# 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/Thaumarchaeota/Candidatus_Caldiarchaeum_subterraneum_uid227223/NC_022786.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/Thaumarchaeota/Candidatus_Caldiarchaeum_subterraneum_uid227223/NC_022786.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Thaumarchaeota/Candidatus_Caldiarchaeum_subterraneum_uid227223/NC_022786.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|557693446|ref|YP_008796500.1|  [L=396]
Description: archaeal cell division control protein 6 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   49.7   0.0    5.7e-13   48.7   0.0    1.5  1  Cdc6_C           CDC6, C terminal winged helix domain
    3.6e-08   34.0   1.4    2.3e-07   31.4   0.2    2.6  2  AAA_16           AAA ATPase domain
    9.4e-08   32.4   0.0    2.3e-07   31.1   0.0    1.7  1  AAA_22           AAA domain
    5.6e-06   26.4   0.2    6.9e-05   22.9   0.1    2.3  2  TIP49_C          TIP49 AAA-lid domain
    4.9e-05   23.8   0.0    0.00012   22.5   0.0    1.7  1  AAA              ATPase family associated with various cellul
     0.0071   16.3   0.2      0.017   15.1   0.0    1.8  2  NACHT            NACHT domain
  ------ inclusion threshold ------
       0.02   13.8   0.0      0.033   13.1   0.0    1.2  1  AFG1_ATPase      AFG1-like ATPase
      0.032   13.9   0.0      0.073   12.8   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
      0.074   13.0   0.0       0.15   12.1   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.078   13.5   0.0       0.18   12.3   0.0    1.7  1  AAA_18           AAA domain
        0.1   11.3   0.4          3    6.5   0.2    2.2  2  AAA_32           AAA domain
       0.11   11.6   0.0       0.22   10.7   0.0    1.5  1  DUF815           Protein of unknown function (DUF815)
       0.12   13.0   0.0       0.33   11.6   0.0    1.7  1  RFX_DNA_binding  RFX DNA-binding domain
       0.15   11.3   0.2       0.51    9.6   0.1    1.8  2  Zeta_toxin       Zeta toxin
       0.17   11.3   0.0       0.35   10.3   0.0    1.4  1  TniB             Bacterial TniB 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 !   48.7   0.0   4.7e-16   5.7e-13       1      75 [.     305     377 ..     305     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 4.7e-16
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEES CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLn 75 
                                       L+++++    ++k +vt+++vye+Yk +Ce++  ++   ++++++l++L +lg+l+l ++s+G r gr++ + L 
  gi|557693446|ref|YP_008796500.1| 305 LLSAARSML-GNKASVTSQDVYETYKLVCEELRQEAKGYTSFWEILQQLQDLGFLRLSVKSEGAR-GRKTFVYLP 377
                                       667777777.89***************************************************97.**9999986 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.2   1.9e-10   2.3e-07       2     146 ..      30     152 ..      29     183 .. 0.68
   2 ?   -0.7   0.1       1.4   1.7e+03     116     138 ..     278     304 ..     203     355 .. 0.56

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.9e-10
                            AAA_16   2 lvGReeeleqLlsalervrsgrp...elvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipy 69 
                                       l  Re+ele L s ++++ +++      v+lsG+ G+GK+sl++ + +++e++      ++ f+  +c+ +      
  gi|557693446|ref|YP_008796500.1|  30 LLFRERELELLFSFFSSLLRDEKsfhVRVFLSGAVGTGKTSLAKLFGQEIERKglglgrKIRFVHVNCRIH------ 100
                                       778*************99999999999**************************544443344444444444...... PP

                            AAA_16  70 salaqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlqw 146
                                               + +l+++l   ae+ +  + ++            +g + + +le + ++l++ ++  r l+l+lD+++ 
  gi|557693446|ref|YP_008796500.1| 101 --------K-SLYTALRKTAEA-LGVEIPR------------RGYSDEEILEIIVSFLRFNKT--R-LILCLDEVEA 152
                                       ........4.555555444222.2222222............222336788888888888877..4.8888888883 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                            AAA_16 116 a.....srllellkrllallsrderplv 138
                                             s      ++ la+l++der +v
  gi|557693446|ref|YP_008796500.1| 278 VrkalaSVYPTIRRENLAYLRPDER-IV 304
                                       1333313333333333344444444.33 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.9e-10   2.3e-07       9     131 ..      59     186 ..      57     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.9e-10
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqa 85 
                                       ++ G +GtGKT l++ + ++ ++      ++ ++v+v++   +s+ + lr+ ++alg+e  +++ s ee+le +   
  gi|557693446|ref|YP_008796500.1|  59 FLSGAVGTGKTSLAKLFGQEIERKGLGLGRKIRFVHVNCRIHKSLYTALRKTAEALGVEIPRRGYSDEEILEIIVSF 135
                                       688*****************965544444*********************************99************* PP

                            AAA_22  86 lraravielliiDEaqhlr....seealeeLrsllnl.srkgvqliLvGtp 131
                                       lr  +++ +l +DE++ l+    s  ++   rs  ++ +  +v+liL+   
  gi|557693446|ref|YP_008796500.1| 136 LRFNKTRLILCLDEVEALIaeegSGPIYLLTRSSEDIeAGALVSLILIFRG 186
                                       ***99999*********9887544555555566666688888888888765 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   5.8e-08   6.9e-05       1      60 [.     219     281 ..     219     283 .. 0.91
   2 ?    0.9   0.0      0.42     5e+02      36      63 ..     305     330 ..     302     332 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 5.8e-08
                           TIP49_C   1 IlkiRakeEgvk..ldeeAldlLakig.tetSLRYaiqLltpasilakkrkkkevevedveev 60 
                                       Il+ Ra e  vk  +++e ld+La+++ +++  RYai Ll  +  +a+ +++  v+ e+v+++
  gi|557693446|ref|YP_008796500.1| 219 ILRYRASEAFVKnaISDEVLDFLAEVAaERKDARYAIDLLWRSGKYAEAEGSSAVTAEHVRKA 281
                                       89999999999666***********97256789***************************987 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.42
                           TIP49_C  36 LltpasilakkrkkkevevedveeveeL 63 
                                       Ll++a+  +++ +k +v+ +dv e ++L
  gi|557693446|ref|YP_008796500.1| 305 LLSAAR--SMLGNKASVTSQDVYETYKL 330
                                       555554..44889999*******99988 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 !   22.5   0.0     1e-07   0.00012       1      74 [.      58     157 ..      58     184 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1e-07
                                       EEEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS.................STTHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel.........gvefleisgsellsk.................yvgesekkirelfk 51 
                                       v l+G  GtGKT+lak   +e+         +++f+ +++     +                   g s ++i e++ 
  gi|557693446|ref|YP_008796500.1|  58 VFLSGAVGTGKTSLAKLFGQEIerkglglgrKIRFVHVNCRIHK-SlytalrktaealgveipRRGYSDEEILEIIV 133
                                       5799*****************85555555555778888885444.34778888999999999966666666655555 PP

                                       H.HHHTSTSEEEEEETGGGHHHHH CS
                               AAA  52 e.akekakpsilfiDEidalaksr 74 
                                       + ++ +++  il +DE++al+ ++
  gi|557693446|ref|YP_008796500.1| 134 SfLRFNKTRLILCLDEVEALIAEE 157
                                       524444445***********9887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.4e-05     0.017       3      98 ..      58     158 ..      56     221 .. 0.78
   2 ?   -4.0   0.0       9.9   1.2e+04      56      80 ..     329     353 ..     319     355 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEE.ETTTTTTS-....-HCHHHCCCCTS--SSS-C....CH CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFfl.slrelsrsgna.rsladllfsqlpepaapvse....vw 73 
                                       v+l G+ G GKT L++ + +++ ++ l  g+ k  F++ ++r  +   +a r  a+ l  + p  +   +e    ++
  gi|557693446|ref|YP_008796500.1|  58 VFLSGAVGTGKTSLAKLFGQEIERKGLGLGR-KIRFVHvNCRIHKSLYTAlRKTAEALGVEIPRRGYSDEEileiIV 133
                                       899**************************98.666665144444444433677777777777777777777777666 PP

                                       HHHCCSCCCEEEEEE-STT-SS-TC CS
                             NACHT  74 avllelperlLlilDglDelvtdlg 98 
                                       ++l  +++rl l lD ++ l ++ g
  gi|557693446|ref|YP_008796500.1| 134 SFLRFNKTRLILCLDEVEALIAEEG 158
                                       6666678888888888887766554 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 9.9
                                       HHHCCCCTS--SSS-CCHHHHCCSC CS
                             NACHT  56 dllfsqlpepaapvsevwavllelp 80 
                                       +l++++l ++a+  + +w++l++l+
  gi|557693446|ref|YP_008796500.1| 329 KLVCEELRQEAKGYTSFWEILQQLQ 353
                                       6778888888888888888887776 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.7e-05     0.033      62     137 ..      55     151 ..      29     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                       AFG1_ATPase  62 vrglYlwGgvGrGKtylmdlffeslpvek...krrvhfhafmarvhdeltklr................kekdplai 119
                                        + ++l G vG GKt l  lf ++++ +    +r++ f +   r+h+ l +                    ++ l+i
  gi|557693446|ref|YP_008796500.1|  55 HVRVFLSGAVGTGKTSLAKLFGQEIERKGlglGRKIRFVHVNCRIHKSLYTALrktaealgveiprrgySDEEILEI 131
                                       45699****************99998765333699999999999999997655588999999999998877777888 PP

                       AFG1_ATPase 120 vad..rlaeearvlCfDEfe 137
                                       ++   r+ +   +lC+DE e
  gi|557693446|ref|YP_008796500.1| 132 IVSflRFNKTRLILCLDEVE 151
                                       87722444555579999975 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.1e-05     0.073      21      59 ..      54      98 ..      39     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
                                      SSS-EEEECSTTSSHHHHHHHHHHHSTT......TTS-EEEEETT CS
                   Sigma54_activat 21 tdlsvlitGesGtGKellaraiheaskr......kekpfvavnca 59
                                       +++v++ G  GtGK+ la++  ++ +r      ++ +fv+vnc 
  gi|557693446|ref|YP_008796500.1| 54 FHVRVFLSGAVGTGKTSLAKLFGQEIERkglglgRKIRFVHVNCR 98
                                      5689******************99888733333345699999995 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   0.00012      0.15      21      43 ..      54      79 ..      33      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                      E...EEEEESTTSSHHHHHHHHHHHT CS
                              TsaE 21 v...ilLeGdLGaGKTtlvrglakal 43
                                      +   ++L+G +G+GKT l++ + +++
  gi|557693446|ref|YP_008796500.1| 54 FhvrVFLSGAVGTGKTSLAKLFGQEI 79
                                      13459***************998876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00015      0.18       1      34 [.      58      96 ..      58     164 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                            AAA_18  1 IlltGtpGvGKttlakeL....skrl.gfgvnlrdvake 34
                                      ++l+G+ G+GKt+lak      ++++ g+g+++r+v+ +
  gi|557693446|ref|YP_008796500.1| 58 VFLSGAVGTGKTSLAKLFgqeiERKGlGLGRKIRFVHVN 96
                                      799************999544433332447777777655 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.033        39      33      56 ..      58      81 ..      49      84 .. 0.84
   2 ?    6.5   0.2    0.0025         3     480     509 ..     254     283 ..     219     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.033
                            AAA_32 33 ifvlGesgtGrttlvkrlleeiak 56
                                      +f++G+ gtG+t+l+k + +ei++
  gi|557693446|ref|YP_008796500.1| 58 VFLSGAVGTGKTSLAKLFGQEIER 81
                                      7**************999888766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0025
                            AAA_32 480 iadllrEAdywakkegaevveaehVekAle 509
                                        +dll  +  +a+ eg+++v+aehV+kAl+
  gi|557693446|ref|YP_008796500.1| 254 AIDLLWRSGKYAEAEGSSAVTAEHVRKALA 283
                                       679999999*******************97 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00018      0.22      55      85 ..      57      93 ..      27     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                            DUF815 55 nvLLwGarGtGKSslvkallneyaeeg......Lrli 85
                                       v+L Ga GtGK sl k   +e++++g      +r++
  gi|557693446|ref|YP_008796500.1| 57 RVFLSGAVGTGKTSLAKLFGQEIERKGlglgrkIRFV 93
                                      479**********************995554445555 PP

>> RFX_DNA_binding  RFX DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028      0.33      16      72 ..     315     375 ..     307     380 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                   RFX_DNA_binding  16 edvsvprqevYaeYlsicsklklkplnaasFgKlirsv....FpnvktrRLgtrgqskYhy 72 
                                       +++sv  q+vY+ Y+ +c++l+ +    +sF  +++++    F ++ ++  g rg+  ++y
  gi|557693446|ref|YP_008796500.1| 315 NKASVTSQDVYETYKLVCEELRQEAKGYTSFWEILQQLqdlgFLRLSVKSEGARGRKTFVY 375
                                       56899**************************999998766667777777778888888887 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00042      0.51      18      43 ..      57      82 ..      48      96 .. 0.89
   2 ?   -1.9   0.0       1.4   1.6e+03     154     174 ..      95     115 ..      86     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00042
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerq 43
                                       ++l+G+ G GK++la+l+ +e+er+
  gi|557693446|ref|YP_008796500.1| 57 RVFLSGAVGTGKTSLAKLFGQEIERK 82
                                      69*******************99754 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                        Zeta_toxin 154 vpkeehdeafeglresveale 174
                                       v++++h+  +++lr+++eal 
  gi|557693446|ref|YP_008796500.1|  95 VNCRIHKSLYTALRKTAEALG 115
                                       68899**********999985 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00029      0.35      37     133 ..      57     155 ..      36     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                              TniB  37 nlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkara.rvskleqqvl 112
                                        + l G   +GKt++++ F ++ +++     +k++ ++v+++ + +     ++  ealg+++  r  + +++ + ++
  gi|557693446|ref|YP_008796500.1|  57 RVFLSGAVGTGKTSLAKLFGQEIERKGLGLGRKIRFVHVNCRIHKSLYTALRKTAEALGVEIPRRGySDEEILEIIV 133
                                       46789*****************999999999***********9999988889999******9888635568899999 PP

                              TniB 113 rllrelkvrv.LiiDEihnlla 133
                                       ++lr  k+r+ L +DE++ l+a
  gi|557693446|ref|YP_008796500.1| 134 SFLRFNKTRLiLCLDEVEALIA 155
                                       ********962679***99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 2617.99
//
Query:       gi|557693447|ref|YP_008796501.1|  [L=409]
Description: replication factor C large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   51.3   0.0    7.2e-13   49.1   0.0    2.2  1  AAA          ATPase family associated with various cellular a
    1.4e-07   31.7   0.0    4.6e-07   29.9   0.0    1.8  2  Rad17        Rad17 P-loop domain
    5.4e-06   26.7   0.9     0.0033   17.7   0.1    3.1  3  AAA_22       AAA domain
    7.4e-06   26.4   0.9    3.3e-05   24.3   0.0    2.5  3  AAA_16       AAA ATPase domain
      8e-06   25.7   0.1    3.6e-05   23.6   0.0    2.1  2  RuvB_N       Holliday junction DNA helicase RuvB P-loop domai
    2.9e-05   24.3   0.0    6.9e-05   23.0   0.0    1.6  1  AAA_2        AAA domain (Cdc48 subfamily)
     0.0002   21.5   0.1    0.00034   20.8   0.1    1.3  1  RFC1         Replication factor RFC1 C terminal domain
    0.00036   19.8   0.0    0.00062   19.0   0.0    1.3  1  DUF815       Protein of unknown function (DUF815)
     0.0004   20.7   0.3     0.0012   19.1   0.2    1.9  1  AAA_assoc_2  AAA C-terminal domain
     0.0019   18.2   0.0     0.0044   17.1   0.0    1.6  1  AAA_14       AAA domain
     0.0021   18.0   0.3       0.03   14.2   0.3    2.4  1  Bac_DnaA     Bacterial dnaA  protein
     0.0024   18.1   0.1      0.011   15.9   0.0    2.1  2  AAA_33       AAA domain
     0.0031   17.5   0.0     0.0097   15.9   0.0    1.9  1  AAA_5        AAA domain (dynein-related subfamily)
     0.0033   17.2   0.3      0.011   15.4   0.3    1.9  1  AAA_30       AAA domain
     0.0034   16.8   0.0       0.18   11.2   0.0    2.5  2  TniB         Bacterial TniB protein
     0.0096   15.4   0.0      0.022   14.3   0.0    1.6  1  AAA_7        P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.023   14.6   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
      0.021   14.9   0.0      0.052   13.6   0.0    1.7  1  MMR_HSR1     50S ribosome-binding GTPase
      0.036   13.8   0.0       0.11   12.3   0.0    1.7  2  IstB_IS21    IstB-like ATP binding protein
       0.05   13.5   0.1       0.23   11.3   0.1    2.1  1  ATPase_2     ATPase domain predominantly from Archaea
      0.057   13.6   0.0       0.18   12.0   0.0    1.8  1  Roc          Ras of Complex, Roc, domain of DAPkinase
      0.071   13.0   0.0        1.4    8.9   0.0    2.4  2  NACHT        NACHT domain
      0.081   12.6   0.0       0.13   12.0   0.0    1.4  1  AAA_24       AAA domain
       0.09   12.8   0.0       0.18   11.8   0.0    1.5  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
       0.12   11.2   0.1       0.75    8.6   0.0    2.0  2  PPV_E1_C     Papillomavirus helicase
       0.14   11.9   0.2       0.37   10.6   0.0    1.8  1  AAA_29       P-loop containing region of AAA domain
       0.14   12.4   0.6       0.93    9.7   0.0    2.4  3  AAA_28       AAA domain
       0.16   10.9   0.0       0.31   10.0   0.0    1.4  1  AAA_6        Hydrolytic ATP binding site of dynein motor regi


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 !   49.1   0.0   1.1e-15   7.2e-13       2     121 ..      45     151 ..      44     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.1e-15
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.....TSEEEEEETGGGHHHH CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka.....kpsilfiDEidalaks 73 
                                       llyGp G+GKT+l++a a+e g e++e+++s+++      + ++i+ ++ +a+ +a     + +i+++DE+d +  +
  gi|557693447|ref|YP_008796501.1|  45 LLYGPAGVGKTSLVHAYASEKGYEVIETNASDFR------TRENIERIVGAASGMAsltmgQRKIILVDEVDGIDAR 115
                                       9*********************************......99999999999988889999767***********555 PP

                                       HTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS CS
                               AAA  74 rsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr 121
                                               +  +v  L   +++       v v++++n+p+++  a lr
  gi|557693447|ref|YP_008796501.1| 116 A-------DAGAVTSLADIISKTH-----VPVVLVANDPWDPRLAPLR 151
                                       5.......6677777777776553.....6899999999888776666 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   7.2e-10   4.6e-07       6      87 ..       2      82 ..       1      93 [. 0.91
   2 ?   -2.3   0.0       5.7   3.7e+03     130     141 ..      98     109 ..      88     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 7.2e-10
                             Rad17  6 nelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslke 84
                                      ++lW ek++P k  e+   k+ +++  ew+      +  k+  L+ GP+G gk+  v+  + e g++++e  n+  ++ 
  gi|557693447|ref|YP_008796501.1|  2 TQLWTEKHRPRKVSEIVGNKEAVQAFLEWMAGWEKGKPSKKAALLYGPAGVGKTSLVHAYASEKGYEVIET-NASDFRT 79
                                      589****************************9999999999****************************95.7777776 PP

                             Rad17 85 pdn 87
                                       +n
  gi|557693447|ref|YP_008796501.1| 80 REN 82
                                      665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.7
                             Rad17 130 rtdkklilvedl 141
                                        +++k+ilv+++
  gi|557693447|ref|YP_008796501.1|  98 MGQRKIILVDEV 109
                                       578999999997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   5.2e-06    0.0033       5     128 ..      41     138 ..      38     147 .. 0.69
   2 ?   -1.1   0.0       3.3   2.1e+03      54      54 ..     255     255 ..     183     304 .. 0.61
   3 ?   -1.8   0.0       5.2   3.3e+03      28      28 ..     293     293 ..     254     367 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.2e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellea 81 
                                       ++  +++G++G+GKT l+  +++++         + ev++ +++   +++++     r++g  +           + 
  gi|557693447|ref|YP_008796501.1|  41 KKAALLYGPAGVGKTSLVHAYASEK---------GYEVIETNASDFRTRENI----ERIVGA-A-----------SG 92 
                                       67899*******************9.........999999999998865554....555552.1...........12 PP

                            AAA_22  82 leqalraravielliiDEaqhlr...seealeeLrsllnlsrkgvqliLv 128
                                       ++  l   ++ +++++DE++ ++    + a++ L ++    +++v+++Lv
  gi|557693447|ref|YP_008796501.1|  93 MAS-LTMGQR-KIILVDEVDGIDaraDAGAVTSLADIIS--KTHVPVVLV 138
                                       333.333333.4777777777765333666666655555..777777777 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.3
                            AAA_22  54 k 54 
                                       +
  gi|557693447|ref|YP_008796501.1| 255 S 255
                                       1 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 5.2
                            AAA_22  28 q 28 
                                       +
  gi|557693447|ref|YP_008796501.1| 293 T 293
                                       0 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   5.2e-08   3.3e-05       3     140 ..      18     138 ..      16     141 .. 0.60
   2 ?   -2.1   0.1       6.8   4.4e+03      88      88 ..     237     237 ..     166     294 .. 0.58
   3 ?   -1.4   0.0       4.1   2.6e+03      36      74 ..     335     374 ..     334     399 .. 0.58

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.2e-08
                            AAA_16   3 vGReeeleqLlsalervrsgrp..elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqala 77 
                                       vG +e ++++l+ +  + +g p   + ll+G++GvGK+slv + +    ++g  ++++++ ++          + + 
  gi|557693447|ref|YP_008796501.1|  18 VGNKEAVQAFLEWMAGWEKGKPskKAALLYGPAGVGKTSLVHAYAS---EKGYEVIETNASDF-------RTRENI- 83 
                                       556667777777777888899999*****************88885...55555799999999.......112222. PP

                            AAA_16  78 reellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlv 140
                                       + +++ +   +   a+l   ++k+      v+e++g +a++ + ++++l++ +s+++ p+vlv
  gi|557693447|ref|YP_008796501.1|  84 E-RIVGAASGM---ASLTMGQRKIIL----VDEVDGIDARADAGAVTSLADIISKTHVPVVLV 138
                                       1.222222222...333333333222....445556666555566666665555555566655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.8
                            AAA_16  88 e 88 
                                       +
  gi|557693447|ref|YP_008796501.1| 237 A 237
                                       0 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.1
                            AAA_16  36 GKsslvrellralekdggiflrgkcdql.....esaipysalaq 74 
                                       G ++ +re l++++++    +  k + +     ++ +py+ ++ 
  gi|557693447|ref|YP_008796501.1| 335 GRTKSIRETLNSISEK----VGKKLHMSarkarTEILPYLKIIM 374
                                       8899999999999999....333333331111122366655444 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 !   23.6   0.0   5.6e-08   3.6e-05       2      98 ..      10     114 ..       9     130 .. 0.76
   2 ?   -2.1   0.0       4.3   2.8e+03      66      88 ..     265     287 ..     256     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 5.6e-08
                            RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaal 78 
                                       rP++++e +g ++  + +   ++  +k + +    llyGp G+Gkt+l +  a+e g ++  t +       ++  +
  gi|557693447|ref|YP_008796501.1|  10 RPRKVSEIVGNKEAVQAFLEWMAGWEKGKPSKKAALLYGPAGVGKTSLVHAYASEKGYEVIETNASDFRTRENIERI 86 
                                       9**********99998888888888888889999*************************999988766555555443 PP

                            RuvB_N  79 l......tn..leekdvlfideihrlsr 98 
                                       +      ++  + +++++++de+  ++ 
  gi|557693447|ref|YP_008796501.1|  87 VgaasgmASltMGQRKIILVDEVDGIDA 114
                                       3111111441145677888888876665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.3
                            RuvB_N  66 gPvlekagdlaalltnleekdvl 88 
                                       +P    ++dla  l nl + d+ 
  gi|557693447|ref|YP_008796501.1| 265 APQQLSPTDLAEALENLAKADLY 287
                                       56666789999999999999964 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.1e-07   6.9e-05       6      91 ..      44     123 ..      40     134 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.1e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG--- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihp 82 
                                        ll gp gvGkt l  a a+        ++i  +as++ ++e++e++v    g +       ++ i+l+DE+d i +
  gi|557693447|ref|YP_008796501.1|  44 ALLYGPAGVGKTSLVHAYASEKGY----EVIETNASDFRTRENIERIVGAASGMASLTM--GQRKIILVDEVDGIDA 114
                                       6889*************9999986....************7777777776666665554..5677**********99 PP

                                       --------- CS
                             AAA_2  83 kessgadvS 91 
                                       +  +ga  S
  gi|557693447|ref|YP_008796501.1| 115 RADAGAVTS 123
                                       755555555 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 !   20.8   0.1   5.2e-07   0.00034       2      92 ..     282     374 ..     281     383 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5.2e-07
                                       HHHHHHHHHHTTSS-GGGHHHHHHHHTHHHHHTT-EE-SS..-----...SHHHHHHHHHHHHHHHHHHHTTTTT-- CS
                              RFC1   2 sdgDlvdkkirseqnWsLlpthavlssvlPaslvrgsleg..risFp...swLGknSktnKnkRllqelqshlrlkt 73 
                                       +++Dl  ++i+++qnW+Ll++   + +   a   + s ++  ++++p   ++LG+   t+  +  l+ ++ ++  k+
  gi|557693447|ref|YP_008796501.1| 282 AKADLYLQRINTRQNWQLLRYAVPMMTAGVALSRKTSPSKfvKFTYPeaiKFLGR---TKSIRETLNSISEKVGKKL 355
                                       799******************7766666543333333344345666688888888...8888899************ PP

                                       ----HHHHHTTTHHHHHHH CS
                              RFC1  74 saskselrldylpllkkkl 92 
                                       ++s ++ r+++lp+lk ++
  gi|557693447|ref|YP_008796501.1| 356 HMSARKARTEILPYLKIIM 374
                                       **************98665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   9.8e-07   0.00062      24     103 ..      11      88 ..       5     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.8e-07
                            DUF815  24 evklddLvgidkqkealventeqfleglpann.vLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklv 99 
                                       + k++++vg ++  +a++e  + + +g+p+++ +LL+G  G+GK slv+a  +   e+g  +ie + +d ++ +++ 
  gi|557693447|ref|YP_008796501.1|  11 PRKVSEIVGNKEAVQAFLEWMAGWEKGKPSKKaALLYGPAGVGKTSLVHAYAS---EKGYEVIETNASDFRTRENIE 84 
                                       5678899999999999999999999***997637***************9876...567788888888887777666 PP

                            DUF815 100 ellr 103
                                       +++ 
  gi|557693447|ref|YP_008796501.1|  85 RIVG 88 
                                       6654 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 !   19.1   0.2   1.9e-06    0.0012       3      41 ..     178     222 ..     176     268 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.9e-06
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......X CS
                       AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeak......e 41 
                                       +++++ +d+l+ ++e ++GD R+a+n L++a +a e        +
  gi|557693447|ref|YP_008796501.1| 178 ENVRVPEDVLRRIVENSEGDLRSAINDLQMASAALEMGlvtgsrD 222
                                       579999************************999887656655551 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.8e-06    0.0044       2      76 ..      41     112 ..      40     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.8e-06
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev 76 
                                       +k+ ++ G+  vGKT l++ +++e+     ++++ n  d r++++ +      + + ++ ++ ++++++ DE+  +
  gi|557693447|ref|YP_008796501.1|  41 KKAALLYGPAGVGKTSLVHAYASEKG---YEVIETNASDFRTRENIERIvGAASGMASLTMG-QRKIILVDEVDGI 112
                                       68899*****************9999...999999999988866443312233444444445.9999*****9876 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.3   4.7e-05      0.03      35     210 ..      42     203 ..      18     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-05
                                       --EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-SEEEEE-GGGGTT CS
                          Bac_DnaA  35 nPlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkvDvLliDDiqflag 111
                                          ++yg+ G+Gkt L++a + e   +  e+  +   + e ++++v a           ++ +  ++l+D++  +  
  gi|557693447|ref|YP_008796501.1|  42 KAALLYGPAGVGKTSLVHAYASEKGYEVIETNASDFRTRENIERIVGAA----SGMASLTMGQRKIILVDEVDGIDA 114
                                       5679***************987766666666655555555555555554....333344556667899999999998 PP

                                       -HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT----T CS
                          Bac_DnaA 112 kektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaeklevpe 188
                                       +   +   ++ +  ++ + +  v+     P+     + rl    +a l+++  +  +   +a lkk + ae++ vpe
  gi|557693447|ref|YP_008796501.1| 115 RA--DAGAVTSLADIISKTHVPVVLVANDPW-----DPRLAPLRDACLMIQFRRIPKPSVAAHLKKIAAAENVRVPE 184
                                       87..455566666666666554444455676.....67888888899999999999999999999999999999999 PP

                                       THHHHHHHH--S-HHHHHHHHH CS
                          Bac_DnaA 189 evlefiaervtdnvRelegaln 210
                                       +vl+ i e+ + ++R   +a+n
  gi|557693447|ref|YP_008796501.1| 185 DVLRRIVENSEGDLR---SAIN 203
                                       999999888877766...4444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.7e-05     0.011       3      33 ..      45      75 ..      44     154 .. 0.85
   2 ?   -0.8   0.1       2.4   1.5e+03      25      43 ..     179     197 ..     166     298 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.7e-05
                            AAA_33  3 llvGlpGsGKstlaerllkklgavllssdtl 33
                                      ll G++G+GK+ l++ ++ + g++++++++ 
  gi|557693447|ref|YP_008796501.1| 45 LLYGPAGVGKTSLVHAYASEKGYEVIETNAS 75
                                      578************************9983 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.4
                            AAA_33  25 avllssdtlrrrlfgtdqq 43 
                                        v++ +d+lrr +++++ +
  gi|557693447|ref|YP_008796501.1| 179 NVRVPEDVLRRIVENSEGD 197
                                       5666666666666663333 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 !   15.9   0.0   1.5e-05    0.0097       3      77 ..      45     112 ..      43     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                                       EEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG- CS
                             AAA_5   3 lLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEvera 77 
                                       lL Gp G+gK++l+  +a+  + ev + + +++ t+e++   +  ++g +s     l+  + + +i+++DEv+ +
  gi|557693447|ref|YP_008796501.1|  45 LLYGPAGVGKTSLVHAYASEKGYEVIETNASDFRTRENIERIVGAASGMAS-----LT--MGQRKIILVDEVDGI 112
                                       8**************************************999886444333.....33..556667777777755 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.3   1.7e-05     0.011      19     122 ..      42     138 ..      38     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrvi.glAptgkaAkvLaeelgieastiakllkrlkgrarlepgtlliv 94 
                                       + a+l GpAG GKt ++ a++    ++g++vi   A+  +  +++++ +g +as +a+l+        + ++++++v
  gi|557693447|ref|YP_008796501.1|  42 KAALLYGPAGVGKTSLVHAYA---SEKGYEVIeTNASDFRTRENIERIVG-AASGMASLT--------MGQRKIILV 106
                                       57899*********9877654...45699999566888888888887766.888889888........23568**** PP

                            AAA_30  95 DEagmv....dtkqlaallkaaekagakvilv 122
                                       DE+  +    d+  +++l+++++k+++ v+lv
  gi|557693447|ref|YP_008796501.1| 107 DEVDGIdaraDAGAVTSLADIISKTHVPVVLV 138
                                       **987733335566777777788888888887 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00028      0.18      18      61 ..      23      67 ..      16      83 .. 0.77
   2 ?    2.9   0.0     0.095        61     112     160 ..      93     138 ..      68     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                              TniB 18 eilerLeeLleypk.rkrmpnlllvGdsnnGKtmivekFarlhpp 61
                                      ++ + Le++  + k +   + +ll+G+  +GKt++v+ +a+++  
  gi|557693447|ref|YP_008796501.1| 23 AVQAFLEWMAGWEKgKPSKKAALLYGPAGVGKTSLVHAYASEKGY 67
                                      4555677888887745566899*****************998754 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.095
                              TniB 112 lrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       ++ l   + +++++DE++ +    ar+   ++ +l  +  + ++p+vlv
  gi|557693447|ref|YP_008796501.1|  93 MASLTMGQRKIILVDEVDGID---ARADAGAVTSLADIISKTHVPVVLV 138
                                       5667777899********998...7888889999999999999999998 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 !   14.3   0.0   3.5e-05     0.022      32      78 ..      40      83 ..      35     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-05
                             AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanql 78
                                      +kk  ll+Gp+G+GKt++++ + ++     y ++  n s   + +++
  gi|557693447|ref|YP_008796501.1| 40 SKKAALLYGPAGVGKTSLVHAYASEKG---YEVIETNASDFRTRENI 83
                                      57999****************998877...55555555555444444 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   3.6e-05     0.023      99     134 ..      41      76 ..      34      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-05
                                       TSEEEEECSTTSSHHHHHHHHCTT-----S------ CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpelelktgevsekl 134
                                       +k ++l G+ GvGK++L+ a ++e+  ++ e+ +++
  gi|557693447|ref|YP_008796501.1|  41 KKAALLYGPAGVGKTSLVHAYASEKGYEVIETNASD 76 
                                       67889******************9988888877655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.2e-05     0.052       3      83 ..      45     138 ..      43     170 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.2e-05
                                       EEEESTTSSHHHHHHHHHTS....TEEESSSTTSSSSEEEEEEE.........ETTEEEEEEECG.GCSSHHHHHHH CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge....kaivsdkpgtTrdinegrvk.........lkgkeielvDtp.Gliegaseekg 65 
                                       +++G   vGK++L+ a   e    + ++++  + Tr+ +e+ v          +++++i+lvD + G i+ a+ + g
  gi|557693447|ref|YP_008796501.1|  45 LLYGPAGVGKTSLVHAYASEkgyeVIETNASDFRTRENIERIVGaasgmasltMGQRKIILVDEVdG-ID-ARADAG 119
                                       6899*************986555356888899********998866666666444688999996525.65.666667 PP

                                       HHHHHHHHHC.TSEEEEEE CS
                          MMR_HSR1  66 lgkaflalee.adlillvv 83 
                                          +++++++ +++ +++v
  gi|557693447|ref|YP_008796501.1| 120 AVTSLADIISkTHVPVVLV 138
                                       7777777555355544444 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 ?   12.3   0.0   0.00017      0.11      47     136 ..      41     130 ..      33     146 .. 0.71
   2 ?   -2.6   0.0         6   3.8e+03     116     141 ..     213     238 ..     185     244 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                         IstB_IS21  47 kenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralk.rllkvdllilDdlgllpl 122
                                       k++ +l Gp+GvGK+ l  a +    ++g++v+ + ++d+ ++ +++r  g ++ +++ ++ + +++++D++   + 
  gi|557693447|ref|YP_008796501.1|  41 KKAALLYGPAGVGKTSLVHAYA---SEKGYEVIETNASDFRTRENIERIVGAASGMASlTMGQRKIILVDEVDGIDA 114
                                       567799***********99976...5789999999999998888887777766554431455668888999855443 PP

                         IstB_IS21 123 ..dqaeaellfeviek 136
                                         d  + + l ++i+k
  gi|557693447|ref|YP_008796501.1| 115 raDAGAVTSLADIISK 130
                                       0133344556666665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6
                         IstB_IS21 116 dlgllpldqaeaellfeviekryerr 141
                                       ++gl++ +++ + ++f  ++  ++ +
  gi|557693447|ref|YP_008796501.1| 213 EMGLVTGSRDRKDEIFTALATIFNAK 238
                                       67777777777777777766666555 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 ?   11.3   0.1   0.00036      0.23      22      51 ..      43      69 ..      28     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00036
                          ATPase_2 22 iyfiYGpegsGKtaLlkeiienledkdkyv 51
                                        ++YGp g+GKt+L+   ++++   +++v
  gi|557693447|ref|YP_008796501.1| 43 AALLYGPAGVGKTSLVHAYASEK---GYEV 69
                                      5789************9988876...4444 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 ?   12.0   0.0   0.00028      0.18       3      39 ..      45      80 ..      43      94 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
                                      EEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEE CS
                               Roc  3 vlvGdsgvGKtsllkrfvedkfsekekstigvdfltk 39
                                      +l G +gvGKtsl++ + ++k  e   +t + df t+
  gi|557693447|ref|YP_008796501.1| 45 LLYGPAGVGKTSLVHAYASEKGYEV-IETNASDFRTR 80
                                      578**************98876543.45556666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0021       1.4       4      22 ..      45      63 ..      42      77 .. 0.86
   2 ?    1.4   0.0      0.41   2.6e+02      81     121 ..     100     136 ..      81     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0021
                                      EEEC-TTTCHHHHHHHHHH CS
                             NACHT  4 ilqGeaGsGKTtLlqklal 22
                                      +l G+aG+GKT L++  a+
  gi|557693447|ref|YP_008796501.1| 45 LLYGPAGVGKTSLVHAYAS 63
                                      799**********997665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.41
                                       CCEEEEEE-STT-SS-TCH.........HHHHHCTTTTT-- CS
                             NACHT  81 erlLlilDglDelvtdlgqkekqpvrtlLselirkkllpea 121
                                       +r  +++D +D + +  ++     + t L+++i+k+++p +
  gi|557693447|ref|YP_008796501.1| 100 QRKIILVDEVDGIDARADA----GAVTSLADIISKTHVPVV 136
                                       5666888999999986666....88999*******999866 PP

>> AAA_24  AAA domain
   #    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 ..      41      64 ..      40     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                            AAA_24  2 klkiliyGpsgiGKTtlakel..g 23
                                      k+  l+yGp+g+GKT+l+  +  +
  gi|557693447|ref|YP_008796501.1| 41 KKAALLYGPAGVGKTSLVHAYasE 64
                                      56789************9888553 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00028      0.18       8      46 ..      25      68 ..      18      80 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                                      HHHHHHHHHCH.....TEEEEEEESTTSSHHHHHHHHHHHTT-- CS
                              TsaE  8 ealgkklakal.....gdvilLeGdLGaGKTtlvrglakalgve 46
                                      +a+ + +a        +++ lL+G+ G+GKT lv++ a++ g+e
  gi|557693447|ref|YP_008796501.1| 25 QAFLEWMAGWEkgkpsKKAALLYGPAGVGKTSLVHAYASEKGYE 68
                                      55555554432444546679*****************9998876 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0012      0.75     245     280 ..      24      59 ..      12      76 .. 0.86
   2 ?   -0.2   0.2      0.53   3.4e+02     139     164 ..     244     269 ..     228     298 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0012
                          PPV_E1_C 245 lisfltalkefLkgvPkknclvllGppntGkslfam 280
                                       + +fl  +  + kg+P k++ +l+Gp+  Gk+ +  
  gi|557693447|ref|YP_008796501.1|  24 VQAFLEWMAGWEKGKPSKKAALLYGPAGVGKTSLVH 59 
                                       5579***************************87765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.53
                          PPV_E1_C 139 eqlaeektfdlsemvqWaydnelede 164
                                       +++a++   d se++qW ++n  ++ 
  gi|557693447|ref|YP_008796501.1| 244 QEAARNIDIDHSELMQWILENAPQQL 269
                                       45567778899*********987654 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 ?   10.6   0.0   0.00057      0.37      23      43 ..      42      62 ..      31      63 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00057
                            AAA_29 23 gatlltGpsGsGKSTllDAiq 43
                                       a ll Gp G+GK++l+ A++
  gi|557693447|ref|YP_008796501.1| 42 KAALLYGPAGVGKTSLVHAYA 62
                                      379**************9985 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0014      0.93       4      34 ..      46      77 ..      43      91 .. 0.84
   2 ?   -0.8   0.0       2.5   1.6e+03      17      54 ..     172     206 ..     164     225 .. 0.68
   3 ?   -1.5   0.0       4.2   2.7e+03      14      48 ..     230     264 ..     227     289 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0014
                            AAA_28  4 itGgestGKTtlleaLaar.gypvvpEaarei 34
                                      + G+ + GKT+l+ a a++ gy+v++  a ++
  gi|557693447|ref|YP_008796501.1| 46 LYGPAGVGKTSLVHAYASEkGYEVIETNASDF 77
                                      78***************665****98776665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.5
                            AAA_28  17 eaLaar.gypvvpEaareileeklakgedalpwvedlla 54 
                                       +++aa  +++v +++ r+i+e+   + + a+++     +
  gi|557693447|ref|YP_008796501.1| 172 KKIAAAeNVRVPEDVLRRIVENSEGDLRSAINDL----Q 206
                                       3444444888889999**9999887777766653....3 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.2
                            AAA_28  14 tlleaLaargypvvpEaareileeklakgedalpw 48 
                                        l+  ++a+ +++ +Eaar i  ++++  + +l+ 
  gi|557693447|ref|YP_008796501.1| 230 ALATIFNAKSFNTAQEAARNIDIDHSELMQWILEN 264
                                       55555667788888999998876666655555544 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 ?   10.0   0.0   0.00049      0.31      35      78 ..      44      87 ..      37      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00049
                             AAA_6 35 gapaGpagtGKtEtvkdLakalakqvvvfncsdqldykslgkif 78
                                      + ++Gpag GKt  v   a++ +  v+ +n sd  + + +++i 
  gi|557693447|ref|YP_008796501.1| 44 ALLYGPAGVGKTSLVHAYASEKGYEVIETNASDFRTRENIERIV 87
                                      6689*****************************99999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      740  (0.0412739); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); 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: 00:00:00.47
# Mc/sec: 2636.36
//
Query:       gi|557693448|ref|YP_008796502.1|  [L=327]
Description: replication factor C small subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   68.1   0.0    2.6e-18   66.2   0.0    2.1  1  Rep_fac_C        Replication factor C C-terminal domain
    5.7e-15   55.9   0.0    1.2e-14   54.9   0.0    1.6  1  AAA              ATPase family associated with various cellul
      1e-14   54.7   0.0    1.6e-09   37.8   0.0    2.3  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    8.2e-07   28.9   0.0    2.7e-06   27.2   0.0    1.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    5.4e-06   26.7   0.1    1.3e-05   25.4   0.1    1.7  1  AAA_assoc_2      AAA C-terminal domain
    1.1e-05   25.3   0.0    1.6e-05   24.7   0.0    1.2  1  DNA_pol3_delta   DNA polymerase III, delta subunit
    1.7e-05   24.8   0.0    3.3e-05   23.9   0.0    1.5  1  Rad17            Rad17 P-loop domain
    2.5e-05   24.7   0.0    0.00018   21.9   0.0    2.0  2  AAA_16           AAA ATPase domain
    0.00024   20.6   0.0     0.0031   16.9   0.0    2.3  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00028   21.1   0.0      0.058   13.7   0.0    2.7  2  AAA_22           AAA domain
    0.00045   20.3   0.0     0.0016   18.5   0.0    1.9  2  AAA_14           AAA domain
    0.00057   19.9   0.0     0.0024   17.9   0.0    1.9  1  ResIII           Type III restriction enzyme, res subunit
     0.0027   17.0   0.0     0.0048   16.1   0.0    1.4  1  TIP49            TIP49 P-loop domain
     0.0092   15.4   0.0       0.22   10.9   0.0    2.2  2  TniB             Bacterial TniB protein
  ------ inclusion threshold ------
      0.016   14.7   0.0      0.037   13.5   0.0    1.6  1  PhoH             PhoH-like protein
      0.017   14.6   0.0      0.032   13.8   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.018   14.9   0.0      0.029   14.2   0.0    1.3  1  AAA_11           AAA domain
      0.025   13.8   0.0       0.08   12.1   0.0    1.8  2  DUF815           Protein of unknown function (DUF815)
      0.028   14.7   0.0      0.058   13.7   0.0    1.6  1  AAA_19           AAA domain
       0.03   14.1   0.0      0.086   12.6   0.0    2.0  1  IstB_IS21        IstB-like ATP binding protein
      0.031   14.0   0.1      0.097   12.4   0.0    1.8  2  Sigma54_activat  Sigma-54 interaction domain
      0.038   13.3   0.0       0.09   12.0   0.0    1.6  1  Zeta_toxin       Zeta toxin
      0.048   13.5   0.0        0.1   12.4   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
      0.061   13.2   0.0       0.13   12.1   0.0    1.6  1  DNA_pol3_gamma3  DNA polymerase III subunits gamma and tau do
       0.08   12.0   0.0       0.17   10.9   0.0    1.6  1  T2SSE            Type II/IV secretion system protein
       0.12   12.6   0.0       0.26   11.5   0.0    1.6  1  AAA_28           AAA domain
       0.12   12.1   0.0       0.35   10.6   0.0    1.8  2  AAA_30           AAA domain
       0.14   12.2   0.0       0.45   10.5   0.0    1.9  2  AAA_5            AAA domain (dynein-related subfamily)
       0.18   12.2   0.0       0.38   11.2   0.0    1.5  1  RNA_helicase     RNA helicase


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 !   66.2   0.0   4.3e-21   2.6e-18       5      88 .]     236     318 ..     232     318 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 4.3e-21
                                       HHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-HHHH CS
                         Rep_fac_C   5 eieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGasehlq 81 
                                       ei+++l+ +l g+f ea++ lrell+ +Gy ++di++ + r ++    ++e+ kl++++l+ge+++r++eG+++++q
  gi|557693448|ref|YP_008796502.1| 236 EITRMLQLVLDGKFIEARNLLRELLYVQGYQPTDIVSSIAREIPLL-PVSEQDKLRLMDLIGETDYRISEGGTPEVQ 311
                                       89******************************************86.69**************************** PP

                                       HHHHHHH CS
                         Rep_fac_C  82 lsallar 88 
                                       l a+la+
  gi|557693448|ref|YP_008796502.1| 312 LQAFLAK 318
                                       *****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 !   54.9   0.0   1.9e-17   1.2e-14       1     129 [.      45     164 ..      45     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.9e-17
                                       EEEESSTTSSHHHHHHHHHHHH.......THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS....TSEEEEEET CS
                               AAA   1 vllyGppGtGKTllakavakel.......gvefleisgsellskyvgesekkirelfkeakeka....kpsilfiDE 66 
                                       +l+ GppGtGKT++a+a a++l       + +f+ei++s+ +   ++   ++++ + +++        +   l++DE
  gi|557693448|ref|YP_008796502.1|  45 MLFAGPPGTGKTATAHAFAQDLfgpryieDGHFIEINASDER--GIETIRERVKTYARSV---PfggiGFRLLLLDE 116
                                       89*******************97666665588**********..4444444444444444...25557779****** PP

                                       GGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                               AAA  67 idalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                        d+l+ +            + ++ + ++++++   ++ +i+a+n+ +++ +++  +R+ +  +
  gi|557693448|ref|YP_008796502.1| 117 SDQLTDAA-----------QHAFRRTMEQFST---TCRFILAANYSNRIIEPIQ-SRCAVLRF 164
                                       ****9999...........*************...69*****************.9**98665 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 !   14.9   0.0   2.7e-05     0.017       2      45 ..      26      68 ..      25      76 .. 0.92
   2 !   37.8   0.0   2.5e-12   1.6e-09      83     163 .]      86     168 ..      70     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
                   DNA_pol3_delta2  2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallc 45
                                      qe++++ l++++ s+++ h +Lf+G+ g+gk ++a ++a+ l+ 
  gi|557693448|ref|YP_008796502.1| 26 QEQVVEALKNIVVSKNVPH-MLFAGPPGTGKTATAHAFAQDLFG 68
                                      899***************9.79******************9986 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 2.5e-12
                   DNA_pol3_delta2  83 ikldqirelieelsrk.pres.kkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqel 157
                                         +++ire  ++  r+ p+ +   +++++++ +++t +A+ a+ +t+E  s+   fiL ++ +n+++++i+SRc +l
  gi|557693448|ref|YP_008796502.1|  86 RGIETIRERVKTYARSvPFGGiGFRLLLLDESDQLTDAAQHAFRRTMEQFSTTCRFILAANYSNRIIEPIQSRCAVL 162
                                       478999966666655515553368***************************************************** PP

                   DNA_pol3_delta2 158 kfspls 163
                                       +f+pls
  gi|557693448|ref|YP_008796502.1| 163 RFKPLS 168
                                       ***985 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 !   27.2   0.0   4.4e-09   2.7e-06       2      59 ..      16      68 ..      15      90 .. 0.86
   2 ?   -2.1   0.0       4.7   2.9e+03      87     112 ..     111     136 ..     109     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.4e-09
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgv 59
                                      rP++l++ + qe+v e lk ++ +     +++ h+l++GpPG Gkt+ a+  a++l  
  gi|557693448|ref|YP_008796502.1| 16 RPRRLDDVVNQEQVVEALKNIVVS-----KNVPHMLFAGPPGTGKTATAHAFAQDLFG 68
                                      9*****************977754.....5789********************99865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.7
                            RuvB_N  87 vlfideihrlsraveevlysamedfr 112
                                       +l++de  +l+ a++  +  +me f+
  gi|557693448|ref|YP_008796502.1| 111 LLLLDESDQLTDAAQHAFRRTMEQFS 136
                                       68899999999999999999999986 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 !   25.4   0.1   2.1e-08   1.3e-05       3      40 ..     183     220 ..     181     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.1e-08
                                       X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                       AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeak 40 
                                       +++kl+d+a++a+ e++ GD+Rka+n+L+ aa+ +++ 
  gi|557693448|ref|YP_008796502.1| 183 ENIKLDDSAIDAIYEFSLGDMRKAINILQSAASISKTI 220
                                       689**************************999888753 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 !   24.7   0.0   2.7e-08   1.6e-05      59     170 ..     110     211 ..      74     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.7e-08
                                       EEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHH CS
                    DNA_pol3_delta  59 rivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwi 135
                                       r+++l+       +++l++  + ++ +++++ ++++ +il a+      ++++  ++++  v+++k+l+++ + + +
  gi|557693448|ref|YP_008796502.1| 110 RLLLLDE------SDQLTDAAQHAFRRTMEQFSTTCRFILAAN----YSNRIIEPIQSRCAVLRFKPLSKDMVETML 176
                                       4444444......57799*************************....56789************************* PP

                                       HHHHHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHH CS
                    DNA_pol3_delta 136 qkraqelglkiekealelLlelvennlsaikqele 170
                                       +k+a+++++k+++ a++ ++e + ++++ + + l+
  gi|557693448|ref|YP_008796502.1| 177 KKIAASENIKLDDSAIDAIYEFSLGDMRKAINILQ 211
                                       **************************999999886 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   5.4e-08   3.3e-05       5      76 ..       7      74 ..       3     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.4e-08
                             Rad17  5 enelWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskel.giklrew 76
                                      +n +W+eky+P  ++++    + +e++k+ + ++ +++      L +GP+G gk+ + +  ++ l g++++e 
  gi|557693448|ref|YP_008796502.1|  7 KNLPWVEKYRPRRLDDVVNQEQVVEALKNIVVSKNVPHM-----LFAGPPGTGKTATAHAFAQDLfGPRYIED 74
                                      6779*************9888888888888887777766.....99***********9999987537787775 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   2.9e-07   0.00018      10      66 ..      27      87 ..      23     135 .. 0.67
   2 ?    0.4   0.1       1.2   7.6e+02     138     161 ..     111     134 ..     106     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.9e-07
                            AAA_16 10 eqLlsale.rvrsgrpelvllsGesGvGKsslvrellralekd....ggiflrgkcdqlesa 66
                                      eq+ +al+  v s   + +l+ G++G+GK++ + ++++ l +     +g+f++ ++ +  ++
  gi|557693448|ref|YP_008796502.1| 27 EQVVEALKnIVVSKNVPHMLFAGPPGTGKTATAHAFAQDLFGPryieDGHFIEINASDE-RG 87
                                      45555666445566669*********************998887886588877777776.33 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
                            AAA_16 138 vlvlDdlqwadeaslqllaaLlrl 161
                                       +l+lD+ +++ +a +++++ +++ 
  gi|557693448|ref|YP_008796502.1| 111 LLLLDESDQLTDAAQHAFRRTMEQ 134
                                       799999999999999999888765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     5e-06    0.0031       2      44 ..      20      64 ..      19      95 .. 0.82
   2 ?    0.4   0.0      0.57   3.5e+02     109     135 ..     111     137 ..     109     151 .. 0.84
   3 ?   -1.0   0.0       1.5   9.5e+02     170     193 ..     136     159 ..     129     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5e-06
                      Mg_chelatase  2 lkdvkGqeeakrale..iaaaGgHnlllvGppGsGKtmlakrlps 44
                                      l dv+ qe+  +al+  +      ++l++GppG+GKt  a+++++
  gi|557693448|ref|YP_008796502.1| 20 LDDVVNQEQVVEALKniVVSKNVPHMLFAGPPGTGKTATAHAFAQ 64
                                      78999******99984333445579*************9998764 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.57
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgev 135
                                       +L+LDE  +++  +  ++R+ +e+ + 
  gi|557693448|ref|YP_008796502.1| 111 LLLLDESDQLTDAAQHAFRRTMEQFST 137
                                       589999999999999999999998765 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.5
                      Mg_chelatase 170 ectcsekeierYlsklsgplldRi 193
                                       ++tc     ++Y +++ +p+  R 
  gi|557693448|ref|YP_008796502.1| 136 STTCRFILAANYSNRIIEPIQSRC 159
                                       556667777889999999988886 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   9.4e-05     0.058       7      60 ..      44      95 ..      38     102 .. 0.78
   2 ?    6.3   0.0     0.018        11      76     129 ..      85     145 ..      78     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.4e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrel 60
                                      +++  G++GtGKT ++  +++ l     + +  e+ ++++++++ + + +++++++
  gi|557693448|ref|YP_008796502.1| 44 HMLFAGPPGTGKTATAHAFAQDL---FGP-RyiEDGHFIEINASDERGIETIRERV 95
                                      67889***************998...222.24677777788888887877777765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.018
                            AAA_22  76 eellealeqalrarav........ielliiDEaqhlrseealeeLrsllnlsrkgvqliLvG 129
                                       e+ +e++++ ++++a+         +ll++DE + l +++a   +r+ ++  ++ +++iL+ 
  gi|557693448|ref|YP_008796502.1|  85 ERGIETIRERVKTYARsvpfggigFRLLLLDESDQL-TDAAQHAFRRTMEQFSTTCRFILAA 145
                                       55567777777777777777888889**********.8777777777777677777777765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       2.5   1.5e+03      70      92 ..      20      41 ..      13      50 .. 0.80
   2 !   18.5   0.0   2.6e-06    0.0016       6      99 ..      46     145 ..      41     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.5
                            AAA_14 70 lDEiqevpewekalkslvdegkn 92
                                      lD + + +++ +alk++v ++ n
  gi|557693448|ref|YP_008796502.1| 20 LDDVVNQEQVVEALKNIVVSK-N 41
                                      899999999******999988.4 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.6e-06
                            AAA_14   6 vitGaRrvGKTtllkqlikell....vkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqevp 77 
                                       +  G+  +GKT  ++ ++++l+    +++ ++++in  der  +   + ++ ++ ++  + + + ++l+lDE  +++
  gi|557693448|ref|YP_008796502.1|  46 LFAGPPGTGKTATAHAFAQDLFgpryIEDGHFIEINASDERGIETIRE-RVKTYARSVpFGGIGFRLLLLDESDQLT 121
                                       5679999********************************999775544.577777776655578899*****97776 PP

                            AAA_14  78 e.wekalkslvdeg.knldvivtG 99 
                                       + +++a ++ +++  + +++i++ 
  gi|557693448|ref|YP_008796502.1| 122 DaAQHAFRRTMEQFsTTCRFILAA 145
                                       626677888888776677777754 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 !   17.9   0.0     4e-06    0.0024       8      56 ..      26      76 ..      23     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4e-06
                                      HHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.......- CS
                            ResIII  8 QeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee..k 56
                                      Qe+++e+l++ + sk+  ++l++ + GtGKT +a ++++ l+  +++e  +
  gi|557693448|ref|YP_008796502.1| 26 QEQVVEALKNIVVSKNVPHMLFAGPPGTGKTATAHAFAQDLFGPRYIEdgH 76
                                      999999999999989999**********************99988877553 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.8e-06    0.0048      29      87 ..      26      84 ..       4      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.8e-06
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXX CS
                             TIP49 29 qkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelg.....edvpfvalsgse 87
                                      q++  ea   + +++ +k++    +L+aGp+gtGkta a a +++l      ed +f+ +++s+
  gi|557693448|ref|YP_008796502.1| 26 QEQVVEA---LKNIVVSKNVP--HMLFAGPPGTGKTATAHAFAQDLFgpryiEDGHFIEINASD 84
                                      5555444...45666777776..79*******************99434444677888888886 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00035      0.22      23      58 ..      30      65 ..      19      80 .. 0.85
   2 ?    2.1   0.0      0.18   1.1e+02     117     144 ..     106     133 ..      86     141 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00035
                              TniB 23 LeeLleypkrkrmpnlllvGdsnnGKtmivekFarl 58
                                       e+L +   +k +p++l++G++ +GKt+ ++ Fa++
  gi|557693448|ref|YP_008796502.1| 30 VEALKNIVVSKNVPHMLFAGPPGTGKTATAHAFAQD 65
                                      4666677778999********************976 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.18
                              TniB 117 elkvrvLiiDEihnllagsarkqrefln 144
                                        ++ r+L++DE ++l  + +++ r++++
  gi|557693448|ref|YP_008796502.1| 106 GIGFRLLLLDESDQLTDAAQHAFRRTME 133
                                       5789***********9988887777765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.1e-05     0.037       8      44 ..      25      67 ..      21      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.1e-05
                                      HHHHHHHHHH....H-S..EEEEE--TTSSTTHHHHHHHHHHH CS
                              PhoH  8 eQkeylealk....knd..ivfaiGpaGtGKtylavalaveal 44
                                      +Q++++ealk    +++   +  +Gp GtGKt  a a a +++
  gi|557693448|ref|YP_008796502.1| 25 NQEQVVEALKnivvSKNvpHMLFAGPPGTGKTATAHAFAQDLF 67
                                      899999999977773333367889************9998765 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 ?   13.8   0.0   5.2e-05     0.032      31      57 ..      40      66 ..      24      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.2e-05
                             AAA_7 31 knkkpvllvGptGtGKtviikdllkkl 57
                                      kn  ++l+ Gp GtGKt++++ + + l
  gi|557693448|ref|YP_008796502.1| 40 KNVPHMLFAGPPGTGKTATAHAFAQDL 66
                                      44457999***********99988776 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.7e-05     0.029       8      42 ..      31      67 ..      24     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-05
                            AAA_11  8 eaiksalsese..itliqGPPGtgKTktivellsqll 42
                                      ea+k+++ +++    l+ GPPGtgKT t  ++ + l 
  gi|557693448|ref|YP_008796502.1| 31 EALKNIVVSKNvpHMLFAGPPGTGKTATAHAFAQDLF 67
                                      5556666555556689***********9999888875 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.08      22     105 ..      15      98 ..       2     103 .. 0.76
   2 ?   -2.7   0.0       4.2   2.6e+03     190     220 ..     162     192 ..     160     198 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                            DUF815  22 vdevklddLvgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeeg....Lrlievekedlke 94 
                                       +++ +ldd+v+    +e++ve  ++ +  ++  ++L+ G  GtGK ++ +a  +++         ++ie++ +d + 
  gi|557693448|ref|YP_008796502.1|  15 YRPRRLDDVVN----QEQVVEALKNIVVSKNVPHMLFAGPPGTGKTATAHAFAQDLFGPRyiedGHFIEINASDERG 87 
                                       44444444443....456788888899999**********************9998776655556899999999888 PP

                            DUF815  95 lpklvellrer 105
                                       ++++ e +++ 
  gi|557693448|ref|YP_008796502.1|  88 IETIRERVKTY 98 
                                       88888888866 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.2
                            DUF815 190 lgFykldqeeYleiveklakklglelekeel 220
                                       l F++l+++   ++++k+a++++++l+++++
  gi|557693448|ref|YP_008796502.1| 162 LRFKPLSKDMVETMLKKIAASENIKLDDSAI 192
                                       7788999999999999999999998887554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.4e-05     0.058       9      89 ..      41     173 ..      33     220 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.4e-05
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkp.eeillvaftgrAakelrerlaalgae................ 68 
                                       + +++l  ++pGtGKT + ++  + l   + ++  + i + a  +r  + +rer++++ ++                
  gi|557693448|ref|YP_008796502.1|  41 NVPHMLFAGPPGTGKTATAHAFAQDLFGPRYIEDgHFIEINASDERGIETIRERVKTYARSvpfggigfrlllldes 117
                                       55678888999*******99999887765555432567777888899999999986666556666666666666666 PP

                            AAA_19  69 ...........atTiHrlal........................ldfddllteale 89 
                                                   +T+ ++++                        l f++l ++++e
  gi|557693448|ref|YP_008796502.1| 118 dqltdaaqhafRRTMEQFSTtcrfilaanysnriiepiqsrcavLRFKPLSKDMVE 173
                                       65555555544222222222444444555666666666666666555555555554 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   0.00014     0.086      37      71 ..      32      66 ..      14     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                         IstB_IS21 37 eLatlsfiekkenivllGpsGvGKshlaialgvea 71
                                      +L +    ++   +++ Gp+G+GK+  a a++++ 
  gi|557693448|ref|YP_008796502.1| 32 ALKNIVVSKNVPHMLFAGPPGTGKTATAHAFAQDL 66
                                      55555555556678999**************9864 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016     0.097       9      59 ..      27      83 ..      22      90 .. 0.77
   2 ?   -2.3   0.1       5.1   3.2e+03      97     119 ..     112     134 ..     110     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHCTSS..S-EEEECSTTSSHHHHHHHHHH....HSTTTTS-EEEEETT CS
                   Sigma54_activat  9 kelleqikkvaktd..lsvlitGesGtGKellaraihe....askrkekpfvavnca 59
                                      ++++e +k+++ ++   ++l  G  GtGK+  a+a  +     +  ++++f+++n +
  gi|557693448|ref|YP_008796502.1| 27 EQVVEALKNIVVSKnvPHMLFAGPPGTGKTATAHAFAQdlfgPRYIEDGHFIEINAS 83
                                      56777777777655557999**********999998776643555588999999976 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.1
                                       EEEETGGGS-HHHHHHHHHHHHH CS
                   Sigma54_activat  97 lfLDeigelplelQekLlrvlqe 119
                                       l+LDe  +l+ ++Q+ + r +++
  gi|557693448|ref|YP_008796502.1| 112 LLLDESDQLTDAAQHAFRRTMEQ 134
                                       89999999999999998888876 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   0.00015      0.09      17      52 ..      44      83 ..      27      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00015
                        Zeta_toxin 17 klillgGqpGAGKselaellkdele.....rqgnvvrldpD 52
                                        +l +G pG GK+++a++++++l      ++g ++++++ 
  gi|557693448|ref|YP_008796502.1| 44 H-MLFAGPPGTGKTATAHAFAQDLFgpryiEDGHFIEINAS 83
                                      4.467*****************9987766677777777765 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   0.00017       0.1       1      91 [.      44     137 ..      44     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00017
                             AAA_3   1 hvllegvPGlaktllvkalakal.dlefkriqftpdllPsdilGtevfeekekef..efkkGpvfanllladeinra 74 
                                       h+l+ g PG++kt +++a+a+ l + ++       ++  sd  G+e ++e+ k++  ++  G +   lll de ++ 
  gi|557693448|ref|YP_008796502.1|  44 HMLFAGPPGTGKTATAHAFAQDLfGPRYIEDGHFIEINASDERGIETIRERVKTYarSVPFGGIGFRLLLLDESDQL 120
                                       99******************976256666666778899999999999999887762245679999999999999999 PP

                             AAA_3  75 ppktqsalleameerqv 91 
                                       +  +q a+  +me+   
  gi|557693448|ref|YP_008796502.1| 121 TDAAQHAFRRTMEQFST 137
                                       99999999999987655 PP

>> DNA_pol3_gamma3  DNA polymerase III subunits gamma and tau domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.13       2      55 ..     221     275 ..     220     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                   DNA_pol3_gamma3   2 saaqVrdmLGladrarlldlleallegdaaaalaelreq.yaaGadpvvvlrdLl 55 
                                       + +++ d++G+++r++++++l+ +l+g+  +a + lre+ y +G+ p  ++++++
  gi|557693448|ref|YP_008796502.1| 221 DSKTIYDVMGVVSRGEITRMLQLVLDGKFIEARNLLRELlYVQGYQPTDIVSSIA 275
                                       567899******************************9953889999998888776 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 ?   10.9   0.0   0.00028      0.17     105     155 ..      20      68 ..      12     102 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                             T2SSE 105 lddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                       ldd++ +e++ e++++++ +   +   +l++G+ g+GKt ++ a  + +  
  gi|557693448|ref|YP_008796502.1|  20 LDDVVNQEQVVEALKNIVVSK--NVPHMLFAGPPGTGKTATAHAFAQDLFG 68 
                                       667777777777777776666..56789*************9998877654 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00041      0.26       3      28 ..      46      73 ..      44     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00041
                            AAA_28  3 vitGgestGKTtlleaLaar..gypvvp 28
                                       + G+++tGKT ++ a+a++  g ++++
  gi|557693448|ref|YP_008796502.1| 46 LFAGPPGTGKTATAHAFAQDlfGPRYIE 73
                                      588***************8777666654 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   0.00056      0.35       4      39 ..      26      63 ..      23     102 .. 0.80
   2 ?   -2.4   0.0       5.3   3.3e+03     157     187 ..     187     216 ..     168     220 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00056
                            AAA_30  4 aeQ.aaavealltsgdr.vavltGpAGtGKttalkalr 39
                                      +eQ  +a+++++ s++   ++  Gp+GtGKt +  a +
  gi|557693448|ref|YP_008796502.1| 26 QEQvVEALKNIVVSKNVpHMLFAGPPGTGKTATAHAFA 63
                                      55523678888888775256789********9988765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.3
                            AAA_30 157 qkeseeraaalalregdaeealealadrgri 187
                                         +++  +a  +++ gd+++a++ l++   i
  gi|557693448|ref|YP_008796502.1| 187 L-DDSAIDAIYEFSLGDMRKAINILQSAASI 216
                                       4.34555666677777777777766665555 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 ?   10.5   0.0   0.00073      0.45       1      23 [.      44      66 ..      44      77 .. 0.85
   2 ?   -2.9   0.0       9.8   6.1e+03      96     121 ..     114     146 ..     110     158 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00073
                                      EEEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal 23
                                      ++l  GppGtgK+  a  +a+ l
  gi|557693448|ref|YP_008796502.1| 44 HMLFAGPPGTGKTATAHAFAQDL 66
                                      68999***********9998765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.8
                                       ..-SSSEEE---.............-EEEEEES CS
                             AAA_5  96 leeggelvkaknddller.......frviatan 121
                                       l+e+++l++a++  + ++        r+i +an
  gi|557693448|ref|YP_008796502.1| 114 LDESDQLTDAAQHAFRRTmeqfsttCRFILAAN 146
                                       444444444444332222445555566666666 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00061      0.38       2      24 ..      46      68 ..      45      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00061
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallk 24
                                      ++ Gp+g+GK+ +a+ +a++l +
  gi|557693448|ref|YP_008796502.1| 46 LFAGPPGTGKTATAHAFAQDLFG 68
                                      689****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2182.96
//
Query:       gi|557693449|ref|YP_008796503.1|  [L=244]
Description: TatD DNase family protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-58  195.8   0.0      9e-58  195.6   0.0    1.0  1  TatD_DNase    TatD related DNase
     0.0091   15.3   0.0      0.038   13.3   0.0    1.9  2  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
      0.042   14.0   0.0      0.073   13.2   0.0    1.4  1  RTC4          RTC4-like domain


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 !  195.6   0.0   1.5e-61     9e-58       1     254 [.       2     242 ..       2     243 .. 0.93

  Alignments for each domain:
  == domain 1  score: 195.6 bits;  conditional E-value: 1.5e-61
                                       EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHH CS
                        TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleel 77 
                                       iD HcHl+++ + ++  e++e+a++++v+a+++ g+ ++d ++vl ++ k   ++y +lGi P+ ++       e++
  gi|557693449|ref|YP_008796503.1|   2 IDVHCHLTEEPLFSNLGEVIEEAKKSSVEAIITSGIGPADCEKVLSIVDK--VYIYGSLGIEPYALEG-----YEQV 71 
                                       8********555699999******************************98..458********77774.....3444 PP

                                       HHHHHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCSEEEE CS
                        TatD_DNase  78 kelanvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaaeakakvvl 154
                                        el   ++++vva+Ge+GLDyy+ +++t+e q +vF+e+++lAk l+lplviH+r+a +  l+il e++++  +vv+
  gi|557693449|ref|YP_008796503.1|  72 IELIMRNRERVVAVGEVGLDYYWGKKETREMQAKVFREFIQLAKSLDLPLVIHSRSAGKYALDILIEERAE--RVVM 146
                                       45546689***********************************************************9755..6*** PP

                                       TT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHH CS
                        TatD_DNase 155 HsfsgsaeeakkflklgyyislsglltfknakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvvekl 231
                                       H f gsa ea++ + +gy++s++  ++   +++ +++v+++ l++lL+E+DaP l p   rg +n+p n+a +++++
  gi|557693449|ref|YP_008796503.1| 147 HAFDGSAGEAARGAAKGYFFSVPPSVVR--SEQKQKMVRRLGLENLLLESDAPVLGP--ERGVVNKPSNIAVSAKTI 219
                                       ************************9888..67889**********************..999*************** PP

                                       HHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 232 aelkaltleelaeitaeNakrlf 254
                                       a lk+++le++ e+t+eNak +f
  gi|557693449|ref|YP_008796503.1| 220 ASLKNIPLEKVLEKTTENAKNIF 242
                                       *********************99 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   6.4e-06     0.038       6     229 ..       1     196 [.       1     202 [. 0.69
   2 ?   -2.4   0.0      0.37   2.2e+03     279     298 ..     224     243 ..     210     244 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.4e-06
                                       EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEEEEEE CS
                      Amidohydro_1   6 lIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglrilgg 82 
                                       +ID+H Hl   +l++         +e ++ea +s +++ + sG++++         +i +    + +l  g++ ++ 
  gi|557693449|ref|YP_008796503.1|   1 MIDVHCHLTEEPLFS-------NLGEVIEEAKKSSVEAIITSGIGPADCEKVL---SIVDKVYIYGSL--GIEPYAL 65 
                                       69******9999877.......699*********************8544443...666666677775..5555555 PP

                                       SSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE.....TS CS
                      Amidohydro_1  83 kvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHa.....le 154
                                             + +e+ ++++ + ++++     + ++++++ + + +e  + ++   +e +++ak  dlp++iH        
  gi|557693449|ref|YP_008796503.1|  66 ------EGYEQVIELIMRNRERV----VAVGEVGLDYYWGKKETREMQAKVFREFIQLAKSLDLPLVIHSrsagkYA 132
                                       ......55555555555555555....55578888999999999999999*******************99633333 PP

                                       SCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE..HHHHHHHHHHHHHHCEEHHHHHHHHSEHHH CS
                      Amidohydro_1 155 tkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt..pteaellkerlkeagvahcpfsnsilrsgr 229
                                       ++  +e++ +  +   +h   +++   + +++     +a+g +++  p+ +++  ++  +++v  +  +n+ l+s+ 
  gi|557693449|ref|YP_008796503.1| 133 LDILIEERAERVV---MH--AFDGSA-GEAARG----AAKGYFFSvpPS-VVRSEQK--QKMVRRLGLENLLLESDA 196
                                       3333333333333...55..444433.344555....888888887444.4444444..777777777777777765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.37
                                       HCHHHHHHHHHTHHHHHHTT CS
                      Amidohydro_1 279 glslkealrmaTingAkalg 298
                                       +++l+++l+++T n+  +++
  gi|557693449|ref|YP_008796503.1| 224 NIPLEKVLEKTTENAKNIFR 243
                                       68899999999999987776 PP

>> RTC4  RTC4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05     0.073      41     105 ..      93     156 ..      67     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                              RTC4  41 YYGlkgqriiseeilkkfkkelrkravkdklvsargvsdFvqaVLvPEvavrLimeDmkvseeeA 105
                                       Y+G k  r +   ++++f  +l k+   + ++++r++ +++  +L+ E a r +m+ ++ s+ eA
  gi|557693449|ref|YP_008796503.1|  93 YWGKKETREMQAKVFREF-IQLAKSLDLPLVIHSRSAGKYALDILIEERAERVVMHAFDGSAGEA 156
                                       89****************.5555557777799************************998888555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1828.72
//
Query:       gi|557693450|ref|YP_008796504.1|  [L=121]
Description: hypothetical protein CSUB_C0005 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 898.08
//
Query:       gi|557693451|ref|YP_008796505.1|  [L=219]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-34  119.8   0.1    1.3e-34  119.5   0.1    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
    9.6e-20   71.0   0.0    1.3e-19   70.6   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0055   16.7   3.2      0.014   15.4   3.2    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.075   14.1   0.0       0.24   12.4   0.0    1.8  2  DUF3298        Protein of unknown function (DUF3298)


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 !  119.5   0.1   2.9e-38   1.3e-34       1     163 []       9     190 ..       9     190 .. 0.91

  Alignments for each domain:
  == domain 1  score: 119.5 bits;  conditional E-value: 2.9e-38
                     Lactamase_B_3   1 eltwlghnsflletagarilvDPfkanlgyeppaeeaDlvlisqaledHahletlkql................... 58 
                                       e+twlgh  f+++ ++ ++++DP++         +  Dlvlis+++ dH  l+ l+++                   
  gi|557693451|ref|YP_008796505.1|   9 EITWLGHDGFRITRGNFVVYIDPYQ-----ITGGPAGDLVLISHDHFDHLSLDDLRKIvsnkttivaarncqkqlge 80 
                                       69**********************9.....455799**********************9999999999999999999 PP

                     Lactamase_B_3  59 ..aenvkvleegeslevggleiravatsh.......davggsergenngflleqdgltiyhlGhlahelsseelkel 126
                                            vk++++g+++ vg+++++av++++        +v  +++ +++gf+l+ +g++iyh G+++     +e k l
  gi|557693451|ref|YP_008796505.1|  81 ikVAAVKYVSPGDEVSVGEAKVKAVHAYNvnkfrepGKVFHPKEYGGVGFVLTLGGVSIYHAGDTDF---IPEMKGL 154
                                       99999999999******************777654433333344569*******************9...8999888 PP

                     Lactamase_B_3 127 grvDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                        rvDv l+Pv g++++ ++ea+e+ak +++k v+Pmh
  gi|557693451|ref|YP_008796505.1| 155 -RVDVALLPVSGTYVMTAAEAVEAAKSMQAKTVIPMH 190
                                       .***********************************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 !   70.6   0.0   2.8e-23   1.3e-19      29     201 .]      38     191 ..      22     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 2.8e-23
                                       .SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEE CS
                     Lactamase_B_2  29 ppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdgglei 105
                                       p+ d+Vl++h+H+DHl  l++lr++  +k +++a + ++++l +         +   +v+ + +g+++++g++  ++
  gi|557693451|ref|YP_008796505.1|  38 PAGDLVLISHDHFDHL-SLDDLRKIVSNKTTIVAARNCQKQLGEI--------K-VAAVKYVSPGDEVSVGEA--KV 102
                                       6779************.6******666567777777777777777........3.55778889*******854..46 PP

                                       EEEEE-EE--C.....TCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT CS
                     Lactamase_B_2 106 tatparhksgr.....rldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemirhmg 177
                                       +a+ a    +       + +++   +G++++ gg ++y++gDt +ipe+ g  l+ +d++ll++          + +
  gi|557693451|ref|YP_008796505.1| 103 KAVHAYNVNKFrepgkVFHPKEYGGVGFVLTLGGVSIYHAGDTDFIPEMKG--LR-VDVALLPVS---------GTY 167
                                       66655544444455777788888999*********************8844..54.99*****88.........889 PP

                                       ---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 178 HltpeeaveaaadlgakrlvliHi 201
                                        +t  eaveaa+ ++ak+++++H+
  gi|557693451|ref|YP_008796505.1| 168 VMTAAEAVEAAKSMQAKTVIPMHY 191
                                       9**********************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.2   3.2e-06     0.014      46     197 .]      41     190 ..      35     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.2e-06
                                       EEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEE CS
                       Lactamase_B  46 davilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrra 122
                                       d v+++H H+DH + l++l++   +++ +va+  +     e + aa++  +++ +vs+    v+         +r+ 
  gi|557693451|ref|YP_008796505.1|  41 DLVLISHDHFDHLS-LDDLRKIVSNKTTIVAARNCQKQLGEIKVAAVKYVSPGDEVSVGEAKVKAVHAYNVNKFREP 116
                                       679*********85.8999999999999999999999999999999999999999********************** PP

                                       EEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 123 lyvtggpghghghgvveygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       ++v++    g++++v+++gg ++  +GD+ +++e   ++     + +  +  ++ + ++++ ++ + a++++p H
  gi|557693451|ref|YP_008796505.1| 117 GKVFHPKEYGGVGFVLTLGGVSIYHAGDTDFIPEMKGLRV-DVALLPVSGTYVMTAAEAVEAAKSMQAKTVIPMH 190
                                       *******************************877665555.4567777777777777788888888888888877 PP

>> DUF3298  Protein of unknown function (DUF3298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.4e-05      0.24      45      76 ..      11      42 ..       6      45 .. 0.89
   2 ?   -1.5   0.0       1.2   5.6e+03      50      61 ..     128     139 ..      63     147 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.4e-05
                                      S-TTTSSEEEETTEEEEEE-TTSSS-GGG-SE CS
                           DUF3298 45 dilgyqnfyltddglviyfppYeiaPyaaGap 76
                                      ++lg + f +t ++ v+y +pY+i  + aG+ 
  gi|557693451|ref|YP_008796505.1| 11 TWLGHDGFRITRGNFVVYIDPYQITGGPAGDL 42
                                      6788999******************9999986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                                       SSEEEETTEEEE CS
                           DUF3298  50 qnfyltddglvi 61 
                                         f+lt +g+ i
  gi|557693451|ref|YP_008796505.1| 128 VGFVLTLGGVSI 139
                                       335555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1572.77
//
Query:       gi|557693452|ref|YP_008796506.1|  [L=150]
Description: hypothetical protein CSUB_C0007 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); 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:                         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: 00:00:00.41
# Mc/sec: 1087.67
//
Query:       gi|557693453|ref|YP_008796507.1|  [L=143]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-10   39.3   0.0      8e-10   39.0   0.0    1.1  1  SnoaL_3    SnoaL-like domain
    0.00011   22.5   0.0    0.00015   22.1   0.0    1.2  1  DUF4440    Domain of unknown function (DUF4440)
  ------ inclusion threshold ------
      0.019   15.1   0.0       0.25   11.5   0.0    2.1  2  CaMKII_AD  Calcium/calmodulin dependent protein kinase II ass


Domain annotation for each model (and alignments):
>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   1.3e-13     8e-10       7     118 ..      18     136 ..      12     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.3e-13
                           SnoaL_3   7 afyeaaaegdfdalfalwaddivfigtgadelltgreevrrslkqifakgegisfeltdvrvtesgdvawvtelldv 83 
                                       + +ea ++gd +++ +l++   + +   ++ +l +ree ++     + +   ++++l++ +   +gdva+++ ll++
  gi|557693453|ref|YP_008796507.1|  18 EALEAGIRGDEETFNDLHSHGYTRYSDLPPYRLQSREEALKLKISLLTQLIDFEYSLENFQTFYHGDVAVACFLLRY 94 
                                       66788899999999999998888888788889999****************************************** PP

                           SnoaL_3  84 ..taa.edgteg....egqlrlTgvlrrtdggWkivhhhlS.v 118
                                           a +d + +    eg  r+T+vl++++++W+i+h hlS v
  gi|557693453|ref|YP_008796507.1|  95 rgM-AvNDYAFEgrmvEGVARCTVVLEKNGDKWRILHEHLSrV 136
                                       652.2366666656658888*********************44 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.5e-08   0.00015      11     107 .]      22     128 ..      11     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.5e-08
                                       HHHCT-HHHHHHCEEEEEEEE-TT..S-EEEHHHHHHHHHCCHCEEEEEEEEEEEEEEE..TTEEEEEEEEEEEE.. CS
                           DUF4440  11 afvagdaealaallapdavlvgps..gtvldkeellealeagfaagrslelteeevrvl..gdlAvvtgrytfeg.. 81 
                                       a  +gd e++++l++   + + +    +++++ee l+   +  ++  ++e++ e  ++   gd+Av+++  +++g  
  gi|557693453|ref|YP_008796507.1|  22 AGIRGDEETFNDLHSHGYTRYSDLppYRLQSREEALKLKISLLTQLIDFEYSLENFQTFyhGDVAVACFLLRYRGma 98 
                                       5557888888888888888887775566678888888877777888888888888877778*******887776633 PP

                                       CCT....TEEEEEEEEEEEEEEEETTEEEE CS
                           DUF4440  82 rgd....gepvegrgrftsvwrkegggWri 107
                                       ++d    g+ veg +r+t v++k+g++Wri
  gi|557693453|ref|YP_008796507.1|  99 VNDyafeGRMVEGVARCTVVLEKNGDKWRI 128
                                       334666688999*****************8 PP

>> CaMKII_AD  Calcium/calmodulin dependent protein kinase II association domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.039   2.3e+02       2      35 ..       9      42 ..       8      60 .. 0.86
   2 ?   11.5   0.0   4.3e-05      0.25      97     127 ..     106     136 ..      73     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.039
                                      HHHHHHHHHHHHHHHHTT-HHHHHHHEEEEEEEE CS
                         CaMKII_AD  2 kqeiiklletlleaisegdfetytklcdpeltvf 35
                                      ++e+ +++ + lea   gd et+++l     t +
  gi|557693453|ref|YP_008796507.1|  9 AEEVYRVVVEALEAGIRGDEETFNDLHSHGYTRY 42
                                      6899999999999999********9988877665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.3e-05
                                       S-EEEEEEEEEEEEEEETTEEEEEEEEEE-X CS
                         CaMKII_AD  97 GkkhtrqseetrVwekrdgkWkivhvHrSaa 127
                                       G+  +  ++ t V ek  +kW+i+h H S  
  gi|557693453|ref|YP_008796507.1| 106 GRMVEGVARCTVVLEKNGDKWRILHEHLSRV 136
                                       5555567899*****************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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 0.28s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1017.89
//
Query:       gi|557693454|ref|YP_008796508.1|  [L=89]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 646.47
//
Query:       gi|557693455|ref|YP_008796509.1|  [L=135]
Description: hypothetical protein CSUB_C0010 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0096   15.8   0.0      0.013   15.3   0.0    1.2  1  DUF3636   Protein of unknown function (DUF3636)


Domain annotation for each model (and alignments):
>> DUF3636  Protein of unknown function (DUF3636)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   7.4e-07     0.013      55     115 ..      73     134 ..      71     135 .] 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 7.4e-07
                                       GGGG--SS-SS----HHHHHHHHHHHHHHHHHHHHHS--T.....TS-TTSHHHHHHHHHHH CS
                           DUF3636  55 LstSvlpdsfGpisseeedqkavekaiidrvsnlLteepr.adegeakvteaeilelrleaL 115
                                       ++tSv + s+ +i+s + +  +  ka ++rv+ +L+e  r ++ +++  ++ e+l +r++ L
  gi|557693455|ref|YP_008796509.1|  73 MQTSVAQVSLNTIPSAALKNIKDVKAFVNRVAEHLSEWARrMPDTNPVKKRVETLLMRVRQL 134
                                       78************************************962566666666677777887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 993.23
//
Query:       gi|557693456|ref|YP_008796510.1|  [L=158]
Description: hypothetical protein CSUB_C0011 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  105.5   0.0    2.4e-30  105.2   0.0    1.1  1  DHNA      Dihydroneopterin aldolase


Domain annotation for each model (and alignments):
>> DHNA  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.0   1.3e-34   2.4e-30       1     107 [.      27     131 ..      27     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 1.3e-34
                                       -HHHHHHHHHHHHHHHHHHHHTT-EESTTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-STS-EE--TTTE CS
                              DHNA   1 tdrerAvFEagiklgalyHqfvGtPvseesaeslekaieesielQPfvedvkvkidrekleekleefgYteLtgeml 77 
                                       +drerAvFEagi+lgal+H  +G P ++e++++leka+e+s++lQPf ++vk+k+   k  +k+  +gY ++  + +
  gi|557693456|ref|YP_008796510.1|  27 SDRERAVFEAGIALGALFHSLIGLPATTETKHILEKAFEKSFSLQPFRKSVKLKLYAVK--RKHGPYGYGSIGPRDI 101
                                       69***************************************************998865..55556*********** PP

                                       EEEEEEEETTEEEEEEEEEETTTTEEEEEE CS
                              DHNA  78 dveitvkyeeaevkarleyieeldYplmkv 107
                                       ++++tv y+ a+++a+++y+++l+Yplm+v
  gi|557693456|ref|YP_008796510.1| 102 SASVTVCYGAATAVAEVRYVASLGYPLMYV 131
                                       *****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1141.62
//
Query:       gi|557693457|ref|YP_008796511.1|  [L=370]
Description: molecular chaperone DnaJ [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  101.7   2.6      3e-29  101.0   2.6    1.4  1  DnaJ           DnaJ domain
    3.1e-20   72.8   0.0    3.8e-20   72.5   0.0    1.1  1  DnaJ_C         DnaJ C terminal domain
    2.9e-10   40.4  16.2    4.6e-10   39.7  16.2    1.3  1  DnaJ_CXXCXGXG  DnaJ central domain
  ------ inclusion threshold ------
        0.7    9.5   2.7        5.4    6.6   0.1    2.2  2  TackOD1        Thaumarchaeal output domain 1
        1.5    8.8  13.9        3.7    7.6   2.6    2.7  2  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi
        2.4    8.1  10.0         15    5.6   0.7    3.5  3  zf-FPG_IleRS   Zinc finger found in FPG and IleRS


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   2.6   9.9e-33     3e-29       1      63 []       7      68 ..       7      68 .. 0.99

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 9.9e-33
                                      HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                              DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                      dyYeiLgv+++a+++eIk+aYr+lal+yHPD+n k+peaeekFkei+eAy vL+d+ekR+ YD
  gi|557693457|ref|YP_008796511.1|  7 DYYEILGVPRNATKEEIKRAYRRLALQYHPDRN-KSPEAEEKFKEISEAYAVLMDDEKRRLYD 68
                                      8********************************.****************************9 PP

>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   1.3e-23   3.8e-20       3     148 .]     126     338 ..     124     338 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 1.3e-23
                                       EEEEE-HHHHHH-.EEE.EEEE....................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                            DnaJ_C   3 veleisleelykGktkkikikrnvi.................................................... 27 
                                       v++eisleely+G  ++i ++  ++                                                    
  gi|557693457|ref|YP_008796511.1| 126 VDVEISLEELYRGGVREIPLETYETcqrcggaggepgyvdkcvecggtgqsvkrvqtgflyftsvqpcgrcggtgrv 202
                                       799*****************99999**************************************************** PP

                                       .................TEEEEEE-TT--TT-EEEETT-SSSS....S---EEEEEEE---SS-EEETTEEEEEEEE CS
                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  28 .............kkekktlevkipaGikdgqkirlegeGdeeg..gepGDlivtikvkphpvFkrkgndlyvevei 89 
                                                    +++++++ v+ip+G+ dg++++l+g+G   +  g +GDl+v+++vk  + F+ ++n l++ +++
  gi|557693457|ref|YP_008796511.1| 203 vrrscsacrgrgmVSRTEKVVVNIPPGVGDGETLVLRGRGLYDMdaGSRGDLLVRVHVKLGRWFRFEDNRLVMLLPV 279
                                       ************9889999*********************955556************9****************** PP

                                       EHHHHHHTEEEEEE-SS-EEEEEE..--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  90 slaeallGgklevptldgkvklki..tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                         +e +  ++++vp +dg++k+k+     ++ l+i+gkG p    +g++ dl +++  ++P
  gi|557693457|ref|YP_008796511.1| 280 APSEVASQREITVPFFDGDIKVKLrrELLDKPLVIRGKGPPMA--GGRKSDLEIRLVLKMP 338
                                       **********************996544567899********9..7********9999998 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7  16.2   1.5e-13   4.6e-10       1      67 []     151     214 ..     151     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 1.5e-13
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                       C++C G g ++g +++C +C+G+G+ +++ + +g+++ +s ++C +C+GtG+v+  ++ C++C+G+g
  gi|557693457|ref|YP_008796511.1| 151 CQRCGGAGGEPGYVDKCVECGGTGQSVKRVQ-TGFLYFTSVQPCGRCGGTGRVV--RRSCSACRGRG 214
                                       *********99*************6544443.5555556789************..556******86 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0018       5.4     146     171 ..     148     173 ..     141     186 .. 0.74
   2 ?    2.7   0.5     0.029        85      72      95 ..     189     212 ..     180     220 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0018
                           TackOD1 146 vykCnsCkslfsepevkarClsCeke 171
                                         +C++C+ +  ep    +C++C+ +
  gi|557693457|ref|YP_008796511.1| 148 YETCQRCGGAGGEPGYVDKCVECGGT 173
                                       45799999999999999999998765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.029
                           TackOD1  72 rirlCpsCksghlnvrevCpkCkS 95 
                                       +++ C +C +    vr +C+ C+ 
  gi|557693457|ref|YP_008796511.1| 189 SVQPCGRCGGTGRVVRRSCSACRG 212
                                       6788******************85 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.6    0.0012       3.7      11      40 ..     149     174 ..     142     183 .. 0.83
   2 ?    6.1   3.6    0.0036        11      12      42 ..     192     216 ..     189     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
                                       EE-TTTTTTSEETTE......E-TTTTTSS CS
                         Anti-TRAP  11 tkCdaCngsGkiepeeprasleCPkCsGkg 40 
                                       ++C+ C g+G +++       +C +C+G g
  gi|557693457|ref|YP_008796511.1| 149 ETCQRCGGAGGEPGY----VDKCVECGGTG 174
                                       689999999998888....668****9987 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0036
                                       E-TTTTTTSEETTE......E-TTTTTSSEE CS
                         Anti-TRAP  12 kCdaCngsGkiepeeprasleCPkCsGkgli 42 
                                       +C  C g+G++          C +C G+g++
  gi|557693457|ref|YP_008796511.1| 192 PCGRCGGTGRVVRR------SCSACRGRGMV 216
                                       8***********99......9********97 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 ?    3.0   0.2     0.031        93       2       9 ..     149     156 ..     149     158 .. 0.84
   2 ?    4.1   0.2     0.014        42       3      15 ..     166     178 ..     165     182 .. 0.88
   3 ?    5.6   0.7     0.005        15       2      12 ..     191     201 ..     191     206 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.031
                                       SB-TTT-- CS
                      zf-FPG_IleRS   2 epCpRCwr 9  
                                       e C RC++
  gi|557693457|ref|YP_008796511.1| 149 ETCQRCGG 156
                                       67****97 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.014
                                       B-TTT--BBEEEE CS
                      zf-FPG_IleRS   3 pCpRCwryiervg 15 
                                       +C  C+++ ++v+
  gi|557693457|ref|YP_008796511.1| 166 KCVECGGTGQSVK 178
                                       9*******99987 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.005
                                       SB-TTT--BBE CS
                      zf-FPG_IleRS   2 epCpRCwryie 12 
                                       +pC RC+++ +
  gi|557693457|ref|YP_008796511.1| 191 QPCGRCGGTGR 201
                                       7******9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2596.03
//
Query:       gi|557693458|ref|YP_008796512.1|  [L=592]
Description: molecular chaperone DnaK [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-223  743.3   5.8   1.4e-220  733.6   5.8    2.0  1  HSP70          Hsp70 protein
    1.7e-18   66.5   3.1    2.1e-17   63.0   3.1    2.3  1  MreB_Mbl       MreB/Mbl protein
      3e-05   23.8   0.0    6.1e-05   22.8   0.0    1.6  1  FGGY_C         FGGY family of carbohydrate kinases, C-termina
     0.0027   17.0   0.0      0.027   13.7   0.1    2.4  3  StbA           StbA protein
  ------ inclusion threshold ------
      0.043   13.0   0.5      0.072   12.2   0.5    1.3  1  NCA2           ATP synthase regulation protein NCA2
      0.064   13.3   0.4       0.14   12.2   0.4    1.5  1  DUF45          Protein of unknown function DUF45
      0.089   12.5   0.1       0.85    9.3   0.0    2.7  2  Raco_middle    RACo middle region
      0.099   11.6   0.1       0.17   10.9   0.1    1.3  1  Emaravirus_P4  P4 movement protein of Emaravirus, and the 30K
       0.11   12.7   3.9       0.19   11.9   3.9    1.4  1  DUF3347        Protein of unknown function (DUF3347)
       0.17   12.3   7.4       0.22   11.9   0.0    3.9  4  FtsA           Cell division protein FtsA
        5.2    7.8   5.9         32    5.3   0.9    3.0  3  CdiI_2         CdiI immunity protein


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  733.6   5.8  8.6e-224  1.4e-220       1     598 [.       5     582 ..       5     583 .. 0.98

  Alignments for each domain:
  == domain 1  score: 733.6 bits;  conditional E-value: 8.6e-224
                                       EEEEEEXSSEEEEEEEETTEEEEEXXTTSX....SSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXB CS
                             HSP70   1 viGiDLGttnsvvavmeggkievianeegn....rttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrk 72 
                                       +iGiDLGt ns+ av+ gg++++i   eg     ++ Ps+va tk+ + lvGe+A+rqav np+ tv++ Kr +G++
  gi|557693458|ref|YP_008796512.1|   5 IIGIDLGTSNSAAAVVIGGRPTIIPSVEGVtlygKAFPSYVAITKEgDLLVGEPARRQAVLNPEGTVTAWKRRMGTD 81 
                                       69**************************963334789*********9*****************************8 PP

                                       TTSHHHHHHHTTXSSEEEEETTSBEEEEEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHH CS
                             HSP70  73 fsdpevqkeikelpykvvkkengkavveveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqR 149
                                       +                            + +g++ftp+q+sa++L+k+k++aea+lg++v++avitvPaYfnd+qR
  gi|557693458|ref|YP_008796512.1|  82 YRY--------------------------NLHGKEFTPQQLSAFLLQKIKRDAEAFLGEPVKKAVITVPAYFNDNQR 132
                                       875..........................23599******************************************* PP

                                       HHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHH CS
                             HSP70 150 qatkdAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedf 226
                                       qatkdAg iAGL+v+Ri+NepTAaalaYGl+k d+e ++lv+DlGggt dv i+e+++Gvfev+aTagDt+lGG d+
  gi|557693458|ref|YP_008796512.1| 133 QATKDAGVIAGLEVVRIINEPTAAALAYGLNKLDQEMKILVFDLGGGTLDVTIMEFGQGVFEVLATAGDTQLGGTDM 209
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTT.EEEEEEEEHHHHHHHH CS
                             HSP70 227 DealvehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedg.kdlseklsRakfeelv 302
                                       D+alv+++v+++++++gidls+dk a++r++eaae+aK+eLSs+++teinl++++ d++g k+l ++++Ra +e+lv
  gi|557693458|ref|YP_008796512.1| 210 DKALVDYIVDTYRRETGIDLSNDKSAMNRIREAAERAKIELSSMTETEINLPYIAYDSSGpKNLYMRINRATLEQLV 286
                                       ***************************************************************************** PP

                                       HHHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCG CS
                             HSP70 303 edllertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgee 379
                                       ++++er+  pv +al+daklk eeid+++lvGG tR+P +q+ +ke++gkep+++v+p e+va+GAA+qa++ sge+
  gi|557693458|ref|YP_008796512.1| 287 KPIVERCRGPVMQALQDAKLKPEEIDKIILVGGPTRMPIIQQFIKEVLGKEPERGVDPMECVAMGAAIQAAIISGEM 363
                                       ***************************************************************************** PP

                                       CSHCCEEEEBESS-EEEEETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEEC CS
                             HSP70 380 evkdllllDvtpLslgietlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldg 456
                                       + kd++llDv+p+slg+etlgg++tk+iernttip ++s++f+taad qt+vei+vlqger +++dn +lg+f+l+g
  gi|557693458|ref|YP_008796512.1| 364 KDKDIVLLDVVPISLGVETLGGIFTKIIERNTTIPVRRSEIFTTAADFQTSVEIHVLQGERPMAADNVSLGRFTLSG 440
                                       ***************************************************************************** PP

                                       ESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH CS
                             HSP70 457 ippaprGvpqieVtfdidanGiltvsakdketgkeeeitieaseglseeeiekmvkdaeesaeedkkkkeaieakne 533
                                       ippaprGvp+ieVtfdi+a+Giltv+akd +tgk+ +++i+a ++ls+ee+e+m+++ae++ae+d++kk+++e +ne
  gi|557693458|ref|YP_008796512.1| 441 IPPAPRGVPKIEVTFDINADGILTVTAKDLGTGKDVSVKITAPHRLSKEEVERMIREAEQFAEQDRRKKQEAELRNE 517
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHHHHHHHHHHHHHHHHHHH CS
                             HSP70 534 aeelvyslekkleeeaekvseaekekvesaieeLkeeleeeekeeieakteelkkvvekiaekly 598
                                       a+ l+y++ek+l+e ++kvs+++k++ve+ +++Lke+l+++++++i++++e+l+++++ki++++y
  gi|557693458|ref|YP_008796512.1| 518 ADGLIYTVEKALKEFGDKVSPEAKKEVEDDLAKLKEALAGKDIQAIKTALEKLRASAQKIGTAVY 582
                                       ************************************************************99876 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   3.1   1.3e-20   2.1e-17      74     318 ..      92     355 ..       3     363 .. 0.66

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 1.3e-20
                                       HHHHHHHH.HHHHHT..SS-S..S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--.TTSS CS
                          MreB_Mbl  74 aeellkyf.ikkvkk..kksl..skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglp.veep 144
                                       + + l  f ++k+k+  + +l  + ++ vi+vP   ++ +r+A k+a   aG + v +i+ep aAA+  gl+ +++ 
  gi|557693458|ref|YP_008796512.1|  92 TPQQLSAFlLQKIKRdaEAFLgePVKKAVITVPAYFNDNQRQATKDAGVIAGLEVVRIINEPTAAALAYGLNkLDQE 168
                                       4445554413455543222223356799*******************************************845667 PP

                                       S-EEEEEE-SS-EEEEEEETTEEE.....EEEEES-SHHHHHHHHHHHHHHHHSEE--HHHHH..HHHHHH-BSS-- CS
                          MreB_Mbl 145 sgnmvvdiGggttevavislggiv.....tsksvrvaGdeldeaiikyirkkynlliGertae..kikieigsavke 214
                                          +v d+Gggt +v+++ +g+ v     t+   +++G ++d+a+++yi  +y+   G   ++  +   +i +a+++
  gi|557693458|ref|YP_008796512.1| 169 MKILVFDLGGGTLDVTIMEFGQGVfevlaTAGDTQLGGTDMDKALVDYIVDTYRRETGIDLSNdkSAMNRIREAAER 245
                                       777899*************997552222255678999************9999988876433200222333333333 PP

                                       HHHH.....EEEEEEEETT..TTCEEE..EEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESG CS
                          MreB_Mbl 215 eeee.....kmeikGrdlv..tglpke..vevsseevrealkepvsaiveavkevLektppeLaadivdrgivltGG 282
                                       ++ e     ++ei+   ++  +  pk+  ++++ +++++ +k  v++    v ++L++  + L  + +d+ i+l+GG
  gi|557693458|ref|YP_008796512.1| 246 AKIElssmtETEINLPYIAydSSGPKNlyMRINRATLEQLVKPIVERCRGPVMQALQD--AKLKPEEIDK-IILVGG 319
                                       3222222234444443333113445542267888888888888888888889999986..4688888888.6777** PP

                                       GGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHHHT CS
                          MreB_Mbl 283 gallkgldkllseetglpvkvaedpltcvakGtgkv 318
                                        + +  ++++++e +g + + + dp++cva G+++ 
  gi|557693458|ref|YP_008796512.1| 320 PTRMPIIQQFIKEVLGKEPERGVDPMECVAMGAAIQ 355
                                       ********************************9865 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 !   22.8   0.0   3.8e-08   6.1e-05     139     196 ..     298     358 ..     209     359 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.8e-08
                            FGGY_C 139 lealekd..sgkpldrlavdGGgskndllmqllAdilg.vpVerpkt.aeatalGaAilAav 196
                                       ++al++   ++ ++d+++++GG ++ + ++q++ ++lg  p er  +  e++a+GaAi Aa+
  gi|557693458|ref|YP_008796512.1| 298 MQALQDAklKPEEIDKIILVGGPTRMPIIQQFIKEVLGkEP-ERGVDpMECVAMGAAIQAAI 358
                                       4445444335777*************************555.665555************96 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.9   3.2e+03      22      61 ..      61      98 ..      53     103 .. 0.78
   2 !   13.7   0.1   1.6e-05     0.027     142     210 ..     147     218 ..     131     260 .. 0.68
   3 ?    1.3   0.0     0.098   1.6e+02     170     292 ..     204     333 ..     202     340 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.9
                              StbA 22 vktlispnsfkeewsvslgdkkpanYlidgekysfdslss 61
                                      ++  + p   +  w+ ++g    + Y + g+ ++ ++ls+
  gi|557693458|ref|YP_008796512.1| 61 RQAVLNPEGTVTAWKRRMG--TDYRYNLHGKEFTPQQLSA 98
                                      5667778888888999987..679999******9999987 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.6e-05
                              StbA 142 vkvlPeslPagfe.alkeldeleslLiiDlGGttLDvakvr..gklegiskvkgdskiGvslitdavkeale 210
                                       v+++ e   a+    l++ld+  + L+ DlGG tLDv+ ++    + ++  + gd ++G   + +a+ +++ 
  gi|557693458|ref|YP_008796512.1| 147 VRIINEPTAAALAyGLNKLDQEMKILVFDLGGGTLDVTIMEfgQGVFEVLATAGDTQLGGTDMDKALVDYIV 218
                                       66677766666541578899999**************97743222445566789999999888888877764 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.098
                              StbA 170 lGGttLDvakvrgklegiskvkgdskiGvslitdavkealetaktrtssfladel.....iknrkdeeyLkrrinde 241
                                       lGGt +D a v   ++   + +g +       ++ ++ea e ak++ ss++  e+       +    + L  rin +
  gi|557693458|ref|YP_008796512.1| 204 LGGTDMDKALVDYIVDTYRRETGIDLSNDKSAMNRIREAAERAKIELSSMTETEInlpyiAYDSSGPKNLYMRINRA 280
                                       66666666666666666655555444443344444555555555554444443332111145556667777778777 PP

                              StbA 242 dkresvlevinekvkkLkerviravsefsgythvmvvGGGae..liaeaikka 292
                                          + v  ++++    + + +++a  + +++ ++++vGG +   +i++ ik+ 
  gi|557693458|ref|YP_008796512.1| 281 TLEQLVKPIVERCRGPVMQALQDAKLKPEEIDKIILVGGPTRmpIIQQFIKEV 333
                                       76666777777777788899999999999999999999987633688888876 PP

>> NCA2  ATP synthase regulation protein NCA2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.5   4.4e-05     0.072     201     276 ..     485     559 ..     462     572 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-05
                              NCA2 201 lrslrnierlltessae.eeekeekeeenelsykdqGllllevhvLrklaekllpkelekefleDledLekvklgve 276
                                       + s +++er++ e  ++  e++++k++e+el+++  Gl+    + L+++++k+ p e +ke+++Dl  L+++ +g++
  gi|557693458|ref|YP_008796512.1| 485 RLSKEEVERMIREA-EQfAEQDRRKKQEAELRNEADGLIYTVEKALKEFGDKVSP-EAKKEVEDDLAKLKEALAGKD 559
                                       55668999999995.44445555556999***********999**********95.6799*********98876444 PP

>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   8.4e-05      0.14      10      72 ..     475     540 ..     469     583 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.4e-05
                             DUF45  10 dgsvevsaPkgvseeeiedfvkkkakwiekklakleer.akeaekelesgesfpl..lGkkyrlkv 72 
                                       d sv+++aP+++s+ee+e+++++ +++ e+ ++k +e+  +++ + l  + +  l  +G k+  + 
  gi|557693458|ref|YP_008796512.1| 475 DVSVKITAPHRLSKEEVERMIREAEQFAEQDRRKKQEAeLRNEADGLIYTVEKALkeFGDKVSPEA 540
                                       5689*************************9999999954333333333333333333444444444 PP

>> Raco_middle  RACo middle region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00052      0.85      51     113 ..     278     340 ..     273     415 .. 0.82
   2 ?   -0.8   0.0      0.68   1.1e+03      49      87 ..     542     580 ..     534     583 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00052
                       Raco_middle  51 eeegleklqkavveeinelieelleeagiekeeiyevvvagNttMlhlllgldpkslakapyv 113
                                       ++ +le+l k +ve  +  + ++l++a++++eei +++++g  t + ++ ++  + l+k+p  
  gi|557693458|ref|YP_008796512.1| 278 NRATLEQLVKPIVERCRGPVMQALQDAKLKPEEIDKIILVGGPTRMPIIQQFIKEVLGKEPER 340
                                       57789************************************9999999888888888888865 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.68
                       Raco_middle  49 keeeegleklqkavveeinelieelleeagiekeeiyev 87 
                                       ke e++l+kl++a+  +  ++i+++le+ + ++++i ++
  gi|557693458|ref|YP_008796512.1| 542 KEVEDDLAKLKEALAGKDIQAIKTALEKLRASAQKIGTA 580
                                       567899999**9999999999999999999999988765 PP

>> Emaravirus_P4  P4 movement protein of Emaravirus, and the 30K superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1    0.0001      0.17     292     327 ..     541     576 ..     495     587 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                     Emaravirus_P4 292 qdeiseakaklsealagidlaiieaakaklvavlrk 327
                                       ++e+ +  akl ealag+d+++i++a  kl a  +k
  gi|557693458|ref|YP_008796512.1| 541 KKEVEDDLAKLKEALAGKDIQAIKTALEKLRASAQK 576
                                       6799999********************999987665 PP

>> DUF3347  Protein of unknown function (DUF3347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.9   0.00012      0.19      25      97 ..     497     588 ..     475     592 .] 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                           DUF3347  25 eeeeeeeekekkkekse............eeee.........kdeklkevlesYlklkdALvaddakeakkaakkle 80 
                                       e+e+  e++++kk++ e            e  +         + e+ kev ++  klk+AL+ +d +++k+a +kl 
  gi|557693458|ref|YP_008796512.1| 497 EAEQFAEQDRRKKQEAElrneadgliytvE--KalkefgdkvSPEAKKEVEDDLAKLKEALAGKDIQAIKTALEKLR 571
                                       222222222222222222233345555441..14556666646666677**************************** PP

                           DUF3347  81 eklkavdtsklkekekk 97 
                                       ++++++ t+ + ++e +
  gi|557693458|ref|YP_008796512.1| 572 ASAQKIGTAVYGQREDQ 588
                                       ******99888554443 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2      0.19   3.1e+02       1      21 [.       6      26 ..       6      40 .. 0.84
   2 ?   -3.1   0.0       6.8   1.1e+04      32      48 ..     103     119 ..     102     121 .. 0.90
   3 ?   11.9   0.0   0.00014      0.22       2      88 ..     173     338 ..     172     360 .. 0.69
   4 ?   -1.1   0.8       1.6   2.6e+03      38      86 ..     492     529 ..     462     580 .. 0.54

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.19
                                      EEEEE-SSSEEEEEEETTEEE CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                              FtsA  1 alvDiGagktdvavaedgalv 21
                                      +++D+G++ + +av+ +g+++
  gi|557693458|ref|YP_008796512.1|  6 IGIDLGTSNSAAAVVIGGRPT 26
                                      58************9998764 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.8
                                       HHHHHHHHHHT--HHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                              FtsA  32 gitkdiakalrtaveeA 48 
                                        i++d++  l+++v++A
  gi|557693458|ref|YP_008796512.1| 103 KIKRDAEAFLGEPVKKA 119
                                       699**********9998 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00014
                                       EEEE-SSSEEEEEEETTEEEEEEEES-......-HHHHHHH...................HHHHHT--HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxx...................xxxxxxxxxxxxxxxxx RF
                              FtsA   2 lvDiGagktdvavaedgalvhlrvigv......ggngitkd...................iakalrtaveeAeriki 53 
                                       + D+G+g+ dv+++e g+ v ++v+ +      gg  ++k                     + a++   e+Aer ki
  gi|557693458|ref|YP_008796512.1| 173 VFDLGGGTLDVTIMEFGQGV-FEVLATagdtqlGGTDMDKAlvdyivdtyrretgidlsnDKSAMNRIREAAERAKI 248
                                       56**************9755.44444445567799999999777777777777776666544455777888999997 PP

                                       HH--S--..................EEEEEHHHHH.......................................... CS
                                       xxxxxxx..................xxxxxxxxxx.......................................... RF
                              FtsA  54 kyGsala..................ekeigrkels.......................................... 70 
                                       +  s  +                                                                      
  gi|557693458|ref|YP_008796512.1| 249 ELSSMTEteinlpyiaydssgpknlY--------Mrinratleqlvkpivercrgpvmqalqdaklkpeeidkiilv 317
                                       77776555555555555555555442........0444444447777777788888888888888888888888888 PP

                                       .GGGGSTTHHHHHHHHH..T- CS
                                       .xxxxxxxxxxxxxxxx..xx RF
                              FtsA  71 .ggsalpnleelaeral..sp 88 
                                        g + +p ++++++++l  +p
  gi|557693458|ref|YP_008796512.1| 318 gGPTRMPIIQQFIKEVLgkEP 338
                                       888888888888888885433 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.6
                                       HHHHT--HHHHHHHHHHH--S--EEEEEHHHHHGGGGSTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              FtsA  38 akalrtaveeAerikikyGsalaekeigrkelsggsalpnleelaeral 86 
                                       ++++r+a + Ae+  +           +++e +  ++  +l+  +e+al
  gi|557693458|ref|YP_008796512.1| 492 ERMIREAEQFAEQDRR-----------KKQEAELRNEADGLIYTVEKAL 529
                                       3444444444443331...........1222223444444444444443 PP

>> CdiI_2  CdiI immunity protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.4   1.4e+04      21      35 ..     206     220 ..     201     226 .. 0.60
   2 ?    5.3   0.9     0.019        32      36      68 ..     487     519 ..     484     524 .. 0.85
   3 ?    3.8   0.1     0.055        90      23      55 ..     524     556 ..     518     572 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.4
                            CdiI_2  21 gdsieeiledYvsse 35 
                                       g++++++l dY+ ++
  gi|557693458|ref|YP_008796512.1| 206 GTDMDKALVDYIVDT 220
                                       556777777776655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                            CdiI_2  36 speevaelideieellassldeeleeaflaelg 68 
                                       s+eev+++i+e e++ +++ +++ e+++++e++
  gi|557693458|ref|YP_008796512.1| 487 SKEEVERMIREAEQFAEQDRRKKQEAELRNEAD 519
                                       689***************998888888877764 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.055
                            CdiI_2  23 sieeiledYvssespeevaelideieellassl 55 
                                       ++e++l+++ ++ spe+ +e+ d++ +l ++  
  gi|557693458|ref|YP_008796512.1| 524 TVEKALKEFGDKVSPEAKKEVEDDLAKLKEALA 556
                                       58999*******************999988654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (592 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1131  (0.0630822); expected 358.6 (0.02)
Passed bias filter:                      709  (0.0395449); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.46
# Mc/sec: 3833.12
//
Query:       gi|557693459|ref|YP_008796513.1|  [L=164]
Description: molecular chaperone GrpE [Candidatus Caldiarchaeum subterraneum]
Scores for 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  133.8   0.7    5.2e-39  133.6   0.7    1.0  1  GrpE          GrpE
  ------ inclusion threshold ------
      0.016   15.4   0.4      0.021   15.0   0.4    1.2  1  MnmE_helical  MnmE helical domain
      0.077   13.0   0.4       0.11   12.6   0.4    1.3  1  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
        1.2    9.3   5.5       0.68   10.0   3.5    1.6  2  COG2          COG (conserved oligomeric Golgi) complex compon


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   0.7   1.2e-42   5.2e-39      18     165 ..       9     156 ..       3     157 .. 0.98

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 1.2e-42
                                       CCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..HHH-HHHHHHH CS
                              GrpE  18 eeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksakeneeekslleG 94 
                                        e leel+++ +el e+l ++lae+ n+r+ +eke + a++ a e+++++L+ v+++ler++ks +++e+  +l++ 
  gi|557693459|ref|YP_008796513.1|   9 AESLEELRAQNRELLERLSYALAEMANMRRVMEKEVSRAEQAAAERLLRKLITVYEDLERVVKSLETSEAPPALAQA 85 
                                       6789************************************************************************* PP

                                       HHHHHHHHHHHHHHTT-EE---TTSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEEE-EEEEEE CS
                              GrpE  95 vemtlkqllkiLekhgvekiepkgepFDpnlheavstveddekeegtvvevvqkGYklkdrvlRpAmVkVs 165
                                       ++m++++l +iL+++gvek++ +g++F+p  heav+ +++d+++ +tv ev+++GY ++d++l+p +VkV+
  gi|557693459|ref|YP_008796513.1|  86 LQMIYRELTNILASEGVEKMDVVGKEFNPFDHEAVEYIDSDTVAVDTVAEVLSNGYRMGDKILKPPRVKVA 156
                                       **********************************************************************8 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.4   4.7e-06     0.021     114     200 ..      16     110 ..       5     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.7e-06
                                       xxxxxxxxxxxxxxxxxxx.x....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      MnmE_helical 114 SaktgegieeLeeaikele.l....eei.eeeplltnaRhkealekalealeeakealeaglpldlvaedLrealea 184
                                        a+++e +e+L  a++e+  +    e+  +  + ++ +R +  l ++ e le++ ++le++ +  ++a  L+  +++
  gi|557693459|ref|YP_008796513.1|  16 RAQNRELLERLSYALAEMAnMrrvmEKEvSRAEQAAAERLLRKLITVYEDLERVVKSLETSEAPPALAQALQMIYRE 92 
                                       577878899999999996645454422244489999*************************9999************ PP

                                       xxxxxxxxxxx..xxxxx RF
                      MnmE_helical 185 LgeItGevvte..dlLde 200
                                       L +I+    +e  d++++
  gi|557693459|ref|YP_008796513.1|  93 LTNILASEGVEkmDVVGK 110
                                       ****99866652255555 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 ?   12.6   0.4   2.4e-05      0.11      20     100 ..      10      99 ..       5     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
                      Baculo_PEP_C  20 nvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt....rldtlltnLtdalnalq.....dtlrneL 87 
                                       + L+ +r+qn ++l  l+ +l+++++    ++++++++ ++ ++    +l t+ + L++ +++l+      +l ++L
  gi|557693459|ref|YP_008796513.1|  10 ESLEELRAQNRELLERLSYALAEMANMRRVMEKEVSRAEQAAAErllrKLITVYEDLERVVKSLEtseapPALAQAL 86 
                                       6799**********************999999999997766666777788999999999999999988888899999 PP

                      Baculo_PEP_C  88 tnlnsiltnLlss 100
                                       + +  +ltn+l+s
  gi|557693459|ref|YP_008796513.1|  87 QMIYRELTNILAS 99 
                                       9999999999876 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 ?   10.0   3.5   0.00015      0.68      69     131 ..      10      75 ..       6      77 .. 0.92
   2 ?   -2.9   0.0       1.5   6.8e+03       7      21 ..     111     125 ..     109     138 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00015
                              COG2  69 eeleevesplaaarkkvesvreklsereeeveskleeakeleekr...ellklllkldevveklea 131
                                       e+lee++ +  ++ ++++ + ++++++++ +e++++ a++++++r   +l+ ++ +l++vv++le 
  gi|557693459|ref|YP_008796513.1|  10 ESLEELRAQNRELLERLSYALAEMANMRRVMEKEVSRAEQAAAERllrKLITVYEDLERVVKSLET 75 
                                       789**********************************99999999888999999999999999996 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.5
                              COG2   7 eFgvpdFdpdqFvse 21 
                                       eF+ +d + ++++ +
  gi|557693459|ref|YP_008796513.1| 111 EFNPFDHEAVEYIDS 125
                                       777778888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1632  (0.0910257); expected 358.6 (0.02)
Passed bias filter:                     1024  (0.0571142); expected 358.6 (0.02)
Passed Vit filter:                       138  (0.00769703); 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 0.27s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1241.20
//
Query:       gi|557693460|ref|YP_008796514.1|  [L=483]
Description: hypothetical protein CSUB_C0015 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.094   12.6   0.0       0.26   11.2   0.0    1.8  1  GIT_CC    GIT coiled-coil Rho guanine nucleotide exchange fac


Domain annotation for each model (and alignments):
>> 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 ?   11.2   0.0   1.4e-05      0.26      13      65 ..     341     393 ..     336     394 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.4e-05
                            GIT_CC  13 VtleeylelKkalaaseakiqqLlkvNtslsdelrlLQskvqkLqaeNaqlrd 65 
                                       V +  +l +K+ +a       qL+k+ tsl++ l +L +++++L++ ++ l++
  gi|557693460|ref|YP_008796514.1| 341 VVVAVFLAVKTTSAPRRTVSPQLKKAQTSLENALDKLLKELETLKPGDKPLKT 393
                                       6677799999999998888899***********************98887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      799  (0.0445647); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3145.55
//
Query:       gi|557693461|ref|YP_008796515.1|  [L=355]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-35  123.2   0.0    1.5e-35  122.9   0.0    1.0  1  DUF354    Protein of unknown function (DUF354)


Domain annotation for each model (and alignments):
>> DUF354  Protein of unknown function (DUF354)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.9   0.0   8.3e-40   1.5e-35       2     324 ..       3     328 ..       2     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 8.3e-40
                            DUF354   2 dvwidltnaphvryfrdlikkfekeGievlltardsGdlaklvklynfv.fksiGkhG.vtlkekliesakrvinls 76 
                                        vw+d+       +fr++ k + k G  v+ t r++ +l+ ++   +f+ f+ +G  G + l+ kl++s +r+ +l 
  gi|557693461|ref|YP_008796515.1|   3 TVWLDILTPKQFWFFRKVAKLLTKRGYRVVATSRNYEQLSSFLVNPGFEgFHVVGEFGgAGLRGKLVKSVERMRGLL 79 
                                       59****************************************999***9457899986268**************** PP

                            DUF354  77 kliaevkpdvalakhsvelprvafGlnipvvyvldnehaeaankltlpladeiikpividendlkktGadpnrirry 153
                                       +++ +   d a++  s e  r+a+Gl+ p v   d   +   n+l+ p++ +i  p ++ ++  k +G +   i  y
  gi|557693461|ref|YP_008796515.1|  80 DVLEDF--DCAVSSGSPEAARIAYGLSQPHVLASDTPES-PVNRLAAPVSKKIATPWIVGKHPWKAYGVRDGDIITY 153
                                       **9886..88999*****************999998765.67****************************999999* PP

                            DUF354 154 eGtsevinvqsyeideeilkdlnlkledektilmrpepslasyl.dadchkdvltkiveklkdrid...ilviprde 226
                                       +    v+ +++++ +++ l++l+  +  e  ++  pe  +asyl ++    +v++ +  ++ + i    ++++pr+ 
  gi|557693461|ref|YP_008796515.1| 154 RALDPVAWIKDHKPNKQTLDELG-LVSMEYVLVRTPEY-KASYLiKSGYQLEVFASVARRVAEMIRprrLVLLPRYV 228
                                       ***********************.67788888888888.88887245556688888888888888777799****99 PP

                            DUF354 227 eqkeiyeev..dnviviketvdalsllkrsdlviGaGGtmnreaallGipvvscypqkllsvdkyliekdlmirstd 301
                                       ++    ++   d ++v+ ++v  l+ll  s + +G GGtm +eaallG+p +s yp  +  v +yl+ k+l+ r + 
  gi|557693461|ref|YP_008796515.1| 229 DEILYLRDRvgDVALVVEKPVTDLTLLSSSLIFVGGGGTMTQEAALLGVPCLSIYPITPPKVIRYLVSKGLVERVKK 305
                                       8776666532367899999*******************************************************999 PP

                            DUF354 302 vdeivntalrllvdklekkklie 324
                                       v+++     r+l+   + + + e
  gi|557693461|ref|YP_008796515.1| 306 VEQLPSKLERMLKTIDKLRDVSE 328
                                       98875544343332222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); 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: 2526.18
//
Query:       gi|557693462|ref|YP_008796516.1|  [L=328]
Description: UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-24   85.8   8.3    3.1e-24   85.8   8.3    1.9  2  Glycos_transf_4  Glycosyl transferase family 4
  ------ inclusion threshold ------
        2.6    8.3   9.2        4.6    7.5   0.1    2.8  3  DUF4293          Domain of unknown function (DUF4293)


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 !   85.8   8.3   3.5e-28   3.1e-24       5     159 ..      77     228 ..      72     229 .. 0.88
   2 ?   -3.3   0.0      0.85   7.7e+03     115     129 ..     303     317 ..     269     321 .. 0.64

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 3.5e-28
                   Glycos_transf_4   5 lltillilllGflDDvlglkarlKlilqilaalililtldlslttlgllltqvlielglilavlltllvivgvtNav 81 
                                       + ++++++l+G+++D+++++++lK +l ++a ++++ ++    ++  l++  +  +l+ il+ ll+ll + +v Nav
  gi|557693462|ref|YP_008796516.1|  77 VGSLAVAALIGLWEDFREINPVLKPVLLVVAGVPVVAAGV-YSPDPVLPFV-GPTRLT-ILYPLLVLLGFSIVCNAV 150
                                       45677899***************************99887.3344444444.466666.778888888899999*** PP

                   Glycos_transf_4  82 NliDGldGlaagvsiiialalvvlaavdgrsellllalallgallGfllfNrypAkvFmGDsgslflGlvlavlail 158
                                       N +D l+G +a++s+ ++l l+++a+++++ e+  l+l+ +++ll fl  N+ypAk F G++gsl++G+v+a++ai+
  gi|557693462|ref|YP_008796516.1| 151 NSLDVLNGSMAATSLTAILPLTIIAYLEKKAEIFSLCLVTAVVLLVFLSKNIYPAKTFAGNVGSLAVGAVIAYVAIV 227
                                       ************************************99999999********************************8 PP

                   Glycos_transf_4 159 g 159
                                       g
  gi|557693462|ref|YP_008796516.1| 228 G 228
                                       7 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.85
                   Glycos_transf_4 115 lllalallgallGfl 129
                                       +l++l+l  a+l +l
  gi|557693462|ref|YP_008796516.1| 303 RLFLLCLYSAVLSLL 317
                                       333334444444444 PP

>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1      0.93   8.4e+03      12      24 ..      10      22 ..       3      35 .. 0.57
   2 ?    5.5   1.6    0.0021        19      56     132 ..     158     227 ..     103     239 .. 0.75
   3 ?    7.5   0.1   0.00051       4.6      37      78 ..     284     325 ..     266     327 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.93
                           DUF4293 12 aailmaaflflpl 24
                                      aa+++ af++lp+
  gi|557693462|ref|YP_008796516.1| 10 AAAAATAFVMLPV 22
                                      3444444444444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0021
                           DUF4293  56 vlvilllliailaliaIflyknRklQlrlclinllllvllyvllallllvnkanaaaeslgesslkiglilpliali 132
                                       ++++ + l+ail l  I   +++   + lcl+++++l++++   ++      a++ a+++  +sl +g+++  +a++
  gi|557693462|ref|YP_008796516.1| 158 GSMAATSLTAILPLTIIAYLEKKAEIFSLCLVTAVVLLVFLSKNIY-----PAKTFAGNV--GSLAVGAVIAYVAIV 227
                                       6788889999999988888888888889999999999999888777.....222222233..356666666666665 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.00051
                           DUF4293  37 yalgvstaeaetsvnvsvwvlvilllliailaliaIflyknR 78 
                                       + + + ta+++ ++   vw l++l l +a+l+l++ fl+ +R
  gi|557693462|ref|YP_008796516.1| 284 TVVRLLTAGEKLTEPAVVWRLFLLCLYSAVLSLLTYFLFIRR 325
                                       44445566788888899**********************888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2224.40
//
Query:       gi|557693463|ref|YP_008796517.1|  [L=88]
Description: hypothetical protein CSUB_C0018 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 636.19
//
Query:       gi|557693464|ref|YP_008796518.1|  [L=348]
Description: hypothetical protein CSUB_C0019 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); 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:                         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 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2669.02
//
Query:       gi|557693465|ref|YP_008796519.1|  [L=328]
Description: dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  112.3   0.1    3.8e-32  111.6   0.1    1.4  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
      1e-05   25.5   0.0    3.2e-05   23.9   0.0    1.9  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
    2.4e-05   25.0   0.1    0.00011   22.9   0.0    1.9  2  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain
    6.7e-05   23.3   0.0    0.00017   22.0   0.0    1.7  2  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
    0.00027   20.9   0.1    0.00068   19.6   0.1    1.6  1  ADH_zinc_N      Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.061   14.0   0.0       0.13   12.9   0.0    1.6  1  CoA_binding     CoA binding domain
       0.08   12.5   0.0       0.21   11.1   0.0    1.8  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.085   12.1   0.4       0.18   11.0   0.3    1.6  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


Domain annotation for each model (and alignments):
>> 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 !  111.6   0.1   1.7e-35   3.8e-32       2     120 .]       3     121 ..       2     121 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 1.7e-35
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHHH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngthee 77 
                                        va++GaG+ g +h+r l+e   + evva++d+d era ++a++fg+e +y++++ +l ++++dav+++tp++th+ 
  gi|557693465|ref|YP_008796519.1|   3 DVAVVGAGFWGVNHIRVLKEL-GESEVVAVCDIDRERAGKAAARFGIEhVYTEVDTMLMETRPDAVTICTPSTTHAS 78 
                                       59*************888888.999**************************************************** PP

                                       HHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  78 lakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       la+++l +g+++++EKP+a tv+ea +++++ +++g++v+vg+
  gi|557693465|ref|YP_008796519.1|  79 LALKLLDHGCDIFIEKPMASTVDEAAKILDKIRETGRVVMVGF 121
                                       *****************************************96 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   1.4e-08   3.2e-05       1      72 [.     133     195 ..     133     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.4e-08
                                       HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEE.EEE.SE CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvva.algrmr 72 
                                       +++Ie+ ++Gev+ +          + ++++w+ ++ ++ Gv+ d +iHd+Dl+ w+f + p +v+ ++gr+r
  gi|557693465|ref|YP_008796519.1| 133 RHMIEDKEIGEVLLF----------YGRRIGWWPERIGDTGVVKDTAIHDLDLVTWIFRTLPDEVYaMCGRLR 195
                                       689999999999999..........778899999999**********************98877774676554 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 !   22.9   0.0   4.8e-08   0.00011       3     112 ..      10     115 ..       8     119 .. 0.81
   2 ?   -0.8   0.0         1   2.3e+03      57      72 ..     242     257 ..     212     279 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.8e-08
                                       SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHHHH CS
                     NAD_binding_3   3 GaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvlka 79 
                                       G  G   ++ lk+     e e+vav+d d + + +++a ++ e +++++d ++ + +pd v  c++s+  a+l+lk 
  gi|557693465|ref|YP_008796519.1|  10 GFWGVNHIRVLKELG---ESEVVAVCDIDRERAGKAAARFGIEHVYTEVDTMLMETRPDAVTICTPSTTHASLALKL 83 
                                       555555556666555...569********666666899****************99********************* PP

                                       HHTTEEEE-S--CGGG-HHHHHHHTSSSTTS-- CS
                     NAD_binding_3  80 LkagkdvvtankgaladealyeeLreaaeanga 112
                                       L +g+d+ +    a +  +  ++++++ +++g+
  gi|557693465|ref|YP_008796519.1|  84 LDHGCDIFIEKPMAST-VDEAAKILDKIRETGR 115
                                       *******999888888.5666777777777776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1
                                       HHS-EEEEE-S--HHH CS
                     NAD_binding_3  57 hldpdvvVEcasseav 72 
                                       +++  vvVE a ++ +
  gi|557693465|ref|YP_008796519.1| 242 FIEQEVVVEKAEQTII 257
                                       3478899999988776 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 !   22.0   0.0   7.7e-08   0.00017       2      93 ..       4      90 ..       3     110 .. 0.86
   2 ?   -2.8   0.0       3.7   8.3e+03      49      77 ..     158     186 ..     117     189 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.7e-08
                                      EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTT.TTTSBHHHHSGGGTTTECEBEEEGGGGGC.TT-SEEEE-SCHHH CS
                    Semialdhyde_dh  2 vaivGatGyvGqellrlLeehpevelvvllsssr.saGkklaeavkaleegkdlkvedvdeeel.kevdivflalpagv 78
                                      va+vG  G  G + +r+L+e  e e+v+++  +r  aGk+ a+       g + ++++vd+  +  + d v  ++p+ +
  gi|557693465|ref|YP_008796519.1|  4 VAVVG-AGFWGVNHIRVLKELGESEVVAVCDIDReRAGKAAARF------GIEHVYTEVDTMLMeTRPDAVTICTPSTT 75
                                      9****.8*************888999998888776799999888......566666666666665899*********** PP

                                      HHHHHHHHHHTTSEE CS
                    Semialdhyde_dh 79 skelapklaeagvkv 93
                                      +++la kl+++g+ +
  gi|557693465|ref|YP_008796519.1| 76 HASLALKLLDHGCDI 90
                                      ************965 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.7
                                       TTTECEBEEEGGGGGCTT-SEEEE-SCHH CS
                    Semialdhyde_dh  49 eegkdlkvedvdeeelkevdivflalpag 77 
                                       + g + +v+d+ + +l+ v  +f  lp +
  gi|557693465|ref|YP_008796519.1| 158 RIGDTGVVKDTAIHDLDLVTWIFRTLPDE 186
                                       44555666667777777777777776666 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1     3e-07   0.00068       4     101 ..      14     133 ..      13     153 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3e-07
                                       HHHHHHHHHTT-.EEEE.EESSHHHH.HHHHHTTESEEEET............TTCHHHHHHHHHT........... CS
                        ADH_zinc_N   4 laavqlAkalGa.evia.vdsseekl.elakklGadeviny............keadlverikelt........... 54 
                                       +  + ++k lG  ev+a  d+++e++ + a+++G ++v+++                        t           
  gi|557693465|ref|YP_008796519.1|  14 VNHIRVLKELGEsEVVAvCDIDRERAgKAAARFGIEHVYTEvdtmlmetrpdaV-----------Tictpstthasl 79 
                                       56678899999999999678999998455555*********7666664444440...........233344466666 PP

                                       ....TTSSEEEEEESSCSHHHHHHHHHCE...EEEEEEEECSC..TSSEEEEEHHH CS
                        ADH_zinc_N  55 ....ggegvdvvfecvGsgatleaalkll...kpgGrlvvvGg..gkgeeefdlrn 101
                                            + g d+ +e +   +t+++a k+l   ++ Gr+v+vG+   +++  +++++
  gi|557693465|ref|YP_008796519.1|  80 alklLDHGCDIFIEKPM-ASTVDEAAKILdkiRETGRVVMVGFieRFNPA-VQFAR 133
                                       6655367**********.*******9998333568*******95444444.44444 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.9e-05      0.13       5      87 ..       3      88 ..       1      92 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.9e-05
                                      EEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEET..TE.EEESCHHHHHHHCTTTEEEEES-HHHHHHHHH CS
                       CoA_binding  5 kviviGagglgiaglyhfkeklkygikavfgvnprkvgtevl..gl.pvyksvdeleektevdvavitvPaesaqeavd 80
                                       v+v+Gag  g     + ke  + +++av +++ + +g+     g+  vy++vd++  +t +d+  i++P++  ++ ++
  gi|557693465|ref|YP_008796519.1|  3 DVAVVGAGFWGVNHIRVLKELGESEVVAVCDIDRERAGKAAArfGIeHVYTEVDTMLMETRPDAVTICTPSTTHASLAL 81
                                      69*********************************99988876655259999999999999***************999 PP

                                      HHHHTT- CS
                       CoA_binding 81 elveagi 87
                                      +l+++g 
  gi|557693465|ref|YP_008796519.1| 82 KLLDHGC 88
                                      9999885 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 ?   11.1   0.0   9.5e-05      0.21       2      38 ..       3      41 ..       2      86 .. 0.85
   2 ?   -2.1   0.0       1.1   2.5e+03     147     166 ..     150     169 ..      93     172 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.5e-05
                                      EEEEE--STTHHHHHHHHHHCT..SEEEEE-S-HHHHHH CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig..hevigvDideekvdk 38
                                       ++v+G+G+ G+ +  vl e+g    v ++Did+e+  k
  gi|557693465|ref|YP_008796519.1|  3 DVAVVGAGFWGVNHIRVLKELGesEVVAVCDIDRERAGK 41
                                      589*******************84556678***998655 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.1
                                       EEEEE------TTSHHHHHH CS
                    UDPG_MGDP_dh_N 147 fdvvsnPEflregsavkdll 166
                                        ++ + PE++ +  +vkd++
  gi|557693465|ref|YP_008796519.1| 150 RRIGWWPERIGDTGVVKDTA 169
                                       45677788888888888875 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 ?   11.0   0.3   8.2e-05      0.18      31      77 ..       4      53 ..       2     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.2e-05
                                      EEEESTSHHHHHHHHHHHHTT-..EEEEEESSHHHHHHHHH.TTTCECEE CS
                       AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglga..kVtvlDvrparleqles.lgakfvev 77
                                      v v+G+G  G++ i++ k+lg   +V v+D++ +r+ +  + +g + v +
  gi|557693465|ref|YP_008796519.1|  4 VAVVGAGFWGVNHIRVLKELGEseVVAVCDIDRERAGKAAArFGIEHVYT 53
                                      89******************963369999**9999988877788776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2506.97
//
Query:       gi|557693466|ref|YP_008796520.1|  [L=212]
Description: hypothetical protein CSUB_C0021 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   58.5   0.0    7.1e-16   58.2   0.0    1.0  1  ATPase    KaiC
    0.00061   19.5   0.0      0.012   15.4   0.0    2.1  2  DUF835    Protein of unknown function (DUF835)
  ------ inclusion threshold ------
      0.061   11.9   0.0      0.061   11.9   0.0    1.2  1  GvpD      GvpD gas vesicle protein
      0.094   12.5   0.0       0.15   11.9   0.0    1.4  1  MEDS      MEDS: MEthanogen/methylotroph, DcmR Sensory domain
       0.15   12.3   0.0       0.22   11.8   0.0    1.2  1  AAA_22    AAA 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 !   58.2   0.0     2e-19   7.1e-16      31     227 ..      14     211 ..      11     212 .] 0.84

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 2e-19
                            ATPase  31 GKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaeesaee....kdked 103
                                       GKt+++ q +   ++k ++++v+  +  +++++ e aks+G ++++  +eg+l+++d  + +e++  +    + +++
  gi|557693466|ref|YP_008796520.1|  14 GKTLLSIQAAEAALSK-NRKTVYALTTMSPQNFLELAKSIGAEFDNHLDEGRLVLVDCHTRGEHTYPAkysiSPEAS 89 
                                       9*******77666666.********************************************9998777455555556 PP

                            ATPase 104 leelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvl.kklgvTailvsekssseeaaggygvee 178
                                       l e+ +++ ea +      +viD +++l ay+ +e+ ++ +      v  ++  ++ai+v ++ ++   + ++ +  
  gi|557693466|ref|YP_008796520.1|  90 LLEIRQTFLEAADYSSNYFLVIDDLSTLlAYIPSENAFKFYQAVASDVRrNGGTCVAIIVPDILEQ---KLTNLLYS 163
                                       6666666666666667799*********99999999998887777777766677999999997555...45555555 PP

                            ATPase 179 fivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvl 227
                                        ++dgv+ +  +e+ ++l+R l+i+ +Rg +h ++  ++ I  +gi+ l
  gi|557693466|ref|YP_008796520.1| 164 -LSDGVVEMMMEEMGGNLRRFLRIRFLRGVRHPTEWSEYVIGLHGIELL 211
                                       .678*****************************************9976 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.04   1.4e+02      53      84 ..      37      70 ..      17      73 .. 0.79
   2 !   15.4   0.0   3.3e-06     0.012      55     132 ..      83     161 ..      72     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.04
                            DUF835 53 entvsPtnlekltetivkflkeaekg..vvliDg 84
                                        t+sP+n+ +l ++i   ++++ ++  +vl+D+
  gi|557693466|ref|YP_008796520.1| 37 LTTMSPQNFLELAKSIGAEFDNHLDEgrLVLVDC 70
                                      34899*********99999998877777999998 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 3.3e-06
                            DUF835  55 tvsPt.nlekltetivkflkeaekgvvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealeekela 130
                                       ++sP+ +l ++++t  ++++  ++ + +iD l  L+++   e+ +kf +++ + v  ++gt + +i +++le+k  +
  gi|557693466|ref|YP_008796520.1|  83 SISPEaSLLEIRQTFLEAADYSSNYFLVIDDLSTLLAYIPSENAFKFYQAVASDVRRNGGTCVAIIVPDILEQKLTN 159
                                       6778625778999999999999999************************************************9888 PP

                            DUF835 131 lL 132
                                       lL
  gi|557693466|ref|YP_008796520.1| 160 LL 161
                                       88 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.7e-05     0.061     152     195 ..     151     193 ..      14     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.7e-05
                              GvpD 152 lvletaansrleyivdGvvtlnvkeddrgrlrrdlrleklrGvr 195
                                        +le +  + l  + dGvv + ++e   g lrr lr+  lrGvr
  gi|557693466|ref|YP_008796520.1| 151 DILEQKLTNLLYSLSDGVVEMMMEEM-GGNLRRFLRIRFLRGVR 193
                                       4789999999999********98887.9***************8 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 ?   11.9   0.0   4.2e-05      0.15      22     129 ..      24     135 ..      18     149 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.2e-05
                              MEDS  22 kaglargekvlyvasastldelrealrkagldvdaalesgqleilda....eetylrgggfdpermlealrralaka 94 
                                       +a+l+++ k +y++++ + +  +e  ++ g + d  l++g+l ++d+    e+ty ++ + +pe+ l ++r+++ +a
  gi|557693466|ref|YP_008796520.1|  24 EAALSKNRKTVYALTTMSPQNFLELAKSIGAEFDNHLDEGRLVLVDChtrgEHTYPAKYSISPEASLLEIRQTFLEA 100
                                       689************99999999999999****************9965556899********99999999999998 PP

                              MEDS  95 ladgyaglrvigemtwalrspaereelleyEalln 129
                                       ++   + + vi + + +l   ++ +++  y a ++
  gi|557693466|ref|YP_008796520.1| 101 ADYSSNYFLVIDDLSTLLAYIPSENAFKFYQAVAS 135
                                       86666667777777766666666666666666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.1e-05      0.22      17     133 ..      14     152 ..      10     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.1e-05
                            AAA_22  17 GKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka....................... 70 
                                       GKT+l  + +e +       ++r++v+  t  s+ +  +l++ +  ++++ l++                       
  gi|557693466|ref|YP_008796520.1|  14 GKTLLSIQAAEAA-----LSKNRKTVYALTTMSPQNFLELAKSIGAEFDNHLDEgrlvlvdchtrgehtypakysis 85 
                                       4444444333333.....34467788899999999***************9999*********************** PP

                            AAA_22  71 erlsseellealeqalraravielliiDEaqhlr....seealeeLrsllnl.srkgvqliLvGtpel 133
                                       +++s+ e+++++ +a++  +   +l+iD+   l     se+a+++    + + +r g + + ++ p++
  gi|557693466|ref|YP_008796520.1|  86 PEASLLEIRQTFLEAADYSSN-YFLVIDDLSTLLayipSENAFKFYQAVASDvRRNGGTCVAIIVPDI 152
                                       9****************9999.********99665887788888886666666666666666666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1648.90
//
Query:       gi|557693467|ref|YP_008796521.1|  [L=118]
Description: hypothetical protein CSUB_C0022 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   24.0   0.0      1e-05   23.7   0.0    1.0  1  PolC_DP2  DNA polymerase II large subunit DP2


Domain annotation for each model (and alignments):
>> 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 !   23.7   0.0   5.6e-10     1e-05       1      48 [.      61     108 ..      61     113 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.6e-10
                          PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllg 48 
                                       eY +++ +e++++y++a++ r+++ +p + vE  +A+ +++Rve l+ 
  gi|557693467|ref|YP_008796521.1|  61 EYRSNILREVDRVYAVASAYRERTREPLPFVETVFADRMEERVELLVP 108
                                       699*****************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); 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: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 951.58
//
Query:       gi|557693468|ref|YP_008796522.1|  [L=281]
Description: hypothetical protein CSUB_C0023 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.3   1.5        1.3    8.9   0.1    2.6  2  Sec34     Sec34-like family
       0.05   13.2   0.0        3.9    7.2   0.0    2.7  2  HTH_50    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.1   0.00015       1.3      65     103 ..     115     155 ..     103     156 .. 0.85
   2 ?    3.7   0.1    0.0057        51     101     128 ..     196     223 ..     189     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00015
                             Sec34  65 eekLkyFeeldpitrkLnspgss..lvksesFlemLkklDe 103
                                       ++ ++ F+ l++++++L++++ +   v ++sF+ ++++++e
  gi|557693468|ref|YP_008796522.1| 115 RQLISSFRRLERTKQRLENQSKDvsDVAKDSFKRLIDHIEE 155
                                       556789***********8887765679*********99986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0057
                             Sec34 101 lDeclefleehpefkeaetYlirfkqcl 128
                                       l e l +++ + +f + ++Yl  f+q  
  gi|557693468|ref|YP_008796522.1| 196 LAELLTYVDFNLSFTDVRLYLGLFRQRI 223
                                       5567899999**********99999854 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0    0.0083        75      28      39 ..      78      89 ..      67      90 .. 0.83
   2 ?    7.2   0.0   0.00043       3.9      15      36 ..     164     185 ..     144     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.0083
                            HTH_50 28 klAkrLGvShta 39
                                      k+ k+LG+S++a
  gi|557693468|ref|YP_008796522.1| 78 KMRKKLGISKSA 89
                                      889******998 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00043
                            HTH_50  15 likkayekYpStRklAkrLGvS 36 
                                       + ++a ++Yp +R +A+ LG++
  gi|557693468|ref|YP_008796522.1| 164 ITEEAERRYPLFRIIAEELGIT 185
                                       5567889*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2208.39
//
Query:       gi|557693469|ref|YP_008796523.1|  [L=235]
Description: hypothetical protein CSUB_C0024 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
       0.54   10.8   5.1        0.5   10.9   1.3    2.5  2  PROL5-SMR  Proline-rich submaxillary gland androgen-regulated


Domain annotation for each model (and alignments):
>> PROL5-SMR  Proline-rich submaxillary gland androgen-regulated family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.038   6.8e+02      39      98 ..      34      93 ..       6      99 .. 0.63
   2 ?   10.9   1.3   2.8e-05       0.5      29      81 ..     144     196 ..     103     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.038
                         PROL5-SMR 39 PdPnkvqfgvpstlPpyglsllapplelllgpgkippsslivyilgeilsqlsalspqrq 98
                                        P +++ ++   lP ++ s   +p   ++++      s      +  + q  a++++ q
  gi|557693469|ref|YP_008796523.1| 34 VSPAGANRTRAGRLPIHSWSHKGRPDTCTVLETSRSSASSACLQAAAAQGQAAAPAAHGQ 93
                                      347777777778888888888888888877766555555555555566666666644444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 2.8e-05
                         PROL5-SMR  29 hdprrplapsPdPnkvqfgvpstlPpyglsllapplelllgpgkippsslivy 81 
                                           r  +p+P+P+  q+g       yg+ +l   l + l pg++  ss+ + 
  gi|557693469|ref|YP_008796523.1| 144 WSQARASQPPPPPHIYQWGGRLVSGVYGMVVLVMGLLVNLCPGFLATSSPHPR 196
                                       345566777799*********999*******************9887776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1848.34
//
Query:       gi|557693470|ref|YP_008796524.1|  [L=1019]
Description: type II restriction enzyme, methylase subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   41.3   0.0    4.7e-05   22.8   0.0    3.3  3  N6_Mtase  N-6 DNA Methylase
    2.9e-08   34.2   0.1    8.2e-08   32.7   0.1    1.7  1  Eco57I    Eco57I restriction-modification methylase
     0.0057   16.4   0.2       0.11   12.1   0.0    2.9  3  UPF0020   Putative RNA methylase family UPF0020


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.021   1.3e+02       5      37 ..     295     324 ..     292     333 .. 0.77
   2 !   12.3   0.0   1.2e-05     0.072      49      99 ..     380     446 ..     369     456 .. 0.78
   3 !   22.8   0.0   7.8e-09   4.7e-05     124     266 ..     548     686 ..     535     746 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.021
                          N6_Mtase   5 llGdvYEyllrkfaeeegksgGeffTPrevskl 37 
                                       llG v E ll++    e  ++G f+TP + + +
  gi|557693470|ref|YP_008796524.1| 295 LLGTVLENLLEEK---ERGEKGTFYTPVNEIGF 324
                                       5788889998875...66677******775555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.2e-05
                          N6_Mtase  49 svyDpacGsggllvqaekvlkee................dgktkelsiyGqeknettyrLakmNlll 99 
                                       +++Dpa+Gsgg+lv + + + +                  + +   ++yG +++++++++a++ + l
  gi|557693470|ref|YP_008796524.1| 380 KILDPAVGSGGFLVVMMQTILQLiqeveeavgwksdleqYKRRIIPNLYGFDIEPEAVEIARLRIWL 446
                                       69************99988865567788888888877644444455788999999999998887766 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 7.8e-09
                          N6_Mtase 124 kkfdvvvaNppfnqkewkektlekderfreavapksnadla.fllhiieslkpkGraavvlangvLfrggkegkIrk 199
                                       + +d+vv Npp+  +e k  +l+kd + +++  +k++  +a f+  ++  lk +G aa++  +  L + + ++++++
  gi|557693470|ref|YP_008796524.1| 548 SLADIVVMNPPYVRQE-KIPKLKKDYYVTNYKLDKTSDIYAyFMVRALRLLKSGGAAALITSDKWL-EVNYGKTLQQ 622
                                       568*********9994.5788899987777777777777777999*************99999988.5677777766 PP

                          N6_Mtase 200 alvekdlveavialpeklFyntsiptcilvlkkekaerkgkvlfidaseefkkkdrkknklteedie 266
                                        l  k ++ a+     + F+   ++t i vlkke++ +++ + fi  ++   +k r+ ++++  +++
  gi|557693470|ref|YP_008796524.1| 623 VL--KPHILAIYGQRMRSFQ-ADVNTVITVLKKEEQPKDKPIQFIYLETYGGEKVRNYKSIERGKLQ 686
                                       44..7789999999999886.589***********99********9999888887888887776666 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.1   1.4e-11   8.2e-08       4      75 ..     551     628 ..     549     655 .. 0.71

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.4e-11
                            Eco57I   4 dviiGNPPYqeseakkelkaleek.......akdiyqkFvekalkle..dkylaliiparflasgkglkefrekllk 71 
                                       d+++ NPPY ++e++ +lk++          ++diy +F+ +al+l    ++ ali++ ++l + +++k++++ l  
  gi|557693470|ref|YP_008796524.1| 551 DIVVMNPPYVRQEKIPKLKKDYYVtnykldkTSDIYAYFMVRALRLLksGGAAALITSDKWL-EVNYGKTLQQVL-- 624
                                       9************776666443337788988***************96668999********.666776666544.. PP

                            Eco57I  72 dkkl 75 
                                       ++++
  gi|557693470|ref|YP_008796524.1| 625 KPHI 628
                                       3444 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.64   3.8e+03     142     178 ..     161     198 ..     148     206 .. 0.73
   2 !   12.1   0.0   1.9e-05      0.11      31      94 ..     380     442 ..     375     455 .. 0.80
   3 ?    0.1   0.1     0.093   5.6e+02     123     134 ..     551     562 ..     545     622 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHHHHH-TT...-EEEEEESSHHHHHCC-- CS
                           UPF0020 142 ekLYseflrelkrvlrgg.grlvlltsenkalekalee 178
                                       ++LY+ + +++k+vl+ + +  +  + ++ ++  +l++
  gi|557693470|ref|YP_008796524.1| 161 RELYERIVKTVKSVLKDNaSSYAQRFLGRLMFLYFLQR 198
                                       789**********9999755555555566666655555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.9e-05
                                       -EEETT-TTSHHHHHHHHHHTT--TTTT-..---SSHHHHHHHHHHHH--.EEEEES-HHHHHHHHH CS
                           UPF0020  31 pllDPmCGsGtilIEaallganiapgllr..efvlelkaeaeeearaelk.lygsDldrrvvqgare 94 
                                       ++lDP  GsG++l+    + ++i  +l++  e+++  k+ +e+ +r+ ++ lyg+D+++++v+ ar 
  gi|557693470|ref|YP_008796524.1| 380 KILDPAVGSGGFLVV---MMQTIL-QLIQevEEAVGWKSDLEQYKRRIIPnLYGFDIEPEAVEIARL 442
                                       79***********94...555555.33330045556999999999999999*************996 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.093
                                       -EEEE------- CS
                           UPF0020 123 dvivtnpPYGer 134
                                       d++v npPY + 
  gi|557693470|ref|YP_008796524.1| 551 DIVVMNPPYVRQ 562
                                       677777777543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1019 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); 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: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.45
# Mc/sec: 6833.09
//
Query:       gi|557693471|ref|YP_008796525.1|  [L=1026]
Description: helicase domain-containing protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-15   57.3   0.0    5.5e-15   55.7   0.0    1.9  1  Helicase_C  Helicase conserved C-terminal domain
    3.3e-11   43.2   0.0    7.8e-11   42.0   0.0    1.7  1  PLDc_2      PLD-like domain
    4.5e-10   38.8   0.7    4.9e-07   28.8   0.0    3.2  3  SNF2_N      SNF2 family N-terminal domain
    4.5e-09   36.5   0.0     0.0049   16.9   0.0    2.8  2  ResIII      Type III restriction enzyme, res subunit
    5.8e-06   26.4   0.0    0.00031   20.8   0.0    2.8  1  Flavi_DEAD  Flavivirus DEAD domain
     0.0001   22.6   0.1      0.001   19.3   0.0    2.8  1  AAA_22      AAA domain
    0.00017   21.4   0.3     0.0013   18.5   0.1    2.5  2  IstB_IS21   IstB-like ATP binding protein
     0.0006   19.6   0.1       0.68    9.7   0.0    3.0  3  DEAD        DEAD/DEAH box helicase
  ------ inclusion threshold ------
       0.11   12.9   0.1        1.7    9.1   0.0    3.0  3  AAA         ATPase family associated with various cellular ac


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.7   0.0   2.7e-18   5.5e-15       6     111 .]     627     737 ..     623     737 .. 0.77

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.7e-18
                                       HHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT.TSTEEEESTT....STHHHHHHHHHHHHTTSSSEEEESGGG CS
                        Helicase_C   6 llellkleeeggkilifvntidrlek.vklllekk.gikvavlhge....lpqnereeileqfnkgesdvLiatdva 76 
                                       l +++k+ +e + ++if+++ d+++   + l+ ++  +  ++  g      ++   ++i+++f ++   +Li+tdv+
  gi|557693471|ref|YP_008796525.1| 627 LQQIMKQIKEPNGVIIFTQYADTAHYlYRRLKASFnRVMLVTGAGGyndkGEKALEDHIVRRF-QKVGGLLISTDVL 702
                                       56667888999***********88545566655555344444444322225555566******.54556******** PP

                                       TSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  77 erGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                       + G +++++++V n+d+p+n+  +iqr+GR+ R+g
  gi|557693471|ref|YP_008796525.1| 703 SAGQNLQNAQYVANYDFPWNPVVLIQRVGRIDRIG 737
                                       *******************************9986 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   3.9e-14   7.8e-11      10     133 .]      24     166 ..      16     166 .. 0.72

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 3.9e-14
                            PLDc_2  10 ksidiatyyfvsdreildallkaakrgvkvrilldskkd.................dagavdeaslkelkellleag 69 
                                       ++i ia+ yf  +   + a+++    ++  ++ll+++ +                 d+++  +  +k+++ +    +
  gi|557693471|ref|YP_008796525.1|  24 DEIAIASAYF--NVRGYGAIAQG-LGDKPMKLLLGREPTetikwedeilqeleqfeDDADYFRLLQKTIQYF-KDDK 96 
                                       6777777777..23334444332.222467788887444777777777766666665555556677777777.7777 PP

                            PLDc_2  70 vevrvfetllgslHaKlylid...gk.....tvivGSsNltkrgldlnlElnvviedkelakeleeeFerlw 133
                                         vr++e+  +++H K+++     +k     + +vGSsNlt+ gl +n+Eln+  +d+e+++el+e+Fe+ w
  gi|557693471|ref|YP_008796525.1|  97 RLVRIMER--RFFHGKAFIGVsldKKevrrgIGVVGSSNLTYGGLVSNRELNMLNTDREVVQELAEWFEEQW 166
                                       77777665..789***988533424478888**************************************999 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 !    5.0   0.0    0.0042       8.5      54     117 ..     233     284 ..     218     299 .. 0.71
   2 !   28.8   0.0   2.5e-10   4.9e-07     170     234 ..     305     372 ..     287     422 .. 0.70
   3 ?    1.2   0.0      0.06   1.2e+02     251     317 ..     600     671 ..     578     713 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0042
                                       TT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHH.HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                            SNF2_N  54 svrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPasll.dqWeneier 117
                                       +  G ++aD +GLGK   +lal +     e+++       +   p L+++P+s+l + We e+++
  gi|557693471|ref|YP_008796525.1| 233 KYGGVLIADSTGLGKSRVALALAH-----EAIR-------EGIRP-LLIAPKSILeTTWEAEMNE 284
                                       4445678********888777777.....3333.......34456.5566775541689999986 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 2.5e-10
                                       .TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-E...EEE-S--SSS-HHHHHHHHHHH-TTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 170 rsvlkqvewkrvvlDEghtlknstskaaeavskLstsnr...wiltGTPiqnsledlygLlkfLreep 234
                                        + + ++  + +++DE+h ++ s ++ + a+++L+++n+   +++t+TP+  sl dly+Ll++  +e 
  gi|557693471|ref|YP_008796525.1| 305 DDYVGEKGPELIIVDEAHYFRRSSTNRYIALRELVNKNQakiVLITATPVNTSLMDLYSLLSLYLPEN 372
                                       55666777899************999999****997765333689****************9866554 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.06
                                       HHHHHHHHHHHTT-ST.....TEE---GGGT--S---EEEEEEEEE--HHHHHHHH................ CS
                                       xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 251 aqaekgrsrLlqllqr.....lmlrrakkdveknlPpkteeiiflklskverksYnrllevlrkkalakllk 317
                                       +++e+ ++ Ll +l +     ++l r+ ++++k++ +++  iif +  +  + +Y rl+ +    +l +   
  gi|557693471|ref|YP_008796525.1| 600 SKDEEAIESLLRMLPNhdekyFLLERRLQQIMKQIKEPNGVIIFTQYADTAHYLYRRLKASFNRVMLVTGAG 671
                                       67888999999999856666699999999999***********************97766655555555444 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 !   16.3   0.0   3.6e-06    0.0072       3      76 ..     215     284 ..     213     288 .. 0.89
   2 !   16.9   0.0   2.5e-06    0.0049     128     169 ..     308     353 ..     285     355 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.6e-06
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkk 76 
                                       +l+++Q+    + +ekl+  +   +li+  TG GK++va++l+ +  ++g   + l+++p+ +l   ++ e+++
  gi|557693471|ref|YP_008796525.1| 215 HLYPHQQLTYIDAKEKLE--KYGGVLIADSTGLGKSRVALALAHEAIREGI--RPLLIAPKSILETTWEAEMNE 284
                                       688999999999999994..888999**********************988..9********999999988765 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.5e-06
                                       HHTTT-SEEEEETGGGTTS.T.....TTHHHHHT---SEEEEEESS- CS
                            ResIII 128 llrdrfdviiiDEaHrlgakk.....swreilekfkeavllglTATp 169
                                        +++  ++ii+DEaH +++++     + re+++k++ a+++ +TATp
  gi|557693471|ref|YP_008796525.1| 308 VGEKGPELIIVDEAHYFRRSStnryiALRELVNKNQ-AKIVLITATP 353
                                       4455556************75556667777788877.555666***9 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.5e-07   0.00031      14     138 ..     244     355 ..     236     360 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.5e-07
                                       TS-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTS-EEE-------------SEEEEEHHHHHHHHHHT CS
                        Flavi_DEAD  14 GaGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeealkglevryktsavkeektgrelvdvmchatftkrllsp 90 
                                       G Gk r  l  l +eai++ +r l++aP  +  +  e  ++++ vr +t +++  +++ ++vd              
  gi|557693471|ref|YP_008796525.1| 244 GLGKSRVAL-ALAHEAIREGIRPLLIAPKSILETTWEAEMNETLVRIDTLSTEMLSQNPDIVDD------------Y 307
                                       677776665.577888888888888888888888888888888888888888888888888873............3 PP

                                       ------SEEEEETTT--SHHHHHHHHHHHHHHHTTS-EEEEEESS-TT CS
                        Flavi_DEAD  91 vrkknyeliimDeahflDPasiaarGyletkaeegeaalilltatPPG 138
                                       v +k  elii+Deah+   +s      l++++++++a+++l+tatP  
  gi|557693471|ref|YP_008796525.1| 308 VGEKGPELIIVDEAHYFRRSSTNRYIALRELVNKNQAKIVLITATPVN 355
                                       4567789*************999989999*****************65 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   5.2e-07     0.001      14     129 ..     243     350 ..     231     357 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.2e-07
                            AAA_22  14 sGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalr 87 
                                       +G GK++++  l++++ +++ ++    +++++++ t  ++++ + ++ + l+            +++  + + +++ 
  gi|557693471|ref|YP_008796525.1| 243 TGLGKSRVALALAHEA-IREGIRPlliAPKSILETTWEAEMNETLVRIDTLSTE---------MLSQNPDIVDDYVG 309
                                       6888888888888887.3322222333333333333333333333322222222.........34444467777888 PP

                            AAA_22  88 aravielliiDEaqhlr..seealeeLrsllnlsrkgvqliLvG 129
                                       +++  el+i+DEa+++r  s + +  Lr+l+n  + + +++L+ 
  gi|557693471|ref|YP_008796525.1| 310 EKGP-ELIIVDEAHYFRrsSTNRYIALRELVN--KNQAKIVLIT 350
                                       8888.***********98669999999*****..*******996 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 ?   -3.6   0.0       3.9   7.7e+03      59      78 ..     109     128 ..     108     129 .. 0.91
   2 !   18.5   0.1   6.4e-07    0.0013      33     100 ..     220     287 ..     205     358 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.9
                         IstB_IS21  59 GKshlaialgveavraglsv 78 
                                       GK+++ ++l ++ vr+g+ v
  gi|557693471|ref|YP_008796525.1| 109 GKAFIGVSLDKKEVRRGIGV 128
                                       9***************9877 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 6.4e-07
                         IstB_IS21  33 rkvkeLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgkla 100
                                       ++++ + + + +ek  ++++   +G GKs +a al++ea+r+g++ l +  + ++e+   a+ ++ l 
  gi|557693471|ref|YP_008796525.1| 220 QQLTYIDAKEKLEKYGGVLIADSTGLGKSRVALALAHEAIREGIRPLLIAPKSILETTWEAEMNETLV 287
                                       5555666666777888899999**********************998888888877766666655544 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0022       4.4      14      71 ..     234     286 ..     218     302 .. 0.78
   2 !    9.7   0.0   0.00034      0.68      99     170 ..     295     354 ..     281     361 .. 0.69
   3 ?   -2.8   0.0       2.4   4.8e+03      93     113 ..     876     900 ..     861     985 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0022
                                       TCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  14 ggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfk 71 
                                        g vl+a  TG GK+ ++l  + +++     ++g + l+++P   L      ++++ +
  gi|557693471|ref|YP_008796525.1| 234 YGGVLIADSTGLGKSRVALALAHEAI-----REGIRPLLIAPKSILETTWEAEMNETL 286
                                       4689***************9999999.....789999999999888766666666555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00034
                                       SEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  99 divvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       +++  +p+ +dd +       +  +++++DEa+ +  ++  + i    ++l       k+q ++++++AT+ 
  gi|557693471|ref|YP_008796525.1| 295 EMLSQNPDIVDDYVG-----EKGPELIIVDEAHYFRRSSTNRYIAL--REL---V--NKNQAKIVLITATPV 354
                                       566666777777662.....256799**********9955555554..444...1..234566*******86 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.4
                                       HHHTTCSEEEEEHHHHHHHH....H CS
                                       xxxxxxxxxxxxxxxxxxxx....x RF
                              DEAD  93 kldngvdivvgtpgrlddll....s 113
                                       +ld++ + +++ p  ++dll    s
  gi|557693471|ref|YP_008796525.1| 876 VLDKDKEKIITSPTEIVDLLlegeS 900
                                       5555555555555555554433331 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 ?   -2.6   0.0       3.4   6.8e+03      80     126 ..      59     104 ..      54     108 .. 0.74
   2 ?    9.1   0.0   0.00083       1.7       6     109 ..     242     352 ..     237     362 .. 0.60
   3 ?   -1.0   0.0       1.1   2.2e+03      43      63 ..     624     643 ..     616     655 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSE CS
                               AAA  80 eeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdr 126
                                       +e+ +  +++l+el++++++ + + ++  t ++ k d+ l+ + ++r
  gi|557693471|ref|YP_008796525.1|  59 TETIKWEDEILQELEQFEDDADYFRLLQKTIQYFKDDKRLV-RIMER 104
                                       66777788999999999999888888888888888888777.34444 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00083
                                       STTSSHHHHHHHHHHHH...THEEEEEETTTCSSS...............STTHHHHHHHHHHHHHHHTS....... CS
                               AAA   6 ppGtGKTllakavakel...gvefleisgsellsk...............yvgesekkirelfkeakeka....... 57 
                                         G GK+ +a a+a+e+   g++ l i  +++l+                +  e+ ++           +       
  gi|557693471|ref|YP_008796525.1| 242 STGLGKSRVALALAHEAireGIRPLLIAPKSILETtweaemnetlvridtLSTEMLSQ-----------Npdivddy 307
                                       679*************876656666666666664434443333444444433333333...........13344444 PP

                                       ....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEE CS
                               AAA  58 ....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigat 109
                                           +p  +++DE++ + +s+            n  ++  + v+k+++k+++i+at
  gi|557693471|ref|YP_008796525.1| 308 vgekGPELIIVDEAHYFRRSS-----------TNRYIALRELVNKNQAKIVLITAT 352
                                       444469**********97777...........444444444444444567777776 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHTSTSEEEE CS
                               AAA  43 ekkirelfkeakekakpsilf 63 
                                       e+++++++k++ke +  +i+f
  gi|557693471|ref|YP_008796525.1| 624 ERRLQQIMKQIKEPN-GVIIF 643
                                       78999******9998.67776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1026 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      762  (0.042501); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.86u 0.33s 00:00:01.19 Elapsed: 00:00:00.46
# Mc/sec: 6705.92
//
Query:       gi|557693472|ref|YP_008796526.1|  [L=108]
Description: hypothetical protein CSUB_C0027 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 784.94
//
Query:       gi|557693473|ref|YP_008796527.1|  [L=134]
Description: hypothetical protein CSUB_C0028 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   18.0   2.2     0.0048   17.5   2.2    1.5  1  Excalibur  Excalibur calcium-binding domain
  ------ inclusion threshold ------
       0.26    9.4  13.6       0.29    9.2  13.6    1.0  1  FSA_C      Fragile site-associated protein C-terminus


Domain annotation for each model (and alignments):
>> Excalibur  Excalibur calcium-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   2.2   5.4e-07    0.0048      26      38 .]     121     133 ..      78     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.4e-07
                         Excalibur  26 kklDrDkDGiACE 38 
                                       +  DrD+DGi+CE
  gi|557693473|ref|YP_008796527.1| 121 HGFDRDGDGIGCE 133
                                       889*********9 PP

>> FSA_C  Fragile site-associated protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  13.6   3.3e-05      0.29     538     606 ..      15      84 ..       3     114 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 3.3e-05
                             FSA_C 538 tsltpklmsaakssleslqgsqdsiaiattasavelndatsstiasaatasslsstkstvtivv..stnds 606
                                       t  t   m a+++    +  + +++  +t++++v+  ++t++t++s +t++ + ++ ++ t++v  s    
  gi|557693473|ref|YP_008796527.1|  15 TMSTTVTMRATATVTALITKTLTATERSTATTTVTTPKTTTTTVTSMTTTTVTMTATTRLTTTVtgS-ATG 84 
                                       3334567778887777788888999999999999999999999988877766655555554444123.222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1622  (0.090468); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); 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):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 1001.69
//
Query:       gi|557693474|ref|YP_008796528.1|  [L=91]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00015   21.6   0.1    0.00018   21.3   0.1    1.1  1  TrmB      Sugar-specific transcriptional regulator TrmB
    0.00031   20.6   0.0    0.00044   20.1   0.0    1.2  1  MarR_2    MarR family
     0.0031   17.4   0.1      0.004   17.1   0.1    1.1  1  DUF977    Bacterial protein of unknown function (DUF977)
  ------ inclusion threshold ------
      0.037   13.6   0.0      0.045   13.3   0.0    1.1  1  HTH_47    winged helix-turn-helix
      0.053   13.1   0.1      0.085   12.4   0.1    1.3  1  HTH_24    Winged helix-turn-helix DNA-binding
      0.058   13.2   0.0      0.091   12.6   0.0    1.3  1  HTH_IclR  IclR helix-turn-helix domain
      0.096   12.6   1.5       0.11   12.3   1.5    1.1  1  RIFIN     Rifin
      0.099   12.8   0.0       0.14   12.3   0.0    1.2  1  DprA_WH   DprA winged helix domain
      0.099   13.3   0.1       0.16   12.7   0.1    1.4  1  RPA_C     Replication protein A C terminal
       0.16   12.5   0.2        1.6    9.3   0.2    2.1  1  HTH_27    Winged helix DNA-binding 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 !   21.3   0.1     1e-07   0.00018      11      65 ..      35      89 ..      31      91 .] 0.89

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1e-07
                                      CCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE- CS
                              TrmB 11 akvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYrav 65
                                      a+v +++ ++g+a+ d+i  ++g+p  +v +++++L+ +G+++++++  k++ +v
  gi|557693474|ref|YP_008796528.1| 35 ARVLAVIRSRGKASLDDIIIISGLPIYSVHNAVNELVARGIIYVKEEDGKIFYTV 89
                                      677788889*************************************998877666 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.4e-07   0.00044       8      60 ..      35      83 ..      33      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.4e-07
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDk 60
                                      arvLa+++ r+    +  ++    gl+  +v++++++Lva+G +  +  +eD+
  gi|557693474|ref|YP_008796528.1| 35 ARVLAVIRSRGK--ASLDDIIIISGLPIYSVHNAVNELVARGIIYVK--EEDG 83
                                      79*********9..9*****************************887..4466 PP

>> DUF977  Bacterial protein of unknown function (DUF977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   2.2e-06     0.004       7      61 ..      27      81 ..      24      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.2e-06
                            DUF977  7 qeereelkeriiGlvkkneritisdleritGvgrtsvrkylvdvlerGdlirpGk 61
                                      + +r e+++r++ +++ +++  ++d+  i G    sv+  + + ++rG ++ +  
  gi|557693474|ref|YP_008796528.1| 27 KRKRSEMLARVLAVIRSRGKASLDDIIIISGLPIYSVHNAVNELVARGIIYVKEE 81
                                      5789********************************************9998654 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.5e-05     0.045      34      76 ..      32      76 ..      22      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.5e-05
                                      HHHHHHHHH..-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-E CS
                            HTH_47 34 mallwvLnl..aDGkrsLldiAeriglpfdrvaaiaraLaeagll 76
                                      + l  vL+   + Gk sL di  ++glp++ v +++++L + g++
  gi|557693474|ref|YP_008796528.1| 32 EMLARVLAVirSRGKASLDDIIIISGLPIYSVHNAVNELVARGII 76
                                      3344566644489******************************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 ?   12.4   0.1   4.7e-05     0.085       7      47 ..      36      76 ..      32      77 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.7e-05
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++L +++  ++ s  ++   +gl++  v+  +++L+  G+I
  gi|557693474|ref|YP_008796528.1| 36 RVLAVIRSRGKASLDDIIIISGLPIYSVHNAVNELVARGII 76
                                      789*************************************9 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 ?   12.6   0.0   5.1e-05     0.091       6      48 ..      35      76 ..      33      80 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.1e-05
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      +++L  +++++ + +l ++   +glp  +vh+ ++ Lv +G++
  gi|557693474|ref|YP_008796528.1| 35 ARVLAVIRSRGKA-SLDDIIIISGLPIYSVHNAVNELVARGII 76
                                      6789999999997.9**************************87 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.5   6.3e-05      0.11     294     309 ..      16      31 ..       2      40 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.3e-05
                             RIFIN 294 mvIIYLiLRYrRKkKm 309
                                       ++II LiLRYr++k+ 
  gi|557693474|ref|YP_008796528.1|  16 IIIIVLILRYRKRKRS 31 
                                       799********99985 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.8e-05      0.14      11      49 ..      31      70 ..      26      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.8e-05
                           DprA_WH 11 ddlerrvLaaLgp.ePvhvDqLvrrtglpaaevsaaLleL 49
                                      ++  +rvLa + +    ++D+++  +glp+ +v  a  eL
  gi|557693474|ref|YP_008796528.1| 31 SEMLARVLAVIRSrGKASLDDIIIISGLPIYSVHNAVNEL 70
                                      67789******6538*****************99887665 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 ?   12.7   0.1   8.7e-05      0.16      70      98 ..      49      77 ..      27      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.7e-05
                                      HHHHHHHSTSXHHHHHHHHHHHHHTTSEE CS
                             RPA_C 70 vdeiaqklrlsvndvkqavdeLsneGiiY 98
                                      +d i    +l+  +v +av+eL+  GiiY
  gi|557693474|ref|YP_008796528.1| 49 LDDIIIISGLPIYSVHNAVNELVARGIIY 77
                                      55555556899****************** 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 ?    9.3   0.2    0.0009       1.6       8      53 ..      37      82 ..      12      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0009
                            HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLv.ertgd 53
                                      vL +ir  r++++l d++    +   ++++++++L+++G + ++++d
  gi|557693474|ref|YP_008796528.1| 37 VLAVIR-SRGKASLDDIIIISGLPIYSVHNAVNELVARGIIyVKEED 82
                                      677788.8888888999999999999999999999999987444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 655.25
//
Query:       gi|557693475|ref|YP_008796529.1|  [L=238]
Description: hypothetical protein CSUB_C0030 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.0        1.8    8.4   0.0    2.1  2  RNaseH_like  Ribonuclease H-like


Domain annotation for each model (and alignments):
>> RNaseH_like  Ribonuclease H-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.014   2.6e+02      95     131 ..      37      73 ..      25      83 .. 0.83
   2 ?    8.4   0.0    0.0001       1.8      62      87 ..     139     164 ..     129     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.014
                       RNaseH_like  95 lkleihiDiGengktkelikevvgmvegsgfeakiKP 131
                                       ++  + iD  ++ kt++ ik+++g+   + + + ++P
  gi|557693475|ref|YP_008796529.1|  37 VTDLVNIDLPRRFKTEDNIKRLLGYSFPVVMVCVVRP 73 
                                       555689*****************99877777777777 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0001
                       RNaseH_like  62 slrekiflEtslslevaskleellle 87 
                                        ++ek++ E+++s+++a++l++l   
  gi|557693475|ref|YP_008796529.1| 139 FVKEKLVDEAKMSVKLAEDLKKLWYM 164
                                       589******************96533 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1698.86
//
Query:       gi|557693476|ref|YP_008796530.1|  [L=291]
Description: cobyrinic acid a,c-diamide synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-57  192.2   0.4      1e-56  191.7   0.4    1.2  1  AAA_31        AAA domain
    2.2e-20   73.0   0.0    3.8e-20   72.2   0.0    1.4  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    1.7e-10   40.7   0.1    1.9e-06   27.6   0.0    2.2  2  ParA          NUBPL iron-transfer P-loop NTPase
    4.5e-10   39.4   0.0    0.00035   20.1   0.0    2.2  2  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
    6.2e-10   38.8   0.1    9.8e-05   21.8   0.0    2.1  2  MipZ          ATPase MipZ
    6.7e-08   32.1   0.0    2.9e-07   30.0   0.0    2.0  2  ArsA_ATPase   Anion-transporting ATPase
    1.6e-05   24.5   0.0    3.3e-05   23.5   0.0    1.5  1  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    6.1e-05   22.4   0.0     0.0019   17.5   0.0    2.1  2  VirC1         VirC1 protein
     0.0013   18.4   0.0     0.0022   17.6   0.0    1.5  1  AAA_25        AAA domain
     0.0095   15.6   0.1       0.38   10.4   0.1    2.2  2  SRP54         SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
      0.054   13.5   0.0       0.11   12.4   0.0    1.5  1  ResIII        Type III restriction enzyme, res subunit
      0.076   12.8   0.1       0.62    9.8   0.1    2.0  1  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.089   13.2   0.0       0.28   11.6   0.0    1.8  2  RNA_helicase  RNA helicase


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 !  191.7   0.4   7.2e-60     1e-56       2     176 ..       3     198 ..       2     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 191.7 bits;  conditional E-value: 7.2e-60
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaala.klgkkvLlvDlDpQanattglgiekne.........iektlyevl..... 63 
                                       kv++++n+KGGvGKTT +v++aaala ++gkkvLlvD+DpQ+nat++l  ++++         + k++++       
  gi|557693476|ref|YP_008796530.1|   3 KVVSFINYKGGVGKTTLAVEIAAALAyHRGKKVLLVDADPQTNATFYLI-SEEDwdvwqknkgTLKNIFDNYlegrd 78 
                                       9*************************9*******************553.333335554422322344433244444 PP

                            AAA_31  64 ..ieeknikeaiiktkvenldlipssidLaeaeielvelekkeei.....lkellekvkdeYDyiiiDcpPsLgllt 133
                                         i+e  ik++ +++++ nl+l+ps+i+L++++ +l++++ ++ i     lk++lekvk++YDy+iiDcpP+L+l+t
  gi|557693476|ref|YP_008796530.1|  79 tdINELIIKDLEVSSRTPNLHLLPSHIELIHIDLKLAGISGSRGIrakglLKKALEKVKQNYDYVIIDCPPNLNLVT 155
                                       44566667777778889999**********************666666659************************** PP

                            AAA_31 134 enaLvasdsviipvqaeayaleGleqllktieevkkklnpkle 176
                                       +n++vasds+ii++++e++++ G++ +l+ i+++ +++n++++
  gi|557693476|ref|YP_008796530.1| 156 QNSIVASDSFIIVLKPEFLSTIGIALILRVINDIVREINDEFQ 198
                                       ***************************************9986 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 !   72.2   0.0   2.8e-23   3.8e-20       2     128 .]       6     265 ..       5     265 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 2.8e-23
                                       EEEESSTTSSHHHHHHHHHHHHHH.TT--EEEEEEEESSCCCCH....HTTEB-HHHH................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx....xxxxxxxxxx................... RF
                              CbiA   2 aiastkGGvGKTtlaanLaralar.rglrVllvDaDpqannlai....leglendiep................... 54 
                                       ++++ kGGvGKTtla+ +a+ala  rg++VllvDaDpq+n++++          d +                    
  gi|557693476|ref|YP_008796530.1|   6 SFINYKGGVGKTTLAVEIAAALAYhRGKKVLLVDADPQTNATFYliseE-----DWDVwqknkgtlknifdnylegr 77 
                                       67899*******************89*****************554441.....333355666778889999***** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|557693476|ref|YP_008796530.1|  78 dtdineliikdlevssrtpnlhllpshielihidlklagisgsrgirakgllkkalekvkqnydyviidcppnlnlv 154
                                       ***************************************************************************** PP

                                       .......................CCHCCCHHHHHHCHCHHHH..............EEEEEEEEESS....-TTCHH CS
                                       .......................xxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxx.xxxxxxx RF
                              CbiA  55 .......................dlkrllellealgkkkall............lkiagvvlnrvdgen.eetllke 95 
                                                              ++  +l+++++++++ +++             ++ g+++n v+     +++++ 
  gi|557693476|ref|YP_008796530.1| 155 tqnsivasdsfiivlkpeflstiGIALILRVINDIVREINDEfqsfgfreeftgPEFSGMIFNFVKYLSgGTRSQEV 231
                                       **************************************99999*********************9864404677777 PP

                                       HHHHHHHHCTS-EEE.EEE--CCHCCCCHHTS-H CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                              CbiA  96 aleelkqrygvpvlg.viprdeavaeapargepv 128
                                        + e+k++y+ +v++ ++++++++ae p ++ p+
  gi|557693476|ref|YP_008796530.1| 232 VINEVKRQYPGKVFKsFLSESVKLAERPVEKIPI 265
                                       888888899******9***********9998876 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 !   27.6   0.0   1.3e-09   1.9e-06       4      41 ..       3      41 ..       1      66 [. 0.88
   2 !   11.2   0.0   0.00013      0.18      92     150 ..     121     176 ..     115     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.3e-09
                              ParA  4 kviavlSgKGGVGKStvavnlAlaLa.kkglkvgllDaD 41
                                      kv+  +  KGGVGK+t+av++A+aLa ++g+kv l+DaD
  gi|557693476|ref|YP_008796530.1|  3 KVVSFINYKGGVGKTTLAVEIAAALAyHRGKKVLLVDAD 41
                                      56667778*****************9899*********9 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                              ParA  92 rGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqeval 150
                                       rG  +++++k+ l++v+ ++ Dy+iiD+PP      +t  + +  +  +iV  p+ +++
  gi|557693476|ref|YP_008796530.1| 121 RGIRAKGLLKKALEKVK-QNYDYVIIDCPPNLN--LVTQNSIVASDSFIIVLKPEFLST 176
                                       8999999********99.569*********853..334444447778888888877665 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.8e-06    0.0025       7      44 ..       8      46 ..       2      74 .. 0.80
   2 !   20.1   0.0   2.6e-07   0.00035     101     151 ..     125     175 ..      93     184 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                          CBP_BcsQ  7 qGvRGGvGttsllaaLawalh.elgesvlviDlspdnlL 44
                                         +GGvG+t+l++ +a al  + g++vl++D+ p+   
  gi|557693476|ref|YP_008796530.1|  8 INYKGGVGKTTLAVEIAAALAyHRGKKVLLVDADPQTNA 46
                                      5568****************735699*******997654 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 2.6e-07
                          CBP_BcsQ 101 kaeallaalkelkeqyrwillDlpagasaltrellaladlvllvvepdanc 151
                                       +++ l++al+++k++y+++++D+p + + +t++ +  +d+ + v++p+  +
  gi|557693476|ref|YP_008796530.1| 125 AKGLLKKALEKVKQNYDYVIIDCPPNLNLVTQNSIVASDSFIIVLKPEFLS 175
                                       56778999***************************************9755 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   7.1e-08   9.8e-05       2      45 ..       4      47 ..       3      76 .. 0.82
   2 !   15.3   0.0   6.8e-06    0.0093      88     133 ..     128     173 ..      77     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.1e-08
                                      EEEE--SSTTSSHHHHHHHHHHHHHT.TT--EEEEE--TTT-HHH CS
                              MipZ  2 vivlgnekGGsGksttavhvavaLlk.kGarvaaidldlrqrtla 45
                                      v+ + n kGG Gk+t av +a aL++ +G++v  +d d + +  +
  gi|557693476|ref|YP_008796530.1|  4 VVSFINYKGGVGKTTLAVEIAAALAYhRGKKVLLVDADPQTN-AT 47
                                      78899*******************9747********997543.33 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 6.8e-06
                                       HHHHHHHHHHHH-SEEEEE--SS--HHHHHHHHT-SEEEEEEESSH CS
                              MipZ  88 eleelvadleaeldfividtPGsdsalsrlahsladtlvtPlndsf 133
                                        l+++++++++++d+++id+P + + +++ +   +d+++  l   f
  gi|557693476|ref|YP_008796530.1| 128 LLKKALEKVKQNYDYVIIDCPPNLNLVTQNSIVASDSFIIVLKPEF 173
                                       4789***************************999999998776665 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   2.1e-10   2.9e-07       5     134 ..       7     149 ..       3     162 .. 0.71
   2 ?   -1.6   0.0      0.86   1.2e+03     207     219 ..     163     175 ..     152     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.1e-10
                                       EEEESTTSSHHHHHHHHHHHHH.HTTS-EEEEE-STTTHHH.........HHHTS--BSS-EEETSSEEEEE--HHH CS
                       ArsA_ATPase   5 lvgGKGGVGKttvsaatavkls.ekgkkvllistDPAhsls.........DsfdqklgkeptkvkeNLsavEidpev 71 
                                       ++  KGGVGKtt++  +a+ l+ + gkkvll+  DP  +           D+++++ g  +   ++ L+  + d+++
  gi|557693476|ref|YP_008796530.1|   7 FINYKGGVGKTTLAVEIAAALAyHRGKKVLLVDADPQTNATfyliseedwDVWQKNKGTLKNIFDNYLEGRDTDINE 83 
                                       6778*****************94568**********99965222223333444444444444445779999999997 PP

                                       HHHHHHCCHHGGGSCCH.HHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHH..CSSSSEEEEESBS CS
                       ArsA_ATPase  72 eleeakqevqkeeeall.gleeledvlaeelaslPGideilsfeellkyvk..eeeydvvvlDtaP 134
                                        + +  +  +++ +  l  ++ +   ++ +la + G   i +   l+k ++  +++yd+v++D +P
  gi|557693476|ref|YP_008796530.1|  84 LIIKDLEVSSRTPNLHLlPSHIELIHIDLKLAGISGSRGIRAKGLLKKALEkvKQNYDYVIIDCPP 149
                                       6666666555555544413334444455566677788888888888888777789********999 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.86
                                       EEEEEEEESSHHH CS
                       ArsA_ATPase 207 tsfrlVvipEkls 219
                                        sf++V++pE+ls
  gi|557693476|ref|YP_008796530.1| 163 DSFIIVLKPEFLS 175
                                       589********98 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 !   23.5   0.0   2.4e-08   3.3e-05       7      47 ..      10      51 ..       5      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.4e-08
                         Fer4_NifH  7 GkGGiGksttsqnlsaalae.mgkkvlivGCDPkaDstrlll 47
                                       kGG+Gk+t +  ++aala+ +gkkvl+v  DP++++t  l+
  gi|557693476|ref|YP_008796530.1| 10 YKGGVGKTTLAVEIAAALAYhRGKKVLLVDADPQTNATFYLI 51
                                      59****************96368**************96655 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.4e-06    0.0019       2      41 ..       3      43 ..       2      63 .. 0.85
   2 ?    2.6   0.0      0.05        69      71     120 ..     128     179 ..     124     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                             VirC1  2 klitfcslkGGaGkttalmglcsala.sdgkrvalfeaden 41
                                      k+++f  +kGG Gktt  + + +ala  +gk+v l +ad  
  gi|557693476|ref|YP_008796530.1|  3 KVVSFINYKGGVGKTTLAVEIAAALAyHRGKKVLLVDADPQ 43
                                      6799*********************94689********965 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.05
                             VirC1  71 lleaayeeaegeGfdyaladtrgGssel.nntiiassdllli..Ptmltpldi 120
                                       ll +a e+++ + +dy+++d       +  n i+as  ++++  P  l+ + i
  gi|557693476|ref|YP_008796530.1| 128 LLKKALEKVK-QNYDYVIIDCPPNLNLVtQNSIVASDSFIIVlkPEFLSTIGI 179
                                       6777777775.5799*9999988776542799****99988755777766665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.6e-06    0.0022      41      89 ..      11      62 ..       3     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                            AAA_25 41 apgtGKttlaldlalava..tGkpwlg.pvapeqgkVlyvsaEdsedelrrR 89
                                       +g+GKttla+++a+a+a  +Gk++l  +  p+  ++ y+  E++ d +++ 
  gi|557693476|ref|YP_008796530.1| 11 KGGVGKTTLAVEIAAALAyhRGKKVLLvDADPQTNATFYLISEEDWDVWQKN 62
                                      58*********************99999778899999999999998888864 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.1   0.00027      0.38      11      39 ..      13      42 ..       3      52 .. 0.86
   2 ?    2.9   0.0     0.053        73      69      91 ..     126     147 ..     107     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                                      TSSHHHHHHHHHHHHHHT.TS-EEEEEEST CS
                             SRP54 11 GaGKTttlaKLaallkke.gkkvllvaaDt 39
                                      G+GKTt +  +aa l  + gkkvllv aD 
  gi|557693476|ref|YP_008796530.1| 13 GVGKTTLAVEIAAALAYHrGKKVLLVDADP 42
                                      8***********9998877*******9996 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.053
                                       HHHHHHHHHHHHHTTSSEEEEEE CS
                             SRP54  69 aavakeavekakeekidvvlvDT 91 
                                         ++k+a+ek k+ ++d+v++D 
  gi|557693476|ref|YP_008796530.1| 126 KGLLKKALEKVKQ-NYDYVIIDC 147
                                       5677899999988.99******5 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 ?   12.4   0.0   8.2e-05      0.11      29     139 ..       8     146 ..       3     147 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.2e-05
                                       EEESTTSTHHHHHHHHHHHH-S.................-EEEEESSH.HHHHHHHHHGGGGTGG........GEEE CS
                            ResIII  29 ikmaTGtGKTlvaaklierllkkgkee............kflflvprk.slleqtleefkkflseayke....igkk 88 
                                       i+   G+GKT +a++++++l+ +++++             f ++  +  ++ ++ + ++k++++++ +     i++ 
  gi|557693476|ref|YP_008796530.1|   8 INYKGGVGKTTLAVEIAAALAYHRGKKvllvdadpqtnaTFYLISEEDwDVWQKNKGTLKNIFDNYLEGrdtdINEL 84 
                                       67778****************98885444444444444333333332234444444444444444443333334444 PP

                                       ESSS-B--.......-SEEEEEHHHHHHTH.....................HHHTTT-SEEEEE CS
                            ResIII  89 vsgdkkkakekdstnkkilvttiqsldadseee.............eeeseellrdrfdviiiD 139
                                       + +d + +  +++ n ++l + i+ ++ d++ +              ++  e+ ++++d++iiD
  gi|557693476|ref|YP_008796530.1|  85 IIKDLEVS--SRTPNLHLLPSHIELIHIDLKLAgisgsrgirakglLKKALEKVKQNYDYVIID 146
                                       33333333..566677777777777777776667777778888778778888888888888887 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 ?    9.8   0.1   0.00045      0.62       6     105 ..      13     154 ..      11     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00045
                        ATP_bind_1   6 GsGKttfvgalse.ilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvale........ 73 
                                       G+GKtt+  +++  ++  rg++v +v  DP  +++ Y        li++ed ++    +++g+l   ++        
  gi|557693476|ref|YP_008796530.1|  13 GVGKTTLAVEIAAaLAYHRGKKVLLVDADPQTNATFY--------LISEEDWDVW--QKNKGTLKNIFDnylegrdt 79 
                                       8999998766655156688999999999999887666........7888888776..56778888888888888888 PP

                        ATP_bind_1  74 ................................................flresldwldeelekeeddyllfDtPGQi 102
                                                                                       +l++ l++++++      dy+++D+P  +
  gi|557693476|ref|YP_008796530.1|  80 dineliikdlevssrtpnlhllpshielihidlklagisgsrgirakgLLKKALEKVKQNY-----DYVIIDCPPNL 151
                                       8888888888899999999999999999999999999998887666656666665555555.....9******9666 PP

                        ATP_bind_1 103 elf 105
                                        l+
  gi|557693476|ref|YP_008796530.1| 152 NLV 154
                                       555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00021      0.28       8      65 ..      13      80 ..       8      99 .. 0.81
   2 ?   -3.2   0.0         8   1.1e+04      43      64 ..     221     242 ..     218     257 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                      RNA_helicase  8 geGKStlakeLakallkkl.........klkkkdsvys.rnpeddfwdgYtgqevvvidDfgqvkdee 65
                                      g+GK+tla e+a+al+ +          + +++ ++y   + + d+w++ +g   +++d   + +d+ 
  gi|557693476|ref|YP_008796530.1| 13 GVGKTTLAVEIAAALAYHRgkkvllvdaDPQTNATFYLiSEEDWDVWQKNKGTLKNIFDNYLEGRDTD 80
                                      9***************7778888999975555677888788888999999999999999988888773 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8
                      RNA_helicase  43 fwdgYtgqevvvidDfgqvkde 64 
                                       +++g t+ + vvi +++++  +
  gi|557693476|ref|YP_008796530.1| 221 YLSGGTRSQEVVINEVKRQYPG 242
                                       6666676666677776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2085.48
//
Query:       gi|557693477|ref|YP_008796531.1|  [L=135]
Description: hypothetical protein CSUB_C0035 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 983.33
//
Query:       gi|557693478|ref|YP_008796532.1|  [L=486]
Description: hypothetical protein CSUB_C0037 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   18.7   0.0     0.0041   17.2   0.0    1.7  2  LSM14     Scd6-like Sm domain
     0.0024   17.7   1.8       0.32   11.0   0.4    3.9  4  PQQ       PQQ enzyme repeat
  ------ inclusion threshold ------
      0.045   13.3   0.0         13    5.3   0.0    3.6  3  PQQ_2     PQQ-like domain
        6.3    7.4   9.1       0.47   11.0   0.3    3.7  5  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> LSM14  Scd6-like Sm domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   9.2e-07    0.0041      19      68 ..     175     224 ..     174     231 .. 0.87
   2 ?   -3.3   0.1       2.3     1e+04      52      61 ..     470     479 ..     466     480 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.2e-07
                             LSM14  19 GilceinledstiaLqnvrsfGteg.rkdneqippskevyeyivFrgsDik 68 
                                       G+l+++++++  i+L  +  +G e  r  +e   ++k+ y+yi+Fr+ ++ 
  gi|557693478|ref|YP_008796532.1| 175 GVLYALDAASGDISLVAIDNMGNELwRSPREP-LVLKDPYQYIIFRAGEVP 224
                                       9***********************95655555.99***********99885 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.3
                             LSM14  52 pskevyeyiv 61 
                                       ++++vy y+v
  gi|557693478|ref|YP_008796532.1| 470 VKDHVYTYVV 479
                                       7899***997 PP

>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.4   7.1e-05      0.32       3      21 ..     168     186 ..     167     187 .. 0.88
   2 ?    0.1   0.0       0.2   8.9e+02      13      26 ..     190     202 ..     188     208 .. 0.76
   3 ?    2.0   0.0     0.049   2.2e+02      19      33 ..     365     379 ..     364     381 .. 0.87
   4 ?   -3.6   0.0         3   1.3e+04       9      15 ..     390     396 ..     385     396 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.1e-05
                                       EEEEETTSEEEEEETTTCC CS
                               PQQ   3 vylgsadGylyAlDadTGk 21 
                                       +++g   G+lyAlDa++G+
  gi|557693478|ref|YP_008796532.1| 168 YFVGAGAGVLYALDAASGD 186
                                       5788999***********8 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.2
                                       EEEETTTCCEEEEE CS
                               PQQ  13 yAlDadTGkvlWrf 26 
                                       +A+D + G++lWr 
  gi|557693478|ref|YP_008796532.1| 190 VAID-NMGNELWRS 202
                                       5666.44*****96 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.049
                                       TCCEEEEEESSSCGS CS
                               PQQ  19 TGkvlWrfktggpvl 33 
                                       +Gk++W+ +  +++l
  gi|557693478|ref|YP_008796532.1| 365 DGKLVWSSNYTPNDL 379
                                       8******99998875 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 3
                                       TSEEEEE CS
                               PQQ   9 dGylyAl 15 
                                       +G lyAl
  gi|557693478|ref|YP_008796532.1| 390 GGSLYAL 396
                                       799**98 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0029        13     167     232 ..     128     186 ..      85     190 .. 0.72
   2 ?    1.4   0.0     0.044     2e+02       5      24 ..     189     219 ..     185     301 .. 0.64
   3 ?    2.1   0.0     0.026   1.2e+02     169     221 ..     415     476 ..     358     484 .. 0.48

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0029
                             PQQ_2 167 grpvvaegtVyassgqgrllal.dlatgrrlwskeissinglpildgdllyvvsa..gelialdratGa 232
                                       g+p++++++ y+   +++l+++ dl +g+  w         ++   g +ly v a  g l+ald a+G 
  gi|557693478|ref|YP_008796532.1| 128 GQPIFDSDKAYFLMENMQLAKIvDLNSGE-MW---------TVDRRGTYLYFVGAgaGVLYALDAASGD 186
                                       66777777777777777777777777776.66.........2334566666666556666777776665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.044
                             PQQ_2   5 vsaldaatGaelWrvdlar............p 24 
                                       ++a+d+  G+elWr+  ++            +
  gi|557693478|ref|YP_008796532.1| 189 LVAIDN-MGNELWRSPREPlvlkdpyqyiifR 219
                                       579996.7999999932333333333334430 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.026
                             PQQ_2 169 pvva..egtVyassgqgrllaldlatgrrlwske.issinglpildgdllyvvsa.......g 221
                                       +v    +gt++a+   + +la +l +g+  ws      i++  i d++l+ ++ a       +
  gi|557693478|ref|YP_008796532.1| 415 LVRIgrDGTINAILSVKDFLAAELFRGEDPWSYRfSDDIHA-IIIDNKLILTTKAsvkdhvyT 476
                                       22222233555555555566666666665565553444555.666666666555336644444 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2       1.5   6.8e+03      18      30 ..      78      91 ..      65      94 .. 0.59
   2 ?   11.0   0.3   0.00011      0.47      25      40 .]     169     184 ..     156     184 .. 0.82
   3 ?   -3.7   0.0         4   1.8e+04       1       8 [.     196     203 ..     196     206 .. 0.79
   4 ?   -1.4   0.0      0.87   3.9e+03      26      36 ..     386     396 ..     384     396 .. 0.76
   5 ?   -3.0   0.0       2.7   1.2e+04       5      23 ..     445     462 ..     445     466 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                             PQQ_3 18 avdgglvyvgtg.d 30
                                       ++ gl+ v+tg d
  gi|557693478|ref|YP_008796532.1| 78 YLAHGLISVVTGqD 91
                                      34555555555555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                             PQQ_3  25 yvgtgdGtlyAlDaet 40 
                                       +vg+g G lyAlDa++
  gi|557693478|ref|YP_008796532.1| 169 FVGAGAGVLYALDAAS 184
                                       67777*********86 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4
                             PQQ_3   1 GevlWsvq 8  
                                       G +lW+ +
  gi|557693478|ref|YP_008796532.1| 196 GNELWRSP 203
                                       8899*965 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.87
                             PQQ_3  26 vgtgdGtlyAl 36 
                                       vg + G+lyAl
  gi|557693478|ref|YP_008796532.1| 386 VGEHGGSLYAL 396
                                       555689***98 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 2.7
                             PQQ_3   5 Wsvqlpgpvnsspavdggl 23 
                                       Ws+++ ++++ +  +d+ l
  gi|557693478|ref|YP_008796532.1| 445 WSYRFSDDIH-AIIIDNKL 462
                                       9999999985.45666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3454.97
//
Query:       gi|557693479|ref|YP_008796533.1|  [L=87]
Description: hypothetical protein CSUB_C0038 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.8   0.1      0.051   13.4   0.1    1.1  1  DUF559    Protein of unknown function (DUF559)


Domain annotation for each model (and alignments):
>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.9e-06     0.051      43     105 ..       4      68 ..       2      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-06
                                       TEEEEEEETTTTEEEEEE-------..----HHHHHHHHHTT-EEEEEEHHHHHH-HHHHHHHHH CS
                            DUF559  43 sYivDfvclkaklivelDGaqhdee..eeyDaeRtelLeslGftvlRfkndevlknieevleeil 105
                                        Y +D + + a ++ve+D  q ++e  ++++ e+ ++ ++ G++ +  +  +v +++ +++e i 
  gi|557693479|ref|YP_008796533.1|   4 GYRIDILITAAMIVVEMDELQNYQErvHAKNLEKFNVSKKRGYEAFMIQAVDVSRDTASIAEMIK 68 
                                       6999***************999888566778888889999**************99999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 627.47
//
Query:       gi|557693480|ref|YP_008796534.1|  [L=145]
Description: hypothetical protein CSUB_C0039 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.1   0.0       0.26   11.1   0.0    2.1  2  DUF5615   Domain of unknown function (DUF5615)


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 ?    0.8   0.0     0.023   4.2e+02       2      16 ..       4      18 ..       3      34 .. 0.71
   2 ?   11.1   0.0   1.4e-05      0.26      36      61 ..     100     125 ..      86     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.023
                           DUF5615  2 klllDenlsprlvel 16
                                      k++lDen+   +++ 
  gi|557693480|ref|YP_008796534.1|  4 KFVLDENIIILAAKM 18
                                      899999997655555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 1.4e-05
                           DUF5615  36 sDeeileyAkeedriivTkDkDFgel 61 
                                       +D ei+++A+  ++++vT D+   e 
  gi|557693480|ref|YP_008796534.1| 100 DDVEIVRLANHANATLVTIDSRLKEA 125
                                       799*****************866665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1046.96
//
Query:       gi|557693481|ref|YP_008796535.1|  [L=431]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  119.9   0.0    3.5e-32  112.5   0.0    2.2  1  AAA_15    AAA ATPase domain
    1.3e-21   77.7   0.3    1.2e-13   51.6   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.6e-09   37.5   0.4    7.6e-07   28.8   0.1    2.3  2  SMC_N     RecF/RecN/SMC N terminal domain
    1.4e-07   31.1   1.8    6.6e-06   25.6   0.2    2.2  2  DUF2813   Protein of unknown function (DUF2813)
    3.4e-07   31.0   0.0    8.8e-07   29.6   0.0    1.7  1  AAA_23    AAA domain
    0.00031   21.3   0.0    0.00065   20.2   0.0    1.6  1  ABC_tran  ABC transporter
    0.00032   21.0   0.0    0.00074   19.9   0.0    1.6  1  DUF3696   Protein of unknown function (DUF3696)
    0.00033   20.3   0.0    0.00091   18.9   0.0    1.8  1  AAA_27    AAA domain
     0.0005   19.7   0.1     0.0024   17.6   0.0    2.0  2  AAA_29    P-loop containing region of AAA domain
    0.00093   19.2   0.1     0.0025   17.8   0.0    1.7  2  ATPase_2  ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.051   14.0   0.1       0.21   12.0   0.0    1.9  2  AAA_16    AAA ATPase domain


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 !  112.5   0.0   2.2e-35   3.5e-32       1     369 []       1     361 [.       1     361 [. 0.69

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 2.2e-35
                            AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn....................... 54 
                                       M I+k++i+ F+slk+v++dl   +tv+iG+N sGKSs+l+al  + +   + +                       
  gi|557693481|ref|YP_008796535.1|   1 M-IEKLTIQGFKSLKNVSLDLGL-ITVIIGPNRSGKSSVLHALAALRQSLGQGHlyangqminlgsyqnilstqske 75 
                                       8.9********************.*********************99966444467756666666666666666666 PP

                            AAA_15  55 .....kkvikiekedleifeniseskdikIdvef......aekekakeyektlkskekkkadlllkkkesdlkktik 120
                                              + +i+  +l    ++s +k   +++++      +            +s e+ ++ l        + ++  
  gi|557693481|ref|YP_008796535.1|  76 ikfvlTGKRFIDPAELAPI-SRSDNKIEYVTYKYgvmfgsD-------AAWVWHSGEISCNGLR------FKATLDS 138
                                       6555544455555555555.455555555555554433220.......2223333333333322......2223335 PP

                            AAA_15 121 dkklklkknelsdekisvekkks..kkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaii 195
                                         +++l+  +++++ i + +  +  +   p+ ++    ++ ++++i    +k+ ++          +++nv+ + ++
  gi|557693481|ref|YP_008796535.1| 139 YGNQELEPRRIQVDEIGAVDLAEapYIAKPIVSTMTFSSNTPTTSIMLRRVKDAYD----------KIFNVIFNDLD 205
                                       55566666677777777776666664444444555555555555556666666666..........678899999** PP

                            AAA_15 196 klllisakRnvsdedsekkssllgklkekileealqekleeelteklkeiqeklkeidkklaeelkkilkkkidkik 272
                                        +++ +  R +++  ++ +  + + + +  +  + +++++  lt   +++++k+++  +k++    ++ +++ d   
  gi|557693481|ref|YP_008796535.1| 206 SFRFVPVLRGFDNHSYKLTGYNSDVIANPNVT-IQAQYASNLLTYRRDKLEDKVSDWTEKITGARIYVRIEPPDL-- 279
                                       *************8887776666665555555.233444556666777777777777777755444433333333.. PP

                            AAA_15 273 kfnykgkkneeieik......ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkv 343
                                                             ++e++l + G+G+++++ ++l ++ a +         i+ iEEPE+hLHp  q  
  gi|557693481|ref|YP_008796535.1| 280 --------------AalrsrdGEVETYLVNDGFGLNQIVIMLLALAVAPEM-------SIIGIEEPEIHLHPRSQAT 335
                                       ..............0233445899***************************.......******************* PP

                            AAA_15 344 likllkelandnktQviitTHSphii 369
                                       l++ l ++a+++k+Q+iitTHS+hi+
  gi|557693481|ref|YP_008796535.1| 336 LADILTDVAKKEKKQLIITTHSEHIL 361
                                       ************************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 !   24.4   0.1   1.4e-08   2.2e-05       1      63 [.      23      83 ..      23     106 .. 0.87
   2 !   51.6   0.0   7.3e-17   1.2e-13     225     302 ..     284     361 ..     188     362 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.4e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63
                                      ++v+iGpN sGKS++L al  l+  ++ ++g  + ++   +++++ + l + ++ei+f+++  
  gi|557693481|ref|YP_008796535.1| 23 ITVIIGPNRSGKSSVLHALAALR--QSLGQGHLYANGQMINLGSYQNILSTQSKEIKFVLTGK 83
                                      79********************9..799999999999999*****************999866 PP

  == domain 2  score: 51.6 bits;  conditional E-value: 7.3e-17
                            AAA_21 225 engdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpl 300
                                        +++  e+ + + + G  ++  +l+al+ a++  s++ i+EpE +LHP+ +++l+++l + +++++ Q+i+tTHS +
  gi|557693481|ref|YP_008796535.1| 284 SRDGEVETYLVNDGFGLNQIVIMLLALAVAPEM-SIIGIEEPEIHLHPRSQATLADILtDVAKKEKKQLIITTHSEH 359
                                       344555555555599*****9999999999999.************************644444789********99 PP

                            AAA_21 301 ll 302
                                       +l
  gi|557693481|ref|YP_008796535.1| 360 IL 361
                                       86 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 !   28.8   0.1   4.6e-10   7.6e-07       1      44 [.       1      41 [.       1     108 [. 0.91
   2 !    6.9   0.0    0.0023       3.7     149     202 ..     306     361 ..     287     370 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 4.6e-10
                                      EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAi 44
                                      ++++l+i++Fks+  k+v+l++   +t+i+GpN SGKs++l A+
  gi|557693481|ref|YP_008796535.1|  1 MIEKLTIQGFKSL--KNVSLDLGL-ITVIIGPNRSGKSSVLHAL 41
                                      699**********..689999887.9**************9997 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0023
                                       HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                             SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreeml 202
                                       +l+A+  +   ++  + e + +L  +  + +a++l   +k+++ Q+i+++++e++l
  gi|557693481|ref|YP_008796535.1| 306 MLLALAVAPEMSIIGIEEPEIHLHPRSQATLADILTdvAKKEKKQLIITTHSEHIL 361
                                       678888899999999********************96566778********99876 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.2   4.1e-09   6.6e-06       3      45 ..       2      44 ..       1      84 [. 0.86
   2 !    4.9   0.1     0.008        13     286     325 ..     318     361 ..     312     381 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 4.1e-09
                           DUF2813  3 LerieisGFRGinrLSlsleentvLiGENaWGKSSLldALsli 45
                                      +e++ i+GF+ ++  Sl l   tv+iG N  GKSS l+AL  +
  gi|557693481|ref|YP_008796535.1|  2 IEKLTIQGFKSLKNVSLDLGLITVIIGPNRSGKSSVLHALAAL 44
                                      68999***********************************876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.008
                           DUF2813 286 illlEdpearLHPtmlaiaWellellP....lQkiltTNSveLl 325
                                       i+ +E+pe +LHP+  a + ++l+ +      Q i+tT S  +l
  gi|557693481|ref|YP_008796535.1| 318 IIGIEEPEIHLHPRSQATLADILTDVAkkekKQLIITTHSEHIL 361
                                       7789**********999988888777522225889999998766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   5.4e-10   8.8e-07       1      40 [.       4      42 ..       4      50 .. 0.96

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 5.4e-10
                            AAA_23  1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAik 40
                                      kL+i++f+s++++++d++  +t+I+GpN +GK+++l A+ 
  gi|557693481|ref|YP_008796535.1|  4 KLTIQGFKSLKNVSLDLG-LITVIIGPNRSGKSSVLHALA 42
                                      79***************9.9*****************996 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0     4e-07   0.00065       5      63 ..      15      78 ..      13     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4e-07
                                      EEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.SEEEEEETTCEGGG....B-HHHCCHCEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx....xxxxxxxxxxxx RF
                          ABC_tran  5 slklkegekvaivGenGaGKStLlkllagllkp.teGeilldgkdlke....qeleslrkeigv 63
                                      +++l  g +++i+G+n +GKS++l +la l +   +G++  +g+ ++     + l+  +kei++
  gi|557693481|ref|YP_008796535.1| 15 NVSLDLGLITVIIGPNRSGKSSVLHALAALRQSlGQGHLYANGQMINLgsyqNILSTQSKEIKF 78
                                      45667799**********************9987889998888777765554444445555554 PP

>> DUF3696  Protein of unknown function (DUF3696)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   4.5e-07   0.00074       1      44 [.     373     412 ..     373     420 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.5e-07
                           DUF3696   1 ispndvalyfferdegkdsaidtevlspiddnGrisnWPeGFFD 44 
                                       +sp++ ++y+fer++g++ +   +    ++++G+++   +GFF 
  gi|557693481|ref|YP_008796535.1| 373 LSPEELKVYYFERVGGETKVTNLA----VNEKGQLEGGLKGFFE 412
                                       589************999999999....9**************6 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   5.6e-07   0.00091       3      50 ..       2      45 ..       1      55 [. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.6e-07
                            AAA_27  3 lerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      +e+L+++ + ++++ sld++     +++i+GpN +GKs++l+A+ +l+
  gi|557693481|ref|YP_008796535.1|  2 IEKLTIQGFKSLKNVSLDLG----LITVIIGPNRSGKSSVLHALAALR 45
                                      78999999999999999999....79******************9997 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 !   17.6   0.0   1.5e-06    0.0024      12      45 ..      10      44 ..       7      48 .. 0.86
   2 ?   -1.4   0.0       1.3     2e+03       5      30 ..      58      83 ..      55      84 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                            AAA_29 12 fdg.htieidlkgatlltGpsGsGKSTllDAiqal 45
                                      f+  + +++dl  +t+++Gp+ sGKS++l A++al
  gi|557693481|ref|YP_008796535.1| 10 FKSlKNVSLDLGLITVIIGPNRSGKSSVLHALAAL 44
                                      6666788888655******************9987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.3
                            AAA_29  5 qlvNWgtfdg.htieidlkg.atlltGp 30
                                      q++N g++++  + +   k+  ++ltG+
  gi|557693481|ref|YP_008796535.1| 58 QMINLGSYQNiLSTQ--SKEiKFVLTGK 83
                                      899999999933333..34557888886 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 !   17.8   0.0   1.5e-06    0.0025      19      94 ..      20      94 ..      11     111 .. 0.77
   2 ?   -3.2   0.0         4   6.5e+03     105     123 ..     335     353 ..     320     361 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-06
                          ATPase_2 19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleei 94
                                         i +i Gp +sGK+++l  ++  ++++++ ++y  + + +++ ++++ + +++++ k+  + +  +  ael  i
  gi|557693481|ref|YP_008796535.1| 20 LGLITVIIGPNRSGKSSVLHALAALRQSLGQGHLY-ANGQMINLGSYQNILSTQSKEIKFVLTGKRFIDPAELAPI 94
                                      56799*************************98887.5789999999999988777777666555555555555555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4
                          ATPase_2 105 aielllekikkkgkkiiii 123
                                        ++++l ++ kk kk  ii
  gi|557693481|ref|YP_008796535.1| 335 TLADILTDVAKKEKKQLII 353
                                       5666777777777663333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.21      24      52 ..      21      51 ..      10      95 .. 0.74
   2 ?   -0.9   0.0       1.2   1.9e+03     106     107 ..     294     314 ..     228     376 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                            AAA_16 24 pelvllsGesGvGKsslvrellralekd...g 52
                                      + +++++G+  +GKss++ +l+ al+++   g
  gi|557693481|ref|YP_008796535.1| 21 GLITVIIGPNRSGKSSVLHALA-ALRQSlgqG 51
                                      57899*************9999.777775432 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.2
                            AAA_16 106 a...................a 107
                                                           +
  gi|557693481|ref|YP_008796535.1| 294 VndgfglnqivimllalavaP 314
                                       034444444444443333331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); 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 0.29s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3140.93
//
Query:       gi|557693482|ref|YP_008796536.1|  [L=305]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  101.1   0.0    1.3e-28  100.7   0.0    1.1  1  DUF72     Protein of unknown function DUF72
  ------ inclusion threshold ------
      0.028   14.5   0.0      0.051   13.7   0.0    1.4  1  DUF5343   Family of unknown function (DUF5343)


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 !  100.7   0.0   1.4e-32   1.3e-28       9     212 ..      19     215 ..      15     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1.4e-32
                                       CHHHHHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS....G-.SCHHHHHHHHHH.CHHHC CS
                             DUF72   9 erLeyYarhfntVEinstFYalpspetvakwaaqtpedFrFavKapraither...ne.daeealerflesalepLg 81 
                                       +rL+ Ya+ f+ VE+ns FY+l+  + va+w++++p++F+F+vK++r+ith +   n+ ++ + le +l+   + L+
  gi|557693482|ref|YP_008796536.1|  19 DRLTKYAKVFDFVEVNSLFYRLLPLDVVASWRKKVPDSFVFTVKCNRKITHIHglaNNrESMKVLEYMLRV-CRLLR 94 
                                       69*************************************************74454222477777777774.77786 PP

                                       T-EEEEEEE--TT--S.HHHHHHHHHHTTTS-...S.EEEE--BGGGHHHHHHHHHTT-EEEEE--SSC-------- CS
                             DUF72  82 eklgpllfQlppsfkfdeenlerLeaflaalp...l.lavEvRhrswfellellrehgvavvldepkkpklpledvt 154
                                       + l  l+++ pp+++ +    e L++f++  p     +a+E+R +s  + le++re+g+++v+d +   ++    + 
  gi|557693482|ref|YP_008796536.1|  95 SPL--LVMETPPTLRVT---CELLRDFFSSSPskdVmYALEIRGESDGKALEAMRELGLIHVVDIS---RQE-PSYY 162
                                       655..99*******444...59*****9999999955********9647**************932...222.2333 PP

                                       SSTEEEEEE--SHHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCHHHHHH CS
                             DUF72 155 tadfvyvRlhgreeryayrYseeelaewaerikawaaegrevyvffnndaegqaplna 212
                                        ++ +y Rl g+     y+++++el e+ ++++a  +  ++v++ f++    ++ ++a
  gi|557693482|ref|YP_008796536.1| 163 HDEITYSRLFGKGVHNIYQFDDDELLEISRKAEASPS--KRVMLSFHT---VKMYEDA 215
                                       36789******9677889*************998766..789999987...4444555 PP

>> DUF5343  Family of unknown function (DUF5343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.7e-06     0.051      22     113 ..     118     213 ..     104     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-06
                           DUF5343  22 PekvtqdflktlglkssnasliiplLkflGfldedGkptelykelrnedtskkalaeaikeaYs....dlFelneda 94 
                                       +++ ++d++  l++ + ++  ++++++ lG++    +  ++ + + +e t+ + + + + + Y+    +l+e+  +a
  gi|557693482|ref|YP_008796536.1| 118 SSSPSKDVMYALEIRGESDGKALEAMRELGLIHVVDISRQEPSYYHDEITYSRLFGKGVHNIYQfdddELLEISRKA 194
                                       5667899********************************************************666669******** PP

                           DUF5343  95 qnldkeelknlfrtvtgks 113
                                          +++ ++  f tv+  +
  gi|557693482|ref|YP_008796536.1| 195 EASPSKRVMLSFHTVKMYE 213
                                       *******999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 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:                        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 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2514.17
//
Query:       gi|557693483|ref|YP_008796537.1|  [L=388]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-59  201.6   0.0    2.4e-59  201.1   0.0    1.2  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 !  201.1   0.0   1.4e-63   2.4e-59       7     217 ..      27     245 ..      24     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: 201.1 bits;  conditional E-value: 1.4e-63
                                       CCC.HHHHHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS...G.-.SCHHHHHHHHHH.CH CS
                             DUF72   7 kke.rLeyYarhfntVEinstFYalpspetvakwaaqtpedFrFavKapraither..n.e.daeealerflesale 78 
                                       k+e +L+ Y++ f+tVEi+stFY+ p ++tva + +++pe+F+F+ K+p ++th+   + +  a ea+erf + +++
  gi|557693483|ref|YP_008796537.1|  27 KSEpKLRRYSNLFETVEIDSTFYSYPGERTVAGMMRAVPESFQFTAKVPGEVTHRLglDvDkGALEAMERFTK-LMR 102
                                       44559*************************************************84442333699********.5** PP

                                       HH..CT-EEEEEEE--TT--S.HHHHHHHHHHTTTS-..S.EEEE--BGGGH..HHHHHHHHTT-EEEE.E--SSC- CS
                             DUF72  79 pL..geklgpllfQlppsfkfdeenlerLeaflaalp..l.lavEvRhrswf..ellellrehgvavvl.depkkpk 147
                                       p+  ++ lg+ll+Qlpps+k+++   e Le+fl+ +     +avE+Rh+sw   e++ llr++++a+++ d   +p 
  gi|557693483|ref|YP_008796537.1| 103 PMlvKGMLGCLLLQLPPSMKYSP---ELLEKFLESVDrgFrYAVEFRHPSWIrkETFTLLRRLEAAYTIvD---EPL 173
                                       *9899**************9999...9*****998888845**********9955***********55549...679 PP

                                       -------SSTEEEEEE--S.H.HTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCHHHHHHHHHHH CS
                             DUF72 148 lpledvttadfvyvRlhgr.e.eryayrYseeelaewaerikawaaegrevyvffnndaegqaplnaraLae 217
                                       lp+  ++t+df+yvR+hgr +  +y+y+Y+e+el+ w++++++++ + r+vy +fnn+++g+a++n+ +  e
  gi|557693483|ref|YP_008796537.1| 174 LPPVVEVTTDFAYVRWHGRgKnPWYNYHYNEAELRGWVDKLQSIKGSVRRVYGYFNNHFHGYAVHNCIQVLE 245
                                       99999999***********9458*******************************************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3225.98
//
Query:       gi|557693484|ref|YP_008796538.1|  [L=162]
Description: hypothetical protein CSUB_C0043 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   10.9   1.2        8.4    6.3   0.0    2.8  3  DUF433    Protein of unknown function (DUF433)


Domain annotation for each model (and alignments):
>> DUF433  Protein of unknown function (DUF433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1    0.0093   1.7e+02      18      37 ..      12      31 ..       9      37 .. 0.91
   2 ?    6.3   0.0   0.00047       8.4      11      30 ..      39      58 ..      33      67 .. 0.88
   3 ?   -0.9   0.0     0.088   1.6e+03       3      20 ..     132     149 ..     131     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.0093
                                      --BTHHHHHHHHTT--HHHH CS
                            DUF433 18 RipVetilellaaGesieei 37
                                      Ri+V +++   ++  s+ ei
  gi|557693484|ref|YP_008796538.1| 12 RIRVGDVVYKEEEETSVTEI 31
                                      9*********9999999998 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00047
                                      S-EETTT--BTHHHHHHHHT CS
                            DUF433 11 kPvIrgtRipVetilellaa 30
                                      +PvI++ R++ et+l+ l++
  gi|557693484|ref|YP_008796538.1| 39 EPVIADVRLSTETLLSTLRM 58
                                      7**************99985 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.088
                                       E-TTSGGGS-EETTT--B CS
                            DUF433   3 idpeilgGkPvIrgtRip 20 
                                       +dp+  + kP+I + Ri+
  gi|557693484|ref|YP_008796538.1| 132 KDPQKNSPKPIIIEGRIR 149
                                       688888889999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1286.01
//
Query:       gi|557693485|ref|YP_008796539.1|  [L=834]
Description: hypothetical protein CSUB_C0044 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   84.9  21.9    0.00012   22.3   0.7    8.4  8  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    2.6e-09   36.9   1.1       0.72    9.9   0.0    7.2  7  CarbopepD_reg_2  CarboxypepD_reg-like domain
    5.7e-09   35.8   0.1       0.72    9.8   0.0    5.3  5  Y_Y_Y            Y_Y_Y domain
    2.2e-05   24.4   0.3         14    5.8   0.3    5.8  4  Big_1            Bacterial Ig-like domain (group 1)
     0.0005   20.2   0.2        5.8    7.0   0.0    4.1  3  DUF2012          Protein of unknown function (DUF2012)
     0.0012   19.3   0.5        9.1    6.6   0.0    4.2  4  DUF4198          Domain of unknown function (DUF4198)
     0.0022   18.3   5.2         83    3.6   0.0    6.4  7  SpaA             Prealbumin-like fold domain
  ------ inclusion threshold ------
       0.04   13.9   0.4        1.8    8.7   0.0    3.5  3  BiPBP_C          Penicillin-Binding Protein C-terminus Family
      0.099   13.4   0.1        6.8    7.5   0.0    3.4  3  DUF4397          Domain of unknown function (DUF4397)
       0.58   10.4   6.2    1.3e+02    2.8   0.0    5.6  7  SdrD_B           SdrD B-like domain


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 !   22.3   0.7   6.6e-08   0.00012       1      59 [.      31      87 ..      31     101 .. 0.80
   2 !   10.1   0.0   0.00043      0.77       5      57 ..     238     293 ..     234     313 .. 0.81
   3 !    8.2   0.0    0.0016       2.9      37      69 ..     353     384 ..     349     392 .. 0.80
   4 ?    1.6   0.1      0.18   3.3e+02      42      65 ..     441     462 ..     440     506 .. 0.69
   5 !   11.0   0.0   0.00022      0.39      33      64 ..     512     543 ..     481     559 .. 0.72
   6 !    5.8   0.0    0.0091        16       5      58 ..     565     615 ..     561     635 .. 0.75
   7 !   19.0   0.2   6.8e-07    0.0012       8      64 ..     644     695 ..     642     709 .. 0.82
   8 !   15.1   0.4   1.1e-05      0.02       2      76 ..     712     780 ..     711     788 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6.6e-08
                   CarboxypepD_reg  1 tisGrVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglpp.gtysvtvsapGy 59
                                      t+  rVtd  +gapi ga+V +   + + +++ +t+++G+ ++++ +   ty vt+s   y
  gi|557693485|ref|YP_008796539.1| 31 TVYVRVTDCiTGAPIQGASVNLD--NPTHRTGGVTNSTGYASIEAFAWfYTYYVTASG--Y 87
                                      57789***77*************..47788999**********977667777777754..4 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00043
                   CarboxypepD_reg   5 rVtda.sgapiagatVtvtnadtgt..vastttdadGafrlrglppgtysvtvsap 57 
                                       +V d+   +p++ga V++  +  ++  + + + d++G+  ++ +  g y  ++++ 
  gi|557693485|ref|YP_008796539.1| 238 QVLDKwGQNPVPGAVVEFIPTLPNVegSFTYRADENGYIDVKRVNDGAYLTRITYL 293
                                       799997889********997655542278889*****************9999875 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0016
                   CarboxypepD_reg  37 dGafrlrglppgtysvtvsapGyatatreevtl 69 
                                       dG  r+ ++ppg+ysv v+    + +t+ ++++
  gi|557693485|ref|YP_008796539.1| 353 DGLARFVNVPPGEYSVSVRWMDVEVYTS-QIRV 384
                                       7999**************9877777774.4555 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.18
                   CarboxypepD_reg  42 lrglppgtysvtvsapGyatatre 65 
                                       ++ lp g+y v+v+a  y+ ++ +
  gi|557693485|ref|YP_008796539.1| 441 FERLPRGEYVVKVQA--YDAYRER 462
                                       678999*******55..3333332 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.00022
                   CarboxypepD_reg  33 ttdadGafrlrglppgtysvtvsapGyatatr 64 
                                       ++ + G+ +l++l+pg+y  ++s +Gy    +
  gi|557693485|ref|YP_008796539.1| 512 VSLRGGKATLTNLTPGPYLFKASWNGYTVLDI 543
                                       67789**********************87665 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.0091
                   CarboxypepD_reg   5 rVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapG 58 
                                       rV   +g+p+  a+  +    +g++++ +t  +G+  ++++p+g +++t+  + 
  gi|557693485|ref|YP_008796539.1| 565 RVLGVDGRPLMKASALLW---QGQSSEQQTVVNGSAVFDQVPAGAHQLTIFLDD 615
                                       677778888888888777...588888889999****************95444 PP

  == domain 7  score: 19.0 bits;  conditional E-value: 6.8e-07
                   CarboxypepD_reg   8 dasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatr 64 
                                       d++gapi+g+++++t    g     +t+adG  rl++ p g+y  t+++ G+  ++ 
  gi|557693485|ref|YP_008796539.1| 644 DQNGAPISGVEIVAT----G-FDVQKTGADGVARLSQKPLGSYGFTARYRGFTVFEG 695
                                       89*************....4.44458**********9999************88774 PP

  == domain 8  score: 15.1 bits;  conditional E-value: 1.1e-05
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqttt 76 
                                       ++ +V+++ ++pi+ a++t+t  +++++ +t t+++  + l  lppg+y +++s    + + +    l++gq   
  gi|557693485|ref|YP_008796539.1| 712 LKATVVNELDTPIE-ASITLT--RGDVSLGTFTGSEAFYHL--LPPGPYVLKASVGTKQAVQQ-VNLLSDGQVYV 780
                                       67799999999998.9*****..7999*************8..9*********7766665554.45556666554 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 !    9.9   0.0    0.0004      0.72       5      56 ..      36      88 ..      35     107 .. 0.80
   2 ?    5.0   0.0     0.013        24       4      54 ..     238     294 ..     238     315 .. 0.77
   3 ?    0.7   0.0      0.29   5.2e+02      39      69 ..     359     389 ..     353     393 .. 0.86
   4 ?    1.4   0.0      0.18   3.2e+02      34      71 ..     517     554 ..     512     563 .. 0.79
   5 ?    0.0   0.0      0.49   8.8e+02      12      50 ..     572     611 ..     565     631 .. 0.83
   6 ?    4.4   0.1     0.021        38       8      66 ..     644     701 ..     642     722 .. 0.77
   7 ?    4.4   0.0     0.022        39      18      66 ..     727     774 ..     712     787 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0004
                   CarbopepD_reg_2  5 VvdketkeplpgatVyvkgtk..kgtvTdenGnFelknlpagkytLvvsyvGyk 56
                                      V+d  t+ p+ ga+V + + +  +g vT++ G+ ++++  a  yt  v++ Gy+
  gi|557693485|ref|YP_008796539.1| 36 VTDCITGAPIQGASVNLDNPThrTGGVTNSTGYASIEAF-AWFYTYYVTASGYR 88
                                      899999***********886434999******9999755.45567677777775 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.013
                   CarbopepD_reg_2   4 tVvdketkeplpgatVyvkgt......kkgtvTdenGnFelknlpagkytLvvsyvG 54 
                                       +V+dk +++p+pga V +  t      ++   +denG+  +k++++g y  +++y++
  gi|557693485|ref|YP_008796539.1| 238 QVLDKWGQNPVPGAVVEFIPTlpnvegSFTYRADENGYIDVKRVNDGAYLTRITYLS 294
                                       6999999*******9988776333222344458************999988888875 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.29
                   CarbopepD_reg_2  39 knlpagkytLvvsyvGyktqekkvtvskekt 69 
                                        n+p+g+y + v+ +  +  + ++ v++   
  gi|557693485|ref|YP_008796539.1| 359 VNVPPGEYSVSVRWMDVEVYTSQIRVEEPLV 389
                                       589*****************99999987655 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.18
                   CarbopepD_reg_2  34 GnFelknlpagkytLvvsyvGyktqekkvtvskektld 71 
                                       G+ +l+nl++g y +++s  Gy+   +  +   ++tl+
  gi|557693485|ref|YP_008796539.1| 517 GKATLTNLTPGPYLFKASWNGYTVLDIMAEPRPGETLT 554
                                       56689*****************9877766666665555 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 0.49
                   CarbopepD_reg_2  12 eplpga.tVyvkgtkkgtvTdenGnFelknlpagkytLvv 50 
                                       +pl  a   +++g++   +T  nG+  ++++pag ++L++
  gi|557693485|ref|YP_008796539.1| 572 RPLMKAsALLWQGQSSEQQTVVNGSAVFDQVPAGAHQLTI 611
                                       5666662456699999999999**************9987 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.021
                   CarbopepD_reg_2   8 ketkeplpgatVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvsk 66 
                                       ++++ p+ g+ ++ +g  +   T ++G  +l+++p g y ++++y G++  e   +  +
  gi|557693485|ref|YP_008796539.1| 644 DQNGAPISGVEIVATGFDV-QKTGADGVARLSQKPLGSYGFTARYRGFTVFEGVAKAGN 701
                                       5678999999998877655.4699************************98776655544 PP

  == domain 7  score: 4.4 bits;  conditional E-value: 0.022
                   CarbopepD_reg_2  18 tVyvkg..tkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvsk 66 
                                       +++++    + gt T ++  ++l  lp+g y L++s vG k++ ++v++ +
  gi|557693485|ref|YP_008796539.1| 727 SITLTRgdVSLGTFTGSEAFYHL--LPPGPYVLKAS-VGTKQAVQQVNLLS 774
                                       444433114799***********..8*******998.67787788888644 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0     0.002       3.5      30      49 ..     355     374 ..     344     384 .. 0.86
   2 !    9.8   0.0    0.0004      0.72      32      52 ..     440     460 ..     432     468 .. 0.86
   3 ?    4.6   0.0     0.018        32      29      45 ..     513     533 ..     500     535 .. 0.75
   4 ?   -1.3   0.0       1.2   2.1e+03      23      48 ..     664     688 ..     660     689 .. 0.79
   5 !    5.9   0.0     0.007        13      27      47 ..     742     761 ..     733     768 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.002
                                       EEEEES--SEEEEEEEEEEE CS
                             Y_Y_Y  30 easytnlppGdYtlkVkakd 49 
                                        a + n ppG+Y + V+ +d
  gi|557693485|ref|YP_008796539.1| 355 LARFVNVPPGEYSVSVRWMD 374
                                       689*************9887 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0004
                                       EEES--SEEEEEEEEEEETTS CS
                             Y_Y_Y  32 sytnlppGdYtlkVkakdndg 52 
                                        +  lp G+Y++kV+a d + 
  gi|557693485|ref|YP_008796539.1| 440 VFERLPRGEYVVKVQAYDAYR 460
                                       5889**************886 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.018
                                       .....EEEEES--SEEEEEEE CS
                             Y_Y_Y  29 q....easytnlppGdYtlkV 45 
                                       +    +a+ tnl pG Y +k+
  gi|557693485|ref|YP_008796539.1| 513 SlrggKATLTNLTPGPYLFKA 533
                                       34445899***********96 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.2
                                       EESSTS.EEEEES--SEEEEEEEEEE CS
                             Y_Y_Y  23 easdysqeasytnlppGdYtlkVkak 48 
                                       ++++ +  a  + +p G+Y ++++++
  gi|557693485|ref|YP_008796539.1| 664 KTGADG-VARLSQKPLGSYGFTARYR 688
                                       566666.7888999*******99875 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.007
                                       TS.EEEEES--SEEEEEEEEE CS
                             Y_Y_Y  27 ysqeasytnlppGdYtlkVka 47 
                                        s ea y  lppG Y+lk+++
  gi|557693485|ref|YP_008796539.1| 742 GS-EAFYHLLPPGPYVLKASV 761
                                       34.99************9876 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 !    5.8   0.3    0.0077        14       8      51 ..      31      72 ..      26      74 .. 0.79
   2 ?    1.9   0.0      0.13   2.3e+02      22      63 ..     108     150 ..     106     150 .. 0.82
   3 ?    4.7   0.0     0.017        31      18      51 ..     245     279 ..     235     291 .. 0.80
   4 ?    3.6   0.0     0.037        66      13      29 ..     642     658 ..     638     674 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0077
                             Big_1  8 tltatvkD.angnpvagatVtfsvsggalsassgtTdanGkatvt 51
                                      t+ ++v+D   g p++ga+V++  +      + g+T++ G a+++
  gi|557693485|ref|YP_008796539.1| 31 TVYVRVTDcITGAPIQGASVNLDNPT---HRTGGVTNSTGYASIE 72
                                      56677777568999999999998554...56689*******9986 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.13
                             Big_1  22 agatVtfsvsggals.assgtTdanGkatvtltstkagtvtvt 63 
                                       + a+  ++v +++l+ ++    +  G a + l++ +ag +++t
  gi|557693485|ref|YP_008796539.1| 108 PEAAGFWRVVADVLAwQGDIHAGGRGWAIIRLKNLEAGVFNIT 150
                                       5566667777777777888888899***************998 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.017
                             Big_1  18 gnpvagatVtfsvsggals.assgtTdanGkatvt 51 
                                        npv+ga V f  +  ++  + + + d+nG + v+
  gi|557693485|ref|YP_008796539.1| 245 QNPVPGAVVEFIPTLPNVEgSFTYRADENGYIDVK 279
                                       59*********999955555999999999987765 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.037
                             Big_1  13 vkDangnpvagatVtfs 29 
                                         D+ng p++g+++  +
  gi|557693485|ref|YP_008796539.1| 642 FHDQNGAPISGVEIVAT 658
                                       579********999755 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0032       5.8       7      64 ..     337     388 ..     331     424 .. 0.79
   2 ?    2.8   0.1     0.067   1.2e+02      33      66 ..     440     478 ..     434     513 .. 0.67
   3 ?    4.9   0.0     0.015        27      12      47 ..     579     612 ..     570     641 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0032
                           DUF2012   7 lantrvlLdsgqqrkfkalvrrDGsFifrdlpegsYlLevespeyvFepyrVdvkdkg 64 
                                       + +t v+L++           +DG   f ++p+g+Y + v+  +++  + +++v ++ 
  gi|557693485|ref|YP_008796539.1| 337 PLETDVYLNGVRA------FSVDGLARFVNVPPGEYSVSVRWMDVEVYTSQIRVEEPL 388
                                       5566666644433......77899999******************9999999998654 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.067
                           DUF2012  33 ifrdlpegsYlLevespeyvFepyrVdvk......dkgka 66 
                                       +f+ lp g+Y+++v++ + ++ +  Vdv       + + +
  gi|557693485|ref|YP_008796539.1| 440 VFERLPRGEYVVKVQAYD-AYRERYVDVGeqyfaiPRDHG 478
                                       6999*********99876.688888999855555433444 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.015
                           DUF2012  12 vlLdsgqqrkfkalvrrDGsFifrdlpegsYlLeve 47 
                                       +lL +gq+   +  + ++Gs +f ++p+g+++L + 
  gi|557693485|ref|YP_008796539.1| 579 ALLWQGQSS--EQQTVVNGSAVFDQVPAGAHQLTIF 612
                                       556555553..444556788999**********985 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0051       9.1     152     210 ..     234     291 ..     215     294 .. 0.83
   2 ?    2.1   0.0      0.12   2.1e+02     167     211 ..     489     535 ..     483     537 .. 0.73
   3 ?   -3.2   0.0       4.9   8.9e+03     153     175 ..     562     585 ..     561     600 .. 0.71
   4 ?    5.5   0.1     0.011        20     185     212 ..     660     688 ..     617     689 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0051
                           DUF4198 152 elevqvl.ldGk.PlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwlleae 210
                                       ++++qvl   G+ P++ga ve+++      + ++ + +++d++G++ ++  + G +l + +
  gi|557693485|ref|YP_008796539.1| 234 SFRIQVLdKWGQnPVPGAVVEFIPT---LPNVEGSFTYRADENGYIDVKRVNDGAYLTRIT 291
                                       6888888755666***********5...7888888888****************9997665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                           DUF4198 167 aeveveyggtryrdapdeikv..ktdadGvvtftlpkaGlwlleaeh 211
                                       a vev+ ++ r+ da+ +i+    +   G++t+t   +G +l++a++
  gi|557693485|ref|YP_008796539.1| 489 AAVEVVDKEGRRIDAELTIEGkpVSLRGGKATLTNLTPGPYLFKASW 535
                                       6677666665555555444447778888***************9986 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.9
                           DUF4198 153 levqvl.ldGkPlagaeveveygg 175
                                       ++++vl +dG+Pl  a+  ++ g+
  gi|557693485|ref|YP_008796539.1| 562 MRLRVLgVDGRPLMKASALLWQGQ 585
                                       678888899999988877766543 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.011
                           DUF4198 185 ikv.ktdadGvvtftlpkaGlwlleaehe 212
                                       + v kt+adGv+ +  +  G ++++a+++
  gi|557693485|ref|YP_008796539.1| 660 FDVqKTGADGVARLSQKPLGSYGFTARYR 688
                                       33469*********************997 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.12   2.2e+02      33      59 ..      56      83 ..      31     100 .. 0.73
   2 ?    3.6   0.0     0.046        83      34      57 ..     264     287 ..     235     289 .. 0.80
   3 ?    0.3   0.0      0.49   8.8e+02      43      58 ..     353     368 ..     339     369 .. 0.89
   4 ?   -1.0   0.0       1.3   2.3e+03      47      59 ..     440     452 ..     437     477 .. 0.83
   5 ?    3.0   0.0     0.073   1.3e+02      39      59 ..     512     532 ..     478     539 .. 0.82
   6 ?   -2.6   0.0       4.1   7.4e+03      38      56 ..     589     607 ..     581     613 .. 0.79
   7 ?    3.2   0.0     0.062   1.1e+02      33      57 ..     658     682 ..     618     708 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.12
                                      CEESEEE-BTTSEEEEEEEESE.EEEEE CS
                              SpaA 33 tevttlttdenGkatfegLplG.tYllv 59
                                      t  t  +t+++G+a++e+ ++  tY+++
  gi|557693485|ref|YP_008796539.1| 56 THRTGGVTNSTGYASIEAFAWFyTYYVT 83
                                      4456779***********9996699986 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.046
                                       EESEEE-BTTSEEEEEEEESEEEE CS
                              SpaA  34 evttlttdenGkatfegLplGtYl 57 
                                        + t+  denG++ ++ ++ G Yl
  gi|557693485|ref|YP_008796539.1| 264 GSFTYRADENGYIDVKRVNDGAYL 287
                                       4456668****************7 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.49
                                       TSEEEEEEEESEEEEE CS
                              SpaA  43 nGkatfegLplGtYll 58 
                                       +G a+f ++p+G+Y +
  gi|557693485|ref|YP_008796539.1| 353 DGLARFVNVPPGEYSV 368
                                       899***********76 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.3
                                       EEEEEESEEEEEE CS
                              SpaA  47 tfegLplGtYllv 59 
                                        fe Lp G+Y+++
  gi|557693485|ref|YP_008796539.1| 440 VFERLPRGEYVVK 452
                                       6899******997 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.073
                                       E-BTTSEEEEEEEESEEEEEE CS
                              SpaA  39 ttdenGkatfegLplGtYllv 59 
                                       ++   Gkat ++L +G Yl++
  gi|557693485|ref|YP_008796539.1| 512 VSLRGGKATLTNLTPGPYLFK 532
                                       55567*************986 PP

  == domain 6  score: -2.6 bits;  conditional E-value: 4.1
                                       EE-BTTSEEEEEEEESEEE CS
                              SpaA  38 lttdenGkatfegLplGtY 56 
                                         t  nG a f+ +p+G  
  gi|557693485|ref|YP_008796539.1| 589 QQTVVNGSAVFDQVPAGAH 607
                                       557779*******999975 PP

  == domain 7  score: 3.2 bits;  conditional E-value: 0.062
                                       CEESEEE-BTTSEEEEEEEESEEEE CS
                              SpaA  33 tevttlttdenGkatfegLplGtYl 57 
                                       t  +  +t+++G a+ +  plG+Y 
  gi|557693485|ref|YP_008796539.1| 658 TGFDVQKTGADGVARLSQKPLGSYG 682
                                       4447889****************95 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 ?    0.8   0.1      0.29   5.2e+02      73      86 ..     489     502 ..     451     507 .. 0.70
   2 ?   -2.4   0.0       2.7   4.9e+03      35      55 ..     553     574 ..     544     593 .. 0.54
   3 ?    8.7   0.0   0.00098       1.8      42      88 ..     604     654 ..     578     655 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.29
                           BiPBP_C  73 hrLtvvDaaGrvdd 86 
                                       + ++vvD++Gr+ d
  gi|557693485|ref|YP_008796539.1| 489 AAVEVVDKEGRRID 502
                                       45677999998876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.7
                           BiPBP_C  35 lqlkarggeaplrWl.ldgepl 55 
                                       l+l+a+  + +lr l +dg+pl
  gi|557693485|ref|YP_008796539.1| 553 LTLSAEIYKMRLRVLgVDGRPL 574
                                       3333333322222221366666 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00098
                           BiPBP_C  42 g.eaplrWlldgepl..aetkrgrelawqpepGrhrLtvvDaaGrvdd.vr 88 
                                       + + +l+++ld++ +  +++k+++e+++  e G ++L  +D++G+  + v+
  gi|557693485|ref|YP_008796539.1| 604 AgAHQLTIFLDDVAVfnGTVKASEEVSVAAEAGWVELFFHDQNGAPISgVE 654
                                       32459********99999**************************8776665 PP

>> DUF4397  Domain of unknown function (DUF4397)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0038       6.8      15      48 ..     340     370 ..     335     393 .. 0.81
   2 ?   -1.5   0.0       2.3   4.2e+03      40      51 ..     476     487 ..     440     507 .. 0.74
   3 ?    1.1   0.0      0.35   6.4e+02      37      77 ..     600     630 ..     587     658 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0038
                           DUF4397  15 vDvyvngkkvlknvaygdvtgylqvpaGqytiel 48 
                                        Dvy+ng   +++++ + +  +++vp+G+y++++
  gi|557693485|ref|YP_008796539.1| 340 TDVYLNG---VRAFSVDGLARFVNVPPGEYSVSV 370
                                       6999995...5669*******************9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.3
                           DUF4397  40 paGqytielnpa 51 
                                       + Gq+ti++  +
  gi|557693485|ref|YP_008796539.1| 476 DHGQHTIRVKVF 487
                                       567888888333 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.35
                           DUF4397  37 lqvpaGqytielnpagnkikagttvallnvditleagteyt 77 
                                        qvpaG+++++++  +        va+ n   t++a +e++
  gi|557693485|ref|YP_008796539.1| 600 DQVPAGAHQLTIFLDD--------VAVFNG--TVKASEEVS 630
                                       5899999999992222........222222..333333333 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.6   2.9e+03      23      49 ..      44      68 ..      40      85 .. 0.73
   2 ?    1.0   0.0      0.26   4.7e+02      20      68 ..     244     294 ..     240     308 .. 0.76
   3 ?    2.1   0.0      0.12   2.2e+02      47      68 ..     353     374 ..     341     388 .. 0.80
   4 ?    2.8   0.0     0.074   1.3e+02      51      79 ..     440     468 ..     402     479 .. 0.82
   5 ?    0.8   0.0       0.3   5.4e+02      12      58 ..     495     537 ..     485     554 .. 0.67
   6 ?   -2.4   0.0         3   5.4e+03      42      71 ..     589     618 ..     583     630 .. 0.72
   7 ?   -2.2   0.0       2.6   4.6e+03      18      54 ..     644     685 ..     642     694 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.6
                            SdrD_B 23 gisgvtVtLkdakgevvatttTdasGk 49
                                       i+g  V+L + +  +    +T+++G+
  gi|557693485|ref|YP_008796539.1| 44 PIQGASVNLDNPTHRT--GGVTNSTGY 68
                                      79999***95555544..467888776 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.26
                            SdrD_B  20 gekgisgvtVtLkdakgevv..atttTdasGkYkFtnltpGeYkVeftapa 68 
                                       g++ + g  V+ + +  +v    t   d++G+   + +++G Y  ++t+ +
  gi|557693485|ref|YP_008796539.1| 244 GQNPVPGAVVEFIPTLPNVEgsFTYRADENGYIDVKRVNDGAYLTRITYLS 294
                                       5677888888886665555532478899***************98887644 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.12
                            SdrD_B  47 sGkYkFtnltpGeYkVeftapa 68 
                                       +G  +F n+ pGeY+V++   +
  gi|557693485|ref|YP_008796539.1| 353 DGLARFVNVPPGEYSVSVRWMD 374
                                       67789***********996644 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.074
                            SdrD_B  51 kFtnltpGeYkVeftapagytvtakkaGs 79 
                                        F+ l  GeY V+++a + y   + + G+
  gi|557693485|ref|YP_008796539.1| 440 VFERLPRGEYVVKVQAYDAYRERYVDVGE 468
                                       69************999888877777665 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.3
                            SdrD_B  12 nknGiqdagekgisgvtVtLkdakgevvatttTd.asGkYkFtnltpG 58 
                                       +k+G   + e +i+g  V+L  + g++   t+T+ + G Y F+   +G
  gi|557693485|ref|YP_008796539.1| 495 DKEGRRIDAELTIEGKPVSL--RGGKA---TLTNlTPGPYLFKASWNG 537
                                       66777777778888888888..33333...334424588888876666 PP

  == domain 6  score: -2.4 bits;  conditional E-value: 3
                            SdrD_B  42 ttTdasGkYkFtnltpGeYkVeftapagyt 71 
                                       + T  +G+  F+++ +G  ++++   +  +
  gi|557693485|ref|YP_008796539.1| 589 QQTVVNGSAVFDQVPAGAHQLTIFLDDVAV 618
                                       567789999999999999998876655544 PP

  == domain 7  score: -2.2 bits;  conditional E-value: 2.6
                            SdrD_B  18 dagekgisgvtVtL....kdakgevv.atttTdasGkYkFtn 54 
                                       d++ + isgv++       +++g    a+   +  G+Y Ft 
  gi|557693485|ref|YP_008796539.1| 644 DQNGAPISGVEIVAtgfdVQKTGADGvARLSQKPLGSYGFTA 685
                                       777788888888764544333333221344444557887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (834 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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):              10  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 5557.35
//
Query:       gi|557693486|ref|YP_008796540.1|  [L=104]
Description: hypothetical protein CSUB_C0045 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 705.95
//
Query:       gi|557693487|ref|YP_008796541.1|  [L=403]
Description: threonine synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-72  242.2   2.7    8.8e-72  242.0   2.7    1.1  1  PALP           Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.077   13.0   0.1       0.15   12.1   0.1    1.5  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.16   11.9   0.1        4.1    7.4   0.0    2.7  2  Rpp20          Rpp20 subunit of nuclear RNase MRP and P
       0.19   11.9   1.1         34    4.7   0.0    3.3  3  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


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 !  242.0   2.7     2e-75   8.8e-72       2     294 .]      72     374 ..      71     374 .. 0.94

  Alignments for each domain:
  == domain 1  score: 242.0 bits;  conditional E-value: 2e-75
                                       GGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaall 77 
                                       +l +g+TPl ++ + ++  gv+ l++K E++nptgSfKdRg++ +++++ e  g+++vv+as+GN+  ++Aa+aa++
  gi|557693487|ref|YP_008796541.1|  72 SLREGGTPLYEASAAARWAGVKkLYVKFEGMNPTGSFKDRGMSVAVSKAVEL-GKRVVVCASTGNTSSSMAAYAAAA 147
                                       6789************************************************.************************ PP

                                       T-EEEEEEETTS-.HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHH CS
                              PALP  78 Glkvtivvpadas.pekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileq 153
                                       Glk+++vvp++   ++k+ ++ l+Ga+ v++++++d a++++  +a    +ayl+++  np++ieg++t+++E++++
  gi|557693487|ref|YP_008796541.1| 148 GLKAVVVVPKTGIaAGKIFQTILHGAQTVQIPEGFDKALSTVISAALG-SEAYLLNSV-NPWRIEGQKTLAYELWSD 222
                                       **********99956**************************8888887.9********.9***************** PP

                                       TTTTEEEEEEE-SSSHHHHHHHHHHHH......HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CCS CS
                              PALP 154 lggkpdavvvpvGgGgliaGiaaglke......rrpd..vrvigvepegsdalarslragrrvtvpvs..dtiadgl 220
                                       lg+ p ++ vpvG+ g+i++i++g++e         +  +r+i+v++eg++++ + +r+g+    pv+  +tia+++
  gi|557693487|ref|YP_008796541.1| 223 LGDTPFHLSVPVGNCGNISAIWKGFRElqrlelV--NtpPRLIAVQAEGASPFVDMVRRGDNMLRPVEkpSTIASAI 297
                                       ***************************8766543..156******************9888754444445******* PP

                                       TCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 221 avg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                       ++g  ++ ++a+++++++ + +  vsd+ +lea+r la++ gi vep+saa+la++ kl+e gel+++++vv++ tg
  gi|557693487|ref|YP_008796541.1| 298 RIGrpVNWTKALKAMKESEGLAEKVSDQLILEAQRVLASAVGIGVEPASAASLAGVkKLVESGELDRSETVVCVATG 374
                                       ***88888999***************************************************************998 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 ?   12.1   0.1   3.4e-05      0.15      68      96 ..       3      31 ..       1      41 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.4e-05
                                      --EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA 68 pvkvrCreCgkefeleekalrCpkCgsad 96
                                      p  +rC +Cg+e++ +e  ++C kCgs  
  gi|557693487|ref|YP_008796541.1|  3 PPYLRCISCGAEWSGDEIIYTCAKCGSLL 31
                                      6789**********8865689*****964 PP

>> Rpp20  Rpp20 subunit of nuclear RNase MRP and P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.22   9.7e+02      68      82 ..     112     126 ..     109     141 .. 0.86
   2 ?    7.4   0.0   0.00092       4.1      12      73 ..     271     377 ..     260     379 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.22
                             Rpp20  68 atGrAiekalsvgrw 82 
                                       ++  A+ ka+++g+ 
  gi|557693487|ref|YP_008796541.1| 112 GMSVAVSKAVELGKR 126
                                       8899********986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00092
                             Rpp20  12 tpfmsavkRvqklLeqaekrataslal.............................................eqkkk 43 
                                       +pf+ +v+R + +L+ +ek +t   a                                              e  ++
  gi|557693487|ref|YP_008796541.1| 271 SPFVDMVRRGDNMLRPVEKPSTIASAIrigrpvnwtkalkamkeseglaekvsdqlileaqrvlasavgigvEPASA 347
                                       78888888888888888888655444468888888887777777777777777777777777777777777777777 PP

                             Rpp20  44 eekkklealekkeeelkkeeVfvkatGrAi 73 
                                       ++    ++l ++ e +++e V+  atG+A 
  gi|557693487|ref|YP_008796541.1| 348 ASLAGVKKLVESGELDRSETVVCVATGHAL 377
                                       778888888888888888888888888886 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 ?    0.9   0.1      0.12   5.3e+02      37      56 ..     125     144 ..     114     165 .. 0.79
   2 ?    3.7   0.1     0.016        71      57      86 ..     318     347 ..     316     350 .. 0.89
   3 ?    4.7   0.0    0.0077        34      50      79 ..     346     375 ..     345     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.12
                                       GB--THHHH-B-GGGHHHHH CS
                     ACP_syn_III_C  37 kvvvnldeyGntsaasipla 56 
                                       k vv  + +Gnts++   +a
  gi|557693487|ref|YP_008796541.1| 125 KRVVVCASTGNTSSSMAAYA 144
                                       55677899999999866665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.016
                                       HHHHHHTTSS-TT-EEEEEEEETTTEEEEE CS
                     ACP_syn_III_C  57 LdeaveegklkpgdlvllvgfGaGltwgaa 86 
                                       L+e v+++ + + ++vl +++G G+  ++a
  gi|557693487|ref|YP_008796541.1| 318 LAEKVSDQLILEAQRVLASAVGIGVEPASA 347
                                       788999999***************987776 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0077
                                       GGHHHHHHHHHHHTTSS-TT-EEEEEEEET CS
                     ACP_syn_III_C  50 aasiplaLdeaveegklkpgdlvllvgfGa 79 
                                       +a ++   +++ve+g+l++ ++v+ v++G 
  gi|557693487|ref|YP_008796541.1| 346 SAASLAGVKKLVESGELDRSETVVCVATGH 375
                                       677788999******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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: 2625.65
//
Query:       gi|557693488|ref|YP_008796542.1|  [L=962]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-154  513.1   0.0   7.2e-154  512.9   0.0    1.0  1  RtcB             tRNA-splicing ligase RtcB
    3.8e-15   56.0   0.0    6.8e-15   55.2   0.0    1.4  1  Intein_splicing  Intein splicing domain
    2.9e-07   30.7   0.4      0.015   15.6   0.0    3.0  2  LAGLIDADG_3      LAGLIDADG-like domain


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 !  512.9   0.0  1.2e-157  7.2e-154       1     412 []      50     962 .]      50     962 .] 0.99

  Alignments for each domain:
  == domain 1  score: 512.9 bits;  conditional E-value: 1.2e-157
                                       HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.......................... RF
                              RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.......................... 48 
                                       q+ nv++lpgivk+++++PD+H G+g+piG+V+a++   gvi+P++VG+DI                          
  gi|557693488|ref|YP_008796542.1|  50 QAVNVSTLPGIVKQMTVLPDAHEGYGFPIGGVAAMDateGVISPGGVGYDInclpagtnvltslgyrlpierfkane 126
                                       899************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|557693488|ref|YP_008796542.1| 127 evvcvnqkrsvpagiifvikkgrdrllrirtksqffltatpdhpvltpngmkpmeqirpgervalfpfegveyedpr 203
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|557693488|ref|YP_008796542.1| 204 dcllldekdvpehvkselkkrgllpikldnpklpylarllgyftgdgafngkttvfygsvegleeirrdierlgykp 280
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|557693488|ref|YP_008796542.1| 281 skihtrrrqniingrkfigaensvrvnsrsftellrrlgapdgkktdaeffvprwillaprwikrlylaglfgaeln 357
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|557693488|ref|YP_008796542.1| 358 kpqtvngynfqvpqltlnkrpdledngrmfleqiaellrelgvettkivsapegrcirlrlliserpqnlirlwgri 434
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              RtcB  49 ............................................................................. 48 
                                                                                                                    
  gi|557693488|ref|YP_008796542.1| 435 gyeynpqrrrlalaavvwlrlkqsvidlriraqeaaiamaadgttiseisevlanefvntrylersvyegredtprv 511
                                       ***************************************************************************** PP

                                       .........................................................-EEEEEEEEEEHHHHGGGHH CS
                                       .........................................................xxxxxxxxxxxxxxxxxxxx RF
                              RtcB  49 .........................................................CGvrllktnltaeeleeklk 68 
                                                                                                CGvrl+ tnlt +++++++ 
  gi|557693488|ref|YP_008796542.1| 512 pknfprfedwvelhldgdivwdevesveeagevndvydltvanpghsfiaegvvvsnCGVRLMVTNLTVNDVRPRIV 588
                                       ***************************************************************************** PP

                                       HHHHHHHHHS-------.------HHHHHHHHHHTHHHHHHT.TSS-GGGGGGBGGG........G--TT--GGGS- CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx........xxxxxxxxxxxx RF
                              RtcB  69 elvkelekavpvglgsk.kkvklskkeleevleegakwavee.glgeeedlekieee........galkeadlekvs 135
                                       elv++++++vp+glgs+ k   +++++l++v  ega++++e+ glg++ed++k+eee        g++ + d++ vs
  gi|557693488|ref|YP_008796542.1| 589 ELVNTVFRNVPAGLGSRrKDFVVTHSDLDRVALEGARYVIEKyGLGWSEDFKKMEEEgrypsykaGNIPDPDPSIVS 665
                                       **************9887999999***************9888**************66666666666666****** PP

                                       HHHHHHHGGGTT---STT-EEEEEEEEEES-HHHHHHHT-.-TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 136 kkakerarkqlGtlGsGNHFiEvqlveeildeeaakalgl.eegqvvvmlHsGSRglGhqiaedylkiakkalkkkg 211
                                       ++ak+r+++q+GtlGsGNHF+E+q v++i+d +aaka+g+ +egq++v++H+GSRg Ghqi++d+l+i+++a++k++
  gi|557693488|ref|YP_008796542.1| 666 REAKARGESQIGTLGSGNHFLEIQRVDKIYDPRAAKAMGItQEGQITVLIHCGSRGYGHQICSDFLRIMERAVAKYN 742
                                       ****************************************889********************************** PP

                                       ---SSGGG--EETTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 212 iklpdrdLaylpagseegqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe 288
                                       ++lpdr+La+ pa+s+e+ +Ylka  +a n+A+aNRq i ++vr+++e+v+k++++d+++++v+dv+HN+ k+E+h+
  gi|557693488|ref|YP_008796542.1| 743 LRLPDRELACTPANSPEATQYLKAFGCAVNFAFANRQAISHWVRQSFEQVFKRSADDMGMQIVYDVCHNVLKFEKHK 819
                                       ******************************************************9********************** PP

                                       .T...EEEEEEEES-EE-.............TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S--------- CS
                                       .x...xxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                              RtcB 289 .d...ekvlVhRKGAtrA.............kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRaka 346
                                        d    +v+VhRKGAtr+             ++gqpv+ipGsmgt+S+++ G+++a+  sfgSt+HGAGR msR+ a
  gi|557693488|ref|YP_008796542.1| 820 vDgsdVDVFVHRKGATRSfpaghplipqvyrEIGQPVLIPGSMGTASWVLLGNEKAMtlSFGSTAHGAGREMSRSGA 896
                                       94567************************************************************************ PP

                                       --------TTTTTCCCT-EEEE------------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 347 kkkfkleevkkdleeqgigvearkkegvleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                       k+++++++v ++le++gi+v+ +++e+v+eE+++aYK++deVve+ ++ g+ ++varl p++vvkg
  gi|557693488|ref|YP_008796542.1| 897 KRRYRGDQVLRELESRGIYVKGDSMETVVEEVDAAYKSVDEVVEVSHQVGIGTKVARLVPIGVVKG 962
                                       *****************************************************************8 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   1.1e-18   6.8e-15      19     134 .]     124     568 ..     109     568 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.1e-18
                                       CTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                   Intein_splicing  19 egeevlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdliavp.. 93 
                                        +eev+ +n  + +   + +  +ik++   l++i+++s+  + aTp+H++l+   +g+  k ++++++g+ +a+   
  gi|557693488|ref|YP_008796542.1| 124 ANEEVVCVN--QKRSVPAGIIFVIKKGRDRLLRIRTKSQFFLTATPDHPVLTP--NGM--KPMEQIRPGERVALFpf 194
                                       445555444..444555668899999999************************..9**..*************999* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|557693488|ref|YP_008796542.1| 195 egveyedprdcllldekdvpehvkselkkrgllpikldnpklpylarllgyftgdgafngkttvfygsvegleeirr 271
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|557693488|ref|YP_008796542.1| 272 dierlgykpskihtrrrqniingrkfigaensvrvnsrsftellrrlgapdgkktdaeffvprwillaprwikrlyl 348
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|557693488|ref|YP_008796542.1| 349 aglfgaelnkpqtvngynfqvpqltlnkrpdledngrmfleqiaellrelgvettkivsapegrcirlrlliserpq 425
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|557693488|ref|YP_008796542.1| 426 nlirlwgrigyeynpqrrrlalaavvwlrlkqsvidlriraqeaaiamaadgttiseisevlanefvntrylersvy 502
                                       ***************************************************************************** PP

                                       ........................HSCEEEEEEEEEEEEECEEEEEEEEETTT.-EEEECTTEEE- CS
                                       ........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                   Intein_splicing  94 ........................dadvvwdkvksievedeeeyVYdltvedn.hNFvangiivHN 134
                                                               d+d+vwd+v+s+e+ +e ++VYdltv +  h F+a+g++v N
  gi|557693488|ref|YP_008796542.1| 503 egredtprvpknfprfedwvelhlDGDIVWDEVESVEEAGEVNDVYDLTVANPgHSFIAEGVVVSN 568
                                       **************************************************87449*******9876 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.2   3.5e-05      0.21       3      82 ..     238     318 ..     237     319 .. 0.62
   2 !   15.6   0.0   2.5e-06     0.015       1      83 []     342     435 ..     342     435 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHHHHHCCECCECSTTTTSEEEEES-..HHHHHHHHHHHH.HCT.HSCEEEE..EEE-SCCCC...ECCCHC CS
                       LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvsisltsss..kelledvqrlLl.rlGIestiyek..kkakgrgvy...rlliis 71 
                                       ++a L G+f++DG ++++ +    + ++s +  +e+ +d+ rl      I+++ +++  + +k          ++++
  gi|557693488|ref|YP_008796542.1| 238 YLARLLGYFTGDGAFNGKTT----VFYGSVEglEEIRRDIERLGYkPSKIHTRRRQNiiNGRKF---IgaeNSVRVN 307
                                       5799***************6....8888776555555555555443334444444443333333...2445777777 PP

                                       HCTTCGGGTTT CS
                       LAGLIDADG_3  72 genlkrFleki 82 
                                       ++++  +l+++
  gi|557693488|ref|YP_008796542.1| 308 SRSFTELLRRL 318
                                       77777777766 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.5e-06
                                       HHHHHHHHHHHHHCCECCECSTTTTS..EEEEES-........HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCEC CS
                       LAGLIDADG_3   1 evkaafLrGlfdaDGsvskskkkgvs..isltsss........kelledvqrlLlrlGIestiyekkkakgrgvyrl 67 
                                       + k+ +L+Glf a+     + ++ +     lt ++        + +le++++lL +lG+e+t   + ++++    rl
  gi|557693488|ref|YP_008796542.1| 342 WIKRLYLAGLFGAELNKPQTVNGYNFqvPQLTLNKrpdledngRMFLEQIAELLRELGVETTKIVSAPEGRCIRLRL 418
                                       5789999999999987777765533367555555567777888***********************99999999999 PP

                                       CCHCH.CTTCGGGTTTX CS
                       LAGLIDADG_3  68 liisg.enlkrFlekig 83 
                                       li+ + +nl r++ +ig
  gi|557693488|ref|YP_008796542.1| 419 LISERpQNLIRLWGRIG 435
                                       99987456777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (962 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 6438.87
//
Query:       gi|557693489|ref|YP_008796543.1|  [L=487]
Description: glyceraldehyde-3-phosphate dehydrogenase (NADP) [Candidatus Caldiarchaeum subterraneum]
Scores for 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-148  493.6   0.9   4.9e-148  493.5   0.9    1.0  1  Aldedh    Aldehyde dehydrogenase family
    7.2e-05   22.3   0.1    0.00023   20.7   0.0    1.8  2  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 !  493.5   0.9  5.5e-152  4.9e-148       3     462 .]      12     468 ..      10     468 .. 0.98

  Alignments for each domain:
  == domain 1  score: 493.5 bits;  conditional E-value: 5.5e-152
                                       T-SSSE.EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHH CS
                            Aldedh   3 eseset.ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletle 78 
                                        s+++  ++v++P++g++ia+v+++++ +  +av+aAke +++ ++l a +R ei++++a++l++++ee+a ++t e
  gi|557693489|ref|YP_008796543.1|  12 VSKEKPvFNVVSPIDGTIIARVQRCGPVETAEAVKAAKENQHKIRSLAAIDRIEIMEETAQILKNHAEEIASVITYE 88 
                                       45555569********************************************************************* PP

                                       H---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEEC.....TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHH CS
                            Aldedh  79 tGkplaearaeveeaidvlryyaelaeklegevlpss.....egklalvrrePlGvvgaItPWNfPlllaawklapa 150
                                       +G pla+a +ev+ +++ l++ +e a+k++ge +p +      gk a+v reP+GvvgaI P+N+Pl+++a k++pa
  gi|557693489|ref|YP_008796543.1|  89 MGRPLADAPGEVNAVVERLKLSMEDARKISGEYIPGDwspdtVGKIAVVLREPVGVVGAIGPFNYPLFIPAAKIIPA 165
                                       *********************************999778888899******************************** PP

                                       HHTT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHC CS
                            Aldedh 151 laaGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaak 227
                                       ++  N+vv KPa+ tp+s ll+a++++ aglP+gvlnvvt +g evg+ l++hp+v +++ft stevg++ia++a  
  gi|557693489|ref|YP_008796543.1| 166 ILGANSVVAKPASATPISLLLFARALQLAGLPDGVLNVVTDPG-EVGAMLASHPDVGMINFTDSTEVGKEIARNAV- 240
                                       ****************************************977.7*****************************98. PP

                                       TTSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTST CS
                            Aldedh 228 nlkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplde 304
                                         kr++lElGGk  +ivl+daD++ a++++v+ga++naGQ+C a+s +lvqe+++defve++++ ++++k gdp+d 
  gi|557693489|ref|YP_008796543.1| 241 -NKRLHLELGGKGYAIVLDDADVELAARKCVEGALRNAGQRCDAVSMVLVQEQVADEFVERVLQIVETWKTGDPRDM 316
                                       .39************************************************************************** PP

                                       T-SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEES CS
                            Aldedh 305 dtdvGPliseaqlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfk 381
                                       +t +GPl+s++++++v+ +v++ +e+ga l +Gg      + ++++ +Ptvl+nv+++++i+ eE+FGPV++++++k
  gi|557693489|ref|YP_008796543.1| 317 STRLGPLVSASAAKRVNTLVKQSIEKGASLAYGG------EVDNAYHQPTVLTNVPDQAPIVWEETFGPVIPIMTVK 387
                                       **********************************......5689********************************* PP

                                       SHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEE CS
                            Aldedh 382 deeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeyte 458
                                       +e++a+++a  ++yGL a+vft++  r+ +va++l +G+v+iNd  ++ +  +pfgGvk+Sg+Greg  +++ee++ 
  gi|557693489|ref|YP_008796543.1| 388 SEADALSVASRSRYGLDAAVFTNNFYRMWKVAKALTVGEVTINDFPRHGVGFFPFGGVKDSGIGREGIGYSIEEMMV 464
                                       *********************************************9999999************************* PP

                                       EEEE CS
                            Aldedh 459 vktv 462
                                       +kt+
  gi|557693489|ref|YP_008796543.1| 465 IKTI 468
                                       **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 !   20.7   0.0   2.6e-08   0.00023       9      58 ..     255     306 ..     252     311 .. 0.84
   2 ?   -2.8   0.0      0.39   3.5e+03     117     167 ..     381     430 ..     375     432 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.6e-08
                           DUF1487   9 vifedgDlnsalealve.slkeP.faegavatvlveesirdefvervrsklk 58 
                                       ++++d+D++ a+++ ve +l++    ++av +vlv+e+++defverv + ++
  gi|557693489|ref|YP_008796543.1| 255 IVLDDADVELAARKCVEgALRNAgQRCDAVSMVLVQEQVADEFVERVLQIVE 306
                                       8999*****9998888746777625689*******************98665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.39
                           DUF1487 117 vTlhtFrnakEvvkllakeslkfasvsvwneklaavyelvarlnvdvftiN 167
                                       + + t ++  ++  ++++ +  +++ +v+ +++  +++++++l v  +tiN
  gi|557693489|ref|YP_008796543.1| 381 IPIMTVKSEADALSVASRSRYGLDA-AVFTNNFYRMWKVAKALTVGEVTIN 430
                                       5556666667777777777777765.6888889999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3531.13
//
Query:       gi|557693490|ref|YP_008796544.1|  [L=350]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.093   13.2   0.0       0.23   11.9   0.0    1.7  1  NERD      Nuclease-related domain
        4.4    7.5   5.4        7.9    6.7   2.8    2.7  3  PYRIN     PAAD/DAPIN/Pyrin domain


Domain annotation for each model (and alignments):
>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.5e-05      0.23      27      53 ..      60      86 ..      35     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.5e-05
                              NERD 27 vrlrpgtgeiDhlvispk.gifviEvKn 53
                                      +++++  g iD+++++ + gi++iE+K 
  gi|557693490|ref|YP_008796544.1| 60 FPVEG-VGSIDIVAVGDGgGIYLIETKL 86
                                      45533.369*********88*******5 PP

>> PYRIN  PAAD/DAPIN/Pyrin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.3   1.2e+04      25      38 ..     222     235 ..     216     240 .. 0.60
   2 ?   -0.8   0.0      0.19   1.7e+03      49      67 ..     288     306 ..     288     308 .. 0.86
   3 ?    6.7   2.8   0.00089       7.9       4      23 ..     327     346 ..     326     350 .] 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                                       --SSSHTTHCCHCT CS
                             PYRIN  25 eeglksiprgelek 38 
                                       e++ ++i+  +l++
  gi|557693490|ref|YP_008796544.1| 222 ENEIQKISDEKLKN 235
                                       55666777666666 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.19
                                       HHHHTCCCCHHHHHHHHHH CS
                             PYRIN  49 vehygedaavevtlkvlek 67 
                                       +++y++  a++  ++ l++
  gi|557693490|ref|YP_008796544.1| 288 IKKYPSVDAWKGFVQSLKD 306
                                       689********99988876 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.00089
                                       CCCCCC-HHHHHHHHHHHHH CS
                             PYRIN   4 lyLeeLseeelkkFKslLke 23 
                                        +L++Ls++e+++F  +L e
  gi|557693490|ref|YP_008796544.1| 327 RKLNDLSDDEFERFLKFLDE 346
                                       68************999954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2643.38
//
Query:       gi|557693491|ref|YP_008796545.1|  [L=130]
Description: hypothetical protein CSUB_C0051 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       457  (0.0254894); 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:                         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 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1014.64
//
Query:       gi|557693492|ref|YP_008796546.1|  [L=118]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   45.6   0.1    4.2e-11   43.4   0.1    1.8  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 !   43.4   0.1   2.3e-15   4.2e-11       4     120 ..       6     108 ..       4     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2.3e-15
                                       -HHHHHHHHTTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHH CS
                               PIN   4 DTsvliallrgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidaeiae 79 
                                       DTsvli            +kl e+   +  +s+++l+E+l+++         a++ ++ + + +++ +++i+ +i +
  gi|557693492|ref|YP_008796546.1|   6 DTSVLI------------KKLKEKKpVDGKISIITLIEMLRGIPE-------AKRGKLKKTIEEGFTVVEITNDIIL 63 
                                       555555............3444444456679**************.......8888888888*************** PP

                                       HHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  80 eaaeialkyg.....llpnDaliaAtAkehgikliatfDedfrrva 120
                                       e+ +++++++      + +D+l+aA Ak++gi+l+ t D+ f+r++
  gi|557693492|ref|YP_008796546.1|  64 EYCKLYDRLKekgqlMNDADLLLAASAKASGIPLL-TLDKGFKRLE 108
                                       **************999******************.*******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 877.91
//
Query:       gi|557693493|ref|YP_008796547.1|  [L=75]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   32.0   4.8    1.8e-07   31.8   4.8    1.0  1  VAPB_antitox  Putative antitoxin
  ------ inclusion threshold ------
      0.063   13.6   0.2      0.076   13.4   0.2    1.1  1  Ras_bdg_2     Ras-binding domain of Byr2


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 !   31.8   4.8     2e-11   1.8e-07       2      69 .]       6      73 ..       5      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2e-11
                      VAPB_antitox  2 tIsIsdevYekLkklKregeSFsdvIerLle.kkkkgkkkellelfgilseeeadeiekaskelrkefk 69
                                      tIs+  +v++ L+k K+  + + + +++L +  ++++kk++l+ l++ lse+e+++i ++s+++r+efk
  gi|557693493|ref|YP_008796547.1|  6 TISVPNDVKKTLEKDKG-SREWGEYLLELYKeATETRKKRALENLAKLLSEKELNNILEESRRFRREFK 73
                                      9****************.888*********95566778899*************************997 PP

>> Ras_bdg_2  Ras-binding domain of Byr2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   8.5e-06     0.076      30      77 ..      13      71 ..       5      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.5e-06
                         Ras_bdg_2 30 lkklglkekeveeydvyvlss...........nekeslrlLsdvELvtichspdrlekn 77
                                      +kk  +k+k ++e++ y+l+              ++ ++lLs+ EL +i ++++r +++
  gi|557693493|ref|YP_008796547.1| 13 VKKTLEKDKGSREWGEYLLELykeatetrkkrALENLAKLLSEKELNNILEESRRFRRE 71
                                      5888889999999****9998999999998877788999****************8885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1301  (0.072564); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); 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: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 532.84
//
Query:       gi|557693494|ref|YP_008796548.1|  [L=200]
Description: transcriptional regulator [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-15   56.9   0.0    2.1e-15   56.4   0.0    1.2  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    4.5e-15   54.9   0.4    7.5e-15   54.2   0.4    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
      7e-14   51.4   1.1    1.2e-13   50.6   1.1    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    2.3e-07   31.0   4.2    4.1e-07   30.2   4.2    1.5  1  Arc_trans_TRASH  Archaeal TRASH domain
      3e-07   30.3   0.1      6e-07   29.3   0.1    1.5  1  MarR             MarR family
    0.00011   22.0   1.1    0.00025   20.9   1.1    1.5  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
    0.00056   19.7   0.1     0.0011   18.8   0.1    1.5  1  MarR_2           MarR family
     0.0006   19.7   0.1     0.0012   18.8   0.1    1.5  1  HTH_11           HTH domain
     0.0017   18.4   0.1     0.0029   17.7   0.1    1.3  1  YHS              YHS domain
     0.0024   17.5   0.1     0.0046   16.6   0.1    1.5  1  GntR             Bacterial regulatory proteins, gntR family
     0.0035   17.1   0.1     0.0068   16.1   0.1    1.5  1  HTH_DeoR         DeoR-like helix-turn-helix domain
     0.0048   16.7   0.0     0.0084   15.9   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
     0.0051   17.5   1.4     0.0091   16.7   1.4    1.4  1  ATPase-cat_bd    Putative metal-binding domain of cation tran
  ------ inclusion threshold ------
      0.018   15.1   0.0      0.042   13.9   0.0    1.7  1  HTH_20           Helix-turn-helix domain
       0.15   12.3   0.0       0.28   11.4   0.0    1.4  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
       0.18   12.4   0.0       0.33   11.6   0.0    1.4  1  Mga              Mga helix-turn-helix domain
       0.23   11.8   0.8       0.63   10.3   0.8    1.7  1  Ta0938           Ta0938


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 !   56.4   0.0     2e-18   2.1e-15       2      74 ..      69     138 ..      66     139 .. 0.92

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2e-18
                                       EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       ++s +p +   + ++ e+l++++eVv +yr+ G++d++++  v++ ++l++f+ +kl++l+g++ ++t+iv +
  gi|557693494|ref|YP_008796548.1|  69 GISAKPAD---IGNVVEQLKNIEEVVGLYRTVGEHDLIVRLSVQSYAELDDFIANKLSTLNGIQGIRTNIVTN 138
                                       56666555...9***********************************************************87 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 !   54.2   0.4   7.1e-18   7.5e-15       1      48 []       3      50 ..       3      50 .. 0.98

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 7.1e-18
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ld++d++IL++Lq+++ri+ + LA++  +S++t ++r++rL++eG+I+
  gi|557693494|ref|YP_008796548.1|  3 LDQIDYRILSILQEDGRIPLSKLARKARVSVPTARQRVNRLVKEGVIQ 50
                                      79********************************************95 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 !   50.6   1.1   1.1e-16   1.2e-13       1      41 [.       3      43 ..       3      44 .. 0.99

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.1e-16
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      LD+iD +IL++Lqed+Ri+ ++LA++  +S +t+++Rv+rL
  gi|557693494|ref|YP_008796548.1|  3 LDQIDYRILSILQEDGRIPLSKLARKARVSVPTARQRVNRL 43
                                      8***************************************9 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   4.2   3.9e-10   4.1e-07       1      34 [.     158     191 ..     158     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.9e-10
                   Arc_trans_TRASH   1 CDYCGkeivgePivyklknkvYyvCCktCkselk 34 
                                       C  CGkei g Pi   +  + Yy+CC++C + + 
  gi|557693494|ref|YP_008796548.1| 158 CTICGKEIEGRPIKRTIEGREYYLCCNSCAEIFD 191
                                       777**************************98775 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.1   5.7e-10     6e-07       6      50 ..       8      52 ..       3      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 5.7e-10
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      ++iL il e g + +s+La+k  vs +t+   + rL+k+G i+R 
  gi|557693494|ref|YP_008796548.1|  8 YRILSILQEDGRIPLSKLARKARVSVPTARQRVNRLVKEGVIQRF 52
                                      89*****************************************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 !   20.9   1.1   2.3e-07   0.00025       6      41 .]     158     190 ..     154     190 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.3e-07
                            zf-FCS   6 CwfCkkyikgkpeftyvlendgvvgqFCStsCldsY 41 
                                       C++C+k+i+g p     ++++g +++ C+ sC+  +
  gi|557693494|ref|YP_008796548.1| 158 CTICGKEIEGRPI---KRTIEGREYYLCCNSCAEIF 190
                                       ************8...9***************9876 PP

>> MarR_2  MarR family
   #    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       8      53 ..       8      51 ..       2      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  8 arvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +r+L  L   ++  +  + lar+ ++s +++ ++++rLv+ G ++r
  gi|557693494|ref|YP_008796548.1|  8 YRILSILQEDGR--IPLSKLARKARVSVPTARQRVNRLVKEGVIQR 51
                                      677777766665..9****************************987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.1e-06    0.0012       4      54 ..       9      64 ..       8      65 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpIesepgr..GY 54
                                       il +L +++g i+ ++LA++  vS  t r+++ +L + g    + I   p+r  GY
  gi|557693494|ref|YP_008796548.1|  9 RILSIL-QEDGRIPLSKLARKARVSVPTARQRVNRLVKEGviqrFTILLNPKRvtGY 64
                                      599999.*********************************99999999999999998 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   2.8e-06    0.0029       6      39 ..     161     192 ..     160     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-06
                               YHS   6 cgmkvdkekaeekseYkGkeYyFcSegCkdkFed 39 
                                       cg+ +  e ++ k + +G+eYy c+ +C ++F++
  gi|557693494|ref|YP_008796548.1| 161 CGKEI--EGRPIKRTIEGREYYLCCNSCAEIFDQ 192
                                       78888..5577788889***************97 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   4.4e-06    0.0046       8      57 ..       5      52 ..       3      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.4e-06
                                      HHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR  8 rLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverr 57
                                      +++ +Ils  l+   ++ + ++La +  Vs +t R+  +rL+ eg+++r 
  gi|557693494|ref|YP_008796548.1|  5 QIDYRILS-ILQEDGRI-PLSKLARKARVSVPTARQRVNRLVKEGVIQRF 52
                                      56667777.88889999.99****************************95 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 !   16.1   0.1   6.4e-06    0.0068       4      46 ..       9      51 ..       7      53 .. 0.96

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.4e-06
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                       il  l+++g + + +l+    vS  T+R   n L+++g++ R
  gi|557693494|ref|YP_008796548.1|  9 RILSILQEDGRIPLSKLARKARVSVPTARQRVNRLVKEGVIQR 51
                                      5999*************************************99 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 !   15.9   0.0   7.9e-06    0.0084       7      50 ..       9      51 ..       8      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.9e-06
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +iL +l e ++   ls lAr++ ++ +t++  ++ Lv++G +++
  gi|557693494|ref|YP_008796548.1|  9 RILSILQEDGR-IPLSKLARKARVSVPTARQRVNRLVKEGVIQR 51
                                      68889998888.8***************************9875 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 !   16.7   1.4   8.6e-06    0.0091       2      35 ..     158     190 ..     157     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.6e-06
                     ATPase-cat_bd   2 CyHCglpveesaklkaeiegeerefCCkGCqava 35 
                                       C+ Cg+++e   ++k++ieg+e ++CC+ C+ ++
  gi|557693494|ref|YP_008796548.1| 158 CTICGKEIEG-RPIKRTIEGREYYLCCNSCAEIF 190
                                       999*****65.79*****************9987 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     4e-05     0.042      13      54 ..       8      49 ..       4      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                      +ril+ L +++   +s la+  ++s  t++++++ L++ g +
  gi|557693494|ref|YP_008796548.1|  8 YRILSILQEDGRIPLSKLARKARVSVPTARQRVNRLVKEGVI 49
                                      69***********************************99987 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 ?   11.4   0.0   0.00027      0.28      13      51 ..      10      48 ..       9      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                                      HHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTS CS
                    Fe_dep_repress 13 IYtlseekkvvktkdlaerLnvspssVsemlkkLekdGy 51
                                      I+++  e + +  ++la+   vs +++ + +++L k+G 
  gi|557693494|ref|YP_008796548.1| 10 ILSILQEDGRIPLSKLARKARVSVPTARQRVNRLVKEGV 48
                                      556666777788899**********************96 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00031      0.33      16      74 ..       5      63 ..       3      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                                      SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHH..HCHCCT-EEETTCCEEES CS
                               Mga 16 slkyqllkflfeeeevsieelaqelyiSestlkrkikelnk..lLkefdleltkknlklrG 74
                                      +++y++l  l e+ ++ + +la++  +S  t+ + +++l k  +++ f + l  ++ +++G
  gi|557693494|ref|YP_008796548.1|  5 QIDYRILSILQEDGRIPLSKLARKARVSVPTARQRVNRLVKegVIQRFTILL--NPKRVTG 63
                                      589******************************9999997745699999999..7777777 PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.8    0.0006      0.63      17      47 ..     158     190 ..     151     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0006
                                       -SS---S---..SS-B-TT--BSSS--SSSS-T CS
                            Ta0938  17 calcgatwgd..yyeevdgeklffccdicakef 47 
                                       c++cg    +     +++g + ++cc+ ca+ f
  gi|557693494|ref|YP_008796548.1| 158 CTICGKEIEGrpIKRTIEGREYYLCCNSCAEIF 190
                                       8888876543226789**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      656  (0.0365888); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1481.61
//
Query:       gi|557693495|ref|YP_008796549.1|  [L=69]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.1   0.9      0.034   13.8   0.9    1.0  1  DUF716    Family of unknown function (DUF716)


Domain annotation for each model (and alignments):
>> DUF716  Family of unknown function (DUF716)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9   1.9e-06     0.034      33      86 ..       5      58 ..       2      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-06
                            DUF716 33 vhlLLvlvvalsllsalleallpksfllelvrsvllilqGtWflqmGfiLytps 86
                                      + +LL l ++ls+++a+  +++    l+    s+ +++  +Wf+ + fi   p 
  gi|557693495|ref|YP_008796549.1|  5 YRSLLTLSICLSFATAITALFIAAATLIGRYTSLDITIGSVWFFTISFIVSLPL 58
                                      789*********************************************976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 534.88
//
Query:       gi|557693496|ref|YP_008796550.1|  [L=845]
Description: Cu2+-exporting ATPase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  192.8   1.0    3.7e-57  192.8   1.0    1.9  2  E1-E2_ATPase  E1-E2 ATPase
    1.9e-46  159.0   2.6    3.5e-46  158.2   2.6    1.5  1  Hydrolase     haloacid dehalogenase-like hydrolase
    1.3e-33  115.2   0.9    5.7e-16   58.7   0.0    2.7  2  HMA           Heavy-metal-associated domain
    6.2e-07   29.4   0.7     0.0028   17.5   0.2    2.6  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
      0.002   18.6   0.0     0.0076   16.7   0.0    2.0  2  HAD           haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.012   15.7   0.1      0.034   14.2   0.1    1.8  1  HAD_2         Haloacid dehalogenase-like hydrolase
      0.015   15.4   0.0       0.18   11.9   0.0    2.8  2  Hydrolase_6   Haloacid dehalogenase-like hydrolase
       0.03   14.5   0.0        0.3   11.3   0.0    2.4  2  LPD22         Large polyvalent protein associated domain 22
       0.13   12.4   0.0         18    5.5   0.0    2.4  2  Tox-PL-2      Papain fold toxin 2
       0.41   11.0   3.4         19    5.7   0.1    3.4  3  Fer2_BFD      BFD-like [2Fe-2S] binding 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 !  192.8   1.0   2.1e-60   3.7e-57       2     180 ..     295     497 ..     294     498 .. 0.97
   2 ?   -3.9   0.1       4.8   8.7e+03     102     144 ..     775     817 ..     767     830 .. 0.52

  Alignments for each domain:
  == domain 1  score: 192.8 bits;  conditional E-value: 2.1e-60
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                       l+p ta+virdg+e+ei+a+++++GD+vl+++g+++p+Dg++veg ++vd+s++TGEs pv+k+ gd+v++ tv++ 
  gi|557693496|ref|YP_008796550.1| 295 LKPLTARVIRDGEEMEIPADDVQIGDVVLVRPGEKIPVDGVVVEGYSSVDQSMITGESIPVDKKVGDEVIGATVNKT 371
                                       78899************************************************************************ PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.......... CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla.......... 145
                                       g +k+++t++g+dt l++i++lve+a+++k p+q+ +d +++++v+++l+i++l+f+++++ g +l           
  gi|557693496|ref|YP_008796550.1| 372 GFLKVRATRVGKDTALAQIVKLVEQAQQTKLPIQRLADWVAGHFVTASLIISMLAFAFWFFAGYQLYfvprggemwa 448
                                       *************************************************************8888888888888889 PP

                                       ..............HHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 146 ..............eallralallvaaiPcaLplavplalalgarrlak 180
                                                     +al+ a+++lv+a+Pca ++a+p a+++g++++a+
  gi|557693496|ref|YP_008796550.1| 449 gfwrivapdttagiFALIIAISILVIACPCAVGIATPAAVMVGTGKAAE 497
                                       9999******************************************997 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.8
                                       --------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSST CS
                      E1-E2_ATPase 102 eeakskktplqkkldklgkvlvpvvlliallvflialllgksl 144
                                         +k++  +++++l   +++ ++++ ++a +++ ++ ++  + 
  gi|557693496|ref|YP_008796550.1| 775 HLSKKTMQKIKQNLLWAFGYNAAAIPIAAGALYPATGFIMSPE 817
                                       4555555555555555555555555555555555555544444 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.2   2.6   1.9e-49   3.5e-46       2     210 .]     515     742 ..     514     742 .. 0.94

  Alignments for each domain:
  == domain 1  score: 158.2 bits;  conditional E-value: 1.9e-49
                                       SEEEEESBTTTBCHHHHHHHHHHHH..............CHHHHHHHHHH...HHCHHHHHHHHHHHHH..HHHH.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxx.. RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa..............alalaaaletg...sehpigkalvaaakar..sgal.. 57 
                                       +++vfDk+GTLt+g+psv+d++                 +++l  + +++   sehp+++a+v++ak++  +  +  
  gi|557693496|ref|YP_008796550.1| 515 DVIVFDKTGTLTRGKPSVTDLVLLKpavkmlanprpiedERDLLLIAAIAekrSEHPLAQAIVEQAKELglE--Ipe 589
                                       79******************999999999999999999966666666666779****************653..444 PP

                                       .HHHHHETTTE........HHHHTHHHHHHHH.HCHHHHHHHHHHHHHHCHHHHHH..TTHHHHHHHHHHTHHBHTT CS
                                       .xxxxxxxxxx........xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  58 .tgfatfigrg........ayaigkpewltal.dippdlgaaigsaqsqgrtvall..qaralavftiadplkvkpe 122
                                        ++f++++g+g        +++ g+++++++      +l+++i  ++++g+tv++   ++  l+++++ad+  +k+ 
  gi|557693496|ref|YP_008796550.1| 590 pEDFEAIPGHGvratyggkTILLGNRKLMESYgVDVAELEERIRMLEDEGKTVMIMafDGAPLGLVAVADT--LKEH 664
                                       8********************************999********************999************..**** PP

                                       HHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 123 aaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGD 198
                                        aeav++L+++g+ev++ltgdn +ta+++a+qlG           i+   a+++p  k + +++Lq ++++v +VGD
  gi|557693496|ref|YP_008796550.1| 665 SAEAVKALQDMGVEVAMLTGDNTRTAQAIARQLG-----------ITRvLAEVLPGEKAEEVKKLQQEGKRVGFVGD 730
                                       **********************************...........5555**************************** PP

                                       SHHHHHHHHHTT CS
                                       xxxxxxxxxxxx RF
                         Hydrolase 199 gvnDaaalaaAg 210
                                       g+nDa+al +A+
  gi|557693496|ref|YP_008796550.1| 731 GINDAPALTQAD 742
                                       **********98 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.0   3.2e-19   5.7e-16       1      61 [.       8      68 ..       8      69 .. 0.97
   2 !   54.1   0.6   8.6e-18   1.5e-14       3      62 .]      78     136 ..      76     136 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 3.2e-19
                               HMA  1 tvrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61
                                      ++++ gmhCa+Ca++ve+ L++l+gV++++v++a++++ Ve+d++ ++l +  +ai+++gy
  gi|557693496|ref|YP_008796550.1|  8 VLQIGGMHCASCAQSVESMLKSLDGVYNASVNFASSRALVEYDPTRVSLAEMERAIKEIGY 68
                                      57899*******************************************************9 PP

  == domain 2  score: 54.1 bits;  conditional E-value: 8.6e-18
                               HMA   3 rvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagyk 62 
                                        v gmhCa+C+++ve +L+e++gV +v+v+l t++++V++ +e  +   +i+a++  gy+
  gi|557693496|ref|YP_008796550.1|  78 GVRGMHCASCVQSVENALKEVEGVVDVSVNLMTGRAVVNVLPET-SKQSLIKAVRGVGYD 136
                                       599*************************************6665.2266*******9996 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0   0.00034      0.62      14      56 ..     659     701 ..     653     707 .. 0.90
   2 !   17.5   0.2   1.5e-06    0.0028     197     247 ..     716     766 ..     710     774 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00034
                                       S---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCS CS
                       Hydrolase_3  14 kkisektkeaikklkekgikvviATGRslravlpvleelgldl 56 
                                        +++e+++ea+k l++ g++v+  TG ++r+++ ++++lg++ 
  gi|557693496|ref|YP_008796550.1| 659 DTLKEHSAEAVKALQDMGVEVAMLTGDNTRTAQAIARQLGITR 701
                                       568899**********************************985 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.5e-06
                                       HHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GG CS
                       Hydrolase_3 197 kelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnn 247
                                       k+l+ + ++v  +GDg ND + L++a++g+A+g++++ + +a + v  + +
  gi|557693496|ref|YP_008796550.1| 716 KKLQQEGKRVGFVGDGINDAPALTQADVGIALGSGTDIAMEAGKIVLVKDD 766
                                       567778889999****************************99998877665 PP

>> HAD  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       4.5   8.1e+03       1      17 [.     517     536 ..     517     571 .. 0.65
   2 !   16.7   0.0   4.2e-06    0.0076      87     187 ..     662     738 ..     625     739 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4.5
                               HAD   1 alfDfDgTLldg.dsle..l 17 
                                       ++fD  gTL++g  s +  +
  gi|557693496|ref|YP_008796550.1| 517 IVFDKTGTLTRGkPSVTdlV 536
                                       68999999999954444433 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.2e-06
                               HAD  87 dpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewla 163
                                       +++  e+++a ++ G++v++++g + + +++++++lg+ +vla+      +l ge         +++ v++l++   
  gi|557693496|ref|YP_008796550.1| 662 KEHSAEAVKALQDMGVEVAMLTGDNTRTAQAIARQLGITRVLAE------VLPGE---------KAEEVKKLQQ--- 720
                                       454455556556********************************......89999.........5555666777... PP

                               HAD 164 aegegidleevvayGDspsDlpll 187
                                             + ++v ++GD+++D p+l
  gi|557693496|ref|YP_008796550.1| 721 ------EGKRVGFVGDGINDAPAL 738
                                       ......44558899******9997 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.9e-05     0.034      80     171 ..     661     741 ..     657     747 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                             HAD_2  80 pydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkeevi 156
                                       + ++  e+++ L+++g++++  T  ++++++   +qlgi++++  ++ +e++e+ K           kl+ + ++v 
  gi|557693496|ref|YP_008796550.1| 661 LKEHSAEAVKALQDMGVEVAMLTGDNTRTAQAIARQLGITRVLAEVLPGEKAEEVK-----------KLQQEGKRVG 726
                                       568999*********************************************99996...........8888888888 PP

                             HAD_2 157 yvGDsptDieaakka 171
                                       +vGD ++D  a  +a
  gi|557693496|ref|YP_008796550.1| 727 FVGDGINDAPALTQA 741
                                       888888887766665 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.8     1e+04       1      13 [.     517     529 ..     517     532 .. 0.88
   2 ?   11.9   0.0    0.0001      0.18      12      51 ..     658     697 ..     652     704 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.8
                                       EEEESTTTSEETT CS
                       Hydrolase_6   1 flfDidGvLwrgd 13 
                                       ++fD  G+L rg+
  gi|557693496|ref|YP_008796550.1| 517 IVFDKTGTLTRGK 529
                                       69*******9986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0001
                                       TTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHH CS
                       Hydrolase_6  12 gdkaipgaaealnalraagkpvvllTNnsskseeeyakkl 51 
                                        d++ +++aea++al+++g++v++lT  ++++ +++a +l
  gi|557693496|ref|YP_008796550.1| 658 ADTLKEHSAEAVKALQDMGVEVAMLTGDNTRTAQAIARQL 697
                                       56777899**************************999987 PP

>> LPD22  Large polyvalent protein associated domain 22
   #    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      40      79 ..     278     317 ..     268     318 .. 0.89
   2 ?   -0.4   0.1      0.76   1.4e+03      20      33 ..     689     702 ..     654     726 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                             LPD22  40 eaferaaeaedwdalledsPatakwladpdnaavAhDDve 79 
                                       e + r  ++e +++l+e +P ta+ ++d + +++ +DDv+
  gi|557693496|ref|YP_008796550.1| 278 ETITRGRTSEAVRRLMELKPLTARVIRDGEEMEIPADDVQ 317
                                       667777899999**************************96 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.76
                             LPD22  20 ralrlaeelGlppd 33 
                                        a+++a++lG+ + 
  gi|557693496|ref|YP_008796550.1| 689 TAQAIARQLGITRV 702
                                       34455555554443 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 ?    5.5   0.0      0.01        18       9      31 ..       7      29 ..       2      38 .. 0.87
   2 ?    4.2   0.0     0.025        46      12      45 ..      78     112 ..      70     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.01
                          Tox-PL-2  9 ivkrfklleCveCAaalekyLke 31
                                      +v ++  ++C +CA+ +e++Lk+
  gi|557693496|ref|YP_008796550.1|  7 VVLQIGGMHCASCAQSVESMLKS 29
                                      66678899************986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.025
                          Tox-PL-2  12 rfklleCveCAaalekyLke.qgisGkrlklktks 45 
                                        ++ ++C +C + +e++Lke +g+    ++l t+ 
  gi|557693496|ref|YP_008796550.1|  78 GVRGMHCASCVQSVENALKEvEGVVDVSVNLMTGR 112
                                       56789*************98345665566666655 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 ?    4.2   0.1     0.031        56      35      50 ..      13      28 ..       9      29 .. 0.87
   2 ?    5.7   0.1     0.011        19      10      51 .]      56      97 ..      52      97 .. 0.65
   3 ?   -1.9   0.0       2.5   4.4e+03      12      31 ..     769     787 ..     766     789 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.031
                          Fer2_BFD 35 gtgCggCrpaieeiLa 50
                                      g+ C++C + +e +L+
  gi|557693496|ref|YP_008796550.1| 13 GMHCASCAQSVESMLK 28
                                      677**********997 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.011
                          Fer2_BFD 10 egeIrdairraglttv.eevkrrtkagtgCggCrpaieeiLae 51
                                        e ++ai++ g + + +++++ ++ g+ C++C++ +e+ L+e
  gi|557693496|ref|YP_008796550.1| 56 LAEMERAIKEIGYRVLkDQITLGVR-GMHCASCVQSVENALKE 97
                                      5566666655543333145555555.899*********99976 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.5
                          Fer2_BFD  12 eIrdairraglttveevkrr 31 
                                       ++++ai+    +t++ +k+ 
  gi|557693496|ref|YP_008796550.1| 769 DVVNAIHL-SKKTMQKIKQN 787
                                       79999955.36999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (845 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1067  (0.0595125); expected 358.6 (0.02)
Passed bias filter:                      784  (0.043728); 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):              10  [number of targets reported over threshold]
# CPU time: 0.73u 0.26s 00:00:00.99 Elapsed: 00:00:00.41
# Mc/sec: 6228.14
//
Query:       gi|557693497|ref|YP_008796551.1|  [L=55]
Description: Cu2+-exporting ATPase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   71.6   1.4      5e-20   71.3   1.4    1.0  1  YHS              YHS domain
     0.0016   18.7   0.2     0.0027   18.0   0.2    1.4  1  Arc_trans_TRASH  Archaeal TRASH domain
  ------ inclusion threshold ------
      0.041   14.1   0.3       0.05   13.8   0.3    1.1  1  Ribosomal_L24e   Ribosomal protein L24e
       0.75    9.8   3.5        0.6   10.1   1.0    2.1  2  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 !   71.3   1.4   1.1e-23     5e-20       1      46 [.       5      50 ..       5      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 1.1e-23
                               YHS  1 vtdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYat 46
                                      v dPvcgm vd+++a++kse++Gk +yFc egCk +Fe++P kY +
  gi|557693497|ref|YP_008796551.1|  5 VVDPVCGMEVDPATARYKSEHGGKVFYFCAEGCKKAFEKNPHKYIK 50
                                      68******************************************75 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2     6e-07    0.0027       4      35 ..      10      43 ..       9      45 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6e-07
                   Arc_trans_TRASH  4 CGkeivgePivyk..lknkvYyvCCktCkselkk 35
                                      CG e+      yk  ++ kv+y+C + Ck+ + k
  gi|557693497|ref|YP_008796551.1| 10 CGMEVDPATARYKseHGGKVFYFCAEGCKKAFEK 43
                                      777765555555522567**************98 PP

>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   1.1e-05      0.05       9      45 ..      10      44 ..       6      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                                      T-SB--SS--EEEE-TTS-EEEESSHHHHHHHHTT-- CS
                    Ribosomal_L24e  9 sgykiyPGhGkrfvrnDgkvfrFlssKceklfkqkrn 45
                                      +g ++ P++ +   ++ gkvf F+ + c+k+f++  n
  gi|557693497|ref|YP_008796551.1| 10 CGMEVDPATARYKSEHGGKVFYFCAEGCKKAFEK--N 44
                                      9999999999999999****************85..4 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 ?   -0.7   0.0      0.33   1.5e+03       7      15 ..       8      16 ..       7      25 .. 0.77
   2 ?   10.1   1.0   0.00013       0.6      19      37 ..      32      50 ..      27      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.33
                           DUF2116  7 ivCGkaIpl 15
                                      +vCG  +++
  gi|557693497|ref|YP_008796551.1|  8 PVCGMEVDP 16
                                      589987665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00013
                           DUF2116 19 fCsekCqeeyekkrkkvar 37
                                      fC e C++++ek+  k ++
  gi|557693497|ref|YP_008796551.1| 32 FCAEGCKKAFEKNPHKYIK 50
                                      9************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); 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:                         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: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 460.54
//
Query:       gi|557693498|ref|YP_008796552.1|  [L=76]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   19.9   0.8      0.001   19.5   0.8    1.3  1  CcdA           Post-segregation antitoxin CcdA
     0.0014   18.5   2.0     0.0014   18.5   2.0    2.4  3  RHH_1          Ribbon-helix-helix protein, copG family
     0.0058   17.4   6.8     0.0066   17.2   6.8    1.1  1  PSK_trans_fac  Rv0623-like transcription factor
  ------ inclusion threshold ------
      0.011   14.6   0.3      0.011   14.5   0.3    1.0  1  ALMT           Aluminium activated malate transporter
      0.015   15.2   0.5      0.015   15.2   0.5    1.6  2  RHH_3          Ribbon-helix-helix domain
      0.042   13.7   0.8      0.042   13.7   0.8    1.6  2  RHH_5          CopG-like RHH_1 or ribbon-helix-helix domain, 
      0.059   11.9   0.4      0.064   11.8   0.4    1.0  1  DUF5357        Family of unknown function (DUF5357)
        0.1   12.8   2.4       0.13   12.5   0.7    1.8  2  XhlA           Haemolysin XhlA
       0.14   12.4   3.6       0.14   12.4   3.6    1.0  1  MCM6_C         MCM6 C-terminal winged-helix domain
        1.7    8.7   6.2       0.32   11.0   0.5    2.1  2  G-gamma        GGL 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 !   19.5   0.8   5.7e-07     0.001       4      44 ..       7      47 ..       5      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.7e-07
                              CcdA  4 vnlsldsdllaqAralgiNlSatleeaLaeevkeekaerwk 44
                                      v+  + ++l ++A +lg+ +S++l +aL+eev++++ e+ +
  gi|557693498|ref|YP_008796552.1|  7 VSTKVRRKLKEEAERLGVKVSEVLRRALEEEVRRRRLEELE 47
                                      56667889************************988876644 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 !   18.5   2.0   7.6e-07    0.0014       6      39 .]       7      40 ..       5      40 .. 0.86
   2 ?   -0.3   0.2      0.64   1.2e+03       8      15 ..      44      51 ..      41      54 .. 0.54
   3 ?   -1.0   0.1       1.1     2e+03      11      20 ..      62      71 ..      56      76 .] 0.51

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.6e-07
                                      EEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHH CS
                             RHH_1  6 ldeellerLdelarrrgrSrSelIReAlreyler 39
                                      ++ ++ ++L e a+r+g+ +Se++R+Al+e + r
  gi|557693498|ref|YP_008796552.1|  7 VSTKVRRKLKEEAERLGVKVSEVLRRALEEEVRR 40
                                      55566689**********************9875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.64
                                      HHHHHHHH CS
                             RHH_1  8 eellerLd 15
                                      eel +rL+
  gi|557693498|ref|YP_008796552.1| 44 EELEKRLE 51
                                      45555555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.1
                                      HHHHHHHHHH CS
                             RHH_1 11 lerLdelarr 20
                                       +r+  ++r+
  gi|557693498|ref|YP_008796552.1| 62 TDRITLMIRE 71
                                      4555555555 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 !   17.2   6.8   3.7e-06    0.0066       8      61 ..       9      62 ..       7      76 .] 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3.7e-06
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--HHHHHHHHHHHHHT CS
                     PSK_trans_fac  8 peverlareLarltgeskteAvrrAleerlerlrreraepllerllallrraaa 61
                                       +v+r+ +e a++ g+   e+ rrAlee+ +r+r e+ e++le+l   l++ ++
  gi|557693498|ref|YP_008796552.1|  9 TKVRRKLKEEAERLGVKVSEVLRRALEEEVRRRRLEELEKRLENLGTALDKLDT 62
                                      5899****************************9877777777777777666665 PP

>> ALMT  Aluminium activated malate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   6.4e-06     0.011     287     342 ..       7      62 ..       2      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.4e-06
                              ALMT 287 apeelrkkfkeelqrvslesakvlrelaesvkkmkklskveellkevkvaaeeLqs 342
                                       +++++r+k+kee +r++ ++++vlr   e+  ++++l++ e+ l+++ +a+++L +
  gi|557693498|ref|YP_008796552.1|   7 VSTKVRRKLKEEAERLGVKVSEVLRRALEEEVRRRRLEELEKRLENLGTALDKLDT 62 
                                       67899*******************98766666777788889***********9975 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.5   8.3e-06     0.015       7      38 ..       5      36 ..       4      36 .. 0.91
   2 ?   -2.8   0.2       3.6   6.4e+03      12      17 ..      45      50 ..      42      53 .. 0.48

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.3e-06
                             RHH_3  7 vsidpelaekLkaLSekTrIprSklldeAiel 38
                                      v++ ++   kLk+  e++++ +S+ l+ A+e+
  gi|557693498|ref|YP_008796552.1|  5 VTVSTKVRRKLKEEAERLGVKVSEVLRRALEE 36
                                      778888889*********************95 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.6
                             RHH_3 12 elaekL 17
                                      el ++L
  gi|557693498|ref|YP_008796552.1| 45 ELEKRL 50
                                      444444 PP

>> 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 ?   13.7   0.8   2.3e-05     0.042       6      42 ..       5      41 ..       4      42 .. 0.94
   2 ?   -2.9   0.4       3.8   6.8e+03      10      17 ..      44      51 ..      44      53 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-05
                             RHH_5  6 vtLPeelleeLeewAdeegRsvSnlaafLvekalrea 42
                                      vt++++++ +L+e+A+  g+ vS +    +e+ +r++
  gi|557693498|ref|YP_008796552.1|  5 VTVSTKVRRKLKEEAERLGVKVSEVLRRALEEEVRRR 41
                                      9***************************999999997 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.8
                             RHH_5 10 eelleeLe 17
                                      eel ++Le
  gi|557693498|ref|YP_008796552.1| 44 EELEKRLE 51
                                      67888887 PP

>> DUF5357  Family of unknown function (DUF5357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   3.5e-05     0.064     186     241 ..      11      66 ..       2      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.5e-05
                           DUF5357 186 vrleekekapkrGvviLnklqplveeqlakkpWsevErwLleadkevkslgkqvld 241
                                       vr + ke+a++ Gv + + l++ +ee+++++   e E+ L +  + + +l+ + + 
  gi|557693498|ref|YP_008796552.1|  11 VRRKLKEEAERLGVKVSEVLRRALEEEVRRRRLEELEKRLENLGTALDKLDTDRIT 66 
                                       566778899999**********************************9999987665 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.85   1.5e+03      33      40 ..      14      21 ..       6      35 .. 0.55
   2 ?   12.5   0.7     7e-05      0.13       4      27 ..      41      64 ..      39      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.85
                              XhlA 33 kiknleed 40
                                      k+k+  e+
  gi|557693498|ref|YP_008796552.1| 14 KLKEEAER 21
                                      33333332 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7e-05
                              XhlA  4 erlerietkldnleervdkleeka 27
                                       rle++e++l+nl++ +dkl+ + 
  gi|557693498|ref|YP_008796552.1| 41 RRLEELEKRLENLGTALDKLDTDR 64
                                      59******************9875 PP

>> MCM6_C  MCM6 C-terminal winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.6   8.1e-05      0.14       9      85 ..       3      75 ..       1      76 [] 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.1e-05
                            MCM6_C  9 kYveianllvlklreeeeeeeeegiekeeLvewYleqieeeleseeeleeekklvekvlkrLvkdkvLlevreeaee 85
                                      +Yv++++ + +kl+ee e+    g++ +e+++  le+ e +    eele++ + +   l++L +d++ l +re++++
  gi|557693498|ref|YP_008796552.1|  3 EYVTVSTKVRRKLKEEAER---LGVKVSEVLRRALEE-EVRRRRLEELEKRLENLGTALDKLDTDRITLMIREDRKS 75
                                      6888888888888777666...9**************.99999****************************999875 PP

>> G-gamma  GGL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.5   0.00018      0.32       5      29 ..       5      30 ..       1      35 [. 0.87
   2 ?    0.5   1.3      0.35   6.2e+02       7      18 ..      39      50 ..      30      60 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                           G-gamma  5 lklkrei.eqLkkeLkrerikvSkAc 29
                                      +++++++  +Lk+e++r ++kvS++ 
  gi|557693498|ref|YP_008796552.1|  5 VTVSTKVrRKLKEEAERLGVKVSEVL 30
                                      57889999***************986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.35
                           G-gamma  7 lkreieqLkkeL 18
                                      + r +e L+k+L
  gi|557693498|ref|YP_008796552.1| 39 RRRRLEELEKRL 50
                                      333344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1724  (0.0961571); expected 358.6 (0.02)
Passed bias filter:                      837  (0.0466841); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 624.90
//
Query:       gi|557693499|ref|YP_008796553.1|  [L=195]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-07   29.5   0.0    1.2e-06   28.6   0.0    1.4  1  Nitrate_red_del  Nitrate reductase delta subunit
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.21   11.4   0.0    1.5  1  TIP120           TATA-binding protein interacting (TIP20)


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 !   28.6   0.0   1.3e-10   1.2e-06      67     129 ..      80     142 ..      69     148 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.3e-10
                   Nitrate_red_del  67 evrefyrqaglevaeefneppDHlaveLeflahLaereaeaeea...eeaealleaqkafleehll 129
                                       +v+efy+ ag + +++    pDHl ++L+f+  L+++e++a  a   +  +++ + q  fl+ hl 
  gi|557693499|ref|YP_008796553.1|  80 MVNEFYKNAGYDCESDN---PDHLTTMLAFINILLREEKKAALAgdlDTLKNIRRIQHRFLNVHLI 142
                                       799**************...*******************999999*99999*************96 PP

>> TIP120  TATA-binding protein interacting (TIP20)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.3e-05      0.21      39      75 ..       5      38 ..       4      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.3e-05
                            TIP120 39 GLelRKaaYetlytlletaldrldlselldrvlaGls 75
                                       +e+R++ Yetly+l++  l++ d    ++++l+Gl+
  gi|557693499|ref|YP_008796553.1|  5 TIEIRQTFYETLYSLFKL-LENGDP--SASQILEGLR 38
                                      58*************998.444333..3455666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.50
# Mc/sec: 1161.72
//
Query:       gi|557693500|ref|YP_008796554.1|  [L=1153]
Description: molybdopterin oxidoreductase, molybdopterin binding subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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   85.6   0.0      2e-19   69.9   0.0    2.8  2  Molybdopterin    Molybdopterin oxidoreductase
    5.2e-11   42.5   0.0    1.5e-10   41.1   0.0    1.7  1  Molydop_binding  Molydopterin dinucleotide binding domain
    2.4e-07   30.6   1.7    5.1e-06   26.4   1.7    2.4  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 !   11.9   0.1   1.3e-05     0.079       1      29 [.     138     166 ..     138     171 .. 0.92
   2 !   69.9   0.0   3.3e-23     2e-19     107     395 ..     321     718 ..     278     723 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                                       B--S-EEECTTTTTSEEEE--HHHHHHHH CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleli 29 
                                       R+ +P++R + rg Gk++ +sW++  +++
  gi|557693500|ref|YP_008796554.1| 138 RVLKPLKRAGPRGSGKWKTISWEQLVKEV 166
                                       999********************988876 PP

  == domain 2  score: 69.9 bits;  conditional E-value: 3.3e-23
                                       CGGGG-SEEEEESS-HHHHSHHH..HHHHHHHHHTTC-EEEEECSSB-H..CGGGCSEEEEEHTTTHHHHHHHHHHH CS
                     Molybdopterin 107 edlensdliilwGsNvreerpil..narirkaalkkkakvivigpryae..llkfadewlaikpgtdaalalamghv 179
                                       +d+  ++++i+ G+ + + +p +  ++ ++ +a ++++kv ++ p+      ++  ++w+++kpg daala+am  +
  gi|557693500|ref|YP_008796554.1| 321 ADVMGAKVVIMAGATMGRQHPGAtgQGLLIERAVEGEVKVYYVNPTAPRtlGTRGSVKWVPVKPGEDAALAMAMIRW 397
                                       48999****************9988999******************9999867889********************* PP

                                       HHHCCCCTCHHHHHHEECHHHCCCCCCCEECCS............................................ CS
                     Molybdopterin 180 ilqelkvdkeflrkytygkeetdmpllvtleee............................................ 212
                                       +++++  dkefl  +++  ++t     v ++                                              
  gi|557693500|ref|YP_008796554.1| 398 MIENNRFDKEFLSITNSEAAKTLRGYPVNTNATwlvifenghprfgehlkasdiglegsqpvvsvngvlmpndavek 474
                                       ***********99999988888888888887779******************************************* PP

                                       .....................................HHHHHHCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTH CS
                     Molybdopterin 213 .....................................tgkkkevvariarelarnaaktagksmiivGaglnhrqdg 252
                                                                             +++++v+++++ e+a ++ ++a+++   +  g+  + +g
  gi|557693500|ref|YP_008796554.1| 475 adiefsgrvqlssgeevlvktpftilkeeafsktleeWSEICGVPVETIVEMAHDFTEAAPRASTYLHRGVCMHPNG 551
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHCTHCSSTTCEEE.....EESSCTTHHHCHHHHTCCTTCCCCCCCTT.................. CS
                     Molybdopterin 253 daiyravinLallvgnvgqpgGgwa.....hlnGqlilagaaekvgalpvllsvkslke.................. 306
                                       + +++a   L ++vgn +++gG +a     ++nG+l+++g+                                    
  gi|557693500|ref|YP_008796554.1| 552 EYAVWAFRVLDIIVGNLNRKGGLMAraahtNYNGYLYNTGTSGFGEPP----------Rlgppvdrhgyayentley 618
                                       *********************998822222345544444433333333..........1333455555588889999 PP

                                       ...........HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHH...CSSEE CS
                     Molybdopterin 307 ...........ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekale...kldlv 369
                                                     +++ + p +      +lf   +      g+++l +   np+ ++    + ++ l+   k  l+
  gi|557693500|ref|YP_008796554.1| 619 llklkrgenpyP--AKRPWYPLTPEESYTELFAA-IAEGYPYGIGALIMYYANPVLSANYGIKFIEVLKntqKIPLF 692
                                       998888766442..33333333333333445543.333445799999999999999999998888877777799*** PP

                                       EEEESCSSHHHHTSSEEEEBE-CCGS CS
                     Molybdopterin 370 vvldgrltstalyaDiiLPaatwyEk 395
                                       +++   +++t  yaD+i P++t++E 
  gi|557693500|ref|YP_008796554.1| 693 IAITTTINETFMYADYIVPDTTYLET 718
                                       ************************96 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   2.5e-14   1.5e-10      29      82 ..     974    1028 ..     951    1046 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.5e-14
                                        S.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEESSHCC CS
                   Molydop_binding   29 p.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmpfgwwe 82  
                                        p ++v inp+dA++  +k+ + Veve+++G +e+ a+v+++v++Gv+++p+g ++
  gi|557693500|ref|YP_008796554.1|  974 PeNFVIINPRDAEKFRVKNSEFVEVETPYGVLEAAAVVEPTVMEGVIAVPYGLGR 1028
                                        456************************************************9887 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   1.7   8.6e-10   5.1e-06       3      54 ..      51     134 ..      49     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 8.6e-10
                                       EEEEE-SSBTT--EEEEEEETTEEE....EEEE-TTSTTTT............................T---HHHH CS
                    Molybdop_Fe4S4   3 vvktaCpyCgvgCglevhvkdgkiv....kvegdpdhpvne............................grlCvKGr 47 
                                       +v ++C  C v+Cg++v  ++  +v    ++eg+p hp n+                            g+lC++G+
  gi|557693500|ref|YP_008796554.1|  51 YVNSVCLGCNVRCGIRVRIVNRDGVdvieRIEGNPYHPYNRavsydrqvkrytqldyqtpveeamamwhGTLCARGQ 127
                                       799****************99999999998999999999988888888888888888888888************** PP

                                       TCHHCCC CS
                    Molybdop_Fe4S4  48 tllervy 54 
                                        ++ +vy
  gi|557693500|ref|YP_008796554.1| 128 DGIHYVY 134
                                       ***9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 7682.10
//
Query:       gi|557693501|ref|YP_008796555.1|  [L=391]
Description: molybdopterin oxidoreductase, membrane subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-44  151.2  22.8    5.1e-44  151.2  22.8    1.3  2  NrfD          Polysulphide reductase, NrfD
  ------ inclusion threshold ------
      0.044   13.5   2.9      0.083   12.6   2.3    1.7  2  DUF3464       Photosynthesis affected mutant 68


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 !  151.2  22.8   5.6e-48   5.1e-44       5     311 ..      12     336 ..       9     337 .. 0.76
   2 ?   -4.3   0.1       1.2   1.1e+04      92      95 ..     364     367 ..     346     378 .. 0.50

  Alignments for each domain:
  == domain 1  score: 151.2 bits;  conditional E-value: 5.6e-48
                              NrfD   5 hsnsvvWglliavylFligisAgalilaillklfkkkegkslkliirtgallaalavlagllilvldlgrperflkl 81 
                                        +++++Wg+li +y++++g+ Ag++i+++l++ f + ++k+  +i   ++lla  ++l++ l l+ dl++p+r + +
  gi|557693501|ref|YP_008796555.1|  12 LAQPAIWGVLITIYPYITGLVAGSFIISSLAYAFGNTRYKKAGGI---AVLLAFTFLLIAPLPLIADLKQPDRAYEI 85 
                                       67899****************************************...78888899999999***********9999 PP

                              NrfD  82 llyynf..s......Simsw.gvlllslyivvlvlyllvifekdlaakglpalgilaklisla.............. 135
                                       ++++    +      S+m++ g  ll +yi ++v+ ++++ ++dl +k+    g l+ l+++               
  gi|557693501|ref|YP_008796555.1|  86 FTRPHLvaTpstpniSPMAVfG-YLLVGYIILMVVEIIFLWRADLVEKA-NRGGKLKTLWRILalgarevsdtmlkr 160
                                       9866654313445566666414.44556666666555677788887777.434455555555335588899999999 PP

                              NrfD 136 .ervakilaiialilavllgsytgfllsavlsrplwnspllpvlFlasaiasGlavlllasllaarfekesedagll 211
                                        ++v+ +la + ++la+l+++y gfl+++++sr lw +p+++v Fl+sai+sG+a+l+++++ +a   + + d g++
  gi|557693501|ref|YP_008796555.1| 161 dKKVVTVLAFVGIPLAALFHAYVGFLFGSMKSRVLWATPFMAVDFLVSAIVSGIALLIIVYYAFAS-HAGRLDKGVV 236
                                       99****************************************************999999555555.4555566666 PP

                              NrfD 212 kklellvilteagllvi.....lfvglaleggekiealeaalsggfltvlFwlgvvllglaiplllslavprlrenv 283
                                       ++l +l+++t+++ l++     l    a+ +++   +lea l      +  +++  ++g  ipl+l l++p+lr+++
  gi|557693501|ref|YP_008796555.1| 237 YGLAGLLAWTLLVDLALkgadeL--YRAYHRTASWPYLEA-LKFDLMVSTGVIEF-VIGAGIPLVL-LLIPSLRRRM 308
                                       66666666666666664222222..334444444444444.33323323333333.455569***9.********** PP

                              NrfD 284 avvviasilalvgvlllrfllliagqlt 311
                                        vv+++s lal+gvl+ r+ ++i gq++
  gi|557693501|ref|YP_008796555.1| 309 SVVLFSSLLALIGVLAYRWNMVIGGQII 336
                                       **************************75 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1.2
                              NrfD  92 swgv 95 
                                       ++ +
  gi|557693501|ref|YP_008796555.1| 364 AMAI 367
                                       1111 PP

>> DUF3464  Photosynthesis affected mutant 68
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0      0.96   8.6e+03      82     111 ..      83     112 ..      70     113 .. 0.72
   2 ?   12.6   2.3   9.3e-06     0.083      54     129 ..     152     236 ..     148     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.96
                           DUF3464  82 ylivskelvdlptwvvllvslvlFglgvlG 111
                                       y i ++ ++ + +  + +  +++Fg  ++G
  gi|557693501|ref|YP_008796555.1|  83 YEIFTRPHLVATPSTPNISPMAVFGYLLVG 112
                                       566666666677777788888888887777 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.3e-06
                           DUF3464  54 vVskRmirR......valfsGiPlalGlatfv..vfylivskelvdlptwvv.llvslvlFglgvlGlsYGvlSasW 121
                                       +Vs+ m++R      v++f+GiPla+ + + v  +f  ++s+ l+  p ++v +lvs+++ g+++l + Y ++ +  
  gi|557693501|ref|YP_008796555.1| 152 EVSDTMLKRdkkvvtVLAFVGIPLAALFHAYVgfLFGSMKSRVLWATPFMAVdFLVSAIVSGIALLIIVYYAFASHA 228
                                       567777777666666899*******99987651166678999999999887769************99998887765 PP

                           DUF3464 122 deereGsl 129
                                           +G +
  gi|557693501|ref|YP_008796555.1| 229 GRLDKGVV 236
                                       55555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2781.22
//
Query:       gi|557693502|ref|YP_008796556.1|  [L=223]
Description: molybdopterin oxidoreductase, iron-sulfur binding subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-26   92.1   9.4    1.9e-26   92.1   9.4    2.0  2  Fer4_11   4Fe-4S dicluster domain
    4.9e-16   59.1  28.4    3.1e-08   34.1   9.4    3.3  3  Fer4_7    4Fe-4S dicluster domain
    1.6e-13   49.9  32.9    5.7e-05   23.0   2.4    4.4  4  Fer4_2    4Fe-4S binding domain
    2.5e-12   46.1  44.6    7.8e-07   28.7   3.8    6.0  5  Fer4      4Fe-4S binding domain
      3e-12   46.5  27.3    2.1e-06   27.7  10.3    3.4  3  Fer4_10   4Fe-4S dicluster domain
    3.1e-11   43.2  25.5      3e-05   24.1  11.7    3.2  4  Fer4_9    4Fe-4S dicluster domain
    5.2e-11   42.1  45.7    3.1e-05   23.9   3.9    5.4  5  Fer4_6    4Fe-4S binding domain
    1.2e-09   38.4  47.2     0.0031   18.3   5.5    4.6  4  Fer4_3    4Fe-4S binding domain
    8.8e-06   26.6  23.6       0.63   11.0   1.3    4.5  4  Fer4_16   4Fe-4S double cluster binding domain
    9.8e-05   22.8  21.3       0.33   11.5   5.7    4.5  5  Fer4_17   4Fe-4S dicluster domain
    0.00016   21.9  36.3      0.057   13.9   3.4    4.6  4  Fer4_4    4Fe-4S binding domain
    0.00048   20.5  30.8          1    9.9  11.7    4.2  2  Fer4_8    4Fe-4S dicluster domain
    0.00065   19.8  29.6      0.024   14.7   9.1    3.7  2  Fer4_21   4Fe-4S dicluster domain
  ------ inclusion threshold ------
        1.4    9.7  22.9        1.2    9.9   0.6    3.9  3  Fer4_15   4Fe-4S single cluster domain
        3.4    8.6  20.5       0.16   12.9   2.6    3.7  4  Fer4_22   4Fe-4S dicluster domain
          5    6.9  24.6        1.1    9.0   3.5    4.1  4  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl


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 ?   -0.4   0.3       1.2   1.3e+03      68      77 ..      50      59 ..      39      70 .. 0.67
   2 !   92.1   9.4   1.7e-29   1.9e-26       4      99 ..      89     182 ..      87     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.2
                           Fer4_11 68 vekCdmcldr 77
                                      v+kC +c++ 
  gi|557693502|ref|YP_008796556.1| 50 VSKCYGCYAC 59
                                      5666666653 PP

  == domain 2  score: 92.1 bits;  conditional E-value: 1.7e-29
                           Fer4_11   4 lflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrvea 80 
                                       +f+p++C+hC+ep+Cv+++p++a +k + +G Vl+d++ +  ++ ++++ cPy + + n  +g++ kC++c +r+ +
  gi|557693502|ref|YP_008796556.1|  89 VFVPKMCNHCEEPSCVEVCPVNATFKAP-NGEVLVDDNVCI-GCGACIQNCPYGARFFNPVKGVADKCTLCRHRIYE 163
                                       79**************************.9**********7.*********************************** PP

                           Fer4_11  81 Gllpacvescptgalnfgd 99 
                                       G+lpacve+cptga+ fgd
  gi|557693502|ref|YP_008796556.1| 164 GKLPACVEACPTGARIFGD 182
                                       *****************98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   3.1   2.8e-05     0.032      29      49 ..      42      64 ..      14      67 .. 0.67
   2 !   28.2  11.5   1.9e-09   2.1e-06       1      52 []      52     111 ..      52     111 .. 0.92
   3 !   34.1   9.4   2.7e-11   3.1e-08       2      52 .]     127     177 ..     126     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.8e-05
                            Fer4_7 29 ekv..eidpekClgCgaCvavCP 49
                                      +++  +id +kC+gC+aC a+C 
  gi|557693502|ref|YP_008796556.1| 42 KRWamVIDVSKCYGCYACLAACA 64
                                      4442277899************6 PP

  == domain 2  score: 28.2 bits;  conditional E-value: 1.9e-09
                            Fer4_7   1 rCigCgaCvaaC......pvkaieldeeenekgtekveidpekClgCga..CvavCPtga 52 
                                       +C gC aC aaC      p ++++++ e +  +   v+++p +C +C++  Cv+vCP++a
  gi|557693502|ref|YP_008796556.1|  52 KCYGCYACLAACaaennvPIGVFRTWIERYVTPGGGVVFVPKMCNHCEEpsCVEVCPVNA 111
                                       7***********999999999999998888888899************999*******97 PP

  == domain 3  score: 34.1 bits;  conditional E-value: 2.7e-11
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCg.........aCvavCPtga 52 
                                       CigCgaC ++Cp++a+ ++++         +++++kC+ C+         aCv++CPtga
  gi|557693502|ref|YP_008796556.1| 127 CIGCGACIQNCPYGARFFNPV---------KGVADKCTLCRhriyegklpACVEACPTGA 177
                                       ******************997.........6799******65555555558*******98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.5   1.3e-05     0.015       1      21 [.      44      64 ..      44      65 .. 0.91
   2 !   16.6   3.3   5.4e-06    0.0061       3      21 ..      88     108 ..      86     109 .. 0.91
   3 !   23.0   2.4   5.1e-08   5.7e-05       3      22 .]     120     139 ..     118     139 .. 0.91
   4 !   12.6   1.8    0.0001      0.12       7      22 .]     151     175 ..     146     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                            Fer4_2  1 apvvvdtdrCigCgaCvsaCP 21
                                      +++v+d  +C gC aC+ aC 
  gi|557693502|ref|YP_008796556.1| 44 WAMVIDVSKCYGCYACLAACA 64
                                      6789****************6 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 5.4e-06
                            Fer4_2   3 vvvdtdrCigCg..aCvsaCP 21 
                                       vv+++ +C++C+  +Cv +CP
  gi|557693502|ref|YP_008796556.1|  88 VVFVPKMCNHCEepSCVEVCP 108
                                       6899*******999******* PP

  == domain 3  score: 23.0 bits;  conditional E-value: 5.1e-08
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       v vd + CigCgaC+++CP+
  gi|557693502|ref|YP_008796556.1| 120 VLVDDNVCIGCGACIQNCPY 139
                                       67999**************5 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.0001
                            Fer4_2   7 tdrCigCg.........aCvsaCPa 22 
                                       +d+C+ C+         aCv aCP+
  gi|557693502|ref|YP_008796556.1| 151 ADKCTLCRhriyegklpACVEACPT 175
                                       79*****8888889**********7 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   4.6   5.5e-05     0.062       2      18 ..      47      63 ..      46      63 .. 0.95
   2 !    7.7   6.8     0.003       3.3       5      22 ..      92     111 ..      88     112 .. 0.70
   3 !   28.7   3.8     7e-10   7.8e-07       3      22 ..     122     141 ..     120     143 .. 0.91
   4 ?    2.4   0.2      0.13   1.5e+02       5      11 ..     151     157 ..     148     158 .. 0.87
   5 !   13.4   1.0   4.5e-05      0.05      13      22 ..     168     177 ..     168     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.5e-05
                                      EEETTTSSS-THHHHHS CS
                              Fer4  2 videekCigCGaCvevC 18
                                      vid +kC gC aC  +C
  gi|557693502|ref|YP_008796556.1| 47 VIDVSKCYGCYACLAAC 63
                                      8**************** PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.003
                                       TTTSSS-T..HHHHHSTTTE CS
                              Fer4   5 eekCigCG..aCvevCPvgA 22 
                                       + +C +C    CvevCPv+A
  gi|557693502|ref|YP_008796556.1|  92 PKMCNHCEepSCVEVCPVNA 111
                                       55666666335********9 PP

  == domain 3  score: 28.7 bits;  conditional E-value: 7e-10
                                       EETTTSSS-THHHHHSTTTE CS
                              Fer4   3 ideekCigCGaCvevCPvgA 22 
                                       +d + CigCGaC++ CP+gA
  gi|557693502|ref|YP_008796556.1| 122 VDDNVCIGCGACIQNCPYGA 141
                                       8999***************9 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.13
                                       TTTSSS- CS
                              Fer4   5 eekCigC 11 
                                        +kC+ C
  gi|557693502|ref|YP_008796556.1| 151 ADKCTLC 157
                                       69***** PP

  == domain 5  score: 13.4 bits;  conditional E-value: 4.5e-05
                                       HHHHHSTTTE CS
                              Fer4  13 aCvevCPvgA 22 
                                       aCve+CP+gA
  gi|557693502|ref|YP_008796556.1| 168 ACVEACPTGA 177
                                       7********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 !   16.2   0.3   7.8e-06    0.0087       2      19 ..      46      63 ..      44      81 .. 0.83
   2 !   24.8  14.1   1.6e-08   1.7e-05       3      56 .]      89     138 ..      87     138 .. 0.94
   3 !   27.7  10.3   1.9e-09   2.1e-06       2      56 .]     120     174 ..     119     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.8e-06
                           Fer4_10  2 vvidddtCirCgkCvkaC 19
                                      +vid ++C +C +C +aC
  gi|557693502|ref|YP_008796556.1| 46 MVIDVSKCYGCYACLAAC 63
                                      789999999999999999 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.6e-08
                           Fer4_10   3 vidddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       v+ ++ C +C+   Cv++CP+      +  ++ ++++v ++   C+gcgaC++ CP
  gi|557693502|ref|YP_008796556.1|  89 VFVPKMCNHCEepSCVEVCPV------NATFKAPNGEVLVDDNVCIGCGACIQNCP 138
                                       677899*****999*******......99**************************9 PP

  == domain 3  score: 27.7 bits;  conditional E-value: 1.9e-09
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgc......g...aCveaCP 56 
                                       v +dd+ Ci+Cg+C + CP+          a   ++v+++ +kCt c      g   aCveaCP
  gi|557693502|ref|YP_008796556.1| 120 VLVDDNVCIGCGACIQNCPY---------GARFFNPVKGVADKCTLCrhriyeGklpACVEACP 174
                                       5689****************.........66666788888999****6666552677******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 !   12.5   3.2   0.00011      0.12      25      47 ..      38      64 ..      15      67 .. 0.69
   2 !   21.6  10.2   1.6e-07   0.00018       1      50 [.      52     111 ..      52     112 .. 0.93
   3 !   24.1  11.7   2.7e-08     3e-05       2      50 ..      95     141 ..      94     142 .. 0.87
   4 !   22.5   9.4   8.2e-08   9.2e-05       2      50 ..     127     177 ..     126     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                            Fer4_9 25 karlraase....eaCigCgaCveaCp 47
                                      + + +++ +    ++C+gC aC++aC 
  gi|557693502|ref|YP_008796556.1| 38 ESSGKRWAMvidvSKCYGCYACLAACA 64
                                      333333333666678999999999997 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.6e-07
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase........eaCigCga..CveaCpkga 50 
                                       kC+gC aC +aC a+ +v+  + r++  r            + C +C++  Cve+Cp +a
  gi|557693502|ref|YP_008796556.1|  52 KCYGCYACLAACAAENNVPIGVFRTWIERYVTPgggvvfvpKMCNHCEEpsCVEVCPVNA 111
                                       7******************9999999987777799******99*****999******985 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 2.7e-08
                            Fer4_9   2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50 
                                       C+ C +  Cve+Cp +++ +  +++    ++     CigCgaC++ Cp ga
  gi|557693502|ref|YP_008796556.1|  95 CNHCEEpsCVEVCPVNATFKAPNGEVLVDDN----VCIGCGACIQNCPYGA 141
                                       ****9666*********99988888888765....4************985 PP

  == domain 4  score: 22.5 bits;  conditional E-value: 8.2e-08
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCga.........CveaCpkga 50 
                                       C+gCgaC++ Cp+g+     +++ a        +C+ C+          CveaCp+ga
  gi|557693502|ref|YP_008796556.1| 127 CIGCGACIQNCPYGARFFNPVKGVAD-------KCTLCRHriyegklpaCVEACPTGA 177
                                       ******************99999999.......5*********************985 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2       2.9   3.3e+03      16      23 ..      14      21 ..      14      21 .. 0.85
   2 !   15.4   2.8   1.3e-05     0.014       2      21 ..      46      65 ..      45      69 .. 0.90
   3 !   17.0   4.3   4.1e-06    0.0046       2      23 ..      88     111 ..      88     112 .. 0.92
   4 !   23.9   3.9   2.8e-08   3.1e-05       2      23 ..     120     141 ..     119     141 .. 0.94
   5 !    6.9   5.8    0.0062         7       7      23 ..     152     177 ..     150     177 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.9
                            Fer4_6 16 vrvCPega 23
                                      v+vC +ga
  gi|557693502|ref|YP_008796556.1| 14 VSVCAAGA 21
                                      689*9997 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 1.3e-05
                            Fer4_6  2 veidpdkCigCgdCvrvCPe 21
                                      ++id +kC gC++C ++C +
  gi|557693502|ref|YP_008796556.1| 46 MVIDVSKCYGCYACLAACAA 65
                                      589***************86 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 4.1e-06
                            Fer4_6   2 veidpdkCigCgd..CvrvCPega 23 
                                       v++ p  C++C++  Cv vCP +a
  gi|557693502|ref|YP_008796556.1|  88 VVFVPKMCNHCEEpsCVEVCPVNA 111
                                       78999******999*******998 PP

  == domain 4  score: 23.9 bits;  conditional E-value: 2.8e-08
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       v +d++ CigCg+C+ +CP+ga
  gi|557693502|ref|YP_008796556.1| 120 VLVDDNVCIGCGACIQNCPYGA 141
                                       679*****************98 PP

  == domain 5  score: 6.9 bits;  conditional E-value: 0.0062
                            Fer4_6   7 dkCigCgd.........CvrvCPega 23 
                                       dkC+ C+          Cv +CP+ga
  gi|557693502|ref|YP_008796556.1| 152 DKCTLCRHriyegklpaCVEACPTGA 177
                                       89999999999999999*******98 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   4.6    0.0076       8.5       1      11 [.      53      63 ..      53      66 .. 0.96
   2 !   17.9   5.8     4e-06    0.0044       1      15 []      95     111 ..      95     111 .. 0.92
   3 !   18.3   5.5   2.8e-06    0.0031       1      15 []     127     141 ..     127     141 .. 0.99
   4 !   18.1   2.3   3.4e-06    0.0038       1      15 []     154     177 ..     154     177 .. 0.95

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0076
                            Fer4_3  1 CtgCgaCvevC 11
                                      C gC+aC+ +C
  gi|557693502|ref|YP_008796556.1| 53 CYGCYACLAAC 63
                                      99********* PP

  == domain 2  score: 17.9 bits;  conditional E-value: 4e-06
                            Fer4_3   1 CtgCg..aCvevCPvgA 15 
                                       C++C+   CvevCPv+A
  gi|557693502|ref|YP_008796556.1|  95 CNHCEepSCVEVCPVNA 111
                                       ****9777*******99 PP

  == domain 3  score: 18.3 bits;  conditional E-value: 2.8e-06
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCgaC + CP+gA
  gi|557693502|ref|YP_008796556.1| 127 CIGCGACIQNCPYGA 141
                                       **************9 PP

  == domain 4  score: 18.1 bits;  conditional E-value: 3.4e-06
                            Fer4_3   1 CtgCg.........aCvevCPvgA 15 
                                       Ct C+         aCve+CP+gA
  gi|557693502|ref|YP_008796556.1| 154 CTLCRhriyegklpACVEACPTGA 177
                                       ****9899999*999********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 !    7.1   0.9    0.0093        10      53      65 ..      52      64 ..      36      67 .. 0.69
   2 !   11.0   1.3   0.00056      0.63       2      17 ..      95     112 ..      94     125 .. 0.81
   3 !   10.3   6.0   0.00095       1.1       2      16 ..     127     141 ..     126     160 .. 0.84
   4 !    8.1   0.0    0.0046       5.2       7      16 ..     168     177 ..     164     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0093
                           Fer4_16 53 aitgCdiCqdvCP 65
                                      +++gC +C ++C 
  gi|557693502|ref|YP_008796556.1| 52 KCYGCYACLAACA 64
                                      4555555555554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00056
                           Fer4_16   2 CgtCgk..CaevCPtnai 17 
                                       C  C++  C+evCP+na 
  gi|557693502|ref|YP_008796556.1|  95 CNHCEEpsCVEVCPVNAT 112
                                       99999888*******995 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00095
                           Fer4_16   2 CgtCgkCaevCPtna 16 
                                       C++Cg+C++ CP +a
  gi|557693502|ref|YP_008796556.1| 127 CIGCGACIQNCPYGA 141
                                       9***********998 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0046
                           Fer4_16   7 kCaevCPtna 16 
                                       +C+e+CPt+a
  gi|557693502|ref|YP_008796556.1| 168 ACVEACPTGA 177
                                       7*******99 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2    0.0019       2.1      44      57 ..      51      64 ..      31      77 .. 0.73
   2 !    7.8   0.9    0.0042       4.7       2      18 ..      95     113 ..      94     123 .. 0.80
   3 !   11.5   5.7   0.00029      0.33       2      25 ..     127     150 ..     126     165 .. 0.76
   4 ?    2.0   0.7      0.28   3.2e+02      51      58 ..     168     175 ..     140     178 .. 0.60
   5 ?    2.6   1.0      0.18     2e+02       7      17 ..     168     178 ..     153     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                           Fer4_17 44 slCieCgeCerkCP 57
                                      s+C +C  C ++C 
  gi|557693502|ref|YP_008796556.1| 51 SKCYGCYACLAACA 64
                                      55666666666664 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0042
                           Fer4_17   2 CiqCgy..ClpeCpsyeay 18 
                                       C++C+   C+++Cp ++  
  gi|557693502|ref|YP_008796556.1|  95 CNHCEEpsCVEVCPVNATF 113
                                       99**9777*****998765 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00029
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkl 25 
                                       Ci+Cg+C+++Cp++++  n  k +
  gi|557693502|ref|YP_008796556.1| 127 CIGCGACIQNCPYGARFFNPVKGV 150
                                       9***********998866655544 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.28
                           Fer4_17  51 eCerkCPq 58 
                                        C+++CP 
  gi|557693502|ref|YP_008796556.1| 168 ACVEACPT 175
                                       35555554 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.18
                           Fer4_17   7 yClpeCpsyea 17 
                                       +C+++Cp++++
  gi|557693502|ref|YP_008796556.1| 168 ACVEACPTGAR 178
                                       38888887766 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   3.6     0.026        29       3      14 ..      52      63 ..      51      66 .. 0.90
   2 !   11.2   3.6   0.00039      0.44       2      17 .]      93     110 ..      92     111 .. 0.86
   3 !   13.9   3.4   5.1e-05     0.057       3      17 .]     126     140 ..     124     140 .. 0.90
   4 !    8.5   2.3    0.0029       3.3       2      17 .]     152     176 ..     151     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                            Fer4_4  3 rCigCgsCvaaC 14
                                      +C gC +C aaC
  gi|557693502|ref|YP_008796556.1| 52 KCYGCYACLAAC 63
                                      799********* PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00039
                            Fer4_4   2 erCigCg..sCvaaCPqg 17 
                                       + C++C   sCv +CP++
  gi|557693502|ref|YP_008796556.1|  93 KMCNHCEepSCVEVCPVN 110
                                       78*****777******75 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 5.1e-05
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                        CigCg+C+  CP+g
  gi|557693502|ref|YP_008796556.1| 126 VCIGCGACIQNCPYG 140
                                       6************86 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0029
                            Fer4_4   2 erCigCg.........sCvaaCPqg 17 
                                       ++C+ C+         +Cv aCP+g
  gi|557693502|ref|YP_008796556.1| 152 DKCTLCRhriyegklpACVEACPTG 176
                                       89999998777777777******86 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9  11.7   0.00089         1       2      64 ..      50     110 ..      49     111 .. 0.82
   2 ?    6.5  11.3      0.01        12       5      22 ..     127     144 ..     124     179 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00089
                            Fer4_8   2 lekCieCgaCqsaCp........vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcga..CtevCpvg 64 
                                       ++kC +C aC +aC         v+r++ ++  ++ g++        v       + C++c++  C+evCpv+
  gi|557693502|ref|YP_008796556.1|  50 VSKCYGCYACLAACAaennvpigVFRTWIERYVTPGGGVVF------V------PKMCNHCEEpsCVEVCPVN 110
                                       79************666666677999999999999999666......3......567****9888******97 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.01
                            Fer4_8   5 CieCgaCqsaCpvlrrtk 22 
                                       Ci+CgaC ++Cp   r+ 
  gi|557693502|ref|YP_008796556.1| 127 CIGCGACIQNCPYGARFF 144
                                       ************766653 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   9.1   2.2e-05     0.024       2      54 ..      47     110 ..      45     115 .. 0.77
   2 !    7.9  12.5     0.003       3.3       3      45 ..     122     158 ..     120     179 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                           Fer4_21   2 ridedkCigCgkCliaCedtshqai.........eidaktvlkvvedeCvGCn..lCssvCPve 54 
                                       +id +kC gC  Cl aC  +    i          +++   +  v + C  C+   C++vCPv+
  gi|557693502|ref|YP_008796556.1|  47 VIDVSKCYGCYACLAACAAENNVPIgvfrtwierYVTPGGGVVFVPKMCNHCEepSCVEVCPVN 110
                                       6999**************8877777777554443344444557789******9556******95 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.003
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCn 45 
                                       +d++ CigCg C++ C+ +   a  +++   +k v+d+C+ C 
  gi|557693502|ref|YP_008796556.1| 122 VDDNVCIGCGACIQNCPYG---ARFFNP---VKGVADKCTLCR 158
                                       8999************953...333332...233566666664 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 ?    9.9   0.6    0.0011       1.2       2      18 ..      47      63 ..      46      73 .. 0.89
   2 ?   -1.1   0.3       2.9   3.2e+03      56      63 ..     104     111 ..     101     113 .. 0.79
   3 ?    6.6   9.8     0.011        13       1      19 [.     120     138 ..     120     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                           Fer4_15  2 vvDrdaCigcglCvaea 18
                                      v+D ++C gc +C+a++
  gi|557693502|ref|YP_008796556.1| 47 VIDVSKCYGCYACLAAC 63
                                      79*************99 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.9
                           Fer4_15  56 araCPvdA 63 
                                       +++CPv A
  gi|557693502|ref|YP_008796556.1| 104 VEVCPVNA 111
                                       57899987 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       V vD + Cigcg+C++++p
  gi|557693502|ref|YP_008796556.1| 120 VLVDDNVCIGCGACIQNCP 138
                                       789***************7 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   1.0    0.0098        11      72      94 ..      43      65 ..      36      67 .. 0.84
   2 ?   -0.7   1.4       2.4   2.7e+03       2      16 ..      95     111 ..      93     120 .. 0.64
   3 ?   12.9   2.6   0.00014      0.16      77      94 ..     122     139 ..     109     141 .. 0.83
   4 ?   -1.4   0.0         4   4.5e+03       8      15 ..     169     176 ..     166     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0098
                           Fer4_22 72 efkekfgesgCvGCgRCieacpv 94
                                       ++  ++ s+C GC  C +ac +
  gi|557693502|ref|YP_008796556.1| 43 RWAMVIDVSKCYGCYACLAACAA 65
                                      5667789999***********86 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.4
                           Fer4_22   2 ClsCg..aCtlvCptCs 16 
                                       C +C   +C  vCp   
  gi|557693502|ref|YP_008796556.1|  95 CNHCEepSCVEVCPVNA 111
                                       55665225777777655 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00014
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                       ++ ++C+GCg Ci++cp 
  gi|557693502|ref|YP_008796556.1| 122 VDDNVCIGCGACIQNCPY 139
                                       57899***********96 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 4
                           Fer4_22   8 CtlvCptC 15 
                                       C  +Cpt 
  gi|557693502|ref|YP_008796556.1| 169 CVEACPTG 176
                                       77777774 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 ?    4.7   0.1     0.022        25      18      43 ..      47      70 ..      32      83 .. 0.80
   2 ?    9.0   3.5     0.001       1.1      23      41 ..      94     112 ..      91     117 .. 0.88
   3 ?    1.7   2.4      0.19   2.2e+02      20      41 ..     123     142 ..     112     154 .. 0.77
   4 ?    4.1   1.4     0.033        37      21      42 ..     151     179 ..     145     181 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.022
                                      HHHHTT----TT-HHHHCSTT---HH CS
                           Fer4_20 18 leeAsRClqCkkapcvkgCPveidip 43
                                      + + s+C+ C    c ++C +e+++p
  gi|557693502|ref|YP_008796556.1| 47 VIDVSKCYGC--YACLAACAAENNVP 70
                                      5567899999..68999999999998 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.001
                                       T----TT-HHHHCSTT--- CS
                           Fer4_20  23 RClqCkkapcvkgCPveid 41 
                                        C +C+++ cv+ CPv+ +
  gi|557693502|ref|YP_008796556.1|  94 MCNHCEEPSCVEVCPVNAT 112
                                       5***************976 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.19
                                       HHTT----TT-HHHHCSTT--- CS
                           Fer4_20  20 eAsRClqCkkapcvkgCPveid 41 
                                       + + C+ C    c+++CP   +
  gi|557693502|ref|YP_008796556.1| 123 DDNVCIGC--GACIQNCPYGAR 142
                                       55679999..78******8765 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.033
                                       HTT----.......TT-HHHHCSTT---H CS
                           Fer4_20  21 AsRClqC.......kkapcvkgCPveidi 42 
                                       A++C  C       k + cv++CP+  +i
  gi|557693502|ref|YP_008796556.1| 151 ADKCTLCrhriyegKLPACVEACPTGARI 179
                                       667777722222224577******99877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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):              16  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1657.16
//
Query:       gi|557693503|ref|YP_008796557.1|  [L=142]
Description: small subunit ribosomal protein S12 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-45  151.2   0.2    9.7e-45  150.9   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 !  150.9   0.2   5.4e-49   9.7e-45       4     114 .]      30     141 ..      27     141 .. 0.97

  Alignments for each domain:
  == domain 1  score: 150.9 bits;  conditional E-value: 5.4e-49
                                       -----S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--.. CS
                   Ribosom_S12_S23   4 lrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrk 80 
                                       l++k+k+d+legap++rG+v++kv++e+++PnsA+Rk+vrv+Likn+k +taf+pg+galn +dEhdev+v+Gi+++
  gi|557693503|ref|YP_008796557.1|  30 LNLKEKTDPLEGAPMARGIVIQKVGIESRQPNSAVRKCVRVQLIKNSKVITAFLPGDGALNVVDEHDEVIVEGIGGS 106
                                       6789***********************************************************************99 PP

                                       ....BTTSTTEEEEBETS---TSSSTTTTT----T CS
                   Ribosom_S12_S23  81 .gkavkDlpGvrykvvkvagvslkalskykkekpk 114
                                        gk+++DlpGvrykv  v+g  l  l+ ++ +kpk
  gi|557693503|ref|YP_008796557.1| 107 mGKSMGDLPGVRYKVTMVNGAPLDLLVTGEVKKPK 141
                                       9**************************99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 00:00:00.41
# Mc/sec: 1033.64
//
Query:       gi|557693504|ref|YP_008796558.1|  [L=347]
Description: molybdenum cofactor biosynthesis protein A [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-33  114.9   0.0    3.6e-33  114.2   0.0    1.3  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    1.1e-30  107.2   0.1    2.1e-30  106.3   0.1    1.4  1  Radical_SAM  Radical SAM superfamily
    6.1e-07   29.8   0.0      1e-06   29.1   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain
    3.5e-06   27.1   0.0    6.9e-06   26.2   0.0    1.5  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 !  114.2   0.0     8e-37   3.6e-33       2     123 ..     201     323 ..     200     328 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 8e-37
                                       EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SST-SSEEEEETTT-.-EEEEE-TTTS--GGG--E CS
                       Mob_synth_C   2 elrfIElmpvgegeewrekkvvsadeilerieerlalleakketkgpakrykikdgk.geiglIapvsepFCasCnR 77 
                                       ++rfIE+mp++  + w+ +++v+  ei+e+i+e++ l e ++e++++a +y+++dg  g++ +I+++++pFC +C+R
  gi|557693504|ref|YP_008796558.1| 201 SIRFIEYMPFDGRHLWDVSRLVPGMEIIEKIREKYGLVELPREPGSTAVVYEFADGAdGNVAVITSMTKPFCGDCDR 277
                                       69***************************************************99888******************* PP

                                       EEE-TTSEEESSSS-SS-EEHHHHHHTT--HHHHHHHHHHHHHT-- CS
                       Mob_synth_C  78 lRltadGklktCLfaeeeidlrdllregaseeeLkelikealarkk 123
                                       +RltadGk+ +CLf+++e d++ llr gas+ee+++ i+e+ ++k 
  gi|557693504|ref|YP_008796558.1| 278 IRLTADGKIVPCLFSRDEYDVKGLLRGGASDEEIAAFIRESFRKKF 323
                                       ****************************************999986 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.3   0.1   4.6e-34   2.1e-30       2     166 ..      34     194 ..      33     195 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.3 bits;  conditional E-value: 4.6e-34
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       +vt  Cn+rC fC   +   + ++ ++l+ ee ++ +++l + ++v  v l+ggepl+++d+++ ++ ++ +     
  gi|557693504|ref|YP_008796558.1|  34 SVTDRCNFRCDFCMPLHP-VWIPHKEILTYEEMARVIRIL-VGMNVTKVRLSGGEPLMRRDLEKGVKLISSIP-GVE 107
                                       6899************96.9********************.9******************************6.999 PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                       +i+++tng+ + eek++ l+e+g+  v+++l+++ +e++ k+++r++ f++vl++l+ ++++g+ ++++++v+ +G 
  gi|557693504|ref|YP_008796558.1| 108 TISMTTNGYFL-EEKAAQLKEAGLQSVTVSLHSLKPERFEKIVGRKDVFSKVLDGLREAKKVGLQPIKINCVVTRGC 183
                                       99*********.***************************************************************** PP

                                       SHHHHHHHHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 156 ndeeleellel 166
                                       nd+e+ +++el
  gi|557693504|ref|YP_008796558.1| 184 NDDEILDFVEL 194
                                       *****999875 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 !   29.1   0.0   2.3e-10     1e-06      12     111 ..      36     133 ..      21     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.3e-10
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdi 88 
                                       + +Cn++C++C+        +++  t e ++++i+ l   +++++ l+GGEPl++   e+ ++l+ ++         
  gi|557693504|ref|YP_008796558.1|  36 TDRCNFRCDFCMPLHPVWIPHKEILTYEEMARVIRILVGMNVTKVRLSGGEPLMRRDLEKGVKLISSIPGVET--IS 110
                                       578*********98766666667777788889999999****************9999999999999988776..78 PP

                           Fer4_12  89 wlytgytleelskkekeellkei 111
                                       + ++gy lee  ++ ke  l+ +
  gi|557693504|ref|YP_008796558.1| 111 MTTNGYFLEEKAAQLKEAGLQSV 133
                                       99*******99887555555555 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 !   26.2   0.0   1.5e-09   6.9e-06       5      94 ..      36     120 ..      33     140 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.5e-09
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       + +Cn+ C +C   +      +++ t+e++ ++++ l   ++   ++ l+GGePL+  + ++ +kl++ +       
  gi|557693504|ref|YP_008796558.1|  36 TDRCNFRCDFCMPLHPVWIPHKEILTYEEMARVIRILVGMNV--TKVRLSGGEPLMRRDLEKGVKLISSIPGVE--- 107
                                       679*********8888888889999999999***87777777..679*********************999877... PP

                           Fer4_14  82 kiwletngtleie 94 
                                        i + tng +  e
  gi|557693504|ref|YP_008796558.1| 108 TISMTTNGYFLEE 120
                                       8999999877633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2675.71
//
Query:       gi|557693505|ref|YP_008796559.1|  [L=449]
Description: cytochrome b/b6 domain-containing protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-32  112.7  11.3    1.8e-32  112.7  11.3    2.6  3  Cytochrome_B     Cytochrome b/b6/petB
    8.6e-27   94.2   9.7    8.6e-27   94.2   9.7    2.9  4  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
      9e-07   29.1   2.0      9e-07   29.1   2.0    3.1  5  Cytochrom_B_C    Cytochrome b(C-terminal)/b6/petD
    1.9e-05   25.1   1.4    1.9e-05   25.1   1.4    4.3  6  DUF4405          Domain of unknown function (DUF4405)
  ------ inclusion threshold ------
      0.049   13.5   0.2       0.21   11.5   0.2    2.1  1  PT-TG            Pre-toxin TG


Domain annotation for each model (and alignments):
>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7  11.3     5e-36   1.8e-32      13     182 ..      46     214 ..      37     217 .. 0.96
   2 ?   -1.6   0.4      0.56     2e+03     115     134 ..     298     317 ..     267     363 .. 0.56
   3 ?    0.2   0.2      0.16   5.7e+02     126     143 ..     392     409 ..     384     441 .. 0.72

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 5e-36
                      Cytochrome_B  13 iynlGsllllvlvlqiltGvalafyytptvtlaflsvqyilrdvnfGwlirsvhangasllflllylhifrglllgg 89 
                                       +  lG+l+ +v++l  +tG +l +yy+p+vt+a+ sv+ i   + fG++ir++h  ++  ++ l + h+f  ++ g 
  gi|557693505|ref|YP_008796559.1|  46 FGYLGTLTAIVFLLLGVTGALLMLYYRPDVTQAYNSVKQIQDGIAFGFFIRNIHYHASNAMVFLAIAHLFYQYFSGR 122
                                       5569************************************************************************* PP

                      Cytochrome_B  90 lkktrelvWviGvillllvivtafiGyvLpwdqmsyWavtvitnllsaiPviGstlvellwgsvsvddatLtrffsl 166
                                       +k + e +Wv+G+il  +++++af+Gy L  +q +  av++  +l ++ P++G +l  ll g+   d   + rf++l
  gi|557693505|ref|YP_008796559.1| 123 FKVKNEVIWVTGIILGTVTVIEAFTGYDLILNQRAMLAVNIAVGLTNSAPFLGAQLAPLLLGGGLYD--LIIRFYAL 197
                                       ***************************************************************9887..478***** PP

                      Cytochrome_B 167 h.fllPflllillllhl 182
                                       h f+lP+++l+l+l+h+
  gi|557693505|ref|YP_008796559.1| 198 HvFILPMVMLLLVLVHF 214
                                       ****************8 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.56
                      Cytochrome_B 115 GyvLpwdqmsyWavtvitnl 134
                                          L w+   ++++  i++l
  gi|557693505|ref|YP_008796559.1| 298 SKKLSWKERPFFTAAGISSL 317
                                       33344444444443333332 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.16
                      Cytochrome_B 126 WavtvitnllsaiPviGs 143
                                       Wav++i +ll++i ++  
  gi|557693505|ref|YP_008796559.1| 392 WAVRIIMGLLAVIGILSL 409
                                       888888888888877754 PP

>> 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 ?   -3.1   0.1       1.9     7e+03      32      48 ..      51      67 ..      48      85 .. 0.65
   2 !   94.2   9.7   2.4e-30   8.6e-27       1     113 [.     104     214 ..     104     217 .. 0.98
   3 ?   -3.3   0.2       2.2   7.9e+03      84     102 ..     275     293 ..     256     295 .. 0.59
   4 ?   -0.9   1.0       0.4   1.4e+03     100     125 ..     346     371 ..     311     419 .. 0.47

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.9
                   Cytochrom_B_N_2 32 vllllltllegflGysL 48
                                       l  ++ ll g++G +L
  gi|557693505|ref|YP_008796559.1| 51 TLTAIVFLLLGVTGALL 67
                                      55555666666666555 PP

  == domain 2  score: 94.2 bits;  conditional E-value: 2.4e-30
                   Cytochrom_B_N_2   1 yimiiliyvHmlrvfftGaYkkpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwlve 77 
                                       ++m+ l+++H++ ++f G +k + e+ W++G++l ++t++e+f+Gy L+ ++ ++ a++++ g+++s P++g  l+ 
  gi|557693505|ref|YP_008796559.1| 104 NAMVFLAIAHLFYQYFSGRFKVKNEVIWVTGIILGTVTVIEAFTGYDLILNQRAMLAVNIAVGLTNSAPFLGAQLAP 180
                                       58*************************************************************************** PP

                   Cytochrom_B_N_2  78 llfGgelpgeallsrlyalHilllpalllalivahl 113
                                       ll+Gg l+  +l+ r+yalH+++lp+++l+l+++h+
  gi|557693505|ref|YP_008796559.1| 181 LLLGGGLY--DLIIRFYALHVFILPMVMLLLVLVHF 214
                                       *******9..8899*********************8 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.2
                   Cytochrom_B_N_2  84 lpgeallsrlyalHilllp 102
                                       +++ a l+ l++l +ll+p
  gi|557693505|ref|YP_008796559.1| 275 FTAGAFLPLLFILFFLLIP 293
                                       4445555555665555555 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.4
                   Cytochrom_B_N_2 100 llpalllalivahlllvekkgqtpsr 125
                                       ++  ll+ l++a +++  k    p+ 
  gi|557693505|ref|YP_008796559.1| 346 IFYPLLAFLVAASFIISYKFIAPPPS 371
                                       44444445555555444433333332 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 ?   -1.3   0.0      0.75   2.7e+03      70      84 ..      51      65 ..      22      86 .. 0.64
   2 ?   -3.9   0.2         5   1.8e+04      72      80 ..     200     208 ..     191     217 .. 0.49
   3 !   29.1   2.0   2.5e-10     9e-07      12      85 ..     256     329 ..     250     348 .. 0.78
   4 ?   -2.4   0.1       1.7     6e+03      73      84 ..     395     406 ..     351     430 .. 0.61
   5 ?   -2.4   0.2       1.7     6e+03      30      38 ..     425     433 ..     397     441 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.75
                                      HHHHHHHHHHHHHHT CS
                     Cytochrom_B_C 70 allvvsfvvLgylGv 84
                                      +l ++ f++Lg+ G+
  gi|557693505|ref|YP_008796559.1| 51 TLTAIVFLLLGVTGA 65
                                      445555666666655 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 5
                                       HHHHHHHHH CS
                     Cytochrom_B_C  72 lvvsfvvLg 80 
                                       +++ +v+L 
  gi|557693505|ref|YP_008796559.1| 200 FILPMVMLL 208
                                       333333332 PP

  == domain 3  score: 29.1 bits;  conditional E-value: 2.5e-10
                                       ---GGGHHHHHHHHCSSSHH.HHHHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHTS CS
                     Cytochrom_B_C  12 aPeWYflpfYaiLraipakl.lGvvamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgylGvq 85 
                                       +PeWY++ +Ya Lr+  +++ +G  + +  i+ ++l+p++drsk  s + r p+++++ +  +v ++v ++ G  
  gi|557693505|ref|YP_008796559.1| 256 VPEWYLTGIYAFLRTGLERFtAGAFLPLLFILFFLLIPFVDRSKKLSWKER-PFFTAAGISSLVLIAVTTVWGFY 329
                                       7**************765552788888999999999***************.77777777666666777777764 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHT CS
                     Cytochrom_B_C  73 vvsfvvLgylGv 84 
                                        + + +L+++G+
  gi|557693505|ref|YP_008796559.1| 395 RIIMGLLAVIGI 406
                                       333333444443 PP

  == domain 5  score: -2.4 bits;  conditional E-value: 1.7
                                       HHHHHHHHH CS
                     Cytochrom_B_C  30 kllGvvamg 38 
                                         lGvv+m+
  gi|557693505|ref|YP_008796559.1| 425 FNLGVVVML 433
                                       345666663 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   1.4   5.4e-09   1.9e-05       4      64 ..      51     116 ..      48     118 .. 0.91
   2 ?   -3.5   0.2       4.4   1.6e+04      15      21 ..     132     138 ..     129     149 .. 0.70
   3 ?   -2.4   2.3       2.1   7.6e+03      50      62 ..     202     214 ..     195     215 .. 0.81
   4 ?   -4.8   1.2         5   1.8e+04       5      13 ..     283     291 ..     282     292 .. 0.65
   5 ?   -3.0   0.4       3.2   1.1e+04      10      24 ..     309     323 ..     308     331 .. 0.66
   6 ?   -1.9   3.3       1.4   5.1e+03      51      65 ..     429     443 ..     393     444 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.4e-09
                           DUF4405   4 lllllsflvlaiSGillsfavlpsgrgaywa...........flglskhqwrdiHeilgllflilvvlHlgl 64 
                                       +l++++fl+l ++G ll   + p++ +ay+            f      ++r+iH  ++ ++++l++ Hl++
  gi|557693505|ref|YP_008796559.1|  51 TLTAIVFLLLGVTGALLMLYYRPDVTQAYNSvkqiqdgiafgF------FIRNIHYHASNAMVFLAIAHLFY 116
                                       7899*******************************88888663......7********************87 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.4
                           DUF4405  15 iSGills 21 
                                       ++Gi+l 
  gi|557693505|ref|YP_008796559.1| 132 VTGIILG 138
                                       7888875 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.1
                           DUF4405  50 lgllflilvvlHl 62 
                                       l +++l+lv++H+
  gi|557693505|ref|YP_008796559.1| 202 LPMVMLLLVLVHF 214
                                       5579999999996 PP

  == domain 4  score: -4.8 bits;  conditional E-value: 5
                           DUF4405   5 llllsflvl 13 
                                       ll+++f++l
  gi|557693505|ref|YP_008796559.1| 283 LLFILFFLL 291
                                       677777765 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 3.2
                           DUF4405  10 flvlaiSGillsfav 24 
                                       f ++ iS+++l +++
  gi|557693505|ref|YP_008796559.1| 309 FTAAGISSLVLIAVT 323
                                       566778888887664 PP

  == domain 6  score: -1.9 bits;  conditional E-value: 1.4
                           DUF4405  51 gllflilvvlHlglh 65 
                                        +++l+ ++ H++ h
  gi|557693505|ref|YP_008796559.1| 429 VVVMLFGAIAHVYRH 443
                                       678999999999977 PP

>> PT-TG  Pre-toxin TG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   5.7e-05      0.21      12      51 ..     133     166 ..     128     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.7e-05
                             PT-TG  12 vpevggvkdaieaitGrDpiTGeklsdwdRllaavalvpg 51 
                                       + +++g  ++iea+tG+D+i    l+  +R++ av++++g
  gi|557693505|ref|YP_008796559.1| 133 TGIILGTVTVIEAFTGYDLI----LN--QRAMLAVNIAVG 166
                                       678899999*********98....55..677777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); 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:                         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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3365.58
//
Query:       gi|557693506|ref|YP_008796560.1|  [L=315]
Description: aspartate carbamoyltransferase catalytic subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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  140.8   0.0    6.1e-41  139.9   0.0    1.5  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    2.8e-28   99.0   0.0      2e-27   96.2   0.0    2.0  2  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 !  139.9   0.0   6.8e-45   6.1e-41       1     148 []       6     149 ..       6     149 .. 0.94

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 6.8e-45
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       +h++s ++++++++  l+++a++lk++ ++++  kl+ +++l+++F epStRTr+Sf  A+krlGg+v+ ++ +e+ 
  gi|557693506|ref|YP_008796560.1|   6 KHVISAKQFDRDTLADLFSTAKALKNRLSEKRGLKLAVDRILMTVFLEPSTRTRLSFVYAMKRLGGEVVDFG-PEE- 80 
                                       79**************************9999999999**********************************.544. PP

                                       CTTTGGSTTSSCHHHHHHHHHHHT.SEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryv.daiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                         +s +kg  E++eDt+r+l++y+ d+iv+R++  ga  +e+  k  +++viNagdg +eHPtQaL+D++ti+e
  gi|557693506|ref|YP_008796560.1|  81 -VTSRAKG--ETFEDTMRMLDGYApDVIVLRSRevGA--AEKASKIVRCSVINAGDGWNEHPTQALLDVYTIWE 149
                                       .3445788..***********************6655..99999999*************************97 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 ?    0.6   0.0     0.058   5.2e+02      14      43 ..      57      88 ..      48     150 .. 0.74
   2 !   96.2   0.0   2.3e-31     2e-27       1     155 [.     155     302 ..     155     304 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.058
                                      HHHHHHHHHHHHCT-EEEEES-TT..SSH-HH CS
                            OTCace 14 nvanslikllarlgmdvvlvaPkg..lepdke 43
                                      ++  s ++++ rlg +vv ++P++   + + e
  gi|557693506|ref|YP_008796560.1| 57 RTRLSFVYAMKRLGGEVVDFGPEEvtSRAKGE 88
                                      66678899999999999999999843333334 PP

  == domain 2  score: 96.2 bits;  conditional E-value: 2.3e-31
                                       CC.EEEEESS.TTSHHHHHHHHHHHH.CT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEE CS
                            OTCace   1 kglkiafvGd.kknnvanslikllar.lgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvv 75 
                                       +gl+ia++Gd  ++++++sl +lla+  ++++++vaP++l+  +evl+e+++      ++++ ++ lee  +++Dv+
  gi|557693506|ref|YP_008796560.1| 155 DGLRIAIMGDlRYGRTPSSLSYLLAKyRDITFHYVAPPQLQIREEVLKEVSH------HDVHQHSRLEEIRDEVDVL 225
                                       599*********************9945899****************87766......89***************** PP

                                       EE--SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHH CS
                            OTCace  76 ytdvwvsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlh 148
                                       y ++++     ker+   + +++l++ y vt +llk+ kk  +++H+LP  r +E+++eV+  p++ +f+qaeN+++
  gi|557693506|ref|YP_008796560.1| 226 YVTRLQ-----KERLgdeNLYQQLRGsYVVTVDLLKKLKKIPLIMHPLP--RVDELSTEVDALPQAKYFQQAENGVY 295
                                       ******.....666555588999*999**********************..************************** PP

                                       HHHHHHH CS
                            OTCace 149 tikAllv 155
                                       +++All 
  gi|557693506|ref|YP_008796560.1| 296 VRAALLT 302
                                       *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2438.03
//
Query:       gi|557693507|ref|YP_008796561.1|  [L=431]
Description: hypothetical protein CSUB_C0067 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); 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):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3252.84
//
Query:       gi|557693508|ref|YP_008796562.1|  [L=324]
Description: pyruvate ferredoxin oxidoreductase, beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   67.8   0.0    1.3e-18   67.3   0.0    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


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 !   67.3   0.0   7.2e-23   1.3e-18       2     150 ..      49     215 ..      48     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 7.2e-23
                                       SSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH............STTSEEEEEEEHHHHHHT.GGGH CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla............kpdrevvaivGDGgflmi.lqel 65 
                                       +Gcltl   +++++++ +s   s +++++  + ++A G+  a             +d +vv+++GDG+ ++i lq +
  gi|557693508|ref|YP_008796562.1|  49 AGCLTL--LQVYPYTPNKS---SWMYTAFASAPAGAQGIRDAldiliekgrvnsIEDLKVVVVTGDGAAYDIgLQST 120
                                       799998..55555544322...5579**************844555666666433478******************* PP

                                       HHHHHTT-SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.......BS----HHHHHHHTTSE.EEEESSH.H CS
                      TPP_enzyme_C  66 atavrrnlpitvvvlnNegygmtggq...qepfggkrksgpagk......dlkpvdfaklaealGak.garvekadv 132
                                       + a++r+l++ ++v++Ne+yg+tg q    +p+g+ + ++p  +      ++ ++d+ ++ +++  +  a+v ++++
  gi|557693508|ref|YP_008796562.1| 121 SGAIERGLDFYYLVYDNEAYGNTGFQksgATPYGSATATTPPTErnptgyTGAKKDLFEIWRSHKPPyIATVAPSHM 197
                                       *****************************99999999999988899999889999************888******* PP

                                       HHHHHHHHHHHCSSSEEE CS
                      TPP_enzyme_C 133 eeleealkealekkgpal 150
                                        ++ +++++a + kgp l
  gi|557693508|ref|YP_008796562.1| 198 VDMLRKIETASQFKGPKL 215
                                       *************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2363.84
//
Query:       gi|557693509|ref|YP_008796563.1|  [L=410]
Description: pyruvate ferredoxin oxidoreductase, alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-56  191.3   0.0    2.6e-56  191.0   0.0    1.1  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    5.2e-24   84.5   0.1    8.3e-24   83.8   0.1    1.3  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0021   17.9   0.0     0.0042   17.0   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain


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 !  191.0   0.0   4.3e-60   2.6e-56       3     227 ..      17     241 ..      15     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 191.0 bits;  conditional E-value: 4.3e-60
                                       HHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCCH CS
                             POR_N   3 aiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmienl 79 
                                       a  a+vd i aYPITP++ei+e+la+++ +g + +++ vq esE++   a+  A+++Gar++TaTS+qGll+  e+l
  gi|557693509|ref|YP_008796563.1|  17 ARIADVDYIPAYPITPQTEIIETLASWISQGLM-KAKLVQLESEHSMLTAAGTASLSGARVFTATSSQGLLYGFEML 92 
                                       667899**************************8.8****************************************** PP

                                       HHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEEEE CS
                             POR_N  80 glaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivlfD 154
                                       + +ag ++P+v+v+v Ra++++ + + +d++D++aard+g+i+l++e+ qe+ dl+l+A+++Ae+  v++Pviv +D
  gi|557693509|ref|YP_008796563.1|  93 YNIAGWRAPLVLVNVSRAVAAP-ITLEPDHNDVLAARDSGFIQLHAEKCQEVLDLILIAYRVAEDhrVMLPVIVNMD 168
                                       **********************.******************************************99********** PP

                                       HHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXX....SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHH CS
                             POR_N 155 gfllshevekvelpdeedelklikekleeyerkey....aldpekpiargtaanpdtglehrekgneaedaaekvve 227
                                       gf ls ++e+v++p++      ++e+l++y++ ++       ++ p + g+  + + + +++e++ +a d +++  +
  gi|557693509|ref|YP_008796563.1| 169 GFYLSFTREPVYIPSKT----DVEEFLPPYNPPHPfragRPVVKGPAVLGGHIYAYFKHNIHESLLRASDVFKEAAA 241
                                       **************999....67777777777775554566668888888888888888888888888887766655 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 !   83.8   0.1   1.4e-27   8.3e-24       1     102 []     262     366 ..     262     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 83.8 bits;  conditional E-value: 1.4e-27
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       Ae+v+v+++s  + a++av +lRe+gi +Gl++l +lrPFP+ ++ e l++ k+v+v+d+nis g  G++++ev+aa
  gi|557693509|ref|YP_008796563.1| 262 AEYVLVVTNSFTSIARKAVVRLREKGIPAGLVKLVMLRPFPSPDIVEKLRGRKAVAVFDQNISPGLGGIIYNEVAAA 338
                                       9**************************************************************************** PP

                                       TGGG...TSEEEEEE--GGG----HHHH CS
                           PFOR_II  78 lkks...kvkvvnfvaglgGrditvedi 102
                                       l++      ++++ ++g+gG+  tve++
  gi|557693509|ref|YP_008796563.1| 339 LYHVknrPETLLSAIGGVGGKYTTVEEF 366
                                       **99774557899************985 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     7e-07    0.0042      13      96 ..     265     346 ..     258     368 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7e-07
                                       EEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCCC CS
                   Transketolase_C  13 tlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeeaf 89 
                                       +lv + s  + a +A+ +L+++gi a +v l  ++p+   +i e + + ++ v v +++++ G+g  + + +a  + 
  gi|557693509|ref|YP_008796563.1| 265 VLVVTNSFTSIARKAVVRLREKGIPAGLVKLVMLRPFPSPDIVE-KLRGRKAVAVFDQNISPGLGGIIYNEVAAAL- 339
                                       66777788999*******************************94.5567777788888999****99999999944. PP

                                       TTCSSEE CS
                   Transketolase_C  90 dgldapv 96 
                                        +++ + 
  gi|557693509|ref|YP_008796563.1| 340 YHVKNRP 346
                                       4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2942.28
//
Query:       gi|557693510|ref|YP_008796564.1|  [L=294]
Description: pyruvate ferredoxin oxidoreductase, gamma subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-27   94.3   0.0    1.1e-26   94.0   0.0    1.1  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase
    7.2e-12   44.6  16.3    9.2e-06   25.3   4.7    2.4  2  Fer4      4Fe-4S binding domain
    8.3e-08   32.3  10.0    1.4e-07   31.5  10.0    1.4  1  Fer4_21   4Fe-4S dicluster domain
    5.1e-07   29.5  15.4    0.00046   20.2   3.2    2.4  2  Fer4_6    4Fe-4S binding domain
    9.6e-07   28.5  14.2     0.0027   17.7   3.2    2.4  2  Fer4_2    4Fe-4S binding domain
    1.9e-06   28.4  10.3    3.7e-06   27.4  10.3    1.5  1  Fer4_7    4Fe-4S dicluster domain
    4.9e-06   27.4   8.6     0.0047   17.8   0.9    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
      2e-05   24.7   9.3    3.2e-05   24.0   9.3    1.4  1  Fer4_9    4Fe-4S dicluster domain
    9.2e-05   22.5  10.8    0.00043   20.3  11.2    1.9  2  Fer4_10   4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.024   15.4  10.7       0.72   10.6   1.0    2.8  3  Fer4_15   4Fe-4S single cluster domain
      0.063   13.8   3.7      0.063   13.8   3.7    2.3  2  Fer4_4    4Fe-4S binding domain
       0.54   10.8  11.5        4.8    7.8   2.6    2.4  3  Fer4_17   4Fe-4S dicluster domain
       0.61   10.6  12.6          3    8.4   2.8    2.4  3  Fer4_8    4Fe-4S dicluster domain
       0.93   10.1  10.3       0.89   10.2   1.2    2.5  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


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 !   94.0   0.0   8.7e-30   1.1e-26       1     176 [.      10     180 ..      10     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 8.7e-30
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH....HHG CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls....ehl 73 
                                       GGqGv t ++il++aa++aG+ +q ++ yg+e+rG+++++  ris +pi ++  + +++++v++d+++l+    + l
  gi|557693510|ref|YP_008796564.1|  10 GGQGVKTSSRILGRAAFSAGLFAQDFPIYGAERRGAPVTAFTRISHSPIMERGYIFNPHIVVVMDETLLAdaqaRPL 86 
                                       9**********************************************999****************99977889*** PP

                                       GGEEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-HHHH CS
                               POR  74 dglkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallglpleal 150
                                       +gl  gg++++ns + +   +++a +            +  +++t+ a +i g ++++++ + +a+a+l gl  +++
  gi|557693510|ref|YP_008796564.1|  87 EGLPRGGVALINSARGPMVSEDQAGHV-----------FMRINFTDPALRIIG-KPIVSVSAAAAAAKLCGLRKQHV 151
                                       *************87777777776664...........679************.*********************** PP

                                       HHHHHCCS-CH....HHHHHHHHHHHHHH CS
                               POR 151 eeaikkrfpkkk...eviekNlkafragy 176
                                       eea+++++++ +   e+++kNl  + + y
  gi|557693510|ref|YP_008796564.1| 152 EEAVREELAELGvrdELLQKNLTLMSETY 180
                                       *********876999******98887776 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   3.7   8.6e-09   1.1e-05       1      24 []     232     255 ..     232     255 .. 0.95
   2 !   25.3   4.7   7.1e-09   9.2e-06       1      24 []     262     285 ..     262     285 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 8.6e-09
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       +v+d+ kC+gC+ C   CP  AI+
  gi|557693510|ref|YP_008796564.1| 232 PVVDYGKCTGCKVCFVYCPDSAIS 255
                                       69********************95 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 7.1e-09
                                       EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   1 vvideekCigCGaCvevCPvgAIt 24 
                                       +vid+e C gC +Cv  CP  AI+
  gi|557693510|ref|YP_008796564.1| 262 PVIDYEHCKGCLICVVECPIRAIS 285
                                       69********************95 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5  10.0   1.1e-10   1.4e-07       2      57 ..     233     284 ..     232     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.1e-10
                           Fer4_21   2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedci 57 
                                       ++d  kC gC+ C++ C+d    ai++da+++  +  ++C GC +C+  CP+  +i
  gi|557693510|ref|YP_008796564.1| 233 VVDYGKCTGCKVCFVYCPD---SAISLDAENKPVIDYEHCKGCLICVVECPI-RAI 284
                                       57889*************9...89****999977889**************9.555 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   3.2   3.6e-07   0.00046       2      24 .]     232     254 ..     231     254 .. 0.95
   2 !   14.9   4.4   1.6e-05     0.021       1      24 []     261     284 ..     261     284 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.6e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPegai 24 
                                       +++d+ kC+gC  C++ CP  ai
  gi|557693510|ref|YP_008796564.1| 232 PVVDYGKCTGCKVCFVYCPDSAI 254
                                       89*****************9998 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.6e-05
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       +++id++ C gC  Cv+ CP  ai
  gi|557693510|ref|YP_008796564.1| 261 KPVIDYEHCKGCLICVVECPIRAI 284
                                       69******************7776 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   3.4   6.8e-06    0.0087       2      21 ..     231     250 ..     230     251 .. 0.91
   2 !   17.7   3.2   2.1e-06    0.0027       2      21 ..     261     280 ..     260     280 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.8e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       ++vvd  +C+gC+ C   CP
  gi|557693510|ref|YP_008796564.1| 231 RPVVDYGKCTGCKVCFVYCP 250
                                       689************777*9 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.1e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       ++v+d ++C gC +Cv  CP
  gi|557693510|ref|YP_008796564.1| 261 KPVIDYEHCKGCLICVVECP 280
                                       589****************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4  10.3   2.9e-09   3.7e-06       1      51 [.     238     282 ..     238     283 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.9e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       +C+gC+ C ++Cp +ai+ld e       k++id+e C gC  Cv +CP  
  gi|557693510|ref|YP_008796564.1| 238 KCTGCKVCFVYCPDSAISLDAE------NKPVIDYEHCKGCLICVVECPIR 282
                                       7******************997......4679*****************65 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 !   17.8   0.9   3.6e-06    0.0047       1      24 [.     238     261 ..     238     267 .. 0.82
   2 !   13.6   1.4   7.5e-05     0.095       1      22 [.     268     289 ..     268     294 .] 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.6e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkeke 24 
                                       +C++C+ C   CP +ai+ ++e++
  gi|557693510|ref|YP_008796564.1| 238 KCTGCKVCFVYCPDSAISLDAENK 261
                                       5*****************995443 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.5e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaikekke 22 
                                       +C++C  C+  CP +ai++ +e
  gi|557693510|ref|YP_008796564.1| 268 HCKGCLICVVECPIRAISSVRE 289
                                       7****************99843 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   9.3   2.5e-08   3.2e-05       1      51 []     238     284 ..     238     284 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.5e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51 
                                       kCtgC+ C   Cp  +++ da ++ +   +     C gC  Cv  Cp  ai
  gi|557693510|ref|YP_008796564.1| 238 KCTGCKVCFVYCPDSAISLDAENKPVIDYE----HCKGCLICVVECPIRAI 284
                                       7********************999999765....6************8766 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3  11.2   3.4e-07   0.00043       3      56 .]     233     280 ..     231     280 .. 0.83
   2 !   13.3   2.1   5.4e-05     0.069       2      23 ..     262     283 ..     261     292 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.4e-07
                           Fer4_10   3 vidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       v+d  +C++C+ C   CP            + e++  +++e+C gc  Cv +CP
  gi|557693510|ref|YP_008796564.1| 233 VVDYGKCTGCKVCFVYCPD------SAISLDAENKPVIDYEHCKGCLICVVECP 280
                                       78999**************......44445555566678**************9 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 5.4e-05
                           Fer4_10   2 vvidddtCirCgkCvkaCPadl 23 
                                       +vid + C +C  Cv  CP  +
  gi|557693510|ref|YP_008796564.1| 262 PVIDYEHCKGCLICVVECPIRA 283
                                       799****************944 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 ?   -2.8   0.1       8.7   1.1e+04      56      59 ..     141     144 ..     134     168 .. 0.58
   2 ?   10.6   0.6    0.0006      0.76       2      20 ..     233     251 ..     233     262 .. 0.86
   3 ?   10.6   1.0   0.00056      0.72       2      19 ..     263     280 ..     263     286 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 8.7
                           Fer4_15  56 araC 59 
                                       a+ C
  gi|557693510|ref|YP_008796564.1| 141 AKLC 144
                                       4444 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0006
                           Fer4_15   2 vvDrdaCigcglCvaeape 20 
                                       vvD  +C+gc +C   +p+
  gi|557693510|ref|YP_008796564.1| 233 VVDYGKCTGCKVCFVYCPD 251
                                       69999************86 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00056
                           Fer4_15   2 vvDrdaCigcglCvaeap 19 
                                       v+D + C gc  Cv e+p
  gi|557693510|ref|YP_008796564.1| 263 VIDYEHCKGCLICVVECP 280
                                       69***************8 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   3.7   4.9e-05     0.063       3      16 ..     238     251 ..     236     253 .. 0.91
   2 ?    3.8   2.0     0.082     1e+02       2      15 ..     267     280 ..     266     288 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.9e-05
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       +C+gC++C  +CP+
  gi|557693510|ref|YP_008796564.1| 238 KCTGCKVCFVYCPD 251
                                       8************6 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.082
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       e C gC  Cv  CP
  gi|557693510|ref|YP_008796564.1| 267 EHCKGCLICVVECP 280
                                       67999999*****9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.6    0.0038       4.8      44      58 ..     237     251 ..     234     254 .. 0.82
   2 ?    6.9   1.7    0.0074       9.5       2      13 ..     269     280 ..     252     284 .. 0.71
   3 ?    6.3   2.2     0.011        14       2      16 ..     269     283 ..     268     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0038
                           Fer4_17  44 slCieCgeCerkCPq 58 
                                       ++C++C+ C  +CP 
  gi|557693510|ref|YP_008796564.1| 237 GKCTGCKVCFVYCPD 251
                                       579999999999986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0074
                           Fer4_17   2 CiqCgyClpeCp 13 
                                       C +C  C+ eCp
  gi|557693510|ref|YP_008796564.1| 269 CKGCLICVVECP 280
                                       666666666666 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.011
                           Fer4_17   2 CiqCgyClpeCpsye 16 
                                       C +C  C+ eCp  +
  gi|557693510|ref|YP_008796564.1| 269 CKGCLICVVECPIRA 283
                                       999999999999755 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.8    0.0023         3      49      62 ..     237     250 ..     212     254 .. 0.78
   2 ?    1.1  13.1      0.42   5.4e+02       4      63 ..     238     281 ..     235     283 .. 0.66
   3 ?    6.2   2.7     0.011        14       3      17 ..     267     281 ..     265     290 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0023
                            Fer4_8  49 wsCttcgaCtevCp 62 
                                       ++Ct+c+ C + Cp
  gi|557693510|ref|YP_008796564.1| 237 GKCTGCKVCFVYCP 250
                                       56666666666666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.42
                            Fer4_8   4 kCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpv 63 
                                       kC++C  C+  Cp        +lda+++        +        ++C +c  C+++Cp+
  gi|557693510|ref|YP_008796564.1| 238 KCTGCKVCFVYCPDS----AISLDAENKPVI-----D-------YEHCKGCLICVVECPI 281
                                       899999999999822....334455555444.....2.......3578888888888886 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.011
                            Fer4_8   3 ekCieCgaCqsaCpv 17 
                                       e+C +C  C  +Cp+
  gi|557693510|ref|YP_008796564.1| 267 EHCKGCLICVVECPI 281
                                       566666666666663 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 ?   10.2   1.2   0.00069      0.89       1      18 [.     234     251 ..     234     252 .. 0.94
   2 ?    4.1   2.3     0.053        67       1      17 [.     264     280 ..     264     281 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00069
                           Fer4_13   1 VDrdtCiacgaCvelaPd 18 
                                       VD  +C++c++C   +Pd
  gi|557693510|ref|YP_008796564.1| 234 VDYGKCTGCKVCFVYCPD 251
                                       8899*************9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.053
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       +D + C +c +Cv  +P
  gi|557693510|ref|YP_008796564.1| 264 IDYEHCKGCLICVVECP 280
                                       7999************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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):              14  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2032.00
//
Query:       gi|557693511|ref|YP_008796565.1|  [L=703]
Description: acetyl-CoA synthetase (ADP-forming), alpha and beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  171.1   0.0    4.4e-50  170.2   0.0    1.3  1  ATP-grasp_5     ATP-grasp domain
      2e-41  141.0   1.4      2e-41  141.0   1.4    2.1  2  Succ_CoA_lig    Succinyl-CoA ligase like flavodoxin domain
    1.2e-18   67.7   0.4    3.4e-17   63.0   0.4    2.7  2  CoA_binding_2   CoA binding domain
    3.9e-09   37.1   0.1    3.2e-06   27.7   0.1    3.1  2  CoA_binding     CoA binding domain
  ------ inclusion threshold ------
      0.019   15.5   0.1      0.068   13.8   0.1    1.9  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
       0.11   12.4   0.1        0.4   10.6   0.0    2.0  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen


Domain annotation for each model (and alignments):
>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.2   0.0   1.5e-53   4.4e-50      16     219 ..     495     694 ..     485     694 .. 0.97

  Alignments for each domain:
  == domain 1  score: 170.2 bits;  conditional E-value: 1.5e-53
                       ATP-grasp_5  16 kelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervkeks 92 
                                        +ll+ yg++ +e rl+ ++++a++aaee+gyp v+Ki+s++i+hK+d+gGv l++++ e+ ++a++++++ +k+  
  gi|557693511|ref|YP_008796565.1| 495 LSLLRVYGVEPAEERLVYNVDDALAAAEELGYPLVMKIASEKISHKSDLGGVVLGINTSEAAAEAFNKLMNLAKR-- 569
                                       5799********************************************************************988.. PP

                       ATP-grasp_5  93 peariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertkaskllkg 169
                                        +   +gv++qe  +  g El+++ ++Dp+ Gpv+++GlGG+++e+ +d     +p+++++a +++++++  ++l+g
  gi|557693511|ref|YP_008796565.1| 570 LGVADDGVVLQETWT--GLELLLSTKTDPSMGPVVTVGLGGVYTELWRDIITYAAPVTEEEALNMLDSLQHVRILNG 644
                                       88999********99..************************************************************ PP

                       ATP-grasp_5 170 vrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDar 219
                                       +r+ ++++++ +++l+vr+s ++ + p I++l+inPl +++e+v a+D+r
  gi|557693511|ref|YP_008796565.1| 645 YRNIPPINRRMIAKLIVRFSSIIPENPSINQLEINPLTIRGENVKAVDIR 694
                                       ************************************************87 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 ?   -1.1   0.1       0.5   1.5e+03      81      99 ..      93     112 ..      79     121 .. 0.77
   2 !  141.0   1.4   6.8e-45     2e-41       1     137 [.     167     304 ..     167     305 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.5
                      Succ_CoA_lig  81 k.kpvvvlksGrseagaraa 99 
                                           vvv+  G seag+r  
  gi|557693511|ref|YP_008796565.1|  93 GaRAVVVISGGFSEAGNREL 112
                                       347899*****9**999876 PP

  == domain 2  score: 141.0 bits;  conditional E-value: 6.8e-45
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarr 77 
                                       +G++a+isqSGala   +d   +rg+g++ ++ +Gn++dv+++ l +y+++dp t+vi+ly+E++ dgr +l+a+ +
  gi|557693511|ref|YP_008796565.1| 167 KGNVAIISQSGALAYHSIDLFGDRGVGLRAAACVGNQVDVNITMLADYFSDDPLTRVIVLYVEGVADGRGLLNAVLK 243
                                       69*************************************************************************** PP

                      Succ_CoA_lig  78 aark.kpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaael 137
                                       a+++ k+vvvlk+Gr++ g raa +ht++++g+ +v++ ++rqaG+++v+ +e+++d+a+l
  gi|557693511|ref|YP_008796565.1| 244 ARHRgKQVVVLKAGRTAVGGRAAYTHTASMVGEWDVFTGCLRQAGAMVVTGVEQMVDVAHL 304
                                       **********************************************************986 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.4   1.1e-20   3.4e-17       2     114 ..      10     136 ..       9     138 .. 0.90
   2 ?    1.5   0.0      0.13     4e+02      23      59 ..     245     280 ..     233     328 .. 0.75

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 1.1e-20
                                       -EEEET--S-TTSHHHHHHHHHHH.......HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGG CS
                     CoA_binding_2   2 tiaVvGasdnpgkfgykvlrylle.......hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpei 71 
                                       +iaVvG+s +p+k g+ + + l++       ++ + ++V    +ei ge+vy++++e   +v+lv+v++p++a+p++
  gi|557693511|ref|YP_008796565.1|  10 SIAVVGVSGDPHKLGRAIYDRLRQnklagvlKS-RLYAVSSSITEIYGERVYRRVSEINDEVELVVVAVPATAVPDV 85 
                                       79**********************999999666.**********************9569***************** PP

                                       HHHHHHH--SEEEE-TT....---HHHHHHHHH....TT-EEE.ES-HHHH CS
                     CoA_binding_2  72 vkealalgakavwlqpg....sedeeaaelaee....agirvvgdrCilve 114
                                       v +a+  ga+av++ +g    + ++e+ +++++     gir++g++ i+++
  gi|557693511|ref|YP_008796565.1|  86 VADAAGHGARAVVVISGgfseAGNRELENRLRQvvveTGIRLLGPNTIGII 136
                                       *****************77775555555555557777***********996 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.13
                                       HHHHT--EEEESSS-SEETTEES----T....T--EE CS
                     CoA_binding_2  23 llehglpvvpVnpkeeeilgekvyaslaedpepvdlv 59 
                                          +g +vv+    ++++ g+ +y  +a+ +++ d+ 
  gi|557693511|ref|YP_008796565.1| 245 R-HRGKQVVVLKAGRTAVGGRAAYTHTASMVGEWDVF 280
                                       2.36779*******************99646777743 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   1.1e-09   3.2e-06       4      94 ..       9     101 ..       6     103 .. 0.89
   2 !    5.8   0.0    0.0073        22      29      61 ..     424     462 ..     413     470 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.1e-09
                                       EEEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEET...TEEEESCHHHHHHHCTTTEEEEES-HHHHH CS
                       CoA_binding   4 tkviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevl...glpvyksvdeleektevdvavitvPaesaq 76 
                                        +++v+G++g  ++++    ++ ++ ++  v       v++ +    g  vy  v+e+ ++  v+  v++vPa+++ 
  gi|557693511|ref|YP_008796565.1|   9 CSIAVVGVSGDPHKLGrAIYDRLRQNKLAGVLKSRLYAVSSSITeiyGERVYRRVSEINDE--VELVVVAVPATAVP 83 
                                       589*************999999999999999888888777555544499************..************** PP

                                       HHHHHHHHTT-SEEEEES CS
                       CoA_binding  77 eavdelveagikgiviit 94 
                                       ++v +++ +g + +v+i+
  gi|557693511|ref|YP_008796565.1|  84 DVVADAAGHGARAVVVIS 101
                                       ****************98 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0073
                                       CEEEEEEC-TTTTTCEET......TEEEESCHHHHHHHC CS
                       CoA_binding  29 gikavfgvnprkvgtevl......glpvyksvdeleekt 61 
                                        ++a++++++ + g+ ++      g+p+++sv+ + + +
  gi|557693511|ref|YP_008796565.1| 424 ATVAAVDTGYSDWGQRIRklltenGVPAFESVEAAAQAL 462
                                       35699****************************998876 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 ?   13.8   0.1   2.3e-05     0.068      33      93 ..      42     101 ..      12     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.3e-05
                                       ESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEE CS
                     F420_oxidored  33 srnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvis 93 
                                       sr      ++ e +g +v     +e  +e + vv+av+ ++v++v++++a +  +  +vis
  gi|557693511|ref|YP_008796565.1|  42 SRLYAVSSSITEIYGERVYR-RVSEINDEVELVVVAVPATAVPDVVADAAGHGARAVVVIS 101
                                       66666667778888888888.999999**********************999888888887 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 ?   10.6   0.0   0.00014       0.4      64     134 ..      64     131 ..      58     133 .. 0.76
   2 ?   -2.8   0.0       1.8   5.4e+03       9      23 ..     435     449 ..     431     464 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00014
                                       HHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SEET.TTEEHHHHHHHHH-S--EEEEESS- CS
                    NAD_Gly3P_dh_N  64 aealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGieegtlkllsevieeelkeekvavlsGps 134
                                        e  ++++++v++vP  a+ +v+++++g+ ++  ++v ++ G++e +++ l++ +++++ e+    l Gp+
  gi|557693511|ref|YP_008796565.1|  64 SEINDEVELVVVAVPATAVPDVVADAAGHGAR--AVVVISGGFSEAGNRELENRLRQVVVET-GIRLLGPN 131
                                       56678899********************7755..5556678998888888888777777666.33455665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHTTT- CS
                    NAD_Gly3P_dh_N   9 swGtalAkvlaengh 23 
                                        wG  + k+l+eng 
  gi|557693511|ref|YP_008796565.1| 435 DWGQRIRKLLTENGV 449
                                       7***********993 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (703 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4970.83
//
Query:       gi|557693512|ref|YP_008796566.1|  [L=196]
Description: hypothetical protein CSUB_C0072 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   20.4   9.1     0.0036   17.4   1.0    2.9  2  DUF350    Domain of Unknown Function (DUF350)


Domain annotation for each model (and alignments):
>> DUF350  Domain of Unknown Function (DUF350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   1.0     2e-07    0.0036       2      49 ..      50     100 ..      50     104 .. 0.82
   2 !    6.4   1.7   0.00054       9.7       7      54 .]     143     191 ..     123     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2e-07
                            DUF350   2 gvvGivllllgffvfdllTp.gklgelIkqgnnAaaivlag..viiglaii 49 
                                       +vv ++l l+ + v+d++Tp +++ e+I++  +A a++ ag  v++++++i
  gi|557693512|ref|YP_008796566.1|  50 FVVVFILGLVSLRVVDWITPgVRELERIRGHPLATALFAAGffVYLSFGYI 100
                                       68899999***********************88999999982244555555 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00054
                            DUF350   7 vllllgffvfdllTp.gklgelIkqgnnAaaivlagviiglaiivaaAi 54 
                                       v+ ++ + ++ ++ p g   + + ++ +A+++ l+g ++ l+++v  A+
  gi|557693512|ref|YP_008796566.1| 143 VFAIVYYRILAKVEPfGLDLDDVDKEPLAVGVYLFGYLVFLGAVVYVAL 191
                                       5556666667777775555566666656*****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1521.54
//
Query:       gi|557693513|ref|YP_008796567.1|  [L=290]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2192.16
//
Query:       gi|557693514|ref|YP_008796568.1|  [L=353]
Description: hypothetical protein CSUB_C0074 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-05   23.9   0.0    0.00014   22.2   0.0    1.9  1  DUF4179       Domain of unknown function (DUF4179)
  ------ inclusion threshold ------
      0.011   15.7   0.2      0.023   14.7   0.2    1.5  1  DUF834        Domain of unknown function (DUF834)
      0.064   13.3   0.7        0.1   12.7   0.7    1.3  1  DZR           Double zinc ribbon
        1.1    9.1   4.0        1.7    8.6   4.0    1.3  1  zf-HIT        HIT zinc finger
        1.9    8.3   4.8         20    5.0   0.6    2.3  2  Rubredoxin_2  Rubredoxin metal binding domain
        5.9    6.4  13.1       0.89    9.0   4.1    2.7  2  SKG6          Transmembrane alpha-helix domain


Domain annotation for each model (and alignments):
>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.8e-08   0.00014      11      72 ..      19      86 ..      12      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.8e-08
                                      XXXXXXXXXXXXXXXXXXXXXXXX......--SS-HHHHT--SS-..HHHHSEEEEEEEEETTEEEEEE CS
                           DUF4179 11 aaaaalvllllssrllspalAsal....n.pvigslfeklsdskg..eqeyvkpvnksaednGitvtvn 72
                                      + aa+++lll + ++ ++++A+        p++  ++++++++++  e+ +   + +s++++Git+ + 
  gi|557693514|ref|YP_008796568.1| 19 I-AAVIALLLTVLMFFNSSWAQGSpppyIqPGLAFVYQLFDQKTQqaENAFQRYIIESVTSQGITISIV 86
                                      3.3344444477*********999999955999999999999998999999999************985 PP

>> DUF834  Domain of unknown function (DUF834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   7.6e-06     0.023      19      42 ..     259     282 ..     258     287 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.6e-06
                            DUF834  19 pavfggnepaAGllLglAePtvaa 42 
                                       ++++++++paAG++L++A P  a+
  gi|557693514|ref|YP_008796568.1| 259 SVSVQAEGPAAGIPLTVAIPVAAV 282
                                       58899***************9886 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.7   3.4e-05       0.1       1      21 [.     331     351 ..     315     353 .] 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                               DZR   1 CpqCgeelppdarfCseCgtk 21 
                                       Cp C+ +l p+  +C +Cg +
  gi|557693514|ref|YP_008796568.1| 331 CPACRFPLYPGEYMCRRCGYR 351
                                       666666666666666666655 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.0   0.00056       1.7       5      22 ..     331     351 ..     327     352 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00056
                                       -TTT-S...B-SEE-TTT--E CS
                            zf-HIT   5 CgvCgf...pakYkCpkCntr 22 
                                       C  C f   p+ Y C++C+ r
  gi|557693514|ref|YP_008796568.1| 331 CPACRFplyPGEYMCRRCGYR 351
                                       999***************987 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2    0.0067        20      10      21 ..     324     335 ..     322     335 .. 0.84
   2 ?    5.0   0.6    0.0066        20       1       9 [.     343     351 ..     343     353 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0067
                      Rubredoxin_2  10 sakwfGrCpsCg 21 
                                       +++ +G Cp+C+
  gi|557693514|ref|YP_008796568.1| 324 FIQPVGACPACR 335
                                       67889******6 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0066
                      Rubredoxin_2   1 YvCsqCGfe 9  
                                       Y C++CG++
  gi|557693514|ref|YP_008796568.1| 343 YMCRRCGYR 351
                                       89*****97 PP

>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.6     0.061   1.8e+02      21      33 ..      21      33 ..      19      34 .. 0.65
   2 ?    9.0   4.1    0.0003      0.89      16      36 ..     275     295 ..     268     296 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.061
                              SKG6 21 aViiivLlailif 33
                                      aVi+++L ++ +f
  gi|557693514|ref|YP_008796568.1| 21 AVIALLLTVLMFF 33
                                      5777777777666 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0003
                              SKG6  16 VaVPVaViiivLlailifvrR 36 
                                       Va+PVa++ii  +++++  rR
  gi|557693514|ref|YP_008796568.1| 275 VAIPVAAVIIGGGIFFVRSRR 295
                                       9*******9975555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2632.18
//
Query:       gi|557693515|ref|YP_008796569.1|  [L=543]
Description: hypothetical protein CSUB_C0075 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.0      0.039   13.7   0.0    1.2  1  VPS13         Vacuolar sorting-associated protein 13, N-termi
      0.043   12.2   6.8       0.48    8.7   0.9    2.7  3  Peptidase_M6  Immune inhibitor A peptidase M6


Domain annotation for each model (and alignments):
>> VPS13  Vacuolar sorting-associated protein 13, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.4e-06     0.039     121     175 ..      19      75 ..      14      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-06
                             VPS13 121 LkPvsgeaklklnkkgetd..apklkldleldevgltLseeqyrdilklleslsrle 175
                                       + Pv+g+ +++ n++ +    +p l l +++++v+l++s++q ++i+k+++s+ r +
  gi|557693515|ref|YP_008796569.1|  19 IYPVTGQEEFEWNRQIPFLgaQPTLVLLVQFSDVKLSISRTQAEQIVKIVDSFVRDA 75 
                                       5688888888888777766667******************************98755 PP

>> Peptidase_M6  Immune inhibitor A peptidase M6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0     0.088   7.9e+02      92     138 ..      91     137 ..      83     138 .. 0.72
   2 ?    5.6   0.7   0.00047       4.2     160     190 ..     138     165 ..     125     171 .. 0.81
   3 ?    8.7   0.9   5.3e-05      0.48     228     265 ..     224     263 ..     207     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.088
                      Peptidase_M6  92 lkvpknaaryGsnssgsdnkapkaardlvkeala..rteaekkidLaqy 138
                                       ++ pk+ ++yG+ s+g +  ++ + r l +  l+  +++++  +dL+qy
  gi|557693515|ref|YP_008796569.1|  91 ITLPKPMSYYGGPSAGAQR-GDDNQRIL-EFHLTtiQLAKKDGVDLSQY 137
                                       5678999*****9999887.66544433.33333347889999999999 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.00047
                      Peptidase_M6 160 DhlmiihagvgeeaGGGalGeDaiWshrskl 190
                                        h+  ihag +e  GG a   + iWsh   +
  gi|557693515|ref|YP_008796569.1| 138 KHVITIHAGKDEATGGSA---NDIWSHCNCV 165
                                       6999******99888764...56****8665 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 5.3e-05
                      Peptidase_M6 228 vfaheyGhDLGLPDeyDtkytG..kgepvgyWslmssGsW 265
                                       v+ahe+ h + + D y     G  +g+ vg+W+ m +Gs+
  gi|557693515|ref|YP_008796569.1| 224 VMAHEFTHSMWISDLYVYAKDGysTGSEVGIWTNMDAGSF 263
                                       99************99655544337999**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (543 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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 0.23s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 4123.30
//
Query:       gi|557693516|ref|YP_008796570.1|  [L=284]
Description: lysine biosynthesis enzyme LysX [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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    1.8e-30  106.0   0.0    1.1  1  RimK             RimK-like ATP-grasp domain
    3.2e-08   33.2   0.0    4.8e-08   32.6   0.0    1.3  1  GSH-S_ATP        Prokaryotic glutathione synthetase, ATP-gras
    4.2e-05   23.6   0.0    6.7e-05   23.0   0.0    1.4  1  ATP-grasp_3      ATP-grasp domain
      0.001   18.7   0.0     0.0018   17.9   0.0    1.4  1  ATP-grasp        ATP-grasp domain
     0.0035   16.9   0.0     0.0069   15.9   0.0    1.5  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
  ------ inclusion threshold ------
      0.014   15.4   0.1      0.025   14.6   0.1    1.4  1  R2K_3            ATP-grasp domain, R2K clade family 3
        0.1   11.8   0.0        0.7    9.1   0.0    2.1  2  ATPgrasp_ST      Sugar-transfer associated ATP-grasp


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 !  106.0   0.0     7e-34   1.8e-30       1     188 []      86     278 ..      86     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 7e-34
                                       HH-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH...... CS
                              RimK   1 ardKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea...... 71 
                                       a dK++++  L  a++++p+ta+  +   aek +ek+  +fP v K   gs G  + l ++ ++ k v e       
  gi|557693516|ref|YP_008796570.1|  86 AGDKVLTVSRLKSANLPIPRTAVGLNTRAAEKALEKV--GFPAVDKPPIGSWGRLIALVRDIDDFKLVAEHremlps 160
                                       5699999999***************************..6*************************999655555444 PP

                                       .GGG--...EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT- CS
                              RimK  72 .lkeai...lvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamel 144
                                            +   ++qeyi+   n+diR lvv+devv+a+ r     d+R+n+ +Gg   ++ l++e+ e+ ++aaka++ 
  gi|557693516|ref|YP_008796570.1| 161 gY---MkthIIQEYIDLP-NRDIRTLVVGDEVVGAIYRYRASNDWRTNVALGGEPVQAFLNDELVEISLRAAKAVKG 233
                                       42...155589****985.79***************9998888********************************** PP

                                       SEEEEEEEEETT.EEEEEEEESS--SHHHHHHHT--HHHHHHHHH CS
                              RimK 145 vvaGvDllrakr.gllvlEvnsspglekiektlgidiakklieai 188
                                       +v+ +D++++ + ++lv Evn  p+ +++ k +g+++ +k+i+++
  gi|557693516|ref|YP_008796570.1| 234 DVVSIDVFETTDgSYLVNEVNGVPEFKGLMKATGVNVPEKIIDYV 278
                                       ********9766268899************************985 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 !   32.6   0.0   1.9e-11   4.8e-08      12     150 ..     103     239 ..      91     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.9e-11
                                       S--EEEES-HHHHHHHHHHHSS.EEEEESS--TTTT-EEE-TT.-TT.HHHHHHHHTTTTTS-EEEEE--GGGGG-E CS
                         GSH-S_ATP  12 ipktlvskdkeeirafleeqgd.vilKPldgkgGegvfrvkks.dpn.lksilellteegkepviaqrylpeikeGD 85 
                                       ip+t v  ++++ ++ le+ g  ++ KP  g+ G+ +  v++  d + +    e+l +   ++ i+q+y++  +  D
  gi|557693516|ref|YP_008796570.1| 103 IPRTAVGLNTRAAEKALEKVGFpAVDKPPIGSWGRLIALVRDIdDFKlVAEHREMLPSGYMKTHIIQEYIDLPN-RD 178
                                       688888888888888888888768889999999998888876523331444567788888999*******8655.5* PP

                                       EEEEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEE CS
                         GSH-S_ATP  86 kRillvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlD 150
                                        R l+v  e +g a+ R  a+++ R+n+a gg+ ++  l+++ +ei+ + a+++k +   +v +D
  gi|557693516|ref|YP_008796570.1| 179 IRTLVVGDEVVG-AIYRYRASNDWRTNVALGGEPVQAFLNDELVEISLRAAKAVKGD---VVSID 239
                                       ************.*********************************99888877765...34555 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   2.6e-08   6.7e-05       1     155 [.      86     254 ..      86     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.6e-08
                                       HTSHHHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE............. CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve...... 64 
                                       a dK+ t+ +Lk a++++P       t++ ++ le++  + v Kp  G+ g  + +v++ ++ +   e+ e      
  gi|557693516|ref|YP_008796570.1|  86 AGDKVLTVSRLKSANLPIPrtavglnTRAAEKALEKVGFPAVDKPPIGSWGRLIALVRDIDDFKLVAEHREmlpsgy 162
                                       67**********************97777778888889**********************999999999989***** PP

                                       ....EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EE CS
                       ATP-grasp_3  65 ....lvqefieGkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGy 137
                                           ++qe+i+  +  + +l+ g + +v a+ r +  + ++ +v  G+  p++  l++e+ve+  ++ ++++g   +
  gi|557693516|ref|YP_008796570.1| 163 mkthIIQEYIDLPNRDIRTLVVG-DEVVGAIYRYRASNDWRTNVALGGE-PVQAFLNDELVEISLRAAKAVKG--DV 235
                                       ***********999999999977.5556678888888888887777774.77777889999988888888853..34 PP

                                       EEEEEEESS.SEEEE.EEE CS
                       ATP-grasp_3 138 vGvDlvlkdeepyvi.EvN 155
                                       v +D+  + ++ y++ EvN
  gi|557693516|ref|YP_008796570.1| 236 VSIDVFETTDGSYLVnEVN 254
                                       5677765544444443666 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     7e-07    0.0018       2     156 ..      97     253 ..      96     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7e-07
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC......GTTCEEEEE-- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal......keekvivEefv 72 
                                       ++++lp+pr ++  ++ ++e+a+e++g+p+v K +  g+ G+   +vr+ +d + ++e          ++ i+ e++
  gi|557693516|ref|YP_008796570.1|  97 KSANLPIPRTAVGLNTRAAEKALEKVGFPAVDK-PPIGSWGRLIALVRDIDDFKLVAEHRemlpsgYMKTHIIQEYI 172
                                       67889999999988899****************.899999**************9999888899987788999**** PP

                                       --.SEEEEEEEEE.ETTC-EEE--EEEEEEETTEEEEEEE..CEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEE CS
                         ATP-grasp  73 pf.ekElsvlvvr.saeGetafypvvetvqedgilrlsva..paevsekaqkkaeeiakkiveeLggvGvfavElFv 145
                                       ++ ++ +  lvv  ++ G+++ y         ++ r++va    +v++  + +  ei  ++++++ g  v+++ +F+
  gi|557693516|ref|YP_008796570.1| 173 DLpNRDIRTLVVGdEVVGAIYRYRAS------NDWRTNVAlgGEPVQAFLNDELVEISLRAAKAVKG-DVVSIDVFE 242
                                       *95689*9999985677855555544......44444443114556666888888999999999887.499****** PP

                                       ETTCTEEEEEE CS
                         ATP-grasp 146 ledgellvnEl 156
                                       ++dg+ lvnE+
  gi|557693516|ref|YP_008796570.1| 243 TTDGSYLVNEV 253
                                       **********9 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 ?   -3.8   0.0         3   7.6e+03      27      43 ..     114     130 ..     107     131 .. 0.77
   2 !   15.9   0.0   2.7e-06    0.0069     108     178 ..     190     259 ..     173     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3
                                       HHHHHHHHC-SSEEEEE CS
                   Dala_Dala_lig_C  27 llekveeelgypvfVKp 43 
                                         ek  e++g+p++ Kp
  gi|557693516|ref|YP_008796570.1| 114 AAEKALEKVGFPAVDKP 130
                                       56788899999998887 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.7e-06
                                       SSSS-HHHHHC.TT-EEES.S----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEESS--- CS
                   Dala_Dala_lig_C 108 kgfydyeakysddkaqlev.paklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNtlPGf 178
                                       +++y+y a + d ++++ +    +++  ++++ e++l+a ka+++ +++ +D+f t++g+ ++nEvN +P f
  gi|557693516|ref|YP_008796570.1| 190 GAIYRYRASN-DWRTNVALgGEPVQAFLNDELVEISLRAAKAVKG-DVVSIDVFETTDGSYLVNEVNGVPEF 259
                                       5677777777.434444331445777889999***********98.6778********************76 PP

>> R2K_3  ATP-grasp domain, R2K clade family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   9.8e-06     0.025      90     183 ..     143     255 ..     117     257 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 9.8e-06
                             R2K_3  90 refeelralaakle.......dtevlvsevvrf.saEwRvFvvdGevvaa.srYrkanddpdl.............e 144
                                       r++ +++  a++ e       +t+ ++ e++++     R+ vv++evv+a  rYr a +d+ +             +
  gi|557693516|ref|YP_008796570.1| 143 RDIDDFKLVAEHREmlpsgymKTH-IIQEYIDLpNRDIRTLVVGDEVVGAiYRYR-ASNDWRTnvalggepvqaflN 217
                                       666777766665555666663333.4667775548899******99997626896.788888877888766666664 PP

                             R2K_3 145 pdlaafaeavralvgappfyvlDvavtadGrwkVVEvnd 183
                                        +l+++   ++++v +  ++++Dv  t+dG ++V Evn 
  gi|557693516|ref|YP_008796570.1| 218 DELVEISLRAAKAV-KGDVVSIDVFETTDGSYLVNEVNG 255
                                       44444444444444.599*******************95 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 ?    9.1   0.0   0.00027       0.7       8      94 ..      75     157 ..      69     175 .. 0.80
   2 ?    0.2   0.0      0.14   3.6e+02     226     269 ..     218     260 ..     202     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00027
                       ATPgrasp_ST   8 rkyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvitered 84 
                                       r +N+ +++ l  dK+++ + ++ a l++p++ + +++ a  ++le++        v Kp  gs+G+ i  + +++d
  gi|557693516|ref|YP_008796570.1|  75 RSINSSEAIYLAGDKVLTVSRLKSANLPIPRTAVGLNTRAAEKALEKVGFP----AVDKPPIGSWGRLIALVRDIDD 147
                                       789****************************99998888777777776433....4789999999999999988877 PP

                       ATPgrasp_ST  85 qdylkssgks 94 
                                        + +++  + 
  gi|557693516|ref|YP_008796570.1| 148 FKLVAEHREM 157
                                       7766665555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.14
                       ATPgrasp_ST 226 eevlelaakaaeklpglgylGwDivldeekgplllElNarpgla 269
                                       +e++e+  +aa+  ++  ++++D+  ++++  l+ E+N  p  +
  gi|557693516|ref|YP_008796570.1| 218 DELVEISLRAAK-AVKGDVVSIDVFETTDGSYLVNEVNGVPEFK 260
                                       578999999999.8889999999999999989999999877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2232.41
//
Query:       gi|557693517|ref|YP_008796571.1|  [L=176]
Description: peptidase, zinc-dependent [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   88.2   0.0    8.9e-25   87.8   0.0    1.2  1  Peptidase_M54  Peptidase family M54
    0.00074   19.4   0.0    0.00076   19.4   0.0    1.2  1  Peptidase_M10  Matrixin
     0.0028   16.7   0.1     0.0041   16.1   0.1    1.2  1  Peptidase_M66  Peptidase M66
  ------ inclusion threshold ------
      0.032   14.7   0.0      0.046   14.3   0.0    1.3  1  Reprolysin_3   Metallo-peptidase family M12B Reprolysin-like
      0.035   12.7   0.2      0.054   12.1   0.2    1.2  1  Metallopep     Putative peptidase family


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 !   87.8   0.0   2.5e-28   8.9e-25      84     190 ..      52     164 ..      26     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 2.5e-28
                                       -..SEE...........EEEESS-EE-TT-S-BSEEE-SSSSEEEEE-T.--........SHHHHHHHHHHHHHHHH CS
                     Peptidase_M54  84 vndDsitkif...gittlplgsrdqyidiykkvlGievsiGnyavlals.ikefyte...dkeLflervvkevlhel 153
                                       +n +++ k +   g   l l++rd y++++++v+G +       vl+++ +k+  +     + L lerv+ke +he+
  gi|557693517|ref|YP_008796571.1|  52 YNAEKLVKHMhaeGSLVLILTDRDLYVEGLNFVFGYAPP--PVGVLSIHrLKPAVEVggsGRSLLLERVLKEAVHEV 126
                                       4444444432122455799****************9876..67788887766655544449**************** PP

                                       HHHTT----S-.TSTTS--SSHHHHHHS-SS--HHHHH CS
                     Peptidase_M54 154 GhlyGLshCke.dCvmnfsndlkdvDrkapkyCksCle 190
                                       Ghl GL+hC+   Cvm+fsn++ +vD k+ + C  C +
  gi|557693517|ref|YP_008796571.1| 127 GHLIGLGHCSArYCVMSFSNSVAEVDSKSGELCDGCRT 164
                                       **********999***********************65 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.1e-07   0.00076     113     134 ..     122     143 ..      36     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHTTBESXSSTTSTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 113 aaHEiGHalGLeHssdkdalmy 134
                                       a+HE+GH++GL H s++  +m 
  gi|557693517|ref|YP_008796571.1| 122 AVHEVGHLIGLGHCSARYCVMS 143
                                       89***************99996 PP

>> Peptidase_M66  Peptidase M66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.1e-06    0.0041     181     211 ..     107     137 ..     103     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-06
                     Peptidase_M66 181 gssGivtgdatltgefiHEqGHalGLpHyla 211
                                       g+sG + + +++ +e +HE+GH +GL+H  a
  gi|557693517|ref|YP_008796571.1| 107 GGSGRSLLLERVLKEAVHEVGHLIGLGHCSA 137
                                       4458889999******************554 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 ?   14.3   0.0   1.3e-05     0.046      60     123 ..      61     134 ..      36     135 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                      Reprolysin_3  60 gqagyDlvhlftardesgvgGlAyvgsvcnsskkagvnsgssvlgkvga...........dtvaHEiGHnfganH 123
                                        +a+  lv ++t+rd   v Gl +v +  ++  ++ ++   ++  +vg            + + HE+GH +g+ H
  gi|557693517|ref|YP_008796571.1|  61 MHAEGSLVLILTDRDL-YVEGLNFVFGYAPPPVGVLSIHRLKPAVEVGGsgrslllervlKEAVHEVGHLIGLGH 134
                                       4556678888899887.8888888855555555554444555555544455566666788999***********9 PP

>> Metallopep  Putative peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   1.5e-05     0.054     319     336 ..     123     142 ..     120     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                        Metallopep 319 lHEiGHllglpHqed..Gvm 336
                                       +HE+GHl+gl+H+++   vm
  gi|557693517|ref|YP_008796571.1| 123 VHEVGHLIGLGHCSAryCVM 142
                                       7***********98755666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1409.78
//
Query:       gi|557693518|ref|YP_008796572.1|  [L=191]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   58.8   0.3    1.9e-15   57.5   0.3    1.7  1  AAA_18           AAA domain
    2.2e-06   27.9   0.0    1.8e-05   24.9   0.0    2.1  2  SKI              Shikimate kinase
    2.5e-06   27.9   0.3    4.1e-05   24.0   0.3    2.3  1  AAA              ATPase family associated with various cellul
    0.00021   21.5   0.7     0.0054   16.9   0.2    2.4  2  AAA_33           AAA domain
    0.00064   20.0   0.1     0.0013   18.9   0.0    1.6  2  AAA_28           AAA domain
     0.0015   18.8   0.2      0.002   18.4   0.2    1.8  1  AAA_22           AAA domain
     0.0022   18.4   0.4        0.2   12.0   0.0    2.3  2  AAA_16           AAA ATPase domain
     0.0028   17.6   0.0       0.12   12.3   0.0    2.2  2  dNK              Deoxynucleoside kinase
     0.0067   16.9   0.2      0.017   15.6   0.2    1.9  1  AAA_17           AAA domain
      0.008   16.3   0.1      0.022   14.9   0.0    1.8  2  Cytidylate_kin2  Cytidylate kinase-like family
  ------ inclusion threshold ------
      0.016   15.0   0.1        2.6    7.7   0.0    3.0  3  PRK              Phosphoribulokinase / Uridine kinase family
      0.017   15.5   0.0      0.031   14.7   0.0    1.5  1  RNA_helicase     RNA helicase
       0.05   13.6   0.1       0.14   12.2   0.0    1.8  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.059   13.3   0.0       0.09   12.7   0.0    1.3  1  Rad17            Rad17 P-loop domain
      0.074   12.8   0.0       0.11   12.3   0.0    1.3  1  AAA_24           AAA domain
      0.074   12.8   0.0       0.12   12.1   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.58   10.0   4.9       0.26   11.2   0.7    2.3  3  NTPase_1         NTPase


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 !   57.5   0.3   1.8e-18   1.9e-15       1     129 [.       3     119 ..       3     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.8e-18
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegkn 76 
                                       I++tGtpGvGKtt ++ L+krlg+  + l + ++ n+l++e+  +    + ++d  +l+++l+ + +        ++
  gi|557693518|ref|YP_008796572.1|   3 IWVTGTPGVGKTTTGRMLAKRLGIgFIDLPEFVSANNLYTERLGD---GTMVVDPRRLERHLSRNVK--------ED 68 
                                       99**********************99999999***********99...5555555554444444444........45 PP

                            AAA_18  77 lvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaeil 129
                                        vi gh+   +    ++  ++vL+++p +l++Rle+Rgy+  k +en eae+l
  gi|557693518|ref|YP_008796572.1|  69 TVIAGHITVRVRGHETR--CIVLRLNPLQLRKRLEERGYSVEKVAENVEAEFL 119
                                       59999999888776653..5*******************************97 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   1.7e-08   1.8e-05       1      28 [.       9      36 ..       9      42 .. 0.90
   2 ?    0.8   0.0      0.46   4.8e+02      99     138 ..      76     114 ..      58     156 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.7e-08
                                      TTSSHHHHHHHHHHHHTSEEEEHHHHHH CS
                               SKI  1 mGaGKstvGkllAkklglefiDlDelie 28
                                      +G+GK+t+G++lAk+lg+ fiDl e+++
  gi|557693518|ref|YP_008796572.1|  9 PGVGKTTTGRMLAKRLGIGFIDLPEFVS 36
                                      69********************988775 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.46
                                       HHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCSSCEE CS
                               SKI  99 lerlkadkeRPllqekskeeelleelaereplyeeaadvv 138
                                         r++  ++R ++   ++  +l++ l+er  + e++a  v
  gi|557693518|ref|YP_008796572.1|  76 TVRVRGHETRCIVLRLNP-LQLRKRLEERGYSVEKVAENV 114
                                       556666666666666666.566666666777666666544 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   0.3   3.9e-08   4.1e-05       3      96 ..       5     159 ..       3     189 .. 0.68

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.9e-08
                                       EESSTTSSHHHHHHHHHHHHTHE...................................................... CS
                               AAA   3 lyGppGtGKTllakavakelgve...................................................... 25 
                                       ++G+pG+GKT++ + +ak lg+                                                       
  gi|557693518|ref|YP_008796572.1|   5 VTGTPGVGKTTTGRMLAKRLGIGfidlpefvsannlyterlgdgtmvvdprrlerhlsrnvkedtviaghitvrvrg 81 
                                       79*****************9876333334444444444555555555555555555555555555555555555555 PP

                                       ......EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTCCCHHHHHHHHHHHHHH CS
                               AAA  26 ......fleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgseseeeervvnqLltel 93 
                                             +l+++  +l+ k ++e+  +++++ ++++++    ++ +D i  ++k+r    + + +e+++vvn  + +l
  gi|557693518|ref|YP_008796572.1|  82 hetrciVLRLNPLQLR-KRLEERGYSVEKVAENVEAEF-LGVVYLDAIRVFGKNRvsqIDVTGKEASDVVNRCVDVL 156
                                       5555444455544444.488999999999999988876.79999999999999998764456667777777776666 PP

                                       HHT CS
                               AAA  94 dgv 96 
                                       +g 
  gi|557693518|ref|YP_008796572.1| 157 EGR 159
                                       665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   5.1e-06    0.0054       2      38 ..       3      45 ..       2      88 .. 0.73
   2 ?    2.7   0.1      0.12   1.3e+02      96     123 ..      81     108 ..      76     119 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.1e-06
                            AAA_33  2 vllvGlpGsGKstlaerllkklg......avllssdtlrrrlf 38
                                      +++ G pG+GK+t  + l+k+lg       +++s ++l++   
  gi|557693518|ref|YP_008796572.1|  3 IWVTGTPGVGKTTTGRMLAKRLGigfidlPEFVSANNLYTERL 45
                                      7899*******************77777777777777776433 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
                            AAA_33  96 gvpvrivvvetdeetlkeRlakRaangd 123
                                       g + r++v++  + +l++Rl++R  + +
  gi|557693518|ref|YP_008796572.1|  81 GHETRCIVLRLNPLQLRKRLEERGYSVE 108
                                       7789*******************98644 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.3e-06    0.0013       2      31 ..       3      35 ..       2      72 .. 0.78
   2 ?   -3.2   0.0       8.3   8.8e+03     143     155 ..      98     110 ..      95     116 .. 0.49

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                            AAA_28  2 ivitGgestGKTtlleaLaar.gypvv..pEaa 31
                                      i +tG+++ GKTt+ + La+r g+  +  pE++
  gi|557693518|ref|YP_008796572.1|  3 IWVTGTPGVGKTTTGRMLAKRlGIGFIdlPEFV 35
                                      779*****************9955544448876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.3
                            AAA_28 143 ealrelgipviiv 155
                                       + l+e+g++v  v
  gi|557693518|ref|YP_008796572.1|  98 KRLEERGYSVEKV 110
                                       4444555554444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   1.9e-06     0.002       7      30 ..       2      25 ..       1     188 [. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                                      i+ vtG +G+GKTt+ r+l+++l 
  gi|557693518|ref|YP_008796572.1|  2 IIWVTGTPGVGKTTTGRMLAKRLG 25
                                      688******************993 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00019       0.2      26      48 ..       2      24 ..       1      42 [. 0.90
   2 ?    4.7   0.1     0.034        36      55     162 ..      77     183 ..      49     190 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                            AAA_16 26 lvllsGesGvGKsslvrellral 48
                                      ++ ++G +GvGK++  r+l+++l
  gi|557693518|ref|YP_008796572.1|  2 IIWVTGTPGVGKTTTGRMLAKRL 24
                                      688**************999987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.034
                            AAA_16  55 f.lrgkcdqlesaipysalaqalareellrqllde..aesaeleawrekleeala................avpela 112
                                       + +rg+ +++        ++  l   +l + l+++  +    +e  +e  e+++                 ++ +++
  gi|557693518|ref|YP_008796572.1|  77 VrVRGHETRC--------IVLRLNPLQLRKRLEERgyS----VEKVAENVEAEFLgvvyldairvfgknrvSQIDVT 141
                                       3566666666........66666565666666555331....33333333333333444555556655555333444 PP

                            AAA_16 113 gaeasrllellkrllallsrderplvlvlDdlqwadeaslqllaaLlrll 162
                                       g+eas++ + + + l    rd+       Dd++w    + ++l++Llr l
  gi|557693518|ref|YP_008796572.1| 142 GKEASDVVNRCVDVL--EGRDAG------DDVEWMSRLDEDILSQLLRYL 183
                                       443333333333333..222233......788888888888888777654 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00011      0.12       1      34 [.       3      38 ..       3      65 .. 0.85
   2 ?    3.5   0.0     0.052        55     126     156 ..      86     119 ..      73     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                      EEEEESTTSSHHHHHHHHHCCST..CEEEE-HHHHC CS
                               dNK  1 ivveGnIgaGKstlvklLskklg..vkvfeEpvdkw 34
                                      i v G+ g+GK+t   +L+k+lg  +  ++E v+ +
  gi|557693518|ref|YP_008796572.1|  3 IWVTGTPGVGKTTTGRMLAKRLGigFIDLPEFVSAN 38
                                      67999*****************96677778988888 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.052
                                       EEEEE--HHHHHHHHHHCTTCCCT...TS-HHHH CS
                               dNK 126 liYLkasletclerikkRgreeek...kieldYl 156
                                        i L++++ ++ +r+++Rg + ek   ++e ++l
  gi|557693518|ref|YP_008796572.1|  86 CIVLRLNPLQLRKRLEERGYSVEKvaeNVEAEFL 119
                                       577999999999*********9996666666655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   1.6e-05     0.017       1      83 [.       6      78 ..       6     116 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                                      EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSH.HHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                            AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklp.leekkelqkeaaekiaeeakkkgvlvdg 78
                                      +G PG+GK+t  + l++++g+ ++   + + +    ++l    +++ ++   ++ ++l + + ++++e     + ++ g
  gi|557693518|ref|YP_008796572.1|  6 TGTPGVGKTTTGRMLAKRLGIGFIDLPEFVSA----NNL--YTERLGDGTmVVDPRRLERHLSRNVKE-----DTVIAG 73
                                      69********************9996555543....344..223333333033445555555555555.....356666 PP

                                      -SEEE CS
                            AAA_17 79 hprik 83
                                      h +++
  gi|557693518|ref|YP_008796572.1| 74 HITVR 78
                                      66654 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     2e-05     0.022       1      30 [.       2      31 ..       2      70 .. 0.90
   2 ?   -1.7   0.0       2.5   2.7e+03     115     128 ..      74      87 ..      35     117 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                   Cytidylate_kin2  1 iITIsreyGsgGetigeaLAekLglpfydr 30
                                      iI ++++ G g++t g++LA++Lg+ f+d 
  gi|557693518|ref|YP_008796572.1|  2 IIWVTGTPGVGKTTTGRMLAKRLGIGFIDL 31
                                      5778899*********************95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.5
                   Cytidylate_kin2 115 vlrvfltapledrv 128
                                       ++ v++ + + +++
  gi|557693518|ref|YP_008796572.1|  74 HITVRVRGHETRCI 87 
                                       33444444444444 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0024       2.6       1      25 [.       2      26 ..       2      68 .. 0.85
   2 ?    2.5   0.0     0.099     1e+02     152     168 ..     100     116 ..      89     120 .. 0.83
   3 ?    1.0   0.1      0.29   3.1e+02     126     152 ..     149     175 ..     141     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0024
                               PRK  1 vIgvagsSGaGkttvarklekifgr 25
                                      +I v+g  G Gktt+ r l k++g 
  gi|557693518|ref|YP_008796572.1|  2 IIWVTGTPGVGKTTTGRMLAKRLGI 26
                                      799******************9984 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.099
                               PRK 152 iaeRGrsleavldsilr 168
                                        +eRG+s+e v +++++
  gi|557693518|ref|YP_008796572.1| 100 LEERGYSVEKVAENVEA 116
                                       689********999875 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.29
                               PRK 126 vaelldlkiyvdisidlelarklqRDi 152
                                       v   +d+  + d+ +d+e++ +l  Di
  gi|557693518|ref|YP_008796572.1| 149 VNRCVDVLEGRDAGDDVEWMSRLDEDI 175
                                       6777889999999**********9997 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.9e-05     0.031       1      24 [.       3      26 ..       3      50 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallk 24
                                      iw++G +g+GK+t+ + Lak+l  
  gi|557693518|ref|YP_008796572.1|  3 IWVTGTPGVGKTTTGRMLAKRLGI 26
                                      8*******************9983 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   0.00013      0.14      22      62 ..       3      43 ..       1      78 [. 0.77
   2 ?   -1.3   0.0       1.9     2e+03      97     105 ..     165     173 ..     110     188 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                      EEEEESTTSSHHHHHHHHHHHTT------TTTTSEEEEEE. CS
                              TsaE 22 ilLeGdLGaGKTtlvrglakalgveevkSPTFtlveeYele 62
                                      i  +G  G+GKTt  r lak lg+  +  P F+ +++  +e
  gi|557693518|ref|YP_008796572.1|  3 IWVTGTPGVGKTTTGRMLAKRLGIGFIDLPEFVSANNLYTE 43
                                      7789999*****************99999999888764343 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.9
                                       EETGGGGCC CS
                              TsaE  97 vEWpeklee 105
                                       vEW ++l+e
  gi|557693518|ref|YP_008796572.1| 165 VEWMSRLDE 173
                                       677777644 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.6e-05      0.09      47      75 ..       2      30 ..       1      49 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.6e-05
                             Rad17 47 iLLisGPsGCgkstvvkvLskelgiklre 75
                                      i+ ++G +G gk+t+ ++L+k lgi +++
  gi|557693518|ref|YP_008796572.1|  2 IIWVTGTPGVGKTTTGRMLAKRLGIGFID 30
                                      6789********************98765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.11       5      25 ..       3      22 ..       1      56 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                            AAA_24  5 iliyGpsgiGKTtlakelgpk 25
                                      i+++G +g+GKTt+ ++l  k
  gi|557693518|ref|YP_008796572.1|  3 IWVTGTPGVGKTTTGRML-AK 22
                                      9*************9998.44 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 ?   12.1   0.0   0.00011      0.12       2      42 ..       4      49 ..       3      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrts....liltvnrptaelltegk.pkl 42
                                       v G pG GK+t  r l++       +l + +++++l+te++ + +
  gi|557693518|ref|YP_008796572.1|  4 WVTGTPGVGKTTTGRMLAKRLgigfIDLPEFVSANNLYTERLgDGT 49
                                      699***************99999999999***********996333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7   0.00025      0.26       2      22 ..       3      23 ..       2      29 .. 0.83
   2 ?    0.1   0.2      0.62   6.5e+02      26      45 ..      67      86 ..      55     143 .. 0.68
   3 ?   -1.6   0.0       2.1   2.2e+03      45      64 ..     103     122 ..      94     160 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                                      EEEE--TTSSHHHHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlel 22
                                      + +TG pGvGKtT  + +++ 
  gi|557693518|ref|YP_008796572.1|  3 IWVTGTPGVGKTTTGRMLAKR 23
                                      689**********87766665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.62
                                      .GGGEEEEEEEEE------- CS
                          NTPase_1 26 sgvkvgGfyteevreggrri 45
                                      ++  ++G +t +vr +++r 
  gi|557693518|ref|YP_008796572.1| 67 EDTVIAGHITVRVRGHETRC 86
                                      45667777777777666653 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.1
                                       -EEEEEET.T--EEEEEETT CS
                          NTPase_1  45 igFkivdlasgeegiLarve 64 
                                        g+++ ++a++ e+++  v 
  gi|557693518|ref|YP_008796572.1| 103 RGYSVEKVAENVEAEFLGVV 122
                                       45555555555555544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 00:00:00.40
# Mc/sec: 1436.53
//
Query:       gi|557693519|ref|YP_008796573.1|  [L=595]
Description: ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  145.1   0.0    4.1e-21   75.9   0.0    2.6  2  ABC_tran      ABC transporter
    8.8e-14   52.0   6.8    0.00039   20.3   0.0    4.2  4  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.4e-11   42.6   1.7     0.0052   16.3   0.0    4.1  4  SMC_N         RecF/RecN/SMC N terminal domain
    2.9e-07   30.0   3.5    2.9e-07   30.0   3.5    2.3  1  Fer4          4Fe-4S binding domain
    1.7e-06   28.2   0.0       0.28   11.3   0.0    3.6  2  AAA_33        AAA domain
    2.5e-06   27.2   1.9    5.7e-06   26.1   1.9    1.7  1  RLI           Possible Fer4-like domain in RNase L inhibitor,
    3.7e-06   26.8  12.1    0.00026   20.9   2.3    2.3  2  Fer4_6        4Fe-4S binding domain
    2.7e-05   24.1   0.0       0.88    9.2   0.0    3.2  3  AAA_15        AAA ATPase domain
    7.3e-05   22.6  11.4      0.014   15.5   1.3    2.4  2  Fer4_2        4Fe-4S binding domain
    0.00013   21.8   0.1       0.14   11.9   0.0    2.4  2  AAA_24        AAA domain
    0.00021   20.6   0.3      0.021   14.0   0.0    2.4  2  NB-ARC        NB-ARC domain
    0.00038   20.9   0.0       0.49   10.8   0.0    2.6  2  AAA           ATPase family associated with various cellular 
    0.00071   19.7   5.6     0.0016   18.6   5.7    1.6  1  Fer4_9        4Fe-4S dicluster domain
    0.00084   19.9   0.2       0.53   10.7   0.1    2.6  2  AAA_23        AAA domain
    0.00094   18.8   1.0      0.024   14.2   0.0    2.9  3  AAA_25        AAA domain
     0.0017   18.9   6.3      0.003   18.1   0.3    2.4  2  Fer4_7        4Fe-4S dicluster domain
      0.002   18.5   0.0        2.4    8.6   0.0    2.5  2  RNA_helicase  RNA helicase
     0.0036   17.4   7.2     0.0061   16.7   7.2    1.4  1  Fer4_21       4Fe-4S dicluster domain
     0.0048   17.0  11.0     0.0076   16.3   1.7    2.3  2  Fer4_10       4Fe-4S dicluster domain
     0.0049   16.8   0.1        1.5    8.7   0.0    2.5  2  RsgA_GTPase   RsgA GTPase
     0.0053   16.5   0.0        1.8    8.4   0.0    2.4  2  AAA_29        P-loop containing region of AAA domain
     0.0073   16.6   0.6        1.7    8.9   0.0    2.9  2  AAA_22        AAA domain
      0.008   16.7   1.1         18    5.9   0.0    3.6  3  AAA_18        AAA domain
  ------ inclusion threshold ------
      0.013   15.9   1.2        4.8    7.5   0.1    3.0  2  AAA_16        AAA ATPase domain
      0.014   15.3   0.0        1.1    9.1   0.0    2.4  2  Rad17         Rad17 P-loop domain
      0.015   16.2   0.3      0.015   16.2   0.3    2.3  1  Fer4_16       4Fe-4S double cluster binding domain
      0.016   15.1   3.1        1.3    8.9   0.0    2.4  2  NACHT         NACHT domain
      0.016   14.9   0.1       0.23   11.2   0.0    2.4  2  IstB_IS21     IstB-like ATP binding protein
      0.023   14.4   1.4       0.47   10.2   0.0    3.0  3  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.066   13.5   0.1         19    5.6   0.0    3.2  2  SbcCD_C       Putative exonuclease SbcCD, C subunit
      0.075   13.1   0.3         13    5.9   0.0    3.1  3  AAA_14        AAA domain
      0.085   13.1   0.1         27    5.0   0.0    3.2  3  AAA_28        AAA domain
       0.12   12.2   2.7         12    5.7   0.2    3.7  4  NTPase_1      NTPase
       0.21   12.0   0.1       0.21   12.0   0.1    2.0  1  Fer4_8        4Fe-4S dicluster domain
       0.31   10.0   1.0        2.9    6.8   0.0    2.2  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.34   10.5   2.6        3.9    7.1   0.1    2.3  2  SRP54         SRP54-type protein, GTPase domain
       0.71    9.6   2.0        2.8    7.7   0.0    2.6  3  MukB          MukB N-terminal
        1.4    9.5   6.6       0.27   11.8   1.8    2.0  2  Fer4_17       4Fe-4S dicluster domain
        2.5    8.9   5.3        5.2    7.9   0.9    2.9  2  Fer4_15       4Fe-4S single cluster 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 !   75.9   0.0     9e-24   4.1e-21       9     136 ..     100     243 ..      99     244 .. 0.84
   2 !   66.4   0.0     8e-21   3.7e-18       8     137 .]     366     486 ..     363     486 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 9e-24
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE...........EETTCEGGG..B-HHHCCHCEEEE-SS--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGei...........lldgkdlke..qeleslrkeigvlpqepqlfp 72 
                                       ++g++v+++G+nG GKSt lk+lag+l p+ G +            ++g  ++e   ++++ ++++++ pq+    p
  gi|557693519|ref|YP_008796573.1| 100 EAGKVVGLLGKNGIGKSTALKILAGQLVPNFGILdrpvtweeasrFFRGSLIQEhlSSISKGKSKVSYKPQNIAEIP 176
                                       589*****************************997777777766644444444466778888999999999966666 PP

                                       TSBHHHH........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  73 eltvren........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++ v  +         + + +e++++kl+l++l d+ +    + LSgG+ qr+a+a++ll+k+++++lDEp+
  gi|557693519|ref|YP_008796573.1| 177 KV-VTGTvkqvlsrlGDAAAVEEVMEKLELTKLSDRDI----RFLSGGELQRLAIAACLLRKADVYILDEPS 243
                                       65.33333567988888888******************....*****************************7 PP

  == domain 2  score: 66.4 bits;  conditional E-value: 8e-21
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren..... 79 
                                       +++ge+++ivG+nG GK+t+++++ag  + ++G               +  k +++ pq pq ++++ v+e+     
  gi|557693519|ref|YP_008796573.1| 366 VYRGEVLGIVGPNGIGKTTFASIIAGVQETDQGFT-------------FDPKAVSYKPQYPQADDRT-VEEHlreaa 428
                                       679**************************999986.............7799999999999999999.999988877 PP

                                       ..HHHTC..HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       ..xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ..esdee..iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                         e+d     + +l+ +gl++l ++++    ++LSgG+ q+v++a++l +k+++++lDEp+a
  gi|557693519|ref|YP_008796573.1| 429 gqEYDTSlyQSLILRPFGLEKLLEKNM----KELSGGELQKVVVAECLSRKADIYVLDEPSA 486
                                       664444444666888999999888888....*****************************75 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 !   13.4   0.7   0.00011      0.05       2      46 ..     105     143 ..     104     154 .. 0.72
   2 !   20.3   0.0   8.6e-07   0.00039     168     303 .]     165     279 ..     138     279 .. 0.83
   3 !   15.2   0.1     3e-05     0.014       3      30 ..     373     400 ..     371     415 .. 0.78
   4 ?    3.7   0.0     0.097        45     234     285 ..     455     503 ..     418     514 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkip 46 
                                        +l G+Ng GKS+ L++l      ++ + +   +l++ +++ + +
  gi|557693519|ref|YP_008796573.1| 105 VGLLGKNGIGKSTALKIL------AGQLVPNFGILDRPVTWEEAS 143
                                       689***************......555556666665555555555 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 8.6e-07
                            AAA_21 168 llnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrl 244
                                       +   +++ +  +k+ + + + v s++ + + ++  +e+ el +++d+++r+                  lS G ++ 
  gi|557693519|ref|YP_008796573.1| 165 VSYKPQNIAEIPKVVTGTVKQVLSRLGDAAAVEEVMEKLELTKLSDRDIRF------------------LSGGELQR 223
                                       555667777788888888888888888888888888888888888888888..................******** PP

                            AAA_21 245 lalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpllld 303
                                       la+++ llr +   +++++DEp ++L+ +   r +e ++++ r +++++++ H+  +ld
  gi|557693519|ref|YP_008796573.1| 224 LAIAACLLRKA---DVYILDEPSSFLDIRQRLRMVEAVRNALRDNVKIVVADHDLAVLD 279
                                       88888888777...************************999999*******99988876 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 3e-05
                            AAA_21   3 vliGpNgsGKSnLLdaldllarldrdve 30 
                                       +++GpNg GK+++  ++ +++ +d+ ++
  gi|557693519|ref|YP_008796573.1| 373 GIVGPNGIGKTTFASIIAGVQETDQGFT 400
                                       79***************99986544333 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.097
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkel 285
                                       + elS G ++   +++ +l++    +++++DEp ++L+ +   + +++lk+l
  gi|557693519|ref|YP_008796573.1| 455 MKELSGGELQK-VVVAECLSRKA--DIYVLDEPSAFLDVEERYHMAKILKRL 503
                                       55678888888.77888887665..9************97776666666554 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 ?    2.3   0.0      0.21        95      10      40 ..      91     118 ..      84     126 .. 0.74
   2 !   15.1   0.0   2.6e-05     0.012     118     195 ..     194     271 ..     129     289 .. 0.73
   3 ?    5.3   0.0     0.026        12      26      42 ..     371     387 ..     354     400 .. 0.85
   4 !   16.3   0.0   1.1e-05    0.0052     134     213 ..     455     532 ..     404     538 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.21
                                       ETTEECEEEEEETTSSEEEEEESTTSSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  10 FksyagktvilpfsksftaivGpNGSGKsnl 40 
                                       Fk +   +   p + ++  ++G+NG GKs  
  gi|557693519|ref|YP_008796573.1|  91 FKLF---RLPYPEAGKVVGLLGKNGIGKSTA 118
                                       5555...3555666678889*********75 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.6e-05
                                       E-HHHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH.CTTS CS
                                       xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                             SMC_N 118 vtkkevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek.skna 190
                                       +  +ev+e le +++s      LSgGe + +a+a        ++a +y+lDe  + LD +++ +++e ++++ ++n+
  gi|557693519|ref|YP_008796573.1| 194 AAVEEVMEKLELTKLSDRdirFLSGGELQRLAIAAC----LLRKADVYILDEPSSFLDIRQRLRMVEAVRNAlRDNV 266
                                       4445555555555554224449*****887666554....588999***********************96515556 PP

                                       EEEEE CS
                                       xxxxx RF
                             SMC_N 191 Qfivi 195
                                        ++v 
  gi|557693519|ref|YP_008796573.1| 267 KIVVA 271
                                       55555 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.026
                                       EEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlld 42 
                                       +  ivGpNG GK+ +  
  gi|557693519|ref|YP_008796573.1| 371 VLGIVGPNGIGKTTFAS 387
                                       567*********98765 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 1.1e-05
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemlekadkl 208
                                       +++LSgGe + v +a        ++a +y+lDe  a LD +++  +a++lk  + +k++ ++ + ++ ++l  a++ 
  gi|557693519|ref|YP_008796573.1| 455 MKELSGGELQKVVVAEC----LSRKADIYVLDEPSAFLDVEERYHMAKILKrlALEKKVYVLLVEHDFTVLDFASSA 527
                                       45899999886655544....568999************************44455667777777777777777777 PP

                                       EEEEE CS
                                       xxxxx RF
                             SMC_N 209 vgvtk 213
                                       + v++
  gi|557693519|ref|YP_008796573.1| 528 LMVFS 532
                                       76665 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   3.5   6.4e-10   2.9e-07       1      24 []      47      70 ..      47      70 .. 0.94

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 6.4e-10
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      ++i e +Ci CG+Cv+ CP++AIt
  gi|557693519|ref|YP_008796573.1| 47 PIISETLCISCGICVKKCPFEAIT 70
                                      5899*******************7 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00083      0.38       2     107 ..     105     274 ..     104     279 .. 0.72
   2 !   11.3   0.0   0.00061      0.28       4     104 ..     374     512 ..     371     518 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00083
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdt............................................ 32 
                                       v l G +G GKst ++ l+ +l   + +l+ ++                                            
  gi|557693519|ref|YP_008796573.1| 105 VGLLGKNGIGKSTALKILAGQLVpnFGILDRPVtweeasrffrgsliqehlssiskgkskvsykpqniaeipkvvtg 181
                                       66789****************9999999****99*******999999999999999999999999999999999888 PP

                            AAA_33  33 ........lrrrlfgtdqqsktdytrvldr........lyqilnelarkalsagrnvildat..nlsrrerarflkl 91 
                                               l ++ +++++  k ++t+++dr          q+l ++a+  l+++  +ild +  +l+ r+r r++++
  gi|557693519|ref|YP_008796573.1| 182 tvkqvlsrLGDAAAVEEVMEKLELTKLSDRdirflsggELQRL-AIAACLLRKADVYILDEPssFLDIRQRLRMVEA 257
                                       8888776633333334444444555554444444444466666.6666556666669**999889999999888888 PP

                            AAA_33  92 arrlgvp..vrivvvetd 107
                                       +r+   +  v+ivv + d
  gi|557693519|ref|YP_008796573.1| 258 VRN-ALRdnVKIVVADHD 274
                                       872.22311455554444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00061
                            AAA_33   4 lvGlpGsGKstlaerllkklg...avllssdt..........................lrrrlfgtdqqskt..... 46 
                                       +vG++G GK+t+a  ++  +    +++ +  +                          +                  
  gi|557693519|ref|YP_008796573.1| 374 IVGPNGIGKTTFASIIAGVQEtdqGFTFDPKAvsykpqypqaddrtveehlreaagqeY------------Dtslyq 438
                                       79***********9986544444766666666555555555555555554444444440............044445 PP

                            AAA_33  47 ...............dytrvldrlyqilnelarkalsagrn.vildat..nlsrrerarflklarrlgvpvrivvv 104
                                                      + ++++    q    +++++ls++++ ++ld +  +l+ +er  + k+++rl  + ++ v+
  gi|557693519|ref|YP_008796573.1| 439 slilrpfglekllekNMKELSGGELQK--VVVAECLSRKADiYVLDEPsaFLDVEERYHMAKILKRLALEKKVYVL 512
                                       555555555444332555555444444..46778999999988889888899999999999999999988877665 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 !   26.1   1.9   1.2e-08   5.7e-06       2      32 ..       6      34 ..       5      37 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.2e-08
                                      -EEEES---------TTHHHHHTTSEEEESS CS
                               RLI  2 rlAivdadqCdPKKCtgkkcarfcpvrlvrt 32
                                      r+A+ d+d+Cd KKC    c+ +cp   vr+
  gi|557693519|ref|YP_008796573.1|  6 RVAVLDRDRCDSKKCGNWPCITYCPP--VRN 34
                                      9*************************..997 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   2.4   0.00074      0.34       4      20 ..      10      30 ..       7      39 .. 0.85
   2 !   20.9   2.3   5.7e-07   0.00026       2      24 .]      47      69 ..      46      69 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00074
                            Fer4_6  4 idpdkCi..gCgd..CvrvCP 20
                                       d+d+C+   Cg+  C++ CP
  gi|557693519|ref|YP_008796573.1| 10 LDRDRCDskKCGNwpCITYCP 30
                                      59*****777*********** PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.7e-07
                            Fer4_6  2 veidpdkCigCgdCvrvCPegai 24
                                      + i + +Ci+Cg Cv+ CP+ ai
  gi|557693519|ref|YP_008796573.1| 47 PIISETLCISCGICVKKCPFEAI 69
                                      668899**************998 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0046       2.1      27      43 ..     106     122 ..      91     124 .. 0.87
   2 !    9.2   0.0    0.0019      0.88      25      44 ..     371     390 ..     352     436 .. 0.82
   3 ?    2.9   0.0      0.15        71     323     356 ..     475     508 ..     464     517 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0046
                            AAA_15  27 vliGkNnsGKSsileal 43 
                                        l GkN++GKS++l++l
  gi|557693519|ref|YP_008796573.1| 106 GLLGKNGIGKSTALKIL 122
                                       578************98 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0019
                            AAA_15  25 ltvliGkNnsGKSsileald 44 
                                       +  ++G+N++GK++++ ++ 
  gi|557693519|ref|YP_008796573.1| 371 VLGIVGPNGIGKTTFASIIA 390
                                       6679************9995 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.15
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnk 356
                                       k +i++++EP a L  +  ++++k lk+la ++k
  gi|557693519|ref|YP_008796573.1| 475 KADIYVLDEPSAFLDVEERYHMAKILKRLALEKK 508
                                       679***************************9986 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   3.1    0.0004      0.18       2      21 ..       7      30 ..       6      31 .. 0.92
   2 !   15.5   1.3     3e-05     0.014       7      21 ..      51      65 ..      45      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0004
                            Fer4_2  2 pvvvdtdrCig..Cg..aCvsaCP 21
                                      ++v d+drC +  Cg  +C++ CP
  gi|557693519|ref|YP_008796573.1|  7 VAVLDRDRCDSkkCGnwPCITYCP 30
                                      5789*****999***********9 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3e-05
                            Fer4_2  7 tdrCigCgaCvsaCP 21
                                      +  Ci+Cg+Cv+ CP
  gi|557693519|ref|YP_008796573.1| 51 ETLCISCGICVKKCP 65
                                      567************ PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0061       2.8       3      23 ..     103     127 ..     101     136 .. 0.77
   2 !   11.9   0.0    0.0003      0.14       5      22 ..     372     389 ..     368     435 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0061
                            AAA_24   3 lkiliyGpsgiGKTtlakel....g 23 
                                       + + + G++giGK+t +k l     
  gi|557693519|ref|YP_008796573.1| 103 KVVGLLGKNGIGKSTALKILagqlV 127
                                       67899***********998854444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0003
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       + i+Gp+giGKTt+a+ +
  gi|557693519|ref|YP_008796573.1| 372 LGIVGPNGIGKTTFASII 389
                                       689************876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3     0.045        21      19      38 ..     102     120 ..      89     240 .. 0.89
   2 !   14.0   0.0   4.5e-05     0.021      22     110 ..     371     482 ..     366     525 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.045
                                       CSEEEEEEESTTSSHHHHHH CS
                            NB-ARC  19 qslvvalvGmgGvGKttlak 38 
                                       +  vv+l G+ G+GK+t +k
  gi|557693519|ref|YP_008796573.1| 102 G-KVVGLLGKNGIGKSTALK 120
                                       4.69************9654 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 4.5e-05
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE...................EEESXXHHHHHHHXXHHHHHC CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdeveg.rFdsvawv...................vvsktdkseeiletilkeLsl 78 
                                       v+++vG  G+GKtt a+ i    ++ +g +Fd  a                       +++++ +  +  il+ ++l
  gi|557693519|ref|YP_008796573.1| 371 VLGIVGPNGIGKTTFASIIAGVQETDQGfTFDPKAVSykpqypqaddrtveehlreAAGQEYDTSLYQSLILRPFGL 447
                                       89**************9998885555557888444336899999999999999999999999999999999999999 PP

                                       CCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEE CS
                            NB-ARC  79 seddleekeeves...lkrklvrlLltkrfllvlD 110
                                       ++   ++++e       k  + + L +k  + vlD
  gi|557693519|ref|YP_008796573.1| 448 EKLLEKNMKELSGgelQKVVVAECLSRKADIYVLD 482
                                       98777777776667766777788888888888888 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 ?    7.4   0.0     0.012       5.6       3      35 ..     107     139 ..     105     186 .. 0.71
   2 !   10.8   0.0    0.0011      0.49       3      21 ..     374     392 ..     372     435 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.012
                                       EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS CS
                               AAA   3 lyGppGtGKTllakavakelgvefleisgsell 35 
                                       l G  G+GK+++ k +a +l  +f  ++ +  +
  gi|557693519|ref|YP_008796573.1| 107 LLGKNGIGKSTALKILAGQLVPNFGILDRPVTW 139
                                       89*****************86655555544444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0011
                                       EESSTTSSHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavake 21 
                                       ++Gp G+GKT++a+ +a  
  gi|557693519|ref|YP_008796573.1| 374 IVGPNGIGKTTFASIIAGV 392
                                       68**************975 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   5.7   3.4e-06    0.0016       4      51 .]      19      69 ..      13      69 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.4e-06
                            Fer4_9  4 gCga..CveaCpagvvveda.aerkarlraaseeaCigCgaCveaCpkgai 51
                                      +Cg+  C++ Cp   ++ +a + +++   + se+ Ci+Cg Cv++Cp +ai
  gi|557693519|ref|YP_008796573.1| 19 KCGNwpCITYCPPVRNNIEAiKMGEDGFPIISETLCISCGICVKKCPFEAI 69
                                      48777799999766665444145555666667799************9876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.021       9.7      21      39 ..     104     122 ..      88     206 .. 0.91
   2 !   10.7   0.1    0.0012      0.53      22      37 ..     372     387 ..     351     392 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.021
                            AAA_23  21 ltlItGpNGaGKTTildAi 39 
                                       ++ + G+NG GK+T l  +
  gi|557693519|ref|YP_008796573.1| 104 VVGLLGKNGIGKSTALKIL 122
                                       67789*********99766 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0012
                            AAA_23  22 tlItGpNGaGKTTild 37 
                                         I+GpNG GKTT+  
  gi|557693519|ref|YP_008796573.1| 372 LGIVGPNGIGKTTFAS 387
                                       57***********975 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.36   1.7e+02      32      51 ..     101     120 ..      97     139 .. 0.85
   2 ?   -2.1   0.1       5.3   2.4e+03     100     150 ..     233     280 ..     196     286 .. 0.56
   3 !   14.2   0.0   5.2e-05     0.024      27     188 ..     363     516 ..     358     517 .. 0.62

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.36
                            AAA_25  32 agelallaGapgtGKttlal 51 
                                       ag+++ l G  g GK+t++ 
  gi|557693519|ref|YP_008796573.1| 101 AGKVVGLLGKNGIGKSTALK 120
                                       789999***********875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.3
                            AAA_25 100 darllvldlagveslpLfakdrggtl.ltadvdaleaaieev.egvrlvviDp 150
                                       +a++++ld +++     f ++r+  + ++a+ +al++ ++ v ++ +l v+D 
  gi|557693519|ref|YP_008796573.1| 233 KADVYILDEPSS-----FLDIRQRLRmVEAVRNALRDNVKIVvADHDLAVLDY 280
                                       566666665444.....223333333334444444444433323445555555 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 5.2e-05
                            AAA_25  27 kgllpagelallaGapgtGKttlaldlalavatGkpwlg.pvapeqgkVlyvsaEdsedelrrRlravgealrddar 102
                                       +g++ +ge+  ++G+ g GKtt+a+ +a    t++ ++  p +    k  y +a+d+  e + R +a+g++++    
  gi|557693519|ref|YP_008796573.1| 363 EGWVYRGEVLGIVGPNGIGKTTFASIIAGVQETDQGFTFdP-KAVSYKPQYPQADDRTVEEHLR-EAAGQEYDTSLY 437
                                       79**********************99888777888777743.4577777888888888555555.336677732222 PP

                            AAA_25 103 llvldlagv.eslpLfakdrggtlltadv.daleaaieevegvrlvviDplsralggdensnsdvgalvealeriar 177
                                         ++ +    +   L++k    +l  +++ + + a++ +  +++  v+D  s++l+ +e       ++ + l+r+a 
  gi|557693519|ref|YP_008796573.1| 438 QSLILR--PfGLEKLLEKN-MKELSGGELqKVVVAECLS-RKADIYVLDEPSAFLDVEER-----YHMAKILKRLAL 505
                                       222221..11233333322.2222222220224566666.45888888888888877776.....666777777777 PP

                            AAA_25 178 rtgaavllvhH 188
                                       ++++ vllv H
  gi|557693519|ref|YP_008796573.1| 506 EKKVYVLLVEH 516
                                       77777777777 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   1.2      0.37   1.7e+02      31      49 ..       8      30 ..       3      32 .. 0.79
   2 !   18.1   0.3   6.6e-06     0.003       2      20 ..      54      72 ..      53      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.37
                            Fer4_7 31 veidpekC..lgCga..CvavCP 49
                                      +++d ++C    Cg+  C++ CP
  gi|557693519|ref|YP_008796573.1|  8 AVLDRDRCdsKKCGNwpCITYCP 30
                                      456889994446**9*******9 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6.6e-06
                            Fer4_7  2 CigCgaCvaaCpvkaield 20
                                      Ci Cg Cv+ Cp +ai++ 
  gi|557693519|ref|YP_008796573.1| 54 CISCGICVKKCPFEAITII 72
                                      ****************975 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0052       2.4       3      27 ..     107     138 ..     105     181 .. 0.72
   2 ?    7.4   0.0     0.012       5.6       3      19 ..     374     390 ..     372     425 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0052
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkkl.......k 27 
                                       l G++g+GKSt+ k La +l  ++        
  gi|557693519|ref|YP_008796573.1| 107 LLGKNGIGKSTALKILAGQLVPNFgildrpvT 138
                                       68***************999977733333333 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.012
                      RNA_helicase   3 lyGpsgeGKStlakeLa 19 
                                       ++Gp+g+GK+t+a  +a
  gi|557693519|ref|YP_008796573.1| 374 IVGPNGIGKTTFASIIA 390
                                       78***********9854 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   7.2   1.3e-05    0.0061       1      58 [.       8      70 ..       8      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-05
                           Fer4_21  1 AridedkC..igCgk..CliaCe..dtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      A++d+d+C   +Cg+  C++ C+   + ++ai++ ++    + e  C+ C +C++ CP  ++i+
  gi|557693519|ref|YP_008796573.1|  8 AVLDRDRCdsKKCGNwpCITYCPpvRNNIEAIKMGEDGFPIISETLCISCGICVKKCPF-EAIT 70
                                      56777777444688666*****944478899999777665566889************7.8887 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6  12.5     0.001      0.48       3      56 .]       9      65 ..       7      65 .. 0.80
   2 !   16.3   1.7   1.7e-05    0.0076       3      23 ..      48      68 ..      46      93 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.001
                           Fer4_10  3 vidddtC..irCg..kCvkaCPadltsvgakgeaseeeavrkkvek.CtgcgaCveaCP 56
                                      v+d+d+C   +Cg   C + CP    +++ ++++++e+   + +e  C+ cg Cv++CP
  gi|557693519|ref|YP_008796573.1|  9 VLDRDRCdsKKCGnwPCITYCPP--VRNNIEAIKMGEDGFPIISETlCISCGICVKKCP 65
                                      7899***7779**999*******..6777777777777777744435***********9 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.7e-05
                           Fer4_10  3 vidddtCirCgkCvkaCPadl 23
                                      +i +  Ci Cg Cvk CP+ +
  gi|557693519|ref|YP_008796573.1| 48 IISETLCISCGICVKKCPFEA 68
                                      688899************955 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    0.0032       1.5      99     123 ..     102     126 ..      91     161 .. 0.90
   2 ?    5.3   0.0     0.037        17      98     123 ..     368     393 ..     360     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0032
                                       TSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpel 123
                                       +k++ l+G+ G+GKSt ++ l+++l
  gi|557693519|ref|YP_008796573.1| 102 GKVVGLLGKNGIGKSTALKILAGQL 126
                                       68999**************999885 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.037
                                       TTSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpel 123
                                       ++++  +vG+ G+GK+t+   +++ +
  gi|557693519|ref|YP_008796573.1| 368 RGEVLGIVGPNGIGKTTFASIIAGVQ 393
                                       5678889***********99888754 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   0.0    0.0039       1.8      20      39 ..      99     119 ..      88     130 .. 0.76
   2 ?    5.4   0.0     0.033        15      24      38 ..     371     385 ..     354     390 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0039
                            AAA_29  20 dlkg.atlltGpsGsGKSTll 39 
                                        ++g ++ l G++G GKST l
  gi|557693519|ref|YP_008796573.1|  99 PEAGkVVGLLGKNGIGKSTAL 119
                                       556767889**********87 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.033
                            AAA_29  24 atlltGpsGsGKSTl 38 
                                       +  ++Gp+G GK+T+
  gi|557693519|ref|YP_008796573.1| 371 VLGIVGPNGIGKTTF 385
                                       5669**********7 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.3     0.073        34      10      30 ..     107     127 ..     100     274 .. 0.84
   2 !    8.9   0.0    0.0038       1.7       8     102 ..     372     486 ..     367     519 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.073
                            AAA_22  10 vtGesGtGKTtllrrlleqld 30 
                                       + G  G+GK+t l+ l+ ql+
  gi|557693519|ref|YP_008796573.1| 107 LLGKNGIGKSTALKILAGQLV 127
                                       67999*********9999885 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0038
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsst.sskdllrellralglelka.......... 70 
                                       l ++G+ G+GKTt +  ++   + +    +    +p+ v+++++ +  + +++ ++l +a g+e ++          
  gi|557693519|ref|YP_008796573.1| 372 LGIVGPNGIGKTTFASIIAGVQETD----QgftFDPKAVSYKPQYPQaDDRTVEEHLREAAGQEYDTslyqslilrp 444
                                       669***********99988876433....234557777777776666655555566666666555555555666655 PP

                            AAA_22  71 ...........erlsseellealeqalraravielliiDEaqh 102
                                                  ++ls  el + +   + +r++  + ++DE   
  gi|557693519|ref|YP_008796573.1| 445 fgleklleknmKELSGGELQKVVVAECLSRKA-DIYVLDEPSA 486
                                       55555656666666666666555555555555.7777777655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.039        18       1      35 [.     105     141 ..     105     211 .. 0.80
   2 ?    3.3   0.0      0.24   1.1e+02      28      85 ..     227     284 ..     216     299 .. 0.82
   3 ?    4.1   0.1      0.14        63       3      19 ..     374     390 ..     372     510 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.039
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.gvnlrdvaken 35 
                                       ++l G+ G GK+t  k L+  l  + g+  r v +e+
  gi|557693519|ref|YP_008796573.1| 105 VGLLGKNGIGKSTALKILAGQLvPNfGILDRPVTWEE 141
                                       6899**************8887533455555555444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.24
                            AAA_18  28 lrdvakenglllevdpe...aldeskrldedkldklldaleenssaleegknlvidghlae 85 
                                         +++++ + ++ ++p    ++++ +r++e ++++l d+++      ++++  v+d +   
  gi|557693519|ref|YP_008796573.1| 227 AACLLRKADVYILDEPSsflDIRQRLRMVEAVRNALRDNVKIVV---ADHDLAVLDYFSDT 284
                                       5678999999999999999999*****************99975...57888888887665 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.14
                            AAA_18   3 ltGtpGvGKttlakeLs 19 
                                       + G+ G GKtt+a  ++
  gi|557693519|ref|YP_008796573.1| 374 IVGPNGIGKTTFASIIA 390
                                       89***********9883 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2     0.035        16      25      52 ..     103     134 ..      97     282 .. 0.73
   2 ?    7.5   0.1      0.01       4.8      25      71 ..     370     410 ..     366     531 .. 0.53

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.035
                            AAA_16  25 elvllsGesGvGKsslvrellralekd....g 52 
                                        +v l G  G+GKs+ ++ l+ +l  +    +
  gi|557693519|ref|YP_008796573.1| 103 KVVGLLGKNGIGKSTALKILAGQLVPNfgilD 134
                                       567799***********999988888844430 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.01
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa 71 
                                       e++ ++G+ G+GK++ +  ++   e+d g+++  k++++       +
  gi|557693519|ref|YP_008796573.1| 370 EVLGIVGPNGIGKTTFASIIAGVQETDQGFTFDPKAVSY------KP 410
                                       66779**********998888544444344444444444......33 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0025       1.1      48      85 ..     105     142 ..      96     200 .. 0.76
   2 ?    3.6   0.0      0.12        57      47      66 ..     371     390 ..     360     419 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0025
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkep 85 
                                       + + G  G gkst++k+L+ +l++++     pv+  e+
  gi|557693519|ref|YP_008796573.1| 105 VGLLGKNGIGKSTALKILAGQLVPNFGILDRPVTWEEA 142
                                       557799*****************998777777766555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.12
                             Rad17  47 iLLisGPsGCgkstvvkvLs 66 
                                       +L i GP G gk+t   +++
  gi|557693519|ref|YP_008796573.1| 371 VLGIVGPNGIGKTTFASIIA 390
                                       889***********988876 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 ?   16.2   0.3   3.4e-05     0.015       2      18 ..      54      70 ..      53      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.4e-05
                           Fer4_16  2 CgtCgkCaevCPtnaik 18
                                      C++Cg C++ CP +ai+
  gi|557693519|ref|YP_008796573.1| 54 CISCGICVKKCPFEAIT 70
                                      ***************97 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.0     0.026        12       2      21 ..     104     123 ..     103     127 .. 0.85
   2 ?    8.9   0.0    0.0029       1.3       3      21 ..     372     390 ..     370     402 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.026
                                       CEEEEC-TTTCHHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqkla 21 
                                       +v l G++G+GK+t l+ la
  gi|557693519|ref|YP_008796573.1| 104 VVGLLGKNGIGKSTALKILA 123
                                       67799**********99877 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0029
                                       EEEEC-TTTCHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqkla 21 
                                       + + G++G+GKTt++  +a
  gi|557693519|ref|YP_008796573.1| 372 LGIVGPNGIGKTTFASIIA 390
                                       5699**********98776 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 ?    0.5   0.0      0.93   4.3e+02      41      62 ..      96     117 ..      88     146 .. 0.81
   2 ?   11.2   0.0   0.00049      0.23      41      68 ..     363     390 ..     354     402 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.93
                         IstB_IS21  41 lsfiekkenivllGpsGvGKsh 62 
                                       l + e+ + + llG  G+GKs 
  gi|557693519|ref|YP_008796573.1|  96 LPYPEAGKVVGLLGKNGIGKST 117
                                       55666777889*********95 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00049
                         IstB_IS21  41 lsfiekkenivllGpsGvGKshlaialg 68 
                                         ++ + e + ++Gp G+GK+ +a  ++
  gi|557693519|ref|YP_008796573.1| 363 EGWVYRGEVLGIVGPNGIGKTTFASIIA 390
                                       56********************997664 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 ?    1.6   0.0      0.46   2.1e+02      36      66 ..     105     135 ..      99     143 .. 0.81
   2 ?   -2.4   0.0       7.6   3.5e+03      84      90 ..     210     216 ..     177     271 .. 0.64
   3 ?   10.2   0.0     0.001      0.47      38      58 ..     374     394 ..     367     407 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.46
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsg 66 
                                       v l G  G+Gk+t  ki+a +l  ++ i   
  gi|557693519|ref|YP_008796573.1| 105 VGLLGKNGIGKSTALKILAGQLVPNFGILDR 135
                                       55899**************999877766555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.6
                            RuvB_N  84 ekdvlfi 90 
                                       ++d+ f+
  gi|557693519|ref|YP_008796573.1| 210 DRDIRFL 216
                                       3333333 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.001
                            RuvB_N  38 lyGpPGlGkttlakiiakelg 58 
                                       ++Gp G+Gktt+a+iia   +
  gi|557693519|ref|YP_008796573.1| 374 IVGPNGIGKTTFASIIAGVQE 394
                                       68**************96555 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 ?    3.8   0.0      0.15        67      26      48 ..     209     231 ..     194     260 .. 0.77
   2 ?    5.6   0.0     0.041        19      22      42 ..     447     467 ..     432     502 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.15
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaa 48 
                                        +r+++ lSGGe q la  a ++
  gi|557693519|ref|YP_008796573.1| 209 SDRDIRFLSGGELQRLAIAACLL 231
                                       5789999******9988777654 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.041
                           SbcCD_C  22 kekelsrssgtlSGGekqfla 42 
                                        ek l++++++lSGGe q+++
  gi|557693519|ref|YP_008796573.1| 447 LEKLLEKNMKELSGGELQKVV 467
                                       56668999********99876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0      0.13        59       2      27 ..     102     127 ..     101     165 .. 0.83
   2 ?   -1.8   0.0       6.4   2.9e+03      62      85 ..     232     254 ..     180     272 .. 0.60
   3 ?    5.9   0.0     0.027        13       3      23 ..     370     390 ..     368     439 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.13
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell 27 
                                       +k++ + G   +GK+t lk l+ +l 
  gi|557693519|ref|YP_008796573.1| 102 GKVVGLLGKNGIGKSTALKILAGQLV 127
                                       589999************99987665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.4
                            AAA_14  62 eekktylflDEiqevpewekalks 85 
                                       + k  + +lDE +   ++++ l+ 
  gi|557693519|ref|YP_008796573.1| 232 R-KADVYILDEPSSFLDIRQRLRM 254
                                       3.5667788887777665555543 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.027
                            AAA_14   3 kilvitGaRrvGKTtllkqli 23 
                                       ++l i+G+  +GKTt++  ++
  gi|557693519|ref|YP_008796573.1| 370 EVLGIVGPNGIGKTTFASIIA 390
                                       7899***********986554 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.058        27       4      36 ..     107     147 ..     104     167 .. 0.76
   2 ?    4.0   0.0      0.12        55       4      20 ..     374     390 ..     372     438 .. 0.84
   3 ?   -1.1   0.0       4.4     2e+03      93     153 ..     460     521 ..     455     526 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.058
                            AAA_28   4 itGgestGKTtlleaLaar........gypvvpEaareile 36 
                                       ++G  + GK+t l+ La +        + pv +E a ++++
  gi|557693519|ref|YP_008796573.1| 107 LLGKNGIGKSTALKILAGQlvpnfgilDRPVTWEEASRFFR 147
                                       78999************666776766667777666666655 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.12
                            AAA_28   4 itGgestGKTtlleaLa 20 
                                       i+G+ + GKTt ++ +a
  gi|557693519|ref|YP_008796573.1| 374 IVGPNGIGKTTFASIIA 390
                                       89**********99888 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 4.4
                            AAA_28  93 ggeaeaeleaaarekrydlvfllppapeidddgeRre..dleereaiderlrealrelgipvi 153
                                       gge ++ ++a++ +++ d ++l +p++++ d +eR +  +  +r a+++++  +l e+++ v+
  gi|557693519|ref|YP_008796573.1| 460 GGELQKVVVAECLSRKADIYVLDEPSAFL-DVEERYHmaKILKRLALEKKVYVLLVEHDFTVL 521
                                       55666667788888889999999999999.777776522445577777777777777777665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0       0.2        92       3      23 ..     106     126 ..     104     144 .. 0.85
   2 ?    0.7   0.0      0.97   4.5e+02      91     130 ..     229     270 ..     216     282 .. 0.66
   3 ?    5.7   0.2     0.027        12       3      21 ..     373     391 ..     371     401 .. 0.81
   4 ?   -1.7   0.0       5.3   2.4e+03      91     103 ..     471     483 ..     461     517 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.2
                                       EEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlell 23 
                                        + G+ G+GK+T +k ++ +l
  gi|557693519|ref|YP_008796573.1| 106 GLLGKNGIGKSTALKILAGQL 126
                                       5779*********99888776 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.97
                                       HHHHHH-EEEE---STTGGG-H..HHHHHHHHHHTTTSEEEE CS
                          NTPase_1  91 kalseadviviDEiGkmElksk..kfkeaveevLksekpvla 130
                                       + l++adv+++DE  ++    +  ++ eav+++L+ ++ +++
  gi|557693519|ref|YP_008796573.1| 229 CLLRKADVYILDEPSSFLDIRQrlRMVEAVRNALRDNVKIVV 270
                                       345899999999977664444311456778888886666554 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.027
                                       EEE--TTSSHHHHHHHHHH CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvle 21 
                                        i Gp G+GKtT+ + ++ 
  gi|557693519|ref|YP_008796573.1| 373 GIVGPNGIGKTTFASIIAG 391
                                       688**********987765 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 5.3
                                       HHHHHH-EEEE-- CS
                          NTPase_1  91 kalseadviviDE 103
                                       +  ++ad++v+DE
  gi|557693519|ref|YP_008796573.1| 471 CLSRKADIYVLDE 483
                                       3447999999999 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00047      0.21       5      17 ..      54      66 ..      52     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00047
                            Fer4_8  5 CieCgaCqsaCpv 17
                                      Ci Cg C ++Cp+
  gi|557693519|ref|YP_008796573.1| 54 CISCGICVKKCPF 66
                                      9999999999994 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 ?    6.8   0.0    0.0062       2.9      27      54 ..     102     127 ..      88     133 .. 0.83
   2 ?    1.3   0.2       0.3   1.4e+02      28      48 ..     368     388 ..     364     398 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0062
                                       S-SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                              MeaB  27 GraqvvGltGvPGaGkstlvealglelr 54 
                                       G  +vvGl G  G Gkst+++ l+ +l+
  gi|557693519|ref|YP_008796573.1| 102 G--KVVGLLGKNGIGKSTALKILAGQLV 127
                                       4..69**************999987775 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.3
                                       -SEEEEEEE-TTSSHHHHHHH CS
                              MeaB  28 raqvvGltGvPGaGkstlvea 48 
                                       r +v+G+ G  G Gk t+ + 
  gi|557693519|ref|YP_008796573.1| 368 RGEVLGIVGPNGIGKTTFASI 388
                                       6789*************9775 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.4      0.14        67       3      24 ..     104     125 ..     102     130 .. 0.85
   2 ?    7.1   0.1    0.0085       3.9       4      23 ..     372     391 ..     370     400 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.14
                                       EEEEEESTTSSHHHHHHHHHHH CS
                             SRP54   3 villvGlqGaGKTttlaKLaal 24 
                                       v+ l+G +G+GK t+l  La +
  gi|557693519|ref|YP_008796573.1| 104 VVGLLGKNGIGKSTALKILAGQ 125
                                       67799**********9998865 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0085
                                       EEEEESTTSSHHHHHHHHHH CS
                             SRP54   4 illvGlqGaGKTttlaKLaa 23 
                                       + +vG++G+GKTt ++ +a 
  gi|557693519|ref|YP_008796573.1| 372 LGIVGPNGIGKTTFASIIAG 391
                                       568**********9887775 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0061       2.8      27      58 ..     103     134 ..      88     147 .. 0.84
   2 ?    0.3   0.0       1.1     5e+02     103     151 ..     153     201 ..     145     217 .. 0.75
   3 ?   -2.4   0.1       7.2   3.3e+03      30      42 ..     373     385 ..     369     393 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0061
                                       HHHHHHS--SHHHHHHHHHHHHHHS--TTT-- CS
                              MukB  27 lvttlsGgnGaGksttmaafvtaliPdlsllh 58 
                                        v  l G nG Gkst++  +   l+P+  +l 
  gi|557693519|ref|YP_008796573.1| 103 KVVGLLGKNGIGKSTALKILAGQLVPNFGILD 134
                                       688999********************998886 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.1
                                       EEEEE-SSTTT-EEEEEEEEES--TT--HH.HHHEE--SSS--EE--HHH CS
                              MukB 103 vrleqvagrdkkvdikpfalqgleedvklt.dvlleklddkkarvrelne 151
                                        +l  +++   kv  kp  + ++++ v+ t + +l++l+d  a v e+ e
  gi|557693519|ref|YP_008796573.1| 153 EHLSSISKGKSKVSYKPQNIAEIPKVVTGTvKQVLSRLGD-AAAVEEVME 201
                                       58899999999*************9987542677888999.555655544 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 7.2
                                       HHHS--SHHHHHH CS
                              MukB  30 tlsGgnGaGkstt 42 
                                        + G nG Gk+t 
  gi|557693519|ref|YP_008796573.1| 373 GIVGPNGIGKTTF 385
                                       57799*****884 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   7.2     0.029        14      45      58 ..      53      66 ..      15      69 .. 0.82
   2 ?   11.8   1.8   0.00058      0.27       2      16 ..      54      68 ..      53      89 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.029
                           Fer4_17 45 lCieCgeCerkCPq 58
                                      lCi+Cg C++kCP 
  gi|557693519|ref|YP_008796573.1| 53 LCISCGICVKKCPF 66
                                      67777777777774 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00058
                           Fer4_17  2 CiqCgyClpeCpsye 16
                                      Ci+Cg C+++Cp+ +
  gi|557693519|ref|YP_008796573.1| 54 CISCGICVKKCPFEA 68
                                      777777777777655 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 ?    1.7   0.2      0.95   4.4e+02       2      10 ..       9      17 ..       8      47 .. 0.70
   2 ?    7.9   0.9     0.011       5.2       5      19 ..      51      65 ..      48      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.95
                           Fer4_15  2 vvDrdaCig 10
                                      v+Drd+C++
  gi|557693519|ref|YP_008796573.1|  9 VLDRDRCDS 17
                                      69*****96 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.011
                           Fer4_15  5 rdaCigcglCvaeap 19
                                      +++Ci+cg Cv+ +p
  gi|557693519|ref|YP_008796573.1| 51 ETLCISCGICVKKCP 65
                                      689*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); 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: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.41
# Mc/sec: 4330.69
//
Query:       gi|557693520|ref|YP_008796574.1|  [L=726]
Description: AAA family ATPase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-101  334.9   0.0    1.1e-49  168.2   0.0    2.5  2  AAA              ATPase family associated with various cellul
      7e-35  118.6   3.0    1.4e-17   63.2   0.5    2.6  2  AAA_lid_3        AAA+ lid domain
    6.9e-31  106.3   0.1    3.8e-30  103.9   0.3    2.2  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.4e-14   53.6   0.6    5.4e-14   51.7   0.6    2.0  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.9e-14   53.7   0.0      9e-07   28.8   0.0    2.9  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      2e-14   54.1   0.0    1.1e-06   28.9   0.0    2.4  2  AAA_2            AAA domain (Cdc48 subfamily)
    8.5e-14   52.3   1.4      3e-05   24.5   0.0    3.9  3  AAA_16           AAA ATPase domain
    7.9e-12   45.0   0.2    0.00014   21.2   0.0    2.8  2  TIP49            TIP49 P-loop domain
    9.6e-11   42.1   0.8     0.0061   16.8   0.1    4.0  3  AAA_22           AAA domain
    1.7e-10   41.0   0.3    0.00036   20.5   0.0    3.7  2  AAA_5            AAA domain (dynein-related subfamily)
    1.1e-09   38.6   0.0     0.0012   19.0   0.0    2.6  2  AAA_33           AAA domain
    6.1e-09   36.0   0.0    0.00047   20.2   0.0    2.4  2  AAA_14           AAA domain
    5.5e-08   32.7   0.0      0.013   15.3   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    1.3e-07   32.2   0.0      0.014   16.0   0.0    2.6  2  AAA_18           AAA domain
    1.9e-07   31.4   0.0      0.019   15.4   0.0    2.5  2  RNA_helicase     RNA helicase
    4.4e-07   30.3   0.0      0.023   15.0   0.0    2.6  2  AAA_28           AAA domain
    5.7e-07   29.1   0.1      0.026   13.9   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    1.9e-06   27.7   0.0       0.09   12.5   0.0    2.6  2  AAA_24           AAA domain
    6.5e-06   26.0   0.0      0.098   12.4   0.0    2.7  2  Sigma54_activat  Sigma-54 interaction domain
    8.6e-06   25.0   0.1      0.038   13.1   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
    1.1e-05   25.4   0.0       0.25   11.4   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    1.2e-05   25.8   0.0       0.11   13.0   0.0    2.5  2  ABC_tran         ABC transporter
    1.9e-05   24.0   0.0      0.049   12.8   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
    1.9e-05   24.0   0.0       0.11   11.7   0.0    2.4  2  Zeta_toxin       Zeta toxin
      2e-05   24.0   0.2      0.096   12.0   0.0    3.3  3  ATPase           KaiC
    2.1e-05   24.4   0.1       0.38   10.8   0.0    2.8  2  Vps4_C           Vps4 C terminal oligomerisation domain
    2.7e-05   23.6   0.0      0.076   12.2   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    2.9e-05   23.7   0.0       0.23   10.9   0.0    2.6  2  AAA_7            P-loop containing dynein motor region
    4.3e-05   23.5   0.2       0.84    9.5   0.0    3.4  3  NACHT            NACHT domain
      7e-05   22.4   0.3       0.37   10.2   0.0    2.4  2  PhoH             PhoH-like protein
    0.00014   21.5   4.6          1    8.9   0.1    4.0  4  AAA_25           AAA domain
    0.00016   21.6   0.0       0.69    9.8   0.0    2.6  2  AAA_3            ATPase family associated with various cellul
     0.0002   21.4   0.3        2.3    8.1   0.0    3.7  3  ATPase_2         ATPase domain predominantly from Archaea
    0.00023   21.0   0.1       0.57    9.9   0.0    2.8  2  AAA_30           AAA domain
    0.00032   21.1   0.0       0.56   10.6   0.0    2.7  2  AAA_17           AAA domain
    0.00047   19.4   0.1       0.76    8.9   0.0    2.6  2  NB-ARC           NB-ARC domain
    0.00048   20.5   0.7        1.1    9.6   0.2    2.9  2  AAA_19           AAA domain
    0.00048   20.0   0.0       0.55   10.0   0.0    2.3  2  AAA_11           AAA domain
     0.0018   18.2   1.6          5    7.0   0.0    3.8  3  NTPase_1         NTPase
      0.004   16.9   0.2        2.6    7.7   0.0    2.6  2  Cytidylate_kin   Cytidylate kinase
     0.0048   16.8   0.0        4.1    7.2   0.0    2.8  2  Bac_DnaA         Bacterial dnaA  protein
     0.0048   16.3   0.1        0.9    8.9   0.0    2.5  2  IPT              Isopentenyl transferase
     0.0096   16.1   0.0        1.2    9.2   0.0    2.3  2  Cytidylate_kin2  Cytidylate kinase-like family
  ------ inclusion threshold ------
      0.011   15.4   1.0        9.4    5.9   0.0    4.2  5  Guanylate_kin    Guanylate kinase
      0.016   15.3   0.0        4.5    7.4   0.0    2.6  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.018   14.0   0.0        6.3    5.6   0.0    3.0  3  AFG1_ATPase      AFG1-like ATPase
       0.02   14.3   0.0         12    5.3   0.0    3.3  3  TniB             Bacterial TniB protein
      0.027   14.6   0.0        4.2    7.5   0.0    2.5  2  SKI              Shikimate kinase
      0.032   14.2   0.0        8.9    6.3   0.0    2.5  2  ResIII           Type III restriction enzyme, res subunit
      0.035   14.0   0.0         18    5.2   0.0    2.9  3  Rad17            Rad17 P-loop domain
      0.044   14.1   0.0        2.4    8.4   0.0    2.4  2  Hydin_ADK        Hydin Adenylate kinase-like domain
      0.057   13.6   0.2       0.19   11.9   0.2    1.9  1  DUF3420          Domain of unknown function (DUF3420)
       0.17   11.0   0.0         19    4.3   0.0    2.4  2  DAP3             Mitochondrial ribosomal death-associated pro
       0.19   10.7   0.0        2.4    7.0   0.0    2.3  2  AAA_6            Hydrolytic ATP binding site of dynein motor 


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 !  168.2   0.0   3.4e-52   1.1e-49       1     131 [.     222     351 ..     222     352 .. 0.98
   2 !  164.4   0.0   5.2e-51   1.7e-48       1     131 [.     495     625 ..     495     626 .. 0.97

  Alignments for each domain:
  == domain 1  score: 168.2 bits;  conditional E-value: 3.4e-52
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       v+lyGppGtGKTl+aka+a+e+g++f++i+g+e++sk+ gese+++re+f+ea+++a psi+fiDE+da+a++r + 
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETGAHFVSINGPEIMSKFYGESEARLREVFQEAEQNA-PSIIFIDELDAIAPKRGEV 297
                                       79******************************************************9.****************999 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLlt +dg+k++ ++v+vigatnr++ +dpal+r gRfdr+i+i+
  gi|557693520|ref|YP_008796574.1| 298 TGEVERRVVSQLLTLMDGLKSR-GQVVVIGATNRIEAIDPALRRpGRFDREIRIG 351
                                       *********************7.66***************************986 PP

  == domain 2  score: 164.4 bits;  conditional E-value: 5.2e-51
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TT CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sg 76 
                                       +llyGppGtGKTllakava+e++++f++++g+e+lsk+vgesek +re+f++a+e a p+i+f+DE+d++a++r  +
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQANFISVKGPEVLSKWVGESEKAVREIFRKARETA-PCIIFFDELDSIAPRRgIH 570
                                       69******************************************************9.****************988 PP

                                       CCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  77 seseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       ++ ++++r+vnqLlte+dg+++ ++ v+v+gatnrpd ldpallr gRfdr+++++
  gi|557693520|ref|YP_008796574.1| 571 TDAGVTDRIVNQLLTEMDGMQSLKG-VVVLGATNRPDILDPALLRpGRFDRVLYVP 625
                                       899*******************877.**************************9987 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.1   1.3e-17   4.4e-15       1      41 [.     374     414 ..     374     433 .. 0.88
   2 !   63.2   0.5   4.3e-20   1.4e-17       1      43 [.     648     692 ..     648     694 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 1.3e-17
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitme 41 
                                       dv+++eLAe T+G++GAD+aal reAa++Alrr +++i+ e
  gi|557693520|ref|YP_008796574.1| 374 DVNIDELAEITHGFVGADIAALTREAAMNALRRFLPQIDLE 414
                                       9********************************87776654 PP

  == domain 2  score: 63.2 bits;  conditional E-value: 4.3e-20
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik.e.itmedf 43 
                                       dvdl++LA++TeGy+GAD++a++reAal A r++i  + ++m++f
  gi|557693520|ref|YP_008796574.1| 648 DVDLEQLAALTEGYTGADIEAVVREAALIAARENINaQvVSMRHF 692
                                       9***********************************647*****9 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 !  103.9   0.3   1.1e-32   3.8e-30       2      84 ..      14      96 ..      13      97 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 1.1e-32
                                      EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEE CS
                           CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtV 80
                                      LrVaea+q+d gr+i+r+d++ m+el+l+pgd +ei+g+r+Tvaivwp ++ed+g+giIr+dg +R+n gvs+G+ V+V
  gi|557693520|ref|YP_008796574.1| 14 LRVAEARQRDIGRKIARVDSQGMKELELSPGDLIEITGRRSTVAIVWPPYKEDDGQGIIRIDGEIRRNSGVSVGEFVRV 92
                                      9****************************************************************************** PP

                                      EEE- CS
                           CDC48_N 81 rkae 84
                                      +k++
  gi|557693520|ref|YP_008796574.1| 93 SKTT 96
                                      *986 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 !   51.7   0.6   1.6e-16   5.4e-14       3      58 ..     114     169 ..     112     176 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.6e-16
                                       SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEE CS
                           CDC48_2   3 dgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielg 58 
                                        gd+   +++q+l+ pv+kGd++v++++g+ ++l+V st+P+ +v +te+T +e++
  gi|557693520|ref|YP_008796574.1| 114 VGDFGRIVRSQLLNMPVAKGDIIVVPVLGMGVELKVSSTSPSPIVMVTESTVVEIS 169
                                       5786669***********************************************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 !   28.8   0.0   2.7e-09     9e-07      35     103 ..     221     297 ..     214     345 .. 0.77
   2 !   21.6   0.0   4.3e-07   0.00014      36      69 ..     495     528 ..     487     618 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.7e-09
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsraveev 103
                                        v+lyGpPG Gkt +ak ia+e g+++ +  gP +      e ++ l  ++++ e++   ++fide+  ++++  ev
  gi|557693520|ref|YP_008796574.1| 221 GVILYGPPGTGKTLIAKAIANETGAHFVSINGPEImskfygESEARLREVFQEAEQNapSIIFIDELDAIAPKRGEV 297
                                       69*******************************9933222223445666666655543379*****99998887776 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 4.3e-07
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvl 69 
                                       +llyGpPG Gkt lak +a+e ++++ +  gP +
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQANFISVKGPEV 528
                                       8****************************99965 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   3.2e-09   1.1e-06       6     105 ..     222     315 ..     218     321 .. 0.91
   2 !   22.6   0.0   2.8e-07   9.4e-05       6     104 ..     495     588 ..     490     592 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 3.2e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ++l gp g+Gkt++aka+a+   +    +++ ++  e++     + + +++   ++  ++ae++   i+++DE+d i
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETGA----HFVSINGPEIMS----KFYGESEARLREVFQEAEQNApsIIFIDELDAI 290
                                       4677*****************996....************....********************9************ PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk ++ + +v r  V+  LL +++g
  gi|557693520|ref|YP_008796574.1| 291 APKrGEVTGEVERR-VVSQLLTLMDG 315
                                       **988888888886.77778999997 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 2.8e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       ill gp g+Gkt+laka+a   ++    ++i +   e+l     + + ++++  ++   +a e    i+++DE+d i
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQA----NFISVKGPEVLS----KWVGESEKAVREIFRKARETApcIIFFDELDSI 563
                                       8999****************9995....***********9....66666666666666666666699********** PP

                                       ------------HH.HHHHHHHHHH CS
                             AAA_2  81 hpkessgadvSreg.VqrdLLqile 104
                                       +p++ +  d   ++ +++ LL  ++
  gi|557693520|ref|YP_008796574.1| 564 APRRGIHTDAGVTDrIVNQLLTEMD 588
                                       ***8888887654437777776555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0     9e-08     3e-05      24     139 ..     219     324 ..     189     326 .. 0.72
   2 !   20.7   0.0   1.3e-06   0.00042      18      60 ..     486     525 ..     482     534 .. 0.78
   3 ?    3.2   0.0      0.31     1e+02     122     147 ..     539     563 ..     535     598 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 9e-08
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                       p  v+l+G++G+GK+ +++++++   ++g++f++ +  +      +s +      e  lr++ +eae+++++     
  gi|557693520|ref|YP_008796574.1| 219 PKGVILYGPPGTGKTLIAKAIAN---ETGAHFVSINGPEI-----MSKFYGE--SEARLREVFQEAEQNAPSIIFID 285
                                       489*****************996...77899*******99.....3333332..23556666666444444444444 PP

                            AAA_16 101 leeala.avpelagaeasrllellkrllallsrderplvl 139
                                        ++a+a   +e++g+ ++r+  +l  l++ l+++++ +v+
  gi|557693520|ref|YP_008796574.1| 286 ELDAIApKRGEVTGEVERRVVSQLLTLMDGLKSRGQ-VVV 324
                                       44444448889999999***********99999777.665 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.3e-06
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkc 60 
                                       r+    p+ +ll+G++G+GK+ l+++++++ +++   f++ k 
  gi|557693520|ref|YP_008796574.1| 486 RLGIRPPRGILLYGPPGTGKTLLAKAVATESQAN---FISVKG 525
                                       555555799*******************987777...655554 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.31
                            AAA_16 122 llkrllallsrderplvlvlDdlqwa 147
                                       +++++++++++   p ++++D+l+ +
  gi|557693520|ref|YP_008796574.1| 539 AVREIFRKARE-TAPCIIFFDELDSI 563
                                       56788899999.667********955 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   4.2e-07   0.00014      51      98 ..     220     265 ..     215     278 .. 0.87
   2 !   20.7   0.0   6.1e-07    0.0002      51     106 ..     493     547 ..     485     550 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.2e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev 98 
                                       ++v+l Gp+gtGkt +a ai++e g   +fv+++g e+ s     +e+
  gi|557693520|ref|YP_008796574.1| 220 KGVILYGPPGTGKTLIAKAIANETG--AHFVSINGPEIMSKFYGESEA 265
                                       799********************99..79*********9987777765 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 6.1e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                       r++Ll Gp+gtGkt la a++ e   +  f++++g ev s  v  +e ++ + +rk+
  gi|557693520|ref|YP_008796574.1| 493 RGILLYGPPGTGKTLLAKAVATES--QANFISVKGPEVLSKWVGESEkAVREIFRKA 547
                                       89*******************985..689**************99984677889997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.8e-05    0.0061       8      51 ..     222     256 ..     217     334 .. 0.59
   2 !   16.7   0.0     2e-05    0.0067       8      41 ..     495     519 ..     489     549 .. 0.74
   3 ?   -1.2   0.0       6.7   2.2e+03      81     112 ..     542     583 ..     533     607 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51 
                                       ++++G++GtGKT+ ++ ++++          ++++v+++ p+ +
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANET---------GAHFVSINGPEIM 256
                                       689******************9.........7888877777655 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpe 41 
                                       ++++G++GtGKT+l++ ++ + +         + 
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQ---------AN 519
                                       89****************99973.........22 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 6.7
                            AAA_22  81 aleqalraravielliiDEaqhlr..s.........eealeeL 112
                                        + + +r++a   ++  DE + +   +         ++++++L
  gi|557693520|ref|YP_008796574.1| 542 EIFRKARETAP-CIIFFDELDSIAprRgihtdagvtDRIVNQL 583
                                       33344444444.89999***99976413444445555555555 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 !   20.5   0.0   1.1e-06   0.00036       1     134 [.     221     338 ..     221     341 .. 0.63
   2 !   16.1   0.1   2.6e-05    0.0086       2      77 ..     495     563 ..     494     614 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.1e-06
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +v+L GppGtgK+ +a+ +a  +++ ++ +++++ +++  + g+ e        +  ++ ++a+   ++i+++DE++
  gi|557693520|ref|YP_008796574.1| 221 GVILYGPPGTGKTLIAKAIANETGAHFVSINGPEIMSK--FYGESEA-------RLREVFQEAEqnAPSIIFIDELD 288
                                       59******************************998875..4555552.......23444444444678888888888 PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHH CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspal 134
                                        + ++  ++     e+r ++  ++ +l++  +     ++ vi+++n+ +     ++pal
  gi|557693520|ref|YP_008796574.1| 289 AIAPKRGEVT-GEVERRVVS--QLLTLMDGLKS--RGQVVVIGATNRIE----AIDPAL 338
                                       7776543333.323333333..44444444332..22266666666666....555555 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.6e-05
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +lL GppGtgK+ la+ +a   ++++  v +++      ++ ++    g+ +    ++ r+ar   ++i+++DE++ 
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQANFISVKGPE------VLSKWV---GESEKAVREIFRKARetAPCIIFFDELDS 562
                                       89****************999999988888876......455555...33334444455555555666777777765 PP

                                       - CS
                             AAA_5  77 a 77 
                                       +
  gi|557693520|ref|YP_008796574.1| 563 I 563
                                       5 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   3.7e-06    0.0012       2      47 ..     222     293 ..     222     366 .. 0.70
   2 !   17.0   0.0   1.5e-05     0.005       2      80 ..     495     604 ..     495     643 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 3.7e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt........................d 47 
                                       v+l G+pG+GK+  a+ +++++g  +v ++ ++++++ +g+ + +++                        +
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETGahFVSINGPEIMSKFYGESEARLRevfqeaeqnapsiifideldaiapK 293
                                       7899*******************999999****999999976666654444444444445555555555551 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.5e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt.............................d 47 
                                       +ll G+pG+GK+ la+ ++ + +  ++ +  ++++++ +g+ ++  +                              
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQanFISVKGPEVLSKWVGESEKAVReifrkaretapciiffdeldsiaprrgihT 571
                                       6789***************9999777777778866666664333333344444444556666666666666666555 PP

                            AAA_33  48 ytrvldrlyqilnelarkalsagrnvildatnl 80 
                                        + v+dr+ ++l    + ++s ++ v+l atn+
  gi|557693520|ref|YP_008796574.1| 572 DAGVTDRIVNQLLTEMDGMQSLKGVVVLGATNR 604
                                       566778877777777778888888888877764 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   1.4e-06   0.00047       5     103 ..     222     330 ..     219     348 .. 0.79
   2 !   13.3   0.0    0.0002     0.065       5      75 ..     495     562 ..     492     592 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.4e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe.kllelileklkeekktylflDEiqev.... 76 
                                       +++ G+  +GKT ++k +++e      +++ in  +   k + ++e +l e+++e   ++  +++f+DE   +    
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETG---AHFVSINGPEIMSKFYGESEaRLREVFQEAE-QNAPSIIFIDELDAIapkr 294
                                       899****************9999...9******999888766665536677777764.4599*********998888 PP

                            AAA_14  77 ........pewekalkslvd.egknldvivtGSnsk 103
                                               +++ + l  l+d  +++++v+v G  + 
  gi|557693520|ref|YP_008796574.1| 295 gevtgeveRRVVSQLLTLMDgLKSRGQVVVIGATNR 330
                                       888888887778888888885335778888887765 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.0002
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqe 75 
                                       +++ G+  +GKT l+k ++ e+     +++ ++  +   k   ++ek  ++i++k++e    ++f+DE   
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQ---ANFISVKGPEVLSKWVGESEKAVREIFRKARETAPCIIFFDELDS 562
                                       6899***************8888...8888888888777777777767777777655558899*****876 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 !   15.3   0.0   3.9e-05     0.013      47      71 ..     219     243 ..     208     276 .. 0.89
   2 !   14.8   0.0   5.5e-05     0.018      48      74 ..     493     519 ..     489     525 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.9e-05
                         IstB_IS21  47 kenivllGpsGvGKshlaialgvea 71 
                                        ++++l Gp+G+GK+ +a a++ e+
  gi|557693520|ref|YP_008796574.1| 219 PKGVILYGPPGTGKTLIAKAIANET 243
                                       5789*****************9876 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 5.5e-05
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavra 74 
                                        +i+l Gp+G+GK+ la a+++e  ++
  gi|557693520|ref|YP_008796574.1| 493 RGILLYGPPGTGKTLLAKAVATESQAN 519
                                       5799****************9987665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.2e-05     0.014       1      25 [.     222     254 ..     222     328 .. 0.69
   2 !   13.6   0.0   0.00022     0.072       1      22 [.     495     516 ..     495     593 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.2e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf........g 25 
                                       ++l G+pG+GKt +ak++++++g          
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETGAhfvsingpE 254
                                       79****************999854456555552 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00022
                            AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                       Ill G+pG+GKt lak+++ + 
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATES 516
                                       99***************97664 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.7e-05     0.019       1      36 [.     222     257 ..     222     283 .. 0.87
   2 !   13.5   0.0   0.00021     0.069       1      26 [.     495     520 ..     495     561 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.7e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                       ++lyGp+g+GK+++ak +a++   ++ +++ ++++s
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETGAHFVSINGPEIMS 257
                                       689******************999997666666654 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00021
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       i+lyGp+g+GK++lak +a++ + ++
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQANF 520
                                       789**************888776555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   6.9e-05     0.023       2      48 ..     222     273 ..     221     305 .. 0.75
   2 !   12.7   0.0   0.00035      0.11       2      36 ..     495     534 ..     494     561 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.9e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvv....pEaareileeklakgedalpw 48 
                                       +++ G+++tGKT +++a+a++ g   v    pE++ +++ e  a+ ++  ++
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANEtGAHFVsingPEIMSKFYGESEARLREVFQE 273
                                       789****************765666552357777777766666655554443 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00035
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareile 36 
                                       i + G+++tGKT l++a a +   ++  v  pE+  + + 
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATEsqaNFISVkgPEVLSKWVG 534
                                       7899***************544444333337777666654 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1    0.0002     0.065      25      43 ..     222     240 ..     219     244 .. 0.91
   2 !   13.9   0.0     8e-05     0.026      25      43 ..     495     513 ..     492     551 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       ++l+GppG+GKt++ak+++
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIA 240
                                       79**************985 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+++
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVA 513
                                       89*************9975 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   0.00029     0.096       5      24 ..     222     245 ..     219     298 .. 0.62
   2 !   12.5   0.0   0.00027      0.09       5      22 ..     495     512 ..     492     532 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00029
                            AAA_24   5 iliyGpsgiGKTtlakel....gp 24 
                                       +++yGp+g+GKT +ak +    g 
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIanetGA 245
                                       789************999553333 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00027
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       il+yGp+g+GKT lak  
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAV 512
                                       89*************987 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00029     0.098      24      62 ..     221     256 ..     211     296 .. 0.83
   2 !   10.6   0.0     0.001      0.35      24      53 ..     494     520 ..     485     532 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00029
                                       -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS- CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavncaaip 62 
                                        v++ G  GtGK+l+a+ai +++    ++fv++n  +i 
  gi|557693520|ref|YP_008796574.1| 221 GVILYGPPGTGKTLIAKAIANET---GAHFVSINGPEIM 256
                                       699****************8765...5789999976654 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.001
                                       -EEEECSTTSSHHHHHHHHHHHSTTTTS-E CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpf 53 
                                        +l+ G  GtGK+lla+a+ ++s+   ++f
  gi|557693520|ref|YP_008796574.1| 494 GILLYGPPGTGKTLLAKAVATESQ---ANF 520
                                       68****************998876...445 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 !   13.1   0.0   0.00012     0.038     117     137 ..     222     242 ..     217     248 .. 0.89
   2 !    9.6   0.0    0.0013      0.42     117     137 ..     495     515 ..     489     519 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v +yGp+ tGkt +a+aIa+ 
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANE 242
                                       789****************86 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0013
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       +++yGp+ tGkt la+a a+ 
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATE 515
                                       89***************9975 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00074      0.25      20      51 ..     220     253 ..     192     265 .. 0.79
   2 !   11.2   0.0   0.00086      0.29      21      51 ..     489     526 ..     459     528 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00074
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       + ++L+G+ G+GKT +++++a++ g +  +++ P
  gi|557693520|ref|YP_008796574.1| 220 KGVILYGPPGTGKTLIAKAIANETGAHfvSINGP 253
                                       4599*******************99876666655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00086
                                       E.....EEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  21 v.....ilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       +     ilL+G+ G+GKT l++++a + + +  +vk P
  gi|557693520|ref|YP_008796574.1| 489 IrpprgILLYGPPGTGKTLLAKAVATESQANfiSVKGP 526
                                       0444449******************9988876677666 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00034      0.11       6      69 ..     214     276 ..     212     335 .. 0.78
   2 !   10.2   0.0    0.0024      0.79       9      65 ..     490     544 ..     486     588 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00034
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pq 69 
                                       l +++ + v + G+ G+GK+ ++k++a+++      + ++g ++ ++   +++++++ ++qe +q
  gi|557693520|ref|YP_008796574.1| 214 LGIEPPKGVILYGPPGTGKTLIAKAIANETGA--HFVSINGPEIMSKFYGESEARLREVFQEaEQ 276
                                       6678888899******************9875..5566688888888888888888888888433 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0024
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlp 65 
                                       ++ + + + G+ G+GK+ L+k++a +++  +  i ++g ++ ++   +++k ++ ++
  gi|557693520|ref|YP_008796574.1| 490 RPPRGILLYGPPGTGKTLLAKAVATESQ--ANFISVKGPEVLSKWVGESEKAVREIF 544
                                       555667899***************9986..566666777776666666666555555 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0028      0.93      49      84 ..     215     250 ..     167     328 .. 0.73
   2 !   12.8   0.0   0.00015     0.049      18     116 ..     448     560 ..     433     562 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0028
                            DUF815  49 eglpannvLLwGarGtGKSslvkallneyaeegLrl 84 
                                         +p + v+L+G  GtGK  + ka+ ne+ ++ + +
  gi|557693520|ref|YP_008796574.1| 215 GIEPPKGVILYGPPGTGKTLIAKAIANETGAHFVSI 250
                                       4567889********************998877444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00015
                            DUF815  18 pveevdevklddLvgidkqkealvente.........qfleglpannvLLwGarGtGKSslvkallneyaeeg..Lr 83 
                                        v e+ +vk+dd+ g+++ k++l e +e         + l  +p + +LL+G  GtGK  l ka+ +e +++   ++
  gi|557693520|ref|YP_008796574.1| 448 VVLEIPNVKWDDIGGLENLKQELREAVEwplkypdvfKRLGIRPPRGILLYGPPGTGKTLLAKAVATESQANFisVK 524
                                       56667778888888888888888777762222221112233467899*********************999984444 PP

                            DUF815  84 lievekedlkelpklvellr...erperfilfvDDL 116
                                         ev  + + e +k v+++    ++   +i+f D L
  gi|557693520|ref|YP_008796574.1| 525 GPEVLSKWVGESEKAVREIFrkaRETAPCIIFFDEL 560
                                       468888777777776666641223345688888876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00035      0.11      14      52 ..     217     253 ..     210     276 .. 0.88
   2 !    9.6   0.0    0.0015      0.49      16      50 ..     492     524 ..     484     528 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00035
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpD 52 
                                       e Pk ++l G pG GK+ +a+++++e+  +  +v +++ 
  gi|557693520|ref|YP_008796574.1| 217 EPPKGVILYGPPGTGKTLIAKAIANET--GAHFVSINGP 253
                                       56999*********************9..8999999875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       P  ill G pG GK+ la+++++e   q n++ ++
  gi|557693520|ref|YP_008796574.1| 492 PRGILLYGPPGTGKTLLAKAVATES--QANFISVK 524
                                       7789********************8..89998876 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0067       2.2      13      37 ..     213     237 ..     208     250 .. 0.83
   2 ?   -1.1   0.0         3   9.8e+02     121     155 ..     280     317 ..     254     330 .. 0.66
   3 !   12.0   0.0   0.00029     0.096      14      43 ..     487     516 ..     460     545 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0067
                            ATPase  13 kgGipegrvvlitGepGtGKtifal 37 
                                       + Gi   + v ++G pGtGKt++a+
  gi|557693520|ref|YP_008796574.1| 213 HLGIEPPKGVILYGPPGTGKTLIAK 237
                                       55777778899***********997 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3
                            ATPase 121 krvviDsitgl...ayeekeavaReilrqlvrvlkklg 155
                                       + + iD ++++     e + +v R+ + ql++ + +l+
  gi|557693520|ref|YP_008796574.1| 280 SIIFIDELDAIapkRGEVTGEVERRVVSQLLTLMDGLK 317
                                       66778877777432445566778999999999886554 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 0.00029
                            ATPase  14 gGipegrvvlitGepGtGKtifalqFlikg 43 
                                        Gi   r +l++G pGtGKt++a+  + ++
  gi|557693520|ref|YP_008796574.1| 487 LGIRPPRGILLYGPPGTGKTLLAKAVATES 516
                                       58888999**************99766665 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 !   10.6   0.1    0.0013      0.43      19      44 ..     418     443 ..     410     447 .. 0.81
   2 !   10.8   0.0    0.0011      0.38      23      49 ..     681     707 ..     665     718 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0013
                            Vps4_C  19 ipsdkllePpvtlkDflkalkkarpt 44 
                                       ip++ l + +vt++Df +al++ +p+
  gi|557693520|ref|YP_008796574.1| 418 IPAEVLEKIKVTREDFANALRTIQPS 443
                                       565556666***************98 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0011
                            Vps4_C  23 kllePpvtlkDflkalkkarptVskeD 49 
                                        + +  v++++f  al+k +p+V +e+
  gi|557693520|ref|YP_008796574.1| 681 NINAQVVSMRHFGLALQKIKPSVGAEE 707
                                       5666789****************9997 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   0.0   0.00023     0.076       4      55 ..     222     267 ..     219     298 .. 0.72
   2 !    9.3   0.0    0.0017      0.58       4      43 ..     495     527 ..     492     557 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakke 55 
                                       v+  G +GtGKt+++ ++++e         a+++s N+p+++ + + + + + 
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANET-------GAHFVSINGPEIMsKFYGESEARL 267
                                       6789***************998.......777888888776535555555555 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0017
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhpl 43 
                                       +l  G +GtGKt+++ ++++e        +a+++sv +p+
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATES-------QANFISVKGPE 527
                                       6789************999998.......55555555555 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    0.0007      0.23      33      58 ..     219     244 ..     209     293 .. 0.85
   2 !    9.8   0.0    0.0015      0.51      34      58 ..     493     517 ..     483     526 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0007
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkld 58 
                                        k v+l+Gp GtGKt+i+k + ++  
  gi|557693520|ref|YP_008796574.1| 219 PKGVILYGPPGTGKTLIAKAIANETG 244
                                       6789***************9988776 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                             AAA_7  34 kpvllvGptGtGKtviikdllkkld 58 
                                       + +ll+Gp GtGKt+++k + ++ +
  gi|557693520|ref|YP_008796574.1| 493 RGILLYGPPGTGKTLLAKAVATESQ 517
                                       679**************99777665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0086       2.8       3      23 ..     222     242 ..     220     246 .. 0.90
   2 ?    1.9   0.0      0.55   1.8e+02      61     115 ..     259     315 ..     253     352 .. 0.73
   3 !    9.5   0.0    0.0025      0.84       3      23 ..     495     515 ..     493     521 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0086
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       vil G++G GKT  ++ +a +
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANE 242
                                       89***************9976 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.55
                                       CCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.............HHHHHCT CS
                             NACHT  61 qlpepaapvsevwavllelperlLlilDglDelvtdlgq....kekqpvrtlLselirk 115
                                        + e++a+ +ev+++  +++ ++ + +D lD ++ + g+     e++ v +lL +l+ +
  gi|557693520|ref|YP_008796574.1| 259 FYGESEARLREVFQEAEQNAPSIIF-IDELDAIAPKRGEvtgeVERRVVSQLL-TLMDG 315
                                       5778999999999999999999988.5*****999999988744444444444.56555 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.0025
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++l G++G GKT L++ +a++
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATE 515
                                       799**************9987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.1    0.0017      0.55      22      41 ..     222     241 ..     215     247 .. 0.87
   2 !   10.2   0.0    0.0011      0.37      24      43 ..     497     516 ..     490     524 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0017
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       v+  Gp GtGKt++a a+a 
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIAN 241
                                       7899***********99985 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0011
                                       EE--TTSSTTHHHHHHHHHH CS
                              PhoH  24 aiGpaGtGKtylavalavea 43 
                                         Gp GtGKt+la a+a e 
  gi|557693520|ref|YP_008796574.1| 497 LYGPPGTGKTLLAKAVATES 516
                                       68*************99875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0061         2      36      52 ..     222     238 ..     215     243 .. 0.86
   2 ?    3.0   0.0       0.2        67     128     176 ..     265     313 ..     246     326 .. 0.81
   3 !    8.9   0.1    0.0031         1      36      54 ..     495     513 ..     488     517 .. 0.87
   4 ?   -1.1   0.0       3.5   1.2e+03     128     172 ..     538     583 ..     533     600 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0061
                            AAA_25  36 allaGapgtGKttlald 52 
                                       ++l+G+pgtGKt +a  
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKA 238
                                       69**********99865 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.2
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeria 176
                                       a ++++ +++e+ + +  + iD l+++ +   +   +v +++v++l  + 
  gi|557693520|ref|YP_008796574.1| 265 ARLREVFQEAEQ-NAPSIIFIDELDAIAPKRGEVTGEVeRRVVSQLLTLM 313
                                       456777888888.67**************977777887799999987765 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0031
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pgtGKt la  +a
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVA 513
                                       69************97666 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3.5
                            AAA_25 128 advdaleaaieevegvrlvviDplsralgg.densnsdv.galveal 172
                                        +v+++ ++++e++ +  + +D l+++ +  + + ++ v +++v++l
  gi|557693520|ref|YP_008796574.1| 538 KAVREIFRKARETA-PCIIFFDELDSIAPRrGIHTDAGVtDRIVNQL 583
                                       57889999999965.999999***99998887777777667777776 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    0.0021      0.69       2      30 ..     222     250 ..     221     293 .. 0.90
   2 !    9.1   0.0    0.0034       1.1       2      30 ..     495     523 ..     494     566 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0021
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       v+l g PG++ktl++ka+a+  +++f  i
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETGAHFVSI 250
                                       7899******************9999877 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0034
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       +ll g PG++ktll+ka+a+  +++f  +
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQANFISV 523
                                       7999****************999998766 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 !    8.1   0.0    0.0068       2.3      18      48 ..     217     246 ..     209     325 .. 0.56
   2 ?    7.2   0.0     0.013       4.2      23      44 ..     495     516 ..     483     524 .. 0.83
   3 ?    0.3   0.0       1.6   5.3e+02     102     130 ..     536     563 ..     517     567 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0068
                          ATPase_2  18 epneiyfiYGpegsGKtaLlkeiienledkd 48 
                                       ep + + +YGp g GKt + k i+++    +
  gi|557693520|ref|YP_008796574.1| 217 EPPKGVILYGPPGTGKTLIAKAIANET-GAH 246
                                       66667889*********8888888776.323 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienl 44 
                                       +++YGp g GKt L k +++++
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATES 516
                                       789************9998876 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.6
                          ATPase_2 102 vfkaielllekikkkgkk...iiiiiDelqkl 130
                                        +ka+ ++++k +    +    ii++Del  +
  gi|557693520|ref|YP_008796574.1| 536 SEKAVREIFRKAR----EtapCIIFFDELDSI 563
                                       4555555555555....444499*****9877 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0017      0.57      17      40 ..     218     241 ..     208     253 .. 0.80
   2 !    7.9   0.0     0.007       2.3      22      42 ..     496     516 ..     485     528 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0017
                            AAA_30  17 gdrvavltGpAGtGKttalkalre 40 
                                       + + ++l Gp+GtGKt + ka+++
  gi|557693520|ref|YP_008796574.1| 218 PPKGVILYGPPGTGKTLIAKAIAN 241
                                       5556899************99975 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.007
                            AAA_30  22 vltGpAGtGKttalkalreaw 42 
                                       +l Gp+GtGKt + ka++   
  gi|557693520|ref|YP_008796574.1| 496 LLYGPPGTGKTLLAKAVATES 516
                                       688**********99997655 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0017      0.56       1      26 [.     225     250 ..     225     295 .. 0.81
   2 ?    7.7   0.0     0.014       4.6       1      25 [.     498     522 ..     498     562 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0017
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa 26 
                                       +G+PG GK+ +++ ++ + g +++s 
  gi|557693520|ref|YP_008796574.1| 225 YGPPGTGKTLIAKAIANETGAHFVSI 250
                                       7*****************99888875 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.014
                                       EE-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                       +G+PG GK+ +++ ++ + +  ++s
  gi|557693520|ref|YP_008796574.1| 498 YGPPGTGKTLLAKAVATESQANFIS 522
                                       7***********9999887666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0023      0.76      23      43 ..     222     242 ..     209     252 .. 0.85
   2 !    7.5   0.0    0.0062         2      23      45 ..     495     517 ..     483     524 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0023
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       v l+G +G GKt +ak i n+
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANE 242
                                       789***************998 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0062
                                       EEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  23 valvGmgGvGKttlakqilnksd 45 
                                       + l+G +G GKt lak +  +s+
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQ 517
                                       679*************9998844 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.2    0.0032       1.1      11      34 ..     220     243 ..     216     288 .. 0.77
   2 ?    7.8   0.0     0.011       3.8      12      32 ..     494     514 ..     489     551 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0032
                            AAA_19  11 kvllvtaGpGtGKTrvlkhivall 34 
                                       k +++ ++pGtGKT + k+i ++ 
  gi|557693520|ref|YP_008796574.1| 220 KGVILYGPPGTGKTLIAKAIANET 243
                                       56899*********9999887665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.011
                            AAA_19  12 vllvtaGpGtGKTrvlkhiva 32 
                                        +l+ ++pGtGKT + k++ +
  gi|557693520|ref|YP_008796574.1| 494 GILLYGPPGTGKTLLAKAVAT 514
                                       5899*********87776654 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0088       2.9      20      39 ..     222     241 ..     202     279 .. 0.81
   2 !   10.0   0.0    0.0017      0.55      20      73 ..     495     546 ..     466     553 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0088
                            AAA_11  20 tliqGPPGtgKTktivells 39 
                                       +++ GPPGtgKT    ++ +
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIAN 241
                                       6789********76655555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0017
                            AAA_11  20 tliqGPPGtgKTktivellsqllsrrkseeeksakpriL..vCapSNaAvDeller 73 
                                        l+ GPPGtgKT    ++  +     + +    ++p++L    ++S++Av e+  +
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATES----QANFISVKGPEVLskWVGESEKAVREIFRK 546
                                       5899********8877777777....334456666666633477888888777655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.026       8.7       2      32 ..     222     252 ..     221     268 .. 0.84
   2 ?    1.4   0.0      0.79   2.6e+02     101     123 ..     457     479 ..     421     484 .. 0.79
   3 ?    7.0   0.0     0.015         5       2      32 ..     495     525 ..     494     541 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.026
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG+GKt + k ++++   + v+++G
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETGAHFVSING 252
                                       7899*********999999988777777666 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.79
                                       E---STTGGG-HHHHHHHHHHHT CS
                          NTPase_1 101 iDEiGkmElkskkfkeaveevLk 123
                                        D iG +E   ++++eave  Lk
  gi|557693520|ref|YP_008796574.1| 457 WDDIGGLENLKQELREAVEWPLK 479
                                       599***************97665 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.015
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       +++ GppG+GKt l k v+ + + + ++v+G
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQANFISVKG 525
                                       6788**************9999888888887 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0079       2.6       3      28 ..     224     249 ..     222     252 .. 0.90
   2 ?    6.5   0.0     0.018         6       3      28 ..     497     522 ..     495     524 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0079
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + GP g+GK  +a+a+a++ g+++++
  gi|557693520|ref|YP_008796574.1| 224 LYGPPGTGKTLIAKAIANETGAHFVS 249
                                       56*******************99975 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
                                       EE-STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyld 28 
                                       + GP g+GK  +a+a+a++ ++++++
  gi|557693520|ref|YP_008796574.1| 497 LYGPPGTGKTLLAKAVATESQANFIS 522
                                       67*******************99986 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0     0.012       4.1      37     113 ..     222     294 ..     217     408 .. 0.62
   2 ?    6.3   0.0     0.022       7.4      37      64 ..     495     522 ..     491     552 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.012
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-.SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv.DvLliDDiqflagk 112
                                       +++yg+ G Gkt + kai+ne+ ++      v +++ e ++++    + +  e f+e  +++  ++ iD++  +a k
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETGAH-----FVSINGPEIMSKFYGESEARLREVFQEAEQNApSIIFIDELDAIAPK 293
                                       789***************9987554.....45677777777777777777777777766644256677777777777 PP

                                       H CS
                          Bac_DnaA 113 e 113
                                        
  gi|557693520|ref|YP_008796574.1| 294 R 294
                                       5 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.022
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenape 64 
                                       +++yg+ G Gkt L ka++ e ++n+ +
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQANFIS 522
                                       79*****************999888755 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0027       0.9       5      32 ..     223     250 ..     220     270 .. 0.93
   2 ?    4.7   0.0     0.052        17       5      31 ..     496     522 ..     493     528 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0027
                               IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                                       +++G+ +tGKt  a ++a+etga  +++
  gi|557693520|ref|YP_008796574.1| 223 ILYGPPGTGKTLIAKAIANETGAHFVSI 250
                                       68*********************99886 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.052
                               IPT   5 lifGatttGKtaeaiklaketgapviv 31 
                                       l++G+ +tGKt  a ++a e  a  i+
  gi|557693520|ref|YP_008796574.1| 496 LLYGPPGTGKTLLAKAVATESQANFIS 522
                                       89****************999888776 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0036       1.2       8      57 ..     228     281 ..     224     328 .. 0.69
   2 ?    4.4   0.0      0.11        36       8      52 ..     501     545 ..     495     600 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0036
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev.eevde...rsrls 57 
                                        G+g++ i++a+A++ g +f++ + +e ++k  g se+ + e ++e   ++++ 
  gi|557693520|ref|YP_008796574.1| 228 PGTGKTLIAKAIANETGAHFVSINGPEIMSKFYGESEARLrEVFQEaeqNAPSI 281
                                       59********************99888888888888888865556642244433 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.11
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeeveevde 52 
                                        G+g++ +++a+A++ + +f++ + +e ++k  g se+ v+e+  
  gi|557693520|ref|YP_008796574.1| 501 PGTGKTLLAKAVATESQANFISVKGPEVLSKWVGESEKAVREIFR 545
                                       69*********************9999999999999999854433 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.2   7.4e+02      30      52 ..     164     185 ..     157     202 .. 0.75
   2 ?    5.9   0.0     0.028       9.4       3      31 ..     220     248 ..     218     255 .. 0.88
   3 ?   -1.8   0.0       6.6   2.2e+03      76      95 ..     257     276 ..     251     290 .. 0.79
   4 ?    3.9   0.0      0.12        39       3      30 ..     493     520 ..     491     528 .. 0.87
   5 ?   -1.3   0.0       4.5   1.5e+03      77      95 ..     531     549 ..     522     559 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.2
                                       EEE--EEESS---TTS-TTTSEE CS
                     Guanylate_kin  30 fgvsvshtTrdprkgevdGkdYy 52 
                                         v +s+tT++ r +ev G  Y 
  gi|557693520|ref|YP_008796574.1| 164 TVVEISSTTAK-RIEEVSGVTYE 185
                                       45789999986.555****9996 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.028
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekfg 31 
                                       + v+l gp g+Gk  + ka+ +e   +f 
  gi|557693520|ref|YP_008796574.1| 220 KGVILYGPPGTGKTLIAKAIANETGAHFV 248
                                       679*****************999988885 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 6.6
                                       TEEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  76 gnlygtsveaieevlekgki 95 
                                       ++ yg+s +  +ev++++ +
  gi|557693520|ref|YP_008796574.1| 257 SKFYGESEARLREVFQEAEQ 276
                                       68899999999999987765 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.12
                                       SEEEEESTTTSSHHHHHHHHHHHSTTTE CS
                     Guanylate_kin   3 rpvvlvgpsgaGksslkkaLlselpekf 30 
                                       r + l gp g+Gk  l ka+ +e + +f
  gi|557693520|ref|YP_008796574.1| 493 RGILLYGPPGTGKTLLAKAVATESQANF 520
                                       6789****************99998888 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 4.5
                                       EEEEEEHHHHHHHHHTTSE CS
                     Guanylate_kin  77 nlygtsveaieevlekgki 95 
                                       +  g+s +a++e++ k+++
  gi|557693520|ref|YP_008796574.1| 531 KWVGESEKAVREIFRKARE 549
                                       66799*********99997 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 ?    7.4   0.0     0.014       4.5      24      47 ..     222     245 ..     217     292 .. 0.84
   2 ?    5.1   0.0     0.067        22      24      47 ..     495     518 ..     490     563 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.014
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       v l G++G+gk+l+A++++++ g 
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETGA 245
                                       7899**************998765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.067
                                       EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgp 47 
                                       ++l G++G+gk+l A++ + +s+ 
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQA 518
                                       799*************99887765 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.9   6.3e+02     235     291 ..       2      58 ..       1      59 [. 0.91
   2 ?    4.3   0.0     0.046        15      58      78 ..     215     235 ..     175     250 .. 0.84
   3 ?    5.6   0.0     0.019       6.3      56      79 ..     486     509 ..     459     516 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.9
                       AFG1_ATPase 235 tsgepeaestlevkaRklrvraaagdlvrfsfaelceaarsqsdYlalaerfhtvll 291
                                        s+ p+++++l+++  ++r r  + +++r++ + + e   s+ d ++++ r +tv +
  gi|557693520|ref|YP_008796574.1|   2 SSPSPTRKKELSLRVAEARQRDIGRKIARVDSQGMKELELSPGDLIEITGRRSTVAI 58 
                                       5678899999999999999999*****************************999975 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.046
                       AFG1_ATPase  58 svepvrglYlwGgvGrGKtyl 78 
                                         ep++g+ l+G+ G GKt +
  gi|557693520|ref|YP_008796574.1| 215 GIEPPKGVILYGPPGTGKTLI 235
                                       468****************76 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.019
                       AFG1_ATPase  56 rksvepvrglYlwGgvGrGKtylm 79 
                                       r   +p+rg+ l+G+ G GKt l 
  gi|557693520|ref|YP_008796574.1| 486 RLGIRPPRGILLYGPPGTGKTLLA 509
                                       44578****************985 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.035        12      25      58 ..     209     242 ..     194     255 .. 0.84
   2 ?   -0.6   0.0       2.3   7.5e+02     115     170 ..     274     335 ..     254     348 .. 0.65
   3 ?    4.4   0.0     0.064        21      35      60 ..     492     517 ..     468     528 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.035
                              TniB  25 eLleypkrkrmpnlllvGdsnnGKtmivekFarl 58 
                                       eL+++   + ++ ++l+G++ +GKt i++  a++
  gi|557693520|ref|YP_008796574.1| 209 ELFRHLGIEPPKGVILYGPPGTGKTLIAKAIANE 242
                                       5777777788899**************9987766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.3
                              TniB 115 lrelkvrvLiiDEihnll..ag..sarkqreflnalksLgnelki..pivlvGteealralr 170
                                        ++  + ++ iDE++ +   +g  + +  r+++ +l +L++ lk    +v++G ++ ++a++
  gi|557693520|ref|YP_008796574.1| 274 AEQNAPSIIFIDELDAIApkRGevTGEVERRVVSQLLTLMDGLKSrgQVVVIGATNRIEAID 335
                                       45566789999999998633341134456777777888887775422688888888777776 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.064
                              TniB  35 mpnlllvGdsnnGKtmivekFarlhp 60 
                                       ++ +ll+G++ +GKt +++  a + +
  gi|557693520|ref|YP_008796574.1| 492 PRGILLYGPPGTGKTLLAKAVATESQ 517
                                       4789*************998776655 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0     0.013       4.2       1      23 [.     228     250 ..     228     278 .. 0.78
   2 ?    4.7   0.0      0.09        30       1      40 [.     501     545 ..     501     551 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.013
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ ++k++A++ g +f+ +
  gi|557693520|ref|YP_008796574.1| 228 PGTGKTLIAKAIANETGAHFVSI 250
                                       69******************866 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.09
                                       TTSSHHHHHHHHHHHHTSEEEEH..HHHHHHHHT...S-HHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl..Deliekrtg...ksiaeife 40 
                                       +G+GK+ ++k++A + + +fi +   e+++k +g   k ++eif+
  gi|557693520|ref|YP_008796574.1| 501 PGTGKTLLAKAVATESQANFISVkgPEVLSKWVGeseKAVREIFR 545
                                       69******************9763334555555433344555555 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     0.051        17      22      47 ..     217     242 ..     183     287 .. 0.83
   2 ?    6.3   0.0     0.027       8.9       5      48 ..     438     516 ..     435     552 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.051
                                       .TTSEEEEEESTTSTHHHHHHHHHHH CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklier 47 
                                       +  k +++  + GtGKTl+a +++ +
  gi|557693520|ref|YP_008796574.1| 217 EPPKGVILYGPPGTGKTLIAKAIANE 242
                                       66778889999********9887765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.027
                                       -HHHHHHHHHHT.........................................TTSEEEEEESTTSTHHHHHHHHHH CS
                            ResIII   5 reyQeeaienlleklks...................................krdkrglikmaTGtGKTlvaaklie 46 
                                       r  Q +a+++++ ++ +                                   +  + +l+  + GtGKTl+a +++ 
  gi|557693520|ref|YP_008796574.1| 438 RTIQPSALREVVLEIPNvkwddigglenlkqelreavewplkypdvfkrlgiRPPRGILLYGPPGTGKTLLAKAVAT 514
                                       66666666666655555555556666666666777888888888888777767777888************966655 PP

                                       HH CS
                            ResIII  47 rl 48 
                                       + 
  gi|557693520|ref|YP_008796574.1| 515 ES 516
                                       54 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.058        19      48      79 ..     222     252 ..     212     287 .. 0.78
   2 ?   -0.3   0.0       2.6   8.7e+02     140     176 ..     254     288 ..     245     298 .. 0.73
   3 ?    5.2   0.0     0.053        18      44      82 ..     491     529 ..     481     569 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.058
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnp 79 
                                       +++ GP+G gk+ + k ++ e g ++   +n+
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETGAHFVS-ING 252
                                       5688*****************9998764.444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 2.6
                             Rad17 140 dlPnkfyrds.dalrevirkylrssealplilviteie 176
                                       ++ +kfy++s  +lrev +++ +     p i+ i e++
  gi|557693520|ref|YP_008796574.1| 254 EIMSKFYGESeARLREVFQEAEQNA---PSIIFIDELD 288
                                       6779999999789999998874433...3355555555 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.053
                             Rad17  44 kkriLLisGPsGCgkstvvkvLskelgiklrewlnpvsl 82 
                                       + r +L+ GP+G gk+   k ++ e   +++    p  l
  gi|557693520|ref|YP_008796574.1| 491 PPRGILLYGPPGTGKTLLAKAVATESQANFISVKGPEVL 529
                                       55667899********99999999988888777766554 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 ?    8.4   0.0    0.0071       2.4       2      32 ..     222     252 ..     221     297 .. 0.87
   2 ?    3.2   0.0      0.29        96       2      30 ..     495     523 ..     494     532 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0071
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAlltiDs 32 
                                       +i+ G+P +GKt +a ++a + +a +++i  
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETGAHFVSING 252
                                       899**********************999975 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.29
                         Hydin_ADK   2 iivhGaPlsGKtatavtLakkYeaAllti 30 
                                       i++ G+P +GKt  a ++a + +a ++++
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTLLAKAVATESQANFISV 523
                                       7889***************9999998887 PP

>> DUF3420  Domain of unknown function (DUF3420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00057      0.19       2      24 ..     408     431 ..     408     443 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00057
                           DUF3420   2 LdreiLEKeL.PievlakIkelRl 24 
                                       L+++ LEKe+ P evl+kIk  R+
  gi|557693520|ref|YP_008796574.1| 408 LPQIDLEKEViPAEVLEKIKVTRE 431
                                       8999*****66*********9997 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 ?    3.8   0.0     0.079        26      23      39 ..     219     235 ..     210     257 .. 0.79
   2 ?    4.3   0.0     0.058        19      26      59 ..     495     527 ..     487     543 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.079
                                       --EEEEE-SSSSSTTTT CS
                              DAP3  23 vkrlvltGekgsGKSvl 39 
                                        k ++l+G +g+GK++ 
  gi|557693520|ref|YP_008796574.1| 219 PKGVILYGPPGTGKTLI 235
                                       5679**********974 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.058
                                       EEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES- CS
                              DAP3  26 lvltGekgsGKSvlLlqalayAlekgwvvlhvpe 59 
                                       ++l+G +g+GK++ L++a+a   +++++ ++ pe
  gi|557693520|ref|YP_008796574.1| 495 ILLYGPPGTGKTL-LAKAVATESQANFISVKGPE 527
                                       689********85.77777776666776666555 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 ?    7.0   0.0    0.0073       2.4      35      68 ..     222     255 ..     216     260 .. 0.87
   2 ?    0.5   0.0      0.69   2.3e+02      37      55 ..     497     515 ..     490     530 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0073
                             AAA_6  35 gapaGpagtGKtEtvkdLakalakqvvvfncsdq 68 
                                         ++Gp gtGKt   k +a++ + ++v +n  + 
  gi|557693520|ref|YP_008796574.1| 222 VILYGPPGTGKTLIAKAIANETGAHFVSINGPEI 255
                                       5679***********************9997665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.69
                             AAA_6  37 paGpagtGKtEtvkdLaka 55 
                                       ++Gp gtGKt   k +a +
  gi|557693520|ref|YP_008796574.1| 497 LYGPPGTGKTLLAKAVATE 515
                                       68********888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 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:                        99  (0.00552178); 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: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.45
# Mc/sec: 4874.34
//
Query:       gi|557693521|ref|YP_008796575.1|  [L=206]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   35.1   3.1    1.2e-08   34.7   3.1    1.3  1  Snf7             Snf7
     0.0024   17.9   1.0       0.05   13.6   1.2    2.6  2  MCC-bdg_PDZ      PDZ domain of MCC-2 bdg protein for Usher sy
     0.0059   16.6   3.1      0.013   15.5   1.2    2.1  2  LOH1CR12         Tumour suppressor protein
  ------ inclusion threshold ------
      0.017   15.4   0.7       0.18   12.1   0.0    2.6  3  DUF948           Bacterial protein of unknown function (DUF94
       0.04   14.0   1.0       0.11   12.6   1.0    1.8  1  Peptidase_S49_N  Peptidase family S49 N-terminal
      0.088   13.3   0.3        0.4   11.2   0.1    2.3  2  Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; D
       0.12   12.2   1.3        1.6    8.5   0.2    2.8  2  DASH_Duo1        DASH complex subunit Duo1
       0.15   12.2   8.4      0.069   13.4   5.1    1.9  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
       0.47   10.9   4.5       0.69   10.4   1.3    2.6  3  UPF0449          Uncharacterised protein family UPF0449


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 !   34.7   3.1   6.1e-12   1.2e-08       4     102 ..      30     128 ..      27     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 6.1e-12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Snf7   4 rsLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksn 80 
                                        +L+ + +kl++ +e+l+ + k+l +++ +  ++++ +ra ++++++ +++k+   l ++  +l++v+l +e+ k  
  gi|557693521|ref|YP_008796575.1|  30 TQLKIQNEKLNRTIERLKHRGKELFEQCVRAEQEKDTARATIYANEIAQLRKMTRTLLASHMSLDKVVLRLETVKEF 106
                                       579999*********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHCTC CS
                              Snf7  81 kevlnamkqgakamkamnkkvd 102
                                        +v+  ++ +++++k+++ +++
  gi|557693521|ref|YP_008796575.1| 107 GDVMHVLGPATQIIKQVQHEIS 128
                                       ******************9887 PP

>> MCC-bdg_PDZ  PDZ domain of MCC-2 bdg protein for Usher syndrome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.037        74      39      61 ..      10      32 ..       5      32 .. 0.83
   2 !   13.6   1.2   2.5e-05      0.05       7      40 ..      30      63 ..      24      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.037
                       MCC-bdg_PDZ 39 snatALvlALeyserlkeayevl 61
                                      ++  A+v  ++y++r++e+  +l
  gi|557693521|ref|YP_008796575.1| 10 AQQPAYVRPVNYQDRMLEILTQL 32
                                      56678888899*******98886 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.5e-05
                       MCC-bdg_PDZ  7 eeLkaqnelLsltleerkqqseeLsldlgkaEsn 40
                                       +Lk qne+L++t+e+ k +  eL  ++ +aE +
  gi|557693521|ref|YP_008796575.1| 30 TQLKIQNEKLNRTIERLKHRGKELFEQCVRAEQE 63
                                      68*****************************966 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   1.2   6.5e-06     0.013      37     125 ..      22     115 ..      18     119 .. 0.78
   2 ?    0.2   0.0      0.35   6.9e+02      89     107 ..     131     149 ..     116     154 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.5e-06
                          LOH1CR12  37 qeHlavcAkavAadqaklverikevdakiitllaelr.ekqk....qyasyaealskvnelsdqlsriqiiledivp 108
                                       q+ +    ++   + +kl ++i  ++++ ++l+++ + ++q+    + + ya+++++++++   l   ++ l+++v 
  gi|557693521|ref|YP_008796575.1|  22 QDRMLEILTQLKIQNEKLNRTIERLKHRGKELFEQCVrAEQEkdtaRATIYANEIAQLRKMTRTLLASHMSLDKVVL 98 
                                       56666666677778889999999999999999998651444411113456*************************** PP

                          LOH1CR12 109 llEtlnelLdedeRLeP 125
                                        lEt+ e+ d+   L P
  gi|557693521|ref|YP_008796575.1|  99 RLETVKEFGDVMHVLGP 115
                                       ******99887666665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.35
                          LOH1CR12  89 vnelsdqlsriqiilediv 107
                                       v e+ + l+r++ +le i+
  gi|557693521|ref|YP_008796575.1| 131 VPEVAHSLRRVDEMLESII 149
                                       3456666666666666665 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 ?    1.0   0.2      0.25     5e+02      29      48 ..      37      56 ..      24     109 .. 0.57
   2 ?   12.1   0.0   8.9e-05      0.18      19      63 ..     104     148 ..      91     157 .. 0.83
   3 ?   -2.6   0.0       3.4   6.8e+03      27      36 ..     172     181 ..     166     202 .. 0.54

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.25
                            DUF948 29 deaaatieelekqvdpilke 48
                                      +++++tie l+++ +++ ++
  gi|557693521|ref|YP_008796575.1| 37 EKLNRTIERLKHRGKELFEQ 56
                                      45555555555444444333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.9e-05
                            DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledv 63 
                                       + +  + ++l  a++ i+++++++ +i+ ev+  l+ v e+le +
  gi|557693521|ref|YP_008796575.1| 104 KEFGDVMHVLGPATQIIKQVQHEISGIVPEVAHSLRRVDEMLESI 148
                                       4455668899999***************************99977 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.4
                            DUF948  27 tldeaaatie 36 
                                       +++eaa+  +
  gi|557693521|ref|YP_008796575.1| 172 IIEEAAEVAA 181
                                       3333333333 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 ?   12.6   1.0   5.3e-05      0.11     106     138 ..      70     102 ..      20     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                   Peptidase_S49_N 106 dikAsevesLreeitavLsvakpeDevllrLes 138
                                        i A+e+++Lr+   ++L+   + D+v+lrLe+
  gi|557693521|ref|YP_008796575.1|  70 TIYANEIAQLRKMTRTLLASHMSLDKVVLRLET 102
                                       689****************************97 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 ?   -1.4   0.0       1.6   3.3e+03      38      53 ..      41      56 ..      24      71 .. 0.50
   2 ?   11.2   0.1    0.0002       0.4      25      70 ..      68     112 ..      66     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.6
                                      HHHHHHHSSSS-HHHH CS
                   Acetyltransf_11 38 kayrllyrsglsleea 53
                                      +  + l ++g++l e 
  gi|557693521|ref|YP_008796575.1| 41 RTIERLKHRGKELFEQ 56
                                      3333333333333333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0002
                                       HTT--HHHHHHHHHHHHHHHSSSS-HHHHHHHHHHHTTTSCCHHHH CS
                   Acetyltransf_11  25 Rrgfseeeikalkkayrllyrsglsleealeeleeeaeespevqel 70 
                                       R+ + ++ei++l+k+ r+l  s +sl++ + +le +++e  +v+++
  gi|557693521|ref|YP_008796575.1|  68 RATIYANEIAQLRKMTRTLLASHMSLDKVVLRLE-TVKEFGDVMHV 112
                                       7888899**********************99995.55555556555 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.22   4.4e+02      43      62 ..      25      44 ..      18      59 .. 0.60
   2 ?    8.5   0.2   0.00081       1.6       4      35 ..      74     105 ..      73     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.22
                         DASH_Duo1 43 LLdkWirIlsqtehtqrlll 62
                                      +L+  +++  q+e+ +r ++
  gi|557693521|ref|YP_008796575.1| 25 MLEILTQLKIQNEKLNRTIE 44
                                      55555555555555555544 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00081
                         DASH_Duo1   4 kEleqLrkinevienviesLkkaksniervke 35 
                                       +E+ qLrk+ +++ +++ sL+k+   +e+vke
  gi|557693521|ref|YP_008796575.1|  74 NEIAQLRKMTRTLLASHMSLDKVVLRLETVKE 105
                                       699*********************99999997 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 ?   13.4   5.1   3.5e-05     0.069      33     123 ..      24     114 ..      24     148 .. 0.84
   2 ?   -0.4   0.1       0.6   1.2e+03      83     109 ..     173     199 ..     166     206 .] 0.62

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
                     Jnk-SapK_ap_N  33 kvLElLeslasrneeeeaeleelreeleqLeteyerekelrkraeeeleeie.dqweeerkelqekveqleeenrel 108
                                       ++LE L +l  +ne+ + ++e+l+   ++L +++ r  +++  a  ++   e  q+++ +++l +   +l++ + +l
  gi|557693521|ref|YP_008796575.1|  24 RMLEILTQLKIQNEKLNRTIERLKHRGKELFEQCVRAEQEKDTARATIYANEiAQLRKMTRTLLASHMSLDKVVLRL 100
                                       58********************************99999999999888777746999*********99999999999 PP

                     Jnk-SapK_ap_N 109 elkaknaadqlsrle 123
                                       e  +k++ d ++ l 
  gi|557693521|ref|YP_008796575.1| 101 E-TVKEFGDVMHVLG 114
                                       9.7777777666665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.6
                     Jnk-SapK_ap_N  83 iedqweeerkelqekveqleeenrele 109
                                       ie++ e  ++ +++ + +l e  ++le
  gi|557693521|ref|YP_008796575.1| 173 IEEAAEVAAQRMKSSFPELPETYQHLE 199
                                       566666666666666666666666666 PP

>> UPF0449  Uncharacterised protein family UPF0449
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.3   0.00035      0.69      66      99 ..      24      57 ..      15      59 .. 0.91
   2 ?   -1.4   0.0       1.7   3.3e+03      57      89 ..      62      94 ..      56     105 .. 0.51
   3 ?    0.1   0.0      0.58   1.1e+03      71      92 ..     181     202 ..     162     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00035
                           UPF0449 66 tylelnerLeeakeeLkqkceeLktageeLeeei 99
                                      ++le+ ++L+ ++e+L++  e+Lk  g+eL e++
  gi|557693521|ref|YP_008796575.1| 24 RMLEILTQLKIQNEKLNRTIERLKHRGKELFEQC 57
                                      689999***********************98775 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.7
                           UPF0449 57 veelYeqvrtylelnerLeeakeeLkqkceeLk 89
                                      +e+   +++ y +   +L++   +L      L 
  gi|557693521|ref|YP_008796575.1| 62 QEKDTARATIYANEIAQLRKMTRTLLASHMSLD 94
                                      444444444555555555555555544444444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.58
                           UPF0449  71 nerLeeakeeLkqkceeLktag 92 
                                        +r+++   eL + +++L++a+
  gi|557693521|ref|YP_008796575.1| 181 AQRMKSSFPELPETYQHLESAA 202
                                       4677777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1566  (0.0873445); expected 358.6 (0.02)
Passed bias filter:                      883  (0.0492498); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1405.42
//
Query:       gi|557693522|ref|YP_008796576.1|  [L=295]
Description: iron complex ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   57.0   0.0    5.1e-15   55.7   0.0    1.6  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 !   55.7   0.0   2.9e-19   5.1e-15       1     235 [.       3     254 ..       3     256 .. 0.88

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.9e-19
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT................TS....-BSBESSSB-HHHHHHH- CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadklee..............ai....vevgadgeidvEklaalk 59 
                                       i+sl ps t+il++lGa d++++v  ++  +++   ++               +i    ++  +   +d+  +a lk
  gi|557693522|ref|YP_008796576.1|   3 IVSLVPSATDILVELGAVDELAAVTYACGVVSKPVVVKPqittenlspeevdrKIssahANGEQLYIVDYGLIASLK 79 
                                       89**********************9999988888877776666666666555522443355555556899******* PP

                                       -SEEEE-GGG.......GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS CS
                      Peripla_BP_2  60 PDlvilskgl....gltdedeellksgiptvivessntgeslkeqiralgellgledeaeklvaeidsklaaaksai 132
                                       PDl++++        + d   e+lks +pt++ ++  +  ++ + i ++g l+ +e+ea +lva i  kl+ +++ +
  gi|557693522|ref|YP_008796576.1|  80 PDLILAQGLCevcgVTGDVVTEKLKSLAPTFTLNPHTV-KEILDDILQVGRLVKREREAVELVAAISAKLEYVREYA 155
                                       *****99988999544566799**************65.************************************** PP

                                       -TT.-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEH..HHHT- CS
                      Peripla_BP_2 133 dsekpkpvlvfggadeggyvvagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgr..aeadn 207
                                       + + +  ++v+ +  +     + s++++ +l++ +g+ ++  +  ++ + +i aE+ila +p+ ++ +++    +++
  gi|557693522|ref|YP_008796576.1| 156 AGLPRVRTAVLEWLHP----PFCSGHWVPELVEMAGGHDLGVA--GKPSRRIRAEEILAHEPEKLVAAPCgySLEKA 226
                                       ***9999999999988....78999***************333..789**********************9999999 PP

                                       S--HHHHT-SHHHHTSHHHHTT-EEEE- CS
                      Peripla_BP_2 208 ktgleflkenpllaelpAvkngrVyald 235
                                          +  +  ++ +++lpA++ g Vya+ 
  gi|557693522|ref|YP_008796576.1| 227 VSEVNRFSGQTWVQQLPAYRLGEVYAVE 254
                                       99999999*****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2156.87
//
Query:       gi|557693523|ref|YP_008796577.1|  [L=255]
Description: undecaprenyl-diphosphatase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-45  154.9  15.5    3.6e-45  154.7  15.5    1.0  1  BacA      Bacitracin resistance protein BacA


Domain annotation for each model (and alignments):
>> BacA  Bacitracin resistance protein BacA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.7  15.5     2e-49   3.6e-45       1     248 [.       6     242 ..       6     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 154.7 bits;  conditional E-value: 2e-49
                              BacA   1 aiilGivqGltefLPvSSsGhlilveellgleked..lllfdvvihlGtllAvlvlfrkdilrllkgllkslkkkkk 75 
                                       a++lG++qG+ e+LPvSS+G ++l+++l+ + +++  +l++ +++hlGtl+A l++ rkd+  +l+g+         
  gi|557693523|ref|YP_008796577.1|   6 ALFLGVIQGFGEWLPVSSEGLVTLFSTLI-FGSSFeyALAVAIWLHLGTLFAALLYLRKDVRLVLQGFKG------- 74 
                                       689*************************9.55444556889*******************9886666333....... PP

                              BacA  76 ekeelrlllliivatipaailglllkdlieellrsplvvaialivtglllllaeklrkkkkksledltlkdalliGl 152
                                       ++e +rll  +ivat+  a+ + +l  +++ l    l    ++i +glll+++  ++++ ++ ++++++++al+ Gl
  gi|557693523|ref|YP_008796577.1|  75 DNEGRRLLRFLIVATLSSAVTAAPLLLFLRGLE---LSEKHFTITVGLLLIVTALVQRRAASGEQKIDTQTALVAGL 148
                                       357899**************9988877775433...223455555555555555444445566779*********** PP

                              BacA 153 aQalAllPGvSRSGaTivaglllglsreaaaefSFllaiPailgagllk.llksaealtasellllvgfvvafvval 228
                                       +Q+l+++PG+SRSG+T+va + lg++ ++a+++S l++iPai++a +l  ll+ +   tas   +++g+++af v+l
  gi|557693523|ref|YP_008796577.1| 149 LQGLSIMPGISRSGITLVALVGLGFNVRDALRLSYLMSIPAIAAAQVLPpLLTRGF--TAS-PEMFAGAFAAFAVGL 222
                                       ************************************************97654432..333.23388********** PP

                              BacA 229 laikfllkllkkkklkvFai 248
                                       l++++ll+ + + + ++F+i
  gi|557693523|ref|YP_008796577.1| 223 LTMRMLLSAAARLDRRLFMI 242
                                       **********9999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1812.35
//
Query:       gi|557693524|ref|YP_008796578.1|  [L=201]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   48.1   1.3    1.2e-06   28.2   0.1    2.4  2  KH_1      KH domain
    5.5e-05   23.2   0.0    8.1e-05   22.6   0.0    1.3  1  KH_8      Krr1 KH1 domain
    0.00064   19.5   0.7      0.069   13.0   0.1    2.3  2  KH_2      KH domain
  ------ inclusion threshold ------
       0.49   10.3   3.2        5.8    6.9   0.1    2.9  2  KH_4      KH domain
       0.79   10.1   3.7        1.7    9.0   0.5    2.3  2  BON       BON 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 !   28.2   0.1   3.4e-10   1.2e-06       3      64 ..      16      79 ..      14      81 .. 0.84
   2 !   18.7   0.2   3.1e-07    0.0011      12      64 ..     122     166 ..     114     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 3.4e-10
                                      EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEE.......E.SHHHHHHHHHHH CS
                              KH_1  3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtis.......G.speavekAkeli 64
                                      ++ +P++ vg +IG gGs+  eI++  g++ +v+ s+     e +v+is       G +p++  kA++ +
  gi|557693524|ref|YP_008796578.1| 16 VVNIPRERVGVLIGEGGSVKAEIERLLGVSLQVD-SS-----EGTVVISlakpveeGgDPASLFKARDIV 79
                                      689**********************77*****87.54.....5799998888888844888888888765 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 3.1e-07
                                       HHHHTGGGHHHHHHHHHH.T-EEEEESSTT...T.-EEEEEESHHHHHHHHHHH CS
                              KH_1  12 griIGkgGsnIkeIreet.gakIkvpksedegsderevtisGspeavekAkeli 64 
                                        r+IG +G++ + I+e t ++ + v  +       ++v i+G+ e+  +A+e++
  gi|557693524|ref|YP_008796578.1| 122 ARVIGTQGKTRRIIEE-TcQVDVSVY-G-------DTVAIIGEYENARAAEEAV 166
                                       69********999999.449999976.4.......59*****9999****9986 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.3e-08   8.1e-05       2      81 .]      14      97 ..      13      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.3e-08
                              KH_8  2 sfevlfpkyrekylkeveekikkllee.kklklevdlkerslkvsTte...kTrDPyiilkardlikLisrgvpleeak 76
                                      sf+v  p  r   l +   ++k+ +e+   ++l+vd +e+++++s  +   +  DP  ++kard+++ i+rg + e+a 
  gi|557693524|ref|YP_008796578.1| 14 SFVVNIPRERVGVLIGEGGSVKAEIERlLGVSLQVDSSEGTVVISLAKpveEGGDPASLFKARDIVTAIGRGFSPEKAL 92
                                      55566666665555555556666664415799************9765222778************************* PP

                              KH_8 77 kvleD 81
                                      k++eD
  gi|557693524|ref|YP_008796578.1| 93 KLVED 97
                                      **998 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   1.9e-05     0.069      25      61 ..      13      48 ..       5      66 .. 0.79
   2 !    4.9   0.1    0.0066        24      36      65 ..     121     149 ..     118     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                                      CEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHH CS
                              KH_2 25 nrviiviresqpgivIGkgGsnikkigkelrkdiekl 61
                                         ++ i  ++ g++IG gGs   +i+  l+  ++ +
  gi|557693524|ref|YP_008796578.1| 13 SSFVVNIPRERVGVLIGEGGSVKAEIERLLGVSLQ-V 48
                                      5667888899******************9998885.4 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0066
                                       HHHHHTGGGHHHHHHHHHHHHHHHHHHTTC CS
                              KH_2  36 pgivIGkgGsnikkigkelrkdieklegkk 65 
                                       +++vIG +G++ + i+++ + d+  + g  
  gi|557693524|ref|YP_008796578.1| 121 KARVIGTQGKTRRIIEETCQVDVS-VYGDT 149
                                       789**************9999995.55555 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0016       5.8      28      49 ..      12      33 ..       9      56 .. 0.91
   2 ?    2.9   0.3     0.027        98      41      50 ..     122     131 ..     119     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0016
                              KH_4 28 eveielnvegedlGrvIGkrGr 49
                                      + ++ +n+  e +G++IG  G 
  gi|557693524|ref|YP_008796578.1| 12 HSSFVVNIPRERVGVLIGEGGS 33
                                      567899*************996 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.027
                              KH_4  41 GrvIGkrGrt 50 
                                       +rvIG +G+t
  gi|557693524|ref|YP_008796578.1| 122 ARVIGTQGKT 131
                                       79*******9 PP

>> BON  BON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1     0.087   3.1e+02      22      36 ..      44      58 ..      32      58 .. 0.68
   2 ?    9.0   0.5   0.00048       1.7      23      50 ..     140     167 ..     118     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.087
                                      CCCEEEEETTCEEEE CS
                               BON 22 adinVevenGvVtLs 36
                                       +++V++++G V++s
  gi|557693524|ref|YP_008796578.1| 44 VSLQVDSSEGTVVIS 58
                                      369********9986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00048
                                       CCEEEEETTCEEEECEEECHHHHHHHHH CS
                               BON  23 dinVevenGvVtLsGtVdseaekekAve 50 
                                        ++V+v+   V + G+  ++ ++e Av+
  gi|557693524|ref|YP_008796578.1| 140 QVDVSVYGDTVAIIGEYENARAAEEAVV 167
                                       699****988**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); 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:                         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: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1517.40
//
Query:       gi|557693525|ref|YP_008796579.1|  [L=265]
Description: RIO kinase 1 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-53  180.2   0.0    4.7e-53  179.6   0.0    1.2  1  RIO1             RIO1 family
      2e-08   34.5   2.5    2.1e-06   27.8   0.0    3.1  3  APH              Phosphotransferase enzyme family
    4.5e-05   23.0   0.0     0.0001   21.8   0.0    1.5  1  Pkinase          Protein kinase domain
    0.00062   19.2   0.0       0.24   10.7   0.0    2.2  2  Kdo              Lipopolysaccharide kinase (Kdo/WaaP) family
  ------ inclusion threshold ------
      0.055   12.7   0.0      0.088   12.1   0.0    1.5  1  Pkinase_Tyr      Protein tyrosine kinase
       0.16   11.2   0.0       0.28   10.3   0.0    1.4  1  Fructosamin_kin  Fructosamine 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 !  179.6   0.0   1.6e-56   4.7e-53       2     183 ..      72     253 ..      71     259 .. 0.97

  Alignments for each domain:
  == domain 1  score: 179.6 bits;  conditional E-value: 1.6e-56
                                       EEEEEETTTEEEEEEEE-S---SS-H.HHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEE CS
                              RIO1   2 VyhavsedgkevaiKiyktstteFkk.rkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpie 77 
                                       Vyh+v+ dg+e a+Kiy ts +eF++ r +yv +++rfk+     + rk v lwa++Ef+nL  +++agv+vPkpi 
  gi|557693525|ref|YP_008796579.1|  72 VYHGVAGDGSETAVKIYLTSSAEFRRnRLQYVVDDPRFKSI--PRDFRKFVYLWAKREFANLVDAYNAGVSVPKPIV 146
                                       9***********************99899**********77..89******************************** PP

                                       EETTEEEEE--EETTEEGGBHHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETT.EEEE--GTTE CS
                              RIO1  78 lkrhvlvmefigedgvaapklkdve.eeeeaeelyeevleemrklykeaglvHaDLSeyNvlvded.kvviIDvsQa 152
                                        ++++lvm+f+ge+gv++p l + + e++e++ + e++le+ +k+y++a lvH+DLSeyNv+v ++  v+iID++Qa
  gi|557693525|ref|YP_008796579.1| 147 QRENILVMQFLGENGVRYPLLVEEKfESDELKMIWEQLLENAAKMYRKAALVHGDLSEYNVVVGRGpAVYIIDFAQA 223
                                       *************************99************************************************** PP

                                       EETTSTTHHHHHHHHHHHHHHHHHTTC---- CS
                              RIO1 153 veldhpnalefLerDveniikfFrrkgvekv 183
                                       v+l hp a+++L +  e ++kfF+++g + v
  gi|557693525|ref|YP_008796579.1| 224 VKLGHPLAETLLLKGFETLAKFFNKRGFS-V 253
                                       **************************988.3 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.6         1     3e+03     122     148 ..      13      40 ..       6      54 .. 0.53
   2 !    4.8   0.1    0.0076        23       5      39 ..      64      98 ..      61     159 .. 0.69
   3 !   27.8   0.0   7.1e-10   2.1e-06     146     204 ..     175     232 ..     159     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1
                                       TCCHHHHHHCHHHCCCGCCTCC.HHHHH CS
                               APH 122 dlellrqlesatarllaselld.lleel 148
                                       +l+++r++ +++   ++sel++ l e +
  gi|557693525|ref|YP_008796579.1|  13 RLREFRKERAQRYLEKRSELDEsLEEVF 40 
                                       4555555555544455555555333333 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0076
                                      E--.SSCEEEEEEETT-.-EEEEEE-TTS-HHHHHH CS
                               APH  5 lsggasnrtylvttpag.ryvlrrnpparaaeeirr 39
                                      +s+g ++r+y+ + ++g + +++++ ++ +ae+ r+
  gi|557693525|ref|YP_008796579.1| 64 ISAGKESRVYHGVAGDGsETAVKIYLTS-SAEFRRN 98
                                      7899999999999999559999998887.5554443 PP

  == domain 3  score: 27.8 bits;  conditional E-value: 7.1e-10
                                       HHHHHHHHHHHHHH--S.SS-EEEE-SS-SGGGEEEC..TTEEEEE---.TT-EEEECCHH CS
                               APH 146 eeleeqvlaalaallpg.elptvllHgDlhpgNllvdpddgrvtGviDf.edaglgpplyD 204
                                        el   ++++l++++++   ++ l+HgDl+  N++v    g+ +++iDf + ++lg+pl++
  gi|557693525|ref|YP_008796579.1| 175 DELKM-IWEQLLENAAKmYRKAALVHGDLSEYNVVVG--RGPAVYIIDFaQAVKLGHPLAE 232
                                       45555.777777777777779****************..66666*****667789999987 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   3.3e-08    0.0001       6     149 ..      63     227 ..      58     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.3e-08
                                       EEEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHH...............HHHHHHHHHHHHHSCTTB--EEEEE CS
                           Pkinase   6 klGeGsfGkVykaveketgkivAvKkikkekakkkke...............kkvlrEikilkklkhpnivrlyevf 67 
                                        +  G+ ++Vy +v + +g + AvK+  +++a+ +++               +++++ + + +k +  n+v  y++ 
  gi|557693525|ref|YP_008796579.1|  63 VISAGKESRVYHGV-AGDGSETAVKIYLTSSAEFRRNrlqyvvddprfksipRDFRKFVYLWAKREFANLVDAYNAG 138
                                       56679999999999.79999999999888888777667778888888866666666667777777788888888887 PP

                                       EE......SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHH.HTTEE-SS-SGGGEEEETTTEE CS
                           Pkinase  68 ee......kdelylvleyveggeladllerkgslseeeakkiakqilegleylH.skgiiHrDlKpeNiLidekgel 137
                                        +      ++e +lv++++ ++ +   l  + +++++e+k i++q+le  + ++ ++ ++H Dl   N+ + +   +
  gi|557693525|ref|YP_008796579.1| 139 VSvpkpivQRENILVMQFLGENGVRYPLLVEEKFESDELKMIWEQLLENAAKMYrKAALVHGDLSEYNVVVGRGPAV 215
                                       779999998888999999987777666667899*********************5666**************8888* PP

                                       EE-SGTTSEESS CS
                           Pkinase 138 KitDFGlakele 149
                                        i+DF  a +l 
  gi|557693525|ref|YP_008796579.1| 216 YIIDFAQAVKLG 227
                                       *****9887775 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   8.1e-05      0.24      42      83 ..     110     149 ..      86     157 .. 0.86
   2 !    6.5   0.0    0.0016       4.9     119     170 ..     176     224 ..     163     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.1e-05
                               Kdo  42 gklskdlyrfklgrtravrEfrllkrLeeagvavpkpvaaga 83 
                                       + + +d  ++k+ ++ a rEf++l   ++agv vpkp+  ++
  gi|557693525|ref|YP_008796579.1| 110 KSIPRD--FRKFVYLWAKREFANLVDAYNAGVSVPKPIVQRE 149
                                       667788..66799999**********************8765 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0016
                               Kdo 119 lkrallkavgrliaklhr.agvnHadlyaknillqqeeeeeaeiwliDldkar 170
                                         +++++++   +ak+ r a + H+dl   n+ +  +      +++iD+ +a 
  gi|557693525|ref|YP_008796579.1| 176 ELKMIWEQLLENAAKMYRkAALVHGDLSEYNVVVGRGP----AVYIIDFAQAV 224
                                       55799***********8737899***********9998....9******8875 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.9e-05     0.088      73     149 ..     147     222 ..      39     229 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                                       SSSEEEEEE--TTEBHHHHHHHTCTTTSBHHHHHHHHHHHHH.HHHHHHHTTEEEST-SGGGEEEEETTEEEE-STT CS
                       Pkinase_Tyr  73 eepllivteyvkgGdLlkfLrkkekekltlkdllsfalqvAk.GmeyLeskklvHrdlaarNvLlsenkvvkisDfG 148
                                       +++ ++v++++ ++ ++  L  +  ek++ ++l  +  q+ + + +   +  lvH dl+  Nv++ ++  v i Df+
  gi|557693525|ref|YP_008796579.1| 147 QRENILVMQFLGENGVRYPLLVE--EKFESDELKMIWEQLLEnAAKMYRKAALVHGDLSEYNVVVGRGPAVYIIDFA 221
                                       34466777777666666666654..677777766666666541455557778************************7 PP

                                       T CS
                       Pkinase_Tyr 149 L 149
                                        
  gi|557693525|ref|YP_008796579.1| 222 Q 222
                                       5 PP

>> Fructosamin_kin  Fructosamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   9.4e-05      0.28     160     213 ..     167     220 ..     154     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.4e-05
                   Fructosamin_kin 160 akekglefakieelvervaellskhqpkpsllHGdLWsgNaaltkdgepvifdP 213
                                       + e++ e ++++ + e++ e  +k   k++l+HGdL + N+ +++    +i+d 
  gi|557693525|ref|YP_008796579.1| 167 LVEEKFESDELKMIWEQLLENAAKMYRKAALVHGDLSEYNVVVGRGPAVYIIDF 220
                                       566778889999999**************************9999877888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2014.33
//
Query:       gi|557693526|ref|YP_008796580.1|  [L=201]
Description: acylphosphatase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   62.1   0.1    9.3e-17   61.2   0.1    1.4  1  Acylphosphatase  Acylphosphatase
     0.0017   18.6   2.5     0.0033   17.6   2.5    1.5  1  Halo_GVPC        Halobacterial gas vesicle protein C (GVPC) r
  ------ inclusion threshold ------
       0.01   15.8   3.7       0.12   12.2   3.6    2.0  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
      0.024   14.7   0.3      0.033   14.3   0.3    1.2  1  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.055   13.9   0.1      0.091   13.2   0.1    1.3  1  CENP-H           Centromere protein H (CENP-H)
      0.057   13.1   0.6      0.082   12.6   0.6    1.2  1  DUF713           Protein of unknown function (DUF713)
      0.066   12.9   1.2      0.097   12.3   1.2    1.2  1  YkyA             Putative cell-wall binding lipoprotein
       0.11   12.8   2.3       0.21   11.8   1.2    1.9  2  TetR_C_24        Tetracyclin repressor-like, C-terminal domai
       0.12   10.9   0.3       0.16   10.5   0.3    1.1  1  FapA             Flagellar Assembly Protein A
       0.42   10.2   3.7       0.21   11.2   1.6    1.5  2  DUF4085          Protein of unknown function (DUF4085)


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 !   61.2   0.1   5.2e-20   9.3e-17       2      76 ..       4      78 ..       3      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 5.2e-20
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveelee 76
                                      +++v+G+VQ vg+R+ v+ +A++lg++G vrNl+dgsVe+ ae +e+ +++f++++  +  +  v ++ ve +e 
  gi|557693526|ref|YP_008796580.1|  4 TVRVFGNVQAVGYRALVKFIARSLGVRGLVRNLDDGSVEVFAEAPEDIMDRFVKMIDVKGRAEDVLSLHVERVEV 78
                                      689*****************************************************9977776666666655443 PP

>> Halo_GVPC  Halobacterial gas vesicle protein C (GVPC) repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.5   1.9e-06    0.0033       3      31 ..     125     153 ..     124     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                         Halo_GVPC   3 aLlaaIaafreefdatqdaFeaYadeFaa 31 
                                       +L+++ +++r ef++ +d+F +Y+ eF +
  gi|557693526|ref|YP_008796580.1| 125 KLVTEFSDLRREFRDYRDEFRDYRNEFRE 153
                                       6889999********************76 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.6   6.7e-05      0.12      63      97 ..     164     198 ..     124     199 .. 0.46

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.7e-05
                                       CCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCH CS
                    Apolipoprotein  63 qlgqnleelrqrlapyteelrerlaadaeelqeql 97 
                                       +  ++++elr++l+++++e+ +rl++d+ e++ +l
  gi|557693526|ref|YP_008796580.1| 164 ETLEEVKELRRDLKTILDERLARLERDISEIKAKL 198
                                       22244556666666666666666666666666554 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 ?   14.3   0.3   1.8e-05     0.033      54     118 ..     132     197 ..     122     201 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                        TPR_MLP1_2  54 edvkelqalreelnelkaeiaelkaeaes.akaeleeseesweeqkeelekelselekriedlneq 118
                                       +  +e +++r+e+ ++++e +e+k+e  s a+++lee +e     k+ l+++l+ le+ i +++++
  gi|557693526|ref|YP_008796580.1| 132 DLRREFRDYRDEFRDYRNEFREFKNESISlANETLEEVKELRRDLKTILDERLARLERDISEIKAK 197
                                       55677889999************9886552789999999999999*************99999875 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 ?   13.2   0.1   5.1e-05     0.091      10      81 ..     125     197 ..     123     201 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-05
                            CENP-H  10 elssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek.eklkeelekleaelkksrqr 81 
                                       +l++e  +l +e r+ ++e  + + e ++ k+++ +la+e le+ ke +++  + l+e+l++le+++ + +++
  gi|557693526|ref|YP_008796580.1| 125 KLVTEFSDLRREFRDYRDEFRDYRNEFREFKNESISLANETLEEVKELRRDLkTILDERLARLERDISEIKAK 197
                                       68899999*********************************75555555544455888888888888777766 PP

>> DUF713  Protein of unknown function (DUF713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.6   4.6e-05     0.082      44      99 ..     123     177 ..     108     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                            DUF713  44 ivklknrfsdfeeeikksdkeekklekedleelqselsnLakkvlsaynkLeeafe 99 
                                        +kl+++fsd++ e+++++ e++ + + +  e+++e  +La+++l+  ++L+++ +
  gi|557693526|ref|YP_008796580.1| 123 FTKLVTEFSDLRREFRDYRDEFRDYRN-EFREFKNESISLANETLEEVKELRRDLK 177
                                       57899**************99999997.999***************9999988765 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   1.2   5.4e-05     0.097      10      72 ..     127     189 ..     122     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.4e-05
                              YkyA  10 leeavelEkefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellek 72 
                                       ++e  +l +ef++  ++  ++ ++  e  +e i+l  + ++++k+l  ++ ++++eR  +le 
  gi|557693526|ref|YP_008796580.1| 127 VTEFSDLRREFRDYRDEFRDYRNEFREFKNESISLANETLEEVKELRRDLKTILDERLARLER 189
                                       5677788899*************************************************9997 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 ?   -1.2   0.0       1.3   2.4e+03      45      59 ..      45      59 ..      24      75 .. 0.65
   2 ?   11.8   1.2   0.00012      0.21       9      63 ..     134     188 ..     131     194 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                                      HHHHHHHHHHHHHHH CS
                         TetR_C_24 45 ralrreyerllrdli 59
                                      ++  +++ +++ ++i
  gi|557693526|ref|YP_008796580.1| 45 AEAPEDIMDRFVKMI 59
                                      444444444444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00012
                                       HHHHHHHHHHHHHTHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         TetR_C_24   9 ralvrahveviaeereeaavllrelraLspehreeiralrreyerllrdlieeGv 63 
                                       r+  r++ + + ++r+e++ + +e  +L  e +ee+++lrr+++++l++ +++  
  gi|557693526|ref|YP_008796580.1| 134 RREFRDYRDEFRDYRNEFREFKNESISLANETLEEVKELRRDLKTILDERLARLE 188
                                       56667777788899*********************************99888765 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   8.9e-05      0.16     332     408 ..     123     198 ..     110     201 .] 0.55

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.9e-05
                              FapA 332 epelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletk.eklkeeleeleeelkelkee 407
                                       + +l  ++++l++e +++++e ++++++++++++++    l  e +e++k+l++++   l e+l+ le+++ e+k++
  gi|557693526|ref|YP_008796580.1| 123 FTKLVTEFSDLRREFRDYRDEFRDYRNEFREFKNES--ISLANETLEEVKELRRDLkTILDERLARLERDISEIKAK 197
                                       555555566666666666666666666666666532..344455555555555555233445555555555555555 PP

                              FapA 408 l 408
                                       l
  gi|557693526|ref|YP_008796580.1| 198 L 198
                                       4 PP

>> DUF4085  Protein of unknown function (DUF4085)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.7   3.1e+03      18      48 ..      48      78 ..      42      81 .. 0.67
   2 ?   11.2   1.6   0.00012      0.21       5      63 ..     128     186 ..     122     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.7
                           DUF4085 18 eetkkdweeelaeekeegedleellkeelee 48
                                      +e + d   ++ + k  +ed+++l+ e++e 
  gi|557693526|ref|YP_008796580.1| 48 PEDIMDRFVKMIDVKGRAEDVLSLHVERVEV 78
                                      5555555556667777888888888888875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00012
                           DUF4085   5 eefeelqsellsfeetkkdweeelaeekeegedleellkeeleelKedLLkfLPkeilp 63 
                                        ef +l++e+    +  +d+ +e +e k+e+  l +   ee++el++dL ++L +++  
  gi|557693526|ref|YP_008796580.1| 128 TEFSDLRREFRDYRDEFRDYRNEFREFKNESISLANETLEEVKELRRDLKTILDERLAR 186
                                       5899*************************************************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1208  (0.0673769); expected 358.6 (0.02)
Passed bias filter:                      904  (0.0504211); expected 358.6 (0.02)
Passed Vit filter:                       116  (0.00646996); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1457.18
//
Query:       gi|557693527|ref|YP_008796581.1|  [L=196]
Description: hypothetical protein CSUB_C0088 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1529.06
//
Query:       gi|557693528|ref|YP_008796582.1|  [L=204]
Description: electron transport protein SCO1/SenC [Candidatus Caldiarchaeum subterraneum]
Scores for 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-44  149.5   0.0      6e-44  149.2   0.0    1.1  1  SCO1-SenC      SCO1/SenC
    7.7e-12   45.2   0.0    1.1e-11   44.7   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
    4.1e-08   33.1   0.0    4.7e-08   32.9   0.0    1.2  1  Redoxin        Redoxin
     0.0002   21.6   0.0    0.00032   21.0   0.0    1.3  1  Thioredoxin_8  Thioredoxin-like
  ------ inclusion threshold ------
      0.051   13.6   1.8        7.7    6.6   1.7    2.4  2  PA             PA domain


Domain annotation for each model (and alignments):
>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.2   0.0   1.7e-47     6e-44       3     126 ..      48     172 ..      46     178 .. 0.96

  Alignments for each domain:
  == domain 1  score: 149.2 bits;  conditional E-value: 1.7e-47
                         SCO1-SenC   3 pFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyl 79 
                                       +F+l+dq+g++++ ++++gk +l++fg+thCpdvCp  +++  ++++alg++a++v ++fiTvDPerD++e++k+y+
  gi|557693528|ref|YP_008796582.1|  48 DFTLTDQNGNPFKLSSVKGKAVLIYFGYTHCPDVCPLVMTKYGQLVKALGNRANDVALIFITVDPERDNVEAMKKYV 124
                                       8**************************************************************************** PP

                         SCO1-SenC  80 eafdpriigltGskeeiakaakefrvyvekvedees.dytvdHsssvy 126
                                       +++++rii+ltGs+eei+++a+ ++vy++k + +e+ +y+vdH + v+
  gi|557693528|ref|YP_008796582.1| 125 AYYSDRIIALTGSPEEIDAVARLYNVYYKKYPPDEKgNYLVDHYALVL 172
                                       ***************************9999988888******98775 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   3.1e-15   1.1e-11       5     117 ..      46     167 ..      43     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 3.1e-15
                                       ----EEESTTCEEEECHHHTTSEEEEEEESTST-C.CHHHHHHHHHHCHHHCC..CTTEEEEEEESSSCHHHHHHHH CS
                          AhpC-TSA   5 apdfelknadgetvslsdykgkpvvlffypkdwcp.vCttelpalaklyeefk..ergvevigvsvdspeshkkfie 78 
                                        pdf+l++++g++++ls +kgk v+++f  + +cp vC+  + ++ +l++++   +++v +i ++vd++ +  + ++
  gi|557693528|ref|YP_008796582.1|  46 LPDFTLTDQNGNPFKLSSVKGKAVLIYFGYT-HCPdVCPLVMTKYGQLVKALGnrANDVALIFITVDPERDNVEAMK 121
                                       7***************************999.88769**************98446699*******99995555555 PP

                                       H-H........SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-T CS
                          AhpC-TSA  79 kes.......lnfpllsDeegkvakaygvlkeekglalratfvidk 117
                                       k+        + ++    e  +va+ y+v+ +++    ++ +++d+
  gi|557693528|ref|YP_008796582.1| 122 KYVayysdriIALTGSPEEIDAVARLYNVYYKKYPPDEKGNYLVDH 167
                                       555555588888888888999***********99999999999996 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   1.3e-11   4.7e-08       3      84 ..      42     128 ..      40     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.3e-11
                                       TSBB.---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-H.HHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH.. CS
                           Redoxin   3 gdka.PdftlplaatdgnsvslsefkgkkvvvnfvpgafcP.tCsaehpyleklaellkekgvdvvavvadndaf.. 75 
                                       g+++ Pdftl++  ++gn+++ls++kgk v+++f  + +cP +C   + +  +l + l+++++dv  + +  d+   
  gi|557693528|ref|YP_008796582.1|  42 GERVlPDFTLTD--QNGNPFKLSSVKGKAVLIYFGYT-HCPdVCPLVMTKYGQLVKALGNRANDVALIFITVDPErd 115
                                       67755****966..***********************.***669999996677766657777777666555555445 PP

                                       HHHHHHH....TT CS
                           Redoxin  76 vkefwgk....eg 84 
                                         e+++k    ++
  gi|557693528|ref|YP_008796582.1| 116 NVEAMKKyvayYS 128
                                       6677766444444 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   8.8e-08   0.00032       1      80 [.      66     150 ..      66     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.8e-08
                                       .SEEEEEE--SSSHH.HHHHHHHHHHHHHHHHH.TTSEEEEEEE-S...S-HHHHHHHGGGS-TTSEE.EE-TT-HH CS
                     Thioredoxin_8   1 gkvvlLyfgaswcpp.ckaftpklkelyeklkk.kkkveivyvsld...kkeeefekylkknkkpwlsvpfddkkrn 72 
                                       gk vl+yfg ++cp+ c  ++ k  +l + l + +++v ++++ +d    + e+++ky++  +   ++++ + ++++
  gi|557693528|ref|YP_008796582.1|  66 GKAVLIYFGYTHCPDvCPLVMTKYGQLVKALGNrANDVALIFITVDperDNVEAMKKYVAYYSDRIIALTGSPEEID 142
                                       689***********99***************999************5422358999999988666666555555688 PP

                                       HHTT-S-- CS
                     Thioredoxin_8  73 klkkkynv 80 
                                       ++++ ynv
  gi|557693528|ref|YP_008796582.1| 143 AVARLYNV 150
                                       88888887 PP

>> PA  PA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.7    0.0022       7.7      35      55 ..       9      29 ..       2      59 .. 0.66
   2 ?    5.5   0.0     0.005        18      14      36 ..      54      86 ..      40     125 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0022
                                PA 35 faeKarnAqaaGAagviivnd 55
                                      f   a+ A aaGAa++++ ++
  gi|557693528|ref|YP_008796582.1|  9 FMGVAALAVAAGAAAAVLSRQ 29
                                      5667899**********9842 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.005
                                PA 14 gisadfegvdvkGkivLvqrtf............a 36
                                       ++++f+ ++vkGk vL+   f             
  gi|557693528|ref|YP_008796582.1| 54 QNGNPFKLSSVKGKAVLI--YFgythcpdvcplvM 86
                                      4456666789********..886666666666662 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1599.24
//
Query:       gi|557693529|ref|YP_008796583.1|  [L=834]
Description: ribonucleoside-diphosphate reductase alpha chain [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-179  598.4   0.0   1.8e-179  597.7   0.0    1.4  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
      3e-23   81.6   0.1    1.1e-22   79.8   0.1    2.1  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
    2.8e-17   63.1   1.0    9.6e-17   61.3   1.0    2.0  1  ATP-cone         ATP cone domain
  ------ inclusion threshold ------
       0.34    9.6   0.0       0.34    9.6   0.0    2.2  2  NRDD             Anaerobic ribonucleoside-triphosphate reduct


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 !  597.7   0.0  3.9e-183  1.8e-179       1     524 []     260     750 ..     260     750 .. 0.97

  Alignments for each domain:
  == domain 1  score: 597.7 bits;  conditional E-value: 3.9e-183
                                       EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC   1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRr 77 
                                       s+Cfvl+ved+++sI++t++eaa ++k+ggGvG+n sklR++g++v++t+g asGpvsfm+++d+v+dvvkqgG+Rr
  gi|557693529|ref|YP_008796583.1| 260 SACFVLDVEDDISSIMRTAEEAAVIFKTGGGVGINYSKLRPEGDVVSSTGGVASGPVSFMRIVDTVTDVVKQGGRRR 336
                                       79*************************************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  78 GAamvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygeefeee 154
                                       GA++++l+++HpDi kfi+aK++        l+n+nisv+v+ +F++ ++ed+ ++L++Pr+               
  gi|557693529|ref|YP_008796583.1| 337 GANIGILNINHPDIDKFISAKQR-----PGFLENFNISVMVTADFWKHYEEDRPYPLVNPRD--------------- 393
                                       *********************66.....67*******************************3............... PP

                                       .............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 155 yeeleekakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNlCgEiplleyesvavCn 231
                                                +  + v+ ++L+++iae+aw+t++Pg+l+ D+iN+ n+l+ a  g I + N+CgE+pl+++es   Cn
  gi|557693529|ref|YP_008796583.1| 394 --------GSVWRLVDTRKLLRQIAENAWKTADPGLLYHDNINELNPLREA-YGDIYCVNPCGEQPLYPHES---CN 458
                                       ........233458**********************************666.5*******************...** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 232 LasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgip 308
                                       L+sinL +fv     ++ + dwd l k ++ +vr+Ldnv+d++k p+++iek t +tRriGlG+mglad+l +l+ip
  gi|557693529|ref|YP_008796583.1| 459 LGSINLHAFV-----KDGRLDWDALGKCVEDAVRFLDNVVDLTKHPTEAIEKMTLRTRRIGLGIMGLADMLYALRIP 530
                                       **********.....358*********************************************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........XXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 309 ydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdefeeke..kedweeLreeikkyGlrn 383
                                       y see+++++r+++e+++y a+++SvelA+ergpfp+f +s +++g+lp+++++e +  k+ w++L+e++kk G+rn
  gi|557693529|ref|YP_008796583.1| 531 YSSEEGFEMMRRVMEYIAYKAVETSVELAEERGPFPDFPRSSWARGELPFRGLREGRelKMYWSRLVEHVKK-GIRN 606
                                       *****************************************************54445599***********.**** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                   Ribonuc_red_lgC 384 amvtalaPTgsiSliagtssgiePifalvykksvtvgeflevnpvfeeeLkklglwseellkkiles...vqgleei 457
                                       ++++++aPTgsiS++a+tssg+eP falvy k+vt+g f++ +pvfe++L+++gl ++e+ +++ e+   vqg++ei
  gi|557693529|ref|YP_008796583.1| 607 SHLLTVAPTGSISMLADTSSGLEPQFALVYRKQVTAGVFYYSDPVFEKALEEYGLPKQEIVRRVAENggsVQGIQEI 683
                                       ****************************************************************555556******* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 458 peeikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524
                                       pe+++rvf+taldi + dh++aq +iqkw+d s+Sktin+p+ +tv+dv ++++ A++lGlKgvt+Y
  gi|557693529|ref|YP_008796583.1| 684 PEDLRRVFVTALDIPWWDHLRAQHEIQKWVDASVSKTINMPSWVTVDDVLKAFIAAHRLGLKGVTVY 750
                                       ******************************************************************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 !   79.8   0.1   2.5e-26   1.1e-22       2      83 .]     102     257 ..     101     257 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.8 bits;  conditional E-value: 2.5e-26
                   Ribonuc_red_lgN   2 kltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealyd............................... 47 
                                        +++nal+ +++rYll+d+ g+++E+p qmf R A+++ +a++ly+                               
  gi|557693529|ref|YP_008796583.1| 102 AFSVNALRLMAARYLLRDRSGRLIERPKQMFQRTAALIVLADILYNpmffdksgqqkkweeddvkleeyadnigvgp 178
                                       799************************************************************************** PP

                   Ribonuc_red_lgN  48 ...........................................kleedkdlaeefydlmssqkflpasPtlmnaGte 81 
                                                                                    ++  + ++++ydlm+ ++flp+sPtl+naGt 
  gi|557693529|ref|YP_008796583.1| 179 sdnmhetkwnihhlerlatlykrlnergmmrkplrevleylksNPSRFYENYRRYYDLMVGKRFLPNSPTLFNAGTV 255
                                       ***************************************99888888888999***********************9 PP

                   Ribonuc_red_lgN  82 lg 83 
                                       lg
  gi|557693529|ref|YP_008796583.1| 256 LG 257
                                       86 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   1.0   2.1e-20   9.6e-17      12      85 ..       2      81 ..       1      82 [. 0.92

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 2.1e-20
                                      E--HHHHHHHHHHHHHH....-HHHHHHHHHHHHHHHHHHHIIT..-BHHHHHHHHHHHHHHSS-HHHHHHHHHHHHHH CS
                          ATP-cone 12 pfdvekIkraiekAceg....seeeideiaeeveaevrkrlrdg..isteeIqdlvektliehpdyavaaayilyrnlr 84
                                      +fd e+I+ ai kA+ +    +e+ ++++++ v +++ +r+ ++  +++eeIqd+ve +l+eh+  +va+ayilyr++r
  gi|557693529|ref|YP_008796583.1|  2 DFDAERIRGAIRKAMAAkqvmDEKVLEKVVASVLEQLSSRFGAEkiPHVEEIQDIVESALMEHGLKEVAKAYILYRHER 80
                                      7*************99988888888999999999999999777779*******************************99 PP

                                      H CS
                          ATP-cone 85 k 85
                                      +
  gi|557693529|ref|YP_008796583.1| 81 T 81
                                      7 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   7.5e-05      0.34     334     396 ..     492     554 ..     475     559 .. 0.78
   2 ?   -2.8   4.3      0.45     2e+03     508     526 ..     804     827 ..     800     833 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 7.5e-05
                                       SS-.GE..............EEEEEEE-HHHHHHHTTEEEE..-HHHHHHHHHHHHHHHHHHHHH CS
                              NRDD 334 ylk.srkkkdeveev.lkngtltiGfiGlaEalkaltgkkigeseeakefalkvlkhmrekadel 396
                                       +++ ++++++ +e++ l++  + +G++Gla++l al    +  see+ e++ +v++++  ka e 
  gi|557693529|ref|YP_008796583.1| 492 VVDlTKHPTEAIEKMtLRTRRIGLGIMGLADMLYAL-RIPY-SSEEGFEMMRRVMEYIAYKAVET 554
                                       554334778888776256669***************.5566.89**************9988776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.45
                                       EEETT.--EESS.....SB-TTT- CS
                              NRDD 508 dvCnecgykgei.....ekCpkCg 526
                                       ++C+ cg + +      ekC +Cg
  gi|557693529|ref|YP_008796583.1| 804 TTCPVCGSTSIVfqegcEKCLECG 827
                                       789999996666687777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (834 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      721  (0.0402142); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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 0.31s 00:00:01.05 Elapsed: 00:00:00.48
# Mc/sec: 5238.86
//
Query:       gi|557693530|ref|YP_008796584.1|  [L=145]
Description: osmotically inducible protein OsmC [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-19   70.5   0.4    1.6e-19   70.2   0.4    1.1  1  OsmC      OsmC-like protein
  ------ inclusion threshold ------
       0.04   13.8   0.1      0.071   13.0   0.1    1.4  1  MORN      MORN repeat


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 !   70.2   0.4   1.8e-23   1.6e-19       4      99 ..      46     140 ..      42     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 70.2 bits;  conditional E-value: 1.8e-23
                                       SSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECTCEEEEEEEEEEE-SS-H..HHHHHHHHH CS
                              OsmC   4 sgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegakgiteirlkvevkipgadseeklkkllek 80 
                                       ++++Peel++aa+a+Cfa++l+ + +k+g + e+lev++e+ ++   + +i+e r++v  k+pg d ++ ++k++++
  gi|557693530|ref|YP_008796584.1|  46 GKTNPEELIAAAHATCFAMALSNIIAKEGKRAEKLEVTAEVVFSIGDQVKISESRITVVGKVPGMD-QASFEKAAQA 121
                                       479**************************************888876669**************99.6********* PP

                                       HHHHSHHHHHHCT-SSSEE CS
                              OsmC  81 aekrCpvsntlkngvkvel 99 
                                       a++ Cpvs++lk +v ++l
  gi|557693530|ref|YP_008796584.1| 122 AKDGCPVSKALKGNVAISL 140
                                       ***************9987 PP

>> MORN  MORN repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   7.9e-06     0.071       5      21 ..      12      28 ..      11      30 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.9e-06
                              MORN  5 WknGkrhGkGvytwpdG 21
                                      W+++++hG+G+  + +G
  gi|557693530|ref|YP_008796584.1| 12 WQGDLFHGQGTVSFDNG 28
                                      ***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1081.79
//
Query:       gi|557693531|ref|YP_008796585.1|  [L=176]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  120.4   0.0    4.3e-35  119.8   0.0    1.3  1  DUF192    Uncharacterized ACR, COG1430
  ------ inclusion threshold ------
       0.09   12.9   0.0       0.23   11.6   0.0    1.7  2  DUF1905   Domain of unknown function (DUF1905)


Domain annotation for each model (and alignments):
>> DUF192  Uncharacterized ACR, COG1430
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.8   0.0   4.8e-39   4.3e-35       2      95 ..      63     169 ..      62     170 .. 0.92

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 4.8e-39
                                       EEEEE-SHHHHHHTTTT-----TTEEEEEEECCEEEEEE--TT--S-EEEEEE-TTSBEEEEEEEE-TT......-. CS
                            DUF192   2 tvevAdteeerarGLmgreslpedegmlfvfdkerehsfwMkntripLdiifldadgriveieealkpq......s. 71 
                                        vevAd+++er rGL+greslpe++gmlfvf+k+ ++sfwM ++r++Ldii++dadgr+v+iee+l+p+      + 
  gi|557693531|ref|YP_008796585.1|  63 YVEVADDDAERGRGLSGRESLPENRGMLFVFEKPGRYSFWMYEMRFALDIIWIDADGRVVHIEENLQPCtpnqvcQs 139
                                       59*******************************************************************76655505 PP

                                       ......ECEEEEEETTHHHHHT--TT-EEE CS
                            DUF192  72 ......vryvLElpaGaakklgikpGdrle 95 
                                             ++yvLE++aG +kk+g+ +Gd +e
  gi|557693531|ref|YP_008796585.1| 140 ytpsadAKYVLEINAGLVKKHGVVVGDFVE 169
                                       56666699*******************887 PP

>> DUF1905  Domain of unknown function (DUF1905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.73   6.5e+03      13      25 ..      60      72 ..      52      82 .. 0.72
   2 ?   11.6   0.0   2.5e-05      0.23      51      80 ..     141     170 ..     135     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.73
                                      S-EEEE--S-HHH CS
                           DUF1905 13 gwtfvevPedvse 25
                                      + ++vev +d +e
  gi|557693531|ref|YP_008796585.1| 60 TIFYVEVADDDAE 72
                                      4678888887776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.5e-05
                                       EESSTT-EEEEE-HHHHHHHT--TTSEEEE CS
                           DUF1905  51 fpmgkggyiLpvkaavrkaigkeaGdtvtv 80 
                                        p+ + +y+L ++a + k+ g+ +Gd v++
  gi|557693531|ref|YP_008796585.1| 141 TPSADAKYVLEINAGLVKKHGVVVGDFVEF 170
                                       688889********************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1277.54
//
Query:       gi|557693532|ref|YP_008796586.1|  [L=466]
Description: Fe-S cluster assembly protein SufB [Candidatus Caldiarchaeum subterraneum]
Scores for 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-75  251.2   0.1    1.1e-74  250.8   0.1    1.1  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 !  250.8   0.1   6.1e-79   1.1e-74       2     218 .]     212     437 ..     211     437 .. 0.97

  Alignments for each domain:
  == domain 1  score: 250.8 bits;  conditional E-value: 6.1e-79
                           UPF0051   2 qfertlivveegaevtiieeyagc............gvveifvgenAklkyvkvqnwsedavnlstkraeegrdakl 66 
                                       qfertli++e+ ++v++i   +gc            +vvei+++++A ++y+++qnws+d++nl+tkra+  ++a++
  gi|557693532|ref|YP_008796586.1| 212 QFERTLIIAEPYSRVHYI---EGCtapiystsslhtAVVEIVAKKGAYVRYTTLQNWSSDVYNLVTKRAHAYEEATV 285
                                       89****************...677777777777777***************************************** PP

                           UPF0051  67 elttvslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkik 143
                                       e++++++g+++t+k+psv+l g+ga+a++ ++++a+++qh+dt+ k+ h +p+t+sri+sk+v+kd++r+++rg ++
  gi|557693532|ref|YP_008796586.1| 286 EWVDANIGSRVTMKYPSVYLLGRGAKADILSVAFAGRGQHQDTGAKAVHLAPDTTSRITSKSVCKDGGRTSYRGLLH 362
                                       ***************************************************************************** PP

                           UPF0051 144 vrkgaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       v+kga++ ++++++++L+l+d +r dt P+ ei+++d +a+H+AtvGki eeqlfYLmsRGlse+eA ++iv gf
  gi|557693532|ref|YP_008796586.1| 363 VAKGAKRVKSSVRCDALILDDISRTDTYPYNEINEEDTTATHEATVGKIGEEQLFYLMSRGLSEQEALNMIVLGF 437
                                       *************************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3284.00
//
Query:       gi|557693533|ref|YP_008796587.1|  [L=759]
Description: xanthine dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-153  512.1   0.7   1.6e-153  512.1   0.7    1.4  2  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    5.1e-27   94.4   0.1    1.4e-26   93.0   0.1    1.8  1  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a
  ------ inclusion threshold ------
      0.064   13.4   0.6        7.2    6.8   0.1    3.7  4  Sigma70_r3     Sigma-70 region 3


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 ?   -3.1   0.2      0.34     2e+03     394     417 ..     104     127 ..     103     135 .. 0.80
   2 !  512.1   0.7  2.7e-157  1.6e-153       1     550 []     152     704 ..     152     704 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.34
                                       HHHHHHHHHHHHHHCTS-CCCEEE CS
                     Ald_Xan_dh_C2 394 eklrerllkiaaellevspedlel 417
                                       + +r++++++aae le+++e++e 
  gi|557693533|ref|YP_008796587.1| 104 RSVRDEVAAVAAETLEAAEEAVEA 127
                                       568889999999999999998876 PP

  == domain 2  score: 512.1 bits;  conditional E-value: 2.7e-157
                                       STTT-STTEEE......EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHH CS
                     Ald_Xan_dh_C2   1 vheeapdnvla......kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphev 71 
                                       vhee ++nv++      + +    +++f++a+ vv+++++++  +  +l t +++a++ ++ gelt+y++tqap+  
  gi|557693533|ref|YP_008796587.1| 152 VHEENRSNVVDlkmrfsTSHSTHLNQVFEKAAAVVSDRYQVHYNNASPLGTMGVIAHY-NHLGELTIYTNTQAPFLY 227
                                       5888888888885533222235679*********************************.88**************** PP

                                       HHHHHHHHT--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE CS
                     Ald_Xan_dh_C2  72 rrlvaevlglpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvga 148
                                       r+ +a++lg+++ k+rvi+p++GG+FG  ++++pl+++aa++++kt+rpVklv++Ree+++++  r+p +i+++++a
  gi|557693533|ref|YP_008796587.1| 228 RHELAKILGINPAKIRVIQPEIGGAFGRGMDVYPLDPIAAVLSMKTRRPVKLVFTREEELQYAPPRQPAIIYMRTAA 304
                                       ***************************99************************************************ PP

                                       -TTS-EEEEEEEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 149 dkdGkitaldvdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlm 225
                                       d+dG+++a +++++ daGay +++p+    ++++++g+Y +p v +e++vvytN+p ++  RG+G+pq +fa+E++m
  gi|557693533|ref|YP_008796587.1| 305 DRDGRLLAREARVILDAGAYVSWGPFDGRVMMATTTGLYTVPEVLFEATVVYTNNPYTGTQRGAGNPQITFAIEQQM 381
                                       ***************************************************************************** PP

                                       HHHHHHHT--HHHHHHHHBCECGCC.SEEETEESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEE CS
                     Ald_Xan_dh_C2 226 delAeelgldplelRrrNlikpgeltpygqpvydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvve 302
                                       d+lAeelg+dp+e+R +N+ +p+++tp g +   +++l+e+l++++e++++++r    a  n     rGig+a++++
  gi|557693533|ref|YP_008796587.1| 382 DALAEELGMDPVEFRIINANRPNTVTPQGLK-ITTCELRECLRRAAEEIGWRGRGM--AGPN-----RGIGFAAFFH 450
                                       ***************************9999.699****************87733..3334.....9******999 PP

                                       EBS--S.EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT CS
                     Ald_Xan_dh_C2 303 giglgftakflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaS 379
                                         g +    +++  g  ++v++ G vtv tg+t++G+G++t++aqi+aeeLg+ple+vrvv+ d +  p+++gt aS
  gi|557693533|ref|YP_008796587.1| 451 VGGGA-RVYRSDGCGTVLSVDDFGLVTVITGSTDLGTGSDTAIAQIVAEELGIPLEKVRVVNDDASIRPWDVGTHAS 526
                                       88644.4456778899************************************************************* PP

                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH..TTSSEEEEEEE CS
                     Ald_Xan_dh_C2 380 rstdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl..ervslsatgfy 451
                                       r+t ++gn+++ Aa+k +e l+k+aae l++ pe+l +e+++v+     +k++++++l+++ ++   + ++  + +y
  gi|557693533|ref|YP_008796587.1| 527 RATFVAGNSALLAAKKAKEILAKAAAEELQTTPENLVFENNTVYDItnhAKKIEFDKLVRRIHFrqGGSNIVVSVYY 603
                                       ********************************************999988999*******9999656669999999* PP

                                       ......EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT--- CS
                     Ald_Xan_dh_C2 452 kt...ldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEel 525
                                       ++   +++e++ g+  a++ +ga++a VevD+et  vkvl++v vhD G+++Npa +egQ++GG+++G+ ++l+Eel
  gi|557693533|ref|YP_008796587.1| 604 DPpteMQDENWMGNLSAAYVFGAQAALVEVDPETRWVKVLKIVSVHDSGRILNPAAAEGQVHGGVAMGLSYTLYEEL 680
                                       99***999********************************************************************* PP

                                       EEETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 526 vydedGqlltasladYkiPtaadiP 550
                                       v+ e+G++++a l+dY++Pta ++P
  gi|557693533|ref|YP_008796587.1| 681 VL-EQGRVVNAALTDYLLPTALETP 704
                                       **.8*****************9998 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 !   93.0   0.1   2.3e-30   1.4e-26       2     109 ..      33     135 ..      32     136 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 2.3e-30
                                       T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEES CS
                      Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkvr 78 
                                       G a+YvdD+++p++ly++++rS ++hA+i++i++++a ++pGV av+t+ d++  +  i   l+d++   l   kvr
  gi|557693533|ref|YP_008796587.1|  33 GAARYVDDVELPNMLYAKILRSRYPHARILRINTEKAWRVPGVRAVVTGYDVQLGRMGI---LQDHP--PLKIGKVR 104
                                       89***************************************************997777...45554..9******* PP

                                       STT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                      Ald_Xan_dh_C  79 svgqavaavvAedeetArkAaklvkveYeel 109
                                       sv ++vaav+Ae+ e+A++A+++++veYe+l
  gi|557693533|ref|YP_008796587.1| 105 SVRDEVAAVAAETLEAAEEAVEAIEVEYEPL 135
                                       *****************************98 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.056   3.3e+02      24      38 ..     229     243 ..     228     246 .. 0.90
   2 ?   -1.8   0.0      0.57   3.4e+03      26      35 ..     384     393 ..     381     398 .. 0.82
   3 ?    6.8   0.1    0.0012       7.2      26      40 ..     496     510 ..     491     515 .. 0.86
   4 ?   -1.3   0.0      0.41   2.4e+03      16      29 ..     727     740 ..     725     749 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.056
                                       HHHHHHHTXXHHHHH CS
                        Sigma70_r3  24 eEiAeeLglseekVr 38 
                                       +E+A+ Lg+ ++k+r
  gi|557693533|ref|YP_008796587.1| 229 HELAKILGINPAKIR 243
                                       7************99 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.57
                                       HHHHHTXXHH CS
                        Sigma70_r3  26 iAeeLglsee 35 
                                       +AeeLg+++ 
  gi|557693533|ref|YP_008796587.1| 384 LAEELGMDPV 393
                                       89****9985 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0012
                                       HHHHHTXXHHHHHHH CS
                        Sigma70_r3  26 iAeeLglseekVrev 40 
                                       +AeeLg+++ekVr v
  gi|557693533|ref|YP_008796587.1| 496 VAEELGIPLEKVRVV 510
                                       8***********976 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.41
                                       HHSSXXXHHHHHHH CS
                        Sigma70_r3  16 elgrePtpeEiAee 29 
                                       e+g+ Ptp+ iA++
  gi|557693533|ref|YP_008796587.1| 727 ETGCIPTPAAIANA 740
                                       899*********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (759 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 4961.65
//
Query:       gi|557693534|ref|YP_008796588.1|  [L=382]
Description: aminotransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-43  149.7   0.0    1.3e-43  149.4   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    3.6e-07   29.7   0.0    5.8e-07   29.0   0.0    1.5  1  Aminotran_1_2    Aminotransferase class I and II
    0.00028   19.5   0.0    0.00047   18.8   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0012   18.2   0.0     0.0016   17.8   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.048   13.0   0.1      0.081   12.2   0.1    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.058   13.7   0.0       0.09   13.1   0.0    1.3  1  DUF2850          Protein of unknown function (DUF2850)
       0.11   11.1   0.0        2.1    6.8   0.0    2.1  2  SHMT             Serine hydroxymethyltransferase


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 !  149.4   0.0   4.9e-47   1.3e-43       2     344 ..       2     329 ..       1     348 [. 0.92

  Alignments for each domain:
  == domain 1  score: 149.4 bits;  conditional E-value: 4.9e-47
                                       EEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHH CS
                       Aminotran_5   2 yldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlva 78 
                                       +l+ +++t++ ++V++a++ +          ++ h++ e+ + ++ + ek +++++a+s++  i ts++t +++++a
  gi|557693534|ref|YP_008796588.1|   2 LLMIPGPTEIDERVIRAMARQ----------MIDHRSDEFRALMKSVVEKSRKIFEANSSDIYILTSSGTGGVEAAA 68 
                                       6999****************9..........99**************************9999************** PP

                                       HHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--..TTEEEEEEESBETTTT CS
                       Aminotran_5  79 lslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldeleklln..ektklvaithvsnvtG 153
                                        +l    +pgd++++ +a+  a++  ++e+  + ga+v++ pl++++  ++ +++kll+  +++++v +  ++++tG
  gi|557693534|ref|YP_008796588.1|  69 SNL---AQPGDKVLILSAGLFAER--MAEAFAAYGANVVKHPLENGQGPNPVAVKKLLEahPDAAIVGFPFNETSTG 140
                                       ***...89****************..44444579************************55599************** PP

                                       E.B--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.ST CS
                       Aminotran_5 154 t.iqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllgg 228
                                       +   +v+eig++++++gal++vDa++avg  ++ v+++++Df +++++K l  P+G+ ++ v+k+++ek+e+ +l  
  gi|557693534|ref|YP_008796588.1| 141 IiSRDVKEIGRICREHGALLVVDAVTAVGGVRVPVDEYNIDFCVAGTQKcLATPPGLALVTVSKRAWEKIEQKKLRP 217
                                       *789*********************************************9999************************ PP

                                       TSEEEEET.TEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B CS
                       Aminotran_5 229 emveevsl.eettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdk 304
                                        +++ v++ +     e+p+     Tp v  + ++ +al+++ e g+e+  +++++ a+ l+++l+s++    +gp  
  gi|557693534|ref|YP_008796588.1| 218 PYFDLVKYrHFMERWETPF-----TPAVTLFWAFDEALNIIFEYGYERWLARHAAGAAGLYAGLRSYGLEFYAGP-- 287
                                       ********88888888888.....*****************************************9876655555.. PP

                                       -CTCBSEEEEEE.TTCSHHHHHHHHHHT.TEEEEEE-TTTHH CS
                       Aminotran_5 305 aerrasivsfnf.kgvhaedvatlLdee.gIavrsGhhcaqp 344
                                         +++ + ++ + +g+    ++  ++++ gI +++G ++ + 
  gi|557693534|ref|YP_008796588.1| 288 GFESPIVAAMHIpPGLTDTAIRETMKKKyGILISGGLAHYKG 329
                                       67777777777777888899999999999*******998744 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 !   29.0   0.0   2.3e-10   5.8e-07      70     195 ..      54     171 ..      19     339 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 2.3e-10
                                       GEEEESHHHHHHHHHHHHHHHTTT-EEEEEE..SS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHC CS
                     Aminotran_1_2  70 avvvgsGagaliealifllklnpgdeilvpd..ptyasyknilrlsggevvryplyseedfhldlealeealkeape 144
                                        ++++sG+g + +a+  l++  pgd++l+ +  ++ + + +++ ++g+ vv+ pl+  ++ + +  a++++l+    
  gi|557693534|ref|YP_008796588.1|  54 YILTSSGTGGVEAAASNLAQ--PGDKVLILSagLFAERMAEAFAAYGANVVKHPLE--NGQGPNPVAVKKLLEA--- 123
                                       799****************8..9999776551144567****************88..************9998... PP

                                       TTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBS CS
                     Aminotran_1_2 145 gnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvf 195
                                           +   +v  p+N t t +   +++++ ++++++++ll+vD + a++  
  gi|557693534|ref|YP_008796588.1| 124 ---HPDAAIVGFPFNETSTGIISRDVKEIGRICREHGALLVVDAVTAVGGV 171
                                       ...4455579*********************************87555554 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 !   18.8   0.0   1.8e-07   0.00047      60     198 ..      44     189 ..      27     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.8e-07
                                       HHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEE.ESTSSHHHHHHHHHTHHHTTCEEEEEST..TSHHHHHHH CS
                   Cys_Met_Meta_PP  60 riaaLeggeaalavssGmaAiaaailallkaGdeivv.sddlYggtqrllkkvlkklgievkfvdt..sdleeleka 133
                                       +i + ++++  +++ssG++ ++aa  +l++ Gd++++ s  l+    +     +    +++   +    ++ +++k 
  gi|557693534|ref|YP_008796588.1|  44 KIFEANSSDIYILTSSGTGGVEAAASNLAQPGDKVLIlSAGLFAERMAEAFAAYGANVVKHPLENGqgPNPVAVKKL 120
                                       4666666777899*********************7551666775433222222222233333333322677789999 PP

                                       CCTTEEEEEEESS-TTTT-...---HHHHHHHHHHTT-EEEEEGTTTHTTTS-GG.GGT-SEEEEETTT CS
                   Cys_Met_Meta_PP 134 ikentklvylEtptnpllk...vvDiekiaklakkagvlvvvDntfaspllqrpl.klgaDivvhSaTK 198
                                       ++ + ++  +  p n +       D+++i ++++++g+l+vvD++ a + +  p+ ++++D  v  + K
  gi|557693534|ref|YP_008796588.1| 121 LEAHPDAAIVGFPFNETSTgiiSRDVKEIGRICREHGALLVVDAVTAVGGVRVPVdEYNIDFCVAGTQK 189
                                       998777776666655554311146********************9998877777735889988876666 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.1e-07    0.0016      13     222 ..      14     226 ..       8     297 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.1e-07
                                       HHHHHHHCS----CCCT--HHHHHHHHHHHHHTT-S...EEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSS CS
                   Beta_elim_lyase  13 amsdaqaaamlGdesYgedktvnrLedavaelfgke...aalfvpqGtaAnsillkillqrgeevivtepahihfde 86 
                                        +++a+a+ m+++ s +    ++ + ++ +++f+++     + + +Gt++ + + + l+q+g++v++ + + +  + 
  gi|557693534|ref|YP_008796588.1|  14 RVIRAMARQMIDHRSDEFRALMKSVVEKSRKIFEANssdIYILTSSGTGGVEAAASNLAQPGDKVLILSAGLFAERM 90 
                                       567788888888888888888888889999999886322456799********************977665555555 PP

                                       TTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-E CS
                   Beta_elim_lyase  87 tgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygip 163
                                       + a a++ g+++++ + ++    ++ +++++++++ +     ++i+    n+t+ G +     ++e+  i++++g  
  gi|557693534|ref|YP_008796588.1|  91 AEAFAAY-GANVVKHPLENGQGPNPVAVKKLLEAHPD-----AAIVGFPFNETSTGII--SRDVKEIGRICREHGAL 159
                                       5555555.5555555555544689999*******444.....5555555666666765..4689************* PP

                                       EEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE-HH................HHHHH CS
                   Beta_elim_lyase 164 lhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvG.gvlafrddel............edylaer 222
                                       l++D+   + a+  ++++v e+   +D ++++  K l ++ G +++ ++++ +            +d +++r
  gi|557693534|ref|YP_008796588.1| 160 LVVDA---VTAVGGVRVPVDEY--NIDFCVAGTQKCLATPPGlALVTVSKRAWekieqkklrppyFDLVKYR 226
                                       ****8...67778889999997..589999999999999999888888887656777777777664444444 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 ?   12.2   0.1   3.2e-05     0.081      40     150 ..      53     169 ..      23     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                                       EEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-TH..HHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE.E CS
                   DegT_DnrJ_EryC1  40 haiavssGtaAlhlaLralgvgpgdeVIvpsltFva..tanavlelgakpvfvDvdpdtynidpaaieaaitert.k 113
                                         i +ssGt +++ a ++l  +pgd+V++ s++ +a   a+a +  ga++v    + +   ++p a++++++    +
  gi|557693534|ref|YP_008796588.1|  53 IYILTSSGTGGVEAAASNLA-QPGDKVLILSAGLFAerMAEAFAAYGANVVKHPLE-NGQGPNPVAVKKLLEAHPdA 127
                                       5678999****999988875.67999999999999944588999999999887776.777899********999857 PP

                                       EEEEB....-GGGB--.-HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1 114 aIlpV....hlyGqva.dmdalkaiaakhglkvieDaAhAlG 150
                                       aI+         G ++ d++++ +i+++hg  ++ Da  A+G
  gi|557693534|ref|YP_008796588.1| 128 AIVGFpfneTSTGIISrDVKEIGRICREHGALLVVDAVTAVG 169
                                       77754222134677778***********************99 PP

>> DUF2850  Protein of unknown function (DUF2850)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.5e-05      0.09       3      45 ..     316     357 ..     314     382 .] 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.5e-05
                           DUF2850   3 yGeWvEqgvapYaaekltlsekGvvvngrlvsTsfefdGktle 45 
                                       yG+ +  g a+Y+ + +++ + G+++++++v+T f   Gktl+
  gi|557693534|ref|YP_008796588.1| 316 YGILISGGLAHYKGKMFRIANIGLITRDKVVNTIFAL-GKTLK 357
                                       9999999***************************986.66665 PP

>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0   0.00083       2.1     281     328 ..      14      61 ..       6      64 .. 0.93
   2 ?    1.8   0.0     0.027        70     184     239 ..     144     196 ..     122     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00083
                                       HHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT-EEGGGS- CS
                              SHMT 281 hviaakavalkealepefkvyqkqvlknakalaealkekgyklvsgGt 328
                                        vi a+a  + +  ++ef++  k v++ ++++ ea  +  y l s Gt
  gi|557693534|ref|YP_008796588.1|  14 RVIRAMARQMIDHRSDEFRALMKSVVEKSRKIFEANSSDIYILTSSGT 61 
                                       6899*******************************************9 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.027
                                       --HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCTSSEEEEESSSTT-S-S- CS
                              SHMT 184 idyarlreiadevgayllvdmahiaGlvaagvipsPfeyadvvtttthktlrGprg 239
                                        d + + +i+ e ga l+vd     G v   v    +   d+  + t k l+ p g
  gi|557693534|ref|YP_008796588.1| 144 RDVKEIGRICREHGALLVVDAVTAVGGVRVPVDEYNI---DFCVAGTQKCLATPPG 196
                                       57788999************98877766655544444...4556677888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2512.02
//
Query:       gi|557693535|ref|YP_008796589.1|  [L=145]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-18   63.9   0.0    1.2e-17   63.6   0.0    1.1  1  MaoC_dehydratas  MaoC like domain
    1.4e-08   35.0   0.0    2.4e-08   34.2   0.0    1.4  1  MaoC_dehydrat_N  N-terminal half of MaoC dehydratase
      0.003   17.9   0.0     0.0057   17.0   0.0    1.4  1  4HBT             Thioesterase superfamily


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 !   63.6   0.0     2e-21   1.2e-17       6     118 ..       8     120 ..       5     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 2e-21
                                       TTSEEEEEEEEEEEHHHHHHHHHHHT---GGGT-HHHHHHTTTSSSB--HHHHHHHHHHHHHHHHS.TTEGGGEEEE CS
                   MaoC_dehydratas   6 igekvetekeitvteadialyalvsgDlnpiHvdpefAkkagfggpIahGmltlaivaklveeelg.dnvvarvgei 81 
                                       +g+++   +e+ vt++di l+a+ +   np+ +++efAk+ gf+++Ia G l+ a++ +l+++ ++ dn+va   ++
  gi|557693535|ref|YP_008796589.1|   8 VGREFVS-RERVVTPSDIDLFATWTWAANPLFLSDEFAKARGFPQRIAPGALVIAFAIGLLYQTGAfDNIVALASID 83 
                                       6677777.8999*************************************************9987626699****** PP

                                       EEEE-S--BTTCEEEEEEEEEEEEEEEEEEEEEEEEE CS
                   MaoC_dehydratas  82 kvrFtkpVlpgdtlkvelevvgkrdvrktkkvevtke 118
                                        ++F +p  pgdtlkv + vv+kr+ +    + v+ e
  gi|557693535|ref|YP_008796589.1|  84 GMSFRSPTHPGDTLKVVARVVEKRESKSPDRGVVKLE 120
                                       *************************998877777665 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 !   34.2   0.0     4e-12   2.4e-08       3     125 ..       8     128 ..       7     135 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 4e-12
                   MaoC_dehydrat_N   3 iGaefepvkaevereavrefakavgetnpayldeeaaraagyrsliaPptflivlatkapellealgidlsrllhge 79 
                                       +G+ef  ++ +v+ +++  fa  + ++np++l++e a+a g+ + iaP  ++i++a+    l+++   d    l   
  gi|557693535|ref|YP_008796589.1|   8 VGREFVSRERVVTPSDIDLFATWTWAANPLFLSDEFAKARGFPQRIAPGALVIAFAIGL--LYQTGAFDNIVALASI 82 
                                       89*******************************************************99..6666667777777777 PP

                   MaoC_dehydrat_N  80 qefeyhepiraGDelttesriadvydkkg..vGalefivvettvtnqr 125
                                         + +  p  +GD+l +++r+ + ++ k+   G +++ v ++ vt  r
  gi|557693535|ref|YP_008796589.1|  83 DGMSFRSPTHPGDTLKVVARVVEKRESKSpdRGVVKLEVACHNVT--R 128
                                       99************************9998999999999998888..4 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   9.6e-07    0.0057      21      58 ..      68     105 ..      57     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9.6e-07
                                       HHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEE CS
                              4HBT  21 lrslggrgilvvvvelsidflrpvrlgdeltvearvlr 58 
                                         + ++++i++ ++ + + f++p ++gd+l v arv++
  gi|557693535|ref|YP_008796589.1|  68 YQTGAFDNIVALASIDGMSFRSPTHPGDTLKVVARVVE 105
                                       4444555999**************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1033.36
//
Query:       gi|557693536|ref|YP_008796590.1|  [L=239]
Description: threonyl/alanyl tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   36.6   0.2    6.7e-09   35.7   0.2    1.5  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    3.7e-08   32.3   0.0    5.1e-08   31.9   0.0    1.1  1  tRNA-synt_2c  tRNA synthetases class II (A)


Domain annotation for each model (and alignments):
>> 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 !   35.7   0.2   7.5e-13   6.7e-09       1      44 []     191     234 ..     191     234 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 7.5e-13
                                       EEEEEE.TT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsi.GdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +r+v+i G  +v++ gG+Hv nT e+g + +++ e+++k++rR+y
  gi|557693536|ref|YP_008796590.1| 191 LRIVEIvG-LDVQADGGPHVGNTVEVGRINVVKLENKGKTNRRLY 234
                                       69****78.8*********************************98 PP

>> 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 !   31.9   0.0   5.7e-12   5.1e-08     473     551 ..      17      93 ..       8      94 .. 0.95

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 5.7e-12
                                       SEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEX CS
                      tRNA-synt_2c 473 kefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevd 549
                                       +ef +ev e++ + vvLdrT+f + +GG  +D G+++  g   rv+++  ++g v h+ +   g  +vg+ v+++vd
  gi|557693536|ref|YP_008796590.1|  17 REFSAEVVEVSGDCVVLDRTVFHPRGGGLVSDVGFLRFGGVVSRVVEAFFTDGGVAHRLEG--GVPRVGEVVEGVVD 91 
                                       58999****************************************************9887..9************* PP

                                       HH CS
                      tRNA-synt_2c 550 ee 551
                                       +e
  gi|557693536|ref|YP_008796590.1|  92 WE 93 
                                       97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1768.32
//
Query:       gi|557693537|ref|YP_008796591.1|  [L=407]
Description: GTPase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-31  109.5   0.1    3.1e-31  108.2   0.0    1.7  2  MMR_HSR1_C     GTPase of unknown function C-terminal
    1.5e-22   79.8   0.0    4.7e-21   75.0   0.0    2.9  3  MMR_HSR1       50S ribosome-binding GTPase
    1.9e-08   34.0   1.0    7.6e-05   22.3   0.1    3.4  2  FeoB_N         Ferrous iron transport protein B
    1.1e-07   31.8   0.0    2.1e-07   30.9   0.0    1.4  1  TGS            TGS domain
    0.00091   19.3   0.0       0.14   12.2   0.0    2.4  2  Dynamin_N      Dynamin family
  ------ inclusion threshold ------
      0.018   14.6   1.5        7.7    6.0   0.0    3.0  2  GTP_EFTU       Elongation factor Tu GTP binding domain
       0.13   11.7   0.0        1.3    8.4   0.0    2.4  1  SRPRB          Signal recognition particle receptor beta subu
       0.14   11.6   0.5          9    5.7   0.0    2.9  3  Arf            ADP-ribosylation factor family
       0.17   11.7   0.0        8.5    6.2   0.0    2.8  2  LexA_DNA_bind  LexA DNA binding 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 ?   -2.7   0.0       4.2   8.4e+03      14      39 ..     168     190 ..     160     192 .. 0.73
   2 !  108.2   0.0   1.6e-34   3.1e-31       2     112 .]     225     332 ..     224     332 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.2
                        MMR_HSR1_C  14 ieklkekypkdkkvvpvsAaaElaLr 39 
                                       +e l+e+ +    v ++ A++E aLr
  gi|557693537|ref|YP_008796591.1| 168 VETLAEALQ---GVKITAAHIEAALR 190
                                       566677766...46788999999987 PP

  == domain 2  score: 108.2 bits;  conditional E-value: 1.6e-34
                        MMR_HSR1_C   2 lNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekir 78 
                                       +NK+Dl++a  n+e l+++  +   v+p+sA+aElaLr+a ++g++kY+pg+edf+i +++  +l+++q+kaLe i+
  gi|557693537|ref|YP_008796591.1| 225 ANKMDLETAGANFEVLRDTLTSYM-VIPASAEAELALRRAVQKGFVKYIPGEEDFRIVDES--KLTAEQRKALEFIE 298
                                       7******************99877.********************************9994..5************* PP

                        MMR_HSR1_C  79 dlvlkrygsTGVqealnaavfelldlivVYPVed 112
                                       + vl +y  TGVq a+n avf+ll++ vVYPV d
  gi|557693537|ref|YP_008796591.1| 299 SRVLGEYMRTGVQFAINVAVFKLLGMGVVYPVSD 332
                                       ********************************87 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.0   2.3e-24   4.7e-21       1      87 [.       4     120 ..       4     163 .. 0.78
   2 ?    0.2   0.0      0.38   7.6e+02      93     114 .]     206     227 ..     157     227 .. 0.62
   3 ?    0.1   0.0      0.41   8.1e+02      47      98 ..     333     395 ..     313     405 .. 0.65

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 2.3e-24
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE...........ETTEE................EEE CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk...........lkgke................iel 50 
                                       +++++G++N+GK+t++na t + a+vs +p+tT+++n+g+             +                    +e+
  gi|557693537|ref|YP_008796591.1|   4 RIGLIGKTNTGKTTFFNAATLQYAEVSTYPFTTKQPNYGTTYaitpcvcrefnV---TdnprnslcidgyrhipVEI 77 
                                       699************************************987554554444331...03444555555555555*** PP

                                       EECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT.....T CS
                          MMR_HSR1  51 vDtpGliegaseekglgkaflalee.adlillvvdas.....e 87 
                                       +D+pGli+ga  +kglg++fl++ + ad++++vvdas     e
  gi|557693537|ref|YP_008796591.1|  78 IDLPGLIKGAWAGKGLGNQFLSVASqADALIHVVDASgsvdeE 120
                                       **********************88879********98444331 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  93 ldeeleelleeakkplilvlnk 114
                                       +d++++e l e  kp+i+++nk
  gi|557693537|ref|YP_008796591.1| 206 EDKKFAEKLLEVSKPMIILANK 227
                                       45666666667899***99998 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.41
                                       EEEEEECGG..C.....SSHHHHHHHHHHHHHHHHCTSEEEEEEETT.....TTCSHHHHHHHH CS
                          MMR_HSR1  47 eielvDtpG..l.....iegaseekglgkaflaleeadlillvvdas.....eeklkpldeele 98 
                                       + +l D +G  l     +  +s+ k+l++a++   e + +l+ vd++      ++++ +d+++ 
  gi|557693537|ref|YP_008796591.1| 333 PAKLSDGAGnvLpdaylMPPNSTVKDLARAIHTELE-KGLLYAVDVRtglhlPGDYRLKDRDVL 395
                                       566777777431222212345566678888887776.9999***98855444234555555555 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 !   22.3   0.1   3.8e-08   7.6e-05       2      44 ..       4      46 ..       3     117 .. 0.71
   2 !    4.7   0.1    0.0099        20      99     141 ..     212     252 ..     205     266 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.8e-08
                                      EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEE CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklkl 44
                                      ++ l+G+ n+Gktt+fna t ++ +v+ +p +t + + g++  
  gi|557693537|ref|YP_008796591.1|  4 RIGLIGKTNTGKTTFFNAATLQYAEVSTYPFTTKQPNYGTTYA 46
                                      688***************************9998888777654 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0099
                                       HHHHHTTSSEEEEEETHHHHHH.TTEEE-HHHHHHHHTS-EEEE CS
                            FeoB_N  99 lqllelgvpvvlalnmideaek.kgieidlkkLsekLgvpvvkt 141
                                        +lle+++p+++  n++d  ++ ++ e+  ++L++     v+++
  gi|557693537|ref|YP_008796591.1| 212 EKLLEVSKPMIILANKMDLETAgANFEVLRDTLTSY---MVIPA 252
                                       689***************643213334444444443...34444 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   1.1e-10   2.1e-07       4      59 ..     343     398 ..     340     399 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.1e-10
                                       EETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                               TGS   4 ytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                       ++Pd+ +  +p ++tv+D+A++Ih++l k ++yA       + + d++L+d dv++Iv
  gi|557693537|ref|YP_008796591.1| 343 VLPDAYL--MPPNSTVKDLARAIHTELEKGLLYAVDVRtgLHLPGDYRLKDRDVLSIV 398
                                       5566666..999***********************988779****************9 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.014        28       1      17 [.       5      21 ..       5      40 .. 0.83
   2 !   12.2   0.0     7e-05      0.14     102     143 ..      74     118 ..      56     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.014
                                      EEEEEBTTTTHHHHHHH CS
                         Dynamin_N  1 iavvGsqSsGKSSvlna 17
                                      i ++G+++ GK+++ na
  gi|557693537|ref|YP_008796591.1|  5 IGLIGKTNTGKTTFFNA 21
                                      789*************8 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7e-05
                                       SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETTS-CC CS
                         Dynamin_N 102 gltlvDlPGldsvnkrdq...elvkeyikkadiilavtsanhdls 143
                                        ++++DlPGl++ +   +   +   + + +ad++++v++a+ ++ 
  gi|557693537|ref|YP_008796591.1|  74 PVEIIDLPGLIKGAWAGKglgNQFLSVASQADALIHVVDASGSVD 118
                                       699*********9999988889999999************98765 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 ?    5.7   0.5    0.0049       9.7       4      32 ..       3      31 ..       1     126 [. 0.56
   2 ?    6.0   0.0    0.0038       7.7     114     147 ..     210     245 ..     199     322 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0049
                                      EEEEEEESTTSSHHHHHHHHHHHTTSSCH CS
                          GTP_EFTU  4 rnigiighvDhGKtTLtdrLlyktgaisk 32
                                      + ig+ig +++GKtT+  + + +  ++s 
  gi|557693537|ref|YP_008796591.1|  3 VRIGLIGKTNTGKTTFFNAATLQYAEVST 31
                                      67999**********99877766666555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0038
                                       HHHHHHHTTTEEEEEEESCGST..HHHHHHHHHHHH CS
                          GTP_EFTU 114 vlrlalkegvpiivfiNKmDrl..kaelkeiveevk 147
                                        ++ +l++  p+i++ NKmD    +a+++ + +++ 
  gi|557693537|ref|YP_008796591.1| 210 FAEKLLEVSKPMIILANKMDLEtaGANFEVLRDTLT 245
                                       56677888999*********9877777777666665 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 ?    8.4   0.0   0.00067       1.3       8      86 ..       7     114 ..       2     126 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00067
                                       EE-STTSSHHHHHHHHHHS..............S---B---SS-EEETTG...............GGTT-SEEEETT CS
                             SRPRB   8 lvGlsdsGKTslftrLttd..............svkktvtSqessaalkv............ksekgskltliDfPG 58 
                                       l+G +++GKT++f+  t +              +   t  ++ +++  ++            ++ ++  +++iD+PG
  gi|557693537|ref|YP_008796591.1|   7 LIGKTNTGKTTFFNAATLQyaevstypfttkqpN-YGTTYAITPCVCREFnvtdnprnslciDGYRHIPVEIIDLPG 82 
                                       8999**********99988878877777655531.223344555555555555555555555667777888888888 PP

                                       -GCCS...HHHHHHHHHHGG.EEEEEEEEETT CS
                             SRPRB  59 heklr...qklleklkakss.lkglvfvvDSt 86 
                                         k +   + l ++++  +s + +l++vvD++
  gi|557693537|ref|YP_008796591.1|  83 LIKGAwagKGLGNQFLSVASqADALIHVVDAS 114
                                       76643111446666655444488888888865 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.06   1.2e+02      15      36 ..       3      24 ..       1      45 [. 0.69
   2 ?   -0.2   0.0      0.29   5.8e+02      81      93 ..     103     115 ..      98     165 .. 0.79
   3 ?    5.7   0.0    0.0045         9     115     136 ..     218     239 ..     196     266 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.06
                                      EEEEEEESTTSSHHHHHHHHHH CS
                               Arf 15 lrilllGLDnaGKtTilkklkl 36
                                      +ri l+G  n+GKtT  +  +l
  gi|557693537|ref|YP_008796591.1|  3 VRIGLIGKTNTGKTTFFNAATL 24
                                      789999*********9875433 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.29
                                       TESEEEEEEETT- CS
                               Arf  81 ktdavifvvDsad 93 
                                       + da+i+vvD++ 
  gi|557693537|ref|YP_008796591.1| 103 QADALIHVVDASG 115
                                       789*******864 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0045
                                       TSEEEEEEE-TTSTTSS-HHHH CS
                               Arf 115 evallvlaNKqDlpealseeel 136
                                       + ++++laNK+Dl++a  + e+
  gi|557693537|ref|YP_008796591.1| 218 SKPMIILANKMDLETAGANFEV 239
                                       4589**********99776554 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 ?    2.0   0.0     0.088   1.8e+02      39      61 ..     252     274 ..     243     276 .. 0.82
   2 ?    6.2   0.0    0.0042       8.5       2      19 ..     284     301 ..     283     306 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.088
                                       .HHHHHHHHHHHHHTTSEE-GGG CS
                     LexA_DNA_bind  39 SpsaveehLkaLerKGyierdpg 61 
                                        ++ +e  L++  +KG+++  pg
  gi|557693537|ref|YP_008796591.1| 252 ASAEAELALRRAVQKGFVKYIPG 274
                                       567788999999*******9998 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0042
                                       X---HHHHHHHHHHHHHH CS
                     LexA_DNA_bind   2 kkLTerQrevldlikasi 19 
                                       +kLT+ Qr+ l++i++ +
  gi|557693537|ref|YP_008796591.1| 284 SKLTAEQRKALEFIESRV 301
                                       79************9977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3058.92
//
Query:       gi|557693538|ref|YP_008796592.1|  [L=290]
Description: sugar kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-45  153.6   0.6    6.8e-45  153.4   0.6    1.0  1  Carb_kinase   Carbohydrate kinase
    1.1e-08   34.8   0.1    1.7e-08   34.2   0.1    1.2  1  HK            Hydroxyethylthiazole kinase family
    8.5e-05   22.0   0.0    0.00017   21.1   0.0    1.5  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase


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 !  153.4   0.6   1.1e-48   6.8e-45       1     240 [.      32     277 ..      32     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 153.4 bits;  conditional E-value: 1.1e-48
                                       EEEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTT....HTTTS....--SSS-SEEE CS
                       Carb_kinase   1 vlvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhpll....edeqa.kileklerldavv 72 
                                       vlv+gGs  y GA+ l   aa+r g++lv  a+ ++ ++++ + +p +iv pl+     ++++  i+  l+ ++a +
  gi|557693538|ref|YP_008796592.1|  32 VLVVGGSWLYHGAPFLVSMAAMRTGVDLVYTAAPEKVATAIRALSPSLIVLPLPdyklTSKSVdRIVRVLDDVNAAA 108
                                       79****************************************************99996677778************ PP

                                       E-TT-SS..SHCHHHHCHHHCCCCS-EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCH.HCCSHHHH CS
                       Carb_kinase  73 iGpGLgr..dekikklleevlekdeplviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivk.keddrlel 146
                                       +GpGL r  ++   kl++   e++  +v+DA +L+       l  r a+ + TPh++Ef rL++   +   ++r+e 
  gi|557693538|ref|YP_008796592.1| 109 VGPGLARgcEKGLLKLVRLLVERNIAVVLDATALFSDVL---LLLRGARAVVTPHAGEFRRLFGEEPGsTLEERVEK 182
                                       *****6632677888*******************97665...489******************98877699****** PP

                                       HHHHHHHHTTEEEEESTTSEEEECTTEEEEE---..-GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHH CS
                       Carb_kinase 147 arelaqklnavvllkgekdvivspegevlinstg..ssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaa 221
                                       + ++a++ +++vllkg++dv+ + + ev+ n +   ssa+++GG+GDvL+G+++++La   ++++aa+aaa+++g+a
  gi|557693538|ref|YP_008796592.1| 183 VYNVAKQFGVTVLLKGHVDVVSD-GVEVVVNRKQplSSAMTVGGTGDVLTGVVAGFLARMVPPFHAAVAAAVANGYA 258
                                       *******************9988.8888888776559**************************************** PP

                                       HHHHCCCT-TS-HCHHHHH CS
                       Carb_kinase 222 sdeaaekkgvgmlatelsk 240
                                       + +aaek g+ +++++++ 
  gi|557693538|ref|YP_008796592.1| 259 GVAAAEKLGLHITPEDVIG 277
                                       *********9999988765 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.1   2.8e-12   1.7e-08     111     225 ..     150     265 ..     138     270 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.8e-12
                                       EEEEHHHHHHHHTSSCCSCSSSSSS-SHHHHHHHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GG..GGGSTT CS
                                HK 111 ikGNasEilslaglelkvkGvDskeaataavaavqkvAqklrvvvvvtGevDvvsdgkkvyklknGtel..lgkita 185
                                       ++G  + ++  ag+  +  G +  ++ ++ v+ v +vA++++v+v++ G+vDvvsdg +v++ +  ++l     + +
  gi|557693538|ref|YP_008796592.1| 150 LRGARAVVTPHAGEFRRLFGEEPGSTLEERVEKVYNVAKQFGVTVLLKGHVDVVSDGVEVVV-NRKQPLssAMTVGG 225
                                       5666666666666666666777777778889**************************98654.44444411446779 PP

                                       HHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH.HHHHH CS
                                HK 186 sGCllgsvvaaflavkkdkllaaveavllykvAgkeaaar 225
                                       +G +l+ vva fla    +  aav+a ++   Ag +aa++
  gi|557693538|ref|YP_008796592.1| 226 TGDVLTGVVAGFLARMVPPFHAAVAAAVANGYAGVAAAEK 265
                                       9*********************************888776 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.8e-08   0.00017     120     225 ..     154     253 ..     128     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.8e-08
                                       -SEEE-BHHHHHHHHT.---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE---.-S CS
                      Phos_pyr_kin 120 atvitPNlpEaeaLlg.ekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleaerie.tk 194
                                         v+tP   E ++L g e+ +t+e+  e   +++k+   +Vl+kG           dv+ dg ev+  +++ ++   
  gi|557693538|ref|YP_008796592.1| 154 RAVVTPHAGEFRRLFGeEPGSTLEERVEKVYNVAKQFGVTVLLKGHV---------DVVSDGVEVVVNRKQPLSsAM 221
                                       479*************666679999999999999988889****953.........888877777666555555055 PP

                                       --BTHHHHHHHHHHHHHHCTSSHHH.HHHHHH CS
                      Phos_pyr_kin 195 nthGtGCtlssaiaaelakgeslee.AvkkAk 225
                                       +  GtG++l  ++a+ la+  ++ + Av+ A 
  gi|557693538|ref|YP_008796592.1| 222 TVGGTGDVLTGVVAGFLARMVPPFHaAVAAAV 253
                                       6679***************9876541555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); 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:                         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: 00:00:00.42
# Mc/sec: 2061.90
//
Query:       gi|557693539|ref|YP_008796593.1|  [L=253]
Description: hypothetical protein CSUB_C0100 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1878.18
//
Query:       gi|557693540|ref|YP_008796594.1|  [L=96]
Description: archaea-specific DNA-binding protein AlbA [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   50.1   0.9    2.7e-13   49.5   0.9    1.3  1  Alba      Alba
  ------ inclusion threshold ------
      0.023   14.7   2.3      0.058   13.4   0.6    2.0  2  Rpp20     Rpp20 subunit of nuclear RNase MRP and P


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 !   49.5   0.9   3.1e-17   2.7e-13       2      66 ..       6      66 ..       5      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 3.1e-17
                                      EEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEEE CS
                              Alba  2 eiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvltss 66
                                      ++ V++ +p m+yv+++   L   + + V+lka+GraI kAv+v+e+++rrf  +   v+++ ++
  gi|557693540|ref|YP_008796594.1|  6 VVLVGR-KPTMNYVLATTLPL--AEGKRVILKARGRAIAKAVDVVEVVRRRFV-QNAVVEKINIG 66
                                      688999.**************..77899************************5.77999999875 PP

>> Rpp20  Rpp20 subunit of nuclear RNase MRP and P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.6   6.4e-06     0.058      60      84 ..      27      51 ..      18      72 .. 0.80
   2 ?    1.5   0.1     0.029   2.6e+02     122     136 ..      72      86 ..      54      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.4e-06
                             Rpp20 60 kkeeVfvkatGrAiekalsvgrwfq 84
                                      + + V++ka GrAi ka+ v +  +
  gi|557693540|ref|YP_008796594.1| 27 EGKRVILKARGRAIAKAVDVVEVVR 51
                                      6789***************987664 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.029
                             Rpp20 122 eepetrtRwvsmvev 136
                                            r+R+vs++e+
  gi|557693540|ref|YP_008796594.1|  72 VGNDGRQRNVSTIEI 86 
                                       556779*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 711.61
//
Query:       gi|557693541|ref|YP_008796595.1|  [L=183]
Description: small GTP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   58.2   0.0    5.9e-13   48.7   0.0    2.0  2  Ras            Ras family
    7.5e-05   22.9   0.0      0.016   15.4   0.1    2.2  2  Roc            Ras of Complex, Roc, domain of DAPkinase
    0.00059   19.9   0.3     0.0032   17.5   0.3    2.1  1  MMR_HSR1       50S ribosome-binding GTPase
     0.0024   17.5   0.0       0.54    9.8   0.0    2.3  2  GTP_EFTU       Elongation factor Tu GTP binding domain
     0.0037   16.8   0.0      0.082   12.4   0.0    2.1  1  FeoB_N         Ferrous iron transport protein B
     0.0089   15.9   0.1        1.4    8.8   0.0    2.1  2  RsgA_GTPase    RsgA GTPase
  ------ inclusion threshold ------
      0.046   13.7   0.0       0.13   12.2   0.0    1.7  2  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
       0.06   13.2   0.0        0.1   12.5   0.0    1.3  1  Ser_hydrolase  Serine hydrolase


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00099       2.2       4      21 ..      22      39 ..      19      62 .. 0.85
   2 !   48.7   0.0   2.7e-16   5.9e-13      71     158 ..      79     165 ..      66     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00099
                                      EEESTTSSHHHHHHHHHH CS
                               Ras  4 lvGdsavGKtslllrfvk 21
                                      ++G+++vGKtsl+ + v 
  gi|557693541|ref|YP_008796595.1| 22 VLGEKNVGKTSLIEKLVA 39
                                      89**********998876 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 2.7e-16
                                       TESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTTTC CS
                               Ras  71 daegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAktne 147
                                       + +++llv+d+++r++f +   ++e++k+  +   p  L++nK+D + +r+v+++e+ ++ak +g++++e+SA +  
  gi|557693541|ref|YP_008796595.1|  79 KMDAALLVFDLSNRRTFVKSLLFFEKLKMLPN-PPPTFLIANKSDETGNRTVEEKEAADVAKAHGATYIEVSASNGF 154
                                       5789***********************99888.69****************************************** PP

                                       THHHHHHHHHH CS
                               Ras 148 nveeafeellr 158
                                       nv+ + e+l++
  gi|557693541|ref|YP_008796595.1| 155 NVDLLREKLIK 165
                                       **988888776 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 !   15.4   0.1   7.1e-06     0.016       3      31 ..      21      50 ..      19      75 .. 0.71
   2 !    5.8   0.0    0.0069        16      80     120 .]      80     123 ..      64     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.1e-06
                                      EEESSTTSSHHHHHHCHCT-.CCC-EEETT CS
                               Roc  3 vlvGdsgvGKtsllkrfved.kfsekekst 31
                                       ++G+++vGKtsl++++v + ++s  + st
  gi|557693541|ref|YP_008796595.1| 21 DVLGEKNVGKTSLIEKLVASsDISAVSGST 50
                                      589*************99740344444444 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0069
                                       SCEEEEEEE...GHHHHCHHHHHHHHHHHCSSS-EEEEEE-TTT CS
                               Roc  80 aalailvyd...srssenlkeWlkelkkvagkspvilvgnkiDl 120
                                        ++a+lv+d   +r++ +    +++lk   +  p +l++nk D+
  gi|557693541|ref|YP_008796595.1|  80 MDAALLVFDlsnRRTFVKSLLFFEKLKMLPNPPPTFLIANKSDE 123
                                       578999999743334444446999999999999********995 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.3   1.4e-06    0.0032       2      34 ..      20      51 ..      19     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                                      EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSS CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltgekaivsdkpgtTr 34
                                      v ++G  NvGK++Li +l+ + + +s+  g T+
  gi|557693541|ref|YP_008796595.1| 20 VDVLGEKNVGKTSLIEKLVAS-SDISAVSGSTT 51
                                      5689***************96.45555555554 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 !    9.8   0.0   0.00024      0.54       6      46 ..      20      60 ..      17      67 .. 0.84
   2 !    5.5   0.0     0.005        11      94     189 ..      80     164 ..      72     169 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00024
                                      EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHS CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtl 46
                                      + ++g  + GKt+L+++L++++ + + +g++++++ ++D+ 
  gi|557693541|ref|YP_008796595.1| 20 VDVLGEKNVGKTSLIEKLVASSDISAVSGSTTSGSWMIDKV 60
                                      56899999************999999888888777777765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.005
                                       -SEEEEEEETTTBSTHH.HHHHHHHHHHTTTE..EEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTT CS
                          GTP_EFTU  94 lDgavlvvdaveGvepq.teevlrlalkegvp..iivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgeke 167
                                       +D a+lv+d ++  +   +   ++ ++ +  p  ++++ NK D+++++  e +e++   +         ++++    
  gi|557693541|ref|YP_008796595.1|  80 MDAALLVFDLSNRRTFVkSLLFFEKLKMLPNPppTFLIANKSDETGNRTVEEKEAAD--V---------AKAH---G 142
                                       677777777765433220222222233322225578888999999888888777776..2.........1122...3 PP

                                       EEEEEEBTTTTBTHHHHHHHHH CS
                          GTP_EFTU 168 vpvvfgSalkgegvktllealv 189
                                        + + +Sa +g++v+ l e l+
  gi|557693541|ref|YP_008796595.1| 143 ATYIEVSASNGFNVDLLREKLI 164
                                       4678888888888887766665 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 !   12.4   0.0   3.7e-05     0.082       2      34 ..      19      50 ..      18     163 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.7e-05
                                      EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSS CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvt 34
                                      +v ++G+ nvGkt+l+++l  + ++++  +G t
  gi|557693541|ref|YP_008796595.1| 19 RVDVLGEKNVGKTSLIEKLVAS-SDISAVSGST 50
                                      57799**************865.4566666655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00061       1.4     104     137 ..      22      53 ..      11      64 .. 0.81
   2 !    5.2   0.0    0.0082        18      19      98 ..      83     164 ..      78     169 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00061
                                       EECSTTSSHHHHHHHHCTT-----S--------- CS
                       RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgrG 137
                                       ++G+  vGK++Li++l+ +    +++vs ++ +G
  gi|557693541|ref|YP_008796595.1|  22 VLGEKNVGKTSLIEKLVAS--SDISAVSGSTTSG 53 
                                       579999***********98..5667777777766 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0082
                                       EEEEEESTTTT--HHHHHHHHHHHHHTT-.....EEEEEEE-GGG--HHH.HHHHHHHHHHHTTSEEEE--TTTHTT CS
                       RsgA_GTPase  19 llivvslkepelslnlldrfLvlaeekgi.....epvivlnKiDlleeee.eleelkeelealgyevllvsaktkeg 89 
                                       +l+v+ l+    + ++  + L+++e+ ++     +  ++ nK D + +++ e +e ++  +a g + + vsa+++ +
  gi|557693541|ref|YP_008796595.1|  83 ALLVFDLS----NRRTFVKSLLFFEKLKMlpnppPTFLIANKSDETGNRTvEEKEAADVAKAHGATYIEVSASNGFN 155
                                       55555555....55555666666666665343323468889***9998886778888999999************** PP

                                       HHHHHHHCT CS
                       RsgA_GTPase  90 leelkellk 98 
                                       ++ l+e+l 
  gi|557693541|ref|YP_008796595.1| 156 VDLLREKLI 164
                                       999999875 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 ?   -2.7   0.0       2.6   5.9e+03      50      65 ..      90     105 ..      79     109 .. 0.77
   2 ?   12.2   0.0     6e-05      0.13      57     102 ..     113     165 ..     112     168 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.6
                      MMR_HSR1_Xtn  50 egnrvYipclyvlNKi 65 
                                       ++ r+++++l+++ K 
  gi|557693541|ref|YP_008796595.1|  90 SNRRTFVKSLLFFEKL 105
                                       5678899999888885 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 6e-05
                      MMR_HSR1_Xtn  57 pclyvlNKiDl.....isleeldelare..pnsvviSaekelnldeLkekiwe 102
                                       p++++ NK D+     ++++e  ++a+     ++ +Sa++++n+d L ek+ +
  gi|557693541|ref|YP_008796595.1| 113 PTFLIANKSDEtgnrtVEEKEAADVAKAhgATYIEVSASNGFNVDLLREKLIK 165
                                       678899****9666555555555555545568999*************99866 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.5e-05       0.1      78     156 ..      77     157 ..      69     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                                       SSSEEEEEEET--SGGS..TT.GGGCGCTTS-SSHHCCHCEEEEETTBTT....C-HHHHHHHHHHCT-EEEEETT- CS
                     Ser_hydrolase  78 akkvagalLVapadveeeaaklaelaefaplpreklpfpslvvaSenDpy....vsfeeaeelaeawgaelvdlgea 150
                                        +k+++alLV  +d +++ +  + l  f++l+  + p p+ ++a + D+     v+ +ea+++a+a ga  ++++ +
  gi|557693541|ref|YP_008796595.1|  77 DDKMDAALLV--FDLSNRRTFVKSLLFFEKLKMLPNPPPTFLIANKSDETgnrtVEEKEAADVAKAHGATYIEVSAS 151
                                       5788999999..566689999999************************86222267899***************999 PP

                                       TTSSGG CS
                     Ser_hydrolase 151 GHinad 156
                                         +n+d
  gi|557693541|ref|YP_008796595.1| 152 NGFNVD 157
                                       888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1392.38
//
Query:       gi|557693542|ref|YP_008796596.1|  [L=340]
Description: hypothetical protein CSUB_C0103 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-38  130.4   1.0    1.9e-37  128.8   0.2    1.8  2  TackOD1          Thaumarchaeal output domain 1
    2.2e-06   27.6   6.9     0.0018   18.2   2.1    2.3  2  DZR              Double zinc ribbon
     0.0001   22.3   7.4       0.11   12.5   0.4    2.6  2  HypA             Hydrogenase/urease nickel incorporation, met
  ------ inclusion threshold ------
       0.07   13.6   7.1       0.23   11.9   1.4    2.4  2  zf-CHY           CHY zinc finger
       0.11   12.0   0.2       0.11   12.0   0.2    2.3  2  RecR             RecR protein
       0.22   12.0   4.9          7    7.2   0.8    2.7  3  zf-C4pol         C4-type zinc-finger of DNA polymerase delta
       0.42   10.6  18.0        3.6    7.7   6.4    4.3  4  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.43   10.7  16.5         12    6.1   3.8    4.5  4  Zn-ribbon_8      Zinc ribbon domain
       0.83    9.7   6.0        8.6    6.5   0.0    3.1  3  zf-BED           BED zinc finger
       0.87    9.6  13.1       0.92    9.5   1.1    3.2  3  zf-C2HC5         Putative zinc finger motif, C2HC5-type
        1.1    9.1   0.0        1.1    9.1   0.0    3.6  4  A2L_zn_ribbon    A2L zinc ribbon domain
        1.2    9.2   9.5         16    5.6   1.7    3.0  2  zinc-ribbons_6   zinc-ribbons
        1.9    8.9   4.7         11    6.4   0.2    3.0  3  zf-Di19          Drought induced 19 protein (Di19), zinc-bind


Domain annotation for each model (and alignments):
>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.8   0.2   1.4e-40   1.9e-37      11     187 .]      13     183 ..       4     183 .. 0.95
   2 ?    0.1   0.0      0.39   5.4e+02      37      67 ..     295     327 ..     266     334 .. 0.63

  Alignments for each domain:
  == domain 1  score: 128.8 bits;  conditional E-value: 1.4e-40
                           TackOD1  11 ekllayllsrdeeklepvldpkskelysypllealskekeeseelleelvkrglleeelvdrirlCpsCksghlnvr 87 
                                       e +l+yl  + +e+++p ++++    y+yp++e +++e  + e++le+l++ g++e++l+d  ++Cp C +    v+
  gi|557693542|ref|YP_008796596.1|  13 ESFLRYLENSGKESIDPLFEKTA---YRYPVAEEFFGE--DAETVLENLAELGIFEKRLMDAAMMCPDCGTIAQVVK 84 
                                       56889999999999999998766...********9986..8999********************************* PP

                           TackOD1  88 evCpkCkSidieeqelihhftCgnvgpeeeflkegkleCpkCktkLrhiGvDYdrplevykCnsCkslfsepevkar 164
                                        vCp C+S ++ + ++i+h+ Cg+v+ e+ef k+g  +C kC ++L+++GvDY+r + +ykC sC+++ + p  ++ 
  gi|557693542|ref|YP_008796596.1|  85 PVCPTCSSGRLVKGNVIEHMLCGYVDFEQEFYKQG-FKCIKCGKELKTLGVDYRRAGVFYKCMSCGRVSAIPVKRFI 160
                                       ********************************999.9**************************************** PP

                           TackOD1 165 ClsCekesesddlkvreiysykl 187
                                       C +C++ s +++l+++ ++sy +
  gi|557693542|ref|YP_008796596.1| 161 CGHCGRASTEEELQLKPVFSYVV 183
                                       *********************76 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.39
                           TackOD1  37 ysypllealskeke.eseelleelvkrglle.e 67 
                                        ++   + l ++++ e+e++l++l+k++l e +
  gi|557693542|ref|YP_008796596.1| 295 LTFTSPDELVEKSKtEIEKILDKLSKKDLYEeA 327
                                       333333444444444999999999999998833 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   0.00015       0.2      28      48 ..      70      90 ..      47      92 .. 0.81
   2 !   18.2   2.1   1.3e-06    0.0018      14      49 .]     121     165 ..     112     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                               DZR 28 edrCpsCgekvdpearfCpeC 48
                                      + +Cp Cg+ ++  + +Cp C
  gi|557693542|ref|YP_008796596.1| 70 AMMCPDCGTIAQVVKPVCPTC 90
                                      568999999999999999888 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.3e-06
                               DZR  14 fCseCgtklkavaa.......edrCpsCgek.vdpearf.CpeCG 49 
                                        C +Cg++lk            ++C+sCg+  + p +rf C++CG
  gi|557693542|ref|YP_008796596.1| 121 KCIKCGKELKTLGVdyrragvFYKCMSCGRVsAIPVKRFiCGHCG 165
                                       6********9555599**************9999999999****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 !   12.5   0.4     8e-05      0.11      66     100 ..      66      96 ..      40     104 .. 0.75
   2 !   12.4   1.7     9e-05      0.12      40      98 ..     112     170 ..     101     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8e-05
                                       EE--EEEETTTS-EEECHHHHHS-TTTSSS-EEEE CS
                              HypA  66 evpvkvrCreCgkefeleekalrCpkCgsadveiv 100
                                        +++ ++C +Cg+  ++ +    Cp+C+s +  +v
  gi|557693542|ref|YP_008796596.1|  66 LMDAAMMCPDCGTIAQVVK--PVCPTCSSGR--LV 96 
                                       567899******9999774..48****9964..44 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9e-05
                                       -HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA  40 epeaLefafellaegtvlegaeLeieevpvkvrCreCgkefeleekalrCpkCgsadve 98 
                                       e+e  ++ f+ ++ g+ l+   +++++  v ++C +Cg+   +  k++ C++Cg+a++e
  gi|557693542|ref|YP_008796596.1| 112 EQEFYKQGFKCIKCGKELKTLGVDYRRAGVFYKCMSCGRVSAIPVKRFICGHCGRASTE 170
                                       567778889999999999999999999999********88887766799*****98765 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   1.0      0.05        69      53      73 ..      69      91 ..      57     108 .. 0.66
   2 ?   11.9   1.4   0.00017      0.23       3      63 ..     103     167 ..     101     176 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.05
                            zf-CHY 53 kavlCkkCkk..efaeyfCpiCk 73
                                      +a++C  C++  ++ + +Cp+C+
  gi|557693542|ref|YP_008796596.1| 69 AAMMCPDCGTiaQVVKPVCPTCS 91
                                      45556666554334444566664 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00017
                            zf-CHY   3 HykravvairapcCkklyaCreCHeeledhelerlev.kevlcllCeteq...ekavlCkkCkke 63 
                                       H+   +v ++ +  k+ ++C +C +el++  ++  ++    +c+ C ++     k  +C++C++ 
  gi|557693542|ref|YP_008796596.1| 103 HMLCGYVDFEQEFYKQGFKCIKCGKELKTLGVDYRRAgVFYKCMSCGRVSaipVKRFICGHCGRA 167
                                       66666777888888999*******9988766654333034679999998833234567****874 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   8.2e-05      0.11      12      36 ..      66      92 ..      64      94 .. 0.81
   2 ?   -2.3   0.8       2.5   3.5e+03      19      34 ..     145     164 ..     144     171 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.2e-05
                                      HHHH-EE-TTT--EESSS..S-CCCCS CS
                              RecR 12 akekvrhCsrCgnlteed..lCaICsd 36
                                      +++    C+ Cg+++     +C+ Cs+
  gi|557693542|ref|YP_008796596.1| 66 LMDAAMMCPDCGTIAQVVkpVCPTCSS 92
                                      7788889*******9985448****98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                                       -TTT--EESSS....S-CCC CS
                              RecR  19 CsrCgnlteed....lCaIC 34 
                                       C  Cg ++       +C  C
  gi|557693542|ref|YP_008796596.1| 145 CMSCGRVSAIPvkrfICGHC 164
                                       66666555444333334444 PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.22   3.1e+02      22      48 ..      50      76 ..      47      83 .. 0.80
   2 ?    7.2   0.8    0.0051         7       1      51 [.      73     127 ..      73     143 .. 0.76
   3 ?    5.7   0.2     0.015        21       1      24 [.     145     172 ..     145     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.22
                          zf-C4pol 22 esllkllsrlkelekklneletvCqsC 48
                                      e++l+ l++l   ek+l +   +C +C
  gi|557693542|ref|YP_008796596.1| 50 ETVLENLAELGIFEKRLMDAAMMCPDC 76
                                      56888899999999999*******999 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0051
                          zf-C4pol   1 ClvCkeklk..kalCkkCrsdkqes...llkllsrlkelekklneletvCqsCaqg 51 
                                       C  C++  +  k++C +C+s +  +   + ++l  + + e+++ +    C +C ++
  gi|557693542|ref|YP_008796596.1|  73 CPDCGTIAQvvKPVCPTCSSGRLVKgnvIEHMLCGYVDFEQEFYKQGFKCIKC-GK 127
                                       999*95333559******97776666657777788888888888888888888.44 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.015
                          zf-C4pol   1 ClvCkeklk....kalCkkCrsdkqesl 24 
                                       C++C++ ++    + +C +C + ++e+ 
  gi|557693542|ref|YP_008796596.1| 145 CMSCGRVSAipvkRFICGHCGRASTEEE 172
                                       9****533356669******86555554 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 ?    2.1   0.1      0.14   1.9e+02      19      26 ..      71      78 ..      57      84 .. 0.74
   2 ?    3.1   0.6      0.07        96      18      27 ..      84      93 ..      79      99 .. 0.83
   3 ?    7.7   6.4    0.0026       3.6      10      45 ..     111     150 ..     110     167 .. 0.75
   4 ?    2.5   0.5      0.11   1.5e+02      18      26 ..     158     166 ..     155     171 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.14
                     Zn_Tnp_IS1595 19 fvCPhCgs 26
                                        CP Cg 
  gi|557693542|ref|YP_008796596.1| 71 MMCPDCGT 78
                                      56****95 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.07
                     Zn_Tnp_IS1595 18 gfvCPhCgsr 27
                                      ++vCP C s 
  gi|557693542|ref|YP_008796596.1| 84 KPVCPTCSSG 93
                                      59*****875 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0026
                     Zn_Tnp_IS1595  10 LealrWpngfvCPhCgsr.kayrikt...rglfqCkeCrk 45 
                                       +e+ ++++gf C +Cg++ k   +        ++C +C++
  gi|557693542|ref|YP_008796596.1| 111 FEQEFYKQGFKCIKCGKElKTLGVDYrraGVFYKCMSCGR 150
                                       578899***********99666555533424678888875 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.11
                     Zn_Tnp_IS1595  18 gfvCPhCgs 26 
                                       +f+C hCg 
  gi|557693542|ref|YP_008796596.1| 158 RFICGHCGR 166
                                       466777774 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.012        16      22      34 ..      68      78 ..      60      84 .. 0.60
   2 ?    6.1   3.8    0.0089        12       8      38 ..      73      97 ..      70      98 .. 0.78
   3 ?    2.4   0.1      0.13   1.8e+02       6      16 ..     120     130 ..     119     139 .. 0.83
   4 ?    5.9   1.8      0.01        14       6      35 ..     143     168 ..     142     173 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                       Zn-ribbon_8 22 sdapltaCPeCgs 34
                                      +  +   CP+Cg 
  gi|557693542|ref|YP_008796596.1| 68 D--AAMMCPDCGT 78
                                      3..3455****97 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0089
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgs.evrr 38
                                      C +Cg+   v+       +++CP+C s ++ +
  gi|557693542|ref|YP_008796596.1| 73 CPDCGTIAQVV-------KPVCPTCSSgRLVK 97
                                      99999666655.......678****9988765 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.13
                       Zn-ribbon_8   6 YrCeeCghefe 16 
                                       ++C +Cg+e  
  gi|557693542|ref|YP_008796596.1| 120 FKCIKCGKELK 130
                                       89999999865 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.01
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgs.e 35 
                                       Y+C +Cg++  + ++        C +Cg   
  gi|557693542|ref|YP_008796596.1| 143 YKCMSCGRVSAIPVKR-----FICGHCGRaS 168
                                       9******777744432.....2399999844 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0062       8.6      14      27 ..     117     130 ..     109     135 .. 0.88
   2 ?   -0.3   0.2      0.79   1.1e+03      17      26 ..     143     152 ..     140     154 .. 0.83
   3 ?    4.6   0.2     0.025        34      15      27 ..     157     169 ..     151     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0062
                                       SS--EETTTTEE-- CS
                            zf-BED  14 eqkavCryCgkils 27 
                                       +q  +C+ Cgk+l+
  gi|557693542|ref|YP_008796596.1| 117 KQGFKCIKCGKELK 130
                                       68899******997 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.79
                                       -EETTTTEE- CS
                            zf-BED  17 avCryCgkil 26 
                                        +C+ Cg+++
  gi|557693542|ref|YP_008796596.1| 143 YKCMSCGRVS 152
                                       58*****987 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.025
                                       S--EETTTTEE-- CS
                            zf-BED  15 qkavCryCgkils 27 
                                       ++ +C +Cg+ ++
  gi|557693542|ref|YP_008796596.1| 157 KRFICGHCGRAST 169
                                       6789*****9876 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 ?    9.5   1.1   0.00067      0.92      13      42 ..      66      92 ..      63     105 .. 0.77
   2 ?    1.0   0.4      0.32   4.4e+02      35      43 ..     120     128 ..     103     132 .. 0.61
   3 ?    6.3   0.5     0.007       9.6      19      43 ..     144     167 ..     139     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00067
                          zf-C2HC5 13 LleaapnClnCGkiiCakeglskpCsfCgs 42
                                      L++aa +C  CG i  + + +   C+ C+s
  gi|557693542|ref|YP_008796596.1| 66 LMDAAMMCPDCGTIAQVVKPV---CPTCSS 92
                                      899**********98777666...999995 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.32
                          zf-C2HC5  35 kpCsfCgsp 43 
                                        +C  Cg++
  gi|557693542|ref|YP_008796596.1| 120 FKCIKCGKE 128
                                       455555555 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.007
                          zf-C2HC5  19 nClnCGkiiCakeglskpCsfCgsp 43 
                                        C++CG +  +  +    C +Cg+ 
  gi|557693542|ref|YP_008796596.1| 144 KCMSCGRVSAIPVKR-FICGHCGRA 167
                                       7*******8887777.89****977 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 ?    9.1   0.0   0.00079       1.1      19      33 .]      68      82 ..      66      82 .. 0.86
   2 ?   -1.7   0.2       1.8   2.5e+03      23      28 ..      86      91 ..      86      92 .. 0.83
   3 ?    2.2   0.4      0.11   1.5e+02       5      12 ..     121     128 ..     117     129 .. 0.78
   4 ?   -3.5   0.7       7.2   9.9e+03       4      10 ..     143     149 ..     143     150 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00079
                     A2L_zn_ribbon 19 qgylvCieCgasfpy 33
                                      ++ + C++Cg+++++
  gi|557693542|ref|YP_008796596.1| 68 DAAMMCPDCGTIAQV 82
                                      56799*******985 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.8
                     A2L_zn_ribbon 23 vCieCg 28
                                      vC+ C+
  gi|557693542|ref|YP_008796596.1| 86 VCPTCS 91
                                      899997 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.11
                     A2L_zn_ribbon   5 vCsvCggn 12 
                                       +C++Cg++
  gi|557693542|ref|YP_008796596.1| 121 KCIKCGKE 128
                                       78888886 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 7.2
                     A2L_zn_ribbon   4 kvCsvCg 10 
                                       ++C  Cg
  gi|557693542|ref|YP_008796596.1| 143 YKCMSCG 149
                                       5666666 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   4.2     0.041        57      18      37 ..      72      92 ..      66     134 .. 0.56
   2 ?    5.6   1.7     0.012        16       2      37 ..     121     166 ..     120     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.041
                                      E-TTT--.EEEEEEE-SSS-S CS
                    zinc-ribbons_6 18 hCeaCqe.dlkkealCpeCeq 37
                                       C  C +    ++++Cp+C++
  gi|557693542|ref|YP_008796596.1| 72 MCPDCGTiAQVVKPVCPTCSS 92
                                      455555422223445555543 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.012
                                       --SSS-S--EE-S.......SEEE-TTT--...EEEEEEE-SSS-S CS
                    zinc-ribbons_6   2 kCpeCqqelekrg.......eqyhCeaCqe...dlkkealCpeCeq 37 
                                       kC +C +el++ g         y+C +C +      k  +C +C+ 
  gi|557693542|ref|YP_008796596.1| 121 KCIKCGKELKTLGvdyrragVFYKCMSCGRvsaIPVKRFICGHCGR 166
                                       6999999999888889998888999999986644456678888875 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 ?   -1.4   0.2       2.2     3e+03       3      10 ..      71      78 ..      69      84 .. 0.66
   2 ?    6.4   0.2    0.0081        11      33      49 ..      86     104 ..      79     108 .. 0.81
   3 ?    3.0   0.0     0.091   1.3e+02       2      18 ..     158     174 ..     157     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.2
                           zf-Di19  3 ftCPyCgk 10
                                      + CP Cg 
  gi|557693542|ref|YP_008796596.1| 71 MMCPDCGT 78
                                      56887775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0081
                           zf-Di19  33 vCPvCa..ekvtkdlvaHl 49 
                                       vCP C+    v+ ++++H+
  gi|557693542|ref|YP_008796596.1|  86 VCPTCSsgRLVKGNVIEHM 104
                                       9999986566889999998 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.091
                           zf-Di19   2 sftCPyCgkeltvkeLv 18 
                                        f C +Cg++ t++eL+
  gi|557693542|ref|YP_008796596.1| 158 RFICGHCGRASTEEELQ 174
                                       699******99999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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):              13  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2176.54
//
Query:       gi|557693543|ref|YP_008796597.1|  [L=348]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2400.73
//
Query:       gi|557693544|ref|YP_008796598.1|  [L=264]
Description: voltage-gated potassium channel [Candidatus Caldiarchaeum subterraneum]
Scores for 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-17   61.5   6.9    5.6e-17   61.5   6.9    2.3  3  Ion_trans_2  Ion channel
    1.2e-13   50.9   6.5    1.6e-13   50.5   6.5    1.1  1  Ion_trans    Ion transport protein
    4.7e-06   26.5   1.1    0.00038   20.3   0.0    2.2  2  Lig_chan     Ligand-gated ion channel
      0.004   17.0   1.5      0.011   15.5   0.1    2.2  2  IRK          Inward rectifier potassium channel transmembrane
  ------ inclusion threshold ------
       0.03   14.8   0.0       0.03   14.8   0.0    2.8  2  SNARE_assoc  SNARE associated Golgi protein


Domain annotation for each model (and alignments):
>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.4      0.47   1.7e+03      53      76 ..      14      37 ..       7      40 .. 0.75
   2 ?   -3.3   0.1       2.5   9.1e+03       8      27 ..      76      91 ..      72      94 .. 0.49
   3 !   61.5   6.9   1.6e-20   5.6e-17       4      77 ..     137     213 ..     132     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.47
                                      HHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2 53 lftivyillGlalfalflavlgkv 76
                                      + +iv+i++ +++ + f +v++++
  gi|557693544|ref|YP_008796598.1| 14 VASIVLIVVEYFVPLSFDQVVAIM 37
                                      456888888888888888888766 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.5
                                      HHHHHHHHT....T---HHH CS
                       Ion_trans_2  8 ifgaviysleegwekwsfld 27
                                      ++ +v+y l    e+++++ 
  gi|557693544|ref|YP_008796598.1| 76 TPMFVLYLL----ETQTIFG 91
                                      444445554....4445554 PP

  == domain 3  score: 61.5 bits;  conditional E-value: 1.6e-20
                                       HHTCHHHHHHHHT.......T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2   4 llvlifgaviysl...eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkvl 77 
                                       l+vl+  +  y l    eg   ++f da+++++ t+tT+GYGd+vp+t agr++  +++++G+a++++f++ lg+++
  gi|557693544|ref|YP_008796598.1| 137 LVVLAGTFSAYLLeagVEGARIHDFGDAFWWALATVTTVGYGDVVPVTVAGRIVGSILMVTGIAILGVFISSLGSAI 213
                                       56666667777778876667899*************************************************99876 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   6.5   4.4e-17   1.6e-13       3     235 ..       4     216 ..       2     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 4.4e-17
                                       HHHHHHHHHHHHHHHHHHCCCSSSSHHHHC.HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCHSHHHHHHHHHH CS
                         Ion_trans   3 vfelfilllillncvflaletyfpedelek.tileilelvftaiftlemllkilalgllikkrYlrdpwnilDflvv 78 
                                       + e ++ +l + ++v++ +  yf ++++++  ++ +++ v++   +++++ + +a g+    rYl +   +  ++++
  gi|557693544|ref|YP_008796598.1|   4 WSETVSSVLAVASIVLIVV-EYFVPLSFDQvVAIMAADGVIVLYLAVDLVRQARASGN--VSRYLIKR--WYEVVAL 75 
                                       5556666666666666666.7888889996666777799******************9..88999997..89***** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHGGGGGGHHH...CHSHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans  79 lpsllslvlseesllllsvlrlfrvlrllkli...srleg.lrtlvtalirsvkdllnvlllllvvlfifaligvql 151
                                       +p ++ + l++ + +  +vlr +r+ rll+++    r ++ l +l+   +  v  l+++ll++++v+++    ++ l
  gi|557693544|ref|YP_008796598.1|  76 TPMFVLYLLET-QTIFGAVLRGMRLTRLLRVVlltARARKsLTHLLE--VVRVSRLGYLLLASALVVLAGTFSAYLL 149
                                       *****995554.45555666666666666666222444443555555..3334589999999999999999999888 PP

                                       HTTSCCCCCCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans 152 fkgklreknecaktwenpnngntnFdnfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsflllNl 228
                                                      ++ +      ++f++a++w++ + tt+g+gd++++t  ++  v+ i++v+ i + ++++ +l
  gi|557693544|ref|YP_008796598.1| 150 E--------------AGVEG--ARIHDFGDAFWWALATVTTVGYGDVVPVTVAGR-IVGSILMVTGIAILGVFISSL 209
                                       8..............23333..3566*****************************.888888888888888888888 PP

                                       HHHHHHH CS
                         Ion_trans 229 liaviad 235
                                         a+i +
  gi|557693544|ref|YP_008796598.1| 210 GSAIIGE 216
                                       7777766 PP

>> Lig_chan  Ligand-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.4    0.0053        19       5      33 ..       4      33 ..       1      84 [. 0.80
   2 !   20.3   0.0   1.1e-07   0.00038      12     105 ..     131     221 ..     123     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0053
                                      XXXXXTX.XXXXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          Lig_chan  5 Wlsvlva.lilvsivlflverfspyewrep 33
                                      W  ++ + l + sivl++ve f+p ++++ 
  gi|557693544|ref|YP_008796598.1|  4 WSETVSSvLAVASIVLIVVEYFVPLSFDQV 33
                                      66665550556789***********99975 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.1e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHH.HXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Lig_chan  12 lilvsivlflverfspyewrepeeaaetveneftlsnslwfslgalvqqG.cdesprsvsgRivvavWwffvlills 87 
                                       l+l s++++l   fs y  +   e      + + + +++w +l++++  G +d  p +v+gRiv ++ ++  + +l 
  gi|557693544|ref|YP_008796598.1| 131 LLLASALVVLAGTFSAYLLEAGVE----GARIHDFGDAFWWALATVTTVGyGDVVPVTVAGRIVGSILMVTGIAILG 203
                                       566677777777777777766632....45678899**************9************************** PP

                                       XXXXXXXXXXXXXXXXXS CS
                                       xxxxxxxxxxxxxxxxxx RF
                          Lig_chan  88 sYtAnLaafltvermqtp 105
                                        ++ +L + ++ e++ t+
  gi|557693544|ref|YP_008796598.1| 204 VFISSLGSAIIGEKLATH 221
                                       **********99998875 PP

>> IRK  Inward rectifier potassium channel transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       0.2   7.2e+02      87     100 ..      78      91 ..      42     111 .. 0.74
   2 !   15.5   0.1   3.2e-06     0.011      81     140 ..     157     219 ..     149     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.2
                               IRK  87 sallfslEtqttig 100
                                        ++l+ lEtqt  g
  gi|557693544|ref|YP_008796598.1|  78 MFVLYLLETQTIFG 91 
                                       34578888887655 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.2e-06
                               IRK  81 nvksftsallfslEtqttigyGsrv...vteeCpeailllviqsivgllidavlvgivlaKla 140
                                       ++++f +a+ ++l t tt+gyG  v   v+ +   +il+++  +i+g++i+++  +i+  Kla
  gi|557693544|ref|YP_008796598.1| 157 RIHDFGDAFWWALATVTTVGYGDVVpvtVAGRIVGSILMVTGIAILGVFISSLGSAIIGEKLA 219
                                       6899******************98621145566778888888899******999999988887 PP

>> SNARE_assoc  SNARE associated Golgi protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   3.8       1.9   6.7e+03      53      53 ..     109     109 ..       9     161 .. 0.61
   2 ?   14.8   0.0   8.4e-06      0.03       6      76 ..     183     255 ..     178     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.9
                       SNARE_assoc  53 e 53 
                                        
  gi|557693544|ref|YP_008796598.1| 109 T 109
                                       1 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 8.4e-06
                       SNARE_assoc   6 llvaaGvlfglllgtlvtslgallGaslayllgrylgr..kalrrkllsekrvkalerlverygflallllrl 76 
                                       ++va+ +++++l++t +++lg++++++ + ++g +l+   ++ + k l +kr++ale+l+e+  + ++ l+ +
  gi|557693544|ref|YP_008796598.1| 183 VTVAGRIVGSILMVTGIAILGVFISSLGSAIIGEKLAThpESDELKELMKKRIDALESLSEEEVSQLVELIKF 255
                                       5566667778999************************9997777778899999*9999999888877766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1254  (0.0699426); expected 358.6 (0.02)
Passed bias filter:                      736  (0.0410508); 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):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1849.11
//
Query:       gi|557693545|ref|YP_008796599.1|  [L=374]
Description: major facilitator superfamily MFS [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   76.2  47.2    3.7e-15   55.7  11.4    2.1  2  MFS_1       Major Facilitator Superfamily
    0.00025   20.0  10.5     0.0072   15.2  10.5    2.8  1  MFS_1_like  MFS_1 like family
     0.0021   16.6   1.2     0.0021   16.6   1.2    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 !   55.7  11.4   6.2e-19   3.7e-15      18     187 ..      28     193 ..      11     207 .. 0.86
   2 !   24.0  30.7   2.7e-09   1.6e-05       6     164 ..     201     363 ..     198     371 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 6.2e-19
                             MFS_1  18 alplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllllfasslwlllvlrv 93 
                                       +lp  ++++lg+++ ++g +l++  l+ ++a +++G l+d+ G  + ++ +g++++++  l++l +s +wll++l +
  gi|557693545|ref|YP_008796599.1|  28 VLP-DYMRQLGMDAFTVGAALGVAELAGWAARPVGGLLADKTGKYSlIVKMGYAGLIVIPLMGL-VSVWWLLVILAF 102
                                       677.67799*************************************999999999999944444.36666******* PP

                             MFS_1  94 lqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfll 170
                                       l  ++ g+ +pa  a+++++  + + g+a+gl  +  ++Ga  gpll+ +++s l  ++v++ l+i ++l+  lf l
  gi|557693545|ref|YP_008796599.1| 103 LERVFRGMRVPARDAMLVRMRGDVKVGKAFGLHELLDQVGAGGGPLLAIAVLSILPTPYVYMSLTIPYILL--LFTL 177
                                       ***********************************************************************..5556 PP

                             MFS_1 171 llpeepperkrkspkee 187
                                        ++ +++e++ +++ e+
  gi|557693545|ref|YP_008796599.1| 178 MFVPSHVEKAHETS-EL 193
                                       66555555555443.33 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 2.7e-09
                             MFS_1   6 flsalarsilgpalpl.alaedlgispseigl....lltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       ++s +a+++++ +lp  +l     +++ + ++    ++t+ +++ ava l+lG + dr+G + v l+  l+ + + +
  gi|557693545|ref|YP_008796599.1| 201 VFSLAAAFNTAGLLPVpLLLYMISLTAGSGSWlipaAYTVAMVVDAVAGLFLGMFFDRWGLKVVALVIPLSVLPT-V 276
                                       455555555566666556766777888889998444555555566**************9999988888888888.6 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...Wr 151
                                       ++   s + ll+v+ +l G+  ga  ++  a++a++++ +  g+a++l++++f++Ga+++  + g++++  g    +
  gi|557693545|ref|YP_008796599.1| 277 FIY--SDVALLMVSAFLLGVVIGAQESIFRAMVAELAHANGLGSAYALYGLAFGVGAAVAGTVFGYMIQ-TGrsvLE 350
                                       666..8989***************************************************999999994.4435655 PP

                             MFS_1 152 avfyilaivslla 164
                                       +v y++a  +  a
  gi|557693545|ref|YP_008796599.1| 351 LVLYAAAMQAGSA 363
                                       5555555544444 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 !   15.2  10.5   1.2e-06    0.0072      25     263 ..      32     318 ..      29     369 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-06
                        MFS_1_like  25 ylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsv 101
                                       y+++ g++a  +g  + ++ l   +++p+ g laD++gk+  +v ++    +v+ l+ l +                
  gi|557693545|ref|YP_008796599.1|  32 YMRQLGMDAFTVGAALGVAELAGWAARPVGGLLADKTGKYSLIVKMGYAGLIVIPLMGL-V---------------- 91 
                                       9*********************************************9988887777222.2................ PP

                        MFS_1_like 102 aqdvdaektfwilfllvvlasfflaailvlldaatlkel..gedrkdyGrqrlfGsvGyaifafitGilidhysvnl 176
                                                 w+l++l +l  +f    ++  da+  ++    +  k +G   l   vG +    +  +++  + +  
  gi|557693545|ref|YP_008796599.1|  92 -------SVWWLLVILAFLERVFRGMRVPARDAMLVRMRgdVKVGKAFGLHELLDQVGAGGGPLLAIAVLSILPT-- 159
                                       .......45666666777777777777788888777777333445668888888887765433333333333333.. PP

                        MFS_1_like 177 lpysallyvlaallvisllvvlilnetekesklkvtksl...................................... 215
                                        py+++ +++  +l++ +l+++  +  ++++  +++  +                                      
  gi|557693545|ref|YP_008796599.1| 160 -PYVYMSLTIPYILLLFTLMFVPSHVEKAHETSELK--Parsvavfslaaafntagllpvplllymisltagsgswl 233
                                       .23333333333333333332222222222222222..122446666677777777777777777777777777777 PP

                        MFS_1_like 216 .....................................qvllnilknpeviifllvalilgmswgiienFlflYLkel 255
                                                                            +vl  ++    v+++++ a++lg++ g+ e+ +     el
  gi|557693545|ref|YP_008796599.1| 234 ipaaytvamvvdavaglflgmffdrwglkvvalviplSVLPTVFIYSDVALLMVSAFLLGVVIGAQESIFRAMVAEL 310
                                       77777777777777777777777777777777777776677777777777777777777777777666544444443 PP

                        MFS_1_like 256 gasntllG 263
                                          n l +
  gi|557693545|ref|YP_008796599.1| 311 AHANGLGS 318
                                       33333333 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.2   3.4e-07    0.0021      89     198 ..      79     189 ..      60     200 .. 0.89
   2 !    2.5   7.8    0.0061        37      84     160 ..     263     339 ..     232     360 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.4e-07
                             MFS_3  89 svlltvlaalgllspw.lllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlva 164
                                        + l+v+ ++gl+s+w ll++l++l  +   +  Pa +A++  +    +v +A  L+ +   +    GP l+  +++
  gi|557693545|ref|YP_008796599.1|  79 YAGLIVIPLMGLVSVWwLLVILAFLERVFRGMRVPARDAMLVRMRGDVKVGKAFGLHELLDQVGAGGGPLLAIAVLS 155
                                       456889999*****972566899****************************************************** PP

                             MFS_3 165 avGaalafavnalsylalivallrwkrevrkssl 198
                                       ++ + +++   ++ y+ l+++l+ +  +v+k + 
  gi|557693545|ref|YP_008796599.1| 156 ILPTPYVYMSLTIPYILLLFTLMFVPSHVEKAHE 189
                                       ***********************99999988765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.0061
                             MFS_3  84 llalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgG 160
                                       ++alv  l ++ +++ + ++ ll+++++l+g+    ++  ++A+v el +++ + +A aL  + + +  +v   + G
  gi|557693545|ref|YP_008796599.1| 263 VVALVIPLSVLPTVFIYSDVALLMVSAFLLGVVIGAQESIFRAMVAELAHANGLGSAYALYGLAFGVGAAVAGTVFG 339
                                       333333344444556677899999************************************99888765555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2604.06
//
Query:       gi|557693546|ref|YP_008796600.1|  [L=316]
Description: threonine dehydratase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-69  235.0   3.0    1.3e-69  234.9   3.0    1.0  1  PALP         Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.046   13.3   0.0      0.077   12.6   0.0    1.4  1  LD_cluster3  SLOG cluster3 family


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 !  234.9   3.0   1.4e-73   1.3e-69       4     294 .]      17     301 ..      14     301 .. 0.98

  Alignments for each domain:
  == domain 1  score: 234.9 bits;  conditional E-value: 1.4e-73
                                       CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-E CS
                              PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlk 80 
                                         +pTPl  +++lskelg+++++KlE+lnpt SfK+Rg  y ++  + +   k+vv+as GNh++++A+ ++l+G++
  gi|557693546|ref|YP_008796600.1|  17 YLKPTPLQYSRKLSKELGADVYVKLENLNPTHSFKVRGGLYYMSLMHDK--VKGVVTASMGNHAQSIAYSGSLYGVE 91 
                                       678*************************************999985555..6************************* PP

                                       EEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTTT CS
                              PALP  81 vtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlggk 157
                                        tiv+p++++p k+++   lGa+v+ +g  ydea+a+a+ +a+e +g ++v++ + +    g +t+ lE++e+l ++
  gi|557693546|ref|YP_008796600.1|  92 TTIVMPSWVNPLKKEAVTDLGAKVITYGAYYDEAAAYAQHYAEE-HGLVFVDPINEVKLYPGVATMHLEVVEEL-PN 166
                                       ********************************************.*****************************.6* PP

                                       EEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHHS CS
                              PALP 158 pdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafelld 234
                                       +++v+ p+GgG+ + G ++ +k+ +p v+v++v++eg++a++ s+++g  ++++  +t a+glav ++ e  +++l+
  gi|557693546|ref|YP_008796600.1| 167 VETVFNPLGGGSGAIGAVTVYKSINPAVKVYAVQAEGAPAFYLSYKKGGLQSTDGVKTRAEGLAVAKAYETPLQILK 243
                                       ***************************************************************************** PP

                                       EEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 235 rlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       +++d++v vsdee+ +a+++l+++ + v+e ++aa+ aa+  + a++++++ +vv++ltg
  gi|557693546|ref|YP_008796600.1| 244 NKLDDVVLVSDEEMEKAVVKLYNTVRQVAELAGAASTAAA-YKFAEKISGK-TVVLMLTG 301
                                       ****************************************.**********.*****998 PP

>> LD_cluster3  SLOG cluster3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.6e-06     0.077      43     153 ..     103     217 ..      62     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.6e-06
                       LD_cluster3  43 laedlgvdyeeavklyqskffkd.efpeeneefenvvyteavdkdr.eksllamReemlseekfkaavf..iGGmeG 115
                                       l ++  +d +++v+ y + + +   +++  +e + +v+++ +++ +    +++m  e+++e     +vf  +GG  G
  gi|557693546|ref|YP_008796600.1| 103 LKKEAVTDLGAKVITYGAYYDEAaAYAQHYAEEHGLVFVDPINEVKlYPGVATMHLEVVEELPNVETVFnpLGGGSG 179
                                       556677788888888877665432578888888999999999875516789***********999***9888***** PP

                       LD_cluster3 116 veeefelfrklqPnakilPvastGgaalelakklgeak 153
                                        +  +++++  +P+ k++ v + G+ a  l  k g ++
  gi|557693546|ref|YP_008796600.1| 180 AIGAVTVYKSINPAVKVYAVQAEGAPAFYLSYKKGGLQ 217
                                       ***************************99988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2163.75
//
Query:       gi|557693547|ref|YP_008796601.1|  [L=111]
Description: translation initiation factor eIF-1A [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   68.8   0.2    3.2e-19   68.5   0.2    1.1  1  eIF-1a          Translation initiation factor 1A / IF-1
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.024   14.6   0.0    1.3  1  Prot_ATP_ID_OB  Proteasomal ATPase OB C-terminal domain


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 !   68.5   0.2   3.6e-23   3.2e-19       2      64 .]      23      85 ..      22      85 .. 0.94

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 3.6e-23
                                      EEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TT.EEEEES- CS
                            eIF-1a  2 evigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydlt.kGrIvyr 64
                                       v+g+V+++ g ++  V ++d gk+++++i+g ++++iwik+Gd VlV++++++ + +G++ +r
  gi|557693547|ref|YP_008796601.1| 23 DVYGVVSKMYGYDRLLVDCSD-GKQRVCRIRGQLKRRIWIKEGDLVLVSPWDFQRDsRGDVWWR 85
                                      689****************85.********************************666****997 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 ?   14.6   0.0   2.7e-06     0.024       4      46 ..      28      70 ..      13      72 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-06
                                      EEEE-TTSSEEEEE-TTS-EEEEEE-GGGSSST.--TTEEEEEE CS
                    Prot_ATP_ID_OB  4 VsEvlddteraiVktssdeevvvslagavprem.LrpgDlVavd 46
                                      Vs++ +  +r++V  s + ++v+++ g ++r   ++ gDlV+v 
  gi|557693547|ref|YP_008796601.1| 28 VSKMYGY-DRLLVDCSDGKQRVCRIRGQLKRRIwIKEGDLVLVS 70
                                      5666666.9*********************9989********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 752.62
//
Query:       gi|557693548|ref|YP_008796602.1|  [L=526]
Description: elongation factor EF-1 alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  101.9   0.0    4.4e-29  101.4   0.0    1.2  1  GTP_EFTU        Elongation factor Tu GTP binding domain
    2.1e-08   34.5   0.3      1e-07   32.2   0.3    2.2  1  GTP_EFTU_D3     Elongation factor Tu C-terminal domain
    3.1e-08   33.9   0.2      1e-07   32.3   0.2    2.0  1  GTP_EFTU_D2     Elongation factor Tu domain 2
     0.0024   17.9   0.0      0.015   15.3   0.0    2.2  1  MMR_HSR1        50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.046   13.4   0.0       0.14   11.9   0.0    1.6  1  CheB_methylest  CheB methylesterase
      0.067   13.1   0.1       0.68    9.8   0.0    2.3  2  RsgA_GTPase     RsgA GTPase
       0.12   12.1   0.0        0.5   10.1   0.0    1.8  2  ATP_bind_1      Conserved hypothetical ATP binding protein


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 !  101.4   0.0   1.7e-32   4.4e-29       3     187 ..     118     328 ..     116     375 .. 0.88

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 1.7e-32
                                       EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE............... CS
                          GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle............... 64 
                                       ++ ++++ghv+hGK+T++ +L++  +++ +      +  +lDtl++E er ++ + + i l                
  gi|557693548|ref|YP_008796602.1| 118 HLVVSVAGHVNHGKSTFLACLITGEKDDGQ------KWLYLDTLPHEVERNLSADLHFIVLGfrgmepnlmknpldr 188
                                       7889******************77766555......2457*********************9*************** PP

                                       ......TTCSSEEEEEEEESSSGGGHHHHHHH..HHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCG CS
                          GTP_EFTU  65 ......ketkkylinliDtPGHvdFskevirg..lrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmD 133
                                             ++++++l++++Dt GH+ + +++irg   + +D+  lvv+a++G+++ t+e+l ++l++g+p+i++i+K+D
  gi|557693548|ref|YP_008796602.1| 189 aerirvTRESERLVSFVDTVGHEPWLRTTIRGilGQEIDYGFLVVAADDGPTHITREHLGIMLAMGIPVIILITKID 265
                                       **9987699***********************98899**************************************** PP

                                       ST.HHHHHHHHHHHHHHHHHH.........HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHH CS
                          GTP_EFTU 134 rl.kaelkeiveevkqklsrk.........eeklekygekgekevpvvfgSalkgegvktllea 187
                                       ++  ++++   +e+ + l+r+          +++e    k +  vpv+ +S+++ +g++ l+  
  gi|557693548|ref|YP_008796602.1| 266 KVpANRVEAAESEIATLLKRVgripfivnsINDVELLIDKVSVVVPVLKISSVTRQGYD-LVYH 328
                                       **8899999999999888776888888877555555544444689999***99999988.3333 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 !   32.2   0.3     4e-11     1e-07       5     111 ..     438     522 ..     434     523 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 4e-11
                                       ECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEEC.CEE CS
                       GTP_EFTU_D3   5 htkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnviveveli.kpi 80 
                                       + +feA+v +l++  +t i +gY+p+ +i+t   t +v+ L    d     +      ++k G++  ve++ + +p 
  gi|557693548|ref|YP_008796602.1| 438 VWSFEAEVTVLSH--PTRISTGYEPIVHIHTIASTTRVKLL----D-----K-----PYLKAGESGRVEMRFKyRPF 498
                                       568**********..********************955555....2.....2.....46788888888888753799 PP

                                       EE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  81 alekgseypqlGrFaiReggrTvaaGvvtei 111
                                        ++ g       rF  Re g+T ++Gvvt+i
  gi|557693548|ref|YP_008796602.1| 499 YIQPGD------RFVFRE-GKTKGIGVVTKI 522
                                       999999......999998.579999999998 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 !   32.3   0.2   3.9e-11     1e-07       1      74 []     358     429 ..     358     429 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 3.9e-11
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEE..EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskke..ivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                       G v+ g+v +G l +G e+ i   +t k +    +r +s+e++  ++ ea++g  +Gv v+++  e  +++G++++
  gi|557693548|ref|YP_008796602.1| 358 GNVVSGSVKQGSLTPGAELLI--GPTRK-GvfVPVRARSIEMHYTRLAEAEPGYIVGVAVKGVREEL-LERGMIVC 429
                                       789******************..55533.447**********************************9.9****987 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   0.0     6e-06     0.015       2     114 .]     121     263 ..     120     263 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6e-06
                                       EEEEESTTSSHHHHHHHHHT.STEEESSSTTSSSSEEEEEEEETTEE.............................. CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.ekaivsdkpgtTrdinegrvklkgke.............................. 47 
                                       v ++G+ N GKSt++  l+  ek   +++    + + e + +l+  +                              
  gi|557693548|ref|YP_008796602.1| 121 VSVAGHVNHGKSTFLACLITgEKDDGQKWLYLDTLPHEVERNLSA-Dlhfivlgfrgmepnlmknpldraerirvtr 196
                                       789**************9651577777777665555555444221.1344555555555666666677777777777 PP

                                       .....EEEEECGGCSSHHHHHHHHHHHHHH..HHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  48 .....ielvDtpGliegaseekglgkafla..leeadlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                            + +vDt+G  e     + l+ +++    +e d  +lvv a  ++ +++ +e   ++   ++p+i++++k
  gi|557693548|ref|YP_008796602.1| 197 eserlVSFVDTVG-HE----PW-LRTTIRGilGQEIDYGFLVVAAD-DGPTHITREHLGIMLAMGIPVIILITK 263
                                       777879*******.44....66.55555552134589999999866.667788888777777788888888876 PP

>> CheB_methylest  CheB methylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.4e-05      0.14      87     122 ..     110     148 ..      87     151 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.4e-05
                                       -.-SS-HHHHHHHHHHHH.G...GEEEEE-SBSS-TTHH CS
                    CheB_methylest  87 kgerpsiDvlfesaaeayge...raigviLtGmgsDGae 122
                                       +++rps+D+l  s+a ++++     ++ ++tG ++DG +
  gi|557693548|ref|YP_008796602.1| 110 TQSRPSVDHLVVSVAGHVNHgksTFLACLITGEKDDGQK 148
                                       457************99865424689***********76 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.21   5.4e+02      99     122 ..     118     141 ..     108     148 .. 0.79
   2 ?    9.8   0.0   0.00026      0.68      16      74 ..     226     281 ..     214     313 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.21
                                       TSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpe 122
                                       + ++ ++G+   GKSt++  l+  
  gi|557693548|ref|YP_008796602.1| 118 HLVVSVAGHVNHGKSTFLACLITG 141
                                       556778999999*****9998764 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00026
                                       --EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHH CS
                       RsgA_GTPase  16 vdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelea 74 
                                       +d  ++vv+++  +  +++    L ++ + gi+++i+++KiD +  ++ +e+ ++e+++
  gi|557693548|ref|YP_008796602.1| 226 IDYGFLVVAAD--DGPTHITREHLGIMLAMGIPVIILITKIDKVPANR-VEAAESEIAT 281
                                       88889999998..555666677899999****************9998.5444444333 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 ?   -1.0   0.0      0.49   1.2e+03       1      18 [.     123     140 ..     123     153 .. 0.80
   2 ?   10.1   0.0   0.00019       0.5     149     235 ..     247     330 ..     236     333 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.49
                        ATP_bind_1   1 vvGpaGsGKttfvgalse 18 
                                       v+G++  GK+tf   l+ 
  gi|557693548|ref|YP_008796602.1| 123 VAGHVNHGKSTFLACLIT 140
                                       899999******987765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00019
                        ATP_bind_1 149 lsamlrlelPhvvvlnkfDllkeklekeleffedvealslllekee.ekykklaeaiaelleefalvlrflplssek 224
                                       l +ml +++P ++ ++k+D +      ++e  e  e  +ll+   +     ++ +++  l+++++ v  +l +ss +
  gi|557693548|ref|YP_008796602.1| 247 LGIMLAMGIPVIILITKIDKVP---ANRVEAAE-SEIATLLKRVGRiPFIVNSINDVELLIDKVSVVVPVLKISSVT 319
                                       679*****************88...33344333.222233333333689999************************* PP

                        ATP_bind_1 225 eesiedllsli 235
                                       +++++ +++l+
  gi|557693548|ref|YP_008796602.1| 320 RQGYDLVYHLL 330
                                       ***99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (526 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3613.62
//
Query:       gi|557693549|ref|YP_008796603.1|  [L=80]
Description: transcriptional regulator, AsnC [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   50.1   0.5    2.2e-13   49.9   0.5    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    0.00038   20.4   0.6    0.00052   20.0   0.6    1.2  1  NapD            NapD protein
  ------ inclusion threshold ------
       0.04   14.0   0.0       0.67   10.1   0.1    2.0  2  ABM             Antibiotic biosynthesis monooxygenase
      0.055   13.7   0.2      0.065   13.4   0.2    1.1  1  Flot            Flotillin


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 !   49.9   0.5     5e-17   2.2e-13       3      73 ..      12      79 ..      10      80 .] 0.96

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 5e-17
                                      EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg  3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                      ++++pg+    ee+  +l++++eV+ + rv G yd+++k+ + +++al +++++++ ++++++++ ++iv+
  gi|557693549|ref|YP_008796603.1| 12 LNVRPGR---EEEVLSQLRAIKEVRDAQRVYGVYDMVVKIEADSMDALKQVVNNRVKKIENITSVISLIVM 79
                                      6789999...9***********************************************************9 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.6   1.2e-07   0.00052       7      66 ..      11      75 ..       8      80 .] 0.74

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.2e-07
                              NapD  7 vVqarperlaavkaalaalpgvEvhasdee.gklVvviEaesedelad....tieaiealpgVls 66
                                      + ++rp+r ++v+ +l+a+++v  +++      +Vv iEa+s d+l +    ++++ie++  V+s
  gi|557693549|ref|YP_008796603.1| 11 LLNVRPGREEEVLSQLRAIKEVRDAQRVYGvYDMVVKIEADSMDALKQvvnnRVKKIENITSVIS 75
                                      6789****************9966666555699***********766610005555666655555 PP

>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00015      0.67       7      31 ..      11      34 ..       5      37 .. 0.83
   2 ?    2.3   0.0     0.041   1.8e+02       7      40 ..      45      77 ..      40      80 .] 0.77

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                                      EEEESTTGHHHHHHHHHHHHHHHHH CS
                               ABM  7 eirvkpgqaeafldafaeaveslla 31
                                       + v+pg++e++l +++++ e ++ 
  gi|557693549|ref|YP_008796603.1| 11 LLNVRPGREEEVLSQLRAIKE-VRD 34
                                      578***************999.864 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.041
                                      EEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEE CS
                               ABM  7 eirvkpgqaeafldafaeavesllaeepGclgye 40
                                       ++++ ++ +a+ +++ ++v+++ ++    ++  
  gi|557693549|ref|YP_008796603.1| 45 VVKIEADSMDALKQVVNNRVKKI-ENITSVISLI 77
                                      67889999999999999999977.7776666655 PP

>> Flot  Flotillin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   1.5e-05     0.065      23      71 ..      25      73 ..      17      78 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.5e-05
                              Flot 23 eAegiralnEAenalseeqialqvklallealPeiieeavkplekidsi 71
                                      +  +i+ + +A+++++   + ++++   ++al +++++ vk +e+i s+
  gi|557693549|ref|YP_008796603.1| 25 QLRAIKEVRDAQRVYGVYDMVVKIEADSMDALKQVVNNRVKKIENITSV 73
                                      556889999*************************************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1168  (0.0651459); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 00:00:00.40
# Mc/sec: 601.55
//
Query:       gi|557693550|ref|YP_008796604.1|  [L=120]
Description: regulatory protein, AsnC/Lrp family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-11   41.6   0.0    1.2e-10   41.2   0.0    1.2  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    1.7e-05   24.8   1.1    3.6e-05   23.7   1.1    1.6  1  UPF0547         Uncharacterised protein family UPF0547
    0.00017   20.9   0.4    0.00026   20.3   0.4    1.3  1  zf-ribbon_3     zinc-ribbon domain
     0.0075   16.0   0.8      0.011   15.4   0.8    1.3  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.5   0.6       0.17   11.6   0.1    2.4  2  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
      0.032   14.3   0.3      0.044   13.8   0.3    1.3  1  DZR             Double zinc ribbon
      0.063   13.7   1.5        5.1    7.7   0.1    2.4  2  zf-H2C2_2       Zinc-finger double domain
       0.12   12.2   0.2       0.12   12.2   0.2    1.9  2  HscB_4_cys      Co-chaperone HscB tetracysteine metal binding
       0.14   11.5   1.4       0.21   10.9   1.4    1.3  1  zf-RanBP        Zn-finger in Ran binding protein and others
       0.14   11.7   1.1       0.27   10.8   1.1    1.4  1  RecR            RecR protein
       0.24   10.6   0.0       0.26   10.5   0.0    1.0  1  DUF4471         Domain of unknown function (DUF4471)
       0.28   11.2   1.8       0.94    9.6   1.8    1.9  1  Elf1            Transcription elongation factor Elf1 like


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 !   41.2   0.0   8.2e-14   1.2e-10       3      73 ..       9      75 ..       7      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 8.2e-14
                                      EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg  3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                      ++++pg        + al+ +p Vv++++v G +d +l v + ++e+l++ + e la+ p+v ++et++++
  gi|557693550|ref|YP_008796604.1|  9 IRTQPGT----SHQIVALRSMPGVVSAHSVFGRFDAVLFVSADSVEQLSQRVYEILAKQPNVVKVETLVCM 75
                                      5555444....3344589**************************************************988 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   1.1   2.4e-08   3.6e-05       2      24 ..      97     119 ..      97     120 .] 0.97

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.4e-08
                           UPF0547   2 vCPeCeakvPvaaqfCphCGyvF 24 
                                       +CP C+a   v+a +C++CGy+F
  gi|557693550|ref|YP_008796604.1|  97 HCPSCRALNEVDALVCSFCGYRF 119
                                       7*********************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 !   20.3   0.4   1.8e-07   0.00026       4      25 ..      97     118 ..      95     119 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.8e-07
                       zf-ribbon_3   4 rCPnCGa.plssddnvCpyCGtk 25 
                                       +CP+C a + + d+ vC  CG++
  gi|557693550|ref|YP_008796604.1|  97 HCPSCRAlN-EVDALVCSFCGYR 118
                                       8******99.***********98 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.8   7.5e-06     0.011       2      22 ..      98     118 ..      97     119 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.5e-06
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtp 22 
                                       Cp+C a ++ +a  C+ CG+ 
  gi|557693550|ref|YP_008796604.1|  98 CPSCRALNEVDALVCSFCGYR 118
                                       *******************85 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 ?   11.6   0.1   0.00012      0.17      33      54 .]      82     105 ..      52     105 .. 0.71
   2 ?    2.1   0.0      0.11   1.6e+02      22      29 ..     109     116 ..     106     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                    zinc_ribbon_10  33 Glap.keeleev.kyrCpkCgaln 54 
                                        + p kee + v ++ Cp+C+aln
  gi|557693550|ref|YP_008796604.1|  82 PVTPrKEEIKLVtSFHCPSCRALN 105
                                       55666889999989********98 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.11
                    zinc_ribbon_10  22 alICskCh 29 
                                       al+Cs C 
  gi|557693550|ref|YP_008796604.1| 109 ALVCSFCG 116
                                       67777774 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   2.9e-05     0.044       1      20 [.      98     117 ..      77     120 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.9e-05
                               DZR   1 CpqCgeelppdarfCseCgt 20 
                                       Cp+C++ ++ da +Cs Cg 
  gi|557693550|ref|YP_008796604.1|  98 CPSCRALNEVDALVCSFCGY 117
                                       78888888888888888875 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 ?    5.0   0.1     0.025        37      14      21 ..      95     102 ..      86     103 .. 0.86
   2 ?    7.7   0.1    0.0034       5.1      16      24 ..     111     119 ..     106     120 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.025
                         zf-H2C2_2  14 pyeCplCd 21 
                                        ++Cp+C+
  gi|557693550|ref|YP_008796604.1|  95 SFHCPSCR 102
                                       59*****7 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0034
                         zf-H2C2_2  16 eCplCdkaF 24 
                                        C++C+++F
  gi|557693550|ref|YP_008796604.1| 111 VCSFCGYRF 119
                                       7*******9 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 ?   12.2   0.2     8e-05      0.12      17      26 ..      95     104 ..      92     105 .. 0.90
   2 ?   -1.8   0.2         2     3e+03      16      23 ..     108     115 ..     107     116 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8e-05
                                       --B-TTT--B CS
                        HscB_4_cys  17 efFCpqCRAL 26 
                                        f Cp CRAL
  gi|557693550|ref|YP_008796604.1|  95 SFHCPSCRAL 104
                                       589******9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2
                                       ---B-TTT CS
                        HscB_4_cys  16 defFCpqC 23 
                                       d + C+ C
  gi|557693550|ref|YP_008796604.1| 108 DALVCSFC 115
                                       56678877 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 ?   10.9   1.4   0.00014      0.21       6      25 ..      97     116 ..      97     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00014
                                       E-SSS--EEESSSSB-TTT- CS
                          zf-RanBP   6 dCskClvqNfawstkCvaCq 25 
                                       +C++C + N+  +++C  C+
  gi|557693550|ref|YP_008796604.1|  97 HCPSCRALNEVDALVCSFCG 116
                                       6****************996 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.1   0.00018      0.27      18      34 ..      97     115 ..      94     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                                       E-TTT--EESSS..S-CCC CS
                              RecR  18 hCsrCgnlteed..lCaIC 34 
                                       hC+ C+ l e d  +C++C
  gi|557693550|ref|YP_008796604.1|  97 HCPSCRALNEVDalVCSFC 115
                                       9***********888**** PP

>> DUF4471  Domain of unknown function (DUF4471)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00017      0.26     224     281 ..      18      77 ..       7      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                           DUF4471 224 kflplesleklkekkkyknlFdii.fvsasmvhllkpelfq.lladdavlivEtakylvd 281
                                       +++ l s++ + + +   ++Fd++ fvsa  v++l++ + + l+++  v+ vEt  ++ +
  gi|557693550|ref|YP_008796604.1|  18 QIVALRSMPGVVSAHSVFGRFDAVlFVSADSVEQLSQRVYEiLAKQPNVVKVETLVCMPS 77 
                                       566777777777787788889865389**************5556668888999877755 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.8   0.00063      0.94      11      34 ..      85     108 ..      79     120 .] 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00063
                              Elf1  11 kkkkkkklptkFdCpfCnheksve 34 
                                       ++k+  kl t+F+Cp C + + v+
  gi|557693550|ref|YP_008796604.1|  85 PRKEEIKLVTSFHCPSCRALNEVD 108
                                       5566677**********9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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 0.28s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 890.23
//
Query:       gi|557693551|ref|YP_008796605.1|  [L=83]
Description: AsnC family transcriptional regulator [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   51.1   0.2      1e-13   51.0   0.2    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.015   15.3   0.2      0.056   13.5   0.2    1.8  1  NapD            NapD protein
      0.019   15.6   0.1      0.021   15.4   0.1    1.1  1  ACT_4           ACT domain
      0.023   14.6   0.0      0.024   14.6   0.0    1.2  1  GYD             GYD domain


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 !   51.0   0.2   2.3e-17     1e-13       1      73 [.       6      78 ..       6      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 2.3e-17
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                      vlvs +pg +e++ +f ++  +++ Vv + +v G yd ++   v+dl+ l+++l + + ++p+v rtet iv+
  gi|557693551|ref|YP_008796605.1|  6 VLVSAKPGTSEDIVRFLKEASAIKGVVAADSVFGRYDAIITLEVEDLRTLSQVLYKVIEKIPNVVRTETCIVM 78
                                      789999999999************************************************************9 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.2   1.2e-05     0.056       6      67 ..       6      72 ..       5      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                              NapD  6 lvVqarperlaavkaalaalpgvE.vhasdee...gklVvviEaesedeladtiea.iealpgVlsa 67
                                      ++V a+p++ +++ + l++   +  v a+d        ++++E e+ ++l + + + ie++p+V+ +
  gi|557693551|ref|YP_008796605.1|  6 VLVSAKPGTSEDIVRFLKEASAIKgVVAADSVfgrYDAIITLEVEDLRTLSQVLYKvIEKIPNVVRT 72
                                      68999******999999876666524444444756779************99876669******987 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   4.7e-06     0.021      11      77 ..       6      71 ..       1      73 [. 0.76

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4.7e-06
                             ACT_4 11 veaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviak.LraipgVis 77
                                      v ++ ++g   di++ ++e+ a    v a++    g  +  it+eV+d++ Ls+v+ k +++ip+V +
  gi|557693551|ref|YP_008796605.1|  6 VLVSAKPGTSEDIVRFLKEASAIKGVVAADS--VFGRYDAIITLEVEDLRTLSQVLYKvIEKIPNVVR 71
                                      6666677888888888887766555555555..468999***************98664899999975 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   5.5e-06     0.024      37      69 ..      31      63 ..       8      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-06
                               GYD 37 leslyatlGeyDvvvivEapDdetaaalslala 69
                                      + +   ++G+yD+++++E++D +t  ++ +++ 
  gi|557693551|ref|YP_008796605.1| 31 VVAADSVFGRYDAIITLEVEDLRTLSQVLYKVI 63
                                      4577889******************99988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         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 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 657.03
//
Query:       gi|557693552|ref|YP_008796606.1|  [L=478]
Description: glutamine synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-126  420.1   0.0   6.8e-126  419.9   0.0    1.0  1  Gln-synt_C  Glutamine synthetase, catalytic domain
    5.6e-30  102.9   0.0    1.3e-29  101.7   0.0    1.7  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 !  419.9   0.0  7.6e-130  6.8e-126       2     345 .]     110     475 ..     109     475 .. 0.96

  Alignments for each domain:
  == domain 1  score: 419.9 bits;  conditional E-value: 7.6e-130
                                       T-HHHHHHHHHHHHHHTTC.EEEEEEEEEEEEESEECCCE...SSEEEEEEE.T........B...B.TSS-TTBHC CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGl.tvvvgpElEFflfdkeedke...asksllevdse........ekgrpaekggyfsva 66 
                                       rdPR+v+++a+++++++G+   + gpE+EFf+fdk++++     ++ +++++s+        +++  + k+gy++v+
  gi|557693552|ref|YP_008796606.1| 110 RDPRYVAQKAEEYVKAQGYdVSYWGPEIEFFVFDKVHWDVktpFEGVSYKIESReaawnsggTQHPIRFKEGYYPVP 186
                                       7******************7789**************98754555666666666*******989999********** PP

                                       CCCCTCCHHHHHHHHH.HHTT--EECCEEECCCT.EEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSS CS
                        Gln-synt_C  67 pvdeaedlrreiveal.ealgieveashhEvatg.QvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKp 141
                                       p+d+ +++r+e++++l + +++ev+a+hhEvat+ Q+Ei+++f+++ ++aD+++t+K+v++ vA++ g+ atFmpKp
  gi|557693552|ref|YP_008796606.1| 187 PQDTLMEYRNEVCRVLsDYFNVEVDAHHHEVATAgQCEIDMRFDTLTRMADKAQTYKYVARVVANSLGMVATFMPKP 263
                                       ***************95679*************99****************************************** PP

                                       STTS---BEEEEEEEEECTTEESSB-TTSGGG.B-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEE CS
                        Gln-synt_C 142 legdnGsgmHvhlSlwdkdgknlfadeddeya.lselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvala 217
                                       ++gdn+sgmHvh+Slw k+g nlf+de+deya ls+l+r+f+gGll+h +alta+t+pt+nS++RlvpgyeaPv +a
  gi|557693552|ref|YP_008796606.1| 264 IFGDNASGMHVHVSLW-KNGVNLFYDENDEYAeLSQLGRYFVGGLLEHSRALTAITNPTTNSFRRLVPGYEAPVFIA 339
                                       ****************.************************************************************ PP

                                       EESS-TTCSEEEE-.....TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH.. CS
                        Gln-synt_C 218 wgarNRsallRipa.....skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer.. 287
                                       w+ +NRsa +Rip      ++ k+kr+E+R+pd+saNPYL++Aa+ aAg+dGi++k++pg+pv++d+y+lspe+r  
  gi|557693552|ref|YP_008796606.1| 340 WSRSNRSANIRIPVyyrgrASMKSKRIEFRTPDPSANPYLCFAAMAAAGIDGIKKKIDPGDPVNEDIYKLSPERRkq 416
                                       *************999999999***************************************************9999 PP

                                       TSS-B--SSHHHHHHHHHCS.HHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 288 kgieelPasleeAlealeed.ellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       +gi+elP sl+eA+e+l +d e+lk v++e++ie y +++ + + ++ ++++++e+  y
  gi|557693552|ref|YP_008796606.1| 417 LGIRELPGSLREAVEELLSDhEFLKPVFTEDLIEVYTEMQLKMFIDVATKPHPYEFYLY 475
                                       9******************************************************9876 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 !  101.7   0.0   1.5e-33   1.3e-29       2      82 ..      19     101 ..      18     102 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 1.5e-33
                                       --EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-E.EEETTSSTTT------EEEEEEEGGGEEE-SS-SS-..EEEE CS
                        Gln-synt_N   2 vkfvdlqFtDikgklkhvtipadelsedaleegv.sFDGSsiegfaeieeSDmlLkPdlstavidPfreek.ktarv 76 
                                       ++f+dlq tD+ gkl+hvt++++ lsed+l+egv ++DGSs++gfa+i+eSDm+LkPd++t++i+P+++ + ktar+
  gi|557693552|ref|YP_008796606.1|  19 IRFIDLQLTDLPGKLHHVTVTSNYLSEDTLQEGVaKLDGSSLRGFADIHESDMVLKPDPRTFAILPWSDGPnKTARM 95 
                                       79*******************************************************************999***** PP

                                       EEEEE- CS
                        Gln-synt_N  77 icdvyd 82 
                                       icdvy 
  gi|557693552|ref|YP_008796606.1|  96 ICDVYR 101
                                       ****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (478 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3569.41
//
Query:       gi|557693553|ref|YP_008796607.1|  [L=130]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   81.4  17.0    7.3e-23   81.1  17.0    1.1  1  VKOR      Vitamin K epoxide reductase family
  ------ inclusion threshold ------
        2.1    8.5   8.3       0.55   10.4   5.6    1.5  2  DUF4870   Domain of unknown function (DUF4870)


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 !   81.1  17.0   8.1e-27   7.3e-23       2     123 ..       5     124 ..       4     125 .. 0.95

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 8.1e-27
                                       HHHHHHHHHHHHHHHHHHHHH...HT---SS-SSSS...HHHHHCSTTSEETTEEHHHHHHHHHHHHHHHHHS-... CS
                              VKOR   2 lllvlalvGllvsiyltleklglktsssaalCdiss.vsCdkvlnSpyasilgvplsllGllayalvlllalapl.. 75 
                                       l+++++l Gl++siyltl          +++C+iss +sCd+vl+Spya++lgvp +++G++++a  + l+++++  
  gi|557693553|ref|YP_008796607.1|   5 LIFAVSLSGLFLSIYLTLLPP-------PPFCEISSfLSCDTVLSSPYAKFLGVPTAFYGVVWFAGAASLSMLASng 74 
                                       6899*************9655.......679****************************************99999* PP

                                       ..HHHHHHHHHHHHHHHHHHHHHHHHTTS----HHHHHHHHHHHHHHHHH CS
                              VKOR  76 ..lwlllllgslagvvfslyLiylslfvigalCpyClvsavlsllllvla 123
                                         l+ l+l +s++gv+++++L+y++l  iga+C++C++++++++++++l+
  gi|557693553|ref|YP_008796607.1|  75 kqLAKLALGWSVIGVAVVAVLVYVELGLIGAVCILCTAAHAMTVAVAALS 124
                                       **9999***************************************99886 PP

>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.35   3.2e+03      87      87 ..      16      16 ..       2      41 .. 0.57
   2 ?   10.4   5.6   6.2e-05      0.55      28      96 ..      58     126 ..      27     130 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.35
                           DUF4870 87 l 87
                                      l
  gi|557693553|ref|YP_008796607.1| 16 L 16
                                      1 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 6.2e-05
                           DUF4870  28 viwllkkdksefvdeqgkealNFqislliysiilivlsllvligflllllllllllnlvlviiaaikan 96 
                                       v+w++   +  +++++gk+     + +++++++++++ + v +g++  + +l  +++ + v +aa+  +
  gi|557693553|ref|YP_008796607.1|  58 VVWFAGAASLSMLASNGKQLAKLALGWSVIGVAVVAVLVYVELGLIGAVCILCTAAHAMTVAVAALSFY 126
                                       89**************************99888887779999998557888888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 954.69
//
Query:       gi|557693554|ref|YP_008796608.1|  [L=197]
Description: thiol-disulfide oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   54.8   0.0    1.1e-14   54.4   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
    2.4e-13   50.0   0.0    3.2e-13   49.6   0.0    1.2  1  Redoxin        Redoxin
    1.7e-12   47.2   0.0    1.2e-07   31.7   0.1    2.2  2  Thioredoxin    Thioredoxin
    3.2e-10   40.2   0.0    4.7e-10   39.7   0.0    1.3  1  Thioredoxin_8  Thioredoxin-like
    8.4e-08   32.6   0.0    1.4e-07   31.9   0.0    1.3  1  Thioredoxin_2  Thioredoxin-like domain
    0.00012   21.0   0.0    0.00016   20.6   0.0    1.1  1  HlyD_2         HlyD family secretion protein
     0.0012   19.0   0.0        1.6    8.9   0.0    2.2  2  Thioredoxin_4  Thioredoxin
     0.0055   16.5   0.1      0.016   15.0   0.0    1.7  2  DSBA           DSBA-like thioredoxin domain
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.026   14.6   0.0    1.6  2  TrbC_Ftype     Type-F conjugative transfer system pilin assem
      0.016   15.1   0.0      0.061   13.1   0.0    1.9  1  TraF           F plasmid transfer operon protein
      0.021   14.5   0.0       0.84    9.3   0.0    2.1  2  Thioredoxin_5  Thioredoxin


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 !   54.4   0.0   6.6e-18   1.1e-14       2     123 ..      55     177 ..      54     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 6.6e-18
                                       TSB----EEE.....STTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEES...SSC CS
                          AhpC-TSA   2 gdkapdfelk.....nadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsv...dsp 70 
                                       gd a  f+l        + e+vs+   +g++  + f+ + wc +C++ +p  ++l++ ++e+gv  i v     ++ 
  gi|557693554|ref|YP_008796608.1|  55 GDIATPFSLDlidetGLKNEKVSFRPDSGQIYFIDFIHE-WCVHCRNMAPIVERLHQTYAEKGVVFITVAGgynTDA 130
                                       788999999988665556799999999************.************************9999987432455 PP

                                       HHHHHHHHH-H.SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  71 eshkkfiekeslnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                       ++ ++fi+ +++++p+  D++ +++++ygv        +++ ++++k+g+i++
  gi|557693554|ref|YP_008796608.1| 131 QKTAQFIKNYRVTWPVGFDPQLEIFRQYGVR------GTPTYVIVNKNGIIAA 177
                                       5999***************************......99************86 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0     2e-16   3.2e-13      29     136 ..      84     184 ..      53     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 2e-16
                                       SEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEE..EESSSHH.HHHHHHHTT-TSEEEE-TTSHHHHHTT CS
                           Redoxin  29 kkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvav..vadndaf.vkefwgkeglkfpvlsDgsaaftkalG 102
                                       +  ++ f    +c  C++ +p +e l + ++ekgv ++ v    ++da+   +f++++ +++pv  D++ ++++++G
  gi|557693554|ref|YP_008796608.1|  84 QIYFIDFIHE-WCVHCRNMAPIVERLHQTYAEKGVVFITVagGYNTDAQkTAQFIKNYRVTWPVGFDPQLEIFRQYG 159
                                       5555666666.*****************************88899999999************************** PP

                                       -TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSC CS
                           Redoxin 103 lrleedaseglrtpryavidedgkvvylevepep 136
                                       +r         +tp+y++++++g + ++  ++ p
  gi|557693554|ref|YP_008796608.1| 160 VR---------GTPTYVIVNKNGIIAAKLEGEQP 184
                                       99.........*************9987666655 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   7.2e-11   1.2e-07      19      58 ..      84     124 ..      73     144 .. 0.78
   2 !   14.2   0.0   1.9e-05     0.032      52     102 ..     142     193 ..     127     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 7.2e-11
                                       SEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEET CS
                       Thioredoxin  19 klvlveFyApwCghCkalaPeleklaeelkd.kvklakvdv 58 
                                       +  +++F  +wC hC+++aP +e+l +++++  v+++ v  
  gi|557693554|ref|YP_008796608.1|  84 QIYFIDFIHEWCVHCRNMAPIVERLHQTYAEkGVVFITVAG 124
                                       6789**************************98777776643 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.9e-05
                                       EEEEEETTTSHHHHHHTT-SSSSEEEEEETTE.EEEEEESS-HHHHHHHHHH CS
                       Thioredoxin  52 klakvdvdenedlakkyevegiPtlklfkngk.evkkyegarekeklaaflk 102
                                       +   v  d + ++ ++y+v+g Pt ++++++   ++k+eg+++ e+la+ l+
  gi|557693554|ref|YP_008796608.1| 142 VTWPVGFDPQLEIFRQYGVRGTPTYVIVNKNGiIAAKLEGEQPYEALARELD 193
                                       45567788899999**********99987766699***********998776 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   2.9e-13   4.7e-10       1      94 [.      83     174 ..      83     175 .. 0.87

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 2.9e-13
                                       .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-S..S-HHHHHHHGGGS-TTSEE.EE-TT-HHHHT CS
                     Thioredoxin_8   1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsld..kkeeefekylkknkkpwlsvpfddkkrnklk 75 
                                       g+++++ f  +wc +c+++ p + +l++++  +k+v+++ v      + +++ +++k+ + +w    fd   + ++ 
  gi|557693554|ref|YP_008796608.1|  83 GQIYFIDFIHEWCVHCRNMAPIVERLHQTYA-EKGVVFITVAGGynTDAQKTAQFIKNYRVTWPV-GFD--PQLEIF 155
                                       578999************************9.699999999765337889999999999666665.555..899*** PP

                                       T-S--TT-SEEEEE-TT-B CS
                     Thioredoxin_8  76 kkynvkaiPtlvvldknge 94 
                                       ++y+v + Pt v+++kng 
  gi|557693554|ref|YP_008796608.1| 156 RQYGVRGTPTYVIVNKNGI 174
                                       *****************96 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   8.7e-11   1.4e-07       5     107 ..      83     190 ..      80     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 8.7e-11
                     Thioredoxin_2   5 gkpvlvvftdpdCpyCkklkkelkel.ddvtvrvllfplkpsfepkavaiwcakekkkafkd...........ieen 69 
                                       g+  +++f  ++C  C+ +   ++ l + +         ++ ++++ va  ++++ +k+ +             + +
  gi|557693554|ref|YP_008796608.1|  83 GQIYFIDFIHEWCVHCRNMAPIVERLhQTY--------AEKGVVFITVAGGYNTDAQKTAQFiknyrvtwpvgFDPQ 151
                                       778899***************999995333........33345555555555555543333344555556666999* PP

                     Thioredoxin_2  70 velarkygvrgtPtivfldgk.eivarlpGyvpaeelea 107
                                        e  r+ygvrgtPt v+ +++  i+a+l+G  p e l+ 
  gi|557693554|ref|YP_008796608.1| 152 LEIFRQYGVRGTPTYVIVNKNgIIAAKLEGEQPYEALAR 190
                                       *********************************999876 PP

>> HlyD_2  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   9.6e-08   0.00016       1      75 [.       1      85 [.       1      89 [. 0.78

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.6e-08
                            HlyD_2  1 Mkkkkkkikrkrfnvlill....vviiliYivv...nlvisiikstieTeivkngeieesikkkgl...iirdekviks 69
                                      M+ kk k kr  +++l +l    +v++++Y++v   +  is+i++t +T++vk g+i   +  + +    +++ekv   
  gi|557693554|ref|YP_008796608.1|  1 MPSKKVKKKRNLSTYLAVLpaalLVVFIAYLIVtppSQSISTISTTGQTNTVKTGDIATPFSLDLIdetGLKNEKVSFR 79
                                      999999999999*****99**99999999*999444468999***************9988776431114566666666 PP

                            HlyD_2 70 naegiv 75
                                      ++ g++
  gi|557693554|ref|YP_008796608.1| 80 PDSGQI 85
                                      666655 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00096       1.6      19      52 ..      89     122 ..      82     140 .. 0.81
   2 !    8.1   0.0    0.0017       2.7     130     165 ..     152     193 ..     148     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00096
                                       EEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEE CS
                     Thioredoxin_4  19 eyedlrCphCakfeeeveklleeyidtGkvkfii 52 
                                        +    C hC++++  ve l + y ++G v +++
  gi|557693554|ref|YP_008796608.1|  89 DFIHEWCVHCRNMAPIVERLHQTYAEKGVVFITV 122
                                       556667*********************9887665 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0017
                                       HHHHHHHT--SS-EEEE.TTEEE.....-TT--HHHHHHHHT CS
                     Thioredoxin_4 130 skeakkagiestPtfii.ngekv.....eepqtyeelkalid 165
                                       ++ +++ g+ +tPt +i n   +     e+ q+ye+l + +d
  gi|557693554|ref|YP_008796608.1| 152 LEIFRQYGVRGTPTYVIvNKNGIiaaklEGEQPYEALARELD 193
                                       57789*********7765554444455599999999998887 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.76   1.2e+03      10      27 ..      95     112 ..      86     144 .. 0.72
   2 !   15.0   0.0     1e-05     0.016     158     192 ..     153     192 ..     121     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.76
                                       BHHHHHHHHHHHHHHHHC CS
                              DSBA  10 CPyCylgkerleklaars 27 
                                       C +C  +++ +e+l + +
  gi|557693554|ref|YP_008796608.1|  95 CVHCRNMAPIVERLHQTY 112
                                       667777777777777766 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1e-05
                                       HHHHHTT-SSSSEEEETTC.....EEEESSSSHHHHHHHH CS
                              DSBA 158 aaaqslgvtGvPtvvvdgk.....rmvfGadrldtladal 192
                                       + ++++gv+G+Pt+v+ +k       + G ++++ la++l
  gi|557693554|ref|YP_008796608.1| 153 EIFRQYGVRGTPTYVIVNKngiiaAKLEGEQPYEALAREL 192
                                       5689************55546677889999*999999987 PP

>> TrbC_Ftype  Type-F conjugative transfer system pilin assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.6   4.2e+03      94     110 ..      48      64 ..      31      66 .. 0.63
   2 ?   14.6   0.0   1.6e-05     0.026      23      82 ..     114     173 ..     101     190 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.6
                        TrbC_Ftype  94 akysvvyGdvsleyale 110
                                       ++ +v +Gd+++  +l+
  gi|557693554|ref|YP_008796608.1|  48 QTNTVKTGDIATPFSLD 64 
                                       23567779998888776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.6e-05
                        TrbC_Ftype  23 gavlvlrGfpegkslketvkalaklleeemekasvqidPll..FrqfkitaVPalvlaeedk 82 
                                       ++ +v+  + +g   ++ ++++a+ +++   +  v  dP+l  Frq++++  P++v+++++ 
  gi|557693554|ref|YP_008796608.1| 114 EKGVVFITVAGG--YNTDAQKTAQFIKNYRVTWPVGFDPQLeiFRQYGVRGTPTYVIVNKNG 173
                                       445666666666..55556666666666667799999**7444**************99765 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.8e-05     0.061     134     202 ..      88     172 ..      77     177 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                              TraF 134 lfFyrgkcpyceaqapilqafadky.glevraVsvdgrplpelpn...............arvdkgqaarlgvkrtP 194
                                       + F  + c  c+ +api++++ ++y +  v++++v g+ +++ ++               + ++ +   ++gv+ tP
  gi|557693554|ref|YP_008796608.1|  88 IDFIHEWCVHCRNMAPIVERLHQTYaEKGVVFITVAGGYNTDAQKtaqfiknyrvtwpvgFDPQLEIFRQYGVRGTP 164
                                       5577788******************667799******9998855544455556666655555666666788888888 PP

                              TraF 195 alvlvdpk 202
                                       + v+v+++
  gi|557693554|ref|YP_008796608.1| 165 TYVIVNKN 172
                                       88888765 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.031        51       3      28 ..      90     115 ..      87     144 .. 0.79
   2 ?    9.3   0.0   0.00052      0.84     143     183 ..     148     187 ..     132     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.031
                     Thioredoxin_5   3 FidPlcseCweiEpelkklkveygek 28 
                                       Fi  +c +C ++ p++ +l ++y ek
  gi|557693554|ref|YP_008796608.1|  90 FIHEWCVHCRNMAPIVERLHQTYAEK 115
                                       89999***************999876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00052
                     Thioredoxin_5 143 fqcDlklakemgvtevPtlvffneneeeeglkveglksyev 183
                                       f+  l++ +++gv+ +Pt v++n+ +     k+eg ++ye 
  gi|557693554|ref|YP_008796608.1| 148 FDPQLEIFRQYGVRGTPTYVIVNK-NGIIAAKLEGEQPYEA 187
                                       556688999**************5.4556778888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1440.59
//
Query:       gi|557693555|ref|YP_008796609.1|  [L=466]
Description: drug resistance transporter EmrB/QacA subfamily [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-50  172.3  51.9    1.4e-50  172.3  51.9    1.7  2  MFS_1     Major Facilitator Superfamily
    7.3e-09   35.0  14.5    7.3e-09   35.0  14.5    2.6  2  Sugar_tr  Sugar (and other) transporter
    0.00034   19.3  38.1      0.023   13.3   8.1    2.4  2  MFS_2     MFS/sugar transport protein
  ------ inclusion threshold ------
       0.52   10.5   3.6        1.5    9.0   0.3    3.4  3  DUF3937   Protein of unknown function (DUF3937)


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 !  172.3  51.9     3e-54   1.4e-50       1     352 [.      11     395 ..      11     396 .. 0.88
   2 ?   -1.4   0.3      0.19   8.6e+02     122     129 ..     437     444 ..     397     461 .. 0.53

  Alignments for each domain:
  == domain 1  score: 172.3 bits;  conditional E-value: 3e-54
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       ll+++fl+a++++++g+alp  + ++l      +++++t+y l++ v+ +++G lsd +Grr ++++g+l+f++g+l
  gi|557693555|ref|YP_008796609.1|  11 LLMGIFLAAIDSTVVGVALP-SIVSSLK-GLNIYSWAFTAYILTSTVTGPLWGKLSDVYGRRFIYVAGVLIFLAGSL 85 
                                       6899****************.8999999.9*********************************************66 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       l+ +a+ +  l+++r +qGlg+gal+ +  +++ ++f+ +er++a+g+ s+ +++++i+gp+lgg++++ +gWr++f
  gi|557693555|ref|YP_008796609.1|  86 LCGLAQDMVQLVLFRGIQGLGGGALLVLTFTIVGEIFTLKERAKATGYTSSVWAVASIVGPPLGGFIVDTVGWRWIF 162
                                       6666555559******************************************************************* PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee.........................................kg 190
                                       +i+ +v+l+++  ++  l ++ +++ +  ++  +                                         ++
  gi|557693555|ref|YP_008796609.1| 163 LINLPVGLFCVATVGRILKTTTRTETKI-DVSGSilfllaasplllylsefqnigetaplilltsgaaftlffynER 238
                                       *********9773333333332222222.23333689**************************************** PP

                             MFS_1 191 tgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrl 267
                                       + p+pl+p   +l++ + l   +++ ll++f+f+g+ +++plylq+vlg+s +  +g+ll  l l+++++a  a++l
  gi|557693555|ref|YP_008796609.1| 239 RSPSPLIP--FHLFREKILRTGFLGNLLAGFVFFGIIAYMPLYLQTVLGYS-ATFSGVLLLPLVLGWVASANAAAQL 312
                                       ********..444444433336677777788********************.78899889999999999999***** PP

                             MFS_1 268 sdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfnta 344
                                       + r  +   +  +l++++l++  ++l  ++++ ++ll +++l G+g+gf+++++l +++ ++p+   g a++l +++
  gi|557693555|ref|YP_008796609.1| 313 AIR--SSLKIPAILSGFFLVSGTVFLSLASQNIPVLLTGFALTGLGMGFTVSTFLIATQTVVPRGVLGVATSLLSFL 387
                                       *55..566888888888888888888888889999999*************************************** PP

                             MFS_1 345 gslggalg 352
                                       +  gga++
  gi|557693555|ref|YP_008796609.1| 388 RLMGGAIS 395
                                       *****997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.19
                             MFS_1 122 aigllsag 129
                                       ai++++++
  gi|557693555|ref|YP_008796609.1| 437 AIAIAASA 444
                                       11111111 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0  14.5   1.6e-12   7.3e-09      48     184 ..      42     172 ..       8     185 .. 0.93
   2 !    4.6   8.7    0.0027        12      44     154 ..     287     395 ..     215     454 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.6e-12
                                       HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                          Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                       +++ + ++++ +++++ + g+l+d++GR+ ++++++++f++g++l+++a+    + +l++ R + G+g G+  vl+ 
  gi|557693555|ref|YP_008796609.1|  42 YSWAFTAYILTSTVTGPLWGKLSDVYGRRFIYVAGVLIFLAGSLLCGLAQ---DMVQLVLFRGIQGLGGGALLVLTF 115
                                       5788999*******************************************...99********************** PP

                                       HHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHH CS
                          Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpalll 184
                                       + ++Ei + k R + ++++ + +++  +v+  +g ++ +t +   wr+ + ++l   l+ 
  gi|557693555|ref|YP_008796609.1| 116 TIVGEIFTLKERAKATGYTSSVWAVASIVGPPLGGFIVDTVG---WRWIFLINLPVGLFC 172
                                       **********************************99999999...999999988888554 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0027
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                       s++ sg+++  +++G ++++  a  l+ r + k   + +++++v g+v   +a   +++ vl++g  l+G+g+G++ 
  gi|557693555|ref|YP_008796609.1| 287 SATFSGVLLLPLVLGWVASANAAAQLAIRSSLKIPAILSGFFLVSGTVFLSLAS--QNIPVLLTGFALTGLGMGFTV 361
                                       56678888889999999*******************************999999..69****************998 PP

                                       HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilva 154
                                        +  + ++ + p  + g  +sl  +   +G  ++
  gi|557693555|ref|YP_008796609.1| 362 STFLIATQTVVPRGVLGVATSLLSFLRLMGGAIS 395
                                       8887777777777777777776666655555444 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   8.1   5.1e-06     0.023     260     376 ..      41     152 ..      11     157 .. 0.88
   2 !   11.5  22.0   1.8e-05      0.08     220     423 ..     249     450 ..     247     455 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-06
                             MFS_2 260 aasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpw 336
                                        +s+ +++ ++ ++++ plw +l   +g++ +y++g l+ +++++l+ l+  ++++ ++++  i g+g g++ +l  
  gi|557693555|ref|YP_008796609.1|  41 IYSWAFTAYILTSTVTGPLWGKLSDVYGRRFIYVAGVLIFLAGSLLCGLA--QDMVQLVLFRGIQGLGGGALLVLTF 115
                                       589999999****************************************9..9***************777777766 PP

                             MFS_2 337 smladvvDygelktGkrregvffavlsfisklatgiglgv 376
                                        +++++   ++lk   +++g + +v++ +s ++  +g+++
  gi|557693555|ref|YP_008796609.1| 116 TIVGEI---FTLKERAKATGYTSSVWAVASIVGPPLGGFI 152
                                       666655...6788899999999999999999887777776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 1.8e-05
                             MFS_2 220 vfrnraflillllfllaalalgvlnglllYyltyvlgngsaasvfllvv.tisallgiplwqplakrlgkkntyllg 295
                                       +fr++ +++ +l+ lla + ++   + + +yl+ vlg  + +s +ll++ +++ ++++  ++ la r + k  ++l+
  gi|557693555|ref|YP_008796609.1| 249 LFREKILRTGFLGNLLAGFVFFGIIAYMPLYLQTVLGYSATFSGVLLLPlVLGWVASANAAAQLAIRSSLKIPAILS 325
                                       799999999999999999999999999999*******9999999999995666667888889999999999999999 PP

                             MFS_2 296 alltivllvlvlllqpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgi 372
                                         ++++++v++ l+  +n+ ++l+ ++++g+g+g+ ++++   + +vv  g         gv++++lsf+  ++++i
  gi|557693555|ref|YP_008796609.1| 326 GFFLVSGTVFLSLA-SQNIPVLLTGFALTGLGMGFTVSTFLIATQTVVPRGV-------LGVATSLLSFLRLMGGAI 394
                                       99999999999999.*****************99999999999999998887.......7***************** PP

                             MFS_2 373 glgvsgllLsaf..gy...rakasvqspqvvlalrllyavlpavlllvallllvry 423
                                       +++v+ l ++a   ++   ++  +v s++ ++a++  ++   a+ ++++++ l +y
  gi|557693555|ref|YP_008796609.1| 395 SAAVLWLPIGALvrDLglqQSVGVVLSEAEKTAFTAGFSQSLAIAIAASAIALALY 450
                                       ****9988887755556686667777888888888888777777777776666665 PP

>> DUF3937  Protein of unknown function (DUF3937)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.37   1.7e+03       3      25 ..       2      24 ..       1      27 [. 0.86
   2 ?   -2.0   0.0      0.88   3.9e+03      51      66 ..     190     205 ..     178     211 .. 0.80
   3 ?    9.0   0.3   0.00034       1.5      12      37 ..     264     289 ..     250     297 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.37
                           DUF3937  3 tnkklirfglslfvflgiinfti 25
                                      t ++l+ +gl + +fl  i+ t+
  gi|557693555|ref|YP_008796609.1|  2 TGQRLLLIGLLMGIFLAAIDSTV 24
                                      67899999********9999886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.88
                           DUF3937  51 ldvpqgilvllgaial 66 
                                       +dv   il ll a  l
  gi|557693555|ref|YP_008796609.1| 190 IDVSGSILFLLAASPL 205
                                       7999999999998655 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00034
                           DUF3937  12 lslfvflgiinftisyfqtyletaad 37 
                                       l+ fvf+gii +   y+qt l  +a 
  gi|557693555|ref|YP_008796609.1| 264 LAGFVFFGIIAYMPLYLQTVLGYSAT 289
                                       677****************9987775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3323.98
//
Query:       gi|557693556|ref|YP_008796610.1|  [L=546]
Description: CTP synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-117  391.6   0.8     2e-117  391.2   0.8    1.1  1  CTP_synth_N    CTP synthase N-terminus
    8.4e-50  169.2   0.0    1.6e-49  168.3   0.0    1.5  1  GATase         Glutamine amidotransferase class-I
    6.1e-06   26.2   0.0    1.9e-05   24.6   0.0    1.8  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.025   14.7   0.0      0.065   13.3   0.0    1.6  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
       0.21   10.7   0.0       0.31   10.2   0.0    1.2  1  ArsA_ATPase    Anion-transporting ATPase


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 !  391.2   0.8  5.5e-121    2e-117       1     265 []       8     270 ..       8     270 .. 0.99

  Alignments for each domain:
  == domain 1  score: 391.2 bits;  conditional E-value: 5.5e-121
                                       EEEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHH CS
                       CTP_synth_N   1 kyilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfl 77 
                                       kyi+vtGGvvS++GkG +aas+g++l  rg+k  ++kiDPY+nvdagtl+p+ hGEvfv+ddGaetDlDlG YeRfl
  gi|557693556|ref|YP_008796610.1|   8 KYIFVTGGVVSSVGKGTVAASIGKILSVRGVKTGFLKIDPYVNVDAGTLNPFSHGEVFVTDDGAETDLDLGWYERFL 84 
                                       8**************************************************************************** PP

                                       T----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHH CS
                       CTP_synth_N  78 dikltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpfle 154
                                       di+++++nnittG+iy +vi +errGdylG++vq++phvtdeik+ri+++++   +dv+ive+gGtvgdie++pfle
  gi|557693556|ref|YP_008796610.1|  85 DITTSRKNNITTGQIYAEVIARERRGDYLGQCVQIVPHVTDEIKRRIREASE--GVDVLIVEVGGTVGDIEGQPFLE 159
                                       *************************************************998..8********************** PP

                                       HHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--G CS
                       CTP_synth_N 155 airqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnvek 231
                                       airq++le g en+l++hv+lv +lka+ge+ktk+ qhsv++lr+lGiqpdiiv+rs+k++++e+++kialf ++++
  gi|557693556|ref|YP_008796610.1| 160 AIRQMRLEEGVENTLFVHVALVLTLKATGEFKTKALQHSVNTLRALGIQPDIIVARSDKPIDQEARRKIALFGTISE 236
                                       ***************************************************************************** PP

                                       GGEEEEE--S-GGGHHHHHHHCTHHHHHHHHTT- CS
                       CTP_synth_N 232 eavisvkdvesiyevpllleeqglaelileklkl 265
                                       +av+s++dv+ +y+vp++le+qg+ ++++++l l
  gi|557693556|ref|YP_008796610.1| 237 KAVFSSHDVDCVYKVPVVLEKQGMGDYLVTRLAL 270
                                       *****************************99976 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.3   0.0   4.4e-53   1.6e-49       2     190 .]     305     531 ..     304     531 .. 0.93

  Alignments for each domain:
  == domain 1  score: 168.3 bits;  conditional E-value: 4.4e-53
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH....THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-E CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile....llknpdgilvsgGpgspgvegkieaikearenkiPi 74 
                                       l D+y sv+e+l ha+v++g+ +e+++++++  e+ +     l ++dg+lv+gG+g +g+eg+ie+i+++r+n+iP+
  gi|557693556|ref|YP_008796610.1| 305 LADSYVSVKEALQHAGVNIGAHLEIDWVNTEEFENGSrsleTLHGYDGVLVPGGFGRRGTEGMIECIRFCRTNDIPF 381
                                       78****************************9999944555359********************************** PP

                                       EEETHHHHHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTTS CS
                            GATase  75 LGICLGmQllaiefgrkvv.......................kekekehhggtmrlgddet........allyglkn 120
                                       LGIC+G+Ql + ef+r+v                        ++++ + +ggtmrlg+           ++lyg  +
  gi|557693556|ref|YP_008796610.1| 382 LGICFGLQLSIVEFARNVCglaganstelnpetphpvidlmpEQRRVSGLGGTMRLGALTVklikdtlaHRLYGA-D 457
                                       ****************9999999999999999999999****88889***********7779************9.* PP

                                       EEEEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHHH CS
                            GATase 121 evierhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflika 190
                                       e++ rhrHryevn++    l ++gl++++ s ++  ++eiie +  + f ++QFHPE+ s+p++p +   +++ka
  gi|557693556|ref|YP_008796610.1| 458 EIRQRHRHRYEVNHTyweTLQKNGLVFSGFSPEG-DRVEIIEYPVnRfFLATQFHPEYLSRPNRPDPAYLGFVKA 531
                                       *************99**7777788*******999.6999999998799*********************999985 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   5.2e-09   1.9e-05      98     216 .]     371     513 ..     365     513 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 5.2e-09
                     Peptidase_C26  98 iraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe............q......saashavkvekg 156
                                       ir + ++++P lgiC Glql  v +  ++   + ++s++ +   ++            +         + +vk+ k+
  gi|557693556|ref|YP_008796610.1| 371 IRFCRTNDIPFLGICFGLQLSIVEFARNVCGLAGANSTELNPETPHpvidlmpeqrrvSglggtmRLGALTVKLIKD 447
                                       55667789************9888776666555543333333333345666666665515555557789999999** PP

                     Peptidase_C26 157 sllaellgseeievnslHhqaike......laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                       +l ++l+g++ei+    H+  +++        ++l  +  ++  + +E ie + ++ f+l+ Q+HPE
  gi|557693556|ref|YP_008796610.1| 448 TLAHRLYGADEIRQRHRHRYEVNHtywetlQKNGLVFSGFSPeGDRVEIIEYPVNR-FFLATQFHPE 513
                                       ***********************99999966778888999996679********76.*********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 ?   13.3   0.0   1.8e-05     0.065       8      55 ..      18     105 ..      10     224 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                                       TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
                              CbiA   8 GGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.............................. 54 
                                       + vGK t+aa+++++l+ rg ++  ++ Dp  n +a   g+ n                                  
  gi|557693556|ref|YP_008796610.1|  18 SSVGKGTVAASIGKILSVRGVKTGFLKIDPYVNVDA---GTLNPFSHgevfvtddgaetdldlgwyerfldittsrk 91 
                                       88****************************999887...55554444555555555555555555555555555555 PP

                                       .............C CS
                                       .............x RF
                              CbiA  55 .............d 55 
                                                     
  gi|557693556|ref|YP_008796610.1|  92 nnittgqiyaeviA 105
                                       55555555555550 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   8.6e-05      0.31       2      61 ..       8      69 ..       7     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8.6e-05
                                      EEEEEEES..TTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSS CS
                       ArsA_ATPase  2 kvilvgGK..GGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeN 61
                                      k+i+v+G     VGK tv+a+++  ls  g k+  +  DP  ++     + +++ +  v++ 
  gi|557693556|ref|YP_008796610.1|  8 KYIFVTGGvvSSVGKGTVAASIGKILSVRGVKTGFLKIDPYVNVDAGTLNPFSHGEVFVTDD 69
                                      6889988433579***************************9888554444466666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); 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:                         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: 00:00:00.41
# Mc/sec: 3961.93
//
Query:       gi|557693557|ref|YP_008796611.1|  [L=421]
Description: ABC-2 type transport system permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-26   92.8  22.1    2.6e-26   92.6  22.1    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
      5e-24   85.1  21.7    6.4e-24   84.7  21.7    1.1  1  ABC2_membrane_2  ABC-2 family transporter protein
      5e-07   29.4  20.2      5e-07   29.4  20.2    2.6  3  ABC2_membrane    ABC-2 type transporter
    0.00013   22.0  14.0    0.00013   22.0  14.0    3.0  4  ABC2_membrane_4  ABC-2 family transporter protein
  ------ inclusion threshold ------
       0.38   10.3  28.8        1.1    8.7  25.3    2.8  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 !   92.6  22.1   7.2e-30   2.6e-26       3     344 ..      20     399 ..      18     400 .. 0.74

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 7.2e-30
                   ABC2_membrane_3   3 fliitlllPiilvlllglifs..nsve.d.dentpiavvdednsslsqqlvealeasps.velvyevdseeeakkal 74 
                                       +li ++l+P++++ l+g+ +   +  e d      + vvd+d+  ++  +veal +++   +  +++++ +++ +++
  gi|557693557|ref|YP_008796611.1|  20 ILIGVVLMPLVIFPLIGFTMApvTMREgDiGARAAVLVVDQDGGKYAALFVEALRKTGLnPQ-PIQLQN-DNLLQLI 94 
                                       5778899999999998888765333333322233336788888*************884244.445555.5599*** PP

                   ABC2_membrane_3  75 kngdidgilvipkgfskdllkgesatvtvlinssnlnss.....kailnalns.llqqlnasalv............ 133
                                       kn +++++++ip+gfs +l++++ +tv++++  + ++++      ai+  +++ ++ + +    +            
  gi|557693557|ref|YP_008796611.1|  95 KNSEASAAVIIPQGFSTQLEQKNKPTVKLFLKLASSSVAeferiGAIRDRIYTaVSLM-GE---Alaseediavsfy 167
                                       *******************************999999999999966666666533222.11...1111223344442 PP

                   ABC2_membrane_3 134 lqseatstsaninvestql..........eeelsnvasf....lvg.liliilifitasfiavsiveEkesrikelq 195
                                                   ++++             ++  + +++f    l++ ++lii+++ +++++a+si  Eke +++e++
  gi|557693557|ref|YP_008796611.1| 168 K----------SPINLSGEvvyrdqtipeTDAGQLFQQFfastLLIpIALIIVVTTSGTIAATSIGLEKEAKTLEML 234
                                       1..........2222222233444445543333444444222233358888888888999***************** PP

                   ABC2_membrane_3 196 lvsgvsplqywlskilgdflvyllqll.lilllafgl.........gipfg....nlglllllfllfglayialgyl 258
                                       l+ ++ +++++ sk+lg+ +v+ll ++ l+++l+f +         +i+f+    +l+ll +++++ + +++ lg l
  gi|557693557|ref|YP_008796611.1| 235 LTYPIARSTILASKLLGSTVVALLGTAsLMTGLIFYFsrvtafagmSISFSlsplSLVLLAVVLFFALVTTLGLGVL 311
                                       ************************99834455666666699999996666653323333336666667788889999 PP

                   ABC2_membrane_3 259 lsslfknsetaqilifivilllsgffgglfp...ledlpsalkwifsiiPffapglgllrlitgdplweillsliil 332
                                        ++l  + +  q+l++++ ++l+++ ++lf+   +++l  +l++i  iiPf++++l+   ++    + +ill+++++
  gi|557693557|ref|YP_008796611.1| 312 AGVLAGDVRGSQQLASLIQVPLILLPLLLFLsggIQSLQQPLATIILIIPFTHVMLATQAILESS-YLNILLHIGVM 387
                                       9*******************9999999998888999**********************9999655.68********* PP

                   ABC2_membrane_3 333 alfavvylllal 344
                                       ++ +v+++ la+
  gi|557693557|ref|YP_008796611.1| 388 VVWTVAVIGLAA 399
                                       *******99997 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 !   84.7  21.7   1.8e-27   6.4e-24       3     284 ..       6     403 ..       4     407 .. 0.83

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 1.8e-27
                   ABC2_membrane_2   3 iakkEfrdlvrsrrfllltvllpli.................................................... 27 
                                       ++ kE+r+l+  +++l+ +vl+pl+                                                    
  gi|557693557|ref|YP_008796611.1|   6 LLSKELRELLSEKTILIGVVLMPLVifpligftmapvtmregdigaraavlvvdqdggkyaalfvealrktglnpqp 82 
                                       688*******************************************9999999999999997777777777777777 PP

                   ABC2_membrane_2  28 .................dvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkv........... 76 
                                                         +a+ + + ++++l++++k ++++ l+l++++ a ++ +         +           
  gi|557693557|ref|YP_008796611.1|  83 iqlqndnllqliknseaSAAVIIPQGFSTQLEQKNKPTVKLFLKLASSSVAEFERIG--------Airdriytavsl 151
                                       777777777777777776777777777777777777777777777777666665554........03444445689* PP

                   ABC2_membrane_2  77 .................................................vstimavlipvi.aalfgadaiagEker 103
                                                                                        +  ++a++i+v    +++a++i  Eke 
  gi|557693557|ref|YP_008796611.1| 152 mgealaseediavsfykspinlsgevvyrdqtipetdagqlfqqffastLLIPIALIIVVTtSGTIAATSIGLEKEA 228
                                       **********************************************999777777777776689************* PP

                   ABC2_membrane_2 104 gTlkllLskPvsRdeillgKfigglaiglaiavallatvll...alaiilalgivlaledllllvvasvlllllvvf 177
                                       +Tl+ lL++P+ R++il++K++g+ +++l++  +l+ ++++    +   ++ +i+++l+ l l+++a+vl+++lv+ 
  gi|557693557|ref|YP_008796611.1| 229 KTLEMLLTYPIARSTILASKLLGSTVVALLGTASLMTGLIFyfsRVTAFAGMSISFSLSPLSLVLLAVVLFFALVTT 305
                                       ***************************8884444444444444477788999999**************99999999 PP

                   ABC2_membrane_2 178 lalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsd 254
                                       l+lg+l  ++a   ++  +   +l+ v +il p++l+  + + +  ++      ++ l+ p+ + ++++++il++s 
  gi|557693557|ref|YP_008796611.1| 306 LGLGVLAGVLAG-DVRGSQQLASLIQVPLILLPLLLFLSGGIQSLQQP----LATIILIIPFTHVMLATQAILESS- 376
                                       ***********9.55555555566666668888887776666665555....66899999****************. PP

                   ABC2_membrane_2 255 lnalgstatnllilllllavllvlgyvlFk 284
                                          ++    ++++++++++++++l++++F+
  gi|557693557|ref|YP_008796611.1| 377 ---YLNILLHIGVMVVWTVAVIGLAAFMFR 403
                                       ...799********************9996 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.16   5.7e+02       9      40 ..       9      39 ..       4      56 .. 0.69
   2 !   29.4  20.2   1.4e-10     5e-07      52     207 ..     195     371 ..     162     373 .. 0.77
   3 ?   -1.3   3.3      0.34   1.2e+03      28      80 ..     354     406 ..     340     413 .. 0.55

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.16
                     ABC2_membrane  9 reflqrwrdpslgllwrliqplllalvfgtvf 40
                                      +e++  +  ++++ +  +++pl+++ ++g+  
  gi|557693557|ref|YP_008796611.1|  9 KELRELLSEKTIL-IGVVLMPLVIFPLIGFTM 39
                                      5666666666455.777777777777777654 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 1.4e-10
                     ABC2_membrane  52 r........pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifll..i 118
                                                p +l++ v++ +  +++++++  e+e ++le +l++p+  +s+++++k+l++ +v+ll ++ +++  i
  gi|557693557|ref|YP_008796611.1| 195 QffastlliPIALIIVVTTSG--TIAATSIGLEKEAKTLEMLLTYPI-ARSTILASKLLGSTVVALLGTASLMTglI 268
                                       134555666999999999999..66666679****************.****************9998888888634 PP

                     ABC2_membrane 119 vyf.....lvgldls......rfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipids 184
                                       +yf     + g+ +s      + +l+ ++l++ ++++++lg+l ++la +++  +qlasl+ +pl+ll   ++    
  gi|557693557|ref|YP_008796611.1| 269 FYFsrvtaFAGMSISfslsplSLVLLAVVLFFALVTTLGLGVLAGVLAGDVRGSQQLASLIQVPLILLPLLLFLSGG 345
                                       444554443366665544344448888888899999999*********************99999888777766666 PP

                     ABC2_membrane 185 m...pkwlqwiaylnPltyavealrs 207
                                       +   ++ l  i  + P+t+++ a ++
  gi|557693557|ref|YP_008796611.1| 346 IqslQQPLATIILIIPFTHVMLATQA 371
                                       64334467789999999999877665 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.34
                     ABC2_membrane  28 qplllalvfgtvfgnlg..nsedglnrpgllffsvlflafsaltsvapvfererg 80 
                                        +++l++ f+ v   ++   ++++ln++  ++ +v++++  a++++a++++r+++
  gi|557693557|ref|YP_008796611.1| 354 ATIILIIPFTHVMLATQaiLESSYLNILLHIGVMVVWTV--AVIGLAAFMFRGER 406
                                       333333333333333333445555566666666666666..66666666666555 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 ?   -1.5   0.1      0.57     2e+03      13     157 ..      18      36 ..       6      47 .. 0.51
   2 !   22.0  14.0   3.6e-08   0.00013      45     153 ..     196     304 ..     177     317 .. 0.64
   3 ?    2.1   2.8     0.046   1.7e+02     101     150 ..     292     341 ..     283     349 .. 0.58
   4 ?   -3.2   6.8       1.9   6.7e+03     110     163 ..     348     403 ..     333     410 .. 0.50

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.57
                   ABC2_membrane_4  13 kivwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPv 89 
                                       k ++++v+++ lv                                                                
  gi|557693557|ref|YP_008796611.1|  18 KTILIGVVLMPLV---------------------------------------------------------------- 30 
                                       3344444433333................................................................ PP

                   ABC2_membrane_4  90 srtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpiia 157
                                                                                                     + p+i 
  gi|557693557|ref|YP_008796611.1|  31 --------------------------------------------------------------IFPLIG 36 
                                       ..............................................................333332 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 3.6e-08
                   ABC2_membrane_4  45 efyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtfl..itvl 119
                                        f s   +++ +l+++++  g ia+++i  E++ +tl  Llt P+ r ++l++Kl+   ++++ l  ++++  + + 
  gi|557693557|ref|YP_008796611.1| 196 FFASTLLIPI-ALIIVVTTSGTIAATSIGLEKEAKTLEMLLTYPIARSTILASKLLGSTVVAL-LGTASLMtgLIFY 270
                                       3333333444.45688899999*********************************87655433.2223333003344 PP

                   ABC2_membrane_4 120 fallsgfvgfsvklvlellkkclelgllvffavl 153
                                       f+ +  f+g+s++  l+ l  +l+ ++l f++v+
  gi|557693557|ref|YP_008796611.1| 271 FSRVTAFAGMSISFSLSPLSLVLLAVVLFFALVT 304
                                       5556666666666655555555555544444443 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.046
                   ABC2_membrane_4 101 vllllsvllmlvtf.litvlfallsgfvgfsvklvlellkkclelgllvff 150
                                       vll +++++ lvt+  + vl+++l+g v+ s +++++l++  l+l  l++f
  gi|557693557|ref|YP_008796611.1| 292 VLLAVVLFFALVTTlGLGVLAGVLAGDVRGS-QQLASLIQVPLILLPLLLF 341
                                       3444444455544415667777777776654.5556666655555444444 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 1.9
                   ABC2_membrane_4 110 mlvtflitvlfallsgfvgfsvklvlellk..kclelgllvffavlpiialvllkk 163
                                       +l + l+t+++ + +++v + ++++le+    ++l +g++v+ +v++i + +++++
  gi|557693557|ref|YP_008796611.1| 348 SLQQPLATIILIIPFTHVMLATQAILESSYlnILLHIGVMVVWTVAVIGLAAFMFR 403
                                       44444555566555666666666666543311333444433333333333355555 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 ?   -1.4   0.1      0.41   1.5e+03      19     129 ..      22      34 ..       6      58 .. 0.53
   2 ?    8.7  25.3   0.00031       1.1      33     191 ..     199     367 ..     192     402 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.41
                   ABC2_membrane_5  19 ivllllaiiiliflndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiail 95 
                                       i ++l++++i+                                                                  
  gi|557693557|ref|YP_008796611.1|  22 IGVVLMPLVIF------------------------------------------------------------------ 32 
                                       22222222222.................................................................. PP

                   ABC2_membrane_5  96 itlllliiavlikgnvtisevllsiliglviali 129
                                                                        +
  gi|557693557|ref|YP_008796611.1|  33 --------------------------------PL 34 
                                       ................................22 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00031
                   ABC2_membrane_5  33 ndsvllifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavlikg 109
                                       ++ ++ i +i++++ s +++ t++  ++ +k+  +llt P+ r++i +sK l+++++ l+++  ++  li  ++ + 
  gi|557693557|ref|YP_008796611.1| 199 STLLIPIALIIVVTTSGTIAATSIGLEKEAKTLEMLLTYPIARSTILASKLLGSTVVALLGTASLMTGLIF-YFSRV 274
                                       444555666777777788889********************************999998887666555432.22222 PP

                   ABC2_membrane_5 110 n..vtisevllsiliglvialiflaivlPlyfkfgvekgri.........vliiiifgiifllvaifslsklelsli 175
                                       +    +s ++  + ++lv+  ++l + l+ ++ +gv  g +         ++ +i + +i l   +f + +++  ++
  gi|557693557|ref|YP_008796611.1| 275 TafAGMSISFSLSPLSLVLLAVVLFFALVTTLGLGVLAGVLagdvrgsqqLASLIQVPLILLPLLLFLSGGIQSLQQ 351
                                       21222222222222333333333333333333333333333333377666444444444444444455566655556 PP

                   ABC2_membrane_5 176 dlsnyilliillviil 191
                                        l ++il+i ++ ++l
  gi|557693557|ref|YP_008796611.1| 352 PLATIILIIPFTHVML 367
                                       6666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2885.42
//
Query:       gi|557693558|ref|YP_008796612.1|  [L=240]
Description: ABC-2 type transport system ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   88.6   0.0    6.7e-25   88.2   0.0    1.2  1  ABC_tran  ABC transporter
    1.4e-11   44.8   0.0    0.00015   21.7   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00044   19.7   0.1       0.32   10.4   0.0    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
    0.00066   20.2   0.0    0.00098   19.7   0.0    1.3  1  AAA_23    AAA domain
     0.0012   18.5   0.1     0.0023   17.6   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
     0.0093   14.7   0.0       0.25    9.9   0.0    2.0  2  AAA_13    AAA domain
  ------ inclusion threshold ------
      0.022   14.5   0.1      0.032   13.9   0.1    1.3  1  AAA_30    AAA domain
      0.047   14.0   0.0       0.07   13.4   0.0    1.4  1  AAA_22    AAA domain
      0.054   13.9   0.0      0.092   13.2   0.0    1.4  1  AAA       ATPase family associated with various cellular acti
      0.081   12.5   0.1       0.16   11.6   0.1    1.4  1  SRP54     SRP54-type protein, GTPase domain
      0.094   12.7   0.0        0.2   11.7   0.0    1.6  1  AAA_5     AAA domain (dynein-related subfamily)
       0.11   12.2   0.0       0.16   11.6   0.0    1.2  1  AAA_15    AAA ATPase 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 !   88.2   0.0   4.5e-28   6.7e-25       1     137 []      21     161 ..      21     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 4.5e-28
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ vsl ++eg + +++G+nGaGK+t++++la ll+p  G+ ++ gkd+ + e +++r+ i +lp+e+ + ++lt r
  gi|557693558|ref|YP_008796612.1|  21 LRGVSLVVEEGGVFGLIGPNGAGKTTMFRILATLLRPSRGTAKVFGKDVVK-EASEVRRMITYLPEEAGVYKNLTGR 96 
                                       6789**********************************************9.9999******************999 PP

                                       HH.HHHTC.....HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.xxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.esdee.....iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       +  ++ ++      +++ + + ++    + v++++ ++S+G+++r+ la +l+ +p+l +lDEpta
  gi|557693558|ref|YP_008796612.1|  97 SFlKMVSRvyglgSSALEKGIAIS-GLGEAVDRKMGEYSKGMRRRILLAGCLMVEPRLAILDEPTA 161
                                       999555553444322333333333.3666777777*****************************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 !   21.7   0.0   9.9e-08   0.00015       2      60 ..      34      90 ..      33      97 .. 0.79
   2 !   21.4   0.0   1.3e-07   0.00019     231     302 ..     127     195 ..     103     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 9.9e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfef 60
                                       +liGpNg+GK++ +++l  l   +++    + +  + +++++  ++  +y pe+++++
  gi|557693558|ref|YP_008796612.1| 34 FGLIGPNGAGKTTMFRILATLL--RPSRGTAKVFGKDVVKEASEVRRMITYLPEEAGVY 90
                                      68****************9998..67777777777777777777777777777777665 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 1.3e-07
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                                       ++ + e S G++r   ll+ +l   +  +l ++DEp +gL+ +    + +++++ ++ g+ +i+++H+ l +
  gi|557693558|ref|YP_008796612.1| 127 DRKMGEYSKGMRRR-ILLAGCLMVEP--RLAILDEPTAGLDVEHSVYVRKIIRQYAEQGTTFIVSSHNMLEV 195
                                       5567899*******.66666666555..**************77777778888888889*********8765 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 !    7.4   0.0    0.0018       2.6      27      42 ..      34      49 ..      25      72 .. 0.86
   2 !   10.4   0.0   0.00022      0.32     161     198 ..     153     191 ..     139     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                                      EEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxx RF
                             SMC_N 27 taivGpNGSGKsnlld 42
                                        ++GpNG+GK+ ++ 
  gi|557693558|ref|YP_008796612.1| 34 FGLIGPNGAGKTTMFR 49
                                      5689********9875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00022
                                       EEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N 161 lyllDeidaaLDeknvkkvaellkekskn.aQfivislr 198
                                       l +lDe  a LD ++   v +++++  ++ + fiv s++
  gi|557693558|ref|YP_008796612.1| 153 LAILDEPTAGLDVEHSVYVRKIIRQYAEQgTTFIVSSHN 191
                                       789*********************999986888888876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   6.6e-07   0.00098      19      43 ..      31      55 ..      15      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 6.6e-07
                            AAA_23 19 kgltlItGpNGaGKTTildAiklaL 43
                                       g++ ++GpNGaGKTT ++ +   L
  gi|557693558|ref|YP_008796612.1| 31 GGVFGLIGPNGAGKTTMFRILATLL 55
                                      699***************9887665 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 !   17.6   0.1   1.5e-06    0.0023      17      50 ..      26      59 ..      20      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      + +++ g++ l+Gp+G+GK+T++  +++lL p++
  gi|557693558|ref|YP_008796612.1| 26 LVVEEGGVFGLIGPNGAGKTTMFRILATLLRPSR 59
                                      5566667999********************9987 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00017      0.25      23      43 ..      38      58 ..      35     134 .. 0.59
   2 ?    2.8   0.0     0.024        36     527     571 ..     151     192 ..     147     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00017
                            AAA_13 23 GwNGaGKTtLSrllrslelge 43
                                      G NGaGKTt+ r+l+ l + +
  gi|557693558|ref|YP_008796612.1| 38 GPNGAGKTTMFRILATLLRPS 58
                                      99*************995433 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.024
                            AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnl 571
                                        +  ++D P   LD +++ +v   i++++   ++   ++++ Hn+
  gi|557693558|ref|YP_008796612.1| 151 PRLAILDEPTAGLDVEHSVYVRKIIRQYA---EQGTTFIVSSHNM 192
                                       566789**********************9...999999*****96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.2e-05     0.032      15      47 ..      29      62 ..      22     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.2e-05
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaa.g.g 47
                                      + +  v  l Gp G+GKtt+ + l+ +++ + g  
  gi|557693558|ref|YP_008796612.1| 29 E-EGGVFGLIGPNGAGKTTMFRILATLLRPSrGtA 62
                                      3.4459999***************99998774452 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   4.7e-05      0.07       6      71 ..      32     115 ..      28     191 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.7e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee...........erpevvfvtlpsst.....sskdllrellralgl 66 
                                       g+  ++G+ G+GKTt  r l+  l      ++           e ++ +++ + + +     + +++l+++ r +gl
  gi|557693558|ref|YP_008796612.1|  32 GVFGLIGPNGAGKTTMFRILATLLRPSRGTAKvfgkdvvkeasEVRRMITYLPEEAGvyknlTGRSFLKMVSRVYGL 108
                                       56669****************99965555555888888888765555556666555577788888888888888887 PP

                            AAA_22  67 elka..e 71 
                                       + +a  +
  gi|557693558|ref|YP_008796612.1| 109 GSSAleK 115
                                       7777441 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 ?   13.2   0.0   6.1e-05     0.092       3      35 ..      36      70 ..      34     101 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
                                      EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelg..vefleisgsell 35
                                      l+Gp G GKT++ + +a+ l   +   ++ g++++
  gi|557693558|ref|YP_008796612.1| 36 LIGPNGAGKTTMFRILATLLRpsRGTAKVFGKDVV 70
                                      89***************998432444555555555 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   0.00011      0.16       6      39 ..      36      69 ..      32      83 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      l+G++GaGKTt    La ll+ +  ++ +   D+
  gi|557693558|ref|YP_008796612.1| 36 LIGPNGAGKTTMFRILATLLRPSRGTAKVFGKDV 69
                                      89***************99998866666666665 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 ?   11.7   0.0   0.00013       0.2       4      34 ..      36      67 ..      34      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                      EE--SSSSHHHHHHHGGGGB.S--EEEEE--T CS
                             AAA_5  4 LvGppGtgKselaerlaaal.nreveyvqltr 34
                                      L+Gp G gK+++ + la +l  ++ + + + +
  gi|557693558|ref|YP_008796612.1| 36 LIGPNGAGKTTMFRILATLLrPSRGTAKVFGK 67
                                      9*******************865555555555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.16      28      59 ..      36      71 ..      22      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                            AAA_15 28 liGkNnsGKSsilealdlFlnnkekkn....kkvik 59
                                      liG+N++GK++  ++l  +l  ++       k+v+k
  gi|557693558|ref|YP_008796612.1| 36 LIGPNGAGKTTMFRILATLLRPSRGTAkvfgKDVVK 71
                                      9******************99883222444544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1777.96
//
Query:       gi|557693559|ref|YP_008796613.1|  [L=283]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   68.1  24.9    1.8e-10   41.1  13.8    2.1  2  EamA      EamA-like transporter family
     0.0053   16.8   4.2        1.7    8.7   0.1    3.5  4  TMEM234   Putative transmembrane family 234


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 !   41.1  13.8     2e-14   1.8e-10       4     136 ..      10     139 ..       7     140 .. 0.95
   2 !   33.0   3.2   6.4e-12   5.7e-08       8     135 ..     156     278 ..     151     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2e-14
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80 
                                       +++ +++a++w+++ ++  ++++k s l++++v+  ++ +lll +  l+++k+  ++ +d+ + +  g+  + l+  
  gi|557693559|ref|YP_008796613.1|  10 AFYGVASAVSWGAGNFYGGYASKKASVLMVVAVSQSLGLVLLLSLGILSGEKP--PTTSDIYWSAAAGF-FSGLGIT 83 
                                       67899************************************************..9999*999888885.556788* PP

                              EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       l++ al+++s + a+++t +  + +   +  +l   ++ +q +g++l++l+++l++
  gi|557693559|ref|YP_008796613.1|  84 LYYAALSRGSMGLAAPVTGVLTAAVPAVAGTFLEGVPSPLQAIGFLLAFLSIFLVT 139
                                       ******************************************************86 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 6.4e-12
                              EamA   8 llaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffy 84 
                                        +a l +++  v++ +++  +  + l++ r++  +++l + ++    +l     ++ l  +  g++ t    ++++ 
  gi|557693559|ref|YP_008796613.1| 156 AAAGLGFGLFLVTIGQVSPGHYYYPLVVSRLVTVSMVLAASLAKGHTSL----SNSRLTTAAAGIFDTGGS-FFYLL 227
                                       5677778888888888877888888888898888887766666655555....778888899999999888.59*** PP

                              EamA  85 alkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       a + +   +a++++sl Pv t++l+  +lgekl++   +gi+++ +++ li
  gi|557693559|ref|YP_008796613.1| 228 ARQQGRLDEAGVLSSLYPVSTVLLAKTILGEKLGKQRTAGIICAAAATTLI 278
                                       **********************************************99987 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.17   1.5e+03      66      96 ..      32      62 ..      16      71 .. 0.76
   2 !    8.7   0.1   0.00019       1.7      57     115 ..      81     138 ..      73     139 .. 0.91
   3 ?    0.6   0.1     0.064   5.7e+02      60      93 ..     177     210 ..     164     227 .. 0.78
   4 !    6.3   0.0     0.001       9.2      59     115 ..     223     278 ..     213     279 .. 0.66

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.17
                           TMEM234 66 gkadlslavpiaNslafvfTvltelllgekv 96
                                      +ka++ ++v+++ sl  v+ +  + l gek 
  gi|557693559|ref|YP_008796613.1| 32 KKASVLMVVAVSQSLGLVLLLSLGILSGEKP 62
                                      5677788888888888888877777777775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00019
                           TMEM234  57 gSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       g  l++++l++ ++ la p++  l+ ++ ++ +++l e v +  + +g ll +++i l+
  gi|557693559|ref|YP_008796613.1|  81 GITLYYAALSRGSMGLAAPVTGVLTAAVPAVAGTFL-EGVPSPLQAIGFLLAFLSIFLV 138
                                       6679**************************999988.6889999999****99999987 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.064
                           TMEM234  60 lfflllgkadlslavpiaNslafvfTvltelllg 93 
                                        ++ l+ +  +++ +++a sla   T l ++ l 
  gi|557693559|ref|YP_008796613.1| 177 YYYPLVVSRLVTVSMVLAASLAKGHTSLSNSRLT 210
                                       4666777888899999999999999988887765 PP

  == domain 4  score: 6.3 bits;  conditional E-value: 0.001
                           TMEM234  59 vlfflllgkadlslavpiaNslafvfTvlte.lllgekvlkkktvlgmllvvvgialc 115
                                        ++ l+ ++  l     +  sl  v Tvl + ++lgek+ k+ +++g++   ++++l+
  gi|557693559|ref|YP_008796613.1| 223 FFYLLARQQGRLDE-AGVLSSLYPVSTVLLAkTILGEKLGKQ-RTAGIICAAAATTLI 278
                                       33333333333333.347789999****99856777777665.567888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); 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:                         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 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2293.93
//
Query:       gi|557693560|ref|YP_008796614.1|  [L=291]
Description: type I restriction enzyme R protein N terminal domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   26.5   0.0      0.022   14.7   0.0    2.3  2  HSDR_N    Type I restriction enzyme R protein N terminus (HSD
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.46   10.6   0.0    1.8  2  Mcp5_PH   Meiotic cell cortex C-terminal pleckstrin homology


Domain annotation for each model (and alignments):
>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.4e-06     0.022       2      36 ..      25      59 ..      24      62 .. 0.91
   2 !   10.2   0.0   6.1e-05      0.55     122     188 ..      61     116 ..      58     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.4e-06
                                      SSHHHHHH.HHHHHHHHTT-EE............. CS
                            HSDR_N  2 lsEaeleqelidellrelGyqvlskkdveiegrrp 36
                                      +sEa ++  lid+llr lG++ ++++ v +e ++p
  gi|557693560|ref|YP_008796614.1| 25 SSEALTRYVLIDPLLRGLGWDTENPELVRPEVSTP 59
                                      79***************************999876 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.1e-05
                                       --EEEEEEETTEEEEEEEE--TT-HHHHHHHHTSS---.---SSSGGGGG-.....-EEEEE-SS-EEEEE- CS
                            HSDR_N 122 rrpDivlfvnglplvviElKrpgtieeAinQikryrkeksdvsipqlfrYl.....qfgvisngketrfyak 188
                                        rpD+ l++ng  l+++ +K  g          +++ +     + q   Y+     +++++++g+ + +y++
  gi|557693560|ref|YP_008796614.1|  61 GRPDYALLHNGQRLAFVGAKPLG----------KQE-D-----LLQQISYCvsegvRYFIATDGSRWEVYDT 116
                                       59*******************54..........233.3.....66777777889999999999999999985 PP

>> Mcp5_PH  Meiotic cell cortex C-terminal pleckstrin homology
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.1e-05      0.46      15      55 ..      12      52 ..       5      59 .. 0.83
   2 ?   -1.9   0.0      0.39   3.5e+03      76     111 ..     238     273 ..     230     275 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.1e-05
                           Mcp5_PH 15 lyKyvrkrkskgssekrhkryvwihpyertllWsskqPkse 55
                                      l K ++  +++ +s++   ryv i+p  r l W +++P+  
  gi|557693560|ref|YP_008796614.1| 12 LKKRIQDYQKELQSSEALTRYVLIDPLLRGLGWDTENPELV 52
                                      556777776777899999********************875 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.39
                           Mcp5_PH  76 enplpkglkefnksililtpdralkltaetrerhev 111
                                       + p  ++ k+f++s  i t   + ++++ ++ rh++
  gi|557693560|ref|YP_008796614.1| 238 TRPVHENGKSFHASKRIGTLYVNTQFKIRDIIRHTI 273
                                       445555556899999999999999999999989876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2114.82
//
Query:       gi|557693561|ref|YP_008796615.1|  [L=139]
Description: nitrogen fixation protein NifU [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  102.3   0.0    2.2e-29  102.2   0.0    1.0  1  NifU_N    NifU-like N terminal domain
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.025   14.4   0.0    1.2  1  SufE      Fe-S metabolism associated domain


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0   2.5e-33   2.2e-29       5     124 ..      16     132 ..      12     137 .. 0.95

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 2.5e-33
                                       HHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHHTTSB CS
                            NifU_N   5 kvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelvkgkt 81 
                                        +ldhy+nPrn G +++++     ++  +p cGD+v + +k++ + +++e a F++ GC++++As+s+l+e ++gk+
  gi|557693561|ref|YP_008796615.1|  16 IILDHYRNPRNYGEMSDASV---KVKDSNPLCGDVVEVFLKINSD-GVVEKATFRGHGCAISQASASMLIESIQGKK 88 
                                       69****************95...88899****************7.******************************* PP

                                       HHHHCCCCHHHHHHHHTC.SCSSSCHCSCHHHHHHHHHHHHHHH CS
                            NifU_N  82 leealkitnkeiaeelgg.lpkeklhcsvlaedalkaavkkYka 124
                                       l+e +++ +++i+e lg  +++++++c+ l  +alkaav++Y +
  gi|557693561|ref|YP_008796615.1|  89 LDELKNLDKQHIFEMLGIeVGPVRVKCALLPLKALKAAVYSYLG 132
                                       ****************866***********************87 PP

>> SufE  Fe-S metabolism associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.8e-06     0.025      44     101 ..      49     107 ..      29     115 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-06
                                       EEEEEEEEET..TSEEEEEEESSHHHHHHHHHHHHHCTTEECCCCTCC-TCHHHHHTTSH CS
                              SufE  44 qvwlaaeled..gklkfeadsdarivkGllalllevlsgktpeeilavdledfleelgls 101
                                       +v+l+++ +   +k +f+++   +i+++ +++l+e ++gk+ +e+ ++d ++++e lg++
  gi|557693561|ref|YP_008796615.1|  49 EVFLKINSDGvvEKATFRGHG-CAISQASASMLIESIQGKKLDELKNLDKQHIFEMLGIE 107
                                       666666655433336666654.5799*******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 981.40
//
Query:       gi|557693562|ref|YP_008796616.1|  [L=388]
Description: metal-dependent phosphohydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-13   50.3   0.8    2.5e-13   50.3   0.8    2.1  3  HD        HD domain
     0.0068   15.9   0.0      0.011   15.2   0.0    1.4  1  HDOD      HDOD domain
  ------ inclusion threshold ------
        0.2   11.2   0.5       0.54    9.8   0.1    1.7  2  MIOX      Myo-inositol oxygenase


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 !   50.3   0.8   4.2e-17   2.5e-13       1      73 [.      51     122 ..      51     160 .. 0.87
   2 ?   -1.9   0.1      0.61   3.7e+03      32      67 ..     208     246 ..     203     311 .. 0.57
   3 ?   -2.1   0.0      0.72   4.3e+03      72     104 ..     295     328 ..     272     363 .. 0.65

  Alignments for each domain:
  == domain 1  score: 50.3 bits;  conditional E-value: 4.2e-17
                                       HHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekr 73 
                                       r++Hsl+ ++la+++a++l++   +r+ll++ aLlHDiG+ pf++ fe+   + ek l+He+ + +i++e  + 
  gi|557693562|ref|YP_008796616.1|  51 RFDHSLGCMHLAGEFADHLNLdTHERNLLRASALLHDIGHTPFSHLFEQL--LMEKRLSHEDMSIKIVQEDDEI 122
                                       79********************99*********************99955..4667789********9998665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.61
                                       HHHTTTTHHHHTS..HHHHHH...CTCCHHHHHHHHHHH CS
                                HD  32 aLlHDiGkgpfgdafekkeee...fekflaHekvgaeil 67 
                                       a +H  ++++f++a   ++ +   + k+l+ e ++ +++
  gi|557693562|ref|YP_008796616.1| 208 ARYHSFINIYFHHAARAAQHLllrAAKMLGDELDFSTMT 246
                                       555555555555544444222233444444444444444 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.72
                                       HHHHHH.HHHHHHHHHTTCCHHHHHHHHHHHHCC CS
                                HD  72 krlgld.ledvaklirehheswegkkrprglaer 104
                                       +r +++ ++++ +li+e  + +++k + +++++ 
  gi|557693562|ref|YP_008796616.1| 295 LRINYSdISLLERLIAEEAGTEPTKIYVDYSYAP 328
                                       4444446677777788877777766666333333 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.9e-06     0.011      96     150 ..      52     108 ..      23     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-06
                                       HHHHHHHHHHHHHHHHHTT-S-H..HHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHH CS
                              HDOD  96 wehslavAlvarelaeelgledp..eeaflaGLLhdiGklvllsllpeeleellekv 150
                                        +hsl +  +a e a++l+l+    + +  ++LLhdiG   + +l+++ l e + + 
  gi|557693562|ref|YP_008796616.1|  52 FDHSLGCMHLAGEFADHLNLDTHerNLLRASALLHDIGHTPFSHLFEQLLMEKRLSH 108
                                       68****************99996235566799*************999877665544 PP

>> MIOX  Myo-inositol oxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.23   1.4e+03      67      91 ..      66      90 ..      50      98 .. 0.77
   2 ?    9.8   0.1   9.1e-05      0.54     176     246 ..     203     283 ..     199     286 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.23
                              MIOX 67 aeairkdypdkdWlqltglihdlGk 91
                                      a+++  d  +++ l+ ++l+hd+G 
  gi|557693562|ref|YP_008796616.1| 66 ADHLNLDTHERNLLRASALLHDIGH 90
                                      556666667788899999****996 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 9.1e-05
                              MIOX 176 ealamiryhsf...ypwhkegaykhlmnek.....dee..llkavkafnkydlyskseekpdveelkPyyqelidky 242
                                       e la+ ryhsf   y +h + a +hl         de    + +v+++ ++d y+      + e+ +Py + l ++ 
  gi|557693562|ref|YP_008796616.1| 203 EELAIARYHSFiniYFHHAARAAQHLLLRAakmlgDELdfSTMTVQEYLQHDDYTTWCLLRSREKSRPYIKMLEKRI 279
                                       568999****977777899999999864431112133211356799*************************999999 PP

                              MIOX 243 lpek 246
                                       lp+ 
  gi|557693562|ref|YP_008796616.1| 280 LPKR 283
                                       9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2925.67
//
Query:       gi|557693563|ref|YP_008796617.1|  [L=67]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   61.9   0.0    2.9e-17   61.7   0.0    1.1  1  GatD_N    GatD N-terminal domain


Domain annotation for each model (and alignments):
>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   1.6e-21   2.9e-17       3      49 ..      20      66 ..      18      67 .] 0.96

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.6e-21
                                      TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT- CS
                            GatD_N  3 vGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieei 49
                                       GD ++v+++g ++ G++m r+e++++d++vlKL nGYN+G++++++
  gi|557693563|ref|YP_008796617.1| 20 LGDEVEVVRNGLRLHGFVMARYEFGEPDVLVLKLPNGYNMGVRVDAS 66
                                      69******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       171  (0.00953762); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 505.95
//
Query:       gi|557693564|ref|YP_008796618.1|  [L=288]
Description: hypothetical protein CSUB_C0125 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.4   0.7      0.029   14.4   0.7    2.0  2  CRISPR_Cas9_WED  CRISPR-Cas9 WED domain
       0.21   10.8   1.4        2.3    7.4   0.8    2.0  2  PPL5             Prim-pol family 5
       0.31   11.6   2.7        1.6    9.4   0.1    2.8  3  PrmC_N           PrmC N-terminal domain
       0.32   11.1   0.2       0.32   11.1   0.2    2.4  2  DUF4145          Domain of unknown function (DUF4145)


Domain annotation for each model (and alignments):
>> CRISPR_Cas9_WED  CRISPR-Cas9 WED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.7   6.5e-06     0.029      36      74 ..      95     140 ..      67     172 .. 0.76
   2 ?   -2.9   0.1       1.4   6.4e+03      40      47 ..     225     232 ..     212     261 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.5e-06
                   CRISPR_Cas9_WED  36 vkkll.......kkdkekflmakkdpktfeklkkilkeysdkkeks 74 
                                       vk l+       kk +e +l+ +k   tf +l+k l++y++  e  
  gi|557693564|ref|YP_008796618.1|  95 VKTLMaieekwfKKVDETYLIMRKKASTFRSLQKTLEQYKNRLEAA 140
                                       3333334444459999************************987654 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                   CRISPR_Cas9_WED  40 lkkdkekf 47 
                                        kk+k+k+
  gi|557693564|ref|YP_008796618.1| 225 NKKKKKKY 232
                                       33333333 PP

>> PPL5  Prim-pol family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.8   0.00051       2.3     174     253 ..      87     165 ..      80     185 .. 0.65
   2 ?    2.1   0.0     0.021        95     116     170 ..     186     238 ..     180     278 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00051
                              PPL5 174 leerlaaeakgveeveeksskkkskekkkklkkktsrkkkkegkkekesekeeededeeddlsdlvnvvegssaaak 250
                                       ++++++a+ k ++ +eek  kk  ++     kk+++ +  ++  ++ ++  e  + de++dl d+v++ e +    +
  gi|557693564|ref|YP_008796618.1|  87 TSKSARADVKTLMAIEEKWFKKVDETYLIMRKKASTFRSLQKTLEQYKNRLEAASGDEREDLLDMVKITEKKLH-RQ 162
                                       55666667777777777666655555544445555555555566666666777889999********9987732.22 PP

                              PPL5 251 kkk 253
                                        k+
  gi|557693564|ref|YP_008796618.1| 163 AKR 165
                                       233 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.021
                              PPL5 116 LPgesaaggekvLlevlnyLevrLpgiGftdPffLvltnevpskdkvsyhvhars 170
                                       + ge +  ++++L e++ y++ r  g+  t  ff ++ n + +k k  y  har 
  gi|557693564|ref|YP_008796618.1| 186 ISGENHILTQEALAEIMMYVDPRW-GLRKTLNFFGLFKNTNKKK-KKKYNGHARK 238
                                       5678888889999********996.8889999999999987655.5589999996 PP

>> PrmC_N  PrmC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.14   6.5e+02      16      58 ..      89     135 ..      76     144 .. 0.64
   2 ?    0.1   0.1      0.28   1.3e+03       3      20 ..     130     146 ..     128     179 .. 0.65
   3 ?    9.4   0.1   0.00036       1.6      18      67 ..     236     285 ..     224     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.14
                            PrmC_N  16 eeaeldAelLla....hvlglsrsdlllrgerelteeqlerfeelie 58 
                                        +a++d++ L+a    +  +++ ++l++r++    ++ ++++e++ +
  gi|557693564|ref|YP_008796618.1|  89 KSARADVKTLMAieekWFKKVDETYLIMRKKASTFRSLQKTLEQYKN 135
                                       56777777777755544556788888887776554444444444444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.28
                            PrmC_N   3 LreaearLkaagieeael 20 
                                       L++ ++rL+aa   +++ 
  gi|557693564|ref|YP_008796618.1| 130 LEQYKNRLEAAS-GDERE 146
                                       677888888873.33332 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00036
                            PrmC_N  18 aeldAelLlahvlglsrsdlllrgerelteeqlerfeelierRaarePlq 67 
                                       a+   e L   v ++++ dl ++ +++l ++ + + ++  ++R+a++P q
  gi|557693564|ref|YP_008796618.1| 236 ARKALERLTITVYKIKPKDLTAKLQKQLLRQIWLTIQQETQERLAGIPAQ 285
                                       55566777788999**********************************99 PP

>> DUF4145  Domain of unknown function (DUF4145)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.5      0.29   1.3e+03      35      59 ..      89     110 ..      69     168 .. 0.61
   2 ?   11.1   0.2   7.2e-05      0.32      17      58 ..     235     279 ..     224     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.29
                           DUF4145  35 kdLknkiealvekgvipeklkelld 59 
                                       k+  + +++l++ +   ek ++++d
  gi|557693564|ref|YP_008796618.1|  89 KSARADVKTLMAIE---EKWFKKVD 110
                                       55555555555554...44444443 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 7.2e-05
                           DUF4145  17 liRraLEkllkdkgiakgkdLknkiealvekgv...ipeklkell 58 
                                       ++R+aLE+l+   +++k kdL +k++++   ++   i+++++e l
  gi|557693564|ref|YP_008796618.1| 235 HARKALERLTITVYKIKPKDLTAKLQKQLLRQIwltIQQETQERL 279
                                       68************************9988877666777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1305  (0.0727871); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2148.72
//
Query:       gi|557693565|ref|YP_008796619.1|  [L=136]
Description: hypothetical protein CSUB_C0126 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 1116.25
//
Query:       gi|557693566|ref|YP_008796620.1|  [L=200]
Description: dTMP kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-49  167.0   0.1    3.9e-49  166.8   0.1    1.0  1  Thymidylate_kin  Thymidylate kinase
    1.5e-11   44.6   0.5      2e-10   40.9   0.5    2.1  1  dNK              Deoxynucleoside kinase
    5.1e-09   36.6   0.0    6.6e-09   36.2   0.0    1.2  1  AAA_28           AAA domain
    3.6e-07   30.7   0.1    1.5e-06   28.6   0.1    2.0  1  AAA_17           AAA domain
    3.7e-07   30.8   0.1    8.3e-07   29.6   0.1    1.6  1  AAA_18           AAA domain
    3.7e-07   30.4   0.1    5.3e-07   29.9   0.1    1.2  1  AAA_33           AAA domain
    4.2e-06   27.0   1.9     0.0069   16.5   0.1    2.4  3  SKI              Shikimate kinase
     0.0021   18.3   0.1      0.024   14.9   0.0    2.2  2  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.015   15.2   0.1      0.035   14.0   0.0    1.7  2  APS_kinase       Adenylylsulphate kinase
       0.02   14.5   0.0      0.043   13.4   0.0    1.5  1  SRP54            SRP54-type protein, GTPase domain
      0.024   15.0   0.0      0.047   14.1   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.031   14.2   0.1      0.091   12.7   0.1    1.9  1  AAA_31           AAA domain
      0.033   14.6   0.1      0.047   14.1   0.1    1.7  1  AAA              ATPase family associated with various cellul
      0.039   14.0   0.0       0.12   12.5   0.0    1.7  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.05   12.6   0.0       0.08   11.9   0.0    1.4  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.072   12.6   0.2       0.57    9.7   0.0    2.0  2  PPK2             Polyphosphate kinase 2 (PPK2)
       0.11   12.3   0.1       0.17   11.6   0.1    1.4  1  AAA_30           AAA domain
       0.12   12.5   0.9         15    5.6   0.1    2.3  2  ADK              Adenylate kinase
       0.15   12.1   0.1       0.91    9.6   0.0    2.0  2  AAA_14           AAA domain
        1.1    9.7   4.0         14    6.2   1.2    3.3  2  CBS              CBS 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 !  166.8   0.1   4.4e-52   3.9e-49       1     185 []       8     185 ..       8     185 .. 0.97

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 4.4e-52
                                       EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHH CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpal 77 
                                       +EG+DGaGKttqa+ll+++l++ g +v+  +ep++++iG +ire+l k+++++e+ +allfaadr  +l+eki  a 
  gi|557693566|ref|YP_008796620.1|   8 VEGIDGAGKTTQAKLLARKLTRHGFRVMNVHEPTDGKIGGLIREALAKRVNMSEEVLALLFAADR-LTLREKIVSAK 83 
                                       7****************************************************************.*********** PP

                                       HTT-EEEEES-HHHHHHHHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHH CS
                   Thymidylate_kin  78 kqgktvivdRylfSslaYqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrk 154
                                       ++g  v++dR ++SslaYq+a+ g + ++v+++n++++ kPd+++++d++pe+alkRl+k+++     +e+  flrk
  gi|557693566|ref|YP_008796620.1|  84 QSGVYVVSDRSVVSSLAYQSAALG-LRNWVYEVNRFAV-KPDIIVYIDISPETALKRLRKKSQ----RYENMVFLRK 154
                                       ********************9886.789**********.************************....6899999999 PP

                                       HHHHHHHHHHTTSTEEEEETTS-HHHHHHHH CS
                   Thymidylate_kin 155 vrerylelakederiliidasksieevheeI 185
                                       v+  y +++ +  r++++d ++++++v e I
  gi|557693566|ref|YP_008796620.1| 155 VKNAYSRVLHDFRRVVVVDGEQPVDAVAETI 185
                                       ***9999999999*************99876 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.5   2.3e-13     2e-10       1     199 [.       6     189 ..       6     194 .. 0.71

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 2.3e-13
                                       EEEEESTTSSHHHHHHHHHCCST.....CEEEE-HHHHCCSSSS...HHHHHHHHSHHH.HHHHHHHHHHHHHHHHH CS
                               dNK   1 ivveGnIgaGKstlvklLskklg.....vkvfeEpvdkwtnvqk...nlLekfYkdpsr.wsfalqtyvllsrlkqq 68 
                                       i+veG  gaGK+t +klL++kl      v  ++Ep d    + +   + L k  +  ++ +++ +    l  r k  
  gi|557693566|ref|YP_008796620.1|   6 IAVEGIDGAGKTTQAKLLARKLTrhgfrVMNVHEPTDGK--IGGlirEALAKRVNMSEEvLALLFAADRLTLREKIV 80 
                                       89******************9964443333355666644..222555777776665555688888888887777766 PP

                                       HCHHSSS-EEEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTT CS
                               dNK  69 lealatkqvvvleRsiysdryiFakalaekgtlseeelkiykelldnlleelakpdlliYLkasletclerikkRgr 145
                                        +a++ +  vv +Rs+ s+       ++++  l   ++         +++ + kpd+++Y+++s+et l+r++k+++
  gi|557693566|ref|YP_008796620.1|  81 -SAKQSGVYVVSDRSVVSSL------AYQSAALGLRNW------VYEVNRFAVKPDIIVYIDISPETALKRLRKKSQ 144
                                       .4548888899999999998......566666666555......4444444446*********************** PP

                                       CCCTTS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS.-TTTHCCHHHHHHHHH CS
                               dNK 146 eeekkieldYlekLhekyeewlkklnevpvlvidveeldlvaeeekredvveev 199
                                        +e+ +   +l+k+++ y+  l+ +    v+v+d+e+      +   e +ve+ 
  gi|557693566|ref|YP_008796620.1| 145 RYENMV---FLRKVKNAYSRVLHDFRR--VVVVDGEQ----PVDAVAETIVEKL 189
                                       **9966...788999999999988554..67778887....4555555555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   7.4e-12   6.6e-09       2     150 ..       6     164 ..       5     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 7.4e-12
                            AAA_28   2 ivitGgestGKTtlleaLa....argypvv..pEaar....eileeklakgedalpwvedllafaervleeqleeea 68 
                                       i++ G  ++GKTt ++ La    ++g++v+  +E+       +++e lak+ +++++v  +l fa+ +l  + +   
  gi|557693566|ref|YP_008796620.1|   6 IAVEGIDGAGKTTQAKLLArkltRHGFRVMnvHEPTDgkigGLIREALAKRVNMSEEV-LALLFAADRLTLREKIVS 81 
                                       7888999********999955545599987779986522226888999*********9.9999*******9999999 PP

                            AAA_28  69 aaaankvlfcDrglldtlaYaraygg..............eaeaeleaaarekrydlvfllppapeidddgeRredl 131
                                       a +++ ++++Dr+++ +laY  a  g              +              d +++ + +pe+     R++++
  gi|557693566|ref|YP_008796620.1|  82 AKQSGVYVVSDRSVVSSLAYQSAALGlrnwvyevnrfavkP--------------DIIVYIDISPETALKRLRKKSQ 144
                                       99*******************99999444444444444440..............5555555555555555555444 PP

                            AAA_28 132 ee.reaiderlrealrelgi 150
                                       ++  + + +++++a+ +  +
  gi|557693566|ref|YP_008796620.1| 145 RYeNMVFLRKVKNAYSRVLH 164
                                       33233444445555555333 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.1   1.7e-09   1.5e-06       2     125 ..      10     145 ..       9     150 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.7e-09
                                       E-TTSSHHHHHHHHHHHH...TEEEEEH........HHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklveky...gfthlsa........Gdllreeakrgglakardemrklpleekkelqkeaaekiae 67 
                                       G+ G+GK+tq++ l++k+   gf +++         G l+re  +++   ++++ ++ l   ++     ++ eki  
  gi|557693566|ref|YP_008796620.1|  10 GIDGAGKTTQAKLLARKLtrhGFRVMNVheptdgkiGGLIREALAKRVN-MSEEVLALLFAADRL----TLREKIVS 81 
                                       899*************999999999986666666668889876665532.344444444444444....45556666 PP

                                       HHHSSEEEEEE-SEEEET..TEEEESSHHHHHH....HH..SEEEEEE--HHHHHHHHHHHTTS CS
                            AAA_17  68 eakkkgvlvdghprikeq..agfldglpkevle....elkpdaiilleadpeeilerrlkdrtr 125
                                       +++++ ++v    ++     + +  gl  +v e     +kpd+i++++++pe+ l+r+ k+ +r
  gi|557693566|ref|YP_008796620.1|  82 AKQSGVYVVSDRSVVSSLayQSAALGLRNWVYEvnrfAVKPDIIVYIDISPETALKRLRKKSQR 145
                                       6677778888887764432255567888888765556789*****************9887665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.1   9.3e-10   8.3e-07       1     116 [.       6     145 ..       6     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 9.3e-10
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenss....... 69 
                                       I++ G+ G+GKtt ak L+++l   g++++ v+   +  ++       e +  + ++ +++l +l ++++       
  gi|557693566|ref|YP_008796620.1|   6 IAVEGIDGAGKTTQAKLLARKLTRhGFRVMNVHEPTDGKIGGLIR---EALAKRVNMSEEVLALLFAADRltlreki 79 
                                       89*******************933466666666665555555555...66666666777888888888778889999 PP

                            AAA_18  70 .......aleegknlvidghlaeleseaakdikk............vvLtaspeelleRlekRgye 116
                                               +   +  v++++  +     ++ +++            v+++ spe+ l+Rl+k +++
  gi|557693566|ref|YP_008796620.1|  80 vsakqsgVYVVSDRSVVSSLAYQSAALGLRNWVYevnrfavkpdiiVYIDISPETALKRLRKKSQR 145
                                       8655444333344447777777777777777777***************************98754 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   5.9e-10   5.3e-07       4     123 ..       8     147 ..       6     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 5.9e-10
                            AAA_33   4 lvGlpGsGKstlaerllkklg.....avllssdt.......lrrrlfgtdqqsktdytrvldrlyq.ilnelarkal 67 
                                       + G  G+GK+t a+ l++kl+     +  + ++t       +r++l+++ + s+ +   +l+ + + +l+e + +a 
  gi|557693566|ref|YP_008796620.1|   8 VEGIDGAGKTTQAKLLARKLTrhgfrVMNVHEPTdgkigglIREALAKRVNMSE-EVLALLFAADRlTLREKIVSAK 83 
                                       78*********************76555577777******76667777655555.4566666666657889999999 PP

                            AAA_33  68 sagrnvildatnlsr.rer......arflklarrlgvp.vrivvvetdeetlkeRlakRaangd 123
                                       ++g  v+ d   +s  + +      ++++  ++r+ v+ + iv+++ ++et+ +Rl+k++++ +
  gi|557693566|ref|YP_008796620.1|  84 QSGVYVVSDRSVVSSlAYQsaalglRNWVYEVNRFAVKpDIIVYIDISPETALKRLRKKSQRYE 147
                                       99999******8885333344456677777777777753899*****************99765 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00094      0.85       2      19 ..      13      30 ..      12      52 .. 0.86
   2 ?   -2.0   0.0       3.8   3.4e+03      96     123 ..      51      78 ..      47     105 .. 0.55
   3 !   16.5   0.1   7.7e-06    0.0069      82     157 ..     120     189 ..     105     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00094
                                      TSSHHHHHHHHHHHHTSE CS
                               SKI  2 GaGKstvGkllAkklgle 19
                                      GaGK+t +kllA+kl ++
  gi|557693566|ref|YP_008796620.1| 13 GAGKTTQAKLLARKLTRH 30
                                      9**************986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.8
                                       HHHHHHHHHTTS.SGGGCSCHHHHHHHHH CS
                               SKI  96 eellerlkadke.RPllqekskeeellee 123
                                       e+l++r+++ +e  +ll + ++   l+e+
  gi|557693566|ref|YP_008796620.1|  51 EALAKRVNMSEEvLALLFAADR-LTLREK 78 
                                       5566666666664444444444.333333 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 7.7e-06
                                       HHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHH.HHHHHHCCSSCEEEECTSSHHHHHHHHHHHHH CS
                               SKI  82 lkekgiviyLdvsleellerlkadkeRPllqekskeeelleela.ereplyeeaadvvvdeseeskeevaeeileal 157
                                       +k   i++y+d+s+e+ l+rl+++++R     ++     l++ + +  ++  ++  vvv + e++ ++vae+i+e+l
  gi|557693566|ref|YP_008796620.1| 120 VK-PDIIVYIDISPETALKRLRKKSQR----YENM--VFLRKVKnAYSRVLHDFRRVVVVDGEQPVDAVAETIVEKL 189
                                       44.789********************6....3333..33444443666888888999999999999*******9987 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   2.7e-05     0.024       8      62 ..       6      55 ..       4      91 .. 0.82
   2 ?    1.3   0.0      0.43   3.8e+02      86     113 ..     159     190 ..      98     195 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.7e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl.lrellr 62
                                      ++v G  G+GKTt ++ l+++l+++      + +v+ v  p +++   l +++l++
  gi|557693566|ref|YP_008796620.1|  6 IAVEGIDGAGKTTQAKLLARKLTRH------GFRVMNVHEPTDGKIGGLiREALAK 55
                                      67899*****************876......9999999999999888884555555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.43
                            AAA_22  86 lrarav...ielliiDEaqhlr..seealeeLr 113
                                        ++      ++++++D  q ++   e+++e+L+
  gi|557693566|ref|YP_008796620.1| 159 YSRV-LhdfRRVVVVDGEQPVDavAETIVEKLS 190
                                       2222.1346678888887777544466666664 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.9e-05     0.035       3      36 ..       4      37 ..       2      80 .. 0.76
   2 ?   -3.0   0.0       6.6   5.9e+03     103     117 ..     124     138 ..     107     149 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.9e-05
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylL 36
                                      + + + G+ g+GK+t a+ l++kL+++g +v+ +
  gi|557693566|ref|YP_008796620.1|  4 FYIAVEGIDGAGKTTQAKLLARKLTRHGFRVMNV 37
                                      567789**********************988765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 6.6
                                       EEEEEE--HHHHHHH CS
                        APS_kinase 103 ievfvdtplevceer 117
                                       i v++d++ e++ +r
  gi|557693566|ref|YP_008796620.1| 124 IIVYIDISPETALKR 138
                                       445666655555544 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.8e-05     0.043       3      33 ..       5      35 ..       3      39 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.8e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EE CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvl 33
                                      +i++ G+ GaGKTt +  La++l+++g +v+
  gi|557693566|ref|YP_008796620.1|  5 YIAVEGIDGAGKTTQAKLLARKLTRHGFRVM 35
                                      68899********************999886 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   5.2e-05     0.047      27     154 ..       6     185 ..       4     194 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.2e-05
                            AAA_16  27 vllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawreklee 103
                                       + + G  G GK++ ++ l+r l+++g+ +++ +            +  ++ r e l++  +++e+ ++  +++  ++
  gi|557693566|ref|YP_008796620.1|   6 IAVEGIDGAGKTTQAKLLARKLTRHGFRVMNVHEPTD------GKIGGLI-R-EALAKRVNMSEEVLALLFAADRLT 74 
                                       5688999******************999988877777......2355555.5.333333333333222222222221 PP

                            AAA_16 104 ala.........................................................avpelagaea....srl 119
                                         +                                                         a + l+ ++       +
  gi|557693566|ref|YP_008796620.1|  75 LREkivsakqsgvyvvsdrsvvsslayqsaalglrnwvyevnrfavkpdiivyidispetALKRLRKKSQryenMVF 151
                                       11134466667777777777777777777777788888888888888888777776655544444444336666777 PP

                            AAA_16 120 lellkrllallsrderplvlvlDdlqwadeaslql 154
                                       l+++k++ ++  +d r  v+v+D  q +d+   ++
  gi|557693566|ref|YP_008796620.1| 152 LRKVKNAYSRVLHDFR-RVVVVDGEQPVDAVAETI 185
                                       7777777744444466.777777777666655555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1    0.0001     0.091      12      91 ..      13      97 ..       6     167 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt..glgi.ekneiektlyevl.i.eeknikeaiiktkvenldlip 85
                                      G GKTT++  la  l++ g +v+ v   + +      +  + ++ +++++++ +l + ++ +++e i+++k++ ++++ 
  gi|557693566|ref|YP_008796620.1| 13 GAGKTTQAKLLARKLTRHGFRVMNVHEPTDGKIGGliREALaKRVNMSEEVLALLfAaDRLTLREKIVSAKQSGVYVVS 91
                                      89*********************99765555444311222213444555666665424777777777777666666665 PP

                            AAA_31 86 ssidLa 91
                                          ++
  gi|557693566|ref|YP_008796620.1| 92 DRSVVS 97
                                      554444 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 ?   14.1   0.1   5.2e-05     0.047       3      35 ..       8      41 ..       6     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.2e-05
                                      EESSTTSSHHHHHHHHHHHHTHE.EEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakelgve.fleisgsell 35
                                      + G  G GKT+ ak +a++l ++ f  ++++e +
  gi|557693566|ref|YP_008796620.1|  8 VEGIDGAGKTTQAKLLARKLTRHgFRVMNVHEPT 41
                                      56899**************964424444554444 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 ?   12.5   0.0   0.00013      0.12       9      31 ..      13      35 ..       6      42 .. 0.90
   2 ?   -1.7   0.0       3.1   2.7e+03     108     108 ..     150     150 ..      94     188 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                      TSSHHHHHHHHHHHHHHTT--EE CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  9 GvGKTtlaanLaralarrglrVl 31
                                      G+GKTt a  Lar l r+g+rV 
  gi|557693566|ref|YP_008796620.1| 13 GAGKTTQAKLLARKLTRHGFRVM 35
                                      89*******************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                                       E CS
                                       x RF
                              CbiA 108 v 108
                                       v
  gi|557693566|ref|YP_008796620.1| 150 V 150
                                       1 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 ?   11.9   0.0     9e-05      0.08      31      76 ..       5      49 ..       2      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9e-05
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----------- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavDPsspftGGsi 76
                                       + + G+ GaGk t  + l+ +l+r+G rv  +  +P+    GG i
  gi|557693566|ref|YP_008796620.1|  5 YIAVEGIDGAGKTTQAKLLARKLTRHGFRVMNVH-EPTDGKIGGLI 49
                                      57899************************97653.78888888876 PP

>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00063      0.57      34      70 ..       6      42 ..       2      47 .. 0.92
   2 ?    0.4   0.0      0.43   3.8e+02     140     157 ..     126     143 ..     111     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00063
                                      EEEEESTTS-HHHHHHHHHTTS-GGG-EEEE--S--H CS
                              PPK2 34 vifegrDaAGKgGaikrvtealnprvarvvalkaPte 70
                                      +  eg D+AGK    k +  +l + + rv+ +++Pt+
  gi|557693566|ref|YP_008796620.1|  6 IAVEGIDGAGKTTQAKLLARKLTRHGFRVMNVHEPTD 42
                                      5689********************************8 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.43
                                       EEEE--HHHHHHHHHHHH CS
                              PPK2 140 fwlsiskeeqleRfkeRr 157
                                       ++++is+e+ l+R++++ 
  gi|557693566|ref|YP_008796620.1| 126 VYIDISPETALKRLRKKS 143
                                       699**********98875 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00018      0.17      21      50 ..       6      35 ..       2     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                            AAA_30 21 avltGpAGtGKttalkalreaweaaggrvi 50
                                       +++G  G+GKtt  k l++ ++++g+rv+
  gi|557693566|ref|YP_008796620.1|  6 IAVEGIDGAGKTTQAKLLARKLTRHGFRVM 35
                                      5799**********************9997 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.019        17       3      21 ..      10      28 ..       8      74 .. 0.84
   2 ?    5.6   0.1     0.017        15      97     132 ..     116     189 ..     109     197 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.019
                                      ESTTSSHHHHHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxxxx RF
                               ADK  3 GaPgaGKGtqaeklvkkyg 21
                                      G  gaGK tqa+ l++k++
  gi|557693566|ref|YP_008796620.1| 10 GIDGAGKTTQAKLLARKLT 28
                                      788**********999865 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
                                       HHHTSEESEEEEEE--HHHHHHHHHT......................................GSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx......................................xxxxxxxxxx RF
                               ADK  97 eeekvkldlvleldvpeevlveRltg......................................DneetvkkRl 132
                                       ++ +vk d+++++d++ e+ ++Rl +                                        +et+ ++l
  gi|557693566|ref|YP_008796620.1| 116 NRFAVKPDIIVYIDISPETALKRLRKksqryenmvflrkvknaysrvlhdfrrvvvvdgeqpvdAVAETIVEKL 189
                                       5667899*****************99888887777777777777777777777777766655533455555555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0     0.001      0.91       5      47 ..       6      46 ..       2      77 .. 0.77
   2 ?    0.5   0.0      0.66   5.9e+02      28      51 ..     120     147 ..     108     192 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                            AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla 47
                                      ++++G+  +GKTt +k l+++l   +  +  +n+ +++d k+ 
  gi|557693566|ref|YP_008796620.1|  6 IAVEGIDGAGKTTQAKLLARKLT--RHGFRVMNVHEPTDGKIG 46
                                      7899***************9988..888888999998885544 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.66
                            AAA_14  28 vkkesilyinldderdkkladpe....k 51 
                                       vk++ i+yi++  e+  k+  ++    +
  gi|557693566|ref|YP_008796620.1| 120 VKPDIIVYIDISPETALKRLRKKsqryE 147
                                       6777788888877766442221112221 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       1.3   1.2e+03      23      39 ..      77      92 ..      56      98 .. 0.71
   2 ?    6.2   1.2     0.016        14       7      35 ..     167     195 ..     114     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.3
                                      HHHHHHTSSEEEEEETT CS
                               CBS 23 elmrekgvsrlPVVded 39
                                      e++++++ s+++VV  d
  gi|557693566|ref|YP_008796620.1| 77 EKIVSAKQSGVYVVS-D 92
                                      445556679999993.3 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.016
                                       SSCEEEETTSBHHHHHHHHHHHTSSEE.EE CS
                               CBS   7 rdvvtvppdttleealelmrekgvsrl.PV 35 
                                       r+vv+v+ ++++  ++e+++ek +sr+ PV
  gi|557693566|ref|YP_008796620.1| 167 RRVVVVDGEQPVDAVAETIVEK-LSRFiPV 195
                                       6789999999999999997543.8888787 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); 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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1409.58
//
Query:       gi|557693567|ref|YP_008796621.1|  [L=563]
Description: dihydroxy-acid dehydratase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-214  711.0   0.2   8.9e-214  710.9   0.2    1.0  1  ILVD_EDD   Dehydratase family
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.31   11.0   0.0    1.7  1  GreA_GreB  Transcription elongation factor, GreA/GreB, C-term
       0.17   11.8   0.0       0.46   10.4   0.0    1.7  1  HTH_25     Helix-turn-helix domain
        0.2   11.6   0.2        1.5    8.8   0.0    2.4  3  TP1        Nuclear transition protein 1


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 !  710.9   0.2    2e-217  8.9e-214       1     517 []      43     560 ..      43     560 .. 0.98

  Alignments for each domain:
  == domain 1  score: 710.9 bits;  conditional E-value: 2e-217
                          ILVD_EDD   1 kpiigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmlea 77 
                                       kp+ig++++ +e++pc+ hl +la+++++gv+e++gv++ef+ti+vsDgi+m++egm+ sL+sRe+iads+e  + a
  gi|557693567|ref|YP_008796621.1|  43 KPFIGVVSTGNEVTPCNLHLTDLAKEARRGVWENNGVGIEFTTIAVSDGISMNTEGMKGSLVSREVIADSIELECFA 119
                                       8**************************************************************************** PP

                          ILVD_EDD  78 qllDalvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaa 152
                                       +++D+lv i+gCDK++Pg++ma+arlniP++f++gG++++gk+   ++++++v+eavg++++g+++ ++l ele+ a
  gi|557693567|ref|YP_008796621.1| 120 ERFDGLVGIAGCDKSLPGTVMAMARLNIPSVFLYGGTILPGKYMgrDVTIQDVYEAVGSYSTGQMTLQQLVELERVA 196
                                       ****************************************99666699***************************** PP

                          ILVD_EDD 153 cpgaGsCsgmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvl 229
                                       cp+ GsC+g++TAntma+++ealG+slpg+asipa++++  + a+++g+++++l+e+ +kprdi+t eafeNAi+v+
  gi|557693567|ref|YP_008796621.1| 197 CPTEGSCAGLYTANTMASAIEALGMSLPGTASIPAVDQRIYDAAYRSGAQVLKLLENGIKPRDIMTYEAFENAITVV 273
                                       ***************************************************************************** PP

                          ILVD_EDD 230 lalGGStNavlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvl 306
                                       +a+GGStN+vlHl+A+A eagv+l++d fd++sr++p++a+++P g++ m dl+r+GGvp+vlk+Ll+agllhgd+l
  gi|557693567|ref|YP_008796621.1| 274 CAMGGSTNSVLHLPAMAYEAGVKLDIDVFDKISRRTPHIADMRPGGRFVMVDLDRVGGVPVVLKKLLDAGLLHGDCL 350
                                       ***************************************************************************** PP

                          ILVD_EDD 307 tvtgktlaenleeaev.keqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseeeave 382
                                       tvtgktlaenl+e ++ +  +v+rpl++p++++gg+a+LkGnLapeG vvK +a +  +  f+gpArvf+seeea++
  gi|557693567|ref|YP_008796621.1| 351 TVTGKTLAENLREMRIgDGGEVVRPLSNPIHPTGGIAILKGNLAPEGGVVKSTASA--VQYFKGPARVFNSEEEAYR 425
                                       ***********995544899**********************************99..8889*************** PP

                          ILVD_EDD 383 ailkgkikagdvvviryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpial 459
                                       a+lk++i++gdv+viryeGPkGgpGm+Eml++t+ ++g+gl++kval+tDGRfSGa++gl++ghvsPEAa+gGpia 
  gi|557693567|ref|YP_008796621.1| 426 ALLKRQIQPGDVIVIRYEGPKGGPGMREMLAVTAIVVGQGLKEKVALLTDGRFSGATHGLMVGHVSPEAAVGGPIAA 502
                                       ***************************************************************************** PP

                          ILVD_EDD 460 vedGDiieidiekrtlelevseeelaaRraawkpekkvktrgllakyaklvssaseGA 517
                                       ++dGDi+eid+++r+l++e+s+ee+++R ++w+p + ++trg+lakyaklv sas+GA
  gi|557693567|ref|YP_008796621.1| 503 LKDGDIVEIDVPNRKLSVELSDEEIRKRMENWTPPPPKYTRGVLAKYAKLVGSASRGA 560
                                       **********************************555556*****************8 PP

>> GreA_GreB  Transcription elongation factor, GreA/GreB, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0     7e-05      0.31      38      72 ..     488     522 ..     457     525 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7e-05
                                       SB--TTSHHHHHHTT--TT-EE---BTTB---EEE CS
                         GreA_GreB  38 gkiSveSPlGkaLlgkkvGdevevkapsgkikveI 72 
                                       g++S+e+ +G  +   k Gd ve+++p+ k++ve 
  gi|557693567|ref|YP_008796621.1| 488 GHVSPEAAVGGPIAALKDGDIVEIDVPNRKLSVEL 522
                                       699*************************9999885 PP

>> HTH_25  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    0.0001      0.46      39      56 ..     537     554 ..     532     558 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0001
                                       S-HHHHHHHHHHHHHHTT CS
                            HTH_25  39 pepvylrgylrnYArlLg 56 
                                       p+p y+rg l +YA+l+g
  gi|557693567|ref|YP_008796621.1| 537 PPPKYTRGVLAKYAKLVG 554
                                       7899************98 PP

>> TP1  Nuclear transition protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00033       1.5       3      25 ..      10      32 ..       8      38 .. 0.88
   2 ?   -2.1   0.0      0.87   3.9e+03      34      42 ..     100     108 ..      97     112 .. 0.80
   3 ?   -1.9   0.0      0.72   3.2e+03      16      35 ..     392     412 ..     390     420 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00033
                               TP1  3 srklkshGmrrGknraPhkGvkr 25
                                       r+l sh +  G  raPh+ + r
  gi|557693567|ref|YP_008796621.1| 10 VRRLYSHEVTEGPERAPHRAMLR 32
                                      599***************98776 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.87
                               TP1  34 kGslksrkr 42 
                                       kGsl sr  
  gi|557693567|ref|YP_008796621.1| 100 KGSLVSREV 108
                                       9*****975 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.72
                               TP1  16 nraPhkGv.krGGskrkyrkG 35 
                                       n aP  Gv k   s  +y kG
  gi|557693567|ref|YP_008796621.1| 392 NLAPEGGVvKSTASAVQYFKG 412
                                       779999963778899999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (563 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:                        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 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3975.94
//
Query:       gi|557693568|ref|YP_008796622.1|  [L=93]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-31  107.2   3.1    3.6e-31  107.1   3.1    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)
  ------ inclusion threshold ------
       0.11   12.5   0.9        3.2    7.7   0.1    2.1  2  PBECR3    phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease3


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 !  107.1   3.1     4e-35   3.6e-31       3      81 .]      10      88 ..       8      88 .. 0.98

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 4e-35
                                      HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHH CS
                           UPF0147  3 ekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEti 81
                                      +k ++v+++Le+ii+d ++PrniRr ak+a ++L +ek ++avraa++i++++ei nDpnmP+++Rt++w+ +s LEti
  gi|557693568|ref|YP_008796622.1| 10 SKRQQVVQILETIINDADTPRNIRRIAKQASTELFNEKLRPAVRAANSIELIEEIINDPNMPSFTRTQLWMAISILETI 88
                                      6789*************************************************************************98 PP

>> PBECR3  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1    0.0028        25      44      65 ..       9      29 ..       4      47 .. 0.77
   2 ?    7.7   0.1   0.00036       3.2      31      63 ..      32      69 ..      28      77 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0028
                            PBECR3 44 ekdrgqidianipdiiknPDkv 65
                                      e +r+q+  + ++ ii+++D  
  gi|557693568|ref|YP_008796622.1|  9 ESKRQQV-VQILETIINDADTP 29
                                      5678999.9***********54 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00036
                            PBECR3 31 ikHilkrH.....gnqstekdrgqidianipdiiknPD 63
                                      i+ i k+       +++ ++ r+   i+ i++ii++P+
  gi|557693568|ref|YP_008796622.1| 32 IRRIAKQAstelfNEKLRPAVRAANSIELIEEIINDPN 69
                                      55555555322222233344444449***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 687.16
//
Query:       gi|557693569|ref|YP_008796623.1|  [L=465]
Description: citrate transporter [Candidatus Caldiarchaeum subterraneum]
Scores for 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-30  104.4  40.8    6.3e-30  104.4  40.8    1.7  2  CitMHS    Citrate transporter
    3.5e-05   23.3  31.3    0.00034   20.1  31.3    2.1  1  ArsB      Arsenical pump membrane protein


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 !  104.4  40.8     7e-34   6.3e-30       9     299 ..      50     402 ..      23     403 .. 0.74
   2 ?   -2.6   0.6      0.27   2.4e+03      80      97 ..     441     455 ..     404     464 .. 0.38

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 7e-34
                                       xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                            CitMHS   9 lrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd.llvllvl 80 
                                       + + v a+++l+l+    +l+ie +++    ++il+l+ +m+++++lee+ +f++++++l  + g++++ ++v++++
  gi|557693569|ref|YP_008796623.1|  50 RFRLVFAFFALALMlgtdLLEIELLIKFAHLDTILFLASMMVVVGYLEEARFFEYVIDRLQAIIGNRPRaMVVFFMA 126
                                       44555566666666799************************************************************ PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxx RF
                            CitMHS  81 ltallsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraa........arpglslp 149
                                       ++a+l+a+v+ ++ +lim++++l+   r + +p++++i+ ++a nig+++t +G+p  +++        a++ ++++
  gi|557693569|ref|YP_008796623.1| 127 MSAMLAALVDEVTSILIMTAVLLDFTSRYNLNPVRFIILSIFATNIGSSATVVGNPVGVMIafqaqlgfADFLRWAT 203
                                       ****************************9999999*********************888889999999966666666 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxx............ RF
                            CitMHS 150 nllllalllvgllplvllfmfgvalalpvnap..............kvkkqkaiieaiarsllpv............ 200
                                        + +  l+l +ll lv++       + + n                +                 +            
  gi|557693569|ref|YP_008796623.1| 204 PISIGSLILCILLSLVIFR------KDIANLSqamtsesgvkiaamE-----------------Kadgghrvdirlp 257
                                       6666555555443333333......1111111122223333333332.................0333333333333 PP

                                       .....xxxxxxx........................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 201 .....atillla........................................ykkveWsvlllfaGvfllvgaleqt 232
                                            atil l+                                          +++W +ll+f   f  vg l++t
  gi|557693569|ref|YP_008796623.1| 258 aaiflATILGLIlhtpieqalglgknamllgvpflfagivllmererarelvETRIDWWTLLFFMIFFASVGTLSHT 334
                                       33333333333344444444444444444444444444444459*******999*********************** PP

                                       xxxxxxxxxx.xx.xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                            CitMHS 233 Gilealadll.ga.ggplvalalv.lgliallsafisnvavaalmapialgmap.algllspsplalalav 299
                                       G  + +a+l+  + g  +++l+++ +++ +l+saf++nv ++a+ +pi+ ++   +   +++ pl++++++
  gi|557693569|ref|YP_008796623.1| 335 GATQVFANLIlANaGDSITTLSIFvMIVAGLMSAFMDNVLAVATWIPIIKTLGEfG---VNVFPLWWTMLF 402
                                       *999999999655654446675553788888********************76643...67*******987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.27
                                       xxxxxxxxxxxxxxxxxx RF
                            CitMHS  80 lltallsafvsndgvvli 97 
                                       +++a+  + v   +++li
  gi|557693569|ref|YP_008796623.1| 441 VGAAITLPTV---ATALI 455
                                       1111111111...22222 PP

>> ArsB  Arsenical pump membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1  31.3   3.8e-08   0.00034      55     421 ..      82     459 ..      56     461 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.8e-08
                              ArsB  55 tlafva.iilislildnigffewaalhmakaakgygvrmfvyvsllgaivaalfandgaaliltpivlamvralhfn 130
                                       t+ f+a ++++   l++  ffe+   ++          m+v+   + a++aal+ +  + li+t ++l +     +n
  gi|557693569|ref|YP_008796623.1|  82 TILFLAsMMVVVGYLEEARFFEYVIDRLQAIIGNRPRAMVVFFMAMSAMLAALVDEVTSILIMTAVLLDFTSRYNLN 158
                                       555665145566689********988876666666677999****************************99887777 PP

                              ArsB 131 eklvfpfiiasgfiadttslpfvvsnlvnivsadyfhitfidyasrmvvpylfsllasiivlylffrksipkrydlt 207
                                           + fii s f ++  s   vv n v ++ a   ++ f d+        + sl+  i++  ++frk i +  +  
  gi|557693569|ref|YP_008796623.1| 159 P---VRFIILSIFATNIGSSATVVGNPVGVMIAFQAQLGFADFLRWATPISIGSLILCILLSLVIFRKDIANLSQAM 232
                                       5...589************************************866665567899999999999******9876544 PP

                              ArsB 208 ..evkkpveai.kdqnmfrlswyilgllligyfaseffsipv......svvagsiaiifliaaqk..spavhtkkvv 273
                                         e    + a+ k +   r+   +   +++  +   ++  p+         a  + + fl a         +++++v
  gi|557693569|ref|YP_008796623.1| 233 tsESGVKIAAMeKADGGHRVDIRLPAAIFLATILGLILHTPIeqalglGKNAMLLGVPFLFAGIVllMERERARELV 309
                                       01433444454233344454444433333333333333333310000022333344445555433113333445555 PP

                              ArsB 274 ke..apwaivffsigmyvvvygvrnagltdvlsdviqaaadqglfagtigmgfiaailssimnnlptvmidalaiag 348
                                       +     w+++ff i ++  v  +  +g t+v++++i a a + + + +i + ++a ++s+ m+n+ +v      i  
  gi|557693569|ref|YP_008796623.1| 310 ETriDWWTLLFFMI-FFASVGTLSHTGATQVFANLILANAGDSITTLSIFVMIVAGLMSAFMDNVLAVATWIPIIKT 385
                                       43114567777766.78889999*********************************************999999999 PP

                              ArsB 349 tdthgmmrealiyanvigsdlgpkitpigslatllwlhvlshk.gmkiswgtyfktgiiltiptllitlvglyi 421
                                          +g+    l ++ +    +  ++t igs a ++ + +l ++  ++i+   ++  g  +t+pt+  +l+ + i
  gi|557693569|ref|YP_008796623.1| 386 LGEFGVNVFPLWWTMLFAGTFWGNLTVIGSTANIVAVGMLERReRIHITLRQWIGVGAAITLPTVATALILIVI 459
                                       999**************999*9*****************98762699*****************9998887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); 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):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3393.86
//
Query:       gi|557693570|ref|YP_008796624.1|  [L=276]
Description: chorismate mutase / prephenate dehydratase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-63  213.0   0.1    3.8e-63  212.6   0.1    1.1  1  PDT       Prephenate dehydratase
    1.6e-11   43.7   0.0      3e-11   42.9   0.0    1.5  1  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 !  212.6   0.1   4.2e-67   3.8e-63       1     182 [.       5     182 ..       5     183 .. 0.99

  Alignments for each domain:
  == domain 1  score: 212.6 bits;  conditional E-value: 4.2e-67
                                       EEEES-TTSHHHHHHCCCS.....EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEE CS
                               PDT   1 vaylGpegtyshqAalkvfkaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivgE 77 
                                       va++G++g+ys++A+ ++f +e+v+++p++si++vf+++e + +dy+vvP+ENs+eGsV et+D++l+ s++k vgE
  gi|557693570|ref|YP_008796624.1|   5 VAFQGEKGAYSEEAIFHFF-GENVQTMPCKSIRDVFKNCEARVVDYGVVPVENSIEGSVFETYDMFLS-SSVKAVGE 79 
                                       89*****************.************************************************.99****** PP

                                       EEEE---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHH CS
                               PDT  78 vvlpiehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaae 154
                                       ++l+i+hcL+a p+ +l+e+++vyShpqal+Qcr +L++   +v+++ +++ta ++k+++++  ++aaa+ase+aae
  gi|557693570|ref|YP_008796624.1|  80 IILRIRHCLIALPDVSLSEVETVYSHPQALAQCRGYLQSL--GVSVEVTYDTAGSVKMIKERGLRNAAAVASERAAE 154
                                       ****************************************..*********************************** PP

                                       HTT-EEEECS-SS-S--EEEEEEEEETT CS
                               PDT 155 lyglkvleeniedkknntTRFlvlakee 182
                                       +yg+k+l++ ied+ +n+TRFlv++ +e
  gi|557693570|ref|YP_008796624.1| 155 IYGMKILAKGIEDYGHNYTRFLVISVKE 182
                                       ************************9765 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   3.4e-15     3e-11       2      65 ..     192     255 ..     191     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 3.4e-15
                                       EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT   2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkkl 65 
                                       +++++ + +PG+L   +ga+a++giN+++ie+r+++ + ++++f+v+ +++++ e+v++al +l
  gi|557693570|ref|YP_008796624.1| 192 SIIFSTAHKPGALYNALGAFARNGINLTKIESRPTRQRPWEYYFFVDFEGHQEEEHVKKALAEL 255
                                       78899999*****************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2200.04
//
Query:       gi|557693571|ref|YP_008796625.1|  [L=299]
Description: 6-phosphogluconate dehydrogenase NAD-binding [Candidatus Caldiarchaeum subterraneum]
Scores for 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-54  181.8   0.3    1.7e-53  181.0   0.3    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    1.6e-32  112.3   0.0    3.4e-32  111.2   0.0    1.5  1  NAD_binding_11   NAD-binding of NADP-dependent 3-hydroxyisobu
    2.5e-06   27.0   0.1    5.6e-06   25.8   0.0    1.6  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    4.1e-06   27.3   0.0    9.7e-06   26.1   0.0    1.6  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    0.00012   21.7   0.0    0.00021   20.9   0.0    1.4  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
    0.00019   21.5   0.0    0.00032   20.8   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.032   14.1   0.0    1.6  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.027   14.7   0.0       0.24   11.7   0.0    2.2  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.049   13.2   0.0        5.6    6.5   0.0    2.4  2  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family


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 !  181.0   0.3   8.4e-57   1.7e-53       1     158 []       3     162 ..       3     163 .. 0.98

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 8.4e-57
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.. CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.. 75 
                                       ++gfiGlG MG++ma+nll++g+k+av+nr+++ +eel++ ga+a++s++e+++s ++vitm++++kav++v+ g  
  gi|557693571|ref|YP_008796625.1|   3 RVGFIGLGLMGKPMAKNLLRRGFKLAVFNRSRSPMEELASLGATACSSPKEVTESSECVITMLPDEKAVEQVLLGrn 79 
                                       58*************************************************************************** PP

                                       .HCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHHHHEE CS
                     NAD_binding_2  76 .llealkkgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvleaiga 151
                                        +le l kg +++d+st+sp  +re+a++++e+g ++ldaPVSG++  Ae+GtL+imvGG+ e fe+++p++ea+g+
  gi|557693571|ref|YP_008796625.1|  80 gVLEGLTKGGVVVDMSTVSPGFSREMARRVEERGGEMLDAPVSGSTMAAEQGTLTIMVGGKPEIFEQIRPIFEAMGK 156
                                       ***************************************************************************** PP

                                       EEEEE-E CS
                     NAD_binding_2 152 kvthviG 158
                                       +++ ++G
  gi|557693571|ref|YP_008796625.1| 157 NIY-YMG 162
                                       **9.556 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 !  111.2   0.0   1.7e-35   3.4e-32       1     122 []     165     285 ..     165     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.2 bits;  conditional E-value: 1.7e-35
                    NAD_binding_11   1 GaGqavKlvnnlllainlaaasEalvlaekaGldpekvlevinassgrsnalenklpqrvlsrdfdpgFaldlmlKD 77 
                                       G+G+ +Kl+n++ + +nl+ ++E l++a+kaGld++kv+evi++++g+s+ l++  p r++ rdf+pgF++++++KD
  gi|557693571|ref|YP_008796625.1| 165 GSGSFTKLCNQVAVSLNLLGVCETLMIAAKAGLDLKKVIEVISTGAGGSWQLSTLGP-RMVVRDFRPGFKVKHLRKD 240
                                       99*******************************************************.8999*************** PP

                    NAD_binding_11  78 lglalelareagaplpllalaeqlyaaaaaegggdaDhsaivrll 122
                                       l+++ e+ +++g+ lp +al+++l++++++ g+g++  +a+v++l
  gi|557693571|ref|YP_008796625.1| 241 LRIVRETTESLGLCLPGVALVSELVKTLDEMGHGENGTQALVEVL 285
                                       ***************************************999875 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 !   25.8   0.0   2.8e-09   5.6e-06      38     109 ..       3      75 ..       1      96 [. 0.84
   2 ?   -2.2   0.0       1.1   2.2e+03      32      66 ..     128     162 ..     104     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.8e-09
                                       EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S--STTTTTSB CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv.sleellaesDivslhlpltpetrhli 109
                                       +vG iGlG +G+ +ak l   g+k+ +++rs+++ ee ++lg++ + s +e+ ++s++v+ +lp +++ ++++
  gi|557693571|ref|YP_008796625.1|   3 RVGFIGLGLMGKPMAKNLLRRGFKLAVFNRSRSPMEELASLGATACsSPKEVTESSECVITMLPDEKAVEQVL 75 
                                       89*****************************************55559****************998877654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                       S-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEES CS
                      2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkafgmkviayd 66 
                                        e    t+ + G  +I +++  +++a+g +++++ 
  gi|557693571|ref|YP_008796625.1| 128 AEQGTLTIMVGGKPEIFEQIRPIFEAMGKNIYYMG 162
                                       45555566666777788888888999998888875 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 !   26.1   0.0   4.9e-09   9.7e-06       1      94 [.       3      94 ..       3      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 4.9e-09
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHH.HHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedv.eevl 78
                                      ++g+iG G mg+ +a++ll++g    ++ v  +r+ + +eela+ lg+++++ + +e+ e+++ v+  ++ e++ e+vl
  gi|557693571|ref|YP_008796625.1|  3 RVGFIGLGLMGKPMAKNLLRRG---FKLAVF-NRSRSPMEELAS-LGATACS-SPKEVTESSECVITMLPDEKAvEQVL 75
                                      69********************...999966.**********76.5889999.9************9999876515555 PP

                                      HHC...GHHHHTTSEEEEE CS
                     F420_oxidored 79 sel...akdalkgklvisv 94
                                             + + kg +v+++
  gi|557693571|ref|YP_008796625.1| 76 LGRngvLEGLTKGGVVVDM 94
                                      3334556667777777765 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 !   20.9   0.0   1.1e-07   0.00021       6      73 ..       3      70 ..       1      97 [. 0.88

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-07
                                      -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHH CS
                              IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelq 73
                                      ++  iG G  G+  a+nl   g++++v +r+ s   + A+  +    + +e++++++ v++++PDe  
  gi|557693571|ref|YP_008796625.1|  3 RVGFIGLGLMGKPMAKNLLRRGFKLAVFNRSRSPMEELASLGATACSSPKEVTESSECVITMLPDEKA 70
                                      6889*************************************************************975 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.6e-07   0.00032      13      57 ..       2      45 ..       1      73 [. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.6e-07
                                      -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT CS
                      Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelk 57
                                      ++v  iG G m++ +ak+Ll++g+k ++v+NR+++ ++ela+   
  gi|557693571|ref|YP_008796625.1|  2 ERVGFIGLGLMGKPMAKNLLRRGFK-LAVFNRSRSPMEELASLGA 45
                                      58999*******************9.**************97554 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 ?   14.1   0.0   1.6e-05     0.032       2      38 ..       4      40 ..       3      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealeka 38
                                      v+ iG G+mG+ +a+ ++++g++  ++++s++ +e+ 
  gi|557693571|ref|YP_008796625.1|  4 VGFIGLGLMGKPMAKNLLRRGFKLAVFNRSRSPMEEL 40
                                      899************************9988777664 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 ?   11.7   0.0   0.00012      0.24       1      98 [.       4     118 ..       4     136 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.............TTTCEEEEE--TTTHHHHH. CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.............lgvrfeaialdaenyeavL. 63 
                                       v +iG G +G+++a+ l+r++ +  +++v  rs++ +e+la+ +             +++ ++++  d + +e+vL 
  gi|557693571|ref|YP_008796625.1|   4 VGFIGLGLMGKPMAKNLLRRG-F--KLAVFNRSRSPMEELAS-LgatacsspkevteSSECVITMLPDEKAVEQVLl 76 
                                       578****************98.5..7**********999975.4466677776666533344444444444444432 PP

                                       .....HHHHTTSSEEEE-SSGG..GHHHHHHHHHHHT-EEEE CS
                   Sacchrp_dh_NADP  64 .....aallkegdlvvnlsppi..ssldvlkaCietgvhyvd 98 
                                             + l++g++vv++s+    +s+++++   e+g  ++d
  gi|557693571|ref|YP_008796625.1|  77 grngvLEGLTKGGVVVDMSTVSpgFSREMARRVEERGGEMLD 118
                                       211111234455666666666666666666666666666666 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 ?    4.3   0.0     0.013        25       2      39 ..       3      40 ..       2      48 .. 0.85
   2 ?    6.5   0.0    0.0028       5.6     106     139 ..      80     113 ..      60     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.013
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHH CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdkl 39
                                      ++ +iGlG +G ++a  l ++g+++ +   +++  ++l
  gi|557693571|ref|YP_008796625.1|  3 RVGFIGLGLMGKPMAKNLLRRGFKLAVFNRSRSPMEEL 40
                                      7999*******************998887777666665 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0028
                                       HHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHH CS
                    UDPG_MGDP_dh_N 106 siaealkkgkvvvvkSTvpvgtaeelvkkileea 139
                                        + e l kg vvv  STv +g  +e+++++ e+ 
  gi|557693571|ref|YP_008796625.1|  80 GVLEGLTKGGVVVDMSTVSPGFSREMARRVEERG 113
                                       56788999*************9998887766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2065.58
//
Query:       gi|557693572|ref|YP_008796626.1|  [L=231]
Description: hypothetical protein CSUB_C0133 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.2   0.2         14    6.2   0.0    2.8  3  MCM_lid   MCM AAA-lid domain


Domain annotation for each model (and alignments):
>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0    0.0042        76      44      61 ..      10      27 ..       1      28 [. 0.79
   2 ?   -1.4   0.0      0.18   3.3e+03       2      19 ..      70      88 ..      67      94 .. 0.65
   3 ?    6.2   0.0    0.0008        14      46      62 ..     128     144 ..     112     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0042
                                      SST--HHHHHHHHHHHHH CS
                           MCM_lid 44 sipitvRqLesliRLseA 61
                                       +p+ v  L sl+RL+ +
  gi|557693572|ref|YP_008796626.1| 10 PVPVRVEDLSSLVRLASS 27
                                      57888889*******987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.18
                                      HHHHHHHH.HHHTT--BET CS
                           MCM_lid  2 llrkYiay.arekikPkls 19
                                      l++kY+ y a ek + +ls
  gi|557693572|ref|YP_008796626.1| 70 LVKKYVVYtALEKEETRLS 88
                                      7899998833444445555 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0008
                                       T--HHHHHHHHHHHHHH CS
                           MCM_lid  46 pitvRqLesliRLseAl 62 
                                       +i vR+L+s++RL  A+
  gi|557693572|ref|YP_008796626.1| 128 KIKVRALDSIMRLVSAM 144
                                       799**********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1813.46
//
Query:       gi|557693573|ref|YP_008796627.1|  [L=49]
Description: CopG/Arc/MetJ family transcriptional regulator [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   34.1   0.1    1.9e-08   33.9   0.1    1.1  1  RHH_1     Ribbon-helix-helix protein, copG family
    0.00054   20.1   0.0    0.00054   20.1   0.0    1.0  1  RHH_8     Ribbon-Helix-Helix transcriptional regulator 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 !   33.9   0.1   2.2e-12   1.9e-08       2      38 ..       4      41 ..       3      42 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.2e-12
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                      +s++++e l++  del++++  +SrS+l+R A+r++l 
  gi|557693573|ref|YP_008796627.1|  4 ISVKMPEALIDGMDELIKKGVyPSRSALMRTAVRDLLR 41
                                      8**********************************996 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 !   20.1   0.0   6.1e-08   0.00054      17      45 ..      15      43 ..       2      49 .] 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 6.1e-08
                             RHH_8 17 qiDlLveeGfYsnRtDlirtairaqLakh 45
                                       +D L+++G Y +R+ l+rta+r+ L+k+
  gi|557693573|ref|YP_008796627.1| 15 GMDELIKKGVYPSRSALMRTAVRDLLRKE 43
                                      6899********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 366.71
//
Query:       gi|557693574|ref|YP_008796628.1|  [L=551]
Description: thermosome subunit alpha [Candidatus Caldiarchaeum subterraneum]
Scores for 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-186  618.6  20.2   8.3e-186  618.4  20.2    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
       0.26   11.2   4.9        2.1    8.2   0.0    3.0  3  Dak2        DAK2 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 !  618.4  20.2  9.3e-190  8.3e-186       1     490 [.      38     528 ..      38     529 .. 0.98

  Alignments for each domain:
  == domain 1  score: 618.4 bits;  conditional E-value: 9.3e-190
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a+++k++lGP+GmdKmlv+++g++v+TnDGatilke+++ehP+ak+lve++++qdeevGDGTt++v+LageLl++a
  gi|557693574|ref|YP_008796628.1|  38 IAETMKSSLGPRGMDKMLVDSFGDIVITNDGATILKEMDVEHPVAKMLVEVSKAQDEEVGDGTTSTVVLAGELLTKA 114
                                       799************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       e+li+++vhpt+iiegy+ka+ kale+L+ei   ++++  +++ L+kva+ts+ skl+++ea++l++lvv+Av+ i 
  gi|557693574|ref|YP_008796628.1| 115 EELIEKEVHPTVIIEGYRKAAVKALEILDEI--GVKVDPTNKDLLKKVAKTSMISKLVAEEADYLADLVVEAVTRIA 189
                                       *******************************..88888889********************************6665 PP

                                       CCS...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                        Cpn60_TCP1 155 ene...keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                       e+     ++dl+ ik++k+eg+sl+d++l+eG+vldk+v++pdmpk ++nak++lld  Leiekte +++++++++e
  gi|557693574|ref|YP_008796628.1| 190 EKVgdkWTVDLDDIKLEKKEGQSLHDTKLIEGVVLDKEVVHPDMPKLVRNAKIALLDAALEIEKTEFDAKLNIESPE 266
                                       55569999********************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGG CS
                        Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledlt 305
                                       ++ +++k+ee++l++++eki+++g+nvv+cqkgiddla+ flak+g+la+rr+kk+d+++lakat+++++s+++dlt
  gi|557693574|ref|YP_008796628.1| 267 QMRAFMKQEEDMLRQMVEKIVSTGANVVLCQKGIDDLAQYFLAKKGVLAVRRIKKSDMDKLAKATKGRVISRIDDLT 343
                                       ***************************************************************************** PP

                                       CGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHH CS
                        Cpn60_TCP1 306 peelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatele 382
                                       pe+lG+a  vee+++g++k+++ie+++++++ til+rg t+ ++de+er+++dA+nvvk +i ++kv++GGGa+ele
  gi|557693574|ref|YP_008796628.1| 344 PEDLGKAALVEERRVGEDKMVFIEGCENPRSLTILIRGGTQRIVDEAERSLKDAINVVKDVIVEGKVIAGGGASELE 420
                                       ***************************************************************************** PP

                                       HHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTX CS
                        Cpn60_TCP1 383 lakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagv 459
                                        a +l++yak+++g+eqla+++fa+ALe+ip +Lae +G+dpie + +l+++h++g++++gi+v ++e  d+++  v
  gi|557693574|ref|YP_008796628.1| 421 TALRLRDYAKTLPGKEQLAVNKFAEALEAIPSQLAESCGMDPIEAIVNLTSKHKEGNINYGINVFKSELADMKQLDV 497
                                       ***************************************************************************** PP

                                       EEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 460 vDplkvkrqalksAteaastiLrideiikak 490
                                       +Dpl vk+q +ksA+eaa++iL+id+ii a 
  gi|557693574|ref|YP_008796628.1| 498 LDPLLVKKQTIKSAVEAAAMILKIDDIIAAS 528
                                       ****************************985 PP

>> Dak2  DAK2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       0.5   4.5e+03      26      51 ..      23      48 ..      14      48 .. 0.75
   2 ?    3.4   0.8    0.0072        65      26     136 ..      77     191 ..      64     195 .. 0.75
   3 ?    8.2   0.0   0.00023       2.1      14      94 ..     382     462 ..     377     466 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.5
                                      --SSHHHHHHHHHHHHHHH--STHHH CS
                              Dak2 26 eeaslaevlkalakallsgagGtsGv 51
                                      + ++++++   +ak+++++++++ G+
  gi|557693574|ref|YP_008796628.1| 23 RGREVQSANIMVAKIIAETMKSSLGP 48
                                      66777778888999999999999986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0072
                                       --SSHHHHHHHHHHHHHHH--..STHHHHHHHHHHHHHHHC........TT---HHHHHHHHHHHHHHHH---TTSS CS
                              Dak2  26 eeaslaevlkalakallsgag..GtsGvlysqflralakalkekee...ldaedlaaalkaaleaiqavgkarpgdk 97 
                                        e+ +a++l +++ka  +++g   ts v ++  l+  a++l eke    + +e   +a+ +ale + ++    ++d 
  gi|557693574|ref|YP_008796628.1|  77 VEHPVAKMLVEVSKAQDEEVGdgTTSTVVLAGELLTKAEELIEKEVhptVIIEGYRKAAVKALEILDEI--GVKVDP 151
                                       457889999999999988885435777777777777777776666656688888999999999999999..778888 PP

                                       STHHHHHHHHHHHHT............T---HHHHHHHHH CS
                              Dak2  98 TmlDvlrpavealekakd.gedlkealekaakaaekgaea 136
                                       T  D l++++++   +k   e+++ +++ +++a ++ ae+
  gi|557693574|ref|YP_008796628.1| 152 TNKDLLKKVAKTSMISKLvAEEADYLADLVVEAVTRIAEK 191
                                       8889999999998887777777777777777777777765 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHC---SSHHHHHHHHHHHHHHH--STHHHHHHHHHHHHHHHC.....TT---HHHHHHHHHHHHHHHH CS
                              Dak2  14 gaeavlkaleeleeaslaevlkalakallsgagGtsGvlysqflralakalkekeeldaedlaaalkaaleaiqavg 90 
                                       g + +++++e+  ++ +  v + + ++ + + gG+s    +  lr  ak+l +ke+l ++++a+al+a  +++ +  
  gi|557693574|ref|YP_008796628.1| 382 GTQRIVDEAERSLKDAINVVKDVIVEGKVIAGGGASELETALRLRDYAKTLPGKEQLAVNKFAEALEAIPSQLAESC 458
                                       778888999988888888888889999999999999999****************************9988887777 PP

                                       ---T CS
                              Dak2  91 karp 94 
                                       +++p
  gi|557693574|ref|YP_008796628.1| 459 GMDP 462
                                       7766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 4030.55
//
Query:       gi|557693575|ref|YP_008796629.1|  [L=85]
Description: DNA-directed RNA polymerase subunit K [Candidatus Caldiarchaeum subterraneum]
Scores for 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   43.0   0.0    4.7e-11   42.4   0.0    1.2  1  RNA_pol_Rpb6  RNA polymerase Rpb6


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 !   42.4   0.0   2.6e-15   4.7e-11       7      49 .]      15      62 ..      12      62 .. 0.92

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 2.6e-15
                                      --HHHHHHHHHHHHHHH....HT.........SS-SSSSTTCHHHHTT-S-- CS
                      RNA_pol_Rpb6  7 ltrYelvriaakRArQieegesl.........etqkpvviAlrEiaegkipi 49
                                      lt+Ye++ri++ RA+Q+    sl           + +++iA rE + g +pi
  gi|557693575|ref|YP_008796629.1| 15 LTKYEKARIIGGRALQL----SLgafplvevrPGESNIDIAKREFERGVLPI 62
                                      8****************....99999999996367***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       162  (0.00903564); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 632.80
//
Query:       gi|557693576|ref|YP_008796630.1|  [L=65]
Description: hypothetical protein CSUB_C0137 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   11.7   0.3       0.16   11.6   0.3    1.0  1  Ac81      Baculoviridae AC81
       0.22   10.3   0.9       0.23   10.2   0.9    1.0  1  DUF2207   Predicted membrane protein (DUF2207)
       0.26   11.0   2.5       0.32   10.8   2.5    1.0  1  SPC25     Microsomal signal peptidase 25 kDa subunit (SPC25)


Domain annotation for each model (and alignments):
>> Ac81  Baculoviridae AC81
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   2.6e-05      0.16     124     163 ..       7      48 ..       3      61 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.6e-05
                              Ac81 124 gvsvqtvlililiavlllaiikfsafllLfi..lfllviLli 163
                                       + +++++++l+++a++l+++  +  f+l f   +f +   ++
  gi|557693576|ref|YP_008796630.1|   7 RGWRDAFILLVAVALVLFTLDVLLGFQLTFQflFFAVYFPIF 48 
                                       67999*************999988888887741333333333 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.9   3.8e-05      0.23     382     435 ..       9      60 ..       3      65 .] 0.66

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.8e-05
                           DUF2207 382 klsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllg 435
                                       +  a++l++++++++++l +ll+++l  + +l++++ +++++++++++f+r l+
  gi|557693576|ref|YP_008796630.1|   9 WRDAFILLVAVALVLFTLDVLLGFQL-TFQFLFFAVYFPIFFSGAVYMFKR-LR 60 
                                       55667777777777777777777777.777777777777777777777754.33 PP

>> SPC25  Microsomal signal peptidase 25 kDa subunit (SPC25)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.5   5.4e-05      0.32      35      78 ..      15      58 ..      13      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.4e-05
                             SPC25 35 lavaiaavaflydykveFeeskpvlaiavvlYfilsgiltlyst 78
                                      l va+a+v+f +d +++F+ + ++l++av + +++sg+++++++
  gi|557693576|ref|YP_008796630.1| 15 LLVAVALVLFTLDVLLGFQLTFQFLFFAVYFPIFFSGAVYMFKR 58
                                      689***************************99999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 504.63
//
Query:       gi|557693577|ref|YP_008796631.1|  [L=364]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-61  208.6   0.0    1.5e-61  208.3   0.0    1.0  1  DUF763    Protein of unknown function (DUF763)


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 !  208.3   0.0   8.5e-66   1.5e-61       1     297 [.       5     314 ..       5     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 208.3 bits;  conditional E-value: 8.5e-66
                            DUF763   1 GiadLpLhegkvPewllermkkLskaiveliveeygkeellerlsdPlwFqslgnvlGmdWdsSGsTtvvlgalkea 77 
                                       G+ dL   +gk+ ++ ++r +++ +++v+  ++ yg++el++ +++P++   + ++ G+d  s  sT  + ++lke+
  gi|557693577|ref|YP_008796631.1|   5 GVKDLRGWSGKAARFHYNRSREIINEVVHSFLNIYGPDELVQGFAEPFFTDFVITAAGLDETSADSTLYMGSMLKEV 81 
                                       677888889******************************************************************** PP

                            DUF763  78 lkseelgilvaGGkGkksrktpeeleklaeklgldeek...lvkasrlvakvdnaalqdgyqlYlhalivsekgkwa 151
                                       ++ +  g +v+GG+ ++  ++p+el ++a+ +g++e+    l ++sr+vak+d++alqdg++lY+h++i+s++g w+
  gi|557693577|ref|YP_008796631.1|  82 ISPR-DGAAVLGGRFATRFRIPNELPEVAKLFGFSETMverLLYCSRMVAKTDSVALQDGFDLYFHMMILSSSGVWT 157
                                       *666.599**************************98878889*********************************** PP

                            DUF763 152 viqQGmneeerlARRYhwlseelesfveephsgiagekkeeevlnlvskeseearkaildlvkekpekllke..lke 226
                                       viqQ +n  ++  RRYhw+s +++sfv+eph+gi++++ +++vl++++k+s+e+r+a+l++++ + +kl++   + +
  gi|557693577|ref|YP_008796631.1| 158 VIQQSLNPYTQAVRRYHWFSGRVKSFVDEPHTGIISDEIRQRVLDMTAKTSSESRRASLEVLEREVSKLQRLhmFGR 234
                                       **************************************************************999988766411333 PP

                            DUF763 227 lkallkgekkl.........klpakhevlekvlekayelqpedfeellllkgvGpktlraLalvaeliygekasfkD 294
                                       l++ ++    l          l+   +++++ + k+ e++p+++eell +k vG+  +r La+   ++yg k+s +D
  gi|557693577|ref|YP_008796631.1| 235 LTNQTT----LdeegksvaeFLRPMERINWTLVYKLGEQTPKSYEELLAVKQVGRGIIRLLAFGVYMMYGVKPSLRD 307
                                       333332....223345556533445566************************************************* PP

                            DUF763 295 Pv....k 297
                                       P+    +
  gi|557693577|ref|YP_008796631.1| 308 PAypasE 314
                                       *955553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2980.14
//
Query:       gi|557693578|ref|YP_008796632.1|  [L=357]
Description: myo-inositol-1-phosphate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-34  117.5   0.0    5.6e-34  116.7   0.0    1.4  1  Inos-1-P_synth  Myo-inositol-1-phosphate synthase
  ------ inclusion threshold ------
       0.03   14.5   0.1       0.07   13.4   0.0    1.7  2  DUF1611_N       Domain of unknown function (DUF1611_N) Rossma


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 !  116.7   0.0   6.2e-38   5.6e-34       1     109 []     191     299 ..     191     299 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 6.2e-38
                                       SHHHHHHHHHHHHHHTT-EEEEEEEEEEE-HHHHHHTTSHHHHHHHHHHHHHHHHHHHSS--EEE....EEE...EE CS
                    Inos-1-P_synth   1 GqTklksvLaellverglkvksivslNilGnnDgknlseeerfksKkisKssvvddivkanellyvdhevvi...kY 74 
                                       G+T+l++vL++l+v+rg+k+++ ++lN++Gn+D++n+ e+er++sKkisK+++v++++ ++  +    +++i   +Y
  gi|557693578|ref|YP_008796632.1| 191 GATILHRVLTKLFVDRGVKIERSYQLNFGGNTDFLNMLERERLQSKKISKTQAVTSLIPYELPA---ENIHIgpsDY 264
                                       9**********************************************************96544...4699999*** PP

                                       -GGGTTEEEEEEEEEEEEGGGEEEEEEEEEEEEH. CS
                    Inos-1-P_synth  75 vpylgDsKvaldeieseiflggkntielkleceDS 109
                                       vp+l+D+K+a++++e+++f++++ ++e+kle++DS
  gi|557693578|ref|YP_008796632.1| 265 VPWLEDRKWAYIRLEGSAFGNAPLNVEVKLEVWDS 299
                                       **********************************9 PP

>> DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.6   1.5e+04      30      40 ..       3      13 ..       2      18 .. 0.77
   2 ?   13.4   0.0   7.8e-06      0.07      44      89 ..     139     182 ..      97     187 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.6
                         DUF1611_N 30 gaevlviGiap 40
                                      ++++ +iG+++
  gi|557693578|ref|YP_008796632.1|  3 KIKTAIIGVGN 13
                                      57899999988 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.8e-06
                         DUF1611_N  44 klpeswreavkeAleaGldvvsGlHerLsddpelaalakkkgvkii 89 
                                           + + +v++Al aG   v+G   +++ +++++++ +k+++ ii
  gi|557693578|ref|YP_008796632.1| 139 ES--ATKWYVEQALVAGTGFVNGIPVFIAREKRWQEIFAKHNIPII 182
                                       33..34569*********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2959.08
//
Query:       gi|557693579|ref|YP_008796633.1|  [L=105]
Description: PadR family transcriptional regulator [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-17   62.8   0.3    2.8e-17   62.5   0.3    1.1  1  PadR         Transcriptional regulator PadR-like family
    1.1e-05   26.1   0.1    1.4e-05   25.7   0.1    1.1  1  RTP          Replication terminator protein
  ------ inclusion threshold ------
       0.01   15.9   0.0        1.6    8.9   0.0    2.4  2  Mrr_N        Mrr N-terminal domain
      0.021   15.0   0.1      0.034   14.3   0.1    1.3  1  HTH_34       Winged helix DNA-binding domain
      0.021   13.2   0.0      0.023   13.1   0.0    1.1  1  DUF505       Protein of unknown function (DUF505)
      0.036   14.0   0.2       0.18   11.7   0.1    2.0  1  TrmB         Sugar-specific transcriptional regulator TrmB
      0.082   12.8   0.1      0.093   12.6   0.1    1.2  1  TFIIE_alpha  TFIIE alpha subunit
       0.13   12.8   0.0       0.31   11.6   0.0    1.6  1  HTH_27       Winged helix DNA-binding domain
       0.14   12.5   0.0       0.18   12.1   0.0    1.3  1  DUF2513      Hypothetical protein (DUF2513)


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 !   62.5   0.3   1.4e-20   2.8e-17       1      74 [.      19      91 ..      19      92 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.4e-20
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S.TSSS-EEEEEESHCCCHHHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglvesewees.gegpprkyYrlTdaGrrela 74
                                      iL ll+++p+yGyei++ +e+ + g +++ e + Y +L rLe+ gl++  +e + ++gp r+yY+lT++G+++l+
  gi|557693579|ref|YP_008796633.1| 19 ILTLLSKRPLYGYEIRNLIEKEF-G-FKPGEVTSYVVLYRLERAGLIKVAEESKsSRGPSRRYYTLTPRGKDTLK 91
                                      89********************7.7.8********************987776669****************997 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.1   6.8e-09   1.4e-05      10      96 ..      15      97 ..       8     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.8e-09
                                      HHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HHH CS
                               RTP 10 lklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkrrkelkekaklqevviYsltdeGkek 88
                                      l ly++tl+ k++lyg+++ + + keF   g+kP + + y  l  l   g++k  +e k  ++     +Y+lt  Gk+ 
  gi|557693579|ref|YP_008796633.1| 15 LWLYILTLLSKRPLYGYEIRNLIEKEF---GFKPGEVTSYVVLYRLERAGLIKVAEESK-SSRGPSRRYYTLTPRGKDT 89
                                      569****************99999765...********************999988888.555566679*********9 PP

                                      HHHHHHHH CS
                               RTP 89 aklykkqv 96
                                      +k  k  +
  gi|557693579|ref|YP_008796633.1| 90 LKKAKTFL 97
                                      99888655 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.013        25       4      39 ..      15      49 ..      12      52 .. 0.88
   2 ?    8.9   0.0   0.00082       1.6      69      86 ..      74      91 ..      53      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                             Mrr_N  4 lmlplLealadgsehrlkeirervaerfglseeera 39
                                      l l +L  l++  ++   eir+ ++++fg+++ e+ 
  gi|557693579|ref|YP_008796633.1| 15 LWLYILTLLSKRPLYG-YEIRNLIEKEFGFKPGEVT 49
                                      66889999*******9.*************998875 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00082
                             Mrr_N 69 spkrgvwkiTekGrevlk 86
                                       p+r ++++T++G+++lk
  gi|557693579|ref|YP_008796633.1| 74 GPSRRYYTLTPRGKDTLK 91
                                      578************998 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 ?   14.3   0.1   1.7e-05     0.034      35      80 .]      54     101 ..      47     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                            HTH_34  35 lkkLekagYievdkefk.gkkp.rtllriTpeGreafkkyvkaLksll 80 
                                       l  Le ag i+v  e k ++ p r  +++Tp G++  kk +  L++l+
  gi|557693579|ref|YP_008796633.1|  54 LYRLERAGLIKVAEESKsSRGPsRRYYTLTPRGKDTLKKAKTFLEELV 101
                                       6679*******9765541454536799***************999986 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05     0.023     369     409 ..      53      98 ..      32     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                            DUF505 369 aLysLesfeLieseveekg.....kevyvlTeyGekvledqekklr 409
                                        Ly+Le  +Li+  +e+k      +++y+lT+ G+  l++ ++ l+
  gi|557693579|ref|YP_008796633.1|  53 VLYRLERAGLIKVAEESKSsrgpsRRYYTLTPRGKDTLKKAKTFLE 98 
                                       7***********99866655568899************98876555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   8.9e-05      0.18       3      36 ..      40      73 ..      36      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.9e-05
                                      HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSC CS
                              TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvpr 36
                                      ++G++  E+  Y++L +l++a   ++aee++ +r
  gi|557693579|ref|YP_008796633.1| 40 EFGFKPGEVTSYVVLYRLERAGLIKVAEESKSSR 73
                                      7899999999999999999999999998888776 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   4.6e-05     0.093      33      81 ..      37      87 ..       3     105 .] 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                                      HHHHHTS-HHHHHH..HHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCH CS
                       TFIIE_alpha 33 lakelkidlnelrk..lLnrLyearlvkykrrrdeekswykyywrinyekl 81
                                      ++ke ++++ e+ +  +L+rL  a+l+k+  +   + +  + y+ ++++  
  gi|557693579|ref|YP_008796633.1| 37 IEKEFGFKPGEVTSyvVLYRLERAGLIKVAEESKSSRGPSRRYYTLTPRGK 87
                                      57888999999987558***************************9998643 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 ?   11.6   0.0   0.00016      0.31      38      68 .]      53      86 ..      49      86 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00016
                            HTH_27 38 slkkLtekGLv.ertgdeadrre..krvrlTdkG 68
                                      +l +L+++GL+ + ++++ +r++  + ++lT+ G
  gi|557693579|ref|YP_008796633.1| 53 VLYRLERAGLIkVAEESKSSRGPsrRYYTLTPRG 86
                                      6789*******8444444444446699*****98 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.9e-05      0.18      45      86 ..      53      94 ..      22      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.9e-05
                           DUF2513 45 hlkllaeagLieaekkkakssiislvvkrLtweGhdFLdsiR 86
                                       l+ l+ agLi++++++++s+ +s  ++ Lt +G d L +++
  gi|557693579|ref|YP_008796633.1| 53 VLYRLERAGLIKVAEESKSSRGPSRRYYTLTPRGKDTLKKAK 94
                                      4667999*****************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); 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:                         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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 888.73
//
Query:       gi|557693580|ref|YP_008796634.1|  [L=657]
Description: enoyl-CoA hydratase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-69  231.8   3.8    9.2e-69  230.9   3.8    1.5  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    9.5e-68  228.2   0.0    1.7e-67  227.4   0.0    1.4  1  ECH_1            Enoyl-CoA hydratase/isomerase
    5.7e-48  164.1   0.8    7.1e-43  147.4   0.0    2.7  3  ECH_2            Enoyl-CoA hydratase/isomerase
    2.1e-47  159.7   0.6    1.8e-26   92.6   0.0    3.6  4  3HCDH            3-hydroxyacyl-CoA dehydrogenase, C-terminal 
    0.00019   20.8   1.3     0.0004   19.7   1.3    1.5  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0007   19.8   2.0     0.0041   17.3   2.0    2.3  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0017   18.0   0.1      0.003   17.2   0.1    1.4  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
      0.003   16.8   0.4     0.0054   16.0   0.4    1.4  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
     0.0086   16.6   0.2      0.025   15.1   0.1    1.9  1  XdhC_C           XdhC Rossmann domain
  ------ inclusion threshold ------
      0.022   14.7   0.2      0.055   13.4   0.2    1.7  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.063   13.2   0.2        0.2   11.5   0.2    1.9  1  UPF0146          Uncharacterised protein family (UPF0146)
      0.067   13.5   0.4       0.16   12.2   0.4    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.11   13.1   0.9       0.34   11.5   0.9    1.9  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
       0.13   12.7   0.0        1.2    9.7   0.0    2.4  2  SeleniumBinding  Selenium binding protein


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 !  230.9   3.8   7.2e-72   9.2e-69       2     179 ..       3     182 ..       2     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: 230.9 bits;  conditional E-value: 7.2e-72
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH. CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav. 77 
                                         v+GaG+mG+gia+v+a ag++Vv+vd++ee+l+k+leki+ slek+vek+++++e ++aa++ri+++t+l+eav 
  gi|557693580|ref|YP_008796634.1|   3 MVVVGAGVMGHGIAEVAALAGFDVVMVDVAEEFLAKGLEKIRWSLEKFVEKKRITKEAADAAFSRIRTSTNLAEAVv 79 
                                       579************************************************************************** PP

                                       C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT CS
                           3HCDH_N  78 dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgek 154
                                       d+dlviEa++E++++K+++f+ l++ a+++aila+nTS+l+i+e+a+a++rpe+v+g+HFfnPpplm+L+Ev++gek
  gi|557693580|ref|YP_008796634.1|  80 DTDLVIEAAPEDIKIKKNIFQVLSQNAPAHAILATNTSTLPITEIASATNRPEKVVGMHFFNPPPLMPLLEVIAGEK 156
                                       ***************************************************************************** PP

                                       --HHHHHHHHHHHHHTT-EEEEE.CS CS
                           3HCDH_N 155 Tseetvatvvelakkigktpvvv.kd 179
                                       Ts+et+a++ve+ kk+gkt+v + kd
  gi|557693580|ref|YP_008796634.1| 157 TSQETLAKAVEIGKKMGKTVVICrKD 182
                                       **********************9777 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.4   0.0   1.3e-70   1.7e-67       5     250 ..     409     656 ..     405     657 .] 0.97

  Alignments for each domain:
  == domain 1  score: 227.4 bits;  conditional E-value: 1.3e-70
                                       TEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHC.HHHHHHHCCHHH CS
                             ECH_1   5 gvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeek.akqallkeevle 79 
                                        v +i lnrP+ +N++++ +++El++al k+  d + r+vvL G g++aF+aGad+++ +e ++ ++++++  +++e
  gi|557693580|ref|YP_008796634.1| 409 PVTKIILNRPHRLNTITPRMIEELMDALLKAWSDSETRVVVLRGaGERAFSAGADITAFTEIKTrQDAEKFLRAFQE 485
                                       6899*********************************************************9885566678889999 PP

                                       HHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT CS
                             ECH_1  80 lwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllg 156
                                       l++ + ++pk viaa+ G+a+gGG+el   cDi+ia d ++fg++e++lGlipgaggtq+l+r +G +kA e++llg
  gi|557693580|ref|YP_008796634.1| 486 LMNIMESMPKAVIAAIDGYALGGGCELIQGCDIRIATDRSEFGQPEINLGLIPGAGGTQRLPRLIGVAKALELTLLG 562
                                       9999999********************************************************************** PP

                                       -EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHH CS
                             ECH_1 157 kkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddi 233
                                       ++isa+ea ++Glv+kvv  e+l++e  +laekla+++p+a+r++k+ +  + e  l ++l++e++ f ++  ++d+
  gi|557693580|ref|YP_008796634.1| 563 NRISAEEAYRIGLVNKVVKPENLEQEVQSLAEKLASQPPLAVRAAKQLIYMTREAPLSRGLAMERMFFADLLFTKDF 639
                                       ***************************************************************************** PP

                                       HHHHHHHHTCSH----- CS
                             ECH_1 234 keGlqaflEkrkpefed 250
                                        eG+ af  krkpef++
  gi|557693580|ref|YP_008796634.1| 640 MEGVSAFFAKRKPEFKG 656
                                       ***************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 ?   -1.4   0.1      0.99   1.3e+03     156     226 ..      20      89 ..      18     120 .. 0.56
   2 !  147.4   0.0   5.5e-46   7.1e-43       2     186 ..     411     594 ..     410     595 .. 0.95
   3 !   17.8   0.0   1.5e-06    0.0019     247     317 ..     587     654 ..     583     657 .] 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.99
                                       -B-HHHHHHTTS--EE--GGGHHHHHHHHHTT...........--------......----SHHHHHHHHHHHT CS
                             ECH_2 156 rlkgadalaaglathyvpseklealeeaLaelessd...eeaveevleelaeeaeeeeeeselaekreaidrlf 226
                                        l g d++ +++a+ ++ +  le+++ +L++  +++   +ea ++++++++++++    ++++ ++   i+++ 
  gi|557693580|ref|YP_008796634.1|  20 ALAGFDVVMVDVAEEFLAKG-LEKIRWSLEKFVEKKritKEAADAAFSRIRTSTNL---AEAVVDTDLVIEAAP 89 
                                       57788888888888888654.78888888777666545455555555555544333...222333334444444 PP

  == domain 2  score: 147.4 bits;  conditional E-value: 5.5e-46
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYk 78 
                                       + i+Lnrp+ lN ++  m+++l +al +  +d+e+++vvl+gage+af+AG D+ a++e ++++++e  +f r+  +
  gi|557693580|ref|YP_008796634.1| 411 TKIILNRPHRLNTITPRMIEELMDALLKAWSDSETRVVVLRGAGERAFSAGADITAFTEIKTRQDAE--KFLRAFQE 485
                                       5799******************99999999*****************************99997755..7******* PP

                                       HHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH- CS
                             ECH_2  79 lnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTG 154
                                       l + ++++pk v+a +dG+++GgG+ l +++ +r++t+r+ f  PE+++Gl+P  Gg+  L+rl g + +l l l G
  gi|557693580|ref|YP_008796634.1| 486 LMNIMESMPKAVIAAIDGYALGGGCELIQGCDIRIATDRSEFGQPEINLGLIPGAGGTQRLPRLIGvAKALELTLLG 562
                                       ****************************************************************88688999***** PP

                                       --B-HHHHHHTTS--EE--GGGHHHHHHHHHT CS
                             ECH_2 155 arlkgadalaaglathyvpseklealeeaLae 186
                                       +r+++++a+ +gl +++v+ e+le+  ++Lae
  gi|557693580|ref|YP_008796634.1| 563 NRISAEEAYRIGLVNKVVKPENLEQEVQSLAE 594
                                       ***********************998888876 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS------- CS
                             ECH_2 247 ewakktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkW 317
                                       + +++ +e+l+++ P++++++ +++  +r++  l+  l+mE  + + ll +kDf+eGv a + ++  kP++
  gi|557693580|ref|YP_008796634.1| 587 QEVQSLAEKLASQPPLAVRAAKQLIYMTREAP-LSRGLAMERMFFADLLFTKDFMEGVSAFFAKR--KPEF 654
                                       5678999************************7.***************************98765..4555 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 ?    0.3   0.0      0.86   1.1e+03      41      90 ..      13      60 ..       4      66 .. 0.65
   2 ?   -2.9   0.1       8.4   1.1e+04      77      94 ..     159     176 ..     154     177 .. 0.79
   3 !   92.6   0.0   1.4e-29   1.8e-26       1      97 []     185     280 ..     185     280 .. 0.98
   4 !   62.3   0.0     4e-20   5.2e-17       7      97 .]     303     392 ..     301     392 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.86
                                      SCHHHHHHHHHHHH.HHHHHH.HHHHHTTTHGGHH-HHHHHHHHTT--BGGG CS
                             3HCDH 41 mGpfelldlvgldv.akkile.vlaeelgerayapsplleklveagrlgrkt 90
                                       G+ e++ l+g dv + +++e  la++l++ ++     lek+ve++r+ +++
  gi|557693580|ref|YP_008796634.1| 13 HGIAEVAALAGFDVvMVDVAEeFLAKGLEKIRWS----LEKFVEKKRITKEA 60
                                      5788888888888624566663334444444444....88888888887765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.4
                                       HHHHHHTT--BGGGTBSS CS
                             3HCDH  77 leklveagrlgrktgkgf 94 
                                        e+l++a ++g+k gk +
  gi|557693580|ref|YP_008796634.1| 159 QETLAKAVEIGKKMGKTV 176
                                       578899999999999876 PP

  == domain 3  score: 92.6 bits;  conditional E-value: 1.4e-29
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GF+vnR+l plln  ++lve+gv ++++iD+a+r++lGlpmG+fel+d++g+dv   +++ ++e+ +++    +  +
  gi|557693580|ref|YP_008796634.1| 185 GFIVNRILTPLLNHSCQLVEDGVYTVAEIDSALRYRLGLPMGAFELADYTGIDVIVLASKSIKERDPNTPPV-CSQF 260
                                       9****************************************************************9999776.9*** PP

                                       HHHHHTT--BGGGTBSSSBC CS
                             3HCDH  78 eklveagrlgrktgkgfyky 97 
                                       ++l+e+g +g k+gkgfy+y
  gi|557693580|ref|YP_008796634.1| 261 QRLYEKGNYGLKSGKGFYEY 280
                                       ******************98 PP

  == domain 4  score: 62.3 bits;  conditional E-value: 4e-20
                                       HHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHT CS
                             3HCDH   7 vlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklvea 83 
                                       ++ap +n a ++v +gvas  d+++ ++lglG+p G+f+ +d++gld + ++l   ae++g+  y+p pl+ +lv++
  gi|557693580|ref|YP_008796634.1| 303 LMAPAINSAAWIVRNGVASLDDVETGVKLGLGWPKGVFQYADELGLDKVAAALTKAAERFGDF-YRPDPLIMELVNQ 378
                                       57899************************************************9999999998.899********** PP

                                       T--BGGGTBSSSBC CS
                             3HCDH  84 grlgrktgkgfyky 97 
                                       g+lg ktg+gfy+y
  gi|557693580|ref|YP_008796634.1| 379 GKLGVKTGAGFYTY 392
                                       ************98 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 !   19.7   1.3   3.2e-07    0.0004      30      99 ..       2      88 ..       1      91 [. 0.89

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.2e-07
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHH.HHH...TTTCECEE.............HCHHHHHHHHHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleq.les...lgakfvev.............lksqeellaeavke 91
                                      k++v+G+Gv G   +++a+  g +V+++Dv ++ l + le+     +kfve              + +++ +laeav +
  gi|557693580|ref|YP_008796634.1|  2 KMVVVGAGVMGHGIAEVAALAGFDVVMVDVAEEFLAKgLEKirwSLEKFVEKkritkeaadaafsRIRTSTNLAEAVVD 80
                                      789****************************998755255566677888888999**********999*********** PP

                                      -SEEEE-- CS
                       AlaDh_PNT_C 92 advvigtv 99
                                      +d+vi ++
  gi|557693580|ref|YP_008796634.1| 81 TDLVIEAA 88
                                      *****886 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 !   17.3   2.0   3.2e-06    0.0041       3      94 ..       4     120 ..       2     143 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.2e-06
                                       EEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........................EEE-SSHHHHHHH CS
                     NAD_binding_2   3 gfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........................akaaesieelvas 55 
                                        ++G GvMG+ +a+  + ag++v+++++ +e + + +++                         +++ ++++e+v +
  gi|557693580|ref|YP_008796634.1|   4 VVVGAGVMGHGIAEVAALAGFDVVMVDVAEEFLAKGLEKIrwslekfvekkritkeaadaafsrIRTSTNLAEAVVD 80 
                                       689************************99866666666646777777778799999999998888888888888888 PP

                                       CSEEEE-SSSHHHHHHHHHS.HCCC--TT-EEEE-S---H CS
                     NAD_binding_2  56 ldvvitmvkagkavdevieg.llealkkgdilidgstssp 94 
                                        d+vi   +++ ++++ i++ l +++ + +il   +++ p
  gi|557693580|ref|YP_008796634.1|  81 TDLVIEAAPEDIKIKKNIFQvLSQNAPAHAILATNTSTLP 120
                                       8999999999999999999944444444444444444333 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 !   17.2   0.1   2.3e-06     0.003       1      81 [.       1      85 [.       1     120 [. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-06
                                      SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHH....HHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHH CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeighevigvDideekv....dklnsgkipiyepgLeelvkkavesgrlsfttdvekave 75
                                      mk++v+G+G +G   a v a +g++v++vD+ ee      +k++ +  +++e++  +  ++ ++ +r++ +t++ +av 
  gi|557693580|ref|YP_008796634.1|  1 MKMVVVGAGVMGHGIAEVAALAGFDVVMVDVAEEFLakglEKIRWSLEKFVEKKRITKEAADAAFSRIRTSTNLAEAVV 79
                                      899****************************998651111455555566666654433333344589999999999999 PP

                                      C-SEEE CS
                    UDPG_MGDP_dh_N 76 eadvif 81
                                      ++d+++
  gi|557693580|ref|YP_008796634.1| 80 DTDLVI 85
                                      999887 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 !   16.0   0.4   4.2e-06    0.0054     144     198 ..       2      56 ..       1      94 [. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.2e-06
                                       EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGv 198
                                       ++vvvG+G+ G  +A ++a +g +v++v+ ++++l +  ++++  le+ +ek+ +
  gi|557693580|ref|YP_008796634.1|   2 KMVVVGAGVMGHGIAEVAALAGFDVVMVDVAEEFLAKGLEKIRWSLEKFVEKKRI 56 
                                       5788999999999999988888898899999888844445666666666666554 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     2e-05     0.025       1      35 [.       3      52 ..       3     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                                      EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG...............- CS
                            XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreefa...............t 35
                                      +v++Gag +++ +a++aa +gf+v++vd  eef                +
  gi|557693580|ref|YP_008796634.1|  3 MVVVGAGVMGHGIAEVAALAGFDVVMVDVAEEFLakglekirwslekfvE 52
                                      69*****************************9886777777775554442 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 ?   13.4   0.2   4.3e-05     0.055       1      99 [.       2     112 ..       2     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                                       -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H...........HHHHHHHHHSSBTTTBTT----TTEEEES-HHHH CS
                    NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree...........elieeineehenvkyLpgiklpenlvattdlaea 66 
                                       k+ v+GaG  G  +A v a +g +v++    e             +e++ e+++ +k   + ++ + ++ +t+laea
  gi|557693580|ref|YP_008796634.1|   2 KMVVVGAGVMGHGIAEVAALAGFDVVMVDVAEeflakglekirWSLEKFVEKKRITKEAADAAF-SRIRTSTNLAEA 77 
                                       5789***********************9999989998887666455555555555555666555.68********** PP

                                       HTT--EEEE---HHH..HHHHHHHHCCC--TT-EE CS
                    NAD_Gly3P_dh_N  67 lkgadiivlvvPsqa..lrevlkklkgllkkkail 99 
                                       + + d+++ + P  +   +++++ l++  +++ail
  gi|557693580|ref|YP_008796634.1|  78 VVDTDLVIEAAPEDIkiKKNIFQVLSQNAPAHAIL 112
                                       ************85411566666667666666655 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00016       0.2      16      92 ..       2      83 ..       1      95 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                                      EEEEET-TT--H.HHHHHHHHS-EEEEE-SS-S.......STTEE---SSS--HHHHTTEEEEEE.ES--TTSHHHHHH CS
                           UPF0146 16 kvvEvGiGrkld.vaealakrgvdlvatDikek...kakegvrivrDDvtdPnleiYkgadliYs.lRpPaelqsaild 89
                                      k+v vG+G   + +ae  a  g+d+v++D+ e+   k  e++r   +  ++ ++   ++ad+ +s +R  ++l +a++d
  gi|557693580|ref|YP_008796634.1|  2 KMVVVGAGVMGHgIAEVAALAGFDVVMVDVAEEflaKGLEKIRWSLEKFVEKKRITKEAADAAFSrIRTSTNLAEAVVD 80
                                      78899***87542888888889*********997444448888888999999999999****99889**********99 PP

                                      HHH CS
                           UPF0146 90 vak 92
                                         
  gi|557693580|ref|YP_008796634.1| 81 TDL 83
                                      755 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 ?   12.2   0.4   0.00013      0.16       2      78 ..       4      89 ..       3      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH........TTTCEEEEE--TT....THHHHHHHHHT CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka........lgvrfeaialdae....nyeavLaallk 68
                                      +++GaG +G+++ae+ a  + +  +++ +d  +e l++ ++k+         ++r++++a da+      +  La+++ 
  gi|557693580|ref|YP_008796634.1|  4 VVVGAGVMGHGIAEVAALAG-F--DVVMVDVAEEFLAKGLEKIrwslekfvEKKRITKEAADAAfsriRTSTNLAEAVV 79
                                      89************999987.5..6***************999**9999997777777777776222223333666666 PP

                                      TSSEEEE-SS CS
                   Sacchrp_dh_NADP 69 egdlvvnlsp 78
                                      ++dlv+ ++p
  gi|557693580|ref|YP_008796634.1| 80 DTDLVIEAAP 89
                                      6699998887 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9   0.00027      0.34       1      52 [.       2      53 ..       2      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TTSSHHHHHHHHHHHHH CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rllDeeaskilqeklek 52
                                      k+vvvG+G+ g   A+++a  g +V +v+ ++++l ++l++ ++  l++ +ek
  gi|557693580|ref|YP_008796634.1|  2 KMVVVGAGVMGHGIAEVAALAGFDVVMVDVAEEFLaKGLEK-IRWSLEKFVEK 53
                                      68*********************************555543.44444444455 PP

>> SeleniumBinding  Selenium binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.4     3e+03      29      68 ..     470     507 ..     464     512 .. 0.69
   2 ?    9.7   0.0    0.0009       1.2      13      55 ..     563     605 ..     558     617 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.4
                   SeleniumBinding  29 vvesdnvdkilkaleekvkekkglaligfkltaidgkllG 68 
                                       +   ++ +k l+a++e++  ++++      ++aidg  lG
  gi|557693580|ref|YP_008796634.1| 470 IKTRQDAEKFLRAFQELMNIMESMPK--AVIAAIDGYALG 507
                                       55667888999999999999998853..234556666666 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0009
                   SeleniumBinding  13 neiPGvelyylgivsavvesdnvdkilkaleekvkekkglali 55 
                                       n i   e y +g+v +vv+ +n+++ ++ l ek  ++  la+ 
  gi|557693580|ref|YP_008796634.1| 563 NRISAEEAYRIGLVNKVVKPENLEQEVQSLAEKLASQPPLAVR 605
                                       67788899*************************9999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      710  (0.0396006); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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 0.29s 00:00:00.99 Elapsed: 00:00:00.46
# Mc/sec: 4305.56
//
Query:       gi|557693581|ref|YP_008796635.1|  [L=409]
Description: cysteine desulfurase / selenocysteine lyase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-151  503.9   0.0   2.7e-151  503.7   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    3.1e-05   23.1   0.0    5.1e-05   22.4   0.0    1.3  1  SelA             L-seryl-tRNA selenium transferase
    0.00064   18.4   0.0     0.0022   16.6   0.0    1.8  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.011   15.1   0.1      0.018   14.4   0.1    1.6  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
       0.11   12.7   0.0       0.38   10.9   0.0    1.9  2  TruB_C_2         tRNA pseudouridylate synthase B C-terminal d


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 !  503.7   0.0  7.7e-155  2.7e-151       1     371 []      25     395 ..      25     395 .. 0.99

  Alignments for each domain:
  == domain 1  score: 503.7 bits;  conditional E-value: 7.7e-155
                                       EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHH CS
                       Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlv 77 
                                       iylds+At+qkp++V++a++e+y++ nanvhr+v++ + eat+a+e+ar+kvae+i+a+s+ ei+f+++ttea+nl 
  gi|557693581|ref|YP_008796635.1|  25 IYLDSTATSQKPAQVVEAVAEFYKKINANVHRGVYEISVEATEAYENARKKVAEFIGARSSREIVFVRNTTEALNLT 101
                                       8**************************************************************************** PP

                                       HHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTT CS
                       Aminotran_5  78 alslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtG 153
                                       a+sl+ + +kpg +iv+t++ehh+n+vpwq +ak   +k+++ip+d++g ldl+e++ +l +++++ ++th+snv+G
  gi|557693581|ref|YP_008796635.1| 102 AYSLGLHrVKPGGKIVLTTMEHHSNIVPWQLIAKINRLKIEYIPFDDQGYLDLSEADRKL-KDADIFSFTHASNVLG 177
                                       ************************************************************.789************* PP

                                       EB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTS CS
                       Aminotran_5 154 tiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKllgPtGiGvlyvrkellekleplllggem 230
                                       ti++ + ++++a+++gal +vDaaq+v+h+p++v+++g+D+lafsghK+lgPtGiGvl++r+elle++ep+++ggem
  gi|557693581|ref|YP_008796635.1| 178 TINDAKMLCRMAHEHGALAIVDAAQSVPHMPVNVQEMGCDLLAFSGHKMLGPTGIGVLFGRRELLEEMEPFQGGGEM 254
                                       ***************************************************************************** PP

                                       EEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CT CS
                       Aminotran_5 231 veevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaer 307
                                       ++ev+l+++ +++ p+kfeaGTpn+ag+iglgaa++yl++ig+e++++he++l++++le ++++ + ++ygp++  +
  gi|557693581|ref|YP_008796635.1| 255 IKEVYLDHSLWNDVPWKFEAGTPNIAGAIGLGAAVDYLRRIGMENVREHEHRLTAKALEIMSEIRHAKVYGPENPLH 331
                                       ***************************************************************************** PP

                                       CBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE--TTS-HHHHHHH CS
                       Aminotran_5 308 rasivsfnfkgvhaedvatlLdeegIavrsGhhcaqplmkrlalegtvRaSlyiynteeevdrl 371
                                       r ++vsfn++++h++d+at+Ld++gI+vr+Ghhca+p++++l++++t RaS+yiynteee++ +
  gi|557693581|ref|YP_008796635.1| 332 RCGLVSFNLADIHPHDLATYLDKHGICVRAGHHCAMPIHTHLGISATTRASFYIYNTEEELEIF 395
                                       ************************************************************9975 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.4e-08   5.1e-05     199     234 ..     211     246 ..     175     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.4e-08
                                       HHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHH CS
                              SelA 199 alaeGvdlvsfsGDkllGgpqaGiivGkkelieklk 234
                                       + + G+dl++fsG k+lG    G++ G++el+e+++
  gi|557693581|ref|YP_008796635.1| 211 VQEMGCDLLAFSGHKMLGPTGIGVLFGRRELLEEME 246
                                       4457*****************************996 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 ?   -1.0   0.0      0.14     5e+02     242     268 ..      54      81 ..      17      95 .. 0.68
   2 !   16.6   0.0   6.1e-07    0.0022     114     201 ..     138     228 ..      97     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.14
                                       HHHHHTTHHHHHHHHHHHHH.HHHHHHH CS
                   Cys_Met_Meta_PP 242 llrGlkTLslRlerhqenAl.kvAefLe 268
                                       ++rG+  +s+   ++ enA  kvAef+ 
  gi|557693581|ref|YP_008796635.1|  54 VHRGVYEISVEATEAYENARkKVAEFIG 81 
                                       5677777777777777777525777765 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 6.1e-07
                                       HTTCEEEEESTTSHHHHHHHCCT..TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGG CS
                   Cys_Met_Meta_PP 114 klgievkfvdtsdleelekaike..ntklvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp.llqrplkl 187
                                       +l+ie+  +d +   +l +a ++    +++ +   +n l  + D + ++++a+++g+l +vD++ + p + ++  ++
  gi|557693581|ref|YP_008796635.1| 138 RLKIEYIPFDDQGYLDLSEADRKlkDADIFSFTHASNVLGTINDAKMLCRMAHEHGALAIVDAAQSVPhMPVNVQEM 214
                                       444444434433333333333333345677777889********************************88899999* PP

                                       T-SEEEEETTTTTT CS
                   Cys_Met_Meta_PP 188 gaDivvhSaTKylg 201
                                       g+D+   S+ K lg
  gi|557693581|ref|YP_008796635.1| 215 GCDLLAFSGHKMLG 228
                                       ********999886 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 ?   14.4   0.1   4.9e-06     0.018      30     150 ..      74     205 ..      42     373 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.9e-06
                                       HHHHHHHT...-SEEEEESSHHHHHHHHHHHTTTT...TT-EEEEES...SS-THHHHHHHHTT.-EEEEE-B-TTT CS
                   DegT_DnrJ_EryC1  30 kafaaylg...vkhaiavssGtaAlhlaLralgvg...pgdeVIvps...ltFvatanavlelg.akpvfvDvdpdt 96 
                                       k++a+++g   ++  + v + t+Al l+   lg+    pg +++ ++   ++++  ++ +++++ +k  ++  d d+
  gi|557693581|ref|YP_008796635.1|  74 KKVAEFIGarsSREIVFVRNTTEALNLTAYSLGLHrvkPGGKIVLTTmehHSNIVPWQLIAKINrLKIEYIPFD-DQ 149
                                       67999999444467899********9987776654444999999887233577778899999873567788888.88 PP

                                       SSB-GGGCGGG--TTE..EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1  97 ynidpaaieaaitert..kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                         +d +++ +++      +   + +++G ++d + l ++a++hg   i DaA+++ 
  gi|557693581|ref|YP_008796635.1| 150 GYLDLSEADRKLKDADifSFTHASNVLGTINDAKMLCRMAHEHGALAIVDAAQSVP 205
                                       899*********999888899999*****************************986 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 ?   10.9   0.0   0.00011      0.38       7      40 ..     279     313 ..     277     327 .. 0.81
   2 ?   -3.4   0.0       3.1   1.1e+04      20      41 ..     330     350 ..     328     354 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                                       HHHHTTS-EEEEEEEEEEETTE.GG-..B-HHHHH CS
                          TruB_C_2   7 iGeaLgcgAhveeLRRtrvgpf.deedmvtledLe 40 
                                       i+ a+g gA v  LRR+ + ++ ++e+ +t + Le
  gi|557693581|ref|YP_008796635.1| 279 IAGAIGLGAAVDYLRRIGMENVrEHEHRLTAKALE 313
                                       77799****************97555556666665 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.1
                                       EEEEEETTEGG-..B-HHHHHH CS
                          TruB_C_2  20 LRRtrvgpfdeedmvtledLed 41 
                                       L+R    +f+ +d +  +dL+ 
  gi|557693581|ref|YP_008796635.1| 330 LHRCGLVSFNLAD-IHPHDLAT 350
                                       8899888998888.77777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2940.30
//
Query:       gi|557693582|ref|YP_008796636.1|  [L=608]
Description: threonyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  134.8   0.0    3.9e-39  133.8   0.0    1.5  1  tRNA-Thr_ED     Archaea-specific editing domain of threonyl-t
    5.8e-19   68.7   0.1    1.3e-18   67.6   0.1    1.6  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.6e-17   63.4   0.2    3.8e-17   62.2   0.2    1.7  1  HGTP_anticodon  Anticodon binding domain
  ------ inclusion threshold ------
      0.028   15.1   0.0        1.6    9.5   0.0    2.6  2  Phage_ABA_S     Phage ABA sandwich domain
      0.097   12.6   0.0       0.76    9.7   0.0    2.4  3  Imm61           Immunity protein 61
        0.2   11.1   0.1       0.49    9.8   0.1    1.6  1  AP_endonuc_2    Xylose isomerase-like TIM barrel


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 !  133.8   0.0   1.3e-42   3.9e-39       1     135 [.       1     132 [.       1     134 [. 0.99

  Alignments for each domain:
  == domain 1  score: 133.8 bits;  conditional E-value: 1.3e-42
                                       -EEEEEEEEEEEEEEEEESSSS-.SS---EEEESSEEEEEEE-BTT--H...HHHHHHHHHHHHHHHHHT-SEEEEE CS
                       tRNA-Thr_ED   1 mrlLlihadeleyeakkkalkeaeeeeekegrleealvvFiavEkeDeeekekvvekavkeikkvakkvkakkvvly 77 
                                       mr+L +h+d +ey+++k++ +++ee +++  r+e+a v++++vE eD+e   +v+e+av++  ++++++k+ ++v+y
  gi|557693582|ref|YP_008796636.1|   1 MRILGLHVDFVEYRPVKRESTVVEEAAPEPVRIEDAYVLLTSVEPEDDE---RVAEAAVADAVEFMSRLKIPRLVIY 74 
                                       9************************************************...9************************ PP

                                       E-STS-SSB--HHHHHHHHHHHHHHHHTT.-EEEE--SSEEEEEEEEE--STTSEEEE CS
                       tRNA-Thr_ED  78 pyaHLssslaspevakeilkkleeklkekglevkraPFGwykefeisckGhpLaelsr 135
                                       p+aHLs++la+pe+a+eil+ +e+  ke+g+ev+r+PFGw k++ +s+kGhpLae sr
  gi|557693582|ref|YP_008796636.1|  75 PFAHLSRELARPEHAVEILALMEKIAKERGVEVHRSPFGWNKALALSVKGHPLAERSR 132
                                       *******************************************************998 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 !   67.6   0.1   4.3e-22   1.3e-18       1     177 [.     271     477 ..     271     479 .. 0.82

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 4.3e-22
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTS.TBC.TTTB-SEEEEEEEEEEES.G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxx.x RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEks.dsr.GLlRvreFhqkdgyvfha.e 73 
                                       Yk+e +  r y+++  ++    +l r++v  s+r LP+ ++++   yR E++ ++  G +R+r++ + d +vf+   
  gi|557693582|ref|YP_008796636.1| 271 YKVEVDG-RPYVMRYAACFQQFALARNWV-ISYRsLPFGMFEVADSYRLEQRgELVlG-FRLRKMSMPDLHVFCRdI 344
                                       8888885.99*****************95.55555****************9977779.***************954 PP

                                       GGHHHHHHHHHHHHHHHHHHTT.SCEEEEEEGTTSC...........................BTTSEEEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........................xxxxxxxxxxxxxx RF
                      tRNA-synt_2b  74 aslddslrdlikaisriferlglefraiielmsaks...........................adykdkkefeavse 123
                                        ++ ++++++  +i+   e+lg  ++ + +l+s+k                                      +v +
  gi|557693582|ref|YP_008796636.1| 345 PEALQIVEKIHDKIYSEIEKLGRDYYSLYNLTSRKFfeenrgffqkllkrekkpvllsfypenS------SYYWVLN 415
                                       5577777777777777778889999999999885436677777777877777777774444443......3333333 PP

                                       T.......TSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EE.HHHHHHHHHH CS
                                       x.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxxxx RF
                      tRNA-synt_2b 124 s.......ltkgieigtiqklgtrlserlgatvldennreksvimicaa.ig.veRllsaile 177
                                       +       +++ +eigt+q +  + +er+g+t++++++++k +++++ a ig veR l a+++
  gi|557693582|ref|YP_008796636.1| 416 IeyhiidkFGRPREIGTVQID-VGNAERFGITYVEKDGEKKYPVILHSAlIGtVERYLYAVVD 477
                                       36666666*************.**************************************997 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.2   1.3e-20   3.8e-17       1      93 [.     495     584 ..     495     585 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.3e-20
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       q  ++plne   ++ + a +lae++ + girv++dd+ e++ kk+ ea++ +ip++ ++G+ke++kgt+++r r ++
  gi|557693582|ref|YP_008796636.1| 495 QLRILPLNE---KYNKRAVQLAEKITKYGIRVDVDDRPETLAKKVYEAETSWIPYVATLGPKEAKKGTLAIRIRGKK 568
                                       6789*****...9*************************************************************999 PP

                                       EEEEEETTHHHHHHHH CS
                    HGTP_anticodon  78 eqervsldelveklke 93 
                                          ++ l+ lv+ +++
  gi|557693582|ref|YP_008796636.1| 569 GVKQMRLKPLVKLIQK 584
                                       999**********998 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 ?    9.5   0.0   0.00053       1.6      35      67 ..     340     371 ..     329     385 .. 0.83
   2 ?    2.5   0.0     0.081   2.4e+02      41      79 ..     508     546 ..     500     551 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00053
                       Phage_ABA_S  35 ysedisaAweVveklknegieikvkslekkyqv 67 
                                       ++ di  A ++vek++ ++i+ ++++l ++y  
  gi|557693582|ref|YP_008796636.1| 340 FCRDIPEALQIVEKIH-DKIYSEIEKLGRDYYS 371
                                       6889************.********99998755 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.081
                       Phage_ABA_S  41 aAweVveklknegieikvkslekkyqvlveidekrvevi 79 
                                        A +++ek+ ++gi ++v++ +++ + +v + e+ ++ +
  gi|557693582|ref|YP_008796636.1| 508 RAVQLAEKITKYGIRVDVDDRPETLAKKVYEAETSWIPY 546
                                       6999***************99999988888888777765 PP

>> Imm61  Immunity protein 61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.5   4.4e+03      35      62 ..      34      61 ..      31      63 .. 0.68
   2 ?   -1.7   0.0      0.79   2.4e+03      84     102 ..     304     322 ..     301     335 .. 0.82
   3 ?    9.7   0.0   0.00025      0.76      34      72 ..     439     479 ..     422     496 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                                      TTEEE.EEEEETT---EEEEEESSHHHHH CS
                             Imm61 35 edryl.ltkaeraeeeevvlaAasldvve 62
                                      ed y+ lt++e+++ e+ v  Aa  d+ve
  gi|557693582|ref|YP_008796636.1| 34 EDAYVlLTSVEPEDDER-VAEAAVADAVE 61
                                      68899678888877666.45566666666 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.79
                                       ---SGGGS-TT-EEEEEEE CS
                             Imm61  84 lPvsaediasgysletree 102
                                       lP+   ++a+ y+le+r e
  gi|557693582|ref|YP_008796636.1| 304 LPFGMFEVADSYRLEQRGE 322
                                       799999********99865 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00025
                                       ETTEEEEEEEETT---E..EEEEESSHHHHHHHHHHHHHHH CS
                             Imm61  34 kedrylltkaeraeeee..vvlaAasldvverylwgllgdd 72 
                                       +++r+ +t +e++ e++  v+l +a + +veryl+ +   +
  gi|557693582|ref|YP_008796636.1| 439 NAERFGITYVEKDGEKKypVILHSALIGTVERYLYAVVDTA 479
                                       467899*******9999999**************9887655 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 ?    9.8   0.1   0.00016      0.49      68     127 ..      52     107 ..      33     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEE CS
                      AP_endonuc_2  68 svdalkraielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvkl 127
                                       + +a+ +a+e++++L +p lv+ p      + + e ++ e+++e l  + ++a+++gv++
  gi|557693582|ref|YP_008796636.1|  52 AEAAVADAVEFMSRLKIPRLVIYPF----AHLSRELARPEHAVEILALMEKIAKERGVEV 107
                                       348999*****************77....556666689*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 4208.86
//
Query:       gi|557693583|ref|YP_008796637.1|  [L=94]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.7   0.0      0.017   15.2   0.0    1.3  1  Bromodomain     Bromodomain
      0.023   14.7   0.2       0.14   12.1   0.2    2.0  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> Bromodomain  Bromodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.9e-06     0.017      13      48 ..      47      83 ..      34      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-06
                                      CGGGGCSTT-GCCSTTHHHH..SS---HHHHHHHHHT CS
                       Bromodomain 13 laepFlepvdpeefpdyyavi.kkPldLstIkkkles 48
                                      + ++ l+p+ ++ + +yy ++ +kP++ + ++kk+++
  gi|557693583|ref|YP_008796637.1| 47 DGSIILRPIRTDPVDEYYGIVkTKPMSVEDMEKKIKE 83
                                      6788899**************89************87 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 ?   12.1   0.2   1.5e-05      0.14       4      44 ..      20      58 ..      17      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                                      TTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCHHS CS
                    MazE_antitoxin  4 GnsgavriPkevrfelgireGdevelevdgd.kiilrplksl 44
                                      + +g+  iPkevr+        e ++e+ +d +iilrp+++ 
  gi|557693583|ref|YP_008796637.1| 20 DHTGRLYIPKEVRDRVAA---EEFTIETLEDgSIILRPIRTD 58
                                      5578999******84444...66999999999******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 716.19
//
Query:       gi|557693584|ref|YP_008796638.1|  [L=121]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   55.0   0.5    1.5e-14   54.5   0.5    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 !   54.5   0.5   8.5e-19   1.5e-14       1     121 [.       2     116 ..       2     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 8.5e-19
                                       EEE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHH CS
                               PIN   1 ivlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidae 76 
                                       i+lD +vl ++l  +  + e+++++l +  + +tsal+++ +l+vl+        +++   +  ++ +l++ p++ +
  gi|557693584|ref|YP_008796638.1|   2 IYLDVNVLQYWLtADPRFGERSKEILKHHRDKATSALTIW-ILFVLNQ------GNEKKIMEAVDAIGLSVAPLTIQ 71 
                                       79**********988899999*****999***********.999****......333333333346788999***** PP

                                       HHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  77 iaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                       +++ a  +++ +gl++ Da+++At+k+ gi++ia++D+df++v++
  gi|557693584|ref|YP_008796638.1|  72 DLRDATTLSESLGLDVEDAIHLATMKRLGIDAIASNDKDFDKVSR 116
                                       ******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 884.98
//
Query:       gi|557693585|ref|YP_008796639.1|  [L=160]
Description: bacterioferritin [Candidatus Caldiarchaeum subterraneum]
Scores for 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-27   95.0   0.6      4e-27   94.9   0.6    1.0  1  Ferritin      Ferritin-like domain
    7.7e-06   26.3   0.2    1.1e-05   25.8   0.2    1.2  1  Rubrerythrin  Rubrerythrin
    0.00021   21.5   1.5      0.089   13.0   0.0    2.3  2  Ferritin_2    Ferritin-like domain
     0.0015   18.9   0.2       0.18   12.1   0.0    2.4  2  DUF2383       Domain of unknown function (DUF2383)
     0.0051   16.6   0.2       0.35   10.6   0.0    2.2  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 !   94.9   0.6   1.1e-30     4e-27       4     139 ..      20     160 .]      17     160 .] 0.96

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 1.1e-30
                                       HHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH......C-S CS
                          Ferritin   4 LneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee......iea 74 
                                       L ++ ade+ a+yqy+  a  +kg++ +++   ++e +++e++ha+kla+ri++lGg+pvl+  +l +      i++
  gi|557693585|ref|YP_008796639.1|  20 LLKAYADEWLAHYQYWVAAVSLKGVDADTFRPVLMEMSQHELKHAEKLAKRIIQLGGKPVLHFEKLLAtsgcgyIPP 96 
                                       78999********************************************************************8877 PP

                                       SSSCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  75 pkefgsveevleaalehekkvteslrelielaeeegDpatadfledfleeqeeheweleallekl 139
                                       p++ ++ e+ ++++l++e ++++ + e++e  +   D +t++++e++le+++e e++ e++l kl
  gi|557693585|ref|YP_008796639.1|  97 PEDPANYEQLIKDILKAEACAIKFYSEMVEKYRVT-DVVTHELFEELLEDEVEDEQTWEDFLAKL 160
                                       77777****************************76.************************99986 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2   3.1e-09   1.1e-05       3     135 ..      20     159 ..      19     160 .] 0.77

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 3.1e-09
                                       HHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.S....SBBS----- CS
                      Rubrerythrin   3 LekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnklleklepelelevk....ekvreyaea 74 
                                       L kA+a E  a+  Y   a  +k       + ++ e+++ E +Ha++l+k + +l ++  l ++    +   +y  +
  gi|557693585|ref|YP_008796639.1|  20 LLKAYADEWLAHYQYWVAAVSLKgVDADTFRPVLMEMSQHELKHAEKLAKRIIQLGGKPVLHFEkllaTSGCGYIPP 96 
                                       67899999999999999999999888888999999**********************99966541222577899*** PP

                                       --TTGGHHHHHH...HHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  75 kpkflttaknLe...eaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrk 135
                                       +++   +++ ++   +a++ a++ ++em ++y  + + +++e  ++l+++  e+E+  e++l+k
  gi|557693585|ref|YP_008796639.1|  97 PEDPANYEQLIKdilKAEACAIKFYSEMVEKYR-VTDVVTHELFEELLEDEVEDEQTWEDFLAK 159
                                       ****99999999666677777777777766664.444466666666667777777777766666 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   2.5e-05     0.089      19      68 ..      31      80 ..      10     108 .. 0.79
   2 !    7.9   0.4   0.00093       3.3      10      56 ..     111     156 ..     105     160 .] 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.5e-05
                        Ferritin_2 19 fYtaalegaslddkalldaevrevaeeiakheeaHveflkaale..Gaaava 68
                                       Y++ +++ sl  k+   ++ r v+ e+ +he +H+e l++ +   G+++v 
  gi|557693585|ref|YP_008796639.1| 31 HYQYWVAAVSL--KGVDADTFRPVLMEMSQHELKHAEKLAKRIIqlGGKPVL 80
                                      45666665554..677777889***************999887779999984 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00093
                        Ferritin_2  10 lnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHvef 56 
                                       l +E  +++fY++++e+++ + +    +   e++e+  ++e++  +f
  gi|557693585|ref|YP_008796639.1| 111 LKAEACAIKFYSEMVEKYRVT-DVVTHELFEELLEDEVEDEQTWEDF 156
                                       689*************87554.3333333344444444444444444 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   5.1e-05      0.18      27      62 ..      44      79 ..      40      85 .. 0.93
   2 ?    4.5   0.1     0.012        42       6      31 ..     107     132 ..     102     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.1e-05
                                      --SHHHHHHHHHHHHHHHHHHHHHHHHHHHCT---- CS
                           DUF2383 27 vkdpqlktlleriaeereeaaeeLqseiralggepe 62
                                      v+ + ++ +l ++++   ++ae+L+++i +lgg+p 
  gi|557693585|ref|YP_008796639.1| 44 VDADTFRPVLMEMSQHELKHAEKLAKRIIQLGGKPV 79
                                      778899****************************96 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHT--SHH CS
                           DUF2383   6 LndLietlkdgeegykeaaekvkdpq 31 
                                       ++d+++++  ++++y+e++ek + ++
  gi|557693585|ref|YP_008796639.1| 107 IKDILKAEACAIKFYSEMVEKYRVTD 132
                                       7999***************9966444 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   9.7e-05      0.35      12      64 ..      26      79 ..      17      92 .. 0.80
   2 !    4.3   0.1    0.0086        31      13      56 ..     114     157 ..      98     160 .] 0.66

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.7e-05
                              COQ7 12 GElgAvaiYkgqlavl.akkdpelkpllkemleqEkeHlatfeellkerrvrps 64
                                       E  A + Y   ++ l   +  +++p+l em ++E +H +++++++ + + +p 
  gi|557693585|ref|YP_008796639.1| 26 DEWLAHYQYWVAAVSLkGVDADTFRPVLMEMSQHELKHAEKLAKRIIQLGGKPV 79
                                      5667777777777777344555699********************999888775 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0086
                              COQ7  13 ElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeell 56 
                                       E +A   Y+  +   + +d  +++l++e le+E e  +t+e+ l
  gi|557693585|ref|YP_008796639.1| 114 EACAIKFYSEMVEKYRVTDVVTHELFEELLEDEVEDEQTWEDFL 157
                                       66777777776666666666667777777777777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      677  (0.0377601); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1178.09
//
Query:       gi|557693586|ref|YP_008796640.1|  [L=188]
Description: hypothetical protein CSUB_C0147 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.3      0.023   14.4   0.3    1.4  1  MukF_M           MukF middle domain
      0.077   13.1   0.4      0.077   13.1   0.4    1.8  2  CRISPR_Cas9_WED  CRISPR-Cas9 WED domain


Domain annotation for each model (and alignments):
>> MukF_M  MukF middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   2.6e-06     0.023      51     112 ..      77     140 ..      66     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-06
                                       HHHHHHHHHHHHHHHHHHHHHHH..HHHGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            MukF_M  51 idltqrvmdeqqqqvkeeiaell..nkdWreaisscekllsetsstlrelqdtleaaGdklqae 112
                                       i  t++ m    ++ ++++  l+  ++ W +a+ +   +++e +st+r lq t+e+  ++l + 
  gi|557693586|ref|YP_008796640.1|  77 IKATRQKMGITSKSARADVRVLMaiEERWFKAVDETYLIMREKASTFRSLQKTIEQYSNRLDSA 140
                                       6677778888888888888877522688**************************9999888764 PP

>> CRISPR_Cas9_WED  CRISPR-Cas9 WED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1      0.95   8.5e+03      42      58 ..      12      29 ..       6      32 .. 0.55
   2 ?   13.1   0.4   8.5e-06     0.077      37      76 ..     102     142 ..      74     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.95
                   CRISPR_Cas9_WED 42 kdkekf.lmakkdpktfe 58
                                      kd++ + + +  d ktf+
  gi|557693586|ref|YP_008796640.1| 12 KDDSCYrITYTTDGKTFK 29
                                      333333255666777775 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.5e-06
                   CRISPR_Cas9_WED  37 kkll.kkdkekflmakkdpktfeklkkilkeysdkkeksek 76 
                                       +++  k  +e +l+ ++   tf +l+k +++ys+  ++ ++
  gi|557693586|ref|YP_008796640.1| 102 EERWfKAVDETYLIMREKASTFRSLQKTIEQYSNRLDSASE 142
                                       44433668899***********************9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1365  (0.0761336); expected 358.6 (0.02)
Passed bias filter:                      734  (0.0409393); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1387.68
//
Query:       gi|557693587|ref|YP_008796641.1|  [L=87]
Description: hypothetical protein CSUB_C0148 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.055   14.1   0.2       0.06   13.9   0.2    1.1  1  PrmC_N    PrmC N-terminal domain


Domain annotation for each model (and alignments):
>> PrmC_N  PrmC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   3.4e-06      0.06      13      67 ..      30      84 ..      19      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-06
                            PrmC_N 13 agieeaeldAelLlahvlglsrsdlllrgerelteeqlerfeelierRaarePlq 67
                                      ++  +a+   + L  +v ++++ +l +++++ l ++ + + ++  ++R+a+ P q
  gi|557693587|ref|YP_008796641.1| 30 RYNGQARKALQRLTIAVYNIKPKELTAKMQKTLLRQIWLTIRQETQERLAGTPAQ 84
                                      556788899999999**************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 604.16
//
Query:       gi|557693588|ref|YP_008796642.1|  [L=412]
Description: GTP-binding protein HflX [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   87.2   0.0      2e-24   86.1   0.0    1.6  1  GTP-bdg_N     GTP-binding GTPase N-terminal
    2.5e-18   66.2   0.0    4.8e-18   65.3   0.0    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
    1.3e-14   54.5   4.5    1.3e-14   54.5   4.5    1.9  2  GTP-bdg_M     GTP-binding GTPase Middle Region
    3.2e-07   30.0   0.1    8.6e-07   28.6   0.0    1.8  2  FeoB_N        Ferrous iron transport protein B
    2.5e-05   23.9   0.2     0.0017   18.0   0.1    2.7  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    5.2e-05   22.8   1.5    0.00015   21.3   0.2    2.3  2  Arf           ADP-ribosylation factor family
    7.2e-05   23.0   0.0    0.00098   19.3   0.0    2.3  1  Roc           Ras of Complex, Roc, domain of DAPkinase
    8.5e-05   22.5   0.1      0.089   12.7   0.0    2.6  2  RsgA_GTPase   RsgA GTPase
    0.00026   20.6   0.0    0.00075   19.1   0.0    1.8  1  Ras           Ras family
    0.00044   20.2   0.0     0.0011   18.9   0.0    1.7  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0073   15.7   0.1      0.049   13.0   0.0    2.4  2  TniB          Bacterial TniB protein
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.024   14.1   0.0    1.4  1  SRPRB         Signal recognition particle receptor beta subun
      0.014   15.2   0.5      0.045   13.5   0.5    1.9  1  NOG1          Nucleolar GTP-binding protein 1 (NOG1)
      0.015   15.8   0.1      0.088   13.3   0.0    2.1  2  ABC_tran      ABC transporter
      0.017   14.9   2.1        5.6    6.7   0.0    2.9  3  OEP           Outer membrane efflux protein
       0.02   15.1   0.0       0.07   13.3   0.0    2.0  1  MnmE_helical  MnmE helical domain
      0.066   12.8   0.1        3.4    7.2   0.0    2.4  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.09   12.8   0.2       0.32   11.0   0.0    2.0  2  Dynamin_N     Dynamin family
       0.12   11.8   0.0       0.21   11.0   0.0    1.4  1  PD-C2-AF1     POU domain, class 2, associating factor 1
        9.4    6.7   7.1        4.9    7.6   0.5    2.5  2  AAA_23        AAA domain


Domain annotation for each model (and alignments):
>> 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 !   86.1   0.0   2.2e-27     2e-24       2      89 .]      15     101 ..      14     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 2.2e-27
                         GTP-bdg_N   2 esleEleeLaktaglevvgevvqkrekpdpatyiGkGkveeikelveeeeadlvifddeLspsqqrnLekelevkVi 78 
                                       ++l+EleeL+++ag++ v ++vq+r  p+++++iG Gkvee++++v++ +++ +++++eL+p+q+ nL k+l++ Vi
  gi|557693588|ref|YP_008796642.1|  15 YNLDELEELCRSAGYTPVYKLVQRR-PPHSKYMIGPGKVEELRRAVKSLKIEKIVTENELKPVQEYNLAKALSIPVI 90 
                                       689********************97.8************************************************** PP

                         GTP-bdg_N  79 DRtqLILdIFA 89 
                                        RtqLIL+ FA
  gi|557693588|ref|YP_008796642.1|  91 TRTQLILETFA 101
                                       **********8 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.3   0.0   5.4e-21   4.8e-18       2     114 .]     188     307 ..     187     307 .. 0.85

  Alignments for each domain:
  == domain 1  score: 65.3 bits;  conditional E-value: 5.4e-21
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC... CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee... 75 
                                       va+ G++N+GK+tL+n+ +ge+  ++ + +tT+ ++ + vk++g++ +l Dt+G+i+  +  + l ++f++  +   
  gi|557693588|ref|YP_008796642.1| 188 VALTGYTNAGKTTLFNRFSGEEHPAGPQLFTTLSTTARIVKFRGRKAYLSDTVGFIK--NLPHLLVESFHSTLSefi 262
                                       99****************************************************988..556678888887544456 PP

                                       .TSEEEEEEETTTT..CSHHHHHHHHHHHHH...TTSEEEEEEES CS
                          MMR_HSR1  76 .adlillvvdasee..klkpldeeleellee...akkplilvlnk 114
                                        adl+llvvd+see   ++ + +++ ++l+e   ++ p+++v+nk
  gi|557693588|ref|YP_008796642.1| 263 yADLLLLVVDISEEksVVESKLNTCLNVLDEvgvKNVPILVVFNK 307
                                       59**********44335566667777777779999999******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 ?   -1.9   0.0       5.8   5.2e+03      39      61 ..      46      67 ..      14      78 .. 0.62
   2 !   54.5   4.5   1.5e-17   1.3e-14       1      79 []     103     180 ..     103     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.8
                                      XXXXXXXXXHHHHHHHHHHHHHH CS
                         GTP-bdg_M 39 trGpGetkleldrrlireriakl 61
                                      + GpG+ + el+r   + +i+k+
  gi|557693588|ref|YP_008796642.1| 46 MIGPGKVE-ELRRAVKSLKIEKI 67
                                      55666665.55555555566666 PP

  == domain 2  score: 54.5 bits;  conditional E-value: 1.5e-17
                                       H--SHHHHHHHHHHHHHHHHHHHC...XXXXXXXXX..X..XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
                         GTP-bdg_M   1 rArtkeaklQVelAqlkyllprLe...glgkelsrqgGgigtrGpGetkleldrrlireriaklkkeLekvkkkrel 74 
                                       rA + eaklQ++lA+l+y+l+r +   +l+k+ ++     g+ G G ++ +++ +++ +ri+++k++L++++ +++l
  gi|557693588|ref|YP_008796642.1| 103 RAASTEAKLQIKLAELQYELSRAKekvRLAKKGEQP----GFHGLGAYEADVYYNEVFRRISTIKQKLKQIRMRKNL 175
                                       9**********************4344455555555....599********************************** PP

                                       ....T CS
                         GTP-bdg_M  75 qrkkR 79 
                                        r++R
  gi|557693588|ref|YP_008796642.1| 176 VRQRR 180
                                       ***98 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 ?   -2.6   0.0       3.9   3.5e+03     124     140 ..      75      91 ..      62      95 .. 0.78
   2 !   28.6   0.0   9.6e-10   8.6e-07       2     155 ..     187     344 ..     186     345 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.9
                                       EE-HHHHHHHHTS-EEE CS
                            FeoB_N 124 eidlkkLsekLgvpvvk 140
                                        +++ +L+++L +pv++
  gi|557693588|ref|YP_008796642.1|  75 PVQEYNLAKALSIPVIT 91 
                                       57788999999999996 PP

  == domain 2  score: 28.6 bits;  conditional E-value: 9.6e-10
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHH...HHHHHHHH CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYslsayseee...kvardfll 75 
                                       tval G  n+Gkttlfn+ +g ++  g    +t   +   +k++g+++ + D  G  +  ++   e   +   +f++
  gi|557693588|ref|YP_008796642.1| 187 TVALTGYTNAGKTTLFNRFSGEEHPAGPQLFTTLSTTARIVKFRGRKAYLSDTVGFIKNLPHLLVEsfhSTLSEFIY 263
                                       79*****************************************************8765444444401133456666 PP

                                       CTSSSEEEEEEEGG.GHHHHHHHHHHHHH....TTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTB CS
                            FeoB_N  76 eeepdvvvnvvdat.nlernLyLtlqlle....lgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkke 147
                                        +   +vv++ + +  +e +L   l++l+     +vp+++++n+id+a + + +i+  +     ++  v++sa +++
  gi|557693588|ref|YP_008796642.1| 264 ADLLLLVVDISEEKsVVESKLNTCLNVLDevgvKNVPILVVFNKIDAAADYREKIESIN----PEFRYVAVSAWTGQ 336
                                       666666666665431356666666666542221568999**********9999997543....34566777888888 PP

                                       THHHHHHH CS
                            FeoB_N 148 gieellka 155
                                       g+++l +a
  gi|557693588|ref|YP_008796642.1| 337 GLDTLEEA 344
                                       88877765 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 ?    2.3   0.0      0.11     1e+02       5      22 ..     187     204 ..     184     215 .. 0.84
   2 !   18.0   0.1   1.8e-06    0.0017      94     189 ..     264     346 ..     254     351 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.11
                                       EEEEEESTTSSHHHHHHH CS
                          GTP_EFTU   5 nigiighvDhGKtTLtdr 22 
                                       ++++ g +++GKtTL  r
  gi|557693588|ref|YP_008796642.1| 187 TVALTGYTNAGKTTLFNR 204
                                       57888999*******987 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.8e-06
                                       -SEEEEEEETTTB...STHHHHHHHHHHHHTTTE...EEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                          GTP_EFTU  94 lDgavlvvdaveG...vepqteevlrlalkegvp...iivfiNKmDrlkaelkeiveevkqklsrkeeklekygekg 164
                                       +D+ +lvvd++e    ve++ ++ l+++ ++gv+   i v+ NK+D + a+++e +e ++ ++              
  gi|557693588|ref|YP_008796642.1| 264 ADLLLLVVDISEEksvVESKLNTCLNVLDEVGVKnvpILVVFNKIDAA-ADYREKIESINPEF-------------- 325
                                       89*********999999*************999988788999****86.67888888888777.............. PP

                                       TTTEEEEEEBTTTTBTHHHHHHHHH CS
                          GTP_EFTU 165 ekevpvvfgSalkgegvktllealv 189
                                             v +Sa++g+g++tl ea+ 
  gi|557693588|ref|YP_008796642.1| 326 ----RYVAVSAWTGQGLDTLEEAVA 346
                                       ....256666666666666666665 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       7.7   6.9e+03     128     153 ..      56      81 ..      53      87 .. 0.66
   2 !   21.3   0.2   1.6e-07   0.00015      19     133 ..     190     316 ..     186     347 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7.7
                                       TTSS-HHHHHHHTTGGGSSSSSSEEE CS
                               Arf 128 pealseeelrellgleelkgkrklei 153
                                       + a+++ +++++++ +elk+ ++ ++
  gi|557693588|ref|YP_008796642.1|  56 RRAVKSLKIEKIVTENELKPVQEYNL 81 
                                       56777777777777777776666555 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1.6e-07
                                       EEESTTSSHHHHHHHHHHSSCEE...CSSSSSEEEEEEEETTEEEEEEE.E-SSGGGGGGGGGGCTTE.......SE CS
                               Arf  19 llGLDnaGKtTilkklkleelvt...tvPTigfnveeleiknlkftvwD.vGGqeklRplWknYfekt.......da 84 
                                       l G  naGKtT+ ++++ ee         T+  + + +++++ k  + D vG  ++l +l  + f++t       d 
  gi|557693588|ref|YP_008796642.1| 190 LTGYTNAGKTTLFNRFSGEEHPAgpqLFTTLSTTARIVKFRGRKAYLSDtVGFIKNLPHLLVESFHSTlsefiyaDL 266
                                       56899************999865444899999****************94565677777666555554333333366 PP

                                       EEEEEETT-CTTHHHHH.HHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-H CS
                               Arf  85 vifvvDsadreRleeak.eeLkalleeeelkevallvlaNKqDlpealse 133
                                       ++ vvD ++++ + e+k +   ++l+e  +k+v++lv+ NK+D++ +  e
  gi|557693588|ref|YP_008796642.1| 267 LLLVVDISEEKSVVESKlNTCLNVLDEVGVKNVPILVVFNKIDAAADYRE 316
                                       777***9999988777735678999******************9877655 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 !   19.3   0.0   1.1e-06   0.00098       2     119 ..     188     309 ..     187     310 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                                       EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-S.........GGCT CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaG.........qerf 69 
                                       v l G +++GKt+l++rf  ++     +  + ++++  +++k++g +           + Dt G          e f
  gi|557693588|ref|YP_008796642.1| 188 VALTGYTNAGKTTLFNRFSGEEHPAGPQLFTTLSTTA-RIVKFRGRKA---------YLSDTVGfiknlphllVESF 254
                                       678899*************999888877777777654.4557776432.........23344442222222226999 PP

                                       TTT-HHHHCTSCEEEEEEE...GHHH...HCHHHHHHHHHHHCS.SS-EEEEEE-TT CS
                               Roc  70 rslhplylreaalailvyd...srss...enlkeWlkelkkvag.kspvilvgnkiD 119
                                       +s+ + ++ ++  ++lv+d   + +s   ++l++ l+ l++v+  + p+++v nkiD
  gi|557693588|ref|YP_008796642.1| 255 HSTLSEFIYADL-LLLVVDiseE-KSvveSKLNTCLNVLDEVGVkNVPILVVFNKID 309
                                       999999998765.5556664332.2223378999******9976156999******9 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0052       4.6     100     125 ..     186     211 ..     152     245 .. 0.77
   2 !   12.7   0.0    0.0001     0.089      18      99 ..     266     347 ..     254     351 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0052
                                       SEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelel 125
                                        t++l G + +GK+tL n++ +e++ 
  gi|557693588|ref|YP_008796642.1| 186 PTVALTGYTNAGKTTLFNRFSGEEHP 211
                                       5789****************998654 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.0001
                                       EEEEEEESTTT.T--HHHHHHHHH...HHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTH CS
                       RsgA_GTPase  18 qllivvslkep.elslnlldrfLv...laeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegl 90 
                                        ll+vv ++e+ ++ ++ l+ +L    ++  k++++++v+nKiD + + +  e++++     +++ ++vsa t++gl
  gi|557693588|ref|YP_008796642.1| 266 LLLLVVDISEEkSVVESKLNTCLNvldEVGVKNVPILVVFNKIDAAADYR--EKIESINP--EFRYVAVSAWTGQGL 338
                                       555555554431344445555555000555678899*********99988..44444443..457788999999*** PP

                                       HHHHHHCTT CS
                       RsgA_GTPase  91 eelkellkd 99 
                                       ++l+e+++d
  gi|557693588|ref|YP_008796642.1| 339 DTLEEAVAD 347
                                       ***999876 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   8.3e-07   0.00075       3     151 ..     189     340 ..     187     350 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.3e-07
                                       EEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETT.........SGGGHHHHHHHHT CS
                               Ras   3 vlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAG.........qeefkslrelyyr 70 
                                        l G ++ GKt+l +rf  ++ +   +       + + ++++g+++ l   DT G          e f+s  + ++ 
  gi|557693588|ref|YP_008796642.1| 189 ALTGYTNAGKTTLFNRFSGEEHPAGPQLFTTLSTTARIVKFRGRKAYL--SDTVGfiknlphllVESFHSTLSEFI- 262
                                       68899*****************98665444467788888888887765..6****554444444477776555544. PP

                                       TESEEEEEEETTBHHHHHTHH.HHHHHHHHHST.TTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTTT CS
                               Ras  71 daegillvyditsresfenvk.kwveeikrvae.envpivLvGnKvDleekravsteegeelakelglkfletSAkt 145
                                        a+ +llv di++++s  + k + + ++ + +  +nvpi++v nK+D + +   + e+      + +++++ +SA t
  gi|557693588|ref|YP_008796642.1| 263 YADLLLLVVDISEEKSVVESKlNTCLNVLDEVGvKNVPILVVFNKIDAAADYREKIES-----INPEFRYVAVSAWT 334
                                       58999***********9988887777777777679************99732211111.....22347777777777 PP

                                       TCTHHH CS
                               Ras 146 nenvee 151
                                        +++++
  gi|557693588|ref|YP_008796642.1| 335 GQGLDT 340
                                       776654 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 !   18.9   0.0   1.3e-06    0.0011      54     103 ..     297     348 ..     274     350 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                      MMR_HSR1_Xtn  54 vYipclyvlNKiDlis..leeldelarepnsvviSaekelnldeLkekiwee 103
                                       + +p l+v+NKiD++    e++++++ e ++v +Sa ++ +ld+L e++ + 
  gi|557693588|ref|YP_008796642.1| 297 KNVPILVVFNKIDAAAdyREKIESINPEFRYVAVSAWTGQGLDTLEEAVADM 348
                                       6689*********9541257778888888*****************998765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   5.5e-05     0.049      32      63 ..     182     214 ..     154     304 .. 0.84
   2 ?   -0.9   0.0         1   9.2e+02     139     156 ..     365     382 ..     359     389 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.5e-05
                              TniB  32 rkrmpnlllvGdsnnGKtmivekFa.rlhppek 63 
                                       +   p + l G +n GKt+++++F+ ++hp+ +
  gi|557693588|ref|YP_008796642.1| 182 EGGLPTVALTGYTNAGKTTLFNRFSgEEHPAGP 214
                                       4446999*****************966676654 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                              TniB 139 qreflnalksLgnelkip 156
                                          +ln +k+++n lki 
  gi|557693588|ref|YP_008796642.1| 365 TPSLLNEIKQFCNVLKIE 382
                                       56789********99995 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 ?   14.1   0.0   2.7e-05     0.024       4     125 ..     186     311 ..     184     323 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                                       -EEEEE-STTSSHHHHHHHHHHSS---B.---SS-EEETTG...GGTT-SEEEETT-GC.CSHHHHHHHHHHGG... CS
                             SRPRB   4 pavllvGlsdsGKTslftrLttdsvkkt.vtSqessaalkvksekgskltliDfPGhek.lrqklleklkakss... 75 
                                       p+v l G +++GKT+lf+r + ++     +     s+++++ + +g k  l D  G  k l + l+e++    s   
  gi|557693588|ref|YP_008796642.1| 186 PTVALTGYTNAGKTTLFNRFSGEEHPAGpQLFTTLSTTARIVKFRGRKAYLSDTVGFIKnLPHLLVESFHSTLSefi 262
                                       78999***************998655441444466777777788999999***999865366666665332222232 PP

                                       .EEEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHHTT---EEEEEE-TTST CS
                             SRPRB  76 .lkglvfvvDStidpkevkevAEllyeilliteklkdavdiliACnKqelf 125
                                        +  l+ vvD + ++  v++      ++l ++    ++v+il+  nK + +
  gi|557693588|ref|YP_008796642.1| 263 yADLLLLVVDISEEKSVVESKLNTCLNVLDEVG--VKNVPILVVFNKIDAA 311
                                       255677889988777666766677777776555..5668899999998865 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 ?   13.5   0.5   5.1e-05     0.045      14      58 .]     264     309 ..     262     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.1e-05
                              NOG1  14 adavlFllDpseecg...ysleeQlsLleeikelfankpvivvlnKiD 58 
                                       ad+ l ++D+see+     +l+  l++l+e+   ++n+p++vv+nKiD
  gi|557693588|ref|YP_008796642.1| 264 ADLLLLVVDISEEKSvveSKLNTCLNVLDEVG--VKNVPILVVFNKID 309
                                       578899*******9855566777777777776..4589*********9 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.4   1.3e+03      28     103 ..      97     177 ..      94     185 .. 0.62
   2 ?   13.3   0.0   9.8e-05     0.088      13      42 ..     187     216 ..     182     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.4
                                       HHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH.....HHHTCHHHHHHHSTTGGTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  28 lkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren.....esdeeiekalsklglkelk 98 
                                       l+++a+    te +++++ ++l++ el++++++++  ++  +  f +l ++e      e  ++i+++ +kl+++ ++
  gi|557693588|ref|YP_008796642.1|  97 LETFARRAASTEAKLQIKLAELQY-ELSRAKEKVRLAKKGeQPGFHGLGAYEAdvyynEVFRRISTIKQKLKQIRMR 172
                                       666777777777777777777777.6666666666555543233333434444565556777788888888888777 PP

                                       CBGES CS
                                       xxxxx RF
                          ABC_tran  99 dtvvk 103
                                       ++ v+
  gi|557693588|ref|YP_008796642.1| 173 KNLVR 177
                                       77774 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 9.8e-05
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGei 42 
                                       +va++G + aGK+tL++ ++g+++p+  ++
  gi|557693588|ref|YP_008796642.1| 187 TVALTGYTNAGKTTLFNRFSGEEHPAGPQL 216
                                       699*********************976555 PP

>> OEP  Outer membrane efflux protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.0     0.018        16      82     128 ..     103     133 ..      89     136 .. 0.57
   2 ?    6.7   0.0    0.0062       5.6      14      77 ..     161     230 ..     155     237 .. 0.81
   3 ?   -0.4   0.0      0.97   8.7e+02     125     174 ..     339     388 ..     334     391 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.018
                               OEP  82 rarvkaakaqleaaeaqleqarqqlrlevaqaylqlllakeqlelae 128
                                       r                 + ++ +l++++a++ ++l  ake ++la+
  gi|557693588|ref|YP_008796642.1| 103 R----------------AASTEAKLQIKLAELQYELSRAKEKVRLAK 133
                                       3................444555555555555555555555555555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0062
                               OEP  14 dlkaaeaeieaaeanlkaakae.flPtlslsgsygyegngsegggddggtgtt.....svgltlsqplfd 77 
                                        +k+  ++i+  ++ +++++ e  lPt++l+g  +    +  + + ++ ++ +     +++ t+++  f+
  gi|557693588|ref|YP_008796642.1| 161 TIKQKLKQIRMRKNLVRQRRLEgGLPTVALTGYTNAGKTTLFNRFSGEEHPAGpqlftTLSTTARIVKFR 230
                                       589999****************78**********999999999988888886666666555555555555 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.97
                               OEP 125 elaeealklaekalelaearykaGlislldvlqaqvrllqaraelaeaeq 174
                                       +++eea++     + +++a++++G+++ + ++++++  + +++e++++ +
  gi|557693588|ref|YP_008796642.1| 339 DTLEEAVADMMGGYIRVRAQLENGETTPSLLNEIKQFCNVLKIEYNSSGY 388
                                       5566666666666778999******9994466666657777777766655 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.8e-05      0.07      62     132 ..     150     349 ..     103     405 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.8e-05
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx........................................ RF
                      MnmE_helical  62 lseeelaekleelkeelekll..atakrgellreGik........................................ 96 
                                       +  +e+ ++++++k++l+++   ++  r+++l+ G+                                         
  gi|557693588|ref|YP_008796642.1| 150 VYYNEVFRRISTIKQKLKQIRmrKNLVRQRRLEGGLPtvaltgytnagkttlfnrfsgeehpagpqlfttlsttari 226
                                       4455788999999999998761145568888889999**************************************** PP

                                       ............................................................................. RF
                      MnmE_helical  97 ............................................................................. 96 
                                                                                                                    
  gi|557693588|ref|YP_008796642.1| 227 vkfrgrkaylsdtvgfiknlphllvesfhstlsefiyadllllvvdiseeksvvesklntclnvldevgvknvpilv 303
                                       *********************************************99999999999999999888888888888888 PP

                                       .........xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      MnmE_helical  97 .........Dllkeke.ekeeeevlkiSaktgegieeLeeaikele 132
                                                D  ++ e  + e + +++Sa tg+g+++Leea+++++
  gi|557693588|ref|YP_008796642.1| 304 vfnkidaaaDYREKIEsINPEFRYVAVSAWTGQGLDTLEEAVADMM 349
                                       88888666665555556556666679****************9855 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 ?    7.2   0.0    0.0038       3.4       1      21 [.     186     206 ..     186     216 .. 0.83
   2 ?    3.0   0.0     0.073        66     102     162 ..     253     321 ..     234     332 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0038
                                       EEEEEEESTTCCHHHHHHHHH CS
                              cobW   1 pvtvltGflGsGKTtLlnhll 21 
                                       p++ ltG+  +GKTtL n+  
  gi|557693588|ref|YP_008796642.1| 186 PTVALTGYTNAGKTTLFNRFS 206
                                       5789************99876 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.073
                                       T.SHHHHHCCCECEEEEEEETTTH....CCHCCHHHHHHHHHHTSS...EEEEE-HHHHCHC...HHHH CS
                              cobW 102 t.eeelksdltldavvavvDaknl...eaeeekieekaedqlaaad...llvlnKtDlldee.allekl 162
                                       + +++l++ + +d ++ vvD ++     +++ ++  ++ d++ + +   l+v+nK+D + +  +++e++
  gi|557693588|ref|YP_008796642.1| 253 SfHSTLSEFIYADLLLLVVDISEEksvVESKLNTCLNVLDEVGVKNvpiLVVFNKIDAAADYrEKIESI 321
                                       257777778888888888888544333222222222223333322233368999999988774555554 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.4     3e+03      64      86 ..     114     136 ..      89     178 .. 0.50
   2 ?   11.0   0.0   0.00036      0.32       1      35 [.     188     221 ..     188     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.4
                                       -CHHHHHHHHHHHHHHHTSSSS- CS
                         Dynamin_N  64 dfsevreeieketekiagankgi 86 
                                       ++ e++ e+++++ek+  a+kg 
  gi|557693588|ref|YP_008796642.1| 114 KLAELQYELSRAKEKVRLAKKGE 136
                                       33333333333333333333332 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00036
                                       EEEEEBTTTTHHHHHHHHHTS--S---SSS---S- CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrp 35 
                                       +a+ G +++GK+++ n   ge+  p gp++ T   
  gi|557693588|ref|YP_008796642.1| 188 VALTGYTNAGKTTLFNRFSGEE-HPAGPQLFTTLS 221
                                       7899******************.999999776544 PP

>> PD-C2-AF1  POU domain, class 2, associating factor 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00023      0.21     213     247 ..      51      87 ..      41      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                         PD-C2-AF1 213 dledtrraissltiekllleeeds..dayalnhtlsv 247
                                       ++e+ rra++sl iek++ e+e +  + y+l+++ls+
  gi|557693588|ref|YP_008796642.1|  51 KVEELRRAVKSLKIEKIVTENELKpvQEYNLAKALSI 87 
                                       57999****************9753378*******98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   1.3      0.42   3.8e+02     148     196 ..     108     170 ..      47     174 .. 0.48
   2 ?    7.6   0.5    0.0055       4.9      21      37 ..     187     203 ..     181     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.42
                            AAA_23 148 lkdkkerleelekeleeledekkllekleqekekek.....................eleeleeeleeil 196
                                       +++ + +l+el+ el  ++++ +l +k        +                     ++++++++l++i 
  gi|557693588|ref|YP_008796642.1| 108 EAKLQIKLAELQYELSRAKEKVRLAKKG-------EqpgfhglgayeadvyynevfrRISTIKQKLKQIR 170
                                       1222224444444444444444333333.......03444444444445555566668888888888775 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0055
                            AAA_23  21 ltlItGpNGaGKTTild 37 
                                        +++tG + aGKTT+++
  gi|557693588|ref|YP_008796642.1| 187 TVALTGYTNAGKTTLFN 203
                                       6789***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       934  (0.0520944); expected 358.6 (0.02)
Passed bias filter:                      712  (0.0397122); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 2739.87
//
Query:       gi|557693589|ref|YP_008796643.1|  [L=154]
Description: RNA binding PUA domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   67.9   0.0    1.1e-18   67.1   0.0    1.4  1  TGT_C2     Patch-forming domain C2 of tRNA-guanine transglyco
    7.1e-11   41.9   5.6    1.1e-10   41.3   5.6    1.3  1  PUA        PUA domain
    8.4e-05   22.8   0.3    0.00012   22.3   0.3    1.2  1  UPF0113    UPF0113 PUA domain
  ------ inclusion threshold ------
      0.042   13.3   0.0      0.054   13.0   0.0    1.2  1  FBPase     Fructose-1-6-bisphosphatase, N-terminal domain
      0.043   14.2   0.2       0.09   13.2   0.2    1.5  1  DraK_HK_N  DraK Histidine Kinase N-terminal domain
       0.12   12.2   1.4        1.4    8.7   0.2    2.6  3  PUA_3      PUA-like domain


Domain annotation for each model (and alignments):
>> 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 !   67.1   0.0   3.8e-22   1.1e-18       2      69 ..      10      77 ..       9      78 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 3.8e-22
                            TGT_C2  2 rlraiadYqFGagagdaLfpedvtitrs.atgrirqvlvdgerlatlraqdgrltLsleGarrlheslp 69
                                      ++r++a +qFG  ag+ ++p+ + +++s +tgr+r + +dg+ lat+ra dg+ltL++ Ga+rl++ l+
  gi|557693589|ref|YP_008796643.1| 10 QVRQLAFFQFGV-AGEMFIPDGCVVEVSpSTGRPRRIWLDGKCLATIRAMDGWLTLTVFGAQRLNSLLE 77
                                      89********87.99*************************************************99876 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   5.6   3.6e-14   1.1e-10       2      73 ..      82     153 ..      81     154 .] 0.98

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3.6e-14
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                       rvvv+++ +++++ g +++   vve++ ++ +g +V +vded +l++vG+a + + e+++  +g +v++++ 
  gi|557693589|ref|YP_008796643.1|  82 RVVVNREGAEKVAAGYDVYGGHVVEADASIVPGMEVLVVDEDYRLLGVGKAVVAGVEMTELRRGAVVKVRHK 153
                                       8*********************************************************************95 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.3   3.9e-08   0.00012       2      53 ..      83     134 ..      82     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 3.9e-08
                           UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirk 53 
                                       vvv+ ++++++  G dv++ ++++ + s+  +  v+V++e+ ++lG+Gk+  
  gi|557693589|ref|YP_008796643.1|  83 VVVNREGAEKVAAGYDVYGGHVVEADASIVPGMEVLVVDEDYRLLGVGKAVV 134
                                       89************************99999******************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 ?   13.0   0.0   1.8e-05     0.054     125     162 ..      65     104 ..      60     127 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                            FBPase 125 tifsiyrkks..edeettidvlqpGkeqvAAgyvvYGsst 162
                                       t+f+  r +s  e     + v + G e+vAAgy vYG + 
  gi|557693589|ref|YP_008796643.1|  65 TVFGAQRLNSllERGRNRVVVNREGAEKVAAGYDVYGGHV 104
                                       56666665554322222336899**************865 PP

>> DraK_HK_N  DraK Histidine Kinase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2     3e-05      0.09      41      83 ..      76     119 ..      62     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                                       -SS-S.EEEEE-TT-.--B-S---.-SSEEEEEEE-TTS-EEEE CS
                         DraK_HK_N  41 vpgdr.yvvVripggtpieaGedpvegrvisatargesgetVtv 83 
                                        + +r +vvV+ +g++++ aG d+ +g+v++a a +  g  V v
  gi|557693589|ref|YP_008796643.1|  76 LERGRnRVVVNREGAEKVAAGYDVYGGHVVEADASIVPGMEVLV 119
                                       5555569*******88********************99999988 PP

>> PUA_3  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.09   2.7e+02      30      43 ..      27      40 ..      11      42 .. 0.79
   2 ?    8.7   0.2   0.00048       1.4       1      49 [.      83     130 ..      83     132 .. 0.92
   3 ?   -1.7   0.0      0.88   2.6e+03      29      39 ..     141     151 ..     134     153 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.09
                             PUA_3 30 ledGdvVdvfsekg 43
                                      ++dG+vV+v  + g
  gi|557693589|ref|YP_008796643.1| 27 IPDGCVVEVSPSTG 40
                                      679*****976666 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00048
                             PUA_3   1 viLkkkaekrlrqGhPwvfsneiasvegeledGdvVdvfsekgkflGtG 49 
                                       v ++++++ ++ +G+  v+ + + + +  + +G  V v++e+ + lG+G
  gi|557693589|ref|YP_008796643.1|  83 VVVNREGAEKVAAGYD-VYGGHVVEADASIVPGMEVLVVDEDYRLLGVG 130
                                       6788889999999986.9*****************************99 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.88
                             PUA_3  29 eledGdvVdvf 39 
                                       el+ G vV+v 
  gi|557693589|ref|YP_008796643.1| 141 ELRRGAVVKVR 151
                                       47889999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1127.88
//
Query:       gi|557693590|ref|YP_008796644.1|  [L=122]
Description: nascent polypeptide-associated complex subunit alpha [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   28.0   0.1    2.8e-06   27.2   0.1    1.4  1  NAC       NAC domain
     0.0032   17.2   0.0     0.0049   16.7   0.0    1.3  1  UBA_4     UBA-like domain
     0.0057   16.7   0.1     0.0093   16.0   0.1    1.5  1  HOIP-UBA  HOIP UBA domain pair
  ------ inclusion threshold ------
      0.081   12.9   0.0        0.2   11.6   0.0    1.7  1  UBA       UBA/TS-N domain


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 !   27.2   0.1   6.3e-10   2.8e-06       5      54 ..      14      66 ..       8      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6.3e-10
                               NAC  5 rkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGea 54
                                       ++lk lgl  +e+  +eeV+i+  +  v+    P V+  k  g ++++++G  
  gi|557693590|ref|YP_008796644.1| 14 ERMLKNLGLnvEEMGQAEEVVIKLGE-RVITLRGPLVYavKTGGEKIFQIIGGE 66
                                      58************************.***********988889*******965 PP

>> UBA_4  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-06    0.0049       1      33 [.      83     115 ..      83     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                             UBA_4   1 deliaqFqaiTGadeekArqlLeannWdLerAi 33 
                                       +e ++  +a TGa+ee+A++ L  +++dL  Ai
  gi|557693590|ref|YP_008796644.1|  83 EEDVSLVMAQTGASEEEAKKALLDSGGDLAKAI 115
                                       5788888999********************998 PP

>> HOIP-UBA  HOIP UBA domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   2.1e-06    0.0093      71      99 ..      93     120 ..      57     122 .] 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-06
                          HOIP-UBA  71 gklsraEakealleagGdvekAvkqclre 99 
                                          s++Eak+all++gGd+ kA+   +r 
  gi|557693590|ref|YP_008796644.1|  93 TGASEEEAKKALLDSGGDLAKAILM-IRS 120
                                       4579******************854.444 PP

>> UBA  UBA/TS-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.5e-05       0.2       2      34 ..      82     115 ..      81     116 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.5e-05
                                       CHHHHHHHHHT.TS-HHHHHHHHHHTTTSHHHHH CS
                               UBA   2 deeaiqrLveM.GFdreevveALratgnNeErAv 34 
                                        ee ++  ++  G ++ee+++AL  +g+++  A+
  gi|557693590|ref|YP_008796644.1|  82 SEEDVSLVMAQtGASEEEAKKALLDSGGDLAKAI 115
                                       68999999999******************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 861.59
//
Query:       gi|557693591|ref|YP_008796645.1|  [L=535]
Description: hypothetical protein CSUB_C0152 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   35.4   0.1    3.9e-08   33.2   0.0    2.3  2  HTH_20    Helix-turn-helix domain
    7.1e-08   32.2   0.6      2e-06   27.6   0.2    3.2  2  HTH_5     Bacterial regulatory protein, arsR family
    3.5e-06   26.9   1.0    6.6e-06   26.0   1.0    1.5  1  HTH_45    Winged helix-turn-helix
    6.9e-05   23.3   0.1    0.00015   22.2   0.1    1.6  1  ATP-cone  ATP cone domain
     0.0087   14.9   0.0      0.029   13.2   0.0    1.7  2  NRDD      Anaerobic ribonucleoside-triphosphate reductase
  ------ inclusion threshold ------
       0.02   14.7   0.2      0.077   12.7   0.1    1.8  2  DUF4364   Domain of unknown function (DUF4364)
      0.049   13.6   0.1       0.14   12.1   0.1    1.8  1  TerB      Tellurite resistance protein TerB
       0.11   12.8   0.1       0.31   11.3   0.1    1.8  2  DUF2513   Hypothetical protein (DUF2513)


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 !   33.2   0.0   1.7e-11   3.9e-08       2      59 ..      18      78 ..      17      80 .. 0.89
   2 ?   -2.2   0.0         2   4.4e+03      47      54 ..     169     176 ..     122     180 .. 0.64

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.7e-11
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHT...S-HHH.HHHHHHHHHHCTTEEEECT CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerld...lsknt.lsyHLrvLeeagLvevvre 59
                                      +i++ La+P R+ ilr L ++ +l  +el++ l+    s++    +HL+ L  agL+++ r+
  gi|557693591|ref|YP_008796645.1| 18 KIFKSLASPNRLSILRKL-EKSPLNYTELMHVLGmnkKSDAGkFAHHLKMLYAAGLITLNRQ 78
                                      79****************.**************7666555555***************9885 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                                       HHHHCTTE CS
                            HTH_20  47 vLeeagLv 54 
                                        L+e+gL 
  gi|557693591|ref|YP_008796645.1| 169 LLVEHGLM 176
                                       35555555 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 !   27.6   0.2   8.9e-10     2e-06       1      45 [.      25      73 ..      25      74 .. 0.91
   2 ?    0.6   0.0      0.24   5.3e+02       6      23 ..     140     159 ..     136     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 8.9e-10
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-H....HHHHHHHHHHHHTTSE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsq....stvShHLkkLreaGLV 45
                                      +p+Rl IL+ L++++l  +el+  lg+++    ++  hHLk+L+ aGL+
  gi|557693591|ref|YP_008796645.1| 25 SPNRLSILRKLEKSPLNYTELMHVLGMNKksdaGKFAHHLKMLYAAGLI 73
                                      69**************************84444689************9 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.24
                                       HHHHHHTT..SSEEHHHHHH CS
                             HTH_5   6 kILklLae..gelcvcelae 23 
                                       kI+kl +e  +el+ +el++
  gi|557693591|ref|YP_008796645.1| 140 KIVKLFEEkvEELKLGELSA 159
                                       89*******99*******97 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   1.0   2.9e-09   6.6e-06      10      74 ..      30     100 ..      28     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.9e-09
                            HTH_45  10 dILeaisegeakkTkimykanLsyk....llnkYLdmLvekgli..kkskekYvlTekGlelleklkelee 74 
                                       +IL++++++  + T++m    ++ k     +   L+mL   gli  + ++++Y+lT kG ++l+ l+e++ 
  gi|557693591|ref|YP_008796645.1|  30 SILRKLEKSPLNYTELMHVLGMNKKsdagKFAHHLKMLYAAGLItlNRQTKNYELTTKGVQVLKILNEMRA 100
                                       79****************9999976323369999*********9888899*****************9985 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   6.9e-08   0.00015       1      69 [.     106     174 ..     106     184 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.9e-08
                                       -EEE-TTS-EEE--HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS CS
                          ATP-cone   1 ikViKRdGtvepfdvekIkraiekAcegseeeideiaeeveaevrkrlrdgisteeIqdlvektliehp 69 
                                       ikV++ d   e+fd++kI+r +   +   ++++d+i++ +e++v++ +  + s   I+++v   l eh+
  gi|557693591|ref|YP_008796645.1| 106 IKVRRSDMVLEDFDRNKITRVLVEEASLPPKTADKIVKLFEEKVEELKLGELSAPLIREMVNALLVEHG 174
                                       6899****************986654445********************************99999887 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.4     9e+02       4      42 ..     199     237 ..     197     252 .. 0.86
   2 !   13.2   0.0   1.3e-05     0.029     278     321 ..     364     407 ..     344     428 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.4
                                       TTHHHHHHHHHHHHHHHHHHHH-H..HHHHHHHHHHHTT CS
                              NRDD   4 nvdskslsglrlklasevskeyalkkllpkevaeaheeg 42 
                                       n  ++ ++ l+ + +++v++ey+ +k+lp+e a+    g
  gi|557693591|ref|YP_008796645.1| 199 NHHQRDFMSLITTASGAVFREYVFHKILPSEAAQLYLVG 237
                                       6777889999999******************99987666 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.3e-05
                                       EEEEHHHHHH..HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              NRDD 278 vtiNlprlaleakgdeekffelLdellelakealeerrkilekl 321
                                        +iN++ l l++ ++e+kf++ L+e+++ ++ a+ +++++l+++
  gi|557693591|ref|YP_008796645.1| 364 ASINMVSLFLRSGSSERKFWDALRETVDTVAAAFSAKKRFLQRF 407
                                       69*********999************************999876 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.4e-05     0.077      14      82 ..      38     107 ..      29     127 .. 0.76
   2 ?   -1.1   0.0       0.6   1.3e+03      75     134 ..     131     189 ..     122     195 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                           DUF4364  14 fpltnsqlseiileneytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfen...ripksir 82 
                                        pl+ ++l++++  n+  +  ++ + l+ L  +gli+   +++++ y++T kG ++l+++++   +i++ i+
  gi|557693591|ref|YP_008796645.1|  38 SPLNYTELMHVLGMNKKSDAGKFAHHLKMLYAAGLITL--NRQTKNYELTTKGVQVLKILNEmraSISQRIK 107
                                       5788888888888888888889999************8..6899**********998876431115555555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.6
                           DUF4364  75 nripksirekideylkenkeelkkesevkadyykkengeytVklkikekdstllelklsv 134
                                        ++p+++ +ki + ++e+ eelk   e++a  +++  +   V+  ++e+ + l +l + v
  gi|557693591|ref|YP_008796645.1| 131 ASLPPKTADKIVKLFEEKVEELKLG-ELSAPLIREMVNALLVEHGLMEHRNRLARLGMPV 189
                                       5788899999999998888887754.4555555555556666666666666666666555 PP

>> TerB  Tellurite resistance protein TerB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.3e-05      0.14      28      80 ..      99     151 ..      78     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.3e-05
                              TerB  28 lalaallaevakaDgqvsesErqafrellksrfglspeeakallelfeeaeee 80 
                                        a+++  ++v ++D  + +  r+++ ++l ++ +l+p+ a+++++lfee +ee
  gi|557693591|ref|YP_008796645.1|  99 RASISQRIKVRRSDMVLEDFDRNKITRVLVEEASLPPKTADKIVKLFEEKVEE 151
                                       677788899****************************************9998 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00014      0.31      10      79 ..      31      89 ..      29      99 .. 0.73
   2 ?   -3.5   0.0       5.6   1.3e+04      48      63 ..     169     184 ..     143     197 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                           DUF2513 10 iLltleeletkeeslddeeeklsaidgyske.eiiyhlkllaeagLieaekkkakssiislvvkrLtweGh 79
                                      iL +le+ + ++++l         +++ s+  +++ hlk+l  agLi  + ++++ +        Lt++G 
  gi|557693591|ref|YP_008796645.1| 31 ILRKLEKSPLNYTELMHV----LGMNKKSDAgKFAHHLKMLYAAGLITLNRQTKNYE--------LTTKGV 89
                                      666777766666666553....3777777777****************999988877........444444 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.6
                           DUF2513  48 llaeagLieaekkkak 63 
                                       ll+e+gL e  ++ a+
  gi|557693591|ref|YP_008796645.1| 169 LLVEHGLMEHRNRLAR 184
                                       6788888887766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (535 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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 0.26s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3723.60
//
Query:       gi|557693592|ref|YP_008796646.1|  [L=333]
Description: ornithine carbamoyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-52  178.2   0.2      2e-52  177.4   0.1    1.4  2  OTCace          Aspartate/ornithine carbamoyltransferase, Asp
    2.4e-46  157.4   0.0    5.3e-46  156.3   0.0    1.6  2  OTCace_N        Aspartate/ornithine carbamoyltransferase, car
    0.00055   20.0   0.0     0.0012   18.9   0.0    1.5  1  Peptidase_C23   Carlavirus endopeptidase
     0.0079   15.8   0.0      0.017   14.7   0.0    1.7  1  PrpR_N          Propionate catabolism activator
  ------ inclusion threshold ------
      0.011   14.5   0.0      0.015   14.1   0.0    1.2  1  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
      0.053   12.9   0.0      0.083   12.3   0.0    1.3  1  PALP            Pyridoxal-phosphate dependent enzyme


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 ?   -3.9   0.0       4.4   1.3e+04      19      44 ..       4      29 ..       3      32 .. 0.70
   2 !  177.4   0.1   6.7e-56     2e-52       3     156 ..     173     326 ..     171     327 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.4
                                      HHHHHHHCT-EEEEES-TTSSH-HHH CS
                            OTCace 19 likllarlgmdvvlvaPkglepdkev 44
                                      ++ ++  ++++++l++ +g+ ++ ++
  gi|557693592|ref|YP_008796646.1|  4 HLLIALSFQVKIKLCSDEGVAKMRHF 29
                                      56667778899999988887666655 PP

  == domain 2  score: 177.4 bits;  conditional E-value: 6.7e-56
                                       .EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE-- CS
                            OTCace   3 lkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdv 79 
                                        k+afvGd+ nnv+ sl++++a  g+d+++++P++++p +e +++a k a+++g+s+ +t+d+ eav +aD+vytdv
  gi|557693592|ref|YP_008796646.1| 173 SKVAFVGDG-NNVCVSLMQVCAAAGVDITVATPPSHRPPEEEVKKALKVAEETGASVILTDDPREAVRNADFVYTDV 248
                                       69*******.****************************9************************************** PP

                                       SSETTCCGGHHHHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                            OTCace  80 wvsmgeekereerlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                       +vsmg+e+er+++l+++ + yqv++ l+++ak+ a+++Hc+P++ geEvt eV  +p+sv+++qaeNr+ht+++ll+
  gi|557693592|ref|YP_008796646.1| 249 FVSMGQEAERNRKLADFLPtYQVNASLMSHAKPTAKFMHCMPMHLGEEVTPEVAYGPQSVIYDQAENRMHTEASLLA 325
                                       ***************************************************************************98 PP

                                       H CS
                            OTCace 156 l 156
                                       +
  gi|557693592|ref|YP_008796646.1| 326 Y 326
                                       7 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 !  156.3   0.0   1.8e-49   5.3e-46       1     147 [.      27     164 ..      27     165 .. 0.96
   2 ?   -2.2   0.0       1.2   3.7e+03     100     140 ..     245     285 ..     215     292 .. 0.70

  Alignments for each domain:
  == domain 1  score: 156.3 bits;  conditional E-value: 1.8e-49
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       rh+l++ dl+++ei+++++ a +++++     +++ l++kt++l+F++pStRTrvSf++A+++lGg+ ++l+  +++
  gi|557693592|ref|YP_008796646.1|  27 RHFLEVGDLKPKEIDAIVSAALRWRKSGY--PRTRPLRDKTVVLVFQKPSTRTRVSFQAAVAKLGGESMYLG-WSEL 100
                                       8************************8876..89999************************************.5599 PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                       ql+     r+Es+eDt +vl+ryvd+iv+R++g+ +l elak+ ++pviNa+ +d++HP+QaLaDl+ti+
  gi|557693592|ref|YP_008796646.1| 101 QLG-----RGESVEDTGKVLARYVDCIVARVFGHGDLVELAKNGRIPVINAL-SDRHHPCQALADLMTIY 164
                                       999.....78************************9999**************.***************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                                       HTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHH CS
                          OTCace_N 100 yvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaL 140
                                       y+d++v   ++ae+ ++la++     +Na   ++  Pt  +
  gi|557693592|ref|YP_008796646.1| 245 YTDVFVSMGQEAERNRKLADFLPTYQVNASLMSHAKPTAKF 285
                                       44777777777777777777777777777777777777655 PP

>> Peptidase_C23  Carlavirus endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     4e-07    0.0012      18      85 ..      82     151 ..      70     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4e-07
                     Peptidase_C23  18 adilAvlekvaseelveevseGrGlsiedvesvleil.d.ivgdvnvggklivlnknGklpisfaledeH 85 
                                       ++ +A+l+  +      e++ GrG s+ed  +vl  + d iv+ v   g+l+ l knG++p+  al+d H
  gi|557693592|ref|YP_008796646.1|  82 QAAVAKLGGESMYLGWSELQLGRGESVEDTGKVLARYvDcIVARVFGHGDLVELAKNGRIPVINALSDRH 151
                                       667788887777777789************9998654254777888899*******************99 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   5.7e-06     0.017      59     128 ..     159     234 ..     117     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.7e-06
                            PrpR_N  59 Dilralkqakklg.ekialvgfen.iikglktlselldldieiytins....eeeaeaavkelkaegvevvvGdgv 128
                                       D++ ++   kk   +k+a+vg +n ++ +l +++++ ++di++ t  s    eee+++a+k + + g +v++ d  
  gi|557693592|ref|YP_008796646.1| 159 DLMTIYMYSKKPYqSKVAFVGDGNnVCVSLMQVCAAAGVDITVATPPShrppEEEVKKALKVAEETGASVILTDDP 234
                                       556555555555548*******998******************99876333367899999999********99865 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 ?   14.1   0.0     5e-06     0.015     266     372 ..     166     270 ..     134     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-06
                                       HHHHHTT-EEEEECSS.HHHHHHHHHHHHHT-EEEEEEESSS-HHHH..HHHHHHS.TT.SEEEES.CHHHHHHHHH CS
                    Oxidored_nitro 266 yheylagkrvaiygdp.drvvalarllkelGmevvaagtetahrdde..erlkaeleegepeviddadleeleelik 339
                                       y ++ ++ +va +gd+    v+l+++++  G+++ +a  ++++++ e  +++ + +ee+   vi + d +e  + + 
  gi|557693592|ref|YP_008796646.1| 166 YSKKPYQSKVAFVGDGnNVCVSLMQVCAAAGVDITVATPPSHRPPEEevKKALKVAEETGASVILTDDPREAVRNAD 242
                                       45666677777777776999***************99999998888767667777777767899999****999999 PP

                                       HHT-SEEEE-CCHHHHHHHTT--EEE-TS-ECC CS
                    Oxidored_nitro 340 elkpdlllggskeryiaeklgiplvrvgfPild 372
                                           d++++  +e +  +kl         P+++
  gi|557693592|ref|YP_008796646.1| 243 FVYTDVFVSMGQEAERNRKL-----ADFLPTYQ 270
                                       99999999999999999988.....44555554 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.8e-05     0.083      48     116 ..     168     239 ..     135     260 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.8e-05
                                       HHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEEETTS-H......HHHHHHHHTT-EEEEECCHHHHHHH CS
                              PALP  48 rlkegtgaktvveassGNhgralAaaaallGlkvtivvpadasp......ekvallrllGaevvevggdydeava 116
                                       + k+  + k+ +++ + N +++l  ++a++G++ t+  p +  p        ++  ++ Ga v+++ +d+ eav+
  gi|557693592|ref|YP_008796646.1| 168 K-KPY-QSKVAFVGDGNNVCVSLMQVCAAAGVDITVATPPSHRPpeeevkKALKVAEETGASVILT-DDPREAVR 239
                                       4.444.4666667777899******************8888886577665777888999******9.33555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.61
# Mc/sec: 1655.46
//
Query:       gi|557693593|ref|YP_008796647.1|  [L=302]
Description: hypothetical protein CSUB_C0154 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   54.4   0.0    3.1e-09   36.6   0.0    2.4  2  Spt5-NGN  Early transcription elongation factor of RNA pol II
    6.9e-05   22.6   0.3    0.00015   21.6   0.3    1.5  1  KOW       KOW motif
     0.0081   16.6   0.0       0.44   11.1   0.0    2.4  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 !   15.3   0.0   2.3e-06     0.014       2      23 ..      11      32 ..      10      38 .. 0.91
   2 !   36.6   0.0   5.1e-13   3.1e-09      32      79 ..     185     232 ..     175     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-06
                          Spt5-NGN  2 iwavkctagqErevalslmkki 23
                                      ++avk+t gqEr+va  l++++
  gi|557693593|ref|YP_008796647.1| 11 YFAVKTTVGQERTVANVLEARF 32
                                      8*****************9985 PP

  == domain 2  score: 36.6 bits;  conditional E-value: 5.1e-13
                          Spt5-NGN  32 leIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqglvpikE 79 
                                         I S+f  + lkGy++vEA++k+++ +al+++++v+++ +  v+++ 
  gi|557693593|ref|YP_008796647.1| 185 PAIASIFILPALKGYVFVEATSKEVIADALQNVRHVKARPPMPVKLET 232
                                       68***********************************99988887765 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.3   2.5e-08   0.00015       2      30 ..     249     277 ..     248     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.5e-08
                                       TSEEEESSSTTTTCEEEEEEEETTTTE.EE CS
                               KOW   2 GdhVkVvsGphkGktGkVvkvdqhkvr.Vf 30 
                                       G++V++vsGp kG +GkV +v++ + r V+
  gi|557693593|ref|YP_008796647.1| 249 GQMVEIVSGPLKGIVGKVIRVEKSR-ReVT 277
                                       99********************998.3354 PP

>> NusG  Transcription termination factor nusG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0      0.02   1.2e+02       2      24 ..      10      31 ..       9      78 .. 0.83
   2 !   11.1   0.0   7.4e-05      0.44      33      71 ..     167     220 ..     133     237 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.02
                                      EEEEEEE-TTTHHHHHHHHHHHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                              NusG  2 kWYvlqvepgkekkvkenLleee 24
                                      +++++++  g+e+ v++ L e +
  gi|557693593|ref|YP_008796647.1| 10 RYFAVKTTVGQERTVANVL-EAR 31
                                      79*************9999.544 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 7.4e-05
                                       EEEEEEETTEEE........................CSSTTEEEEEE---CHHHHHHHCSTTE CS
                                       xxxxxxxxxxxx........................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              NusG  33 eekveirqgkkk........................klfpgyifikadmndkllmairktpgV 71 
                                       +e         +                        + ++gy+f++a+ ++    a++++++V
  gi|557693593|ref|YP_008796647.1| 167 QE---------EwrddarlplfkliekpaiasifilPALKGYVFVEATSKEVIADALQNVRHV 220
                                       22.........1222223466667777888889999************998888888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 2031.87
//
Query:       gi|557693594|ref|YP_008796648.1|  [L=162]
Description: large subunit ribosomal protein L11 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-22   78.8   0.6    4.6e-22   78.3   0.6    1.2  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
      1e-17   63.7   0.0    1.8e-17   62.9   0.0    1.4  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain


Domain annotation for each model (and alignments):
>> 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 !   78.3   0.6   5.1e-26   4.6e-22       2      70 .]      70     137 ..      69     137 .. 0.99

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 5.1e-26
                                       --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                     Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                       tP+ts+lL +aag++kgsg+ g++ vG++++ ++++IA+ K +d++++ +l+aavk++lg++ smGikV
  gi|557693594|ref|YP_008796648.1|  70 TPSTSALLASAAGVQKGSGTAGRDYVGDLKFTEIVKIAEKKLQDMRSK-TLKAAVKEVLGSCVSMGIKV 137
                                       9*********************************************99.*******************9 PP

>> 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 !   62.9   0.0     2e-21   1.8e-17       6      64 ..       4      63 ..       2      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 2e-21
                   Ribosomal_L11_N  6 kvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitv.yqdrs 64
                                      k+++  v++Gk+t++PplGpaLGplGln+  + +e n  T++++g+r+p ++ v  ++++
  gi|557693594|ref|YP_008796648.1|  4 KTFRFLVEGGKVTAGPPLGPALGPLGLNVLAVAEEANRLTQEFNGMRVPIEVVVdTDTKK 63
                                      78999*************************************************556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1204.85
//
Query:       gi|557693595|ref|YP_008796649.1|  [L=218]
Description: large subunit ribosomal protein L1 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-40  139.5   2.4    1.4e-40  139.3   2.4    1.0  1  Ribosomal_L1  Ribosomal protein L1p/L10e family
  ------ inclusion threshold ------
        2.4    8.6   7.3        5.9    7.4   0.1    3.5  5  Cep57_MT_bd   Centrosome microtubule-binding domain of Cep57


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 !  139.3   2.4   1.5e-44   1.4e-40       6     203 ..      21     211 ..      11     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: 139.3 bits;  conditional E-value: 1.5e-44
                                       -SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSC.S-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHH CS
                      Ribosomal_L1   6 kkkfdesveialnlttkkpkkadqrkpgkipLphplgke.vkiclitkdpqaeyakeakeagriakviglkklkkky 81 
                                       ++kf++sve+ +n+t+++  k+++r+++ i Lp+ lg++  ki++i+ ++ a   +  k++g +a+vi+ ++l++ +
  gi|557693595|ref|YP_008796649.1|  21 NTKFKQSVELVINVTGVDLTKPQNRFSEVIELPNDLGRKrRKILVIASGNLAL--EASKTPG-VARVIQKEELEALV 94 
                                       45999******************************998879*********999..4667777.************** PP

                                       T-HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEE CS
                      Ribosomal_L1  82 ksfeakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtcls 158
                                         +++ +k+++e+d++l++++++ l  ++LG  +g r+k+Pip+   g    d++k v+++ + +vv  l+k+  ++
  gi|557693595|ref|YP_008796649.1|  95 GRKKEAKKIAAEYDFVLVEPALVGLAARVLGAALGARGKTPIPI-PPG---SDIQKLVKRYEN-SVVATLRKSPQVA 166
                                       ********************************************.334...59********99.666666******* PP

                                       EEEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS CS
                      Ribosomal_L1 159 vkvGklsftaeelaeNieavvkalvekvpkkwkniksiylkttms 203
                                       + vG  + ++e++aeN+e+v++ +vek++kk +ni s+y+kttm+
  gi|557693595|ref|YP_008796649.1| 167 CLVGVEEDPDEKIAENVETVLNRVVEKLEKKRRNIASVYVKTTMG 211
                                       ********************************************9 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.2     0.011        94      32      60 ..       3      31 ..       1      35 [. 0.87
   2 ?   -3.2   0.0       1.4   1.2e+04      43      53 ..      54      64 ..      43      65 .. 0.70
   3 ?   -1.0   0.1      0.27   2.5e+03      51      76 ..      84     108 ..      81     109 .. 0.70
   4 ?   -2.6   0.0      0.86   7.7e+03      57      65 ..     144     152 ..     141     162 .. 0.61
   5 ?    7.4   0.1   0.00066       5.9      52      75 ..     182     205 ..     174     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.011
                       Cep57_MT_bd 32 qelaaqynaldpslgkrkRkdLaeeleel 60
                                      +ela++ +al ++ ++rk ++ ++++e +
  gi|557693595|ref|YP_008796649.1|  3 SELAKTVEALKKAKQNRKNTKFKQSVELV 31
                                      799*****************999998866 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.4
                       Cep57_MT_bd 43 pslgkrkRkdL 53
                                        lg+++Rk+L
  gi|557693595|ref|YP_008796649.1| 54 NDLGRKRRKIL 64
                                      45778888876 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.27
                       Cep57_MT_bd  51 kdLaeeleelvkrlEaKadqIykLyd 76 
                                        + +eele+lv r  + a++I++ yd
  gi|557693595|ref|YP_008796649.1|  84 VIQKEELEALVGRKKE-AKKIAAEYD 108
                                       5567888888877655.667777776 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 0.86
                       Cep57_MT_bd  57 leelvkrlE 65 
                                       +++lvkr E
  gi|557693595|ref|YP_008796649.1| 144 IQKLVKRYE 152
                                       455555554 PP

  == domain 5  score: 7.4 bits;  conditional E-value: 0.00066
                       Cep57_MT_bd  52 dLaeeleelvkrlEaKadqIykLy 75 
                                       +++  l+++v++lE+K   I+++y
  gi|557693595|ref|YP_008796649.1| 182 NVETVLNRVVEKLEKKRRNIASVY 205
                                       5677899*************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1620.18
//
Query:       gi|557693596|ref|YP_008796650.1|  [L=287]
Description: large subunit ribosomal protein L10 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-20   73.0   0.0    4.5e-20   71.4   0.0    1.8  2  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    3.6e-18   65.6   1.3    7.2e-18   64.6   0.9    1.7  2  Ribosomal_L10  Ribosomal protein L10


Domain annotation for each model (and alignments):
>> 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 !   71.4   0.0   5.1e-24   4.5e-20       1      71 []     112     182 ..     112     182 .. 0.99
   2 ?   -2.5   0.0      0.58   5.2e+03      11      29 ..     199     217 ..     194     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 5.1e-24
                      RL10P_insert   1 AraGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                       A+aG++A+ d+++p+ +++l Pg+i + + kl++pt+++ G++++ +d+lv+kkGe++++  a+lL +L+i
  gi|557693596|ref|YP_008796650.1| 112 AKAGEKADFDIWVPETNTGLPPGPILSDFGKLKIPTRIEGGQVWIAKDTLVAKKGEEISQLLASLLAKLDI 182
                                       9********************************************************************98 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.58
                      RL10P_insert  11 viipagplelaPgsiepeL 29 
                                       vi++a +l   P +i +e+
  gi|557693596|ref|YP_008796650.1| 199 VILKAEELLIDPVKIGQEI 217
                                       7888888888888887765 PP

>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   0.9     8e-22   7.2e-18       5      98 ..      12     106 ..       9     108 .. 0.95
   2 ?   -2.6   0.0      0.67     6e+03      47      60 ..     151     164 ..     147     179 .. 0.73

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 8e-22
                                       CHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS..S.SCGCCSSSE CS
                     Ribosomal_L10   5 kKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeee.k.lkellkgpv 79 
                                       kK++lv+e+ el+ ky +v+++d++  +++ ++e+Rkklr+  +e++v K tl+ +A + +g+ e + l e++k p+
  gi|557693596|ref|YP_008796650.1|  12 KKAKLVEEVAELIRKYPVVAIFDLRSTRANTIHEMRKKLRGV-CEIRVLKRTLFVKACRLAGKPElEkLVENIKAPI 87 
                                       8*****************************************.****************99998654699******* PP

                                       EEEEESS-TCHHHHCCCCC CS
                     Ribosomal_L10  80 alvftnedpvalakvleef 98 
                                       +++f++ + ++la +le++
  gi|557693596|ref|YP_008796650.1|  88 GFIFSSVNSFQLAFTLEKN 106
                                       *************999998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.67
                                       GCEEEEESCCCCCC CS
                     Ribosomal_L10  47 gaelkvvKntlmrr 60 
                                       g+++ ++K tl+ +
  gi|557693596|ref|YP_008796650.1| 151 GGQVWIAKDTLVAK 164
                                       56777888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1953.58
//
Query:       gi|557693597|ref|YP_008796651.1|  [L=909]
Description: alanyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-113  379.3   0.0   3.9e-113  378.9   0.0    1.2  1  tRNA-synt_2c  tRNA synthetases class II (A)
    3.2e-13   49.5   0.4    6.2e-13   48.6   0.4    1.5  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi
    1.9e-07   31.6   1.1    1.9e-07   31.6   1.1    2.0  2  DHHA1         DHHA1 domain
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.033   14.1   0.0    1.4  1  DrsE_2        DsrE/DsrF/DrsH-like family
      0.087   12.0   0.0       0.15   11.3   0.0    1.4  1  tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
        0.3   11.3   0.8        3.6    7.8   0.0    2.3  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 !  378.9   0.0  1.3e-116  3.9e-113       1     552 []      64     586 ..      64     586 .. 0.96

  Alignments for each domain:
  == domain 1  score: 378.9 bits;  conditional E-value: 1.3e-116
                                       HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTT CS
                      tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVG 77 
                                       e r++F++fF+++gH+++k +++v++++++l+++ A++++f+p+++++ a p+++++v+sQ+c R+     Dl+++G
  gi|557693597|ref|YP_008796651.1|  64 EARQSFIEFFAQRGHAPIKPYPIVARWRTDLYLTDASIVDFQPWVTNGIAPPPANPLVISQPCARLV----DLDKIG 136
                                       569****************************************************************....****** PP

                                       TS.SS--SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGGG CS
                      tRNA-synt_2c  78 kt.arHhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpeer 146
                                        t +rH+T+FeM G+++f+     +Y+k+e+ e+++e++t++lg+++ +l+++++++++  + +++ e ++g+ e +
  gi|557693597|ref|YP_008796651.1| 137 LTfGRHLTVFEMGGHHAFNypekkIYWKSETAEYCHEFMTSVLGVPTGELVYKESWWAGggNEGPCLEVIAGGLELA 213
                                       *978******************************************************999**************** PP

                                       EEEE-HHHHEEESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTTSHEEEEEEEEEE CS
                      tRNA-synt_2c 147 ilrfgekdnfwemgdtgpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnreedgtlkpLpkksid 223
                                       +l+f   ++f+++  ++ + p + +++++g e+ ++ +++++ a d+++ e++ +v + + ++   +++ L k ++ 
  gi|557693597|ref|YP_008796651.1| 214 TLVF---MQFKTLDGERAETPIKTVDTGYGIERLAWFSQQTPSAFDAIYGELLAKVRELIPVN-RPDEELLIKYAKY 286
                                       ****...**************************************************999998.78999******** PP

                                       EEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT--SSSSHHHHH CS
                      tRNA-synt_2c 224 tGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvvpsnegrgYv 300
                                       tG+      a + e+r ++++  +++v+   e+i++         +e+++   D  +a+af++a+Gvvpsn++ gY+
  gi|557693597|ref|YP_008796651.1| 287 TGLVKPGADATVSELRRKVASMAGISVETVNEQIVP---------YEKVYQALDYSKAIAFIVAEGVVPSNVKTGYL 354
                                       ************************************.........57788888************************ PP

                                       HHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCC CS
                      tRNA-synt_2c 301 lRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklk 377
                                        R+l+Rra r++++++++ek l +lv+++++  ++ +p l+e++e+v +i+e+E ++F++T++rG++ + +++++  
  gi|557693597|ref|YP_008796651.1| 355 TRLLIRRAYRLLRMVDAEEK-LLDLVDLQIRYWEKDFPHLSEMREEVLDIVEHEVNKFRETIKRGTETVLRELRS-- 428
                                       ********************.899********************************************9999998.. PP

                                       CCSEEXHHHHHHHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXXTTSHCHHCCT CS
                      tRNA-synt_2c 378 kkkelsgedafkLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekklikkdvealkelkkteef 454
                                        +k++s e++++ yd  G+++d+++e+a+++g++v +++++++++++r+  +k +k++    ++  ++++++kt++ 
  gi|557693597|ref|YP_008796651.1| 429 -TKAISVEKLIQYYDDKGLTPDIVAEVAAKQGVEVTVPENFYELVASRHLREKPVKTTM---QKQIDVSSYPKTHK- 500
                                       .679*********************************************9987777755...44556778888888. PP

                                       STTTXXXXXXTSXXXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEX CS
                      tRNA-synt_2c 455 lgyeeleaeakvlallkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkg 531
                                       l+ye+           ++ +f ++v  +e+++v+Ld T fY+e+GG  gD+G++ ++++  +v+d+q  + vv+h++
  gi|557693597|ref|YP_008796651.1| 501 LYYEQ----------PNSYSFRAKVLGVENGYVILDATLFYPEGGGAVGDTGTLVCRDKVCTVVDTQILEDVVVHRV 567
                                       9****..........78899********************************************************* PP

                                       SS.XSXXXTTSEEEEEEXHHH CS
                      tRNA-synt_2c 532 kleegklkvgdkvkaevdeer 552
                                       +       vg++v++ vd er
  gi|557693597|ref|YP_008796651.1| 568 EGP--VPDVGEEVEGYVDAER 586
                                       996..999*********9875 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 !   48.6   0.4   2.1e-16   6.2e-13       1      44 []     685     728 ..     685     728 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 2.1e-16
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                                       +rvv+i  ++ e+CgG H++nT ++g++ki+s e+i++g+ RI+
  gi|557693597|ref|YP_008796651.1| 685 IRVVEIPGWDAEACGGIHCENTEDVGLIKIVSSERIQDGVERIE 728
                                       7*****66***********************************7 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.6   4.8e+03      12      61 ..     405     456 ..     395     457 .. 0.59
   2 !   31.6   1.1   6.4e-11   1.9e-07       2     113 ..     765     877 ..     761     890 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.6
                                       HHHHHCHHHHHHHHHHHHHHHTCEEEC...TCEEEEEECHCCHHHHHHHHHHH CS
                             DHHA1  12 ekeleelkealaklkaeellekaeevk...gvkvlvaevgeewdagalgiaad 61 
                                       e e+++++e +++ ++ ++l +++ +k     k++  +++++  +++++++a 
  gi|557693597|ref|YP_008796651.1| 405 EHEVNKFRETIKRGTE-TVLRELRSTKaisVEKLIQYYDDKGLTPDIVAEVAA 456
                                       4555555555555443.344444555556466666666667777788888775 PP

  == domain 2  score: 31.6 bits;  conditional E-value: 6.4e-11
                                       HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHH.HHHHHHHHHHHTHGBT.TCEEEEE CS
                             DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewda.galgiaadklksklkk.pvivfva 76 
                                        +l e+++ l+k ++ l+e+l    a+e+ +    v+   ++++e   e+d    l  +a ++ +   + p +++++
  gi|557693597|ref|YP_008796651.1| 765 AELDENLRILRKTVKTLSEKLIVYRAAEIRSVGIAVDSLLLYISEE--EYDDeEYLIKLAAEIVK--VDkPAVALAY 837
                                       5777888888888888888888888888877666665666666666..44443666666666666..555******* PP

                                       EEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCCEEE CS
                             DHHA1  77 keegdkvkvsarskkd....gvdagelakeaaaklgggGGG 113
                                       +     +kv+a ++++    gv++ge++++  +  gggGGG
  gi|557693597|ref|YP_008796651.1| 838 AGTP-SAKVVAVANDKavaaGVNVGEVLRKFLQLAGGGGGG 877
                                       *998.7777777777778************99999999998 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 ?   14.1   0.0   1.1e-05     0.033      12      70 ..     440     498 ..     432     515 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                       --H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GGG---TT--HHHHHHHHHS-S CS
                            DrsE_2  12 gtldkalaalilAsgAaalglevtiFftFwGLnilrkeekkkvkkkslekmamkmvtrk 70 
                                        ++dk l + i+A++Aa+ g+evt+   F+ L + r+ ++k vk ++ ++  ++  +++
  gi|557693597|ref|YP_008796651.1| 440 YYDDKGLTPDIVAEVAAKQGVEVTVPENFYELVASRHLREKPVKTTMQKQIDVSSYPKT 498
                                       5789******************************9999999999888877777666655 PP

>> tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.1e-05      0.15     119     179 ..     197     261 ..     186     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.1e-05
                                       TEEEEEEEEEETTCEEEEEEEEE..EETTE.E-SS-.-EEEEEEHHHHHHHHCT-SSGGG-ECCT CS
                      tRNA-synt_2e 119 GawGlGwevwldGmeitqftYfq..qvggl.elkpv.sveityGleRlamylqevdnvydlewne 179
                                       G  G   ev   G+e++ + ++q   + g    +p+ +v+  yG+eRla + q++ + +d  + e
  gi|557693597|ref|YP_008796651.1| 197 GNEGPCLEVIAGGLELATLVFMQfkTLDGErAETPIkTVDTGYGIERLAWFSQQTPSAFDAIYGE 261
                                       66788899********99887662244443133344278999******************99976 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 ?    1.2   0.1      0.13   3.8e+02      76     111 ..     394     430 ..     372     442 .. 0.79
   2 ?    7.8   0.0    0.0012       3.6      70     118 ..     737     785 ..     716     789 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHHHHH CS
                         Fib_alpha  76 dnvikksskeleeeilrlketidaqe.snirvLqnvl 111
                                       +++ +++ + +e+e+++++eti++   + +r+L+++ 
  gi|557693597|ref|YP_008796651.1| 394 SEMREEVLDIVEHEVNKFRETIKRGTeTVLRELRSTK 430
                                       556678889999**********998878999999865 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  70 kskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqki 118
                                       + +++ ++++++++++l+  ++++ +++ +  +n+r L+++++++++k+
  gi|557693597|ref|YP_008796651.1| 737 HRYQGMETMLHEVAEKLQAPVEDIPKKVAELDENLRILRKTVKTLSEKL 785
                                       55666799999*******************************9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (909 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); 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: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 5872.76
//
Query:       gi|557693598|ref|YP_008796652.1|  [L=482]
Description: hypothetical protein CSUB_C0159 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3290.79
//
Query:       gi|557693599|ref|YP_008796653.1|  [L=245]
Description: ABC-2 type transport system ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-30  104.7   0.0    6.9e-30  104.4   0.0    1.1  1  ABC_tran  ABC transporter
    2.1e-14   54.1   0.1      1e-07   32.1   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    0.00064   19.5   0.0       0.99    9.0   0.0    2.1  2  AAA_15    AAA ATPase domain
     0.0075   16.0   0.1      0.013   15.2   0.1    1.3  1  AAA_29    P-loop containing region of AAA domain
     0.0093   15.7   0.0      0.014   15.1   0.0    1.4  1  AAA_30    AAA domain
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.023   15.1   0.0    1.5  1  AAA_16    AAA ATPase domain
      0.019   15.5   0.0       0.03   14.8   0.0    1.3  1  AAA_23    AAA domain
      0.031   14.7   0.0       0.17   12.3   0.0    2.0  1  AAA       ATPase family associated with various cellular acti
      0.037   13.6   0.0      0.061   12.9   0.0    1.2  1  AAA_27    AAA domain
      0.053   12.6   0.1        0.1   11.7   0.1    1.4  1  T2SSE     Type II/IV secretion system protein
       0.16   12.3   0.1       0.38   11.1   0.1    1.6  1  AAA_19    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 !  104.4   0.0   4.2e-33   6.9e-30       2     137 .]      21     163 ..      20     163 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 4.2e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + vsl l++g++++++G+nG+GK+t lk++ gllkp++G +++ g++ +    + +r ++g++p++p+l + ltv+e
  gi|557693599|ref|YP_008796653.1|  21 RGVSLRLEAGQVHGLLGPNGSGKTTSLKCIVGLLKPDKGIVTVFGEKPSA--NNGYRMKLGYVPENPSLPDYLTVQE 95 
                                       679*****************************************888887..799********************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                                       ++++++++++++l+++ d+ v    ++LS+G +qr+a+a++l++ p++l+lDEp++
  gi|557693599|ref|YP_008796653.1|  96 FlifsarlkglvgdSVRSRVSELMESYELHQVSDRLV----YELSKGIRQRLAIAASLVSSPTVLILDEPFN 163
                                       ***********98888888******************....*****************************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 !   20.4   0.0   2.3e-07   0.00037       2      71 ..      33     102 ..      32     114 .. 0.88
   2 !   32.1   0.0   6.3e-11     1e-07     233     297 ..     131     192 ..      96     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-07
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvr 71 
                                        +l GpNgsGK++ L+++ +l   d+ +     e+++ ++   +   + + +p+ p+ +++ efl+ + r
  gi|557693599|ref|YP_008796653.1|  33 HGLLGPNGSGKTTSLKCIVGLLKPDKGIVTVFGEKPSANNGYRMKLGYVPENPSLPDYLTVQEFLIFSAR 102
                                       679******************9999999999999999999999999999999999999999888877665 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 6.3e-11
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkll..rrll..ellkelsrngaQviltTH 297
                                        ++elS G ++ la++++l + +   ++l++DEp ngL+P+++  +rl+  e++++    g+ v+++TH
  gi|557693599|ref|YP_008796653.1| 131 LVYELSKGIRQRLAIAASLVSSP---TVLILDEPFNGLDPEAQkvTRLYinEIIED----GGGVLISTH 192
                                       5799*****************99...**************9885566665666655....566*****9 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00082       1.3      28      50 ..      35      57 ..      23      91 .. 0.86
   2 !    9.0   0.0   0.00061      0.99     323     364 ..     152     192 ..     130     193 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00082
                            AAA_15 28 liGkNnsGKSsilealdlFlnnk 50
                                      l G+N+sGK++ l+ +  +l+ +
  gi|557693599|ref|YP_008796653.1| 35 LLGPNGSGKTTSLKCIVGLLKPD 57
                                      77*************99888865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00061
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++ +l+++EP + L p+aqkv   ++ e+++d+   v+i+TH
  gi|557693599|ref|YP_008796653.1| 152 SPTVLILDEPFNGLDPEAQKVTRLYINEIIEDGG-GVLISTH 192
                                       467899***************************8.9****** 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 !   15.2   0.1   8.2e-06     0.013      16      50 ..      24      58 ..      17      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.2e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +++++  +++ l Gp+GsGK+T l  i  lL p+k
  gi|557693599|ref|YP_008796653.1| 24 SLRLEAGQVHGLLGPNGSGKTTSLKCIVGLLKPDK 58
                                      566664448889************99999999987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.6e-06     0.014      17      62 ..      29      76 ..      18     161 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.6e-06
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaag..grviglAptgkaAkvL 62
                                        +v+ l Gp G+GKtt+lk ++ +++ ++   +v+g  p+++   ++
  gi|557693599|ref|YP_008796653.1| 29 AGQVHGLLGPNGSGKTTSLKCIVGLLKPDKgiVTVFGEKPSANNGYRM 76
                                      446999******************999996244555544555444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.4e-05     0.023      29     143 ..      35     160 ..      15     190 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                            AAA_16  29 lsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleea 104
                                       l G+ G+GK++ ++++   l+ d+gi+ + g+  +   +  y + + +  ++  l + l+    +e+  ++++l++ 
  gi|557693599|ref|YP_008796653.1|  35 LLGPNGSGKTTSLKCIVGLLKPDKGIVtVFGEKPSA--NNGYRMKLGYVPENPSLPDYLTV---QEFLIFSARLKGL 106
                                       68***************9999998777555555555..34455544444444555555555...4445555555555 PP

                            AAA_16 105 la.........avpelagaea.........srllellkrll.allsrder....plvlvlDd 143
                                       ++                             rl ++l++ + ++l+  ++    p+vl+lD+
  gi|557693599|ref|YP_008796653.1| 107 VGdsvrsrvseL--------MesyelhqvsDRLVYELSKGIrQRLAIAASlvssPTVLILDE 160
                                       553333322220........122333444444444444444434333333444499999995 PP

>> AAA_23  AAA 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      0.03      23      40 ..      34      51 ..      14      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.8e-05
                            AAA_23 23 lItGpNGaGKTTildAik 40
                                       + GpNG+GKTT l +i 
  gi|557693599|ref|YP_008796653.1| 34 GLLGPNGSGKTTSLKCIV 51
                                      578************995 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   0.0   0.00011      0.17       3      66 ..      35     160 ..      34     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                       EESSTTSSHHHHHHHHHHHHTHE....................................................EE CS
                               AAA   3 lyGppGtGKTllakavakelgve....................................................fl 27 
                                       l Gp G GKT+  k ++  l+ +                                                      
  gi|557693599|ref|YP_008796653.1|  35 LLGPNGSGKTTSLKCIVGLLKPDkgivtvfgekpsanngyrmklgyvpenpslpdyltvqeflifsarlkglvgdS- 110
                                       78*****************974444444556666666777777777777777777777777775555555544442. PP

                                       EEETTTCSSS...................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  28 eisgsellsk...................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                                    +v e +k ir+ ++ a +   +p++l++DE
  gi|557693599|ref|YP_008796653.1| 111 ---------VrsrvselmesyelhqvsdrLVYELSKGIRQRLAIAASLVsSPTVLILDE 160
                                       .........04444445555777777777999999999999988877667889999998 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   3.7e-05     0.061       9      50 ..      12      54 ..      10      55 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                            AAA_27  9 eryGkftd.rsldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      +r+G+++  r ++++ e+ ++h ++GpN +GK+t+l+ i  ll
  gi|557693599|ref|YP_008796653.1| 12 KRFGRVEAvRGVSLRLEAGQVHGLLGPNGSGKTTSLKCIVGLL 54
                                      57888765245777777999*****************998876 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 ?   11.7   0.1   6.2e-05       0.1     136     163 ..      37      63 ..      31      67 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.2e-05
                             T2SSE 136 GgTgsGKttllyallkeinksderivtv 163
                                       G+ gsGKtt+l  ++  ++ + + ivtv
  gi|557693599|ref|YP_008796653.1|  37 GPNGSGKTTSLKCIVGLLKPD-KGIVTV 63 
                                       9*****************999.899987 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00024      0.38      11      37 ..      31      57 ..      23      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                            AAA_19 11 kvllvtaGpGtGKTrvlkhivallvel 37
                                      +v  ++++ G+GKT+ lk+iv ll+  
  gi|557693599|ref|YP_008796653.1| 31 QVHGLLGPNGSGKTTSLKCIVGLLKPD 57
                                      667799***************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1838.60
//
Query:       gi|557693600|ref|YP_008796654.1|  [L=103]
Description: large subunit ribosomal protein L12 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   55.3  13.0    8.9e-15   55.1  13.0    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
  ------ inclusion threshold ------
        2.3    8.3   7.4        4.1    7.5   5.5    2.1  2  PepSY_2        Peptidase propeptide and YPEB 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 !   55.1  13.0   9.9e-19   8.9e-15       2      88 .]      17     102 ..      16     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 9.9e-19
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX CS
                     Ribosomal_60s   2 ptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEe 78 
                                       +++e +k v++aag++ + +++k l +al++ +i+e+l++++a+ +a+aaa+a+aaaa++ a+a +ek+kee++   
  gi|557693600|ref|YP_008796654.1|  17 IDEEGLKRVVEAAGITPDMSKIKSLSAALAEINIDEVLKQATAAPVAVAAAPASAAAASKPAEAPAEKPKEEKQ--Q 91 
                                       78999***************************************88*************************998..6 PP

                                       --SS--.STTT CS
                     Ribosomal_60s  79 edddmG.fgLF 88 
                                       e+   G  +LF
  gi|557693600|ref|YP_008796654.1|  92 EEALSGlSALF 102
                                       77788877777 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 ?    0.6   0.0     0.066   5.9e+02      28      49 ..      15      38 ..      10      52 .. 0.65
   2 ?    7.5   5.5   0.00046       4.1       3      36 ..      60      96 ..      56     103 .] 0.71

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.066
                           PepSY_2 28 dwlpreklvakleaqGy..kvkki 49
                                      + +++e l++ +ea+G   + +ki
  gi|557693600|ref|YP_008796654.1| 15 KKIDEEGLKRVVEAAGItpDMSKI 38
                                      455667777777777764444454 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00046
                           PepSY_2  3 alalalallaaaAlA...grrdtdspkadwlpreklv 36
                                      a ++++a++a+aA A   ++   ++pk++ +++e+l+
  gi|557693600|ref|YP_008796654.1| 60 APVAVAAAPASAAAAskpAEAPAEKPKEEKQQEEALS 96
                                      4456777777777778888888888888888666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1102  (0.0614647); expected 358.6 (0.02)
Passed bias filter:                      625  (0.0348597); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 790.53
//
Query:       gi|557693601|ref|YP_008796655.1|  [L=366]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-97  324.9   0.0    5.6e-97  324.7   0.0    1.0  1  DUF763    Protein of unknown function (DUF763)


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 !  324.7   0.0  3.1e-101   5.6e-97       1     312 []       5     325 ..       5     325 .. 0.95

  Alignments for each domain:
  == domain 1  score: 324.7 bits;  conditional E-value: 3.1e-101
                            DUF763   1 GiadLpLhegkvPewllermkkLskaiveliveeygkeellerlsdPlwFqslgnvlGmdWdsSGsTtvvlgalkea 77 
                                       G+a+L+L eg vP+  +++m++L+++i+++++ ++g ee+++r++dP+w+ sl+++lG++Wd+SG+Ttv+l+al  +
  gi|557693601|ref|YP_008796655.1|   5 GTATLWLTEGPVPH--FREMVELGREIMRALCAQVGYEETVRRFADPFWLSSLACALGFEWDTSGQTTVTLKALSLG 79 
                                       89***********9..89*********************************************************** PP

                            DUF763  78 lkseelgilvaGGkGkksrktpeeleklaeklgldeek.lvkasrlvakvdnaalqdgyqlYlhalivsekgkwavi 153
                                       l+ +++ ++v+GGkG+++r  + e  kl  ++g+ e   + +a+rl++ vdnaalqd+y++Y++a  vse+g+wa+i
  gi|557693601|ref|YP_008796655.1|  80 LMGTDIPVRVLGGKGAEMRMAQLEAGKLLAEIGVREVGeIRRAMRLTTSVDNAALQDSYDIYFQAAAVSESGQWAII 156
                                       **********************************88767************************************** PP

                            DUF763 154 qQGmneeerlARRYhwlseelesfveephsgiagekkeeevlnlvskeseearkaildlvkekp.ekllkelkelka 229
                                       +QGmn+ +++ARRYhw  ++    veeph++i +++ e+ vl+l+s++s+e+r++il++++++p ++l+++l+++ka
  gi|557693601|ref|YP_008796655.1| 157 NQGMNTVNKTARRYHWS-SDRGLGVEEPHTEILSDTVEDVVLDLTSTTSAETRQTILEVLEDTPpSRLNEDLAQVKA 232
                                       ****************7.778889************************************8876599********** PP

                            DUF763 230 llkgekkl........klpakhev....lekvlekayelqpedfeellllkgvGpktlraLalvaeliygekasfkD 294
                                       +++++++l        ++p++ +      e+++++a  +++++f+ell+++gvG++tlr La++a l+yg+k+s++D
  gi|557693601|ref|YP_008796655.1| 233 IARKQHTLtstfeelpTIPKHLSPpnrlDEETIRRA--KNVSSFDELLTTQGVGAATLRGLAYIAALVYGSKVSWRD 307
                                       ***999999988888844444443555589999999..799************************************ PP

                            DUF763 295 PvkysfavGgKdgvPypv 312
                                       Pvk+s+a+G+K g Pypv
  gi|557693601|ref|YP_008796655.1| 308 PVKFSYAFGTKSGKPYPV 325
                                       *****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2684.78
//
Query:       gi|557693602|ref|YP_008796656.1|  [L=96]
Description: elongation factor EF-1 beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   54.8   0.1      9e-15   54.6   0.1    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain


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 !   54.6   0.1     5e-19     9e-15       2      90 .]      14      96 .]      13      96 .] 0.95

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 5e-19
                                      EEEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S.....S CS
                           EF1_GNE  2 vvlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiegeledlV 79
                                      +v+++ P+d++tdl+el+++v+s kl++ + + +  ++e+i+fGlk+L + + +++  +  ++le+ ++++e+     V
  gi|557693602|ref|YP_008796656.1| 14 MVVRILPKDSDTDLDELARAVES-KLPKdVRVSD-KRVEDIGFGLKALLMGFLMPEVDGVGEALEQYLSTVEL-----V 85
                                      689********************.****999995.**********************************9999.....9 PP

                                      EEEEEEEEEE- CS
                           EF1_GNE 80 qsveivsfnkl 90
                                      +++++ s++++
  gi|557693602|ref|YP_008796656.1| 86 GEYDVQSVTRI 96
                                      99999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 771.93
//
Query:       gi|557693603|ref|YP_008796657.1|  [L=299]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-26   91.2   0.3    1.5e-25   90.4   0.3    1.4  1  NTP_transf_3  MobA-like NTP transferase domain
    0.00028   20.9   0.0    0.00042   20.3   0.0    1.3  1  CTP_transf_3  Cytidylyltransferase
     0.0044   16.5   1.0     0.0078   15.7   1.0    1.3  1  SNAP          Soluble NSF attachment protein, SNAP


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 !   90.4   0.3   2.5e-29   1.5e-25       1     132 [.       8     142 ..       8     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 2.5e-29
                                       EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH....CHHHHHHTTCTS-EEE-TTSS-SHH CS
                      NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggd....eevlaalarlgvrvvededpgkgpl 73 
                                       +viL GG S+R+ggdKal+ l+g+pl+++v+++l++a v+ev+++++d    e++ +a++++   +++de  ++gpl
  gi|557693603|ref|YP_008796657.1|   8 GVILSGGVSKRFGGDKALALLNGEPLIRHVAKSLHEA-VEEVWLSVRDaergEQLMKACEPFVKGYIVDE-FSAGPL 82 
                                       79***********************************.*********94333355556666666677776.699*** PP

                                       HHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECC..E CS
                      NTP_transf_3  74 aslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpl..l 132
                                       +++++a++++ +ad v+  ++D+P +++++ ++l++++  ++a+v+ +++ +++ + l  +
  gi|557693603|ref|YP_008796657.1|  83 SGFLSAANRL-EADVVVTSPADVPRIKAATFQKLVEKFLHHSASVASVVWGNGAVETLvqV 142
                                       *********9.9***************************************9998887443 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     7e-08   0.00042       5     122 ..      11     135 ..       7     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7e-08
                                       EE-SSSSSSTT.GGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTT...SEEEE--TTCSSHHHHH CS
                      CTP_transf_3   5 pARsgSkRlpg.KnlldlggkpliayvleaalkskafekvivaTDseeiknvakefg...asvlvtrsslesdterf 77 
                                       ++   SkR+ g K+l+ l+g+pli++v + + +  a+e+v+++  + e  + + +++   ++ +  ++     ++ f
  gi|557693603|ref|YP_008796657.1|  11 LSGGVSKRFGGdKALALLNGEPLIRHVAKSLHE--AVEEVWLSVRDAERGEQLMKACepfVKGYIVDEFSAGPLSGF 85 
                                       555669999744*********************..89******8665555555555548888888888888889999 PP

                                       HHHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTTS.........S CS
                      CTP_transf_3  78 levvkaflmseneeiivnlqGdnPllqeevikkaietlkenqed.........y 122
                                       l +  +++++    ++v   +d P ++  + +k++e+ +               
  gi|557693603|ref|YP_008796657.1|  86 LSAANRLEAD----VVVTSPADVPRIKAATFQKLVEKFLHHSASvasvvwgngA 135
                                       9999999999....9999999999999999999999988885545533333332 PP

>> SNAP  Soluble NSF attachment protein, SNAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.0   1.3e-06    0.0078      33      97 ..     220     284 ..     216     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHHHHHHHTT-THHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT.-HHHHHHHH CS
                              SNAP  33 eAadlyeqAAnayklakkweeAgeaflkaAecqeklkekdeaanayveAakcykkv.speeAveal 97 
                                       e +  + qAA a   +k+++e+++ ++  A +  + + ++ a++a+++Aak++++  spe+A  + 
  gi|557693603|ref|YP_008796657.1| 220 ESSQHFRQAAAA-AAEKRFKESAQEYVSEALVLLSYGVAHLAGHALADAAKMFETGrSPEAALICS 284
                                       566778888877.689**************************************996677776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2328.43
//
Query:       gi|557693604|ref|YP_008796658.1|  [L=175]
Description: molybdopterin-guanine dinucleotide biosynthesis protein B [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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    1.4e-27   96.2   0.1    1.1  1  MobB       Molybdopterin guanine dinucleotide synthesis prote
  ------ inclusion threshold ------
      0.024   14.7   0.2      0.063   13.3   0.1    1.6  1  CbiA       CobQ/CobB/MinD/ParA nucleotide binding domain
      0.058   13.4   0.0      0.067   13.2   0.0    1.2  1  AAA_14     AAA domain
        0.1   12.7   0.0       0.17   12.0   0.0    1.3  1  Torsin     Torsin
       0.11   12.2   0.0       0.14   11.9   0.0    1.2  1  PduV-EutP  Ethanolamine utilisation - propanediol utilisation


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 !   96.2   0.1   3.8e-31   1.4e-27       2     113 ..       4     123 ..       3     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 3.8e-31
                              MobB   2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikeleeae 78 
                                       l+i+g++++GKT L +k+i+ l   g+rv+++Kh hh+f +d++gkD++r++++GA+ v+ +s++++a+i   +++e
  gi|557693604|ref|YP_008796658.1|   4 LAIMGFKKTGKTFLATKIIEDLVGDGYRVAAVKHVHHEFTIDTEGKDTWRMARSGASIVTSISPNEMAIIFPKQTHE 80 
                                       789*******************************************************************999999* PP

                              MobB  79 lsleellarl.se..vDlvlvEGfkke.....alpkievlrae 113
                                       ++ +ell ++ +e  +D+v+ EGf k      ++ ki  +r++
  gi|557693604|ref|YP_008796658.1|  81 TNRDELLGKIfQEegIDVVVYEGFAKLyggspHVYKILTVRKS 123
                                       *******99975579*********9752222244556555555 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   0.1   1.8e-05     0.063      10      34 ..      12      36 ..       4      38 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                                      SSHHHHHHHHHHHHHHTT--EEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA 10 vGKTtlaanLaralarrglrVllvD 34
                                      +GKT+la++++  l  +g+rV++v+
  gi|557693604|ref|YP_008796658.1| 12 TGKTFLATKIIEDLVGDGYRVAAVK 36
                                      8**********************98 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.9e-05     0.067       4      28 ..       3      32 ..       1      94 [. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                            AAA_14  4 ilvitGaRrvGKTtllkqlikell.....v 28
                                       l+i+G +++GKT+l+ ++i++l      v
  gi|557693604|ref|YP_008796658.1|  3 HLAIMGFKKTGKTFLATKIIEDLVgdgyrV 32
                                      689*****************9988544441 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.8e-05      0.17      56      92 ..       4      40 ..       2      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.8e-05
                                      EEEEE-TTSSHHHHHHHHHHHHSTTGGGSTTEEEEEH CS
                            Torsin 56 lsfhGwtGtGknfvaeiiaenlyrdGlrsdyvkkfva 92
                                      l++ G+  tGk f+a  i+e+l  dG r   vk++  
  gi|557693604|ref|YP_008796658.1|  4 LAIMGFKKTGKTFLATKIIEDLVGDGYRVAAVKHVHH 40
                                      6678999***********************9998755 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.8e-05      0.14       1      96 [.       1      99 [.       1     128 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                         PduV-EutP  1 mkkilliGkvgsGKttLtqalkgeel..kYkktqaief.sdeviDtPGeylenrklysalivtsaeadvialvqdatee 76
                                      mk++ ++G  ++GKt L+ ++ ++ +   Y+     ++ ++ +iDt G+       + a ivts++ + +a++   +++
  gi|557693604|ref|YP_008796658.1|  1 MKHLAIMGFKKTGKTFLATKIIEDLVgdGYRVAAVKHVhHEFTIDTEGKDTWRMARSGASIVTSISPNEMAIIFPKQTH 79
                                      89999************99987766632466655444414556******99999999999************9999999 PP

                         PduV-EutP 77 esvfppgfasvfnkeviGii 96
                                      e+   + + ++f+ e i ++
  gi|557693604|ref|YP_008796658.1| 80 ETNRDELLGKIFQEEGIDVV 99
                                      88888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1376.52
//
Query:       gi|557693605|ref|YP_008796659.1|  [L=224]
Description: ribose 5-phosphate isomerase A [Candidatus Caldiarchaeum subterraneum]
Scores for 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-53  179.7   0.0    4.5e-53  179.4   0.0    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    2.7e-06   27.4   0.0    1.8e-05   24.7   0.0    1.9  2  DeoRC           DeoR C terminal sensor 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 !  179.4   0.0     5e-57   4.5e-53       2     171 ..      48     214 ..      47     216 .. 0.97

  Alignments for each domain:
  == domain 1  score: 179.4 bits;  conditional E-value: 5e-57
                                       EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESS CS
                    Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlvek 78 
                                       ++p S q+  +a elg+ ++sld++++ d+++D  D+v++d ++iKGgGga+lrEK++a+a+++ +++ d+ Klvek
  gi|557693605|ref|YP_008796659.1|  48 IIPASWQSYYEAIELGLMVSSLDQHPCPDVYLDSFDQVTRDGAMIKGGGGAMLREKVLASASRNRVFVGDHGKLVEK 124
                                       79*************************************************************************** PP

                                       TTSS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEE CS
                    Rib_5-P_isom_A  79 lgkfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVve 155
                                       l   pvP+e++pfa++ v ++l+++ g+k ++R++++k+gp+v+dngn+i D++f ++i++p+++ek lk+ipGVve
  gi|557693605|ref|YP_008796659.1| 125 LR-RPVPLEIIPFAYKFVENRLREK-GVKLVMRTSQAKNGPTVSDNGNIIGDADF-GEIDEPAQVEKFLKEIPGVVE 198
                                       *5.9*******************87.*****************************.5688***************** PP

                                       ESEE-S--SEEEEEET CS
                    Rib_5-P_isom_A 156 tGlFlgladkvlvgke 171
                                       +G+F+gl+d+++++++
  gi|557693605|ref|YP_008796659.1| 199 SGIFMGLVDTLIIAHD 214
                                       *************986 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.0   2.1e-09   1.8e-05       3      47 ..       4      49 ..       3      62 .. 0.86
   2 ?    0.2   0.0     0.073   6.5e+02     121     139 ..     103     121 ..      83     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.1e-09
                             DeoRC  3 aeeKrrIAkaAaeliedgdtifldaGtTtlelaraLaekk.nltvv 47
                                      +e+K+r Ak+A++++ dg ++ +++GtT+ ++ ++La+   +++++
  gi|557693605|ref|YP_008796659.1|  4 VEAKKRAAKEAVKFVDDGFVVGVGSGTTVSLILSELAAAGkKIVII 49
                                      689*********************************9875466665 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.073
                             DeoRC 121 ralieaarrvillaDssKf 139
                                       + l++a+r+ + + D+ K+
  gi|557693605|ref|YP_008796659.1| 103 KVLASASRNRVFVGDHGKL 121
                                       667889999999****997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1764.97
//
Query:       gi|557693606|ref|YP_008796660.1|  [L=194]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  21.7    1.3e-33  116.2  21.7    1.5  2  DUF996        Protein of unknown function (DUF996)
  ------ inclusion threshold ------
      0.081   12.6  33.8      0.077   12.7  32.7    1.4  1  Yip1          Yip1 domain
        2.4    8.3  10.6        1.2    9.3   1.1    2.8  3  DUF962        Protein of unknown function (DUF962)


Domain annotation for each model (and alignments):
>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.98   5.9e+03     116     124 ..      13      21 ..       5      26 .. 0.59
   2 !  116.2  21.7   2.1e-37   1.3e-33       1     135 []      30     169 ..      30     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.98
                            DUF996 116 iGaiLtivl 124
                                       iG+iL+++ 
  gi|557693606|ref|YP_008796660.1|  13 IGSILLVLT 21 
                                       444444443 PP

  == domain 2  score: 116.2 bits;  conditional E-value: 2.1e-37
                            DUF996   1 lsivGliLvlvalkeiskavndekifsnaliafilsiialvvailalllvlgalatalelpgleeaas......lil 71 
                                       lsivG+iLvl+alk +s++v++++if+nal+a+i++i++ v+a+++ +++l ++a++ +++g     +      l++
  gi|557693606|ref|YP_008796660.1|  30 LSIVGFILVLLALKYVSDTVQQPAIFQNALYAVIIGIVGAVIAMVLGGAAL-FAAVGPGFGGGFGDGVsgdffsLLA 105
                                       69*************************************999766555555.5556666665555454589999*** PP

                            DUF996  72 llllvliiayvlliisavflkksyellgkrtgvklFetagllyfiGaiLtivlvGliilliaei 135
                                       +++++l+++++++++sa+fl+ks++l+++ +gvklF+t+gll+f+GaiLti+lvG+i++l+a++
  gi|557693606|ref|YP_008796660.1| 106 GVVVALVVVWIFAVVSAFFLRKSLYLTSDVLGVKLFRTGGLLLFLGAILTIILVGFILSLVAYV 169
                                       **************************************************************97 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  32.7   1.3e-05     0.077      26     155 ..      27     179 ..      23     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                              Yip1  26 llllalltlllgllaslnlgqtlasgeevqgltlssllga.iiggylglllgllllalllhliakllg......gkg 95 
                                       +++l +++++l+lla   +++t++++       +  +l a iig++ ++++++l  a+l+  ++  +g       +g
  gi|557693606|ref|YP_008796660.1|  27 GPVLSIVGFILVLLALKYVSDTVQQP-----AIFQNALYAvIIGIVGAVIAMVLGGAALFAAVGPGFGggfgdgVSG 98 
                                       799*************8888888877.....3344444440444444444555555555555777777766677999 PP

                              Yip1  96 sfkqtlsvvgyallPlilgaliaillllllgt.....................llllvgllaliWslvllylglkaa 151
                                       +f  +l+ v+ al++++++a++++++l  + +                     ++l ++l+++i slv+ +l   a+
  gi|557693606|ref|YP_008796660.1|  99 DFFSLLAGVVVALVVVWIFAVVSAFFLRKSLYltsdvlgvklfrtgglllflgAILTIILVGFILSLVAYVLLAVAF 175
                                       9***********************99999999********************9999999999999999999999888 PP

                              Yip1 152 hnls 155
                                       ++++
  gi|557693606|ref|YP_008796660.1| 176 FQIP 179
                                       8887 PP

>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.1    0.0002       1.2      27      87 ..      12      69 ..       5      78 .. 0.78
   2 ?    4.7   0.7    0.0052        31      44      65 ..     104     125 ..      69     136 .. 0.73
   3 ?    1.3   3.0     0.062   3.7e+02      48      65 ..     108     125 ..     106     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0002
                            DUF962 27 gvplilltvlllllraklklllalfvvgyifafvGHfvfEkrkPAlfknplqsllidplmv 87
                                      g+  ill+++++   +++  ++   +v  ++ +v++     ++PA+f+n l++++i+++ +
  gi|557693606|ref|YP_008796660.1| 12 GIGSILLVLTIVPNVGPVLSIVGFILVLLALKYVSDT---VQQPAIFQNALYAVIIGIVGA 69
                                      4556666666777777788888888899999999999...69**************99854 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0052
                            DUF962  44 lklllalfvvgyifafvGHfvf 65 
                                       l+ +++++vv +ifa v+ f++
  gi|557693606|ref|YP_008796660.1| 104 LAGVVVALVVVWIFAVVSAFFL 125
                                       566789999********99976 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.062
                            DUF962  48 lalfvvgyifafvGHfvf 65 
                                       ++++vv +ifa v+ f++
  gi|557693606|ref|YP_008796660.1| 108 VVALVVVWIFAVVSAFFL 125
                                       566777777777777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1398  (0.0779742); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 1346.36
//
Query:       gi|557693607|ref|YP_008796661.1|  [L=239]
Description: hypothetical protein CSUB_C0169 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-15   57.2   0.2    7.1e-14   51.4   0.0    2.3  2  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0081   15.9   0.0      0.019   14.7   0.0    1.6  1  DUF4423   Domain of unknown function (DUF4423)
  ------ inclusion threshold ------
      0.052   13.4   0.0       0.19   11.6   0.0    1.8  2  SMC_Nse1  Nse1 non-SMC component of SMC5-6 complex
        0.1   12.4   0.0       0.29   11.0   0.0    1.8  1  HTH_IclR  IclR 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 !   51.4   0.0   1.6e-17   7.1e-14       1      64 [.       4      67 ..       4      70 .. 0.93
   2 !    4.2   0.1    0.0087        39      13      55 ..      70     112 ..      65     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1.6e-17
                                      HH.HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                              TrmB  1 Lq.klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64
                                      Lq ++G+++y ak+Yla+l +g ++  ++a+++++p ++vY+vL+sL + G+ +r    +++ ++
  gi|557693607|ref|YP_008796661.1|  4 LQkVFGFNKYQAKAYLAVL-QGYSKPADVARKSKIPITRVYDVLSSLCENGFLTRTSDGYRVTEP 67
                                      7889***************.9**********************************9988887666 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0087
                                       HCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB  13 vYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55 
                                       +++  l++++a+++ +  e ++   ++  ++++L ++G Ve e
  gi|557693607|ref|YP_008796661.1|  70 AFTFWLERERARIESLMMEKKRMVEQIIPTVSRLRERGAVENE 112
                                       566668888888888888888888999999**********987 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.2e-06     0.019      29      82 ..      19      68 ..       6      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.2e-06
                           DUF4423 29 llplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqteks 82
                                      l+ l+ + ++p+ +a++ +  i+  +v + l+ L+++g+l+++ d  yr+te +
  gi|557693607|ref|YP_008796661.1| 19 LAVLQGY-SKPADVARKSK--IPITRVYDVLSSLCENGFLTRTSD-GYRVTEPA 68
                                      4445555.99*********..***********************9.9**99865 PP

>> SMC_Nse1  Nse1 non-SMC component of SMC5-6 complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.3e-05      0.19     153     183 ..      32      62 ..       5      68 .. 0.84
   2 ?   -0.9   0.0      0.29   1.3e+03     101     139 ..      90     127 ..      89     163 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.3e-05
                          SMC_Nse1 153 aadkgLtaseaeklLkrLveegWleksreGf 183
                                       a+++++  + + ++L++L+e+g+l ++++G+
  gi|557693607|ref|YP_008796661.1|  32 ARKSKIPITRVYDVLSSLCENGFLTRTSDGY 62 
                                       566788899999*****************97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.29
                          SMC_Nse1 101 Krlldamfet.sntrrlevmaitesqavvlelarilaaar 139
                                       Kr++++++ t s+ r  e +a++++ a+ + l+ ++++ r
  gi|557693607|ref|YP_008796661.1|  90 KRMVEQIIPTvSRLR--ERGAVENEAAILRGLQPVVVKLR 127
                                       677777777755444..45677777776666666554443 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 ?   11.0   0.0   6.4e-05      0.29      20      50 ..      27      57 ..      18      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
                                      BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 20 tlselArrtglpkStvhRlLqtLvelGyveq 50
                                      + +++Ar++ +p + v+  L++L e G++++
  gi|557693607|ref|YP_008796661.1| 27 KPADVARKSKIPITRVYDVLSSLCENGFLTR 57
                                      5689*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1778.92
//
Query:       gi|557693608|ref|YP_008796662.1|  [L=234]
Description: ubiquinone/menaquinone biosynthesis methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-20   71.9   0.0    5.6e-20   71.7   0.0    1.0  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    7.1e-16   58.6   0.0    1.1e-15   58.0   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    4.1e-13   49.8   0.0    6.5e-13   49.2   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    1.4e-11   44.5   0.0    1.6e-11   44.3   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    3.8e-08   34.0   0.0    5.8e-08   33.4   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    2.6e-07   30.5   0.0    3.5e-07   30.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
     0.0054   16.6   0.0     0.0079   16.1   0.0    1.2  1  Methyltransf_8   Hypothetical methyltransferase
     0.0054   16.8   0.0       0.02   15.0   0.0    2.0  1  FtsJ             FtsJ-like methyltransferase
     0.0074   15.8   0.0      0.014   14.9   0.0    1.4  1  MTS              Methyltransferase small domain
     0.0075   16.0   0.0      0.011   15.4   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.011   15.0   0.0        1.7    7.8   0.0    2.2  2  NNMT_PNMT_TEMT   NNMT/PNMT/TEMT family
       0.11   12.1   0.0       0.19   11.3   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW


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 !   71.7   0.0   3.8e-23   5.6e-20       9     228 ..      15     231 ..      10     234 .] 0.86

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 3.8e-23
                                       XXXXXX-HHHHHHHHHHHHHTTTHHHHHH.HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHH CS
                   Ubie_methyltran   9 vkevfesvaskyDlmndvlslgihrlWkk.fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenm 84 
                                       v    e++a  yD +n+ +s++     ++  ++  v+v+   +vlD  +G g ++ +l+++ + +g+vv+lD  ++m
  gi|557693608|ref|YP_008796662.1|  15 VMRSLEKLAPMYDRLNKTISFNTDIRLRAeCLNGNVGVL--DRVLDAGSGPGVFTETLLRTQNWRGEVVMLDPLPSM 89 
                                       5566789999************99877763444444444..48********************************** PP

                                       HHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHH CS
                   Ubie_methyltran  85 LkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpl 161
                                          ++kk+ ++   ++   +a  e++pf d+ fD+v ++f lr+ +++ kaL e +++l+ GGrl+v+++ k+ + l
  gi|557693608|ref|YP_008796662.1|  90 HMLARKKVPQNISHQV---VAVFEQMPFRDGVFDTVLMGFSLRDAANMAKALTETRKILRKGGRLLVVDLGKPANIL 163
                                       ********99888775...67789***************************************************** PP

                                       HHHHHHHHHH.HHHHHHHH.HHS-HHHHHHHHHHHHHS--HHHHHHHHHHTTEEEEEE.EEEGGGTEEE CS
                   Ubie_methyltran 162 lsqayelyskevlPvlGkl.lakdldsyryLvesirafPdqetlkeliedaGfksvey.esltgGvvai 228
                                        + a  +y   + P l  l l k   +   +  + r+ P +++lk l++   f++ve  e++ gGvv i
  gi|557693608|ref|YP_008796662.1| 164 KKIAIGVYWALLAPLLAALkLGKTGLEAAAIYLTYRRLPTNKELKYLLK-TFFETVEVgEKMLGGVVVI 231
                                       **********9***99887456666666767778899999999999986.5688887636677777766 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   7.3e-19   1.1e-15       1      96 []      57     153 ..      57     153 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 7.3e-19
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+G+G G ++e l ++    ++vv +D+ + m+ la++k++++      vva +e++pf+d+ fD v++ ++l   
  gi|557693608|ref|YP_008796662.1|  57 LDAGSGPGVFTETLLRTQnwrGEVVMLDPLPSMHMLARKKVPQNI--SHQVVAVFEQMPFRDGVFDTVLMGFSLRDA 131
                                       8**************666679**********************99..556*************************** PP

                                       CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                       ++++kal e +++L++gG+l++
  gi|557693608|ref|YP_008796662.1| 132 ANMAKALTETRKILRKGGRLLV 153
                                       *******************975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   4.4e-16   6.5e-13       1      97 []      56     149 ..      56     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 4.4e-16
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEE.EESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvef.vqgdaedlpfedgsfDlvvssgalh 75 
                                       vLd+G G+G +t+ l++  + +++v+++D+ ++m   ar+++ +   n++  v++ +e++pf dg fD v++  +++
  gi|557693608|ref|YP_008796662.1|  56 VLDAGSGPGVFTETLLRTQNwRGEVVMLDPLPSMHMLARKKVPQ---NISHqVVAVFEQMPFRDGVFDTVLM--GFS 127
                                       9***************998679********************43...6665256777***************..577 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       + + ++++kal e +++L++gG
  gi|557693608|ref|YP_008796662.1| 128 LRDAANMAKALTETRKILRKGG 149
                                       88999****************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   1.1e-14   1.6e-11      24     124 ..      31     160 ..       4     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 1.1e-14
                   Methyltransf_23  24 g.......................rvLdiGcGtGillevl.rengf..svtgvDlspeaveiae.....kakkaqkd 69 
                                       +                       rvLd G G G ++e l r++ +  +v++ D+ p ++ +a+     +    +++
  gi|557693608|ref|YP_008796662.1|  31 KtisfntdirlraeclngnvgvldRVLDAGSGPGVFTETLlRTQNWrgEVVMLDPLPSMHMLARkkvpqN----ISH 103
                                       345555666666666666777777*************99998887779***************9955553....444 PP

                   Methyltransf_23  70 qfdeq..eaaepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl 124
                                       q+ +   + ++ +g fd++ + ++l    +++++l+  +++l+ gG+ll+ + ++++
  gi|557693608|ref|YP_008796662.1| 104 QVVAVfeQMPFRDGVFDTVLMGFSLRDAANMAKALTETRKILRKGGRLLVVDLGKPA 160
                                       44333115577999**************************************99876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   3.8e-11   5.8e-08       1      99 []      57     151 ..      57     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3.8e-11
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L+ G+G G +++ ll+    + e++ +D+ ps+   a++k  +++ ++  +  +e+     +dg   fD+v++ + l
  gi|557693608|ref|YP_008796662.1|  57 LDAGSGPGVFTETLLRTQnWRGEVVMLDPLPSMHMLARKKVPQNISHQ-VVAVFEQMP--FRDG--VFDTVLMGFSL 128
                                       89************9998899*************99*******99754.333333343..4555..9********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGrl 99 
                                          ++++++l + rk L++gGrl
  gi|557693608|ref|YP_008796662.1| 129 RDAANMAKALTETRKILRKGGRL 151
                                       *********************97 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   2.4e-10   3.5e-07       6     113 ..      55     157 ..      52     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.4e-10
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsn 81 
                                       rvlD+G+G G +t  l ++ + ++evv +D  + +  lAr+    +  +n++ ++  ++e ++  + d  fD +l  
  gi|557693608|ref|YP_008796662.1|  55 RVLDAGSGPGVFTETLLRTQNWRGEVVMLDPLPSMHMLARK----KVPQNISHQVVAVFEqMP--FRDGVFDTVLMG 125
                                       89***************99999*********9999888888....5678999999999999**..************ PP

                   Methyltransf_31  82 evlnaladpdkileeiervlkpggilliedpr 113
                                         l + a+++k+l e  + l++gg+ll+ d  
  gi|557693608|ref|YP_008796662.1| 126 FSLRDAANMAKALTETRKILRKGGRLLVVDLG 157
                                       ***************************99876 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   5.3e-06    0.0079     112     158 ..     108     155 ..      94     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-06
                                       -TTS-S--TT-EEEEEEES---.SS-HHHHHHHHHHHEEEEEEEEEEE CS
                    Methyltransf_8 112 dlakvPledesvdvavfclslm.gtnladflkeanrvlkvGGllkvae 158
                                        + ++P  d+  d +++ +sl  + n+a+ l e +++l++GG l v +
  gi|557693608|ref|YP_008796662.1| 108 VFEQMPFRDGVFDTVLMGFSLRdAANMAKALTETRKILRKGGRLLVVD 155
                                       4689*****************7468******************99876 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-05      0.02       4     157 ..      17     220 ..      14     222 .. 0.46

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                       CHHHHHHHHHHHHT...-S-TT..................-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHH CS
                              FtsJ   4 RsayKLleidekfk...lfkpg..................ktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmap 59 
                                       Rs  KL+ + ++ +                          ++v+D g++PG +++ ll+  + +g vv +D  p   
  gi|557693608|ref|YP_008796662.1|  17 RSLEKLAPMYDRLNktiS---FntdirlraeclngnvgvlDRVLDAGSGPGVFTETLLRTQNWRGEVVMLDPLPSMH 90 
                                       777777777666662211...122345555555555555566***************99964467777777766644 PP

                                       HTTEEEECS-CCCSSHHHHHCHCHHH..............................SSEEEEEE--S-SS-CHHHHH CS
                              FtsJ  60 lpgvttiqgditdpetiekikealse..............................rkvdlvvsDgapdvsgvhdld 106
                                       +   + +  +i ++ ++   +  + +                              ++  l v D++   +  +++ 
  gi|557693608|ref|YP_008796662.1|  91 MLARKKVPQNISHQVVAVFEQMPFRDgvfdtvlmgfslrdaanmakaltetrkilrKGGRLLVVDLGKPANILKKIA 167
                                       43333333444444443333333333122222222222222222222222333443455555555554443333333 PP

                                       HHHH...CCCCHHHHCCHCCCCECCCEEEECCCHCCCHH.HHHHHHHCCEEEEEE CS
                              FtsJ 107 eylq...sqLllaalelalkllkpggtfvlkifrgeete.allkqlkkfFekvsv 157
                                         +    +  llaal+l+ + l+     +  ++r+  t+ +l + lk+fFe+v+v
  gi|557693608|ref|YP_008796662.1| 168 IGVYwalLAPLLAALKLGKTGLEAA--AIYLTYRRLPTNkELKYLLKTFFETVEV 220
                                       3333111122333333333333322..3333444555553666667777777765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   9.7e-06     0.014      30     138 ..      49     154 ..      38     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.7e-06
                                       C..TCSEEEEET-TTSHHHHHHHHHTT.C.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE CS
                               MTS  30 e..lsgkvlDlGcGaGvlgaalakesp.eaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivs 103
                                       +    ++vlD G+G Gv + +l++ ++ + ev+++d       +a++ + +n    +vva      + ++ fd++++
  gi|557693608|ref|YP_008796662.1|  49 NvgVLDRVLDAGSGPGVFTETLLRTQNwRGEVVMLDPLPSMHMLARKKVPQNIS-HQVVAVFEQMPFRDGVFDTVLM 124
                                       4444568************999887662567*****988888888888888765.4555554555667899****** PP

                                       ---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEE CS
                               MTS 104 NPPfhagkatelavaeeliaeAkeaLkegGeLliV 138
                                          +++  +     + + ++e +++L++gG+Ll+V
  gi|557693608|ref|YP_008796662.1| 125 GFSLRDAAN-----MAKALTETRKILRKGGRLLVV 154
                                       988887777.....55566789***********99 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 !   15.4   0.0   7.7e-06     0.011      53     130 ..      30     109 ..      20     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.7e-06
                                       TEEE--HHHHHHHHHHTT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEE CS
                              PCMT  53 natiSaphmvalalelle..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvi 127
                                       n+tiS    + l  e l+  +   +rvL+ GsG G  t  l r  + +g vv ++  +++   a++++ ++ +++v+
  gi|557693608|ref|YP_008796662.1|  30 NKTISFNTDIRLRAECLNgnVGVLDRVLDAGSGPGVFTETLLRTQNWRGEVVMLDPLPSMHMLARKKVPQNISHQVV 106
                                       5666666666666777776667779*******************************************999999887 PP

                                       EEE CS
                              PCMT 128 vvv 130
                                        v+
  gi|557693608|ref|YP_008796662.1| 107 AVF 109
                                       654 PP

>> NNMT_PNMT_TEMT  NNMT/PNMT/TEMT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0082        12      57      76 ..      53      72 ..      37      88 .. 0.78
   2 ?    7.8   0.0    0.0011       1.7     147     199 ..     104     155 ..      93     160 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0082
                                      ECEEEEET-TT--GGGTTGG CS
                    NNMT_PNMT_TEMT 57 gdtllDiGaGPTvyqllsar 76
                                       d +lD G+GP v++   +r
  gi|557693608|ref|YP_008796662.1| 53 LDRVLDAGSGPGVFTETLLR 72
                                      489**********9876555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0011
                                       STTTTSS-SS..EEEEEEESSHHHH-SSHHHHHHHHHHHHTTEEEEEEEEEEE CS
                    NNMT_PNMT_TEMT 147 pvvlagvqlpkkadvvvtifcleaacedleeylralrnlasllkpGGhlvlgg 199
                                       +vv    q+p   d v  +  +  + +d ++  +al+++ + l++GG+l++++
  gi|557693608|ref|YP_008796662.1| 104 QVVAVFEQMPF-RDGVFDTVLMGFSLRDAANMAKALTETRKILRKGGRLLVVD 155
                                       44544467776.688888888999999**********************9875 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.19      15     103 ..      54     146 ..      42     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                              MetW  15 srvldlGcGdGellellkeekqvdgrGleldeegvaecvakG.l..sviqgdld.kdlenfedksfdyvvlsqtlqa 87 
                                        rvld G+G G + e l  +++ +g+ + ld    ++ +a+  +  ++ ++ +   +   f+d  fd v++  +l+ 
  gi|557693608|ref|YP_008796662.1|  54 DRVLDAGSGPGVFTETLLRTQNWRGEVVMLDPLPSMHMLARKkVpqNISHQVVAvFEQMPFRDGVFDTVLMGFSLRD 130
                                       69**************99************9988777777641221333333221344568999************* PP

                              MetW  88 trnpkevldellrigr 103
                                         n ++ l e  +i r
  gi|557693608|ref|YP_008796662.1| 131 AANMAKALTETRKILR 146
                                       *******999766654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1788.29
//
Query:       gi|557693609|ref|YP_008796663.1|  [L=485]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-05   24.7   3.9    3.3e-05   23.8   3.9    1.5  1  V4R       V4R domain


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   3.9   1.9e-09   3.3e-05       3      59 ..     425     481 ..     423     484 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.9e-09
                                       EEEEEES-S-TT---SS---H.HHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEE CS
                               V4R   3 lsieespelaglpgkeePvCy.leaGllagalsellgkrveveEveCaaeGhdhCeFe 59 
                                       ++++++ ++ +   ++eP C  ++  +  g+ls  l++r+e+ Ev+C a+G + C+F+
  gi|557693609|ref|YP_008796663.1| 425 FEVRNCHLCGD-AVSDEPFCDkFVSSVVVGVLSVCLKRRFECFEVSCKAVGNESCIFK 481
                                       6899*******.599*****658999*******************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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 0.26s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3607.40
//
Query:       gi|557693610|ref|YP_008796664.1|  [L=285]
Description: 4-hydroxybenzoate octaprenyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-28   97.1  29.9    2.2e-27   96.0  29.9    1.5  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.013   15.6   0.0      0.024   14.8   0.0    1.4  1  SoPB_HTH  Centromere-binding protein HTH domain


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 !   96.0  29.9   2.4e-31   2.2e-27       8     235 ..      34     265 ..      26     284 .. 0.80

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 2.4e-31
                              UbiA   8 g...lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgl 81 
                                       +   + +++ g +dl   ++++l ++l +a+ n +N++ D+++D +   + n Pl+sG+isp+ea +f++++li+++
  gi|557693610|ref|YP_008796664.1|  34 SvtiMIITGEGLLDL---WVFWLYFFLSTAFLNSFNNLMDIKSDYI--TKNNFPLPSGLISPREASLFSAATLIAAV 105
                                       334477777777777...56666779********************..666************************** PP

                              UbiA  82 lll..alllnpltallgllalllyvvYt.g.lrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavfl 154
                                       + l  +l +n  +a+++l+ ll++++Y+ + +rlKr+++l+   + i+ +++pl+     ++   +  l++ ++v l
  gi|557693610|ref|YP_008796664.1| 106 ATLipILEVNASAAGILLIDLLIGYFYSaPkIRLKRYPVLKATMLIIHTAILPLIVGLTLANKSIADYLAIVFPVYL 182
                                       ***9*************************99*******************8888777775555579999999***** PP

                              UbiA 155 ltwaialandlrdregDrkagiktlpvvlGrkaarillalllavllla..llllllalllllylllalllaalallr 229
                                       + +a+++ +d+ d+ gD   g kt+p  lG k+++ l +ll +++ ++  l++   +  l ++l+++ ++++++l++
  gi|557693610|ref|YP_008796664.1| 183 MGLAVHTLQDIGDVVGDVLMGDKTFPSMLGMKNSVLLTVLLFMLAAIFtwLVFDASYRILIMFLFFSQIVLSMLLFI 259
                                       ************************************74433333333344445555555555555555566666665 PP

                              UbiA 230 aarlvr 235
                                        + l++
  gi|557693610|ref|YP_008796664.1| 260 RVNLWK 265
                                       555554 PP

>> SoPB_HTH  Centromere-binding protein HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.6e-06     0.024      28      55 ..       2      29 ..       1      36 [. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-06
                          SoPB_HTH 28 aeklskkilskmlrvaklPdavvalFas 55
                                      + k+sk ++ km+  a+lP++  +lF+s
  gi|557693610|ref|YP_008796664.1|  2 RVKMSKYFIQKMIGFATLPKSYFSLFTS 29
                                      679***********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1008  (0.0562218); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2023.06
//
Query:       gi|557693611|ref|YP_008796665.1|  [L=386]
Description: hypothetical protein CSUB_C0173 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.6   0.1      0.061   13.3   0.1    1.6  1  DUF1077   Protein of unknown function (DUF1077)
       0.09   12.9   0.1       0.18   12.0   0.1    1.4  1  CDC37_C   Cdc37 C terminal domain


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 ?   13.3   0.1   6.8e-06     0.061      37      85 ..      95     146 ..      80     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.8e-06
                           DUF1077  37 nslqifsimmvlmllvnpikallsvnkaFkkleseks...ksklllqklvyv 85 
                                       +  qifs +++ m+l+  ik l ++n++F++ e++++   ++k  +++ +y+
  gi|557693611|ref|YP_008796665.1|  95 TRAQIFSTVLAKMALIISIKVLDNINDTFHTTEEAEQslqRQKKAIEEGIYI 146
                                       568*****************************99877443445555555555 PP

>> CDC37_C  Cdc37 C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1     2e-05      0.18      12      58 ..      93     137 ..      88     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                           CDC37_C  12 eqkkvevFeklppelqkAlktksLdevnkvlakmkveeAeeilellg 58 
                                       +  + ++F+++  ++   +  k Ld++n+++     eeAe+ l++ +
  gi|557693611|ref|YP_008796665.1|  93 KATRAQIFSTVLAKMALIISIKVLDNINDTFHT--TEEAEQSLQRQK 137
                                       56789**************************96..69****999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); 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 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2749.90
//
Query:       gi|557693612|ref|YP_008796666.1|  [L=244]
Description: hypothetical protein CSUB_C0175 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   33.4  29.9    6.3e-05   21.9   4.8    2.6  2  Presenilin       Presenilin
    2.5e-06   27.2  13.2    2.5e-06   27.2  13.2    2.0  2  SPP              Signal-peptide peptidase, presenilin asparty
  ------ inclusion threshold ------
       0.87   10.2   4.5        4.9    7.8   2.0    2.4  2  Phage_holin_1    Bacteriophage holin


Domain annotation for each model (and alignments):
>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8  16.8   3.8e-07    0.0023      62     199 ..      27     154 ..      16     163 .. 0.61
   2 !   21.9   4.8   1.1e-08   6.3e-05     320     392 ..     170     241 ..     155     243 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.8e-07
                        Presenilin  62 lnalililvivvvtfllvlLykyrcykvikgwlilsslllLflvsglllaevlkaynipldyitlllllwnfgvvGv 138
                                       ln+l +i+v+++ ++ ++  + +r+ + + +  i+s  ++Lf  ++ ++  +l +     + + +++ +++ g+v +
  gi|557693612|ref|YP_008796666.1|  27 LNSLLVIAVMFLGSLAML--WLIRFRRALAV--IVS--VVLFTTAVSVTFLLLFVSTSLGEELLAAVSILVGGMV-L 96 
                                       567777777766666555..55666666553..333..3333333333333333333333344444444444444.3 PP

                        Presenilin 139 iaifw..kgplllqqaYlilisalmAlvfikylpewTtwvlLvvisiyDlvAVLcPkGPLrlL 199
                                         +f       +l  aY+ + s    +vf   lp wT  vlL+++s+yD+vAV   kG L+ L
  gi|557693612|ref|YP_008796666.1|  97 AGVFSrkGLFNVLAAAYVASAS---GVVFGSSLPFWTSLVLLAAVSVYDVVAVF--KGHLKRL 154
                                       4445521233467888876666...6789999*********************7..6777776 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.1e-08
                        Presenilin 320 rgvkLGLGDFiFYSvLvgkAalsgdlntvvacfvailiGLclTLllLaifkkalPALPisialGlvfyfltrl 392
                                       +g  +GLGD  FYSv ++ +  +  +   +a+  + ++G  +T+  La ++   P LP+ ++ ++ f f+++l
  gi|557693612|ref|YP_008796666.1| 170 EGFSIGLGDLFFYSVVLSFSVNNLGWLPGIAASAGLIVGYLATI-KLAETRPVFPGLPLTLLAAMGFAFISYL 241
                                       58889**************************************7.589********************99876 PP

>> SPP  Signal-peptide peptidase, presenilin aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2  13.2   4.2e-10   2.5e-06      24     157 ..      18     149 ..       8     161 .. 0.76
   2 ?    1.6   2.1     0.027   1.6e+02     203     269 ..     172     231 ..     158     244 .] 0.69

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 4.2e-10
                               SPP  24 qatedPtqvlnsvvyivlllvftlfvlivi..kkdkkliiskviyvivvavifyvflvllsivlvvaglvnlaslvv 98 
                                           +P   lns++ i+++++ +l +l  i  ++   +i+s v++++ v+v f +++v  s+   +     +  lv 
  gi|557693612|ref|YP_008796666.1|  18 AVLGSPAPYLNSLLVIAVMFLGSLAMLWLIrfRRALAVIVSVVLFTTAVSVTFLLLFVSTSLGEELLA--AVSILVG 92 
                                       456789999************99998766611566677888888999999999999988888755444..3344555 PP

                               SPP  99 aialvvllyaypeWyvidlaGvilavGvsalfGislgvlpavvllialavydaisvykt 157
                                        ++l +++  +  + v+ +a v  a G   +fG sl  ++ +vll a+ vyd ++v+k 
  gi|557693612|ref|YP_008796666.1|  93 GMVLAGVFSRKGLFNVLAAAYVASASG--VVFGSSLPFWTSLVLLAAVSVYDVVAVFKG 149
                                       677777666666666666655555555..59**************************96 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.027
                               SPP 203 lfiGlGdavlPsilvvsaavfleshilaglelavllalaGtlvGllvlsilvlrgrpaaGlPllnsG 269
                                       + iGlGd  + s+++   +v  ++  l g  l+ ++a aG +vG+l  + l       +GlPl    
  gi|557693612|ref|YP_008796666.1| 172 FSIGLGDLFFYSVVLS-FSV--NN--L-G-WLPGIAASAGLIVGYLATIKLAETRPVFPGLPLTLLA 231
                                       7799999998887543.222..22..2.1.368899999*****99999977666668999985433 PP

>> Phage_holin_1  Bacteriophage holin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   2.0   0.00081       4.9       5      60 ..      47      99 ..      44     103 .. 0.84
   2 ?    2.3   0.0     0.042   2.5e+02      11      35 ..     127     151 ..     120     171 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00081
                     Phage_holin_1  5 vRlknkafwvalisavlllilavlglfgldltvaklaeqllqivsavlsllaalGv 60
                                      +R++     +a+i +v+l++ av   f l + +++l+e+ll++vs+++  +++ Gv
  gi|557693612|ref|YP_008796666.1| 47 IRFRRA---LAVIVSVVLFTTAVSVTFLLLFVSTSLGEELLAAVSILVGGMVLAGV 99
                                      555554...68999999******999999999999**********99987777776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.042
                     Phage_holin_1  11 afwvalisavlllilavlglfgldl 35 
                                        fw++l+++ ++ +  v+++f+  l
  gi|557693612|ref|YP_008796666.1| 127 PFWTSLVLLAAVSVYDVVAVFKGHL 151
                                       69*******9999999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1775.26
//
Query:       gi|557693613|ref|YP_008796667.1|  [L=291]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-54  182.9   0.1    1.1e-53  182.8   0.1    1.0  1  CitG          ATP:dephospho-CoA triphosphoribosyl transferase
  ------ inclusion threshold ------
      0.022   14.8   0.1      0.037   14.1   0.1    1.3  1  HTH_Tnp_Mu_2  Mu DNA binding, I gamma subdomain
      0.043   12.6   0.0      0.059   12.1   0.0    1.1  1  DUF935        Protein of unknown function (DUF935)


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 !  182.8   0.1   1.8e-57   1.1e-53       1     280 [.      10     283 ..      10     284 .. 0.93

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 1.8e-57
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXHHHHHHHHHTTHHHHHHHH...........HH--HHHHHHHHHH CS
                              CitG   1 aelavlAlllEvsatpKPGlVdrrdsgahdDmdfetFlaSaealapyfeeaaaaGleakalfeelrsiGelaekaml 77 
                                       a++++l lllE++++pKPGlVdr ++    D  ++ F aSa+al+p+f +aa           +  s+G+++    +
  gi|557693613|ref|YP_008796667.1|  10 ARCCTLGLLLELATSPKPGLVDRLSNP---D-VYACFTASAVALYPCFLKAA-----------QGTSVGDAVLCSTR 71 
                                       7899**********************9...4.79******************...........56789999887777 PP

                                       HH...------HHHHHHHHHHHHTTTTS-.......SHHHHHHHHHHHHHT--HHHHHHH.HHHHHH--........ CS
                              CitG  78 aa...tggvNThkGaifllgllaaaagrraaeeeeasleelveeaaevlaeltvedavaf.rairlakv........ 142
                                       ++   ++g+NTh+G ++ll+++a aa ++       ++e+l+  ++++l++++++d++++ +ai+++ +        
  gi|557693613|ref|YP_008796667.1|  72 EMmswQKGGNTHLGSLLLLTPIAKAAVEA------GKIERLRGSLEKTLKQMDYRDLHKIlKAIKMVGPgglgkvay 142
                                       77777**********************66......689*******************************99998876 PP

                                       ..---...HHHHHH.TT--HHHHHHTS-TT-HHHHHHHHTSHHHHHHHH........HH-SSHHHHHHHHHHHHHHS CS
                              CitG 143 ..eel...kdelvekksltlgevlelsygvdgirgeaasgFpsvfeialpalrealasgadlndalvqallallael 214
                                           +   + +lv+++++++ e+    ++++ +++e+ ++++ ++ +++ +lr+ + +++d n a ++++l++l++l
  gi|557693613|ref|YP_008796667.1| 143 ldV-NnakTYNLVKQRKTSVIEAFNPYAQWEVVAHEYCTNYQASIMHGYMFLRKRI-EQEDWNTAGINTFLNILQHL 217
                                       651.144566777789**************************************87.568***************** PP

                                       --HHHHHHHHHHHHHHHHHHHH..........H-SHHHHHHHHHHHHHHT---HHHHHHHHHHHHH CS
                              CitG 215 pDtnilrrgGaegaeevqeeArallaaggvaaeaglealeeldrelvernisPGgsADllaatlfl 280
                                       pD+++ rr+G+++a+  +++A+++l+aggv++e+g ++ +++ +  ++ ++ P  +AD+la+++ l
  gi|557693613|ref|YP_008796667.1| 218 PDSHVSRRQGRHAAKILSRMAKQVLDAGGVGTEEGGRRYTQFIKHVKRAGMKPAAAADVLAVSYTL 283
                                       **************************************************************9875 PP

>> HTH_Tnp_Mu_2  Mu DNA binding, I gamma subdomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   6.2e-06     0.037      21     101 ..     155     233 ..     143     241 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.2e-06
                                       XXSXX--TT--S-HHHHHHHHHHHTSTT---HHHHHHHHHHHHHHHT-----HHHHHHHH.HHH-CHHHHHHH--HH CS
                      HTH_Tnp_Mu_2  21 aaakkekevaeideeawqflkadYlrpekPtlaacyerlkkaAqekGwaiPslkslkrrleeavpetevvllRegeh 97 
                                       +++k+++  a+ + + w+++  +Y  + + ++ + y  l+k   ++ w+   ++++   l +++p+ + v +R+g+h
  gi|557693613|ref|YP_008796667.1| 155 KQRKTSVIEAFNPYAQWEVVAHEYCTNYQASIMHGYMFLRKRIEQEDWNTAGINTFLNIL-QHLPD-SHVSRRQGRH 229
                                       4666777777888899****************************************9999.9***9.889******* PP

                                       HH-X CS
                      HTH_Tnp_Mu_2  98 aLkk 101
                                       a k 
  gi|557693613|ref|YP_008796667.1| 230 AAKI 233
                                       9664 PP

>> DUF935  Protein of unknown function (DUF935)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     1e-05     0.059     469     511 ..      89     131 ..      55     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1e-05
                            DUF935 469 llapvlelleeaesleelrerlaelypdmdaeelaelLaralf 511
                                       ll+p+ +++ ea+++e lr +l++ +++md ++l++ L+ + +
  gi|557693613|ref|YP_008796667.1|  89 LLTPIAKAAVEAGKIERLRGSLEKTLKQMDYRDLHKILKAIKM 131
                                       89***********************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2140.35
//
Query:       gi|557693614|ref|YP_008796668.1|  [L=96]
Description: hypothetical protein CSUB_C0177 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.083   12.5   4.0      0.037   13.6   1.9    1.5  1  Ni_hydr_CYTB  Prokaryotic cytochrome b561
       0.15   12.0   6.0      0.083   12.8   3.4    1.7  1  DUF5453       Family of unknown function (DUF5453)
        0.2   12.4   6.9        0.1   13.3   4.3    1.7  2  DUF4728       Domain of unknown function (DUF4728)
       0.94    9.1   5.1       0.62    9.6   0.4    2.0  2  Saf_2TM       SAVED-fused 2TM effector domain
        1.9    8.6   5.5          4    7.5   5.5    1.6  1  Vma12         Endoplasmic reticulum-based factor for assembly


Domain annotation for each model (and alignments):
>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.9     1e-05     0.037     106     167 ..       5      58 ..       3      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHHHHHHHHTHHHHHHHH...HTS-THHHHHHH.HHHHHHH.HHHHHHHHHHHH CS
                      Ni_hydr_CYTB 106 lllyvllvvliltGlllsfaatagfplllddkggaqlarelHellaaall.afvvlHiaaall 167
                                       +l+ +l+ ++i+tGll+s          +++   ++ ar+    + +al  +f++ H++aa +
  gi|557693614|ref|YP_008796668.1|   5 WLINILISLMIVTGLLYSL---------RNYLLTRKYARTKFTNALVALTsVFLIQHLYAAYV 58 
                                       8999*************65.........35888899999999888888888999999999864 PP

>> DUF5453  Family of unknown function (DUF5453)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   3.4   2.3e-05     0.083      91     132 ..       5      47 ..       3      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.3e-05
                           DUF5453  91 fllnillgvlllvllvnfltnqileekysll.ltnalpllyss 132
                                       +l+nil++++++  l++ l+n  l++ky +  +tnal  l s 
  gi|557693614|ref|YP_008796668.1|   5 WLINILISLMIVTGLLYSLRNYLLTRKYARTkFTNALVALTSV 47 
                                       89***************************999**998777665 PP

>> DUF4728  Domain of unknown function (DUF4728)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   4.3   2.8e-05       0.1      31      85 ..       5      60 ..       3      67 .. 0.77
   2 ?    0.5   0.5      0.27   9.8e+02      29      71 ..      74      84 ..      49      94 .. 0.36

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                           DUF4728 31 WLinslvslvleigilvalv.llvsvieakidrlialliifflllvLniyiyygiy 85
                                      WLin l+sl++ +g+l++l  +l++ + a +++ +al  ++ ++l+ ++y  y+ y
  gi|557693614|ref|YP_008796668.1|  5 WLINILISLMIVTGLLYSLRnYLLTRKYARTKFTNALVALTSVFLIQHLYAAYVFY 60
                                      *****************997666777777777777777666666666677666655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.27
                           DUF4728 29 lPWLinslvslvleigilvalvllvsvieakidrlialliiff 71
                                       P                                l++l +i f
  gi|557693614|ref|YP_008796668.1| 74 TP--------------------------------LLMLNVIGF 84
                                      12................................222222322 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 ?    9.6   0.4   0.00017      0.62      69     100 ..       5      36 ..       3      41 .. 0.88
   2 ?    2.3   0.6     0.033   1.2e+02      26      79 ..      43      87 ..      32      94 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00017
                           Saf_2TM  69 aiilvigvllivvGavllilryvneakrqskk 100
                                       ++i+++ +l+iv+G++ ++++y+ ++k    k
  gi|557693614|ref|YP_008796668.1|   5 WLINILISLMIVTGLLYSLRNYLLTRKYARTK 36 
                                       8899******************9999976655 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.033
                           Saf_2TM 26 ftigvalllailgtdwalkialkla.ggslevsfssseipeivlaiilvigvlli 79
                                        ++           +++++++     + ++vs+s++  ++  l++++vig++ +
  gi|557693614|ref|YP_008796668.1| 43 ALTS----------VFLIQHLYAAYvFYMMSVSYSEEMHIATPLLMLNVIGFAGF 87
                                      2223..........44444444444445566666666655555566666655433 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 ?    7.5   5.5    0.0011         4      80     131 ..       6      63 ..       2      95 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0011
                             Vma12  80 vlNiliSvvavffavwialrsartp.slpvrvllslvvallVgv.....AEvvvyaky 131
                                        +NiliS ++v+  ++++ +++ t     +++  +lv+ + V++     A  v+y+  
  gi|557693614|ref|YP_008796668.1|   6 LINILISLMIVTGLLYSLRNYLLTRkYARTKFTNALVALTSVFLiqhlyAAYVFYMMS 63 
                                       79*******************9888645566767777766666611111444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); 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 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 694.97
//
Query:       gi|557693615|ref|YP_008796669.1|  [L=109]
Description: transcriptional regulator, ArsR family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   45.8   0.1    7.4e-12   44.9   0.1    1.5  1  HTH_5     Bacterial regulatory protein, arsR family
    2.1e-05   24.4   0.1    3.4e-05   23.7   0.1    1.4  1  HTH_45    Winged helix-turn-helix
    5.1e-05   23.3   0.0      9e-05   22.5   0.0    1.4  1  HTH_20    Helix-turn-helix domain
    0.00019   21.3   0.0    0.00036   20.4   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0003   20.5   0.0    0.00036   20.3   0.0    1.1  1  DUF4423   Domain of unknown function (DUF4423)
     0.0014   18.2   0.1     0.0025   17.3   0.1    1.5  1  HTH_24    Winged helix-turn-helix DNA-binding
     0.0093   16.3   0.0      0.014   15.7   0.0    1.4  1  Rrf2      Transcriptional regulator
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.018   15.0   0.0    1.2  1  HTH_11    HTH domain
      0.017   15.1   0.0      0.079   13.0   0.0    1.9  2  HTH_29    Winged helix-turn helix
      0.052   13.4   0.0      0.071   13.0   0.0    1.2  1  HxlR      HxlR-like helix-turn-helix
       0.11   12.4   0.0       0.18   11.7   0.0    1.3  1  RuvB_C    RuvB C-terminal winged helix 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 !   44.9   0.1   4.5e-15   7.4e-12       2      46 ..      21      65 ..      20      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 4.5e-15
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      ptRl IL  L++g++ + +la++l+l+  t+ hHL +L e +LVe
  gi|557693615|ref|YP_008796669.1| 21 PTRLLILLKLRDGPANANQLAKALHLNYKTILHHLEFLIENNLVE 65
                                      9*******************************************7 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   2.1e-08   3.4e-05      11      58 ..      26      73 ..      24      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.1e-08
                            HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvl 58
                                      IL ++++g a+  ++ ++  L+yk++   L++L+e++l++ +++ Y +
  gi|557693615|ref|YP_008796669.1| 26 ILLKLRDGPANANQLAKALHLNYKTILHHLEFLIENNLVEADEGRYDV 73
                                      7888999***********************************999965 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   5.5e-08     9e-05      10      57 ..      21      67 ..      19      71 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.5e-08
                                      HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 10 PvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      P+R+ il  L r++++ a++la++l l  +t+ +HL+ L e  Lve  
  gi|557693615|ref|YP_008796669.1| 21 PTRLLILLKL-RDGPANANQLAKALHLNYKTILHHLEFLIENNLVEAD 67
                                      9*********.**********************************965 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.2e-07   0.00036      17      64 ..      27      77 ..      23      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.2e-07
                                      HH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT.EEEE CS
                              TrmB 17 Ll..klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk.lYra 64
                                      Ll  + gpa+a+++a++l + + ++   L+ L++  lVe  +gr+  +Yr 
  gi|557693615|ref|YP_008796669.1| 27 LLklRDGPANANQLAKALHLNYKTILHHLEFLIENNLVEADEGRYDvKYRL 77
                                      554488**************************************7658875 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.2e-07   0.00036      26      82 ..      24      77 ..      21      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.2e-07
                           DUF4423 26 irellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqteks 82
                                      ++ ll+l+d+ a+ ++lak+l+  ++ + + + lefL +++l++ de g+y +  + 
  gi|557693615|ref|YP_008796669.1| 24 LLILLKLRDGPANANQLAKALH--LNYKTILHHLEFLIENNLVEADE-GRYDVKYRL 77
                                      56699*****************..***********************.799887655 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 !   17.3   0.1   1.5e-06    0.0025      14      48 .]      30      65 ..      22      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.5e-06
                            HTH_24 14 k.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                        ++  + ++LA++l+l   t++ +l+ L+e+ l++
  gi|557693615|ref|YP_008796669.1| 30 LrDGPANANQLAKALHLNYKTILHHLEFLIENNLVE 65
                                      36999***************************9996 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.9e-06     0.014      12      61 ..      23      70 ..      20      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.9e-06
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                      ++l+ L+++++  p++++++a+   ++ + + + l+ L +++lv++ +G+
  gi|557693615|ref|YP_008796669.1| 23 RLLILLKLRDG--PANANQLAKALHLNYKTILHHLEFLIENNLVEADEGR 70
                                      56677777766..79*********************************98 PP

>> HTH_11  HTH 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     0.018       4      51 ..      23      69 ..      22      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIesepg 51
                                       +l+lL+  +gp ++++LA+ L++  +t+  +++ L e    +e++ g
  gi|557693615|ref|YP_008796669.1| 23 RLLILLKLRDGPANANQLAKALHLNYKTILHHLEFLIENN-LVEADEG 69
                                      589999999999***********************98876.6666665 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       0.7   1.1e+03      27      35 ..       7      15 ..       7      21 .. 0.74
   2 ?   13.0   0.0   4.8e-05     0.079       1      36 [.      23      58 ..      23      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.7
                            HTH_29 27 rtvyrwlkr 35
                                      +t++rw+ +
  gi|557693615|ref|YP_008796669.1|  7 KTFFRWVLL 15
                                      69****987 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.8e-05
                            HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrf 36
                                      R+++ll+l++G  +  q+Ak+l l ++t+ ++l+  
  gi|557693615|ref|YP_008796669.1| 23 RLLILLKLRDGPANANQLAKALHLNYKTILHHLEFL 58
                                      899********99****************8888765 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.3e-05     0.071       8      77 ..      24      89 ..      19      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                                      HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHH CS
                              HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlq 77
                                      llil +l +g+   ++l++al ++  k++ ++L  L +++l+e+++       v+Y+l++   + +++l+
  gi|557693615|ref|YP_008796669.1| 24 LLILLKLRDGPANANQLAKAL-HLNYKTILHHLEFLIENNLVEADEGR---YDVKYRLSQVVSENMDILD 89
                                      79*******************.9*******************987654...4567888877666666665 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 ?   11.7   0.0   0.00011      0.18      14      56 ..      26      66 ..      21      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                      HHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEE CS
                            RuvB_C 14 llkekfkggpvglktlaailgeeketiedviEPyLlkeglIer 56
                                      +l  k ++gp+  + la++l ++ +ti +  E +L++++l+e 
  gi|557693615|ref|YP_008796669.1| 26 ILL-KLRDGPANANQLAKALHLNYKTILHHLE-FLIENNLVEA 66
                                      343.4589************************.9******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 856.71
//
Query:       gi|557693616|ref|YP_008796670.1|  [L=264]
Description: cyclase family protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  112.8   0.0    2.1e-32  112.2   0.0    1.3  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 !  112.2   0.0   1.2e-36   2.1e-32       1     134 [.      10     199 ..      10     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 1.2e-36
                           Cyclase   1 idLshplsedtpvwp.dp..............................islsehtGTHlDapgHfae.....kti.. 39 
                                       +dL++p+ +++pv+p dp                              + +s+h+GTH+Da +H+a+     +    
  gi|557693616|ref|YP_008796670.1|  10 YDLGQPYFNGMPVHPeDPpysmviyryheytkklfekvapgfsdsmelVITSMHSGTHIDAKCHMARngllyN-Gvk 85 
                                       7*************6555789999999********************888999***********988544331.035 PP

                           Cyclase  40 ...............delpleelvgpavvldvsak...aaa..edyeiitaedleaalakqgveikpgdivlirTgw 96 
                                                      +e+p   +v +av+ld+ a    +    ++y  ita+dle+al+ q++eik+gd+vlirTg+
  gi|557693616|ref|YP_008796670.1|  86 aaeivkhsgytkygtEEIP--IYVKRAVLLDIPASknlD-IlpPRYG-ITAQDLEQALKLQKTEIKEGDAVLIRTGY 158
                                       5555666666666657787..89*********5543341.1335665.5**************************** PP

                           Cyclase  97 skrl.edkeky..rnpglseeaaewlaekgvkavGvDtlsv 134
                                       s+++ +dkeky  +  g++ee a+wl++++++++G+D+l++
  gi|557693616|ref|YP_008796670.1| 159 SRYFtTDKEKYlhDFAGITEESAKWLIDRKISLLGIDNLAM 199
                                       *99998899**8888***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2153.92
//
Query:       gi|557693617|ref|YP_008796671.1|  [L=400]
Description: formyl-CoA transferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-116  388.1   0.0   4.7e-116  387.9   0.0    1.0  1  CoA_transf_3  CoA-transferase family III
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.38   10.8   0.0    1.8  2  SAM_4         SAM domain (Sterile alpha motif)
       0.17   12.1   0.0       0.45   10.8   0.0    1.7  1  PIN_10        PIN like domain


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 !  387.9   0.0  7.8e-120  4.7e-116       1     368 []       7     374 ..       7     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: 387.9 bits;  conditional E-value: 7.8e-120
                      CoA_transf_3   1 LaGvrVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegre 77 
                                       L++v Vl++++ +aGpl++ +LA++GA+VIkvE+p++gD+aR++g+   kges+yf ++nrnK s+a+D+k++eg +
  gi|557693617|ref|YP_008796671.1|   7 LDDVSVLEIGTAIAGPLCGAILAEMGAKVIKVEHPSRGDDARHFGRIV-KGESLYFFNYNRNKLSLAVDIKKKEGLA 82 
                                       89******************************************8766.5*************************** PP

                      CoA_transf_3  78 llkrLvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdg 154
                                       ++k+L+++ DV+ieN+rpg+l +lgl ye++++ n r+iy+s+sg+G++G +++  gyD+v+qa+sGlm+++ e+d 
  gi|557693617|ref|YP_008796671.1|  83 IVKELIRRVDVLIENYRPGTLSKLGLAYEQVKRLNKRIIYCSISGFGSHGVYRDFKGYDVVVQAMSGLMWMNREQDA 159
                                       ***************************************************************************** PP

                      CoA_transf_3 155 pPvkvgvplgDivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrdpaaapy 231
                                       +P++   pl+Di++++ aa a++aal+ r+r  k+ +i++sll+  la +++ l+++  t+e+ ++ gn+ pa+apy
  gi|557693617|ref|YP_008796671.1| 160 EPMRLPAPLTDILAAYSAATAVCAALHLRKRLKKAVKIEASLLQMGLAAVSQWLVDTWVTKEEVKPFGNKYPALAPY 236
                                       *********************************************************9999999999********** PP

                      CoA_transf_3 232 gvyrtkdgwvaiaaatdkqwaalckalgrpelaedprfatnasrlenr..aeldaelaewlaertaaewlellaaag 306
                                       + +rtkdgw+++a+++d+qw +lcka gr +l +d+rf+tn++r++ +    l  el++ l ert +ew++l+++ g
  gi|557693617|ref|YP_008796671.1| 237 EPFRTKDGWIVVAVGNDEQWLSLCKATGRLDLMQDERFRTNQDRINPNnrSYLASELQKTLVERTSKEWVTLFQKMG 313
                                       ********************************************8755448889*********************** PP

                      CoA_transf_3 307 vpaapvntleevlddpqlaarglvvevddpdygevpvvglpvrlsetparvkraaPklGedt 368
                                       +pa+pv +l +vl+d+ l   gl+  +++p++gev +v+l +++++++a ++r+ P+lGe+t
  gi|557693617|ref|YP_008796671.1| 314 IPAGPVYSLTDVLNDENLSSLGLFSPTRHPTIGEVLAVRLTAFFQGFTA-YQRPSPRLGEHT 374
                                       **********************************************955.***********8 PP

>> SAM_4  SAM domain (Sterile alpha motif)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       2.1   1.2e+04      44      62 ..      70      88 ..      63      91 .. 0.67
   2 ?   10.8   0.0   6.3e-05      0.38       6      28 ..     300     322 ..     295     335 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 2.1
                             SAM_4 44 dlskeimnelgitvvgdii 62
                                       l+ +i ++ g+++v ++i
  gi|557693617|ref|YP_008796671.1| 70 SLAVDIKKKEGLAIVKELI 88
                                      5666777777777776665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 6.3e-05
                             SAM_4   6 latsewiqffkeagipaglavny 28 
                                        ++ ew+ +f++ gipag+  + 
  gi|557693617|ref|YP_008796671.1| 300 RTSKEWVTLFQKMGIPAGPVYSL 322
                                       5677**************97655 PP

>> PIN_10  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.5e-05      0.45      40      70 ..     252     282 ..     245     290 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.5e-05
                            PIN_10  40 kDeeWiaalaeggwvvltkDrrirkrpaEra 70 
                                        De+W+++ +++g   l++D+r+r++++ + 
  gi|557693617|ref|YP_008796671.1| 252 NDEQWLSLCKATGRLDLMQDERFRTNQDRIN 282
                                       6*************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 3263.13
//
Query:       gi|557693618|ref|YP_008796672.1|  [L=265]
Description: 3-hydroxybutyryl-CoA dehydratase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-55  187.6   0.0    2.8e-55  187.4   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    3.9e-39  135.1   0.0    6.7e-34  117.9   0.0    2.0  2  ECH_2     Enoyl-CoA hydratase/isomerase
  ------ inclusion threshold ------
      0.049   12.7   0.0      0.062   12.4   0.0    1.1  1  ICE2      ICE2


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 !  187.4   0.0   4.7e-59   2.8e-55       4     250 ..      15     264 ..      13     265 .] 0.94

  Alignments for each domain:
  == domain 1  score: 187.4 bits;  conditional E-value: 4.7e-59
                                       TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEE.BTSEEEEEB-HHHHHHHHC....HHHHHHHC CS
                             ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtG.gdkaFaaGadlkemaeeek....akqallke 75 
                                       + vavi++nrPea Na+s ++ltE+++al+k+ dd++v  +++tG gdkaF++G+d ke +++ +    ++ ++++ 
  gi|557693618|ref|YP_008796672.1|  15 DKVAVITFNRPEARNAMSVAMLTEFNDALHKAADDPEVWSIIVTGaGDKAFCSGGDAKEFLANVEagkiSEIEKFNR 91 
                                       579********************************************************998866553444555666 PP

                                       CHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHH CS
                             ECH_1  76 evlelwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeei 152
                                         l+ w+ + ++ kp+iaavnG+++   +e+  a D+via++na+fgl+e+ +G+ pgag+t +l+r + k  A++ 
  gi|557693618|ref|YP_008796672.1|  92 FNLDVWRFMEKMRKPIIAAVNGFCN---IEVIQAVDLVIASQNAKFGLPEVTIGVSPGAGITVRLPRFLSKYWAKYF 165
                                       67789*******************9...8************************************************ PP

                                       HHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                             ECH_1 153 lllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfs 229
                                       l +g+ +sa+e  + G v+kvvp+e+l+eea++la+k+++++p+a+ + k+ +n   e+   e++e + k    +f 
  gi|557693618|ref|YP_008796672.1| 166 LFTGEWVSAEEGYRLGFVNKVVPHEKLMEEAMALARKINKNAPLAVGATKACVNLGGEMPIDEGMEYQLKESILMFY 242
                                       ***************************************************************************** PP

                                       SHHHHHHHH.HHHTCSH----- CS
                             ECH_1 230 kddikeGlq.aflEkrkpefed 250
                                       ++d keG+  +f Ekr+p+f++
  gi|557693618|ref|YP_008796672.1| 243 TQDLKEGIRaRFYEKREPRFTG 264
                                       *******9626*********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 !  117.9   0.0   1.1e-37   6.7e-34       2     185 ..      18     200 ..      17     202 .. 0.96
   2 !   17.1   0.0   5.2e-07    0.0031     249     317 ..     196     262 ..     193     265 .] 0.91

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 1.1e-37
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THH.HHHHHHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkee.eeffreeY 77 
                                       +vit+nrp+a Na+s +m++++++al++ ++d+ev  ++++gag+kafC+GgD +++  + ++gk +e e+f r + 
  gi|557693618|ref|YP_008796672.1|  18 AVITFNRPEARNAMSVAMLTEFNDALHKAADDPEVWSIIVTGAGDKAFCSGGDAKEFLANVEAGKISEiEKFNRFNL 94 
                                       79**************************************************************999999******* PP

                                       HHHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCS.STTHHHHHHHH CS
                             ECH_2  78 klnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrl.pgelGlylalT 153
                                       ++   +++++kp++a ++G++    + + +   + +++++++f  PE++IG+ P  G +  L+r  ++  ++y+  T
  gi|557693618|ref|YP_008796672.1|  95 DVWRFMEKMRKPIIAAVNGFC---NIEVIQAVDLVIASQNAKFGLPEVTIGVSPGAGITVRLPRFlSKYWAKYFLFT 168
                                       ********************8...699*************************************64899******** PP

                                       ---B-HHHHHHTTS--EE--GGGHHHHHHHHH CS
                             ECH_2 154 GarlkgadalaaglathyvpseklealeeaLa 185
                                       G+ +++++ + +g+ +++vp+ekl + + aLa
  gi|557693618|ref|YP_008796672.1| 169 GEWVSAEEGYRLGFVNKVVPHEKLMEEAMALA 200
                                       **********************9987666665 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 5.2e-07
                                       HHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS------- CS
                             ECH_2 249 akktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkW 317
                                       a + +++++k++P+++ +t + ++ g ++  ++e ++  l+ +  ++ ++D+ eG+ra++ +k ++P++
  gi|557693618|ref|YP_008796672.1| 196 AMALARKINKNAPLAVGATKACVNLGGEMP-IDEGMEYQLKESILMFYTQDLKEGIRARFYEK-REPRF 262
                                       5677899**********************7.****99999999999999*************9.78887 PP

>> ICE2  ICE2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     1e-05     0.062      98     137 ..      85     124 ..      28     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1e-05
                              ICE2  98 lseyleklvvkpWkklLsnstpvftllEGfcslLvIQaig 137
                                         e ++++ +  W+++ ++  p++  + Gfc + vIQa+ 
  gi|557693618|ref|YP_008796672.1|  85 EIEKFNRFNLDVWRFMEKMRKPIIAAVNGFCNIEVIQAVD 124
                                       3455688999****************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2132.71
//
Query:       gi|557693619|ref|YP_008796673.1|  [L=194]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-47  161.6   0.5    2.1e-47  161.4   0.5    1.0  1  DUF655       Protein of unknown function (DUF655)
     0.0015   18.7   0.0     0.0044   17.3   0.0    1.7  1  HHH_6        Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.078   12.7   0.0       0.24   11.1   0.0    1.9  2  XPC-binding  XPC-binding domain
       0.09   13.0   0.0       0.18   12.1   0.0    1.5  1  HHH_3        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 !  161.4   0.5   4.7e-51   2.1e-47       2     181 .]       8     188 ..       7     188 .. 0.97

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 4.7e-51
                                       --EEEEEEEETT--TT--S-GGG---..EEEEEETTT--EEEEEE-TT----TT-EEE-SSS--SSEEEEEEE--GG CS
                            DUF655   2 eeeaivLDylpeGypddkhrehrdkp..vvqalgereltLlelvplkevdilkldevaigkgksdkivkikreisye 76 
                                       e++ +vLD +p  +  + +++h+dk   +vq lge+ +tLle+ ++++   +   +++ig++   +i +i r+i y 
  gi|557693619|ref|YP_008796673.1|   8 EDYGYVLDVFPAQQRAGFQKFHHDKNeyIVQLLGEDFFTLLEVAVNEKFKPKPGTKLYIGRDVPREILRIVRRIDYT 84 
                                       8899*********999999999776444************************************************* PP

                                       GS-HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHSTT CS
                            DUF655  77 dLtdvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvkg 153
                                       dLt+++ a+L+ +v+kiv+e+ +rf +f n++  +t R+HaLel+pg+gkk+++k l eR++  F+sFedvk+r  g
  gi|557693619|ref|YP_008796673.1|  85 DLTETSIANLEPAVYKIVEEHPQRFLDFINNSGMLTPRMHALELVPGIGKKMLQKFLTERDNASFTSFEDVKNRT-G 160
                                       **************************************************************************9.6 PP

                                       ---HHHHHHHHHHHHHH-TTSS--SS-- CS
                            DUF655 154 lkdpaeilverileEiedktekYylFve 181
                                       l +p+e++v+ri++Ei++k+ekY+lFv+
  gi|557693619|ref|YP_008796673.1| 161 LPNPVEAIVKRIVQEIKNKDEKYRLFVR 188
                                       **************************95 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   9.7e-07    0.0044      28      67 ..     125     162 ..     123     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 9.7e-07
                             HHH_6  28 GLaaikglgeaaaerivaeRekegpfksledlarrvdsln 67 
                                       +L+ + g+g++ +++ ++eR+ + +f+s+ed+ +r++ l 
  gi|557693619|ref|YP_008796673.1| 125 ALELVPGIGKKMLQKFLTERD-NASFTSFEDVKNRTG-LP 162
                                       7999****************9.9*************9.44 PP

>> XPC-binding  XPC-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.7   7.4e+03      46      55 ..      33      42 ..      30      43 .. 0.72
   2 ?   11.1   0.0   5.4e-05      0.24      31      56 ..      91     116 ..      89     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.7
                       XPC-binding 46 qeeFlqlLne 55
                                       e+ +qlL+e
  gi|557693619|ref|YP_008796673.1| 33 NEYIVQLLGE 42
                                      5778888887 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.4e-05
                       XPC-binding  31 laqsnPqllqlIqqnqeeFlqlLnep 56 
                                       +a+ +P+++++ +++++ Fl+++n++
  gi|557693619|ref|YP_008796673.1|  91 IANLEPAVYKIVEEHPQRFLDFINNS 116
                                       78889*******************86 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.1e-05      0.18      15      52 ..     125     161 ..     120     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.1e-05
                             HHH_3  15 eLqklpGlgpklAknIvayReknGpfksreeLlkvkgl 52 
                                        L+ +pG+g+k+ ++ +  R  n  f+s+e+ ++  gl
  gi|557693619|ref|YP_008796673.1| 125 ALELVPGIGKKMLQKFLTER-DNASFTSFEDVKNRTGL 161
                                       6999****************.788*******9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1537.64
//
Query:       gi|557693620|ref|YP_008796674.1|  [L=118]
Description: DNA-directed RNA polymerase subunit F [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-07   32.2   0.2    1.2e-07   32.1   0.2    1.1  1  RNA_pol_Rpb4  RNA polymerase Rpb4
  ------ inclusion threshold ------
      0.059   13.8   0.1      0.082   13.3   0.1    1.1  1  NAPRTase_C    Nicotinate phosphoribosyltransferase C-terminal


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 !   32.1   0.2   1.3e-11   1.2e-07      32     120 ..      18     110 ..       2     113 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.3e-11
                                       HHSHCHTCHHCHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTST.STHHHHHHHHHCSTSSHHHHHHHSTTGTT.. CS
                      RNA_pol_Rpb4  32 sekeevkgnlnkilkktleyltnkfsrlkneekfnelvellksfe.LtkaEklqlvnlkPesavelktlieelee.. 105
                                       + +e+  ++ln  + ++++y ++ +++l  +++++ lv++l +   Lt+ E++q+ + +P++++el+++    +   
  gi|557693620|ref|YP_008796674.1|  18 KLMEQRAEDLNSLQTRVYTYAKK-YAKLS-PDQAELLVQKLMTDVgLTREEAVQVADTCPRNVEELRAILSGYKRlv 92 
                                       56788999**************9.****9.999********96656***********************98777655 PP

                                       ...TSTSHHHHHHHHHHH CS
                      RNA_pol_Rpb4 106 ...rfedeqleeiLdelk 120
                                           f++e++   +++++
  gi|557693620|ref|YP_008796674.1|  93 sflLFSEEKMRTVVKLVE 110
                                       554457777777777776 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 ?   13.3   0.1   9.2e-06     0.082       8      94 ..       6      92 ..       3      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.2e-06
                        NAPRTase_C  8 ydkdgkalaDlialadekepkegkeilclhpfdekkrveitpsrvekLlkkvfkdGklv.yelpsleeireyvkeqlae 85
                                       +k++ ++a ++ l+++ + ++ +++  +  +++kk +++ p ++e L +k+++d  l+ +e  ++++   +  e+l++
  gi|557693620|ref|YP_008796674.1|  6 LSKTEVPMATVVKLMEQ-RAEDLNSLQTRVYTYAKKYAKLSPDQAELLVQKLMTDVGLTrEEAVQVADTCPRNVEELRA 83
                                      56777799999999999.8999999999999**********************98555515667788888888888888 PP

                        NAPRTase_C 86 lrpehkRll 94
                                      +   +kRl+
  gi|557693620|ref|YP_008796674.1| 84 ILSGYKRLV 92
                                      899999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 872.95
//
Query:       gi|557693621|ref|YP_008796675.1|  [L=95]
Description: large subunit ribosomal protein L21e [Candidatus Caldiarchaeum subterraneum]
Scores for 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-27   93.9   0.4    5.4e-27   93.6   0.4    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 !   93.6   0.4     3e-31   5.4e-27       1      97 [.       1      91 [.       1      94 [. 0.97

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 3e-31
                                      X--S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEE CS
                    Ribosomal_L21e  1 mknskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkk 79
                                      m++skg+rr++r  ++k+   +  p++  ylreyk Gd+V + i+psvqkg ph+ryhGk+g++  v+kr++g++v  k
  gi|557693621|ref|YP_008796675.1|  1 MPQSKGFRRKSRGYLKKPRGSRSGPRPDIYLREYKPGDRVLLAIEPSVQKGSPHRRYHGKIGVI--VEKRGRGYVV--K 75
                                      899*************************************************************..*********9..6 PP

                                      ETTE..EEEEEE-GGGEE CS
                    Ribosomal_L21e 80 vggkileKriivriehlk 97
                                      vg++  eK++ + ++h++
  gi|557693621|ref|YP_008796675.1| 76 VGDE--EKTLSILPDHIR 91
                                      7888..99********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 649.50
//
Query:       gi|557693622|ref|YP_008796676.1|  [L=439]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   33.8   2.5    3.7e-08   33.6   0.3    2.1  3  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 !   33.6   0.3   2.1e-12   3.7e-08      64     139 ..     102     189 ..      56     191 .. 0.90
   2 ?   -1.4   0.0      0.12   2.2e+03      43      77 ..     296     330 ..     257     334 .. 0.64
   3 ?   -3.2   0.1      0.44   7.9e+03      56      73 ..     364     380 ..     344     399 .. 0.46

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.1e-12
                                       HHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTS...............SSHHHHHHHHHHHHHHCCTT-EE-SSS- CS
                             THUMP  64 ledileaakeivkkkfeeeketFaVrvkrrgkhf...............eftsreinrevGkaivektglkVdlenP 125
                                       + +  e+a e+ ++  +e   tF V++k+ g+ +               e +++ei+re+ + + + tg+k d ++P
  gi|557693622|ref|YP_008796676.1| 102 FRKAAEKAAELLHDIEFE---TFLVGAKASGDVVntedrlralagltegENIRNEIKREISRVFANITGKKLDHSSP 175
                                       455567777778877777...***********99******************************************* PP

                                       SEEEEEEEETTEEE CS
                             THUMP 126 divvrveiikdkay 139
                                       d+v+ v++++dk++
  gi|557693622|ref|YP_008796676.1| 176 DVVITVDLFRDKVE 189
                                       ***********985 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.12
                                       HHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHH CS
                             THUMP  43 alekargiqrvipvcevceadledileaakeivkk 77 
                                       +++   g++ v+ + +++++ + +i+ aa+ + k+
  gi|557693622|ref|YP_008796676.1| 296 INTNTQGLVTVYLEAYTTRRQVRQIKLAASTAAKT 330
                                       33344488888888999999999999988887776 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 0.44
                                       EEEEEESSHHHHHHHHHH CS
                             THUMP  56 vcevceadledileaake 73 
                                         +v +++ e++ ++++ 
  gi|557693622|ref|YP_008796676.1| 364 L-RVLRRRAEKLRRKTVY 380
                                       3.4444444444333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3163.45
//
Query:       gi|557693623|ref|YP_008796677.1|  [L=466]
Description: signal recognition particle, subunit SRP54 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-71  238.8   0.0    5.3e-71  238.3   0.0    1.2  1  SRP54            SRP54-type protein, GTPase domain
    4.1e-26   91.5   0.0    1.1e-25   90.1   0.0    1.8  1  SRP_SPB          Signal peptide binding domain
    7.5e-15   54.9   1.7    1.6e-14   53.9   0.1    2.4  2  SRP54_N          SRP54-type protein, helical bundle domain
      4e-06   26.9   0.0    1.2e-05   25.4   0.0    1.8  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00012   22.7   0.3      0.017   15.6   0.1    3.0  2  AAA_18           AAA domain
    0.00013   21.4   0.0    0.00046   19.5   0.0    1.9  2  Zeta_toxin       Zeta toxin
    0.00064   20.0   0.2     0.0061   16.8   0.0    2.6  2  AAA_22           AAA domain
    0.00097   18.5   0.0     0.0015   17.8   0.0    1.3  1  6PF2K            6-phosphofructo-2-kinase
     0.0012   18.0   0.3     0.0025   16.9   0.3    1.5  1  IMPDH            IMP dehydrogenase / GMP reductase domain
     0.0014   18.1   0.0     0.0029   17.1   0.0    1.5  1  ParA             NUBPL iron-transfer P-loop NTPase
     0.0015   17.5   0.5      0.033   13.2   0.2    2.4  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0017   18.6   0.2      0.023   14.9   0.1    2.4  2  AAA_28           AAA domain
     0.0021   17.7   2.1      0.067   12.8   2.1    2.3  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0025   17.5   0.0      0.016   15.0   0.0    2.2  2  AAA_30           AAA domain
      0.003   17.7   0.0       0.01   16.0   0.0    1.9  1  AAA_33           AAA domain
     0.0035   17.8   0.5      0.018   15.5   0.1    2.4  2  AAA_17           AAA domain
     0.0039   17.1   0.2       0.01   15.7   0.1    1.8  1  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0062   16.9   0.0       0.08   13.3   0.0    2.5  2  AAA_16           AAA ATPase domain
      0.007   16.1   0.0      0.016   14.9   0.0    1.7  1  AAA_24           AAA domain
     0.0089   15.9   0.0      0.023   14.6   0.0    1.7  1  APS_kinase       Adenylylsulphate kinase
  ------ inclusion threshold ------
       0.01   16.3   2.0      0.026   14.9   1.0    2.3  1  AAA              ATPase family associated with various cellul
      0.013   14.9   0.1      0.034   13.6   0.1    1.7  1  TniB             Bacterial TniB protein
      0.017   15.1   0.0      0.035   14.1   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4
      0.019   14.9   1.5      0.034   14.1   0.1    2.1  2  NTPase_1         NTPase
      0.025   14.5   0.5      0.084   12.8   0.3    1.8  1  AAA_31           AAA domain
      0.033   13.5   0.6        1.3    8.2   0.6    2.4  1  MipZ             ATPase MipZ
      0.042   13.7   1.3       0.54   10.0   1.3    2.2  1  AAA_26           AAA domain
      0.044   13.7   0.0       0.15   12.0   0.0    2.0  2  NACHT            NACHT domain
      0.057   12.9   0.0        0.1   12.1   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.061   13.0   0.3        0.2   11.3   0.3    1.9  1  Thymidylate_kin  Thymidylate kinase
      0.084   12.9   0.7       0.51   10.3   0.3    2.4  3  AAA_5            AAA domain (dynein-related subfamily)
      0.086   12.8   0.1       0.18   11.8   0.1    1.6  1  ResIII           Type III restriction enzyme, res subunit
      0.095   12.1   0.1       0.24   10.8   0.0    1.7  1  KTI12            Chromatin associated protein KTI12
      0.098   12.4   0.4        4.2    7.1   0.0    2.7  3  AAA_11           AAA domain
        0.1   12.9   0.0       0.82   10.0   0.0    2.6  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
       0.12   11.4   0.7       0.28   10.3   0.2    1.7  2  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
       0.12   12.4   0.3        1.1    9.3   0.1    2.5  2  AAA_14           AAA domain
        0.2   11.2   1.8          8    6.0   0.2    2.6  2  AAA_25           AAA domain
        3.2    7.4   5.4         18    5.0   1.0    2.9  2  GGA_N-GAT        GGA N-GAT 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 !  238.3   0.0   1.1e-73   5.3e-71       2     195 ..     126     319 ..     125     320 .. 0.99

  Alignments for each domain:
  == domain 1  score: 238.3 bits;  conditional E-value: 1.1e-73
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                        v++l+G+qG+GKTtt+aKLa++lk  g+kv +v+aDt+R+aA++QLk+l e  ++pv+++ e+++p+++a++++e+
  gi|557693623|ref|YP_008796677.1| 126 YVVMLLGIQGTGKTTTAAKLANYLKVGGYKVGVVCADTYRPAAYQQLKHLLEPRQIPVYGEPENNNPVEIARKGLEH 202
                                       69*************************************************************************** PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                       +k+ ++dvv++DTaGr++++++lm+e+k ++k +kpde++lv+d+t+gq+a ++a aF++a+ ++++i+tklD++ +
  gi|557693623|ref|YP_008796677.1| 203 FKQMGVDVVIIDTAGRHRQQESLMDEMKMLEKELKPDENILVIDGTIGQQAGAHAAAFHKATPVGSIIITKLDTSGR 279
                                       ***************************************************************************** PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                                       gG+al+++ae++ Pikf+gvGe++ed+++f+p++++ +ll
  gi|557693623|ref|YP_008796677.1| 280 GGGALAAVAETGAPIKFVGVGESVEDFQPFNPSSYIASLL 319
                                       *************************************998 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0   2.4e-28   1.1e-25       1      99 []     350     450 ..     350     450 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 2.4e-28
                                       SSCTHHHHHHHHHHHCCCCCCHHHHCCC........H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHH CS
                           SRP_SPB   1 eftlrdlleqlqqikkmGplskllsmiP..gmsae.akaeeeaekklkrieaiidSMTkeErdspekllkesRkrRi 74 
                                       +ftl+d+ eq+++++k+Gpl+kll ++P  g+ a   ++ e+a++++++++aii+SMT+eE+++p+ +l+ sR+rRi
  gi|557693623|ref|YP_008796677.1| 350 KFTLEDMVEQVNSLTKLGPLKKLLAKLPfpGIDALpDDQLEKAQDRIRKWNAIIKSMTAEEKNDPS-ILDGSRIRRI 425
                                       6*************************772254443644458899**********************.9999****** PP

                                       HHHTTS-HHHHHHHHHHHHHHHHHT CS
                           SRP_SPB  75 ArGsGtsvqevnellkqfeqmkkmm 99 
                                       A G+G+  ++v+ell++++  kkmm
  gi|557693623|ref|YP_008796677.1| 426 AYGAGVLERDVRELLRSYQASKKMM 450
                                       ************************9 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 !   53.9   0.1   3.4e-17   1.6e-14       2      75 .]      31     107 ..      30     107 .. 0.95
   2 ?   -1.9   0.1       8.6     4e+03      47      72 ..     327     348 ..     324     350 .. 0.49

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 3.4e-17
                                       HHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS....S-HHHHHHHHHHHH CS
                           SRP54_N   2 gkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk....lkpkqqvkkivkde 74 
                                       g++l+++++k+  + + d+  +ee+++ ++++Ll+aDV v++v+k+ e+++ +a + +k    +++k++v kiv++e
  gi|557693623|ref|YP_008796677.1|  31 GRSLKEVFRKFLASPSADKSSVEELVRGIQRSLLMADVKVELVQKISERIRARAFE-EKlppgVSRKDSVAKIVYEE 106
                                       899***********************************************998777.556***************** PP

                                       H CS
                           SRP54_N  75 L 75 
                                       L
  gi|557693623|ref|YP_008796677.1| 107 L 107
                                       8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.6
                                       HHHHHHHHHHCTTSS-.HHHHHHHHHH CS
                           SRP54_N  47 lienvkkkavgekklk.pkqqvkkivk 72 
                                       ++e     +v+  +l+ + +q++ i+k
  gi|557693623|ref|YP_008796677.1| 327 IVE-----RVKLAELTaDEKQFEAILK 348
                                       333.....4443443336667766665 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 !   25.4   0.0   2.5e-08   1.2e-05       9      55 ..     135     276 ..     132     375 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 2.5e-08
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH.............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.............................. RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep.............................. 54 
                                       G+GKTt+aa+La +l+ +g++V +v aD+ ++++   l   +  +ep                              
  gi|557693623|ref|YP_008796677.1| 135 GTGKTTTAAKLANYLKVGGYKVGVVCADTYRPAAYQqL---KHLLEPrqipvygepennnpveiarkglehfkqmgv 208
                                       9*******************************987452...333333444699999999999987777777777777 PP

                                       ...................................................................C CS
                                       ...................................................................x RF
                              CbiA  55 ...................................................................d 55 
                                                                                                          +
  gi|557693623|ref|YP_008796677.1| 209 dvviidtagrhrqqeslmdemkmlekelkpdenilvidgtigqqagahaaafhkatpvgsiiitkldT 276
                                       77777777777776666666666666666666666666655555555555555555555555555551 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   3.8e-05     0.017       1      40 [.     128     168 ..     128     263 .. 0.64
   2 ?    3.8   0.0      0.17        78      47      82 ..     379     420 ..     340     440 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.8e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakengllle 40 
                                       ++l G++G+GKtt a  L++ l++ g++++ v+++ +    
  gi|557693623|ref|YP_008796677.1| 128 VMLLGIQGTGKTTTAAKLANYLKVgGYKVGVVCADTYRPAA 168
                                       789***************99987785555554444332222 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.17
                            AAA_18  47 deskrldedkldklldaleenss......aleegknlvidgh 82 
                                       +  + l +d+l+k++d ++++++      a+e++++ ++dg 
  gi|557693623|ref|YP_008796677.1| 379 PGIDALPDDQLEKAQDRIRKWNAiiksmtAEEKNDPSILDGS 420
                                       567788999*******************99999***9**986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     1e-06   0.00046      12     110 ..     121     223 ..     112     235 .. 0.76
   2 ?   -1.1   0.0       2.1   9.7e+02      34      81 ..     230     277 ..     227     294 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1e-06
                        Zeta_toxin  12 sqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeyeeilka.dpkkaseltqkdas...el 83 
                                        +++P +++l G +G GK+++a++l+++l+  + +v ++ +D++R+    y+++    +p++   + +++     e+
  gi|557693623|ref|YP_008796677.1| 121 GGKKPYVVMLLGIQGTGKTTTAAKLANYLKvGGYKVGVVCADTYRPAA--YQQLKHLlEPRQIPVYGEPENNnpvEI 195
                                       459**************************95455566889*****998..888777557888777777665422267 PP

                        Zeta_toxin  84 vekllqeaiengyni.ivegtlrspdvv 110
                                       ++k l++  ++g+++ i++++ r+ ++ 
  gi|557693623|ref|YP_008796677.1| 196 ARKGLEHFKQMGVDVvIIDTAGRHRQQE 223
                                       8888899999999962467776666655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.1
                        Zeta_toxin  34 ellkdelerqgnvvrldpDdlRelhPeyeeilkadpkkaseltqkdas 81 
                                       ++l++el++++n++++d++  ++   ++++  ka p    + t+ d+s
  gi|557693623|ref|YP_008796677.1| 230 KMLEKELKPDENILVIDGTIGQQAGAHAAAFHKATPVGSIIITKLDTS 277
                                       68999999********99877777777777777666666666666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       4.4     2e+03      57      91 ..      34      68 ..      18      84 .. 0.70
   2 !   16.8   0.0   1.3e-05    0.0061       5     105 ..     125     222 ..     121     245 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4.4
                            AAA_22 57 lrellralglelkaerlsseellealeqalrarav 91
                                      l+e++r++  + +a   s eel++ +++ l  ++v
  gi|557693623|ref|YP_008796677.1| 34 LKEVFRKFLASPSADKSSVEELVRGIQRSLLMADV 68
                                      55556655555555577788888888888877766 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.3e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.....erlsse 76 
                                        +++++ G  GtGKTt++++l++ l+        +++vv  +   +      +++l + l+ ++       e+++  
  gi|557693623|ref|YP_008796677.1| 125 PYVVMLLGIQGTGKTTTAAKLANYLKVG----GYKVGVVCADTYRPAA----YQQLKHLLEPRQIPvygepENNNPV 193
                                       5678999*****************9443....2466666444444332....3444444443333344466668999 PP

                            AAA_22  77 ellealeqalraravielliiDEaqhlr.s 105
                                       e+ ++  +++++ +v  ++iiD a + r +
  gi|557693623|ref|YP_008796677.1| 194 EIARKGLEHFKQMGV-DVVIIDTAGRHRqQ 222
                                       999999999999999.9*****99887652 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.3e-06    0.0015      11      59 ..     123     171 ..     115     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-06
                                       .S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHSS CS
                             6PF2K  11 nsklvivlvGLpargKtyiskkltrylkwlgvrtkvFnvgkyrreaska 59 
                                       +++ v++l+G+  +gKt+++ kl  ylk  g++  v  +  yr  a ++
  gi|557693623|ref|YP_008796677.1| 123 KKPYVVMLLGIQGTGKTTTAAKLANYLKVGGYKVGVVCADTYRPAAYQQ 171
                                       678999***************************9999999999887776 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.3   5.4e-06    0.0025     109     199 ..     200     290 ..     192     300 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.4e-06
                                       HHHHHHTT-SEEEEE-S..TSSSHHHHHHHHHHHHHTT...TSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTB CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 109 vkalveagvdvlvvdsa..hghsekvleavkeikkkve...eveviaGnvataegakaLieagadavkvGiGpGsiC 180
                                       ++++ + gvdv+++d+a  h ++e  ++ +k + k+++   ++ vi G + +++ga+a + + a  v      Gsi 
  gi|557693623|ref|YP_008796677.1| 200 LEHFKQMGVDVVIIDTAgrHRQQESLMDEMKMLEKELKpdeNILVIDGTIGQQAGAHAAAFHKATPV------GSII 270
                                       5677899**********444445678999999999986543599***********999887777665......8999 PP

                                       HHHH.HCSB---HHHHHHHH CS
                                       xxxx.xxxxxxxxxxxxxxx RF
                             IMPDH 181 ttrv.vagvGvpqltAvaev 199
                                       +t+   +g G + l Avae+
  gi|557693623|ref|YP_008796677.1| 271 ITKLdTSGRGGGALAAVAET 290
                                       99964678898889888876 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   0.0   6.2e-06    0.0029      11      49 ..     132     170 ..     123     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.2e-06
                              ParA  11 gKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsipr 49 
                                       g  G GK+t+a++lA  L+  g+kvg++ aD y p   +
  gi|557693623|ref|YP_008796677.1| 132 GIQGTGKTTTAAKLANYLKVGGYKVGVVCADTYRPAAYQ 170
                                       66699**************************99887554 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 !   13.2   0.2   7.3e-05     0.033      30      66 ..     126     162 ..     116     168 .. 0.87
   2 ?    1.8   0.0       0.2        94     112     132 ..     198     218 ..     193     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.3e-05
                                       EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB  30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                        vv l G+ G+Gk t+  +l+  l+  G++v+v+  D
  gi|557693623|ref|YP_008796677.1| 126 YVVMLLGIQGTGKTTTAAKLANYLKVGGYKVGVVCAD 162
                                       578899****************************988 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.2
                                       HHHHHHHHTT-SEEEEEEESS CS
                              MeaB 112 evvllleaaGfDvvlietvGv 132
                                       + ++ +  +G Dvv+i+t G 
  gi|557693623|ref|YP_008796677.1| 198 KGLEHFKQMGVDVVIIDTAGR 218
                                       55677889**********995 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1     5e-05     0.023       2      38 ..     128     171 ..     127     246 .. 0.83
   2 ?    1.1   0.0      0.92   4.2e+02      40      95 ..     378     434 ..     369     452 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar....gyp..vv.pEaareileek 38 
                                       ++++G ++tGKTt++++La+     gy+  vv ++++r    ++
  gi|557693623|ref|YP_008796677.1| 128 VMLLGIQGTGKTTTAAKLANYlkvgGYKvgVVcADTYRPAAYQQ 171
                                       7899***************9888887775545577766666555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.92
                            AAA_28  40 akgedalpwvedllafaervleeql..eeeaaaaankvlfcDrglldtlaYaraygge 95 
                                       + g dalp+ ++l + ++r+ ++ +  +  +a ++n+  ++D + +  +aY     ++
  gi|557693623|ref|YP_008796677.1| 378 FPGIDALPD-DQLEKAQDRIRKWNAiiKSMTAEEKNDPSILDGSRIRRIAYGAGVLER 434
                                       667788888.5788888777777652255566699*************9998655444 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   2.1   0.00015     0.067       4     156 ..     129     280 ..     126     295 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                                       EEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCC...CCCHCCCT.EEEETTTTECCHCTT-HHHHHHH CS
                              cobW   4 vltGflGsGKTtLlnhll..enraglklavivNefgevsiDa...ellretgveivelenGciCctlredllkelea 75 
                                       +l G  G+GKTt   +l    +  g+k+ v+  + +  +  +   +ll+ ++ ++    +   +      + k le+
  gi|557693623|ref|YP_008796677.1| 129 MLLGIQGTGKTTTAAKLAnyLKVGGYKVGVVCADTYRPAAYQqlkHLLEPRQIPVYGEPENNNPVE---IARKGLEH 202
                                       566666667766666666555566666677666666433222000233333333333333333333...44555556 PP

                                       HHHHHTT-SEEEEEECTTTTHHHHHTT.SHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HH CS
                              cobW  76 leereerldviliEttGlaePapvaft.eeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtD 151
                                       ++++   +dv++i t G    +++++   + l+++l+ d  + v+D+  +  ++   +  a ++ +    ++++K D
  gi|557693623|ref|YP_008796677.1| 203 FKQMG--VDVVIIDTAGRHRQQESLMDeMKMLEKELKPDENILVIDG-TI-GQQAGAHAAAFHKATPVGSIIITKLD 275
                                       65655..9*********88888885554899999*************.44.5777788888888888899999***9 PP

                                       HHCHC CS
                              cobW 152 lldee 156
                                       +    
  gi|557693623|ref|YP_008796677.1| 276 TSGRG 280
                                       87665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.4e-05     0.016      19      60 ..     126     168 ..     118     246 .. 0.69
   2 ?   -0.7   0.0       2.2     1e+03      97     141 ..     316     357 ..     316     366 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.4e-05
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrv.iglAptgkaAk 60 
                                        v++l G  GtGKtt+ ++l++ ++  g++v +++A t + A+
  gi|557693623|ref|YP_008796677.1| 126 YVVMLLGIQGTGKTTTAAKLANYLKVGGYKVgVVCADTYRPAA 168
                                       488999************************9557888877554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.2
                            AAA_30  97 agmvdtkqlaallkaaekagakvilvGDerQlasVeaGgv.lrdlv 141
                                       a+++++ ++++++++++       l  De+Q +++ +G+  l+d+v
  gi|557693623|ref|YP_008796677.1| 316 ASLLGMPDIESIVERVKL----AELTADEKQFEAILKGKFtLEDMV 357
                                       567777777777777777....45788********99985255554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.2e-05      0.01       1      42 [.     127     173 ..     127     240 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-05
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.....avllssdtlrrrlfgtdq 42 
                                       +v+l G +G+GK+t a +l++ l+     + ++  dt+r + + + +
  gi|557693623|ref|YP_008796677.1| 127 VVMLLGIQGTGKTTTAAKLANYLKvggykVGVVCADTYRPAAYQQLK 173
                                       89*****************9888888877777889998877776332 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   3.8e-05     0.018       1     108 [.     131     244 ..     131     249 .. 0.71
   2 ?   -1.5   0.1       6.8   3.1e+03      49      80 ..     392     421 ..     382     461 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.8e-05
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC....TSHHHHHHHHHHHHHHHHHHHH...H CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr....klpleekkelqkeaaekiaeea...k 70 
                                       lG+ G GK+t ++kl+  +++  +  G +  ++ ++   ++ ++ ++     ++ e+++    e+a+k  e+    +
  gi|557693623|ref|YP_008796677.1| 131 LGIQGTGKTTTAAKLANYLKVGGYKVGVVCADTYRPAAYQQLKHLLEprqiPVYGEPENNNPVEIARKGLEHFkqmG 207
                                       79*****************9999999999999888887655555444555523444444444444444444441114 PP

                                       SSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                            AAA_17  71 kkgvlvdghprikeqagfldglpkevleelkpdaiill 108
                                        + v++d+  r ++q+ ++d+++   ++elkpd  il+
  gi|557693623|ref|YP_008796677.1| 208 VDVVIIDTAGRHRQQESLMDEMKM-LEKELKPDENILV 244
                                       4569*******9999999998885.899****876654 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.8
                                       SHHHHHHHHHHHHHHHHHHHHHSSEEEEEE-S CS
                            AAA_17  49 lpleekkelqkeaaekiaeeakkkgvlvdghp 80 
                                       ++ +++k + ++++ ++  e+k++  ++dg  
  gi|557693623|ref|YP_008796677.1| 392 AQDRIRK-WNAIIK-SMTAEEKNDPSILDGSR 421
                                       4433333.333333.44444466677777764 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 !   15.7   0.1   2.3e-05      0.01       1      33 [.     127     159 ..     127     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-05
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvgti 33 
                                       v+ + g +g+GKTt   kl + lk  g++vg++
  gi|557693623|ref|YP_008796677.1| 127 VVMLLGIQGTGKTTTAAKLANYLKVGGYKVGVV 159
                                       67899**************************98 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   0.00017      0.08      25     141 ..     126     245 ..     105     261 .. 0.63
   2 ?    0.8   0.0       1.2   5.7e+02      98     127 ..     340     403 ..     295     443 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00017
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekl 101
                                        +v+l G +G+GK++ + +l+++l+  gg+ +   c +  + ++y++l  +l+  + +   +++ e++++ + ++k 
  gi|557693623|ref|YP_008796677.1| 126 YVVMLLGIQGTGKTTTAAKLANYLKV-GGYKVGVVCADTYRPAAYQQLKHLLEP-RQIPVYGEP-ENNNPVEIARKG 199
                                       6799*****************76665.467777777777666777777777766.333433333.333444444444 PP

                            AAA_16 102 eeala........avpelagaea....srllellkrllallsrderplvlvl 141
                                       +e ++        +  +     +    ++l +++k l + l++de   +lv+
  gi|557693623|ref|YP_008796677.1| 200 LEHFKqmgvdvviIDTAG----RhrqqESLMDEMKMLEKELKPDEN--ILVI 245
                                       444444545443222222....122335666666555555555444..5555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.2
                            AAA_16  98 rekleeala..................................avpelagaeasrllellkrll 127
                                        +++e+ l+                                  a p++  ++a++  +++++++
  gi|557693623|ref|YP_008796677.1| 340 EKQFEAILKgkftledmveqvnsltklgplkkllaklpfpgidALPDDQLEKAQDRIRKWNAII 403
                                       4444444444444444444444444444444444444444333222222222233333333333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.6e-05     0.016       2      75 ..     125     217 ..     124     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-05
                            AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfidtek.Glksldadkfpdieswedfldevvel.................. 59 
                                       ++ +++ G +g+GKTt+a++l  + l +   k G+     ++  ++ +++++++ ++                    
  gi|557693623|ref|YP_008796677.1| 125 PYVVMLLGIQGTGKTTTAAKL-ANYLKVGGYKvGV---VCADTYRPAAYQQLKHLLEPRqipvygepennnpveiar 197
                                       6899*****************.8888777666333...333333455777777777777777777777777888887 PP

                            AAA_24  60 ....aaeladyktlviDtid 75 
                                             ++ + ++++iDt++
  gi|557693623|ref|YP_008796677.1| 198 kgleHFKQMGVDVVIIDTAG 217
                                       77777777777888888876 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.9e-05     0.023       2      51 ..     125     174 ..     124     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.9e-05
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--S CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLgf 51 
                                       + vv+l G+ g+GK+t a +l+++L+  g++v ++  d+ R   +++L  
  gi|557693623|ref|YP_008796677.1| 125 PYVVMLLGIQGTGKTTTAAKLANYLKVGGYKVGVVCADTYRPAAYQQLKH 174
                                       789********************************999999888777765 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 ?   14.9   1.0   5.7e-05     0.026       1      25 [.     128     152 ..     128     248 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.7e-05
                                       EEEESSTTSSHHHHHHHHHHHHTHE CS
                               AAA   1 vllyGppGtGKTllakavakelgve 25 
                                       v+l G  GtGKT++a  +a+ l+v 
  gi|557693623|ref|YP_008796677.1| 128 VMLLGIQGTGKTTTAAKLANYLKVG 152
                                       6899*****************9753 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   7.3e-05     0.034      36     154 ..     126     237 ..     100     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-05
                              TniB  36 pnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgapl...kararvskleq 109
                                         ++l+G + +GKt+ + k a+  +        kv v+ +++   +  ++l +++Le  + p+    ++++  ++ +
  gi|557693623|ref|YP_008796677.1| 126 YVVMLLGIQGTGKTTTAAKLANYLK----VGGYKVGVVCADTYRPAAYQQL-KHLLEPRQIPVygePENNNPVEIAR 197
                                       5678888899999998888776544....4457888888888777766666.789998888852223556778999* PP

                              TniB 110 qvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelk 154
                                       + l+ +++++v v+iiD      ag++r+q+ ++  +k+L  elk
  gi|557693623|ref|YP_008796677.1| 198 KGLEHFKQMGVDVVIID-----TAGRHRQQESLMDEMKMLEKELK 237
                                       *****************.....68*****************9996 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.7e-05     0.035       5      81 ..     139     216 ..     136     221 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.7e-05
                    Glyco_transf_4   5 erhvleLaraLarrGheVtvvtpgddgpleeev.elvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahs 80 
                                        + +  La++L   G++V vv+ ++ +p+++++ +++ +++ +p  + + + + +  +r+  +++k+ ++Dvv + +
  gi|557693623|ref|YP_008796677.1| 139 TTTAAKLANYLKVGGYKVGVVCADTYRPAAYQQlKHLLEPRQIPVYGEPENNNPVEIARKGLEHFKQMGVDVVIIDT 215
                                       577889***************9999999999999***************************************8877 PP

                    Glyco_transf_4  81 p 81 
                                       +
  gi|557693623|ref|YP_008796677.1| 216 A 216
                                       5 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   7.4e-05     0.034       2      38 ..     128     164 ..     127     171 .. 0.85
   2 ?   -1.8   0.1       5.6   2.6e+03      94     106 ..     206     218 ..     191     246 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.4e-05
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteev 38 
                                       v++ G +G+GKtT   k+++ lk  g+kvg + +  +
  gi|557693623|ref|YP_008796677.1| 128 VMLLGIQGTGKTTTAAKLANYLKVGGYKVGVVCADTY 164
                                       678899**********************976655555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.6
                                       HHH-EEEE---ST CS
                          NTPase_1  94 seadviviDEiGk 106
                                        + dv++iD  G+
  gi|557693623|ref|YP_008796677.1| 206 MGVDVVIIDTAGR 218
                                       4667888887775 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3   0.00018     0.084      12      40 ..     135     163 ..     132     178 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00018
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                       G GKTTt+ +la  l   g+kv +v +D+
  gi|557693623|ref|YP_008796677.1| 135 GTGKTTTAAKLANYLKVGGYKVGVVCADT 163
                                       89*********************999997 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.6    0.0029       1.3      11      42 ..     135     166 ..     126     248 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0029
                                       TSSHHHHHHHHHHHHHTTT--EEEEE--TTT- CS
                              MipZ  11 GsGksttavhvavaLlkkGarvaaidldlrqr 42 
                                       G+Gk+tta  +a  L   G +v+++  d+ + 
  gi|557693623|ref|YP_008796677.1| 135 GTGKTTTAAKLANYLKVGGYKVGVVCADTYRP 166
                                       999*********99999999999999887543 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.3    0.0012      0.54      10     111 ..     134     252 ..     127     261 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
                            AAA_26  10 tgvGKTvvslgLvralkrkgvkvgyfKPiqtgie.................ededselikellgldqtyelpeplal 69 
                                       +g GKT++++ L+++lk  g+kvg+++                         + +++   e++   +  e+ +++ +
  gi|557693623|ref|YP_008796677.1| 134 QGTGKTTTAAKLANYLKVGGYKVGVVCADTYRPAayqqlkhlleprqipvyGEPENNNPVEIA--RKGLEHFKQMGV 208
                                       578999999999999999999999987644444422222344444333332111333333333..334446677777 PP

                            AAA_26  70 saplspelaarqegedidlekiv...kelekdadivvVEGagglg 111
                                       +  +    a+r+ +++  ++++    kel+ d++i+v++G+ g  
  gi|557693623|ref|YP_008796677.1| 209 D-VVIIDTAGRHRQQESLMDEMKmleKELKPDENILVIDGTIGQQ 252
                                       6.56777889999999999999999999************98755 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         7   3.2e+03      52      91 ..      32      70 ..      17      94 .. 0.56
   2 ?   12.0   0.0   0.00032      0.15       2      31 ..     127     156 ..     126     247 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 7
                                      .-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-ST CS
                             NACHT 52 rsladllfsqlpepaapvsevwavllelperlLlilDglD 91
                                      rsl+++ ++ l  p+a+ s  +++l++  +r Ll  D   
  gi|557693623|ref|YP_008796677.1| 32 RSLKEVFRKFLASPSADKSS-VEELVRGIQRSLLMADVKV 70
                                      44555444444444444444.5555555555555555444 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00032
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpq 31 
                                       +v+l G +G GKTt ++kla  ++ g ++ 
  gi|557693623|ref|YP_008796677.1| 127 VVMLLGIQGTGKTTTAAKLANYLKVGGYKV 156
                                       799********************9998665 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   0.00022       0.1      34      99 ..     126     189 ..     118     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                             AAA_7  34 kpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpgg 99 
                                       + v+l G +GtGKt+++ +l + l+   y++ ++            + ++  le r+  vyg p +
  gi|557693623|ref|YP_008796677.1| 126 YVVMLLGIQGTGKTTTAAKLANYLKVGGYKVGVVCADT--YRPAAYQQLKHLLEPRQIPVYGEPEN 189
                                       569*********************98888888775444..44444556788888888888887766 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00043       0.2       3      27 ..     132     156 ..     130     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                                       ESTTSSHHHHHHHHHHHHHHTTE.E CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikv 27 
                                       G+ G+GKtt a++l+++lk  g+kv
  gi|557693623|ref|YP_008796677.1| 132 GIQGTGKTTTAAKLANYLKVGGYKV 156
                                       9******************999883 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 ?   -1.3   0.0       4.2   1.9e+03      12      40 ..      69      97 ..      68     107 .. 0.81
   2 ?   10.3   0.3    0.0011      0.51       2      24 ..     128     153 ..     127     178 .. 0.82
   3 ?   -2.0   0.0       7.1   3.2e+03      78     124 ..     165     220 ..     161     230 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 4.2
                                      HHHHHHHGGGGBS--EEEEE--TT--HHH CS
                             AAA_5 12 Kselaerlaaalnreveyvqltrdtteed 40
                                      K el+++++++++++ ++  l+ + +++d
  gi|557693623|ref|YP_008796677.1| 69 KVELVQKISERIRARAFEEKLPPGVSRKD 97
                                      7899********99999988888777766 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0011
                                       EEEE--SSSSHHHHHHHGGGGB...S CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal...n 24 
                                       v+L+G +GtgK++ a +la  l   +
  gi|557693623|ref|YP_008796677.1| 128 VMLLGIQGTGKTTTAAKLANYLkvgG 153
                                       89*****************9986543 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 7.1
                                       -HHHHHHHHHHHHSSEEE.....-SSSEEE---.................-EEEEEESS-- CS
                             AAA_5  78 esevlnsLlslleerrlll...eeggelvkaknddller...........frviatanpld 124
                                       ++++ + L  lle r++++   +e+++ v  ++     +           + +i ta + +
  gi|557693623|ref|YP_008796677.1| 165 RPAAYQQLKHLLEPRQIPVygePENNNPVEIAR-----KglehfkqmgvdVVIIDTAGRHR 220
                                       567778888999998887322233333333333.....22333445666666665555555 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 ?   11.8   0.1   0.00039      0.18      27      82 ..     128     184 ..      70     247 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00039
                                       EEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSH...HHHHHHHHHGGGGTGG.. CS
                            ResIII  27 glikmaTGtGKTlvaaklierllkkgkeekflflvprk...slleqtleefkkflseay 82 
                                       +++    GtGKT +aakl+ +l+  g+  k+ +++  +   + ++q+++ ++  + + y
  gi|557693623|ref|YP_008796677.1| 128 VMLLGIQGTGKTTTAAKLANYLKVGGY--KVGVVCADTyrpAAYQQLKHLLEPRQIPVY 184
                                       4566678************99998766..565555433243666666655555444444 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00053      0.24       4      41 ..     128     165 ..     125     177 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00053
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                                       v+l G+  +GK+t a++La++l+  +++v v+  ++++
  gi|557693623|ref|YP_008796677.1| 128 VMLLGIQGTGKTTTAAKLANYLKVGGYKVGVVCADTYR 165
                                       7789999************************9988876 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0091       4.2       8      42 ..      97     150 ..      93     189 .. 0.74
   2 ?    2.4   0.0      0.25   1.2e+02     209     228 ..     201     218 ..     193     226 .. 0.76
   3 ?   -1.6   0.0       3.9   1.8e+03     149     150 ..     412     435 ..     320     463 .. 0.48

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0091
                            AAA_11   8 eaiksalseseitliqGPP...................GtgKTktivellsqll 42 
                                       +++++++ e+ i l+ G+P                   GtgKT+t ++l ++l 
  gi|557693623|ref|YP_008796677.1|  97 DSVAKIVYEELINLLGGKPaqfstggkkpyvvmllgiqGTGKTTTAAKLANYLK 150
                                       55666666777778888877777777777888888888*************994 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.25
                            AAA_11 209 klleklakkfdvviIDEAaq 228
                                       + ++++  ++dvviID A++
  gi|557693623|ref|YP_008796677.1| 201 EHFKQM--GVDVVIIDTAGR 218
                                       455666..9*******9986 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.9
                            AAA_11 149 k......................e 150
                                       +                      +
  gi|557693623|ref|YP_008796677.1| 412 NdpsildgsrirriaygagvlerD 435
                                       122244444444343333333331 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 ?   10.0   0.0    0.0018      0.82      13      50 ..     140     177 ..     126     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHST CS
                           PFOR_II  13 gtaksavdelReegikvGllrlrtlrPFPeeelkellk 50 
                                        ta + ++ l+  g+kvG++   t+rP  +++lk+ll+
  gi|557693623|ref|YP_008796677.1| 140 TTAAKLANYLKVGGYKVGVVCADTYRPAAYQQLKHLLE 177
                                       5677788999************************9985 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2    0.0006      0.28      45      71 ..     133     159 ..     123     170 .. 0.92
   2 ?   -2.0   0.0       3.2   1.5e+03     200     214 ..     227     241 ..     198     263 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0006
                                       SS-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK  45 vGGtGKTPlvialvkllqarglkvgvl 71 
                                       + GtGKT +++ l+++l+  g+kvgv+
  gi|557693623|ref|YP_008796677.1| 133 IQGTGKTTTAAKLANYLKVGGYKVGVV 159
                                       56************************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.2
                                       SSS-EEEEEEEE.EE CS
                              LpxK 200 ksipvlrmrlepkkl 214
                                        ++++l+ +l+p++ 
  gi|557693623|ref|YP_008796677.1| 227 DEMKMLEKELKPDEN 241
                                       334444444444443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0024       1.1       4      40 ..     127     163 ..     124     231 .. 0.80
   2 ?   -0.2   0.0       2.1   9.5e+02      75     103 ..     395     423 ..     393     450 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0024
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldd 40 
                                       ++++ G+  +GKTt + +l++ l v   ++  +  d+
  gi|557693623|ref|YP_008796677.1| 127 VVMLLGIQGTGKTTTAAKLANYLKVGGYKVGVVCADT 163
                                       7899***************977766555555555555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.1
                            AAA_14  75 evpewekalkslvdegknldvivtGSnsk 103
                                       ++++w  ++ks+  e+kn   i+ GS   
  gi|557693623|ref|YP_008796677.1| 395 RIRKWNAIIKSMTAEEKNDPSILDGSRIR 423
                                       6789**********999999999999754 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.017         8      35      54 ..     127     146 ..     123     152 .. 0.91
   2 ?    3.7   0.0     0.085        39     131     153 ..     197     218 ..     158     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.017
                            AAA_25  35 lallaGapgtGKttlaldla 54 
                                       +++l G +gtGKtt a  la
  gi|557693623|ref|YP_008796677.1| 127 VVMLLGIQGTGKTTTAAKLA 146
                                       899*************9987 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.085
                            AAA_25 131 daleaaieevegvrlvviDplsr 153
                                       ++  ++ ++  gv++v+iD+  r
  gi|557693623|ref|YP_008796677.1| 197 RKGLEHFKQ-MGVDVVIIDTAGR 218
                                       445678999.58*******9876 PP

>> GGA_N-GAT  GGA N-GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.15        69      26      36 ..     400     410 ..     394     412 .. 0.87
   2 ?    5.0   1.0     0.039        18       6      18 ..     451     463 ..     448     464 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.15
                         GGA_N-GAT  26 NrLIKsmVked 36 
                                       N++IKsm  e+
  gi|557693623|ref|YP_008796677.1| 400 NAIIKSMTAEE 410
                                       9******9988 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.039
                         GGA_N-GAT   6 ksklLarLLkSkn 18 
                                       ks++L++LLkS++
  gi|557693623|ref|YP_008796677.1| 451 KSRQLRQLLKSSR 463
                                       89*********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); 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:                        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: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 3026.63
//
Query:       gi|557693624|ref|YP_008796678.1|  [L=318]
Description: UDP-glucose 4-epimerase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-46  158.4   0.0    2.6e-46  158.1   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.4e-43  148.3   0.0    2.4e-41  142.3   0.0    2.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    7.3e-19   67.9   0.0    9.5e-19   67.6   0.0    1.1  1  RmlD_sub_bind    RmlD substrate binding domain
    2.2e-14   53.1   0.0    1.4e-12   47.2   0.0    2.2  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.3e-12   47.5   0.0    2.8e-11   43.1   0.0    2.4  3  Polysacc_synt_2  Polysaccharide biosynthesis protein
      4e-11   42.6   0.0    1.7e-09   37.2   0.0    2.7  2  NAD_binding_4    Male sterility protein
    1.1e-05   25.4   0.0    2.3e-05   24.4   0.0    1.6  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.027   14.4   0.4       0.14   12.0   0.1    2.1  2  KR               KR domain
       0.17   11.4   0.0       0.34   10.4   0.0    1.5  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase


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 !  158.1   0.0   1.3e-49   2.6e-46       1     241 []      16     237 ..      16     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: 158.1 bits;  conditional E-value: 1.3e-49
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       +l+tG  Gf+G++l ++l  +g  v+g d  s a+          +++d+td +++ + f++++++av+hlAav+++
  gi|557693624|ref|YP_008796678.1|  16 VLITGSEGFVGRHLREYLGGRGFVVVGADISSGAD----------IRMDVTDFDSVLKTFEQNRFEAVVHLAAVADI 82 
                                       79**************************9994433..........69****************************** PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklve 154
                                       + s+ dp ++++ n+ g+ln+leaar+ gv+r++ +sS+  YG++ + p +e+t   p +p++pY ++K+a e++++
  gi|557693624|ref|YP_008796678.1|  83 PLSMRDPHRCFKVNVYGSLNVLEAARRMGVRRVVVFSSANYYGAPVKLPVTEDT---PPNPRTPYDYSKVALENVAW 156
                                       *******************************************99999999999...******************** PP

                                       HHHHHHT-EEEEEEESEEESTTS-TTS.TTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHT CS
                         Epimerase 155 ayaaqyglnaiilrlfnlyGprngege.vsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvd 230
                                       +y++ +g++ ++lr+   +G++    e  ++++p++++ +l+ + ++ l++ g  + d  +v+ ++ a+ l l + d
  gi|557693624|ref|YP_008796678.1| 157 SYHRNHGVPLTVLRPWKAFGEY----EpGEKMVPRFVKACLASE-PIPLFNGGADVTDPYHVDNLCHAVELGLIK-D 227
                                       **********************....5599**************.*************************99999.3 PP

                                       T-STTEEEEES CS
                         Epimerase 231 agdkgeiyniG 241
                                         + ge++n+G
  gi|557693624|ref|YP_008796678.1| 228 -EAVGEAFNVG 237
                                       .36799***99 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 !  142.3   0.0   1.2e-44   2.4e-41       1     331 [.      17     302 ..      17     303 .. 0.87

  Alignments for each domain:
  == domain 1  score: 142.3 bits;  conditional E-value: 1.2e-44
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       LiTG  Gf+G +l e+L  +g+ v+g +            + a+            +++D+tD +s+ + +++ +++
  gi|557693624|ref|YP_008796678.1|  17 LITGSEGFVGRHLREYLGGRGFVVVGADIS----------SGAD------------IRMDVTDFDSVLKTFEQNRFE 71 
                                       9***********************995422..........2121............579****************** PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       +v++LAA   ++ s+ +P++ ++vnv G l++Lea+r++g++   r++  S++  YG + + p+tE+tp +Pr PY 
  gi|557693624|ref|YP_008796678.1|  72 AVVHLAAVADIPLSMRDPHRCFKVNVYGSLNVLEAARRMGVR---RVVVFSSANYYGAPVKLPVTEDTPPNPRTPYD 145
                                       ****************************************97...89999*************************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                        +K++ + ++ +y++++g++ ++ +     + +      ++ ++r+v   ++ + +++ +  +  + d  hv+  ++
  gi|557693624|ref|YP_008796678.1| 146 YSKVALENVAWSYHRNHGVPLTVLRPWKAFGEYE---PGEKMVPRFVKACLASE-PIPLFNGGADVTDPYHVDNLCH 218
                                       *********************************6...45699999998888866.5555555666999********* PP

                                       HHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B CS
                     GDP_Man_Dehyd 232 amwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllg 308
                                       a+ l l +d+      a ge ++v++ + l++ el ++i+  +          +s++++ ++ p++  ++   + + 
  gi|557693624|ref|YP_008796678.1| 219 AVELGLIKDE------AVGEAFNVGTGNALSVRELAEKIKQLT----------NSSSKLESLPPRTPAEATPMKSIP 279
                                       *********9......799999999999999999998876543..........23333444444444444445679* PP

                                       -THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 309 daskakeeLgWkpkvsfeelvre 331
                                        ++k+ ++Lg++p+vs+e+++++
  gi|557693624|ref|YP_008796678.1| 280 SIKKIATKLGYTPQVSLEQGLKR 302
                                       ********************986 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   4.7e-22   9.5e-19       1     282 [.      14     304 ..      14     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 4.7e-22
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.....T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre.....eldltdaeavaellkeakpdvvvnaAAytavDkaEseee 72 
                                       mk+l+tG++G +G++L++ l  +g+ v++ + +     ++d+td ++v +++++++ ++vv++AA  ++     +++
  gi|557693624|ref|YP_008796678.1|  14 MKVLITGSEGFVGRHLREYLGGRGFVVVGADISsgadiRMDVTDFDSVLKTFEQNRFEAVVHLAAVADIPLSMRDPH 90 
                                       89***************************988889999*************************************** PP

                                       HHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSE....E CS
                     RmlD_sub_bind  73 aayavnaeavealAeaaaavgal.LihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkka....l 144
                                       + ++vn+ ++ ++ eaa+++g+  ++  S+   + +  k p +ed +++P++ Y  +K+a E++  +++ ++    +
  gi|557693624|ref|YP_008796678.1|  91 RCFKVNVYGSLNVLEAARRMGVRrVVVFSSANYYGAPVKLPVTEDTPPNPRTPYDYSKVALENVAWSYHRNHgvplT 167
                                       *********************96355556666678889999**********************99886666533338 PP

                                       EEEE-SEESS..SSS-HHHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS- CS
                     RmlD_sub_bind 145 ivRtswvyge..kgknfvktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeekelagvyHlanege 217
                                       ++R    +ge   g+ +v ++++    +e++ +++    +  P ++++l ++   +    ++++++ + + ++  ++
  gi|557693624|ref|YP_008796678.1| 168 VLRPWKAFGEyePGEKMVPRFVKACLASEPIPLFNGgaDVTDPYHVDNLCHA---VELGLIKDEAVGEAFNVGTGNA 241
                                       8999999999445789999999999888888888751156667666666554...4455555566789999999999 PP

                                       EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT---.-BHHHHHHHHH CS
                     RmlD_sub_bind 218 tswlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfgikl.rewrealkevl 282
                                       +s  e+A++i + ++++s +++  +    p++A  P +S  + +k++++ g ++  + +++lk+v+
  gi|557693624|ref|YP_008796678.1| 242 LSVRELAEKIKQLTNSSS-KLESLPP-RTPAEA-TPMKSIPSIKKIATKLGYTPqVSLEQGLKRVI 304
                                       999999999988888755.5555533.334444.37777777777766655443145666666665 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 ?    3.4   0.4     0.016        32       1      14 [.      17      30 ..      17      39 .. 0.87
   2 !   47.2   0.0   7.1e-16   1.4e-12      50     224 ..      51     219 ..      40     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.016
                         3Beta_HSD  1 vvtGgaGFlGralv 14
                                      ++tG+ GF+Gr+l 
  gi|557693624|ref|YP_008796678.1| 17 LITGSEGFVGRHLR 30
                                      69**********95 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 7.1e-16
                         3Beta_HSD  50 iegDvtdkdkleealeg..vdvvihlaslvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpn 123
                                       i  Dvtd d++ +  e+   ++v+hla++ d+   +    ++ kvnv+G  nvlea++++gvr++v  Ssa+  g  
  gi|557693624|ref|YP_008796678.1|  51 IRMDVTDFDSVLKTFEQnrFEAVVHLAAVADIPLsMRDPHRCFKVNVYGSLNVLEAARRMGVRRVVVFSSANYYGA- 126
                                       789**********998622589*********975488999*******************************99888. PP

                         3Beta_HSD 124 slgeeilngdEeleyeslhqdaypesKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvp.llkqla 197
                                         + +++     +  ++++  +y +sK   E+ v  +     +n g  +T+ LRp   +Ge+++  ++vp ++k ++
  gi|557693624|ref|YP_008796678.1| 127 PVKLPVT-----EDTPPNPRTPYDYSKVALEN-VAWSYH---RNHGVPLTV-LRPWKAFGEYEPgeKMVPrFVKACL 193
                                       5566666.....566789999*****987776.555666...788866775.********97642245550555555 PP

                         3Beta_HSD 198 klglalfkigdeevlsdrvYvgNvawa 224
                                        ++  +        ++d+  v+N+ +a
  gi|557693624|ref|YP_008796678.1| 194 ASE-PIPLFNGGADVTDPYHVDNLCHA 219
                                       555.55555556666899999999887 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1   2.3e+03       1      14 [.      16      29 ..      16      33 .. 0.87
   2 !   43.1   0.0   1.4e-14   2.8e-11      61     128 ..      53     120 ..      44     126 .. 0.96
   3 ?    1.4   0.0     0.071   1.4e+02     220     251 ..     228     259 ..     205     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                                      EEEETTTSHHHHHH CS
                   Polysacc_synt_2  1 vlvtGagGsiGsel 14
                                      vl+tG+ G +G++l
  gi|557693624|ref|YP_008796678.1| 16 VLITGSEGFVGRHL 29
                                      89*********987 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 1.4e-14
                                       --TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  61 gdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                        dv+d +++ k++e+ + ++v+h AA+  +Pl  + p+ ++k Nv+g+ nv+eaa ++gv++vv+ S+
  gi|557693624|ref|YP_008796678.1|  53 MDVTDFDSVLKTFEQNRFEAVVHLAAVADIPLSMRDPHRCFKVNVYGSLNVLEAARRMGVRRVVVFSS 120
                                       69***************************************************************996 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.071
                                       --SS-EEEE--.-EEEHHHHHHHH........ CS
                   Polysacc_synt_2 220 akggeifvldmGepvkivdlakalielsglee 251
                                          ge f +  G+++++++la+++ +l++ ++
  gi|557693624|ref|YP_008796678.1| 228 EAVGEAFNVGTGNALSVRELAEKIKQLTNSSS 259
                                       5678999999**************99987655 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.047        94       1      14 [.      18      31 ..      18      33 .. 0.87
   2 !   37.2   0.0   8.6e-13   1.7e-09      86     255 ..      68     218 ..      50     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.047
                                      EE-TTSHHHHHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLle 14
                                      +TG+ GF+G++L e
  gi|557693624|ref|YP_008796678.1| 18 ITGSEGFVGRHLRE 31
                                      8**********955 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 8.6e-13
                                       HH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H...... CS
                     NAD_binding_4  86 eevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekee 159
                                       ++ ++++h aA  ++  ++++   +++vNv G  +vle a+++   +v+++ S  y     +               
  gi|557693624|ref|YP_008796678.1|  68 NRFEAVVHLAAVADIPLSMRDphrCFKVNVYGSLNVLEAARRMGVRRVVVFSSANYYGAPVKL-------------- 130
                                       67899********9987766555599*****************99955555555544444443.............. PP

                                       HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST---TTSHHHHHHHHHHHH-EEES CS
                     NAD_binding_4 160 kldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGwingsdlgirgllgliakgvlpe 236
                                            ++++  +  + Y +sK++ E++  +++r++g+p++++Rp    ge ++G     ++++r+++++ a + +p 
  gi|557693624|ref|YP_008796678.1| 131 ---PVTEDTPPNPRTPYDYSKVALENVAWSYHRNHGVPLTVLRPWKAFGEYEPG----EKMVPRFVKACLASEPIPL 200
                                       ...356788889999**********************************99996....5668889999999999997 PP

                                       -SB---TT--EEEHHHHHH CS
                     NAD_binding_4 237 ilgdkeavldlvpvDyvan 255
                                       ++g +  v d   vD ++ 
  gi|557693624|ref|YP_008796678.1| 201 FNGGA-DVTDPYHVDNLCH 218
                                       76664.5677777777666 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 !   24.4   0.0   1.2e-08   2.3e-05      43     143 ..      40     171 ..      20     186 .. 0.60

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.2e-08
                                       EEE--TT-CCHHHHHHTT-SEEEES---TCC..HHHH.........................HHHHHHHHHHCT--E CS
                    NAD_binding_10  43 vvegdvtdvedlaealkgadaVvsalggggk..deeg.........................aknivdaakeagvkR 92 
                                       vv +d+++ +d++  +++ d V+ ++ +++      +                           n+++aa++ gv+R
  gi|557693624|ref|YP_008796678.1|  40 VVGADISSGADIRMDVTDFDSVLKTFEQNRFeaV--VhlaavadiplsmrdphrcfkvnvygSLNVLEAARRMGVRR 114
                                       4555555555555555555555555533222110..1222222333333444557777778899************* PP

                                       EEEEEETTTTSGCGCHHHHHHHH.....CCHHHH..HHHHHHHHHHHHSSSEEEEEEE CS
                    NAD_binding_10  93 fvlvsaigvgdevpgefgewnke.....llkayl..aakraaeellrasgldwTivrp 143
                                       +v+ s+++ +  +p +++ + ++     +  +y   a  + a  + r+ g+  T++rp
  gi|557693624|ref|YP_008796678.1| 115 VVVFSSANYYG-APVKLPVTEDTppnprTPYDYSkvALENVAWSYHRNHGVPLTVLRP 171
                                       ********995.455444433321111144444322345567778899*********9 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.34   6.8e+02       3      24 ..      16      37 ..      15      44 .. 0.87
   2 ?   12.0   0.1   7.2e-05      0.14      58     137 ..      51     121 ..      35     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.34
                                      EEEETTTSHHHHHHHHHHHHHH CS
                                KR  3 ylitGGlGgLGlelarwlaekg 24
                                      +litG  G +G++l + l  +g
  gi|557693624|ref|YP_008796678.1| 16 VLITGSEGFVGRHLREYLGGRG 37
                                      69***********999987666 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.2e-05
                                       ----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEE CS
                                KR  58 vaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlf 134
                                       +++Dv+d d+v +++e+ +      + v+h A v++  +   +++ d +++++  v G+ n+ e+ ++  +  +v+f
  gi|557693624|ref|YP_008796678.1|  51 IRMDVTDFDSVLKTFEQNR-----FEAVVHLAAVADI-P---LSMRDPHRCFKVNVYGSLNVLEAARRMGVRRVVVF 118
                                       5678888888877777765.....788*****99764.3...466788999************************** PP

                                       EEH CS
                                KR 135 SSi 137
                                       SS+
  gi|557693624|ref|YP_008796678.1| 119 SSA 121
                                       **7 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 ?   10.4   0.0   0.00017      0.34      43     118 ..      47     112 ..      34     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                                       SEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCT CS
                      adh_short_C2  43 aev.lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreefdraldvnlyslfllakaalplmk 118
                                       + + +++DVtd ++v +++e+     +++  +v+ a++a+        +s  + +r ++vn+y+ +++++aa+++  
  gi|557693624|ref|YP_008796678.1|  47 SGAdIRMDVTDFDSVLKTFEQ-----NRFEAVVHLAAVADI------PLSMRDPHRCFKVNVYGSLNVLEAARRMGV 112
                                       445689999999999999998.....7899**********8......68999********************99754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2185.70
//
Query:       gi|557693625|ref|YP_008796679.1|  [L=250]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   49.1   0.0    8.2e-13   48.3   0.0    1.4  1  MOSC_N    MOSC N-terminal beta barrel domain
    1.7e-10   41.0   0.0    2.6e-10   40.4   0.0    1.3  1  MOSC      MOSC domain


Domain annotation for each model (and alignments):
>> MOSC_N  MOSC N-terminal beta barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   9.1e-17   8.2e-13       2      71 ..       4      71 ..       3     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 9.1e-17
                            MOSC_N  2 arvssLyvyPiKsckgvslseaevtaaGllalDReflvvd.edGkfltqrrePrlalirteldeedglLtl 71
                                      +rv++L++yP+Ks+ g+++ +++v  +G+   DR f+vvd  +G +l ++ ePrl  i ++l   dg L l
  gi|557693625|ref|YP_008796679.1|  4 FRVVRLFRYPVKSLLGEEVADVDVSFEGFD-GDRLFAVVDpVTGYALSAKGEPRLLQIGATLV--DGELGL 71
                                      79**************************96.*********999****************9995..555544 PP

>> MOSC  MOSC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   2.9e-14   2.6e-10       2     129 ..     126     238 ..     125     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 2.9e-14
                                       XX---GGGGSEEEEETHHHHHHHHHS..GGGGG-STTTT--SEEES-.......-TTT-BTT-E.EEETT....... CS
                              MOSC   2 rkihggdekavllisresldalneelkegrsveldpgrfreNivvggaaafeEdtwkelrigdrrfrlggacsRcqm 78 
                                       r+ +++d+ +++li+   l+++  ++  ++     ++rfr+Niv + +++ e+     l  g++ ++++++++Rc +
  gi|557693625|ref|YP_008796679.1| 126 RETRFHDSMPIHLINLRTLEKMGLSI--DE-----AARFRPNIVFSAEQNDESLVGGYLDTGEALLKIVKPTRRCIV 195
                                       567899****************9999..54.....56********8834444444445555999************* PP

                                       .........EE----THHHHHTTHHHHHHHHT---EEEEEEE-EEEETTS- CS
                              MOSC  79 vnvdqetgarprepcktlakfrrvdkrvkgkgrfGvylrvleegtvrvGde 129
                                       ++ +q++  r+   ++tl +         ++grfG y+ v+++g ++v+ +
  gi|557693625|ref|YP_008796679.1| 196 ITHQQKNLSRNLDLLRTLRAN--------SEGRFGLYATVVKPGKISVDAR 238
                                       **9999999999999999986........679***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1836.07
//
Query:       gi|557693626|ref|YP_008796680.1|  [L=327]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   62.6   0.0    7.2e-15   55.1   0.0    2.5  2  LAGLIDADG_3  LAGLIDADG-like domain
     0.0062   16.7   0.0      0.016   15.3   0.0    1.7  2  Hom_end      Homing endonuclease
  ------ inclusion threshold ------
      0.026   14.5   0.1      0.043   13.8   0.1    1.3  1  Imm43        Immunity protein 43


Domain annotation for each model (and alignments):
>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0042        25       3      42 ..      92     135 ..      90     173 .. 0.80
   2 !   55.1   0.0   1.2e-18   7.2e-15       2      83 .]     188     281 ..     187     281 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0042
                                       HHHHHHHHHHHCCECCECSTTTTS....EEEEES-HHHHHHHHH CS
                       LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvs....isltssskelledvqr 42 
                                        +a+L G  ++D +++k+ +++++    i l+ ++ke++++++ 
  gi|557693626|ref|YP_008796680.1|  92 DLAYLIGTEAGDAYATKTDEGTRGekyiIGLKVKDKEFADEYAT 135
                                       5799999999*********9999999*************99865 PP

  == domain 2  score: 55.1 bits;  conditional E-value: 1.2e-18
                                       HHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCC............. CS
                       LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvy............. 65 
                                       ++a+fLrG+fd++G+v+k++     +++++++++ll +v++lL++lGIe+t  + k++ + g+              
  gi|557693626|ref|YP_008796680.1| 188 CVAMFLRGFFDSEGCVDKRGA----MTVYNTDYQLLLYVMYLLKKLGIETTSDTPKIKTRGGTSfkdpkkgktyhhn 260
                                       689*****************7....9*****************************77777777788*********** PP

                                       ...ECCCHCHCTTCGGGTTTX CS
                       LAGLIDADG_3  66 ...rlliisgenlkrFlekig 83 
                                          ++l+i++ + ++F++ +g
  gi|557693626|ref|YP_008796680.1| 261 kdyYYLRIRMPSNETFYNWVG 281
                                       ****************99887 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.99   5.9e+03      28      56 ..     106     141 ..      93     144 .. 0.48
   2 !   15.3   0.0   2.8e-06     0.016      16      68 ..     191     241 ..     180     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.99
                           Hom_end  28 vkkeked......satvktedksvmeg.ivklarsL 56 
                                        +k++e+       + +k  dk+  ++  +++ar L
  gi|557693626|ref|YP_008796680.1| 106 ATKTDEGtrgekyIIGLKVKDKEFADEyATRIARVL 141
                                       555544444444444444444444443134555555 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.8e-06
                           Hom_end  16 aFlaGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvktkeek 68 
                                       +Fl G+ ds+g v+k+  + +tv  +d +++  ++ l ++LGi+++ +t + k
  gi|557693626|ref|YP_008796680.1| 191 MFLRGFFDSEGCVDKR--GAMTVYNTDYQLLLYVMYLLKKLGIETTSDTPKIK 241
                                       6***************..89*************************99884433 PP

>> Imm43  Immunity protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   7.3e-06     0.043      78     116 ..     252     288 ..     221     300 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.3e-06
                             Imm43  78 kkgeslksdknYyalRvkkldndlFldlknsdleedrkk 116
                                       kkg++ +++k+Yy+lR++   n+ F++    +   +rkk
  gi|557693626|ref|YP_008796680.1| 252 KKGKTYHHNKDYYYLRIRMPSNETFYNWVGFTI--ERKK 288
                                       8999*********************66555443..3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2311.66
//
Query:       gi|557693627|ref|YP_008796681.1|  [L=456]
Description: gylcosyl transferase group 1 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-42  143.6   0.0    5.7e-42  143.2   0.0    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    4.2e-27   95.2   0.0    7.9e-27   94.3   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    8.9e-08   32.4   0.0    1.7e-07   31.5   0.0    1.4  1  Glyco_trans_1_2  Glycosyl transferases group 1
    0.00061   18.6   0.0       0.21   10.2   0.0    2.6  2  Glyco_transf_20  Glycosyltransferase family 20
  ------ inclusion threshold ------
       0.19   12.2   0.0       0.35   11.3   0.0    1.5  1  Tex_YqgF         Tex protein YqgF-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 !  143.2   0.0   1.6e-45   5.7e-42       6     171 ..     255     433 ..     250     434 .. 0.97

  Alignments for each domain:
  == domain 1  score: 143.2 bits;  conditional E-value: 1.6e-45
                                       HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES................STTHHHHHHHHH CS
                   Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...............ngeeekelkklae 67 
                                        +k+g+ e++ +i  v+rl++ Kg+d+++ka+a++ k   +nvkl+i+G               +++++ +l+ l++
  gi|557693627|ref|YP_008796681.1| 255 ADKHGLGEDDGVISIVARLDPLKGHDRALKALAKVVK--THNVKLLIVGngsfssskkglglskGEAWRTYLQTLVK 329
                                       5789999****************************97..6************************99*********** PP

                                       HHCTTCGGGEEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT- CS
                   Glycos_transf_1  68 elelsdnviflgevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnn 144
                                       +l+l+++vif+g+vs+++le +++ +d +vlps  EgfG+v++E+  +g+pv++s+a g+ae+++dg++G+lv p +
  gi|557693627|ref|YP_008796681.1| 330 NLGLEKHVIFTGHVSQKELECVYTLSDFTVLPSVAEGFGLVVVESWLFGKPVVVSKAAGIAELIVDGVNGYLVGPDD 406
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHSHHHHHHHHHHHHH CS
                   Glycos_transf_1 145 aealaeairklledeelrerlgenark 171
                                       +  la+++r lle++ l e++g+n+r+
  gi|557693627|ref|YP_008796681.1| 407 VSGLADRMRTLLENPSLTEEMGKNGRE 433
                                       *************************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 !   94.3   0.0   2.2e-30   7.9e-27       3     134 .]     266     420 ..     264     420 .. 0.87

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 2.2e-30
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.HEEEEEES---.................HHHHHHHT..T-T.TEEEE- CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.dvrlvivGdgp.rp..............eeleelaa..gleerveftG 61 
                                       vi  v rl ++ kg+d  l+a++++ k  +v+l+ivG+g+  +                l+ l++  gle++v+ftG
  gi|557693627|ref|YP_008796681.1| 266 VISIVARL-DPLKGHDRALKALAKVVKThNVKLLIVGNGSfSSskkglglskgeawrTYLQTLVKnlGLEKHVIFTG 341
                                       577899**.788**********88887746*******985533345666666655556677677568999******* PP

                                       --..THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  62 fv..edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLl 132
                                       +v  ++l+ ++  +d +v+Ps  egfgl+++E+  +g+pvV+++++giae++  g+ng+lv p+d++ la+++ +Ll
  gi|557693627|ref|YP_008796681.1| 342 HVsqKELECVYTLSDFTVLPSvaEGFGLVVVESWLFGKPVVVSKAAGIAELIvdGVNGYLVGPDDVSGLADRMRTLL 418
                                       **9778*********************************************9************************* PP

                                       H- CS
                   Glyco_trans_1_4 133 ed 134
                                       e+
  gi|557693627|ref|YP_008796681.1| 419 EN 420
                                       97 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 !   31.5   0.0   4.7e-11   1.7e-07       3      77 ..     359     435 ..     354     446 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 4.7e-11
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarerv 77 
                                       + ps +e++ l+++E   +G ++++++a g++el+ +g  + l+   d+  la+++r ll+np + +++++++re +
  gi|557693627|ref|YP_008796681.1| 359 VLPSVAEGFGLVVVESWLFGKPVVVSKAAGIAELIVDGVNGYLVGpdDVSGLADRMRTLLENPSLTEEMGKNGRETA 435
                                       679999**************************************99****************************985 PP

>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.4   0.0    0.0017         6      93     176 ..     104     188 ..      87     194 .. 0.74
   2 !   10.2   0.0   5.9e-05      0.21     355     442 ..     337     422 ..     246     439 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0017
                                       CHHHHCHHHHHTT-GG....G----HHHHHH...HHHHHHHHHHHHHCC--..TT-EEEEESGGGTTHHHHHHHCCT CS
                   Glyco_transf_20  93 gfsksvLWpllHYklpdsseekefersawda...YvkvnklFAdkiveeik..dgdliwvhDYhLmllPellRkkle 164
                                       g +k+ +W llH  ++d+   +  e ++ d+   Y   n++ ++++++  +  d dl+ +hD++ + + e++    +
  gi|557693627|ref|YP_008796681.1| 104 GAAKEEMWKLLH-GVQDERPLSLLELAWTDEyayYNLYNRVCSETALALDRelDFDLFYIHDFQQLPMGEMMGTLKP 179
                                       468999******.5555555555565555541115667888899888877777889********9999999988777 PP

                                       TSEEEEEE-S-- CS
                   Glyco_transf_20 165 dakigfflHiPF 176
                                       ++   f  HiPF
  gi|557693627|ref|YP_008796681.1| 180 KL---FRWHIPF 188
                                       75...6677777 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 5.9e-05
                                       EEEES---HHHHHHHHHH-SEEEE--SSBSS-CHHHHHHHCSTTT--EEEEETTBGGGGT-TTTS..EEE-TT-HHH CS
                   Glyco_transf_20 355 vylersldfeeliallaaadvllvtslRdGmnlvakeyvvcqqekkgvLiLSeFaGaaqsLkdaa..ilvNPwdiee 429
                                       v ++ +++++el  +++ +d  +  s+ +G  lv  e     +    ++++S+ aG a+   d++  +lv P d++ 
  gi|557693627|ref|YP_008796681.1| 337 VIFTGHVSQKELECVYTLSDFTVLPSVAEGFGLVVVESWLFGK----PVVVSKAAGIAELIVDGVngYLVGPDDVSG 409
                                       4567789***************************999887765....5*************99854489******** PP

                                       HHHHHHHHHC--H CS
                   Glyco_transf_20 430 vaeaikeaLkmse 442
                                       +a+ +++ L+ + 
  gi|557693627|ref|YP_008796681.1| 410 LADRMRTLLENPS 422
                                       ***9999887654 PP

>> Tex_YqgF  Tex protein YqgF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   9.8e-05      0.35      35      68 ..     274     307 ..     253     326 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.8e-05
                                       TTT--HHHHHHHHHHHHHHTT--EEEEESSTTHH CS
                          Tex_YqgF  35 epkkkveeakkklkklvkkykveliaiGnGtasr 68 
                                       +p k  ++a k+l+k+vk+++v+l+ +GnG  s 
  gi|557693627|ref|YP_008796681.1| 274 DPLKGHDRALKALAKVVKTHNVKLLIVGNGSFSS 307
                                       4666788999********************9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); 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 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3225.88
//
Query:       gi|557693628|ref|YP_008796682.1|  [L=255]
Description: small conductance mechanosensitive ion channel, MscS family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-22   78.1   0.0    6.6e-22   78.1   0.0    1.3  2  MS_channel  Mechanosensitive ion channel


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 ?   -3.6   0.3      0.39   6.9e+03      36      48 ..      19      31 ..       8      38 .. 0.49
   2 !   78.1   0.0   3.7e-26   6.6e-22       5     202 ..      57     249 ..      54     252 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 0.39
                                      HHHHHHHCHHHHH CS
                        MS_channel 36 lalglalkdlisn 48
                                      +a++l +    + 
  gi|557693628|ref|YP_008796682.1| 19 VAIMLLVTAFAAR 31
                                      3333333333333 PP

  == domain 2  score: 78.1 bits;  conditional E-value: 3.7e-26
                                       HHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-S CS
                        MS_channel   5 kiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedigl 81 
                                       +i i++vg+l +  +lg n+ +ll ++G++g+a  +a++d++sn+ +  ++    pf++GD  +++ ++G+V++i+ 
  gi|557693628|ref|YP_008796682.1|  57 SIFIWLVGLLFIVNQLGLNLDILLLLMGLAGVAAIIAARDILSNISSRYLIGSFIPFNVGDEMQVSSFRGKVVEINP 133
                                       6899************************************************************************* PP

                                       SEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHHHHHH-TTB-TTS-EEE CS
                        MS_channel  82 rttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelkealkekpevlkdkellv 158
                                        +  + + +g++ ++Pns l+++   Nls     rri++s++v+ + +v  +e    +lk + k  ++++++ ++lv
  gi|557693628|ref|YP_008796682.1| 134 VASLLLSEEGTLAVVPNSVLLKEISLNLSP-YASRRITISVHVPQEVNVPDAEAE--VLKLCNKYRSKLDQRFPPLV 207
                                       ******************************.*****************6655555..55555555566667789*** PP

                                       EEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHH CS
                        MS_channel 159 vldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileee 202
                                        ++  g+  + +e+  ++ +  pe++ ++ +e+  +i + +e+ 
  gi|557693628|ref|YP_008796682.1| 208 SVKSSGQADVVLELVLLAAQ--PEKRNELAAELGAKISELMEKM 249
                                       ********************..**************99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1830.06
//
Query:       gi|557693629|ref|YP_008796683.1|  [L=295]
Description: methionyl aminopeptidase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-35  120.8   0.0      8e-35  120.4   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24


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 !  120.4   0.0   4.4e-39     8e-35       5     208 ..       9     287 ..       6     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 4.4e-39
                                       HHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC...SSSB--TTEEEE CS
                     Peptidase_M24   5 kaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp...ndrvlkegdlvl 78 
                                       +a+++a++++ a+ + + pg +  ++a+ +e++ + ++g+ ++afp  + +++ + ++hy+p   ++ +l+++ + +
  gi|557693629|ref|YP_008796683.1|   9 RAGEVARRIRMAIPSLVSPGASLLQIAEQVEKM-ILDNGC-QPAFP--CNVSVDSVAAHYSPipgDTSTLHRNFIAK 81 
                                       79*****************************87.778887.589**..8888999999**777765677******** PP

                                       EEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEE CS
                     Peptidase_M24  79 idagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGH 155
                                       id+g+ +dgy++D+++Tv     t+  + l +av+ea++aa+k v +Gv++s+i+ ++++vl+++g+ k++++++GH
  gi|557693629|ref|YP_008796683.1|  82 IDFGVMVDGYIADTAVTVTD---TAVGEMLKTAVEEALKAAVKTVAAGVKVSAIGSVVQNVLTRYGV-KPIRNLTGH 154
                                       ******************65...44455689************************************.********* PP

                                       EESS.SSSEE..EEEESSSTTCSSB--TTBEEEEEE......EEEEETTT........................... CS
                     Peptidase_M24 156 gvGl.evhde..gpsvsresndgrkleeGmvftiEp......giyfapge........................... 196
                                        + + ++h +   p+++  s++g kl+eG+v++iEp      g                                  
  gi|557693629|ref|YP_008796683.1| 155 EIQRyNLHAGvsIPNIA--SGEGAKLQEGHVYAIEPfatvadG------Fgeviehrtatifrlwktfagqvsspes 223
                                       ***99***883444455..789**************5444442......3334444556666666677777777888 PP

                                       ...................................................E.EEEEBEEEEEE CS
                     Peptidase_M24 197 ...................................................g.gvriedtvlvt 208
                                                                                          + +++ e+tvlv 
  gi|557693629|ref|YP_008796683.1| 224 nllktlserfnglpysprwltdlgpdalsihqrlvktgrvkaypvlverlnKpVAQAEHTVLVE 287
                                       8888888888888888888999999999999999999999999999999986699999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2072.35
//
Query:       gi|557693630|ref|YP_008796684.1|  [L=58]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0007   19.6   0.2       0.12   12.4   0.0    2.1  2  DUF2752          Protein of unknown function (DUF2752)
     0.0016   18.2   1.1        1.4    8.9   0.1    2.1  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.002   17.6   2.6       0.49    9.9   0.1    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0032   17.6   1.7     0.0065   16.6   1.7    1.5  1  Zn-ribbon_8      Zinc ribbon domain
     0.0078   16.1   2.2        0.1   12.5   0.5    2.2  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
  ------ inclusion threshold ------
       0.03   14.7   0.1        3.6    8.0   0.1    2.1  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.034   14.2   0.1      0.041   13.9   0.1    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.056   13.1   4.4        1.8    8.3   1.2    2.3  2  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
      0.056   13.4   0.4        1.4    8.9   0.1    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.061   13.1   5.7        1.9    8.3   0.6    2.3  2  zinc_ribbon_2    zinc-ribbon domain
      0.068   13.1   1.0        9.8    6.2   0.1    2.1  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.12   11.8   3.4       0.34   10.4   0.3    2.1  2  zf-ribbon_3      zinc-ribbon domain
       0.12   12.0   2.3        9.2    6.1   0.1    2.1  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.15   11.5   1.8       0.27   10.6   0.4    1.9  2  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge


Domain annotation for each model (and alignments):
>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.013        17       6      16 ..       5      15 ..       3      18 .. 0.90
   2 !   12.4   0.0   9.6e-05      0.12      10      19 ..      35      44 ..      28      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.013
                           DUF2752  6 ltGipCPGCGl 16
                                      lt ++C  CG+
  gi|557693630|ref|YP_008796684.1|  5 LTFLKCLNCGV 15
                                      899*******6 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 9.6e-05
                           DUF2752 10 pCPGCGltRa 19
                                      +CP CG+tR+
  gi|557693630|ref|YP_008796684.1| 35 KCPKCGGTRS 44
                                      7********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 !    8.9   0.1    0.0011       1.4      25      35 ..       4      14 ..       3      16 .. 0.86
   2 !    8.4   0.1    0.0014       1.9       2      10 ..      35      43 ..      34      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                           TFIIS_C 25 mtvfykCtkCg 35
                                      + +f kC++Cg
  gi|557693630|ref|YP_008796684.1|  4 PLTFLKCLNCG 14
                                      579*******8 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0014
                           TFIIS_C  2 kCpkCgsre 10
                                      kCpkCg+++
  gi|557693630|ref|YP_008796684.1| 35 KCPKCGGTR 43
                                      8*****987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.3    0.0014       1.8       2      21 ..       9      27 ..       8      27 .. 0.80
   2 !    9.9   0.1   0.00038      0.49       2      10 ..      35      43 ..      34      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0014
                                      EETTTTCEECHEETSTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelv 21
                                      kC nCg +n  +++ ++++v
  gi|557693630|ref|YP_008796684.1|  9 KCLNCGVEN-SRPFRENDYV 27
                                      9******99.7777777776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00038
                                      EETTTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstn 10
                                      kCP+Cg+t+
  gi|557693630|ref|YP_008796684.1| 35 KCPKCGGTR 43
                                      8******86 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.7   5.1e-06    0.0065       7      39 ..       9      46 ..       7      47 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.1e-06
                       Zn-ribbon_8  7 rCeeCghefevlqsisdap.......ltaCPeCgsevrrv 39
                                      +C +Cg   e  +++ +++       +++CP+Cg++  r+
  gi|557693630|ref|YP_008796684.1|  9 KCLNCG--VENSRPFRENDyvlkiveDEKCPKCGGTRSRI 46
                                      8*****..565555555555666774666******76666 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 ?    3.4   0.1     0.055        71       2       8 ..       8      14 ..       7      16 .. 0.87
   2 !   12.5   0.5   8.1e-05       0.1       2      14 ..      34      46 ..      33      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.055
                                      SB-TTT- CS
                      zf-FPG_IleRS  2 epCpRCw 8 
                                       +C  C+
  gi|557693630|ref|YP_008796684.1|  8 LKCLNCG 14
                                      69****8 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8.1e-05
                                      SB-TTT--BBEEE CS
                      zf-FPG_IleRS  2 epCpRCwryierv 14
                                      e+Cp C+++ +r+
  gi|557693630|ref|YP_008796684.1| 34 EKCPKCGGTRSRI 46
                                      9********9987 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 ?    5.1   0.0     0.023        30      28      39 ..       7      19 ..       2      29 .. 0.69
   2 ?    8.0   0.1    0.0028       3.6       5      16 ..      35      46 ..      32      56 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.023
                   Lar_restr_allev 28 cvyCadCga.stp 39
                                      +  C +Cg+ ++ 
  gi|557693630|ref|YP_008796684.1|  7 FLKCLNCGVeNSR 19
                                      578*****95333 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0028
                   Lar_restr_allev  5 pCPfCggravle 16
                                       CP Cgg    +
  gi|557693630|ref|YP_008796684.1| 35 KCPKCGGTRSRI 46
                                      7*****987655 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 ?   13.9   0.1   3.2e-05     0.041      71     100 ..       8      47 ..       3      50 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                                       EEETTTS-EEECHHHHH...........S-TTTSSS-EEEE CS
                              HypA  71 vrCreCgkefeleekal...........rCpkCgsadveiv 100
                                       ++C +Cg e +   + +           +CpkCg+++ +i+
  gi|557693630|ref|YP_008796684.1|   8 LKCLNCGVENSRPFR-EndyvlkivedeKCPKCGGTRSRII 47 
                                       68*****77774332.123478899999*******998876 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 ?    5.8   0.1    0.0079        10      12      20 ..       9      17 ..       7      20 .. 0.91
   2 ?    8.3   1.2    0.0014       1.8      12      22 ..      35      42 ..      34      46 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0079
                           zf-tcix 12 kCpkCGtyN 20
                                      kC +CG++N
  gi|557693630|ref|YP_008796684.1|  9 KCLNCGVEN 17
                                      9******99 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0014
                           zf-tcix 12 kCpkCGtyNGt 22
                                      kCpkCG   Gt
  gi|557693630|ref|YP_008796684.1| 35 KCPKCG---GT 42
                                      9****9...44 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 ?    3.1   0.0     0.073        93      20      30 ..       9      19 ..       3      27 .. 0.74
   2 ?    8.9   0.1    0.0011       1.4      20      30 ..      35      45 ..      32      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.073
                     Zn_Tnp_IS1595 20 vCPhCgsrkay 30
                                       C +Cg++ ++
  gi|557693630|ref|YP_008796684.1|  9 KCLNCGVENSR 19
                                      59999999443 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0011
                     Zn_Tnp_IS1595 20 vCPhCgsrkay 30
                                       CP+Cg+++++
  gi|557693630|ref|YP_008796684.1| 35 KCPKCGGTRSR 45
                                      5*****99654 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.5    0.0026       3.4       1      10 [.       9      18 ..       9      20 .. 0.88
   2 ?    8.3   0.6    0.0015       1.9       1       6 [.      35      40 ..      32      42 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0026
                     zinc_ribbon_2  1 fCpnCGaelq 10
                                      +C nCG e++
  gi|557693630|ref|YP_008796684.1|  9 KCLNCGVENS 18
                                      7*****9985 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0015
                     zinc_ribbon_2  1 fCpnCG 6 
                                      +Cp+CG
  gi|557693630|ref|YP_008796684.1| 35 KCPKCG 40
                                      577776 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 ?    5.9   0.1    0.0096        12       6      19 ..       9      22 ..       9      25 .. 0.90
   2 ?    6.2   0.1    0.0076       9.8       6      20 ..      35      46 ..      34      49 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0096
                    Zn_ribbon_SprT  6 rCtgCgreythhls 19
                                      +C +Cg e  ++++
  gi|557693630|ref|YP_008796684.1|  9 KCLNCGVENSRPFR 22
                                      6*****99999987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0076
                    Zn_ribbon_SprT  6 rCtgCgreythhlsi 20
                                      +C+ Cg   + +++i
  gi|557693630|ref|YP_008796684.1| 35 KCPKCG---GTRSRI 46
                                      599999...777766 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   0.2     0.086   1.1e+02      18      24 ..       9      15 ..       8      17 .. 0.73
   2 ?   10.4   0.3   0.00026      0.34      16      24 ..      33      41 ..      31      42 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.086
                       zf-ribbon_3 18 vCpyCGt 24
                                      +C +CG 
  gi|557693630|ref|YP_008796684.1|  9 KCLNCGV 15
                                      5888885 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00026
                       zf-ribbon_3 16 dnvCpyCGt 24
                                      d +Cp+CG+
  gi|557693630|ref|YP_008796684.1| 33 DEKCPKCGG 41
                                      788999995 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 ?    6.1   0.1    0.0072       9.2       7      19 ..      13      25 ..      11      25 .. 0.89
   2 ?    5.9   0.4    0.0079        10       5      14 ..      34      43 ..      32      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0072
                           zf-RRN7  7 CgvCgcrsftldd 19
                                      Cgv+++r f+++d
  gi|557693630|ref|YP_008796684.1| 13 CGVENSRPFREND 25
                                      ********99976 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0079
                           zf-RRN7  5 ppCgvCgcrs 14
                                      + C+ Cg+++
  gi|557693630|ref|YP_008796684.1| 34 EKCPKCGGTR 43
                                      78*****964 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00021      0.27      32      45 ..       6      19 ..       2      37 .. 0.83
   2 ?    0.8   0.2      0.26   3.3e+02      29      36 ..      32      39 ..      21      42 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                       Vps36-NZF-N 32 plPpClaCGvkpdl 45
                                      ++ +Cl+CGv+ ++
  gi|557693630|ref|YP_008796684.1|  6 TFLKCLNCGVENSR 19
                                      5789******9876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.26
                       Vps36-NZF-N 29 astplPpC 36
                                      +++++P+C
  gi|557693630|ref|YP_008796684.1| 32 EDEKCPKC 39
                                      56677777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 427.37
//
Query:       gi|557693631|ref|YP_008796685.1|  [L=382]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-140  468.1   5.8   1.9e-140  467.9   5.8    1.0  1  DUF1512     Protein of unknown function (DUF1512)
     0.0055   17.1   1.8        1.1    9.6   0.5    2.5  2  DUF3496     Domain of unknown function (DUF3496)
     0.0083   16.0   0.4       0.84    9.5   0.0    2.6  3  CK2S        Casein Kinase 2 substrate
  ------ inclusion threshold ------
       0.57   10.2   3.2        2.4    8.2   0.0    2.7  3  HU-DNA_bdg  DNA-binding domain


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 !  467.9   5.8  4.2e-144  1.9e-140       2     356 .]      22     380 ..      21     380 .. 0.98

  Alignments for each domain:
  == domain 1  score: 467.9 bits;  conditional E-value: 4.2e-144
                           DUF1512   2 isliifllllill..llglnqklqlavllrdiekklakleklaeeakkkvvellkklg..kedpkklverlleffvi 74 
                                       ++ ++++++l+++  ++++ q++ql+++lrd+ekkl+kl+ +++e ++ +ve++k++g  ++dp+  ++rl+eff+i
  gi|557693631|ref|YP_008796685.1|  22 LLSLVWFAFLMIFflYPSFGQRMQLSYMLRDLEKKLNKLKLIKDEINQITVETIKRVGkpEKDPAPDINRLSEFFII 98 
                                       567899999988854569***************************************99999*************** PP

                           DUF1512  75 ePvdlePtgivkrlehllrtsedklkklvekllpeadeversnvetaleiasalnliykvvrHylllakktknlvll 151
                                       +P +++P+g+v +leh+l+t e+ ++++v+kl+p+a+e++++++++++e+++ +n+iy+vvrHy+ll+kkt n++++
  gi|557693631|ref|YP_008796685.1|  99 QPESMDPYGLVYKLEHILETGESVYEQEVAKLAPHATEHQVKSLTNLVEVLRGINTIYRVVRHYYLLGKKTANIYMV 175
                                       ***************************************************************************** PP

                           DUF1512 152 lqlqmllplllklaeayekalkaflkgkPvGDgaGplvaakllekkekksleaakdtviaevelegrkvivvkaeGp 228
                                       lq+qm+lp+++++ae+y++a+ af+kg+P+GDg+Gplvaakl++ +ek++ e+akdtv++e+ele+rkv+vv+a Gp
  gi|557693631|ref|YP_008796685.1| 176 LQIQMVLPQIIEIAESYRQAAVAFSKGQPIGDGVGPLVAAKLVNGMEKERYEIAKDTVVQEIELENRKVYVVRAIGP 252
                                       ***************************************************************************** PP

                           DUF1512 229 gstvGrlgeavekiveklkekvdliitvDAalkLEGEetgsvaeGvGvaiGdpGvekikiErvatkygipldaviik 305
                                       g+tvGr+ge+v+++ve+l e+++liit+DAalkLEGEetg++aeGvGvaiG+pGv+k+kiE++a+++gipl+a++i 
  gi|557693631|ref|YP_008796685.1| 253 GGTVGRPGEGVKQLVERLPENPKLIITIDAALKLEGEETGKIAEGVGVAIGGPGVDKYKIEELAKSRGIPLYAFVIF 329
                                       ***************************************************************************** PP

                           DUF1512 306 msleeAitaMtkeiaeavdkavervkeiikektkegetvivvGvGNtvGva 356
                                       +s++eAit M+++ia+a+d+++e+vk++i ek k+ge+v+v+G+GNt+Gv+
  gi|557693631|ref|YP_008796685.1| 330 QSITEAITPMRESIAKAADQVLEKVKQLILEKVKSGESVVVAGIGNTIGVG 380
                                       *************************************************96 PP

>> DUF3496  Domain of unknown function (DUF3496)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.5   0.00026       1.1       2      35 ..      44      77 ..      43      79 .. 0.91
   2 !    6.0   0.0    0.0033        15      14      47 ..     335     368 ..     327     370 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00026
                           DUF3496  2 sqmElrikdLeselskmKtsqedsnkteLEkykq 35
                                       q+  +++dLe +l k+K  + ++n++ +E+ k+
  gi|557693631|ref|YP_008796685.1| 44 MQLSYMLRDLEKKLNKLKLIKDEINQITVETIKR 77
                                      6888999***********************9886 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0033
                           DUF3496  14 elskmKtsqedsnkteLEkykqlyleelkvrksL 47 
                                        +  m+ s +++  + LEk kql le++k  +s+
  gi|557693631|ref|YP_008796685.1| 335 AITPMRESIAKAADQVLEKVKQLILEKVKSGESV 368
                                       5678999999999999*************99886 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0   0.00019      0.84      64     102 ..      42      80 ..      39     100 .. 0.85
   2 ?    3.8   0.0     0.011        49      87     142 ..     110     165 ..     106     171 .. 0.81
   3 ?   -2.4   0.0      0.84   3.7e+03      60      78 ..     339     357 ..     327     364 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00019
                              CK2S  64 qlealeevlakLrekleelqkvrdsleklvrdalqlyee 102
                                       q+++l  +l++L++kl++l+ ++d+++++  ++ + + +
  gi|557693631|ref|YP_008796685.1|  42 QRMQLSYMLRDLEKKLNKLKLIKDEINQITVETIKRVGK 80 
                                       8999************************99888877654 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.011
                              CK2S  87 dsleklvrdalqlyeekadklslkeliersavtPsladmlewlqdiermyrseyll 142
                                        +le +++++ ++ye++ +kl  ++   +      l ++l ++ +i+r+ r  yll
  gi|557693631|ref|YP_008796685.1| 110 YKLEHILETGESVYEQEVAKLAPHATEHQVKSLTNLVEVLRGINTIYRVVRHYYLL 165
                                       57888999999999999999999998888887778888888888888888888776 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.84
                              CK2S  60 LrekqlealeevlakLrek 78 
                                       +re +++a+++vl+k ++ 
  gi|557693631|ref|YP_008796685.1| 339 MRESIAKAADQVLEKVKQL 357
                                       5667777888888877765 PP

>> HU-DNA_bdg  DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       1.5   6.5e+03     103     121 ..      56      74 ..      51      76 .. 0.70
   2 ?    8.2   0.0   0.00054       2.4      33      69 ..     216     254 ..     209     259 .. 0.80
   3 ?    1.8   0.1     0.052   2.3e+02      37      72 ..     335     369 ..     327     377 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.5
                                       EEEE-HHHHHHHHTEEEEE CS
                        HU-DNA_bdg 103 sltqgkeLrealakikvei 121
                                       +l+  k +++++++i ve 
  gi|557693631|ref|YP_008796685.1|  56 KLNKLKLIKDEINQITVET 74 
                                       5666677788888888875 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00054
                                       HHHHHHHHH-TTS-HHHHHHHHHHHHHHHH..HHHTTT- CS
                        HU-DNA_bdg  33 dIidemvkegtevrketienilnlykrevs..eaileGy 69 
                                       ++++ m ke+ e+ k t+++ ++l +r+v+  +ai  G 
  gi|557693631|ref|YP_008796685.1| 216 KLVNGMEKERYEIAKDTVVQEIELENRKVYvvRAIGPGG 254
                                       67899**********************986225565555 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.052
                                       HHHHH-TTS-HHHHHHHHHHHHHHHHHHHTTT-EEE CS
                        HU-DNA_bdg  37 emvkegtevrketienilnlykrevseaileGysVn 72 
                                       ++   +  + k+ + ++l+ +k+ + e +++G+sV+
  gi|557693631|ref|YP_008796685.1| 335 AITPMRESIAKA-ADQVLEKVKQLILEKVKSGESVV 369
                                       555555555443.46778888888899999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      695  (0.038764); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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 0.28s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2690.71
//
Query:       gi|557693632|ref|YP_008796686.1|  [L=606]
Description: DNA topoisomerase III [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-100  336.7   0.0   2.8e-100  336.2   0.0    1.2  1  Topoisom_bac  DNA topoisomerase
    4.4e-12   46.1   0.1    9.5e-12   45.1   0.1    1.6  1  Toprim        Toprim domain
  ------ inclusion threshold ------
       0.03   14.4   1.1      0.098   12.7   1.1    2.0  1  Exonuc_VII_S  Exonuclease VII small subunit


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 !  336.2   0.0  4.6e-104  2.8e-100       2     411 ..     151     551 ..     150     553 .. 0.92

  Alignments for each domain:
  == domain 1  score: 336.2 bits;  conditional E-value: 4.6e-104
                      Topoisom_bac   2 inenlvdaaeaRrelDwliGinlsrlltkklkg...kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkk 75 
                                       +n++ v++a  R++ D++ G++++rllt+++++    +v+s G +qtptL ++veRe+ei++F+p++yw +eatl k
  gi|557693632|ref|YP_008796686.1| 151 LNMRWVEKARFRQIFDLVTGAAFTRLLTLSTRRlapVRVISWGSCQTPTLNFVVEREKEIQQFKPQKYWVIEATLRK 227
                                       58999************************66656668999**********************************955 PP

                      Topoisom_bac  76 ekkekekkkkkkkerikdkeeaeaileklkkk.eakvesvekkekkkppplpfdtttLqkeasrklglsakktlsia 151
                                       +++e+   +k++ ++i++++eae+++ek +k  ea+v+s++k+ek+ p+plp++t++ +++ +r+ g+sa++ ls++
  gi|557693632|ref|YP_008796686.1| 228 ASGEE---FKAATQQIWNRDEAEQVFEKARKAgEAVVTSYTKSEKTLPRPLPMRTDDVLRDLTRITGVSANRLLSMM 301
                                       55544...7999*****************99669******************************************* PP

                      Topoisom_bac 152 qkLYekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpk 228
                                       ++LY + g+i+YpRTd++r+ + +++++ l+a++     ++l+ a+  ++++  +   ++ +++aH++I+P++    
  gi|557693632|ref|YP_008796686.1| 302 EELYAE-GYISYPRTDTNRYRRGFDFQTPLKAVTAA---DALRDAKPDKAEPDPR--NGSRDDGAHPPIYPVATF-- 370
                                       *****7.****************99********994...4555555555555544..456666*********553.. PP

                      Topoisom_bac 229 lkelsddekklYelIvrrfla.slmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelke 304
                                         + s+   +++e+I+ rf a ++ +da+ ++ ++++ +++  f+a+g+ ++++G+++v+ + + ++++  lpel +
  gi|557693632|ref|YP_008796686.1| 371 --RGSGVLMQIWEYIACRFYAnAFFDDAVQSTAKAEIGIDGIAFSAEGSSVTKQGYLQVFSYFRPRDKP--LPELMV 443
                                       ..57888999********9984799**************************************9*9986..****** PP

                      Topoisom_bac 305 geevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellek 381
                                       ge++++ +v+++e +Tkpp+r+tea+L+++mek+giGt+aTra+  + ++er+Y++r ++ ++pt+lG+al+e l +
  gi|557693632|ref|YP_008796686.1| 444 GEKLQIIDVTIREDETKPPPRLTEADLLRLMEKNGIGTDATRASFPQLITERNYAVRAGRFFKPTPLGMALIESLAE 520
                                       *********************************************************88****************77 PP

                      Topoisom_bac 382 f.kdlvspelTaeleekLdeIaegkadakev 411
                                          +l+ pe+++ +e+ +++I++g+ + +e 
  gi|557693632|ref|YP_008796686.1| 521 AdTRLITPETRRLVEDYMAKIERGETSFQES 551
                                       7799*********************998875 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.1   1.6e-15   9.5e-12       2     102 ..      16     134 ..      15     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.6e-15
                                       EEEESSHHHHHHHHHTHT..STEEEEEEESSSSEEEHS....TTEEEEE............ECTTTHHHHHHHHHHH CS
                            Toprim   2 lvivEgpsdaktiakalg..sgfqavtaslGhildlet....efkpvye............eiedkkkvlkalkela 60 
                                       ++++E+ s a++i+ + +  + + +v +++Gh+++ +     e     +            ++ dk++   ++++l 
  gi|557693632|ref|YP_008796686.1|  16 IIVAEKASVARAIKAVVSaaKANAVVSSVRGHMMEADLpdgyE-----WgakhpfeiiklrKVVDKISDNRVFEQLV 87 
                                       79**************9999999************99966663.....04444464444453333333333455555 PP

                                       ...HHHSEEEEECSSSHHHHHHHHHHHHHHT..HHHTTTEEEEEESS CS
                            Toprim  61 ...kradeiilatDpDreGeaiawellevlk..ellenkigrvefse 102
                                          +    +++atD+D eGe i++e+l+v +   + e  ++r++f++
  gi|557693632|ref|YP_008796686.1|  88 kvfSGGGVLVIATDNDSEGELIGYEILQVYRrvTGGEPVVYRMRFNS 134
                                       2336666**********************9977666668******97 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 ?   12.7   1.1   1.6e-05     0.098       9      50 ..     535     577 ..     529     579 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                      Exonuc_VII_S   9 eeIvekLEsgel....sLeeslklyeeGvkLlkeCekkLdeaeqkv 50 
                                       e+  +k+E ge+    sLe+sl lyee   Ll++C++k+de+ +++
  gi|557693632|ref|YP_008796686.1| 535 EDYMAKIERGETsfqeSLEQSLSLYEE---LLRRCSDKIDEISRRL 577
                                       556678888887444479999****95...***********98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (606 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       800  (0.0446204); expected 358.6 (0.02)
Passed bias filter:                      638  (0.0355848); 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: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 4372.36
//
Query:       gi|557693633|ref|YP_008796687.1|  [L=176]
Description: hypothetical protein CSUB_C0196 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       291  (0.0162307); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1384.73
//
Query:       gi|557693634|ref|YP_008796688.1|  [L=266]
Description: 3-oxoacyl-[acyl-carrier protein] reductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-61  208.3   0.0    1.8e-61  207.7   0.0    1.2  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    1.9e-45  154.8   0.0    2.2e-45  154.5   0.0    1.1  1  adh_short        short chain dehydrogenase
    2.2e-08   34.2   0.0    3.1e-08   33.8   0.0    1.2  1  KR               KR domain
    3.4e-05   23.4   0.0    0.00015   21.3   0.0    1.8  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.017   15.0   0.1      0.025   14.5   0.1    1.2  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.11   11.6   0.0       0.15   11.2   0.0    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
       0.12   12.6   0.0        0.2   11.9   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.21   10.7   0.0        0.3   10.1   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding 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 !  207.7   0.0     8e-65   1.8e-61       1     233 [.      21     263 ..      21     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 207.7 bits;  conditional E-value: 8e-65
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilv 74 
                                       GaasgIGr + +++ae+Ga++vl+d+ne +  + + ++++++g ev   ++D +++ ++++l + ++e+    Dilv
  gi|557693634|ref|YP_008796688.1|  21 GAASGIGRSVSERFAEAGASLVLVDINEPSlTSVASAIKDRYGVEVeaKKADLSRKREIDELWAGLKERA--PDILV 95 
                                       9*****************************9999999******99666********************96..8**** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSCCEEEEEEEGGGTSB.STTTTHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeggsivnlssvgaerv.vpnynaygaaKaale 149
                                       nnagi +    +fle++++ ++r+ldvnl+s+f++++++++    +gg ivn+ss+ a +  v++ ++yg++K +l+
  gi|557693634|ref|YP_008796688.1|  96 NNAGIYEF--RDFLEVDEDFLERTLDVNLKSVFYMCQHMVRtRGDRGGVIVNVSSIEAVIHlVKGLTHYGVSKIGLV 170
                                       ********..*******************************444566*********99877689999********** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT...HHH.......HHHHHHHHSTTSS-B-HHHHHHHHHHHCS CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgikg...fde.......lleelearaplgrlgtpeevaeaalfLas 216
                                       +ltr+lA+e+g kg RvNav pg i+T+ ++++++   + +          ++ +r+pl+rlg+p+eva+++lfLas
  gi|557693634|ref|YP_008796688.1| 171 GLTRALAREYGGKGFRVNAVMPGGIHTPGTDKVRNealK-RlqlgffiTGMNFISRIPLKRLGEPDEVARVILFLAS 246
                                       ********************************9975431.233333223456789********************** PP

                                       GGGTT--SEEEEESTTG CS
                      adh_short_C2 217 deasyitGqtlvvDgGl 233
                                       d++sy++G++lvvDgG+
  gi|557693634|ref|YP_008796688.1| 247 DLSSYVNGSVLVVDGGY 263
                                       ****************9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.5   0.0     1e-48   2.2e-45       2     192 ..      16     205 ..      15     208 .. 0.96

  Alignments for each domain:
  == domain 1  score: 154.5 bits;  conditional E-value: 1e-48
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgk 77 
                                        +lvtGa+sGIGr +++++a++Ga++v+vd++e  l  va+ +k+  g ++ a ++D++ ++e+++l +  +++   
  gi|557693634|ref|YP_008796688.1|  16 KALVTGAASGIGRSVSERFAEAGASLVLVDINEPSLTSVASAIKDRyGVEVEAKKADLSRKREIDELWAGLKERAP- 91 
                                       69*********************************************************************99987. PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB.-TTBHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvp.vagvaaYsAsK 153
                                        d+LvnNAGi ++++f e++e+  er+++vNl++vf ++++++++    ++G IvnvsS+ +  + v+g++ Y+ sK
  gi|557693634|ref|YP_008796688.1|  92 -DILVNNAGIYEFRDFLEVDEDFLERTLDVNLKSVFYMCQHMVRT-RGDRGGVIVNVSSIEAVIHlVKGLTHYGVSK 166
                                       .99******************************************.99*************966526889******* PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmakelre 192
                                        +++gltr+la+e+  +g rvnav+PG++ T+ + ++r+
  gi|557693634|ref|YP_008796688.1| 167 IGLVGLTRALAREYGGKGFRVNAVMPGGIHTPGTDKVRN 205
                                       ********************************9999876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   1.4e-11   3.1e-08       4     141 ..      18     153 ..      16     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 1.4e-11
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaee 79 
                                       l+tG++ g+G+++++  ae ga+ lvl+  ++++  + +   ++++++ g+eve+ +aD+s k ++ +l + +k+++
  gi|557693634|ref|YP_008796688.1|  18 LVTGAASGIGRSVSERFAEAGAS-LVLVDINEPSLTSVA---SAIKDRyGVEVEAKKADLSRKREIDELWAGLKERA 90 
                                       9********************96.667766645444444...5555555**************************** PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT...S--SEEEEEEEHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled...esldffvlfSSiagll 141
                                       p i   ++ Ag+ + + + e++++ le+ l   +k +  + + + +   ++  ++v +SSi +++
  gi|557693634|ref|YP_008796688.1|  91 PDI--LVNNAGIYEFRDFLEVDEDFLERTLDVNLKSVFYMCQHMVRtrgDRGGVIVNVSSIEAVI 153
                                       999..7************************99999999887776663345566888899988876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   6.7e-08   0.00015       1     170 [.      17     193 ..      17     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 6.7e-08
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHH...HHHHT-S CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerl...fkeeqpd 66 
                                       +lVtGa+  iG+ + ++++e+g  ++ +d ++ +  + + + +        e  ++dl  + ++++l   +ke +pd
  gi|557693634|ref|YP_008796688.1|  17 ALVTGAASGIGRSVSERFAEAGASLVLVDINEPSLTSVASA-IkdrygvevEAKKADLSRKREIDELwagLKERAPD 92 
                                       59********************9988888774443333333.14678999999*********999884446788*** PP

                                       EEEE--S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.......EEEEEEEGGGGTSCSSSSBSTCSTTS-- CS
                         Epimerase  67 avihlAavggvaassedpadfieknlqgtlnlleaarkagvk.......rllflsSsevYGkdaeqpkeettltgpl 136
                                       + ++ A++   ++  e  +df+e++l ++l+ + ++ ++ v+        ++++sS            e ++   +l
  gi|557693634|ref|YP_008796688.1|  93 ILVNNAGIYEFRDFLEVDEDFLERTLDVNLKSVFYMCQHMVRtrgdrggVIVNVSS-----------IEAVI---HL 155
                                       ***********************999999999999998877655556666777777...........45555...55 PP

                                       .--SSHHHHHHHHHHHHHHHHHHHHT...-EEEEEEES CS
                         Epimerase 137 .kpnspYaaaKlageklveayaaqyg...lnaiilrlf 170
                                        k  + Y+++K+    l++a+a++yg   +++ ++++ 
  gi|557693634|ref|YP_008796688.1| 156 vKGLTHYGVSKIGLVGLTRALAREYGgkgFRVNAVMPG 193
                                       67888999999999999999999996455666666655 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 ?   14.5   0.1   1.1e-05     0.025      10      56 ..      26      72 ..      16      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                                      CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS- CS
                           3HCDH_N 10 mGagiaavfasagleVvlvdiseealekalekieksleklvekgklk 56
                                      +G+++ + fa+ag + vlvdi+e +l++++++i++++   ve++k++
  gi|557693634|ref|YP_008796688.1| 26 IGRSVSERFAEAGASLVLVDINEPSLTSVASAIKDRYGVEVEAKKAD 72
                                      8**********************************888888877776 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.6e-05      0.15       2      81 ..      18      94 ..      17     106 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.6e-05
                                      EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SE CS
                   Polysacc_synt_2  2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdv 80
                                      lvtGa+  iG+++ +++++  + +++l++ +E +l ++++ +++++   +++++  + +   r+ ++l   l+e  +d+
  gi|557693634|ref|YP_008796688.1| 18 LVTGAASGIGRSVSERFAEAGA-SLVLVDINEPSLTSVASAIKDRYGV-EVEAK-KADLSRKREIDELWAGLKERAPDI 93
                                      8***************998765.7999************998666544.34333.334444444444444555555555 PP

                                      E CS
                   Polysacc_synt_2 81 v 81
                                      +
  gi|557693634|ref|YP_008796688.1| 94 L 94
                                      5 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   8.9e-05       0.2       3      87 ..      19     108 ..      17     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.9e-05
                                       EE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHHHHHHH...HTTS.. CS
                   Sacchrp_dh_NADP   3 iiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka...lgvrfeaialdaenyeavLaal...lkeg.. 70 
                                       + Ga  ++G++v e  a+ +     ++++d ++ +l  +a+++    gv++ea++ d + +++ +++l   lke+  
  gi|557693634|ref|YP_008796688.1|  19 VTGAaSGIGRSVSERFAEAGAS---LVLVDINEPSLTSVASAIkdrYGVEVEAKKADLSRKRE-IDELwagLKERap 91 
                                       6677789999999999999986...6777777766666665556669**********999999.77774557888** PP

                                       SEEEE-SSGGGHHHHHH CS
                   Sacchrp_dh_NADP  71 dlvvnlsppissldvlk 87 
                                       d++vn ++ ++ +d l+
  gi|557693634|ref|YP_008796688.1|  92 DILVNNAGIYEFRDFLE 108
                                       *******9999888765 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 ?   10.1   0.0   0.00014       0.3       2      82 ..      16     125 ..      15     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00014
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT......................T--TTSHHHHHHHH...HHH--S CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre......................eldltdaeavaell...keakpd 53 
                                       k lvtGa   +G+ + +++ae+g++++ ++ +                      ++dl+++ +++el    ke  pd
  gi|557693634|ref|YP_008796688.1|  16 KALVTGAASGIGRSVSERFAEAGASLVLVDINepsltsvasaikdrygveveakKADLSRKREIDELWaglKERAPD 92 
                                       679**********************9999888899******************99*****99999986555899999 PP

                                       EEEE--.----HHHHHHSH...HHHHHHHTHHH CS
                     RmlD_sub_bind  54 vvvnaA.AytavDkaEsee...eaayavnaeav 82 
                                       ++vn A  y   D  E +e   e+   vn ++v
  gi|557693634|ref|YP_008796688.1|  93 ILVNNAgIYEFRDFLEVDEdflERTLDVNLKSV 125
                                       888655267777766665411145566666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1935.82
//
Query:       gi|557693635|ref|YP_008796689.1|  [L=223]
Description: methylated-DNA-[protein]-cysteine S-methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-28   98.7   0.0    2.5e-28   98.0   0.0    1.3  1  DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA b


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 !   98.0   0.0   1.4e-32   2.5e-28       2      81 .]     127     206 ..     126     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 1.4e-32
                                       HHHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHH CS
                     DNA_binding_1   2 fqqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLea 78 
                                       f+ +V++++ +Ip+G+v +Y ++A  +g+pka raVg+a+a+np++i++PcHRVv++dg++g y g  + k++lL++
  gi|557693635|ref|YP_008796689.1| 127 FAGKVLNVVASIPFGEVRSYRDVAVSVGSPKAYRAVGNAVARNPVPIIIPCHRVVKSDGSIGLYGGDENVKAWLLRH 203
                                       7789************************************************************************* PP

                                       TTS CS
                     DNA_binding_1  79 Egv 81 
                                       Eg+
  gi|557693635|ref|YP_008796689.1| 204 EGI 206
                                       *96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       235  (0.0131073); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); 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 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1543.93
//
Query:       gi|557693636|ref|YP_008796690.1|  [L=84]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-18   66.5   0.0      2e-18   66.3   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 !   66.3   0.0   1.1e-22     2e-18       1      73 [.       4      79 ..       4      80 .. 0.93

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 1.1e-22
                                      EEEEEEETTTTTHHHHHHHHHHHHHHCCC...CSSEEEEEEESTT-EEEEETTEEEEEHHHHTSS--HHHHHHHHH CS
                               Rdx  1 rvtIeYCtqCkwmlraaelaqellstfpe...slgevalqpstgGaFeVtldgelvwsrkeeggfpetkelkqrvr 73
                                      +v+I YC  C+  ++a ela++lls++++   +  +v+l +s gG+FeV++dge ++sr+e  +fp+ +e+ ++v+
  gi|557693636|ref|YP_008796690.1|  4 NVRIVYCVPCGHLPTALELAKNLLSRYGQrlnKKFSVTLDTSDGGTFEVYIDGERIFSRHEARRFPTLDEIAEQVD 79
                                      59***************************555446899999*******************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 638.97
//
Query:       gi|557693637|ref|YP_008796691.1|  [L=634]
Description: quinoprotein alcohol dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-30  101.5   0.2    2.5e-06   27.2   0.0    7.2  8  PQQ       PQQ enzyme repeat
    3.2e-18   66.2   0.0    5.5e-07   29.4   0.0    3.6  3  PQQ_2     PQQ-like domain
    2.8e-09   37.2   4.4      0.074   13.6   0.1    6.8  6  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.4e-07   0.00082       1      28 [.     110     137 ..     110     143 .. 0.95
   2 !    4.5   0.0    0.0062        37       5      23 ..     161     179 ..     158     179 .. 0.87
   3 ?   -3.2   0.0       1.7     1e+04      19      25 ..     234     240 ..     233     240 .. 0.89
   4 ?   -3.4   0.0       1.9   1.1e+04      20      27 ..     249     256 ..     249     259 .. 0.85
   5 !   16.1   0.0   1.3e-06    0.0081      11      32 ..     336     357 ..     332     358 .. 0.89
   6 !   27.2   0.0   4.1e-10   2.5e-06       3      32 ..     375     405 ..     374     410 .. 0.88
   7 !   20.2   0.0   6.7e-08    0.0004       5      26 ..     477     499 ..     475     504 .. 0.88
   8 !    4.3   0.0    0.0071        43       2      22 ..     514     535 ..     513     543 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-07
                                       TEEEEEETTSEEEEEETTTCCEEEEEES CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfkt 28 
                                       gvvyl+++   ++A+ a++G++lW++++
  gi|557693637|ref|YP_008796691.1| 110 GVVYLATNTPSILAVEASNGRILWEYRP 137
                                       79************************98 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0062
                                       EEETTSEEEEEETTTCCEE CS
                               PQQ   5 lgsadGylyAlDadTGkvl 23 
                                       ++s+d  +  +Da+TG+++
  gi|557693637|ref|YP_008796691.1| 161 YPSPDCSIKLVDASTGTEK 179
                                       568999**********986 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.7
                                       TCCEEEE CS
                               PQQ  19 TGkvlWr 25 
                                       +G++lWr
  gi|557693637|ref|YP_008796691.1| 234 NGTMLWR 240
                                       79****7 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 1.9
                                       CCEEEEEE CS
                               PQQ  20 GkvlWrfk 27 
                                       G+ lW f+
  gi|557693637|ref|YP_008796691.1| 249 GDQLWDFR 256
                                       899**998 PP

  == domain 5  score: 16.1 bits;  conditional E-value: 1.3e-06
                                       EEEEEETTTCCEEEEEESSSCG CS
                               PQQ  11 ylyAlDadTGkvlWrfktggpv 32 
                                        + A++++TG++lW +++++++
  gi|557693637|ref|YP_008796691.1| 336 SVIAINITTGDMLWFYQVVSHD 357
                                       689**************99886 PP

  == domain 6  score: 27.2 bits;  conditional E-value: 4.1e-10
                                       EEEE.ETTSEEEEEETTTCCEEEEEESSSCG CS
                               PQQ   3 vylg.sadGylyAlDadTGkvlWrfktggpv 32 
                                       +++  +++G l+Al+a++G++lWrf++++ v
  gi|557693637|ref|YP_008796691.1| 375 MVIKgCKNGELVALNASNGDLLWRFNPQSLV 405
                                       67777*********************99865 PP

  == domain 7  score: 20.2 bits;  conditional E-value: 6.7e-08
                                       EE.ETTSEEEEEETTTCCEEEEE CS
                               PQQ   5 lg.sadGylyAlDadTGkvlWrf 26 
                                       ++ + ++++yA+D+++G+v+W+f
  gi|557693637|ref|YP_008796691.1| 477 APtPINTTIYAVDLSNGEVKWSF 499
                                       666889***************99 PP

  == domain 8  score: 4.3 bits;  conditional E-value: 0.0071
                                       EEEEE.ETTSEEEEEETTTCCE CS
                               PQQ   2 vvylg.sadGylyAlDadTGkv 22 
                                       +++++ + +     lDa+TGk 
  gi|557693637|ref|YP_008796691.1| 514 GMVIAsTVNRGMIFLDAETGKP 535
                                       56777799999999******96 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   6.6e-06      0.04      67     111 ..     100     143 ..      83     208 .. 0.75
   2 !   18.3   0.0   2.3e-07    0.0013      87     147 ..     336     398 ..     309     403 .. 0.84
   3 !   29.4   0.0   9.2e-11   5.5e-07      45     107 ..     482     544 ..     462     570 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.6e-06
                             PQQ_2  67 pvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrseepae 111
                                        v g+plv +g v+++++  +++a++a +G+ lW+ ++ + ++ +
  gi|557693637|ref|YP_008796691.1| 100 GVIGPPLVIDGVVYLATNTPSILAVEASNGRILWE-YRPRLQKIP 143
                                       56667888888888888888888888888888888.655545554 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.3e-07
                             PQQ_2  87 qlialdaedGkrlWstqqrseepae..lrssaspavagdtvvvgessgklvaldpkdGkvlWe 147
                                       ++ia+++++G+ lW  q  s+   +   + ++  a++ + v+ g+ +g+lval++++G++lW 
  gi|557693637|ref|YP_008796691.1| 336 SVIAINITTGDMLWFYQVVSHDFYDhdCAWNTVLAKTLNMVIKGCKNGELVALNASNGDLLWR 398
                                       89************9555554333334555777777799***********************6 PP

  == domain 3  score: 29.4 bits;  conditional E-value: 9.2e-11
                             PQQ_2  45 ggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrse 107
                                         +++a+d ++G+v+W++ +++  +g  + ++g+v++ + ++ +i ldae+Gk  +s+ ++++
  gi|557693637|ref|YP_008796691.1| 482 NTTIYAVDLSNGEVKWSFFVDSAYRGWLTATGGMVIASTVNRGMIFLDAETGKPIHSISLDGT 544
                                       679******************************************************999983 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.1   1.2e-05     0.074       3      39 ..      84     127 ..      83     128 .. 0.88
   2 ?    2.5   0.0     0.037   2.2e+02       1      40 []     129     175 ..     129     175 .. 0.82
   3 ?   -3.0   0.0         2   1.2e+04      22      30 ..     309     317 ..     292     319 .. 0.78
   4 ?   -0.9   0.0      0.45   2.7e+03      30      39 ..     382     391 ..     377     392 .. 0.85
   5 ?    3.3   0.1     0.021   1.2e+02      12      38 ..     434     490 ..     393     492 .. 0.66
   6 !   12.0   0.1   3.7e-05      0.22       1      40 []     493     532 ..     493     532 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                             PQQ_3   3 vlWsv.......qlpgpvnsspavdgglvyvgtgdGtlyAlDae 39 
                                       v+Ws        +l++ v ++p+v +g+vy +t   ++ A++a 
  gi|557693637|ref|YP_008796691.1|  84 VVWSIeiprfmdGLGYGVIGPPLVIDGVVYLATNTPSILAVEAS 127
                                       7888877777778899999**********************996 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.037
                             PQQ_3   1 GevlWsv.......qlpgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       G++lW++       +l  p   +  +++g +   ++d ++  +Da t
  gi|557693637|ref|YP_008796691.1| 129 GRILWEYrprlqkiPLTPPHIHGINYYNGFILYPSPDCSIKLVDAST 175
                                       89*****9999988776776788899999999999998887777765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2
                             PQQ_3  22 glvyvgtgd 30 
                                       g+ yv+t++
  gi|557693637|ref|YP_008796691.1| 309 GVAYVSTSN 317
                                       889999987 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.45
                             PQQ_3  30 dGtlyAlDae 39 
                                       +G l+Al+a 
  gi|557693637|ref|YP_008796691.1| 382 NGELVALNAS 391
                                       8*******96 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.021
                             PQQ_3  12 pvnsspavdgglvyvgtg..............................dGtlyAlDa 38 
                                        + s  a++ g+v+v+ +                              + t+yA+D 
  gi|557693637|ref|YP_008796691.1| 434 GIESDIALAYGKVFVAVMnlctvhvptpveqygevvkgsvyniaptpiNTTIYAVDL 490
                                       555666999999999988777777777777777777777777777777777777775 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 3.7e-05
                             PQQ_3   1 GevlWsvqlpg..pvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       Gev+Ws+ +++  +++  +++ gg v ++t + ++  lDaet
  gi|557693637|ref|YP_008796691.1| 493 GEVKWSFFVDSayRGW--LTATGGMVIASTVNRGMIFLDAET 532
                                       9******776634777..8999******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (634 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4316.36
//
Query:       gi|557693638|ref|YP_008796692.1|  [L=202]
Description: hypothetical protein CSUB_C0201 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1532.04
//
Query:       gi|557693639|ref|YP_008796693.1|  [L=158]
Description: hypothetical protein CSUB_C0202 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1216.83
//
Query:       gi|557693640|ref|YP_008796694.1|  [L=370]
Description: ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-33  115.7   0.0      5e-33  114.5   0.0    1.6  2  ABC_tran     ABC transporter
    2.4e-08   34.0   0.1    3.7e-07   30.2   0.0    2.7  3  TOBE_2       TOBE domain
    5.4e-06   26.4   0.0       0.03   14.1   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0011   19.4   0.2      0.002   18.5   0.2    1.6  1  AAA_16       AAA ATPase domain
     0.0022   18.0   0.0     0.0031   17.5   0.0    1.3  1  Rad17        Rad17 P-loop domain
     0.0032   17.7   0.0      0.029   14.7   0.0    2.4  1  TOBE         TOBE domain
     0.0036   17.6   0.8      0.015   15.6   0.7    1.9  1  AAA_22       AAA domain
     0.0054   17.1   0.1      0.017   15.6   0.1    1.9  1  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
      0.029   14.3   0.1      0.077   12.9   0.0    1.7  2  RsgA_GTPase  RsgA GTPase
      0.091   12.5   0.0       0.17   11.6   0.0    1.4  1  IstB_IS21    IstB-like ATP binding protein
       0.15   12.3   0.1        1.1    9.5   0.1    2.1  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.19   11.5   0.0        0.4   10.5   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
       0.23   12.0   0.1       0.54   10.7   0.1    1.6  1  AAA_23       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 !  114.5   0.0   3.6e-36     5e-33       2     136 ..      24     169 ..      23     170 .. 0.95
   2 ?   -3.4   0.0       9.3   1.3e+04     106     118 ..     347     360 ..     328     361 .. 0.68

  Alignments for each domain:
  == domain 1  score: 114.5 bits;  conditional E-value: 3.6e-36
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqepqlfpeltv 76 
                                       + v++++++ge++a++G++G+GK+t l+++agl+k ++Gei++ ++ + +  + l+  ++ +g+++q   l+p++tv
  gi|557693640|ref|YP_008796694.1|  24 DGVTFNVEKGECLALLGPSGCGKTTTLRCVAGLEKADMGEIRIGDRVVFSkdTFLPPEKRGVGMVFQSYALWPHMTV 100
                                       789****************************************98887664577899999***************** PP

                                       HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        +n             e ++++++al+ +gl +++++      s+LSgGq+qrvalara++ +p+l+llDEp 
  gi|557693640|ref|YP_008796694.1| 101 FDNvayplkirkyqktEIKNRVSHALELVGLAGFENRYP----SQLSGGQQQRVALARAIVYEPSLILLDEPL 169
                                       ************999999999****************99....*****************************7 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.3
                                       S.GGS-HHHHHHHH CS
                                       x.xxxxxxxxxxxx RF
                          ABC_tran 106 p.ssLSgGqkqrva 118
                                         ++LS G+k+ + 
  gi|557693640|ref|YP_008796694.1| 347 NiEELSVGKKVHLY 360
                                       34899999998765 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.2   8.5e+03      56      67 ..      62      73 ..      53      75 .. 0.73
   2 ?    0.2   0.0      0.62   8.6e+02      20      51 ..     123     154 ..     108     160 .. 0.78
   3 !   30.2   0.0   2.7e-10   3.7e-07       2      74 ..     289     367 ..     288     368 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.2
                            TOBE_2 56 salapGdtVels 67
                                        +++Gd+V  s
  gi|557693640|ref|YP_008796694.1| 62 GEIRIGDRVVFS 73
                                      478999999765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.62
                            TOBE_2  20 sGtVedveylGsstryvvelaggqlvvvrqpn 51 
                                       s   e v   G + ry  +l ggq+++v+ + 
  gi|557693640|ref|YP_008796694.1| 123 SHALELVGLAGFENRYPSQLSGGQQQRVALAR 154
                                       5556667778999999999*****99998765 PP

  == domain 3  score: 30.2 bits;  conditional E-value: 2.7e-10
                            TOBE_2   2 aiRPEklrla..aagga...nglsGtVedveylGsstryvvelaggqlvvvrqpnadr.d..salapGdtVelswdp 70 
                                       +iR   + +   +  ++   n+l+G+V+ +e++G +++++v++++g ++vv+++   + +  + l +G +V+l ++p
  gi|557693640|ref|YP_008796694.1| 289 VIRSNEIAIRssG--REnglNTLTGHVSFIEFRGQYIDLRVDVGNGVEMVVSTHRFCGvAniEELSVGKKVHLYIEP 363
                                       6899999998552..32234899****************************888877766678999*********** PP

                            TOBE_2  71 ddav 74 
                                       d++ 
  gi|557693640|ref|YP_008796694.1| 364 DAIT 367
                                       *986 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 !   10.3   0.0   0.00032      0.44       3      52 ..      37      74 ..      35      84 .. 0.75
   2 !   14.1   0.0   2.2e-05      0.03     232     298 ..     137     201 ..     103     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00032
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldly 52
                                      +l Gp g+GK++ L++  +l            e+ + g+ir+ ++  +++
  gi|557693640|ref|YP_008796694.1| 37 ALLGPSGCGKTTTLRCVAGL------------EKADMGEIRIGDRVVFSK 74
                                      799**************999............566666666655555554 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.2e-05
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHS 298
                                       + +++lS G+++  al+ a+ + +   sl+l+DEp ++L+ kl ++    l ++l++ g   + +TH+
  gi|557693640|ref|YP_008796694.1| 137 RYPSQLSGGQQQRVALARAIVYEP---SLILLDEPLSNLDAKLREKMRVELkRLLKKIGLTTLYVTHD 201
                                       567899*****999********99...****************9998855523333345666666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   1.5e-06     0.002      22      51 ..      33      59 ..      21     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd 51
                                      g  e++ l G+sG+GK++ +r+++  lek+
  gi|557693640|ref|YP_008796694.1| 33 G--ECLALLGPSGCGKTTTLRCVA-GLEKA 59
                                      3..89******************9.56665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.2e-06    0.0031      43     112 ..      31     104 ..      19     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.2e-06
                             Rad17  43 rkkriLLisGPsGCgkstvvkvLskelgiklrewl..npvslkepdnqksdfkgltekesrf..lsqiesfkel 112
                                       +k + L + GPsGCgk+t+++ ++     ++ e    + v + +  +   + +g+  +++++   + + +f ++
  gi|557693640|ref|YP_008796694.1|  31 EKGECLALLGPSGCGKTTTLRCVAGLEKADMGEIRigDRVVFSKDTFLPPEKRGVGMVFQSYalWPHMTVFDNV 104
                                       455689999************99877666665543114566777777777777777777766656777777664 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.1e-05     0.029       4      60 ..     306     364 ..     303     368 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                              TOBE   4 rNqlpgtVvvveplgseveVrvdlgggatLtArvtr....rsaeeLgLapGeeVfalikaa 60 
                                        N+l+g+V+ +e++g    +rvd+g g +++++  r    +  ee  L++G++V++ i + 
  gi|557693640|ref|YP_008796694.1| 306 LNTLTGHVSFIEFRGQYIDLRVDVGNGVEMVVSTHRfcgvANIEE--LSVGKKVHLYIEPD 364
                                       7***************************88887543222245556..77777777777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.7   1.1e-05     0.015       4      29 ..      32      57 ..      30     201 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      +  +l++ G+sG+GKTt+lr ++   
  gi|557693640|ref|YP_008796694.1| 32 KGECLALLGPSGCGKTTTLRCVAGLE 57
                                      5679****************998765 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 !   15.6   0.1   1.2e-05     0.017       2      34 ..      37      69 ..      36     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTC CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgsel 34
                                       l Gp G+GKT++ + va   ++++ ei   + 
  gi|557693640|ref|YP_008796694.1| 37 ALLGPSGCGKTTTLRCVAGLEKADMGEIRIGDR 69
                                      589***************988887777766554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.6e-05     0.077      96     131 ..      29      65 ..      11      69 .. 0.85
   2 ?   -3.2   0.0       4.9   6.8e+03      63      88 ..     179     204 ..     169     214 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                                       HCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--- CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelelktgevs 131
                                       ++++ ++ +l+G+SG GK+t +  +++ +++ +ge++
  gi|557693640|ref|YP_008796694.1|  29 NVEKgECLALLGPSGCGKTTTLRCVAGLEKADMGEIR 65 
                                       55555999*******************9999999997 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.9
                                       HHHHHHHHHHHHTTSEEEE--TTTHT CS
                       RsgA_GTPase  63 eeleelkeelealgyevllvsaktke 88 
                                       +   elk  l+++g+++l+v  +++e
  gi|557693640|ref|YP_008796694.1| 179 KMRVELKRLLKKIGLTTLYVTHDQEE 204
                                       33556777788888888888666554 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 ?   11.6   0.0   0.00012      0.17      44      68 ..      30      55 ..      19      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                         IstB_IS21 44 iekkenivllGpsGvGKsh.laialg 68
                                      +ek e+++llGpsG GK+  l +  g
  gi|557693640|ref|YP_008796694.1| 30 VEKGECLALLGPSGCGKTTtLRCVAG 55
                                      7999*************842555555 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 ?    9.5   0.1    0.0008       1.1      32      84 ..     141     180 ..     108     185 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0008
                           SbcCD_C  32 tlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatl 84 
                                       +lSGG++q    +ala a   +          ++l++LDE  s+lD++ ++++
  gi|557693640|ref|YP_008796694.1| 141 QLSGGQQQR---VALARA--IV--------YEPSLILLDEPLSNLDAKLREKM 180
                                       455555532...222222..22........23689************999886 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 ?   10.5   0.0   0.00029       0.4      13      39 ..      24      50 ..      21      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00029
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      dg t++++  +   l GpsG GK+T l
  gi|557693640|ref|YP_008796694.1| 24 DGVTFNVEKGECLALLGPSGCGKTTTL 50
                                      67888998656999**********976 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   0.00039      0.54      13      39 ..      26      53 ..      14      55 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00039
                            AAA_23 13 qeidFsk.gltlItGpNGaGKTTildAi 39
                                      ++++ +k    ++ Gp G+GKTT l+++
  gi|557693640|ref|YP_008796694.1| 26 VTFNVEKgECLALLGPSGCGKTTTLRCV 53
                                      55666552466899***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2730.37
//
Query:       gi|557693641|ref|YP_008796695.1|  [L=314]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   33.4   0.0    3.6e-07   30.4   0.0    2.2  1  NMT1            NMT1/THI5 like
    1.1e-05   25.0   0.0    2.4e-05   23.9   0.0    1.7  2  SBP_bac_3       Bacterial extracellular solute-binding protei
    1.1e-05   25.1   0.0    3.5e-05   23.5   0.0    1.5  2  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
     0.0013   18.3   0.0       0.02   14.3   0.0    2.0  2  NMT1_3          NMT1-like family
  ------ inclusion threshold ------
       0.05   13.4   0.0      0.083   12.7   0.0    1.3  1  DUF592          Protein of unknown function (DUF592)


Domain annotation for each model (and alignments):
>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   9.9e-11   3.6e-07       6     156 ..      33     192 ..      30     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 9.9e-11
                                       HHHHHHHTTHHHHTTEEEEEE--.....SSTTHHHHHHHCTS-SE.EEE-HHHHH..HHHHTT--EEEE..EEEE-S CS
                              NMT1   6 glyvAkekGYFkeeGldVeivep.....adpsdatelvasgkadf.gvsyqesll..aarakglpvvsv..aallqe 72 
                                       + +vA e+G+F e+Gl  e+ve      + +   ++++ +gk df  + +   ++  ++  +g  v +   a    +
  gi|557693641|ref|YP_008796695.1|  33 PELVALEHGFFGENGLRCELVELrgggvEKSDLYVDALRTGKTDFyHCGEWVGVVrvLKNTAGKIVAQSkpAPGTLN 109
                                       779***************999973111122344678999******65555555553233333433332222334456 PP

                                       --EEEEEECCC--SSGGGGTTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHH.HHHCTSSSEEECEE CS
                              NMT1  73 plsglivlkdsgikspkDLkGkrigyvgspfekallkallakdggdpsdvtlvnvggtslak.alltgkvDaaiggy 148
                                       + ++++v++dsgi+sp+DL+Gk i++   + ++    ++  +  ++ +++ l++v+  ++   al++g+v aa   +
  gi|557693641|ref|YP_008796695.1| 110 SSFTIFVRQDSGISSPRDLAGKSIAVEA-GTGSFYAARMDLEPYVKSEEIRLISVSEPHARLkALMDGRVSAAS-LL 184
                                       78899********************988.899999999999999***********98887645*******9997.66 PP

                                       TTTHHHHH CS
                              NMT1 149 enwegvel 156
                                         w ++ +
  gi|557693641|ref|YP_008796695.1| 185 GPWTKIAV 192
                                       66666665 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.1     4e+03      47      61 ..      63      77 ..      46      85 .. 0.66
   2 !   23.9   0.0   6.8e-09   2.4e-05      83     168 ..     108     193 ..      96     251 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.1
                                      GGGHHHHHHTTSSSE CS
                                      xxxxxxxxxxxxxxx RF
                         SBP_bac_3 47 wdelipalksgkvDi 61
                                       d  ++al++gk D+
  gi|557693641|ref|YP_008796695.1| 63 SDLYVDALRTGKTDF 77
                                      455566777777664 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 6.8e-09
                                       EEEEEEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHC......TSEEEEESSHHHHHHHHHTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3  83 fsagqvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkk......gaeivefdtleealqaLkngrv 153
                                       ++++ +++vr +d    s+i+s+ dL+gk+++v ag+ +  +++  l +      +++++++    + l+aL +grv
  gi|557693641|ref|YP_008796695.1| 108 LNSSFTIFVR-QD----SGISSPRDLAGKSIAVEAGTGSFYAARMDL-EpyvkseEIRLISVSEPHARLKALMDGRV 178
                                       5778899***.54....4899999************99774444333.24677678899999888888********* PP

                                       SEEEEEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                         SBP_bac_3 154 davvadspvlaylvk 168
                                        a+    p  + +vk
  gi|557693641|ref|YP_008796695.1| 179 SAASLLGPWTKIAVK 193
                                       **9876666666555 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   9.7e-09   3.5e-05      43     161 ..      67     181 ..      63     189 .. 0.78
   2 ?   -2.1   0.0      0.64   2.3e+03      14      48 ..     203     237 ..     190     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 9.7e-09
                                       HHHHHTTS-SEEE--HHHHHHHHHHS.-EEEEEEEEETT--SEEEEEEEEETTSS--SHHHHGG-EEEE--TT-TTT CS
                    Phosphonate-bd  43 vealragqvDiaflgplayvqardqa.gveplatrvrsdGsasyrsviivradsdiqsledLkgktiafvspsStsG 118
                                       v alr+g++D+   g   +v+ + ++ + + +a+++   G    +  i+vr+ds+i s  dL+gk+ia+++   t++
  gi|557693641|ref|YP_008796695.1|  67 VDALRTGKTDFYHCGEWVGVVRVLKNtAGKIVAQSKPAPGTLNSSFTIFVRQDSGISSPRDLAGKSIAVEA--GTGS 141
                                       789**************99998888735599999999999999999**********************976..5677 PP

                                       THHHHHHTCCCCT--HHHHSSEEEE--HHHHHHHHHTTSSSEE CS
                    Phosphonate-bd 119 ylvpaalLvkeagldpeddfsevfsgshdaavlavlsgdadaa 161
                                       +++ ++ L +++ +     ++   ++   a ++a+++g++ aa
  gi|557693641|ref|YP_008796695.1| 142 FYAARMDL-EPYVKSE--EIRLISVSEPHARLKALMDGRVSAA 181
                                       88888888.6665443..3444444444445566666666665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHHHHHSSEEEEE--SSHHHHHHHHHT CS
                    Phosphonate-bd  14 eayqpladyLseelGvevelvvatdyaavvealra 48 
                                       ++  p + ++s++lG e  ++  ++++ +ve + +
  gi|557693641|ref|YP_008796695.1| 203 KRDNPTLLIVSDRLGDETVVRLIKSINKAVEKINS 237
                                       55567777899999999999999999999998876 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   5.5e-06      0.02      91     167 ..     110     184 ..     106     193 .. 0.89
   2 ?    1.6   0.0     0.041   1.5e+02     227     263 ..     208     244 ..     206     253 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.5e-06
                            NMT1_3  91 evfqlvvskdsgigsiadlkgkrvsvGpegsGtegsarailealglsekdlklleelgygesadalkdgqldgaalv 167
                                         f++ v++dsgi+s  dl gk+++v ++g+G+  +ar  le +  ++++++l++  ++    +al+dg++ +a+l 
  gi|557693641|ref|YP_008796695.1| 110 SSFTIFVRQDSGISSPRDLAGKSIAV-EAGTGSFYAARMDLEPYV-KSEEIRLISVSEPHARLKALMDGRVSAASLL 184
                                       568999********************.7799*9999999999776.78899999999****************9886 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.041
                            NMT1_3 227 nflvvradldeelvYeitkaifenldelnsihkaake 263
                                        +l+v++ l +e+v  ++k+i    +++ns  +a ++
  gi|557693641|ref|YP_008796695.1| 208 TLLIVSDRLGDETVVRLIKSINKAVEKINSDPSAYSD 244
                                       689*******************999999987777655 PP

>> DUF592  Protein of unknown function (DUF592)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.3e-05     0.083     100     130 ..     212     242 ..     192     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                            DUF592 100 leDpLekkeivrlikdLqkainkvlstrlrl 130
                                       + D L ++++vrlik ++ka++k++s  +  
  gi|557693641|ref|YP_008796695.1| 212 VSDRLGDETVVRLIKSINKAVEKINSDPSAY 242
                                       6799********************9987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); 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:                         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 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2084.21
//
Query:       gi|557693642|ref|YP_008796696.1|  [L=564]
Description: iron complex ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-16   60.0  48.0    2.9e-10   40.2  13.7    3.1  4  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        2.5    7.8   5.0         26    4.6   0.1    3.7  3  MotA_ExbB     MotA/TolQ/ExbB proton channel family


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 ?   -0.6   1.0      0.11   9.7e+02     114     170 ..      64     114 ..      58     129 .. 0.45
   2 !   40.2  13.7   3.3e-14   2.9e-10       6     183 ..      83     281 ..      78     283 .. 0.80
   3 ?   -0.9   0.1      0.13   1.2e+03     107     162 ..     319     368 ..     307     389 .. 0.48
   4 !   32.4  17.9   7.7e-12   6.9e-08       3     176 ..     380     555 ..     375     563 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.11
                      BPD_transp_1 114 lilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnl 170
                                       l+++f+++ g a+l+  +g     +tl + a+    +   + ++++ l+ + ++ ++
  gi|557693642|ref|YP_008796696.1|  64 LLNTFVFAAGSALLATVVG-----STLAFLASRTDVFFKKT-VVYASLITFAIPSSV 114
                                       4444455555555555444.....33333333333333333.344444444444444 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 3.3e-14
                      BPD_transp_1   6 ilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf.................vilsilghlilpviillll 62 
                                       + +a    +   +++k +   + +++++Ps v  i +++++                     +  ++  ++ +++ +
  gi|557693642|ref|YP_008796696.1|  83 STLAflaSRTDVFFKKTVVYASLITFAIPSSVESIGWTYLLsprtglvnmaymrltgfEEPLVNLYTLQGMTLVMGI 159
                                       44444445888888888999999999999999555555544555555555566677763333444888889****** PP

                      BPD_transp_1  63 saapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgt 139
                                        ++p++++i++  +   +++l+e  r+ G + +q+++++vlP+++p+i++ +++ f+ +l ++  + ++g  +   +
  gi|557693642|ref|YP_008796696.1| 160 NLTPVALMITAPTFTLFDRSLEEIGRISGGGLFQVYKRIVLPLSAPSIASAFLYCFIVALEAFDTPAIIGIPS-GVY 235
                                       **********************************************************************444.344 PP

                      BPD_transp_1 140 llleailgydyseis..nggvlalviavlllnlvadilqrlldprv 183
                                       +++++i ++ +se    +g++ a++  +l +++++ i++ +++++ 
  gi|557693642|ref|YP_008796696.1| 236 VITTTIYSQLVSEVPprYGSATAYATTLLTISILLIIVYNWFSKKA 281
                                       55555555555555599999*******************9999985 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.13
                      BPD_transp_1 107 lppiitglilafggllggavlleflgswpGlgtllleailgydyseis..nggvlalv 162
                                       +p i+t+++ +f      +  +e+l+     + +l + i  ++y+ +s  ++ +l++ 
  gi|557693642|ref|YP_008796696.1| 319 IPLIATLAAASFQK----YWNPEYLF----TNITLDNYIKFFNYPTTSqaFVNSLVVS 368
                                       44444444444444....44455555....5555666666666666665522222222 PP

  == domain 4  score: 32.4 bits;  conditional E-value: 7.7e-12
                      BPD_transp_1   3 llGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.vilsilghlilpviillllsaapyvrlirraalrs 78 
                                       +lG +  ++r  ++ ++l++l  ++l++P++vla+ +++ + +i+ +l+ +i++++ ++ l ++p+v+++ ++ l +
  gi|557693642|ref|YP_008796696.1| 380 FLGTYFSVRRPIRGGRALTTLLSIPLAFPPIVLAVGIFWSViYIDIGLYGTIWALVYAYSLRYIPLVIRFLSGSLLQ 456
                                       56666669999*********************8887776556999999***************************** PP

                      BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllleailgydyseis 154
                                       + +dl+  a + G + ++++ ++++P++ + + + ++++f++ +++  ++ +l + +  + +++l a+++    ++ 
  gi|557693642|ref|YP_008796696.1| 457 IHRDLEDSAIVHGGGVFTTITRITIPLLRTAVSSAALYVFIRTITDLGVAVLLVTHNStVLSTTLFALWNTGEKLTV 533
                                       *********************************************99777666655442444444444444444444 PP

                      BPD_transp_1 155 nggvlalviavlllnlvadilq 176
                                       ++g l+++  ++ l+++a  + 
  gi|557693642|ref|YP_008796696.1| 534 VAGGLIYTTTLMCLLFIAHRFG 555
                                       5555555555555555555544 PP

>> MotA_ExbB  MotA/TolQ/ExbB proton channel family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.5     0.021   1.9e+02      92     108 ..      74      90 ..      65     101 .. 0.83
   2 ?    4.6   0.1    0.0029        26     101     122 ..     264     285 ..     252     288 .. 0.79
   3 ?   -0.1   0.0      0.08   7.2e+02      59      70 ..     425     436 ..     421     439 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHH CS
                         MotA_ExbB  92 eALiaTalGlvvAipav 108
                                        AL+aT++G  +A +a 
  gi|557693642|ref|YP_008796696.1|  74 SALLATVVGSTLAFLAS 90 
                                       7************8875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHHHHHHHHHHHHHH CS
                         MotA_ExbB 101 lvvAipavlaynklkrkverlv 122
                                       l ++i+++++yn++++k++r +
  gi|557693642|ref|YP_008796696.1| 264 LTISILLIIVYNWFSKKADRYE 285
                                       6789*************99875 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.08
                                       HHHHHHHHHHHH CS
                         MotA_ExbB  59 lGLlGTVlGlie 70 
                                       +GL GT++ l+ 
  gi|557693642|ref|YP_008796696.1| 425 IGLYGTIWALVY 436
                                       8*******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 4058.42
//
Query:       gi|557693643|ref|YP_008796697.1|  [L=449]
Description: iron complex ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-24   86.1   0.1    3.8e-24   85.4   0.1    1.3  1  SBP_bac_6   Bacterial extracellular solute-binding protein
    4.3e-17   62.6   0.1    7.6e-17   61.8   0.1    1.4  1  SBP_bac_11  Bacterial extracellular solute-binding protein
    2.6e-16   60.3   0.2    6.2e-16   59.0   0.0    1.6  2  SBP_bac_8   Bacterial extracellular solute-binding protein
    5.4e-10   39.7   0.3    7.6e-06   26.1   0.2    2.4  2  SBP_bac_1   Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
       0.17   11.8   0.0       0.35   10.8   0.0    1.5  1  HSBP1       Heat shock factor binding protein 1


Domain annotation for each model (and alignments):
>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.1   1.1e-27   3.8e-24       2     219 ..     190     403 ..     189     431 .. 0.92

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 1.1e-27
                         SBP_bac_6   2 plpdlilsfdkdflekfieeglfqpldpanlpnvnkdfaeeglkdpdgkyypygvgplvlavnkdrlkgrpvPksWa 78 
                                       p++dl++  +     ++++e+ + p+ ++++++++     e+lkd +g+++++   p+ +a+n+d++k+   P++ +
  gi|557693643|ref|YP_008796697.1| 190 PTADLVV-ISHTTGIRLAQEKHYLPYVSPSAASYP-----EMLKDRNGEWTAFVLLPIAFAYNTDKVKQP--PSTLD 258
                                       899****.9999999999999999***********.....***************************877..***** PP

                         SBP_bac_6  79 DLldPeykgkvalpgnngsdlfealllalykdfgedgvkkllrnlkanlhpaq...mvkaagslesgepavsvvpyf 152
                                        L+dP+++gkv +++   ++  +  l++l+   ge +  ++++ l+ n++p+    + + a +++sge ++  +++ 
  gi|557693643|ref|YP_008796697.1| 259 QLTDPQWQGKVIMHDITLGTVGTQYLVTLKNIIGETAWNRFIERLATNVKPVLdisTATVAEKVASGE-YYIGLIAN 334
                                       ****************************************************99999**********9.56667999 PP

                         SBP_bac_6 153 fadilpekkkgknlkvvwPedGalvspifmlvkkg..kkkelakafidfllspevqailakaggvfPvv 219
                                         di++ k +g++++   P +  l+ + + +   +  k+++ ak ++d+lls+e+q+i+ +    fP+ 
  gi|557693643|ref|YP_008796697.1| 335 LHDIVRLKMQGAPVDYFLPSEVPLLTTFAHVAIINttKNPNSAKLLVDYLLSQEGQTIIGNTPVRFPAR 403
                                       9********************9999999888888889**********************9999899986 PP

>> 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 !   61.8   0.1   2.1e-20   7.6e-17       3     224 ..     142     393 ..     140     396 .. 0.83

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 2.1e-20
                                       EEE-SSTHHHHHHHHHHHHHH.H---EEEEESSHHHHHHHH.....HHH..-SEEEESSH.HHHHHHHH...GGGGG CS
                        SBP_bac_11   3 vaaagslaaalrelaaaFeah.tgvkvevsaggsgklarqi.....adgarpDvwipassawlellaaa...glvqa 70 
                                       v+ + + +a ++   +aF+a+ + ++v++++  + +++ ++     a++  +D+++   ++ ++l++++        
  gi|557693643|ref|YP_008796697.1| 142 VYGSVD-YADIKSTLDAFQAKyPFIQVVYESMRPPEVYTRVtseisANKPTADLVVISHTTGIRLAQEKhylP---Y 214
                                       555555.77899999***775277***************99666655555****************9995553...3 PP

                                       ................GG-EEEEEEEEEEEESTT-TT.---SHHHHHHSS-..-EEEE--T-TTTTHH.HHHHGGG- CS
                        SBP_bac_11  71 ................esavplassplviavpkgnpk.kikgwadLlkpgl..klavadPttspsGlaalalleaag 128
                                                       ++ ++++  p+++a+++++ k +++++++L++p++  k+++ d t  ++G++ l +l++  
  gi|557693643|ref|YP_008796697.1| 215 vspsaasypemlkdrnGEWTAFVLLPIAFAYNTDKVKqPPSTLDQLTDPQWqgKVIMHDITLGTVGTQYLVTLKNII 291
                                       44588889********99*****************6658999*********999********************763 PP

                                       -....HHHHHHHHHTEE.EEESSHHHHHHHHHTTT-SEEE.EEHHHHH..H.STTSSEEEE--TTT--...EEEEEE CS
                        SBP_bac_11 129 a....qellkalekkvv.klgessrqlltaveageadagi.vyeseakaae.ngdkleavylpeglnldpldypaav 198
                                       +    ++++++l+ +v  +l  s+ ++++ v++ge+ +g+ ++++++ + + +g++++++ ++e  +l ++   +a+
  gi|557693643|ref|YP_008796697.1| 292 GetawNRFIERLATNVKpVLDISTATVAEKVASGEYYIGLiANLHDIVRLKmQGAPVDYFLPSEVPLL-TTFAHVAI 367
                                       324556899999999762445555778888*****99877355676655544999*****99888888.7888999* PP

                                       EE-TT--HHHHHHHHHTTSHHHHHHH CS
                        SBP_bac_11 199 lkkaakreaAraFlafLrspeaqail 224
                                       ++++++++ A+ ++++L+s+e+q+i+
  gi|557693643|ref|YP_008796697.1| 368 INTTKNPNSAKLLVDYLLSQEGQTII 393
                                       ***********************997 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.1   3.8e+03      23      60 ..      31      65 ..      29      99 .. 0.59
   2 !   59.0   0.0   1.7e-19   6.2e-16       4     269 ..     156     407 ..     154     418 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                                      SHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB- CS
                         SBP_bac_8 23 dleqklkaalaagtapdidvvwanedalatlaeeglla 60
                                      ++ q + a +aag++p +  +   +  ++ l ++g++a
  gi|557693643|ref|YP_008796697.1| 31 TILQRFMAGAAAGKTPLL--IAVVAVLIS-LLAAGYTA 65
                                      566777777888887742..222223333.33345554 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 1.7e-19
                                       HHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGS.TTHHH-HHHHHTT CS
                         SBP_bac_8   4 kefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdl.dnlddltdalaav 78 
                                       ++f++k+  ++v ++++  +++ + ++++++a++ p++d+v++++    +la+e+   +  ++ + +++++  l++ 
  gi|557693643|ref|YP_008796697.1| 156 DAFQAKYpFIQVVYESMRPPEVYTRVTSEISANK-PTADLVVISHTTGIRLAQEKHYLP--YVsPSAASYPEMLKDR 229
                                       89*****55********99***********9998.899*******99999999776555..4448999999999987 PP

                                       --TS.----EEEEEEE-EEEEEHHHHHHS.---BHHHHHHHHHHHHHH-SEGG---GGG.GGGTHHETTEE---H.. CS
                         SBP_bac_8  79 gydgklygvPyasetpyvliynkdllekaedpktwdellaaakklkgkfglpdpasgwl.qaallakdgksldddgg 154
                                        +++   ++ +    p +++yn+d++++  +p t+d+l++  ++++gk++++d + g++  ++l+  +        g
  gi|557693643|ref|YP_008796697.1| 230 NGEW--TAFVLL---PIAFAYNTDKVKQ--PPSTLDQLTD--PQWQGKVIMHDITLGTVgTQYLVT-LKNII----G 292
                                       7777..555555...78**********6..**********..************999651445555.43333....3 PP

                                       HHH.HHHHHHHHHHHHTT-EE-.S..--SSTTTTTSBSEEE.E-TTHHHHHH-TTTSEEEE--S--.EEEEEEEEEE CS
                         SBP_bac_8 155 kdglkealellkklkdngktyd.tgadavsefanGevafti.ngswdiaaaqkagkklgaivpkqg.sfaggkglav 228
                                       + ++ +++e l++ ++   ++d + a++ +++a+Ge+ +++ +   di  ++ +g ++ + +p +  +++ ++ +a+
  gi|557693643|ref|YP_008796697.1| 293 ETAWNRFIERLATNVKP--VLDiSTATVAEKVASGEYYIGLiANLHDIVRLKMQGAPVDYFLPSEVpLLTTFAHVAI 367
                                       43555555555555544..45545688889*********996788******************88757888889*** PP

                                       BTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TT CS
                         SBP_bac_8 229 pknaknedlaAldFlkwltspenqaalaektgyipvnksaa 269
                                        + +kn++  A+ ++ +l+s e+q+   ++   +p+++  +
  gi|557693643|ref|YP_008796697.1| 368 INTTKNPNS-AKLLVDYLLSQEGQTIIGNTPVRFPARPQTP 407
                                       ********8.***************9999888889888765 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 !   26.1   0.2   2.1e-09   7.6e-06      15     140 ..     155     262 ..     144     271 .. 0.81
   2 !   11.4   0.0   6.2e-05      0.22     287     314 ..     363     390 ..     273     391 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.1e-09
                                       HHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBEC.CHHHHHHTTECTTCCTE CS
                         SBP_bac_1  15 akafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllp.ldpyvkaylapgvkdaa 90 
                                        +af++++p i+V++es    ++++ +t  i+a+++ aD++ +++++  rla+++ +lp ++p ++ y ++  k   
  gi|557693643|ref|YP_008796697.1| 155 LDAFQAKYPFIQVVYESMRPPEVYTRVTSEISANKPTADLVVISHTTGIRLAQEKHYLPyVSPSAASY-PEMLK--- 227
                                       37788889***********************************999999*****66666155555555.45544... PP

                                       EEEHHHHTHHHHCEEEESEEEEEEEEEEEETTTHHCTTGGGSHBHHHHHH CS
                         SBP_bac_1  91 dklsssvlpkildskvlyvPlyaargliYNkdlfekagldppwtWdelve 140
                                        + ++++++ +l           + +++YN+d++++    pp t d+l++
  gi|557693643|ref|YP_008796697.1| 228 -DRNGEWTAFVLL----------PIAFAYNTDKVKQ----PPSTLDQLTD 262
                                       .467889999999..........************5....5678888876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 6.2e-05
                                       EEEEEBTTCSTHHHHHHHHHHHTSHHHH CS
                         SBP_bac_1 287 yglaipkgsknpeaAkkFldfllspeaq 314
                                        ++ai +++knp  Ak ++d+lls e+q
  gi|557693643|ref|YP_008796697.1| 363 AHVAIINTTKNPNSAKLLVDYLLSQEGQ 390
                                       469***********************99 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   0.0   9.7e-05      0.35      24      43 ..      82     101 ..      78     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.7e-05
                             HSBP1  24 qilsriDdMssriDdLEksi 43 
                                       qi  +iD ++sr+D+LEk i
  gi|557693643|ref|YP_008796697.1|  82 QIQPKIDYLQSRLDSLEKLI 101
                                       7889**************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2992.79
//
Query:       gi|557693644|ref|YP_008796698.1|  [L=235]
Description: hypothetical protein CSUB_C0207 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   32.0   0.0    2.8e-07   30.3   0.0    1.9  2  MarR_2          MarR family
    4.5e-06   26.6   0.0    9.3e-06   25.6   0.0    1.5  1  HTH_20          Helix-turn-helix domain
    8.3e-06   25.3   0.0    1.9e-05   24.1   0.0    1.7  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00018   21.3   0.1    0.00053   19.8   0.0    1.8  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0022   17.9   0.0     0.0052   16.7   0.0    1.6  1  MarR            MarR family
     0.0035   17.5   0.3      0.016   15.3   0.1    2.1  2  B-block_TFIIIC  B-block binding subunit of TFIIIC
     0.0041   16.9   0.0     0.0075   16.0   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.031   14.2   0.0    1.7  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.029   14.3   0.0      0.051   13.5   0.0    1.4  1  HTH_11          HTH domain
      0.032   14.6   0.0        0.1   12.9   0.0    1.8  2  Rrf2            Transcriptional regulator
      0.033   14.2   0.0      0.085   12.8   0.0    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.066   13.7   0.0       0.29   11.6   0.0    2.1  2  HTH_27          Winged helix DNA-binding domain
       0.15   11.6   0.0       0.28   10.8   0.0    1.5  1  HTH_CodY        CodY helix-turn-helix domain
       0.19   11.3   0.1        1.5    8.5   0.0    2.1  2  RP-C            Replication protein C N-terminal 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 !   30.3   0.0   2.2e-10   2.8e-07      17      56 ..       4      41 ..       1      47 [. 0.84
   2 ?   -3.3   0.0       6.9   8.8e+03      38      53 ..     163     178 ..     155     180 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2.2e-10
                                      TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      +++  lt+++la rlg++++ v++++k L++ GL++ ++ 
  gi|557693644|ref|YP_008796698.1|  4 AGP--LTISQLAFRLGIPRQLVHYHVKHLQSEGLIRVKDV 41
                                      344..9*****************************98865 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.9
                                       HHHHHHHHHHTTSEEE CS
                            MarR_2  38 vsrilkrLvaaGLver 53 
                                       +s  l+ + + GL+  
  gi|557693644|ref|YP_008796698.1| 163 ASANLAMMNENGLIHF 178
                                       6777777888888865 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   7.2e-09   9.3e-06      19      57 ..       2      39 ..       1      43 [. 0.93

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 7.2e-09
                                      HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      L  a++lt s+la rl+++++ ++yH++ L++ gL++v 
  gi|557693644|ref|YP_008796698.1|  2 L-AAGPLTISQLAFRLGIPRQLVHYHVKHLQSEGLIRVK 39
                                      6.799*******************************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 !   24.1   0.0   1.5e-08   1.9e-05      16      48 .]       5      37 ..       1      37 [. 0.93

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.5e-08
                            HTH_24 16 prisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      + +++++LA rlg++++ v++++k L++eGlI+
  gi|557693644|ref|YP_008796698.1|  5 GPLTISQLAFRLGIPRQLVHYHVKHLQSEGLIR 37
                                      679*****************************7 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 !   19.8   0.0   4.1e-07   0.00053      10      46 ..       1      37 [.       1      38 [. 0.96
   2 ?   -1.9   0.0       2.5   3.1e+03      36      45 ..     167     176 ..     164     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.1e-07
                                      HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 10 lLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +La g+l++++la  lg+++  v +H k L  +GL++
  gi|557693644|ref|YP_008796698.1|  1 MLAAGPLTISQLAFRLGIPRQLVHYHVKHLQSEGLIR 37
                                      6999*******************************96 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                                       HHHHHHTTSE CS
                             HTH_5  36 LkkLreaGLV 45 
                                       L+++ e GL+
  gi|557693644|ref|YP_008796698.1| 167 LAMMNENGLI 176
                                       8999*****8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.1e-06    0.0052      15      49 ..       4      38 ..       3      47 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.1e-06
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                       gpl++s+La +lg+ +  v   +++L  +Gli+ 
  gi|557693644|ref|YP_008796698.1|  4 AGPLTISQLAFRLGIPRQLVHYHVKHLQSEGLIRV 38
                                      59*******************************86 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 !   15.3   0.1   1.3e-05     0.016      22      70 ..      10      56 ..       7      57 .. 0.82
   2 ?   -1.2   0.0       1.9   2.4e+03      35      45 ..     104     114 ..      94     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.3e-05
                    B-block_TFIIIC 22 sdLakeskqdprslfyrlksLekkgLIvkqsiidsatkksistsllvlk 70
                                      s+La  +++    ++y++k+L++ gLI  + +  ++t++  s++  +lk
  gi|557693644|ref|YP_008796698.1| 10 SQLAFRLGIPRQLVHYHVKHLQSEGLIRVKDV--VKTGRRVSSKAYMLK 56
                                      5666667777788*******************..999999888877765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                    B-block_TFIIIC  35 lfyrlksLekk 45 
                                       +fy+l+ L+++
  gi|557693644|ref|YP_008796698.1| 104 FFYHLMRLCSN 114
                                       89******985 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 !   16.0   0.0   5.9e-06    0.0075      16      49 ..       4      37 ..       2      40 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.9e-06
                                      BSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR 16 pqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      +++lt+s+lA r+g+p+  vh +++ L+ +G+++
  gi|557693644|ref|YP_008796698.1|  4 AGPLTISQLAFRLGIPRQLVHYHVKHLQSEGLIR 37
                                      689*****************************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 ?   14.2   0.0   2.4e-05     0.031      18      56 ..       2      40 ..       1      53 [. 0.92
   2 ?   -3.6   0.0       8.5   1.1e+04      40      48 ..     196     204 ..     195     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                      l+ gp+t++++a +lg+pr+ v   ++ L + Gl+++++
  gi|557693644|ref|YP_008796698.1|  2 LAAGPLTISQLAFRLGIPRQLVHYHVKHLQSEGLIRVKD 40
                                      789********************************9875 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.5
                                       HHHHHHHHH CS
                              TrmB  40 YevLrsLed 48 
                                        +vLr+L++
  gi|557693644|ref|YP_008796698.1| 196 HSVLRRLVN 204
                                       579999997 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     4e-05     0.051      13      46 ..       4      38 ..       1      47 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4e-05
                            HTH_11 13 rgpisgeeLAeeLnvSrrtvrrdIkaLeelg.vpI 46
                                       gp+++++LA +L++ r+ v+ ++k L++ g +++
  gi|557693644|ref|YP_008796698.1|  4 AGPLTISQLAFRLGIPRQLVHYHVKHLQSEGlIRV 38
                                      578***************************97443 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.1e-05       0.1      24      59 ..       5      40 ..       2      61 .. 0.88
   2 ?   -2.5   0.0       5.2   6.6e+03      41      56 ..     162     177 ..     159     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.1e-05
                                      C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      +p++++++a r +i+++ +   +++L+ +gl++++ 
  gi|557693644|ref|YP_008796698.1|  5 GPLTISQLAFRLGIPRQLVHYHVKHLQSEGLIRVKD 40
                                      579*****************************9875 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.2
                                       HHHHHHHHHHHTTSEE CS
                              Rrf2  41 ylekilakLrkaglvk 56 
                                       +++  la+++++gl++
  gi|557693644|ref|YP_008796698.1| 162 FASANLAMMNENGLIH 177
                                       6667789999999996 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 ?   12.8   0.0   6.6e-05     0.085      21      54 ..       6      39 ..       3      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.6e-05
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrg 54
                                      plt  +lA +lG+ r+ v    ++L+ egli+ +
  gi|557693644|ref|YP_008796698.1|  6 PLTISQLAFRLGIPRQLVHYHVKHLQSEGLIRVK 39
                                      8999***************************943 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 ?   11.6   0.0   0.00023      0.29      17      50 ..       5      37 ..       2      50 .. 0.87
   2 ?   -2.2   0.0       4.8   6.1e+03      35      45 ..     195     205 ..     192     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00023
                            HTH_27 17 rrkkladlcgrlnvedshisyslkkLtekGLver 50
                                      ++ ++++l++rl +  + ++y +k+L   GL+ r
  gi|557693644|ref|YP_008796698.1|  5 GPLTISQLAFRLGIPRQLVHYHVKHLQSEGLI-R 37
                                      6789***************************9.3 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.8
                            HTH_27  35 isyslkkLtek 45 
                                       i+++l++L+++
  gi|557693644|ref|YP_008796698.1| 195 IHSVLRRLVNA 205
                                       67999**9986 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 ?   10.8   0.0   0.00022      0.28       3      36 ..       5      38 ..       3      47 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                          HTH_CodY  3 GrLtaskiaDriGitrsvivnaLrkLesaGiies 36
                                      G Lt s++a r+Gi r  +   ++ L s G+i  
  gi|557693644|ref|YP_008796698.1|  5 GPLTISQLAFRLGIPRQLVHYHVKHLQSEGLIRV 38
                                      889****************************975 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 ?    8.5   0.0    0.0012       1.5      76     113 ..      11      49 ..       9      58 .. 0.86
   2 ?   -0.1   0.0      0.49   6.2e+02      87     114 ..     198     225 ..     188     233 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0012
                              RP-C  76 qLsralglsestlrrhlaaLveaGliirrDs.pngkRya 113
                                       qL+ +lg++++ + +h+++L   Gli  +D   +g+R  
  gi|557693644|ref|YP_008796698.1|  11 QLAFRLGIPRQLVHYHVKHLQSEGLIRVKDVvKTGRRVS 49 
                                       8999**************************625666655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.49
                              RP-C  87 tlrrhlaaLveaGliirrDspngkRyar 114
                                        lrr++ a    ++++++  pngk y +
  gi|557693644|ref|YP_008796698.1| 198 VLRRLVNAYLGGRFVVHKFPPNGKTYSY 225
                                       44444444445577999999***99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1775.07
//
Query:       gi|557693645|ref|YP_008796699.1|  [L=208]
Description: pyrroloquinoline-quinone synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-33  116.5   0.0    1.6e-33  116.3   0.0    1.0  1  TENA_THI-4       TENA/THI-4/PQQC family
  ------ inclusion threshold ------
       0.13   12.6   0.0        0.5   10.7   0.0    2.0  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like 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 !  116.3   0.0   1.8e-37   1.6e-33      20     209 ..       4     193 ..       1     194 [. 0.96

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 1.8e-37
                                       HHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCH.....HHHHHHHHHHTT-HHH CS
                        TENA_THI-4  20 lakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgee.....ielhlrlaealGlsre 91 
                                        ++G+l+ +q+++++i++y+y+++++ +++iils+ + +  r+ + +r+++ +g       +e + ++aea G+   
  gi|557693645|ref|YP_008796699.1|   4 FYNGKLTPQQVRGWIINRYYYQRQIPVKDSIILSNITEPVSRKMWLQRMMKREGLGayrgdVEGWAKFAEAAGIAST 80 
                                       689***********************************************98877777999**************** PP

                                       HHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHHS-TSCHHHHHHHHHCSHHHHHHHH CS
                        TENA_THI-4  92 elsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklralegpeyyewvkeyaseefraave 168
                                        l+k   +p+++ +v+++++++r+ s+ e +aa+l++lf+ +e  +r++ + +      +y w+++++ e+f ++++
  gi|557693645|ref|YP_008796699.1|  81 TLEKMDILPGVRMAVDAYINFVRTVSWFEGAAASLSELFALDELPKRITALRN------HYNWIDQRGVEFFLERLS 151
                                       *************************************************7766......****************** PP

                                       HHHHHHHHHHHTSHHHH.HHHHHHHHHHHHHHHHHHHHHHHT CS
                        TENA_THI-4 169 eakrllerllakvsdeq.leelqeiflkalefetsfltmald 209
                                        +k++++ +l+ v+++   +e+ +  l+a  f +++ +++ld
  gi|557693645|ref|YP_008796699.1| 152 YLKEDVDLVLELVAPHIrGREMLKKCLQAAAFNCDVHWSMLD 193
                                       ****************999*********************98 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 ?   10.7   0.0   5.6e-05       0.5       6      49 ..      45      87 ..      44     120 .. 0.86
   2 ?   -1.6   0.0      0.38   3.4e+03      68      80 ..     126     138 ..     123     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.6e-05
                                      HHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHH CS
                   Phage_int_SAM_1  6 eyLikerglspnTlraYrrdLrrflkflaergkesleqlttedv 49
                                      +  +++r + +  l aYr d++ + kf++   + + ++l+ +d+
  gi|557693645|ref|YP_008796699.1| 45 RKMWLQRMMKREGLGAYRGDVEGWAKFAEA-AGIASTTLEKMDI 87
                                      567999************************.8888889999888 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHHHH CS
                   Phage_int_SAM_1  68 rrlsalrsFfqfl 80 
                                       +r+ alr+ + + 
  gi|557693645|ref|YP_008796699.1| 126 KRITALRNHYNWI 138
                                       5899***999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1490.76
//
Query:       gi|557693646|ref|YP_008796700.1|  [L=289]
Description: hypothetical protein CSUB_C0209 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
        1.7    8.1   5.9       0.12   11.8   0.3    2.1  2  DUF1129   Protein of unknown function (DUF1129)
        1.7    8.5   5.9         32    4.5   0.2    3.6  3  DUF2631   Protein of unknown function (DUF2631)
        1.8    7.9   9.7          4    6.7   9.7    2.0  1  YdjM      LexA-binding, inner membrane-associated putative hy


Domain annotation for each model (and alignments):
>> DUF1129  Protein of unknown function (DUF1129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.4      0.71   4.2e+03     161     187 ..      10      36 ..       5      64 .. 0.57
   2 ?   11.8   0.3   2.1e-05      0.12     113     176 ..     103     167 ..      76     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.71
                           DUF1129 161 lvlftlvallpaviNpvLpplvliiig 187
                                       +v ++lv+ll  ++   L  + l+  g
  gi|557693646|ref|YP_008796700.1|  10 FVGVFLVSLLVDNMAMDLRMYLLTRGG 36 
                                       555556666666666655555544433 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.1e-05
                           DUF1129 113 litl.llvalvgGlamvlvyrlltrekkkkkrpplwkrllilllllvvwlvlftlvallpaviNp 176
                                       + ++ +++ l +G++++ +   ++ ++++k r++ w   +++ l++++w++++  v  l +++  
  gi|557693646|ref|YP_008796700.1| 103 IFSIvISTQLSMGAFLLGYRLPMQLRHSTKTRNEDWSLETYAGLSVLFWFAVMPGVDALGNNVYS 167
                                       444415677999***99999999999***************************999887766544 PP

>> DUF2631  Protein of unknown function (DUF2631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2     0.027   1.6e+02      32      51 ..       3      22 ..       1      28 [. 0.87
   2 ?    4.5   0.2    0.0053        32      38      63 ..      55      80 ..      49      83 .. 0.83
   3 ?    2.4   0.1     0.024   1.4e+02      24      48 ..     188     212 ..     187     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.027
                           DUF2631 32 ttriaGlisvlallamliGn 51
                                       ++ a+l++ ++l+ +l+ n
  gi|557693646|ref|YP_008796700.1|  3 FAKAAALFVGVFLVSLLVDN 22
                                      56889************998 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0053
                           DUF2631 38 lisvlallamliGnhqGhvedifLig 63
                                      l +++++ ++l G + G+ e++fL++
  gi|557693646|ref|YP_008796700.1| 55 LTIIFLVYGLLQGSQLGRGEEVFLVF 80
                                      5567778899**************97 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.024
                           DUF2631  24 GWsgespkttriaGlisvlallaml 48 
                                       GW +  ++ + ++G+++v ++la +
  gi|557693646|ref|YP_008796700.1| 188 GWTNYVHRFALLTGFCVVALVLASV 212
                                       9***************999999866 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 ?    6.7   9.7   0.00068         4      79     154 ..     176     255 ..       4     268 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00068
                              YdjM  79 lalvlllllrlfgrsa........lrlglllllgvlsHlllDlltkyGvpllwPfskkkvrlsllfiiidplltlls 147
                                       l+l+l+ ++++ g  +        l +g+++++ vl  +++D+l+++G+ l +P+ ++ ++l ++    ++ +++l+
  gi|557693646|ref|YP_008796700.1| 176 LSLLLITFMFFKG--WtnyvhrfaLLTGFCVVALVLASVFADVLWRAGTLLVLPLPENIYYLVAQAF--QGFFLALA 248
                                       2333333333222..2235555544555567777999******************764444444333..33334444 PP

                              YdjM 148 rrglval 154
                                       ++++++l
  gi|557693646|ref|YP_008796700.1| 249 ASSGIWL 255
                                       5555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); 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:                         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 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2180.47
//
Query:       gi|557693647|ref|YP_008796701.1|  [L=159]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-05   22.7   0.0     0.0084   16.2   0.0    2.2  1  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
      0.067   13.1   0.0       0.11   12.4   0.0    1.4  2  HIRAN         HIRAN domain


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.4e-07    0.0084       4      92 ..      14     137 ..       6     150 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.4e-07
                      Cupredoxin_1   4 alavllllsskaaaaaektveitvkdggfePs....kievkagekvklkiknkdkt..................... 55 
                                       ++av+ +++  ++  + ++ ++tv + g+  +    +i  kage+v++ ++n+++                      
  gi|557693647|ref|YP_008796701.1|  14 VAAVAGFFTMLSQRPEVRSLTVTVYEFGYRVDggepTIRMKAGEEVRILFENRGTHdhefllvrdkdeaigvvekkl 90 
                                       3445556666777888888999999888888655558*******************444444444444444444444 PP

                      Cupredoxin_1  56 ...peefesed.............lgeekvlapgktttitiaplkpGeYeftc 92 
                                          +      +             +g++ + +pg t+++ ++  +pG+Y f c
  gi|557693647|ref|YP_008796701.1|  91 eagA------SdaeldrlkaemalMGVRFESEPGGTSVFRLRLTEPGTYYFLC 137
                                       4331......0333333445555566666667777777777777777777766 PP

>> HIRAN  HIRAN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05      0.11       4      57 ..      33      89 ..      30     107 .. 0.83
   2 ?   -2.9   0.0      0.73   6.6e+03      17      32 ..     125     140 ..     102     148 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                      EEEEEECGGGC.CT.....---TTEEEEEEE-TT-SS-TT-EEEEETTS-EEEEE-HH CS
                             HIRAN  4 fevsvvglsyy.sg...tgylkpgtevilerepnnpadanavrvlnergfeiGrlpre 57
                                      + v+v  + y+ +g   t  +k g+ev++ +e+   +d++   v++++++ iG + ++
  gi|557693647|ref|YP_008796701.1| 33 LTVTVYEFGYRvDGgepTIRMKAGEEVRILFENRGTHDHEFLLVRDKDEA-IGVVEKK 89
                                      5667777777754467789**************************87776.9988775 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.73
                                       ..---TTEEEEEEE-T CS
                             HIRAN  17 tgylkpgtevilerep 32 
                                        +  +pgt  +l+ e+
  gi|557693647|ref|YP_008796701.1| 125 LRLTEPGTYYFLCLET 140
                                       3555666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1156.48
//
Query:       gi|557693648|ref|YP_008796702.1|  [L=355]
Description: sugar ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  126.0   0.0    2.7e-36  125.1   0.0    1.5  1  ABC_tran  ABC transporter
      1e-11   45.2   0.7    7.4e-06   26.0   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.4e-06   28.3   0.4    6.8e-06   26.2   0.4    2.1  2  TOBE_2    TOBE domain
    0.00042   20.3   0.0    0.00068   19.6   0.0    1.3  1  Rad17     Rad17 P-loop domain
    0.00043   20.0   0.0    0.00092   18.9   0.0    1.5  1  AAA_29    P-loop containing region of AAA domain
    0.00053   19.5   0.1     0.0083   15.6   0.1    2.1  1  SMC_N     RecF/RecN/SMC N terminal domain
     0.0017   18.9   3.1     0.0059   17.1   3.1    1.9  1  AAA_23    AAA domain
     0.0025   18.2   0.0     0.0042   17.5   0.0    1.5  1  AAA_16    AAA ATPase domain
     0.0035   17.3   0.0     0.0064   16.4   0.0    1.5  1  ATPase_2  ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.015   15.6   0.2       0.17   12.2   0.2    2.4  2  AAA_19    AAA domain
      0.019   15.4   0.0      0.056   13.9   0.0    1.9  1  AAA       ATPase family associated with various cellular acti
      0.019   14.7   0.4       0.17   11.6   0.2    2.0  2  AAA_15    AAA ATPase domain
      0.037   14.3   0.1      0.082   13.2   0.1    1.8  1  AAA_22    AAA domain
      0.071   12.8   0.0       0.16   11.6   0.0    1.5  1  AAA_30    AAA domain
        0.1   11.7   0.0       0.15   11.2   0.0    1.2  1  G-alpha   G-protein alpha subunit
       0.11   13.1   1.0       0.51   10.9   0.1    2.3  2  AAA_18    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 !  125.1   0.0   2.4e-39   2.7e-36       1     136 [.      19     161 ..      19     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 2.4e-39
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       lkn++l++++ge   i+G++G+GK+t+l+++agl+kp++G++ +++ ++++  ++  ++e+++++q   l p+ltv 
  gi|557693648|ref|YP_008796702.1|  19 LKNITLEIRKGEFFTILGPSGSGKTTILRIIAGLEKPDQGKVYFNNINVTD--TPAHDREVSMIFQSLALYPHLTVF 93 
                                       79*******************************************999999..999********************* PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             + ++ + +++s+l+++++ ++++    ssLSgG+kqrvalaral+ +pk++l+DEp 
  gi|557693648|ref|YP_008796702.1|  94 ENiafplrvrkrgeeDVKKTVREIASTLRIEDILNRNI----SSLSGGEKQRVALARALIYQPKIFLMDEPL 161
                                       *********99986555555*****************9....*****************************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 !   18.0   0.1   1.8e-06     0.002       2      33 ..      32      66 ..      31     104 .. 0.70
   2 !   26.0   0.0   6.6e-09   7.4e-06     220     299 ..     117     194 ..      87     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.8e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl...drdveglt 33
                                        + Gp gsGK+++L+++ +l        ++++ +
  gi|557693648|ref|YP_008796702.1| 32 FTILGPSGSGKTTILRIIAGLEKPdqgKVYFNNIN 66
                                      6799**************99954455544444444 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 6.6e-09
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvilt 295
                                          +l  +d  ++++++lS G k+  al+ al++++   +++l DEp +gL+P++  +l + ++  +r +g+  + +
  gi|557693648|ref|YP_008796702.1| 117 IASTLRIEDILNRNISSLSGGEKQRVALARALIYQP---KIFLMDEPLTGLEPAFRQELRREIRTIQRsTGITTVYV 190
                                       5566677888999*********************99...9***********************66666699****** PP

                            AAA_21 296 THSp 299
                                       TH+ 
  gi|557693648|ref|YP_008796702.1| 191 THDQ 194
                                       **96 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       2.4   2.7e+03       5      24 ..     225     247 ..     224     250 .. 0.82
   2 !   26.2   0.4     6e-09   6.8e-06       2      76 .]     280     348 ..     279     348 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 2.4
                            TOBE_2   5 PEklrla...aagganglsGtVe 24 
                                       PE+l +a   ++++ n ++GtVe
  gi|557693648|ref|YP_008796702.1| 225 PENLFVAkfvGDTPLNMFTGTVE 247
                                       999999988877777999***98 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 6e-09
                            TOBE_2   2 aiRPEklrlaaaggan.glsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                       a R E+ r+   + ++ +lsG+V+ +e lG+ ++y+v++ g ++ vv++ + +    ++   +++l++d d+++++
  gi|557693648|ref|YP_008796702.1| 280 AARAEAFRV---DENHaALSGVVVGREVLGDRIVYTVDVKGREI-VVKTGADT---IHNKSAQIRLAVDVDKLMLF 348
                                       679******...55444************************988.66666666...77888888888888888876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.1e-07   0.00068      34     112 ..      18      96 ..      10     138 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.1e-07
                             Rad17  34 wlkadvLesrkkriLLisGPsGCgkstvvkvLskelgi.klrewlnpvslkepdnqksdfkgltekesrflsqiesf 109
                                        lk  +Le rk +   i GPsG gk+t++++++    + + + + n +++ +++ +  ++  +++    + + + +f
  gi|557693648|ref|YP_008796702.1|  18 VLKNITLEIRKGEFFTILGPSGSGKTTILRIIAGLEKPdQGKVYFNNINVTDTPAHDREVSMIFQSLA-LYPHLTVF 93 
                                       5788899***999*******************975554167789999999999999988877766665.77888888 PP

                             Rad17 110 kel 112
                                       +++
  gi|557693648|ref|YP_008796702.1|  94 ENI 96 
                                       765 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 !   18.9   0.0   8.3e-07   0.00092      16      56 ..      23      64 ..      18      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 8.3e-07
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfNk 56
                                      t+ei+  +++ + GpsGsGK+T+l  i+ l  p++ kv fN+
  gi|557693648|ref|YP_008796702.1| 23 TLEIRKGEFFTILGPSGSGKTTILRIIAGLEKPDQgKVYFNN 64
                                      6778755599**************888888888888888886 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 !   15.6   0.1   7.4e-06    0.0083      24     202 ..      29     195 ..      11     212 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.4e-06
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevsi 99 
                                        +f  i+Gp GSGK+ +l  i    G ++    + + + + i+   +   ++  ev+++f+        +  e++  
  gi|557693648|ref|YP_008796702.1|  29 GEFFTILGPSGSGKTTILRII---AGLEKP--DQGKVYFNNIN--VTDTPAHDREVSMIFQSLALYpHLTVFENIAF 98 
                                       35889************9999...554333..22333333333..4678888999*****99887744445566777 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDe 173
                                         rv + ge ++     + t +e+++ l+ ++i   ++++LSgGek+ vala  +    ++p+ ++l+De    L  
  gi|557693648|ref|YP_008796702.1|  99 PLRVRKRGEEDV-----KKTVREIASTLRIEDIlnrNISSLSGGEKQRVALARAL---IYQPK-IFLMDEPLTGLEP 166
                                       777777777444.....44445555555555552224678*******99998653...35555.7899999888888 PP

                                       HHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 174 knvkkvaellkeksknaQfivislreeml 202
                                       + ++++ + +++ + ++ +  + ++++++
  gi|557693648|ref|YP_008796702.1| 167 AFRQELRREIRTIQRSTGITTVYVTHDQV 195
                                       88888888888666555554444444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   3.1   5.2e-06    0.0059      10      40 ..      12      50 ..       3     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.2e-06
                            AAA_23 10 f.......rdqeidF.skgltlItGpNGaGKTTildAik 40
                                              ++ +++  +  ++ I Gp G+GKTTil+ i 
  gi|557693648|ref|YP_008796702.1| 12 TfggkpvlKNITLEIrKGEFFTILGPSGSGKTTILRIIA 50
                                      335544446666677444799**************9885 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   3.8e-06    0.0042      25     107 ..      30     130 ..      19     221 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.8e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekd...ggiflrgkcdql.esaipysalaqalareellrqlldeaesaeleaw 97 
                                       e   + G+sG+GK++++r ++  lek    +++f + + ++    +++ s++ q l    l+  l   ++ a + + 
  gi|557693648|ref|YP_008796702.1|  30 EFFTILGPSGSGKTTILRIIA-GLEKPdqgKVYFNNINVTDTpAHDREVSMIFQSL---ALYPHLTVFENIAFPLRV 102
                                       67889***************9.5666668559996666666643445556666666...344444333444455555 PP

                            AAA_16  98 rekleeala..................a 107
                                       r++ ee ++                   
  gi|557693648|ref|YP_008796702.1| 103 RKRGEEDVKktvreiastlriedilnrN 130
                                       5555555554333333333333333441 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 !   16.4   0.0   5.7e-06    0.0064      18      68 ..      27      76 ..      19     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.7e-06
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68
                                       + e+  i Gp gsGKt++l+ ii  le+ d+ ++y+++++  ++   d+ 
  gi|557693648|ref|YP_008796702.1| 27 RKGEFFTILGPSGSGKTTILR-IIAGLEKPDQGKVYFNNINVTDTPAHDRE 76
                                      5567889***********987.66777788999*****9998777766665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00015      0.17       9     116 ..      28     223 ..      20     242 .. 0.52
   2 ?   -2.5   0.0       5.3   5.9e+03      65      76 ..     322     333 ..     287     349 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae................. 68 
                                       k + + ++++ G+GKT++l+ i  l +  +g    + + v+ t    +e++   ++l +                  
  gi|557693648|ref|YP_008796702.1|  28 KGEFFTILGPSGSGKTTILRIIAGLEKPDQGKVYFNNINVTDTPAHDREVSMIFQSLALYphltvfeniafplrvrk 104
                                       567889***********998776655544444445555555555444444444333333233333333333333333 PP

                            AAA_19  69 ......atTiHrlal.............................................................. 77 
                                              +T+ ++a                                                               
  gi|557693648|ref|YP_008796702.1| 105 rgeedvKKTVREIAStlriedilnrnisslsggekqrvalaraliyqpkiflmdepltglepafrqelrreirtiqr 181
                                       33333322333222255555555555555555666666666666666666666666666555555555555555555 PP

                            AAA_19  78 ........ldfddlltealelleeaeeekklqeeellivDEfqdvde 116
                                               ++ d+   ea++l   a++   l+e+ l  vDE q v+e
  gi|557693648|ref|YP_008796702.1| 182 stgittvyVTHDQV--EAFSL---ADRVALLHEGVLQCVDEPQRVYE 223
                                       55555532222222..23333...34444454444556666666665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.3
                            AAA_19  65 lgaeatTiHrla 76 
                                       ++  a+TiH+ +
  gi|557693648|ref|YP_008796702.1| 322 VKTGADTIHNKS 333
                                       333488888543 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 ?   13.9   0.0     5e-05     0.056       3      52 ..      34      83 ..      32     160 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-05
                                      EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfke 52
                                      + Gp G GKT++ + +a        +v+f +i++++       +  ++++++f++
  gi|557693648|ref|YP_008796702.1| 34 ILGPSGSGKTTILRIIAGLEkpdqgKVYFNNINVTDTP-----AHDREVSMIFQS 83
                                      68***************985333335999999999888.....566666666665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00015      0.17      14      50 ..      19      56 ..      18     131 .. 0.81
   2 ?    1.1   0.0      0.22   2.5e+02     324     365 ..     152     193 ..     142     195 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      lk++++++ +  + ++ G+ +sGK++il+++  + + +
  gi|557693648|ref|YP_008796702.1| 19 LKNITLEIRKGeFFTILGPSGSGKTTILRIIAGLEKPD 56
                                      78999999998899999*************97666554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.22
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++i+l++EP + L p + ++l + ++ + +++   +++ TH 
  gi|557693648|ref|YP_008796702.1| 152 PKIFLMDEPLTGLEPAFRQELRREIRTIQRSTGITTVYVTHD 193
                                       689*************************99998899999996 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.3e-05     0.082       4      29 ..      28      53 ..      25     195 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.3e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      +  + ++ G+sG+GKTt lr ++   
  gi|557693648|ref|YP_008796702.1| 28 KGEFFTILGPSGSGKTTILRIIAGLE 53
                                      567889*************9877654 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00014      0.16      20      44 ..      31      55 ..      21      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                            AAA_30 20 vavltGpAGtGKttalkalreawea 44
                                      + ++ Gp G+GKtt+l+ ++ + + 
  gi|557693648|ref|YP_008796702.1| 31 FFTILGPSGSGKTTILRIIAGLEKP 55
                                      77899************99877655 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.15      27     148 ..      33     190 ..      18     217 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                                       EEEESTTSSHHHHHHHHHHHCS--................--HHHH.HCCHHHHHHHHHHHHHHHHHHHHHT...T. CS
                           G-alpha  27 lllGqseSGKsTilkqlkllykkg................fseeel.atwraviqlnivrsiktilealesl...es 83 
                                        +lG s+SGK+Til+ +  l+k+                 +++ e+  +++++     ++ +++i + l+     e+
  gi|557693648|ref|YP_008796702.1|  33 TILGPSGSGKTTILRIIAGLEKPDqgkvyfnninvtdtpaHDR-EVsMIFQSLALYPHLTVFENIAFPLRVRkrgEE 108
                                       689***************9998887788766655555442222.231334444433333333333333333211022 PP

                                       ......HHHC-SS-SCCCS-HCHHHH...................................HHCCHHC-HCHHHHHH CS
                           G-alpha  84 elsesfelqelkerldplkkveasliaklssateee.........................qeiefnpraevgedik 135
                                             + ++  ++++  + +e+ l++++ss +  e                          e  f  r+e++++i+
  gi|557693648|ref|YP_008796702.1| 109 ------DVKKTVREIASTLRIEDILNRNISSLSGGEkqrvalaraliyqpkiflmdepltgLEPAF--RQELRREIR 177
                                       ......234444444444555555555555555444555777776666654444444333333333..447777888 PP

                                       HHCCSHHHHHHHC CS
                           G-alpha 136 aLwndpgiqelye 148
                                       ++  + gi  +y 
  gi|557693648|ref|YP_008796702.1| 178 TIQRSTGITTVYV 190
                                       8777777777765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00045      0.51       3      21 ..      34      52 ..      33      83 .. 0.78
   2 ?   -0.2   0.1       1.2   1.4e+03     109     121 ..     101     113 ..      89     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00045
                            AAA_18  3 ltGtpGvGKttlakeLskr 21
                                      + G++G+GKtt+ + ++ +
  gi|557693648|ref|YP_008796702.1| 34 ILGPSGSGKTTILRIIAGL 52
                                      89***********999755 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
                            AAA_18 109 RlekRgyeeakik 121
                                       R++kRg+e+ k++
  gi|557693648|ref|YP_008796702.1| 101 RVRKRGEEDVKKT 113
                                       99******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2370.80
//
Query:       gi|557693649|ref|YP_008796703.1|  [L=294]
Description: multiple sugar ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   25.7  16.2      8e-06   25.7  16.2    2.2  1  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 !   25.7  16.2   4.5e-10     8e-06       2     155 ..      76     263 ..      37     288 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 4.5e-10
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf.................vilsilghlilpviil 59 
                                       +llG+laa  ++  + +++++ ++  v+l++ +++ +i++   +                 +  ++   ++  +++ 
  gi|557693649|ref|YP_008796703.1|  76 LLLGVLAAfvVRGVGGGRRVVEGFLAVPLAVSPILAGIVWSPPAvwddlntvlhhvfglgfIDVTDPLVYFPVMVLS 152
                                       78999999776677777888888888888888888666655544666788888888888633334444444447778 PP

                      BPD_transp_1  60 lllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG 136
                                        ++ + p+++l +  +l+++p+d +eaa++ Gasr qif  v lP++l++ +  +++a   ++  +   e+ ++w  
  gi|557693649|ref|YP_008796703.1| 153 EAWVWSPLFMLAVVVVLDNIPRDCMEAAELTGASRLQIFNLVYLPAILRSRVVAMLVA-LKVVDFFRSFEIPFAW-- 226
                                       8***********************************************9988876554.4666666666777766.. PP

                      BPD_transp_1 137 lgtllleailgydyseis...................n 155
                                        + ++ e++lg +++  s                   +
  gi|557693649|ref|YP_008796703.1| 227 -SFWVRESQLGAPTDTLSlmlfkllltprpdgtipipY 263
                                       .5777777777777766666666666777776665431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2061.95
//
Query:       gi|557693650|ref|YP_008796704.1|  [L=279]
Description: multiple sugar ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-16   60.1  18.1    2.3e-16   60.1  18.1    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        6.3    7.1   7.6         21    5.4   7.6    1.8  1  DUF4519       Domain of unknown function (DUF4519)


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 ?   -2.6   6.2      0.43   3.8e+03      16      55 ..       4      85 ..       1     106 [. 0.54
   2 !   60.1  18.1   2.6e-20   2.3e-16       2     179 ..      88     276 ..      87     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.43
                      BPD_transp_1 16 ldkllrpliivllslPsfvlaillvlvf..........................................vilsilghl 52
                                      l++l +++  ++++ P++v+++  + +                                           +++ ++g +
  gi|557693650|ref|YP_008796704.1|  4 LTYLTLTILALFYYYPIIVIVLEGFDADispllapgirliggvpyysggftpslvyyvdmfttqsfqrliINSLVIGVG 82
                                      5666677777777777777555554333555555555666666666666666666666775555544444333333333 PP

                      BPD_transp_1 53 ilp 55
                                       ++
  gi|557693650|ref|YP_008796704.1| 83 STA 85
                                      333 PP

  == domain 2  score: 60.1 bits;  conditional E-value: 2.6e-20
                      BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilp.viillllsaapyvrlirr 73 
                                       +l+G++aa   +++ k  +   + ++ v++s+P+f+l+i+l+l    ls+lg +   p +i+ +l+ + p+++li+r
  gi|557693650|ref|YP_008796704.1|  88 LLVGLFAAyglTFYFKQMSGKYDYVMLVMRSVPPFLLIIPLLL---TLSSLGmWDTYPgMILSYLILNSPIAYLIMR 161
                                       789999998888888888888999************9999995...677777655555599999************* PP

                      BPD_transp_1  74 aalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydy 150
                                       + l ++p+d v  a ++G+++ + ++kvv+P ++p+i+ ++++ f++ +++++l++ l++     +++    ++   
  gi|557693650|ref|YP_008796704.1| 162 SLLAEMPRDIVDSAMVMGCRPLTAVVKVVVPVLIPSILVSVVFMFVLTWNEFLLASVLTGP--YARTVSVGVWSGVG 236
                                       ***********************************************************44..44444444444444 PP

                      BPD_transp_1 151 seis...........nggvlalviavlllnlvadilqrll 179
                                        +i            ++g++al+ a ll++l+ + l+rl+
  gi|557693650|ref|YP_008796704.1| 237 EQIGtfrtvefeaqaAAGTVALIPASLLILLIRRRLVRLF 276
                                       4444666688977666777777777777777777777665 PP

>> DUF4519  Domain of unknown function (DUF4519)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   7.6    0.0023        21      30      53 ..     186     209 ..     184     211 .. 0.94

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0023
                           DUF4519  30 vttvVlPvlavlillivvfvYlkT 53 
                                       v++vV+Pvl+  il+ vvf+++ T
  gi|557693650|ref|YP_008796704.1| 186 VVKVVVPVLIPSILVSVVFMFVLT 209
                                       89*******************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1886.38
//
Query:       gi|557693651|ref|YP_008796705.1|  [L=400]
Description: kelch repeat protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-53  175.6   4.0    5.2e-11   41.9   0.1    6.2  6  Kelch_1   Kelch motif
    3.4e-35  119.2   0.0    1.3e-08   34.8   0.0    6.2  6  Kelch_6   Kelch motif
    5.4e-25   87.1   0.2    0.00019   21.6   0.0    5.8  5  Kelch_3   Galactose oxidase, central domain
    3.5e-24   83.8   0.0    0.00031   20.6   0.0    6.1  6  Kelch_2   Kelch motif
    3.1e-22   78.3   0.0    1.2e-05   25.2   0.0    5.6  5  Kelch_4   Galactose oxidase, central domain
    1.1e-11   44.4   3.6      0.028   14.4   0.0    6.2  7  Kelch_5   Kelch motif
  ------ inclusion threshold ------
       0.14   12.7   6.4       0.58   10.7   0.0    4.2  6  PQQ_3     PQQ-like domain
        3.7    6.6  11.0          6    6.0  11.0    1.2  1  Med3      Mediator complex subunit 3 fungal


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 !   24.4   0.0     7e-09   1.6e-05       4      46 .]     126     169 ..     123     169 .. 0.95
   2 !   28.7   0.0   3.3e-10   7.4e-07       2      46 .]     172     217 ..     171     217 .. 0.96
   3 !   37.8   0.0   4.4e-13     1e-09       2      46 .]     220     264 ..     219     264 .. 0.95
   4 !   33.7   0.0   8.9e-12     2e-08       2      46 .]     267     315 ..     266     315 .. 0.94
   5 !   41.9   0.1   2.3e-14   5.2e-11       1      45 [.     317     361 ..     317     362 .. 0.98
   6 !    5.1   0.1    0.0076        17       1      20 [.     364     383 ..     364     393 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 7e-09
                                       SEEEEEETTEEEEEEEBCS.SSBEEEEEEEETTTTEEEEECCCS CS
                           Kelch_1   4 gagavvvggkiYviGGsdg.gnalssvevyDpetntWrelpsMp 46 
                                        +++v+ g  ++  GG    gna+s ++ y++e ++Wrel++Mp
  gi|557693651|ref|YP_008796705.1| 126 EVAMVSDGKSLFLAGGLTAeGNASSHFFSYNVELKKWRELAPMP 169
                                       6799***************************************7 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 3.3e-10
                                       BBSEEEEEETTEEEEEEEBCS.SSBEEEEEEEETTTTEEEEECCCS CS
                           Kelch_1   2 ragagavvvggkiYviGGsdg.gnalssvevyDpetntWrelpsMp 46 
                                        +++g v++++++Y +GG+d+ +na + +++y +  + W+el+++p
  gi|557693651|ref|YP_008796705.1| 172 LHHVGLVYLNNRVYLLGGYDNrWNAQRKAYAYRVNRDVWEELSPLP 217
                                       6899****************************************97 PP

  == domain 3  score: 37.8 bits;  conditional E-value: 4.4e-13
                                       BBSEEEEEETTEEEEEEEBCSSSBEEEEEEEETTTTEEEEECCCS CS
                           Kelch_1   2 ragagavvvggkiYviGGsdggnalssvevyDpetntWrelpsMp 46 
                                       ra  +a +v + +Y++GG +g+ +l+  e+yDp++n+W ++++M+
  gi|557693651|ref|YP_008796705.1| 220 RAALTAQAVKDVLYAVGGARGNMPLNINEAYDPTSNEWKPMAPMS 264
                                       77788999************************************6 PP

  == domain 4  score: 33.7 bits;  conditional E-value: 8.9e-12
                                       BBSEEEEEETTEEEEEEEBCS....SSBEEEEEEEETTTTEEEEECCCS CS
                           Kelch_1   2 ragagavvvggkiYviGGsdg....gnalssvevyDpetntWrelpsMp 46 
                                       r + ++ +v gk+Y+iGG+       + l+ ve yD+e+n Wr   +Mp
  gi|557693651|ref|YP_008796705.1| 267 REHLTSGAVEGKMYAIGGRVVsantMTNLNVVEEYDVEKNVWRFRKPMP 315
                                       5677899*************************************99997 PP

  == domain 5  score: 41.9 bits;  conditional E-value: 2.3e-14
                                       BBBSEEEEEETTEEEEEEEBCSSSBEEEEEEEETTTTEEEEECCC CS
                           Kelch_1   1 aragagavvvggkiYviGGsdggnalssvevyDpetntWrelpsM 45 
                                       ar+g +a+vvgg iYv+GG +  +    ve+yDp+++tW ++++M
  gi|557693651|ref|YP_008796705.1| 317 ARSGLAAAVVGGLIYVCGGESQVKTFGEVEAYDPVSDTWLKVAEM 361
                                       69*****************************************99 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.0076
                                       BBBSEEEEEETTEEEEEEEB CS
                           Kelch_1   1 aragagavvvggkiYviGGs 20 
                                       +r+g g+++ g+ki+ + G+
  gi|557693651|ref|YP_008796705.1| 364 PRHGLGVAAAGDKIFTVAGG 383
                                       79***************996 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   3.5e-09   7.8e-06       6      49 ..     128     171 ..     125     172 .. 0.95
   2 !   34.8   0.0   5.8e-12   1.3e-08       5      50 .]     175     220 ..     173     220 .. 0.95
   3 !    9.5   0.0   0.00056       1.3      14      50 .]     232     267 ..     227     267 .. 0.91
   4 !   10.3   0.0    0.0003      0.66      10      50 .]     275     318 ..     271     318 .. 0.87
   5 !   30.9   0.0     1e-10   2.3e-07       2      50 .]     318     365 ..     317     365 .. 0.95
   6 ?    1.5   0.0      0.18   4.1e+02       1      19 [.     364     382 ..     364     392 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 3.5e-09
                           Kelch_6   6 slvsvggkiYifGGytdsspylnkvwvydpetksWeqlpplpvp 49 
                                       ++vs g +++++GG+t+ +++++ ++ y++e k+W++l+p+p p
  gi|557693651|ref|YP_008796705.1| 128 AMVSDGKSLFLAGGLTAEGNASSHFFSYNVELKKWRELAPMPAP 171
                                       69****************************************87 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 5.8e-12
                           Kelch_6   5 hslvsvggkiYifGGytdsspylnkvwvydpetksWeqlpplpvpr 50 
                                       + lv  ++++Y++GGy++ +++++k + y++  ++We+l+plpv+r
  gi|557693651|ref|YP_008796705.1| 175 VGLVYLNNRVYLLGGYDNRWNAQRKAYAYRVNRDVWEELSPLPVAR 220
                                       678999*************************************998 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00056
                           Kelch_6  14 iYifGGytdsspylnkvwvydpetksWeqlpplpvpr 50 
                                       +Y++GG+ + +++ln  + ydp ++ W++ +p+ ++r
  gi|557693651|ref|YP_008796705.1| 232 LYAVGGARG-NMPLNINEAYDPTSNEWKPMAPMSIAR 267
                                       799999988.8*********************98876 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.0003
                           Kelch_6  10 vggkiYifGGytds...spylnkvwvydpetksWeqlpplpvpr 50 
                                       v gk Y++GG++ s    + ln v+ yd+e ++W++  p+p++r
  gi|557693651|ref|YP_008796705.1| 275 VEGKMYAIGGRVVSantMTNLNVVEEYDVEKNVWRFRKPMPTAR 318
                                       6789999****9999985557999***********999999887 PP

  == domain 5  score: 30.9 bits;  conditional E-value: 1e-10
                           Kelch_6   2 raghslvsvggkiYifGGytdsspylnkvwvydpetksWeqlpplpvpr 50 
                                       r g ++++vgg iY++GG ++  +++  v+ ydp +++W +++ + +pr
  gi|557693651|ref|YP_008796705.1| 318 RSGLAAAVVGGLIYVCGGESQ-VKTFGEVEAYDPVSDTWLKVAEMVTPR 365
                                       788999***************.8*********************99988 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.18
                           Kelch_6   1 praghslvsvggkiYifGG 19 
                                       pr+g  ++++g+ki+ + G
  gi|557693651|ref|YP_008796705.1| 364 PRHGLGVAAAGDKIFTVAG 382
                                       7999**********98866 PP

>> Kelch_3  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.4e-07   0.00076       2      48 ..     134     179 ..     133     180 .. 0.91
   2 !   15.7   0.1   6.2e-06     0.014       1      42 [.     181     221 ..     181     225 .. 0.96
   3 ?    5.3   0.0     0.011        24       2      37 ..     230     263 ..     229     273 .. 0.81
   4 !   17.6   0.0   1.6e-06    0.0035       2      48 ..     277     325 ..     276     326 .. 0.91
   5 !   21.6   0.0   8.4e-08   0.00019       1      48 [.     327     372 ..     327     373 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.4e-07
                           Kelch_3   2 drlyifGGlgddgqdrlndvyvydldtntWaeiaslppaRaghaata 48 
                                        +l++ GGl++  +++++ +++y+++  +W+e+a++p + +++ +++
  gi|557693651|ref|YP_008796705.1| 134 KSLFLAGGLTA-EGNASSHFFSYNVELKKWRELAPMPAPLHHVGLVY 179
                                       679*******5.499**************************998876 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 6.2e-06
                           Kelch_3   1 gdrlyifGGlgddgqdrlndvyvydldtntWaeiaslppaRa 42 
                                       ++r+y+ GG++ ++ ++    y+y ++++ W+e+++lp aRa
  gi|557693651|ref|YP_008796705.1| 181 NNRVYLLGGYD-NRWNAQRKAYAYRVNRDVWEELSPLPVARA 221
                                       79*********.99*************************997 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.011
                           Kelch_3   2 drlyifGGlgddgqdrlndvyvydldtntWaeiasl 37 
                                       d ly +GG++  g+ +ln   +yd+ +n+W+  a++
  gi|557693651|ref|YP_008796705.1| 230 DVLYAVGGAR--GNMPLNINEAYDPTSNEWKPMAPM 263
                                       6788899999..8888888889*********98877 PP

  == domain 4  score: 17.6 bits;  conditional E-value: 1.6e-06
                           Kelch_3   2 drlyifGGlgd..dgqdrlndvyvydldtntWaeiaslppaRaghaata 48 
                                       +++y +GG+    ++ ++ln v +yd+++n W+   ++p+aR+g aa++
  gi|557693651|ref|YP_008796705.1| 277 GKMYAIGGRVVsaNTMTNLNVVEEYDVEKNVWRFRKPMPTARSGLAAAV 325
                                       68*********88889999**************779*******999886 PP

  == domain 5  score: 21.6 bits;  conditional E-value: 8.4e-08
                           Kelch_3   1 gdrlyifGGlgddgqdrlndvyvydldtntWaeiaslppaRaghaata 48 
                                       g+ +y+ GG+     +  ++v +yd++++tW ++a++ ++R+g  ++a
  gi|557693651|ref|YP_008796705.1| 327 GGLIYVCGGES--QVKTFGEVEAYDPVSDTWLKVAEMVTPRHGLGVAA 372
                                       5779*******..77888************************987776 PP

>> Kelch_2  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.016        35      11      49 .]     133     169 ..     123     169 .. 0.82
   2 !   15.2   0.0   6.8e-06     0.015       2      49 .]     172     217 ..     171     217 .. 0.93
   3 !   17.6   0.0   1.2e-06    0.0028       2      48 ..     220     263 ..     219     264 .. 0.91
   4 !   20.6   0.0   1.4e-07   0.00031       5      49 .]     270     315 ..     266     315 .. 0.92
   5 !   15.3   0.0   6.6e-06     0.015       1      45 [.     317     358 ..     317     361 .. 0.91
   6 ?    2.4   0.0     0.074   1.7e+02       1      33 [.     364     394 ..     364     395 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.016
                           Kelch_2  11 ggkiyvvGGahtdnpnlsssdvhvldlekhvWeevtplg 49 
                                       g  +++ GG  + ++ +s++    ++ e ++W+e++p++
  gi|557693651|ref|YP_008796705.1| 133 GKSLFLAGGLTAEGNASSHFFS--YNVELKKWRELAPMP 169
                                       6679999999888888888888..99999*****99997 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 6.8e-06
                           Kelch_2   2 rgghsssvpggkiyvvGGahtdnpnlsssdvhvldlekhvWeevtplg 49 
                                       ++++  +++++++y+ GG+  dn   ++++ + ++ +  vWee++pl+
  gi|557693651|ref|YP_008796705.1| 172 LHHVGLVYLNNRVYLLGGY--DNRWNAQRKAYAYRVNRDVWEELSPLP 217
                                       5677789************..9999********************987 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 1.2e-06
                           Kelch_2   2 rgghsssvpggkiyvvGGahtdnpnlsssdvhvldlekhvWeevtpl 48 
                                       r+  ++  + + +y vGGa ++n++l ++    +d+ +++W++++p+
  gi|557693651|ref|YP_008796705.1| 220 RAALTAQAVKDVLYAVGGA-RGNMPLNINEA--YDPTSNEWKPMAPM 263
                                       66677888999********.***********..***********998 PP

  == domain 4  score: 20.6 bits;  conditional E-value: 1.4e-07
                           Kelch_2   5 hsssvpggkiyvvGGa.htdnpnlsssdvhvldlekhvWeevtplg 49 
                                        +s  ++gk+y +GG+  + n+    + v  +d ek+vW+  +p++
  gi|557693651|ref|YP_008796705.1| 270 LTSGAVEGKMYAIGGRvVSANTMTNLNVVEEYDVEKNVWRFRKPMP 315
                                       567799**********************************999997 PP

  == domain 5  score: 15.3 bits;  conditional E-value: 6.6e-06
                           Kelch_2   1 rrgghsssvpggkiyvvGGahtdnpnlsssdvhvldlekhvWeev 45 
                                       +r+g +++v+gg iyv+GG      +  +  v  +d+ + +W +v
  gi|557693651|ref|YP_008796705.1| 317 ARSGLAAAVVGGLIYVCGGE---SQVKTFGEVEAYDPVSDTWLKV 358
                                       699*****************...9999999999999999999655 PP

  == domain 6  score: 2.4 bits;  conditional E-value: 0.074
                           Kelch_2   1 rrgghsssvpggkiyvvGGahtdnpnlsssdvh 33 
                                       +r+g  ++  g+ki+ v G   + p+l+ sdv+
  gi|557693651|ref|YP_008796705.1| 364 PRHGLGVAAAGDKIFTVAGG--PRPGLYVSDVN 394
                                       6788888999*******999..99999999986 PP

>> Kelch_4  Galactose oxidase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   5.3e-09   1.2e-05       6      48 ..     128     169 ..     125     170 .. 0.92
   2 !    5.7   0.1    0.0065        15       6      48 ..     176     217 ..     173     218 .. 0.79
   3 !   19.8   0.0   2.6e-07   0.00059       1      47 [.     219     263 ..     219     264 .. 0.93
   4 !    8.0   0.0    0.0012       2.7       6      49 .]     271     316 ..     266     316 .. 0.85
   5 !   12.3   0.0   5.7e-05      0.13       1      45 [.     317     359 ..     317     365 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.3e-09
                           Kelch_4   6 satsipdgtiylfGGrgedgtllndlylldlstntWrrlgslP 48 
                                       +++s++  +++l GG +++g ++++ + ++++ ++Wr+l+++P
  gi|557693651|ref|YP_008796705.1| 128 AMVSDG-KSLFLAGGLTAEGNASSHFFSYNVELKKWRELAPMP 169
                                       678885.8**********************************9 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0065
                           Kelch_4   6 satsipdgtiylfGGrgedgtllndlylldlstntWrrlgslP 48 
                                       +++++ ++++yl GG+ +   +   +y++ +    W++l++lP
  gi|557693651|ref|YP_008796705.1| 176 GLVYL-NNRVYLLGGYDNRWNAQRKAYAYRVNRDVWEELSPLP 217
                                       57888.79********986677777888888888888888877 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 2.6e-07
                           Kelch_4   1 pRaghsatsipdgtiylfGGrgedgtllndlylldlstntWrrlgsl 47 
                                       +Ra  +a ++ ++ +y +GG+ +++ +ln   ++d ++n+W++++++
  gi|557693651|ref|YP_008796705.1| 219 ARAALTAQAV-KDVLYAVGGARGNM-PLNINEAYDPTSNEWKPMAPM 263
                                       68888999**.79***********7.******************987 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0012
                           Kelch_4   6 satsipdgtiylfGGrgedg...tllndlylldlstntWrrlgslPs 49 
                                       ++ ++  g+ y +GGr   +   t ln +  +d++ n Wr  +++P+
  gi|557693651|ref|YP_008796705.1| 271 TSGAV-EGKMYAIGGRVVSAntmTNLNVVEEYDVEKNVWRFRKPMPT 316
                                       66777.5899********9989999999999********98888885 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 5.7e-05
                           Kelch_4   1 pRaghsatsipdgtiylfGGrgedgtllndlylldlstntWrrlg 45 
                                       +R g +a +++ g iy+ GG++   ++++++ ++d  + tW +++
  gi|557693651|ref|YP_008796705.1| 317 ARSGLAAAVVG-GLIYVCGGESQV-KTFGEVEAYDPVSDTWLKVA 359
                                       67888888885.9**********9.9***************5554 PP

>> Kelch_5  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1         3   6.8e+03       9      22 ..      31      46 ..      29      50 .. 0.66
   2 !    6.3   0.0    0.0043       9.7       4      38 ..     123     156 ..     120     158 .. 0.76
   3 !   10.6   0.0    0.0002      0.45       1      24 [.     168     191 ..     168     210 .. 0.92
   4 ?    2.6   0.0     0.063   1.4e+02       1      23 [.     216     238 ..     216     250 .. 0.90
   5 !    5.2   0.0    0.0094        21      10      39 ..     272     303 ..     265     306 .. 0.71
   6 !   14.4   0.0   1.3e-05     0.028       1      38 [.     314     349 ..     314     353 .. 0.89
   7 ?   -1.2   0.0      0.99   2.2e+03       4      18 ..     364     378 ..     363     383 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3
                           Kelch_5  9 cavtvs..ekiYvyGG 22
                                      ++++++  + iY ++G
  gi|557693651|ref|YP_008796705.1| 31 SVAAAGafYLIYSFSG 46
                                      3444557777887777 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0043
                           Kelch_5   4 pRaghcavtvsekiYvyGGkvgrdgsvsddvyvLd 38 
                                       +++  ++v ++ ++++ GG ++ +g++s++++ ++
  gi|557693651|ref|YP_008796705.1| 123 ALTEVAMVSDGKSLFLAGGLTA-EGNASSHFFSYN 156
                                       56667888889**********8.777777776555 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0002
                           Kelch_5   1 iPppRaghcavtvsekiYvyGGkv 24 
                                       +P+p+++   v++++ +Y+ GG++
  gi|557693651|ref|YP_008796705.1| 168 MPAPLHHVGLVYLNNRVYLLGGYD 191
                                       7**********************8 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.063
                           Kelch_5   1 iPppRaghcavtvsekiYvyGGk 23 
                                       +P++Ra   a +v++ +Y  GG 
  gi|557693651|ref|YP_008796705.1| 216 LPVARAALTAQAVKDVLYAVGGA 238
                                       69*******************96 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.0094
                           Kelch_5  10 avtvsekiYvyGGkv.g.rdgsvsddvyvLdl 39 
                                       + +v++k+Y +GG+v + +++   + v  +d+
  gi|557693651|ref|YP_008796705.1| 272 SGAVEGKMYAIGGRVvSaNTMTNLNVVEEYDV 303
                                       55789*********943566666666666666 PP

  == domain 6  score: 14.4 bits;  conditional E-value: 1.3e-05
                           Kelch_5   1 iPppRaghcavtvsekiYvyGGkvgrdgsvsddvyvLd 38 
                                       +P++R+g +a++v++ iYv GG ++   + +++v  +d
  gi|557693651|ref|YP_008796705.1| 314 MPTARSGLAAAVVGGLIYVCGGESQ--VKTFGEVEAYD 349
                                       7***********************5..88888887776 PP

  == domain 7  score: -1.2 bits;  conditional E-value: 0.99
                           Kelch_5   4 pRaghcavtvsekiY 18 
                                       pR+g  ++++++ki+
  gi|557693651|ref|YP_008796705.1| 364 PRHGLGVAAAGDKIF 378
                                       89999999*****98 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         3   6.7e+03      18      29 ..     130     141 ..     111     149 .. 0.60
   2 ?   -2.2   0.0         3   6.8e+03      18      34 ..     178     201 ..     166     206 .. 0.59
   3 ?   -2.4   0.0       3.4   7.7e+03      22      30 ..     230     239 ..     215     242 .. 0.72
   4 ?   -1.9   0.0       2.4   5.5e+03      28      36 ..     274     282 ..     261     287 .. 0.65
   5 ?   10.7   0.0   0.00026      0.58       5      38 ..     308     350 ..     305     352 .. 0.75
   6 ?    1.9   0.3      0.16   3.5e+02      16      29 ..     369     382 ..     362     393 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3
                             PQQ_3  18 avdgglvyvgtg 29 
                                       + dg  ++ ++g
  gi|557693651|ref|YP_008796705.1| 130 VSDGKSLFLAGG 141
                                       444555887776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3
                             PQQ_3  18 avdgglvyvgtg.......dGtly 34 
                                       ++ +++vy  +g       + + y
  gi|557693651|ref|YP_008796705.1| 178 VYLNNRVYLLGGydnrwnaQRKAY 201
                                       555666666665554444444455 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.4
                             PQQ_3  22 glvyvgtg.d 30 
                                       +++y+++g  
  gi|557693651|ref|YP_008796705.1| 230 DVLYAVGGaR 239
                                       6788888744 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 2.4
                             PQQ_3  28 tgdGtlyAl 36 
                                       +  G++yA+
  gi|557693651|ref|YP_008796705.1| 274 AVEGKMYAI 282
                                       335777776 PP

  == domain 5  score: 10.7 bits;  conditional E-value: 0.00026
                             PQQ_3   5 Wsvqlpgpvn.ssp..avdgglvyvgtg......dGtlyAlDa 38 
                                       W+++ p p+  s++  av+ggl+yv +g       G + A+D+
  gi|557693651|ref|YP_008796705.1| 308 WRFRKPMPTArSGLaaAVVGGLIYVCGGesqvktFGEVEAYDP 350
                                       7775554333166688999********9888888888888886 PP

  == domain 6  score: 1.9 bits;  conditional E-value: 0.16
                             PQQ_3  16 spavdgglvyvgtg 29 
                                       ++a++g+++++++g
  gi|557693651|ref|YP_008796705.1| 369 GVAAAGDKIFTVAG 382
                                       5799******9998 PP

>> Med3  Mediator complex subunit 3 fungal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.0    0.0027         6     142     200 ..      52     113 ..      20     115 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0027
                              Med3 142 pssaastPtttatPgantktaak..slpapnatatigtpt..nsaaaaattatttssqakkPr 200
                                         + ++t ttt tP  +t+++a   sl++p++t  +  p   ++ +a  t++tt++++  +Pr
  gi|557693651|ref|YP_008796705.1|  52 RPTSGATETTTMTPYHTTQNTATdtSLTTPATTV-VQQPHhtTQVTAKETSTTTAATTGIQPR 113
                                       456789999999**88887776511345555444.4444432444444455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2821.65
//
Query:       gi|557693652|ref|YP_008796706.1|  [L=159]
Description: hypothetical protein CSUB_C0215 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
       0.48   10.5  13.4        1.1    9.4   1.3    2.9  3  DUF1206   Domain of Unknown Function (DUF1206)


Domain annotation for each model (and alignments):
>> DUF1206  Domain of Unknown Function (DUF1206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2     0.028     5e+02       7      17 ..      46      56 ..      44      58 .. 0.87
   2 ?    7.2   2.5    0.0003       5.4       5      39 ..      55      89 ..      52     101 .. 0.88
   3 ?    9.4   1.3   6.2e-05       1.1      13      59 ..     108     151 ..      97     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.028
                           DUF1206  7 Gvvylllglla 17
                                      G+vy +lg++ 
  gi|557693652|ref|YP_008796706.1| 46 GAVYMVLGYFS 56
                                      89******985 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0003
                           DUF1206  5 arGvvylllgllalqaalggggssasgsdgalatl 39
                                      ++ +vy++lg+l + aa     +sa+g d al  l
  gi|557693652|ref|YP_008796706.1| 55 FSFLVYGVLGALGWAAAYRLLDESAQGYDKALTYL 89
                                      5779*******************999999999877 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 6.2e-05
                           DUF1206  13 lgllalqaalggggssasgsdgalatlleqpfGrvllglvglgllgy 59 
                                        g+l ++++  g++    ++ ga++++ e p+G +++ +++  l+g+
  gi|557693652|ref|YP_008796706.1| 108 GGYLGARLVYEGRPV---QAVGAIMEVVEIPAGLFIMLAIASTLMGI 151
                                       468888888888888...77*********************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1217.85
//
Query:       gi|557693653|ref|YP_008796707.1|  [L=738]
Description: quinoprotein alcohol dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-26   90.9  13.2    6.8e-06   25.8   0.1    7.2  7  PQQ             PQQ enzyme repeat
    4.9e-16   59.0   3.2    0.00039   20.1   0.1    4.2  4  PQQ_2           PQQ-like domain
    7.2e-12   45.4  20.8    5.2e-05   23.6   0.6    7.8  7  PQQ_3           PQQ-like domain
  ------ inclusion threshold ------
      0.072   12.3   0.3       0.12   11.6   0.3    1.3  1  Attachment_P66  Borrelia burgdorferi attachment protein P66


Domain annotation for each model (and alignments):
>> PQQ  PQQ enzyme repeat
   #    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      21      36 ..      60      75 ..      60      77 .. 0.90
   2 !   25.8   0.1   1.5e-09   6.8e-06       1      31 [.      92     122 ..      92     124 .. 0.93
   3 ?   -3.7   0.1       3.3   1.5e+04       9      17 ..     328     336 ..     323     337 .. 0.77
   4 !   13.8   0.1   9.6e-06     0.043      11      33 ..     366     388 ..     359     392 .. 0.91
   5 !   24.0   0.0   5.4e-09   2.4e-05       5      27 ..     414     437 ..     410     438 .. 0.87
   6 !   15.4   0.0   2.9e-06     0.013       7      24 ..     550     567 ..     545     574 .. 0.90
   7 !   12.3   0.0   2.7e-05      0.12       1      23 [.     585     607 ..     585     620 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.035
                                      CEEEEEESSSCGSSES CS
                               PQQ 21 kvlWrfktggpvlslp 36
                                      +++W f+++++ +++p
  gi|557693653|ref|YP_008796707.1| 60 EIKWAFPVPPASVGDP 75
                                      68**********9998 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.5e-09
                                       TEEEEEETTSEEEEEETTTCCEEEEEESSSC CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktggp 31 
                                       gvvy  +++ ++yAlD++TGk lW+  +++p
  gi|557693653|ref|YP_008796707.1|  92 GVVYFVTNWHRVYALDLATGKTLWTQTLQPP 122
                                       799**********************998876 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.3
                                       TSEEEEEET CS
                               PQQ   9 dGylyAlDa 17 
                                       +G  yA+D 
  gi|557693653|ref|YP_008796707.1| 328 WGGAYAVDE 336
                                       88999*995 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 9.6e-06
                                       EEEEEETTTCCEEEEEESSSCGS CS
                               PQQ  11 ylyAlDadTGkvlWrfktggpvl 33 
                                        ++Al+++TG+ +W ++t  ++l
  gi|557693653|ref|YP_008796707.1| 366 SILALNIETGQPIWGVQTTTHDL 388
                                       589***************99875 PP

  == domain 5  score: 24.0 bits;  conditional E-value: 5.4e-09
                                       EE.ETTSEEEEEETTTCCEEEEEE CS
                               PQQ   5 lg.sadGylyAlDadTGkvlWrfk 27 
                                       +  +++G++yAl+a++G +lW f+
  gi|557693653|ref|YP_008796707.1| 414 IKgCKNGVVYALNAEDGSLLWAFN 437
                                       455******************996 PP

  == domain 6  score: 15.4 bits;  conditional E-value: 2.9e-06
                                       ETTSEEEEEETTTCCEEE CS
                               PQQ   7 sadGylyAlDadTGkvlW 24 
                                       + +++lyA+D++TG+v+W
  gi|557693653|ref|YP_008796707.1| 550 PTNTTLYAIDVATGRVVW 567
                                       6789************** PP

  == domain 7  score: 12.3 bits;  conditional E-value: 2.7e-05
                                       TEEEEEETTSEEEEEETTTCCEE CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvl 23 
                                       g v+ + +dG+++ +DadTG +l
  gi|557693653|ref|YP_008796707.1| 585 GLVFTTFNDGTIRVFDADTGAEL 607
                                       56888899************998 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.1e-07    0.0005      29      65 ..      84     120 ..      60     134 .. 0.59
   2 !   18.3   0.0     3e-07    0.0013       4      61 ..     102     181 ..     101     194 .. 0.82
   3 !   15.4   0.3   2.4e-06     0.011      87     147 ..     366     435 ..     332     447 .. 0.82
   4 !   20.1   0.1   8.7e-08   0.00039       3      72 ..     553     620 ..     528     636 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.1e-07
                             PQQ_2  29 vsravlsggtlfvatgggrlvaldaatGkvlWettle 65 
                                       + ++++ +g+++ +t   r++ald atGk lW++tl+
  gi|557693653|ref|YP_008796707.1|  84 IHTPLVYKGVVYFVTNWHRVYALDLATGKTLWTQTLQ 120
                                       2344445555555555555555555555555555553 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 3e-07
                             PQQ_2   4 vvsaldaatGaelWrvdlarp......................lgggvsravlsggtlfvatgggrlvaldaatGkv 58 
                                       +v+ald atG++lW+++l++p                      +  ++     ++ +lf  t +  lva+d++tG +
  gi|557693653|ref|YP_008796707.1| 102 RVYALDLATGKTLWTQTLQPPkefvdeltagkppiwepffrghFHQIHIFEIDGRPYLFLITNYYYLVAIDPFTGDI 178
                                       79***************99844555555555666777777777888888899999999999**************99 PP

                             PQQ_2  59 lWe 61 
                                       + +
  gi|557693653|ref|YP_008796707.1| 179 RLR 181
                                       876 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 2.4e-06
                             PQQ_2  87 qlialdaedGkrlWstqqrseepae....lrssaspava.......gdtvvvgessgklvaldpkdGkvlWe 147
                                       +++al++e+G+  W +q +++   +     +++  +  +       +d v+ g+ +g ++al+++dG++lW 
  gi|557693653|ref|YP_008796707.1| 366 SILALNIETGQPIWGVQTTTHDLYDwdcsWSVVYLK--DvqiggqrRDAVIKGCKNGVVYALNAEDGSLLWA 435
                                       6789***********888886555554332222222..25588999999999999****************5 PP

  == domain 4  score: 20.1 bits;  conditional E-value: 8.7e-08
                             PQQ_2   3 gvvsaldaatGaelWrv...dlarplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvgap 72 
                                        +++a+d atG+++W v   d+  p +gg+  ++  +g +f++   g++  +da tG++l +    gpv + p
  gi|557693653|ref|YP_008796707.1| 553 TTLYAIDVATGRVVWNVfipDV--PYRGGI--TT-TNGLVFTTFNDGTIRVFDADTGAELRRIMIAGPVMTQP 620
                                       4667777777777777755544..667777..66.67777777777777777777777777777777766665 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   2.5e-08   0.00011       2      40 .]      60     110 ..      60     110 .. 0.91
   2 ?   -1.1   0.1      0.69   3.1e+03       1       9 [.     111     119 ..     111     126 .. 0.84
   3 ?    1.1   0.1      0.14   6.2e+02      11      29 ..     325     346 ..     319     374 .. 0.64
   4 ?    2.9   0.0     0.036   1.6e+02      30      40 .]     419     429 ..     405     429 .. 0.83
   5 ?    2.3   0.9     0.058   2.6e+02      12      40 .]     499     562 ..     491     562 .. 0.65
   6 !   23.6   0.6   1.2e-08   5.2e-05       1      40 []     563     603 ..     563     603 .. 0.96
   7 ?   -1.7   0.0         1   4.7e+03      10      23 ..     613     629 ..     607     630 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.5e-08
                             PQQ_3   2 evlWsvqlpgpvnssp............avdgglvyvgtgdGtlyAlDaet 40 
                                       e++W++++p + ++ p            +v+ g+vy++t  +++yAlD +t
  gi|557693653|ref|YP_008796707.1|  60 EIKWAFPVPPASVGDPffsgsegvihtpLVYKGVVYFVTNWHRVYALDLAT 110
                                       689***9998777888899999999999********************998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.69
                             PQQ_3   1 GevlWsvql 9  
                                       G++lW+++l
  gi|557693653|ref|YP_008796707.1| 111 GKTLWTQTL 119
                                       9*****987 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.14
                             PQQ_3  11 gpvnssp.avdg..glvyvgtg 29 
                                       g++++++ avd+  g+ +v+t 
  gi|557693653|ref|YP_008796707.1| 325 GAGWGGAyAVDEdkGVAFVATN 346
                                       4566666666653356777776 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.036
                             PQQ_3  30 dGtlyAlDaet 40 
                                       +G +yAl+ae+
  gi|557693653|ref|YP_008796707.1| 419 NGVVYALNAED 429
                                       9********96 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.058
                             PQQ_3  12 pvnsspavdg..glvyvgtg.................................dGtlyAlDaet 40 
                                        + s pa+d   ++++v+ +                                 + tlyA+D +t
  gi|557693653|ref|YP_008796707.1| 499 GIESDPAYDPvrNRLFVAVYnspsafslanvgpgtgwpngwgvafetlptqptNTTLYAIDVAT 562
                                       5666666663336666666666666666666666666666666666666667788999999887 PP

  == domain 6  score: 23.6 bits;  conditional E-value: 1.2e-08
                             PQQ_3   1 GevlWsvqlpg.pvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       G+v+W+v +p+ p+ ++ ++ +glv+++  dGt++ +Da+t
  gi|557693653|ref|YP_008796707.1| 563 GRVVWNVFIPDvPYRGGITTTNGLVFTTFNDGTIRVFDADT 603
                                       99*****99999999************************98 PP

  == domain 7  score: -1.7 bits;  conditional E-value: 1
                             PQQ_3  10 pgpvnssp...avdggl 23 
                                        gpv ++p   ++++g+
  gi|557693653|ref|YP_008796707.1| 613 AGPVMTQPaiaTTADGK 629
                                       68999999554445666 PP

>> Attachment_P66  Borrelia burgdorferi attachment protein P66
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   2.8e-05      0.12     132     170 ..     651     688 ..     647     718 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.8e-05
                    Attachment_P66 132 gwiasiglydllreksksndiisaltentstkttttnle 170
                                       g+++s+gl d++ e++++++++ +l+ +  t+t+t++++
  gi|557693653|ref|YP_008796707.1| 651 GFVTSLGLPDVVAERTVQQTVVQTLSTEV-TRTQTQEVT 688
                                       89*****************9998886664.556665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (738 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.41
# Mc/sec: 5387.16
//
Query:       gi|557693654|ref|YP_008796708.1|  [L=259]
Description: short-chain dehydrogenase/reductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-58  196.2   0.1    4.9e-58  195.8   0.1    1.1  1  adh_short        short chain dehydrogenase
    5.1e-46  157.1   0.0    6.6e-46  156.8   0.0    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    2.1e-09   37.6   0.1    2.9e-09   37.1   0.1    1.1  1  KR               KR domain
     0.0014   18.2   0.0     0.0018   17.7   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
     0.0038   16.6   0.0     0.0093   15.4   0.0    1.5  2  DUF1776          Fungal family of unknown function (DUF1776)
     0.0043   17.3   0.1       0.01   16.1   0.1    1.6  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.095   12.6   0.6        9.8    6.2   0.1    2.5  2  DUF4322          Domain of unknown function (DUF4322)
       0.16   11.8   0.2       0.53   10.1   0.1    1.9  2  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 


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 !  195.8   0.1   2.2e-61   4.9e-58       2     188 ..       9     195 ..       8     198 .. 0.99

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 2.2e-61
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                       vvlvtGassGIGra+a e+a+ G +vv v+r+ ++l +va+e  + g ++ ++++Dv+d+e+v ++v++ v+++g++
  gi|557693654|ref|YP_008796708.1|   9 VVLVTGASSGIGRATALEFARLGSTVVGVARRLDELLKVAEEAASFGGRFKPLRCDVSDKEQVYNTVKETVENYGRV 85 
                                       89****************************************9999******************************* PP

                                       SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHH CS
                         adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaa 155
                                       dvLvnNAG    g+f+++  ee+e  ++vNl+gv+  ++avlp+ml q+ GrIvnvsS ag+  v+ +  Y+A K a
  gi|557693654|ref|YP_008796708.1|  86 DVLVNNAGFGLYGEFKDFGLEEVEYQVSVNLMGVIYFVKAVLPHMLGQRFGRIVNVSSLAGFITVPKMNLYCAVKSA 162
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHH CS
                         adh_short 156 vagltrslakelaptgirvnavaPGlvdTdmak 188
                                       v+ l+r+l ++l++++irv+av+PG vdT++ +
  gi|557693654|ref|YP_008796708.1| 163 VTVLSRALDMQLKKHNIRVSAVCPGSVDTAFFQ 195
                                       *****************************9876 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 !  156.8   0.0   2.9e-49   6.6e-46       1     213 [.      14     222 ..      14     229 .. 0.93

  Alignments for each domain:
  == domain 1  score: 156.8 bits;  conditional E-value: 2.9e-49
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvn 75 
                                       Ga sgIGra+A ++a+ G +vv + ++ ++  +v+e a+++g ++  l+cDV+d+eqv ++v+e+ve++g++D+lvn
  gi|557693654|ref|YP_008796708.1|  14 GASSGIGRATALEFARLGSTVVGVARRLDELLKVAEEAASFGGRFkpLRCDVSDKEQVYNTVKETVENYGRVDVLVN 90 
                                       899***********************99998899999999**99889****************************** PP

                                       -----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHH CS
                      adh_short_C2  76 nagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalea 150
                                       nag+     g+f ++  ee++  ++vnl ++++++ka+lp+m  +  g+ivn+ss+++ ++vp+ n y+a+K a+  
  gi|557693654|ref|YP_008796708.1|  91 NAGFGLY--GEFKDFGLEEVEYQVSVNLMGVIYFVKAVLPHMLGQrfGRIVNVSSLAGFITVPKMNLYCAVKSAVTV 165
                                       *******..*******************************7766669****************************** PP

                                       HHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHH CS
                      adh_short_C2 151 ltrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalf 213
                                       l+r+l ++l +++iRv av+pg ++T   ++ +       +++   plg l+++e+va++++ 
  gi|557693654|ref|YP_008796708.1| 166 LSRALDMQLKKHNIRVSAVCPGSVDTAFFQNPS------FYSRGGRPLGPLIKAEKVAKTIVS 222
                                       *************************98876665......566788899999999999999875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.1   1.3e-12   2.9e-09       3     157 ..      10     164 ..       9     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 1.3e-12
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                       +l+tG+  g+G+++a   a+ g + +v ++R+   de   +  +e ++ g + + +++Dvsdk++v ++++e  ++ 
  gi|557693654|ref|YP_008796708.1|  10 VLVTGASSGIGRATALEFARLGST-VVGVARR--LDEL-LKVAEEAASFGGRFKPLRCDVSDKEQVYNTVKETVENY 82 
                                       79******************9975.6677777..3444.4588999999**************************** PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaa 152
                                       +++   ++ Ag+   + +++   e++e  ++  + G+    +++ +    ++   +v +SS+ag++  ++   Y a 
  gi|557693654|ref|YP_008796708.1|  83 GRVDVLVNNAGFGLYGEFKDFGLEEVEYQVSVNLMGVIYFVKAVLPhmlgQRFGRIVNVSSLAGFITVPKMNLYCAV 159
                                       *************************************999888877677788899***************9999998 PP

                                       HHHHH CS
                                KR 153 NaflD 157
                                        + + 
  gi|557693654|ref|YP_008796708.1| 160 KSAVT 164
                                       77665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   8.3e-07    0.0018       1      77 [.      10      97 ..      10     147 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.3e-07
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HH....HHHHHHHHH.T-SEE CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrs....alerlfkee.qpdav 68
                                      +lVtGa+  iG+a++ ++++ g +v+g++r+ ++  + ++e +      +  ++d+ d++     +++ ++++ ++d+ 
  gi|557693654|ref|YP_008796708.1| 10 VLVTGASSGIGRATALEFARLGSTVVGVARRLDELLKVAEEAAsfggrfKPLRCDVSDKEqvynTVKETVENYgRVDVL 88
                                      79*****************************5555444444449***9999********95555566666666777777 PP

                                      EE--S---H CS
                         Epimerase 69 ihlAavggv 77
                                      ++ A+ g +
  gi|557693654|ref|YP_008796708.1| 89 VNNAGFGLY 97
                                      777765544 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 ?   -1.9   0.0      0.76   1.7e+03       5      46 ..       9      49 ..       6      77 .. 0.76
   2 !   15.4   0.0   4.2e-06    0.0093      98     202 ..      89     191 ..      85     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.76
                           DUF1776  5 vvlvlGsptePltRsialDLerrGFiVfvtvesaeeeklves 46
                                      vvlv G +   + R+ al++ r G +V+ +++  +e  +v +
  gi|557693654|ref|YP_008796708.1|  9 VVLVTG-ASSGIGRATALEFARLGSTVVGVARRLDELLKVAE 49
                                      444444.67789999999999999999877776666555555 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.2e-06
                           DUF1776  98 vPslsy.ptgpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssa 173
                                       v +  +  +g ++  +l++++ ++  +l+  i +++a lp++     q+   iv   s+   + +p   +   v sa
  gi|557693654|ref|YP_008796708.1|  89 VNNAGFgLYGEFKDFGLEEVEYQVSVNLMGVIYFVKAVLPHMLG---QRFGRIVNVSSLAGFITVPKMNLYCAVKSA 162
                                       5566677788999999999************************9...8999999999******************** PP

                           DUF1776 174 lsalfevLkrelrphnidvtqikLGnldl 202
                                       ++ l ++L+ +l++hni v+ +  G++d 
  gi|557693654|ref|YP_008796708.1| 163 VTVLSRALDMQLKKHNIRVSAVCPGSVDT 191
                                       *******************9998887775 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 !   16.1   0.1   4.6e-06      0.01       1      76 [.      10      91 ..      10      96 .. 0.84
   2 ?   -3.0   0.0       3.7   8.3e+03      22      36 ..     158     172 ..     146     184 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-06
                                      EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..TTTCEEEEE--TTTHHHHHHHHHTTS...... CS
                   Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaaka..lgvrfeaialdaenyeavLaallkeg...... 70
                                      vl+ Ga  ++G+a+a + ar ++    ++ + r +++l ++a++a   g rf++  +d++++e+ +   +ke+      
  gi|557693654|ref|YP_008796708.1| 10 VLVTGAsSGIGRATALEFARLGST---VVGVARRLDELLKVAEEAasFGGRFKPLRCDVSDKEQ-VYNTVKETvenygr 84
                                      78999999*************997...777777788888888887789****************.77778887677677 PP

                                      .SEEEE- CS
                   Sacchrp_dh_NADP 71 .dlvvnl 76
                                       d++vn 
  gi|557693654|ref|YP_008796708.1| 85 vDVLVNN 91
                                      7777775 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.7
                                       CT-GEEEEEESSHHH CS
                   Sacchrp_dh_NADP  22 dvdaeitvadrskek 36 
                                        v++ +tv +r ++ 
  gi|557693654|ref|YP_008796708.1| 158 AVKSAVTVLSRALDM 172
                                       455567777776665 PP

>> DUF4322  Domain of unknown function (DUF4322)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.018        41      46      63 ..      65      82 ..      61      84 .. 0.90
   2 ?    6.2   0.1    0.0044       9.8      28      40 ..     212     224 ..     210     231 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.018
                           DUF4322 46 ienkskaynvspqtvrny 63
                                      + +k + yn    tv ny
  gi|557693654|ref|YP_008796708.1| 65 VSDKEQVYNTVKETVENY 82
                                      77899************* PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0044
                           DUF4322  28 kaeevakvLvsaa 40 
                                       kae vak++vsaa
  gi|557693654|ref|YP_008796708.1| 212 KAEKVAKTIVSAA 224
                                       9***********8 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 ?   10.1   0.1   0.00024      0.53      42      71 ..       9      37 ..       2      40 .. 0.78
   2 ?   -2.1   0.0       1.5   3.3e+03      31      54 ..      76      96 ..      60      97 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00024
                                      EEEEESTSSHHHHHHHHHHHHSS--EEEEE CS
                   Eno-Rase_NADH_b 42 kvLviGaStGYGLAsriaaafgagadtigV 71
                                       vLv GaS+G G A+ +  a+  g + +gV
  gi|557693654|ref|YP_008796708.1|  9 VVLVTGASSGIGRATALEFARL-GSTVVGV 37
                                      79************98877765.5555665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                                      HHS-----.-SEEEEESTSSHHHH CS
                   Eno-Rase_NADH_b 31 ksqkkiekgpkkvLviGaStGYGL 54
                                      k+  +   +  +v v+   +G+GL
  gi|557693654|ref|YP_008796708.1| 76 KETVE---NYGRVDVLVNNAGFGL 96
                                      32222...2446666667778887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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 0.28s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1947.87
//
Query:       gi|557693655|ref|YP_008796709.1|  [L=283]
Description: hypothetical protein CSUB_C0218 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
        1.1    7.2   5.1        1.1    7.1   5.1    1.1  1  Dicty_REP  Dictyostelium (Slime Mold) REP protein


Domain annotation for each model (and alignments):
>> Dicty_REP  Dictyostelium (Slime Mold) REP protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   5.1   6.2e-05       1.1     249     303 ..      39      98 ..      27     188 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 6.2e-05
                         Dicty_REP 249 pskeknkttttttttttttsqartrkrkaidddklsenqakekkknskksdddp......q 303
                                         k+++ tt+tttt++ tt+q++t+ + +  + +++ +++ +++++++ ++ +       +
  gi|557693655|ref|YP_008796709.1|  39 TTKSPTVTTQTTTTLSPTTPQTTTTIQTTSPPTTIT-TTQTTPTQTTTTPTFQVnlrsffN 98 
                                       456777788888888888888888777755555555.567777788887777664544431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2051.79
//
Query:       gi|557693656|ref|YP_008796710.1|  [L=169]
Description: hypothetical protein CSUB_C0219 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); 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: 00:00:00.42
# Mc/sec: 1218.74
//
Query:       gi|557693657|ref|YP_008796711.1|  [L=171]
Description: hypothetical protein CSUB_C0220 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   12.4   1.0       0.32   11.2   1.0    1.6  1  DUF4731         Domain of unknown function (DUF4731)
       0.72    9.2   4.5       0.19   11.1   1.1    1.7  2  Zn_peptidase_2  Putative neutral zinc metallopeptidase
        4.8    7.7   5.7        7.1    7.2   0.8    2.2  2  DUF4231         Protein of unknown function (DUF4231)


Domain annotation for each model (and alignments):
>> DUF4731  Domain of unknown function (DUF4731)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   5.4e-05      0.32      29      70 ..      77     118 ..      69     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.4e-05
                           DUF4731  29 easslkrisrklctGklgialkvlggvalfwvvfilGYvtGy 70 
                                       + +s + +  kl+  kl+++  +l  va + v f++GY +Gy
  gi|557693657|ref|YP_008796711.1|  77 HYLSATLLNIKLLRRKLVVTHLILHNVAAYGVGFLMGYGAGY 118
                                       55566677889999***************************9 PP

>> Zn_peptidase_2  Putative neutral zinc metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       0.2   1.2e+03     127     132 ..      54      59 ..      17      90 .. 0.54
   2 ?   11.1   1.1   3.3e-05      0.19      89     147 ..     102     160 ..      85     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.2
                    Zn_peptidase_2 127 illlig 132
                                       +++++ 
  gi|557693657|ref|YP_008796711.1|  54 WMFIAY 59 
                                       333332 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 3.3e-05
                    Zn_peptidase_2  89 avAAHevGhaiqhaegyaplklrsalvpvvnigsklslillliglllslsslllligii 147
                                        vAA+ vG+ + +  gy   + r + v v+ i+  +s+ ++ ig+l+ +  l +++g++
  gi|557693657|ref|YP_008796711.1| 102 NVAAYGVGFLMGYGAGYVGGTARLEGVGVAVITALISWTVIPIGILIFIGLLSAILGVF 160
                                       69******************************************887554445566665 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.3     0.022   1.3e+02      14      42 ..      15      51 ..      10      83 .. 0.65
   2 ?    7.2   0.8    0.0012       7.1      24      77 ..     126     170 ..     120     171 .] 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.022
                           DUF4231 14 krrfrllrlitivlgallpilvs........sklgag 42
                                       r+f ++ ++ i++++l+++ v         + ++++
  gi|557693657|ref|YP_008796711.1| 15 ARYFLFTTFVNICAAVLITTPVLvarlalplKLTEWP 51
                                      4566777778888888776555544665555322333 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0012
                           DUF4231  24 tivlgallpilvssklgagvsvlkiltallsalvailaaleeffrykerWrryR 77 
                                       + v++a++++l+s         +++++ ++ +++ +l+a+ ++f + + W+  R
  gi|557693657|ref|YP_008796711.1| 126 EGVGVAVITALIS---------WTVIPIGILIFIGLLSAILGVFTVLDGWTMSR 170
                                       5689999999999.........89999999999999999999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 1163.40
//
Query:       gi|557693658|ref|YP_008796712.1|  [L=492]
Description: multiple sugar ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-17   62.4   3.2    1.2e-16   61.6   3.2    1.3  1  SBP_bac_1  Bacterial extracellular solute-binding protein
    1.5e-12   47.9   0.0      1e-11   45.2   0.0    1.9  2  SBP_bac_8  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> 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 !   61.6   3.2   1.3e-20   1.2e-16      69     310 ..     149     392 ..     134     396 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 1.3e-20
                                       TSBECCHHHHHHTTECTTCCTEEEEHHHHTHHHHCE.EE.............ES.EEEEE.EEEEEEETTTHHCTTG CS
                         SBP_bac_1  69 glllpldpyvkaylapgvkdaadklsssvlpkilds.kv.............ly.vPlya.argliYNkdlfekagl 129
                                       ++++p+++++++y  ++++++ +++   +lp  l+  +v             ++ +P+ + ++  +Y+ d++ek g 
  gi|557693658|ref|YP_008796712.1| 149 NYFTPVQDFMEKYREYTYEKFRLDD---FLPESLNLvGVyppkldsggekgnVVmLPFSTpTMINFYRRDIYEKNGH 222
                                       6999*****************9996...9******98889************************************* PP

                                       GGSHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT....HHCSHHHHSHHHHHHH CS
                         SBP_bac_1 130 dppwtWdelveaakklkekgkkpiggarggsasgtayyfalalakslggkvfdkdgg....gldnpegvtaatylvk 202
                                       +pp tW+e +e +k l  + ++ ++ a +          +++l  s+gg++f    g     +d+++ v+a++ +  
  gi|557693658|ref|YP_008796712.1| 223 EPPATWEEYLEDLKALNNPSEGFFATAQQVGSDVGIVTEFNNLVHSFGGRLFEVSDGkiipVMDSDAVVEALKMYSS 299
                                       *********************99*****************************9999889999999999999999999 PP

                                       HHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTT CS
                         SBP_bac_1 203 lyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkgg 279
                                                 ++++ + ++d++a+++++ +G++  ai +  +a        +  +++  + + +++g+ p Pag+ g
  gi|557693658|ref|YP_008796712.1| 300 IR-------PYADPASISYDWDAVATAMRRGRIVQAILWQDYA--------WMMDDPVRSVVVNKVGYKPNPAGPAG 361
                                       99.......9**********************99999887773........33566666777788999999999999 PP

                                       TSEEEEEEEEEEBTTCSTHHHHHHHHHHHTS CS
                         SBP_bac_1 280 kpgilgayglaipkgsknpeaAkkFldflls 310
                                          +++++g++++k+ knp+a + +l+++++
  gi|557693658|ref|YP_008796712.1| 362 SFHQFVGDGVGLVKNGKNPVAMWLWLQWATE 392
                                       8888************************996 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.052   4.6e+02     154     203 ..      57     104 ..      16     134 .. 0.69
   2 !   45.2   0.0   1.2e-15     1e-11      70     268 ..     163     414 ..     116     428 .. 0.67

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.052
                                       .HHH.HHHHHHHHHHHHTT-EE-S...--SSTTTTTSBSEEEE-TTHHHHH CS
                         SBP_bac_8 154 gkdglkealellkklkdngktydtg.adavsefanGevaftingswdiaaa 203
                                        +d+++e++e+l++ ++n+   +tg + av+++a+  +++++  +++++ a
  gi|557693658|ref|YP_008796712.1|  57 PPDQYVEFMEWLAEVSKNI---ETGkEPAVALMAESAALAVQRIDGEFFLA 104
                                       3566788999999999888...44425566677766666666666666555 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 1.2e-15
                                       H.....................-HHHHHTT--TS.----EEEEEEE-EEEEEHHHHHHS...---BHHHHHHHHHHH CS
                         SBP_bac_8  70 d.....................ltdalaavgydgklygvPyasetpyvliynkdlleka..edpktwdellaaakkl 123
                                       +                     ++++l++ g +g++  +P+ + t ++ +y+ d++ek+  e+p+tw+e+l+ +k+l
  gi|557693658|ref|YP_008796712.1| 163 EytyekfrlddflpeslnlvgvYPPKLDSGGEKGNVVMLPFSTPT-MINFYRRDIYEKNghEPPATWEEYLEDLKAL 238
                                       2333445555555566667776789******************98.9***********8999**********99999 PP

                                       HHH-SEGG---GGGGGGTHH........................ETTEE---H....HHH.HHHHHHHHHHHHTT-. CS
                         SBP_bac_8 124 kgkfglpdpasgwlqaalla........................kdgksldddg..gkdglkealellkklkdngk. 173
                                              +p++g++ +a++                         +dgk        ++d+++eal+++ +++++ + 
  gi|557693658|ref|YP_008796712.1| 239 ------NNPSEGFFATAQQVgsdvgivtefnnlvhsfggrlfevSDGKII---PvmDSDAVVEALKMYSSIRPYADp 306
                                       ......33333333333333333333344445555545544444455555...04579****************987 PP

                                       ..EE-S..--SSTTTTTSBSEEE...E-TTHHHH.HH-T.TTSEEEE-.-..S--...EEEEEEEEEEBTTS-HHHH CS
                         SBP_bac_8 174 ..tydtgadavsefanGevafti...ngswdiaa.aqka.gkklgaiv.p..kqg...sfaggkglavpknaknedl 237
                                         +  +++++  +++ G+++ +i    + w + + ++     k+g+ + p  + g   +f+g  g+   kn kn+  
  gi|557693658|ref|YP_008796712.1| 307 asISYDWDAVATAMRRGRIVQAIlwqDYAWMMDDpVRSVvVNKVGYKPnPagPAGsfhQFVGD-GVGLVKNGKNPV- 381
                                       753357888889******999993333556666424444234777776333323433344444.688899999999. PP

                                       HHHHHHHHHTTSHHHHHHHH..HH---BS-S-T CS
                         SBP_bac_8 238 aAldFlkwltspenqaalae..ktgyipvnksa 268
                                       a + +l+w+t+      l+   k  ++p++ s+
  gi|557693658|ref|YP_008796712.1| 382 AMWLWLQWATEVGTRIILMLdeKARVVPIRRSV 414
                                       599999999876555554443455556666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3444.96
//
Query:       gi|557693659|ref|YP_008796713.1|  [L=150]
Description: hypothetical protein CSUB_C0222 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.35u 0.30s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1097.15
//
Query:       gi|557693660|ref|YP_008796714.1|  [L=451]
Description: major facilitator superfamily MFS [Candidatus Caldiarchaeum subterraneum]
Scores for 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-40  137.6  38.4    4.7e-40  137.6  38.4    2.4  2  MFS_1            Major Facilitator Superfamily
      0.004   16.2   6.8      0.004   16.2   6.8    2.4  2  PUCC             PUCC protein
     0.0091   14.9  20.1       0.02   13.8   0.5    3.2  3  Sugar_tr         Sugar (and other) transporter
  ------ inclusion threshold ------
       0.74   10.3   6.4         24    5.4   0.2    4.1  4  FeoB_associated  FeoB-associated Cys-rich membrane protein
       0.91    9.6   3.4        3.3    7.8   3.4    2.0  1  DUF4337          Domain of unknown function (DUF4337)
          3    7.2   8.9          7    6.0   3.1    3.3  2  Ceramidase       Ceramidase


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 !  137.6  38.4   1.6e-43   4.7e-40      34     352 ..       2     390 ..       1     391 [. 0.92
   2 ?   -2.0   0.9      0.43   1.3e+03     154     170 ..     426     442 ..     410     447 .. 0.70

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 1.6e-43
                             MFS_1  34 igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgagalfpagaal 109
                                       +g++  +y ++  +++++lG  sd  +r+ ++++gll+fa++ ++l+  a +++ llv r+lqG+ga+++++++ al
  gi|557693660|ref|YP_008796714.1|   2 AGWVPITYLIVITALMPLLGQYSDSKSRKNMFIVGLLIFASA-AYLSsTAFTIYELLVYRALQGIGAALVLANSRAL 77 
                                       79***********************98999************.555522255777********************** PP

                             MFS_1 110 iadwfpkeergraigllsagfslGailgpllggllasslg...Wravfyilaivsllafvlfllllpeepperkrks 183
                                       i+d+f ++  g+a+g+  a +  + ++gpllgg+++++ +   Wr vf+++ +v+l+++ l+++ +p+e+  +k+++
  gi|557693660|ref|YP_008796714.1|  78 IVDVFEEKGGGLAMGVHVAVIYSALLMGPLLGGVILTLTSligWRDVFLLNVPVCLVSAALVYITYPREKALHKKSA 154
                                       *********************************6655544555********************************** PP

                             MFS_1 184 pkeee.....................................................................kgt 191
                                       +k ++                                                                      ++
  gi|557693660|ref|YP_008796714.1| 155 EKIDWlsgillligvfnllggvtlwpihkgiievlveevrifglylrpffyisfpawlmvalgllsvmlyvfreRRK 231
                                       *************************************************************************9999 PP

                             MFS_1 192 gpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrls 268
                                         ++++p +k+l ++  l ++ +a+ll   ++ g+ + + +yl   +gl+  ++ag++l++l l ++++++++g ls
  gi|557693660|ref|YP_008796714.1| 232 SDSQVIP-LKLLSTNTRLRSASLAILLLYSAHHGVWVVVSFYLTALMGLD-PVTAGFVLGVLPLTVLAVSPIGGLLS 306
                                       9999999.********99755555555555999999999999999*****.8************************* PP

                             MFS_1 269 drlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntag 345
                                       d++g     +l+l++++la+++l l++  ss + ++++l ++G+g g++ ++ ++ a  ++ pe +++++gl+++++
  gi|557693660|ref|YP_008796714.1| 307 DKYGYSAVSTLGLFICSLALFALSLVSQQSSIIYVAISLTILGIGIGLFAAPNTNSALASVEPETRAQVNGLMGFMR 383
                                       ****9888888888888888888888888888888889999************************************ PP

                             MFS_1 346 slggalg 352
                                       +lg  l+
  gi|557693660|ref|YP_008796714.1| 384 HLGQTLS 390
                                       ***9875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.43
                             MFS_1 154 fyilaivsllafvlfll 170
                                       f++ ++++++a+v++l+
  gi|557693660|ref|YP_008796714.1| 426 FLLGGVIAAIAAVIVLW 442
                                       66677777777665433 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   6.0     0.055   1.7e+02     282     391 ..      36     137 ..      10     145 .. 0.67
   2 !   16.2   6.8   1.3e-06     0.004     264     362 ..     302     400 ..     280     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.055
                              PUCC 282 llgllsflllilaallenvallvagvlllGlasGlfavaaltlmldlaaeeraglalGaWGaaQaiaaglavllgga 358
                                        l + ++ + + +++++   llv   +l G+++ l+ + + +l++d+  e+  gla+G+  a+   a  ++ llgg+
  gi|557693660|ref|YP_008796714.1|  36 GLLIFASAAYLSSTAFTIYELLVYR-ALQGIGAALVLANSRALIVDVFEEKGGGLAMGVHVAVIYSALLMGPLLGGV 111
                                       3344444555555555555555443.456777778888888888888888888899999999999999999999999 PP

                              PUCC 359 lrdllkalaandaalayglVfaleavlliisil 391
                                       ++ l  ++        +  Vf+l++ + ++s++
  gi|557693660|ref|YP_008796714.1| 112 ILTLTSLIG-------WRDVFLLNVPVCLVSAA 137
                                       887766554.......45555555555555544 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.3e-06
                              PUCC 264 glvlsrglkkarlaslgvllgllsflllilaallenvallvagvlllGlasGlfavaaltlmldlaaeeraglalGa 340
                                       g +ls + +   + +lg+ ++ l++++l l ++++++  ++ ++ +lG++ Glfa+  + ++l+ + +e+ +   G+
  gi|557693660|ref|YP_008796714.1| 302 GGLLSDKYGYSAVSTLGLFICSLALFALSLVSQQSSIIYVAISLTILGIGIGLFAAPNTNSALASVEPETRAQVNGL 378
                                       55778888899999*************************************************************** PP

                              PUCC 341 WGaaQaiaaglavllggalrdl 362
                                        G    + + l+++l+ +++d 
  gi|557693660|ref|YP_008796714.1| 379 MGFMRHLGQTLSIALSTIILDY 400
                                       ***9999999999999999885 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.5   6.8e-06      0.02      65     118 ..      19      69 ..       3      79 .. 0.88
   2 ?    2.2   0.6     0.022        67      46      95 ..      93     141 ..      75     149 .. 0.83
   3 !    7.4   6.3   0.00059       1.8      47     161 ..     283     397 ..     228     442 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.8e-06
                                       HHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHH CS
                          Sugar_tr  65 fagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGl 118
                                       ++g  +d  +Rk+ ++++ ++f  +a l+ +a    +++ l+v R l Gig+ l
  gi|557693660|ref|YP_008796714.1|  19 LLGQYSDSKSRKNMFIVGLLIFASAAYLSSTAF---TIYELLVYRALQGIGAAL 69 
                                       46788999************************9...9*************9866 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.022
                                       .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH- CS
                          Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaa 95 
                                       v + +i s++l G ++G++++  l+  +G ++++l  + +++++a+l ++
  gi|557693660|ref|YP_008796714.1|  93 VHVAVIYSALLMGPLLGGVILT-LTSLIGWRDVFLLNVPVCLVSAALVYI 141
                                       5667899999999999999998.899999999999999888888888765 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00059
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv 123
                                       + g++++++ +  ++ s ++gll+d++G+  +   + ++++ + +   +  +++s+  ++++  ++Gig+Gl+ +  
  gi|557693660|ref|YP_008796714.1| 283 TAGFVLGVLPLTVLAVSPIGGLLSDKYGYSAVSTLGLFICSLALFALSLVSQQSSIIYVAISLTILGIGIGLFAA-- 357
                                       566777777777777788999999999999999998888888887777777688888899999999999998764.. PP

                                       HHHHHTTS..-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 124 PmyisEiA..pkklRgalvslyqlaitfGilvaaifglgl 161
                                       P + s +A   ++ R ++ +l  ++  +G+ +++ + +++
  gi|557693660|ref|YP_008796714.1| 358 PNTNSALAsvEPETRAQVNGLMGFMRHLGQTLSIALSTII 397
                                       5555555544677777777777777777777777666665 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 ?    5.4   0.2    0.0082        24       2      16 ..      32      46 ..      31      57 .. 0.82
   2 ?   -3.2   0.0       4.1   1.2e+04      10      18 ..     134     143 ..     131     153 .. 0.58
   3 ?    2.0   0.0     0.095   2.8e+02       2      23 ..     211     232 ..     210     235 .. 0.83
   4 ?    3.0   0.5     0.046   1.4e+02       2      17 ..     425     440 ..     424     450 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0082
                   FeoB_associated  2 tiIVgliiaaavafv 16
                                      ++IVgl+i+a +a++
  gi|557693660|ref|YP_008796714.1| 32 MFIVGLLIFASAAYL 46
                                      58*******999987 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.1
                   FeoB_associated  10 a.aavafvir 18 
                                       + aa++++ +
  gi|557693660|ref|YP_008796714.1| 134 VsAALVYITY 143
                                       3256666655 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.095
                   FeoB_associated   2 tiIVgliiaaavafvirrlikk 23 
                                       ++ V+l +++++++v+r  +k+
  gi|557693660|ref|YP_008796714.1| 211 WLMVALGLLSVMLYVFRERRKS 232
                                       5678999999******999886 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.046
                   FeoB_associated   2 tiIVgliiaaavafvi 17 
                                       +++ g++iaa++a+++
  gi|557693660|ref|YP_008796714.1| 425 NFLLGGVIAAIAAVIV 440
                                       6788999999888875 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   3.4    0.0011       3.3     123     160 ..     319     356 ..     306     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0011
                           DUF4337 123 lLqiaIvlaaialltkkklllylslvlglvGlvlflag 160
                                       l+  +++l a++l+++++ ++y+++ l+++G++++l++
  gi|557693660|ref|YP_008796714.1| 319 LFICSLALFALSLVSQQSSIIYVAISLTILGIGIGLFA 356
                                       344579***************************99876 PP

>> Ceramidase  Ceramidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   3.1    0.0024         7      89     189 ..      12     180 ..       5     233 .. 0.75
   2 ?    1.7   0.3     0.048   1.4e+02      91     175 ..     296     380 ..     241     390 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0024
                        Ceramidase  89 iyatalvlyavfsekksrstrvllgvlltalavvvtllylvlkepvlhqvafalltvlvllrsiyliekkv...... 159
                                       +++++++l   +s++ksr++  ++g+l++a a+ ++ +++++ e  +   + ++ ++lvl+ s++li  +v      
  gi|557693660|ref|YP_008796714.1|  12 VITALMPLLGQYSDSKSRKNMFIVGLLIFASAAYLSSTAFTIYELLVYRALQGIGAALVLANSRALIV-DVfeekgg 87 
                                       4555666666777899999**************99999999999999999************999993.33466667 PP

                        Ceramidase 160 ...............................................................dksdeaakkevkkl 173
                                                                                                      +ks e+++     l
  gi|557693660|ref|YP_008796714.1|  88 glamgvhvaviysallmgpllggviltltsligwrdvfllnvpvclvsaalvyityprekalhKKSAEKIDWLSGIL 164
                                       77777777777777777777777777777777777777777777777777777777666655544444444445555 PP

                        Ceramidase 174 allgliifllgfliWn 189
                                       +l+g++ +l g+++W 
  gi|557693660|ref|YP_008796714.1| 165 LLIGVFNLLGGVTLWP 180
                                       5566666666666665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.048
                        Ceramidase  91 atalvlyavfsekksrstrvllgvlltalavvvtllylvlkep..vlhqvafalltvlvllrsiyliekkvdksdea 165
                                       +++ ++  ++s   ++ ++++++++l++ ++++ +l+lv+++   ++ ++++ +l + + l ++  +++ + + +++
  gi|557693660|ref|YP_008796714.1| 296 LAVSPIGGLLS--DKYGYSAVSTLGLFICSLALFALSLVSQQSsiIYVAISLTILGIGIGLFAAPNTNSALASVEPE 370
                                       44444444444..3455666666666777666667776666551144555555555555555555555555666666 PP

                        Ceramidase 166 akkevkklal 175
                                       ++ +v+ l+ 
  gi|557693660|ref|YP_008796714.1| 371 TRAQVNGLMG 380
                                       6666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); 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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3089.82
//
Query:       gi|557693661|ref|YP_008796715.1|  [L=630]
Description: quinoprotein alcohol dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   78.8   6.0    0.00091   19.0   0.0    7.3  7  PQQ       PQQ enzyme repeat
    3.5e-22   79.1   0.1    2.3e-08   33.9   0.1    4.1  4  PQQ_2     PQQ-like domain
    6.2e-21   74.3  11.2    2.9e-08   33.9   0.1    7.8  8  PQQ_3     PQQ-like domain


Domain annotation for each model (and alignments):
>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1     2e-06     0.012       1      29 [.      90     118 ..      90     122 .. 0.86
   2 ?    2.0   0.0     0.038   2.3e+02       3      22 ..     144     163 ..     142     164 .. 0.80
   3 ?   -0.8   0.1      0.29   1.7e+03       9      24 ..     207     222 ..     202     223 .. 0.79
   4 !   16.0   0.0   1.4e-06    0.0084      11      28 ..     313     330 ..     309     335 .. 0.89
   5 !    9.1   0.0   0.00022       1.3       4      22 ..     359     378 ..     356     380 .. 0.75
   6 !   19.0   0.0   1.5e-07   0.00091       9      27 ..     471     489 ..     469     499 .. 0.88
   7 !   12.0   0.1   2.6e-05      0.15       1      23 [.     504     526 ..     504     533 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-06
                                       TEEEEEETTSEEEEEETTTCCEEEEEESS CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktg 29 
                                       g vy +++ ++++Al  dTG+++W+++++
  gi|557693661|ref|YP_008796715.1|  90 GIVYFATPYNRVVALRSDTGNLVWQYQVN 118
                                       5788886666****************987 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.038
                                       EEEEETTSEEEEEETTTCCE CS
                               PQQ   3 vylgsadGylyAlDadTGkv 22 
                                       +y+   d  +  lDa++G+ 
  gi|557693661|ref|YP_008796715.1| 144 IYMMASDCSVHVLDASNGRP 163
                                       666678999*********85 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.29
                                       TSEEEEEETTTCCEEE CS
                               PQQ   9 dGylyAlDadTGkvlW 24 
                                        G + A+D+++ +++W
  gi|557693661|ref|YP_008796715.1| 207 RGFIAAYDINNFNLVW 222
                                       6899****99866666 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 1.4e-06
                                       EEEEEETTTCCEEEEEES CS
                               PQQ  11 ylyAlDadTGkvlWrfkt 28 
                                        ++Al+a+TG++lW ++t
  gi|557693661|ref|YP_008796715.1| 313 SIVALNASTGDLLWFYQT 330
                                       799*************97 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.00022
                                       EEE.ETTSEEEEEETTTCCE CS
                               PQQ   4 ylg.sadGylyAlDadTGkv 22 
                                       +++  +  y+y lDa+TG+ 
  gi|557693661|ref|YP_008796715.1| 359 VMAaAKSDYIYVLDARTGQP 378
                                       44555666**********86 PP

  == domain 6  score: 19.0 bits;  conditional E-value: 1.5e-07
                                       TSEEEEEETTTCCEEEEEE CS
                               PQQ   9 dGylyAlDadTGkvlWrfk 27 
                                       + +lyA+D++TG++lW+f+
  gi|557693661|ref|YP_008796715.1| 471 NSTLYAVDIRTGRILWKFE 489
                                       668***************8 PP

  == domain 7  score: 12.0 bits;  conditional E-value: 2.6e-05
                                       TEEEEEETTSEEEEEETTTCCEE CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvl 23 
                                       gvvy+ ++ G+ly +Da+TG++l
  gi|557693661|ref|YP_008796715.1| 504 GVVYAVDRAGVLYMVDAETGRLL 526
                                       799*****************987 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0     9e-11   5.4e-07      26     106 ..      79     171 ..      58     222 .. 0.52
   2 ?    1.7   0.0     0.027   1.6e+02      69     101 ..     185     223 ..     178     242 .. 0.79
   3 !    9.1   0.0   0.00014      0.85       4      58 ..     313     378 ..     309     381 .. 0.64
   4 !   33.9   0.1   3.8e-12   2.3e-08      84     191 ..     470     575 ..     411     610 .. 0.63

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 9e-11
                             PQQ_2  26 gggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvga............plvaegrvvvvasdgqlia 90 
                                       +g+ +++++ +g ++ at ++r+val   tG ++W+++++ ++ ++                +g ++ +asd ++  
  gi|557693661|ref|YP_008796715.1|  79 QGIETTPLVVNGIVYFATPYNRVVALRSDTGNLVWQYQVNMTTFTSkpywayvanqksISYHGGAIYMMASDCSVHV 155
                                       44445556666666666666666666666666666666644444444566655555555555566666666666666 PP

                             PQQ_2  91 ldaedGkrlWstqqrs 106
                                       lda +G+ l  +q ++
  gi|557693661|ref|YP_008796715.1| 156 LDASNGRPLRIVQGET 171
                                       6666666655544444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.027
                             PQQ_2  69 vgaplvaegrvvvva......sdgqlialdaedGkrlWs 101
                                         ap v ++ v+v+a      + g ++a+d+++ +++W+
  gi|557693661|ref|YP_008796715.1| 185 EQAPIVYRNLVIVRAstaafgGRGFIAAYDINNFNLVWR 223
                                       567999999999999777764445888899999999998 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00014
                             PQQ_2   4 vvsaldaatGaelWrv........dlarp......lgggvsravlsggtlfvatgggrlvaldaatGkv 58 
                                       +++al+a tG +lW                     + + v+ a  +++++ +a +++ ++ lda tG+ 
  gi|557693661|ref|YP_008796715.1| 313 SIVALNASTGDLLWFYqtiphalvA---VepgwsvILADVEIAGAPRKVVMAAAKSDYIYVLDARTGQP 378
                                       4678888888888877433332221...03334456666666777888888888888888888888875 PP

  == domain 4  score: 33.9 bits;  conditional E-value: 3.8e-12
                             PQQ_2  84 sdgqlialdaedGkrlWstqqrseepaelrssaspavagdtvvvgessgklvaldpkdGkvlWerel.aaprgtsel 159
                                       ++ +l+a+d+++G+ lW  ++         ++as +v+g++v++++  g l+++d+++G++l   +l + +  +++ 
  gi|557693661|ref|YP_008796715.1| 470 QNSTLYAVDIRTGRILWK-FEMPNRY----QAASVVVSGGVVYAVDRAGVLYMVDAETGRLLRRISLgGLGAAGVS- 540
                                       334788888888888888.6666333....3355566688888888888888888888888888887555444444. PP

                             PQQ_2 160 srvgdisgrpvva....egtVyassgqgrllaldla 191
                                          +di+g+p++     +g++     +g+++a++l+
  gi|557693661|ref|YP_008796715.1| 541 -ISTDIQGEPILLvptgGGELGGTYTPGVVAAFKLS 575
                                       .45888888887766543355555555555555555 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00017         1      13      40 .]      81     108 ..      60     108 .. 0.87
   2 !   10.9   0.0   8.6e-05      0.51       1      39 [.     109     159 ..     109     160 .. 0.88
   3 ?   -2.0   0.0      0.98   5.8e+03      29      38 ..     206     215 ..     188     217 .. 0.68
   4 ?   -0.2   0.1      0.27   1.6e+03      11      29 ..     273     293 ..     263     321 .. 0.71
   5 !    4.9   0.1    0.0068        40       1      40 []     322     375 ..     322     375 .. 0.72
   6 !   13.9   0.0   9.8e-06     0.058      11      40 .]     421     481 ..     416     481 .. 0.94
   7 !   33.9   0.1   4.9e-12   2.9e-08       1      40 []     482     522 ..     482     522 .. 0.95
   8 ?   -1.9   0.1      0.93   5.5e+03       6      32 ..     528     559 ..     523     561 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00017
                             PQQ_3  13 vnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       + ++p+v++g+vy++t+ ++++Al  +t
  gi|557693661|ref|YP_008796715.1|  81 IETTPLVVNGIVYFATPYNRVVALRSDT 108
                                       66789******************98665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.6e-05
                             PQQ_3   1 GevlWsvqlpg.pvnssp...........avdgglvyvgtgdGtlyAlDae 39 
                                       G ++W++q+     +s p            + gg +y+ ++d +++ lDa 
  gi|557693661|ref|YP_008796715.1| 109 GNLVWQYQVNMtTFTSKPywayvanqksiSYHGGAIYMMASDCSVHVLDAS 159
                                       7899***9987567778888888999999999*****************96 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.98
                             PQQ_3  29 gdGtlyAlDa 38 
                                       g G + A+D 
  gi|557693661|ref|YP_008796715.1| 206 GRGFIAAYDI 215
                                       3588888886 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.27
                             PQQ_3  11 gpvnsspavdg..glvyvgtg 29 
                                       g++++  avd+  g++y++ g
  gi|557693661|ref|YP_008796715.1| 273 GALWGLIAVDEssGVLYATVG 293
                                       466666688766688888876 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.0068
                             PQQ_3   1 GevlWsvql..pg.....pvnssp......avdgglvyvgtg.dGtlyAlDaet 40 
                                       G++lW +q+  ++     p++s        a + ++v++++     +y lDa+t
  gi|557693661|ref|YP_008796715.1| 322 GDLLWFYQTipHAlvavePGWSVIladveiAGAPRKVVMAAAkSDYIYVLDART 375
                                       8889999776444222335554447777777778999999999*********98 PP

  == domain 6  score: 13.9 bits;  conditional E-value: 9.8e-06
                             PQQ_3  11 gpvnsspavdgglvyvgtg...............................dGtlyAlDaet 40 
                                       g v s+pa+++g++yv+t                                + tlyA+D +t
  gi|557693661|ref|YP_008796715.1| 421 GGVESPPAFANGILYVATQrachriskgpvfykneviegfisqidpsiqqNSTLYAVDIRT 481
                                       5788999***************************************************998 PP

  == domain 7  score: 33.9 bits;  conditional E-value: 4.9e-12
                             PQQ_3   1 GevlWsvqlpgpvn.sspavdgglvyvgtgdGtlyAlDaet 40 
                                       G++lW+++ p +++ +s++v+gg+vy+++  G ly++Daet
  gi|557693661|ref|YP_008796715.1| 482 GRILWKFEMPNRYQaASVVVSGGVVYAVDRAGVLYMVDAET 522
                                       99*********6666999**********************9 PP

  == domain 8  score: -1.9 bits;  conditional E-value: 0.93
                             PQQ_3   6 svqlpgpvnsspavdggl.....vyvgtgdGt 32 
                                       + +l+g + +++ ++ ++     + v tg G 
  gi|557693661|ref|YP_008796715.1| 528 RISLGGLGAAGVSISTDIqgepiLLVPTGGGE 559
                                       66778867778877765333333899998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (630 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 4289.98
//
Query:       gi|557693662|ref|YP_008796716.1|  [L=304]
Description: ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-28  100.3   0.0    2.4e-28   99.4   0.0    1.5  1  ABC_tran     ABC transporter
    1.7e-10   41.2   0.1    0.00061   19.7   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00021   21.9   0.1     0.0006   20.4   0.0    1.8  2  AAA_23       AAA domain
    0.00027   21.5   1.7       0.86   10.2   0.0    3.2  3  AAA_18       AAA domain
     0.0065   16.2   0.0      0.014   15.1   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0084   15.9   0.0       0.11   12.2   0.0    2.4  2  IstB_IS21    IstB-like ATP binding protein
     0.0092   16.4   0.0      0.016   15.6   0.0    1.5  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.031   13.9   0.0    1.4  1  AAA_27       AAA domain
      0.016   15.7   0.2       0.12   12.8   0.2    2.4  1  AAA          ATPase family associated with various cellular a
      0.034   14.0   0.3        0.3   11.0   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
      0.036   14.4   1.0       0.17   12.2   0.7    2.3  1  AAA_19       AAA domain
      0.084   13.1   2.0       0.33   11.2   1.0    2.6  2  AAA_22       AAA domain
      0.093   12.8   0.1       0.78    9.8   0.0    2.5  3  AAA_14       AAA domain
        0.2   11.4   0.5        0.5   10.1   0.0    2.0  3  AAA_24       AAA domain
       0.23   10.8   0.4       0.85    9.0   0.0    2.0  3  SMC_N        RecF/RecN/SMC N terminal domain
       0.24   11.3   1.8        1.1    9.1   0.1    2.3  2  NTPase_1     NTPase


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 !   99.4   0.0   2.1e-31   2.4e-28       1     136 [.      20     159 ..      20     160 .. 0.96

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 2.1e-31
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l +vs++ ++ge +ai+G+nGaGK+tLlk+ +gll+   G+i++dg d+ + +  ++r+++g++pq++ l ++l++ 
  gi|557693662|ref|YP_008796716.1|  20 LADVSFNARKGEALAILGPNGAGKTTLLKCCLGLLD-FDGKITVDGVDVGT-NGAVARSKMGYVPQKTALHDKLRII 94 
                                       579********************************9.59***********9.99*********************77 PP

                                       HH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++           +++++ ++l+ lg  e ++++v     sLS+G+kqr++l  +ll  p++lllDEp 
  gi|557693662|ref|YP_008796716.1|  95 DEmklmarikgiRDEQRCREVLEMLGFWERRKDPV----GSLSQGMKQRLMLGFTLLAMPDVLLLDEPL 159
                                       777********999999******************....*****************************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 !   19.3   0.0   7.1e-07   0.00079       3      26 ..      34      63 ..      33     102 .. 0.76
   2 !   19.7   0.0   5.4e-07   0.00061     231     297 ..     126     189 ..     120     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.1e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl......d 26
                                      ++ GpNg+GK++LL++  +l ++      d
  gi|557693662|ref|YP_008796716.1| 34 AILGPNGAGKTTLLKCCLGLLDFdgkitvD 63
                                      699**************9998874433331 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 5.4e-07
                            AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       + p+ +lS+G+k+   +l   l a +  ++ll+DEp ++++ + + +ll  l+e +r+g  +++++H
  gi|557693662|ref|YP_008796716.1| 126 KDPVGSLSQGMKQR-LMLGFTLLAMP--DVLLLDEPLSNIDVEGQISLLNQLDEIKREGKTILISSH 189
                                       568899********.67776666666..9***********************999999********* PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.4e-07    0.0006      23      40 ..      34      51 ..      13     111 .. 0.87
   2 ?   -1.2   0.0       2.1   2.4e+03     142     189 ..     225     242 ..     158     259 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.4e-07
                            AAA_23 23 lItGpNGaGKTTildAik 40
                                      +I GpNGaGKTT+l ++ 
  gi|557693662|ref|YP_008796716.1| 34 AILGPNGAGKTTLLKCCL 51
                                      7*************9975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                            AAA_23 142 rfeefelkdkkerleelekeleeledekkllekleqekekekeleele 189
                                       ++ +                              +++++ke+   +le
  gi|557693662|ref|YP_008796716.1| 225 NKLY------------------------------IKLNDKEAVSRALE 242
                                       2222..............................22222222222222 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   0.00077      0.86       3      71 ..      35     109 ..      33     139 .. 0.77
   2 !    7.3   0.1    0.0058       6.5      51      89 ..     161     196 ..     151     230 .. 0.82
   3 ?    2.0   0.1      0.26   2.9e+02      48      97 ..     225     280 ..     210     304 .] 0.58

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00077
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf.......gvnlrdvakenglllevdpealdeskrldedkldklldaleenssal 71 
                                       + G+ G+GKttl k    +l f       gv ++ + +  ++  ++ p+++  +++l++   +kl+  ++++++ +
  gi|557693662|ref|YP_008796716.1|  35 ILGPNGAGKTTLLKCCLGLLDFdgkitvdGVDVGTNGAVARSKMGYVPQKTALHDKLRIIDEMKLMARIKGIRD-E 109
                                       89***********9886766779999999888888888888888888886667777777777777777777665.3 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0058
                            AAA_18  51 rldedkldklldaleenssaleegknlvidghlaelese 89 
                                        +d + + +ll++l+e+    +egk+++i++h++ +   
  gi|557693662|ref|YP_008796716.1| 161 NIDVEGQISLLNQLDEIK---REGKTILISSHIVGMGNV 196
                                       578889999*******96...6***********998765 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.26
                            AAA_18  48 eskrldedkldklldaleenssaleegknlvidghlaele.seaakdikk.......v 97 
                                       +++ ++ +  +++++alee    +++g+++ ++   ++l+ + + +d+ +        
  gi|557693662|ref|YP_008796716.1| 225 NKLYIKLNDKEAVSRALEEK--LMQQGDVYAVQRMDEWLIvECESRDKARvisivldS 280
                                       55556666667777777776..378888888887777777333334433355644440 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   0.0   1.3e-05     0.014      20      40 ..      28      48 ..      16      60 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                            AAA_29 20 dlkg.atlltGpsGsGKSTllD 40
                                      + kg a  + Gp+G+GK+Tll 
  gi|557693662|ref|YP_008796716.1| 28 R-KGeALAILGPNGAGKTTLLK 48
                                      3.456999************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 !   12.2   0.0   9.9e-05      0.11      36      68 ..      18      52 ..       5     100 .. 0.83
   2 ?    0.8   0.0      0.31   3.5e+02     102     148 ..     143     189 ..     121     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.9e-05
                         IstB_IS21 36 keLatlsfie.kkenivllGpsGvGKshl.aialg 68
                                      ++La  sf + k e++++lGp G+GK+ l  + lg
  gi|557693662|ref|YP_008796716.1| 18 EALADVSFNArKGEALAILGPNGAGKTTLlKCCLG 52
                                      588999996516699***********865267777 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.31
                         IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfeviek.ryerrsiiitsn 148
                                         + l+++d+l+lD+  l ++d + +  l++ +++ + e ++i+i+s 
  gi|557693662|ref|YP_008796716.1| 143 GFTLLAMPDVLLLDEP-LSNIDVEGQISLLNQLDEiKREGKTILISSH 189
                                       556788899****994.7888888777777777662456666666664 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   1.5e-05     0.016      19      51 ..      27      57 ..      15     159 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                            AAA_16 19 vrsgrpelvllsGesGvGKsslvrellralekd 51
                                      +r+  +e++ + G+ G GK++l++++l  l  d
  gi|557693662|ref|YP_008796716.1| 27 ARK--GEALAILGPNGAGKTTLLKCCLGLLDFD 57
                                      333..489*****************99755555 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   2.8e-05     0.031       9      50 ..      12      54 ..      10      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                            AAA_27  9 eryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      +ryGk +    ++f+a + +   i+GpN AGK+t+l+    ll
  gi|557693662|ref|YP_008796716.1| 12 KRYGKHEALaDVSFNARKGEALAILGPNGAGKTTLLKCCLGLL 54
                                      588888764379999988888899************9887776 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 ?   12.8   0.2    0.0001      0.12       3      99 ..      35     128 ..      33     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                                       EESSTTSSHHHHHHHHHHHHTHEE.EEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCC CS
                               AAA   3 lyGppGtGKTllakavakelgvef.leisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgse 78 
                                       + Gp G GKT+l k     l+++  ++++g ++   + g+ +++  +++ +  +    +  +iDE+  +a+ + g  
  gi|557693662|ref|YP_008796716.1|  35 ILGPNGAGKTTLLKCCLGLLDFDGkITVDGVDVG--TNGAVARSKMGYVPQKTALH-DKLRIIDEMKLMARIK-GIR 107
                                       68******************98755999999999..44554444444444322332.4888999999999998.778 PP

                                       CHHHHHHHHHHHHHHHHTTTS CS
                               AAA  79 seeeervvnqLlteldgvkkk 99 
                                       +e++ r v ++l ++++ k+ 
  gi|557693662|ref|YP_008796716.1| 108 DEQRCREVLEMLGFWERRKDP 128
                                       888888888888888888775 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00027       0.3      86     120 ..      16      51 ..       6      85 .. 0.83
   2 ?    0.8   0.1      0.35     4e+02      45      97 ..     195     245 ..     153     253 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                                       ++e+l++++ + ++ +  +++G+ G+GK+tL++  l
  gi|557693662|ref|YP_008796716.1|  16 KHEALADVSFNARKgEALAILGPNGAGKTTLLKCCL 51 
                                       56777788877777799**************98765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.35
                                       TT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                       RsgA_GTPase  45 kgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                       + i+ v+vlnK  ++   e ++e+ ++l+  +   ++++ k ++  ++l+e+l
  gi|557693662|ref|YP_008796716.1| 195 NVIDRVLVLNKGHVAAFGE-INEVLSRLRVRNKLYIKLNDK-EAVSRALEEKL 245
                                       4567788999998888888.888888888777666666555.44455666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.7   0.00016      0.17       7     125 ..      27     174 ..      21     192 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelre...rlaalgaeatTiHrlal... 77 
                                       a k + l+++++ G GKT++lk+ + ll   g++ ++ + + +    A +++     ++ al  + +      +   
  gi|557693662|ref|YP_008796716.1|  27 ARKGEALAILGPNGAGKTTLLKCCLGLLDFDGKITVDGVDVGTNGAVARSKMGYvpqKT-ALHDKLR------Iide 96 
                                       66788999*****************9999999888888887777777777776421122.2222222......1222 PP

                            AAA_19  78 ......................ldfddlltealelle.........eaeeekklqeeellivDE.fqdvd.elqyrL 121
                                                             l+f ++ +++++ l               + l   ++l+ DE  +++d e q +L
  gi|557693662|ref|YP_008796716.1|  97 mklmarikgirdeqrcrevlemLGFWERRKDPVGSLSqgmkqrlmlG---FTLLAMPDVLLLDEpLSNIDvEGQISL 170
                                       22344455555555555555553333333333333334333322110...134445557777775577777777777 PP

                            AAA_19 122 lkal 125
                                       l++l
  gi|557693662|ref|YP_008796716.1| 171 LNQL 174
                                       7766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   0.00029      0.33       5      29 ..      30      54 ..      27     200 .. 0.87
   2 ?   -1.6   0.0       2.7     3e+03      82      91 ..     241     250 ..     212     292 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                         l++ G+ G+GKTtll+  l  l
  gi|557693662|ref|YP_008796716.1| 30 GEALAILGPNGAGKTTLLKCCLGLL 54
                                      56799*************9776655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                            AAA_22  82 leqalrarav 91 
                                       le+ l ++++
  gi|557693662|ref|YP_008796716.1| 241 LEEKLMQQGD 250
                                       3333333333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0007      0.78       3      74 ..      31      98 ..      29     115 .. 0.61
   2 ?   -2.0   0.0         3   3.4e+03      10      21 ..     177     188 ..     164     204 .. 0.80
   3 ?   -0.9   0.0       1.4   1.5e+03      31      58 ..     224     247 ..     210     279 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0007
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiq 74
                                      ++l+i G+  +GKTtllk ++  ll + +  + ++  d  +  +    + + ++ +k ++ ++++ ++DE++
  gi|557693662|ref|YP_008796716.1| 31 EALAILGPNGAGKTTLLKCCL-GLL-DFDGKITVDGVDVGTNGAVAR-SKMGYVPQK-TALHDKLRIIDEMK 98
                                      7899************98776.444.455555555444444332212.234444444.22345666666665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3
                            AAA_14  10 aRrvGKTtllkq 21 
                                       ++r GKT l+  
  gi|557693662|ref|YP_008796716.1| 177 IKREGKTILISS 188
                                       467788888765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.4
                            AAA_14  31 esilyinldderdkkladpekllelile 58 
                                       ++ lyi+l+d++  ++a +e     +++
  gi|557693662|ref|YP_008796716.1| 224 RNKLYIKLNDKEAVSRALEE----KLMQ 247
                                       56677777776665544443....2222 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00045       0.5       5      22 ..      33      50 ..      29     108 .. 0.85
   2 ?   -3.7   0.0       7.2     8e+03     113     162 ..     195     243 ..     193     247 .. 0.61
   3 ?   -2.0   0.1       2.2   2.5e+03      60      85 ..     267     292 ..     233     297 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00045
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++i Gp+g+GKTtl+k  
  gi|557693662|ref|YP_008796716.1| 33 LAILGPNGAGKTTLLKCC 50
                                      79************9976 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.2
                            AAA_24 113 rllkklqelrk.nvifiahektrkdedpegeakytrlepklgkktanelke 162
                                       ++++++  l+k +v + ++  +     + ++  + +++++ ++ ++++l+e
  gi|557693662|ref|YP_008796716.1| 195 NVIDRVLVLNKgHVAAFGEINEVLSRLRVRN--KLYIKLNDKEAVSRALEE 243
                                       5666666666667766666666666665555..566666666666666665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.2
                            AAA_24  60 aaeladyktlviDtideleelclaev 85 
                                       ++++a+  ++v+D+  +l +++++ v
  gi|557693662|ref|YP_008796716.1| 267 SRDKARVISIVLDSGYQLADIVSEAV 292
                                       56677777888888888888887765 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 ?    9.0   0.0   0.00075      0.85      26      43 ..      32      49 ..      15      59 .. 0.83
   2 ?   -1.8   0.0       1.5   1.7e+03     162     204 ..     153     196 ..     111     209 .. 0.70
   3 ?   -2.0   0.1       1.8     2e+03     101     130 ..     219     248 ..     171     249 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00075
                                      EEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldA 43
                                        ai+GpNG+GK+ ll  
  gi|557693662|ref|YP_008796716.1| 32 ALAILGPNGAGKTTLLKC 49
                                      568**********99875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                                       EEECTTTTTS-HHHHHHHHHHHHHHCTTSEEE.EE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N 162 yllDeidaaLDeknvkkvaellkeksknaQfi.vislreemlek 204
                                        llDe  +++D +    + + l+e + +   i + s+  +m + 
  gi|557693662|ref|YP_008796716.1| 153 LLLDEPLSNIDVEGQISLLNQLDEIKREGKTIlISSHIVGMGNV 196
                                       57888888888888888888888766665444044555555555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.8
                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesa 130
                                        r+   ++  +k+n+ke+ ++ ++e l ++
  gi|557693662|ref|YP_008796716.1| 219 SRLRVRNKLYIKLNDKEAVSRALEEKLMQQ 248
                                       333444455778888888888887777665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1     0.001       1.1       3      33 ..      34      65 ..      32      81 .. 0.83
   2 ?    1.4   0.2      0.23   2.6e+02      72     134 ..     225     290 ..     199     304 .] 0.70

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.001
                                      EEE--TTSSHHHHHHHHHHHH...G.GGEEEE CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssg.vkvgGf 33
                                      +i Gp G GKtTl+k  l ll+ +g ++v+G+
  gi|557693662|ref|YP_008796716.1| 34 AILGPNGAGKTTLLKCCLGLLDFDGkITVDGV 65
                                      688*************9999987642677776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.23
                                       TTEEE-HHHHHHHHHHHHHHHH.HHH-...EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--S CS
                          NTPase_1  72 gkyvvdvesfeelalealrkal.sead...viviDEiGkmElkskkfkeaveevLksekpvlavihr 134
                                        k ++++++ e + ++al+++l ++ d   v  +DE    E +s+  ++ +  vL+s+ ++  ++ +
  gi|557693662|ref|YP_008796716.1| 225 NKLYIKLNDKEAV-SRALEEKLmQQGDvyaVQRMDEWLIVECESRDKARVISIVLDSGYQLADIVSE 290
                                       4667777775555.67777766577775555567999999999999999999999988877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2072.81
//
Query:       gi|557693663|ref|YP_008796717.1|  [L=275]
Description: ABC-2 type transport system permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   63.8  30.7    3.8e-16   59.2  30.7    2.1  1  ABC2_membrane_2  ABC-2 family transporter protein
    3.5e-08   33.6  17.5    3.5e-08   33.6  17.5    2.1  2  ABC2_membrane_4  ABC-2 family transporter protein
    2.4e-07   30.2  31.6    2.4e-07   30.2  31.6    1.5  1  ABC2_membrane_3  ABC-2 family transporter protein
    2.1e-05   24.0  25.9    2.1e-05   24.0  25.9    2.0  2  ABC2_membrane    ABC-2 type transporter
  ------ inclusion threshold ------
        4.7    6.7  30.6      0.009   15.6  16.9    2.5  3  ABC2_membrane_5  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 !   59.2  30.7     1e-19   3.8e-16      77     283 ..      59     269 ..       6     274 .. 0.76

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 1e-19
                   ABC2_membrane_2  77 vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalg 153
                                       ++++ + ++p++ + ++a++i++Eke+g l+ +Ls+PvsR ++l++K+ g +++   + + ++ ++l+  a  l++g
  gi|557693663|ref|YP_008796717.1|  59 LMALSFPFLPLLSLPLAATSIVDEKESGLLEYMLSNPVSRLSYLMSKLAGLFLS---TTLVVVGGYLI--AAFLSYG 130
                                       5678899***********************************************...99999999999..6666788 PP

                   ABC2_membrane_2 154 ivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqein 230
                                       i ++ +  +l ++ s +ll ++ +l lgll+S+v++ + +a+ + +++++++ +l++i ++ ++   ag+a+   i 
  gi|557693663|ref|YP_008796717.1| 131 IRINQMGAILPLLGSAMLLNTI-MLLLGLLISIVSKRKITAMMIGIFFWFMFTVLSDIGSLSILVSIAGAAP---IV 203
                                       8888877777777777666655.89***********************************************...88 PP

                   ABC2_membrane_2 231 dflsllsptsayntllneilagsdlna.............lgstatnllilllllavllvlgyvlF 283
                                       +fl+ l+p+ a ++l    + + ++ +              g+  + l + l +   ll+l++ +F
  gi|557693663|ref|YP_008796717.1| 204 LFLTALNPIEAARLLGIYGTRNVGFTElgsiglilrqligEGAPLFILSVQLMWVGLLLILCINIF 269
                                       888888888887776544444444444666666666653322222222233455555556665555 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 !   33.6  17.5   9.8e-12   3.5e-08      14     177 ..      23     179 ..      18     185 .. 0.70
   2 ?   -1.6   2.1      0.64   2.3e+03     140     164 ..     248     272 ..     195     275 .] 0.66

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 9.8e-12
                   ABC2_membrane_4  14 ivwllvlaallvpl..lallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiP 88 
                                       iv+ lv+ +l + +  ++l+  ++l +++l+    y+ + ++   + +lpl+   +a+++i +E++++ l ++l  P
  gi|557693663|ref|YP_008796717.1|  23 IVYTLVFFMLAINVpmIVLISARYLPPDYLE---AYL-TGLMALSFPFLPLLSLPLAATSIVDEKESGLLEYMLSNP 95 
                                       5666666555554410555555666655554...333.23444445689999999********************** PP

                   ABC2_membrane_4  89 vsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfs.vklvlellkkclelgllvffavlpiialvllkks 164
                                       vsr ++l++Kl+ l+l + l+++  +l   ++a ls +++++ ++++l ll   ++l+ +++   l  ++++++ k 
  gi|557693663|ref|YP_008796717.1|  96 VSRLSYLMSKLAGLFLSTTLVVVGGYL---IAAFLSYGIRINqMGAILPLLGSAMLLNTIML---LLGLLISIVSKR 166
                                       ***************998888776665...45556666665425667788887776666555...444578888888 PP

                   ABC2_membrane_4 165 yvlpliltlvyti 177
                                        ++++++ +++ +
  gi|557693663|ref|YP_008796717.1| 167 KITAMMIGIFFWF 179
                                       8888888888766 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.64
                   ABC2_membrane_4 140 kclelgllvffavlpiialvllkks 164
                                        +++ + l+++ +l i+++ ++ +s
  gi|557693663|ref|YP_008796717.1| 248 LFILSVQLMWVGLLLILCINIFIRS 272
                                       3444445555555666666555554 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 !   30.2  31.6   6.6e-11   2.4e-07     154     325 ..      50     250 ..      31     271 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 6.6e-11
                   ABC2_membrane_3 154 eelsnvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlll.ill.. 226
                                       ++l+ +   l++  + +++++  ++ +a+siv Ekes+++e +l+ +vs+l+y++sk+ g+fl   l+++  +l+  
  gi|557693663|ref|YP_008796717.1|  50 DYLEAYLTGLMAlSFPFLPLLSLPL-AATSIVDEKESGLLEYMLSNPVSRLSYLMSKLAGLFLSTTLVVVGgYLIaa 125
                                       5666777777776777888888888.7889**********************************9999964233322 PP

                   ABC2_membrane_3 227 .lafglgipfgnlglll.llfllfgl..ayialgyllsslfknsetaqilifivilllsgf..fgglfpledlpsal 297
                                        l +g  i ++++g++l ll   ++l  +++ lg+l+s ++k+  ta+ + +++++++ ++  +g l +l ++++ +
  gi|557693663|ref|YP_008796717.1| 126 fLSYG--IRINQMGAILpLLGSAMLLntIMLLLGLLISIVSKRKITAMMIGIFFWFMFTVLsdIGSLSILVSIAG-A 199
                                       24777..9999999999966666666669999***************9999999984444433222233334444.5 PP

                   ABC2_membrane_3 298 kwifsiiPffapglgllrli.tgdplwe........................i 325
                                       + i  ++    p+++   l+ +g+   +                        i
  gi|557693663|ref|YP_008796717.1| 200 APIVLFLTALNPIEAARLLGiYGT--RNvgftelgsiglilrqligegaplfI 250
                                       556666666666666655533444..223344566655655555555555532 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0  25.9     6e-09   2.1e-05      32     176 ..      21     185 ..       4     215 .. 0.76
   2 ?   -2.9   0.5         1   3.7e+03      52      59 ..     257     264 ..     231     272 .. 0.50

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6e-09
                     ABC2_membrane  32 lalvfgtvfgnlg.nsedglnr....................pgllffsvlflaf..saltsvapvferergvlere 85 
                                       + +v+++vf+ l  n                            gl++ s+ fl +  + l+++++v e+e g+le +
  gi|557693663|ref|YP_008796717.1|  21 WVIVYTLVFFMLAiN------VpmivlisarylppdyleaylTGLMALSFPFLPLlsLPLAATSIVDEKESGLLEYM 91 
                                       455666666643321......1222333445666666777786666666666554116678888999********** PP

                     ABC2_membrane  86 lvsplyslsayvlakvlvelpvsllqalifll.ivyflvgldls...rfflflllllltalaasslgllisalapsf 158
                                       l++p+ s+ +y+++k+++ ++ ++l+++   l  +++  g++++   +++ +l  ++l+  +++ lgllis++++  
  gi|557693663|ref|YP_008796717.1|  92 LSNPV-SRLSYLMSKLAGLFLSTTLVVVGGYLiAAFLSYGIRINqmgAILPLLGSAMLLNTIMLLLGLLISIVSKRK 167
                                       *****.**********99966666666655550555557****9865559999999********************* PP

                     ABC2_membrane 159 edasqlaslvllplllls 176
                                        +a++++ ++ +++++ls
  gi|557693663|ref|YP_008796717.1| 168 ITAMMIGIFFWFMFTVLS 185
                                       ***************999 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1
                     ABC2_membrane  52 rpgllffs 59 
                                        +gll ++
  gi|557693663|ref|YP_008796717.1| 257 WVGLLLIL 264
                                       12222222 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 ?    1.3   1.7     0.061   2.2e+02     110     155 ..      17      67 ..       1      73 [. 0.56
   2 ?   15.6  16.9   2.5e-06     0.009      38     186 ..      62     208 ..      51     215 .. 0.61
   3 ?   -1.4   0.5       0.4   1.4e+03     182     194 ..     256     264 ..     230     274 .. 0.49

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.061
                   ABC2_membrane_5 110 n....vtise.vllsiliglvialiflaivlPlyfkfgvekgrivliiiif 155
                                            v++ + v+++++i + ++++++a +lP  ++  + +g ++l + ++
  gi|557693663|ref|YP_008796717.1|  17 LrarwVIVYTlVFFMLAINVPMIVLISARYLPPDYLEAYLTGLMALSFPFL 67 
                                       333333333314444555566777778888888887777777777666665 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.5e-06
                   ABC2_membrane_5  38 lifsilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitlllliiavl.ikgnvti 113
                                       l f +l+ ++s  l+ t++  ++ s+   y l+ Pv+r  +  sK  ++++ ++++++ ++l+++  ++ i+ n ++
  gi|557693663|ref|YP_008796717.1|  62 LSFPFLP-LLSLPLAATSIVDEKESGLLEYMLSNPVSRLSYLMSKLAGLFLSTTLVVVGGYLIAAFLSYgIRIN-QM 136
                                       3333333.3344445567776778***********************************999986544414444.33 PP

                   ABC2_membrane_5 114 sevllsiliglvialiflaivlPlyfkfgvekgrivliiiifgiif.llvaifslsklelslidlsnyilliil 186
                                         +l  +  + ++ +i+l + l + +  + +k++ ++i i+f ++f +l+ i s  ++ +s+ +   ++l++ +
  gi|557693663|ref|YP_008796717.1| 137 GAILPLLGSAMLLNTIMLLLGLLISIVSK-RKITAMMIGIFFWFMFtVLSDIGS-LSILVSIAGAAPIVLFLTA 208
                                       44445544444444444444444444444.555544444444444423333333.3456777777777777665 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.4
                   ABC2_membrane_5 182 lliillviillli 194
                                       ++++ll+    ++
  gi|557693663|ref|YP_008796717.1| 256 MWVGLLL----IL 264
                                       1111111....11 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); 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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1888.29
//
Query:       gi|557693664|ref|YP_008796718.1|  [L=662]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-18   63.6   0.4    5.4e-06   26.1   0.0    6.5  6  PQQ       PQQ enzyme repeat
    4.1e-17   62.6   0.0    3.3e-05   23.6   0.0    3.4  3  PQQ_2     PQQ-like domain
      3e-07   30.7   6.4     0.0088   16.5   0.6    5.3  5  PQQ_3     PQQ-like domain
  ------ inclusion threshold ------
       0.12   12.4   0.3       0.33   11.0   0.3    1.7  1  SBBP      Beta-propeller repeat
       0.24   11.0   2.7       0.12   11.9   0.3    1.6  2  DUF5336   Family of unknown function (DUF5336)
        5.2    7.1   4.6          1    9.4   0.5    1.9  2  DUF4083   Domain of unknown function (DUF4083)


Domain annotation for each model (and alignments):
>> PQQ  PQQ enzyme repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.031        94       3      33 ..     103     133 ..     101     138 .. 0.85
   2 ?    4.0   0.0     0.017        51       4      23 ..     161     180 ..     159     185 .. 0.88
   3 !    7.2   0.0    0.0017         5      12      35 ..     350     373 ..     346     376 .. 0.83
   4 !   26.1   0.0   1.8e-09   5.4e-06       1      29 [.     385     413 ..     385     419 .. 0.87
   5 !   13.0   0.0   2.4e-05     0.073      12      31 ..     500     519 ..     495     524 .. 0.89
   6 ?    0.7   0.0      0.19   5.7e+02       3      28 ..     531     556 ..     529     564 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.031
                                       EEEEETTSEEEEEETTTCCEEEEEESSSCGS CS
                               PQQ   3 vylgsadGylyAlDadTGkvlWrfktggpvl 33 
                                        y+ ++++ +y +D++ Gk+ W+ ++++p+ 
  gi|557693664|ref|YP_008796718.1| 103 GYAVTNGYLVYSFDLRGGKIFWTIELQPPPA 133
                                       577799999**************99999875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.017
                                       EEEETTSEEEEEETTTCCEE CS
                               PQQ   4 ylgsadGylyAlDadTGkvl 23 
                                       ++g+ + ++y lD  TG+++
  gi|557693664|ref|YP_008796718.1| 161 VVGTSWQRIYLLDSFTGRLV 180
                                       799**********9999875 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0017
                                       EEEEETTTCCEEEEEESSSCGSSE CS
                               PQQ  12 lyAlDadTGkvlWrfktggpvlsl 35 
                                       ++Al ++TG+vlW f++ +++++ 
  gi|557693664|ref|YP_008796718.1| 350 VLALKVETGEVLWLFQAIPHDVWG 373
                                       889999*******99988888776 PP

  == domain 4  score: 26.1 bits;  conditional E-value: 1.8e-09
                                       TEEEEEETTSEEEEEETTTCCEEEEEESS CS
                               PQQ   1 gvvylgsadGylyAlDadTGkvlWrfktg 29 
                                       ++v + + +G+lyAlD dTG++lW f+++
  gi|557693664|ref|YP_008796718.1| 385 NTVLALCGNGVLYALDKDTGQMLWMFEPP 413
                                       577788******************99987 PP

  == domain 5  score: 13.0 bits;  conditional E-value: 2.4e-05
                                       EEEEETTTCCEEEEEESSSC CS
                               PQQ  12 lyAlDadTGkvlWrfktggp 31 
                                       ly +D++TG++lW++k++g+
  gi|557693664|ref|YP_008796718.1| 500 LYSVDLSTGRLLWEKKLEGV 519
                                       899**************997 PP

  == domain 6  score: 0.7 bits;  conditional E-value: 0.19
                                       EEEEETTSEEEEEETTTCCEEEEEES CS
                               PQQ   3 vylgsadGylyAlDadTGkvlWrfkt 28 
                                       v + +    ly +  ++G+++ ++++
  gi|557693664|ref|YP_008796718.1| 531 VLVQTSSSGLYIFSEKDGEIKYSKPA 556
                                       4444888889***********98875 PP

>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   1.3e-05      0.04       4      67 ..     111     188 ..      90     212 .. 0.75
   2 !   23.6   0.0   1.1e-08   3.3e-05       3      71 ..     348     419 ..     346     437 .. 0.78
   3 !   21.3   0.0   5.6e-08   0.00017      38     106 ..     488     557 ..     453     584 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                             PQQ_2   4 vvsaldaatGaelWrvdlarp...............lgggvsravlsggtlfvatgggrlvaldaatGkvlWettle 65 
                                        v+ +d + G++ W+ +l++p                +  + +a  s+  l+v+t   r++ ld +tG+++  ++l 
  gi|557693664|ref|YP_008796718.1| 111 LVYSFDLRGGKIFWTIELQPPpalnpsvsserlghiYQVLLVKAG-SDELLVVGTSWQRIYLLDSFTGRLVHAVDLL 186
                                       368888888888888888774455555566666666566666666.8888888888888888888888888777775 PP

                             PQQ_2  66 gp 67 
                                        p
  gi|557693664|ref|YP_008796718.1| 187 TP 188
                                       55 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 1.1e-08
                             PQQ_2   3 gvvsaldaatGaelWrv.....dl.arplgggvsravlsggtlfvatgggrlvaldaatGkvlWettlegpvvga 71 
                                       ++v al  +tG++lW +     d+ + + +ggv   +  g+t+++  g g l+ald+ tG+ lW +++++ + g+
  gi|557693664|ref|YP_008796718.1| 348 SSVLALKVETGEVLWLFqaiphDVwGYGCNGGV--SL-VGNTVLALCGNGVLYALDKDTGQMLWMFEPPVNTGGN 419
                                       678899999999999996665533255788888..66.8888888889999999999999999999987766655 PP

  == domain 3  score: 21.3 bits;  conditional E-value: 5.6e-08
                             PQQ_2  38 tlfva..tgggrlvaldaatGkvlWettlegpvvgaplvaegrvvvvasdgqlialdaedGkrlWstqqrs 106
                                        +f+   +    l+++d +tG++lWe++leg   +    a + v+v++s   l+ ++ +dG+ ++s + + 
  gi|557693664|ref|YP_008796718.1| 488 NVFSQsqQSNLMLYSVDLSTGRLLWEKKLEGVGSSFISAASDIVLVQTSSSGLYIFSEKDGEIKYS-KPAI 557
                                       333331222223556666777777777776654444566666666666666777777777777666.4444 PP

>> PQQ_3  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       3.7   1.1e+04      25      37 ..     104     116 ..      81     118 .. 0.61
   2 !    5.6   0.0    0.0079        24       3      37 ..     122     173 ..     120     176 .. 0.69
   3 ?    0.2   0.0       0.4   1.2e+03      17      29 ..     307     329 ..     295     345 .. 0.70
   4 !   16.5   0.6     3e-06    0.0088       1      40 []     358     403 ..     358     403 .. 0.79
   5 !    6.6   0.0    0.0037        11       1      36 [.     508     543 ..     508     547 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.7
                             PQQ_3  25 yvgtgdGtlyAlD 37 
                                       y++t    +y++D
  gi|557693664|ref|YP_008796718.1| 104 YAVTNGYLVYSFD 116
                                       5555544455555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0079
                             PQQ_3   3 vlWsvql..pgpvnssp...............avdgglvyvgtgdGtlyAlD 37 
                                       + W+ +l  p ++n s+               a ++ l++vgt+  ++y lD
  gi|557693664|ref|YP_008796718.1| 122 IFWTIELqpPPALNPSVsserlghiyqvllvkAGSDELLVVGTSWQRIYLLD 173
                                       55666554223444444666666666667777889**************999 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.4
                             PQQ_3  17 p........avdg..glvyvgtg 29 
                                       +        a+d+  g+vyvg +
  gi|557693664|ref|YP_008796718.1| 307 VmaswmngwALDEdaGVVYVGVS 329
                                       35555555566653489***976 PP

  == domain 4  score: 16.5 bits;  conditional E-value: 3e-06
                             PQQ_3   1 GevlWsv.....ql.pgpvnsspavdgglvyvgtgdGtlyAlDaet 40 
                                       GevlW +     ++ ++  n+++ ++g++v + +g+G lyAlD +t
  gi|557693664|ref|YP_008796718.1| 358 GEVLWLFqaiphDVwGYGCNGGVSLVGNTVLALCGNGVLYALDKDT 403
                                       78888885555544334555888********************987 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.0037
                             PQQ_3   1 GevlWsvqlpgpvnsspavdgglvyvgtgdGtlyAl 36 
                                       G++lW+++l g + s   ++ ++v v t+  +ly +
  gi|557693664|ref|YP_008796718.1| 508 GRLLWEKKLEGVGSSFISAASDIVLVQTSSSGLYIF 543
                                       99********96666669999999999999988865 PP

>> SBBP  Beta-propeller repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00011      0.33      15      32 ..     203     220 ..     197     222 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                              SBBP  15 gngIavDsnGNiYvtGsT 32 
                                       + +Ia Ds  Ni +tGsT
  gi|557693664|ref|YP_008796718.1| 203 PVNIAYDSRRNILITGST 220
                                       679**************9 PP

>> DUF5336  Family of unknown function (DUF5336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.4   4.2e+03     102     121 ..      19      38 ..      10      47 .. 0.65
   2 ?   11.9   0.3   4.2e-05      0.12      88     154 ..     587     651 ..     561     653 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.4
                           DUF5336 102 ktavaAvlsvlgfLlvlaev 121
                                        +a+a vlsv+ +L + +  
  gi|557693664|ref|YP_008796718.1|  19 MRALALVLSVIMLLTMFSSA 38 
                                       56777777777666665544 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.2e-05
                           DUF5336  88 gLlAgvslLPkqksktavaAvlsvlgfLlvlaevinap.egvsiawglwvvlvlallqaaaAvaaLLf 154
                                       g +A   lLPk  ++++ ++v+     +     +++++ + ++ + g wv+ v++++ aa A++ L f
  gi|557693664|ref|YP_008796718.1| 587 GYIASFRLLPKNMEQNGTVSVITEHTTIT---RTVTMQlNIADFSGGGWVLYVIVVVLAASALTSLFF 651
                                       7899************9998877655544...333333134589999999999999999999999987 PP

>> DUF4083  Domain of unknown function (DUF4083)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.3       1.5   4.6e+03      16      30 ..      22      36 ..       8      42 .. 0.67
   2 ?    9.4   0.5   0.00034         1       3      29 ..     630     656 ..     630     662 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                           DUF4083 16 lllvfsftlfiRrvv 30
                                      l+lv s+++++   +
  gi|557693664|ref|YP_008796718.1| 22 LALVLSVIMLLTMFS 36
                                      566667766665544 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00034
                           DUF4083   3 gdliyliivivLilllvfsftlfiRrv 29 
                                       g ++ ++iv+vL    + s+ +++Rr 
  gi|557693664|ref|YP_008796718.1| 630 GGWVLYVIVVVLAASALTSLFFVLRRS 656
                                       66999********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (662 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 4548.37
//
Query:       gi|557693665|ref|YP_008796719.1|  [L=130]
Description: hypothetical protein CSUB_C0228 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   35.6   0.0    8.7e-09   35.4   0.0    1.1  1  Cupredoxin_1  Cupredoxin-like domain
     0.0014   19.0   0.0      0.024   15.1   0.0    2.2  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
  ------ inclusion threshold ------
      0.011   15.9   0.0      0.016   15.3   0.0    1.3  1  SPRY          SPRY domain
      0.029   14.0   0.0      0.034   13.8   0.0    1.1  1  Pox_VP8_L4R   Poxvirus nucleic acid binding protein VP8/L4R


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   1.9e-12   8.7e-09       3      93 ..      18     109 ..       7     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.9e-12
                      Cupredoxin_1   3 aalavllllsskaaaaaektveitvkdggfePskievkagekvklkiknkdktpeefesed..lgeekvlapgkttt 77 
                                       +al+ + ++  ++++a+ekt ++ + +  f+P++i+v  + kv + ++n+++ p++ +  +   +   vl pg++++
  gi|557693665|ref|YP_008796719.1|  18 TALFTI-FFMVEQSEAGEKTTTVYMYEYYFSPDEITVGRNVKVLIVFVNNGTYPHNAYLSQekKDLAPVLYPGDSAS 93 
                                       344444.444556788999***********************************98888874466779********* PP

                      Cupredoxin_1  78 itiaplkpGeYeftcd 93 
                                       +++   ++G +e  c 
  gi|557693665|ref|YP_008796719.1|  94 VELFFRERGVFEVLCT 109
                                       ************9997 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 !   15.1   0.0   5.4e-06     0.024      12      98 ..      44     129 ..      33     130 .] 0.74

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.4e-06
                                       SEEESSEEEEETTEEE..EEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEE..SSEEEEEEE CS
                       Copper-bind  12 lqFetkeitvkkgekv..tfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfd..eagtYkffC 84 
                                         F++ eitv    kv  +fvn+  ++HN  l++++     d   +       +  +G++ sv++   e g +++ C
  gi|557693665|ref|YP_008796719.1|  44 YYFSPDEITVGRNVKVliVFVNNGTYPHNAYLSQEKK----D---L-----APVLYPGDSASVELFfrERGVFEVLC 108
                                       5699999999988885337999999****99998873....1...1.....23455677777765544999999999 PP

                                       T.....T..TTTTTSEEEEEE CS
                       Copper-bind  85 s.....P..HaaagMkgkvtv 98 
                                       +     P  H+ +gM++k++v
  gi|557693665|ref|YP_008796719.1| 109 TvsypaPvsHYELGMRAKIVV 129
                                       555634699999999999998 PP

>> SPRY  SPRY domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   3.6e-06     0.016      62     118 ..      44      99 ..      17     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.6e-06
                                       SSSTTSEEEEEEETTTTEEEEEETTEEEEEEEESTTTSSEEEEEEE.STCEEEEESS CS
                              SPRY  62 paregdviGvalDleegelsFtkngknlgvaFrnvrgaelfPvvslgngaslkinlg 118
                                        + ++d i v+ +++   + F +ng++  +a+ + +++ l Pv + g  as++  + 
  gi|557693665|ref|YP_008796719.1|  44 YYFSPDEITVGRNVK-VLIVFVNNGTYPHNAYLSQEKKDLAPVLYPGDSASVELFFR 99 
                                       3448999******99.89*****************************9999998775 PP

>> Pox_VP8_L4R  Poxvirus nucleic acid binding protein VP8/L4R
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   7.5e-06     0.034      25     120 ..       7     107 ..       4     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.5e-06
                       Pox_VP8_L4R  25 lelvqtetitGvvlttvynirknLgleeekltieaiekyy......LdknndvltLivnntdlselgvprkksrrkk 95 
                                       l lv++ ++t  +l t++ + ++ + +e++ t+   e y+      + +n+ vl + vnn    +  ++  ++++  
  gi|557693665|ref|YP_008796719.1|   7 LMLVAAAAVTATALFTIFFMVEQSEAGEKTTTVYMYEYYFspdeitVGRNVKVLIVFVNNGTYPHN-AYLSQEKKDL 82 
                                       56899999999988888888888888899999998888884433333468999********99998.6677777779 PP

                       Pox_VP8_L4R  96 npvifrkgsaPlllvfesrkkvdiy 120
                                        pv++   sa + l f+ r   +++
  gi|557693665|ref|YP_008796719.1|  83 APVLYPGDSASVELFFRERGVFEVL 107
                                       ****************999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 940.18
//
Query:       gi|557693666|ref|YP_008796720.1|  [L=138]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   54.6  23.9    1.4e-14   54.4  23.9    1.0  1  EamA      EamA-like transporter family
    0.00013   21.3   5.7    0.00015   21.1   5.7    1.2  1  UAA       UAA transporter family
  ------ inclusion threshold ------
      0.011   15.8   5.7      0.019   15.0   5.7    1.6  1  TMEM234   Putative transmembrane family 234
          9    4.5  16.9         11    4.2  16.9    1.0  1  DUF2070   Predicted membrane protein (DUF2070)


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 !   54.4  23.9   3.1e-18   1.4e-14       2     136 ..       4     136 ..       3     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 3.1e-18
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       +++ ++ll  ++w++++v+++++ + +     ++v  +   i+ l+++  ++ +   +  ++w++ ll g+lg++ +
  gi|557693666|ref|YP_008796720.1|   4 RWVAVVLLTLFIWGVWGVVARVGASALGWRDSAAVAAIGHMIVSLMFIISSRAQV-IPASQAWFAALLAGALGFL-G 78 
                                       578899*****************99998888888888766666666666666666.5556667777777776655.5 PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                        ++f+ al   ++s+++++tsl P++tlils+l+++e ltl+q++g++++l +++li+
  gi|557693666|ref|YP_008796720.1|  79 AVAFYLALDLNPSSIVVVATSLYPLVTLILSYLFFNEALTLRQIIGVAFALTALVLIS 136
                                       59******************************************************97 PP

>> UAA  UAA transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   5.7   3.4e-08   0.00015     215     297 ..      52     134 ..      12     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.4e-08
                               UAA 215 esedvallslpsklfylllnvltqyvcikgVlilisefgaltvtlvltlRKfvslllSillFknpltlqhlvgtllV 291
                                        s++++++   + +f +ll   +++++    ++      + +v++ ++l  +v+l+lS+l+F++ ltl +++g+++ 
  gi|557693666|ref|YP_008796720.1|  52 ISSRAQVIPASQAWFAALLAGALGFLGAVAFYLALDLNPSSIVVVATSLYPLVTLILSYLFFNEALTLRQIIGVAFA 128
                                       3455566888899*****************999999999************************************99 PP

                               UAA 292 flglll 297
                                       + +l+l
  gi|557693666|ref|YP_008796720.1| 129 LTALVL 134
                                       988877 PP

>> TMEM234  Putative transmembrane family 234
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   5.7   4.3e-06     0.019      48     115 ..      69     135 ..       9     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-06
                           TMEM234  48 liplllNqsgSvlfflllgkadlslavpiaNslafvfTvltelllgekvlkkktvlgmllvvvgialc 115
                                       l++ +l  +g v f+l+l   + s+ v++a sl  ++T++ ++l  ++ l+ ++++g+++ +++++l+
  gi|557693666|ref|YP_008796720.1|  69 LLAGALGFLGAVAFYLALDLNPSSI-VVVATSLYPLVTLILSYLFFNEALTLRQIIGVAFALTALVLI 135
                                       445568889*********9888665.67899******************************9999987 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2  16.9    0.0024        11      60     170 ..      24     134 ..       3     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0024
                           DUF2070  60 rilggr....ltykrslflalltelivviisllaillsall.qalvllalvlslalvfalrllvlvavsdesllkav 131
                                       r         l ++ s+ +a++  +iv++++++++ + ++  ++  + al+ + al f   +  ++a++ +  + +v
  gi|557693666|ref|YP_008796720.1|  24 R----VgasaLGWRDSAAVAAIGHMIVSLMFIISSRAQVIPaSQAWFAALLAG-ALGFLGAVAFYLALDLNPSSIVV 95 
                                       2....1333599*****************999999999776644444444444.78888888888888888888889 PP

                           DUF2070 132 lpaliqpllailllvlyfspesfllllllslifalavyl 170
                                       + ++++pl+ ++l++l+f+++ +l+ ++ +++ + a++l
  gi|557693666|ref|YP_008796720.1|  96 VATSLYPLVTLILSYLFFNEALTLRQIIGVAFALTALVL 134
                                       999**************7666666666655555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); 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:                         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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1012.32
//
Query:       gi|557693667|ref|YP_008796721.1|  [L=480]
Description: methylmalonate-semialdehyde dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-126  421.3   0.5   4.2e-126  421.2   0.5    1.0  1  Aldedh     Aldehyde dehydrogenase family
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.024   14.3   0.0    1.6  1  LUD_dom    LUD domain
       0.09   12.7   0.4       0.29   11.1   0.1    2.0  2  TetR_C_36  Tetracyclin repressor-like, C-terminal domain


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 !  421.2   0.5  7.1e-130  4.2e-126       3     462 .]      14     475 ..      12     475 .. 0.95

  Alignments for each domain:
  == domain 1  score: 421.2 bits;  conditional E-value: 7.1e-130
                                       T-SS.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHH CS
                            Aldedh   3 eses.etievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletle 78 
                                       es+s e+i+v nPa ++ ia vp +t+e+v aav+a  +af++++k+ ++eR ++L k+++l+ ++ e la++++ +
  gi|557693667|ref|YP_008796721.1|  14 ESKSsEKIPVKNPAFDTDIAYVPVSTEEEVAAAVEAGVAAFEKFRKTAPTERVSYLLKIRELMIRDTELLAKILVDN 90 
                                       5566478********************************************************************** PP

                                       H---HHHHHHHHHHHHHHHHHHHHHHHH.HSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHT CS
                            Aldedh  79 tGkplaearaeveeaidvlryyaelaek.legevlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaa 153
                                        G ++aea +ev+++++ ++ +a+la +  +ge + + s++ ++   rePlG  ++ItP+N Pl+ ++  +  a+a 
  gi|557693667|ref|YP_008796721.1|  91 HGRTYAEAVGEVKRSLENVEAAASLAYTlAKGEKMVNiSPEIDQELIREPLGCFAVITPFNIPLHAWSSYVPYAIAL 167
                                       ****************************55665555549************************************** PP

                                       T-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTS CS
                            Aldedh 154 GNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlk 230
                                       G tvvlKP+e tp++a  +a++++eag+P+gv++vv+g+g+ v+e lv+hp+v+ v f+Gst++g+ +++ aak+ k
  gi|557693667|ref|YP_008796721.1| 168 GATVVLKPSEVTPVVANEVARIVKEAGVPAGVMSVVHGDGR-VAEKLVRHPDVQGVGFIGSTKTGKFLYELAAKEGK 243
                                       **************************************886.99********************************* PP

                                       EEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-S CS
                            Aldedh 231 rvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtd 307
                                       r ++  G+kn+liv++daD+ k+++a+v ++fg +GQ+C aas l+v ++  +++v+ + e+  +lk+g ++d++t+
  gi|557693667|ref|YP_008796721.1| 244 RASINAGAKNHLIVMPDADFVKTADAAVSSFFGMSGQRCLAASNLVVVKGA-ERVVDLVRERS-ALKLGYGMDKETE 318
                                       *************************************************98.77777666665.9************ PP

                                       B---SSHHHHHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSH CS
                            Aldedh 308 vGPliseaqlekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkde 383
                                       +GP++s+a lekv+k++e ++e g kll++g+ ++  ++ +gyfv Pt++++++p +++a+eEiFGPV+s++ ++++
  gi|557693667|ref|YP_008796721.1| 319 MGPMASRAGLEKVMKFIELGEEYG-KLLVDGRkNKPVKPLNGYFVGPTIFTDISPTAPLAKEEIFGPVVSILHAESL 394
                                       **********************88.77777776889999************************************** PP

                                       HHHHHHHH.SSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSH.HHHHHHTEE CS
                            Aldedh 384 eeaieiaN.dteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGregg.kegleeyte 458
                                       + aie+ N +t+yG+aa++ft+++++a+r++ ++++Gnv++N    + +  +p gG kqS +G  ++  + ++++te
  gi|557693667|ref|YP_008796721.1| 395 DAAIELINkNTPYGNAASIFTSNPNTARRFVLDVNVGNVGVNIGVPQPMAYFPLGGRKQSFFGTAHSrVDTIRFFTE 471
                                       ********5589********************************8888888************6666599******9 PP

                                       EEEE CS
                            Aldedh 459 vktv 462
                                        k v
  gi|557693667|ref|YP_008796721.1| 472 HKIV 475
                                       9976 PP

>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     4e-06     0.024     104     172 ..     237     302 ..     218     309 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4e-06
                           LUD_dom 104 lvdnegnrraltflpkvhivvvginkivpdledavkrlktaprnatrlqkktpyvsfisgpsrtadiel 172
                                       l   eg+r++++ + k+h++v++    v++ + av+      ++++r     +++ +++g +r+ d  +
  gi|557693667|ref|YP_008796721.1| 237 LAAKEGKRASINAGAKNHLIVMPDADFVKTADAAVSSFFG--MSGQR-CLAASNLVVVKGAERVVDLVR 302
                                       56789*******************************9999..99999.778889999999999988765 PP

>> TetR_C_36  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.8e-05      0.29      22      70 ..      71     119 ..      51     124 .. 0.90
   2 ?   -2.4   0.0      0.79   4.7e+03      40      64 ..     174     197 ..     168     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.8e-05
                         TetR_C_36  22 plraflrrEPeralRllttkagevqrrvvaavaelleeevaageleppl 70 
                                       ++r+++ r++e+ +++l++++g+  + +v  v++ le+ +aa++l  +l
  gi|557693667|ref|YP_008796721.1|  71 KIRELMIRDTELLAKILVDNHGRTYAEAVGEVKRSLENVEAAASLAYTL 119
                                       579999**********************************999887655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.79
                         TetR_C_36  40 tkagevqrrvvaavaelleeevaag 64 
                                       ++ +ev + v++ va++++e+   +
  gi|557693667|ref|YP_008796721.1| 174 KP-SEVTPVVANEVARIVKEAGVPA 197
                                       44.8888888888888888776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3327.22
//
Query:       gi|557693668|ref|YP_008796722.1|  [L=202]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-70  234.1   0.1      8e-70  233.9   0.1    1.0  1  AA_synth  Amino acid synthesis


Domain annotation for each model (and alignments):
>> AA_synth  Amino acid synthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.9   0.1   4.5e-74     8e-70       1     175 []      10     188 ..      10     188 .. 0.99

  Alignments for each domain:
  == domain 1  score: 233.9 bits;  conditional E-value: 4.5e-74
                          AA_synth   1 irkivtvveeilheggkaadkplrkvavaavlknpfagryvedlsplmeaaeelgeelaerllealgv.aerieaYG 76 
                                       irk++++v+e+++e+gk ++kp+rk a+aav+knp+agryv+dl+ l++a++ lg  la++++ealg+ ++++e+YG
  gi|557693668|ref|YP_008796722.1|  10 IRKVAVYVDEVFMEMGKGLQKPVRKSAAAAVIKNPYAGRYVDDLQLLIDAGDFLGGFLARKAREALGIaPADVESYG 86 
                                       9**************************************************************************** PP

                          AA_synth  77 KaaivGlagelEhgaAllhtkfgkamRealgga...kaivpstkkvgaagtaldvplthknaayvrshfdtievrvp 150
                                       Kaai+Gl gelEhg+A+lh+kfg+ +Re++gg    kai+ps++k ga+gta+dvpl++k+aa+vrsh+d++evrvp
  gi|557693668|ref|YP_008796722.1|  87 KAAIIGLGGELEHGHAILHPKFGRGLREECGGQdvcKAIIPSSAKLGAPGTAIDVPLHYKRAAFVRSHYDAVEVRVP 163
                                       ******************************9766669**************************************** PP

                          AA_synth 151 daPaadEivvalavatggRvhaRvG 175
                                       daP +dEivv+ av+++gR+ +R+G
  gi|557693668|ref|YP_008796722.1| 164 DAPLPDEIVVIAAVTDSGRPLPRIG 188
                                       ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1513.46
//
Query:       gi|557693669|ref|YP_008796723.1|  [L=322]
Description: branched-chain amino acid ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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  106.8  39.1    1.4e-30  106.4  39.1    1.1  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 !  106.4  39.1   7.9e-35   1.4e-30       2     268 .]      34     302 ..      33     304 .. 0.84

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 7.9e-35
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvl 78 
                                        +++l++ + ++i+A +++++fg+++++ l +g+f ++Gay+++++l  + + +  a++++ +v a++gl++ +l++
  gi|557693669|ref|YP_008796723.1|  34 AVFILAQMTFFTIFAYSFNFLFGFTRQLFLCIGAFTGIGAYITGIILRDGIAGPVGAVALSTVVVAFIGLAVSILSV 110
                                       5789************************************************************************* PP

                      BPD_transp_2  79 rlkvdeliitllllsvlvgltlllltg...itsgvkgqssvkellgfagallsflsaviv..llalllvlavllllr 150
                                       r k+  + +++ +l + +++ + l+tg   +t+g++g +     l f ++l  ++   +    ++l++++++++l++
  gi|557693669|ref|YP_008796723.1| 111 RRKLVAIFTGIFTLAITLVFSN-LVTGlvdLTGGETGFRIRGVSLLFLDNLPYYMRYYYIalTTLLIVTVIAFYLIY 186
                                       ****999666665555444444.33330004445555545555555555555555544448778888999999**** PP

                      BPD_transp_2 151 rtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp..nigvglgfnaiaavvlGga 225
                                       +tr+G+a r + ++e  a+++Ginv rvk+lt ++++al g++Gal+ l+++ i+p  ++   + + + ++v+lGg 
  gi|557693669|ref|YP_008796723.1| 187 YTRTGYAYRCIIDDELSAELVGINVQRVKTLTSLLASALLGFSGALYGLFSQLISPsyYAFGSIDLPVQIIVILGGR 263
                                       ********************************************************954444599************ PP

                      BPD_transp_2 226 gsllgtviGaliigvvksllltllgiptelarvllgallilvl 268
                                        sllg+ iG+ ii+vv+++l++l      l+++l g++l+l+l
  gi|557693669|ref|YP_008796723.1| 264 TSLLGPYIGSAIIAVVNESLRFLG----PLTQLLYGLILMLLL 302
                                       ******************777776....578888888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2256.14
//
Query:       gi|557693670|ref|YP_008796724.1|  [L=290]
Description: branched-chain amino acid ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  110.6  47.5      1e-31  110.1  47.5    1.1  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
       0.46   10.8   0.1       0.46   10.8   0.1    2.6  2  DUF2649       Protein of unknown function (DUF2649)


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 !  110.1  47.5   1.1e-35     1e-31       2     267 ..       9     277 ..       8     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 1.1e-35
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvl 78 
                                       +l +++ +++l ++A Gl+l++g+aGv+nl+hg+++++  ++aa+l+ ll+ +l+lal+v++++ +av+++l + vl
  gi|557693670|ref|YP_008796724.1|   9 LLDGVVFGLVLSLIAAGLTLIYGLAGVLNLAHGELLVVTTVTAAVLSGLLGLPLPLALIVGIAATLAVAVVLDRVVL 85 
                                       67789999*********************************************************999999987766 PP

                      BPD_transp_2  79 ..rlkvdeliitllllsvlvgltlllltgitsg....vkgqssvkellgfagallsflsavivllalllvlavllll 149
                                          +k++    +ll+l++ +++  +l+ gi+      + +++ +++ +++ g ++ +++    +l ++++l ++l+l
  gi|557693670|ref|YP_008796724.1|  86 spIYKLEGEERVLLGLYITLAFSIFLHSGIITTfplaYLTVNLPTPNIEVLGLSFRTAQLLAGVLSAVILLGIYLFL 162
                                       224555555556666666666666667777665111144556666777777777777777777************** PP

                      BPD_transp_2 150 rrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGgag 226
                                       ++t  Gra+r +++ne+ a ++G++vk++++l+f+++g+l glaG++ + + +++p   g+++++ ++++ v+Gg+ 
  gi|557693670|ref|YP_008796724.1| 163 KKTWSGRAIRSLTQNETGALLVGVSVKKYRMLVFMVGGVLVGLAGIVRSIIATVAP-ESGLEFTILGLLVTVVGGIR 238
                                       ****************************************************9999.******************** PP

                      BPD_transp_2 227 sllgtviGaliigvvksllltllgiptelarvllgallilv 267
                                       s+ gt++++l+igvv+++l  ++g    la+v l +l++++
  gi|557693670|ref|YP_008796724.1| 239 SVSGTIAAGLVIGVVYTFLVVVVGT--YLAYVALLILIMVL 277
                                       *****************88888766..66666666666654 PP

>> DUF2649  Protein of unknown function (DUF2649)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   5.1e-05      0.46      14      49 ..     157     191 ..     152     206 .. 0.77
   2 ?   -3.2   2.8       1.2   1.1e+04      38      59 ..     257     276 ..     248     282 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.1e-05
                           DUF2649  14 yiflfidkanvesiimwnltqneyltlmvgvwvvil 49 
                                        i+lf+ k+      +  ltqne  +l+vgv v   
  gi|557693670|ref|YP_008796724.1| 157 GIYLFLKKTWSGR-AIRSLTQNETGALLVGVSVKKY 191
                                       6899999997655.5679*************88654 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                           DUF2649  38 ltlmvgvwvvilfltwfllwmv 59 
                                       l ++vg ++   +++ ++l mv
  gi|557693670|ref|YP_008796724.1| 257 LVVVVGTYL--AYVALLILIMV 276
                                       344444433..33333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1026  (0.0572257); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1895.44
//
Query:       gi|557693671|ref|YP_008796725.1|  [L=239]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-33  116.1   0.1    2.5e-33  115.5   0.1    1.3  1  ABC_tran      ABC transporter
    1.1e-11   45.1   2.7    1.9e-05   24.7   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    6.6e-05   23.4   0.1     0.0001   22.7   0.1    1.4  1  AAA_16        AAA ATPase domain
     0.0001   22.1   1.2    0.00036   20.3   0.9    2.0  1  AAA_30        AAA domain
     0.0004   20.4   0.0      0.026   14.4   0.0    2.1  2  Rad17         Rad17 P-loop domain
    0.00092   19.6   1.8     0.0033   17.8   1.7    1.9  1  AAA_19        AAA domain
     0.0013   18.4   0.1     0.0029   17.3   0.1    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0016   19.0   1.4     0.0055   17.2   0.1    2.0  2  AAA_23        AAA domain
     0.0019   17.1   0.4     0.0029   16.5   0.4    1.2  1  DLIC          Dynein light intermediate chain (DLIC)
     0.0035   16.7   1.1      0.086   12.2   0.1    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.004   16.8   0.5      0.095   12.3   0.4    2.1  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
     0.0049   16.3   1.1       0.17   11.3   0.1    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0055   15.9   0.2      0.015   14.5   0.1    1.7  2  PIF1          PIF1-like helicase
     0.0064   16.1   1.1      0.013   15.1   1.1    1.5  1  SRP54         SRP54-type protein, GTPase domain
     0.0072   16.4   0.2       0.31   11.1   0.1    2.2  2  AAA_14        AAA domain
     0.0087   16.0   2.2     0.0097   15.8   0.3    2.0  2  NACHT         NACHT domain
  ------ inclusion threshold ------
      0.013   15.8   1.6        0.2   11.9   0.2    2.1  2  AAA_22        AAA domain
      0.013   15.2   0.0       0.17   11.5   0.0    2.0  2  AAA_15        AAA ATPase domain
      0.018   13.9   0.7        1.2    7.9   0.4    2.1  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.023   14.3   0.2      0.044   13.3   0.2    1.4  1  AAA_25        AAA domain
      0.032   14.2   0.3       0.11   12.4   0.1    1.8  2  ATPase_2      ATPase domain predominantly from Archaea
      0.035   14.0   0.2      0.063   13.2   0.2    1.4  1  RsgA_GTPase   RsgA GTPase
       0.04   14.2   0.4       0.48   10.7   0.3    2.1  2  AAA_28        AAA domain
      0.044   13.5   0.1      0.066   12.9   0.1    1.3  1  AAA_24        AAA domain
      0.061   12.4   0.2       0.11   11.5   0.2    1.3  1  T2SSE         Type II/IV secretion system protein
      0.064   12.8   0.0       0.12   11.9   0.0    1.4  1  AAA_27        AAA domain
      0.065   12.5   0.1        2.3    7.5   0.1    2.1  2  Zeta_toxin    Zeta toxin
       0.11   12.5   0.1       0.21   11.6   0.1    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.12   12.7   1.4       0.19   12.1   1.4    1.7  1  AAA           ATPase family associated with various cellular 
       0.13   12.5   0.3       0.59   10.4   0.3    2.0  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.14   11.3   1.4       0.28   10.3   0.2    1.9  3  NB-ARC        NB-ARC domain
       0.15   12.2   0.3       0.23   11.6   0.3    1.6  1  AAA_33        AAA domain
       0.16   11.7   0.0       0.43   10.3   0.0    1.9  1  PRK           Phosphoribulokinase / Uridine kinase family
        0.2   11.6   1.9       0.46   10.4   0.6    2.0  2  NTPase_1      NTPase


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 !  115.5   0.1   4.7e-36   2.5e-33       3     136 ..      22     165 ..      20     166 .. 0.89

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 4.7e-36
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvre 78 
                                       nvsl++++ge+va++G+nGaGK+tLlk++ag  kp++G++ll+gk ++   +++++++ ++    e++lfp +tv+e
  gi|557693671|ref|YP_008796725.1|  22 NVSLTVEKGEVVAVLGPNGAGKTTLLKTIAGIIKPKKGKVLLEGKRIDGqPPEKIVEEGVALALAEKELFPLMTVHE 98 
                                       9***********************************************9778999999******************* PP

                                       H........HHHTCHHHHHHHSTTGG.TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x........xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n........esdeeiekalsklglke.lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n         +++++++ l+ +  +  + ++++++++ ++SgG++q++a+ ral++++kllllDEp+
  gi|557693671|ref|YP_008796725.1|  99 NlllgafnkRARQKLDENLEMVYSIFpKLKERASQKAGTMSGGEQQMLAIGRALMTDSKLLLLDEPS 165
                                       *****87654444466666555444357788888999*****************************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 !   20.7   0.3   5.9e-07   0.00031       2      39 ..      33      58 ..      32      82 .. 0.72
   2 !   24.7   0.1   3.5e-08   1.9e-05     233     287 ..     134     185 ..      96     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.9e-07
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsgg 39
                                       ++ GpNg+GK++LL+++ ++            +++++
  gi|557693671|ref|YP_008796725.1| 33 VAVLGPNGAGKTTLLKTIAGI------------IKPKK 58
                                      6899**************888............44444 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 3.5e-08
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr 287
                                        a  +S G +++   +   l +++  +lll+DEp +gL P l++++++ l++l +
  gi|557693671|ref|YP_008796725.1| 134 KAGTMSGGEQQM-LAIGRALMTDS--KLLLLDEPSTGLAPLLVKTIFQALRKLME 185
                                       45678*******.66666666665..8*********************9965544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1     2e-07    0.0001      21     135 ..      29     157 ..      11     195 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2e-07
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql..esaipy....salaqalareellrqllde.. 88 
                                       +g  e+v + G+ G GK++l+++++  ++ ++g + l+gk  +   +           +a ala++el+  +  +  
  gi|557693671|ref|YP_008796725.1|  29 KG--EVVAVLGPNGAGKTTLLKTIAGIIKPKKGKVlLEGKRIDGqpP----EkiveEGVALALAEKELFPLMTVHen 99 
                                       34..89************************98888788888887331....12222234444444455554433334 PP

                            AAA_16  89 .aesaeleawrekleeala.......avpelagaea...srllellkrllallsrder 135
                                        +  a   ++r+kl+e+l+         +e a+++a   s   +++ ++ + l +d++
  gi|557693671|ref|YP_008796725.1| 100 lLLGAFNKRARQKLDENLEmvysifpKLKERASQKAgtmSGGEQQMLAIGRALMTDSK 157
                                       4444455556666666666777777633333333334444444444444444444343 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.9   6.9e-07   0.00036      14      96 ..      26     163 ..      18     195 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.9e-07
                            AAA_30  14 ltsgdrvavltGpAGtGKttalkalreaweaa.g......................................grvig 51 
                                       + ++  v+++ Gp G+GKtt+lk+++ +++ + g                                      +++++
  gi|557693671|ref|YP_008796725.1|  26 TVEKGEVVAVLGPNGAGKTTLLKTIAGIIKPKkGkvllegkridgqppekiveegvalalaekelfplmtvhENLLL 102
                                       44555699**********************99457777776666666666666666666666666666666556666 PP

                            AAA_30  52 lAptgkaAkvLaeelgieastiakllkrlk................grarlepgtllivDE 96 
                                        A +++a ++L e+l++  s   kl +r                  gra +++++ll+ DE
  gi|557693671|ref|YP_008796725.1| 103 GAFNKRARQKLDENLEMVYSIFPKLKERASqkagtmsggeqqmlaiGRALMTDSKLLLLDE 163
                                       6666666666666666554444444444445555555555666666555556666666666 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     5e-05     0.026      38     130 ..      23     118 ..      16     126 .. 0.77
   2 ?    3.9   0.0     0.082        43     121     171 ..     144     195 ..     131     204 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5e-05
                             Rad17  38 dvLesrkkriLLisGPsGCgkstvvkvLskelgiklrew.lnpvsl..kepdnqksdfkgltekesrflsqiesfke 111
                                        +L  +k +++ + GP G gk+t +k ++ +  +k  +  l +  +  + p+  +++  +l   e+++ +++ ++++
  gi|557693671|ref|YP_008796725.1|  23 VSLTVEKGEVVAVLGPNGAGKTTLLKTIAGIIKPKKGKVlLEGKRIdgQPPEKIVEEGVALALAEKELFPLMTVHEN 99 
                                       5677777889999****************9998876554156665521344556788888888999999*****999 PP

                             Rad17 112 leLkdakylklqklGddlr 130
                                       l+L + +    qkl ++l+
  gi|557693671|ref|YP_008796725.1| 100 LLLGAFNKRARQKLDENLE 118
                                       9999888888888888775 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.082
                             Rad17 121 klqklGddlrtdkklilvedlPnkfyrds.dalrevirkylrssealplilv 171
                                       ++   G  l td kl+l+++        + +++ + +rk + +++ l+++lv
  gi|557693671|ref|YP_008796725.1| 144 QMLAIGRALMTDSKLLLLDEPSTGLAPLLvKTIFQALRKLMETKRELSILLV 195
                                       45668999**********9955555555579999999****99999999887 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.7   6.2e-06    0.0033       9      66 ..      29     121 ..      23     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.2e-06
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkp...................................eeillvaf 50 
                                       k +v++v+++ G GKT++lk+i  +++  +g  +                                   e++ll af
  gi|557693671|ref|YP_008796725.1|  29 KGEVVAVLGPNGAGKTTLLKTIAGIIKPKKGKVLlegkridgqppekiveegvalalaekelfplmtvhENLLLGAF 105
                                       56899*****************9999998877669*********************************999****** PP

                            AAA_19  51 tgrAakelrerlaalg 66 
                                       ++rA ++l e+l+++ 
  gi|557693671|ref|YP_008796725.1| 106 NKRARQKLDENLEMVY 121
                                       ************5543 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 !   17.3   0.1   5.4e-06    0.0029      18      50 ..      26      58 ..      19      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.4e-06
                            AAA_29 18 eidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                      +++ kg ++ + Gp+G+GK+Tll  i+ ++ p+k
  gi|557693671|ref|YP_008796725.1| 26 TVE-KGeVVAVLGPNGAGKTTLLKTIAGIIKPKK 58
                                      555.44599**************99999988877 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1     1e-05    0.0055      21      40 ..      32      51 ..      14      59 .. 0.85
   2 ?    0.7   0.1       1.2   6.4e+02     116     166 ..     108     191 ..      87     209 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1e-05
                            AAA_23 21 ltlItGpNGaGKTTildAik 40
                                      ++++ GpNGaGKTT+l  i 
  gi|557693671|ref|YP_008796725.1| 32 VVAVLGPNGAGKTTLLKTIA 51
                                      77899***********9875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.2
                            AAA_23 116 eleqfisellgskkiilnlilflgqer.................................feefelkdkkerleele 159
                                         +q+++e+l+  ++i++ +   ++++                                  ++++ k+ +++l++l 
  gi|557693671|ref|YP_008796725.1| 108 RARQKLDENLEMVYSIFPKLKERASQKagtmsggeqqmlaigralmtdsklllldepstgLAPLLVKTIFQALRKLM 184
                                       45677888888888888777666666667777776666666555555433333333333322222244444444444 PP

                            AAA_23 160 keleele 166
                                       + ++el+
  gi|557693671|ref|YP_008796725.1| 185 ETKRELS 191
                                       4444443 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.4   5.5e-06    0.0029      25      57 ..      30      62 ..      19      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.5e-06
                              DLIC 25 gksvlvlGedgsGkttliaklqGveeekkGrGl 57
                                      g  v vlG +g+Gkttl+  + G+ ++kkG+ l
  gi|557693671|ref|YP_008796725.1| 30 GEVVAVLGPNGAGKTTLLKTIAGIIKPKKGKVL 62
                                      66799*************************865 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   0.00016     0.086      24      60 ..      32      68 ..      14      81 .. 0.85
   2 ?    3.6   0.1     0.068        36      44     134 ..      89     188 ..      80     205 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllpplseeealevaki 60
                                       + ++Gp G+GKt l k +++++ p + +  le ++i
  gi|557693671|ref|YP_008796725.1| 32 VVAVLGPNGAGKTTLLKTIAGIIKPKKGKVLLEGKRI 68
                                      56789********************999999998877 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.068
                      Mg_chelatase  44 sllpplseeealevakiasvag.kkeeekllkrrpfraphhsaskaa..lvGggs.kpkpGeislahnGvLfLDE.. 114
                                       +l+p ++ +e l   + +  a+ k +e+  +    f + ++ as+ a  + Gg +     G   ++   +L+LDE  
  gi|557693671|ref|YP_008796725.1|  89 ELFPLMTVHENLLLGAFNKRARqKLDENLEMVYSIFPKLKERASQKAgtMSGGEQqMLAIGRALMTDSKLLLLDEps 165
                                       566666666666666665555523334444556667676666666543377886646778999999999*****955 PP

                      Mg_chelatase 115 ...lpefkrkvlevLRePledge 134
                                          +p + ++++++LR+ +e+++
  gi|557693671|ref|YP_008796725.1| 166 tglAPLLVKTIFQALRKLMETKR 188
                                       55556788999999999999763 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   0.4   0.00018     0.095       2      21 ..      32      51 ..      31      65 .. 0.78
   2 ?    2.6   0.0      0.18        92      59      91 ..     167     198 ..     127     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                      EEEEEESTTCCHHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhll 21
                                      v+ + G+ G+GKTtLl+++ 
  gi|557693671|ref|YP_008796725.1| 32 VVAVLGPNGAGKTTLLKTIA 51
                                      67899************997 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.18
                                       TTECCHCTT-HHHHHHHHHHHHTT-SEEEEEEC CS
                              cobW  59 GciCctlredllkelealeereerldviliEtt 91 
                                       G  +    + + ++l++l+e++++l+++l+E+ 
  gi|557693671|ref|YP_008796725.1| 167 GLAPLL-VKTIFQALRKLMETKRELSILLVEQR 198
                                       555544.45678899****************75 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 !   11.3   0.1   0.00032      0.17      25      45 ..      31      51 ..      22      65 .. 0.84
   2 ?    4.1   0.2      0.05        27     136     189 ..     137     186 ..      57     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                                      SEEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAil 45
                                      ++ a++GpNG+GK+ ll  i 
  gi|557693671|ref|YP_008796725.1| 31 EVVAVLGPNGAGKTTLLKTIA 51
                                      5789************99985 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.05
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn 189
                                       ++SgGe++++a+   +    +  + l llDe    L    vk + + l++  ++
  gi|557693671|ref|YP_008796725.1| 137 TMSGGEQQMLAIGRAL----MTDSKLLLLDEPSTGLAPLLVKTIFQALRKLMET 186
                                       8*******99875432....3455677777777777777777777777766554 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   2.9e-05     0.015      16      54 ..      24      62 ..      17      65 .. 0.89
   2 ?   -1.7   0.0       2.4   1.3e+03      57      84 ..     164     189 ..     147     212 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-05
                                      ....HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEE CS
                              PIF1 16 avlnekgklfFvtGsgGtgKtflwkallkklrsegkivl 54
                                      +++ ekg+++ v G  G+gKt l+k++  ++++++ +vl
  gi|557693671|ref|YP_008796725.1| 24 SLTVEKGEVVAVLGPNGAGKTTLLKTIAGIIKPKKGKVL 62
                                      566799***************************998887 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                                       ESSHHHHHCC.TSEECHHHHT-TTSSS- CS
                              PIF1  57 AssGvAalllegGrtahsrfkiplekde 84 
                                        s+G+A ll+   ++  ++ k+  +k e
  gi|557693671|ref|YP_008796725.1| 164 PSTGLAPLLV--KTIFQALRKLMETKRE 189
                                       3455555554..2333444444444444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.1   2.5e-05     0.013       3      34 ..      32      63 ..      30      66 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvll 34
                                      v++++G++GaGKTt l  +a ++k ++ kvll
  gi|557693671|ref|YP_008796725.1| 32 VVAVLGPNGAGKTTLLKTIAGIIKPKKGKVLL 63
                                      8999**********************999997 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00059      0.31       2      23 ..      30      51 ..      29      73 .. 0.88
   2 ?    3.3   0.0      0.15        80      58      96 ..     150     193 ..      97     197 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00059
                            AAA_14  2 rkilvitGaRrvGKTtllkqli 23
                                      ++++++ G+  +GKTtllk+++
  gi|557693671|ref|YP_008796725.1| 30 GEVVAVLGPNGAGKTTLLKTIA 51
                                      5799**************9987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.15
                            AAA_14  58 eklkeekktylflDEiqev......pewekalkslvdegknldvi 96 
                                       + l++ + ++l+lDE +        +++++al++l++++++l ++
  gi|557693671|ref|YP_008796725.1| 150 RALMT-DSKLLLLDEPSTGlapllvKTIFQALRKLMETKRELSIL 193
                                       33344.688999999987666666699999999999999888776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3   1.8e-05    0.0097       2      25 ..      32      55 ..      31      62 .. 0.86
   2 ?   -1.6   0.0       4.1   2.2e+03      54      71 ..     172     189 ..     141     202 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                      +v++ G++G GKTtLl+ +a  ++
  gi|557693671|ref|YP_008796725.1| 32 VVAVLGPNGAGKTTLLKTIAGIIK 55
                                      799****************97665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.1
                                       HCHHHCCCCTS--SSS-C CS
                             NACHT  54 ladllfsqlpepaapvse 71 
                                       l +++f+ l ++ ++ +e
  gi|557693671|ref|YP_008796725.1| 172 LVKTIFQALRKLMETKRE 189
                                       333333334444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00038       0.2       5      26 ..      30      51 ..      27      69 .. 0.89
   2 ?    3.3   0.1      0.17        91      63     128 ..     126     195 ..      78     202 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00038
                            AAA_22  5 agilvvtGesGtGKTtllrrll 26
                                        +++v G+ G+GKTtll++++
  gi|557693671|ref|YP_008796725.1| 30 GEVVAVLGPNGAGKTTLLKTIA 51
                                      56789*************9875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.17
                            AAA_22  63 alglelkaerlsseellealeqalrarav.ielliiDEaqh.lrs...eealeeLrsllnlsrkgvqliLv 128
                                       +l+++++ + ++ +   +++    ra ++  +ll++DE    l +   +++++ Lr+l++  +  ++++Lv
  gi|557693671|ref|YP_008796725.1| 126 KLKERASQKAGTMSGGEQQMLAIGRALMTdSKLLLLDEPSTgLAPllvKTIFQALRKLME-TKRELSILLV 195
                                       33333333222223333555555556665999******9988852556999999999888.6666777766 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00033      0.17      25      56 ..      32      59 ..      20     134 .. 0.79
   2 ?    1.8   0.0      0.29   1.5e+02     322     356 ..     154     188 ..     107     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                            AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekknkk 56
                                      +  + G+N++GK+++l+ +  +++ k    k 
  gi|557693671|ref|YP_008796725.1| 32 VVAVLGPNGAGKTTLLKTIAGIIKPK----KG 59
                                      78899**************9999888....33 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.29
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnk 356
                                       +++++ll++EP + L p + k ++++l++l ++++
  gi|557693671|ref|YP_008796725.1| 154 TDSKLLLLDEPSTGLAPLLVKTIFQALRKLMETKR 188
                                       35589999999999999999999999999998765 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 ?    7.9   0.4    0.0022       1.2     240     265 ..      25      51 ..      23      57 .. 0.89
   2 ?    4.2   0.0     0.028        15     310     349 ..     125     164 ..     110     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0022
                                       EEE-SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 240 mgipkG.vtlIvGggfhGKsTLLeAle 265
                                       + + kG v+++ G++  GK+TLL+ ++
  gi|557693671|ref|YP_008796725.1|  25 LTVEKGeVVAVLGPNGAGKTTLLKTIA 51 
                                       5688999*****************996 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.028
                                       CCC--STTEEESS--HHHHHHHHHHHHHHTT-SEEEEEGG CS
                        ABC_ATPase 310 PegkdttkfstedASGStsqAanimealeagakllLiDED 349
                                       P+ k+  +    + SG   q  +i +al  ++kllL+DE 
  gi|557693671|ref|YP_008796725.1| 125 PKLKERASQKAGTMSGGEQQMLAIGRALMTDSKLLLLDEP 164
                                       555565666677889************************6 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   8.4e-05     0.044      24      52 ..      21      49 ..      16      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.4e-05
                            AAA_25 24 wlvkgllpagelallaGapgtGKttlald 52
                                      w v   + +ge++++ G+ g+GKttl+  
  gi|557693671|ref|YP_008796725.1| 21 WNVSLTVEKGEVVAVLGPNGAGKTTLLKT 49
                                      88898999*****************9855 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 ?   12.4   0.1   0.00021      0.11      18      42 ..      28      52 ..      22      63 .. 0.82
   2 ?   -1.8   0.0       4.6   2.4e+03     139     162 ..     170     193 ..     158     213 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00021
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkeiie 42
                                      e+ e++ + Gp g GKt+Llk i+ 
  gi|557693671|ref|YP_008796725.1| 28 EKGEVVAVLGPNGAGKTTLLKTIAG 52
                                      6789999**************9975 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.6
                          ATPase_2 139 ellvkeLlnliesltkekhlcvvi 162
                                        llvk +++++ +l++ k+   ++
  gi|557693671|ref|YP_008796725.1| 170 PLLVKTIFQALRKLMETKRELSIL 193
                                       567777777777777766665554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   0.00012     0.063      98     127 ..      29      58 ..      18      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                                       TTSEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelkt 127
                                       k+++++++G+ G+GK+tL++++++  + k 
  gi|557693671|ref|YP_008796725.1|  29 KGEVVAVLGPNGAGKTTLLKTIAGIIKPKK 58 
                                       56999****************998666555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   0.00091      0.48       2      20 ..      33      51 ..      32      64 .. 0.88
   2 ?    1.4   0.0      0.65   3.4e+02      29      82 ..     163     217 ..     137     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00091
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      ++++G+ ++GKTtll+ +a
  gi|557693671|ref|YP_008796725.1| 33 VAVLGPNGAGKTTLLKTIA 51
                                      899************9887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.65
                            AAA_28  29 Eaareileeklakgedalpwv.edllafaervleeqleeeaaaaankvlfcDrgl 82 
                                       E+ + +   + ++ ++al++  e++ ++ ++++e++  ++a+ ++++++++   +
  gi|557693671|ref|YP_008796725.1| 163 EPSTGLAPLLVKTIFQALRKLmETKRELSILLVEQRTVQAAQLSDRGYVLSNGRI 217
                                       5555555556666677788888889999999888888777777899998886655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00012     0.066       4      23 ..      32      55 ..      29      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            AAA_24  4 kiliyGpsgiGKTtlakel....g 23
                                       +++ Gp+g+GKTtl+k++    +
  gi|557693671|ref|YP_008796725.1| 32 VVAVLGPNGAGKTTLLKTIagiiK 55
                                      689**************9966663 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 ?   11.5   0.2   0.00021      0.11     126     161 ..      27      62 ..      16      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                             T2SSE 126 vrerglilvsGgTgsGKttllyallkeinksderiv 161
                                       v++  ++ v G+ g GKttll ++  +i+ ++ +++
  gi|557693671|ref|YP_008796725.1|  27 VEKGEVVAVLGPNGAGKTTLLKTIAGIIKPKKGKVL 62 
                                       5666778899******************99977665 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00024      0.12      20      47 ..      24      51 ..      12      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                            AAA_27 20 dfsaeeadlhliyGpNEAGKstalrAis 47
                                      ++  e+ ++  ++GpN AGK+t+l+ i 
  gi|557693671|ref|YP_008796725.1| 24 SLTVEKGEVVAVLGPNGAGKTTLLKTIA 51
                                      55666788899*************9986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0043       2.3      17      49 ..      31      63 ..      22      74 .. 0.80
   2 ?    3.1   0.0     0.097        51     128     163 ..     183     227 ..     145     231 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0043
                        Zeta_toxin 17 klillgGqpGAGKselaellkdelerqgnvvrl 49
                                       ++ + G  GAGK++l++ ++  ++++++ v l
  gi|557693671|ref|YP_008796725.1| 31 EVVAVLGPNGAGKTTLLKTIAGIIKPKKGKVLL 63
                                      567778999**********99988877766666 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.097
                        Zeta_toxin 128 vvavkkelSrlgvldRyeee.vae.........gRlvpkeehdeaf 163
                                       ++ +k+elS+l v++R  +              gR+v +  ++ea+
  gi|557693671|ref|YP_008796725.1| 183 LMETKRELSILLVEQRTVQAaQ-LsdrgyvlsnGRIVYEGDIKEAV 227
                                       67899***********999851.23467888878999888888776 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    0.0004      0.21      19      41 ..      30      52 ..      17      61 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0004
                                      TEEEEEEESTTSSHHHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrglak 41
                                      g+v++  G+ GaGKTtl + +a 
  gi|557693671|ref|YP_008796725.1| 30 GEVVAVLGPNGAGKTTLLKTIAG 52
                                      7899***************9986 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 ?   12.1   1.4   0.00037      0.19       2      23 ..      34      55 ..      33     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00037
                                      EEESSTTSSHHHHHHHHHHHHT CS
                               AAA  2 llyGppGtGKTllakavakelg 23
                                       + Gp G GKT+l k +a  ++
  gi|557693671|ref|YP_008796725.1| 34 AVLGPNGAGKTTLLKTIAGIIK 55
                                      578***************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 ?   10.4   0.3    0.0011      0.59      24      42 ..     129     147 ..     108     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                           SbcCD_C  24 kelsrssgtlSGGekqfla 42 
                                       ++ s+++gt+SGGe+q+la
  gi|557693671|ref|YP_008796725.1| 129 ERASQKAGTMSGGEQQMLA 147
                                       457999*********9876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00054      0.28      21      41 ..      31      51 ..      17      59 .. 0.85
   2 ?   -1.4   0.0         2   1.1e+03      70     110 ..     121     162 ..     111     166 .. 0.66
   3 ?   -2.7   0.1         5   2.6e+03      92     106 ..     176     190 ..     143     194 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00054
                                      EEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqil 41
                                       vva+ G  G GKttl+k i 
  gi|557693671|ref|YP_008796725.1| 31 EVVAVLGPNGAGKTTLLKTIA 51
                                      49***************9985 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                                       HXXHHHHHCCCTTSS.SS-STTSHHHHHHHHCCCTTEEEEEE CS
                            NB-ARC  70 etilkeLslseddle.ekeeveslkrklvrlLltkrfllvlD 110
                                        +i  +L+++ ++    ++ +e+    + r+L t   ll+lD
  gi|557693671|ref|YP_008796725.1| 121 YSIFPKLKERASQKAgTMSGGEQQMLAIGRALMTDSKLLLLD 162
                                       556666665544443144455557788899999999999998 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5
                                       HHHHHHHHCCCTTEE CS
                            NB-ARC  92 lkrklvrlLltkrfl 106
                                       + + l++l++tkr l
  gi|557693671|ref|YP_008796725.1| 176 IFQALRKLMETKREL 190
                                       334455555555555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   0.00043      0.23       1      20 [.      32      51 ..      32     158 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00043
                            AAA_33  1 lvllvGlpGsGKstlaerll 20
                                      +v + G++G+GK+tl++ ++
  gi|557693671|ref|YP_008796725.1| 32 VVAVLGPNGAGKTTLLKTIA 51
                                      78899**********99864 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00082      0.43       1      27 [.      32      58 ..      32     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00082
                               PRK  1 vIgvagsSGaGkttvarklekifgrek 27
                                      v++v g+ GaGktt+ +++  i++ +k
  gi|557693671|ref|YP_008796725.1| 32 VVAVLGPNGAGKTTLLKTIAGIIKPKK 58
                                      789*****************9998433 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00087      0.46       2      27 ..      33      58 ..      32      67 .. 0.86
   2 ?   -0.4   0.0       1.8   9.6e+02      88     135 ..     148     198 ..     126     212 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00087
                                      EEEE--TTSSHHHHHHHHHHHH...G CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssg 27
                                      v++ Gp G GKtTl+k ++  +k + 
  gi|557693671|ref|YP_008796725.1| 33 VAVLGPNGAGKTTLLKTIAGIIKPKK 58
                                      6788***************9998664 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                                       HHHHHHHHH-EEEE--..-STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS CS
                          NTPase_1  88 alrkalseadviviDE..iGkmElkskkfkeaveevLk.sekpvlavihrr 135
                                       + r  ++++ ++++DE   G   l +k++ +a++++++ + +  +  + +r
  gi|557693671|ref|YP_008796725.1| 148 IGRALMTDSKLLLLDEpsTGLAPLLVKTIFQALRKLMEtKRELSILLVEQR 198
                                       444444677777788766677778888888999999985555556555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 1629.35
//
Query:       gi|557693672|ref|YP_008796726.1|  [L=248]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-26   91.3   0.0    1.3e-25   90.5   0.0    1.4  2  ABC_tran      ABC transporter
    2.8e-08   33.5   0.3    6.4e-08   32.3   0.3    1.7  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
    0.00024   21.0   0.3     0.0013   18.6   0.2    1.8  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    0.00088   19.8   0.2    0.00088   19.8   0.2    1.5  2  AAA_23        AAA domain
     0.0021   17.8   0.0     0.0042   16.8   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
     0.0043   17.3   0.1        1.6    9.0   0.0    2.2  2  AAA_22        AAA domain
     0.0044   16.8   0.1      0.054   13.2   0.0    2.1  2  AAA_30        AAA domain
  ------ inclusion threshold ------
       0.01   14.7   0.4        2.7    6.7   0.0    2.5  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.017   14.5   0.2       0.21   11.0   0.1    2.0  2  TniB          Bacterial TniB protein
      0.022   14.3   0.0        4.4    6.8   0.0    2.3  2  AAA_25        AAA domain
      0.023   14.1   0.2      0.066   12.6   0.1    1.7  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.024   14.5   0.0      0.047   13.6   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.026   14.3   0.2        5.7    6.6   0.1    2.3  2  IstB_IS21     IstB-like ATP binding protein
      0.026   14.2   0.2      0.035   13.8   0.2    1.1  1  AAA_15        AAA ATPase domain
      0.049   13.5   0.1        0.2   11.6   0.0    1.8  2  ATPase_2      ATPase domain predominantly from Archaea
       0.05   11.7   0.1      0.059   11.4   0.1    1.0  1  PEPcase       Phosphoenolpyruvate carboxylase
      0.066   12.8   0.0       0.13   11.9   0.0    1.4  1  AAA_27        AAA domain
       0.13   12.0   0.1       0.34   10.6   0.0    1.7  2  Phage_tail_X  Phage Tail Protein X


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 !   90.5   0.0   1.3e-28   1.3e-25       1     135 [.      20     165 ..      20     167 .. 0.95
   2 ?   -3.0   0.0       9.9   9.8e+03      86     113 ..     196     222 ..     176     233 .. 0.61

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 1.3e-28
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       lkn++l+++++e+ ai+G+nGaGK+tL++++ g +kp +G+i +dgkd++   ++e+++  ++   q p+ f++ltv
  gi|557693672|ref|YP_008796726.1|  20 LKNINLEIEANEIRAIIGPNGAGKTTLFNVVNGVYKPSAGKIFFDGKDITGkPPHEIFKLGMSRTLQIPRPFKDLTV 96 
                                       79************************************************98899********************** PP

                                       HHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                        en              e +++++++l++lgl e+ + ++      L   ++++v+laral++kp++l++DE 
  gi|557693672|ref|YP_008796726.1|  97 WENvlagglfnervdrtELEKHVSTLLDRLGLAEKSEMKA----GLLNLQERKKVELARALASKPRVLMVDEY 165
                                       ***********99999888888***********9777777....99999**********************95 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 9.9
                                       HHHHHHSTTGGTTCBGESTTSGGS-HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  86 ekalsklglkelkdtvvksspssLSgGq 113
                                       e+++s +    +k tv+ +++++L +G 
  gi|557693672|ref|YP_008796726.1| 196 EHVISAVASLADKVTVL-NQGAKLAEGR 222
                                       44444444444333333.4445555554 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.3   6.4e-11   6.4e-08       2      23 .]     217     238 ..     216     238 .. 0.97

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 6.4e-11
                      BCA_ABC_TP_C   2 vIAeGtPaEvrndPrVieAYLG 23 
                                       ++AeG P+Ev+ d +V+eAYLG
  gi|557693672|ref|YP_008796726.1| 217 KLAEGRPEEVVMDQEVVEAYLG 238
                                       89*******************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 !   18.6   0.2   1.3e-06    0.0013       3      63 ..      34      82 ..      32     101 .. 0.75
   2 ?   -0.5   0.0      0.84   8.4e+02     254     287 ..     153     186 ..     142     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.3e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63
                                      ++iGpNg+GK++L+    ++             +++ g+i  + + ++++ p + f+++ +
  gi|557693672|ref|YP_008796726.1| 34 AIIGPNGAGKTTLFNVVNGVY------------KPSAGKIFFDGKDITGKPPHEIFKLGMS 82
                                      69*************999885............4666666666666666666666666655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.84
                            AAA_21 254 alkkgsllliDEpEngLHPkllrrllellkelsr 287
                                       +++k+++l +DE  +gL+ + +++ ++l+++l+r
  gi|557693672|ref|YP_008796726.1| 153 LASKPRVLMVDEYMSGLNTAEVEEAVDLFRDLRR 186
                                       456679*******9***99999999999998877 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   8.9e-07   0.00088      16      37 ..      24      48 ..      12      53 .. 0.75
   2 ?   -3.2   0.1       9.8   9.7e+03     173     173 ..     130     130 ..     106     156 .. 0.45

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 8.9e-07
                            AAA_23 16 dF...skgltlItGpNGaGKTTild 37
                                      ++    + + +I+GpNGaGKTT+++
  gi|557693672|ref|YP_008796726.1| 24 NLeieANEIRAIIGPNGAGKTTLFN 48
                                      44335557889************98 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 9.8
                            AAA_23 173 e 173
                                       e
  gi|557693672|ref|YP_008796726.1| 130 E 130
                                       2 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 !   16.8   0.0   4.2e-06    0.0042      17      50 ..      25      58 ..      19      65 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.2e-06
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +ei+ +++  ++Gp+G+GK+Tl+  ++ +  p+ 
  gi|557693672|ref|YP_008796726.1| 25 LEIEANEIRAIIGPNGAGKTTLFNVVNGVYKPSA 58
                                      677777899*************987777766665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0016       1.6       7      23 ..      32      48 ..      27      55 .. 0.86
   2 ?    6.2   0.1     0.012        12      74     126 ..     140     193 ..     106     196 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0016
                            AAA_22  7 ilvvtGesGtGKTtllr 23
                                      i +++G+ G+GKTtl +
  gi|557693672|ref|YP_008796726.1| 32 IRAIIGPNGAGKTTLFN 48
                                      5589**********975 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.012
                            AAA_22  74 sseell.ealeqalraravielliiDEaqh.lr..s.eealeeLrsllnlsrkgvqli 126
                                       +++e     l++al ++  +++l++DE    l+  + eea+  +r+l    ++g++++
  gi|557693672|ref|YP_008796726.1| 140 NLQERKkVELARALASK--PRVLMVDEYMSgLNtaEvEEAVDLFRDLRR--EYGLTIV 193
                                       33333334455555555..55******9999954314555555566665..8888876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   5.4e-05     0.054      18      48 ..      30      60 ..      24      85 .. 0.87
   2 ?    1.4   0.0      0.22   2.2e+02      71     110 ..     133     179 ..     100     195 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.4e-05
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggr 48
                                      + + ++ Gp G+GKtt+ ++++ +++ + g+
  gi|557693672|ref|YP_008796726.1| 30 NEIRAIIGPNGAGKTTLFNVVNGVYKPSAGK 60
                                      56899*****************999987555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.22
                            AAA_30  71 stiakllkrlk......grarlepg.tllivDE.agmvdtkqlaallk 110
                                       +  a ll+ ++      +r +l+++ ++l+vDE ++ ++t+++++ ++
  gi|557693672|ref|YP_008796726.1| 133 EMKAGLLNLQErkkvelAR-ALASKpRVLMVDEyMSGLNTAEVEEAVD 179
                                       3344444333366677643.44445599****9445566666655554 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 ?    5.6   0.1    0.0056       5.6     246     271 ..      32      56 ..      17      68 .. 0.82
   2 ?    6.7   0.0    0.0027       2.7     355     413 ..     160     214 ..     157     234 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0056
                                       EEEEEE-TTSSHHHHHHHHHHCCSEE CS
                        ABC_ATPase 246 vtlIvGggfhGKsTLLeAlekGvynh 271
                                       + +I+G++  GK+TL + + +Gvy+ 
  gi|557693672|ref|YP_008796726.1|  32 IRAIIGPNGAGKTTLFNVV-NGVYKP 56 
                                       889************9965.689875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0027
                                       HH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEET CS
                        ABC_ATPase 355 lmirDermqelvskekepitplvdrvrelykklgvstilvvggsgdyldvAdtvilmee 413
                                       lm+ De+m+ l       ++  vd+ r+l++++g++++ v   +++  ++Ad+v ++++
  gi|557693672|ref|YP_008796726.1| 160 LMV-DEYMSGLN---TAEVEEAVDLFRDLRREYGLTIVWVEHVISAVASLADKVTVLNQ 214
                                       555.99999998...4458999********************************99986 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.17   1.7e+02      39      53 ..      34      48 ..      17      58 .. 0.86
   2 ?   11.0   0.1   0.00021      0.21     108     160 ..     143     195 ..     110     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.17
                              TniB 39 llvGdsnnGKtmive 53
                                       ++G+   GKt++++
  gi|557693672|ref|YP_008796726.1| 34 AIIGPNGAGKTTLFN 48
                                      79**********976 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00021
                              TniB 108 eqqvlrllr..elkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       e++ ++l r  + k+rvL++DE  + l  +  + +e++ + + L +e+ ++iv v
  gi|557693672|ref|YP_008796726.1| 143 ERKKVELARalASKPRVLMVDEYMSGL--NTAEVEEAVDLFRDLRREYGLTIVWV 195
                                       344444544114689********9999..788999*****************987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.013        13      30      49 ..      27      46 ..      17      51 .. 0.87
   2 ?    6.8   0.0    0.0044       4.4     162     189 ..     171     198 ..     128     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.013
                            AAA_25 30 lpagelallaGapgtGKttl 49
                                      + a+e+ +++G+ g+GKttl
  gi|557693672|ref|YP_008796726.1| 27 IEANEIRAIIGPNGAGKTTL 46
                                      567888999**********8 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0044
                            AAA_25 162 nsdvgalvealeriarrtgaavllvhHv 189
                                        ++v+++v+ +++++r++g +++ v Hv
  gi|557693672|ref|YP_008796726.1| 171 TAEVEEAVDLFRDLRREYGLTIVWVEHV 198
                                       466899*********************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 ?   12.6   0.1   6.6e-05     0.066      24      43 ..      30      49 ..      18      54 .. 0.79
   2 ?   -1.3   0.0       1.2   1.2e+03     162     208 ..     160     206 ..     117     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.6e-05
                                      SSEEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldA 43
                                      +++ ai+GpNG+GK+ l++ 
  gi|557693672|ref|YP_008796726.1| 30 NEIRAIIGPNGAGKTTLFNV 49
                                      4589***********99875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                                       EEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 162 yllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadkl 208
                                        ++De  + L  ++v++ ++l++  + +  + ++ +++ + + a+  
  gi|557693672|ref|YP_008796726.1| 160 LMVDEYMSGLNTAEVEEAVDLFRDLRREYGLTIVWVEHVISAVASLA 206
                                       46788888888888888888888888777777766666666555554 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.7e-05     0.047      94     123 ..      24      54 ..      15      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.7e-05
                                       HHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  94 kellkd.ktsvlvGqSGvGKStLinallpel 123
                                       + +++  ++ +++G+ G+GK+tL n++++  
  gi|557693672|ref|YP_008796726.1|  24 NLEIEAnEIRAIIGPNGAGKTTLFNVVNGVY 54 
                                       5555555999***************998755 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 ?    5.7   0.0     0.011        11      44      63 ..      27      46 ..      19      53 .. 0.88
   2 ?    6.6   0.1    0.0057       5.7      95     141 ..     143     191 ..     123     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                         IstB_IS21 44 iekkenivllGpsGvGKshl 63
                                      ie++e  +++Gp G+GK+ l
  gi|557693672|ref|YP_008796726.1| 27 IEANEIRAIIGPNGAGKTTL 46
                                      67888899*********987 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0057
                         IstB_IS21  95 rdgklaralkrllkvdllilDdl..gllpldqaeaellfeviekryerr 141
                                       +  k++ a +   k+++l++D++  gl++ + +ea +lf+ + + y+ +
  gi|557693672|ref|YP_008796726.1| 143 ERKKVELARALASKPRVLMVDEYmsGLNTAEVEEAVDLFRDLRREYGLT 191
                                       3444444444556899******7779**************999999865 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   3.5e-05     0.035      15      43 ..      21      50 ..      19      80 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsileal 43
                                      k++ ++++ + +  +iG+N++GK+++ ++ 
  gi|557693672|ref|YP_008796726.1| 21 KNINLEIEANeIRAIIGPNGAGKTTLFNVV 50
                                      55444444444**************98765 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 ?   11.6   0.0    0.0002       0.2      15      40 ..      25      50 ..      17      69 .. 0.81
   2 ?   -0.3   0.0      0.84   8.4e+02      71     107 ..     142     179 ..      92     213 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                          ATPase_2 15 lerepneiyfiYGpegsGKtaLlkei 40
                                      le e nei  i Gp g GKt+L++ +
  gi|557693672|ref|YP_008796726.1| 25 LEIEANEIRAIIGPNGAGKTTLFNVV 50
                                      56788*****************9865 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.84
                          ATPase_2  71 eeeekkklekalgiavpkaeleeilk.eksklvfkaie 107
                                       +e++k +l++al+++ +   ++e ++  ++++v++a++
  gi|557693672|ref|YP_008796726.1| 142 QERKKVELARALASKPRVLMVDEYMSgLNTAEVEEAVD 179
                                       33333334444444444444444444444444444444 PP

>> PEPcase  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   5.9e-05     0.059     303     393 ..     130     219 ..      98     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
                                       HHTTS.--GGGS-HHHHHHHHHHHHH-SS--S-TT----HHHHHHHHHHHHHHHS.-...TTSE.EEEEEET--SHH CS
                           PEPcase 303 eylglekdYaelseeervelLlreLeskrplipkelelseeteevldvlrviaelqeefgkeii.etyviSmaeeas 378
                                       e+ +++    +l+e+++vel  +  +++r l+ +e     +t+ev + ++ +++l++e+g +i+  ++viS   ++ 
  gi|557693672|ref|YP_008796726.1| 130 EKSEMKAGLLNLQERKKVELARALASKPRVLMVDEYMSGLNTAEVEEAVDLFRDLRREYGLTIVwVEHVISAVASLA 206
                                       444555666789*******99999999**********99*********************99873689*****9999 PP

                                       HHHHHHHHHHHTT-. CS
                           PEPcase 379 dvLevllLakeagll 393
                                       d   v++L + a+l+
  gi|557693672|ref|YP_008796726.1| 207 DK--VTVLNQGAKLA 219
                                       95..55566666555 PP

>> AAA_27  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      0.13      18      46 ..      22      50 ..      10      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAi 46
                                      +++++ e++++  i+GpN AGK+t+++ +
  gi|557693672|ref|YP_008796726.1| 22 NINLEIEANEIRAIIGPNGAGKTTLFNVV 50
                                      5677778999**************98765 PP

>> Phage_tail_X  Phage Tail Protein X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.9   5.8e+03      17      40 ..      12      37 ..      10      38 .. 0.57
   2 ?   10.6   0.0   0.00034      0.34      16      49 ..     185     218 ..     172     219 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.9
                                      HTTS--..TTTHHHHHHHSTTTTTT- CS
                      Phage_tail_X 17 ryYGrt..lgvveavleaNPgLAelg 40
                                      +y+G +  l+ ++  +eaN   A +g
  gi|557693672|ref|YP_008796726.1| 12 KYFGGLpaLKNINLEIEANEIRAIIG 37
                                      77776633444555577776666655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00034
                                       HHTTS--TTTHHHHHHHSTTTTTT-S---TTEEE CS
                      Phage_tail_X  16 wryYGrtlgvveavleaNPgLAelgpvLphGtav 49 
                                       +r YG t   ve+v+ a   LA+   vL +G ++
  gi|557693672|ref|YP_008796726.1| 185 RREYGLTIVWVEHVISAVASLADKVTVLNQGAKL 218
                                       578*************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1810.12
//
Query:       gi|557693673|ref|YP_008796727.1|  [L=405]
Description: branched-chain amino acid ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  192.8   0.5    1.4e-56  192.6   0.5    1.1  1  Peripla_BP_6   Periplasmic binding protein
    2.4e-22   79.5   0.0    3.2e-22   79.1   0.0    1.1  1  ANF_receptor   Receptor family ligand binding region
      6e-22   78.1   0.0    1.9e-21   76.5   0.0    1.6  1  Peripla_BP_5   Periplasmic binding protein domain
  ------ inclusion threshold ------
       0.21   12.2   1.1       0.86   10.2   1.1    2.2  1  LPAM_1         Prokaryotic membrane lipoprotein lipid attachm


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.6   0.5   3.2e-60   1.4e-56       1     319 [.      36     352 ..      36     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 192.6 bits;  conditional E-value: 3.2e-60
                                       EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEETTEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE-B CS
                      Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaGGinGrkielverDdaydpdraaeaarrlvdqdgvdalvgpl 77 
                                       ++kiG+l+pl+Gp+a +g   l+g++ a++e+Na+GG++G ++ lve+D ++d+++a++ ++r+ + d v+a+vg+ 
  gi|557693673|ref|YP_008796727.1|  36 EVKIGALVPLTGPFAVYGSYTLDGMRFAVDELNARGGVLGARVVLVEADEKNDAKEAVAIFKRMAEVDRVTAVVGTI 112
                                       69*************************************************************************** PP

                                       SHHHHHHHHHHHHHHT-EEEESS-HH...CCTTSTTEEES.S--HHHHHHHHHHHHHHHTTSCEEEEEEESSHHHHH CS
                      Peripla_BP_6  78 ssavaaavaevlakdgvpvigpaglt...gekcspyvfsl.gpsysaqasalveylakelggkkvalvyadyafgre 150
                                       ss++ a ++  +++++vp++ +a+++    +k s+y+f++ +p + + ++ l+++ +++ g k+v++v a y +g +
  gi|557693673|ref|YP_008796727.1| 113 SSGIGAVLSAEAEQAKVPLFLVAAGShtiLTKESRYTFRTcLPPAPTNGELLANF-VRDKGYKRVGVVIASYEWGFA 188
                                       *********************8866633358*******99457777888888887.7778***************** PP

                                       HHHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEECCC- CS
                      Peripla_BP_6 151 giaalkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillvswsg 227
                                       +++ l + +k++ g  ++ e+ plg+tdf++++++++  ++++ +l+g ++ ++++ k+a e G++    + ++ s+
  gi|557693673|ref|YP_008796727.1| 189 IRDVLDQRLKQLQGVQYQIEEAPLGETDFTTVLRKLQPLQPEVMILTGHPPGFPTITKQAIELGFQS---AYYIASV 262
                                       ***********9777779************************************************7...4567777 PP

                                       CHHHHHHHHH.HHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCTHCCHHH CS
                      Peripla_BP_6 228 seedlkalgg.eaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaagsltrea 303
                                        +++l+  g  +   g l++t+ +++ + p+ ++++++++++yg+  + +  a+ gy++++++++a++++ s+++ +
  gi|557693673|ref|YP_008796727.1| 263 QPPELMLRGVgDIGLGKLVTTTCVNS-EAPEYKQLAEKFYQKYGK--FFDHNAVTGYVTVMMIADAVEKTRSVDPVT 336
                                       77776666552346677777777766.58***************9..7***************************** PP

                                       HHHHHHHS-BECCCTC CS
                      Peripla_BP_6 304 vraaleslgfdgllgp 319
                                       v++ +++ ++++++  
  gi|557693673|ref|YP_008796727.1| 337 VANHIRTSEYNSPIFA 352
                                       **********997543 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 !   79.1   0.0   7.2e-26   3.2e-22       4     307 ..      58     343 ..      56     364 .. 0.86

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 7.2e-26
                                       HHHHHHHHHHHT-TTSSTTEEEEEEEEE-TT-HHHHHHHHHHHCCC.CEEEEEE-SSHHHHHHHHHHHCCTT-EEEE CS
                      ANF_receptor   4 eAmklAveeinsdpnllpgiklgyeiidtccdfslaleaaldflkg.kvvaviGpssssvsdavaslanlfkiPvis 79 
                                         m++Av+e+n+++++l+  ++ +   d+++d + a++++  + +   v av+G  ss+  ++++  a+++k+P++ 
  gi|557693673|ref|YP_008796727.1|  58 DGMRFAVDELNARGGVLGA-RVVLVEADEKNDAKEAVAIFKRMAEVdRVTAVVGTISSGIGAVLSAEAEQAKVPLFL 133
                                       57***********999976.999999*******************735***************************** PP

                                       SS---GG.GG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHHHHHHTT.-EEEEEE CS
                      ANF_receptor  80 ygstspe.lsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqaleeeleerg.icvalke 154
                                       +++ s + l++ +ry  f +  p++ + ++ +++ ++  g+k+v++++++ ++g  + + l ++l++ + ++ + +e
  gi|557693673|ref|YP_008796727.1| 134 VAAGSHTiLTKESRYT-FRTCLPPAPTNGELLANFVRDKGYKRVGVVIASYEWGFAIRDVLDQRLKQLQgVQYQIEE 209
                                       *******899988866.7777899999************************9**99999999999888856666666 PP

                                       EESTCHHHCHHHHHHHHHHTTT--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC..HHHH. CS
                      ANF_receptor 155 kipessnddevvrkllkeikskarvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpeltglea. 230
                                           +++++ v+rkl+     ++ v +l  +++    + k+a +lg+++    +ia        +++ pel  + + 
  gi|557693673|ref|YP_008796727.1| 210 APLGETDFTTVLRKLQ---PLQPEVMILTGHPPGFPTITKQAIELGFQS--AYYIA--------SVQPPELMLRGVg 273
                                       6554777777777776...8899**************************..77884........3333432233336 PP

                                       ...HTT-EEEEE--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSHCCB CS
                      ANF_receptor 231 ...aegvlgfrlkdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgrals 304
                                          ++++++ + ++++ p++++           +++y+++gk+ ++ +a + Y +V+++a A++k+++ ++ + a++
  gi|557693673|ref|YP_008796727.1| 274 digLGKLVTTTCVNSEAPEYKQLA---------EKFYQKYGKF-FDHNAVTGYVTVMMIADAVEKTRSVDPVTVANH 340
                                       668999999999************.........999*******.899*******************97775555555 PP

                                       -HH CS
                      ANF_receptor 305 cnt 307
                                        +t
  gi|557693673|ref|YP_008796727.1| 341 IRT 343
                                       544 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   4.3e-25   1.9e-21       1     315 [.      37     349 ..      37     352 .. 0.89

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 4.3e-25
                      Peripla_BP_5   1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvlgrkieavvvdpasdwelfaekaeklieedkvevvfGcwt 77 
                                       +k+G L  l+G  a+  + ++d++++a++e na+gGvlg ++  v +d + d++   +  +++ e d+v++v+G++ 
  gi|557693673|ref|YP_008796727.1|  37 VKIGALVPLTGPFAVYGSYTLDGMRFAVDELNARGGVLGARVVLVEADEKNDAKEAVAIFKRMAEVDRVTAVVGTIS 113
                                       69************************************************************************987 PP

                      Peripla_BP_5  78 SasRkavlpv.veelnalLfYpvqYEG...eEssknviYtGaapnqqaipavdyllselgakrvflvGsdyvypret 150
                                       S    avl+   e+ +  Lf          +  s+  + t   p     ++++ +++++g krv +v + y +    
  gi|557693673|ref|YP_008796727.1| 114 SGIG-AVLSAeAEQAKVPLFLVAAGSHtilTKESRYTFRTCLPPAPTNGELLANFVRDKGYKRVGVVIASYEWGFAI 189
                                       7665.5655516666666665443322112456888888999999988888888888889***************** PP

                      Peripla_BP_5 151 nrilkallkakggevvgeeYlplgssdvqkivakikkakpdvvlstinGdsnvafykelkeagikaekipvvslsva 227
                                         +l + lk+ +g + + e +plg++d++++++k++  +p+v++ t       ++ k+  e g+++  ++++s++  
  gi|557693673|ref|YP_008796727.1| 190 RDVLDQRLKQLQGVQYQIEEAPLGETDFTTVLRKLQPLQPEVMILTGHPPGFPTITKQAIELGFQS-AYYIASVQPP 265
                                       *************9999999************************9988888888888888889976.689******* PP

                      Peripla_BP_5 228 eeelaaidaealvGhlaawnYfqsvdtpenkafvakfkarvgedrvtndpmeaayiqvklwaqAvekagstdvekvr 304
                                       e  l++++     G+l +++  +s + pe k+  +kf +++g+    ++++ + y++v+++a Avek  s d+ +v 
  gi|557693673|ref|YP_008796727.1| 266 ELMLRGVGD-IGLGKLVTTTCVNS-EAPEYKQLAEKFYQKYGK--FFDHNAVTGYVTVMMIADAVEKTRSVDPVTVA 338
                                       *******98.778***99999998.89*************997..899999************************** PP

                      Peripla_BP_5 305 eallgqelkap 315
                                       ++++ +e+++p
  gi|557693673|ref|YP_008796727.1| 339 NHIRTSEYNSP 349
                                       ******99988 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.1   0.00019      0.86       1      16 [.       1      17 [.       1      17 [. 0.97

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00019
                            LPAM_1  1 MKKi.llalgalllLsG 16
                                      MK++ l+a++a++++++
  gi|557693673|ref|YP_008796727.1|  1 MKRSvLVAIVAVVVVAA 17
                                      ***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3121.12
//
Query:       gi|557693674|ref|YP_008796728.1|  [L=328]
Description: luciferase family protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-51  174.5   0.0    1.5e-49  169.2   0.0    2.2  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.2   0.0   8.2e-54   1.5e-49       2     260 ..       2     288 ..       1     297 [. 0.86

  Alignments for each domain:
  == domain 1  score: 169.2 bits;  conditional E-value: 8.2e-54
                    Bac_luciferase   2 efgvflptrqggalgaasaslrylvelaraaEelGfdavwvaehhggpgga.....ldaftllaalaaaTerirlgt 73 
                                       ++g+ lpt     ++++  s++ l++++ +aE+lG ++++v +h++ ++ a     +d++  l+ +aaaT++  +g 
  gi|557693674|ref|YP_008796728.1|   2 KLGLRLPTYA---RPGEFSSYETLKNYVAKAEDLGVEGFFVIDHLLTSRPAystswHDPLIALSFIAAATRKAIIGP 75 
                                       5555555555...222225899************************99888************************** PP

                    Bac_luciferase  74 avtplytrhPavlAqqaatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGef 150
                                       ++++l+ r+P++lA+q a+Ld  sgGRf+lg g g+++ e+r    + ++r a ++E++ +l++lw++++++feG+f
  gi|557693674|ref|YP_008796728.1|  76 MILVLPFRNPYLLAKQLASLDVYSGGRFVLGAGVGWNPDEFRLLNTPLEKRGAIMDEYLVLLKKLWTDDKITFEGKF 152
                                       ******************************************************************99999****** PP

                    Bac_luciferase 151 fsvkgalllprpgqgpiP.vyvaaas.p.............aglelaarhadglllag.eppeeaaelierlragaa 211
                                       f+v+++ l p+p q+p+P ++++++s p             + l   a++adg+++++ ++pe a++  e++++ a 
  gi|557693674|ref|YP_008796728.1| 153 FNVRDLVLEPKPLQKPHPpIWIGGGSqPheilygaaakgidRVLYRVAKFADGWIPHSsSTPEMARQDWEKVKKYAT 229
                                       ****************44488877775533333333322225677899***************************** PP

                    Bac_luciferase 212 eagrdpadirvgisltviva...dteeeAraea.......raliagldfyaldsegagr 260
                                       e grdp +i+ ++s ++++     ++eeA +++       +++++ ++ y + +e+a+ 
  gi|557693674|ref|YP_008796728.1| 230 ELGRDPYKIQKVYSNFIYIKspgSSDEEAVKRFslysgmnLDYWRTFYLYGTVEELAEK 288
                                       *****************998888999999999977777777777666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2619.17
//
Query:       gi|557693675|ref|YP_008796729.1|  [L=394]
Description: amidohydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-11   44.3   1.7    2.1e-10   40.4   1.7    2.2  1  Amidohydro_1   Amidohydrolase family
    3.8e-09   36.5   2.5     0.0003   20.4   0.2    3.0  2  Amidohydro_3   Amidohydrolase family
    4.8e-06   26.1   0.0    7.2e-06   25.6   0.0    1.3  1  TatD_DNase     TatD related DNase
     0.0028   17.4   0.2      0.011   15.5   0.1    2.1  2  FAD_binding_4  FAD binding domain
  ------ inclusion threshold ------
      0.023   14.3   0.0      0.037   13.6   0.0    1.3  1  MR_MLE_C       Enolase C-terminal domain-like


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 !   40.4   1.7   5.9e-14   2.1e-10       1     341 [.      55     364 ..      55     366 .. 0.65

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 5.9e-14
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH........HHHHHHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst........gieallea 69 
                                       +v+PGl D+HvH  ++             + t ++ +  +i+  + +G+ t++ +g+++ +        + +al+  
  gi|557693675|ref|YP_008796729.1|  55 TVMPGLFDSHVHPVFG-------------DFTPRQNTLGFIESSVHGGVATFISAGEVHLPgrprgdkeASKALAII 118
                                       69**********8644.............456678999***********************6555555433333333 PP

                                       HHT.....SSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHH CS
                      Amidohydro_1  70 aee.....lplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealke 140
                                       a++      plg  i++g + l  +++ t+ +  e ++ag+    +     +v  v+l   + ++ + +e +++++ 
  gi|557693675|ref|YP_008796729.1| 119 AHKsfkniHPLGAKIHAGALLL--EKGMTDADFEEVVRAGV----W-----LVGeVGL---GSVQDP-DEAAAMVRT 180
                                       3331212333333333333333..44455555555555555....2.....2222222...344443.477788889 PP

                                       HHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHH..HHHHHHHHHHHHCE CS
                      Amidohydro_1 141 akkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpt..eaellkerlkeagv 215
                                       a k++++v+iH+++ +   + + +a +        l+v+ +        +    g + +p+  +++ ++e+l+ + +
  gi|557693675|ref|YP_008796729.1| 181 AQKHGMKVVIHTGGASIPGSTINNAEV-------VLKVRPD-------VVSHINGGPTSPSlqDIRKIIENLN-SAI 242
                                       ************777777756666666.......7788555.......3444556666677779999999943.333 PP

                                       EHHHHHHHHSEHHHHHHHHHHHH.TSC.EEEEEECTTSSCCG..GHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHH CS
                      Amidohydro_1 216 ahcpfsnsilrsgrealrkalde.Gvk.vglgtDgaasgnsl..nlleelrlalklqrgllyedeegglslkealrm 288
                                         +++ n   rs +e +r + ++  ++  ++g D  +   ++   +++++ + +          +++++++++++ +
  gi|557693675|ref|YP_008796729.1| 243 EVVQCGN--FRSMLETVRILKHRnELHrLIIGNDAPSGTGVIplGIIRTISFIA----------SNTDVEAEKIVCA 307
                                       3344444..5666666666666656656******66555555345555555555..........5889********* PP

                                       HTHHHHHHTT-TTTSSSS-TTSB--EEEECC..CT....CGGGTTTCTSEEEEEEEETT CS
                      Amidohydro_1 289 aTingAkalglddkvGsievGkdADlvvvdl..di....laafvglkkdgnvkkvivkG 341
                                       a+ n+ +++gl  + G ie G++ADlvv+d    +      + + + +   +++v+++G
  gi|557693675|ref|YP_008796729.1| 308 ASGNTGRVFGL--REGIIETGRPADLVVIDApyGSvakdAVEAFSIGDIPGIAMVMIDG 364
                                       ***********..****************998722455544444444555588888888 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.2   1.1e-05      0.04       2      21 ..      48      67 ..      47      78 .. 0.89
   2 !   20.4   0.2   8.3e-08    0.0003     262     469 ..     170     364 ..     128     368 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                      Amidohydro_3  2 viDakGrlvlPGFvDsHtHl 21
                                      v D ++++v+PG+ DsH H 
  gi|557693675|ref|YP_008796729.1| 48 VFDINNMTVMPGLFDSHVHP 67
                                      7899***************4 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 8.3e-08
                      Amidohydro_3 262 dea.laelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegv.tesqiervaalqvaagvqp 336
                                       d +  a++v+ a+++g+ v ih+ g++    +++  e + +  ++     ++h  g  t   +++++++       +
  gi|557693675|ref|YP_008796729.1| 170 DPDeAAAMVRTAQKHGMKVVIHTGGASIPGSTINNAEVVLKVRPD----VVSHINGGpTSPSLQDIRKIIENLNSAI 242
                                       444488888888888888888888887777777777666333333....4666666665555555555544444442 PP

                      Amidohydro_3 337 vfnfedelldsrlg.perargstpvkellnagvkvalgsD.apvgpfdpwprigaavmrktrrggevlrpdeelsle 411
                                        ++          g    +  + ++   +n  ++++ g+D + ++ + p+  i++               + +++ e
  gi|557693675|ref|YP_008796729.1| 243 EVVQ-------C-GnFRSMLETVRILKHRNELHRLIIGNDaPSGTGVIPLGIIRTISF---------IASNTDVEAE 302
                                       2222.......1.223444444666666677788888888777777777666555554.........3457889*** PP

                      Amidohydro_3 412 ealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear......vrltvvdG 469
                                       +++++ + ++ +++gl++  G +e G +ADlvv+da    v ++++          + ++++dG
  gi|557693675|ref|YP_008796729.1| 303 KIVCAASGNTGRVFGLRE--GIIETGRPADLVVIDAPYGSVAKDAVEAFSigdipgIAMVMIDG 364
                                       ******************..***************77666665533222244666666666666 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0     2e-09   7.2e-06       1     254 [.      61     316 ..      61     317 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2e-09
                                       EEEEE-TTSCCC..TTTHHHHHHHHHHTTEEEEEEE-SSG.........GGHHHHHHHHTT..TTTEEEEE---GGG CS
                        TatD_DNase   1 iDaHcHldskef..eedreeileraeeagvaavvvvgtss.........kdskavlelakk.ypnkvyavlGiHPne 65 
                                       +D+H+H+ + +f   ++  + +e+  ++gva++++ g  +         ++ska+  +a+k ++n       iHP  
  gi|557693675|ref|YP_008796729.1|  61 FDSHVHPVFGDFtpRQNTLGFIESSVHGGVATFISAGEVHlpgrprgdkEASKALAIIAHKsFKN-------IHPLG 130
                                       7********8885566688999************7777667777777745666666666665555.......77754 PP

                                       GGCC.CCHH.......HHHHHHHHCCCTSEEEEEEEEEET-CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-H CS
                        TatD_DNase  66 vdeasedll.......eelkelanvkhskvvaiGeiGLDyysreestkeaqeevFeeqlrlAkelklplviHlrkae 135
                                       ++ +   ll       ++++e   v +  v ++Ge+GL  + +++++         +++r A++++  +viH++ a 
  gi|557693675|ref|YP_008796729.1| 131 AKIHAGALLlekgmtdADFEE---VVRAGVWLVGEVGLGSV-QDPDEA-------AAMVRTAQKHGMKVVIHTGGAS 196
                                       444322332332222234444...4556999*******993.332222.......46899***************99 PP

                                       HHHHHHHHHCGGCCS..EEEETT....--S-HHHHHHHH.HTTEEEEE-GGGGTTTTHHHHHHH.HHS-GGGEEE-- CS
                        TatD_DNase 136 edlleilkeaaeaka..kvvlHs....fsgsaeeakkfl.klgyyislsglltfknakelrelv.kavpldrlLiET 204
                                            i +++   k+   vv H     +s s + ++k++ +l++ i +  + +f++  e+ +++  + +l rl+i+ 
  gi|557693675|ref|YP_008796729.1| 197 IPGSTINNAEVVLKVrpDVVSHInggpTSPSLQDIRKIIeNLNSAIEVVQCGNFRSMLETVRILkHRNELHRLIIGN 273
                                       98888888887777777*****99999************888**************9999999977899******** PP

                                       -TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
                        TatD_DNase 205 DaPyltpkpyrgkrnepanvayvveklaelkaltleelaeitaeNakrlf 254
                                       DaP +t          p  + +++  +a  ++++ e++  +++ N+ r+f
  gi|557693675|ref|YP_008796729.1| 274 DAPSGTG-------VIPLGIIRTISFIASNTDVEAEKIVCAASGNTGRVF 316
                                       *987776.......778888888888888888888888888888887777 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   3.1e-06     0.011       7      51 ..     168     212 ..     164     222 .. 0.89
   2 ?   -2.7   0.0       1.3   4.6e+03     112     137 ..     243     268 ..     239     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-06
                                       ESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEET CS
                     FAD_binding_4   7 peseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldls 51 
                                       +++++e aa +r a+++g++v++  gG s+ g+ +++  vvl+++
  gi|557693675|ref|YP_008796729.1| 168 VQDPDEAAAMVRTAQKHGMKVVIHTGGASIPGSTINNAEVVLKVR 212
                                       6789******************************99999999883 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                       TEEGG--HHGTEEEEEEEETTSEEEE CS
                     FAD_binding_4 112 gsekyGlirdnvlglevvladGevvr 137
                                        + + G++r++++ ++++  + e++r
  gi|557693675|ref|YP_008796729.1| 243 EVVQCGNFRSMLETVRILKHRNELHR 268
                                       56778999999999999887777665 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 ?   13.6   0.0     1e-05     0.037     109     172 ..     145     210 ..     135     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                                       SHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCS.S.HHHHHHHHHHHHT CS
                          MR_MLE_C 109 sradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgs.g.glglaaslhlaaa 172
                                       + adf+e+++ag+  +  + ++ v  ++ea ++++ a+++g++v++H+g+ + + +++ ++ +   
  gi|557693675|ref|YP_008796729.1| 145 TDADFEEVVRAGVWLVGEVGLGSVQDPDEAAAMVRTAQKHGMKVVIHTGGaSiPGSTINNAEVVLK 210
                                       6789********************************************643457777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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 0.24s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2974.38
//
Query:       gi|557693676|ref|YP_008796730.1|  [L=768]
Description: molybdopterin binding oxidoreductase large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-166  554.6   0.7   2.8e-166  554.2   0.1    1.4  2  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    7.5e-19   68.1   0.0    1.5e-18   67.1   0.0    1.6  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 ?   -2.7   0.0      0.16   1.5e+03     207     234 ..      86     115 ..      84     118 .. 0.73
   2 !  554.2   0.1  3.2e-170  2.8e-166       1     550 []     136     704 ..     136     704 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.16
                                       E-SSTTTHHHHHHHHHHHHHHH..HHHHT- CS
                     Ald_Xan_dh_C2 207 tafRGfGgpqamfalErlmdel..Aeelgl 234
                                       + +R fG+p am+a+E+l d+l  A+e+ +
  gi|557693676|ref|YP_008796730.1|  86 GKVRFFGEPVAMVAAETLGDALdaADEVSV 115
                                       5678899********999886422555555 PP

  == domain 2  score: 554.2 bits;  conditional E-value: 3.2e-170
                                       STTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHH CS
                     Ald_Xan_dh_C2   1 vheeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlv 75 
                                       vhe++++nv+   ++ +G+ve++faead+vv+++f++ r + +++Et++++avp ++dg+ltvy + q+p+  r+ +
  gi|557693676|ref|YP_008796730.1| 136 VHENLGSNVALsrRFVFGEVEKVFAEADTVVKEKFYFDRYASAPIETCGVVAVP-GKDGSLTVYDNQQTPQLFRKSI 211
                                       68999999999888889*************************************.99******************** PP

                                       HHHHT--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS CS
                     Ald_Xan_dh_C2  76 aevlglpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdG 152
                                       a+ lg+ ++k+r+i  ++GGGFG+K+  +p+ +l ++aA+k++rpVk+v++R+e+++a ++ ++  + ++++++kdG
  gi|557693676|ref|YP_008796730.1| 212 AQSLGIRPEKLRFIEHDIGGGFGVKIMLYPYVFLTCFAALKLRRPVKWVETRQEHLTAMAHNSNRVTVAEMALRKDG 288
                                       ***************************************************************************** PP

                                       -EEEEEEEEEEEESSTHHH.CHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 153 kitaldvdlladaGayadl.spavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdel 228
                                       ++t+++  ++ d+Gaya l  p+ + r l++  g+Y+i+nv +e++vv tN++p++++RG+G  qa+f+lEr+md +
  gi|557693676|ref|YP_008796730.1| 289 RVTGYRTSFIEDVGAYARLpDPGGTVRSLMTYLGCYDIQNVAIEFKVVLTNKCPTGPVRGYGCQQAYFVLERMMDIA 365
                                       ****************86615566669999999******************************************** PP

                                       HHHHT--HHHHHHHHBCECGCC.SEEET...EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEE CS
                     Ald_Xan_dh_C2 229 AeelgldplelRrrNlikpgeltpygqp...vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvve 302
                                       A+elgl p+e+R +N++++++  py++    +yd gd++++l k+ + s+ e+        ++    +G+g+a+vve
  gi|557693676|ref|YP_008796730.1| 366 ARELGLTPVEIRLKNMVEKENQ-PYRTVfgsLYDGGDYKATLLKAWSLSQAEKY-----LVKD---DVGVGVACVVE 433
                                       *****************99999.****88899************9998855433.....2222...49********* PP

                                       EBS--S...EETTEE............EEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-S CS
                     Ald_Xan_dh_C2 303 giglgf..takflnq............egalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvveg 365
                                       +++++   +     +            ega vr++++G +t++ ++ ++GqG+ t+l++i++e Lgv++e+vrvv g
  gi|557693676|ref|YP_008796730.1| 434 PAVTNLarN-----KllfpelessgsgEGAVVRLEESGMITLYAASIPQGQGHATVLTEIVSELLGVKPEQVRVVFG 505
                                       **8887652.....223335677888899************************************************ PP

                                       BTTSS...S----S-TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET..EEEECHHHHHHH CS
                     Ald_Xan_dh_C2 366 dtdkv...pngsgtaaSrstdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk..eksvslaelaaa 437
                                       dtd v   p  +gt+aSr ++++ +Avkk +e+l++r+l+iaae+le+s+edle++dgk++vk  + s+sl++laa 
  gi|557693676|ref|YP_008796730.1| 506 DTDFVypsP-YGGTWASRFSVMTVAAVKKSCETLKQRILEIAAEILETSTEDLEIRDGKISVKgsDVSISLEKLAAI 581
                                       ****96433.446**************************************************999999******** PP

                                       HHH.......TTSSEEEEEEE......EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHH CS
                     Ald_Xan_dh_C2 438 ayl.......ervslsatgfykt...ldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpai 504
                                       ay+       +  sl+a+ fy+     + e gk ++ a++ + a+va+V+vD+etgevk+lr+v+vhD+Gk++N++i
  gi|557693676|ref|YP_008796730.1| 582 AYRnslttngRHTSLQAEYFYEFptfNTGEPGKINMSATYGNSAHVAVVKVDRETGEVKILRYVAVHDCGKILNKKI 658
                                       **99999988888********887765666667777889999*********************************** PP

                                       HHHHHHHHHHHHHHHHHT---EEETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 505 vegQieGGfvqGiGlalmEelvydedGqlltasladYkiPtaadiP 550
                                       v+gQi+GG++qGiG++l+E++vyde+Gqllt+ ++dY++Pta+++P
  gi|557693676|ref|YP_008796730.1| 659 VDGQIMGGVMQGIGATLYEKIVYDENGQLLTSHFSDYLLPTARETP 704
                                       *******************************************998 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 !   67.1   0.0   1.7e-22   1.5e-18       2     110 .]      15     121 ..      14     121 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 1.7e-22
                                       T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEES CS
                      Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkvr 78 
                                       Ge+ ++dD+++p++++l fvrS++ hA+i+si+  ++l+    va i++k +++e k   + ++d + + +a  kvr
  gi|557693676|ref|YP_008796730.1|  15 GEGLFIDDLAFPKMVHLVFVRSPYGHANIKSINSGESLRRA--VAAIDGKTVATETKPLYTLIRDVPYYGIAVGKVR 89 
                                       999*******************************9999888..999************99999999999******** PP

                                       STT-EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                      Ald_Xan_dh_C  79 svgqavaavvAedeetArkAaklvkveYeelp 110
                                       + g++va+v+Ae+   A +Aa+ v+v+Ye+lp
  gi|557693676|ref|YP_008796730.1|  90 FFGEPVAMVAAETLGDALDAADEVSVDYEPLP 121
                                       *****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (768 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 5249.93
//
Query:       gi|557693677|ref|YP_008796731.1|  [L=249]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-40  139.6   3.4    2.5e-40  139.1   3.4    1.2  1  SIMPL     Protein of unknown function (DUF541)


Domain annotation for each model (and alignments):
>> SIMPL  Protein of unknown function (DUF541)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.1   3.4   1.4e-44   2.5e-40       1     200 []      49     246 ..      49     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: 139.1 bits;  conditional E-value: 1.4e-44
                             SIMPL   1 ItVtGsaevevapDqatltlsvesegkdaaeakaevaekmnavlealkklgikekdiqtsslslkpeysy.engknk 76 
                                       ++VtG+a+++++pD+  +t+ v++++++++ea a+++ek+n+v++a+  lgi+ ++i+t+s++++pey+y ++++++
  gi|557693677|ref|YP_008796731.1|  49 LSVTGTAQATIVPDTLAITFVVQEKAPTPSEALAKLSEKANRVVSAVLGLGISSENIKTTSVNISPEYTYpDKEPPR 125
                                       58********************************************99779*999********************** PP

                             SIMPL  77 itgyeasqsltvkfrdldklgevldaavka.aneingvsfsls.de.delrdeareeAvkdArakAealAkalgvkl 150
                                       + gy+a+ s++v+++   ++g+++d+av+a a++++g+ f++s ++ +  +++++ +A+ dA+akAe + + l+++ 
  gi|557693677|ref|YP_008796731.1| 126 LIGYVATYSIEVRTKRVADAGTLIDTAVNAgADQVSGLYFTVSpEQySTVYRQLLSAAIGDAEAKAESVLRPLNLRK 202
                                       **************99999************************433566699*******************999877 PP

                             SIMPL 151 gkvvsisesgsnpyappapamaaaaaaaasaatpfepgeievtasVtvvf 200
                                        +v+s+s+   +p      a +a+aaa+as+++p+ +g++++t+sV+vv+
  gi|557693677|ref|YP_008796731.1| 203 TGVKSVSVMDVQP------AYPARAAAEASSGPPILAGTTTLTVSVNVVY 246
                                       7899999832222......23333344799******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1778.61
//
Query:       gi|557693678|ref|YP_008796732.1|  [L=285]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-31  107.7  41.7    4.8e-19   68.9  16.0    2.0  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 !   45.2  17.7   5.7e-16     1e-11       4     134 ..       7     136 ..       4     139 .. 0.89
   2 !   68.9  16.0   2.7e-23   4.8e-19       2     136 ..     150     284 ..     149     285 .] 0.95

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 5.7e-16
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80 
                                       +l  + a +f++++ ++ +  l+ v+ +t++++r l+ag+ll+++a+++ +++ + + + +   + l  +   + f+
  gi|557693678|ref|YP_008796732.1|   7 VLQGVGAGFFFGTASIFVRF-LAGVDAFTIVVFRVLVAGLLLSVLAAFFFRSDVVNTFRKFPREIPLLGFLLSFHFI 82 
                                       5567899***********88.7********************99998888888455556666667777777788889 PP

                              EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvll 134
                                       +f+ ++++ts+ na+ +++++P+++l +++ l   k+t   ++g+vl+++G + 
  gi|557693678|ref|YP_008796732.1|  83 FFVLGVQNTSVVNATTLVNTTPAMALAIGWGLGWTKPTNVNVIGLVLAVAGSAT 136
                                       ***************************************************876 PP

  == domain 2  score: 68.9 bits;  conditional E-value: 2.7e-23
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       lg ++a+l+a+fwa+y v+ k++ ++v+ +++++  +l+ ++  l+ a l ++ l  l+  + l+ll l+l++tvl+
  gi|557693678|ref|YP_008796732.1| 150 LGNVYAVLGAFFWALYLVVGKRVRQEVNIFAVFGPLLLFTSLPALAAAYLLGRGLYPLNTAQTLFLLALALFPTVLG 226
                                       68999*****************************99999999999999999999967777789999*********** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       ++l+f++l+ + + +as + +leP+++++l+++ll e  +  ++lg++ ++lG++l++
  gi|557693678|ref|YP_008796732.1| 227 HGLQFSSLRGLHPYQASSLALLEPIVAALLAAVLLAEVAGPVTYLGAAAVILGIYLVI 284
                                       ********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); 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 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1944.52
//
Query:       gi|557693679|ref|YP_008796733.1|  [L=329]
Description: ornithine cyclodeaminase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-79  266.6   0.1    2.6e-79  266.5   0.1    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    0.00031   20.8   0.0    0.00068   19.7   0.0    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0013   19.2   0.0     0.0032   18.0   0.0    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.054   14.3   0.0      0.096   13.5   0.0    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


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 !  266.5   0.1   5.7e-83   2.6e-79       4     312 ..      15     324 ..      12     329 .] 0.96

  Alignments for each domain:
  == domain 1  score: 266.5 bits;  conditional E-value: 5.7e-83
                                       EEE-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCC CS
                   OCD_Mu_crystall   4 avltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkks 80 
                                       ++lt  ev  ++   ++++ave a+  ++ g+v +p+r ++e +++ g+l +mp   +  + +++Klv+++p n ++
  gi|557693679|ref|YP_008796733.1|  15 KFLTDDEVAFLVDPVKVVEAVERAYILYSTGRVVMPVRSRVENREQGGDLLMMPCLVPDMGIFSLKLVTVYPRNLEK 91 
                                       6778888888888889************************************************************* PP

                                       TSSSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEE CS
                   OCD_Mu_crystall  81 glptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikev 157
                                       glpt +a+v+ +d +tG+p ++ +a  lt lRTaA+ av+ k+Lar+d ++++iiG G qa+ ql+++ a  + +  
  gi|557693679|ref|YP_008796733.1|  92 GLPTINATVIALDASTGMPRLVAEARALTGLRTAAATAVSIKHLARRDFTRVGIIGTGYQARWQLRVVAANHPHTVF 168
                                       ***************************************************************************** PP

                                       EEE-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-H CS
                   OCD_Mu_crystall 158 riydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLdd 234
                                       + yd+d +  + f++++ + + +v+ +  +ee v   d+v+tvT++k+p++ ++wvk+G+hi a+g+  p+  e+++
  gi|557693679|ref|YP_008796733.1| 169 KAYDIDSRRLNEFVTEMGRLGHDVKPSPTAEELVRWSDVVITVTTSKQPVVLKSWVKEGTHISAIGGYTPEMVEIEP 245
                                       ***************************************************************************** PP

                                       HHHHCCEEEESHHHHH.HHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHHH CS
                   OCD_Mu_crystall 235 dilkradifvdseaqa.reeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaaklv 310
                                        +++ ++++vds ++  +e G+i  +i +g+++ +++ ae+ge+ aG kpGR +++eit+f+svGlav+D a+akl 
  gi|557693679|ref|YP_008796733.1| 246 VLVAGSKLVVDSREAVrEEAGDILKPIMLGLMRFEDIYAEIGEIAAGLKPGRIDEREITVFKSVGLAVQDAATAKLL 322
                                       **********6666551567*******************************************************98 PP

                                       HH CS
                   OCD_Mu_crystall 311 ye 312
                                        +
  gi|557693679|ref|YP_008796733.1| 323 ID 324
                                       76 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.5e-07   0.00068      13     100 ..     141     229 ..     129     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-07
                                       -EEEEES-SHHHHHHHHHHHCCT-CEEE.EEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS- CS
                      Shikimate_DH  13 kkvlliGaGemaelvakhLlakgvkkvv.vaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseep 88 
                                        +v +iG+G  a+  ++  +a++ + v+     + +r +e+++e++     +++    +el++ +dvvi+ t s++p
  gi|557693679|ref|YP_008796733.1| 141 TRVGIIGTGYQARWQLRVVAANHPHTVFkAYDIDSRRLNEFVTEMGRLGHDVKPSPTAEELVRWSDVVITVTTSKQP 217
                                       6899**************99999998772457789999*******999999************************** PP

                                       SB-HHHHHCCHH CS
                      Shikimate_DH  89 ilekeeveealk 100
                                       ++ k++v+e  +
  gi|557693679|ref|YP_008796733.1| 218 VVLKSWVKEGTH 229
                                       *******99765 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 !   18.0   0.0   7.1e-07    0.0032       1      81 [.     142     223 ..     142     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.1e-07
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.....-EEECECHHHHHHH-SEEEE-S-HH CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.....vkvtavdneeaaeeadvvvlavkpe 72 
                                       ++giiG+G +++  ++ ++a+   ph +  a + +  +++e+  e+g     vk ++ ++ee+++ +dvv+ +v ++
  gi|557693679|ref|YP_008796733.1| 142 RVGIIGTGYQARWQLRVVAANH--PHTVFKAYDIDSRRLNEFVTEMGrlghdVKPSP-TAEELVRWSDVVI-TVTTS 214
                                       69**********9999666665..**************************9999999.99*****999875.67777 PP

                                       HHHHHHHHC CS
                     F420_oxidored  73 dveevlsel 81 
                                       + + vl+++
  gi|557693679|ref|YP_008796733.1| 215 KQPVVLKSW 223
                                       777777776 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 ?   13.5   0.0   2.1e-05     0.096       2      59 ..     142     203 ..     141     231 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.1e-05
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH.....HHHTTHEEESSHHHHHT CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeav.....aesfgveaysdleella 59 
                                       rv+iiG+G+ ++++lr + ++ + + v  ++d+d+ r  ++     +   +v+     eel++
  gi|557693679|ref|YP_008796733.1| 142 RVGIIGTGYQARWQLRVVAAN-HPHTVFKAYDIDSRRLNEFvtemgRLGHDVKPSPTAEELVR 203
                                       89*************666555.9999************9994442222222223334555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); 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:                         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: 00:00:00.42
# Mc/sec: 2355.67
//
Query:       gi|557693680|ref|YP_008796734.1|  [L=759]
Description: hypothetical protein CSUB_C0243 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  156.3   4.1    3.2e-26   92.3   0.9    2.5  3  Peptidase_S8  Subtilase family
  ------ inclusion threshold ------
      0.086   12.9   0.4       0.19   11.8   0.4    1.6  1  Osw5          Outer spore wall 5


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 ?   -3.1   0.0      0.42   3.7e+03     247     260 ..      41      54 ..      40      55 .. 0.88
   2 !   64.2   0.0   1.3e-21   1.2e-17       1     210 [.      94     312 ..      94     340 .. 0.72
   3 !   92.3   0.9   3.5e-30   3.2e-26     171     298 .]     402     547 ..     385     547 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.42
                                       HHHCHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx RF
                      Peptidase_S8 247 TSmAsPnaagaaAl 260
                                       +S AsP+++ ++A 
  gi|557693680|ref|YP_008796734.1|  41 SSGASPVVSEMLAE 54 
                                       699********995 PP

  == domain 2  score: 64.2 bits;  conditional E-value: 1.3e-21
                                       -TT-EEEEECS-B-TT-TTTGGGEEE..EEEE---TTSG...........GGEETT-SS-TT-SC-SSS.....HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                      Peptidase_S8   1 gkgvlvavlDtGvdpshpdlsvttdgerklvdvideegag..........fngadsettstnwarddngnsie.HGt 66 
                                       g+gvl+av+DtGvd+ hp ++  t +   +v + d+++ g                +  +  +++  + +  + HGt
  gi|557693680|ref|YP_008796734.1|  94 GRGVLIAVVDTGVDYRHPAFR--TGNGTRIVAIWDQTVEGkppqgfgygyE----CDRQEILSGTCPQRDT-VgHGT 163
                                       89*******************..8888999999999888888888653332....2222222222222323.24*** PP

                                       HHHHHHH-B..SSSSSB-SSTTSEEEEEE-SSTTSB-HH..HHHHHH..HHHHHHCT-S.........EEEE-EESC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.........xxxxxxxxx RF
                      Peptidase_S8  67 hvAGiaaanapeegekngvapgakilsvkvldtsggsmetgtelira..ieeaaedkvd.........vinmslges 132
                                        vA+iaa++   +    gva g ++  vk +++  +     ++  +   + + +   vd         v+ +slg +
  gi|557693680|ref|YP_008796734.1| 164 VVASIAAGGVYGDWVLRGVAAGSELVVVKTGGPACSGT---RWFFSEkgLLDGVAYTVDkakqlgrrlVVVLSLGTD 237
                                       *********99999************999886544332...222222222222222222333566778*******77 PP

                                       ETTCHHCHHHHHHHHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTSTTCEEEEEESTTSSB-TT--B-TT. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 133 tslpktgrsiealainravnkkgvlvviSaGNngktgsslqagspvgtpstsknvitvgayttegkiapfSsrGpss 209
                                           + ++  e+ a++++ +++gv++v++aGN+ ++  ++ ++ + g   t +  +t+   tte+ ++  + +G+++
  gi|557693680|ref|YP_008796734.1| 238 IGAHDGSTPLEK-ALDKWAEENGVVFVVAAGNSANDSRHIETTLTQGIQLTLR--MTIPEQTTEAALSLVTHSGNVM 311
                                       777777776664.888888899************8888777777777777766..7777777777777777777776 PP

                                       . CS
                                       x RF
                      Peptidase_S8 210 d 210
                                       +
  gi|557693680|ref|YP_008796734.1| 312 E 312
                                       5 PP

  == domain 3  score: 92.3 bits;  conditional E-value: 3.5e-30
                                       EEE-TTCEECTTTSTTCEEEEEES................TTSSB-TT--B-TT.......-EEEE-S-CCCCCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 171 slqagspvgtpstsknvitvgayt................tegkiapfSsrGpssdgklkpdivapGgnivstwsrq 231
                                       s++++ +v  p+t++ v+tvgay+                t g+i  +S rGp++dg+ kpdi+apGg +++  sr+
  gi|557693680|ref|YP_008796734.1| 402 SITSSYTVTIPGTARKVLTVGAYNtrktwtaggetwsvggTVGDIEFYSGRGPTTDGRTKPDITAPGGVVFAARSRD 478
                                       678999***************************************************************88888888 PP

                                       CHHHTTTHH..EEEE-SHHHCHHHHHHHHHHHHHHHTT--HHHHHHHHHCCS-EE......SSSSSSTT CS
                                       xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 232 snnsaglss..yqsmsGTSmAsPnaagaaAlllsalpkltpetvraallntAqdlgkadniesfaqGaG 298
                                       +  +a + s  +    GTSmA+P+aag+aAl+l+  p l+pe+v +++ ntA+  +    ++s+  G+G
  gi|557693680|ref|YP_008796734.1| 479 APRQAFSPSeeTAVSRGTSMAAPHAAGVAALILQLAPTLSPEEVFEIIRNTARQDSYTGDAVSNTWGHG 547
                                       7655544447899***************************************99988889999999998 PP

>> Osw5  Outer spore wall 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   2.1e-05      0.19      12      38 ..       3      30 ..       1      36 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.1e-05
                              Osw5 12 liigviaslfilPLLgiSfifat.gvvv 38
                                      +++g +a+l+i+ LL+iS +f++ gvv 
  gi|557693680|ref|YP_008796734.1|  3 VLVGRAATLLIIALLTISSVFSShGVVA 30
                                      57899****************9835555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (759 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.26s 00:00:00.90 Elapsed: 00:00:00.42
# Mc/sec: 5375.46
//
Query:       gi|557693681|ref|YP_008796735.1|  [L=211]
Description: adenine phosphoribosyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   49.2   0.1    4.7e-13   49.0   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 !   49.0   0.1   2.6e-17   4.7e-13       2     144 ..      37     194 ..      36     204 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 2.6e-17
                                       HHHTTT---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE....... CS
                      Pribosyltran   2 gsellenpaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssde 78 
                                       + ++ + p++++a+arl + +  + ++  d+v+ +++ G   + +la+eL+ p++ + k k+   +++++a+g+s+ 
  gi|557693681|ref|YP_008796735.1|  37 WLNVVHEPEVFRAIARLVKIHAAKMGYDADAVASVETSGAKYGLALANELGKPYFSIHKAKKLIFQQPVTAEGFSVT 113
                                       7788899*******************************************************999999999999988 PP

                                       .........EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE.......E-HHHHHHHHHH-TTS CS
                      Pribosyltran  79 s........rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlv.......dkpateeevdknakrv 140
                                                 ++     + V+++DD+  t +T++ a++lL e+g+++  + v++        +p ++ ++++++ +v
  gi|557693681|ref|YP_008796735.1| 114 EskpvtlhlDKAVASQFRNVFLIDDVRRTSTTINTAADLLNECGAQVTACYVIIdlafaghPRPVKVPRDRYHPLFV 190
                                       88999**9888888999*************************************88888777788888888888877 PP

                                       .... CS
                      Pribosyltran 141 fsls 144
                                       +s  
  gi|557693681|ref|YP_008796735.1| 191 ISSV 194
                                       7544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1562.39
//
Query:       gi|557693682|ref|YP_008796736.1|  [L=373]
Description: major facilitator superfamily MFS [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   88.8  51.0    4.1e-25   88.5  42.3    2.0  2  MFS_1       Major Facilitator Superfamily
    2.3e-08   33.7  31.8      3e-08   33.4  31.8    1.0  1  MFS_4       Uncharacterised MFS-type transporter YbfB
  ------ inclusion threshold ------
       0.17   10.2   7.2      0.096   11.0   2.5    2.3  2  OATP        Organic Anion Transporter Polypeptide (OATP) fami
       0.47    9.3  18.1      0.086   11.7  11.4    2.4  2  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 !   88.5  42.3     9e-29   4.1e-25       1     353 []       8     331 ..       8     331 .. 0.86
   2 !   12.6   9.8   1.1e-05     0.048      95     175 ..     288     364 ..     281     371 .. 0.86

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 9e-29
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalgl 76 
                                       l++a++ + + ++ l p+lp +la +   s++++ l+ t+y  +a+++++ +G++ dr  ++  ++ lgl+l ++++
  gi|557693682|ref|YP_008796736.1|   8 LFFAHLANDTLYTSLPPLLP-LLAAQQKTSAATLALIPTVYLMTASFLQIAVGFFFDRR-PKTvLMPLGLFLGGVAV 82 
                                       68999999999999******.67777778*****************************7.8888************5 PP

                             MFS_1  77 llllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                        ++ f+ s++l+l+l +l G+g++++ p + ++++ + ++ +r++ ++++++g  +G ++g  l+   +   g +++
  gi|557693682|ref|YP_008796736.1|  83 SAIGFVESFPLILLLGFLGGVGSALFHPPATSMAS-V-SE-KRASSVSFFMSGGDIGLAVGSFLATTAYVVMGAQGT 156
                                       5555779999************8888888766654.3.33.7*********************************** PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkr.kspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltl 229
                                        +++ +  l a++   ll+ +++p ++r +++++                ++k     ++l+a++l +++  +++t+
  gi|557693682|ref|YP_008796736.1| 157 GLLIILPVLAAAM---LLVGVRQPLEARvQNSVRP--------------DVRKLG---LALAAAVLRAVAALSFVTF 213
                                       9999999999988...5555555555550554444..............455555...388888888888888**** PP

                             MFS_1 230 lplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllv 306
                                       lply  + +gls + +ag++l ++ l+ga+++l ag+++ ++g++r+ +l+lll+ l+    +l++      l++++
  gi|557693682|ref|YP_008796736.1| 214 LPLY-LTKRGLS-FSMAGTVLTVMILAGAGGMLSAGYVAEKIGKKRAVTLFLLLTGLWIPVAVLTPEE----LAYFS 284
                                       ****.*******.****************************************999999999999999....66667 PP

                             MFS_1 307 lvliGfglgfvfpsllalasdlappeeagtasglfn.tagslggalgp 353
                                       + ++Gf  + v p+l a+  dl+p ++ g+as+l+  ++++lg ++ p
  gi|557693682|ref|YP_008796736.1| 285 YGVLGFLIFAVHPILVAYSHDLLP-QNLGAASALMYgLTFGLGHLIVP 331
                                       77789988888************8.88888999888899999999876 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.1e-05
                             MFS_1  95 qGlgagalfpagaaliadwfpkeergraigllsa.gfslGailgpllggllasslgWravfyilaivsllafvlfll 170
                                        G+   a+ p+ +a+  d+ p+ + g a +l+++ +f+lG ++ p +g+++  ++g+++v + la++ + a++   l
  gi|557693682|ref|YP_008796736.1| 288 LGFLIFAVHPILVAYSHDLLPQ-NLGAASALMYGlTFGLGHLIVPFVGAAVD-AYGYQSVLLSLAFMPFTAAL---L 359
                                       566677899*************.*******988879********99988887.99****************99...5 PP

                             MFS_1 171 llpee 175
                                       + +++
  gi|557693682|ref|YP_008796736.1| 360 FQWTP 364
                                       55555 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 !   33.4  31.8   6.7e-12     3e-08      12     340 ..      22     340 ..      19     361 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 6.7e-12
                             MFS_4  12 ytpiLPallaegqlslsqagllaaaNy..lGYLvGallaafalsagaeRlrllagllatvllllamaltesfaafll 86 
                                       + p+LP l a+++ s++ ++l+ ++ +  + +L  a+ + f +  +++ + +  gl++  +++ a +++esf ++ll
  gi|557693682|ref|YP_008796736.1|  22 LPPLLPLLAAQQKTSAATLALIPTVYLmtASFLQIAVGFFFDR--RPKTVLMPLGLFLGGVAVSAIGFVESFPLILL 96 
                                       569*******************998652245676666664444..444456899*********************** PP

                             MFS_4  87 iRflaGvasAvvlvfgsslvlahaaaarrervgallfaGvGlGiavsgllvlll.lqlglsasslWlalavlsavll 162
                                       + fl Gv+sA+      ++++a ++++r+++v +++ +G  +G av++ l++ + +++g+++  l ++l vl+a++l
  gi|557693682|ref|YP_008796736.1|  97 LGFLGGVGSALFH--PPATSMASVSEKRASSV-SFFMSGGDIGLAVGSFLATTAyVVMGAQGTGLLIILPVLAAAML 170
                                       **********865..45555666666666665.7889999********99987615566777777999999999998 PP

                             MFS_4 163 llvalllpraalreasaaaeaakaeqkslpllalllaYglaGfGYiitatFlvaiardgaggalleallWllvGlaa 239
                                       l+ +         ea  +  +       + l   l+a  l +++     tFl+++  +++ +  ++  + +++ la 
  gi|557693682|ref|YP_008796736.1| 171 LVGVRQPL-----EARVQNSV---RPDVRKLGLALAAAVLRAVAALSFVTFLPLYLTKRGLSFSMAGTVLTVMILAG 239
                                       77654444.....33333333...2234455555666678999999999**************************** PP

                             MFS_4 240 ivgvlvwlrvakrsglrralaaallieavgvllsllspsplglivssvllGltflaitalvlqlarelappatrrll 316
                                       + g+l    va++ g +ra+++ ll+ ++ + +++l p   +   s  +lG   +a+ ++ +++++ l p++  ++ 
  gi|557693682|ref|YP_008796736.1| 240 AGGMLSAGYVAEKIGKKRAVTLFLLLTGLWIPVAVLTPEE-LAYFSYGVLGFLIFAVHPILVAYSHDLLPQNLGAAS 315
                                       **************************99888888875554.556788899***********************9999 PP

                             MFS_4 317 glm.TasfgigQilGpllasllaea 340
                                       +lm  ++fg+g ++ p + +++ ++
  gi|557693682|ref|YP_008796736.1| 316 ALMyGLTFGLGHLIVPFVGAAVDAY 340
                                       998569**********997776543 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 ?    1.2   0.1     0.019        87      33      80 ..      35      82 ..       8      93 .. 0.87
   2 ?   11.0   2.5   2.1e-05     0.096     300     368 ..     197     263 ..     192     277 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.019
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 33 lpsstsgliassneignillilfvsYfggrghrPrwigigallmalgs 80
                                       + +t  li +++ +++ +l + v++f +r+ ++ ++ +g++l +++ 
  gi|557693682|ref|YP_008796736.1| 35 TSAATLALIPTVYLMTASFLQIAVGFFFDRRPKTVLMPLGLFLGGVAV 82
                                      566788999****************************99999988765 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.1e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 300 ilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvkklklsakklakl 368
                                       + ++v+ ++++  f+tFlp yl ++ +ls s+A +++ +v+i+++a G+l +G++ +k+  +   +++l
  gi|557693682|ref|YP_008796736.1| 197 LAAAVLRAVAALSFVTFLPLYLTKR-GLSFSMAGTVL-TVMILAGAGGMLSAGYVAEKIGKKRAVTLFL 263
                                       567899999*************877.99999999997.567788999*********9986554444444 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 ?    0.6   1.3     0.044     2e+02     284     339 ..      62     117 ..      29     156 .. 0.77
   2 ?   11.7  11.4   1.9e-05     0.086     228     370 ..     193     334 ..     135     351 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.044
                        MFS_1_like 284 leklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvs 339
                                       +++   ++l+ ++l++  +  + ++++e++ l+l++ +L g+  +l++  a++ +s
  gi|557693682|ref|YP_008796736.1|  62 FDRRPKTVLMPLGLFLGGVAVSAIGFVESFPLILLLGFLGGVGSALFHPPATSMAS 117
                                       55555678888999999999999***********************9988777665 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.9e-05
                        MFS_1_like 228 iifllvalilgmswgi.ienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilr 303
                                       +++ l+a++l ++ ++ + +Fl lYL + g s +++G+++++  +a     + a ++ ek+G  + +++ ll++ l 
  gi|557693682|ref|YP_008796736.1| 193 LGLALAAAVLRAVAALsFVTFLPLYLTKRGLSFSMAGTVLTVMILAGAGGMLSAGYVAEKIGKKRAVTLFLLLTGL- 268
                                       56778888888777763679*********************************************99998887776. PP

                        MFS_1_like 304 fllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliG 370
                                       ++ +a+++   l+ +     g+ + +++ ++v y++++ p++l a   +l+ gl+fglG+ +  ++G
  gi|557693682|ref|YP_008796736.1| 269 WIPVAVLTPEELAYFSYGVLGFLIFAVHPILVAYSHDLLPQNLGA-ASALMYGLTFGLGHLIVPFVG 334
                                       9999999666666666666688888899*************9977.57999********98877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2469.70
//
Query:       gi|557693683|ref|YP_008796737.1|  [L=380]
Description: acyl-CoA dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  122.2   0.1    2.7e-35  121.8   0.1    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    3.3e-19   68.9   0.0    6.4e-19   68.0   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.9e-16   60.6   0.1    3.2e-16   59.8   0.1    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    5.8e-14   52.7   0.0    1.3e-13   51.6   0.0    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.078   13.2   0.0    1.9  1  Nterm_IS4      Insertion element 4 transposase N-terminal


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 !  121.8   0.1   7.6e-39   2.7e-35       2     148 ..     226     372 ..     225     374 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.8 bits;  conditional E-value: 7.6e-39
                                       BHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH-- CS
                     Acyl-CoA_dh_1   2 kGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaeal 78 
                                       +G+++  ++ln  R++ aa a+g a  a+ +a +ya +rk fgkp++++q +++ la++++e+eaarll+++aa+++
  gi|557693683|ref|YP_008796737.1| 226 NGWKALAHALNPDRIVYAAVAVGSALFAIKTATSYASERKVFGKPIGAYQGIQFPLASLYTETEAARLLTLDAAAKF 302
                                       7**************************************************************************** PP

                                       ------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHH CS
                     Acyl-CoA_dh_1  79 dagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarr 148
                                       d+g++++++a +aK+fase++ +++ +a+q+lGg+Gyl+e ++er +rd+ +lr g  t+e  +  ia+ 
  gi|557693683|ref|YP_008796737.1| 303 DRGEDASVAACLAKYFASEVVFKAVGQAVQVLGGYGYLKESGLERVLRDIYLLRSGPITQELALAFIAEK 372
                                       *****************************************************99999999999888875 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 !   68.0   0.0   1.8e-22   6.4e-19       2      97 .]     116     213 ..     115     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.8e-22
                                       EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE...TS---.----EEEEEEE..GGGEE CS
                     Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar...tekpd.rarglslflvprdapgvs 74 
                                       + +TE+++Gsdv s+ktta  ++gg+yv+nGeK++++n   at++l+ ar    e+++ ++ gl+lf+++ +a g+s
  gi|557693683|ref|YP_008796737.1| 116 LSITEKESGSDVLSIKTTA-VKQGGKYVINGEKMYVNNFDRATHMLLAARttpLEHAAkKSLGLTLFVLDMKAGGLS 191
                                       789**************55.555669************************86633444789**************** PP

                                       E-----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  75 vrrieeklGlrglptgelvfedv 97 
                                       ++++ +k+G++  +tg +++e+v
  gi|557693683|ref|YP_008796737.1| 192 FSEL-PKMGTNYFRTGVMRLENV 213
                                       ****.69************9997 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 !   59.8   0.1     9e-20   3.2e-16       2     127 ..     241     356 ..     240     361 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 9e-20
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       + aava+G A  a++ ++++a er+   +g+++   + +q+ la + ++ +AAr+l+++aaa+     ++g+     
  gi|557693683|ref|YP_008796737.1| 241 VYAAVAVGSALFAIKTATSYASERKV--FGKPIGAYQGIQFPLASLYTETEAARLLTLDAAAK----FDRGEDA--- 308
                                       789***********************..***********************************....9999997... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHC CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaa 127
                                           a +a+ +a+e   +av +++++ Gg++++kes l+R++RD+  ++
  gi|557693683|ref|YP_008796737.1| 309 -SVAACLAKYFASEVVFKAVGQAVQVLGGYGYLKESGLERVLRDIYLLR 356
                                       .77899***************************************8765 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 !   51.6   0.0   3.5e-17   1.3e-13      23     113 .]      21     111 ..       7     111 .. 0.91

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 3.5e-17
                                       HHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHHHHHHHHHTTHHHHHHHS-H CS
                     Acyl-CoA_dh_N  23 aaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglalllgvhsslvapailrfGte 99 
                                        +++ ++g fp+e+w+++++  l g  +p  ygG+g ++ e + ++  l+ +++g+al++ +++++ + +i + Gte
  gi|557693683|ref|YP_008796737.1|  21 WEKMSNSGLFPEEFWRECGRRRLPGFLIPATYGGLGKTVGELVEAVIYLTMHGCGTALYPLLSNNMSSLVINKSGTE 97 
                                       455667778***************************988899999999999999999999999999999******** PP

                                       HHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N 100 eqkrryLpklasge 113
                                       +q++r Lp+lasge
  gi|557693683|ref|YP_008796737.1|  98 KQRQRLLPRLASGE 111
                                       *************8 PP

>> Nterm_IS4  Insertion element 4 transposase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.2e-05     0.078      14      63 ..      85     134 ..      76     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.2e-05
                         Nterm_IS4  14 elvdevlaetgtaevRkrkLPaevvvylvlalaLfrdesyeevvrrLtag 63 
                                       ++ + v++++gt ++R+r+LP      ++++l++ ++es ++v++  t++
  gi|557693683|ref|YP_008796737.1|  85 NMSSLVINKSGTEKQRQRLLPRLASGEYIMGLSITEKESGSDVLSIKTTA 134
                                       5556799*********************************9999865555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2744.01
//
Query:       gi|557693684|ref|YP_008796738.1|  [L=325]
Description: ornithine cyclodeaminase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-63  214.7   0.2    1.8e-63  214.4   0.2    1.0  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    4.5e-07   30.0   0.0    1.1e-06   28.7   0.0    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.029   14.9   0.1       0.08   13.5   0.1    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.047   14.1   0.0       0.13   12.7   0.0    1.8  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.087   13.3   0.1        0.2   12.1   0.1    1.5  1  NAD_binding_7    Putative NAD(P)-binding
       0.11   12.5   0.0       0.33   11.0   0.0    1.8  2  OTCace           Aspartate/ornithine carbamoyltransferase, As


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 !  214.4   0.2   5.9e-67   1.8e-63       6     310 ..       5     310 ..       2     318 .. 0.95

  Alignments for each domain:
  == domain 1  score: 214.4 bits;  conditional E-value: 5.9e-67
                                       E-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCC.T CS
                   OCD_Mu_crystall   6 ltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkks.g 81 
                                        +++e+e+ l ++  +k ve+ fr +   k   ppr++  v++ + +   mpa++   + ++vKl+n + +n+   g
  gi|557693684|ref|YP_008796738.1|   5 ISRNELENWLDMKTSVKIVEDFFRDYGDEKYVAPPRMVTAVEERDAVYLNMPAASLHVGGYAVKLINEYRKNPVLhG 81 
                                       5778999999*********************************9999999*******9***************988* PP

                                       SSSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEE CS
                   OCD_Mu_crystall  82 lptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikevr 158
                                       +    ++v+ +d etG    ++da  lt+lRT+A+++v+akyLa+ d++ +a+iG G+ a+tql al+ v++i++++
  gi|557693684|ref|YP_008796738.1|  82 IEAAHGVVLFFDIETGLLNGVVDAVALTSLRTGAIGGVGAKYLAPDDSRSAALIGSGRTAWTQLTALHTVRNIERLK 158
                                       ***************************************************************************** PP

                                       EE-SSHHHHHHHHHHCCS..CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-H CS
                   OCD_Mu_crystall 159 iydrdeeaaekfaenlqe.fefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLdd 234
                                       iy  ++ ++ek+ae++++  +++ +a++s++eave+ad+v ++T + +p+++ ew+ + +h++ +ga  p ++eLd 
  gi|557693684|ref|YP_008796738.1| 159 IYSPTKTNREKLAEKASKtLGIDAKAVDSPREAVENADVVLAATNSAEPVFSGEWLAENVHVTSIGA-LPTRRELDL 234
                                       ******************77**********************************************9.799****** PP

                                       HHHHCCEEEE..SHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHH CS
                   OCD_Mu_crystall 235 dilkradifv..dseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaakl 309
                                       +  +rad++    ++  +re G+i  a+ekgv+++ +kv el ev++ +++ R ++  + l +svG+a  D+     
  gi|557693684|ref|YP_008796738.1| 235 ETFRRADLIAadLKKSVLREAGDIMAAVEKGVVDP-YKVLELHEVVKQNLK-RPRNVHVSLLKSVGFAALDLYFTSR 309
                                       ********9965566779************99876.6789***********.****************999876655 PP

                                       H CS
                   OCD_Mu_crystall 310 v 310
                                       v
  gi|557693684|ref|YP_008796738.1| 310 V 310
                                       5 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   3.8e-10   1.1e-06      12      99 ..     129     218 ..     121     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.8e-10
                                       T-EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH  12 ekkvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaeadvvisatase 86 
                                       ++ + liG G++a   +++L++  +++++ +   t ++ ++lae+  k+  i a+++++ +e++++advv++at+s 
  gi|557693684|ref|YP_008796738.1| 129 SRSAALIGSGRTAWTQLTALHTVrNIERLKIYSPTKTNREKLAEKAsKTLGIDAKAVDSPREAVENADVVLAATNSA 205
                                       56789********9999999985499*******************95566799************************ PP

                                       S-SB-HHHHHCCH CS
                      Shikimate_DH  87 epilekeeveeal 99 
                                       ep+++ e++ e +
  gi|557693684|ref|YP_008796738.1| 206 EPVFSGEWLAENV 218
                                       ****999987765 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 ?   13.5   0.1   2.7e-05      0.08       3      69 ..     133     202 ..     131     209 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                                       EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......-EEECECHHHHHHH-SEEEE-S CS
                     F420_oxidored   3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......vkvtavdneeaaeeadvvvlav 69 
                                       ++iG+G+ + + +  l +   + + +  + s+++  +e+lae+++      +k+   +  ea+e+advv+ a 
  gi|557693684|ref|YP_008796738.1| 133 ALIGSGRTAWTQLTALHTVR-NIERLK-IYSPTKTNREKLAEKASktlgidAKAVD-SPREAVENADVVLAAT 202
                                       67888888776666555553.344444.3366666666666666656665544444.689*********9986 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 ?   12.7   0.0   4.5e-05      0.13       2      76 ..     132     204 ..     131     226 .. 0.86
   2 ?   -2.0   0.0       1.5   4.5e+03      58      95 ..     230     268 ..     204     279 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                                       EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCH CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpa 76 
                                       +a++G +G +    l+ L++  ++e + ++s ++ + +klae+++  + g d k  d   e+++++d+v+ a+++
  gi|557693684|ref|YP_008796738.1| 132 AALIG-SGRTAWTQLTALHTVRNIERLKIYSPTKTNREKLAEKAS-KTLGIDAKAVDSPREAVENADVVLAATNS 204
                                       6899*.****************************88889999877.56677777777789999*******99976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
                                       E.GGGGGCTT-SEEEE-SCHHHHHHHHHHHHHTTSEEEE CS
                    Semialdhyde_dh  58 d.vdeeelkevdivflalpagvskelapklaeagvkviD 95 
                                          d e ++++d++   l ++v +e  + +a+ +  v+D
  gi|557693684|ref|YP_008796738.1| 230 ReLDLETFRRADLIAADLKKSVLREAGDIMAAVEKGVVD 268
                                       336777788888877777777777776666666666655 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 ?   12.1   0.1   6.8e-05       0.2       8      73 ..     130     206 ..     127     208 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.8e-05
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleag..akvtvvapevkeeleelvklaeeel..........ekdlegadlviaatddr 72 
                                       ++  ++G G+ A + +  l       ++++++p+   + e+l + a+++l          ++ +e+ad+v+aat+ +
  gi|557693684|ref|YP_008796738.1| 130 RSAALIGSGRTAWTQLTALHTVRniERLKIYSPTK-TNREKLAEKASKTLgidakavdspREAVENADVVLAATNSA 205
                                       67789**********999987655599*******5.444554443333322211112444567***********986 PP

                     NAD_binding_7  73 e 73 
                                       e
  gi|557693684|ref|YP_008796738.1| 206 E 206
                                       5 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 ?   11.0   0.0   0.00011      0.33      26      77 ..     152     200 ..     129     220 .. 0.71
   2 ?   -3.0   0.0       2.2   6.6e+03      52      85 ..     282     315 ..     260     317 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                                       CT-E.EEEES-TTSSH-HHHHHHHHHHHHHH.T-EEEEESSCHHHHTT-SEEEE CS
                            OTCace  26 lgmd.vvlvaPkglepdkevleeakknakks.ggsititedleeavkgaDvvyt 77 
                                        +++ +++ +P++++      e+++++a+k+ g + +  +++ eav++aDvv  
  gi|557693684|ref|YP_008796738.1| 152 RNIErLKIYSPTKTNR-----EKLAEKASKTlGIDAKAVDSPREAVENADVVLA 200
                                       4555566666666555.....566666666669******************976 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.2
                                       HHHHT-EEEEESSCHHHHTT-SEEEE--SSETTC CS
                            OTCace  52 akksggsititedleeavkgaDvvytdvwvsmge 85 
                                       + k  ++++++   +  ++  D  +t ++ sm+e
  gi|557693684|ref|YP_008796738.1| 282 NLKRPRNVHVSLLKSVGFAALDLYFTSRVLSMAE 315
                                       3344455555555556777778888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 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:                        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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2290.60
//
Query:       gi|557693685|ref|YP_008796739.1|  [L=436]
Description: phenylacetate-CoA ligase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-23   82.1   0.1    4.6e-23   81.3   0.1    1.4  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain
    6.2e-13   48.1   2.6    2.9e-12   45.9   2.6    1.8  1  AMP-binding      AMP-binding enzyme
    6.9e-05   22.1   0.0      0.021   13.9   0.0    2.1  2  LuxE             Acyl-protein synthetase, LuxE


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 !   81.3   0.1   7.8e-27   4.6e-23       1      96 []     340     434 ..     340     434 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 7.8e-27
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT----HHHHHHHHHHHHHHHHHHHSS--EEEEE CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsdelkelealekkiakklksklgvsvkvelv 77 
                                       Gv v+Ps++e+vl + +e++peYqi+v re++lD+++v  E+++++ +  +e eal+++++++l+++l   v+vel 
  gi|557693685|ref|YP_008796739.1| 340 GVAVWPSAVEAVLLKHRELGPEYQIIVWREKGLDKMKVVAELAHELKS--DEAEALRSRLESELRETLLTGVQVELA 414
                                       9*******************************************9955..59************************* PP

                                       -TT-S-----.----EEE-S CS
                   AMP-binding_C_2  78 epgtlprseg.KakrviDkR 96 
                                       ep +lpr+e  KakrviDkR
  gi|557693685|ref|YP_008796739.1| 415 EPLSLPRQEVgKAKRVIDKR 434
                                       *******9966********9 PP

>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   2.6   4.9e-16   2.9e-12     167     371 ..      94     291 ..      54     339 .. 0.75

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 4.9e-16
                                       E--SSSS-EEEEEEHHHH.HHHHHHHH.HHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCC CS
                       AMP-binding 167 TSGTTGkPKGVmlshrnl.vanvaslk.letr.fklkeddvvlsilplahifglilelllallsGatvvllpkdaal 240
                                       TSGTTG P    ++ + + v++  s+  l     +l+++dv+  + ++   +g  ++ ++   + ++++++++  + 
  gi|557693685|ref|YP_008796739.1|  94 TSGTTGVPTLGFYTKNDIeVWAEVSARsL--AmSGLTREDVFQITPSFGMFTGG-FGFYYGARKIGAMIVPTGAGF- 166
                                       *************9988874443333222..22446667777666666666665.777777777777889888888. PP

                                       HHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT.-SEEEEESS-EBHHHHHHHHHHHTCEEEEEE CS
                       AMP-binding 241 dpklllelieklkvtviagvPrvlealle.sgalkaakkakdlss.lrlvllggeplspellrffralfgeevlegY 315
                                        +++ ++++ +++ t++++v + + +l+e + +      akd    +r  ++g e   +e+ +++ ++    v+++Y
  gi|557693685|ref|YP_008796739.1| 167 -SRRQIQYMLDFGTTMVCAVVSYILRLTEtALEMG-VDPAKD--TlVRKGVFGSEMWTSEMKKWVAEKWNMDVYDIY 239
                                       .345689********************88554443.333333..569999*******************99****** PP

                                       EEGGGSSECEECHCTTTCTSTTS-BEE-T..TEEEEEE-TTTSCBEETTSEEEEEEEE CS
                       AMP-binding 316 GlTEttgvvtvlpleedkkklgsvGkplp..gvevkivDeetgepvpdgeeGellvrg 371
                                       G TE +g  + ++  ++  +  + G  l+  +  v+++D++tgepv+++e+Gel++  
  gi|557693685|ref|YP_008796739.1| 240 GFTELCGPGV-AN--DC-FV--HDGLHLWedHFLVEVIDPKTGEPVGPEEKGELVFTT 291
                                       *********9.55..23.23..3477775448999*******************9865 PP

>> LuxE  Acyl-protein synthetase, LuxE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.0   0.00083         5      19     104 ..      14     102 ..       4     133 .. 0.74
   2 !   13.9   0.0   3.6e-06     0.021     265     356 ..     234     329 ..     223     343 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00083
                              LuxE  19 lseeekeklrkkflldelvnhykhneeyrkycqknkvddlvtegevddiPviPvsvfk....aigtkllsvsedeik 91 
                                       +s ++ e+ r+k l   +++ y+ n  yr+     kv +  ++  vdd+  +P              +l+v   e+ 
  gi|557693685|ref|YP_008796739.1|  14 MSRKDIEENRDKMLRWTVRHAYRNNPFYRRKLDEAKVSPDDVN-SVDDLVKLPFTTKDelrsLYPYGILAVPRSEVL 89 
                                       57777788899999999********************998777.7***99999754330000233456666666666 PP

                              LuxE  92 aklqssatsGlks 104
                                           +s+t+G+++
  gi|557693685|ref|YP_008796739.1|  90 EVHATSGTTGVPT 102
                                       6666677777765 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 3.6e-06
                              LuxE 265 dvvdiygfteqve...lntpdfkdelkrkrvysdviirdeetlkvvgdGkvGlleyvdalstsyPafvvltddlG.v 337
                                       dv diygfte  +    n ++++d+l+    +  v + d++t ++vg+   G l +   + ++ P       d+  v
  gi|557693685|ref|YP_008796739.1| 234 DVYDIYGFTELCGpgvANDCFVHDGLHLWEDHFLVEVIDPKTGEPVGPEEKGELVFTTLTKEAAPLLRYRCRDISyV 310
                                       89********99755569*********99999999999******************999999999888888888724 PP

                              LuxE 338 ieeslcegqkaGklvkvlr 356
                                        +   c+++++  ++  +r
  gi|557693685|ref|YP_008796739.1| 311 YDARSCDCGRTHLRLGYIR 329
                                       5556789998888776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3093.52
//
Query:       gi|557693686|ref|YP_008796740.1|  [L=321]
Description: fumarylacetoacetate hydrolase family protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-65  219.8   0.0    4.1e-65  219.5   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
  ------ inclusion threshold ------
       0.13   12.0   0.0        0.3   10.8   0.0    1.6  1  Scm3           Centromere protein Scm3


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 !  219.5   0.0   4.6e-69   4.1e-65       1     218 []     106     319 ..     106     319 .. 0.92

  Alignments for each domain:
  == domain 1  score: 219.5 bits;  conditional E-value: 4.6e-69
                                       .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T-- CS
                     FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevls 77 
                                       ki+ ++ n++eh++ea+ka+ e p    p+  + flk++++++gp d+i++P+ +++ldyE+E+a+vigk+ + + +
  gi|557693686|ref|YP_008796740.1| 106 KIIHTAGNFREHAKEAEKAKWEFPI---PQ-WISFLKSPTAVIGPYDNIVYPKYTKELDYELEMAIVIGKRGKYI-P 177
                                       6889999*********877433333...44.679*****************************************.9 PP

                                       HHHHHTTEEEEEEEEEEE-SBGGG---.HHHHHH.TGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEG CS
                     FAA_hydrolase  78 veeAedaiaGytllnDvsaRdlqaeekaplgwfl.gksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsnt 153
                                        e+A d++aG++++nD++aRd+q++e+ + g ++ gk+ dtf+p+Gp +vt+de+++p++l+++lrvnge++q++nt
  gi|557693686|ref|YP_008796740.1| 178 KERAFDYVAGFMVFNDITARDIQRQEM-KNGLLNfGKNLDTFAPLGPYLVTKDEVSNPHNLKMELRVNGEVRQSGNT 253
                                       ***************************.4466666****************************************** PP

                                       GGTTTSHHHHHHHHHHHH-B-TT-EEEEEES.........S--EE--TT-EEEEEETTTEEEEEEE. CS
                     FAA_hydrolase 154 kdmifspaeliahlsagltLepGdliltGTpsgvga..eeeslkflkdgDeveveieglGelrnrVa 218
                                       + + ++ +e+i+h s +  LepGd+i+tGT+sgv a  e+ ++++lk+gD+ve eie+lG +rn+V+
  gi|557693686|ref|YP_008796740.1| 254 NRLSVTLQEIIEHYSWV-MLEPGDIITTGTISGVAAfrENPEKYYLKPGDVVESEIESLGVMRNPVV 319
                                       ***************99.6**************9644467899*********************995 PP

>> Scm3  Centromere protein Scm3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.4e-05       0.3       8      35 ..     252     278 ..     246     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHHHHHHHHHHHSG..GGSS--B CS
                              Scm3   8 sderlkkrwesifeKYeridfedqgDEI 35 
                                       +++rl+ ++++i+e+Y+ + +e  gD+I
  gi|557693686|ref|YP_008796740.1| 252 NTNRLSVTLQEIIEHYSWVMLEP-GDII 278
                                       789***************99977.**99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2340.59
//
Query:       gi|557693687|ref|YP_008796741.1|  [L=401]
Description: carboxyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-65  220.9   0.1    2.9e-65  220.5   0.1    1.2  1  HMGL-like  HMGL-like
     0.0029   17.5   0.0     0.0092   15.9   0.0    1.9  2  RelB       RelB antitoxin


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 !  220.5   0.1   3.2e-69   2.9e-65       1     264 []      31     289 ..      31     289 .. 0.97

  Alignments for each domain:
  == domain 1  score: 220.5 bits;  conditional E-value: 3.2e-69
                                       B-EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHH CS
                         HMGL-like   1 kvkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekd 77 
                                       k++i d+tLRDGeq++++ l+++ekl+iakaLde+gv+ +E+g+p+ se+df++v+ ia+++  a++ + +r++++d
  gi|557693687|ref|YP_008796741.1|  31 KIEIYDVTLRDGEQTPGVVLKASEKLEIAKALDELGVHRLEAGMPVVSEEDFNAVKIIANEGLRAKVFGFARLVKED 107
                                       689************************************************************************** PP

                                       HHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHH CS
                         HMGL-like  78 ikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevvea 154
                                       i+aa +    a +  + +  ++      ++++   e+v++ka+ +v++a+++g  ++++  d +r+d++fl  ++++
  gi|557693687|ref|YP_008796741.1| 108 IDAALK----ADVSGIVTEGPVGV-PKLMQFGWRPEDVVEKAVTHVQYAKDHGLYTVFFGVDGTRADINFLKHIYKR 179
                                       ******....***********998.67789*********************************************98 PP

                                       H.HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SS CS
                         HMGL-like 155 a.eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGer 230
                                       + +ea ++ +++ Dt G+++P+ ++ l+ ++++ v   v+++vHcHnd+G+++a ++a++ aGa++v ++vnG+Ger
  gi|557693687|ref|YP_008796741.1| 180 VvDEAKPDAVAVVDTFGCASPEGFRYLVGEIVQTVR--VPVEVHCHNDFGMGTAVSIAGLSAGARVVHVSVNGIGER 254
                                       62689*******************************..*************************************** PP

                                       BBB-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 231 aGnaaleelvaalealg.vdtgldlqklrsiaalv 264
                                       aGnaalee+++ le l     gl l+kl ++++lv
  gi|557693687|ref|YP_008796741.1| 255 AGNAALEEVALSLELLYgRRLGLRLEKLVEVSRLV 289
                                       **************9866999**********9997 PP

>> RelB  RelB antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.2   1.1e+04      13      25 ..      55      67 ..      53      68 .. 0.86
   2 !   15.9   0.0     1e-06    0.0092       4      52 ..     176     224 ..     173     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.2
                                      HHHHHHHHHCCT- CS
                              RelB 13 KaeatdvlekmGl 25
                                      K+e +++l+++G+
  gi|557693687|ref|YP_008796741.1| 55 KLEIAKALDELGV 67
                                      8899999999997 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1e-06
                                       EEEEEEHHHHHHHHHHHHCCT--HHHHHHHHHHHHHHHTS-STT-CHHH CS
                              RelB   4 islRidedlKaeatdvlekmGltiSqairlfLekiaktkalPfdlrlpe 52 
                                       i  R++++ K  a +v++ +G    + +r ++ +i++t ++P+++   +
  gi|557693687|ref|YP_008796741.1| 176 IYKRVVDEAKPDAVAVVDTFGCASPEGFRYLVGEIVQTVRVPVEVHCHN 224
                                       667*****************************************98874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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 0.27s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3069.77
//
Query:       gi|557693688|ref|YP_008796742.1|  [L=358]
Description: pyruvate dehydrogenase E1 component subunit alpha [Candidatus Caldiarchaeum subterraneum]
Scores for 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-83  280.7   0.0    1.2e-83  280.5   0.0    1.0  1  E1_dh           Dehydrogenase E1 component
    2.7e-06   26.8   0.0    4.3e-06   26.1   0.0    1.4  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
      5e-05   23.1   0.4    0.00047   20.0   0.4    2.1  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.5   0.0   2.1e-87   1.2e-83       2     299 ..      39     335 ..      38     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 280.5 bits;  conditional E-value: 2.1e-87
                                       HHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-TT CS
                             E1_dh   2 klvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkvk 78 
                                       + +++ r +d+ + +++  ++ + y++  gqea  vg+ ++l + D+ +++YRe  v l+rg++l+ ++  +     
  gi|557693688|ref|YP_008796742.1|  39 RDMVVLRAFDQWMLKIHPLGKASRYAPVEGQEASVVGSVHSLSDVDWTFPTYRELTVGLLRGAPLTTLIHRMFATSL 115
                                       679999***********************************************************999999999999 PP

                                       TSSGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EE CS
                             E1_dh  79 gkggsrhelmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvi 155
                                       ++ ++     y+ k  ri+ g g v++  p++ G+a+aak +g+kev +++ GDgA+++Gd++ea+n a ++k pvi
  gi|557693688|ref|YP_008796742.1| 116 DHMKGHEITLYGDKRYRIVVGAGAVSLMCPVAVGMAMAAKKRGEKEVFLVYLGDGATSKGDFHEAINWAGVFKPPVI 192
                                       9999999556688888************************************************************* PP

                                       EEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SST CS
                             E1_dh 156 fvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyggHse 232
                                       f+v+NN+++is + +k++as+++a +a+++gipg+rVdgnD+lavy +++  +e ar+g+g +lie+vtYR+g+H++
  gi|557693688|ref|YP_008796742.1| 193 FFVQNNQWAISIPFKKQTASPTIAVKAKAYGIPGIRVDGNDVLAVYTVCRRFVEKARAGEGAVLIEAVTYRMGPHTT 269
                                       ***************************************************************************** PP

                                       TSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS----G CS
                             E1_dh 233 sDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskkelep 299
                                        Ddps+yr+ +evee+r+  dp++r++ +L+ +g++s ee+++i ++ r e   a+++ae+++ ++p
  gi|557693688|ref|YP_008796742.1| 270 ADDPSKYRSEKEVEEMRAF-DPLKRMRIYLTRNGLWSPEEEQKIVESFRDELRRATEEAEKTPPPHP 335
                                       ******************9.*******************************************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 !   26.1   0.0   7.2e-10   4.3e-06     109     177 ..     136     204 ..     130     261 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 7.2e-10
                    DXP_synthase_N 109 eagHsstsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisk 177
                                       +ag  s    +a+G+a+a++++gek+  +  +GDga + G  +ea+n +g  k  ++  + +N+++is 
  gi|557693688|ref|YP_008796742.1| 136 GAGAVSLMCPVAVGMAMAAKKRGEKEVFLVYLGDGATSKGDFHEAINWAGVFKPPVIFFVQNNQWAISI 204
                                       556666667789*****************************************************9985 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 !   20.0   0.4   7.8e-08   0.00047      26     152 ..     136     258 ..     118     259 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.8e-08
                                       TTS-TTTHHHHHHHHHHH..ST.TSEEE.EEEEHHHHHHT.GGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTC CS
                      TPP_enzyme_C  26 glgtmGyglpaAiGakla..kp.drevv.aivGDGgflmi.lqelatavrrnlpitvvvlnNegygmtggqqepfgg 97 
                                       g g+     p+A+G+++a  k+ ++ev+ ++ GDG++    ++e ++ +    p +++ ++N+ ++     + pf +
  gi|557693688|ref|YP_008796742.1| 136 GAGAVSLMCPVAVGMAMAakKRgEKEVFlVYLGDGATSKGdFHEAINWAGVFKPPVIFFVQNNQWAI----SIPFKK 208
                                       66677777899999999533223566654899********999999988887755555555555543....334554 PP

                                       CTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHH....HHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  98 krksgpagkdlkpvdfaklaealGakgarvekadveel....eealkealekkgpalie 152
                                       ++          ++ +a  a+a+G++g+rv+ +dv  +    ++ +++a++ +g +lie
  gi|557693688|ref|YP_008796742.1| 209 QT---------ASPTIAVKAKAYGIPGIRVDGNDVLAVytvcRRFVEKARAGEGAVLIE 258
                                       33.........23478999*********9999988888444455566666999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 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:                        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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2903.17
//
Query:       gi|557693689|ref|YP_008796743.1|  [L=286]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-10   38.7   0.0    4.7e-09   35.6   0.0    2.0  1  DUF1015   Protein of unknown function (DUF1015)
    5.5e-08   33.0   0.0    1.1e-07   32.1   0.0    1.4  1  ParBc     ParB-like nuclease domain


Domain annotation for each model (and alignments):
>> DUF1015  Protein of unknown function (DUF1015)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   5.2e-13   4.7e-09     285     380 ..     119     204 ..      22     206 .. 0.62

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 5.2e-13
                           DUF1015 285 fglylkdgkwyklltlkdkavrsLdvsvlqelllepilgiedprkderidyvhgleeavekvdsgeagvafllnpts 361
                                         ++++dg   ++l++k+   +  d s   + + e++  i++  ++  i+yv++  +++e v++g++ ++ ll+p +
  gi|557693689|ref|YP_008796743.1| 119 ARFMWSDG---YVLQVKH--RE--DLS--TRQVYEKLSIIDQSLQHLGISYVRD-GDVEELVKQGKHVFGYLLRPLR 185
                                       45555566...3444355..22..333..334778877779999999*******.********************** PP

                           DUF1015 362 veelfavadagevmPrKST 380
                                       +ee+ +++++g ++P+KST
  gi|557693689|ref|YP_008796743.1| 186 KEEVVSIVKQGYRLPPKST 204
                                       ******************9 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   1.2e-11   1.1e-07      11      75 ..      14      77 ..       7      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.2e-11
                             ParBc 11 nplqprkd.spekieelvasIkkkGll.qPiivrktrqgryeiiaGerRlrAakrlglkevpvivle 75
                                      ++l+p+ +  p+ +  +++ I +kG   +P+iv+ +      +++G +R++Aa rlgl ++pv+  +
  gi|557693689|ref|YP_008796743.1| 14 KDLHPHEQsIPQTVSRIAEDIAQKGRFiDPVIVDAET---GLVVDGTHRVEAAIRLGLGKIPVYTVD 77
                                      4566676677999**********99666********9...89*********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2088.98
//
Query:       gi|557693690|ref|YP_008796744.1|  [L=310]
Description: D-3-phosphoglycerate dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-70  234.3   0.1    8.2e-70  233.8   0.1    1.2  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    5.5e-32  110.2   0.3    6.3e-32  110.1   0.3    1.0  1  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    5.9e-10   39.4   0.2    1.1e-09   38.6   0.2    1.4  1  AdoHcyase_NAD   S-adenosyl-L-homocysteine hydrolase, NAD bind
      8e-10   39.1   0.5    3.2e-09   37.2   0.1    2.0  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    3.9e-05   23.0   0.8     0.0001   21.6   0.8    1.7  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      9e-05   22.1   0.1    0.00026   20.6   0.0    1.8  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
     0.0019   18.1   0.3     0.0019   18.1   0.3    2.0  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0097   16.4   0.0      0.038   14.5   0.0    2.0  2  XdhC_C          XdhC Rossmann domain
  ------ inclusion threshold ------
      0.019   15.5   0.1      0.078   13.6   0.1    2.2  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.045   13.5   0.1      0.082   12.6   0.1    1.4  1  ELFV_dehydrog   Glutamate/Leucine/Phenylalanine/Valine dehydr
      0.046   12.4   0.1       0.24   10.1   0.1    1.9  2  Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
      0.075   13.4   0.0       0.17   12.3   0.0    1.6  1  Gp_dh_N         Glyceraldehyde 3-phosphate dehydrogenase, NAD
       0.13   12.4   0.0       0.32   11.1   0.0    1.7  1  DpaA_N          Dipicolinate synthase subunit A N-terminal do
       0.15   12.3   1.3       0.47   10.7   0.1    2.5  3  TrkA_N          TrkA-N domain
       0.24   11.5   1.6        0.7   10.0   0.7    2.3  2  DapB_N          Dihydrodipicolinate reductase, N-terminus


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 !  233.8   0.1   6.9e-73   8.2e-70       1     178 []     108     283 ..     108     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 233.8 bits;  conditional E-value: 6.9e-73
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77 
                                       ++l++a++r++a+ d++vr+g+w  +++ +g el+gkt+G++G+GrIG++va++++a+gmkv+ayd+ + +ee  ++
  gi|557693690|ref|YP_008796744.1| 108 IGLMIAVARKIAWCDKQVRSGKW-PKSEAMGVELAGKTLGVVGYGRIGRRVAEIAHAMGMKVVAYDVIPIPEEVLAK 183
                                       589********************.9999*********************************************99** PP

                                       HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                        g++l+slee+l+++D+++lh+pltpetrhli+a++l++mk++ai+iN++RG+++deeaL++aLk+g+iaga+lDvf
  gi|557693690|ref|YP_008796744.1| 184 AGAKLTSLEEVLKTADVITLHVPLTPETRHLIDASKLEMMKPKAIIINASRGEVIDEEALYNALKNGRIAGAGLDVF 260
                                       ***************************************************************************** PP

                                       SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eeeplpedspllelpnviltPHia 178
                                       e+ep++  s+llel+nv+ltPHi+
  gi|557693690|ref|YP_008796744.1| 261 EKEPPT-GSKLLELDNVVLTPHIG 283
                                       *****9.66*************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 !  110.1   0.3   5.2e-35   6.3e-32       1     126 [.       5     307 ..       5     310 .] 0.99

  Alignments for each domain:
  == domain 1  score: 110.1 bits;  conditional E-value: 5.2e-35
                                       EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHH.TT--EEEESSSSCTTB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevleal.pkLkviaragvGvDnvD 76 
                                       vl+ +p++ ++++ l+++g++v+++  ++ eel + + ++d+l+vr +tkvta+v+e+  p Lkv++ragvG DnvD
  gi|557693690|ref|YP_008796744.1|   5 VLVADPVDRSAVDMLERAGFTVDLRPGISAEELESVIGGYDVLLVRGRTKVTAKVIERGvPVLKVVGRAGVGLDNVD 81 
                                       7999*************999**************************************99***************** PP

                                       HHHHHHTT-EEEE-TTTTHHHHHHHH................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                        2-Hacid_dh  77 ldaakerGilVtnvpgystesvAElt................................................... 102
                                       l+aa+++G++V n+p++stesvAEl+                                                   
  gi|557693690|ref|YP_008796744.1|  82 LEAAARHGVKVLNTPESSTESVAELViglmiavarkiawcdkqvrsgkwpkseamgvelagktlgvvgygrigrrva 158
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|557693690|ref|YP_008796744.1| 159 eiahamgmkvvaydvipipeevlakagakltsleevlktadvitlhvpltpetrhlidasklemmkpkaiiinasrg 235
                                       ***************************************************************************** PP

                                       ................................................T-BHHHHHHHHHHHHHHHHHHHTT CS
                                       ................................................xxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ................................................aaTeeaqeniaeeaaenlvaflkg 126
                                                                                       a T eaqe++a++ a++++++++ 
  gi|557693690|ref|YP_008796744.1| 236 evideealynalkngriagagldvfekepptgsklleldnvvltphigAQTLEAQEAAATMLAKKVIEAFAS 307
                                       ***********************************************999******************9986 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 !   38.6   0.2   9.2e-13   1.1e-09      18     111 ..     137     234 ..     132     259 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 9.2e-13
                                       -S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE....-SSSSS CS
                     AdoHcyase_NAD  18 dvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadivvt....ttGnkd 90 
                                        v laGk+  v+GyG +G+  a+  +++G +v+  +v Pi     a  G +++ leev+k+ad++      t  ++ 
  gi|557693690|ref|YP_008796744.1| 137 GVELAGKTLGVVGYGRIGRRVAEIAHAMGMKVVAYDVIPIPEEVLAKAGAKLTSLEEVLKTADVITLhvplTPETRH 213
                                       6779**************************************9999*****************98532222557899 PP

                                       SB-HHHHCCS-TTEEEEE-SS CS
                     AdoHcyase_NAD  91 iitlehlkkmkddaivcniGh 111
                                       +i + +l+ mk +ai+ n   
  gi|557693690|ref|YP_008796744.1| 214 LIDASKLEMMKPKAIIINASR 234
                                       ****************99754 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 ?   -0.5   0.0       1.1   1.3e+03      36      57 ..      83     105 ..      43     120 .. 0.68
   2 !   37.2   0.1   2.7e-12   3.2e-09       2     108 ..     145     251 ..     144     259 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                                       HHHHHTTEEE-SSHHHHHHHC.S CS
                     NAD_binding_2  36 eelvaegakaaesieelvasl.d 57 
                                       e+++ +g+k+++++e+ ++s+ +
  gi|557693690|ref|YP_008796744.1|  83 EAAARHGVKVLNTPESSTESVaE 105
                                       34444445555555555554442 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 2.7e-12
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       +g++G G +G+  a+   + g+kv++y++ +   e l+++ga  ++s+ee+++++dv+ + v+ +++++++i+   l
  gi|557693690|ref|YP_008796744.1| 145 LGVVGYGRIGRRVAEIAHAMGMKVVAYDVIPIPEEVLAKAGA-KLTSLEEVLKTADVITLHVPLTPETRHLIDAsKL 220
                                       79****************************988888888887.7899***************************889 PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHHHTT CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelkekg 108
                                       e +k+ +i+i+ s  ++ d + l+++lk+  
  gi|557693690|ref|YP_008796744.1| 221 EMMKPKAIIINASRGEVIDEEALYNALKNGR 251
                                       9********************9999998765 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 !   21.6   0.8   8.8e-08    0.0001      31     126 ..     145     231 ..     130     238 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 8.8e-08
                                       EEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS.- CS
                       AlaDh_PNT_C  31 vlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipGkk.a 106
                                         v+G G  G   +++a+++g kV+++Dv p   e l + gak          +l+e +k+adv+  t ++p  + +
  gi|557693690|ref|YP_008796744.1| 145 LGVVGYGRIGRRVAEIAHAMGMKVVAYDVIPIPEEVLAKAGAK--------LTSLEEVLKTADVI--TLHVPLTPeT 211
                                       359****************************************........4578999*****98..6778766515 PP

                                       --SC-HHHHHTS-TTEEEEE CS
                       AlaDh_PNT_C 107 PkLvteemvksMkpgsVivD 126
                                        +L++++ ++ Mkp ++i+ 
  gi|557693690|ref|YP_008796744.1| 212 RHLIDASKLEMMKPKAIIIN 231
                                       67****************95 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 ?   -2.0   0.0       1.9   2.3e+03      40      60 ..      81     101 ..      67     113 .. 0.70
   2 !   20.6   0.0   2.2e-07   0.00026       2      87 ..     140     225 ..     139     244 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.9
                                       HHHHHHHTT-EEEEHHHHHHT CS
                              IlvN  40 svkkAkeegfevltvaeavkk 60 
                                        ++ A ++g++vl++ e +++
  gi|557693690|ref|YP_008796744.1|  81 DLEAAARHGVKVLNTPESSTE 101
                                       578899999999998887654 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 2.2e-07
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHH.HHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDel.qkevy 77 
                                       l gk++ v+GyG  G+  a+  +  g++vv          +   ++g + ++++e+ k+adv+++ +P +   ++++
  gi|557693690|ref|YP_008796744.1| 140 LAGKTLGVVGYGRIGRRVAEIAHAMGMKVVAYDVIPI-PEEVLAKAGAKLTSLEEVLKTADVITLHVPLTPeTRHLI 215
                                       789*************************975444444.56666788*******************999653034455 PP

                                       HHHTGGG--T CS
                              IlvN  78 eeeiepnlke 87 
                                       +++  + +k 
  gi|557693690|ref|YP_008796744.1| 216 DASKLEMMKP 225
                                       4444455555 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 ?   -3.2   0.1       5.5   6.6e+03      14      39 ..      79     104 ..      67     118 .. 0.57
   2 !   18.1   0.3   1.6e-06    0.0019       2      49 ..     145     194 ..     144     206 .. 0.85
   3 ?   -1.1   0.0       1.2   1.5e+03     140     175 ..     264     302 ..     189     306 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.5
                                       HHHHHHHTT-EEEEE-S-HHHHHHHH CS
                           3HCDH_N  14 iaavfasagleVvlvdiseealekal 39 
                                          + a+a + V+++++ e++ e+++
  gi|557693690|ref|YP_008796744.1|  79 NVDLEAAARHGVKVLNTPESSTESVA 104
                                       55555555555555555555554444 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.6e-06
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S...-HHHHHHHHHHHHHHHHCC CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdi...seealekalekiekslekl 49 
                                       ++v+G G +G+ +a+++ + g++Vv +d+    ee l+ka +k+++ le++
  gi|557693690|ref|YP_008796744.1| 145 LGVVGYGRIGRRVAEIAHAMGMKVVAYDVipiPEEVLAKAGAKLTS-LEEV 194
                                       79**************************988889999999999886.5554 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.2
                                       STTT--EEE...EEE-TT--HHHHHHHHHHHHHTT-EEE CS
                           3HCDH_N 140 PpplmkLvE...vvrgekTseetvatvvelakkigktpv 175
                                       Pp+  kL+E   vv +++   +t+++  + a+ + k+++
  gi|557693690|ref|YP_008796744.1| 264 PPTGSKLLEldnVVLTPHIGAQTLEAQEAAATMLAKKVI 302
                                       555555555333566666677777777666666666666 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.7   6.8e+03       6      24 ..       8      26 ..       5      31 .. 0.83
   2 !   14.5   0.0   3.2e-05     0.038       2      66 ..     146     248 ..     145     257 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.7
                                      -STTHHHHHHHHHHHTEEE CS
                            XdhC_C  6 aghvaqalarlaaalgfrv 24
                                      a++v ++ +++++++gf+v
  gi|557693690|ref|YP_008796744.1|  8 ADPVDRSAVDMLERAGFTV 26
                                      6788999999999999998 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.2e-05
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-G.GGG....................-GGG-TT-SE............. CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpre.efa....................tkerfpeade............. 44 
                                        ++G g +++ +a++a+a+g++v+ +d  +   +                    +                      
  gi|557693690|ref|YP_008796744.1| 146 GVVGYGRIGRRVAEIAHAMGMKVVAYDVIPiP-EevlakagakltsleevlktaD--------Vitlhvpltpetrh 213
                                       699************************98843.3355666666665444444440........15555555555555 PP

                                       .............-EEEE--S-HHHHHHHHHHHSS CS
                            XdhC_C  45 .............tavvvlthdhklDaealeaalr 66 
                                                    ++++ ++++  +D+eal +al+
  gi|557693690|ref|YP_008796744.1| 214 lidasklemmkpkAIIINASRGEVIDEEALYNALK 248
                                       66666688888877777788999999999999995 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   0.1   6.5e-05     0.078       2      72 ..     145     208 ..     144     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpe 72 
                                       +g++G+G++g+ +a+ + a g    ++v a +  p   e l +++g+k+t+   ee+++ adv+ l v+ +
  gi|557693690|ref|YP_008796744.1| 145 LGVVGYGRIGRRVAEIAHAMG---MKVV-AYDVIPIPEEVL-AKAGAKLTS--LEEVLKTADVITLHVPLT 208
                                       89*******************...7777.655555544445.555778888..9************99964 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 ?   12.6   0.1   6.9e-05     0.082      29     137 ..     139     249 ..     132     255 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.9e-05
                                       -STTEEEEEE--SHHHHHHHHHHHHCT-EEEE..EEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHHSTSTSEEE CS
                     ELFV_dehydrog  29 slegkrvaisGsGnvgsyaallltelgakvva..vsDssGviydpeGldieellelkeerksvkeykkssekkaeyi 103
                                       +l+gk++ + G+G +g  +a++++ +g+kvva  v+     +  + G ++ +l e+ +    ++       ++ + i
  gi|557693690|ref|YP_008796744.1| 139 ELAGKTLGVVGYGRIGRRVAEIAHAMGMKVVAydVIPIPEEVLAKAGAKLTSLEEVLKTADVITLHVPLTPETRHLI 215
                                       599****************************9555666677778888877777777555555433332333344555 PP

                                       SHHSHHHHS.S-SEEEE-SSTTSB-HHHHTHTHHT CS
                     ELFV_dehydrog 104 eneeellel.kvdilvPcAtqneideenakalikn 137
                                       + + +l  + +  i++ + + ++idee + + +kn
  gi|557693690|ref|YP_008796744.1| 216 DAS-KLEMMkPKAIIINASRGEVIDEEALYNALKN 249
                                       554.5544446667777777777777777666665 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 ?   -0.2   0.0      0.26   3.2e+02     327     373 ..      30      69 ..      10      76 .. 0.74
   2 ?   10.1   0.1    0.0002      0.24     265     332 ..     135     201 ..      85     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.26
                                       ES.CHHHHHHHHHHHT-SEEEE-CCHHHHHHHTT--EEE-TS-ECCT CS
                    Oxidored_nitro 327 ddadleeleelikelkpdlllggskeryiaeklgiplvrvgfPildr 373
                                        + + eele+ i  + + l+ g++k ++   ++       g+P+l  
  gi|557693690|ref|YP_008796744.1|  30 PGISAEELESVIGGYDVLLVRGRTKVTAKVIER-------GVPVLKV 69 
                                       567789999999999999999999977777777.......5555544 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0002
                                       HHHHHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS.TT.SEEEES.CHH CS
                    Oxidored_nitro 265 dyheylagkrvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkaeleegepeviddadle 332
                                       ++   lagk+  ++g++ +   +a++ + +Gm+vva  +    +++ +++ a+l   e ev+ +ad  
  gi|557693690|ref|YP_008796744.1| 135 AMGVELAGKTLGVVGYGRIGRRVAEIAHAMGMKVVAYDVIPIPEEVLAKAGAKLTSLE-EVLKTADVI 201
                                       455679*****************************98777777777777777777774.777776665 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 ?   12.3   0.0   0.00014      0.17       3      29 ..     145     170 ..     143     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                       EEEESTSHHHHHHHHHHHHHTTCEEEE CS
                           Gp_dh_N   3 vainGfGRIGrlvlralleekelevva 29 
                                       +++ G+GRIGr v+ ++     ++vva
  gi|557693690|ref|YP_008796744.1| 145 LGVVGYGRIGRRVAEIAH-AMGMKVVA 170
                                       7899*********98776.33555554 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 ?   11.1   0.0   0.00027      0.32      16      68 ..     159     214 ..     155     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                                       HHHHHTT-EEEEES-...TSSS-BTTEEEE-GGGS-GGG-SEEE--TT-BETTTEE CS
                            DpaA_N  16 rkLaekgakvslygl...eleekiegvekaesleealedadviilPvpgtkdggei 68 
                                       +   ++g kv +y +   ++e   +  +k +slee+l++advi l vp+t + +++
  gi|557693690|ref|YP_008796744.1| 159 EIAHAMGMKVVAYDVipiPEEVLAKAGAKLTSLEEVLKTADVITLHVPLTPETRHL 214
                                       5556789999999999998999999999**********************998887 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       2.1   2.5e+03      23      52 ..      45      74 ..      34     108 .. 0.62
   2 ?   10.7   0.1   0.00039      0.47       3      28 ..     147     172 ..     145     200 .. 0.79
   3 ?   -3.2   0.0         8   9.5e+03      42      58 ..     225     241 ..     215     246 .. 0.48

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.1
                                      EEEEEESSHHHHHHHHHTTSEEEES-TTSH CS
                            TrkA_N 23 dvvvidkdeerveelreeglevvvgdatde 52
                                      dv+++  + ++ +++ e+g++v++  +   
  gi|557693690|ref|YP_008796744.1| 45 DVLLVRGRTKVTAKVIERGVPVLKVVGRAG 74
                                      466777777777777777777666544444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00039
                                       EES-SHHHHHHHHHHHHTTEEEEEEE CS
                            TrkA_N   3 iiGlGrvGrslaeeLseggkdvvvid 28 
                                       ++G+Gr+Gr++ae  ++ g++vv+ d
  gi|557693690|ref|YP_008796744.1| 147 VVGYGRIGRRVAEIAHAMGMKVVAYD 172
                                       8*************999554687655 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 8
                                       SEEEES-TTSHHHHHHT CS
                            TrkA_N  42 levvvgdatdeevLeea 58 
                                        ++++ +a++ ev++e 
  gi|557693690|ref|YP_008796744.1| 225 PKAIIINASRGEVIDEE 241
                                       33444555554444444 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.2   1.4e+03      26      71 ..      64     107 ..      19     111 .. 0.68
   2 ?   10.0   0.7   0.00058       0.7       3      34 ..     145     174 ..     143     238 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.2
                                       EEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH.-SEE CS
                            DapB_N  26 lelvaavdrkeselegkdagellglgklgvavtddleevlek.advl 71 
                                       + + ++v r +   +g d  +l    ++gv+v ++ e+ +e+ a+ +
  gi|557693690|ref|YP_008796744.1|  64 VPVLKVVGRAG---VGLDNVDLEAAARHGVKVLNTPESSTESvAELV 107
                                       44444555544...444555555555667777777776666655555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00058
                                       EEEETTTSHHHHHHHHHHHHSTTEEEEEEEET CS
                            DapB_N   3 vavvGasGrmGkevvkaveeaedlelvaavdr 34 
                                       ++vvG+ Gr+G++v++ +++  ++++va    
  gi|557693690|ref|YP_008796744.1| 145 LGVVGY-GRIGRRVAEIAHA-MGMKVVAYDVI 174
                                       68****.*********9998.88888875443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2204.13
//
Query:       gi|557693691|ref|YP_008796745.1|  [L=94]
Description: small subunit ribosomal protein S26e [Candidatus Caldiarchaeum subterraneum]
Scores for 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   1.4    5.4e-19   68.6   1.4    1.1  1  Ribosomal_S26e   Ribosomal protein S26e
  ------ inclusion threshold ------
      0.017   15.1   0.4        2.7    8.0   0.0    2.3  2  zf-dskA_traR     Prokaryotic dksA/traR C4-type zinc finger
      0.059   13.8   0.2       0.22   11.9   0.1    1.8  2  Lar_restr_allev  Restriction alleviation protein Lar


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 !   68.6   1.4   9.1e-23   5.4e-19       1      94 [.       1      90 [.       1      93 [. 0.91

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 9.1e-23
                                      X--S-SSTT----S-S---EEE-TTT--EEES----EEEEEEESS-SSSHHHHTTSBSSSS----EEEEEEE--HHHHH CS
                    Ribosomal_S26e  1 mtkKRrnngrnkkgrghvkivrCsncarlvpkdKaikrfvvrniveaaavrdlseasvyeeyalPklYiklaycvscai 79
                                      m++KR+++gr+k  +g++ +v+C+nc+  vp++K  + +   ++v  + +r+l++a +y + +     + ++ c+scai
  gi|557693691|ref|YP_008796745.1|  1 MPFKRKSRGRSKGAKGKEPTVQCDNCGAYVPRSKVQRVTRRVSLVRGDLARELKQAGAYLAEN----IVVKNLCISCAI 75
                                      9*********************************99999999**************8775444....356689****** PP

                                      HTTSS----TTTTS- CS
                    Ribosomal_S26e 80 hskvvrvRsredrkn 94
                                      h  v++vR+r++rk 
  gi|557693691|ref|YP_008796745.1| 76 HYGVLKVRARDERKP 90
                                      *************95 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 ?    8.0   0.0   0.00046       2.7       5      21 ..      20      38 ..      16      44 .. 0.79
   2 ?    5.3   0.1    0.0032        19      24      31 ..      67      74 ..      65      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00046
                      zf-dskA_traR  5 s..CeeCGEpIpeaRlral 21
                                      +  C+ CG  +p  +++++
  gi|557693691|ref|YP_008796745.1| 20 TvqCDNCGAYVPRSKVQRV 38
                                      346*********9998876 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0032
                      zf-dskA_traR 24 arlCveCq 31
                                      ++lC++C+
  gi|557693691|ref|YP_008796745.1| 67 KNLCISCA 74
                                      689****9 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 ?   11.9   0.1   3.7e-05      0.22      19      37 ..      12      31 ..       3      44 .. 0.63
   2 ?    0.3   0.0      0.15   9.1e+02      27      32 ..      55      74 ..      32      89 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.7e-05
                   Lar_restr_allev 19 qrvvaeigqcvyCadCga..s 37
                                      + ++++++++v+C++Cga   
  gi|557693691|ref|YP_008796745.1| 12 K-GAKGKEPTVQCDNCGAyvP 31
                                      2.2333455*********542 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.15
                   Lar_restr_allev 27 q..............cvyCa 32
                                      q              c++Ca
  gi|557693691|ref|YP_008796745.1| 55 QagaylaenivvknlCISCA 74
                                      13444455555666688885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 677.11
//
Query:       gi|557693692|ref|YP_008796746.1|  [L=322]
Description: peptidase M48 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-40  136.6   0.0    1.2e-39  136.1   0.0    1.2  1  Peptidase_M48  Peptidase family M48
    0.00013   21.3   0.2    0.00028   20.2   0.0    1.6  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 !  136.1   0.0   1.4e-43   1.2e-39       5     194 ..      85     316 ..      81     318 .. 0.85

  Alignments for each domain:
  == domain 1  score: 136.1 bits;  conditional E-value: 1.4e-43
                                       SHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   5 aelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrhs 80 
                                       ++++e v++l  +ag+ ++++k+yv++ +  NAFa g   +   +++t+ L+ + l +ee++aV+GHElGHikhr++
  gi|557693692|ref|YP_008796746.1|  85 GWVEEAVNRLSMAAGM-EKPPKTYVAEIDIPNAFAFGSPLTGpMVAVTRRLV-ESLPREEVEAVIGHELGHIKHRDV 159
                                       699*************.9999********99*********************.************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT......HHHHHHHHHHHHHHHHTTT.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxx. RF
                     Peptidase_M48  81 vvslivsllasillllglallisraeedaagafldalavliglliillfl......alSRkrEyqADeagvellkr. 150
                                       ++++ +s ++ i+++lg++l++s a + ++++ + +  + i+ l++++f+      ++SR rEy+AD ++++++ + 
  gi|557693692|ref|YP_008796746.1| 160 AFMMAISIIPAIIYYLGYTLFVSGAYSGRREGGAYTFLIGIA-LMVFSFIfnifvfYMSRLREYYADYFAAKTVPNg 235
                                       ********************9999988888777656655544.5667777889999****************99763 PP

                                       HHHHHHHHHHHHHHTT-...-S---HHHH.....................................HHS-SS--HHH CS
                                       xxxxxxxxxxxxxxxxx...xxxxxxxxx.....................................xxxxxxxxxxx RF
                     Peptidase_M48 151 akdlvraliklakdler...qdvsaslrs.....................................ellstHPplle 187
                                       a++l+ral+++   + r   ++v++                                         el+stHP+ ++
  gi|557693692|ref|YP_008796746.1| 236 ARNLQRALVRIMMLAGRlrrEEVAH---VeqfkaffiadpevklqafgdidrvveevknrkpstvaELFSTHPDPAK 309
                                       6788999999887776633333333...33346777777777777777777777777777888999*********** PP

                                       HHHHHHH CS
                                       xxxxxxx RF
                     Peptidase_M48 188 Riqalke 194
                                       R++al++
  gi|557693692|ref|YP_008796746.1| 310 RLRALDN 316
                                       *****97 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.2e-08   0.00028     143     227 ..      90     174 ..      39     176 .. 0.68
   2 ?   -2.2   0.1      0.21   1.9e+03     109     136 ..     196     220 ..     193     236 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.2e-08
                     Peptidase_M56 143 lkeaLkeakeemqlkrnikirlsssidsPavlg....llkprIvlPadflkklsdeeleyillHElaHlkrkDllvn 215
                                       ++++L   + + ++ +++k +++ +id P  ++    l  p++ +   ++++l  ee e ++ HEl H+k++D+ + 
  gi|557693692|ref|YP_008796746.1|  90 AVNRL---SMAAGMEKPPKTYVA-EIDIPNAFAfgspLTGPMVAVTRRLVESLPREEVEAVIGHELGHIKHRDVAFM 162
                                       44444...444556677776664.6888877661133356899******************************9988 PP

                     Peptidase_M56 216 llvavlqclfwf 227
                                       + + ++  ++++
  gi|557693692|ref|YP_008796746.1| 163 MAISIIPAIIYY 174
                                       777766666654 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.21
                     Peptidase_M56 109 Wivgalilllyliaallvlkkrfvrklg 136
                                       +++g++++++ +i+ ++v++ +   +l+
  gi|557693692|ref|YP_008796746.1| 196 FLIGIALMVFSFIFNIFVFYMS---RLR 220
                                       5778888888888888888733...333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       984  (0.0548832); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2293.11
//
Query:       gi|557693693|ref|YP_008796747.1|  [L=484]
Description: prolyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  113.0   0.0    4.3e-32  111.5   0.0    1.8  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.3e-17   63.7   0.8    3.5e-17   62.3   0.4    2.0  2  HGTP_anticodon  Anticodon binding domain
    1.1e-13   51.2   0.1    2.4e-13   50.1   0.1    1.6  1  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
  ------ inclusion threshold ------
      0.091   11.7   0.1       0.17   10.8   0.1    1.4  1  Vps53_N         Vps53-like, N-terminal


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 ?   -4.0   0.0       2.7   1.2e+04      86     101 ..      19      34 ..      15      43 .. 0.78
   2 !  111.5   0.0   9.6e-36   4.3e-32       9     179 .]     111     281 ..     102     281 .. 0.94

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.7
                                       HHHHHHHHTT.SCEEE CS
                                       xxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  86 aisriferlglefrai 101
                                         s++f +l+le r +
  gi|557693693|ref|YP_008796747.1|  19 NFSEWFDKLLLEARIV 34 
                                       6789999999998754 PP

  == domain 2  score: 111.5 bits;  conditional E-value: 9.6e-36
                                       EEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                      tRNA-synt_2b   9 reyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrdl 83 
                                        ++i++Pt+e+ ++ +++ + +rs  +LPl ++q   +yR+E++++r+LlRvre+ +++++ +ha +a++++++r+ 
  gi|557693693|ref|YP_008796747.1| 111 VKLIVRPTSETIMYPMFKLW-IRShADLPLLVHQSNMVYRHETKATRPLLRVREIPWNEAHTVHAtAAEAEQQVRKA 186
                                       579***************88.***777**************************************99********** PP

                                       HHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  84 ikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvi 160
                                       ++ + +++ +lgl + ++++   +k + + ++  f+a+ +  +++ +++t+++lg+++s+ +++++  +++++++++
  gi|557693693|ref|YP_008796747.1| 187 VEIYRKVLDQLGLAYLVLKRPDFDKFPGARYSIAFDAWNP-DGRVNQVATVHNLGKNFSKVFEIEFETRDGKRENPH 262
                                       **************88777774445599************.9*********************************** PP

                                       EEEEEEEHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 161 micaaigveRllsaileqn 179
                                        +c+++g +R+l+a+++q+
  gi|557693693|ref|YP_008796747.1| 263 QLCYGFGYSRVLAALISQH 281
                                       ***************9985 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.5   6.6e+03      41      51 ..      53      63 ..      26      82 .. 0.60
   2 !   62.3   0.4   7.7e-21   3.5e-17       1      92 [.     297     389 ..     297     391 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.5
                                      HHHHHHHHHHT CS
                    HGTP_anticodon 41 igkkireadll 51
                                      i +++re+ ++
  gi|557693693|ref|YP_008796747.1| 53 ILRRVREMLEK 63
                                      33333333332 PP

  == domain 2  score: 62.3 bits;  conditional E-value: 7.7e-21
                                       SEEEEESSSS..HHHHHHHHHHHHHHHHTTTSEEEEES.SSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET CS
                    HGTP_anticodon   1 qvvviplnek..aeeleeyakklaeeLraagirveldd.snesigkkireadllgipfavvvGekelekgtvtvrdr 74 
                                       +vv++p+  k  +e +++++ +lae+L++    v++dd ++ ++g+k+ ++++lg+p+++++G++e+ ++  t+ +r
  gi|557693693|ref|YP_008796747.1| 297 HVVIVPIVFKgqEESIKQFCHSLAERLQKFA--VKVDDrEDVTPGEKFYHWEKLGVPVRLEIGPREVAENRATLFRR 371
                                       69******9999999*************765..9****99************************************* PP

                                       TTCEEEEEETTHHHHHHH CS
                    HGTP_anticodon  75 dtreqervsldelveklk 92 
                                       dt e++ v+++e++ +++
  gi|557693693|ref|YP_008796747.1| 372 DTLEKQVVAVEEIERAVE 389
                                       *************99886 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 !   50.1   0.1   5.3e-17   2.4e-13       2      69 .]     418     484 .]     417     484 .] 0.95

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 5.3e-17
                                       HHHHHHHHTT-EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                         ProRS-C_1   2 eefkealekkgfvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                                       +e k+ ++++++++  Wcg+ ec e++k   g + ++  fd+  +  +  C+vcgk+a ++v+f+r+Y
  gi|557693693|ref|YP_008796747.1| 418 DEAKKVISERRIARLDWCGSVECAEQLKAAAGGELRGSRFDE-LEVPSGPCVVCGKNAAEVVYFARAY 484
                                       89***************************************7.5667889*****************9 PP

>> Vps53_N  Vps53-like, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   3.8e-05      0.17      39     105 ..     363     425 ..     346     432 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.8e-05
                           Vps53_N  39 deiksvvraqanvgekgkealeeaqkaieelfqkikeikdkaekseemvkeitrdIkqLDiAKknlt 105
                                       ++ +++ r ++   ek   a+ee+++a+e+++ ++   ++ ae+s  +++++  +++ +D AKk ++
  gi|557693693|ref|YP_008796747.1| 363 ENRATLFRRDT--LEKQVVAVEEIERAVENVLTNMG--QSLAERSWRIMRQMVVEVSSIDEAKKVIS 425
                                       55555555555..5666789*************998..79***********************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      715  (0.0398795); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3178.02
//
Query:       gi|557693694|ref|YP_008796748.1|  [L=101]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   24.4   1.4    3.4e-05   24.1   0.3    1.7  2  DUF4258   Domain of unknown function (DUF4258)
    0.00057   19.8   0.2    0.00074   19.5   0.2    1.1  1  PBECR3    phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease3
     0.0025   18.1   0.2      0.003   17.9   0.2    1.1  1  PBECR2    phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease2
  ------ inclusion threshold ------
        0.1   12.5   0.0       0.14   12.0   0.0    1.2  1  GSAP-16   gamma-Secretase-activating protein C-term


Domain annotation for each model (and alignments):
>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.3   7.6e-09   3.4e-05       1      62 [.       6      75 ..       6      76 .. 0.86
   2 ?   -1.6   0.0      0.82   3.7e+03      40      49 ..      89      98 ..      81     101 .] 0.66

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 7.6e-09
                           DUF4258  1 fsaHArermaeRgIseedieevlenGe.iieeys.....lvlgktsegrpl..hvvvapdedpvvviTvy 62
                                      +s+HA+e+ + R+++ e i +vl+++e i ++        ++ ++ +++ +  +v+++ ++d + + Tvy
  gi|557693694|ref|YP_008796748.1|  6 LSRHASEKIKLRRLRMELINQVLNSPEhIYFDVVtrlyvAIRKVEFHDEKIplVVIYRTEDDSYYIATVY 75
                                      69************************97777777999996667777777666599999999999*****9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.82
                           DUF4258 40 segrplhvvv 49
                                      ++gr+++v v
  gi|557693694|ref|YP_008796748.1| 89 KKGRWIKVGV 98
                                      5677777766 PP

>> PBECR3  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   1.6e-07   0.00074      34     111 ..       5      80 ..       3      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-07
                            PBECR3  34 ilkrHgnqstekdrgqi.dianipdiiknPDkviyggknkkeksieyvKki...nngylvvvevdkkknelyvktmy 106
                                       il+rH   ++ek++     ++ i++++++P ++ ++ +++     + ++k+   ++++ +vv  ++++++ y++t y
  gi|557693694|ref|YP_008796748.1|   5 ILSRH---ASEKIKLRRlRMELINQVLNSPEHIYFDVVTRL---YVAIRKVefhDEKIPLVVIYRTEDDSYYIATVY 75 
                                       78899...344444333569******************997...56666666899999999999************* PP

                            PBECR3 107 kikek 111
                                       + ke 
  gi|557693694|ref|YP_008796748.1|  76 PCKEF 80 
                                       *9986 PP

>> PBECR2  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   6.6e-07     0.003      40     112 ..      13      88 ..       3      95 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.6e-07
                            PBECR2  40 krg.rerylplLaetledPdeIwldeeeskklrrrylkrfkd.rglfavfelgedggwsgitafpk..denylekqr 112
                                       k + r   ++l+ ++l++P+ I+ d+ ++  + +r + + ++  +l+++++++ d+ + ++t++p    e++++++ 
  gi|557693694|ref|YP_008796748.1|  13 KIKlRRLRMELINQVLNSPEHIYFDVVTRLYVAIRKVEFHDEkIPLVVIYRTE-DDSYYIATVYPCkeFEEEVDRKV 88 
                                       334477789*****************995544455555554455888888888.66********8755455555554 PP

>> GSAP-16  gamma-Secretase-activating protein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.2e-05      0.14      13      51 ..      12      51 ..       2      52 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                           GSAP-16 13 kkagl.dpllelidelksseelalFhllerllealeelaf 51
                                      +k +l   ++eli++  +s e++ F +++rl+ a++++ f
  gi|557693694|ref|YP_008796748.1| 12 EKIKLrRLRMELINQVLNSPEHIYFDVVTRLYVAIRKVEF 51
                                      45555455778************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 741.83
//
Query:       gi|557693695|ref|YP_008796749.1|  [L=72]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   65.9   3.1    3.8e-18   65.4   3.1    1.2  1  DUF2283   Protein of unknown function (DUF2283)


Domain annotation for each model (and alignments):
>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   3.1   2.1e-22   3.8e-18       1      49 []       2      50 ..       2      50 .. 0.98

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 2.1e-22
                           DUF2283  1 kitYDpeaDalYIylsegpveeseevdddiilDfDedGrlvGIEiLnAS 49
                                      k+tYDpeaD+ Y  l +g+v++s+e ++di l++D++G+l+GIEi+nA+
  gi|557693695|ref|YP_008796749.1|  2 KVTYDPEADIIYMVLRDGEVYDSREENEDIRLEYDKEGQLIGIEIMNAR 50
                                      8**********************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 551.98
//
Query:       gi|557693696|ref|YP_008796750.1|  [L=227]
Description: V-type H+-transporting ATPase subunit D [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  180.9   9.0    2.7e-53  180.7   9.0    1.0  1  ATP-synt_D  ATP synthase subunit D


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 !  180.7   9.0   1.5e-57   2.7e-53       1     195 [.      22     211 ..      22     212 .. 0.97

  Alignments for each domain:
  == domain 1  score: 180.7 bits;  conditional E-value: 1.5e-57
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-. CS
                        ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkl 77 
                                       eLir ++ l++a+ ++++L++Krd+L++++ ++++ ++  re++e+ l++ay sl +a+a +g+ ++e++++ +++ 
  gi|557693696|ref|YP_008796750.1|  22 ELIRARRSLQVAKSIYRILEDKRDVLVRRLNDLVEVAEAEREKMEQPLRQAYMSLFKAYAEMGSVKVEAIAATTPP- 97 
                                       79******************************************************************99997777. PP

                                       .TSS-SEEEEEEBTTSEEEEEEE-..S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  78 akvvkvelktenvaGVkvpvfeleeeksdstelygllrtgaqldeavealrellellvelasletslelLdeeikkt 154
                                        + ++v+++++ + G+++p++e+ +  ++   +ygll+t +++deav+++re++ +l ++a++e+++ +L+ee+kkt
  gi|557693696|ref|YP_008796750.1|  98 -S-IEVKVSEKTILGIRIPTLEIAS--TKIPLNYGLLDTASSFDEAVRNFREIIATLCRVAEIENTIFRLAEELKKT 170
                                       .5.99****************9965..567799******************************************** PP

                                       HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 155 nrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvk 195
                                       +r  NaLe+ +IPr++e+ik+I+  L+E+ere+f+ lk vk
  gi|557693696|ref|YP_008796750.1| 171 QRLLNALEHLIIPRYQEAIKFISASLEEREREDFVKLKHVK 211
                                       ****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 1823.98
//
Query:       gi|557693697|ref|YP_008796751.1|  [L=211]
Description: hypothetical protein CSUB_C0260 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.7   3.6      0.012   15.7   3.6    2.4  2  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


Domain annotation for each model (and alignments):
>> 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 ?   15.7   3.6   6.8e-07     0.012      58     134 ..       6      83 ..       2      86 .. 0.83
   2 ?    2.0   1.3     0.011     2e+02      65     115 ..     113     158 ..     110     193 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 6.8e-07
                   Polysacc_synt_C  58 aaiatvlallvvavlnlyalrrllgikl.ellrrllkpllaalvmgivvylllllllgllllaal..alllavlvga 131
                                       aa+at++a +++++l +y l r l +    ++ +++ +++aa++ + + ++ ++l+ +l  +  +   ++++++++ 
  gi|557693697|ref|YP_008796751.1|   6 AAAATIIAVFAYIALFHYPLVRGLELTNlLFYMDVWPTFIAAVGYSTAYLTSTRLNTNLGKP--WsrYIGFGAAAAL 80 
                                       8************************999988*****************44444444444444..3359999998888 PP

                   Polysacc_synt_C 132 lvY 134
                                       ++Y
  gi|557693697|ref|YP_008796751.1|  81 IFY 83 
                                       888 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.011
                   Polysacc_synt_C  65 allvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllgl 115
                                       ++++v vl+++a  + ++ ++   r     ++++ vmg+  ++l+l++ +l
  gi|557693697|ref|YP_008796751.1| 113 SYFIVGVLIYFA-AKDFNKPW---REA-LAIAFGKVMGWYGFYLTLVTEPL 158
                                       566666655444.44444444...444.45777777777755555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1759.54
//
Query:       gi|557693698|ref|YP_008796752.1|  [L=136]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-06   29.1   0.1    1.4e-06   28.8   0.1    1.2  1  Asp_protease_2   Aspartyl protease
    5.9e-06   26.7   0.0    8.5e-06   26.2   0.0    1.2  1  gag-asp_proteas  gag-polyprotein putative aspartyl protease
  ------ inclusion threshold ------
      0.017   15.5   0.1      0.035   14.5   0.1    1.6  1  CBS              CBS domain


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 !   28.8   0.1   2.4e-10   1.4e-06       6      88 ..      25     104 ..      18     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.4e-10
                    Asp_protease_2   6 nGk..pvrfllDTGasttlispelaeklglkvreseltvrvsgaggevkarlvrldslklggltlknvpalvldlge 80 
                                       +Gk   +r+l+D+Ga++t++ +++++ lgl++ ++   + + +a+g++ +r+v    ++l g   ++ p++  +  e
  gi|557693698|ref|YP_008796752.1|  25 GGKsaAARLLVDSGATYTVLKKDVWTILGLEPLGE---IDLVLADGTTITRKVSEAIIELPGYGERHTPVVLGE--E 96 
                                       45432569**************************6...999*********************999999998888..7 PP

                    Asp_protease_2  81 eidglLGm 88 
                                       e++ lLG+
  gi|557693698|ref|YP_008796752.1|  97 EDENLLGI 104
                                       88888885 PP

>> gag-asp_proteas  gag-polyprotein putative aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.4e-09   8.5e-06      10      90 ..      31     107 ..      22     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.4e-09
                                       EEEEEETT-SS-EEEHHHHHHTTGGGGEB..TT--EE-TTSTT-EEEEEEEEEE.EETTEEEEEEEEEESSSSEEEE CS
                   gag-asp_proteas  10 vkflvDTGAsstiiseelaerlglsrkedkgkvevktangeveakrvrldsvkiggielrnvsavvlegelddlLLG 86 
                                        ++lvD+GA+ t++++++++ lgl+++    +  +  a+g++ +++v  + +++ g   r+ ++v l +e d+ LLG
  gi|557693698|ref|YP_008796752.1|  31 ARLLVDSGATYTVLKKDVWTILGLEPLG---EIDLVLADGTTITRKVSEAIIELPGYGERHTPVV-LGEEEDENLLG 103
                                       689************************9...69*********************99999987666.5579999**** PP

                                       HHHH CS
                   gag-asp_proteas  87 ldfL 90 
                                          L
  gi|557693698|ref|YP_008796752.1| 104 IVTL 107
                                       8665 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   5.9e-06     0.035      18      48 ..      74     107 ..      58     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.9e-06
                                       HHHHHHHHHHHTS..SEEEEE...ETTTBEEEEEEH CS
                               CBS  18 leealelmrekgv..srlPVV...dedgklvGivtl 48 
                                       ++ea+ ++   g+  ++ PVV   +ed++l+Givtl
  gi|557693698|ref|YP_008796752.1|  74 VSEAIIEL--PGYgeRHTPVVlgeEEDENLLGIVTL 107
                                       67777777..67522699**99*877778******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1018.31
//
Query:       gi|557693699|ref|YP_008796753.1|  [L=135]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-27   95.8   0.1    2.1e-27   95.6   0.1    1.0  1  HEPN      HEPN domain
  ------ inclusion threshold ------
       0.15   10.8   0.0       0.16   10.7   0.0    1.1  1  Vps52     Vps52 / Sac2 family


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 !   95.6   0.1   2.4e-31   2.1e-27       1     117 [.       8     130 ..       8     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 2.4e-31
                                       HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--..SSCCHHHHHHCCHHHT...-HHHHHH CS
                              HEPN   1 aeewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkgge.ppkthdlreLleelkkelkeseelree 76 
                                       ae+w++++ ed++ Ae+ll++g+y++++f  +qaaek l  l+++  +e pp+ h+l+eL e l+k +++  e++++
  gi|557693699|ref|YP_008796753.1|   8 AEYWFKQGVEDFRLAEKLLSDGRYNYSAFLTHQAAEKTLTTLIIEVLREiPPRIHNLLELGESLRKTGIDMAEVEDD 84 
                                       69*******************************************99999*************************** PP

                                       HHHHHCCCHHCCCTSS--S.....--HHHHHHHHHHHHHHHHHHHH CS
                              HEPN  77 leeLekayiesrYpdakee.....yteedaeealkdaeevlelvee 117
                                       l++L+++y +srYpda+++     y+++ ae +l+ a +vl+++e+
  gi|557693699|ref|YP_008796753.1|  85 LKYLNPHYLTSRYPDAANGiptevYSRRMAELCLQSAARVLAWAEN 130
                                       *******************************************987 PP

>> Vps52  Vps52 / Sac2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   1.8e-05      0.16     383     422 ..      57      99 ..      45     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 1.8e-05
                             Vps52 383 lWPRFqlvldlnveSlrkadittlve....kdtrPHeltrryae 422
                                       + PR + +l+l  eSlrk+ i         k ++PH+lt ry +
  gi|557693699|ref|YP_008796753.1|  57 IPPRIHNLLELG-ESLRKTGIDMAEVeddlKYLNPHYLTSRYPD 99 
                                       669999999986.9******9987655788889*********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); 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:                         2  (0.000111551); expected 0.2 (1e-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: 970.01
//
Query:       gi|557693700|ref|YP_008796754.1|  [L=151]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-07   30.5   0.1    4.2e-07   30.2   0.1    1.3  1  NTP_transf_2  Nucleotidyltransferase domain
    9.6e-07   28.8   0.0    1.3e-06   28.4   0.0    1.2  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.022   14.6   0.0    1.4  1  DUF294        Putative nucleotidyltransferase DUF294
      0.025   14.8   0.1      0.079   13.2   0.0    1.9  2  PMBR          Pseudomurein-binding repeat


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 !   30.2   0.1   9.4e-11   4.2e-07       5      45 ..      18      59 ..      14     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 9.4e-11
                                      HHHHHHHTT.TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCH CS
                      NTP_transf_2  5 leelkelep.vakvvlfGSyarGtalkgSDiDllvvlpeevs 45
                                       ++++e+   v+++vlfGS+arG  l  SD+Dll+vl++ ++
  gi|557693700|ref|YP_008796754.1| 18 VNAVRENGFdVVSAVLFGSRARGRELVSSDVDLLLVLSNCSY 59
                                      56777766689***********************99998855 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   2.9e-10   1.3e-06       9      89 ..      24     111 ..      13     113 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.9e-10
                                       HHHHHHSTTEEEEEE-S------EEEEEEEESS-.....--HHHHHHHHHHHHHH...SSSEEEEEETTTS-HHHHH CS
                           Polbeta   9 kekeielaylFGSrakgkareeSDiDlavllkek.....ldleeelelaaeledi..klgkkvDlvdlneappllly 78 
                                       +  ++  a+lFGSra+g+   +SD+Dl ++l++      +++e   +++    ++  ++  k +++ l e  +  ly
  gi|557693700|ref|YP_008796754.1|  24 NGFDVVSAVLFGSRARGRELVSSDVDLLLVLSNCsygfiERIEALSKFWRHELSLevFPYTKDEVMRLFERGSITLY 100
                                       4468999************************9998877744444444443322223447777777777766677777 PP

                                       HHHHS-EEEES CS
                           Polbeta  79 eilkegkllys 89 
                                         l++g ++y+
  gi|557693700|ref|YP_008796754.1| 101 DSLEHGVIIYD 111
                                       77777777775 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     5e-06     0.022      53     111 ..      32      89 ..       4      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5e-06
                            DUF294  53 lvmGSeGReEqtlktDqDnalvledeeeeaareyfaelaervneaLaalGyplCpggim 111
                                       + +GS +R+  ++++D D  lvl++  +    e++++l+++  ++L+   +p+ + ++m
  gi|557693700|ref|YP_008796754.1|  32 VLFGSRARGRELVSSDVDLLLVLSN-CSYGFIERIEALSKFWRHELSLEVFPYTKDEVM 89 
                                       679**********************.888888899999999999999888888888888 PP

>> PMBR  Pseudomurein-binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.8e-05     0.079       2      25 ..       2      25 ..       2      25 .. 0.94
   2 ?   -2.0   0.0       1.1     5e+03       6      16 ..      84      94 ..      83      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.8e-05
                              PMBR  2 sgkisyeeyldmasrvlafiesng 25
                                      +gk+++ee+++m s++++ +++ng
  gi|557693700|ref|YP_008796754.1|  2 GGKLTREEVTQMVSNYVNAVRENG 25
                                      69****************999998 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                              PMBR  6 syeeyldmasr 16
                                      +++e+ +++ r
  gi|557693700|ref|YP_008796754.1| 84 TKDEVMRLFER 94
                                      899*9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1090.85
//
Query:       gi|557693701|ref|YP_008796755.1|  [L=288]
Description: UTP--glucose-1-phosphate uridylyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   93.5   0.0    2.6e-26   92.7   0.0    1.3  1  NTP_transferase  Nucleotidyl transferase
    1.5e-08   35.2   0.0    2.5e-08   34.4   0.0    1.3  1  NTP_transf_3     MobA-like NTP transferase domain


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 !   92.7   0.0   2.9e-30   2.6e-26       2     241 ..       5     275 ..       4     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 2.9e-30
                                       EEEE--S--GGGTTCCTTSSGGGSEETTE....T....ETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGG CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgk....e....rliqatlsrlansgieeiivvltqehsflveeqlkegsk 70 
                                        vI a G GtRL P t++++k ++p++      +    +l+qa +++l + g+++  +v+ + ++  +e++++  ++
  gi|557693701|ref|YP_008796755.1|   5 VVITAAGLGTRLLPTTKEMPKEMLPIYVRagngSvtlkPLLQALFEQLYSFGFRQFCFVVGRGKR-AIEDHFTPDWD 80 
                                       6999*********************98542233223459****************8888886665.56777776666 PP

                                       GT........................SEEEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHH CS
                   NTP_transferase  71 fg........................vevlialepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeav 123
                                       f                           +  + +p+++g  dAv+ a+ +++d++    +l  +gD +i  + + ++
  gi|557693701|ref|YP_008796755.1|  81 FVekmdkmgkystvsdlvtfykmleeSVIVWVSQPSPRGFGDAVRTARHFVGDDN----FLLCAGDTIILGNNTHFL 153
                                       667999999**************8776677788*******************999....799999999999888888 PP

                                       HHHHTHSST.T.SEEEEEEESS-CTTSEEEEEC..TTS..BEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCC CS
                   NTP_transferase 124 kkaiekaak.g.tvtfgivpveeateyGviead..eeg..rverfvEKPkeakaselassGiYvfnsevllflakdl 194
                                       k+  e+a + + ++++++++ve++++yGv+  +  ++   +v + vEKPk+++ s+la +  Y+f++ +++ l + +
  gi|557693701|ref|YP_008796755.1| 154 KRLFEAAPRnMlDAVLLVQKVENPQQYGVVVSQplNQTlhQVFKVVEKPKTPP-SNLAIMPFYIFTPYIMKAL-DMI 228
                                       8766655542689*******************98844357*************.*************999998.99* PP

                                       HHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEEXSSHHHHHHH CS
                   NTP_transferase 195 eelkrgedeitdilpkaleegkvalaflfkdaeyWsDvGtldsllea 241
                                       +e   ge ++td+++k+++ g + la+   d+e   D+Gt++ ++ea
  gi|557693701|ref|YP_008796755.1| 229 SEGVGGELQLTDAIQKLIDMGGKVLAVELLDNEMRLDIGTPETYMEA 275
                                       ********************************************998 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 !   34.4   0.0   2.8e-12   2.5e-08       1     127 [.       5     176 ..       5     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2.8e-12
                                       EEEEEESS-TTT....TT.THHHHCC...CCC......CHHHHHHHHHCTT.-CEEEEECSH..CHHHH........ CS
                      NTP_transf_3   1 aviLAGGrSsRm....gg.dKallpl...ggk......pllervldalraagvdevvvvggd..eevla........ 53 
                                       +vi A+G ++R+    ++ +K +lp+   +g       pll+ ++++l + g+++ + v+g+  +++++        
  gi|557693701|ref|YP_008796755.1|   5 VVITAAGLGTRLlpttKEmPKEMLPIyvrAGNgsvtlkPLLQALFEQLYSFGFRQFCFVVGRgkRAIEDhftpdwdf 81 
                                       5899********7765347*******766444889999***************998888877556777799999999 PP

                                       ....................HHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHH..HHHHH CS
                      NTP_transf_3  54 ....................alarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPlltpel..verll 108
                                                            + +  v v++ +++ +g + ++++a + + ++d +l++a+D++ l  ++  ++rl+
  gi|557693701|ref|YP_008796755.1|  82 vekmdkmgkystvsdlvtfyKMLEESVIVWVSQPSPRGFGDAVRTARHFV-GDDNFLLCAGDTIILGNNThfLKRLF 157
                                       999999999999999998885566778888887889***********999.9***********998765545***** PP

                                       HCHHHHTSSEEEEESSSEE CS
                      NTP_transf_3 109 aaaaasgadvvvptyeger 127
                                       +aa ++  d+v ++ + e 
  gi|557693701|ref|YP_008796755.1| 158 EAAPRNMLDAVLLVQKVEN 176
                                       **98777777776665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2020.86
//
Query:       gi|557693702|ref|YP_008796756.1|  [L=437]
Description: UDP-glucose 6-dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-55  188.0   0.0      2e-55  187.3   0.0    1.3  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    4.6e-37  126.1   0.1    9.1e-37  125.2   0.1    1.5  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
      1e-32  112.6   0.0    2.1e-32  111.6   0.0    1.6  1  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
    1.8e-07   31.5   0.0    0.00031   20.9   0.0    2.6  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    6.9e-07   29.3   0.0    4.5e-06   26.7   0.0    2.3  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    2.8e-06   27.8   0.2      0.017   15.7   0.0    3.3  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    5.7e-06   25.8   0.1     0.0022   17.4   0.0    2.5  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    5.2e-05   23.3   0.0    0.00051   20.1   0.0    2.5  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    0.00024   20.8   0.0    0.00064   19.4   0.0    1.7  2  ApbA            Ketopantoate reductase PanE/ApbA
    0.00034   20.8   0.1     0.0078   16.5   0.0    2.5  2  TrkA_N          TrkA-N domain
    0.00048   20.5   0.1        3.6    8.1   0.0    3.2  3  NAD_binding_7   Putative NAD(P)-binding
     0.0034   17.0   0.6     0.0083   15.7   0.6    1.6  2  DAO             FAD dependent oxidoreductase
     0.0087   16.2   0.1      0.062   13.4   0.0    2.3  2  Ldh_1_N         lactate/malate dehydrogenase, NAD binding dom
  ------ inclusion threshold ------
      0.011   15.1   0.6      0.019   14.3   0.1    1.7  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.064   13.5   0.2       0.17   12.2   0.2    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.073   13.6   0.6       0.41   11.2   0.2    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.077   12.2   0.2       0.23   10.6   0.2    1.7  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
        0.1   12.6   0.0        0.2   11.7   0.0    1.5  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
        0.2   10.9   0.0       0.28   10.4   0.0    1.2  1  FAD_binding_3   FAD binding domain


Domain annotation for each model (and alignments):
>> 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 !  187.3   0.0   2.1e-58     2e-55       1     175 [.       1     173 [.       1     182 [. 0.96

  Alignments for each domain:
  == domain 1  score: 187.3 bits;  conditional E-value: 2.1e-58
                                       SEEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC- CS
                    UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveea 77 
                                       mki+viGlGYvGl+taa+la++g++v+g+Did++kv+++n+gk p+ ep L++l+k+      l+ +td+ +a  +a
  gi|557693702|ref|YP_008796756.1|   1 MKIAVIGLGYVGLTTAACLASRGFKVTGIDIDKHKVETINEGKTPFKEPRLDKLLKRSG----LRCSTDYAEA-VDA 72 
                                       8*******************************************************999....********95.579 PP

                                       SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHC...EEEEEE-S---TTHHHHCHHHHHHHHCSS-.TTCEEEE CS
                    UDPG_MGDP_dh_N  78 dvifiaVgTPskkkgkaaDlkyvesaarsiaealkk...gkvvvvkSTvpvgtaeelvkkileeaskkk.gvdfdvv 150
                                       d +fi+VgTP+   g ++Dl+yv  aars++e+l +    ++vvv+STv++gt++ +vk+ le+ s k+ g+d+ + 
  gi|557693702|ref|YP_008796756.1|  73 DFVFISVGTPAGP-GGEIDLSYVAGAARSLGEVLASrrkPCTVVVRSTVVPGTTRGIVKNELEKSSGKRvGEDLFLC 148
                                       *************.9999****************8876689**********************9999889******* PP

                                       E------TTSHHHHHHS-S-EEEEE CS
                    UDPG_MGDP_dh_N 151 snPEflregsavkdllnpdrvviGv 175
                                       +nPEflreg+av+d++npdr+viG 
  gi|557693702|ref|YP_008796756.1| 149 VNPEFLREGNAVHDTFNPDRIVIGD 173
                                       ************************6 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.2   0.1   9.7e-40   9.1e-37       2      92 ..     204     295 ..     203     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 9.7e-40
                      UDPG_MGDP_dh   2 tAEliKlaaNaflatkIsfiNelanlceal.gidveeVieavgldprigpkflkpglGvGGsclpkDvkaLvalaee 77 
                                       +AE+iK+a+Nafla +Is+iNe+an+c+++ g+dv+ V +a+gld+rigp fl++glG+GGsc+pkDvkaL+++ae+
  gi|557693702|ref|YP_008796756.1| 204 NAEMIKYASNAFLAARISLINEIANICQHIpGADVTVVSKAIGLDKRIGPYFLNAGLGYGGSCFPKDVKALIKYAEK 280
                                       69***************************99********************************************** PP

                      UDPG_MGDP_dh  78 lgleaelleavrevN 92 
                                       lg ++++leav++vN
  gi|557693702|ref|YP_008796756.1| 281 LGETPRVLEAVDKVN 295
                                       *************** 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 !  111.6   0.0   2.3e-35   2.1e-32       1     105 []     319     421 ..     319     421 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 2.3e-35
                                       EEE-SSSSTT-S--TT-HHHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--G CS
                    UDPG_MGDP_dh_C   1 ailGlafKkdtdDlReSpaldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehd 77 
                                       ailGlafK++tdD+Re+ +l+ii++Lle+g+ vk+yDP + e+a++  +  ++v++++s+ee+l++ad ++i+te++
  gi|557693702|ref|YP_008796756.1| 319 AILGLAFKPNTDDIREAVSLKIIKTLLEKGCTVKAYDPAAIENARKVLG--DTVNYASSAEECLTDADFCIIATEWK 393
                                       8********************************************9987..59************************ PP

                                       GGGGS-HHHHHHCCSS-EEEESSS-CCC CS
                    UDPG_MGDP_dh_C  78 efkeldlaklkelmkpavvfDgrnvldp 105
                                       ef+ l  +++++lm+++vv+Dgr+++dp
  gi|557693702|ref|YP_008796756.1| 394 EFRRLGPDDFRKLMRDPVVVDGRRIYDP 421
                                       *************************996 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 !   20.9   0.0   3.3e-07   0.00031       1      65 [.       2      81 ..       2     137 .. 0.80
   2 !    7.9   0.0    0.0035       3.3      14      61 ..     340     388 ..     338     397 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 3.3e-07
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT................EEE-SSHHHHHHHCSEEEE-S CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg................akaaesieelvasldvvitmv 63
                                      ki++iGlG  G   a  l+++g+kv++++ +k kve++ + +                ++  ++ +e+v+ +d+v++ v
  gi|557693702|ref|YP_008796756.1|  2 KIAVIGLGYVGLTTAACLASRGFKVTGIDIDKHKVETINEGKtpfkeprldkllkrsgLRCSTDYAEAVD-ADFVFISV 79
                                      79**********************************9988777888888888877654444444444443.38888877 PP

                                      SS CS
                     NAD_binding_2 64 ka 65
                                        
  gi|557693702|ref|YP_008796756.1| 80 GT 81
                                      65 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0035
                                       HHHHHHHTT-EEEEE-.SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE CS
                     NAD_binding_2  14 malnllkagykvavyn.rtkekveelvaegakaaesieelvasldvvit 61 
                                       +++ ll++g++v +y+    e++++++ + ++ a+s+ee+++++d+ i+
  gi|557693702|ref|YP_008796756.1| 340 IIKTLLEKGCTVKAYDpAAIENARKVLGDTVNYASSAEECLTDADFCII 388
                                       67889***********556799**********************99886 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 !   26.7   0.0   4.8e-09   4.5e-06       1      83 [.       2      76 ..       2      79 .. 0.82
   2 ?   -1.4   0.0       1.9   1.8e+03      14      47 ..     340     371 ..     336     386 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 4.8e-09
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHC..EEEES-HHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalar..isfttdleeav 77
                                      k+aviG G +G   aa +as+g++V+ +di+++++e+ +e  +           +ke   +++l+r  ++ +td++eav
  gi|557693702|ref|YP_008796756.1|  2 KIAVIGLGYVGLTTAACLASRGFKVTGIDIDKHKVETINEGKTP----------FKEPRLDKLLKRsgLRCSTDYAEAV 70
                                      69******************************999987776554..........444444455544338999******* PP

                                      C-SEEE CS
                           3HCDH_N 78 dadlvi 83
                                      dad+v+
  gi|557693702|ref|YP_008796756.1| 71 DADFVF 76
                                      ***996 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.9
                                       HHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHH CS
                           3HCDH_N  14 iaavfasagleVvlvdiseealekalekieksle 47 
                                       i + ++++g++V+ +d   +a+e+a++ + ++++
  gi|557693702|ref|YP_008796756.1| 340 IIKTLLEKGCTVKAYDP--AAIENARKVLGDTVN 371
                                       66778899999999986..566666666665444 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 !   15.7   0.0   1.8e-05     0.017       1      70 [.       2      80 ..       2      85 .. 0.74
   2 ?   -2.5   0.0       8.6   8.1e+03      54      80 ..     203     229 ..     191     244 .. 0.66
   3 !    8.1   0.0    0.0043       4.1      34      93 ..     354     414 ..     337     415 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                                      EEEEETTSHHHHHHHHHHHHTTS.......-GGCEEEEEES....SCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE- CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaaga.......qpheivvansr....npekaeelaeelgvkvtavdneeaaeeadvvvla 68
                                      ki++iG G +g + a  l+++g+       ++h++  +n+     ++ ++++l ++ g ++++ d++ea++ ad+v+++
  gi|557693702|ref|YP_008796756.1|  2 KIAVIGLGYVGLTTAACLASRGFkvtgidiDKHKVETINEGktpfKEPRLDKLLKRSGLRCST-DYAEAVD-ADFVFIS 78
                                      79********************85655566566665554431111234566666666699999.******8.******* PP

                                      S- CS
                     F420_oxidored 69 vk 70
                                      v 
  gi|557693702|ref|YP_008796756.1| 79 VG 80
                                      96 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8.6
                                       CHHHHHHH-SEEEE-S-HHHHHHHHHH CS
                     F420_oxidored  54 dneeaaeeadvvvlavkpedveevlse 80 
                                        n+e+++ a   +la + + + e+++ 
  gi|557693702|ref|YP_008796756.1| 203 VNAEMIKYASNAFLAARISLINEIANI 229
                                       577888888888888777766666654 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0043
                                       SSCCCHHHHHHHHC..-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEEEE CS
                     F420_oxidored  34 rnpekaeelaeelg..vkvtavdneeaaeeadvvvlavkpedveevlselakdalkgklvis 93 
                                        +p  +e +++ lg  v+  + ++ee++++ad+ ++a  ++ +  +  + ++++ ++ +v++
  gi|557693702|ref|YP_008796756.1| 354 YDPAAIENARKVLGdtVNYAS-SAEECLTDADFCIIATEWKEFRRLGPDDFRKLMRDPVVVD 414
                                       566666666666665566666.9********************9998888888888888887 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 !   17.4   0.0   2.4e-06    0.0022      38      92 ..       2      58 ..       1      60 [. 0.88
   2 !    5.7   0.0     0.009       8.4      47      99 ..     336     390 ..     288     397 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.4e-06
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH..CHHHHTCEECSHHHHHHH- CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee..eeeelgvelvsleellaes 92
                                      ++++iGlG +G ++a +l++ g+kv+++d  k+k e  +e ++ ++   l++ll++s
  gi|557693702|ref|YP_008796756.1|  2 KIAVIGLGYVGLTTAACLASRGFKVTGIDIDKHKVEtiNEGKTPFKEPRLDKLLKRS 58
                                      799****************************99988666667777888999999987 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.009
                                       HHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEEC.SHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C  47 IGqavakrlkafgmkviaydrskkkee.eeeelgvelv.sleellaesDivslhl 99 
                                       +  +++k+l + g+ v ayd+   +++ ++    v+++ s ee l ++D+ ++++
  gi|557693702|ref|YP_008796756.1| 336 VSLKIIKTLLEKGCTVKAYDPAAIENArKVLGDTVNYAsSAEECLTDADFCIIAT 390
                                       556789999999**********9977753333344444499*********98876 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 !   20.1   0.0   5.4e-07   0.00051       1      79 [.       2      81 ..       2      85 .. 0.90
   2 ?   -1.9   0.0       3.1   2.9e+03      55     106 ..     196     247 ..     192     252 .. 0.72
   3 ?   -1.2   0.0       1.9   1.8e+03      53      83 ..     366     396 ..     361     409 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.4e-07
                                      -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTT..TBTT----TTEEEES-HHHHHTT--EEEE-- CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvk..yLpgiklpenlvattdlaealkgadiivlvv 77
                                      kiav+G G  G + A+ la++g +v+ +  +++ +e+ine ++  k   L+++   + l+ +td aea++ ad++++ v
  gi|557693702|ref|YP_008796756.1|  2 KIAVIGLGYVGLTTAACLASRGFKVTGIDIDKHKVETINEGKTPFKepRLDKLLKRSGLRCSTDYAEAVD-ADFVFISV 79
                                      7***************************************998655226899999999**********98.99999998 PP

                                      -H CS
                    NAD_Gly3P_dh_N 78 Ps 79
                                       +
  gi|557693702|ref|YP_008796756.1| 80 GT 81
                                      65 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.1
                                       TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SE CS
                    NAD_Gly3P_dh_N  55 enlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGi 106
                                       +++  +t  ae +k a+  +l+   + ++e+++ ++++  +++++vs + G+
  gi|557693702|ref|YP_008796756.1| 196 ATILTNTVNAEMIKYASNAFLAARISLINEIANICQHIPGADVTVVSKAIGL 247
                                       5566666667777778888888888888888888888888888888777666 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.9
                                       --TTEEEES-HHHHHTT--EEEE---HHHHH CS
                    NAD_Gly3P_dh_N  53 lpenlvattdlaealkgadiivlvvPsqalr 83 
                                       l +++   +  +e+l++ad+ +++   + +r
  gi|557693702|ref|YP_008796756.1| 366 LGDTVNYASSAEECLTDADFCIIATEWKEFR 396
                                       66789999999*********99998766665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   6.8e-07   0.00064       1      76 [.       3      79 ..       3      83 .. 0.80
   2 ?   -2.6   0.0       4.1   3.8e+03      75      93 ..     350     367 ..     340     390 .. 0.51

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.8e-07
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCH.SCCCCS-ESEEEE-S CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsae.ekselepidlvivtv 76
                                      ia++G+G +G + aa+La  g +vt i+ ++ ++e++++    +++++   +l+++  l+++ + +e+ ++d v+++v
  gi|557693702|ref|YP_008796756.1|  3 IAVIGLGYVGLTTAACLASRGFKVTGIDIDKhKVETINEGKTPFKEPR-LDKLLKRSGLRCStDYAEAVDADFVFISV 79
                                      89*************************************999999999.33444444444443466667777777765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                                       -SSGGGHHHHHHHHGGGEC CS
                              ApbA  75 tvKayqteealeeikplld 93 
                                       tvKay+ ++ +e+++++l+
  gi|557693702|ref|YP_008796756.1| 350 TVKAYDPAA-IENARKVLG 367
                                       344444332.333333333 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.2e-06    0.0078       1      41 [.       3      43 ..       3      59 .. 0.90
   2 ?    1.4   0.0       0.4   3.7e+02      26      71 ..     351     391 ..     330     407 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.2e-06
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTT CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeg 41
                                      i++iGlG vG + a  L ++g +v++id d+ +ve++ e +
  gi|557693702|ref|YP_008796756.1|  3 IAVIGLGYVGLTTAACLASRGFKVTGIDIDKHKVETINEGK 43
                                      79*****************7756************998765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.4
                                       EEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SS CS
                            TrkA_N  26 vidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatg 71 
                                       v   d++++e++r      v gd  + +  +e  + +ad  i+at+
  gi|557693702|ref|YP_008796756.1| 351 VKAYDPAAIENAR-----KVLGDTVNYASSAEECLTDADFCIIATE 391
                                       4444555555544.....5667777777777777777777777776 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 !    8.1   0.0    0.0038       3.6       9      46 ..       2      47 ..       1      84 [. 0.66
   2 ?    0.7   0.0      0.77   7.3e+02      30      40 ..     235     245 ..     227     297 .. 0.77
   3 !    7.5   0.0    0.0058       5.5      19      73 ..     337     394 ..     334     401 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0038
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele.........e 46
                                      k+ v+G G v+++ +  l++ g kvt ++ +   ++e         +
  gi|557693702|ref|YP_008796756.1|  2 KIAVIGLGYVGLTTAACLASRGFKVTGIDIDK-HKVEtinegktpfK 47
                                      688***********************999884.22223334333330 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.77
                     NAD_binding_7  30 gakvtvvapev 40 
                                       ga+vtvv++++
  gi|557693702|ref|YP_008796756.1| 235 GADVTVVSKAI 245
                                       79******996 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0058
                     NAD_binding_7  19 Aarkvrklleagakvtvvapevkeeleelvklaeeel......ekdlegadlviaatddre 73 
                                        ++ +++lle+g++v+ ++p+   ++e+  k+  +++      e+ l++ad+ i+at+ +e
  gi|557693702|ref|YP_008796756.1| 337 SLKIIKTLLEKGCTVKAYDPA---AIENARKVLGDTVnyassaEECLTDADFCIIATEWKE 394
                                       566689***************...6665555433332222222788999**9999998666 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.6   8.8e-06    0.0083       1      27 [.       2      30 ..       2      34 .. 0.92
   2 ?   -3.5   0.0       6.2   5.9e+03     102     140 ..     274     318 ..     264     321 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.8e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEE CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtlle 27
                                      ++++iG G++Gl+tA  La rg  Vt ++
  gi|557693702|ref|YP_008796756.1|  2 KIAVIGLGYVGLTTAACLASRGfkVTGID 30
                                      59********************9999877 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.2
                                       HHHHHHHTTTTEEEEEH.HHHHHHSTT..ST...TTSEEEEETTE CS
                               DAO 102 llallleagldaellda.eevrelepa..lp...gllgalfypdt 140
                                       l++ ++++g   ++l+a ++v+ ++p   ++   +llg+l+ +++
  gi|557693702|ref|YP_008796756.1| 274 LIKYAEKLGETPRVLEAvDKVNMMQPLkaVElaeKLLGSLHGKTA 318
                                       444445667666888888888888886542255677777776665 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 !   13.4   0.0   6.5e-05     0.062       1      86 [.       1      88 [.       1     118 [. 0.76
   2 ?   -0.7   0.0       1.4   1.3e+03      57      76 ..     370     389 ..     346     393 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.5e-05
                                      EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHH...HHHHHHHHHHHCHCC..STS-EEEEESSGGGGTTESEEE CS
                           Ldh_1_N  1 vkvavvGaaGgiGqslalllankkladelaLlDiake...kleGvaldlshistf..lsvkvkvsekeeealkdadvvv 74
                                      +k+av+G  G +G ++a  la++++    + +Di+k+    ++   + +++  +   l++++   +++++   dad+v 
  gi|557693702|ref|YP_008796756.1|  1 MKIAVIGL-GYVGLTTAACLASRGFKV--TGIDIDKHkveTINEGKTPFKEPRLDklLKRSGLRCSTDYAEAVDADFVF 76
                                      69******.**************9865..7788888733323333344555444400444444555999********** PP

                                      E--S-SS-TTTT CS
                           Ldh_1_N 75 itagvprkpGet 86
                                      i  g p  pG +
  gi|557693702|ref|YP_008796756.1| 77 ISVGTPAGPGGE 88
                                      *********965 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                                       EEEEESSGGGGTTESEEEE- CS
                           Ldh_1_N  57 vkvsekeeealkdadvvvit 76 
                                       v+  ++ ee+l+dad+ +i 
  gi|557693702|ref|YP_008796756.1| 370 VNYASSAEECLTDADFCIIA 389
                                       555668999*******9996 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 ?   14.3   0.1     2e-05     0.019      30      73 ..       2      45 ..       1     130 [. 0.73
   2 ?   -3.0   0.1       3.8   3.6e+03      78      96 ..     222     240 ..     197     245 .. 0.51

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTC CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgak 73
                                      k+ viG G +Gl  +a  ++ g kVt +D+++++ e +++ +  
  gi|557693702|ref|YP_008796756.1|  2 KIAVIGLGYVGLTTAACLASRGFKVTGIDIDKHKVETINEGKTP 45
                                      799********************************999984444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.8
                                       HCHHHHHHHHHHHH-SEEE CS
                       AlaDh_PNT_C  78 lksqeellaeavkeadvvi 96 
                                       l ++ +++ +++  adv +
  gi|557693702|ref|YP_008796756.1| 222 LINEIANICQHIPGADVTV 240
                                       3344556666666666655 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 ?   12.2   0.2   0.00018      0.17       1      27 [.       5      31 ..       5      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                      EE--SHHHHHHHHHHHCCTEEEEEE-S CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllek 27
                                      ++G G  Gl++A+ La +gf+v+ ++ 
  gi|557693702|ref|YP_008796756.1|  5 VIGLGYVGLTTAACLASRGFKVTGIDI 31
                                      8999******************98886 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00043      0.41       1      29 [.       2      30 ..       2      41 .. 0.91
   2 ?   -1.9   0.0       5.4   5.1e+03      15      48 ..     102     131 ..      98     138 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00043
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEE CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvve 29
                                      k++v+G Gy+gl  A+ la  g kVt ++
  gi|557693702|ref|YP_008796756.1|  2 KIAVIGLGYVGLTTAACLASRGFKVTGID 30
                                      79***********************9776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.4
                                       HHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHH CS
                         Pyr_redox  15 AgalaelgkkVtvversdkllrllDeeaskilqe 48 
                                       +++la  +k  tvv+rs  +      +++ i+++
  gi|557693702|ref|YP_008796756.1| 102 GEVLASRRKPCTVVVRSTVVP----GTTRGIVKN 131
                                       678888899999999986544....445555555 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 ?   10.6   0.2   0.00025      0.23       2      33 ..       2      42 ..       1      88 [. 0.61

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00025
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEE.........TTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.........leg 33
                                      +++viG G  Gl++a  la  g+kvt ++          eg
  gi|557693702|ref|YP_008796756.1|  2 KIAVIGLGYVGLTTAACLASRGFKVTGIDidkhkvetiNEG 42
                                      45555555555555555555555555554334333344444 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 ?   11.7   0.0   0.00021       0.2      20      55 ..      16     228 ..      11     305 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                       HHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................... RF
                              CbiA  20 aralarrglrVllvDaDpqannlaileglendiep.......................................... 54 
                                       a++la rg++V  +D D   +  +i eg+ +++ep                                          
  gi|557693702|ref|YP_008796756.1|  16 AACLASRGFKVTGIDIDKH-KVETINEGKTPFKEPrldkllkrsglrcstdyaeavdadfvfisvgtpagpggeidl 91 
                                       7899999***********9.555569999999999****************************************99 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|557693702|ref|YP_008796756.1|  92 syvagaarslgevlasrrkpctvvvrstvvpgttrgivknelekssgkrvgedlflcvnpeflregnavhdtfnpdr 168
                                       99999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ...........................................................C CS
                                       ...........................................................x RF
                              CbiA  55 ...........................................................d 55 
                                                                                                  +
  gi|557693702|ref|YP_008796756.1| 169 ivigddwgsggknllrlyhrfyrrrkpatiltntvnaemikyasnaflaarislineiaN 228
                                       999999988555555555555555555555555555555555555555555555555550 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00029      0.28       3      58 ..       2      60 ..       1     114 [. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEE..SSSS.SCCSSS--EEEHHHHHHHHHTT- CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlve..krst.tvvlpradglnqrtmellrqlGl 58
                                      +++++G G +Gl++a  L+++G +v+ ++  k++  t+++++    ++r   ll+  Gl
  gi|557693702|ref|YP_008796756.1|  2 KIAVIGLGYVGLTTAACLASRGFKVTGIDidKHKVeTINEGKTPFKEPRLDKLLKRSGL 60
                                      678*******************9988765116654133444776666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3025.68
//
Query:       gi|557693703|ref|YP_008796757.1|  [L=321]
Description: glycosyl transferase family 1 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  132.9   0.0    1.1e-38  132.5   0.0    1.1  1  Glycos_transf_1  Glycosyl transferases group 1
    2.2e-27   96.1   0.0      4e-27   95.3   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
      3e-13   50.0   0.0    5.2e-13   49.2   0.0    1.3  1  Glyco_trans_1_2  Glycosyl transferases group 1
    1.2e-07   32.3   0.7    3.6e-07   30.7   0.7    1.7  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 !  132.5   0.0   2.4e-42   1.1e-38      10     171 ..     134     294 ..     126     295 .. 0.96

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 2.4e-42
                                       TTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSH CS
                   Glycos_transf_1  10 gknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredl 86 
                                       + +e+  ++++ +rl++eKg+dll++a++ll ++  p++ + i G+g+++k+l+ la el+++d v+flg  +++dl
  gi|557693703|ref|YP_008796757.1| 134 NPDERGHVVVTAARLVPEKGLDLLLRAVPLLLQD-FPDLEVRILGEGPMRKSLQGLAGELGVGDVVKFLGWAPVDDL 209
                                       45677789***********************987.****************************************** PP

                                       HHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHH CS
                   Glycos_transf_1  87 eellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelre 163
                                        + ++ a +fv++s++Eg + ++ EA ++ +p +++ +g ++ev++dge+ llv+  +++ lae+i++ll+d+++r+
  gi|557693703|ref|YP_008796757.1| 210 VKHYNEAAVFVCTSHYEGGPRTVFEAASCLTPSVSTPVGIVPEVLRDGESVLLVERRDPDLLAEKIAQLLHDRDKRR 286
                                       ***************************************************************************** PP

                                       HHHHHHHH CS
                   Glycos_transf_1 164 rlgenark 171
                                       rl e+ar+
  gi|557693703|ref|YP_008796757.1| 287 RLAEKARE 294
                                       *****996 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 !   95.3   0.0     9e-31     4e-27       2     134 .]     140     281 ..     139     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 9e-31
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHHT..T-T.TEEEE---..THHHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleelaa..gleerveftGfv..edlaella 71 
                                       +v+++  rl+++ kg+dlll+avpll+++  d+++ i G+gp r ++l+ la   g+ + v+f+G+   +dl ++++
  gi|557693703|ref|YP_008796757.1| 140 HVVVTAARLVPE-KGLDLLLRAVPLLLQDfpDLEVRILGEGPmR-KSLQGLAGelGVGDVVKFLGWApvDDLVKHYN 214
                                       6899999**655.**************88855**********65.699988855999899*******9999****** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       +a vfv++s  eg + ++ Ea+++ +p V+t+vg ++ev+  ge+ llv+ +dp+ lae+i++Ll+d
  gi|557693703|ref|YP_008796757.1| 215 EAAVFVCTShyEGGPRTVFEAASCLTPSVSTPVGIVPEVLrdGESVLLVERRDPDLLAEKIAQLLHD 281
                                       *********************************667**99*99999*******************97 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 !   49.2   0.0   1.2e-16   5.2e-13       4      90 ..     221     309 ..     218     311 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.2e-16
                   Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervl 78 
                                        +s++e+    +fEaa c ++ ++++   ++e +++g++v+l+e  d++ laeki++ll ++++rr++ae+are vl
  gi|557693703|ref|YP_008796757.1| 221 CTSHYEGGPRTVFEAASCLTPSVSTPVGIVPEVLRDGESVLLVErrDPDLLAEKIAQLLHDRDKRRRLAEKAREIVL 297
                                       567777777899*************99************************************************** PP

                   Glyco_trans_1_2  79 aehtydhraeql 90 
                                       +e+ + + +e++
  gi|557693703|ref|YP_008796757.1| 298 REFEWSKSVERY 309
                                       *****9988875 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 !   30.7   0.7   8.1e-11   3.6e-07      57     158 ..      17     120 ..       2     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 8.1e-11
                   Glyco_trans_4_4  57 laalralrrll....rqrrerpdvvhahspt..aglaarlarrrrgiplvvtlhglllrrg.sgavrrlyralerrl 126
                                       l+++++  ++     + r  r+d+v+a++pt  +gl+a+l +   ++ l+ ++hg+ lr+   +++ rl+++l   +
  gi|557693703|ref|YP_008796757.1|  17 LRRYWGTVDVAtglhAPRFTRYDLVIAQEPTikIGLPALLQAKLSNAALITEVHGDYLRGNfLPWKDRLFAWL---V 90 
                                       44443332322333444789*********9878788887666599***********99988*********998...9 PP

                   Glyco_trans_4_4 127 lrradavlvvseaeaeelralgvpadrvvvvp 158
                                       lr+ d v +v  ++a  l+ +g+   +v+vvp
  gi|557693703|ref|YP_008796757.1|  91 LRSSDFVRAVNSGIAWNLQSRGLS--NVHVVP 120
                                       ***********************9..999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2316.43
//
Query:       gi|557693704|ref|YP_008796758.1|  [L=314]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   62.8   0.0    4.5e-17   62.1   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    4.8e-11   43.2   0.0    9.4e-11   42.3   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.2e-07   31.9   0.6    1.8e-07   31.3   0.6    1.3  1  Glyco_transf_4   Glycosyltransferase Family 4
    0.00015   22.3   0.5    0.00032   21.2   0.1    1.8  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain
     0.0028   17.7   0.0     0.0068   16.4   0.0    1.7  1  Glyco_trans_4_2  Glycosyl transferase 4-like


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 !   62.1   0.0   1.2e-20   4.5e-17       8     103 ..     197     293 ..     191     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 1.2e-20
                                       HTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...STTHHHHHHHHHHHCTTCGGGEEECCH CS
                   Glycos_transf_1   8 klgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG..ngeeekelkklaeelelsdnviflgevs 82 
                                        ++++ ++k il+vgr++++Kgv+ l+kaf+ +  +++ ++ l iaG  +  + ++l +++ + +l d v+flg v+
  gi|557693704|ref|YP_008796758.1| 197 LEELKRGRKCILYVGRVNEKKGVEDLVKAFRIV-STMHRDCILAIAGagEAGYVEKLLEEVNKTGLDDSVFFLGPVP 272
                                       45667899***********************88.568**********99889************************* PP

                                       SSSHHHHHHCESEEEEEESSB CS
                   Glycos_transf_1  83 redleellknadifvlpsisE 103
                                       +++++ l+++ad++++ s+ E
  gi|557693704|ref|YP_008796758.1| 273 NSEIPMLYRSADVVAYASRGE 293
                                       ****************99866 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 !   42.3   0.0   2.6e-14   9.4e-11       2      82 ..     205     292 ..     204     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2.6e-14
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---.....HHHHHHHT..T-T.TEEEE---..THHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgprp...eeleelaa..gleerveftGfv..edlael 69 
                                       + il+vGr++e +kgv+ l++a+  +     d+ l i+G g+ +   e+l e+++  gl+++v f+G v  ++++ l
  gi|557693704|ref|YP_008796758.1| 205 KCILYVGRVNE-KKGVEDLVKAFRIVSTMhrDCILAIAGAGE-AgyvEKLLEEVNktGLDDSVFFLGPVpnSEIPML 279
                                       679******65.5**************55326*******996.32345665566569************8777**** PP

                                       HHH-SEEEE---- CS
                   Glyco_trans_1_4  70 laaadvfvaPseg 82 
                                       +++adv+   s+g
  gi|557693704|ref|YP_008796758.1| 280 YRSADVVAYASRG 292
                                       ********99954 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.6     5e-11   1.8e-07      24     168 ..      44     184 ..      28     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 5e-11
                    Glyco_transf_4  24 vvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrr.rlgipl 99 
                                       vv+++ d p+  e   +v +p+++  ++k ++ +   +  ++ +l+r ++Dv+ ++++ +  +++l+  r  ++ip 
  gi|557693704|ref|YP_008796758.1|  44 VVSRRLDTPPNME---IVKLPAIR--IPKIYGATKILFYGFKPVLDRDNVDVLYVRTFSPPELSALWFGRlFSDIPS 115
                                       4555555555555...55555555..555555555556678999*************99998888888888****** PP

                    Glyco_transf_4 100 VltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelreryg..vppekitVipnGvDl 168
                                       Vl + g++    +++  k ++r++r+++rr+l+++ +++  S+++  e++  y+  ++ +k++ i+n+v++
  gi|557693704|ref|YP_008796758.1| 116 VLVLPGTW-LFGHPSSAKGKERFYRWFLRRALDSCEKIVLYSRHMLPEVLL-YHpkLDVSKVVYIHNAVNI 184
                                       ********.788899999999******************************.77588889*********96 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 !   21.2   0.1   8.9e-08   0.00032      47     145 ..      45     164 ..      14     181 .. 0.67
   2 ?   -1.9   0.0       1.1   4.1e+03     126     141 ..     279     294 ..     277     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 8.9e-08
                   Glyco_trans_4_4  47 vprrpspladlaal..................ralrrllrqrrerpdvvhahs.ptaglaarlarrrr.giplvvtl 103
                                       v+rr +++++++ +                   +++ +l  +r ++dv+++ + ++  l a++  r   +ip v+ l
  gi|557693704|ref|YP_008796758.1|  45 VSRRLDTPPNMEIVklpairipkiygatkilfYGFKPVL--DRDNVDVLYVRTfSPPELSALWFGRLFsDIPSVLVL 119
                                       333333333333333333334555555555556788889..*********9985455555555543444******** PP

                   Glyco_trans_4_4 104 hgll.lrrg..sgavrrlyralerrllrradavlvvseaeaeelr 145
                                        g++ + ++  +  + r+yr++ rr+l ++  ++  s+++  e+ 
  gi|557693704|ref|YP_008796758.1| 120 PGTWlFGHPssAKGKERFYRWFLRRALDSCEKIVLYSRHMLPEVL 164
                                       99875333335777999*******************999976655 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                   Glyco_trans_4_4 126 llrradavlvvseaea 141
                                       l+r+ad+v + s++e+
  gi|557693704|ref|YP_008796758.1| 279 LYRSADVVAYASRGER 294
                                       6899****99999886 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 !   16.4   0.0   1.9e-06    0.0068      57     135 ..      70     152 ..      30     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-06
                   Glyco_trans_4_2  57 pleylk.af.klkklikkikPDvvhahyakpygllgslaarlsgvipvvlsvwGldvlkfpkksk....lkklllkl 127
                                        ++  k +f  +k ++++++ Dv+++ + +p+ l +  + rl   ip vl   G+  + +p  +k    ++++ l+ 
  gi|557693704|ref|YP_008796758.1|  70 GAT--KiLFyGFKPVLDRDNVDVLYVRTFSPPELSALWFGRLFSDIPSVLVLPGTWLFGHPSSAKgkerFYRWFLRR 144
                                       333..434458999***************************8889**********9999998888666777777777 PP

                   Glyco_trans_4_2 128 alkkatkv 135
                                       al + +k+
  gi|557693704|ref|YP_008796758.1| 145 ALDSCEKI 152
                                       77776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2287.02
//
Query:       gi|557693705|ref|YP_008796759.1|  [L=335]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-22   78.3   0.0    7.4e-22   78.0   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.1e-12   46.6   0.2    2.8e-12   46.2   0.2    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.2e-11   44.7   0.0    4.7e-11   42.7   0.0    1.7  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    4.8e-09   35.7   0.0    6.9e-09   35.2   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    2.3e-06   27.0   1.9      0.023   13.9   0.3    2.7  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0016   18.4   0.2     0.0023   17.9   0.2    1.3  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.013   15.1   0.1      0.026   14.1   0.1    1.5  1  NmrA             NmrA-like family
      0.019   15.2   0.5       0.04   14.2   0.5    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.046   14.3   0.4       0.35   11.5   0.5    2.4  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
       0.11   12.0   0.2       0.31   10.5   0.2    1.7  1  adh_short        short chain dehydrogenase
       0.19   11.1   0.1       0.44    9.9   0.0    1.6  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


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 !   78.0   0.0   4.5e-25   7.4e-22       1     236 [.       5     236 ..       5     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 4.5e-25
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---H CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggv 77 
                                       ++V G++GfiGsa++++l ++g +v + d  + ++  +    +e+ve+d++dr a+ r++   ++ + ++  a+  +
  gi|557693705|ref|YP_008796759.1|   5 VVVFGGSGFIGSAVANYLSDAGLKVRVADVVRPRGDLG----VEFVECDVRDRGAVLRALG--DARVAVNT-AIVQI 74 
                                       689**********************9999994444433....39*****************..78999999.67888 PP

                                       HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSSSS.BSTCSTTS--...--SSHHHHHHHHH CS
                         Epimerase  78 aassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdaeqp.keettltgpl...kpnspYaaaKlag 149
                                       ++ +e+p   +e n++gt+n++ea+  +g    ++++++ ++ G+   +   +e+  + p    +  + Ya++K++ 
  gi|557693705|ref|YP_008796759.1|  75 PRINEEPRLGYEVNVIGTQNVCEAVAGSGSClGMVQAGTWHTIGETGLSGvVDEEFGYRPDkveERARVYALSKVCQ 151
                                       9999999999****************9977669***********99995347788888888889999********** PP

                                       HHHHHHHHHHH.T-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHH..HHHHHHH CS
                         Epimerase 150 eklveayaaqy.glnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyve..Dvaeail 223
                                       e++v+ +   + +  ++++r  ++ Gp+  ++e +     +i+++  gk ++t +   +  R+ lyv+  Dva+a+ 
  gi|557693705|ref|YP_008796759.1| 152 ESVVRLFSYMFrEKAYVVIRTGTVLGPN--MPE-QTAAKIFIKNAVGGK-PLTPYR-HSMYRPILYVDvgDVAKAYE 223
                                       **********99999*************..333.33344579****9*9.999997.6667887765444******* PP

                                       HHHHHHTT-STTE CS
                         Epimerase 224 lvlehvdagdkge 236
                                        v+++  +gd ++
  gi|557693705|ref|YP_008796759.1| 224 VVVKKILDGDMRG 236
                                       **99977776644 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 !   46.2   0.2   1.7e-15   2.8e-12       1     235 [.       6     232 ..       6     268 .. 0.72

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 1.7e-15
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       vv Gg+GF+G+a+ + L +++   +vrv+D++           ++v+ ++e+Dv+d   + +al ++ v + +a ++
  gi|557693705|ref|YP_008796759.1|   6 VVFGGSGFIGSAVANYLSDAG--LKVRVADVVRPRG------DLGVE-FVECDVRDRGAVLRALGDARVAVNTAIVQ 73 
                                       79***************9999..69*****987554......48999.*************************6665 PP

                         3Beta_HSD  78 dvagkltedeimkvnvkGTrnvleacvkag.vrvlvYtSsaevvgpnslgeeilngdEeleyesl....hqdaypes 149
                                         + + +    ++vnv GT+nv ea   +g    +v   +   +g+ +    ++  dEe  y +        +y+ s
  gi|557693705|ref|YP_008796759.1|  74 IPRINEEPRLGYEVNVIGTQNVCEAVAGSGsCLGMVQAGTWHTIGE-TGLSGVV--DEEFGYRPDkveeRARVYALS 147
                                       55557777888**************98776266799*********9.5555566..56655544323446679**** PP

                         3Beta_HSD 150 KalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkqlaklglal.fkigdeevlsdrvY..vgNvaw 223
                                       K   E +v      ++++      + +R  ++ G+  ++ +++   +++    + +    +++     Y  vg va+
  gi|557693705|ref|YP_008796759.1| 148 KVCQESVVRLFSY-MFREK---AYVVIRTGTVLGPNMPEQTAAKIFIKNAVGGKpLTPYRHSMYRPILYvdVGDVAK 220
                                       *999999988776.88888...5577999999998876655443333333333303333344444444522577777 PP

                         3Beta_HSD 224 ahilAaralqdp 235
                                       a+ + +++++d 
  gi|557693705|ref|YP_008796759.1| 221 AYEVVVKKILDG 232
                                       777777777766 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 !   42.7   0.0   2.9e-14   4.7e-11       2     318 ..       7     305 ..       6     321 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 2.9e-14
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       + G++GfiGs +a++L + g +v + +                      +  ++++++D++D+ ++ r+l ++++  
  gi|557693705|ref|YP_008796759.1|   7 VFGGSGFIGSAVANYLSDAGLKVRVADVVRPR--------------G--DLGVEFVECDVRDRGAVLRALGDARVA- 66 
                                       89*******************99664332222..............1..22478******************9765. PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S.SSSB-TTS----..... CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq.evpqtEttpfyP..... 149
                                        +n  A   +++  e+P   +evnv+Gt+++ ea+   g  +   ++qa+t    G++  +  ++E+  ++P     
  gi|557693705|ref|YP_008796759.1|  67 -VN-TAIVQIPRINEEPRLGYEVNVIGTQNVCEAVAGSG--SCLGMVQAGTWHTIGETGlSGVVDEEFGYRPdkvee 139
                                       .66.68899**************************8777..589**************945668***9999977777 PP

                                       .-SHHHHHHHHHHHHHHHHHHHH---EEEEE.E-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EEC.TTTT-EEEE CS
                     GDP_Man_Dehyd 150 .rsPYaaaKlyadwivvnyreayglfavngi.lfnhesprrgetfvtrkitravarialgkqevlyl.GnldakRdw 223
                                           Ya +K+ ++ +v+ +   +   a + i +    +p +     +++  ++  + a+g ++ + +   ++    +
  gi|557693705|ref|YP_008796759.1| 140 rARVYALSKVCQESVVRLFSYMFREKAYVVIrTGTVLGPNMP----EQTAAKIFIKNAVGGKPLTPYrHSMYRPILY 212
                                       6679*************9999888776654415556666655....5555555555566655655553777777788 PP

                                       EEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--S CS
                     GDP_Man_Dehyd 224 ghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrp 300
                                         v D+++a+  ++++      + + ++++++     ++++el +t++ +  +e   gr++   +vv +  p  f p
  gi|557693705|ref|YP_008796759.1| 213 VDVGDVAKAYEVVVKKILDG-DMRGVNNVFNLVYPEPMTVIELAETVKRSV-EELTGGRISPAVEVVDKGIPPLFTP 287
                                       8999******9999876644.455777889999999999999998877654.4455577777777777888889999 PP

                                       S--SB--B-THHHHHHH- CS
                     GDP_Man_Dehyd 301 gevdlllgdaskakeeLg 318
                                        + ++ +  ++++   Lg
  gi|557693705|ref|YP_008796759.1| 288 DDKNRFVCKIDRITAILG 305
                                       999999999999988887 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 !   35.2   0.0   4.2e-12   6.9e-09       3     233 ..       5     264 ..       3     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 4.2e-12
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...........T--TTSHHHHHHHHHHH--SEEEE------HHHHH CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre...........eldltdaeavaellkeakpdvvvnaAAytavDkaE 68 
                                       ++v+G++G +Gs++a+ l+ +gl+v   +             e+d++d+ av ++l +a+  v vn+A   ++ +  
  gi|557693705|ref|YP_008796759.1|   5 VVVFGGSGFIGSAVANYLSDAGLKVRVADVVrprgdlgvefvECDVRDRGAVLRALGDAR--VAVNTAI-VQIPRIN 78 
                                       79********************999888666679***********************955..6889876.5788999 PP

                                       HSHHHHHHHHTHHHHHHHHHHHHCT-EE..EEEEEGGGS-S-.......TTS-B-TTS----SSHHHHHHHHHHHHH CS
                     RmlD_sub_bind  69 seeeaayavnaeavealAeaaaavgalL..ihvStDyVFdGe.......kkrpYeeddetsPlnvYGrtKlaGEqav 136
                                       +e+++ y+vn+ +++++ ea a  g+ L  ++  t      +       ++  Y++d   +   vY+ +K+  E +v
  gi|557693705|ref|YP_008796759.1|  79 EEPRLGYEVNVIGTQNVCEAVAGSGSCLgmVQAGTWHTIGETglsgvvdEEFGYRPDKVEERARVYALSKVCQESVV 155
                                       9************************9865599999988776688888855556************************ PP

                                       HH.....H-SSEEEEEE-SEESS..SSS-HHHHHHHHHHH-SEEEEESS-EE--...EEHHHHHHHHHHHHHHCHH. CS
                     RmlD_sub_bind 137 la.....agkkalivRtswvyge..kgknfvktmlrlakereelkvvaDqlgsP...TsardlAevllqllekaaee 203
                                       +        k ++++Rt+ v+g    ++  +k +++ a   ++l+     + +P     + d+A++   +++k+++ 
  gi|557693705|ref|YP_008796759.1| 156 RLfsymfREKAYVVIRTGTVLGPnmPEQTAAKIFIKNAVGGKPLTPYRHSMYRPilyVDVGDVAKAYEVVVKKILDG 232
                                       *98888788999*********98555778899999999****************33335778888888888888876 PP

                                       GGG..-EEEE---BS-EEHHHHHHHHHHHHCH CS
                     RmlD_sub_bind 204 kel..agvyHlanegetswlefArailkeaga 233
                                            + v+ l+  + ++  e+A+ + +++++
  gi|557693705|ref|YP_008796759.1| 233 DMRgvNNVFNLVYPEPMTVIELAETVKRSVEE 264
                                       66577999999999999999999999887765 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.3   1.4e-05     0.023      59     116 ..      46     100 ..       5     125 .. 0.87
   2 !   11.5   0.1   7.4e-05      0.12     129     247 ..     135     262 ..     131     281 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                                       .E--TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHH CS
                   Polysacc_synt_2  59 vigdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaai 116
                                       v +dvrd+  + +al + +v       A+ ++P ++e+p  + + Nv+gt+nv+ea  
  gi|557693705|ref|YP_008796759.1|  46 VECDVRDRGAVLRALGDARV---AVNTAIVQIPRINEEPRLGYEVNVIGTQNVCEAVA 100
                                       5589*****99999994444...3456889************************9975 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.4e-05
                                       GGGSS--SHHHHHHHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT...TSSHHHHHHHHHTTSSEEES-TT-EEE CS
                   Polysacc_synt_2 129 DKAvnPtnvmGatKrlaekllqalakeseekktkfvvvRfGNVlgSr...GSviplFkkqikeggpvtvTdpemtRy 202
                                       DK  +   v+ ++K ++e ++  ++     +++++vv+R G Vlg +        +F k    g+p+t   ++m R 
  gi|557693705|ref|YP_008796759.1| 135 DKVEERARVYALSKVCQESVVRLFSYMF--REKAYVVIRTGTVLGPNmpeQTAAKIFIKNAVGGKPLTPYRHSMYRP 209
                                       88888899*************9999998..7899***********86333688999********************8 PP

                                       EE-.....HHHHHHHHHHHH...HH--SS-EEEE--.-EEEHHHHHHHH.... CS
                   Polysacc_synt_2 203 fmt.....ieeavqLvlqal...alakggeifvldmGepvkivdlakaliels 247
                                       ++      +++a ++v++ +    +   +++f l   ep+++++la+++ + +
  gi|557693705|ref|YP_008796759.1| 210 ILYvdvgdVAKAYEVVVKKIldgDMRGVNNVFNLVYPEPMTVIELAETVKRSV 262
                                       8862222246899999998733244455679*99999**********997654 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 !   17.9   0.2   1.4e-06    0.0023       1      89 [.       9     103 ..       9     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.4e-06
                                       TTTSHHHHHHHHHHHHC-.T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-S.EEEES-......- CS
                    NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgad.aVvsal......g 69 
                                       G++G +G+++++ l ++g +++v  +vR   +        g+e ve dv d  ++ +al +a  aV +a+      +
  gi|557693705|ref|YP_008796759.1|   9 GGSGFIGSAVANYLSDAGlKVRVADVVRPRGD-------LGVEFVECDVRDRGAVLRALGDARvAVNTAIvqipriN 78 
                                       9****************744444445555544.......5699*******************945666666533221 PP

                                       -TCCHHHH..........HHHHHHHHHHCT CS
                    NAD_binding_10  70 gggkdeeg..........aknivdaakeag 89 
                                           +e            ++n+++a+  +g
  gi|557693705|ref|YP_008796759.1|  79 ----EE-PrlgyevnvigTQNVCEAVAGSG 103
                                       ....22.12455556677999999987655 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   1.6e-05     0.026       1      69 [.       5      67 ..       5      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEE CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvf 69
                                      ++v+G++G +G++v+++l +ag kvr+       ++++   + Gve+v+ d+ d+  + +al ++ v+ 
  gi|557693705|ref|YP_008796759.1|  5 VVVFGGSGFIGSAVANYLSDAGLKVRV------ADVVRPRGDLGVEFVECDVRDRGAVLRALGDARVAV 67
                                      78************************8......567777788899999999999998888888888765 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 ?   14.2   0.5   2.5e-05      0.04       1      77 [.       5      70 ..       5      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                      EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77
                                      v+++G+ G++G+ava +l++ +    ++ vad  + +            +e++++d+ ++ avL a l ++ + vn +
  gi|557693705|ref|YP_008796759.1|  5 VVVFGGsGFIGSAVANYLSDAGL---KVRVADVVRPR--------GDLGVEFVECDVRDRGAVLRA-LGDARVAVNTA 70
                                      7899999*************984...7**********........6678999**********7777.68888888865 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   0.00022      0.35       2      27 ..       6      31 ..       5      46 .. 0.89
   2 ?   -1.4   0.0       2.2   3.5e+03      23      44 ..     164     186 ..     160     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00022
                                      EEEECSSHHHHHHHHHHHHTTSEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtv 27
                                      vv+ G+G+ig  +A++l++ g kV v
  gi|557693705|ref|YP_008796759.1|  6 VVFGGSGFIGSAVANYLSDAGLKVRV 31
                                      567799***************99987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                                       SEEEEEESSSSSS.TTSSHHHHH CS
                         Pyr_redox  23 kkVtvversdkll.rllDeeask 44 
                                        k +vv r  ++l ++++e++++
  gi|557693705|ref|YP_008796759.1| 164 EKAYVVIRTGTVLgPNMPEQTAA 186
                                       67789999999999888877654 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00019      0.31       3      72 ..       5      64 ..       4      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00019
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekav 72
                                      v+v G+s+ IG a+a+ l  +G kv v+d    +       l+     + ++++Dv+dr +v +++ +a+
  gi|557693705|ref|YP_008796759.1|  5 VVVFGGSGFIGSAVANYLSDAGLKVRVADVVRPRG-----DLG-----VEFVECDVRDRGAVLRALGDAR 64
                                      899**********************9988776665.....555.....7789999999988888877665 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 ?    9.9   0.0   0.00027      0.44      42      83 ..       9      46 ..       4      60 .. 0.80
   2 ?   -2.7   0.0         2   3.2e+03      36      60 ..      84     108 ..      55     112 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                                      ES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC CS
                      2-Hacid_dh_C 42 iGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv 83
                                       G G IG+ava++l+  g+kv + d+ + + +    lgve+v
  gi|557693705|ref|YP_008796759.1|  9 GGSGFIGSAVANYLSDAGLKVRVADVVRPRGD----LGVEFV 46
                                      589**********************9988655....444444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                                       TSEEEEES-SHHHHHHHHHHHHTT- CS
                      2-Hacid_dh_C  36 gktvGiiGlGrIGqavakrlkafgm 60 
                                       g +v +iG+ ++ +ava   + +gm
  gi|557693705|ref|YP_008796759.1|  84 GYEVNVIGTQNVCEAVAGSGSCLGM 108
                                       5567788998888888887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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 0.29s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2341.56
//
Query:       gi|557693706|ref|YP_008796760.1|  [L=209]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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    6.3e-10   39.6   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.8e-08   34.9   0.0    2.8e-08   34.4   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    9.4e-08   32.1   0.0    1.2e-07   31.7   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    3.2e-05   23.8   0.0    4.3e-05   23.3   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    0.00011   22.9   0.0    0.00015   22.5   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.026   13.8   0.0      0.036   13.4   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.047   12.2   0.0      0.085   11.4   0.0    1.3  1  Methyltransf_29  Putative S-adenosyl-L-methionine-dependent m
      0.061   12.2   0.0      0.071   12.0   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
       0.16   12.3   0.0       0.29   11.4   0.0    1.4  1  CpcD             CpcD/allophycocyanin linker domain


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 !   39.6   0.0   3.1e-13   6.3e-10       2      94 ..      31     126 ..      30     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 3.1e-13
                                       EET-..T.TSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCC..TSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   2 dvGc..G.tGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaek..lpfednsfDlvvssevlhh 73 
                                       dvGc  G +G +++a+a r  +vvg+D+ +  lk+ +e ++  ++    ++ d+ek  +p++d+  Dl ++ ev++h
  gi|557693706|ref|YP_008796760.1|  31 DVGCrlGwAGHMLAAIAGRPVEVVGLDVYEPYLKTLSEISKIYKP----IKVDLEKepIPLPDGFADLTICIEVIEH 103
                                       999944445666666665559************999776666654....8888887779****************** PP

                                       -..CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  74 v..edpekalkeiaRvLkpgGll 94 
                                       +  +   ++++e+ R+ ++gG++
  gi|557693706|ref|YP_008796760.1| 104 LskPAGYRLMDEMERITRKGGYI 126
                                       *888889**************98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   1.4e-11   2.8e-08       1      97 []      29     124 ..      29     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.4e-11
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCG..BSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvefvqgdaed..lpfedgsfDlvvssgal 74 
                                       v+d+Gc  G    +la+  g   +v+g+D+ e +l++  e  +      + ++ d+e+  +p++dg  Dl +++ ++
  gi|557693706|ref|YP_008796760.1|  29 VVDVGCRLGWAGHMLAAIAGrPVEVVGLDVYEPYLKTLSEISK----IYKPIKVDLEKepIPLPDGFADLTICIEVI 101
                                       89*******9999999888668****************99884....567888888665589***********988* PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                       +hls++   ++++e+ r++++gG
  gi|557693706|ref|YP_008796760.1| 102 EHLSKPAGYRLMDEMERITRKGG 124
                                       **********************9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0     6e-11   1.2e-07      23     122 ..      26     133 ..      12     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 6e-11
                   Methyltransf_23  23 ggrvLdiGcGtGi...llevlrengfsvtgvDlspeaveiae...kakkaqkdqfdeqeaaepqgkfdlIvlrevle 93 
                                          v+d+Gc  G    +l  ++ ++++v+g D ++   + ++   k++k +k+    + ++ p+g  dl +++ev+e
  gi|557693706|ref|YP_008796760.1|  26 LRVVVDVGCRLGWaghMLAAIAGRPVEVVGLDVYEPYLKTLSeisKIYKPIKVDLEKEPIPLPDGFADLTICIEVIE 102
                                       5689******9953447888899999999888776544444466699999999998888888*************** PP

                   Methyltransf_23  94 hvpdpp..ellrqiatllkpgGylllsepla 122
                                       h+  p+  +l++ + ++++ gGy+ l++p+ 
  gi|557693706|ref|YP_008796760.1| 103 HLSKPAgyRLMDEMERITRKGGYIHLTTPNG 133
                                       ****998899******************974 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   2.2e-08   4.3e-05       6     119 ..      28     138 ..      24     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.2e-08
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       +v+D+GC  G  ++ la  +g   evvG+D  e  ++   e+++  +   v +e+++i      l d   Dl ++ e
  gi|557693706|ref|YP_008796760.1|  28 VVVDVGCRLGWAGHMLAAIAGRPVEVVGLDVYEPYLKTLSEISKIYKPIKVDLEKEPIP-----LPDGFADLTICIE 99 
                                       699***************9999********************88666666666666664.....456888******* PP

                   Methyltransf_31  83 vlnaladpdki..leeiervlkpggilliedprllaelp 119
                                       v+ +l+ p+ +  + e+er  ++gg++ +++p++++  +
  gi|557693706|ref|YP_008796760.1| 100 VIEHLSKPAGYrlMDEMERITRKGGYIHLTTPNGWRPTD 138
                                       **9998888643288******************887666 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   7.4e-08   0.00015       1      98 [.      30     125 ..      30     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 7.4e-08
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       +++Gc  G   ++l++   +++e++g+D+ +  + ++  +++k+ +    +v+le++ +   dg    Dl ++++v+
  gi|557693706|ref|YP_008796760.1|  30 VDVGCRLGWAGHMLAAIAgRPVEVVGLDVYEPYL-KTLSEISKIYKPI--KVDLEKEPIPLPDG--FADLTICIEVI 101
                                       59****99999998887789**************.9999999988755..66666666665555..69********* PP

                   Methyltransf_12  77 hhlkdir..evldnirklLkpgGr 98 
                                       +hl +++  +++d++ +  ++gG+
  gi|557693706|ref|YP_008796760.1| 102 EHLSKPAgyRLMDEMERITRKGGY 125
                                       ***666657999999999999997 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.8e-05     0.036      66     166 ..      29     130 ..      19     158 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.8e-05
                                       EEEES-..TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGT CS
                              CMAS  66 lLdiGc..GWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehv 140
                                       ++d+Gc  GW + +  a++   v+vvgl + +   k+   ++ ++    kv+++       d+  d  + ++++eh+
  gi|557693706|ref|YP_008796760.1|  29 VVDVGCrlGWAGHMLAAIAGRPVEVVGLDVYEPYLKTL-SEISKIYKPIKVDLEKEPIPLPDGFADLTICIEVIEHL 104
                                       79****99***********99********987766655.567888888888888877766666889999******** PP

                                       SGGGHHHHHHHHHHHS-TT-EEEEEE CS
                              CMAS 141 gkenydtffkklkkllkedGllllht 166
                                        k    + +++++++++++G + l t
  gi|557693706|ref|YP_008796760.1| 105 SKPAGYRLMDEMERITRKGGYIHLTT 130
                                       99999999************998876 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 ?   11.4   0.0   4.3e-05     0.085     113     221 ..      21     132 ..      13     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.3e-05
                   Methyltransf_29 113 aaggkvrtvlDvGCgvasfgayllsrdvltlslapkDeheaqvqfaLe.Rgvpa.ilavlgtkrlpyPsrsfdlihC 187
                                       + g+++r+v+DvGC     g +l       + +   D++e  ++   e  ++   i   l ++ +p P    dl  C
  gi|557693706|ref|YP_008796760.1|  21 ELGDELRVVVDVGCRLGWAGHMLAAIAGRPVEVVGLDVYEPYLKTLSEiSKIYKpIKVDLEKEPIPLPDGFADLTIC 97 
                                       468899********98766666666677788888999999999876663345440555599999************* PP

                   Methyltransf_29 188 srCridwteedgilll.evdRvlRpgGyfvlsapp 221
                                            + ++  g  l+ e++R+ R gGy  l++p+
  gi|557693706|ref|YP_008796760.1|  98 IEVIEHLSKPAGYRLMdEMERITRKGGYIHLTTPN 132
                                       **9999999999866659**********9888775 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 ?   12.0   0.0   3.6e-05     0.071     117     198 ..      27     107 ..      14     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.6e-05
                                       -EEEEET-TTSH..HHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T---E.EEEEEES CS
                    Methyltransf_9 117 rtildvGcgnGy..hlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpeleaf.dtvfsmG 190
                                       r+++dvGc  G+  h+   ++  +  vvG+d  e +l ++  + k+     + +++ l  e +p  ++f d    + 
  gi|557693706|ref|YP_008796760.1|  27 RVVVDVGCRLGWagHMLAAIAGRPVEVVGLDVYEPYLKTLSEISKIY----KPIKVDLEKEPIPLPDGFaDLTICIE 99 
                                       89******99987799999999**************99999999887....34455556666666666645555666 PP

                                       -GGG-S-H CS
                    Methyltransf_9 191 vlyhrrsP 198
                                       v+ h + P
  gi|557693706|ref|YP_008796760.1| 100 VIEHLSKP 107
                                       66665555 PP

>> CpcD  CpcD/allophycocyanin linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.29      35      50 ..     111     126 ..     109     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                              CpcD  35 rLsqemqrInrqGGkI 50 
                                       rL +em rI+r+GG I
  gi|557693706|ref|YP_008796760.1| 111 RLMDEMERITRKGGYI 126
                                       899***********88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1593.10
//
Query:       gi|557693707|ref|YP_008796761.1|  [L=496]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 4150.40
//
Query:       gi|557693708|ref|YP_008796762.1|  [L=288]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-21   75.0   0.0    1.3e-20   74.2   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
      3e-14   52.9   0.0    4.7e-14   52.3   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.1e-08   35.3   0.0    1.8e-08   34.6   0.0    1.3  1  Glyco_trans_1_2  Glycosyl transferases group 1
      3e-08   33.9   0.2    8.1e-08   32.4   0.0    1.9  2  Glyco_transf_4   Glycosyltransferase Family 4
    6.5e-06   26.7   0.1      2e-05   25.1   0.0    1.8  2  Glyco_trans_4_4  Glycosyl transferase 4-like domain


Domain annotation for each model (and alignments):
>> 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 !   74.2   0.0   3.5e-24   1.3e-20       2     134 .]     113     251 ..     112     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 3.5e-24
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---....HHHHHHHTT-T.TEEEE---..THHHHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgprp..eeleelaagleerveftGfv..edlaellaa 72 
                                       pv+l+ G + ++ +++ ll++ v+++ +   dvr++++Gd p+p  + l+++a g  e+ve+ Gf+  ++l++++++
  gi|557693708|ref|YP_008796762.1| 113 PVVLYYGTF-QP-HRANLLIKVVEKITSIrsDVRFLLIGDVPKPmvDTLRRMA-G--EKVELPGFIprDKLPPFIQR 184
                                       89*******.55.89999**999999954336*******98855457787555.4..89*******9666******* PP

                                       -SEEEE--.-....--SHHHHHHHHTT-EEEE-TGGG.TTT--TTSS.EE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  73 advfvaPs.e....gfglkllEamaaglpvVatdvgg.iaevvgeng.llvppgdpealaeailrLled 134
                                       +++++++  +      + kll++ma+g+pvV+t+v   ++    e+g  l+ p d++++aea+++Ll+d
  gi|557693708|ref|YP_008796762.1| 185 SKICIFTQdRslggRHPAKLLDYMASGRPVVTTNVDEsFPI--RESGaGLITPVDADKMAEAVVKLLDD 251
                                       ********85444347*******************642222..44443366678*************98 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 !   52.3   0.0   1.3e-17   4.7e-14       6     169 ..     104     262 ..      99     265 .. 0.86

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1.3e-17
                                       HHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCH CS
                   Glycos_transf_1   6 rkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevs 82 
                                       +k +++  +++++l++g +++  + +llik+++++   ++++v+++++G+++  k + +    +  +++v++ g+++
  gi|557693708|ref|YP_008796762.1| 104 FKPSPL-PDEPVVLYYGTFQP-HRANLLIKVVEKITS-IRSDVRFLLIGDVP--KPMVDT-LRRMAGEKVELPGFIP 174
                                       555555.699***********.789**********76.7**********444..344444.5677899********* PP

                                       SSSHHHHHHCESEEEEEESS...BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHH CS
                   Glycos_transf_1  83 redleellknadifvlpsis...EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkll 156
                                       r++l+ ++++++i +++  +      +  ll +ma+g pv+++n+     + ++g    l+ p++a+++aea+ kll
  gi|557693708|ref|YP_008796762.1| 175 RDKLPPFIQRSKICIFTQDRslgGRHPAKLLDYMASGRPVVTTNVDESFPIRESGA--GLITPVDADKMAEAVVKLL 249
                                       *****************999999999******************777777888887..5677777************ PP

                                       HSHHHHHHHHHHH CS
                   Glycos_transf_1 157 edeelrerlgena 169
                                       +d+ l++++  ++
  gi|557693708|ref|YP_008796762.1| 250 DDDALARQMAARG 262
                                       *****99998776 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 !   34.6   0.0   5.1e-12   1.8e-08      11      90 ..     200     278 ..     182     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 5.1e-12
                   Glyco_trans_1_2  11 pnlrlfEaaacGafaltddaegleelftpgkevilfe.dleelaekiryllanpeerraiaeaarervlaehtydhr 86 
                                       +  +l++++a+G++++t+  ++   + + g  +i+   d + +ae++ +ll++++++r++a+++ +   +++++++ 
  gi|557693708|ref|YP_008796762.1| 200 HPAKLLDYMASGRPVVTTNVDESFPIRESGAGLIT-PvDADKMAEAVVKLLDDDALARQMAARGVQY-AKRFDWRNM 274
                                       55699*************87777777778855555.45**************************999.89******9 PP

                   Glyco_trans_1_2  87 aeql 90 
                                       ++++
  gi|557693708|ref|YP_008796762.1| 275 VNKY 278
                                       9987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   2.3e-11   8.1e-08     124     169 ..      58     102 ..      10     103 .. 0.85
   2 ?   -2.6   0.1       1.3   4.7e+03      11      21 ..     254     264 ..     253     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2.3e-11
                    Glyco_transf_4 124 ralerrllrradrviavSeatadelrerygvppekitVipnGvDle 169
                                       +++   + +r++++++++e +++ +++ +gv++eki+VipnGvD e
  gi|557693708|ref|YP_008796762.1|  58 NEMRMLMDKRVRKIVVTTEIIRRKFVK-LGVDEEKIEVIPNGVDSE 102
                                       4444455789*****************.****************87 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                    Glyco_transf_4  11 LaraLarrGhe 21 
                                       Lar++a+rG++
  gi|557693708|ref|YP_008796762.1| 254 LARQMAARGVQ 264
                                       9********97 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 !   25.1   0.0   5.7e-09     2e-05      73     160 .]      10      98 ..       3      98 .. 0.79
   2 ?   -1.9   0.1       1.1   3.9e+03       9      20 ..     253     264 ..     252     267 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.7e-09
                   Glyco_trans_4_4  73 rpdvvhahsptaglaarlarrrrgiplvvtlhg....lllrrg.sgavrrlyralerrllrradavlvvseaeaeel 144
                                       + dvv++++  ++la        + p+v+++ +    l +++  +  + +l+ ++ +++ +r++ ++v++e +++++
  gi|557693708|ref|YP_008796762.1|  10 GADVVWLFDTATALAPN----FLHSPVVLDVDDpkvvLPVDELaKQSKLSLVNEMRMLMDKRVRKIVVTTEIIRRKF 82 
                                       67999999974443333....44689*****97544333444466667788999999999***************** PP

                   Glyco_trans_4_4 145 ralgvpadrvvvvpng 160
                                       + lgv+ ++++v+png
  gi|557693708|ref|YP_008796762.1|  83 VKLGVDEEKIEVIPNG 98 
                                       ***************8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                   Glyco_trans_4_4   9 elaraLaarGhe 20 
                                       +lar++aarG++
  gi|557693708|ref|YP_008796762.1| 253 ALARQMAARGVQ 264
                                       578888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 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:                        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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2366.34
//
Query:       gi|557693709|ref|YP_008796763.1|  [L=367]
Description: glycosyl transferases group 1 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-46  157.4   0.1    3.3e-46  157.0   0.1    1.2  1  Glycos_transf_1  Glycosyl transferases group 1
    1.2e-33  116.4   0.0    2.8e-33  115.2   0.0    1.6  2  Glyco_trans_1_4  Glycosyl transferases group 1
    3.5e-16   59.7   0.1      7e-16   58.7   0.0    1.5  2  Glyco_transf_4   Glycosyltransferase Family 4
    9.6e-10   38.7   0.0      2e-09   37.7   0.0    1.5  1  Glyco_trans_1_2  Glycosyl transferases group 1
    6.9e-09   36.3   0.0    1.2e-08   35.6   0.0    1.3  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    2.2e-06   27.8   0.1    5.2e-06   26.5   0.1    1.6  1  Glyco_trans_4_2  Glycosyl transferase 4-like
  ------ inclusion threshold ------
      0.023   13.3   0.0      0.031   12.8   0.0    1.2  1  Glycogen_syn     Glycogen synthase


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 !  157.0   0.1   1.3e-49   3.3e-46       2     171 ..     179     344 ..     178     345 .. 0.97

  Alignments for each domain:
  == domain 1  score: 157.0 bits;  conditional E-value: 1.3e-49
                                       HHHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEE CS
                   Glycos_transf_1   2 kekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnvifl 78 
                                        ek +++++++ ++k+il+ +rl+k+K++++l++a+++++    ++ kl+iaG+g+ +++l + ++  +l+dnvifl
  gi|557693709|ref|YP_008796763.1| 179 HEKFSNSTEHQPDQKTILTAARLDKVKDIETLLHAIEDIEP--MNRPKLLIAGDGPLRETLTEIVKTKKLQDNVIFL 253
                                       57889999*******************************86..6999****************************** PP

                                       ECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHH CS
                   Glycos_transf_1  79 gevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkl 155
                                       g+    d+e+l+ +a+if+lpsi+E+fG+++ EA+aag+pviasn+gg++e+v +g++Gll+ p+n+++la++i+kl
  gi|557693709|ref|YP_008796763.1| 254 GHRT--DVEKLMAKASIFILPSIYEPFGMAAAEALAAGKPVIASNIGGLREIVDHGVNGLLFTPKNHHELAQHITKL 328
                                       ***9..*********************************************************************** PP

                                       HHSHHHHHHHHHHHHH CS
                   Glycos_transf_1 156 ledeelrerlgenark 171
                                       l+d++l   +++nar+
  gi|557693709|ref|YP_008796763.1| 329 LQDKKLWTTFSQNARE 344
                                       **************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 ?   -2.6   0.0       2.6   6.8e+03      54      88 ..      53      90 ..      42      92 .. 0.73
   2 !  115.2   0.0   1.1e-36   2.8e-33       2     134 .]     193     331 ..     192     331 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.6
                                      T.TEEEE---THHHHHHHH-SEEEE--...---SHHHH CS
                   Glyco_trans_1_4 54 eerveftGfvedlaellaaadvfvaPs...egfglkll 88
                                      e++v +   +  ++ +l+  ++f+ ++   + +g+k++
  gi|557693709|ref|YP_008796763.1| 53 EKSVLIIEARRRMKGVLHWLWLFLTTLrlaRKLGVKII 90
                                      45677777777889999999999999877668888876 PP

  == domain 2  score: 115.2 bits;  conditional E-value: 1.1e-36
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HH.EEEEEES---...HHHHHHHT..T-T.TEEEE---THHHHHHHH-S CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkd.vrlvivGdgp.rpeeleelaa..gleerveftGfvedlaellaaad 74 
                                       ++il+  rl ++vk ++ ll+a++ +   +  +l+i+Gdgp r e l e ++  +l+++v+f+G+++d+++l+a+a+
  gi|557693709|ref|YP_008796763.1| 193 KTILTAARL-DKVKDIETLLHAIEDIEPMNrPKLLIAGDGPlR-ETLTEIVKtkKLQDNVIFLGHRTDVEKLMAKAS 267
                                       789******.788**************66569*********66.59998776779********************** PP

                                       EEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  75 vfvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       +f++Ps  e fg+++ Ea+aag+pv+a+++gg++e+v  g+ngll+ p++ ++la++i +Ll+d
  gi|557693709|ref|YP_008796763.1| 268 IFILPSiyEPFGMAAAEALAAGKPVIASNIGGLREIVdhGVNGLLFTPKNHHELAQHITKLLQD 331
                                       **************************************************************98 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.0   2.7e-19     7e-16       1     169 [.      12     180 ..      12     181 .. 0.79
   2 ?   -3.8   0.0       4.3   1.1e+04      83     101 ..     278     294 ..     275     296 .. 0.61

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 2.7e-19
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev....elvvrvprvplpllkrllrslaflrrlrrllkrekp 73 
                                       vGG+   +l+L  +L+ +G++  ++tp+++   +       e  v ++  +++  k+ l+ l+ ++   rl+++ ++
  gi|557693709|ref|YP_008796763.1|  12 VGGATLAMLHLMLGLPSQGIQPILLTPTTSAIDPSLAkklvEKSVLIIEARRRM-KGVLHWLWLFLTTLRLARKLGV 87 
                                       79***********************88776554444444553333333333344.44444455555566789999** PP

                    Glyco_transf_4  74 DvvHahspaalgaallalrrrlgiplVltvHglye.krllkarlkplsrllralerrllrradrviavSeatadelr 149
                                        ++H+h+p  +  ++la++  l++++V+tv g     ++ ++   ++++ ++ l +  lr ad v+ +S+++a +++
  gi|557693709|ref|YP_008796763.1|  88 KIIHTHGPKEAAIMGLAAKI-LRLKHVYTVEGDPViETFINKSGLKATITNKLLFKIGLRLADEVVGCSRWMATHIE 163
                                       *******************9.************9976666666667777777777777******************* PP

                    Glyco_transf_4 150 erygvppekitVipnGvDle 169
                                       + yg   +k t i n++D e
  gi|557693709|ref|YP_008796763.1| 164 KTYG---RKATPIWNPIDHE 180
                                       ****...678999*****88 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.3
                    Glyco_transf_4  83 algaallalrrrlgiplVl 101
                                       +++aa+ al+   g+p+++
  gi|557693709|ref|YP_008796763.1| 278 FGMAAAEALA--AGKPVIA 294
                                       3444545555..7999987 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 !   37.7   0.0   7.8e-13     2e-09       1      91 [.     268     359 ..     268     360 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 7.8e-13
                   Glyco_trans_1_2   1 ivLnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaare 75 
                                       i++ ps +e + +   Ea+a+G +++++ + gl+e+++ g  ++lf   +++ela++i +ll++ +++   +++are
  gi|557693709|ref|YP_008796763.1| 268 IFILPSIYEPFGMAAAEALAAGKPVIASNIGGLREIVDHGVNGLLFTpkNHHELAQHITKLLQDKKLWTTFSQNARE 344
                                       57789999********************************************************************* PP

                   Glyco_trans_1_2  76 rvlaehtydhraeqll 91 
                                       +  a +  ++ a+++l
  gi|557693709|ref|YP_008796763.1| 345 K-SAIYKPENIAKRYL 359
                                       9.77777777766665 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 !   35.6   0.0   4.6e-12   1.2e-08       1     153 [.      13     172 ..      13     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 4.6e-12
                   Glyco_trans_4_4   1 gGigryvaelaraLaarGheVtvltpapapgapeleedgvrvhrl..pvprrpspladlaalralrrll.rqrrerp 74 
                                       gG++  + +l  +L  +G +  +ltp+  + +p l    v+   l   ++rr    + l +l+ +  +l  +r+ ++
  gi|557693709|ref|YP_008796763.1|  13 GGATLAMLHLMLGLPSQGIQPILLTPTTSAIDPSLAKKLVEKSVLiiEARRRM--KGVLHWLWLFLTTLrLARKLGV 87 
                                       79999999***********************9998877777554411455554..456777888888887669**** PP

                   Glyco_trans_4_4  75 dvvhahspt.aglaarlarrrrgiplvvtlhglllrrg....sgavrrly.ralerrllrradavlvvseaeaeelr 145
                                        ++h+h+p+ a++ +++a+   ++++v+t+ g+ + +     sg ++ +  + l +  lr ad v+  s+++a +++
  gi|557693709|ref|YP_008796763.1|  88 KIIHTHGPKeAAIMGLAAK-ILRLKHVYTVEGDPVIETfinkSGLKATITnKLLFKIGLRLADEVVGCSRWMATHIE 163
                                       ********86888888888.99*********9775555566588888887777899********************* PP

                   Glyco_trans_4_4 146 a.lgvpadr 153
                                         +g+ a+ 
  gi|557693709|ref|YP_008796763.1| 164 KtYGRKATP 172
                                       988887765 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 !   26.5   0.1     2e-09   5.2e-06      36     134 ..      46     150 ..      13     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2e-09
                   Glyco_trans_4_2  36 a.kdeleaegihvhrlkvdrkgpleylkaf.klkklikkikPDvvhahyakpygllgslaarlsgvipvvlsvwGld 110
                                       +  ++l+++ + +++ + + kg l +l +f +  +l +k++  ++h+h +k  +++g laa++++  + v++v G  
  gi|557693709|ref|YP_008796763.1|  46 SlAKKLVEKSVLIIEARRRMKGVLHWLWLFlTTLRLARKLGVKIIHTHGPKEAAIMG-LAAKILR-LKHVYTVEGDP 120
                                       2356777888889999988999*****9777**********************9999.******9.9999******* PP

                   Glyco_trans_4_2 111 v.lkfpkksk.....lkklllklalkkatk 134
                                       v  +f +ks        kll+k+ l+ a+ 
  gi|557693709|ref|YP_008796763.1| 121 ViETFINKSGlkatiTNKLLFKIGLRLADE 150
                                       964446666644445556677777776665 PP

>> Glycogen_syn  Glycogen synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.2e-05     0.031     461     508 ..     258     305 ..     246     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                                       -HHHHHHH-SEEE---SSBSS-HHHHHHHHTT--EEEETTBHHHHHHH CS
                      Glycogen_syn 461 dyeefvrGchlGvfpsyyepwGytpaectvmGipsvttnlsGfGcfme 508
                                       d e+++  + + ++ps yep+G + ae    G p +++n+ G+   ++
  gi|557693709|ref|YP_008796763.1| 258 DVEKLMAKASIFILPSIYEPFGMAAAEALAAGKPVIASNIGGLREIVD 305
                                       56666777778899***************************9865544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2724.54
//
Query:       gi|557693710|ref|YP_008796764.1|  [L=321]
Description: NAD-dependent epimerase/dehydratase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-59  200.9   0.0    8.3e-59  199.6   0.0    1.5  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    9.9e-54  182.3   0.0    1.2e-53  182.0   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.4e-18   67.0   0.0    1.3e-17   63.9   0.0    2.0  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.2e-13   50.9   0.0    1.8e-13   50.2   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
    2.1e-11   43.3   0.0      3e-11   42.8   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    6.2e-11   41.9   0.0    8.8e-10   38.2   0.0    2.5  1  NAD_binding_4    Male sterility protein
    7.4e-06   26.0   0.0    1.6e-05   24.9   0.0    1.5  2  NAD_binding_10   NAD(P)H-binding
    0.00013   22.0   0.0    0.00023   21.1   0.0    1.4  1  KR               KR domain
  ------ inclusion threshold ------
      0.012   15.1   0.0      0.022   14.2   0.0    1.6  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 !  199.6   0.0   4.2e-62   8.3e-59       1     331 [.       3     307 ..       3     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: 199.6 bits;  conditional E-value: 4.2e-62
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       ++TG  GfiGs+l+e Ll+kg +v+g+ + +   n  +i+ l++++   + +nl++++ Dl++ ++++++++   p+
  gi|557693710|ref|YP_008796764.1|   3 IVTGALGFIGSHLTEALLDKGEQVVGVSHPKPPEN--NINILTSHK---AASNLRIIYSDLKNLDEVKQIMKTNAPT 74 
                                       59************************987776655..887787654...468************************* PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        vy+LAA    + s+++P +++e+n+l tl++Lea+r++  e+  r++++S+s +YG+ +  p +E+ + +Pr PYa
  gi|557693710|ref|YP_008796764.1|  75 HVYHLAALASHRLSMSEPYKYLENNILTTLNILEAARIT--EPGPRIVFSSSSSIYGNNT-PPLREDMKPDPRGPYA 148
                                       **************************************7..5789*************86.99************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHH.HHHTTS-C-EECTTTT-.EEEEEEHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitrava.rialgkqevlylGnlda.kRdwghvkDy 229
                                        +K +++ ++ +y + ygl +v+ ++fn  + r   ++v r + + ++ +i+l+    ++ G  ++  Rd+++vkD 
  gi|557693710|ref|YP_008796764.1| 149 LSKWICEELCSQYVRDYGLNVVTVRYFNVVGERCRGNIVFRVFAEHASkNIDLEVYGRYINGVFKPaARDFTYVKDA 225
                                       *********************************999*****999876516777777777778877549********* PP

                                       HHHHHHHHHC.SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB CS
                     GDP_Man_Dehyd 230 veamwlmlqq.dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdl 305
                                       v++  l+ ++ +k e y+i+ g+ +sv++++el +++lg +                      ++ +k  +p e  +
  gi|557693710|ref|YP_008796764.1| 226 VQGTILAAEKgGKGEVYNIGFGRPVSVKTVAELIIKNLGSR---------------------SKIVEKELKPHESLE 281
                                       ******99984667788888888888888888888888753.....................3566788999***** PP

                                       --B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 306 llgdaskakeeLgWkpkvsfeelvre 331
                                        + d++ka+++LgWkp +++ee+v++
  gi|557693710|ref|YP_008796764.1| 282 SYSDNTKARKQLGWKPVTDIEEMVKK 307
                                       ************************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 !  182.0   0.0   6.2e-57   1.2e-53       1     241 []       2     245 ..       2     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 182.0 bits;  conditional E-value: 6.2e-57
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHHHT-SEEEE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfkeeqpdavih 70 
                                       i+VtGa GfiGs+l++all+kg +v+g+++ +  +n+ ++ +        ++++ dl++ +++++++k+++p++v+h
  gi|557693710|ref|YP_008796764.1|   2 IIVTGALGFIGSHLTEALLDKGEQVVGVSHPKPPENNINILTShkaasnlRIIYSDLKNLDEVKQIMKTNAPTHVYH 78 
                                       89*****************************887777766666899******************************* PP

                                       --S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHH CS
                         Epimerase  71 lAavggvaassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdaeqpkeettltgplkpnspYaaaK 146
                                       lAa ++ + s+++p +++e+n+  tln+leaar +++  r++f sSs++YG++++ p  e++   +  p+ pYa++K
  gi|557693710|ref|YP_008796764.1|  79 LAALASHRLSMSEPYKYLENNILTTLNILEAARITEPGpRIVFSSSSSIYGNNTP-PLREDM---KPDPRGPYALSK 151
                                       *********************************996666****************.999999...999********* PP

                                       HHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEET......TST-EEEEEEHHH CS
                         Epimerase 147 lageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllg......dgtalRdflyveD 217
                                          e+l+ +y ++ygln++++r+fn++G+r     + ++++++ +  +++  ++ ++g         a Rdf yv+D
  gi|557693710|ref|YP_008796764.1| 152 WICEELCSQYVRDYGLNVVTVRYFNVVGER----CRGNIVFRVFAEHASKNIDLEVYGryingvFKPAARDFTYVKD 224
                                       ******************************....54455555444444444488888888855555789******** PP

                                       HHHHHHHHHHHHTT-STTEEEEES CS
                         Epimerase 218 vaeaillvlehvdagdkgeiyniG 241
                                       ++++ +l++e+   g kge+yniG
  gi|557693710|ref|YP_008796764.1| 225 AVQGTILAAEK---GGKGEVYNIG 245
                                       ***********...99*******9 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   6.5e-21   1.3e-17       1     252 [.       2     268 ..       2     280 .. 0.80

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 6.5e-21
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       ++vtGa G iGs+l++ +l+k   +++ +++      +i+  ++++++ ++l+     +  d+++ +++++++++  
  gi|557693710|ref|YP_008796764.1|   2 IIVTGALGFIGSHLTEALLDKGE-QVVGVSHPKPPENNINILTSHKAA-SNLR----IIYSDLKNLDEVKQIMKTNA 72 
                                       79***************999865.566667777777777765543333.3453....4589**************** PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS--SH..............HHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAvnPtnv..............mGa 140
                                       +  v+h AAl    l  ++p++ +++N+l t n++eaa  ++    ++ S+   ++  n+              + +
  gi|557693710|ref|YP_008796764.1|  73 PTHVYHLAALASHRLSMSEPYKYLENNILTTLNILEAARITEPGPRIVFSSSSSIYGNNTpplredmkpdprgpYAL 149
                                       **************************************999887777777766665444322233323333222899 PP

                                       HHHHHHHHHHHGGG--SSS--EEEEEEE-EETT..GTTSSH.HHHHHHHHTTSSEEES-TT-.......EEEEE-HH CS
                   Polysacc_synt_2 141 tKrlaekllqalakeseekktkfvvvRfGNVlg..SrGSvi.plFkkqikeggpvtvTdpem.......tRyfmtie 207
                                       +K ++e l+ ++ +       ++v+vR+ NV+g   rG ++  +F +  +++ ++ v  + +        R f  ++
  gi|557693710|ref|YP_008796764.1| 150 SKWICEELCSQYVRDY---GLNVVTVRYFNVVGerCRGNIVfRVFAEHASKNIDLEVYGRYIngvfkpaARDFTYVK 223
                                       ********99998888...89***********944469876379********999998877633333336999**** PP

                                       HHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH......... CS
                   Polysacc_synt_2 208 eavqLvlqalalakggeifvldmGepvkivdlakalielsgleek 252
                                       +avq  + a++++ +ge++    G pv+++ +a+ +i+  g ++k
  gi|557693710|ref|YP_008796764.1| 224 DAVQGTILAAEKGGKGEVYNIGFGRPVSVKTVAELIIKNLGSRSK 268
                                       *************************************99987665 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 !   50.2   0.0   9.3e-17   1.8e-13       3     242 ..       2     278 ..       1     310 [. 0.83

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 9.3e-17
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT......................T--TTSHHHHHHHHHHH--SEEEE CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre......................eldltdaeavaellkeakpdvvvn 57 
                                       i+vtGa G +Gs+L+++l  +g +v++++ +                        dl++ ++v++++k + p  v++
  gi|557693710|ref|YP_008796764.1|   2 IIVTGALGFIGSHLTEALLDKGEQVVGVSHPkppenniniltshkaasnlriiYSDLKNLDEVKQIMKTNAPTHVYH 78 
                                       89**************************8889********************99*********************** PP

                                       ------HHHHHHSHHHHHHHHTHHHHHHHHHHH..HCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHH CS
                     RmlD_sub_bind  58 aAAytavDkaEseeeaayavnaeavealAeaaa..avgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaG 132
                                       +AA        se+ +  + n   + ++ eaa+  + g  +++ S+  ++ G+++ p +ed +++P++ Y+ +K+  
  gi|557693710|ref|YP_008796764.1|  79 LAALASHRLSMSEPYKYLENNILTTLNILEAARitEPGPRIVFSSSSSIY-GNNTPPLREDMKPDPRGPYALSKWIC 154
                                       ****************************9999722568899999999998.677899*******************9 PP

                                       H....HHHHHH-SSEEEEEE-SEESS.SSS-HH.HHHHHHHHH-SEEEEESS-EE...--.....EEHHHHHHHHHH CS
                     RmlD_sub_bind 133 E....qavlaagkkalivRtswvyge.kgknfv.ktmlrlakereelkvvaDqlg...sP.....TsardlAevllq 195
                                       E    q v+++g +++ vR   v ge  + n v +++ + a+++  l+v    +    +P     T+++d  + ++ 
  gi|557693710|ref|YP_008796764.1| 155 EelcsQYVRDYGLNVVTVRYFNVVGErCRGNIVfRVFAEHASKNIDLEVYGRYINgvfKPaardfTYVKDAVQGTIL 231
                                       9444446888999********99999645555515667788999999986543321113423333677777777777 PP

                                       HHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTT....SEEEEE- CS
                     RmlD_sub_bind 196 llekaaeekelagvyHlanegetswlefArailkeagads....eevkpis 242
                                       ++ek  +     +vy ++  + +s   +A+ i+k++g++s    +e+kp +
  gi|557693710|ref|YP_008796764.1| 232 AAEKGGK----GEVYNIGFGRPVSVKTVAELIIKNLGSRSkiveKELKPHE 278
                                       7666666....8899999999999999999999999998866665566554 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 !   42.8   0.0   1.5e-14     3e-11       1     231 [.       3     235 ..       3     272 .. 0.72

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.5e-14
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk...viegDvtdkdkleealegv..dvvih 72 
                                       +vtG+ GF+G++l ++L++ +e + v v   +  ++  + l++ + ++   +i+ D+++ d++++ ++      v h
  gi|557693710|ref|YP_008796764.1|   3 IVTGALGFIGSHLTEALLDKGE-QVVGVSHPKPPENNINILTSHKAASnlrIIYSDLKNLDEVKQIMKTNapTHVYH 78 
                                       69*******************8.6666666444333334444444443566**************986542267999 PP

                         3Beta_HSD  73 laslvdvag.kltedeimkvnvkGTrnvleacvkag.vrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdayp 147
                                       la+l   +  + +  ++ + n+  T n+lea++ ++  +++v+ Ss ++ g+  +  +++     + +++ +  +y+
  gi|557693710|ref|YP_008796764.1|  79 LAALASHRLsMSEPYKYLENNILTTLNILEAARITEpGPRIVFSSSSSIYGN--NTPPLR-----EDMKPDPRGPYA 148
                                       9998776644889999****************87762689***********9..456676.....56778899**** PP

                         3Beta_HSD 148 esKalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdk...llvpllkqlaklg.lal....fkigdeevlsdrv 216
                                        sK + E+l  +     +++   l+ + +R   + Ge+++   ++  +++++ k+  l++    ++ + + +  d++
  gi|557693710|ref|YP_008796764.1| 149 LSKWICEELCSQ----YVRDY-GLNVVTVRYFNVVGERCRgniVFRVFAEHASKNIdLEVygryINGVFKPAARDFT 220
                                       ********9864....46676.5888999********98733233444555554421222111023344667899** PP

                         3Beta_HSD 217 YvgNvawahilAara 231
                                       Yv   ++  ilAa +
  gi|557693710|ref|YP_008796764.1| 221 YVKDAVQGTILAAEK 235
                                       ***********9965 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   4.4e-13   8.8e-10       1     214 [.       4     185 ..       4     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 4.4e-13
                                       EE-TTSHHHHHHHHHHHHHS-.TEEEEEE-SSSHHHHHHHHHHHT-SS-HHHHHHHHHTTTEEEEE--TTSGGGG-- CS
                     NAD_binding_4   1 lTGaTGFLGkvLlekLLrttpevkiyllvRaksgesaeeRleeelekkelfsallkelaerikvveGDlseprlGLs 77 
                                       +TGa GF+G++L e LL++ +  +++ + ++k     e+ + + l+++++        a++++++  Dl++    L+
  gi|557693710|ref|YP_008796764.1|   4 VTGALGFIGSHLTEALLDKGE--QVVGVSHPKPP---ENNI-NILTSHKA--------ASNLRIIYSDLKN----LD 62 
                                       7******************99..78888888855...6666.55555555........56678******97....56 PP

                                       HHHHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS CS
                     NAD_binding_4  78 eedlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekv 151
                                       e +    ++  ++++h aA  ++  +++e    l+ N++ t ++le a+ ++    +++ S++ ++g+++  +    
  gi|557693710|ref|YP_008796764.1|  63 EVKQIMKTNAPTHVYHLAALASHRLSMSEpykYLENNILTTLNILEAARITEPGPRIVFSSSSSIYGNNTPPL---- 135
                                       76666668999*********9999888875556789*************777776899999999999999554.... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SSST- CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitgesktGw 214
                                                     ++ + +    Y  sK++ E+l+ ++ r  gl+vv vR  +++ge   G 
  gi|557693710|ref|YP_008796764.1| 136 -------------REDMKPDPRGPYALSKWICEELCSQYVRDYGLNVVTVRYFNVVGERCRGN 185
                                       .............44555666779********************************9988776 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 !   24.9   0.0   7.8e-09   1.6e-05       1     143 [.       6     174 ..       6     196 .. 0.70
   2 ?   -3.1   0.0       3.2   6.3e+03     165     180 ..     247     262 ..     225     264 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 7.8e-09
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT..H.HHCH...HHHCTTTCEEEE--TT-CCHHHHHHTT-S..EE..EES CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..p.ekla...eleaeeglevvegdvtdvedlaealkgad..aV..vsa 67 
                                       GA G +G++l++ ll++g  +v+ +     p + ++   + +a+++l+++  d+ + +++++ +k      V  ++a
  gi|557693710|ref|YP_008796764.1|   6 GALGFIGSHLTEALLDKG-EQVVGVSHPkpPeNNINiltSHKAASNLRIIYSDLKNLDEVKQIMKTNAptHVyhLAA 81 
                                       99***************6.78877665433212332222556789*******************9665435633344 PP

                                       ---TCC...HHHH..........HHHHHHHHHHCT.--EEEEEEETTTTSGCGCHHHH.HHHHCCHHHH....HHHH CS
                    NAD_binding_10  68 lggggk...deeg..........aknivdaakeag.vkRfvlvsaigvgdevpgefge.wnkellkayl....aakr 125
                                       l++++    +             + ni++aa+ ++   R+v+ s+  ++ +   ++ e ++ +  ++y+    +  +
  gi|557693710|ref|YP_008796764.1|  82 LASHRLsmsE--PykylenniltTLNILEAARITEpGPRIVFSSSSSIYGNNTPPLREdMKPDPRGPYAlskwICEE 156
                                       4554445540..14555566799********9766479*********997655555440445566777622223355 PP

                                       HHHHHHHHSSSEEEEEEE CS
                    NAD_binding_10 126 aaeellrasgldwTivrp 143
                                          +++r+ gl+ + vr 
  gi|557693710|ref|YP_008796764.1| 157 LCSQYVRDYGLNVVTVRY 174
                                       666678889999999885 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.2
                                       --EEEHHHHHHHHHHH CS
                    NAD_binding_10 165 ggsisradVAdvlvav 180
                                       g+ +s + VA+++++ 
  gi|557693710|ref|YP_008796764.1| 247 GRPVSVKTVAELIIKN 262
                                       5678889999998875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.2e-07   0.00023       3     144 ..       2     131 ..       1     133 [. 0.78

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                        ++tG+lG +G +l++ l++kg++ + +   + +++++   +i + ++   + +++  D+ + d+v++++++     
  gi|557693710|ref|YP_008796764.1|   2 IIVTGALGFIGSHLTEALLDKGEQVVGVSHPK-PPENN--INILTSHKAASNLRIIYSDLKNLDEVKQIMKTNAP-- 73 
                                       58********************8755544444.33333..234444555779999*************9988763.. PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHHH--T CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagllgsa 144
                                          + v+h A ++  +    +++++  + l+  +  + n+ e+ + ++    ++fSS ++++g++
  gi|557693710|ref|YP_008796764.1|  74 ---THVYHLAALASHR----LSMSEPYKYLENNILTTLNILEAARITEPGPRIVFSSSSSIYGNN 131
                                       ...4699*99998765....466677778888899999999999999999999999999999986 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.1e-05     0.022       3      70 ..       2      70 ..       1     126 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvek 70
                                      ++vtGa + IG  + ++l+ +G +vv v+  +   e+ ++ l ++  ++++ +i  D+++ +ev++++++
  gi|557693710|ref|YP_008796764.1|  2 IIVTGALGFIGSHLTEALLDKGEQVVGVSHPKP-PENNINILTSHkaASNLRIIYSDLKNLDEVKQIMKT 70
                                      89***********************99876644.44555555554467889***************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2357.72
//
Query:       gi|557693711|ref|YP_008796765.1|  [L=97]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-05   25.5   0.0    1.3e-05   25.3   0.0    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 !   25.3   0.0   7.3e-10   1.3e-05      35      93 ..       1      64 [.       1      78 [. 0.91

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 7.3e-10
                                      HHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT........-HHHHHHHHHHHCCCHHCCCTSS- CS
                              HEPN 35 aekalKAlllkkggeppkthdlreLleelkkelke.....seelreeleeLekayiesrYpdak 93
                                      +e++lKA+l   g eppk hd+  +l++ +   +      ++el+ + + L+k + ++ Y+d +
  gi|557693711|ref|YP_008796765.1|  1 MELSLKAALRPFGVEPPKWHDVGPILRRERSRFPPwmneqIDELASISRALRKERETAMYGDEE 64
                                      79*************************888888888877888888888*************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 715.95
//
Query:       gi|557693712|ref|YP_008796766.1|  [L=173]
Description: DNA polymerase beta domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   38.6   0.0    1.7e-09   37.9   0.0    1.4  1  NTP_transf_2  Nucleotidyltransferase domain
    1.3e-07   31.5   0.0    2.6e-07   30.6   0.0    1.5  2  Polbeta       Polymerase beta, Nucleotidyltransferase
    0.00022   21.1   0.0    0.00051   19.9   0.0    1.5  2  DUF294        Putative nucleotidyltransferase DUF294


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 !   37.9   0.0   2.8e-13   1.7e-09       3      56 ..      16      66 ..      14      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.8e-13
                                      HHHHHHHHHTT..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHH CS
                      NTP_transf_2  3 klleelkelep..vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeeglekl 56
                                      kl e+l+++ +   ++vv+fGS+arG+a+k+SD+D+ vv ++        ++l++ 
  gi|557693712|ref|YP_008796766.1| 16 KLVESLRRRLGerLVSVVVFGSAARGEAGKESDLDVMVVCEKLPM-----NRLDRT 66
                                      78899999999999*************************998754.....444444 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   4.4e-11   2.6e-07       6      54 ..      20      71 ..      15      85 .. 0.70
   2 ?   -3.2   0.0       1.5     9e+03      77      92 ..     109     124 ..     104     125 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.4e-11
                                      THHHH..HHHHSTTEEEEEE-S------EEEEEEEESS-.....--HHHHHHHHHH CS
                           Polbeta  6 ileke..keielaylFGSrakgkareeSDiDlavllkek.....ldleeelelaae 54
                                       l+++  + +  +++FGS a+g+a +eSD+D++v++++      +    + el  e
  gi|557693712|ref|YP_008796766.1| 20 SLRRRlgERLVSVVVFGSAARGEAGKESDLDVMVVCEKLpmnrlD----RTELFIE 71
                                      555554457899*************************99844333....3333333 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.5
                                       HHHHHHS-EEEES-SH CS
                           Polbeta  77 lyeilkegkllyskde 92 
                                       l  ++++ ++ly++d+
  gi|557693712|ref|YP_008796766.1| 109 LLDMTEDAIILYDRDS 124
                                       5566777888888885 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   8.6e-08   0.00051      23      79 ..       5      61 ..       3      88 .. 0.78
   2 ?   -2.1   0.0       0.5     3e+03      60     102 ..     104     141 ..      96     144 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.6e-08
                            DUF294 23 lvselndallrrlielaeeelgkppvpfallvmGSeGReEqtlktDqDnalvled..ee 79
                                      l++e +++l+++l+e + ++lg++   ++++v+GS++R+E+  ++D D   v e+   +
  gi|557693712|ref|YP_008796766.1|  5 LLAEPYRTLAQKLVESLRRRLGER--LVSVVVFGSAARGEAGKESDLDVMVVCEKlpMN 61
                                      677888999999999999998875..67899*********************9996433 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.5
                            DUF294  60 ReEqtlktDqDnalvledeeeeaareyfaelaervneaLaalG 102
                                       R   +l    + a++l d      +  + +l + + ++L+++G
  gi|557693712|ref|YP_008796766.1| 104 RIPSILLDMTEDAIILYD-----RDSFLTNLLNSLKANLKKMG 141
                                       555555555566666666.....44455566666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1261.19
//
Query:       gi|557693713|ref|YP_008796767.1|  [L=51]
Description: small subunit ribosomal protein S30e [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-12   47.9   1.0    1.3e-12   47.7   1.0    1.0  1  Ribosomal_S30  Ribosomal protein S30


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 !   47.7   1.0   7.1e-17   1.3e-12       3      44 ..       4      44 ..       3      51 .] 0.90

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 7.1e-17
                                      BX-STTTTHHHHHS-------------THHHHHHHHHHHTTS CS
                     Ribosomal_S30  3 hGsLarAGKVrnqTPKveKqekkKkptGRakkRlqYnrRfvn 44
                                      hGs+++AGKVr+qTPK e +  +K+p  R + R+ Y +R  +
  gi|557693713|ref|YP_008796767.1|  4 HGSITKAGKVRSQTPKLEAK-PRKSPFPRQRNRQNYLKRVLA 44
                                      ******************99.9*****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      137  (0.00764125); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 381.96
//
Query:       gi|557693714|ref|YP_008796768.1|  [L=431]
Description: hypothetical protein CSUB_C0277 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3137.74
//
Query:       gi|557693715|ref|YP_008796769.1|  [L=212]
Description: hypothetical protein CSUB_C0278 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1617.61
//
Query:       gi|557693716|ref|YP_008796770.1|  [L=130]
Description: hypothetical protein CSUB_C0279 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
        1.7    9.3   3.5        3.9    8.1   2.4    2.0  2  LPAM_1    Prokaryotic membrane lipoprotein lipid attachment s


Domain annotation for each model (and alignments):
>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.4   0.00022       3.9       1      15 [.       2      17 ..       2      18 .. 0.88
   2 ?   -0.3   0.0      0.11     2e+03       3       9 ..     118     124 ..     117     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00022
                            LPAM_1  1 MKKi.llalgalllLs 15
                                      MKK  l++l++ll Ls
  gi|557693716|ref|YP_008796770.1|  2 MKKVvLVFLLILLGLS 17
                                      ****999999999998 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.11
                            LPAM_1   3 Killalg 9  
                                       Ki++a+g
  gi|557693716|ref|YP_008796770.1| 118 KIFSAIG 124
                                       9****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1007.98
//
Query:       gi|557693717|ref|YP_008796771.1|  [L=392]
Description: pre-mRNA processing ribonucleoprotein, binding region [Candidatus Caldiarchaeum subterraneum]
Scores for 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-59  201.8   0.0    1.4e-59  201.4   0.0    1.2  1  Nop       snoRNA binding domain, fibrillarin
  ------ inclusion threshold ------
        0.1   12.5   1.4        7.3    6.6   0.1    2.9  3  T2SSF     Type II secretion system (T2SS), protein F
       0.18   12.0   0.0       0.37   11.0   0.0    1.4  1  TrbH      Conjugal transfer protein TrbH


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 !  201.4   0.0   2.3e-63   1.4e-59       2     229 ..     142     366 ..     141     367 .. 0.92

  Alignments for each domain:
  == domain 1  score: 201.4 bits;  conditional E-value: 2.3e-63
                                       HHHHHHHHHHHHHHHHHHHTTTSTCHHHHS-SHHHHHHHHHHCCCCHCCT.HH..TT...HHHHHHHHHHHHCHHHH CS
                               Nop   2 ldeidkeintlhkrvrewYswhFpELeslvkdnleYakvvkligneredlekk..ee..deelakevimaakvtast 74 
                                       ld+++k+ n+l+ rvrewYs hFpEL+sl+++  +++k+v++    r+ l+++  ++    +lak+v++aa+     
  gi|557693717|ref|YP_008796771.1| 142 LDDLEKTKNQLYVRVREWYSVHFPELSSLLTEGDDFLKLVSVPV-LRHGLDERmvSKllGPDLAKRVLEAAEK---- 213
                                       89**************************************8876.5566655522223323389999999999.... PP

                                       -SSS-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHT CS
                               Nop  75 smgaelseedlknikelcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiq 151
                                       s g ++ + d + +++ ++  l++++l ++ +eY+++ m+  APNlsa+ G+ +++rLis aGgL++La++Pastiq
  gi|557693717|ref|YP_008796771.1| 214 SVGGDMGPGDAAMLSATASLGLDVSRLAEKTAEYIRELMASEAPNLSAVAGPVLGSRLISLAGGLERLARLPASTIQ 290
                                       ***************************************************************************** PP

                                       TTT-HHHHCCCHH.T---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHH CS
                               Nop 152 ilGaekalfralk.kkntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekk 227
                                       +lGaekalfr lk +  +pk+G+i++++l++ + p+++++kiaR+la+K+++aaRiD f  ++++ G +lre +ek+
  gi|557693717|ref|YP_008796771.1| 291 VLGAEKALFRFLKtGRGSPKHGVIFQHPLIHMS-PKWQRGKIARALATKISIAARIDYF--SKEDRGAQLREALEKR 364
                                       *************7779**************77.*************************..57788*********** PP

                                       HH CS
                               Nop 228 lk 229
                                       ++
  gi|557693717|ref|YP_008796771.1| 365 VE 366
                                       97 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 ?   -2.6   0.0      0.82   4.9e+03      46      52 ..     123     129 ..     102     171 .. 0.58
   2 ?    6.6   0.1    0.0012       7.3      50     114 ..     209     274 ..     198     278 .. 0.83
   3 ?    4.1   0.0    0.0071        43       6      44 ..     332     370 ..     330     390 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.82
                                       SSHHHHH CS
                             T2SSF  46 gslseal 52 
                                         ++ea 
  gi|557693717|ref|YP_008796771.1| 123 RIMAEAG 129
                                       3333333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0012
                                       HHHCT-TT.TS.-HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXX CS
                             T2SSF  50 ealertpssef.pelvvqlirageeggnLaevLerlaeyleeerelrrkllaallepllllvvall 114
                                       ea e++   ++ p  +++l+++++ g +++   e+ aey++e  ++++ +l+a ++p+l   +++l
  gi|557693717|ref|YP_008796771.1| 209 EAAEKSVGGDMgPGDAAMLSATASLGLDVSRLAEKTAEYIRELMASEAPNLSAVAGPVLGSRLISL 274
                                       56665555566699999***************************************9987666655 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.0071
                                       HHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHT CS
                             T2SSF   6 atllsaGvplveaLellaeeaengplaeelkriarrlra 44 
                                       a++l++ +++++ ++++++e++  +l+e+l++ ++++r 
  gi|557693717|ref|YP_008796771.1| 332 ARALATKISIAARIDYFSKEDRGAQLREALEKRVEEIRR 370
                                       667777777777777777777777777777776666664 PP

>> TrbH  Conjugal transfer protein TrbH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.1e-05      0.37      30      58 ..      43      71 ..      36      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.1e-05
                              TrbH 30 kvpdefGaaLvkelrekGyavlefapera 58
                                       +p  f +a++kelr++Gy+vl + +er 
  gi|557693717|ref|YP_008796771.1| 43 DLPSGFVEAFLKELRDRGYSVLVYWDERV 71
                                      6788999***************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2710.88
//
Query:       gi|557693718|ref|YP_008796772.1|  [L=231]
Description: fibrillarin-like pre-rRNA processing protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-91  303.4   0.0    7.5e-91  303.3   0.0    1.0  1  Fibrillarin      Fibrillarin
    0.00018   22.2   0.0    0.00028   21.5   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    0.00041   20.2   0.0    0.00052   19.8   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00049   19.8   0.0    0.00061   19.6   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
  ------ inclusion threshold ------
      0.039   14.6   0.1       0.12   13.1   0.0    1.8  2  Methyltransf_11  Methyltransferase domain
       0.11   12.6   0.0       0.14   12.2   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase


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 !  303.3   0.0   2.5e-94   7.5e-91       1     224 [.       5     229 ..       5     231 .] 0.99

  Alignments for each domain:
  == domain 1  score: 303.3 bits;  conditional E-value: 2.5e-94
                                       EEEECSSTTEEEEETTSSEEEEEE-SSTT--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEE CS
                       Fibrillarin   1 veeheklegvyivkekgdarlatknlvpgekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYl 77 
                                       +++h ++egvy+v++ +  r atk+l pg +vYgE l++  + EyRvWnpfrsKlaaail+++ke+ i++gs+vLYl
  gi|557693718|ref|YP_008796772.1|   5 IRPHPRFEGVYLVEGVEGLRPATKSLDPGFQVYGEELVRAVDGEYRVWNPFRSKLAAAILRDVKEIFIRPGSRVLYL 81 
                                       579***********99999********************************************************** PP

                                       STTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHH.HHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTH CS
                       Fibrillarin  78 GaasGttvsHvsDivgeegvvyavefsprvlreli.evakkRknivPileDArkPekYralvekvDvifaDvaqpdq 153
                                       G+asGttvsHvsDivg +gvvy+v+f+p+v++++i +va++R+n+vPil+DA+kPe+Y++lv  vDvi+aDva p q
  gi|557693718|ref|YP_008796772.1|  82 GSASGTTVSHVSDIVGLRGVVYGVDFAPKVMQQFIqKVAERRNNVVPILADASKPESYAHLVGVVDVIYADVAWPAQ 158
                                       **********************************9789*************************************** PP

                                       HHHHHHHHHHHEEEEEEEEEEEEHHHHHSSSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEEEEE CS
                       Fibrillarin 154 arilaknaklflkeggyllisikarsidvtkepeevfkeeveklkeeglkvleqvklepyekdhalvvgky 224
                                       a+++a na+l l++gg +l+++karsid++++p +v  +ev++l ++g+++ e++ lep+ekdh++v ++y
  gi|557693718|ref|YP_008796772.1| 159 ADLVAANARLMLRKGGGVLLAVKARSIDSVEDPGKVVDREVRTLASSGFEIRETLGLEPFEKDHVMVAAVY 229
                                       *******************************************************************9987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   9.3e-08   0.00028       1      97 []      78     174 ..      78     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.3e-08
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBS...SSTTTEEEEEEEST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvefvqgdaedlp...fedgsfDlvvssga 73 
                                       vL lG  +G+++ ++++ +g ++ v+gvD++++ +++  ++++e++ nv  + +da++ +      g +D++++   
  gi|557693718|ref|YP_008796772.1|  78 VLYLGSASGTTVSHVSDIVGlRGVVYGVDFAPKVMQQFIQKVAERRNNVVPILADASKPEsyaHLVGVVDVIYA--- 151
                                       8999**************9889********************99999*********775511155667777777... PP

                                       GGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  74 lhhlsdedlekalkeiarvLkpgG 97 
                                         + ++++++ + ++++ +L++gG
  gi|557693718|ref|YP_008796772.1| 152 -DVAWPAQADLVAANARLMLRKGG 174
                                       .345677888999999999**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 !   19.8   0.0   1.7e-07   0.00052      69     132 ..      67     132 ..      54     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.7e-07
                                       TT...--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES- CS
                              PCMT  69 le...lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD 132
                                       ++   +++g+rvL +Gs sG     ++ +vg +g v +++  ++++++  +++ +   +nv+ + +D
  gi|557693718|ref|YP_008796772.1|  67 VKeifIRPGSRVLYLGSASGTTVSHVSDIVGLRGVVYGVDFAPKVMQQFIQKVAERR-NNVVPILAD 132
                                       4445599*****************************************999997654.455555555 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0     2e-07   0.00061      35     141 ..      69     176 ..      60     211 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2e-07
                             GCD14  35 kLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevs 111
                                       ++ ++pGs+v+  G  sg+  + ++  v+ +G ++ ++f  + +++ +++  e++ +++v +   D+ k    +++ 
  gi|557693718|ref|YP_008796772.1|  69 EIFIRPGSRVLYLGSASGTTVSHVSDIVGLRGVVYGVDFAPKVMQQFIQKVAERR-NNVVPI-LADASKPESYAHLV 143
                                       5669****************99******************999999999988775.344444.56777655548888 PP

                             GCD14 112 gkvDavfLDlPaPwea..ip.haakalkkeggr 141
                                       g+vD ++ D+  P +a  +  +a  +l+k gg+
  gi|557693718|ref|YP_008796772.1| 144 GVVDVIYADVAWPAQAdlVAaNARLMLRKGGGV 176
                                       **********98887743330333344555555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.9e-05      0.12       1      92 [.      79     174 ..      79     178 .. 0.73
   2 ?   -1.7   0.0       1.5   4.6e+03      70      92 ..     184     206 ..     176     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.9e-05
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-T..T-EEEEEEES-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadaekl.pfed..nsfDlvvssevl 71 
                                       L +G+ +G  + ++ + +   + v+gvD++++++++  +k+ e++++v  + ada+k   ++   + +D++++  ++
  gi|557693718|ref|YP_008796772.1|  79 LYLGSASGTTVSHVSDIVglrGVVYGVDFAPKVMQQFIQKVAERRNNVVPILADASKPeSYAHlvGVVDVIYADVAW 155
                                       5689999999999997777889************9999999999998888999999843344433677777776654 PP

                                       CC-CCHHHHHHHHHHHEEEEE CS
                   Methyltransf_11  72 hhvedpekalkeiaRvLkpgG 92 
                                             + + ++++ +L++gG
  gi|557693718|ref|YP_008796772.1| 156 PAQ--ADLVAANARLMLRKGG 174
                                       444..3445555555666666 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                                       -CCC-CCHHHHHHHHHHHEEEEE CS
                   Methyltransf_11  70 vlhhvedpekalkeiaRvLkpgG 92 
                                       +++ vedp k+++  +R L   G
  gi|557693718|ref|YP_008796772.1| 184 SIDSVEDPGKVVDREVRTLASSG 206
                                       67889999999999999998877 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   4.8e-05      0.14      17      97 ..      69     155 ..      56     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.8e-05
                                       T-S.-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS..........HHHTTEEEECS-CCCSSHHHHHCHC CS
                              FtsJ  17 klf.kpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm..........aplpgvttiqgditdpetiekikea 82 
                                       ++f +pg +v+ lg+a G     ++  +g +g+v++vD  p           + +++v  i +d  +pe    +   
  gi|557693718|ref|YP_008796772.1|  69 EIFiRPGSRVLYLGSASGTTVSHVSDIVGLRGVVYGVDFAPKvmqqfiqkvaERRNNVVPILADASKPESYAHLVG- 144
                                       34427************************9*********8888898887774445899999999999999998875. PP

                                       HHHSSEEEEEE--S- CS
                              FtsJ  83 lserkvdlvvsDgap 97 
                                            vd++ +D+a 
  gi|557693718|ref|YP_008796772.1| 145 ----VVDVIYADVAW 155
                                       ....59999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1637.45
//
Query:       gi|557693719|ref|YP_008796773.1|  [L=189]
Description: ribonuclease HII [Candidatus Caldiarchaeum subterraneum]
Scores for 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  127.8   0.0    5.6e-37  127.5   0.0    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 !  127.5   0.0   3.1e-41   5.6e-37       1     175 [.       3     177 ..       3     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 127.5 bits;  conditional E-value: 3.1e-41
                                       EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH..SEEEEEEE-HHHHH..HHTTT CS
                         RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklik..kkiekrklvaeeiky.asene 74 
                                       +G+DEaGrG+v+Gplvvaava e ++ + l++lgv+DSK+Ls+++ree++++++   ++ +  ++   i+   ++n+
  gi|557693719|ref|YP_008796773.1|   3 CGVDEAGRGCVVGPLVVAAVAAERDELPLLRALGVADSKTLSPRRREEIFEKLRasFRVGYMLVSPRRISScLRVNG 79 
                                       7*****************************************************77556666666666665544444 PP

                                       S-.HHHHHHHHHHHHHHHHHHTCEECCECCCE--SSHHHHHHHHHHHHCCEEEEETTGGGT-HHHHHHHHHHHHHHH CS
                         RNase_HII  75 in.lneikaaltlaviklleklgvkvdeilvdgvttpeslkkkleqiikikvtvekkadekyllvaaASiiAkverd 150
                                        + ln+++  +++++++  ++    vd+ + d  ++  +l +kl   +   v    ++d++++lvaaAS++Akv rd
  gi|557693719|ref|YP_008796773.1|  80 GDgLNDLEYGVMAELARSFRPRILFVDSPDRDVRRARRRLLEKLGVEMD--VRCMVRGDRRHVLVAAASVVAKVVRD 154
                                       444899999999********************88888888888877777..777789******************** PP

                                       HHHHHHHHHCSH.--TTSSTTSHHH CS
                         RNase_HII 151 eelellkrkpgtldkgsGyasdekt 175
                                        ++  l+r  g  d+gsGy+sd++ 
  gi|557693719|ref|YP_008796773.1| 155 RKVAMLRRRLG--DFGSGYPSDPRH 177
                                       *********98..*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); 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:                         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 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1319.86
//
Query:       gi|557693720|ref|YP_008796774.1|  [L=174]
Description: nucleotide kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-51  172.5   0.1    7.7e-51  172.3   0.1    1.0  1  NTPase_1  NTPase
    0.00037   20.3   0.1    0.00064   19.5   0.1    1.5  1  AAA_30    AAA domain
     0.0034   17.0   0.0     0.0058   16.3   0.0    1.4  1  DUF2478   Protein of unknown function (DUF2478)
     0.0079   16.5   0.3       0.12   12.7   0.3    2.2  1  AAA_19    AAA domain
     0.0081   15.2   0.3      0.017   14.1   0.3    1.5  1  MeaB      Methylmalonyl Co-A mutase-associated GTPase MeaB
  ------ inclusion threshold ------
      0.022   14.7   0.1      0.054   13.4   0.1    2.0  1  NACHT     NACHT domain
      0.037   13.3   0.0       0.07   12.4   0.0    1.4  1  VirC1     VirC1 protein
      0.039   14.3   0.1       0.11   12.9   0.1    1.9  1  AAA_16    AAA ATPase domain
      0.056   13.3   0.1      0.098   12.6   0.1    1.4  1  MobB      Molybdopterin guanine dinucleotide synthesis protei
      0.072   13.4   0.1       0.53   10.6   0.1    2.3  1  AAA_22    AAA domain
      0.084   13.3   0.0       0.16   12.4   0.0    1.7  1  AAA       ATPase family associated with various cellular acti
      0.095   12.4   0.0       0.69    9.6   0.0    2.1  1  AAA_24    AAA domain
       0.17   11.9   0.2       0.57   10.2   0.1    1.9  2  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain


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 !  172.3   0.1   5.6e-54   7.7e-51       4     167 ..       1     164 [.       1     165 [. 0.99

  Alignments for each domain:
  == domain 1  score: 172.3 bits;  conditional E-value: 5.6e-54
                                       EE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE-HHH CS
                          NTPase_1   4 iTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvdves 80 
                                       +TG+pGvGKtT +  v+ell+++gv+vgGfyt+e re+g r gF++vd+ sge++ La+v+++ +pr+g+yvv +++
  gi|557693720|ref|YP_008796774.1|   1 MTGRPGVGKTTALMSVVELLRKDGVRVGGFYTRELRETGVRKGFEVVDIISGETALLASVSTTPGPRIGRYVVMLDN 77 
                                       5**************************************************************************** PP

                                       HHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE--T CS
                          NTPase_1  81 feelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfevte 157
                                       +e+l++ +l+k l+++dv+ +DE+G+mEl s+kf e+ve++L+s+kp ++++h++ ++++ +++r+ ++ +++ ++ 
  gi|557693720|ref|YP_008796774.1|  78 LERLGVGSLEKGLETCDVLAVDEVGPMELLSNKFVETVEKILRSGKPSIFTVHVSATHPVAKSVRKLAGENLYLLDT 154
                                       ***************************************************************************** PP

                                       TTTTTHHHHH CS
                          NTPase_1 158 enrdalleei 167
                                        nrd++++ +
  gi|557693720|ref|YP_008796774.1| 155 VNRDRVPQVV 164
                                       *****99865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   4.7e-07   0.00064      24     100 ..       2     104 ..       1     126 [. 0.69

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.7e-07
                            AAA_30  24 tGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgi......eastiakllkrlk............. 81 
                                       tG++G GKttal +++e+++++g rv g+   +     +++++++      e++ +a++ ++ +             
  gi|557693720|ref|YP_008796774.1|   2 TGRPGVGKTTALMSVVELLRKDGVRVGGFYTRELRETGVRKGFEVvdiisgETALLASVSTTPGprigryvvmldnl 78 
                                       8**********************999988776666666776555444443344444444433336666666666677 PP

                            AAA_30  82 ........grarlepgtllivDEagmv 100
                                               + + le+ ++l vDE+g +
  gi|557693720|ref|YP_008796774.1|  79 erlgvgslE-KGLETCDVLAVDEVGPM 104
                                       777777642.45666677777777755 PP

>> DUF2478  Protein of unknown function (DUF2478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.2e-06    0.0058      10     132 ..       7     131 ..       1     146 [. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.2e-06
                           DUF2478  10 eavdalLaafaerlraeGlrvaGvvqenaeeaegkkcdmeledlatgeri...risqdlgsgsqgCrLdpeaLaeaa 83 
                                           + L +++e lr++G+rv+G+  ++ +e+ g ++  e++d+ +ge+    ++s + g++     +  ++L++  
  gi|557693720|ref|YP_008796774.1|   7 VGKTTALMSVVELLRKDGVRVGGFYTRELRET-GVRKGFEVVDIISGETAllaSVSTTPGPRIGRYVVMLDNLERLG 82 
                                       556678999****************8888765.7788**********986222556666777767778889999987 PP

                           DUF2478  84 aaveralaegadlvivnkFGkqEaeGrGlreeiaaalaagiPvltaVse 132
                                           ++  e +d++ v   G  E   + + e ++++l +g P + +V+ 
  gi|557693720|ref|YP_008796774.1|  83 VGSLEKGLETCDVLAVDEVGPMELLSNKFVETVEKILRSGKPSIFTVHV 131
                                       7666666699999999999999999999999999999999999999875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.3   8.7e-05      0.12      16     124 ..       2     114 ..       1     129 [. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.7e-05
                            AAA_19  16 taGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal..........ldfdd 82 
                                       t+ pG GKT+ l+ +v+ll + g v +  ++   + +  +++  e ++ + +e+  + ++++          + +d+
  gi|557693720|ref|YP_008796774.1|   2 TGRPGVGKTTALMSVVELLRKDG-VRVGGFYTRELRETGVRKGFEVVDIISGETALLASVSTtpgprigryvVMLDN 77 
                                       799**************999887.44544444444444444444444444444333333333444444445444555 PP

                            AAA_19  83 lltealelleeaeeekklqeeellivDEfqdvdelqyrLlka 124
                                       l+   ++ le     k l+ +++l vDE+  ++ l ++++++
  gi|557693720|ref|YP_008796774.1|  78 LERLGVGSLE-----KGLETCDVLAVDEVGPMELLSNKFVET 114
                                       5544444444.....355455566666666666666666655 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 !   14.1   0.3   1.2e-05     0.017      34      61 ..       1      28 [.       1      30 [. 0.96

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                      EEE-TTSSHHHHHHHHHHHHHCTT--EE CS
                              MeaB 34 ltGvPGaGkstlvealglelrrrGkrva 61
                                      +tG PG+Gk t++  +++ lr+ G rv+
  gi|557693720|ref|YP_008796774.1|  1 MTGRPGVGKTTALMSVVELLRKDGVRVG 28
                                      69************************96 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.9e-05     0.054       6      29 ..       2      25 ..       1     170 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.9e-05
                                      EC-TTTCHHHHHHHHHHHHCTS-S CS
                             NACHT  6 qGeaGsGKTtLlqklalawaegkl 29
                                      +G++G+GKTt l +++++++++  
  gi|557693720|ref|YP_008796774.1|  2 TGRPGVGKTTALMSVVELLRKDGV 25
                                      7******************99875 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.1e-05      0.07      12      40 ..       6      34 ..       2      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
                             VirC1 12 GaGkttalmglcsalasdgkrvalfeade 40
                                      G Gkttalm++   l  dg rv+ f + e
  gi|557693720|ref|YP_008796774.1|  6 GVGKTTALMSVVELLRKDGVRVGGFYTRE 34
                                      99********************9997665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   7.6e-05      0.11      30      61 ..       2      33 ..       1     129 [. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.6e-05
                            AAA_16 30 sGesGvGKsslvrellralekdggif..lrgkcd 61
                                      +G +GvGK++ + ++ + l+kdg+ +  +   ++
  gi|557693720|ref|YP_008796774.1|  2 TGRPGVGKTTALMSVVELLRKDGVRVggF--YTR 33
                                      799*************9999997776333..333 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 ?   12.6   0.1   7.1e-05     0.098       5      31 ..       2      28 ..       1      32 [. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.1e-05
                              MobB  5 vgksgsGKTtLleklipelkarglrvg 31
                                      +g+ g GKTt l  +++ l++ g+rvg
  gi|557693720|ref|YP_008796774.1|  2 TGRPGVGKTTALMSVVELLRKDGVRVG 28
                                      68899*********************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00038      0.53      11      30 ..       2      21 ..       1     135 [. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00038
                            AAA_22 11 tGesGtGKTtllrrlleqld 30
                                      tG +G+GKTt l  ++e l 
  gi|557693720|ref|YP_008796774.1|  2 TGRPGVGKTTALMSVVELLR 21
                                      8***********99999884 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       4      30 ..       2      28 ..       1     104 [. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                                      ESSTTSSHHHHHHHHHHHHTHEEEEEE CS
                               AAA  4 yGppGtGKTllakavakelgvefleis 30
                                      +G pG+GKT++  +v++ l  + +++ 
  gi|557693720|ref|YP_008796774.1|  2 TGRPGVGKTTALMSVVELLRKDGVRVG 28
                                      79**************99853333332 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0005      0.69       8      88 ..       2     115 ..       1     145 [. 0.62

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0005
                            AAA_24   8 yGpsgiGKTtlakel....gpkplfi................dtekGlksldadkfpdie.............swed 51 
                                       +G +g+GKTt + +                             + kG+  +d + ++++               +  
  gi|557693720|ref|YP_008796774.1|   2 TGRPGVGKTTALMSVvellR-----KdgvrvggfytrelretGVRKGFEVVDIISGETALlasvsttpgprigRYVV 73 
                                       69999999999988845441.....1222334555555444433333333333333322233333333333337777 PP

                            AAA_24  52 fldevvel.....aaeladyktlviDtideleelclaevirq 88 
                                       +ld ++ l     ++ l+++++l +D ++ +e l  + v + 
  gi|557693720|ref|YP_008796774.1|  74 MLDNLERLgvgslEKGLETCDVLAVDEVGPMELLSNKFVETV 115
                                       777777779999999999999999999988876665555555 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 ?   10.2   0.1   0.00041      0.57       9      30 ..       6      27 ..       1      30 [. 0.91
   2 ?   -1.1   0.0       1.3   1.8e+03      30      43 ..      95     109 ..      85     169 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00041
                                      TSSHHHHHHHHHHHHHHTT--E CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  9 GvGKTtlaanLaralarrglrV 30
                                      GvGKTt + +   +l ++g rV
  gi|557693720|ref|YP_008796774.1|  6 GVGKTTALMSVVELLRKDGVRV 27
                                      9********************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                                       EEEEE.EEESSCCCC CS
                                       xxxxx.xxxxxxxxx RF
                              CbiA  30 VllvD.aDpqannla 43 
                                       Vl+vD ++p+  +++
  gi|557693720|ref|YP_008796774.1|  95 VLAVDeVGPMELLSN 109
                                       666666666655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); 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: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1168.40
//
Query:       gi|557693721|ref|YP_008796775.1|  [L=366]
Description: tRNA (guanine-N2-)-methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-88  297.8   0.0    1.5e-88  297.5   0.0    1.0  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    4.1e-07   29.9   0.0    6.3e-07   29.3   0.0    1.2  1  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.022   15.8   0.0       0.06   14.4   0.0    1.7  2  Methyltransf_24  Methyltransferase domain
      0.029   13.8   0.1      0.041   13.3   0.1    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.038   13.6   0.0      0.067   12.8   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
        0.1   12.1   0.0       0.18   11.4   0.0    1.3  1  MTS              Methyltransferase small domain
        0.1   12.0   0.0       0.17   11.3   0.0    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
       0.18   11.6   0.0        0.3   10.9   0.0    1.3  1  Methyltransf_31  Methyltransferase 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 !  297.5   0.0   6.8e-92   1.5e-88      15     373 ..      16     362 ..       6     365 .. 0.95

  Alignments for each domain:
  == domain 1  score: 297.5 bits;  conditional E-value: 6.8e-92
                                       -TT--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHH CS
                               TRM  15 skkeeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelik 91 
                                       +++++VFYNP  +  RDl+v++          +g  + v+++L++sG+RaiR ++E+++v ++l+NDi+++Av++++
  gi|557693721|ref|YP_008796775.1|  16 PTRSPVFYNPYSALSRDLTVVL---AR----TFGDGVVVAEPLAGSGVRAIRLLVETNTVARALMNDINPNAVKVMR 85 
                                       6789*****************9...44....4455689*************************************** PP

                                       HHHHHTT--GGEEEE-S-HHHHHC...--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHH CS
                               TRM  92 eNvklneveeivvineddAnvlla...ekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspe 165
                                        N++ n v+e+ ++ e+dA+v+l+    ++ r +++D+DP G+p++f+++ +++v+++g++ v aTD+a+L G++pe
  gi|557693721|ref|YP_008796775.1|  86 LNAEWNGVAERCEVFEGDAAVFLTrlsGWRDRVHYVDVDPVGAPVKFVENSLRAVANGGYIGVSATDLAPLVGNHPE 162
                                       ***********************9888999*********************************************** PP

                                       HHHHHHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEE CS
                               TRM 166 kclrkYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhC 242
                                       +c+rkYg  + k+ +  E alR+l ++v ++ a  + a +p+ls+++ ++vrvf++v +g  +v k+lek+g ++ C
  gi|557693721|ref|YP_008796775.1| 163 TCFRKYGLLSGKTFFPKEAALRLLASFVIQRGAALNIAATPVLSVQHRHFVRVFFHVLRGRSRVIKLLEKIGWIKSC 239
                                       ****************************************************************************8 PP

                                       TTT--EEEE--GGG--.SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS-- CS
                               TRM 243 sgClseekvkglakfk.aecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeEllda 318
                                        +Cl  ++v +l+ f  + c+ cg +  ++GP wlgpl++ e+ve++l+   +        + +k+L+ i+ E  d+
  gi|557693721|ref|YP_008796775.1| 240 -NCLY-KEVFSLQDFPdRVCPRCGGEAAVVGPAWLGPLHNGELVEKMLALSTD------LPKAQKILERIRGE-DDV 307
                                       .7988.5666677765488******************************9999......46889*********.9** PP

                                       SS-EEHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHHH CS
                               TRM 319 plyydlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavve 373
                                       ++yy ++++a+v  ++ ++   +v+ l+++g+++s+tH+ p+a+kT+aple +++
  gi|557693721|ref|YP_008796775.1| 308 VGYYPVDRIAHVRGVTPRSPLVLVASLRSMGYRASLTHVDPTAVKTDAPLEDLLK 362
                                       **************************************************99876 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   2.8e-10   6.3e-07      93     195 ..      36     144 ..      19     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 2.8e-10
                                       HHHTT--TT-EEEETT-TTTCCHHHCCHHTTSS.EEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---..T CS
                            Met_10  93 rlaklveegevVvdvfAGiGpfaipiakyskak.rvlaidlnPesvkylkeniklNkvekvvkpileDgrevir..e 166
                                        la+++ +g vV + +AG G  ai + + ++ + r l +d+nP++vk ++ n + N v+++ +++++D++ +++  +
  gi|557693721|ref|YP_008796775.1|  36 VLARTFGDGVVVAEPLAGSGVRAIRLLVETNTVaRALMNDINPNAVKVMRLNAEWNGVAERCEVFEGDAAVFLTrlS 112
                                       47889*******************99887665426899*********************************997665 PP

                                       T-EE..EEE.E--TTTGGGGHHHHHHHEEEEE CS
                            Met_10 167 qlad..rvv.mnlpksaieFldkvlaalkdgg 195
                                          d  ++v  + +   ++F+++ l+a+ +gg
  gi|557693721|ref|YP_008796775.1| 113 GWRDrvHYVdVDPVGAPVKFVENSLRAVANGG 144
                                       55553334423445556777777777776665 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.7e-05      0.06      12     101 ..      59     146 ..      51     149 .. 0.78
   2 ?   -3.4   0.0         8   1.8e+04      12      33 ..     328     350 ..     325     358 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.7e-05
                   Methyltransf_24  12 lwllralrrngagrlvavdhdpgaeeaaalare.aglddrvrlikadseealaslaagsiD.llfiDgghaaeavle 86 
                                       + l  +++ n   r ++ d +p a ++++l +e +g+++r ++ ++d+   l++l+ g+ D + ++D +++++ v++
  gi|557693721|ref|YP_008796775.1|  59 IRL--LVETNTVARALMNDINPNAVKVMRLNAEwNGVAERCEVFEGDAAVFLTRLS-GWRDrVHYVDVDPVGAPVKF 132
                                       333..35666667788888888655555555558**********************.66664889*****9999998 PP

                   Methyltransf_24  87 dleallprlapggvv 101
                                        +e+ l+ +a+gg++
  gi|557693721|ref|YP_008796775.1| 133 -VENSLRAVANGGYI 146
                                       .************97 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8
                   Methyltransf_24  12 lwllralrrnga.grlvavdhdp 33 
                                       l+l++ lr+ g   +l+ vd+ +
  gi|557693721|ref|YP_008796775.1| 328 LVLVASLRSMGYrASLTHVDPTA 350
                                       56666777777666788888765 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   0.1   1.8e-05     0.041     170     216 ..      52     100 ..      42     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                              PrmA 170 tGSGiLaiaaa..kLgakkvvavDiDevAvkvakeNaelNkveakleva 216
                                       +GSG+ ai  +      ++++  Di++ Avkv + Nae N+v++++ev+
  gi|557693721|ref|YP_008796775.1|  52 AGSGVRAIRLLveTNTVARALMNDINPNAVKVMRLNAEWNGVAERCEVF 100
                                       58999888654113345667778**********************9994 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     3e-05     0.067      44     142 ..      46     146 ..      32     152 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3e-05
                                       EEEETT-TTSHHHHHHH..HTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEEEE CS
                     Cons_hypoth95  44 rvLDlfaGsGalglEAl..SRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdivf 118
                                        v +  aGsG+ ++  l     +++a++ + +++avk+++ n e  ++ e+++++  da+  l +l++   ++ +v 
  gi|557693721|ref|YP_008796775.1|  46 VVAEPLAGSGVRAIRLLveTNTVARALMNDINPNAVKVMRLNAEWNGVAERCEVFEGDAAVFLTRLSGWRDRVHYVD 122
                                       55666788887777666224568899*************************************************** PP

                                       E--SSSTTCH.HHHHHHHHHTT-E CS
                     Cons_hypoth95 119 lDPPyakellieevlelleekkll 142
                                       +DP  a ++++e+ l+++++ + +
  gi|557693721|ref|YP_008796775.1| 123 VDPVGAPVKFVENSLRAVANGGYI 146
                                       ***999999999999999887766 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0     8e-05      0.18      40      89 ..      52     104 ..      34     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8e-05
                                       -TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC..EEEEE-ST CS
                               MTS  40 cGaGvlgaalakespeae.vtlvdvdarAlesakenleankle..vevvasdv 89 
                                       +G Gv ++ l+ e+++++   + d++ +A+++ + n+e n+++  +ev++ d+
  gi|557693721|ref|YP_008796775.1|  52 AGSGVRAIRLLVETNTVArALMNDINPNAVKVMRLNAEWNGVAerCEVFEGDA 104
                                       799999999998888877699********************998888888886 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.6e-05      0.17      32     109 ..      58     131 ..      51     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.6e-05
                                       HHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEESTCHHHHCTCSS-EEEEEEECCSTTCSSC CS
                    Spermine_synth  32 vlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklvlgdgfkflkayekkfdvvivdsldpvgpae 108
                                       ++r +v  ntv ++ + di  +++++++ +     +     +r++++ gd+  fl++++   d v ++ +dpvg   
  gi|557693721|ref|YP_008796775.1|  58 AIRLLVETNTVARALMNDINPNAVKVMRLNAEWNGVA----ERCEVFEGDAAVFLTRLSGWRDRVHYVDVDPVGAPV 130
                                       67889999******************99876655555....********************************9765 PP

                                       G CS
                    Spermine_synth 109 n 109
                                       +
  gi|557693721|ref|YP_008796775.1| 131 K 131
                                       5 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00013       0.3       5      67 ..      45     109 ..      42     174 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.le 67 
                                       ++v ++ +G+G  +++l  e ++ a+    Di+++a++++r na+ +g+  ++e+ +gd+   l 
  gi|557693721|ref|YP_008796775.1|  45 VVVAEPLAGSGVRAIRLLVETNTVARALMNDINPNAVKVMRLNAEWNGVAeRCEVFEGDAAVfLT 109
                                       5666677899999999999*******999********************99******99987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2537.41
//
Query:       gi|557693722|ref|YP_008796776.1|  [L=224]
Description: ribosomal RNA large subunit methyltransferase E FtsJ [Candidatus Caldiarchaeum subterraneum]
Scores for 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-43  146.9   0.0    7.6e-43  146.7   0.0    1.0  1  FtsJ             FtsJ-like methyltransferase
    1.7e-06   27.9   0.0    2.1e-06   27.6   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    1.4e-05   24.3   0.0    2.3e-05   23.6   0.0    1.4  1  Fibrillarin      Fibrillarin
    0.00011   21.9   0.0     0.0002   21.1   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0022   18.6   0.1     0.0041   17.7   0.1    1.5  1  Methyltransf_11  Methyltransferase domain
     0.0064   16.1   0.0      0.008   15.7   0.0    1.1  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.019   14.8   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
      0.029   15.1   0.1       0.07   13.8   0.1    1.7  1  Methyltransf_25  Methyltransferase domain
      0.035   14.0   0.0      0.076   12.8   0.0    1.7  1  Methyltransf_23  Methyltransferase domain
       0.24   10.7   0.0       0.33   10.3   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.7   0.0   4.2e-46   7.6e-43       1     177 []      24     201 ..      24     201 .. 0.98

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 4.2e-46
                                       CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHH.TTEEEECS-CCCSSHH CS
                              FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmapl.pgvttiqgditdpeti 76 
                                       y sR+a+KLlei+++ k++++g++v+DlgaaPGg + v++  +g+kg vvavD qp ++  p++ tiq+di + +  
  gi|557693722|ref|YP_008796776.1|  24 YPSRAAFKLLEIQSRWKIIREGQRVLDLGAAPGGMAAVASDIVGEKGLVVAVDRQPLQLTrPNIVTIQADIYEARLT 100
                                       779******************************************************9888**************** PP

                                       HHHCHCHHHSSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCCEE CS
                              FtsJ  77 ekikealserkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkfFe 153
                                       + +++al+e+ +d+vvsD++p  sg  dl   +q++Ll+a+l+l+ + l++gg+ v+k+f+ ++  +++k++ ++F 
  gi|557693722|ref|YP_008796776.1| 101 RDVQTALGEEFCDVVVSDLSPHHSGDYDLLVEQQIDLLEASLNLCHRFLRRGGNAVFKAFEHPRLRDFEKRMMRCFW 177
                                       ***********************************************************************9999** PP

                                       EEEEEE-SS--CCG-EEEEEEEEC CS
                              FtsJ 154 kvsvvkPkssrsesseeflvcrgf 177
                                       kv+ + P+s++++sse+fl+ +g+
  gi|557693722|ref|YP_008796776.1| 178 KVERYVPRSTKKGSSEIFLLGLGY 201
                                       *******************99875 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 !   27.6   0.0   1.2e-09   2.1e-06      32     108 ..       5      79 ..       1     109 [. 0.80

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.2e-09
                                       GGSSCGGGGGTTSSS-EEEETTEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBH CS
                              PCMT  32 efvpesfkekaYedaplsigynatiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierik 108
                                       +++++  +e +Y  ++ ++gy +   a ++  +   +  +++g+rvL++G+  G  +av + +vgekg+vv+++r++
  gi|557693722|ref|YP_008796776.1|   5 QWLQR-RREDPYWRKAKEMGYPSR-AAFKLLEIQSRWKIIREGQRVLDLGAAPGGMAAVASDIVGEKGLVVAVDRQP 79 
                                       55655.466888888888888876.46677778888888***********************************997 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.3e-08   2.3e-05      67     107 ..      41      81 ..      24     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.3e-08
                                       S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                       Fibrillarin  67 pikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                        i++g++vL lGaa G  ++  sDivge+g+v av+  p  
  gi|557693722|ref|YP_008796776.1|  41 IIREGQRVLDLGAAPGGMAAVASDIVGEKGLVVAVDRQPLQ 81 
                                       589********************************987753 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 !   21.1   0.0   1.1e-07    0.0002       7      47 ..      43      83 ..      40     120 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.1e-07
                                      -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHH CS
                   Methyltr_RsmB-F  7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlk 47
                                      +e++++lDl aaPGg  +  ++++ +kg vvAvd++   l 
  gi|557693722|ref|YP_008796776.1| 43 REGQRVLDLGAAPGGMAAVASDIVGEKGLVVAVDRQPLQLT 83
                                      6899******************************9876554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   2.3e-06    0.0041       1      96 []      49     157 ..      49     157 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.3e-06
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECC...CTSS-TT-EEEEEEES-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseeglkvefvvadae...klpfednsfDlvvssevl 71 
                                       Ld+G+  G +a+   + +   + vv+vD  + +l   + ++++ +   ++ +a+++   ++ + ++ +D+vvs  + 
  gi|557693722|ref|YP_008796776.1|  49 LDLGAAPGGMAAVASDIVgekGLVVAVDRQPLQL--TRPNIVTIQ--ADIYEARLTrdvQTALGEEFCDVVVSDLSP 121
                                       89999999999999977677789*****988888..555555555..456666666322479*************** PP

                                       CC-...C........CHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  72 hhv...e........dpekalkeiaRvLkpgGllvi 96 
                                       hh    +         +e+ l+ ++R L+ gG  v+
  gi|557693722|ref|YP_008796776.1| 122 HHSgdyDllveqqidLLEASLNLCHRFLRRGGNAVF 157
                                       ***86615555556599999************8876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   4.5e-06     0.008      31     136 ..      44     156 ..      31     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.5e-06
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE-. CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivsN. 104
                                       + ++vlDlG+  G ++a++ +   e    +v vd + l++++ n+ + +++     +++dv  ++ e+ +d++vs  
  gi|557693722|ref|YP_008796776.1|  44 EGQRVLDLGAAPGGMAAVASDIVGEKG-LVVAVDRQPLQLTRPNIVTIQADiyEARLTRDVQTALGEEFCDVVVSDl 119
                                       4678*****************999965.567788999**********999985556789***************985 PP

                                       --STTTC.....HCHHHHHHHHHHHHHHHEEEEEEEE CS
                               MTS 105 PPfhagk.....atelavaeeliaeAkeaLkegGeLl 136
                                        P h+g      +++ ++ e+ ++  +++L+ gG+ +
  gi|557693722|ref|YP_008796776.1| 120 SPHHSGDydllvEQQIDLLEASLNLCHRFLRRGGNAV 156
                                       6888876322223445555555666667777777655 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     1e-05     0.019       2      95 ..      43     132 ..      42     176 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDl 77 
                                       ++g rvlDlG++ G  + ++ + +g+k+ vv +D+++  +++ +  + +  + ++++   d+++ l +    e  D+
  gi|557693722|ref|YP_008796776.1|  43 REGQRVLDLGAAPGGMAAVASDIVGEKGLVVAVDRQPLQLTRPNIVTIQADIYEARLT-RDVQTaLGE----EFCDV 114
                                       57889********************************999888886665555545544.455553553....44588 PP

                   Methyltransf_31  78 ilsnevlnaladpdkile 95 
                                       ++s+   ++  d d   e
  gi|557693722|ref|YP_008796776.1| 115 VVSDLSPHHSGDYDLLVE 132
                                       888855544444444444 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   3.9e-05      0.07       1      97 []      48     153 ..      48     153 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-05
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC.CG..BSSSTTTEEEEEEEST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeeglnvefvqgda.ed..lpfedgsfDlvvssga 73 
                                       vLdlG+ +G +++ +++ +g k+ v++vD ++ +l + +       ++++++++ + +d    + ++ +D+vvs  +
  gi|557693722|ref|YP_008796776.1|  48 VLDLGAAPGGMAAVASDIVGeKGLVVAVDRQPLQLTRPNIVT----IQADIYEARLtRDvqTALGEEFCDVVVSDLS 120
                                       9*************999997699******9998876544333....4555555555322212356779999999555 PP

                                       GGGSSHHHH.........HHHHHHHHHHEEEEE CS
                   Methyltransf_25  74 lhhlsdedl.........ekalkeiarvLkpgG 97 
                                        hh  d dl         e+ l+ ++r L+ gG
  gi|557693722|ref|YP_008796776.1| 121 PHHSGDYDLlveqqidllEASLNLCHRFLRRGG 153
                                       555443332222222333556666677776666 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.3e-05     0.076      20      58 ..      42     125 ..      15     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-05
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlre.............................................ngfsvtgvD 51 
                                        r+g+rvLd+G++ G ++ v+++                                             ++++v++ D
  gi|557693722|ref|YP_008796776.1|  42 IREGQRVLDLGAAPGGMAAVASDivgekglvvavdrqplqltrpnivtiqadiyearltrdvqtalgeEFCDVVVSD 118
                                       68899************887777666667777777777777777777777777777777777777776889999999 PP

                   Methyltransf_23  52 lspeave 58 
                                       lsp+ ++
  gi|557693722|ref|YP_008796776.1| 119 LSPHHSG 125
                                       9998666 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00019      0.33     157     232 ..      40     117 ..      29     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                              PrmA 157 klvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk...eekadvi 230
                                       k+++eg++vlD+G+  G +a +a+ +  +k + v +D + ++ ++ N+   + +   e  l++++++   ee  dv+
  gi|557693722|ref|YP_008796776.1|  40 KIIREGQRVLDLGAAPGGMAAVASDIVGEKGLVVAVDRQPLQLTRPNIVTIQADI-YEARLTRDVQTalgEEFCDVV 115
                                       56999********997766655555555555566677777899999987655543.334455555544446777999 PP

                              PrmA 231 va 232
                                       v+
  gi|557693722|ref|YP_008796776.1| 116 VS 117
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1689.19
//
Query:       gi|557693723|ref|YP_008796777.1|  [L=115]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   16.5   0.4       0.44    9.9   0.0    2.2  2  RNA_pol_Rpc34  RNA polymerase Rpc34 subunit
  ------ inclusion threshold ------
      0.017   15.1   0.0      0.026   14.5   0.0    1.4  1  MarR           MarR family
      0.067   13.4   0.0      0.092   12.9   0.0    1.2  1  HTH_34         Winged helix DNA-binding domain


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 !    5.3   0.1    0.0018        11     125     140 ..      45      60 ..      19      67 .. 0.78
   2 !    9.9   0.0   7.4e-05      0.44     301     336 .]      77     112 ..      64     112 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0018
                                       HHHHTTXXEEEEXSSS CS
                     RNA_pol_Rpc34 125 sLeskkyiksvksvka 140
                                        Le k+yik vk +++
  gi|557693723|ref|YP_008796777.1|  45 KLERKGYIKRVKAFSN 60 
                                       69************98 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 7.4e-05
                                       SSTTXXSSXSSSSSXXTSSSSSSSSSSTTSSSSXXX CS
                     RNA_pol_Rpc34 301 sglveapcgecpvfdlceeggavspkncvYlkeWle 336
                                       ++l+++pc  c   ++c   g+ + k+c+ l+eWl+
  gi|557693723|ref|YP_008796777.1|  77 QPLIGVPCPSCVYDNVCGPRGEPHYKTCILLEEWLS 112
                                       7899******************************96 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.3e-06     0.026      17      52 ..      22      57 ..       5      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.3e-06
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                      ++ +seL+ klgv++   +r+  +Le+kG+i+R k 
  gi|557693723|ref|YP_008796777.1| 22 GMLQSELWHKLGVTSREGSRIGIKLERKGYIKRVKA 57
                                      47899****************************886 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   0.0   1.5e-05     0.092       5      53 ..      12      61 ..       8      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                            HTH_34  5 vlsyLas.vdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgk 53
                                      +l++L++ +  +  +el  +l++t+ + s    kLe +gYi++ k+f++ 
  gi|557693723|ref|YP_008796777.1| 12 ALALLMQnEVGMLQSELWHKLGVTSREGSRIGIKLERKGYIKRVKAFSND 61
                                      788899944467889999999999999999999**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 912.62
//
Query:       gi|557693724|ref|YP_008796778.1|  [L=235]
Description: transcription initiation factor TFIIB [Candidatus Caldiarchaeum subterraneum]
Scores for 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-23   80.4   1.1    1.6e-13   50.5   0.1    2.2  2  TFIIB     Transcription factor TFIIB repeat
    0.00018   21.8   0.1       0.11   12.8   0.0    2.4  2  Rrf2      Transcriptional regulator
    0.00087   19.5   0.6     0.0066   16.7   0.0    2.2  2  DUF4129   Domain of unknown function (DUF4129)
  ------ inclusion threshold ------
      0.088   12.5   0.0        0.2   11.4   0.0    1.5  1  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 !   29.0   0.1   1.8e-10   7.9e-07       4      66 ..      61     122 ..      58     127 .. 0.95
   2 !   50.5   0.1   3.6e-17   1.6e-13       1      71 []     151     221 ..     151     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.8e-10
                                       HHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS- CS
                             TFIIB   4 fadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqV 66 
                                       +ad+++Lp + a+ A ela++a++ kv+k rs    aAA +y+ +  +++ ++ +ei+s + V
  gi|557693724|ref|YP_008796778.1|  61 IADKIGLPRQAAEGAGELARKAVSSKVVK-RSRRPAAAALVYLSANNNGLCKSIEEIASAADV 122
                                       79**************************9.999999***********************9988 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 3.6e-17
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       i ++   leLp + a+ A  +++ a++ + ++Gr+pa+i AA++y+Acr+e+vk+ ++ +s+ + +s+ t+
  gi|557693724|ref|YP_008796778.1| 151 IDKLTRTLELPPTTANTACRIYQSAASLGKISGRKPAAISAAAVYLACRREGVKKPLSTVSEAAGISVLTL 221
                                       6788899*********************************************************9998775 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   2.5e-05      0.11       9      49 ..      94     134 ..      87     136 .. 0.90
   2 !    6.6   0.0    0.0022       9.8      13      52 ..     192     231 ..     180     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHH CS
                              Rrf2   9 yalhallyLakeeeeepvsseeiaerqnispsylekilakL 49 
                                        a  al+yL++++++   s+eeia+  +++ + l + ++kL
  gi|557693724|ref|YP_008796778.1|  94 PAAAALVYLSANNNGLCKSIEEIASAADVPLNQLNREISKL 134
                                       5889************9******************999988 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0022
                                       HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHT CS
                              Rrf2  13 allyLakeeeeepvsseeiaerqnispsylekilakLrka 52 
                                       a +yLa ++e+ +  +++++e  +is   l+k +a L+ a
  gi|557693724|ref|YP_008796778.1| 192 AAVYLACRREGVKKPLSTVSEAAGISVLTLRKAIALLESA 231
                                       5689******999**********************99876 PP

>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.5e-06    0.0066       9      42 ..      61      99 ..      56     122 .. 0.77
   2 ?    0.7   0.1      0.14   6.3e+02       4      42 ..     149     192 ..     147     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.5e-06
                           DUF4129  9 Laer.gldrrpgeTprEyarrv.......riapspaaalaal 42
                                       a++ gl+r+++e ++E+ar +       r   s + a+aal
  gi|557693724|ref|YP_008796778.1| 61 IADKiGLPRQAAEGAGELARKAvsskvvkR---SRRPAAAAL 99
                                      68999*****************99885542...333344443 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
                           DUF4129   4 allraLaer.gldrrpgeTprEyarrv....riapspaaalaal 42 
                                       al + L++   l++ ++ T+  + + +     i++   aa+ a+
  gi|557693724|ref|YP_008796778.1| 149 ALIDKLTRTlELPPTTANTACRIYQSAaslgKISGRKPAAISAA 192
                                       77888889989999999999888877766665555555555543 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.5e-05       0.2      37      93 ..     150     206 ..     143     224 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.5e-05
                                       HHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS-- CS
                          Cyclin_N  37 wlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeispp 93 
                                        + ++++ ++l p t+ +a +++    s  +++ +k   + a++++lA++ e ++ p
  gi|557693724|ref|YP_008796778.1| 150 LIDKLTRTLELPPTTANTACRIYQSAASLGKISGRKPAAISAAAVYLACRREGVKKP 206
                                       67789999*****************************************99877644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1971.72
//
Query:       gi|557693725|ref|YP_008796779.1|  [L=82]
Description: RNA-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   41.1   0.0    1.5e-10   41.1   0.0    1.0  1  Gar1      Gar1/Naf1 RNA binding region
  ------ inclusion threshold ------
      0.017   15.2   0.1      0.023   14.7   0.1    1.4  1  PRC       PRC-barrel domain


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 !   41.1   0.0   1.7e-14   1.5e-10      19      95 ..       9      75 ..       2      82 .] 0.88

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 1.7e-14
                                      -EEEEEEEEEEETTEEEEEE---S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE--GGHHHHHHHTTTTS CS
                              Gar1 19 evleiGtvssivenevviksttsgekkvldfnsilflenktqiGkVdEifGpvnepyysVklnsseeikaksfkvgd 95
                                      +++ +G+v +   + +vi++       v+  +  +++ +++++G V  ifGpv epy++Vk+  + e+ +     g+
  gi|557693725|ref|YP_008796779.1|  9 RLKLLGEVLHSRRDYLVIRAY-----TVPRLGDKVYNGKGREVGHVSNIFGPVAEPYVAVKPAAEAEVVE-----GE 75
                                      67899***************9.....69***********************************7776665.....44 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.6e-06     0.023      11      30 ..      35      53 ..      34      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-06
                                      T-EEEETTSSEEEEEEEEEE CS
                               PRC 11 GkeVytedGeklGkVkDvvi 30
                                      G +Vy+++G+++G+V+++ +
  gi|557693725|ref|YP_008796779.1| 35 GDKVYNGKGREVGHVSNI-F 53
                                      889**************9.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 616.75
//
Query:       gi|557693726|ref|YP_008796780.1|  [L=95]
Description: signal recognition particle subunit SRP19 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-20   74.2   0.1    1.5e-20   73.9   0.1    1.1  1  SRP19     SRP19 protein


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 !   73.9   0.1   8.2e-25   1.5e-20       1      94 []       8      93 ..       8      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 8.2e-25
                                      EEECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCC.EEEEEC-..........SS CS
                             SRP19  1 viYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanp.GrVrvklkedgkevnekik 78
                                      +++PvY+dsk +rk+GRrv++ lav++P+a+++a a+++lg+ev+ + + +yPr+w ++ G+V vk +         + 
  gi|557693726|ref|YP_008796780.1|  8 ILWPVYFDSKSSRKQGRRVSRGLAVQRPSADDLAAACRRLGYEVEKN-DAAYPRRWSRRtGYVVVKPR--------PKI 77
                                      69******************************************977.********9777******85........345 PP

                                      -CHHHHHHHHHHHHHH CS
                             SRP19 79 nkkellkkiaellkel 94
                                      +k+  lk++ae+l+++
  gi|557693726|ref|YP_008796780.1| 78 SKNMFLKMVAEELRKH 93
                                      8999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 715.20
//
Query:       gi|557693727|ref|YP_008796781.1|  [L=129]
Description: small subunit ribosomal protein S8e [Candidatus Caldiarchaeum subterraneum]
Scores for 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   93.7   2.1    1.3e-26   93.4   2.1    1.2  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 !   93.4   2.1   7.2e-31   1.3e-26       5     137 .]       5     124 ..       1     124 [. 0.96

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 7.2e-31
                                       XXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEEE CS
                     Ribosomal_S8e   5 rdskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlgV 81 
                                       ++  hkrk+tG+ka++ r +rk e g + +   lg+++v + rv gG+ k + l +k+anv+     v+k+l+Il+V
  gi|557693727|ref|YP_008796781.1|   5 HSDLHKRKKTGAKAHPARGRRKRERGGEINLVSLGEQKVVTRRVSGGNLKAAVLSTKTANVAV--GPVVKRLEILRV 79 
                                       5668**********************************************************9..6799******** PP

                                       ECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                     Ribosomal_S8e  82 kknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                       + npsn++y r++v+tKg+ ie++ +            A+vts PgqdG vnavl+
  gi|557693727|ref|YP_008796781.1|  80 VSNPSNRDYDRRKVITKGTLIETSEGL-----------ARVTSSPGQDGTVNAVLV 124
                                       ***********************9998...........****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 964.30
//
Query:       gi|557693728|ref|YP_008796782.1|  [L=198]
Description: segregation and condensation protein B [Candidatus Caldiarchaeum subterraneum]
Scores for 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-34  117.3   0.1    5.8e-34  117.0   0.1    1.1  1  SMC_ScpB  Segregation and condensation complex subunit ScpB
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.19   11.9   0.0    1.4  1  NitrOD5   Nitrosopumilus output domain 5
       0.11   12.6   0.0       0.33   11.0   0.0    1.9  2  HTH_20    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> 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 !  117.0   0.1   9.6e-38   5.8e-34       3     153 ..       2     145 ..       1     153 [. 0.96

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 9.6e-38
                          SMC_ScpB   3 iEAiLfvageplsleeLakilels.keeveealeeLkeeyeeedrglelvev.aggyrlvtkpelaevvkklvkekk 77 
                                        EA+Lf++++p+++++L+++l+++ +e+v++++e Lk+ey  ++r++e+ve+ +g+y ++++p+la  vkk++++  
  gi|557693728|ref|YP_008796782.1|   2 AEALLFASDKPVDIKTLQRALKTRsPEKVRKIVETLKNEY--SGRAVEIVELdGGRYYMRLRPDLAAHVKKYTRR-- 74 
                                       69*******************9778***************..**********5677******************9.. PP

                          SMC_ScpB  78 ktrLsqaaletLaiIaykqpvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglks 153
                                        + L +  l+tLa Iay qp+  + +++iRG++s+++++ L+ergl+e+++    +gr+ +++t++ F + fg+++
  gi|557693728|ref|YP_008796782.1|  75 -RMLPHGVLKTLATIAYYQPIPLSTLAAIRGKDSYRQIKILQERGLVESEK----KGRTSVLRTSRLFADFFGVEN 145
                                       .9***********************************************99....9******************97 PP

>> NitrOD5  Nitrosopumilus output domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.2e-05      0.19      42      82 ..      24      64 ..      13      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                           NitrOD5 42 yedPkkFkeaveeLFGeysarllellliselkellglkedv 82
                                       + P+k ++ ve L  eys+r +e++ ++  + ++ l++d 
  gi|557693728|ref|YP_008796782.1| 24 TRSPEKVRKIVETLKNEYSGRAVEIVELDGGRYYMRLRPDL 64
                                      689*********************99998888888777775 PP

>> HTH_20  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       0.5     3e+03      20      40 ..       8      28 ..       3      38 .. 0.68
   2 ?   11.0   0.0   5.5e-05      0.33      29      61 .]      98     127 ..      72     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.5
                                      STCTTB-HHHHHHHHTS-HHH CS
                            HTH_20 20 araegltaselaerldlsknt 40
                                      a+++++  + l ++l ++  +
  gi|557693728|ref|YP_008796782.1|  8 ASDKPVDIKTLQRALKTRSPE 28
                                      778888888888888666555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.5e-05
                                       HHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  29 elaerldlskntlsyHLrvLeeagLvevvregr 61 
                                        la+   ++ +  ++++++L+e gLve+++ gr
  gi|557693728|ref|YP_008796782.1|  98 TLAA---IRGKDSYRQIKILQERGLVESEKKGR 127
                                       4444...67777899**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1413.54
//
Query:       gi|557693729|ref|YP_008796783.1|  [L=229]
Description: segregation and condensation protein A [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-07   30.9   0.3      0.005   16.8   0.0    2.1  2  SMC_ScpA    Segregation and condensation protein ScpA
    0.00021   20.5   0.0    0.00049   19.3   0.0    1.6  1  Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
  ------ inclusion threshold ------
       0.18   12.3   0.0       0.41   11.2   0.0    1.6  1  SANTA       SANTA (SANT Associated)


Domain annotation for each model (and alignments):
>> SMC_ScpA  Segregation and condensation protein ScpA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   8.3e-07     0.005       6      62 ..      27      82 ..      23      89 .. 0.93
   2 !   12.0   0.6   2.5e-05      0.15     132     238 ..     110     213 ..      97     215 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.3e-07
                                      HHHHTSSSSXXXXHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHSXXXXXXX CS
                          SMC_ScpA  6 eldvtdvavakvtdqflayiktllnkleleesteylviastlvelKaasLlpleqve 62
                                      ++ v++v + +v ++f + +++     + ++ + +   a+ + ++K+++Ll+++q +
  gi|557693729|ref|YP_008796783.1| 27 RVKVWEVRLSEVLTEFAQVLRIQ-GYIDFNICGIAVHSAAIIHRIKSEKLLQADQPP 82
                                      6789******************9.89***************************9865 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.5e-05
                                       XXXXXXXXXXXX...XXXXXXXXXXXX...HHHHHHHHHHHH...............HHHTS-EEGGGSSTT...-- CS
                          SMC_ScpA 132 fklieafnkllk...rakivalaekqiseleisieeqleellaqleqflqarlkevLldlrswvdlseLladnkled 205
                                        +++ a++k l    r k++a  + qi e ++  +e   ++  +l++f +   +  + ++r  + +seL++      
  gi|557693729|ref|YP_008796783.1| 110 QEIVTALQKALSqsgRSKTEAAPP-QIMENRLILNEFIVKIEEELDKFIEKLRE--IFSVRTSITFSELVEG---MP 180
                                       444455555443122455666656.68777777777777777777777754333..4678888*********...67 PP

                                       HHHHHHHHHHHHHHHHTT-EEEEESSTTS-EEE CS
                          SMC_ScpA 206 kkelvgvFlAlLeLiknqavaleQeeflddLqv 238
                                       + e   +F+ lL     + v l Q++ ++dL +
  gi|557693729|ref|YP_008796783.1| 181 RLEAAKTFILLLFAAARRYVLLLQADEFSDLVI 213
                                       7788999***********************987 PP

>> Rad21_Rec8  Conserved region of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   8.1e-08   0.00049       5      50 ..     169     214 ..     166     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.1e-08
                                       HTT----------HHHHHHHHHHHHHHHHTSEEEEESSTT--EEEE CS
                        Rad21_Rec8   5 kdslsllpagktRkeAArlFyelLvLatkgvIkvkQeaPYgdIlit 50 
                                       ++ +s+l +g++R eAA++F  lL  a ++++ + Q+  ++d++i 
  gi|557693729|ref|YP_008796783.1| 169 SITFSELVEGMPRLEAAKTFILLLFAAARRYVLLLQADEFSDLVIL 214
                                       66789*********************************9**99985 PP

>> SANTA  SANTA (SANT Associated)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   6.9e-05      0.41       5      51 ..      30      79 ..      27      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.9e-05
                             SANTA  5 dWwlkkvekete..k.laveGfrkdseeqqvfhSsaIvkrvdsttletas 51
                                       W ++ +e  te  + l+++G++  +     +hS+aI +r++s +l  a+
  gi|557693729|ref|YP_008796783.1| 30 VWEVRLSEVLTEfaQvLRIQGYIDFNICGIAVHSAAIIHRIKSEKLLQAD 79
                                      5777776665556666******888888889************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); 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:                         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: 00:00:00.42
# Mc/sec: 1643.27
//
Query:       gi|557693730|ref|YP_008796784.1|  [L=1119]
Description: chromosome segregation protein SMC [Candidatus Caldiarchaeum subterraneum]
Scores for 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-60  202.2   9.4      3e-59  200.1   9.4    2.2  1  SMC_N            RecF/RecN/SMC N terminal domain
    8.9e-12   45.4  14.2    2.3e-06   27.6   0.1    4.8  5  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.2e-06   28.2   0.0    2.8e-05   23.8   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.028   14.5  72.9      0.031   14.3   5.6    8.1  9  DUF1664          Protein of unknown function (DUF1664)
      0.077   12.9   1.0       0.27   11.2   1.0    1.9  1  DNAPolymera_Pol  DNA polymerase catalytic subunit Pol
       0.34   11.4   0.0       0.34   11.4   0.0    7.2  5  ABC_tran         ABC transporter
       0.56   10.5   0.0       0.56   10.5   0.0    6.1  7  AAA_22           AAA domain
        1.3    9.5 128.8    8.7e+02    0.3  67.8    7.4  3  AAA_23           AAA domain


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 !  200.1   9.4   1.4e-62     3e-59       6     216 ..       2    1103 ..       1    1106 [. 1.00

  Alignments for each domain:
  == domain 1  score: 200.1 bits;  conditional E-value: 1.4e-62
                                        EEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N    6 eienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeve 80  
                                         i++Fks+ +k++++++ +++ +i+GpNG GKs +ldA++F LGe sa++lr +++s+l+h+ ++k    +a v+
  gi|557693730|ref|YP_008796784.1|    2 AITGFKSFGNKRTVIKLPPGLVVITGPNGGGKSTVLDAVKFALGELSAHNLRVDRFSKLLHE-SSKGTDAQALVT 75  
                                        689**********************************************************9.89999999**** PP

                                        EEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.................... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                             SMC_N   81 itfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.................... 135 
                                        +t+dn+d++++i++eev+isrr++ +gesey++n++ v+++e+  +l+ a+i+++                    
  gi|557693730|ref|YP_008796784.1|   76 LTLDNSDRSIPIDSEEVVISRRLYATGESEYMLNNRIVSRNELLTILSAANIKPDglnlvtqgsvvgiaemtsre 150 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|557693730|ref|YP_008796784.1|  151 lrevledaagisgykkrrdeaykeleiaqknidiakaatsevrsrvkqlelernqllrktlaekilntlkslsli 225 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|557693730|ref|YP_008796784.1|  226 neynshaqalreldaraaellnklaekqaeaeqvrarvsalkneveelerrqrevatevskidravlsleteksr 300 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|557693730|ref|YP_008796784.1|  301 kiaeknsaenalkqldlqrrsletrvakwrerqqqlkeesekktqqvenlreqwavreaeyneskklleelqkev 375 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|557693730|ref|YP_008796784.1|  376 deaenryaakveelrflklsddgksllldniqkqltrkqqekeeaekrvaetrnslsekteqltrltesmekltq 450 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|557693730|ref|YP_008796784.1|  451 lletqtntaknirrelesrrekiasidkllektrllkaagqqlretlqaavkedkktsglktvrevfgekltgih 525 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|557693730|ref|YP_008796784.1|  526 ravlgdwlnavyvadaeagfslareaaekkiplkivaesleldslvkalthgagfravdsvkqlqpgdryvatmd 600 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|557693730|ref|YP_008796784.1|  601 gvyvdepgiisvagemsetvaaervnrsmerletieakllnareafdkevklaekrlreteaeaeetrrqlnika 675 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|557693730|ref|YP_008796784.1|  676 lektrletelnnlsksaenslqrlkqleeevarlvqekekltqllsdktdeitalthlrqsvaekkqvlrkaeed 750 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|557693730|ref|YP_008796784.1|  751 mrrksqessttyrayvnaererdrilielknieeslagaekefeqialrerelateleqirgmieeldqkiveas 825 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|557693730|ref|YP_008796784.1|  826 elkekmdnelsqltgvlaeksrevkqleqhlttllnevsalekennnlaiervriettlksigerlqsftsaeea 900 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|557693730|ref|YP_008796784.1|  901 etslpldlipqletevaeipvvnqlaamqydgivenyrlrstrinelemerkrildliesinreevdafrraldr 975 
                                        *************************************************************************** PP

                                        ...............................................CS-HHHHHHHHHHHHHHHHCCS--SEEE CS
                                        ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  136 ...............................................lLSgGektLvalaLlfAiqkvkpaplyl 163 
                                                                                       ++SgGek+++a+aL++A+q   pa +y+
  gi|557693730|ref|YP_008796784.1|  976 vsdsfsfyfnqltggegflklenpddplnsgvemlvkfvgkqtrstvSISGGEKSVSAVALILALQDLTPAQFYM 1050
                                        *************************************************************************** PP

                                        ECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEEEET CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  164 lDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtkven 216 
                                        +Deida+LD  +vk++++llk+ s++ Q+i+i+l++ + e+ad+l+gv+++++
  gi|557693730|ref|YP_008796784.1| 1051 FDEIDAHLDVVYVKNLVNLLKKMSTKKQIIIITLKDIIAEQADALYGVYMANE 1103
                                        **************************************************554 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 !   21.3   0.0   8.9e-08    0.0002       1      26 [.      22      55 ..      22     101 .. 0.74
   2 ?   -1.2   0.1      0.62   1.4e+03     122     165 ..     167     218 ..     160     285 .. 0.62
   3 ?   -0.2   1.6       0.3   6.8e+02      95     204 ..     327     411 ..     304     441 .. 0.57
   4 ?    1.4   0.1       0.1   2.3e+02      86     190 ..     644     752 ..     569     783 .. 0.72
   5 !   27.6   0.1     1e-09   2.3e-06     124     296 ..     935    1083 ..     917    1083 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.9e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl........d 26
                                      l v++GpNg GKS++Lda +++ +         d
  gi|557693730|ref|YP_008796784.1| 22 LVVITGPNGGGKSTVLDAVKFALGElsahnlrvD 55
                                      579******************9875555554432 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.62
                            AAA_21 122 vsvfslkelsvsepndlqfgkaltditsrawsllllldglrke........r 165
                                       ++++  kel++++ n+++ ++a+ +++sr  +l+l+ + l+ +        +
  gi|557693730|ref|YP_008796784.1| 167 RRDEAYKELEIAQKNIDIAKAATSEVRSRVKQLELERNQLLRKtlaekilnT 218
                                       5666777777888888888888888888877777777776644443333322 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.3
                            AAA_21  95 esgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllni 171
                                        ++                          +++++ ++ se  ++q + ++     r +++++++  l + ++ + ++
  gi|557693730|ref|YP_008796784.1| 327 AKWR-------------------------ERQQQLKEESEKKTQQVENLREQWAVREAEYNESKKLLEELQKEVDEA 378
                                       3444.........................444444444444444444444444444444444444444445555555 PP

                            AAA_21 172 fadyfgfakekrllqrlvrslklveielsdlge 204
                                        ++y+ + +e+r+l+   ++ +l  +++++ + 
  gi|557693730|ref|YP_008796784.1| 379 ENRYAAKVEELRFLKLSDDGKSLLLDNIQKQLT 411
                                       566666666666666666555555555555544 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.1
                            AAA_21  86 klssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglr 162
                                         +++e +l    l+  +++ ee +   + +   +++ + +l +ls+s +n+lq+ k+l + ++r+++ ++ l  l+
  gi|557693730|ref|YP_008796784.1| 644 EAFDKEVKLAEKRLRETEAEAEETRRQLNIKALEKTRLETELNNLSKSAENSLQRLKQLEEEVARLVQEKEKLTQLL 720
                                       36777777888888888899999999999999999999999999999999999999999999999998888887776 PP

                            AAA_21 163 ke....rigllnifadyfgfakekrllqrlvr 190
                                               +l ++ ++ + ++ ++r +++ +r
  gi|557693730|ref|YP_008796784.1| 721 SDktdeITALTHLRQSVAEKKQVLRKAEEDMR 752
                                       65666655555555555555555555555555 PP

  == domain 5  score: 27.6 bits;  conditional E-value: 1e-09
                            AAA_21  124 vfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveie 198 
                                        ++++  ++++++ ++++++ l++i s +++  + ++       ++ + f  yf++   ++ + +l+++ ++ ++ 
  gi|557693730|ref|YP_008796784.1|  935 ENYRLRSTRINELEMERKRILDLIESINREEVDAFRRA---LDRVSDSFSFYFNQLTGGEGFLKLENPDDPLNSG 1006
                                        55555555555555555555555555555555544444...8899999999999999999999999999999999 PP

                            AAA_21  199 lsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkg.sllliDEpEngLHP 272 
                                        +++l +++ +++++ + +                     S G k++ a++++l+ ++  +  ++ +DE++++L+ 
  gi|557693730|ref|YP_008796784.1| 1007 VEMLVKFVGKQTRSTVSI---------------------SGGEKSVSAVALILALQDLTPaQFYMFDEIDAHLDV 1060
                                        999999999999999887.....................*******866666666666666************** PP

                            AAA_21  273 kllrrllellkelsrngaQviltT 296 
                                          ++ l+ llk+ s+ + Q+i+ T
  gi|557693730|ref|YP_008796784.1| 1061 VYVKNLVNLLKKMST-KKQIIIIT 1083
                                        **********99999.9***9988 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 !   23.8   0.0   1.2e-08   2.8e-05      16      46 ..      15      44 ..       6      51 .. 0.79
   2 ?    1.3   0.0      0.13     3e+02      32      50 ..     396     414 ..     394     418 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.2e-08
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      +i++   g +++tGp+G GKST+lDA+++ L
  gi|557693730|ref|YP_008796784.1| 15 VIKLP-PGLVVITGPNGGGKSTVLDAVKFAL 44
                                      44554.4579****************99876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.13
                            AAA_29  32 GsGKSTllDAiqalLvpak 50 
                                         GKS llD iq  L+ ++
  gi|557693730|ref|YP_008796784.1| 396 DDGKSLLLDNIQKQLTRKQ 414
                                       56*********98887665 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3      0.48   1.1e+03      62      94 ..     169     201 ..     135     225 .. 0.65
   2 ?   13.6   4.0   2.3e-05     0.052      52     122 ..     226     296 ..     207     298 .. 0.85
   3 ?    8.3   5.5     0.001       2.3      51     122 ..     309     380 ..     303     382 .. 0.93
   4 ?    4.8   6.2     0.013        28      51     102 ..     429     479 ..     400     500 .. 0.55
   5 ?    5.7   4.7    0.0062        14      45     122 ..     627     704 ..     617     706 .. 0.90
   6 ?    0.1   4.3      0.34   7.6e+02      48     103 ..     700     755 ..     690     768 .. 0.73
   7 ?   -0.8   3.0      0.64   1.4e+03      41     118 ..     722     794 ..     716     811 .. 0.61
   8 ?   14.3   5.6   1.4e-05     0.031      39     122 ..     782     868 ..     772     870 .. 0.86
   9 ?   -1.3   0.0      0.92   2.1e+03      61     102 ..     937     979 ..     919     989 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.48
                           DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevre 94 
                                       ++  ++++  +k++d  k++++e+++ v++++ 
  gi|557693730|ref|YP_008796784.1| 169 DEAYKELEIAQKNIDIAKAATSEVRSRVKQLEL 201
                                       344444444555555555555555555555443 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.3e-05
                           DUF1664  52 qvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       + ++s a++ r+L +r +++ +kl e ++ ++++++ v++++++++e+++  ++v + v++++  + ++e+
  gi|557693730|ref|YP_008796784.1| 226 NEYNSHAQALRELDARAAELLNKLAEKQAEAEQVRARVSALKNEVEELERRQREVATEVSKIDRAVLSLET 296
                                       4457888999*****************************************************99999986 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.001
                           DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                       e+  ++l  ++r L+ r+++  +++++ ke s++ +++v+++re+ +  + + ++ k++ e+l++++++ e+
  gi|557693730|ref|YP_008796784.1| 309 ENALKQLDLQRRSLETRVAKWRERQQQLKEESEKKTQQVENLREQWAVREAEYNESKKLLEELQKEVDEAEN 380
                                       677889999*********************************************************998875 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.013
                           DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseiged 102
                                       +++se+  ++  +L++ ++++ + l+ q++++k+i++e+++ re++++i++ 
  gi|557693730|ref|YP_008796784.1| 429 NSLSEKT-EQLTRLTESMEKLTQLLETQTNTAKNIRRELESRREKIASIDKL 479
                                       2222221.22234555555555555555555555555555555555555543 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.0062
                           DUF1664  45 svskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       +  ++le++ ++l ++++ + ++++  +k+l e+++ ++e++++++    + ++++++++++++  e+  ++l+++e
  gi|557693730|ref|YP_008796784.1| 627 RSMERLETIEAKLLNAREAFDKEVKLAEKRLRETEAEAEETRRQLNIKALEKTRLETELNNLSKSAENSLQRLKQLE 703
                                       4456789999************************************9999999**********99999999999998 PP

                           DUF1664 122 e 122
                                       e
  gi|557693730|ref|YP_008796784.1| 704 E 704
                                       6 PP

  == domain 6  score: 0.1 bits;  conditional E-value: 0.34
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedv 103
                                       kqle+  + l + k++L++ +    +++ + +++ ++++e+ + +r+  +++++++
  gi|557693730|ref|YP_008796784.1| 700 KQLEEEVARLVQEKEKLTQLLSDKTDEITALTHLRQSVAEKKQVLRKAEEDMRRKS 755
                                       67888888888888888888887777777777777777777666666666666554 PP

  == domain 7  score: -0.8 bits;  conditional E-value: 0.64
                           DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                       d  ++++  l+++ +s+a+ k+ L +  + + +k +e++ + ++      +++++ ++i  ++++++e   g e++ 
  gi|557693730|ref|YP_008796784.1| 722 DKTDEIT-ALTHLRQSVAEKKQVLRKAEEDMRRKSQESSTTYRA----YVNAERERDRILIELKNIEESLAGAEKEF 793
                                       5555554.589999999999999999988888887776655433....22333444444444444444444444443 PP

                           DUF1664 118 e 118
                                       e
  gi|557693730|ref|YP_008796784.1| 794 E 794
                                       3 PP

  == domain 8  score: 14.3 bits;  conditional E-value: 1.4e-05
                           DUF1664  39 lsdavesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                       +++ ++   k+ eq+     +la+  +++   i+++d+k+ e +e+++++++e++++ + l+e +++v+++++  ++
  gi|557693730|ref|YP_008796784.1| 782 IEESLAGAEKEFEQIAlreRELATELEQIRGMIEELDQKIVEASELKEKMDNELSQLTGVLAEKSREVKQLEQHLTT 858
                                       5555555566666665444788999999999********************************************** PP

                           DUF1664 113 leskleriee 122
                                       l ++++ +e+
  gi|557693730|ref|YP_008796784.1| 859 LLNEVSALEK 868
                                       *****99997 PP

  == domain 9  score: -1.3 bits;  conditional E-value: 0.92
                           DUF1664  61 krhLssridrvdkkldeqkeiskeik.eevtevredlseiged 102
                                        r  s ri++++ + +   +++++i+ eev++ r+ l+++++ 
  gi|557693730|ref|YP_008796784.1| 937 YRLRSTRINELEMERKRILDLIESINrEEVDAFRRALDRVSDS 979
                                       5555789999999999999999998626799999998888776 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 ?   11.2   1.0   0.00012      0.27      19      30 ..     662     673 ..     660     675 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                   DNAPolymera_Pol  19 ieaEETRRkLhr 30 
                                       +eaEETRR L++
  gi|557693730|ref|YP_008796784.1| 662 AEAEETRRQLNI 673
                                       79*********8 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.34      13      31 ..      22      40 ..      15      66 .. 0.91
   2 ?   -9.1  11.7         8   1.8e+04      55      64 ..     257     266 ..     164     389 .. 0.60
   3 ?   -0.1   6.0      0.53   1.2e+03      23     102 ..     398     493 ..     394     509 .. 0.59
   4 ?    5.3   0.8     0.011        26      33     111 ..     601     690 ..     595     697 .. 0.63
   5 ?   -3.3   6.1       5.4   1.2e+04      98      98 ..     893     893 ..     690    1056 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                      EEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkll 31
                                      +v+i+G+nG GKSt+l ++
  gi|557693730|ref|YP_008796784.1| 22 LVVITGPNGGGKSTVLDAV 40
                                      689************9875 PP

  == domain 2  score: -9.1 bits;  conditional E-value: 8
                                       HHCCHCEEEE CS
                                       xxxxxxxxxx RF
                          ABC_tran  55 eslrkeigvl 64 
                                       e++r++++ l
  gi|557693730|ref|YP_008796784.1| 257 EQVRARVSAL 266
                                       2222223222 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.53
                                       SHHHHHHHHTTSS--SEEEEEETTCEGGG.........B-HHHCCHCEEEE-SS--S-TTSBHHHH.........HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xx RF
                          ABC_tran  23 GKStLlkllagllkpteGeilldgkdlke.........qeleslrkeigvlpqepqlfpeltvren.........es 81 
                                       GKS Ll  + ++l+ ++ e +  +k + e         ++l++l ++++ l+q  + + ++  ++n         e+
  gi|557693730|ref|YP_008796784.1| 398 GKSLLLDNIQKQLTRKQQEKEEAEKRVAEtrnslsektEQLTRLTESMEKLTQLLETQTNT--AKNirrelesrrEK 472
                                       9*******99998874444322233333335455555666666666666666663333333..23345557544433 PP

                                       HTCHHHHHHHSTTGGTTCBGE CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  82 deeiekalsklglkelkdtvv 102
                                        + i+k+l+k +l + + + +
  gi|557693730|ref|YP_008796784.1| 473 IASIDKLLEKTRLLKAAGQQL 493
                                       333888888877777555554 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.011
                                       TSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTSBHHHH..........HHHTCHHHHHHHSTTGG CS
                                       xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxx RF
                          ABC_tran  33 gllkpteGeilldgkdlke...qeleslrkeigvlpqepqlfpeltvren..........esdeeiekalsklglke 96 
                                       g + ++ G i + g+ +++   ++ +++ +++++++ +  l +  ++ ++          e ++e+e+ +++l++k 
  gi|557693730|ref|YP_008796784.1| 601 GVYVDEPGIISVAGEMSETvaaERVNRSMERLETIEAK--LLNAREAFDKevklaekrlrETEAEAEETRRQLNIKA 675
                                       55666677777776666664332222222223333322..2222222222455555599999999************ PP

                                       TTCBGESTTSGGS-H CS
                                       xxxxxxxxxxxxxxx RF
                          ABC_tran  97 lkdtvvksspssLSg 111
                                       l++t+++++ ++LS+
  gi|557693730|ref|YP_008796784.1| 676 LEKTRLETELNNLSK 690
                                       ******9999***97 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 5.4
                                       T CS
                                       x RF
                          ABC_tran  98 k 98 
                                        
  gi|557693730|ref|YP_008796784.1| 893 S 893
                                       0 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00025      0.56       6      38 ..      21      55 ..      17     111 .. 0.74
   2 ?   -2.4   1.1       2.3   5.2e+03      80      99 ..     209     227 ..     146     288 .. 0.61
   3 ?    0.3   0.8      0.35   7.9e+02      30      78 ..     331     389 ..     321     397 .. 0.62
   4 ?    1.3   5.9      0.17   3.9e+02      17      87 ..     398     494 ..     395     503 .. 0.54
   5 ?   -2.3   1.4       2.2     5e+03      48      91 ..     663     715 ..     627     764 .. 0.60
   6 ?   -1.4   0.9       1.1   2.6e+03      19     101 ..     731     818 ..     730     860 .. 0.54
   7 ?    0.3   0.0      0.35   7.9e+02      91     124 ..    1045    1080 ..    1001    1084 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaee..e 38
                                      g++v+tG+ G GK+t+l  ++  l e ++++    
  gi|557693730|ref|YP_008796784.1| 21 GLVVITGPNGGGKSTVLDAVKFALGELSAHNLrvD 55
                                      789**************999988876666655442 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                            AAA_22  80 ealeqalraravielliiDE 99 
                                       ++l++ + ++ + +l +i E
  gi|557693730|ref|YP_008796784.1| 209 KTLAEKILNTLK-SLSLINE 227
                                       444444443333.3444443 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.35
                            AAA_22  30 deeakaee......erpevv....fvtlpsstsskdllrellralglelkaerlsseel 78 
                                       +++++ +e      +++e +     v  ++ ++sk+ll+el +++++  +++ ++ eel
  gi|557693730|ref|YP_008796784.1| 331 ERQQQLKEesekktQQVENLreqwAVREAEYNESKKLLEELQKEVDEAENRYAAKVEEL 389
                                       33333333344355333333555589999999999999999999998877766665555 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.17
                            AAA_22  17 GKTtllrrlleqldeeakaee..............erpevvfvtlpsstsskdllrellralglelka......... 70 
                                       GK++ll ++++ql++ ++ +e              e+ e++       t +++ +++l + l+ ++++         
  gi|557693730|ref|YP_008796784.1| 398 GKSLLLDNIQKQLTRKQQEKEeaekrvaetrnslsEKTEQL-------TRLTESMEKLTQLLETQTNTaknirrele 467
                                       9************8776666696666654444444222222.......23333333333333333333333333333 PP

                            AAA_22  71 ..........erlsseellealeqalr 87 
                                                 + l++ +ll+a  q+lr
  gi|557693730|ref|YP_008796784.1| 468 srrekiasidKLLEKTRLLKAAGQQLR 494
                                       333337777766666666666655555 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 2.2
                            AAA_22  48 psstsskdllrellralglelka.........erlsseellealeqalrarav 91 
                                        +++++++l  + l+++ le++          + +++++l e +++ ++++ +
  gi|557693730|ref|YP_008796784.1| 663 EAEETRRQLNIKALEKTRLETELnnlsksaenSLQRLKQLEEEVARLVQEKEK 715
                                       44445555555555444443333444444444444444444555555544444 PP

  == domain 6  score: -1.4 bits;  conditional E-value: 1.1
                            AAA_22  19 Ttllrrlleqldeeakaee.......erpevvfvtlpsstsskdl...lrellralglelkaerlsseell.ealeq 84 
                                       T+l + ++e+++   kaee       e++++++ +++++ +++ +   l+++ + l    k+   ++ +l+ + l+ 
  gi|557693730|ref|YP_008796784.1| 731 THLRQSVAEKKQVLRKAEEdmrrksqESSTTYRAYVNAERERDRIlieLKNIEESLAGAEKE--FEQIALReRELAT 805
                                       56666777777666667667777776666666555555554444400444444444433333..4444444444444 PP

                            AAA_22  85 alraravielliiDEaq 101
                                        l++ +     +i+E +
  gi|557693730|ref|YP_008796784.1| 806 ELEQIRG----MIEELD 818
                                       4444444....444444 PP

  == domain 7  score: 0.3 bits;  conditional E-value: 0.35
                            AAA_22   91 vielliiDEaqh.lr...seealeeLrsllnlsrkgvq 124 
                                          ++ + DE++  l+    +++++ L++++   +k++ 
  gi|557693730|ref|YP_008796784.1| 1045 PAQFYMFDEIDAhLDvvyVKNLVNLLKKMST--KKQII 1080
                                        368999*****99965433888888888877..66655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3  67.8      0.39   8.7e+02       4     194 ..       3     349 ..       1     500 [. 0.63
   2 ?  -28.3  50.2         8   1.8e+04     106     197 ..     670     861 ..     613     892 .. 0.46
   3 ?   -1.6   0.2       1.5   3.3e+03      87     110 ..     936     959 ..     857    1083 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.39
                            AAA_23   4 ienfrsf..rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvelt 78 
                                       i +f+sf  +++ i + +gl++ItGpNG GK+T+ldA+k+aL++ ++ + r ++  f k   e +++++ +a v+lt
  gi|557693730|ref|YP_008796784.1|   3 ITGFKSFgnKRTVIKLPPGLVVITGPNGGGKSTVLDAVKFALGELSAHNLRVDR--FSKLLHESSKGTDAQALVTLT 77 
                                       88*****655567*******************************8866655443..555555555566767779999 PP

                            AAA_23  79 fenkdgry..................................................................... 86 
                                       + n d+                                                                       
  gi|557693730|ref|YP_008796784.1|  78 LDNSDRSIpidseevvisrrlyatgeseymlnnrivsrnelltilsaanikpdglnlvtqgsvvgiaemtsrelrev 154
                                       97766655999999999999999999999999999999999999999999999999999999999999999999888 PP

                            AAA_23  87 ....................................................trsiererelskkkgkttkkaklel 111
                                                                                                                    
  gi|557693730|ref|YP_008796784.1| 155 ledaagisgykkrrdeaykeleiaqknidiakaatsevrsrvkqlelernqlL------------------------ 207
                                       88888888877776555555555544333333333333222221111111110........................ PP

                            AAA_23 112 leideleqfisellgskkiilnlilflgqer....................feefelkdkke............... 153
                                             ++++ e++ ++ ++l   +++ + +                    +         e               
  gi|557693730|ref|YP_008796784.1| 208 ------RKTLAEKILNTLKSL---SLINEYNshaqalreldaraaellnklA---------Ekqaeaeqvrarvsal 266
                                       ......111111111111111...1111111111222344443332222210.........0122233333433333 PP

                            AAA_23 154 .....................................rleelekeleeledekkllekl.....eqekekekeleel 188
                                                                            + +++e++l++l  +++ le++     e++++ ++e e++
  gi|557693730|ref|YP_008796784.1| 267 kneveelerrqrevatevskidravlsleteksrkiaEKNSAENALKQLDLQRRSLETRvakwrERQQQLKEESEKK 343
                                       33333444444445555555555444444444444442222233333333233333322444443333333333333 PP

                            AAA_23 189 eeelee 194
                                        ++ e+
  gi|557693730|ref|YP_008796784.1| 344 TQQVEN 349
                                       333333 PP

  == domain 2  score: -28.3 bits;  conditional E-value: 8
                            AAA_23 106 kaklelleideleqfisellgskkiilnlilflgqerfeefelkdkke............................. 153
                                       + + + le++ le ++++l +s +++l+++  l +e +   ++k+k+                              
  gi|557693730|ref|YP_008796784.1| 670 QLNIKALEKTRLETELNNLSKSAENSLQRLKQLEEEVARLVQEKEKLTqllsdktdeitalthlrqsvaekkqvlrk 746
                                       22222222222333333322222222222222222221111111111111111111222111111111111112222 PP

                            AAA_23 154 ..............................................................rleelekeleelede 168
                                                                                                     +++ +++el+++  e
  gi|557693730|ref|YP_008796784.1| 747 aeedmrrksqessttyrayvnaererdrilielknieeslagaekefeqialrerelateleQIRGMIEELDQKIVE 823
                                       22233333345566666666666666666665555555555555555555553333333333444444444444444 PP

                            AAA_23 169 kkllekl.......eqekekek........eleeleeeleeilk 197
                                       +++l+++       +               e ++le+ l+++l+
  gi|557693730|ref|YP_008796784.1| 824 ASELKEKmdnelsqL------TgvlaeksrEVKQLEQHLTTLLN 861
                                       444444443333330......13333333355555555555555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.5
                            AAA_23  87 trsiererelskkkgkttkkakle 110
                                       +++++ +r +  ++++++  +  e
  gi|557693730|ref|YP_008796784.1| 936 NYRLRSTRINELEMERKRILDLIE 959
                                       222222222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3206  (0.178816); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                       269  (0.0150036); expected 17.9 (0.001)
Passed Fwd filter:                       132  (0.00736237); 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: 3.12u 0.39s 00:00:03.51 Elapsed: 00:00:00.74
# Mc/sec: 4563.58
//
Query:       gi|557693731|ref|YP_008796785.1|  [L=287]
Description: hypothetical protein CSUB_C0294 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-24   84.2   0.0    1.2e-23   83.9   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24


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 !   83.9   0.0   6.6e-28   1.2e-23       1     208 [.      69     270 ..      69     271 .. 0.95

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 6.6e-28
                                       HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEE CS
                     Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlv 77 
                                       elirka+ i+s a+e v e i  g+t  ++ +++ +   +++   +l ++p +++ge + +   +p +r ++eg++v
  gi|557693731|ref|YP_008796785.1|  69 ELIRKASSIVSFAMEIVREVIAGGTTASDIRRALADN--IYRLEADLPYSPHISIGEDTFLNTDSPPSRGIREGEIV 143
                                       689**************999***************99..7778999**************9999************* PP

                                       EEEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSE CS
                     Peptidase_M24  78 lidagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglG 154
                                       +i+++a ++gy+s+i+rT++  k +++ ++ y+ + +  e +++++    ++  +++ ar+++ + gl      + G
  gi|557693731|ref|YP_008796785.1| 144 KITFAASVQGYISQISRTYFYKKSQEKIKKTYQQLIRLKEYITSLLSVWSSAVSVYDRARAFAMEIGLDPTSLTLFG 220
                                       *******************999898999*************************************99*55556699* PP

                                       EEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                     Peptidase_M24 155 HgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                        gvGle  +  p++   + +++ ++eG v+++ p +   pg +g  + d +lvt
  gi|557693731|ref|YP_008796785.1| 221 RGVGLEAEEH-PFID--AASTDIIREGSVISVGPDLL-LPGRYGLSVSDIYLVT 270
                                       ********98.***9..678*****************.99*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2115.94
//
Query:       gi|557693732|ref|YP_008796786.1|  [L=260]
Description: undecaprenyl pyrophosphate synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-75  251.8   0.0    6.1e-75  251.6   0.0    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


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 !  251.6   0.0   3.4e-79   6.1e-75       1     224 []      35     259 ..      35     259 .. 0.92

  Alignments for each domain:
  == domain 1  score: 251.6 bits;  conditional E-value: 3.4e-79
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHH...HHHHHH CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellk...eellke 74 
                                       i+DGNrRwA+ rg  + + Gh aGa++++eil++ lelg+k+vt+Y +SteN++R+ +ev+++++l++    +ll  
  gi|557693732|ref|YP_008796786.1|  35 ILDGNRRWARVRGWPPWK-GHAAGADRVEEILDWLLELGIKTVTLYILSTENLRRPMHEVEEIFRLIEekaYSLL-- 108
                                       89***********66666.************************************************95322233.. PP

                                       HHHHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GG CS
                      Prenyltransf  75 elkellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.ee 150
                                       +  ++ k++v+v+viG++++lp++v ealek+e+at+++++   ln+a++Yg+r ei+eavr++++++++ + + e+
  gi|557693732|ref|YP_008796786.1| 109 RDPKIYKHRVKVKVIGRKDMLPPNVVEALEKLEHATERHDN-RFLNLAIAYGGRLEILEAVRQIAEQVKTGQLSpEQ 184
                                       34699********************************7666.9*********************9998766665588 PP

                                       HSHHHHHCTSTT..T.SSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                      Prenyltransf 151 ideetlekhlytaka.lpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                       ide+t+ekhlyt+    p+pDl+iRtsGe+R+SnFllwq+ayse++f dv  Pdf+  dll+a+++yq+rerrfg
  gi|557693732|ref|YP_008796786.1| 185 IDEKTFEKHLYTNGVpNPEPDLIIRTSGETRISNFLLWQSAYSEFVFQDVNLPDFRYIDLLRAIRTYQSRERRFG 259
                                       89*********966688********************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1901.33
//
Query:       gi|557693733|ref|YP_008796787.1|  [L=394]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-93  312.2   4.0    6.1e-93  311.9   4.0    1.1  1  DUF373    Domain of unknown function (DUF373)
     0.0067   16.6   0.2       0.94    9.7   0.1    2.3  2  CnrY      Anti-sigma factor CnrY


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 !  311.9   4.0   6.8e-97   6.1e-93       1     334 [.       7     361 ..       7     371 .. 0.90

  Alignments for each domain:
  == domain 1  score: 311.9 bits;  conditional E-value: 6.8e-97
                            DUF373   1 ktLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLka..egedvevavvtGde 75 
                                       ++L+++vDrDdDlg kagv++PvvGr+a+l+aav+laladPeD+D+Nalf a+k+yd+L++  +ge+veva++tG++
  gi|557693733|ref|YP_008796787.1|   7 RLLIIVVDRDDDLGVKAGVSGPVVGRDANLDAAVRLALADPEDPDANALFYAVKLYDQLTQskTGEEVEVATLTGSR 83 
                                       68**********************************************************9777************* PP

                            DUF373  76 kvgveadrkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyll....kkal 148
                                       k+g+ead++i +ql+evl+k++a+++i+VsDG++D+ v pii+s+v ++sv+rV Vkqs+++E+++ +l    +  +
  gi|557693733|ref|YP_008796787.1|  84 KEGMEADMNIFNQLREVLEKFPAQRCIFVSDGETDAIVTPIISSQVAIASVQRVTVKQSQTVEQSWLILgkylRLGI 160
                                       *********************************************************************88888889 PP

                            DUF373 149 kdpelrktiLvplGlllliyalllllglpelalaiillllGlylllrGfgldelleelle...klkesleegritfv 222
                                       +dp+++k+i++++G ++ + all ++gl++   +i+ll+lGl+l+l+Gf++d +l++l++   k++++   g+i+ +
  gi|557693733|ref|YP_008796787.1| 161 TDPRYAKFIIGIPGGFIALSALLNIFGLAQ--PSILLLFLGLLLFLWGFRIDIHLSRLFTgfyKISQMPAIGQIRAF 235
                                       9*************************9865..9999**********************998889999999******* PP

                            DUF373 223 tyvvallllligiisgyislesvss............asvssglltlilafiygavewlalailtaslgkiideylk 287
                                       +y+ a ++llig++ g++s+ +++             +   ++ l l  +fi+++++++a+++++++l+++i  y+ 
  gi|557693733|ref|YP_008796787.1| 236 AYLGAGASLLIGLYLGLSSTYTTYVslnlsgeqlldpTILLPTALRLSGVFISQSIDFIAISAILVVLSNMIYYYI- 311
                                       **************999996666656878887555444444455555556**************************. PP

                            DUF373 288 reekdiarllllpflvlaiglvlygasaylls........lsilalslvvgivva 334
                                        ++  ++r++++ +l+++++++l +a   l +              s++++i++a
  gi|557693733|ref|YP_008796787.1| 312 IRYYGFWRTIHAGVLAIWLWALLKRAGVLLQQpqpttiteS-----STFLFILTA 361
                                       779***********************999966999555441.....444444433 PP

>> CnrY  Anti-sigma factor CnrY
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1    0.0001      0.94       8      70 ..      79     140 ..      73     152 .. 0.86
   2 !    4.6   0.0    0.0041        37      43      84 ..     314     353 ..     282     359 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHT----HHHHHT-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CnrY   8 lssaakvsleasiGvdlasleeqldkemaqivlvarrdaqraivcaalaalvafvainrvatl 70 
                                       l+ ++k  +ea + +    l+e l+k +aq+ +        aiv   +++ va ++++rv+  
  gi|557693733|ref|YP_008796787.1|  79 LTGSRKEGMEADMNI-FNQLREVLEKFPAQRCIFVSDGETDAIVTPIISSQVAIASVQRVTVK 140
                                       777899999999999.99**************************************9999654 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0041
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              CnrY  43 rrdaqraivcaalaalvafvainrvatlmlekaaptwlasps 84 
                                           +r+i  + la  + + a+ + a ++l+++ pt ++  s
  gi|557693733|ref|YP_008796787.1| 314 YYGFWRTIHAGVLAIWL-W-ALLKRAGVLLQQPQPTTITESS 353
                                       55679**9999997644.3.4445677899*****9887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       896  (0.0499749); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2909.23
//
Query:       gi|557693734|ref|YP_008796788.1|  [L=129]
Description: DNA polymerase beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   56.7   0.0    2.6e-15   56.3   0.0    1.2  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    4.5e-06   26.9   0.1    7.1e-06   26.2   0.1    1.3  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   2.9e-19   2.6e-15       2      92 ..      16     103 ..      15     104 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 2.9e-19
                                       STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHH CS
                           Polbeta   2 kikeilekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneappllly 78 
                                       k+++++e+ +ei++a++FGS ++ ++ +  DiD+av+ + +l+l + +e+a+ led+ lg  vDl+ +++++p  + 
  gi|557693734|ref|YP_008796788.1|  16 KVRAFFERMPEIRFAVIFGSAVRRRLVR--DIDIAVYARPELSLRKLIEVANVLEDL-LGTPVDLIPIEQTSPKQRV 89 
                                       8999***********************9..***************************.9****************** PP

                                       HHHHS-EEEES-SH CS
                           Polbeta  79 eilkegkllyskde 92 
                                       +il+eg+ ++ +d+
  gi|557693734|ref|YP_008796788.1|  90 KILTEGIRVITRDS 103
                                       *********99996 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.1   7.9e-10   7.1e-06       2      92 ..      15      95 ..      14      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 7.9e-10
                                      HHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECC CS
                      NTP_transf_2  2 kklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekle 80
                                      +k++ +++++  +  +v+fGS++r  +    DiD++v+ + e        +l+kl+e   +le llg +vdl+++e+  
  gi|557693734|ref|YP_008796788.1| 15 DKVRAFFERMPEIRFAVIFGSAVRRRLV--RDIDIAVYARPE-------LSLRKLIEVANVLEDLLGTPVDLIPIEQTS 84
                                      5677777777778889********9887..79**********.......679************************999 PP

                                      CCTEEEEEECEE CS
                      NTP_transf_2 81 dpllvksileer 92
                                       p+++ +il e+
  gi|557693734|ref|YP_008796788.1| 85 -PKQRVKILTEG 95
                                      .77777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1027.11
//
Query:       gi|557693735|ref|YP_008796789.1|  [L=136]
Description: hypothetical protein CSUB_C0298 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   53.5   0.0    2.5e-14   53.1   0.0    1.1  1  DUF86     Protein of unknown function DUF86


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0   1.4e-18   2.5e-14      16     116 ..      26     127 ..      12     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 1.4e-18
                                       TSTSCCG.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSC..HHHHHHHTTSS-HHHHHHHHHHHCCHHHH CS
                             DUF86  16 deeefls.deleydavernlqvigEaaidiakhlakklgikkpgdy..ifeilaekgviaeepeepwrkmiglRNrL 89 
                                       + + f + d  +++++ +nl  ++E++  ++ hl+ +  +k p++y  +++  ae+ +++    +++++++g+RN L
  gi|557693735|ref|YP_008796789.1|  26 TSRPFSElDVDQRYSMRYNLIALVESLVSLCTHLCMEAYGKTPTSYreAIKCVAERLTLSC--VKDLQALVGFRNLL 100
                                       4555664477889999******************************877777776665555..569*********** PP

                                       HT-CCCTTHHHHHHHHHHTCHHHHHHH CS
                             DUF86  90 vHgYlgidpeivwsiikenlpdleefl 116
                                       +H+Y+++d+e+v++ i ++ + +eefl
  gi|557693735|ref|YP_008796789.1| 101 IHRYWTVDDERVYREILDDFKCVEEFL 127
                                       ********************9999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1081.04
//
Query:       gi|557693736|ref|YP_008796790.1|  [L=117]
Description: hypothetical protein CSUB_C0299 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   17.8   1.9     0.0049   16.9   1.9    1.4  1  AKAP7_RIRII_bdg  PKA-RI-RII subunit binding domain of A-kinas


Domain annotation for each model (and alignments):
>> AKAP7_RIRII_bdg  PKA-RI-RII subunit binding domain of A-kinase anchor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.9   2.7e-07    0.0049      22      48 ..      82     108 ..      79     114 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.7e-07
                   AKAP7_RIRII_bdg  22 KAVqqYLEETqnkarqadGssvKaeea 48 
                                       K +qq LEE q k++q++  ++K  e 
  gi|557693736|ref|YP_008796790.1|  82 KGIQQLLEEAQQKEKQLEAHTLKEVEK 108
                                       89****************999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1763  (0.0983323); expected 358.6 (0.02)
Passed bias filter:                      749  (0.0417759); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 939.01
//
Query:       gi|557693737|ref|YP_008796791.1|  [L=139]
Description: small subunit ribosomal protein S19 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  109.0   0.1    1.1e-31  108.5   0.1    1.2  1  Ribosomal_S19  Ribosomal protein S19


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 !  108.5   0.1   6.3e-36   1.1e-31       4      81 .]      39     122 ..      35     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 6.3e-36
                                       HSS.TTCCCHHHHHHHHHH.....TS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT- CS
                     Ribosomal_S19   4 kkg.pfvqesllkkvrkak.....aekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFsp 74 
                                       k+g +  q +ll k+rkak      +k +++ikth+Rd+ IlPemvglt++V+nGk+f+pvei++em+Gh+LgE+++
  gi|557693737|ref|YP_008796791.1|  39 KRGlTPAQSRLLLKIRKAKkllesGQKLEKPIKTHCRDMFILPEMVGLTIHVHNGKEFTPVEITPEMIGHRLGEYAI 115
                                       66777789999999**9998987656699************************************************ PP

                                       SS----S CS
                     Ribosomal_S19  75 Trkpvkh 81 
                                       T+k+v h
  gi|557693737|ref|YP_008796791.1| 116 TNKRVIH 122
                                       ****988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 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:                        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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1127.33
//
Query:       gi|557693738|ref|YP_008796792.1|  [L=95]
Description: hypothetical protein CSUB_C0301 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   22.3   0.0    0.00019   22.0   0.0    1.1  1  RHH_6     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> RHH_6  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.1e-08   0.00019       5      47 ..      17      59 ..      13      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.1e-08
                             RHH_6  5 wnvavspetdqavrafLAsqGggrkGdLSrfieeAVrayllel 47
                                      + + +s+ + +  r ++A++ g+++G+LSr +e+ + + + e+
  gi|557693738|ref|YP_008796792.1| 17 LKIEISRHIAEKFRRWVAERYGMKRGALSRAVEDLIAKTIGEN 59
                                      57899*****************************999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 772.99
//
Query:       gi|557693739|ref|YP_008796793.1|  [L=241]
Description: large subunit ribosomal protein L2 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-36  124.0   0.6    5.9e-36  123.4   0.6    1.2  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    3.8e-11   42.8   0.0    1.1e-10   41.3   0.0    1.8  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 !  123.4   0.6   6.6e-40   5.9e-36       2     121 ..      91     215 ..      90     223 .. 0.93

  Alignments for each domain:
  == domain 1  score: 123.4 bits;  conditional E-value: 6.6e-40
                                       SSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT CS
                    Ribosomal_L2_C   2 vGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehke 78 
                                       +Gn+lp++++peG +v  +e  pg+ggkl+rs+G+ya v a+ g+++++klpS++  +vs+++ A++Gvv++g++ e
  gi|557693739|ref|YP_008796793.1|  91 PGNILPVGKVPEGGVVSTVERIPGDGGKLVRSSGAYALVAAQLGDRTVLKLPSKKDVEVSAKAFAVMGVVAGGGRGE 167
                                       7****************************************989********************************* PP

                                       ----STTHHHHT.....TBS----SSSS-TTTSSS--SSSS--SSSST CS
                    Ribosomal_L2_C  79 kklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGeGktksrkap 121
                                       k+++kAg+k++l     + +pk rGvam p+ Hp+GGG+ k ++r + 
  gi|557693739|ref|YP_008796793.1| 168 KPFLKAGAKYYLmrarhRYWPKSRGVAMVPAVHPFGGGSHKRIGRPET 215
                                       ************9***99*********************666555333 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 !   41.3   0.0   1.2e-14   1.1e-10       1      76 [.      11      82 ..      11      83 .. 0.75

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.2e-14
                                      TB-TT--BSSTT--------EE-B--S---SS--EEEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                      Ribosomal_L2  1 GrnnsgritvrhrggGhkkkyrlidfkrnkekvkgkVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                      Gr+++  i+++hr+      y+   f   k+ + ++V +i +DpgR Ap+A +   dg ++y+ a+eg+ vG++++
  gi|557693739|ref|YP_008796793.1| 11 GRGSPRFIASKHRRY--MVGYPSQLF-SGKNLITAVVSDIVHDPGRGAPVAVL-RHDGAEFYVPAVEGMYVGQVIE 82
                                      566664444444444..455555445.3467799*****************66.5677****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       254  (0.014167); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1953.19
//
Query:       gi|557693740|ref|YP_008796794.1|  [L=86]
Description: large subunit ribosomal protein L23 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   56.8   7.0    1.1e-14   54.6   7.0    1.8  1  Ribosomal_L23  Ribosomal protein L23


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 !   54.6   7.0   6.1e-19   1.1e-14       1      72 [.       5      75 ..       5      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 6.1e-19
                                      SSEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESSSSSEEBE--EE CS
                     Ribosomal_L23  1 dvilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrvgrkvgrrksyK 72
                                      dv+++ +it  +++l e+ nk+vF V+++a K+ ik+ave+l++VkV+kVntl+  + +k+   +v+ +++yK
  gi|557693740|ref|YP_008796794.1|  5 DVVKRIYITQDTVSLIESeNKLVFIVDLKADKHTIKNAVEQLYNVKVDKVNTLITSRGEKKA--FVKLKPEYK 75
                                      689999***********988**********************************99877663..444455554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 690.64
//
Query:       gi|557693741|ref|YP_008796795.1|  [L=272]
Description: large subunit ribosomal protein L4e [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-40  138.6   0.1    2.2e-40  138.4   0.1    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family


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 !  138.4   0.1   1.2e-44   2.2e-40       1     192 []      30     270 ..      30     270 .. 0.94

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 1.2e-44
                                       EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT............S CS
                      Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir............s 64 
                                       ++L p++F+ap+r+dl+ ra+    ++  q+++++k +++++s   +++++  G G AR+ +i+            +
  gi|557693741|ref|YP_008796795.1|  30 ITL-PSIFSAPLREDLVSRAYIHLATHSLQPKGASKmSGHKHSI--ESWGP--GFGIARISRIKgrgtpkygaggmV 101
                                       568.9***************************************..6****..************************ PP

                                       TTSTT---SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES.....---.-S............S--HHH CS
                      Ribosomal_L4  65 piargGgvahgpkperdystklnkKvrrlAlrsaLsakakqglllvvd.....nleple............esktke 124
                                       p a+gG+ +h+p+pe+++++++nkK+ r Al  aL+ +a+ + ++ ++     +                  skt e
  gi|557693741|ref|YP_008796795.1| 102 PSAVGGRPTHPPTPEKKIHKQINKKELRNALLAALAFTASPQHVKTRGhriteQ----TllpiivddgleaLSKTAE 174
                                       ************************************************644431....1446778899999****** PP

                                       HHHHHHHTT-.........................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHS CS
                      Ribosomal_L4 125 lvellkklgl.........................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllka 176
                                       ++++l klgl                         ++k++Livv + d+++ +aa n+pgvev+++++l+v++l+++
  gi|557693741|ref|YP_008796795.1| 175 VRRVLIKLGLgdelkrcgvkkvragkgkmrgrrykRRKGPLIVVAA-DRGVGKAASNIPGVEVVTAKDLSVLHLAPG 250
                                       *******9999999999999999999999999999999******97.****************************** PP

                                       SE....EEEEHHHHHHHHHH CS
                      Ribosomal_L4 177 dk....vvitksavekleek 192
                                       +k    +++tksa++ lee+
  gi|557693741|ref|YP_008796795.1| 251 AKpgrlTLFTKSALKALEER 270
                                       ******************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2137.49
//
Query:       gi|557693742|ref|YP_008796796.1|  [L=320]
Description: large subunit ribosomal protein L3 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-70  238.5   0.0    7.7e-48  163.3   0.0    2.0  2  Ribosomal_L3  Ribosomal protein L3
    7.2e-07   29.0   0.3    9.4e-07   28.6   0.3    1.1  1  ATP-grasp_2   ATP-grasp domain


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 !   73.3   0.0     2e-24   1.8e-20       1     117 [.       1     112 [.       1     116 [. 0.96
   2 !  163.3   0.0   8.6e-52   7.7e-48     151     349 ..     126     308 ..     120     318 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 2e-24
                                       XX.S.SXXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEE CS
                      Ribosomal_L3   1 mshrkfeaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavt 77 
                                       m +rk+++prhgsl +lpr+Ra++ +++vk +P  +      + +f+GyK Gmt +   ++ p+s++++ ev++a t
  gi|557693742|ref|YP_008796796.1|   1 MGRRKYSRPRHGSLAYLPRGRAASILPRVKHWPDGEG-----VLGFIGYKVGMTMVHYIDNTPNSPTQGSEVAKACT 72 
                                       889******************************7665.....69**********9999999**************** PP

                                       EEEC--EEEEEEEEEEEETTEEEEEEEEESSS.SHHHHCC CS
                      Ribosomal_L3  78 vvetppmvivgvvgyvetprGlrslktvwaehlseevkrr 117
                                       vv  pp++++g+ +y ++   l  + + w++++ e+vkrr
  gi|557693742|ref|YP_008796796.1|  73 VVAAPPLKVIGISLYRNVDGELVNIGKYWSKEVPEDVKRR 112
                                       ***************************************8 PP

  == domain 2  score: 163.3 bits;  conditional E-value: 8.6e-52
                                       HHHHHSCSCEEEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE--- CS
                      Ribosomal_L3 151 eeikkeasvvrviahtvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGk 227
                                        ++++    vr+++ t+ r +   a K++ + Ei++ gG+ ae l+ a++ + k   v++vF++g+++Dvi+vtkGk
  gi|557693742|ref|YP_008796796.1| 126 GQLEDDVDEVRIVVATQPRLVG--AGKAPRIAEIKI-GGKPAEALEKAKQLVGKDLRVTDVFKEGQFVDVIAVTKGK 199
                                       566778889**********998..99*********9.799************************************* PP

                                       EEE-HHHHCT----STTTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.S CS
                      Ribosomal_L3 228 GfeGvvkRWgvkklprkthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdlt 304
                                       Gf+GvvkR+gv  l+rk  +++R vaaig+w+p  V++tv+r+Gq+Gyh+Rte+nk+i rig+              
  gi|557693742|ref|YP_008796796.1| 200 GFQGVVKRYGVSILQRKSRKTRRGVAAIGPWNPHYVMYTVPRSGQMGYHRRTEFNKRILRIGD-------------D 263
                                       ***************************************************************.............3 PP

                                       S..SS.TTTCTTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGG CS
                      Ribosomal_L3 305 ekeitPmGGfvhyGevkndfilvkGsvpGpkkrlvklrkslltqt 349
                                         +i+P+ G+ ++G vk d+++++Gsv+G+  r + lr   ++ +
  gi|557693742|ref|YP_008796796.1| 264 PASINPKSGWHRFGLVKSDYLVLEGSVAGTPLRPLVLRAPARPPK 308
                                       568***************************999999998777755 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.3   1.1e-10   9.4e-07       2     103 ..      97     201 ..      96     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.1e-10
                                       E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCT...TCEEEESSHHHHHHHHHCC CS
                       ATP-grasp_2   2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKa...gGvklvkskeeakeaakel 75 
                                       +  y +ke+ ++   + p+++   saee+ +  ++++e ++vv +Q    G GKa   + +k+  ++ ea e+ak+l
  gi|557693742|ref|YP_008796796.1|  97 IGKYWSKEVPEDVKRRNPTFRPMPSAEEIGQLEDDVDEVRIVVATQPRLVGAGKApriAEIKIGGKPAEALEKAKQL 173
                                       567999999999999****************************************999999**************** PP

                                       TTSEEE-TTS-TT-EEE--EEEEE---E CS
                       ATP-grasp_2  76 lgkelvtkqtgkeGkkvekvlveealdi 103
                                       +gk+l+ +   keG+ v+ + v++   +
  gi|557693742|ref|YP_008796796.1| 174 VGKDLRVTDVFKEGQFVDVIAVTKGKGF 201
                                       **********************987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2508.60
//
Query:       gi|557693743|ref|YP_008796797.1|  [L=177]
Description: hypothetical protein CSUB_C0306 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   12.4   0.2        4.5    7.5   0.0    2.7  3  KIP1      KIP1-like protein


Domain annotation for each model (and alignments):
>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.11     2e+03      24      37 ..      23      36 ..      16      51 .. 0.75
   2 ?    1.4   0.0     0.019   3.4e+02      55      73 ..      66      84 ..      64      85 .. 0.92
   3 ?    7.5   0.0   0.00025       4.5      37      72 ..     111     146 ..     101     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.11
                              KIP1 24 dekvkemlklieed 37
                                      de ++e+++li  +
  gi|557693743|ref|YP_008796797.1| 23 DEVTDEIISLITAE 36
                                      67778888888765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.019
                              KIP1 55 LielveefyrsyrsLaery 73
                                      ++++v+ + +++ +L e y
  gi|557693743|ref|YP_008796797.1| 66 VVKMVDGVRKTFSVLVEAY 84
                                      799*************998 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.00025
                              KIP1  37 dadsfakraemyykkrpeLielveefyrsyrsLaer 72 
                                       d+    kr e+ y+  ++L++ ve + rs+ s++ r
  gi|557693743|ref|YP_008796797.1| 111 DGGRVLKRREAAYRDGEDLFSRVERVRRSFYSVYSR 146
                                       6677789************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1334.35
//
Query:       gi|557693744|ref|YP_008796798.1|  [L=399]
Description: hypothetical protein CSUB_C0307 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-19   71.1   0.7    2.7e-18   66.8   0.4    2.0  2  Asn_synthase  Asparagine synthase
  ------ inclusion threshold ------
       0.13   11.3   0.1        0.2   10.7   0.1    1.3  1  NAD_synthase  NAD synthase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.4     3e-22   2.7e-18       2     145 ..     155     294 ..     154     319 .. 0.86
   2 !    2.8   0.0    0.0085        77     241     270 ..     334     367 ..     294     398 .. 0.78

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 3e-22
                      Asn_synthase   2 lrelLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelv 78 
                                       + e+L++aV++ +    +v++++SGGlDS ++a l +  s s     ++g+   +s + ++a+ +a  lg+e  ++v
  gi|557693744|ref|YP_008796798.1| 155 VLEALRHAVEKFC--PHRVSVFFSGGLDSLILAKLIQDRSGS-PLLLTVGT--VESHDFAAAESAASFLGLEVEKVV 226
                                       6789999999877..667899******************985.55789**9..9*********************** PP

                      Asn_synthase  79 lteeelldalpdviyhlee..pfadrsaiplyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsr 145
                                       ++e+ +++al+ +  +l     + ++ a+++ylls++a + g+  +  G+GaDElfgGY   y + l +
  gi|557693744|ref|YP_008796798.1| 227 VEEKNVAEALEMLENVLGPlgDMDAAIAVAMYLLSKKAVEAGCGTAVLGQGADELFGGYM-KYERILHE 294
                                       ****999987777777776766788999**********9999999999***********8.77766544 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0085
                      Asn_synthase 241 flDhrlvevalrlppelklrg....gieKyiLRe 270
                                       +l +++v +al+ p+e+k+         K++LR 
  gi|557693744|ref|YP_008796798.1| 334 YLTRNVVSAALSTPVEHKIHVqggrVVRKHVLRI 367
                                       6899***************995555566777765 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   2.3e-05       0.2       6      84 ..     156     230 ..     153     264 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---H CS
                      NAD_synthase   6 vdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidik 82 
                                        + l++ v+k   + v +  SGG+DS + a+l ++  g+   l++     + + +d  +a   a  lg+ev+++ ++
  gi|557693744|ref|YP_008796798.1| 156 LEALRHAVEKFCPHRVSVFFSGGLDSLILAKLIQDRSGSPLLLTV----GTVESHDFAAAESAASFLGLEVEKVVVE 228
                                       56799999999999999****************999866554444....4466677777777777777777777665 PP

                                       HH CS
                      NAD_synthase  83 pi 84 
                                       + 
  gi|557693744|ref|YP_008796798.1| 229 EK 230
                                       54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 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:                        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 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3004.24
//
Query:       gi|557693745|ref|YP_008796799.1|  [L=155]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  112.4   0.0    2.5e-32  112.1   0.0    1.0  1  HD_3           HD domain
      4e-14   52.8   0.0    4.7e-14   52.6   0.0    1.1  1  HD_2           HD containing hydrolase-like enzyme
    6.2e-06   26.4   0.1    9.3e-06   25.9   0.1    1.2  1  HD             HD domain
  ------ inclusion threshold ------
      0.062   12.5   0.0      0.076   12.2   0.0    1.1  1  Peptidase_S32  Equine arteritis virus serine endopeptidase S3


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 !  112.1   0.0   5.5e-36   2.5e-32       4     132 ..      11     139 ..      10     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 5.5e-36
                              HD_3   4 LKfqkRqgwlqtgrvreesvaeHmwrvalmalllseelkekvdiarvikmfLiHDlvEiltgDiispd..elakeek 78 
                                       LK+ +R+gwl+ g++++esva H++ +a+m+++ +e+ +  +d+ +++km+L+HDl+E++tgD+++    ++ k + 
  gi|557693745|ref|YP_008796799.1|  11 LKRLPRTGWLEEGVKNPESVASHSYSLAVMTMVEAEARG--LDVCKAVKMALLHDLAESYTGDLTPATkkKIPKNIL 85 
                                       899*******************************99999..*************************99756****** PP

                              HD_3  79 eeeekeaaerilkllpeelaeellalweEFeeretkeakfakdlDklepllqal 132
                                       ++ ek++ +++++ lp ++a+++ +l +E+  r t+ea+++++lD+ e++  al
  gi|557693745|ref|YP_008796799.1|  86 QQVEKAIVRELFSSLPPKIAQQYTELHQEYLGRRTPEARLVHKLDRRELVEEAL 139
                                       **********************************************99987665 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 !   52.6   0.0     1e-17   4.7e-14      15     134 ..      19     131 ..       3     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1e-17
                              HD_2  15 walmrntreenvaeHslevaliahalalienkkfggkldaerlallalyHDasEiitGDlptpvKyanpeireayke 91 
                                       w  +   ++e+va Hs++ a++++    +e +   + ld+ +++++al+HD++E  tGDl   +K + p  ++ +++
  gi|557693745|ref|YP_008796799.1|  19 WLEEGVKNPESVASHSYSLAVMTM----VEAEA--RGLDVCKAVKMALLHDLAESYTGDLTPATKKKIP--KNILQQ 87 
                                       444445789***********9765....55555..67***********************999998877..5899** PP

                              HD_2  92 vEeeaeekllelLpeelreeyeella.deeaeeeekklvkaaDk 134
                                       vE++  ++l+++Lp ++ ++y+el +     ++ e +lv+  D+
  gi|557693745|ref|YP_008796799.1|  88 VEKAIVRELFSSLPPKIAQQYTELHQeYLGRRTPEARLVHKLDR 131
                                       ************************94344555668999988886 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   2.1e-09   9.3e-06       2     120 ..      31     133 ..      30     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.1e-09
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHH..CTCCHHHHHHHHHHHHHHHHHHHH CS
                                HD   2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeee..fekflaHekvgaeilrevekrlgl 76 
                                       + Hs+  a ++   ae +g   d+ +++++aLlHD+++ ++gd    ++++  +++++  ek  ++ l  ++ ++  
  gi|557693745|ref|YP_008796799.1|  31 ASHSYSLAVMTMVEAEARG--LDVCKAVKMALLHDLAESYTGDLTPATKKKipKNILQQVEKAIVRELFSSLPPK-- 103
                                       5788888888888899999..9********************944444443566666666666665555555555.. PP

                                       HHHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHH CS
                                HD  77 dledvaklirehheswegkkrprglaerqlslearivklaDrla 120
                                          ++++  + h+e                ++ear+v  +Dr +
  gi|557693745|ref|YP_008796799.1| 104 ---IAQQYTELHQEYLG-----------RRTPEARLVHKLDRRE 133
                                       ...66666666666665...........78***********975 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 ?   12.2   0.0   1.7e-05     0.076     246     286 ..      56      97 ..      34     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                                       SS-EEHHHHHTT--SSEEE--S.---TTEE--SS.EEEHHHH CS
                     Peptidase_S32 246 vaevkLselskhfaGplvpvstvklpkniiaDve.avpsdLa 286
                                       v+   L +l++ ++G l+p ++ k+pkni++ ve a+ ++L 
  gi|557693745|ref|YP_008796799.1|  56 VKMALLHDLAESYTGDLTPATKKKIPKNILQQVEkAIVRELF 97 
                                       4455689*************************9725667665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1078.69
//
Query:       gi|557693746|ref|YP_008796800.1|  [L=357]
Description: DNA primase large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-26   91.6   0.0      9e-26   90.8   0.0    1.4  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
  ------ inclusion threshold ------
      0.043   13.7   0.2      0.099   12.6   0.2    1.6  1  Erythro-docking  Erythronolide synthase, docking
       0.14   10.4   0.0       0.17   10.1   0.0    1.1  1  COG6             Conserved oligomeric complex COG6
       0.14   12.3   0.1        1.9    8.7   0.0    2.7  4  PAS_7            PAS fold


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 !   90.8   0.0     2e-29     9e-26       3     206 ..     137     319 ..     135     344 .. 0.85

  Alignments for each domain:
  == domain 1  score: 90.8 bits;  conditional E-value: 2e-29
                                       EEEEHHHHHHHTT..-G......GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---HHH CS
                   DNA_primase_lrg   3 ykvpfedvldlvk..rr......rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikederekl 71 
                                       + ++f d+l+ +   ++      +++l+kGy+ ++++e+++l+++  +k + + le++   +p     + e+  e l
  gi|557693746|ref|YP_008796800.1| 137 FWIHFVDYLKHATplNEprfklvNRILDKGYVAVTRSEAITLVKNGLEKLIHQRLEKMGSLTPPP---FLEKHVERL 210
                                       566777777666655336799999*********************************88887754...46666667* PP

                                       HHHHCT--.............TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHHHH CS
                   DNA_primase_lrg  72 eellealsesyvaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsldeil 148
                                       ++lle ++              + +a    +l  +  PpCm++l ++l +++  +h g ++ ++F+  ig+++de++
  gi|557693746|ref|YP_008796800.1| 211 KKLLESVH--------------QREAAPAVRLDPDKWPPCMQALRKRLLAGEPVSHFGNFAAAAFMLRIGMTVDEVV 273
                                       *******9..............33333445789999***************************************** PP

                                       CCCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S.-H CS
                   DNA_primase_lrg 149 elwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg.Cp 206
                                       ++ ++       +Fd    ry+++h++G +g+rt+ys++ C+++         ++hg C 
  gi|557693746|ref|YP_008796800.1| 274 NIYSQR-----GDFDPrIARYQVEHIAGLKGSRTKYSVPRCATM---------QTHGlCI 319
                                       ****97.....9****8889************************.........9999995 PP

>> Erythro-docking  Erythronolide synthase, docking
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   2.2e-05     0.099      33      54 ..      47      68 ..      30      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                                      HHHHHHHHHHHHHHH-S--S-- CS
                   Erythro-docking 33 aRLeaLLRRWnsRRadetetva 54
                                       R+e  LRRW +RR++  et+ 
  gi|557693746|ref|YP_008796800.1| 47 RRVEEALRRWPARRPQPLETSD 68
                                      699************9888875 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   3.8e-05      0.17     381     448 ..     175     244 ..     158     303 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.8e-05
                              COG6 381 ffsllkdklakll.pelpp.sdLspPewlsealskllelletyesslaseaser.ekdfeevlsalldpll 448
                                        ++l+k+ l+kl  + l++   L+pP++l + ++ l++lle+++++ a+  + r ++d  +++ ++l + l
  gi|557693746|ref|YP_008796800.1| 175 AITLVKNGLEKLIhQRLEKmGSLTPPPFLEKHVERLKKLLESVHQREAA-PAVRlDPDKWPPCMQALRKRL 244
                                       4555556666665222222367*******************99997666.455556666666666666655 PP

>> PAS_7  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.72   3.2e+03      39      67 ..      15      46 ..       6      77 .. 0.53
   2 ?   -1.6   0.0      0.64   2.9e+03      70     102 ..      88     120 ..      66     123 .. 0.73
   3 ?   -1.8   0.0      0.77   3.5e+03      57      80 ..     181     204 ..     167     220 .. 0.73
   4 ?    8.7   0.0   0.00043       1.9      34      74 ..     262     302 ..     256     321 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.72
                             PAS_7 39 vp.leellrynaergefg.....agdveaeverrl 67
                                       p l+e+ +y a++g        +   ++++e+ +
  gi|557693746|ref|YP_008796800.1| 15 FPfLREVRDYVAQQGLRLedfdgN---NEYLEAAV 46
                                      554566666666666543222111...22222222 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.64
                             PAS_7  70 aragkphsfererpdgrvievrgnplpdgGfVt 102
                                        ++++  ++e er +    ++r+ ++   G+V+
  gi|557693746|ref|YP_008796800.1|  88 FAKRRFAAYEAERYATMLKNIREDQVKAVGYVM 120
                                       445566677777777788888888888888887 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.77
                             PAS_7  57 gdveaeverrlaaaragkphsfer 80 
                                       +  e+ +++rl+++ + +p+ f  
  gi|557693746|ref|YP_008796800.1| 181 NGLEKLIHQRLEKMGSLTPPPFLE 204
                                       557888999999998866665544 PP

  == domain 4  score: 8.7 bits;  conditional E-value: 0.00043
                             PAS_7  34 lvqvgvpleellrynaergefgagdveaeverrlaaaragk 74 
                                       ++++g++++e++++ ++rg+f+++ ++ +ve++     +++
  gi|557693746|ref|YP_008796800.1| 262 MLRIGMTVDEVVNIYSQRGDFDPRIARYQVEHIAGLKGSRT 302
                                       789*******************9998888888875444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2561.60
//
Query:       gi|557693747|ref|YP_008796801.1|  [L=380]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  37.8    3.3e-15   55.9  17.8    2.1  2  MFS_1     Major Facilitator Superfamily
    7.8e-07   28.3  11.0    7.8e-07   28.3  11.0    2.4  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 !   53.9  19.9   1.4e-18   1.3e-14      19     245 ..      12     234 ..       1     241 [. 0.73
   2 !   55.9  17.8   3.7e-19   3.3e-15       4     166 ..     208     373 ..     205     378 .. 0.84

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.4e-18
                             MFS_1  19 lplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa..sslw.lllvlr 92 
                                       +p+++ + lg s++ +gl  +l   g +v+++ +Grl+dr+Gr +v+  g+++ al++++++f   + +  ++l + 
  gi|557693747|ref|YP_008796801.1|  12 VPITI-SLLGGSAALAGLGSALMWGGRIVTTYQMGRLMDRVGRMPVIYSGMVVAALSAAAAAFFyqQRFMeAFLMVI 87 
                                       45333.457889999998777777788******************************566664335889999***** PP

                             MFS_1  93 vlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg..Wravfyilaivsllafv 166
                                       vl G+g g++  + + ++ d+ p+e+rg+++g++ +g+ +G++  p++ +++   s+g    a++++l+++++ +f 
  gi|557693747|ref|YP_008796801.1|  88 VLFGVGRGMADYGRM-AAGDMLPPEKRGLGTGVILTGSMVGTLAVPPIIAAVQmLSGGenIAATYLALTPFAAGGFA 163
                                       ******877776665.58************************9997777766625555999999***********77 PP

                             MFS_1 167 lfllllpeepperkrkspkeee..kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls 241
                                          ++ + ++p    k + +++  + t ++++++ ++++ +++    +++a++++++ +  +++++ l     l+l+
  gi|557693747|ref|YP_008796801.1| 164 A--AYAVKPDPLQIAK-TLRQGnpSETHQQAVRK-ISEIINRR----MVFAIVSAAVSTGVMVAYMSL-GSLLLHLG 231
                                       4..4444444444444.44443456666666666.999*****....555555555444455555555.45555555 PP

                             MFS_1 242 glll 245
                                        +++
  gi|557693747|ref|YP_008796801.1| 232 -HVE 234
                                       .444 PP

  == domain 2  score: 55.9 bits;  conditional E-value: 3.7e-19
                             MFS_1   4 aaflsalarsilgpalplalaedlg.ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       + + ++++ ++++++l   l  +lg +  ++i+ ++tl  +g+ ++s+plG  +d +Gr +v l+g+++ ++g++++
  gi|557693747|ref|YP_008796801.1| 208 VSAAVSTGVMVAYMSLG-SLLLHLGhVETTVISAVVTLHVIGMYAFSIPLGKAADIVGRVPVTLVGVIVCSIGSYIM 283
                                       44444445555555555.6667777466777999***************************************8888 PP

                             MFS_1  80 lfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...Wra 152
                                       ++   +  ++ ++ +l G+g +a++ a++ali+d + + erg+a+gl  ++++l ++ +p+l +++ +++g     +
  gi|557693747|ref|YP_008796801.1| 284 SV-GKSLdIVTIGMFLVGVGWSAATVASIALISDETQPAERGKAMGLNDTATALTSLTTPILLSVIFQNYGdtaLGL 359
                                       86.77777**************************************************************9766556 PP

                             MFS_1 153 vfyilaivsllafv 166
                                       + +++a  ++++++
  gi|557693747|ref|YP_008796801.1| 360 AGLAAATPTIILAI 373
                                       66666666666655 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   8.6    0.0011       9.9      45     151 ..      23     128 ..       5     159 .. 0.80
   2 !   28.3  11.0   8.7e-11   7.8e-07      44     170 ..     234     357 ..     181     375 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0011
                                       ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS
                          Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121
                                       + l gl  +++  G+i++ + +g l+dr+GR +++  + v++  +a+  a+  +++ +e++++  vl G+g G+a +
  gi|557693747|ref|YP_008796801.1|  23 AALAGLGSALMWGGRIVTTYQMGRLMDRVGRMPVIYSGMVVAALSAAAAAFFYQQRFMEAFLMVIVLFGVGRGMADY 99 
                                       55778888889999999999999999999999999999999999999999999888888888888999999998877 PP

                                       HHHHHHHTTS-SCCHHHHHHHHHHHHHHHH CS
                          Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGi 151
                                          m ++ + p+++Rg  +++  ++  +G 
  gi|557693747|ref|YP_008796801.1| 100 G-RMAAGDMLPPEKRGLGTGVILTGSMVGT 128
                                       6.4777777777777766665555555554 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 8.7e-11
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                        ++ ++++v + ++G  + s+ +g+++d++GR ++ l+++++++ig+ ++ + k   s+ ++++g +lvG+g+ +a+
  gi|557693747|ref|YP_008796801.1| 234 ETTVISAVVTLHVIGMYAFSIPLGKAADIVGRVPVTLVGVIVCSIGSYIMSVGK---SLDIVTIGMFLVGVGWSAAT 307
                                       5788999***********************************************...******************** PP

                                       HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHH CS
                          Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsnadgw 170
                                       v +  +is  + ++ Rg+ ++l+++a+++  l + i+  ++ +++++ +  
  gi|557693747|ref|YP_008796801.1| 308 VASIALISDETQPAERGKAMGLNDTATALTSLTTPILLSVIfQNYGD-TAL 357
                                       *****************************999998765555477766.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 2830.09
//
Query:       gi|557693748|ref|YP_008796802.1|  [L=203]
Description: superoxide dismutase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-36  122.9   0.8    7.6e-36  122.4   0.8    1.2  1  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do
    4.7e-31  107.1   2.1    6.9e-31  106.6   0.4    1.9  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 !  122.4   0.8   8.5e-40   7.6e-36       1     102 []      95     197 ..      95     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 122.4 bits;  conditional E-value: 8.5e-40
                                       --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTH CS
                          Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYy 76 
                                       p g++a++i++dfgs+e+fkk+f++aa +v++ Gwa+L++d++ ++L i+++++q+ +   +   lL+lDvwehAYy
  gi|557693748|ref|YP_008796802.1|  95 PGGAIADQINKDFGSFENFKKQFSDAAKNVEAVGWAILTYDPEsETLVIYQVEKQNFMHPPDLPLLLTLDVWEHAYY 171
                                       6799*************************************98679*9**99999976665444579********** PP

                                       HHHTT-HHHHHHHHGGGBBHHHHHHH CS
                          Sod_Fe_C  77 ldyqnkradYieafwnvvnWkeveer 102
                                       l+y+n+ra+Y++++w+vvnW++ve+r
  gi|557693748|ref|YP_008796802.1| 172 LQYKNDRAAYVDKWWEVVNWDDVEKR 197
                                       ***********************997 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 !  106.6   0.4   7.7e-35   6.9e-31       1      82 []       5      86 ..       5      86 .. 0.98
   2 ?   -0.5   0.1       0.2   1.8e+03      26      43 ..     173     190 ..     165     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 7.7e-35
                                      S------SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Sod_Fe_N  1 kyeLpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakkkleelvlkklekalrnnagghvnHslfwk 79
                                      ky+Lp+LpYay+aLeP+is+e+++lHh+kHh++Yvn++N+ale+le+++k  +   ++++ ++l++n +gh +Hs+fw 
  gi|557693748|ref|YP_008796802.1|  5 KYSLPPLPYAYNALEPVISAEIMTLHHTKHHQAYVNGANAALERLEKQRKGENPENIRGILRDLSFNLSGHKLHSVFWP 83
                                      69************************************************9999999********************** PP

                                      TB- CS
                          Sod_Fe_N 80 nls 82
                                      n++
  gi|557693748|ref|YP_008796802.1| 84 NMA 86
                                      995 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.2
                                       HHHTHHHHHHHHHHHHHH CS
                          Sod_Fe_N  26 HhdkHhktYvnnlNkale 43 
                                        ++   ++Yv+++ ++++
  gi|557693748|ref|YP_008796802.1| 173 QYKNDRAAYVDKWWEVVN 190
                                       577788999999877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 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:                        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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1614.86
//
Query:       gi|557693749|ref|YP_008796803.1|  [L=321]
Description: hypothetical protein CSUB_C0312 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-23   83.1  69.1    1.2e-17   63.9  32.5    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 !   63.9  32.5   6.8e-22   1.2e-17      51     310 ..       2     238 ..       1     242 [. 0.82
   2 !   32.7  28.5   2.1e-12   3.8e-08       4     166 ..     148     310 ..     142     318 .. 0.91

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 6.8e-22
                             MFS_1  51 plGrlsdrfGrrrvlllglllfalg.lllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigl 125
                                       p++ l++r+G  rv+ +gl+++a++ +++++  ss w  +l+ r+lqG+ +ga+f   + l+ ++  + +r++a+g+
  gi|557693749|ref|YP_008796803.1|   2 PFAMLAERLGVVRVVSAGLVVYAVFhFVFAT--SSTWnEILFYRFLQGFVGGAVFIPTLQLAFEVGDE-RRSFATGF 75 
                                       8899*********************666666..89999**************************8887.******** PP

                             MFS_1 126 lsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawka 202
                                       ++ gf++G+ lg+  + + +  + W+a  + +++v++ ++ ++ +l+++ +++r  k+p++                
  gi|557693749|ref|YP_008796803.1|  76 VACGFNAGTGLGAYYSFAAS-GGKWQAGLVSATLVFAALIPVASILMFTAQRRRLEKRPTDF--------------- 136
                                       ************77754444.556*9887777777777777888888888888888877555............... PP

                             MFS_1 203 llkdpvlw.illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrll 278
                                         k+  ++ + +++++    ++ +++t++p+ l + +glsg  +a+++ ++l+++g+++  ++g+l d lg+ r l+
  gi|557693749|ref|YP_008796803.1| 137 -SKNSGFYfLNILHFVRL-GVIIAATTWMPTALASLHGLSG-DSAAFYASILQMAGIVSLTVGGYLTDMLGKGRVLV 210
                                       .34444442355555555.49999****************7.999999************************99999 PP

                             MFS_1 279 lallllllaalglallavtssavllllvlvli 310
                                       +++++l++a++   +++      lll  ++l+
  gi|557693749|ref|YP_008796803.1| 211 MNVAALAAALAVSQFVPGW----LLLPYVALL 238
                                       9999999888777666666....222233334 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 2.1e-12
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                       ++f+    + ++++++p ala+ +g+s++++ + +++   + +v+  ++G+l+d +G  rvl++ ++++a++ l+ +
  gi|557693749|ref|YP_008796803.1| 148 LHFVRLGVIIAATTWMPTALASLHGLSGDSAAFYASILQMAGIVSLTVGGYLTDMLGKGRVLVMNVAALAAA-LAVS 223
                                       556666666778899999999999************************************************.5555 PP

                             MFS_1  81 .fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfy 155
                                        f+++ wlll   +l G+   + +pa+ a+++d+++    + a g+l++++++Gai  p l g+l   + g+ ++fy
  gi|557693749|ref|YP_008796803.1| 224 qFVPG-WLLLPYVALLGFLIYLPTPAAFAILRDMYHAGGASVAAGYLNTSAAAGAITMPYLFGVLHdVLHGFASSFY 299
                                       69666.779999******************************************************88999****** PP

                             MFS_1 156 ilaivsllafv 166
                                       ++a+++l+++ 
  gi|557693749|ref|YP_008796803.1| 300 LAAALYLILLP 310
                                       ********954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2284.92
//
Query:       gi|557693750|ref|YP_008796804.1|  [L=400]
Description: hypothetical protein CSUB_C0313 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   12.4   1.1       0.22   11.8   1.1    1.2  1  Shisa     Wnt and FGF inhibitory regulator


Domain annotation for each model (and alignments):
>> Shisa  Wnt and FGF inhibitory regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.1   1.2e-05      0.22      92     154 ..      25      88 ..       6     106 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.2e-05
                             Shisa  92 ifivfvivgvvvivcccgclkkkqrekrpgrenlssalaev.gpivte..ttsattvvhsrysepq 154
                                        +iv v+v+++ +v +  +l   + +k+p+r  ++++  ++  +++t+  tt++++ + s++++ +
  gi|557693750|ref|YP_008796804.1|  25 TVIVAVLVIAILFVGL--VLDDAEAAKNPRRTRTRTRTSTTlSTTPTStiTTTSSQTTTSQQYSDT 88 
                                       3444444444444444..788888888899999888888886444443344444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      711  (0.0396564); 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 0.25s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2707.00
//
Query:       gi|557693751|ref|YP_008796805.1|  [L=217]
Description: endonuclease III [Candidatus Caldiarchaeum subterraneum]
Scores for 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-22   78.4   0.0    7.2e-22   77.9   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    1.9e-08   33.7   0.1    4.7e-08   32.5   0.1    1.7  1  HHH            Helix-hairpin-helix motif
    5.1e-05   23.8   0.0      0.069   13.8   0.1    2.5  2  HHH_5          Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.028   14.7   3.2      0.058   13.7   3.2    1.5  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 !   77.9   0.0   1.6e-25   7.2e-22       1     105 [.      36     169 ..      36     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 1.6e-25
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       v+a+ls +t+de + +++ +lf  f   +p d+a+ad   ++ li+++Gfyr+Kak+ik+lA+i+            
  gi|557693751|ref|YP_008796805.1|  36 VGAVLSHRTRDEKTDEAYHNLFTWF--NDPRDIASADVRTVARLIKPVGFYRQKAKRIKQLAKIVYgklggrvpdnr 110
                                       789*********************6..5************************************************* PP

                                       ......................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHH CS
                                       ......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ......................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleel 105
                                                             ++p+  i+vD+hv  ++krl++++ k  +++v+k+l  l
  gi|557693751|ref|YP_008796805.1| 111 aellklpgvgpksadivlsiafNRPE--IAVDTHVETVAKRLGIADGKAGYEEVKKALTTL 169
                                       ********************877777..****************************99655 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   0.1     1e-11   4.7e-08       2      30 .]     102     130 ..     101     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1e-11
                                       HHHHHTSSHHHHHTSTT-SHHHHHHHHHH CS
                               HHH   2 leglipasreeLlalPGVGpktAeaIlsy 30 
                                       l+g +p++r+eLl+lPGVGpk A+ +ls+
  gi|557693751|ref|YP_008796805.1| 102 LGGRVPDNRAELLKLPGVGPKSADIVLSI 130
                                       7899*********************9996 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0012       5.6      23      53 ..      60      93 ..      54      96 .. 0.75
   2 !   13.8   0.1   1.5e-05     0.069       3      42 ..     112     151 ..     109     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
                                      --SHHHHHHS-...HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5 23 iesvedlaaad...veeLakipGiGkktAeriil 53
                                      ++ + d+a+ad   v++L k  G+   +A+ri++
  gi|557693751|ref|YP_008796805.1| 60 FNDPRDIASADvrtVARLIKPVGFYRQKAKRIKQ 93
                                      67899*****833345566669999999999975 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.5e-05
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTT CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipG 42 
                                       eLl+++G+Gpk A  +ls  ++ +e  ++  ve++ak  G
  gi|557693751|ref|YP_008796805.1| 112 ELLKLPGVGPKSADIVLSIAFNRPEIAVDTHVETVAKRLG 151
                                       6888888888888888887555555555666666666555 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 ?   13.7   3.2   1.3e-05     0.058       5      17 .]     194     206 ..     191     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                     EndIII_4Fe-2S   5 kPkCeaCPLaDlC 17 
                                       +P+C  CP+ ++C
  gi|557693751|ref|YP_008796805.1| 194 RPRCSLCPITEYC 206
                                       8************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1570.81
//
Query:       gi|557693752|ref|YP_008796806.1|  [L=152]
Description: peroxiredoxin Q/BCP [Candidatus Caldiarchaeum subterraneum]
Scores for 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-44  148.7   0.0    8.7e-44  148.4   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    6.3e-27   94.1   0.0    7.5e-27   93.8   0.0    1.0  1  Redoxin        Redoxin
    4.7e-05   23.5   0.0    6.8e-05   23.0   0.0    1.3  1  AhpC-TSA_2     AhpC/TSA antioxidant enzyme
    5.8e-05   22.7   0.0    6.6e-05   22.5   0.0    1.1  1  DUF899         Bacterial protein of unknown function (DUF899)
    6.4e-05   23.2   0.0      9e-05   22.7   0.0    1.2  1  Thioredoxin_8  Thioredoxin-like
     0.0022   17.9   0.0      0.003   17.5   0.0    1.2  1  SCO1-SenC      SCO1/SenC
     0.0042   16.8   0.2       0.95    9.3   0.0    3.0  3  ACT            ACT domain
  ------ inclusion threshold ------
       0.14   12.5   0.0       0.38   11.1   0.0    1.7  1  Radical_SAM    Radical SAM superfamily


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 !  148.4   0.0   3.9e-47   8.7e-44       2     123 ..       6     129 ..       5     130 .. 0.99

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 3.9e-47
                                       TSB----EEESTTCEEEECHHH..TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHH CS
                          AhpC-TSA   2 gdkapdfelknadgetvslsdy..kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkf 76 
                                       gd+apdfel++++g++ sl+++  +g+ +vl+fypkd++p+Ctte++ +++ +e++ ++gv+v+g+svdspesh+kf
  gi|557693752|ref|YP_008796806.1|   6 GDRAPDFELPDHQGRKTSLKQLlsNGRALVLYFYPKDDTPGCTTEACGFRDSMEKLSKHGVNVVGISVDSPESHQKF 82 
                                       9**********************999*************************************************** PP

                                       HHH-H.SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  77 iekeslnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                       i+k++lnf+llsD+ gkva+ y+ + eekg ++r+tf+id++g+ir+
  gi|557693752|ref|YP_008796806.1|  83 IAKYGLNFTLLSDSGGKVARLYNSYSEEKGRCIRKTFIIDRDGVIRA 129
                                       *********************************************97 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0   3.4e-30   7.5e-27       2     136 ..       5     136 ..       4     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 3.4e-30
                                       TTSBB---ECCEETTCEEEEEHHH..HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHH CS
                           Redoxin   2 agdkaPdftlplaatdgnsvslse..fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafv 76 
                                       agd+aPdf+lp+   +g ++sl++   +g+ +v++f+p  ++P C++e++ +++  e+l+++gv+vv++++d+ +  
  gi|557693752|ref|YP_008796806.1|   5 AGDRAPDFELPD--HQGRKTSLKQllSNGRALVLYFYPKDDTPGCTTEACGFRDSMEKLSKHGVNVVGISVDSPESH 79 
                                       8*********99..**********9888999*******************777776667****************** PP

                                       HHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSC CS
                           Redoxin  77 kefwgkeglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepep 136
                                       ++f++k+gl+f++lsD ++++++ ++ + +e ++   +++ +++id+dg++++ +  +  
  gi|557693752|ref|YP_008796806.1|  80 QKFIAKYGLNFTLLSDSGGKVARLYNSY-SEEKG--RCIRKTFIIDRDGVIRAAFHKVVA 136
                                       **************************66.55544..4****************9988766 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 !   23.0   0.0     3e-08   6.8e-05       3      57 ..      55     110 ..      53     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3e-08
                        AhpC-TSA_2   3 srdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalglkrgl 57 
                                       +++ ++l+++gv++v+i++++p s +kF++  g +f l+ D  +k+ ++ + ++  
  gi|557693752|ref|YP_008796806.1|  55 RDSMEKLSKHGVNVVGISVDSPeSHQKFIAKYGLNFTLLSDSGGKVARLYNSYSEE 110
                                       45679*****************77******************99999988877654 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 !   22.5   0.0   2.9e-08   6.6e-05      58     175 ..      22     131 ..       9     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.9e-08
                            DUF899  58 vsLadlFegrsqLivyhfmfgpdaeegCpgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwv 134
                                       +sL++l ++ + L++y   f p+     pgC++ a  +  ++++L++++v+++ +s    e+ +++ ++ G ++ + 
  gi|557693752|ref|YP_008796806.1|  22 TSLKQLLSNGRALVLY---FYPKD--DTPGCTTEACGFRDSMEKLSKHGVNVVGISVDSPESHQKFIAKYGLNFTLL 93 
                                       5677777766777766...44444..458************************************************ PP

                            DUF899 135 ssaesdfnrdfnvsleeeqaseelpglsvflrdd.grvfhtY 175
                                       s+ + ++ r +n  ++ee   + +   ++f+ d  g ++  +
  gi|557693752|ref|YP_008796806.1|  94 SDSGGKVARLYNS-YSEE---KGRCIRKTFIIDRdGVIRAAF 131
                                       ************6.5554...455666666666536666555 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0     4e-08     9e-05       2      95 .]      32     127 ..      30     127 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 4e-08
                                       SEEEEEE--SSSHH.HHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT- CS
                     Thioredoxin_8   2 kvvlLyfgaswcpp.ckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkkk 77 
                                       + ++Lyf+ +++ p c++      + +ekl+ k++v++v +s+d+  e+ +k+++k + +++     +++  k+++ 
  gi|557693752|ref|YP_008796806.1|  32 RALVLYFYPKDDTPgCTTEACGFRDSMEKLS-KHGVNVVGISVDSP-ESHQKFIAKYGLNFTL---LSDSGGKVARL 103
                                       667888887665555***************9.7************6.999*******555555...44445555555 PP

                                       S--TT......-SEEEEE-TT-BE CS
                     Thioredoxin_8  78 ynvka......iPtlvvldkngev 95 
                                       yn  +      i +++++d++g +
  gi|557693752|ref|YP_008796806.1| 104 YNSYSeekgrcIRKTFIIDRDGVI 127
                                       554444447889999999999976 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.3e-06     0.003       2     104 ..      10     108 ..       9     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.3e-06
                         SCO1-SenC   2 gpFelvdqdgeavteedl..egkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlk 76 
                                        +Fel d++g++ + ++l  +g+  +++f     +  C+t+    ++ +++l +    v+++ i+v    D+pe  +
  gi|557693752|ref|YP_008796806.1|  10 PDFELPDHQGRKTSLKQLlsNGRALVLYFYPKDDTPGCTTEACGFRDSMEKLSKH--GVNVVGISV----DSPESHQ 80 
                                       58***********999984457888888888888889***************999..788888888....5899*** PP

                         SCO1-SenC  77 eyleafdpriigltGskeeiakaakefr 104
                                       +++++++ +++ l++s  ++a++++++ 
  gi|557693752|ref|YP_008796806.1|  81 KFIAKYGLNFTLLSDSGGKVARLYNSYS 108
                                       ********************99999985 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.72   1.6e+03      41      64 ..       6      29 ..       2      32 .. 0.79
   2 !    9.3   0.0   0.00042      0.95      21      39 ..      61      79 ..      59      97 .. 0.84
   3 ?    4.2   0.0     0.017        38      46      66 ..     131     151 ..     118     152 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.72
                                      CEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT 41 agivfvvivvdeedleevlealkk 64
                                      ++++  ++++d+++ ++ l++l +
  gi|557693752|ref|YP_008796806.1|  6 GDRAPDFELPDHQGRKTSLKQLLS 29
                                      567788999999999999999876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00042
                                      HHHTTSEEEEEEEEEESTT CS
                               ACT 21 ladrgiNidsieqrssedk 39
                                      l+++g+N++ i++ s e +
  gi|557693752|ref|YP_008796806.1| 61 LSKHGVNVVGISVDSPESH 79
                                      89***********999886 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.017
                                       EEEEEEHHHHHHHHHHHHTTC CS
                               ACT  46 vvivvdeedleevlealkkle 66 
                                       +  vv + ++eevle++kkl+
  gi|557693752|ref|YP_008796806.1| 131 FHKVVADGHAEEVLETIKKLG 151
                                       567889999**********96 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00017      0.38      80     116 ..      47      91 ..      20     151 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                                       EEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH...........H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........x RF
                       Radical_SAM  80 itvetngtlpdeeklerllelgvdrvslgleaadde...........k 116
                                       +t e++g+++    +e+l + gv++v ++++++ +            +
  gi|557693752|ref|YP_008796806.1|  47 CTTEACGFRD---SMEKLSKHGVNVVGISVDSPESHqkfiakyglnfT 91 
                                       5667777776...9*******************996444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); 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: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1033.13
//
Query:       gi|557693753|ref|YP_008796807.1|  [L=117]
Description: iron-sulfur cluster assembly accessory protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-21   74.4   0.0    8.4e-21   74.2   0.0    1.0  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   4.7e-25   8.4e-21       2     110 ..       9     111 ..       8     112 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 4.7e-25
                                       EEEE-HHHHHHHHHHHHCTTEC....EEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEEETTEEEEEEGG CS
                       Fe-S_biosyn   2 kitlteaAaeklkkllaedkke....lrLdvddgggpyskggCsiggkyslvlvdeedeeydevlesnggkvyvksy 74 
                                       k+t+te+Aa+k+ +l++++++     lr+++  gg       Cs g++y + l ++   e+d+v++ +g+kv+v+s 
  gi|557693753|ref|YP_008796807.1|   9 KLTVTERAAKKIAQLIEQEGGSdkmaLRIYITGGG-------CS-GYRYGMALDENV-YEDDVVVNAHGVKVVVDSF 76 
                                       89****************99889999999999999.......**.**********99.******************* PP

                                       GHHHS.TTEEEEEEEETTEEEEEEETCCEEEEEEEE CS
                       Fe-S_biosyn  75 slvfldeglvldfvedlgtlgLksdngilddnvglg 110
                                       s++fl eg ++d+ ed +++g+  +n+++ +++g+g
  gi|557693753|ref|YP_008796807.1|  77 SAPFL-EGSEIDYIEDVMGSGFAINNPNVVSSCGCG 111
                                       *****.9****************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 874.88
//
Query:       gi|557693754|ref|YP_008796808.1|  [L=215]
Description: DNA-directed RNA polymerase subunit D [Candidatus Caldiarchaeum subterraneum]
Scores for 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   84.5   0.0    8.9e-24   84.0   0.0    1.2  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    5.1e-11   41.9   0.0    6.8e-11   41.4   0.0    1.2  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation 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 !   84.0   0.0   9.9e-28   8.9e-24       3     112 .]      44     156 ..      42     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 9.9e-28
                                       EEECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSEC...EEGGGCBES..SS CS
                     RNA_pol_A_bac   3 ieentsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpge...vtagdlkle..da 74 
                                       ++en+s + +Ev+aHr++lip++++ + +  +  +e+  +   g+e++ v + L+++  ++   v+++d+k e  d+
  gi|557693754|ref|YP_008796808.1|  44 VIENSSPMTNEVLAHRISLIPFITDLDNF--NVAEECSCQSRLGCEKCVVRFVLRAEAADQpvtVYSRDIKPErhDT 118
                                       679********************888777..666777436789***************999999********98888 PP

                                       SCEESSTTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                     RNA_pol_A_bac  75 dveivnpdilIakLrkgqeleleakvkkGiGkehakfs 112
                                       +v +++ +i+I+ L++ q++ele++v+ G+G++hak++
  gi|557693754|ref|YP_008796808.1| 119 KVAPFDGNIPIVVLAPRQKIELELYVRLGRGRKHAKWQ 156
                                       89999********************************6 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 !   41.4   0.0   7.6e-15   6.8e-11       5      67 ..      16     194 ..      12     196 .. 0.79

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 7.6e-15
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                         RNA_pol_L   5 rgvdhtlgNaLRrillsevpgvaiea................................................... 30 
                                        +  h l+NaLRr+++ evp++a+e+                                                   
  gi|557693754|ref|YP_008796808.1|  16 TDLPHPLANALRRMIIREVPTMAVEEilviensspmtnevlahrislipfitdldnfnvaeecscqsrlgcekcvvr 92 
                                       667899********************************999999999999999999999999999999999999888 PP

                                       ...................................xx................xxxx................xxxx RF
                         RNA_pol_L  31 ...................................pv................vkvn................tdkd 40 
                                                                          p+                                    ++ +
  gi|557693754|ref|YP_008796808.1|  93 fvlraeaadqpvtvysrdikperhdtkvapfdgniPIvvlaprqkielelyvrL--GrgrkhakwqsgiatlyQENS 167
                                       888888888866666666666666665555555552266666666555555440..2555555566677777799** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  41 klilevetdgslkPeealkeAlkiLke 67 
                                       +  l ve+ g l+P+ +++eA++i k 
  gi|557693754|ref|YP_008796808.1| 168 RWLLYVESYGFLPPRRMVLEAARIVKT 194
                                       ***********************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1534.23
//
Query:       gi|557693755|ref|YP_008796809.1|  [L=107]
Description: large subunit ribosomal protein L18e [Candidatus Caldiarchaeum subterraneum]
Scores for 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-11   43.0   1.3    3.5e-10   40.6   1.3    1.9  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27
    5.1e-09   35.8   0.1    6.4e-09   35.5   0.1    1.0  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
  ------ inclusion threshold ------
       0.22   11.8   1.6       0.77   10.1   0.5    2.1  2  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4


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 !   40.6   1.3   5.9e-14   3.5e-10      62     126 ..      22      87 ..       2      89 .. 0.73

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 5.9e-14
                                       TTGTTS------EEEGGGTTTTSSS....SE..EEE--S---.--EEEESEE-HHHHHHHHHTT-EE CS
                    Ribosomal_L27A  62 deerleladeaeeidleelaeaglikkkdgv..KvlgkgeltkklkvkaskfSkkAkekIeaaGGkv 126
                                       +e+r++   ++ e+++++l+++ + ++   v  Kvlg+g+ltkkl+v a +fS++A++kI++aGG++
  gi|557693755|ref|YP_008796809.1|  22 KELRRSR-RSTREVNISRLQRNTMDNEVVFVpgKVLGQGSLTKKLTVGAFSFSQSAIQKIQKAGGRA 87 
                                       2333321.3567888888855555555333345********************************97 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 !   35.5   0.1   1.1e-12   6.4e-09      40     134 ..      14     102 ..       8     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.1e-12
                     Ribosomal_L18  40 skFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsvaALrftetararilkaG 116
                                       ++F k +lk L  sr+  + + +srl +++     +++++ v g+v+    l++  kl+v A+ f+++a ++i kaG
  gi|557693755|ref|YP_008796809.1|  14 TRFAKRLLKELRRSRRSTREVNISRLQRNTM----DNEVVFVPGKVLGQGSLTK--KLTVGAFSFSQSAIQKIQKAG 84 
                                       68************************99887....5689999*******99986..9******************** PP

                     Ribosomal_L18 117 GeiltlDqLalraPtGkn 134
                                       G  l l+++  +  +G+ 
  gi|557693755|ref|YP_008796809.1|  85 GRALLLEEFLREFGKGSG 102
                                       *****9998887777776 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 ?   10.1   0.5   0.00013      0.77       9      41 ..      12      41 ..       9      48 .. 0.74
   2 ?    0.3   0.0      0.14   8.5e+02       1      17 [.      49      65 ..      49      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00013
                                      EE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TT CS
                    RNA_pol_Rpb2_4  9 GvtrdpkklvetlRelRRkgkiseevsivlnek 41
                                      G tr  k+l+++lR+ RR+ +   ev+i++ ++
  gi|557693755|ref|YP_008796809.1| 12 GKTRFAKRLLKELRRSRRSTR---EVNISRLQR 41
                                      667888888888888888766...888887665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.14
                                      EECTT-BEEE-S-HCCH CS
                    RNA_pol_Rpb2_4  1 VfvNGrllGvtrdpkkl 17
                                      Vfv G++lG  +  kkl
  gi|557693755|ref|YP_008796809.1| 49 VFVPGKVLGQGSLTKKL 65
                                      9*******976666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 772.38
//
Query:       gi|557693756|ref|YP_008796810.1|  [L=145]
Description: large subunit ribosomal protein L13 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   46.5   0.3    4.8e-10   39.8   0.2    2.4  1  Ribosomal_L13  Ribosomal protein L13
  ------ inclusion threshold ------
      0.033   14.3   0.1       0.31   11.2   0.0    2.2  2  PHB_acc_N      PHB/PHA accumulation regulator DNA-binding dom
      0.077   13.1   1.6        1.2    9.3   0.1    2.4  2  TEA            TEA/ATTS domain


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 !   39.8   0.2     8e-14   4.8e-10       4     117 ..       1     104 [.       1     111 [. 0.79

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 8e-14
                                       EEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEE.EE-SSTTSEEEEEHHHH CS
                     Ribosomal_L13   4 viDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyy.rhtgypgglkevtakel 79 
                                       ++DAeg  lgrlas +ak+L              G  v +inaek ++tg+k +   +y    ++ +  ++ +++  
  gi|557693756|ref|YP_008796810.1|   1 MVDAEGYRLGRLASYVAKLLLK------------GHRVTIINAEKTVITGNKPAILEHYlMLRNRKQFSSHKKITVW 65 
                                       58****************9975............55689*************8765444144445444555666667 PP

                                       HCCSHHHHHHHHHHCCS-SSH.HHHHHGCTEEEESSSTT CS
                     Ribosomal_L13  80 lekkpeeilekaVkgmLpknk.lgrrrlkrLkvyageeh 117
                                         +kp+ il++a+ +mLp++k  gr+  krL v +g++ 
  gi|557693756|ref|YP_008796810.1|  66 YPTKPDAILRLAITRMLPRKKpRGREAAKRLVVLKGPAN 104
                                       899***************8763778888*******9976 PP

>> PHB_acc_N  PHB/PHA accumulation regulator DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.13   7.6e+02      23      40 ..      15      32 ..      13      37 .. 0.85
   2 ?   11.2   0.0   5.2e-05      0.31       9      32 ..     119     144 ..     118     145 .] 0.84

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.13
                         PHB_acc_N 23 diaelvregeevkVvDak 40
                                       +a+l  +g++v ++ a+
  gi|557693756|ref|YP_008796810.1| 15 YVAKLLLKGHRVTIINAE 32
                                      589999*******99876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 5.2e-05
                         PHB_acc_N   9 rLYdtets..sYitlediaelvrege 32 
                                       +LY+ +++  +Yitle+++++ r g+
  gi|557693756|ref|YP_008796810.1| 119 KLYNRSAKiiRYITLEELSKMLRGGR 144
                                       79998776559***********9886 PP

>> TEA  TEA/ATTS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0002       1.2      45      61 ..      43      59 ..      13      63 .. 0.91
   2 ?    3.1   0.3     0.017        99      29      52 ..      94     138 ..      61     142 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0002
                               TEA 45 IlkktgkertrKQvsSh 61
                                      Il++ ++ r+rKQ sSh
  gi|557693756|ref|YP_008796810.1| 43 ILEHYLMLRNRKQFSSH 59
                                      6888999********** PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.017
                               TEA  29 k.....................legklhgRnelIseyIlkktgke 52 
                                       k                       +kl++R   I  yI+ + + +
  gi|557693756|ref|YP_008796810.1|  94 KrlvvlkgpanvegekiefedaKLTKLYNRSAKIIRYITLEELSK 138
                                       355555555555555555555544788999999999997766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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:                         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 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1041.36
//
Query:       gi|557693757|ref|YP_008796811.1|  [L=131]
Description: small subunit ribosomal protein S9 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  108.1   0.0    4.2e-31  108.0   0.0    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16
  ------ inclusion threshold ------
       0.18   12.0   1.1       0.29   11.3   1.1    1.3  1  DUF3886       Protein of unknown function (DUF3886)


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 !  108.0   0.0   4.7e-35   4.2e-31       1     121 []      10     131 .]      10     131 .] 0.95

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 4.7e-35
                                       EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSSS.EEEEEEEESS-HHHHHHHHHHHHHH CS
                      Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllgk.fdvfvkvkgGGlsgqaeAirlgiar 76 
                                       G+rK+svA+v +++gkg+i vn+++le  f+ e  r+kvl pl l+ +  k  d++v+vkgGG+++ aeAi+ ++++
  gi|557693757|ref|YP_008796811.1|  10 GKRKTSVAKVFLRPGKGNIFVNKTPLEL-FN-EFFRSKVLTPLLLLPEFWKkHDFHVTVKGGGVMSSAEAIAIAVSK 84 
                                       8***************************.87.899*******9998776544************************* PP

                                       HHHHHHHHHHHHHC..TCCCTS-B--------TTSSCTTB----S-- CS
                      Ribosomal_S9  77 aLvalekeekkeLk..kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                       a +a ++e+k+ L+  +++ll+ DpR+ E+kK+++++AR+k+q+s+R
  gi|557693757|ref|YP_008796811.1|  85 AAAAESEEYKQRLEsyDRSLLVDDPRRAEPKKPNRRGARRKPQKSYR 131
                                       ***999988*****999****************************99 PP

>> DUF3886  Protein of unknown function (DUF3886)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.1   3.3e-05      0.29      14      51 ..      91     128 ..      89     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.3e-05
                           DUF3886  14 edvlekLkakkkeLkeeeekrkeeekarreeerkarek 51 
                                       e+ +++L +  ++L   + +r e++k+ r+ +r++ +k
  gi|557693757|ref|YP_008796811.1|  91 EEYKQRLESYDRSLLVDDPRRAEPKKPNRRGARRKPQK 128
                                       78899******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 993.33
//
Query:       gi|557693758|ref|YP_008796812.1|  [L=72]
Description: DNA-directed RNA polymerase subunit N [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  100.4   0.5      6e-29  100.1   0.5    1.1  1  RNA_pol_N       RNA polymerases N / 8 kDa subunit
    0.00075   19.7   0.2    0.00094   19.4   0.2    1.2  1  Chordopox_RPO7  Chordopoxvirus DNA-directed RNA polymerase 7 


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 !  100.1   0.5   6.7e-33     6e-29       1      59 []       1      59 [.       1      59 [. 0.99

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 6.7e-33
                                      ----SS-TTT--B-STHHHHHHHHHHTT--HHHHHHHHT--SHHHHHHHHTB--THHHH CS
                         RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekgeepkdaLdaLglkryCCrrmllthvdliekl 59
                                      M++P+rCF+CG+vi++kw+ey++++++g++p+d+Ld+Lg+kryCCrrm+++ v+++++l
  gi|557693758|ref|YP_008796812.1|  1 MMFPIRCFSCGRVIAHKWDEYQRRVSEGQHPRDVLDSLGFKRYCCRRMFISAVNVMDEL 59
                                      9*******************************************************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 !   19.4   0.2   1.1e-07   0.00094       1      41 [.       1      46 [.       1      59 [. 0.79

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-07
                    Chordopox_RPO7  1 mvfplvCstCGrDlsee..ryrLlv.kkkkLkdvlat..vkrkCCr 41
                                      m+fp+ C +CGr ++++   y+  v + ++ +dvl++  +kr CCr
  gi|557693758|ref|YP_008796812.1|  1 MMFPIRCFSCGRVIAHKwdEYQRRVsEGQHPRDVLDSlgFKRYCCR 46
                                      99*************9633576555166889****984469****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 583.05
//
Query:       gi|557693759|ref|YP_008796813.1|  [L=414]
Description: enolase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-59  200.9   0.0    3.6e-59  200.4   0.0    1.1  1  Enolase_C       Enolase, C-terminal TIM barrel domain
    1.1e-25   90.3   0.0    1.7e-25   89.7   0.0    1.4  1  Enolase_N       Enolase, N-terminal domain
    1.8e-11   44.0   0.0    2.8e-11   43.4   0.0    1.3  1  MR_MLE_C        Enolase C-terminal domain-like
  ------ inclusion threshold ------
      0.021   14.6   0.0      0.043   13.6   0.0    1.4  1  Succ_CoA_lig    Succinyl-CoA ligase like flavodoxin domain
       0.11   11.7   0.0       0.17   11.0   0.0    1.3  1  MAAL_C          Methylaspartate ammonia-lyase C-terminus
       0.11   12.7   0.1       0.34   11.1   0.0    1.8  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
        1.8    9.2   5.3       0.59   10.8   0.3    2.6  3  Ribosomal_60s   60s Acidic ribosomal protein


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 !  200.4   0.0   1.4e-62   3.6e-59       3     261 ..     138     385 ..     136     392 .. 0.95

  Alignments for each domain:
  == domain 1  score: 200.4 bits;  conditional E-value: 1.4e-62
                                       EE-EE-EEEEE-GGGSSS.S--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SS CS
                         Enolase_C   3 vlPvPalnvinGGshagn.klalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqs 78 
                                       v P+P+ nv+ GG hag+ + ++qef++ P    s++ea+r+ +ev+++l +vl kk g   +  GdeG +aP +++
  gi|557693759|ref|YP_008796813.1| 138 VYPIPLGNVLGGGAHAGEgAPDIQEFLVFPRKPGSVEEAVRMNVEVHKRLGKVLAKKVGGYGGGKGDEGAYAPPVDD 214
                                       68**************86267******************************************************87 PP

                                       HHHHHHHHHHHHHHCT-TCTBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEE CS
                         Enolase_C  79 nkealdliveaiekaGykgkvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsie 155
                                       + +al+     +++a    +v  +ldva+s +y++  k+y+   ++      k+lt eq +++  elv+ky i  +e
  gi|557693759|ref|YP_008796813.1| 215 E-KALEA----VKEASEGLDVGFGLDVAASSLYDAARKNYHYRNRG------KHLTREQHMQHISELVEKYGISYVE 280
                                       5.68865....555666679****************9***999888......99*********************** PP

                                       S-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEE CS
                         Enolase_C 156 dpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvv 232
                                       dp++e d e++++l +    k+ + Gddl+vt ++ ++ a ek+a  a++lk nq+G++t+++ea+k a++ g   v
  gi|557693759|ref|YP_008796813.1| 281 DPFEETDVEGFAELCKAFP-KLLVCGDDLVVTRAELIRWASEKRAVKAVILKPNQVGTITDTVEAAKEAEKRGIVRV 356
                                       ******************9.9******************************************************** PP

                                       EE--SC--S--HHHHHHHHCT-SEEE--- CS
                         Enolase_C 233 vshrsGetedttiadlavglsaGqiktGa 261
                                       vshrsGet d+++++la+gl    ik+G 
  gi|557693759|ref|YP_008796813.1| 357 VSHRSGETCDSFLTHLAIGLGGKFIKAGV 385
                                       **************************996 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7   0.0   6.8e-29   1.7e-25       1     131 []       8     129 ..       8     129 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 6.8e-29
                                       EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHT CS
                         Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapali 77 
                                       I++ +a  +ldSrG+ T+ev+++   ++ ++a++psG S g++ea+ + +g        g +++v+ +++ ++++l+
  gi|557693759|ref|YP_008796813.1|   8 ITDAEAWVVLDSRGSETIEVTLYSG-KVSATASAPSGKSRGSREAVPFPEG--------GAKQSVKLFTSSLRSRLV 75 
                                       67888999****************6.5678****************66665........9***************** PP

                                       TSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                         Enolase_N  78 gldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                       g d++dq++iD+ll e+Dgten sk+G+N ++avS + +k aA  k+ p +r++
  gi|557693759|ref|YP_008796813.1|  76 GRDPADQTDIDTLLKEVDGTENFSKIGGNLAYAVSACSVKLAAMLKQKPTWRHV 129
                                       **************************************************9996 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 !   43.4   0.0   1.1e-14   2.8e-11      25     156 ..     200     360 ..     173     390 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.1e-14
                                       S.........HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTS..................BHHHHHHHHHHHGG.GT CS
                          MR_MLE_C  25 d.........dvaedvervravreavgpgddvdlmvDanqaw..................dlatAirvarelee.ld 73 
                                       +          + +d + ++av+ea  +g dv + +D+ ++                   ++++ ++ + el e ++
  gi|557693759|ref|YP_008796813.1| 200 GgkgdegayaPPVDDEKALEAVKEAS-EGLDVGFGLDVAASSlydaarknyhyrnrgkhlTREQHMQHISELVEkYG 275
                                       14455566678899999999999997.89999*****99995568899999999999999************555** PP

                                       ESEEESSSSTTTHHHHHHHHHHHH..SSEEEESTTSSSHHHHHHHHHH.TSESEEEEBHHHHTSHHHHHHHHHHHHH CS
                          MR_MLE_C  74 llwlEEPvppeddleglaelrara..sipiaagEslysradfrellea.gavdivqpdvsrvgGitearkvaalaea 147
                                       + ++E+P+    d+eg ael  +a  ++ ++++  + +ra++ +++++ +av +v +++++vg it +++ a+ ae+
  gi|557693759|ref|YP_008796813.1| 276 ISYVEDPFEE-TDVEGFAELC-KAfpKLLVCGDDLVVTRAELIRWASEkRAVKAVILKPNQVGTITDTVEAAKEAEK 350
                                       *********9.67********.666899*************998886527*************************** PP

                                       TT-.EEEEBS CS
                          MR_MLE_C 148 fgv.pvapHs 156
                                       +g+ +v+ H 
  gi|557693759|ref|YP_008796813.1| 351 RGIvRVVSHR 360
                                       **62576666 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 ?   13.6   0.0   1.7e-05     0.043      28      92 ..     298     364 ..     293     373 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                      Succ_CoA_lig  28 fskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarraark..kpvvvlksGrs 92 
                                       f k++ +G+ + v+ a+l+++ +e+ ++k+++l   +++     ++aa++a ++  ++vv  +sG++
  gi|557693759|ref|YP_008796813.1| 298 FPKLLVCGDDLVVTRAELIRWASEKRAVKAVILKPNQVGTITDTVEAAKEAEKRgiVRVVSHRSGET 364
                                       5677889*********************************************988888998888876 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.7e-05      0.17     143     206 ..     304     368 ..     262     383 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.7e-05
                            MAAL_C 143 vaDeWcntled.irefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsa 206
                                         D+   t  + ir   +++a+++v +k   +G+i++t+ea   ++++g+   +   + et  s 
  gi|557693759|ref|YP_008796813.1| 304 CGDDLVVTRAElIRWASEKRAVKAVILKPNQVGTITDTVEAAKEAEKRGIVRVVSHRSGETCDSF 368
                                       55666666555156666789*****************************9988888777776665 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 ?   -2.1   0.0       1.7   4.4e+03      91     111 ..     110     130 ..     103     132 .. 0.82
   2 ?   11.1   0.0   0.00013      0.34      14      62 ..     314     362 ..     237     367 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHCTT---HHHHH CS
                    Asparaginase_C  91 eaarikLmlllgkgldpaevr 111
                                        a+ +kL+ +l+++ + + v+
  gi|557693759|ref|YP_008796813.1| 110 SACSVKLAAMLKQKPTWRHVA 130
                                       689999*99999998888776 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00013
                                       HHHHHHHHT.T--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSS CS
                    Asparaginase_C  14 kvlkallkk.gakGvvlegtGvGnlpsallealkeakargivvvatsqcp 62 
                                       ++++ + +k  +k+v+l+   vG +++ ++ea+kea +rgiv v++ +  
  gi|557693759|ref|YP_008796813.1| 314 ELIRWASEKrAVKAVILKPNQVGTITD-TVEAAKEAEKRGIVRVVSHRSG 362
                                       555555555489************985.789**************99975 PP

>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.3   3.4e+03      42      59 ..      32      43 ..      12      56 .. 0.53
   2 ?   10.8   0.3   0.00023      0.59      32      87 ..     180     234 ..     168     234 .. 0.88
   3 ?   -2.3   0.1       2.8   7.2e+03      56      61 ..     342     347 ..     313     351 .. 0.50

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                                      XXXXXXXXXXXXXXXXXX CS
                     Ribosomal_60s 42 gaaklaaaaaaaaaaaaa 59
                                      g+      ++a+a+a   
  gi|557693759|ref|YP_008796813.1| 32 GK------VSATASAPSG 43
                                      32......2223332222 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX--S.S--STT CS
                     Ribosomal_60s  32 gkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeEeedd.dmGfgL 87 
                                       ++++++ l+++ ak   +++ +   + ++a a++ +++k+ e  +E ++  d GfgL
  gi|557693759|ref|YP_008796813.1| 180 NVEVHKRLGKVLAK--KVGGYGGGKGDEGAYAPPVDDEKALEAVKEASEGlDVGFGL 234
                                       67899999999999..9999999999999999999999999999999999******9 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.8
                                       XXXXXX CS
                     Ribosomal_60s  56 aaaaaa 61 
                                        +aa++
  gi|557693759|ref|YP_008796813.1| 342 VEAAKE 347
                                       222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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 0.22s 00:00:00.73 Elapsed: 00:00:00.37
# Mc/sec: 3313.36
//
Query:       gi|557693760|ref|YP_008796814.1|  [L=208]
Description: small subunit ribosomal protein S2 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   83.5   1.5    3.6e-12   46.0   0.2    2.0  2  Ribosomal_S2  Ribosomal protein S2
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.32   11.2   0.0    1.8  1  PYRIN         PAAD/DAPIN/Pyrin domain


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 !   37.5   0.1   1.6e-13   1.4e-09       1      98 [.      15     108 ..      15     114 .. 0.90
   2 !   46.0   0.2     4e-16   3.6e-12     147     213 ..     113     179 ..     109     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.6e-13
                      Ribosomal_S2   1 LLeagvhfGhqtrrwnpkmkpyIyger.ngihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaa 76 
                                       L++ +vh+G + +   ++m+pyI+  r +g+++++++k+l+ l+ a+k+++    + +++l v+t+    +av++ a
  gi|557693760|ref|YP_008796814.1|  15 LVKYNVHVGSRIK--VKHMEPYIFRMRyDGVYLFEVKKILTRLNLAAKLIS--YYDPSEVLAVSTHVFGMKAVQKFA 87 
                                       67889****8777..688******76648*********************9..568899****************** PP

                      Ribosomal_S2  77 krangyyvnerWlgGtLTNfkt 98 
                                       + ++g+ +  + + G+LTN +t
  gi|557693760|ref|YP_008796814.1|  88 ELTGGMAMAGKMMAGMLTN-RT 108
                                       *******************.44 PP

  == domain 2  score: 46.0 bits;  conditional E-value: 4e-16
                      Ribosomal_S2 147 klPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladaie 213
                                       + P++v++ dp+ +  a++Ea+ ++ipvia++ t+   ++vd +Ip+N+ s  s+   + +la+ + 
  gi|557693760|ref|YP_008796814.1| 113 TEPSIVIISDPRYDAQALEEAAIARIPVIAMCSTDNTCSNVDLVIPMNNRSRTSLPYAFWYLARRVL 179
                                       579***************************************************9998888888776 PP

>> PYRIN  PAAD/DAPIN/Pyrin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.6e-05      0.32      35      66 ..      47      79 ..      29      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.6e-05
                                      CHCT.-SHHHHHHHHHHHHTCCCCHHHHHHHHH CS
                             PYRIN 35 elek.adrvdladlLvehygedaavevtlkvle 66
                                      e++k  +r++la +L+++y  ++++ v  +v+ 
  gi|557693760|ref|YP_008796814.1| 47 EVKKiLTRLNLAAKLISYYDPSEVLAVSTHVFG 79
                                      6788889************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); 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 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1516.09
//
Query:       gi|557693761|ref|YP_008796815.1|  [L=715]
Description: DNA polymerase I [Candidatus Caldiarchaeum subterraneum]
Scores for 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-20   72.3   0.0    3.7e-19   68.8   0.0    2.2  1  DNA_pol_B       DNA polymerase family B
    1.2e-09   37.8   0.0    2.5e-09   36.7   0.0    1.4  2  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain


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 !   68.8   0.0   4.1e-23   3.7e-19      45     413 ..     346     673 ..     310     694 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 4.1e-23
                                       ----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---H CS
                         DNA_pol_B  45 qGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvaseeeakeleaedeyleveveprlvefvkksvregl 121
                                        G+ +l+ + g+y  +v  lDF SLYP ++++hN++ +t+ ++  + +++++      ++v +         + +g+
  gi|557693761|ref|YP_008796815.1| 346 RGGWILDHQPGVYW-NVGELDFHSLYPMLMLKHNISGETVNCRCCSGDDIPELG----YHVCG---------KWRGI 408
                                       69999999999997.6999*************************9999988754....66665.........579** PP

                                       HHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHH CS
                         DNA_pol_B 122 lpklLkdllakRkaikkelkeekdefekalldkqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektk 198
                                       +p+ +++ l +R ++k+  +e  d+    ++ ++  alK +  + +G++G+++ ++ + +    v +  R++L++  
  gi|557693761|ref|YP_008796815.1| 409 VPRAIEEPLRRRLEYKRLYQEGGDK----VYKARADALKWILVTSFGYLGYRKAKFGSREAHMAVCALARDTLLRSV 481
                                       ****************999988888....9999999***************************************** PP

                                       HHHHHT...SSGGGT-SS.....T-EEEEEBSSEEEEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEE CS
                         DNA_pol_B 199 elvekkaellskllalpeeaeeeklkviYGDTDSvfielkvkdveellkigkelaeevseklfkkplklefekvykk 275
                                       +l e++                 ++kv  G  D ++i  +  + e+  ++g++l++++          + +e ++k 
  gi|557693761|ref|YP_008796815.1| 482 KLAEEH-----------------GFKVLHGIVDCLWIWRRDASEEDYRAFGEALEKRLGL-------PVGYEGTFKW 534
                                       ****88.................9******************************998765.......5899****** PP

                                       EEEEETT.........EEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHH CS
                         DNA_pol_B 276 llLisKK.........kYaglkvektskanklliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealk 343
                                       + ++            +Y g +v+     +++ ++Gv+  Rrd  +lv+++ +++l++l +     r+++++le+ +
  gi|557693761|ref|YP_008796815.1| 535 IAFLDSRtspgrpvnnRYFGAYVD-----GRIKCRGVEARRRDTPPLVRRMQQELLTKLAEV-CSPRDVPQKLEECH 605
                                       999987622222222266666666.....69***************************9999.8889********** PP

                                       HHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS CS
                         DNA_pol_B 344 silkdvleeleenkvplekfvlskelskepenyksknlphlevakrlkkrneeapevgdrisYvivekkk 413
                                       +i+k+ l+ +  ++v +e++ +++++s + e+y   ++ h+e+ak + k+ ++ +++g  +sYv+ + + 
  gi|557693761|ref|YP_008796815.1| 606 EIFKRYLRMVYLGSVGVEELAVTRSVSGPVESYGR-RIKHVEAAK-MLKQMGASVSPGQSVSYVVKHGAG 673
                                       ****************************9999944.346999876.5555699***********876654 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 ?   -4.1   0.0      0.73   6.5e+03      95     118 ..     102     125 ..     100     132 .. 0.82
   2 !   36.7   0.0   2.8e-13   2.5e-09     202     319 ..     167     274 ..     149     279 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 0.73
                                       CCCCCSSS--HHHHHHHHCTS-TT CS
                    DNA_pol_B_exo1  95 ivdvyeydvdylerflidnkivgf 118
                                       +++vy++d ++   fl+ +++ + 
  gi|557693761|ref|YP_008796815.1| 102 GIRVYNVDLPPAQEFLYSHGLATT 125
                                       5789***********999988765 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 2.8e-13
                                       EEEEEEECCCTSS----EE--SSTCSTTEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCC CS
                    DNA_pol_B_exo1 202 arklftlrecaseeeedfeltpkpeypgvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakely 278
                                       +r++ +l++               +  g +++   +E ++L++ + ++ + d dv+++Y +d+F +pY+  Ra+ ++
  gi|557693761|ref|YP_008796815.1| 167 PRFIHPLKNVK------------VVCGGEEIVLDGDEEKVLMELVHVLDEFDVDVVVTYGGDSFLMPYLRYRAR-VN 230
                                       55555555555............3433448888899**************************************.99 PP

                                       TCCHCG.SCCS.CTCEECCCCESEE.....EEEECEEEETTSEEEEH CS
                    DNA_pol_B_exo1 279 kvklsklgrln.kggrskvseigfs.....kqarekvkisgrihlDl 319
                                       +v+l+ lgr +  +gr   + ++++      ++++ ++++gr+h+D 
  gi|557693761|ref|YP_008796815.1| 231 NVELR-LGREEdPRGR--SRGFSYMsygrvYHSYSGYRLRGRLHIDA 274
                                       99976.5988554444..4445555557999***************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (715 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 4852.05
//
Query:       gi|557693762|ref|YP_008796816.1|  [L=308]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-60  202.9   0.0    9.8e-58  196.0   0.0    2.0  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
        0.1   11.9   0.0        0.2   11.0   0.0    1.5  1  TMP-TENI        Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.0   0.0   1.1e-61   9.8e-58      16     312 ..      12     281 ..       1     282 [. 0.87

  Alignments for each domain:
  == domain 1  score: 196.0 bits;  conditional E-value: 1.1e-61
                    Bac_luciferase  16 gaasaslrylvelaraaEelGfdavwvaehhggpgga..ldaftllaalaaaTerirlgtavtplytrhPavlAqqa 90 
                                       +++ +++r +v+ +++ EelGf +vwv++h+++ + +  l+++tllaala++T+  rlgt v++ + rhP +lA++a
  gi|557693762|ref|YP_008796816.1|  12 PRYDVDFRKVVDTVVMFEELGFSSVWVTDHLQPRRASriLESWTLLAALAPVTDA-RLGTVVLCSCYRHPSLLAKMA 87 
                                       445579**************************98888****************86.********************* PP

                    Bac_luciferase  91 atLdhlsgGRfglglgtggpaveerrf..Gv...dhderyarlrEfvevlrrlwrg.eevdfeGeffsvkgalllpr 161
                                       atLd +s+GR++lg+gtg+ ++ e++   G+   +  e  +r++E+vevl+ l+++ ++v +eG+f+s++ al+  +
  gi|557693762|ref|YP_008796816.1|  88 ATLDTISNGRLELGVGTGSEPQTEEMQalGMetwPPKEKIQRFKEYVEVLKLLLSDgGPVIYEGKFYSLRAALRNTP 164
                                       *****************99999988885566***********************663777*********77777777 PP

                    Bac_luciferase 162 pgqgpiP.vyvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeA 237
                                       + q+p+P ++++a + ++++laa+++dg+ + ge++ e++e+++ ++   a+ gr   ++  +i + + + +++++ 
  gi|557693762|ref|YP_008796816.1| 165 SIQKPHPpIWIGARGRKMVKLAAEIGDGWNFYGETLTEYREAVKLFDDESAKLGR---KPSKAIFTNLLLYKDDADK 238
                                       77777555***********************************************...999**************** PP

                    Bac_luciferase 238 raearaliagldfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagv 312
                                        +++++l                           + +++++a +         t+l+Gtp+qv++++++++e gv
  gi|557693762|ref|YP_008796816.1| 239 MEKMKHLG--------------------------SHGSEQEALRKT------YTLLHGTPDQVIKQVEELQERGV 281
                                       ***96666..........................223333333332......36679999999999999998886 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.2e-05       0.2      13      51 ..     267     305 ..     259     308 .] 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.2e-05
                          TMP-TENI  13 eellevveealkggvtlvqlRekeldarellelaeklaa 51 
                                       ++++++vee+ + gv l+ lR+ + +a+++++ a+++ +
  gi|557693762|ref|YP_008796816.1| 267 DQVIKQVEELQERGVGLIILRDMDPEASSIKAFAKEITP 305
                                       6789*******************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); 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 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2181.91
//
Query:       gi|557693763|ref|YP_008796817.1|  [L=150]
Description: PilT protein domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-08   34.5   0.2    3.3e-08   34.1   0.2    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 !   34.1   0.2   1.8e-12   3.3e-08       1     120 [.       5     139 ..       5     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.8e-12
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS.......SCHCHHHHHHHHHHHHH.H CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleel....eelvtsalvlaEllyvlar.......rkskrekaaelvellll.l 65 
                                       ++lDTs++++ + +++++e +r l+ ++     +l++s+  + E+l vl +       +  ++ +a+++++ +l   
  gi|557693763|ref|YP_008796817.1|   5 VYLDTSAIVKRYVDDPGSEFVRSLYRKAytgeIKLASSIWNVGEMLGVLDKayavgriNGGDHVAARRRFLNELNrQ 81 
                                       69*******************************************************94444444444444444447 PP

                                       HTSEEEE...BCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  66 salkilp...idaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                        ++  l    +  +i+   +++++k+ +  +Dal +  Ak+  ++ i+ +D+++++va
  gi|557693763|ref|YP_008796817.1|  82 TRFGTLTiihLRVSILINSWQLIEKHHIYQADALQITSAKYVSADQIVVADKKLYDVA 139
                                       766555555599*****************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1061.34
//
Query:       gi|557693764|ref|YP_008796818.1|  [L=90]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   12.9   0.8        0.6   10.0   0.1    2.3  3  RHH_4     Ribbon-helix-helix domain


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 ?   10.0   0.1   3.3e-05       0.6      11      53 ..       5      46 ..       3      50 .. 0.82
   2 ?    1.3   0.0     0.017   3.1e+02      23      36 ..      48      61 ..      42      63 .. 0.88
   3 ?   -1.7   0.0      0.16   2.8e+03      37      48 ..      74      81 ..      67      89 .. 0.46

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.3e-05
                                      EEEEEEEEHHHHHHHHHHHHHTT--HHHHHHHH.HHHHSS.TH CS
                             RHH_4 11 hrTSirLEpafWdaLeeiArregltvnaLiaeidadrrgeanL 53
                                      ++ S+ +  ++W+ +++ A++++ + + L++e+  +++   nL
  gi|557693764|ref|YP_008796818.1|  5 VKSSVYIDGEIWRRFKKYAAEQEREASVLLEEL-MREELMLNL 46
                                      678999999************************.555344465 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.017
                                      HHHHHHHHHTT--H CS
                             RHH_4 23 daLeeiArregltv 36
                                      daLee+ ++eg+++
  gi|557693764|ref|YP_008796818.1| 48 DALEELTEQEGIEL 61
                                      89********9976 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.16
                                      HHHHHHH.HHHH CS
                             RHH_4 37 naLiaeidadrr 48
                                      ++L+ e+    r
  gi|557693764|ref|YP_008796818.1| 74 SSLVREM----R 81
                                      3333333....2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 647.55
//
Query:       gi|557693765|ref|YP_008796819.1|  [L=70]
Description: hypothetical protein CSUB_C0328 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 523.92
//
Query:       gi|557693766|ref|YP_008796820.1|  [L=140]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-36  124.8   0.0      2e-36  124.6   0.0    1.1  1  UPF0047   Uncharacterised protein family UPF0047
  ------ inclusion threshold ------
       0.11   12.4   0.0        1.4    8.8   0.0    2.3  3  DUF1495   Winged helix DNA-binding domain (DUF1495)


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 !  124.6   0.0   2.2e-40     2e-36       1     115 []      22     137 ..      22     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 2.2e-40
                                       E-HHHHHHHHHHHT.SEEEEEEEESSSSEEEEEEESSSHHHHHHHHHHHHHHSTTT.T-GGG.TTS..THHHHHHHH CS
                           UPF0047   1 diteeveeavkesgvkeGlvlvfsrhttasltinEnadpdvqeDleealeklvpee.eYrhn.aegpdnadaHlkss 75 
                                       d+++eve++v+ sgvk+Glv+vfs+htt +l++nEn ++++++D+ e+lekl+p++  Y+h+ ++ + n+ +Hl+s+
  gi|557693766|ref|YP_008796820.1|  22 DVSHEVERVVAASGVKQGLVNVFSQHTTFALYLNEN-ESNLRRDVLEFLEKLAPQReGYHHDtIDPTANTFSHLRSI 97 
                                       6899********************************.******************99****9778889********* PP

                                       HH-SEEEEEEETTEE---TTEEEEEEESS-SSEEEEEEEE CS
                           UPF0047  76 llgssltipvedgklalGtwqsiylveldgpreRkvvvqv 115
                                       ll++ +t+p++dgk++ Gtwqsi+ +e+dgpr+R+++vqv
  gi|557693766|ref|YP_008796820.1|  98 LLSHVITLPIRDGKVVRGTWQSIIAAEFDGPRTRRLLVQV 137
                                       ************************************9986 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 ?   -0.2   0.0     0.099   8.9e+02      57      66 ..      33      42 ..       4      50 .. 0.64
   2 ?    1.0   0.0     0.043   3.9e+02      58      77 ..      34      53 ..      30      57 .. 0.81
   3 ?    8.8   0.0   0.00015       1.4       6      37 ..      57      89 ..      53     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.099
                           DUF1495 57 ssLielGLve 66
                                       s +++GLv+
  gi|557693766|ref|YP_008796820.1| 33 ASGVKQGLVN 42
                                      3446666665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.043
                           DUF1495 58 sLielGLveeeeeseglklY 77
                                      s +++GLv+  +++  ++lY
  gi|557693766|ref|YP_008796820.1| 34 SGVKQGLVNVFSQHTTFALY 53
                                      7799****988888887777 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00015
                           DUF1495  6 nkSkvRkkvllyLysiypek.snlqeisrrvrs 37
                                      n+S++R++vl++L +  p++  + ++ +  ++ 
  gi|557693766|ref|YP_008796820.1| 57 NESNLRRDVLEFLEKLAPQReGYHHDTIDPTAN 89
                                      78************9988651455555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); 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: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 942.63
//
Query:       gi|557693767|ref|YP_008796821.1|  [L=180]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-73  245.2   0.0    3.3e-73  245.0   0.0    1.0  1  DUF4256   Protein of unknown function (DUF4256)


Domain annotation for each model (and alignments):
>> DUF4256  Protein of unknown function (DUF4256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.0   0.0   1.8e-77   3.3e-73       2     173 .]       9     180 .]       8     180 .] 0.98

  Alignments for each domain:
  == domain 1  score: 245.0 bits;  conditional E-value: 1.8e-77
                           DUF4256   2 lkilkerfeknkerhk..gleWekvqakleakpeklwsleemeetgGepdvvaldkktdeyifvdcsaesPkgrrsl 76 
                                       l+il++rfe  +er+   g+ We+v + l+ +++kl++l++meetgGep++va+ +  d+y+f+dcsaesPkgrrsl
  gi|557693767|ref|YP_008796821.1|   9 LNILRQRFEWARERFPldGVVWERVVDALQGERDKLTVLRRMEETGGEPCLVAYVD--DMYVFMDCSAESPKGRRSL 83 
                                       899***********96669***********************************99..9****************** PP

                           DUF4256  77 CydrealesrkenkPensavelaaemgiellteeqyrelqklgefdlktssWiktpeeirklgGalfcdrrydtvfv 153
                                       Cydrea + rk  kP+++++++a++mg+e+lteeqyr lq++g+fd++tssW+ktpe+irklgGa+++++ry+tvf+
  gi|557693767|ref|YP_008796821.1|  84 CYDREAEKLRKGVKPRGNVLDVANSMGVEVLTEEQYRWLQSFGDFDTRTSSWLKTPEKIRKLGGAIYGEKRYGTVFI 160
                                       ***************************************************************************** PP

                           DUF4256 154 yhngaesyyaargfrgllrv 173
                                        +n+a+s+y+ rgfrgll+v
  gi|557693767|ref|YP_008796821.1| 161 GANSAQSFYGGRGFRGLLKV 180
                                       ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1307.38
//
Query:       gi|557693768|ref|YP_008796822.1|  [L=186]
Description: hypothetical protein CSUB_C0331 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-11   44.6   0.0    2.8e-11   43.9   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    6.9e-10   39.5   0.0    1.1e-09   38.8   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    6.2e-06   26.1   0.0    7.8e-06   25.8   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    7.8e-05   22.1   0.0    9.1e-05   21.9   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0068   16.3   0.0     0.0088   15.9   0.0    1.2  1  Methyltransf_8   Hypothetical methyltransferase
  ------ inclusion threshold ------
      0.029   15.1   0.0      0.049   14.4   0.0    1.4  1  Methyltransf_12  Methyltransferase domain


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 !   43.9   0.0   9.4e-15   2.8e-11      13      96 .]      67     152 ..      59     152 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 9.4e-15
                                       HHHHTTSEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHH CS
                   Methyltransf_11  13 alakrgarvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRv 87 
                                       +l+k+ ++++ vD+s    + a+++a+ ++l  +  ++v+d+++lp++++ +D+ +s+ +++hv++ + a+ e aRv
  gi|557693768|ref|YP_008796822.1|  67 YLMKNDRELILVDISSGIAEKASQRAKAKRLhsRTHIIVGDFRRLPLRSECVDMSCSFGSIEHVPEYDVAFYEQARV 143
                                       5666678999**************9999999998899**************************************** PP

                                       EEEEEEEEE CS
                   Methyltransf_11  88 LkpgGllvi 96 
                                       +++gG +++
  gi|557693768|ref|YP_008796822.1| 144 VRNGGEVIV 152
                                       *****9885 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   3.8e-13   1.1e-09      18      97 .]      71     148 ..      61     148 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 3.8e-13
                                       TSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHH CS
                   Methyltransf_25  18 rlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarv 92 
                                       +  + +++ vDis++  e+a +ra++++l  + ++++gd+++lp+ ++ +D+ +s+g+++h++  +++ a+ e arv
  gi|557693768|ref|YP_008796822.1|  71 N--DRELILVDISSGIAEKASQRAKAKRLhsRTHIIVGDFRRLPLRSECVDMSCSFGSIEHVP--EYDVAFYEQARV 143
                                       3..5899*******************99999999*********************988***98..56688******* PP

                                       EEEEE CS
                   Methyltransf_25  93 LkpgG 97 
                                       +++gG
  gi|557693768|ref|YP_008796822.1| 144 VRNGG 148
                                       ****9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.6e-09   7.8e-06      25     113 ..      69     156 ..      58     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.6e-09
                   Methyltransf_31  25 lgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsnevlnaladpdkileeierv 100
                                       +  + e++++Dis    e+A ++a+ + l  + +  +gd+  l+  l  e++D+ +s++ + ++++ d ++ e  rv
  gi|557693768|ref|YP_008796822.1|  69 MKNDRELILVDISSGIAEKASQRAKAKRLHsRTHIIVGDFRRLP--LRSECVDMSCSFGSIEHVPEYDVAFYEQARV 143
                                       4457789**********************99*************..889*********************9999*** PP

                   Methyltransf_31 101 lkpggilliedpr 113
                                       +++gg++++  p+
  gi|557693768|ref|YP_008796822.1| 144 VRNGGEVIVGVPN 156
                                       ********99888 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0     3e-08   9.1e-05      71     151 ..      71     152 ..      41     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3e-08
                                       HHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS-T-EEEEEEES-.GGG-S-HHHHHHHHHHHEEE CS
                   Ubie_methyltran  71 ekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfeddsfDvvtvsfG.lrnvtDklkaLkeayrvlkp 145
                                       +  +++++Di++ + + + +++k +    + + ++++  +Lp   +  D+   sfG +  v++++ a+ e  rv++ 
  gi|557693768|ref|YP_008796822.1|  71 NDRELILVDISSGIAEKASQRAKAKRLHsRTHIIVGDFRRLPLRSECVDM-SCSFGsIEHVPEYDVAFYEQARVVRN 146
                                       455899*****************998776999*****************7.57999799****************** PP

                                       EEEEEE CS
                   Ubie_methyltran 146 GGrlvv 151
                                       GG+++v
  gi|557693768|ref|YP_008796822.1| 147 GGEVIV 152
                                       **9976 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.9e-06    0.0088      69     156 ..      70     152 ..      58     180 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.9e-06
                                       TS-TTS-EEEES-TT-HHHHH--S-..EEEEESS-SSTTEEES-TTS-S--TT-EEEEEEES---.SS-HHHHHHHH CS
                    Methyltransf_8  69 kkkdnlvvadlGcGeakiaeavrekekvrsfdlvavnervvacdlakvPledesvdvavfclslm.gtnladflkea 144
                                       k + +l+++d+  G a  a++  + ++++s        ++++ d++++Pl  e vd+     s+  + ++ +   e 
  gi|557693768|ref|YP_008796822.1|  70 KNDRELILVDISSGIAEKASQRAKAKRLHS------RTHIIVGDFRRLPLRSECVDMSCSFGSIEhVPEYDVAFYEQ 140
                                       566677888999998888866666655555......5799******************9999985267888899*** PP

                                       HHHEEEEEEEEE CS
                    Methyltransf_8 145 nrvlkvGGllkv 156
                                        rv+++GG + v
  gi|557693768|ref|YP_008796822.1| 141 ARVVRNGGEVIV 152
                                       ********8766 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.6e-05     0.049      13      98 ..      67     149 ..      54     150 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                   Methyltransf_12  13 alleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldni 89 
                                       +l ++  d e++ vDis+   e+a+++ ++++ ++ +++ + +   l l + + +D+  +++ ++h+++ + ++ + 
  gi|557693768|ref|YP_008796822.1|  67 YLMKN--DRELILVDISSGIAEKASQRAKAKRLHSRTHIIVGDFRRLPLRS-ECVDMSCSFGSIEHVPEYDVAFYEQ 140
                                       45555..8999*********************9998887777777665544.6**************9999999999 PP

                   Methyltransf_12  90 rklLkpgGr 98 
                                       ++++++gG 
  gi|557693768|ref|YP_008796822.1| 141 ARVVRNGGE 149
                                       999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1369.77
//
Query:       gi|557693769|ref|YP_008796823.1|  [L=418]
Description: hypothetical protein CSUB_C0332 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   53.3   9.9    3.5e-14   53.3   9.9    3.0  2  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer
    2.7e-08   33.7   3.5    0.00063   19.4   4.6    4.3  4  PMT       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 !   53.3   9.9   3.9e-18   3.5e-14       2     133 ..      59     196 ..      58     227 .. 0.82
   2 ?   -3.8   9.8       1.4   1.3e+04      96     144 ..     344     395 ..     300     416 .. 0.46

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 3.9e-18
                             PMT_2   2 hPPliawllalftklfgfselairlvsalagvltilllyllarrlfgkraal.....laalllavvplfvalsalft 73 
                                       hPPl   l+al++  fg++ ++ r++s++ag  +i ++yl++ rlf+ r  +     la++l ++ +l ++ s+  +
  gi|557693769|ref|YP_008796823.1|  59 HPPLGKMLIALGMLAFGDNPFGWRIMSVIAGTAAIPIFYLVVSRLFQDRKEFnyatpLATFLFSFETLTFYFSRVAR 135
                                       9*********************************************9664443333489999999999999999*** PP

                             PMT_2  74 pdaplvllwalalylllraleknklkywllagvlfGlgflsKytaallliaallyllis.....a 133
                                       +d+++++++++ +y+ll    k+k    ++a++lf+ +fl K  a+++++++lly+ ++     +
  gi|557693769|ref|YP_008796823.1| 136 IDIFMLVFLLAGIYFLLDNRFKRK----IMAAPLFATSFLAKESALVVIVPLLLYAGLKtvekaK 196
                                       ***************997766666....7*************************99888543230 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.4
                             PMT_2  96 nklkywllagvlfGlgflsKytaallliaall.yllis..arrilkekkpyl 144
                                       + + + ++ +v+ Gl++l+    +l ++ +++ y+l +  ++    +++++ 
  gi|557693769|ref|YP_008796823.1| 344 GLMGWVVVNMVFRGLIYLFYILTLLPPVIIAIsYFLGKrlHEESSGKSVKWT 395
                                       3334555556666666665544444444333366666654333333344443 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   8.8e-08   0.00079       2      61 ..      10      75 ..       9      78 .. 0.75
   2 !   19.4   4.6   7.1e-08   0.00063      80     154 ..      76     154 ..      72     173 .. 0.87
   3 ?   -1.5   2.9      0.17   1.5e+03     131     219 ..     175     270 ..     160     287 .. 0.51
   4 ?   -5.8   7.8         2   1.8e+04     141     205 ..     314     380 ..     302     413 .. 0.51

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 8.8e-08
                               PMT  2 iltllallirlwrlslpnsvvfdevhfgkfasdYlehsffmd......vhpplgkmllalggyLag 61
                                      +lt++++lir+++l++p   + dev++   a   l ++   +       hpplgkml+alg+  +g
  gi|557693769|ref|YP_008796823.1| 10 ALTIVSFLIRVYKLDVPDRQIGDEVYYVPDARSILGQNEQGLpidprsGHPPLGKMLIALGMLAFG 75
                                      699************************76655555544444322233247**********997666 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 7.1e-08
                               PMT  80 vpyvslRlfsallgslivplvyltllelgfsk....ltallaallvllenslitlsryilldspLlfftllsmyclv 152
                                        + ++ R++s ++g+ + p+ yl++ +l +++     ++ la++l+ +e++ +  sr + +d+++l f+l+++y+l+
  gi|557693769|ref|YP_008796823.1|  76 DNPFGWRIMSVIAGTAAIPIFYLVVSRLFQDRkefnYATPLATFLFSFETLTFYFSRVARIDIFMLVFLLAGIYFLL 152
                                       688999*********************9998744434788**********************************998 PP

                               PMT 153 kf 154
                                         
  gi|557693769|ref|YP_008796823.1| 153 DN 154
                                       65 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.17
                               PMT 131 sryilldspLlfftllsmyclvkferkapfsrswwlwllltgvalg..lavsvKwvglftvllvgllliwelwqllg 205
                                       s ++++ + Ll+  l ++    k e +  + r  w ++l+++ a g  +a++  +    ++++ ++ l+ +++ ++ 
  gi|557693769|ref|YP_008796823.1| 175 SALVVIVPLLLYAGLKTVEKAKKKE-HGRLLRYDWRTVLALFAATGvsVALLWYMLEWVILVPRYSNLVERILAMFS 250
                                       4444444444444444444444444.222333333333333332220023333333334445666666777777777 PP

                               PMT 206 dkslllksi......vkhll 219
                                       ++s ++ s+      +++++
  gi|557693769|ref|YP_008796823.1| 251 RLSISNPSAvgrseiWQWFF 270
                                       77777776677777655554 PP

  == domain 4  score: -5.8 bits;  conditional E-value: 2
                               PMT 141 lfftllsmyclvkferkapfsrswwlwllltgvalglavsvK....wvglftvllvgllliwelwqllg 205
                                       + f++ +m+++++    ++ +++ +++l+ +g  +g +v        + lf +l ++  +i+ + + lg
  gi|557693769|ref|YP_008796823.1| 314 IVFMVPTMMYMLWLA--RKDTLGRFTSLYWFGGLMGWVVVNMvfrgLIYLFYILTLLPPVIIAISYFLG 380
                                       667777777777776..2345555555555554444444332100122222223344444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2928.95
//
Query:       gi|557693770|ref|YP_008796824.1|  [L=350]
Description: glutamate dehydrogenase (NAD(P)+) [Candidatus Caldiarchaeum subterraneum]
Scores for 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-26   91.0   0.0    1.5e-25   90.3   0.0    1.3  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    5.6e-16   58.6   0.0      9e-16   57.9   0.0    1.3  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 


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 !   90.3   0.0   1.7e-29   1.5e-25      10     220 ..     137     336 ..     134     348 .. 0.82

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 1.7e-29
                                       HHHHHHHHHHHHHHHTTTS.-STT.EEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE-HHHHHHHHH CS
                     ELFV_dehydrog  10 TglGvvyyveemlkklkld.sleg.krvaisGsGnvgsyaallltelgakvvavsDssGviydpeGldieellelke 84 
                                       Tgl v+  +++ ++ l+   ++e+ + +  +G+Gn+g +aa ll ++g  +vavs+   +++dp+Gldi++ll+l++
  gi|557693770|ref|YP_008796824.1| 137 TGLAVAESLHASIEALRHIkNIEDvEMFSLQGFGNMGTAAAHLLGRRGYIMVAVSNRYHTLFDPKGLDIDQLLDLRT 213
                                       66666666666666554322444413489**********************************************99 PP

                                       CSSS..STTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHHHHHHH CS
                     ELFV_dehydrog  85 erks..vkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeAkeile 159
                                       ++++  ++ y++++  + + ++   ++ ++k+di+vP A+++ i++      i   +++v+  AN p++    +ile
  gi|557693770|ref|YP_008796824.1| 214 RHGEncLRIYAERNP-ASRLLPPT-DITNIKTDIFVPGARPKTITG-----PIP--CRIVAPIANYPISVTTARILE 281
                                       999998999997665.57899995.*******************97.....466..99******************* PP

                                       HTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                     ELFV_dehydrog 160 eagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeyk 220
                                       + g+ ++pd+++ aGG + S+l +l+       + ee ++ + ki +  +k+ v++a+++ 
  gi|557693770|ref|YP_008796824.1| 282 HTGINIIPDIISTAGGAIASALTLLNR------SFEENRKTISKITHYNMKKAVTMAQRKI 336
                                       ************************997......5566666666666666666666666543 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 !   57.9   0.0     1e-19     9e-16      33     125 ..      28     116 ..      12     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1e-19
                                       SSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES-GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEE CS
                   ELFV_dehydrog_N  33 gPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvkidpkklseeeleritrrfvrelakkfiGpgiDv 109
                                       g   GG+R++++v+  e++ La+lmt+K +l+++p+GGak g+  dp + ++++l + + + ++el      +g  +
  gi|557693770|ref|YP_008796824.1|  28 GISWGGVRIASDVTRAETEMLARLMTLKSSLAGIPVGGAKTGIAADPLNVDKKNLIQKFVEKTKELL----VKGSYI 100
                                       5667********************************************9998876544444444444....466678 PP

                                       EEBBTTB-HHHHHHHH CS
                   ELFV_dehydrog_N 110 pApDvgtgaremawla 125
                                       p  D+g +++++++l+
  gi|557693770|ref|YP_008796824.1| 101 PGSDIGFSEEDLQYLY 116
                                       ***********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2460.83
//
Query:       gi|557693771|ref|YP_008796825.1|  [L=390]
Description: peptidase M24 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-36  126.4   0.0    1.5e-36  126.1   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24


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 !  126.1   0.0   8.3e-41   1.5e-36       2     208 ..     150     374 ..     149     375 .. 0.88

  Alignments for each domain:
  == domain 1  score: 126.1 bits;  conditional E-value: 8.3e-41
                                       HHHHHHHHHHHHHHHHHHHHHTT.............CBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTB CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpg.............vterelaaeieattlkrhgarglafppivasgenaavlhyt 65 
                                        +r+a+r + a++++v + +++               t + l ++++++ ++++g + +    i+a+g+++a +hy+
  gi|557693771|ref|YP_008796825.1| 150 RVREAGRKTVAVVQRVEKILEESrvagdkvlyenkpLTANVLRQAVRQA-CAEQGLNLVE-GFIIAVGAESADPHYS 224
                                       68**************987887433444444444446999999999999.8888866664.568************7 PP

                                       CS.SSB--TTEEEEEEEEEEET.TEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHH CS
                     Peptidase_M24  66 pn.drvlkegdlvlidagaeyd.gyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevl 140
                                          d+++k+g++vl+d+ +    gy  D trT++vG+ +p  r++y+ + eaq+ a++++++ + +++    ++++ 
  gi|557693771|ref|YP_008796825.1| 225 GEkDTPIKPGEPVLLDIFPADTtGYRYDFTRTYCVGRAKPLLRKMYADTVEAQRIALDMIRENIGCEAPFIRVCRLY 301
                                       754999***********987556***********************************************9999999 PP

                                       HHTTB.........CCGBSSCSEEEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                     Peptidase_M24 141 esagl.........akffphglGHgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                        ++g+         ++ f hglGHg+Gl + +e p++ r   ++++l  G+v+t+Epg+y ++g ggvr+ed+vlv 
  gi|557693771|ref|YP_008796825.1| 302 MARGWptplsrqpvERGFVHGLGHGLGLTIGEE-PYLTR--FSRDPLLSGDVVTVEPGLY-EKGFGGVRVEDVVLVE 374
                                       999999999999999999**************9.**995..789****************.78************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2787.89
//
Query:       gi|557693772|ref|YP_008796826.1|  [L=267]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-55  185.6   8.9    1.1e-54  185.3   8.9    1.0  1  DUF92            Integral membrane protein DUF92
  ------ inclusion threshold ------
      0.027   14.1   1.4      0.051   13.2   1.4    1.4  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.069   12.7   0.3       0.21   11.2   0.3    1.8  1  Kelch_1          Kelch motif
       0.58   10.2   5.2       0.29   11.2   1.0    2.7  2  Kelch_5          Kelch motif
        2.3    8.6   4.6       0.64   10.4   0.2    2.4  3  Kelch_6          Kelch motif
        2.4    8.0   5.9       0.91    9.4   0.2    2.7  3  DUF2976          Protein of unknown function (DUF2976)


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  185.3   8.9   3.8e-58   1.1e-54       2     235 ..      12     255 ..      11     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 185.3 bits;  conditional E-value: 3.8e-58
                             DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKakleeekegaRdavqV 78 
                                       ++++++++al  + L+++Ga aav++g++i++ +++ + fllllvFf+++   t++++++K +  e  +g R++ +V
  gi|557693772|ref|YP_008796826.1|  12 VIAVVGAVALAGRFLDLRGAGAAVVLGYMIYIFGGR-MHFLLLLVFFIVSGFSTRYRYREKYG--EYGRGVRTWSNV 85 
                                       6789999**************************888.7********************99986..555799****** PP

                             DUF92  79 lanslvalllally...lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsllGllas 152
                                       ++n+l+a+l+a +    +   + l  ++++++av aDT+++ElG +lsk++p+lit+lkk++pGt GgV++lGl+ +
  gi|557693772|ref|YP_008796826.1|  86 ISNGLAAALIASAGyflIDPATALPLYIGAVSAVFADTMSTELG-LLSKRPPILITSLKKTEPGTPGGVTPLGLMSA 161
                                       *******9988887554225566799******************.88899*************************** PP

                             DUF92 153 llGalliallavlllllel.......lillltlaGllGsllDSlLGatlqasvvdkrtgkvvegegge....kvvsG 218
                                       ++ +++ a+++++ + ++l       ++l+ +++G++Gsl+DS++G+++q+++++k +g+ ve +++      +  G
  gi|557693772|ref|YP_008796826.1| 162 FVTGFITAATVFIYTGFSLdtlplskVALVSVFSGFTGSLFDSVVGGLVQSRYRCKVCGRAVEVRRHCgvetIYLGG 238
                                       ********8866666666677899989999*********************************97766999877799 PP

                             DUF92 219 ldlLdNnaVNllsallt 235
                                        ++++N+ VN+l++l +
  gi|557693772|ref|YP_008796826.1| 239 SRVINNDVVNFLTSLYG 255
                                       *************9976 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.4   1.7e-05     0.051       7      18 ..     214     225 ..     210     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                                       EE-TTT--EEEE CS
                   Desulfoferrod_N   7 YkCevCGniVeV 18 
                                       Y+C+vCG  VeV
  gi|557693772|ref|YP_008796826.1| 214 YRCKVCGRAVEV 225
                                       ***********9 PP

>> Kelch_1  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   7.1e-05      0.21       6      21 ..      33      48 ..      29      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.1e-05
                                      EEEEETTEEEEEEEBC CS
                           Kelch_1  6 gavvvggkiYviGGsd 21
                                      +avv+g  iY++GG+ 
  gi|557693772|ref|YP_008796826.1| 33 AAVVLGYMIYIFGGRM 48
                                      89************86 PP

>> Kelch_5  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   9.6e-05      0.29       7      23 ..      31      47 ..      29      49 .. 0.87
   2 ?   -1.7   0.2         1   3.1e+03      19      33 ..     193     204 ..     193     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.6e-05
                           Kelch_5  7 ghcavtvsekiYvyGGk 23
                                       ++av++++ iY++GG+
  gi|557693772|ref|YP_008796826.1| 31 AGAAVVLGYMIYIFGGR 47
                                      5789999*********6 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                           Kelch_5  19 vyGGkvgrdgsvsdd 33 
                                       v++G++   gs++d 
  gi|557693772|ref|YP_008796826.1| 193 VFSGFT---GSLFDS 204
                                       799***...788886 PP

>> Kelch_6  Kelch motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00022      0.64       5      22 ..      32      49 ..      29      64 .. 0.82
   2 ?   -2.0   0.1       1.7     5e+03      16      22 ..     205     211 ..     191     216 .. 0.60
   3 ?   -3.6   0.0       5.6   1.7e+04      13      22 ..     233     242 ..     232     246 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
                           Kelch_6  5 hslvsvggkiYifGGytd 22
                                      +++v+ g  iYifGG+ +
  gi|557693772|ref|YP_008796826.1| 32 GAAVVLGYMIYIFGGRMH 49
                                      67899**********987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                           Kelch_6  16 ifGGytd 22 
                                       ++GG+++
  gi|557693772|ref|YP_008796826.1| 205 VVGGLVQ 211
                                       4566655 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 5.6
                           Kelch_6  13 kiYifGGytd 22 
                                       +iY+ G ++ 
  gi|557693772|ref|YP_008796826.1| 233 TIYLGGSRVI 242
                                       6888888765 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       1.4   4.1e+03      66      73 ..      12      19 ..       4      24 .. 0.55
   2 ?    9.4   0.2   0.00031      0.91      23      86 ..      44     107 ..      32     109 .. 0.82
   3 ?    0.9   0.1      0.14     4e+02      14      45 ..     164     195 ..     150     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                           DUF2976 66 ltlvvGvv 73
                                      +++vvG+v
  gi|557693772|ref|YP_008796826.1| 12 VIAVVGAV 19
                                      34444444 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00031
                           DUF2976  23 ylkdgvillgLvlaavaflaVakaalkkfneisegkaewgkfgltlvvGvvllvvviwLltkAa 86 
                                       ++  +  ll Lv+  v+ +   +   +k+ e+ +g  +w+++++  + ++++  +  +L+  A+
  gi|557693772|ref|YP_008796826.1|  44 FGGRMHFLLLLVFFIVSGFSTRYRYREKYGEYGRGVRTWSNVISNGLAAALIASAGYFLIDPAT 107
                                       555555666667777777777888899***********************99999999998886 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.14
                           DUF2976  14 gdllelikgylkdgvillgLvlaavaflaVak 45 
                                       +++++    +++ g+ l  L l+ va++ V +
  gi|557693772|ref|YP_008796826.1| 164 TGFITAATVFIYTGFSLDTLPLSKVALVSVFS 195
                                       56777778899999999999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 1721.91
//
Query:       gi|557693773|ref|YP_008796827.1|  [L=349]
Description: histidyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-69  233.3   0.0    4.4e-69  233.1   0.0    1.0  1  tRNA-synt_His  Histidyl-tRNA synthetase
    1.6e-11   44.5   0.0    2.6e-11   43.8   0.0    1.5  1  tRNA-synt_2b   tRNA synthetase class II core domain (G, H, P,
    0.00017   21.2   0.0    0.00028   20.4   0.0    1.3  1  tRNA-synt_2d   tRNA synthetases class II core domain (F)
    0.00062   18.9   0.1       0.39    9.7   0.0    2.4  2  tRNA-synt_2    tRNA synthetases class II (D, K and N)


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 !  233.1   0.0   9.8e-73   4.4e-69       1     310 []       8     316 ..       8     316 .. 0.97

  Alignments for each domain:
  == domain 1  score: 233.1 bits;  conditional E-value: 9.8e-73
                                       T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH.HS-EEE-TTSSEEEE-SSSHHHHH CS
                     tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld.qtfklvDqsgrllglRaDiTpqva 76 
                                       g++dllpee++ ++++   + ++++ +GYe+V +P+lEyl+ +++++ge+ + ++f + D  gr l lR+++T++va
  gi|557693773|ref|YP_008796827.1|   8 GMDDLLPEEFAVKQRIVDVIREIYRLYGYEEVETPTLEYLELFEAKSGEEIRhRMFVFDDPHGRKLVLRPEVTASVA 84 
                                       899***********************************************99689999889**************** PP

                                       HHHHHHHH.TSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEE CS
                     tRNA-synt_His  77 Riaahrln.rerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlg 152
                                       R++a  l+ r+ plRl Y+++++r  + + gr+r + Q G El+G+ ++ +d+E++    ++++  +g+ e r+++g
  gi|557693773|ref|YP_008796827.1|  85 RLVASKLSrRPLPLRLGYIADCYRYDEPQWGRRRRFWQGGLELFGSRDPMSDAEIILASRDVFQ-RLGLVEQRFKIG 160
                                       ******999******************************************************7.************ PP

                                       ETCHHHHHHHHTT--HHHHHHHHHHHHCT-HHHHHHHHHCCTTHHHCCHCC....HCCHCCCHHHHCHCCHCTHHHH CS
                     tRNA-synt_His 153 hvglvralleaaglsesleeallaalarkdlaelkelaaeaglkealrellkal.elygdaevleealealaaapal 228
                                       hvg++r ++++++  +++++ +l++++rk  +e ++l+++ +l+++++e+l  l e +g+ ev+e+a+  ++  p++
  gi|557693773|ref|YP_008796827.1| 161 HVGIMRGIMDNVE--QKTQDIILSLIDRKMFTEARQLMEQ-HLDKDAVETLWRLaEHRGGLEVVERARDMVSPWPKA 234
                                       **********866..999********************97.7*****************************99**** PP

                                       HHHHHHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-SS-SEEEEEECTTTGGG.T---EEEEEE CS
                     tRNA-synt_His 229 qaaldeleelaallealakpevrvtlDlaelrgyeYytGlvFaayaegvgqaiarGGrYdelgaaf.grarpAtGfs 304
                                        + l++le +++l+ +++ p++++ +Dl+  rg+eYytG++F+   eg++  + +GGrYd+l++ f g++ pA+G s
  gi|557693773|ref|YP_008796827.1| 235 MQSLENLETIVSLIMNVD-PNISIEVDLGFARGLEYYTGMIFEQKLEGEQLSFNGGGRYDGLVELFgGKPTPAVGCS 310
                                       ****************95.9********************************************************* PP

                                       EEHHHH CS
                     tRNA-synt_His 305 ldleal 310
                                       + ++++
  gi|557693773|ref|YP_008796827.1| 311 IGITRI 316
                                       *99876 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 !   43.8   0.0   5.7e-15   2.6e-11       1     101 [.      63     159 ..      63     285 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 5.7e-15
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasld 77 
                                       + ++d  +r+++L+P+ ++ +++l+  + l  + LPl+l +i  +yR+ ++ + G  R r F q + + f++ +  +
  gi|557693773|ref|YP_008796827.1|  63 FVFDDPHGRKLVLRPEVTASVARLVASK-LSRRPLPLRLGYIADCYRYDEP-QWG--RRRRFWQGGLELFGSRD--P 133
                                       6689999*******************99.65556*****************.99*..***************99..9 PP

                                       HHHHHHHHHHHHHHHHTT.SC..EEE CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxx RF
                      tRNA-synt_2b  78 dslrdlikaisriferlglef..rai 101
                                        s++++i a  ++f+rlgl +  ++i
  gi|557693773|ref|YP_008796827.1| 134 MSDAEIILASRDVFQRLGLVEqrFKI 159
                                       999***************95533233 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 !   20.4   0.0   6.3e-08   0.00028      19     127 ..      20     123 ..      10     161 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.3e-08
                                       HHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCH.TTSEBTCTSSS-ECESEEE-SSTHHHHHHH CS
                      tRNA-synt_2d  19 ltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdm.qdtFylkkpekaveekllLRthttavqirt 94 
                                        +++++ i+ei++ +g+eeve p +e        L++ + ++  ++ +  F++++p+    +kl+LR   ta  +r 
  gi|557693773|ref|YP_008796827.1|  20 KQRIVDVIREIYRLYGYEEVETPTLE-------YLELFEAKSGEEIrHRMFVFDDPH---GRKLVLRPEVTASVARL 86 
                                       5789999*****************93.......444434344444306677775555...589************99 PP

                                       H....TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEE CS
                      tRNA-synt_2d  95 l....ekkkppikiisigrvfRrdavDathlaeFhqv 127
                                       +    +++ +p+++  i  ++R d+    +   F q 
  gi|557693773|ref|YP_008796827.1|  87 VasklSRRPLPLRLGYIADCYRYDEPQWGRRRRFWQG 123
                                       888879999***************9888888888875 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 !    9.7   0.0   8.8e-05      0.39      21      50 ..      16      45 ..       9      58 .. 0.89
   2 !    7.1   0.1   0.00056       2.5     252     311 ..     274     331 ..     163     334 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 8.8e-05
                                      HHHHHHHHHHHHHHHHHHTT-EE----SEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 21 vlrlrstvtkavrkyleengfieietPiLs 50
                                       + +++++++ +r+++   g+ e+etP+L 
  gi|557693773|ref|YP_008796827.1| 16 EFAVKQRIVDVIREIYRLYGYEEVETPTLE 45
                                      68899***********************96 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00056
                                       HHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 252 eleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFP 311
                                       + e+kl+ ++l+ +   +++ ++e++     p  G+ +G+ R+ m llg +   ++++FP
  gi|557693773|ref|YP_008796827.1| 274 IFEQKLEGEQLSFNGGGRYDGLVELFGGKPTPAVGCSIGITRIQMHLLGRKT--QTTPFP 331
                                       455666666666666678999*******9*******************9874..666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 00:00:00.40
# Mc/sec: 2586.09
//
Query:       gi|557693774|ref|YP_008796828.1|  [L=382]
Description: 2-alkenal reductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-36  125.0   0.9    9.4e-36  124.0   0.9    1.6  1  Trypsin_2      Trypsin-like peptidase domain
    3.2e-15   56.2   1.9    3.3e-13   49.7   1.9    2.7  1  PDZ_2          PDZ domain
    9.4e-15   55.0   0.2    3.1e-14   53.3   0.2    1.8  1  Trypsin        Trypsin
    1.8e-09   37.8   2.8    0.00032   21.0   0.4    2.9  2  PDZ            PDZ domain
    9.3e-08   31.8  11.8    0.00034   20.4   1.1    3.6  4  PDZ_6          PDZ domain
  ------ inclusion threshold ------
      0.032   12.9   1.5      0.036   12.7   0.3    1.5  2  Peptidase_S46  Peptidase S46
      0.043   13.8   1.2       0.15   12.1   0.5    2.2  2  Tricorn_PDZ    Tricorn protease PDZ domain


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 !  124.0   0.9   3.7e-39   9.4e-36       1     150 []      97     235 ..      97     235 .. 0.99

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 3.7e-39
                         Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgp 77 
                                       GsGf+++ +g+i+Tn+Hvv++a++ +v         ++ +g+ ++a+vv++d ++DlA++k+ ++++++l pl+lg+
  gi|557693774|ref|YP_008796828.1|  97 GSGFVYDTEGHIVTNNHVVAGASSIRV---------VFYNGEMYAARVVGTDVDSDLAVIKL-ENPPKNLKPLKLGN 163
                                       9**************************.........**************************.************** PP

                         Trypsin_2  78 sealkggepvyvvGyplggeksgsvssGivsgvve.sesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                       s++l+ ge+v+++G+p g e+  ++++G+vs+  +  ++ ++++ ++++qtdaa++pG+SGGpl++ +G+vvG+
  gi|557693774|ref|YP_008796828.1| 164 STELRIGEEVIAIGNPFGLEG--TLTTGVVSQKGRlLPTGRGYSIPGVIQTDAAINPGNSGGPLLNMRGEVVGV 235
                                       *********************..9*************************************************8 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   1.9   1.3e-16   3.3e-13       3      82 .]     273     378 ..     271     378 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.3e-16
                                       ..XX------............-EEEEEE-TTSGGGGT.--T...............T-EEEEETTB--SSHHHHHH CS
                             PDZ_2   3 lGvsvsdeed..........tggvlvvsVkeggPaakaglka...............gDvilkvdgkkvksledlis 54 
                                       +G+s + ++           t+gvl+ +V +++Pa+ agl+                gDvi++v+g++++s ++l  
  gi|557693774|ref|YP_008796828.1| 273 MGISGTTLDMdiaaaggynvTRGVLISQVVNNSPAQSAGLRGgdrtvvvngvqvivgGDVIVAVNGVPINSIDELLV 349
                                       5666666666677777777799******************************************************* PP

                                       HHH.TS-TT-EEEEEEEETTEEEEEEEE- CS
                             PDZ_2  55 lll.kkkpGdtVkltvlRdgkkktvevkl 82 
                                       ++  k++pG+t++l++ R+++  tv+++l
  gi|557693774|ref|YP_008796828.1| 350 YMEeKTSPGQTITLNIVRNNQFITVSLTL 378
                                       ***9******************9999987 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.2   1.2e-17   3.1e-14      25     215 ..      95     253 ..      82     259 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.2e-17
                                       EEEEEEEEETT.EEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTS CS
                           Trypsin  25 hlCgGslisen.wvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvkl 100
                                        + +G++++++  ++T++H+v +as+++vv+        +g   +++ ++v+        ++d D+a++kl++p   
  gi|557693774|ref|YP_008796828.1|  95 AVGSGFVYDTEgHIVTNNHVVAGASSIRVVFY-------NG---EMYAARVVG------TDVDSDLAVIKLENP--- 152
                                       5667999999889**********999988443.......45...456666433......44577**********... PP

                                       BSSBHCCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHH.HHHHHTTTTSTTTEEEEESTTSSSBC CS
                           Trypsin 101 gdtvrpiclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsre.tcksaykgkvtenmlcagakeggkda 176
                                        ++ +p++l   s +l +g    v+++g+++  +   tl+   + vvs++ +   + +g+  +  ++++a     ++
  gi|557693774|ref|YP_008796828.1| 153 PKNLKPLKLGN-STELRIG--EEVIAIGNPFGLE--GTLT---TGVVSQKgRLLPTGRGYSIPGVIQTDA-----AI 216
                                       ***********.6656666..7788888987777..5555...6666666444444677788********.....** PP

                                       TTTTTTSEEEETTTEEEEEEEEESSSSCTTSEEEEEEGG CS
                           Trypsin 177 cqGDSGGPlvcsdgelvGivswgkgcakgnrpgvytkvs 215
                                       ++G+SGGPl+++ ge+vG++++ +  + g  +g +++ s
  gi|557693774|ref|YP_008796828.1| 217 NPGNSGGPLLNMRGEVVGVNTAIEPGGVG--IGYAVPSS 253
                                       **********************9888877..66666655 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.4   1.2e-07   0.00032      12      58 ..     273     326 ..     262     329 .. 0.79
   2 !   16.3   0.2   3.5e-06     0.009      47      81 ..     330     365 ..     325     366 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.2e-07
                                       SSEEEEEETTSS.......SSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEET CS
                               PDZ  12 lGfslkggsdqr.......gdkgifvsevlpggaaeadglkvGDkIlsvNgvdv 58 
                                       +G+s+   + +          +g+ +s+v+ +++a+ +gl+ GD+ + vNgv v
  gi|557693774|ref|YP_008796828.1| 273 MGISGTTLDMDIaaaggynVTRGVLISQVVNNSPAQSAGLRGGDRTVVVNGVQV 326
                                       5555555444445557777789*****************************976 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 3.5e-06
                                       TEEEEEETTEETTTSHHHHHHHHHHTTTS.EEEEEE CS
                               PDZ  47 GDkIlsvNgvdvenvsheeavqaikgskg.kvtLti 81 
                                       GD+I++vNgv+++++ ++ +  + k s g ++tL+i
  gi|557693774|ref|YP_008796828.1| 330 GDVIVAVNGVPINSIDELLVYMEEKTSPGqTITLNI 365
                                       9**************777776665555555****98 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.45   1.2e+03      29      53 ..      33      56 ..      32      57 .. 0.83
   2 ?   -3.4   0.0       3.6   9.3e+03      16      26 ..     167     177 ..     166     178 .. 0.85
   3 !   20.4   1.1   1.3e-07   0.00034       2      30 ..     298     326 ..     297     329 .. 0.95
   4 !   17.4   0.1   1.1e-06    0.0028      19      54 ..     330     365 ..     327     367 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.45
                             PDZ_6 29 pveglsladvaallr.gsagesvvlv 53
                                      +v  l l+++++ l+ +++++ v+lv
  gi|557693774|ref|YP_008796828.1| 33 DV--LGLQQAVSSLQtQAVEKTVTLV 56
                                      57..7899999999989999999987 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.6
                             PDZ_6  16 lrvGDiilsvN 26 
                                       lr+G  +++++
  gi|557693774|ref|YP_008796828.1| 167 LRIGEEVIAIG 177
                                       89999999997 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 1.3e-07
                             PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpv 30 
                                       +++V+ +sPA  AGlr GD+ + vNG+ v
  gi|557693774|ref|YP_008796828.1| 298 ISQVVNNSPAQSAGLRGGDRTVVVNGVQV 326
                                       899************************98 PP

  == domain 4  score: 17.4 bits;  conditional E-value: 1.1e-06
                             PDZ_6  19 GDiilsvNGqpveglsladvaallr..gsagesvvlvv 54 
                                       GD+i++vNG+p+   s++++  +++  +s+g+ ++l +
  gi|557693774|ref|YP_008796828.1| 330 GDVIVAVNGVPI--NSIDELLVYMEekTSPGQTITLNI 365
                                       9***********..*****9999985556666666665 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.49   1.3e+03      49      69 ..      97     117 ..      66     119 .. 0.76
   2 ?   12.7   0.3   1.4e-05     0.036     627     651 ..     212     236 ..     185     240 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.49
                                       EE-EE-STT-EEEE-HHHHHH CS
                     Peptidase_S46  49 CtasfVSpeGLvlTNHHCayg 69 
                                        ++ +   eG ++TN H++ g
  gi|557693774|ref|YP_008796828.1|  97 GSGFVYDTEGHIVTNNHVVAG 117
                                       355555679********9976 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.4e-05
                                       ES----TT-TT-EEE-TTS-EEEEE CS
                     Peptidase_S46 627 stnDitGGNSGSPvlngkgelvGla 651
                                       +++ i  GNSG P+ln +ge+vG++
  gi|557693774|ref|YP_008796828.1| 212 TDAAINPGNSGGPLLNMRGEVVGVN 236
                                       7788899****************97 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1       0.2     5e+02      28      54 ..     302     326 ..     280     328 .. 0.76
   2 ?   12.1   0.5   5.7e-05      0.15      36      78 ..     322     367 ..     318     374 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.2
                                       S-B-GGGGGS---.TT-EEEEETTEE- CS
                       Tricorn_PDZ  28 earSPLaepGvnvreGdlilavdgepv 54 
                                        ++SP +  G++   Gd  + v+g++v
  gi|557693774|ref|YP_008796828.1| 302 VNNSPAQSAGLR--GGDRTVVVNGVQV 326
                                       467899999998..8999999999887 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.7e-05
                                       GS---.T.T-EEEEETTEE-BTTB-HHHHHHTTTT..SEEEEEEE- CS
                       Tricorn_PDZ  36 pGvnvre.GdlilavdgepvskekgiaelLvgkag..keveLtvkr 78 
                                        Gv+v + Gd+i+av+g+p+++ +++  ++++k+   ++++L++ r
  gi|557693774|ref|YP_008796828.1| 322 NGVQVIVgGDVIVAVNGVPINSIDELLVYMEEKTSpgQTITLNIVR 367
                                       588876537***********98777777777776433777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2687.57
//
Query:       gi|557693775|ref|YP_008796829.1|  [L=308]
Description: 5-carboxymethyl-2-hydroxymuconate isomerase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-64  216.5   0.0    4.2e-64  216.2   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
  ------ inclusion threshold ------
       0.15   12.0   0.0       0.32   10.9   0.0    1.5  1  DUF4751        Domain of unknown function (DUF4751)


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 !  216.2   0.0   4.7e-68   4.2e-64       1     216 [.      92     303 ..      92     305 .. 0.95

  Alignments for each domain:
  == domain 1  score: 216.2 bits;  conditional E-value: 4.7e-68
                                       .EEEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T-- CS
                     FAA_hydrolase   1 kivcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevls 77 
                                       ki+c+++ny+ h +e++    ++p+     +p+ff k  ++l+g+g++i +P+ s+ +dyE ELavvigk+ + + +
  gi|557693775|ref|YP_008796829.1|  92 KILCVAANYVMHGQEMK---ITVPE-----KPYFFGKFGNTLIGHGENIIIPRTSTMVDYEIELAVVIGKKGKYI-P 159
                                       689************97...67888.....899******************************************.9 PP

                                       HHHHHTTEEEEEEEEEEE-SBGGG---..HH......HHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEE CS
                     FAA_hydrolase  78 veeAedaiaGytllnDvsaRdlqaeek.apl......gwflgksfdtftpiGpwivtpdeledpedlelrlrvngee 147
                                       +++A+++iaGy+++nDvs Rd q +   ++       +w+lgks dt++p Gp +vt+de+++p  l+l l vnge+
  gi|557693775|ref|YP_008796829.1| 160 AKQADEYIAGYMVFNDVSFRDKQLPPGwPEKlnpfgqNWILGKSLDTAAPCGPYLVTRDEVGSPYPLRLVLKVNGEV 236
                                       ***********************876654334666999*************************************** PP

                                       EEEEEGGGTTTSHHHHHHHHHHHH-B-TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEE CS
                     FAA_hydrolase 148 vqdsntkdmifspaeliahlsagltLepGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnr 216
                                       +q+++t++m f++ eli+++s gltLepGd+i+tGTp+gv   ++++++l+dgD ve+eie++G lrnr
  gi|557693775|ref|YP_008796829.1| 237 RQNGSTDEMFFKIGELIEYISDGLTLEPGDIIATGTPAGVA--AAGKRYLRDGDLVEAEIEKVGLLRNR 303
                                       ***************************************87..699*********************98 PP

>> DUF4751  Domain of unknown function (DUF4751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.5e-05      0.32      68     104 ..      98     134 ..      91     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.5e-05
                           DUF4751  68 inyllngqkwqstiedyiffhalegkelrgyydnvik 104
                                        ny+++gq+ + t+ +  +f    g+ l g+ +n+i 
  gi|557693775|ref|YP_008796829.1|  98 ANYVMHGQEMKITVPEKPYFFGKFGNTLIGHGENIII 134
                                       69********************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       256  (0.0142785); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2297.12
//
Query:       gi|557693776|ref|YP_008796830.1|  [L=494]
Description: methylmalonate-semialdehyde dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-136  456.0   0.0   1.3e-136  455.8   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 !  455.8   0.0  7.2e-141  1.3e-136       1     462 []      22     490 ..      22     490 .. 0.96

  Alignments for each domain:
  == domain 1  score: 455.8 bits;  conditional E-value: 7.2e-141
                                       EET-SSSE.EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHH CS
                            Aldedh   1 wveseset.ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaelet 76 
                                       w++s++e   +v++P  g++ia+vp at e+v++av+aA+eaf++w+++p+ eR ++L ++ ++le++ +ela++ t
  gi|557693776|ref|YP_008796830.1|  22 WMDSRTEVwRPVYDPGAGRIIAEVPYATDEEVNSAVEAAAEAFEKWSRTPFLERVKYLFEVKHVLENHLDELAAINT 98 
                                       77777777789****************************************************************** PP

                                       HHH---HHHHHHHHHHHHHHHHHHHHHHHH.HSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHH CS
                            Aldedh  77 letGkplaearaeveeaidvlryyaelaek.legevlps.segklalvrrePlGvvgaItPWNfPlllaawklapal 151
                                       l+ Gk+l e+r+++++ai+ ++ ++++a +  +ge+l   s++ + ++++ePlGv ++I+P+NfP++++ w +  a+
  gi|557693776|ref|YP_008796830.1|  99 LNHGKTLDESRGDLRRAIENVDAAIAAAYTlAKGEMLHEiSPRIDEYSVKEPLGVFAVISPFNFPIMIPFWFFPYAI 175
                                       ******************************55569999999************************************ PP

                                       HTT-EEEEEE-TTSHHHHHHHHHHHHH.TTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHC CS
                            Aldedh 152 aaGNtvvlKPaeetplsalllaelfee.aglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaak 227
                                       a GNtvv+KP++ tp+ +++++e++++ ++lP+gvln+v+g g+e++ealv+hp+v+ v f+Gst+ +r+i++ a++
  gi|557693776|ref|YP_008796830.1| 176 ALGNTVVIKPSDVTPVPMTRVMEILQQeVKLPPGVLNLVHG-GKETAEALVKHPHVKGVCFVGSTPAARNIYRLAGE 251
                                       ************************97549************.*********************************** PP

                                       TTSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHH.HHHHHHHHHHHHHHT--BS-TTS CS
                            Aldedh 228 nlkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqes.iydefveklveaakklkvgdpld 303
                                       + kr+++  G+kn ++v++daD+d ++ a+v ++fgn+GQ+C a+s llv ++   + f++k+  + k+l +g++l 
  gi|557693776|ref|YP_008796830.1| 252 HGKRCIAQGGAKNYIVVMPDADMDVTIPATVSSFFGNTGQRCLAGSNLLVVDKgFKKSFLDKFSRRSKELVIGHGLV 328
                                       *********************************************9988766627777******************* PP

                                       TT-SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEE CS
                            Aldedh 304 edtdvGPliseaqlekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvik 379
                                       + +++GPl+++a++ +v+ yve+++eega+lll+g+  + ++  +g+++   ++++vtpdm+ia+eEiFGPV+svi+
  gi|557693776|ref|YP_008796830.1| 329 QGVEMGPLVNKAAQTRVKTYVEKGVEEGARLLLDGTeVSVQQFPDGFYLGANIFDEVTPDMTIAREEIFGPVASVIT 405
                                       *********************************99988899************************************ PP

                                       ESSHHHHHHHHH.SSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSH.HHHHH CS
                            Aldedh 380 fkdeeeaieiaN.dteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGregg.kegle 454
                                       +++++eaie  N  t+yG+ a++ft++ ++a +++++++aGn+++N   ++ a  +pf G k+S +G  +g  ++++
  gi|557693776|ref|YP_008796830.1| 406 ASSLDEAIETINtRTDYGNMACIFTSSGSNAAKFIKNVNAGNIGVNIGVAAPAAYFPFAGRKNSFYGVLHGqIDSVD 482
                                       ************559*********************************88888889***********77776999** PP

                                       HTEEEEEE CS
                            Aldedh 455 eytevktv 462
                                       ++t  k+v
  gi|557693776|ref|YP_008796830.1| 483 FFTDKKVV 490
                                       *9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3435.13
//
Query:       gi|557693777|ref|YP_008796831.1|  [L=557]
Description: phenylalanyl-tRNA synthetase beta chain [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-41  141.3   0.0    7.4e-41  139.9   0.0    1.7  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    2.6e-22   78.9   0.2    4.7e-15   55.6   0.1    2.6  2  B5               tRNA synthetase B5 domain
    2.7e-08   33.7   0.0    4.9e-08   32.9   0.0    1.4  1  B3_4             B3/4 domain
    3.7e-05   23.9   0.0    0.00067   19.8   0.0    2.7  1  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain
     0.0022   17.6   0.1       0.04   13.6   0.0    2.5  2  HTH_33           Winged helix-turn helix
  ------ inclusion threshold ------
       0.15   12.4   0.0        1.6    9.1   0.0    2.6  2  HTH_18           Helix-turn-helix 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       1.6   4.8e+03     139     164 ..      49      73 ..      43      81 .. 0.77
   2 !  139.9   0.0   2.5e-44   7.4e-41       4     213 ..     348     543 ..     345     544 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.6
                   tRNA_synthFbeta 139 ravdfydlkgivealleslgiekvef 164
                                       +  df  + g++ al + lgi +  +
  gi|557693777|ref|YP_008796831.1|  49 NRPDFSSVYGVAAALRSYLGI-ETGL 73 
                                       567999*********999999.4444 PP

  == domain 2  score: 139.9 bits;  conditional E-value: 2.5e-44
                   tRNA_synthFbeta   4 tlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlp 80 
                                       + P+ +t +  l ++  + +k+++++ g+G++Ev +  +++e++  ++ +  de ++v+lanP + +++++RtsL+p
  gi|557693777|ref|YP_008796831.1| 348 VAPQSNTYGS-LRPQTTFYEKVAETMLGLGFTEVHNLMLTNEQTHYQM-SGLDEIEHVTLANPATREYTMVRTSLIP 422
                                       5688888888.99***********************************.5669************************ PP

                   tRNA_synthFbeta  81 glLevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealles 156
                                       +lL +la+N ++  +  r+FE+g++++ + ++ e+    ++la++++  +           +++ ++k ++++ll+ 
  gi|557693777|ref|YP_008796831.1| 423 SLLATLANNTDNLYP-QRIFELGDIIHIEpAAPEKTVRMKKLAAAIAYAE-----------AGYSEAKSVLDELLKL 487
                                       ***************.*************988888888888888888888...........8*************** PP

                   tRNA_synthFbeta 157 lgiekvefepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEld 213
                                       l++ k e+ pa+  ++  gr+A +++dg + G++Ge++p vle+f+++ +v +fE++
  gi|557693777|ref|YP_008796831.1| 488 LQL-KPEYIPATMGTFIEGRCAALTIDGSKAGIVGEVSPTVLENFGIEMPVTLFEIE 543
                                       ***.***************************************************97 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.3e-07   0.00038       1      51 [.       4      53 ..       4      57 .. 0.95
   2 !   55.6   0.1   1.6e-18   4.7e-15       3      67 .]     279     342 ..     277     342 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-07
                                      EEEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5  1 vslrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDl 51
                                      v+++vek+++l+G +l+ eei + L +lg+ + e+++d l+V+  + R+D 
  gi|557693777|ref|YP_008796831.1|  4 VNIDVEKLRRLVGRSLTLEEISDNLAALGMSV-EETGDILRVEYNPNRPDF 53
                                      6789**************************98.****************97 PP

  == domain 2  score: 55.6 bits;  conditional E-value: 1.6e-18
                                       EEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   3 lrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                       l++e +++l+G++ls  e +++L+r+g+e +  +++ l+V  P +R D+++++Dl+E++a++yGY
  gi|557693777|ref|YP_008796831.1| 279 LDMELVKRLTGLQLSLREATRLLRRMGME-PRVKGKRLRVLYPRHRADILHPVDLVEDIAIAYGY 342
                                       67899************************.5999999***************************9 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   1.6e-11   4.9e-08      37     165 ..     115     244 ..      94     253 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.6e-11
                                       HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEE.EEE--TTEEEEBTTS-EEEE-T................... CS
                              B3_4  37 nvVDitNyvmlelgq.....PlhafDldkiqgdiv.vrlakegeklvtldgkerelde................... 88 
                                        ++++++ ++  +g+     +++ +Dl+ i+++++ ++   ++ ++v+l++  r +++                   
  gi|557693777|ref|YP_008796831.1| 115 EFIAMQEDLHWIIGRnrrktAIGLHDLSAISPPFTyKAVGMDEVRFVPLKDY-RAMTPrevlskseigrkhawllkd 190
                                       57888888888899999999***************777777778*****955.6666668***************** PP

                                       ..TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHHHHHHHHHTT---HHHHHHHH---TTTHHHHH CS
                              B3_4  89 ..edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpvsirktarrlglrseaskrfergvdpekleaal 162
                                         + +vi+ds+++v s++++++   ++++   +++f+ +++ d                           ek+++al
  gi|557693777|ref|YP_008796831.1| 191 asKAPVIVDSRGQVfSMPPIVNASITELTPGRRDIFIDVTGTD--------------------------WEKVNQAL 241
                                       *****************************************55..........................55555555 PP

                                       HHH CS
                              B3_4 163 dra 165
                                       + +
  gi|557693777|ref|YP_008796831.1| 242 NIL 244
                                       544 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 !   19.8   0.0   2.3e-07   0.00067       1      82 [.       1      68 [.       1      69 [. 0.93

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.3e-07
                         PhetRS_B1  1 MPtisvkkeaLfkalgkelteeeledllfefGlElDeiveeeekkkadkkseeviykidipAnryDLLcleglaralkv 79
                                      MP+++++ e+L +++g++lt ee++d l+ +G+ +    ee+            i++++   nr+D  ++ g+a al+ 
  gi|557693777|ref|YP_008796831.1|  1 MPVVNIDVEKLRRLVGRSLTLEEISDNLAALGMSV----EETG----------DILRVEYNPNRPDFSSVYGVAAALRS 65
                                      9*******************************975....4455..........79***********************9 PP

                         PhetRS_B1 80 Flg 82
                                      +lg
  gi|557693777|ref|YP_008796831.1| 66 YLG 68
                                      986 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.12   3.5e+02      14      38 ..      11      35 ..       8      38 .. 0.89
   2 !   13.6   0.0   1.3e-05      0.04      12      39 ..     282     309 ..     281     310 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.12
                            HTH_33 14 ieerfgvsysvsgvyrlLkrlGfsy 38
                                      +++  g s++   +++ L  lG+s 
  gi|557693777|ref|YP_008796831.1| 11 LRRLVGRSLTLEEISDNLAALGMSV 35
                                      78899*****************995 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.3e-05
                            HTH_33  12 qlieerfgvsysvsgvyrlLkrlGfsyq 39 
                                       +l+++ +g+++s +  +rlL+r+G+ ++
  gi|557693777|ref|YP_008796831.1| 282 ELVKRLTGLQLSLREATRLLRRMGMEPR 309
                                       799*********************9876 PP

>> HTH_18  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.65     2e+03      17      43 ..     164     190 ..     163     197 .. 0.80
   2 ?    9.1   0.0   0.00053       1.6       5      60 ..     290     345 ..     288     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.65
                                       HHHTSS-HHHHHHHHHHHHHHHHHHSS CS
                            HTH_18  17 krvlgltpkeylrrlRlerArrlLlen 43 
                                       k++  +tp+e+l +  + r ++ Ll++
  gi|557693777|ref|YP_008796831.1| 164 KDYRAMTPREVLSKSEIGRKHAWLLKD 190
                                       788899******999999999999874 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00053
                                       HT--HHHHHHHHHHHTSS-HHHHHHHHHHHHHHHHHHS..SS---HHHHHHHTT-S-H CS
                            HTH_18   5 lgvsrrtLqrlfkrvlgltpkeylrrlRlerArrlLle..ntglsvaeiAlalGFsdl 60 
                                       l +s r  +rl++r +g+ p+   +rlR+ + r++  +  ++ + v +iA a+G++++
  gi|557693777|ref|YP_008796831.1| 290 LQLSLREATRLLRR-MGMEPRVKGKRLRVLYPRHRA-DilHPVDLVEDIAIAYGYNNM 345
                                       67899999******.**************9766543.3335**************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3968.07
//
Query:       gi|557693778|ref|YP_008796832.1|  [L=533]
Description: phenylalanyl-tRNA synthetase alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-90  300.9   0.0      9e-90  300.4   0.0    1.2  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    2.3e-06   26.9   0.0      0.013   14.6   0.0    3.2  3  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    4.3e-06   26.3   0.1    0.00043   19.8   0.0    2.7  3  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
     0.0042   17.3   0.2      0.011   15.9   0.0    1.9  2  PheRS_DBD3       PheRS DNA binding domain 3
  ------ inclusion threshold ------
      0.018   14.3   0.0       0.04   13.1   0.0    1.5  1  RepC             Replication protein C (RepC)
      0.031   14.2   0.2       0.07   13.1   0.1    1.6  2  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
       0.26   11.0   0.0        1.7    8.3   0.0    2.0  2  DUF4364          Domain of unknown function (DUF4364)
          1    9.6   4.1        1.9    8.7   1.6    2.9  3  AbiEi_4          Transcriptional regulator, AbiEi antitoxin


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 !  300.4   0.0     4e-93     9e-90       2     244 ..     252     520 ..     251     521 .. 0.98

  Alignments for each domain:
  == domain 1  score: 300.4 bits;  conditional E-value: 4e-93
                                       .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-.. CS
                      tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka.. 76 
                                       +dv++p+++i a+k+hplt++++ +++ ++e+gfee+egp ve  f+nfdaL++pqdhpaR+mqdtFyl +p+    
  gi|557693778|ref|YP_008796832.1| 252 YDVKAPTPPIFAAKRHPLTELIRMVRQAYVEMGFEEIEGPIVELAFWNFDALFQPQDHPAREMQDTFYLLEPRAGdp 328
                                       9********************************************************************9999889* PP

                                       ..............................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-S CS
                      tRNA-synt_2d  77 ..............................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathla 122
                                                                     ++++llLRthtta++ir+l + k+pp+k+++++r+fR+++vD +hla
  gi|557693778|ref|YP_008796832.1| 329 paqhveavrkvhenggdtgskgwrykwsleEARRLLLRTHTTATTIRHLaTVKQPPVKVFCVDRIFRNEKVDWKHLA 405
                                       ******************************999****************77788*********************** PP

                                       EEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHH CS
                      tRNA-synt_2d 123 eFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpev 199
                                       eFhq+eg+vv+++ sl+ l+gvl++++++l g + ++rf+psyfp+tePs+ev+v l   +++wlEl+g+G++rpe 
  gi|557693778|ref|YP_008796832.1| 406 EFHQIEGIVVERDASLRMLMGVLRDFYSRL-GLR-EIRFKPSYFPYTEPSMEVEVRL---GGRWLELGGSGIFRPET 477
                                       ******************************.999.********************99...9**************** PP

                                       HHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                      tRNA-synt_2d 200 leavgideevsgfafGlGveRlamlkygieDiRelvendlrflrq 244
                                       + ++g+  + +++a+GlG+eRlam+ yg+eDiR ++ ndl +lr+
  gi|557693778|ref|YP_008796832.1| 478 TYPFGV--KHPVLAWGLGLERLAMVIYGLEDIRTFHLNDLGWLRS 520
                                       ******..**********************************986 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 ?    3.5   0.0     0.014        32      27      49 ..     271     293 ..     265     322 .. 0.86
   2 !   14.6   0.0   5.9e-06     0.013      93     119 ..     386     411 ..     377     437 .. 0.86
   3 !    4.8   0.0    0.0054        12     287     306 ..     490     509 ..     484     524 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHTT-EE----SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  27 tvtkavrkyleengfieietPiL 49 
                                       +++++vr+ + e gf eie Pi+
  gi|557693778|ref|YP_008796832.1| 271 ELIRMVRQAYVEMGFEEIEGPIV 293
                                       67899****************97 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.9e-06
                                       EEEEEEEEE--S--BTTB-S-CEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqie 119
                                       +vf++ r FR+E+++  +hlaEF qie
  gi|557693778|ref|YP_008796832.1| 386 KVFCVDRIFRNEKVD-WKHLAEFHQIE 411
                                       8**************.67888*****9 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0054
                                       EEEEHHHHHHHHCT-SSGGG CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIrd 306
                                       +glGl+Rl m++ g+e+Ir 
  gi|557693778|ref|YP_008796832.1| 490 WGLGLERLAMVIYGLEDIRT 509
                                       79****************96 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 ?   -1.5   0.1      0.64   1.4e+03     146     197 ..     186     238 ..     182     241 .. 0.79
   2 ?    3.1   0.0     0.024        54       6      37 ..     257     288 ..     254     314 .. 0.91
   3 !   19.8   0.0   1.9e-07   0.00043      90     209 ..     378     489 ..     356     494 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.64
                   tRNA_synthFbeta 146 lkgivealleslgiekvefep.aehpalhpgrsAeikvdgkevGvlGelhpev 197
                                       l ++v++ll++ ++ k+  +p  +  + ++gr A   +++++v  +  l pe+
  gi|557693778|ref|YP_008796832.1| 186 LREVVDELLRRQRVVKLVERPvRKVVLTEKGREAVSLLEETVVPEVTRLTPEL 238
                                       678999****9999555444458888889999999999999888888888876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.024
                   tRNA_synthFbeta   6 PkapttegelnkeqklrrklrdllagaGlnEv 37 
                                       P+ p+ ++++++  +l r +r++ +++G+ E+
  gi|557693778|ref|YP_008796832.1| 257 PTPPIFAAKRHPLTELIRMVRQAYVEMGFEEI 288
                                       77777888899********************8 PP

  == domain 3  score: 19.8 bits;  conditional E-value: 1.9e-07
                   tRNA_synthFbeta  90 largnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefe 165
                                          +++ v++F + ++f+++  + +  +e +++ ++++ ++           ++   l g+++ + ++lg+++++f+
  gi|557693778|ref|YP_008796832.1| 378 ATVKQPPVKVFCVDRIFRNEkVDWKHLAEFHQIEGIVVERD-----------ASLRMLMGVLRDFYSRLGLREIRFK 443
                                       5567888************97777889**************...........************************* PP

                   tRNA_synthFbeta 166 paehpalhpgrsAeikvdgk..evGvlGelhpevleafdlkqrvyv 209
                                       p+  p+ +p    e++++g+  e+G  G + pe+   f++k++v +
  gi|557693778|ref|YP_008796832.1| 444 PSYFPYTEPSMEVEVRLGGRwlELGGSGIFRPETTYPFGVKHPVLA 489
                                       *******************999********************9987 PP

>> PheRS_DBD3  PheRS DNA binding domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         7   1.6e+04      37      44 ..      65      72 ..      63      77 .. 0.80
   2 !   15.9   0.0   5.1e-06     0.011       2      53 ..     103     153 ..     103     159 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 7
                        PheRS_DBD3 37 AmknkWik 44
                                      A +++W++
  gi|557693778|ref|YP_008796832.1| 65 AKACGWLR 72
                                      8899**97 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 5.1e-06
                        PheRS_DBD3   2 hEarvfaavppegg.isqkelkklggdpvakiGfskAmknkWikkdkgdg.kvv 53 
                                       +E rv + +   gg  s +e+ +l +   a+iG+  A + +W+++ k++g  vv
  gi|557693778|ref|YP_008796832.1| 103 PERRVVEFLQRRGGeASVDEVRAL-E-R-ADIGLMWARRRGWVEFAKKNGaTVV 153
                                       799999999656666******888.5.4.******************7776554 PP

>> RepC  Replication protein C (RepC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.8e-05      0.04     186     240 ..     117     171 ..      80     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
                              RepC 186 ridleevralktdparlihqrlsGwidaGksgrveldtlcgyvwpdeaneealkk 240
                                         +++evral+     l+  r  Gw++  k++  ++  l g+v p+   e+ l+ 
  gi|557693778|ref|YP_008796832.1| 117 EASVDEVRALERADIGLMWARRRGWVEFAKKNGATVVVLKGHVPPSTDVENFLRE 171
                                       5679****************************************99999988875 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 ?   13.1   0.1   3.1e-05      0.07       1      98 [.     353     439 ..     353     459 .. 0.80
   2 ?   -3.7   0.0       4.5     1e+04     157     175 ..     484     501 ..     481     502 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.1e-05
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasld 77 
                                       Yk + ++ r++ L+   ++t ++      +++   P+k++ + +++R+Ek d +    + eFhq +g v+  +a   
  gi|557693778|ref|YP_008796832.1| 353 YKWSLEEARRLLLRTHTTATTIRHLA-T-VKQP--PVKVFCVDRIFRNEKVDWKH---LAEFHQIEGIVVERDA--- 419
                                       66666777888888777666666555.3.5666..***************98998...78*******9998877... PP

                                       HHHHHHHHHHHHHHHHTT.SC CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  78 dslrdlikaisriferlglef 98 
                                        slr l+ +  ++++rlgl +
  gi|557693778|ref|YP_008796832.1| 420 -SLRMLMGVLRDFYSRLGLRE 439
                                       .78889999999999999875 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.5
                                       EEEEEEEEEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 157 ksvimicaaigveRllsai 175
                                       k++ ++  ++g+eRl  +i
  gi|557693778|ref|YP_008796832.1| 484 KHP-VLAWGLGLERLAMVI 501
                                       677.78899*****97776 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.3   6.8e+02      42      69 ..      70      97 ..      62     100 .. 0.86
   2 ?    8.3   0.0   0.00077       1.7      36      83 ..     186     233 ..     185     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.3
                           DUF4364 42 eLvesglieeeekenktlykiTekGket 69
                                       L ++g++++e+++++++ ++  +G+e 
  gi|557693778|ref|YP_008796832.1| 70 WLRDKGYVTVEQETSRKFVALDAEGEEY 97
                                      5889*********************986 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00077
                           DUF4364  36 lqqalseLvesglieeeekenktlykiTekGketlelfenripksire 83 
                                       l ++++eL+  + + +  ++      +TekG+e+++l+e+++ +++  
  gi|557693778|ref|YP_008796832.1| 186 LREVVDELLRRQRVVKLVERPVRKVVLTEKGREAVSLLEETVVPEVTR 233
                                       578999****9999999999********************99888765 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         3   6.7e+03      14      37 ..      54      76 ..      41      78 .. 0.59
   2 ?    8.7   1.6   0.00085       1.9       1      39 [.     105     143 ..     105     143 .. 0.97
   3 ?   -3.1   0.0       4.1   9.1e+03      18      34 ..     260     277 ..     258     278 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3
                           AbiEi_4 14 fttreleaaGispsalrrLvrkGw 37
                                       ++ e++ + i   a+  L++kG 
  gi|557693778|ref|YP_008796832.1| 54 GRDGEAMLSSIAK-ACGWLRDKGY 76
                                      5666665555555.5666777775 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00085
                           AbiEi_4   1 erlpelasrqvGlfttreleaaGispsalrrLvrkGwLv 39 
                                       +r++e++ r++G ++++e++a+ + +  l  ++r+Gw++
  gi|557693778|ref|YP_008796832.1| 105 RRVVEFLQRRGGEASVDEVRALERADIGLMWARRRGWVE 143
                                       799**********************************97 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 4.1
                           AbiEi_4  18 eleaaGisp.salrrLvr 34 
                                       ++ aa ++p + l r+vr
  gi|557693778|ref|YP_008796832.1| 260 PIFAAKRHPlTELIRMVR 277
                                       566888999777888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3681.01
//
Query:       gi|557693779|ref|YP_008796833.1|  [L=207]
Description: hypothetical protein CSUB_C0342 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0095   16.2  20.6      0.094   13.0   2.7    2.1  2  DUF996    Protein of unknown function (DUF996)


Domain annotation for each model (and alignments):
>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   2.7   5.2e-06     0.094      73     135 .]      30      89 ..      13      89 .. 0.78
   2 !    7.2  15.5   0.00033       5.9      29     131 ..      81     182 ..      71     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.2e-06
                            DUF996  73 lllvliiayvlliisavflkksyellgkrtgvklFetagllyfiGaiLtivlvGliilliaei 135
                                       +  vl i+ +++i++ +++  +++++g+rtg++lF+ +g l+++   ++   vG+++ + ++i
  gi|557693779|ref|YP_008796833.1|  30 IGYVLNIIPLANIVAPLLIGVAWYQVGSRTGQSLFRATGVLMVV---TFLASVGFLVFFLGSI 89 
                                       44444566788999999999*********************985...6667799999988876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00033
                            DUF996  29 aliafilsiialvvailalllvlgalatalelpgleeaaslilllllvliiayvlliisavflkksyellgkrtgvk 105
                                       +l+ f+ sii++++    +++  + + ta+ ++ l +++ +++++l++ ++++ l +++ v+   s  + +k +++ 
  gi|557693779|ref|YP_008796833.1|  81 FLVFFLGSIIGVIM-STPFAIGGENFSTAVASALLPQIMGYLAVFLAAAVTLAALGLATFVLELGSHFRAAKVLNSV 156
                                       34444444444333.33334444444444444444554449*************************9999******* PP

                            DUF996 106 lFetagllyfiGaiLtivlvGliill 131
                                        F++a+   +++ +L+ v+v +++ l
  gi|557693779|ref|YP_008796833.1| 157 WFRRAAVARIVALVLVLVFVAVVLAL 182
                                       ********************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1460  (0.0814323); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1403.97
//
Query:       gi|557693780|ref|YP_008796834.1|  [L=385]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   37.4   0.0    5.6e-09   35.9   0.0    1.8  1  SIS       SIS domain
    0.00042   20.3   0.1     0.0021   18.1   0.0    2.2  2  SIS_2     SIS domain
  ------ inclusion threshold ------
       0.19   11.6   0.0       0.64    9.8   0.0    1.8  2  TssD      Hemolysin coregulated protein Hcp (TssD)


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 !   35.9   0.0   9.4e-13   5.6e-09       9     109 ..     241     339 ..     233     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 9.4e-13
                                       EEEESHHHHHHHHHHHHHHHHHHTSEEE.EEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEE CS
                               SIS   9 yvlGaGtsyaiakelalkleeiggivve.vedaselkhgvlalideddlvilisfsgetkdlvaaaelakergakii 84 
                                       ++ G G+sy +a+  a  + +i+  + + v+ a e   +  +  +++dl+i+is sget  +    +  k+ g++i 
  gi|557693780|ref|YP_008796834.1| 241 FFGGLGSSYEVARMTAVRVSHIKRAIGDqVYVARE---SSTPAPRQGDLLIVISSSGETEIVSTWCKSFKRMGGQIA 314
                                       899******************99866441444444...558999********************************* PP

                                       EEESSTTSHHHHHSSEEEEEEEECH CS
                               SIS  85 aITdskgsplareadlalyinaepe 109
                                       a+ ++++s++a +ad +l+i++ +e
  gi|557693780|ref|YP_008796834.1| 315 AVVGNADSTIASMADSVLEIPVKNE 339
                                       *********************9887 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.49   2.9e+03      29      53 ..      30      54 ..      10      67 .. 0.73
   2 !   18.1   0.0   3.5e-07    0.0021      88     138 .]     268     318 ..     243     318 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.49
                                      HHHHHTT--EEEEESGGGHHHHHHT CS
                             SIS_2 29 adslenggkvlvfGsGhSaalaeel 53
                                       + +++ g+++ +G G S+ + + +
  gi|557693780|ref|YP_008796834.1| 30 LHDIQSAGVIIPLGEGRSKGALSIA 54
                                      5567788888888888887665544 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.5e-07
                                       -TTHHHHHHHHTT--TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                             SIS_2  88 degyakqilrlvrlkpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                       d++y+ + ++    ++gD+L+viS+sG+ ++v   ++ +k++g ++ A+++
  gi|557693780|ref|YP_008796834.1| 268 DQVYVARESSTPAPRQGDLLIVISSSGETEIVSTWCKSFKRMGGQIAAVVG 318
                                       555555555555669*********************************986 PP

>> TssD  Hemolysin coregulated protein Hcp (TssD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.55   3.3e+03      60      75 ..      57      72 ..      33      81 .. 0.74
   2 ?    9.8   0.0   0.00011      0.64      36      80 ..     280     324 ..     272     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.55
                              TssD 60 nsnkekdGeivfykrd 75
                                      +  k++dG+iv+ + d
  gi|557693780|ref|YP_008796834.1| 57 EMAKMRDGKIVIDRGD 72
                                      5678999999997765 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00011
                              TssD  36 evrGgkisvtiestpdtellewmlnsnkekdGeivfykrdeeskl 80 
                                        +r g++ ++i+s+++te+++  ++s+k++ G+i  +  +++s++
  gi|557693780|ref|YP_008796834.1| 280 APRQGDLLIVISSSGETEIVSTWCKSFKRMGGQIAAVVGNADSTI 324
                                       6899****************9999**********98887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2766.94
//
Query:       gi|557693781|ref|YP_008796835.1|  [L=360]
Description: F420-dependent glucose-6-phosphate dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-58  197.0   0.1    6.1e-58  196.7   0.1    1.1  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.7   0.1   3.4e-62   6.1e-58      12     261 ..      23     272 ..      13     319 .. 0.85

  Alignments for each domain:
  == domain 1  score: 196.7 bits;  conditional E-value: 3.4e-62
                    Bac_luciferase  12 ggalgaasaslrylvelaraaEelGfdavwvaehhggpgga....ldaftllaalaaaTerirlgtavtply.trhP 83 
                                       g ++g ++ +++++v++  +aE++Gfd + +++h ++++ +      ++ +laa+a++T++++lgtavt+++ ++hP
  gi|557693781|ref|YP_008796835.1|  23 GYWAGLEQYDPARIVAHSIHAEAVGFDIIALSDHFHPWSDTggqaGFPWIVLAAVAEHTKKVELGTAVTTPFfRYHP 99 
                                       4456666689****************************999****88****************************** PP

                    Bac_luciferase  84 avlAqqaatLdhlsgGRfglglgtggpaveerrfGv...dhderyarlrEfvevlrrlwrgeevdfeGeffsvkgal 157
                                       a++Aq++atLd l++GR+ + +gtg++++e +  G     ++e ++rlrE++e+++ lw+g+ vd+eG++++++ a 
  gi|557693781|ref|YP_008796835.1| 100 AIVAQAFATLDYLYPGRIFITVGTGHAMNE-TPLGFkwpGYREKVERLREAIEIIQLLWKGDFVDYEGKYYQLRSAK 175
                                       ******************************.777888999*******************88888*********8888 PP

                    Bac_luciferase 158 llprpgqgpiPvyvaaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadte 234
                                       l  +p  + iP+yva ++   +e+a++ +dg+l+++   +++ e i+ l++ga++ag+dp+++  ++ + v+++++ 
  gi|557693781|ref|YP_008796835.1| 176 LYTKPLTK-IPIYVATSNATVAEIAGELCDGILTNPRGMDKYMEIIAALEKGARKAGKDPSKLSKCLEFKVSYDHDY 251
                                       88888778.******************************************************************** PP

                    Bac_luciferase 235 eeAraearaliagldfyaldsegagre 261
                                       + A + a+ ++a+     +  ++ +re
  gi|557693781|ref|YP_008796835.1| 252 DRAYKAAL-FWAP-----TAIPREKRE 272
                                       ***99985.5522.....222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2475.13
//
Query:       gi|557693782|ref|YP_008796836.1|  [L=217]
Description: cyclase family protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-26   90.7   0.0    1.2e-25   90.4   0.0    1.1  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 !   90.4   0.0   6.5e-30   1.2e-25       1     134 [.       3     156 ..       3     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 6.5e-30
                           Cyclase   1 idLshplsedtpvwp...dp..................islsehtGTHlDapgHfae..ktidelpleelvg.pavv 53 
                                       i Lsh l++++p+++    p                  i+l +h+GTH+Dap+Hf +  ++i++++++elv+ + ++
  gi|557693782|ref|YP_008796836.1|   3 IYLSHILTRNSPCYDdgpRPeftpdkqiargdssntyfIKLLNHIGTHVDAPYHFDPngRKISSYRADELVFeKPLL 79 
                                       579***********5466226777999****************************99999***********999*** PP

                           Cyclase  54 ldvsakaaaedyeiitaedleaalakqgveikpgdivlirTgwskrl.edkeky..rnpglseeaaewlaekg.vka 126
                                       +dvs+       e+it++dle+       ++ + d +lirT +++++ +d+e++  r+p ls+eaa +l++ g ++a
  gi|557693782|ref|YP_008796836.1|  80 IDVSKD----AGELITVSDLEKH----SQTLHNVDLLLIRTSFQRYReKDPEAFmrRGPCLSAEAASFLRQFGtLRA 148
                                       ***875....34589*****764....55799***********998876679999999******************* PP

                           Cyclase 127 vGvDtlsv 134
                                       +GvDt+s+
  gi|557693782|ref|YP_008796836.1| 149 LGVDTISI 156
                                       ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1612.63
//
Query:       gi|557693783|ref|YP_008796837.1|  [L=280]
Description: 4-hydroxybenzoate octaprenyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  136.3  16.5    1.4e-39  135.9  16.5    1.2  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 !  135.9  16.5   7.7e-44   1.4e-39       2     247 ..      19     263 ..      18     276 .. 0.94

  Alignments for each domain:
  == domain 1  score: 135.9 bits;  conditional E-value: 7.7e-44
                              UbiA   2 lipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivlli 78 
                                       ++++l+g++++++  +++++++ ++++ + ++++++alNdyfDre D    + p+RP++sG++sp  a++++ +l+ 
  gi|557693783|ref|YP_008796837.1|  19 FFAVLIGVLFSETRAINPQQIFYAFVTSFGLTGSSMALNDYFDREVDLV--NNPRRPIPSGEVSPTSAVALSSILAG 93 
                                       6899*********************************************..9************************* PP

                              UbiA  79 lgllllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavfll 155
                                       +gll + +l +  ++l++++al++ +vY+ ++lK+ +l+g++ ++++ + p+l g  ++ g +s+ ++++ ++ fl 
  gi|557693783|ref|YP_008796837.1|  94 AGLLTA-FLSSTACFLMAAVALAVSTVYN-MFLKKAGLVGNFAVSFTVVAPFLYGSLLADGYVSWRVVVFVVLAFLA 168
                                       *****9.999999999999999999****.5********************************************** PP

                              UbiA 156 twaialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalallraa 231
                                        ++  +++ + d+egD+ +g+ t++ + G ++a ++ + +++a+++l++l +ll  ++ lyl l++++ a +++ ++
  gi|557693783|ref|YP_008796837.1| 169 NTGREVIKGITDVEGDAVRGVATIARKSGLRTASRVgAGFYIAAVMLSPLPYLLKVVNILYLPLVAAADAGFVYSSI 245
                                       ***********************************976666666666699*************************** PP

                              UbiA 232 rlvrrrdakkaakff..l 247
                                       r++++ ++++a+k     
  gi|557693783|ref|YP_008796837.1| 246 RIIKNPEPAEAKKQKnlT 263
                                       *********999988551 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2032.15
//
Query:       gi|557693784|ref|YP_008796838.1|  [L=174]
Description: tRNA-intron endonuclease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   47.4   0.3    3.2e-12   46.3   0.3    1.5  1  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    2.3e-07   30.4   2.6    3.4e-07   29.8   0.6    2.2  3  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
  ------ inclusion threshold ------
      0.076   13.1   0.2       0.52   10.4   0.0    2.0  2  HU-HIG           HU domain fused to wHTH, Ig, or Glycine-rich
       0.12   12.1   0.0       0.19   11.4   0.0    1.3  1  NdhN             NADH-quinone oxidoreductase cyanobacterial s
       0.21   11.8   0.8       0.37   11.0   0.1    1.8  2  tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-t


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 !   46.3   0.3     9e-16   3.2e-12       2      85 .]      79     163 ..      78     163 .. 0.93

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 9e-16
                                       HHHHHHHHHHHHTT-EEEECGGGTSSEEEE.TSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEE CS
                     tRNA_int_endo   2 alkyavyrdLrekGyvvrsGlkFGadFrvY.qrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaiv 77 
                                       ++ y++y dLr++ yvv++G+     Frv+ +++   + ++ylV  + e+e +++ +l++ vr ++ ++K +++a+ 
  gi|557693784|ref|YP_008796838.1|  79 WRDYVIYMDLRKRRYVVKEGFGPKLRFRVFeRGEYPAKPAKYLVIPLYEGESVSVDELISLVRSCRAMDKVAVVAVL 155
                                       899*****************776689****66667899*************************************** PP

                                       TTTSCEEE CS
                     tRNA_int_endo  78 daegdvty 85 
                                       d+  +v y
  gi|557693784|ref|YP_008796838.1| 156 DRRNEVVY 163
                                       **999987 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 !   29.8   0.6   9.6e-11   3.4e-07      22      67 .]      23      68 ..       5      68 .. 0.89
   2 ?   -2.7   0.0       1.4     5e+03       8      28 ..      81     100 ..      77     110 .. 0.64
   3 ?   -0.8   0.0      0.34   1.2e+03      53      67 .]     122     137 ..     117     137 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 9.6e-11
                                      HHTTT-SEECCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHHH CS
                   tRNA_int_endo_N 22 yekgfYGkplidepLqLslvEAlYLlekGklevvkggeplsfeell 67
                                      +++++YG ++ +++ + s vE+lYL+ +Gk ev+++g++l+f ell
  gi|557693784|ref|YP_008796838.1| 23 FRERGYGDMRGEKRYFFSQVETLYLVNHGKAEVYRSGRKLGFSELL 68
                                      67899**************************************995 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                                       TEEEESSHHHHHHHHHTTT-S CS
                   tRNA_int_endo_N   8 drvlvedeeaakrlyekgfYG 28 
                                       d v+  d  +++ + ++g +G
  gi|557693784|ref|YP_008796838.1|  81 DYVIYMDLRKRRYVVKEG-FG 100
                                       666766656556555554.66 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.34
                                       EEE.TTSEEE-HHHHH CS
                   tRNA_int_endo_N  53 evv.kggeplsfeell 67 
                                        +  ++ge++s++el+
  gi|557693784|ref|YP_008796838.1| 122 VIPlYEGESVSVDELI 137
                                       5556899999999985 PP

>> HU-HIG  HU domain fused to wHTH, Ig, or Glycine-rich motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.19   6.8e+02      65      82 ..       6      24 ..       3      26 .. 0.86
   2 ?   10.4   0.0   0.00014      0.52       3      63 ..     103     162 ..     102     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.19
                            HU-HIG 65 eaLadGerVeL.gelGyFs 82
                                      e L+dGe+V + g+lG+F+
  gi|557693784|ref|YP_008796838.1|  6 ELLNDGEVVFVeGDLGWFR 24
                                      67999999988689***98 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00014
                            HU-HIG   3 lkYdlvkrpnkkgegekkklyarvvskgtvdfeeLceeiskrstlsrgdvkavldaledel 63 
                                       l++++++r +  ++  +k l+  + + ++v+++eL++ + +  ++ +  v avld+ ++++
  gi|557693784|ref|YP_008796838.1| 103 LRFRVFERGEYPAKP-AKYLVIPLYEGESVSVDELISLVRSCRAMDKVAVVAVLDRRNEVV 162
                                       678888888877777.7777888888899**************************987765 PP

>> NdhN  NADH-quinone oxidoreductase cyanobacterial subunit N
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.3e-05      0.19     102     146 ..     117     161 ..     106     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.3e-05
                              NdhN 102 kskglvlWliegkvlskqEleylvklpkkeprlkvvvElggdrsl 146
                                        +k lv+ l+eg+ +s +El +lv+ +++ +++ vv  l    ++
  gi|557693784|ref|YP_008796838.1| 117 PAKYLVIPLYEGESVSVDELISLVRSCRAMDKVAVVAVLDRRNEV 161
                                       5799*******************************9877666555 PP

>> tRNA_int_end_N2  tRNA-splicing endonuclease subunit sen54 N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0001      0.37      25      71 ..      12      56 ..       7      57 .. 0.78
   2 ?   -2.5   0.1       1.7   6.1e+03      15      30 ..     150     165 ..     142     172 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                   tRNA_int_end_N2 25 rvvvvespkarGkhfktmGvsra.rrgrlwLlpeEaLYLvErGsldir 71
                                       vv ve +     +f+  G+ +   ++r      E+LYLv  G+ +++
  gi|557693784|ref|YP_008796838.1| 12 EVVFVEGD---LGWFRERGYGDMrGEKRYFFSQVETLYLVNHGKAEVY 56
                                      56666633...56789888776559*****************998876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                   tRNA_int_end_N2  15 lvraiwfprdrvvvve 30 
                                        v+a+ + r+ vv+ +
  gi|557693784|ref|YP_008796838.1| 150 AVVAVLDRRNEVVYYH 165
                                       5777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1287.62
//
Query:       gi|557693785|ref|YP_008796839.1|  [L=258]
Description: hypothetical protein CSUB_C0348 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   17.2   0.2      0.009   16.0   0.2    1.6  1  OppC_N    N-terminal TM domain of oligopeptide transport perm
  ------ inclusion threshold ------
      0.075   13.1   0.2       0.13   12.4   0.2    1.4  1  DUF2012   Protein of unknown function (DUF2012)


Domain annotation for each model (and alignments):
>> 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 !   16.0   0.2     1e-06     0.009      10      37 ..      13      42 ..      11      61 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1e-06
                            OppC_N 10 FkrNklAvvglvilllllliaif..aPlia 37
                                      + +N++Av+ l++++ll+ +++f   P i+
  gi|557693785|ref|YP_008796839.1| 13 LVKNPRAVLLLAVVALLTGFSLFeiVPPIS 42
                                      679********************5556664 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   1.5e-05      0.13      22      83 ..      89     149 ..      75     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                           DUF2012  22 fkalvrrDGsFifrdlpegsYlLevespeyvFepyrVdvkdkgkakasklrivetaevnvvd 83 
                                       f+++++ +G  +f    +g++++ v s + + ++y+Vdv       + ++r+vet  ++++ 
  gi|557693785|ref|YP_008796839.1|  89 FTTVTNLSGY-AFFTTTPGKHVISVASTTATLPTYAVDVEVTTRITELVIRFVETRLSLQSL 149
                                       4555555554.5556678**********************9999999999999998887743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 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:                        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 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1953.02
//
Query:       gi|557693786|ref|YP_008796840.1|  [L=149]
Description: hypothetical protein CSUB_C0349 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0052   17.0   0.1      0.011   15.9   0.0    1.6  2  DUF4129          Domain of unknown function (DUF4129)
  ------ inclusion threshold ------
      0.038   13.8   0.4      0.062   13.1   0.4    1.3  1  PqiA             Paraquat-inducible protein A
      0.069   13.2   0.3      0.089   12.9   0.3    1.1  1  Peptidase_S49_N  Peptidase family S49 N-terminal
      0.073   13.1   0.1       0.13   12.3   0.1    1.4  1  HTH_56           Cch helix turn helix domain
      0.076   13.2   0.0       0.17   12.1   0.0    1.6  1  Acetyltransf_19  Acetyltransferase (GNAT) domain
       0.11   12.4   0.0       0.15   12.0   0.0    1.2  1  CYTL1            Cytokine-like protein 1


Domain annotation for each model (and alignments):
>> DUF4129  Domain of unknown function (DUF4129)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.8e-06     0.011      21      66 ..      91     136 ..      83     139 .. 0.81
   2 ?   -1.8   0.0       1.3   3.9e+03      42      52 ..     138     148 ..     131     149 .] 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.8e-06
                           DUF4129  21 TprEyarrvriapspaaalaalaelfeearYGgrpasaeeyrrlve 66 
                                       T rE++   ri+ + aa l    e+fe +rYG   +++e+++   e
  gi|557693786|ref|YP_008796840.1|  91 TFREVLNSGRIPQTFAAYLSSMYEVFEPVRYGEMKPTEETLAKFEE 136
                                       445555555999999************************9987765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                           DUF4129  42 laelfeearYG 52 
                                       l +l ee +Y 
  gi|557693786|ref|YP_008796840.1| 138 LHRLSEEFWYD 148
                                       55777999995 PP

>> PqiA  Paraquat-inducible protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   2.1e-05     0.062      95     118 ..       6      29 ..       2      33 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                              PqiA  95 eflgrWsMldVfvvgilvalvklg 118
                                         +  W Ml +f+v+ +v+lv ++
  gi|557693786|ref|YP_008796840.1|   6 YNVSFWLMLNIFLVAAIVSLVLVN 29 
                                       56778***************9775 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 ?   12.9   0.3     3e-05     0.089       2      82 ..       4      84 ..       3      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                   Peptidase_S49_N  2 flleyglFlaklvtlvvailvvvvlivalaakkkkekgelevtkLneeykelkeeleealldeeelkaaekkekkeeke 80
                                      +l++++++l+  + lv+ai+ +v++  + +++k+  + + ++ +L+ee +  k+ l++   +++ +k + +  kk  k+
  gi|557693786|ref|YP_008796840.1|  4 LLYNVSFWLMLNIFLVAAIVSLVLVNQSRSKNKQPPNSSQQIITLKEEEELFKQLLQKGEKRDAVVKVFPQVFKKICKT 82
                                      57888889999999999999988666666666668889999***************99999999999988888887776 PP

                   Peptidase_S49_N 81 ek 82
                                       +
  gi|557693786|ref|YP_008796840.1| 83 AN 84
                                      65 PP

>> HTH_56  Cch helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   4.4e-05      0.13       9      66 ..      21      88 ..      18     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
                            HTH_56  9 filqwiaqnqskFkeegkeasnpn........eiwGkiekkkekte...........vyIlknvfdkileeagFedt 66
                                      +i++ +  nqs+ k++++++s ++        e +          +           v ++++vf+ki++ a+ e  
  gi|557693786|ref|YP_008796840.1| 21 AIVSLVLVNQSRSKNKQPPNSSQQiitlkeeeELFK---------QllqkgekrdavVKVFPQVFKKICKTANVETR 88
                                      799999999999999999976544344444433333.........145555566799*************9998655 PP

>> Acetyltransf_19  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.6e-05      0.17      64     112 ..      48      94 ..      44      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.6e-05
                                       HHHHHHHHHHHHTT----EEEEETT-HHHHHHHHHHEEEEEEEEEEEEE CS
                   Acetyltransf_19  64 lklaeeiFseiieeeeiksafvstadplflslcldnnksikvnsylFqd 112
                                       lk  ee+F++++++ e + a+v+ + ++f + c    +++++ +y F++
  gi|557693786|ref|YP_008796840.1|  48 LKEEEELFKQLLQKGEKRDAVVKVFPQVFKKICKT--ANVETRGYTFRE 94 
                                       57789****************************86..568889999986 PP

>> CYTL1  Cytokine-like protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.9e-05      0.15      10      60 ..      25      80 ..      14     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
                             CYTL1 10 lllla.....eaaPPtcysrvlslskeitesleklqksertescvevlPklyldih 60
                                      l+l+      +  PP    ++++l +e     + lqk e++++ v+v+P+++  i 
  gi|557693786|ref|YP_008796840.1| 25 LVLVNqsrskNKQPPNSSQQIITLKEEEELFKQLLQKGEKRDAVVKVFPQVFKKIC 80
                                      2222233444789****99*****99988888889****************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1355  (0.0755759); expected 358.6 (0.02)
Passed bias filter:                      937  (0.0522617); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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 0.25s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 1208.70
//
Query:       gi|557693787|ref|YP_008796841.1|  [L=90]
Description: hypothetical protein CSUB_C0350 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.6   0.0      0.025   14.4   0.0    1.1  1  DUF3015          Protein of unknown function (DUF3015)
      0.056   13.4   0.2      0.083   12.8   0.2    1.2  1  Gram_pos_anchor  LPXTG cell wall anchor motif
        0.1   13.0   0.1       0.14   12.6   0.1    1.2  1  HycH             Formate hydrogenlyase maturation protein Hyc


Domain annotation for each model (and alignments):
>> DUF3015  Protein of unknown function (DUF3015)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.2e-06     0.025      73     135 ..      29      89 ..      17      90 .] 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.2e-06
                           DUF3015  73 LaediakGeGealaalavllgveaedraafkavlqenfsslfaseevtseevlkaikevlkkd 135
                                         +d+a+GeG  l+ +a l++  ++   +++++l+     + ++ +++ +++lk+++++l+k+
  gi|557693787|ref|YP_008796841.1|  29 KRKDVARGEGVVLDQYADLVKLVMD--GEVREALKRVRRYVEKETDTERRRLLKNVEAELRKH 89 
                                       579*******************999..89******99999999999***********999876 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.4e-05     0.083      16      41 ..       4      29 ..       3      32 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor 16 gnifltaaGllallggllLlvkrRKk 41
                                      +n+f+ +++l+++ + +lL++ r Kk
  gi|557693787|ref|YP_008796841.1|  4 ENAFFILLALMLAGALSLLAIPREKK 29
                                      58999999977777777775555544 PP

>> HycH  Formate hydrogenlyase maturation protein HycH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.3e-05      0.14      50      95 ..      41      86 ..      38      90 .] 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                              HycH 50 leeyeklvalleegearrKlegllkfgEieidkehvellaaaldel 95
                                      l++y++lv+l+ +ge r+ l+ ++++ E e d+e+ +ll +  +el
  gi|557693787|ref|YP_008796841.1| 41 LDQYADLVKLVMDGEVREALKRVRRYVEKETDTERRRLLKNVEAEL 86
                                      689*****************************99998887655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
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 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 650.97
//
Query:       gi|557693788|ref|YP_008796842.1|  [L=318]
Description: methanol dehydrogenase regulator [Candidatus Caldiarchaeum subterraneum]
Scores for 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-62  207.7   0.0    7.5e-62  207.0   0.0    1.4  1  AAA_3            ATPase family associated with various cellul
    4.6e-19   68.0   0.3    9.8e-19   67.0   0.1    1.7  1  AAA_lid_2        AAA lid domain
    1.3e-16   60.8   0.0    2.9e-16   59.7   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
    5.5e-06   26.8   0.0    1.6e-05   25.3   0.0    1.8  1  AAA              ATPase family associated with various cellul
    1.8e-05   24.0   0.0      3e-05   23.2   0.0    1.3  1  MCM              MCM P-loop domain
    3.3e-05   23.4   1.0     0.0065   15.9   0.2    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00011   22.0   0.0    0.00099   18.9   0.0    2.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0003   20.6   0.0     0.0045   16.7   0.0    2.1  2  Sigma54_activat  Sigma-54 interaction domain


Domain annotation for each model (and alignments):
>> 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 !  207.0   0.0   3.4e-65   7.5e-62       1     131 []      40     170 ..      40     170 .. 1.00

  Alignments for each domain:
  == domain 1  score: 207.0 bits;  conditional E-value: 3.4e-65
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       hv++egvPGlaktll+k++a +l+l+fkriqft+d+lPsdi+G  v+++k+ e+efk+Gpvfan++l deinrapp+
  gi|557693788|ref|YP_008796842.1|  40 HVIMEGVPGLAKTLLAKSFAMSLGLSFKRIQFTTDILPSDIIGGLVLNRKTGELEFKPGPVFANVVLIDEINRAPPR 116
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                       +qsalleam+erqvtveg t+klpepflv+atqnP+e eGt+plpea++drf++
  gi|557693788|ref|YP_008796842.1| 117 SQSALLEAMQERQVTVEGVTYKLPEPFLVIATQNPVELEGTFPLPEAEIDRFMM 170
                                       ****************************************************98 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.1   4.4e-22   9.8e-19       2      60 ..     233     290 ..     232     299 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 4.4e-22
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepe 60 
                                       ++r+++++ lg+s+r a++all aA+AlAal++r yV+p+Dvk+++  VL+HRl ++pe
  gi|557693788|ref|YP_008796842.1| 233 RSRKDTRLMLGASPR-AEIALLYAAKALAALNNRVYVIPDDVKRVCYRVLNHRLMPKPE 290
                                       57899999*******.**************************************98886 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 !   59.7   0.0   1.3e-19   2.9e-16       1     138 []      40     168 ..      40     168 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 1.3e-19
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEve 75 
                                       +v++ G pG +K+ la+++a  l+ ++  +q+t d+ ++d++g++ ++   g+ +++++p+      + ++++DE++
  gi|557693788|ref|YP_008796842.1|  40 HVIMEGVPGLAKTLLAKSFAMSLGLSFKRIQFTTDILPSDIIGGLVLNrkTGELEFKPGPVF-----ANVVLIDEIN 111
                                       79**********************************************999***********.....9********* PP

                                       G--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  76 raesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       ra++  +++Ll  + er++   eg ++   ++      f viat np++  +  +l +a ++Rf
  gi|557693788|ref|YP_008796842.1| 112 RAPPRSQSALLEAMQERQVT-VEGVTYKLPEP------FLVIATQNPVElEGTFPLPEAEIDRF 168
                                       *******************9.77888887888......***********999999999999998 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 !   25.3   0.0   7.1e-09   1.6e-05       1     111 [.      41     151 ..      41     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 7.1e-09
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS..SSSTTHHHHHHHHHHHHHHHTS........TSEEEEEETG CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsell..skyvgesekkirelfkeakeka........kpsilfiDEi 67 
                                       v++ G pG  KTllak+ a +lg +f +i+ ++ +  s+++g      r++       +           +++iDEi
  gi|557693788|ref|YP_008796842.1|  41 VIMEGVPGLAKTLLAKSFAMSLGLSFKRIQFTTDIlpSDIIGGLV-LNRKTG------ElefkpgpvFANVVLIDEI 110
                                       5789*************************9876553344333221.112222......122323344338******* PP

                                       GGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS CS
                               AAA  68 dalaksrsgseseeeervvnqLlteldgvkkk........eskvivigatnr 111
                                        +  +++           +++Ll+++++ +           ++++vi++ n 
  gi|557693788|ref|YP_008796842.1| 111 NRAPPRS-----------QSALLEAMQERQVTvegvtyklPEPFLVIATQNP 151
                                       ***9999...........**********999999999998665777777664 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   1.3e-08     3e-05      57     175 ..      38     153 ..      10     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.3e-08
                                       S-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESSSSSS...SHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESG CS
                               MCM  57 dinvllvgdpgtaKsqlLkyveklapravytsgkgssa...agLtaavvrdeetgefvleaGalvladkGvcciDef 130
                                         +v++ g pg+aK+ l k+ + ++    +  ++ ++    +++    v +++tge+ ++ G +      v++iDe+
  gi|557693788|ref|YP_008796842.1|  38 GGHVIMEGVPGLAKTLLAKSFA-MSLGLSFKRIQFTTDilpSDIIGGLVLNRKTGELEFKPGPVFA---NVVLIDEI 110
                                       5699999999999998888877.5555556666666652225778888889999********9875...49****** PP

                                       GGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SS CS
                               MCM 131 dkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpka 175
                                       ++   + +sal+Eam + ++++   G++++L+    v+a  np++
  gi|557693788|ref|YP_008796842.1| 111 NRAPPRSQSALLEAMQERQVTVE--GVTYKLPEPFLVIATQNPVE 153
                                       ******************99996..9*****************84 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   2.9e-06    0.0065       5      44 ..      21      60 ..      18      73 .. 0.90
   2 !    6.2   0.0    0.0027         6     108     159 ..     103     152 ..      77     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.9e-06
                      Mg_chelatase  5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlps 44
                                      v+G ++a + l ia   g ++++ G pG  Kt+lak ++ 
  gi|557693788|ref|YP_008796842.1| 21 VVGMHDAIESLIIALLTGGHVIMEGVPGLAKTLLAKSFAM 60
                                      8999**********999999***************98765 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0027
                      Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                        v+++DE+     +   +L e +++++vt++  ++k   p  f ++a+ Np 
  gi|557693788|ref|YP_008796842.1| 103 NVVLIDEINRAPPRSQSALLEAMQERQVTVEGVTYK--LPEPFLVIATQNPV 152
                                       5899**************************987765..68889*******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 !   18.9   0.0   4.4e-07   0.00099      34     114 ..      39     131 ..      34     138 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.4e-07
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaa.lltnleek...........dvlfideihrlsr 98 
                                        hv++ G PGl kt lak  a  lg ++k     +   ++d+++ l+ n +++           +v++idei r  +
  gi|557693788|ref|YP_008796842.1|  39 GHVIMEGVPGLAKTLLAKSFAMSLGLSFKRIQFTTDILPSDIIGgLVLNRKTGelefkpgpvfaNVVLIDEINRAPP 115
                                       5*************************998776555555666654244433332111112222337899********* PP

                            RuvB_N  99 aveevlysamedfrld 114
                                         +  l  am++ ++ 
  gi|557693788|ref|YP_008796842.1| 116 RSQSALLEAMQERQVT 131
                                       **********998876 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.098   2.2e+02       8      42 ..      24      58 ..      20      72 .. 0.86
   2 !   16.7   0.0     2e-06    0.0045      96     142 ..     104     150 ..      87     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.098
                                      HHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHH CS
                   Sigma54_activat  8 lkelleqikkvaktdlsvlitGesGtGKellarai 42
                                      +++++e++  +  t  +v+++G  G  K+lla++ 
  gi|557693788|ref|YP_008796842.1| 24 MHDAIESLIIALLTGGHVIMEGVPGLAKTLLAKSF 58
                                      6677788888888999****************975 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2e-06
                                       EEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatn 142
                                       ++++Dei++ p++ Q+ Ll+++qe++v+  G + + +  + +ia+ n
  gi|557693788|ref|YP_008796842.1| 104 VVLIDEINRAPPRSQSALLEAMQERQVTVEGVTYKLPEPFLVIATQN 150
                                       6789************************9999999988887776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2273.83
//
Query:       gi|557693789|ref|YP_008796843.1|  [L=418]
Description: hypothetical protein CSUB_C0352 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-11   42.9   0.0    9.6e-11   41.8   0.0    1.5  1  DUF58     Protein of unknown function DUF58


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   5.3e-15   9.6e-11       4      84 ..     202     281 ..     200     283 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 5.3e-15
                             DUF58   4 faglReYvpgDplrrIdWkatARt.gelyvrefeaerartvllvldlspemslgstgdekletavsaaaslarqlld 79 
                                       f+++  Y+ g pl+ +dW+ tAR  ge +vr f+++ + ++ lvld s  + lg+   + l+  v a+++la ++l+
  gi|557693789|ref|YP_008796843.1| 202 FREITRYEEGQPLKAVDWRRTAREnGEIFVRRFDKQNRLRICLVLDYSHGNILGNP--SLLDSVVGAVSTLASSVLE 276
                                       88999******************6599************************99985..******************* PP

                             DUF58  80 egdrv 84 
                                       +gd v
  gi|557693789|ref|YP_008796843.1| 277 RGDSV 281
                                       **998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2948.41
//
Query:       gi|557693790|ref|YP_008796844.1|  [L=237]
Description: hypothetical protein CSUB_C0353 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1690.32
//
Query:       gi|557693791|ref|YP_008796845.1|  [L=505]
Description: hypothetical protein CSUB_C0354 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   11.9   0.0        6.3    6.8   0.0    2.7  3  CE2_N     Carbohydrate esterase 2 N-terminal


Domain annotation for each model (and alignments):
>> CE2_N  Carbohydrate esterase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0   0.00035       6.3      15      85 ..     114     179 ..     105     188 .. 0.86
   2 ?    1.5   0.0     0.016   2.8e+02      50      88 ..     212     250 ..     196     254 .. 0.90
   3 ?   -2.2   0.0      0.22     4e+03      20      36 ..     365     381 ..     350     397 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00035
                                       E-STT-EEEEEEEEEEEEEEEEE..SSS-EEEEEEETTS--EEEEE-SS-EEEEEEEEEEEEEEEEEEEE- CS
                             CE2_N  15 fawpGtsvefrftGtslsvrlkdkedkgknrlaviiDgkrvkdlkldgeektytlaeglepgehtvrlvkr 85 
                                       +a p ++v +rf+G  + ++++       n +a+++Dg+   +++  g+      ++g ++ +++v++++r
  gi|557693791|ref|YP_008796845.1| 114 LAKPPVQVLARFEGPFVVLTVST----SPNTYALFLDGRGEGEVVAAGSSI-ELGLKGFNDTRVRVEIIRR 179
                                       6678899****************....*************99998888887.4455999999999999987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.016
                                       ETTS--EEEEE-SS-EEEEEEEEEEEEEEEEEEEE-S-G CS
                             CE2_N  50 iDgkrvkdlkldgeektytlaeglepgehtvrlvkrtEa 88 
                                       i++++v +++l++++++++ +++   g h +rl+  ++ 
  gi|557693791|ref|YP_008796845.1| 212 INDSTVFSVRLPADGEQVSGLRKMGLGPHLIRLYSVSDK 250
                                       899999999999999999***************999885 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.22
                                       -EEEEEEEEEEEEEEEE CS
                             CE2_N  20 tsvefrftGtslsvrlk 36 
                                       t+v+++f+ tsl++ l+
  gi|557693791|ref|YP_008796845.1| 365 TNVSLNFNATSLTLPLT 381
                                       78899999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3735.62
//
Query:       gi|557693792|ref|YP_008796846.1|  [L=376]
Description: fructose-1,6-bisphosphatase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-172  571.2   0.0     1e-171  571.0   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 !  571.0   0.0  5.7e-176    1e-171       1     361 []       2     370 ..       2     370 .. 0.98

  Alignments for each domain:
  == domain 1  score: 571.0 bits;  conditional E-value: 5.7e-176
                          FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafk 77 
                                       ++t+svikaDvGs+aGh+k+h++++e ++ +l+ea+++gl++  y t++GDDi l+m+h kg+dn e+h+law++f+
  gi|557693792|ref|YP_008796846.1|   2 RTTVSVIKADVGSIAGHHKPHPKMMELASGKLAEAENTGLIKSGYATHCGDDIILVMSHGKGEDNPEIHGLAWNIFR 78 
                                       68*************************************************************************** PP

                          FBPase_3  78 eat.evakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaG 153
                                       e+t +vak +klygaGqDlL+dafsGnv+GlGPgvae+efeeRks+pv+vfaaDktepga+nlply+ifa p ntaG
  gi|557693792|ref|YP_008796846.1|  79 EITeKVAKPMKLYGAGQDLLSDAFSGNVRGLGPGVAEIEFEERKSDPVIVFAADKTEPGAWNLPLYRIFASPENTAG 155
                                       ***789*********************************************************************** PP

                          FBPase_3 154 lvidpklheGfkfevlDvieekkillsapeelydllallgakeryvikrvyskkdeeiaavvsterlsliaGkYvGk 230
                                       lvidp+lh+Gf+fevlD++e+ ++ll++peelydl+allg+ +ry++++vy+ +d+e+aa++st+rlsliaG+YvGk
  gi|557693792|ref|YP_008796846.1| 156 LVIDPTLHDGFRFEVLDLVESWSVLLKTPEELYDLVALLGTVGRYAVSKVYRASDGEPAAAASTTRLSLIAGRYVGK 232
                                       ***************************************************************************** PP

                          FBPase_3 231 DDPvaivRaqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakp..trfdgpprvvalgfqlkegklvg. 304
                                       DDPv+ivRaq+g+Pavgevl +fa+p +v+GwmrGsh gplmPvs+++ ++  ++fdgpprv+a+g+q+++g+lvg 
  gi|557693792|ref|YP_008796846.1| 233 DDPVMIVRAQAGFPAVGEVLAAFATPFIVSGWMRGSHRGPLMPVSFRRGQNvvSYFDGPPRVMAMGWQVSNGRLVGq 309
                                       **********************************************977653499********************99 PP

                          FBPase_3 305 ....pvDlfddpafdeaRekaaeiadelRrqGpfephrlpeeeleYttlpevleklkerfe 361
                                           pvDlf+dp +d++R+kaa++a +lR++G fep+rl +ee+eYttlp+++eklk rf+
  gi|557693792|ref|YP_008796846.1| 310 dgvePVDLFEDPFWDTVRNKAADLALTLRTMGEFEPARLGHEEMEYTTLPQIIEKLKPRFK 370
                                       99999******************************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 3039.58
//
Query:       gi|557693793|ref|YP_008796847.1|  [L=58]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   21.4   0.0    0.00031   21.0   0.0    1.3  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
  ------ inclusion threshold ------
      0.052   13.9   0.0      0.068   13.5   0.0    1.2  1  Histone        Core histone H2A/H2B/H3/H4
       0.14   12.5   0.5       0.49   10.7   0.0    1.7  2  CENP-X         CENP-S associating Centromere protein X


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   5.2e-08   0.00031      23      60 ..      24      57 ..      11      58 .] 0.75

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.2e-08
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHH CS
                     CBFD_NFYB_HMF 23 kdAkeliaecveefieelaseAaeickkekrKtikaeh 60
                                      +dA e ++e+v    + l ++A+++c++++rKt+++e+
  gi|557693793|ref|YP_008796847.1| 24 SDALEGLNEAV----KALIEKAVKRCQANGRKTLMKED 57
                                      56666666555....556679****************9 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.1e-05     0.068      80     123 ..      18      57 ..       7      58 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                                       SSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHH CS
                           Histone  80 edlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkD 123
                                       e++r+ ++a++ l+ea++al++     A + +  + R+T++++D
  gi|557693793|ref|YP_008796847.1|  18 EGIRLGSDALEGLNEAVKALIE----KAVKRCQANGRKTLMKED 57 
                                       799***************9886....566667789999999998 PP

>> CENP-X  CENP-S associating Centromere protein X
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.16   9.7e+02      32      43 ..       4      15 ..       3      19 .. 0.80
   2 ?   10.7   0.0   8.2e-05      0.49      16      52 ..      19      55 ..      16      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.16
                                      HHHHHHHHHHHH CS
                            CENP-X 32 klFvrEavaRaa 43
                                      + Fv+E  +R a
  gi|557693793|ref|YP_008796847.1|  4 ESFVVESRVREA 15
                                      579999999965 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.2e-05
                                      T-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-S CS
                            CENP-X 16 ktkItkdalelvaeylklFvrEavaRaaeeaeeegke 52
                                       +++ +dale ++e +k +++ av R+ ++ ++  ++
  gi|557693793|ref|YP_008796847.1| 19 GIRLGSDALEGLNEAVKALIEKAVKRCQANGRKTLMK 55
                                      58999**********************9998876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 429.44
//
Query:       gi|557693794|ref|YP_008796848.1|  [L=104]
Description: hypothetical protein CSUB_C0357 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   25.8   0.0    1.1e-05   25.5   0.0    1.1  1  ABM       Antibiotic biosynthesis monooxygenase
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.015   15.5   0.0    1.1  1  DUF4937   Domain of unknown function (DUF4937
      0.073   13.4   0.0      0.092   13.1   0.0    1.2  1  DUF4188   Domain of unknown function (DUF4188)


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 !   25.5   0.0   1.8e-09   1.1e-05       1      67 [.       4      70 ..       4      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.8e-09
                                      CEEEEEEEEESTTGHHHHHHH.HHHHHHHHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHH CS
                               ABM  1 mviviaeirvkpgqaeaflda.faeavesllaeepGclgyellrstedpdevvvieeWeseaaleahl 67
                                      m+  + +  +k+g ++af++  ++ea + +l+++ Gcl + +  +  +p   vv++ W+++++l+a++
  gi|557693794|ref|YP_008796848.1|  4 MILRVWTCPIKKGMEKAFEEFaLKEATQ-ILEKQAGCLNAFFGIDYGEPSVGVVVTLWRDIESLKAFT 70
                                      56666677799*********83555555.88**********************************987 PP

>> DUF4937  Domain of unknown function (DUF4937
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   2.5e-06     0.015       2      65 ..       6      71 ..       5      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-06
                           DUF4937  2 vklirCevkdekkeaFska..qakWaalkgveGFigqlGGWekeeeaeavilalWedraaydeFma 65
                                      +++ +C +k+ +++aF++   +++ + l++  G ++ + G    e++  v+++lW+d +++++F  
  gi|557693794|ref|YP_008796848.1|  6 LRVWTCPIKKGMEKAFEEFalKEATQILEKQAGCLNAFFGIDYGEPSVGVVVTLWRDIESLKAFTG 71
                                      56789***********98522456678999********************************9975 PP

>> DUF4188  Domain of unknown function (DUF4188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.5e-05     0.092      23      71 ..      14      72 ..       3      84 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                           DUF4188 23 leamprmlreleekk.......elGlLgaeslig...srevllvqYwrdvesLeafaks 71
                                       + m++ ++e + k+       ++G+L+a   i    +   ++v  wrd+esL+af+ +
  gi|557693794|ref|YP_008796848.1| 14 KKGMEKAFEEFALKEatqilekQAGCLNAFFGIDygePSVGVVVTLWRDIESLKAFTGD 72
                                      4455555555444440011111556665555552676666778999**********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 787.24
//
Query:       gi|557693795|ref|YP_008796849.1|  [L=127]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (127 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:                        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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 890.40
//
Query:       gi|557693796|ref|YP_008796850.1|  [L=260]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-35  120.8   1.2    1.1e-34  120.5   1.2    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 !  120.5   1.2   5.9e-39   1.1e-34      12     215 ..      24     249 ..      19     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 5.9e-39
                                       HHHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCC.......S..................G-. CS
                             DUF72  12 eyYarhfntVEinstFYalpspetvakwaaqtpedFrFavKapraith.......e............r.....ne. 63 
                                       e+Y ++f+t+Ei+ tFY+lp++etv +w++++p +F+F++Ka++a++h       +            r        
  gi|557693796|ref|YP_008796850.1|  24 EAYYQKFPTIEIQETFYKLPRTETVMRWREKAPRGFVFCMKAWQAVSHpvssptwRrsglqpgkreatRygwlrPVk 100
                                       68**********************************************66555551555555554444144442121 PP

                                       SCHHHHHHHHHH.CHHHCT-EEEEEEE--TT--S.HHHHHHHHHHTTTS-...S.EEEE--BGGGH..H.HHHHHHH CS
                             DUF72  64 daeealerflesalepLgeklgpllfQlppsfkfdeenlerLeaflaalp...l.lavEvRhrswf..e.llellre 133
                                       ++ +a+++  e   ++   ++ ++++Q p+s+  d++  +++ +f+++     l +a+E R +       l +++++
  gi|557693796|ref|YP_008796850.1| 101 ENFAAWDKTAEV-AKA--MQAHVVVIQTPASMPDDQKTQQNVMKFFEHASthhLtIAWEPRGKLAKnkTfLQKVCEK 174
                                       344555555553.444..57899*********77788999999998866566755*******8665754689***** PP

                                       TT-EEEEE--SSC--------SSTEEEEEE--S...HHTTB----HHHHHHHHHHHHHHHTCSSEEEEEE-SBCCCH CS
                             DUF72 134 hgvavvldepkkpklpledvttadfvyvRlhgr...eeryayrYseeelaewaerikawaaegrevyvffnndaegq 207
                                       hg+++v+d      l+ e++t+++  y Rlhg    e +y+yrYs+++l+ +ae+i+a++   +e yvffnn + ++
  gi|557693796|ref|YP_008796850.1| 175 HGIIHVTD-----ILKSEPATQHKIFYTRLHGLgrgEVNYRYRYSDQDLRLLAEKIDAINF--DEGYVFFNNLWMAE 244
                                       *******9.....6788999*9**********9986589*******************976..89*******76544 PP

                                       HHHHHHHH CS
                             DUF72 208 aplnaraL 215
                                           a+++
  gi|557693796|ref|YP_008796850.1| 245 D---AERF 249
                                       4...4333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1751.44
//
Query:       gi|557693797|ref|YP_008796851.1|  [L=341]
Description: pyruvate dehydrogenase E1 component subunit alpha [Candidatus Caldiarchaeum subterraneum]
Scores for 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-83  279.8   0.0    2.3e-83  279.6   0.0    1.0  1  E1_dh            Dehydrogenase E1 component
    9.5e-07   28.7   0.3    4.7e-06   26.5   0.3    1.9  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    1.1e-05   24.8   0.0    0.00028   20.2   0.0    2.1  2  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    3.9e-05   22.8   0.0    5.6e-05   22.3   0.0    1.2  1  Transketolase_N  Transketolase, thiamine diphosphate binding 


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.6   0.0   5.1e-87   2.3e-83       1     298 [.      20     316 ..      20     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 279.6 bits;  conditional E-value: 5.1e-87
                                       HHHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-T CS
                             E1_dh   1 eklvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkv 77 
                                       ++ ++l+r++d+++++++r +++  y +s gqea+ v++ +a  + D+i+++YRe g ++arg++le ++a   g+v
  gi|557693797|ref|YP_008796851.1|  20 YREMVLARLFDSAMVKLQRAGKVAAYTSSEGQEAVSVAAVNAASPLDWIFPTYRETGAFIARGVPLETLIARQLGRV 96 
                                       5789************************************************************************* PP

                                       TTSSGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--E CS
                             E1_dh  78 kgkggsrhelmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpv 154
                                        + +++   l ++ k  ri++g g+v+a  p++ G  +aa+ +g++ v ++++GDgA+++Gd++e+ln a ++k p+
  gi|557693797|ref|YP_008796851.1|  97 GDPLKGHEVLLFGDKRYRIVTGPGPVAAHIPVAVGFGYAARRKGEDCVMLVFFGDGATSKGDFHEGLNVAGVFKTPT 173
                                       ********788899999************************************************************ PP

                                       EEEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SS CS
                             E1_dh 155 ifvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyggHs 231
                                       +f+++NN+y+is+++++++as+++a +a ++g  g++V+gn ++++y+ v  A+e ar+g+gp+lie++tYR+  Hs
  gi|557693797|ref|YP_008796851.1| 174 VFICQNNQYAISVPRHQQTASETIAVKAEAYGFEGVTVNGNNIEEMYKIVSRAVEKARNGEGPTLIEAITYRLAAHS 250
                                       ***************************************************************************** PP

                                       TTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS---- CS
                             E1_dh 232 esDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskkele 298
                                       + Ddp++yrt +eve +r++ dpi++ ++lL++k+++s+e+++++  ++r++ e+ ++++e++++ +
  gi|557693797|ref|YP_008796851.1| 251 TADDPTKYRTVQEVEMWRSQ-DPITICRKLLIEKNLLSDEKDNQLWTSLRQMLEQKIEEVEKTPIIP 316
                                       ******************99.*****************************************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 !   26.5   0.3   1.1e-09   4.7e-06      26     152 ..     118     240 ..     103     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.1e-09
                                       TTS-TTTHHHHHHHHHHH...ST.TSEEEEEEEHHHHHHT..GGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHT CS
                      TPP_enzyme_C  26 glgtmGyglpaAiGakla...kp.drevvaivGDGgflmi..lqelatavrrnlpitvvvlnNegygmtggqqepfg 96 
                                       g g     +p+A+G   a   k  d  + ++ GDG++     ++ l  a   + p ++++ nN++   + ++q+ + 
  gi|557693797|ref|YP_008796851.1| 118 GPGPVAAHIPVAVGFGYAarrKGeDCVMLVFFGDGATSKGdfHEGLNVAGVFKTPTVFICQNNQYAISVPRHQQTAS 194
                                       567777889999999995332222568889******99888355677777788899999999998877766665554 PP

                                       CCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH....CSSSEEEEE CS
                      TPP_enzyme_C  97 gkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkeal....ekkgpalie 152
                                       +               +a  aea+G +g++v+ +++ee+ +++ +a+    + +gp+lie
  gi|557693797|ref|YP_008796851.1| 195 E--------------TIAVKAEAYGFEGVTVNGNNIEEMYKIVSRAVekarNGEGPTLIE 240
                                       3..............36677*******************7766666666669*******8 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 !   20.2   0.0   6.4e-08   0.00028     115     176 ..     124     185 ..     116     197 .. 0.93
   2 ?    2.3   0.0     0.018        82     244     273 .]     210     243 ..     189     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.4e-08
                    DXP_synthase_N 115 tsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsis 176
                                       + i +a+G+  a++ kge+  ++   GDga + G  +e+ln +g  k+  + i  +N+ +is
  gi|557693797|ref|YP_008796851.1| 124 AHIPVAVGFGYAARRKGEDCVMLVFFGDGATSKGDFHEGLNVAGVFKTPTVFICQNNQYAIS 185
                                       678899****************************************************9997 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.018
                    DXP_synthase_N 244 pidGhdleelikvl....eevkklkgpvllhvvt 273
                                        ++G+++ee+ k++    e++++ +gp+l+  +t
  gi|557693797|ref|YP_008796851.1| 210 TVNGNNIEEMYKIVsravEKARNGEGPTLIEAIT 243
                                       599*****99887611115667779999998776 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   1.2e-08   5.6e-05     144     243 ..     142     243 ..     120     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.2e-08
                                       ---EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEESSEETTE.EGGGT--S-HHHHHHHTT-EEEEE..TTTT CS
                   Transketolase_N 144 dhytyvilgDgclmeGvsseasslagtlkLgkLivlyDdnkisidG.eteisftedvakrfeaygWhviev..edge 217
                                       d  + v+ gDg    G  +e  ++ag+ k    + +  +n+ +i     +++ +e +a + eayg++ ++v  ++ e
  gi|557693797|ref|YP_008796851.1| 142 DCVMLVFFGDGATSKGDFHEGLNVAGVFKTPT-VFICQNNQYAISVpRHQQTASETIAVKAEAYGFEGVTVngNNIE 217
                                       556789**********************9876.4455666655554144667889999*********8887333334 PP

                                       -H.HHHHHHHHHHHH-TTS-EEEEEE- CS
                   Transketolase_N 218 dv.eaikaaieeakaekdkPsliklrt 243
                                       ++ + +++a+e+a++  + P+li+  t
  gi|557693797|ref|YP_008796851.1| 218 EMyKIVSRAVEKARNG-EGPTLIEAIT 243
                                       55145689*****998.89****8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); 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:                         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: 00:00:00.43
# Mc/sec: 2373.26
//
Query:       gi|557693798|ref|YP_008796852.1|  [L=241]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-07   29.5  16.7    1.1e-06   28.8  16.7    1.3  1  SpoIIM     Stage II sporulation protein M


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 !   28.8  16.7   6.1e-11   1.1e-06       5     151 ..      83     229 ..      74     232 .. 0.69

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 6.1e-11
                            SpoIIM   5 flvgillgallaa..........snfaeqisseskensalslflaifanNlrvalllf..llGllllgiptilvl.l 68 
                                       +l+g+l++a+la           +    q++  +     +++ + if+nNl  +ll++  +     lg++++ ++  
  gi|557693798|ref|YP_008796852.1|  83 LLIGLLAAAALAPmpfvdaealvN----QFE--EMLPRLTETPVMIFLNNLAASLLMMipV-----LGMALAGLIvY 148
                                       334444444444455554433321....222..223333457799*************444.....46666666624 PP

                            SpoIIM  69 inGfvlGavaalvaefgglllflllilPhgilelpaiiiagaaglrlgkalrsrrkalkeakrellklllllvplll 145
                                        +G+v+Ga++a+ +    lll++ +i   g++e+ a+ +a++ g+ l ++    +k+l+++ r+l   + ++v+lll
  gi|557693798|ref|YP_008796852.1| 149 NTGAVIGAFSAVSNVPVALLLLIPFITVYGFIEMLAYGFAVSQGFFLTTSAF--KKQLRKEVRSLPYTVAVVVLLLL 223
                                       56*******999999888*****************************88773..35666677776666666666888 PP

                            SpoIIM 146 iAaliE 151
                                       ++a++E
  gi|557693798|ref|YP_008796852.1| 224 AGAVLE 229
                                       888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1789.49
//
Query:       gi|557693799|ref|YP_008796853.1|  [L=237]
Description: archaeal preflagellin peptidase FlaK [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   31.3   7.9    2.1e-07   31.3   7.9    1.8  2  Peptidase_A24  Type IV leader peptidase family
    2.7e-07   31.0   2.1    2.3e-06   28.0   0.3    2.9  2  Arc_PepC_II    Archaeal Peptidase A24 C-terminus Type II
  ------ inclusion threshold ------
      0.076   12.9   0.2        2.1    8.3   0.1    2.4  2  TRIQK          Triple QxxK/R motif-containing protein family
        4.9    7.4   5.7        1.5    9.0   0.3    2.5  3  DPM3           Dolichol-phosphate mannosyltransferase subunit


Domain annotation for each model (and alignments):
>> Peptidase_A24  Type IV leader peptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   7.9   4.7e-11   2.1e-07       3      92 ..       9     107 ..       7     129 .. 0.83
   2 ?   -1.9   0.1      0.96   4.3e+03      28      39 ..     204     213 ..     197     231 .. 0.50

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 4.7e-11
                     Peptidase_A24   3 lltillvlsviDldtrtlpdeltlpllllgvlfa..qllllglpnlaqavlgalvgalvlllislvdeqamGgGDvk 77 
                                       + + ll+ s+ D+++r+++d ++++  +lg+l++  + + +g+  l  + +++lv a+v ++  l+  +  Gg+D+k
  gi|557693799|ref|YP_008796853.1|   9 VSLTLLYSSYLDIKKREVDDIVWVIPSILGLLLNlyTVYVVGFDYLVRYGAAVLVSAGVGFA--LYFAGLYGGADAK 83 
                                       56789****************************977666778999999999999********..************* PP

                     Peptidase_A24  78 laavlgaflgwerl.........l 92 
                                        +++++++ ++ ++         l
  gi|557693799|ref|YP_008796853.1|  84 ALVTIALVQPFSYTglqlhgvtsL 107
                                       *******99988876666655542 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.96
                     Peptidase_A24  28 llllgvlfaqll 39 
                                       ++ l v+f   +
  gi|557693799|ref|YP_008796853.1| 204 GIPLLVFFT--V 213
                                       555555554..1 PP

>> 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 ?    0.9   0.1      0.14   6.5e+02      59      73 ..      22      36 ..      14      51 .. 0.66
   2 !   28.0   0.3   5.1e-10   2.3e-06      52      91 ..     189     223 ..     149     224 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.14
                       Arc_PepC_II 59 kkglieetvWvtygv 73
                                      kk+ +++ vWv + +
  gi|557693799|ref|YP_008796853.1| 22 KKREVDDIVWVIPSI 36
                                      445588889996654 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 5.1e-10
                       Arc_PepC_II  52 kelkkykkkglieetvWvtygvPflipitaGfiialvlGD 91 
                                       +el+k+ +     ++vWvt+g+P+l++ t+G+ + l+ G 
  gi|557693799|ref|YP_008796853.1| 189 EELEKVDR-----DDVWVTPGIPLLVFFTVGYFFNLFAGE 223
                                       34444433.....44*********************9995 PP

>> TRIQK  Triple QxxK/R motif-containing protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00046       2.1      48      69 ..      26      47 ..      18      53 .. 0.84
   2 ?    2.0   0.0     0.045     2e+02      40      76 ..     187     223 ..     175     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00046
                             TRIQK 48 ikevllvlvailvlllalYalf 69
                                      + ++++v+ +il lll lY+++
  gi|557693799|ref|YP_008796853.1| 26 VDDIVWVIPSILGLLLNLYTVY 47
                                      689****************986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.045
                             TRIQK  40 eakksasgikevllvlvailvlllalYalfflnlske 76 
                                        +     + ++ ++v+ +i +l++   + ff  ++ e
  gi|557693799|ref|YP_008796853.1| 187 GIEELEKVDRDDVWVTPGIPLLVFFTVGYFFNLFAGE 223
                                       5555556778889999999999999999999888765 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 ?    9.0   0.3   0.00034       1.5      19      60 ..      12      52 ..       3      56 .. 0.79
   2 ?    0.0   0.2      0.22   9.9e+02       8      60 ..      62     113 ..      55     121 .. 0.67
   3 ?   -2.1   0.0         1   4.6e+03      37      49 ..     198     210 ..     186     221 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00034
                              DPM3 19 lalllrlvslplskvqdevvpvlPlwalvlfGayslatlgyg 60
                                      ++l+ + ++++ ++++d++v+v+P ++ +l+ +y ++++g++
  gi|557693799|ref|YP_008796853.1| 12 TLLYSSYLDIK-KREVDDIVWVIPSILGLLLNLYTVYVVGFD 52
                                      34555555666.899***********************9975 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.22
                              DPM3   8 lalallllalwlalllrlvslplskvqdevvpvlPlwalvlfGayslatlgyg 60 
                                       l+ a + +al++a l++  + +   v   +v+ +++  l l G+ sl++l  g
  gi|557693799|ref|YP_008796853.1|  62 LVSAGVGFALYFAGLYGGADAK-ALVTIALVQPFSYTGLQLHGVTSLTVLTNG 113
                                       5555666677777777777666.555555566666677888888888887665 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1
                              DPM3  37 vvpvlPlwalvlf 49 
                                        v+v+P + l++f
  gi|557693799|ref|YP_008796853.1| 198 DVWVTPGIPLLVF 210
                                       4555555544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); 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:                         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 0.27s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1547.92
//
Query:       gi|557693800|ref|YP_008796854.1|  [L=417]
Description: glutamate dehydrogenase (NAD(P)+) [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  247.5   0.1    2.8e-73  246.6   0.1    1.4  2  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    1.2e-57  193.4   0.0    1.9e-57  192.7   0.0    1.3  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
     0.0026   17.1   0.0     0.0052   16.2   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.051   12.8   0.1       0.42    9.8   0.0    2.0  2  Thi4             Thi4 family
      0.091   13.1   0.0       0.24   11.7   0.0    1.8  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
       0.14    9.6   0.0        0.2    9.1   0.0    1.1  1  Bac_GDH          Bacterial NAD-glutamate dehydrogenase
       0.16   12.4   0.0       0.37   11.3   0.0    1.6  1  NAD_binding_7    Putative NAD(P)-binding


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 ?   -3.4   0.0       2.5   6.3e+03      66      85 ..     108     127 ..     106     135 .. 0.75
   2 !  246.6   0.1   1.1e-76   2.8e-73       2     241 ..     182     412 ..     182     414 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.5
                                       EEEEETTEE-HHHHHHHHHC CS
                     ELFV_dehydrog  66 GviydpeGldieellelkee 85 
                                       Gv +dp+ l+++el ++ ++
  gi|557693800|ref|YP_008796854.1| 108 GVACDPKNLSKNELERITRR 127
                                       77889999999999988655 PP

  == domain 2  score: 246.6 bits;  conditional E-value: 1.1e-76
                                       --TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHC.T-EEEEEEESSEEEEETTEE-HH CS
                     ELFV_dehydrog   2 GsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltel.gakvvavsDssGviydpeGldie 77 
                                       Gsl+r +aT++G++y+++e +k+++   +++++v+i+G+Gnvg +aa++l+e  gak++avsDs+G +y p+G + +
  gi|557693800|ref|YP_008796854.1| 182 GSLGRHDATSRGAAYIIREYFKTINKP-VKDAKVVIQGYGNVGYNAAKILHEEyGAKIIAVSDSKGGVYLPNGAHPD 257
                                       9**********************8887.**********************9877*********************** PP

                                       HHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HHH CS
                     ELFV_dehydrog  78 ellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqeA 154
                                       ++le+k++++sv +++     + + ++ne ell++++dil+P+A++n+i++e a  +++  +k+vvEgAN+ptt+eA
  gi|557693800|ref|YP_008796854.1| 258 KILEHKQKTGSVINFP-----GSKPLTNE-ELLTTPCDILIPAALENSITKEIAG-KVE--AKVVVEGANGPTTKEA 325
                                       ****************.....34789**7.*************************.888..**************** PP

                                       HHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHHH CS
                     ELFV_dehydrog 155 keileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkganiag 231
                                       + +l e+++ v+pd+++NaGGVtvS+lE++qnl+r +wt eev++kl+++m + f++v+++ ++y+++l++ga+i +
  gi|557693800|ref|YP_008796854.1| 326 DMVLFERKIPVIPDILSNAGGVTVSYLEWVQNLKRETWTLEEVHAKLEAKMVKGFHDVMNTSKKYETPLRQGAMIFA 402
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                     ELFV_dehydrog 232 fekvaeamka 241
                                       +++vaea + 
  gi|557693800|ref|YP_008796854.1| 403 VDRVAEAINY 412
                                       ******9765 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 !  192.7   0.0   7.4e-61   1.9e-57       1     130 []      35     163 ..      35     163 .. 0.99

  Alignments for each domain:
  == domain 1  score: 192.7 bits;  conditional E-value: 7.4e-61
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       p+rv+ v+vpvk+d+G+l+v++g+r+qh++a+gP+kGG+R+ p+v+ dev aLa+lmt+K+a++dlp+GGakggv +
  gi|557693800|ref|YP_008796854.1|  35 PKRVVVVSVPVKMDDGSLRVFTGIRVQHNNARGPYKGGVRYYPTVDVDEVTALAMLMTFKCAVTDLPYGGAKGGVAC 111
                                       89*************************************************************************** PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeykk 130
                                       dpk+ls++eleritrr++  ++ ++iGp iD+p pDv+t+a++maw++d+y++
  gi|557693800|ref|YP_008796854.1| 112 DPKNLSKNELERITRRYTAMIY-EVIGPYIDIPGPDVYTDAQTMAWMVDTYSM 163
                                       **********************.****************************97 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   0.0     2e-06    0.0052      23      68 ..     196     244 ..     178     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-06
                                       C..HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSS CS
                      2-Hacid_dh_C  23 w..ksekallgkelsgktvGiiGlGrIGqavakrlk.afgmkviaydrs 68 
                                       +  ++  ++  k +++ +v i G+G++G ++ak+l+ + g+k+ia++ s
  gi|557693800|ref|YP_008796854.1| 196 YiiREYFKTINKPVKDAKVVIQGYGNVGYNAAKILHeEYGAKIIAVSDS 244
                                       44445556778899*********************999*******9977 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00016      0.42       4      48 ..     197     242 ..     194     264 .. 0.82
   2 ?    0.6   0.0      0.11   2.8e+02       8      57 ..     300     347 ..     294     361 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHT.EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                              Thi4   4 iveryfedllkya.esDvvivGaGssGLtaayylakkpdlkvaile 48 
                                       i+++yf+ + k + ++ vvi G G  G  aa++l ++ + k++ + 
  gi|557693800|ref|YP_008796854.1| 197 IIREYFKTINKPVkDAKVVIQGYGNVGYNAAKILHEEYGAKIIAVS 242
                                       78999999988652689********************998887554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.11
                                       HHHHHHHHTEEEEEEE--.SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                              Thi4   8 yfedllkyaesDvvivGa.GssGLtaayylakkpdlkvailersvspGGGa 57 
                                         +++   +e+ vv+ Ga G++   a  +l ++   k+ ++   +s  GG+
  gi|557693800|ref|YP_008796854.1| 300 ITKEIAGKVEAKVVVEGAnGPTTKEADMVLFER---KIPVIPDILSNAGGV 347
                                       567777789999***998789999999999999...999999999999997 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 ?   11.7   0.0   9.5e-05      0.24       2      35 ..     213     246 ..     212     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.5e-05
                                       EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS- CS
                           Gp_dh_N   2 kvainGfGRIGrlvlralleekelevvaindltd 35 
                                       kv+i G+G +G +++++l ee   +++a+ d+  
  gi|557693800|ref|YP_008796854.1| 213 KVVIQGYGNVGYNAAKILHEEYGAKIIAVSDSKG 246
                                       89***************************99654 PP

>> Bac_GDH  Bacterial NAD-glutamate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0     8e-05       0.2    1052    1099 ..     306     353 ..     302     360 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 8e-05
                           Bac_GDH 1052 kelrakvvgEGgNLGltQlgRiEyalkggrintDaiDNsaGVdcSDhE 1099
                                         +++akvv EG+N   t  + +   ++++ +  D + N++GV +S  E
  gi|557693800|ref|YP_008796854.1|  306 GKVEAKVVVEGANGPTTKEADMVLFERKIPVIPDILSNAGGVTVSYLE 353 
                                        5789***************************************99766 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 ?   11.3   0.0   0.00014      0.37       5      83 ..     209     309 ..     205     328 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklle.agakvtvvapev......keele.elvklaeee...........lekd.... 58 
                                       +k+ kv++ G G+v+++ ++ l e +gak++ v+         + +++ +++++++++           l       
  gi|557693800|ref|YP_008796854.1| 209 VKDAKVVIQGYGNVGYNAAKILHEeYGAKIIAVSDSKggvylpNGAHPdKILEHKQKTgsvinfpgskpL--Tneel 283
                                       6899****************9998689******9996665555222223444444443333333322221..02222 PP

                     NAD_binding_7  59 .legadlviaatddrelneriaeaak 83 
                                         +  d++i a  ++++ ++ia + +
  gi|557693800|ref|YP_008796854.1| 284 lTTPCDILIPAALENSITKEIAGKVE 309
                                       22336666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2806.34
//
Query:       gi|557693801|ref|YP_008796855.1|  [L=201]
Description: phosphoribosyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   88.8   0.0      5e-25   87.9   0.0    1.4  2  Pribosyltran  Phosphoribosyl transferase domain
    7.3e-06   25.6   0.0      1e-05   25.1   0.0    1.1  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
       0.09   12.3   0.0       0.15   11.6   0.0    1.3  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 !   87.9   0.0   8.4e-29     5e-25       8     153 ..      16     155 ..      12     157 .. 0.87
   2 ?   -2.8   0.0      0.65   3.9e+03       5      25 ..     167     187 ..     164     195 .. 0.67

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 8.4e-29
                                       ---EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE--- CS
                      Pribosyltran   8 npaildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlled 84 
                                       +  +++ ++ la++i++  + + d+++g++rgG+++a+ l+d L+v+ +yv   + ++++ ++  +   d   +le 
  gi|557693801|ref|YP_008796855.1|  16 WGDVERGADALAEKIVDG-GCSVDTIIGVLRGGMIVADFLSDILDVREVYVIGCRSYTGTVSTELKIYHDL--ALER 89 
                                       556677888999999999.***************************9887776666666666666555554..9*** PP

                                       -TTSEEEEE-SEESSSHHHHHHHH.HHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEEEE- CS
                      Pribosyltran  85 pagkkVliVDDildtGgTllaale.lLkekgpeevriavlvdkpateeevdknakrvfslspdnfvavvg 153
                                       ++g+ Vl+VDD+ dtG+Tl aa+e +Lk ++p +v +a+l++kp ++  +d+ +++++     ++v++++
  gi|557693801|ref|YP_008796855.1|  90 LDGRNVLLVDDVADTGSTLDAAVEkILKPRNPNSVTTATLLKKPWSRYTPDYFVDETD----AWIVFPWE 155
                                       **************************************************99888887....89999885 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.65
                                       TTT---EEEEEEETTEEEEEE CS
                      Pribosyltran   5 llenpaildavarlaaeilee 25 
                                       + en+ + +av++laa ++ +
  gi|557693801|ref|YP_008796855.1| 167 FVENMGFDAAVDELAALTRLD 187
                                       667777778888888877666 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   1.7e-09     1e-05      71     159 ..      40     129 ..      32     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.7e-09
                           UPRTase  71 lVpilRaGegmeealrellpearvghlglqreeetlepv.eyynkLPkki.aertvlllDpviaTGgsaaaaiqlLk 145
                                       ++ +lR+G   ++ l+++l   +v+ +g+     t +++  +y+ L  +  + r+vll+D v  TG+++ aa+++++
  gi|557693801|ref|YP_008796855.1|  40 IIGVLRGGMIVADFLSDILDVREVYVIGCRSYTGTVSTElKIYHDLALERlDGRNVLLVDDVADTGSTLDAAVEKIL 116
                                       7899*************************9999887766468888987666***********************998 PP

                           UPRTase 146 ergvgeekIlvlsv 159
                                       +   + ++++ +++
  gi|557693801|ref|YP_008796855.1| 117 KPR-NPNSVTTATL 129
                                       843.4455666655 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   2.4e-05      0.15     120     159 ..      91     130 ..      76     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklprkryvvvslv 159
                                       + ++++LvDD + tG+t+ + ++++ +  + +++++++l+
  gi|557693801|ref|YP_008796855.1|  91 DGRNVLLVDDVADTGSTLDAAVEKILKPRNPNSVTTATLL 130
                                       45789********************999999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); 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:                         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 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1479.71
//
Query:       gi|557693802|ref|YP_008796856.1|  [L=432]
Description: 2-methylthioadenine synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   82.4   0.0    1.3e-22   81.0   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
    5.5e-21   74.4   0.0    9.5e-21   73.7   0.0    1.3  1  UPF0004      Uncharacterized protein family UPF0004
    3.7e-08   33.2   0.1    8.4e-08   32.1   0.1    1.6  1  TRAM         TRAM 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 ?   -2.0   0.0      0.67     4e+03     114     144 ..      48      80 ..      36      94 .. 0.66
   2 !   81.0   0.0   2.1e-26   1.3e-22       1     167 []     143     317 ..     143     317 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.67
                                       HH..HHHHHHT.CTSHHHHHHHHHHHHHHTTSET CS
                                       xx..xxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 114 de..kvlklmn.rghtfeevlealeklreagikr 144
                                       +   +vl  +  +++t ++ +  ++k+ ++ ++r
  gi|557693802|ref|YP_008796856.1|  48 EAdyVVLVTCAvKKPTADRMIHRIKKFSSL-GPR 80 
                                       444455556666778888888888888887.454 PP

  == domain 2  score: 81.0 bits;  conditional E-value: 2.1e-26
                                       EEEESEESS-.-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.........TTHHHHH CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlr.CsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.........pdfvell 67 
                                       v+v++gC+   CsfC++p+   +++ ++s +v+ +++ev+++ ++ g++ev+l++++   y         p+++e +
  gi|557693802|ref|YP_008796856.1| 143 VPVSEGCRWSrCSFCIVPR---SRPGYESYPVRAVVDEVRKA-VNEGCREVWLTSQDMGSYglesgrnllPELIESV 215
                                       57899**9877*******8...7*******************.9**********99999999999998889999999 PP

                                       HHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT.....-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  68 erlaklavpgiritvetngtlpdeeklerllelg.....vdrvslgleaaddekvlklmnrghtfeevlealeklre 139
                                         l  +     ri +  n++ + + +l++l+++         +++++++++d+ vlk mnrgh+++ ++ ++e++r+
  gi|557693802|ref|YP_008796856.1| 216 NSLEGK--FYTRIGMM-NPIYL-KPILQKLVKAYsgekiYKFIHVPVQSGSDK-VLKDMNRGHSVQLFYHVVEAFRR 287
                                       999998..35555554.44444.788899998888999***************.*********************** PP

                                       TTSET...EEEEEEEBTTTSHHHHHHHHHHH CS
                                       xxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 140 agikr...vvdrivglpGendeeleellell 167
                                       + +++   ++d ivg p e+de++e++l+l+
  gi|557693802|ref|YP_008796856.1| 288 R-FPSitvSTDLIVGYPTETDEDFEQTLKLV 317
                                       *.**************************986 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   1.6e-24   9.5e-21       1      93 [.      13     102 ..      13     105 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.6e-24
                                       XEEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEH CS
                           UPF0004   1 kvaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGC 77 
                                       kv+ e +GC+ N++d e+ +++L+k+gy +ve+++eAd+v++ TCav++ + +++i++++++++l     +++v+GC
  gi|557693802|ref|YP_008796856.1|  13 KVYAEVYGCSANQADGEIALGILQKQGYIMVERPNEADYVVLVTCAVKKPTADRMIHRIKKFSSLG---PRLIVAGC 86 
                                       799*************************************************************99...79****** PP

                                       HHHS-HHHHHHH-TTS CS
                           UPF0004  78 maqrekeellkeepev 93 
                                       ma  e e++ + +pe+
  gi|557693802|ref|YP_008796856.1|  87 MATGEAERVRRVAPEA 102
                                       *******999988874 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.1   1.4e-11   8.4e-08       9      62 .]     377     429 ..     372     429 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.4e-11
                                       EEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   9 eVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                       eVl+++++ ++g ++Gr+ ++++++++ + +++G+fVe+++ +v+++yL G++l
  gi|557693802|ref|YP_008796856.1| 377 EVLINEVG-KKGKMMGRNFAYRPIVLDAPRESLGRFVEAEVVDVEKNYLLGRVL 429
                                       9*******.*******************9777*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3208.15
//
Query:       gi|557693803|ref|YP_008796857.1|  [L=207]
Description: hypothetical protein CSUB_C0366 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   27.4   0.2    3.8e-05   24.1   0.2    2.0  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
    0.00033   20.7   0.0    0.00049   20.2   0.0    1.3  1  Cupredoxin_1  Cupredoxin-like domain


Domain annotation for each model (and alignments):
>> 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 !   24.1   0.2   4.2e-09   3.8e-05      14      99 .]     124     198 ..     118     198 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.2e-09
                                       EESSEEEEETTEEEEEEEE....SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEEEETT CS
                       Copper-bind  14 Fetkeitvkkgekvtfvnl....avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkffCsP 86 
                                       +++++++v +g + t ++       +gH v  d++               +  l+g+ e+   tf  ag Y ++C+P
  gi|557693803|ref|YP_008796857.1| 124 YSPANVRVLAGYNSTVIWVngetVNVGHTVTSDQGL---------F----DSGLFGPNETWVFTFGRAGIYPYHCTP 187
                                       666666666665555555411222223333333222.........2....23488999******************* PP

                                       TTTTTSEEEEEEE CS
                       Copper-bind  87 HaaagMkgkvtve 99 
                                       H    M+g vtve
  gi|557693803|ref|YP_008796857.1| 188 HP--WMQGVVTVE 198
                                       **..69*****96 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   5.4e-08   0.00049      30     104 .]     122     197 ..     106     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.4e-08
                      Cupredoxin_1  30 ggfePskievkagekvklkiknkdktp..eefesed.lgeekvlapgktttitiaplkpGeYeftcdmhmdakGkli 103
                                       ++++P+++ v ag + ++ ++n  +    ++++s++ l  +    p++t ++t+    +G Y+++c  h+ ++G+++
  gi|557693803|ref|YP_008796857.1| 122 ETYSPANVRVLAGYNSTVIWVNGETVNvgHTVTSDQgLFDSGLFGPNETWVFTF--GRAGIYPYHCTPHPWMQGVVT 196
                                       68********************9998678*******544446668999999999..9*************99****9 PP

                      Cupredoxin_1 104 V 104
                                       V
  gi|557693803|ref|YP_008796857.1| 197 V 197
                                       8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1482.98
//
Query:       gi|557693804|ref|YP_008796858.1|  [L=218]
Description: NADPH-dependent F420 reductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-13   51.6   1.0    3.4e-13   50.0   0.5    1.9  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    5.5e-05   22.9   0.1    7.4e-05   22.4   0.1    1.2  1  ApbA            Ketopantoate reductase PanE/ApbA
    0.00026   21.0   0.4     0.0011   18.9   0.4    1.9  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
    0.00034   20.8   0.1    0.00057   20.1   0.1    1.4  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00046   19.7   2.9    0.00075   19.0   0.9    2.0  2  adh_short       short chain dehydrogenase
    0.00087   19.2   1.1     0.0012   18.7   0.4    1.6  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0014   18.3   0.1     0.0026   17.4   0.1    1.4  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
  ------ inclusion threshold ------
      0.013   14.5   0.3      0.023   13.7   0.2    1.4  1  PDH             Prephenate dehydrogenase
       0.04   14.4   1.0       0.12   12.8   0.2    2.0  2  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai
      0.043   13.7   1.2      0.052   13.5   0.3    1.5  2  KR              KR domain
       0.07   12.7   2.6      0.046   13.3   0.9    1.5  2  NmrA            NmrA-like family
       0.14   11.6   0.1       0.25   10.8   0.1    1.4  1  Epimerase       NAD dependent epimerase/dehydratase family
       0.17   11.7   1.7       0.26   11.1   1.4    1.5  1  Rossmann-like   Rossmann-like domain


Domain annotation for each model (and alignments):
>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.5   2.4e-16   3.4e-13       3      94 ..       4      97 ..       3     100 .. 0.89
   2 ?   -0.3   0.0       1.2   1.7e+03      69      95 ..      97     125 ..      91     127 .. 0.71

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 2.4e-16
                                      EEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.....-EEECECHHHHHHH-SEEEE-S-HHHHH CS
                     F420_oxidored  3 gii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.....vkvtavdneeaaeeadvvvlavkpedve 75
                                      +++ G+G++g++la +l++ag    ++v++ sr  e+a e+ae++       +v +  n +a++ a+vv+++v++e + 
  gi|557693804|ref|YP_008796858.1|  4 AVLgGTGDLGFGLAARLAKAG---VDVVIG-SRRLERAVEAAEKIRalvgrENVNGAVNRDAVKAAEVVFFSVPYEGLV 78
                                      6888*****************...****88.***************999998899999********************* PP

                                      HHHHHCGHHHHTTSEEEEE CS
                     F420_oxidored 76 evlselakdalkgklvisv 94
                                      e+++++a+ ++  ++ +s+
  gi|557693804|ref|YP_008796858.1| 79 EIARDVAPFLQPFTVSVSC 97
                                      ***9996666665555665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                                       S-HHHHHHHHHHC..GHHHHTTSEEEEES CS
                     F420_oxidored  69 vkpedveevlsel..akdalkgklvisvl 95 
                                       +  + +e+v+++   a+++++g  v+s+l
  gi|557693804|ref|YP_008796858.1|  97 CVVSFAEDVCAAEmlAENLQQGAKVVSAL 125
                                       55566777776655588889999999875 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   5.3e-08   7.4e-05       5     133 ..       8     134 ..       4     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 5.3e-08
                                       S-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSGGGH CS
                              ApbA   5 GaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppealsaeekselepidlvivtvKayqt 81 
                                       G+G +G  laa+Lakag dv++  r  rle+ +++  +++   g e++   ++ +a+     + +++v+++v+   +
  gi|557693804|ref|YP_008796858.1|   8 GTGDLGFGLAARLAKAGVDVVIGSR--RLERAVEAAEKIRALVGRENVNGAVNRDAV-----KAAEVVFFSVPYEGL 77 
                                       89***************99986666..479988888889999988888888888888.....89************* PP

                                       HHHHHHHGGGECTCE....EEEEESSSSCHHHHHTTTSTTS.EEEEEEEE-EEEEEE CS
                              ApbA  82 eealeeikplldpnt....vvlllqNGlgheeelrealpkp.rvlggvtthgatreg 133
                                       +e +++++p+l+p t     v+++ + + ++e l+e l++  +v++++ t++a  ++
  gi|557693804|ref|YP_008796858.1|  78 VEIARDVAPFLQPFTvsvsCVVSFAEDVCAAEMLAENLQQGaKVVSALHTVSASLLS 134
                                       *************987777999****************8855999999999988776 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 !   18.9   0.4   8.3e-07    0.0011       3     126 ..       4     119 ..       2     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 8.3e-07
                                       EEE.--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE--- CS
                    NAD_Gly3P_dh_N   3 avl.GaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvP 78 
                                       avl G+G  G  lA+ la++g +v++ +r+ e +    e+ e  + L g    en+    + ++a+k a+++++ vP
  gi|557693804|ref|YP_008796858.1|   4 AVLgGTGDLGFGLAARLAKAGVDVVIGSRRLERA---VEAAEKIRALVG---RENVNGAVN-RDAVKAAEVVFFSVP 73 
                                       5662579**************9999987765433...344455555555...778877766.689999********* PP

                                       HHHHHHHHHHHCCC--TT-EEEE---SEET.TTEEHHHHHHHHH-S-- CS
                    NAD_Gly3P_dh_N  79 sqalrevlkklkgllkkkailvsliKGieegtlkllsevieeelkeek 126
                                        + l e++++++++l++ ++ vs++  + e       e+++e+l++ +
  gi|557693804|ref|YP_008796858.1|  74 YEGLVEIARDVAPFLQPFTVSVSCVVSFAE--DVCAAEMLAENLQQGA 119
                                       ************************988866..3556677777776664 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 !   20.1   0.1   4.1e-07   0.00057       6      96 ..       8     104 ..       4     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.1e-07
                                       --SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.......EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS CS
                     NAD_binding_2   6 GlGvMGsnmalnllkagykvavynrtkekveelvaeg.......akaaesieelvasldvvitmvkagkavdevieg 75 
                                       G+G +G  +a +l+kag +v++  r+ e++ e++++         +  +  +++v++++vv++ v+ +  v e+ ++
  gi|557693804|ref|YP_008796858.1|   8 GTGDLGFGLAARLAKAGVDVVIGSRRLERAVEAAEKIralvgreNVNGAVNRDAVKAAEVVFFSVPYEGLV-EIARD 83 
                                       99*********************99987777777764566666555556668999999********97766.57788 PP

                                       HCCC--TT-EEEE-S---HHH CS
                     NAD_binding_2  76 llealkkgdilidgstssped 96 
                                       +++ l++ ++ + +  s +ed
  gi|557693804|ref|YP_008796858.1|  84 VAPFLQPFTVSVSCVVSFAED 104
                                       899888888888776665555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.9   5.4e-07   0.00075       3      49 ..       3      50 ..       1      69 [. 0.88
   2 ?    0.3   0.0      0.29   4.1e+02      17      79 ..     111     171 ..     104     172 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.4e-07
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TS CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.ga 49
                                      + v G+++ +G  +a +lak+G++vv+ +r+ e++ e+a++++++ g+
  gi|557693804|ref|YP_008796858.1|  3 AAVLGGTGDLGFGLAARLAKAGVDVVIGSRRLERAVEAAEKIRALvGR 50
                                      789***************************************998644 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.29
                                       HHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                         adh_short  17 akelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkld 79 
                                         e +++Gakvv +  + +  + +++ + ++ ++ ++i +D +d+++  a + k v+ l ++d
  gi|557693804|ref|YP_008796858.1| 111 LAENLQQGAKVVSALHTVS--ASLLSDISRAVNSDTFIFGDDRDAKKKVANLLKLVEGLRPVD 171
                                       4556789999998666655..347888888855556666666655555554445556666666 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 !   18.7   0.4   8.8e-07    0.0012       3      63 ..       4      64 ..       2      84 .. 0.84
   2 ?   -2.8   0.0       3.5   4.8e+03      85     101 ..     110     126 ..      96     145 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.8e-07
                                      EEE--.SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCC CS
                           3HCDH_N  3 aviGa.GtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaa 63
                                      av+G  G +G g+aa +a+ag++Vv+  ++ e++ +a+eki++ + +   +g+++++ v+ a
  gi|557693804|ref|YP_008796858.1|  4 AVLGGtGDLGFGLAARLAKAGVDVVIGSRRLERAVEAAEKIRALVGRENVNGAVNRDAVK-A 64
                                      777655*************************************99999989998866554.3 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.5
                                       -S-SSHHHHHHHHHHHH CS
                           3HCDH_N  85 avvEnlelKrkvfaele 101
                                         +Enl+  +kv  +l+
  gi|557693804|ref|YP_008796858.1| 110 MLAENLQQGAKVVSALH 126
                                       33344433333333333 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 !   17.4   0.1   1.9e-06    0.0026      11      86 ..       8      89 ..       2     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.9e-06
                                      S-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHH.......TT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHHHHTG CS
                              IlvN 11 GyGsqGhaqalnlrdsgldvvvglregsksvkkAke.......egfevltvaeavkkadvvmiliPDelqkevyeeeie 82
                                      G G  G   a  l  +g+dvv+g r+ ++ v+ A++       e+++ +  ++avk+a+vv++ +P e   e+  ++++
  gi|557693804|ref|YP_008796858.1|  8 GTGDLGFGLAARLAKAGVDVVIGSRRLERAVEAAEKiralvgrENVNGAVNRDAVKAAEVVFFSVPYEGLVEIA-RDVA 85
                                      689999999*******************9999999733332224455566789*************99988887.6777 PP

                                      GG-- CS
                              IlvN 83 pnlk 86
                                      p l+
  gi|557693804|ref|YP_008796858.1| 86 PFLQ 89
                                      7775 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   1.6e-05     0.023      22      71 ..      36      90 ..      16     128 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHTTS..SSEEES-...GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-T CS
                               PDH 22 ekaeaalelgl..vdeatdd...ieavkeadivvlavPvevilevlkelaphlke 71
                                       + eaa+++ +  + e+ +     +avk a++v+ +vP e + e+++++ap l++
  gi|557693804|ref|YP_008796858.1| 36 RAVEAAEKIRAlvGRENVNGavnRDAVKAAEVVFFSVPYEGLVEIARDVAPFLQP 90
                                      44444444433112333222222479*************************9886 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 ?   12.8   0.2   8.6e-05      0.12       2      86 ..       3      84 ..       2      90 .. 0.72
   2 ?   -0.7   0.0       1.3   1.9e+03      67      95 ..      95     123 ..      83     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.6e-05
                                      EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEE.GGGGGCTT-SEEEE-SCHHHH CS
                    Semialdhyde_dh  2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkved.vdeeelkevdivflalpagvs 79
                                      +a++G+tG  G  l+ +L++   + + v+++s+r   +++++a k+ + +   +v+  v+ +++k++++vf+++p +  
  gi|557693804|ref|YP_008796858.1|  3 AAVLGGTGDLGFGLAARLAK---AGVDVVIGSRR-LERAVEAAEKIRALVGRENVNGaVNRDAVKAAEVVFFSVPYEGL 77
                                      59****************98...44555556666.455555555533333333444446889*************9877 PP

                                      HHHHHHH CS
                    Semialdhyde_dh 80 kelapkl 86
                                       e+a+++
  gi|557693804|ref|YP_008796858.1| 78 VEIARDV 84
                                      7777665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                                       -SEEEE-SCHHHHHHHHHHHHHTTSEEEE CS
                    Semialdhyde_dh  67 vdivflalpagvskelapklaeagvkviD 95 
                                       v +v++ ++   ++e+ ++ +++g+kv++
  gi|557693804|ref|YP_008796858.1|  95 VSCVVSFAEDVCAAEMLAENLQQGAKVVS 123
                                       55566666666677777777899999987 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   3.7e-05     0.052       5      65 ..       5      64 ..       2      70 .. 0.80
   2 ?   -2.8   0.0       3.7   5.1e+03      54      55 ..     120     121 ..      94     147 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                                      EETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-H CS
                                KR  5 itGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdk 65
                                      + GG+G LG  la  la+ g   +v+ sR+ +   +++++i++l  ++    +v+ D  ++
  gi|557693804|ref|YP_008796858.1|  5 VLGGTGDLGFGLAARLAKAGV-DVVIGSRRLERAVEAAEKIRALVGRENVNGAVNRDAVKA 64
                                      89****************997.578899998888888899999988876555666665555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.7
                                       EE CS
                                KR  54 ev 55 
                                       +v
  gi|557693804|ref|YP_008796858.1| 120 KV 121
                                       22 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.9   3.4e-05     0.046       2      78 ..       4      79 ..       3      85 .. 0.78
   2 ?   -3.1   0.0       3.3   4.6e+03      80      88 ..     116     124 ..     102     140 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---GG.S-H CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgfy.ske 78
                                      +v+G+TG +G  +++ l+kag +v +  R +++  a + +e+   lv  +  + ++ + a+k ++vvf+++++    e
  gi|557693804|ref|YP_008796858.1|  4 AVLGGTGDLGFGLAARLAKAGVDVVIGSRRLER--AVEAAEKIRALVGRENVNGAVNRDAVKAAEVVFFSVPYEgLVE 79
                                      79**********************999998854..334445555677777777788899***********99654334 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.3
                                       HHHHHHHHH CS
                              NmrA  80 edgkklvdA 88 
                                       ++g k+v+A
  gi|557693804|ref|YP_008796858.1| 116 QQGAKVVSA 124
                                       333333333 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00018      0.25       2      39 ..       4      42 ..       3      74 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                                      EEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHH CS
                         Epimerase  2 lVtGatGfiGsalvkallekgye.vigldrlssasntar 39
                                       V+G+tG +G  l+ +l+++g++ vig  rl++a + a+
  gi|557693804|ref|YP_008796858.1|  4 AVLGGTGDLGFGLAARLAKAGVDvVIGSRRLERAVEAAE 42
                                      59*********************7777777766555443 PP

>> Rossmann-like  Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.4   0.00019      0.26      18      95 ..       9      89 ..       3     127 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                     Rossmann-like 18 aGrvGtalgaaleraghvvv.gis....aisaasreraerrlPdvpvlevedvaaraellllavPdaelpglvkglaat 91
                                      +G +G  l+a l++ag  vv g      a+ aa + ra     +v+ +  +d ++ ae++ ++vP   l ++ +++a  
  gi|557693804|ref|YP_008796858.1|  9 TGDLGFGLAARLAKAGVDVViGSRrlerAVEAAEKIRALVGRENVNGAVNRDAVKAAEVVFFSVPYEGLVEIARDVAPF 87
                                      689999999999999975541543233377888888888888888888889************************9965 PP

                     Rossmann-like 92 gavr 95
                                        ++
  gi|557693804|ref|YP_008796858.1| 88 --LQ 89
                                      ..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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):              13  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1606.10
//
Query:       gi|557693805|ref|YP_008796859.1|  [L=449]
Description: phosphomannomutase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-33  115.2   0.0    3.9e-33  114.1   0.0    1.6  1  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.8e-22   79.1   0.1    5.2e-22   78.2   0.1    1.5  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.9e-21   76.6   0.0    6.7e-21   74.9   0.0    1.9  2  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.7e-07   30.7   0.0    1.1e-06   28.7   0.0    2.0  2  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 !  114.1   0.0   8.7e-37   3.9e-33       3     131 ..       7     130 ..       5     136 .. 0.95

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 8.7e-37
                                       GBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-H CS
                         PGM_PMM_I   3 kfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllpt 79 
                                       +f+++++Rg++ ++ l+++l++++g+a++++++      kvvvGrD R s++ l +al+ gl+ +G +v++lg+++t
  gi|557693805|ref|YP_008796859.1|   7 IFRAYDIRGVYRVD-LDESLAYSVGRAFGKIVTG-----KVVVGRDVRRSGESLVKALCDGLTDAGHDVLNLGVCTT 77 
                                       79**********77.9****************96.....8************************************* PP

                                       HHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHH.HHHHHHHH CS
                         PGM_PMM_I  80 PavsfairklkadagimitaSHnppeyngiKvylsnGgpispev.eekIeaii 131
                                       Pa++f  r ++a +g+m+taSHnpp+ ng+K++l +G  +s+ + +ekI++ i
  gi|557693805|ref|YP_008796859.1|  78 PACYFGGRFYRAGGGVMVTASHNPPDWNGFKMFLGDGETVSQGAgMEKIRDMI 130
                                       ***************************************99988788888776 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 !   78.2   0.1   1.2e-25   5.2e-22       2     113 ..     254     359 ..     253     360 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 1.2e-25
                                       HHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETT CS
                       PGM_PMM_III   2 gdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifld 78 
                                       gd  +a+l k l +    +g  +v +v +s+al+++a+klg + +e+kvG  ++ ++++e gav+GgE+S h++f++
  gi|557693805|ref|YP_008796859.1| 254 GDIAMAVLLKTLDK----KGI-IVYDVNSSTALKEMAEKLGFTPMEWKVGRAFLHRKVRELGAVMGGEKSNHLYFGE 325
                                       88899999998855....476.******************************************************* PP

                                       TBSS--HHHHHHHHHHHHHHHTS-HHHHHHHHHHH CS
                       PGM_PMM_III  79 eattkDGilaallvleilaetgkslselleellkk 113
                                          ++D+i+aal+++ +l +t++sls+ ++e++ k
  gi|557693805|ref|YP_008796859.1| 326 LEGDDDAIYAALKMATLLHRTKTSLSKHVDEIP-K 359
                                       *9***************************6654.4 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 !   74.9   0.0   1.5e-24   6.7e-21       3     103 .]     154     249 ..     152     249 .. 0.96
   2 ?   -2.0   0.0       1.3   5.7e+03      13      29 ..     278     294 ..     264     318 .. 0.62

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1.5e-24
                                       HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGG CS
                        PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvk 79 
                                       Yi++++++++       gl++++d   G+++ ++++++++lg+ + +ln +pd+ f +++p+p+e e++++l ++v 
  gi|557693805|ref|YP_008796859.1| 154 YIQHIVSRFS----PMYGLRMAADFSDGSASLCFPQICEKLGITLRQLNNNPDGYFRGHMPEPTE-ENISELKQVVI 225
                                       9999999998....67899**********************************************.*********** PP

                                       GGG-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  80 kegadlglafDgDaDRlgvvderG 103
                                       +e+ d+g+afDgDaDR ++vd+ G
  gi|557693805|ref|YP_008796859.1| 226 AEKLDFGVAFDGDADRAVFVDDMG 249
                                       ********************9765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                                       HHHHHHHT-EEEEE-TT CS
                        PGM_PMM_II  13 seaikksglkvvidplh 29 
                                       s+a+k+   k+ ++p++
  gi|557693805|ref|YP_008796859.1| 278 STALKEMAEKLGFTPME 294
                                       34444444444444443 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 ?   -3.9   0.0       3.6   1.6e+04      37      45 ..      40      51 ..      36      63 .. 0.67
   2 !   28.7   0.0   2.4e-10   1.1e-06      23      66 ..     389     435 ..     368     442 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 3.6
                                      EEE....EEEET CS
                        PGM_PMM_IV 37 rrla...vRpSG 45
                                       +++   vR SG
  gi|557693805|ref|YP_008796859.1| 40 KVVVgrdVRRSG 51
                                      455556688887 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 2.4e-10
                                       H....HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHH CS
                        PGM_PMM_IV  23 a....sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarla 66 
                                            ++ +g+k  +e+G++l +R+S+T p ++  +Eak+ e l+ l+
  gi|557693805|ref|YP_008796859.1| 389 MgfktNNLDGVKAYGEEGWIL-IRASNTMPQIKMSIEAKKAESLNMLR 435
                                       25666799*************.*****************999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); 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:                         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: 00:00:00.43
# Mc/sec: 3166.19
//
Query:       gi|557693806|ref|YP_008796860.1|  [L=209]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-15   58.0   1.3    1.2e-15   58.0   1.3    2.7  3  SNARE_assoc  SNARE associated Golgi protein
  ------ inclusion threshold ------
       0.19   10.9   2.7        6.4    5.9   0.2    2.1  2  ArsP_2       Putative, 10TM heavy-metal exporter
          2    8.8   6.5       0.62   10.4   1.2    2.8  3  DUF1056      Protein of unknown function (DUF1056)


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 ?    1.2   0.4     0.085   5.1e+02      10      29 ..       8      27 ..       4      29 .. 0.87
   2 !   58.0   1.3   2.1e-19   1.2e-15       1     117 [.      32     144 ..      32     147 .. 0.90
   3 ?   -0.0   0.0       0.2   1.2e+03      23      63 ..     163     203 ..     154     207 .. 0.54

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.085
                       SNARE_assoc 10 aGvlfglllgtlvtslgall 29
                                       +v++g+l ++ v++lg++l
  gi|557693806|ref|YP_008796860.1|  8 IAVTYGPLGVFAVSLLGSIL 27
                                      568999**********9976 PP

  == domain 2  score: 58.0 bits;  conditional E-value: 2.1e-19
                       SNARE_assoc   1 lPsevllvaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrll 77 
                                       +P+ +++v+++ ++++l+  l++ +g ++G++++y++gr    + l     ++k ++ l +++ +yg + ++++ l+
  gi|557693806|ref|YP_008796860.1|  32 VPYLIVVVLLSDTVNPLILGLAAGIGGSIGKITSYIIGRLGY-RLLSD--EKKKSMDTLREFIGKYGDIGVFIFALT 105
                                       699999********************************8554.33333..46677777******************* PP

                       SNARE_assoc  78 pivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyayl 117
                                       p +P+d+  ++aG+ ++sf+rF+la+ +G+i+ a+++a+l
  gi|557693806|ref|YP_008796860.1| 106 P-LPDDVYIIPAGMVKLSFWRFLLANTAGKILLAIIVALL 144
                                       *.79********************************9987 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.2
                       SNARE_assoc  23 tslgallGaslayllgrylgrkalrrkllsekrvkalerlv 63 
                                       + +ga++++++  ++  +   ++l + + ++ + + l ++v
  gi|557693806|ref|YP_008796860.1| 163 STAGAVVAMVVLTIILLRTDWEKLLKTWEERGWRGVLREWV 203
                                       44444444444444433333366666666666666666665 PP

>> ArsP_2  Putative, 10TM heavy-metal exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0011       6.4      56      80 ..      49      73 ..      41      77 .. 0.90
   2 ?    5.4   0.2    0.0015         9     173     222 ..     135     184 ..     115     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0011
                            ArsP_2 56 llGllPGCGGAivvitlyvrgkvsF 80
                                      +lGl  G GG i  it y+ g++++
  gi|557693806|ref|YP_008796860.1| 49 ILGLAAGIGGSIGKITSYIIGRLGY 73
                                      79********************997 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0015
                            ArsP_2 173 lvpalivalllafqvdveallsleeksiellgavlavlslllwaltrele 222
                                       ++ a+ivall ++ ++ ++l+  e++ ++++gav+a+++l++ +l ++ e
  gi|557693806|ref|YP_008796860.1| 135 ILLAIIVALLSKTYFEYSKLFLGETSWLSTAGAVVAMVVLTIILLRTDWE 184
                                       567899***************88889999*******99999887766655 PP

>> DUF1056  Protein of unknown function (DUF1056)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.69   4.1e+03      10      22 ..      91     103 ..      87     116 .. 0.78
   2 ?   10.4   1.2    0.0001      0.62      15      49 ..     110     144 ..     100     147 .. 0.89
   3 ?   -1.2   0.3      0.43   2.6e+03      35      48 ..     163     176 ..     159     181 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.69
                           DUF1056  10 iWklfDVLlFiaa 22 
                                       i k+ D+ +Fi a
  gi|557693806|ref|YP_008796860.1|  91 IGKYGDIGVFIFA 103
                                       5678888888866 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0001
                           DUF1056  15 DVLlFiaamivltytaFlfnataGvlvisvvlflv 49 
                                       DV +  a+m+ l +  Fl+  taG + +++++ l+
  gi|557693806|ref|YP_008796860.1| 110 DVYIIPAGMVKLSFWRFLLANTAGKILLAIIVALL 144
                                       8888889**********************998775 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.43
                           DUF1056  35 ataGvlvisvvlfl 48 
                                        taG +v  vvl +
  gi|557693806|ref|YP_008796860.1| 163 STAGAVVAMVVLTI 176
                                       67777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1532.44
//
Query:       gi|557693807|ref|YP_008796861.1|  [L=106]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.3   0.0      0.069   13.1   0.0    1.1  1  Pesticin  Bacterial toxin homologue of phage lysozyme, C-term


Domain annotation for each model (and alignments):
>> Pesticin  Bacterial toxin homologue of phage lysozyme, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.8e-06     0.069      60     107 ..      20      68 ..       9      83 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-06
                                       TTTTT-BCHH.HHHHHHHS--B--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Pesticin  60 epYlglkkqe.AkdflaknPLslseeeaklldkavkdkaldklakeynk 107
                                       + Y gl+ +   + ++a+ PL+++++ ++ ++ +vk k+l +++key +
  gi|557693807|ref|YP_008796861.1|  20 KLYHGLEPKYyVEVKVADRPLKVNKDALEVVKGVVKGKMLTRMKKEYVD 68 
                                       55666664431456799******************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 821.86
//
Query:       gi|557693808|ref|YP_008796862.1|  [L=81]
Description: hypothetical protein CSUB_C0371 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   24.5   0.4    2.8e-05   24.5   0.4    1.0  1  zf-C4H2          Zinc finger-containing protein
    0.00029   20.9   2.4    0.00048   20.1   2.4    1.3  1  UPF0547          Uncharacterised protein family UPF0547
    0.00091   18.6   2.9     0.0013   18.1   2.9    1.3  1  zf-ribbon_3      zinc-ribbon domain
     0.0019   18.2   0.5     0.0024   17.9   0.5    1.1  1  DZR              Double zinc ribbon
     0.0026   17.5   3.4     0.0036   17.1   3.4    1.1  1  zf-RING_4        RING/Ubox like zinc-binding domain
     0.0026   17.4   1.8     0.0036   17.0   1.8    1.2  1  zinc_ribbon_2    zinc-ribbon domain
  ------ inclusion threshold ------
      0.032   15.0   0.1      0.038   14.8   0.1    1.1  1  zinc_ribbon_15   zinc-ribbon family
      0.066   12.7   0.6        1.7    8.2   0.1    2.1  2  DUF4044          Protein of unknown function (DUF4044)
       0.15   12.1   0.0       0.19   11.7   0.0    1.2  1  DUF952           Protein of unknown function (DUF952)
       0.16   12.0   0.0       0.16   12.0   0.0    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
        9.3    5.1   6.0         11    4.9   6.0    1.0  1  Pex24p           Integral peroxisomal membrane peroxin
        9.7    6.2   8.0        3.2    7.8   0.2    2.1  2  Gram_pos_anchor  LPXTG cell wall anchor motif


Domain annotation for each model (and alignments):
>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.4   1.9e-08   2.8e-05     176     201 ..      55      80 ..      26      81 .] 0.84

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.9e-08
                           zf-C4H2 176 PPMKsClsChqqIHRNAPiCPlCKaK 201
                                       P  K C  C qqI   A iCP CK K
  gi|557693808|ref|YP_008796862.1|  55 PGKKFCWHCYQQIPADAGICPHCKLK 80 
                                       55799*******************98 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   2.4   3.2e-07   0.00048       3      20 ..      60      77 ..      58      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.2e-07
                           UPF0547  3 CPeCeakvPvaaqfCphC 20
                                      C  C +++P++a +CphC
  gi|557693808|ref|YP_008796862.1| 60 CWHCYQQIPADAGICPHC 77
                                      778*************** PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.9   8.5e-07    0.0013       2      25 ..      57      80 ..      56      81 .] 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.5e-07
                       zf-ribbon_3  2 tvrCPnCGaplssddnvCpyCGtk 25
                                      +++C++C +++ +d+ +Cp+C  k
  gi|557693808|ref|YP_008796862.1| 57 KKFCWHCYQQIPADAGICPHCKLK 80
                                      689******99**********986 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.5   1.6e-06    0.0024      28      48 ..      57      77 ..      42      80 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.6e-06
                               DZR 28 edrCpsCgekvdpearfCpeC 48
                                      +++C++C ++++++a +Cp+C
  gi|557693808|ref|YP_008796862.1| 57 KKFCWHCYQQIPADAGICPHC 77
                                      566666666666666666666 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 !   17.1   3.4   2.4e-06    0.0036      23      44 ..      58      78 ..      56      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.4e-06
                         zf-RING_4 23 qiClfCyhrileeeegrCPaCr 44
                                      ++C+ Cy++i ++ +g+CP C+
  gi|557693808|ref|YP_008796862.1| 58 KFCWHCYQQIPAD-AGICPHCK 78
                                      79*********76.9******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 !   17.0   1.8   2.4e-06    0.0036       1      19 [.      59      77 ..      59      78 .. 0.99

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.4e-06
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyC 19
                                      fC++C  +++ +a  Cp+C
  gi|557693808|ref|YP_008796862.1| 59 FCWHCYQQIPADAGICPHC 77
                                      9****************** PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   2.5e-05     0.038      64      85 ..      56      77 ..      36      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                    zinc_ribbon_15 64 ekkeCknCgkeveeefkyCpkC 85
                                       kk C++C +++ ++   Cp+C
  gi|557693808|ref|YP_008796862.1| 56 GKKFCWHCYQQIPADAGICPHC 77
                                      3899****************** PP

>> DUF4044  Protein of unknown function (DUF4044)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1    0.0012       1.7      11      22 ..      12      23 ..      12      24 .. 0.94
   2 ?    2.9   0.0     0.053        79       8      21 ..      27      40 ..      26      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                           DUF4044 11 iTkvvvwlMlia 22
                                      iT++++++M++a
  gi|557693808|ref|YP_008796862.1| 12 ITLIFGVFMAFA 23
                                      9********987 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.053
                           DUF4044  8 FqKiTkvvvwlMli 21
                                      F++i ++ +++M +
  gi|557693808|ref|YP_008796862.1| 27 FSYIFLFSGIIMTV 40
                                      99999999999965 PP

>> DUF952  Protein of unknown function (DUF952)
   #    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      52      86 ..      37      71 ..      29      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                      EEEEESGGGTTTEEEEEGGGGSEEEEESS-EEGGG CS
                            DUF952 52 llkidasklaaavkweaseggelfPHlYgplplka 86
                                      ++++  + l+++v +e+ +g++ + H Y+++p++a
  gi|557693808|ref|YP_008796862.1| 37 IMTVLGAFLKPPVSVEPDPGKKFCWHCYQQIPADA 71
                                      566666779999********************986 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 ?   12.0   0.0   0.00011      0.16      63      94 ..      50      79 ..      27      81 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      EEEEE--EEEETTTS-EEECHHHHHS-TTTSS CS
                              HypA 63 eieevpvkvrCreCgkefeleekalrCpkCgs 94
                                      ++e  p k  C +C +++  ++    Cp+C+ 
  gi|557693808|ref|YP_008796862.1| 50 SVEPDPGKKFCWHCYQQIPADA--GICPHCKL 79
                                      5899999***********9884..58****85 PP

>> Pex24p  Integral peroxisomal membrane peroxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   6.0    0.0075        11     152     186 ..       5      39 ..       2      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0075
                            Pex24p 152 tllfltllltpililllsrlipwrlillvlgaill 186
                                       +l+f +l+ +++ +++ +  +p ++i+l++g+i++
  gi|557693808|ref|YP_008796862.1|   5 SLFFSGLITLIFGVFMAFAGLPFSYIFLFSGIIMT 39 
                                       689999*************************7665 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   2.9      0.21   3.2e+02      19      32 ..      12      25 ..       9      25 .. 0.83
   2 ?    7.8   0.2    0.0021       3.2      17      34 ..      28      45 ..      27      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.21
                                      XXXXXXXXXXXXXX CS
                   Gram_pos_anchor 19 fltaaGllallggl 32
                                      +++++G++++ +gl
  gi|557693808|ref|YP_008796862.1| 12 ITLIFGVFMAFAGL 25
                                      79999*99998886 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0021
                                      XXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor 17 nifltaaGllallggllL 34
                                      ++++++ G++++++g++L
  gi|557693808|ref|YP_008796862.1| 28 SYIFLFSGIIMTVLGAFL 45
                                      689************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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):              12  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 631.97
//
Query:       gi|557693809|ref|YP_008796863.1|  [L=812]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-31  109.0   1.6    2.8e-31  109.0   0.2    1.8  1  HAD_2            Haloacid dehalogenase-like hydrolase
      2e-22   80.5   1.0    2.5e-21   77.0   0.4    2.9  1  Hydrolase        haloacid dehalogenase-like hydrolase
      4e-11   43.7   0.0    9.7e-11   42.4   0.0    1.7  1  HAD              haloacid dehalogenase-like hydrolase
    6.6e-11   42.1   0.0    4.6e-10   39.4   0.0    2.4  2  Hydrolase_like   HAD-hyrolase-like
    8.5e-11   41.4   0.0    2.2e-10   40.0   0.0    1.7  1  T2SSE            Type II/IV secretion system protein
    5.5e-05   22.9   0.9    0.00013   21.7   0.1    2.1  1  KH_1             KH domain
    7.3e-05   23.0   0.0      0.046   13.9   0.0    3.2  3  AAA_33           AAA domain
    8.7e-05   22.3   0.2     0.0013   18.5   0.2    2.3  1  NIF              NLI interacting factor-like phosphatase
     0.0003   20.3   0.0      0.018   14.4   0.1    2.4  2  Put_Phosphatase  Putative Phosphatase
    0.00033   20.5   0.1        4.7    6.9   0.0    3.5  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
    0.00067   20.2   0.0     0.0038   17.8   0.0    2.4  1  AAA_18           AAA domain
    0.00086   19.2   2.2      0.028   14.2   0.0    2.7  2  ATP_bind_1       Conserved hypothetical ATP binding protein
    0.00093   19.0   0.3     0.0047   16.8   0.3    2.2  1  KH_4             KH domain
    0.00095   19.4   0.3      0.086   13.1   0.0    2.9  2  AAA_22           AAA domain
     0.0011   19.2   1.0       0.11   12.8   0.0    3.0  2  PIN_4            PIN domain
     0.0012   19.2   0.2     0.0069   16.8   0.0    2.4  1  AAA_16           AAA ATPase domain
     0.0017   18.8   0.6       0.24   11.8   0.0    3.3  3  AAA              ATPase family associated with various cellul
     0.0019   17.8   0.0      0.012   15.2   0.0    2.4  2  AAA_25           AAA domain
     0.0022   17.6   0.0     0.0046   16.6   0.0    1.4  1  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph
     0.0037   17.1   1.5      0.016   15.1   1.5    2.1  1  KH_2             KH domain
     0.0044   17.1   0.0      0.047   13.8   0.0    2.8  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase
     0.0052   17.3   0.1      0.034   14.6   0.0    2.3  2  ABC_tran         ABC transporter
  ------ inclusion threshold ------
      0.011   15.3   0.0       0.31   10.6   0.0    2.6  2  SRP54            SRP54-type protein, GTPase domain
      0.013   15.2   0.0      0.031   14.0   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
      0.015   15.0   0.3      0.089   12.5   0.0    2.4  2  Thymidylate_kin  Thymidylate kinase
      0.017   15.1   0.2        2.8    7.9   0.1    2.5  2  ADH_zinc_N       Zinc-binding dehydrogenase
      0.018   14.8   0.2       0.23   11.2   0.0    2.7  2  AAA_30           AAA domain
      0.019   15.0   0.0      0.061   13.3   0.0    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
      0.021   13.7   0.0      0.034   13.0   0.0    1.2  1  PPV_E1_C         Papillomavirus helicase
      0.022   14.5   0.0      0.056   13.2   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
      0.027   14.2   0.1      0.091   12.5   0.1    1.9  1  AAA_24           AAA domain
      0.034   14.3   0.0       0.13   12.3   0.0    2.0  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.06   12.6   0.1       0.39   10.0   0.0    2.3  2  Zeta_toxin       Zeta toxin
      0.066   13.7   1.0       0.12   12.8   0.1    1.9  1  Peptidase_S8_N   N-terminal of Subtilase family
      0.072   13.5   0.4       0.47   10.9   0.0    2.7  1  AAA_17           AAA domain
      0.082   13.1   1.0        1.1    9.5   0.0    2.9  2  AAA_28           AAA domain
      0.086   12.7   0.5       0.32   10.9   0.0    2.3  1  NACHT            NACHT domain
      0.093   13.1   0.2       0.58   10.5   0.1    2.2  2  PG_binding_2     Putative peptidoglycan binding domain
      0.096   12.9   1.5        1.2    9.4   0.0    2.6  2  DUF1827          Domain of unknown function (DUF1827)
       0.11   13.1   0.8       0.28   11.7   0.1    2.2  1  PIN              PIN domain
       0.11   11.9   0.0       0.56    9.6   0.0    1.9  2  DUF705           Protein of unknown function (DUF705)
       0.15   12.4   0.0       0.43   11.0   0.0    1.8  1  RNA_helicase     RNA helicase
       0.16   12.1   0.0        2.3    8.3   0.0    2.5  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.22   11.6   0.7         27    4.9   0.1    2.9  2  LAGLIDADG_WhiA   WhiA LAGLIDADG-like domain
       0.22   10.8   1.4       0.47    9.8   0.0    2.0  2  Mg_chelatase     Magnesium chelatase, subunit ChlI


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 !  109.0   0.2   7.1e-34   2.8e-31       2     178 .]       2     178 ..       1     178 [. 0.86

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 7.1e-34
                             HAD_2   2 iFDlDgTlldteeliiqafn...elleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkk 75 
                                       ++DlDgTl+  +  i+q+ +   e+++++g++  ++e ++ ++   +     +l +  e  +++ee+ ++ ++e  k
  gi|557693809|ref|YP_008796863.1|   2 VMDLDGTLIKMKFDIFQVKKrvsEVAKQHGFELRENESIQDFLDRAS-----HLLPPHEFAKLREEIQNILRNEDRK 73 
                                       78***********9999876111566778898888899999998888.....4445445555555555555555555 PP

                             HAD_2  76 ..kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklkl 150
                                         ++ +  +g+ ++Le+Lk  g+kl ++T+++reavee l+++g+++yF++++t +dvek KP p++++k+ e + +
  gi|557693809|ref|YP_008796863.1|  74 saEQAEATPGIADVLEKLKTLGFKLVVATNSHREAVEEALKKTGLDKYFEHVYTRDDVEKMKPRPDILLKIAEDMRI 150
                                       5569************************************************************************* PP

                             HAD_2 151 kkeeviyvGDsptDieaakkagikviav 178
                                         ++++yvGDs +D+ aa++ag ++iav
  gi|557693809|ref|YP_008796863.1| 151 PISSIVYVGDSVNDLRAAREAGARFIAV 178
                                       **************************97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.4   6.2e-24   2.5e-21       5     210 .]       2     172 ..       1     172 [. 0.81

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 6.2e-24
                                       EEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   5 vfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewltald 81 
                                       v+D+dGTL++ +  + +v +++                     + ak+++++l +++            +++l++  
  gi|557693809|ref|YP_008796863.1|   2 VMDLDGTLIKMKFDIFQVKKRV--------------------SEVAKQHGFELRENES----------IQDFLDRA- 47 
                                       89*******8887776666666....................8999999999988888..........45555555. PP

                                       CHHHHHHHHHHHH.HHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT. CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                         Hydrolase  82 ippdlgaaigsaq.sqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG. 156
                                         ++l    + a  ++    +l   ++++  + + +    p++a+++++Lk  g+++v++t++++e +e+a+++ G 
  gi|557693809|ref|YP_008796863.1|  48 --SHLLPPHEFAKlREEIQNILR--NEDRKSAEQAE--ATPGIADVLEKLKTLGFKLVVATNSHREAVEEALKKTGl 118
                                       ..222222333330344444444..44444444445..99************************************* PP

                                       GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 157 ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                       d+yf++v+++d+++  kp p++++++++ ++++++ ++ VGD+vnD+ a+++Ag
  gi|557693809|ref|YP_008796863.1| 119 DKYFEHVYTRDDVEKMKPRPDILLKIAEDMRIPISSIVYVGDSVNDLRAAREAG 172
                                       *****************************************************8 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   2.4e-13   9.7e-11       2     188 .]       2     169 ..       1     169 [. 0.68

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 2.4e-13
                               HAD   2 lfDfDgTLldgdslelllrfllrrgaprlwralrek..lllalfrellrldraglaelleallaglseelaaelerf 76 
                                       + D+DgTL+    +++ +++++ + a++ + +lre   +   l r    l   ++a+l e++   l+ e+ + +e++
  gi|557693809|ref|YP_008796863.1|   2 VMDLDGTLIKMKFDIFQVKKRVSEVAKQHGFELRENesIQDFLDRASHLLPPHEFAKLREEIQNILRNEDRKSAEQA 78 
                                       78*********777777776777766666666666643222223333333444555555555555555555556666 PP

                               HAD  77 vaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrg.e 152
                                                 +pg+ ++l++ +  G+++vv ++++r+ ve+ l++ g    l+       ++     +  ++v + +
  gi|557693809|ref|YP_008796863.1|  79 E--------ATPGIADVLEKLKTLGFKLVVATNSHREAVEEALKKTG----LDK------YFEHV--YTRDDVEKmK 135
                                       6........77************************************....888......44444..2222222213 PP

                               HAD 153 gkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                        +++ l +   ae   i+++++v++GDs++Dl ++r
  gi|557693809|ref|YP_008796863.1| 136 PRPDILLK--IAEDMRIPISSIVYVGDSVNDLRAAR 169
                                       44444444..56688999999*************97 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   1.2e-12   4.6e-10       4      71 ..     135     199 ..     133     208 .. 0.88
   2 ?   -1.5   0.0       6.9   2.7e+03      22      46 ..     280     305 ..     268     309 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.2e-12
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SE CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvadd 71 
                                       KP p ++  ++e++ ++ + ++++GD+   D+++A++aG+++++V+ G +++e+    e ++t +a +
  gi|557693809|ref|YP_008796863.1| 135 KPRPDILLKIAEDMRIPISSIVYVGDS-VNDLRAAREAGARFIAVAWGLHSAEKFM--ENGATEIAHN 199
                                       9**************************.***********************98865..4566666655 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 6.9
                                       GGEEEEES-T.TTHHHHHHHCT-EEE CS
                    Hydrolase_like  22 eevlmiGDrl.atDiagAnnaGwksv 46 
                                        ++ ++G r+   Di+ A++  ++ +
  gi|557693809|ref|YP_008796863.1| 280 LNIRIVGERPsLEDIKLARKGRIDAI 305
                                       5667889988458*****99887765 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 !   40.0   0.0   5.6e-13   2.2e-10      47     244 ..     393     582 ..     375     606 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 5.6e-13
                             T2SSE  47 lerlisriaalakldiseerplqd.arlp..ekgvrlrvvllPvvagealviRkksakeltlddlgaeealkekiae 120
                                       l+ li+++   a+ + + +  ++  +++    +++r+ v+ +P + g +++i +    +l+++d+   ++l e+   
  gi|557693809|ref|YP_008796863.1| 393 LNNLIKEVTEYARVKPEANIEIVRaGAFVaqIGNYRIAVARPPFSSGLEVTIVR-PIVKLRIEDYKLPPKLLER--- 465
                                       4555555555554444433333330333366679*************6665543.5677899**9887766555... PP

                             T2SSE 121 vlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnakkakvtfadllraaLR 197
                                        l+k       il++G+ gsGK+t++ +l ++     + + t+E p+ +q+ g++ +q  +   + +f++  + +L 
  gi|557693809|ref|YP_008796863.1| 466 -LEKK---AEGILIAGPPGSGKSTFAASLAEFYSRMGKIVKTLESPRDLQV-GPDITQYGPL--EGDFEKTAEILLL 535
                                       .5555...5889*************9888888888877777*********9.4566666666..66899******** PP

                             T2SSE 198 lrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagalerLe 244
                                        rPD  +  EiR    +++ + +     g ++ +Ha +a++a++r  
  gi|557693809|ref|YP_008796863.1| 536 VRPDYTVFDEIRRDRDFQVFSDMRLAGIGMIGVVHASEAVSAIQRFI 582
                                       ************999999966666555666***************75 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   3.3e-07   0.00013       4      37 ..     698     731 ..     695     755 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.3e-07
                                       EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES CS
                              KH_1   4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpk 37 
                                       ++v+++  ++iIG++G+nI ++++e g++ +v++
  gi|557693809|ref|YP_008796863.1| 698 VKVDREVLPKIIGRRGENIARLEKELGVSLDVEP 731
                                       799999******************88*****984 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.069        28      55     112 ..     222     295 ..     209     316 .. 0.82
   2 ?   -1.9   0.0       8.7   3.5e+03      17      39 ..     307     329 ..     304     372 .. 0.62
   3 !   13.9   0.0   0.00012     0.046       2      21 ..     473     492 ..     473     503 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.069
                            AAA_33  55 lyqilnelarkalsagrnvildat................nlsrrerarflklarrlgvpvrivvvetdeetlk 112
                                       ++++l +l+++ l  g+ vil a                 ++  +e ++++++a+++  ++riv  +++ e +k
  gi|557693809|ref|YP_008796863.1| 222 INGTLTQLVEQGLLDGCEVILPAAaidelqaqasqkrepgFVGLNELKKVRSIAEQHRLNIRIVGERPSLEDIK 295
                                       66778888888899999999988877777777777777778888999*****************9888888876 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 8.7
                            AAA_33  17 erllkklgavllssdtlrrrlfg 39 
                                       ++ +k++ avl++sd++ + +++
  gi|557693809|ref|YP_008796863.1| 307 REAAKRENAVLITSDYVQSLVAE 329
                                       56677788999999997665554 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 0.00012
                            AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                       +l+ G+pGsGKst+a +l++
  gi|557693809|ref|YP_008796863.1| 473 ILIAGPPGSGKSTFAASLAE 492
                                       5789************9984 PP

>> NIF  NLI interacting factor-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   3.3e-06    0.0013       4     117 ..       2     165 ..       1     177 [. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.3e-06
                               NIF   4 VLDLDetLvhskl.....eksk............................................klkvegekvev 31 
                                       V+DLD+tL+  k+     +  k                                             l+ e++k   
  gi|557693809|ref|YP_008796863.1|   2 VMDLDGTLIKMKFdifqvK--KrvsevakqhgfelrenesiqdfldrashllpphefaklreeiqnILRNEDRKSAE 76 
                                       99*******9997544331..14556777788888888888898888888888887776655443222333666677 PP

                               NIF  32 svlkRpgldefLkelskl.yevvifTasseeyaeavidildpekkllshrlyrescvkkkg......eyvKdLsllg 101
                                       +    pg  + L++l  l +++v+ T+s++e +e+ +++   +k +++h+++r+++ k k       +   d+    
  gi|557693809|ref|YP_008796863.1|  77 QAEATPGIADVLEKLKTLgFKLVVATNSHREAVEEALKKTGLDK-YFEHVYTRDDVEKMKPrpdillKIAEDM---- 148
                                       77777**********9999*********************9998.7*********942222233222222222.... PP

                               NIF 102 r.dlsrvvivDdspdsf 117
                                       r + s++v v ds +  
  gi|557693809|ref|YP_008796863.1| 149 RiPISSIVYVGDSVNDL 165
                                       13777777777766655 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   4.6e-05     0.018       4     121 ..       2     127 ..       1     133 [. 0.64
   2 ?    3.3   0.0      0.11        46     169     185 ..     152     168 ..     139     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.6e-05
                   Put_Phosphatase   4 vfDFDktiidedsdnwvvdelpatelfeelretlrkglwnelmdrvlkel..heqgvseadi........kkvlrsi 70 
                                       v+D D t+i+ + d   v++   +   ++  e  +++  ++++dr  + l  he  +  ++i        +k  ++ 
  gi|557693809|ref|YP_008796863.1|   2 VMDLDGTLIKMKFDIFQVKKRVSEVAKQHGFELRENESIQDFLDRASHLLppHEFAKLREEIqnilrnedRKSAEQA 78 
                                       56666666666666555544444444343334444445556666554444222222333344000100114556678 PP

                   Put_Phosphatase  71 plspglvelikslakkkleldliiiSDaNsffieeileaagledlFseift 121
                                        ++pg+ +++++l  k+l++ l++  ++ +  +ee+l+++gl ++F++++t
  gi|557693809|ref|YP_008796863.1|  79 EATPGIADVLEKL--KTLGFKLVVATNSHREAVEEALKKTGLDKYFEHVYT 127
                                       99***********..789********************************9 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.11
                   Put_Phosphatase 169 yerliYvGDganDlCpv 185
                                        + ++YvGD+ nDl + 
  gi|557693809|ref|YP_008796863.1| 152 ISSIVYVGDSVNDLRAA 168
                                       5689*********9765 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.062        25       2      33 ..       2      33 ..       1      35 [. 0.86
   2 ?    6.9   0.0     0.012       4.7      17      58 ..      81     122 ..      75     125 .. 0.89
   3 ?    4.7   0.0     0.053        21     192     217 ..     141     166 ..     139     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.062
                                      EEEIIIIIS-TTS---HHHHHHHHHHHHTTSE CS
                       Hydrolase_3  2 alDlDGTLlnsdkkisektkeaikklkekgik 33
                                      ++DlDGTL++ +  i +  k++ + +k++g++
  gi|557693809|ref|YP_008796863.1|  2 VMDLDGTLIKMKFDIFQVKKRVSEVAKQHGFE 33
                                      79********9999999999998888888875 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.012
                                       -HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                       Hydrolase_3  17 sektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                       ++ ++++++klk  g+k+v+AT  + +av++ l++ gld ++
  gi|557693809|ref|YP_008796863.1|  81 TPGIADVLEKLKTLGFKLVVATNSHREAVEEALKKTGLDKYF 122
                                       677899*******************************99775 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.053
                                       HHHHHHHCT--GGGEEEEESSGGGHH CS
                       Hydrolase_3 192 lkklakelnisleeviafGDgeNDie 217
                                       l k+a+ ++i+ + ++ +GD+ ND+ 
  gi|557693809|ref|YP_008796863.1| 141 LLKIAEDMRIPISSIVYVGDSVNDLR 166
                                       56899*******************96 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   9.6e-06    0.0038       1      21 [.     473     493 ..     473     556 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.6e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                                       Il++G+pG+GK+t+a  L++ 
  gi|557693809|ref|YP_008796863.1| 473 ILIAGPPGSGKSTFAASLAEF 493
                                       99****************764 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 !   14.2   0.0   7.2e-05     0.028       1      28 [.     475     502 ..     475     505 .. 0.88
   2 ?    3.9   0.1     0.095        38     167     224 ..     635     695 ..     628     701 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.2e-05
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsva 28 
                                       ++Gp+GsGK+tf  +l+e+++  g+ v+
  gi|557693809|ref|YP_008796863.1| 475 IAGPPGSGKSTFAASLAEFYSRMGKIVK 502
                                       79*****************999887665 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.095
                        ATP_bind_1 167 Dllkeklekeleffedvealslllekee...ekykklaeaiaelleefalvlrflplssek 224
                                       D l ++le+e+  f + + +  ++++++   + +++l e+i+e+l  f+++ ++ ++s++k
  gi|557693809|ref|YP_008796863.1| 635 DFLTDELEYEIYTFGEENVIIPVKKLHDevrSETRELREKIVEALRSFDENVQVEMVSRKK 695
                                       6667677788888877776665555555666999*****************9999999987 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3   1.2e-05    0.0047       3      51 ..     671     716 ..     669     719 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-05
                              KH_4   3 lvedilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtl 51 
                                       l e+i++al    e+v+v++    ++++  ++v+ e l ++IG+rG+++
  gi|557693809|ref|YP_008796863.1| 671 LREKIVEALRSFDENVQVEMV---SRKKAIVKVDREVLPKIIGRRGENI 716
                                       66899999999999******9...789999*****************98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0      0.28   1.1e+02      91     135 ..     235     293 ..     191     294 .. 0.67
   2 !   13.1   0.0   0.00022     0.086       4      30 ..     469     495 ..     465     523 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.28
                            AAA_22  91 v......ielliiDEaqh.lr.s.......eealeeLrsllnlsrkgvqliLvGtp.elrk 135
                                               ++  iDE q   + +        + l+++rs+++  ++ + + +vG + +l++
  gi|557693809|ref|YP_008796863.1| 235 LdgceviLPAAAIDELQAqASqKrepgfvgLNELKKVRSIAE--QHRLNIRIVGERpSLED 293
                                       233335667889******553515678555666666688888..*******9999878876 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00022
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqld 30 
                                       +a  +++ G++G+GK+t ++ l+e + 
  gi|557693809|ref|YP_008796863.1| 469 KAEGILIAGPPGSGKSTFAASLAEFYS 495
                                       566799****************99985 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00026      0.11       2     127 ..     215     335 ..     214     338 .. 0.69
   2 ?    3.4   0.2      0.21        85      15      65 ..     645     693 ..     636     722 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00026
                             PIN_4   2 VlDTnvlLhdpealksf.....keehdvviPitVleELdklKkgsse.relarlarqanrlldellekesgrlkvqt 72 
                                       V DT+++++    l ++      +  +v++P   ++EL+++ ++++e   ++ +  + +r +    e++  ++++  
  gi|557693809|ref|YP_008796863.1| 215 VPDTSTIINGT--LTQLveqglLDGCEVILPAAAIDELQAQASQKREpGFVGLNELKKVRSIA---EQHRLNIRIVG 286
                                       88999999876..4444556678999**************99999976455555445556555...44555666666 PP

                             PIN_4  73 saeelpee.eseseknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgiea 127
                                       ++ +l++   +++ + D  I ++a    +   +++ vL++ D    + A+a+g+++
  gi|557693809|ref|YP_008796863.1| 287 ERPSLEDIkLARKGRIDAIIREAA----K---RENAVLITSDYVQSLVAEAEGVQV 335
                                       666666542333445665555544....3...357899999999999999999986 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.21
                             PIN_4  15 lksfkeehdvviPitVleELdklKkgsserelarlarqanrlldelleke...s 65 
                                       +++f +e +v+iP+  l+  d+++++++  el++++ +a+r +de ++ e    
  gi|557693809|ref|YP_008796863.1| 645 IYTF-GEENVIIPVKKLH--DEVRSETR--ELREKIVEALRSFDENVQVEmvsR 693
                                       5778.8999999998887..67888887..9************99988765542 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.7e-05    0.0069      15      57 ..     462     504 ..     460     601 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.7e-05
                            AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekdggif.lr 57 
                                       +ler+ +   e +l+ G++G+GKs+ + +l++ +++ g i+ + 
  gi|557693809|ref|YP_008796863.1| 462 LLERLEKKA-EGILIAGPPGSGKSTFAASLAEFYSRMGKIVkTL 504
                                       566666665.89*******************9888876444444 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 ?    3.1   0.1      0.29   1.2e+02      65     120 ..      61     114 ..      18     124 .. 0.81
   2 ?   -1.0   0.0       5.4   2.2e+03      64     128 ..     247     306 ..     192     319 .. 0.62
   3 !   11.8   0.0    0.0006      0.24       1      21 [.     473     493 ..     473     510 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.29
                                       ETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS.GGGSTHHHH CS
                               AAA  65 DEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr.pdkldpall 120
                                       +Ei ++ +++ +++s e+ ++ + +  +l+++k+    + +++atn+  + +++al 
  gi|557693809|ref|YP_008796863.1|  61 EEIQNILRNE-DRKSAEQAEATPGIADVLEKLKTL--GFKLVVATNShREAVEEALK 114
                                       6999999999.88899999999************6..599******95566666665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 5.4
                                       EETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEE CS
                               AAA  64 iDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrki 128
                                       iDE+ a a+++    +e +   +n+L ++ +  ++  +++ + +++ rp+  d +l r gR+d +i
  gi|557693809|ref|YP_008796863.1| 247 IDELQAQASQK----REPGFVGLNELKKVRSIAEQ--HRLNIRIVGERPSLEDIKLARkGRIDAII 306
                                       55555555554....45555556666666666666..34555555666666666777777777666 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.0006
                                       EEEESSTTSSHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavake 21 
                                       +l+ GppG GK+++a ++a+ 
  gi|557693809|ref|YP_008796863.1| 473 ILIAGPPGSGKSTFAASLAEF 493
                                       699**************9975 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       6.3   2.5e+03     125     155 ..     297     327 ..     268     331 .. 0.73
   2 !   15.2   0.0   2.9e-05     0.012      27      59 ..     464     496 ..     456     604 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.3
                            AAA_25 125 lltadvdaleaaieevegvrlvviDplsral 155
                                       ++++ +da+++++ ++e+++l+  D +++++
  gi|557693809|ref|YP_008796863.1| 297 ARKGRIDAIIREAAKRENAVLITSDYVQSLV 327
                                       3678899999999999999999888777765 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.9e-05
                            AAA_25  27 kgllpagelallaGapgtGKttlaldlalavat 59 
                                       ++l  + e +l+aG+pg+GK+t+a +la  +++
  gi|557693809|ref|YP_008796863.1| 464 ERLEKKAEGILIAGPPGSGKSTFAASLAEFYSR 496
                                       55556677789****************988874 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 !   16.6   0.0   1.2e-05    0.0046     113     215 ..      76     174 ..      71     188 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                                       TGGCCECCHHHHHHHHHHTTEEEEEEEEEECCCHHHHHHHHHHCT-TT.BSCCEEECCSTTC---HHHHHHHHHHHH CS
                   Acid_phosphat_B 113 geakaipgalelikkvverGvkiffvsgRseeqkaaTvenLkkagfss.weklilkgkkdkqkksvvsyKeerrqkl 188
                                        +a+a pg  ++++k++ +G+k++  ++  +e   a +e Lkk g ++  e+++ +++ +  k   ++   +   k+
  gi|557693809|ref|YP_008796863.1|  76 EQAEATPGIADVLEKLKTLGFKLVVATNSHRE---AVEEALKKTGLDKyFEHVYTRDDVE--K---MKPRPDILLKI 144
                                       578999*********************96666...6778889999765146788777665..3...34677788888 PP

                                       HHTTEEE....EEEEESSGGGCHCCHHCTCC CS
                   Acid_phosphat_B 189 ekkGyni....vlniGDnlsDlngakeaear 215
                                        ++ ++i    ++++GD+ +Dl +a+ea+ar
  gi|557693809|ref|YP_008796863.1| 145 AED-MRIpissIVYVGDSVNDLRAAREAGAR 174
                                       888.9998888889**********8888876 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.5   3.9e-05     0.016       2      59 ..     671     728 ..     669     747 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.9e-05
                                       HHHHHHHHT.ECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2   2 ipeslavei.kkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdie 59 
                                       ++e + + + ++ ++ +ve   +++++i+ +  +    +IG++G+ni +++kel+  ++
  gi|557693809|ref|YP_008796863.1| 671 LREKIVEALrSFDENVQVEM-VSRKKAIVKVDREVLPKIIGRRGENIARLEKELGVSLD 728
                                       56666666666666777776.45799999999999999****************98884 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   0.00012     0.047       2      61 ..       2     123 ..       1     134 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00012
                                       EEESTTTSE.................................................................ETT CS
                       Hydrolase_6   2 lfDidGvLw.................................................................rgd 13 
                                       ++D+dG+L+                                                                 ++ 
  gi|557693809|ref|YP_008796863.1|   2 VMDLDGTLIkmkfdifqvkkrvsevakqhgfelrenesiqdfldrashllpphefaklreeiqnilrnedrksaEQA 78 
                                       67778888777888888888888888888888888888888888888888888888888887777777777777789 PP

                                       EE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GG CS
                       Hydrolase_6  14 kaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditee 61 
                                       +a pg a++l+ l+  g ++v+ TN+ ++   ++ + l+k g+d   e
  gi|557693809|ref|YP_008796863.1|  79 EATPGIADVLEKLKTLGFKLVVATNSHRE---AVEEALKKTGLDKYFE 123
                                       9************************7755...5666667777665555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       8.5   3.4e+03      54      95 ..      77     119 ..      20     132 .. 0.54
   2 !   14.6   0.0   8.6e-05     0.034      11      42 ..     470     500 ..     467     585 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 8.5
                                       HHHCCHCEEEE-SS.--S-TTSBHHHHHHHTCHHHHHHHSTTG CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  54 leslrkeigvlpqe.pqlfpeltvrenesdeeiekalsklglk 95 
                                         ++   i+ + ++ ++l  +l v++n  +e +e+al+k gl+
  gi|557693809|ref|YP_008796863.1|  77 QAEATPGIADVLEKlKTLGFKLVVATNSHREAVEEALKKTGLD 119
                                       2222222222222223333333344445555566666666655 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 8.6e-05
                                       TSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGei 42 
                                        e + i G+ G+GKSt+++ la+ ++  +G+i
  gi|557693809|ref|YP_008796863.1| 470 AEGILIAGPPGSGKSTFAASLAEFYS-RMGKI 500
                                       567889******************98.69998 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.5     2e+02     155     186 ..     137     169 ..      72     176 .. 0.72
   2 ?   10.6   0.0   0.00078      0.31       4      31 ..     473     500 ..     470     504 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.5
                                       STTHHHHHHHHHTS-EEEE.E-SSSTTGEEE-- CS
                             SRP54 155 kgGaalsiaaelklPikfi.gvGekiedleefd 186
                                       +  ++l+ia+ + +Pi+ i  vG++++dl++++
  gi|557693809|ref|YP_008796863.1| 137 RPDILLKIAEDMRIPISSIvYVGDSVNDLRAAR 169
                                       5567899*********865168*******9876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00078
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS- CS
                             SRP54   4 illvGlqGaGKTttlaKLaallkkegkk 31 
                                       il++G+ G+GK t +a La+ ++++gk 
  gi|557693809|ref|YP_008796863.1| 473 ILIAGPPGSGKSTFAASLAEFYSRMGKI 500
                                       89********************999875 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 ?   14.0   0.0   7.8e-05     0.031      45      78 ..     468     501 ..     462     542 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.8e-05
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavraglsv 78 
                                       +k+e+i++ Gp+G GKs +a++l+    r g+ v
  gi|557693809|ref|YP_008796863.1| 468 KKAEGILIAGPPGSGKSTFAASLAEFYSRMGKIV 501
                                       57899******************98777766655 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.3   2.5e+03      31      64 ..      52      86 ..      42     111 .. 0.57
   2 ?   12.5   0.0   0.00022     0.089       3      61 ..     477     535 ..     475     558 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.3
                                      SSSTTSHHHHHHHHHHH.TCS---HHHHHHHHHHH CS
                   Thymidylate_kin 31 repggteiGekirelll.keeeleeqteallfaad 64
                                      ++ ++ +++e i+++l  + ++ +eq+ea    ad
  gi|557693809|ref|YP_008796863.1| 52 PPHEFAKLREEIQNILRnEDRKSAEQAEATPGIAD 86
                                      55666666666666666444444444454443333 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00022
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHH CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallf 61 
                                       G  G+GK+t+a+ l+e ++++g+ v +   p++ ++G  i ++   e ++e+ +e ll+
  gi|557693809|ref|YP_008796863.1| 477 GPPGSGKSTFAASLAEFYSRMGKIVKTLESPRDLQVGPDITQYGPLEGDFEKTAEILLL 535
                                       778*******************7677778899******999997756666666655554 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1     0.007       2.8      26      68 ..      87     127 ..      80     134 .. 0.74
   2 ?    4.3   0.0     0.092        37       9      41 ..     167     199 ..     164     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.007
                                       HHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCS CS
                        ADH_zinc_N  26 klelakklGadevinykeadlverikeltggegvdvvfecvGs 68 
                                        le++k lG + v+ +++    e+++e+ ++ g+d +fe+v +
  gi|557693809|ref|YP_008796863.1|  87 VLEKLKTLGFKLVVATNS--HREAVEEALKKTGLDKYFEHVYT 127
                                       58999***********55..4455555555559******9965 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.092
                                       HHHHTT-EEEEEESSHHHHHHHHHTTESEEEET CS
                        ADH_zinc_N   9 lAkalGaeviavdsseeklelakklGadeviny 41 
                                       +A+ +Ga+ iav+   + +e+ +++Ga+e+ ++
  gi|557693809|ref|YP_008796863.1| 167 AAREAGARFIAVAWGLHSAEKFMENGATEIAHN 199
                                       7999************************98766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       1.6   6.5e+02      96     131 ..     259     294 ..     258     324 .. 0.83
   2 ?   11.2   0.0   0.00058      0.23      20      49 ..     472     501 ..     462     507 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1.6
                            AAA_30  96 EagmvdtkqlaallkaaekagakvilvGDerQlasV 131
                                       E g v+ ++l+++ ++ae++   +++vG +  l+ +
  gi|557693809|ref|YP_008796863.1| 259 EPGFVGLNELKKVRSIAEQHRLNIRIVGERPSLEDI 294
                                       668899999999*******99******998766665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00058
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrv 49 
                                         ++ Gp+G+GK+t  ++l+e + + g+ v
  gi|557693809|ref|YP_008796863.1| 472 GILIAGPPGSGKSTFAASLAEFYSRMGKIV 501
                                       56899******************9988655 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 ?   13.3   0.0   0.00015     0.061       2      27 ..     473     498 ..     472     551 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00015
                                       EEEE--SSSSHHHHHHHGGGGBS--E CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnrev 27 
                                       +l+ GppG+gKs++a +la+++ r  
  gi|557693809|ref|YP_008796863.1| 473 ILIAGPPGSGKSTFAASLAEFYSRMG 498
                                       7999****************995443 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.6e-05     0.034     261     292 ..     469     502 ..     459     514 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.6e-05
                          PPV_E1_C 261 kknclvllGppntGkslfamslikfLk..Gkvls 292
                                       k + +++ Gpp +Gks+fa sl +f +  Gk++ 
  gi|557693809|ref|YP_008796863.1| 469 KAEGILIAGPPGSGKSTFAASLAEFYSrmGKIVK 502
                                       55789*******************9743377765 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 ?   13.2   0.0   0.00014     0.056      20      38 ..     469     486 ..     463     492 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                            AAA_29  20 dlkgatlltGpsGsGKSTl 38 
                                       + +g +l++Gp GsGKST+
  gi|557693809|ref|YP_008796863.1| 469 KAEG-ILIAGPPGSGKSTF 486
                                       4456.9************7 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00023     0.091       5      22 ..     473     490 ..     469     502 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00023
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       ili Gp+g+GK+t+a++l
  gi|557693809|ref|YP_008796863.1| 473 ILIAGPPGSGKSTFAASL 490
                                       89*************998 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 ?   12.3   0.0   0.00034      0.13      14      53 ..     463     502 ..     460     512 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00034
                                       HHHHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE--SS CS
                   Sigma54_activ_2  14 LeqaaqsklpvfltGekGsgkelvArlLhknsgpwleifv 53 
                                       Le ++++   ++++G++Gsgk+++A  L+++ ++  +i++
  gi|557693809|ref|YP_008796863.1| 463 LERLEKKAEGILIAGPPGSGKSTFAASLAEFYSRMGKIVK 502
                                       7889999999********************9999877765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.5     1e+03      34      64 ..     303     333 ..     297     345 .. 0.78
   2 ?   10.0   0.0   0.00099      0.39      18      47 ..     472     501 ..     461     504 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.5
                        Zeta_toxin  34 ellkdelerqgnvvrldpDdlRelhPeyeei 64 
                                       +++ +e ++++n+v +  D +++l  e+e++
  gi|557693809|ref|YP_008796863.1| 303 DAIIREAAKRENAVLITSDYVQSLVAEAEGV 333
                                       445555568**********999998777765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00099
                        Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvv 47 
                                        il++G pG+GKs+ a+ l++   r g++v
  gi|557693809|ref|YP_008796863.1| 472 GILIAGPPGSGKSTFAASLAEFYSRMGKIV 501
                                       59*************999988776666666 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 ?   12.8   0.1   0.00031      0.12       6      70 ..      58     124 ..      56     136 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00031
                    Peptidase_S8_N   6 klkeeaaealeaaaatrgesvrsgiksldevlaelgavelervfpvd...gkfeertrkaGLhlWYdv 70 
                                       kl+ee++++l+++ ++++e   ++++ + +vl++l++  ++ v++++   + +ee  +k+GL++ ++ 
  gi|557693809|ref|YP_008796863.1|  58 KLREEIQNILRNEDRKSAE-QAEATPGIADVLEKLKTLGFKLVVATNshrEAVEEALKKTGLDKYFEH 124
                                       9**********99999888.78888888888888888888888887611145778899*****99874 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0012      0.47       2      19 ..     477     494 ..     476     501 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0012
                                       E-TTSSHHHHHHHHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklveky 19 
                                       G+PGsGK+t ++ l+e y
  gi|557693809|ref|YP_008796863.1| 477 GPPGSGKSTFAASLAEFY 494
                                       9*************9977 PP

>> AAA_28  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       1.1       2      21 ..     473     492 ..     472     508 .. 0.87
   2 ?    0.6   0.1       1.5     6e+02     121     149 ..     660     687 ..     634     697 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0028
                            AAA_28   2 ivitGgestGKTtlleaLaa 21 
                                       i i G++++GK+t ++ La+
  gi|557693809|ref|YP_008796863.1| 473 ILIAGPPGSGKSTFAASLAE 492
                                       789***************96 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.5
                            AAA_28 121 idddgeRredleereaiderlrealrelg 149
                                       +  d++R e+ e re+i e+lr++ ++ +
  gi|557693809|ref|YP_008796863.1| 660 L-HDEVRSETRELREKIVEALRSFDENVQ 687
                                       4.79***************9998766555 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    0.0008      0.32       3      22 ..     473     492 ..     471     498 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0008
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       +++ G++GsGK+t++++la+
  gi|557693809|ref|YP_008796863.1| 473 ILIAGPPGSGKSTFAASLAE 492
                                       789**************985 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 ?   10.5   0.1    0.0015      0.58       9      49 ..      73     115 ..      66     131 .. 0.79
   2 ?   -0.9   0.0       5.1     2e+03      33      52 ..     665     684 ..     664     705 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0015
                      PG_binding_2   9 eervlaedv..aeevqaaLsrLGyydgeaggafrealrdALra 49 
                                       + ++ ae++  +  v ++L+ LG++   a+ + rea+++AL++
  gi|557693809|ref|YP_008796863.1|  73 KSAEQAEATpgIADVLEKLKTLGFKLVVATNSHREAVEEALKK 115
                                       4444444442245799*************************85 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 5.1
                      PG_binding_2  33 geaggafrealrdALrafia 52 
                                       ++ ++ +re+  +ALr+f +
  gi|557693809|ref|YP_008796863.1| 665 RSETRELREKIVEALRSFDE 684
                                       567899999999***99965 PP

>> DUF1827  Domain of unknown function (DUF1827)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0031       1.2       2      31 ..      97     128 ..      96     134 .. 0.88
   2 ?    1.5   0.4      0.87   3.5e+02      26      65 ..     643     680 ..     631     701 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0031
                                       -EEE-GGG-HHHHHHHHHHS..S-SEEEEEEE CS
                           DUF1827   2 kLinvtnsyselvkkqLenT..daklvkvYsl 31 
                                       kL+  tns++e v++ L++T  d  + +vY+ 
  gi|557693809|ref|YP_008796863.1|  97 KLVVATNSHREAVEEALKKTglDKYFEHVYTR 128
                                       899*****************888888899985 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.87
                                       EEEEEETTEEEEEEEETTEEEEEEEESSS---HHHHHHHH CS
                           DUF1827  26 vkvYslGnttvvyteapkhveivlsnkkRaikeeEiefvl 65 
                                        ++Y+ G+ +v+   ++ h e+    ++R+++e+ +e ++
  gi|557693809|ref|YP_008796863.1| 643 YEIYTFGEENVIIPVKKLHDEV--RSETRELREKIVEALR 680
                                       689*********9999999997..6788888888777655 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00069      0.28       4     116 ..     217     324 ..     214     330 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00069
                                       -HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.SCHCHHHHHHHHHHHHHHHTSEEEEBCHHHHH CS
                               PIN   4 DTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.rkskrekaaelvelllllsalkilpidaeiae 79 
                                       DTs +i   +g   +     ll++  e++++a+++ El + ++  r+++   ++el++++ +++++++     + + 
  gi|557693809|ref|YP_008796863.1| 217 DTSTII---NGTLTQLVEQGLLDG-CEVILPAAAIDELQAQASQkREPGFVGLNELKKVRSIAEQHRLNIRIVGERP 289
                                       666666...344444444556655.7999999999999999999988888888888888877666555543444444 PP

                                       HHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHH CS
                               PIN  80 eaaeialkygllpnDaliaAtAkehgikliatfDedf 116
                                         ++i+l + ++ +Da+i   Ak++++ li t D   
  gi|557693809|ref|YP_008796863.1| 290 SLEDIKLAR-KGRIDAIIREAAKRENAVLI-TSDYVQ 324
                                       444444444.689**************999.**9765 PP

>> DUF705  Protein of unknown function (DUF705)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.9   7.5e+02     137     157 ..       1      24 [.       1      40 [. 0.66
   2 ?    9.6   0.0    0.0014      0.56     157     202 ..      82     127 ..      71     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.9
                            DUF705 137 vvfDlDstLit...deeevelRdh 157
                                       +v+DlD tLi    d ++v+ R  
  gi|557693809|ref|YP_008796863.1|   1 MVMDLDGTLIKmkfDIFQVKKRVS 24 
                                       59********73334455555554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0014
                            DUF705 157 havydsLdelkerh.vlvLWsYGnaehvaeslrevglerslFkiils 202
                                       + + d L++lk+ +  lv+     +e v+e+l++ gl+ ++F+ + +
  gi|557693809|ref|YP_008796863.1|  82 PGIADVLEKLKTLGfKLVVATNSHREAVEEALKKTGLD-KYFEHVYT 127
                                       7799**********999*********************.9**98866 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    0.0011      0.43       1      20 [.     473     492 ..     473     511 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0011
                      RNA_helicase   1 iwlyGpsgeGKStlakeLak 20 
                                       i++ Gp+g GKSt+a +La+
  gi|557693809|ref|YP_008796863.1| 473 ILIAGPPGSGKSTFAASLAE 492
                                       6899*************876 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 ?    0.3   0.0       1.7   6.8e+02      54      87 ..     115     217 ..      36     251 .. 0.67
   2 ?    8.3   0.0    0.0057       2.3       9      30 ..     480     501 ..     473     580 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.7
                                       H.................................................................CCHCCCHHHHH CS
                                       x.................................................................xxxxxxxxxxx RF
                              CbiA  54 p.................................................................dlkrllellea 65 
                                       +                                                                 +l + ++++e+
  gi|557693809|ref|YP_008796863.1| 115 KtgldkyfehvytrddvekmkprpdillkiaedmripissivyvgdsvndlraareagarfiavawGLHSAEKFMEN 191
                                       35666666666666666666666666666666667777777777777777777777777777777755555556655 PP

                                       HCHCHHHH......EEEEEEEEESS. CS
                                       xxxxxxxx....xxxxxxxxxxxxxx RF
                              CbiA  66 lgkkkall....lkiagvvlnrvdge 87 
                                         ++ a++    l+ +gv l++v ++
  gi|557693809|ref|YP_008796863.1| 192 GATEIAHNpselLNHLGVHLTKVVPD 217
                                       55555555556788888888888877 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0057
                                       TSSHHHHHHHHHHHHHHTT--E CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   9 GvGKTtlaanLaralarrglrV 30 
                                       G+GK+t+aa+La   +r g+ V
  gi|557693809|ref|YP_008796863.1| 480 GSGKSTFAASLAEFYSRMGKIV 501
                                       9************999988755 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0      0.15        61      40      72 ..      13      45 ..       6      50 .. 0.87
   2 ?    4.9   0.1     0.068        27      19      58 ..     657     698 ..     652     705 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.15
                    LAGLIDADG_WhiA 40 llnefeleakilerrkkyvvylKkaeqIvdlLk 72
                                        + f+++ +++e+ k+  + l++ e+I+d+L 
  gi|557693809|ref|YP_008796863.1| 13 KFDIFQVKKRVSEVAKQHGFELRENESIQDFLD 45
                                      45678999************************6 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.068
                    LAGLIDADG_WhiA  19 ekkyhLEivspdeelaeqlqkllnef..eleakilerrkkyv 58 
                                        kk h E++s++ el e++ ++l++f  +++ +++ r+k  v
  gi|557693809|ref|YP_008796863.1| 657 VKKLHDEVRSETRELREKIVEALRSFdeNVQVEMVSRKKAIV 698
                                       566789******************997678888888887665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0012      0.47      25      48 ..     473     496 ..     469     507 .. 0.86
   2 ?   -1.4   0.3       3.3   1.3e+03     114     142 ..     667     696 ..     665     704 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                      Mg_chelatase  25 lllvGppGsGKtmlakrlpsllpp 48 
                                       +l++GppGsGK+  a+ l++  ++
  gi|557693809|ref|YP_008796863.1| 473 ILIAGPPGSGKSTFAASLAEFYSR 496
                                       899*************99887665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.3
                      Mg_chelatase 114 ElpefkrkvlevLRePledgevt.israka 142
                                       E+ e+++k++e+LR+  e+ +v+ +sr+ka
  gi|557693809|ref|YP_008796863.1| 667 ETRELREKIVEALRSFDENVQVEmVSRKKA 696
                                       78899**********999999962566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (812 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1084  (0.0604607); expected 358.6 (0.02)
Passed bias filter:                      936  (0.0522059); expected 358.6 (0.02)
Passed Vit filter:                       168  (0.00937029); 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: 0.92u 0.31s 00:00:01.23 Elapsed: 00:00:00.45
# Mc/sec: 5452.09
//
Query:       gi|557693810|ref|YP_008796864.1|  [L=394]
Description: acetyl-CoA C-acyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   96.5   0.0    5.2e-27   94.8   0.0    1.8  1  Thiolase_N       Thiolase, N-terminal domain
    6.5e-11   42.0   0.1    2.4e-08   33.7   0.0    2.9  2  Thiolase_C       Thiolase, C-terminal domain
    8.7e-06   25.5   1.2    0.00062   19.6   0.2    2.4  2  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
    0.00013   21.7  14.4    0.00014   21.6   5.3    3.6  5  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
     0.0039   17.2   0.4          3    7.9   0.0    3.2  3  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 !   94.8   0.0   1.5e-30   5.2e-27       1     260 []       4     223 ..       4     223 .. 0.96

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 1.5e-30
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSE CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevp 77 
                                       v+iv+   +p+g+     +d  ++eL+ +a+k++l++ag+++++v  v v+nv    ++  +a  +   ag+   v 
  gi|557693810|ref|YP_008796864.1|   4 VAIVGVGQSPFGR----ASDKGINELAWQAIKQALQDAGITQKDVGFVSVANVGGWSAEPLPAVSVNEYAGL-TGVG 75 
                                       799**********....9******************************************************.9*** PP

                                       EEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT..TGGSSSSEEEEEHHHHHHTEETTTT CS
                        Thiolase_N  78 avtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr..sglklgdekakdllipdgladafne 152
                                       + +v+ +c+Sg +a+++aa+ + +g++d+++a+GvE+m ++pt ++++++  +g  + + ++ +l+ p+        
  gi|557693810|ref|YP_008796864.1|  76 TYRVEAACASGSAALVTAANLVSSGAVDIALAVGVERMNESPTPTAVELIgrAGNYFWEFEMFGLTFPS-------- 144
                                       *****************************************999999987558888899999*******........ PP

                                       SEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS CS
                        Thiolase_N 153 ehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLakl 229
                                          +l a  + +ky+++ e++++  vk+h  a+ +  a  F++ +              + +e ++s+ +a +L+ l
  gi|557693810|ref|YP_008796864.1| 145 -YYALYATAYMNKYGATEEDLAKISVKNHFYASFNEYAA-FRKRV--------------TVEEVLKSRPVAWPLKLL 205
                                       .899**********************************9.***77..............899*************** PP

                                       -BSSSTTSS-BTTSB--BEEEEEEEEEEEHH CS
                        Thiolase_N 230 kpaFkkeGtvtAgnasqisDGaaavllmses 260
                                                    ++s+i+DGaaav+l+se+
  gi|557693810|ref|YP_008796864.1| 206 -------------DCSPITDGAAAVVLASED 223
                                       .............***************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 !    4.9   0.0    0.0053        19      26      47 ..      28      49 ..      17      57 .. 0.89
   2 !   33.7   0.0   6.6e-12   2.4e-08      24     114 ..     259     371 ..     240     381 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0053
                                      HHHHHHHHHHT--GGGESEEEE CS
                        Thiolase_C 26 yaikkvlkkagltvedidlfEi 47
                                       aik++l++ag+t +d+ ++ +
  gi|557693810|ref|YP_008796864.1| 28 QAIKQALQDAGITQKDVGFVSV 49
                                      69***************98865 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 6.6e-12
                                       HHHHHHHHHHHHT--....GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH CS
                        Thiolase_C  24 Payaikkvlkkaglt....vedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaial 78 
                                          a+ ++ kkag++    v++ d++E+++ F+   + + ++l++++                    vN+ GG  a 
  gi|557693810|ref|YP_008796864.1| 259 TRKAAAEAYKKAGVDpskpVKSFDVVEVHDCFTIAEILAYEDLGFAApgqgymlaregetykgglIPVNLDGGLKAK 335
                                       4568888999999975556889*****************************************9999********** PP

                                       -B-TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTT CS
                        Thiolase_C  79 GHPlGasGaRivvtllselkkeggklgvaalCiggg 114
                                       GHP+Ga+G+ +++ ++++l++e      a +  g g
  gi|557693810|ref|YP_008796864.1| 336 GHPIGATGVSMAAEITKQLRQEAPAERQADIVKGMG 371
                                       ********************9876655555555555 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 !   19.6   0.2   1.7e-07   0.00062       3      38 ..      79     114 ..      77     121 .. 0.94
   2 !    4.4   0.0    0.0097        35      53      65 ..     211     223 ..     204     233 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.7e-07
                                       EE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGG CS
                       ACP_syn_III   3 lnaaCsgfvyalsvAdaliesgaakrvLvigaetls 38 
                                       ++aaC++  +al +A++l++sga+  +L +g e++ 
  gi|557693810|ref|YP_008796864.1|  79 VEAACASGSAALVTAANLVSSGAVDIALAVGVERMN 114
                                       789******************************986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0097
                                       -EEEEEEEEEEES CS
                       ACP_syn_III  53 GDGAgAvvlease 65 
                                        DGA+Avvl  ++
  gi|557693810|ref|YP_008796864.1| 211 TDGAAAVVLASED 223
                                       6********9864 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 !    4.8   0.1    0.0051        18      91     123 ..      25      57 ..      19      72 .. 0.80
   2 !   21.6   5.3   3.8e-08   0.00014     158     207 ..      65     115 ..      47     128 .. 0.83
   3 ?   -3.0   0.0       1.2   4.4e+03     239     251 ..     211     223 ..     209     225 .. 0.82
   4 ?   -2.9   0.0       1.1   4.1e+03      94     109 ..     261     276 ..     256     285 .. 0.79
   5 ?   -1.0   0.1      0.29     1e+03     200     239 ..     330     373 ..     321     378 .. 0.66

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHHTS-HHTCTTGGEEEEEEESS CS
                     ketoacyl-synt  91 llleaawealedagltpeeldgsrvgvfiGvga 123
                                       l+ +a ++al+dag+t++++   +v+++ G +a
  gi|557693810|ref|YP_008796864.1|  25 LAWQAIKQALQDAGITQKDVGFVSVANVGGWSA 57 
                                       78899************9986666777766665 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 3.8e-08
                                       HHHHHT--SS.EEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                     ketoacyl-synt 158 isyalglrGp.svtvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                       ++   gl+G+ ++ v++AC+S+ +a+  a + + sg +d+ala Gve + +
  gi|557693810|ref|YP_008796864.1|  65 VNEYAGLTGVgTYRVEAACASGSAALVTAANLVSSGAVDIALAVGVERMNE 115
                                       45557888864789********99988888*****************9875 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.2
                                       B-EEEEEEEEECH CS
                     ketoacyl-synt 239 GEGvGavvLkrle 251
                                       ++G++avvL +++
  gi|557693810|ref|YP_008796864.1| 211 TDGAAAVVLASED 223
                                       69*******9876 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHTS-HHT CS
                     ketoacyl-synt  94 eaawealedagltpee 109
                                       +aa+ea ++ag++p +
  gi|557693810|ref|YP_008796864.1| 261 KAAAEAYKKAGVDPSK 276
                                       6899999999999854 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.29
                                       EEEE---SHHHHHHHHHTTBB-TT..SGGGTTBTTB..-SB-BB CS
                     ketoacyl-synt 200 GGvellltpeavagfsaagllspd..grckafdpka..dGfvlG 239
                                       GG ++  +p +  g s+a+ ++++  +   a ++++  +G+ l+
  gi|557693810|ref|YP_008796864.1| 330 GGLKAKGHPIGATGVSMAAEITKQlrQEAPAERQADivKGMGLA 373
                                       89999999999999999995555543334444444477777666 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 !    7.9   0.0   0.00082         3      28      51 ..      28      51 ..      15      60 .. 0.86
   2 !    4.8   0.0    0.0076        27      23      51 ..     256     288 ..     234     294 .. 0.72
   3 ?   -0.3   0.0      0.29     1e+03      88     109 ..     336     357 ..     333     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00082
                                      HHHHHHHHHHT--GGGEEEEE-SS CS
                   Ketoacyl-synt_C 28 raiekalaeagvdpedvdyveahg 51
                                      +ai++al++ag++ +dv+ v+   
  gi|557693810|ref|YP_008796864.1| 28 QAIKQALQDAGITQKDVGFVSVAN 51
                                      78*****************98765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0076
                                       HHHHHHHHHHHHHHHT--G....GGEEEEE-SS CS
                   Ketoacyl-synt_C  23 geaqaraiekalaeagvdp....edvdyveahg 51 
                                        +a ++a ++a+++agvdp    ++ d+ve h+
  gi|557693810|ref|YP_008796864.1| 256 LRATRKAAAEAYKKAGVDPskpvKSFDVVEVHD 288
                                       5678899***********933334688888887 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.29
                                       -B-GGGHHHHHHHHHHHHHHHT CS
                   Ketoacyl-synt_C  88 GHleaAaGvaelikvvlalkhg 109
                                       GH  +A Gv  ++ + ++l+++
  gi|557693810|ref|YP_008796864.1| 336 GHPIGATGVSMAAEITKQLRQE 357
                                       9********9999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2823.67
//
Query:       gi|557693811|ref|YP_008796865.1|  [L=182]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   59.0   0.0    5.3e-16   58.4   0.0    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    5.9e-08   32.4   0.1    1.2e-07   31.5   0.1    1.5  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)


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 !   58.4   0.0   5.9e-20   5.3e-16       1      64 [.     103     166 ..     103     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 5.9e-20
                                       EEEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE- CS
                     OB_aCoA_assoc   1 wvelsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravf 64 
                                       wve+ g+Gt+ ++tvv+ +p ++  ++ y++++ +++eg  i++++  +dp  +riGm+Vr+v+
  gi|557693811|ref|YP_008796865.1| 103 WVEIRGKGTLITYTVVNVKPASYLHYPDYIIAIARMEEGFNILCWMAVDDPSKLRIGMPVRLVV 166
                                       9************************************************************997 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 !   31.5   0.1   1.3e-11   1.2e-07       1      36 [.      66     101 ..      66     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.3e-11
                           DUF35_N   1 wdaaaegrLvgqrCpdCGtvqfPPravCphCgsddl 36 
                                       +d+++eg++ ++rCp  G ++fPP+a Cp C   +l
  gi|557693811|ref|YP_008796865.1|  66 FDGLKEGKVYATRCPVQGVYFFPPQADCPFCMDENL 101
                                       69*****************************65565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1374.42
//
Query:       gi|557693812|ref|YP_008796866.1|  [L=132]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   67.9   0.1    8.2e-19   67.6   0.1    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
    8.8e-12   45.2   0.0    1.1e-11   44.9   0.0    1.1  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase
      7e-06   25.7   0.0    8.7e-06   25.4   0.0    1.1  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like
  ------ inclusion threshold ------
       0.02   13.7   0.0      0.023   13.5   0.0    1.0  1  HlyD_2          HlyD family secretion protein


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.6   0.1   1.8e-22   8.2e-19       6      87 ..       9      88 ..       4      89 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 1.8e-22
                                      HHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEEEEE CS
                    Putative_PNPOx  6 reflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGtaelv 84
                                      r f+++ ++++lAT de+ +P+v+pv +++ + +  +++at+ d+rkl+n+++n++val+++  + +r v+++G a+++
  gi|557693812|ref|YP_008796866.1|  9 RRFVEANELCRLATTDENSQPHVVPVAYIYYNNK--FYIATDLDTRKLANIRRNNKVALVIDKTNPNRAVMVQGLATIL 85
                                      789*******************************..*****************************************99 PP

                                      SCH CS
                    Putative_PNPOx 85 sdg 87
                                       +g
  gi|557693812|ref|YP_008796866.1| 86 LRG 88
                                      776 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   2.5e-15   1.1e-11       7     126 ..      10     117 ..       6     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 2.5e-15
                                       HHHHC-SEEEEEEEETTE.EEEEEEEEEEETTEEEEEEETTSHCCHCCC.T--ECEEEEEEEEEEE-SEGGEEEEEE CS
                      Pyridox_ox_2   7 alLdegevgrlafvddge.pvilPvnyvvdgdslyfhgakgsrlaaalr.gapvcvvvtevdglvlarsfnslnyrS 81 
                                       ++++++e++rla++d++  p+++Pv+y + ++++y+ +   +r++a +r +++v+ v+ +++             r 
  gi|557693812|ref|YP_008796866.1|  10 RFVEANELCRLATTDENSqPHVVPVAYIYYNNKFYIATDLDTRKLANIRrNNKVALVIDKTNP-----------NRA 75 
                                       68999**********5555***********************999999944447777777555...........388 PP

                                       EEEEEEEEEE--HHHHHHHCCCHHHHHSTTTGGCSB---CCCCCT CS
                      Pyridox_ox_2  82 VvvrGraeevtdeeekaealellvekivpgrwenlrpptrkelka 126
                                       V+v+G a+ +   ee +++ + + ++++   w    p +++e + 
  gi|557693812|ref|YP_008796866.1|  76 VMVQGLATILLRGEEYRTVYKIFYDRFA---WVRRDPWQEGEAAF 117
                                       ************************9993...44333444555444 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.9e-09   8.7e-06      10      87 ..      12      87 ..       8     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.9e-09
                     Pyrid_ox_like 10 vkdiktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdeskkkyvsvsGtaevved 87
                                      v+  + + L+tt+++++ ++ P a   +  +++++  t+ d++k ++ir++++v l++ +++ +  v+v+G a++   
  gi|557693812|ref|YP_008796866.1| 12 VEANELCRLATTDENSQPHVVPVAY--IYYNNKFYIATDLDTRKLANIRRNNKVALVIDKTNPNRAVMVQGLATILLR 87
                                      67778999****99999****9875..677899****************************************99754 PP

>> HlyD_2  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.1e-06     0.023     257     296 ..      32      71 ..      12      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.1e-06
                            HlyD_2 257 dpifkivnnqkwYlvtlvekeevkslkegkkvkvkvddee 296
                                        p+++i  n+k Y++t ++  ++++++++ kv + +d+ +
  gi|557693812|ref|YP_008796866.1|  32 VPVAYIYYNNKFYIATDLDTRKLANIRRNNKVALVIDKTN 71 
                                       5899*********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1018.35
//
Query:       gi|557693813|ref|YP_008796867.1|  [L=463]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-69  232.6   0.0    9.2e-69  232.4   0.0    1.1  1  Amidohydro_1  Amidohydrolase family
    6.8e-21   75.3   0.5      5e-15   55.9   0.0    2.3  2  Amidohydro_3  Amidohydrolase family
    0.00051   19.5   0.0      0.001   18.5   0.0    1.4  1  A_deaminase   Adenosine/AMP deaminase


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 !  232.4   0.0   1.5e-72   9.2e-69       2     344 .]      59     424 ..      58     424 .. 0.94

  Alignments for each domain:
  == domain 1  score: 232.4 bits;  conditional E-value: 1.5e-72
                                       EEE-EEEEEEECETTECSSS.....GHHHHH..........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHH CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrga.....tledwl..........vppetaaealesgiktalksGtttvadmgattstgi 63 
                                       ++PGlID+HvHl q llrg+     tl  wl           + ++a++ ++ +i ++lk Gtt++++++ +  +g+
  gi|557693813|ref|YP_008796867.1|  59 IIPGLIDTHVHLAQALLRGVvpdnlTLIPWLrdwvwrflgvYDNMDAKASAALCILEMLKTGTTSFIEIHLHSRYGF 135
                                       89*********************996666667777******9999**************************9888** PP

                                       HHHHHHHHTSSSEEEEEEESSEGGS............GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCC CS
                      Amidohydro_1  64 ealleaaeelplglrilggkvsldr............gsaetskasreklkagaaetikgkadgvvkvalapheapa 128
                                       + ++e +++   g+r +++k+++d+            +  e  +a+++++k+   +++ g adg+++v+l+ ++a a
  gi|557693813|ref|YP_008796867.1| 136 DGIAEVVKQS--GIRGVLSKTIMDMkgyateenlmppSMIEDGEACIREFKQMY-QKWNGQADGRIDVWLGLRSAGA 209
                                       *********9..*************************88888889999998885.999******************* PP

                                       SHHHHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHH CS
                      Amidohydro_1 129 fsdeelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteael 205
                                       +sd + +ea++ ak++d+ ++ H++e +++ e+ ++a+g     ++   ++e++ +l+e k + ah+v+l  ++++ 
  gi|557693813|ref|YP_008796867.1| 210 VSDKLFYEAAEIAKEYDTGITNHVAEVREDLEYYRRAYG-----TGVAGYLEKFNMLGE-KHVYAHCVWLNEEDMKK 280
                                       ***************************************.....56666667799****.***************** PP

                                       HHHHHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTT..TTHCHC CS
                      Amidohydro_1 206 lkerlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllye..deeggl 280
                                        +e   ++ v+hcp+sn++l+sg++++ ++l+ Gv+v+lg+Dg  s++s ++++e+++a+ lq++   +  d+++ +
  gi|557693813|ref|YP_008796867.1| 281 FAET--GTTVSHCPSSNMKLGSGIAPVSDMLKHGVNVALGCDGGPSNDSYDMIREMKMAACLQKV---RtlDPRV-I 351
                                       ****..******************************************************77773...2469899.* PP

                                       HHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC.....CT....CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 281 slkealrmaTingAkalglddkvGsievGkdADlvvvdl.....di....laafvglkkdgnvkkvivkGklv 344
                                       s+ ++l+maT ngA+a+g  + +Gs+e+Gk+AD+v+v l     ++     + +v+ ++   v+ v+++Gk v
  gi|557693813|ref|YP_008796867.1| 352 SAWDVLTMATRNGARAMGKLNMLGSLEPGKKADIVIVSLtrpsvTPisnpVSLLVYAASGADVRDVMIDGKFV 424
                                       ***************************************976652267779*******************986 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.7e-07    0.0022       1      25 [.      50      74 ..      50      83 .. 0.90
   2 !   55.9   0.0   8.3e-19     5e-15     309     473 .]     264     425 ..     218     425 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.7e-07
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlaggg 25
                                      ev+Da+ +l +PG++D H Hla + 
  gi|557693813|ref|YP_008796867.1| 50 EVVDAEKCLIIPGLIDTHVHLAQAL 74
                                      79******************99876 PP

  == domain 2  score: 55.9 bits;  conditional E-value: 8.3e-19
                      Amidohydro_3 309 r.rlehaegvtesqiervaalqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsD..apvgpfd 382
                                           +h+ +++e++++++a+ + + + +p +n            + ++g++pv  +l++gv+valg D  +  +++d
  gi|557693813|ref|YP_008796867.1| 264 KhVYAHCVWLNEEDMKKFAETGTTVSHCPSSNM-----------KLGSGIAPVSDMLKHGVNVALGCDggPSNDSYD 329
                                       4477899999*******************9999...........78999*******************9999999** PP

                      Amidohydro_3 383 pwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.........adpl 450
                                        + ++  a  ++++r      + + +s  ++l + Tr++A+a+g+    G+Le+G++AD+v+ +          +p+
  gi|557693813|ref|YP_008796867.1| 330 MIREMKMAACLQKVRTL----DPRVISAWDVLTMATRNGARAMGKLNMLGSLEPGKKADIVIVSltrpsvtpiSNPV 402
                                       *************7665....999****************************************7555544443333 PP

                      Amidohydro_3 451 dvdppelaear.........vrltvvdGrvvy 473
                                                 +         vr +++dG++v+
  gi|557693813|ref|YP_008796867.1| 403 S---------LlvyaasgadVRDVMIDGKFVV 425
                                       3.........2355556666999999999996 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.7e-07     0.001     232     297 ..     279     341 ..     269     351 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-07
                                       HHHHHCT-EEEE-HHHHCCCSST-TTTT-CHHHHHHTT-EEEE--BS.CCCCT-SHHHHHHHHHHHH CS
                       A_deaminase 232 yllalaqiplevcPlSNvalgafleyaenPlkeflerglnvslntDD.PlqfgttLieeYaiaaqvf 297
                                       +++a+  +++  cP+SN++l         P+ + l++g+nv+l+ D  P   ++++i e+++aa   
  gi|557693813|ref|YP_008796867.1| 279 KKFAETGTTVSHCPSSNMKL----GSGIAPVSDMLKHGVNVALGCDGgPSNDSYDMIREMKMAACLQ 341
                                       678899999***********....66788*****************735555666********9665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3469.31
//
Query:       gi|557693814|ref|YP_008796868.1|  [L=339]
Description: coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-56  191.1   0.4    3.8e-56  190.8   0.4    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.8   0.4   2.1e-60   3.8e-56      20     313 ..      22     316 ..      10     317 .. 0.88

  Alignments for each domain:
  == domain 1  score: 190.8 bits;  conditional E-value: 2.1e-60
                    Bac_luciferase  20 aslrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhl 96 
                                        +lr+  ++ar+aE+ Gf+++w +e+ +     +d++  +aal a+Te+i+lgt+v+ ++tr+ ++lA ++ tLd+l
  gi|557693814|ref|YP_008796868.1|  22 TPLRDEMDYARLAERGGFTSIWQGESRTS----RDSTISIAALGAVTEKIKLGTGVLHTWTRNVVTLATTFTTLDEL 94 
                                       389999**********************9....******************************************** PP

                    Bac_luciferase  97 sgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaa 173
                                       ++GR+ lg+g  + +    + G+++++ ++ + E v+vl++l++geev feGef++v+g++l   p q  +Pvyv+a
  gi|557693814|ref|YP_008796868.1|  95 TNGRACLGIGVLWEPMA-SKIGIERRKTLQAMFEHVTVLKKLFSGEEVFFEGEFVKVRGVRLERVPSQ--VPVYVGA 168
                                       ***********999888.899************************************99999999965..5****** PP

                    Bac_luciferase 174 aspaglelaarhadglllag.eppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearaliagld 249
                                       ++ +++ela+++adg+ll+   +pe  ++++++++ ga++agr  +di+    l v++  + e+A ++ar ++a++ 
  gi|557693814|ref|YP_008796868.1| 169 TGFKMMELAGEIADGVLLNYlVSPEYNRKALQHIENGAKKAGRKLDDIDRPQLLAVAYSVDLEKAYRRARLMVAEYL 245
                                       *********************************************************************55555554 PP

                    Bac_luciferase 250 ......fyaldsegagreaeaa.eiqeeedanlwagaadavpdelvaatal.vGtpeqvaerlaayaeagvd 313
                                             + a+  ++   ++ ++ + + + + ++ ++a+++v de +a+t++ vG+ ++v  ++ +y+eag +
  gi|557693814|ref|YP_008796868.1| 246 amephiALASGVSEKITGEIREiTGGWPTTERKLEQAMELV-DEKLASTLMaVGDLKTVKRKIIEYVEAGCT 316
                                       55566533333333333333335668888888889999998.5555555555******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2599.25
//
Query:       gi|557693815|ref|YP_008796869.1|  [L=445]
Description: N-ethylammeline chlorohydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-49  169.4   0.0    1.5e-49  169.1   0.0    1.0  1  Amidohydro_1  Amidohydrolase family
    5.8e-20   72.2   1.7    2.9e-16   60.0   0.1    2.4  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 !  169.1   0.0   1.7e-53   1.5e-49       1     344 []      63     416 ..      63     416 .. 0.90

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 1.7e-53
                                       EEEE-EEEEEEECETTECSSS.......GHHHHH...........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSS CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga.......tledwl...........vppetaaealesgiktalksGtttvadmgatt 59 
                                       i+lPGl+ aH H ++ l  g+       +++d+l           ++++ a++a+  ++++ l+ Gtt vad+ ++ 
  gi|557693815|ref|YP_008796869.1|  63 IILPGLVSAHDHMYGVLAHGIpvksqlkDFWDFLknfwwpyvedrLDKNLAEAAVHYAAAERLRTGTTCVADILEA- 138
                                       79***********97777777999*888888888*****************************************5. PP

                                       THHHHHHHH....HHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHH.CTTTCEEEEEEECGTCCSHH CS
                      Amidohydro_1  60 stgiealle....aaeelplglrilggkvsldrgsaetskasreklkagaaetikg.kadgvvkvalapheapafsd 131
                                       +++++ +le    a+e+l  glr+++++   +r s+e+ +   e+ k+ +   +k  + + +vk     h  +++s+
  gi|557693815|ref|YP_008796869.1| 139 PNALPNVLEtearAVESL--GLRAVLSFEATERMSPENGIQGLEENKRFI---EKMnTRPRLVKGMHCLHTTFTCSP 210
                                       555555555544488887..*************88888888888887776...33304556667999********** PP

                                       HHHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHH CS
                      Amidohydro_1 132 eelkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellke 208
                                       + ++ +   a+  ++ ++iH+ e ++e ++a++++g     +++   +e+lg+ ++  +++ ++v  t +e+++l++
  gi|557693815|ref|YP_008796869.1| 211 DFIRRCRADADMTKAGIHIHFEEGSYETQQALKKYG-----KYPAQLYEELGFWRD-DVLASQCVKTTSDELNILAK 281
                                       ************************************.....55*************.***********99******* PP

                                       HHHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHH CS
                      Amidohydro_1 209 rlkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkea 285
                                       +  +++++h p sn  ++ g++++ ++l++G+ v lgtD    g  ++++e +r+  ++++  ++++ +g ++++ +
  gi|557693815|ref|YP_008796869.1| 282 Y--DVKISHQPLSNGEVGGGIAPVPEMLQRGLTVCLGTD----GFIVDMFEVMRNTWLIHK--AAKENAGVMPAETV 350
                                       *..************************************....9999**********9999..4444588899999* PP

                                       HHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC...CT......CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 286 lrmaTingAkalglddkvGsievGkdADlvvvdl...di......laafvglkkdgnvkkvivkGklv 344
                                       +rmaT ngAk lg   + G+ie+G++ADlv++     ++      l+++v  ++  +v++viv+Gk+v
  gi|557693815|ref|YP_008796869.1| 351 FRMATENGAKTLGY--RGGRIEKGYKADLVLLQNkfpTPvtpenvLTQVVVYASGSWVDTVIVDGKVV 416
                                       **************..****************8876633777999*********************98 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.3   1.8e-05      0.16       1      25 [.      55      79 ..      55      88 .. 0.91
   2 !   60.0   0.1   3.2e-20   2.9e-16     291     473 .]     240     417 ..     107     417 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.8e-05
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlaggg 25
                                      +++Da+G++ lPG+v +H H++g+ 
  gi|557693815|ref|YP_008796869.1| 55 KTVDASGMIILPGLVSAHDHMYGVL 79
                                      68******************99875 PP

  == domain 2  score: 60.0 bits;  conditional E-value: 3.2e-20
                      Amidohydro_3 291 dvldafeaa....aekngnqdrrrlehaegv.tesqiervaalqvaagvqpvfnfedelldsrlgperargstpvke 362
                                       ++l+ + ++     e++g+     l+ +++  t ++++ +a+  v ++ qp +n            e + g++pv e
  gi|557693815|ref|YP_008796869.1| 240 QALKKYGKYpaqlYEELGFWRDDVLASQCVKtTSDELNILAKYDVKISHQPLSNG-----------EVGGGIAPVPE 305
                                       6666666665555444443322234444444688889999999999999988888...........566789***** PP

                      Amidohydro_3 363 llnagvkvalgsDapvgpfdpwprig..aavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevG 437
                                       +l+ g++v+lg+D   g + ++ +++  +++ +k+++++        ++ e+++++ T+++Ak+lg +   G++e+G
  gi|557693815|ref|YP_008796869.1| 306 MLQRGLTVCLGTD---GFIVDMFEVMrnTWLIHKAAKEN-----AGVMPAETVFRMATENGAKTLGYRG--GRIEKG 372
                                       *************...55555555542268889998775.....999**********************..****** PP

                      Amidohydro_3 438 adADlvvld.adpldvdppelaear........vrltvvdGrvvy 473
                                       ++ADlv+l  + p  v+p+++ +++        v  ++vdG+vv+
  gi|557693815|ref|YP_008796869.1| 373 YKADLVLLQnKFPTPVTPENVLTQVvvyasgswVDTVIVDGKVVV 417
                                       ********96778888888888888******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3121.90
//
Query:       gi|557693816|ref|YP_008796870.1|  [L=774]
Description: molybdenum hydroxylase family, large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-138  462.6   0.0   1.9e-138  462.4   0.0    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    1.4e-18   67.3   0.0    3.6e-18   65.9   0.0    1.8  2  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a
  ------ inclusion threshold ------
       0.14   12.4   0.0        1.8    8.9   0.0    2.3  2  Peptidase_Prp  Cysteine protease Prp


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 !  462.4   0.0  3.1e-142  1.9e-138       3     550 .]     143     708 ..     141     708 .. 0.92

  Alignments for each domain:
  == domain 1  score: 462.4 bits;  conditional E-value: 3.1e-142
                                       TT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHH CS
                     Ald_Xan_dh_C2   3 eeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvae 77 
                                       e+ ++n +a  + ++Gd+   +++a++vve++++t+r++++++Et++++a +d   g ltv+s +q+ph++r++++e
  gi|557693816|ref|YP_008796870.1| 143 EDWENNTMAkfSRKFGDPFHELERAKVVVEERITTHRVAPAPIETRGVVASYDAGRGFLTVWSPNQNPHMHRTVLSE 219
                                       567788888455556************************************************************** PP

                                       HHT--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-E CS
                     Ald_Xan_dh_C2  78 vlglpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGki 154
                                       vl+lpe+k+rvi+p++GGGFG K ++++++v++a++++ tgrpVk++++R+e+++a+++ +++ + +k+gad++G+i
  gi|557693816|ref|YP_008796870.1| 220 VLNLPESKIRVIAPNIGGGFGQKGHTYAEDVVVAALSMLTGRPVKWIEERRENLTAAAQSREQVHLIKIGADRNGRI 296
                                       ***************************************************************************** PP

                                       EEEEEEEEEEESST..HHHCHCCHCCTTGGGT.TTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 155 taldvdlladaGay..adlspavleralshld.gpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdel 228
                                       +al  + + d Gay   ++s   l++++  +  gpY+i+n+ +e+ +v tN++p++a+RGfG+p+a+f+ Er++d l
  gi|557693816|ref|YP_008796870.1| 297 KALIDEAYLDLGAYplIPHSYLELAHVVIDMLpGPYRIENYAAEVSLVATNKTPAGAYRGFGHPEATFVRERALDIL 373
                                       **************4435555555544444445******************************************** PP

                                       HHHHT--HHHHHHHHBCECGCC.SEEET...EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEE CS
                     Ald_Xan_dh_C2 229 AeelgldplelRrrNlikpgeltpygqp...vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvve 302
                                       Aee+gldp+ +R+rNli   ++ p+  +   ++dsg+  e++++l +++  +       +  +g   +G+g+a++v+
  gi|557693816|ref|YP_008796870.1| 374 AEEIGLDPVTIRKRNLISSADI-PCMAAtgmIFDSGRPLETFETLVQQAAHH-------DCGDG-EVVGVGYAVGVK 441
                                       **********************.86555478899999999999999987332.......22233.469********* PP

                                       EBS--S....EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S CS
                     Ald_Xan_dh_C2 303 giglgf...takflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgt 376
                                       g++  +    +++ ++e+a+vr+  dG+ +v++g+++mG+ l+  la+i+++ L vp edv+vv gdt ++p+++g 
  gi|557693816|ref|YP_008796870.1| 442 GSVPTMsgvSQRWGSSEAAMVRLSMDGKPVVFSGAVSMGTRLDKLLAKIVSDILSVPEEDVEVVLGDTLSTPFSTGL 518
                                       **7666766666777799*********************************************************** PP

                                       -TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH........TT CS
                     Ald_Xan_dh_C2 377 aaSrstdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl........er 442
                                       ++Sr+++++g+Av+kA   lr++++ i + l+e++ped+ le+g+v+v+   e+ ++l+ela + y+         +
  gi|557693816|ref|YP_008796870.1| 519 WGSRGAVMVGGAVAKASTMLRKKIQHISSILFECRPEDVVLENGRVFVRdamENGLTLSELAWKVYNhpnmfpqdID 595
                                       *************************************************9988889*********999999996666 PP

                                       SSEEEEEEE........EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 443 vslsatgfykt.....ldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfv 514
                                        sl a++ y++      ++e g+ ++ a+++  a++a V++D+et evkv+++v +   G+ + p+ v+ Q+ GG++
  gi|557693816|ref|YP_008796870.1| 596 LSLMAEALYDPpniwqAPDELGRMNAAAAVSTIACAAFVTLDVETFEVKVKKLVLAENGGTYLSPEDVDEQLIGGAI 672
                                       6999*****99***776667777777789999********************************************* PP

                                       HHHHHHHT---EEETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 515 qGiGlalmEelvydedGqlltasladYkiPtaadiP 550
                                       q++G+ l+Ee+vy+++  ++t+++++Y++Ptaa++P
  gi|557693816|ref|YP_008796870.1| 673 QAYGASLFEEVVYSNEAMPMTTTFSEYLLPTAAETP 708
                                       **********************************98 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 !   65.9   0.0     6e-22   3.6e-18       1     110 []      18     129 ..      18     129 .. 0.88
   2 ?   -4.1   0.0         3   1.8e+04      22      36 ..     625     639 ..     621     642 .. 0.80

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 6e-22
                                       TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT..TSSS-EEEESS-SS CS
                      Ald_Xan_dh_C   1 tGeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig..siledeedallaed 75 
                                       tG+a +vdD+++p++l+  fvrS+++hA +  +++ ++l+  ++++    +++    + +   +  ++ e   la++
  gi|557693816|ref|YP_008796870.1|  18 TGRASFVDDVALPKMLHCVFVRSSYPHAVVHGLRTPENLSEAKIFTWRMLSEIVRPFSLSFpfEGCKRLEVSPLANT 94 
                                       8****************************************9776666666666655444455555566689***** PP

                                       EESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                      Ald_Xan_dh_C  76 kvrsvgqavaavvAedeetArkAaklvkveYeelp 110
                                       kvr+vg++vaav+Aed +tA + a+ v+veYe+lp
  gi|557693816|ref|YP_008796870.1|  95 KVRYVGEPVAAVLAEDLYTAYDVANSVEVEYEPLP 129
                                       ********************************986 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3
                                       E-SSSSEEEEEEE-H CS
                      Ald_Xan_dh_C  22 rStkahAkivsidvs 36 
                                        St+a A  v +dv+
  gi|557693816|ref|YP_008796870.1| 625 VSTIACAAFVTLDVE 639
                                       699999999999987 PP

>> Peptidase_Prp  Cysteine protease Prp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0003       1.8      16      74 ..     239     303 ..     234     310 .. 0.64
   2 ?    0.2   0.0      0.15   9.2e+02      34      58 ..     623     646 ..     619     685 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0003
                                       EEEESTSS-SSHHHHHHHHHHHHHHHHHHHHHHHHS----..............TTTTSHHHHHHHHHH CS
                     Peptidase_Prp  16 fevsGHAgyaeaGeDiVCAavSalvittvnaleevlkekvelee..........seeekekaqllletl 74 
                                       f  +GH+ ya   eD+V Aa S+l+   v+ +ee  ++     +            + + +++ l+++ 
  gi|557693816|ref|YP_008796870.1| 239 FGQKGHT-YA---EDVVVAALSMLTGRPVKWIEERRENLTAAAQsreqvhlikiGADRNGRIKALIDEA 303
                                       5556776.44...7*******************933333322223334555555444455666666555 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHS----... CS
                     Peptidase_Prp  34 AavSalvittvnaleevlkekvele 58 
                                       AavS+++ ++  +l+  +  +v+++
  gi|557693816|ref|YP_008796870.1| 623 AAVSTIACAAFVTLDV-ETFEVKVK 646
                                       9999999999999983.44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (774 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); 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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 5421.15
//
Query:       gi|557693817|ref|YP_008796871.1|  [L=196]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00015   21.0  26.0    0.00068   18.9  26.2    1.7  1  MASE1     MASE1
  ------ inclusion threshold ------
       0.15   11.5   0.6       0.27   10.7   0.6    1.4  1  FAM70     FAM70 protein


Domain annotation for each model (and alignments):
>> MASE1  MASE1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9  26.2   7.5e-08   0.00068       5     170 ..      16     182 ..      13     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.5e-08
                             MASE1   5 llllyallialglslalalvssggvplW.lPsGlalaalllfgrrgwpgil...laavlasislfllfagnlllala 77 
                                       l++l+++ +a+    +l   +s ++p++ + s ++ ++++  +  +w+gi+   ++++l+ ++++ l + + + a+a
  gi|557693817|ref|YP_008796871.1|  16 LVALFIVSAAITA--VLGAFGSIVFPFLaPISSFYPGVAFQVSFGVWFGIVgalAGGFLGPFIGIVLTGTSAPIAAA 90 
                                       5556666666665..5556667777777777778888888888888888888879999999**************** PP

                             MASE1  78 iaavntleallgalllrrllpsrnrletlkdwllfvvaaaiiaalllaiiglalllllgliplaslssswltwwlgs 154
                                       +a++++++a++  l++r   ++++ +++  dw++ +v+ +iia +++a+ig+++l+++g +p +   ++wl w+ ++
  gi|557693817|ref|YP_008796871.1|  91 VAVGDFFQAFIPMLAFRLGKFDPRLKSSK-DWAGHIVFNVIIAQAVGATIGSGSLAAFGVFPWDIWPIAWLGWFGSN 166
                                       ******************99999999998.*****************************888777777777777777 PP

                             MASE1 155 atGvlvvaplllllrr 170
                                       ++ v v++  l+ ++ 
  gi|557693817|ref|YP_008796871.1| 167 VVVVGVITTILFKVFS 182
                                       7777777766666665 PP

>> FAM70  FAM70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.6     3e-05      0.27      18      73 ..       9      66 ..       1      68 [. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3e-05
                             FAM70 18 rrkrtsllvtvsLLvvsvlil.tvGLaattrten.vtvggyYpGii..LgfGsfLGiiGi 73
                                      rr  +s    v+L++vs  i  ++G   +       +++++YpG+   ++fG ++Gi+G+
  gi|557693817|ref|YP_008796871.1|  9 RR--RSPTTLVALFIVSAAITaVLGAFGSIVFPFlAPISSFYPGVAfqVSFGVWFGIVGA 66
                                      33..3444556788888777525677666655541579*******73469*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1459.60
//
Query:       gi|557693818|ref|YP_008796872.1|  [L=275]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   88.8  13.5    3.9e-25   88.8  13.5    1.6  2  CbiQ      Cobalt transport protein
  ------ inclusion threshold ------
       0.63    9.7   2.2        1.2    8.8   2.2    1.4  1  GET2      GET complex subunit GET2


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 !   88.8  13.5   4.3e-29   3.9e-25       6     215 ..      23     234 ..      18     237 .. 0.85
   2 ?   -1.7   0.6      0.21   1.9e+03      38      64 ..     248     274 ..     242     275 .] 0.67

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 4.3e-29
                                       CS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---....HHHHHHHCCCHCHHHHHHHHHHE..... CS
                              CbiQ   6 hrldprvkliwlfllllalvlapnlvtlliiiallllllllvilp....rvlaqalilpllflllgllillfqlitt 78 
                                        ++ p vkl++++ +++a+ l pn  ++l+  +l+ ++++++ +p    r+++++++  +++l+  + + +f    +
  gi|557693818|ref|YP_008796872.1|  23 VKVHPAVKLFVVIVFSFAALLTPNHSLALVNLILISVTVVVARVPakalRLYTFVIG--WMLLVSFIFYSFF-TPIR 96 
                                       568899*******************99977777777777777777766556666555..3333333333333.3446 PP

                                       ..EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHH CS
                              CbiQ  79 egefvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLle 155
                                       +g ++ ++g  ++i +e+ +  ll+al++l+++ +++ll++TT+  +l+ +l++++ P +++++++ ++R + ++  
  gi|557693818|ref|YP_008796872.1|  97 SGPVMATIGP-LKIGYENFMAWLLVALKFLAVSYVTALLLATTKHRDLAVALRTWRLPYVVSFTFASILRNLAVVSV 172
                                       8899999999.****************************************************************** PP

                                       HHHHHHHHHHHTTTTS...SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS..... CS
                              CbiQ 156 evqrikqAqklRlgds.klgirrslrslgkliaalflralkraervalAmeaRGYtg.seer 215
                                        + +i +Aq++R++++ k +  ++l +  ++ ++l+  +lkr+e++  Am++RG++  +e+ 
  gi|557693818|ref|YP_008796872.1| 173 DLFTIIDAQSSRGLNFrKGNPIQRLAKFVRVGIPLIYVSLKRTEEMSNAMASRGFKVrGEKT 234
                                       *****************9888888*******************************9855554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.21
                                       HHHHHHHTTS---HHHHHHHCCCHCHH CS
                              CbiQ  38 allllllllvilprvlaqalilpllfl 64 
                                       ++ l++l lvi+  vl+  l +p +++
  gi|557693818|ref|YP_008796872.1| 248 VAGLFTLHLVIVLAVLLGLLKFPNFLF 274
                                       567777777777777776666665554 PP

>> GET2  GET complex subunit GET2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.2   0.00013       1.2     180     254 ..      68     146 ..      60     170 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00013
                              GET2 180 vkklkarfllvrllllllnfvYhvfrssks.alvralteas..vrnFftv.FltfEvvllsiyylllkkiekenkvk 252
                                       +k l++++ ++ ++ll+ +++Y +f++ +s  ++ ++ + +   +nF+ +  +++  +++s+   ll   +k+ +++
  gi|557693818|ref|YP_008796872.1|  68 AKALRLYTFVIGWMLLVSFIFYSFFTPIRSgPVMATIGPLKigYENFMAWlLVALKFLAVSYVTALLLATTKHRDLA 144
                                       6889**********************999974444444444556899866156888888888888887777776666 PP

                              GET2 253 tl 254
                                        +
  gi|557693818|ref|YP_008796872.1| 145 VA 146
                                       55 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:                      260  (0.0145016); 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):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1933.35
//
Query:       gi|557693819|ref|YP_008796873.1|  [L=427]
Description: amidohydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-07   31.8   0.3    0.00021   20.9   0.1    2.3  2  Amidohydro_3  Amidohydrolase family
    1.9e-06   27.5   0.2     0.0038   16.6   0.0    2.2  2  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 !   20.9   0.1   2.4e-08   0.00021       2      25 ..      51      74 ..      50     111 .. 0.80
   2 !    8.8   0.0   0.00011         1     412     472 ..     311     380 ..     305     380 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.4e-08
                      Amidohydro_3  2 viDakGrlvlPGFvDsHtHlaggg 25
                                      viDa+G++v P ++D+HtHl  g 
  gi|557693819|ref|YP_008796873.1| 51 VIDADGMTVSPTLIDPHTHLSFGD 74
                                      9******************76554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00011
                      Amidohydro_3 412 ealalyTrgpAkalgled...rkGtLevGadADlvvldadpldvdppelaear......vrltvvdGrvv 472
                                       +a+a+ T +    +g+     + G +e+G  +Dl v da p  v  ++l +++      +  ++vdG+ v
  gi|557693819|ref|YP_008796873.1| 311 KAIATATGNILDCYGKYSeefNMGKIEPGRAGDLLVMDAPPGSVGNDALESIEagdmigIAGVIVDGNLV 380
                                       55555555555555544433366**********************99999999999999********977 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.1   8.5e-05      0.76       1      18 [.      58      75 ..      58     113 .. 0.74
   2 !   16.6   0.0   4.2e-07    0.0038     243     344 .]     278     380 ..     263     380 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 8.5e-05
                                      EEEE-EEEEEEECETTEC CS
                      Amidohydro_1  1 ivlPGlIDaHvHleqsll 18
                                      +v P lID H+Hl+++ +
  gi|557693819|ref|YP_008796873.1| 58 TVSPTLIDPHTHLSFGDF 75
                                      589**********87753 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.2e-07
                                       EEEEECT.TSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TT...TSSSS-TTSB--EE CS
                      Amidohydro_1 243 glgtDga.asgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalgldd...kvGsievGkdADlv 315
                                       ++g+D   + g  +  + + +l l          + +gl++++a++ aT n  +++g ++   + G+ie+G+  Dl 
  gi|557693819|ref|YP_008796873.1| 278 IVGSDTPtGQGYLPVAIHRAILFL---------SSICGLPAEKAIATATGNILDCYGKYSeefNMGKIEPGRAGDLL 345
                                       566665533333333333333333.........44699*******************9765558************* PP

                                       EECCCT.......CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 316 vvdldi.......laafvglkkdgnvkkvivkGklv 344
                                       v+d  +       l++++       +++viv+G+lv
  gi|557693819|ref|YP_008796873.1| 346 VMDAPPgsvgndaLESIEAGDM-IGIAGVIVDGNLV 380
                                       ****555677665666666644.5699999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3219.52
//
Query:       gi|557693820|ref|YP_008796874.1|  [L=281]
Description: cobalt/nickel ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-28   97.7   0.0    1.3e-27   97.0   0.0    1.4  1  ABC_tran      ABC transporter
    1.4e-08   34.9   0.4     0.0012   18.7   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    7.2e-05   22.7   0.1      0.001   18.9   0.0    2.0  2  AAA_15        AAA ATPase domain
    0.00017   21.9   0.2     0.0043   17.3   0.2    2.4  1  AAA_22        AAA domain
    0.00058   19.4   0.2     0.0065   15.9   0.2    2.2  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00074   19.2   0.1     0.0013   18.4   0.1    1.3  1  AAA_29        P-loop containing region of AAA domain
    0.00083   19.1   0.0     0.0022   17.7   0.0    1.7  1  AAA_30        AAA domain
     0.0021   17.5   0.0     0.0035   16.7   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0031   17.5   0.1      0.044   13.8   0.0    2.3  2  AAA_5         AAA domain (dynein-related subfamily)
     0.0034   17.3   0.2      0.045   13.6   0.0    2.2  2  NTPase_1      NTPase
     0.0041   17.5   0.1     0.0083   16.5   0.1    1.8  1  AAA_16        AAA ATPase domain
     0.0045   16.7   0.0     0.0092   15.7   0.0    1.6  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
     0.0056   16.6   0.1      0.015   15.2   0.1    1.7  1  NACHT         NACHT domain
      0.006   15.3   0.0       0.19   10.3   0.0    2.0  2  AAA_13        AAA domain
     0.0063   17.0   0.1      0.011   16.2   0.1    1.4  1  AAA_23        AAA domain
     0.0097   15.6   0.2        0.2   11.4   0.0    2.4  2  AAA_24        AAA domain
  ------ inclusion threshold ------
      0.011   15.9   0.3      0.024   14.8   0.3    1.8  1  AAA_33        AAA domain
      0.011   14.9   0.7      0.024   13.8   0.7    1.8  1  NB-ARC        NB-ARC domain
      0.012   15.0   0.4       0.52    9.6   0.0    2.2  2  ATPase        KaiC
      0.012   16.0   0.1       0.04   14.4   0.1    2.1  1  AAA           ATPase family associated with various cellular 
      0.016   15.7   0.1       0.11   13.0   0.0    2.2  2  AAA_18        AAA domain
       0.02   14.5   0.0      0.053   13.1   0.0    1.6  2  SRP54         SRP54-type protein, GTPase domain
      0.023   14.3   0.0      0.054   13.1   0.0    1.6  1  AAA_25        AAA domain
      0.025   14.1   0.1       0.26   10.7   0.1    2.1  2  RecA          recA bacterial DNA recombination protein
      0.048   13.4   0.0        0.1   12.3   0.0    1.5  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.051   13.5   0.1       0.42   10.5   0.0    2.1  2  ATPase_2      ATPase domain predominantly from Archaea
      0.058   13.1   0.2       0.63    9.8   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
      0.065   12.4   0.0       0.15   11.2   0.0    1.7  1  G-alpha       G-protein alpha subunit
      0.076   12.5   0.2         11    5.4   0.0    2.2  2  Pox_A32       Poxvirus A32 protein
       0.09   12.7   0.1       0.21   11.5   0.1    1.6  1  RsgA_GTPase   RsgA GTPase
      0.092   12.7   0.0       0.18   11.8   0.0    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.14   11.6   0.0       0.34   10.3   0.0    1.6  2  KTI12         Chromatin associated protein KTI12
       0.21   11.8   0.5        1.3    9.2   0.1    2.3  3  AAA_28        AAA domain
       0.22   11.9   1.2       0.93    9.8   1.0    2.1  2  AAA_19        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 !   97.0   0.0   2.5e-30   1.3e-27       1     136 [.      23     168 ..      23     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 2.5e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltv 76 
                                       l+nv++++++ge va++G+nG+GK+tL+k + gllkpt+G+i + g d++e +   l k++g+++q+ ++    +tv
  gi|557693820|ref|YP_008796874.1|  23 LNNVNITIRRGEFVALIGHNGSGKTTLAKHINGLLKPTSGQIIVHGIDTREASVADLAKKVGYVFQNpDHQLCMKTV 99 
                                       79*****************************************************************6445555559 PP

                                       HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        e+             e ++ ++++l+ +gl++ +d +       LS   + rval+ +l  +p+ l++DEpt
  gi|557693820|ref|YP_008796874.1| 100 WEElafgprnlgtpedEVKQVVDEILRLFGLEHYRDVHP----FLLSRADRLRVALCSVLTMRPETLVVDEPT 168
                                       9999********997777777************777776....*****************************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 !   14.7   0.1   3.8e-05      0.02       1      23 [.      35      57 ..      35      85 .. 0.81
   2 !   18.7   0.0   2.3e-06    0.0012     244     302 ..     149     203 ..     102     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      + +liG NgsGK++L + + +l 
  gi|557693820|ref|YP_008796874.1| 35 FVALIGHNGSGKTTLAKHINGLL 57
                                      679************99998885 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.3e-06
                            AAA_21 244 llalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSplll 302
                                       + al + l  ++    +l++DEp +g + +   +++e+lk+l+++g  v++ TH+  l+
  gi|557693820|ref|YP_008796874.1| 149 V-ALCSVLTMRP---ETLVVDEPTTGQDMRQSYEVMEILKKLHKEGRTVVFITHNMRLV 203
                                       3.6777777777...89**************************************9887 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   1.9e-06     0.001      16      50 ..      25      60 ..      22     106 .. 0.78
   2 ?    1.7   0.0      0.31   1.6e+02     325     365 ..     160     199 ..     154     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-06
                            AAA_15 16 dveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      +v i +    +  liG+N+sGK+++++ ++ +l+ +
  gi|557693820|ref|YP_008796874.1| 25 NVNITIRRGeFVALIGHNGSGKTTLAKHINGLLKPT 60
                                      566666665699*****************9999876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.31
                            AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        +l+++EP + +   + +++++ lk+l ++++  v++ TH+
  gi|557693820|ref|YP_008796874.1| 160 ETLVVDEPTTGQDMRQSYEVMEILKKLHKEGR-TVVFITHN 199
                                       6799***************************9.78888997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.2   8.1e-06    0.0043       4     116 ..      32     187 ..      29     204 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 8.1e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee............................erpevv....fvtlp 48 
                                       +  +++++G+ G+GKTtl++ +   l+  + +                               + ++v     + + 
  gi|557693820|ref|YP_008796874.1|  32 RGEFVALIGHNGSGKTTLAKHINGLLKPTSGQIIvhgidtreasvadlakkvgyvfqnpdhqLCMKTVweelAFGPR 108
                                       56799*****************9999644333337777777777777775555555544444333333444422222 PP

                            AAA_22  49 sst....sskdllrellralglelka.....erlsseellealeqalraravielliiDE...aqhlr.seealeeL 112
                                       +++    + k++  e+lr +gle+ +        + ++l+ al   l  r     l++DE    q +r s e++e L
  gi|557693820|ref|YP_008796874.1| 109 NLGtpedEVKQVVDEILRLFGLEHYRdvhpfLLSRADRLRVALCSVLTMRPE--TLVVDEpttGQDMRqSYEVMEIL 183
                                       2222223455555555555555555577776666666666666666666655..77777733334444445555555 PP

                            AAA_22 113 rsll 116
                                       ++l+
  gi|557693820|ref|YP_008796874.1| 184 KKLH 187
                                       5555 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 !   15.9   0.2   1.2e-05    0.0065      24      94 ..      33      98 ..      12     218 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                                      SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEE.EEEEEEEETTEESSSSS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkka.eveitfdnedkklkiek 94
                                       +f a++G+NGSGK+ l   i           l+ ++ + ++h   ++e + ++ a +v  +f+n+d++l +++
  gi|557693820|ref|YP_008796874.1| 33 GEFVALIGHNGSGKTTLAKHING--------LLKPTSGQIIVHGidTREASVADLAkKVGYVFQNPDHQLCMKT 98
                                      4699*************999932........4666666667776653444444444258888888888855544 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   0.1   2.5e-06    0.0013      14      49 ..      25      60 ..      20      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.5e-06
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                      +  i+i++ +++ l+G++GsGK+Tl   i+ lL p+
  gi|557693820|ref|YP_008796874.1| 25 NVNITIRRGEFVALIGHNGSGKTTLAKHINGLLKPT 60
                                      5678898667***************88888887776 PP

>> AAA_30  AAA domain
   #    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      17     121 ..      32     195 ..      25     204 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.3e-06
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv..Laeelgieastiakllkrlk.......... 81 
                                       +  +++l G  G+GKtt+ k+++ +++   g++i+     + A v  La+++g   ++ ++ l   +          
  gi|557693820|ref|YP_008796874.1|  32 RGEFVALIGHNGSGKTTLAKHINGLLKPTSGQIIVHGIDTREASVadLAKKVGYVFQNPDHQLCMKTvweelafgpr 108
                                       445899***********************888888877777776645887777544433333322223445555555 PP

                            AAA_30  82 ............................................grarlepg.tllivDEag....mvdtkqlaall 109
                                                                                   +   l+ + + l+vDE      m  + ++ ++l
  gi|557693820|ref|YP_008796874.1| 109 nlgtpedevkqvvdeilrlfglehyrdvhpfllsradrlrvalcSV--LTMRpETLVVDEPTtgqdMRQSYEVMEIL 183
                                       5555555555555555577777777777777777777777776532..22222666777754111133444455555 PP

                            AAA_30 110 kaaekagakvil 121
                                       k+++k+g +v++
  gi|557693820|ref|YP_008796874.1| 184 KKLHKEGRTVVF 195
                                       555555666665 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   0.0   6.7e-06    0.0035      16      67 ..      27      80 ..      16      99 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.7e-06
                      Mg_chelatase 16 eiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealev..akiasvagkk 67
                                      +i++  g  + l+G  GsGKt lak +++ll p s + ++    ++ asva+  
  gi|557693820|ref|YP_008796874.1| 27 NITIRRGEFVALIGHNGSGKTTLAKHINGLLKPTSGQIIVHGidTREASVADLA 80
                                      566666667899********************9998866653113344555544 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 !   13.8   0.0   8.3e-05     0.044       3      39 ..      37      74 ..      36      81 .. 0.83
   2 ?    1.1   0.0      0.66   3.5e+02      19      48 ..     151     180 ..     144     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.3e-05
                                      EEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HH CS
                             AAA_5  3 lLvGppGtgKselaerlaaal.nreveyvqltrdttee 39
                                       L+G  G+gK++la+++  +l  ++ +++    dt+e+
  gi|557693820|ref|YP_008796874.1| 37 ALIGHNGSGKTTLAKHINGLLkPTSGQIIVHGIDTREA 74
                                      69******************988887777777666665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.66
                                       GGGGBS--EEEEE--TT--HHHHH--B--. CS
                             AAA_5  19 laaalnreveyvqltrdtteedlkgrreik 48 
                                       l+++l+ + e+    + tt +d+++++e++
  gi|557693820|ref|YP_008796874.1| 151 LCSVLTMRPETLVVDEPTTGQDMRQSYEVM 180
                                       566678888999999999999999999986 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   8.6e-05     0.045       2      46 ..      36      84 ..      35      93 .. 0.80
   2 ?    1.3   0.0      0.55   2.9e+02      99     163 ..     162     228 ..     138     231 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.6e-05
                                      EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE-..------E CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfyteevr..eggrrig 46
                                      v++ G+ G+GKtTl k +  llk    ++ v+G+ t+e    +  +++g
  gi|557693820|ref|YP_008796874.1| 36 VALIGHNGSGKTTLAKHINGLLKPTsgQIIVHGIDTREASvaDLAKKVG 84
                                      57889*****************96544899****999975334455555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.55
                                       EEE--..-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE--TTTTTTH CS
                          NTPase_1  99 iviDE..iGkmElkskkfkeaveevLksekpvlavihrrk.dlalveeirerkdvkvfevteenrdal 163
                                       +v+DE   G+   +s ++ e ++++ k+++ v+++ h+ +   +  e+    kd+kvf +++  r+al
  gi|557693820|ref|YP_008796874.1| 162 LVVDEptTGQDMRQSYEVMEILKKLHKEGRTVVFITHNMRlVAEYAERCIIMKDGKVF-IDKPTREAL 228
                                       5566544455556677777888888888888888888886666777777777888888.777777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.6e-05    0.0083      22      51 ..      31      60 ..      22     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.6e-05
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd 51
                                       r+e v l+G+ G+GK++l++++   l+ +
  gi|557693820|ref|YP_008796874.1| 31 RRGEFVALIGHNGSGKTTLAKHINGLLKPT 60
                                      34589****************998655555 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 !   15.7   0.0   1.7e-05    0.0092       8      63 ..      27      83 ..      19     222 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
                                      HS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSS.EEEEEEESEEHHHHHHHHHHC CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  8 lfpivqGqrtlipgafgvGktvisqslskqsnsdd.aiiyvgiGergnevaevleef 63
                                       ++i +G+ ++++g +g Gkt++++++    + ++  ii+ gi  r+ +va++ +++
  gi|557693820|ref|YP_008796874.1| 27 NITIRRGEFVALIGHNGSGKTTLAKHINGLLKPTSgQIIVHGIDTREASVADLAKKV 83
                                      47999*******************888777666655888899666666666555443 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.9e-05     0.015       3      24 ..      36      57 ..      34      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.9e-05
                                      EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                      v+l G +GsGKTtL++++  ++
  gi|557693820|ref|YP_008796874.1| 36 VALIGHNGSGKTTLAKHINGLL 57
                                      899**************97655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00037      0.19      23      39 ..      40      56 ..      33      81 .. 0.83
   2 ?    2.9   0.0     0.063        33     528     580 ..     160     209 ..     154     235 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00037
                            AAA_13 23 GwNGaGKTtLSrllrsl 39
                                      G NG+GKTtL++ ++ l
  gi|557693820|ref|YP_008796874.1| 40 GHNGSGKTTLAKHINGL 56
                                      9************9998 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.063
                            AAA_13 528 kivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkn 580
                                       ++ v+D P    D   ++ v+  +k+     k+ + +   THn+ +  e  ++
  gi|557693820|ref|YP_008796874.1| 160 ETLVVDEPTTGQDMRQSYEVMEILKKLH---KEGRTVVFITHNMRLVAEYAER 209
                                       6789***********************8...777777778****998887665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.2e-05     0.011      10      40 ..      23      54 ..      15      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.2e-05
                            AAA_23 10 frdqeidFsk.gltlItGpNGaGKTTildAik 40
                                      +++++i   +  +++++G+NG+GKTT+   i 
  gi|557693820|ref|YP_008796874.1| 23 LNNVNITIRRgEFVALIGHNGSGKTTLAKHIN 54
                                      566777775525789************98876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00037       0.2       5      22 ..      36      53 ..      33      82 .. 0.86
   2 ?    1.7   0.0      0.33   1.8e+02     110     131 ..     178     199 ..     155     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00037
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++++G +g+GKTtlak++
  gi|557693820|ref|YP_008796874.1| 36 VALIGHNGSGKTTLAKHI 53
                                      689*************98 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.33
                            AAA_24 110 efrrllkklqelrknvifiahe 131
                                       e++++lkkl++ + +v+fi h 
  gi|557693820|ref|YP_008796874.1| 178 EVMEILKKLHKEGRTVVFITHN 199
                                       78899999999999*****996 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   4.5e-05     0.024       2      19 ..      36      53 ..      35     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.5e-05
                            AAA_33  2 vllvGlpGsGKstlaerl 19
                                      v l+G++GsGK+tla+++
  gi|557693820|ref|YP_008796874.1| 36 VALIGHNGSGKTTLAKHI 53
                                      679************986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   4.5e-05     0.024      22      44 ..      35      57 ..      29     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.5e-05
                                      EEEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC 22 vvalvGmgGvGKttlakqilnks 44
                                      +val G  G+GKttlak+i+  +
  gi|557693820|ref|YP_008796874.1| 35 FVALIGHNGSGKTTLAKHINGLL 57
                                      89****************98655 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00098      0.52      16      43 ..      30      55 ..      17      99 .. 0.77
   2 ?    3.5   0.1     0.071        37     121     182 ..     160     209 ..     147     245 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00098
                            ATPase 16 ipegrvvlitGepGtGKtifalqFlikg 43
                                      i +g+ v + G+ G+GKt++a++  i+g
  gi|557693820|ref|YP_008796874.1| 30 IRRGEFVALIGHNGSGKTTLAKH--ING 55
                                      7899*****************97..555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.071
                            ATPase 121 krvviDsitglayeekeavaReilrqlvrvlkklgvTailvsekssseeaaggygveefivd 182
                                       + +v+D  t+     +++    +++++++ l+k g T ++++             v+e++  
  gi|557693820|ref|YP_008796874.1| 160 ETLVVDEPTTG----QDMRQSYEVMEILKKLHKEGRTVVFITHNMR--------LVAEYAER 209
                                       55666655554....66777789999999**999999999987332........33333333 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 ?   14.4   0.1   7.5e-05      0.04       2      52 ..      37      89 ..      36     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.5e-05
                                      EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelfke 52
                                       l+G  G GKT+lak +   l+  +  + + g + ++  v + +kk+  +f++
  gi|557693820|ref|YP_008796874.1| 37 ALIGHNGSGKTTLAKHINGLLKptSGQIIVHGIDTREASVADLAKKVGYVFQN 89
                                      699***************99974444577777777777777777777777776 PP

>> AAA_18  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      0.11       1      39 [.      36      87 ..      36     163 .. 0.65
   2 ?    0.1   0.0       2.2   1.1e+03      14      89 ..     182     257 ..     173     271 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00021
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf.............gvnlrdvakenglll 39
                                      ++l G  G+GKttlak+++ +l+                 + d+ak+ g+++
  gi|557693820|ref|YP_008796874.1| 36 VALIGHNGSGKTTLAKHINGLLKPtsgqiivhgidtrEASVADLAKKVGYVF 87
                                      6799**************7776324655555555555555555555555444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 2.2
                            AAA_18  14 lakeLskrlgfgvnlrdvakenglllevdpe..aldeskrldedkldklldaleenss.aleegknlvidghlaele 87 
                                       + k L k+   g+ + ++  + +l+ e+ +     ++ k++ ++ + ++l+ +e+ ++  l  +++ +++ +la+  
  gi|557693820|ref|YP_008796874.1| 182 ILKKLHKE---GRTVVFITHNMRLVAEYAERciIMKDGKVFIDKPTREALTDFEKLRQaQLKPPQVTILSARLANIG 255
                                       45556665...888888888888888888887755666666666666777777776666666666667777777666 PP

                            AAA_18  88 se 89 
                                       +e
  gi|557693820|ref|YP_008796874.1| 256 FE 257
                                       55 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.053       4      48 ..      36      79 ..      34     102 .. 0.84
   2 ?   -2.3   0.0       5.5   2.9e+03     119     132 ..     163     175 ..     139     200 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHH CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQL 48
                                      ++l+G +G+GKTt +  +  llk    ++++   Dt R a v  L
  gi|557693820|ref|YP_008796874.1| 36 VALIGHNGSGKTTLAKHINGLLKPTSGQIIVHGIDT-REASVADL 79
                                      789***********9999999999999999999998.66655554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.5
                                       EEEETTBHTHHHHH CS
                             SRP54 119 lvldattgqeavkq 132
                                       +v + ttgq++ +q
  gi|557693820|ref|YP_008796874.1| 163 VVDEPTTGQDM-RQ 175
                                       22223333332.22 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0    0.0001     0.054      30      50 ..      30      50 ..      24      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +++ge+++l+G+ g+GKttla
  gi|557693820|ref|YP_008796874.1| 30 IRRGEFVALIGHNGSGKTTLA 50
                                      789*****************9 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0005      0.26      33     102 ..      15      84 ..       5      93 .. 0.76
   2 ?    1.0   0.0      0.46   2.4e+02      72     103 ..     181     212 ..     152     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0005
                                       EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEE..EESS----HHHHHHTT CS
                              RecA  33 tissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaaf..idaehaldpkyakklG 102
                                       ++s G +al++      + +G  + + G + sGkttla h+    + ++g++    id+  a  ++ akk+G
  gi|557693820|ref|YP_008796874.1|  15 VYSNGVVALNNVNI--TIRRGEFVALIGHNGSGKTTLAKHINGLLKPTSGQIIVhgIDTREASVADLAKKVG 84 
                                       56777777776432..5889********************98888777665432238888888888888877 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.46
                                       HHHHHHHHTT--EEEEESS----HHHHHHTT- CS
                              RecA  72 haiaeaqkkggvaafidaehaldpkyakklGv 103
                                       +++ +  k+g +++fi  +  l ++ya++  +
  gi|557693820|ref|YP_008796874.1| 181 EILKKLHKEGRTVVFITHNMRLVAEYAERCII 212
                                       56777889999999999999999999987655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0002       0.1       4      24 ..      36      56 ..      34      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0002
                         PduV-EutP  4 illiGkvgsGKttLtqalkge 24
                                      + liG+ gsGKttL+++++g 
  gi|557693820|ref|YP_008796874.1| 36 VALIGHNGSGKTTLAKHINGL 56
                                      679***************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 ?   10.5   0.0   0.00079      0.42       8      69 ..      23      83 ..      17     134 .. 0.75
   2 ?    0.8   0.1      0.73   3.8e+02      38      82 ..     180     224 ..     174     280 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00079
                          ATPase_2  8 lkeleeilerepneiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefi 69
                                      l++++  ++r   e++ + G  gsGKt+L k+i   l   +++ ++  i+ re s + l +++
  gi|557693820|ref|YP_008796874.1| 23 LNNVNITIRR--GEFVALIGHNGSGKTTLAKHINGLLkPTSGQIIVHGIDTREASVADLAKKV 83
                                      5566655665..5677888*************9988844566678888888888877776665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.73
                          ATPase_2  38 keiienledkdkyviyyialreesiskldefieeeeekkklekal 82 
                                       +ei+++l++ +  v++++   +   +++++ i  ++ k +++k++
  gi|557693820|ref|YP_008796874.1| 180 MEILKKLHKEGRTVVFITHNMRLVAEYAERCIIMKDGKVFIDKPT 224
                                       455555555555666666665555555555555444444444444 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 ?    9.8   0.0    0.0012      0.63      44      67 ..      30      53 ..      10      85 .. 0.84
   2 ?    1.2   0.0      0.49   2.6e+02     107     150 ..     157     201 ..     140     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                         IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                      i++ e ++l+G+ G GK+ la  +
  gi|557693820|ref|YP_008796874.1| 30 IRRGEFVALIGHNGSGKTTLAKHI 53
                                      789999**************9765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.49
                         IstB_IS21 107 lkvdllilDdlgllpldqaeaellfeviekry..errsiiitsnlp 150
                                       ++++ l++D+  +   d  ++ +++e+++k    +r+ + it n+ 
  gi|557693820|ref|YP_008796874.1| 157 MRPETLVVDEPTTG-QDMRQSYEVMEILKKLHkeGRTVVFITHNMR 201
                                       56789999997664.4677778889999987622466677888875 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00028      0.15      26      50 ..      36      60 ..      22     275 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                                      EEEEESTTSSHHHHHHHHHHHCS-- CS
                           G-alpha 26 llllGqseSGKsTilkqlkllykkg 50
                                      + l+G+++SGK+T+ k++  l k++
  gi|557693820|ref|YP_008796874.1| 36 VALIGHNGSGKTTLAKHINGLLKPT 60
                                      679***************9888777 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.025        13      16      30 ..      36      50 ..      28      59 .. 0.83
   2 ?    5.4   0.0     0.021        11     178     237 ..     176     235 ..     143     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.025
                           Pox_A32 16 lalvGgsGsGktvyL 30
                                      +al+G  GsGkt+  
  gi|557693820|ref|YP_008796874.1| 36 VALIGHNGSGKTTLA 50
                                      69**********965 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.021
                           Pox_A32 178 llkvlnilrsaeqkkrkvl.iiedsvfsegeariCldsaDesviekeldksillkqfshmk 237
                                         +v++il++ +++ r v+ i ++  +  + a  C++++D +v + +   + l ++f +++
  gi|557693820|ref|YP_008796874.1| 176 SYEVMEILKKLHKEGRTVVfITHNMRLVAEYAERCIIMKDGKVFIDKPTREAL-TDFEKLR 235
                                       46799*****999999998567777777888899*********9999887765.5666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00041      0.21      97     126 ..      30      60 ..       9      89 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00041
                                       CTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  97 lkd.ktsvlvGqSGvGKStLinallpelelk 126
                                       ++  ++++l+G+ G GK+tL +++++ l+  
  gi|557693820|ref|YP_008796874.1|  30 IRRgEFVALIGHNGSGKTTLAKHINGLLKPT 60 
                                       5444999**************9998865544 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00035      0.18      19      40 ..      33      54 ..      11      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00035
                                      TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                      g++++L G  G+GKTtl++++ 
  gi|557693820|ref|YP_008796874.1| 33 GEFVALIGHNGSGKTTLAKHIN 54
                                      778****************985 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00064      0.34       4      40 ..      36      72 ..      34      91 .. 0.86
   2 ?   -2.1   0.0       3.9     2e+03      20      29 ..     181     190 ..     143     236 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00064
                                      EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHH CS
                             KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvviddesl 40
                                      v l G+  sGK+t+ak+++  l+ +  +++v+  ++ 
  gi|557693820|ref|YP_008796874.1| 36 VALIGHNGSGKTTLAKHINGLLKPTSGQIIVHGIDTR 72
                                      7799********************9999999986654 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.9
                                       HHHHHHHHTT CS
                             KTI12  20 eLakaleeek 29 
                                       e+ k+l++e+
  gi|557693820|ref|YP_008796874.1| 181 EILKKLHKEG 190
                                       2222223333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0025       1.3       2      20 ..      36      54 ..      35      81 .. 0.89
   2 ?   -0.2   0.0         2     1e+03      98     154 ..     138     195 ..     120     209 .. 0.67
   3 ?   -1.3   0.0       4.2   2.2e+03      22      43 ..     198     219 ..     181     240 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0025
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      ++++G  ++GKTtl+++++
  gi|557693820|ref|YP_008796874.1| 36 VALIGHNGSGKTTLAKHIN 54
                                      89*************9975 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2
                            AAA_28  98 aeleaaarekrydl..vfllppapeidddgeRredleereaiderlrealrelgipvii 154
                                       + l + a + r +l  v+ ++p+  ++d  +  +d+++  ++ e+l+++ +e g  v+ 
  gi|557693820|ref|YP_008796874.1| 138 PFLLSRADRLRVALcsVLTMRPETLVVDEPTTGQDMRQSYEVMEILKKLHKE-GRTVVF 195
                                       5555566666665544555556666667777778888888888888877776.444444 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.2
                            AAA_28  22 rgypvvpEaareileeklakge 43 
                                       ++++ v+E+a + +  k  k +
  gi|557693820|ref|YP_008796874.1| 198 HNMRLVAEYAERCIIMKDGKVF 219
                                       5778888888777665554444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.0    0.0018      0.93       9      45 ..      32      64 ..      25     203 .. 0.62
   2 ?    0.7   0.1       1.2   6.1e+02     116     135 ..     177     196 ..     156     266 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0018
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeei 45
                                      + + +++++  G+GKT++ khi  ll+ + g    +i
  gi|557693820|ref|YP_008796874.1| 32 RGEFVALIGHNGSGKTTLAKHINGLLKPTSG----QI 64
                                      567899***************9999987774....34 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.2
                            AAA_19 116 elqyrLlkallgekkklllv 135
                                          +++lk+l +e+ +++++
  gi|557693820|ref|YP_008796874.1| 177 YEVMEILKKLHKEGRTVVFI 196
                                       33444555555444434443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 1987.01
//
Query:       gi|557693821|ref|YP_008796875.1|  [L=288]
Description: cobalt/nickel ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-28   98.7   0.0    5.1e-28   98.3   0.0    1.2  1  ABC_tran        ABC transporter
    8.9e-08   32.3   0.1    0.00084   19.2   0.0    2.2  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    4.7e-07   29.5   0.0      1e-06   28.3   0.0    1.5  1  SMC_N           RecF/RecN/SMC N terminal domain
     0.0001   22.6   0.3      0.001   19.3   0.2    2.5  2  AAA_22          AAA domain
    0.00013   22.6   0.1    0.00026   21.6   0.1    1.6  1  AAA_23          AAA domain
    0.00023   20.3   0.0    0.00075   18.6   0.0    1.8  3  T2SSE           Type II/IV secretion system protein
    0.00055   20.4   0.0    0.00098   19.5   0.0    1.5  1  AAA_16          AAA ATPase domain
    0.00059   19.6   0.2      0.021   14.6   0.0    2.1  2  IstB_IS21       IstB-like ATP binding protein
     0.0011   18.5   0.9     0.0028   17.3   0.1    1.9  2  AAA_25          AAA domain
     0.0022   17.7   0.0     0.0043   16.8   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
     0.0095   15.9   1.7      0.053   13.4   0.2    2.1  2  NTPase_1        NTPase
  ------ inclusion threshold ------
      0.012   16.0   1.3       0.16   12.4   1.4    2.5  2  AAA             ATPase family associated with various cellula
      0.013   16.1   0.1      0.041   14.4   0.1    1.9  1  AAA_18          AAA domain
      0.013   15.1   0.0      0.023   14.3   0.0    1.4  1  Peripla_BP_4    Periplasmic binding protein domain
      0.018   14.5   0.0      0.037   13.5   0.0    1.4  1  PhoH            PhoH-like protein
       0.02   14.8   0.0       0.07   13.0   0.0    1.8  2  RsgA_GTPase     RsgA GTPase
      0.031   14.5   0.2      0.074   13.3   0.2    1.6  1  AAA_28          AAA domain
       0.05   13.2   0.5       0.16   11.6   0.1    1.9  2  cobW            CobW/HypB/UreG, nucleotide-binding domain
       0.05   13.3   1.7       0.27   10.9   1.7    2.0  1  AAA_30          AAA domain
      0.061   12.1   0.1        7.7    5.2   0.0    2.3  2  ABC_ATPase      Predicted ATPase of the ABC class
      0.081   12.3   0.5       0.65    9.3   0.1    2.2  2  ATPase          KaiC
      0.084   12.3   0.1        2.5    7.5   0.0    2.3  2  TniB            Bacterial TniB protein
      0.085   12.8   0.0       0.14   12.0   0.0    1.5  1  ATPase_2        ATPase domain predominantly from Archaea
       0.11   12.5   0.0       0.21   11.6   0.0    1.5  1  TsaE            Threonylcarbamoyl adenosine biosynthesis prot
       0.12   12.0   0.0        0.2   11.2   0.0    1.3  1  AAA_27          AAA domain
       0.12   12.1   0.0       0.17   11.6   0.0    1.3  1  Cytidylate_kin  Cytidylate kinase
       0.13   12.0   0.1       0.32   10.7   0.0    1.6  1  PduV-EutP       Ethanolamine utilisation - propanediol utilis
       0.14   11.8   0.3       0.52    9.9   0.1    1.9  2  SRP54           SRP54-type protein, GTPase domain
       0.14   12.6   0.0       0.27   11.6   0.0    1.6  1  RNA_helicase    RNA helicase
       0.14   11.4   0.1       0.42    9.9   0.0    1.7  2  DnaB_C          DnaB-like helicase C terminal domain
       0.16   12.0   0.1       0.61   10.1   0.1    2.0  2  AAA_14          AAA domain
       0.16   11.7   0.1       0.32   10.8   0.1    1.6  1  DEAD            DEAD/DEAH box helicase
       0.17   11.6   0.5       0.57    9.9   0.1    1.9  2  AAA_24          AAA domain
       0.19   11.5   0.0       0.35   10.6   0.0    1.4  1  AAA_11          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 !   98.3   0.0   9.6e-31   5.1e-28       1     136 [.      23     173 ..      23     174 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 9.6e-31
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqe.pqlf 71 
                                       l++++++++ege v+i+G++GaGK+tL+ ++agl          G++ + gkd+ + +   + + +g+++q+ ++ f
  gi|557693821|ref|YP_008796875.1|  23 LSDINFSVREGEFVVITGPTGAGKTTLCLAMAGLIPYhyngtLRGKVYVFGKDTYTLSSADMASLVGIVFQDpESQF 99 
                                       689*******************************9888777778899999**********************76677 PP

                                       TTSBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  72 peltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                        +++v+++             e++e++++a++ ++ ++l ++      ++LSgGqkqrva+a+al+ kpk+l+lDEp
  gi|557693821|ref|YP_008796875.1| 100 LTMSVEDEiafglenlalpleEMKERVHEAAKLVKVEDLLERAP----YELSGGQKQRVAIAAALAMKPKVLVLDEP 172
                                       77779999******************************999998....***************************** PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                       t
  gi|557693821|ref|YP_008796875.1| 173 T 173
                                       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 !   11.2   0.0   0.00045      0.24       1      22 [.      35      56 ..      35      86 .. 0.85
   2 !   19.2   0.0   1.6e-06   0.00084     220     294 ..     129     200 ..      92     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00045
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + v++Gp g+GK++L  a+ +l
  gi|557693821|ref|YP_008796875.1| 35 FVVITGPTGAGKTTLCLAMAGL 56
                                      68*************9999988 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.6e-06
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                          +++ +d  e+ ++elS G+k+  a+++al+  +   ++l++DEp   L+P   ++++ +l +l++ g+ +i+
  gi|557693821|ref|YP_008796875.1| 129 AAKLVKVEDLLERAPYELSGGQKQRVAIAAALAMKP---KVLVLDEPTGQLDPIGKEEVVNVLQSLKKQGITIIV 200
                                       5667889999***********************988...9********999994447777777777777777776 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 !   28.3   0.0     2e-09     1e-06      24     196 ..      33     202 ..      24     219 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 2e-09
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEE.EEEEEEETTEESSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkae.veitfdnedkklkiekeev 97 
                                        +f +i+Gp G+GK+ l+ A+  ++  + + +lr + +   ++   + + +s++ a+ v i+f+++++++ + + e 
  gi|557693821|ref|YP_008796875.1|  33 GEFVVITGPTGAGKTTLCLAMAGLIPYHYNGTLRGKVY---VFGkdTYTLSSADMASlVGIVFQDPESQFLTMSVED 106
                                       4799******************99*9999999998865...333233444444444338999***999965555555 PP

                                       EEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkgeseykingkevtkkevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                       +i   ++   +    +++ + + +e ++l++ +++ +    +LSgG+k+ va+a  +A+   kp+   +lDe   +L
  gi|557693821|ref|YP_008796875.1| 107 EIAFGLE---NLALPLEEMKERVHEAAKLVKVEDLLERapyELSGGQKQRVAIAAALAM---KPKV-LVLDEPTGQL 176
                                       5544333...33556666666666666666666665443338***********988776...5665.689******* PP

                                       -HHHHHHHHHHHHHHCTT.SEEEEE- CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxx RF
                             SMC_N 172 Deknvkkvaellkekskn.aQfivis 196
                                       D    ++v+++l++ +k+   +iv+ 
  gi|557693821|ref|YP_008796875.1| 177 DPIGKEEVVNVLQSLKKQgITIIVVE 202
                                       *************9997644555544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   1.9e-06     0.001       4      38 ..      32      83 ..      30     203 .. 0.54
   2 ?   -1.0   0.0       3.6   1.9e+03      73     104 ..     247     277 ..     226     286 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.9e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaee.................e 38
                                      +  ++v+tG++G+GKTtl+  ++   + +++ +                   
  gi|557693821|ref|YP_008796875.1| 32 EGEFVVITGPTGAGKTTLCLAMAGLIPYHYNGTLrgkvyvfgkdtytlssaD 83
                                      56799**************999988876655555444444444444444430 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.6
                            AAA_22  73 lsseellealeqalraravielliiDEaqhlr 104
                                        +  el  +l++ l++      + ++Ea+hl+
  gi|557693821|ref|YP_008796875.1| 247 PQVVELTLLLRKELNTELE-IPITLEEAEHLM 277
                                       5556666667777777777.778899999984 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   4.9e-07   0.00026      14      40 ..      25      54 ..       8     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.9e-07
                            AAA_23 14 eidF...skgltlItGpNGaGKTTildAik 40
                                      +i+F   +  +++ItGp+GaGKTT+  A+ 
  gi|557693821|ref|YP_008796875.1| 25 DINFsvrEGEFVVITGPTGAGKTTLCLAMA 54
                                      48998888899*************987776 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 !   18.6   0.0   1.4e-06   0.00075     118     155 ..      22      59 ..       9      65 .. 0.84
   2 ?   -2.3   0.0       3.6   1.9e+03     132     132 ..     167     167 ..     125     218 .. 0.56
   3 ?   -2.5   0.0       3.9     2e+03      66      74 ..     222     230 ..     167     267 .. 0.53

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                             T2SSE 118 iaevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                       + + ++ +vre   ++++G+Tg GKttl  a+   i+ 
  gi|557693821|ref|YP_008796875.1|  22 VLSDINFSVREGEFVVITGPTGAGKTTLCLAMAGLIPY 59 
                                       5566788999999***************9999888875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                             T2SSE 132 i 132
                                       +
  gi|557693821|ref|YP_008796875.1| 167 L 167
                                       2 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.9
                             T2SSE  66 rplqdarlp 74 
                                       r+l d+ + 
  gi|557693821|ref|YP_008796875.1| 222 RILYDGDFR 230
                                       344444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.9e-06   0.00098      20     107 ..      31     142 ..      23     204 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.9e-06
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaelea 96 
                                       r+g  e v+++G+ G GK++l  + +  +  ++  +lrgk   +++++  +  a+++   +l+  + +++es ++  
  gi|557693821|ref|YP_008796875.1|  31 REG--EFVVITGPTGAGKTTLCLAMAGLIPYHYNGTLRGKVYVFGKDTYTLSSADMA---SLVGIVFQDPES-QFLT 101
                                       444..89****************9999999999999999999997775444444444...777777777444.3333 PP

                            AAA_16  97 wrekleeala..............................a 107
                                        + + e a++                              a
  gi|557693821|ref|YP_008796875.1| 102 MSVEDEIAFGlenlalpleemkervheaaklvkvedllerA 142
                                       33322222223333333333333333333355444444441 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 !   14.6   0.0     4e-05     0.021      44      68 ..      30      54 ..      17      57 .. 0.88
   2 ?    3.0   0.0      0.14        75      82     145 ..     134     199 ..     114     211 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-05
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                      +++ e +v++Gp+G+GK+ l  a++
  gi|557693821|ref|YP_008796875.1| 30 VREGEFVVITGPTGAGKTTLCLAMA 54
                                      678899****************997 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                         IstB_IS21  82 rvedLveelkrarr...dgklaralkrllkvdllilDdlgllpldqaeaellfeviekryerrsiii 145
                                       +vedL+e+   + +   ++++a a++  +k+++l+lD+    +ld   +e++ +v+++  ++  +ii
  gi|557693821|ref|YP_008796875.1| 134 KVEDLLERAPYELSggqKQRVAIAAALAMKPKVLVLDEPT-GQLDPIGKEEVVNVLQSLKKQGITII 199
                                       5666666554444300034455556667788******964.45677777777777766665555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   5.3e-06    0.0028      30      54 ..      30      54 ..      16      57 .. 0.85
   2 ?   -1.1   0.1       2.3   1.2e+03     167     188 ..     183     203 ..     122     204 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5.3e-06
                            AAA_25 30 lpagelallaGapgtGKttlaldla 54
                                      +++ge+++++G++g+GKttl+l +a
  gi|557693821|ref|YP_008796875.1| 30 VREGEFVVITGPTGAGKTTLCLAMA 54
                                      579*******************998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.3
                            AAA_25 167 alvealeriarrtgaavllvhH 188
                                       ++v+ l+++ ++ g+++++v H
  gi|557693821|ref|YP_008796875.1| 183 EVVNVLQSL-KKQGITIIVVEH 203
                                       455555555.566666666666 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 !   16.8   0.0   8.1e-06    0.0043      17      43 ..      28      54 ..      14      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.1e-06
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTllDAiq 43
                                      +++++ g ++++tGp+G+GK+Tl  A++
  gi|557693821|ref|YP_008796875.1| 28 FSVRE-GeFVVITGPTGAGKTTLCLAMA 54
                                      44554.3599*************87776 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.2    0.0001     0.053       2      23 ..      36      57 ..      35      73 .. 0.85
   2 ?    1.7   0.1      0.42   2.2e+02      94     135 ..     162     204 ..     130     224 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                                      EEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlell 23
                                      v+iTGp G GKtTl+  ++ l+
  gi|557693821|ref|YP_008796875.1| 36 VVITGPTGAGKTTLCLAMAGLI 57
                                      79*************9887765 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.42
                                       HHH-EEEE--.-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS CS
                          NTPase_1  94 seadviviDE.iGkmElkskkfkeaveevLksekpvlavihrr 135
                                        ++ v+v+DE  G++    k+    v + Lk++ + ++v+ + 
  gi|557693821|ref|YP_008796875.1| 162 MKPKVLVLDEpTGQLDPIGKEEVVNVLQSLKKQGITIIVVEHI 204
                                       5788999999779999999988888889998666666666544 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   1.4    0.0003      0.16       1      66 [.      36     171 ..      36     224 .. 0.53
   2 ?   -1.3   0.0       5.2   2.7e+03      24      57 ..     213     240 ..     186     250 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0003
                                       EEEESSTTSSHHHHHHHHHHHH..........THE...............EEEEETTTCSSS............... CS
                               AAA   1 vllyGppGtGKTllakavakel..........gve...............fleisgsellsk............... 37 
                                       v+++Gp G GKT+l+ a+a  +          +v+                                          
  gi|557693821|ref|YP_008796875.1|  36 VVITGPTGAGKTTLCLAMAGLIpyhyngtlrgKVYvfgkdtytlssadmaS----------Lvgivfqdpesqfltm 102
                                       5789***************98633333333331223333322222222220..........1333333333334444 PP

                                       .........................................STTHHHHHHHHHHHHHHHTSTSEEEEEET CS
                               AAA  38 .........................................yvgesekkirelfkeakekakpsilfiDE 66 
                                                                                y   + +k r  +++a +++ p++l++DE
  gi|557693821|ref|YP_008796875.1| 103 svedeiafglenlalpleemkervheaaklvkvedllerapYELSGGQKQRVAIAAALAMK-PKVLVLDE 171
                                       4444444455555555555555555555555555555554444444444444444444443.56666665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5.2
                                       HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS CS
                               AAA  24 vefleisgsellskyvgesekkirelfkeakeka 57 
                                        +++ ++g ++l         ++r++fk+a+e +
  gi|557693821|ref|YP_008796875.1| 213 DRLVVMNGGRIL------YDGDFRGFFKDAEEVS 240
                                       556666666666......5667777777777665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   7.7e-05     0.041       1      19 [.      36      54 ..      36      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.7e-05
                            AAA_18  1 IlltGtpGvGKttlakeLs 19
                                      +++tG+ G+GKttl+ + +
  gi|557693821|ref|YP_008796875.1| 36 VVITGPTGAGKTTLCLAMA 54
                                      79*************8765 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.3e-05     0.023      14      88 ..     120     203 ..     108     221 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.3e-05
                                       HHHHHHHHHHHHHTTCEEEEE.ECSTT-H.HHHHHHHHHHHHTT-SEEE.......E--SSHHHHHHHHHHHHHTT- CS
                      Peripla_BP_4  14 saaregleeaakelgaevtvv.gdaenda.aeQvaqiedaiakgvdgii.......vapvdstalapalkkakaaGI 81 
                                       ++++e + eaak  ++e  +  ++ e +  ++Q  +i +a+a ++++++       ++p+  +++  +l+ +k++GI
  gi|557693821|ref|YP_008796875.1| 120 EEMKERVHEAAKLVKVEDLLErAPYELSGgQKQRVAIAAALAMKPKVLVldeptgqLDPIGKEEVVNVLQSLKKQGI 196
                                       468999999999988888888977777777*******************8888888899999*************** PP

                                       EEEEEST CS
                      Peripla_BP_4  82 pVvafds 88 
                                        ++++  
  gi|557693821|ref|YP_008796875.1| 197 TIIVVEH 203
                                       ***9876 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     7e-05     0.037      17      40 ..      31      54 ..      21      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7e-05
                                      HH-SEEEEE--TTSSTTHHHHHHH CS
                              PhoH 17 kkndivfaiGpaGtGKtylavala 40
                                      ++ ++v+++Gp+G+GKt l +a+a
  gi|557693821|ref|YP_008796875.1| 31 REGEFVVITGPTGAGKTTLCLAMA 54
                                      57789****************998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00013      0.07      88     120 ..      21      54 ..       4      82 .. 0.82
   2 ?   -1.2   0.0       3.1   1.6e+03     100     125 ..     165     194 ..     121     207 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinall 120
                                         l++++  +++ +++v+ G++G+GK+tL  a++
  gi|557693821|ref|YP_008796875.1|  21 WVLSDINFSVREgEFVVITGPTGAGKTTLCLAMA 54 
                                       45678888888879***************87665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.1
                                       SEEEEECSTT....SSHHHHHHHHCTT--- CS
                       RsgA_GTPase 100 ktsvlvGqSG....vGKStLinallpelel 125
                                       k+ vl  ++G    +GK  ++n+l++ +++
  gi|557693821|ref|YP_008796875.1| 165 KVLVLDEPTGqldpIGKEEVVNVLQSLKKQ 194
                                       555554455544446777777777765444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   0.00014     0.074       2      20 ..      36      54 ..      35      76 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00014
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      +vitG+ ++GKTtl+ a+a
  gi|557693821|ref|YP_008796875.1| 36 VVITGPTGAGKTTLCLAMA 54
                                      8*************99887 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   0.1    0.0003      0.16       3      18 ..      36      51 ..      34      71 .. 0.88
   2 ?   -0.8   0.0       1.9     1e+03      66      89 ..     181     202 ..     120     222 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                                      EEEEESTTCCHHHHHH CS
                              cobW  3 tvltGflGsGKTtLln 18
                                      +v+tG+ G+GKTtL  
  gi|557693821|ref|YP_008796875.1| 36 VVITGPTGAGKTTLCL 51
                                      79***********975 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.9
                                       TT-HHHHHHHHHHHHTT-SEEEEE CS
                              cobW  66 redllkelealeereerldviliE 89 
                                       +e+++++l++l+++   + +i++E
  gi|557693821|ref|YP_008796875.1| 181 KEEVVNVLQSLKKQG--ITIIVVE 202
                                       344444444444444..4444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.7   0.00051      0.27      18      42 ..      33      57 ..      27     202 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00051
                            AAA_30 18 drvavltGpAGtGKttalkalreaw 42
                                        ++v+tGp G+GKtt+  a++ ++
  gi|557693821|ref|YP_008796875.1| 33 GEFVVITGPTGAGKTTLCLAMAGLI 57
                                      3589************987777665 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 ?    4.6   0.1     0.022        12     242     274 ..      30      63 ..      28      87 .. 0.80
   2 ?    5.2   0.0     0.015       7.7     324     393 ..     147     217 ..     143     226 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.022
                                       E-SS.EEEEEE-TTSSHHHHHHHHHHCCSEE-TT CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAlekGvynhvpg 274
                                       +++G  ++I+G+   GK+TL  A++  +  h  g
  gi|557693821|ref|YP_008796875.1|  30 VREGeFVVITGPTGAGKTTLCLAMAGLIPYHYNG 63 
                                       67777899*************9998777666665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HH.HCHHHHHHHH--EEEE CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplv.drvrelykklgvstil 393
                                       SG   q ++i+ al ++ k+l++DE t     + + e ++ l s +k++it +v + + e  + + + +++
  gi|557693821|ref|YP_008796875.1| 147 SGGQKQRVAIAAALAMKPKVLVLDEPTGQLDPIGKEEVVNVLQSLKKQGITIIVvEHILEELAPFTDRLVV 217
                                       899999999****************9999999999999999999999999876523444433555555554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0012      0.65      17      38 ..      31      52 ..      26      72 .. 0.84
   2 ?    0.5   0.0      0.59   3.1e+02     139     164 ..     179     204 ..     153     214 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                            ATPase 17 pegrvvlitGepGtGKtifalq 38
                                       eg+ v itG +G+GKt+++l 
  gi|557693821|ref|YP_008796875.1| 31 REGEFVVITGPTGAGKTTLCLA 52
                                      68999**************974 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.59
                            ATPase 139 vaReilrqlvrvlkklgvTailvsek 164
                                         +e++ ++++ lkk g+T i v+ +
  gi|557693821|ref|YP_008796875.1| 179 IGKEEVVNVLQSLKKQGITIIVVEHI 204
                                       456789999999*******9998765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.19     1e+02      38      52 ..      36      50 ..      27      69 .. 0.86
   2 ?    7.5   0.0    0.0047       2.5     103     158 ..     147     199 ..     133     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.19
                              TniB 38 lllvGdsnnGKtmiv 52
                                      +++ G++  GKt+++
  gi|557693821|ref|YP_008796875.1| 36 VVITGPTGAGKTTLC 50
                                      6899*********98 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0047
                              TniB 103 rvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipiv 158
                                       +  ++++ +++   ++k++vL++DE    l      ++e++n+l+sL+ +  i+i+
  gi|557693821|ref|YP_008796875.1| 147 SGGQKQRVAIAAALAMKPKVLVLDEPTGQL--DPIGKEEVVNVLQSLKKQ-GITII 199
                                       556777788888889**********99999..78889999****999865.45555 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 ?   12.0   0.0   0.00027      0.14      20      66 ..      33      83 ..      23     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeiienl.edkdk.....yviyyialreesiskld 66
                                       e+++i+Gp g GKt+L   ++       ++      ++y++   ++ +s++d
  gi|557693821|ref|YP_008796875.1| 33 GEFVVITGPTGAGKTTLCLAMAGLIpY--HYngtlrGKVYVFGKDTYTLSSAD 83
                                      6899*************9887765522..222345566666666666666555 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   0.0    0.0004      0.21      19      40 ..      33      54 ..      17      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0004
                                      TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                      g++++++G+ GaGKTtl+ ++a
  gi|557693821|ref|YP_008796875.1| 33 GEFVVITGPTGAGKTTLCLAMA 54
                                      6789*************98776 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   0.00039       0.2      19      49 ..      26      56 ..      21      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00039
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      ++fs  e ++ +i Gp  AGK+t+  A+  l
  gi|557693821|ref|YP_008796875.1| 26 INFSVREGEFVVITGPTGAGKTTLCLAMAGL 56
                                      7899999*****************9999876 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00032      0.17       2      29 ..      37      64 ..      36     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                                      EEE-STTSSHHHHHHHHHHHHT-EEEEH CS
                    Cytidylate_kin  2 aiDGPagsGKssvaralaeklglkyldt 29
                                       i GP+g+GK +++ a+a  + ++y  t
  gi|557693821|ref|YP_008796875.1| 37 VITGPTGAGKTTLCLAMAGLIPYHYNGT 64
                                      689***************9999998766 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00061      0.32       4      24 ..      36      56 ..      34      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00061
                         PduV-EutP  4 illiGkvgsGKttLtqalkge 24
                                      +++ G++g+GKttL+ a+ g 
  gi|557693821|ref|YP_008796875.1| 36 VVITGPTGAGKTTLCLAMAGL 56
                                      6889************99984 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00099      0.52       4      40 ..      36      77 ..      34      91 .. 0.72
   2 ?   -1.0   0.0       2.1   1.1e+03      47      74 ..     175     202 ..     153     242 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00099
                                      EEEEESTTSSHHHHHHHHHHHHHHT.....TS-EEEEEESTS CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkke.....gkkvllvaaDtf 40
                                      +++ G++GaGKTt +  +a l+  +       kv +   Dt+
  gi|557693821|ref|YP_008796875.1| 36 VVITGPTGAGKTTLCLAMAGLIPYHyngtlRGKVYVFGKDTY 77
                                      7899**********9999865433322234556666666666 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.1
                                       HHHHHHHHTTEEEEESSTTSCHHHHHHH CS
                             SRP54  47 QLktlaeklgvpvikkkeeadpaavake 74 
                                       QL  ++++  v+v+++ +++    ++ e
  gi|557693821|ref|YP_008796875.1| 175 QLDPIGKEEVVNVLQSLKKQGITIIVVE 202
                                       4444444444444444333333333334 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00052      0.27       1      41 [.      36      76 ..      36     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00052
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnped 41
                                      ++++Gp+g GK+tl+  +a  +  +++ + +++vy+ ++++
  gi|557693821|ref|YP_008796875.1| 36 VVITGPTGAGKTTLCLAMAGLIPYHYNGTLRGKVYVFGKDT 76
                                      689**************999999999888889999866655 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 ?    9.9   0.0   0.00079      0.42      15      48 ..      29      62 ..      22      87 .. 0.80
   2 ?   -1.7   0.0       2.8   1.5e+03      83     137 ..     145     203 ..     100     205 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00079
                                      SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCST CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 15 GlqkgdliiiAarpsmGktalalniaenaavkek 48
                                       +++g++++i +  + Gkt+l+l +a  +  +++
  gi|557693821|ref|YP_008796875.1| 29 SVREGEFVVITGPTGAGKTTLCLAMAGLIPYHYN 62
                                      5789*********************987765444 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.8
                                       TSXHHHHHHHHHHHHHHHHSEEEEEEXSSXCHHHH.....HHHHHHHHHHTTEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  83 klkeedweklteaieelseaklfiddtpaltvsei.....rskarrlkkekglgliviDy 137
                                       +l+  + ++++ a++   + k+++ d+p+ ++  i      + ++ l k++g+ +iv+ +
  gi|557693821|ref|YP_008796875.1| 145 ELSGGQKQRVAIAAALAMKPKVLVLDEPTGQLDPIgkeevVNVLQSL-KKQGITIIVVEH 203
                                       45544555555555555555566666555544444211102222223.236677777665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0012      0.61       3      23 ..      34      54 ..      32      64 .. 0.87
   2 ?   -1.2   0.0       3.6   1.9e+03      47      47 ..     147     147 ..      77     200 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0012
                            AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                      + +vitG+  +GKTtl+  ++
  gi|557693821|ref|YP_008796875.1| 34 EFVVITGPTGAGKTTLCLAMA 54
                                      689*************98765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.6
                            AAA_14  47 a 47 
                                       +
  gi|557693821|ref|YP_008796875.1| 147 S 147
                                       0 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0006      0.32      13      48 ..      32     164 ..      22     225 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0006
                                       TTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx...................................... RF
                              DEAD  13 gggdvlvaaeTGsGKTlaflipvlqivyet....kgktg...................................... 47 
                                       +g+ v++ ++TG+GKT+  l  +  i y+     +   g                                      
  gi|557693821|ref|YP_008796875.1|  32 EGEFVVITGPTGAGKTTLCLAMAGLIPYHYngtlR---Gkvyvfgkdtytlssadmaslvgivfqdpesqfltmsve 105
                                       78899***********9866555444444322330...023344444455555555555555555555555555555 PP

                                       ..........................................................- CS
                                       ..........................................................x RF
                              DEAD  48 ..........................................................p 48 
                                                                                                 p
  gi|557693821|ref|YP_008796875.1| 106 deiafglenlalpleemkervheaaklvkvedllerapyelsggqkqrvaiaaalamkP 164
                                       55555555555555555555555555555555555555555555555555555555554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0011      0.57       5      22 ..      36      53 ..      33      88 .. 0.89
   2 ?   -1.0   0.0       2.4   1.2e+03     110     133 ..     183     206 ..     180     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++i+Gp g+GKTtl++ +
  gi|557693821|ref|YP_008796875.1| 36 VVITGPTGAGKTTLCLAM 53
                                      79************9987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
                            AAA_24 110 efrrllkklqelrknvifiahekt 133
                                       e++++l+ l++ + ++i++ h  +
  gi|557693821|ref|YP_008796875.1| 183 EVVNVLQSLKKQGITIIVVEHILE 206
                                       555555555555559999999665 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00066      0.35       9      41 ..      25      57 ..      17      83 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00066
                            AAA_11  9 aiksalseseitliqGPPGtgKTktivellsql 41
                                       i++ ++e e+++i GP G gKT+  +++   +
  gi|557693821|ref|YP_008796875.1| 25 DINFSVREGEFVVITGPTGAGKTTLCLAMAGLI 57
                                      578899999***************999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 2027.94
//
Query:       gi|557693822|ref|YP_008796876.1|  [L=450]
Description: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-111  370.6   0.1     1e-110  370.4   0.1    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 !  370.4   0.1  5.6e-115    1e-110       8     403 ..      17     397 ..       8     400 .. 0.94

  Alignments for each domain:
  == domain 1  score: 370.4 bits;  conditional E-value: 5.6e-115
                                       TSEEEEESEB-TBTHHHHHHHHHHHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHHHHHHHHH CS
                              UbiD   8 gelvrikeevdpelEiaeiarrvleeggpallFenvkgkgskfpvltnlfgtrervalalglssleeileklaelle 84 
                                       +e v+i+e+v+ e+Ei+++ +   ++g p+l+Fe+v  +g+++pv++n+fg+r rva+++g +++ ++++k+ e ++
  gi|557693822|ref|YP_008796876.1|  17 EEFVKISEQVSLEYEITAVWKMFERKGNPVLFFEKV--QGCDMPVVANVFGSRARVARMIG-ADMWNFYDKWLEKTS 90 
                                       6889********************************..5689*******************.779999999999877 PP

                                       S..----EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEEEEEE-TTTT-EEEEEEEEEEEETTEE CS
                              UbiD  85 pkppippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlglvitrdpetgkrnlgiyRmqvldknkl 161
                                           ++p+ v  +++p++ ev +  ++vdL +LP+l+++ +DgG+yit+g+v++ +petg+ nl+++R++v+d+nkl
  gi|557693822|ref|YP_008796876.1|  91 V--IVEPEYV--STGPVK-EVKHLSSEVDLGTLPALKFFVEDGGRYITSGIVVANHPETGEVNLSFARLMVKDRNKL 162
                                       5..59*****..56****.564558**************************************************** PP

                                       EE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TCHHHHHHHHTS--EEEE-SSSSSEEET CS
                              UbiD 162 glhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsElefaGalrgepvelvkcetvdlevpa 238
                                       g+ ++++ +  +++++a + g+  l vav+iG++P l+laA++    + +E+++aGal  epv+lvkcet+d++vp+
  gi|557693822|ref|YP_008796876.1| 163 GVSIHSRGNLWRYFNRATELGRPWLNVAVVIGCNPTLYLAAAT---RTTDEYKMAGALASEPVQLVKCETNDVHVPS 236
                                       *****9999899999999999656******************9...577**************************** PP

                                       T-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EEEE-SSSCCSHHHHCHHHHHHHHHHHH CS
                              UbiD 239 dAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiypttvvgkppeedallgkalealflpl 315
                                       dAEivleG++ ++  ++EGPf ++tGy s+ +    v+ +++ithR++pi++t+++ +  e+ +l g++++a +++ 
  gi|557693822|ref|YP_008796876.1| 237 DAEIVLEGRMLTNVYEDEGPFSEYTGYVSGRST-RNVMIIDCITHRRNPIFQTIIPTNSSEHLLLGGLPMQANVYKR 312
                                       ****************************98887.6************************9***************** PP

                                       HHCCSTTEEEEEE-GGGTTTCEEEEECHHH.TCCHHHHHHHHHHCCTTGGC-SEEEEEEETTS-TTSHHHHHHHHHH CS
                              UbiD 316 lkkqvpevkdvhlpeeggfhllavvsikkr.ypghakkvmealwalkqqlsltKlvivvDedvdvrdlkevlwaiat 391
                                       lk+ +pevk +++p  g+ h++a++s++k+  +g + +++++l+++++   + K+vi+vD+d+dv+d  +vlwa+at
  gi|557693822|ref|YP_008796876.1| 313 LKESIPEVKGINFPVWGT-HFVAILSVDKEgKEGVQIRAAMLLMGANP---YVKYVILVDDDIDVFDEMQVLWAVAT 385
                                       **************9866.88******66637************9988...88************************ PP

                                       C--CCCCEEEEC CS
                              UbiD 392 rvdpdrDlviie 403
                                       r +pdr +++++
  gi|557693822|ref|YP_008796876.1| 386 RSQPDRSMHLFP 397
                                       *********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3440.69
//
Query:       gi|557693823|ref|YP_008796877.1|  [L=317]
Description: F420-dependent N5,N10-methenyltetrahydromethanopterin reductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-51  176.0   0.0    1.5e-51  175.7   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.7   0.0   8.2e-56   1.5e-51      28     313 ..      20     299 ..       3     300 .. 0.89

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 8.2e-56
                    Bac_luciferase  28 laraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglg 104
                                       + + aE++G+d+vwv+eh++g     +af+ll+a+aa T++irlgtav+ + +rhPav+A +aatL ++sgGRf lg
  gi|557693823|ref|YP_008796877.1|  20 YGVSAEKVGYDSVWVPEHLNG----GEAFSLLGAIAAKTSKIRLGTAVVSINLRHPAVTALAAATLSDVSGGRFTLG 92 
                                       5678*****************....**************************************************** PP

                    Bac_luciferase 105 lgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiP.vyvaaaspagle 180
                                       +g g  ++     G+  d++++ + E+v+++r+++ ++ +dfeG  f+  +++ + rp++   P +++aa+++++l+
  gi|557693823|ref|YP_008796877.1|  93 IGLGDLTQLRNSLGIIDDKPVKSMVEAVKICRQIF-RGSSDFEGIRFR-SHLQHIIRPKSS--PkIFIAAVGEQMLK 165
                                       ***************99******************.8899****8866.566666666556..66************ PP

                    Bac_luciferase 181 laarhadglllag.eppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearaliagldfyaldse 256
                                        aarh+dg+++    +pe++++  + ++   + ++++++ ++++  l ++  +  ++ r+ a+ ++++  +++   +
  gi|557693823|ref|YP_008796877.1| 166 AAARHGDGVIFSIfMSPESIKKSTAVIKT-TSGFSARRDYFEFMGLLATATEKHIQQLRELAAVFLSWPGRAERSLP 241
                                       ***********999999999999998886.6666666789**********************999988777777777 PP

                    Bac_luciferase 257 gagreaeaaei.qeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvd 313
                                        + + +   e+ + + +++++ +aa++v+de+++++a +G+ ++++ ++ ++ +ag++
  gi|557693823|ref|YP_008796877.1| 242 NNLFNKIDVEKlSMHVSRGQKGKAAELVDDEVLEEFACIGSLKTIRRKIGEFIDAGLT 299
                                       7777666665527777777777777888***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2520.17
//
Query:       gi|557693824|ref|YP_008796878.1|  [L=159]
Description: hypothetical protein CSUB_C0387 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   40.7   0.6    3.6e-10   39.6   0.6    1.5  1  PCuAC     Copper chaperone PCu(A)C


Domain annotation for each model (and alignments):
>> PCuAC  Copper chaperone PCu(A)C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.6     2e-14   3.6e-10      11     107 ..      41     144 ..      34     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 2e-14
                                       TS-SEEEEEEEEEECSSSEEEEEEEE-TT.......CCEEEEE.EETTTCEEEEEECS.SEEEETTEEEEE-TT... CS
                             PCuAC  11 pgakvsaaymtirNtgdeddkLvaassdv.......aasvelh.tvvedgvmkmrqveegieipaggqveLkpg... 76 
                                       +g++++++++ ++N+g   d +v++++           ++elh tv+ed+vmkm +v+ ++ +++ ++v+++     
  gi|557693824|ref|YP_008796878.1|  41 KGTNSAGIFFDLHNRGFLRDCVVGVEVLGeghmgeeVLQAELHrTVMEDNVMKMVKVD-KVCVEPFSTVKMRGAege 116
                                       46778999*****************964411222224578***77777*********9.************753335 PP

                                       SCEEEEECESS-B-TTEEEEEEEEETTTEEE CS
                             PCuAC  77 gfhvMliglkrdlkaGdevtltLtfekggti 107
                                       g+hvM++g   +++  d++++ L++e+g+ i
  gi|557693824|ref|YP_008796878.1| 117 GYHVMVFG---EVEHFDSFHVHLKMESGKVI 144
                                       ********...6778999********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1276.62
//
Query:       gi|557693825|ref|YP_008796879.1|  [L=431]
Description: elongation factor EF-1 alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-51  173.0   0.0      1e-50  172.0   0.0    1.5  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.3e-33  115.6   0.1    3.1e-33  114.4   0.1    1.6  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    1.2e-15   57.7   1.4    4.7e-15   55.7   0.3    2.4  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00026   21.0   0.0      0.004   17.2   0.0    2.3  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
       0.02   14.8   1.0      0.067   13.1   1.0    1.9  1  GTP_EFTU_D4  Elongation factor Tu domain 4
      0.063   12.6   0.2       0.76    9.1   0.0    2.5  2  Gtr1_RagA    Gtr1/RagA G protein conserved region
      0.082   13.5   0.7       0.27   11.9   0.0    1.9  2  Amelogenin   Amelogenin


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 !  172.0   0.0     4e-54     1e-50       1     189 [.       4     220 ..       4     225 .. 0.92
   2 ?   -3.2   0.0         2     5e+03     119     134 ..     352     367 ..     345     376 .. 0.77

  Alignments for each domain:
  == domain 1  score: 172.0 bits;  conditional E-value: 4e-54
                                       TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH.HHHST.............HCHSHHHHHHTSCSSCEEEEE CS
                          GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgeka.eeerv.............lDtlkeErergiTiksaaisl 63 
                                       k+++n+++ighvDhGK+T++++ lyk gai++++ k+ e e++             lD+ keErerg+Ti+ a  ++
  gi|557693825|ref|YP_008796879.1|   4 KPHMNLVVIGHVDHGKSTTMGHFLYKMGAIDERTLKTyE-EEAkkigkesfkyawvLDRVKEERERGLTIDLAFQKF 79 
                                       579******************************999953.33336899999************************** PP

                                       ETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.......STHHHHHHHHHHHHTTTE.EEEEEESC CS
                          GTP_EFTU  64 eketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.......vepqteevlrlalkegvp.iivfiNKm 132
                                       e  t+ky ++liD+PGH+dF+k++i+g++++D a++vv+a++G       +  qt+e+++l   +g++ iiv+iNKm
  gi|557693825|ref|YP_008796879.1|  80 E--TRKYYFTLIDAPGHRDFVKNMITGASQADAAIMVVSAKKGeaevgiaPGGQTREHAYLSFVLGIRqIIVLINKM 154
                                       *..**********************************************9*************************** PP

                                       GST.....HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHHHHH CS
                          GTP_EFTU 133 Drl.....kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............tllealv 189
                                       D       ka+++e+++++++        l+ +g++   +++++++S++ g++++            tlleal+
  gi|557693825|ref|YP_008796879.1| 155 DDSsvnwaKARYEEVKQMASDL-------LKTIGYNIA-KINFIPVSGWLGDNLTekssnmpwyngpTLLEALD 220
                                       **99999899999998888855.......588899985.9************9998888888888887888776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2
                                       HHTTTEEEEEEESCGS CS
                          GTP_EFTU 119 lkegvpiivfiNKmDr 134
                                        +  v+++ +i KmD 
  gi|557693825|ref|YP_008796879.1| 352 AQTAVKFVELIQKMDP 367
                                       4677899999999995 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 !  114.4   0.1   1.2e-36   3.1e-33       2     111 ..     320     427 ..     319     428 .. 0.98

  Alignments for each domain:
  == domain 1  score: 114.4 bits;  conditional E-value: 1.2e-36
                                       -EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECC CS
                       GTP_EFTU_D3   2 ikphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelik 78 
                                       i  +++f  q+y++ +  +t+i  gY+pvl+i+ta+ ++k+veL++k+d++t++ +ek+p+f+k+Gd ++v++++ +
  gi|557693825|ref|YP_008796879.1| 320 IPVAKEFIGQIYVIYH--PTAIAVGYTPVLHIHTAQTAVKFVELIQKMDPRTGQITEKNPSFLKTGDVAVVRLRPLN 394
                                       56789***********..*********************************************************** PP

                                       EEEE--TTTHCCCCEEEEECTTCEEEEEEEEEE CS
                       GTP_EFTU_D3  79 pialekgseypqlGrFaiReggrTvaaGvvtei 111
                                       p+a+e  s  p+lGrFaiR+ g TvaaGvv+ei
  gi|557693825|ref|YP_008796879.1| 395 PVAIEPASVSPELGRFAIRDSGMTVAAGVVKEI 427
                                       *******************************99 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 ?   -0.4   0.0      0.62   1.6e+03      14      47 ..       4      35 ..       3      50 .. 0.82
   2 !   55.7   0.3   1.8e-18   4.7e-15       1      74 []     247     314 ..     247     314 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.62
                                      ETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESE CS
                       GTP_EFTU_D2 14 kkGdevrilg.ndtskkeivtrissletfhedede 47
                                      k+ ++++++g +d +k+   t+ +  +  ++  de
  gi|557693825|ref|YP_008796879.1|  4 KPHMNLVVIGhVDHGKS---TTMGHFLYKMGAIDE 35
                                      67789999999999999...999999988887777 PP

  == domain 2  score: 55.7 bits;  conditional E-value: 1.8e-18
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                                       G+v  grv++G+lk+Gd v i +   + k    +++s+e++h+ +++a++g+n+G+++++++ ++ + +G+++t
  gi|557693825|ref|YP_008796879.1| 247 GVVPVGRVEQGVLKPGDIVAIYPG--GLK---AEVKSIEMHHQSLQQAIPGDNIGFNLKGVEKNQ-LSRGMVVT 314
                                       8899*****************664..245...9********************************.9****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 !   17.2   0.0   1.6e-06     0.004       3      87 ..      10     122 ..       8     165 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.6e-06
                                       EEEESTTSSHHHHHHHHH...............T................STEEESSSTTSSSSEEEEEEEETTEEE CS
                          MMR_HSR1   3 aivGrpNvGKStLinalt...............g................ekaivsdkpgtTrdinegrvklkgkei 48 
                                       +++G+   GKSt +   +               +                ++++ +++ g T+d  + ++++++  +
  gi|557693825|ref|YP_008796879.1|  10 VVIGHVDHGKSTTMGHFLykmgaidertlktyeEeakkigkesfkyawvlDRVKEERERGLTIDLAFQKFETRKYYF 86 
                                       6777777777777777774443333333333330333333344444333367777888888888888888877788* PP

                                       EEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT...T CS
                          MMR_HSR1  49 elvDtpGliegaseekglgkaflaleeadlillvvdas...e 87 
                                       +l+D pG  +    +  +++ +    +ad++++vv+a+    
  gi|557693825|ref|YP_008796879.1|  87 TLIDAPG--H----RDFVKNMITGASQADAAIMVVSAKkgeA 122
                                       *******..3....2346666666777999999999774430 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 ?   13.1   1.0   2.6e-05     0.067      21      72 ..     251     301 ..     236     311 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEES CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisieg 72 
                                       vG +v +Gv+kpg  +    G    e+++i+ ++++l++a  G++++  ++g
  gi|557693825|ref|YP_008796879.1| 251 VG-RVEQGVLKPGDIVAIYPGGLKAEVKSIEMHHQSLQQAIPGDNIGFNLKG 301
                                       78.9*********999999998999*********************998887 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 ?    9.1   0.0    0.0003      0.76      30     158 ..      67     193 ..      46     197 .. 0.71
   2 ?   -2.9   0.0       1.3   3.4e+03     104     123 ..     348     367 ..     343     376 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0003
                         Gtr1_RagA  30 rlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvliyVfDvesreleedletlkeilealr 106
                                       + g tid+  +++  +++ ++ l+D +G ++fv+++++       ++ ++ i V+ +++ e e  ++   ++ e+++
  gi|557693825|ref|YP_008796879.1|  67 ERGLTIDLAFQKF-ETRKYYFTLIDAPGHRDFVKNMITG-----ASQADAAIMVVSAKKGEAEVGIAPGGQTREHAY 137
                                       5577888888888.47889999***********998554.....456678888888888877777776666555443 PP

                         Gtr1_RagA 107 ..qyspeakvfvlihKmDliqedereeifeerkeeireeiekleke..eiqffaTS 158
                                          +    ++ vli+KmD  + +  +  +ee k+  ++ ++ ++ +  +i+f   S
  gi|557693825|ref|YP_008796879.1| 138 lsFVLGIRQIIVLINKMDDSSVNWAKARYEEVKQMASDLLKTIGYNiaKINFIPVS 193
                                       10344455799999999999877777777777777777666554443366666655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                         Gtr1_RagA 104 alrqyspeakvfvlihKmDl 123
                                       ++++ +  +k+  li KmD 
  gi|557693825|ref|YP_008796879.1| 348 HIHTAQTAVKFVELIQKMDP 367
                                       57777888899999999995 PP

>> Amelogenin  Amelogenin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0001      0.27      30      91 ..     184     246 ..     174     269 .. 0.85
   2 ?   -0.7   0.2      0.74   1.9e+03      79     137 ..     311     371 ..     270     396 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                        Amelogenin  30 ypsyGyepmgGwlhhavvpvlsqltfqqhpsvhsll.hhvvpklpalqpflvpqqplvpvpgq 91 
                                         +  + p++Gwl ++++   s ++  + p+    l     p+ p  +p  +p q + ++ g 
  gi|557693825|ref|YP_008796879.1| 184 IAKINFIPVSGWLGDNLTEKSSNMPWYNGPTLLEALdMLEEPPKPIDKPLRIPIQGVYSIKGV 246
                                       5567899************************8777647789****************999875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.74
                        Amelogenin  79 lvpqqplvpvpgqhslipq.fqpalggpiqqplqpqavehplkp.tqlsnpvhpleplkpd 137
                                       +v  +p +p+p  + +i q +   +++ i   ++p    h  +   +  + ++ ++p   +
  gi|557693825|ref|YP_008796879.1| 311 MVVTKPDTPIPVAKEFIGQiYVIYHPTAIAVGYTPVLHIHTAQTaVKFVELIQKMDPRTGQ 371
                                       5566777777777777775244556666777777765544443303334445666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); 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:                         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 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3140.49
//
Query:       gi|557693826|ref|YP_008796880.1|  [L=105]
Description: small subunit ribosomal protein S10 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   86.7   0.3    1.1e-24   86.5   0.3    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
    0.00023   21.9   0.0    0.00037   21.2   0.0    1.3  1  PriA_C         Primosomal protein N C-terminal domain


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 !   86.5   0.3   1.2e-28   1.1e-24       1      97 [.       6     100 ..       6     101 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 1.2e-28
                                       EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HH CS
                     Ribosomal_S10   1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatke 76 
                                       ri+++S++ + Le+++++i+++a+++g+k++gp+plP k++ ++++ksp+++ +k++ + ++r+h+Rlid+   +++
  gi|557693826|ref|YP_008796880.1|   6 RIKVTSTNLTKLEEVCREIKDIAEKTGTKISGPIPLPVKKLVIPTRKSPCGEgTKTWRKHQMRIHRRLIDLGITDQR 82 
                                       89*********************************************************************99999* PP

                                       HHHHHS-...S---SS-EEEE CS
                     Ribosomal_S10  77 tidtllkllqlnlpegVsvev 97 
                                       +++++++   +++p+ V++e+
  gi|557693826|ref|YP_008796880.1|  83 VMRQIMR---IQIPDDVAIEM 100
                                       *******...********996 PP

>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   4.1e-08   0.00037       3      51 ..       2      46 ..       1      51 [. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.1e-08
                            PriA_C  3 srlalirvsgkdeekveeaaeelaellkealkleeveilgpapapiaki 51
                                      +++++i+v++++  k+ee+++e++++ ++    ++ +i gp+p p++k+
  gi|557693826|ref|YP_008796880.1|  2 TQIVRIKVTSTNLTKLEEVCREIKDIAEK----TGTKISGPIPLPVKKL 46
                                      689***********************999....4567*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 836.64
//
Query:       gi|557693827|ref|YP_008796881.1|  [L=253]
Description: ABC-2 type transport system permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-11   42.1  14.7    7.5e-11   41.8  14.7    1.2  1  ABC2_membrane_2  ABC-2 family transporter protein
    1.2e-05   24.6  17.5    1.4e-05   24.4  17.5    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
    0.00069   19.2   3.7      0.001   18.7   3.7    1.3  1  ABC2_membrane_5  ABC-2 family transporter protein
     0.0031   17.5   5.0     0.0084   16.1   4.5    2.0  2  ABC2_membrane_4  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 !   41.8  14.7   1.7e-14   7.5e-11      80     288 .]      38     248 ..       7     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.7e-14
                   ABC2_membrane_2  80 imavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaii.lalgiv 155
                                       + a+l+ v+a+++g+   a+E+e gT    +++P  R+++ lgK iggl++   + ++++   ll+l ++  ++g +
  gi|557693827|ref|YP_008796881.1|  38 PSAGLLHVLALTIGSSTSAEEYELGTADYWMTQPLRRSSYFLGKTIGGLVL---LFLIIFTYSLLSLSVSwYVFGPQ 111
                                       67899999*******************************************...44444444455555551678999 PP

                   ABC2_membrane_2 156 laledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqeindf 232
                                        ++e + l +++s+++++   f a+gl++  ++r s  ++ +a ++f++ a++ +++   + +l ag    qe   f
  gi|557693827|ref|YP_008796881.1| 112 SKVETFPLALAVSTASAA--PFYAIGLAFGELLRRSMMSTIVAGAVFFASALVQTYAN--FVALIAGDLTLQEFVRF 184
                                       99************9999..88**************************9998888777..44666665554666777 PP

                   ABC2_membrane_2 233 lsllsptsayntllneilagsdlna.........lgstatnllilllllavllvlgyvlFkrkDl 288
                                       l +  pt    t+l      + +n+             +  ++ l+ + av++ +++ +F+  D+
  gi|557693827|ref|YP_008796881.1| 185 LPTWAPTGLTPTILTDAVGLG-INTpgapfagfgAENLWLAAANLVTYSAVFFLVAWLRFRHSDV 248
                                       777788888877776666666.45568***99988888999999****************99986 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 !   24.4  17.5   3.1e-09   1.4e-05     154     345 .]      27     241 ..      14     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.1e-09
                   ABC2_membrane_3 154 eelsnvasflvg..liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllillla 228
                                       + +  +  ++++   +l +l++ ++s   +  +eE e ++    ++ ++++++y+l+k +g +++ +l+++ + ll 
  gi|557693827|ref|YP_008796881.1|  27 SGAAWTLGIIAPsaGLLHVLALTIGS---STSAEEYELGTADYWMTQPLRRSSYFLGKTIGGLVLLFLIIFTYSLLS 100
                                       45555555555544333333333333...3458*************************************9999986 PP

                   ABC2_membrane_3 229 fgl.......gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgf...fgglfpledlps 295
                                       +++       +  ++ + l+l ++   +  + a+g++++ l ++s +  i++++v++ +s++   +++++ l + + 
  gi|557693827|ref|YP_008796881.1| 101 LSVswyvfgpQSKVETFPLALAVSTASAAPFYAIGLAFGELLRRSMMSTIVAGAVFF-ASALvqtYANFVALIAGDL 176
                                       666656556688888999999999999999999************999999888888.66662334445559999** PP

                   ABC2_membrane_3 296 alkwifsiiPffapglgllrli.......tgdplwe.............illsliilalfavvylllall 345
                                       +l+ + +++P++ap+ +  +++             +             ++l+ + l+  ++v++l+a+l
  gi|557693827|ref|YP_008796881.1| 177 TLQEFVRFLPTWAPTGLTPTILtdavglgI-----NtpgapfagfgaenLWLAAANLVTYSAVFFLVAWL 241
                                       ***************999899866666553.....13444477777778999999999999999999985 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 !   18.7   3.7   2.3e-07     0.001      45     170 ..      43     168 ..      11     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.3e-07
                   ABC2_membrane_5  45 lvisiililttlsyDek.skwnkylltLPvtrkeiVksKYlfvlililiailitlllli.iavlikgnvtisevlls 119
                                       l +++++i ++ s +e+  ++  y +t P++r+ +   K +++l+l ++ i+ ++ll++ ++ ++ g+    + + +
  gi|557693827|ref|YP_008796881.1|  43 LHVLALTIGSSTSAEEYeLGTADYWMTQPLRRSSYFLGKTIGGLVLLFLIIFTYSLLSLsVSWYVFGPQ---SKVET 116
                                       44556667777777776368889*********************9999988888888752677777775...36899 PP

                   ABC2_membrane_5 120 iliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifsl.skl 170
                                       + ++l+++++  a ++ + + fg+   r ++ +i++g++f+ +a++++  ++
  gi|557693827|ref|YP_008796881.1| 117 FPLALAVSTASAAPFYAIGLAFGELLRRSMMSTIVAGAVFFASALVQTyANF 168
                                       999********************99999************999999865444 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 !   16.1   4.5   1.9e-06    0.0084      60     149 ..      43     132 ..       3     174 .. 0.76
   2 ?    0.3   0.4      0.13     6e+02      15     126 ..     147     168 ..     128     199 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-06
                   ABC2_membrane_4  60 lplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvle 136
                                       l ++   i+s    +E++ +t  + +t P  r +++l+K i  l+l +l++++  l+++ +++ + +++ +v+++  
  gi|557693827|ref|YP_008796881.1|  43 LHVLALTIGSSTSAEEYELGTADYWMTQPLRRSSYFLGKTIGGLVLLFLIIFTYSLLSLSVSWYVFGPQSKVETFPL 119
                                       4444555899999********************************99999999999999999999999998888777 PP

                   ABC2_membrane_4 137 llkkclelgllvf 149
                                       +l  ++  ++  +
  gi|557693827|ref|YP_008796881.1| 120 ALAVSTASAAPFY 132
                                       6665554444222 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.13
                   ABC2_membrane_4  15 vwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsr 91 
                                       +  +v+                                                                       
  gi|557693827|ref|YP_008796881.1| 147 MSTIVA----------------------------------------------------------------------- 152
                                       222222....................................................................... PP

                   ABC2_membrane_4  92 tklllaKlivllllsvllmlvtflitvlfallsgf 126
                                                           + f++++l+   + f
  gi|557693827|ref|YP_008796881.1| 153 -------------------GAVFFASALVQTYANF 168
                                       ...................2223333333333333 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:                      310  (0.0172904); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1982.99
//
Query:       gi|557693828|ref|YP_008796882.1|  [L=314]
Description: ABC-2 type transport system ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-26   93.3   0.0    2.1e-25   89.9   0.0    2.0  2  ABC_tran         ABC transporter
    2.5e-12   47.2   0.2    1.8e-05   24.7   0.1    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    1.2e-06   29.1   0.2    3.5e-06   27.7   0.1    1.9  1  DUF4162          Domain of unknown function (DUF4162)
    0.00038   20.2   0.1     0.0019   17.9   0.0    2.1  2  AAA_30           AAA domain
    0.00039   21.0   0.1    0.00062   20.3   0.1    1.6  1  AAA_23           AAA domain
    0.00089   18.8   0.0      0.037   13.5   0.1    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00092   18.9   0.2     0.0021   17.7   0.2    1.6  1  AAA_29           P-loop containing region of AAA domain
     0.0015   18.9   0.6      0.003   18.0   0.6    1.5  1  HMA              Heavy-metal-associated domain
     0.0075   16.0   0.0      0.012   15.3   0.0    1.4  1  AAA_15           AAA ATPase domain
  ------ inclusion threshold ------
      0.019   15.3   0.1       0.19   12.0   0.0    2.2  2  AAA_19           AAA domain
       0.02   14.8   0.3       0.14   12.1   0.0    2.2  2  NTPase_1         NTPase
      0.021   15.2   1.5        0.2   12.1   1.5    2.4  1  AAA              ATPase family associated with various cellul
      0.027   14.2   1.6        3.2    7.4   0.3    2.5  2  AAA_24           AAA domain
      0.028   14.8   0.1      0.045   14.1   0.1    1.7  1  AAA_16           AAA ATPase domain
      0.033   13.8   0.1      0.071   12.7   0.1    1.5  1  SRP54            SRP54-type protein, GTPase domain
      0.043   12.8   0.0      0.077   12.0   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.058   13.0   0.1       0.15   11.6   0.0    1.6  2  AAA_27           AAA domain
      0.061   13.2   0.1       0.16   11.9   0.1    1.6  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.076   12.6   0.3       0.16   11.6   0.3    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.079   12.0   1.4       0.17   10.9   0.3    1.9  2  T2SSE            Type II/IV secretion system protein
      0.082   13.2   0.3       0.26   11.6   0.2    2.1  1  AAA_22           AAA domain
       0.15   12.2   0.3       0.34   11.1   0.3    2.0  1  AAA_33           AAA domain
       0.16   11.6   0.1        3.3    7.3   0.0    2.5  3  Thymidylate_kin  Thymidylate kinase
       0.21   10.4   0.5        1.5    7.7   0.0    2.2  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN


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 !   89.9   0.0   2.7e-28   2.1e-25       3     136 ..      24     165 ..      22     166 .. 0.94
   2 ?    1.8   0.0      0.43   3.2e+02      22      80 ..     171     247 ..     165     294 .. 0.63

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 2.7e-28
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                        +sl+++ege++++vG+nG+GK+t l++++gllkp  G++ + g +  +   e+++++ig+ p+ p+  p  t+++ 
  gi|557693828|ref|YP_008796882.1|  24 PISLHVYEGEVYGLVGPNGSGKTTTLRAILGLLKPSGGKVSVYGLNPYS-HPEKANQKIGYSPEIPNYPPFFTAEKL 99 
                                       589*************************************999766655.58999*****************87777 PP

                                       .............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       .............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 .............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                    ++d+e+ ++l+  gl++ +d+++     ++S+G+ qr+++ +al+ +p+ll+lDEp+
  gi|557693828|ref|YP_008796882.1| 100 lrvtcsmkkifgkDADNEVRRVLDLTGLVNHADRKI----GNFSKGMVQRLSIGQALVGDPPLLVLDEPM 165
                                       ************999999*****************9....*****************************6 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.43
                                       SSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................... RF
                          ABC_tran  22 aGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren................... 79 
                                        G   +  +l++l k +  +i + +++l e   ++l+ +++++   +++f+++   +                    
  gi|557693828|ref|YP_008796882.1| 171 VGRAHIRDVLTQLRK-QGKTIIFSSHELYE--VQRLSDRVAMVYRGKTVFEDMV-MNLlnnsshtrvvaelaaepdg 243
                                       566666666666655.56677788888888..9999999999999989888884.3333456666666655554444 PP

                                       ...H CS
                                       ...x RF
                          ABC_tran  80 ...e 80 
                                          +
  gi|557693828|ref|YP_008796882.1| 244 klaK 247
                                       3330 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 !   24.7   0.1   2.5e-08   1.8e-05       2      51 ..      35      70 ..      34     107 .. 0.70
   2 !   20.5   0.0   4.6e-07   0.00035     234     300 ..     135     198 ..     112     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.5e-08
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldl 51
                                       +l+GpNgsGK++ L+a+ +l                 +g ++  + l++
  gi|557693828|ref|YP_008796882.1| 35 YGLVGPNGSGKTTTLRAILGLLK--------------PSGGKVSVYGLNP 70
                                      58****************99953..............3444444444444 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 4.6e-07
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                       + ++S G+ + l +  al  ++   +ll++DEp +g +P   +++ ++l +l++ g  +i+++H  +
  gi|557693828|ref|YP_008796882.1| 135 IGNFSKGMVQRLSIGQALVGDP---PLLVLDEPMLGVDPVGRAHIRDVLTQLRKQGKTIIFSSHELY 198
                                       6788999999889999999888...***************************************765 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   4.6e-09   3.5e-06      21      81 .]     246     308 ..     226     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 4.6e-09
                                       -----..---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---HHHHHHHHH CS
                           DUF4162  21 aeelleepgveeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsLndIFiekv 81 
                                       a++l+e+ gv +v  e +++++++++  + ++++ +++ + g+ +r+F++ +PsL+++Fi  v
  gi|557693828|ref|YP_008796882.1| 246 AKALEEITGVLKVAIEANRVVIHVDSsLDPREKIAEKIvKLGYGLREFRLSQPSLEEVFINRV 308
                                       678889999*****999********9788889999999778888****************876 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   2.6e-06    0.0019      19      52 ..      33      66 ..      26     194 .. 0.74
   2 ?   -0.7   0.0       1.3   9.6e+02      30      68 ..     213     255 ..     212     280 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.6e-06
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvigl 52
                                       v  l+Gp G+GKtt+l+a+  +++ +gg+v ++
  gi|557693828|ref|YP_008796882.1| 33 EVYGLVGPNGSGKTTTLRAILGLLKPSGGKVSVY 66
                                      47889**********************8666543 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                            AAA_30  30 GKttalkalreaweaa.ggrvi...glAptgkaAkvLaeelgi 68 
                                       GKt     + ++++++   rv+   ++ p gk Ak+L+e +g+
  gi|557693828|ref|YP_008796882.1| 213 GKTVFEDMVMNLLNNSsHTRVVaelAAEPDGKLAKALEEITGV 255
                                       6666666666666666555555432334889999999997775 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   8.3e-07   0.00062      21      43 ..      34      56 ..      16     208 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.3e-07
                            AAA_23 21 ltlItGpNGaGKTTildAiklaL 43
                                      ++ ++GpNG+GKTT l+Ai   L
  gi|557693828|ref|YP_008796882.1| 34 VYGLVGPNGSGKTTTLRAILGLL 56
                                      6789***************7655 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 !   13.5   0.1     5e-05     0.037      25      45 ..      33      53 ..       7      62 .. 0.81
   2 ?    3.0   0.0     0.076        57     159     199 ..     156     196 ..     139     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
                                      SEEEEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAil 45
                                      ++  +vGpNGSGK+  l Ail
  gi|557693828|ref|YP_008796882.1| 33 EVYGLVGPNGSGKTTTLRAIL 53
                                      56679**************95 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.076
                                       -SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 159 aplyllDeidaaLDeknvkkvaellkeksknaQfivislre 199
                                        pl +lDe     D   ++ + ++l + +k+   i+ s +e
  gi|557693828|ref|YP_008796882.1| 156 PPLLVLDEPMLGVDPVGRAHIRDVLTQLRKQGKTIIFSSHE 196
                                       69*****************************9988877543 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 !   17.7   0.2   2.9e-06    0.0021      23      50 ..      32      60 ..      19      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.9e-06
                            AAA_29 23 g.atlltGpsGsGKSTllDAiqalLvpak 50
                                      g ++ l+Gp+GsGK+T l Ai  lL p+ 
  gi|557693828|ref|YP_008796882.1| 32 GeVYGLVGPNGSGKTTTLRAILGLLKPSG 60
                                      336779*******************9986 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.6     4e-06     0.003      15      61 ..     244     288 ..     242     289 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4e-06
                               HMA  15 kvekvLselpgVesvkvdlatktvtVegdaestklrkiieaiekagy 61 
                                       k  k+L+e++gV +  v  ++++v++ +d + ++ +ki e+i k+gy
  gi|557693828|ref|YP_008796882.1| 244 KLAKALEEITGVLK--VAIEANRVVIHVDSSLDPREKIAEKIVKLGY 288
                                       5679********55..555667999999999977799*********9 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   1.6e-05     0.012      28      50 ..      37      59 ..      26     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.6e-05
                            AAA_15 28 liGkNnsGKSsilealdlFlnnk 50
                                      l+G+N+sGK++ l+a+  +l+ +
  gi|557693828|ref|YP_008796882.1| 37 LVGPNGSGKTTTLRAILGLLKPS 59
                                      9***************9999876 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00026      0.19      10      38 ..      32      60 ..      26      81 .. 0.84
   2 ?    0.6   0.0      0.85   6.3e+02      22      68 ..     213     259 ..     205     292 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00026
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                       +v  ++++ G+GKT++l++i+ ll+  g
  gi|557693828|ref|YP_008796882.1| 32 GEVYGLVGPNGSGKTTTLRAILGLLKPSG 60
                                      6778899**************99998766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.85
                            AAA_19  22 GKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae 68 
                                       GKT    ++++ll++  +  +   l++ + g+ ak l+e + +l+++
  gi|557693828|ref|YP_008796882.1| 213 GKTVFEDMVMNLLNNSSHTRVVAELAAEPDGKLAKALEEITGVLKVA 259
                                       89999999999999999999999999999999999999998766665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00018      0.14       4      46 ..      37      82 ..      34      85 .. 0.75
   2 ?    0.1   0.1      0.89   6.7e+02     113     158 ..     216     263 ..     212     284 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00018
                                      EE--TTSSHHHHHHHHHHHH...G..GGEEEEEEEEE-.------E CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkssg..vkvgGfyteevr.eggrrig 46
                                      + Gp G+GKtT ++ +l llk sg  v+v G+    +  + +++ig
  gi|557693828|ref|YP_008796882.1| 37 LVGPNGSGKTTTLRAILGLLKPSGgkVSVYGLNPYSHPeKANQKIG 82
                                      77*******************9973356667776666634455666 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.89
                                       HHHHHHHHHHT..TTSEEEEE--SS--SHHHHHHHT-TT-EEEE--TT CS
                          NTPase_1 113 kfkeaveevLk..sekpvlavihrrkdlalveeirerkdvkvfevtee 158
                                       +f+++v ++L+  s++ v+a +  + d +l + ++e ++v  + + ++
  gi|557693828|ref|YP_008796882.1| 216 VFEDMVMNLLNnsSHTRVVAELAAEPDGKLAKALEEITGVLKVAIEAN 263
                                       688888888987778888888888878888888888754444433333 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 ?   12.1   1.5   0.00027       0.2       3      23 ..      37      57 ..      35     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                                      EESSTTSSHHHHHHHHHHHHT CS
                               AAA  3 lyGppGtGKTllakavakelg 23
                                      l+Gp G GKT++ +a+   l+
  gi|557693828|ref|YP_008796882.1| 37 LVGPNGSGKTTTLRAILGLLK 57
                                      89**************98875 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.3    0.0043       3.2       5      22 ..      35      52 ..      31      62 .. 0.84
   2 ?    5.4   0.1     0.017        13     110     172 ..     175     237 ..     172     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0043
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      + ++Gp+g+GKTt+++ +
  gi|557693828|ref|YP_008796882.1| 35 YGLVGPNGSGKTTTLRAI 52
                                      5799*********99865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.017
                            AAA_24 110 efrrllkklqelrknvifiahektrkdedpegeakytrlepklgkktanelkeevDlvlranl 172
                                        +r++l++l++ +k++if +he  + +   ++ a+  r ++  ++ ++n+l++ +++ + a+l
  gi|557693828|ref|YP_008796882.1| 175 HIRDVLTQLRKQGKTIIFSSHELYEVQRLSDRVAMVYRGKTVFEDMVMNLLNNSSHTRVVAEL 237
                                       567899999999**********99999999888889999999999999999888887777665 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   0.1   6.1e-05     0.045      29      61 ..      37      70 ..      29     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-05
                            AAA_16 29 lsGesGvGKsslvrellralekdggif.lrgkcd 61
                                      l+G+ G+GK++ +r++l  l+ +gg + ++g + 
  gi|557693828|ref|YP_008796882.1| 37 LVGPNGSGKTTTLRAILGLLKPSGGKVsVYGLNP 70
                                      89***************99999977766555444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   9.5e-05     0.071       4      34 ..      35      65 ..      33      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.5e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEE CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvll 34
                                      + lvG++G+GKTttl  +  llk +g kv +
  gi|557693828|ref|YP_008796882.1| 35 YGLVGPNGSGKTTTLRAILGLLKPSGGKVSV 65
                                      569************9988888888777765 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 ?   12.0   0.0    0.0001     0.077      30      70 ..      33      73 ..      24      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                                      EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                      +v Gl G  G+Gk t++ a+   l+  G +v+v  ++P s 
  gi|557693828|ref|YP_008796882.1| 33 EVYGLVGPNGSGKTTTLRAILGLLKPSGGKVSVYGLNPYSH 73
                                      688********************************999885 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    0.0002      0.15      31      50 ..      37      56 ..      21      57 .. 0.88
   2 ?   -3.4   0.0       8.3   6.2e+03     156     172 ..     174     190 ..     172     206 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                            AAA_27 31 iyGpNEAGKstalrAisdll 50
                                      ++GpN +GK+t+lrAi  ll
  gi|557693828|ref|YP_008796882.1| 37 LVGPNGSGKTTTLRAILGLL 56
                                      69**************9887 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.3
                            AAA_27 156 aslrevleaLeaeadel 172
                                       a++r+vl++L+++ +++
  gi|557693828|ref|YP_008796882.1| 174 AHIRDVLTQLRKQGKTI 190
                                       56677777777666554 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   0.1   0.00021      0.16       2      32 ..      35      65 ..      34      68 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                              MobB  2 lgivgksgsGKTtLleklipelkarglrvgt 32
                                       g+vg +gsGKTt l  ++  lk +g +v++
  gi|557693828|ref|YP_008796882.1| 35 YGLVGPNGSGKTTTLRAILGLLKPSGGKVSV 65
                                      579************************9986 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   0.3   0.00021      0.16       2      28 ..      34      62 ..      33      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                                      EEEEEESTTCCHHHHHHHHH..CT--SS- CS
                              cobW  2 vtvltGflGsGKTtLlnhll..enraglk 28
                                      v++l+G+ GsGKTt l+++l   + +g k
  gi|557693828|ref|YP_008796882.1| 34 VYGLVGPNGSGKTTTLRAILglLKPSGGK 62
                                      7899**************99765555555 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 ?   10.9   0.3   0.00022      0.17     135     156 ..      38      59 ..      31      65 .. 0.87
   2 ?   -0.7   0.0      0.81   6.1e+02     141     168 ..     213     240 ..     179     273 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                             T2SSE 135 sGgTgsGKttllyallkeinks 156
                                        G+ gsGKtt+l a+l  ++ s
  gi|557693828|ref|YP_008796882.1|  38 VGPNGSGKTTTLRAILGLLKPS 59 
                                       59**************999876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.81
                             T2SSE 141 GKttllyallkeinksderivtvEDpvE 168
                                       GKt++  ++++ +n+s++  v++E ++E
  gi|557693828|ref|YP_008796882.1| 213 GKTVFEDMVMNLLNNSSHTRVVAELAAE 240
                                       6777777777777666555555554444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00035      0.26      10      29 ..      37      56 ..      30     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                            AAA_22 10 vtGesGtGKTtllrrlleql 29
                                      ++G+ G+GKTt+lr +l  l
  gi|557693828|ref|YP_008796882.1| 37 LVGPNGSGKTTTLRAILGLL 56
                                      89************998766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00045      0.34       4      20 ..      37      53 ..      34     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00045
                            AAA_33  4 lvGlpGsGKstlaerll 20
                                      lvG++GsGK+t ++ +l
  gi|557693828|ref|YP_008796882.1| 37 LVGPNGSGKTTTLRAIL 53
                                      79**********99875 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0045       3.3       3      26 ..      39      62 ..      37      72 .. 0.88
   2 ?   -2.7   0.0       5.3   3.9e+03      67      86 ..     174     193 ..     172     196 .. 0.79
   3 ?    1.3   0.0      0.31   2.3e+02       8      45 ..     213     252 ..     212     285 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0045
                                      ESTTSSHHHHHHHHHHHHHHTTE. CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegik 26
                                      G +G+GKtt ++++   lk +g k
  gi|557693828|ref|YP_008796882.1| 39 GPNGSGKTTTLRAILGLLKPSGGK 62
                                      899************999998866 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.3
                                       HTTHHHHHHHHHTT-EEEEE CS
                   Thymidylate_kin  67 ehleekikpalkqgktvivd 86 
                                        h+++++ +  kqgkt+i++
  gi|557693828|ref|YP_008796882.1| 174 AHIRDVLTQLRKQGKTIIFS 193
                                       57888888888999999975 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.31
                                       SHHHHHHHHHHHHHHTTE..EE..EESSSTTSHHHHHHHHH CS
                   Thymidylate_kin   8 GKttqaellkerlkeegik.vv..ltrepggteiGekirel 45 
                                       GKt + +++++ l+++ +  vv  l  ep+ +++++ + e+
  gi|557693828|ref|YP_008796882.1| 213 GKTVFEDMVMNLLNNSSHTrVVaeLAAEPD-GKLAKALEEI 252
                                       9************99998875522234444.6666666655 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 ?    7.7   0.0     0.002       1.5      14      47 ..      31      64 ..      20      69 .. 0.77
   2 ?   -0.0   0.0      0.43   3.2e+02     112     173 ..     212     271 ..     200     284 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.002
                     TrwB_AAD_bind 14 etqhilivGttGsGKtqalekllrairargdrai 47
                                      e +   +vG  GsGKt++l+++l  ++  g ++ 
  gi|557693828|ref|YP_008796882.1| 31 EGEVYGLVGPNGSGKTTTLRAILGLLKPSGGKVS 64
                                      45556799**************988877776665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.43
                     TrwB_AAD_bind 112 aartvlaetlrelvrekkksnaallralltadleeLkellagteaaalvaeeaertaasira 173
                                        ++tv+++++ +l+++ ++   + +++l+ ++  +L+++l++      va ea+r+   + +
  gi|557693828|ref|YP_008796882.1| 212 RGKTVFEDMVMNLLNNSSH--TRVVAELAAEPDGKLAKALEEITGVLKVAIEANRVVIHVDS 271
                                       5789999999999999444..45777788888888888888777666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.38
# Mc/sec: 2452.36
//
Query:       gi|557693829|ref|YP_008796883.1|  [L=278]
Description: hypothetical protein CSUB_C0392 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   12.6   0.0       0.41   10.8   0.0    2.0  1  PilN      Fimbrial assembly protein (PilN)


Domain annotation for each model (and alignments):
>> PilN  Fimbrial assembly protein (PilN)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.3e-05      0.41      24      59 ..      57      93 ..      54     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.3e-05
                              PilN 24 nqltitGsAvsndeVaefmrnLegspffk.nidlksa 59
                                      ++l + G+A+ nd Va+f +nL +s f    +dl + 
  gi|557693829|ref|YP_008796883.1| 57 GRLRLRGVATFNDGVATFEKNLPQSYFSPpAVDLAEY 93
                                      6799********************8776666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2310.81
//
Query:       gi|557693830|ref|YP_008796884.1|  [L=464]
Description: aspartate aminotransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-56  190.3   0.0    7.3e-56  189.9   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
    1.4e-08   33.7   0.0    2.6e-08   32.8   0.0    1.5  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    1.5e-07   31.7   2.5    4.3e-07   30.2   2.5    1.9  1  CM_2             Chorismate mutase type II
    1.1e-06   27.8   0.0    1.7e-06   27.2   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
    1.3e-05   24.7   0.0    2.3e-05   23.9   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00012   21.5   0.0    0.00025   20.4   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.077   11.8   0.0       0.26   10.1   0.0    1.8  2  Alliinase_C      Allinase
       0.79   10.0   5.1         25    5.2   0.3    4.1  5  DUF1059          Protein of unknown function (DUF1059)


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 !  189.9   0.0   3.2e-59   7.3e-56       3     354 ..     109     443 ..     107     450 .. 0.92

  Alignments for each domain:
  == domain 1  score: 189.9 bits;  conditional E-value: 3.2e-59
                                       EEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHH CS
                     Aminotran_1_2   3 vinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGaga 79 
                                       v  L ++e++ +     +pev++ ++   +  +++++y +++gl+el++++   + ++++l++++e +vv ++G   
  gi|557693830|ref|YP_008796884.1| 109 VHRLEVGEPDLG----APPEVRQSAAN--ALLEGYARYIDSRGLAELRTQIVNQVYEKHGLEITPE-NVVITPGGRF 178
                                       66799*******....*********98..9999*******************999999********.8888888887 PP

                                       HHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEES CS
                     Aminotran_1_2  80 liealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilves 156
                                       +i +++  l l  gde +v dp++++y +++   g+  v +++  e++++  ++a+e+ ++        tk i+++ 
  gi|557693830|ref|YP_008796884.1| 179 AIYLAAKTL-LREGDELIVIDPSWPMYRQVAPFVGARSVHVKTLFEDGWTPSIDAVEKHISP------STKAIILNY 248
                                       777777777.67*************************************************9......99******* PP

                                       S-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEE CS
                     Aminotran_1_2 157 phNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyi 233
                                       p+NPtG+++++ +  kl++la+ +++ +++De+Ya+ v +   +v+++ n   +   ++ +s+sK++G++G R+Gy+
  gi|557693830|ref|YP_008796884.1| 249 PNNPTGKILDRTTFNKLVELATDHGITVISDEVYADYVRDG--HVSILDNDLGKQ-HVLIQSFSKSYGMTGYRIGYV 322
                                       ****************************************5..566444544444.5******************** PP

                                       EEEHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEE CS
                     Aminotran_1_2 234 lgnaavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmfl 308
                                       ++++++v  ++++   ++   ++  q+ +++als  +      +e ++ + +r ++ + eL++ g +++ +++gm++
  gi|557693830|ref|YP_008796884.1| 323 IADKNLVAKMASIIGLVITcvPEFIQRGALTALSLRD----APKEYAAIMMRRMEKAVHELEKVGAEFYRPDGGMYV 395
                                       ****************99999*************999....89********************************** PP

                                       EEEETHH..CHHHHHHHHHHTCTEEEEEGGGGTS.TTEEEEECTTS-HH CS
                     Aminotran_1_2 309 ltdlsae..takelskkLleevgvyvtpgtsftv.pgrlRitvAgltee 354
                                       + ++ ++  +a++ + +Lle +gv+v pg+ f+   +++Ri++ g ++e
  gi|557693830|ref|YP_008796884.1| 396 FPRVGKLgeDAMATAFELLESKGVAVAPGSLFGGyDEFIRISL-GAPDE 443
                                       *******6666666666****************99********.66555 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 !   32.8   0.0   1.2e-11   2.6e-08      68     176 ..     168     282 ..     145     336 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.2e-11
                                       SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEEST..TSHHHHHHHCCTTEEEE CS
                   Cys_Met_Meta_PP  68 eaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdt..sdleelekaikentklv 141
                                       e++++++ G  Ai +a  +ll++Gde++v d  +   +++   v  + +++++ f d    +++++ek+i++ tk++
  gi|557693830|ref|YP_008796884.1| 168 ENVVITPGGRFAIYLAAKTLLREGDELIVIDPSWPMYRQVAPFVGARsVHVKTLFEDGwtPSIDAVEKHISPSTKAI 244
                                       788999**************************99998888888877768999999997446789************* PP

                                       EEESS-TTTT----...HHHHHHHHHHTT-EEEEEGTT CS
                   Cys_Met_Meta_PP 142 ylEtptnpllkvvD...iekiaklakkagvlvvvDntf 176
                                        l  p np+ k++D   ++k+++la ++g++v+ D ++
  gi|557693830|ref|YP_008796884.1| 245 ILNYPNNPTGKILDrttFNKLVELATDHGITVISDEVY 282
                                       *************9777789999**********99876 PP

>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   2.5   1.9e-10   4.3e-07      10      74 ..      14      82 ..       5      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.9e-10
                                      HHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHH....S-HHHHHHHHHHHHHHHHHHH CS
                              CM_2 10 eileLLaeRaelakevgeyKkeeglpvydpeReaevlerleega....ldeeaierifreiisasralq 74
                                      e+++ La R el+ +++e K++ g++   p+ e+ev + + e+a    ++e++i+ri + i+s ++++q
  gi|557693830|ref|YP_008796884.1| 14 ELVKVLAARRELVNKIAEHKRALGQQAVLPDVEKEVRRAMLEEAsrhgIPEDTINRIATIIFSDAVEQQ 82
                                      89****************************************667788*****************9998 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.0   7.8e-10   1.7e-06      59     222 ..     166     333 ..     121     366 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 7.8e-10
                                       STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEE..BETTSCBEGGGHH CS
                       Aminotran_5  59 eseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvip..ldeegeldldele 133
                                       +  e+++ t G+  ai l+a++l   l++gde +v +      +    ++a + ga+ ++++  ++++++  +d++e
  gi|557693830|ref|YP_008796884.1| 166 T-PENVVITPGGRFAIYLAAKTL---LREGDELIVIDPSWPMYR----QVAPFVGARSVHVKtlFEDGWTPSIDAVE 234
                                       3.378999999999*********...*********998777666....555555555333321157889999***** PP

                                       HH--TTEEEEEEESBETTTTEB--...HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTES.....EEEEETTTT CS
                       Aminotran_5 134 kllnektklvaithvsnvtGtiqp...veeigklakkkgalvlvDaaqavghipidvkklgvD.....flafsghKl 202
                                       k++++ tk+++++  +n tG i +   ++++++la ++g+ v+ D + a   +   v+ l+ D     +l  s  K 
  gi|557693830|ref|YP_008796884.1| 235 KHISPSTKAIILNYPNNPTGKILDrttFNKLVELATDHGITVISDEVYADYVRDGHVSILDNDlgkqhVLIQSFSKS 311
                                       *********************8763336778888999********99887777777766666633333488888889 PP

                                       TSSTT..-EEEEEEHHHHHTS. CS
                       Aminotran_5 203 lgPtG..iGvlyvrkellekle 222
                                       +g tG  iG +++ k+l  k+ 
  gi|557693830|ref|YP_008796884.1| 312 YGMTGyrIGYVIADKNLVAKMA 333
                                       9988888888888888888884 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 !   23.9   0.0     1e-08   2.3e-05      53     144 ..     180     279 ..     165     287 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1e-08
                                       HHHHH.TTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-.TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB- CS
                   DegT_DnrJ_EryC1  53 laLra.lgvgpgdeVIvpsltFvatanavlelgakpvfvDvd.pdtynidpaaieaaitertkaIl...pVhlyGqv 124
                                       + L a   + +gde+Iv   ++    +++  +ga+ v v    +d ++++ +a+e+ i + tkaI+   p +  G++
  gi|557693830|ref|YP_008796884.1| 180 IYLAAkTLLREGDELIVIDPSWPMYRQVAPFVGARSVHVKTLfEDGWTPSIDAVEKHISPSTKAIIlnyPNNPTGKI 256
                                       44555334568****************************97626789******************955567999*99 PP

                                       --...HHHHHHHHHHCT-EEEEE CS
                   DegT_DnrJ_EryC1 125 ad...mdalkaiaakhglkvieD 144
                                        d   +++l ++a++hg+ vi+D
  gi|557693830|ref|YP_008796884.1| 257 LDrttFNKLVELATDHGITVISD 279
                                       8645589999************9 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.1e-07   0.00025      13     167 ..     124     279 ..     120     281 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.1e-07
                                       HHHHHH.HCS----CCCT--HHHHHHHHHHHH........HTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT- CS
                   Beta_elim_lyase  13 amsdaq.aaamlGdesYgedktvnrLedavae........lfgkeaalfvpqGtaAnsillkillqrgeevivtepa 80 
                                       ++++    a+  G + Y ++++  +L  ++ +         +  e ++ +p G+ A  ++ k+ll+ g+e iv +p+
  gi|557693830|ref|YP_008796884.1| 124 EVRQSAaNALLEGYARYIDSRGLAELRTQIVNqvyekhglEITPENVVITPGGRFAIYLAAKTLLREGDELIVIDPS 200
                                       5666663444456667888888888887766633333333222345566**************************** PP

                                       HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHH CS
                   Beta_elim_lyase  81 hihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaia 157
                                         + +     +   +v++++l  +   + +++++e++i +       +k+i+l   nn   G+++     +++ ++a
  gi|557693830|ref|YP_008796884.1| 201 WPMYRQVAPFVGARSVHVKTLFEDG-WTPSIDAVEKHISP------STKAIILNYPNNP-TGKILDRTTFNKLVELA 269
                                       **99999999999*********999.9************9......589*********5.9**************** PP

                                       HHCT-EEEEE CS
                   Beta_elim_lyase 158 kkygiplhlD 167
                                        ++gi+++ D
  gi|557693830|ref|YP_008796884.1| 270 TDHGITVISD 279
                                       *******988 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00012      0.26     142     221 ..     245     336 ..     190     355 .. 0.71
   2 ?   -1.6   0.0      0.41   9.2e+02     317     345 ..     410     438 ..     401     450 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                                       EEESS-TTT--------........-TT-EEEEEE-TT..-S..TTTS---S-.B--SEEEEEHHHHHS-GGG-EEE CS
                       Alliinase_C 142 lvtsPnnPdgllreavv........kgseakviyDlay..YW..Phytpitsk.adedimLftlskltGhaGsrlGW 205
                                       +   PnnP g++ +           +++   vi D +y  Y    h + + +    + + + ++sk  G +G r+G+
  gi|557693830|ref|YP_008796884.1| 245 ILNYPNNPTGKILDRTTfnklvelaTDHGITVISDEVYadYVrdGHVSILDNDlGKQHVLIQSFSKSYGMTGYRIGY 321
                                       45679999998754322122235544455567889887444322345555444135678899**************9 PP

                                       EEES-HHHHHHHHHHH CS
                       Alliinase_C 206 alvkdkevakklveyi 221
                                        ++ dk++  k+ + i
  gi|557693830|ref|YP_008796884.1| 322 -VIADKNLVAKMASII 336
                                       .578999999998876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.41
                                       HHHHHHTTTEEEEEGGGGTS-TTEEEEES CS
                       Alliinase_C 317 caevlrekkiltrsGevfeaesryvrlsl 345
                                         e+l++k++    G+ f+   +++r+sl
  gi|557693830|ref|YP_008796884.1| 410 AFELLESKGVAVAPGSLFGGYDEFIRISL 438
                                       56889999********************8 PP

>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3     0.011        25      23      54 ..      23      53 ..      20      55 .. 0.87
   2 ?   -0.7   0.0      0.79   1.8e+03      36      52 ..      59      72 ..      56      75 .. 0.80
   3 ?    2.6   0.0     0.073   1.6e+02      23      46 ..     147     170 ..     141     172 .. 0.80
   4 ?    0.1   0.0      0.43   9.6e+02      35      46 ..     270     281 ..     267     284 .. 0.86
   5 ?   -3.4   0.0       5.4   1.2e+04      34      45 ..     374     385 ..     373     386 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
                           DUF1059 23 eEvlrkvaeHakaaHglteippelvekiksaI 54
                                       E+++k+aeH +a  g + + p++ +++++a+
  gi|557693830|ref|YP_008796884.1| 23 RELVNKIAEHKRAL-GQQAVLPDVEKEVRRAM 53
                                      59********8887.66***********9985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.79
                           DUF1059 36 aHglteippelvekiks 52
                                       Hg   ip++++++i +
  gi|557693830|ref|YP_008796884.1| 59 RHG---IPEDTINRIAT 72
                                      678...9*****99976 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.073
                           DUF1059  23 eEvlrkvaeHakaaHglteippel 46 
                                       +E+ +++++ + + Hgl+  p+++
  gi|557693830|ref|YP_008796884.1| 147 AELRTQIVNQVYEKHGLEITPENV 170
                                       5889999*********66555554 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.43
                           DUF1059  35 aaHglteippel 46 
                                       ++Hg+t i++e+
  gi|557693830|ref|YP_008796884.1| 270 TDHGITVISDEV 281
                                       79*******997 PP

  == domain 5  score: -3.4 bits;  conditional E-value: 5.4
                           DUF1059  34 kaaHglteippe 45 
                                       ka+H l+++ +e
  gi|557693830|ref|YP_008796884.1| 374 KAVHELEKVGAE 385
                                       789*99999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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 0.24s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 3627.85
//
Query:       gi|557693831|ref|YP_008796885.1|  [L=277]
Description: prephenate dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   67.5   0.1    1.1e-18   67.3   0.1    1.1  1  PDH              Prephenate dehydrogenase
    3.8e-16   59.6   0.0    7.3e-16   58.7   0.0    1.4  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    2.4e-09   37.6   0.2    6.9e-09   36.2   0.2    1.8  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    2.4e-06   26.5   0.8    3.8e-06   25.9   0.1    1.7  2  HI0933_like      HI0933-like protein
      4e-06   26.9   0.2    8.8e-06   25.8   0.2    1.6  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    9.4e-06   25.6   0.2    2.6e-05   24.2   0.2    1.9  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    9.4e-06   26.0   0.0    3.7e-05   24.1   0.0    2.2  1  NAD_binding_7    Putative NAD(P)-binding
    1.7e-05   25.0   0.1    4.8e-05   23.5   0.0    1.8  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    3.2e-05   23.7   0.0     0.0002   21.1   0.0    1.9  2  DAO              FAD dependent oxidoreductase
    3.5e-05   24.1   0.0    9.3e-05   22.8   0.0    1.7  1  UDPG_MGDP_dh_C   UDP-glucose/GDP-mannose dehydrogenase family
    3.6e-05   23.2   0.0    8.5e-05   22.0   0.0    1.7  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    8.9e-05   21.9   1.3    0.00011   21.5   0.1    1.7  2  FAD_binding_3    FAD binding domain
    0.00011   21.6   0.1    0.00031   20.1   0.1    1.8  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    0.00012   22.1   0.0    0.00059   19.9   0.0    2.1  2  DpaA_N           Dipicolinate synthase subunit A N-terminal d
     0.0013   19.0   0.1     0.0038   17.5   0.1    1.8  1  TrkA_N           TrkA-N domain
     0.0023   18.5   0.0      0.007   16.9   0.0    1.9  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
     0.0037   17.5   0.1     0.0089   16.3   0.1    1.7  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0041   16.8   0.1     0.0065   16.1   0.1    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.005   16.3   0.1      0.014   14.9   0.0    1.8  2  Glu_dehyd_C      Glucose dehydrogenase C-terminus
      0.007   16.3   0.7       0.84    9.6   0.2    2.7  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
     0.0071   15.9   0.1      0.019   14.5   0.1    1.9  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0095   15.3   0.3      0.019   14.3   0.3    1.5  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.022   14.2   0.1        0.1   12.1   0.0    1.9  2  adh_short        short chain dehydrogenase
      0.036   13.3   0.0        0.1   11.9   0.0    1.6  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
       0.07   13.6   0.0       0.12   12.9   0.0    1.6  1  XdhC_C           XdhC Rossmann domain
      0.081   13.5   0.0       0.22   12.2   0.0    1.7  1  TIR_2            TIR domain
        0.1   12.5   0.1       0.18   11.7   0.1    1.4  1  NAD_binding_10   NAD(P)H-binding
       0.11   12.5   0.0       0.25   11.3   0.0    1.6  1  NAD_binding_9    FAD-NAD(P)-binding
       0.12   11.9   0.0       0.22   11.1   0.0    1.5  1  DUF364           Putative heavy-metal chelation
       0.16   11.4   0.0       0.23   10.9   0.0    1.4  1  Epimerase        NAD dependent epimerase/dehydratase family
       0.23   10.5   0.1       0.31   10.1   0.1    1.2  1  FAD_binding_2    FAD binding domain


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 !   67.3   0.1   1.8e-21   1.1e-18       1     253 [.      18     259 ..      18     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 1.8e-21
                                       HHHHHHHTT--SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE CS
                               PDH   1 laralrrkgfkvtvigydideekaeaalelglvdeatddieavkeadivvlavPvevilevlkelaphlkedalitD 77 
                                       +ar l ++g +  v+ yd++ +k ++ +  g+  ++    ea++   +vvlav     +  l  l ++++ + +i D
  gi|557693831|ref|YP_008796885.1|  18 MARNLVKRGYR--VTVYDKKRNKLKKIEGGGISAAKSL-KEALSSSSLVVLAVGASNAATLLSSLMSTVS-GKIILD 90 
                                       58999999955..5556666666666644666655555.6899************************765.77999* PP

                                       --S--CHHHHHHHHHCC..GCEEEEEES---S-SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEE CS
                               PDH  78 vgsvKekvvreleellkegksfvgghPmaGteksGvdaareelfenavviLtPtektdkealekvkelleevgarvi 154
                                       ++svK+ v+++l ++ ++ + +v  hP++G+         ++ +e++ v+  P   +++e      e+++++  ++ 
  gi|557693831|ref|YP_008796885.1|  91 ISSVKTPVAKALAKHRRSSNMVVLIHPLFGP--------GTKKLEDKSVVFIPFR-KPEEEYRVCTEVFHPC--KIL 156
                                       *******************************........67889**********9.66699999******98..599 PP

                                       E--HHHHHHHHHHHTHHHHHHHHHHHHHHHCHHCCCCHHHHCGTCCHHHHH.CGGGS-HHHHHHHHHHTHH...... CS
                               PDH 155 lmspeeHDrvvavvshlphvvaialaatlkekkndekeirklasggfrdvt.RiaksnPelwadilleNke...... 224
                                        ms e+HDr +a    lp ++   l    + + ++       + + + +v   i + +P l+++i  +N +      
  gi|557693831|ref|YP_008796885.1| 157 RMSVETHDRKMASAMALPRLLILTLLRSWSMDDVK---PLTVSQKALMLVAsPILSESPSLFKEITEKNPYtekali 230
                                       *************************9944433333...344455556555448999999999999999987333222 PP

                                       HHHHHHHHHHHHHHHHHHHHHTT-HHHHH CS
                               PDH 225 avlealdkfikelkklkelienedaeeLv 253
                                       + l+ l++f+++   ++++ ++ ++ +Lv
  gi|557693831|ref|YP_008796885.1| 231 NALKTLNQFRNNPSTASKIFKQLQTKKLV 259
                                       34556666666666666666666666666 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 !   58.7   0.0   1.3e-18   7.3e-16       4     117 ..       8     119 ..       6     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 1.3e-18
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC- CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieglleal 80 
                                       +iG G MG  ma+nl+k+gy+v+vy+ +++k++++   g++aa+s++e+++s  +v++ v a++a  +++++l++++
  gi|557693831|ref|YP_008796885.1|   8 VIGAGPMGLWMARNLVKRGYRVTVYDKKRNKLKKIEGGGISAAKSLKEALSSSSLVVLAVGASNA-ATLLSSLMSTV 83 
                                       7************************************************************9766.56777788776 PP

                                       -TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEE CS
                     NAD_binding_2  81 kkgdilidgstsspedtrelakelkekglkfldaPVS 117
                                        +g+i++d s+++   ++ lak  +++++ +l  P  
  gi|557693831|ref|YP_008796885.1|  84 -SGKIILDISSVKTPVAKALAKHRRSSNMVVLIHPLF 119
                                       .8********************999988887766665 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 !   36.2   0.2   1.2e-11   6.9e-09       4      95 ..       8      92 ..       5      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.2e-11
                                      EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCG CS
                     F420_oxidored  4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlsela 82
                                      +iGaG mg  +a++l+++g   + ++v  +++ +k+++++   g+++ + + +ea++++  vvlav  ++++ +ls+l 
  gi|557693831|ref|YP_008796885.1|  8 VIGAGPMGLWMARNLVKRG---YRVTVY-DKKRNKLKKIEGG-GISAAK-SLKEALSSSSLVVLAVGASNAATLLSSL- 79
                                      79*****************...****55.9999999999555.788888.9***************************. PP

                                      HHHHTTSEEEEES CS
                     F420_oxidored 83 kdalkgklvisvl 95
                                       ++ +gk++++++
  gi|557693831|ref|YP_008796885.1| 80 MSTVSGKIILDIS 92
                                      8889******996 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.1   6.6e-09   3.8e-06       3      43 ..       6      46 ..       4      49 .. 0.93
   2 ?   -3.3   0.1       4.9   2.8e+03     240     251 ..      83      94 ..      56     111 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 6.6e-09
                                      EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                       +viG+G+ Gl  A ++ krg rV++++k+++ ++Ki   G
  gi|557693831|ref|YP_008796885.1|  6 ALVIGAGPMGLWMARNLVKRGYRVTVYDKKRNKLKKIEGGG 46
                                      68**********************************98665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.9
                                       EESHHHHHHTTT CS
                       HI0933_like 240 lsGpailqlSsy 251
                                       +sG +il +Ss+
  gi|557693831|ref|YP_008796885.1|  83 VSGKIILDISSV 94 
                                       566777777665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2   1.5e-08   8.8e-06      11     112 ..       2      92 ..       1     112 [. 0.85

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.5e-08
                                       TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS CS
                      Shikimate_DH  11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatasee 87 
                                       +++++l+iGaG m+  +a++L+++g++ v+v    +++ k++          + + ++lke+l+++ +v+ a+++++
  gi|557693831|ref|YP_008796885.1|   2 DKRRALVIGAGPMGLWMARNLVKRGYR-VTVYDKKRNKLKKIEGG---G---ISAAKSLKEALSSSSLVVLAVGASN 71 
                                       5789**********************9.*****999999988332...2...678899*****************99 PP

                                       -SB-HHHHHCCHHH.S..EEEEE-- CS
                      Shikimate_DH  88 pilekeeveealkkrkkplllvDia 112
                                       +    ++++++++     ++++Di+
  gi|557693831|ref|YP_008796885.1|  72 AATLLSSLMSTVSG----KIILDIS 92 
                                       98888888777744....6888887 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 !   24.2   0.2   4.6e-08   2.6e-05       4      51 ..       8      55 ..       5     113 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 4.6e-08
                                      EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTT CS
                           3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdiseealekalekieksleklve 51
                                      viGaG mG  +a  ++++g++V+++d ++++l+k +    +  ++l+e
  gi|557693831|ref|YP_008796885.1|  8 VIGAGPMGLWMARNLVKRGYRVTVYDKKRNKLKKIEGGGISAAKSLKE 55
                                      9********************************988765554544443 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 !   24.1   0.0   6.5e-08   3.7e-05       5      73 ..       1      71 [.       1     175 [. 0.80

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.5e-08
                     NAD_binding_7  5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk....laeeelekdlegadlviaatddre 73
                                      +++++ lv+G+G++++  +r+l++ g +vtv++++  ++l+ +++     a + l++ l+   lv+ a+   +
  gi|557693831|ref|YP_008796885.1|  1 MDKRRALVIGAGPMGLWMARNLVKRGYRVTVYDKKR-NKLK-KIEgggiSAAKSLKEALSSSSLVVLAVGASN 71
                                      5789*******************************4.3333.2332332345557777777788887776554 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 !   23.5   0.0   8.3e-08   4.8e-05       1      28 [.       8      35 ..       8      38 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 8.3e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekr 28
                                      ++GaG  Gl +A+ L k+g++v++++k 
  gi|557693831|ref|YP_008796885.1|  8 VIGAGPMGLWMARNLVKRGYRVTVYDKK 35
                                      8*************************96 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.4e-07    0.0002       2      29 ..       6      35 ..       5      38 .. 0.93
   2 ?    0.4   0.0      0.68   3.9e+02     192     268 ..      59     148 ..      36     186 .. 0.56

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.4e-07
                                      EEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg..Vtllekg 29
                                       ++iG+G +Gl+ A+ L +rg  Vt+++k+
  gi|557693831|ref|YP_008796885.1|  6 ALVIGAGPMGLWMARNLVKRGyrVTVYDKK 35
                                      58**************************98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.68
                                       EEEEEEE--GGGHH..HH.HTT.....CTTTSEEEEEEEEEEEE.EECCTHSTGSGCSEEEEE...EEETTTTEEEE CS
                               DAO 192 aadavVnaaGawsd..ll.gll.....keldlpispvrgqvlvl.kplseklvspaailpvpe...tdddgrgvyvt 256
                                       +   vV+a Ga     ll  l+     k + l is v+  v    ++  ++ ++  +i p++    +  ++++v ++
  gi|557693831|ref|YP_008796885.1|  59 SSSLVVLAVGASNAatLLsSLMstvsgK-IILDISSVKTPVAKAlAKHRRSSNMVVLIHPLFGpgtKKLEDKSVVFI 134
                                       3255999999886554442222222211.124445555555444233333333334555555566666666666666 PP

                                       E..ETTSEEEEEES CS
                               DAO 257 p..rkdgrvlvGgt 268
                                       p   ++ + +v+++
  gi|557693831|ref|YP_008796885.1| 135 PfrKPEEEYRVCTE 148
                                       64324555666665 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 !   22.8   0.0   1.6e-07   9.3e-05      23     102 ..      19      94 ..      16      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.6e-07
                                       HHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGGS-HHHHHHCCSS-EEEES CS
                    UDPG_MGDP_dh_C  23 ieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefkeldlaklkelmkpavvfDg 99 
                                       +++L ++g++v++yD k ++ ++ +     g++ ++sl+eal++++++v+++  ++  +l l++l ++++ ++++D+
  gi|557693831|ref|YP_008796885.1|  19 ARNLVKRGYRVTVYDKKRNKLKKIE---GGGISAAKSLKEALSSSSLVVLAVGASNAATL-LSSLMSTVSGKIILDI 91 
                                       789*****************99999...689***************************97.88888889*****999 PP

                                       SS- CS
                    UDPG_MGDP_dh_C 100 rnv 102
                                         v
  gi|557693831|ref|YP_008796885.1|  92 SSV 94 
                                       766 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 !   22.0   0.0   1.5e-07   8.5e-05      36     102 ..       3      70 ..       1      82 [. 0.89

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.5e-07
                                       TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC.EECSHHHHHHH-SEEEE-S--S CS
                      2-Hacid_dh_C  36 gktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv.elvsleellaesDivslhlplt 102
                                       +++  +iG+G +G  +a+ l + g +v++yd++++k ++ e  g+    sl+e+l++s  v+l++ ++
  gi|557693831|ref|YP_008796885.1|   3 KRRALVIGAGPMGLWMARNLVKRGYRVTVYDKKRNKLKKIEGGGIsAAKSLKEALSSSSLVVLAVGAS 70 
                                       56789******************************99999999995555**************98765 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     2e-07   0.00011       4      45 ..       6      47 ..       3      53 .. 0.91
   2 ?   -2.0   0.2       2.9   1.7e+03       4      49 ..      64     108 ..      62     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2e-07
                                      EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EE CS
                     FAD_binding_3  4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradgl 45
                                       l++GaGp Gl  a+ L ++G rv++ +k +++ ++  ++g+
  gi|557693831|ref|YP_008796885.1|  6 ALVIGAGPMGLWMARNLVKRGYRVTVYDKKRNKLKKIEGGGI 47
                                      69******************************9998877776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.9
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHH CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrt 49 
                                       Vl VGa+ a  +l++l+s+     ++++  s +++  +a   + r+
  gi|557693831|ref|YP_008796885.1|  64 VLAVGASNAATLLSSLMSTV-SGKIILDISSVKTPVAKALAKHRRS 108
                                       88899999999999999998.7788999999998888888888776 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 !   20.1   0.1   5.4e-07   0.00031       3      33 ..       6      40 ..       4     132 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.4e-07
                                      EEEE--SHHHHHHHHHHHHHTS-EEEEE....TTH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx RF
                       Pyr_redox_2  3 vvviGgGpAGlaaaltlaqagakvtlve....leg 33
                                       +viG+Gp Gl++a++l + g++vt+++    + +
  gi|557693831|ref|YP_008796885.1|  6 ALVIGAGPMGLWMARNLVKRGYRVTVYDkkrnKLK 40
                                      58*************************84433333 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 !   19.9   0.0     1e-06   0.00059      12      73 ..      16      81 ..       7     106 .. 0.85
   2 ?   -1.4   0.0       4.2   2.5e+03      68      95 ..     236     261 ..     228     275 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1e-06
                                      HHHHHHHHHTT-EEEEES-....TSSS-BTTEEEE-GGGS-GGG-SEEE--TT-BETTTEE-BSS- CS
                            DpaA_N 12 lylarkLaekgakvslygl....eleekiegvekaesleealedadviilPvpgtkdggeintpfs 73
                                      l++ar L ++g++v++y       ++ +  g+  a+sl+eal+ + +++l v  ++    +++ +s
  gi|557693831|ref|YP_008796885.1| 16 LWMARNLVKRGYRVTVYDKkrnkLKKIEGGGISAAKSLKEALSSSSLVVLAVGASNAATLLSSLMS 81
                                      789**************55554447778899*********************99988877777665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.2
                                       E-BSS-SS-EE-HHHHHTS-TT-EEEES CS
                            DpaA_N  68 intpfseeklsleelleklkkgqllfgG 95 
                                       +n  f +++ + ++++++l+ ++l+  G
  gi|557693831|ref|YP_008796885.1| 236 LNQ-FRNNPSTASKIFKQLQTKKLV-KG 261
                                       555.888888889999999999854.44 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   6.5e-06    0.0038       2      79 ..       7      76 ..       6     114 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.5e-06
                                      EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHH CS
                            TrkA_N  2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanila 79
                                      ++iG+G +G  +a++L + g+ +v+v dk+++++++++  g+          + L+ea +++ ++v+ a+g   a +l+
  gi|557693831|ref|YP_008796885.1|  7 LVIGAGPMGLWMARNLVKrGY-RVTVYDKKRNKLKKIEGGGIS-------AAKSLKEA-LSSSSLVVLAVGASNAATLL 76
                                      79****************777.6*************8866643.......33334443.33333444444444333333 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.2e-05     0.007       1      37 [.       5      42 ..       5      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-05
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS.TT CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll.rl 37
                                      +++v+G+G  gl +A +l + g +Vtv + + + l + 
  gi|557693831|ref|YP_008796885.1|  5 RALVIGAGPMGLWMARNLVKRGYRVTVYDKKRNKLkKI 42
                                      579************************99887766444 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 !   16.3   0.1   1.5e-05    0.0089       2      77 ..       7      92 ..       6     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-05
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...........TTTCEEEEE--TTTHHHHHHHHHTT CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka...........lgvrfeaialdaenyeavLaallke 69
                                      l+iGaG +G  +a+ l++++ +  ++tv d++++kl+++               +++++   a+ a+n + +L++l++ 
  gi|557693831|ref|YP_008796885.1|  7 LVIGAGPMGLWMARNLVKRG-Y--RVTVYDKKRNKLKKIEGGGisaakslkealSSSSLVVLAVGASNAATLLSSLMST 82
                                      89****************98.6..9***********9996544777788888888888888888888888888888877 PP

                                      S..SEEEE-S CS
                   Sacchrp_dh_NADP 70 g..dlvvnls 77
                                         +++++ s
  gi|557693831|ref|YP_008796885.1| 83 VsgKIILDIS 92
                                      6656666654 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.1e-05    0.0065       2      47 ..       7      53 ..       6     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg 47
                                      +++GaG +G  +a +L k g+ vt+++++r +l++++  G++  ++ 
  gi|557693831|ref|YP_008796885.1|  7 LVIGAGPMGLWMARNLVKRGYRVTVYDKKRnKLKKIEGGGISAAKSL 53
                                      79*********************************999999877766 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 !   14.9   0.0   2.3e-05     0.014      31      72 ..       3      41 ..       1      74 [. 0.87
   2 ?   -2.3   0.0       4.6   2.6e+03      12      34 ..     224     246 ..     218     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                       Glu_dehyd_C 31 pesalvlGaGslGLLalalleaeerglervyvlgrrdrpdpt 72
                                       ++alv+GaG++GL ++  l   +rg+  v+v +++ ++ ++
  gi|557693831|ref|YP_008796885.1|  3 KRRALVIGAGPMGLWMARNLV--KRGYR-VTVYDKKRNKLKK 41
                                      689*************99997..59995.9999987665555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.6
                       Glu_dehyd_C  12 iveKaielaeasrsafewepesa 34 
                                        +eKa+  a ++ ++f+ +p++a
  gi|557693831|ref|YP_008796885.1| 224 YTEKALINALKTLNQFRNNPSTA 246
                                       58999999999999999999987 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 !    9.6   0.2    0.0014      0.84       4      73 ..       8      63 ..       6     113 .. 0.69
   2 ?   -2.2   0.0         6   3.5e+03     102     106 ..     232     236 ..     194     268 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                                      EE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EE CS
                    NAD_Gly3P_dh_N  4 vlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadii 73
                                      v+GaG  G  +A+ l ++g +v+++ ++++ +++i+                 + a + l+eal+ ++++
  gi|557693831|ref|YP_008796885.1|  8 VIGAGPMGLWMARNLVKRGYRVTVYDKKRNKLKKIEGG--------------GISAAKSLKEALSSSSLV 63
                                      78888888888888888888888888888888877643..............234444444444444444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6
                                       ---SE CS
                    NAD_Gly3P_dh_N 102 liKGi 106
                                       ++K +
  gi|557693831|ref|YP_008796885.1| 232 ALKTL 236
                                       33333 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 !   14.5   0.1   3.3e-05     0.019       4      47 ..       7      50 ..       4     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-05
                                      EEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS- CS
                    UDPG_MGDP_dh_N  4 sviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiy 47
                                       viG+G +Gl +a  l ++g  v++ D+ ++k +k++ g i+  
  gi|557693831|ref|YP_008796885.1|  7 LVIGAGPMGLWMARNLVKRGYRVTVYDKKRNKLKKIEGGGISAA 50
                                      69**********************************99988754 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 !   14.3   0.3   3.2e-05     0.019      30     109 ..       5      75 ..       1     104 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-05
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS- CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipGkka 106
                                       + lviG+G  Gl  +++ ++ g +Vtv+D++ ++l+++e  g +        +++l+ea++++ +v+ +  + +++a
  gi|557693831|ref|YP_008796885.1|   5 RALVIGAGPMGLWMARNLVKRGYRVTVYDKKRNKLKKIEGGGIS-------AAKSLKEALSSSSLVVLA--VGASNA 72 
                                       789*********************************99974433.......555666666666666655..334445 PP

                                       --S CS
                       AlaDh_PNT_C 107 PkL 109
                                       ++L
  gi|557693831|ref|YP_008796885.1|  73 ATL 75 
                                       555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00017       0.1       3      40 ..       6      42 ..       4      44 .. 0.91
   2 ?   -1.0   0.1       1.7   9.9e+02     115     139 ..      72      96 ..      44     104 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                                      EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHH CS
                         adh_short  3 vlvtGassGIGraiakelakeGakvvvvdrseekleev 40
                                      +lv+Ga+  +G+ +a++l+k+G++v+v+d++ +kl+++
  gi|557693831|ref|YP_008796885.1|  6 ALVIGAG-PMGLWMARNLVKRGYRVTVYDKKRNKLKKI 42
                                      8999998.8************************99875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHCTTEEEE.EEEEGGG CS
                         adh_short 115 ltravlpamlkqssGrIv.nvsSvag 139
                                       ++  +l  +++  sG+I+  +sSv +
  gi|557693831|ref|YP_008796885.1|  72 AAT-LLSSLMSTVSGKIIlDISSVKT 96 
                                       443.4455566777777635888765 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 ?   11.9   0.0   0.00017       0.1       1      30 [.       7      35 ..       7      43 .. 0.89
   2 ?   -2.0   0.0       2.9   1.7e+03     253     275 ..      55      77 ..      36      95 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      ++iGaGP Gl +a +l k g  ++++ +k+
  gi|557693831|ref|YP_008796885.1|  7 LVIGAGPMGLWMARNLVKRGY-RVTVYDKK 35
                                      69******************9.78998886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.9
                       Pyr_redox_3 253 kkvevkddvvlatGykpdlsflk 275
                                       + +++++ vvla+G ++ +++l+
  gi|557693831|ref|YP_008796885.1|  55 EALSSSSLVVLAVGASNAATLLS 77 
                                       34555566667777776666665 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0002      0.12       2      65 ..       7      80 ..       6     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0002
                                      EEE--STTHHHHHHHHHHHTEEEEEEES-G.GGG........-GGG-TT-SE....-EEEE--S-HHHHHHHHHHHS CS
                            XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpre.efa........tkerfpeade....tavvvlthdhklDaealeaal 65
                                      +++Gag+++  +ar + + g+rvtv+d+++ +++        ++++++   e    + +vvl  + +  a +l+ ++
  gi|557693831|ref|YP_008796885.1|  7 LVIGAGPMGLWMARNLVKRGYRVTVYDKKRnKLKkiegggisAAKSLK---EalssSSLVVLAVGASNAATLLSSLM 80
                                      699*************************99444466665555333333...13446666666666666666666555 PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00037      0.22      14     107 ..      16     137 ..      13     145 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00037
                             TIR_2  14 eklaeaLeaagirv.wldrw.....dlkpge.dweeeieeaiessdvvlvvlspayles.................e 66 
                                        ++a++L ++g+rv ++d++     +++ g+ +  + ++ea+ ss+ v++ ++ + ++                   
  gi|557693831|ref|YP_008796885.1|  16 LWMARNLVKRGYRVtVYDKKrnklkKIEGGGiSAAKSLKEALSSSSLVVLAVGASNAATllsslmstvsgkiildiS 92 
                                       599**********9568885332223555556**************9999888776655566677777777776666 PP

                             TIR_2  67 wcreeleaaleaaeegkkrlipvlle....pekpp...l..aslqyidls 107
                                       ++++ +  al+  +++++  ++vl++    p   +   l  +s+ +i ++
  gi|557693831|ref|YP_008796885.1|  93 SVKTPVAKALA--KHRRSSNMVVLIHplfgP---GtkkLedKSVVFIPFR 137
                                       66666666665..222222333333323322...2112345666677776 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 ?   11.7   0.1   0.00031      0.18       3      73 ..      11      72 ..      10     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00031
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk 73
                                       G  G   ++ l++r g++vt++  + +kl+++e         g ++ +++l+eal+  + Vv a+g+++ 
  gi|557693831|ref|YP_008796885.1| 11 AGPMGLWMARNLVKR-GYRVTVYDKKRNKLKKIE--------GGGISAAKSLKEALSSSSLVVLAVGASNA 72
                                      6899***********.5******99999999876........58899999****************98765 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 ?   11.3   0.0   0.00044      0.25       2      34 ..       8      35 ..       7      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00044
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdps 34
                                      ++GaGp Gl ++++L++r       ++t++d++
  gi|557693831|ref|YP_008796885.1|  8 VIGAGPMGLWMARNLVKRG-----YRVTVYDKK 35
                                      8****************94.....888888874 PP

>> DUF364  Putative heavy-metal chelation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00038      0.22      15      68 ..       7      65 ..       2     101 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                            DUF364 15 vvVGyfap....vlkklkekgaeltvlelnpnlleeeegdl..pdeaaeellpeadvvii 68
                                       v+G+  p    +++ l ++g+++tv++ ++n+l++ eg     ++  +e+l+++ +v++
  gi|557693831|ref|YP_008796885.1|  7 LVIGAG-PmglwMARNLVKRGYRVTVYDKKRNKLKKIEGGGisAAKSLKEALSSSSLVVL 65
                                      567762.33445788999********************9887744444555555555443 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0004      0.23       2      73 ..       7      68 ..       6     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAa 73
                                      lV+Ga G +G  ++++l ++gy+v++ d+++++ +       ++  + +  +++l+++++      v+++ +
  gi|557693831|ref|YP_008796885.1|  7 LVIGA-GPMGLWMARNLVKRGYRVTVYDKKRNKLK-------KIEGGGISAAKSLKEALS--SSSLVVLAVG 68
                                      78887.************************44444.......566899999999999998..5666666643 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   0.00054      0.31       2      33 ..       6      37 ..       5      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00054
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      ++ViG+G  GL  A ++ ++G +v+v +k+ +
  gi|557693831|ref|YP_008796885.1|  6 ALVIGAGPMGLWMARNLVKRGYRVTVYDKKRN 37
                                      69***************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 1838.55
//
Query:       gi|557693832|ref|YP_008796886.1|  [L=173]
Description: nitroreductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  101.6   0.3    1.4e-13   51.2   0.0    2.1  2  Nitroreductase  Nitroreductase family
    7.4e-12   45.3   0.0    5.1e-06   26.2   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 !   49.1   0.0     7e-17   6.3e-13       4      54 ..      13      63 ..      10      76 .. 0.90
   2 !   51.2   0.0   1.6e-17   1.4e-13      88     170 .]      73     143 ..      66     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 7e-17
                                      --B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHH CS
                    Nitroreductase  4 RrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelrykla 54
                                       r +R+F d+pv+ ++++kilea+rra sa+n+qpw+f+++++ke ++kl 
  gi|557693832|ref|YP_008796886.1| 13 KRETREFLDKPVDMDTISKILEAGRRAGSAKNRQPWQFILIREKENLRKLS 63
                                      5779*************************************8888887775 PP

  == domain 2  score: 51.2 bits;  conditional E-value: 1.6e-17
                                       HHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SEEEE CS
                    Nitroreductase  88 agapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeeeivv 164
                                         a++ ivi          + ++ y  + +dag aaqn++LaA+ lGlgscpi+   e+a   +++l++p++++i  
  gi|557693832|ref|YP_008796886.1|  73 PSAAFAIVI----------TIPDKYFQDRFDAGRAAQNMMLAAHILGLGSCPITLHSEEA--AKNHLNIPGDQRIAI 137
                                       567777777..........778999999********************************..9*******99***** PP

                                       EEEEE- CS
                    Nitroreductase 165 liavGy 170
                                       +ia+G+
  gi|557693832|ref|YP_008796886.1| 138 CIAFGH 143
                                       *****7 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.2e-07    0.0019     158     197 ..      27      66 ..      12      72 .. 0.78
   2 !   26.2   0.0   5.7e-10   5.1e-06      65     153 ..      75     166 ..      61     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHHTS--GGG----EEE.E-SSEE......EEE CS
                    TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfelkdddeikika.svlg 197
                                       + + +ilea r A sA N+qpw+f l  + + ++++ s++g
  gi|557693832|ref|YP_008796886.1|  27 DTISKILEAGRRAGSAKNRQPWQFILIRE-KENLRKlSNFG 66 
                                       67899*******************98775.44443335555 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 5.7e-10
                                       SSSEEEE----SSHHHHHHHHHHHHHHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS----.. CS
                    TM1586_NiRdase  65 gvpnyialvgekkedleekaGYygeqlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyaktklv.. 138
                                        +  +++ + +k  + +  aG   ++++L +  lGlg+c + +  ++  k +++++ +++++i Ia+G +k ++   
  gi|557693832|ref|YP_008796886.1|  75 AAFAIVITIPDKYFQDRFDAGRAAQNMMLAAHILGLGSCPITLHSEEaAKNHLNIPGDQRIAICIAFGHPKPSKPlg 151
                                       45555556666668888999**********************98777677889*****************9888556 PP

                                       .-----HHHHBSS-G CS
                    TM1586_NiRdase 139 eakrkpleelcevke 153
                                       +  rkpl e++++++
  gi|557693832|ref|YP_008796886.1| 152 KIIRKPLHEILHLEK 166
                                       999999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1239.59
//
Query:       gi|557693833|ref|YP_008796887.1|  [L=340]
Description: hypothetical protein CSUB_C0396 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-05   23.3   0.0    0.00015   21.5   0.0    1.9  1  TrmB           Sugar-specific transcriptional regulator TrmB
    5.9e-05   22.9   0.1    0.00021   21.1   0.0    1.9  2  MarR_2         MarR family
    6.9e-05   22.7   0.1       0.33   10.9   0.1    3.0  3  TBPIP          TBPIP/Hop2 winged helix domain
     0.0002   21.1   0.0    0.00055   19.8   0.0    1.7  1  HTH_5          Bacterial regulatory protein, arsR family
    0.00024   21.0   0.0    0.00091   19.2   0.0    1.9  2  HTH_45         Winged helix-turn-helix
     0.0004   20.8   0.0     0.0014   19.1   0.0    1.9  1  HTH_27         Winged helix DNA-binding domain
    0.00067   20.0   0.1     0.0028   17.9   0.0    2.0  2  Rrf2           Transcriptional regulator
     0.0016   18.4   0.0      0.005   16.9   0.0    1.8  1  HTH_20         Helix-turn-helix domain
     0.0041   16.7   1.8       0.08   12.6   0.1    3.0  3  GntR           Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.052   13.5   0.0    2.1  2  MarR           MarR family
      0.025   14.1   0.5         13    5.5   0.0    3.3  3  HTH_47         winged helix-turn-helix
      0.027   14.4   0.2       0.56   10.2   0.0    2.8  3  BLACT_WH       Beta-lactamase associated winged helix domain
      0.028   14.7   0.0      0.064   13.6   0.0    1.5  1  DUF3085        Protein of unknown function (DUF3085)
      0.035   13.8   0.0      0.088   12.5   0.0    1.6  1  HrcA_DNA-bdg   Winged helix-turn-helix transcription represso
      0.065   13.2   0.3       0.23   11.5   0.1    2.0  2  DUF910         Bacterial protein of unknown function (DUF910)
      0.067   13.0   0.1       0.64    9.9   0.1    2.4  1  DUF1495        Winged helix DNA-binding domain (DUF1495)
       0.07   13.1   0.0       0.67    9.9   0.0    2.5  2  PadR           Transcriptional regulator PadR-like family
      0.088   12.8   0.0        1.2    9.1   0.0    2.4  3  Dimerisation2  Dimerisation domain
      0.097   11.8   0.0       0.13   11.4   0.0    1.1  1  RPE65          Retinal pigment epithelial membrane protein


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 !   21.5   0.0   1.6e-07   0.00015      20      63 ..      20      63 ..      13      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.6e-07
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63
                                       gp +++e+ +++  +r+ v ++L+sL++ GlVe+e+g++ +Y 
  gi|557693833|ref|YP_008796887.1| 20 DGPHSVTELVSAVRASRQGVIKTLKSLMSEGLVEKEPGKRGMYM 63
                                      58999**********************************88885 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.2e-07   0.00021       9      60 ..      13      58 ..      10      60 .. 0.93
   2 ?   -1.8   0.0       3.2     3e+03       8      29 ..     223     245 ..     218     273 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.2e-07
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSS CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDk 60
                                      +vL aL ++p    +v+el+ + + s++ v ++lk L + GLve++pg   k
  gi|557693833|ref|YP_008796887.1| 13 DVLDALFDGPH---SVTELVSAVRASRQGVIKTLKSLMSEGLVEKEPG---K 58
                                      89*******95...********************************98...4 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.2
                                       HHHHHHHHCTTTS.EEEHHHHHH CS
                            MarR_2   8 arvLaaLgrrpgr.dltvgelar 29 
                                       +++L++L   + r + t  ++ r
  gi|557693833|ref|YP_008796887.1| 223 LMILHFLNTFEQRgNATCVDIIR 245
                                       67778777776665445555554 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0026       2.4      17      60 ..      23      63 ..      21      65 .. 0.79
   2 ?   -1.4   0.0       2.5   2.4e+03      36      51 ..     258     273 ..     241     275 .. 0.83
   3 !   10.9   0.1   0.00035      0.33      35      53 ..     290     308 ..     278     315 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0026
                             TBPIP 17 fsvqdvvanlqkklgKtavqkaLdeLvdegkiieKeyGKqkiYl 60
                                       sv++ v++   + + + v k+L +L +eg+ +eKe GK  +Y+
  gi|557693833|ref|YP_008796887.1| 23 HSVTELVSAV--RASRQGVIKTLKSLMSEGL-VEKEPGKRGMYM 63
                                      5555555554..568999************6.68999**99997 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.5
                             TBPIP  36 qkaLdeLvdegkiieK 51 
                                       +k L+  v+++ki+ +
  gi|557693833|ref|YP_008796887.1| 258 TKLLEAAVNQQKIKRR 273
                                       799999999**99865 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00035
                             TBPIP  35 vqkaLdeLvdegkiieKey 53 
                                       + +aL++L+++gki eK y
  gi|557693833|ref|YP_008796887.1| 290 IKEALETLRSSGKIDEKSY 308
                                       789***************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 !   19.8   0.0   5.8e-07   0.00055       4      47 .]      11      54 ..       9      54 .. 0.97

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 5.8e-07
                                      HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      R ++L +L +g+++v+el+ +++ s+  v   Lk L+ +GLVek
  gi|557693833|ref|YP_008796887.1| 11 RKDVLDALFDGPHSVTELVSAVRASRQGVIKTLKSLMSEGLVEK 54
                                      7889**************************************97 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   9.6e-07   0.00091      10      64 ..      13      70 ..       7      79 .. 0.88
   2 ?   -2.5   0.0       5.6   5.3e+03       2      19 ..     284     301 ..     283     312 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 9.6e-07
                            HTH_45 10 dILeaisegeakkTkimykanLsykllnkYLdmLvekglikk...skekYvlTekGle 64
                                      d+L+a+ +g  + T+++ ++  s + + k L+ L+++gl++k   + ++Y+lTekG  
  gi|557693833|ref|YP_008796887.1| 13 DVLDALFDGPHSVTELVSAVRASRQGVIKTLKSLMSEGLVEKepgKRGMYMLTEKGYS 70
                                      89999999********************************66456789********75 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.6
                            HTH_45   2 RskleIiadILeaisege 19 
                                       R +l+ i + Le +++++
  gi|557693833|ref|YP_008796887.1| 284 RARLSLIKEALETLRSSG 301
                                       667777777777765544 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 !   19.1   0.0   1.5e-06    0.0014      16      68 .]      20      68 ..      14      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-06
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +++ + ++l+ ++  + + +++ lk L   GLv   ++ +++++  + lT+kG
  gi|557693833|ref|YP_008796887.1| 20 DGPHSVTELVSAVRASRQGVIKTLKSLMSEGLV---EK-EPGKRGMYMLTEKG 68
                                      5677779**************************...55.5899*********9 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     3e-06    0.0028      24      69 ..      21      66 ..      15      70 .. 0.92
   2 ?   -2.1   0.0       5.5   5.2e+03       8      31 ..     220     243 ..     215     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3e-06
                                      C-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESS CS
                              Rrf2 24 epvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLak 69
                                      +p s++e+ + +  s++ + k l+ L  +glv+ + Gk+G y+L++
  gi|557693833|ref|YP_008796887.1| 21 GPHSVTELVSAVRASRQGVIKTLKSLMSEGLVEKEPGKRGMYMLTE 66
                                      568999**************************************86 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.5
                                       HHHHHHHHHHHHSSTCC-B-HHHH CS
                              Rrf2   8 eyalhallyLakeeeeepvsseei 31 
                                         al +l +L + e+++ ++  +i
  gi|557693833|ref|YP_008796887.1| 220 AAALMILHFLNTFEQRGNATCVDI 243
                                       568999999999998887776655 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   5.3e-06     0.005      11      58 ..      10      56 ..       8      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.3e-06
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                       R ++l+aL  +++++++el  +++ s++ + + L+ L + gLve + 
  gi|557693833|ref|YP_008796887.1| 10 LRKDVLDAL-FDGPHSVTELVSAVRASRQGVIKTLKSLMSEGLVEKEP 56
                                      79*******.***********************************886 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   8.5e-05      0.08      26      60 ..      24      58 ..      23      61 .. 0.94
   2 ?    1.5   0.0      0.25   2.3e+02      15      37 ..     171     192 ..     166     194 .. 0.85
   3 ?   -1.2   0.0       1.7   1.6e+03      41      54 ..     290     303 ..     287     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.5e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                              GntR 26 sereLaaefgVsrttvReALrrLeaeglverrqgr 60
                                      s+ eL+++   sr+ v + L+ L +eglve ++g+
  gi|557693833|ref|YP_008796887.1| 24 SVTELVSAVRASRQGVIKTLKSLMSEGLVEKEPGK 58
                                      5789**************************99997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.25
                                       TTSS-TTSB---HHHHHHHHTS- CS
                              GntR  15 sgelrpGdkLPsereLaaefgVs 37 
                                       + el+ G+ L se+ + +e+ +s
  gi|557693833|ref|YP_008796887.1| 171 NYELNEGEEL-SEETIGTELSFS 192
                                       56899*****.*******99988 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHTTSE CS
                              GntR  41 vReALrrLeaeglv 54 
                                       + eAL +L + g +
  gi|557693833|ref|YP_008796887.1| 290 IKEALETLRSSGKI 303
                                       789*****999876 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.5e-05     0.052      16      51 ..      21      56 ..      20      59 .. 0.95
   2 ?   -2.1   0.0       3.9   3.7e+03      24      46 ..     230     252 ..     213     252 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.5e-05
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRsk 51
                                      gp+sv+eL +++  s+  v ++l+ L  +Gl+e+++
  gi|557693833|ref|YP_008796887.1| 21 GPHSVTELVSAVRASRQGVIKTLKSLMSEGLVEKEP 56
                                      89*******************************987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.9
                                       HHHHTS-HHHHHHHHHHHHHTTS CS
                              MarR  24 akklgvskstvtrvldrLekkGl 46 
                                         + +  ++t   +++  e++G+
  gi|557693833|ref|YP_008796887.1| 230 NTFEQRGNATCVDIIRFFERRGW 252
                                       34444445555556666666665 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.013        13      41      77 ..      17      53 ..       5      54 .. 0.91
   2 ?    4.2   0.1     0.032        31      15      37 ..      57      79 ..      55      81 .. 0.85
   3 ?   -0.1   0.0      0.76   7.1e+02      23      70 ..     185     232 ..     183     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.013
                                      HH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 41 nlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                      +l DG +s+ ++ + + ++ + v++ +++L  +gl++
  gi|557693833|ref|YP_008796887.1| 17 ALFDGPHSVTELVSAVRASRQGVIKTLKSLMSEGLVE 53
                                      688********************************97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.032
                                      TS----------------HHHHH CS
                            HTH_47 15 GrrGLYrtiggkntakqaemall 37
                                      G+rG+Y  + +++++++ ++++l
  gi|557693833|ref|YP_008796887.1| 57 GKRGMYMLTEKGYSEHHSRREML 79
                                      9*******999998788888887 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.76
                                       ----------HHHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHH CS
                            HTH_47  23 iggkntakqaemallwvLnlaDGkrsLldiAeriglpfdrvaaiaraL 70 
                                       ig++ + +++    l++ ++ D ++ ++d A   ++ +  +++ ++  
  gi|557693833|ref|YP_008796887.1| 185 IGTELSFSAKLSLSLDFTAFQDPEKKIVDKARMKQAAALMILHFLNTF 232
                                       666666666777789999999999999999999998888877776665 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 ?   10.2   0.0   0.00059      0.56      19      43 ..      33      57 ..      29      60 .. 0.86
   2 ?    0.6   0.0       0.6   5.6e+02      16      38 ..     216     238 ..     214     243 .. 0.86
   3 ?   -2.2   0.0       4.6   4.4e+03      27      42 ..     292     307 ..     288     309 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00059
                          BLACT_WH 19 paAergvlahLeKLeeeGkVkregd 43
                                      +a ++gv+ +L+ L++eG+V++e +
  gi|557693833|ref|YP_008796887.1| 33 RASRQGVIKTLKSLMSEGLVEKEPG 57
                                      67789****************9974 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.6
                          BLACT_WH  16 slhpaAergvlahLeKLeeeGkV 38 
                                       ++ +aA+  +l+ L+  e++G +
  gi|557693833|ref|YP_008796887.1| 216 RMKQAAALMILHFLNTFEQRGNA 238
                                       7889**********999999865 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.6
                          BLACT_WH  27 ahLeKLeeeGkVkreg 42 
                                         Le L++ Gk+ +++
  gi|557693833|ref|YP_008796887.1| 292 EALETLRSSGKIDEKS 307
                                       579999999*998865 PP

>> DUF3085  Protein of unknown function (DUF3085)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.8e-05     0.064       8      37 ..      58      88 ..      56      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.8e-05
                           DUF3085  8 deGvYllsngg.kladgqkklvaYaeecdPk 37
                                       +G+Y+l+++g + ++ ++++++Y eec+Pk
  gi|557693833|ref|YP_008796887.1| 58 KRGMYMLTEKGySEHHSRREMLVYDEECEPK 88
                                      68*********9999999************8 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 ?   12.5   0.0   9.3e-05     0.088      39      72 ..      39      71 ..      24      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.3e-05
                      HrcA_DNA-bdg 39 tvRNqlqsLkalgLvegvpGPkGGYkPtlkayea 72
                                       +   l+sL + gLve  pG +G Y+ t k y++
  gi|557693833|ref|YP_008796887.1| 39 VI-KTLKSLMSEGLVEKEPGKRGMYMLTEKGYSE 71
                                      33.357788888******************9986 PP

>> DUF910  Bacterial protein of unknown function (DUF910)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.4   4.2e+03      34      46 ..      43      55 ..      41      66 .. 0.83
   2 ?   11.5   0.1   0.00025      0.23      11      54 ..     270     314 ..     267     320 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.4
                                      HHHHHHTTSS-HH CS
                            DUF910 34 lkeLykaglidkk 46
                                      lk+L+++gl++k+
  gi|557693833|ref|YP_008796887.1| 43 LKSLMSEGLVEKE 55
                                      7999999999997 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00025
                                       HHTTS-----.S-HHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHH CS
                            DUF910  11 LKkfGiiiYv.gdrladlelmeiElkeLykaglidkkeYltAkli 54 
                                        K+ +ii +  +d  a l l+++ l++L ++g id+k Y +A+ i
  gi|557693833|ref|YP_008796887.1| 270 IKRRNIIMHKkTDNRARLSLIKEALETLRSSGKIDEKSYKQAMKI 314
                                       55556666641467789*************************977 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 ?    9.9   0.1   0.00068      0.64      55      84 ..      42      69 ..       5      73 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00068
                           DUF1495 55 sessLielGLveeeeeseglklYklteeGi 84
                                      + +sL++ GLve+e +++g  +Y lte+G 
  gi|557693833|ref|YP_008796887.1| 42 TLKSLMSEGLVEKEPGKRG--MYMLTEKGY 69
                                      3479*******86555555..799***996 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00071      0.67      36      72 ..      41      71 ..      22      74 .. 0.76
   2 ?   -0.4   0.0       1.2   1.1e+03      25      36 ..     130     141 ..     117     150 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00071
                                      HHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                              PadR 36 paLkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                      ++Lk+L  eglve+e        +r +Y lT++G +e
  gi|557693833|ref|YP_008796887.1| 41 KTLKSLMSEGLVEKEPG------KRGMYMLTEKGYSE 71
                                      78***********9966......59*********876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                                       T-CCTTHHHHHH CS
                              PadR  25 gllelseGslYp 36 
                                        +++l++G++Y+
  gi|557693833|ref|YP_008796887.1| 130 RFFTLEHGRVYQ 141
                                       478999*****7 PP

>> Dimerisation2  Dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0    0.0013       1.2      23      78 ..      14      66 ..      10      70 .. 0.90
   2 ?   -3.0   0.0       7.8   7.4e+03      28      46 ..     175     193 ..     166     199 .. 0.58
   3 ?    0.3   0.0      0.75     7e+02      39      58 ..     247     266 ..     216     284 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0013
                     Dimerisation2 23 vFdlLkeeeplsaeevaeelgasvkGterLldacvaLgLLerekkeekkalYsnte 78
                                      v d+L + +p+s+ e+ +++ as +G+   l+ +++ gL e  k+ +k+++Y  te
  gi|557693833|ref|YP_008796887.1| 14 VLDALFD-GPHSVTELVSAVRASRQGVIKTLKSLMSEGLVE--KEPGKRGMYMLTE 66
                                      7788888.*********************************..55677799*9997 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.8
                     Dimerisation2  28 keeeplsaeevaeelgasv 46 
                                       +e e+ls e++ +el++s+
  gi|557693833|ref|YP_008796887.1| 175 NEGEELSEETIGTELSFSA 193
                                       4455566666666665554 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.75
                     Dimerisation2  39 aeelgasvkGterLldacva 58 
                                        e+ g+ +kG + Ll+a v 
  gi|557693833|ref|YP_008796887.1| 247 FERRGWAPKGWTKLLEAAVN 266
                                       46889999999999999986 PP

>> RPE65  Retinal pigment epithelial membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.13     255     302 ..     213     260 ..     196     312 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                                       ...EEEEE--SEEEEEEEEEEET.TCEEEEEEEEE.SS..--STTS-CT CS
                             RPE65 255 akfrwfeteaffvfHtaNayeeeedgevvvdlcryedae.vldnlylen 302
                                       +k r  ++ a +++H++N++e++ ++++ vd++r+ ++   + + + + 
  gi|557693833|ref|YP_008796887.1| 213 DKARMKQAAALMILHFLNTFEQR-GNATCVDIIRFFERRgWAPKGWTKL 260
                                       33333334699**********96.555669****966543444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2602.27
//
Query:       gi|557693834|ref|YP_008796888.1|  [L=139]
Description: hypothetical protein CSUB_C0397 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   55.2   0.0    1.3e-14   54.9   0.0    1.1  1  Prim-Pol  Bifunctional DNA primase/polymerase, N-terminal


Domain annotation for each model (and alignments):
>> Prim-Pol  Bifunctional DNA primase/polymerase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   7.1e-19   1.3e-14       2     137 ..      10     131 ..       9     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 7.1e-19
                          Prim-Pol   2 leyaergwpvvPlppggKrPlgkkwekdattdpeqirawwkkhpranvglatgpsglvvlDvDgkeagaealarLar 78 
                                        +y++rg+ v+Pl  g+KrP+ ++w+k+   ++e++ a +++h  +n+g+++    l vlD+ +    +  ++  ++
  gi|557693834|ref|YP_008796888.1|  10 DDYFSRGLVVIPLVRGDKRPMVSEWQKK---SREELFAVFREHSGCNIGIRLD--SLTVLDIEHARLWRLFFE--TE 79 
                                       5899******************999986...6789999*************98..9*********76666666..33 PP

                          Prim-Pol  79 eegplPe.tvtvttgstgggrhlyfraPdglalpnsagklapgldlr.geggyvvappsvh 137
                                        + +l + t + +tg   gg+h+yf+     + p++a       +lr ge+++vvapp+ +
  gi|557693834|ref|YP_008796888.1|  80 PR-ELASkTWVSRTGG--GGYHVYFKG---STTPSKADGY---AELRsGEKQFVVAPPQHT 131
                                       33.5555366666666..********3...3333333333...99**8888*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1017.73
//
Query:       gi|557693835|ref|YP_008796889.1|  [L=146]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1023.71
//
Query:       gi|557693836|ref|YP_008796890.1|  [L=426]
Description: hypothetical protein CSUB_C0399 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   18.9   0.0     0.0026   18.3   0.0    1.3  1  AAA_23      AAA domain
     0.0029   17.8   0.8     0.0049   17.0   0.8    1.3  1  CEP209_CC5  Coiled-coil region of centrosome protein CE290
  ------ inclusion threshold ------
      0.012   15.8   0.0      0.021   15.1   0.0    1.3  1  DUF3631     Protein of unknown function (DUF3631)
       0.21   11.3   0.0       0.37   10.4   0.0    1.4  2  AAA_15      AAA ATPase domain


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.7e-07    0.0026      24     189 ..     112     310 ..      98     348 .. 0.52

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.7e-07
                            AAA_23  24 ItGpNGaGKTTildAiklaLygetprlsrks..........grgfeksdveiesegkvkayveltfenkdgrytrsi 90 
                                       ++G+N++GK+  l+ +++ +y  +++ s +           g  +   + e++ +++++  +++  +  +++     
  gi|557693836|ref|YP_008796890.1| 112 LVGDNESGKSHTLNLFTWLCYRPFSGVSHTAadlysyleddGLPLTIIEDEFQGSEEDNDKMKIYKSGYKRG----A 184
                                       79********************99999888888776666442233333333444466667777775543332....4 PP

                            AAA_23  91 ererelskkkgkttkkaklelleideleqfisellgskki..ilnlilflgqer..................feefe 147
                                       +  r ++++ g++++  ++ +++i + e++i+++   + +  i +l+  ++ ++                  +++++
  gi|557693836|ref|YP_008796890.1| 185 RVGRVVTYEGGRRIDYFNTYGMKIMAGERLIENKGLLQ-RciIVELVEGYPVKDhydesdyfrfralrndllKWRMK 260
                                       44555555555555555555555555455555422221.11222333333333222222233332222244433333 PP

                            AAA_23 148 l....kdkke..........rleelekeleeledekkllekleqekekekeleele 189
                                            +              r +el + l    +  ++ ek+    e+ k+le+ +
  gi|557693836|ref|YP_008796890.1| 261 VlagdE---HleqpvtelkgRARELYTPLLAVLKGHEFYEKV---IEWIKKLEQQK 310
                                       333331...022233333333333333332222222222222...23333333322 PP

>> CEP209_CC5  Coiled-coil region of centrosome protein CE290
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.8   1.1e-06    0.0049       9      74 ..     251     317 ..     245     325 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                        CEP209_CC5   9 kakleeelkkleeerrkaeskavelelklkgL.eelistlkdakgaqkvleWhkkieelrlqelklk 74 
                                       +++l + + k+    +++e+ ++el+ + ++L   l++ lk +   +kv+eW kk+e+ ++ e +l+
  gi|557693836|ref|YP_008796890.1| 251 RNDLLKWRMKVLAGDEHLEQPVTELKGRARELyTPLLAVLKGHEFYEKVIEWIKKLEQQKMAEKQLS 317
                                       555666666667777889999999999*99994469**************************98876 PP

>> DUF3631  Protein of unknown function (DUF3631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   4.6e-06     0.021      16     130 ..     240     350 ..     230     368 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.6e-06
                           DUF3631  16 errdeeelealrdrLaawaesvaeevaeaepempegveDRaadvwepLlavadlaggewpetaraAcvklvaeakae 92 
                                        ++d   ++alr++L +w  +v +  ++ e  +  +++ Ra + + pLlav++  g e  e   +  +kl +++ ae
  gi|557693836|ref|YP_008796890.1| 240 DESDYFRFRALRNDLLKWRMKVLAGDEHLEQPVT-ELKGRARELYTPLLAVLK--GHEFYEKVIEWIKKLEQQKMAE 313
                                       455677899************9999888877766.8**************975..8888888888888886666555 PP

                           DUF3631  93 eesslgvrLLadirevfekkdadrlstaelleeLnede 130
                                       ++ s++  L + + + + +k++++l+  ++ ++L +  
  gi|557693836|ref|YP_008796890.1| 314 KQLSVEGLLAKILLDSV-RKGENELALDKIWQALLQFA 350
                                       55777766666666666.77777788888888777665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   8.3e-05      0.37      25      83 ..     109     163 ..      98     218 .. 0.72
   2 ?   -3.4   0.0       1.3     6e+03     176     189 ..     302     317 ..     269     351 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.3e-05
                            AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef 83 
                                       +  l+G N sGKS  l+++ ++  +  +++  v  ++++ +++  +++      I+ ef
  gi|557693836|ref|YP_008796890.1| 109 YLYLVGDNESGKSHTLNLFTWLCYR--PFS-GVSHTAADLYSYL-EDDGLPLTIIEDEF 163
                                       5679*****************9994..444.3333444444444.66666666677777 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
                            AAA_15 176 leeslkkee..elknv 189
                                       ++++l++++  e++ +
  gi|557693836|ref|YP_008796890.1| 302 WIKKLEQQKmaEKQLS 317
                                       2222222222222333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); 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: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2700.49
//
Query:       gi|557693837|ref|YP_008796891.1|  [L=475]
Description: ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-08   34.4   0.0     0.0013   19.2   0.0    2.4  2  ABC_tran         ABC transporter
    1.2e-06   28.8   0.0    7.3e-05   23.1   0.0    2.4  2  AAA_22           AAA domain
    4.2e-05   23.8   0.0    0.00018   21.8   0.0    2.0  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00026   21.4   0.0    0.00091   19.6   0.0    1.9  2  AAA_16           AAA ATPase domain
     0.0019   18.1   0.0      0.062   13.2   0.0    2.7  3  NACHT            NACHT domain
     0.0034   17.8   0.0     0.0078   16.6   0.0    1.6  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0086   16.0   0.0      0.021   14.8   0.0    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.025   13.8   0.0      0.042   13.0   0.0    1.3  1  PIF1             PIF1-like helicase
      0.026   14.9   0.0       0.14   12.6   0.0    2.2  2  AAA              ATPase family associated with various cellul
      0.027   14.6   0.0      0.066   13.3   0.0    1.7  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
       0.03   13.8   0.0      0.061   12.8   0.0    1.5  2  Acetyltransf_15  Putative acetyl-transferase
      0.032   14.6   0.0       0.16   12.4   0.0    2.0  2  RNA_helicase     RNA helicase
      0.036   14.1   0.0      0.087   12.9   0.0    1.6  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.056   13.1   0.0       0.14   11.8   0.0    1.6  1  SH3_2            Variant SH3 domain
      0.075   13.6   0.0       0.16   12.5   0.0    1.6  1  AAA_18           AAA domain
      0.082   12.7   0.0       0.17   11.7   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
       0.11   12.0   0.5        1.1    8.8   0.1    2.4  2  AAA_25           AAA domain
       0.17   11.6   0.0       0.54    9.9   0.0    1.8  1  AAA_30           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 !   19.2   0.0   1.3e-06    0.0013       2      37 ..      56      91 ..      55      98 .. 0.90
   2 !   13.0   0.0   0.00012      0.11     104     135 ..     140     171 ..     102     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                                      EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  2 knvslklkegekvaivGenGaGKStLlkllagllkp 37
                                      k+ ++++++g +v ++Ge+G GKS Ll+ la+++++
  gi|557693837|ref|YP_008796891.1| 56 KDSEINFEAGDVVYVTGESGGGKSLLLRHLAKQMRN 91
                                      677899*************************98765 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00012
                                       TTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 104 sspssLSgGqkqrvalarallkkpkllllDEp 135
                                       ++  +LS Gqk r   a+al + ++ +++DE 
  gi|557693837|ref|YP_008796891.1| 140 RRFDELSDGQKMRFIFAKALDTGARTIIIDEF 171
                                       4459**************************95 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   7.4e-08   7.3e-05       7     127 ..      67     200 ..      62     208 .. 0.72
   2 ?    3.1   0.0       0.1     1e+02      53     114 ..     377     443 ..     357     455 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 7.4e-08
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee..........erpevv.........fvtlpsstsskdllrellral 64 
                                       +++vtGesG GK++llr l++q  + ++ +           ++++++          v++ s  +++d+++++ r+ 
  gi|557693837|ref|YP_008796891.1|  67 VVYVTGESGGGKSLLLRHLAKQMRNNPEFAPvacswrlnipRDKPLIdcvgrdvkeAVEVLSAAGLSDVFTWFRRFD 143
                                       789********************888777778888888888444444444555556777777777777777776665 PP

                            AAA_22  65 glelkaerlsseellealeqalraravielliiDEaqh.lrseealeeLrsllnl.srkgvqliL 127
                                       +l       + + ++  +++al++ a+   +iiDE+   l++e+a  +  ++++l +r g++li+
  gi|557693837|ref|YP_008796891.1| 144 EL------SDGQKMRFIFAKALDTGAR--TIIIDEFCSvLDRETAKATAYTMQKLaRRRGITLIV 200
                                       53......4678999999999999999..******999665444444443343333377777766 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.1
                            AAA_22  53 skdllrellralglelkaerlsseellealeqalrarav...ielliiDEaqhlr.....s...eealeeLrs 114
                                        k ll+e+  ++g++  +  +      +++ +++++++     +  ++D+ +++      s   +++l++L+s
  gi|557693837|ref|YP_008796891.1| 377 KKALLKEFRDKFGVDVMR--HGV----DQILRYINEKGLlneLRRWLLDNLEKFAdaaasSrdtANMLKTLKS 443
                                       566667777777766665..444....4444444444444444889999999987776642566777777754 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       9.4   9.3e+03      79      93 ..      79      94 ..      79     100 .. 0.81
   2 !   21.8   0.0   1.8e-07   0.00018      18      82 ..     249     336 ..     235     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.4
                                      HHHHHHHHHHHHHT.T CS
                    Acetyltransf_1 79 saLlealeeraree.g 93
                                      s+Ll++l++++r++ +
  gi|557693837|ref|YP_008796891.1| 79 SLLLRHLAKQMRNNpE 94
                                      689******9999855 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 1.8e-07
                                       HHHHHH...HHHHHHSTTC...EEEE.EEETTEEEEEEEEEEEET.................TSTTEEEEEEEEESG CS
                    Acetyltransf_1  18 daseee...feesfsleae...gllv.aeedgeliGfisllkipd.................ekggvayieslaVsp 70 
                                       +++ ++   f ++ s +++    + + a  +g+++G + + k +                    ++v  i +++V+p
  gi|557693837|ref|YP_008796891.1| 249 STEDWRllsFLHYRSHHTPaavKI-FrAVLNGRVVGVVVYAKPYLhatgysrffrpdwylreRMNHVLRISRVVVHP 324
                                       445555455555555566643333.269999*******999999988888888888889998778999999****** PP

                                       GGTTSSHHHHHH CS
                    Acetyltransf_1  71 eyrgkGlGsaLl 82 
                                       ++rg G++++Ll
  gi|557693837|ref|YP_008796891.1| 325 SFRGIGVARKLL 336
                                       ***********8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   9.1e-07   0.00091      25      86 ..      66     124 ..      54     201 .. 0.69
   2 ?   -2.1   0.0       4.4   4.4e+03      84     112 ..     403     431 ..     385     465 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 9.1e-07
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysa.laqalareellrqll 86 
                                        +v+++GesG GKs l+r+l+++++ +   f  +++ ++ +   ip++  l+++  r ++ ++  
  gi|557693837|ref|YP_008796891.1|  66 DVVYVTGESGGGKSLLLRHLAKQMRNN-PEFapVACSWRLN---IPRDKpLIDCVGR-DV-KEAV 124
                                       5799********************999.4443488888888...8886668888833.33.3333 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.4
                            AAA_16  84 qlldeaesaeleawrekleealaavpela 112
                                        ++++   +el++w    +e +a++++ +
  gi|557693837|ref|YP_008796891.1| 403 YINEKGLLNELRRWLLDNLEKFADAAASS 431
                                       44444444455555554444444333322 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   6.3e-05     0.062       2      26 ..      67      91 ..      66      98 .. 0.89
   2 ?    1.5   0.0      0.26   2.6e+02      52      99 ..     161     213 ..     133     241 .. 0.72
   3 ?   -2.0   0.0         3   2.9e+03     102     141 ..     406     443 ..     389     459 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.3e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                      +v ++Ge+G GK+ Ll++la +++ 
  gi|557693837|ref|YP_008796891.1| 67 VVYVTGESGGGKSLLLRHLAKQMRN 91
                                      899*****************98875 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.26
                                       .-HCHHHCCCCTS--SSS-C.....CHHHHCCSCCCEEEEEE-STT-SS-TCH CS
                             NACHT  52 rsladllfsqlpepaapvse.....vwavllelperlLlilDglDelvtdlgq 99 
                                       ++ ++++ ++++   ++ +       ++ l++++  +L++  ++D+lv+dl++
  gi|557693837|ref|YP_008796891.1| 161 TGARTIIIDEFCSVLDRETAkatayTMQKLARRRGITLIVATAIDDLVEDLNP 213
                                       45555555555555555555555588999999999999999999999999988 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3
                                       .......HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSC CS
                             NACHT 102 kqpvrtlLselirkkllpeasllltvrpralrdleeqlee 141
                                       ++ + + L++++  +l + a   +++r +a   + ++l++
  gi|557693837|ref|YP_008796891.1| 406 EKGLLNELRRWLLDNLEKFADAAASSRDTAN--MLKTLKS 443
                                       4566667777777777777777777777766..5444444 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   7.8e-06    0.0078      24      46 ..     304     336 ..     268     364 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.8e-06
                                       S..........TCTEEEEE-GGGTTSSHHHHHH CS
                    Acetyltransf_7  24 d..........aeitrlaVdpeyrgkGiGraLl 46 
                                       d            i r++V+p++rg G++r+Ll
  gi|557693837|ref|YP_008796891.1| 304 DwylrermnhvLRISRVVVHPSFRGIGVARKLL 336
                                       2555555544455666****************9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) 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     0.021      53      77 ..     316     340 ..     306     350 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                   Acetyltransf_10  53 hisllfVdpeyrgqGigkaLleave 77 
                                       +is+++V+p++rg G++++Ll + +
  gi|557693837|ref|YP_008796891.1| 316 RISRVVVHPSFRGIGVARKLLIESL 340
                                       8*******************98765 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.3e-05     0.042      17      51 ..      60      94 ..      54     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                                      ...HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCC CS
                              PIF1 17 vlnekgklfFvtGsgGtgKtflwkallkklrsegk 51
                                      ++ e g +++vtG +G gK+ l+++l k++r++ +
  gi|557693837|ref|YP_008796891.1| 60 INFEAGDVVYVTGESGGGKSLLLRHLAKQMRNNPE 94
                                      45689*************************98754 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 ?   12.6   0.0   0.00014      0.14       1     111 [.      68     204 ..      68     228 .. 0.54
   2 ?   -1.6   0.0       3.4   3.4e+03      62      88 ..     416     440 ..     379     468 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                       EEEESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSS..................................STTH CS
                               AAA   1 vllyGppGtGKTllakavakel..gvefleisgsellsk..................................yvge 41 
                                       v+++G  G GK+ll + +ak++  + ef  + +s  l+                                    + e
  gi|557693837|ref|YP_008796891.1|  68 VYVTGESGGGKSLLLRHLAKQMrnNPEFAPVACSWRLNIprdkplidcvgrdvkeavevlsaaglsdvftwfrRFDE 144
                                       6899*****************94423343343333332233344444333344444555555555556666665555 PP

                                       HHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS CS
                               AAA  42 sekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr 111
                                        ++  ++ f  ak+   +   ++iDE+ ++  ++          ++++    ++++ ++ + +++i+at  
  gi|557693837|ref|YP_008796891.1| 145 LSDGQKMRFIFAKALDtGARTIIIDEFCSVLDRE----------TAKATAYTMQKLARR-RGITLIVATAI 204
                                       5555555544444444435777788887777666..........222222222222222.22555555555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.4
                                       EEEETGGGHHHHHTTCCCHHHHHHHHH CS
                               AAA  62 lfiDEidalaksrsgseseeeervvnq 88 
                                        ++D+++++a +   ++s+++ +++++
  gi|557693837|ref|YP_008796891.1| 416 WLLDNLEKFADAA--ASSRDTANMLKT 440
                                       4677777777776..222222222222 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 ?   13.3   0.0   6.7e-05     0.066      19      46 ..     309     336 ..     273     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.7e-05
                   Acetyltransf_CG  19 vrkegvldfthTeVpeelrGkGiAkkLv 46 
                                       +r ++vl +  ++V++++rG G+A+kL 
  gi|557693837|ref|YP_008796891.1| 309 ERMNHVLRISRVVVHPSFRGIGVARKLL 336
                                       78899*********************97 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       5.7   5.6e+03     169     200 ..     188     219 ..     168     226 .. 0.68
   2 ?   12.8   0.0   6.1e-05     0.061      69     101 ..     311     343 ..     238     387 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.7
                   Acetyltransf_15 169 ekrseekgkylamfckvndflnkkkiraeemk 200
                                       +k ++ +g  l++++ ++d+ +  + + + +k
  gi|557693837|ref|YP_008796891.1| 188 QKLARRRGITLIVATAIDDLVEDLNPNLLIIK 219
                                       55677788888888888888776665555555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.1e-05
                   Acetyltransf_15  69 eknvleiYtlyvsekyrgkGlakklLeeslkel 101
                                        ++vl i  ++v++ +rg G+a+klL esl +l
  gi|557693837|ref|YP_008796891.1| 311 MNHVLRISRVVVHPSFRGIGVARKLLIESLPRL 343
                                       467999**********************98766 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00016      0.16       1      25 [.      68      92 ..      68     104 .. 0.89
   2 ?   -1.3   0.0       2.8   2.8e+03      49      73 ..     162     187 ..     159     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                      ++++G+sg GKS+l ++Lak++ ++
  gi|557693837|ref|YP_008796891.1| 68 VYVTGESGGGKSLLLRHLAKQMRNN 92
                                      79*****************999754 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.8
                      RNA_helicase  49 gqevvvidDfgqvkdee.npsdlael 73 
                                       g   ++id+f++v d+e  +    ++
  gi|557693837|ref|YP_008796891.1| 162 GARTIIIDEFCSVLDREtAKATAYTM 187
                                       56778999999999887444455544 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.8e-05     0.087      56     102 ..     297     343 ..     261     356 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.8e-05
                                       EEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHHHHH CS
                    Acetyltransf_9  56 qlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaraleem 102
                                         ++++ +++++++  ++  ++ V v+p  rg gv++kLl ++l ++
  gi|557693837|ref|YP_008796891.1| 297 YSRFFRPDWYLRERMNHVLRISRVVVHPSFRGIGVARKLLIESLPRL 343
                                       56788899999*****************************9998665 PP

>> SH3_2  Variant SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014      0.14      13      34 ..      57      76 ..      51      82 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                                      CCB--B-TTEEEEEE..EEEEC CS
                             SH3_2 13 kseLsfkkGdvikvlslgskds 34
                                       se++f++Gdv++v+  g+++ 
  gi|557693837|ref|YP_008796891.1| 57 DSEINFEAGDVVYVT--GESGG 76
                                      579************..44333 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00016      0.16       2      86 ..      69     175 ..      68     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                            AAA_18   2 lltGtpGvGKttlakeLskrl.gf...........................gvnlrdvakenglllevdpealdesk 50 
                                        +tG +G GK+ l ++L+k + ++                           + +  +v++  gl++ ++++  ++++
  gi|557693837|ref|YP_008796891.1|  69 YVTGESGGGKSLLLRHLAKQMrNNpefapvacswrlniprdkplidcvgrdVKEAVEVLSAAGLSDVFTWF--RRFD 143
                                       69******************977799999999999999999999999866666666666666666666666..8888 PP

                            AAA_18  51 rldedkldklldaleenssaleegknlvidghlael 86 
                                       +l +++    ++ + + +   + + +++id + + l
  gi|557693837|ref|YP_008796891.1| 144 ELSDGQ---KMRFIFAKAL-DTGARTIIIDEFCSVL 175
                                       888888...4444444443.5667788888877766 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 ?   11.7   0.0   0.00017      0.17      12      39 ..      55      82 ..      51      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                                      f++ +i+++  +++ +tG+sG GKS ll
  gi|557693837|ref|YP_008796891.1| 55 FKDSEINFEAGDVVYVTGESGGGKSLLL 82
                                      788899999777*************886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0011       1.1      31     160 ..      63     180 ..      53     222 .. 0.63
   2 ?   -3.0   0.0       4.4   4.4e+03     126     138 ..     410     422 ..     378     442 .. 0.52

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                            AAA_25  31 pagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvld 107
                                        ag+++ ++G +g GK+ l+ +la  +    p + pv         + +  ++   ++ + +vg+++  ++ + vl+
  gi|557693837|ref|YP_008796891.1|  63 EAGDVVYVTGESGGGKSLLLRHLAKQMRN-NPEFAPV------ACSWRLNIPR--DKPLIDCVGRDV--KEAVEVLS 128
                                       46677777777777777777777766543.3333322......2222222333..123344444444..67777777 PP

                            AAA_25 108 lagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggden 160
                                       +ag  ++  ++ ++++    ++++ + a++ +  g+r ++iD + ++l+ +  
  gi|557693837|ref|YP_008796891.1| 129 AAGLSDVFTWFRRFDELSDGQKMRFIFAKALD-TGARTIIIDEFCSVLDRETA 180
                                       76666667777777777777777777777777.56777777777777766554 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.4
                            AAA_25 126 ltadvdaleaaie 138
                                       l++  ++l + +e
  gi|557693837|ref|YP_008796891.1| 410 LNELRRWLLDNLE 422
                                       3333333333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00054      0.54      17     100 ..      65     174 ..      59     202 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00054
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa............eelgi.eastiakllkrl 80 
                                       gd v+ +tG  G GK+ +l++l++ ++++  + + +A + +                  e++++  a+ +  + ++ 
  gi|557693837|ref|YP_008796891.1|  65 GD-VVYVTGESGGGKSLLLRHLAKQMRNNP-EFAPVACSWRLNIPRDkplidcvgrdvkEAVEVlSAAGLSDVFTWF 139
                                       44.899*****************9999884.4444444444321111111111111111122212333333333333 PP

                            AAA_30  81 k...............grarlepg.tllivDEagmv 100
                                       +               + ++l++g + +i+DE   v
  gi|557693837|ref|YP_008796891.1| 140 RrfdelsdgqkmrfifA-KALDTGaRTIIIDEFCSV 174
                                       35555666666766642.455555567777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.47
# Mc/sec: 3051.36
//
Query:       gi|557693838|ref|YP_008796892.1|  [L=154]
Description: hypothetical protein CSUB_C0401 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   11.8   2.7      0.033   11.9   2.7    1.1  1  ACR_tran         AcrB/AcrD/AcrF family
      0.082   13.3   0.6      0.082   13.3   0.6    1.6  2  DUF2663          Protein of unknown function (DUF2663)
       0.43   10.6   7.1       0.84    9.7   7.1    1.7  1  p53-inducible11  Tumour protein p53-inducible protein 11
       0.98    7.6  10.7        1.4    7.1  10.7    1.2  1  DUF2070          Predicted membrane protein (DUF2070)
        2.3    8.1  15.5       0.17   11.8   3.6    2.6  2  DUF2721          Protein of unknown function (DUF2721)
        3.8    7.4   7.3        1.1    9.1   0.2    3.1  3  LapA_dom         Lipopolysaccharide assembly protein A domain
        5.7    7.4  12.7    1.4e+02    2.9  12.7    2.3  1  CPBP             CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.7   1.3e-05     0.033     431     480 ..      32      81 ..      13     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                          ACR_tran 431 iqgalvaialvllavflPilflgGveGklfrqfaltivlaillsvlvalt 480
                                       i  a+v+i + lla f+P+++l+ + G +f   ++  +++++l ++  + 
  gi|557693838|ref|YP_008796892.1|  32 IIIAIVSIGFALLALFMPTFLLHTIAGTIFTHEIIESSFSVALLLVCTVF 81 
                                       789***************************98888777777776665554 PP

>> DUF2663  Protein of unknown function (DUF2663)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.6   3.2e-05     0.082       7      73 ..      15      87 ..      12      95 .. 0.85
   2 ?   -0.6   0.1      0.65   1.7e+03      24      40 ..      96     112 ..      83     154 .] 0.45

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                           DUF2663  7 krKkkweklekrllllsllallvlllfliyvlik......ssslssllsallessvlllllllvallyvavkl 73
                                       +Kk   +l +rl l+s++  +v++ f+++ l++      + + + + + ++ess+++ lll+ ++ +++++ 
  gi|557693838|ref|YP_008796892.1| 15 DKKKDLSRLMRRLPLWSIIIAIVSIGFALLALFMptfllhTIAGTIFTHEIIESSFSVALLLVCTVFFFTAYK 87
                                      68999****************99999999998888998855566889999********999999888887664 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.65
                           DUF2663  24 llallvlllfliyvlik 40 
                                       +l+l++l++ +i   + 
  gi|557693838|ref|YP_008796892.1|  96 ILSLTSLAIPFIVFHQL 112
                                       44444444333322122 PP

>> p53-inducible11  Tumour protein p53-inducible protein 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   7.1   0.00033      0.84      48     125 ..      22      95 ..       9     152 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00033
                   p53-inducible11  48 rlPlGlrlWqllsavvftalallalvfPdtlvevvfseeladtkisilalrlyGgallalalilWnalttaekviir 124
                                       rl + l lW ++ a+v + +allal++P  l++++  +  +++ i +     +  all ++ +++ +++ + k i+ 
  gi|557693838|ref|YP_008796892.1|  22 RLMRRLPLWSIIIAIVSIGFALLALFMPTFLLHTIAGTIFTHEIIES----SFSVALLLVCTVFFFTAYKPWKKIVA 94 
                                       5666788*********************9999998888877777765....56677777777777666666666654 PP

                   p53-inducible11 125 w 125
                                        
  gi|557693838|ref|YP_008796892.1|  95 T 95 
                                       3 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1  10.7   0.00054       1.4       9     151 ..      25     131 ..      17     153 .. 0.34

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00054
                           DUF2070   9 frlPswkvsllliillalligllaflssklfgillfglpalvaflltlpvlrilggrltykrslflalltelivvii 85 
                                        rlP w+                                                        +++a+++  ++++ 
  gi|557693838|ref|YP_008796892.1|  25 RRLPLWS--------------------------------------------------------IIIAIVSIGFALLA 45 
                                       4444443........................................................33333333333333 PP

                           DUF2070  86 sllaillsall.qalvllalvls.lalvfalrllvlvavsdesllkavlpaliqpllailllvly............ 148
                                       ++++++l + +  +++++ ++ s +++++ l+  v+++++ + ++k+v+  l  + lai+++v+             
  gi|557693838|ref|YP_008796892.1|  46 LFMPTFLLHTIaGTIFTHEIIESsFSVALLLVCTVFFFTAYKPWKKIVATILSLTSLAIPFIVFHqltnrlreiakp 122
                                       33333333333322222222222233333333333333333333333333333333333333333455555555555 PP

                           DUF2070 149 ......fsp 151
                                             f+p
  gi|557693838|ref|YP_008796892.1| 123 veayftFGP 131
                                       333332222 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   3.6   6.6e-05      0.17      50     116 ..      17      84 ..       6      87 .. 0.90
   2 ?    1.7   4.1     0.084   2.1e+02      94     114 ..     129     149 ..      90     151 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.6e-05
                           DUF2721  50 akeiknlrrRarlirrailllvlsallvvlvvlllflsall.sldlsllaailfvlalllllvslllf 116
                                       +k +++l rR+ l +  i+++ ++++l++l + + +l  +  ++ ++ +++  f +alll+++  +++
  gi|557693838|ref|YP_008796892.1|  17 KKDLSRLMRRLPLWSIIIAIVSIGFALLALFMPTFLLHTIAgTIFTHEIIESSFSVALLLVCTVFFFT 84 
                                       56799********************************999999999***********99988766665 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.084
                           DUF2721  94 lsllaailfvlalllllvsll 114
                                       +   a+ lf++++l+l++sll
  gi|557693838|ref|YP_008796892.1| 129 FGPGASSLFLAGILMLVASLL 149
                                       55568899**********997 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 ?    9.1   0.2   0.00043       1.1      17      38 ..      27      48 ..      14      55 .. 0.88
   2 ?   -0.3   0.1      0.37   9.5e+02      16      28 ..      69      81 ..      60      87 .. 0.66
   3 ?    0.5   0.2      0.21   5.4e+02      27      45 ..     137     152 ..     128     154 .] 0.48

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00043
                          LapA_dom 17 lpLsllllvafgiGallgwlls 38
                                      lpL+ ++++ + iG+ l  l++
  gi|557693838|ref|YP_008796892.1| 27 LPLWSIIIAIVSIGFALLALFM 48
                                      8**************9988887 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.37
                          LapA_dom 16 elpLsllllvafg 28
                                      +++++lll+ +++
  gi|557693838|ref|YP_008796892.1| 69 SFSVALLLVCTVF 81
                                      5566666666655 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.21
                          LapA_dom  27 fgiGallgwllslwsylrl 45 
                                       f++G+l+ +   lw   r+
  gi|557693838|ref|YP_008796892.1| 137 FLAGILMLVASLLW---RK 152
                                       33333333333333...44 PP

>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9  12.7     0.055   1.4e+02      30      84 ..      22      75 ..      17     154 .] 0.90

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.055
                                      HHHHH...S-HHHHHHHHHHHHHCSGGGHHHHHHHHHHHHHHHHHHHHTT-HHHHHH CS
                              CPBP 30 llqer..gsstlailissilFglaHlpngpsvllaalaGlvlgylylktgsllaail 84
                                      +l++r   +  ++i+i si F+l+ l   p++ll ++aG +++  ++++  + +a+l
  gi|557693838|ref|YP_008796892.1| 22 RLMRRlpLW-SIIIAIVSIGFALLALFM-PTFLLHTIAGTIFTHEIIESS-FSVALL 75
                                      566676778.899*************99.899999999999999888877.666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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):               7  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1083.15
//
Query:       gi|557693839|ref|YP_008796893.1|  [L=355]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   87.7   0.0      2e-24   86.3   0.0    1.7  2  Phage_integrase  Phage integrase family
     0.0001   22.5   0.1     0.0003   21.0   0.1    1.7  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    0.00018   21.9   0.0    0.00041   20.8   0.0    1.5  1  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain


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 ?   -2.4   0.0      0.59   3.6e+03      87     109 ..      53      85 ..      37     101 .. 0.57
   2 !   86.3   0.0   3.3e-28     2e-24       5     167 ..     128     292 ..     124     297 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.59
                                       H.........CHCCTTTSBSSBET.TSSB--HH CS
                   Phage_integrase  87 a.........leeaeksellfask.rgkplsrq 109
                                       +         ++++ek+ +lf+++ r++ l  q
  gi|557693839|ref|YP_008796893.1|  53 CgfsdlvdaaMRAEEKDLVLFIRHlRDEGLAPQ 85 
                                       444444444366677777788887644444443 PP

  == domain 2  score: 86.3 bits;  conditional E-value: 3.3e-28
                                       HHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHH CS
                   Phage_integrase   5 edeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellk 81 
                                        d+ve+ l+++++    +++l++ l+++tGlRi+E+lsLr  d+d+     ++     K+   r+vpl+  ++e+lk
  gi|557693839|ref|YP_008796893.1| 128 RDVVEAVLENMDN---STKRLAIWLIWATGLRIGEALSLRARDIDFTIDPPKLTVISEKTHEPREVPLPTDIAEALK 201
                                       6889999999999...999***************************999999988999******************* PP

                                       HHHHHHCHCCTTTSBSSBET..TSSB--HHHHHHHHHHHHHHCT-S........SC--TTHHHHHHHHHHHHHCTSH CS
                   Phage_integrase  82 ellskaleeaeksellfask..rgkplsrqtvrkafkraveeagie........kpltpHtlRhsfataLleagvdl 148
                                       + l++     ++ +++f  +  + kpl r ++r+af++a  +a+           + t H lR+s+ t+L++agv+ 
  gi|557693839|ref|YP_008796893.1| 202 QHLQRL----QPGDFIFHPRgnPSKPLARTKLRAAFRSALIKANRAerdksgigWRYTIHGLRRSYETNLVRAGVNS 274
                                       ******....********9999********************9998899999999********************** PP

                                       HHHHHHHT-SSCCHHHHHH CS
                   Phage_integrase 149 rvvqkllGHssisttqiYt 167
                                       +vv  llGH+ i + q+Y 
  gi|557693839|ref|YP_008796893.1| 275 MVVGLLLGHR-IGIEQHYL 292
                                       *********6.55556665 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 !   21.0   0.1     5e-08    0.0003      17      78 ..      37      99 ..      26     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5e-08
                                      HHHHHHHHHHHHHHHHHHH..TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHH CS
                   Phage_int_SAM_1 17 nTlraYrrdLrrflkflae.rgkesleqlttedvraflaeleeeglsatslarrlsalrsFfq 78
                                       T ++Yr + rrf++     +   ++ +++++d++ f+++l++egl+  s++++  a++sF++
  gi|557693839|ref|YP_008796893.1| 37 TTAENYRAAMRRFVTTCGFsDLVDAAMRAEEKDLVLFIRHLRDEGLAPQSIRLHYQAVKSFLS 99
                                      599************998867888899**********************************98 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 !   20.8   0.0   6.8e-08   0.00041      14      76 ..      34      99 ..      30     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.8e-08
                   Phage_int_SAM_4 14 lserTiksYlsaikrflrflkkk....apeeltkedieaYlnyLanerklsastqknalnalsffyk 76
                                      ++ +T ++Y  a +rf+  +       a    +++d+ +++ +L+ ++ l++++++ + +a ++f +
  gi|557693839|ref|YP_008796893.1| 34 KTGTTAENYRAAMRRFVTTCGFSdlvdAAMRAEEKDLVLFIRHLR-DEGLAPQSIRLHYQAVKSFLS 99
                                      5679****************73346669999**************.***************999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2493.50
//
Query:       gi|557693840|ref|YP_008796894.1|  [L=284]
Description: hypothetical protein CSUB_C0403 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   16.9   0.7     0.0088   16.0   0.7    1.5  1  TMEM154   TMEM154 protein family


Domain annotation for each model (and alignments):
>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.7   4.9e-07    0.0088      37      84 ..     236     283 ..     205     284 .] 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.9e-07
                           TMEM154  37 qeeakeslssaelsnesdqlelvlmiiiPlvllillllvviiliqkkk 84 
                                       q  ++ ++ s++ s + +q+ +++m+i  +vll ll+++ +il++ +k
  gi|557693840|ref|YP_008796894.1| 236 QRADNTTQTSPQQSSTPEQKYILIMLIAQSVLLTLLVILSLILVKSCK 283
                                       6678899999999*******************************7665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2077.65
//
Query:       gi|557693841|ref|YP_008796895.1|  [L=576]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   56.4   0.3    3.7e-15   56.4   0.3    1.8  2  Glyco_trans_2_3  Glycosyl transferase family group 2
    3.3e-11   43.5   0.0      5e-11   42.9   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.011   14.2   0.0      0.017   13.7   0.0    1.1  1  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 ?   -3.4   1.4       1.3   7.7e+03     168     180 ..      17      29 ..       3      79 .. 0.55
   2 !   56.4   0.3   6.2e-19   3.7e-15       1     191 [.     309     514 ..     309     518 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.3
                   Glyco_trans_2_3 168 plhlallllfsll 180
                                       ++ ++l++lf+ l
  gi|557693841|ref|YP_008796895.1|  17 LAVIVLSILFPAL 29 
                                       2222222222222 PP

  == domain 2  score: 56.4 bits;  conditional E-value: 6.2e-19
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvl.vm.nvanwleelaalffaedhgkdilvrealgrvvpsv. 73 
                                       +i++ D++t + +d +++i + +   ++++i+   ++ ++    +  ++ +   ++ d  ++ l ++++g+  + + 
  gi|557693841|ref|YP_008796895.1| 309 WIYHQDDETKVGEDTILGIMDYIInAGDHDIYAAGIInYAdSLTYTPSRAQEPSRSYDDFRILLTTKTNGKLSFGHh 385
                                       9******************99766369***9997777344255667788888889999999**********999888 PP

                   Glyco_trans_2_3  74 GsgaflrrsalqevggwdgdessvsEDfdmglrlqrkG..yrvrfvpeslvkekspltlraalrQrkRwayGc.el. 146
                                       Gs  ++r+++  +v gwd+  +  +ED+ +gl ++++    ++++      +ek plt ++ l+Qr+Rwa G+ ++ 
  gi|557693841|ref|YP_008796895.1| 386 GSHLLVRADVEAAV-GWDFG-DVKTEDWMFGLMMWQRHrpGKTILKG--YGYEKPPLTTKDLLKQRRRWAHGAmQIv 458
                                       *********99999.***65.899**********9877345555555..56*********************97446 PP

                   Glyco_trans_2_3 147 .....eklil.....lvrll.gylgsllwsalplhlallllfsllalalvllllll 191
                                            +++++      v+++   l+sl+++a+++ +    lf+ + +++ + ++ l
  gi|557693841|ref|YP_008796895.1| 459 fdkriRPRYRlaalyGVVSWmSALPSLIAFAVSIIYPTGGLFPASGIIAGFTWYSL 514
                                       53333222223333322233133455555555554444444444446666666655 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 !   42.9   0.0   8.4e-15     5e-11      59     229 ..     269     452 ..     245     453 .. 0.81

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 8.4e-15
                   Glyco_tranf_2_3  59 vrvrvvvna.rnl.gstgksralnealravk.......sdlvllvDdDtvvePdtlkrllqff...ltpkvgavgtp 123
                                       +rv +v+++ +   g++ k+ral+ a +  +       ++++ + Dd+t v+ dt+  +  ++    ++++ a+g  
  gi|557693841|ref|YP_008796895.1| 269 ARVIIVPREfNTVnGTRYKARALVYANKVMAeeglvnkDTWIYHQDDETKVGEDTILGIMDYIinaGDHDIYAAGII 345
                                       3666666654323488999999999999855456665688***********************84333455555555 PP

                   Glyco_tranf_2_3 124 vfllnrstlvsalgalefaerhlrflaarralg.v.ltlnGsgslirrevlkelegldplflltdDyelglrlrrag 198
                                        +++  +++ s+++      +++r+l+++++ g      +Gs +l+r++v ++  g+d++ ++t+D+  gl+++++ 
  gi|557693841|ref|YP_008796895.1| 346 NYADSLTYTPSRAQEPSRSYDDFRILLTTKTNGkLsFGHHGSHLLVRADVEAAV-GWDFGDVKTEDWMFGLMMWQRH 421
                                       5666777888888888888999999999999986435566**************.********************** PP

                   Glyco_tranf_2_3 199 frtayvpgaavrevfpsslkayikqrnRwvy 229
                                        + ++  +   +e  p ++k++ kqr+Rw+ 
  gi|557693841|ref|YP_008796895.1| 422 RPGKTILKGYGYEKPPLTTKDLLKQRRRWAH 452
                                       ****988888*******************85 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.8e-06     0.017     412     509 ..     396     499 ..     391     506 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-06
                    Cellulose_synt 412 GkeiGwiyGsv.tedvltGfkmharGwrsvycvtkrdafkGsapinlsdrlhqvlrwalGsveiffsrnn......a 481
                                          +Gw +G v ted + G  m +r  r    + k   +    p+   d l+q  rwa G+++i+f ++       a
  gi|557693841|ref|YP_008796895.1| 396 EAAVGWDFGDVkTEDWMFGLMMWQRH-RPGKTILKGYGYE-KPPLTTKDLLKQRRRWAHGAMQIVFDKRIrpryrlA 470
                                       5689*****9989*******999885.5555666666665.579**********************98642222224 PP

                    Cellulose_synt 482 lfagykkklklle.rlaylnviiypftsi 509
                                        ++g+ + +  l   +a+  +iiyp   +
  gi|557693841|ref|YP_008796895.1| 471 ALYGVVSWMSALPsLIAFAVSIIYPTGGL 499
                                       56666677776641468888899997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 4007.03
//
Query:       gi|557693842|ref|YP_008796896.1|  [L=322]
Description: sugar phosphate isomerase/epimerase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  115.7   0.0    3.3e-33  114.9   0.0    1.3  1  AP_endonuc_2    Xylose isomerase-like TIM barrel
    1.5e-17   63.0   0.0      3e-17   62.1   0.0    1.5  1  AP_endonuc_2_N  AP endonuclease family 2 C terminus


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 !  114.9   0.0   3.7e-37   3.3e-33       4     194 ..      22     246 ..      20     266 .. 0.89

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 3.7e-37
                                       HHHCT-SEEEEECCTCSHHHHC...HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC.........HTTCS..HH CS
                      AP_endonuc_2   4 aaeaGfdgvElfgrdlvpvsel...sdeelrelrkaldelglriaslslftrfgypded.........erear..re 66 
                                       +a+ G+++vEl+++ +    +       +++e++++++ + l i+++s +   + ++            ++++   +
  gi|557693842|ref|YP_008796896.1|  22 IASFGYEAVELACWRGSLHLDIdkaLGGGAQEIKRIIENNQLLISAVSNHLEGQLVLGPhdastdgifKGSPEekVK 98 
                                       79************99999888889***********************9999999888866666666633333789* PP

                                       HHHHHHHHHHHHHHHHTBSEEEEEBCC........GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTT CS
                      AP_endonuc_2  67 esvdalkraielaaaLGapllvlhpGt........agagpkgseeeawerlaeslneladyaekegvklalEtlags 135
                                         ++++k++++ a+ L++p++v ++G         +++g+++  e+ +e++ae++ e++dy   +gvk+a E ++ +
  gi|557693842|ref|YP_008796896.1|  99 YGIERMKKTCDVANLLDVPVVVGFIGCpnwgawynFPFGYDKIFESYFELFAERWGEILDYYSSCGVKFAHEVHPQE 175
                                       **************************9**9*99999999999999******************************** PP

                                       TSSSTCHHHHHHHHHHTTTT.EEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESS............T CS
                      AP_endonuc_2 136 gvelgdeelarlldavdspn.vgvclDtgHlliaeedvddalraladrikhvHikDakg............d 194
                                        +++  e++++ l+a+++++ +g+++D++Hl+++  d+  ++++++dri+h H+kD+++            +
  gi|557693842|ref|YP_008796896.1| 176 LAYNV-ETAEQALKAINWKKeFGFNFDPSHLIWQLIDPVVFIKKFGDRIFHSHAKDGELvaenlstsgaipT 246
                                       *****.***************************************************997776666555552 PP

>> AP_endonuc_2_N  AP endonuclease family 2 C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   0.0   3.3e-21     3e-17       1      55 [.     267     320 ..     267     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 3.3e-21
                    AP_endonuc_2_N   1 dwkdifsaLrqiGYdgplSiEwEDslmsreeGareAvaflkdkllieeseaafdw 55 
                                       +wk++++a +++GYd+++S E+ED++ms+e+G+++ +++lk+ lli+++ ++++w
  gi|557693842|ref|YP_008796896.1| 267 PWKRVITAFAEVGYDYVMSYEHEDPVMSQEDGLEKTIQYLKP-LLIKKRLTEIWW 320
                                       6****************************************8.***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2281.47
//
Query:       gi|557693843|ref|YP_008796897.1|  [L=720]
Description: inorganic pyrophosphatase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-227  756.5  36.0   3.1e-227  756.3  36.0    1.0  1  H_PPase   Inorganic H+ pyrophosphatase
  ------ inclusion threshold ------
      0.098   12.9  38.7        3.6    7.8   0.0    4.4  4  EI24      Etoposide-induced protein 2.4 (EI24)


Domain annotation for each model (and alignments):
>> H_PPase  Inorganic H+ pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  756.3  36.0  3.5e-231  3.1e-227       3     650 .]      16     709 ..      14     709 .. 0.97

  Alignments for each domain:
  == domain 1  score: 756.3 bits;  conditional E-value: 3.5e-231
                                       HHHHHHHHHHHHHTS--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT............HHHHH CS
                           H_PPase   3 allfalvllkkvlkedegtekmkeiaeaikegaeaflkrqykviailvvvlavlllllal.........lsvltaia 70 
                                       + l a+ +++ v++ ++g  ++ ++ +ai+eg+ a+lkrqy++i+i++v++++l+++  +         +++++  +
  gi|557693843|ref|YP_008796897.1|  16 GALSAVGFVALVNRYPKGGPEFVSVWSAIREGSIAYLKRQYRTIFIISVFIFILIIVSFAafpqmgglvYGLQIGGS 92 
                                       55678889999*******************************************9997668999999988889**** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS-EE-HH CS
                           H_PPase  71 flvGallSalagyigmkvavranvrtakaarkslkkalkvafrsGavmgllvvglallgvsllllllkaaalelekl 147
                                       fl+G+++S +a+ i+m  a+ranvrt+ aa+k+  +al+va  +Ga  gl+v++++llg+++l++++++        
  gi|557693843|ref|YP_008796897.1|  93 FLLGVAFSLIAATIAMDSATRANVRTTYAASKDSVSALRVATMGGAALGLAVIAMSLLGLTILYIVFRD-------- 161
                                       *********************************************************************........ PP

                                       HHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHTCHHHHTS---TT-TT-TTHHHHHHHHHHHHTHHHHHHHHHHHH CS
                           H_PPase 148 lellvgfglGaslvalfarvgGGiytKaADvGaDLvGKveagipEDdprnpaviADnvGDnvGDvaGmgADlfesyv 224
                                       + +l+gfg+Gasl alfa++gGGiytK+AD+GaDLvGKveagipEDdprnpaviAD+vGDnvGD aG+gADlfes++
  gi|557693843|ref|YP_008796897.1| 162 PGVLAGFGFGASLAALFAQLGGGIYTKSADIGADLVGKVEAGIPEDDPRNPAVIADQVGDNVGDEAGRGADLFESVT 238
                                       9**************************************************************************** PP

                                       HHHHHHHHH...........SHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHSS--HHHHHHHHHHHHHHHHH CS
                           H_PPase 225 asivaamvlg..........aavklvllpllvaavgilasiigillvktkedasskkkeellkaLkkgllvsavlsv 291
                                       a+ ++ m+++          ++ ++v+lpl+v+avg++a+++g+  +  +     k+ +e  + L++gl++++++++
  gi|557693843|ref|YP_008796897.1| 239 AENLGGMIVAliisiilfekINETYVVLPLVVRAVGVIATLAGVGWALYQ-----KSFKESIEPLRNGLIITSIVAA 310
                                       **********99998877654899********************998433.....4456789*************** PP

                                       HHHHHHHH-S-TTTTSHHHHHHHHHHHHHHHHHHHHHHHH-TTSHHHHHHHHHGGG-HHHHHHHHHHHHHHHTHHHH CS
                           H_PPase 292 vlvallslllkeaaalklflavlvGlvagllivllteyytsteykpvkeiaeasetGaatniisGlavgmestvlpv 368
                                       vl++l++ ++     l lf+++lvGlvag+li++++e+yts ++++v  ia++se+G+a++++sGl+vgm st+lpv
  gi|557693843|ref|YP_008796897.1| 311 VLMYLVTSTVFGGGFLPLFVTMLVGLVAGILIMFYSEIYTSLKSRHVSLIATNSESGPALTVVSGLSVGMISTALPV 387
                                       ***999999988899************************************************************** PP

                                       HHHHHHHHHHHHHH...............HHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHT--SHHHHH CS
                           H_PPase 369 lviavaillsylla...............glygialaavgmLstlgitlavdayGPiaDNAggiaemseleeevrei 430
                                       +++++ai +s+ll+               g++g+++a++gmLst+g++l++d  GPi+DNAggiaem++ ++++r++
  gi|557693843|ref|YP_008796897.1| 388 ITVVIAIAISFLLGiewakvvglpdlflgGVFGTTMATMGMLSTAGFVLTMDGLGPIVDNAGGIAEMANAPKTIRDR 464
                                       *************99999999999999999*********************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT...........................HHCS--BTTSHHH CS
                           H_PPase 431 tdklDavGNttkAitKgfaigsAalaalaLfaaylee...........................aklekvdllnpev 480
                                       ++ lDa+GNttkA+tK++a+gsAalaal+Lf+a+l e                           +  ++++l++p v
  gi|557693843|ref|YP_008796897.1| 465 LEPLDALGNTTKALTKSYAMGSAALAALLLFQAFLLEvgrymagivelshltpelsakllnnieQLSTQLQLNSPAV 541
                                       *************************************************************99866789******** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTTTSS---HHHHHHHHHHHHHHTTHHHHHHHHHH CS
                           H_PPase 481 lvglliGamlvflfsaltmkaVgkaAeevveevrrqfkeipgilegkekpdykkcveistkaalkemilpgllavla 557
                                       l+gl+iGaml+flfs++++kaVg++A ++veevrrqf+ei+gilegk++p+y +cv+ist++al+ m++p+l++ l+
  gi|557693843|ref|YP_008796897.1| 542 LIGLFIGAMLPFLFSGYAVKAVGTGAFQMVEEVRRQFREIKGILEGKARPEYGRCVDISTRTALRLMVAPTLIVTLS 618
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTT.SSSHHHHHHHHHHHHHHHHHCTHHH CS
                           H_PPase 558 pivvglllgaealagllagalvsgvllAifmanaGgawDNAKkyiEegelggkgseahkaaVvGDtVGDPfKDtagp 634
                                       piv+g++lg +a+++l++ga+vs++ lAi+   +G+a DNAKky+E    g kgs+ahkaaVvGDtVGDP+KDt +p
  gi|557693843|ref|YP_008796897.1| 619 PIVLGIFLGWRAVGALVIGATVSAIPLAILGFYGGAAMDNAKKYLEI--AGRKGSDAHKAAVVGDTVGDPMKDTYAP 693
                                       **********************************************8..689************************* PP

                                       HHHHHHHHHHHHHHHH CS
                           H_PPase 635 slniliklmsivslvi 650
                                       sl+ilikl++++slv+
  gi|557693843|ref|YP_008796897.1| 694 SLHILIKLLNTLSLVF 709
                                       **************97 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 ?    1.5  10.7     0.033     3e+02      27     123 ..      17     172 ..       2     183 .. 0.48
   2 ?    7.8  16.2   0.00041       3.6      18     125 ..     263     400 ..     245     404 .. 0.71
   3 ?    4.0   1.7    0.0057        51      23     128 ..     498     628 ..     414     631 .. 0.68
   4 ?    7.8   0.0    0.0004       3.6      13      60 ..     602     717 ..     592     720 .] 0.53

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHH.....................-.................TTHHHHHHHHHHHHHHHHHH.....H CS
                              EI24  27 lllfllllvlll.....................w.................vllasllvllllllplwlfp.....l 60 
                                       +l         +                     w                 +++ s+++++l+++ +  fp     +
  gi|557693843|ref|YP_008796897.1|  17 AL---------SavgfvalvnrypkggpefvsvWsairegsiaylkrqyrtIFIISVFIFILIIVSFAAFPqmgglV 84 
                                       22.........122333445888998888888856677777777788888855555666666666656666555554 PP

                                       HHHHHHHHH.....HHHHHHHH........HH.HH................CCTTSHHHHHHHHHHHHHHHHHHHHH CS
                              EI24  61 valllaapf.....ygllaekv........ekrhl................glvkslaeslkslllllllllvllpl 108
                                         l +++ f     ++l+a+ +        +   +                +++ + a +l  +++ ll l +l+++
  gi|557693843|ref|YP_008796897.1|  85 YGLQIGGSFllgvaFSLIAATIamdsatraN---VrttyaaskdsvsalrvATMGGAALGLAVIAMSLLGLTILYIV 158
                                       4444444444444466666666333222221...0222344443344432322223335555555555555544444 PP

                                       HH..TTHHH....HHHH CS
                              EI24 109 li..Pvvglilspllls 123
                                        +  P+v  ++ + +++
  gi|557693843|ref|YP_008796897.1| 159 -FrdPGV--LAGFGFGA 172
                                       .347755..44444444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00041
                                       HHHHHHHHHHHHHHHHHHHHH-............................TTHHHHHHHHHHHHHHHHHH..HHHHH CS
                              EI24  18 llllplllnlllfllllvlllw............................vllasllvllllllplwlfp..lvall 64 
                                       +++lpl++ ++ +++ l+ ++w                            + l+   v+ + +lpl+++   +++  
  gi|557693843|ref|YP_008796897.1| 263 YVVLPLVVRAVGVIATLAGVGWalyqksfkesieplrngliitsivaavlMYLVTSTVFGGGFLPLFVTMlvGLVAG 339
                                       67888888888888776666666666666677777777753333333333222234444444444555542344444 PP

                                       HHHHHHHHHHHHHHH.HHCCTTSHHHHHHHHHHHHHHHHHHHHH.HHTTHHH....HHHHHH CS
                              EI24  65 laapfygllaekvekrhlglvkslaeslkslllllllllvllpl.liPvvglilsplllswl 125
                                       +  +fy++++  +++rh++l+++  es   l +++ l + ++ + l Pv+ ++++++++++l
  gi|557693843|ref|YP_008796897.1| 340 ILIMFYSEIYTSLKSRHVSLIATNSESGPALTVVSGLSVGMISTaL-PVITVVIAIAISFLL 400
                                       44555************9777777799************9999955.****99999999987 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.0057
                                       HHHHHHHHHHHHHHHH..........................-.........TTHHHHHHHHHHHHHHHHHHHHHHH CS
                              EI24  23 lllnlllfllllvlll..........................w.........vllasllvllllllplwlfplvall 64 
                                       +l             l                          +            a+l++l + +++ +lf++ a+ 
  gi|557693843|ref|YP_008796897.1| 498 FL-------------LevgrymagivelshltpelsakllnnIeqlstqlqlNSPAVLIGLFIGAMLPFLFSGYAVK 561
                                       22.............12335544444444665555555444404444444442222555555555555777777777 PP

                                       HHHHHHHHHHHHHHH.HH....CCTTSHH.HHHHHHHHHHHHHHHHHHHHHTTHHH....HHHHHHHHH CS
                              EI24  65 laapfygllaekvekrhl....glvksla.eslkslllllllllvllplliPvvglilsplllswltay 128
                                        +++   +++e+v++ ++    g++++ a  ++ + + +++++++ l +  P + ++lsp++l+++ ++
  gi|557693843|ref|YP_008796897.1| 562 AVGTGAFQMVEEVRR-QFreikGILEGKArPEYGRCVDISTRTALRLMVA-PTLIVTLSPIVLGIFLGW 628
                                       777777778888875.3324444444444778888888888888888886.888899999999998888 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0004
                                       TTTHHHHHHHHHHHHHHHHHHHHHHH.................................................-. CS
                              EI24  13 pkllallllplllnlllfllllvlll.................................................w. 39 
                                       +  l+l++ p+l+  l  ++l+++l+                                                   
  gi|557693843|ref|YP_008796897.1| 602 RTALRLMVAPTLIVTLSPIVLGIFLGwravgalvigatvsaiplailgfyggaamdnakkyleiagrkgsdahkaAv 678
                                       56677777777777777776777777244444444555555555555444444444444444444444443333303 PP

                                       ..................TTHHHHHHHHHHHHHHHHHHH CS
                              EI24  40 ..................vllasllvllllllplwlfpl 60 
                                                         +l+++l +l+l+++pl+++ l
  gi|557693843|ref|YP_008796897.1| 679 vgdtvgdpmkdtyapslhILIKLLNTLSLVFIPLFIYGL 717
                                       344444444555555566666666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (720 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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):               2  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.44
# Mc/sec: 4911.15
//
Query:       gi|557693844|ref|YP_008796898.1|  [L=297]
Description: hypothetical protein CSUB_C0407 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   11.5   1.0        7.5    6.4   0.1    2.5  2  Sec34     Sec34-like family
       0.34   10.6   3.1       0.63    9.7   0.0    2.8  4  DUF2312   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1   0.00083       7.5      65     103 ..     143     183 ..     101     184 .. 0.88
   2 ?    3.3   0.1    0.0078        70     102     128 ..     225     251 ..     221     274 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00083
                             Sec34  65 eekLkyFeeldpitrkLnspgss..lvksesFlemLkklDe 103
                                       ++ ++ F+ l++++++L+++  +   v ++sF+ ++++++e
  gi|557693844|ref|YP_008796898.1| 143 RQLISPFRRLERTKQRLENQYKDvpDVAKQSFKRLIDHIEE 183
                                       566789***********877666578**********99986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0078
                             Sec34 102 DeclefleehpefkeaetYlirfkqcl 128
                                        e l +++  ++f + ++Yl  f+q  
  gi|557693844|ref|YP_008796898.1| 225 AELLTYVDFSRSFTDVRIYLGLFRQRI 251
                                       56688999999********99999854 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 ?   -1.9   0.0      0.29   2.6e+03      24      43 ..     105     124 ..      86     127 .. 0.60
   2 ?    9.7   0.0     7e-05      0.63       5      34 ..     142     171 ..     140     175 .. 0.92
   3 ?   -1.7   0.0      0.27   2.4e+03       4      19 ..     173     185 ..     170     193 .. 0.60
   4 ?   -0.9   0.1      0.14   1.3e+03      47      66 ..     269     288 ..     252     293 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.29
                           DUF2312  24 edikdvyaeaKseGfdtkvl 43 
                                       +  k +  e Ks+  d+++l
  gi|557693844|ref|YP_008796898.1| 105 QMRKRLGIESKSAKTDVRIL 124
                                       33344445566666666665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 7e-05
                           DUF2312   5 LrqfieRiErleeEkkaiaedikdvyaeaK 34 
                                       +rq+i+ + rle  k+ ++++ kdv   aK
  gi|557693844|ref|YP_008796898.1| 142 MRQLISPFRRLERTKQRLENQYKDVPDVAK 171
                                       79***********************88887 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.27
                           DUF2312   4 qLrqfieRiErleeEk 19 
                                        ++++i+ iE   eEk
  gi|557693844|ref|YP_008796898.1| 173 SFKRLIDHIE---EEK 185
                                       5555665555...555 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 0.14
                           DUF2312  47 vklrkkdkdereEeeallel 66 
                                       +++ +k++  r+Eee  +++
  gi|557693844|ref|YP_008796898.1| 269 MSITNKEPRARDEEEIAFKI 288
                                       56778899999999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2147.19
//
Query:       gi|557693845|ref|YP_008796899.1|  [L=204]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-38  129.6   0.1    1.4e-37  129.0   0.1    1.3  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 !  129.0   0.1   7.6e-42   1.4e-37       3     172 .]      22     167 ..      20     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 7.6e-42
                                       ----.GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHH CS
                    Oxidored_molyb   3 avpkvdpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlr 79 
                                        +pk+d+e +rl+v+glve+p+++s+++L ++  ve++  ++C++              +w   ++  ++WtGv+++
  gi|557693845|ref|YP_008796899.1|  22 GTPKIDVEGYRLRVTGLVEEPREYSYQELLEMADVEYVKPFHCVT--------------KW---SIREVRWTGVSMK 81 
                                       57999****************************************..............8*...9************ PP

                                       HHHHHTTB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBT CS
                    Oxidored_molyb  80 dvLekagvkkpearhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvK 156
                                        +Le+ +vk +e ++++f +ad      +y+a +pl++al++++++A++m+g+pL++d+G+P R ++p+l+g++s+K
  gi|557693845|ref|YP_008796899.1|  82 RLLENSRVK-KEGKWLMFVCAD------GYTAPVPLDDALSEEAIVALKMDGRPLEVDQGFPARPFIPHLYGWKSAK 151
                                       ********7.9**********9......5***********99*********************************** PP

                                       TEEEEEEESS---SHH CS
                    Oxidored_molyb 157 wlkrievsdeesegyw 172
                                       wl ++ev ++  +gyw
  gi|557693845|ref|YP_008796899.1| 152 WLVEMEVIPTYVDGYW 167
                                       **********999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1520.90
//
Query:       gi|557693846|ref|YP_008796900.1|  [L=120]
Description: hypothetical protein CSUB_C0409 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   59.4   0.0    4.5e-16   59.3   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 !   59.3   0.0   2.5e-20   4.5e-16      53     147 ..       2      93 ..       1     108 [. 0.90

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.5e-20
                                       HHHSEEEEEEEBCCGHHHHHHTCS...SCCCCCCCCCCCEEECT.CCCSEEETTCSEEEEEEEEEEECCTTEEEEEE CS
                     Flavin_Reduct  53 keagefvinllsesqealadafsqksgprtddksifagltwees.ptgapallgalasleCqvvgsvelgdhelfig 128
                                       +++++f +n ls+++ + ++ +++++ p t+dk++ +gl  +++ +tgap+l +a a+leCqv  ++++gdh l+++
  gi|557693846|ref|YP_008796900.1|   2 EKSHHFSVNWLSHEHVEKMELLAKPAEPTTVDKLKESGLMHRPGeNTGAPILVDASAYLECQVTTRLDAGDHILYVA 78 
                                       6899*********************************999999999******************************* PP

                                       EEEEEEESTTECTTBEECC CS
                     Flavin_Reduct 129 eVvavkvgddadeepLlyw 147
                                       +Vv+++  dd  +e   yw
  gi|557693846|ref|YP_008796900.1|  79 QVVDARAVDD-FGE---YW 93 
                                       ******9998.555...33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 841.91
//
Query:       gi|557693847|ref|YP_008796901.1|  [L=184]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   60.4   0.7    2.5e-16   60.1   0.7    1.0  1  NT5C       5' nucleotidase, deoxy (Pyrimidine), cytosolic typ
  ------ inclusion threshold ------
       0.15   12.4   4.0       0.32   11.3   4.0    1.7  1  HAD_SAK_2  HAD domain in Swiss Army Knife RNA repair proteins


Domain annotation for each model (and alignments):
>> NT5C  5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.7   2.7e-20   2.5e-16       4     175 ..       3     179 ..       1     183 [. 0.82

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 2.7e-20
                              NT5C   4 vlvDlDgvladlygkmlevankrfeatllpeevsswdleefvkPeqreslyrfltep..glFadlepipg.arevLe 77 
                                       + +D+Dgvladl g  +++++++ ++  +++ ++  ++e +vk +   + +  l  +    +++l+pi++   e +e
  gi|557693847|ref|YP_008796901.1|   3 IALDVDGVLADLAGMIIRLYEEDTGRRISRDMIT--EWEFWVKLSMTRQEFIDLITRswRRWTELQPIEDdVAEDVE 77 
                                       789*******************************..788898887765555544444024589*****9725699** PP

                              NT5C  78 eladegrlvvitaallqfydavkekveWldehlplipyrnlvlv...kekdlvrgDvlidDapknleklrgrs...i 148
                                       +l   g++ ++t+++     +v+   +Wl++h  +i yr  + v     k+    Dv+idD+p+  ekl   +    
  gi|557693847|ref|YP_008796901.1|  78 KLNTVGEVDILTQRPAE---TVEYVKQWLKQH--GIMYRRFMWVplkASKTSFVYDVYIDDSPHLAEKLANTQrmvF 149
                                       ****************9...8899999*****..999999886533268999999********97777665544448 PP

                              NT5C 149 lfdsptnrhie...delRaasWqevedlil 175
                                       l+d+  nr ++   +++R+ s  e+++l++
  gi|557693847|ref|YP_008796901.1| 150 LYDQNWNRRVKpapNIKRISSLDEAYQLLV 179
                                       899999**997444689**********996 PP

>> HAD_SAK_2  HAD domain in Swiss Army Knife RNA repair proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   4.0   3.6e-05      0.32       2     111 ..       3     116 ..       2     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.6e-05
                         HAD_SAK_2   2 iFLDiDGVLnpekskkrregeedea........ldpeaverlkriveatgakiVlsstWrrred.eelkallkaag. 68 
                                       i LD+DGVL + +    r +eed+          ++e   +l    ++ +    ++ +Wrr+ + + +++  +++  
  gi|557693847|ref|YP_008796901.1|   3 IALDVDGVLADLAGMIIRLYEEDTGrrisrdmiTEWEFWVKLSM--TRQEFIDLITRSWRRWTElQPIEDDVAEDVe 77 
                                       679********999988888877778988888877774444444..333333368999******9889999999999 PP

                         HAD_SAK_2  69 rpriigvtpdlpeeeseeekksRaqeilewlrrh...eeveawval 111
                                       + + +g ++ l+++ +     + ++ +++wl++h      ++++++
  gi|557693847|ref|YP_008796901.1|  78 KLNTVGEVDILTQRPA-----ETVEYVKQWLKQHgimY--RRFMWV 116
                                       8999998888887754.....669999******98543..444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1300.21
//
Query:       gi|557693848|ref|YP_008796902.1|  [L=1046]
Description: DEAD/DEAH box helicase domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   58.0   0.0    2.1e-15   56.9   0.0    1.6  1  DEAD        DEAD/DEAH box helicase
      3e-14   53.3   0.1    6.5e-13   49.0   0.1    2.4  2  Helicase_C  Helicase conserved C-terminal domain
      0.001   18.8   0.0     0.0031   17.2   0.0    1.9  2  AAA_30      AAA domain
  ------ inclusion threshold ------
      0.023   14.7   0.0      0.046   13.7   0.0    1.5  1  ResIII      Type III restriction enzyme, res subunit
      0.026   14.9   0.0      0.049   14.0   0.0    1.5  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 !   56.9   0.0   5.8e-19   2.1e-15       3     171 ..      63     234 ..      61     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 5.8e-19
                                       HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                        Q+ea++ + +g++++++a TGsGKT+a+++            ++ k+l v Pt +L ++++++l+ ++  ++l+++
  gi|557693848|ref|YP_008796902.1|  63 HQKEAFDSLARGENLVLKAGTGSGKTEAWFLYTA--------AHRVKTLAVYPTLALSNDQVERLNDYCMSLGLKAV 131
                                       69**************************999888........56789***********************9997776 PP

                                       EE........ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHH......HCTSSH..CTTEEEEEEETHHHHHHTTTHH CS
                                       xx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  80 li........iggvaardqlskldngvdivvgtpgrlddll......stgkln..lsqvrflVlDEadrlldqgfsd 140
                                       +i        +  + ar  ++ + +++d+v+++p  l++ l      +   l+  l +v ++VlDE d +     s 
  gi|557693848|ref|YP_008796902.1| 132 AIdalrkeelVRRSGARVVRNMV-KEADLVITNPAYLLNELkrigagKPAFLRdfLGEVGLVVLDEFDFYGPR--SI 205
                                       66432211113344444444444.88*************8867765422224478***************998..44 PP

                                       HHHHHHHHSHHHCTTSTTTSEEEEEESSBSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 141 finrilnqlpqitcdgklqrqvivlSATlpk 171
                                        i   ++q+ + + +     q+++++AT+ +
  gi|557693848|ref|YP_008796902.1| 206 AILLGMAQILHEYVN--PRFQLVIMTATIAD 234
                                       444445666444444..4567*******984 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     0.099   3.6e+02      13      50 ..     219     266 ..     208     326 .. 0.55
   2 !   49.0   0.1   1.8e-16   6.5e-13      13     109 ..     338     437 ..     329     439 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.099
                                       TTTTSEEEEEESSHH...HHHHHHHHHHHTTSTEEEESTT.........S CS
                        Helicase_C  13 eeeggkilifvntid...rlekvklllekkgikvavlhge.........l 50 
                                        + + + +i++ ti    ++  +++l+e +g k+a+++g+         l
  gi|557693848|ref|YP_008796902.1| 219 VNPRFQLVIMTATIAdptEA--AQILTEINGRKTAIVDGQpyrsenrtyL 266
                                       47788889999999954333..79999999********974333333330 PP

  == domain 2  score: 49.0 bits;  conditional E-value: 1.8e-16
                                       TTTTSEEEEEESSHHHHHH.HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTT CS
                        Helicase_C  13 eeeggkilifvntidrlek.vklllekk....gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipk 84 
                                         ++  +l+f++ i ++e+ ++ ++  +    + ++a +h  l   +r+ei ++ ++g ++++ + + +++Gidi  
  gi|557693848|ref|YP_008796902.1| 338 VDDEALTLVFTTGIASAEEfARKVK--NevgeSHRIASHHHLLLRTQRREIEQAAREGVVKLIFTPRTLSQGIDIGL 412
                                       4677789**********86656663..246788******************************************** PP

                                       ESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  85 vnlVinfdlprnvtsyiqriGRtgR 109
                                       ++ V++++lp++v++y+qr GR gR
  gi|557693848|ref|YP_008796902.1| 413 IRRVVHLGLPQTVREYWQREGRKGR 437
                                       ************************9 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   8.7e-07    0.0031       4      92 ..      62     160 ..      59     214 .. 0.76
   2 ?   -4.1   0.1       3.1   1.1e+04      51      78 ..     350     376 ..     347     392 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 8.7e-07
                            AAA_30   4 aeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrvi.glAptgkaAkvLae...elgieastiakl 76 
                                         Q++a+++l+ +++   vl+++ G+GKt a   +++a++ +   v   lA ++ + ++L++   +lg++a  i+ l
  gi|557693848|ref|YP_008796902.1|  62 IHQKEAFDSLARGEN--LVLKAGTGSGKTEAWFLYTAAHRVKTLAVYpTLALSNDQVERLNDycmSLGLKAVAIDAL 136
                                       57**********998..99***********************9999878************7666888888888877 PP

                            AAA_30  77 lkrlk..............grarlepgtll 92 
                                        k+                +      ++l+
  gi|557693848|ref|YP_008796902.1| 137 RKEELvrrsgarvvrnmvkE------ADLV 160
                                       75544555556664333330......3333 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 3.1
                            AAA_30  51 glAptgkaAkvLaeelgieastiakllk 78 
                                       g+A+ ++ A+++++e+g e+++ia+  +
  gi|557693848|ref|YP_008796902.1| 350 GIASAEEFARKVKNEVG-ESHRIASHHH 376
                                       78888888999998888.5555555443 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 ?   13.7   0.0   1.3e-05     0.046       4     169 ..      60     232 ..      54     234 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                                       E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG CS
                            ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflse 80 
                                       l+ +Q+ea ++l+      r +++++k+ TG+GKT   +  +     ++++ k+l + p+++l +   e+++++  +
  gi|557693848|ref|YP_008796902.1|  60 LYIHQKEAFDSLA------RGENLVLKAGTGSGKTEAWFLYT-----AAHRVKTLAVYPTLALSNDQVERLNDYCMS 125
                                       6667888887775......7899************8665444.....444459**********99999888777666 PP

                                       ............GEEEESSS-B--.......-SEEEEEHHHHHHTH...........HHHTTT-SEEEEETGGGTTS CS
                            ResIII  81 ayke........igkkvsgdkkkakekdstnkkilvttiqsldadseee...eeeseellrdrfdviiiDEaHrlga 146
                                          +        +++ v+  + +  ++  +++++++t+   l +++++    + +  +   ++  +++ DE   +g 
  gi|557693848|ref|YP_008796902.1| 126 LGLKavaidalrKEELVRRSGARVVRNMVKEADLVITNPAYLLNELKRIgagKPAFLRDFLGEVGLVVLDEFDFYGP 202
                                       55544543444333333333333377888999999999999999994334444444444445555999999977766 PP

                                       .T.....TTHHH.HHT---.SEEEEEESS- CS
                            ResIII 147 kk.....swrei.lekfke.avllglTATp 169
                                        +      + +i  e++++ + l+ +TAT+
  gi|557693848|ref|YP_008796902.1| 203 RSiaillGMAQIlHEYVNPrFQLVIMTATI 232
                                       535566688887456665536667789997 PP

>> AAA_19  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     0.049       1     112 [.      64     198 ..      64     220 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-05
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrv.lkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrl 75 
                                       q+ea +  ++ ++l++ aG G+GKT+       a+ v++  v    +  +a+ +  +++l++ + +lg++a  i +l
  gi|557693848|ref|YP_008796902.1|  64 QKEAFDsLARGENLVLKAGTGSGKTEAwFLYTAAHRVKTLAV----YPTLALSNDQVERLNDYCMSLGLKAVAIDAL 136
                                       889998789999*************87244556666666644....5678888999******99999*999999998 PP

                            AAA_19  76 al................ldfddlltealelle.........eaeeekklqeee.llivDEfq 112
                                                          ++d  +t+++ ll+          a  +++l  e  l++ DEf 
  gi|557693848|ref|YP_008796902.1| 137 RKeelvrrsgarvvrnmvKEADLVITNPAYLLNelkrigagkPAFLRDFL-GEVgLVVLDEFD 198
                                       65777777777777777644555555566666566666666422233344.444477777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1046 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.45
# Mc/sec: 6915.90
//
Query:       gi|557693849|ref|YP_008796903.1|  [L=147]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-18   66.6   0.1    3.5e-18   66.4   0.1    1.1  1  GGACT     Gamma-glutamyl cyclotransferase, AIG2-like
    2.1e-12   47.2   0.1    2.8e-12   46.9   0.1    1.2  1  AIG2_2    AIG2-like family
  ------ inclusion threshold ------
      0.015   15.4   0.6      0.035   14.2   0.3    1.7  2  ChaC      ChaC-like protein


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 !   66.4   0.1   5.8e-22   3.5e-18       1     110 [.       5     111 ..       5     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 5.8e-22
                                       EEESSTTSTTSCCCHHHHCSECEEEEEEEECCTBEEEE.......ETTTEEEETTSSE.EEEEEEEE-HHHHHHHHH CS
                             GGACT   1 vFvYGtLkrgepnhqrlllgarflesgpatlkgyrlyd......lggkypalvpgdgekVkGelyevddeelarLDe 71 
                                       +F+YG+    +++ +r   g + l ++pa+l++y+++       + g++ ++ +++g+ V+G +y +++++l++LD+
  gi|557693849|ref|YP_008796903.1|   5 YFAYGSNL--DQEGMRRRVG-EWLDLKPAILRDYKIVFnvfsssWRGGVANIEESPGSVVYGAVYLLEESQLEKLDK 78 
                                       7*******..5555555558.9*************995555567777889999************************ PP

                                       CT.TTTTSEEEEEEEEEC.TTS-EEEEEEEEETT..GGG CS
                             GGACT  72 lEpeepseYereevkvevledgeqveawvYvyageeeeg 110
                                       +E + p++Y+r++++vev  +g+++ea+vYv+++    +
  gi|557693849|ref|YP_008796903.1|  79 YE-GVPHLYHRRKMTVEV--GGRPLEAYVYVATN---PR 111
                                       **.9********999999..************66...22 PP

>> AIG2_2  AIG2-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9   0.1   4.7e-16   2.8e-12       2      81 ..      61     139 ..      60     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 4.7e-16
                            AIG2_2   2 VfGvlweidlenlkdLDkqEgvedgiyrpievrVstatgeevlaraYvlsn.qpetkPsetYlkvlvkGAeesglPe 77 
                                       V+G+++ +++++l++LDk+Egv++ +y++ +++V+   g+ ++a +Yv++n +p++ Ps  Yl  ++kG ++ g ++
  gi|557693849|ref|YP_008796903.1|  61 VYGAVYLLEESQLEKLDKYEGVPH-LYHRRKMTVEV-GGRPLEAYVYVATNpRPRLTPSSSYLALVLKGLKKLGYSD 135
                                       9**********************9.9*********9.888********9995688**************99999888 PP

                            AIG2_2  78 dYvk 81 
                                       d ++
  gi|557693849|ref|YP_008796903.1| 136 DVIH 139
                                       7665 PP

>> ChaC  ChaC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   5.8e-06     0.035       1     124 [.       3     115 ..       3     122 .. 0.79
   2 ?   -1.0   0.0      0.26   1.5e+03     147     177 ..     118     146 ..     114     147 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-06
                                       EEEEESSHHHHS--T.....T-SEEEEEEEETEEEEEEEEESSSSS-SSS-EEEEEEEEHHH-EEEEEEEEE-GGGG CS
                              ChaC   1 lwvfgYGSLiwkpdf.....eytesrravihgyaRrfwlsstdhRGteekPGrvltLiedeegstiGvvyripaeea 72 
                                       +w f+YGS + + ++     e+ +  +a+++ y+  f + s ++RG       v+ ++e  +++++G vy +++++ 
  gi|557693849|ref|YP_008796903.1|   3 VWYFAYGSNLDQEGMrrrvgEWLDLKPAILRDYKIVFNVFSSSWRGG------VANIEESPGSVVYGAVYLLEESQ- 72 
                                       69999999866555422222788999*******************85......788999999*********99888. PP

                                       GGGGGGGGGSTT..TTEEEEEEEEEE-EETTTS-EEEEEEEEEE-TTSTTB- CS
                              ChaC  73 eevleyLeeRElvtnGytlkevevylkkdakeekvvlealvyvatikneqya 124
                                          le+L++ E v + y+ ++++v +    ++++   ea vyvat   ++ +
  gi|557693849|ref|YP_008796903.1|  73 ---LEKLDKYEGVPHLYHRRKMTVEV----GGRPL--EAYVYVATNPRPRLT 115
                                       ...67799999888877777777665....66777..999999988776655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHTS-----BHHHHHHHHHHH CS
                              ChaC 147 aeYlfelakaleklgigirDehLeeleelvk 177
                                         Yl+ + k l+klg   +D+ + ++  +v+
  gi|557693849|ref|YP_008796903.1| 118 SSYLALVLKGLKKLG--YSDDVIHSIRMQVE 146
                                       579999999999997..99999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1141.99
//
Query:       gi|557693850|ref|YP_008796904.1|  [L=423]
Description: glycine/D-amino acid oxidase (deaminating) [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  152.2   0.0    3.3e-44  151.9   0.0    1.0  1  DAO             FAD dependent oxidoreductase
    4.4e-06   26.2   0.2      0.048   12.9   0.0    2.4  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.6e-05   24.2   0.8    0.00025   20.3   0.8    2.1  2  FAD_binding_2   FAD binding domain
    2.2e-05   23.8   0.7    0.00012   21.4   0.2    2.1  2  Thi4            Thi4 family
    4.3e-05   23.7   1.2    9.2e-05   22.6   1.2    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0014   19.2   0.8      0.023   15.2   0.3    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0025   16.4   0.0     0.0034   16.0   0.0    1.1  1  Mqo             Malate:quinone oxidoreductase (Mqo)
     0.0058   15.8   0.2        2.3    7.2   0.2    2.2  2  GIDA            Glucose inhibited division protein A
     0.0085   15.5   0.2      0.012   15.0   0.2    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
     0.0094   14.7   0.3          1    8.0   0.2    2.2  2  HI0933_like     HI0933-like protein
  ------ inclusion threshold ------
      0.031   13.3   0.3       0.73    8.8   0.2    2.2  2  Lycopene_cycl   Lycopene cyclase protein
      0.059   12.6   0.8        2.5    7.3   0.5    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.21   11.6   3.8        6.1    6.8   0.2    3.0  3  NAD_binding_9   FAD-NAD(P)-binding
       0.32    9.8   0.4       0.46    9.3   0.4    1.2  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 !  151.9   0.0   2.6e-47   3.3e-44       1     349 [.       5     386 ..       5     388 .. 0.78

  Alignments for each domain:
  == domain 1  score: 151.9 bits;  conditional E-value: 2.6e-47
                                       EEEEECTSHHHHHHHHHHH.HTT...EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLa.rrg...VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelrelee 73 
                                       dvv++GGGi Gl+ Ay+    +g   V+++e+g+++g+g + r+ g  ++g+  + +  +   l++ ++++lre e+
  gi|557693850|ref|YP_008796904.1|   5 DVVVVGGGILGLASAYYIKsLHGelsVAVIERGRDVGQGNTARSVGGYRQGIF-TSYVNR--VLAETTIQHLREAEA 78 
                                       9*****************537899****************************5.444223..4666669***99999 PP

                                       HHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.ST.............TTSEEEE CS
                               DAO  74 elgididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa.lp.............gllgalf 136
                                       + +  +  r+ G+l+l  d++ l +++  ++  l+ g    ll++e + e+  + ++             +++++lf
  gi|557693850|ref|YP_008796904.1|  79 SGETSLNMREVGYLILL-DDNRLKNVETVVETFLKEGKA-ILLNPETLSEKLHMrTDftgdeeamlmglsNIKAGLF 153
                                       9666699*********8.666788888888877666643.367776666666554334556677888888******* PP

                                       ETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEE..EEEE..............TCEEEEEEECTEEEEEEEEEE CS
                               DAO 137 ypdtgqvdpakltaalaraaealGveilegtevtgl..eeed..............gkvwgverttpgendaadavV 197
                                        p +g +d +k+++ + +++ + Gve+++g +v++l  e  +               +v+gv  +++ge+ +a +vV
  gi|557693850|ref|YP_008796904.1| 154 APRCGFLDVEKVVNLYKKRCIDVGVELILGKRVEKLllEP-EnplgipreprawqkVRVAGV--VADGEVIKAGKVV 227
                                       ******************************9999974433.236666667656544455555..55577734466** PP

                                       E--GGGHH.HHHTTCTT..TSEEEEEEEEEEEEEECCTHSTGS.....GCSEEEEEEEETTTTEEEEEETTSE.EEE CS
                               DAO 198 naaGawsd.llgllkel..dlpispvrgqvlvlkplseklvsp.....aailpvpetdddgrgvyvtprkdgr.vlv 265
                                       +a+G w+  ll    +l  d+ i++ + q +v++   e l++      + + p+p       g+y++pr +++ ++v
  gi|557693850|ref|YP_008796904.1| 228 VATGSWTPqLL---DPLgvDCFIKAKKRQLFVISAEGE-LQRLltntwDGGRPMP-MMFFPNGLYIVPRMSDKaFWV 299
                                       *******9777...666669*************66555.2222345656777777.899999******976663778 PP

                                       EESSE..EETTCSSTSCSHHHHHHHHHHHHHHSGGG..CGEEEEEEEEEEE..TTSSEEEEEEETEEEEEEEEECTT CS
                               DAO 266 Ggtad..eesgdddpevdeedidellealrklfPql..gdvlrkwaGlrpl..pdglpligetpgvkglylatGhsg 336
                                         t++    +g dd + ++  +d +++ l k++Pq+  ++ ++ waG + +   dg+pli +   + + +++tG+sg
  gi|557693850|ref|YP_008796904.1| 300 SLTDEfgRGFGLDDEPEPSYYLDNVYPPLVKYYPQFlnARPSSMWAGTYSMnyLDGNPLIFR---FLNCLVVTGASG 373
                                       999977755566664555567888***********73566778*******5458******99...68********** PP

                                       THHHHHHHHHHHH CS
                               DAO 337 hGltlapatGkll 349
                                       +G++ + a+G+++
  gi|557693850|ref|YP_008796904.1| 374 SGVMKSDAIGRIA 386
                                       **********985 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 !   12.9   0.0   3.7e-05     0.048       2     176 ..       5      39 ..       3     142 .. 0.73
   2 !   10.7   0.0   0.00017      0.22      81     114 ..     205     237 ..     201     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.7e-05
                                       SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCE CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevv 76 
                                       dvvv+GgG+ Gla a +++    ++ v+++e                                              
  gi|557693850|ref|YP_008796904.1|   5 DVVVVGGGILGLASAYYIKSlhGELSVAVIE---------------------------------------------- 35 
                                       5777777777777777777754466777775.............................................. PP

                                       EEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  77 kidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyi 153
                                                                                                                    
  gi|557693850|ref|YP_008796904.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       HHHHHHHHHHHT-EEEEEESSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 154 GvElAaalaklgkevtlveardr 176
                                                          ++  
  gi|557693850|ref|YP_008796904.1|  36 -------------------RGRD 39 
                                       ...................3322 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00017
                                       SCEEEEETEEECTCEEEEEESEEEE---EEE-BC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  81 gkkkvklekkkegdeekiaydklvlAtGssprdl 114
                                       +++kv +   +  d+e i+++k+v+AtGs++  l
  gi|557693850|ref|YP_008796904.1| 205 AWQKVRVAGVV-ADGEVIKAGKVVVATGSWTPQL 237
                                       56788887766.899**************77665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.8     2e-07   0.00025       1      45 [.       5      52 ..       5      81 .. 0.93
   2 ?    1.6   0.0     0.088   1.1e+02     143     207 ..     165     238 ..     146     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2e-07
                                      SEEEE--SHHHHHHHHHHHH.TTT.-EEEEESSSGGGS.GGGG--S-E CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaae.aGl.kvavvekeqefgg.atawsqGgi 45
                                      Dv+V+G+G+ GLa+A+ ++  +G  +vav+e +  +g  +ta s Gg 
  gi|557693850|ref|YP_008796904.1|  5 DVVVVGGGILGLASAYYIKSlHGElSVAVIERGRDVGQgNTARSVGGY 52
                                      9******************998888********999877*****9985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.088
                                       HHHHHHHHHHTCTEEEEESEEEEEEEECTT...............EEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 143 llarlvesarkagvdfqerteadeLivedg...............rvtGavvenpesgrevrirakavvlatgGfgr 204
                                       ++    +++ + gv++    ++++L+ e +               rv G+v+      +ev i+a +vv+atg +  
  gi|557693850|ref|YP_008796904.1| 165 VVNLYKKRCIDVGVELILGKRVEKLLLEPEnplgipreprawqkvRVAGVVAD-----GEV-IKAGKVVVATGSWTP 235
                                       55566677777889999999999999996667777777888887778887777.....444.7899*******9976 PP

                                       ... CS
                     FAD_binding_2 205 all 207
                                       +ll
  gi|557693850|ref|YP_008796904.1| 236 QLL 238
                                       444 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   9.3e-08   0.00012      18      58 ..       4      45 ..       1      80 [. 0.78
   2 ?    0.3   0.0      0.26   3.3e+02     107     167 ..     173     231 ..     161     238 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.3e-08
                                      EEEEEE--SHHHHHHHHHHHHC.TTS-EEEEESSSS--TTTT CS
                              Thi4 18 sDvvivGaGssGLtaayylakk.pdlkvailersvspGGGaw 58
                                       Dvv+vG+G  GL++ayy+     +l va++er   +G G  
  gi|557693850|ref|YP_008796904.1|  4 LDVVVVGGGILGLASAYYIKSLhGELSVAVIERGRDVGQGNT 45
                                      6******************98879********9988887754 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.26
                                       HHTSTTEEEEESEEEEEEEEETB..TEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEEE--G CS
                              Thi4 107 vlqlanvkllnavaveDlivreg..egvaGvvinwtlvelahdtqscvDPlvirakvvvdatG 167
                                        ++  +v l+ +  ve l++ ++   g+      w+ v +a     + D  vi+a  vv atG
  gi|557693850|ref|YP_008796904.1| 173 CID-VGVELILGKRVEKLLLEPEnpLGIPREPRAWQKVRVAG---VVADGEVIKAGKVVVATG 231
                                       344.88999999999999999832344444555666666665...678888888888888887 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 !   22.6   1.2   7.1e-08   9.2e-05       1      37 [.       8      47 ..       8      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 7.1e-08
                                      EE--SHHHHHHHHHHHCC..TEEEEEE-SSSSSS.GGG-E CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrdrlG.Graas 37
                                      +vG+G+ Gl+ Ay+++     ++v ++e+++++G G+ a+
  gi|557693850|ref|YP_008796904.1|  8 VVGGGILGLASAYYIKSLhgELSVAVIERGRDVGqGNTAR 47
                                      8**************9955788***********8665543 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   1.8e-05     0.023       2      35 ..       6      41 ..       5      78 .. 0.89
   2 ?    1.6   0.0      0.34   4.3e+02      44      66 ..     167     189 ..     160     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                                      EEEECSSHHHHHHHHHHHHTT..SEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg..kkVtvversdkll 35
                                      vvvvGgG +gl  A +++ l    +V v+er+  + 
  gi|557693850|ref|YP_008796904.1|  6 VVVVGGGILGLASAYYIKSLHgeLSVAVIERGRDVG 41
                                      8******************7756799****998776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.34
                                       HHHHHHHHHTTEEEECSEEEEEE CS
                         Pyr_redox  44 kilqeklekngievllntkveei 66 
                                       ++ +++  + g+e++l+++ve++
  gi|557693850|ref|YP_008796904.1| 167 NLYKKRCIDVGVELILGKRVEKL 189
                                       5667777788**********997 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.7e-06    0.0034       3      44 ..       4      45 ..       2      50 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.7e-06
                               Mqo  3 vdvvliGaGimsatlgvllkelepelsievlerldkvaeess 44
                                       dvv++G+Gi+  + + ++k+l+ els++v+er  +v++ ++
  gi|557693850|ref|YP_008796904.1|  4 LDVVVVGGGILGLASAYYIKSLHGELSVAVIERGRDVGQGNT 45
                                      69********************************99998765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.2    0.0018       2.3       1      53 [.       5      58 ..       5      74 .. 0.79
   2 !    6.4   0.0    0.0031       3.9     127     152 ..     210     234 ..     178     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0018
                                      CEEEE-SSHHHHHHHHHHHHT..T--EEEEES-GGGTT--SSSSEEE-TTHHHHH CS
                              GIDA  1 dviViGgGhAGceAAlaaarl..GakvlLithkldtiaelsCnpsiggiakgllv 53
                                      dv+V+GgG  G++ A+ ++ l   ++v+ i ++  ++++     s+gg  +g+ +
  gi|557693850|ref|YP_008796904.1|  5 DVVVVGGGILGLASAYYIKSLhgELSVAVI-ERGRDVGQGNTARSVGGYRQGIFT 58
                                      79**************99886223555555.888888888888888888887765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0031
                                       EEEEEEETTS-EEEECEEEE--TT-B CS
                              GIDA 127 kvkgvvtedgetikakavviatGtfl 152
                                       +v+gv  +dge+ika +vv+atG++ 
  gi|557693850|ref|YP_008796904.1| 210 RVAGV-VADGEVIKAGKVVVATGSWT 234
                                       45555.5799*************964 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   9.2e-06     0.012       1      77 [.       5      84 ..       5     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.2e-06
                      FAD_oxidored  1 DvvVvGGgpaGvaAA..iaAaraGakvlLveergvlG.Glltsglvatdignkaeeqvvtgiareflerlrqrgga.rl 75
                                      DvvVvGGg+ G+a A  i +     +v+++e+ + +G G++++ +++   g    + v++ +a+  +++lr+ +++ ++
  gi|557693850|ref|YP_008796904.1|  5 DVVVVGGGILGLASAyyIKSLHGELSVAVIERGRDVGqGNTARSVGGYRQGIF-TSYVNRVLAETTIQHLREAEASgET 82
                                      9**************5557778889************8888888888888866.4569999999999999885444222 PP

                      FAD_oxidored 76 kk 77
                                      + 
  gi|557693850|ref|YP_008796904.1| 83 SL 84
                                      22 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.2   0.00082         1       2      37 ..       5      42 ..       4      48 .. 0.88
   2 !    4.5   0.0    0.0091        12     109     164 ..     163     232 ..     157     237 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00082
                                      SEEEE--SHHHHHHHHHH..HHTT--EEEE-SSSSS-H CS
                       HI0933_like  2 dviviGgGaAGlmaAisa..akrgkrVlllekakklgr 37
                                      dv+v+GgG  Gl  A  +   + + +V+++e+++ +g+
  gi|557693850|ref|YP_008796904.1|  5 DVVVVGGGILGLASAYYIksLHGELSVAVIERGRDVGQ 42
                                      8**************8874356789********99985 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0091
                                       HHHHHHHHHHHHHHT-EEE-S--EEEE...............ECETTE.EEEEE...TTEEEEESEEEE---- CS
                       HI0933_like 109 edivdallkelkeagvklrletevksv...............ekeedgkfrvkt..kseeeleadklvlAtGG 164
                                       e++v++++k++ + gv+l l ++v+++               +    +k+rv+    ++e ++a k+v+AtG+
  gi|557693850|ref|YP_008796904.1| 163 EKVVNLYKKRCIDVGVELILGKRVEKLllepenplgipreprA---WQKVRVAGvvADGEVIKAGKVVVATGS 232
                                       789***********************99999999999885432...33344432235999**********996 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2   0.00057      0.73       1      37 [.       5      41 ..       5      52 .. 0.91
   2 ?    2.2   0.0     0.057        73     120     172 ..     211     276 ..     203     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00057
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsll 37
                                      Dvvv+G+G  gl+ A  + + + +l+v +ie + ++ 
  gi|557693850|ref|YP_008796904.1|  5 DVVVVGGGILGLASAYYIKSLHGELSVAVIERGRDVG 41
                                      9*****************99999********999884 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.057
                     Lycopene_cycl 120 slvvleggrkirarlvvdarglaslk.............karrlglQtfyGvevevdnppfdldkm 172
                                       +  v+++g+ i+a  vv+a+g   ++             k+r+l +  + G + ++ ++ +d +++
  gi|557693850|ref|YP_008796904.1| 211 VAGVVADGEVIKAGKVVVATGSWTPQlldplgvdcfikaKKRQLFVISAEGELQRLLTNTWDGGRP 276
                                       455899***************666557777777777777777777777777777777777776655 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 ?    7.3   0.5     0.002       2.5       1      32 [.       7      40 ..       7      45 .. 0.83
   2 ?    3.4   0.0     0.029        37     116     138 ..     214     235 ..     208     256 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.002
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkka.gledylilEkg.ni 32
                                      +++G+G  Gla+a+ +k + g  ++ ++E+g  +
  gi|557693850|ref|YP_008796904.1|  7 VVVGGGILGLASAYYIKSLhGELSVAVIERGrDV 40
                                      79**************987244699*****9555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.029
                       Pyr_redox_3 116 vetsketyeAkkviiAtGefdkP 138
                                       v ++ e+++A kv++AtG +  P
  gi|557693850|ref|YP_008796904.1| 214 VVADGEVIKAGKVVVATGSW-TP 235
                                       667889************95.45 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 ?    6.8   0.2    0.0047       6.1       1      44 [.       7      48 ..       7      50 .. 0.90
   2 ?    1.7   0.1      0.18   2.3e+02      96     150 ..      49     107 ..      46     109 .. 0.79
   3 ?    3.1   0.0     0.065        83     137     154 ..     214     231 ..     202     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0047
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgagrvwrt 44
                                      ++vG+G+ Gla +  + +    + +l++ ++++ +  g+g  +r+
  gi|557693850|ref|YP_008796904.1|  7 VVVGGGILGLASAYYIKSL---HGELSVAVIERgRDVGQGNTARS 48
                                      69************99999...6**********888899988875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                     NAD_binding_9  96 yGrYlrdlfeellarlpegvtvevhra.evv...dleeradgqavlladgaslaadaVv 150
                                       +G Y + +f++ ++r+ +++t++++r+ e+    +l+ r+ g+ +ll+d++   ++ Vv
  gi|557693850|ref|YP_008796904.1|  49 VGGYRQGIFTSYVNRVLAETTIQHLREaEASgetSLNMREVGYLILLDDNRLKNVETVV 107
                                       6889999*********9999***997647753336777888888888888877777776 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.065
                     NAD_binding_9 137 lladgaslaadaVvLAlG 154
                                       + adg+ ++a +Vv+A+G
  gi|557693850|ref|YP_008796904.1| 214 VVADGEVIKAGKVVVATG 231
                                       4699*************9 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.4   0.00036      0.46       1      33 [.       5      36 ..       5      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00036
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                                      ++v+vGGG+ G  +A +++  + g+l+v ++e 
  gi|557693850|ref|YP_008796904.1|  5 DVVVVGGGILGLASAYYIKSLH-GELSVAVIER 36
                                      69**********9999999988.88******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 00:00:00.40
# Mc/sec: 3201.38
//
Query:       gi|557693851|ref|YP_008796905.1|  [L=359]
Description: diphthamide synthase subunit DPH2 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-64  218.6   0.0    1.5e-64  218.3   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein
     0.0043   16.7   0.0       0.43   10.2   0.0    2.6  3  DUF1847          Protein of unknown function (DUF1847)
  ------ inclusion threshold ------
      0.021   14.6   0.0       0.05   13.4   0.0    1.6  1  ACT_7            ACT domain


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 !  218.3   0.0   2.5e-68   1.5e-64       2     299 ..      31     327 ..      30     331 .. 0.95

  Alignments for each domain:
  == domain 1  score: 218.3 bits;  conditional E-value: 2.5e-68
                   Diphthamide_syn   2 PegllpdsaeiadileefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvdrlpvlYvfveie..ldv 76 
                                       P gl   +a +a++l++ + ev++++  ++G C++   +a+ l++d+++H Ghs +   d+lp++Y  ++      v
  gi|557693851|ref|YP_008796905.1|  31 PLGLRGVAASVAEQLKSNKFEVLMSSSNCWGGCDIAYTEASGLDVDAIIHLGHSRFLRHDKLPTIYLECRYAdpSPV 107
                                       6688999************************************************************9996522579 PP

                   Diphthamide_syn  77 ehlvetlkknfkekkkivlvstiqyahaleevkeeleeegyevv.kvpqsekplspgevlgctspklkeeeeevdai 152
                                        +l+++++++++  kk+++ +++q+ + l+ vke l ++g++ v  +p+     ++++vlgc+ ++lk+ e++vd++
  gi|557693851|ref|YP_008796905.1| 108 YDLMDRIAAELTGYKKVGVGASVQWLDYLSFVKESLARRGVDAVtAMPDM-YSVYESQVLGCDVSALKKLEKNVDCF 183
                                       9**********9999**********************9999888677777.999*********************99 PP

                   Diphthamide_syn 153 lyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlelver 229
                                       l++g+  fh l++++s +k pvy++dp ++++++ ++  +++lr+Rya+i +++++++vG++v+ + +q+rl l+++
  gi|557693851|ref|YP_008796905.1| 184 LVLGS-VFHGLGIAVSSSK-PVYAADPHTQRVENLDKMRERILRQRYAQIIRFRESRTVGVLVSIKPGQKRLGLAKK 258
                                       99997.9**********77.********************************************************* PP

                   Diphthamide_syn 230 lkkllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalgerewt 299
                                       l++ l+++gk+s++v+ +e++ a + +   ++afV++aCprlsi d+++F+kPvl p+E+ va+g  ew+
  gi|557693851|ref|YP_008796905.1| 259 LNNILNQHGKNSTIVSADEITSATILEN-GFEAFVNTACPRLSIEDQSRFTKPVLLPVEALVAVGLMEWE 327
                                       ************************9998.9***********************************99996 PP

>> DUF1847  Protein of unknown function (DUF1847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   7.2e-05      0.43      42      85 ..      10      53 ..       3      67 .. 0.90
   2 !    3.3   0.0    0.0094        56      50      97 ..     116     163 ..     100     183 .. 0.82
   3 ?   -2.0   0.0       0.4   2.4e+03      51      62 ..     246     257 ..     203     287 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.2e-05
                           DUF1847 42 RveeiiefakrmgykkiGiafCvglleeakalakileakgfevv 85
                                       +ee +e  +rm++ ++ +   +gl+  a  +a+ l+++ fev 
  gi|557693851|ref|YP_008796905.1| 10 EIEEAVEQLRRMNVSRVLVQSPLGLRGVAASVAEQLKSNKFEVL 53
                                      489***************************************96 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0094
                           DUF1847  50 akrmgykkiGiafCvglleeakalakileakgfevvsviCkvgsvdke 97 
                                       a+ +gykk+G+   v  l+    +++ l ++g++ v+++  + sv  +
  gi|557693851|ref|YP_008796905.1| 116 AELTGYKKVGVGASVQWLDYLSFVKESLARRGVDAVTAMPDMYSVYES 163
                                       5778*****************************999988777666555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.4
                           DUF1847  51 krmgykkiGiaf 62 
                                        + g k++G+a 
  gi|557693851|ref|YP_008796905.1| 246 IKPGQKRLGLAK 257
                                       344556666654 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.4e-06      0.05      12      43 ..      29      57 ..      18      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.4e-06
                                      -S-.---SS--HHHHHHHHHHTTT---EEEE- CS
                             ACT_7 12 vgsglpfdvtGivaklaspLaeagIsifqiSt 43
                                      +    p+++ G++a++a+ L  ++++++++S+
  gi|557693851|ref|YP_008796905.1| 29 Q---SPLGLRGVAASVAEQLKSNKFEVLMSSS 57
                                      3...345889*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2632.86
//
Query:       gi|557693852|ref|YP_008796906.1|  [L=190]
Description: exosome complex component CSL4 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.2     0.0033   17.3   0.2    1.3  1  Prok-RING_1     Prokaryotic RING finger family 1
     0.0074   15.7   3.7       0.23   10.9   4.2    2.4  2  zf-ribbon_3     zinc-ribbon domain
     0.0093   15.7   0.8      0.022   14.5   0.8    1.7  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.013   15.3   0.1      0.052   13.4   0.0    2.0  2  ECR1_N          Exosome complex exonuclease RRP4 N-terminal r
      0.043   13.8   0.5       0.16   12.0   0.5    1.8  2  zf-C2HC5        Putative zinc finger motif, C2HC5-type
      0.092   12.3   3.9       0.91    9.1   3.9    2.3  1  RecR            RecR protein
       0.14   12.1   1.2       0.24   11.3   1.2    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.16   11.9   2.4       0.24   11.3   2.4    1.2  1  PHD             PHD-finger
       0.28   10.9   1.9       0.61    9.9   1.9    1.5  1  A2L_zn_ribbon   A2L zinc ribbon domain
       0.72    9.4   6.2        1.9    8.1   4.1    2.4  1  TF_Zn_Ribbon    TFIIB zinc-binding


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 !   17.3   0.2   1.8e-06    0.0033       6      33 ..     144     171 ..     141     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.8e-06
                       Prok-RING_1   6 kCpvCgkelkeedDiVvCpeCgtpyHra 33 
                                       +C+vCg+ l++ d i  C  Cg    r+
  gi|557693852|ref|YP_008796906.1| 144 ICSVCGNVLDKRDNILSCSRCGNKERRK 171
                                       7*********************876665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   4.2   0.00013      0.23       4      25 ..     144     167 ..     141     167 .. 0.86
   2 ?    4.5   0.6     0.013        23       4      11 ..     160     167 ..     159     173 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00013
                       zf-ribbon_3   4 rCPnCGaplssddnv..CpyCGtk 25 
                                        C+ CG++l+++dn+  C  CG k
  gi|557693852|ref|YP_008796906.1| 144 ICSVCGNVLDKRDNIlsCSRCGNK 167
                                       7******99*****7779999975 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.013
                       zf-ribbon_3   4 rCPnCGap 11 
                                       +C++CG++
  gi|557693852|ref|YP_008796906.1| 160 SCSRCGNK 167
                                       7*****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 !   14.5   0.8   1.2e-05     0.022       2      21 ..     145     166 ..     144     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                     zinc_ribbon_2   2 CpnCGaelqdnakF..CpyCGt 21 
                                       C+ CG+ l+++++   C++CG 
  gi|557693852|ref|YP_008796906.1| 145 CSVCGNVLDKRDNIlsCSRCGN 166
                                       *********************7 PP

>> 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 ?   13.4   0.0   2.9e-05     0.052       1      33 [.       5      38 ..       5      42 .. 0.86
   2 ?   -1.4   0.0       1.2   2.2e+03      17      29 ..     127     135 ..     122     151 .. 0.43

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-05
                                      EE-TT-EEEETTTSEE-TTEEE.ETTEEEESSSE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYv.rggtiyAsvaG 33
                                      +V+PGevl+  eef++  G +v  +g++ A v+G
  gi|557693852|ref|YP_008796906.1|  5 LVVPGEVLCVLEEFLPRLGSFVnGEGKVKARVLG 38
                                      6***************999998667778888877 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                                       -TTEEEETTEEEE CS
                            ECR1_N  17 GhGTYvrggtiyA 29 
                                       G +T+     +y+
  gi|557693852|ref|YP_008796906.1| 127 GINTF----DVYS 135
                                       44444....3322 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 ?   -1.5   0.0       1.5   2.6e+03      24      32 ..       9      17 ..       8      21 .. 0.84
   2 ?   12.0   0.5   8.7e-05      0.16      17      43 ..     142     167 ..     139     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
                          zf-C2HC5 24 GkiiCakeg 32
                                      G ++C+ e+
  gi|557693852|ref|YP_008796906.1|  9 GEVLCVLEE 17
                                      899**9987 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.7e-05
                          zf-C2HC5  17 apnClnCGkiiCakeglskpCsfCgsp 43 
                                       + +C  CG+++ +++++  +Cs Cg++
  gi|557693852|ref|YP_008796906.1| 142 LAICSVCGNVLDKRDNI-LSCSRCGNK 167
                                       679**************.******964 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   3.9   0.00051      0.91      19      39 ..     145     169 ..     142     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00051
                                       -TTT--EESSS....S-CCCCSTTS CS
                              RecR  19 CsrCgnlteed....lCaICsdprR 39 
                                       Cs+Cgn+ ++      C+ C +++R
  gi|557693852|ref|YP_008796906.1| 145 CSVCGNVLDKRdnilSCSRCGNKER 169
                                       9999999666446655999999988 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 ?   11.3   1.2   0.00014      0.24      30      58 ..     144     170 ..     143     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfeadr 58 
                                        Cs+Cg ++++   ++ + C++Cg +  r
  gi|557693852|ref|YP_008796906.1| 144 ICSVCGNVLDK--RDNILSCSRCGNKERR 170
                                       6**********..9**********99777 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.4   0.00014      0.24       1      23 [.     144     166 ..     144     168 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                       SBTTTTSTTSTTSCEEEETTTSC CS
                               PHD   1 rCavCkkksdeeeelvqCdgCkr 23 
                                       +C+vC++  d+ +++++C +C++
  gi|557693852|ref|YP_008796906.1| 144 ICSVCGNVLDKRDNILSCSRCGN 166
                                       6******999***********86 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 ?    9.9   1.9   0.00034      0.61       5      29 ..     144     166 ..     142     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00034
                     A2L_zn_ribbon   5 vCsvCggngilnseqgylvCieCga 29 
                                       +CsvCg+  +l + +++l+C  Cg+
  gi|557693852|ref|YP_008796906.1| 144 ICSVCGN--VLDKRDNILSCSRCGN 166
                                       7****95..5559***********7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.1     0.001       1.9       2      27 ..     144     166 ..     143     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
                                       EETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGl 27 
                                       +C +Cg+   v+D   + l C++CG+
  gi|557693852|ref|YP_008796906.1| 144 ICSVCGN---VLDKRDNILSCSRCGN 166
                                       5888998...7888888889999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1421.59
//
Query:       gi|557693853|ref|YP_008796907.1|  [L=92]
Description: DNA-directed RNA polymerase subunit L [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   53.6   0.0    1.8e-14   53.2   0.0    1.1  1  RNA_pol_L_2    RNA polymerase Rpb3/Rpb11 dimerisation domain
     0.0034   16.8   0.0     0.0054   16.1   0.0    1.3  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
      0.085   12.8   0.2       0.14   12.1   0.2    1.4  1  TBPIP          TBPIP/Hop2 winged helix domain
       0.11   11.9   0.0       0.12   11.8   0.0    1.1  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2


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 !   53.2   0.0     4e-18   1.8e-14       3      74 ..      14      86 ..      13      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 4e-18
                                      EEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTTSEEEEEEEEST.SS-HHHHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2  3 tfeingEDhTLgnlLrhlllknpsVefagYkipHPlepkmnlriqtks.snnpleaLkkalkdlldicdelee 74
                                       +++++ D +++nl ++ l++ ++V +agY+++HPl+ ++++ i+ +s +++p++a++kal++l+++++ l +
  gi|557693853|ref|YP_008796907.1| 14 AISVYDVDQSILNLFTETLNSIEGVSYAGYRVEHPLTGEITVSIKVEStKITPRKAVQKALERLQETFKILDK 86
                                      5788999******************************99999999988677****************998865 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 !   16.1   0.0   1.2e-06    0.0054       6      68 ..      19      80 ..      15      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-06
                                      xxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  6 gvdhtlgNaLRrillsevpgvaiea.....pvvkvntdkdklilevetdgslkPeealkeAlkiLkek 68
                                      +vd ++ N +  +l  +++gv  ++     p     t +    ++ve++  ++P++a+++Al+ L+e 
  gi|557693853|ref|YP_008796907.1| 19 DVDQSILNLFTETLN-SIEGVSYAGyrvehPL----TGEITVSIKVESTK-ITPRKAVQKALERLQET 80
                                      578999999999999.9999999998666644....66667888999765.57************996 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   3.1e-05      0.14      32      52 ..      67      87 ..      55      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.1e-05
                             TBPIP 32 KtavqkaLdeLvdegkiieKe 52
                                       +avqkaL+ L+++ ki  Ke
  gi|557693853|ref|YP_008796907.1| 67 RKAVQKALERLQETFKILDKE 87
                                      579**************9886 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 ?   11.8   0.0   2.7e-05      0.12       9      52 ..      10      55 ..       5      87 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
                     tRNA-synt_1_2  9 Gleiefkvees.eeklevfttrpdtlfGvtfvalapehplvekl.a 52
                                      G  + ++v +  ++ l+ ft+  + + Gv++     ehpl+ ++  
  gi|557693853|ref|YP_008796907.1| 10 GDFLAISVYDVdQSILNLFTETLNSIEGVSYAGYRVEHPLTGEItV 55
                                      55566666666456789************************99952 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 665.63
//
Query:       gi|557693854|ref|YP_008796908.1|  [L=110]
Description: DNA-directed RNA polymerase subunit M [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-20   72.8  16.2    2.1e-20   72.3   5.2    3.1  3  TFIIS_C          Transcription factor S-II (TFIIS)
    1.3e-08   34.7   7.9    0.00017   21.5   0.7    2.2  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    1.4e-07   30.7   9.6      0.076   12.5   0.2    4.1  4  zf-ribbon_3      zinc-ribbon domain
    2.8e-06   27.1   6.2    5.2e-06   26.2   0.4    3.2  3  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    8.9e-06   25.3  14.1      0.041   13.6   0.2    4.2  4  zinc_ribbon_2    zinc-ribbon domain
    1.9e-05   24.6   9.2     0.0012   18.9   0.7    2.8  2  DZR              Double zinc ribbon
    9.5e-05   21.8  11.6      0.033   13.7   1.2    3.6  3  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00011   22.3   7.4      0.024   14.8   1.8    2.4  2  DUF2387          Probable metal-binding protein (DUF2387)
    0.00067   19.5  11.4      0.069   13.1   3.5    3.7  3  Nudix_N_2        Nudix N-terminal
     0.0011   18.8   9.8       0.14   12.1   1.8    2.5  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0011   18.5   7.7        1.4    8.6   0.1    4.1  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
     0.0017   18.3  13.8       0.35   10.8   0.7    4.0  3  zinc_ribbon_4    zinc-ribbon domain
     0.0023   17.2   1.1     0.0023   17.2   1.1    2.6  2  zf-TFIIB         Transcription factor zinc-finger
     0.0031   17.6  12.9        1.1    9.5   0.1    3.9  3  Zn-ribbon_8      Zinc ribbon domain
     0.0045   16.7  17.7       0.55   10.0   1.2    4.1  4  Rubredoxin_2     Rubredoxin metal binding domain
     0.0056   16.3   8.1        4.4    7.1   1.8    3.6  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit
     0.0059   16.7   8.0        9.3    6.5   0.1    4.1  4  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
     0.0068   16.3   8.1        2.8    8.0   1.2    3.9  3  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
     0.0073   16.4  15.4        3.2    7.9   0.2    4.2  4  UPF0547          Uncharacterised protein family UPF0547
     0.0084   16.5   8.2       0.13   12.7   0.5    2.4  2  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.011   15.4   3.2       0.62    9.7   0.3    2.3  2  TackOD1          Thaumarchaeal output domain 1
      0.012   15.3   0.3      0.012   15.3   0.3    2.8  3  Baculo_LEF5_C    Baculoviridae late expression factor 5 C-ter
      0.014   15.6   6.5        1.3    9.3   1.1    3.1  3  IBR              IBR domain, a half RING-finger domain
      0.021   14.7   7.7        1.2    9.0   0.5    3.0  3  eIF-5_eIF-2B     Domain found in IF2B/IF5
      0.026   14.5   7.3       0.21   11.6   0.4    2.4  2  zinc-ribbons_6   zinc-ribbons
      0.026   14.2  10.1        6.6    6.6   0.0    4.0  4  A2L_zn_ribbon    A2L zinc ribbon domain
       0.04   13.9   8.3          1    9.4   0.7    3.0  2  HypA             Hydrogenase/urease nickel incorporation, met
      0.055   13.2   8.2       0.21   11.3   1.4    3.6  3  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
      0.056   13.1   0.4       0.12   12.1   0.4    1.5  1  zf-SNAP50_C      snRNA-activating protein of 50kDa MW C termi
      0.064   13.2   7.3        1.2    9.1   0.5    2.8  3  Prok-RING_1      Prokaryotic RING finger family 1
      0.089   13.2   0.2       0.14   12.6   0.2    1.2  1  DUF104           Protein of unknown function DUF104
      0.093   12.8   8.2         10    6.2   0.2    3.2  2  Elf1             Transcription elongation factor Elf1 like
       0.11   12.8   7.0       0.63   10.4   0.2    3.3  3  zinc_ribbon_9    zinc-ribbon
       0.11   12.1   6.2        6.6    6.4   0.1    4.0  4  zf_C2H2_13       Zinc finger domain
       0.12   12.8  10.1        6.8    7.2   0.2    3.9  4  zf-IS66          zinc-finger binding domain of transposase IS
       0.19   11.3   8.8         14    5.4   0.0    3.9  4  Sgf11            Sgf11 (transcriptional regulation protein)
       0.31   11.1  11.7         15    5.6   0.1    3.9  3  CpXC             CpXC protein
       0.43   10.6   0.1       0.43   10.6   0.1    3.7  4  PriA_CRR         PriA DNA helicase Cys-rich region (CRR) doma
       0.45   10.1   3.2        4.9    6.8   0.3    2.2  2  DpnI             Dam-replacing family
       0.48   10.7   7.1         16    5.8   0.0    3.7  3  Ribosomal_L32p   Ribosomal L32p protein family
       0.64    9.4   7.9        2.6    7.5   1.5    2.5  2  NMD3             NMD3 family
          1    9.5  11.8          9    6.5   3.1    3.2  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
        1.2    9.5   4.6        1.6    9.2   0.6    2.6  2  ribosomal_L24    Ribosomal proteins 50S L24/mitochondrial 39S
        1.3    9.1   9.9         28    4.8   0.1    4.2  4  YhfH             YhfH-like protein
        1.4    9.0   9.0         14    5.9   2.6    3.0  2  Ribosomal_L37ae  Ribosomal L37ae protein family
        1.6    8.9   9.7        5.9    7.1   2.6    3.0  3  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
        1.8    9.1  15.8        5.8    7.5   4.6    3.7  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
          2    8.5   9.6    1.4e+02    2.5   5.7    3.3  2  zf-RING_5        zinc-RING finger domain
        2.5    8.3  14.9        4.7    7.4   1.0    3.8  4  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
        2.5    7.9   8.4       0.38   10.6   0.2    2.8  2  zf-ZPR1          ZPR1 zinc-finger domain
        2.6    7.8  17.6        1.6    8.5   0.2    3.7  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
        2.9    8.3   8.8         21    5.6   0.4    3.3  4  GFA              Glutathione-dependent formaldehyde-activatin
        3.5    7.7  10.5         26    4.9   0.2    4.0  4  ADK_lid          Adenylate kinase, active site lid
        4.6    8.1  12.0        1.3    9.9   0.6    3.2  3  zinc_ribbon_15   zinc-ribbon family
        5.4    6.5   9.5        2.9    7.4   0.6    2.8  2  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
        5.5    7.0   7.4         42    4.2   2.8    2.9  3  RNHCP            RNHCP domain
        6.2    6.9  14.1        2.2    8.4   1.2    3.8  4  Zn_Tnp_IS91      Transposase zinc-binding domain
        6.8    6.8  11.6        3.1    7.9   2.6    3.2  2  Ogr_Delta        Ogr/Delta-like zinc finger
          7    6.4  12.9         14    5.4   0.3    3.9  4  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
        7.4    6.5  16.8        6.9    6.6   4.9    3.7  3  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
        8.6    6.4  11.1        5.5    7.1   1.3    3.3  3  DUF1610          Domain of unknown function (DUF1610)


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 ?    4.7   0.2     0.096        28       3       9 ..       4      10 ..       2      12 .. 0.82
   2 ?    3.0   0.2      0.33        96      29      37 ..      22      30 ..      19      31 .. 0.74
   3 !   72.3   5.2   7.1e-23   2.1e-20       2      39 .]      70     107 ..      69     107 .. 0.98

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.096
                           TFIIS_C  3 CpkCgsr 9 
                                      CpkCg++
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKT 10
                                      9999986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.33
                           TFIIS_C 29 ykCtkCghr 37
                                       +C+ Cg++
  gi|557693854|ref|YP_008796908.1| 22 LVCKRCGYQ 30
                                      578888875 PP

  == domain 3  score: 72.3 bits;  conditional E-value: 7.1e-23
                           TFIIS_C   2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39 
                                        Cp+Cg++ea ++++QtRsaDEpmt f++C+kCgh+Wr
  gi|557693854|ref|YP_008796908.1|  70 VCPQCGHNEAKWWTVQTRSADEPMTQFFRCVKCGHTWR 107
                                       6************************************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 !   17.2   1.3   1.3e-05    0.0038      21      46 .]       4      30 ..       2      30 .. 0.96
   2 !   21.5   0.7   5.9e-07   0.00017      19      46 .]      69     105 ..      59     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-05
                     Zn_Tnp_IS1595 21 CPhCgsr.kayriktrglfqCkeCrkq 46
                                      CP+Cg++ ++ r+ +   + Ck+C++q
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTlTPSRVGGKAMLVCKRCGYQ 30
                                      *************************98 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 5.9e-07
                     Zn_Tnp_IS1595  19 fvCPhCgsr..kayrikt.......rglfqCkeCrkq 46 
                                       +vCP Cg+   k ++++t        + f+C +C+++
  gi|557693854|ref|YP_008796908.1|  69 VVCPQCGHNeaKWWTVQTrsadepmTQFFRCVKCGHT 105
                                       89******999***********************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 !   12.4   0.1   0.00027      0.08       2      14 ..       1      13 [.       1      16 [. 0.72
   2 ?    3.9   0.1      0.13        38      17      25 ..      22      30 ..      19      30 .. 0.83
   3 !   12.5   0.2   0.00026     0.076      13      24 ..      65      76 ..      61      79 .. 0.70
   4 ?    5.9   0.1     0.029       8.6       3      10 ..      97     104 ..      95     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00027
                       zf-ribbon_3  2 tvrCPnCGa.plss 14
                                      + +CP+CG+ + ++
  gi|557693854|ref|YP_008796908.1|  1 MEFCPKCGKtL-TP 13
                                      67899999955.54 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.13
                       zf-ribbon_3 17 nvCpyCGtk 25
                                       vC+ CG++
  gi|557693854|ref|YP_008796908.1| 22 LVCKRCGYQ 30
                                      58*****86 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 0.00026
                       zf-ribbon_3 13 ssddnvCpyCGt 24
                                      +++d+vCp CG+
  gi|557693854|ref|YP_008796908.1| 65 TTSDVVCPQCGH 76
                                      667777777776 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.029
                       zf-ribbon_3   3 vrCPnCGa 10 
                                        rC +CG+
  gi|557693854|ref|YP_008796908.1|  97 FRCVKCGH 104
                                       69*****8 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 !   26.2   0.4   1.8e-08   5.2e-06       1      35 [.       1      35 [.       1      36 [. 0.88
   2 ?    1.6   0.1      0.85   2.5e+02       4       8 ..      71      75 ..      63      78 .. 0.70
   3 ?    0.5   0.1       1.9   5.6e+02      22      28 ..      97     103 ..      87     104 .. 0.66

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.8e-08
                                      EEBESTTTSBEEEEECSCCCEEEESSSS-EEESSC CS
                    RNA_POL_M_15KD  1 lkFCpkCgNlLlpkedkegknfeCrqCgYeepadq 35
                                      ++FCpkCg  L p +   +  + C  CgY +p ++
  gi|557693854|ref|YP_008796908.1|  1 MEFCPKCGKTLTPSRVGGKAMLVCKRCGYQKPLEG 35
                                      99***********9866666689*********986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.85
                                      ESTTT CS
                    RNA_POL_M_15KD  4 CpkCg 8 
                                      Cp Cg
  gi|557693854|ref|YP_008796908.1| 71 CPQCG 75
                                      66665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 1.9
                                       EEESSSS CS
                    RNA_POL_M_15KD  22 feCrqCg 28 
                                       f C +Cg
  gi|557693854|ref|YP_008796908.1|  97 FRCVKCG 103
                                       6677775 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   0.00014     0.041       1      11 [.       3      13 ..       3      16 .. 0.81
   2 ?    5.3   0.4     0.059        17       2       8 ..      24      30 ..      23      37 .. 0.78
   3 !    9.9   0.1     0.002      0.59      12      22 ..      67      77 ..      61      77 .. 0.75
   4 ?    4.2   0.6      0.13        37       2       7 ..      99     104 ..      96     105 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00014
                     zinc_ribbon_2  1 fCpnCGaelqd 11
                                      fCp+CG++l +
  gi|557693854|ref|YP_008796908.1|  3 FCPKCGKTLTP 13
                                      89999999865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.059
                     zinc_ribbon_2  2 CpnCGae 8 
                                      C++CG++
  gi|557693854|ref|YP_008796908.1| 24 CKRCGYQ 30
                                      9999987 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.002
                     zinc_ribbon_2 12 nakFCpyCGtp 22
                                       ++ Cp+CG++
  gi|557693854|ref|YP_008796908.1| 67 SDVVCPQCGHN 77
                                      56779999985 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.13
                     zinc_ribbon_2   2 CpnCGa 7  
                                       C +CG+
  gi|557693854|ref|YP_008796908.1|  99 CVKCGH 104
                                       777775 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.7     4e-06    0.0012      13      41 ..       2      34 ..       1      37 [. 0.85
   2 !    8.8   2.2    0.0056       1.6      13      37 ..      69     105 ..      58     110 .] 0.63

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4e-06
                               DZR 13 rfCseCgtklkavaa.....edrCpsCgekvdpe 41
                                      +fC++Cg++l +  +     + +C +Cg++ ++e
  gi|557693854|ref|YP_008796908.1|  2 EFCPKCGKTLTPS-RvggkaMLVCKRCGYQKPLE 34
                                      69********854.36999**********97765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0056
                               DZR  13 rfCseCgtk......lkavaa.........edrCpsCgek 37 
                                        +C++Cg++      ++   +           rC++Cg+ 
  gi|557693854|ref|YP_008796908.1|  69 VVCPQCGHNeakwwtVQ---TrsadepmtqFFRCVKCGHT 105
                                       47888887754443322...14457777777788888765 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   3.3    0.0021       0.6       3      27 ..       4      29 ..       2      30 .. 0.77
   2 !    7.8   0.2    0.0079       2.3      16      27 ..      65      76 ..      64      80 .. 0.79
   3 !   13.7   1.2   0.00011     0.033       2      27 ..      70     104 ..      69     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0021
                                      ETTTTCEECHEE...TSTTCEEESSSSB CS
                      TF_Zn_Ribbon  3 CPnCgstnlveD...pergelvCtdCGl 27
                                      CP+Cg t +  +      + lvC++CG+
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLT--PsrvGGKAMLVCKRCGY 29
                                      *****9854..3334778899******7 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0079
                                      STTCEEESSSSB CS
                      TF_Zn_Ribbon 16 ergelvCtdCGl 27
                                       + ++vC+ CG 
  gi|557693854|ref|YP_008796908.1| 65 TTSDVVCPQCGH 76
                                      577889999985 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 0.00011
                                       EETTTTCEEC.........HEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon   2 kCPnCgstnl.........veDpergelvCtdCGl 27 
                                       +CP Cg+ +            +p++  ++C +CG 
  gi|557693854|ref|YP_008796908.1|  70 VCPQCGHNEAkwwtvqtrsADEPMTQFFRCVKCGH 104
                                       8******99779****997777************7 PP

>> DUF2387  Probable metal-binding protein (DUF2387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.3    0.0019      0.55      11      62 ..       4      53 ..       2      62 .. 0.85
   2 !   14.8   1.8   8.1e-05     0.024       9      39 ..      69     105 ..      67     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0019
                           DUF2387 11 CPrCsemDkirmweedeveyrECvsCgftdelsekgqsvakelktrvnkdee 62
                                      CP+C ++  +   +  ++ +  C  Cg+   l+ ++  ++ e ++ v k+ +
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKT--LTPSRVGGKAMLVCKRCGYQKPLEGEKVVIKLEKENTVSKNVA 53
                                      9999985..77788999******************99999999999998865 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 8.1e-05
                           DUF2387   9 avCPrCsemD....kirmweede..veyrECvsCgft 39 
                                       +vCP+C +      ++++ + de  +++  Cv+Cg+t
  gi|557693854|ref|YP_008796908.1|  69 VVCPQCGHNEakwwTVQTRSADEpmTQFFRCVKCGHT 105
                                       7*****99987777666666666679999*******8 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   3.5   0.00023     0.069       2      30 ..       3      29 ..       2      29 .. 0.84
   2 ?    7.0   0.1     0.019       5.5       3       8 ..      71      76 ..      69      91 .. 0.81
   3 ?    2.7   0.1      0.42   1.2e+02      25      30 ..      99     104 ..      95     108 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00023
                                      B-TTT--B-EEE--TT-SS-EEEETTTTE CS
                         Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCgt 30
                                      FC++CG++++      + +  lvC++Cg+
  gi|557693854|ref|YP_008796908.1|  3 FCPKCGKTLTPSRV--GGKAMLVCKRCGY 29
                                      9********98886..445569*****97 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.019
                                      -TTT-- CS
                         Nudix_N_2  3 CsqCGt 8 
                                      C+qCG+
  gi|557693854|ref|YP_008796908.1| 71 CPQCGH 76
                                      666665 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.42
                                       ETTTTE CS
                         Nudix_N_2  25 CpaCgt 30 
                                       C +Cg+
  gi|557693854|ref|YP_008796908.1|  99 CVKCGH 104
                                       555555 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 !   11.1   1.3   0.00094      0.28      31      55 ..       4      30 ..       2      32 .. 0.85
   2 !   12.1   1.8   0.00047      0.14      29      56 ..      69     106 ..      53     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00094
                    OrfB_Zn_ribbon 31 CseCgsknke..alsgrtfkCpnCgfe 55
                                      C++Cg+++++     +  ++C++Cg++
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLTPsrVGGKAMLVCKRCGYQ 30
                                      **********755567789******86 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00047
                    OrfB_Zn_ribbon  29 ktCseCgsknke..........alsgrtfkCpnCgfea 56 
                                         C++Cg++  +          ++ ++ f+C +Cg+++
  gi|557693854|ref|YP_008796908.1|  69 VVCPQCGHNEAKwwtvqtrsadEPMTQFFRCVKCGHTW 106
                                       68************99999988888899*******987 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1    0.0046       1.4       4      14 ..       3      13 ..       1      17 [. 0.82
   2 ?    4.3   0.1      0.11        31       3       9 ..      22      28 ..      20      37 .. 0.80
   3 ?    6.7   0.1     0.018       5.4       2      11 ..      68      77 ..      67      85 .. 0.84
   4 ?    1.4   0.2      0.82   2.4e+02       3      11 ..      97     105 ..      95     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0046
                            zf_UBZ  4 lCerCgkeipe 14
                                      +C++Cgk++ +
  gi|557693854|ref|YP_008796908.1|  3 FCPKCGKTLTP 13
                                      8******9866 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.11
                            zf_UBZ  3 ylCerCg 9 
                                       +C+rCg
  gi|557693854|ref|YP_008796908.1| 22 LVCKRCG 28
                                      69****9 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.018
                            zf_UBZ  2 tylCerCgke 11
                                       ++C++Cg++
  gi|557693854|ref|YP_008796908.1| 68 DVVCPQCGHN 77
                                      589*****86 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.82
                            zf_UBZ   3 ylCerCgke 11 
                                       + C +Cg++
  gi|557693854|ref|YP_008796908.1|  97 FRCVKCGHT 105
                                       88****985 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   3.6      0.13        37       5      33 ..       4      29 ..       3      30 .. 0.78
   2 ?    7.0   0.0     0.018       5.4      21      33 ..      64      76 ..      56      77 .. 0.68
   3 !   10.8   0.7    0.0012      0.35      26      36 .]      97     107 ..      91     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.13
                     zinc_ribbon_4  5 CpsCkakyeiddeklpakgvkvrCskCgh 33
                                      Cp+C++  ++ ++++ +k +++ C++Cg 
  gi|557693854|ref|YP_008796908.1|  4 CPKCGK--TLTPSRVGGK-AMLVCKRCGY 29
                                      899998..5888888888.6677999985 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.018
                     zinc_ribbon_4 21 akgvkvrCskCgh 33
                                      ++++ v C+ Cgh
  gi|557693854|ref|YP_008796908.1| 64 PTTSDVVCPQCGH 76
                                      6667778888887 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0012
                     zinc_ribbon_4  26 vrCskCghvFr 36 
                                        rC kCgh++r
  gi|557693854|ref|YP_008796908.1|  97 FRCVKCGHTWR 107
                                       69********7 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   1.1   7.7e-06    0.0023       2      26 ..       4      28 ..       3      28 .. 0.98
   2 ?    2.9   3.3      0.24        71       2      26 ..      71     103 ..      70     106 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.7e-06
                          zf-TFIIB  2 CPkCqdeleeserggveidyCpqCr 26
                                      CPkC+ +l++s++gg    +C +C+
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLTPSRVGGKAMLVCKRCG 28
                                      ************************7 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.24
                          zf-TFIIB   2 CPkCqd.ele....eser.gg..veidyCpqCr 26 
                                       CP C++ e +    ++++ ++   ++++C +C+
  gi|557693854|ref|YP_008796908.1|  71 CPQCGHnEAKwwtvQTRSaDEpmTQFFRCVKCG 103
                                       999987578888653333533347888888886 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.7     0.015       4.5       8      33 ..       4      28 ..       2      34 .. 0.83
   2 !    9.5   0.1    0.0037       1.1      25      36 ..      67      79 ..      52      81 .. 0.75
   3 ?    5.6   0.5     0.061        18       6      14 ..      97     105 ..      96     109 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.015
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCg 33
                                      C +Cg++ ++ + +  +++ +C++Cg
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLTPSR-VGGKAMLVCKRCG 28
                                      999999999887.6666788899998 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0037
                       Zn-ribbon_8 25 pltaCPeCgs.ev 36
                                      ++++CP+Cg+ e+
  gi|557693854|ref|YP_008796908.1| 67 SDVVCPQCGHnEA 79
                                      3677*****9554 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.061
                       Zn-ribbon_8   6 YrCeeCghe 14 
                                       +rC +Cgh+
  gi|557693854|ref|YP_008796908.1|  97 FRCVKCGHT 105
                                       8******97 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.4      0.73   2.2e+02      17      21 ..       4       8 ..       3      10 .. 0.80
   2 !    8.0   0.1    0.0082       2.4       2      10 ..      23      31 ..      23      33 .. 0.88
   3 !   10.0   1.2    0.0019      0.55       2      14 ..      70      82 ..      70      82 .. 0.93
   4 ?    7.5   0.6     0.011       3.3       1      10 [.      97     106 ..      97     110 .] 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.73
                      Rubredoxin_2 17 CpsCg 21
                                      Cp Cg
  gi|557693854|ref|YP_008796908.1|  4 CPKCG 8 
                                      88887 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0082
                      Rubredoxin_2  2 vCsqCGfes 10
                                      vC++CG++ 
  gi|557693854|ref|YP_008796908.1| 23 VCKRCGYQK 31
                                      7******96 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0019
                      Rubredoxin_2  2 vCsqCGfesakwf 14
                                      vC qCG+  akw+
  gi|557693854|ref|YP_008796908.1| 70 VCPQCGHNEAKWW 82
                                      7***********7 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.011
                      Rubredoxin_2   1 YvCsqCGfes 10 
                                       ++C +CG++ 
  gi|557693854|ref|YP_008796908.1|  97 FRCVKCGHTW 106
                                       8******985 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 ?    7.1   1.8     0.015       4.4       3      25 ..       4      29 ..       3      30 .. 0.69
   2 ?    5.8   0.0     0.036        11      11      25 ..      62      76 ..      58      77 .. 0.78
   3 ?    5.2   0.1     0.059        17      19      25 ..      98     104 ..      92     105 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.015
                                      -SSS--...B----SSS----SSS-- CS
                    DNA_RNApol_7kD  3 CgeCga...evslkkgdpiRCkeCGh 25
                                      C +Cg+   + ++  ++ + Ck CG+
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKtltPSRVGGKAMLVCKRCGY 29
                                      555655111456888999*******8 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.036
                                      ---SSS----SSS-- CS
                    DNA_RNApol_7kD 11 slkkgdpiRCkeCGh 25
                                       l  +  + C +CGh
  gi|557693854|ref|YP_008796908.1| 62 PLPTTSDVVCPQCGH 76
                                      566777789*****9 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.059
                                       --SSS-- CS
                    DNA_RNApol_7kD  19 RCkeCGh 25 
                                       RC +CGh
  gi|557693854|ref|YP_008796908.1|  98 RCVKCGH 104
                                       9*****9 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 ?    3.0   0.2      0.41   1.2e+02       2       8 ..       4      10 ..       3      15 .. 0.84
   2 ?    6.0   0.0     0.045        13      36      44 ..      22      30 ..      20      42 .. 0.82
   3 ?    6.5   0.1     0.032       9.3       1      16 [.      70      85 ..      70      90 .. 0.82
   4 ?    3.5   0.2      0.27        78       1       8 [.      98     105 ..      98     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.41
                    zinc_ribbon_13  2 CpKCgnt 8 
                                      CpKCg+t
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKT 10
                                      *****87 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.045
                    zinc_ribbon_13 36 vsCknCgYt 44
                                        Ck+CgY 
  gi|557693854|ref|YP_008796908.1| 22 LVCKRCGYQ 30
                                      68*****97 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.032
                    zinc_ribbon_13  1 kCpKCgnteaevkeva 16
                                      +Cp+Cg++ea+  +v+
  gi|557693854|ref|YP_008796908.1| 70 VCPQCGHNEAKWWTVQ 85
                                      6********9977776 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.27
                    zinc_ribbon_13   1 kCpKCgnt 8  
                                       +C+KCg+t
  gi|557693854|ref|YP_008796908.1|  98 RCVKCGHT 105
                                       59999997 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   1.2    0.0095       2.8       5      28 ..       4      30 ..       3      30 .. 0.73
   2 ?    6.9   0.1     0.021       6.2      21      27 ..      70      76 ..      60      77 .. 0.84
   3 ?    1.9   0.0      0.74   2.2e+02      20      29 ..      97     106 ..      92     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0095
                    PhnA_Zn_Ribbon  5 CplCaSeytY.....edgallvCpeCahE 28
                                      Cp+C+   t+      ++a+lvC  C+++
  gi|557693854|ref|YP_008796908.1|  4 CPKCG--KTLtpsrvGGKAMLVCKRCGYQ 30
                                      56665..455556656789********98 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.021
                    PhnA_Zn_Ribbon 21 vCpeCah 27
                                      vCp C+h
  gi|557693854|ref|YP_008796908.1| 70 VCPQCGH 76
                                      9****99 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.74
                    PhnA_Zn_Ribbon  20 lvCpeCahEw 29 
                                       + C +C+h w
  gi|557693854|ref|YP_008796908.1|  97 FRCVKCGHTW 106
                                       5589999988 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.7     0.044        13      14      21 ..       1       8 [.       1       9 [. 0.91
   2 ?    6.2   0.1     0.037        11      13      22 ..      20      29 ..      19      30 .. 0.88
   3 ?    7.9   0.2     0.011       3.2      16      22 ..      70      76 ..      66      77 .. 0.71
   4 ?    5.0   0.6      0.09        26      17      25 ..      99     107 ..      97     108 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.044
                           UPF0547 14 aqfCphCG 21
                                      ++fCp CG
  gi|557693854|ref|YP_008796908.1|  1 MEFCPKCG 8 
                                      789****9 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.037
                           UPF0547 13 aaqfCphCGy 22
                                      a+ +C  CGy
  gi|557693854|ref|YP_008796908.1| 20 AMLVCKRCGY 29
                                      8999*99**9 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.011
                           UPF0547 16 fCphCGy 22
                                      +Cp CG+
  gi|557693854|ref|YP_008796908.1| 70 VCPQCGH 76
                                      5777776 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.09
                           UPF0547  17 CphCGyvFq 25 
                                       C  CG+ + 
  gi|557693854|ref|YP_008796908.1|  99 CVKCGHTWR 107
                                       989****96 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 !   12.7   0.5   0.00043      0.13       6      37 ..       4      34 ..       1      61 [. 0.77
   2 ?    7.5   1.9     0.018       5.4       6      36 ..      71     104 ..      69     110 .] 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00043
                   Lar_restr_allev  6 CPfCggravlersqrvvaeigqcvyCadCga....s 37
                                      CP Cg+  +  r ++++     +  C+ Cg+     
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLTPSRVGGKA-----MLVCKRCGYqkplE 34
                                      *****999999997777.....9********55441 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.018
                   Lar_restr_allev   6 CPfCggra.vlersqrvvaeigq...cvyCadCga 36 
                                       CP Cg+ + ++ + q ++a+ ++   ++ C +Cg 
  gi|557693854|ref|YP_008796908.1|  71 CPQCGHNEaKWWTVQTRSAD-EPmtqFFRCVKCGH 104
                                       *****854144444444443.33468999999997 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2     0.018       5.3      88     116 ..       2      34 ..       1      44 [. 0.75
   2 ?    9.7   0.3    0.0021      0.62      74     112 ..      69     105 ..      41     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.018
                           TackOD1  88 evCpkCkSi....dieeqelihhftCgnvgpee 116
                                       e CpkC+ +    ++  ++++ + +Cg+++p e
  gi|557693854|ref|YP_008796908.1|   2 EFCPKCGKTltpsRVGGKAMLVCKRCGYQKPLE 34 
                                       679999864222267788999999999988865 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0021
                           TackOD1  74 rlCpsCksghlnvrevCpkCkSidieeqelihhftCgnv 112
                                       ++Cp+C +++ +   v  + +S+d   ++++ +++Cg++
  gi|557693854|ref|YP_008796908.1|  69 VVCPQCGHNEAKWWTV--QTRSADEPMTQFFRCVKCGHT 105
                                       68****9998877765..889****************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 ?    0.1   0.2       2.2   6.5e+02      36      41 ..       3       8 ..       1       9 [. 0.82
   2 ?   -1.1   0.5       5.4   1.6e+03      36      41 ..      23      28 ..      21      29 .. 0.84
   3 ?   15.3   0.3   4.1e-05     0.012      12      41 ..      73     103 ..      69     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 2.2
                     Baculo_LEF5_C 36 yCskCg 41
                                       C kCg
  gi|557693854|ref|YP_008796908.1|  3 FCPKCG 8 
                                      6****9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5.4
                     Baculo_LEF5_C 36 yCskCg 41
                                      +C++Cg
  gi|557693854|ref|YP_008796908.1| 23 VCKRCG 28
                                      6****9 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 4.1e-05
                     Baculo_LEF5_C  12 qClHdfv.tiEiQnRagDEivsfvryCskCg 41 
                                       qC H+       Q+R+ DE       C+kCg
  gi|557693854|ref|YP_008796908.1|  73 QCGHNEAkWWTVQTRSADEPMTQFFRCVKCG 103
                                       577766665557*******6666666****9 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 ?    9.3   1.1    0.0044       1.3      20      47 ..       3      30 ..       1      31 [. 0.85
   2 ?    4.9   0.0       0.1        30      32      46 ..      58      76 ..      37      78 .. 0.69
   3 ?    3.5   0.1      0.28        82      49      57 ..      99     107 ..      83     110 .] 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0044
                               IBR 20 wCprpdCeaiiekseg..cksvtCskCgfe 47
                                       Cp  +C++ + +s    ++++ C++Cg++
  gi|557693854|ref|YP_008796908.1|  3 FCP--KCGKTLTPSRVggKAMLVCKRCGYQ 30
                                      7*9..******999997677788****986 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.1
                               IBR 32 kseg....cksvtCskCgf 46
                                       +e     +++v C++Cg+
  gi|557693854|ref|YP_008796908.1| 58 AEEAplptTSDVVCPQCGH 76
                                      3333444445599****98 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.28
                               IBR  49 CfnCkkewH 57 
                                       C++C++ w 
  gi|557693854|ref|YP_008796908.1|  99 CVKCGHTWR 107
                                       888888875 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 ?    7.6   0.5     0.011       3.3      90     116 ..       4      29 ..       3      30 .. 0.91
   2 ?    1.3   0.0         1   3.1e+02      15      37 ..      37      58 ..      31      62 .. 0.78
   3 ?    9.0   0.5    0.0042       1.2      88     116 ..      69     104 ..      66     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.011
                                       TSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  90 CkeCkspetelekeerllvlkCkaCga 116
                                       C++C++  t   + ++ + l Ck Cg 
  gi|557693854|ref|YP_008796908.1|   4 CPKCGKTLTPSRVGGKAM-LVCKRCGY 29 
                                       *********999999998.9*****97 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1
                                      T--EEEETT.EEEETTHHHHHHH CS
                      eIF-5_eIF-2B 15 klqvkvegkkktvivNfeeiaka 37
                                      k+ +k e + +tv +N++ i++a
  gi|557693854|ref|YP_008796908.1| 37 KVVIKLEKE-NTVSKNVAAIVEA 58
                                      556677777.99****9999875 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0042
                                       TSTSSSTSTCEEECC.......SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  88 VlCkeCkspetelek.......eerllvlkCkaCga 116
                                       V+C++C++ e +  +       e ++++++C +Cg+
  gi|557693854|ref|YP_008796908.1|  69 VVCPQCGHNEAKWWTvqtrsadEPMTQFFRCVKCGH 104
                                       89******99987666667776788999******97 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00071      0.21      30      55 ..       2      27 ..       1      37 [. 0.91
   2 ?    6.1   1.5     0.036        11       2      25 ..      70     105 ..      69     110 .] 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00071
                                      EE-SSS-S---EEEETTEEEE--TTT CS
                    zinc-ribbons_6 30 alCpeCeqelevlkaCgavdyfCnkc 55
                                       +Cp+C++ l   +  g++   C++c
  gi|557693854|ref|YP_008796908.1|  2 EFCPKCGKTLTPSRVGGKAMLVCKRC 27
                                      58****************9999*999 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.036
                                       --SSS-S--E.E-S...........SEEE-TTT--E CS
                    zinc-ribbons_6   2 kCpeCqqele.krg...........eqyhCeaCqed 25 
                                        Cp+C ++   + +           + ++C +C + 
  gi|557693854|ref|YP_008796908.1|  70 VCPQCGHNEAkWWTvqtrsadepmtQFFRCVKCGHT 105
                                       6****9876656665677777777666777777665 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 ?    6.1   0.1     0.031       9.2      22      28 ..       2       8 ..       1      11 [. 0.89
   2 ?    6.6   0.0     0.022       6.6      21      32 ..      21      32 ..      19      33 .. 0.78
   3 ?    5.7   0.1     0.043        13      20      28 ..      67      75 ..      65      80 .. 0.67
   4 ?   -0.5   0.5       3.8   1.1e+03       6      11 ..      99     104 ..      98     105 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.031
                     A2L_zn_ribbon 22 lvCieCg 28
                                      ++C++Cg
  gi|557693854|ref|YP_008796908.1|  2 EFCPKCG 8 
                                      8*****9 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.022
                     A2L_zn_ribbon 21 ylvCieCgasfp 32
                                       lvC+ Cg+  p
  gi|557693854|ref|YP_008796908.1| 21 MLVCKRCGYQKP 32
                                      589*****9655 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.043
                     A2L_zn_ribbon 20 gylvCieCg 28
                                      ++ vC+ Cg
  gi|557693854|ref|YP_008796908.1| 67 SDVVCPQCG 75
                                      566777777 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 3.8
                     A2L_zn_ribbon   6 CsvCgg 11 
                                       C +Cg+
  gi|557693854|ref|YP_008796908.1|  99 CVKCGH 104
                                       445554 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 ?    9.4   0.7    0.0034         1      72     108 ..       3      41 ..       1      44 [. 0.76
   2 ?    7.0   5.0     0.019       5.7      70      98 ..      21      80 ..      19     110 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0034
                                       EETTTS-EEECHH...H.HHS-TTTSSS-EEEEESSSEEEE CS
                              HypA  72 rCreCgkefelee...k.alrCpkCgsadveivsGeellvk 108
                                        C +Cgk+ + ++   k  l C++Cg +  + ++Ge + +k
  gi|557693854|ref|YP_008796908.1|   3 FCPKCGKTLTPSRvggKaMLVCKRCGYQ--KPLEGEKVVIK 41 
                                       5********977655545679****996..46778877775 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.019
                                      EEEETTTS-EEECHHHHH...............................S-TTTSSS-EE CS
                              HypA 70 kvrCreCgkefeleekal...............................rCpkCgsadve 98
                                       + C++Cg++  le +++                                Cp+Cg+++ +
  gi|557693854|ref|YP_008796908.1| 21 MLVCKRCGYQKPLEGEKVviklekentvsknvaaiveaeeaplpttsdvVCPQCGHNEAK 80
                                      678999999988776433467788999999999999999999999999999999988765 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 ?    1.0   0.2       1.2   3.5e+02      47      52 ..       4       9 ..       3      11 .. 0.77
   2 ?    2.5   0.0       0.4   1.2e+02      22      29 ..      21      28 ..      13      33 .. 0.82
   3 ?   11.3   1.4   0.00072      0.21      17      53 ..      63     105 ..      48     106 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 1.2
                    zinc_ribbon_10 47 CpkCga 52
                                      CpkCg 
  gi|557693854|ref|YP_008796908.1|  4 CPKCGK 9 
                                      999986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.4
                    zinc_ribbon_10 22 alICskCh 29
                                       l+C+ C 
  gi|557693854|ref|YP_008796908.1| 21 MLVCKRCG 28
                                      68999995 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00072
                    zinc_ribbon_10  17 aknryalICskChshnGlap....keeleev..kyrCpkCgal 53 
                                         + + ++C++C ++         +++ e++   +rC kCg++
  gi|557693854|ref|YP_008796908.1|  63 LPTTSDVVCPQCGHNEAKWWtvqtRSADEPMtqFFRCVKCGHT 105
                                       5667789*****98766433344645555553369******85 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 ?   12.1   0.4    0.0004      0.12     143     178 ..      65     102 ..      60     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0004
                       zf-SNAP50_C 143 klrrkkCkvCekfsakwvvlndkll..pedpsyfCdkC 178
                                       ++    C  C +++akw +++ + +  p ++++ C kC
  gi|557693854|ref|YP_008796908.1|  65 TTSDVVCPQCGHNEAKWWTVQTRSAdePMTQFFRCVKC 102
                                       667789**************97666225688999**** 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 ?    9.1   0.5    0.0042       1.2       6      27 ..       3      28 ..       1      31 [. 0.88
   2 ?    7.5   0.1     0.013       3.8      21      27 ..      69      75 ..      60      80 .. 0.83
   3 ?   -1.3   0.1       7.3   2.2e+03       7      12 ..      99     104 ..      96     108 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0042
                       Prok-RING_1  6 kCpvCgkelkee....dDiVvCpeCg 27
                                       Cp Cgk+l++     + + vC  Cg
  gi|557693854|ref|YP_008796908.1|  3 FCPKCGKTLTPSrvggKAMLVCKRCG 28
                                      5*********987777999******9 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.013
                       Prok-RING_1 21 VvCpeCg 27
                                      VvCp+Cg
  gi|557693854|ref|YP_008796908.1| 69 VVCPQCG 75
                                      89****9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 7.3
                       Prok-RING_1   7 CpvCgk 12 
                                       C  Cg+
  gi|557693854|ref|YP_008796908.1|  99 CVKCGH 104
                                       555554 PP

>> DUF104  Protein of unknown function DUF104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00047      0.14      24      51 ..      34      60 ..      33      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00047
                            DUF104 24 EGeevkikIeeakeilkklkgilkeade 51
                                      EGe+v+ik+e+  +++k++ +i+  a+e
  gi|557693854|ref|YP_008796908.1| 34 EGEKVVIKLEKENTVSKNVAAIVE-AEE 60
                                      9******************99987.443 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   2.9     0.086        25      24      54 ..       4      30 ..       3      79 .. 0.85
   2 ?    6.2   0.2     0.035        10      14      30 ..      89     105 ..      80     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.086
                              Elf1 24 CpfCnheksvevkldkkekiaevsCkvCges 54
                                      Cp C+++     + ++  ++a++ Ck Cg +
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKT----LTPSRVGGKAMLVCKRCGYQ 30
                                      8888888....78888899999999999975 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.035
                              Elf1  14 kkkklptkFdCpfCnhe 30 
                                         +++ + F+C  C+h+
  gi|557693854|ref|YP_008796908.1|  89 ADEPMTQFFRCVKCGHT 105
                                       34459999*******96 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.8      0.24        70       4      27 ..       3      27 ..       1      30 [. 0.57
   2 ?   10.4   0.2    0.0021      0.63      18      29 ..      65      76 ..      56      77 .. 0.77
   3 ?    0.3   0.0         3   8.9e+02      21      28 ..      91     103 ..      80     105 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.24
                     zinc_ribbon_9  4 WChqCdrfVsvspdedsdv.lCPhC 27
                                      +C  C +++++s+    +  +C +C
  gi|557693854|ref|YP_008796908.1|  3 FCPKCGKTLTPSRVGGKAMlVCKRC 27
                                      5556666666666644442256666 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0021
                     zinc_ribbon_9 18 edsdvlCPhCgg 29
                                      ++sdv+CP+Cg 
  gi|557693854|ref|YP_008796908.1| 65 TTSDVVCPQCGH 76
                                      577777****85 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 3
                     zinc_ribbon_9  21 d......vlCPhCg 28 
                                       +        C  Cg
  gi|557693854|ref|YP_008796908.1|  91 EpmtqffR-CVKCG 103
                                       33343334.99998 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2       0.3        87      20      27 ..       4      11 ..       2      14 .. 0.84
   2 ?    6.4   0.1     0.022       6.6      19      37 ..      23      43 ..      21      45 .. 0.83
   3 ?    1.9   0.0      0.59   1.7e+02      19      24 ..      70      75 ..      59      77 .. 0.87
   4 ?    1.2   0.0      0.98   2.9e+02      15      24 ..      94     103 ..      88     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.3
                        zf_C2H2_13 20 CnkCGkPi 27
                                      C kCGk +
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTL 11
                                      9****965 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.022
                        zf_C2H2_13 19 vCnkCG..kPisleaivdHLe 37
                                      vC+ CG  kP+  e +v  Le
  gi|557693854|ref|YP_008796908.1| 23 VCKRCGyqKPLEGEKVVIKLE 43
                                      9*****999999888876666 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.59
                        zf_C2H2_13 19 vCnkCG 24
                                      vC +CG
  gi|557693854|ref|YP_008796908.1| 70 VCPQCG 75
                                      9***** PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.98
                        zf_C2H2_13  15 lnYRvCnkCG 24 
                                       +++  C kCG
  gi|557693854|ref|YP_008796908.1|  94 TQFFRCVKCG 103
                                       67777***** 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 ?    7.2   0.2     0.023       6.8       3      15 ..       3      17 ..       2      20 .. 0.72
   2 ?    4.2   0.2       0.2        60       3      20 ..      23      39 ..      22      45 .. 0.77
   3 ?    6.0   0.1     0.053        16       3      10 ..      70      78 ..      68      86 .. 0.84
   4 ?   -0.8   0.2       7.1   2.1e+03       4      10 ..      99     105 ..      98     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.023
                           zf-IS66  3 tCpcCGg.l.lkpig 15
                                       Cp+CG+ l  +++g
  gi|557693854|ref|YP_008796908.1|  3 FCPKCGKtLtPSRVG 17
                                      6*****955666666 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.2
                           zf-IS66  3 tCpcCGgllkpigedrvr 20
                                      +C+ CG + kp+++++v 
  gi|557693854|ref|YP_008796908.1| 23 VCKRCGYQ-KPLEGEKVV 39
                                      6999*997.788888775 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.053
                           zf-IS66  3 tCpcCGg.l 10
                                      +Cp+CG+ +
  gi|557693854|ref|YP_008796908.1| 70 VCPQCGHnE 78
                                      6*****955 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 7.1
                           zf-IS66   4 CpcCGgl 10 
                                       C +CG++
  gi|557693854|ref|YP_008796908.1|  99 CVKCGHT 105
                                       8889984 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.046        14       7      18 ..       4      15 ..       3      16 .. 0.90
   2 ?    0.2   0.1       1.9   5.5e+02       4      11 ..      21      28 ..      18      30 .. 0.76
   3 ?    4.5   0.2     0.085        25       2      11 ..      66      75 ..      65      77 .. 0.83
   4 ?    4.2   0.2      0.11        31       2      11 ..      94     103 ..      93     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.046
                                      -TTTSSEEEGGG CS
                             Sgf11  7 CpnCgRqiaasR 18
                                      Cp Cg++   sR
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLTPSR 15
                                      *******99888 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.9
                                      EEE-TTTS CS
                             Sgf11  4 yvtCpnCg 11
                                        +C+ Cg
  gi|557693854|ref|YP_008796908.1| 21 MLVCKRCG 28
                                      56899997 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.085
                                      C-EEE-TTTS CS
                             Sgf11  2 seyvtCpnCg 11
                                      + +v+Cp Cg
  gi|557693854|ref|YP_008796908.1| 66 TSDVVCPQCG 75
                                      5689*****8 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.11
                                       C-EEE-TTTS CS
                             Sgf11   2 seyvtCpnCg 11 
                                       +++++C  Cg
  gi|557693854|ref|YP_008796908.1|  94 TQFFRCVKCG 103
                                       689******8 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1      0.15        45      40      48 ..       4      12 ..       2      16 .. 0.80
   2 ?    5.6   0.1     0.051        15      38      62 ..      22      46 ..      17      68 .. 0.81
   3 ?    2.5   3.8       0.5   1.5e+02       2      18 ..      70      85 ..      69     109 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.15
                              CpXC 40 CpkCgatak 48
                                      CpkCg+t +
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLT 12
                                      999999876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.051
                              CpXC 38 atCpkCgatakleapllyhdpekel 62
                                       +C +Cg++  le + ++++ eke 
  gi|557693854|ref|YP_008796908.1| 22 LVCKRCGYQKPLEGEKVVIKLEKEN 46
                                      68*******9999988887777765 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.5
                              CpXC  2 tCpaCgkefeaeiwtsi 18
                                       Cp+Cg++ ea+ wt+ 
  gi|557693854|ref|YP_008796908.1| 70 VCPQCGHN-EAKWWTVQ 85
                                      57777664.45555544 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 ?    2.5   0.2      0.52   1.5e+02       1       9 [.       4      12 ..       4      12 .. 0.93
   2 ?   10.6   0.1    0.0015      0.43      15      27 .]      20      32 ..      18      32 .. 0.89
   3 ?    2.0   0.1      0.73   2.1e+02      18      24 ..      70      76 ..      66      78 .. 0.67
   4 ?   -0.5   0.2       4.3   1.3e+03      18      25 ..      98     105 ..      95     107 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.52
                          PriA_CRR  1 CpnCdvslt 9 
                                      Cp C  +lt
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLT 12
                                      ****99998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0015
                          PriA_CRR 15 nrLrCHyCgyteP 27
                                        L+C  Cgy++P
  gi|557693854|ref|YP_008796908.1| 20 AMLVCKRCGYQKP 32
                                      679*********9 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.73
                          PriA_CRR 18 rCHyCgy 24
                                      +C +Cg+
  gi|557693854|ref|YP_008796908.1| 70 VCPQCGH 76
                                      5666776 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 4.3
                          PriA_CRR  18 rCHyCgyt 25 
                                       rC  Cg+t
  gi|557693854|ref|YP_008796908.1|  98 RCVKCGHT 105
                                       56669987 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.087        26      33      69 ..       3      37 ..       1      63 [. 0.66
   2 ?    6.8   0.3     0.017       4.9      30      61 ..      67     104 ..      64     109 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.087
                                      --TTT--SS-EE--------EEE-TTT--EEEEEEEE CS
                              DpnI 33 yCpkCgskklsefennkpvaDfyCesckeefeLkskk 69
                                      +CpkCg++ l+  +   + a + C++c  +  L  +k
  gi|557693854|ref|YP_008796908.1|  3 FCPKCGKT-LTPSRVGGK-AMLVCKRCGYQKPLEGEK 37
                                      9*****99.665555554.347888887555554444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.017
                                       HH---TTT--SS-EE--------E.....EE.-TTT-- CS
                              DpnI  30 knlyCpkCgskklsefennkpvaD.....fy.Cescke 61 
                                       +++ Cp+Cg+++ + ++  ++ aD     f+ C +c  
  gi|557693854|ref|YP_008796908.1|  67 SDVVCPQCGHNEAKWWTVQTRSADepmtqFFrCVKCGH 104
                                       5789******9887776666665544444544777765 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   3.0      0.38   1.1e+02      29      49 ..       4      31 ..       1      38 [. 0.67
   2 ?    5.8   0.0     0.055        16      40      47 ..      69      76 ..      50      81 .. 0.68
   3 ?   -0.2   0.0       4.3   1.3e+03      25      35 ..      95     105 ..      88     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.38
                                      ETTTCCEECTTC.......-BTTTTBSS CS
                    Ribosomal_L32p 29 cpncgelklpHr.......vcpscGyYk 49
                                      cp+cg++  p r       vc+ cGy k
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLTPSRvggkamlVCKRCGYQK 31
                                      8888877777663333333688888876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.055
                                      C-BTTTTB CS
                    Ribosomal_L32p 40 rvcpscGy 47
                                      +vcp+cG+
  gi|557693854|ref|YP_008796908.1| 69 VVCPQCGH 76
                                      45555555 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 4.3
                                       -EEEETTTCCE CS
                    Ribosomal_L32p  25 nlvecpncgel 35 
                                       ++ +c +cg++
  gi|557693854|ref|YP_008796908.1|  95 QFFRCVKCGHT 105
                                       55678888875 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   1.0     0.042        12       1      21 [.       4      29 ..       4      44 .. 0.79
   2 ?    7.5   1.5    0.0087       2.6     100     154 ..      37      89 ..      30     102 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.042
                              NMD3  1 CcrCGkeieeling.....lCedCll 21
                                      C++CGk+ +++  g     +C++C  
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLTPSRVGgkamlVCKRCGY 29
                                      9******9644333688889****65 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0087
                              NMD3 100 rikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqk 154
                                       ++ +k++ +++v++++ +i++ e     +++  +Cp+C   +++ ++  vQ R+ 
  gi|557693854|ref|YP_008796908.1|  37 KVVIKLEKENTVSKNVAAIVEAEEAPLPTTSDVVCPQCGHNEAKWWT--VQTRSA 89 
                                       55566666777766666666666666667788999999999999995..788877 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 ?    1.9   7.0      0.81   2.4e+02       2      24 ..       4      29 ..       3      81 .. 0.57
   2 ?    6.5   3.1     0.031         9       2      24 ..      71     104 ..      70     107 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.81
                          zf-Mss51  2 CPvpkhkqt...apkhvdfeCpdCGi 24
                                      CP + ++ t      +  + C++CG+
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLTpsrVGGKAMLVCKRCGY 29
                                      77777777766644455555555554 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.031
                          zf-Mss51   2 CPvpkhkqt...........apkhvdfeCpdCGi 24 
                                       CP + h+++           +p  + f C +CG 
  gi|557693854|ref|YP_008796908.1|  71 CPQCGHNEAkwwtvqtrsadEPMTQFFRCVKCGH 104
                                       ****999999*********99************6 PP

>> ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.6    0.0053       1.6      34      63 ..       3      29 ..       1      31 [. 0.75
   2 ?    1.8   0.3       1.1   3.3e+02      23      40 ..      60      76 ..      36     105 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0053
                     ribosomal_L24 34 vdpkcgkp...trvgfrlkedgkkvRvskksge 63
                                      ++pkcgk    +rvg      gk   v+k++g 
  gi|557693854|ref|YP_008796908.1|  3 FCPKCGKTltpSRVG------GKAMLVCKRCGY 29
                                      7*****985445555......56789*****96 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 1.1
                     ribosomal_L24 23 EapIhv.SnVmlvdpkcgk 40
                                      Eap+   S   +v+p cg 
  gi|557693854|ref|YP_008796908.1| 60 EAPLPTtSD--VVCPQCGH 76
                                      455544444..47777764 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.097        28      16      23 ..       4      11 ..       2      13 .. 0.88
   2 ?    0.8   0.2       1.7   4.9e+02      15      20 ..      23      28 ..      21      31 .. 0.81
   3 ?    3.4   0.2      0.25        74      15      21 ..      70      76 ..      66      78 .. 0.88
   4 ?    3.7   0.1      0.21        62      16      25 ..      99     108 ..      91     110 .] 0.79

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.097
                              YhfH 16 CteCGkei 23
                                      C++CGk +
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTL 11
                                      *****975 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.7
                              YhfH 15 kCteCG 20
                                      +C  CG
  gi|557693854|ref|YP_008796908.1| 23 VCKRCG 28
                                      599999 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.25
                              YhfH 15 kCteCGk 21
                                      +C++CG 
  gi|557693854|ref|YP_008796908.1| 70 VCPQCGH 76
                                      6*****7 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.21
                              YhfH  16 CteCGkeieE 25 
                                       C++CG    E
  gi|557693854|ref|YP_008796908.1|  99 CVKCGHTWRE 108
                                       *****87665 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.7     0.059        17      36      60 ..       4      30 ..       2      57 .. 0.72
   2 ?    5.9   2.6     0.047        14      33      58 ..      68      93 ..      46     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.059
                                      ESSSSSS.EEEEEE.TTEEEETTTTEE CS
                   Ribosomal_L37ae 36 Cpfcgkt.kvkRka.vgiwkCkkcgkt 60
                                      Cp+cgkt + +R++   +  Ck+cg++
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTlTPSRVGgKAMLVCKRCGYQ 30
                                      9*****987888762468899999875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.047
                                      -BEESSSSSSEEEEEETTEEEETTTT CS
                   Ribosomal_L37ae 33 kytCpfcgktkvkRkavgiwkCkkcg 58
                                      +  Cp+cg+++ k++ v   + ++ +
  gi|557693854|ref|YP_008796908.1| 68 DVVCPQCGHNEAKWWTVQTRSADEPM 93
                                      557************99877665544 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 ?    7.1   2.6      0.02       5.9      17      40 .]       3      28 ..       1      28 [. 0.89
   2 ?    4.3   0.1      0.15        45      31      40 .]      66      75 ..      60      75 .. 0.70
   3 ?    0.6   0.1       2.2   6.3e+02      35      40 .]      98     103 ..      87     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.02
                     Auto_anti-p27 17 tCpvCgvPLmrdr..kggkvyCvaCd 40
                                       Cp+Cg  L  +r  ++  ++C +C+
  gi|557693854|ref|YP_008796908.1|  3 FCPKCGKTLTPSRvgGKAMLVCKRCG 28
                                      6************98778899**996 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.15
                     Auto_anti-p27 31 ggkvyCvaCd 40
                                      + +v+C+ C+
  gi|557693854|ref|YP_008796908.1| 66 TSDVVCPQCG 75
                                      4578888885 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 2.2
                     Auto_anti-p27  35 yCvaCd 40 
                                        Cv C+
  gi|557693854|ref|YP_008796908.1|  98 RCVKCG 103
                                       699996 PP

>> Zn_ribbon_recom  Recombinase zinc beta ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.6      0.02       5.8       7      32 ..       3      27 ..       1      32 [. 0.83
   2 ?    2.5   3.6      0.73   2.1e+02       7      29 ..      70      99 ..      67     107 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.02
                   Zn_ribbon_recom  7 rCgeCGspmtrrkrkgkrhyYrCsty 32
                                      +C +CG+++t ++  g++   +C+++
  gi|557693854|ref|YP_008796908.1|  3 FCPKCGKTLTPSRV-GGKAMLVCKRC 27
                                      8**********987.88988888875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.73
                   Zn_ribbon_recom  7 rCgeCGsp....mtrrkrkgkr...hyYrC 29
                                      +C +CG++     t+++r+        +rC
  gi|557693854|ref|YP_008796908.1| 70 VCPQCGHNeakwWTVQTRSADEpmtQFFRC 99
                                      777777775555455554422234433333 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 ?    2.5   5.7      0.48   1.4e+02      25      43 ..       4      28 ..       3      76 .. 0.44
   2 ?    2.5   0.1       0.5   1.5e+02      13      23 ..      95     105 ..      85     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.48
                         zf-RING_5 25 CekClkkll......ekeavCpiCr 43
                                      C kC k+l+      +++ vC  C+
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLTpsrvggKAMLVCKRCG 28
                                      4444444444444444444444332 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.5
                         zf-RING_5  13 ekfyltsCgHi 23 
                                       + f  ++CgH+
  gi|557693854|ref|YP_008796908.1|  95 QFFRCVKCGHT 105
                                       45777888886 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 ?    7.4   1.0     0.016       4.7      24      32 ..       2      10 ..       1      18 [. 0.81
   2 ?    2.2   0.1      0.69     2e+02      26      35 ..      24      34 ..      16      61 .. 0.66
   3 ?    7.0   0.1     0.021       6.3      21      44 ..      66      89 ..      56      98 .. 0.78
   4 ?    0.6   0.6       2.2   6.6e+02      25      31 ..      97     104 ..      86     108 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.016
                      NOB1_Zn_bind 24 kFCpkCGnk 32
                                      +FCpkCG+ 
  gi|557693854|ref|YP_008796908.1|  2 EFCPKCGKT 10
                                      6******73 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.69
                      NOB1_Zn_bind 26 CpkCGn.ktLk 35
                                      C++CG  k L+
  gi|557693854|ref|YP_008796908.1| 24 CKRCGYqKPLE 34
                                      99999845564 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.021
                      NOB1_Zn_bind 21 mtkkFCpkCGnktLkrvavsvden 44
                                      ++ + Cp+CG++  k  +v++++ 
  gi|557693854|ref|YP_008796908.1| 66 TSDVVCPQCGHNEAKWWTVQTRSA 89
                                      56678******9888777777655 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 2.2
                      NOB1_Zn_bind  25 F.CpkCGn 31 
                                       F C kCG+
  gi|557693854|ref|YP_008796908.1|  97 FrCVKCGH 104
                                       34667765 PP

>> zf-ZPR1  ZPR1 zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   3.3       3.3   9.7e+02      32      39 ..      23      30 ..       2      61 .. 0.61
   2 ?   10.6   0.2    0.0013      0.38       2      42 ..      70     108 ..      69     110 .] 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 3.3
                           zf-ZPR1 32 eCehCgyk 39
                                      +C++Cgy+
  gi|557693854|ref|YP_008796908.1| 23 VCKRCGYQ 30
                                      45555554 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0013
                           zf-ZPR1   2 lCpsCgkengetrllltkiPyfkeviimsfeCehCgyknne 42 
                                        Cp+Cg +  e + ++++     e +   f+C +Cg++ +e
  gi|557693854|ref|YP_008796908.1|  70 VCPQCG-H-NEAKWWTVQTRSADEPMTQFFRCVKCGHTWRE 108
                                       5****8.4.68999999999****************98766 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 ?    5.2   5.9     0.055        16       5      28 ..       3      28 ..       1      30 [. 0.69
   2 ?    8.5   0.2    0.0053       1.6      23      29 ..      70      76 ..      62      78 .. 0.86
   3 ?   -0.9   0.5       4.4   1.3e+03      24      29 ..      99     104 ..      98     105 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.055
                     zf-NADH-PPase  5 FCgrCGaptepaegg..warvCpaCg 28
                                      FC++CG    p++ g   ++vC  Cg
  gi|557693854|ref|YP_008796908.1|  3 FCPKCGKTLTPSRVGgkAMLVCKRCG 28
                                      ******99988875311334677776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0053
                     zf-NADH-PPase 23 vCpaCgl 29
                                      vCp+Cg+
  gi|557693854|ref|YP_008796908.1| 70 VCPQCGH 76
                                      8999998 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 4.4
                     zf-NADH-PPase  24 CpaCgl 29 
                                       C  Cg+
  gi|557693854|ref|YP_008796908.1|  99 CVKCGH 104
                                       555665 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.4      0.07        21      50      62 ..       2      14 ..       1      25 [. 0.70
   2 ?    0.4   0.0       2.9   8.5e+02      51      60 ..      23      32 ..      16      43 .. 0.75
   3 ?    5.0   0.6      0.11        31      25      58 ..      44      77 ..      23      87 .. 0.61
   4 ?    1.7   0.3       1.1   3.4e+02      41      57 ..      87     104 ..      76     108 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.07
                               GFA 50 sfCpeCgsplyse 62
                                      +fCp+Cg +l+ +
  gi|557693854|ref|YP_008796908.1|  2 EFCPKCGKTLTPS 14
                                      6*******99853 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2.9
                               GFA 51 fCpeCgsply 60
                                      +C++Cg +  
  gi|557693854|ref|YP_008796908.1| 23 VCKRCGYQKP 32
                                      7999998755 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.11
                               GFA 25 ealellegelkeykktadsgnkvtrsfCpeCgsp 58
                                      ++ ++++  ++ ++ +++   + +  +Cp+Cg +
  gi|557693854|ref|YP_008796908.1| 44 KENTVSKNVAAIVEAEEAPLPTTSDVVCPQCGHN 77
                                      33333444555555557777888889*****975 PP

  == domain 4  score: 1.7 bits;  conditional E-value: 1.1
                               GFA  41 adsgnkvtr.sfCpeCgs 57 
                                           +++t+   C +Cg 
  gi|557693854|ref|YP_008796908.1|  87 RSADEPMTQfFRCVKCGH 104
                                       344556666477****96 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 ?    4.9   0.2      0.09        26       4      10 ..       4      10 ..       2      12 .. 0.64
   2 ?    1.8   0.1      0.82   2.4e+02       3       8 ..      23      28 ..      20      30 .. 0.83
   3 ?    4.0   0.1      0.17        51       3       9 ..      70      76 ..      63      77 .. 0.85
   4 ?    1.6   0.2      0.98   2.9e+02       4      11 ..      99     106 ..      97     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.09
                                      -TTT--E CS
                           ADK_lid  4 CpkCGrs 10
                                      CpkCG++
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKT 10
                                      6777654 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.82
                                      E-TTT- CS
                           ADK_lid  3 vCpkCG 8 
                                      vC+ CG
  gi|557693854|ref|YP_008796908.1| 23 VCKRCG 28
                                      888888 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.17
                                      E-TTT-- CS
                           ADK_lid  3 vCpkCGr 9 
                                      vCp+CG 
  gi|557693854|ref|YP_008796908.1| 70 VCPQCGH 76
                                      8999985 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.98
                                       -TTT--EE CS
                           ADK_lid   4 CpkCGrsY 11 
                                       C kCG ++
  gi|557693854|ref|YP_008796908.1|  99 CVKCGHTW 106
                                       89999875 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.9      0.57   1.7e+02      80      86 .]       2       8 ..       1       8 [. 0.88
   2 ?    9.9   0.6    0.0043       1.3      35      73 ..      19      76 ..      12      83 .. 0.77
   3 ?    4.2   1.4      0.26        76      38      74 ..      69     105 ..      64     109 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.57
                    zinc_ribbon_15 80 kyCpkCg 86
                                      ++CpkCg
  gi|557693854|ref|YP_008796908.1|  2 EFCPKCG 8 
                                      8*****9 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0043
                    zinc_ribbon_15 35 kpylacskCkslleaskelg.keiekkesse..................kkeCknCgk 73
                                      k++l+c++C++  + + e+   ++ek+++++                    +C++Cg+
  gi|557693854|ref|YP_008796908.1| 19 KAMLVCKRCGYQKPLEGEKVvIKLEKENTVSknvaaiveaeeaplpttsDVVCPQCGH 76
                                      8899******998888754413444444444899999999999999999999999987 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.26
                    zinc_ribbon_15  38 lacskCkslleaskelgkeiekkessekkeCknCgke 74 
                                       ++c +C+++ ++  +++++  ++  ++  +C +Cg++
  gi|557693854|ref|YP_008796908.1|  69 VVCPQCGHNEAKWWTVQTRSADEPMTQFFRCVKCGHT 105
                                       5667777666666656666666666667777777765 PP

>> Vps36-NZF-N  Vacuolar protein sorting 36 NZF-N zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.6    0.0097       2.9      31      62 ..      19      50 ..       3      53 .. 0.85
   2 ?    2.7   2.7      0.28        81      11      40 ..      70     103 ..      60     105 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0097
                       Vps36-NZF-N 31 tplPpClaCGvkpdlelikksikasasskkse 62
                                      + + +C  CG + +le  k  ik +++++ s+
  gi|557693854|ref|YP_008796908.1| 19 KAMLVCKRCGYQKPLEGEKVVIKLEKENTVSK 50
                                      6789************9999999999998776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.28
                       Vps36-NZF-N  11 vCpICsfsNevpsnfdp....nastplPpClaCG 40 
                                       vCp C  +     +++     + +t++  C+ CG
  gi|557693854|ref|YP_008796908.1|  70 VCPQCGHNEAKWWTVQTrsadEPMTQFFRCVKCG 103
                                       78888765443333333445588999999****9 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.8      0.14        42       6      33 ..       4      31 ..       2      83 .. 0.83
   2 ?   -0.1   0.1       3.2   9.5e+02       4      12 ..      69      77 ..      66      88 .. 0.66
   3 ?    3.7   0.9       0.2        60      63      76 ..      93     106 ..      73     110 .] 0.69

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.14
                             RNHCP  6 CeeCgkeveklaagsakrnHCpsCLlsk 33
                                      C +Cgk++++++ g +    C +C + k
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTLTPSRVGGKAMLVCKRCGYQK 31
                                      9999999999999999999999997655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.2
                             RNHCP  4 ftCeeCgke 12
                                       +C +Cg++
  gi|557693854|ref|YP_008796908.1| 69 VVCPQCGHN 77
                                      556666654 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.2
                             RNHCP  63 wvivhrCekCgelk 76 
                                       ++  +rC kCg++ 
  gi|557693854|ref|YP_008796908.1|  93 MTQFFRCVKCGHTW 106
                                       45568888888865 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 ?    3.1   0.3      0.34     1e+02      59      66 ..       3      10 ..       1      16 [. 0.80
   2 ?    2.2   0.1      0.62   1.8e+02      36      49 ..      18      31 ..      13      34 .. 0.78
   3 ?    8.4   1.2    0.0075       2.2      58      77 ..      69      88 ..      56     100 .. 0.77
   4 ?    0.9   0.2       1.7   4.9e+02      40      48 ..      97     105 ..      90     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.34
                       Zn_Tnp_IS91 59 hCpsCqkk 66
                                      +Cp+C+k 
  gi|557693854|ref|YP_008796908.1|  3 FCPKCGKT 10
                                      8****986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.62
                       Zn_Tnp_IS91 36 GfaryeCeeCghek 49
                                      G a++ C+ Cg +k
  gi|557693854|ref|YP_008796908.1| 18 GKAMLVCKRCGYQK 31
                                      67788999999876 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0075
                       Zn_Tnp_IS91 58 rhCpsCqkkateewlekqqe 77
                                        Cp+C++++++ w  ++++
  gi|557693854|ref|YP_008796908.1| 69 VVCPQCGHNEAKWWTVQTRS 88
                                      56********9999876665 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 1.7
                       Zn_Tnp_IS91  40 yeCeeCghe 48 
                                       ++C +Cgh+
  gi|557693854|ref|YP_008796908.1|  97 FRCVKCGHT 105
                                       678888886 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 ?    2.7   1.8      0.44   1.3e+02       2       9 ..       4      11 ..       3      31 .. 0.85
   2 ?    7.9   2.6      0.01       3.1       2      36 ..      71     105 ..      70     108 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.44
                         Ogr_Delta  2 CPhCgapa 9 
                                      CP+Cg+  
  gi|557693854|ref|YP_008796908.1|  4 CPKCGKTL 11
                                      *****865 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.01
                         Ogr_Delta   2 CPhCgap.aaartsrnlskdvre.ryyqCsnfeCgat 36 
                                       CP+Cg++ a  +t++  s+d     ++ C    Cg+t
  gi|557693854|ref|YP_008796908.1|  71 CPQCGHNeAKWWTVQTRSADEPMtQFFRCVK--CGHT 105
                                       *****97256667777676544467777766..7776 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 ?    1.5   0.1      0.85   2.5e+02       6      11 ..       3       8 ..       1      11 [. 0.74
   2 ?    5.3   0.3     0.052        15      22      29 ..      22      29 ..      21      31 .. 0.80
   3 ?    5.4   0.3     0.049        14       5      11 ..      69      75 ..      66      79 .. 0.83
   4 ?    0.6   0.4       1.5   4.5e+02      24      29 ..      99     104 ..      96     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.85
                           zf-RRN7  6 pCgvCg 11
                                       C+ Cg
  gi|557693854|ref|YP_008796908.1|  3 FCPKCG 8 
                                      688888 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.052
                           zf-RRN7 22 yyCrrCht 29
                                       +C+rC+ 
  gi|557693854|ref|YP_008796908.1| 22 LVCKRCGY 29
                                      59****95 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.049
                           zf-RRN7  5 ppCgvCg 11
                                       +C++Cg
  gi|557693854|ref|YP_008796908.1| 69 VVCPQCG 75
                                      5899998 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 1.5
                           zf-RRN7  24 CrrCht 29 
                                       C+ C++
  gi|557693854|ref|YP_008796908.1|  99 CVKCGH 104
                                       777776 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 ?    6.6   4.9     0.023       6.9       2      27 ..       2      27 ..       2      27 .. 0.96
   2 ?    4.7   0.1     0.097        29       3       9 ..      70      76 ..      67      77 .. 0.70
   3 ?    1.6   0.7      0.91   2.7e+02       3      10 ..      98     105 ..      96     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.023
                                      SB-TTT--BBEEEECTTEEEEE-TTT CS
                      zf-FPG_IleRS  2 epCpRCwryiervgqagrstyfCprC 27
                                      e Cp C+ +++  +++g    +C rC
  gi|557693854|ref|YP_008796908.1|  2 EFCPKCGKTLTPSRVGGKAMLVCKRC 27
                                      67***********************9 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.097
                                      B-TTT-- CS
                      zf-FPG_IleRS  3 pCpRCwr 9 
                                      +Cp+C++
  gi|557693854|ref|YP_008796908.1| 70 VCPQCGH 76
                                      4777775 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.91
                                       B-TTT--B CS
                      zf-FPG_IleRS   3 pCpRCwry 10 
                                       +C  C+++
  gi|557693854|ref|YP_008796908.1|  98 RCVKCGHT 105
                                       6*****97 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   1.3     0.019       5.5      19      24 .]       4       9 ..       3       9 .. 0.91
   2 ?    4.8   0.1     0.098        29      19      23 ..      71      75 ..      67      76 .. 0.90
   3 ?   -0.9   0.4       5.7   1.7e+03      17      23 ..      97     103 ..      96     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.019
                           DUF1610 19 CPNCGE 24
                                      CP+CG+
  gi|557693854|ref|YP_008796908.1|  4 CPKCGK 9 
                                      *****8 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.098
                           DUF1610 19 CPNCG 23
                                      CP CG
  gi|557693854|ref|YP_008796908.1| 71 CPQCG 75
                                      ****9 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 5.7
                           DUF1610  17 FpCPNCG 23 
                                       F C +CG
  gi|557693854|ref|YP_008796908.1|  97 FRCVKCG 103
                                       6677888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        77  (0.00429472); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              61  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 682.18
//
Query:       gi|557693855|ref|YP_008796909.1|  [L=234]
Description: adenine phosphoribosyltransferase, fused to N-terminal DNA-binding [Candidatus Caldiarchaeum subterraneum]
Scores for 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   16.6   0.0      0.013   15.6   0.0    1.6  1  HTH_3     Helix-turn-helix
  ------ inclusion threshold ------
      0.029   14.8   0.0      0.064   13.7   0.0    1.5  1  HTH_26    Cro/C1-type HTH DNA-binding domain
       0.03   14.3   0.0        0.1   12.6   0.0    1.8  1  RHH_3     Ribbon-helix-helix domain
       0.11   11.1   0.0       0.16   10.6   0.0    1.1  1  Rabaptin  Rabaptin


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 !   15.6   0.0   2.8e-06     0.013       9      46 ..      23      60 ..      15      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.8e-06
                                      THHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHH CS
                             HTH_3  9 glsqeeLAeklGvsrstisriEnGernPsletlkklak 46
                                      g++ + L++ +G+++st++r+  ++++P  +++  l +
  gi|557693855|ref|YP_008796909.1| 23 GMDYKILSKQTGIPVSTLTRYVTNKTIPHGKRAAVLIE 60
                                      6777779*********************9998876665 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   0.0   1.4e-05     0.064      10      34 ..      23      47 ..      20      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.4e-05
                            HTH_26 10 gitkseLargtgisaatlsrlvkgk 34
                                      g+ ++ L+++tgi  +tl+r+v++k
  gi|557693855|ref|YP_008796909.1| 23 GMDYKILSKQTGIPVSTLTRYVTNK 47
                                      8999********************9 PP

>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.3e-05       0.1      18      33 ..      27      42 ..      25      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.3e-05
                             RHH_3 18 kaLSekTrIprSklld 33
                                      k LS++T+Ip+S l++
  gi|557693855|ref|YP_008796909.1| 27 KILSKQTGIPVSTLTR 42
                                      78**********9987 PP

>> Rabaptin  Rabaptin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   3.6e-05      0.16      16      91 ..     140     218 ..     132     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.6e-05
                          Rabaptin  16 enaefyrlkqqleaefnqkrakf.kelylakeedlkrq...navlqaaqeeldalrvqlaearaelenikavatvse 88 
                                       +n+e y   + le  + +k+a++ + ly+  e  lk      a +  +++ l ++r++++ ar el  + a+a+  e
  gi|557693855|ref|YP_008796909.1| 140 QNTESYASDRWLEIRYKNKQARLvQRLYVPSE-ALKNHilvSAGVLDSHVPLREIRTHIVSARGELVGVCAIAASQE 215
                                       68999999*************97356887765.56654222677778999***********************9887 PP

                          Rabaptin  89 ntk 91 
                                         k
  gi|557693855|ref|YP_008796909.1| 216 FLK 218
                                       655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1696.18
//
Query:       gi|557693856|ref|YP_008796910.1|  [L=727]
Description: molybdenum hydroxylase family protein, large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-153  510.1   0.1   9.2e-153  509.6   0.1    1.2  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    5.3e-27   94.4   0.3    1.1e-26   93.4   0.3    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 !  509.6   0.1    1e-156  9.2e-153       6     550 .]     136     658 ..     131     658 .. 0.92

  Alignments for each domain:
  == domain 1  score: 509.6 bits;  conditional E-value: 1e-156
                                       STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHHT CS
                     Ald_Xan_dh_C2   6 pdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevlg 80 
                                       ++n+l+  k++kGd+ ++f+e+d++ve+efrt++q++++lE++aa+avp ++dg+lt+y s q+p++v + v+++lg
  gi|557693856|ref|YP_008796910.1| 136 ENNLLRhyKLRKGDITRGFNESDVIVEEEFRTQMQDPAPLEPEAAYAVP-EKDGTLTIYGSIQNPFYVLTGVSRILG 211
                                       35555567789************99************************.89************************* PP

                                       --GGGEEEE-SB-S--TTTT..SS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EE CS
                     Ald_Xan_dh_C2  81 lpenkvrvivprvGGGFGgK..tqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkit 155
                                       lp+++++++v  +GG+FGgK    ++ + ++a laA+ktg+p  +++ R+e+m+a+++rhp  ++yk+ga+ dG+++
  gi|557693856|ref|YP_008796910.1| 212 LPRDRINLVVMAIGGTFGGKsdEAPWDVCAMAGLAALKTGKPAACIYGRDESMIAHSHRHPAVMRYKIGATTDGRLK 288
                                       ********************43344555667889******************************************* PP

                                       EEEEEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 156 aldvdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeel 232
                                       ald+dl+ d+Gaya+++p v+ ra++h+ gpY ++nvrv++++vytN+ +++ +RGfG+pq+ fa+E++md lA++l
  gi|557693856|ref|YP_008796910.1| 289 ALDADLYFDTGAYASVGPLVMLRAVTHAAGPYVVENVRVDSYLVYTNNLTAGSMRGFGSPQVHFAVESMMDILADKL 365
                                       ***************************************************************************** PP

                                       T--HHHHHHHHBCECGCC.SEEETEESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S. CS
                     Ald_Xan_dh_C2 233 gldplelRrrNlikpgeltpygqpvydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgft 309
                                       g+dp+elR +N+ ++g +t  +  ++d+ d+  l  ++ e++++++ ++e           G+g+a++ +g +lg++
  gi|557693856|ref|YP_008796910.1| 366 GMDPVELRLKNAWRQGVVTASDAVLMDNPDFGVLASRVCEELGWRRGEKE---PD-----EGVGIAFMAHGNSLGPE 434
                                       ******************98888899******************544333...22.....4899********88884 PP

                                       EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHHHHH CS
                     Ald_Xan_dh_C2 310 akflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstdlng 386
                                           ++++a+vr+ +dG v+v+t++te G+G+   +a+iaa++Lgvp e+v v    t+kvp+++gt+aSrst ++g
  gi|557693856|ref|YP_008796910.1| 435 --GEDKSSATVRISPDGVVHVATSLTEYGTGASRGFAKIAASVLGVPEERVVVDRVETKKVPDSGGTFASRSTLMGG 509
                                       ..478999********************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEETEEEECHHHHHHHHHHTTSSEEEEEEE.......EEEET CS
                     Ald_Xan_dh_C2 387 nAvkkAaeklrerllkiaaellevspedleledgkvvvkeksvslaelaaaaylervslsatgfykt....ldeetg 459
                                       nAv+ Aa++l+e+++k+ +   e   +               +++a+ ++  ++e+v  s+ + +k     ++ etg
  gi|557693856|ref|YP_008796910.1| 510 NAVYLAAKRLKEKIEKLMK---ESGRSG--------------LDVADFVRDVFHEEV--SEYAEFKLpvcdYNPETG 567
                                       *******************...444444..............466777777755555..444444445688899*** PP

                                       HCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEESS- CS
                     Ald_Xan_dh_C2 460 kgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqllta 536
                                       kg+p+ +++yg++ + V+vD+e g v+v+++v++ DvG+++N      Q+eGG++qG+++ l+Eel++ ++ ++l+ 
  gi|557693856|ref|YP_008796910.1| 568 KGTPYLQYTYGVVGVRVKVDRELGVVRVKDIVAAFDVGRVVNEGYLTAQLEGGITQGVAYGLLEELLIGKKHKVLNP 644
                                       ***************************************************************************** PP

                                       STTTS----GGGS- CS
                     Ald_Xan_dh_C2 537 sladYkiPtaadiP 550
                                       +ladY++Ptaad+P
  gi|557693856|ref|YP_008796910.1| 645 NLADYLVPTAADMP 658
                                       *************9 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 !   93.4   0.3   1.2e-30   1.1e-26       2     109 ..      13     117 ..      12     118 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 1.2e-30
                                       T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEES CS
                      Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkvr 78 
                                       G  +Y++Di  ++ l ++ +rS ++hA i+++dvsaal++pGVvav+ta d+p+en +++ ++ d +  +la +kvr
  gi|557693856|ref|YP_008796910.1|  13 GAPIYTEDIVPEDSLCVKALRSEHSHALIKRVDVSAALEVPGVVAVLTARDIPGENITGA-VILDRP--FLAYEKVR 86 
                                       7789***************************************************99996.666766..******** PP

                                       STT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                      Ald_Xan_dh_C  79 svgqavaavvAedeetArkAaklvkveYeel 109
                                       +  +++a+v+A deetA+kA++++ v+Ye l
  gi|557693856|ref|YP_008796910.1|  87 CLADPIALVAAVDEETADKAIEKIVVDYEVL 117
                                       *****************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (727 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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 0.28s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 5163.72
//
Query:       gi|557693857|ref|YP_008796911.1|  [L=154]
Description: molybdenum hydroxylase family protein, small subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   88.9   0.1    2.9e-25   88.1   0.1    1.4  1  Fer2_2           [2Fe-2S] binding domain
    1.1e-06   28.5   2.5    1.2e-06   28.4   0.4    2.0  2  Fer2             2Fe-2S iron-sulfur cluster binding domain
     0.0023   17.9   0.5     0.0031   17.5   0.5    1.4  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
       0.18   11.6   4.8       0.55   10.1   4.8    1.8  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
       0.19   11.7   0.0       0.33   11.0   0.0    1.4  1  CE2_N            Carbohydrate esterase 2 N-terminal


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 !   88.1   0.1     8e-29   2.9e-25       1      75 [.      73     145 ..      73     146 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 8e-29
                            Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                       Tveg+  e e+lhp+q a+++  asqCG+C pG++m+a+ + ++  p+ +e++ir+ l  n+CRC+gY++ivdAv
  gi|557693857|ref|YP_008796911.1|  73 TVEGITPE-EKLHPIQSALLDYTASQCGFCIPGIIMTAKYIADNY-PDADEQTIRHILIANICRCGGYTKIVDAV 145
                                       9****966.78******************************9888.88888***********************9 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 !   28.4   0.4   3.2e-10   1.2e-06       3      52 ..       8      55 ..       6      75 .. 0.84
   2 ?   -0.4   0.1      0.31   1.1e+03      38      44 ..      96     102 ..      87     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3.2e-10
                                      TTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSSSSTTEEEEEESCE CS
                              Fer2  3 idgkevevevadgettlldaaeenggidipysCggggCgtClvevlegev 52
                                      ++gk+v++e   +e+ l+d +++ g   ++ +Cg g Cg+C v v+ g+ 
  gi|557693857|ref|YP_008796911.1|  8 LNGKQVSAELRGNER-LMDLLRRLGMKSVKEACGTGDCGSCNVIVD-GKL 55
                                      79*************.*******99*****************9655.554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.31
                                       SSSSTTE CS
                              Fer2  38 ggCgtCl 44 
                                       ++Cg C 
  gi|557693857|ref|YP_008796911.1|  96 SQCGFCI 102
                                       5688886 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 !   17.5   0.5   8.8e-07    0.0031      49      83 ..      36      70 ..      11     101 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.8e-07
                            Fer2_3 49 rasCregiCGscavainGkptlaCtatikdlakqk 83
                                      +  C+ g CGsc v ++Gk    C     +   ++
  gi|557693857|ref|YP_008796911.1| 36 KEACGTGDCGSCNVIVDGKLINSCMMLAVQARGKT 70
                                      578*****************999998777665544 PP

>> 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 ?   10.1   4.8   0.00015      0.55       5      21 ..      38      54 ..      38      61 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                                      SSSSSSS-TTEEEETTC CS
                   DHODB_Fe-S_bind  5 aCGvGaClgCvvktkgg 21
                                      aCG+G C++C v ++g+
  gi|557693857|ref|YP_008796911.1| 38 ACGTGDCGSCNVIVDGK 54
                                      8**********999765 PP

>> CE2_N  Carbohydrate esterase 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.1e-05      0.33      22      77 ..       4      81 ..       2     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.1e-05
                                      EEEEEEEEEEEEEEEE.....................SSS-EEEEEEETTS--EEEEE...-SS-EEEEEEEEEEEEE CS
                             CE2_N 22 vefrftGtslsvrlkd...................kedkgknrlaviiDgkrvkdlkl...dgeektytlaeglepge 77
                                      +ef  +G+++s++l++                     + +  + +vi+Dgk +++ ++   ++++kt+t++eg +p+e
  gi|557693857|ref|YP_008796911.1|  4 IEFVLNGKQVSAELRGnerlmdllrrlgmksvkeaCGTGDCGSCNVIVDGKLINSCMMlavQARGKTVTTVEGITPEE 81
                                      7899999999999999999999999***9999775555566789********777666677999999***99999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1113.95
//
Query:       gi|557693858|ref|YP_008796912.1|  [L=289]
Description: molybdenum hydroxylase family protein, medium subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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   95.1   0.0    6.3e-27   94.4   0.0    1.3  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
      2e-14   53.6   0.0    3.1e-14   53.0   0.0    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 !   94.4   0.0   7.1e-31   6.3e-27       2     143 ..       6     147 ..       5     158 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 7.1e-31
                                       EEEEEE-SSHHHHHHHHHH.CTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHH CS
                     FAD_binding_5   2 kfeylrpasleealallaa.epdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlsel 77 
                                       +fe+++p+sl+e+l+++++ ++++ l aGgtdl++ m+++++rp++++d++g+ el++++++++ +++G ++t++el
  gi|557693858|ref|YP_008796912.1|   6 SFEVYTPSSLQEVLNIYSSlDEEVVLYAGGTDLMPFMRRGKVRPRAVVDLSGVGELRYVRREGDFIHVGGLTTVHEL 82 
                                       699****************99******************************************************** PP

                                       HHHHHHHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEE CS
                     FAD_binding_5  78 aaealvrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerev 143
                                       a+++++ e+y +++ + + ++ +  R++aT+GGNla +    D++++++ ld +v++++ +ger v
  gi|557693858|ref|YP_008796912.1|  83 ATSPAIPENYFSIRWLSKYFGAETTRHMATVGGNLASGG-ERDIPAIMASLDGQVKIMGIDGERVV 147
                                       ***********************************9998.78********************9976 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 !   53.0   0.0   3.4e-18   3.1e-14       3     100 ..     176     274 ..     174     276 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 3.4e-18
                                       E.EEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS.-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHH CS
                     CO_deh_flav_C   3 y.klsrrrendiaivnaAfrveleedgkiedariafggvapt.pvraekaeaaLiGkplseelleeaakaleeelsp 77 
                                       + k+++r++n i +v+aA++++  ++ ++e++ +++  v  + + r + +e+ L+Gk ++ +ll +a+++  + ++p
  gi|557693858|ref|YP_008796912.1| 176 FgKFEKRASNGIGVVTAAVSMKAVHG-VVEKIAVVLNRVEGRtMGRLTDLEDILTGKAINPSLLRAAVEESVSRIRP 251
                                       789********************999.************98857799****************************** PP

                                       HTCTTC-HHHHHHHHHHHHHHHH CS
                     CO_deh_flav_C  78 asdprasaeYRrslavsllfrfl 100
                                       asd ras  +R+++ ++l++r l
  gi|557693858|ref|YP_008796912.1| 252 ASDFRASSSFRKHVSKVLVRRGL 274
                                       ********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2233.98
//
Query:       gi|557693859|ref|YP_008796913.1|  [L=480]
Description: dihydropyrimidinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-28   97.9   0.1    9.6e-28   97.5   0.1    1.1  1  Amidohydro_1  Amidohydrolase family
      1e-13   51.6   0.5    4.8e-07   29.6   0.0    3.1  2  Amidohydro_3  Amidohydrolase family
    6.1e-06   26.6   0.2    1.4e-05   25.4   0.2    1.5  1  Urease_alpha  Urease alpha-subunit, N-terminal domain
  ------ inclusion threshold ------
       0.11   12.3   0.0       0.28   10.9   0.0    1.6  1  Amidohydro_2  Amidohydrolase


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 !   97.5   0.1   2.1e-31   9.6e-28       1     343 [.      71     455 ..      71     456 .. 0.74

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 2.1e-31
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.....HHHHHHHHHHT CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.....giealleaaee 72 
                                       +vlPG ID HvH+                + + a  + +g+++a  +G+tt++d+ + +++       ++ +ea   
  gi|557693859|ref|YP_008796913.1|  71 YVLPGAIDGHVHFKLKY----------FEDVYTADDFYTGTVAAACGGVTTIIDFVTPETKdyvedFRRRKAEAD-G 136
                                       69***********7332..........777889999*********************988896653333333344.3 PP

                                       .SSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEE CS
                      Amidohydro_1  73 .lplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpv 148
                                        ++++++++++           + +++ ++++   e++     +v + + + +    + d   ++++k+++++++ v
  gi|557693859|ref|YP_008796913.1| 137 dVVVDYGLHVS--------VTDFDEKIARMLTNLFEKEG--LASVKMFTAYSRRGLMLDDGKAYKLMKLCREKNVLV 203
                                       59999999977........44556666666666633333..33333356777778888888**************** PP

                                       EEEETSSCHHHHHHHHHHTTTEEEETTTTSTCC............HHTTTHCCEEEHCTCEEE.HHHHHHHHHHHHH CS
                      Amidohydro_1 149 aiHaletkgevedaeaafgetiehgthlevaes............lglldeiklilahgvhlt.pteaellkerlke 212
                                       ++Ha + ++ +   +++f++  +   + + a s            +++l  ++ +   +vh++ ++ ++++ e+ ++
  gi|557693859|ref|YP_008796913.1| 204 MVHAEN-EHLINTLLEEFVSQGKT-EPIYHAWSrpdfveaeaverVAFLAGLTGAEILIVHVSsAMGLNTILEA-RR 277
                                       ****55.55555666666633333.45555555689*********88888888888899999964444443333.45 PP

                                       HCEE..............HHHHHHHH................SEHHHHHHHHHHHHTSCEEEEEECT........TS CS
                      Amidohydro_1 213 agva..............hcpfsnsi................lrsgrealrkaldeGvkvglgtDga........as 251
                                       +gv               +      +                 + + e l+k l  + ++++g+D+a        + 
  gi|557693859|ref|YP_008796913.1| 278 KGVKihgetcphylmfteD------VykrpdgakfimspplkKEHDKEGLWKGLLTDGFSVVGSDHAcfnlsqklG- 347
                                       5555558877764444440......35555555556666666**************88*******99***999963. PP

                                       SCCGGHHHHHHHHHHHHHHCCTT..TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC..CT... CS
                      Amidohydro_1 252 gnslnlleelrlalklqrgllye..deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl..di... 321
                                        +s++ + ++  ++++ ++ ly+  + + g++l+++++++  n+Ak +g++ ++G i vG dAD+ ++d+  +    
  gi|557693859|ref|YP_008796913.1| 348 HKSFTTVPGGVAGTEVINMILYSegVVKRGMPLSRFVDLTAHNPAKLYGIYPRKGVIRVGADADFYILDPsqKTrlt 424
                                       444444466666666656666666988999***************************************98622667 PP

                                       .........CGGGTTTCTSEEEEEEEETTEE CS
                      Amidohydro_1 322 .........laafvglkkdgnvkkvivkGkl 343
                                                 + ++ ++ ++ ++ ++ +G++
  gi|557693859|ref|YP_008796913.1| 425 renlhsnidHSIYEDVEVSCRIVATFARGEQ 455
                                       788899999999999999999****999986 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.2   6.5e-07    0.0029       2      25 ..      64      86 ..      63     110 .. 0.74
   2 !   29.6   0.0   1.1e-10   4.8e-07     261     470 ..     185     454 ..     162     457 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.5e-07
                      Amidohydro_3  2 viDakGrlvlPGFvDsHtHlaggg 25
                                      + Da Gr+vlPG +D H H ++ +
  gi|557693859|ref|YP_008796913.1| 64 TYDAGGRYVLPGAIDGHVH-FKLK 86
                                      78*****************.5555 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1.1e-10
                      Amidohydro_3 261 edealaelvaaadergldvaihaigdaavddvldafeaaaekngnqdrrrlehaegvtesqiervaalqvaagvqpv 337
                                       +d++  +l+++++e+ + v +ha  +  +  +l++f ++++ ++ +     +   +v ++ +erva l +  g ++ 
  gi|557693859|ref|YP_008796913.1| 185 DDGKAYKLMKLCREKNVLVMVHAENEHLINTLLEEFVSQGKTEPIYH--AWSRPDFVEAEAVERVAFLAGLTGAEIL 259
                                       55556666666666666666666666666666666666644444443..3444444444555555555555555544 PP

                      Amidohydro_3 338 fnf.......edelldsrlgperargs.......................................tpvkellnagv 368
                                        ++       +       + ++r++g+                                         +k ll +g 
  gi|557693859|ref|YP_008796913.1| 260 IVHvssamglN------TILEARRKGVkihgetcphylmftedvykrpdgakfimspplkkehdkeGLWKGLLTDGF 330
                                       44443333331......222222222222222223333333333333333344477777777777777888888888 PP

                      Amidohydro_3 369 kvalgsD...apvgpfdpwprigaavmrktrrgg.......evlrpdeelsleealalyTrgpAkalgledrkGtLe 435
                                       +v+ gsD    +++    + ++ ++v++  ++ +            ++ ++l   ++l+  +pAk++g   rkG ++
  gi|557693859|ref|YP_008796913.1| 331 SVV-GSDhacFNLSQKLGHKSF-TTVPGGVAGTEvinmilySEGVVKRGMPLSRFVDLTAHNPAKLYGIYPRKGVIR 405
                                       877.778533333332233333.333333333335777777333345679*************************** PP

                      Amidohydro_3 436 vGadADlvvld.adpldvdppelaear.............vrltvvdGr 470
                                       vGadAD+ +ld  +  +++ ++l++               +++t  +G+
  gi|557693859|ref|YP_008796913.1| 406 VGADADFYILDpSQKTRLTRENLHSNIdhsiyedvevscrIVATFARGE 454
                                       ***********87777777777777656666666666666666666655 PP

>> Urease_alpha  Urease alpha-subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.2     3e-09   1.4e-05      63      99 ..      20      56 ..      13      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3e-09
                      Urease_alpha 63 eealDlvitnavilDatgivkadigikdgrivaiGka 99
                                      ++  Dl++ n  i+D+ g++ adig+  gri+aiG+ 
  gi|557693859|ref|YP_008796913.1| 20 KDGFDLLVRNCRIVDVEGVYEADIGVVGGRIAAIGRN 56
                                      5578*******************************96 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.3e-05      0.28      66     148 ..      91     206 ..      74     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.3e-05
                                       HHHHHHHHHHHHHHHCTTCBECEEECTSSHCHHHHHHHHHH................................HHTT CS
                      Amidohydro_2  66 crgannrvlaeaakrpdrfvggaavvpldpedaaaelerav................................eelg 110
                                       +++a++ ++  +a++++++ + +++v ++ +d ++ ++r+                                 e+ g
  gi|557693859|ref|YP_008796913.1|  91 VYTADDFYTGTVAAACGGVTTIIDFVTPETKDYVEDFRRRKaeadgdvvvdyglhvsvtdfdekiarmltnlfEKEG 167
                                       56778888888888888888888888888888888888888777777777777777777777777777777778888 PP

                                       ECEEEEESSTT..TCCTTTCGGHHHHHHHHHHHT-EEEEE CS
                      Amidohydro_2 111 fkGvrlnphvg..gddllgdrldrpifealeelglpvdih 148
                                       +  v++ +++   g  l++    ++++++++e ++ v++h
  gi|557693859|ref|YP_008796913.1| 168 LASVKMFTAYSrrGLMLDDGKA-YKLMKLCREKNVLVMVH 206
                                       8889999988521444444444.6**************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (480 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3692.63
//
Query:       gi|557693860|ref|YP_008796914.1|  [L=284]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-77  260.0   0.0    2.2e-77  259.8   0.0    1.0  1  Memo      Memo-like protein
  ------ inclusion threshold ------
      0.018   14.1   0.0       0.04   13.0   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 !  259.8   0.0   2.5e-81   2.2e-77       2     269 ..       7     276 ..       6     278 .. 0.98

  Alignments for each domain:
  == domain 1  score: 259.8 bits;  conditional E-value: 2.5e-81
                              Memo   2 aavAGsfYpedeeelkkqleeflekntgkkei.........arviisPHagyvysgevaakayaeles.skvervvi 68 
                                       +avAG fY+   e+l +q+e+++++  g++++         a ++isPHag++ysg+vaa++y+el + + +e vv+
  gi|557693860|ref|YP_008796914.1|   7 PAVAGYFYEGSREALLRQVEHCFLSPHGPGKTparewgkrrAPALISPHAGLMYSGPVAAHGYYELTKyAVPESVVV 83 
                                       89***************************999999999766667788*********************999****** PP

                              Memo  69 lGpsHtilgskvsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivP 145
                                       +Gp+H+++g+ vs+++ + + TPlG++k+De+l+ e+  ++e++ lde+++  EHS+EvqlpfL++l  +  f+ vP
  gi|557693860|ref|YP_008796914.1|  84 FGPNHYGVGTVVSIYPGGSWVTPLGEVKIDEKLAAEIAGQREFFYLDEVSHSREHSIEVQLPFLQYLYGD--FQFVP 158
                                       **********************************************************************..***** PP

                              Memo 146 ilvsaqseetakevgealakvikdesnlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylektn 222
                                       i++  qs et  e+gea+ +v+   ++l+i+S+D++Hy+     p+e + ++ Dr +++++e+l+ e+l+ ++e+ +
  gi|557693860|ref|YP_008796914.1| 159 ICINDQSLETCVEIGEAVGEVVDGRNILMIASTDFTHYE-----PHETVLKK-DRLALERIERLDVEGLYGVIERHD 229
                                       ***************************************.....********.************************ PP

                              Memo 223 nticGekpiavilkalkklgakkakllkYaqssdvtsdtdsvVsyas 269
                                       +t+cG++ +a++l a+kklga +a +lk a+s+d+ +d+ svV+ya+
  gi|557693860|ref|YP_008796914.1| 230 ITMCGYGAVAALLTAAKKLGAVEATVLKQATSGDTGGDYGSVVGYAA 276
                                       *********************************************97 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 ?   13.0   0.0   4.4e-06      0.04      43     188 ..      78     201 ..      30     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.4e-06
                              LigB  43 PdtiivvsphhltdvnpvfvlgvaeefeaiddfgkflprleyelkgnpeLaekiaealkksgidlavesnsmklDHG 119
                                       P+ ++v+ p h+     v  +       +i+   ++   + +e+k++ +La++ia + +    d  ++s+s++    
  gi|557693860|ref|YP_008796914.1|  78 PESVVVFGPNHYGVGT-V--V-------SIYPG-GSWVTPLGEVKIDEKLAAEIAGQREFFYLD--EVSHSREHSIE 141
                                       5556666665555222.2..1.......22222.245567788889999998888766655555..33555544444 PP

                              LigB 120 tlvP.LelmlpdeakvpvikvslntvaypllsferlykLGeAlrkaveeld.knvlilgsGglsHqlegde 188
                                       +  P L+++++     + +++ +n       s e + ++GeA+++ v   d +n+l+++s +++H+ + + 
  gi|557693860|ref|YP_008796914.1| 142 VQLPfLQYLYG---DFQFVPICIND-----QSLETCVEIGEAVGEVV---DgRNILMIASTDFTHYEPHET 201
                                       56664678888...59999999999.....8****************...52689**********866555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2015.67
//
Query:       gi|557693861|ref|YP_008796915.1|  [L=319]
Description: mevalonate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-17   61.4   1.2    3.2e-16   59.5   0.2    2.3  2  GHMP_kinases_C   GHMP kinases C terminal
      2e-15   56.8   0.2    4.9e-15   55.5   0.2    1.7  1  GHMP_kinases_N   GHMP kinases N terminal domain
    3.1e-05   23.4   0.0    6.5e-05   22.4   0.0    1.6  1  GalKase_gal_bdg  Galactokinase galactose-binding signature


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 ?    0.1   0.1      0.17     1e+03      53      64 ..     101     112 ..      74     126 .. 0.87
   2 !   59.5   0.2   5.4e-20   3.2e-16       2      84 ..     225     303 ..     224     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.17
                    GHMP_kinases_C  53 lsGaGgGptvfa 64 
                                       +sG G+G++ ++
  gi|557693861|ref|YP_008796915.1| 101 ISGGGLGSSAAV 112
                                       799999999876 PP

  == domain 2  score: 59.5 bits;  conditional E-value: 5.4e-20
                    GHMP_kinases_C   2 lealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvara 78 
                                        eal +gd++++g+l +l++   l+  vg++  +lee++++l++ +++gakl+GaGgG++v+a++  + +a ++a+a
  gi|557693861|ref|YP_008796915.1| 225 KEALVEGDFQAVGRLFTLNHL--LLRSVGVSDNVLEEIVRKLRNKDVYGAKLTGAGGGGCVIAVA--DGRAVEIAEA 297
                                       699******************..899***************************************..********** PP

                    GHMP_kinases_C  79 lreefe 84 
                                       ++++++
  gi|557693861|ref|YP_008796915.1| 298 MARLYP 303
                                       *99986 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 !   55.5   0.2   8.1e-19   4.9e-15       2      66 .]      94     160 ..      93     160 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 8.1e-19
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHH...HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglslee...aklaleaerlaqggngsggDvaasvyGg 66 
                                       ++i+s++  g GLGSSAA++val++A+  l +++l++    + al+ae++++ g++sg+D + s+ Gg
  gi|557693861|ref|YP_008796915.1|  94 VEIESDLISGGGLGSSAAVSVALAKAVSLLHEIQLSKdqlINYALKAEKEFH-GRPSGIDPTISTVGG 160
                                       689****************************999944478************.************998 PP

>> GalKase_gal_bdg  Galactokinase galactose-binding signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.1e-08   6.5e-05      14      48 ..       7      41 ..       2      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.1e-08
                                      EEEEEEEEEE--S-TTTT-EEEEEEEEEEEEEEEE CS
                   GalKase_gal_bdg 14 asAPGRvnLiGEHtDYngGfVlpmAieqdiyiavs 48
                                      ++APG v L GEH   +g+  + +Ai++++++ ++
  gi|557693861|ref|YP_008796915.1|  7 VFAPGKVILFGEHFVVSGYPAIVTAIDRGVTVTAK 41
                                      79*****************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2200.91
//
Query:       gi|557693862|ref|YP_008796916.1|  [L=260]
Description: acetylglutamate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-47  160.4   0.4    6.3e-47  160.2   0.4    1.0  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 !  160.2   0.4   3.5e-51   6.3e-47       2     241 .]       4     237 ..       3     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: 160.2 bits;  conditional E-value: 3.5e-51
                                       EEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HH CS
                         AA_kinase   2 rvVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstlee 72 
                                       +vV+K+GGs++tdk++      +++ r+a++ia+      +lv++hG+gsf++  +++ + +++g+ +     + + 
  gi|557693862|ref|YP_008796916.1|   4 LVVLKIGGSVITDKKRenffrqDVMARIAKEIARC--WPTPLVIIHGAGSFGHPVAKQ-YSVDKGYRE-----QGQL 72 
                                       89**********99999******************..5578*****************.******998.....7899 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEE CS
                         AA_kinase  73 agevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigl 149
                                       +g+v t +++ +l++ +v  l++ g+ avg++a+ l +t++g+       +e    + +   l+ gv+pv++g++++
  gi|557693862|ref|YP_008796916.1|  73 EGFVKTLQSVKTLNQHVVNTLIETGIGAVGMPASTLFITRKGI-------IETAHLDLVLSALDLGVIPVTCGDAVF 142
                                       9***************************************999.......*************************** PP

                                       ETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH.....CSSS.TTTHHHH CS
                         AA_kinase 150 deegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee.....saselatgGmkv 221
                                       d+e +++++s+D+ia +lA+ l+A ++++++dVdGVyd d       rll+++++++        +++e++tgGm  
  gi|557693862|ref|YP_008796916.1| 143 DRELKFTVLSGDQIAIHLAKSLKASRIVFASDVDGVYDVDRETG-EKRLLDKLDYRKHTTllyggVEGEDITGGMFY 218
                                       ***************************************97666.89****************************** PP

                                       CHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 222 khpaalaaarrggipvvItn 241
                                       k++  ++a++ g  +vvI+n
  gi|557693862|ref|YP_008796916.1| 219 KVENGFEAVKAG-AEVVIVN 237
                                       ************.*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1938.47
//
Query:       gi|557693863|ref|YP_008796917.1|  [L=358]
Description: isopentenyl-diphosphate delta-isomerase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  104.0   0.1    1.9e-26   92.9   0.1    2.2  1  FMN_dh        FMN-dependent dehydrogenase
    1.1e-07   31.1   2.3    0.00015   20.9   0.3    3.4  4  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0001   21.6   2.2    0.00033   19.9   2.2    1.7  1  Glu_synthase  Conserved region in glutamate synthase
    0.00039   19.7   0.1    0.00082   18.7   0.1    1.7  1  DHO_dh        Dihydroorotate dehydrogenase
     0.0012   18.3   1.6     0.0016   17.9   0.4    1.7  2  NMO           Nitronate monooxygenase
     0.0018   17.5   0.0     0.0064   15.7   0.0    1.8  2  DUF561        Protein of unknown function (DUF561)
  ------ inclusion threshold ------
       0.42    9.9   6.4        4.5    6.5   0.1    2.9  3  ThiG          Thiazole biosynthesis protein ThiG


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 !   92.9   0.1   7.4e-30   1.9e-26      21     343 ..      19     334 ..       3     338 .. 0.81

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 7.4e-30
                                       HHHHHHHHGGGGEEE---SSSS-SS-..B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEET CS
                            FMN_dh  21 vtlrenraaferirlrprvlrdvskv..dlsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlst 95 
                                       v++r + + +e ++l+++++ ++     +++t +lG+++s+P++i ++   ++ +++ + +l +aaa +++p+++++
  gi|557693863|ref|YP_008796917.1|  19 VSYR-KSTWLEYVELVHQAAPEIDPDdiQTETIFLGRRFSHPFIIESMTGGTAEAERINANLGEAAAIFKVPMGVGS 94 
                                       5544.456688899999999999877224556689*************99999999******************998 PP

                                       T-SS-HHHHHHHHTT-EEEEEE-CSSHHHHHHHHHHHHHCTESEEEEESSTSS---BHHHHHCT--BSTT-T.G.TT CS
                            FMN_dh  96 vastsleevaaaaegplwfqlyvpkdrelteellkraeaagykalvltvDtpvlgkRerdlrngfslppklklrnll 172
                                       +   +   v+     + ++ +   +++   + l+ ++ a ++    +++ +      ++d  + ++l+        l
  gi|557693863|ref|YP_008796917.1|  95 Q---RAGVVKP----ETVYTFRAAREHGPDAFLIGNIGAVQLVENGVEMGVKAVEMIDADALA-VHLN-------PL 156
                                       8...3344433....678888999999999999999988876666666666555544444333.4444.......45 PP

                                       GGGSTSGSCCTTH..THHHHHHCCCHB-TC--HHHHHHHHHHHSSEEEEEEE...-SHHHHHHHHHTTESEEEE--G CS
                            FMN_dh 173 qelakpewaaealkkasaaaefvgkqldpsltwddikwlreqtklplvvKGv...ltaedakraveaGvdgivvSNH 246
                                       qe  +p+++a++            +        +++++lr+++++p+++K++   l+ e + +a eaGvd+  v+  
  gi|557693863|ref|YP_008796917.1| 157 QEIIQPDGKARFR-----------N------LSKTLEKLRKEVSVPIILKEIgcgLSREVVAMADEAGVDAFDVAGS 216
                                       89999***99999...........1......13589*****************9*********************** PP

                                       GG........................TSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEE CS
                            FMN_dh 247 GG........................RqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavll 299
                                       GG                          l+  ++t  +  e v+a     +v+++gG r+G D++kA+alGA++ +l
  gi|557693863|ref|YP_008796917.1| 217 GGtnwtmiemiraeemrdiekkalaeVFLEWGIPTAAAVMEAVDATT--KPVIASGGLRTGLDAAKAIALGASMAGL 291
                                       ***********999996666655555445555555555555555554..7*************************** PP

                                       SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHHC CS
                            FMN_dh 300 GRpflyglaagGeeGvervleilraelertmallGvksvaeldr 343
                                       +Rpfl   a++  e v  +l+ l+++l+++m l+G++sv+el++
  gi|557693863|ref|YP_008796917.1| 292 ARPFLEP-ATKSVEDVLATLKRLSDQLKTSMFLTGCRSVDELRQ 334
                                       ****877.8899*****************************987 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1       0.1   2.6e+02     254     320 ..      83     166 ..      57     190 .. 0.54
   2 ?   -1.3   0.0      0.33   8.4e+02     107     138 ..     198     229 ..     172     236 .. 0.81
   3 !   20.9   0.3   5.7e-08   0.00015     188     233 ..     247     289 ..     240     295 .. 0.86
   4 !    6.8   0.0    0.0012         3     298     332 ..     305     339 ..     296     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.1
                                       TEEEEEEEETTSHHHHHH-SS-TT.S-...-..............-SS-SBEEEEEE--B-HH.HHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xx.xxx..............xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx RF
                             IMPDH 254 grkyKeyrGmgslgamkkgskdry.fq.kke..............klvpeGvegrvpykgsvk.evveqlvgglrsg 313
                                          +K+  G+gs +a   + +  y f+ ++e              +lv++Gve  v++   ++ + +   ++ l++ 
  gi|557693863|ref|YP_008796917.1|  83 AAIFKVPMGVGSQRAGVVKPETVYtFRaAREhgpdaflignigavQLVENGVEMGVKAVEMIDaDALAVHLNPLQEI 159
                                       44567777777777763333333312211112344455555666677777777777666555324555555555555 PP

                                       HHHHT-S CS
                                       xxxxxxx RF
                             IMPDH 314 mgylGak 320
                                       ++  G +
  gi|557693863|ref|YP_008796917.1| 160 IQPDGKA 166
                                       5555555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.33
                                       HHHHHHHHTT-SEEEEE-STSSSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 107 ervkalveagvdvlvvdsahghsekvleavke 138
                                       e v++  eagvd+  v  + g + +++e++++
  gi|557693863|ref|YP_008796917.1| 198 EVVAMADEAGVDAFDVAGSGGTNWTMIEMIRA 229
                                       45666678999999999999999999999875 PP

  == domain 3  score: 20.9 bits;  conditional E-value: 5.7e-08
                                       B---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 188 vGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadav 233
                                        G+p + Av+e+++a++    pvia GG+++  d +kA+a+Ga++ 
  gi|557693863|ref|YP_008796917.1| 247 WGIPTAAAVMEAVDATT---KPVIASGGLRTGLDAAKAIALGASMA 289
                                       69999999999887765...59*********************975 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0012
                                       -HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 298 svkevveqlvgglrsgmgylGaktieelkekakfv 332
                                       +v +++++l  +l+++m  +G+++++el++  k+v
  gi|557693863|ref|YP_008796917.1| 305 DVLATLKRLSDQLKTSMFLTGCRSVDELRQAPKVV 339
                                       5667789999*******************987765 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 !   19.9   2.2   1.3e-07   0.00033     188     304 ..     169     293 ..     154     297 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.3e-07
                                       HHHHHHHHHHHHH-TTSEEEEE.EE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHHH........HH...B- CS
                      Glu_synthase 188 edlaqliedLkevnkeakvsvK.lvaeagvetiaagvakanadiilidGleGGTGAspkssi........kh...aG 252
                                        +l++ +e+L++   ++++  K ++++   e++a+ + +a++d+  + G+ GGT  +  ++i        ++   a 
  gi|557693863|ref|YP_008796917.1| 169 RNLSKTLEKLRKEV-SVPIILKeIGCGLSREVVAM-ADEAGVDAFDVAGS-GGTNWTMIEMIraeemrdiEKkalAE 242
                                       57888889998765.67888776999999999999.99999999999996.67765544443111111112222255 PP

                                       --HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SH CS
                      Glu_synthase 253 lPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigt 304
                                       + le +++ +  ++ + +   +  +ia+Ggl+tg d +ka+alGA   g+++
  gi|557693863|ref|YP_008796917.1| 243 VFLEWGIPTAAAVMEAVDATTK-PVIASGGLRTGLDAAKAIALGASMAGLAR 293
                                       6788899999988888888776.6789******************9998887 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   3.2e-07   0.00082     228     287 ..     250     306 ..     166     313 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 3.2e-07
                                       HHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHH CS
                            DHO_dh 228 dialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakki 287
                                       ++a +v+ ++ +++k   p+I++GG+ +g Da   i  GAs+  +   +     k+++++
  gi|557693863|ref|YP_008796917.1| 250 PTAAAVMEAVDATTK---PVIASGGLRTGLDAAKAIALGASMAGLARPFLEPATKSVEDV 306
                                       567777777777777...************************987666655555555555 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.1   2.8e+03     146     162 ..     105     121 ..      97     152 .. 0.64
   2 !   17.9   0.4   6.2e-07    0.0016     185     235 ..     255     305 ..     246     329 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.1
                               NMO 146 vkearkvearGaDaliv 162
                                       v+  r++ + G+Da+ +
  gi|557693863|ref|YP_008796917.1| 105 VYTFRAAREHGPDAFLI 121
                                       55556666666666543 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 6.2e-07
                               NMO 185 vpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakd 235
                                       v +++da   PviA GG+ ++ + a a+alGAs + ++  fL      ++d
  gi|557693863|ref|YP_008796917.1| 255 VMEAVDATTKPVIASGGLRTGLDAAKAIALGASMAGLARPFLEPATKSVED 305
                                       3344555559****************************9999655444444 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.33   8.5e+02     180     203 ..     177     203 ..     127     214 .. 0.66
   2 !   15.7   0.0   2.5e-06    0.0064     146     237 ..     224     317 ..     219     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.33
                            DUF561 180 eiskkvslPvic...asGlsdvtvpla 203
                                       ++ k+vs+P+i      Gls   v +a
  gi|557693863|ref|YP_008796917.1| 177 KLRKEVSVPIILkeiGCGLSREVVAMA 203
                                       355666666664111345554444444 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.5e-06
                            DUF561 146 vdliqteGkitsiskakkvndliekslstlastyeiskkvslPvicasGl.sdvtvplalslgasGiGigsav.s.k 219
                                       +++i++e  + +i k+   +  +e  ++t a++ e + +++ Pvi++ Gl + + +  a++lgas  G+ +   +  
  gi|557693863|ref|YP_008796917.1| 224 IEMIRAEE-MRDIEKKALAEVFLEWGIPTAAAVMEAVDATTKPVIASGGLrTGLDAAKAIALGASMAGLARPFlEpA 299
                                       78999997.8899999999999****************************557999**********99976541313 PP

                            DUF561 220 lndeeemvallseikkai 237
                                        ++ e++ a l+++++++
  gi|557693863|ref|YP_008796917.1| 300 TKSVEDVLATLKRLSDQL 317
                                       556677777777777766 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.2      0.17   4.3e+02     182     230 ..      97     150 ..      67     164 .. 0.54
   2 ?    6.5   0.1    0.0018       4.5     164     208 ..     172     218 ..     159     242 .. 0.77
   3 ?    5.0   0.3     0.005        13     160     199 ..     248     287 ..     239     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.17
                                       S---SHHHHH...HHHHTT-SEEEES..HHHHTSSSHHHHHHHHHHHHHHHHHH CS
                              ThiG 182 AGigspsdaa...qamelGadavlln..tavaeakdpvamArafklaveaGrla 230
                                       AG+ +p+ +    +a e G da l+    av   ++ v+m       ++a  la
  gi|557693863|ref|YP_008796917.1|  97 AGVVKPETVYtfrAAREHGPDAFLIGniGAVQLVENGVEMGVKAVEMIDADALA 150
                                       555555544311135555666655541235555555555554444444444444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHH-SS-BEE.ES---SHHHH.HHHHHTT-SEEEESHHHH CS
                              ThiG 164 kealkiiieeakvPviv.DAGigspsda.aqamelGadavllntava 208
                                        ++l+ +++e++vP+i+ + G g + ++ a+a e G+da  ++ +  
  gi|557693863|ref|YP_008796917.1| 172 SKTLEKLRKEVSVPIILkEIGCGLSREVvAMADEAGVDAFDVAGSGG 218
                                       678999**********945899999886267889****987766555 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.005
                                       --S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-S CS
                              ThiG 160 GllnkealkiiieeakvPvivDAGigspsdaaqamelGad 199
                                       G+ +++a+   ++ ++ Pvi   G+++  daa+a+ lGa+
  gi|557693863|ref|YP_008796917.1| 248 GIPTAAAVMEAVDATTKPVIASGGLRTGLDAAKAIALGAS 287
                                       77788888888999999*********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2584.64
//
Query:       gi|557693864|ref|YP_008796918.1|  [L=574]
Description: glutamyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-71  240.1   0.0    3.2e-71  239.8   0.0    1.1  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
      6e-28   97.9   0.0      1e-27   97.1   0.0    1.4  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo
  ------ inclusion threshold ------
      0.057   13.4   0.0       0.14   12.2   0.0    1.6  1  Lig_C           Ligase Pab1020 C-terminal region


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 !  239.8   0.0   5.3e-75   3.2e-71       1     313 [.     100     405 ..     100     406 .. 0.96

  Alignments for each domain:
  == domain 1  score: 239.8 bits;  conditional E-value: 5.3e-75
                                       S-EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGG CS
                      tRNA-synt_1c   1 kVrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsdr 77 
                                       kV+tR +PeP+Gy+H+Gha a l+n ++A++++Gk+ lR+eDT+p +   e+ es  +   wlgi+wd     +sd 
  gi|557693864|ref|YP_008796918.1| 100 KVVTRLPPEPSGYMHLGHALAGLINEHYARRYGGKLWLRFEDTNPRKARLEFYESFRKGYRWLGIEWDF-EKNNSDD 175
                                       79*****************************************************************75.6899*** PP

                                       HHHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTS CS
                      tRNA-synt_1c  78 fdelkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkidees 154
                                       ++ ++ yae++i++G  Y c+c++ee++++r +   +g+k+r    e  l+ + e++ ++ + +++++ Rl  +++s
  gi|557693864|ref|YP_008796918.1| 176 MESYYMYAERMIREGFLYPCFCSSEEMHRQRAQ--GIGCKHRGLVGEAGLETW-EKALNRVYGEGEVSFRLVGEMSS 249
                                       *******************************99..99999*************.99999****************** PP

                                       S.GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EE CS
                      tRNA-synt_1c 155 s.vefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevppf 230
                                       + +++rD+v+ ri  +p   h+l ++ + + PtYdfa +++Dal ++thvlr  ef  +++ + ++   lgl  +p+
  gi|557693864|ref|YP_008796918.1| 250 PnTALRDPVMFRIVDHP---HPLKGREYVVWPTYDFAAAVQDALCGVTHVLRSSEFAFRDELQNMIRGILGLS-NPV 322
                                       *****************...*****************************************************.999 PP

                                       EEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHH.HHHCCCSSS.EEEEHHHHHH CS
                      tRNA-synt_1c 231 iheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelf.treeliksfdlnreskslea 306
                                       + e++r  + +   SKR++  l++ek v +wdd+r+ +++++ r+G+ p+++re+  t  +++++      ++ l++
  gi|557693864|ref|YP_008796918.1| 323 YVEFSRFEFRGATTSKREIRSLIEEKVVSGWDDPRLSTIEAVKRRGILPQAIREFTlTYAGVTQAK-KIFDWSLLHS 398
                                       99****************************************************972556777666.7788999999 PP

                                       HHHHHHH CS
                      tRNA-synt_1c 307 fdrkkLe 313
                                       ++rk+L+
  gi|557693864|ref|YP_008796918.1| 399 INRKHLD 405
                                       9999886 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 !   97.1   0.0   1.7e-31     1e-27       1     174 []     408     562 ..     408     562 .. 0.87

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 1.7e-31
                    tRNA-synt_1c_C   1 ApRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfskeiyiereDakrlkpgeevrLkelynikveev 77 
                                       A+R+++V +pvk+++ n++   + e+evp+hp+  ++g+r v+ ++++yi+  Da++l  ge +rLk l n+kv e 
  gi|557693864|ref|YP_008796918.1| 408 ARRLWFVASPVKLRLINHK---RAEVEVPYHPS-TNMGKRVVKAGETLYISGPDAENLGVGEVFRLKLLTNVKVVEK 480
                                       89************99876...689********.8***************************************654 PP

                    tRNA-synt_1c_C  78 ekdesgevtelkleydgesleearkkkgiihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepal 154
                                           +gev+     ++g  l    k   ii+Wvs+ ++ +++v  Y  Lf+e+      +  +sl+v eeglae a+
  gi|557693864|ref|YP_008796918.1| 481 ---GAGEVVG--EVVEGPPL----KDGRIIQWVSE-DNRRVKVIRYGPLFTED----GSVDRKSLWV-EEGLAEAAV 542
                                       ...3556655..23344445....6677******6.7788889*******974....45899***98.9******** PP

                    tRNA-synt_1c_C 155 anlkkgdivQfeRiGyfrvd 174
                                       ++++ +++vQfeR+G++r d
  gi|557693864|ref|YP_008796918.1| 543 ETVAFEEVVQFERYGFVRRD 562
                                       *****************976 PP

>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.4e-05      0.14       7      43 ..     174     211 ..     170     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                                       CGS-STSCH.HHHHHHHHHHHHH--SHHHHHHHHHHHH CS
                             Lig_C   7 felgrdFlf.sRviReafqavefeeseeelrerakeLG 43 
                                        ++++ +++ +R+iRe+f    f+ see  r+ra+ +G
  gi|557693864|ref|YP_008796918.1| 174 DDMESYYMYaERMIREGFLYPCFCSSEEMHRQRAQGIG 211
                                       57888888637************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 4337.28
//
Query:       gi|557693865|ref|YP_008796919.1|  [L=123]
Description: large subunit ribosomal protein L7Ae [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  104.6   0.1      2e-30  104.4   0.1    1.1  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
      0.014   15.5   0.0      0.015   15.3   0.0    1.1  1  RNase_P_pop3    RNase P subunit Pop3


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 !  104.4   0.1   2.2e-34     2e-30       2      92 ..      18     108 ..      17     111 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 2.2e-34
                                       HHHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSS CS
                    Ribosomal_L7Ae   2 aieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkr 78 
                                       a+ e++++ak +gk+++G++ev+ka+erg+ak+v++A dv+p+e++++l++lc+e+++ y++v+sk++LGe++g+++
  gi|557693865|ref|YP_008796919.1|  18 AALEAVRLAKTSGKVKKGVNEVIKAIERGQAKFVLIATDVDPPEIVAFLPTLCEERKISYIFVNSKAQLGEVAGLSV 94 
                                       567899*********************************************************************** PP

                                       ECSEEEEEESTTTH CS
                    Ribosomal_L7Ae  79 pvsalaikdegdsk 92 
                                       p+s++a++d+g++k
  gi|557693865|ref|YP_008796919.1|  95 PASSVAVVDPGEAK 108
                                       ***********987 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 ?   15.3   0.0   1.7e-06     0.015      53     123 ..      29      93 ..      13     122 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-06
                      RNase_P_pop3  53 eseltvglneivelLecsesddvvllvcnkDtPsvLlsqlpllvavanltvklvqlpksaqakldeklGls 123
                                         ++  g+ne+++ +e  ++++ vl++ + D P  ++  lp l++  +  +  + ++  ++a+l e+ Gls
  gi|557693865|ref|YP_008796919.1|  29 SGKVKKGVNEVIKAIE-RGQAKFVLIATDVD-PPEIVAFLPTLCEERK--ISYIFVN--SKAQLGEVAGLS 93 
                                       568999**********.9999999****999.88899********998..4444444..344555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       665  (0.0370907); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 982.09
//
Query:       gi|557693866|ref|YP_008796920.1|  [L=73]
Description: small subunit ribosomal protein S28e [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-30  104.8   4.5    1.9e-30  104.7   4.5    1.0  1  Ribosomal_S28e  Ribosomal protein S28e


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 !  104.7   4.5     1e-34   1.9e-30       2      64 .]      10      72 ..       9      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 1e-34
                                      --EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                    Ribosomal_S28e  2 eaklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                      e ++A V++v+grtG++GevtqVrv++l+gkd+gr+i RnVkGPvr+GDiL+Ll+terEA+++
  gi|557693866|ref|YP_008796920.1| 10 EPVPAVVEQVVGRTGVTGEVTQVRVRILKGKDEGRVISRNVKGPVRVGDILMLLDTEREAEKI 72
                                      6789********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); 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: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.42
# Mc/sec: 524.82
//
Query:       gi|557693867|ref|YP_008796921.1|  [L=57]
Description: large subunit ribosomal protein L24e [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   67.7   2.0    8.4e-19   67.6   2.0    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
    8.4e-05   22.4   2.6    0.00014   21.8   2.6    1.3  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
    0.00095   19.5   0.2      0.001   19.4   0.2    1.0  1  DUF3268         zinc-finger-containing domain
     0.0083   15.6   2.5      0.016   14.6   2.5    1.5  1  zf-FLZ          zinc-finger of the FCS-type, C2-C2
  ------ inclusion threshold ------
      0.079   12.9   2.9      0.085   12.8   2.2    1.6  1  zf-C4_ClpX      ClpX C4-type zinc finger
        2.6    8.2  12.2          1    9.5   6.7    2.5  2  DUF2256         Uncharacterized protein conserved in bacteria


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 !   67.6   2.0   2.8e-22   8.4e-19       2      54 ..       3      56 ..       2      57 .] 0.96

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 2.8e-22
                                      XX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHH.HHHHHTT--GGGSTTSTT CS
                    Ribosomal_L24e  2 ktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKc.eklfkqkrnPrklkWTka 54
                                      +t++CsF+g++   G+G+++v+nDg+ + F+s+Kc   ++++ + PrklkWTka
  gi|557693867|ref|YP_008796921.1|  3 RTHRCSFCGREFTHGKGMLYVKNDGTLLWFCSRKCrIYMVEHGKDPRKLKWTKA 56
                                      899********************************77999************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 !   21.8   2.6   4.5e-08   0.00014       4      38 ..       5      38 ..       3      38 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 4.5e-08
                            zf-FCS  4 krCwfCkkyikgkpeftyvlendgvvgqFCStsCl 38
                                       rC+fC+++++ +++   ++ ndg    FCS+ C+
  gi|557693867|ref|YP_008796921.1|  5 HRCSFCGREFTHGKG-MLYVKNDGTLLWFCSRKCR 38
                                      59********88884.59****************7 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.2   3.5e-07     0.001       2      45 ..       4      46 ..       3      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.5e-07
                           DUF3268  2 ttrCpyCGekvilvsaseiYkerskgkllylC.pkCdayvgvhkg 45
                                      t+rC++CG++ +   +  +Y  ++ g+ll+ C +kC  y+  h +
  gi|557693867|ref|YP_008796921.1|  4 THRCSFCGREFTHG-KGMLY-VKNDGTLLWFCsRKCRIYMVEHGK 46
                                      689******98765.56799.888999*****99****9987765 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 !   14.6   2.5   5.5e-06     0.016      15      46 ..       6      40 ..       4      47 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.5e-06
                            zf-FLZ 15 aCflCkkkLgegkDiymYrGdka...FCSeeCRqq 46
                                       C++C +++++gk +   + d     FCS  CR  
  gi|557693867|ref|YP_008796921.1|  6 RCSFCGREFTHGKGMLYVKNDGTllwFCSRKCRIY 40
                                      7************8877777765667*******65 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.2   2.9e-05     0.085       2      17 ..       6      21 ..       5      35 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.9e-05
                        zf-C4_ClpX  2 rCSFCgksesevkklI 17
                                      rCSFCg++ +  k ++
  gi|557693867|ref|YP_008796921.1|  6 RCSFCGREFTHGKGML 21
                                      9******977766665 PP

>> DUF2256  Uncharacterized protein conserved in bacteria (DUF2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   6.7   0.00034         1       5      38 ..       2      38 ..       1      39 [. 0.80
   2 ?   -1.6   0.2         1   3.1e+03      15      21 ..      49      55 ..      48      56 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00034
                           DUF2256  5 lpsKiCavCgrpftwRkkWe...kdWdeVkyCSerCr 38
                                      +++  C  Cgr+ft  k      +d     +CS++Cr
  gi|557693867|ref|YP_008796921.1|  2 VRTHRCSFCGREFTHGKGMLyvkNDGTLLWFCSRKCR 38
                                      57889************76433366777889*****9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1
                           DUF2256 15 rpftwRk 21
                                      r+++w k
  gi|557693867|ref|YP_008796921.1| 49 RKLKWTK 55
                                      5566665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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):               6  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 438.02
//
Query:       gi|557693868|ref|YP_008796922.1|  [L=138]
Description: nucleoside diphosphate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-50  170.1   0.0    2.7e-50  169.9   0.0    1.0  1  NDK       Nucleoside diphosphate kinase
  ------ inclusion threshold ------
      0.071   13.6   0.1       0.12   12.9   0.1    1.3  1  MycE_N    MycE methyltransferase N-terminal
      0.088   12.6   0.0       0.13   12.1   0.0    1.3  1  DUF2840   Protein of unknown function (DUF2840)


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 !  169.9   0.0   4.5e-54   2.7e-50       2     131 ..       3     132 ..       2     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 4.5e-54
                                       EEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTT CS
                               NDK   2 rtlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvleged 78 
                                       rt+v++KP+av+rgl+geiisr+e+kglk +a+++ +lt+++a ++Y+ h+gkpf+e+l++ +t+gpvv++vleg++
  gi|557693868|ref|YP_008796922.1|   3 RTFVILKPNAVSRGLVGEIISRFERKGLKPLAIQLKQLTRDEAARLYEVHRGKPFYEDLLTAITKGPVVLMVLEGRQ 79 
                                       9**************************************************************************** PP

                                       HHHHHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHST CS
                               NDK  79 aiekvreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFk 131
                                       a+e+vr+liGat+p +a+pgtiR+d+g+++++NlvH+Sds e+ +re ++fF+
  gi|557693868|ref|YP_008796922.1|  80 AVEVVRKLIGATDPVKAEPGTIRGDYGLDITDNLVHASDSAEAYQRESAIFFT 132
                                       ****************************************************7 PP

>> MycE_N  MycE methyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     2e-05      0.12      24     107 ..      10      96 ..       6      98 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                            MycE_N  24 lervarvLvdElvfRadleelpvdevsvqlalsaggeelsvlvaVgkggpvveagesaaaaa.....tve.qdleel 94 
                                       +++v r Lv E+++R ++++l++  + +ql+   ++e ++ l  V  g+p  e+  +a ++      ++e   ++e+
  gi|557693868|ref|YP_008796922.1|  10 PNAVSRGLVGEIISRFERKGLKP--LAIQLKQLTRDE-AARLYEVHRGKPFYEDLLTAITKGpvvlmVLEgRQAVEV 83 
                                       7899999**************99..999999777765.66789******9865555554444544545554578999 PP

                            MycE_N  95 vralfGPvrevsa 107
                                       vr l G + +v+a
  gi|557693868|ref|YP_008796922.1|  84 VRKLIGATDPVKA 96 
                                       9999998888766 PP

>> DUF2840  Protein of unknown function (DUF2840)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.1e-05      0.13      75     138 ..      62     126 ..      47     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                           DUF2840  75 lpfvrpGgeiLLrvegwpkVervleaidavealgidpadvapdhWrhvhnrl.aageepraytae 138
                                       l+ ++ G  +L+ +eg++ Ve v ++i a + +  +p ++  d+   +++ l +a  + +ay +e
  gi|557693868|ref|YP_008796922.1|  62 LTAITKGPVVLMVLEGRQAVEVVRKLIGATDPVKAEPGTIRGDYGLDITDNLvHASDSAEAYQRE 126
                                       678999**************************************999876551677777888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1127.66
//
Query:       gi|557693869|ref|YP_008796923.1|  [L=412]
Description: translation initiation factor eIF-2 gamma subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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   93.7   0.0    5.9e-26   91.2   0.0    1.9  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.7e-24   85.9   0.3    3.2e-24   85.0   0.3    1.5  1  eIF2_C       Initiation factor eIF2 gamma, C terminal
    1.4e-07   31.8   2.8    1.9e-07   31.4   0.8    2.2  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00038   20.5   0.0     0.0008   19.5   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0038   16.3   0.0      0.014   14.4   0.0    1.8  2  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
  ------ inclusion threshold ------
      0.092   12.6   0.1        1.2    9.0   0.0    2.3  2  RsgA_GTPase  RsgA GTPase


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 !   91.2   0.0     2e-29   5.9e-26       4     192 ..       9     199 ..       6     201 .. 0.90

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 2e-29
                                       EEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................ CS
                          GTP_EFTU   4 rnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................ 64 
                                       +nig++ghvD GK+T++ +++    a               +++eE +rgiTi +  +                   
  gi|557693869|ref|YP_008796923.1|   9 VNIGTLGHVDNGKSTIVQSITGVWTA---------------KHSEELKRGITIRIGYADAAiyicprctppynhysv 70 
                                       7*******************944333...............456899999999999988888899999999999999 PP

                                       ........TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEES CS
                          GTP_EFTU  65 ........ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNK 131
                                               +++ ++ +++iD+PGH + + ++  g++  Dga++v d+++  ++pq  e+l  a+ +g++ ++++ NK
  gi|557693869|ref|YP_008796923.1|  71 ekcpihgtANEFQRVVSFIDCPGHHSLMVTMLSGAALFDGAIFVTDVRQKfPQPQDGEHLLAAKILGIKnLVIAQNK 147
                                       9***998669999***********************************9889************************* PP

                                       CGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
                          GTP_EFTU 132 mDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvell 192
                                       +D + k++ +e  ee+ + l       ek g+++    p++++S+ +g g+++ll a+ + +
  gi|557693869|ref|YP_008796923.1| 148 IDLVdKKRAEENYEEIVDYL-------EKNGFERP---PIIPVSGQHGVGIEPLLYAIQHVI 199
                                       ****8889999999999666.......88888875...******************998766 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 !   85.0   0.3   1.1e-27   3.2e-24       2      86 .]     325     409 ..     324     409 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 1.1e-27
                                       EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSE CS
                            eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrW 78 
                                       +l++ey+l+e+++g++ + +v+++++kE L++n+ sa++ gvv++ +++ +++ L++P++ae g+k a+sR+v++ W
  gi|557693869|ref|YP_008796923.1| 325 TLTLEYQLFEKVLGLEGNVAVKQIAEKEALVINVSSAVSSGVVAKRSSNRIEIVLSRPLVAEPGSKAAISRKVGAGW 401
                                       699************************************************************************** PP

                                       EEEEEEEE CS
                            eIF2_C  79 rLiGwGei 86 
                                       rLiG+G+i
  gi|557693869|ref|YP_008796923.1| 402 RLIGYGII 409
                                       ******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 ?   -1.0   0.0      0.81   2.4e+03      26      42 ..      19      35 ..      11      53 .. 0.55
   2 !   31.4   0.8   6.3e-11   1.9e-07       1      61 [.     232     299 ..     232     308 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.81
                                      TTSEEEEEEEEEEEEET CS
                       GTP_EFTU_D2 26 tskkeivtrissletfh 42
                                       +k+ iv  i++++t +
  gi|557693869|ref|YP_008796923.1| 19 NGKSTIVQSITGVWTAK 35
                                      55555666666665542 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 6.3e-11
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEE......EEEEEEEEEEETEEESEEETTSEEEEEEEES CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke......ivtrissletfhededeavaganaGvivaik 61 
                                       G v++g++ +G+l++Gde++i + + ++k +        t++  + +  ++++ea++g+  Gv + ++
  gi|557693869|ref|YP_008796923.1| 232 GAVIGGSITQGVLRVGDEIEIQPgLAKQKMGktvyepLYTDVANIVAGGKNVEEAYPGGLTGVETTLD 299
                                       89*********************99986666*****************************99987765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   2.7e-07    0.0008       2      94 ..      11     126 ..      10     180 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.7e-07
                                       EEEEESTTSSHHHHHHHHHTS.TEEESSST..TSSSSEEEEEEE....ETTEE........................ CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkp..gtTrdinegrvk....lkgke........................ 47 
                                       ++ +G+   GKSt+++++tg  +a+ s++   g T+ i ++  +        +                        
  gi|557693869|ref|YP_008796923.1|  11 IGTLGHVDNGKSTIVQSITGVwTAKHSEELkrGITIRIGYADAAiyicP---Rctppynhysvekcpihgtanefqr 84 
                                       7889****************87776666652366776666665544431...1333444455555566666666666 PP

                                       .EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHH CS
                          MMR_HSR1  48 .ielvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpld 94 
                                        + ++D+pG  +      +l  ++l+     d +++v d++++  +p+d
  gi|557693869|ref|YP_008796923.1|  85 vVSFIDCPG-HH------SLMVTMLSGAAlFDGAIFVTDVRQKFPQPQD 126
                                       6********.44......6777777666646999999998855444443 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 ?   -1.5   0.1      0.34     1e+03      32      50 ..      11      29 ..       8      36 .. 0.83
   2 !   14.4   0.0   4.6e-06     0.014     141     230 ..     113     200 ..      71     211 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.34
                                      EEEEE-TTSSHHHHHHHHH CS
                              MeaB 32 vGltGvPGaGkstlvealg 50
                                      +G  G    Gkst+v+ ++
  gi|557693869|ref|YP_008796923.1| 11 IGTLGHVDNGKSTIVQSIT 29
                                      788899999******9876 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.6e-06
                                       TT-SEEEEEEESSTTTTTTT--CCCHHH-SEE.EEE---HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTB CS
                              MeaB 141 evvdtfvvlllpeaGDelqgikkGileiaDii.vvnkaDkkeaekaarelraaleleeekekeWrpkvlktsavege 216
                                        v+d+      p+ G++l + k  il i +++ + nk D+ + ++a+++++ +++ +e++    rp+++ +s+++g 
  gi|557693869|ref|YP_008796923.1| 113 FVTDVRQKFPQPQDGEHLLAAK--ILGIKNLViAQNKIDLVDKKRAEENYEEIVDYLEKNGF-ERPPIIPVSGQHGV 186
                                       4556666666667777776666..78888765157******************999887644.48************ PP

                                       SHHHHHHHHHHHHH CS
                              MeaB 217 Gidelvdaieehre 230
                                       Gi+ l+ ai++  +
  gi|557693869|ref|YP_008796923.1| 187 GIEPLLYAIQHVIK 200
                                       ********997655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.12   3.6e+02     106     137 ..      15      43 ..       9      45 .. 0.80
   2 ?    9.0   0.0   0.00042       1.2      13      77 ..     105     172 ..      82     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.12
                                       CSTTSSHHHHHHHHCTT-----S--------- CS
                       RsgA_GTPase 106 GqSGvGKStLinallpelelktgevseklgrG 137
                                       G+   GKSt++ ++++     t++ se+l+rG
  gi|557693869|ref|YP_008796923.1|  15 GHVDNGKSTIVQSITGV---WTAKHSEELKRG 43 
                                       66667********9987...677777777777 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00042
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH...HHHHHHHHHHHTTS CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee...eleelkeelealgy 77 
                                       +a  d ++ v+ +  +++ + +    L++a+  gi ++vi+ nKiDl+++++   ++ee+ + le+ g+
  gi|557693869|ref|YP_008796923.1| 105 AALFDGAIFVTDVR-QKFPQPQDGEHLLAAKILGIkNLVIAQNKIDLVDKKRaeeNYEEIVDYLEKNGF 172
                                       56677788888888.66666666777888999999678999********99856667777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 00:00:00.38
# Mc/sec: 3261.66
//
Query:       gi|557693870|ref|YP_008796924.1|  [L=119]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   54.9   0.0    1.1e-14   54.7   0.0    1.0  1  PIN_9     PIN like domain
  ------ inclusion threshold ------
      0.036   14.0   0.1       0.28   11.1   0.0    2.2  2  RHH_5     CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5
        0.1   12.9   0.0       0.11   12.8   0.0    1.2  1  PIN_4     PIN domain
       0.18   11.8   1.6       0.26   11.3   0.1    2.0  2  RHH_1     Ribbon-helix-helix protein, copG family


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 !   54.7   0.0   2.5e-18   1.1e-14      10     109 ..       3     102 ..       1     106 [. 0.87

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 2.5e-18
                             PIN_9  10 ipvqfgvdifeelerll.gsvelvvpkavleELerlakagkgkertaakvalsLaerceiveae.eekaDdailela 84 
                                         ++ gvd ++ le  l ++ elvvp++v+eEL+rla++g g ++  a+val++ +  e +  + +e++Dd++l+l 
  gi|557693870|ref|YP_008796924.1|   3 FCAERGVDYLSVLENKLgERLELVVPSSVVEELRRLAAKG-GGKSMLARVALEILKDAEQLPGKvGENVDDVLLQLG 78 
                                       567889*******99997899***************5555.5567899******99988888775888********* PP

                             PIN_9  85 keldaavlvTnDreLkkrllekgip 109
                                       +e+++ vl T D+ L +rl  ++++
  gi|557693870|ref|YP_008796924.1|  79 RETGYPVL-TVDARLMRRLAARNLE 102
                                       ********.**********999875 PP

>> 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 ?    0.1   0.0      0.17   7.5e+02      32      40 ..       2      10 ..       1      12 [. 0.83
   2 ?   11.1   0.0   6.3e-05      0.28       2      22 ..      21      41 ..      20      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.17
                             RHH_5 32 afLvekalr 40
                                       f++e++++
  gi|557693870|ref|YP_008796924.1|  2 LFCAERGVD 10
                                      69*****98 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.3e-05
                             RHH_5  2 kRvnvtLPeelleeLeewAde 22
                                      +R  +++P+ + eeL+++A++
  gi|557693870|ref|YP_008796924.1| 21 ERLELVVPSSVVEELRRLAAK 41
                                      7999***************86 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.4e-05      0.11      18      60 ..      19      59 ..       9      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.4e-05
                             PIN_4 18 fkeehdvviPitVleELdklKkgsserelarlarqanrlldel 60
                                      + e +++v+P  V+eEL++l  +      + lar a+++l+++
  gi|557693870|ref|YP_008796924.1| 19 LGERLELVVPSSVVEELRRLAAKGG--GKSMLARVALEILKDA 59
                                      378899*************988887..6777777777777655 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 ?   11.3   0.1   5.9e-05      0.26       2      25 ..      23      47 ..      22      54 .. 0.87
   2 ?   -1.7   0.1      0.72   3.2e+03      28      34 ..      92      98 ..      87     102 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.9e-05
                                      EEEEEEHHHHHHHHHHHHHHT.SSH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSr 25
                                      +++ ++++++e+L++la+++g +S+
  gi|557693870|ref|YP_008796924.1| 23 LELVVPSSVVEELRRLAAKGGgKSM 47
                                      5666899**************8885 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.72
                                      HHHHHHH CS
                             RHH_1 28 lIReAlr 34
                                      l+R++++
  gi|557693870|ref|YP_008796924.1| 92 LMRRLAA 98
                                      3454444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 910.62
//
Query:       gi|557693871|ref|YP_008796925.1|  [L=187]
Description: DNA-directed RNA polymerase subunit E' [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   53.4   0.0    4.2e-14   52.7   0.0    1.4  1  SHS2_Rpb7-N  SHS2 domain found in N terminus of Rpb7p/Rpc25p/
    1.4e-13   51.0   0.1    3.1e-13   49.8   0.1    1.6  1  S1           S1 RNA binding domain


Domain annotation for each model (and alignments):
>> 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 !   52.7   0.0   4.7e-18   4.2e-14       3      70 .]      10      77 ..       8      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 4.7e-18
                                      EEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTTEEEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                       SHS2_Rpb7-N  3 tvrlePsylgstledallerllekyegkvvpslGvivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                      +v ++P ++g++le+ +l +l+++yeg v+++lG+i+ v d + ++ g++l+ +Gs+y+r tf++l +
  gi|557693871|ref|YP_008796925.1| 10 IVGIPPADFGKPLEKVVLNELRKRYEGAVDEELGYIIMVIDAKVDKVGRILPRDGSTYHRSTFTLLTY 77
                                      799*************************************************************9975 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.1   3.5e-17   3.1e-13       5      62 ..      82     148 ..      79     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 3.5e-17
                                       TCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEE CS
                                S1   5 gevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlk 62 
                                       +evv GeV+++t++G fV++g +++g++++s++++d            +++++++l vGd v+ ++  
  gi|557693871|ref|YP_008796925.1|  82 NEVVLGEVVEITDFGCFVRIG-PIDGLIHISQIMDDyitydeknnmLVGRKSGRKLLVGDDVRGRINA 148
                                       79*******************.**************77777777776667777777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1356.43
//
Query:       gi|557693872|ref|YP_008796926.1|  [L=63]
Description: DNA-directed RNA polymerase subunit E'' [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   51.3   0.3    1.1e-13   51.1   0.3    1.1  1  Spt4         Spt4/RpoE2 zinc finger
  ------ inclusion threshold ------
       0.01   16.0   0.9      0.013   15.6   0.9    1.2  1  Laminin_EGF  Laminin EGF domain


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 !   51.1   0.3   1.2e-17   1.1e-13       2      77 .]       6      63 .]       5      63 .] 0.98

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.2e-17
                              Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                      rAC++Ck+++  ++     C++C           +s+++s++++Glv+ild e+S++Ak   l+ ++ g YA+kv+
  gi|557693872|ref|YP_008796926.1|  6 RACRNCKRIVVGKT-----CDVC-----------GSSNLSTSYSGLVIILDVESSEIAKE--LGIRKSGRYAVKVD 63
                                      9************9.....****...........**************************..************95 PP

>> Laminin_EGF  Laminin EGF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.9   1.5e-06     0.013      19      36 ..       7      25 ..       3      33 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-06
                                      CES.BTTTEESTTS-EE-T CS
                       Laminin_EGF 19 qCl.CkenveGrkCdrCkp 36
                                      +C+ Ck+ v G++Cd C +
  gi|557693872|ref|YP_008796926.1|  7 ACRnCKRIVVGKTCDVCGS 25
                                      7****************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 479.01
//
Query:       gi|557693873|ref|YP_008796927.1|  [L=168]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  111.6   0.5    2.6e-32  111.1   0.5    1.2  1  DUF359    Protein of unknown function (DUF359)


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 !  111.1   0.5   1.5e-36   2.6e-32       4     124 ..      53     165 ..      50     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 1.5e-36
                            DUF359   4 nllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdGEED 80 
                                       ++++ag++Pd+++vD k++R+       + e+ + +++ev++v+N aG+i+ e+ ea+ +a+ ++ + +++VdGEED
  gi|557693873|ref|YP_008796927.1|  53 RMIEAGLRPDVVVVDAKVMRN-------AAEMPRLEGYEVTRVRNMAGVIEPEAAEAVMSAV-KKGRGAVFVDGEED 121
                                       789******************.......2334567899************************.89999********* PP

                            DUF359  81 LavlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellek 124
                                       L++lpai ++p+g vvvYGqp++G v+vk++ ++k+ +ee++++
  gi|557693873|ref|YP_008796927.1| 122 LLALPAIHALPDGGVVVYGQPRQGYVVVKASVKVKKLVEEIISM 165
                                       *****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1283.42
//
Query:       gi|557693874|ref|YP_008796928.1|  [L=52]
Description: small subunit ribosomal protein S27Ae [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   54.5   2.9    1.1e-14   54.3   2.9    1.1  1  Ribosomal_S27   Ribosomal protein S27a
    0.00033   20.5   0.9    0.00045   20.1   0.9    1.3  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
     0.0016   18.5   2.4     0.0021   18.2   2.4    1.2  1  Ribosomal_L37e  Ribosomal protein L37e
     0.0027   17.9   0.1     0.0035   17.5   0.1    1.1  1  IBR             IBR domain, a half RING-finger domain
     0.0038   16.7   3.3     0.0057   16.2   3.3    1.3  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.021   14.7   2.8       0.45   10.5   2.4    2.4  2  zinc_ribbon_4   zinc-ribbon domain
      0.027   13.9   1.1      0.075   12.5   0.0    1.9  2  Mu-like_Com     Mu-like prophage protein Com
      0.031   14.2   1.8       0.06   13.3   1.8    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.044   13.7   1.0        1.1    9.3   0.0    2.1  2  zf-DNL          DNL zinc finger
      0.071   12.7   1.0        9.1    5.9   0.1    2.2  2  zf_C2H2_10      C2H2 type zinc-finger
      0.072   13.1   0.1      0.072   13.1   0.1    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.086   12.8   4.9        1.2    9.1   4.9    2.1  1  Nudix_N_2       Nudix N-terminal
       0.24   11.5   4.2        2.8    8.1   0.3    2.1  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
       0.35   10.8   6.4        4.1    7.4   0.2    2.3  2  zf-HIT          HIT zinc finger
       0.42   10.3   3.1         11    5.7   0.1    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.86    9.5   4.1         30    4.6   4.9    2.1  2  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        1.6    8.3   6.6          2    7.9   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain


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 !   54.3   2.9   1.1e-17   1.1e-14       6      45 .]      11      48 ..       7      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.1e-17
                                      CESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
                     Ribosomal_S27  6 kvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                                       ++d g  e++   Cpr CG G+fMA+h +R++CGkCg+T
  gi|557693874|ref|YP_008796928.1| 11 VLKD-GRLEKTLVSCPR-CGVGYFMADHGNRYTCGKCGYT 48
                                      5555.9999999*****.*********************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 !   20.1   0.9   4.2e-07   0.00045      10      46 .]      12      48 ..       6      48 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.2e-07
                     Zn_Tnp_IS1595 10 LealrWpngfv.CPhCgsrkayrikt.rglfqCkeCrkq 46
                                      L++ r   + v CP+Cg    y++++   ++ C +C+++
  gi|557693874|ref|YP_008796928.1| 12 LKDGRLEKTLVsCPRCG--VGYFMADhGNRYTCGKCGYT 48
                                      566667777666*****..7888888779*******985 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   2.4     2e-06    0.0021      13      41 ..      18      49 ..      13      52 .] 0.78

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-06
                    Ribosomal_L37e 13 kktHilCrrCgkrsy...hvqkktCascGyps 41
                                      +kt + C rCg   +   h ++ tC++cGy +
  gi|557693874|ref|YP_008796928.1| 18 EKTLVSCPRCGVGYFmadHGNRYTCGKCGYTR 49
                                      6899*******9999444666789******54 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 !   17.5   0.1   3.3e-06    0.0035       4      46 ..       8      47 ..       6      49 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-06
                               IBR  4 eklklkkslesdpnlkwCprpdCeaiieksegcksvtCskCgf 46
                                      +++ lk+    +++l+ Cp   C+  +   ++ ++ tC kCg+
  gi|557693874|ref|YP_008796928.1|  8 KRYVLKDG-RLEKTLVSCP--RCGVGYFMADHGNRYTCGKCGY 47
                                      66667763.55789*****..899777777776778*****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 !   16.2   3.3   5.4e-06    0.0057       3      27 ..      24      47 ..      22      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.4e-06
                                      ETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGl 27
                                      CP Cg  ++  D+  + ++C++CG+
  gi|557693874|ref|YP_008796928.1| 24 CPRCGVGYFMADHG-NRYTCGKCGY 47
                                      *******999**88.889******6 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.3    0.0024       2.6      12      32 ..      10      28 ..       8      29 .. 0.63
   2 ?   10.5   2.4   0.00042      0.45       3      33 ..      22      47 ..      21      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0024
                     zinc_ribbon_4 12 yeiddeklpakgvkvrCskCg 32
                                      y + d +l ++   v C++Cg
  gi|557693874|ref|YP_008796928.1| 10 YVLKDGRLEKT--LVSCPRCG 28
                                      66666666555..77788886 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00042
                     zinc_ribbon_4  3 itCpsCkakyeiddeklpakgvkvrCskCgh 33
                                      ++Cp+C+  y  +d     +g + +C kCg 
  gi|557693874|ref|YP_008796928.1| 22 VSCPRCGVGYFMAD-----HGNRYTCGKCGY 47
                                      89********9999.....799999999996 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 ?   12.5   0.0   7.1e-05     0.075      11      31 ..       8      28 ..       3      34 .. 0.87
   2 ?    0.3   0.3      0.47     5e+02       7      10 ..      42      45 ..      38      49 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.1e-05
                       Mu-like_Com 11 aRLLaKaeAlDeltiKCPRCG 31
                                      +R + K + l++  + CPRCG
  gi|557693874|ref|YP_008796928.1|  8 KRYVLKDGRLEKTLVSCPRCG 28
                                      68888999999999******9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.47
                       Mu-like_Com  7 CGeC 10
                                      CG+C
  gi|557693874|ref|YP_008796928.1| 42 CGKC 45
                                      6766 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 ?   13.3   1.8   5.6e-05      0.06      29      55 ..      22      48 ..       7      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.6e-05
                    OrfB_Zn_ribbon 29 ktCseCgsknkealsgrtfkCpnCgfe 55
                                       +C++Cg     a++g++++C +Cg++
  gi|557693874|ref|YP_008796928.1| 22 VSCPRCGVGYFMADHGNRYTCGKCGYT 48
                                      68*****9888899***********96 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0     0.001       1.1      28      43 ..      21      36 ..      18      39 .. 0.93
   2 ?    3.4   0.6     0.072        76       4      13 ..      40      49 ..      37      52 .] 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.001
                            zf-DNL 28 ivqCpgCknrHliaDn 43
                                      +v+Cp C     +aD+
  gi|557693874|ref|YP_008796928.1| 21 LVSCPRCGVGYFMADH 36
                                      89*************9 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.072
                            zf-DNL  4 ftCkaCetrs 13
                                      +tC +C+   
  gi|557693874|ref|YP_008796928.1| 40 YTCGKCGYTR 49
                                      9*****9754 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 ?    5.6   0.1     0.011        11       4       9 ..      23      28 ..      22      32 .. 0.89
   2 ?    5.9   0.1    0.0086       9.1       3      10 ..      40      47 ..      39      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.011
                        zf_C2H2_10  4 sCPKCq 9 
                                      sCP+C+
  gi|557693874|ref|YP_008796928.1| 23 SCPRCG 28
                                      9****7 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0086
                        zf_C2H2_10  3 fsCPKCqe 10
                                      + C KC++
  gi|557693874|ref|YP_008796928.1| 40 YTCGKCGY 47
                                      79*****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 ?   13.1   0.1   6.8e-05     0.072      67      97 ..      18      50 ..       1      52 [] 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.8e-05
                                      E--EEEETTTS-EEECHHH..HHS-TTTSSS-E CS
                              HypA 67 vpvkvrCreCgkefeleek..alrCpkCgsadv 97
                                      ++  v C +Cg  + ++++  +++C+kCg +++
  gi|557693874|ref|YP_008796928.1| 18 EKTLVSCPRCGVGYFMADHgnRYTCGKCGYTRF 50
                                      567799*****998877644689*****98765 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   4.9    0.0012       1.2       3      31 ..      24      48 ..      23      51 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                                      -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCgti 31
                                      C+ CG    + +   D+  R++C +Cg++
  gi|557693874|ref|YP_008796928.1| 24 CPRCGVG--YFM--ADHGNRYTCGKCGYT 48
                                      6666644..333..59999********97 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 ?    8.1   0.3    0.0026       2.8      17      28 ..      22      33 ..      10      37 .. 0.81
   2 ?    5.6   0.4     0.016        17      15      25 ..      38      48 ..      34      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0026
                          zf-Mss51 17 feCpdCGiptyc 28
                                      + Cp+CG+ +++
  gi|557693874|ref|YP_008796928.1| 22 VSCPRCGVGYFM 33
                                      78*****98875 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.016
                          zf-Mss51 15 vdfeCpdCGip 25
                                       +++C +CG+ 
  gi|557693874|ref|YP_008796928.1| 38 NRYTCGKCGYT 48
                                      68*******96 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0039       4.1      15      23 ..      23      31 ..      19      31 .. 0.86
   2 ?    5.9   1.7     0.011        12      13      20 ..      39      46 ..      37      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0039
                                      E-TTT--EE CS
                            zf-HIT 15 kCpkCntry 23
                                      +Cp+C++ y
  gi|557693874|ref|YP_008796928.1| 23 SCPRCGVGY 31
                                      7*****876 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                                      SEE-TTT- CS
                            zf-HIT 13 kYkCpkCn 20
                                      +Y+C kC+
  gi|557693874|ref|YP_008796928.1| 39 RYTCGKCG 46
                                      8******8 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.011        11       3       9 ..      22      28 ..      20      29 .. 0.85
   2 ?    5.3   0.5     0.014        15       2       9 ..      39      46 ..      38      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.011
                            zf_UBZ  3 ylCerCg 9 
                                      + C+rCg
  gi|557693874|ref|YP_008796928.1| 22 VSCPRCG 28
                                      68****8 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.014
                            zf_UBZ  2 tylCerCg 9 
                                       y+C +Cg
  gi|557693874|ref|YP_008796928.1| 39 RYTCGKCG 46
                                      69*****8 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 ?    3.0   0.2     0.087        92      17      28 ..      16      28 ..      11      32 .. 0.65
   2 ?    4.6   4.9     0.029        30      16      30 ..      34      48 ..      24      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.087
                                      SCCCE.EEESSSS CS
                    RNA_POL_M_15KD 17 kegkn.feCrqCg 28
                                      ++ k  + C  Cg
  gi|557693874|ref|YP_008796928.1| 16 RLEKTlVSCPRCG 28
                                      5555556677775 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.029
                                      CSCCCEEEESSSS-E CS
                    RNA_POL_M_15KD 16 dkegknfeCrqCgYe 30
                                      ++ g+++ C +CgY 
  gi|557693874|ref|YP_008796928.1| 34 ADHGNRYTCGKCGYT 48
                                      5678789*******5 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0019         2       3       9 ..      22      28 ..      21      29 .. 0.87
   2 ?    3.1   1.6     0.062        65      18      24 ..      41      47 ..      40      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0019
                       zf-ribbon_3  3 vrCPnCG 9 
                                      v+CP+CG
  gi|557693874|ref|YP_008796928.1| 22 VSCPRCG 28
                                      7899999 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.062
                       zf-ribbon_3 18 vCpyCGt 24
                                      +C +CG+
  gi|557693874|ref|YP_008796928.1| 41 TCGKCGY 47
                                      6999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 385.85
//
Query:       gi|557693875|ref|YP_008796929.1|  [L=99]
Description: small subunit ribosomal protein S24e [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   50.7   0.0      2e-13   50.1   0.0    1.3  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 !   50.1   0.0   1.1e-17     2e-13      12      78 ..      32      98 ..      24      99 .] 0.95

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.1e-17
                                      --HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS---S CS
                    Ribosomal_S24e 12 pskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekkk 78
                                      ++++e ++ +a+ + +dp  vvv+++  h G +   ++a++Yd++e  k fEp ++l+Rn+lae  k
  gi|557693875|ref|YP_008796929.1| 32 ITRDEAKQLIAAHLSIDPARVVVRKLVYHTGSRLVDVYANVYDKVEGIKVFEPLYILIRNKLAERPK 98
                                      5799************************************************************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 737.37
//
Query:       gi|557693876|ref|YP_008796930.1|  [L=141]
Description: small subunit ribosomal protein S6e [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-46  156.9   0.8    5.1e-46  155.7   0.8    1.5  1  Ribosomal_S6e  Ribosomal protein S6e
  ------ inclusion threshold ------
       0.14   12.2   1.5       0.25   11.3   1.5    1.4  1  KH_7           KH domain


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 !  155.7   0.8   5.7e-50   5.1e-46       2     122 ..       9     141 .]       9     141 .] 0.99

  Alignments for each domain:
  == domain 1  score: 155.7 bits;  conditional E-value: 5.7e-50
                                       EEEEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEET CS
                     Ribosomal_S6e   2 klnisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlsk 78 
                                       ++++sdp+++k+++i+++ ++l+ ligkrige+vdg+++G  +kgy++kitggsdk+Gfpm+++v++p++vr+Lls+
  gi|557693876|ref|YP_008796930.1|   9 RMVLSDPVQKKASTIQLTPQQLTLLIGKRIGETVDGGVFG--YKGYLIKITGGSDKDGFPMRPDVSGPRKVRVLLSG 83 
                                       699*************************************..*********************************** PP

                                       TSSSS-SSS...............SS-EEEEEEE-SB--SSEEEEEEEEEE--SS--TT CS
                     Ribosomal_S6e  79 ggvgyrprr...............kGerkrksvrGcivsadisqlnlvivkkgekdieg 122
                                        g+g++prr               kG rkr++vrG+++s++i+q+n+++vkkge+d++g
  gi|557693876|ref|YP_008796930.1|  84 -GPGFHPRRkpaskrkkkrarrlvKGLRKRVTVRGDTISEAIAQINAILVKKGEQDVAG 141
                                       .********************************************************87 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.5   2.8e-05      0.25      46      64 ..     100     118 ..      91     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.8e-05
                              KH_7  46 dlirklAkelrkRiviRpD 64 
                                       +  r+l+k lrkR+++R D
  gi|557693876|ref|YP_008796930.1| 100 KRARRLVKGLRKRVTVRGD 118
                                       56799************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1095.33
//
Query:       gi|557693877|ref|YP_008796931.1|  [L=748]
Description: translation initiation factor IF-2 unclassified subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-32  110.4   5.1    3.4e-32  110.2   2.8    2.5  2  GTP_EFTU_D4      Elongation factor Tu domain 4
      3e-29  102.0   0.0    3.4e-26   92.0   0.0    2.4  2  GTP_EFTU         Elongation factor Tu GTP binding domain
    1.3e-15   57.4   0.3    3.4e-15   56.1   0.3    1.7  1  IF-2             Translation-initiation factor 2
      1e-11   44.9   0.0      3e-11   43.4   0.0    1.8  2  Intein_splicing  Intein splicing domain
    1.5e-06   28.4   6.3    0.00026   21.3   0.0    3.4  3  GTP_EFTU_D2      Elongation factor Tu domain 2
     0.0013   18.8   0.0     0.0053   16.8   0.0    2.1  2  MMR_HSR1         50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.037   13.8   0.0       0.07   12.9   0.0    1.4  1  ATP_bind_1       Conserved hypothetical ATP binding protein


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 ?   -3.5   0.0         4     1e+04      60      76 ..     463     479 ..     447     485 .. 0.57
   2 !  110.2   2.8   1.3e-35   3.4e-32       1      86 []     620     705 ..     620     705 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4
                                       EETT-EEEEEEESS-TT CS
                       GTP_EFTU_D4  60 akaGqevaisiegkivG 76 
                                       a   + va ++e++++G
  gi|557693877|ref|YP_008796931.1| 463 AAGVKMVAEMLEEAVAG 479
                                       33334455555555555 PP

  == domain 2  score: 110.2 bits;  conditional E-value: 1.3e-35
                                       S-CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTT CS
                       GTP_EFTU_D4   1 rPgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGr 77 
                                       +Pgkikil++++frrs+paivGvev++G ++pgv+l++++G++vG+++qiqd+g++++ akaG++va+si++++vGr
  gi|557693877|ref|YP_008796931.1| 620 KPGKIKILKDFIFRRSEPAIVGVEVVAGEVRPGVQLVNKTGKTVGQLSQIQDRGQAISLAKAGMKVAVSIRDAVVGR 696
                                       7**************************************************************************** PP

                                       S--TT-EEE CS
                       GTP_EFTU_D4  78 qikegdily 86 
                                       +i+ +++ly
  gi|557693877|ref|YP_008796931.1| 697 TIHGDEELY 705
                                       *******98 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 !    7.4   0.0    0.0011       2.8       5      26 ..       7      28 ..       4      49 .. 0.79
   2 !   92.0   0.0   1.3e-29   3.4e-26      50     189 ..     193     372 ..     171     377 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0011
                                      EEEEEESTTSSHHHHHHHHHHH CS
                          GTP_EFTU  5 nigiighvDhGKtTLtdrLlyk 26
                                       ++++ghvDhGK     +L+++
  gi|557693877|ref|YP_008796931.1|  7 IVVVLGHVDHGKCVAPWTLVHE 28
                                      589*********7665555555 PP

  == domain 2  score: 92.0 bits;  conditional E-value: 1.3e-29
                                       HHHTSCSSCEEEEEE...............T.TCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHH CS
                          GTP_EFTU  50 rergiTiksaaisle...............k.etkkylinliDtPGHvdFskevirglrvlDgavlvvdaveGvepq 110
                                       ++ giT ++ a+ +                k + +   i +iDtPGH+ Fs+   rg +v+D+a+lvvd+++Gv++q
  gi|557693877|ref|YP_008796931.1| 193 EAGGITQHIGATIFPiraieetcrqllgelKvKLEIPGILFIDTPGHAAFSNLRKRGGSVADMAILVVDVMKGVQEQ 269
                                       56789999999999999999999999998745899999*************************************** PP

                                       HHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHHHHHHHHH....HHHHHHHHHTTT....... CS
                          GTP_EFTU 111 teevlrlalkegvpiivfiNKmDrl...........kaelkeiveevkqklsrk....eeklekygekge....... 165
                                       t+e ++l++++++p++v+ NK+D++           +++++++ ++v ++l+++    +++l+  g++++       
  gi|557693877|ref|YP_008796931.1| 270 TRESIQLLRSRKTPFVVAANKIDMItgwrptpnapfIKTYNNQHKTVAEDLDNRiynlMGELSFLGFRSDlytrirs 346
                                       ********************************999966666666666666644455566666666666668888888 PP

                                       ..TTEEEEEEBTTTTBTHHHHHHHHH CS
                          GTP_EFTU 166 ..kevpvvfgSalkgegvktllealv 189
                                         ++v +v++Sa++geg+ +ll  l 
  gi|557693877|ref|YP_008796931.1| 347 ftDTVAIVPVSAKTGEGIPDLLLLLL 372
                                       8899****************998776 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.3   1.3e-18   3.4e-15      11     105 .]     505     600 ..     493     600 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 1.3e-18
                                       CSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHH..ST....EEEEEESSSCTHHHH CS
                              IF-2  11 egkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasa..sn....aiiigFnvkvskkak 81 
                                       ++++++v++kaD  G+leA  ++L++ +     v +  +++G+++++Dv  a++  ++    ++i+++ v+v+++ +
  gi|557693877|ref|YP_008796931.1| 505 STDKIGVVVKADALGTLEAAVNYLREKG-----VLIRLADIGDVSKRDVVEAHVvrQKdellGVILAYGVRVDPELE 576
                                       45899*********************84.....89999**************9965225899*************** PP

                                       HCCCCCTSEEEEESSHHHHHHHHH CS
                              IF-2  82 klaekegvkirlynvIYkliddvk 105
                                        +a+++gv+i++++v+++li+d++
  gi|557693877|ref|YP_008796931.1| 577 YEAQSKGVRIFKNDVLFRLIEDYE 600
                                       *********************985 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   1.2e-14     3e-11      37     134 .]      77     177 ..      30     177 .. 0.85
   2 ?   -2.8   0.0       2.2   5.6e+03      51      92 ..     494     536 ..     455     601 .. 0.63

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.2e-14
                                       EEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCT.TEEEEEECCC--TT-EEEEEHSC.EEEEEEEEEEEEEC. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx. RF
                   Intein_splicing  37 svkkliklklkelyeiklesgrkikaTpeHkllvvrd.egivEkradeLkegdliavpdad.vvwdkvksievede. 110
                                        v    + + +++++i+ ++g+++ +TpeH++         + +rad L++gd +   +++ v+   v+++e+ +  
  gi|557693877|ref|YP_008796931.1|  77 AVMLWRRQAPETVIRIHFSNGETVETTPEHPYARAYSsSFYIFTRADRLRPGDRVLSMRKNqVASVAVENVEQVKPc 153
                                       34444455556*********************98877666667***********9998888799999****998876 PP

                                       EEEEEEEEETTT-EEEECTTEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing 111 eeyVYdltvednhNFvangiivHN 134
                                         yVYd+tv+ +h + a++ii+HN
  gi|557693877|ref|YP_008796931.1| 154 YPYVYDFTVPPTHFYEAQEIILHN 177
                                       89*********************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.2
                                       EEEETTS-EEEEETT-EEEECCT.TEEEEEECCC--TT-EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  51 eiklesgrkikaTpeHkllvvrd.egivEkradeLkegdliav 92 
                                       ++  e+++ i  T +  + v  d  g++E  ++ L+e+ +++ 
  gi|557693877|ref|YP_008796931.1| 494 RVAEEAQEFILSTDKIGVVVKADaLGTLEAAVNYLREKGVLIR 536
                                       4444444444445555555555555555555555555555544 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 ?   -1.0   0.0      0.95   2.4e+03      13      26 ..     125     139 ..     124     151 .. 0.70
   2 !   21.3   0.0     1e-07   0.00026       1      73 [.     404     482 ..     404     483 .. 0.88
   3 !    6.3   2.6    0.0049        12       3      73 ..     639     698 ..     638     699 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.95
                                       EETTEEEEEEC.TCT CS
                       GTP_EFTU_D2  13 lkkGdevrilg.ndt 26 
                                       l++Gd+v  ++ n++
  gi|557693877|ref|YP_008796931.1| 125 LRPGDRVLSMRkNQV 139
                                       89******9765544 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 1e-07
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEE...........ETTSEEEEEEEESSCCSG CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededea...........vaganaGvivaikgleda 66 
                                       G +a + + +Gtl++Gd+v +  + t + +i++r+++l+ + +++de               a+aGv+  +  le+a
  gi|557693877|ref|YP_008796931.1| 404 GATANILIHTGTLRVGDKVAF--L-TRRGPITSRVKALLLP-KPLDEIrdprdrlknisQISAAAGVKMVAEMLEEA 476
                                       567778899************..7.45779***********.77999989999999999999999999999999997 PP

                                       SSTTCEE CS
                       GTP_EFTU_D2  67 iivGdtl 73 
                                        ++G+++
  gi|557693877|ref|YP_008796931.1| 477 -VAGSPI 482
                                       .999876 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0049
                                       EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       ++++ v+ G++++G ++++  + t +k    ++++l    +d  +a+  a aG +va+  + da +vG t+
  gi|557693877|ref|YP_008796931.1| 639 IVGVEVVAGEVRPGVQLVN--K-T-GK----TVGQLSQI-QDRGQAISLAKAGMKVAV-SIRDA-VVGRTI 698
                                       78999*************9..6.5.44....79999999.88999************5.99998.999998 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.8   1.2e+04       2      41 ..       8      49 ..       8      55 .. 0.72
   2 !   16.8   0.0   2.1e-06    0.0053      47     114 .]     217     290 ..     178     290 .. 0.61

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.8
                                      EEEEESTTSSHHHHHHHHHTS..TEEESSSTTSSSSEEEEEE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge..kaivsdkpgtTrdinegrv 41
                                      v+++G+   GK     +l+ e  +  vs++   Tr ++ grv
  gi|557693877|ref|YP_008796931.1|  8 VVVLGHVDHGKCVAPWTLVHEagEGYVSAEDIFTRYTRDGRV 49
                                      678888888988777777776555677777777777777766 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 2.1e-06
                                       E.............EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEE CS
                          MMR_HSR1  47 e.............ielvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkpli 109
                                       +             i ++DtpG  +       +++  ++  + ad+++lvvd+  ++++++ +e  +ll+++k p++
  gi|557693877|ref|YP_008796931.1| 217 QllgelkvkleipgILFIDTPG--H-----AAFSNLRKRGGSvADMAILVVDVM-KGVQEQTRESIQLLRSRKTPFV 285
                                       144444444444559*******..3.....22333333333347********87.77999*********99****** PP

                                       EEEES CS
                          MMR_HSR1 110 lvlnk 114
                                       +++nk
  gi|557693877|ref|YP_008796931.1| 286 VAANK 290
                                       **998 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 ?   12.9   0.0   2.7e-05      0.07      66     234 ..     202     370 ..     187     377 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                        ATP_bind_1  66 galvvaleflresldwldeeleke.ed.dyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptk 140
                                       ga+++ +  ++e++ +l  el+ + e    l +DtPG   + ++++ +         ++a +++ +vD+    +  +
  gi|557693877|ref|YP_008796931.1| 202 GATIFPIRAIEETCRQLLGELKVKlEIpGILFIDTPGHAAFSNLRKRGG--------SVADMAILVVDVMKGVQEQT 270
                                       788888889999999999999766555678999**************99........88888999999877666444 PP

                        ATP_bind_1 141 fisgllsalsamlrlelPhvvvlnkfDllkek....lekeleffedvealslllekee............ekykkla 201
                                         s     ++ + + ++P+vv+ nk+D++       +   ++ ++  ++ + ++++++            +      
  gi|557693877|ref|YP_008796931.1| 271 RES-----IQLLRSRKTPFVVAANKIDMITGWrptpNAPFIKTYN-NQHKTVAEDLDNriynlmgelsflG----FR 337
                                       433.....4667779*************99667544222222222.1222222333336787776643333....34 PP

                        ATP_bind_1 202 eaiaelleefalvlrflplssekeesiedllsl 234
                                       +++   +  f+ +  ++p+s++++e+i dll l
  gi|557693877|ref|YP_008796931.1| 338 SDLYTRIRSFTDTVAIVPVSAKTGEGIPDLLLL 370
                                       556666666666666779999999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (748 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); 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 0.27s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 5181.40
//
Query:       gi|557693878|ref|YP_008796932.1|  [L=326]
Description: O-sialoglycoprotein endopeptidase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-78  262.9   0.1    4.6e-78  262.6   0.1    1.0  1  Peptidase_M22    Glycoprotease family
     0.0024   17.4   0.0        1.5    8.2   0.0    2.1  2  BcrAD_BadFG      BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
       0.09   12.8   0.1       0.16   12.0   0.1    1.4  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
       0.14   12.4   0.6        7.1    6.9   0.3    2.2  2  baeRF_family10   Bacterial archaeo-eukaryotic release factor 


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 !  262.6   0.1     1e-81   4.6e-78       2     271 .]      25     292 ..      24     292 .. 0.96

  Alignments for each domain:
  == domain 1  score: 262.6 bits;  conditional E-value: 1e-81
                                       CEXEEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHH CS
                     Peptidase_M22   2 vlanvvasqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglal 78 
                                       +lan+ + +k   +++GG++P++a+++H+ +  +++eea+++ag++++++da+a+++gPG++++Lr G+++A+++a 
  gi|557693878|ref|YP_008796932.1|  25 ILANIQKIYK---PAKGGIHPREAAQHHAAKAAEALEEAFKKAGIKPSEIDAVAFSQGPGMGPCLRTGATVARTIAT 98 
                                       5655555555...889************************************************************* PP

                                       HCT--EEEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCC CS
                     Peptidase_M22  79 alnkPlvgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypgg 155
                                        l kPl+gVnh +ah++ ++l ++  +Pvvl+v Gg+t + +  ++ry+ilgetld+aag++ld+++ + g++  + 
  gi|557693878|ref|YP_008796932.1|  99 VLRKPLIGVNHGIAHIEIGKLVTGCGEPVVLYVAGGNTLLTAFVNKRYRILGETLDIAAGNCLDSFGITAGIGPMPA 175
                                       **********************87789****************99****************************9999 PP

                                       HHHHHHHCTC.S.......EETTEEE.CHHHHHHHHHHST.T.HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEE CS
                     Peptidase_M22 156 pkieklakeg.kkiefprplkgldfsfsGlktavlkelek.e.vedlaasfqeavvdhlvekteralklpkakelvi 229
                                       p+i+  a+eg + +e+p+ +kg+d+sfsG+ ta  k+l++ + + d++ s++e+v ++l+e++eral+  ++++l++
  gi|557693878|ref|YP_008796932.1| 176 PEIK--ASEGnTIYELPYRVKGMDVSFSGILTASEKLLQQgKpIPDVCLSLTETVYSMLTEVAERALAMLDKSSLLL 250
                                       9999..999*666*************************88769********************************** PP

                                       ESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
                     Peptidase_M22 230 lGGvaankrLrealeeeaeelglkliiPplkyctdnaamiaw 271
                                       +GG a  +rL ++le++++++g+++++ p +y  dn+amiaw
  gi|557693878|ref|YP_008796932.1| 251 VGGLARSRRLYNMLETMCRDRGARVYVVPDEYAGDNGAMIAW 292
                                       *****************************************9 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 !    7.3   0.0   0.00066         3      38      67 ..      47      76 ..      10     144 .. 0.82
   2 !    8.2   0.0   0.00034       1.5     186     260 ..     212     288 ..     203     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00066
                                      ........HHHHHHHHHHT--GGGECEE.. CS
                       BcrAD_BadFG 38 eaaekvleealtealerageeeadieetyl 67
                                      +  +    eal+ea+++ag ++++i+ +++
  gi|557693878|ref|YP_008796932.1| 47 QHHAAKAAEALEEAFKKAGIKPSEIDAVAF 76
                                      345667889***************998865 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00034
                                       HTT--HHHHHHHHHHHHHHHHHHHHHTT---SS...EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHH CS
                       BcrAD_BadFG 186 sggekaedIlaglhraialrvialisrsggvtde..vtltGGvakneaavkelrklvkenygevkininpdsiytga 260
                                       ++g+   d+   l + + + + ++++r  +  d+  ++l+GG+a++  ++++l+++   +  +v++  + ++  +ga
  gi|557693878|ref|YP_008796932.1| 212 QQGKPIPDVCLSLTETVYSMLTEVAERALAMLDKssLLLVGGLARSRRLYNMLETMCRDRGARVYVVPDEYAGDNGA 288
                                       55555666666777777778888888877777777899*************************97655555555544 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 ?   12.0   0.1   3.7e-05      0.16      13      48 ..      39      75 ..      26      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.7e-05
                                      -.STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE CS
                   Ketoacyl-synt_C 13 g.ahnsltapngeaqaraiekalaeagvdpedvdyve 48
                                      g +   + + +++++a+a+e+a+++ag++p+++d v 
  gi|557693878|ref|YP_008796932.1| 39 GiHPREAAQHHAAKAAEALEEAFKKAGIKPSEIDAVA 75
                                      55555666778888899*****************985 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 ?    6.9   0.3    0.0016       7.1      66      89 ..      43      66 ..      39      68 .. 0.90
   2 ?    3.6   0.0     0.017        75      69     124 ..     225     280 ..     223     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0016
                    baeRF_family10 66 eeqaerhlkevAellaklleergv 89
                                      +e a++h+ ++Ae+l++++++ g+
  gi|557693878|ref|YP_008796932.1| 43 REAAQHHAAKAAEALEEAFKKAGI 66
                                      7899****************9987 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.017
                    baeRF_family10  69 aerhlkevAellaklleergverlvlgGdeeetaalldrlpkalrarvvgtlplpv 124
                                       +e  +  ++e+++++l+  +   l+l+G+ +    l + l    r+r +   ++p+
  gi|557693878|ref|YP_008796932.1| 225 TETVYSMLTEVAERALAMLDKSSLLLVGGLARSRRLYNMLETMCRDRGARVYVVPD 280
                                       677899999*********99999***999999999999999988888777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2444.93
//
Query:       gi|557693879|ref|YP_008796933.1|  [L=214]
Description: Mn2+-dependent serine/threonine protein kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   35.2   0.0    1.3e-08   34.6   0.0    1.3  1  RIO1         RIO1 family
    1.2e-08   35.2   1.6      3e-05   24.1   0.1    2.2  2  APH          Phosphotransferase enzyme family
    1.4e-07   31.0   0.0    1.3e-06   27.9   0.0    2.0  1  Kdo          Lipopolysaccharide kinase (Kdo/WaaP) family
    3.7e-07   29.8   0.0      5e-07   29.4   0.0    1.2  1  Pkinase      Protein kinase domain
    0.00095   18.5   0.0     0.0016   17.8   0.0    1.5  1  Pkinase_Tyr  Protein tyrosine kinase
  ------ inclusion threshold ------
      0.023   14.0   0.0      0.025   13.9   0.0    1.1  1  DUF4135      Domain of unknown function (DUF4135)
      0.085   12.2   0.0       0.12   11.7   0.0    1.3  1  APH_6_hur    Aminoglycoside/hydroxyurea antibiotic resistance


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 !   34.6   0.0   5.2e-12   1.3e-08      50     150 ..      50     144 ..      30     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 5.2e-12
                                       HHHHHHHHHHHHHHHHHHTT--S--EE..EEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHT CS
                              RIO1  50 lvklwaekEfrnLkrleeagvpvPkpi..elkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklyke 124
                                       + +  +  E + L+ l+e g pvP ++  +l + ++ m+fi+  gv++   +  +     +e + e+++     ++ 
  gi|557693879|ref|YP_008796933.1|  50 VRRSRTLHEAKVLSHLSENGQPVPLVLflDLANSIIYMQFIE--GVELRSHHSPQ---RYAERLGEIVS----SMHS 117
                                       55666789****************995338899*********..88876655555...44555555555....5556 PP

                                       STEEESS-STTSEEEETT.EEEE--GT CS
                              RIO1 125 aglvHaDLSeyNvlvded.kvviIDvs 150
                                       + +vH+DL   N+l  ed +++++D++
  gi|557693879|ref|YP_008796933.1| 118 MDIVHGDLTLANILAGEDtGLWLVDFG 144
                                       77***********************97 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   1.2e-08     3e-05      34     109 ..      52     119 ..       9     120 .. 0.82
   2 !   10.9   0.2   0.00012      0.31     168     196 ..     120     146 ..     119     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.2e-08
                                       HHHHHHHHHHHHHHHHTT-B--B-CTTBS-EEETTEEEEEEE----EE-SSHHHHHHHHHHHHHHHHHHCCHHCH. CS
                               APH  34 aeeirrevallrlLakagvpvPevlagdtddeeigllfalieyvpgrsllrklsaaqlpellealgeflaalhqvd 109
                                         ++  e+++l +L+++g pvP vl +d  +  i+  +++ie+v+ rs +        ++++e+lge    +h++d
  gi|557693879|ref|YP_008796933.1|  52 RSRTLHEAKVLSHLSENGQPVPLVLFLDLANSIIY--MQFIEGVELRSHHS------PQRYAERLGEIVSSMHSMD 119
                                       446778999*****************755555555..9*************......8999999999999999885 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00012
                                       EE-SS-SGGGEEEC..TTEEEEE---TT- CS
                               APH 168 llHgDlhpgNllvdpddgrvtGviDfeda 196
                                       ++HgDl + N+l  +d g    ++Df+++
  gi|557693879|ref|YP_008796933.1| 120 IVHGDLTLANILAGEDTGLW--LVDFGLS 146
                                       79************666666..****986 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0     5e-10   1.3e-06     115     202 ..      96     179 ..       4     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 5e-10
                               Kdo 115 laeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliDldkarlrlradrwrekdLarLkrsfl 191
                                        ++++ ++  +++g +++ +h++++ H+dl   nil  ++      +wl+D+  ++  +     +  d++ L+rs+ 
  gi|557693879|ref|YP_008796933.1|  96 RSHHSPQRYAERLGEIVSSMHSMDIVHGDLTLANILAGEDT----GLWLVDFGLSAFNA-DLEEKAVDIHLLERSAA 167
                                       467889999***************************99888....9*******999998.77788889999999977 PP

                               Kdo 192 .kielteadwea 202
                                        +   + +++ +
  gi|557693879|ref|YP_008796933.1| 168 gSFPDKAREFMQ 179
                                       655555555444 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.9e-10     5e-07      70     147 ..      71     148 ..      22     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.9e-10
                                       SSEEEEEEE--TTEBHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSE CS
                           Pkinase  70 kdelylvleyveggeladllerkgslseeeakkiakqilegleylHskgiiHrDlKpeNiLidekgelKitDFGlak 146
                                       +  l+l+l++++   +++++e     s++  +++a+++ e ++ +Hs+ i+H Dl  +NiL  e+  l ++DFGl++
  gi|557693879|ref|YP_008796933.1|  71 PVPLVLFLDLANSIIYMQFIEGVELRSHHSPQRYAERLGEIVSSMHSMDIVHGDLTLANILAGEDTGLWLVDFGLSA 147
                                       4445566666666666666665555666677999*****************************9999********97 PP

                                       E CS
                           Pkinase 147 e 147
                                        
  gi|557693879|ref|YP_008796933.1| 148 F 148
                                       6 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.2e-07    0.0016     115     152 ..     111     148 ..      11     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.2e-07
                                       HHHHHHHTTEEEST-SGGGEEEEETTEEEE-STTTHEE CS
                       Pkinase_Tyr 115 GmeyLeskklvHrdlaarNvLlsenkvvkisDfGLard 152
                                        ++ ++s+++vH dl+  N+L  e++   + DfGL+  
  gi|557693879|ref|YP_008796933.1| 111 IVSSMHSMDIVHGDLTLANILAGEDTGLWLVDFGLSAF 148
                                       4566899****************************975 PP

>> DUF4135  Domain of unknown function (DUF4135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.7e-06     0.025     106     175 ..      61     147 ..      28     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-06
                           DUF4135 106 vlkvldr..............geYgWvefvehqpcaseeeverfYrraGallallyllgg..tDlheeNliasgeq. 165
                                       vl  l+               ++  +++f+e  +++s+ + +r+ +r+G+++  ++ +++   Dl   N++a  +  
  gi|557693879|ref|YP_008796933.1|  61 VLSHLSEngqpvplvlfldlaNSIIYMQFIEGVELRSHHSPQRYAERLGEIVSSMHSMDIvhGDLTLANILAGEDTg 137
                                       4444444555555555555558889*********************************99446*******9987776 PP

                           DUF4135 166 pvliDlEtll 175
                                       ++l+D+    
  gi|557693879|ref|YP_008796933.1| 138 LWLVDFGLSA 147
                                       9999987554 PP

>> APH_6_hur  Aminoglycoside/hydroxyurea antibiotic resistance kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.8e-05      0.12     146     181 ..     105     141 ..      47     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.8e-05
                         APH_6_hur 146 aaiaaeLleepselrpLHgdlhhenvLagerrg.Wla 181
                                       a    e++++ + +   Hgdl  +n+Lage+ g Wl+
  gi|557693879|ref|YP_008796933.1| 105 AERLGEIVSSMHSMDIVHGDLTLANILAGEDTGlWLV 141
                                       555567899999999****************986775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1570.49
//
Query:       gi|557693880|ref|YP_008796934.1|  [L=192]
Description: nucleoside-triphosphatase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-48  164.3   0.0    3.2e-48  164.1   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 !  164.1   0.0   1.8e-52   3.2e-48       1     187 []       6     181 ..       6     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 164.1 bits;  conditional E-value: 1.8e-52
                                       EEEC-S-HHHHHHHHHHTTTECCCE...EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGG CS
                        Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevk..slkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaL 73 
                                       ++f+T+N++K++ev++i+++++l++k  s+      ++ E+q ++++e+a + a +a++  ++p++++DsgL+++aL
  gi|557693880|ref|YP_008796934.1|   6 LIFVTSNPHKAEEVSQIFKKHGLRLKihSM------KTLEVQsTSLAEIACISAAQAYAnLEKPLFVEDSGLFIEAL 76 
                                       69****************996665553244......434999999*********9988646788************* PP

                                       TTTBGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTT CS
                        Ham1p_like  74 nglPGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGy 150
                                       +g+PG+ys+++      ++ +l+ +l+ +    e+r+A f+++++l+   +++ ++f+Ge  G+i+eeprg +gfG+
  gi|557693880|ref|YP_008796934.1|  77 KGFPGPYSSYVY-----KTIGLDGVLKLVG---ERREAVFKSIICLYGL-KDRPIFFSGESLGSIAEEPRGVHGFGF 144
                                       ***********6.....356999******6...469**********986.7777*********************** PP

                                       GGGEEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHHH CS
                        Ham1p_like 151 DpiFvpeegektfaelskeeknaiShRgkAlekllef 187
                                       DpiF+p+++ kt+ae+s eekn++ShRg+A+e+l+++
  gi|557693880|ref|YP_008796934.1| 145 DPIFIPRGSRKTLAEMSLEEKNRFSHRGRAVESLVKW 181
                                       ******76566***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1394.46
//
Query:       gi|557693881|ref|YP_008796935.1|  [L=144]
Description: small subunit ribosomal protein S15 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-28   98.1   0.4    3.5e-28   97.4   0.4    1.4  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
      1e-11   44.9   0.4    1.4e-11   44.4   0.4    1.2  1  Ribosomal_S15    Ribosomal protein S15
  ------ inclusion threshold ------
      0.022   14.3   0.1      0.088   12.4   0.1    1.8  2  NUDIX_2          Nucleotide hydrolase


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 !   97.4   0.4   5.9e-32   3.5e-28       1      60 []       1      60 [.       1      60 [. 1.00

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 5.9e-32
                                      X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                   Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                      Marmh++++GkSgS+rP+++ +p Wlkl +eeve+l++k+ak+G++pS+IGv+LRDq+Gv
  gi|557693881|ref|YP_008796935.1|  1 MARMHASKRGKSGSTRPLSKIPPPWLKLMPEEVESLVIKYAKEGMPPSMIGVVLRDQHGV 60
                                      ***********************************************************8 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.4   2.4e-15   1.4e-11       4      67 ..      74     133 ..      72     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 2.4e-15
                                       HHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Ribosomal_S15   4 likefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkd 67 
                                       +++e++ ++     +++++ +l e+I++++ hl++nk D h+  +L++++sk r+l+kY+k++ 
  gi|557693881|ref|YP_008796935.1|  74 ILEENNLKP----PVPEDLQNLLEKIRRMRIHLEKNKSDGHNIHRLQLVESKVRRLVKYYKSRG 133
                                       678888888....899*********************************************976 PP

>> NUDIX_2  Nucleotide hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.5e-05     0.088      27      79 ..      30      82 ..      25     116 .. 0.71
   2 ?    0.2   0.0      0.08   4.8e+02      19      42 ..     111     134 ..     100     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                           NUDIX_2 27 eeklkrlkesyekeglrrtveavllvhrhelphvLlLqielqefkLpggklks 79
                                       e+++ l  +y+keg+  ++ +v+l ++h++p v     ++    L +++lk+
  gi|557693881|ref|YP_008796935.1| 30 PEEVESLVIKYAKEGMPPSMIGVVLRDQHGVPLVKTVTGKTILQILEENNLKP 82
                                      678889999***********************997766666556666666664 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.08
                           NUDIX_2  19 lkekdksveeklkrlkesyekegl 42 
                                       + ++ ++ve+k++rl + y+++g+
  gi|557693881|ref|YP_008796935.1| 111 NIHRLQLVESKVRRLVKYYKSRGI 134
                                       4556689999*********99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       680  (0.0379274); 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:                         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 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1057.66
//
Query:       gi|557693882|ref|YP_008796936.1|  [L=488]
Description: archaea-specific RecJ-like exonuclease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   59.5   0.2    1.5e-15   57.9   0.2    2.0  1  DHHA1           DHHA1 domain
  ------ inclusion threshold ------
      0.079   12.5   0.0       0.13   11.8   0.0    1.3  1  VitK2_biosynth  Menaquinone biosynthesis


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 !   57.9   0.2   1.6e-19   1.5e-15      42     137 ..     371     472 ..     332     473 .. 0.78

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.6e-19
                                       EEEEECHCCHHHHHHHHHHHHHHTHG...BT.TCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCC CS
                             DHHA1  42 vlvaevgeewdagalgiaadklkskl...kk.pvivfvakeegdkvkvsarskkd....gvdagelakeaaaklggg 110
                                       ++v + g+ +d + + ++a+ l s     ++ p i+++ + +  +vk+sar++k+    g+++g++++++ a++gg+
  gi|557693882|ref|YP_008796936.1| 371 IVVLKGGDVIDYRQVSSVASILSSSGllpPDkPLIALANAGK--TVKISARASKQlvdrGLNLGAILSRLGAQFGGK 445
                                       444444577777889999999999656675547777776654..9********99********************** PP

                                       EEEETCEEEEEEEHCHHHHHHHHHHHH CS
                             DHHA1 111 GGGHdlAaGagipaekleealealeea 137
                                       GGGH+ AaGa ip + + ++l++l++ 
  gi|557693882|ref|YP_008796936.1| 446 GGGHNIAAGAEIPYDHMIKFLAELDKT 472
                                       ***********************9987 PP

>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.4e-05      0.13      32      96 ..     276     340 ..     265     356 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.4e-05
                                       EEEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEEESSSSEEEEESS-CCC-SS CS
                    VitK2_biosynth  32 ivledpetlnrallegelDvakiSsaayariaddyalLpdlsisalGrvygvllvskvpleeleg 96 
                                       + ++ p+t++++l  +++D++k S+  y+  a ++a L ++++ + +   g+l+      e le+
  gi|557693882|ref|YP_008796936.1| 276 VSKNLPTTIANELIGKTYDLVKESVWTYLSDAREFATLLNACGKSGKAWAGILVAMGARSEALEE 340
                                       566789***********************************************998444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3487.52
//
Query:       gi|557693883|ref|YP_008796937.1|  [L=82]
Description: hypothetical protein CSUB_C0446 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.036   14.2   0.1      0.045   13.9   0.1    1.3  1  Pcc1      Transcription factor Pcc1
       0.13   12.2   0.0       0.18   11.8   0.0    1.2  1  DUF3501   Protein of unknown function (DUF3501)


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     5e-06     0.045       4      63 ..       5      65 ..       2      76 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-06
                                      EEEE-SSHHHHHHHHHHHHHHCHC-TTECEEEEEEETTEEEEEEEE.SSHHHHHHHHHHHH CS
                              Pcc1  4 isvpfpterlAsialrtLqvDkelsplavkrslslegnvLqveykA.ttnrmLRvavngfl 63
                                      i++  +++++A +++++L++D ++ p    ++ + e+  ++v++     + ++ ++v+ +l
  gi|557693883|ref|YP_008796937.1|  5 ITIRPKNSQDAIAIYNALKPDDKPLPRGLFVETRQENDAVVVDIVCeRGLASFLATVDDIL 65
                                      677778999************7777766888888888888886655223444444444444 PP

>> DUF3501  Protein of unknown function (DUF3501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     2e-05      0.18      65      99 ..       9      43 ..       4      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2e-05
                                      HHHHHHHHHHHGGGS--SSEEEEEEEE--SSHHHH CS
                           DUF3501 65 eeeiqeeleaYneLlPdgselkatlfieiededer 99
                                      +++ q+++ +Yn+L Pd++ l   lf+e ++e++ 
  gi|557693883|ref|YP_008796937.1|  9 PKNSQDAIAIYNALKPDDKPLPRGLFVETRQENDA 43
                                      67889************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 00:00:00.41
# Mc/sec: 602.72
//
Query:       gi|557693884|ref|YP_008796938.1|  [L=206]
Description: small subunit ribosomal protein S3Ae [Candidatus Caldiarchaeum subterraneum]
Scores for 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-56  189.4   0.5    6.5e-56  189.1   0.5    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family


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 !  189.1   0.5   3.6e-60   6.5e-56       3     200 ..       4     190 ..       2     191 .. 0.98

  Alignments for each domain:
  == domain 1  score: 189.1 bits;  conditional E-value: 3.6e-60
                                       ----S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCS.HTSSSEEEEEEEEEE CS
                    Ribosomal_S3Ae   3 kkkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtnde.keqafrklklkieev 78 
                                       +kkv ++ k K+ y+v+aP +fg r +G+t++       ++++k+ grv+ +sl+ +t+d+ k+  ++ +++ki+ev
  gi|557693884|ref|YP_008796938.1|   4 SKKVSEQKKPKKVYEVYAPPYFGGRWLGSTVA-------DDPSKVLGRVLRTSLYAITDDFtKQ--YMLMRFKITEV 71 
                                       6899****************************.......**********************666..*********** PP

                                       ESSEEEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHH CS
                    Ribosomal_S3Ae  79 qgknaltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilte 155
                                       +++ + t F+g+e+ r++lrslv++++++Ie i+dv+t Dg+++rv +v+fT++r   + ss+k+aIrk+m+e+l+e
  gi|557693884|ref|YP_008796938.1|  72 KDSVCNTVFYGHEYGREYLRSLVKRGTNKIEYIFDVTTRDGFVIRVYPVVFTTSR---ISSSKKRAIRKTMREVLEE 145
                                       *******************************************************...******************* PP

                                       HHHHS-HHHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE CS
                    Ribosomal_S3Ae 156 easeldlkelvkklipeslgkeiekeakkIyplrnveirKvkvlk 200
                                        a++l+ ++l ++l+  +++++i++++kkI+  r+v ++K+k++k
  gi|557693884|ref|YP_008796938.1| 146 AAANLTHDQLAQELVLGKTASDIYNRVKKIVLPRHVGVYKSKIIK 190
                                       ****************77*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1564.90
//
Query:       gi|557693885|ref|YP_008796939.1|  [L=109]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   88.8   0.9    3.6e-25   88.4   0.9    1.2  1  DUF2095       Uncharacterized protein conserved in archaea (D
  ------ inclusion threshold ------
      0.033   13.5   0.3      0.036   13.4   0.3    1.1  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
        1.4    8.8   4.6        3.8    7.4   0.0    2.7  3  SHOCT         Short C-terminal domain


Domain annotation for each model (and alignments):
>> DUF2095  Uncharacterized protein conserved in archaea (DUF2095)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.9     6e-29   3.6e-25      14     127 ..       2     108 ..       1     109 [] 0.88

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 6e-29
                           DUF2095  14 eydleefkrrfpalareleeer.gleidairldeeevleeeeeegkidfsgynptiidflrrcetdeealeiinwme 89 
                                       e d+eef+rrfpal +e+ e r  l i+++r  +e + +e         +   pt+id+lrrc+t+e+  e+in++ 
  gi|557693885|ref|YP_008796939.1|   2 EIDVEEFRRRFPALYKEMVERRmALRISGVRNMKEFAEDEA--------AHKGPTVIDYLRRCDTEEQGREVINYLR 70 
                                       78***************977653799999997655442222........2357************************ PP

                           DUF2095  90 ergeithemakelrvvlvkkgvrafgpkkewgwyerhg 127
                                       +rgei++e a  l   l +kg+r+fg +k+ g y r g
  gi|557693885|ref|YP_008796939.1|  71 NRGEISEETAESLLKQLDEKGIRSFGSRKQPGHYLREG 108
                                       **********************************9987 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3     6e-06     0.036     101     173 ..       4      73 ..       1      89 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6e-06
                                       SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHH..HHHHHHHHHHTT---B-TT-...................... CS
                      FtsK_SpoIIIE 101 dperalraleeLvkemeeryalfreagvrsiaa..ydgeiaedpldifgdvflvlDnyddlaaene...ritsLsnq 172
                                       d+e+ +r + +L kem er   +r +gvr+++    d+ + + p+        v+D  +   +e++    i+ L n+
  gi|557693885|ref|YP_008796939.1|   4 DVEEFRRRFPALYKEMVERRMALRISGVRNMKEfaEDEAAHKGPT--------VIDYLRRCDTEEQgreVINYLRNR 72 
                                       78999999************************9533333333333........456666666666666677788887 PP

                                       . CS
                      FtsK_SpoIIIE 173 g 173
                                       g
  gi|557693885|ref|YP_008796939.1|  73 G 73 
                                       7 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2     0.017     1e+02      14      23 ..       2      11 ..       2      11 .. 0.90
   2 ?    7.4   0.0   0.00063       3.8       9      18 ..      69      78 ..      66      79 .. 0.92
   3 ?   -3.3   0.1       1.4   8.7e+03       3       8 ..      84      89 ..      82      89 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.017
                             SHOCT 14 eIteEEFeak 23
                                      eI+ EEF+++
  gi|557693885|ref|YP_008796939.1|  2 EIDVEEFRRR 11
                                      8999***997 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00063
                             SHOCT  9 LyarGeIteE 18
                                      L+ rGeI+eE
  gi|557693885|ref|YP_008796939.1| 69 LRNRGEISEE 78
                                      899******9 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.4
                             SHOCT  3 LekLke 8 
                                      L++L+e
  gi|557693885|ref|YP_008796939.1| 84 LKQLDE 89
                                      666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
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 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 864.96
//
Query:       gi|557693886|ref|YP_008796940.1|  [L=402]
Description: translation-associated GTPase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  114.9   0.1    4.2e-33  114.3   0.1    1.3  1  MMR_HSR1_C     GTPase of unknown function C-terminal
    1.7e-20   73.2   0.0    8.5e-20   71.0   0.0    2.2  2  MMR_HSR1       50S ribosome-binding GTPase
    1.9e-08   34.0   0.7    5.9e-07   29.1   0.2    2.7  3  FeoB_N         Ferrous iron transport protein B
    3.8e-08   33.3   0.0    7.7e-08   32.3   0.0    1.5  1  TGS            TGS domain
      0.008   15.7   0.1        4.1    6.9   0.0    2.7  2  GTP_EFTU       Elongation factor Tu GTP binding domain
     0.0095   15.7   0.0       0.75    9.5   0.0    2.6  3  ATP_bind_1     Conserved hypothetical ATP binding protein
  ------ inclusion threshold ------
       0.11   13.0   0.2       0.32   11.5   0.0    1.9  2  CoA_binding_2  CoA binding domain
       0.16   12.6   0.0       0.45   11.1   0.0    1.7  1  AAA_18         AAA domain
        0.2   11.6   0.0       0.37   10.7   0.0    1.4  1  YARHG          YARHG domain
       0.21   11.4   0.4         21    5.0   0.0    2.5  3  RsgA_GTPase    RsgA GTPase


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 !  114.3   0.1   2.3e-36   4.2e-33       1     112 []     224     330 ..     224     330 .. 0.97

  Alignments for each domain:
  == domain 1  score: 114.3 bits;  conditional E-value: 2.3e-36
                        MMR_HSR1_C   1 alNKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLeki 77 
                                       a+NKaD++ +++n+ekl ++     +vvpvsA+aE  Lr aa++gl+kY +gd+dfe+ +d+  +l+ +qkkaLe+i
  gi|557693886|ref|YP_008796940.1| 224 AANKADVKGSEKNVEKLVQHGY---DVVPVSAEAERTLRLAASKGLVKYVSGDSDFEVVDDS--KLTPQQKKALEYI 295
                                       89******************77...59**********************************5..5************ PP

                        MMR_HSR1_C  78 rdlvlkrygsTGVqealnaavfelldlivVYPVed 112
                                       r++v++r+g+TGVq+++n a  e l++i+VYPVe+
  gi|557693886|ref|YP_008796940.1| 296 RENVFERWGGTGVQKLVNMAYLEKLGYIPVYPVEN 330
                                       *********************************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 !   71.0   0.0   4.7e-23   8.5e-20       3      87 ..       5     123 ..       3     165 .. 0.76
   2 ?   -1.5   0.0       1.5   2.6e+03      95     114 .]     208     227 ..     152     227 .. 0.69

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 4.7e-23
                                       EEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEE.......ETTEE....................EEEEE CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvk.......lkgke....................ielvD 52 
                                       +ivG+pNvGKStL++al+  +++++++p+tT+++n g          +   +                    i+++D
  gi|557693886|ref|YP_008796940.1|   5 GIVGKPNVGKSTLFSALSMVNVEIANYPFTTKKTNVGVTYvrvecvcK---KlgikdnprnsiciegvrlvpIQIID 78 
                                       8************************************76633334330...034444456667777777777***** PP

                                       CGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT.........T CS
                          MMR_HSR1  53 tpGliegaseekglgkaflalee.adlillvvdas.........e 87 
                                       +pG+i +a+++kglg +fl+ ++ a+l+++v d+s          
  gi|557693886|ref|YP_008796940.1|  79 CPGIIREAHKGKGLGLKFLDEIRqASLLIIVADVSgatladgtpA 123
                                       ***9999************977769********886555544440 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                                       HHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  95 eeleelleeakkplilvlnk 114
                                        +l+ +++++ kp+i+++nk
  gi|557693886|ref|YP_008796940.1| 208 LRLATMIRRRSKPFIVAANK 227
                                       34566666688888888887 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 !   29.1   0.2   3.3e-10   5.9e-07       5      42 ..       6      43 ..       2      60 .. 0.84
   2 ?   -3.0   0.0       2.5   4.5e+03      49      57 ..      74      82 ..      70      90 .. 0.86
   3 ?    2.3   0.0      0.06   1.1e+02      95     148 ..     208     257 ..     165     263 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.3e-10
                                      EEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEE CS
                            FeoB_N  5 lvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegkl 42
                                      +vG+pnvGk+tlf al+ ++ +++N+p +t + + g +
  gi|557693886|ref|YP_008796940.1|  6 IVGKPNVGKSTLFSALSMVNVEIANYPFTTKKTNVGVT 43
                                      89*************************99977776654 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.5
                                      EEEEE---- CS
                            FeoB_N 49 veivDlPGi 57
                                      ++i+D PGi
  gi|557693886|ref|YP_008796940.1| 74 IQIIDCPGI 82
                                      789****98 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.06
                                       HHHHHHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBT CS
                            FeoB_N  95 LyLtlqllelgvpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkeg 148
                                       L L + +   ++p+++a n+ d+   kg e +++kL ++ g +vv++sa+ ++ 
  gi|557693886|ref|YP_008796940.1| 208 LRLATMIRRRSKPFIVAANKADV---KGSEKNVEKLVQH-GYDVVPVSAEAERT 257
                                       66777788888999999999886...6677788999876.99999999988765 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.0   4.3e-11   7.7e-08      12      59 ..     344     396 ..     334     397 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 4.3e-11
                                       E...EETTB-HHHHHHHHSTTHHHHEEEEEECS..EEEETTSBB-SSEEEEEE CS
                               TGS  12 d...lprgatveDfAykIhrslakkfiyAlVnG..qrvgldhvLedgdvveIv 59 
                                       d   +pr++t++++AykIh++l++  +yA   +   r   dh L+ g +v+Iv
  gi|557693886|ref|YP_008796940.1| 344 DvylMPRNSTPRQLAYKIHTELGEGYLYAVDAKtgLRLADDHLLQPGEIVSIV 396
                                       35559**************************99889****************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 !    6.9   0.0    0.0023       4.1       6      39 ..       4      37 ..       1      84 [. 0.60
   2 !    6.0   0.0    0.0043       7.8     115     150 ..     211     248 ..     204     319 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0023
                                      EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHH CS
                          GTP_EFTU  6 igiighvDhGKtTLtdrLlyktgaiskkgekaee 39
                                       gi+g  + GK+TL  +L + + +i++   ++++
  gi|557693886|ref|YP_008796940.1|  4 AGIVGKPNVGKSTLFSALSMVNVEIANYPFTTKK 37
                                      589***************9999999886555543 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0043
                                       HHHHHHTTTEEEEEEESCGST..HHHHHHHHHHHHHHH CS
                          GTP_EFTU 115 lrlalkegvpiivfiNKmDrl..kaelkeiveevkqkl 150
                                       + +++++  p+iv+ NK+D    +++++++v+  ++ +
  gi|557693886|ref|YP_008796940.1| 211 ATMIRRRSKPFIVAANKADVKgsEKNVEKLVQHGYDVV 248
                                       4567788888*********9988788888888777665 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 ?    3.5   0.0      0.03        54       1      20 [.       6      25 ..       6      34 .. 0.86
   2 ?   -2.7   0.0       2.3   4.2e+03      95     103 ..      76      84 ..      74     113 .. 0.69
   3 !    9.5   0.0   0.00042      0.75     137     180 ..     198     242 ..     170     298 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.03
                        ATP_bind_1  1 vvGpaGsGKttfvgalseil 20
                                      +vG + +GK+t+ +als + 
  gi|557693886|ref|YP_008796940.1|  6 IVGKPNVGKSTLFSALSMVN 25
                                      79*************99765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                        ATP_bind_1  95 lfDtPGQie 103
                                       ++D+PG i+
  gi|557693886|ref|YP_008796940.1|  76 IIDCPGIIR 84 
                                       89***9776 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00042
                        ATP_bind_1 137 dptkfisgllsalsamlrl.elPhvvvlnkfDllkeklekeleff 180
                                       +p+++ +g l+ l++m+r  + P++v+ nk+D+  ++++ e  + 
  gi|557693886|ref|YP_008796940.1| 198 KPVSWREGDLLRLATMIRRrSKPFIVAANKADVKGSEKNVEKLVQ 242
                                       5888899999999999975268***********664433333333 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00018      0.32       5      46 ..     222     263 ..     219     297 .. 0.82
   2 ?   -3.3   0.0         7   1.3e+04      21      34 ..     315     329 ..     313     338 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                                       EET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES- CS
                     CoA_binding_2   5 VvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvy 46 
                                       +v a + + k + k ++ l++hg++vvpV   +e+ l   + 
  gi|557693886|ref|YP_008796940.1| 222 IVAANKADVKGSEKNVEKLVQHGYDVVPVSAEAERTLRLAAS 263
                                       677888888999999***************999887765554 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7
                                       HHHHHHT.--EEEES CS
                     CoA_binding_2  21 ryllehg.lpvvpVn 34 
                                       +yl + g +pv+pV 
  gi|557693886|ref|YP_008796940.1| 315 AYLEKLGyIPVYPVE 329
                                       566666635677763 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.45       3      37 ..       6      56 ..       5      67 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf.................gvnlrdvakengl 37
                                      + G+p vGK+tl  +Ls  + +                  v++ +v+k+ g+
  gi|557693886|ref|YP_008796940.1|  6 IVGKPNVGKSTLFSALSMVN-VeianypfttkktnvgvtYVRVECVCKKLGI 56
                                      89**************5543.2335556666666667777777777777665 PP

>> YARHG  YARHG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00021      0.37       3      76 ..     269     341 ..     267     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                                       THHHH.HH-TTHHHHHHTS-HHHHHHHHHHHHHTTT----SHHHHHHHHT-TT----TT..--GGG--HHHHHH CS
                             YARHG   3 yilpesssrylteeelsnlskeeLkilRNeiYArhGycFktpdlkdyFsskswYepesspefdevvLsedekkn 76 
                                       y++ +s+ + +++++l  + k+ L+++R+ ++ r G    ++  +  + +k+ Y p+++  ++  +L+++e ++
  gi|557693886|ref|YP_008796940.1| 269 YVSGDSDFEVVDDSKLTPQQKKALEYIRENVFERWGGTGVQKLVNMAYLEKLGYIPVYP-VENPHTLTDHEGRV 341
                                       66667777888999999999**************************************5.45589999988665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.024        42     104     121 ..       6      23 ..       2      43 .. 0.83
   2 ?   -4.1   0.0         7   1.3e+04     154     161 ..      75      82 ..      69      83 .. 0.77
   3 ?    5.0   0.0     0.012        21      42      90 ..     214     258 ..     201     274 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.024
                                       EECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase 104 lvGqSGvGKStLinallp 121
                                       +vG+  vGKStL  al  
  gi|557693886|ref|YP_008796940.1|   6 IVGKPNVGKSTLFSALSM 23 
                                       899999******999975 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 7
                                       EEESS-SS CS
                       RsgA_GTPase 154 lliDtPGf 161
                                        +iD PG+
  gi|557693886|ref|YP_008796940.1|  75 QIIDCPGI 82 
                                       39*****8 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.012
                                       HHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTH CS
                       RsgA_GTPase  42 aeekgiepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegl 90 
                                       + ++  + +++ nK+D+  +e+      e+l + gy+v+ vsa+ +++l
  gi|557693886|ref|YP_008796940.1| 214 IRRRSKPFIVAANKADVKGSEK----NVEKLVQHGYDVVPVSAEAERTL 258
                                       4444445667789***998888....67778899*******99966554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3034.83
//
Query:       gi|557693887|ref|YP_008796941.1|  [L=143]
Description: large subunit ribosomal protein L15e [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-43  148.2   3.5    2.5e-43  148.0   3.5    1.0  1  Ribosomal_L15e  Ribosomal L15
  ------ inclusion threshold ------
      0.041   14.1   0.1      0.068   13.4   0.0    1.5  2  GGDEF_2         GGDEF-like domain


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 !  148.0   3.5   2.8e-47   2.5e-43       1     143 [.       3     142 ..       3     143 .] 0.97

  Alignments for each domain:
  == domain 1  score: 148.0 bits;  conditional E-value: 2.8e-47
                                       -SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..--- CS
                    Ribosomal_L15e   1 gaykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskg 77 
                                       ++yk++++lw+++  ++lr  lr+r++ +r+  av+rve+p r+drAr+LGYkakqG+vv+ vrvrrGg  k  ++ 
  gi|557693887|ref|YP_008796941.1|   3 SMYKMMQKLWRERP-EALRSQLRKRMVAWRRMRAVERVEKPLRIDRARELGYKAKQGYVVALVRVRRGGFSK--PRP 76 
                                       79*********885.599999***************************************************..*** PP

                                       SS---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT CS
                    Ribosomal_L15e  78 ktgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairn 143
                                       ++gr+ k  gv + k + s+++ a +r  +++pnl+ L+ Y +++D+ y++yEv+ vDpsh+a++ 
  gi|557693887|ref|YP_008796941.1|  77 RSGRRQKALGVVRHKVNVSMKEEAVQRFIKHFPNLKPLGAYPLAQDSLYRWYEVVAVDPSHPAVQA 142
                                       ***************************************************************986 PP

>> GGDEF_2  GGDEF-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.1   9.5e+03      77      81 ..      20      24 ..      10      36 .. 0.48
   2 ?   13.4   0.0   7.6e-06     0.068       9      31 ..      45      76 ..      37     125 .. 0.68

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.1
                           GGDEF_2 77 lerla 81
                                       ++l+
  gi|557693887|ref|YP_008796941.1| 20 RSQLR 24
                                      22222 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 7.6e-06
                           GGDEF_2  9 lerarrlgldldgpyvvvviel.........e 31
                                      ++rar+lg+  ++ yvv+++++         +
  gi|557693887|ref|YP_008796941.1| 45 IDRARELGYKAKQGYVVALVRVrrggfskprP 76
                                      79********************5555555441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 00:00:00.41
# Mc/sec: 1056.33
//
Query:       gi|557693888|ref|YP_008796942.1|  [L=133]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-24   85.0   0.0    5.5e-24   84.7   0.0    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 !   84.7   0.0   3.1e-28   5.5e-24       2     117 ..       7     117 ..       6     119 .. 0.93

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 3.1e-28
                                       EEEEEEE-TTC-HHHHHHHHHTTSTTSE---EEEEEE-CCC-EEEEEEEEESSHHH.HHHHHHHHHHHCCCCHHHHH CS
                       RNA_binding   2 ievrafvhaTEdeekVlealsnllpeeeveieeeeaeGhygnpitileaelekkka.kkvlkkllellreeeikeLl 77 
                                       +++r++v++TE+ ekV++a++n+l e+    ++++++Gh+g++it+le+  e+ ++  +++k+++ ++  +      
  gi|557693888|ref|YP_008796942.1|   7 LTCRTHVYSTENIEKVKKAVKNILGENILPSSKTSLTGHFGDNITVLEYVGENPDQvGEIFKRVVARVGMSV----- 78 
                                       689**********************9977789*************************************995..... PP

                                       HCCHCCB-TTSEEEEEEEHHHHHTT---BESSSSEEEEEE CS
                       RNA_binding  78 keleervdekgklylrldKQaaylgklslvegddvIkvki 117
                                        ++eer   +gkl++rldKQ+aylg+++  e+ d+Ik+++
  gi|557693888|ref|YP_008796942.1|  79 VGVEERGGGGGKLHIRLDKQKAYLGEVAA-EDIDPIKLEF 117
                                       79**************************9.5567888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 960.59
//
Query:       gi|557693889|ref|YP_008796943.1|  [L=203]
Description: hypothetical protein CSUB_C0452 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1568.04
//
Query:       gi|557693890|ref|YP_008796944.1|  [L=102]
Description: hypothetical protein CSUB_C0453 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   28.1   0.1    5.4e-06   26.6   0.1    1.7  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 !   26.6   0.1     3e-10   5.4e-06      21      98 ..      26      98 ..      11     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 3e-10
                                      HHHHHHHHHHHHHHHHHHHHH--..EEEEEETTTTEEEEEEEGGGHHHHHHHHHT--EETTEEEEEEEEEEESSHHHH CS
                     RNase_P_Rpp14 21 llkairesvqelfGdyglgklgsslsvkyfspatstaiiRcsresyrlvwaaLtlitkiegrpvvfrvvrvsGTikka 98
                                      l +a++e   +l+G  gl + g      ++s   +  +  c +  +  ++ aLtl+++i+++pvv+++v+vsGT++++
  gi|557693890|ref|YP_008796944.1| 26 LENAVKECFIRLYGVEGLVQSGL----RRVSV-GGQPVFLCGHLWVPRLVLALTLVRHIGDTPVVLKTVKVSGTVRSL 98
                                      66777778888888877777766....23333.3455677899999999**************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 731.87
//
Query:       gi|557693891|ref|YP_008796945.1|  [L=223]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   51.9   0.4    7.1e-14   51.9   0.4    2.8  2  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   3.5      0.15   2.8e+03      24      24 ..      68      68 ..      12     109 .. 0.58
   2 !   51.9   0.4     4e-18   7.1e-14       5      92 .]     117     203 ..     113     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.15
                                      T CS
                              CPBP 24 R 24
                                      R
  gi|557693891|ref|YP_008796945.1| 68 R 68
                                      2 PP

  == domain 2  score: 51.9 bits;  conditional E-value: 4e-18
                                       HHHHHHHHHHHHHHHHHHHTTCHHHHHHHH.S-HHHHHHHHHHHHHCSGGGHHHHHHHHHHHHHHHHHHHHTT-HHH CS
                              CPBP   5 llvfllalllapllEEllfRglllqllqergsstlailissilFglaHlpngpsvllaalaGlvlgylylktgslla 81 
                                       ll + l++++++ +EE++fRg++ ++l++  ++ +a ++ss +F+laHl     + +++++Gl+l+    + +sl +
  gi|557693891|ref|YP_008796945.1| 117 LLYIGLTIFVVAPAEEIIFRGIVHEKLSKIMKRGFADVVSSTVFALAHLDL-SRLGPTFVLGLFLAHSVDRARSLTP 192
                                       5566678888999*****************8889**************987.35*********************** PP

                                       HHHHHHHHHHH CS
                              CPBP  82 aillHallnll 92 
                                       a+++Ha++n++
  gi|557693891|ref|YP_008796945.1| 193 AVIIHAINNTV 203
                                       *********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1614.17
//
Query:       gi|557693892|ref|YP_008796946.1|  [L=287]
Description: sec-independent protein translocase protein TatC [Candidatus Caldiarchaeum subterraneum]
Scores for 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-38  130.5  22.5    8.7e-38  130.2  22.5    1.1  1  TatC            Sec-independent protein translocase protein (
    0.00013   21.6   5.3    0.00021   20.9   5.3    1.3  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.012   16.3   0.2      0.024   15.4   0.2    1.5  1  zinc_ribbon_15  zinc-ribbon family
      0.097   12.7   2.1       0.15   12.1   2.1    1.2  1  DZR             Double zinc ribbon
       0.12   11.8   2.3       0.21   11.1   2.3    1.3  1  zf-ribbon_3     zinc-ribbon domain
        4.9    6.8   4.8         58    3.4   3.6    2.7  2  RecR            RecR protein
        9.2    6.3   6.2        1.6    8.7   1.1    2.4  2  DUF4006         Family of unknown function (DUF4006)


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 !  130.2  22.5   3.4e-41   8.7e-38       1     207 []      11     237 ..      11     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 130.2 bits;  conditional E-value: 3.4e-41
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCCHHHHC.C...............TTS-EE--SSS-HHHHHHH CS
                              TatC   1 ehLeeLrkrlirallavaiafiitfvfaeeliafllepleeae...............eevelivlspleafllklk 62 
                                       ehL+eL+ r+  +++ +++a+i++++f ++l++++ +p   ++               +++e+i  s++ +f + + 
  gi|557693892|ref|YP_008796946.1|  11 EHLRELKDRVKVVMISFVVALIFWLAFPADLTEIIRNPEFYEPmvtlvlkrivqdlagARIEIIGCSMTSPFEIFFL 87 
                                       8***********************99*999988888774443245555555555555534889999999******** PP

                                       HHHHHHHHHSHHHHHHHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHH...HHT.TTTSSTTE CS
                              TatC  63 vslvaglvlasPvilyqlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlk...fll.seevepll 135
                                       ++ +++l+  +Pvi y+++a+v p+Ly+herrl++ f +a ++lf++G +f+yfv +pl+++   f++  ++v+p++
  gi|557693892|ref|YP_008796946.1|  88 AAAFLALATIMPVIGYETYAYVDPALYPHERRLIYGFTLAFVALFAVGGVFGYFVAAPLIMRamvFFFeLAGVIPTV 164
                                       **************************************************************6654446567899** PP

                                       EHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S..SHHHHHHHHHH CS
                              TatC 136 slseylsfvlllllafgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltP.pdvisqlllavP 207
                                        + +++s+v++++l++g++F  P+vlvll+r+g++s + ++++r y++ ++ ++ a++tP   ++   +l++P
  gi|557693892|ref|YP_008796946.1| 165 CAMDFYSLVFTTVLLIGVVFTSPVVLVLLVRFGIISTDLISRNRLYVYGILYILVAIITPdGWLVGNAVLFLP 237
                                       ************************************************************6666666666655 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   5.3   8.4e-08   0.00021       1      21 [.     264     284 ..     264     285 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8.4e-08
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGt 21 
                                       +C+ CG+ l +n+ FC++CG 
  gi|557693892|ref|YP_008796946.1| 264 YCKFCGNGLRENEIFCSKCGR 284
                                       8*******************5 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   0.2   9.3e-06     0.024      57      86 .]     252     283 ..     240     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.3e-06
                    zinc_ribbon_15  57 iekkesse..kkeCknCgkeveeefkyCpkCg 86 
                                       +e+++ ++  + +Ck Cg+ + e+  +C+kCg
  gi|557693892|ref|YP_008796946.1| 252 VERNRLKSmiVGYCKFCGNGLRENEIFCSKCG 283
                                       343333335699*******************9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.1   5.8e-05      0.15       1      20 [.     265     284 ..     263     287 .] 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.8e-05
                               DZR   1 CpqCgeelppdarfCseCgt 20 
                                       C+ Cg+ l+++ +fCs+Cg 
  gi|557693892|ref|YP_008796946.1| 265 CKFCGNGLRENEIFCSKCGR 284
                                       88888888888888888886 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.3   8.2e-05      0.21       4      23 ..     264     283 ..     263     284 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.2e-05
                       zf-ribbon_3   4 rCPnCGa.plssddnvCpyCG 23 
                                       +C  CG+ + ++  ++C +CG
  gi|557693892|ref|YP_008796946.1| 264 YCKFCGNgL-RENEIFCSKCG 283
                                       7999***77.**********9 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.13   3.3e+02       4      17 ..       8      21 ..       7      22 .. 0.89
   2 ?    3.4   3.6     0.023        58      16      34 ..     262     282 ..     261     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.13
                                      HHHHHHHHHHHH-E CS
                              RecR  4 eLaeaLqeakekvr 17
                                      +L+e L+e+k++v+
  gi|557693892|ref|YP_008796946.1|  8 PLIEHLRELKDRVK 21
                                      6999********97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.023
                                       -EE-TTT--E.ESSSS.-CCC CS
                              RecR  16 vrhCsrCgnl.teedl.CaIC 34 
                                       v++C+ Cgn   e+++ C+ C
  gi|557693892|ref|YP_008796946.1| 262 VGYCKFCGNGlRENEIfCSKC 282
                                       789****99548888778888 PP

>> DUF4006  Family of unknown function (DUF4006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   1.1   0.00064       1.6       8      31 ..     131     154 ..     129     173 .. 0.76
   2 ?   -1.4   0.5      0.87   2.2e+03      20      29 ..     175     184 ..     169     198 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00064
                           DUF4006   8 lFglnGitGmliavvLLLsilavL 31 
                                       lF++ G+ G+++a  L +  ++++
  gi|557693892|ref|YP_008796946.1| 131 LFAVGGVFGYFVAAPLIMRAMVFF 154
                                       8*************9998655544 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.87
                           DUF4006  20 avvLLLsila 29 
                                        +vLL ++++
  gi|557693892|ref|YP_008796946.1| 175 TTVLLIGVVF 184
                                       5788888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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):               7  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1993.44
//
Query:       gi|557693893|ref|YP_008796947.1|  [L=97]
Description: sec-independent protein translocase protein TatA [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   53.7   1.1    1.2e-13   50.2   0.6    2.1  2  MttA_Hcf106  mttA/Hcf106 family
  ------ inclusion threshold ------
      0.024   14.3   0.5      0.028   14.1   0.5    1.1  1  GrpE         GrpE
        1.6    8.8   4.7        2.6    8.1   4.6    1.4  1  OapA_N       Opacity-associated protein A N-terminal motif


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 !   50.2   0.6     2e-17   1.2e-13       5      51 ..       7      55 ..       3      57 .. 0.93
   2 ?    2.0   0.0     0.021   1.3e+02      20      29 ..      64      73 ..      63      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 2e-17
                                      HHHHHHHHHHHHS..-TTTHHHHHHHHHHHHHHHHHHHHHHHH---XXX CS
                       MttA_Hcf106  5 elliIlvValllF..GpkkLPEvaraLGktLreFkkavkeleeenekea 51
                                      e+++++vV+l+lF  Gp+kLP +a++ G++ reF ka+k+leee +k a
  gi|557693893|ref|YP_008796947.1|  7 EWIVVAVVVLVLFlwGPDKLPKIAKSIGQAKREFEKAQKGLEEEISKAA 55
                                      9**********9999****************************988765 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.021
                                      TTHHHHHHHH CS
                       MttA_Hcf106 20 kkLPEvaraL 29
                                      +kL EvaraL
  gi|557693893|ref|YP_008796947.1| 64 DKLLEVARAL 73
                                      6999*****8 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   4.6e-06     0.028      30      96 ..      28      94 ..      23      97 .] 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-06
                                      SCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..HHH-HHHHHHHHH CS
                              GrpE 30 elkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksakeneeekslleGve 96
                                      ++ +++ +++ efe+++k +e+e+++a+ +a +   ++LL+v+ +l+  ++ ++ ++  k+++e  +
  gi|557693893|ref|YP_008796947.1| 28 KIAKSIGQAKREFEKAQKGLEEEISKAATTAASPPDDKLLEVARALNISTEGKTRDQIAKEIVEKSQ 94
                                      67788899***********************************999999998778888888887665 PP

>> OapA_N  Opacity-associated protein A N-terminal motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.6   0.00043       2.6      14      28 .]       9      24 ..       9      27 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00043
                            OapA_N 14 iaLslvvlvlllw.Ps 28
                                      i+ ++vvlvl+lw P+
  gi|557693893|ref|YP_008796947.1|  9 IVVAVVVLVLFLWgPD 24
                                      5789*********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1269  (0.0707792); expected 358.6 (0.02)
Passed bias filter:                      763  (0.0425568); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
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: 712.57
//
Query:       gi|557693894|ref|YP_008796948.1|  [L=256]
Description: 3-oxoacyl-[acyl-carrier protein] reductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  169.0   0.3    1.4e-49  168.8   0.3    1.0  1  adh_short_C2    Enoyl-(Acyl carrier protein) reductase
    6.9e-35  120.3   0.1    8.1e-35  120.0   0.1    1.1  1  adh_short       short chain dehydrogenase
      1e-11   45.1   0.1    1.5e-11   44.6   0.1    1.2  1  KR              KR domain
     0.0001   21.9   0.3    0.00034   20.2   0.3    1.9  1  Epimerase       NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.015   15.2   0.1      0.025   14.5   0.1    1.5  1  NAD_binding_10  NAD(P)H-binding
      0.018   14.4   0.0      0.024   14.1   0.0    1.2  1  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
      0.033   13.7   0.1       0.29   10.6   0.1    2.0  2  NmrA            NmrA-like family
      0.077   12.1   0.0       0.14   11.2   0.0    1.4  1  RmlD_sub_bind   RmlD substrate binding 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 !  168.8   0.3   6.3e-53   1.4e-49       1     232 [.      13     252 ..      13     254 .. 0.92

  Alignments for each domain:
  == domain 1  score: 168.8 bits;  conditional E-value: 6.3e-53
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSE.E..EE--TTSHHHHHHHHHHHHHHHSSEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgae.v..lecDVtdeeqvealveevvekfgklDil 73 
                                       Ga   IGra+A  + e+Ga v +  ++ +  ++  ++ a+++g+  v    ++V+de++ve++v+++ e+fg++D +
  gi|557693894|ref|YP_008796948.1|  13 GASGDIGRAVADWFLEQGAFVSAGARRLQVlRELEKTWAARYGSVkVhvDMLNVADEKSVESFVAKTLERFGRIDAV 89 
                                       67778*****************9999999977777788888885544436689************************ PP

                                       EE-----EG...CSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHH CS
                      adh_short_C2  74 vnnagiapk...lkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaK 145
                                       vn ag++ +    ++ ++et+ +e+ ++++v+l + f+++k+ ++ m ++  g  vn ss+ a  + +   ay+ aK
  gi|557693894|ref|YP_008796948.1|  90 VNVAGYVLEprlWNKGLAETTTQEIIDVMSVDLLGSFNMVKHTIERMVKQrgGVYVNFSSTPAITGYDRGLAYTLAK 166
                                       *******9999999*******************************55544469************************ PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT- CS
                      adh_short_C2 146 aalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyi 222
                                        a+ +lt+ +A+e+g+ g+R  +   g i+T+ +++   +++ +++l+a++plgr+g+peeva++a fL+sd+as+i
  gi|557693894|ref|YP_008796948.1| 167 SAILGLTKHIAYEYGRFGVRAYTLVLGSIETEPSTKHL-TKADYAALAAESPLGRWGRPEEVAAVAGFLCSDMASFI 242
                                       *******************************9966665.467789999***************************** PP

                                       -SEEEEESTT CS
                      adh_short_C2 223 tGqtlvvDgG 232
                                       +Gq +vvDgG
  gi|557693894|ref|YP_008796948.1| 243 NGQSIVVDGG 252
                                       ********** PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.0   0.1   3.6e-38   8.1e-35       1     189 [.       7     202 ..       7     208 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 3.6e-38
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT..TSEEEEEE-TTTSHHHHHHHHHHHHHHH CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee..gakalaiqvDvtdreevealvekavkkl 75 
                                       k+ +vtGas+ IGra+a+ ++++Ga v + +r+ + l+e+ k   +   + k+++  ++v+d+++ve +v+k  +++
  gi|557693894|ref|YP_008796948.1|   7 KICIVTGASGDIGRAVADWFLEQGAFVSAGARRLQVLRELEKTWAARygSVKVHVDMLNVADEKSVESFVAKTLERF 83 
                                       6889***************************************99999999************************** PP

                                       SSESEEEE---S.....S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBH CS
                         adh_short  76 gkldvLvnNAGi.....tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagva 147
                                       g++d++vn AG       +++  +e++ +e+ +v++v l g f+++++ ++ m+kq++G  vn sS+ +  ++  + 
  gi|557693894|ref|YP_008796948.1|  84 GRIDAVVNVAGYvleprLWNKGLAETTTQEIIDVMSVDLLGSFNMVKHTIERMVKQRGGVYVNFSSTPAITGYDRGL 160
                                       ****************999********************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                         adh_short 148 aYsAsKaavagltrslakelaptgirvnavaPGlvdTdmake 189
                                       aY+ +K a+ glt+ +a e+ + g+r  +++ G ++T+  ++
  gi|557693894|ref|YP_008796948.1| 161 AYTLAKSAILGLTKHIAYEYGRFGVRAYTLVLGSIETEPSTK 202
                                       *************************************97665 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.1   6.5e-15   1.5e-11       4     161 ..      10     174 ..       8     193 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 6.5e-15
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       ++tG+ G +G+++a+w +e+ga  +   +R+ ++ ++ + ++ + +   ++v+v  + v+d+++ve+ +++  ++++
  gi|557693894|ref|YP_008796948.1|  10 IVTGASGDIGRAVADWFLEQGAF-VSAGARRLQVLRELE-KTWAARYGSVKVHVDMLNVADEKSVESFVAKTLERFG 84 
                                       8********************95.333444434333333.333344447899999999******************* PP

                                       ---EEEE------.....---TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HH CS
                                KR  81 pikGvihaAgvlr.....dklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqan 148
                                       +i  v++ Ag +      +k l+e+t++++  v++  + G+ n+ + + +    ++  + v fSS  +++g     +
  gi|557693894|ref|YP_008796948.1|  85 RIDAVVNVAGYVLeprlwNKGLAETTTQEIIDVMSVDLLGSFNMVKHTIErmvkQRGGVYVNFSSTPAITGYDRGLA 161
                                       *********975423333677999*******************9888877566677789****************** PP

                                       HHHHHHHHHHHHH CS
                                KR 149 YaaaNaflDalae 161
                                       Y+ a + + +l +
  gi|557693894|ref|YP_008796948.1| 162 YTLAKSAILGLTK 174
                                       **99887766655 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.3   1.5e-07   0.00034       2     101 ..      10     125 ..       9     227 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.5e-07
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.............EEEE--TT-HHHHHHHHHH... CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl.............elveldltdrsalerlfke... 62 
                                       +VtGa+G iG+a+++ +le+g  v + +r+ +      l++l             ++  l++ d++++e ++++   
  gi|557693894|ref|YP_008796948.1|  10 IVTGASGDIGRAVADWFLEQGAFVSAGARRLQ-----VLRELektwaarygsvkvHVDMLNVADEKSVESFVAKtle 81 
                                       8********************88777777722.....2222223357899999998889999999977766654222 PP

                                       .H.T-SEEEE--S.---HHHHHHSHHHHHHHHTH..HHHHHHHH CS
                         Epimerase  63 .e.qpdavihlAa.vggvaassedpadfieknlq..gtlnllea 101
                                        + ++dav+++A+ v  ++ +++  a++  + ++  ++++ll  
  gi|557693894|ref|YP_008796948.1|  82 rFgRIDAVVNVAGyVLEPRLWNKGLAETTTQEIIdvMSVDLLGS 125
                                       2679*********9999999988888777666541133444444 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 ?   14.5   0.1   1.1e-05     0.025       1      85 [.      13     118 ..      13     150 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTT.......TCEEEE--TT-CCHHHHHHT.......T-SE CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaee.......glevvegdvtdvedlaealk.......gada 63 
                                       GA+G +Gr++++  l++g   v a +R+ + l ele++        +++v  ++v d++++++ ++        +da
  gi|557693894|ref|YP_008796948.1|  13 GASGDIGRAVADWFLEQG-AFVSAGARRLQVLRELEKTWaarygsvKVHVDMLNVADEKSVESFVAktlerfgRIDA 88 
                                       9****************6.89********999999965412222223333345555666666666656666666688 PP

                                       EEES-........--TCC...HHHHHHHHHHHH CS
                    NAD_binding_10  64 Vvsal........ggggk...deegaknivdaa 85 
                                       Vv  +            +    e++++ i+d++
  gi|557693894|ref|YP_008796948.1|  89 VVNVAgyvleprlW---NkglAETTTQEIIDVM 118
                                       77777444433332...0333555566666666 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 ?   14.1   0.0   1.1e-05     0.024       1      85 [.      10      95 ..      10     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                      EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH..... CS
                     GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev..... 74
                                      ++TG +G iG  +a+++le+g  v    rr +   ++++e+    +    + ++++   ++ D++s+e+ +a++     
  gi|557693894|ref|YP_008796948.1| 10 IVTGASGDIGRAVADWFLEQGAFVSAGARRLQV--LRELEKTWAAR--YGSVKVHVDMLNVADEKSVESFVAKTlerfg 84
                                      59*********************9988777665..44666655433..3345788888999*********999988889 PP

                                      T-SEEEE--S- CS
                     GDP_Man_Dehyd 75 qpdevynLAAq 85
                                      ++d+v+n A+ 
  gi|557693894|ref|YP_008796948.1| 85 RIDAVVNVAGY 95
                                      99*****9986 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00013      0.29       2      33 ..      10      43 ..       9      84 .. 0.75
   2 ?    0.8   0.0      0.14   3.1e+02     122     147 ..     130     156 ..     121     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S..- CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdt..k 33
                                      +v+Ga+G +G++v++ +l++g  v a  R +   
  gi|557693894|ref|YP_008796948.1| 10 IVTGASGDIGRAVADWFLEQGAFVSAGARRLqvL 43
                                      69**********************9988877442 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHC.TS-EEEEEE-EEGGG CS
                              NmrA 122 Kaeieeyvral.gipytfvyagffmen 147
                                       K++ie++v++  g+   f  +++ +++
  gi|557693894|ref|YP_008796948.1| 130 KHTIERMVKQRgGVYVNFSSTPAITGY 156
                                       9********996666677777666666 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 ?   11.2   0.0   6.4e-05      0.14       4      61 ..      10      95 ..       7      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.4e-05
                                      EEESTTSHHHHHHHHHCTTTSEEEEEE-TT.......................T--TTSHHHHHHHH.....HHH--SE CS
                     RmlD_sub_bind  4 lvtGanGqlGseLakqlaeeglevlaltre.......................eldltdaeavaell.....keakpdv 54
                                      +vtGa+G +G+++a+ + e+g+ v a  r+                        l+++d+++v++++     +  + d+
  gi|557693894|ref|YP_008796948.1| 10 IVTGASGDIGRAVADWFLEQGAFVSAGARRlqvlrelektwaarygsvkvhvdMLNVADEKSVESFVaktleRFGRIDA 88
                                      79*******************9999988889*******************999999********999444433347889 PP

                                      EEE---- CS
                     RmlD_sub_bind 55 vvnaAAy 61
                                      vvn+A y
  gi|557693894|ref|YP_008796948.1| 89 VVNVAGY 95
                                      ***9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1833.59
//
Query:       gi|557693895|ref|YP_008796949.1|  [L=161]
Description: small subunit ribosomal protein S13 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-38  131.5   0.1    2.6e-38  131.3   0.1    1.1  1  Ribosomal_S13  Ribosomal protein S13/S18
  ------ inclusion threshold ------
      0.077   13.2   0.0       0.21   11.8   0.0    1.7  2  U-box          U-box domain
        0.2   11.6   0.2       0.41   10.6   0.2    1.6  1  DUF3944        Domain of unknown function (DUF3944)


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 !  131.3   0.1   4.4e-42   2.6e-38       1     128 []      10     138 ..      10     138 .. 0.99

  Alignments for each domain:
  == domain 1  score: 131.3 bits;  conditional E-value: 4.4e-42
                     Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdi 76 
                                       R+l+td+dg+ ++ +al+ +kGiG +   +i+++a++d  +r+g+lte++iekie+i  n++++ ip+w+ nr+ d 
  gi|557693895|ref|YP_008796949.1|  10 RVLNTDVDGTLRLPYALARVKGIGVNLGYAIARAAGIDPATRLGNLTEKQIEKIEQIARNPTRFGIPAWLlNRRFDP 86 
                                       99*************************************************************************** PP

                     Ribosomal_S13  77 kdGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                                        +G+d h++  dl+  ++edi+ +++ +s++G+RH+ GlkvRGQrT+ttgR+
  gi|557693895|ref|YP_008796949.1|  87 VTGEDRHLTGADLELAIKEDIQTMMRTKSWKGIRHSLGLKVRGQRTRTTGRK 138
                                       **************************************************95 PP

>> U-box  U-box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.79   4.7e+03      41      54 ..      46      60 ..      41      66 .. 0.65
   2 ?   11.8   0.0   3.5e-05      0.21      31      73 .]      75     116 ..      70     116 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.79
                                      B-TTT-S.B--GGGS CS
                             U-box 41 tdPftre.pltqdql 54
                                       dP tr   lt++q+
  gi|557693895|ref|YP_008796949.1| 46 IDPATRLgNLTEKQI 60
                                      689996515555554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.5e-05
                                       HHHHHTT.SSB-TTT-SB--GGGSEE-HHHHHHHHHHHHHCTC CS
                             U-box  31 iekhllsrdktdPftrepltqdqlipnlelKekIdefleekre 73 
                                       i ++ll+  ++dP+t e      +  +l++Ke I++ +++k++
  gi|557693895|ref|YP_008796949.1|  75 IPAWLLN-RRFDPVTGEDRHLTGADLELAIKEDIQTMMRTKSW 116
                                       889****.9******999999999999*********9999986 PP

>> DUF3944  Domain of unknown function (DUF3944)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   6.9e-05      0.41      15      35 .]       2      22 ..       1      22 [. 0.95

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.9e-05
                           DUF3944 15 sedLedLfdiLthdkdGkkRl 35
                                      s dL+ ++++L  d dG++Rl
  gi|557693895|ref|YP_008796949.1|  2 SKDLRLIVRVLNTDVDGTLRL 22
                                      78******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
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: 00:00:00.42
# Mc/sec: 1151.87
//
Query:       gi|557693896|ref|YP_008796950.1|  [L=356]
Description: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-17   62.2   0.0    3.9e-16   59.2   0.0    2.3  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
    0.00034   20.2   0.0    0.00054   19.6   0.0    1.2  1  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai


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 !   59.2   0.0   4.3e-20   3.9e-16      44     288 ..      68     328 ..      49     338 .. 0.80

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 4.3e-20
                                       HHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTEE--SS--EEEETTEEE---EE-SS---SS-SSTHHHHHHTTS-S CS
                       Meth_synt_2  44 vrrqeelgvDvlvhgepeRgdmveyfgealdgfaftkngwvqsygsrcvrppiivgdvsrpaamtvkesalaqsltd 120
                                       +r  e +g+Dv+ +ge  R +m e+    +dgf  +  g v    + ++r   +v      ++  + e +  +   +
  gi|557693896|ref|YP_008796950.1|  68 LRFFESAGLDVVYDGEQRRVEMYEHPLRFIDGF--EYRGVVRVWDNEFYRKAAVVKRPRLIQPYHIDELQFNKKHAK 142
                                       5677899******************99999997..67899999****99999999999******************* PP

                                       S-BEEEEE-HHHHHHTSEE-..............TTS-HHHHHHHHH.HHHHHHHHHHHHTT-SEEEEE-TTSSTT- CS
                       Meth_synt_2 121 kpvkglltGpvtilnwsfvr..............ddvdraeaaaqia.lalrdevkdLeaaGikviQiDepalreGl 182
                                       kp+k  +t   t+++wsf +                  r++ + +++  +lr  v +L++ G+  iQ+Depa+ +  
  gi|557693896|ref|YP_008796950.1| 143 KPLKVPVTSAYTLVDWSFDEyyakhaagedlvakTGAARRDFVLDLVkEVLRPVVMALDSEGVDYIQLDEPAAATKP 219
                                       ******************99999999995444443345566666665247888888****************98754 PP

                                       -SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCHHHHHTT--SEEEESBSSS-S............. CS
                       Meth_synt_2 183 plkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndilsaiaaldvDvitieasrsde............. 246
                                          +   ++          ++++  ++ ++ ++H+Cy +++ + +a+ +l++Dv++i  s+ d+             
  gi|557693896|ref|YP_008796950.1| 220 HESE-LVVES---------INETFRSVGAKKAVHICYTDYKALFPALLELKIDVLSISCSNADTtrlgtdpdartgf 286
                                       3333.22222.........33333344445578************************99988753333333333334 PP

                                       SGGGGTTTT---SEEEEBSS-TTSSS--THHHHHHHHHCHHC CS
                       Meth_synt_2 247 ellealeevkygrgvglGvydihsprvpsmeeiaalikkald 288
                                       e+l +++e +++ +v +G++d+h++ ++  e +++  ++ l+
  gi|557693896|ref|YP_008796950.1| 287 EVLRVFKEYDVKFKVAPGLVDVHTDFIEPPELVREGSSTLLR 328
                                       68999**********************999999887666655 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 !   19.6   0.0     6e-08   0.00054     173     264 ..     182     270 ..     171     280 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6e-08
                                       HCHHHHHHHHHHHHHHHHHHHTT-SEEEEE-GGGGSSGCHHHHHHHHHHHHHHTCCTTTSEEEEE--SS-.CCHHHH CS
                       Meth_synt_1 173 klellekLlpvYkelleeLkeagvewvqidEPalvldlekeelealkeaYeelakekkelklllatyFdsvaealel 249
                                       +  +l+ + +v + ++  L+++gv+++q+dEPa +++ +++e  +++++ e++  ++ ++k  ++  + + ++ + +
  gi|557693896|ref|YP_008796950.1| 182 RDFVLDLVKEVLRPVVMALDSEGVDYIQLDEPAAATKPHESE-LVVESINETF--RSVGAKKAVHICYTDYKALFPA 255
                                       4445666678999999*****************999864443.3444444444..4556777777788888999999 PP

                                       HTTSSTSEEEEETSS CS
                       Meth_synt_1 250 laelpveglglDlvr 264
                                       l+el+++ l++   +
  gi|557693896|ref|YP_008796950.1| 256 LLELKIDVLSISCSN 270
                                       999999999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2666.74
//
Query:       gi|557693897|ref|YP_008796951.1|  [L=315]
Description: methylcobalamin:homocysteine methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-17   64.5   0.0    2.1e-17   63.6   0.0    1.4  1  Meth_synt_1  Cobalamin-independent synthase, N-terminal domai
    1.7e-13   50.5   0.0    2.1e-13   50.2   0.0    1.0  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain


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 !   63.6   0.0   2.3e-21   2.1e-17     107     311 ..      80     275 ..      69     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 2.3e-21
                                       EEEESTTSS-EEEE-BE-SS.----S-THHHHHHHHHHHTTGGEEEEEE-HHHHHHT-EETTCC.-HCHHHHHHHHH CS
                       Meth_synt_1 107 emtkwFntnYHYlvPelekdtefklaseklleevkeakalgieakpvllGpltflkLskakeekveklellekLlpv 183
                                        + +wF+ n+ Y  P ++    ++l+++   + + +++    + k+v+  pltf kLs +k  + +  el+ ++ ++
  gi|557693897|ref|YP_008796951.1|  80 GLSRWFDNNFFYKAPVITGR--LSLRNKIDTSPFFHQSIETAKRKIVVPEPLTFAKLSINKFYN-RLDELVYDVAQA 153
                                       578**************975..66666666667777777788999*************999888.777788888888 PP

                                       HHHHHHHHHHTT-SEEEEE-GGGGSSG.CHHHHHHHHHHHHHHTCCTTTSEEEEE--SS-.CCHHHHHTTSSTSEEE CS
                       Meth_synt_1 184 YkelleeLkeagvewvqidEPalvldl.ekeelealkeaYeelakekkelklllatyFdsvaealellaelpveglg 259
                                        +  l++L e     vq+  P lv    ++e+le+ ++a e l +++ +++l+l+  F+s++++le  +++pv+ +g
  gi|557693897|ref|YP_008796951.1| 154 LALYLKQLGEF--AQVQLTAPFLVSGKiSPEDLELSRSAVEVL-RRTVDAELMLHLQFGSAEKNLEDFLDFPVDVIG 227
                                       88888888765..79*********9875999************.699****************************** PP

                                       EETSSHCHHHHHHHHCTT.TTSEEEEEEE-SSS-B---HHHHHHHHHHHHHC CS
                       Meth_synt_1 260 lDlvraeenlealkkaglpedkvLsaGvidGrniWradlekalelleelaek 311
                                       lD+ +  +++e l+  gl++dk +++G++dGrn    d + +++lle+++++
  gi|557693897|ref|YP_008796951.1| 228 LDMFK--TRVECLR--GLNTDKSIFLGLVDGRNTLLEDAAPTVSLLEKVSSM 275
                                       ***95..5566665..4778***************************99875 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 !   50.2   0.0   2.4e-17   2.1e-13       6     320 ..       6     306 ..       1     311 [. 0.89

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 2.4e-17
                                       -SB---SS-----------------HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTE.E--SS CS
                       Meth_synt_2   6 iGSfPqtaevrearaevkkgelseeeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgf.aftkn 81 
                                       +G  P t+++ +a +++ k+++ e    + ++    + ++ q + g   +++g    +d    f+  l+ + +   +
  gi|557693897|ref|YP_008796951.1|   6 VGALPRTEKLIKAYRDRAKNKIPETALLNELETTSLAYIEAQRRNGFTYIIDGMLGWNDLLRPFASSLENVaVNGLS 82 
                                       99*********************************************************************777788 PP

                                       --EEEETTEEE---EE-SS---SS-SSTHHHHHHTTS-SS-BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHHHHHHH CS
                       Meth_synt_2  82 gwvqsygsrcvrppiivgdvsrpaamtvkesalaqsltdkpvkglltGpvtilnwsfvrddvdraeaaaqialalrd 158
                                        w +   + ++++p+i g +s ++++       +++ t k  k ++  p t  + s  +    ++e ++++a al  
  gi|557693897|ref|YP_008796951.1|  83 RWFDN--NFFYKAPVITGRLSLRNKIDTSPFFHQSIETAKR-KIVVPEPLTFAKLSINKFYNRLDELVYDVAQALAL 156
                                       89985..56889************99988766655555555.*****************9999************** PP

                                       HHHHHHHTT-SEEEEE-TTSSTT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCHHHHHTT--S CS
                       Meth_synt_2 159 evkdLeaaGikviQiDepalreGlplkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndilsaiaaldvD 235
                                        +k+L +   + +Q+  p+l  G +  +      l+ +  a  +      +d+++ +Hl     +++l++  ++ vD
  gi|557693897|ref|YP_008796951.1| 157 YLKQLGEF--AQVQLTAPFLVSGKISPE-----DLELSRSAVEVLRR--TVDAELMLHLQFGSAEKNLEDFLDFPVD 224
                                       *****998..899**********99888.....33333334333333..569999999999999************* PP

                                       EEEESBSSS-SSGGGGTTTT---SEEEEBSS-TTSSS--THHHHHHHHHCHHCTS-STSB-BB-SS-STTS-HHHHH CS
                       Meth_synt_2 236 vitieasrsdeellealeevkygrgvglGvydihsprvpsmeeiaalikkaldvapkerlwvnPdCGLktrkreear 312
                                       vi +++ +     +e l+  + ++ + lG++d      + +    +l++k+  +a   +l v P+C L  ++ e a 
  gi|557693897|ref|YP_008796951.1| 225 VIGLDMFKTR---VECLRGLNTDKSIFLGLVDGRNTLLEDAAPTVSLLEKVSSMASFRELHVGPNCELEHLPHEYAL 298
                                       ******9999...788888888*****************999999*********999*****************999 PP

                                       HHHHHHHH CS
                       Meth_synt_2 313 aalknmvd 320
                                       +++    +
  gi|557693897|ref|YP_008796951.1| 299 KKIDVLGE 306
                                       99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2260.83
//
Query:       gi|557693898|ref|YP_008796952.1|  [L=336]
Description: thioredoxin reductase (NADPH) [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  115.2   0.0    4.1e-33  114.9   0.0    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    3.5e-24   85.6   0.0    3.8e-21   75.6   0.0    2.0  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    3.4e-14   53.2   0.3      8e-10   39.1   0.1    3.4  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    4.6e-07   29.3   0.0    9.9e-05   21.6   0.0    2.8  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    1.4e-06   28.2   1.2      0.028   14.0   0.1    2.8  3  DAO            FAD dependent oxidoreductase
      2e-06   26.8   0.0     0.0024   16.6   0.1    3.0  3  HI0933_like    HI0933-like protein
    1.6e-05   24.2   0.1       0.75    8.8   0.0    3.8  4  FAD_binding_2  FAD binding domain
    1.8e-05   24.1   0.0    0.00017   20.9   0.0    2.2  2  Thi4           Thi4 family
     0.0001   22.5   0.0    0.00025   21.2   0.0    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00055   18.5   0.0    0.00085   17.9   0.0    1.2  1  FMO-like       Flavin-binding monooxygenase-like
    0.00085   18.8   0.0     0.0039   16.6   0.0    1.9  2  FAD_oxidored   FAD dependent oxidoreductase
  ------ inclusion threshold ------
       0.04   14.4   0.0      0.093   13.2   0.0    1.8  1  NAD_binding_7  Putative NAD(P)-binding
      0.053   13.1   0.0       0.17   11.5   0.0    1.8  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
      0.055   12.5   0.0        1.3    8.1   0.0    2.6  3  GIDA           Glucose inhibited division protein A
       0.11   11.7   0.2          1    8.5   0.0    2.5  3  FAD_binding_3  FAD binding domain
       0.11   12.5   0.1         29    4.6   0.0    3.1  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 !  114.9   0.0   3.7e-36   4.1e-33       1     290 [.      11     300 ..      11     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 3.7e-36
                                       CSEEEE--SHHHHHHHHHHHH.HTS-EEEEE..TTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq.agakvtlve..legtclnggcllskallgvaedaeias........evvkklnqg 66 
                                       +d+ +iG+Gp Gl aa ++a   ++k+ ++e  ++    + +  + k +  va++++i+s        e+ + +n  
  gi|557693898|ref|YP_008796952.1|  11 YDITIIGAGPTGLFAAFYAAGmRSMKTKVIEalDTYGGQLTTLYPDKFIYDVAGFPKILSkdlaknlyEQASAYNPT 87 
                                       689*****************988*******96533333444456699********************9999999999 PP

                                       CCCCHCCTCEEEE.ESCEEEEETEEECTCEEEEEE.SEEEE---E...EE-BCTCTTC.TTBEECCSECHHHHHHCC CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  67 ielllgeevvkid.pgkkkvklekkkegdeekiay.dklvlAtGs...sprdlgipGvaenvgklvrtldsaealkl 138
                                       +++  +  v+++   + + ++l+++k+     + + +++++A G    +pr+lg p v+    k+  +++  +++  
  gi|557693898|ref|YP_008796952.1|  88 FHFSER--VLNLTrLDGGIIELTTDKG-----VHFsKTVLIAAGHgafTPRKLGNPSVERFENKG-VYYTVRDKWMF 156
                                       998888..8888744557888866663.....33449*******633466666888886666555.56666666655 PP

                                       SS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       Pyr_redox_2 139 kllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge. 214
                                        ++  r+v+vGgG  +v+ A  l+++++ev+lv++r+++  a++      + e l ++ v+v    +vke+ g ++ 
  gi|557693898|ref|YP_008796952.1| 157 RNK--RVVIVGGGDSAVDWALNLKDIASEVYLVHRRSEFR-AHE----GSVIE-LFHSPVKVLIPYEVKEAHGGEHl 225
                                       555..5*********************************6.333....33333.44557****************98 PP

                                       .EEE...EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--H CS
                                       .xxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 215 .kle...vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpela 287
                                        k++    +++++++i++d +++  G   + +l+ +k gl + e+++i+++ +++tn+pg+ya+GD+a   ++p+++
  gi|557693898|ref|YP_008796952.1| 226 eKITvynNKTGEETTIECDALLLQLGHIVDVSLF-KKWGLDM-EGNAIKINARCETNIPGVYAAGDIA---TQPDSV 297
                                       855563466777777******************9.*******.*************************...777777 PP

                                       HHH CS
                                       xxx RF
                       Pyr_redox_2 288 qaA 290
                                       + A
  gi|557693898|ref|YP_008796952.1| 298 KLA 300
                                       655 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 !    8.2   0.0    0.0011       1.3       2      29 ..      15      42 ..      14      59 .. 0.83
   2 !   75.6   0.0   3.4e-24   3.8e-21      82     305 .]      72     288 ..      61     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0011
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEk 29
                                      IiGaGP Gl aa  +  +   +  ++E 
  gi|557693898|ref|YP_008796952.1| 15 IIGAGPTGLFAAFYAAGMRSMKTKVIEA 42
                                      9***********9998888878888886 PP

  == domain 2  score: 75.6 bits;  conditional E-value: 3.4e-24
                       Pyr_redox_3  82 ealeYlrevaksfelpiklfeeVesvkk.edegfevetsketyeAkkviiAtGefd.kPnklnipGeek..lvkhys 154
                                       ++++ l e a+ ++   +  e+V ++++ +++  e++t+k++  +k+v+iA+G     P+kl+ p  e+  ++ +y+
  gi|557693898|ref|YP_008796952.1|  72 DLAKNLYEQASAYNPTFHFSERVLNLTRlDGGIIELTTDKGVHFSKTVLIAAGHGAfTPRKLGNPSVERfeNKGVYY 148
                                       556666667777888899**********555669******************9855259999998888544777999 PP

                       Pyr_redox_3 155 kvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlf 231
                                       +v++   +++++vv++Gg++SavD Al+l +  +eV +v+r+se +++e     s+    ++ ++ l+  e  +++ 
  gi|557693898|ref|YP_008796952.1| 149 TVRDKWMFRNKRVVIVGGGDSAVDWALNLKDIASEVYLVHRRSEFRAHE----GSVIELFHSPVKVLIPYEVKEAHG 221
                                       9998879************************************999985....7888889999998888877799** PP

                       Pyr_redox_3 232 naevkeikekeeeykvktedgkkvevkddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                        +++++i+        + ++g++++++ d +l+ +G   d+s++kk +++   +g     ++ +etn+pg++ aG
  gi|557693898|ref|YP_008796952.1| 222 GEHLEKITVY------NNKTGEETTIECDALLLqLGHIVDVSLFKKWGLDM--EGNAIKINARCETNIPGVYAAG 288
                                       *******975......344556666777777776***********666655..66666667899*********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 !    8.0   0.0    0.0038       4.3       2      35 ..      13      47 ..      12      53 .. 0.86
   2 ?    2.1   0.0      0.26     3e+02      38      72 ..      69     103 ..      62     112 .. 0.82
   3 !   39.1   0.1   7.2e-13     8e-10       1      78 [.     160     230 ..     160     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0038
                                      EEEECSSHHHHHHHHHHHHTTS.EEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgk.kVtvversdkll 35
                                      ++++G+G +gl +A ++a +++ k++v+e+ d+  
  gi|557693898|ref|YP_008796952.1| 13 ITIIGAGPTGLFAAFYAAGMRSmKTKVIEALDTYG 47
                                      79************99999885499****999765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.26
                                       SSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  38 lDeeaskilqeklekngievllntkveeiegsedg 72 
                                       l ++++k+l e+ ++ + +++++++v +++  + g
  gi|557693898|ref|YP_008796952.1|  69 LSKDLAKNLYEQASAYNPTFHFSERVLNLTRLDGG 103
                                       478999*********************99987777 PP

  == domain 3  score: 39.1 bits;  conditional E-value: 7.2e-13
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       +vv+vGgG++++++A +l++++++V++v+r+++++      a +    +l +  ++vl   +v+e +g e  +e+++
  gi|557693898|ref|YP_008796952.1| 160 RVVIVGGGDSAVDWALNLKDIASEVYLVHRRSEFR------AHEGSVIELFHSPVKVLIPYEVKEAHGGEH-LEKIT 229
                                       79*********************************......888888888888899999999988888776.67777 PP

                                       E CS
                         Pyr_redox  78 l 78 
                                       +
  gi|557693898|ref|YP_008796952.1| 230 V 230
                                       6 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 ?    4.0   0.0      0.02        23       2      35 ..      10      42 ..       9      50 .. 0.85
   2 !   21.6   0.0   8.9e-08   9.9e-05     114     241 ..      89     204 ..      75     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.02
                       K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalfler 35
                                      ++D+ +iG+Gp  L  a  ++ ++  +k+ ++e 
  gi|557693898|ref|YP_008796952.1| 10 VYDITIIGAGPTGLFAAFYAAGMR-SMKTKVIEA 42
                                      89************9999998888.888888876 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 8.9e-08
                       K_oxygenase 114 rfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkee.ll 189
                                       +f+e+v +++  +     + ++++     ++  + +++++++ G  +  P  l + +  er+  +  y + +++   
  gi|557693898|ref|YP_008796952.1|  89 HFSERVLNLTRLDGG---IIELTT-----DKGVHFSKTVLIAAGHGAFTPRKLGNPS-VERFENKGVYYTVRDKwMF 156
                                       556666655555542...455554.....5678999*****************9877.4777777777776666688 PP

                       K_oxygenase 190 akkriaVvGsGqSaaeifedllrrqkkvelklvtrsealeplddspfvneif 241
                                       ++kr+++vG+G Sa + + +l + ++  e+ lv r++++++ + s +  e+f
  gi|557693898|ref|YP_008796952.1| 157 RNKRVVIVGGGDSAVDWALNLKDIAS--EVYLVHRRSEFRAHEGSVI--ELF 204
                                       99**************9999987766..9***********9998876..544 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.1   2.5e-05     0.028       1      33 [.      12      47 ..      12      52 .. 0.83
   2 !   11.4   0.0   0.00016      0.18     147     227 ..      72     150 ..      68     160 .. 0.77
   3 ?   -0.4   0.1      0.61   6.9e+02       1      32 [.     160     193 ..     160     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                                      EEEEECTSHHHHHHHHHHH.HTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLa.rrg..Vtllekgdiag 33
                                      d+ iiG+G +Gl++A+++a  r   + ++e+ d  g
  gi|557693898|ref|YP_008796952.1| 12 DITIIGAGPTGLFAAFYAAgMRSmkTKVIEALDTYG 47
                                      89****************844558899999876666 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT..CTTTSEEEE CS
                               DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gll..keldlpisp 219
                                        l++ l+++a a   ++++ ++v +l + dg++ ++  tt+ g  ++ ++v +aaG+++ ++ ++l  + +      
  gi|557693898|ref|YP_008796952.1|  72 DLAKNLYEQASAYNPTFHFSERVLNLTRLDGGIIEL--TTDkGVHFS-KTVLIAAGHGA-FTpRKLgnPSV--ERFE 142
                                       688999********************9989999999..888898666.89******997.55666642222..2244 PP

                                       EEEEEEEE CS
                               DAO 220 vrgqvlvl 227
                                        +g ++++
  gi|557693898|ref|YP_008796952.1| 143 NKGVYYTV 150
                                       67777777 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.61
                                       EEEEECTSHHHHHHHHHHHHT..T.EEEEESSSST CS
                               DAO   1 dvviiGGGiiGlstAyeLarr..g.Vtllekgdia 32 
                                       +vvi+GGG   +  A+ L +     V l+ +++++
  gi|557693898|ref|YP_008796952.1| 160 RVVIVGGGDSAVDWALNL-KDiaSeVYLVHRRSEF 193
                                       59******8777777777.4322367777777655 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   2.1e-06    0.0024       2      36 ..      12      47 ..      11      52 .. 0.86
   2 !    5.9   0.0     0.004       4.5     102     165 ..      65     126 ..      64     136 .. 0.85
   3 ?   -0.3   0.0      0.31   3.5e+02       2      32 ..     160     190 ..     159     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-06
                                      SEEEE--SHHHHHHHHHH.HHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisa.akrgkrVlllekakklg 36
                                      d+ +iG+G+ Gl+aA  a + r  ++ ++e+ ++ g
  gi|557693898|ref|YP_008796952.1| 12 DITIIGAGPTGLFAAFYAaGMRSMKTKVIEALDTYG 47
                                      899************988689999*****9988776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.004
                                       EETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 102 FpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                       Fp+   ++d+ + l +++++ + +++ +++v ++++ ++g+++++t +++   ++++++A G  
  gi|557693898|ref|YP_008796952.1|  65 FPKI-LSKDLAKNLYEQASAYNPTFHFSERVLNLTRLDGGIIELTT-DKGVHFSKTVLIAAGHG 126
                                       5555.689999***********************************.77777778888888844 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.31
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVllleka 32 
                                       +v+++GgG + +  A+++++  ++V l+ + 
  gi|557693898|ref|YP_008796952.1| 160 RVVIVGGGDSAVDWALNLKDIASEVYLVHRR 190
                                       79********999999999999999988765 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   0.0   0.00067      0.75       1      38 [.      12      50 ..      12      52 .. 0.86
   2 ?    3.3   0.0     0.032        36     142     175 ..      72     105 ..      66     143 .. 0.82
   3 ?   -0.3   0.0      0.38   4.2e+02       2      37 ..     161     196 ..     160     198 .. 0.89
   4 !    6.8   0.0    0.0027         3     376     402 ..     271     291 ..     224     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00067
                                      SEEEE--SHHHHHHHHHHHH.TTT-EEEEESSSGGGSGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaae.aGlkvavvekeqefggat 38
                                      D+ +iG+G  GL AA  aa  +  k+ v+e  +  gg++
  gi|557693898|ref|YP_008796952.1| 12 DITIIGAGPTGLFAAFYAAGmRSMKTKVIEALDTYGGQL 50
                                      788**************9995555*****9999888875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEE CS
                     FAD_binding_2 142 allarlvesarkagvdfqerteadeLivedgrvt 175
                                        l++ l+e+a +++ +f+++ ++++L++ dg++ 
  gi|557693898|ref|YP_008796952.1|  72 DLAKNLYEQASAYNPTFHFSERVLNLTRLDGGII 105
                                       68899*********************99888664 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.38
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37 
                                       v+++G+G +    Al++++   +v +v   +ef+ +
  gi|557693898|ref|YP_008796952.1| 161 VVIVGGGDSAVDWALNLKDIASEVYLVHRRSEFRAH 196
                                       9**************999999999999998888865 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0027
                                       EEBETTSBESTTEEESSBTEEE-STCE CS
                     FAD_binding_2 376 vetdengrvldadgqpipGLYAaGeva 402
                                       +++++++++      +ipG YAaG  a
  gi|557693898|ref|YP_008796952.1| 271 IKINARCET------NIPGVYAAGDIA 291
                                       567778888......*********988 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.5e-07   0.00017      13      55 ..       6      48 ..       1      52 [. 0.88
   2 ?    0.2   0.0      0.32   3.6e+02      15      35 ..     156     176 ..     146     191 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.5e-07
                                      HHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 13 lkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                        + + D+ i+GaG++GL aa+y a    +k+ ++e+  ++GG
  gi|557693898|ref|YP_008796952.1|  6 EPFDVYDITIIGAGPTGLFAAFYAAGMRSMKTKVIEALDTYGG 48
                                      557789*******************999********9888887 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.32
                                       HTEEEEEEE--SHHHHHHHHH CS
                              Thi4  15 yaesDvvivGaGssGLtaayy 35 
                                       + +  vvivG+G s +  a  
  gi|557693898|ref|YP_008796952.1| 156 FRNKRVVIVGGGDSAVDWALN 176
                                       66788*******998776655 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 !   21.2   0.0   2.3e-07   0.00025       1      46 [.      15      61 ..      15      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.3e-07
                                      EE--SHHHHHHHHHHHC.CTEEEEEE-SSSSSSGGG-EECETTCEEC CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLak.agfdvlllekrdrlGGraasyevpgvrvd 46
                                      I+GaG +Gl aA ++a  +  +  ++e+ d  GG++++   +++++d
  gi|557693898|ref|YP_008796952.1| 15 IIGAGPTGLFAAFYAAGmRSMKTKVIEALDTYGGQLTTLYPDKFIYD 61
                                      9***********999973699****************9877777766 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   7.6e-07   0.00085     141     216 ..     118     191 ..     105     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.6e-07
                          FMO-like 141 avmvctGhhvnphlple.sfpGiekf..kGqyfhsrdykepevfkgkrvlviGlGnsggdiavelsrtaeqvllstr 214
                                       +v++ +Gh   +  p++   p +e+f  kG y+  rd     +f++krv+++G G+s+ d a +l   a +v+l  r
  gi|557693898|ref|YP_008796952.1| 118 TVLIAAGHGAFT--PRKlGNPSVERFenKGVYYTVRD---KWMFRNKRVVIVGGGDSAVDWALNLKDIASEVYLVHR 189
                                       567777775443..33325699999955666776666...468******************************9988 PP

                          FMO-like 215 sG 216
                                       + 
  gi|557693898|ref|YP_008796952.1| 190 RS 191
                                       75 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.4e-06    0.0039       1      41 [.      12      53 ..      12      98 .. 0.81
   2 ?   -0.5   0.0      0.52   5.9e+02       2      31 ..     161     190 ..     160     193 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.4e-06
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAara.GakvlLveergvlGGlltsg 41
                                      D+ ++G+gp G+ AA  Aa +   k+ ++e  +  GG+lt  
  gi|557693898|ref|YP_008796952.1| 12 DITIIGAGPTGLFAAFYAAGMrSMKTKVIEALDTYGGQLTTL 53
                                      9**************988876267***************974 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.52
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveer 31 
                                       vv+vGGg + v  A+  +    +v Lv++r
  gi|557693898|ref|YP_008796952.1| 161 VVIVGGGDSAVDWALNLKDIASEVYLVHRR 190
                                       9*********99999999999999999887 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 ?   13.2   0.0   8.3e-05     0.093       3      40 ..     154     191 ..     153     281 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.3e-05
                     NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                       + +++k+v++vGgG+ A   + +l +   +v +v  ++
  gi|557693898|ref|YP_008796952.1| 154 WMFRNKRVVIVGGGDSAVDWALNLKDIASEVYLVHRRS 191
                                       6789**********************999999998884 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 ?   -2.4   0.0       2.8   3.2e+03       7      34 ..      13      43 ..      11      51 .. 0.69
   2 ?   11.5   0.0   0.00015      0.17       2      38 ..     156     192 ..     155     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.8
                                      EEEES-SHHHHH...HHHHHHHTT--EEEEE CS
                              IlvN  7 iaviGyGsqGha...qalnlrdsgldvvvgl 34
                                      i++iG G  G      a  +r  + +v+ +l
  gi|557693898|ref|YP_008796952.1| 13 ITIIGAGPTGLFaafYAAGMRSMKTKVIEAL 43
                                      8899999988641124567777777777665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00015
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT- CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregs 38 
                                       +++k+++++G G  +  +alnl+d   +v +  r+++
  gi|557693898|ref|YP_008796952.1| 156 FRNKRVVIVGGGDSAVDWALNLKDIASEVYLVHRRSE 192
                                       689*************************998887765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0011       1.3       1      28 [.      12      40 ..      12      58 .. 0.79
   2 ?    1.4   0.0      0.12   1.4e+02       2      29 ..     161     194 ..     160     222 .. 0.82
   3 ?   -2.6   0.0       1.9   2.1e+03     347     364 ..     274     290 ..     269     291 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0011
                                      CEEEE-SSHHHHHHHHHHHHT.T--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarl.GakvlLi 28
                                      d+++iG+G  G+ AA+ aa +  +k++ i
  gi|557693898|ref|YP_008796952.1| 12 DITIIGAGPTGLFAAFYAAGMrSMKTKVI 40
                                      799*************9997724566555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.12
                                       EEEE-SSHHHHHHHHHHHHTT--EEEE......E CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLi......t 29 
                                       v+++GgG + +  Al+++    +v L+       
  gi|557693898|ref|YP_008796952.1| 161 VVIVGGGDSAVDWALNLKDIASEVYLVhrrsefR 194
                                       99***********************994444442 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.9
                                       -TTSBBSSSBTEEE-CGG CS
                              GIDA 347 lntLetkkvkgLflAGqi 364
                                       +++ et+ ++g+++AG+i
  gi|557693898|ref|YP_008796952.1| 274 NARCETN-IPGVYAAGDI 290
                                       5566776.9*******99 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0009         1       3      17 ..      12      26 ..      10      45 .. 0.83
   2 ?   -1.1   0.0      0.75   8.4e+02       3      35 ..     160     192 ..     158     198 .. 0.81
   3 ?   -1.2   0.0      0.83   9.3e+02     134     156 ..     222     244 ..     205     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0009
                                      EEEEE--SHHHHHHH CS
                     FAD_binding_3  3 dVlIVGaGpaGlmla 17
                                      d+ I+GaGp+Gl +a
  gi|557693898|ref|YP_008796952.1| 12 DITIIGAGPTGLFAA 26
                                      789**********99 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.75
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                        V+IVG+G + +  al L+    +v lv +rs+
  gi|557693898|ref|YP_008796952.1| 160 RVVIVGGGDSAVDWALNLKDIASEVYLVHRRSE 192
                                       699*****9988888888888777888888776 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.83
                                       CCCCCCCEEEECCTTEEEEEEEE CS
                     FAD_binding_3 134 deegvtaevrdketgeeetvrak 156
                                        e  ++ +v++++tgee+t++++
  gi|557693898|ref|YP_008796952.1| 222 GEHLEKITVYNNKTGEETTIECD 244
                                       4555677889999********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 ?    4.6   0.0     0.025        29       2      15 ..      15      28 ..      14      56 .. 0.78
   2 ?    3.9   0.0     0.043        48     103     155 ..      73     125 ..      70     126 .. 0.75
   3 ?   -1.2   0.0       1.6   1.7e+03       1      16 [.     162     177 ..     162     195 .. 0.82
   4 ?   -2.7   0.0       4.5     5e+03     138     155 ..     235     252 ..     223     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.025
                     NAD_binding_9  2 ivGaGprGlavler 15
                                      i+GaGp+Gl ++  
  gi|557693898|ref|YP_008796952.1| 15 IIGAGPTGLFAAFY 28
                                      9********98865 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.043
                     NAD_binding_9 103 lfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       l+++l +++++     +++++v++l++ ++g   l++d+  +  + V +A Gh
  gi|557693898|ref|YP_008796952.1|  73 LAKNLYEQASAYNPTFHFSERVLNLTRLDGGIIELTTDKGVHFSKTVLIAAGH 125
                                       55666667765444456699**********986667777788889999****9 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.6
                     NAD_binding_9   1 aivGaGprGlavlerL 16 
                                       +ivG+G +++  + +L
  gi|557693898|ref|YP_008796952.1| 162 VIVGGGDSAVDWALNL 177
                                       69****9999888877 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 4.5
                     NAD_binding_9 138 ladgaslaadaVvLAlGh 155
                                       + +++++++da+ L lGh
  gi|557693898|ref|YP_008796952.1| 235 TGEETTIECDALLLQLGH 252
                                       445678999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2268.64
//
Query:       gi|557693899|ref|YP_008796953.1|  [L=330]
Description: phosphate uptake regulator [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   41.1   1.2    8.9e-10   38.9   0.8    2.2  2  PhoU            PhoU domain
    2.5e-10   40.1   0.0    5.7e-10   38.9   0.0    1.7  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
       0.01   15.7   0.2      0.081   12.8   0.0    2.4  2  TOBE_3          TOBE-like domain
       0.12   11.7   0.0       0.19   11.1   0.0    1.3  1  YPEB            YpeB sporulation


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 !   38.9   0.8     2e-13   8.9e-10       1      87 [.     136     225 ..     136     226 .. 0.83
   2 ?   -0.4   0.0      0.37   1.6e+03      16      75 ..     257     312 ..     242     319 .. 0.55

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2e-13
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HH..HGG-SHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeierslleal.ak..rqplaedlrellsllriard 74 
                                       lrr  ++v  m+++a+ ++  +d  lar  + rd+e+drl++ + r l  al      + l++    ll+++ +a+ 
  gi|557693899|ref|YP_008796953.1| 136 LRRQYNLVMGMVEYAVNSVLMDDSSLARVAVTRDEEVDRLYFTLVRVLRSALvDPalAKRLNTSPLSLLDIRVAAKF 212
                                       578889**************************************77755555333334445445555789999**** PP

                                       HHHHHHHHHHHHH CS
                              PhoU  75 lERigDhavniae 87 
                                       +E  gD+a+++a+
  gi|557693899|ref|YP_008796953.1| 213 IEDAGDQAAEMAK 225
                                       ***********98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.37
                                       HHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHH CS
                              PhoU  16 lealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardl 75 
                                       +ea+++ +  l+++v  ++ e  +  +e+ r+ +   ++  +l    +  ++l r++ dl
  gi|557693899|ref|YP_008796953.1| 257 IEAFFSHEITLVNRVTGLRTEFMKRSEEFLRK-VSGRGETASLY---KLHFHLARVCEDL 312
                                       67777777777777776666666666666555.43333333333...3322344444443 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   1.3e-13   5.7e-10       2      43 ..      10      52 ..       9      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.3e-13
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCHH CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgd.kiilrplks 43
                                      ++G+s  v++Pke+++ +g+++G+ v++++ +d ++ ++p k+
  gi|557693899|ref|YP_008796953.1| 10 TGGSSFTVTLPKEWVERMGLSKGSQVIIRPAEDgGLYIYPDKP 52
                                      89*******************************9999999876 PP

>> TOBE_3  TOBE-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05     0.081      32      59 ..      12      39 ..       3      40 .. 0.91
   2 ?   -0.7   0.1      0.31   1.4e+03      25      43 ..     111     127 ..     105     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                            TOBE_3 32 geliEvelprdrfeelglaeGetvylrP 59
                                      g+ ++v lp++  e++gl++G++v +rP
  gi|557693899|ref|YP_008796953.1| 12 GSSFTVTLPKEWVERMGLSKGSQVIIRP 39
                                      7899***********************9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.31
                            TOBE_3  25 LerlgdtgeliEvelprdr 43 
                                       +  +++++e +Ev++  d+
  gi|557693899|ref|YP_008796953.1| 111 I--VDEADESVEVQIVLDE 127
                                       4..3458889999986555 PP

>> YPEB  YpeB sporulation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.2e-05      0.19      73     118 ..     194     240 ..     159     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.2e-05
                              YPEB  73 enlgqLPlstlelsktekFLsqvgdfsyslakkdldge.pLteeeyk 118
                                       + l++ Pls l+++ ++kF++  gd + ++ak++l+++ p++++  +
  gi|557693899|ref|YP_008796953.1| 194 KRLNTSPLSLLDIRVAAKFIEDAGDQAAEMAKEKLRNKkPMSDDVKQ 240
                                       568888**************************999877477776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2296.15
//
Query:       gi|557693900|ref|YP_008796954.1|  [L=152]
Description: large subunit ribosomal protein L22 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   82.3   0.1      3e-23   82.0   0.1    1.1  1  Ribosomal_L22  Ribosomal protein L22p/L17e


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 !   82.0   0.1   1.7e-27     3e-23       2     100 ..      20     146 ..      19     148 .. 0.96

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 1.7e-27
                                       EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT.-SST...........................THHHHHHHHHHH CS
                     Ribosomal_L22   2 kgsnlrvsfkklrevarlIrgmkveeAlkyLkf.skkk...........................aakfvlklLkna 50 
                                       + +++ vs+k +rev+++++g ++ eA++ L++  +k+                           +++++lkl+++ 
  gi|557693900|ref|YP_008796954.1|  20 SLREIDVSPKWAREVCEALKGLTIPEAKRLLEDvINKRrmipykryrkkrahhaetkgpggypvkVSQYLLKLVESL 96 
                                       6799*****************************955556************************************** PP

                                       HHHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEE CS
                     Ribosomal_L22  51 eanaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchiev 100
                                       eanae kgld+++  I+++  +kg+ l++   rA Gr +p+++ ++hie+
  gi|557693900|ref|YP_008796954.1|  97 EANAEFKGLDPEKTEIVHAASHKGRVLRKNIERAFGRSSPYNRTYVHIEL 146
                                       ************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1121.99
//
Query:       gi|557693901|ref|YP_008796955.1|  [L=203]
Description: small subunit ribosomal protein S3 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   76.6   0.2      3e-21   75.7   0.2    1.5  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    5.1e-12   45.4   0.1    1.1e-11   44.4   0.1    1.6  1  KH_2            KH domain
      0.009   15.8   0.1      0.045   13.6   0.0    2.1  2  KH_1            KH domain
       0.01   15.8   0.1      0.021   14.7   0.1    1.5  1  Tautomerase     Tautomerase enzyme


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 !   75.7   0.2   6.8e-25     3e-21       1      83 []      99     182 ..      99     182 .. 0.99

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 6.8e-25
                                       HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTE CS
                    Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyG 75 
                                       ia+ l +++++Rr+   a++r+m+agakG+++ +sG+L+ + ++r+ek++eG +p+  + +++++ ++++++ +k G
  gi|557693901|ref|YP_008796955.1|  99 IAQDLARGLRYRRVGFWAVKRIMEAGAKGVEVHISGKLT-SARSRTEKFTEGFMPKsgELAMNYVLEGKSSVLLKTG 174
                                       89*************************************.*****************99****************** PP

                                       EEEEEEEE CS
                    Ribosomal_S3_C  76 iiGvkVwI 83 
                                        +Gv+V I
  gi|557693901|ref|YP_008796955.1| 175 LFGVRVLI 182
                                       ******87 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.1   2.4e-15   1.1e-11       2      77 ..      17      89 ..      16      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 2.4e-15
                                      HHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTTG CS
                              KH_2  2 ipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkkpe 77
                                      i e+l +++k+a  ++v I  t+ +++++i++ +p +vIG +G+ ik+i+++l+k+++ +e+  V   +v+V+ pe
  gi|557693901|ref|YP_008796955.1| 17 IEEYLREKLKNAFFGGVSISFTPLGTRVTIYAMRPSRVIGPKGKVIKEITEALEKQFG-VENPVVT--VVEVEVPE 89
                                      889****************99************************************7.8888777..77887776 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0     1e-05     0.045      12      27 ..      52      67 ..      42      70 .. 0.90
   2 ?   -1.3   0.0      0.45     2e+03      23      35 ..     118     130 ..     117     142 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                                      HHHHTGGGHHHHHHHH CS
                              KH_1 12 griIGkgGsnIkeIre 27
                                      +r+IG++G++IkeI e
  gi|557693901|ref|YP_008796955.1| 52 SRVIGPKGKVIKEITE 67
                                      59************87 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.45
                                       HHHHHHHT-E.EEE CS
                              KH_1  23 keIreetgak.Ikv 35 
                                       k+I+e  gak + v
  gi|557693901|ref|YP_008796955.1| 118 KRIME-AGAKgVEV 130
                                       67777.56554443 PP

>> Tautomerase  Tautomerase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   4.7e-06     0.021      16      53 ..      58      95 ..      49     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.7e-06
                                      HHHHHHHHHHHHHHHHTS-GGG-EEEEEEE-TTSEEET CS
                       Tautomerase 16 KaeLaervTealvealgaprsaivVvieEvpaenwgvg 53
                                      K ++++++Teal +++g+ ++ ++Vv  Evp+ n +v 
  gi|557693901|ref|YP_008796955.1| 58 KGKVIKEITEALEKQFGVENPVVTVVEVEVPELNPYVM 95
                                      6789**********************999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1458.82
//
Query:       gi|557693902|ref|YP_008796956.1|  [L=66]
Description: large subunit ribosomal protein L29 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   55.7   4.2    4.3e-15   55.4   4.2    1.1  1  Ribosomal_L29  Ribosomal L29 protein
     0.0011   18.9   8.4      0.017   15.2   0.7    2.1  2  DUF1192        Protein of unknown function (DUF1192)
  ------ inclusion threshold ------
      0.054   14.0   0.7       0.09   13.3   0.7    1.4  1  DUF2482        Hypothetical protein of unknown function (DUF2
      0.063   13.0   1.8      0.064   12.9   1.8    1.0  1  HBB            Helical and beta-bridge domain
      0.099   12.5   2.7       0.19   11.6   2.7    1.4  1  Takusan        Takusan
       0.13   12.5   2.8       0.21   11.8   2.8    1.4  1  DUF1811        Protein of unknown function (DUF1811)
        4.4    7.6   5.7         16    5.8   5.7    2.0  1  VPS11_C        Vacuolar protein sorting protein 11 C terminal


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 !   55.4   4.2   1.7e-18   4.3e-15       1      57 []       4      61 ..       4      61 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.7e-18
                                      HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHHH CS
                     Ribosomal_L29  1 kelrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlrer 57
                                      +elre++++eL ek++elk+eL +       g  +enp+r r++Rk+IAR +Tvl e+
  gi|557693902|ref|YP_008796956.1|  4 QELREMNEKELAEKIEELKAELRQVVSEIGKGgMVENPMRKRELRKEIARAYTVLAEK 61
                                      69***************************999899*********************97 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.7   6.6e-06     0.017      15      44 ..       4      33 ..       1      40 [. 0.88
   2 !    8.4   1.7   0.00085       2.2      30      50 ..      45      65 ..      42      66 .] 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.6e-06
                           DUF1192 15 qDLslLSveELeerIalLeaEIaRleaaia 44
                                      q+L  ++ +EL e I++L+aE   +  +i 
  gi|557693902|ref|YP_008796956.1|  4 QELREMNEKELAEKIEELKAELRQVVSEIG 33
                                      88999****************998887775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00085
                           DUF1192 30 alLeaEIaRleaaiakkkasr 50
                                       +L++EIaR+ + +a+k+ ++
  gi|557693902|ref|YP_008796956.1| 45 RELRKEIARAYTVLAEKRRQK 65
                                      589**************9876 PP

>> DUF2482  Hypothetical protein of unknown function (DUF2482)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.7   3.5e-05      0.09       2      30 ..       5      33 ..       4      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.5e-05
                           DUF2482  2 efKdmtqeeikdllaeKskeLyelieeik 30
                                      e+++m+++e+ + ++e + eL++++ ei 
  gi|557693902|ref|YP_008796956.1|  5 ELREMNEKELAEKIEELKAELRQVVSEIG 33
                                      899************************96 PP

>> HBB  Helical and beta-bridge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.8   2.5e-05     0.064       2      55 ..       3      55 ..       2      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                                      CHCHCCCCHHCCCCCCCHHHHHHHHHCCCCHHHHSTTTECCHCHHHHHCHCHHH CS
                               HBB  2 ikeaketdepklqdeysrLvegLreaeeereeeyvleeepilpdeileeavpgl 55
                                      ++e++e +e++l+++++ L   Lr++ +e  +  ++e+ p++ +e+ +e++ + 
  gi|557693902|ref|YP_008796956.1|  3 LQELREMNEKELAEKIEELKAELRQVVSEIGKGGMVEN-PMRKRELRKEIARAY 55
                                      689*************************9999999999.*******99987765 PP

>> Takusan  Takusan
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.7   7.4e-05      0.19       9      32 ..       8      31 ..       4      32 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.4e-05
                           Takusan  9 ilekeqakkklEeLkleLrkitre 32
                                       ++++++ +k+EeLk eLr++ +e
  gi|557693902|ref|YP_008796956.1|  8 EMNEKELAEKIEELKAELRQVVSE 31
                                      6899****************9776 PP

>> DUF1811  Protein of unknown function (DUF1811)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.8   8.3e-05      0.21       4      52 ..       7      60 ..       4      65 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.3e-05
                                      HT--HHHHHHHHHHHHHHHHHHH.HT..T-HHH..HHHHHHHHHHHHHHHS-GG CS
                           DUF1811  4 SemseeeLkqeiaklkekarkae.ql..givne..lavlerkialAksYlldps 52
                                       em+e+eL ++i++lk + r+   +   g + e  +   e + ++A++Y++ ++
  gi|557693902|ref|YP_008796956.1|  7 REMNEKELAEKIEELKAELRQVVsEIgkGGMVEnpMRKRELRKEIARAYTVLAE 60
                                      69***************9998641332233434013444447789****98555 PP

>> VPS11_C  Vacuolar protein sorting protein 11 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   5.7    0.0064        16       4      44 ..       3      37 ..       1      38 [. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0064
                           VPS11_C  4 irelrraQees.adrhdlFkaaLeeseDrFkvvadyFGRGvm 44
                                       +elr+++e+  a++ + +ka+L++      vv++ +G+G+m
  gi|557693902|ref|YP_008796956.1|  3 LQELREMNEKElAEKIEELKAELRQ------VVSE-IGKGGM 37
                                      689999887655***********99......6666.777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1711  (0.095432); expected 358.6 (0.02)
Passed bias filter:                      828  (0.0461822); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 506.51
//
Query:       gi|557693903|ref|YP_008796957.1|  [L=79]
Description: ribonuclease P subunit P29 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-07   30.5   0.3    2.9e-07   30.3   0.3    1.2  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 !   30.3   0.3   1.6e-11   2.9e-07      26      82 ..      23      73 ..       5      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.6e-11
                                      EEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHHHH CS
                           UPF0086 26 ikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpadRa 82
                                       +G+Vv+Et+n+  + t  ++ k  pK +svF ++ k      v+G ++  rp +R 
  gi|557693903|ref|YP_008796957.1| 23 SEGVVVSETRNMVMVKT-MKGAKSFPKMNSVFIVDGK-----VVEGVRMVARPFERL 73
                                      58***************.899***************7.....89***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.33u 0.28s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 572.14
//
Query:       gi|557693904|ref|YP_008796958.1|  [L=109]
Description: small subunit ribosomal protein S17 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   92.8   2.3    1.3e-26   92.4   2.3    1.1  1  Ribosomal_S17    Ribosomal protein S17
  ------ inclusion threshold ------
      0.054   13.9   0.8        0.1   13.0   0.0    1.8  2  Ribosomal_S17_N  Ribosomal_S17 N-terminal
       0.46   10.3   3.2       0.94    9.3   3.2    1.4  1  zf-C3H1          Putative zinc-finger domain


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 !   92.4   2.3   2.2e-30   1.3e-26       1      68 []      38     106 ..      38     106 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 2.2e-30
                                       EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
                     Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                                       GvV ++km+kTvvV+ e+ v+ +kyk+y++rr++++ah ++++ + vGD+Vr +ecrPlSkt++fvv+e
  gi|557693904|ref|YP_008796958.1|  38 GVVYKKKMNKTVVVENEHIVYVKKYKRYMRRRSRISAHLPPCIdADVGDRVRLGECRPLSKTVSFVVLE 106
                                       99*****************************************************************86 PP

>> Ribosomal_S17_N  Ribosomal_S17 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.7e-05       0.1      34      69 .]       5      36 ..       2      36 .. 0.83
   2 ?   -1.4   0.2      0.53   3.2e+03      21      21 ..      58      58 ..      40      72 .. 0.45

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.7e-05
                                      ----TT----GGGGS-----TTSSSSSS----S-EE CS
                   Ribosomal_S17_N 34 knvglgfktPkeAiegtYiDkKCPFtGnvsirGriL 69
                                      +n+g+  + Pk+  +    D  CPF G+ s+rG +L
  gi|557693904|ref|YP_008796958.1|  5 RNIGIPVNPPKTSCN----DPDCPFHGKLSVRGILL 36
                                      677777777887777....899***********766 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.53
                                      - CS
                   Ribosomal_S17_N 21 e 21
                                       
  gi|557693904|ref|YP_008796958.1| 58 Y 58
                                      1 PP

>> zf-C3H1  Putative zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.2   0.00016      0.94      11      18 ..      18      25 ..      17      25 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00016
                           zf-C3H1 11 CnDpsCef 18
                                      CnDp+C+f
  gi|557693904|ref|YP_008796958.1| 18 CNDPDCPF 25
                                      ******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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: 00:00:00.40
# Mc/sec: 809.68
//
Query:       gi|557693905|ref|YP_008796959.1|  [L=144]
Description: large subunit ribosomal protein L14 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  110.7   0.2    5.2e-32  110.5   0.2    1.1  1  Ribosomal_L14  Ribosomal protein L14p/L23e
  ------ inclusion threshold ------
       0.07   13.0   0.8          1    9.3   0.2    2.2  2  DUF1952        Domain of unknown function (DUF1952)


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 !  110.5   0.2   5.7e-36   5.2e-32       4     122 .]      26     144 .]      23     144 .] 0.93

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 5.7e-36
                                       SS-EEE--SSSSBSEEEEEEETT-.--....-EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-E CS
                     Ribosomal_L14   4 lktrlkvaDNsgakevecikvlggkkr....kaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsv 76 
                                        ++ +++aDNsga+ +++i+v g ++r    +aa vGd++ v+vkk++      +++ ++a+v+r++k++rr+dG++
  gi|557693905|ref|YP_008796959.1|  26 PGSLITCADNSGAQILKIIQVHGVSTRlrrvPAAAVGDKVSVTVKKGSA---DLRKKPMHAIVIRQRKPYRRSDGTW 99 
                                       67899******************994445569**************998...899999******************* PP

                                       EEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
                     Ribosomal_L14  77 irfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApevl 122
                                       i+f++ aaVl++ +g+++Gt+i+gpva+e++e+ ++++++ A++++
  gi|557693905|ref|YP_008796959.1| 100 ISFEETAAVLVTPEGDLKGTEIKGPVAKEAAER-WPRVANAASMIV 144
                                       ********************************9.********9986 PP

>> DUF1952  Domain of unknown function (DUF1952)
   #    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      27      45 ..      45      63 ..      38      75 .. 0.85
   2 ?    9.3   0.2   0.00011         1      27      72 ..      94     141 ..      85     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.02
                           DUF1952 27 rldGavvrfrelePlkvGs 45
                                      ++ G   r+r ++   vG 
  gi|557693905|ref|YP_008796959.1| 45 QVHGVSTRLRRVPAAAVGD 63
                                      689999********99995 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00011
                           DUF1952  27 rldGavvrfrelePlkv...GslrisrleveveGeeaerWaeriavaas 72 
                                       r dG+++ f e     v   G l+ ++++  v  e aerW  r+a aas
  gi|557693905|ref|YP_008796959.1|  94 RSDGTWISFEETAAVLVtpeGDLKGTEIKGPVAKEAAERWP-RVANAAS 141
                                       789*******999888767799******************5.7777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1127.62
//
Query:       gi|557693906|ref|YP_008796960.1|  [L=119]
Description: large subunit ribosomal protein L24 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-27   93.3   0.8    1.2e-26   92.9   0.8    1.1  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    3.5e-06   26.8   2.9    5.8e-06   26.1   2.9    1.4  1  KOW            KOW motif
  ------ inclusion threshold ------
       0.08   13.1   0.2       0.22   11.7   0.1    1.7  2  LAL_C2         L-amino acid ligase C-terminal domain 2
      0.094   12.5   0.6       0.25   11.1   0.1    1.9  2  Mitoc_L55      Mitochondrial ribosomal protein L55


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 !   92.9   0.8   2.7e-30   1.2e-26       1      81 [.       3     116 ..       3     117 .. 0.99

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 2.7e-30
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................xx RF
                     Ribosomal_L26   1 sssrrkqrKahfnapshirrklmsapLskeLrekygvrslpir................................gv 45 
                                       s s+rkqr +++nap+hi  k++sa+Ls eLr+kyg+r++++r                                +v
  gi|557693906|ref|YP_008796960.1|   3 SASPRKQRLRRYNAPKHILGKFLSAHLSPELRNKYGRRAVRLRqgdtvkvikgtfkniegkvkrvdvkrqmayveNV 79 
                                       789************************************************************************** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                     Ribosomal_L26  46 trekangttvpvgihpSkvvItklkl.DkdrkkiLer 81 
                                       + +ka+g+tv v+i+  +++It+l+l Dk rk+ Le 
  gi|557693906|ref|YP_008796960.1|  80 SIKKADGSTVDVPIRIPNLMITQLNLdDKYRKEKLED 116
                                       ***********************************95 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   2.9   1.3e-09   5.8e-06       2      32 .]      47      77 ..      46      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.3e-09
                                      TSEEEESSSTTTTCEEEEEEEETTTTEEEEE CS
                               KOW  2 GdhVkVvsGphkGktGkVvkvdqhkvrVfvd 32
                                      Gd+VkV+ G++k+ +GkV++vd ++  ++v+
  gi|557693906|ref|YP_008796960.1| 47 GDTVKVIKGTFKNIEGKVKRVDVKRQMAYVE 77
                                      9**********************99555554 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 ?   -1.0   0.0      0.45     2e+03      31      41 ..      42      52 ..      22      58 .. 0.71
   2 ?   11.7   0.1   4.9e-05      0.22       8      42 ..      61      92 ..      54      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.45
                            LAL_C2 31 ltvkpGdevrp 41
                                      ++ + Gd+v+ 
  gi|557693906|ref|YP_008796960.1| 42 VRLRQGDTVKV 52
                                      44578888876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.9e-05
                            LAL_C2  8 pGrlkaveGleearalpgvveveltvkpGdevrpp 42
                                      +G++k+v+     r++++v+ v+++++ G++v  p
  gi|557693906|ref|YP_008796960.1| 61 EGKVKRVDVK---RQMAYVENVSIKKADGSTVDVP 92
                                      5888888887...9******************877 PP

>> Mitoc_L55  Mitochondrial ribosomal protein L55
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.23     1e+03      58      82 ..      13      36 ..       8      63 .. 0.62
   2 ?   11.1   0.1   5.6e-05      0.25      36      72 ..      71     105 ..      50     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.23
                         Mitoc_L55 58 ryrEPrrilampvdldtLseeerra 82
                                      ry+ P++il   +   +Ls+e r  
  gi|557693906|ref|YP_008796960.1| 13 RYNAPKHILGKFLS-AHLSPELRNK 36
                                      56777777766665.4577765543 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.6e-05
                         Mitoc_L55  36 rqayarlYpvllvkqDGsTikiryrEPrrilampvdl 72 
                                       rq  a + +v + k DGsT+ + +r P  +++  ++l
  gi|557693906|ref|YP_008796960.1|  71 RQ-MAYVENVSIKKADGSTVDVPIRIPNLMITQ-LNL 105
                                       33.3445678899**************998863.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 889.25
//
Query:       gi|557693907|ref|YP_008796961.1|  [L=238]
Description: small subunit ribosomal protein S4e [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-20   72.9   0.0    2.8e-20   72.0   0.0    1.5  1  Ribosomal_S4e  Ribosomal family S4e
    7.5e-10   38.4   0.0    1.5e-09   37.4   0.0    1.5  1  S4             S4 domain
      2e-08   34.2   5.2    3.9e-08   33.3   5.2    1.4  1  RS4NT          RS4NT (NUC023) domain


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 !   72.0   0.0   4.7e-24   2.8e-20       2      75 .]      89     168 ..      88     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 4.7e-24
                                       TEEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEES......STT-STTEEEEEETTT CS
                     Ribosomal_S4e   2 genyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtiryp......dpdikvnDtvkidlee 72 
                                       genyr+l+++ + ++l k +seea +K+c++ +k  v++g +++ +hdGrti+++         ik+ Dt+ki +++
  gi|557693907|ref|YP_008796961.1|  89 GENYRVLIKPGKGLTLAKTSSEEAGFKICQVVRKNHVRGGALMIGLHDGRTILFRgemldkGRAIKTLDTLKIAVPS 165
                                       8*****************************************************999**99667************* PP

                                       TEE CS
                     Ribosomal_S4e  73 nkI 75 
                                       ++I
  gi|557693907|ref|YP_008796961.1| 166 QEI 168
                                       *98 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   2.5e-13   1.5e-09      11      48 .]      46      83 ..      40      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.5e-13
                                      TSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                                S4 11 glassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                       +a     Ar+lI++G++ V+G+vvkdp ++++ +Dv+
  gi|557693907|ref|YP_008796961.1| 46 NYADNAHTARRLIKQGKFMVDGRVVKDPRFPLGLMDVL 83
                                      67888899****************************85 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   5.2   6.5e-12   3.9e-08       6      36 ..       3      31 ..       2      32 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 6.5e-12
                                      -EETTTS-TTS---SSSSSEE----SSSS-T CS
                             RS4NT  6 HLKrlaAPkhWpldkkegvfavkPspGPHkl 36
                                      HLK laAP+h+p  kk  vf+v PspGPH++
  gi|557693907|ref|YP_008796961.1|  3 HLKTLAAPRHYP--KKATVFTVAPSPGPHAK 31
                                      **********85..***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1807.15
//
Query:       gi|557693908|ref|YP_008796962.1|  [L=174]
Description: large subunit ribosomal protein L5 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   73.4   0.0    3.2e-20   72.1   0.0    1.8  2  Ribosomal_L5_C  ribosomal L5P family C-terminus
    1.1e-17   64.1   0.2    3.2e-17   62.6   0.1    1.8  2  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 ?   -2.1   0.0      0.49   4.4e+03      21      23 ..      41      43 ..      29      60 .. 0.46
   2 !   72.1   0.0   3.6e-24   3.2e-20       1      82 [.      64     142 ..      64     171 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.49
                    Ribosomal_L5_C 21 lev 23
                                      ++ 
  gi|557693908|ref|YP_008796962.1| 41 VNQ 43
                                      432 PP

  == domain 2  score: 72.1 bits;  conditional E-value: 3.6e-24
                    Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivtta 77 
                                       pi+++vtLr++ ++efl+k l +v +r++      kss+d+ G +sfGike++++p+ +y+++ gi Gmd+t+++ +
  gi|557693908|ref|YP_008796962.1|  64 PIALRVTLRKAAAEEFLRKGLAAVNNRIK------KSSIDSMGSFSFGIKEHLDIPGTRYNPELGIIGMDVTVHLVK 134
                                       79***************************......****************************************99 PP

                    Ribosomal_L5_C  78 k...tdee 82 
                                       +   ++++
  gi|557693908|ref|YP_008796962.1| 135 PgyrVSKR 142
                                       97664442 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.1   3.6e-21   3.2e-17       4      56 ..      10      59 ..       8      60 .. 0.97
   2 ?   -2.1   0.0      0.56     5e+03      16      36 ..     150     166 ..     148     167 .. 0.62

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 3.6e-21
                                      TS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCS CS
                      Ribosomal_L5  4 qvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFki 56
                                      + Pr+eK+v+n+ vGe g++   le+a k+L++++ QkP v+ka+k+i++F+i
  gi|557693908|ref|YP_008796962.1| 10 RRPRIEKVVVNCAVGEGGAR---LERAQKILESLVNQKPEVRKARKTIRGFGI 59
                                      78******************...****************************98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.56
                                       E-SSSSSCHHHHHCCHHHHCC CS
                      Ribosomal_L5  16 gvGeagedkkllekaakeLae 36 
                                       g+G+ +     +++a+++L++
  gi|557693908|ref|YP_008796962.1| 150 GMGQRV----SVDEAIEFLRQ 166
                                       555433....37888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1234.50
//
Query:       gi|557693909|ref|YP_008796963.1|  [L=53]
Description: small subunit ribosomal protein S14 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   35.1   1.6    9.1e-09   34.9   1.6    1.0  1  Ribosomal_S14   Ribosomal protein S14p/S29e
     0.0064   16.1   7.1       0.39   10.4   0.3    2.2  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
  ------ inclusion threshold ------
      0.017   15.1   2.2       0.02   14.8   2.2    1.1  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.022   14.8   0.1      0.026   14.5   0.1    1.2  1  DZR             Double zinc ribbon
      0.051   13.5   3.7        0.4   10.6   0.6    2.1  2  zf-C4_ClpX      ClpX C4-type zinc finger
      0.054   13.8   0.3      0.061   13.6   0.3    1.1  1  C1_2            C1 domain
      0.063   13.2   5.9       0.14   12.0   5.9    1.6  1  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
      0.074   12.7   0.4        6.7    6.4   0.0    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
      0.094   13.0   2.2        0.2   12.0   0.9    1.8  2  DUF3268         zinc-finger-containing domain
       0.13   12.1   6.8       0.85    9.6   6.5    2.0  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.15   12.2   2.5        4.2    7.6   0.3    2.1  2  SR1P            SR1 protein
       0.21   11.8   3.7        1.9    8.8   0.2    2.1  2  DUF2757         Protein of unknown function (DUF2757)
       0.25   11.4   0.3        0.3   11.1   0.3    1.1  1  DUF1451         Zinc-ribbon containing domain
       0.34   11.4   3.3        7.1    7.1   0.2    2.1  2  OrsD            Orsellinic acid/F9775 biosynthesis cluster pr
        0.4   10.6   8.6        2.9    7.8   0.3    2.3  2  zf-CCHC_2       Zinc knuckle
        1.5    8.4   8.0       0.19   11.2   1.0    2.1  2  DUF2688         Protein of unknown function (DUF2688)
        4.5    7.8   6.0         16    6.1   0.4    2.0  2  DUF1660         Prophage protein (DUF1660)


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 !   34.9   1.6   8.7e-12   9.1e-09       4      50 ..       4      49 ..       2      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 8.7e-12
                                      ----SS..CTTT---SSS--SSSEE-GGG-..EHHHHHHHTTT...TT- CS
                     Ribosomal_S14  4 klprnssptrirnrCrvtGrprGvirkfgL..sRicfRelAlkgelpGv 50
                                      k p++ + +++ + Cr +G + Gvirk+gL  +R c+ e A k    G+
  gi|557693909|ref|YP_008796963.1|  4 KPPKQRKFGKGVHVCRRCGTSVGVIRKYGLyiCRRCINEIAPK---LGF 49
                                      78999999*******************************9988...665 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 !    9.1   1.6   0.00095         1      23      31 ..      17      25 ..      14      26 .. 0.82
   2 !   10.4   0.3   0.00037      0.39      20      27 ..      32      39 ..      32      42 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00095
                           zf-RRN7 23 yCrrChtqe 31
                                      +CrrC+t +
  gi|557693909|ref|YP_008796963.1| 17 VCRRCGTSV 25
                                      9*****965 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00037
                           zf-RRN7 20 GfyyCrrC 27
                                      G+y+CrrC
  gi|557693909|ref|YP_008796963.1| 32 GLYICRRC 39
                                      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 ?   14.8   2.2   1.9e-05      0.02      15      43 ..      11      39 ..       7      42 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                     Zn_Tnp_IS1595 15 Wpng.fvCPhCgsrkayriktrglfqCkeC 43
                                      ++ g +vC +Cg +++  i++ gl+ C++C
  gi|557693909|ref|YP_008796963.1| 11 FGKGvHVCRRCG-TSVGVIRKYGLYICRRC 39
                                      6777678*****.889999999******** PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.5e-05     0.026      10      41 ..      13      46 ..       5      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                               DZR 10 pdarfCseCgtklkavaa..edrCpsCgekvdpe 41
                                      ++ ++C +Cgt++    +   + C +C  ++ p+
  gi|557693909|ref|YP_008796963.1| 13 KGVHVCRRCGTSVGVIRKygLYICRRCINEIAPK 46
                                      56789*******875555889******8887665 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.036        38      20      29 ..      13      21 ..       7      25 .. 0.86
   2 ?   10.6   0.6   0.00038       0.4      22      32 ..      32      42 ..      24      45 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.036
                        zf-C4_ClpX 20 pngvyICdeC 29
                                        gv++C +C
  gi|557693909|ref|YP_008796963.1| 13 K-GVHVCRRC 21
                                      3.7******9 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00038
                        zf-C4_ClpX 22 gvyICdeCvel 32
                                      g+yIC +C+++
  gi|557693909|ref|YP_008796963.1| 32 GLYICRRCINE 42
                                      68*******86 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   5.8e-05     0.061      14      38 ..      11      39 ..       2      44 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.8e-05
                              C1_2 14 dssesfnCsaCgrk...idgff.YsCseC 38
                                        ++ + C+ Cg++   i ++  Y+C +C
  gi|557693909|ref|YP_008796963.1| 11 FGKGVHVCRRCGTSvgvIRKYGlYICRRC 39
                                      5678899*******886555559***999 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 ?   12.0   5.9   0.00013      0.14       3      28 ..      17      40 ..      16      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                      B-TTT--BBEEEECTTEEEEE-TTTT CS
                      zf-FPG_IleRS  3 pCpRCwryiervgqagrstyfCprCq 28
                                      +C+RC++ +  +++  ++ y+C rC 
  gi|557693909|ref|YP_008796963.1| 17 VCRRCGTSVGVIRK--YGLYICRRCI 40
                                      8*************..*********7 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   0.0    0.0063       6.7       3      12 ..      16      25 ..      14      28 .. 0.87
   2 ?    5.0   0.1     0.017        18       3      13 ..      34      44 ..      32      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0063
                            zf_UBZ  3 ylCerCgkei 12
                                      ++C rCg+++
  gi|557693909|ref|YP_008796963.1| 16 HVCRRCGTSV 25
                                      69*****987 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.017
                            zf_UBZ  3 ylCerCgkeip 13
                                      y+C rC  ei 
  gi|557693909|ref|YP_008796963.1| 34 YICRRCINEIA 44
                                      9*****88886 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.9   0.00019       0.2      23      45 ..       8      30 ..       4      37 .. 0.88
   2 ?    1.3   0.2       0.4   4.2e+02      30      37 ..      33      40 ..      28      46 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                           DUF3268 23 erskgkllylCpkCdayvgvhkg 45
                                      +r++gk +++C++C+++vgv ++
  gi|557693909|ref|YP_008796963.1|  8 QRKFGKGVHVCRRCGTSVGVIRK 30
                                      7899***************9765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.4
                           DUF3268 30 lylCpkCd 37
                                      ly+C++C 
  gi|557693909|ref|YP_008796963.1| 33 LYICRRCI 40
                                      79999995 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 ?    8.3   0.6     0.002       2.1      24      32 ..      11      24 ..       2      30 .. 0.66
   2 ?    9.6   6.5   0.00081      0.85       4      34 ..      15      43 ..      15      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.002
                    Zn_ribbon_SprT 24 n....YrCrrCk.g 32
                                           + CrrC+ +
  gi|557693909|ref|YP_008796963.1| 11 FgkgvHVCRRCGtS 24
                                      3666689****844 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00081
                    Zn_ribbon_SprT  4 vYrCtgCgreythhlsirrhnYrCrrCkgtL 34
                                      v++C +Cg+ ++++++     Y+CrrC +++
  gi|557693909|ref|YP_008796963.1| 15 VHVCRRCGTSVGVIRKYGL--YICRRCINEI 43
                                      579*9**************..******7666 PP

>> SR1P  SR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.3     0.004       4.2       2      13 ..      14      25 ..      13      29 .. 0.84
   2 ?    5.1   0.1     0.024        25       2       9 ..      32      39 ..      31      44 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                              SR1P  2 GtIvCqtCnatI 13
                                      G+ vC++C++ +
  gi|557693909|ref|YP_008796963.1| 14 GVHVCRRCGTSV 25
                                      888*****9876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.024
                              SR1P  2 GtIvCqtC 9 
                                      G+ +C++C
  gi|557693909|ref|YP_008796963.1| 32 GLYICRRC 39
                                      899***** PP

>> DUF2757  Protein of unknown function (DUF2757)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0018       1.9       6      19 ..      17      30 ..      14      33 .. 0.87
   2 ?    4.7   0.4     0.035        37       5      15 ..      34      44 ..      31      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
                                      EETTT--BTT-SST CS
                           DUF2757  6 rCrhCgkkigtlek 19
                                       Cr+Cg+++g ++k
  gi|557693909|ref|YP_008796963.1| 17 VCRRCGTSVGVIRK 30
                                      7*********9976 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.035
                                      EEETTT--BTT CS
                           DUF2757  5 YrCrhCgkkig 15
                                      Y Cr+C ++i+
  gi|557693909|ref|YP_008796963.1| 34 YICRRCINEIA 44
                                      99****99885 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.3   0.00029       0.3     111     140 ..      12      41 ..       9      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                           DUF1451 111 glGtlvCekCgkelalkkteeippCpkCga 140
                                       g G+ vC++Cg+++ + +   +  C +C +
  gi|557693909|ref|YP_008796963.1|  12 GKGVHVCRRCGTSVGVIRKYGLYICRRCIN 41 
                                       889*************************65 PP

>> 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 ?    5.8   0.4     0.017        18      10      21 ..      14      25 ..       8      29 .. 0.84
   2 ?    7.1   0.2    0.0067       7.1       6      23 ..      28      45 ..      26      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.017
                              OrsD 10 rvliCreCkyav 21
                                      +v +Cr+C ++v
  gi|557693909|ref|YP_008796963.1| 14 GVHVCRRCGTSV 25
                                      799*****9998 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0067
                              OrsD  6 neeyrvliCreCkyavlp 23
                                      +++y++ iCr+C   ++p
  gi|557693909|ref|YP_008796963.1| 28 IRKYGLYICRRCINEIAP 45
                                      5799********887776 PP

>> zf-CCHC_2  Zinc knuckle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.3    0.0028       2.9       5      11 ..      17      23 ..      17      24 .. 0.88
   2 ?    6.0   2.9      0.01        11       4       9 ..      34      39 ..      34      41 .. 0.96

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0028
                         zf-CCHC_2  5 vChiCgk 11
                                      vC++Cg+
  gi|557693909|ref|YP_008796963.1| 17 VCRRCGT 23
                                      8****96 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.01
                         zf-CCHC_2  4 YvChiC 9 
                                      Y+C++C
  gi|557693909|ref|YP_008796963.1| 34 YICRRC 39
                                      ****** PP

>> DUF2688  Protein of unknown function (DUF2688)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   1.0   0.00018      0.19      10      22 ..      18      30 ..      15      35 .. 0.83
   2 ?    1.4   1.0      0.22   2.3e+02      10      14 ..      36      40 ..      34      46 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                           DUF2688 10 CrRCGkslstlsr 22
                                      CrRCG+s+  +++
  gi|557693909|ref|YP_008796963.1| 18 CRRCGTSVGVIRK 30
                                      *******987765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.22
                           DUF2688 10 CrRCG 14
                                      CrRC 
  gi|557693909|ref|YP_008796963.1| 36 CRRCI 40
                                      88885 PP

>> DUF1660  Prophage protein (DUF1660)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.6     0.016        17       9      29 ..       2      23 ..       1      32 [. 0.65
   2 ?    6.1   0.4     0.015        16      19      31 ..      30      42 ..      24      51 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.016
                           DUF1660  9 gHKwdenpaadseelyCeRC.e 29
                                      +HK  ++        +C+RC +
  gi|557693909|ref|YP_008796963.1|  2 KHKPPKQRKFGKGVHVCRRCgT 23
                                      6888755544555559****33 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                           DUF1660 19 dseelyCeRCeiv 31
                                      ++   +C+RC+++
  gi|557693909|ref|YP_008796963.1| 30 KYGLYICRRCINE 42
                                      566679****554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 394.93
//
Query:       gi|557693910|ref|YP_008796964.1|  [L=127]
Description: small subunit ribosomal protein S8 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-23   82.3   0.0    3.6e-23   81.9   0.0    1.2  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 !   81.9   0.0     2e-27   3.6e-23       1     127 []       3     127 .]       3     127 .] 0.83

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 2e-27
                                       -HHHHHHHHHHHHHHTT-SEEEEE--HHHHHHHHHHHHCTSEEEEEEECCCCCC...EEEEE-BSSS-SBSSSEEEE CS
                      Ribosomal_S8   1 DpiadmltrirNaekakkeevevpasklkeeilkvLkeeGyikdfeveeekkkk...ikielkynkkkksvikklkr 74 
                                       D ++ ++t+++N+e+++++e+ v+as+l +eilkvL++ Gyi  fe+ ++ +     +++ +++n+  +  i+    
  gi|557693910|ref|YP_008796964.1|   3 DLVSALFTTLQNNEMVRNRECIVKASNLVAEILKVLQRTGYIGAFEYIDNGRGGlfrVQLLGRINR--SAPIRPRMS 77 
                                       778999*****************************************7444333555777778877..788887666 PP

                                       -SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                      Ribosomal_S8  75 vskpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                       v+    +++  ++ lp   +++Gi++v+T+kGvm++++A+k+k+GG++l yv+
  gi|557693910|ref|YP_008796964.1|  78 VKANQFEMFE-QRYLP--ARNVGILVVTTPKGVMSHEDAKKMKTGGRLLGYVY 127
                                       6665555433.34454..689*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 981.84
//
Query:       gi|557693911|ref|YP_008796965.1|  [L=180]
Description: large subunit ribosomal protein L6 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   68.0  10.2    3.5e-09   37.2   2.9    2.1  2  Ribosomal_L6  Ribosomal protein L6
     0.0048   17.5   0.3     0.0048   17.5   0.3    1.8  2  FecR          FecR protein
  ------ inclusion threshold ------
       0.23   11.8   7.6       0.89    9.9   2.2    3.2  3  YbbR          YbbR-like protein


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 !   35.6   0.8   1.8e-12   1.1e-08       1      76 []      12      84 ..      12      84 .. 0.94
   2 !   37.2   2.9   5.9e-13   3.5e-09       1      76 []      96     170 ..      96     170 .. 0.98

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.8e-12
                                      CSTTEEEEEETTTEEEEEESSEEEEEE-CTT.SEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                      Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipeg.vtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                      iP++v+v i+g +++ + G kg +  +i++   +v+   e++k+++ v+  ++k+k+ l+gt  s+ +n  +GVt+g
  gi|557693911|ref|YP_008796965.1| 12 IPDKVNVRIDG-KTLVFEGTKGRVLKDISHIpAEVK--IEDGKIVFRVPGRSRKAKA-LLGTLVSIARNAATGVTKG 84
                                      8*********8.******************855666..77*****************.*****************98 PP

  == domain 2  score: 37.2 bits;  conditional E-value: 5.9e-13
                                       CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHH CS
                      Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGV 73 
                                       +P+ v+v + ++ + +++G+k  ++++i  +v+v+vk     +++i+++g d+e v    A+i+ ++++ +++ +++
  gi|557693911|ref|YP_008796965.1|  96 FPITVKVVGGEVHITNFIGEKYVRRAKIVGDVKVQVK-----GDEIIITGVDRESVgqtaANIENATRIPRKDPRKF 167
                                       7999*******************************99.....*********************************** PP

                                       HTC CS
                      Ribosomal_L6  74 teg 76 
                                        +g
  gi|557693911|ref|YP_008796965.1| 168 LDG 170
                                       997 PP

>> FecR  FecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.3     8e-07    0.0048      11      95 ..       8     107 ..       4     108 .. 0.84
   2 ?   -1.4   0.1      0.64   3.8e+03      47      67 ..     125     141 ..     114     158 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8e-07
                              FecR  11 aeilleDgsvvrlnenssl......ekaadsskrrrevsllkGevlfdvakdkkrp.....fevktp.satigvrg. 74 
                                       +e++++D+  vr++ ++ +      ++ +d s+  +ev+++ G++ f+v +++++        v+ + +a +gv++ 
  gi|557693911|ref|YP_008796965.1|   8 EEFQIPDKVNVRIDGKTLVfegtkgRVLKDISHIPAEVKIEDGKIVFRVPGRSRKAkallgTLVSIArNAATGVTKg 84 
                                       6899***********************************************99955556664444433777777762 PP

                              FecR  75 tef..rvrksdkqtevavleGeV 95 
                                         +  +v +s+ +++v+v+ GeV
  gi|557693911|ref|YP_008796965.1|  85 YVYkmKVVSSHFPITVKVVGGEV 107
                                       55588888999999****99999 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.64
                              FecR  47 Gevlfdvakdkkrpfevktps 67 
                                       G v+++v++d+    ++ t+ 
  gi|557693911|ref|YP_008796965.1| 125 GDVKVQVKGDE----IIITGV 141
                                       55555555543....244443 PP

>> YbbR  YbbR-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1     0.029   1.7e+02      23      51 ..      13      47 ..       9      65 .. 0.58
   2 ?    0.8   0.1      0.11   6.3e+02      14      34 ..      83     106 ..      76     112 .. 0.65
   3 ?    9.9   2.2   0.00015      0.89       7      55 ..     108     157 ..      96     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.029
                                      .-EEEEEEEE-HHHH........HHHTTS----EEE- CS
                              YbbR 23 pepvtVtvtGpesvl........dkieevkaevyvDl 51
                                      p++v+V++ G   v         ++i+++ aev   +
  gi|557693911|ref|YP_008796965.1| 13 PDKVNVRIDGKTLVFegtkgrvlKDISHIPAEV--KI 47
                                      566666665544222333333337777777766..44 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                                       TT-EEEE--.....-EEEEEEEE-H CS
                              YbbR  14 egyvvvsgtp....epvtVtvtGpe 34 
                                       +gy v ++++     p tV+v G e
  gi|557693911|ref|YP_008796965.1|  83 KGY-VYKMKVvsshFPITVKVVGGE 106
                                       566.333333366678888888866 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00015
                                       ..EE--TTT-EEEE--.-EEEEEEEE-HHHHHHHTTS--..--EEE-TT-- CS
                              YbbR   7 entgelaegyvvvsgtpepvtVtvtGpesvldkieevka..evyvDlsglk 55 
                                        +t+ ++e+yv    ++  v+V+v+G+e ++  +++ ++  ++ +++++++
  gi|557693911|ref|YP_008796965.1| 108 HITNFIGEKYVRRAKIVGDVKVQVKGDEIIITGVDRESVgqTA-ANIENAT 157
                                       55777889999999999***************99999886544.5887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1289.41
//
Query:       gi|557693912|ref|YP_008796966.1|  [L=128]
Description: large subunit ribosomal protein L32e [Candidatus Caldiarchaeum subterraneum]
Scores for 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  117.6   0.0    3.8e-34  117.4   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 !  117.4   0.0   2.1e-38   3.8e-34       1     108 []      16     121 ..      16     121 .. 0.99

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 2.1e-38
                                       ------TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE CS
                    Ribosomal_L32e   1 tkkFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenk 77 
                                       t+kF r++s+ryv+l++ +r+prG+d+r+r + +g +++ kiGYgspk  rgl+psG+++vlV +v+eLe l +e++
  gi|557693912|ref|YP_008796966.1|  16 TPKFVRQESWRYVRLETGYRRPRGKDSRMRLQKSGSPPLAKIGYGSPKTYRGLHPSGLRDVLVASVAELERLSPERD 92 
                                       79*************************************************************************** PP

                                       ..EEEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                    Ribosomal_L32e  78 syaaeiahsVsskkrkeiverAaelgikVtN 108
                                         a++i+   + +k++e+ e A++ g+kV+N
  gi|557693912|ref|YP_008796966.1|  93 --AVRISGRLGLRKKQEVFEAAKSRGFKVLN 121
                                       ..****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 00:00:00.40
# Mc/sec: 949.50
//
Query:       gi|557693913|ref|YP_008796967.1|  [L=146]
Description: large subunit ribosomal protein L19e [Candidatus Caldiarchaeum subterraneum]
Scores for 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-47  160.2   3.1    3.9e-47  159.9   3.1    1.1  1  Ribosomal_L19e  Ribosomal protein L19e
  ------ inclusion threshold ------
      0.016   15.3   0.2       0.14   12.3   0.0    2.1  2  CtsR_C          CtsR C-terminal dimerization domain
       0.11   12.4   0.5       0.81    9.7   0.1    2.2  2  HTH_Crp_2       Crp-like helix-turn-helix domain


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 !  159.9   3.1   6.5e-51   3.9e-47       2     143 ..       3     137 ..       2     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 159.9 bits;  conditional E-value: 6.5e-51
                                       THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG CS
                    Ribosomal_L19e   2 lklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGk 78 
                                       l++qkrlaa++lk+G++rv++dpe+le+i++Aitr++ir likdg+I k p+kg srar+       ++gr+rg+G+
  gi|557693913|ref|YP_008796967.1|   3 LEMQKRLAADLLKCGVTRVRFDPERLEDIESAITRDEIRGLIKDGAIYKVPEKGVSRARV-------ERGRKRGEGS 72 
                                       789********************************************************9.......58******** PP

                                       --S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT-X CS
                    Ribosomal_L19e  79 rkGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiekk 143
                                       rkG+k++ +p+k++W++r+Ra+Rr+Lk+lrek+ id++ Yr +Y  +k+g+fk++a+L+e+i++k
  gi|557693913|ref|YP_008796967.1|  73 RKGAKHSLVPRKRMWMTRVRAQRRFLKQLREKGLIDSRGYRLIYSFVKAGNFKSVASLREFIKSK 137
                                       **************************************************************986 PP

>> CtsR_C  CtsR C-terminal dimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.11   6.5e+02      11      27 ..      29      45 ..      26      46 .. 0.81
   2 ?   12.3   0.0   2.4e-05      0.14      23      60 ..      95     132 ..      90     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.11
                            CtsR_C 11 nsigdsiseqdaeaiiq 27
                                      + i+++i+  +++ +i+
  gi|557693913|ref|YP_008796967.1| 29 EDIESAITRDEIRGLIK 45
                                      67899999999999886 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.4e-05
                            CtsR_C  23 eaiiqrLleegliterEakLmkaalsdrvLdlpleerd 60 
                                       ++++++L e gli+ r ++L+ + +   +++  + +r+
  gi|557693913|ref|YP_008796967.1|  95 RRFLKQLREKGLIDSRGYRLIYSFVKAGNFKSVASLRE 132
                                       789********************999888877777666 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 ?    0.3   0.0      0.12   6.9e+02       2      27 ..       8      40 ..       7      45 .. 0.54
   2 ?    9.7   0.1   0.00013      0.81      40      56 ..      96     113 ..      86     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.12
                                      HHHHHHHHH....HCT..TTC...EEEEEHHHHHH CS
                         HTH_Crp_2  2 RlArfLlrl....aer..agg...eielpltqeel 27
                                      RlA+ Ll+       r  + +    ie  +t++e+
  gi|557693913|ref|YP_008796967.1|  8 RLAADLLKCgvtrV-RfdP-ErleDIESAITRDEI 40
                                      77777777643320.1211.123456667777765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00013
                                       HHHHHHHHTTSEE.ETEE CS
                         HTH_Crp_2  40 rilseLkreglis.rgrr 56 
                                       r l++L+++gli+ rg+r
  gi|557693913|ref|YP_008796967.1|  96 RFLKQLREKGLIDsRGYR 113
                                       89***********77765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); 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:                         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 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1133.62
//
Query:       gi|557693914|ref|YP_008796968.1|  [L=192]
Description: large subunit ribosomal protein L18 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-27   94.2   1.6    2.3e-18   66.7   0.7    2.3  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
    0.00027   21.3   0.8    0.00039   20.8   0.8    1.3  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


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 !   66.7   0.7   2.6e-22   2.3e-18       4      99 ..       7      95 ..       6      98 .. 0.96
   2 !   26.8   0.0     5e-10   4.5e-06     128     162 ..      97     131 ..      94     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 2.6e-22
                     Ribosomal_L5e  4 qvkfrrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelpkygvkvgltny 82
                                      +vk rrrr+g tdY++r +l+            Rlv+r   ++i++qi+++k  gd++l+++ s+ l+kyg +++l++ 
  gi|557693914|ref|YP_008796968.1|  7 RVKPRRRRQGYTDYRKRLKLVKSGL-------ERLVIRRGSRRIVVQIVKSKAGGDETLVTVGSEVLRKYGWRASLKSV 78
                                      699******************7665.......59********************************************* PP

                     Ribosomal_L5e 83 aaaYatglllarrllkk 99
                                       aaY+tgll ++++l+k
  gi|557693914|ref|YP_008796968.1| 79 PAAYLTGLLAGKKALEK 95
                                      **************997 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 5e-10
                     Ribosomal_L5e 128 afkaiLdvGLartttgakvfgalkgavdgglsiph 162
                                         kai+d+G+ r+ +g+++++++kga+d+gl+ip 
  gi|557693914|ref|YP_008796968.1|  97 VEKAIVDIGVYRSVKGSRLYAVVKGALDAGLEIPV 131
                                       5689*****************************96 PP

>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.8   4.4e-08   0.00039       7     115 ..      11     128 ..       5     129 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.4e-08
                                       HCHHH..HHHTTT--.TTSSS-EEEEEE-SS-EEEEEE-TTT-..-EEEEE.CS-SCCCT.S-SSSCHHHHHHHHHH CS
                    Ribosomal_L18p   7 rkrRh..kRirkkls.gtaerprlvvfrsnrhiyaQviddvkg..ktlasa.stlekelk.lkstknkeaakkvgel 76 
                                       r+rR+  +  rk+l+  ++   rlv+ r  r i++Q++ +++g  +tl+++ s +  +     s k+  aa   g l
  gi|557693914|ref|YP_008796968.1|  11 RRRRQgyTDYRKRLKlVKSGLERLVIRRGSRRIVVQIVKSKAGgdETLVTVgSEVLRKYGwRASLKSVPAAYLTGLL 87 
                                       4444322344555554444466****************998753378877624444444445677777778888888 PP

                                       HHHHHCHHCHTC-EE--TTSSS..-CHHHHHHHHHHCTSSB CS
                    Ribosomal_L18p  77 iAerakekgiekvvfDrggykY..hGrvaalAdaaReaGlk 115
                                         ++a+ekg+ek++ D g y+     r+ a+ ++a +aGl+
  gi|557693914|ref|YP_008796968.1|  88 AGKKALEKGVEKAIVDIGVYRSvkGSRLYAVVKGALDAGLE 128
                                       889**************998742134788888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1390.49
//
Query:       gi|557693915|ref|YP_008796969.1|  [L=204]
Description: small subunit ribosomal protein S5 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-26   90.7   1.2    7.3e-26   89.9   1.2    1.4  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
    2.3e-20   71.8   0.1      5e-20   70.7   0.0    1.6  2  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


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 !   89.9   1.2   8.2e-30   7.3e-26       1      64 [.      45     108 ..      45     109 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 8.2e-30
                                       XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE- CS
                      Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpv 64 
                                       l+++v+++k vq++t++G +t+f+alvvvG+++G++G+G+gk+++v  Ai+kAi++Ak+n+vpv
  gi|557693915|ref|YP_008796969.1|  45 LEQEVIDVKLVQRQTDAGEKTRFKALVVVGNRDGYIGIGTGKSTQVVLAIEKAIRNAKLNIVPV 108
                                       789************************************************************9 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 ?   -2.9   0.0      0.54   4.8e+03      44      61 ..      83     100 ..      82     103 .. 0.68
   2 !   70.7   0.0   5.5e-24     5e-20       1      65 [.     130     195 ..     130     201 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.54
                                       S-SSHHHHHHHHHHHHHH CS
                    Ribosomal_S5_C  44 gsrnpinvvkAtfeALkk 61 
                                       g+     vv A+ +A+++
  gi|557693915|ref|YP_008796969.1|  83 GTGKSTQVVLAIEKAIRN 100
                                       555667788888888776 PP

  == domain 2  score: 70.7 bits;  conditional E-value: 5.5e-24
                                       EEEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT CS
                    Ribosomal_S5_C   1 tgkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrsp 65 
                                       +gk+g+v+v l paprG G++ag   + vl laG+kD++++s g +r+ + vv A++eALk++  +
  gi|557693915|ref|YP_008796969.1| 130 EGKYGSVRVQLLPAPRGLGLVAGESQKVVLALAGVKDCWTRSFGeTRTSLSVVGAVYEALKRTAEA 195
                                       59***********************************************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1569.33
//
Query:       gi|557693916|ref|YP_008796970.1|  [L=136]
Description: large subunit ribosomal protein L30 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   42.2   0.6    8.5e-11   41.6   0.1    1.7  2  Ribosomal_L30  Ribosomal protein L30p/L7e
  ------ inclusion threshold ------
      0.085   12.7   0.1       0.12   12.3   0.1    1.2  1  PCRF           PCRF domain


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 !   41.6   0.1   9.5e-15   8.5e-11       2      50 ..       5      53 ..       4      54 .. 0.88
   2 ?   -3.3   0.1      0.98   8.8e+03      35      45 ..      59      69 ..      58      70 .. 0.59

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 9.5e-15
                                      EEEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCG CS
                     Ribosomal_L30  2 fVtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhl 50
                                      +V+ri++ +g++p ++ktL++L L k ++    + + +++GmLkk + +
  gi|557693916|ref|YP_008796970.1|  5 AVIRIKGHVGIKPEIKKTLESLKLDKAFKAALFNESDTLNGMLKKAQRY 53
                                      7***************************55555555*********9877 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.98
                                      -SSHHHHHHHH CS
                     Ribosomal_L30 35 lntpsirGmLk 45
                                      +n+ +i  +Lk
  gi|557693916|ref|YP_008796970.1| 59 PNKHTILTLLK 69
                                      56666666666 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   1.3e-05      0.12      60     122 ..      28      86 ..       8      91 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.3e-05
                                       ...-S-..-GGGTHHHHHHHHHH..HHHHHT-..SSSTTSEEEEEEEE-SSTHHHHHHHHHHH CS
                              PCRF  60 edeelaelaeeeleelekeleeleeelkklLlpkdendeknaileiraGaGGdeaalfaedLl 122
                                        d+ +++     l + +++l+ + ++ ++ L+   +n +   +l  +aG+GG++ + fae+L 
  gi|557693916|ref|YP_008796970.1|  28 LDKAFKA----ALFNESDTLNGMLKKAQRYLTWGRPNKHTILTLLKKAGVGGEDVETFAEKLE 86 
                                       4444444....44445555555556669999989999999999999**************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1093.46
//
Query:       gi|557693917|ref|YP_008796971.1|  [L=140]
Description: large subunit ribosomal protein L15 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   63.6   1.3    2.7e-17   63.6   1.3    1.5  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


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 !   63.6   1.3   1.5e-21   2.7e-17       2     126 ..      32     131 ..      31     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.5e-21
                                       GGGTSSTTTTTTTTT-S--........S--.........---GGG..---EEEEHHHHHHTTTTGTTS------EEE CS
                    Ribosomal_L27A   2 GktgGrGhkGqkkrsgvkk.kpg.feGGqmplyrrlpkrGfknskfkkeykvvnlkdLdelideerleladeaeeid 76 
                                       G +gGrG++G +k++++k  + + f  G+          Gf   + ++e+k+ nl ++  l+++        ++ i+
  gi|557693917|ref|YP_008796971.1|  32 GAKGGRGMAGGHKHKWTKLlNTDyF--GKN---------GFAPLV-RREEKTANLLTVSMLAEKSG------NNLIN 90 
                                       99**************888777779..***.........**9866.899999***99996666654......489** PP

                                       GGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EE CS
                    Ribosomal_L27A  77 leelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkv 126
                                       l e           g+ K+lg+g++t++l++ ++k SkkA+ek+++aGG+ 
  gi|557693917|ref|YP_008796971.1|  91 LVEA----------GYtKLLGDGKITTPLTIVVEKWSKKAEEKVKQAGGNL 131
                                       ****..........***********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1116.35
//
Query:       gi|557693918|ref|YP_008796972.1|  [L=477]
Description: preprotein translocase subunit SecY [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-65  220.6  23.0    3.3e-65  220.3  23.0    1.1  1  SecY      SecY translocase
  ------ inclusion threshold ------
      0.081   13.1   0.4         21    5.3   0.3    2.8  3  Popeye    Popeye protein conserved region


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 !  220.3  23.0   3.7e-69   3.3e-65       1     306 []      78     455 ..      78     455 .. 0.84

  Alignments for each domain:
  == domain 1  score: 220.3 bits;  conditional E-value: 3.7e-69
                                       BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC.......HH.H CS
                              SecY   1 sifaLGImPyitasIilqLl.tvvipkleelkkegeegrkkinqitryltvvlalvqalgialslg.......lall 69 
                                       ++++LGI+P++ta++ilqLl ++   +l +l+  ++e+r +++++ ++l +v+al+q+++++++ g       ++ +
  gi|557693918|ref|YP_008796972.1|  78 TLITLGIGPIVTAGLILQLLvGA---ELIKLDLSKPEDRGLFTSTSKLLGIVIALFQSAAYVYA-GffgptnaTQNI 150
                                       799*****************999...666666559************************97643.56789***899* PP

                                       HHHHHHHHHHHHHHHHHHHHHH.HSSTTHHHHHHHHHHHHHHCCHSS..................-HHHHSS..... CS
                              SecY  70 livlqltagtvllmwLgEqite.kGiGnGisllifagivarlpkals..................glielale.... 123
                                        i++ql+a+t+l+m+L+E++++ +G+G+Gisl+i+ag++++++ al                   +           
  gi|557693918|ref|YP_008796972.1| 151 AIFIQLVAATILIMLLDELVQKgWGLGSGISLFIVAGVAEEIFVALFspiilpdqayqgiilasiQ------Aiftg 221
                                       *******************************************55553666666555543333331......02233 PP

                                       ..........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT....S.S-EEEEETTCCCSCHHHHHHHHHH.. CS
                              SecY 124 .........gilallllllvtllvillvvyveeaerripvqyakrgrkggqssylPlklnyagviPiIfasslla.. 189
                                                +  + l+ l+ t++++l+++y+e ++++ip++yak    +g + ++P+kl+y +++PiIfa+++++  
  gi|557693918|ref|YP_008796972.1| 222 nlpsilvrqSGYPDLVGLFSTIFLVLALIYIEAIRVEIPISYAKF---QGYRAKYPVKLLYVSNVPIIFATTVFSni 295
                                       344334455557*******************************98...799************************99 PP

                                       ............................................H..HHCCCCS.TCCCSTHHHHHHHHHHHHHHHH CS
                              SecY 190 ............................................l..pstiaqfllallspsvlyvvlyvlliifFa 220
                                                                                   +  p+ ia++l++ +   v++++l +++ ++Fa
  gi|557693918|ref|YP_008796972.1| 296 fylgslvwsrfnpnndniflnligtyrfdeqlgtvvstgglayyVigPRGIASVLQDPV-RAVVHAALLIVFAVLFA 371
                                       99999988888888888887777777766666665555554444145777766554333.457888888888888** PP

                                       HHHHTCT.THHHHHHHCCHHTBSSSCTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHH CS
                              SecY 221 yfyteit.fnpkevaenlkksggfipgir.pgketakyLekvlsritliGalflaliavlpdllgasligafggtsl 295
                                       +f+++++ + p++vae+l + g+++pg+r + + +a ++ k++ ++t++G+l+++l+a ++d++    +g  +g +l
  gi|557693918|ref|YP_008796972.1| 372 KFWVQVSgLAPEKVAEQLIQAGMQVPGFRrSPEVIAAVIGKYIGTVTILGGLIIGLVASVADYVAV--FG--SGIGL 444
                                       *****************************999**********************************..87..***** PP

                                       HHHHHHHHHHH CS
                              SecY 296 LivVgvaletv 306
                                       L+++g+  +++
  gi|557693918|ref|YP_008796972.1| 445 LLTIGILQQYY 455
                                       ******98875 PP

>> Popeye  Popeye protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.77   6.9e+03      54      80 ..      34      60 ..      31      74 .. 0.68
   2 ?    5.3   0.3    0.0023        21       5      43 ..     129     166 ..     127     175 .. 0.84
   3 ?    4.7   0.0    0.0036        32      84     115 ..     189     270 ..     184     372 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.77
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Popeye 54 flWnlllvlinlaqllyllyklrpvkf 80
                                      ++W++l ++i +     +ly l + ++
  gi|557693918|ref|YP_008796972.1| 34 LVWTALALIIYTWMGHTILYGLPQGTQ 60
                                      789888888888777777777665555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0023
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            Popeye   5 lfhlanillllaflapsgvlgllvlrsllvlGflllalw 43 
                                       lf+ a   + ++f++p++ ++ + +++ lv++++l++l 
  gi|557693918|ref|YP_008796972.1| 129 LFQSAA-YVYAGFFGPTNATQNIAIFIQLVAATILIMLL 166
                                       566664.5678***********************99885 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0036
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................. RF
                            Popeye  84 leelYkklFqplkvsrkeFkklvseeeakil.............................................. 114
                                       +ee++ +lF+p+ ++ ++++ ++ ++ + i+                                              
  gi|557693918|ref|YP_008796972.1| 189 AEEIFVALFSPIILPDQAYQGIILASIQAIFtgnlpsilvrqsgypdlvglfstiflvlaliyieairveipisyak 265
                                       689*******************9977777776666666666666555555555555555555555555555555555 PP

                                       ....x RF
                            Popeye 115 ....e 115
                                           +
  gi|557693918|ref|YP_008796972.1| 266 fqgyR 270
                                       55550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3660.03
//
Query:       gi|557693919|ref|YP_008796973.1|  [L=180]
Description: hypothetical protein CSUB_C0482 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-11   43.9   3.5    3.9e-11   43.0   3.5    1.5  1  EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
     0.0063   17.3   0.2     0.0098   16.7   0.2    1.3  1  ATP-synt_G  Mitochondrial ATP synthase g subunit


Domain annotation for each model (and alignments):
>> 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 !   43.0   3.5   4.4e-15   3.9e-11      24     168 ..      12     146 ..       2     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 4.4e-15
                        EMC3_TMCO1  24 giltgllsellqkllidkkkmekeqkre.kelqkrarelqkngdklklkklekrqeelmedqsemmmdqmkpmivtm 99 
                                       +++ +  ++ ++k++  k+  + +++ e + + ++  ++++++d++  +kl+k+q ++ + + e++++ m  m++ +
  gi|557693919|ref|YP_008796973.1|  12 AAAISASTTAIRKIVFKKE--DLAKMAEiQSYNRELMNATRKKDQKTIQKLQKKQDYIRQINAEVTKKNMITMFASL 86 
                                       4555555667777663333..444433323455555666669999******************************** PP

                        EMC3_TMCO1 100 ipqiliffwlnsffsgfvvaklpfpltgrfksllqrglesldvrfvssiswYflcsfglsqiirklLge 168
                                       +++++i+ +l  ff   ++  +p+ l + f   +       d    ++  w++l+ fg+s+ i+k++g 
  gi|557693919|ref|YP_008796973.1|  87 LIFFTIYPTLGGFFGTQMLGYVPAGLDIPFV--T-------DSGKLYFYGWFILSFFGVSSPITKIFGL 146
                                       ***************9999999999999998..5.......77888999*****************996 PP

>> ATP-synt_G  Mitochondrial ATP synthase g subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   1.1e-06    0.0098      12      87 ..      14      92 ..       7     107 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                        ATP-synt_G 12 yyskvglelskqvakkeklapPtvaefqslykqllktalaspskpqeller.......lknlkkeeallagv.vaaevl 82
                                      + s  + ++ k+v+kke  +  ++ae+qs+ ++l+++  +++   q+++++       +++++ e   ++ + ++a +l
  gi|557693919|ref|YP_008796973.1| 14 AISASTTAIRKIVFKKE--DLAKMAEIQSYNRELMNA-TRKKD--QKTIQKlqkkqdyIRQINAEVTKKNMItMFASLL 87
                                      5667788899****999..7779*************9.55554..4445552224444556665555554431457788 PP

                        ATP-synt_G 83 gfFsv 87
                                       fF++
  gi|557693919|ref|YP_008796973.1| 88 IFFTI 92
                                      88887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2362  (0.131742); expected 358.6 (0.02)
Passed bias filter:                      839  (0.0467957); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1397.88
//
Query:       gi|557693920|ref|YP_008796974.1|  [L=200]
Description: cytidylate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   56.2   2.3    8.4e-14   52.1   2.3    2.0  1  Cytidylate_kin2  Cytidylate kinase-like family
      4e-12   46.8   0.0    7.8e-12   45.9   0.0    1.5  1  AAA_18           AAA domain
    1.9e-09   37.6   1.9     0.0005   19.9   0.1    2.2  2  Cytidylate_kin   Cytidylate kinase
    4.7e-07   30.1   0.3     0.0053   16.9   0.1    2.3  2  SKI              Shikimate kinase
    9.2e-06   26.1   0.0    1.9e-05   25.1   0.0    1.7  1  AAA_17           AAA domain
  ------ inclusion threshold ------
      0.015   15.4   1.6       0.21   11.8   1.6    2.4  2  AAA_33           AAA domain
      0.028   14.3   0.4       0.14   12.0   0.1    2.0  2  dNK              Deoxynucleoside kinase
      0.033   14.0   0.4        9.1    6.2   0.0    2.6  2  LacI             Bacterial regulatory proteins, lacI family
      0.074   12.8   0.0       0.12   12.2   0.0    1.3  1  Amidohydro_2     Amidohydrolase


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 !   52.1   2.3   4.2e-17   8.4e-14       1     178 [.       6     170 ..       6     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 4.2e-17
                   Cytidylate_kin2   1 iITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevdersrlssflskllaarvagdtldek 76 
                                       +I++++  + g++t+g+ +A++Lgl++++  + ++e+a e+g  +      + ++   +fls   +ar      d +
  gi|557693920|ref|YP_008796974.1|   6 VICLAGFAAVGKSTVGKIVAKRLGLKYVSGgDALKELAAEMGYRPGGPGWWETAKG-IEFLSL--RAR------DPS 73 
                                       89***************************99***********99998877777444.344432..221......455 PP

                   Cytidylate_kin2  77 lddelfeaqervirelaaeesvVivGRgadliLkdrpnvlrvfltapledrvkrvaereglseeearekiketDkrr 153
                                       +d +    ++++++ + ++ +vV+  +    + k+  ++++v+lta+  +r++r+a+r ++s ++a ++++++D++ 
  gi|557693920|ref|YP_008796974.1|  74 FDRK---VDRKLLEICRRG-GVVVDSWVMPWLYKG--RAFKVWLTADYRSRAERMAKRSKISVKQASRLLRSRDRKS 144
                                       5555...445555555455.9*********99999..57************************************** PP

                   Cytidylate_kin2 154 akyykkytgqdw.gdaenYdlvlnts 178
                                       a+ y+++++  +  d +  +l+++ts
  gi|557693920|ref|YP_008796974.1| 145 AAIYERLYDIRIgRDFSPLHLIVDTS 170
                                       *********99967888889998887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   3.9e-15   7.8e-12       1     121 [.       7     133 ..       7     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 3.9e-15
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe........aldeskrldedkldklldal 64 
                                       I+l+G ++vGK+t++k ++krlg+     g+ l+++a+e g++ +            ++ + +  d  ++ k+ ++l
  gi|557693920|ref|YP_008796974.1|   7 ICLAGFAAVGKSTVGKIVAKRLGLkyvsgGDALKELAAEMGYRPGGP-GwwetakgiEFLSLRARDPSFDRKVDRKL 82 
                                       9*********************9998999999999999987764321.12336789977777777777888999999 PP

                            AAA_18  65 eenssaleegknlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakik 121
                                        e+++     + +v+d+ +  +++  + + k v+Lta++  ++eR++kR++ + k++
  gi|557693920|ref|YP_008796974.1|  83 LEICR---R-GGVVVDSWVMPWLYKGRAF-K-VWLTADYRSRAERMAKRSKISVKQA 133
                                       99987...4.5557877666666555554.3.9*****************9999987 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   2.5e-07    0.0005       1      34 [.       7      40 ..       7      47 .. 0.87
   2 !   17.4   0.1   1.4e-06    0.0028      93     210 ..      69     186 ..      59     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.5e-07
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYR 34
                                      i + G a+ GKs+v++++a++lglky++ g   +
  gi|557693920|ref|YP_008796974.1|  7 ICLAGFAAVGKSTVGKIVAKRLGLKYVSGGDALK 40
                                      678899*********************9997655 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.4e-06
                                       TTSHHHHHHHHHHHHTT-BSSBEEEEESSIIIIISTT-SEEEEEE--HHHHHHHHHHHHHHTT----HHHHHHHHHH CS
                    Cytidylate_kin  93 aaipavRailvkklrelvkkarvvveGRDigtvvfpdaelKifldAsveeRakRRlkqlkakgtsvsleellaeike 169
                                       a  p++ +++ +kl e+ ++++vvv+   +   + +   +K++l+A  + Ra+R +k  k +     +++  + ++ 
  gi|557693920|ref|YP_008796974.1|  69 ARDPSFDRKVDRKLLEICRRGGVVVDSWVM-PWLYKGRAFKVWLTADYRSRAERMAKRSKIS-----VKQASRLLRS 139
                                       555666666667777777777777776544.456677789*************998884333.....3444444555 PP

                                       HHHHHHC..TSSS-S---TT....-EEEETTTS-HHHHHHHHHHHHH CS
                    Cytidylate_kin 170 RDklDke..revgpLklaed....aliidtskltieevvekilelik 210
                                       RD++  +   +++ +++ +d     li+dts l+ ++v e ++++++
  gi|557693920|ref|YP_008796974.1| 140 RDRKSAAiyERLYDIRIGRDfsplHLIVDTSGLSPKQVAEVVVQTAR 186
                                       55544432256777888888444359****************99876 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   2.7e-06    0.0053       2      23 ..      14      35 ..      13      49 .. 0.78
   2 !   11.4   0.0   0.00013      0.26      70     145 ..      89     162 ..      76     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.7e-06
                                      TSSHHHHHHHHHHHHTSEEEEH CS
                               SKI  2 GaGKstvGkllAkklglefiDl 23
                                      ++GKstvGk++Ak+lgl+++  
  gi|557693920|ref|YP_008796974.1| 14 AVGKSTVGKIVAKRLGLKYVSG 35
                                      58****************9976 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00013
                                       TTGGGSHHHH.HHHHHHSEEEEEE--HHHHHHHHHHTTSSGGGCSCHHHHHHHHHHHHHHHHHCCSSCEEEECTSSH CS
                               SKI  70 GGavlseenr.ellkekgiviyLdvsleellerlkadkeRPllqekskeeelleelaereplyeeaadvvvdesees 145
                                       GG+v+++  + +l k ++  ++L ++  + +er++++++ + +++ s+   l++  ++  ++ye++ d+ + ++ ++
  gi|557693920|ref|YP_008796974.1|  89 GGVVVDSWVMpWLYKGRAFKVWLTADYRSRAERMAKRSK-ISVKQASR--LLRSRDRKSAAIYERLYDIRIGRDFSP 162
                                       66666666651555688899***************9999.66666666..666666688899999866666555444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   9.6e-09   1.9e-05       2      80 ..      11      97 ..      10     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 9.6e-09
                                      E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTT.......SHSSHHHHCTSHHHH.HHHHHHHHHHHHHHHHHSS CS
                            AAA_17  2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgg.......lakardemrklplee.kkelqkeaaekiaeeakkk 72
                                      G   +GK+t+ + +++++g++++s Gd l e a++ g         ++ + ++ l+l+  +  +++++ +k+ e ++++
  gi|557693920|ref|YP_008796974.1| 11 GFAAVGKSTVGKIVAKRLGLKYVSGGDALKELAAEMGyrpggpgWWETAKGIEFLSLRArDPSFDRKVDRKLLEICRRG 89
                                      67789******999********************998565555423444445545544425578999999999999999 PP

                                      EEEEEE-S CS
                            AAA_17 73 gvlvdghp 80
                                      gv+vd   
  gi|557693920|ref|YP_008796974.1| 90 GVVVDSWV 97
                                      99999765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.6    0.0001      0.21       1     122 [.       6     129 ..       6     151 .. 0.69
   2 ?   -1.7   0.0       1.5   2.9e+03      69      89 ..     161     181 ..     130     194 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                            AAA_33   1 lvllvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkal.sagrnvild 76 
                                       ++ l G +++GKst+ + ++k+lg   +s  ++++ l+++   ++   + +++ +++i  e++  ++    ++  +d
  gi|557693920|ref|YP_008796974.1|   6 VICLAGFAAVGKSTVGKIVAKRLGLKYVSGGDALKELAAEMGYRPGG-PGWWETAKGI--EFLSLRArDPSFDRKVD 79 
                                       68899*******************99999999999888855544432.3455444444..34433330444667778 PP

                            AAA_33  77 atnlsrrer.....arflklarrlgvpvrivvvetdeetlkeRlakRaang 122
                                         +l+ ++r     + ++  +   g +   v++++d +  +eR akR++ +
  gi|557693920|ref|YP_008796974.1|  80 RKLLEICRRggvvvDSWVMPWLYKG-RAFKVWLTADYRSRAERMAKRSKIS 129
                                       8888877777777767777666555.5566888888888888888888765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                            AAA_33  69 agrnvildatnlsrrerarfl 89 
                                       +  ++i+d   ls+++ a+++
  gi|557693920|ref|YP_008796974.1| 161 SPLHLIVDTSGLSPKQVAEVV 181
                                       445677777777777775443 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   6.8e-05      0.14       1      27 [.       7      33 ..       7      39 .. 0.93
   2 ?    0.0   0.0      0.32   6.4e+02     123     145 ..     105     127 ..      93     167 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.8e-05
                                      EEEEESTTSSHHHHHHHHHCCSTCEEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvf 27
                                      i++ G  ++GKst+ k+ +k+lg k +
  gi|557693920|ref|YP_008796974.1|  7 ICLAGFAAVGKSTVGKIVAKRLGLKYV 33
                                      89********************98876 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.32
                                       -SEEEEEE--HHHHHHHHHHCTT CS
                               dNK 123 pdlliYLkasletclerikkRgr 145
                                         + ++L a++ +  er+ kR++
  gi|557693920|ref|YP_008796974.1| 105 RAFKVWLTADYRSRAERMAKRSK 127
                                       56678888888889999998876 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0082        16       6      45 ..      10      50 ..       9      51 .. 0.76
   2 ?    6.2   0.0    0.0046       9.1       6      33 ..     123     150 ..     122     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0082
                                      HHHCTS-HHHHHHHCTTS...SSSTHHHHHHHHHHHHHTTB-T CS
                              LacI  6 ArlAGVSkaTVSrvLnnk...erVseetrerVeaameelnYiP 45
                                      A  A V k+TV +++ ++   ++Vs    +   + ++e++Y+P
  gi|557693920|ref|YP_008796974.1| 10 AGFAAVGKSTVGKIVAKRlglKYVSG--GDALKELAAEMGYRP 50
                                      67799**********99988888875..445556666777766 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0046
                                       HHHCTS-HHHHHHHCTTSSSSTHHHHHH CS
                              LacI   6 ArlAGVSkaTVSrvLnnkerVseetrer 33 
                                       A++++ S+  +Sr L++++r s+++ er
  gi|557693920|ref|YP_008796974.1| 123 AKRSKISVKQASRLLRSRDRKSAAIYER 150
                                       99****************9999998887 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.8e-05      0.12     111     160 ..      59     113 ..      34     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.8e-05
                                       ECEEEEESSTTTCCTTTCGGHHHHHHHHHHHT-EEEEE.........CHHHCHHH CS
                      Amidohydro_2 111 fkGvrlnphvggddllgdrldrpifealeelglpvdihtGps.....pewlfggp 160
                                       +kG+++ +    d+  ++  dr+++e++++ g++vd  + p+     +  ++  +
  gi|557693920|ref|YP_008796974.1|  59 AKGIEFLSLRARDPSFDRKVDRKLLEICRRGGVVVDSWVMPWlykgrAFKVWLTA 113
                                       689*********************************8866666666644444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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 0.28s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1505.11
//
Query:       gi|557693921|ref|YP_008796975.1|  [L=107]
Description: large subunit ribosomal protein L14e [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00071   19.4   7.5     0.0011   18.9   7.5    1.3  1  KOW             KOW motif
     0.0018   18.7   0.1     0.0023   18.4   0.1    1.2  1  Ribosomal_L14e  Ribosomal protein L14


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 !   18.9   7.5   1.2e-07    0.0011       1      29 [.       7      36 ..       7      38 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.2e-07
                                      TTSEEEESSSTTTTCEEEEEEEETTT.TEE CS
                               KOW  1 pGdhVkVvsGphkGktGkVvkvdqhk.vrV 29
                                      +G++V  ++G+++G +G+Vv+v+ +  v V
  gi|557693921|ref|YP_008796975.1|  7 VGRVVVKTRGRDAGLKGVVVSVYGDGyVLV 36
                                      79**********************996666 PP

>> Ribosomal_L14e  Ribosomal protein L14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   2.6e-07    0.0023       2      50 ..      47      95 ..      46     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.6e-07
                    Ribosomal_L14e  2 RqaiplkrlkLtkivlklprgartgavkkawekadveekwaksawakkl 50
                                      R  ++ ++++ t+ +l+++++a+ + v ka+++a++e+  a+    k+ 
  gi|557693921|ref|YP_008796975.1| 47 RRRVNASHIIPTPHKLSITKEASDEDVMKAIKEAGLEKYMAEPHAIKQS 95
                                      8899********************************9988887776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 813.33
//
Query:       gi|557693922|ref|YP_008796976.1|  [L=240]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-20   73.1   0.1    2.5e-20   72.4   0.1    1.4  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
      6e-17   61.4   2.0      1e-16   60.6   2.0    1.4  1  PUA       PUA domain
    2.2e-05   24.9   0.0     0.0018   18.7   0.0    2.4  1  TruB_N    TruB family pseudouridylate synthase (N terminal do
      0.003   17.8   0.1     0.0079   16.4   0.0    1.7  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 !   72.4   0.1   5.5e-24   2.5e-20       1      63 [.      80     145 ..      80     146 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 5.5e-24
                                       HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT..--H.HHHHEEEGGGGG CS
                          TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke..dee.LdrlllPlesal 63 
                                       R++c+D+G++Lg+gAh+eeLRRtr+g+++e++ vtl ++ +a+++y+e  dee +++++ P+e++l
  gi|557693922|ref|YP_008796976.1|  80 RKICHDMGLYLGVGAHMEELRRTRAGSLEEKNSVTLLQVYEAFEKYREtgDEEaVRKVVYPVEKCL 145
                                       9***********************************************998888*********987 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   2.0   2.3e-20     1e-16       1      74 []     149     222 ..     149     222 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 2.3e-20
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveiervl 74 
                                       ++v + d Av+a+++ga+L+++Gv  ++ d+ e+ +Va+++ ++elva+G+a ++++ + ++ +g++v++ rv+
  gi|557693922|ref|YP_008796976.1| 149 PKVYILDTAVDAVCHGADLMVAGVSMIDSDVAENSEVAVMTLKNELVALGKAAMDAQSILEASEGMAVDVTRVI 222
                                       68999*****************************************************************9985 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 !   18.7   0.0     4e-07    0.0018      72     149 .]      19      79 ..       6      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4e-07
                                       --HHHHHHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTT CS
                            TruB_N  72 lteekleevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtY 148
                                       ++++kl e++k ftG+++qvpp+ ++v                  r++r  ++y ++lle + +++ +++ cs GtY
  gi|557693922|ref|YP_008796976.1|  19 VSDDKLLEAFKIFTGDVYQVPPVRASVA-----------------RRPRIRRVYYFDLLERDGRYILFRIGCSGGTY 78 
                                       6677788888888888888888887776.................99****************************** PP

                                       H CS
                            TruB_N 149 i 149
                                       +
  gi|557693922|ref|YP_008796976.1|  79 V 79 
                                       8 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.7   7.6e+03      67      74 ..      83      90 ..      74      91 .. 0.62
   2 !   16.4   0.0   1.8e-06    0.0079       2      56 ..     151     206 ..     150     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.7
                           UPF0113 67 laDiGeYl 74
                                        D+G Yl
  gi|557693922|ref|YP_008796976.1| 83 CHDMGLYL 90
                                      35888887 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.8e-06
                           UPF0113   2 vvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt.k 56 
                                       v++   a   +  G d++  ++  i+++v en  v+V+  ++e++++Gk++ d  +
  gi|557693922|ref|YP_008796976.1| 151 VYILDTAVDAVCHGADLMVAGVSMIDSDVAENSEVAVMTLKNELVALGKAAMDAqS 206
                                       6677778888899*************************************998862 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1892.93
//
Query:       gi|557693923|ref|YP_008796977.1|  [L=128]
Description: signal-transduction protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  101.2   4.2    1.8e-16   60.3   0.3    2.0  2  CBS              CBS domain
     0.0013   18.9   1.0       0.22   11.8   0.1    2.5  2  IF3_N            Translation initiation factor IF-3, N-termin
  ------ inclusion threshold ------
        0.1   12.5   0.0         10    6.1   0.0    2.1  2  Acetyltransf_10  Acetyltransferase (GNAT) 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 !   42.8   0.4   8.9e-15   5.3e-11       2      56 ..       4      57 ..       3      58 .. 0.90
   2 !   60.3   0.3   2.9e-20   1.8e-16       1      55 [.      66     120 ..      66     122 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 8.9e-15
                                      HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                      +++ +r ++t++ ++tl +++++m+e +++ + VV e+g+ vG++++rD++r l+
  gi|557693923|ref|YP_008796977.1|  4 KQLVRRGPITIDSSATLYDVVRIMAEQNIGFI-VVLENGRMVGVLSERDVVRTLA 57
                                      6788999**********************666.7669**************9987 PP

  == domain 2  score: 60.3 bits;  conditional E-value: 2.9e-20
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       Vg+i+ rd++t+p d+++e+a+e+m +++++++ VVd+ gklvG+v+ rD+l+ l
  gi|557693923|ref|YP_008796977.1|  66 VGEICKRDIITLPADASVEDAAEEMGRHRIRHIVVVDNAGKLVGVVSARDVLQEL 120
                                       89************************9******889****************987 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 !    5.6   0.1    0.0032        19      12      34 ..      36      58 ..      24      68 .. 0.87
   2 !   11.8   0.1   3.7e-05      0.22       6      32 ..      94     120 ..      92     128 .] 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0032
                                      EE-SSS-EEEEEEHHHHHHHHHH CS
                             IF3_N 12 lvdedGeqlGvistreAlrlaee 34
                                      +v e+G ++Gv+s r+++r+  e
  gi|557693923|ref|YP_008796977.1| 36 VVLENGRMVGVLSERDVVRTLAE 58
                                      77799************998766 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 3.7e-05
                                       -SSEEEEE-SSS-EEEEEEHHHHHHHH CS
                             IF3_N   6 rarevrlvdedGeqlGvistreAlrla 32 
                                       r r++ +vd+ G+ +Gv+s r++l+  
  gi|557693923|ref|YP_008796977.1|  94 RIRHIVVVDNAGKLVGVVSARDVLQEL 120
                                       5799********************964 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0045        27      25      47 ..      26      48 ..      13      60 .. 0.81
   2 ?    6.1   0.0    0.0017        10      20      50 ..      84     115 ..      68     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0045
                   Acetyltransf_10 25 rieegealllvaeeggkivGvie 47
                                       ++e++  ++v+ e+g++vGv++
  gi|557693923|ref|YP_008796977.1| 26 IMAEQNIGFIVVLENGRMVGVLS 48
                                      3468889999999*******985 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0017
                   Acetyltransf_10  20 ealreri.eegealllvaeeggkivGvielrd 50 
                                       e  +e++ ++   +++v+++ gk+vGv++ rd
  gi|557693923|ref|YP_008796977.1|  84 EDAAEEMgRHRIRHIVVVDNAGKLVGVVSARD 115
                                       455566657888899999999*******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 894.93
//
Query:       gi|557693924|ref|YP_008796978.1|  [L=318]
Description: peptide/nickel ABC transporter ATPase subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  103.6   0.0    1.7e-29  103.1   0.0    1.2  1  ABC_tran   ABC transporter
    1.7e-22   79.7   0.3    2.9e-22   78.9   0.3    1.4  1  oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal reg
     0.0066   16.7   0.3      0.029   14.6   0.3    1.9  1  AAA_22     AAA domain
  ------ inclusion threshold ------
      0.012   15.0   0.0        0.4   10.1   0.0    2.2  2  TniB       Bacterial TniB protein
      0.014   15.1   0.1      0.024   14.4   0.1    1.3  1  AAA_29     P-loop containing region of AAA domain
      0.051   13.0   0.1          3    7.2   0.0    2.1  2  SMC_N      RecF/RecN/SMC N terminal domain
      0.063   12.8   0.3       0.58    9.7   0.1    2.2  2  AAA_25     AAA domain
      0.084   13.2   0.2       0.14   12.6   0.2    1.6  1  AAA_16     AAA ATPase domain
       0.15   11.4   0.1       0.29   10.5   0.1    1.4  1  ATPase     KaiC


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 !  103.1   0.0   8.3e-33   1.7e-29       2     136 ..      27     179 ..      26     180 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 8.3e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + vsl++ e+e va+vGe+G+GK+t+ kl ++llkp  G+i +dg d+++   ++l +lr+e ++++q+  ++l+p 
  gi|557693924|ref|YP_008796978.1|  27 DGVSLSIPENEAVALVGESGSGKTTVGKLSIRLLKPLTGRIFYDGLDVTRlpeNRLGKLRRETRMIFQDpyASLNPY 103
                                       78************************************************999999*************999***** PP

                                       SBHHHH.............HHHTC....HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxx.............xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdee....iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       ++v+e              +   e    ++kal++++l+  +++ +++ p+ LSgGq+qrva+ara++ kp+ l++D
  gi|557693924|ref|YP_008796978.1| 104 MSVGEFveepllihgvedkA---ErveiVYKALEEVRLTP-PQDFAQKYPHMLSGGQRQRVAIARAIVLKPRYLVAD 176
                                       ***************96541...345679*********99.88888899**************************** PP

                                       STT CS
                                       xxx RF
                          ABC_tran 134 Ept 136
                                       Ep 
  gi|557693924|ref|YP_008796978.1| 177 EPV 179
                                       **7 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 !   78.9   0.3   1.5e-25   2.9e-22       1      65 []     231     297 ..     231     297 .. 0.99

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 1.5e-25
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd..klekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE+g+++++++eplHPYT++L++s+p++d++++  + e+i+ge+ps++++++GC+F+pRCp a e C
  gi|557693924|ref|YP_008796978.1| 231 VEMGEVEEILSEPLHPYTQGLIASIPEPDPGNRfvERETIQGEPPSPQNIPSGCRFHPRCPKAFERC 297
                                       8****************************************************************99 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.3   1.4e-05     0.029       8     127 ..      39     207 ..      35     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.4e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.....................erpevv....fvtlpsstsskdllre 59 
                                       ++++GesG+GKTt+ +   + l+                            ++ + +    +  l+  +s  ++ +e
  gi|557693924|ref|YP_008796978.1|  39 VALVGESGSGKTTVGKLSIRLLKP--LT-GrifydgldvtrlpenrlgklrRETRMIfqdpYASLNPYMSVGEFVEE 112
                                       789************998888732..22.135677788888888777777655555566666666666677777777 PP

                            AAA_22  60 llralglelka................erlsseellealeqalrarav.........ielliiDEaqhlr...s.ee 107
                                        l + g+e ka                ++++  + + ++    ++++v         ++ l+ DE   ++   s +e
  gi|557693924|ref|YP_008796978.1| 113 PLLIHGVEDKAerveivykaleevrltPPQDFAQKYPHMLSGGQRQRVaiaraivlkPRYLVADEPVSMIdasSrAE 189
                                       77777777777778888888888777766666666666666666666677777777778888888777655752588 PP

                            AAA_22 108 aleeLrsllnlsrkgvqliL 127
                                       +le L++l++  ++ +++++
  gi|557693924|ref|YP_008796978.1| 190 VLEVLKTLQK--DYRMAILY 207
                                       8888888877..66666665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.036        73      37      51 ..      38      52 ..      31      60 .. 0.86
   2 ?   10.1   0.0    0.0002       0.4     118     160 ..     168     208 ..     143     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.036
                              TniB 37 nlllvGdsnnGKtmi 51
                                       + lvG+s  GKt++
  gi|557693924|ref|YP_008796978.1| 38 AVALVGESGSGKTTV 52
                                      689**********98 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0002
                              TniB 118 lkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       lk+r L+ DE  +++   a+++ e+l++lk+L+ +++++i ++
  gi|557693924|ref|YP_008796978.1| 168 LKPRYLVADEPVSMI--DASSRAEVLEVLKTLQKDYRMAILYI 208
                                       6899*********99..778899**************999876 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   0.1   1.2e-05     0.024      13      38 ..      27      52 ..      24      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTl 38
                                      dg +++i +++a+ l+G+sGsGK+T+
  gi|557693924|ref|YP_008796978.1| 27 DGVSLSIPENEAVALVGESGSGKTTV 52
                                      67788999888*************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 ?    3.8   0.1     0.016        32      24      40 ..      36      52 ..      23      58 .. 0.84
   2 ?    7.2   0.0    0.0015         3     135     197 ..     150     208 ..      86     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                                      SSEEEEEESTTSSHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnl 40
                                      ++  a+vG+ GSGK+ +
  gi|557693924|ref|YP_008796978.1| 36 NEAVALVGESGSGKTTV 52
                                      45789*********987 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0015
                                       TCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 elLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivisl 197
                                       ++LSgG+++ va+a  +     kp+ l + De  + +D++ +++v e+lk+ +k+  + +  +
  gi|557693924|ref|YP_008796978.1| 150 HMLSGGQRQRVAIARAIV---LKPRYL-VADEPVSMIDASSRAEVLEVLKTLQKDYRMAILYI 208
                                       39*******999986543...345543.67********************9999865544433 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00029      0.58      30      49 ..      33      52 ..      23      68 .. 0.91
   2 ?    0.7   0.0      0.17   3.4e+02     161     188 ..     183     210 ..     114     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00029
                            AAA_25 30 lpagelallaGapgtGKttl 49
                                      +p++e ++l+G +g+GKtt+
  gi|557693924|ref|YP_008796978.1| 33 IPENEAVALVGESGSGKTTV 52
                                      89****************97 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.17
                            AAA_25 161 snsdvgalvealeriarrtgaavllvhH 188
                                       ++s  ++++e l+ +++ ++ a+l + H
  gi|557693924|ref|YP_008796978.1| 183 DASSRAEVLEVLKTLQKDYRMAILYIAH 210
                                       5556688899999999999999999988 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   6.8e-05      0.14      23      42 ..      35      54 ..      25     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.8e-05
                            AAA_16 23 rpelvllsGesGvGKsslvr 42
                                      + e+v l+GesG+GK+++ +
  gi|557693924|ref|YP_008796978.1| 35 ENEAVALVGESGSGKTTVGK 54
                                      4489*************965 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00014      0.29      16      36 ..      33      53 ..      23      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                            ATPase 16 ipegrvvlitGepGtGKtifa 36
                                      ipe+++v ++Ge+G+GKt+++
  gi|557693924|ref|YP_008796978.1| 33 IPENEAVALVGESGSGKTTVG 53
                                      8*****************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2039.44
//
Query:       gi|557693925|ref|YP_008796979.1|  [L=226]
Description: hypothetical protein CSUB_C0488 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.027   14.7   0.6      0.038   14.2   0.6    1.2  1  CwsA      Cell wall synthesis protein CwsA
      0.067   14.3   0.0       0.21   12.7   0.0    1.9  2  PPC       Bacterial pre-peptidase C-terminal domain


Domain annotation for each model (and alignments):
>> CwsA  Cell wall synthesis protein CwsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.6   4.2e-06     0.038      35     125 ..     127     222 ..      92     225 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.2e-06
                              CwsA  35 staeelrrryresrlarelaa.aqeaiaqelaaaqevvaglPqaledarkkrrrkrplllag...vavavla.GGav 106
                                        t + +r +  ++ +++ +++   e++++++  ++ vv++   ++ d+++ + +k p+  ag   +a+a+l  G a+
  gi|557693925|ref|YP_008796979.1| 127 LTISVIRPKTVTQTVTAVVTErVTETVTTHVFNTNTVVSERIVTVVDTERVEVEKAPWTAAGlaiLAAALLYtGHAA 203
                                       3557778787778887777653689**********************************999444456777515566 PP

                              CwsA 107 afsivrrssrPePsslpPs 125
                                       + ++  r ++P  + +pPs
  gi|557693925|ref|YP_008796979.1| 204 SEALKSRHKQPPEEQKPPS 222
                                       6677778889966677887 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 ?   12.7   0.0   2.3e-05      0.21       4      68 ..      53     115 ..      50     117 .. 0.80
   2 ?   -3.9   0.0         2   1.8e+04      61      68 ..     122     129 ..     121     130 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.3e-05
                                       EEEEEE-TT-E.EE.EEES-TT..SEEEEE-TT..-SS-EE-ST.T-TTS-TTS-EE-SSSEEEEEEE CS
                               PPC   4 vysfevpagds.lt.ididggtidldLylldsngtsvaaydans.apsgsdeyieftapqaGtYyvaV 68 
                                       ++++ ++ gd  +  + +  ++ d+dLyll++   ++      s   +g    +e+ta ++G  y+ V
  gi|557693925|ref|YP_008796979.1|  53 FFKIMLEPGDIlVAkVRMAANQ-DFDLYLLNPL-REIVG---QSvRATGLTDAVEYTAVEKGPHYIVV 115
                                       7888888888855478899999.**********.44444...2335588999**************98 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2
                                       SEEEEEEE CS
                               PPC  61 aGtYyvaV 68 
                                       aG+Y + +
  gi|557693925|ref|YP_008796979.1| 122 AGVYSLTI 129
                                       89998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1591.65
//
Query:       gi|557693926|ref|YP_008796980.1|  [L=80]
Description: hypothetical protein CSUB_C0489 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       140  (0.00780858); expected 358.6 (0.02)
Passed bias filter:                      127  (0.0070835); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); 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: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 632.17
//
Query:       gi|557693927|ref|YP_008796981.1|  [L=573]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   48.8   0.2    3.4e-10   39.7   0.0    2.9  2  BNR_2           BNR repeat-like domain
    1.7e-06   27.1  26.6       0.18   11.9   0.4    6.4  6  BNR             BNR/Asp-box repeat
    0.00018   21.0   0.1     0.0018   17.7   0.1    2.1  2  BNR_4           BNR repeat-containing family member
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.042   13.9   0.1    1.9  1  TIG             IPT/TIG domain
       0.18   10.6   4.3        4.2    6.1   1.6    3.6  3  Sortilin-Vps10  Sortilin, neurotensin receptor 3,
        0.2   11.7   0.0        0.4   10.7   0.0    1.5  1  FAST_1          FAST kinase-like protein, subdomain 1


Domain annotation for each model (and alignments):
>> BNR_2  BNR repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.0    0.0027         8     186     203 ..      50      67 ..      40      89 .. 0.64
   2 !   39.7   0.0   1.1e-13   3.4e-10      16     209 ..     129     353 ..     125     362 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0027
                                       EEEEEESSTTSS-EEE-E CS
                             BNR_2 186 ileseSedgGetWskvel 203
                                       + +s S+dgG +Ws++++
  gi|557693927|ref|YP_008796981.1|  50 VTVSVSKDGGLSWSAPHV 67 
                                       444555555555555543 PP

  == domain 2  score: 39.7 bits;  conditional E-value: 1.1e-13
                                       EEEEEEEEEETTEEE.EEEEEE-TTS-.....BTTEEEEEEEEEEET.TTEEEEEEEEEETT--HHT----E.EEES CS
                             BNR_2  16 pdvaiwvsvsdkgsneWsapqvvadreq..srearkklgNPvlfqdp.sgtliLfykvgvsvggwagskitr.vtSk 88 
                                        +v+i +  s++g+ +W++p+ v+   +   + + ++l     ++ + +gt++  y  + + g  +g  + +   S+
  gi|557693927|ref|YP_008796981.1| 129 IEVSIKLVKSTDGGLTWTSPVAVSPVYSglAGDEEARLVQGSHVHVAeDGTVYVAYYDSRDDGPFKGLFTPMvTVSR 205
                                       5789999999***********999888777555555555555555444999999885555555566666555589** PP

                                       STTSS----EHHHGG................EEEEEE-SS--..EE--T--EEEEEE..SS--.EEEEEEEESSTTS CS
                             BNR_2  89 DdGktWsaprrlpks................pflnisgpvknkpiqladGrlilPsshelagk.wrallelsddggk 148
                                       D+G+tWs+p +++++                ++  +  +  n p   ++  ++ +  ++  g+   +++  s dgg 
  gi|557693927|ref|YP_008796981.1| 206 DGGRTWSKPSPVIPGgtweqpffltptyfrsWSSMFPVLKTN-PANSNEVYIVFGATGTNSGDlSDVYFSKSVDGGA 281
                                       **********99999777666666555554444444433333.444445566666655544445788899999**** PP

                                       S-EE----S...SSEEEEEEEE.EEETTEEEEE...EEE.........EEEEEEESSTTSS-EE.E-EEEEE-- CS
                             BNR_2 149 tWkkgrvve...qisgeiqpsilvekdgslval...aRsrka......aileseSedgGetWsk.veltslpnp 209
                                       tW+k + v+   +++++  p++ v+++g ++++   +R+  +      +i+ ++S+dgG+t+ +  ++t++p++
  gi|557693927|ref|YP_008796981.1| 282 TWSKPKRVNddlTLRNQFFPTMAVSPNGTIHIIwgdMRD--DpdnyryHIYYTRSTDGGATFMEnSRVTDYPSN 353
                                       ***9888888999999************99998444566..1345679**************554889999865 PP

>> BNR  BNR/Asp-box repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.1   0.00062       1.9       2      11 ..      54      63 ..      53      64 .. 0.90
   2 !    9.4   0.5   0.00041       1.2       3      11 ..     138     146 ..     136     147 .. 0.90
   3 !   11.9   0.4   6.2e-05      0.18       2      12 .]     203     213 ..     202     213 .. 0.92
   4 ?   -1.7   0.5       1.9   5.8e+03       7      11 ..     220     224 ..     220     225 .. 0.86
   5 !    8.9   0.2    0.0006       1.8       3      12 .]     276     285 ..     275     285 .. 0.92
   6 ?    4.7   0.2     0.015        44       2      10 ..     333     341 ..     332     341 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00062
                                      EESSTTSS-E CS
                               BNR  2 yStDgGktWs 11
                                      +S+DgG +Ws
  gi|557693927|ref|YP_008796981.1| 54 VSKDGGLSWS 63
                                      7********9 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00041
                                       ESSTTSS-E CS
                               BNR   3 StDgGktWs 11 
                                       StDgG tW+
  gi|557693927|ref|YP_008796981.1| 138 STDGGLTWT 146
                                       9*******7 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 6.2e-05
                                       EESSTTSS-EE CS
                               BNR   2 yStDgGktWsk 12 
                                       +S+DgG+tWsk
  gi|557693927|ref|YP_008796981.1| 203 VSRDGGRTWSK 213
                                       7********97 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.9
                                       TSS-E CS
                               BNR   7 GktWs 11 
                                       G tW+
  gi|557693927|ref|YP_008796981.1| 220 GGTWE 224
                                       89**8 PP

  == domain 5  score: 8.9 bits;  conditional E-value: 0.0006
                                       ESSTTSS-EE CS
                               BNR   3 StDgGktWsk 12 
                                       S DgG tWsk
  gi|557693927|ref|YP_008796981.1| 276 SVDGGATWSK 285
                                       89******97 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.015
                                       EESSTTSS- CS
                               BNR   2 yStDgGktW 10 
                                        StDgG t+
  gi|557693927|ref|YP_008796981.1| 333 RSTDGGATF 341
                                       5******97 PP

>> BNR_4  BNR repeat-containing family member
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.099     3e+02     228     266 ..     169     212 ..     137     225 .. 0.74
   2 !   17.7   0.1   6.1e-07    0.0018     105     196 ..     252     344 ..     241     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.099
                                       S-EEEE-TT--EEEEEEE--TT-.....SS-EEEEEEE-SS-EE CS
                             BNR_4 228 qesvavDkegnpvvlyskfddag.....atqkyyyrkanggaWe 266
                                         +v v ++g+++v+y++ +d+g      t+   + +  g++W 
  gi|557693927|ref|YP_008796981.1| 169 GSHVHVAEDGTVYVAYYDSRDDGpfkglFTPMVTVSRDGGRTWS 212
                                       55788889999999999999988776663333333335555555 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 6.1e-07
                                       G-EEEEEEE-TTSS-EEEEEEEETTTTEEEEEES-.SB--T.TT-EEEEEE.EE-TTS-EEEEEEEE-SSSGGGEEE CS
                             BNR_4 105 gkLllsyRdgksgngnavlneYdektdkwktlgekqlldgeegqrnaYlkglsygkdgrihvtwtwretpdaetnhd 181
                                       +++++++  +++  g+   + ++++ d   t+++ + ++   + rn ++  + + ++g+ih++w +    + + +  
  gi|557693927|ref|YP_008796981.1| 252 NEVYIVFGATGTNSGDLSDVYFSKSVDGGATWSKPKRVNDDLTLRNQFFPTMAVSPNGTIHIIWGDMRDDPDNYRYH 328
                                       667888888888888888889999999999999998888877**********************9754456666667 PP

                                       EEEEEESSTTSS-.B- CS
                             BNR_4 182 lyYaysddggrtw.en 196
                                       +yY +s+dgg t+ en
  gi|557693927|ref|YP_008796981.1| 329 IYYTRSTDGGATFmEN 344
                                       **********998344 PP

>> TIG  IPT/TIG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.4e-05     0.042       6      53 ..     409     452 ..     407     472 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                               TIG   6 isPnsgsasgGttititGtnFgtnssdssvtiggtpctvtasvssttl 53 
                                       isP++g+a  G+ iti G++F    ++  v i  + ++v+++ +++  
  gi|557693927|ref|YP_008796981.1| 409 ISPPQGPA--GQVITIIGDGF--APRQREVFIEFDGVVVSSFATDSVG 452
                                       89******..***********..5555555555555555545555544 PP

>> Sortilin-Vps10  Sortilin, neurotensin receptor 3,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.055   1.6e+02     378     390 ..      51      63 ..      39      70 .. 0.80
   2 ?    0.1   0.0     0.089   2.7e+02     382     391 ..     138     147 ..     125     156 .. 0.82
   3 ?    6.1   1.6    0.0014       4.2       3     109 ..     201     341 ..     199     350 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.055
                                       EEEEESSSSSS-E CS
                    Sortilin-Vps10 378 dtfiSrDaGltWk 390
                                        + +S+D+Gl+W+
  gi|557693927|ref|YP_008796981.1|  51 TVSVSKDGGLSWS 63 
                                       5668999999997 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.089
                                       ESSSSSS-EE CS
                    Sortilin-Vps10 382 SrDaGltWke 391
                                       S+D+GltW++
  gi|557693927|ref|YP_008796981.1| 138 STDGGLTWTS 147
                                       8999999975 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0014
                                       EEEESSTTSS-EE-GGGGTTEEBE..................-EEE-STTS--EEEEEE..........S-EEEEES CS
                    Sortilin-Vps10   3 vyiSeDeGktwkkvkeklkgeaiq..................eivvhpfdkkkaylltd..........skklyvtt 51 
                                       v +S+D G+tw+k + ++ g +++                   + ++p +++++y++            +  +  + 
  gi|557693927|ref|YP_008796981.1| 201 VTVSRDGGRTWSKPSPVIPGGTWEqpffltptyfrswssmfpVLKTNPANSNEVYIVFGatgtnsgdlsDVYFSKSV 277
                                       67888888888888888888888888888888888888777777788888888887765677777774333333456 PP

                                       STTSSEEE.EE-SS-BS......S--EEESSETTEEEEE.......BTTS-EEEE..SSTTSSE CS
                    Sortilin-Vps10  52 DrGktwkk.fklpfkpsl...saeplsfhakdkdwlialgekkeskdckkkayys..tdggksw 109
                                       D G+tw+k  +++++ +l     +++++ ++   ++i+  ++ + ++ +  +yy+  tdgg+++
  gi|557693927|ref|YP_008796981.1| 278 DGGATWSKpKRVNDDLTLrnqFFPTMAVSPNGTIHIIWGDMRDDPDNYRYHIYYTrsTDGGATF 341
                                       8888888844455555555556777888888888888887776666666666665225677665 PP

>> FAST_1  FAST kinase-like protein, subdomain 1
   #    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      18      50 ..     522     554 ..     507     564 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                            FAST_1  18 eeFfeklesrlepylsslspeelldavwsLcil 50 
                                       + + ++l++rl+p+ls+  ++ +ld+v+ L+i+
  gi|557693927|ref|YP_008796981.1| 522 DRLADALTERLKPQLSQTGSSAMLDIVLGLAIV 554
                                       678899*************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 3815.86
//
Query:       gi|557693928|ref|YP_008796982.1|  [L=838]
Description: peptide/nickel ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  101.0   2.3    1.5e-24   86.7   0.0    3.0  3  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


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 !   86.7   0.0   8.6e-29   1.5e-24     147     367 ..      29     263 ..      19     272 .. 0.88
   2 !    2.5   0.1    0.0031        55       8      49 ..     455     494 ..     451     511 .. 0.77
   3 !   10.1   0.1   1.6e-05      0.28     112     160 ..     642     702 ..     593     718 .. 0.77

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 8.6e-29
                                       TSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTT.....STG CS
                         SBP_bac_5 147 ggkpkldriefkvipdsdaraaalqsGeiddv.aepppsdieqlkeakglkvlyespgggvtylafNtk.....kpp 217
                                       +  p+ d i+++ +  ++ + + l++G+id +  ++  s +++l++++g+k+   ++++    + +N +      +p
  gi|557693928|ref|YP_008796982.1|  29 KPGPATDVIRVRAY-AEEIAPQVLEKGDIDLYlYNMRVSRVQALENNPGIKM--VKAPSLLLSIILNPApdpngLNP 102
                                       55578899999999.777777888*****999899*****************..9999999999*****9999977* PP

                                       GGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH...SHHHHHHHH....HHHTT-BCS CS
                         SBP_bac_5 218 fddkrvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka...ydpekAkkl....LkeaGykdg 287
                                       f+ k+vR+A++y ++r+ +vk++++gya p++++l+p  + + + +++  ++   ydpe A +l    L +aG +++
  gi|557693928|ref|YP_008796982.1| 103 FSIKEVRKAFQYLVNRDYVVKELYRGYASPMTTPLSPYDYDYAQFFESILETgirYDPEYASRLitaaLTSAGAEKR 179
                                       **********************************9998888888877766559********9884444677899999 PP

                                       STSCEETCEEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHH....HHHHHHHHCTTESEEEEEEECTTS CS
                         SBP_bac_5 288 dggglrekklkltlllasgspaekaiaeliqqqlkkiGikvevktvdwa....atylervkdgdfdmillgwgadyp 360
                                       dg+++  +k++ + ++  +   ++++ +l++++l+k G++ve  ++++a    ++y+++ ++ ++ ++  gwg +  
  gi|557693928|ref|YP_008796982.1| 180 DGKWFYRDKPVSVKFVIRTEDERRELGDLVASELEKTGFTVERIYLPFAqaiaRVYTTDPSEFTWHLYTEGWGRGAL 256
                                       99999999999999999999999***********************8888***********************9988 PP

                                       TTHHHHH CS
                         SBP_bac_5 361 dpdnfln 367
                                       + +++++
  gi|557693928|ref|YP_008796982.1| 257 EKYDSTS 263
                                       7776655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.0031
                                       EEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHH CS
                         SBP_bac_5   8 eswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferll 49 
                                       ++  +v   + t+ + L    k++ G p+t +D+ + ++ + 
  gi|557693928|ref|YP_008796982.1| 455 TN--TVAISKVTFDYSLYTSSKWHHGIPITMADILYRIYQTF 494
                                       55..55555667777788888***************766554 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 1.6e-05
                                       TTGTTTSE-BSSSEEEEEEETTT...EEEEEE-TTS.T........TTSCSSSSEEEEEE- CS
                         SBP_bac_5 112 dkdtnekpvgtGPYklkefkpgq...kivlernpdY.w........gggkpkldriefkvi 160
                                        +++n ++v++GPY l++f+p +   +++ +r p Y +          +kp++ ri+ +v+
  gi|557693928|ref|YP_008796982.1| 642 VNTYNLAVVSNGPYILAAFDPASqfaELRAYRDPSYpFkpgkwffgAVEKPRITRIQGSVV 702
                                       6789999**************6655555555666696245555995449999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (838 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); 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: 0.69u 0.28s 00:00:00.97 Elapsed: 00:00:00.44
# Mc/sec: 5674.09
//
Query:       gi|557693929|ref|YP_008796983.1|  [L=291]
Description: hypothetical protein CSUB_C0492 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-05   23.3   9.5    9.8e-05   22.7   9.5    1.3  1  ATG16            Autophagy protein 16 (ATG16)
    0.00014   22.6   0.4    0.00026   21.7   0.4    1.4  1  DUF2203          Uncharacterized conserved protein (DUF2203)
    0.00017   20.7   6.8    0.00026   20.1   6.8    1.2  1  IFT57            Intra-flagellar transport protein 57
    0.00017   20.6   0.3    0.00027   20.0   0.3    1.3  1  DUF677           Protein of unknown function (DUF677)
    0.00022   20.4   6.2     0.0003   20.0   6.2    1.1  1  Atg14            Vacuolar sorting 38 and autophagy-related su
    0.00023   20.6  11.9    0.00052   19.4  11.9    1.5  1  GAS              Growth-arrest specific micro-tubule binding
    0.00029   19.2  11.9    0.00039   18.8  11.9    1.0  1  FPP              Filament-like plant protein, long coiled-coi
    0.00035   21.1   5.0    0.00049   20.6   5.0    1.2  1  Fez1             Fez1
    0.00048   20.5   9.5      0.038   14.4   2.5    3.0  3  FlaC_arch        Flagella accessory protein C (FlaC)
    0.00053   18.7   0.7    0.00067   18.4   0.7    1.1  1  FapA             Flagellar Assembly Protein A
    0.00063   20.4   7.4     0.0011   19.7   7.4    1.3  1  DUF4472          Domain of unknown function (DUF4472)
    0.00064   19.8   7.2     0.0012   18.8   7.2    1.4  1  Laminin_II       Laminin Domain II
    0.00068   18.7   4.8    0.00091   18.2   4.8    1.1  1  DUF812           Protein of unknown function (DUF812)
    0.00086   17.2   2.9     0.0011   16.9   2.9    1.1  1  Nup88            Nuclear pore component
     0.0012   18.9  10.6     0.0012   18.9  10.6    1.9  1  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
     0.0013   18.4   1.6     0.0016   18.0   1.6    1.1  1  Exonuc_VII_L     Exonuclease VII, large subunit
     0.0013   18.7  12.0       0.77    9.9   2.1    2.5  2  TolA_bind_tri    TolA binding protein trimerisation
     0.0015   18.7   8.6      0.003   17.7   8.5    1.6  1  Nup54            Nucleoporin complex subunit 54
     0.0015   17.9   3.3     0.0025   17.2   3.3    1.4  1  HemX             HemX, putative uroporphyrinogen-III C-methyl
     0.0015   17.9   3.0     0.0024   17.3   3.0    1.2  1  Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
     0.0016   18.1   6.1     0.0025   17.4   6.1    1.3  1  Filament         Intermediate filament protein
     0.0016   18.6   4.8     0.0033   17.6   4.8    1.5  1  FliJ             Flagellar FliJ protein
     0.0017   17.8   8.8     0.0025   17.2   7.5    1.6  1  Tropomyosin      Tropomyosin
     0.0017   18.4  11.4     0.0036   17.4  11.4    1.6  1  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
      0.002   17.9   4.4     0.0032   17.2   4.4    1.3  1  DUF745           Protein of unknown function (DUF745)
      0.002   17.0   8.2     0.0027   16.5   8.2    1.1  1  Tektin           Tektin family
      0.002   17.8   3.0      0.002   17.8   3.0    1.5  1  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
     0.0021   18.1   2.7     0.0038   17.3   2.7    1.4  1  Rootletin        Ciliary rootlet component, centrosome cohesi
     0.0023   16.9  10.1     0.0036   16.2  10.1    1.2  1  Spc7             Spc7 kinetochore protein
     0.0024   16.6   0.7     0.0033   16.2   0.7    1.3  1  AAA_13           AAA domain
     0.0024   17.4  16.2      0.033   13.8  17.6    1.9  2  MscS_porin       Mechanosensitive ion channel porin domain
     0.0027   17.3   5.9     0.0039   16.8   5.9    1.2  1  HAUS-augmin3     HAUS augmin-like complex subunit 3
     0.0028   17.3   5.5     0.0041   16.8   5.5    1.1  1  PTRF_SDPR        PTRF/SDPR family
     0.0028   17.3   0.4     0.0048   16.5   0.4    1.4  1  Vps5             Vps5 C terminal like
     0.0029   16.0   4.5     0.0039   15.6   4.5    1.1  1  Gp58             gp58-like protein
      0.003   16.2   4.9     0.0038   15.9   4.9    1.0  1  Macoilin         Macoilin family
     0.0032   18.3  10.9     0.0053   17.6  10.9    1.3  1  PRKG1_interact   cGMP-dependent protein kinase interacting do
     0.0032   16.8   6.4       0.21   10.9   0.2    2.2  2  CASP_C           CASP C terminal
     0.0035   17.6   5.9      0.093   13.0   2.6    2.5  2  Rx_N             Rx N-terminal domain
     0.0038   17.4   2.7     0.0063   16.6   2.7    1.3  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
     0.0042   17.6  10.4      0.011   16.3  10.4    1.6  1  APG6_N           Apg6 coiled-coil region
     0.0044   15.3   4.3     0.0068   14.6   4.3    1.2  1  EzrA             Septation ring formation regulator, EzrA
      0.005   16.9   5.0      0.018   15.0   5.0    2.0  1  DUF1664          Protein of unknown function (DUF1664)
     0.0057   17.0  11.3       0.62   10.5   6.2    3.0  3  CLZ              C-terminal leucine zipper domain of cyclic n
      0.006   15.9   2.8     0.0092   15.3   2.8    1.3  1  TMPIT            TMPIT-like protein
     0.0078   13.8   7.1       0.01   13.4   7.1    1.1  1  DUF3584          Protein of unknown function (DUF3584)
      0.008   16.6   7.2       0.31   11.4   0.6    3.2  2  LPP              Lipoprotein leucine-zipper
      0.008   16.7   2.3      0.013   16.0   2.3    1.3  1  T3SSipB          Type III cell invasion protein SipB
  ------ inclusion threshold ------
      0.011   16.0   8.0      0.024   14.8   8.0    1.5  1  Fib_alpha        Fibrinogen alpha/beta chain family
      0.012   14.6   9.9      0.016   14.1   9.9    1.1  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
      0.012   15.7  12.2       0.14   12.2   3.6    2.5  2  bZIP_1           bZIP transcription factor
      0.012   15.2   6.4      0.018   14.7   6.4    1.2  1  DUF2968          Protein of unknown function (DUF2968)
      0.013   14.6   3.4      0.018   14.0   3.4    1.2  1  TTKRSYEDQ        Predicted coiled-coil domain-containing prot
      0.013   15.0   9.0      0.021   14.3   9.0    1.3  1  HMMR_N           Hyaluronan mediated motility receptor N-term
      0.014   14.9   8.6      0.021   14.3   8.6    1.2  1  Golgin_A5        Golgin subfamily A member 5
      0.014   13.8   6.8       0.02   13.3   6.8    1.1  1  MAD              Mitotic checkpoint protein
      0.015   15.3   2.4      0.033   14.2   0.3    2.0  2  DUF4446          Protein of unknown function (DUF4446)
      0.017   15.5   5.2      0.028   14.8   5.2    1.2  1  DUF4200          Domain of unknown function (DUF4200)
      0.024   14.9   3.6      0.049   14.0   3.6    1.5  1  OmpH             Outer membrane protein (OmpH-like)
      0.026   14.6  12.3       0.04   14.0  11.5    1.6  1  ADIP             Afadin- and alpha -actinin-Binding
      0.027   14.5   7.6       0.05   13.7   4.9    2.2  2  DUF2730          Protein of unknown function (DUF2730)
      0.028   14.8  10.5      0.048   14.0  10.5    1.4  1  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
      0.028   14.5   5.7       0.71   10.0   1.3    2.6  2  Vps51            Vps51/Vps67
      0.031   14.3  13.5       0.29   11.2  12.7    2.0  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.031   14.0   1.2       0.05   13.4   1.2    1.3  1  dCache_1         Cache domain
      0.038   13.8   5.5      0.059   13.2   5.5    1.2  1  DUF724           Protein of unknown function (DUF724)
      0.038   11.9   2.3      0.055   11.4   2.3    1.2  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.04   14.2   0.1      0.059   13.7   0.1    1.3  1  RskA             Anti-sigma-K factor rskA
       0.04   14.4   7.7       0.14   12.7   7.7    1.9  1  DUF16            Protein of unknown function DUF16
      0.058   13.5   2.7      0.091   12.8   1.0    1.9  2  DUF3568          Protein of unknown function (DUF3568)
      0.064   12.6  11.6       0.24   10.7   8.1    2.1  2  DUF3450          Protein of unknown function (DUF3450)
      0.069   13.4   6.6        0.2   11.9   2.0    2.7  2  XhlA             Haemolysin XhlA
       0.07   12.3   0.2       0.13   11.4   0.2    1.5  1  AI-2E_transport  AI-2E family transporter
      0.071   13.3  10.1      0.086   13.0   8.8    1.6  1  Tropomyosin_1    Tropomyosin like
      0.076   13.3   7.0       0.57   10.5   7.0    2.2  1  DUF641           Plant protein of unknown function (DUF641)
      0.082   12.5   5.4       0.24   11.0   5.4    1.8  1  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
      0.083   12.6   4.4       0.15   11.7   4.4    1.4  1  LXG              LXG domain of WXG superfamily
      0.085   11.7   0.1        0.1   11.5   0.1    1.2  1  LMBR1            LMBR1-like membrane protein
      0.088   13.2   9.6       0.19   12.2   9.6    1.5  1  CENP-H           Centromere protein H (CENP-H)
      0.093   13.1  12.9       0.18   12.2   6.1    2.6  2  Csm1_N           Csm1 N-terminal domain
        0.1   12.6  15.5      0.031   14.3   8.3    2.7  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        0.1   12.7   5.6        1.1    9.4   5.6    2.2  1  COG2             COG (conserved oligomeric Golgi) complex com
       0.11   12.7  12.8       0.65   10.3   4.4    2.3  2  Spc24            Spc24 subunit of Ndc80
       0.11   12.7   8.2        3.5    8.0   8.3    2.8  1  DUF948           Bacterial protein of unknown function (DUF94
       0.12   12.6   4.0       0.24   11.7   3.6    1.7  1  ABC_tran_CTD     ABC transporter C-terminal domain
       0.13   10.9   8.2       0.17   10.5   8.2    1.1  1  GOLGA2L5         Putative golgin subfamily A member 2-like pr
       0.13   10.9   9.7        0.3    9.7   9.8    1.4  1  WEMBL            Weak chloroplast movement under blue light
       0.13   12.2  10.5        1.6    8.7   2.7    2.6  3  Prefoldin_2      Prefoldin subunit
       0.14   11.8   8.1        2.6    7.6   8.0    2.3  1  DUF4795          Domain of unknown function (DUF4795)
       0.14   12.5   4.7        1.1    9.7   1.8    2.1  2  HrpB7            Bacterial type III secretion protein (HrpB7)
       0.14   11.5   4.3       0.23   10.8   4.3    1.3  1  Not3             Not1 N-terminal domain, CCR4-Not complex com
       0.15   12.4   1.3       0.23   11.7   1.3    1.3  1  zf-C4H2          Zinc finger-containing protein
       0.15   11.8   3.5       0.21   11.4   2.4    1.8  1  USP8_interact    USP8 interacting
       0.16   12.3  10.4        5.4    7.4   6.9    2.5  2  DUF4164          Domain of unknown function (DUF4164)
       0.17   12.0   6.6       0.35   10.9   6.6    1.5  1  SPATA1_C         Spermatogenesis-associated C-terminus
       0.17   11.0   3.3       0.27   10.4   3.3    1.3  1  Tho2             Transcription factor/nuclear export subunit 
       0.19   11.8   9.6        0.1   12.6   3.9    2.2  2  BRE1             BRE1 E3 ubiquitin ligase
       0.19   10.6   3.1       0.26   10.1   3.1    1.2  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
       0.19   11.6   7.9        3.3    7.7   1.6    2.5  2  Prefoldin        Prefoldin subunit
        0.2   11.9   8.4       0.38   11.0   8.4    1.5  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
        0.2   11.0   7.9       0.55    9.6   2.6    2.1  2  DUF4618          Domain of unknown function (DUF4618)
        0.2   11.4  11.1       0.34   10.7   2.6    3.0  3  DivIC            Septum formation initiator
       0.21   11.2   9.6        0.3   10.6   9.6    1.1  1  TMCO5            TMCO5 family
       0.22    9.5   3.6       0.31    9.0   3.6    1.2  1  Prominin         Prominin
       0.22   12.2  11.1        2.5    8.8   5.6    2.6  2  SlyX             SlyX
       0.22   11.4   6.8       0.81    9.5   0.3    2.4  2  CdvA             CdvA-like coiled-coil domain
       0.22   11.0   4.1       0.36   10.4   4.1    1.3  1  HXXSHH           Protein of unknown function (DUF1552)
       0.22   12.0  10.8       0.28   11.6   6.7    2.9  2  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.23   11.8   2.7        4.7    7.7   0.8    2.5  2  Alanine_zipper   Alanine-zipper, major outer membrane lipopro
       0.23   11.3   4.7       0.54   10.1   4.7    1.6  1  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
       0.23    9.5  10.3       0.32    9.1  10.3    1.1  1  HOOK             HOOK protein
       0.24   11.7  10.6        1.8    8.9   4.7    3.1  3  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.27   10.9   5.5        1.4    8.5   0.8    2.3  2  DUF4988          Domain of unknown function
       0.28   11.9   7.1        1.9    9.2   7.1    2.1  1  AATF-Che1        Apoptosis antagonizing transcription factor
       0.33   11.3   6.2        0.6   10.5   4.8    2.0  2  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
       0.33   11.2   8.5       0.64   10.3   8.5    1.4  1  KLRAQ            Predicted coiled-coil domain-containing prot
       0.37   10.9  11.1        1.1    9.3  11.1    1.8  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.41   10.5   7.5        1.2    9.0   7.4    1.9  1  Sec34            Sec34-like family
       0.47   10.4   7.3        2.3    8.1   3.8    2.1  2  YscO             Type III secretion protein YscO
       0.49    9.9   9.5        2.3    7.7   3.7    2.1  2  PspA_IM30        PspA/IM30 family
       0.57    9.2  13.1        1.9    7.6  13.1    1.6  1  CCDC144C         CCDC144C protein coiled-coil region
        0.6    9.4   9.4       0.57    9.4   5.7    2.0  2  DUF4763          Domain of unknown function (DUF4763)
       0.61   10.2  11.5        1.4    9.1   2.0    3.7  4  DMPK_coil        DMPK coiled coil domain like
       0.66   10.5   7.6        7.1    7.1   7.6    2.3  1  DUF4140          N-terminal domain of unknown function (DUF41
       0.66    9.2   5.5        4.8    6.4   0.6    2.2  2  HlyE             Haemolysin E (HlyE)
       0.67    9.3   8.2          1    8.7   8.2    1.3  1  NBP1             Fungal Nap binding protein NBP1
        0.7   10.1   7.1        2.4    8.4   6.5    2.0  1  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.79    9.0  10.3       0.23   10.8   7.0    1.7  1  CorA             CorA-like Mg2+ transporter protein
       0.83    8.5   4.4        1.9    7.3   4.1    1.6  1  FemAB            FemAB family
       0.95    9.9   9.4         16    6.0  10.0    2.6  1  Snapin_Pallidin  Snapin/Pallidin
        1.1    9.2   6.5        9.3    6.1   6.6    2.1  1  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
        1.4    9.0   6.1          5    7.1   6.1    1.9  1  DUF1043          Protein of unknown function (DUF1043)
        1.4    9.5  10.5        4.9    7.8   9.3    2.2  3  BST2             Bone marrow stromal antigen 2
        1.6    9.0   9.6        3.1    8.1   3.8    2.2  2  KxDL             Uncharacterized conserved protein
        1.7    8.9   9.1        9.4    6.5   9.1    2.2  1  Cnn_1N           Centrosomin N-terminal motif 1
        1.8    7.7   6.3       0.87    8.7   2.7    1.8  2  DLP_helical      Dynamin-like helical domain
        1.8    8.7  17.8        0.2   11.8   3.9    3.2  2  Cep57_CLD_2      Centrosome localisation domain of PPC89
        1.8    8.5   7.7         11    6.0   0.8    2.6  2  Flg_hook         Flagellar hook-length control protein FliK
        1.8    9.2  11.9        6.1    7.5  11.0    2.1  1  HIP1_clath_bdg   Clathrin-binding domain of Huntingtin-intera
        1.9    8.7  14.5          3    8.1   1.7    2.8  2  JIP_LZII         JNK-interacting protein  leucine zipper II
          2    8.5   5.1        5.7    7.0   4.5    2.0  1  Noelin-1         Neurogenesis glycoprotein
        2.1    7.9   6.3        2.5    7.6   4.3    1.7  2  Fzo_mitofusin    fzo-like conserved region
        2.2    8.3  12.5        5.7    7.0   4.7    2.3  2  Sec2p            GDP/GTP exchange factor Sec2p
        2.4    8.7   9.0         29    5.2   1.9    3.3  2  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
        2.5    8.8   6.6        7.9    7.2   6.6    1.9  1  YabA             Initiation control protein YabA
        2.9    7.9   5.8        1.3    9.0   2.2    2.2  2  DUF1515          Protein of unknown function (DUF1515)
        3.6    7.8   8.1        2.8    8.1   1.4    2.7  2  Swi5             Swi5
        3.6    8.1  18.7       0.22   12.0   7.5    2.7  2  ZapB             Cell division protein ZapB
        3.7    7.9   8.7        5.9    7.2   7.5    1.9  1  Muted            Organelle biogenesis, Muted-like protein
        3.9    7.0   6.9         12    5.5   6.9    1.6  1  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
          4    7.5   7.8         11    6.1   7.8    1.7  1  DivIVA           DivIVA protein
        4.5    7.2  14.4        1.6    8.7   2.2    3.1  2  Shugoshin_N      Shugoshin N-terminal coiled-coil region
        6.4    6.1  10.6         13    5.2  10.6    1.5  1  DUF3552          Domain of unknown function (DUF3552)
        6.8    7.3  10.4        7.5    7.2   8.1    2.3  1  Syntaxin-6_N     Syntaxin 6, N-terminal
        7.1    6.3   7.7        7.1    6.3   2.8    2.4  1  GrpE             GrpE
        7.1    7.3  14.8        3.2    8.5   1.5    3.1  2  DUF4404          Domain of unknown function (DUF4404)


Domain annotation for each model (and alignments):
>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   9.5   8.5e-07   9.8e-05      68     145 ..      90     167 ..      64     184 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.5e-07
                             ATG16  68 snskqsakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdree 144
                                       +n + s+++++ e+++ +lr++ + l+ s ++  qr ++l+e+++ le++l++ +++l+++++e+++l+t++++ ++
  gi|557693929|ref|YP_008796983.1|  90 QNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKD 166
                                       34455566666666666666666666666666666666666666666666666666666666666666665554444 PP

                             ATG16 145 e 145
                                        
  gi|557693929|ref|YP_008796983.1| 167 V 167
                                       3 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.4   2.2e-06   0.00026      16     104 ..      99     185 ..      76     186 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.2e-06
                           DUF2203  16 kelleelralrkeleeleeeleeakaeaekseaaeleaeleeleaeieelveeieelGvevkdlea...glvDFpak 89 
                                       +e  + +++lr+++++l+++l++a ++     a++l ++++ le+++++l +e+e+   evk+l+     + D  + 
  gi|557693929|ref|YP_008796983.1|  99 TEAENTVNKLRSDITSLQTSLQTADQR-----AQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTnmeSVKDVLSL 170
                                       333334445555555555555555555.....7888999999999999999999999999999765111456999** PP

                           DUF2203  90 ldgeevllCWklgEe 104
                                       l++++vl++W   E+
  gi|557693929|ref|YP_008796983.1| 171 LENDRVLISWLRSEP 185
                                       **********98875 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   6.8   2.3e-06   0.00026     241     329 ..      74     162 ..      70     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.3e-06
                             IFT57 241 petksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekv 317
                                        et+   +kl +d++ +   +++r +  ++ +++l ++  ++q++l+++ ++ +qlse+v  l++ l+++s ele++
  gi|557693929|ref|YP_008796983.1|  74 GETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAA 150
                                       6789999********************************************************************** PP

                             IFT57 318 kqemeergssmt 329
                                        +e+++  ++m 
  gi|557693929|ref|YP_008796983.1| 151 NTEVKSLRTNME 162
                                       *****9998885 PP

>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.3   2.3e-06   0.00027     184     307 ..      47     171 ..      26     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.3e-06
                            DUF677 184 nvvfvaafvaVlvlSvvlaalaapavva.vagalav...Pleavgkwvasawkkyeealkrqkeivssmekgievak 256
                                        +++vaa+v  l+l  ++aa+a   v++   +        l++    +++++++ e+++ + +  ++s+++ +++a 
  gi|557693929|ref|YP_008796983.1|  47 KAILVAAVVVSLFLGAAAAAVAYSFVLGeTEARYQKlldDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTAD 123
                                       467888888888888888888888888854443333011333444444599************************** PP

                            DUF677 257 kdvenisilverleseiksilktvefAvekeeneaavklaleeikkkvekl 307
                                       +  +++s +v+ le + + ++   e A ++ +   + +  +e +k+ +  l
  gi|557693929|ref|YP_008796983.1| 124 QRAQQLSEKVRLLENRLNQLSSELEAANTEVK---SLRTNMESVKDVLSLL 171
                                       *************************9988877...9999999998766655 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 !   20.0   6.2   2.6e-06    0.0003      27     112 ..      80     162 ..      76     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.6e-06
                             Atg14  27 lrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkk 103
                                       +++ l +lks++  l +++++a+++ +   +l+++i +++++l++  ++ ++l+e++++l+ +l ql +e+e++  +
  gi|557693929|ref|YP_008796983.1|  80 YQKLLDDLKSQNLDLSNRLTEAENTVN---KLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTE 153
                                       788999***************999999...99999999999999999999999999999999999999999999999 PP

                             Atg14 104 laklsdklk 112
                                       +++l+ ++ 
  gi|557693929|ref|YP_008796983.1| 154 VKSLRTNME 162
                                       999887764 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 !   19.4  11.9   4.5e-06   0.00052      40     133 ..      75     164 ..      72     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.5e-06
                               GAS  40 kkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfe 116
                                       + e+r +k+l++++++n +l+  L++ae+ v++Lr ++   +    sl+ + +r ++l ++++ l+   ++l+ ++e
  gi|557693929|ref|YP_008796983.1|  75 ETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQT---SLQTADQRAQQLSEKVRLLENRLNQLSSELE 148
                                       678999*****************************99998876...9999999999999999999999999999999 PP

                               GAS 117 kvekerdelykkfeaai 133
                                       ++  e + l+ + e+ +
  gi|557693929|ref|YP_008796983.1| 149 AANTEVKSLRTNMES-V 164
                                       999999999988876.4 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 !   18.8  11.9   3.4e-06   0.00039     713     793 ..      86     166 ..      75     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.4e-06
                               FPP 713 satenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyesletrateleaelnelkqkieaLeveLe 789
                                       + ++++  l ++l+e E+++++l+s+++sl+ s + a++  ++ +e  + le r+++l +el+ +++++++L  ++e
  gi|557693929|ref|YP_008796983.1|  86 DLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNME 162
                                       55566778999***************************************************************999 PP

                               FPP 790 eekk 793
                                       + k+
  gi|557693929|ref|YP_008796983.1| 163 SVKD 166
                                       8765 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   5.0   4.3e-06   0.00049      15      99 ..      87     171 ..      80     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 4.3e-06
                              Fez1  15 LKqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvek 91 
                                       LK+Q  d  + +t+  + + +l++++  l+++l++ ++++++l+e+++  ++ l+++ +el+ +++e++ lr ++e+
  gi|557693929|ref|YP_008796983.1|  87 LKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMES 163
                                       89999999999999999999999999999999999999999999999999999999999999999999999999988 PP

                              Fez1  92 leeelkel 99 
                                       +++ l+ l
  gi|557693929|ref|YP_008796983.1| 164 VKDVLSLL 171
                                       87766555 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 ?    3.8   0.1      0.67        77      16      40 ..      84     108 ..      79     112 .. 0.87
   2 !   11.1   0.6    0.0034      0.39       1      38 [.      97     134 ..      97     136 .. 0.89
   3 !   14.4   2.5   0.00033     0.038       1      40 [.     132     167 ..     132     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.67
                         FlaC_arch  16 letvkkeneelsksveelkenVkdl 40 
                                       l+ +k++n +ls+ ++e + +V++l
  gi|557693929|ref|YP_008796983.1|  84 LDDLKSQNLDLSNRLTEAENTVNKL 108
                                       7789999999999999999999887 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0034
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVk 38 
                                       r+ e En ++kl + +++++++++   +  ++l e+V+
  gi|557693929|ref|YP_008796983.1|  97 RLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVR 134
                                       77899999999999999999999999999999999997 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 0.00033
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       ++  lEn+l++ls+ele + +e ++l+++ e +k+    +
  gi|557693929|ref|YP_008796983.1| 132 KVRLLENRLNQLSSELEAANTEVKSLRTNMESVKD----V 167
                                       67789************************987765....4 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.7   5.8e-06   0.00067     334     411 ..      86     164 ..      35     177 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.8e-06
                              FapA 334 elkeklkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelkeele 409
                                       +lk++  +l ++l e e+ ++kl+++i++l+ + +  +q  ++ +e++  l++ +++l++ele+ ++e k+l  ++e
  gi|557693929|ref|YP_008796983.1|  86 DLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQtADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNME 162
                                       34444445555555556666666666666655444344455566677777777777777777777777777777777 PP

                              FapA 410 sk 411
                                       s 
  gi|557693929|ref|YP_008796983.1| 163 SV 164
                                       66 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   7.4   9.2e-06    0.0011      32     103 ..      86     157 ..      77     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 9.2e-06
                           DUF4472  32 elknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqel 103
                                       +lk++ l l nr++e e + +k++++i+sl++ l+++++ +++l+e++  l++++ +l+ e+e+ +++ + l
  gi|557693929|ref|YP_008796983.1|  86 DLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSL 157
                                       699***********************************************************9988776655 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   7.2   1.1e-05    0.0012       4      82 ..      97     175 ..      77     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkq 80 
                                        ++ea++t+++  ++++ l++ l+   + ++++ ++v+  ++ +++++  ++ A+++vk L  +++ + d l+ l++
  gi|557693929|ref|YP_008796983.1|  97 RLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVLSLLEN 173
                                       57899999999999999999999999999999999999999999999999999999999999999999999888887 PP

                                       HH CS
                        Laminin_II  81 le 82 
                                        +
  gi|557693929|ref|YP_008796983.1| 174 DR 175
                                       76 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   4.8     8e-06   0.00091     314     396 ..      94     176 ..      63     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8e-06
                            DUF812 314 lakkaeteeelkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlel 390
                                       l+++ ++ e++ +k   ++++lq+ ++++++++++l+e+++ le++++q+++ele+ ++e + l  +++  k +l+l
  gi|557693929|ref|YP_008796983.1|  94 LSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVLSL 170
                                       33455566666666667999**************************************************9999999 PP

                            DUF812 391 lpdaee 396
                                       l+++  
  gi|557693929|ref|YP_008796983.1| 171 LENDRV 176
                                       998765 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.9   9.6e-06    0.0011     621     709 ..      71     161 ..      63     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9.6e-06
                             Nup88 621 pvlseaeremkkelekikeklkslknalkqvkkkldkqrkqiakskeeekk...sslelsekqkktikeiLkeegee 694
                                       +vl e+e   +k l  +k++   l n+l +++++++k r+ i+  +++ ++   ++ +ls ++ + +++ L+++++e
  gi|557693929|ref|YP_008796983.1|  71 FVLGETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTadqRAQQLS-EKVRLLENRLNQLSSE 146
                                       5677889999*******************************9987665554110444444.55688*********** PP

                             Nup88 695 ieelikqvkdikkiv 709
                                       +e   ++vk++++ +
  gi|557693929|ref|YP_008796983.1| 147 LEAANTEVKSLRTNM 161
                                       ***********9876 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 !   18.9  10.6     1e-05    0.0012      21     109 ..      83     169 ..      73     174 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1e-05
                      Baculo_PEP_C  21 vLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdtlrneLtnlnsil 94 
                                       +L+++++qn  +    ++ l++ e+++n+l +d++sl ++l+t   r ++l++++    n+l+ +l++eL++ n+++
  gi|557693929|ref|YP_008796983.1|  83 LLDDLKSQNLDL----SNRLTEAENTVNKLRSDITSLQTSLQTadqRAQQLSEKVRLLENRLN-QLSSELEAANTEV 154
                                       688999998777....55555556666777777777777777655555555555555555555.6778888888888 PP

                      Baculo_PEP_C  95 tnLlssvtNinstLn 109
                                        +L +++  ++  L+
  gi|557693929|ref|YP_008796983.1| 155 KSLRTNMESVKDVLS 169
                                       888877766666654 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 !   18.0   1.6   1.4e-05    0.0016     171     257 ..      84     169 ..      48     205 .. 0.48

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-05
                      Exonuc_VII_L 171 leklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlkekleekkerlkklkerle....lle 243
                                       l+ l+s+  + +++l+++++ +++l++++++ l+++l+++ +r ++l+e+    ++  ++rl++l+++le    +++
  gi|557693929|ref|YP_008796983.1|  84 LDDLKSQNLDLSNRLTEAENTVNKLRSDITS-LQTSLQTADQRAQQLSEK----VRLLENRLNQLSSELEaantEVK 155
                                       1122211122233333333333333333333.333333333333333322....22222222222222222222222 PP

                      Exonuc_VII_L 244 ekkerleeleekle 257
                                       + ++++e++++ l+
  gi|557693929|ref|YP_008796983.1| 156 SLRTNMESVKDVLS 169
                                       22223333333333 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 !    9.7   7.5    0.0075      0.86       3      61 ..      77     132 ..      75     141 .. 0.85
   2 !    9.9   2.1    0.0067      0.77      13      52 ..     136     172 ..     127     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0075
                     TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYld 61 
                                       e+r ++L   l++    +l+l ++l + ++ +++LR +i  lq  l+++ +r ++l ++
  gi|557693929|ref|YP_008796983.1|  77 EARYQKLLDDLKS---QNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEK 132
                                       5666666666666...79***********************************999765 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0067
                     TolA_bind_tri  13 learsqlllelqqqlealqqelreLRGqiEelqyqleqle 52 
                                       le+    l +l ++lea ++e+++LR  +E  +  l+ le
  gi|557693929|ref|YP_008796983.1| 136 LEN---RLNQLSSELEAANTEVKSLRTNMESVKDVLSLLE 172
                                       343...5889********************9887777665 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   8.5   2.6e-05     0.003      56     126 ..      81     150 ..      65     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.6e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHHHHHHHS-H CS
                             Nup54  56 sdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarletleaqlndp 126
                                       ++ l++l+ +++l++s+rl +a ++  +l + +++l + l+ + +r+++l+++ + l++rl++l+++l++ 
  gi|557693929|ref|YP_008796983.1|  81 QKLLDDLK-SQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAA 150
                                       44456666.99*********************************************************974 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 !   17.2   3.3   2.2e-05    0.0025      16     100 ..      58     151 ..      45     181 .. 0.40

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-05
                              HemX  16 lavgag......lyylgqqqvqeltaev..aelqqqlaaleqqlaq....veaekeqkqeleerlqqlaeklealek 80 
                                       l +ga+         lg+ ++ +++  +  ++l++q   l++ l++    v++++++ + l+++lq+++++ ++l++
  gi|557693929|ref|YP_008796983.1|  58 LFLGAAaaavaySFVLGETEA-RYQ--KllDDLKSQNLDLSNRLTEaentVNKLRSDITSLQTSLQTADQRAQQLSE 131
                                       333333223322112222221.122..12344444444444433333444333333333333444444444444444 PP

                              HemX  81 eleqlqkqleelqqqlskvs 100
                                       ++  l+++l++l+++l++ +
  gi|557693929|ref|YP_008796983.1| 132 KVRLLENRLNQLSSELEAAN 151
                                       44444444444444433322 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 !   17.3   3.0   2.1e-05    0.0024     166     247 ..      85     169 ..      75     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.1e-05
                   Phlebovirus_NSM 166 ediknqv..lhseieqlknelqkkRndikrgqek.rdakklveesmArvkdlkeelkiltdelsqikseiqilrkki 239
                                       +d k+q   l +++   +n ++k+R di   q   + a+++ +++  +v+ l ++l +l+ el+ + +e+++lr  +
  gi|557693929|ref|YP_008796983.1|  85 DDLKSQNldLSNRLTEAENTVNKLRSDITSLQTSlQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNM 161
                                       55666641146788999***********9999763789************************************998 PP

                   Phlebovirus_NSM 240 kdfetvvp 247
                                          + v+ 
  gi|557693929|ref|YP_008796983.1| 162 ESVKDVLS 169
                                       88777765 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   6.1   2.2e-05    0.0025     188     280 ..      75     163 ..      70     174 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 188 eaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqekl 264
                                       e e+ y++ l++l+++    s+ l +a++ +++lr  i sl++ l+   + +++l ++++ le+rl+    +l ++l
  gi|557693929|ref|YP_008796983.1|  75 ETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLN----QLSSEL 147
                                       7899*********************************************999999999999998864....344444 PP

                                       HHHHHHHHHHHHHHHH CS
                          Filament 265 seleeelaeireemar 280
                                       ++ ++e++++r +m+ 
  gi|557693929|ref|YP_008796983.1| 148 EAANTEVKSLRTNMES 163
                                       4445555555555443 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   4.8   2.9e-05    0.0033      15      94 ..      78     159 ..      73     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.9e-05
                              FliJ  15 qqaeekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqer 89 
                                       +++++ l+ l+++  +++++l ++  + +   +++  +q  +++ d++ +q+ +++  +e+++++  +e+ +a+ e+
  gi|557693929|ref|YP_008796983.1|  78 ARYQKLLDDLKSQNLDLSNRLTEAEnTvNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEV 154
                                       57788899999999999999999996666678999****************************************** PP

                              FliJ  90 kklek 94 
                                       k+l++
  gi|557693929|ref|YP_008796983.1| 155 KSLRT 159
                                       **987 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   7.5   2.2e-05    0.0025     141     213 ..      96     168 ..      84     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-05
                       Tropomyosin 141 skiveLeeeLkvvgnnlksLevseekaseredeyeeeirtLeekLkeaeeRaeeAErsvqkLekevdrledel 213
                                       ++ +e e+++      + sL+ s + a +r ++  e++r Le++L +     e+A  +v+ L  +++++ d l
  gi|557693929|ref|YP_008796983.1|  96 NRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVL 168
                                       5677778888888888888888888888888888888888888888888888888888888888888887766 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 !   17.4  11.4   3.1e-05    0.0036       4      91 ..      85     172 ..      76     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.1e-05
                        TPR_MLP1_2   4 ksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaea 80 
                                       + l+++  +l+++ +eae++++kl++d+++ + ++++a q+ ++   k     + l++l +el+ +++e+++l+++ 
  gi|557693929|ref|YP_008796983.1|  85 DDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNM 161
                                       679999999*******************************99999999999999*********************** PP

                        TPR_MLP1_2  81 esakaeleese 91 
                                       es+k  l+  e
  gi|557693929|ref|YP_008796983.1| 162 ESVKDVLSLLE 172
                                       ****9998766 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   4.4   2.7e-05    0.0032      67     136 ..      94     163 ..      74     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.7e-05
                            DUF745  67 leqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelae 136
                                       l + l+eae+ v++  + ++s ++++++a + a+q  +++  l++ l++ +++le a++  ++  +++++
  gi|557693929|ref|YP_008796983.1|  94 LSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMES 163
                                       778899*************************************************999887777777665 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   8.2   2.3e-05    0.0027     251     355 ..      75     176 ..      62     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.3e-05
                            Tektin 251 krieetedaknkleeqlkkvleeiaeleknieeLekairdkeaplklaqtRlenRtqRpnvElcrDeaqyrLveEvk 327
                                       +  + +++  + l++q   + ++++e+e+++++L+++i + + +l+ a  R ++ +++ ++   r    ++L +E++
  gi|557693929|ref|YP_008796983.1|  75 ETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENR---LNQLSSELE 148
                                       55567899999*******************************************99887765444...379****** PP

                            Tektin 328 eleetieaLkeklaeaeaslkaLertrl 355
                                         ++++++L+ +++ +++ l+ Le+ r+
  gi|557693929|ref|YP_008796983.1| 149 AANTEVKSLRTNMESVKDVLSLLENDRV 176
                                       ************************9987 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   3.0   1.7e-05     0.002     116     204 ..      70     160 ..      67     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-05
                           HAUS6_N 116 sfVlkkvlkeksk...klalevreaaskkaqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelra 189
                                       sfVl ++ ++ +k   +l+ ++ +++++ + + +++v + r  ++ +++ +++ad+  q+++e+++lle++  +l +
  gi|557693929|ref|YP_008796983.1|  70 SFVLGETEARYQKlldDLKSQNLDLSNRLT-EAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSS 145
                                       688888888888888777778888888877.99******************************************** PP

                           HAUS6_N 190 eleelqaelkaekea 204
                                       ele+ + e+k  + +
  gi|557693929|ref|YP_008796983.1| 146 ELEAANTEVKSLRTN 160
                                       ****99988843333 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   2.7   3.3e-05    0.0038      59     141 ..      82     163 ..      48     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.3e-05
                         Rootletin  59 releeeesadleealakLeeErqrseklaqvnslLreqleearqaneaLtedlqkltkdwerlreeleqkekewree 135
                                       + l++ +s++l  + ++L e  +  +kl +  + L++ l+ a+q  ++L+e ++ l++ +++l  ele  ++e ++ 
  gi|557693929|ref|YP_008796983.1|  82 KLLDDLKSQNL-DLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSL 157
                                       34555667777.78899999999999999999999999999999999999999999999999999999988888877 PP

                         Rootletin 136 eeafne 141
                                       ++++++
  gi|557693929|ref|YP_008796983.1| 158 RTNMES 163
                                       776654 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  10.1   3.1e-05    0.0036     143     229 ..      79     168 ..      72     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.1e-05
                              Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeie 216
                                       ++++ l++l++++  L+++  e+++ +++l++  ++l+  l++  ++a++l++   + +++L++l +el+++++e++
  gi|557693929|ref|YP_008796983.1|  79 RYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEkvrLLENRLNQLSSELEAANTEVK 155
                                       56777888999999999999999999999999999999999999998888776544446777777777777777777 PP

                              Spc7 217 ekkkelaelqeql 229
                                       +++++++++++ l
  gi|557693929|ref|YP_008796983.1| 156 SLRTNMESVKDVL 168
                                       7777776666554 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.7   2.8e-05    0.0033     379     457 ..      88     165 ..      62     230 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.8e-05
                            AAA_13 379 akhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrd 455
                                       ++ N   +n  +e+e+  +kl+ ++ + l+  l++ ++  ++l++++  le++l++ ++el++++ e+k L++++++
  gi|557693929|ref|YP_008796983.1|  88 KSQNLDLSNRLTEAENTVNKLRSDITS-LQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMES 163
                                       333333333334444444444443333.4444444445555555555555555555555555555555555554444 PP

                            AAA_13 456 ek 457
                                       +k
  gi|557693929|ref|YP_008796983.1| 164 VK 165
                                       44 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 !   13.8  17.6   0.00028     0.033      80     169 ..      84     172 ..      75     175 .. 0.80
   2 ?   -0.5   0.0       6.3   7.3e+02      31      60 ..     213     242 ..     209     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00028
                        MscS_porin  80 leeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaage.alsqaqrtalq 155
                                       l++L ++ l+ s++l e++++ ++l s++++lqt++++a q+  + +++   ++nrLn++  ++e + ++++  +l+
  gi|557693929|ref|YP_008796983.1|  84 LDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQL--SSElEAANTEVKSLR 158
                                       678888888899999999999999999999999999999999999999999999999999..555688888888888 PP

                        MscS_porin 156 aelaaleaqieele 169
                                       ++ ++ ++ +++le
  gi|557693929|ref|YP_008796983.1| 159 TNMESVKDVLSLLE 172
                                       88777777666665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 6.3
                        MscS_porin  31 kidkskkkaeelqkaiddaPkelrelqqel 60 
                                       +idk  + ++ + + ++++P++++  + el
  gi|557693929|ref|YP_008796983.1| 213 TIDKILDNLDLYYDWVEQFPQLTDVTRDEL 242
                                       78899999999************9999888 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 !   16.8   5.9   3.4e-05    0.0039      67     165 ..      78     175 ..      68     190 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.4e-05
                      HAUS-augmin3  67 ellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaet 143
                                         +++ l++++++  +L + l e++++ + + +    Lq    ++ q+ ++l+e+    +++l+++ +el+a+n e+
  gi|557693929|ref|YP_008796983.1|  78 ARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEV 154
                                       45567788889999999999999999999999999999999999999999999999999999999999999999999 PP

                      HAUS-augmin3 144 navLqqlteeakqlaeyfeeae 165
                                       +++  + +e++k + + +e+++
  gi|557693929|ref|YP_008796983.1| 155 KSL-RTNMESVKDVLSLLENDR 175
                                       765.555555999999888876 PP

>> PTRF_SDPR  PTRF/SDPR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   5.5   3.6e-05    0.0041      16      96 ..      82     162 ..      78     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         PTRF_SDPR  16 givdsvqesqkrlEerqaelenavksiqgdllkLakshssTsntvnklleksrkvsvnvkevrerlekqavqvkklE 92 
                                       +++d ++++   l +r +e en+v+ + +d++ L  s ++  +  ++l ek+r   +++ ++ ++le  +++vk l 
  gi|557693929|ref|YP_008796983.1|  82 KLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLR 158
                                       678999999999***************************99**********************************99 PP

                                       HHHH CS
                         PTRF_SDPR  93 anea 96 
                                       +n +
  gi|557693929|ref|YP_008796983.1| 159 TNME 162
                                       9876 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.4   4.2e-05    0.0048     129     195 ..      90     156 ..      56     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.2e-05
                              Vps5 129 qRvklwqkwqsaeqelskkkeqleKlekaaksqqdklqqlkkeveelerkvqeaekeFeeisetikk 195
                                       q ++l +++ +ae++++k +++ + l+++ +++ +++qql + v+ le+++++++ e e   +++k+
  gi|557693929|ref|YP_008796983.1|  90 QNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKS 156
                                       6667788899**********************************************99999888885 PP

>> Gp58  gp58-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   4.5   3.4e-05    0.0039     260     343 ..      89     172 ..      75     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.4e-05
                              Gp58 260 stakqisqeiknregavsrvqqdldsyqrrlqdaeknyssLtqtvkGlqstvsdpnsklesrvtqLadlieqkvtrg 336
                                       s    +s ++ ++e+ v +++ d+ s+q  lq a++    L++ v+ l++++++ +s+le+  t +++l  +  +  
  gi|557693929|ref|YP_008796983.1|  89 SQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVK 165
                                       55667899*****************************************************9999999988888888 PP

                              Gp58 337 dvesiir 343
                                       dv s+++
  gi|557693929|ref|YP_008796983.1| 166 DVLSLLE 172
                                       8888775 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   4.9   3.3e-05    0.0038     388     457 ..      94     164 ..      63     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.3e-05
                          Macoilin 388 pnnqlskkdalv.rLeadikkLkaeLqasrqteqelrskissltseerslkselqqlkkendllqtklhel 457
                                        +n+l++ ++ v +L +di  L++ Lq++ q  q+l +k+ +l ++  +l sel++ + e  +l+t ++++
  gi|557693929|ref|YP_008796983.1|  94 LSNRLTEAENTVnKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESV 164
                                       3566677666666*****************************************************99876 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 !   17.6  10.9   4.6e-05    0.0053       2      88 ..      80     166 ..      79     173 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.6e-05
                    PRKG1_interact   2 YkkLYeeekeenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeelkelee 78 
                                       Y+kL  + k++n  L ++L+e+e+ +++l+s +++l+++ q+  ++ ++l+e  +  ++ l++  sele  ++e++ 
  gi|557693929|ref|YP_008796983.1|  80 YQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKS 156
                                       99***********************************99888888888888989999999999999*********** PP

                    PRKG1_interact  79 LraenqrLkd 88 
                                       Lr++ +  kd
  gi|557693929|ref|YP_008796983.1| 157 LRTNMESVKD 166
                                       ****999987 PP

>> CASP_C  CASP C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.2     0.011       1.3      97     137 ..      88     135 ..      80     138 .. 0.63
   2 !   10.9   0.2    0.0019      0.21      98     148 ..     138     187 ..     136     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.011
                            CASP_C  97 rkrnaeLEeelrkqeetvsslraeiaslqk.......DNlkLYEkvRY 137
                                       +++n +L + l + e+tv++lr++i+slq+          +L EkvR 
  gi|557693929|ref|YP_008796983.1|  88 KSQNLDLSNRLTEAENTVNKLRSDITSLQTslqtadqRAQQLSEKVRL 135
                                       667777777777777777777777777775111111035667777775 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0019
                            CASP_C  98 krnaeLEeelrkqeetvsslraeiaslqkDNlkLYEkvRYlqsYnrgskas 148
                                       +r ++L +el+  +++v+slr++++s++ D l+L E  R l s+ r++   
  gi|557693929|ref|YP_008796983.1| 138 NRLNQLSSELEAANTEVKSLRTNMESVK-DVLSLLENDRVLISWLRSEPPG 187
                                       699***********************96.99*****999999998877654 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   2.6   0.00081     0.093       7      69 ..      81     148 ..      77     151 .. 0.88
   2 ?    8.0   0.7     0.029       3.4       8      46 ..     135     173 ..     129     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00081
                              Rx_N   7 qkLadllaeea....kllkgvkeeleklkdeLesiqavLedaeerqi.kdeavkeWlkelrdlaydae 69 
                                       qkL d l+++     ++l + ++ ++kl++   s+q  L+ a++r +  +e v+   ++l +l+ ++e
  gi|557693929|ref|YP_008796983.1|  81 QKLLDDLKSQNldlsNRLTEAENTVNKLRSDITSLQTSLQTADQRAQqLSEKVRLLENRLNQLSSELE 148
                                       77887788887899999***************************877589****99999999988776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.029
                              Rx_N   8 kLadllaeeakllkgvkeeleklkdeLesiqavLedaee 46 
                                        L++ l +  + l+    e+++l++++es++ vL+  e+
  gi|557693929|ref|YP_008796983.1| 135 LLENRLNQLSSELEAANTEVKSLRTNMESVKDVLSLLEN 173
                                       577777777788999999****************98876 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 !   16.6   2.7   5.5e-05    0.0063      88     171 ..      81     167 ..      52     176 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.5e-05
                           UPF0242  88 eealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae...dfeelkleleeqLaekqellqeyqetieeq 161
                                       ++ l +l++++ +L ++l + e+++++l+ +  +Lq  l+ + +   + +e  + le++L++    l+  + +++++
  gi|557693929|ref|YP_008796983.1|  81 QKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQraqQLSEKVRLLENRLNQLSSELEAANTEVKSL 157
                                       44566777777777777777777777777777777777666655444555666666777777777777777777777 PP

                           UPF0242 162 rsvlekrqdq 171
                                       r  +e+ +d 
  gi|557693929|ref|YP_008796983.1| 158 RTNMESVKDV 167
                                       7777766555 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  10.4   9.2e-05     0.011      26     123 ..      78     172 ..      72     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.2e-05
                            APG6_N  26 daYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfw 102
                                         Y++ l+ lk+++ + +   + l e+e+ + kl+++  +l++ L+ +++  ++l ++++ le+ l++l  e e+  
  gi|557693929|ref|YP_008796983.1|  78 ARYQKLLDDLKSQNLDLS---NRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAAN 151
                                       568888999998866654...68888888888888888888888888888888888888888888888888888888 PP

                            APG6_N 103 reynelqlelleleeeldsle 123
                                       +e ++l++++++ ++ l  le
  gi|557693929|ref|YP_008796983.1| 152 TEVKSLRTNMESVKDVLSLLE 172
                                       888888888877777666555 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   4.3   5.9e-05    0.0068      76     149 ..      90     165 ..      65     174 .. 0.45

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-05
                                       HTHHHHHT-GGGT--S-SHH..HHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHH CS
                              EzrA  76 klpeieellfeaeelldkyk..fkkakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelr 149
                                       +  +++++l+eae+ ++k +  + +++++l++++++ +++ ek++ + + l++l +  e   +e+++l+++ ++++
  gi|557693929|ref|YP_008796983.1|  90 QNLDLSNRLTEAENTVNKLRsdITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVK 165
                                       3334444444444444443211334444444444444444444444444444444444444444444444444433 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   5.0   0.00016     0.018      50     121 ..      94     165 ..      64     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 0.00016
                           DUF1664  50 leqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerie 121
                                       l +  ++ ++t ++L s+i +++++l+   + +++++e+v  +++ l+++++++e+ ++ v++l +++e+++
  gi|557693929|ref|YP_008796983.1|  94 LSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVK 165
                                       334445556677788899999999999999999999999999999999999999999999999998888875 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 ?    7.5   0.2     0.044       5.1      45      70 ..      78     103 ..      73     104 .. 0.92
   2 ?    5.0   0.1      0.28        32      28      48 ..     100     120 ..      99     121 .. 0.90
   3 !   10.5   6.2    0.0054      0.62      21      69 ..     114     162 ..     106     164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.044
                               CLZ  45 trlarLlaeyessqrkLkqRitkLEk 70 
                                        r+++Ll++++s +  L +R+t+ E+
  gi|557693929|ref|YP_008796983.1|  78 ARYQKLLDDLKSQNLDLSNRLTEAEN 103
                                       799*******************9997 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.28
                               CLZ  28 eleekverLessLeaLqtrla 48 
                                       e+e+ v++L s + +Lqt l+
  gi|557693929|ref|YP_008796983.1| 100 EAENTVNKLRSDITSLQTSLQ 120
                                       6899**************986 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0054
                               CLZ  21 kagaeqkeleekverLessLeaLqtrlarLlaeyessqrkLkqRitkLE 69 
                                       + ++  +++++++++L +++  L++rl++L +e+e+++++ k+  t++E
  gi|557693929|ref|YP_008796983.1| 114 SLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNME 162
                                       5566778999**************************9999998766666 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   2.8     8e-05    0.0092      15      93 ..      74     151 ..      68     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8e-05
                             TMPIT  15 eetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesllpk 91 
                                        et+ +y++ l++l++++ ++s+++++ ++ +++l+s++++l++s+ +  ++++++l+e+++  ++ l++++s l +
  gi|557693929|ref|YP_008796983.1|  74 GETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSL-QTADQRAQQLSEKVRLLENRLNQLSSELEA 149
                                       5778899999999999999999999999999999999999999997.577888999999999999999998888876 PP

                             TMPIT  92 kn 93 
                                        n
  gi|557693929|ref|YP_008796983.1| 150 AN 151
                                       54 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   7.1     9e-05      0.01     591     661 ..      91     165 ..      72     175 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9e-05
                           DUF3584 591 ridvpdyaasee....eLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlq 661
                                       ++d  + + + e    +Lr+ +  l++ lq+a ++++q++e++  l++ l++++ +++ a+t++k  r ++e ++
  gi|557693929|ref|YP_008796983.1|  91 NLDLSNRLTEAEntvnKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVK 165
                                       333333222222345577777777777777777777777777777777777777777777777777777776655 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.8     0.044       5.1       5      37 ..      94     126 ..      90     128 .. 0.87
   2 !   11.4   0.6    0.0027      0.31       3      32 ..     127     156 ..     125     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.044
                               LPP   5 LssqVsqLkskvdqlssdvnsakaaaqaakeEA 37 
                                       Ls+ + + ++ v++l sd++s+++ +q+a + A
  gi|557693929|ref|YP_008796983.1|  94 LSNRLTEAENTVNKLRSDITSLQTSLQTADQRA 126
                                       788888889999***********9999998877 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.0027
                               LPP   3 deLssqVsqLkskvdqlssdvnsakaaaqa 32 
                                       ++Ls+ V  L++  +qlss++++a++++++
  gi|557693929|ref|YP_008796983.1| 127 QQLSEKVRLLENRLNQLSSELEAANTEVKS 156
                                       689999999999999999998888887765 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 !   16.0   2.3   0.00011     0.013      29     105 ..      79     152 ..      72     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 0.00011
                                       HHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHH CS
                           T3SSipB  29 awkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekaklea 105
                                        +++     + +++ lS+ l +a +  +++  d++  +  +++a++ a+++ +kv    +rl++L   + e  +++ 
  gi|557693929|ref|YP_008796983.1|  79 RYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQL---SSELEAANT 152
                                       5777777788999***************************************************9...333333333 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 ?   14.8   8.0   0.00021     0.024      26     124 ..      73     174 ..      70     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 0.00021
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHCCCHHHHHHHC CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksske...leeeilrlketida 99 
                                       l ++e  ++k l++l+++  ++sn+ +eae++v+++++ +++ q+s +  d+  +++s++   le++ ++l  ++ a
  gi|557693929|ref|YP_008796983.1|  73 LGETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKvrlLENRLNQLSSELEA 149
                                       56778889999*********************************999999999999998833357899999999999 PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 100 qesnirvLqnvlesneqkiqkLeqd 124
                                         ++++ L++++es +  ++ Le+d
  gi|557693929|ref|YP_008796983.1| 150 ANTEVKSLRTNMESVKDVLSLLEND 174
                                       9999999999999999999988876 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 ?   14.1   9.9   0.00014     0.016     158     257 ..      76     172 ..      72     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 0.00014
                          CALCOCO1 158 rakkalaqrkeeeaerkqlqakleqseeelrslskelqelrnslaerdtqvlqLqdtittltqkLttAqrkeaenEa 234
                                       +  + ++++ + ++++ +l ++l ++e+ +++l +++ +l+ sl+  d +++qL +++  l+++L++      e Ea
  gi|557693929|ref|YP_008796983.1|  76 TEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQL---SSELEA 149
                                       55566677778888888999999999999999999999999999999999999999999999999864...567788 PP

                          CALCOCO1 235 llkelrslqerlaaSerkvegLk 257
                                       +  e++sl+  +++ +    +L+
  gi|557693929|ref|YP_008796983.1| 150 ANTEVKSLRTNMESVKDVLSLLE 172
                                       88888888777776665555555 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.6     0.014       1.7      35      63 ..      84     112 ..      78     113 .. 0.89
   2 ?   12.2   3.6    0.0012      0.14      26      63 ..     124     161 ..     122     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  35 vkaLekeNksLkseleelkkevekLkskv 63 
                                        + L+++N +L+++l e +++v+kL+s++
  gi|557693929|ref|YP_008796983.1|  84 LDDLKSQNLDLSNRLTEAENTVNKLRSDI 112
                                       678***********************976 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  26 aeieeLerrvkaLekeNksLkseleelkkevekLkskv 63 
                                       ++ ++L+++v  Le+   +L+sele  + ev++L+++ 
  gi|557693929|ref|YP_008796983.1| 124 QRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNM 161
                                       5789******************************9875 PP

>> DUF2968  Protein of unknown function (DUF2968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   6.4   0.00015     0.018     104     178 ..      87     161 ..      67     163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00015
                           DUF2968 104 leaqkaqlerqiaasearaerLqadlavarqQeqavaerQkqarkeaaaLeaqreaaqaqlralqrqirqLqaqq 178
                                       l++q+  l + ++++e+ +++L++d++  ++  q+  +r +q+ ++++ Le+  +++ ++l+a+  ++++L  + 
  gi|557693929|ref|YP_008796983.1|  87 LKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNM 161
                                       7899999****************************************************************8776 PP

>> TTKRSYEDQ  Predicted coiled-coil domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.4   0.00016     0.018     421     484 ..     106     169 ..      70     174 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00016
                         TTKRSYEDQ 421 shytariaeLtsqlqlaDskavhfhaecraLakRlalaekskeklteelklakqnisrlqDela 484
                                       +   + i+ L + lq aD +a ++   +r L+ Rl++   + e  + e+k+ + n++ ++D l 
  gi|557693929|ref|YP_008796983.1| 106 NKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVLS 169
                                       4456778888888888888888888888888888888888888888888888888888888775 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 ?   14.3   9.0   0.00018     0.021     245     327 ..      93     174 ..      74     178 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00018
                            HMMR_N 245 kykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekekeel...vreeeekeqtlsaEleelk 318
                                         + +++++e+++++  ++i sL++sL+  +q    ++++l+ek++lle+ +++l   ++ +++  ++l + +e++k
  gi|557693929|ref|YP_008796983.1|  93 DLSNRLTEAENTVNKLRSDITSLQTSLQTADQ----RAQQLSEKVRLLENRLNQLsseLEAANTEVKSLRTNMESVK 165
                                       34667788888888888888888888887777....77888888888885555441115566677788899999999 PP

                            HMMR_N 319 eklklkeqe 327
                                       + l l e++
  gi|557693929|ref|YP_008796983.1| 166 DVLSLLEND 174
                                       999988887 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 ?   14.3   8.6   0.00019     0.021     123     202 ..      80     163 ..      67     175 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00019
                         Golgin_A5 123 lryleeelvrskatlqsrikdrekeieklrnqlttkslsss....seselesRlkqLtesLiqKQtvlEalstekns 195
                                        + l ++l+ +  +l +r+++ e+ ++klr+++t+ + s        ++l+++++ L + L q    lEa +te +s
  gi|557693929|ref|YP_008796983.1|  80 YQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQtadqRAQQLSEKVRLLENRLNQLSSELEAANTEVKS 156
                                       44556666777777777777777777777777665433221112244566666666666666666666666666666 PP

                         Golgin_A5 196 lvlQLeR 202
                                       l   +e 
  gi|557693929|ref|YP_008796983.1| 157 LRTNMES 163
                                       6666554 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   6.8   0.00017      0.02      81     173 ..      80     165 ..      71     178 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00017
                               MAD  81 kkknlealnkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqq 157
                                       ++k l+ l++++ + +++l+ea+++ ++l+ ++  l+++++ +++  ++ +++++ l++rl+ l  +l+ ++  +++
  gi|557693929|ref|YP_008796983.1|  80 YQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKS 156
                                       44444444444445555555555555555555555555555555544444444444444444444444444444444 PP

                               MAD 158 lekkqkelaeaeqrik 173
                                       l ++ ++        k
  gi|557693929|ref|YP_008796983.1| 157 LRTNMESV-------K 165
                                       44444333.......3 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3   0.00029     0.033       4      84 ..      53     135 ..      47     137 .. 0.77
   2 ?    1.7   0.2         2   2.3e+02      43      73 ..     136     166 ..     130     173 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00029
                           DUF4446   4 lvlavlvvillillivllvklkklkkkykklmk..gkdgksleellkekleeveelkeeseelekeieeleeklkks 78 
                                       +v++ l++ +  ++++ +  l +++ +y+kl+   ++++ +l + l e  ++v++l+++ ++l++++++ +++ ++ 
  gi|557693929|ref|YP_008796983.1|  53 AVVVSLFLGAAAAAVAYSFVLGETEARYQKLLDdlKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQL 129
                                       222333333344566667778899*********444466678899******************************** PP

                           DUF4446  79 lqkvgl 84 
                                        +kv+l
  gi|557693929|ref|YP_008796983.1| 130 SEKVRL 135
                                       999987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 2
                           DUF4446  43 leellkekleeveelkeeseelekeieelee 73 
                                       le+ l++  +e+e++++e+++l++++e++++
  gi|557693929|ref|YP_008796983.1| 136 LENRLNQLSSELEAANTEVKSLRTNMESVKD 166
                                       6777777777777777777777777777665 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   5.2   0.00024     0.028      15     110 ..      73     168 ..      68     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 0.00024
                           DUF4200  15 leakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeiet 91 
                                       l++ ++ +q+l + lk++  +l ++  e e++++k+   + + +   + a ++a++ +++ +  e+ +++l +e+e+
  gi|557693929|ref|YP_008796983.1|  73 LGETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEA 149
                                       677889999******************************************************************** PP

                           DUF4200  92 lkseiekleekleeykkYe 110
                                        ++e + l  ++e++k   
  gi|557693929|ref|YP_008796983.1| 150 ANTEVKSLRTNMESVKDVL 168
                                       ******9999999888655 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.6   0.00043     0.049      17      90 ..      80     154 ..      64     172 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00043
                                       HHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  17 gkaaqeqlekkf.......kklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkk 86 
                                       +++  ++l+++        ++ ++++++++ ++++lq+ lq    +    +++q+l +k++ l+++++q   el+++
  gi|557693929|ref|YP_008796983.1|  80 YQKLLDDLKSQNldlsnrlTEAENTVNKLRSDITSLQTSLQ----T--ADQRAQQLSEKVRLLENRLNQLSSELEAA 150
                                       56666666666633333336666677777777777777775....2..67888888888888888888888888888 PP

                                       HHHH CS
                              OmpH  87 qqel 90 
                                       + e+
  gi|557693929|ref|YP_008796983.1| 151 NTEV 154
                                       7663 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0  11.5   0.00035      0.04      55     118 ..      98     161 ..      87     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00035
                              ADIP  55 reslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeel 118
                                        ++ + t++kl+++i++lq++ +  +++ +ql  ++ l++++++ql  +l+++++ +k+++  +
  gi|557693929|ref|YP_008796983.1|  98 LTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNM 161
                                       4677889999999999999999999999999999999999999999999999999999998766 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.4    0.0074      0.85      27      89 ..      78     136 ..      58     137 .. 0.73
   2 ?   13.7   4.9   0.00044      0.05      32     100 ..     109     175 ..     107     177 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0074
                           DUF2730  27 skYakredleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrql 89 
                                        +Y k      l+ +  +  +rlte+e +v++L  ++d+ +L++ l+  + + ++l+++vr l
  gi|557693929|ref|YP_008796983.1|  78 ARYQKLL--DDLKSQNLDLSNRLTEAENTVNKL--RSDITSLQTSLQTADQRAQQLSEKVRLL 136
                                       5555543..345555667789999999999999..7899999999999999999999998866 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00044
                           DUF2730  32 redleklaekveendkrlteletkvenLPtakdlekLkllladlrgelkaleaevrqlshqvdLLLene 100
                                       r+d+++l+ ++++ d+r ++l  kv  L +   l++L+ +l+  + e+k l+ ++++++  + LL +++
  gi|557693929|ref|YP_008796983.1| 109 RSDITSLQTSLQTADQRAQQLSEKVRLLEN--RLNQLSSELEAANTEVKSLRTNMESVKDVLSLLENDR 175
                                       89**************************65..599*************************999986665 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 ?   14.0  10.5   0.00041     0.048       4      77 ..      78     156 ..      75     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00041
                       Uso1_p115_C   4 seleseaaslkdeneklkaelqslskalesleqk.....eakkaaesqakeleaenkklekeleklraelkeekeke 75 
                                       + +++   +lk++n +l ++l ++++ +++l++       +++ a+++a++l++++  le++l +l++el++++ + 
  gi|557693929|ref|YP_008796983.1|  78 ARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDitslqTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEV 154
                                       56788888899999999999999999999999988888888999999999999999999**9999999999987766 PP

                       Uso1_p115_C  76 ke 77 
                                       k 
  gi|557693929|ref|YP_008796983.1| 155 KS 156
                                       54 PP

>> Vps51  Vps51/Vps67
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.3    0.0062      0.71      51      86 ..      96     131 ..      76     132 .. 0.85
   2 ?    5.8   0.1      0.13        15      55      78 ..     149     172 ..     145     174 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0062
                             Vps51  51 skLisasdtIrkmksemdkldqklselkqaiskiae 86 
                                       ++L +a +t++k++s++++l+++l++ +q+ ++++e
  gi|557693929|ref|YP_008796983.1|  96 NRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSE 131
                                       6788999*********************99999887 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.13
                             Vps51  55 sasdtIrkmksemdkldqklselk 78 
                                       +a+ ++++++++m+++++ ls l 
  gi|557693929|ref|YP_008796983.1| 149 AANTEVKSLRTNMESVKDVLSLLE 172
                                       6899999******99999988775 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 ?    6.8   1.0     0.056       6.4      55      90 ..      85     120 ..      75     121 .. 0.52
   2 ?   11.2  12.7    0.0025      0.29      33     118 ..      91     176 ..      85     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.056
                    CENP-F_leu_zip  55 etlkeeieelaeelreleldLvalrsekeeLekelq 90 
                                         lk++   l+++l+e e  +++lrs+  +L+ +lq
  gi|557693929|ref|YP_008796983.1|  85 DDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQ 120
                                       345555555555555555555555555555555554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0025
                    CENP-F_leu_zip  33 lemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenl 109
                                         ++ + +++++  + + +  + +l++ +++  ++ ++l+ ++  l +  ++L  el+  + +v++L +  +s++ +
  gi|557693929|ref|YP_008796983.1|  91 NLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDV 167
                                       445555666677777778889999***************************************************** PP

                    CENP-F_leu_zip 110 leekEqekv 118
                                       l+ +E+++v
  gi|557693929|ref|YP_008796983.1| 168 LSLLENDRV 176
                                       **9999987 PP

>> dCache_1  Cache domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.2   0.00044      0.05      15     117 ..      87     203 ..      76     218 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00044
                          dCache_1  15 aeqlanniedvldslenlaetlasnps.lqdlleepnra.......neasreslqallksilksn............ 71 
                                       +++   ++++ l+++en+++ l s+++ lq +l+  ++             + l+++l+++ +              
  gi|557693929|ref|YP_008796983.1|  87 LKSQNLDLSNRLTEAENTVNKLRSDITsLQTSLQTADQRaqqlsekV----RLLENRLNQLSSELeaantevkslrt 159
                                       55555566777777777777777776557777776666666643331....33333333332222333344444444 PP

                          dCache_1  72 ..pdisgv.ylvdadGqviassdpssppnlegtddpadrdwykealagg 117
                                         +++++v +l+ ++ +v+ s+ +s pp++       dr++++e++a  
  gi|557693929|ref|YP_008796983.1| 160 nmESVKDVlSLL-ENDRVLISWLRSEPPGT----REGDREYWNETRALA 203
                                       447886663555.77778776666655554....9*********99876 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   5.5   0.00051     0.059      98     173 ..      92     167 ..      76     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00051
                            DUF724  98 lslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleee 173
                                       l l ++ t+++++ +kl ++i+  +++ + +++  ++l++k++ le++l +l ++ eaa+ e+++l++++e++++ 
  gi|557693929|ref|YP_008796983.1|  92 LDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDV 167
                                       7788899999999999999999999999999999999999999999999999999999999999999999988765 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 ?   11.4   2.3   0.00048     0.055      30     115 ..      96     177 ..      75     207 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00048
                        V_ATPase_I  30 rrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkelnelvelk 106
                                        r+ e e++++ l++ i++l++  ++    +++++++ ++++  le++l++l +el+  n++ ++l+++++++++  
  gi|557693929|ref|YP_008796983.1|  96 NRLTEAENTVNKLRSDITSLQTSLQT----ADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVL 168
                                       46667777777777777664444433....34577777778888888888888888888888888888888888888 PP

                        V_ATPase_I 107 avlekakef 115
                                       ++le+ + +
  gi|557693929|ref|YP_008796983.1| 169 SLLENDRVL 177
                                       777766555 PP

>> RskA  Anti-sigma-K factor rskA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   0.00052     0.059      42     124 ..      53     182 ..      17     190 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00052
                                       ......XXXXXXXXXX..XXXX.......................................XXXXXXXXXXXXXXXX CS
                              RskA  42 r.....laaaaAaall..lvlg.............................qlavasaaldplrqsaaqaeavvavl 82 
                                       +     +++aaAaa++  +vlg                             ++ +++++++ l++s + a+++++ l
  gi|557693929|ref|YP_008796983.1|  53 AvvvslFLGAAAAAVAysFVLGetearyqkllddlksqnldlsnrlteaenTVNKLRSDITSLQTSLQTADQRAQQL 129
                                       0445554445555555458888**********************999999955555555555555555555555555 PP

                                       XXX.............XXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              RskA  83 aap.............daagatatvvdsasggalvldvsglpalpagkvyqlWli 124
                                       +++             + ++a + v + +++ + v dv +l  l+ ++v+  Wl 
  gi|557693929|ref|YP_008796983.1| 130 SEKvrllenrlnqlssELEAANTEVKSLRTNMESVKDVLSL--LENDRVLISWLR 182
                                       55555555558777765555666666777777777777777..677777777776 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   7.7    0.0012      0.14      23      93 ..      82     169 ..      74     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0012
                                       HHHHHB-.....BHHHHHHHHHHHH.................HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...... CS
                             DUF16  23 kqlnefkds...nkqrLkkieakvd..............klgeqinkleqkvekqgekikelkveqkaqgeelnkvd 82 
                                       k l++ k +     +rL++ e++v+              + +++ ++l +kv+ +++++++l+ e +a + e++++ 
  gi|557693929|ref|YP_008796983.1|  82 KLLDDLKSQnldLSNRLTEAENTVNklrsditslqtslqTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLR 158
                                       66677666533346788888888887777777766666677788888888888888888888888888888888777 PP

                                       .HHHHHHHHHH CS
                             DUF16  83 etleliletLq 93 
                                         +e++ + L 
  gi|557693929|ref|YP_008796983.1| 159 TNMESVKDVLS 169
                                       77777766665 PP

>> DUF3568  Protein of unknown function (DUF3568)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.0    0.0008     0.091       5      51 ..      41      88 ..      37     137 .. 0.77
   2 ?    0.3   0.1       5.9   6.7e+02      52      96 ..     121     165 ..     106     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0008
                           DUF3568  5 llllsislillasC.aalvagaaagagtvayvnGelkaeyeanlkkvy 51
                                      ++++ + +il+a++  +l +gaaa+a ++ +v Ge +a y++ l++  
  gi|557693929|ref|YP_008796983.1| 41 RVVIGMKAILVAAVvVSLFLGAAAAAVAYSFVLGETEARYQKLLDDLK 88
                                      56777788777777799***********************99887764 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 5.9
                           DUF3568  52 kAtlkaiedlnvlsvvekskdsssatieakaaedktvfiklekld 96 
                                       +A ++a + ++++++ e++ ++ s ++ea++ e k  + ++e+++
  gi|557693929|ref|YP_008796983.1| 121 TADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVK 165
                                       455666677778999999999999999999988777777666665 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   5.9    0.0047      0.54      21      88 ..      66     133 ..      47     138 .. 0.79
   2 ?   10.7   8.1     0.002      0.24      21      93 ..     101     166 ..      96     173 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0047
                           DUF3450  21 alkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqi 88 
                                       a + +    +++a+ qk  d+l+ +  +l+++++++++ +++l+     l+ ++++++q+ ++l e+ 
  gi|557693929|ref|YP_008796983.1|  66 AVAYSFVLGETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKV 133
                                       444455556789999*********************************************99999876 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.002
                           DUF3450  21 alkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                       a+++ +k         + i++l+   q+  ++ ++l+e++  le   +ql++ ++++++e++sl++++e+++ 
  gi|557693929|ref|YP_008796983.1| 101 AENTVNK-------LRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKD 166
                                       3444444.......44445555555555555555555555555555555555555555555555555555543 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.0    0.0017       0.2       3      46 ..      95     138 ..      93     141 .. 0.91
   2 ?    5.9   1.2      0.13        15       4      44 ..     131     164 ..     128     173 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0017
                              XhlA   3 kerlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                         rl++ e+ +++l ++++ l+    +a++++++l e++  le+
  gi|557693929|ref|YP_008796983.1|  95 SNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLEN 138
                                       579**********************************9987776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.13
                              XhlA   4 erlerietkldnleervdkleekaaeaeekiknleedlkkl 44 
                                       e++  +e++l+ l+++        + a +++k+l  ++++ 
  gi|557693929|ref|YP_008796983.1| 131 EKVRLLENRLNQLSSE-------LEAANTEVKSLRTNMESV 164
                                       5566666666666665.......444444444444444444 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 ?   11.4   0.2    0.0011      0.13      42     128 ..      40     132 ..      30     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0011
                   AI-2E_transport  42 L.kkrgvkrvlavllvlllllvllvll..vlllvplliaqltqlvkslpayidslqnilnelpslleele.n..liq 112
                                       L  + g+k++l++++v+ l+l++++    + +++ +  a  ++l+++l+  + +l+n l+e ++ +++l  +   +q
  gi|557693929|ref|YP_008796983.1|  40 LrVVIGMKAILVAAVVVSLFLGAAAAAvaYSFVLGETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRsDitSLQ 116
                                       55677999999999999999987665500556888999999999999999999999999999999999986587444 PP

                   AI-2E_transport 113 alkqslskilsnilss 128
                                       ++ q++++ ++++ ++
  gi|557693929|ref|YP_008796983.1| 117 TSLQTADQRAQQLSEK 132
                                       4444444444444444 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   8.8   0.00075     0.086      11      87 ..     100     173 ..      92     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00075
                     Tropomyosin_1  11 eaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealtrkiqlLEe 87 
                                       ea + +++l++++ +l+ + +  +q  ++L++k+++le+ +++l+++l+ a++   e ++++tn e+++  + lLE+
  gi|557693929|ref|YP_008796983.1| 100 EAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANT---EVKSLRTNMESVKDVLSLLEN 173
                                       44555677888888888888888888888888888888888888888877665...445677777777777777776 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 ?   10.5   7.0    0.0049      0.57      71     121 ..     117     167 ..      62     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0049
                            DUF641  71 aeeseleaeiqeqrsllktyeitvkkleaelkakdseieeLkekLeeaeks 121
                                       ++ ++ ++++q++ ++++ +e ++++l +el+a ++e+++L+ ++e+++  
  gi|557693929|ref|YP_008796983.1| 117 TSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDV 167
                                       444556667778889999999999999999999999999999999987765 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 ?   11.0   5.4    0.0021      0.24      10     105 ..      82     176 ..      73     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0021
                     PI3K_P85_iSH2  10 gdleklseklrevskqlqekskeydqlkeeynkiseeiqlkrqaleaFneaikmFeeqiklqekfskeaqehEiekl 86 
                                       + l+ l  +  ++s+ l+e +++ ++l  + ++++  +q+  q  ++ +e ++++e+ ++     + ea ++E+++l
  gi|557693929|ref|YP_008796983.1|  82 KLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLS-SELEAANTEVKSL 157
                                       556667777778899999999999999999999999999999999999999999999998554.4889999999999 PP

                     PI3K_P85_iSH2  87 qenleqlksrlkelhsske 105
                                        +n+e +k+ l+ l++ + 
  gi|557693929|ref|YP_008796983.1| 158 RTNMESVKDVLSLLENDRV 176
                                       9999999999998888775 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   4.4    0.0013      0.15      96     190 ..      68     162 ..      60     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0013
                               LXG  96 dedfLeqelenglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksal 172
                                         +f+  e e +++k+  +++++   + + l ++  +v+  + d+ ++++slq a++ +q+  ek+  +++ ++++ 
  gi|557693929|ref|YP_008796983.1|  68 AYSFVLGETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLS 144
                                       55777778888888888889999999999999999999999*****************************9988887 PP

                               LXG 173 anlesdlkalktyvseLe 190
                                       ++le+  +++k++  ++e
  gi|557693929|ref|YP_008796983.1| 145 SELEAANTEVKSLRTNME 162
                                       777776666666544444 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00089       0.1     173     276 ..      54     160 ..      39     245 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00089
                             LMBR1 173 vllilllGyGlvelPrslwr.eiksdldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyle 248
                                       v++ l+lG + +++  s +  e +++ ++ l+ l+ +   l+++++eae+ +++l ++++ l++s++  d++ + l+
  gi|557693929|ref|YP_008796983.1|  54 VVVSLFLGAAAAAVAYSFVLgETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLS 130
                                       66778888888888888777877888888899999999999999999999999999999999999999997667777 PP

                             LMBR1 249 eilkkvPeeiaeklks.....nenkteeslakl 276
                                       e ++   + +++  ++     +     +sl  +
  gi|557693929|ref|YP_008796983.1| 131 EKVRLLENRLNQLSSEleaanT---EVKSLRTN 160
                                       7777666655555444442221...22222222 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 ?   12.2   9.6    0.0016      0.19       4      90 ..      87     169 ..      83     172 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0016
                            CENP-H   4 lieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesekeklkeelekleaelkksrq 80 
                                       l  q+ +ls +l + ++ +++l++++t+++ +   + ++ ++l ++++ l++  +    +l++ele++ +e+k  r 
  gi|557693929|ref|YP_008796983.1|  87 LKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLN----QLSSELEAANTEVKSLRT 159
                                       5567889999999999999999999999999999999999999999944443333....345788888888888888 PP

                            CENP-H  81 rwrvvknvas 90 
                                       +++ vk v+s
  gi|557693929|ref|YP_008796983.1| 160 NMESVKDVLS 169
                                       8888888877 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   6.1    0.0015      0.18      12      63 ..      95     146 ..      84     150 .. 0.92
   2 ?    7.6   1.2     0.041       4.7      28      61 ..     137     172 ..     134     176 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0015
                            Csm1_N  12 qerldsAdllvsklvhENsvLsqkletkdqeiesLkeqlaeleekvkeleer 63 
                                        +rl +A+  v+kl    + L++ l+t dq+ ++L e++  le+++++l ++
  gi|557693929|ref|YP_008796983.1|  95 SNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSE 146
                                       589******************************************9998765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.041
                            Csm1_N  28 ENsv..LsqkletkdqeiesLkeqlaeleekvkele 61 
                                       EN++  Ls +le  ++e++sL+ ++++++  ++ le
  gi|557693929|ref|YP_008796983.1| 137 ENRLnqLSSELEAANTEVKSLRTNMESVKDVLSLLE 172
                                       6664448999*****************998776665 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 ?   14.3   8.3   0.00027     0.031      23      72 ..      93     142 ..      81     144 .. 0.93
   2 ?    6.0   4.7      0.11        12      22      67 ..     127     172 ..     124     174 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00027
                        TMF_DNA_bd  23 kLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                       +Ls    + +nt+ kLr+++  l +++++ +++ ++l++++  le+rl +
  gi|557693929|ref|YP_008796983.1|  93 DLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQ 142
                                       588899999**************************************987 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.11
                        TMF_DNA_bd  22 ekLskkelklnntikkLrkknkelekeikelkkkleklekeleele 67 
                                       ++Ls k + l+n + +L ++++ +++e+k+l    e++   l+ le
  gi|557693929|ref|YP_008796983.1| 127 QQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVLSLLE 172
                                       6777777777777777777777777777777777666666666665 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 ?    9.4   5.6    0.0092       1.1      62     119 ..     110     167 ..      80     173 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0092
                              COG2  62 ghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellkll 119
                                       +  ++lq++l++ ++  +++ +kv+ +++ l++ ++e+e+   e k+l+ + e++k++
  gi|557693929|ref|YP_008796983.1| 110 SDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDV 167
                                       2334444444444444444444444444444444444444444444444444444444 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   4.4    0.0057      0.65       2      43 ..      87     128 ..      86     137 .. 0.88
   2 ?    7.0   4.4     0.058       6.7       3      43 ..     123     163 ..     121     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0057
                             Spc24   2 ldnekfriakelsdleselesleselaelkeeleeleeesee 43 
                                       l+++++++++ l+++e+++++l+s  ++l++ l++ ++  ++
  gi|557693929|ref|YP_008796983.1|  87 LKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQ 128
                                       78999*****************************99998887 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.058
                             Spc24   3 dnekfriakelsdleselesleselaelkeeleeleeesee 43 
                                       d++ ++++++++ le+ l++l+sel+  ++e++ l ++ e+
  gi|557693929|ref|YP_008796983.1| 123 DQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMES 163
                                       67778899999999999999999999999999999887777 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 ?    8.0   8.3      0.03       3.5      23      85 ..      93     155 ..      48     173 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.03
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvs 85 
                                        l++ l+ea++t+++l+++++++ + ++++ + +++l e v+   +++++l ++++ + + v+
  gi|557693929|ref|YP_008796983.1|  93 DLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVK 155
                                       335555555555555555555555555555555555555555555555555555555555554 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 ?   11.7   3.6    0.0021      0.24       9      60 ..      97     150 ..      89     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0021
                      ABC_tran_CTD   9 eleeleaeIeaLEeeiaeleaeladpelysdp..eklaelsaeleeleaeLeel 60 
                                       +l e e++ ++L  +i++l++ l+ ++  +++  ek+  l ++l++l +eLe++
  gi|557693929|ref|YP_008796983.1|  97 RLTEAENTVNKLRSDITSLQTSLQTADQRAQQlsEKVRLLENRLNQLSSELEAA 150
                                       6889999*****************999776666788888899999999999987 PP

>> GOLGA2L5  Putative golgin subfamily A member 2-like protein 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   8.2    0.0015      0.17     163     238 ..      89     164 ..      84     173 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0015
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          GOLGA2L5 163 sqnreLkeqLaeLqngFvkltnenmeltsalqseqhvkkelakklGqlqeelgelketlelksqeaqslqeqrdqy 238
                                       sqn +L ++L e  n   kl  +   l ++lq+  +  + l+ k+  l ++l++l  +le+ ++e++sl  + + +
  gi|557693929|ref|YP_008796983.1|  89 SQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESV 164
                                       8*********************************999*******************************99877655 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 ?    9.7   9.8    0.0026       0.3     176     251 ..      99     170 ..      73     191 .. 0.43

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0026
                             WEMBL 176 kevekaveeltielialkesLesahaahleaeEkrlgaalareqdklnwekeLkqaeeelqrLneellsakdlksk 251
                                        e+e +v++l  ++++l+ sL++a    ++  Ek   + l  e+   ++ +eL+ a+ e++ L+ ++ s kd+ s 
  gi|557693929|ref|YP_008796983.1|  99 TEAENTVNKLRSDITSLQTSLQTADQRAQQLSEK---VRL-LENRLNQLSSELEAANTEVKSLRTNMESVKDVLSL 170
                                       2333444444444444444333333333332222...111.12333334444444444444444444444444444 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   2.8      0.15        17      62     101 ..      82     121 ..      76     132 .. 0.68
   2 ?    8.5   3.5     0.016       1.8      59      99 ..     121     161 ..     112     165 .. 0.71
   3 ?    8.7   2.7     0.014       1.6      67      97 ..     136     166 ..     127     177 .. 0.44

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  62 evkeeLeerketlekeiktlekqleklekeleelkeelqk 101
                                       +++++L+ +  +l+ ++++ e+   kl+ +++ l+++lq 
  gi|557693929|ref|YP_008796983.1|  82 KLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQT 121
                                       5666666667777777777777777777777777777664 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.016
                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  59 dkeevkeeLeerketlekeiktlekqleklekeleelkeel 99 
                                       + ++  ++L e+   le ++++l+++le  ++e++ l+++ 
  gi|557693929|ref|YP_008796983.1| 121 TADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNM 161
                                       44555677777777788888888888888888877777765 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  67 Leerketlekeiktlekqleklekeleelke 97 
                                       Le+r+++l+ e+++ + + ++l++++e +k+
  gi|557693929|ref|YP_008796983.1| 136 LENRLNQLSSELEAANTEVKSLRTNMESVKD 166
                                       3333333444444444444444444433333 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   8.0     0.022       2.6       8      58 ..      83     133 ..      76     214 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.022
                           DUF4795   8 llkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvk 58 
                                       ll+ l+++ ++l+++l + e++v++l +++  ++ +l++  + +++l ++ 
  gi|557693929|ref|YP_008796983.1|  83 LLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKV 133
                                       555555555555555555555555555555555555555555555554432 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.8    0.0092       1.1      73     137 ..      65     133 ..      59     137 .. 0.65
   2 ?    7.1   0.3     0.058       6.6      83     117 ..     128     162 ..     126     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0092
                             HrpB7  73 dylacrayrdvlegrvra....aeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraa 137
                                       ++ a+  ++++ e+r ++    ++++   + ++l +ae+ v++ +  i +++ +++  ++r+++l ++ 
  gi|557693929|ref|YP_008796983.1|  65 AAVAYSFVLGETEARYQKllddLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKV 133
                                       445555555555555544111145566677788888888888888888888888888888888887664 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.058
                             HrpB7  83 vlegrvraaeaelaaarqaldaaedavaatarkia 117
                                       +l+++vr +e++l ++  +l+aa+ +v+  ++++ 
  gi|557693929|ref|YP_008796983.1| 128 QLSEKVRLLENRLNQLSSELEAANTEVKSLRTNME 162
                                       78999999999999999999999999988777655 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 ?   10.8   4.3     0.002      0.23     115     194 ..      95     176 ..      76     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.002
                              Not3 115 dpkekekeearewlkdaideLneqvekleaeieklsskkkkkkk..skekarveeleklierhkfhieklelllrll 189
                                       +++  e+e++ + l++ i++L++++++ ++ +++ls+k +  ++  ++ ++++e++++ +++ ++ +e+++++l ll
  gi|557693929|ref|YP_008796983.1|  95 SNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENrlNQLSSELEAANTEVKSLRTNMESVKDVLSLL 171
                                       56667888999999999****************999998554443355556999999******************** PP

                              Not3 190 eneel 194
                                       en+++
  gi|557693929|ref|YP_008796983.1| 172 ENDRV 176
                                       **997 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.3     0.002      0.23      14      87 ..      93     166 ..      78     206 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.002
                           zf-C4H2  14 klknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklye 87 
                                       +l+n+l+++ ++++k ++ +++ +  l++ +q  ++ +e++rl+++ +n+l s ++ a++e +   ++++++ +
  gi|557693929|ref|YP_008796983.1|  93 DLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKD 166
                                       56777777777777777777777777777777777777777777777777777777777766554444444333 PP

>> USP8_interact  USP8 interacting
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.4    0.0019      0.21       2      69 ..     115     183 ..     114     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0019
                     USP8_interact   2 Lrelvqkqqqkiaelkkevaeqkqqlseqkrelellkeyiralrstnpvlraladqlerdev.lrWves 69 
                                       L++ +q+  q+ ++l+++v+  +++l++   ele  ++ +++lr+  ++++ + + le+d v + W++s
  gi|557693929|ref|YP_008796983.1| 115 LQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVLSLLENDRVlISWLRS 183
                                       77889999************************************999**********996651679876 PP

>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.9     0.047       5.4      23      81 ..      87     145 ..      73     149 .. 0.85
   2 ?    6.7   0.2     0.076       8.7      63      88 ..     145     169 ..     143     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.047
                           DUF4164  23 avdrrleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaie 81 
                                          + l+  +   e+e+++++l++d + L   L  a  ra++l+e  r + +rL+ +  
  gi|557693929|ref|YP_008796983.1|  87 LKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSS 145
                                       4456677778889***********************************99999998765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.076
                           DUF4164  63 arleevnrEvsrrLkaaietiravLa 88 
                                       ++le++n Ev+  L + +e++++vL+
  gi|557693929|ref|YP_008796983.1| 145 SELEAANTEVK-SLRTNMESVKDVLS 169
                                       689******97.5***********96 PP

>> SPATA1_C  Spermatogenesis-associated C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   6.6     0.003      0.35      68     152 .]      75     165 ..      72     165 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.003
                          SPATA1_C  68 elellykkllaqlkardnkkkeknvakseelkneliiqiiaaqheidelkrkledak.......mklvaElklRkqa 137
                                       e+e+ y+kll  lk+++    +++ +++e++ n+l  +i+ +q+ ++   ++ ++          +l +   + + a
  gi|557693929|ref|YP_008796983.1|  75 ETEARYQKLLDDLKSQNL-DLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSekvrlleNRLNQLSSELEAA 150
                                       78999**********998.7788888888899999999999998886555444444311112223333333344566 PP

                          SPATA1_C 138 aeelkaLraelsqkk 152
                                       ++e+k Lr++++++k
  gi|557693929|ref|YP_008796983.1| 151 NTEVKSLRTNMESVK 165
                                       77*********9987 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.3    0.0023      0.27      28      93 ..     102     167 ..      78     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0023
                              Tho2  28 ekeieklkseieelakdrsderaaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkeekks 93 
                                       e++++kl+s+i++l+++ ++++++a++ +++ + l+++ ++L++E+++  ++v+  ++ ++++k+ 
  gi|557693929|ref|YP_008796983.1| 102 ENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDV 167
                                       68899*********888888899999999999999************************9999975 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.4       0.4        46      12      41 ..      84     113 ..      75     118 .. 0.64
   2 ?   12.6   3.9   0.00091       0.1       3      61 ..     110     168 ..     108     174 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.4
                              BRE1  12 feelseqlskkvkeltileekklrleaeka 41 
                                        ++l++q+ ++ + lt  e+ +++l ++++
  gi|557693929|ref|YP_008796983.1|  84 LDDLKSQNLDLSNRLTEAENTVNKLRSDIT 113
                                       456666666666666666666666666665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00091
                              BRE1   3 kELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenel 61 
                                       + + +l++  + +++ ++++ +++  le+++++l++e + a  + ++++ ++++++  l
  gi|557693929|ref|YP_008796983.1| 110 SDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVL 168
                                       6788999**********************************************988765 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 ?   10.1   3.1    0.0023      0.26     181     247 ..      85     154 ..      75     191 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0023
                        Fmp27_WPPW 181 eeleeqiekleekleelelkseke...deelkeeieelekeikelkeklefletlledlkeseesseeee 247
                                       ++l++q  +l+++l e+e++ +k     ++l++ +++  + +++l ek+++le+ l++l+++ e++++e 
  gi|557693929|ref|YP_008796983.1|  85 DDLKSQNLDLSNRLTEAENTVNKLrsdITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEV 154
                                       5566666666666666666666655545566667777777777777777777777777777666433111 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.6     0.029       3.3      82     118 ..      94     130 ..      84     132 .. 0.83
   2 ?    7.3   0.9     0.037       4.2      80     115 ..     134     169 ..     128     174 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  82 lkkkleelekqlekleeeleklkdqittleanlaqly 118
                                       l ++l+e+e+++ kl  +++ l++ ++t+ + ++ql+
  gi|557693929|ref|YP_008796983.1|  94 LSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLS 130
                                       5678888999999999999999999999998888886 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  80 ellkkkleelekqlekleeeleklkdqittleanla 115
                                       +ll+++l++l++ le  + e++ l+++++++ + l+
  gi|557693929|ref|YP_008796983.1| 134 RLLENRLNQLSSELEAANTEVKSLRTNMESVKDVLS 169
                                       678888999999999999999999888888877665 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 ?   11.0   8.4    0.0033      0.38      43     123 ..      96     172 ..      76     183 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0033
                     Jnk-SapK_ap_N  43 srneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadql 119
                                       +r  e e ++++lr ++++L+t ++   +  ++  e++ ++e+ ++    +l++++e  ++e++ l + +++++d l
  gi|557693929|ref|YP_008796983.1|  96 NRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLN----QLSSELEAANTEVKSLRTNMESVKDVL 168
                                       3334455555555555555555555555444444444444444433....344444444444444444444666666 PP

                     Jnk-SapK_ap_N 120 srle 123
                                       s le
  gi|557693929|ref|YP_008796983.1| 169 SLLE 172
                                       6555 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.3     0.038       4.3     173     228 ..      76     131 ..      67     134 .. 0.80
   2 ?    9.6   2.6    0.0048      0.55      67     112 ..     114     162 ..     109     168 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.038
                           DUF4618 173 tlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeepre 228
                                       t +++q+ L +   +n +l++ + +  + +++l+ +i  L+ ++++  ++a++  e
  gi|557693929|ref|YP_008796983.1|  76 TEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSE 131
                                       55678888888999999999999999999999999999999999988888887655 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0048
                           DUF4618  67 qakaeLqew...eekeekklekLeqqleqlnakvqklqeelnvLstYkD 112
                                       +++  Lq+    ++++++k++ Le+ l+ql ++++ +++e++ L+t ++
  gi|557693929|ref|YP_008796983.1| 114 SLQTSLQTAdqrAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNME 162
                                       4444444441114556677888888888888888888888888888776 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1      0.51        59      26      53 ..      84     111 ..      64     111 .. 0.82
   2 ?   10.7   2.6     0.003      0.34      18      52 ..     104     138 ..      98     141 .. 0.92
   3 ?    5.4   0.6      0.13        15      18      55 ..     139     176 ..     137     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.51
                                       HHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                             DivIC  26 iaalqaelaklkaeneeLeaevkdLksd 53 
                                       +++l+ ++  l+++  e e  v++L+sd
  gi|557693929|ref|YP_008796983.1|  84 LDDLKSQNLDLSNRLTEAENTVNKLRSD 111
                                       5689999999999999999999999865 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                       ++ +l+++i+ lq  l++  ++ ++L ++v++L++
  gi|557693929|ref|YP_008796983.1| 104 TVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLEN 138
                                       7889****************************964 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                             DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLksded 55 
                                       ++ ql +e++a + e+++l+   e+ ++ +++L++d+ 
  gi|557693929|ref|YP_008796983.1| 139 RLNQLSSELEAANTEVKSLRTNMESVKDVLSLLENDRV 176
                                       67899999*******************99999988765 PP

>> TMCO5  TMCO5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   9.6    0.0026       0.3      12      98 ..      84     172 ..      76     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0026
                             TMCO5  12 lqrldeaNqslLrkiqekeetiqslereitkldsllereedeeenfsenekedalke.Leletaklekkn...eiLl 84 
                                       l  l+ +N +l +++ e+e+t+++l+++it l+  l+  ++  ++   +ek + l + L++ ++ le  n   + L 
  gi|557693929|ref|YP_008796983.1|  84 LDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQL--SEKVRLLENrLNQLSSELEAANtevKSLR 158
                                       667899999**************************99999998655..57888888889999999999998778888 PP

                             TMCO5  85 kevveLqkkisrke 98 
                                        ++ +++  +s +e
  gi|557693929|ref|YP_008796983.1| 159 TNMESVKDVLSLLE 172
                                       88888887666555 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.6    0.0027      0.31     631     709 ..      78     155 ..      59     174 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0027
                          Prominin 631 ekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkkldeensdlqesikkllaaveraenf 707
                                       ++ ++l ++l++++ +l+++l+++ ++++++ ++++  l++s+++  ++ ++l+e+ + l++++++l +++e+a+ +
  gi|557693929|ref|YP_008796983.1|  78 ARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDIT-SLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTE 153
                                       445555555555555666666666666666655543.4555566666666666666666666666666666665555 PP

                          Prominin 708 lk 709
                                       +k
  gi|557693929|ref|YP_008796983.1| 154 VK 155
                                       44 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.3      0.15        17      25      54 ..      76     105 ..      72     111 .. 0.85
   2 ?    8.8   5.6     0.021       2.5       3      55 ..     110     162 ..     108     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHHHHT-XXXXXXX CS
                              SlyX  25 vvaeqqqqidrlqrqlrllaerlkeleess 54 
                                       + a+ q+ +d l+ q   l +rl e+e++ 
  gi|557693929|ref|YP_008796983.1|  76 TEARYQKLLDDLKSQNLDLSNRLTEAENTV 105
                                       66899******************9999875 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXX CS
                              SlyX   3 erleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkeleessg 55 
                                       + ++ L++ l   ++  ++L++ v   + ++ +l  +l++ + ++k+l+++++
  gi|557693929|ref|YP_008796983.1| 110 SDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNME 162
                                       56888888888888888888888888888888888888888888888887765 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3     0.007      0.81      64     118 ..      65     119 ..      60     124 .. 0.81
   2 ?    4.4   2.1      0.28        32      29      66 ..     124     161 ..     115     172 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.007
                              CdvA  64 anlkisyasGEidEeaYksaieairellesaleekeeikkllekl.skleleeeev 118
                                       a++  s++ GE  E  Y++  + ++++   ++++++e++++++kl s++++ +++ 
  gi|557693929|ref|YP_008796983.1|  65 AAVAYSFVLGE-TEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLrSDITSLQTSL 119
                                       56666777777.69999999999999999999999999999999988888776665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.28
                              CdvA  29 ealkklkekakelkeklkkrlkeledqikslekalanl 66 
                                       +  ++l ek   l ++l++  +ele   ++++++ +n+
  gi|557693929|ref|YP_008796983.1| 124 QRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNM 161
                                       33444555555555555555555555555555555554 PP

>> HXXSHH  Protein of unknown function (DUF1552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.1    0.0031      0.36     140     219 ..      80     155 ..      75     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0031
                            HXXSHH 140 FsrLFgsgaggseeaeaaarrlarrksvlDlvledakslkrkLgaadrqKLdeylesvreiekrlekaekwaptaka 216
                                       +++L+ ++++++    + ++rl + ++ +  +++d++sl+ +L +ad+ + ++  e+vr +e+rl++ +++ ++a+ 
  gi|557693929|ref|YP_008796983.1|  80 YQKLLDDLKSQN---LDLSNRLTEAENTVNKLRSDITSLQTSLQTADQ-RAQQLSEKVRLLENRLNQLSSELEAANT 152
                                       888888887744...45678999999999******************8.57999***********888887776666 PP

                            HXXSHH 217 eag 219
                                       e +
  gi|557693929|ref|YP_008796983.1| 153 EVK 155
                                       652 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.5       1.8   2.1e+02      36      63 ..      93     117 ..      79     122 .. 0.47
   2 ?   11.6   6.7    0.0025      0.28       8      66 ..     107     169 ..      93     178 .. 0.68

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 1.8
                           NPV_P10  36 dvtelnekLdaqsaqLaeletkvenIqd 63 
                                       d   l+++L +  +++++l + +++ q 
  gi|557693929|ref|YP_008796983.1|  93 D---LSNRLTEAENTVNKLRSDITSLQT 117
                                       3...444444444444444444444443 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0025
                           NPV_P10   8 vIradikavddkVdalqqqvddvqenl....pdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                         r+di+ +++ ++  +q+ ++++e++    + +++l+++L+a ++++++l t++e+++d+L+
  gi|557693929|ref|YP_008796983.1| 107 KLRSDITSLQTSLQTADQRAQQLSEKVrlleNRLNQLSSELEAANTEVKSLRTNMESVKDVLS 169
                                       456666666666666665556666655111134456888888888888888889999999987 PP

>> Alanine_zipper  Alanine-zipper, major outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.8     0.041       4.7       3      33 ..      98     128 ..      93     134 .. 0.82
   2 ?    3.9   0.0      0.59        68       2      28 ..     132     158 ..     131     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.041
                    Alanine_zipper   3 veelqakadqaeqdaaaaksaadeAkskAde 33 
                                       ++e++++++++ +d+ +++ + ++A ++A++
  gi|557693929|ref|YP_008796983.1|  98 LTEAENTVNKLRSDITSLQTSLQTADQRAQQ 128
                                       5788999999999999999999999999987 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.59
                    Alanine_zipper   2 qveelqakadqaeqdaaaaksaadeAk 28 
                                       +v  l+++++q++++ +aa+ + ++ +
  gi|557693929|ref|YP_008796983.1| 132 KVRLLENRLNQLSSELEAANTEVKSLR 158
                                       67889***************9998866 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.7    0.0047      0.54     100     158 ..     105     166 ..      75     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0047
                      Bacillus_HBL 100 kaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdv...deltsilagdsg 158
                                        ++l ++++ Lq+++q+  + ++ql+++++ l+++l++ s++++++    + l   +++ + 
  gi|557693929|ref|YP_008796983.1| 105 VNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANtevKSLRTNMESVKD 166
                                       45677888889999999999999988888888888888777776544111444444444444 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  10.3    0.0028      0.32     481     569 ..      78     163 ..      73     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0028
                              HOOK 481 telqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqeelqkkk 557
                                       ++ q+ll+d + ++ +L +    a++ + +L++ +  lq++lq+ +++a++   l +k+  + ++l+++ +el+  +
  gi|557693929|ref|YP_008796983.1|  78 ARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQ---LSEKVRLLENRLNQLSSELEAAN 151
                                       567999999999999999999999999999999999999999999998887...44444444444444444544444 PP

                              HOOK 558 eqleelepklss 569
                                         + +l  +++s
  gi|557693929|ref|YP_008796983.1| 152 TEVKSLRTNMES 163
                                       444444443333 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 ?    8.9   4.7     0.016       1.8      32      95 ..      76     140 ..      72     141 .. 0.85
   2 ?    5.6   0.6      0.17        20      35      69 ..     132     166 ..     130     174 .. 0.52
   3 ?    2.6   0.0       1.5   1.7e+02      60      93 ..     260     291 .]     255     291 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.016
                           BLOC1_2  32 asekykklkdvaaslekkl.eklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEakf 95 
                                       ++++y+kl d ++s + +l ++l e +++++++ + i  +++++++  + +++L e ++ LE+++
  gi|557693929|ref|YP_008796983.1|  76 TEARYQKLLDDLKSQNLDLsNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRL 140
                                       78899999888888776652678888889999999999999999999999999999999999987 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.17
                           BLOC1_2  35 kykklkdvaaslekkleklnekyeelqpylqqidq 69 
                                       k+  l++++++l+++le+ n + ++l+ +++++++
  gi|557693929|ref|YP_008796983.1| 132 KVRLLENRLNQLSSELEAANTEVKSLRTNMESVKD 166
                                       44445555555555555555555555555544444 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 1.5
                           BLOC1_2  60 lqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                       +++y + ++q+ ++v  L ++++++D+ s+ LE+
  gi|557693929|ref|YP_008796983.1| 260 VDEYNNAVNQLREEV--LLTVIAHIDSLSRVLES 291
                                       678999999999998..999*********99996 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.4      0.19        21       8      33 ..      94     119 ..      87     133 .. 0.60
   2 ?    8.5   0.8     0.012       1.4       1      33 [.     136     168 ..     129     184 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.19
                           DUF4988   8 lkdrvaaleeqvkelndniealkkll 33 
                                       l +r +  e++v++l ++i++l++ l
  gi|557693929|ref|YP_008796983.1|  94 LSNRLTEAENTVNKLRSDITSLQTSL 119
                                       56666666666666666666665433 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.012
                           DUF4988   1 leddvndlkdrvaaleeqvkelndniealkkll 33 
                                       le+++n+l ++ +a +++vk+l +n+e++k +l
  gi|557693929|ref|YP_008796983.1| 136 LENRLNQLSSELEAANTEVKSLRTNMESVKDVL 168
                                       567777777777777777777777777776655 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   7.1     0.016       1.9      43     129 ..      86     158 ..      36     217 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.016
                         AATF-Che1  43 eflesseefeealeeaekalkklleslleLreelleqne.ikkla.............eskeeeekkkskrkrkkkk 105
                                       ++++++ +++++l+eae+ ++kl +++++L+++l +  +  ++l+             +                  
  gi|557693929|ref|YP_008796983.1|  86 DLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQrAQQLSekvrllenrlnqlS------------------ 144
                                       333446788999999*******************3333333333344444444443331.................. PP

                         AATF-Che1 106 keetsleelwkeleklekalkpfr 129
                                                 +ele+ ++++k+ r
  gi|557693929|ref|YP_008796983.1| 145 ----------SELEAANTEVKSLR 158
                                       ..........22222222222222 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 ?    7.8   1.8     0.037       4.3      13      52 ..      88     127 ..      75     138 .. 0.70
   2 ?   10.5   4.8    0.0052       0.6       5      62 ..     101     162 ..      96     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.037
                            CC2-LZ  13 keeieeLkaqlqaaeealaakqeeidelkeeikkkeeele 52 
                                       k++  +L+++l++ae+ +++ +++i  l+++++  ++  +
  gi|557693929|ref|YP_008796983.1|  88 KSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQ 127
                                       6667788899999999999999999999888877766444 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0052
                            CC2-LZ   5 akeaekvk.keeieeLkaqlqaaeealaakqeeidelkeeikkkeeele....tisvlkaQae 62 
                                       a+++   k +++i++L++ lq+a++  ++ +e++  l++ +++ ++ele    +++ l++ +e
  gi|557693929|ref|YP_008796983.1| 101 AENTV-NKlRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEaantEVKSLRTNME 162
                                       34444.4449************************************99988888888887765 PP

>> KLRAQ  Predicted coiled-coil domain-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   8.5    0.0056      0.64       9      83 ..      86     160 ..      78     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0056
                             KLRAQ   9 KlraqakvLkkavleEqskeaslkeelkekeqslrkseqEvdsLtFrNkqLekrvellqeeleveekkvkskskn 83 
                                        l++q+  L   + e  + +++l+ ++ + ++sl++++q  + L+ + + Le r+++l  ele ++ +vks  +n
  gi|557693929|ref|YP_008796983.1|  86 DLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTN 160
                                       479************************************************************988665444443 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  11.1    0.0098       1.1      45     117 ..      87     160 ..      73     182 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0098
                             Mod_r  45 laeknlslepeleelrselqekleelkelekefeekeqeldellqkfspd.allarLqtavaeaeeeSealaee 117
                                       l ++nl+l ++l+e  + +++ ++ +++l+++++   q+ ++l++k+ +  + l++L  ++++a+ e ++l  +
  gi|557693929|ref|YP_008796983.1|  87 LKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLeNRLNQLSSELEAANTEVKSLRTN 160
                                       44566666666777666666666667777777777777776666666543133444555555555555544443 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   7.4      0.01       1.2       3      69 ..      96     162 ..      80     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.01
                             Sec34   3 dqLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                       ++L++ e+++++l +++++++++L++  ++ ++ sek + l+++ +ql +e +  ++ +++++++++
  gi|557693929|ref|YP_008796983.1|  96 NRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNME 162
                                       67999999999*******************************9999999999999998888888876 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   6.4     0.028       3.2      76     140 ..      85     149 ..      78     153 .. 0.86
   2 ?    8.1   3.8      0.02       2.3      67     111 ..     118     162 ..     113     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  76 alLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvraeasrqqerkEe 140
                                         L+ +  +l +++ ea++++++ r   ++++  lq a +  + + e +rl++   +++   +E 
  gi|557693929|ref|YP_008796983.1|  85 DDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEA 149
                                       56899999**********************************99999999999988888877775 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  67 elekvkqqvalLrekeaelekqveeakqqleaerealrqarkelq 111
                                        l ++ q+ + L ek++ le+++ ++  +lea+ ++++++r +++
  gi|557693929|ref|YP_008796983.1| 118 SLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNME 162
                                       57788899*****************************99998875 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.7      0.02       2.3      88     149 ..      66     126 ..      61     134 .. 0.74
   2 ?    6.0   3.4     0.069       7.9      93     139 ..     119     165 ..     117     177 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.02
                         PspA_IM30  88 ealaeikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaakaqe 149
                                       +++++ + l ++ ++++++l+ ++s+  +l + l+++e  +++l++ ++ l+  +++a  ++
  gi|557693929|ref|YP_008796983.1|  66 AVAYSFV-LGETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRA 126
                                       4444444.444556899999999999999999999999999999999999999888875443 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.069
                         PspA_IM30  93 ikslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellk 139
                                       ++++ + a++l++++  ++    ql  +lea+ t ++ l++ +e +k
  gi|557693929|ref|YP_008796983.1| 119 LQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVK 165
                                       56666777777777777777777777777777777777776666654 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  13.1     0.016       1.9      55     154 ..      74     169 ..      70     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.016
                          CCDC144C  55 tktvfqyngqLnvlkaentmlnskLekekqnkerleaevesyrsrLaaAiqdheqsqtskrdlelalqrerdewlrl 131
                                        +t ++y++ L++lk++n  l+++L +  ++ ++l  ++ s+++ L++A q ++q  +  r le  l++   e    
  gi|557693929|ref|YP_008796983.1|  74 GETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSEL--- 147
                                       56778899999999999999999999999999999999999999999998888888888888888777777654... PP

                          CCDC144C 132 qdklnfdvsnlkdknevLsqqLs 154
                                        +  n +v +l+ + e+++  Ls
  gi|557693929|ref|YP_008796983.1| 148 -EAANTEVKSLRTNMESVKDVLS 169
                                       .5566666677777777666666 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.7     0.005      0.57     101     152 ..      83     134 ..      75     139 .. 0.91
   2 ?    1.5   0.2       1.4   1.6e+02     112     140 ..     136     164 ..     131     173 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.005
                           DUF4763 101 eileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrln 152
                                        + +L+ +n  L  +l+e++   ++ r++++ l++sl+   +r+++l+++  
  gi|557693929|ref|YP_008796983.1|  83 LLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVR 134
                                       5789********************************************9876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 1.4
                           DUF4763 112 Lrqqlaelqqhlkasrkslkelreslcqe 140
                                       L  +l +l++ l+a ++++k lr+ + + 
  gi|557693929|ref|YP_008796983.1| 136 LENRLNQLSSELEAANTEVKSLRTNMESV 164
                                       56677777777777777777777776655 PP

>> DMPK_coil  DMPK coiled coil domain like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0       1.4   1.7e+02      26      49 ..      65      88 ..      63      90 .. 0.82
   2 ?    9.1   2.0     0.012       1.4      17      54 ..      81     118 ..      75     120 .. 0.90
   3 ?    3.9   2.5      0.49        57      33      59 ..     118     144 ..     116     151 .. 0.85
   4 ?    0.0   0.1       8.1   9.3e+02      46      58 ..     152     164 ..     143     166 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 1.4
                         DMPK_coil 26 anlafeskLkeaEkknreLeeele 49
                                      a +a +  L e+E++ + L+++l+
  gi|557693929|ref|YP_008796983.1| 65 AAVAYSFVLGETEARYQKLLDDLK 88
                                      5666777899*********99986 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.012
                         DMPK_coil  17 qeeLekvkaanlafeskLkeaEkknreLeeeleqLkke 54 
                                       q+ L   k  nl  + +L eaE     L +++ +L+  
  gi|557693929|ref|YP_008796983.1|  81 QKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTS 118
                                       5568899****************************976 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.49
                         DMPK_coil  33 kLkeaEkknreLeeeleqLkkemEelr 59 
                                        L+ a ++ ++L e+++ L +++ +l 
  gi|557693929|ref|YP_008796983.1| 118 SLQTADQRAQQLSEKVRLLENRLNQLS 144
                                       589999999999999999999998765 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 8.1
                         DMPK_coil  46 eeleqLkkemEel 58 
                                        e+++L+ +mE +
  gi|557693929|ref|YP_008796983.1| 152 TEVKSLRTNMESV 164
                                       5889999999875 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 ?    7.1   7.6     0.062       7.1      48      95 ..     111     161 ..      56     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.062
                           DUF4140  48 tildvqvervpnreaeee...elkalraeleeledelaaledelaaaearl 95 
                                        i+++q++ ++ ++ +++   +++ l+++l++l  el+a++ e +++++ +
  gi|557693929|ref|YP_008796983.1| 111 DITSLQTSLQTADQRAQQlseKVRLLENRLNQLSSELEAANTEVKSLRTNM 161
                                       466777777666666666664377777777777777777777777777655 PP

>> HlyE  Haemolysin E (HlyE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.6     0.042       4.8     194     261 ..      51     118 ..      33     129 .. 0.72
   2 ?    5.0   1.0      0.11        13     226     279 ..     125     178 ..     117     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.042
                                       S-HHHHHHHHHHH.....H.HHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              HlyE 194 aGPiGlilalaiafppaia.avvkGkliaelkeklksvqafftilddrvkkaskiidaikldlaedkaa 261
                                          + ++l l  a   a+a + v G+  a +++ l  +++    l++r+ +a++ +++++ d++  +++
  gi|557693929|ref|YP_008796983.1|  51 VAAVVVSLFLGAAA-AAVAySFVLGETEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTS 118
                                       33333444444442.244427899**************999999*************999988875555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH............. CS
                              HlyE 226 klksvqafftilddrvkkaskiidaikldlaedkaalgelkgllsaadrnkqll 279
                                       + + + +   +l++r+++ s +++a++ ++   +++++ +k +ls  + ++ l+
  gi|557693929|ref|YP_008796983.1| 125 RAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVLSLLENDRVLI 178
                                       555666667889999***999999999999999999999999999887766553 PP

>> NBP1  Fungal Nap binding protein NBP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   8.2    0.0087         1     159     229 ..     102     172 ..      75     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0087
                              NBP1 159 kqmleqLrrgrssnkserrvslrnnnleeDqvvlLqkkikklesklkdlekeLeitkkkLkFakeknkLle 229
                                       ++ +++Lr+   s + + ++  +  +  + +v+lL++++++l s+l++++ e ++++ +++ +k+  +Lle
  gi|557693929|ref|YP_008796983.1| 102 ENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVLSLLE 172
                                       45566666666666665555556667777888888888888888888888888888888888888888887 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 ?    8.4   6.5     0.021       2.4      34     100 ..      87     157 ..      75     164 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  34 ldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekl 100
                                       l ++   l ++l e+ +  N+l   I ++  +     + a++l ++v+ l ++l++l+ el+++++e+++l
  gi|557693929|ref|YP_008796983.1|  87 LKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLqtadQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSL 157
                                       45555566666777777777777777776665544445677777777777777777777777777777655 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   7.0     0.002      0.23     120     218 ..      77     171 ..      64     178 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.002
                              CorA 120 vdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeyl 194
                                         r+ +ll++l+++  +l+++l   ++t ++++++++ l+++l +  + + ++ e + rll+ ++ ++l++e    l
  gi|557693929|ref|YP_008796983.1|  77 EARYQKLLDDLKSQNLDLSNRLteAENTVNKLRSDITSLQTSLQTADQRAQQLSEKV-RLLE-NRLNQLSSE----L 147
                                       445666666666666666666666666666666666666666666666666666666.6666.555555555....3 PP

                              CorA 195 rdlldelerllemlealrerlesl 218
                                       +    e+++l   +e+++++l+ l
  gi|557693929|ref|YP_008796983.1| 148 EAANTEVKSLRTNMESVKDVLSLL 171
                                       555555555555555555555544 PP

>> FemAB  FemAB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.1     0.016       1.9     237     298 ..      91     154 ..      76     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.016
                             FemAB 237 elnlaeylkelqekleklekklakleekleknpe..kkkkkklkelekqlaslekelkeaeefi 298
                                       +l+l+++l+e ++  +kl+++++ l+ +l+++++  ++  +k++ le+ l++l+ el+ a+   
  gi|557693929|ref|YP_008796983.1|  91 NLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQraQQLSEKVRLLENRLNQLSSELEAANTEV 154
                                       5788888888888888888888888888888887775555555555555555555555555433 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  10.0      0.14        16      17      86 ..      93     161 ..      80     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.14
                   Snapin_Pallidin  17 eldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRa 86 
                                       +l ++l e +++ ++L++++++l+++L+ + + ++ ++ ++++   ++L+++  ++++ n+ +++l+  +
  gi|557693929|ref|YP_008796983.1|  93 DLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQ-QLSEKVRLLENRLNQLSSELEAANTEVKSLRTNM 161
                                       56677778888888888888888888887777766.6777777777777777777777777777776554 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 ?    6.1   6.6     0.081       9.3      96     139 ..     118     159 ..      55     178 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.081
                       EMP24_GP25L  96 evgseasdykdsakkekletleselkkleekldsikreqkylre 139
                                        ++    d+ + + +ek+  le++l++l++ l+   +e+k+lr+
  gi|557693929|ref|YP_008796983.1| 118 SLQT--ADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRT 159
                                       2211..12333444555555555555555555555555555555 PP

>> DUF1043  Protein of unknown function (DUF1043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   6.1     0.044         5       2     100 ..      55     146 ..      50     177 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.044
                           DUF1043   2 liglvvGiiiGalilrltnsklkkqkklekelekakaeleeqkqeledHfaqsaelLetlaedyqkLyqhlakssee 78 
                                       +++l++G+   a+++ ++ ++      +e++ +k  + l+ q+ +l++ ++++ + +++l +d + L++ l++  ++
  gi|557693929|ref|YP_008796983.1|  55 VVSLFLGAAAAAVAYSFVLGE------TEARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQR 125
                                       455666666666666665555......88888999999999999999999999999999999999999999866655 PP

                           DUF1043  79 Llpeleeqelfqqkkleekkae 100
                                          +l+e+   ++++l++ ++e
  gi|557693929|ref|YP_008796983.1| 126 A-QQLSEKVRLLENRLNQLSSE 146
                                       4.23333333333333333322 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3       3.4     4e+02      64      89 ..      80     105 ..      73     107 .. 0.66
   2 ?    7.8   9.3     0.042       4.9      33      89 ..      98     154 ..      82     156 .. 0.65
   3 ?    7.2   2.3     0.067       7.7      13      53 ..     127     167 ..     123     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHHHHHHHHHHHHHHHC CS
                              BST2  64 qqakvqelqgeikkLnqkLqdaeaev 89 
                                        q+ + +l+ ++ +L ++L +ae  v
  gi|557693929|ref|YP_008796983.1|  80 YQKLLDDLKSQNLDLSNRLTEAENTV 105
                                       45667777777777777777777665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.042
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                              BST2  33 lreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaeaev 89 
                                       l eae  ++   + + +L+ sL+    ++q+  +kv+ l++ +++L  +L+ a++ev
  gi|557693929|ref|YP_008796983.1|  98 LTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEV 154
                                       444444555555556667777777777777777777777777777777777777766 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.067
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  13 qecrnvtrlLerqLtqaqeslreaeaqaatcnqtvvtLkas 53 
                                       q+++++ rlLe++L+q   +l+ a++++ +    +++ k+ 
  gi|557693929|ref|YP_008796983.1| 127 QQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDV 167
                                       678899999*******9999999999999988777777665 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   3.9      0.27        31      23      78 ..      78     133 ..      73     137 .. 0.72
   2 ?    8.1   3.8     0.027       3.1      21      71 ..     118     168 ..     110     174 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.27
                              KxDL  23 grlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkakl 78 
                                       +r++k    L+ +n  +++rl+++++ +++   ++ +++  L++  ++ ++l +k+
  gi|557693929|ref|YP_008796983.1|  78 ARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKV 133
                                       55666666777777777888888888888888888888888888777777777765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.027
                              KxDL  21 tsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkki 71 
                                        +++  +  ++L+e   l+++rl++l+++++   + +k+++ ++es++  +
  gi|557693929|ref|YP_008796983.1| 118 SLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVL 168
                                       345556667788888888888888888888888888888888888877655 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 ?    6.5   9.1     0.081       9.4       4      67 ..     100     162 ..      76     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.081
                            Cnn_1N   4 EqeeqidkLkKENFdLKLriyfLeerleklseeqkeellkenielkveveslqkelkekkkllr 67 
                                       E e++++kL+ +  +L+  +++ ++r ++lse +++ l++ + +l  e+e    e+k+++  ++
  gi|557693929|ref|YP_008796983.1| 100 EAENTVNKLRSDITSLQTSLQTADQRAQQLSE-KVRLLENRLNQLSSELEAANTEVKSLRTNME 162
                                       78888888888888888888999999888888.6777777777777777777777777666554 PP

>> DLP_helical  Dynamin-like helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.2       0.9     1e+02      87     129 ..      77     119 ..      59     122 .. 0.54
   2 ?    8.7   2.7    0.0076      0.87      72     119 ..     115     162 ..     111     174 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.9
                       DLP_helical  87 ekevekleesakriekelaelkkeieearielreelkayfsdL 129
                                       e+  +kl +++k ++ +l++   e e++ ++lr  ++++ + L
  gi|557693929|ref|YP_008796983.1|  77 EARYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSL 119
                                       3444444444444444444444444444444444444444433 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0076
                       DLP_helical  72 lerqlpeaeerleelekevekleesakriekelaelkkeieearielr 119
                                       l+  l++a +r+++l+++v+ le++++++++el+ ++ e++  r++++
  gi|557693929|ref|YP_008796983.1| 115 LQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNME 162
                                       5678999*************************************9986 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 ?    3.2   4.3       0.8        92      10      53 ..      89     132 ..      83     135 .. 0.55
   2 ?   11.8   3.9    0.0017       0.2       4      32 ..     132     160 ..     129     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.8
                       Cep57_CLD_2  10 nrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkae 53 
                                        ++  l+ +l ++e + ++L+++  s  ++L+ A +++++L+++
  gi|557693929|ref|YP_008796983.1|  89 SQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEK 132
                                       44444555555555555555555555555555555555555555 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0017
                       Cep57_CLD_2   4 evktLqnrLdsltrklqvheeelkrLnkE 32 
                                        v  L+nrL++l+++l+++ +e k+L++ 
  gi|557693929|ref|YP_008796983.1| 132 KVRLLENRLNQLSSELEAANTEVKSLRTN 160
                                       45668*********************984 PP

>> Flg_hook  Flagellar hook-length control protein FliK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.5      0.13        15      44      75 ..      99     130 ..      87     134 .. 0.88
   2 ?    6.0   0.8     0.095        11      51      76 ..     134     159 ..     128     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.13
                                       E-SCHHHHHHHHTHHHHHHHHHCCTTCCEEEE CS
                          Flg_hook  44 aenpetrelLeqnlprLreaLaaaGlklddls 75 
                                       +e + t + L++++ +L+++L+ a    ++ls
  gi|557693929|ref|YP_008796983.1|  99 TEAENTVNKLRSDITSLQTSLQTADQRAQQLS 130
                                       788999****************9998887765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.095
                                       HHHHHTHHHHHHHHHCCTTCCEEEEE CS
                          Flg_hook  51 elLeqnlprLreaLaaaGlklddlsv 76 
                                       +lLe+ l++L ++L+aa+ ++++l  
  gi|557693929|ref|YP_008796983.1| 134 RLLENRLNQLSSELEAANTEVKSLRT 159
                                       79*******************98765 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 ?    7.5  11.0     0.053       6.1       6      79 ..      89     165 ..      86     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.053
                    HIP1_clath_bdg   6 rKnAevtkqlsvarqaqeeverekkeleeelerlkeeaerkle...eqkeelekLkreleakraelarlkssLesse 79 
                                        +n ++   l+ a ++ + +      l+++l+ + + a++  e     +  l++L +elea ++e+++l++ +es +
  gi|557693929|ref|YP_008796983.1|  89 SQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEkvrLLENRLNQLSSELEAANTEVKSLRTNMESVK 165
                                       5688888999999999999999999******99988777654422155678999******************99876 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 ?    7.5   2.7      0.04       4.6      29      70 ..      92     133 ..      81     134 .. 0.89
   2 ?    8.1   1.7     0.026         3      33      68 ..     138     173 ..     135     175 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.04
                          JIP_LZII  29 ddLIarvdeLtsereiLreEleslqkakerlesrikelEeel 70 
                                        dL +r++e  +  + Lr++++slq+++++  +r ++l e++
  gi|557693929|ref|YP_008796983.1|  92 LDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKV 133
                                       58999*******************************998876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.026
                          JIP_LZII  33 arvdeLtsereiLreEleslqkakerlesrikelEe 68 
                                       +r+ +L+se e+ + E++sl+++ e++++ ++ lE+
  gi|557693929|ref|YP_008796983.1| 138 NRLNQLSSELEAANTEVKSLRTNMESVKDVLSLLEN 173
                                       699**********************99998888876 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   4.5      0.05       5.7      40      95 ..     104     159 ..      89     166 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.05
                          Noelin-1  40 qlrqllekvqnlsqsievldlRtsrdlqyvrktetllktlesklkvveedrkelsa 95 
                                        + +l   +  l +s++  d+R ++  + vr  e+ l++l+s+l+ ++ + k+l +
  gi|557693929|ref|YP_008796983.1| 104 TVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRT 159
                                       56778888889999999999999999999999999999999999999888887765 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.6     0.031       3.6     104     157 ..      92     145 ..      72     153 .. 0.58
   2 ?    7.6   4.3     0.022       2.5      78     143 ..     106     173 ..     101     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.031
                     Fzo_mitofusin 104 arlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfee 157
                                         l+++  e+e+++++  +++++  ++l+++ ++a++l +k  lle++L++ ++
  gi|557693929|ref|YP_008796983.1|  92 LDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSS 145
                                       445555444444444444444444455556666666666666666666666544 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.022
                     Fzo_mitofusin  78 ekLrlivs..ltsancshqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrn 143
                                       +kLr+ ++  +ts +   q  q+ls+ +  l+++ ++ ++ele+  +e+++  +++e+v+  + ll n
  gi|557693929|ref|YP_008796983.1| 106 NKLRSDITslQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVLSLLEN 173
                                       56666554335777888888888888888888888888888888777777777777777777777766 PP

>> Sec2p  GDP/GTP exchange factor Sec2p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   3.8       0.2        23      45      89 ..      84     128 ..      75     131 .. 0.87
   2 ?    7.0   4.7      0.05       5.7      41      85 ..     122     166 ..     120     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXXXXXXX CS
                             Sec2p  45 kealekkneklkeqLkeketlleslqeqLkeLkevlekmeeesee 89 
                                        ++l+ +n  l ++L+e+e+ +++l ++  +L++ l++ +++ ++
  gi|557693929|ref|YP_008796983.1|  84 LDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQ 128
                                       578999*******************************99887765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.05
                                       HHHHHHHHHHHHHHHHHHHTTHCHCCCHCTSSSSHHHHCTTTXXX CS
                             Sec2p  41 arkekealekkneklkeqLkeketlleslqeqLkeLkevlekmee 85 
                                       a ++ ++l +k + l+++L++  + le+ +++ k+L++ +e++++
  gi|557693929|ref|YP_008796983.1| 122 ADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKD 166
                                       566777788888888888888888888888888888888887765 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   3.2      0.89     1e+02      37      71 ..      95     129 ..      72     138 .. 0.61
   2 ?    5.2   1.9      0.25        29      28      64 ..     136     164 ..     123     176 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.89
                       Fungal_TACC  37 qkkldklelenkslkqeieqLkkqleaerkEKqeL 71 
                                       +++l + e+  ++l+++i++L+  l+++ +  q+L
  gi|557693929|ref|YP_008796983.1|  95 SNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQL 129
                                       34455555555667777777777777666655555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.25
                       Fungal_TACC  28 lkkgyeakyqkkldklelenkslkqeieqLkkqleae 64 
                                       l        +++l++l+ e ++ ++e+++L+ ++e++
  gi|557693929|ref|YP_008796983.1| 136 L--------ENRLNQLSSELEAANTEVKSLRTNMESV 164
                                       3........4555566666666666666665555544 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   6.6     0.068       7.9       5      75 ..      93     163 ..      81     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.068
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   5 elfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLar 75 
                                       +l ++l+e e+++++l +++++l+++l++  ++ ++L+   + l +rl++ +++ ++ ++e+++ ++n++ 
  gi|557693929|ref|YP_008796983.1|  93 DLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMES 163
                                       56778888888888888888888888888888888888888888888866666666666666666666654 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1       0.1        12      42      68 ..      91     117 ..      73     125 .. 0.83
   2 ?    9.0   2.2     0.012       1.3       9      70 ..     104     168 ..      99     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.1
                           DUF1515  42 mdelvervtalegsvvklkaditsvke 68 
                                         +l +r+t  e +v kl++dits++ 
  gi|557693929|ref|YP_008796983.1|  91 NLDLSNRLTEAENTVNKLRSDITSLQT 117
                                       457899*****************9875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.012
                           DUF1515   9 qlgtllaevkelredlkrsedrsdasrak...myrkmdelvervtalegsvvklkaditsvkevt 70 
                                       ++++l ++++ l+  l+ +++r++    k   + +++++l   ++a ++ v  l++++ svk+v 
  gi|557693929|ref|YP_008796983.1| 104 TVNKLRSDITSLQTSLQTADQRAQQLSEKvrlLENRLNQLSSELEAANTEVKSLRTNMESVKDVL 168
                                       5678999**********9999998654441124689999999999*99**************985 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   1.6     0.053       6.1       2      44 ..      95     137 ..      75     139 .. 0.92
   2 ?    8.1   1.4     0.024       2.8       2      43 ..     130     171 ..     122     173 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.053
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHH CS
                              Swi5   2 eaeikeleeqleelekelaelkeelkekkdpeetvkrhIklLh 44 
                                       ++++ e e+++++l++++ +l+  l+  ++ ++ ++++++lL 
  gi|557693929|ref|YP_008796983.1|  95 SNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLE 137
                                       5678899999****************999***********997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHH CS
                              Swi5   2 eaeikeleeqleelekelaelkeelkekkdpeetvkrhIklL 43 
                                       +++++ le++l++l +el++++ e k+  +  e vk+ ++lL
  gi|557693929|ref|YP_008796983.1| 130 SEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDVLSLL 171
                                       334444555555555555555555555446666666666665 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.9       0.3        35      14      62 ..      81     119 ..      72     121 .. 0.60
   2 ?   12.0   7.5    0.0019      0.22       8      61 ..     114     167 ..     111     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.3
                              ZapB  14 qkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerl 62 
                                       qk           +++Lk +n  l+++  e e  +++l+ + +++q  l
  gi|557693929|ref|YP_008796983.1|  81 QK----------LLDDLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSL 119
                                       33..........3456666666666666666666666666666665555 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0019
                              ZapB   8 qLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqer 61 
                                        L+++ q+a ++ ++L+++++ L+ + ++l++e ++ + e++ l+++ e++++ 
  gi|557693929|ref|YP_008796983.1| 114 SLQTSLQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVKDV 167
                                       588888888888888888888888888888888888888888888888877765 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   7.5     0.051       5.9      63     136 ..      94     165 ..      72     175 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.051
                             Muted  63 mkenLselnkkleaalekverllqkeleeekrkseqlqekeeerkaeweeflkelqekkeevDeefeekveelk 136
                                       ++++L+e ++ +++++++++ l++  l++  ++++ql+ek + ++++ +++ +el+  + ev  + + ++e +k
  gi|557693929|ref|YP_008796983.1|  94 LSNRLTEAENTVNKLRSDITSLQTS-LQTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVK-SLRTNMESVK 165
                                       5566667777777777777777766.4444446677777777777777777777766666663.3444444444 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   6.9       0.1        12     187     252 ..      89     151 ..      60     176 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.1
                         Phage_GPO 187 kkkksddarfadveeavelvAeevkelsekveallaleaelaalkkeveklkaeleaLkekLsktd 252
                                       +++ + ++r ++ e++v+++ + +++l+++++   ++++++++l+++v+ l+++l++L+++L++ +
  gi|557693929|ref|YP_008796983.1|  89 SQNLDLSNRLTEAENTVNKLRSDITSLQTSLQ---TADQRAQQLSEKVRLLENRLNQLSSELEAAN 151
                                       22222244444444444444444444444444...3344444444444444444444444444433 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   7.8     0.095        11      36     124 ..      86     169 ..      73     174 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.095
                                       HHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  36 allkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeakki 112
                                       +l ++n +l +++ e+e+++++ ++  ++L+ +l +a + a+++     ++ +l+ +  ++  ++ +e a+ e+k +
  gi|557693929|ref|YP_008796983.1|  86 DLKSQNLDLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQLS----EKVRLLENRLNQL-SSELEAANTEVKSL 157
                                       455556666666666666666666666666666655555554443....3344444444444.44457999999999 PP

                                       XXXXXXXXXXXX CS
                            DivIVA 113 aeeieelkrqar 124
                                       ++++e++k    
  gi|557693929|ref|YP_008796983.1| 158 RTNMESVKDVLS 169
                                       999999987765 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.2     0.014       1.6       4      40 ..      79     115 ..      77     119 .. 0.87
   2 ?    5.5   0.9      0.13        15      18      36 ..     128     146 ..     125     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.014
                       Shugoshin_N   4 kylrqNreLAKsNsalslkirelekevseLlsENlnL 40 
                                       +y + + +L  +N  ls ++ e e++v++L+s + +L
  gi|557693929|ref|YP_008796983.1|  79 RYQKLLDDLKSQNLDLSNRLTEAENTVNKLRSDITSL 115
                                       566778888889********************98777 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.13
                       Shugoshin_N  18 alslkirelekevseLlsE 36 
                                       +ls k+r le+++++L sE
  gi|557693929|ref|YP_008796983.1| 128 QLSEKVRLLENRLNQLSSE 146
                                       7899************887 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2  10.6      0.11        13      54     130 ..      97     165 ..      46     183 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.11
                           DUF3552  54 alleakeeihklreelekelkerrnelqrlekRll...qkeetLdrkeeslekkeesleekekelkqkeqsleekee 127
                                        l           +e+e+ +++ r+++++l++ l+   q+ ++L +k + le++ ++l+++ +  +++ +sl+++ e
  gi|557693929|ref|YP_008796983.1|  97 RL-----------TEAENTVNKLRSDITSLQTSLQtadQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNME 162
                                       33...........4556666666666666665554333555566666666666655555555544444444444444 PP

                           DUF3552 128 ele 130
                                       +++
  gi|557693929|ref|YP_008796983.1| 163 SVK 165
                                       444 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 ?    7.2   8.1     0.065       7.5      26      92 ..      97     165 ..      72     184 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.065
                      Syntaxin-6_N  26 rlledtssstseeldetrteLrkalrsiewdledLeetvrivek..np..skfkidekelsrrrafveevr 92 
                                       rl e +  +t ++l++  t L+++l+++++  ++L e vr +e+  n+  s+ +  ++e+++ r  +e+v+
  gi|557693929|ref|YP_008796983.1|  97 RLTEAE--NTVNKLRSDITSLQTSLQTADQRAQQLSEKVRLLENrlNQlsSELEAANTEVKSLRTNMESVK 165
                                       222222..246677777777777777777777777777777766221121335555555555555555444 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.8     0.062       7.1       8      53 ..     120     165 ..     114     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.062
                                       TTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHH CS
                              GrpE   8 eeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekek 53 
                                       + ++++ ++l e++  le+++++l+++l+ ++ e++ lr ++e  k
  gi|557693929|ref|YP_008796983.1| 120 QTADQRAQQLSEKVRLLENRLNQLSSELEAANTEVKSLRTNMESVK 165
                                       5667788888888888999999999999999999998888887655 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   6.6       2.2   2.6e+02       3      56 ..      82     136 ..      80     139 .. 0.68
   2 ?    8.5   1.5     0.028       3.2       1      78 [.     136     221 ..     136     222 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 2.2
                           DUF4404   3 elLekLhee...LeqnesldeetralLeslaedieellaeedaaaeeeelaerlnea 56 
                                       +lL++L+++   L++  +  e+t ++L+s ++ ++  l++ d++a++  l+e+++ +
  gi|557693929|ref|YP_008796983.1|  82 KLLDDLKSQnldLSNRLTEAENTVNKLRSDITSLQTSLQTADQRAQQ--LSEKVRLL 136
                                       66777776553355666666777777777777777777777777777..99988765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.028
                           DUF4404   1 LkelLekLheeLeqnesldeetralLeslaedieellaeedaaaeeee........laerlneaverFeeeHPklag 69 
                                       L+++L++L++eLe  ++  ++ r ++es+++ ++ l ++    +  ++          e +ne+ +   ++ P+l  
  gi|557693929|ref|YP_008796983.1| 136 LENRLNQLSSELEAANTEVKSLRTNMESVKDVLSLLENDRVLISWLRSeppgtregDREYWNETRALAVKSDPNLVL 212
                                       6789*************999999999999988874433322222111123344445666677777777777777777 PP

                           DUF4404  70 vlreildsL 78 
                                       ++++ild L
  gi|557693929|ref|YP_008796983.1| 213 TIDKILDNL 221
                                       777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1993  (0.111161); expected 358.6 (0.02)
Passed bias filter:                     1227  (0.0684366); expected 358.6 (0.02)
Passed Vit filter:                       352  (0.019633); expected 17.9 (0.001)
Passed Fwd filter:                       160  (0.00892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             156  [number of targets reported over threshold]
# CPU time: 1.12u 0.35s 00:00:01.47 Elapsed: 00:00:00.50
# Mc/sec: 1766.53
//
Query:       gi|557693930|ref|YP_008796984.1|  [L=348]
Description: peptide/nickel ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-35  120.2  11.4    8.1e-35  120.2  11.4    2.2  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 ?   -1.3   1.2     0.086   1.5e+03     157     172 ..      13      28 ..       2      42 .. 0.50
   2 ?   -1.5   0.0       0.1   1.8e+03     100     122 ..     121     143 ..     110     144 .. 0.72
   3 !  120.2  11.4   4.5e-39   8.1e-35       1     184 [.     142     347 ..     142     348 .] 0.99

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.086
                      BPD_transp_1 157 gvlalviavlllnlva 172
                                       ++++++++vll+++v+
  gi|557693930|ref|YP_008796984.1|  13 TLVFVLLSVLLMVAVV 28 
                                       3333333333333333 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.1
                      BPD_transp_1 100 kvvlPnalppiitglilafggll 122
                                         +lP +l  + t +++++++ +
  gi|557693930|ref|YP_008796984.1| 121 MERLPYSLLLVTTAVVISAVAGI 143
                                       56788888888888888877655 PP

  == domain 3  score: 120.2 bits;  conditional E-value: 4.5e-39
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.......................vilsilghlil 54 
                                       gi +G+ aa++r++ +dkl++    + ++lPs + +++l+lvf                       ++l+ l+h++l
  gi|557693930|ref|YP_008796984.1| 142 GINFGLRAATRRGSLFDKLVSYTAAASYGLPSWWTGLILLLVFyfylrllppggimstppptepvaKVLDMLWHTVL 218
                                       6779******************************99999999999******************************** PP

                      BPD_transp_1  55 pviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllefl 131
                                       p+++l+++  +++++++r  +l++ ++d+v +a+a+G+++  + r+++l+ a+ppi+t +++a++g+lgga+l+e++
  gi|557693930|ref|YP_008796984.1| 219 PLMTLVVVIVGGWAYVTRTIVLNITQEDFVTVAKAKGLPENLLRRRYILRPAAPPIATNIVFAIAGSLGGAILTETV 295
                                       ***************************************************************************** PP

                      BPD_transp_1 132 gswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       ++wpG+g+l  +ai ++d  +   ++++++++++++  +++ +l+++ldprvr
  gi|557693930|ref|YP_008796984.1| 296 FNWPGMGRLYYDAITAFDEGLVV-ALTFVYTLIYIAARFIIEVLVAVLDPRVR 347
                                       ***********************.****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2514.90
//
Query:       gi|557693931|ref|YP_008796985.1|  [L=321]
Description: peptide/nickel ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   77.8   0.0    1.5e-21   77.4   0.0    1.2  1  ABC_tran    ABC transporter
      6e-19   68.3   0.3    9.5e-19   67.7   0.3    1.3  1  oligo_HPY   Oligopeptide/dipeptide transporter, C-terminal re
    1.1e-10   41.9   0.3      7e-10   39.2   0.0    2.0  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    9.7e-06   25.2   0.2    4.8e-05   22.9   0.2    1.9  1  SMC_N       RecF/RecN/SMC N terminal domain
    2.1e-05   24.8   0.1      0.063   13.6   0.0    2.2  2  AAA_22      AAA domain
    0.00027   20.4   0.2     0.0025   17.3   0.1    2.2  2  TniB        Bacterial TniB protein
     0.0014   19.1   0.4      0.014   15.8   0.4    2.1  1  AAA         ATPase family associated with various cellular ac
  ------ inclusion threshold ------
      0.019   13.8   0.2      0.096   11.5   0.2    1.8  1  ABC_ATPase  Predicted ATPase of the ABC class
      0.045   14.0   0.1       0.16   12.2   0.1    2.0  1  DUF3265     Protein of unknown function (DUF3265)
      0.071   12.8   0.1       0.92    9.2   0.0    2.5  3  PRK         Phosphoribulokinase / Uridine kinase family
       0.16   11.5   0.2        2.8    7.5   0.0    2.3  2  AAA_25      AAA domain
       0.18   12.3   0.2       0.31   11.5   0.2    1.3  1  PhoU        PhoU domain
        0.2   11.9   0.0       0.69   10.2   0.0    1.9  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 !   77.4   0.0   1.1e-24   1.5e-21       2     137 .]      22     179 ..      21     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 1.1e-24
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG.....B-HHHCCHCEEEE-SS.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx.. RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke.....qeleslrkeigvlpqe.. 67 
                                       + v++++ e e +++vGe+G+GK++   +++++l p      G+il++g d+ +       +e   ++i++++q   
  gi|557693931|ref|YP_008796985.1|  22 DGVDFSVGEAEALGLVGESGCGKTSTGLAVMRMLPPnvvkLGGKILFEGIDILSmnprdFAEEYQWRKISMVFQGam 98 
                                       789*********************998888888888788789*********9999888745555567899****988 PP

                                       --S-TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  68 pqlfpeltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       ++++p l+v+ +            ++e ++++ + +++++l+ + v++ p++LSgG+kqr  +a+al+ +p+l++lD
  gi|557693931|ref|YP_008796985.1|  99 NSFNPVLKVGLQvaeplmvkegaSKTEALNRVKQVFRQVGLPPEYVDRYPHELSGGMKQRALVAMALIMQPRLIILD 175
                                       5666666666556777***99974444456666666666677799999***************************** PP

                                       STTT CS
                                       xxxx RF
                          ABC_tran 134 Epta 137
                                       Ept+
  gi|557693931|ref|YP_008796985.1| 176 EPTS 179
                                       **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 !   67.7   0.3   6.9e-22   9.5e-19       1      65 []     230     293 ..     230     293 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 6.9e-22
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE gps+k+++ plHPY+ +Ll+s+prl+ +++ l  i+g +psl++ ++GC+F+pRC+ + e+C
  gi|557693931|ref|YP_008796985.1| 230 VELGPSEKILRTPLHPYSSKLLSSTPRLKGPRK-LDYIPGAPPSLTDPPTGCRFHPRCHRVFEKC 293
                                       8***************************99999.******************************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 ?    0.7   0.1      0.27   3.7e+02       3      19 ..      35      51 ..      34      77 .. 0.69
   2 !   39.2   0.0     5e-13     7e-10     220     302 ..     134     214 ..      77     215 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.27
                            AAA_21  3 vliGpNgsGKSnLLdal 19
                                      +l+G  g+GK++   a 
  gi|557693931|ref|YP_008796985.1| 35 GLVGESGCGKTSTGLAV 51
                                      69*********976665 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 5e-13
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvilt 295
                                       +     ++ + ++ ++elS G+k+ + ++ al+ ++   +l+++DEp + L+ ++++ ++ +lk+l+r +g   i+ 
  gi|557693931|ref|YP_008796985.1| 134 FRQVGLPPEYVDRYPHELSGGMKQRALVAMALIMQP---RLIILDEPTSALDVSIQTQIMNMLKRLKReHGLSMIFI 207
                                       555556677888999**********56666666555...************************888888******** PP

                            AAA_21 296 THSplll 302
                                       TH+  l+
  gi|557693931|ref|YP_008796985.1| 208 THDLALV 214
                                       ***9997 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 !   22.9   0.2   3.5e-08   4.8e-05     116     209 ..     123     221 ..      27     230 .. 0.64

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.5e-08
                                       EEE-HHHHHHHHHCTT-STT.......CS-HH..HHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx.......xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 116 kevtkkevsellesagiske.......lLSgG..ektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaell 183
                                       k+   + v+++++++g+ +e       +LSgG  +++Lva+aL+     ++p+ l +lDe  +aLD +  +++ ++l
  gi|557693931|ref|YP_008796985.1| 123 KTEALNRVKQVFRQVGLPPEyvdryphELSGGmkQRALVAMALI-----MQPR-LIILDEPTSALDVSIQTQIMNML 193
                                       333446677777777777777777777*****666789999999.....4554.89********************* PP

                                       HHHCTT..SEEEEE-SSHHHCCC-SCEE CS
                                       xxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 184 kekskn..aQfivislreemlekadklv 209
                                       k+ + +    +i i+++  ++++    +
  gi|557693931|ref|YP_008796985.1| 194 KRLKREhgLSMIFITHDLALVSDIADDI 221
                                       *665553488999999988887764444 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   0.00093       1.3       8      29 ..      34      55 ..      28      89 .. 0.83
   2 !   13.6   0.0   4.6e-05     0.063      50     128 ..     123     207 ..     110     213 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00093
                            AAA_22  8 lvvtGesGtGKTtllrrlleql 29
                                      l ++GesG+GKT +   +++ l
  gi|557693931|ref|YP_008796985.1| 34 LGLVGESGCGKTSTGLAVMRML 55
                                      6689*********999888887 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 4.6e-05
                            AAA_22  50 stsskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr...seealeeLrsllnl 118
                                       +t+  +  ++++r++gl+ ++     +el   + ++al a a    ++l+i+DE    l+   + ++++ L++l   
  gi|557693931|ref|YP_008796985.1| 123 KTEALNRVKQVFRQVGLPPEYVDRYPHELSgGMKQRALVAMALimqPRLIILDEPTSaLDvsiQTQIMNMLKRLKR- 198
                                       55666668999999999999944444555546666666666667779*********999896559999999999**. PP

                            AAA_22 119 srkgvqliLv 128
                                        ++g+++i++
  gi|557693931|ref|YP_008796985.1| 199 -EHGLSMIFI 207
                                       .*******98 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.21   2.8e+02      37      51 ..      33      47 ..      28      63 .. 0.82
   2 !   17.3   0.1   1.8e-06    0.0025     108     160 ..     157     207 ..     119     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.21
                              TniB 37 nlllvGdsnnGKtmi 51
                                       l lvG+s +GKt+ 
  gi|557693931|ref|YP_008796985.1| 33 ALGLVGESGCGKTST 47
                                      5679*********85 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.8e-06
                              TniB 108 eqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       +++ +++   +++r++i+DE  ++l   ++ q +++n+lk+L++e  ++++ +
  gi|557693931|ref|YP_008796985.1| 157 QRALVAMALIMQPRLIILDEPTSAL--DVSIQTQIMNMLKRLKREHGLSMIFI 207
                                       444455555689*************..7778999***************9987 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 !   15.8   0.4   1.1e-05     0.014       3      38 ..      36     143 ..      34     222 .. 0.57

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                                       EESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.......................................... CS
                               AAA   3 lyGppGtGKTllakavakelgvefleisgsellsk.......................................... 37 
                                       l+G  G+GKT++  av++ l  +++++ g+ l++                                           
  gi|557693931|ref|YP_008796985.1|  36 LVGESGCGKTSTGLAVMRMLPPNVVKLGGKILFEGidilsmnprdfaeeyqwrkismvfqgamnsfnpvlkvglqva 112
                                       89*****************9666555555555533344444444433335555555555555555555555555555 PP

                                       ..............................S CS
                               AAA  38 ..............................y 38 
                                                                     y
  gi|557693931|ref|YP_008796985.1| 113 eplmvkegasktealnrvkqvfrqvglppeY 143
                                       5555555555555555555555555555553 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 ?   11.5   0.2   6.9e-05     0.096     324     418 ..     152     231 ..     147     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.9e-05
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GC CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgd 400
                                       SG + q a ++ al ++ +l+++DE tsA    i+                 +++++++l +++g+s+i ++  +  
  gi|557693931|ref|YP_008796985.1| 152 SGGMKQRALVAMALIMQPRLIILDEPTSALDVSIQT---------------QIMNMLKRLKREHGLSMIFITHDLAL 213
                                       999999999999999999999999999998877733...............34567778888889999999888888 PP

                                       CTTT-SEEEEEETTEEEE CS
                        ABC_ATPase 401 yldvAdtvilmeeykpkd 418
                                         d+Ad + +m + k+ +
  gi|557693931|ref|YP_008796985.1| 214 VSDIADDIAVMYAGKVVE 231
                                       888888888887766655 PP

>> DUF3265  Protein of unknown function (DUF3265)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00012      0.16       9      25 ..      33      49 ..      32      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                           DUF3265  9 AVsFgvEvglrkfglag 25
                                      A+++++E+g++k + ++
  gi|557693931|ref|YP_008796985.1| 33 ALGLVGESGCGKTSTGL 49
                                      89**********88776 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.3       1.2   1.6e+03     110     134 ..       5      28 ..       1      29 [. 0.80
   2 ?    9.2   0.0   0.00066      0.92       3      42 ..      35      77 ..      33     104 .. 0.67
   3 ?   -0.3   0.0      0.53   7.3e+02       9      34 ..     120     145 ..     116     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.2
                               PRK 110 advlviEGlhalydervaelldlki 134
                                        d++v+ Gl + +++ v   +d+++
  gi|557693931|ref|YP_008796985.1|   5 MDLVVYYGLGGKVVKAVDG-VDFSV 28 
                                       589***********99854.67777 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00066
                               PRK  3 gvagsSGaGkttvarklekifgrekvkaaei....egdsflrld 42
                                      g+ g+SG+Gkt++  ++  ++  + vk  ++    eg+ +l+++
  gi|557693931|ref|YP_008796985.1| 35 GLVGESGCGKTSTGLAVMRMLPPNVVK-LGGkilfEGIDILSMN 77
                                      899**********99999998854444.3334556666666665 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.53
                               PRK   9 GaGkttvarklekifgrekvkaaeie 34 
                                       Ga kt   ++++++f+++++++ +++
  gi|557693931|ref|YP_008796985.1| 120 GASKTEALNRVKQVFRQVGLPPEYVD 145
                                       8999***************9998874 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.11   1.6e+02      37      52 ..      35      50 ..      27      67 .. 0.84
   2 ?    7.5   0.0     0.002       2.8     138     188 ..     164     209 ..     106     210 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.11
                            AAA_25 37 llaGapgtGKttlald 52
                                       l+G +g+GKt   l 
  gi|557693931|ref|YP_008796985.1| 35 GLVGESGCGKTSTGLA 50
                                      589********87665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.002
                            AAA_25 138 eevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                         + ++rl+++D  ++al+ + +     ++++++l+r++r++g   +++ H
  gi|557693931|ref|YP_008796985.1| 164 ALIMQPRLIILDEPTSALDVSIQ-----TQIMNMLKRLKREHGLSMIFITH 209
                                       34456999999999999999888.....9*******************999 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00023      0.31      33      86 ..     174     222 ..     169     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                                       HHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  33 rddeidrlekeiersllealakrqplaedlrellsllriardlERigDhavnia 86 
                                       +d+   +l   i+ +++++l++ +      +  ls++ i++dl  ++D a +ia
  gi|557693931|ref|YP_008796985.1| 174 LDEPTSALDVSIQTQIMNMLKRLKR-----EHGLSMIFITHDLALVSDIADDIA 222
                                       57777889999*********77554.....45699******************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 ?   10.2   0.0    0.0005      0.69      63      89 ..     168     194 ..     132     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                           SbcCD_C  63 alrlvfLDEAFsklDeesiatllelle 89 
                                       ++rl++LDE  s lD   +++++++l+
  gi|557693931|ref|YP_008796985.1| 168 QPRLIILDEPTSALDVSIQTQIMNMLK 194
                                       589*********************997 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:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2356.53
//
Query:       gi|557693932|ref|YP_008796986.1|  [L=466]
Description: peptide/nickel ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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   79.1  14.1    3.5e-22   79.1  14.1    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.073   13.0   0.1      0.073   13.0   0.1    3.1  3  OppC_N        N-terminal TM domain of oligopeptide transport 
        6.8    6.3   7.6        3.9    7.1   0.8    2.8  2  DUF4131       Domain of unknown function (DUF4131)


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 ?   -2.5   0.3      0.62   3.7e+03     157     171 ..      19      33 ..       6      39 .. 0.54
   2 !   79.1  14.1   5.8e-26   3.5e-22       1     185 []     278     464 ..     278     464 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.62
                      BPD_transp_1 157 gvlalviavlllnlv 171
                                       + ++l+i++l++++ 
  gi|557693932|ref|YP_008796986.1|  19 AGVVLLILYLVISVY 33 
                                       344455555555443 PP

  == domain 2  score: 79.1 bits;  conditional E-value: 5.8e-26
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilp.viillllsaapyvrlirraal 76 
                                       g llG+l++ + ++k+d ++++  ++l  +P + l+i+++       il  +i+  ++il+++++ ++++++r+ ++
  gi|557693932|ref|YP_008796986.1| 278 GSLLGMLSG-YIGGKTDTIIQRTCDILNNIPLLPLLIFFT------FILRPSIWIiIAILVAFGWSGLAIVVRNIVM 347
                                       679******.******************************......67887777769******************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       ++   ++ve a+  G++r +i+r++++P+++p +i++li++ ++++ + ++l+flg    lg++   +++g+ + ++
  gi|557693932|ref|YP_008796986.1| 348 QAKTAQFVESAESIGVPRGRILRRYIFPQIAPFLIAQLIFSTPSAILAEAALSFLG----LGDP-SLPSWGQILEYA 419
                                       ********************************************************....9976.557777777777 PP

                      BPD_transp_1 154 s.............nggvlalviavlllnlvadilqrlldprvrk 185
                                                       + + ++++ + ++ +++ l  +++pr+r+
  gi|557693932|ref|YP_008796986.1| 420 FrsggvnlglwwwvLPPGALIALLSFTFVMLSMGLEPVVSPRLRR 464
                                       77799********999999**********************9985 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 ?   13.0   0.1   1.2e-05     0.073       2      42 ..       3      48 ..       2      62 .. 0.69
   2 ?   -5.5   5.9         3   1.8e+04      21      30 ..     324     339 ..     322     390 .. 0.58
   3 ?   -3.1   0.3       1.4   8.2e+03      16      28 ..     438     450 ..     436     460 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                            OppC_N  2 lwqdawrrFkrNklAvvglvilllllliaifaPliaPydp.....q 42
                                      l    wr F++  +  +g v+l+l l+i+++  + +P d      +
  gi|557693932|ref|YP_008796986.1|  3 LSESSWRVFWSSNMSKAGVVLLILYLVISVYVVVSYPLDFgtrfwN 48
                                      55678*************************9644444333444441 PP

  == domain 2  score: -5.5 bits;  conditional E-value: 3
                            OppC_N  21 villlllli......a 30 
                                       +i++++l++      a
  gi|557693932|ref|YP_008796986.1| 324 WIIIAILVAfgwsglA 339
                                       4555554433444441 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.4
                            OppC_N  16 Avvglvillllll 28 
                                       A+++l  + ++ l
  gi|557693932|ref|YP_008796986.1| 438 ALIALLSFTFVML 450
                                       6666666666655 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.8   0.00066       3.9      12      53 ..     308     344 ..     304     369 .. 0.80
   2 ?    1.8   1.0     0.029   1.7e+02       3      23 ..     427     447 ..     425     465 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00066
                           DUF4131  12 lllllllllllllrrrprrrvllllllllllallgfalrapq 53 
                                       ll ll+++ ++l     r+ +++++++l +++++g+a+ +++
  gi|557693932|ref|YP_008796986.1| 308 LLPLLIFFTFIL-----RPSIWIIIAILVAFGWSGLAIVVRN 344
                                       555666666665.....8*****************9998776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.029
                           DUF4131   3 lplalvllallllllllllll 23 
                                       l+l++++l  ++l++ll + +
  gi|557693932|ref|YP_008796986.1| 427 LGLWWWVLPPGALIALLSFTF 447
                                       556666666666666555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3503.08
//
Query:       gi|557693933|ref|YP_008796987.1|  [L=106]
Description: hypothetical protein CSUB_C0496 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.0     0.0056   16.5   0.0    1.2  1  MarR_2     MarR family
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.019   14.9   0.1    1.3  1  MarR       MarR family
      0.012   15.4   0.0      0.017   15.0   0.0    1.2  1  TrmB       Sugar-specific transcriptional regulator TrmB
      0.024   14.7   0.0      0.037   14.1   0.0    1.3  1  z-alpha    Adenosine deaminase z-alpha domain
      0.026   14.5   0.0      0.045   13.7   0.0    1.4  1  HTH_Crp_2  Crp-like helix-turn-helix domain
      0.032   14.6   0.0      0.067   13.5   0.0    1.5  2  Rrf2       Transcriptional regulator
        0.1   12.5   0.0       0.13   12.1   0.0    1.1  1  SMC_Nse1   Nse1 non-SMC component of SMC5-6 complex


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 !   16.5   0.0   2.2e-06    0.0056       4      54 ..      16      65 ..      12      70 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.2e-06
                                      -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      t ++ rv   L+ ++ +  t  +la+ +gls +++ +il++L  + +v r 
  gi|557693933|ref|YP_008796987.1| 16 TYQHIRVVKTLAEHGKP-ATKYALAKFTGLSLQRLDKILRELITQRWVNRH 65
                                      678999999******98.7*****************************875 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   7.3e-06     0.019       2      49 ..      16      64 ..      15      68 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.3e-06
                                      -HHHHHHHHHHHHSTTEEHH.HHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  2 tltqfviLrilyeqgplsvs.eLakklgvskstvtrvldrLekkGlieR 49
                                      t+++++++ +l+e+g +  +  Lak+ g+s   + ++l++L+ + +++R
  gi|557693933|ref|YP_008796987.1| 16 TYQHIRVVKTLAEHGKPATKyALAKFTGLSLQRLDKILRELITQRWVNR 64
                                      7899***********966666**************************99 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   0.0   6.7e-06     0.017      13      63 ..      22      73 ..      16      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.7e-06
                                      HCHHHHHHC.CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                              TrmB 13 vYlaLlklg.patadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63
                                      v ++L ++g pat + +a+ +g++ ++  ++Lr+L+   +V+r   +p +Y+
  gi|557693933|ref|YP_008796987.1| 22 VVKTLAEHGkPATKYALAKFTGLSLQRLDKILRELITQRWVNRHSTTPPKYS 73
                                      556777554389************************************9996 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 ?   14.1   0.0   1.4e-05     0.037       8      64 ..      21      75 ..      15      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                                      HHHHHHHHC-TTCECCHHHHH..HHHCC-HHHHHHHHHHHHHTTSEEEESSSSEEEEE- CS
                           z-alpha  8 kilelLeelgekkaatalale..rgLstpkreiNrvLydlerkgkvyredgtPPlWflt 64
                                      ++++ L e g  k+at++al+   gLs   +   ++L +l  +  v r  +tPP  +l 
  gi|557693933|ref|YP_008796987.1| 21 RVVKTLAEHG--KPATKYALAkfTGLS--LQRLDKILRELITQRWVNRHSTTPPKYSLN 75
                                      7999999999..777766655116777..68899********************99886 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 ?   13.7   0.0   1.8e-05     0.045      21      53 ..      32      64 ..      12      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisr 53
                                      p t+  lA + Gl+ + + +il+eL  + ++ r
  gi|557693933|ref|YP_008796987.1| 32 PATKYALAKFTGLSLQRLDKILRELITQRWVNR 64
                                      889************************999985 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05     0.067      11      67 ..      20      74 ..      11      81 .. 0.80
   2 ?   -1.4   0.0       1.2   3.2e+03      38      55 ..      77      94 ..      72      96 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                                      HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEE CS
                              Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrL 67
                                      ++++  La++ +  p++  ++a+ +++s + l kil++L  + +v+        y+L
  gi|557693933|ref|YP_008796987.1| 20 IRVVKTLAEHGK--PATKYALAKFTGLSLQRLDKILRELITQRWVNRHSTTPPKYSL 74
                                      677777887777..89****************************9876655555555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.2
                                      -HHHHHHHHHHHHHTTSE CS
                              Rrf2 38 spsylekilakLrkaglv 55
                                        ++l k l+ L++a+++
  gi|557693933|ref|YP_008796987.1| 77 DNQMLGKFLTFLSEANYL 94
                                      567888999999999886 PP

>> SMC_Nse1  Nse1 non-SMC component of SMC5-6 complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     5e-05      0.13     147     186 ..      33      74 ..       7      76 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5e-05
                          SMC_Nse1 147 lsqeeaaadkgLtaseaeklLkrLveegWleksre..GfysL 186
                                       +++++ a+ +gL+ +  +k+L +L++++W ++ ++   +ysL
  gi|557693933|ref|YP_008796987.1|  33 ATKYALAKFTGLSLQRLDKILRELITQRWVNRHSTtpPKYSL 74 
                                       2223357899********************998763346665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 794.88
//
Query:       gi|557693934|ref|YP_008796988.1|  [L=379]
Description: archaeal cell division control protein 6 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   37.2   0.0    7.7e-09   35.9   0.0    1.6  1  AAA_22      AAA domain
    2.8e-06   27.4   0.0    5.1e-06   26.6   0.0    1.5  1  ATPase_2    ATPase domain predominantly from Archaea
      1e-05   26.0   1.9    0.00027   21.4   0.3    2.9  2  AAA_16      AAA ATPase domain
     0.0013   18.6   0.0       0.12   12.2   0.0    2.5  2  Bac_DnaA    Bacterial dnaA  protein
     0.0015   18.9   0.0     0.0031   17.9   0.0    1.5  1  AAA         ATPase family associated with various cellular ac
     0.0062   15.8   0.1      0.015   14.5   0.0    1.6  2  NB-ARC      NB-ARC domain
  ------ inclusion threshold ------
      0.013   15.6   0.1        4.8    7.4   0.0    2.6  2  TIP49_C     TIP49 AAA-lid domain
      0.019   14.8   0.0      0.037   13.8   0.0    1.5  1  ATP_bind_1  Conserved hypothetical ATP binding protein
      0.021   14.8   0.1      0.065   13.2   0.0    1.9  2  Cdc6_C      CDC6, C terminal winged helix domain
      0.025   14.5   0.0      0.047   13.6   0.0    1.4  1  NACHT       NACHT domain
      0.036   13.8   0.0      0.074   12.8   0.0    1.5  1  RuvB_N      Holliday junction DNA helicase RuvB P-loop domain
      0.061   13.6   1.2         12    6.1   0.1    2.9  4  TFIID_NTD2  WD40 associated region in TFIID subunit, NTD2 dom
      0.061   13.9   0.0       0.14   12.7   0.0    1.6  1  AAA_18      AAA domain
      0.079   12.2   0.0       0.17   11.2   0.0    1.6  1  Zeta_toxin  Zeta toxin
        0.1   13.1   0.0       0.21   12.1   0.0    1.6  1  ABC_tran    ABC transporter
       0.17   11.6   0.1       0.46   10.2   0.0    1.7  2  PduV-EutP   Ethanolamine utilisation - propanediol utilisatio


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 !   35.9   0.0   6.9e-12   7.7e-09      10     117 ..      52     161 ..      50     177 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 6.9e-12
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsst.sskdllrellralglelkaerlsseellealeq 84 
                                       v+G++G+GKTtl+ +  ++ ++     +++ +   +v+l   t s  +++r l++ + +e+ +  ls eelle l +
  gi|557693934|ref|YP_008796988.1|  52 VVGPVGAGKTTLCLMAGQEMQRK----HRNLT-HaYVNLRRFTsSKVSIYRYLVKSVAEEAYSVSLSAEELLENLLH 123
                                       89**************9998532....23444.36********999999**************************** PP

                            AAA_22  85 alraravielliiDEaqh.lr.s...eealeeLrslln 117
                                        l++++ + ++  D+a++ ++ s   e+++ ++ +l++
  gi|557693934|ref|YP_008796988.1| 124 FLKNTGQRLIITFDDADYhVSmSrgrETVVYDFTRLHE 161
                                       *******99999*****977562455666666666555 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 !   26.6   0.0   4.5e-09   5.1e-06       4     202 ..      24     214 ..      21     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.5e-09
                          ATPase_2   4 Rekelkeleeile....repneiy...fiYGpegsGKtaLlkeiienledkdk.yviyyialreesiskldefieee 72 
                                       Reke + l++ le    r+ + +y    + Gp g GKt+L   + ++ + k+      y +lr+  +sk++ +    
  gi|557693934|ref|YP_008796988.1|  24 REKEFSLLRKFLEagveRGDDVFYsrvQVVGPVGAGKTTLCLMAGQEMQRKHRnLTHAYVNLRRFTSSKVSIY---- 96 
                                       666665555555411113344333221588**********999999986555525555678999999999998.... PP

                          ATPase_2  73 eekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnli 149
                                          ++l k ++++  +++l          +++ +e+ll  +k++g+++ii +D++ + +++  +g e +v+++ +l 
  gi|557693934|ref|YP_008796988.1|  97 ---RYLVKSVAEEAYSVSL---------SAEELLENLLHFLKNTGQRLIITFDDADYHVSMS-RGRETVVYDFTRLH 160
                                       ...8899999888899888.........7899***************************665.88********9998 PP

                          ATPase_2 150 esl.tkekhlcvviclsSeglfiervyneselegrhkyilvddldketalnflk 202
                                       e    +  ++  v+  s e+    ++++  +    ++ + +++ ++e+  ++l 
  gi|557693934|ref|YP_008796988.1| 161 EFSsVRPLNVLGVVFVSRESGYGGYLDRAETSSLGASVLRLEPYTREQLIDILA 214
                                       854044566777777777777777777776666666666666666666666655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.3   2.4e-07   0.00027       1     145 [.      20     140 ..      20     167 .. 0.72
   2 ?   -0.4   0.1       1.2   1.4e+03      77     144 ..     205     274 ..     184     320 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 2.4e-07
                            AAA_16   1 rlvGReeeleqLlsale.rvrsgrp...elvllsGesGvGKsslvrellralekd.....ggiflrgkcdqlesaip 68 
                                       rl  Re+e + L+  le  v +g+    + v ++G+ G GK++l  ++ ++++++     ++++   +++++     
  gi|557693934|ref|YP_008796988.1|  20 RLLHREKEFSLLRKFLEaGVERGDDvfySRVQVVGPVGAGKTTLCLMAGQEMQRKhrnltHAYVNLRRFTSS----- 91 
                                       5788*************777777779*******************999999999976666666666666666..... PP

                            AAA_16  69 ysalaqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlq 145
                                                + +++r l       + ea++  l +            a+ lle l ++l   +++++ l++++Dd++
  gi|557693934|ref|YP_008796988.1|  92 ---------KVSIYRYLVKS---VAEEAYSVSL-S------------AEELLENLLHFL---KNTGQRLIITFDDAD 140
                                       .........33555555544...1222333321.1............134555555555...555556999999998 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.2
                            AAA_16  77 areellrqllde.aesaeleawrekleealaavpelagaea.srllellkrll.allsrderplvlvlDdl 144
                                       +re+l+  l+d+ +e+  ++a ++   e +a+v + ++ +   rl+  l   + +l+++d+r  v+ +Dd+
  gi|557693934|ref|YP_008796988.1| 205 TREQLIDILADRvSEAFVRGAVPDNVVEYVADVVSKPPYSGdVRLALDLLLYAgNLAENDGR-DVVKVDDV 274
                                       46666666666644444455555555555554444444433466666666666566666555.56666665 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00011      0.12      35      84 ..      48      97 ..      39     136 .. 0.85
   2 ?    3.6   0.0     0.045        50     161     199 ..     199     239 ..     187     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                                      --EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHH CS
                          Bac_DnaA 35 nPlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalr 84
                                        + + g+vG Gkt L   +g+e+++++++l   Y++  +F+++ v++ r
  gi|557693934|ref|YP_008796988.1| 48 SRVQVVGPVGAGKTTLCLMAGQEMQRKHRNLTHAYVNLRRFTSSKVSIYR 97
                                      5567889***********************************99998765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.045
                                       EE-----HHHHHHHHHHHHHHTT--..--TTHHHHHHHH-- CS
                          Bac_DnaA 161 vdieppdletrlailkkkieaekle..vpeevlefiaervt 199
                                         +ep  +e  ++il  +++++ +   vp++v+e++a+ v+
  gi|557693934|ref|YP_008796988.1| 199 LRLEPYTREQLIDILADRVSEAFVRgaVPDNVVEYVADVVS 239
                                       57899999999********99987777**********9886 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 !   17.9   0.0   2.8e-06    0.0031       3      74 ..      52     146 ..      50     164 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
                                       EESSTTSSHHHHHHHHHHHHTHE.....EEEEETTTCSSS..................STTHHHHHHHHHHHHHHHT CS
                               AAA   3 lyGppGtGKTllakavakelgve.....fleisgsellsk..................yvgesekkirelfkeakek 56 
                                       ++Gp G GKT+l+    +e++++        +++ +++s+                  +   +e+ +++l+  +k+ 
  gi|557693934|ref|YP_008796988.1|  52 VVGPVGAGKTTLCLMAGQEMQRKhrnltHAYVNLRRFTSSkvsiyrylvksvaeeaysVSLSAEELLENLLHFLKNT 128
                                       79*****************9533333334555555555333566666666666667656667777788888877777 PP

                                       STSEEEEEETGGGHHHHH CS
                               AAA  57 akpsilfiDEidalaksr 74 
                                        +  i+ +D++d  ++ +
  gi|557693934|ref|YP_008796988.1| 129 GQRLIITFDDADYHVSMS 146
                                       6569******99877766 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.3e-05     0.015      22     111 ..      49     138 ..      30     145 .. 0.72
   2 ?   -2.7   0.0       2.3   2.6e+03      67      88 ..     299     320 ..     295     329 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                       EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEEEEEES.XXHHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHH CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFdsvawvvvsk.tdkseeiletilkeLslseddleekeeveslkrklv 97 
                                        v +vG  G GKttl   + ++  + ++r   +a+v + + t+++ +i + ++k + ++     + + +e l ++l 
  gi|557693934|ref|YP_008796988.1|  49 RVQVVGPVGAGKTTLCLMAGQE-MQRKHRNLTHAYVNLRRfTSSKVSIYRYLVKSVAEEAYS-VSLSAEE-LLENLL 122
                                       589************9888888.444444446777777662344456777777777555333.3333344.899999 PP

                                       HHCCCT..TEEEEEEE CS
                            NB-ARC  98 rlLltk..rfllvlDD 111
                                       ++L++   r ++ +DD
  gi|557693934|ref|YP_008796988.1| 123 HFLKNTgqRLIITFDD 138
                                       9999888899999**9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                                       HHHHXXHHHHHCCCTTSSSS-S CS
                            NB-ARC  67 eiletilkeLslseddleekee 88 
                                        +l +i+k+L+++++++ e +e
  gi|557693934|ref|YP_008796988.1| 299 AVLLSIAKVLQRRDEQTAELKE 320
                                       5667788888888777666554 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0043       4.8      31      60 ..     248     277 ..     231     279 .. 0.91
   2 ?    5.5   0.1     0.017        19      36      65 ..     301     329 ..     299     330 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0043
                           TIP49_C  31 RYaiqLltpasilakkrkkkevevedveev 60 
                                       R a+ Ll  a  la+  +++ v+v+dv+ +
  gi|557693934|ref|YP_008796988.1| 248 RLALDLLLYAGNLAENDGRDVVKVDDVRYA 277
                                       899************************865 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.017
                           TIP49_C  36 LltpasilakkrkkkevevedveeveeLFl 65 
                                       Ll++a++l ++r +++ e+++++e+ +LF 
  gi|557693934|ref|YP_008796988.1| 301 LLSIAKVL-QRRDEQTAELKEIREMFSLFC 329
                                       9999**99.8888999*************6 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 ?   13.8   0.0   3.3e-05     0.037       1      32 [.      52      85 ..      52      88 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.3e-05
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsv..avvNL 32
                                      vvGp+G+GKtt++    + ++ + r++  a+vNL
  gi|557693934|ref|YP_008796988.1| 52 VVGPVGAGKTTLCLMAGQEMQRKHRNLthAYVNL 85
                                      89***********999999988776642267887 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 ?   -3.0   0.0       6.5   7.2e+03      33      47 ..     200     214 ..     196     217 .. 0.81
   2 ?   13.2   0.0   5.8e-05     0.065       1      46 [.     301     346 ..     301     375 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.5
                                       T-----HHHHHHHHH CS
                            Cdc6_C  33 gvdpltqrevsdlls 47 
                                        ++p t+++  d+l+
  gi|557693934|ref|YP_008796988.1| 200 RLEPYTREQLIDILA 214
                                       689999999999987 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 5.8e-05
                                       HHHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHH CS
                            Cdc6_C   1 LcalvlllrksgkeevttgevyevYkslCesegvdpltqrevsdll 46 
                                       L++++++l+++++ ++ ++e+ e+++  Ces g++       +++l
  gi|557693934|ref|YP_008796988.1| 301 LLSIAKVLQRRDEQTAELKEIREMFSLFCESHGLSESGFDKALSYL 346
                                       89*****************************998554444444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   4.2e-05     0.047       3      95 ..      50     144 ..      48     162 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                                       EEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C........ CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse........ 71 
                                       v + G+ G GKTtL     +++++++ +        +++lr+++ s+ + s+ ++l++   e+a  vs         
  gi|557693934|ref|YP_008796988.1|  50 VQVVGPVGAGKTTLCLMAGQEMQRKHRNL----THAYVNLRRFTSSK-V-SIYRYLVKSVAEEAYSVSLsaeellen 120
                                       6799*********9877777777777554....56789999999987.4.788888888888887777766667776 PP

                                       CHHHHCCSCCCEEEEEE-STT-SS CS
                             NACHT  72 vwavllelperlLlilDglDelvt 95 
                                          +l    +rl +++D++D+ v+
  gi|557693934|ref|YP_008796988.1| 121 LLHFLKNTGQRLIITFDDADYHVS 144
                                       8888888888899*******9876 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 ?   12.8   0.0   6.6e-05     0.074      19      63 ..      31      77 ..      15      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.6e-05
                            RuvB_N 19 lkifieaakkreeal..dhvllyGpPGlGkttlakiiakelgvklki 63
                                      l+ f+ea  +r++ +    v ++Gp G Gkttl+ +  +e++ k + 
  gi|557693934|ref|YP_008796988.1| 31 LRKFLEAGVERGDDVfySRVQVVGPVGAGKTTLCLMAGQEMQRKHRN 77
                                      6667888888887652367999*******************998775 PP

>> TFIID_NTD2  WD40 associated region in TFIID subunit, NTD2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.5   8.4e+03       8      19 ..      25      36 ..      23      40 .. 0.67
   2 ?    6.1   0.1     0.011        12       3      31 ..      74     102 ..      72     104 .. 0.87
   3 ?    6.0   0.1     0.012        13      91     123 ..     101     134 ..      98     137 .. 0.83
   4 ?   -1.3   0.0       2.1   2.3e+03      90     114 ..     133     157 ..     130     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.5
                                      HHHHHHHHHHHH CS
                        TFIID_NTD2  8 ekayelLkkwie 19
                                      ek+++lL+k++e
  gi|557693934|ref|YP_008796988.1| 25 EKEFSLLRKFLE 36
                                      566777777766 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                                       XXHHHHHHHHHHHHHHHTS-HHHHHHHGG CS
                        TFIID_NTD2   3 dpekyekayelLkkwiessldiykpeLsr 31 
                                       +++++++ay +L+++ +s  +iy++ +++
  gi|557693934|ref|YP_008796988.1|  74 KHRNLTHAYVNLRRFTSSKVSIYRYLVKS 102
                                       678999******************87765 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.012
                                       HHHHHS-EEEEEEH.HHHHHHHHHHHHTT-HHHH CS
                        TFIID_NTD2  91 kafrenkyriklsk.aafelLlrfLeekekavll 123
                                       k+  e+ y+++ls  + +e+Ll+fL+++ + +++
  gi|557693934|ref|YP_008796988.1| 101 KSVAEEAYSVSLSAeELLENLLHFLKNTGQRLII 134
                                       6677899*****962678**********999876 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 2.1
                                       HHHHHHS-EEEEEEHHHHHHHHHHH CS
                        TFIID_NTD2  90 akafrenkyriklskaafelLlrfL 114
                                       + +f++  y++++s+   +   +f 
  gi|557693934|ref|YP_008796988.1| 133 IITFDDADYHVSMSRGRETVVYDFT 157
                                       66899999*****998777776665 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   0.00012      0.14       3      70 ..      52     144 ..      50     179 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                            AAA_18   3 ltGtpGvGKttlakeL....skrl.gf..................gvnlrdvakenglllevdpealdeskrldedk 56 
                                       + G+ G+GKttl+       ++++ ++                   + +++va e +++    +e l++ + + ++ 
  gi|557693934|ref|YP_008796988.1|  52 VVGPVGAGKTTLCLMAgqemQRKHrNLthayvnlrrftsskvsiyRYLVKSVAEEAYSVSLSAEELLENLLHFLKNT 128
                                       89***********8775444444434488889999666666666666666666666666666666444444444444 PP

                            AAA_18  57 ldklldaleenss..a 70 
                                        ++l+ +++ ++   +
  gi|557693934|ref|YP_008796988.1| 129 GQRLIITFDDADYhvS 144
                                       4444444444444553 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   0.00015      0.17      19      97 ..      50     131 ..      48     154 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                        Zeta_toxin  19 illgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeyeeilk...adpkkaseltqkdaselvekllqea 91 
                                       ++++G  GAGK++l  ++ +e++ +++n  +    +lR++     +i++   + +++ +  ++  a el e+ll  +
  gi|557693934|ref|YP_008796988.1|  50 VQVVGPVGAGKTTLCLMAGQEMQrKHRNL-THAYVNLRRFTSSKVSIYRylvKSVAEEAYSVSLSAEELLENLLHFL 125
                                       68999******************545554.44444566666555666654444555555555666666666666555 PP

                        Zeta_toxin  92 iengyn 97 
                                        + g+ 
  gi|557693934|ref|YP_008796988.1| 126 KNTGQR 131
                                       555555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00019      0.21      13      36 ..      49      72 ..      47     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00019
                                      EEEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllk 36
                                      +v++vG+ GaGK+tL+ +  ++++
  gi|557693934|ref|YP_008796988.1| 49 RVQVVGPVGAGKTTLCLMAGQEMQ 72
                                      799************966555444 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   0.0   0.00041      0.46       3      27 ..      49      72 ..      47      85 .. 0.78
   2 ?   -2.1   0.0       2.6   2.9e+03     114     142 ..      98     126 ..      89     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00041
                         PduV-EutP  3 killiGkvgsGKttLtqalkgeelk 27
                                      ++ ++G+vg+GKttL+  + g+e++
  gi|557693934|ref|YP_008796988.1| 49 RVQVVGPVGAGKTTLCL-MAGQEMQ 72
                                      7899************5.4556555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                         PduV-EutP 114 lLksaGaekifevsavekegieellkyle 142
                                       +L +  ae+ ++vs   +e +e+ll++l+
  gi|557693934|ref|YP_008796988.1|  98 YLVKSVAEEAYSVSLSAEELLENLLHFLK 126
                                       56666789999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 2706.64
//
Query:       gi|557693935|ref|YP_008796989.1|  [L=88]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   42.9   0.0    4.1e-11   42.7   0.0    1.1  1  GYD             GYD domain
  ------ inclusion threshold ------
      0.011   15.7   0.0      0.016   15.2   0.0    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
      0.049   13.8   0.0       0.38   11.0   0.0    2.0  2  FlaG            FlaG protein


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 !   42.7   0.0   6.9e-15   4.1e-11      18      89 ..      14      83 ..       7      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 6.9e-15
                               GYD 18 sperreeakealveslGgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrtetlrafteeefde 89
                                      ++e++++  + ++e+  +k++++ +t+G+yD + + EapD et  ++ l+ + +  ++tetl af++e++ +
  gi|557693935|ref|YP_008796989.1| 14 TKEDVDRTDRIIRENPSVKVREMLWTFGHYDGILVAEAPDAETYLKFILQFTDY--LSTETLAAFPREQALK 83
                                      5788999999999999***********************************998..7***********9876 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 ?   15.2   0.0   2.6e-06     0.016       3      70 ..       7      73 ..       5      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-06
                                      EEE-GGG..TTHHHHHHHHHHTSTT..EEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEE CS
                    AsnC_trans_reg  3 vslepgh..peqleefeealaelpe..VvecyrvtGdydyllkvvvrdlealerflreklaslpgvartets 70
                                      ++ + ++  +e++++  + ++e p   V+e   + G yd +l + ++d e + +f    + +  ++ +tet+
  gi|557693935|ref|YP_008796989.1|  7 IRFK-KKltKEDVDRTDRIIRENPSvkVREMLWTFGHYDGILVAEAPDAETYLKF----ILQFTDYLSTETL 73
                                      5666.44578889999999999886225799************************....8888888888886 PP

>> FlaG  FlaG protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.3e-05      0.38      71     101 .]      20      50 ..      18      50 .. 0.93
   2 ?    0.7   0.0     0.099   5.9e+02      68      88 ..      65      85 ..      55      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.3e-05
                                       TT-SEEEEE-HHHHHHHHHHHHHHHHHHS-T CS
                              FlaG  71 etgevIrqiPseevldlakklkelaGllvde 101
                                        t+++Ir+ Ps +v +++  +  + G+lv e
  gi|557693935|ref|YP_008796989.1|  20 RTDRIIRENPSVKVREMLWTFGHYDGILVAE 50 
                                       69**************************975 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.099
                                      EETTT-SEEEEE-HHHHHHHH CS
                              FlaG 68 iDketgevIrqiPseevldla 88
                                      +D  + e++  +P e++l+la
  gi|557693935|ref|YP_008796989.1| 65 TDYLSTETLAAFPREQALKLA 85
                                      566677888899******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 661.64
//
Query:       gi|557693936|ref|YP_008796990.1|  [L=97]
Description: hypothetical protein CSUB_C0499 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   12.5   0.0        0.2   11.9   0.0    1.3  1  DUF5495   Family of unknown function (DUF5495)


Domain annotation for each model (and alignments):
>> DUF5495  Family of unknown function (DUF5495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.1e-05       0.2      21      39 ..      33      51 ..      23      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.1e-05
                           DUF5495 21 igltqiegngfileyefsq 39
                                      +g+ +iegn file ef  
  gi|557693936|ref|YP_008796990.1| 33 VGVGRIEGNRFILEEEFVA 51
                                      7999************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 756.76
//
Query:       gi|557693937|ref|YP_008796991.1|  [L=392]
Description: FAD dependent oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-62  209.8   0.3    9.6e-62  209.6   0.3    1.0  1  DAO             FAD dependent oxidoreductase
    3.9e-07   29.6   0.3     0.0016   17.7   0.0    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.8e-06   27.1   1.2     0.0013   17.6   0.8    2.1  2  Trp_halogenase  Tryptophan halogenase
    6.3e-06   25.8   0.3      0.021   14.2   0.2    2.1  2  FAD_oxidored    FAD dependent oxidoreductase
      5e-05   22.6   0.4    0.00012   21.5   0.2    1.7  2  Thi4            Thi4 family
    9.5e-05   21.7   0.7    0.00015   21.0   0.4    1.5  2  FAD_binding_2   FAD binding domain
     0.0003   20.9   1.0    0.00081   19.6   1.0    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00032   20.1   0.0       0.27   10.4   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0033   16.7   1.2      0.012   14.8   0.8    1.9  2  FAD_binding_3   FAD binding domain
     0.0037   16.0   0.3        1.5    7.4   0.2    2.1  2  HI0933_like     HI0933-like protein
     0.0059   16.0   0.2       0.39   10.0   0.0    2.2  2  GMC_oxred_N     GMC oxidoreductase
  ------ inclusion threshold ------
       0.02   15.4   0.6      0.077   13.6   0.3    2.0  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.043   12.9   0.5      0.079   12.0   0.5    1.4  1  GIDA            Glucose inhibited division protein A
      0.045   13.1   0.1      0.081   12.3   0.1    1.3  1  ThiF            ThiF family
       0.13   12.5   0.5       0.51   10.6   0.2    2.0  2  TrkA_N          TrkA-N domain
       0.19   11.7   1.5        1.8    8.5   0.1    2.1  2  NAD_binding_9   FAD-NAD(P)-binding
       0.26   11.1   0.3       0.55   10.1   0.3    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD 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 !  209.6   0.3   9.1e-65   9.6e-62       1     351 [.       4     356 ..       4     357 .. 0.88

  Alignments for each domain:
  == domain 1  score: 209.6 bits;  conditional E-value: 9.1e-65
                                       EEEEECTSHHHHHHHHHHHHTT...EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg...VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleee 74 
                                       dvv++GGG +G+s+Ay+La rg   V+l+ek+ ++g+g++gr++++++ ++++ p    l +++le+++ lr +e+ 
  gi|557693937|ref|YP_008796991.1|   4 DVVVVGGGSTGSSIAYYLASRGagkVALVEKQ-RVGWGQTGRSTAVVRLHYSTEP----LIKMALESWKILRNMEKV 75 
                                       9******************99888********.****************887444....55**************** PP

                                       HSSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..STTTSEEEEETTEEEEEHHHHH CS
                               DAO  75 lgididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa..lpgllgalfypdtgqvdpaklt 149
                                        g + ++ + G l+ a ++e+l++l+++++l++++g++++ll +eevre+ p+  ++ l++a ++p +g +dp   +
  gi|557693937|ref|YP_008796991.1|  76 VGGPSGFTEVGFLIFA-GHEDLNGLKRNVELQKKLGVETRLLGPEEVREILPQtsTDSLAAAAYEPFSGYADPVTTA 151
                                       9999***********9.6668***********99******************9755488899*************** PP

                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT.CTTTSEEEEEEEE CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gll.keldlpispvrgq 223
                                       + +a+aa + Gv +le +ev ++++++ ++ g+  +t+ g   +ad +Vna+G+w + + +++  ++  p++  + +
  gi|557693937|ref|YP_008796991.1| 152 QTYASAAVREGVALLEDCEVHSVRRDGRRILGL--ETSkGLL-EADVIVNATGVWCNRFfEMTgVQM--PVKIYKEE 223
                                       ***********************9988899999..7777986.569***********5558887666..9999**** PP

                                       EEEEEECCT.HSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSE.........EETTCSSTSCSHHHHHHHHH CS
                               DAO 224 vlvlkplse.klvspaailpvpetdddgrgvyvtprkdgrvlvGgtad.........eesgdddpevdeedidelle 290
                                       ++v k++s  +        p  +  d    +y++p  + ++++G+            ++++ +  +v  e + ++ e
  gi|557693937|ref|YP_008796991.1| 224 IVVWKRPSSfEG-----NHP--VVGDLPNNYYMRPAGETQTYMGSINPdlsnprryaTDFDLE-ERVGIETATRYGE 292
                                       ****66555122.....233..477888899*****999****99766899988854444444.599999******* PP

                                       HHHHHSGGGCG..EEEEEEEEEE.ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                               DAO 291 alrklfPqlgd..vlrkwaGlrp.lpdglpligetpgvkglylatGhsghGltlapatGkllae 351
                                       a++k+fP  ++  ++  w+Gl++ +pd lp+ig +  v++l+ a G sghG++l+pa+G l+++
  gi|557693937|ref|YP_008796991.1| 293 AVSKRFPVMAEagFVGGWVGLYDvTPDWLPVIGFSQDVENLFNAVGMSGHGFKLCPAIGILASD 356
                                       ********75623667*******77*********88999********************99877 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 !   17.7   0.0   1.5e-06    0.0016       1      37 [.       3      38 ..       3     127 .. 0.78
   2 !   10.1   0.0   0.00032      0.34     186     252 ..     151     215 ..     144     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.5e-06
                                      CSEEEE--SHHHHHHHHHHHH.HTS-EEEEETTHCHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaq.agakvtlvelegtcln 37
                                      +dvvv+GgG  G + a +la    +kv+lve++   ++
  gi|557693937|ref|YP_008796991.1|  3 FDVVVVGGGSTGSSIAYYLASrGAGKVALVEKQ--RVG 38
                                      589999999999999999999558899999533..233 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 186 saaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglel 252
                                       +++++ a  +eGv++   ++v+ ++++g+++   ++++  ++ad +v a+Gv  ++ +  e  g+++
  gi|557693937|ref|YP_008796991.1| 151 AQTYASAAVREGVALLEDCEVHSVRRDGRRILGLETSKGLLEADVIVNATGVWCNRFF--EMTGVQM 215
                                       57788888899*****************977766666777************999755..5555544 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.8   1.3e-06    0.0013       1      45 [.       4      46 ..       4      55 .. 0.93
   2 !    7.8   0.0    0.0012       1.3     156     209 ..     150     202 ..     125     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeat 45
                                      ++v+vGGG+ G+  A +la  + g  +v lve++ +g  + G++t
  gi|557693937|ref|YP_008796991.1|  4 DVVVVGGGSTGSSIAYYLASRGAG--KVALVEKQRVGWGQTGRST 46
                                      69******************9966..9****************98 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGG CS
                    Trp_halogenase 156 yakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGf 209
                                        a+     a ++Gv  +e++ v+ + ++  r+ +l++++g  +ead ++ ++G 
  gi|557693937|ref|YP_008796991.1| 150 TAQTYASAAVREGVALLEDCEVHSVRRDGRRILGLETSKGL-LEADVIVNATGV 202
                                       56666788999**********9999999*********9998.**********96 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2     2e-05     0.021       1      36 [.       4      40 ..       4      71 .. 0.86
   2 !    9.7   0.0   0.00046      0.49      83     144 ..     144     201 ..     110     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGa.kvlLveergvlGG 36
                                      DvvVvGGg+ G   A+  a +Ga kv+Lve+++v  G
  gi|557693937|ref|YP_008796991.1|  4 DVVVVGGGSTGSSIAYYLASRGAgKVALVEKQRVGWG 40
                                      9***********999999999988******9987555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00046
                      FAD_oxidored  83 tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                         +p + ++++     ++gv +l ++++++v+++g+ri ++++     +  ++A+v++ ATg
  gi|557693937|ref|YP_008796991.1| 144 YADPVTTAQTYASAAVREGVALLEDCEVHSVRRDGRRILGLETS----KGLLEADVIVNATG 201
                                       567777777777777666*****************99******5....799**********8 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   1.1e-07   0.00012      18      50 ..       3      35 ..       1      47 [. 0.86
   2 ?   -2.8   0.0       2.8   2.9e+03     157     167 ..     191     201 ..     149     211 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.1e-07
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailers 50
                                       Dvv+vG+Gs+G + ayyla +   kva++e++
  gi|557693937|ref|YP_008796991.1|  3 FDVVVVGGGSTGSSIAYYLASRGAGKVALVEKQ 35
                                      7*********************999*****975 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.8
                                       EEEEEEEE--G CS
                              Thi4 157 irakvvvdatG 167
                                       ++a v+v+atG
  gi|557693937|ref|YP_008796991.1| 191 LEADVIVNATG 201
                                       45556666665 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.4   1.4e-07   0.00015       1      46 [.       4      50 ..       4      67 .. 0.90
   2 ?   -2.9   0.0       2.5   2.6e+03      84     105 ..     153     175 ..     127     205 .. 0.56

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                                      SEEEE--SHHHHHHHHHHHHTTT.-EEEEESSSGGGSGGGG--S-EE CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGl.kvavvekeqefggatawsqGgid 46
                                      Dv+V+G+G  G + A+ +a +G+ kva+vek  +  g+t  s + + 
  gi|557693937|ref|YP_008796991.1|  4 DVVVVGGGSTGSSIAYYLASRGAgKVALVEKQRVGWGQTGRSTAVVR 50
                                      9*******************************998889988877665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.5
                                       HHHH.THHHHHHHHHHTT----B CS
                     FAD_binding_2  84 afve.aapeavdeLeelgvpfsr 105
                                       ++++ a++e v+ Le++ v   r
  gi|557693937|ref|YP_008796991.1| 153 TYASaAVREGVALLEDCEVHSVR 175
                                       33333444444444444333333 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 !   19.6   1.0   7.7e-07   0.00081       1      31 [.       7      37 ..       7      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.7e-07
                                      EE--SHHHHHHHHHHHCCTE.EEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllekrdrl 31
                                      +vG+G +G+++Ay+La +g+ +v l+ek+ r+
  gi|557693937|ref|YP_008796991.1|  7 VVGGGSTGSSIAYYLASRGAgKVALVEKQ-RV 37
                                      8*******************9*******8.44 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 !    7.5   0.0     0.002       2.1       1      33 [.       6      38 ..       2      75 .. 0.62
   2 !   10.4   0.0   0.00026      0.27      83     135 ..     150     203 ..     112     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.002
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                      +++G+G  G ++a+ l   g  ++  +Ek+++g
  gi|557693937|ref|YP_008796991.1|  6 VVVGGGSTGSSIAYYLASRGAGKVALVEKQRVG 38
                                      355555555555555555555555555555544 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00026
                       Pyr_redox_3  83 aleYlrevaksfelpiklfeeVesvkke.degfevetsketyeAkkviiAtGef 135
                                        ++ +++ a ++ +   +++eV sv ++ ++   +etsk+ +eA+ ++ AtG +
  gi|557693937|ref|YP_008796991.1| 150 TAQTYASAAVREGVALLEDCEVHSVRRDgRRILGLETSKGLLEADVIVNATGVW 203
                                       455666777778999999*********7256699******************86 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.8   1.2e-05     0.012       2      34 ..       3      36 ..       2      49 .. 0.87
   2 ?   -0.3   0.0      0.46   4.8e+02      50     137 ..     103     180 ..      98     225 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                                      EEEEEE--SHHHHHHHHHHHHTTHH.EEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvr.vvlvekrs 34
                                       dV++VG+G +G + a  L+++G   v lvek++
  gi|557693937|ref|YP_008796991.1|  3 FDVVVVGGGSTGSSIAYYLASRGAGkVALVEKQR 36
                                      69*********************97699999987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.46
                                       HHHHHHTT-HHHHHHHSEECCCCEEEEEEECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSE CS
                     FAD_binding_3  50 mellrqlGledrilaegapnelmgealynelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfkt 126
                                       +el ++lG+e r+l    ++e+  ++   +      a a +e  s++ ++ +  qt+      ++a+++g+ + ++ 
  gi|557693937|ref|YP_008796991.1| 103 VELQKKLGVETRLLGPEEVREILPQTSTDS-----LAAAAYEPFSGYADPVTTAQTYA-----SAAVREGVALLEDC 169
                                       566666666666655554444444333333.....55555553344555555555443.....45677778888888 PP

                                       EEECCEECCCC CS
                     FAD_binding_3 127 evesleqdeeg 137
                                       ev+s+++d+  
  gi|557693937|ref|YP_008796991.1| 170 EVHSVRRDGRR 180
                                       88888887765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.2    0.0014       1.5       1      32 [.       3      35 ..       3      39 .. 0.87
   2 !    6.6   0.0    0.0025       2.7     114     163 ..     153     201 ..     142     204 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0014
                                      -SEEEE--SHHHHHHHHHHHHTT-.-EEEE-SS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgk.rVllleka 32
                                      +dv+v+GgG  G   A  +a+rg+ +V+l+ek+
  gi|557693937|ref|YP_008796991.1|  3 FDVVVVGGGSTGSSIAYYLASRGAgKVALVEKQ 35
                                      59**************9998887659****997 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       ++ +++ ++gv l  ++ev+sv+++  +++ ++t s++ lead +v AtG
  gi|557693937|ref|YP_008796991.1| 153 TYASAAVREGVALLEDCEVHSVRRDGRRILGLET-SKGLLEADVIVNATG 201
                                       556777889*************************.9************99 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0   0.00037      0.39       1      32 [.       3      34 ..       3      80 .. 0.84
   2 ?    4.0   0.0     0.026        28     194     236 ..     150     189 ..     147     202 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00037
                       GMC_oxred_N  1 vdelveggGsagsvvAaRLsedpstsvlvlea 32
                                      +d +v+ggGs+gs +A+ L+  ++ +v ++e 
  gi|557693937|ref|YP_008796991.1|  3 FDVVVVGGGSTGSSIAYYLASRGAGKVALVEK 34
                                      6889*************************996 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.026
                       GMC_oxred_N 194 tarawLrpalerpnleiltgakaekiilegrkkravGVeasdk 236
                                       ta+++   a+++ ++ +l+++++  +  +  ++r++G+e+s+ 
  gi|557693937|ref|YP_008796991.1| 150 TAQTYASAAVRE-GVALLEDCEVHSV--RRDGRRILGLETSKG 189
                                       789999999999.*************..989*******99875 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   7.3e-05     0.077       2      31 ..       5      35 ..       4      46 .. 0.90
   2 ?   -1.6   0.0       3.9   4.1e+03      50      72 ..     158     180 ..     148     188 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-05
                                      EEEECSSHHHHHHHHHHHHTTS.EEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgk.kVtvvers 31
                                      vvvvGgG +g   A +la  g+ kV +ve +
  gi|557693937|ref|YP_008796991.1|  5 VVVVGGGSTGSSIAYYLASRGAgKVALVEKQ 35
                                      8****************99995499999975 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.9
                                       HHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  50 lekngievllntkveeiegsedg 72 
                                         ++g+ +l + +v +++ +++ 
  gi|557693937|ref|YP_008796991.1| 158 AVREGVALLEDCEVHSVRRDGRR 180
                                       45679999999999999988765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   7.5e-05     0.079       1      30 [.       4      34 ..       4      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.5e-05
                                      CEEEE-SSHHHHHHHHHHHHTT-.-EEEEES CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGa.kvlLith 30
                                      dv+V+GgG  G+  A+ +a +Ga kv+L+ +
  gi|557693937|ref|YP_008796991.1|  4 DVVVVGGGSTGSSIAYYLASRGAgKVALVEK 34
                                      79*******************9868999844 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   7.7e-05     0.081      20      57 ..       4      41 ..       2      48 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.7e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGG CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 20 kvllvGaGglGsellknLalsGvgkltlvDnDkielsN 57
                                       v++vG G  Gs ++ +La  G gk+ lv   ++ +  
  gi|557693937|ref|YP_008796991.1|  4 DVVVVGGGSTGSSIAYYLASRGAGKVALVEKQRVGWGQ 41
                                      599**************************998887665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2   0.00049      0.51       1      30 [.       5      35 ..       5      42 .. 0.88
   2 ?   -1.3   0.0       2.3   2.5e+03       4      14 ..      37      47 ..      36      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00049
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESS CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkd 30
                                      ++++G G +G+s+a +L + g  +v +++k+
  gi|557693937|ref|YP_008796991.1|  5 VVVVGGGSTGSSIAYYLASrGAGKVALVEKQ 35
                                      79*****************55556*999996 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.3
                                      ES-SHHHHHHH CS
                            TrkA_N  4 iGlGrvGrsla 14
                                      +G+G++Grs a
  gi|557693937|ref|YP_008796991.1| 37 VGWGQTGRSTA 47
                                      7*******987 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 ?    8.5   0.1    0.0017       1.8       1      44 [.       6      45 ..       6      58 .. 0.85
   2 ?    2.2   0.1      0.15   1.6e+02     117     154 ..     163     201 ..     145     202 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0017
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrt 44
                                      ++vG+G +G +++  L++r       ++ l++++  g g+  r+
  gi|557693937|ref|YP_008796991.1|  6 VVVGGGSTGSSIAYYLASR----GAGKVALVEKQRVGWGQTGRS 45
                                      69****************9....5999******99986766555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.15
                     NAD_binding_9 117 vevhra.evvdleeradgqavlladgaslaadaVvLAlG 154
                                       v ++++ ev+++++++++   l++++  l+ad +v A+G
  gi|557693937|ref|YP_008796991.1| 163 VALLEDcEVHSVRRDGRRILGLETSKGLLEADVIVNATG 201
                                       5555555999999999999888999999**********9 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 ?   10.1   0.3   0.00052      0.55       2      30 ..       5      34 ..       4      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00052
                                      EEEE--SCCHHHHHHHHHHTT-.EEEEE-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagl.eVvlvdi 30
                                      v v+G G  G++ia+ +as+g  +V lv+ 
  gi|557693937|ref|YP_008796991.1|  5 VVVVGGGSTGSSIAYYLASRGAgKVALVEK 34
                                      89******************9747888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2829.25
//
Query:       gi|557693938|ref|YP_008796992.1|  [L=337]
Description: hypothetical protein CSUB_C0501 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   12.9   0.1       0.18   11.6   0.1    1.7  1  HTH_23    Homeodomain-like domain


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 ?   11.6   0.1     1e-05      0.18      26      49 ..     305     328 ..     283     331 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1e-05
                            HTH_23  26 eLgvsrrTvyrwlkryreeGlegl 49 
                                       eLg +   +yrw+k+yr+e  e l
  gi|557693938|ref|YP_008796992.1| 305 ELGKTLDAIYRWKKTYRRETQERL 328
                                       799999**********97665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2427.05
//
Query:       gi|557693939|ref|YP_008796993.1|  [L=186]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-38  130.8   5.3    1.5e-37  129.2   5.3    1.6  1  CarS-like        CDP-archaeol synthase
     0.0016   18.3   5.4     0.0016   18.3   5.4    2.2  2  CTP_transf_1     Cytidylyltransferase family
  ------ inclusion threshold ------
       0.21   11.8   3.5       0.45   10.7   3.5    1.5  1  Bacteriocin_IIc  Bacteriocin class II with double-glycine lea


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 !  129.2   5.3   2.5e-41   1.5e-37       6     175 .]      20     186 .]      16     186 .] 0.87

  Alignments for each domain:
  == domain 1  score: 129.2 bits;  conditional E-value: 2.5e-41
                         CarS-like   6 lksiylllpayvanasavl....vGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqglleklsilal 78 
                                       l+ + +++payvanas v+    +   +p+d G+ +vdGrr++GdG+t  G+v+Gvl+G l+g +   l        
  gi|557693939|ref|YP_008796993.1|  20 LMGLAYIFPAYVANASPVVaakiLRKTRPIDCGRVFVDGRRVLGDGKTVEGFVVGVLAGFLTGFVMSFL-------- 88 
                                       66788*********99775222167899***********************************998887........ PP

                         CarS-like  79 dssgsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllaypvkllp....ieliiliv 151
                                           s l ++   +ll++GallGd+ G+f+krrl+++ G+pa++ldql f+ +alll + +  lp    +  ++ + 
  gi|557693939|ref|YP_008796993.1|  89 ---WSWLFGLFEVFLLSLGALLGDVGGAFVKRRLGLKTGSPAPVLDQLSFLTAALLLIHLFHGLPpwmdTATLASLF 162
                                       ...4566678889*********************************************9877776441134455667 PP

                         CarS-like 152 litlvlhlsaniiayklglkdvwy 175
                                       l+t+++h+++n  ay +glk+ wy
  gi|557693939|ref|YP_008796993.1| 163 LFTIFMHIATNSFAYLVGLKNKWY 186
                                       89********************98 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   5.4   2.6e-07    0.0016     170     233 ..      65     122 ..      61     128 .. 0.85
   2 !    4.5   1.0    0.0043        26     130     156 ..     155     181 ..     127     184 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.6e-07
                                       --BHHHHHHHHHHHHHHHHHHHHHHHCTS---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT-S CS
                      CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskalalsllhllllslllslvavfGDLveSglKRafgiK 233
                                       +KTveGf+ G++a ++ g++++ + s+        +l+  +llsl a +GD+    +KR++g K
  gi|557693939|ref|YP_008796993.1|  65 GKTVEGFVVGVLAGFLTGFVMSFLWSWL------FGLFEVFLLSLGALLGDVGGAFVKRRLGLK 122
                                       6******************999988873......444455667789999**999*******999 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0043
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      CTP_transf_1 130 ikeglllvllllalvvaaDigaYffGk 156
                                         + + l+l+ +++ +a+ ++aY++G 
  gi|557693939|ref|YP_008796993.1| 155 TATLASLFLFTIFMHIATNSFAYLVGL 181
                                       344456799999999**********95 PP

>> Bacteriocin_IIc  Bacteriocin class II with double-glycine leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.5   7.5e-05      0.45      23      61 ..      66     114 ..      62     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.5e-05
                   Bacteriocin_IIc  23 gtvggivggalaGaatGaa..........tlgilgaavGavvGavvGai 61 
                                       +tv+g+v+g laG  tG++          ++ ++    Ga++G v+Ga+
  gi|557693939|ref|YP_008796993.1|  66 KTVEGFVVGVLAGFLTGFVmsflwswlfgLFEVFLLSLGALLGDVGGAF 114
                                       799**************************66666666677777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1336.36
//
Query:       gi|557693940|ref|YP_008796994.1|  [L=151]
Description: hypothetical protein CSUB_C0503 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   18.6   0.0     0.0018   18.3   0.0    1.1  1  RNase_H_2       RNase_H superfamily
  ------ inclusion threshold ------
      0.064   12.9   0.0       0.09   12.4   0.0    1.3  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
       0.15   11.1   0.0       0.16   11.0   0.0    1.2  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain


Domain annotation for each model (and alignments):
>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     3e-07    0.0018      43     100 ..      44     104 ..      41     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3e-07
                         RNase_H_2  43 eekailelflellekkkalvtfngksFDvpflkrlfkkyklde...eefrhiDLlkelrkk 100
                                       +ek +l+ fl++  + + +vt+ g+sF +p+l  ++ + +ld+    e +h+DL + + k 
  gi|557693940|ref|YP_008796994.1|  44 DEKTFLRSFLKFCMDVDIFVTWGGESFAFPLLTAKIIRNRLDPaplYEAYHLDLKTFFGKT 104
                                       799999******************************7767777667888*****9887654 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 ?   12.4   0.0   1.5e-05      0.09      36      87 ..      44      94 ..      28     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                    DNA_pol_B_exo2 36 sekelikkffegvekkkpqlVsfngrgfDlpvleyralkhgvsapkyfdegd 87
                                      +ek+++++f+++       +V++ g++f +p+l+ + +++++  + ++++ +
  gi|557693940|ref|YP_008796994.1| 44 DEKTFLRSFLKFCMDVD-IFVTWGGESFAFPLLTAKIIRNRLDPAPLYEAYH 94
                                      79999*****9888776.8*********************999888777655 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 ?   11.0   0.0   2.7e-05      0.16     236     274 ..      43      79 ..      11     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.7e-05
                                       SSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHH CS
                    DNA_pol_B_exo1 236 dsEkelLqaflefikqydPdvitgYNidnFDlpYilnRa 274
                                        +Ek+ L+ fl+f  ++  d+ +++ +++F +p + +++
  gi|557693940|ref|YP_008796994.1|  43 GDEKTFLRSFLKFCMDV--DIFVTWGGESFAFPLLTAKI 79 
                                       58************988..**************988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1147.96
//
Query:       gi|557693941|ref|YP_008796995.1|  [L=435]
Description: adenosylhomocysteinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-62  211.1   0.0      8e-61  205.8   0.0    2.0  1  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    5.2e-54  182.7   2.0    9.4e-54  181.8   0.7    2.0  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    2.6e-11   43.2   0.4    4.7e-11   42.4   0.4    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    8.8e-05   22.9   0.2    0.00024   21.5   0.2    1.7  1  NAD_binding_7  Putative NAD(P)-binding
    0.00012   22.3   0.1     0.0003   21.0   0.1    1.7  1  TrkA_N         TrkA-N domain
    0.00037   20.1   0.4    0.00075   19.1   0.4    1.5  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
  ------ inclusion threshold ------
      0.041   13.6   0.3      0.064   13.0   0.3    1.3  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
      0.049   14.1   0.1       0.17   12.4   0.1    1.9  2  XdhC_C         XdhC Rossmann domain
      0.064   13.2   0.5        0.3   11.1   0.2    2.2  2  ADH_zinc_N     Zinc-binding dehydrogenase
       0.09   12.7   2.2       0.13   12.1   1.4    1.8  2  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
       0.17   12.5   0.4       0.45   11.1   0.4    1.8  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
       0.38   10.0   4.3        1.2    8.4   4.0    1.8  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain


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 !  205.8   0.0   5.3e-64     8e-61       2     286 ..       5     429 ..       4     435 .] 0.95

  Alignments for each domain:
  == domain 1  score: 205.8 bits;  conditional E-value: 5.3e-64
                                       -B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase   2 ykvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifs 78 
                                       ++vkd+slae G  +i lae+ mp l  lr++ya+ekp++g r++ +lh+t +tavL   L + Ga+v  ++ n  s
  gi|557693941|ref|YP_008796995.1|   5 FHVKDLSLAEKGASRIMLAESMMPVLSLLRRKYADEKPFEGYRVSMCLHVTKETAVLCRVLREGGAKVALCASNPLS 81 
                                       89*************************************************************************** PP

                                       --HHHHHHHCCTTEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHHHHHHHH.....S..SHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  79 tqdeaaaaiaeagvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhkgvkeeesvlekeedeee 155
                                       tqd++aaa+a +g +v+a++g++++ey   + ++l++     +p+l++DdG Dl + +h+ +   + +++       
  gi|557693941|ref|YP_008796995.1|  82 TQDDVAAALAVEGFNVYAFRGMSTQEYYGALGKVLSH-----GPHLLVDDGADLITSLHRLI---HGLPDV------ 144
                                       ***********************************55.....8****************922...222222...... PP

                                       HHHHHHHHHHHHTT.THHCCCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                         AdoHcyase 156 ekvvlellkksleedkkytellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD............ 220
                                           le +++ ++        + ++ G +eetttGv rL  l  +g L +p i vnd+++ks fD            
  gi|557693941|ref|YP_008796995.1| 145 ---HLEDVRRGMD-----GADVPRVWGATEETTTGVTRLRALDGEGLLAFPVIAVNDALSKSLFDnplgtgqsaldg 213
                                       ...2222222222.....34467899*************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|557693941|ref|YP_008796995.1| 214 vlratnlllagktvvvagygrvgagiaerakgmgarvvvvepdpikalqaymngftvtsmskaseigdvfitatgni 290
                                       ***************************************************************************** PP

                                       .........................................................................S-HH CS
                                       .........................................................................xxxx RF
                         AdoHcyase 221 .........................................................................hpsf 224
                                                                                                                hps 
  gi|557693941|ref|YP_008796995.1| 291 dvirgehfekmkdgvflanaghmdveinkqdlkqlavsvetirenvtlyrlrngrklflladgrlvnlvcaegHPSE 367
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHTTSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 225 vmsasftnqvlaqielfkkekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyig 286
                                       vm+ sf+ q+ +   l k+ +k  k+vy++p+++De va+l+l+++g++l++lt +q +y+ 
  gi|557693941|ref|YP_008796995.1| 368 VMDLSFSLQAESLRYLIKNVEKLGKHVYTVPREIDEAVAALKLAAFGVELEKLTPRQLDYMR 429
                                       *******************999**************************************96 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   0.0       1.1   1.7e+03      39      71 ..      62      99 ..      45     106 .. 0.71
   2 !  181.8   0.7   6.3e-57   9.4e-54       4     162 .]     205     363 ..     202     363 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.1
                                      HHHHHHCT-EEEEE-S-HHH.....HHHHHCTT-EE-- CS
                     AdoHcyase_NAD 39 aaslkglGarvivtevdPic.....alqaameGfevvt 71
                                      ++ l++ Ga+v +   +P++     a   a+eGf+v  
  gi|557693941|ref|YP_008796995.1| 62 CRVLREGGAKVALCASNPLStqddvAAALAVEGFNVYA 99
                                      46788899999998888886222112334578888865 PP

  == domain 2  score: 181.8 bits;  conditional E-value: 6.3e-57
                                       HHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-S CS
                     AdoHcyase_NAD   4 gcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkad 80 
                                       g+ +s +dg+ rat++llaGk++vvaGyG vG G a+  kg+Garv+v e dPi alqa m+Gf v+ + ++ + +d
  gi|557693941|ref|YP_008796995.1| 205 GTGQSALDGVLRATNLLLAGKTVVVAGYGRVGAGIAERAKGMGARVVVVEPDPIKALQAYMNGFTVTSMSKASEIGD 281
                                       777999*********************************************************************** PP

                                       EEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSBCHH CS
                     AdoHcyase_NAD  81 ivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrllnl 157
                                       +++t+tGn d+i+ eh++kmkd + ++n Gh+d ei+ + l++ a+++e+++ +v  ++l++g+k+ lla+Grl+nl
  gi|557693941|ref|YP_008796995.1| 282 VFITATGNIDVIRGEHFEKMKDGVFLANAGHMDVEINKQDLKQLAVSVETIRENVTLYRLRNGRKLFLLADGRLVNL 358
                                       ***************************************************************************** PP

                                       HTS-- CS
                     AdoHcyase_NAD 158 gcatg 162
                                        ca g
  gi|557693941|ref|YP_008796995.1| 359 VCAEG 363
                                       **975 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 !   42.4   0.4   3.2e-14   4.7e-11      33     131 ..     221     315 ..     208     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 3.2e-14
                                       -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSB CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpltpetrhli 109
                                        l+gktv + G+Gr+G  +a+r+k++g++v+++++ + k  ++  +g++++s+ ++ +  D+ + ++     + ++i
  gi|557693941|ref|YP_008796995.1| 221 LLAGKTVVVAGYGRVGAGIAERAKGMGARVVVVEPDPIKALQAYMNGFTVTSMSKASEIGDVFITATG----NIDVI 293
                                       589*********************************99888888888888888888877777766554....889** PP

                                       SHHHHHCSTTTEEEEESS-GGG CS
                      2-Hacid_dh_C 110 naeelakmkkgailiNtaRGgl 131
                                         e+++kmk+g++l N++  ++
  gi|557693941|ref|YP_008796995.1| 294 RGEHFEKMKDGVFLANAGHMDV 315
                                       *****************98665 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 !   21.5   0.2   1.6e-07   0.00024       5      77 ..     222     320 ..     219     336 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.6e-07
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele.........................elvkla.eeel 55 
                                       l gk+v+v+G G+v+a  +++    ga+v+vv p+  ++l+                         ++++++  e++
  gi|557693941|ref|YP_008796995.1| 222 LAGKTVVVAGYGRVGAGIAERAKGMGARVVVVEPDPIKALQaymngftvtsmskaseigdvfitatGNIDVIrGEHF 298
                                       689********************************655555777777777777677777666666655554414557 PP

                     NAD_binding_7  56 ekdlegadlviaatddrelner 77 
                                       ek  +g++l+ a   d e+n++
  gi|557693941|ref|YP_008796995.1| 299 EKMKDGVFLANAGHMDVEINKQ 320
                                       8888888888777777777765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1     2e-07    0.0003       1      44 [.     227     270 ..     227     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2e-07
                                       EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEE CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglev 44 
                                       ++++G+GrvG  +ae+ +  g  +vvv++ d+ ++ ++  +g++v
  gi|557693941|ref|YP_008796995.1| 227 VVVAGYGRVGAGIAERAKGmGA-RVVVVEPDPIKALQAYMNGFTV 270
                                       79*****************666.6********9998888888776 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 !   19.1   0.4     5e-07   0.00075       2      92 ..     222     308 ..     221     328 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 5e-07
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78 
                                       l gk+++v GyG  G   a+  +  g  vvv   +   ++ +A  +gf+v+++++a++  dv ++ +    + +v++
  gi|557693941|ref|YP_008796995.1| 222 LAGKTVVVAGYGRVGAGIAERAKGMGARVVVVEPDP-IKALQAYMNGFTVTSMSKASEIGDVFITATG---NIDVIR 294
                                       789*************************99966555.58889*******************9876543...345555 PP

                                       HHTGGG--TT-EEE CS
                              IlvN  79 eeiepnlkegkala 92 
                                        e  +++k+g  la
  gi|557693941|ref|YP_008796995.1| 295 GEHFEKMKDGVFLA 308
                                       55555556555555 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 ?   13.0   0.3   4.3e-05     0.064      20      62 ..     213     254 ..     205     335 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
                                       HHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEE CS
                     ELFV_dehydrog  20 emlkklkldslegkrvaisGsGnvgsyaallltelgakvvavs 62 
                                        +l+  +l  l+gk+v++ G+G vg   a+ ++ +ga+vv v 
  gi|557693941|ref|YP_008796995.1| 213 GVLRATNLL-LAGKTVVVAGYGRVGAGIAERAKGMGARVVVVE 254
                                       566666666.99***************************9875 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.2   3.3e+03      12      40 ..      60      87 ..      51     117 .. 0.73
   2 ?   12.4   0.1   0.00012      0.17       1      47 [.     227     283 ..     227     329 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.2
                                      HHHHHHHHHTEEEEEEES-GGGG-GGG-T CS
                            XdhC_C 12 alarlaaalgfrvtvvdpreefatkerfp 40
                                       l+r++++ g +v ++ +++   t+++++
  gi|557693941|ref|YP_008796995.1| 60 VLCRVLREGGAKVALCASNPL-STQDDVA 87
                                      578888888999999988884.3444444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00012
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG........-GGG-TT-SE..-EE CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefa........tkerfpeade..tav 47 
                                       +v+ G g v++ +a+ a+ +g rv+vv+p++  a        t++++ +a+e  +++
  gi|557693941|ref|YP_008796995.1| 227 VVVAGYGRVGAGIAERAKGMGARVVVVEPDPIKAlqaymngfTVTSMSKASEigDVF 283
                                       689****************************54645666666555555444455333 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.9   2.9e+03      77     123 ..      63     110 ..      53     117 .. 0.51
   2 ?   11.1   0.2    0.0002       0.3       2      61 ..     235     292 ..     235     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.9
                                       HCEEEEE.EEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHH CS
                        ADH_zinc_N  77 kllkpgG.rlvvvGg.gkgeeefdlrnlllkeksilGsllgslreefke 123
                                       ++l++gG ++++++  +   ++  ++ l+ +  +++ + + s ++e++ 
  gi|557693941|ref|YP_008796995.1|  63 RVLREGGaKVALCASnPLSTQDDVAAALAVEGFNVYAFRGMS-TQEYYG 110
                                       567777425556665422222222222334444444444444.555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                                       HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEE CS
                        ADH_zinc_N   2 vGlaavqlAkalGaeviavdsseeklelakklGadevinykea.dlverikeltggegvdv 61 
                                       vG    + Ak +Ga+v++v +++ k+ +a  +G +++  + +a ++ +    +tg  ++dv
  gi|557693941|ref|YP_008796995.1| 235 VGAGIAERAKGMGARVVVVEPDPIKALQAYMNGFTVTSMS-KAsEIGDVFITATG--NIDV 292
                                       67788889*********************99**9999888.44488888888884..5665 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 ?   12.1   1.4   8.9e-05      0.13       1      38 [.     226     263 ..     226     338 .. 0.86
   2 ?   -3.2   0.0       4.5   6.7e+03      18      67 ..     359     408 ..     355     412 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.9e-05
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealeka 38 
                                       +v v G G +Gagia+ +   g +Vv+v+ ++ ++ +a
  gi|557693941|ref|YP_008796995.1| 226 TVVVAGYGRVGAGIAERAKGMGARVVVVEPDPIKALQA 263
                                       5899*************************988555444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.5
                                       HHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCE CS
                           3HCDH_N  18 fasagleVvlvdiseealekalekieksleklvekgklkeeeveaalari 67 
                                       ++++g++  ++d s +  +++l+ + k++ekl ++  +   e+++a+a +
  gi|557693941|ref|YP_008796995.1| 359 VCAEGHPSEVMDLSFSLQAESLRYLIKNVEKLGKHVYTVPREIDEAVAAL 408
                                       55667777777777777777777777777777666665566666666555 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 ?   11.1   0.4    0.0003      0.45       3      68 ..     228     286 ..     225     293 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0003
                                       EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE- CS
                     F420_oxidored   3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvla 68 
                                        + G+G++g+++a+++   g     +vv+ +++p ka  l +++  + t ++ ++a e  dv + a
  gi|557693941|ref|YP_008796995.1| 228 VVAGYGRVGAGIAERAKGMG---ARVVVV-EPDPIKA--L-QAYMNGFTVTSMSKASEIGDVFITA 286
                                       445*****************...999988.6666655..4.4455566666788888888887766 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 ?    8.4   4.0   0.00078       1.2      30      72 ..     226     266 ..     214     304 .. 0.78
   2 ?    0.0   0.1      0.29   4.4e+02     114     143 ..     269     297 ..     262     326 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00078
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTT CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslga 72 
                                       +v+v G G +G   ++ akg+ga+V+v++ +p   + l+++ +
  gi|557693941|ref|YP_008796995.1| 226 TVVVAGYGRVGAGIAERAKGMGARVVVVEPDPI--KALQAYMN 266
                                       68999**********************886664..44444333 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.29
                                       HHHTS-TTEEEEETTGGGT-SBTT--TBBT CS
                       AlaDh_PNT_C 114 mvksMkpgsVivDvAidqGGnvetsrltth 143
                                       +v sM + s i Dv i + Gn++ +r  +h
  gi|557693941|ref|YP_008796995.1| 269 TVTSMSKASEIGDVFITATGNIDVIR-GEH 297
                                       58999999999999999999999555.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2999.35
//
Query:       gi|557693942|ref|YP_008796996.1|  [L=144]
Description: translation initiation factor eIF-2 beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-27   94.8   0.0    3.6e-27   94.6   0.0    1.1  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
     0.0039   17.5   0.4     0.0064   16.8   0.4    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0073   15.8   1.0      0.013   15.0   0.5    1.7  2  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
      0.054   13.2   0.7         11    5.8   0.0    2.3  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.14   11.6   0.9         13    5.4   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
       0.22   11.3   1.0        7.1    6.4   0.1    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain


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 !   94.6   0.0   1.2e-30   3.6e-27      15     117 .]      38     138 ..      26     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 1.2e-30
                                       T--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHHHHHHHHHTSTS CS
                      eIF-5_eIF-2B  15 klqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakkleklldkyieeyVlCk 91 
                                       ++++ ++ k +t ++N+ ++ak+Lnr+p h++++llke g +g + ++++l+++g++ ++++++lld yi+e+V C+
  gi|557693942|ref|YP_008796996.1|  38 SPNLVIDAK-NTFFTNLGQVAKMLNREPAHLARFLLKETGRAGAV-SDDKLVIQGRMMHDEVKRLLDLYIKEFVRCP 112
                                       566777777.9**********************************.999**************************** PP

                                       SSTSTCEEECCSSSCEEEEESSSTCE CS
                      eIF-5_eIF-2B  92 eCkspetelekeerllvlkCkaCgak 117
                                        C+  +t+++ e+r  +l C+aCgak
  gi|557693942|ref|YP_008796996.1| 113 VCNGIDTRIVSEKRFRFLVCDACGAK 138
                                       ************************85 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 !   16.8   0.4   2.1e-06    0.0064       3      36 ..     108     137 ..     106     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.1e-06
                   Lar_restr_allev   3 LkpCPfCggravlersqrvvaeigqcvyCadCga 36 
                                          CP C+g ++ + s+++      +  C+ Cga
  gi|557693942|ref|YP_008796996.1| 108 FVRCPVCNGIDTRIVSEKRFR----FLVCDACGA 137
                                       568*****************9....********* 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       1.1   3.4e+03       8      20 ..      38      50 ..      38      51 .. 0.76
   2 !   15.0   0.5   4.2e-06     0.013       2      29 ..     110     139 ..     109     144 .] 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                                      CEECHEETSTTCE CS
                      TF_Zn_Ribbon  8 stnlveDpergel 20
                                      s+nlv D++++ +
  gi|557693942|ref|YP_008796996.1| 38 SPNLVIDAKNTFF 50
                                      5788999998876 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 4.2e-06
                                       EETTTTC.EECHEETSTTCE.EESSSSBEE CS
                      TF_Zn_Ribbon   2 kCPnCgs.tnlveDpergel.vCtdCGlVl 29 
                                       +CP+C++ ++ ++ ++r  + vC +CG+  
  gi|557693942|ref|YP_008796996.1| 110 RCPVCNGiDTRIVSEKRFRFlVCDACGAKS 139
                                       7******76667777777777******875 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 ?    5.6   0.2    0.0042        12       6      12 ..     110     116 ..     109     124 .. 0.82
   2 ?    5.8   0.0    0.0036        11      22      30 ..     130     138 ..     129     140 .. 0.59

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0042
                           zf-RRN7   6 pCgvCgc 12 
                                       +C+vC++
  gi|557693942|ref|YP_008796996.1| 110 RCPVCNG 116
                                       8*****8 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0036
                           zf-RRN7  22 yyCrrChtq 30 
                                        +C+ C+ +
  gi|557693942|ref|YP_008796996.1| 130 LVCDACGAK 138
                                       566666654 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   0.1    0.0044        13       2       9 ..     108     115 ..     107     120 .. 0.84
   2 ?    4.7   0.1    0.0069        21       5      11 ..     132     138 ..     129     142 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0044
                       zf-ribbon_3   2 tvrCPnCG 9  
                                        vrCP C+
  gi|557693942|ref|YP_008796996.1| 108 FVRCPVCN 115
                                       69*****7 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0069
                       zf-ribbon_3   5 CPnCGap 11 
                                       C +CGa+
  gi|557693942|ref|YP_008796996.1| 132 CDACGAK 138
                                       7777763 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.1     0.022        66      16      22 ..     110     116 ..     109     119 .. 0.82
   2 ?    6.4   0.1    0.0024       7.1       2      11 ..     131     140 ..     131     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.022
                      Rubredoxin_2  16 rCpsCgs 22 
                                       rCp C+ 
  gi|557693942|ref|YP_008796996.1| 110 RCPVCNG 116
                                       8****96 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0024
                      Rubredoxin_2   2 vCsqCGfesa 11 
                                       vC++CG++s+
  gi|557693942|ref|YP_008796996.1| 131 VCDACGAKSP 140
                                       7******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1061.07
//
Query:       gi|557693943|ref|YP_008796997.1|  [L=95]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-19   70.5   0.1    1.2e-19   70.4   0.1    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 !   70.4   0.1   6.7e-24   1.2e-19       4      90 ..       8      94 ..       4      95 .] 0.94

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 6.7e-24
                                      TTE.EEEEEEEGGGTT-EEEETT.EEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EEE CS
                            DUF424  4 ddllklvavcdkellgktfkege.lllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlvi 81
                                      +++ ++va+cd+ llg++++    ++++v+e+fy+g l+ e ++ +  +  ti+N++ge+av+ avk G+  ++s++++
  gi|557693943|ref|YP_008796997.1|  8 TGE-VVVAICDEMLLGRKLRLSTgVSVEVQESFYKGVLVCETDLEDYFRMGTIINLLGENAVKAAVKLGYASEKSIIYV 85
                                      455.9***************8877******************************************************* PP

                                      TTEEEEEEE CS
                            DUF424 82 dgvphaqig 90
                                      dgvph q++
  gi|557693943|ref|YP_008796997.1| 86 DGVPHIQLF 94
                                      ******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 733.17
//
Query:       gi|557693944|ref|YP_008796998.1|  [L=113]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-05   22.9   0.1    9.9e-05   22.4   0.1    1.2  1  MazG       MazG nucleotide pyrophosphohydrolase domain
  ------ inclusion threshold ------
      0.014   15.7   0.0       0.02   15.1   0.0    1.4  1  MazG-like  MazG-like family
      0.046   13.9   0.5       0.23   11.7   0.1    2.3  3  DUF3782    Protein of unknown function (DUF3782)
      0.047   13.6   0.1       0.18   11.8   0.0    1.9  2  SUV3_C     Mitochondrial degradasome RNA helicase subunit C t


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 !   22.4   0.1   2.2e-08   9.9e-05       4      69 ..      25      98 ..      22     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.2e-08
                                      HHHHHHHHHHHHHHHHHHHT...T-HH...........HHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHH CS
                              MazG  4 etllaylleEvgEvaeaIkk...edrd...........eleeELGDvLlqvlflaniaeeeggidledvaetileKler 68
                                        + a+l+eE+ E+ + I +   +  +           +l++E +  L   ++lan    + g+dle+++++ ++K+e+
  gi|557693944|ref|YP_008796998.1| 25 SLIYAHLIEEITEIGRFILEkegY--KrsglghsspgeDLDSEFAQSLTLFVQLAN----RFGVDLEKALAKEMAKMEK 97
                                      567899************664451..355666667777******************....5****************** PP

                                      H CS
                              MazG 69 R 69
                                      R
  gi|557693944|ref|YP_008796998.1| 98 R 98
                                      9 PP

>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   4.5e-06      0.02      34      74 ..      62     103 ..      30     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.5e-06
                         MazG-like  34 ildeLAdviiylylLAdrlGidfee.ideklkkklkkypvek 74 
                                       +  e A+ +++ + LA+r+G+d+e+ + ++++k +k+ ++e+
  gi|557693944|ref|YP_008796998.1|  62 LDSEFAQSLTLFVQLANRFGVDLEKaLAKEMAKMEKRFNAEE 103
                                       556789999999*********************999887776 PP

>> DUF3782  Protein of unknown function (DUF3782)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       0.3   1.3e+03      44      44 ..      20      20 ..       2      40 .. 0.59
   2 ?   -0.8   0.0       0.4   1.8e+03      44      61 ..      20      37 ..      19      50 .. 0.56
   3 ?   11.7   0.1     5e-05      0.23      18      60 ..      60     101 ..      49     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.3
                           DUF3782 44 e 44
                                      +
  gi|557693944|ref|YP_008796998.1| 20 D 20
                                      2 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.4
                           DUF3782 44 eafReglk..eiLeealgvk 61
                                      ++fRe+l   +++ee+  ++
  gi|557693944|ref|YP_008796998.1| 20 DSFRESLIyaHLIEEI--TE 37
                                      5777776411455555..34 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 5e-05
                           DUF3782  18 eelekeieklertigaLGaRWGlvsEeafReglkeiLeealgv 60 
                                       e+l++e+++  + +  L+ R+G++ E+a+ + ++++ e+ +++
  gi|557693944|ref|YP_008796998.1|  60 EDLDSEFAQSLTLFVQLANRFGVDLEKALAKEMAKM-EKRFNA 101
                                       6677788888888999*************9999875.555455 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 ?   -1.6   0.0      0.61   2.8e+03      32      40 ..       4      12 ..       2      13 .. 0.81
   2 ?   11.8   0.0     4e-05      0.18       9      36 ..      68      94 ..      65      97 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.61
                                      HHHHHHHHH CS
                            SUV3_C 32 eelkkevee 40
                                       el+k+vee
  gi|557693944|ref|YP_008796998.1|  4 SELQKRVEE 12
                                      689999998 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 4e-05
                                      HHHHHHHHHHHH-------HHHHHHHHH CS
                            SUV3_C  9 kvldLYlWLSyRfpevFpdrelaeelkk 36
                                      + l+L+ +L++Rf+    +++la e+ k
  gi|557693944|ref|YP_008796998.1| 68 QSLTLFVQLANRFGVD-LEKALAKEMAK 94
                                      89**************.9*****99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 906.88
//
Query:       gi|557693945|ref|YP_008796999.1|  [L=432]
Description: 3-hydroxy-3-methylglutaryl-CoA reductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-113  379.6   2.8   1.8e-113  379.3   2.8    1.1  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
     0.0013   19.3   1.0        6.2    7.4   0.1    3.9  4  FliG_N       FliG N-terminal domain


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 !  379.3   2.8    2e-117  1.8e-113       2     367 .]      15     379 ..      14     379 .. 0.96

  Alignments for each domain:
  == domain 1  score: 379.3 bits;  conditional E-value: 2e-117
                                       HHHHHHHHHH...S-HHHHHHHTT----HHHHHHHSSS---------EEEEEEEETTEEEEEEE---STTHHHHHHH CS
                       HMG-CoA_red   2 veeRrkllee...lteeeleelkeesldeevadkmiEnviGyvqlPlGvagpllingkeylvPmAteEgslvAsasr 75 
                                        eeR+++++e   lt+ee + +++ +ld ++a +miEnv+G+++lPlG+a ++ling++ylvPmA+eE+s+vA+as+
  gi|557693945|ref|YP_008796999.1|  15 PEERLRVVAEfaqLTDEEKKLISSCGLDIATASRMIENVVGVFPLPLGIAANFLINGRDYLVPMAVEEPSVVAAASN 91 
                                       5899999988887999999999******************************************************* PP

                                       HHHHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHH.HTHHHHHHHHHHCSHH..CCT-EEEEEEE.EE-.. CS
                       HMG-CoA_red  76 gakainesgGvkttvlkdgmtraqvvllesvedaaelkkwi.ekkeeleelanaaest..srggglkdiev.vla.. 146
                                       +ak+++++gG+      ++++++qv+l+ +v+++ ++k  i ++++e+ + an+++++  + ggg+kd+e+ vl+  
  gi|557693945|ref|YP_008796999.1|  92 AAKMARDGGGI-FSFQPSQLMIGQVQLV-EVSNPFHAKMEIlRNRDEILARANECDPVlvNLGGGAKDVEArVLEte 166
                                       ***********.8888888*********.9999999999999*****************************888899 PP

                                       .SSEEEEEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHH CS
                       HMG-CoA_red 147 .grlvvlrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigee 222
                                        g++vv++l vd++DAmGaN+vn+++e +a+++ +  g++  l+i sNl+++++a+a ++++ +++        g e
  gi|557693945|ref|YP_008796999.1| 167 lGPMVVVHLIVDVRDAMGANAVNTMAESVAPFLARLSGGKFRLRIISNLADKRIARAYARVPAESV-------GGVE 236
                                       999***********************************************************9999.......99** PP

                                       HHHHHHHHHHHHHH-HHHH..HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTT.......SEEE...T CS
                       HMG-CoA_red 223 vvekilkasaealvdlnranigtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaa.......leev...e 289
                                       v++ i++a+++a++d++ra  +t+nkGi       +Ngi+Av++AtG+D++a+e+++ha+aa       l+ +   +
  gi|557693945|ref|YP_008796999.1| 237 VARGIVEAYQFAKADPYRA--ATHNKGI-------MNGIDAVAIATGNDWRAIEAGAHAYAArngryepLTIWeqtP 304
                                       *******************..*******.......**********************************55555449 PP

                                       TTEEEEEEEEE.----SBSHHHHH-HHHHHH.HHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHHHH CS
                       HMG-CoA_red 290 dgdlygsvtlPsleVGtvGGgtklppqaell.kllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHmkl 365
                                        gdlyg ++lP l+VG+vGG+++++p a+ + k+lg+k+a+   eLae++aavgL+q+l+alrALaaeg+q+gHm+l
  gi|557693945|ref|YP_008796999.1| 305 SGDLYGVIELP-LAVGIVGGAVRTNPVAKTClKILGIKSAR---ELAEVMAAVGLVQNLAALRALAAEGIQAGHMSL 377
                                       999********.**************998777*********...********************************* PP

                                       HH CS
                       HMG-CoA_red 366 hr 367
                                       h+
  gi|557693945|ref|YP_008796999.1| 378 HA 379
                                       96 PP

>> FliG_N  FliG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0047        42      43      73 ..      11      42 ..       4      55 .. 0.71
   2 ?    2.5   0.0     0.024   2.2e+02      66     100 ..     150     184 ..     129     187 .. 0.84
   3 ?   -1.2   0.0      0.32   2.9e+03      20      47 ..     331     358 ..     328     368 .. 0.81
   4 !    7.4   0.1   0.00069       6.2      28      60 ..     389     421 ..     377     429 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0047
                                      TTXXHHHHHHHHHHHHHHHHCCCCH.HCHHHH CS
                            FliG_N 43 ksvskeeveaVleefleeleaqeyl.seggee 73
                                       ++++ee+ +V++ef + + ++++l s+ g +
  gi|557693945|ref|YP_008796999.1| 11 YTLKPEERLRVVAEFAQLTDEEKKLiSSCGLD 42
                                      67899**************6665550444544 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.024
                                       CHHCHHHHHHHHHHHHHHSHHHHHHHCHHHHXXXX CS
                            FliG_N  66 ylseggeeyarelLekalgeekaeellerltaeaq 100
                                       +l++g+++ + ++Le  lg+  + +l+ +++  ++
  gi|557693945|ref|YP_008796999.1| 150 NLGGGAKDVEARVLETELGPMVVVHLIVDVRDAMG 184
                                       6889999*************999999998887665 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.32
                                       HHHHHTTSXHHHHHHHHHHHHCHTTXXH CS
                            FliG_N  20 aaevlkhLdeeeiekltkeiaslksvsk 47 
                                       a+  lk L  +  ++l++ +a ++ v++
  gi|557693945|ref|YP_008796999.1| 331 AKTCLKILGIKSARELAEVMAAVGLVQN 358
                                       6677888999999999999999988775 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.00069
                                       XHHHHHHHHHHHHCHTTXXHHHHHHHHHHHHHH CS
                            FliG_N  28 deeeiekltkeiaslksvskeeveaVleeflee 60 
                                       + eei  +++e+++ k++  +++e++l+e +++
  gi|557693945|ref|YP_008796999.1| 389 TGEEIDLVAEEMVRQKTIRVDKAEEILAELRSR 421
                                       56899***********************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 00:00:00.38
# Mc/sec: 3404.34
//
Query:       gi|557693946|ref|YP_008797000.1|  [L=206]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   24.1   0.0    6.1e-05   23.2   0.0    1.4  1  DUF4443         Domain of unknown function (DUF4443)
     0.0035   17.5   0.4     0.0075   16.5   0.4    1.6  1  PaaX            PaaX-like protein
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.052   13.5   0.0    1.4  1  HTH_45          Winged helix-turn-helix
      0.039   14.4   0.0      0.076   13.5   0.0    1.5  1  DUF4093         Domain of unknown function (DUF4093)
       0.04   14.1   0.0       0.12   12.6   0.0    1.8  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.069   12.2   0.0      0.081   11.9   0.0    1.1  1  Topoisom_bac    DNA topoisomerase


Domain annotation for each model (and alignments):
>> DUF4443  Domain of unknown function (DUF4443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0     2e-08   6.1e-05      15     106 ..     108     200 ..      99     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2e-08
                           DUF4443  15 ayaivvknppqfks..ielrdeairffakgamilivkngepvfpederplrdtmeelamnieevlnfsdgdlivvtw 89 
                                        y +vvk   +  s  +e rdea+r  a  am+l        +p     l     e+a +++  ++   gd+i++t 
  gi|557693946|ref|YP_008797000.1| 108 NYGLVVKGLAERIStgLEERDEAVRHGASAAMVLTFLSDGVHMPR-VSNLSVERPEFAEQVKSFFKPEVGDVIIITG 183
                                       5888999876654422789***************98776666665.5678888899********************* PP

                           DUF4443  90 aenpsdamksayhvalt 106
                                       ae+   am sa   al 
  gi|557693946|ref|YP_008797000.1| 184 AEDEPRAMYSALAAALK 200
                                       ***********999986 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.4   2.5e-06    0.0075      31      66 ..      45      76 ..      41      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.5e-06
                              PaaX 31 aelGiseslvRaalsRlakaGwlvrekegrrsfYrL 66
                                      + l ++e++vR+ +sRl k+G+ v+++ g     +L
  gi|557693946|ref|YP_008797000.1| 45 ELLQLGEGSVRTMVSRLMKRGLAVSTRGG----VAL 76
                                      567789********************999....445 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.8e-05     0.052      36      72 ..      54      90 ..      46      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
                            HTH_45 36 lnkYLdmLvekglikkskekYvlTekGlelleklkel 72
                                      ++ +++ L+++gl   + +   lTekG+e++e+lk+l
  gi|557693946|ref|YP_008797000.1| 54 VRTMVSRLMKRGLAVSTRGGVALTEKGEEVYERLKKL 90
                                      6788999***************************987 PP

>> DUF4093  Domain of unknown function (DUF4093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05     0.076      10      70 ..       2      62 ..       1      68 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                           DUF4093 10 ealreaLaeveeeekekeitkedLlelgLvggadskkrReklgekLgigyangkqllkrLn 70
                                      ealr+ L+  e ++++ ++t  +L+ l ++ g++    R++l e L++g+++ +++++rL 
  gi|557693946|ref|YP_008797000.1|  2 EALRKILSVKEGKGPSPTFTEPQLVYLIFLIGSEPYIGRKRLKELLQLGEGSVRTMVSRLM 62
                                      677777774455999999*************9***************************96 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     4e-05      0.12      17      52 ..      32      67 ..      26      73 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                                      HHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress 17 seekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                       +++ ++++k+l e L+    sV  m+++L k G+ 
  gi|557693946|ref|YP_008797000.1| 32 IGSEPYIGRKRLKELLQLGEGSVRTMVSRLMKRGLA 67
                                      567889****************************95 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.7e-05     0.081     346     395 ..      54     104 ..       8     106 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                      Topoisom_bac 346 raeiieklvergYverkkkslvptelGkalvellekf.kdlvspelTaele 395
                                         +++++l++rg +++ ++ +  te+G++++e l+k+ + l + ++   +e
  gi|557693946|ref|YP_008797000.1|  54 VRTMVSRLMKRGLAVSTRGGVALTEKGEEVYERLKKLvSPLRKISFKMPWE 104
                                       5689************9999**************98878899998888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); 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:                         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 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1581.11
//
Query:       gi|557693947|ref|YP_008797001.1|  [L=302]
Description: signal recognition particle receptor [Candidatus Caldiarchaeum subterraneum]
Scores for 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-67  224.4   0.2    1.4e-66  223.8   0.2    1.2  1  SRP54            SRP54-type protein, GTPase domain
    7.4e-07   29.3   1.6    1.9e-06   28.0   0.3    2.4  2  SRP54_N          SRP54-type protein, helical bundle domain
    1.5e-06   28.7   0.0    2.8e-06   27.8   0.0    1.5  1  AAA_16           AAA ATPase domain
    2.3e-06   27.1   0.0    4.5e-06   26.1   0.0    1.5  1  Zeta_toxin       Zeta toxin
    6.3e-06   26.3   0.0    2.3e-05   24.4   0.0    2.1  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    7.8e-06   25.7   0.8    1.2e-05   25.1   0.8    1.3  1  AAA_30           AAA domain
    8.7e-06   26.2   0.0    1.9e-05   25.1   0.0    1.6  1  AAA_17           AAA domain
    1.1e-05   25.1   1.4    6.9e-05   22.5   0.2    2.4  2  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00012   22.0   0.0    0.00025   21.0   0.0    1.5  1  APS_kinase       Adenylylsulphate kinase
    0.00017   21.6   0.3     0.0012   18.8   0.3    2.3  1  NTPase_1         NTPase
    0.00024   21.3   0.0    0.00044   20.4   0.0    1.5  1  AAA_33           AAA domain
    0.00025   21.5   0.1     0.0035   17.8   0.0    2.5  2  AAA              ATPase family associated with various cellul
    0.00038   20.8   0.0     0.0012   19.1   0.0    1.8  2  AAA_22           AAA domain
    0.00069   19.5   0.1          1    9.1   0.0    2.3  2  CLP1_P           mRNA cleavage and polyadenylation factor CLP
     0.0011   18.9   0.0     0.0031   17.4   0.0    1.8  1  MobB             Molybdopterin guanine dinucleotide synthesis
     0.0014   18.6   0.2     0.0048   16.8   0.0    1.9  2  AAA_31           AAA domain
     0.0015   18.0   0.0     0.0026   17.2   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
     0.0017   17.4   0.2     0.0036   16.3   0.2    1.7  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
     0.0019   18.2   0.0     0.0031   17.5   0.0    1.4  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0042   16.9   0.4      0.018   14.8   0.1    2.3  2  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0044   17.0   0.0     0.0071   16.4   0.0    1.5  1  ResIII           Type III restriction enzyme, res subunit
     0.0044   17.3   0.1      0.014   15.6   0.1    1.7  1  AAA_28           AAA domain
      0.006   16.4   0.0      0.013   15.4   0.0    1.6  1  AAA_11           AAA domain
     0.0062   16.2   0.0      0.031   14.0   0.0    2.0  2  Thymidylate_kin  Thymidylate kinase
     0.0088   16.4   0.1      0.017   15.5   0.1    1.5  1  AAA_19           AAA domain
  ------ inclusion threshold ------
       0.01   14.9   0.1      0.039   13.0   0.0    1.9  2  T2SSE            Type II/IV secretion system protein
      0.012   15.1   0.0      0.022   14.3   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
      0.015   15.3   0.0        1.2    9.2   0.0    2.6  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.02   15.4   0.0      0.028   14.9   0.0    1.4  1  ABC_tran         ABC transporter
       0.02   15.4   0.0      0.033   14.7   0.0    1.4  1  AAA_23           AAA domain
       0.02   14.3   0.0        1.1    8.6   0.0    2.5  2  SRPRB            Signal recognition particle receptor beta su
      0.022   14.7   0.0      0.038   13.9   0.0    1.4  1  Rad17            Rad17 P-loop domain
      0.031   14.2   0.0      0.079   12.9   0.0    1.6  1  ATPase_2         ATPase domain predominantly from Archaea
      0.049   13.4   0.0       0.11   12.3   0.0    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.057   12.3   0.0        0.1   11.5   0.0    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
       0.06   12.5   0.1       0.21   10.7   0.0    1.9  2  ArsA_ATPase      Anion-transporting ATPase
      0.064   13.2   0.0       0.12   12.3   0.0    1.4  1  NACHT            NACHT domain
      0.065   13.0   0.1       0.32   10.7   0.0    2.1  2  IstB_IS21        IstB-like ATP binding protein
      0.066   13.3   0.0       0.13   12.3   0.0    1.6  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.067   12.9   0.0        7.1    6.2   0.0    2.1  2  SWI2_SNF2        SWI2/SNF2 ATPase
      0.073   12.2   0.0       0.11   11.7   0.0    1.3  1  G-alpha          G-protein alpha subunit
      0.088   12.1   0.0       0.13   11.6   0.0    1.3  1  6PF2K            6-phosphofructo-2-kinase
      0.096   12.2   0.4       0.31   10.6   0.4    2.0  1  AAA_25           AAA domain
       0.11   12.6   1.0       0.55   10.3   0.2    2.4  2  MMR_HSR1         50S ribosome-binding GTPase
       0.13   11.7   0.0       0.23   10.8   0.0    1.4  1  SMC_N            RecF/RecN/SMC N terminal domain
       0.15   12.7   0.0       0.51   11.0   0.0    1.9  1  TIR_2            TIR domain
       0.18   11.5   0.1       0.49   10.1   0.1    1.7  1  AAA_24           AAA domain
       0.22   11.2   0.0       0.36   10.5   0.0    1.3  1  AAA_15           AAA ATPase domain
       0.23   11.2   0.3       0.35   10.6   0.3    1.2  1  AAA_21           AAA domain, putative AbiEii toxin, Type IV T


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 !  223.8   0.2   3.9e-69   1.4e-66       1     194 [.     106     299 ..     106     300 .. 0.98

  Alignments for each domain:
  == domain 1  score: 223.8 bits;  conditional E-value: 3.9e-69
                                       SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHH CS
                             SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeave 77 
                                       p vil+vG++G+GKTtt+ KLa++l+k+g++v+l++aDtfRa+A+eQL+tl++++g  v++++ +adpaava +a++
  gi|557693947|ref|YP_008797001.1| 106 PAVILFVGPNGSGKTTTVVKLAHYLRKRGYSVILASADTFRAGAIEQLETLGQRAGFMVVSQSYGADPAAVAVDALN 182
                                       579************************************************************************** PP

                                       HHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSS CS
                             SRP54  78 kakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgda 154
                                       ka + +++vvl+DTaGr + d+ l+ee++k+k+vvkpd v+++ da++g++av+qak F+e+vgi+ vil+k+D+da
  gi|557693947|ref|YP_008797001.1| 183 KASSMRVNVVLIDTAGRTELDRGLLEEMRKLKRVVKPDFVIYTGDALAGNAAVQQAKMFDEVVGIDYVILSKVDADA 259
                                       ***************************************************************************** PP

                                       STTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHH CS
                             SRP54 155 kgGaalsiaaelklPikfigvGekiedleefdperlvsrl 194
                                       kgG+a+si++++++P+ f+gvG++++dl    +e+l+++l
  gi|557693947|ref|YP_008797001.1| 260 KGGSAISISHSTGKPLLFLGVGQELDDLVDKPAEKLLEAL 299
                                       ****************************998888887765 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 !   28.0   0.3   5.1e-09   1.9e-06      12      74 ..      15      76 ..       5      82 .. 0.72
   2 ?   -1.7   0.0       9.7   3.5e+03      13      31 ..     197     214 ..     188     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 5.1e-09
                                      HCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTSS-HHHHHHHHHHHH CS
                           SRP54_N 12 lsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekklkpkqqvkkivkde 74
                                        +  k + + +e++l +   +L+eaDV+v++++ ++++++ + ++  ++ +  + + ++k++
  gi|557693947|ref|YP_008797001.1| 15 TVKTAKPSPKEVENVLSDFYLQLVEADVAVETADAIVNSLRHTLLE-MDVPRFGDREAVLKEA 76
                                      34445668999*****************************997766.5555444444444433 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 9.7
                                       CCSSCGHHHHHHHHHHHHH CS
                           SRP54_N  13 sgkskideedleealkele 31 
                                        g++++d  +lee +++l+
  gi|557693947|ref|YP_008797001.1| 197 AGRTELDRGLLEE-MRKLK 214
                                       6788999999999.66665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   7.7e-09   2.8e-06      18      88 ..     100     159 ..      86     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 7.7e-09
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde 88 
                                       + ++grp ++l++G+ G+GK++ v +l+++l+k+g  ++ + +d +         a a+   e l+ l+++
  gi|557693947|ref|YP_008797001.1| 100 ARKQGRPAVILFVGPNGSGKTTTVVKLAHYLRKRGYSVILASADTF--------RAGAI---EQLETLGQR 159
                                       6678999**************************9888899999999........33344...223333333 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.2e-08   4.5e-06      10     100 ..     100     193 ..      91     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.2e-08
                        Zeta_toxin  10 ypsqerPklillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelhPeyeeilk..adpkkaseltqkdasel 83 
                                         +q rP++il +G  G+GK+++  +l+ +l+ r+ +v+  ++D++R+   e  e l   a  + +s+   +d   +
  gi|557693947|ref|YP_008797001.1| 100 ARKQGRPAVILFVGPNGSGKTTTVVKLAHYLRkRGYSVILASADTFRAGAIEQLETLGqrAGFMVVSQSYGADPAAV 176
                                       4578****************************56666777799****966554444442247788888899999999 PP

                        Zeta_toxin  84 vekllqeaiengyniiv 100
                                       +  +l++a ++++n+++
  gi|557693947|ref|YP_008797001.1| 177 AVDALNKASSMRVNVVL 193
                                       99999999999999875 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 !   24.4   0.0   6.3e-08   2.3e-05       9      38 ..     116     145 ..     109     293 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 6.3e-08
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpq 38 
                                       G+GKTt++++La +l +rg+ V+l  aD+ 
  gi|557693947|ref|YP_008797001.1| 116 GSGKTTTVVKLAHYLRKRGYSVILASADTF 145
                                       9***********************999976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.8   3.3e-08   1.2e-05      19     151 ..     107     252 ..      95     257 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.3e-08
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa...............eelgieastiakllkrl 80 
                                        v + +Gp G+GKtt++ +l++ ++++g++vi+++     A +++               ++ g  a+         
  gi|557693947|ref|YP_008797001.1| 107 AVILFVGPNGSGKTTTVVKLAHYLRKRGYSVILASADTFRAGAIEqletlgqragfmvvsQSYG--AD--------- 172
                                       47788***************************99888777777773323332222222221222..22......... PP

                            AAA_30  81 k........grarlepgtllivDEagmv.....dtkqlaallkaaekagakvilvGDe.rQlasVeaGgvlrdlvea 143
                                                ++a+  + +++++D ag +       +++++l + ++     vi  GD  +  a+V++ ++++++v  
  gi|557693947|ref|YP_008797001.1| 173 PaavavdalNKASSMRVNVVLIDTAGRTeldrgLLEEMRKLKRVVKP--DFVIYTGDAlAGNAAVQQAKMFDEVV-- 245
                                       133333333324445669********995533333455555555555..88999999846788999999999885.. PP

                            AAA_30 144 agigtaeL 151
                                        gi+ + L
  gi|557693947|ref|YP_008797001.1| 246 -GIDYVIL 252
                                       .4555555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   5.3e-08   1.9e-05       1     107 [.     112     224 ..     112     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 5.3e-08
                                       EE-TTSSHHHHHHHHH...HHHTEEEE.EHHHHHHHHHHTT.TSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH..H CS
                            AAA_17   1 lGgPGsGKgtqceklv...ekygfthl.saGdllreeakrg.glakardemrklpleekkelqkeaaekiaeea..k 70 
                                       +G+ GsGK+t + kl+   +k g++++    d +r+ a ++ +   +r  ++ ++++   +  + a +++++++  +
  gi|557693947|ref|YP_008797001.1| 112 VGPNGSGKTTTVVKLAhylRKRGYSVIlASADTFRAGAIEQlETLGQRAGFMVVSQSYGADPAAVAVDALNKASsmR 188
                                       79*************9444566999872558****988766565578888999999999999999999999998533 PP

                                       SSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEE CS
                            AAA_17  71 kkgvlvdghprikeqagfldglpkevleelkpdaiil 107
                                        + vl+d+  r++ ++g+l+++ k  ++ +kpd++i+
  gi|557693947|ref|YP_008797001.1| 189 VNVVLIDTAGRTELDRGLLEEMRK-LKRVVKPDFVIY 224
                                       3569*****************985.99*********9 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 ?    1.0   0.1      0.78   2.9e+02      87     155 ..      12     102 ..       6     108 .. 0.60
   2 !   22.5   0.2   1.9e-07   6.9e-05       2     152 ..     108     257 ..     106     267 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.78
                                       EEEECTTTTHHHH.HTT..SHHHHHCCCECEEEEEEETTTH.....................CCHCCHHHHHHHHHH CS
                              cobW  87 liEttGlaePapv.aft..eeelksdltldavvavvDaknl....................eaeeekieekaedqla 140
                                       +iEt+  a+P p  + +  ++ + + +++d+ v   Da  +                       +e  ++ +e  ++
  gi|557693947|ref|YP_008797001.1|  12 FIETVKTAKPSPKeVENvlSDFYLQLVEADVAVETADA--IvnslrhtllemdvprfgdreAVLKEALKKAIEPLIK 86 
                                       67777777777763211333333333333333333333..2344555778888888888765557778888888899 PP

                                       TSSE.EEEE-HHHHCH CS
                              cobW 141 aadl.lvlnKtDllde 155
                                       +ad+ lvl  +D + +
  gi|557693947|ref|YP_008797001.1|  87 VADVnLVLKRVDEARK 102
                                       9998567777777765 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.9e-07
                                       EEEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SS...CHCCCCCC..HCCCT.EEEETTTTECCHCTT-HHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhllenraglklavivNefge...vsiDaell..retgveivelenGciCctlredllkel 73 
                                       v++++G+ GsGKTt + +l +  +++ + vi+    +    +i++     +++g ++v+ + G  + +++ d+l+++
  gi|557693947|ref|YP_008797001.1| 108 VILFVGPNGSGKTTTVVKLAHYLRKRGYSVILASADTfraGAIEQLETlgQRAGFMVVSQSYGADPAAVAVDALNKA 184
                                       68899***************777777777777655531013333322222333666999999999999766666554 PP

                                       HHHHHHHTT-SEEEEEECTTTTHHHH.HTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE- CS
                              cobW  74 ealeereerldviliEttGlaePapv.afteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnK 149
                                       +   ++  r++v+li t G  e     + + ++lk+ ++ d+v++  Da  l  +   ++ k+ d++   d ++l+K
  gi|557693947|ref|YP_008797001.1| 185 S---SM--RVNVVLIDTAGRTELDRGlLEEMRKLKRVVKPDFVIYTGDA--LAGNAAVQQAKMFDEVVGIDYVILSK 254
                                       4...44..4899*******666555525669******************..4467788899999************* PP

                                       HHH CS
                              cobW 150 tDl 152
                                       +D 
  gi|557693947|ref|YP_008797001.1| 255 VDA 257
                                       **6 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.8e-07   0.00025       1      49 [.     105     153 ..     105     160 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.8e-07
                                       S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                        APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                                       r++v+++ G  gsGK+t  ++l+++L+++g+sv+l   d+ R g  ++L
  gi|557693947|ref|YP_008797001.1| 105 RPAVILFVGPNGSGKTTTVVKLAHYLRKRGYSVILASADTFRAGAIEQL 153
                                       589***************************************9977766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3   3.2e-06    0.0012       3      78 ..     110     196 ..     108     225 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.2e-06
                                       EEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-........------EEEEEET.T--EEEEEETT...---S CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyteevr........eggrrigFkivdlasgeegiLarve...akre 68 
                                       +  Gp G+GKtT v k+++ l+++g++v    +   r          g+r gF +v+ + g       v+   + ++
  gi|557693947|ref|YP_008797001.1| 110 LFVGPNGSGKTTTVVKLAHYLRKRGYSVILASADTFRagaieqleTLGQRAGFMVVSQSYGADPAAVAVDalnKASS 186
                                       5679**********************996555555543222233356999999999987777666666664545555 PP

                                       SEETTEEE-H CS
                          NTPase_1  69 prvgkyvvdv 78 
                                       +rv    +d+
  gi|557693947|ref|YP_008797001.1| 187 MRVNVVLIDT 196
                                       5555555554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   1.2e-06   0.00044       1      39 [.     108     152 ..     108     219 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.2e-06
                            AAA_33   1 lvllvGlpGsGKstlaerl...lkklg..avllssdtlrr.rlfg 39 
                                       ++l+vG++GsGK+t + +l   l+k+g  ++l s dt+r  +++ 
  gi|557693947|ref|YP_008797001.1| 108 VILFVGPNGSGKTTTVVKLahyLRKRGysVILASADTFRAgAIEQ 152
                                       89*************999855577777755556777766633333 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 ?    0.8   0.0       1.6   5.9e+02      14      53 ..      46      80 ..      45     106 .. 0.72
   2 !   17.8   0.0   9.6e-06    0.0035       1      65 [.     109     195 ..     109     226 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.6
                                      HHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHH CS
                               AAA 14 lakavakelgvefleisgsellskyvgesekkirelfkea 53
                                      +a a++++l  ++le++++++      ++e+ ++e +k+a
  gi|557693947|ref|YP_008797001.1| 46 TADAIVNSLRHTLLEMDVPRFG-----DREAVLKEALKKA 80
                                      588999999999*****99998.....4444444444443 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 9.6e-06
                                       EEEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS....................STTHHHHHHHHHHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakel...gvefleisgsellsk....................yvgesekkirelfkeak 54 
                                       +l++Gp G GKT+++  +a+ l   g +++  s+ +++                      y  + ++   + +++a+
  gi|557693947|ref|YP_008797001.1| 109 ILFVGPNGSGKTTTVVKLAHYLrkrGYSVILASADTFRAGaieqletlgqragfmvvsqsYGADPAAVAVDALNKAS 185
                                       69*******************95444666666666666334555555555555555555333333333345555555 PP

                                       HTSTSEEEEEE CS
                               AAA  55 ekakpsilfiD 65 
                                       +++   +++iD
  gi|557693947|ref|YP_008797001.1| 186 SMR-VNVVLID 195
                                       554.5666666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       6.9   2.5e+03      37      68 ..      49      84 ..      19     105 .. 0.66
   2 !   19.1   0.0   3.3e-06    0.0012       6     115 ..     107     213 ..     100     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 6.9
                            AAA_22 37 e....erpevvfvtlpsstsskdllrellralglel 68
                                            r +++++++p  ++++ +l+e l++  ++l
  gi|557693947|ref|YP_008797001.1| 49 AivnsLRHTLLEMDVPRFGDREAVLKEALKKAIEPL 84
                                      344444566667777777777777776666655555 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 3.3e-06
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka......erlsse 76 
                                        +++ +G+ G+GKTt++ +l++ l         r++ ++v l+s  + +  + e l+ lg+++        ++++  
  gi|557693947|ref|YP_008797001.1| 107 AVILFVGPNGSGKTTTVVKLAHYL---------RKRGYSVILASADTFRAGAIEQLETLGQRAGFmvvsqsYGADPA 174
                                       67999*******************.........99999999999999999999999999988888999999888888 PP

                            AAA_22  77 ell.ealeqalraravielliiDEaqhlr.seealeeLrsl 115
                                       ++  +al++a++ r    +++iD a +      +lee r+l
  gi|557693947|ref|YP_008797001.1| 175 AVAvDALNKASSMRVN--VVLIDTAGRTElDRGLLEEMRKL 213
                                       8886888877777777..99999998863346666666555 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 !    8.1   0.0    0.0057       2.1       1      31 [.     113     143 ..     113     148 .. 0.93
   2 !    9.1   0.0    0.0028         1      94     151 ..     180     239 ..     171     260 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0057
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlD 31 
                                       Gp+ sGK+T +  L+ y+ ++g+++++  +D
  gi|557693947|ref|YP_008797001.1| 113 GPNGSGKTTTVVKLAHYLRKRGYSVILASAD 143
                                       899**********************998887 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0028
                            CLP1_P  94 kleenkkakasgliIntpGwvk.glg.aellleliealepdvvvvldqeellnelkrdlp 151
                                        l++ ++++ ++++I+t G  + + g +e + +l ++++pd v+++++    n   ++++
  gi|557693947|ref|YP_008797001.1| 180 ALNKASSMRVNVVLIDTAGRTElDRGlLEEMRKLKRVVKPDFVIYTGDALAGNAAVQQAK 239
                                       56778899***********998445745889999************99666666666655 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 !   17.4   0.0   8.5e-06    0.0031       1      30 [.     108     137 ..     108     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.5e-06
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrv 30 
                                       v+ +vg +gsGKTt + kl + l++rg++v
  gi|557693947|ref|YP_008797001.1| 108 VILFVGPNGSGKTTTVVKLAHYLRKRGYSV 137
                                       6889************************98 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       4.6   1.7e+03      78     113 ..      44      79 ..      15      83 .. 0.71
   2 !   16.8   0.0   1.3e-05    0.0048      12      40 ..     116     144 ..     108     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.6
                            AAA_31  78 venldlipssidLaeaeielvelekkeeilkellek 113
                                       ve+ d i+ s+    +e+++ ++ ++e +lke+l+k
  gi|557693947|ref|YP_008797001.1|  44 VETADAIVNSLRHTLLEMDVPRFGDREAVLKEALKK 79 
                                       456677777777777788888888888888888887 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.3e-05
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                       G GKTTt+v+la  l k+g+ v+l  +D+
  gi|557693947|ref|YP_008797001.1| 116 GSGKTTTVVKLAHYLRKRGYSVILASADT 144
                                       99**********************99997 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.2e-06    0.0026       3      43 ..     108     148 ..     106     202 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.2e-06
                                       EEEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH.T CS
                             KTI12   3 LvvltGlPssGKstrakeLakaleeekrsvvviddeslgie 43 
                                        +++ G   sGK+t + +La++l+++++sv++ + ++++  
  gi|557693947|ref|YP_008797001.1| 108 VILFVGPNGSGKTTTVVKLAHYLRKRGYSVILASADTFRAG 148
                                       58999*99***************************999843 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 !   16.3   0.2   9.9e-06    0.0036      24      66 ..     101     143 ..      80     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.9e-06
                                       GG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB  24 akaGraqvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                        k Gr  v+ + G  G+Gk t+v +l+  lr+rG+ v + + D
  gi|557693947|ref|YP_008797001.1| 101 RKQGRPAVILFVGPNGSGKTTTVVKLAHYLRKRGYSVILASAD 143
                                       578********************************99655544 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 !   17.5   0.0   8.5e-06    0.0031       2      46 ..     109     154 ..     108     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.5e-06
                                       EEEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT--HHHHH--B- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal.nreveyvqltrdtteedlkgrre 46 
                                       +l vGp G+gK++ + +la+ l +r + +++ ++dt ++  + ++e
  gi|557693947|ref|YP_008797001.1| 109 ILFVGPNGSGKTTTVVKLAHYLrKRGYSVILASADTFRAGAIEQLE 154
                                       589*******************99**********997766666555 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 ?   -2.3   0.0       8.6   3.1e+03     197     228 ..      19      50 ..       7      57 .. 0.73
   2 !   14.8   0.1   4.9e-05     0.018       1      28 [.     111     138 ..     111     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.6
                        ATP_bind_1 197 ykklaeaiaelleefalvlrflplssekeesi 228
                                        k +++++ ++l++f+l+l+   +++e+ ++i
  gi|557693947|ref|YP_008797001.1|  19 AKPSPKEVENVLSDFYLQLVEADVAVETADAI 50 
                                       45677889999999999977777777776665 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 4.9e-05
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsva 28 
                                       +vGp GsGKtt v +l+ +l++rg+sv 
  gi|557693947|ref|YP_008797001.1| 111 FVGPNGSGKTTTVVKLAHYLRKRGYSVI 138
                                       58*********************98876 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 !   16.4   0.0   1.9e-05    0.0071      12      60 ..      94     139 ..      72     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-05
                                       HHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                            ResIII  12 ienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60 
                                       ++++ e++k+ r   +l++ + G+GKT + +kl+ +l+k g+    ++l
  gi|557693947|ref|YP_008797001.1|  94 LKRVDEARKQGRPAVILFVGPNGSGKTTTVVKLAHYLRKRGYS---VIL 139
                                       44555556545666788*********************98773...444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   3.9e-05     0.014       2      31 ..     109     142 ..     108     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.9e-05
                            AAA_28   2 ivitGgestGKTtlleaLa....argypvvpEaa 31 
                                       i ++G+ ++GKTt++ +La    +rgy+v+  +a
  gi|557693947|ref|YP_008797001.1| 109 ILFVGPNGSGKTTTVVKLAhylrKRGYSVILASA 142
                                       889****************666555***994433 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.4e-05     0.013      16      44 ..     105     133 ..      93     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.4e-05
                            AAA_11  16 eseitliqGPPGtgKTktivellsqllsr 44 
                                       ++++ l+ GP G+gKT+t+v+l ++l +r
  gi|557693947|ref|YP_008797001.1| 105 RPAVILFVGPNGSGKTTTVVKLAHYLRKR 133
                                       45588999******************533 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   8.3e-05     0.031       3      29 ..     113     139 ..     111     153 .. 0.90
   2 ?   -0.9   0.0       3.1   1.1e+03     109     124 ..     211     225 ..     200     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.3e-05
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEE CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvl 29 
                                       G +G+GKtt + +l+ +l+++g++v+l
  gi|557693947|ref|YP_008797001.1| 113 GPNGSGKTTTVVKLAHYLRKRGYSVIL 139
                                       89*********************9665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.1
                                       HHGGGTTSE-SEEEEE CS
                   Thymidylate_kin 109 slnedvllkPdltfll 124
                                       ++ + v+ kPd++++ 
  gi|557693947|ref|YP_008797001.1| 211 RKLKRVV-KPDFVIYT 225
                                       4455666.9****995 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   4.7e-05     0.017      10      55 ..     106     148 ..      98     228 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.7e-05
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAa 55 
                                         v+l +++ G+GKT+++++  ++l ++g      il+ a t rA 
  gi|557693947|ref|YP_008797001.1| 106 PAVILFVGPNGSGKTTTVVKLAHYLRKRG-Y--SVILASADTFRAG 148
                                       5677888999*******998887777777.4..5677777777763 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 ?   13.0   0.0   0.00011     0.039     128     161 ..     105     138 ..      60     145 .. 0.78
   2 ?   -1.9   0.0       3.8   1.4e+03     237     256 ..     147     166 ..     134     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                             T2SSE 128 erglilvsGgTgsGKttllyallkeinksderiv 161
                                       +  +il+ G+ gsGKtt++  l +++ k+   ++
  gi|557693947|ref|YP_008797001.1| 105 RPAVILFVGPNGSGKTTTVVKLAHYLRKRGYSVI 138
                                       45789**************999999999855554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.8
                             T2SSE 237 agalerLeqlgaeveaaelk 256
                                       aga+e+Le+lg+++    ++
  gi|557693947|ref|YP_008797001.1| 147 AGAIEQLETLGQRAGFMVVS 166
                                       6899******9875555544 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 ?   14.3   0.0     6e-05     0.022      36      65 ..     109     138 ..      82     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6e-05
                             AAA_7  36 vllvGptGtGKtviikdllkkldkekylsl 65 
                                       +l+vGp G+GKt+++ +l + l k+ y+++
  gi|557693947|ref|YP_008797001.1| 109 ILFVGPNGSGKTTTVVKLAHYLRKRGYSVI 138
                                       79******************9999998876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0032       1.2      19      44 ..     106     131 ..      75     147 .. 0.78
   2 ?    3.4   0.0       0.2        72      30      56 ..     197     224 ..     177     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0032
                                       TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalg 44 
                                        +vil+ G+ G+GKTt v +la+ l 
  gi|557693947|ref|YP_008797001.1| 106 PAVILFVGPNGSGKTTTVVKLAHYLR 131
                                       457***************99998875 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.2
                                       SSHHHHHHHHHHHTT--.----TTTTSE CS
                              TsaE  30 aGKTtlvrglakalgve.evkSPTFtlv 56 
                                       aG T l rgl++++    +v  P F++ 
  gi|557693947|ref|YP_008797001.1| 197 AGRTELDRGLLEEMRKLkRVVKPDFVIY 224
                                       9*************76459999*99986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   7.8e-05     0.028      13      52 ..     108     151 ..      94     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.8e-05
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlke....q 52 
                                       ++ +vG+nG+GK+t +  la+ l++   ++ l ++d+ +    +
  gi|557693947|ref|YP_008797001.1| 108 VILFVGPNGSGKTTTVVKLAHYLRKRGYSVILASADTFRagaiE 151
                                       6789**********999999888877666666655555545553 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   8.9e-05     0.033      21      35 ..     108     122 ..      75     124 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 8.9e-05
                            AAA_23  21 ltlItGpNGaGKTTi 35 
                                       + l++GpNG+GKTT 
  gi|557693947|ref|YP_008797001.1| 108 VILFVGPNGSGKTTT 122
                                       789***********5 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 ?    8.6   0.0    0.0031       1.1       5      31 ..     108     134 ..     104     155 .. 0.79
   2 ?    3.2   0.0      0.15        53      44      78 ..     184     218 ..     162     256 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0031
                                       EEEEE-STTSSHHHHHHHHHHSS---B CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkkt 31 
                                        +l+vG+  sGKT+   +L     k+ 
  gi|557693947|ref|YP_008797001.1| 108 VILFVGPNGSGKTTTVVKLAHYLRKRG 134
                                       5789************99987655554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.15
                                       ...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEE CS
                             SRPRB  44 ksekgskltliDfPGheklrqklleklkaksslkg 78 
                                        s+   ++ liD  G  +l   lle++++ +++ +
  gi|557693947|ref|YP_008797001.1| 184 ASSMRVNVVLIDTAGRTELDRGLLEEMRKLKRVVK 218
                                       355567889****************9877666433 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0    0.0001     0.038      27      69 ..      86     130 ..      75     163 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.0001
                             Rad17  27 kieevkewlkadvLesrkkr....iLLisGPsGCgkstvvkvLskel 69 
                                       k+ +v+  lk     +++k+    ++L  GP G gk+t+v  L+  l
  gi|557693947|ref|YP_008797001.1|  86 KVADVNLVLKRVD--EARKQgrpaVILFVGPNGSGKTTTVVKLAHYL 130
                                       5556665555433..33333458899**************9999755 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   0.00022     0.079       8      53 ..      94     139 ..      88     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00022
                          ATPase_2   8 lkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviy 53 
                                       lk++ e  ++++  +++  Gp gsGKt+ + +++  l++ ++ vi 
  gi|557693947|ref|YP_008797001.1|  94 LKRVDEARKQGRPAVILFVGPNGSGKTTTVVKLAHYLRKRGYSVIL 139
                                       7888888899999999999*******************99999985 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 ?   12.3   0.0    0.0003      0.11      24      38 ..     108     122 ..      96     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0003
                            AAA_29  24 atlltGpsGsGKSTl 38 
                                       ++l++Gp+GsGK+T 
  gi|557693947|ref|YP_008797001.1| 108 VILFVGPNGSGKTTT 122
                                       689**********96 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 ?   11.5   0.0   0.00028       0.1      18      48 ..     109     139 ..      99     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                     TrwB_AAD_bind  18 ilivGttGsGKtqalekllrairargdraiv 48 
                                       il+vG  GsGKt+++ kl + +r+rg  +i 
  gi|557693947|ref|YP_008797001.1| 109 ILFVGPNGSGKTTTVVKLAHYLRKRGYSVIL 139
                                       899***********************99886 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00058      0.21       3      38 ..     108     143 ..     106     147 .. 0.95
   2 ?   -2.1   0.0       4.8   1.8e+03     121     133 ..     185     197 ..     158     252 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00058
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                       vil+ G  G GKtt    +a +l + g++v+l s D
  gi|557693947|ref|YP_008797001.1| 108 VILFVGPNGSGKTTTVVKLAHYLRKRGYSVILASAD 143
                                       799*******************************99 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.8
                                       HCSSSSEEEEESB CS
                       ArsA_ATPase 121 keeeydvvvlDta 133
                                       +++  +vv++Dta
  gi|557693947|ref|YP_008797001.1| 185 SSMRVNVVLIDTA 197
                                       3333344444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00033      0.12       2      28 ..     108     134 ..     107     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00033
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegk 28 
                                       +++  G++GsGKTt + kla+ ++++ 
  gi|557693947|ref|YP_008797001.1| 108 VILFVGPNGSGKTTTVVKLAHYLRKRG 134
                                       68899***************9999876 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 ?   10.7   0.0   0.00088      0.32      48      84 ..     107     143 ..      95     168 .. 0.89
   2 ?   -0.6   0.0       2.5   9.3e+02     106     124 ..     186     204 ..     175     238 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00088
                         IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsvlfvrve 84 
                                       + i+++Gp G GK+   + l++   ++g+sv+  +++
  gi|557693947|ref|YP_008797001.1| 107 AVILFVGPNGSGKTTTVVKLAHYLRKRGYSVILASAD 143
                                       56899**************************987765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.5
                         IstB_IS21 106 llkvdllilDdlgllpldq 124
                                        ++v+++++D  g ++ld+
  gi|557693947|ref|YP_008797001.1| 186 SMRVNVVLIDTAGRTELDR 204
                                       5667777777777777765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00036      0.13       5      75 ..     108     195 ..     105     210 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00036
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS........... CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG........... 70 
                                        il++gp+g+Gkt +  +la +l+ k+  ++i a a ++     + + ++ l + + ++v  +  G           
  gi|557693947|ref|YP_008797001.1| 108 VILFVGPNGSGKTTTVVKLAHYLR-KRGYSVILASADTFRA--GAIEQLETLGQRAGFMVVSQSYGadpaavavdal 181
                                       79**********************.7777777777777766..3344444555555555555555555553333333 PP

                                       .........EEEEE CS
                             AAA_2  71 .........ivllD 75 
                                                +vl+D
  gi|557693947|ref|YP_008797001.1| 182 nkassmrvnVVLID 195
                                       35566666666665 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.019       7.1      26      44 ..     114     132 ..      79     140 .. 0.71
   2 ?    4.4   0.0     0.069        25     113     174 ..     181     246 ..     142     268 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.019
                         SWI2_SNF2  26 tqGSGKsltmvflakklle 44 
                                         GSGK+ t v+la+ l++
  gi|557693947|ref|YP_008797001.1| 114 PNGSGKTTTVVKLAHYLRK 132
                                       47*************9998 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.069
                         SWI2_SNF2 113 levlsereniivlvDEaHRsqyg.elakklrka..lpnaafigFTGTPilkkd.kktkevFgeyid 174
                                       l++ s+ +  +vl+D a R++ + +l +++rk   + +  f+ +TG  +  +   + +++F+e++ 
  gi|557693947|ref|YP_008797001.1| 181 LNKASSMRVNVVLIDTAGRTELDrGLLEEMRKLkrVVKPDFVIYTGDALAGNAaVQQAKMFDEVVG 246
                                       4555555667999*******9987666777654113455688899988886542556777877764 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   0.0   0.00029      0.11      12      44 ..      95     127 ..      49     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00029
                                       XXXXXXXXE..EEEEEEEESTTSSHHHHHHHHH CS
                           G-alpha  12 kaerkarkkkrevkllllGqseSGKsTilkqlk 44 
                                       k+  +ark+ r+  +l++G ++SGK+T++ +l 
  gi|557693947|ref|YP_008797001.1|  95 KRVDEARKQGRPAVILFVGPNGSGKTTTVVKLA 127
                                       44566777788999*************987665 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00035      0.13       9      51 ..     102     149 ..      95     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00035
                                       T..S-EEEEEESSTTSSHHHHHHHHHHHHH.....HTT--EEEEEHHH CS
                             6PF2K   9 lknsklvivlvGLpargKtyiskkltrylk.....wlgvrtkvFnvgk 51 
                                       ++ ++ vi++vG    gKt++ +kl +yl+      +  ++ +F +g 
  gi|557693947|ref|YP_008797001.1| 102 KQGRPAVILFVGPNGSGKTTTVVKLAHYLRkrgysVILASADTFRAGA 149
                                       4678999***********************444444444555555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.4   0.00084      0.31      34      55 ..     107     128 ..     100     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00084
                            AAA_25  34 elallaGapgtGKttlaldlal 55 
                                       +++l++G+ g+GKtt ++ la+
  gi|557693947|ref|YP_008797001.1| 107 AVILFVGPNGSGKTTTVVKLAH 128
                                       799****************996 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       5.5     2e+03      75      91 ..      39      52 ..      21     102 .. 0.51
   2 ?   10.3   0.2    0.0015      0.55       2      86 ..     109     229 ..     108     254 .. 0.55

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 5.5
                                      CTSEEEEEEETTTTCSH CS
                          MMR_HSR1 75 eadlillvvdaseeklk 91
                                      ead+++   da    ++
  gi|557693947|ref|YP_008797001.1| 39 EADVAVETADAI---VN 52
                                      444444444422...11 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0015
                                       EEEEESTTSSHHHHHHHHHT.......STEEESSSTTSSSSEEEEEEEETTEE........................ CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.......ekaivsdkpgtTrdinegrvklkgke........................ 47 
                                       +++vG   +GK+t + +l         ++  +s+  +    i++ +    g++                        
  gi|557693947|ref|YP_008797001.1| 109 ILFVGPNGSGKTTTVVKLAHylrkrgySVILASADTFRAGAIEQLETL--GQRagfmvvsqsygadpaavavdalnk 183
                                       678888888888888888864333222122222222222222222211..111344444455555566666666666 PP

                                       .......EEEEECGGCSSHHHHHHHHHHHHHHHHC...TSEEEEEEETT CS
                          MMR_HSR1  48 .......ielvDtpGliegaseekglgkaflalee...adlillvvdas 86 
                                              ++l+Dt+G     + ++gl +++++l++    d +++  da 
  gi|557693947|ref|YP_008797001.1| 184 assmrvnVVLIDTAGRT---ELDRGLLEEMRKLKRvvkPDFVIYTGDAL 229
                                       6666666********33...46666555555554432169999988865 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 ?   10.8   0.0   0.00064      0.23      22      50 ..     104     132 ..      94     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00064
                                       TTSSEEEEEESTTSSHHHHHHHHHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  22 fsksftaivGpNGSGKsnlldAilFvLGe 50 
                                         + +   vGpNGSGK+  +  + ++L +
  gi|557693947|ref|YP_008797001.1| 104 GRPAVILFVGPNGSGKTTTVVKLAHYLRK 132
                                       56777889*********998888887765 PP

>> TIR_2  TIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0014      0.51      11      67 ..     121     174 ..     114     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0014
                             TIR_2  11 ewaeklaeaLeaagirvwldrwd.lkpgedweeeieeaiessdvvlvvlspaylesew 67 
                                         + kla++L+++g++v l + d +++g    e++e   +  ++  +v+s++y +++ 
  gi|557693947|ref|YP_008797001.1| 121 TTVVKLAHYLRKRGYSVILASADtFRAGA--IEQLETLGQ--RAGFMVVSQSYGADPA 174
                                       5689*************987766255554..666644333..4557788888886654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0013      0.49       3      22 ..     107     126 ..     105     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                            AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                                       + il +Gp+g+GKTt++ +l
  gi|557693947|ref|YP_008797001.1| 107 AVILFVGPNGSGKTTTVVKL 126
                                       78999***********9888 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00097      0.36      25      40 ..     108     123 ..      94     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00097
                            AAA_15  25 ltvliGkNnsGKSsil 40 
                                       + +++G+N+sGK++ +
  gi|557693947|ref|YP_008797001.1| 108 VILFVGPNGSGKTTTV 123
                                       789**********976 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   0.3   0.00096      0.35       2      14 ..     109     121 ..     108     127 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00096
                            AAA_21   2 nvliGpNgsGKSn 14 
                                        +++GpNgsGK++
  gi|557693947|ref|YP_008797001.1| 109 ILFVGPNGSGKTT 121
                                       689*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       767  (0.0427799); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); expected 358.6 (0.02)
Passed Vit filter:                       157  (0.00875676); expected 17.9 (0.001)
Passed Fwd filter:                        49  (0.002733); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              49  [number of targets reported over threshold]
# CPU time: 0.62u 0.30s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 2138.59
//
Query:       gi|557693948|ref|YP_008797002.1|  [L=146]
Description: prefoldin subunit alpha [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   70.2   0.6      2e-19   69.7   0.6    1.2  1  Prefoldin      Prefoldin subunit
     0.0042   17.3   2.7        0.6   10.4   0.3    2.2  2  BLOC1_2        Biogenesis of lysosome-related organelles comp
     0.0062   16.8   6.5       0.08   13.2   1.2    2.5  2  Lzipper-MIP1   Leucine-zipper of ternary complex factor MIP1
     0.0063   16.5   3.4     0.0063   16.5   3.4    2.7  3  Exonuc_VII_S   Exonuclease VII small subunit
     0.0094   16.0  10.5      0.027   14.5   2.5    2.1  2  DHR10          Designed helical repeat protein 10 domain
     0.0095   16.4   0.1          1    9.9   0.0    2.2  2  HMA            Heavy-metal-associated domain
  ------ inclusion threshold ------
      0.034   14.3   4.4       0.36   11.0   0.1    2.1  2  Tropomyosin_1  Tropomyosin like
      0.054   13.0   0.2      0.084   12.3   0.1    1.4  1  adh_short      short chain dehydrogenase
      0.058   12.3   5.1       0.56    9.0   0.4    2.0  2  Spc7           Spc7 kinetochore protein
       0.16   11.3   8.5        1.5    8.1   1.4    2.1  2  DUF3450        Protein of unknown function (DUF3450)
       0.24   11.4   6.9        2.5    8.2   1.7    2.2  2  TMF_DNA_bd     TATA element modulatory factor 1 DNA binding
       0.24   11.7   2.9          1    9.7   0.2    2.2  2  KxDL           Uncharacterized conserved protein
       0.26   10.6   3.8       0.41    9.9   0.3    2.0  2  FmiP_Thoc5     Fms-interacting protein/Thoc5
       0.27   12.3   0.8        0.9   10.6   0.0    2.0  2  DUF5320        Family of unknown function (DUF5320)
       0.32   10.8   6.9       0.81    9.5   0.2    2.2  2  DivIC          Septum formation initiator
        1.2    9.6  12.1        4.9    7.7   2.4    2.3  2  ZapB           Cell division protein ZapB
        3.1    7.9   7.7       0.69   10.0   0.7    2.1  2  DivIVA         DivIVA protein
        6.3    7.5  12.6        5.3    7.7   1.5    3.1  3  SlyX           SlyX


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 !   69.7   0.6     2e-22     2e-19       2     116 ..      23     137 ..      22     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 2e-22
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHH CS
                         Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeA 78 
                                       ++ ++ lqa++ +l+ +  e e++ + +++++k++ ++++lvp+g+g +++a++++ +kv+v+lGag+y+ k le+ 
  gi|557693948|ref|YP_008797002.1|  23 ERLVADLQARILTLQRSVAEHEEAVKLIEEIRKSGGSMKILVPIGSGTFAEASLQSVEKVTVSLGAGVYAVKALEDT 99 
                                       567889*********************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  79 iellkkkleelekqlekleeeleklkdqittleanlaq 116
                                         ll k+ + l++ ++ l + l + + ++++l++ l++
  gi|557693948|ref|YP_008797002.1| 100 QQLLTKRNQALQAYVDALAKRLSEYAGRAEELRRFLNR 137
                                       *************************9999999877665 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 !   10.4   0.3    0.0006       0.6       8      55 ..       5      52 ..       1      61 [. 0.82
   2 !    7.3   0.1    0.0059       5.9      20      64 ..      91     135 ..      74     141 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0006
                           BLOC1_2  8 skyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklne 55
                                      s++ eae++ + e+++lLe+l    ++++  l++++a+ e+ ++ ++e
  gi|557693948|ref|YP_008797002.1|  5 SAMSEAEVAQALEELQLLERLVADLQARILTLQRSVAEHEEAVKLIEE 52
                                      566788999999999999999999999999999999999988887766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0059
                           BLOC1_2  20 edyklLeklNeaasekykklkdvaaslekkleklnekyeelqpyl 64 
                                         +k Le   +  +++ ++l+  ++ l+k l+++  + eel+ +l
  gi|557693948|ref|YP_008797002.1|  91 YAVKALEDTQQLLTKRNQALQAYVDALAKRLSEYAGRAEELRRFL 135
                                       556677777777777777777777777777777777777777766 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 !   13.2   1.2   8.1e-05      0.08      47      82 ..       6      41 ..       2      43 .. 0.88
   2 ?    6.0   0.3     0.014        14       4      37 ..     105     142 ..     103     146 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.1e-05
                      Lzipper-MIP1 47 tllpkkakellkeiallEeevvkLEqkllsLyrklf 82
                                      +++  ++++ l+e+ llE  v+ L+ ++l+L+r++ 
  gi|557693948|ref|YP_008797002.1|  6 AMSEAEVAQALEELQLLERLVADLQARILTLQRSVA 41
                                      55667899*************************976 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.014
                      Lzipper-MIP1   4 ekrssLeqeveqLqerLqe....eeklrraLekalsss 37 
                                       +++++L+  v  L +rL+e     e+lrr+L +al+s+
  gi|557693948|ref|YP_008797002.1| 105 KRNQALQAYVDALAKRLSEyagrAEELRRFLNRALTSQ 142
                                       678899999********9633336899******99433 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 !   16.5   3.4   6.3e-06    0.0063       3      41 ..      17      55 ..      14      56 .. 0.92
   2 ?   -2.0   0.1         4     4e+03      34      45 ..      94     105 ..      92     112 .. 0.48
   3 ?   -0.8   0.1       1.6   1.6e+03      31      45 ..     127     141 ..     117     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.3e-06
                      Exonuc_VII_S  3 ealaeLeeIvekLEsgelsLeeslklyeeGvkLlkeCek 41
                                      e l+ Le +v+ L+   l+L  s+++ ee+vkL++e +k
  gi|557693948|ref|YP_008797002.1| 17 EELQLLERLVADLQARILTLQRSVAEHEEAVKLIEEIRK 55
                                      567889****************************99876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                      Exonuc_VII_S  34 kLlkeCekkLde 45 
                                       k l+  ++ L++
  gi|557693948|ref|YP_008797002.1|  94 KALEDTQQLLTK 105
                                       444444455544 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.6
                      Exonuc_VII_S  31 eGvkLlkeCekkLde 45 
                                       ++++L ++++  L+ 
  gi|557693948|ref|YP_008797002.1| 127 RAEELRRFLNRALTS 141
                                       788999999988876 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 !   14.5   2.5   2.7e-05     0.027       2      47 ..      10      55 ..       9      61 .. 0.94
   2 !    6.5   1.1    0.0084       8.4      46     112 ..      73     139 ..      71     144 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.7e-05
                             DHR10  2 eslaeekeelaelErkarelqakidalqvvekdlrsciklleeiea 47
                                      +++a++ eel+ lEr   +lqa+i +lq+  ++ ++++kl+eei +
  gi|557693948|ref|YP_008797002.1| 10 AEVAQALEELQLLERLVADLQARILTLQRSVAEHEEAVKLIEEIRK 55
                                      679999*************************************976 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0084
                             DHR10  46 eaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaakarl 112
                                       ea l+++e++   l +   a++ +e +++ l+++ + lq  ++   ++l+ +  +aee r+  +++l
  gi|557693948|ref|YP_008797002.1|  73 EASLQSVEKVTVSLGAGVYAVKALEDTQQLLTKRNQALQAYVDALAKRLSEYAGRAEELRRFLNRAL 139
                                       5667777777777777777777778888888888888888888888888887777777776555555 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0     0.001         1       8      60 ..       4      57 ..       1      59 [. 0.89
   2 ?    4.7   0.0     0.042        42      22      43 ..      75      98 ..      74     121 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                               HMA  8 hCagCaakvekvLselpgVesvkvdlatktvtVegdaes.tklrkiieaiekag 60
                                        a ++a v ++L+el+  e  + dl ++ +t   ++++  +  k+ie+i+k+g
  gi|557693948|ref|YP_008797002.1|  4 FSAMSEAEVAQALEELQLLERLVADLQARILTLQRSVAEhEEAVKLIEEIRKSG 57
                                      566789999************************9988887999********987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.042
                               HMA 22 elpgVesvkvdlatktvtVeg..d 43
                                      +l++Ve+v+v+l+++   V+   d
  gi|557693948|ref|YP_008797002.1| 75 SLQSVEKVTVSLGAGVYAVKAleD 98
                                      6889*********99999888533 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.9     0.025        25      21      63 ..      10      52 ..       5      61 .. 0.75
   2 ?   11.0   0.1   0.00037      0.36      33      68 ..      96     131 ..      72     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.025
                     Tropomyosin_1 21 ekvKeleqenlekeqeiksLtkknqqleeevekleeklkeake 63
                                      ++v ++ +e +  e  +++L+ ++ +l+  v + ee++k  +e
  gi|557693948|ref|YP_008797002.1| 10 AEVAQALEELQLLERLVADLQARILTLQRSVAEHEEAVKLIEE 52
                                      5555666667778889999999999999999999999886555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00037
                     Tropomyosin_1  33 keqeiksLtkknqqleeevekleeklkeakekaees 68 
                                        e+  + Ltk+nq+l++ v+ l ++l+e+   aee 
  gi|557693948|ref|YP_008797002.1|  96 LEDTQQLLTKRNQALQAYVDALAKRLSEYAGRAEEL 131
                                       57777889*********************9999985 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   8.4e-05     0.084      26     104 ..      11      82 ..       4     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.4e-05
                                       EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHHHHH CS
                         adh_short  26 kvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselseeewe 102
                                       +v+ + ++ + le++++ l++   ++l++q  v+++ee+ +l+e+++k  g++ +Lv   +     +f+e s + +e
  gi|557693948|ref|YP_008797002.1|  11 EVAQALEELQLLERLVADLQA---RILTLQRSVAEHEEAVKLIEEIRKSGGSMKILVPIGSG----TFAEASLQSVE 80 
                                       455555555566666666665...7*******************************986555....57777777777 PP

                                       HH CS
                         adh_short 103 rv 104
                                       +v
  gi|557693948|ref|YP_008797002.1|  81 KV 82 
                                       65 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.5    0.0054       5.4     199     238 ..      10      49 ..       2      59 .. 0.45
   2 ?    9.0   0.4   0.00056      0.56     148     192 ..      93     137 ..      77     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0054
                              Spc7 199 eeLeelreelaelkaeieekkkelaelqeqleeleekiee 238
                                       +e++++ eel+ l+  ++ +++++ +lq+ ++e ee+++ 
  gi|557693948|ref|YP_008797002.1|  10 AEVAQALEELQLLERLVADLQARILTLQRSVAEHEEAVKL 49 
                                       3333444444444444444444444444444444444433 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00056
                              Spc7 148 legleedkelLekqeeeldellpeleeekaeleeeleklqeaaee 192
                                       +++le+ ++lL+k+++ l++++++l ++ +e   ++e+l+++ + 
  gi|557693948|ref|YP_008797002.1|  93 VKALEDTQQLLTKRNQALQAYVDALAKRLSEYAGRAEELRRFLNR 137
                                       6789999999****************************9997665 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.4    0.0015       1.5      50      96 ..       9      55 ..       4      57 .. 0.90
   2 ?    7.5   0.9    0.0022       2.2      53      93 ..      93     133 ..      72     144 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0015
                           DUF3450 50 laeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeier 96
                                      +ae+ ++ eel+ le   + l++ + ++++++a+ ee  + ieei++
  gi|557693948|ref|YP_008797002.1|  9 EAEVAQALEELQLLERLVADLQARILTLQRSVAEHEEAVKLIEEIRK 55
                                      789999999****************************9999999986 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0022
                           DUF3450  53 yralkeeleslevyneqlerlvasqeqeiasleeqieeiee 93 
                                       ++al++ ++ l++ n+ l+++v+++ +++++   + ee+++
  gi|557693948|ref|YP_008797002.1|  93 VKALEDTQQLLTKRNQALQAYVDALAKRLSEYAGRAEELRR 133
                                       56777777788888888888888888888777777777665 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 ?    8.2   1.7    0.0025       2.5      11      50 ..       9      48 ..       6      58 .. 0.90
   2 ?    6.1   0.3     0.011        11      31      72 ..      96     137 ..      92     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0025
                        TMF_DNA_bd 11 DeqIaqLmeEGekLskkelklnntikkLrkknkelekeik 50
                                      ++++aq +eE++ L+    +l + i  L+  ++e+e+ +k
  gi|557693948|ref|YP_008797002.1|  9 EAEVAQALEELQLLERLVADLQARILTLQRSVAEHEEAVK 48
                                      6899********************************9886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.011
                        TMF_DNA_bd  31 lnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                       l+ t+  L k n+ l   ++ l k+l+++    eel+++l +
  gi|557693948|ref|YP_008797002.1|  96 LEDTQQLLTKRNQALQAYVDALAKRLSEYAGRAEELRRFLNR 137
                                       566777788888888888888888888888888888888776 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.3      0.19   1.9e+02      30      58 ..      20      48 ..       5      55 .. 0.74
   2 ?    9.7   0.2     0.001         1      22      65 ..      93     136 ..      75     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.19
                              KxDL 30 reLlelnalsqerlaklrarfkqgtkllk 58
                                      + L++l a +q+r   l+  ++++ +++k
  gi|557693948|ref|YP_008797002.1| 20 QLLERLVADLQARILTLQRSVAEHEEAVK 48
                                      45777888888888888888888876665 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.001
                              KxDL  22 sgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLe 65 
                                       ++ l+++++ L++ n+ +q+ +  l +r+ +++  + e+++ L+
  gi|557693948|ref|YP_008797002.1|  93 VKALEDTQQLLTKRNQALQAYVDALAKRLSEYAGRAEELRRFLN 136
                                       67899999999999999999999999999999999999988776 PP

>> FmiP_Thoc5  Fms-interacting protein/Thoc5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3     0.097        96      87     122 ..      15      51 ..       3      63 .. 0.58
   2 ?    9.9   0.3   0.00042      0.41     111     163 ..      93     145 ..      90     146 .] 0.93

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.097
                        FmiP_Thoc5  87 adehelmlaRLewEleqRke.laeqlkeleekkkkle 122
                                       a e+ + l+RL  +l+ R+  l+  + e ee +k +e
  gi|557693948|ref|YP_008797002.1|  15 ALEELQLLERLVADLQARILtLQRSVAEHEEAVKLIE 51 
                                       3566677778888888887514444444444444443 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00042
                        FmiP_Thoc5 111 lkeleekkkkleqeieekkkfLssLppkLkslkkatkplqealglpltkerkq 163
                                       +k+le  ++ l + ++  +++ ++L+++L++ +  +++l++ l+  lt++++q
  gi|557693948|ref|YP_008797002.1|  93 VKALEDTQQLLTKRNQALQAYVDALAKRLSEYAGRAEELRRFLNRALTSQQRQ 145
                                       699*****************************************999977765 PP

>> DUF5320  Family of unknown function (DUF5320)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3       2.5   2.5e+03      68      94 ..      12      38 ..       3      43 .. 0.62
   2 ?   10.6   0.0   0.00091       0.9      65      98 ..      90     123 ..      64     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.5
                           DUF5320 68 easkeeekelLeeqaeaLeeeleaikk 94
                                       a++ ee +lLe+  + L++++ ++++
  gi|557693948|ref|YP_008797002.1| 12 VAQALEELQLLERLVADLQARILTLQR 38
                                      445556777777777777766666555 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00091
                           DUF5320  65 etaeaskeeekelLeeqaeaLeeeleaikkrlke 98 
                                        +a ++ e++++lL+++ +aL++ ++a+ krl+e
  gi|557693948|ref|YP_008797002.1|  90 VYAVKALEDTQQLLTKRNQALQAYVDALAKRLSE 123
                                       45677889************************98 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.1     0.046        46      17      49 ..      17      49 ..       7      56 .. 0.70
   2 ?    9.5   0.2   0.00081      0.81      14      50 ..      88     124 ..      82     133 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.046
                                      XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                             DivIC 17 laykqlkqeiaalqaelaklkaeneeLeaevkd 49
                                        ++ l++ +a+lqa + +l+   +e e+ vk+
  gi|557693948|ref|YP_008797002.1| 17 EELQLLERLVADLQARILTLQRSVAEHEEAVKL 49
                                      455666777777777777777777777777765 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00081
                                       XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC  14 kgllaykqlkqeiaalqaelaklkaeneeLeaevkdL 50 
                                        g++a+k+l+   + l++ +++l+a  ++L+++++++
  gi|557693948|ref|YP_008797002.1|  88 AGVYAVKALEDTQQLLTKRNQALQAYVDALAKRLSEY 124
                                       5667777777777777777777777777777776665 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.3    0.0074       7.4      10      51 ..       9      50 ..       8      59 .. 0.81
   2 ?    7.7   2.4    0.0049       4.9      14      52 ..      94     132 ..      92     145 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0074
                              ZapB 10 EskiqkaidtitlLqmeieeLkeeneelkeenreleeeneql 51
                                      E+ + +a+++++lL   +++L+++  +l++  +e ee ++  
  gi|557693948|ref|YP_008797002.1|  9 EAEVAQALEELQLLERLVADLQARILTLQRSVAEHEEAVKLI 50
                                      677899999999999999999999999999998888776654 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0049
                              ZapB  14 qkaidtitlLqmeieeLkeeneelkeenreleeeneqlk 52 
                                       +++ dt +lL +++++L++ + +l+++  e     e+l+
  gi|557693948|ref|YP_008797002.1|  94 KALEDTQQLLTKRNQALQAYVDALAKRLSEYAGRAEELR 132
                                       556688888999999999999888888888876666665 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.2      0.25   2.5e+02      33      59 ..      18      44 ..       6      56 .. 0.42
   2 ?   10.0   0.7    0.0007      0.69      33      69 ..      99     135 ..      93     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.25
                                      HHHHHHHHHHHHHHHHHCCCCTXXXXX CS
                            DivIVA 33 dyeallkeneelkekvkeleeklkeyk 59
                                      +++ l + +++l++++ +l+++++e++
  gi|557693948|ref|YP_008797002.1| 18 ELQLLERLVADLQARILTLQRSVAEHE 44
                                      222222333333333333333333333 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0007
                                       HHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXX CS
                            DivIVA  33 dyeallkeneelkekvkeleeklkeykeleetLkktl 69 
                                       + + l k+n++l++ v++l ++l+ey+ + e+L++ l
  gi|557693948|ref|YP_008797002.1|  99 TQQLLTKRNQALQAYVDALAKRLSEYAGRAEELRRFL 135
                                       45567899***********************999765 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   1.5    0.0053       5.3      16      52 ..      16      52 ..       8      61 .. 0.57
   2 ?    4.4   0.5     0.058        57      19      53 ..      93     127 ..      90     134 .. 0.69
   3 ?    2.3   0.2      0.27   2.7e+02      22      32 ..     135     145 ..     128     146 .] 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0053
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXX CS
                              SlyX 16 edtieeLndvvaeqqqqidrlqrqlrllaerlkelee 52
                                       + ++ L + va+ q +i  lqr +++ +e +k +ee
  gi|557693948|ref|YP_008797002.1| 16 LEELQLLERLVADLQARILTLQRSVAEHEEAVKLIEE 52
                                      4445555666666666666666666666665555544 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.058
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX  19 ieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                       +++L d+     ++ ++lq+ +++la+rl+e + +
  gi|557693948|ref|YP_008797002.1|  93 VKALEDTQQLLTKRNQALQAYVDALAKRLSEYAGR 127
                                       55666666666777778888888888888776554 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHH CS
                              SlyX  22 Lndvvaeqqqq 32 
                                       Ln++++ qq+q
  gi|557693948|ref|YP_008797002.1| 135 LNRALTSQQRQ 145
                                       9********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1438  (0.0802053); expected 358.6 (0.02)
Passed bias filter:                      780  (0.0435049); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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):              18  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1003.05
//
Query:       gi|557693949|ref|YP_008797003.1|  [L=222]
Description: translation initiation factor eIF-6 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-57  193.5   4.8    3.1e-57  193.2   4.8    1.1  1  eIF-6     eIF-6 family


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 !  193.2   4.8   1.7e-61   3.1e-57       4     197 .]       8     202 ..       6     202 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.2 bits;  conditional E-value: 1.7e-61
                                       BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHHHHH CS
                             eIF-6   4 iegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeeleklk 80 
                                       + gs e+G+fa  t++y++++++++ ++v++++++Lkv+++ t++a+s lv  +++gNsngll++++v deel+k+k
  gi|557693949|ref|YP_008797003.1|   8 VLGSAEVGLFALPTDRYVILSKEINPSKVRVFQQVLKVDTILTSLADSILVAPFAAGNSNGLLLSKLVVDEELKKIK 84 
                                       5799************************************************************************* PP

                                       HHHH.---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE-T CS
                             eIF-6  81 eslk.leverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllvhp 156
                                        +l+ l+++rl++k+tA+GN+il+ND++A+v++ l k++++++advLg e+v++t+a+ + vGs++++tn g+lv  
  gi|557693949|ref|YP_008797003.1|  85 AALPdLNIHRLDTKYTAVGNLILCNDRGAVVSSLLGKNVAKVVADVLGTETVSSTVANRSYVGSLVAATNVGALVFV 161
                                       ****99*********************************************************************** PP

                                       T--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                             eIF-6 157 kateeeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                       +a+++el+ +e++l+v+v++gTvN G+ + +sg+ aN++ga
  gi|557693949|ref|YP_008797003.1| 162 DAEDDELKLVEDVLHVNVDTGTVNGGVLFPRSGIAANSSGA 202
                                       **************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1649.51
//
Query:       gi|557693950|ref|YP_008797004.1|  [L=93]
Description: large subunit ribosomal protein L31e [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   37.8   0.2    2.2e-09   37.4   0.2    1.2  1  Ribosomal_L31e  Ribosomal protein L31e


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 !   37.4   0.2   1.2e-13   2.2e-09      19      79 ..      20      77 ..       7      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.2e-13
                    Ribosomal_L31e 19 gfkkraprAlkeikkfamkemgtpdvridtrLnkavwakgirnvpyrirvrlsrkrnedEd 79
                                      ++ +r   A++ +k++am++ + + v+i +++n+ +wa++ +++p+rirv l++   edEd
  gi|557693950|ref|YP_008797004.1| 20 SRLRRTDAAVRLVKEYAMRHGKASVVKISPKVNEILWANSRQSPPRRIRVVLEK---EDED 77
                                      56689999******************************************9987...4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 698.10
//
Query:       gi|557693951|ref|YP_008797005.1|  [L=417]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-91  304.2   0.0    5.5e-91  303.8   0.0    1.2  1  DUF1116   Protein of unknown function (DUF1116)


Domain annotation for each model (and alignments):
>> DUF1116  Protein of unknown function (DUF1116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.8   0.0   3.1e-95   5.5e-91       1     215 []      87     302 ..      87     302 .. 0.94

  Alignments for each domain:
  == domain 1  score: 303.8 bits;  conditional E-value: 3.1e-95
                                       SEEEEGGGGTB--STT--B-TTSEEEEEEETTT--EEEEE----SSSSGGGT--SHHHHHHHHHHHHTHHHHHHHHH CS
                           DUF1116   1 ielepchdhsavgpmagvvspsmpvlvvenktegnrayctlneGlgkvlrfGayseevlerLrwmrdvlapvlkeal 77 
                                       i lep+h+hsavgpmagv+spsm v+vv++ +   +a+++lneGlgkvlr+Gayse+vl++L++++  +a+vl++a+
  gi|557693951|ref|YP_008797005.1|  87 IVLEPNHHHSAVGPMAGVISPSMKVFVVSDGEV--KAFSNLNEGLGKVLRYGAYSEDVLKKLKYLNGPFADVLADAI 161
                                       679***************************876..9****************************9977666666555 PP

                                       H....-TT-EEHHHHHHHHTTTT--SSS--HHHHHHHHHHHHHHHHTSSS-HHHHHHHHHHHTS-TTTTHHHHHHHH CS
                           DUF1116  78 e....keggidlkaliaqalqmGDelHnRnkaatslllrelapalveldadkkelaevlkflaendqfflnlamaaa 150
                                       +    ++ggidl+++iaqa++mGDe+HnRn+aatsl++re+++++v+++ + k+++evl+++++n+ fflnlama++
  gi|557693951|ref|YP_008797005.1| 162 RdavkEKGGIDLRNIIAQAVHMGDECHNRNIAATSLFFREITSHVVKVADT-KTAQEVLTTINANNLFFLNLAMASC 237
                                       4211166***************************************98665.99*********************** PP

                                       HHHHHHTSS-TT--BEEEEEEESSEEEEEETTT-T--EEEE----BS-B-TT--GGGB---EEST CS
                           DUF1116 151 kavldaaegiegstlvtamarNGtefGirvsglgdeWftapanapegllfpgfseedanpdiGDS 215
                                       k+++d+a++i++st+vt+++rNGt++GirvsglgdeWftapa++p+gl+fpgf+e+d+npdiGDS
  gi|557693951|ref|YP_008797005.1| 238 KLMTDKAHNIKYSTIVTTISRNGTDLGIRVSGLGDEWFTAPAPVPKGLYFPGFTENDSNPDIGDS 302
                                       ****************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2719.11
//
Query:       gi|557693952|ref|YP_008797006.1|  [L=288]
Description: cyclase family protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-32  111.8   0.0    3.9e-32  111.3   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 !  111.3   0.0   2.2e-36   3.9e-32       1     136 []      35     197 ..      35     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 2.2e-36
                           Cyclase   1 idLshplsedtpvwp..dp..................islsehtGTHlDapgHfae..ktidelpleelvgpavvld 55 
                                       +dLs+p+s + p +    p                  i+ + h+GTH+D+ +Hf++  k+i +++++ ++g++vv+d
  gi|557693952|ref|YP_008797006.1|  35 YDLSQPTSTKAPPFMwyPPfkatwikrlsehnvnamyIEGPLHHGTHFDGQLHFMTggKDIASIDINYFIGEGVVVD 111
                                       79*****999976643422456779999999*****99999***************999****************** PP

                           Cyclase  56 vsakaaaedyeiitaedleaalakqgveikpgdivlirTgwskrl.....edkeky..rnpglseeaaewlaekgvk 125
                                       +s+k+  +dy+i+t+e +e a++++g ei+p di++i+Tg+s+++     +d+ +y  ++pg++  +a+w +ek+++
  gi|557693952|ref|YP_008797006.1| 112 ISRKV--GDYDIYTPETIEGAAKEAGLEIRPDDILIIYTGYSRYAwcgqePDEVRYicKHPGPDVRFAKWCIEKKIR 186
                                       *9998..9*********************************9998***998889999*9****************** PP

                           Cyclase 126 avGvDtlsvDa 136
                                       ++GvD+ s D+
  gi|557693952|ref|YP_008797006.1| 187 WLGVDAASQDH 197
                                       *******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2065.60
//
Query:       gi|557693953|ref|YP_008797007.1|  [L=516]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  102.6   0.0      5e-29  101.1   0.0    1.8  2  Ligase_CoA   CoA-ligase
     0.0001   22.9   5.9     0.0024   18.5   0.3    3.2  3  CoA_binding  CoA binding domain


Domain annotation for each model (and alignments):
>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         1   9.2e+03      87     121 ..      16      46 ..       9      51 .. 0.58
   2 !  101.1   0.0   5.5e-33     5e-29       2     148 ..     340     490 ..     339     495 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1
                                       EHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH CS
                        Ligase_CoA  87 ahedpaaellkaikeakaegrelpvvarvaGtead 121
                                       + + +  e+ + ik++k     ++  a v+Gt  +
  gi|557693953|ref|YP_008797007.1|  16 RDSVQLMEVSESIKRLK----GVVDAAVVMGTVSN 46 
                                       55555555555555554....66667777777665 PP

  == domain 2  score: 101.1 bits;  conditional E-value: 5.5e-33
                                       ESSHHHHHHHHHHHHHT....................T--BSEEEE-TSS--..........HHHHHHHHHHHHS-T CS
                        Ligase_CoA   2 vnGGtLayeamdlikealgdvasn......kklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadp 72 
                                       ++GGtLa e++++ ++a  +++sn      ++l n  +s +++i+d G ++ft+GrpHP+iDpt r+ ++  +++ +
  gi|557693953|ref|YP_008797007.1| 340 YSGGTLATETAYVWNKAGLEIYSNiglswtRRLDNPYTSIGATIVDYGSEEFTEGRPHPIIDPTLRNRRIVTELESD 416
                                       99*************************************************************************** PP

                                       T-SEEEEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH......HHHHHHHTTTSSEEE-SSHHHH CS
                        Ligase_CoA  73 evkvilldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqels.eqakaleeagveiasskaqalr 148
                                       +++ i +d+++Gyga +++++++ ++i ea  ++r++ + +rv+Gt++d   ++  q   +e+ gv + ss+a a+ 
  gi|557693953|ref|YP_008797007.1| 417 STNSIAMDLIIGYGAPDNIVSKVFDEIGEAVLKNRKKRLAVRVVGTDKD---YQwPQVSGIEKFGVLTSSSNAMAAV 490
                                       ******************************88*****************...4448899999999999999988765 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.29   2.6e+03      43      72 ..      17      46 ..       9      51 .. 0.73
   2 !    5.4   0.2    0.0032        29      28      90 ..      76     139 ..      66     142 .. 0.89
   3 !   18.5   0.3   2.7e-07    0.0024       4      69 ..     188     251 ..     186     271 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.29
                                      CEETTEEEESCHHHHHHHCTTTEEEEES-H CS
                       CoA_binding 43 tevlglpvyksvdeleektevdvavitvPa 72
                                      + v+ ++v +s++ l+  +++ v + tv++
  gi|557693953|ref|YP_008797007.1| 17 DSVQLMEVSESIKRLKGVVDAAVVMGTVSN 46
                                      567888888999999999666666666665 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0032
                                       ECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHC.TTTEEEEES-HHHHHHHHHHHHHTT-SEE CS
                       CoA_binding  28 ygikavfgvnprkvgtevlglpvyksvdeleekt.evdvavitvPaesaqeavdelveagikgi 90 
                                        +i+++  ++ + + +++ + p y s++e+ +   +v+ a i +P   ++e++++l+e ++++ 
  gi|557693953|ref|YP_008797007.1|  76 GNIEEILETSKKLLFETHVTAPKYISIEEALNANpDVKFASISIPGGYVEEVAVKLIEGNVNLF 139
                                       6788888999999999999999999*****999977**********************999875 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 2.7e-07
                                       EEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEE CS
                       CoA_binding   4 tkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavit 69 
                                       ++v+v+   g+gi++ ++  + +++g+++++gv+ r++ ++v+g++++k+++ l  +   d++ i+
  gi|557693953|ref|YP_008797007.1| 188 GNVGVVASAGSGIQEFVTLLDAYGIGVSHAIGVGARDLTEKVGGIMAQKALRLLNGD--SDTKFIA 251
                                       689999999***************************************999999888..7776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 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:                        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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3552.20
//
Query:       gi|557693954|ref|YP_008797008.1|  [L=51]
Description: hypothetical protein CSUB_C0517 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 366.70
//
Query:       gi|557693955|ref|YP_008797009.1|  [L=268]
Description: hypothetical protein CSUB_C0518 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   68.4   0.0    1.2e-18   67.8   0.0    1.2  1  DUF2877   Protein of unknown function (DUF2877)


Domain annotation for each model (and alignments):
>> DUF2877  Protein of unknown function (DUF2877)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.8   0.0   6.5e-23   1.2e-18       2     107 ..     160     258 ..     159     260 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.8 bits;  conditional E-value: 6.5e-23
                           DUF2877   2 iGlGpGlTPsgDDfLvGllaalrllgqkeekelaaalaevakakkrttdvSaalLkaalegefseellallkalsse 78 
                                       +G+GpGlTP+gDDf++G+l+ lrllg k+++++  +     ka+k+ ++ S +++++a++g++ +++++l++++  +
  gi|557693955|ref|YP_008797009.1| 160 VGRGPGLTPAGDDFVSGVLLGLRLLGLKADASELFQ-----KARKSSRWPSWKMMEHAHHGCTFSPIYNLCREILMG 231
                                       8*************************9998887766.....57899******************************* PP

                           DUF2877  79 eeeelekalekllaiGhtSGadlllGlll 107
                                        ++   +++ +  +iG ++G ++l+Gll 
  gi|557693955|ref|YP_008797009.1| 232 GDC--VEHVFEAVRIGGSTGLATLAGLLE 258
                                       999..99999****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1950.25
//
Query:       gi|557693956|ref|YP_008797010.1|  [L=246]
Description: hypothetical protein CSUB_C0519 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1724.86
//
Query:       gi|557693957|ref|YP_008797011.1|  [L=740]
Description: molybdenum hydroxylase family protein, large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-177  591.2   0.0   2.2e-177  590.9   0.0    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    8.4e-25   87.3   0.0    8.4e-25   87.3   0.0    2.4  3  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 !  590.9   0.0  2.4e-181  2.2e-177       1     550 []     120     673 ..     120     673 .. 0.97

  Alignments for each domain:
  == domain 1  score: 590.9 bits;  conditional E-value: 2.4e-181
                                       STTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHH CS
                     Ald_Xan_dh_C2   1 vheeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlv 75 
                                       vhe++p+n++a   i+ Gd      +ad v++++f ++r + + +Et++++a++d ++g+ltv+ stqap  +r+++
  gi|557693957|ref|YP_008797011.1| 120 VHEDVPNNIAAhhIIRVGDS-TLAGNADLVIREKFVFNRGAGASIETRGVVAHYDAKTGQLTVWDSTQAPIPIRNTL 195
                                       799********855667*97.66779*************************************************** PP

                                       HHHHT--GGGEEEE-SB-S--TTTT.SS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TT CS
                     Ald_Xan_dh_C2  76 aevlglpenkvrvivprvGGGFGgK.tqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkd 151
                                       ++++++p + vrvi+p++GGGFG K +  +p+e+l ++aA k+grpVk++++R+e m+at++++ + +++++++ +d
  gi|557693957|ref|YP_008797011.1| 196 SKLFNIPLHLVRVIAPDIGGGFGPKiMLFYPEEILTTFAAIKLGRPVKWIEERREYMVATNQQRIQVHYVEAAFGRD 272
                                       ***************************************************************************** PP

                                       S-EEEEEEEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 152 GkitaldvdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdel 228
                                       G+++ ++ ++l d+Gay++++ +v+  + +++ gpYkip++++e+  vytN++ ++++RG+G+p a++++Er+md +
  gi|557693957|ref|YP_008797011.1| 273 GRLLSFRDRFLVDTGAYTPYGIMVPIITSGTMPGPYKIPAMEIEFMSVYTNKTVVSPVRGAGRPDAVYVMERVMDIA 349
                                       ***************************************************************************** PP

                                       HHHHT--HHHHHHHHBCECGCC.SEEET.........EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEE CS
                     Ald_Xan_dh_C2 229 AeelgldplelRrrNlikpgeltpygqp.........vydsgdlpelldklkessdyeerraeqaefnagwkkrGig 296
                                       A++lgld++e+RrrNlik +e+ py++           ydsg+++ ll+ l+e+++y+++ +++++++a+++ +G+g
  gi|557693957|ref|YP_008797011.1| 350 AQKLGLDRVEVRRRNLIKSNEF-PYDTGiiyqdggpvKYDSGNYESLLNLLLEKIHYKSWPERKQRYRAQGRYVGLG 425
                                       **********************.***955555566678******************************88899**** PP

                                       EEEEEEEBS--S.EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS-- CS
                     Ald_Xan_dh_C2 297 lapvvegiglgftakflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpng 373
                                       la++veg+g+g+       e a+v+v+++G+++v+tg+ ++GqG+ t+laqiaa++Lg +++dv+vv gdt+++p+g
  gi|557693957|ref|YP_008797011.1| 426 LALYVEGAGVGP------YEMAKVTVTPSGRIVVATGVGSQGQGHFTVLAQIAADVLGASVDDVDVVVGDTAHMPWG 496
                                       ********9998......368******************************************************** PP

                                       --S-TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH......T CS
                     Ald_Xan_dh_C2 374 sgtaaSrstdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl......e 441
                                       +gt+aSrs++++gnAv+ Aa ++r++++++aa+l+e++ped+e++ g+v+v+   +ks +l ela  a+       +
  gi|557693957|ref|YP_008797011.1| 497 VGTFASRSATIAGNAVHLAAMDVRKKAAEVAAKLFEANPEDIEFQGGRVFVRghpDKSYTLGELAVYAHPirglikR 573
                                       *****************************************************999999*******88778899989 PP

                                       TSSEEEEEEE...EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 442 rvslsatgfyktldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiG 518
                                       +++l+at f+         +p++++fa g ++aeVe+D+etg+ ++lr+vivhD+G +iNp ivegQi+GG+  G+G
  gi|557693957|ref|YP_008797011.1| 574 EPGLEATRFF---------SPEQSVFASGGHAAEVEIDPETGKLHILRYVIVHDCGPMINPLIVEGQIHGGLSNGLG 641
                                       99********.........89999***************************************************** PP

                                       HHHT---EEETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 519 lalmEelvydedGqlltasladYkiPtaadiP 550
                                        a++Ee+v de+Gq+l ++++dY+iP+a+++P
  gi|557693957|ref|YP_008797011.1| 642 GAVYEEIVHDESGQPLATTFSDYLIPSATEMP 673
                                       *******************************9 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 !   87.3   0.0   9.4e-29   8.4e-25      17     110 .]       2     104 ..       1     104 [. 0.90
   2 ?   -2.0   0.3      0.51   4.6e+03      71     101 ..     499     530 ..     481     534 .. 0.70
   3 ?   -5.3   1.1         2   1.8e+04      83      92 ..     702     711 ..     698     714 .. 0.78

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 9.4e-29
                                       EEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT.........TSSS-EEEESS-SSEESSTT-EE CS
                      Ald_Xan_dh_C  17 ylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig.........siledeedallaedkvrsvgqav 84 
                                       ++a++rS++ahA+i++id + alal+GVvav+ta+dl + n             +i+   ++++la++kvr+vg++v
  gi|557693957|ref|YP_008797011.1|   2 HAAVLRSPYAHARITKIDKTRALALKGVVAVYTADDLGQLNGPLPpsvsplpqyPIPYMRTHYALAKEKVRYVGEPV 78 
                                       899***********************************9988776555566666555555689************** PP

                                       EEEEESSHHHHHHHHHT-EEEEEE-- CS
                      Ald_Xan_dh_C  85 aavvAedeetArkAaklvkveYeelp 110
                                       a++vAe++++A++Aa++v+veYe+lp
  gi|557693957|ref|YP_008797011.1|  79 AFIVAENKYVAKDAAEMVEVEYEPLP 104
                                       ***********************986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.51
                                       SS-SSEESSTT-EEEEEEESSH.HHHHHHHHT CS
                      Ald_Xan_dh_C  71 llaedkvrsvgqavaavvAede.etArkAakl 101
                                        +a++ ++++g+av + + + + ++A+ Aakl
  gi|557693957|ref|YP_008797011.1| 499 TFASRSATIAGNAVHLAAMDVRkKAAEVAAKL 530
                                       57888888888888876666540445556665 PP

  == domain 3  score: -5.3 bits;  conditional E-value: 2
                                       EEEEEEESSH CS
                      Ald_Xan_dh_C  83 avaavvAede 92 
                                       +vaav+A   
  gi|557693957|ref|YP_008797011.1| 702 PVAAVIASAV 711
                                       7999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (740 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 5087.65
//
Query:       gi|557693958|ref|YP_008797012.1|  [L=467]
Description: propionyl-CoA carboxylase beta chain [Candidatus Caldiarchaeum subterraneum]
Scores for 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-110  368.9   0.8   4.7e-110  368.6   0.8    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    9.7e-06   25.2   0.2    2.7e-05   23.8   0.0    1.8  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 !  368.6   0.8  5.2e-114  4.7e-110      10     481 ..       6     456 ..       3     466 .. 0.93

  Alignments for each domain:
  == domain 1  score: 368.6 bits;  conditional E-value: 5.2e-114
                                       EEEEEHTTSGGGEBEHHHHHHHHHHHHHHHHHT..EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCEEECHHH CS
                    Carboxyl_trans  10 areridllldpgsFgeledlffhrvtelgrkkklprdgvvtgsGaviGravevvaqdktvlggslgpakgekllkaq 86 
                                       +++ri+ lld+gsF+++   +++  +++  +   p+dgvv+g G++ Gr v+v+a+d  + ggslg++ ++k+ k  
  gi|557693958|ref|YP_008797012.1|   6 VFDRINSLLDAGSFRPILSGVEQHGADMPHR---PGDGVVAGFGKIGGRNVAVFAHDPAFAGGSLGEVGVRKIAKLY 79 
                                       679************************9965...******************************************* PP

                                       HHHHHHTEEEEEEEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHHTSEEEEETTE CS
                    Carboxyl_trans  87 eeaikagepligindsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpalgdrvimveet 163
                                       e+a++ g p+ig+ ds+Ga  riqeg  sl  +G++ +   ka g+Ipqi +++   +Gg+a+ +a+gd+vi v++t
  gi|557693958|ref|YP_008797012.1|  80 ELAARFGYPIIGLADSSGA--RIQEGARSLIAVGELIKTANKAHGKIPQINVIIAGGVGGAAFTAAVGDVVIGVAKT 154
                                       *******************..******************************************************** PP

                                       EEEESSTHHHHHHHHSSCC-SSCHHHHSHHHHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGSS----ECSS CS
                    Carboxyl_trans 164 skifltGpdvikkvlgreevtseelgGatqhmtksGvahltaeddeealelirkllsylPkkasnnresaPivetad 240
                                       +++fl Gp+++k ++g ++v+  elg +++ ++ sG+++++ ed+ +a++l++kllsylP   sn  +++P   +++
  gi|557693958|ref|YP_008797012.1| 155 GYMFLHGPRAVKHATG-QDVSIMELGSVKTLAASSGLIDFVTEDEAQAISLVKKLLSYLP---SNYLATPPTSIATE 227
                                       ****************.*******************************************...77666767655433 PP

                                       GSSSH..HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEEEEEEEETTEEEEEEEE--SEEETTEE-HHHHH CS
                    Carboxyl_trans 241 epdrdlieivPdnakkpyDvreviarlvdegeFlEikegyAktvVvGfArlgGipvGvvAnetrveaGqvlfidsav 317
                                       +  +         + ++ + r +ia++ d g FlE+k++yA+++++G++r++G  vGvvAne++v+ G  ++ ++ v
  gi|557693958|ref|YP_008797012.1| 228 STIK------Q--DLESTETRRLIAEIIDPGTFLEFKADYARNLITGLGRVDGLVVGVVANEPNVFKG-YIDGKACV 295
                                       3333......2..367779*************************************************.******** PP

                                       HHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEEHHHHHTTTGGGSTT CS
                    Carboxyl_trans 318 KaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkayGGayvvmdskinga 394
                                       K +rf+ +c+ +n+P+++++d++Gf +G ++e+ggi++ G  +  ++ +a+vPk+t+i +kayGGay++m+sk +ga
  gi|557693958|ref|YP_008797012.1| 296 KLSRFVDFCNSFNIPVLTIVDTPGFEPGVAAEHGGIIREGTWVYRSYLNATVPKVTLIAGKAYGGAYIAMCSKGIGA 372
                                       ***************************************************************************** PP

                                       TTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHHHHT CS
                    Carboxyl_trans 395 dlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargfaDavidpsetrak 471
                                       d+v+a p+a++aV + e  +eilfrke+++      d++a + ++  e+ +++++     ++g+aD +++ +e++++
  gi|557693958|ref|YP_008797012.1| 373 DYVLALPDAEVAVQPLEVSAEILFRKELEKLPD---DQKAAAFAQYVEALRTKSRGDALLSIGVADVIVKREEVKKT 446
                                       ***************************999993...34444444555555555999999****************99 PP

                                       TSSSEEEHGG CS
                    Carboxyl_trans 472 lvialelewk 481
                                       ++  l+ +++
  gi|557693958|ref|YP_008797012.1| 447 VSSVLHSLYD 456
                                       9988877765 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.25   2.3e+03      94     112 ..      75      93 ..      72     115 .. 0.76
   2 !   23.8   0.0     3e-09   2.7e-05      65     177 ..     309     421 ..     271     456 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.25
                                       HHHHHHHHHHHT--EEEEE CS
                              MdcE  94 lakalarArlaGhpvigll 112
                                       +ak + +A   G p+igl 
  gi|557693958|ref|YP_008797012.1|  75 IAKLYELAARFGYPIIGLA 93 
                                       6888999999999999984 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 3e-09
                                       -EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEEHHHHHHT...TTT-SEEEEEET-E CS
                              MdcE  65 rpilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkavsGaflah...glqanrlialpgvq 138
                                        p+l +vD+++   g   E  Gi    + +  ++++A +   p ++l+ Gka  Ga++a+   g+ a+ ++alp+++
  gi|557693958|ref|YP_008797012.1| 309 IPVLTIVDTPGFEPGVAAEHGGIIREGTWVYRSYLNATV---PKVTLIAGKAYGGAYIAMcskGIGADYVLALPDAE 382
                                       699999999999999999999999999999999999986...99*************985344899*********** PP

                                       EESS-HHHHHHHH.T--HHHHHHHGGCSGGG--SHHHHHT CS
                              MdcE 139 vavmdkasaArvT.krsveaLealaksipvfAydvdnyar 177
                                       vav  +   A +  ++ +e+L +   + + fA  v+ + +
  gi|557693958|ref|YP_008797012.1| 383 VAVQPLEVSAEILfRKELEKLPDDQ-KAAAFAQYVEALRT 421
                                       *******999996255677776543.45667777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 00:00:00.42
# Mc/sec: 3343.05
//
Query:       gi|557693959|ref|YP_008797013.1|  [L=787]
Description: molybdenum hydroxylase family protein, large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-162  539.6   0.0   9.7e-162  539.2   0.0    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    5.7e-28   97.5   0.0    1.4e-27   96.2   0.0    1.7  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 !  539.2   0.0  1.1e-165  9.7e-162       7     550 .]     164     714 ..     158     714 .. 0.95

  Alignments for each domain:
  == domain 1  score: 539.2 bits;  conditional E-value: 1.1e-165
                                       TTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHHT- CS
                     Ald_Xan_dh_C2   7 dnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevlgl 81 
                                       +n+++  +++kGdve++f+e+d+++e+ef++++++h+ lEt++++ ++   dg++++++s q p+ vr++++  lg+
  gi|557693959|ref|YP_008797013.1| 164 TNIANkfTLRKGDVEKGFRESDVIIENEFSMPQVSHTQLETHVTIGQY-LPDGNVKIWTSAQSPFTVRHILSVSLGI 239
                                       4555566889************99************************.67************************** PP

                                       -GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHH.TS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEE CS
                     Ald_Xan_dh_C2  82 penkvrvivprvGGGFGgKtqsvplevlaalaAkkt.grpVklvldReedmlatgkrhpfkikykvgadkdGkital 157
                                       pe+k+ v vp+vGG+FGgK   +  e+l+++++k + g+pVkl l+Ree+++++  r+ +++k+k+g+++ G+i a 
  gi|557693959|ref|YP_008797013.1| 240 PEHKISVYVPYVGGAFGGK-AGINFEPLVVMLSKIVgGKPVKLELTREEQFTTAPVRQGMYAKVKTGVKRSGEIMAE 315
                                       *******************.9***************9**************************************** PP

                                       EEEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT- CS
                     Ald_Xan_dh_C2 158 dvdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgl 234
                                       ++ ++ daGayad++  +  +a   ++gpY +pnv++++ +vytN+p+ tafRGfG+ + ++a+Er+md +A+elg+
  gi|557693959|ref|YP_008797013.1| 316 KLFYVYDAGAYADYGVNIGRAAGYSCTGPYYVPNVEADSLTVYTNHPWGTAFRGFGHFEFLWAIERQMDIVANELGI 392
                                       ***************************************************************************** PP

                                       -HHHHHHHHBCECGCC.SEEET.EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S.E CS
                     Ald_Xan_dh_C2 235 dplelRrrNlikpgeltpygqp.vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgfta 310
                                       dp+e+R +N++ pg +tp+g+    d g+++e+++++++++++ ++ + +       k rG g+a+ +++ ++ ++ 
  gi|557693959|ref|YP_008797013.1| 393 DPVEFRLKNALLPGLTTPTGEVlRQDAGRIDECIKAVASAIGWGKKSENITG-----KPRGKGIAALWKAPAMPPN- 463
                                       *********************976799****************877666554.....3499*******99966653. PP

                                       ETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-S.BTTSSS----S-TT-HHHHHH CS
                     Ald_Xan_dh_C2 311 kflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvveg.dtdkvpngsgtaaSrstdlng 386
                                           +++a +++n+dG++++ +g te+GqG+et+laqiaaeeLg+ple+++vv+   td  p++++t+aSr+  + g
  gi|557693959|ref|YP_008797013.1| 464 ---ASSSAIIKFNEDGTAELLLGITEIGQGSETALAQIAAEELGIPLEKIKVVPFrHTDVSPYSWQTVASRGLFMDG 537
                                       ...3678***********************************************98********************* PP

                                       HHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH.....TTSSEEEEEEE.... CS
                     Ald_Xan_dh_C2 387 nAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl.....ervslsatgfykt.. 453
                                       +Av+ Aa++ ++++l+iaa++l+v+++dl le+++v+vk   e  ++l+++++  ++      + ++  +gfy++  
  gi|557693959|ref|YP_008797013.1| 538 KAVQMAARDAKNQILEIAAQVLRVQKDDLVLENERVFVKgrpEVGLELRQIVNGYTYpngnvVGGPVIGRGFYSAsr 614
                                       ***************************************8766667999***94433687778889*******99** PP

                                       ....EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EE CS
                     Ald_Xan_dh_C2 454 ...ldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvy 527
                                          ld etg+g p   +++ga+++eVevD++tg vkvl++v + D+Gk+iNp +v+ Qi+GG+vq + l l+E +vy
  gi|557693959|ref|YP_008797013.1| 615 ltyLDPETGQGLPALKWTFGAHAVEVEVDPDTGMVKVLKLVSAFDIGKAINPLTVKSQIYGGAVQSMSLGLYEGYVY 691
                                       ***9************************************************************************* PP

                                       ETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 528 dedGqlltasladYkiPtaadiP 550
                                       de+G+ll+ +l+dYki +a+diP
  gi|557693959|ref|YP_008797013.1| 692 DENGRLLNYNLTDYKIARARDIP 714
                                       **********************9 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 !   96.2   0.0   1.6e-31   1.4e-27       1     110 []      25     129 ..      25     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 1.6e-31
                                       TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEE CS
                      Ald_Xan_dh_C   1 tGeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkv 77 
                                       tG a Y  Di++pg+ly+++++S+++hAkivsi+v++a++ pGVv v  ++d p +   +    +d  +++la +kv
  gi|557693959|ref|YP_008797013.1|  25 TGVAEYAGDIELPGMLYAKLLLSPYPHAKIVSINVEKAKRCPGVVGVAVGEDFPFRVGLY---VND--RYILAYKKV 96 
                                       799***************************************************995544...444..47******* PP

                                       SSTT-EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                      Ald_Xan_dh_C  78 rsvgqavaavvAedeetArkAaklvkveYeelp 110
                                       r +g++vaavvAe+ e+A++A++l++v+Ye+lp
  gi|557693959|ref|YP_008797013.1|  97 RWAGEPVAAVVAESLEQAEEAVELIDVNYEPLP 129
                                       ******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (787 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 5387.22
//
Query:       gi|557693960|ref|YP_008797014.1|  [L=289]
Description: molybdenum hydroxylase family protein, medium subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-48  162.5   0.0    1.1e-47  162.0   0.0    1.2  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
    1.8e-20   73.0   0.3    3.2e-20   72.2   0.3    1.4  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 !  162.0   0.0   1.2e-51   1.1e-47       2     170 ..       4     174 ..       3     175 .. 0.98

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 1.2e-51
                                       EEEEEE-SSHHHHHHHHHH.CTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEE.SSEEEEETTSBHHH CS
                     FAD_binding_5   2 kfeylrpasleealallaa.epdaklvaGgtdlgvlmkekvarpehliditgipelkeieet.eggleiGAavtlse 76 
                                       kf y+ p+sl+eal+l+++ + dak++aGgtdl+v ++ek+ +p+++id+++i+el++++ + ++gl iGA+vt+++
  gi|557693960|ref|YP_008797014.1|   4 KFVYHAPKSLQEALDLMSSyGRDAKPLAGGTDLLVDLREKKSKPKAVIDLKNIKELNKLSYErGSGLVIGATVTYEQ 80 
                                       688****************999*************************************9998************** PP

                                       HHHHHHHHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETT CS
                     FAD_binding_5  77 laaealvrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkgpg 153
                                       + + + +r+ry  l ea+++iA++ iR +aT+ GN++t sp++D+ap+Ll++dA v++ s++g re+p+e+f+ g +
  gi|557693960|ref|YP_008797014.1|  81 ILSFEPIRRRYTVLWEAVKTIADEIIRMRATLVGNICTSSPAADTAPPLLVYDAVVKTLSKNGAREIPIEKFFIGVK 157
                                       ***************************************************************************** PP

                                       EESS-TT-EEEEEEEE- CS
                     FAD_binding_5 154 ktalepgelitaveiPa 170
                                       k++le+ge++++v +P 
  gi|557693960|ref|YP_008797014.1| 158 KNVLEAGEIVESVYLPE 174
                                       ****************7 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 !   72.2   0.3   3.6e-24   3.2e-20       2     102 ..     182     279 ..     181     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 3.6e-24
                                       EE.EEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHH CS
                     CO_deh_flav_C   2 ay.klsrrrendiaivnaAfrveleedgkiedariafggvaptpvraekaeaaLiGkplseelleeaakaleeelsp 77 
                                       ay k++r  ++d+a+v++A++v  ++     d+r+a+ +vaptpvra+kae++  G  + +e +e+a++ +++ +sp
  gi|557693960|ref|YP_008797014.1| 182 AYlKAMRTWSEDLALVGVAVLVADRGR----DVRLAYASVAPTPVRARKAEDVFRGDGPLREKIEQAVEIAAASVSP 254
                                       799******************988655....********************************************** PP

                                       HTCTTC-HHHHHHHHHHHHHHHHHH CS
                     CO_deh_flav_C  78 asdprasaeYRrslavsllfrflle 102
                                       ++d+ras+eYR +l++++++ +ll+
  gi|557693960|ref|YP_008797014.1| 255 ITDVRASKEYRLHLVKTFTRNALLK 279
                                       *********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2186.71
//
Query:       gi|557693961|ref|YP_008797015.1|  [L=155]
Description: molybdenum hydroxylase family protein, small subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   87.2   0.0    5.6e-25   87.2   0.0    1.7  2  Fer2_2    [2Fe-2S] binding domain
    1.5e-07   31.3   2.9    1.8e-07   31.0   0.2    2.1  2  Fer2      2Fe-2S iron-sulfur cluster binding domain
    0.00029   20.8   1.2    0.00032   20.7   0.3    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 ?   -2.6   0.8      0.99   5.9e+03      26      31 ..      45      50 ..      39      51 .. 0.83
   2 !   87.2   0.0   9.4e-29   5.6e-25       1      75 [.      75     147 ..      75     148 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.99
                            Fer2_2 26 qCGyCt 31
                                       CG Ct
  gi|557693961|ref|YP_008797015.1| 45 DCGLCT 50
                                      6****9 PP

  == domain 2  score: 87.2 bits;  conditional E-value: 9.4e-29
                            Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                       Tvegl+++  el pvq++f+++ga+qCG Ctp fv+  + l++++ +k ++e +++al+g lCRCtgYr+i+dA+
  gi|557693961|ref|YP_008797015.1|  75 TVEGLARN-GELTPVQKSFIKHGALQCGICTPAFVIMGHWLVQNE-KKLDRERVADALDGILCRCTGYRQIIDAI 147
                                       9*****88.78*******************************998.66666***********************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 !   31.0   0.2     3e-11   1.8e-07       1      58 [.       7      67 ..       7      84 .. 0.83
   2 ?    0.6   0.2     0.091   5.4e+02      38      44 ..      96     104 ..      93     138 .. 0.58

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3e-11
                                      EETTTEEEEEEEETTTHBHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCE.CTT...SSS CS
                              Fer2  1 itidgkevevevadgettlldaaee.nggidipysCggggCgtClvevlegev.qsd...ete 58
                                      +t++g e+ +ev+d++t ll  ++e  +  +++++C  g Cg C+v ++ g+  +s+   ++e
  gi|557693961|ref|YP_008797015.1|  7 VTVNGVERFAEVEDHKT-LLWLLREkFKLKGTKHGCDRGDCGLCTVLLN-GKPvKSClvlAAE 67
                                      689*********99999.9999999889******************888.4443555455444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.091
                                       SS..SSTTE CS
                              Fer2  38 gg..CgtCl 44 
                                       g+  Cg C+
  gi|557693961|ref|YP_008797015.1|  96 GAlqCGICT 104
                                       444699998 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 !   20.7   0.3   5.4e-08   0.00032      49      91 ..      38      79 ..      16      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.4e-08
                            Fer2_3 49 rasCregiCGscavainGkptlaCtatikdlakqkseielepl 91
                                      ++ C  g CG c+v +nGkp   C     +++ ++  +++e l
  gi|557693961|ref|YP_008797015.1| 38 KHGCDRGDCGLCTVLLNGKPVKSCLVLAAEVDGST-ILTVEGL 79
                                      579**********************9999988765.5677766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1185.80
//
Query:       gi|557693962|ref|YP_008797016.1|  [L=109]
Description: molybdopterin converting factor, small subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   41.1   0.7    2.6e-09   37.6   0.7    2.0  1  ThiS      ThiS family
     0.0046   17.3   0.0     0.0054   17.0   0.0    1.1  1  Urm1      Urm1 (Ubiquitin related modifier)
  ------ inclusion threshold ------
      0.025   14.6   0.0      0.035   14.1   0.0    1.3  1  TGS       TGS domain
      0.086   12.8   0.0      0.093   12.7   0.0    1.2  1  MIT_C     Phospholipase D-like domain at C-terminus of MIT


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 !   37.6   0.7   5.9e-13   2.6e-09       6      77 .]      20     109 .]      16     109 .] 0.88

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 5.9e-13
                                       CCHHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHG...........TTTTEEEEETTEEEGC.CTTTSB--TTC... CS
                              ThiS   6 elrelag.eeelelaegstvaelleaLgerypela...........lerrvavavNgeivpr.lwldtelkdgD... 66 
                                        lr++ag e+  +++++ tv+ell+ L+++ ++ +           l+r ++++vNg  ++  ++ldt+l + D   
  gi|557693962|ref|YP_008797016.1|  20 YLRRAAGgETIRLEESPRTVRELLDLLAAKLGKSFeelvydprqktLKRAIVLLVNGHSIKMlKGLDTPLHPDDnvs 96 
                                       589999*************************9999***********99**************88******8876111 PP

                                       ..EEEEEESTTC- CS
                              ThiS  67 ..evailppVaGG 77 
                                         +v+++ +V+GG
  gi|557693962|ref|YP_008797016.1|  97 idTVEVIEVVGGG 109
                                       1156889999998 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.2e-06    0.0054      25      88 ..      31      96 ..      12     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.2e-06
                                      -SSSSS-BHHHHHHHHCCCC-SSGHHHCBS..TTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEE CS
                              Urm1 25 eieseevnleeliayikknlikerkevFle..kdkvrPGilvLindaDwellgekdyelkdkDkiv 88
                                        e+++ +++el++ ++ +l k  +e+  +  +++++  i+ L+n   +++l+ +d+ l+ +D+++
  gi|557693962|ref|YP_008797016.1| 31 RLEESPRTVRELLDLLAAKLGKSFEELVYDprQKTLKRAIVLLVNGHSIKMLKGLDTPLHPDDNVS 96
                                      34588999***************77776644799*****************************996 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   7.9e-06     0.035      16      58 ..      51      97 ..      39      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.9e-06
                                      TB-HHHHHHHHSTTHHHHEEEEEECS....EEEETTSBB-SSEEEEE CS
                               TGS 16 gatveDfAykIhrslakkfiyAlVnG....qrvgldhvLedgdvveI 58
                                      g++ e++ y   +   k++i+ lVnG    ++ gld++L  +d v+I
  gi|557693962|ref|YP_008797016.1| 51 GKSFEELVYDPRQKTLKRAIVLLVNGhsikMLKGLDTPLHPDDNVSI 97
                                      5666677777777778999999***********************99 PP

>> MIT_C  Phospholipase D-like domain at C-terminus of MIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.1e-05     0.093      61     125 ..      35     100 ..       5     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.1e-05
                             MIT_C  61 eedeqkenleelkesleklgielevef.sstihdreirldngwiikigrGLdifkkseskfslgsv 125
                                       + ++++e l+ l+++l k   el ++  ++t++   + l ng+ ik+ +GLd   ++++++s+ +v
  gi|557693962|ref|YP_008797016.1|  35 SPRTVRELLDLLAAKLGKSFEELVYDPrQKTLKRAIVLLVNGHSIKMLKGLDTPLHPDDNVSIDTV 100
                                       4566777777888888888888888883455555555679*************9999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 792.56
//
Query:       gi|557693963|ref|YP_008797017.1|  [L=417]
Description: cytosine deaminase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   94.9   0.5      1e-20   74.7   0.2    2.1  2  Amidohydro_3  Amidohydrolase family
    4.8e-10   39.3   0.3    1.3e-07   31.3   0.3    2.2  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 !   19.0   0.0   8.8e-08   0.00078       1      26 [.      46      78 ..      46     143 .. 0.69
   2 !   74.7   0.2   1.1e-24     1e-20     223     450 ..     155     382 ..     111     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.8e-08
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlaggg.......v 26
                                      +viDa Grlv+ +Fv +H+Hl+++        +
  gi|557693963|ref|YP_008797017.1| 46 RVIDAGGRLVTEPFVNPHLHLCKVYtfhmigdQ 78
                                      69********************99754333333 PP

  == domain 2  score: 74.7 bits;  conditional E-value: 1.1e-24
                      Amidohydro_3 223 s..................pgseeltigavklfadgvlgsrtalltepyftgwpdfedea...laelvaaadergld 278
                                                          pg eel  +av+++ d+v+g+++++ +            e+   + ++++ a++   d
  gi|557693963|ref|YP_008797017.1| 155 AdvltiqvvafpqegvvrdPGAEELVWKAVEMGCDVVGGIPWIENSPK----------EQrlhVDKMFEIAKAFNRD 221
                                       1222233333355555555***************************84..........3335599************ PP

                      Amidohydro_3 279 vaihaigdaavd.dvldafeaaaekngnqdrrrlehaegv...tesqiervaalqvaagvqpvfnfedelldsrlgp 351
                                       va++++++++ + ++ + + + a ++ + +r++++h++++    e ++e++  l       +v+n+           
  gi|557693963|ref|YP_008797017.1| 222 VAMLTDDAGDPSlRTTEMLVRKALEEKWVGRVSAHHSRAMalyEEGYLEDLIQLLRMTEANIVSNP----------- 287
                                       ************99999999999999999999**********************************........... PP

                      Amidohydro_3 352 erargstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg.evlrpdeelsleealalyTrgpAkalgl 427
                                       + +++++pvk l++ gv+valg+D   ++ d ++++g++ m++ +  + ++lr+  + ++ +++ ++T ++Aka++ 
  gi|557693963|ref|YP_008797017.1| 288 HTGPLHAPVKKLIDRGVNVALGQD---DVADAYYPFGRNKMLEVAFLAsHILRMLSKSDIMKLFNMITFNAAKAMRI 361
                                       889*********************...*****************9999***************************** PP

                      Amidohydro_3 428 edrkGtLevGadADlvvldadpl 450
                                       +   +t+e+G dA +++lda+ +
  gi|557693963|ref|YP_008797017.1| 362 PR--YTVEKGSDATFIILDAESI 382
                                       **..9*************95543 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.3   1.5e-11   1.3e-07     224     328 ..     288     389 ..      58     402 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.5e-11
                                       HSEHHHHHHHHHHHHTSCEEEEEECTTSSCCG....GHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHH CS
                      Amidohydro_1 224 ilrsgrealrkaldeGvkvglgtDgaasgnsl....nlleelrlalklqrgllyedeegglslkealrmaTingAka 296
                                         ++  ++++k++d+Gv+v+lg D++a    +    ++   l +a++ ++ l +     + +++++++m T+n+Aka
  gi|557693963|ref|YP_008797017.1| 288 HTGPLHAPVKKLIDRGVNVALGQDDVADAYYPfgrnKM---LEVAFLASHILRM---LSKSDIMKLFNMITFNAAKA 358
                                       45666689******************888888555444...3444433444444...345689999*********** PP

                                       TT-TTTSSSS-TTSB--EEEECC.CTCGGGTTT CS
                      Amidohydro_1 297 lglddkvGsievGkdADlvvvdl.dilaafvgl 328
                                       ++++    ++e+G dA ++++d   i  af+ +
  gi|557693963|ref|YP_008797017.1| 359 MRIP--RYTVEKGSDATFIILDAeSIHHAFATQ 389
                                       ***6..447************996444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3028.26
//
Query:       gi|557693964|ref|YP_008797018.1|  [L=519]
Description: sugar ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-50  171.6   0.0    3.3e-31  108.6   0.0    2.2  2  ABC_tran       ABC transporter
    3.1e-07   30.5   0.1     0.0043   16.9   0.0    2.2  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
     0.0032   17.4   0.2      0.061   13.2   0.0    2.7  3  RsgA_GTPase    RsgA GTPase
     0.0074   16.0   0.1      0.028   14.2   0.0    2.0  2  AAA_29         P-loop containing region of AAA domain
  ------ inclusion threshold ------
       0.01   16.4   0.1      0.032   14.7   0.0    1.8  2  AAA_23         AAA domain
      0.013   14.9   0.0        1.8    8.0   0.0    2.5  3  SMC_N          RecF/RecN/SMC N terminal domain
      0.035   14.4   0.1       0.23   11.7   0.1    2.3  1  AAA_22         AAA domain
      0.053   13.1   0.0        0.1   12.2   0.0    1.4  1  AAA_27         AAA domain
      0.089   11.6   0.0       0.58    8.9   0.0    2.0  2  DLIC           Dynein light intermediate chain (DLIC)
       0.14   11.1   0.0       0.24   10.4   0.0    1.3  1  Histidinol_dh  Histidinol dehydrogenase


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 !  108.6   0.0   1.9e-34   3.3e-31       1     137 []      30     178 ..      30     178 .. 0.97
   2 !   61.1   0.0   8.4e-20   1.5e-16       2     136 ..     284     439 ..     283     440 .. 0.89

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 1.9e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l++v+l++k+ge++a++GenGaGK+tL+++l g+l+p+eGei l g++++   +l   +k ig+++q+ +l + +tv
  gi|557693964|ref|YP_008797018.1|  30 LDHVDLEMKAGEIHAVLGENGAGKTTLMNILFGMLQPDEGEIYLFGEKVRFrSPLDAINKGIGMVHQHRKLISAHTV 106
                                       789********************************************999989************************ PP

                                       HHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        en               e+++eie++ +k+g k + d +v     +LS G+kq v++++ l + +++l+lDEpt+
  gi|557693964|ref|YP_008797018.1| 107 FENiilghprvgrlikksEARAEIEELCRKFGFKIDLDARV----WQLSAGEKQLVEIVKNLYRGARILILDEPTS 178
                                       ***************98888888************999999....9****************************96 PP

  == domain 2  score: 61.1 bits;  conditional E-value: 8.4e-20
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS...--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe...pqlfpel 74 
                                       kn++++++ege+ +i G +G G   L+++++gl kp  G+il++gkd+++   le+++  i ++p e     l  el
  gi|557693964|ref|YP_008797018.1| 284 KNINFSVYEGEIFGIAGVTGNGQQELVETIYGLRKPLTGRILFQGKDITKtSVLERMKMGIVYIPPErlnFALIGEL 360
                                       8************************************************98899***********997777788888 PP

                                       BHHHH....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEE CS
                                       xxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpklll 131
                                       ++ +n                    +++e +e+++s+++ +    +    +++ LSgG +q+++l r+ll+ pkl++
  gi|557693964|ref|YP_008797018.1| 361 SLVDNvlmttyfnqgmskrglinykTAKEYCERVISEFNVVAP-SSST--KAAYLSGGNQQKIVLGRVLLSSPKLII 434
                                       888889********99999999876666669********9993.3333..569***********************9 PP

                                       EESTT CS
                                       xxxxx RF
                          ABC_tran 132 lDEpt 136
                                       +  pt
  gi|557693964|ref|YP_008797018.1| 435 ANLPT 439
                                       86555 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 !   16.9   0.0   2.4e-06    0.0043       2      72 ..      43     107 ..      42     112 .. 0.77
   2 !   11.5   0.0   0.00011      0.19     230     297 ..     143     218 ..     113     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.4e-06
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvry 72 
                                        ++ G Ng+GK++L+ +l      +++++++  e   +g+    +s ld +++ i ++++ +++ s ++++
  gi|557693964|ref|YP_008797018.1|  43 HAVLGENGAGKTTLMNIL------FGMLQPDEGEIYLFGEKVRFRSPLDAINKGIGMVHQHRKLISAHTVF 107
                                       6899**************......66667888888888888888888888888777777777666666666 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00011
                            AAA_21 230 qelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr...........ngaQvilt 295
                                        +  +++lS G k+l  ++  l+r +   ++l++DEp + L P  +  +l+ l++ s+           ++  v+++
  gi|557693964|ref|YP_008797018.1| 143 LDARVWQLSAGEKQLVEIVKNLYRGA---RILILDEPTSVLTPPEIDAFLDSLRAVSKekislmpfvthKLPEVFAV 216
                                       5567899*****************99...*********************999888885556666666666666666 PP

                            AAA_21 296 TH 297
                                       +H
  gi|557693964|ref|YP_008797018.1| 217 SH 218
                                       66 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   3.4e-05     0.061      96     129 ..      36      70 ..      27      74 .. 0.79
   2 ?   -0.4   0.0      0.53   9.6e+02      97     148 ..     291     339 ..     264     347 .. 0.72
   3 ?   -0.7   0.0      0.67   1.2e+03      32      79 ..     447     492 ..     440     510 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.4e-05
                                       HCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                       ++k  ++ +++G+ G+GK+tL+n l + l+   ge
  gi|557693964|ref|YP_008797018.1|  36 EMKAgEIHAVLGENGAGKTTLMNILFGMLQPDEGE 70 
                                       44444999*****************9887766555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.53
                                       CTTSEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEE CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavelle 148
                                        ++++  ++G +G G   L++++ +  +  tg +     +Gk  T+++ l +
  gi|557693964|ref|YP_008797018.1| 291 YEGEIFGIAGVTGNGQQELVETIYGLRKPLTGRILF---QGKDITKTSVLER 339
                                       445888999***********9999987888887744...5666666666555 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEE CS
                       RsgA_GTPase  32 lnlldrfLvlaeekgiepvivlnKiDlleeeeeleelkeelealgyev 79 
                                       +n++ r L++ +++gi+ ++v   +D + e +  ++++  +e + ++v
  gi|557693964|ref|YP_008797018.1| 447 ENFVRRKLLESKTHGISTILVSEDLDEIMELS--DRVAPIYEGVFVKV 492
                                       67899999999999999999998888887776..55555555555555 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   1.6e-05     0.028      13      42 ..      31      60 ..      28      71 .. 0.77
   2 ?   -3.9   0.0       6.8   1.2e+04      23      34 ..     293     305 ..     282     310 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAi 42
                                      d+ ++e++  +++ + G++G+GK+Tl+  +
  gi|557693964|ref|YP_008797018.1| 31 DHVDLEMKAGEIHAVLGENGAGKTTLMNIL 60
                                      55678888666***************9655 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.8
                            AAA_29  23 g.atlltGpsGsG 34 
                                       g ++ ++G +G+G
  gi|557693964|ref|YP_008797018.1| 293 GeIFGIAGVTGNG 305
                                       3367788888888 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.8e-05     0.032      21      41 ..      42      62 ..      27      82 .. 0.84
   2 ?   -2.7   0.1         4   7.2e+03      15      31 ..     286     305 ..     268     339 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                            AAA_23 21 ltlItGpNGaGKTTildAikl 41
                                      + ++ G+NGaGKTT+++ +  
  gi|557693964|ref|YP_008797018.1| 42 IHAVLGENGAGKTTLMNILFG 62
                                      56789***********98765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4
                            AAA_23  15 idF...skgltlItGpNGaG 31 
                                       i+F   +  ++ I G +G G
  gi|557693964|ref|YP_008797018.1| 286 INFsvyEGEIFGIAGVTGNG 305
                                       44444555555555555544 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 ?    8.0   0.0   0.00099       1.8      25      44 ..      41      60 ..      29      67 .. 0.80
   2 ?    4.2   0.0     0.014        25     117     184 ..     124     193 ..     105     241 .. 0.66
   3 ?   -2.9   0.0       2.1   3.7e+03     101     101 ..     369     369 ..     284     424 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00099
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      ++ a++G+NG+GK+ l++ +
  gi|557693964|ref|YP_008797018.1| 41 EIHAVLGENGAGKTTLMNIL 60
                                      5789***********99754 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.014
                                       EE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHH.....HHCCS--SEEEECTTTTTS-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 117 evtkkevsellesagiske......lLSgGektLvalaLlfA.....iqkvkpaplyllDeidaaLDeknvkkvael 182
                                       +  ++e++el ++ g++++      +LS Gek+Lv +   +      +   +p+++    eida LD          
  gi|557693964|ref|YP_008797018.1| 124 SEARAEIEELCRKFGFKIDldarvwQLSAGEKQLVEIVKNLYrgariLILDEPTSVLTPPEIDAFLDS--------- 191
                                       44568999999999999999999999********9885443333343333445555555556666654......... PP

                                       HH CS
                                       xx RF
                             SMC_N 183 lk 184
                                       l+
  gi|557693964|ref|YP_008797018.1| 192 LR 193
                                       33 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.1
                                       E CS
                                       x RF
                             SMC_N 101 r 101
                                       +
  gi|557693964|ref|YP_008797018.1| 369 T 369
                                       0 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00013      0.23       7      38 ..      42     113 ..      36     214 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee........................................e 38 
                                       i +v Ge G+GKTtl++ l+  l+ ++   +                                         
  gi|557693964|ref|YP_008797018.1|  42 IHAVLGENGAGKTTLMNILFGMLQPDEGEIYlfgekvrfrspldainkgigmvhqhrklisahtvfeniilG 113
                                       67899*************999997554444466666666655555555555555555555555555444442 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.6e-05       0.1      18      52 ..      32      62 ..      25      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.6e-05
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdllfG 52
                                      ++d++ ++ ++h ++G N AGK+t+++    +lfG
  gi|557693964|ref|YP_008797018.1| 32 HVDLEMKAGEIHAVLGENGAGKTTLMN----ILFG 62
                                      688999999***************986....4455 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00032      0.58      29      54 ..      44      69 ..      35      74 .. 0.84
   2 ?   -0.3   0.0      0.21   3.7e+02     288     330 ..      88     131 ..      82     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00032
                              DLIC 29 lvlGedgsGkttliaklqGveeekkG 54
                                       vlGe+g+Gkttl+  l G+ ++  G
  gi|557693964|ref|YP_008797018.1| 44 AVLGENGAGKTTLMNILFGMLQPDEG 69
                                      69***************999877766 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.21
                              DLIC 288 ekkiailyenlqtvkaedsyedvik.kPPvrklvhekeiqaede 330
                                       +k i+++++  + + a+  +e++i  +P v +l+++ e  ae e
  gi|557693964|ref|YP_008797018.1|  88 NKGIGMVHQHRKLISAHTVFENIILgHPRVGRLIKKSEARAEIE 131
                                       57899*****************9963688999999999999866 PP

>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00013      0.24     266     336 ..     442     512 ..     424     515 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                                       HHHHHCC-TTHHHHHHHHCCH-EEEE-SSHHHHHHHHHHH--SEEEEESTTHHHHGGG--S-SEEEESTT- CS
                     Histidinol_dh 266 vekqleelprkeiaekslekqsaiilvedleeaielaneyApEHlelqvedpeellekiknaGaiflGeys 336
                                       ++  +e+  r++++e+  +  s+i++ edl+e++el++++Ap +  + v+  +++  k +++Ga+  G+ys
  gi|557693964|ref|YP_008797018.1| 442 LDIAAENFVRRKLLESKTHGISTILVSEDLDEIMELSDRVAPIYEGVFVKVLQNIDLKKEEVGAMIAGAYS 512
                                       566778889999999999**************************999999999999999999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); 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 0.27s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 3823.42
//
Query:       gi|557693965|ref|YP_008797019.1|  [L=358]
Description: sugar ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  113.5  23.9    9.3e-33  113.5  23.9    1.6  2  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
       0.15   11.5   0.2       0.31   10.4   0.2    1.5  1  NAR2          High-affinity nitrate transporter accessory


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 ?   -2.3   0.4      0.22     2e+03     226     262 ..      23      57 ..      13      58 .. 0.53
   2 !  113.5  23.9     1e-36   9.3e-33       5     249 ..      67     320 ..      63     344 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.22
                      BPD_transp_2 226 gsllgtviGaliigvvksllltllgiptelarvllga 262
                                        s++ t++  +++++v s    + +  t++++++++a
  gi|557693965|ref|YP_008797019.1|  23 ISIYSTIASFIVFSIVLS-VEGADPL-TAYQNMFSFA 57 
                                       455666666666666665.3333333.6666666666 PP

  == domain 2  score: 113.5 bits;  conditional E-value: 1e-36
                      BPD_transp_2   5 lltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl.....lllallvallvgaavglllgll 76 
                                       ++ +++++++  l++ +   +aG +n+g +g++ lG + a+ ++++l+       ++l++l ++++ga+ g+l g+l
  gi|557693965|ref|YP_008797019.1|  67 TIHRSMLILFSTLAFIVPL-RAGFWNIGMEGQFYLGTIGAFFVAYSLPDYppevlIPLMILSGMVFGALYGALAGIL 142
                                       56789999999********.****************99999999998888999************************ PP

                      BPD_transp_2  77 vlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsavivllalllvlavllllrrtr 153
                                         +++v+e+++tl+l+ +++++++ll  g+ +  +  s+  +l ++a+a ++ +  + ++la++++++++++l +t+
  gi|557693965|ref|YP_008797019.1| 143 RGKFNVNEVVVTLMLNNIAFWMVYLLTVGGPWAGTAESTSRPLPKNAQAPFILGTPFTTFLAIAFAFILYFFLSKTV 219
                                       ************************99999999999999999999999999999999999****************** PP

                      BPD_transp_2 154 fGralravgeneeaaralGinvkrvklltfvisgalAglaGall....alllgsipp...nigvglgfnaiaavvlG 223
                                        G+++r +g +++aa+++Gi+ +++ +l++ ++galAg+aG ++     ++l +  p    +   l++ +i++ ++ 
  gi|557693965|ref|YP_008797019.1| 220 AGFKIRILGHSPTAAKFVGIDEFKTAVLVMSLGGALAGVAGYHMwagdPAYLRIPRPdayKAVGDLTYWGIIIGLVC 296
                                       *******************************************9333335777777787777777999999999999 PP

                      BPD_transp_2 224 gagsllgtviGaliigvvksllltll 249
                                        + +++ ++ +++ ig +   ++t+l
  gi|557693965|ref|YP_008797019.1| 297 LL-NPIPAMPASFFIGSIIV-GSTVL 320
                                       99.99999999999998766.55544 PP

>> NAR2  High-affinity nitrate transporter accessory
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   3.5e-05      0.31     130     161 ..       7      38 ..       3      43 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.5e-05
                              NAR2 130 akttnlfevkaitgrhasldiaaavfsvfSvv 161
                                        k + l ++ +i g++ s+  + a f+vfS+v
  gi|557693965|ref|YP_008797019.1|   7 LKRERLVTISGIRGVQISIYSTIASFIVFSIV 38 
                                       567899************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2535.21
//
Query:       gi|557693966|ref|YP_008797020.1|  [L=297]
Description: sugar ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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  106.9  28.7    2.2e-30  105.8  28.7    1.5  1  BPD_transp_2     Branched-chain amino acid transport system /


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 !  105.8  28.7   1.2e-34   2.2e-30       2     268 .]      12     270 ..      11     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 1.2e-34
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvl 78 
                                       i ++l +++il++aA+G  l+  ++Gvin g++g+m+ G+ +a+l ++l++  +l++++v+  vg ++gl+  +l++
  gi|557693966|ref|YP_008797020.1|  12 ITRFLEVSTILLLAAMGELLTQ-RSGVINVGIEGLMLAGGASAFLTAQLYG--PLAGFVVGTFVGTLLGLFHSFLSV 85 
                                       668999****************.**************************99..5*********************** PP

                      BPD_transp_2  79 rlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv..llalllvlavllllrrtr 153
                                         +v+++i++ ++ +++vg++      ++ + ++ +    + +++g             ++al  +++++++l +t 
  gi|557693966|ref|YP_008797020.1|  86 SMRVNQIISGMGVWLFAVGFVT-----YWADRYTGPLRYSIPRINGL--------SPalFIALGSLIVIWYVLSYTH 149
                                       **********************.....33333333333333333333........2222688999************ PP

                      BPD_transp_2 154 fGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGgagsll 229
                                       fG+++r vgen+ aa+a+G+nv++++ l   i+g l+g+aGa+l l++ +++      glg+ a+  v+   + ++ 
  gi|557693966|ref|YP_008797020.1| 150 FGLKIRSVGENPAAAEASGVNVEKIRYLCTTIGGSLGGFAGAVLLLSYLGAWShLPTKGLGWLAFGLVMFSLW-RPG 225
                                       ****************************************************9888889**************.*** PP

                      BPD_transp_2 230 gtviGaliigvvksllltllgi......ptelarvllgallilvl 268
                                         ++Gal +g+v +++++   i      p  ++r++ ++l i++l
  gi|557693966|ref|YP_008797020.1| 226 ILLAGALSFGFVWQFGISPETIypgfpaPLPVNRMMPFLLTIIIL 270
                                       **************88877766888888899*********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2057.76
//
Query:       gi|557693967|ref|YP_008797021.1|  [L=469]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   84.5   0.0    8.6e-24   84.0   0.0    1.2  1  Bmp       ABC transporter substrate-binding protein PnrA-like


Domain annotation for each model (and alignments):
>> Bmp  ABC transporter substrate-binding protein PnrA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.0   4.8e-28   8.6e-24       2     250 ..      86     337 ..      85     352 .. 0.88

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 4.8e-28
                                       EEEEEECSS-TTTSCHHHHHHHHHHHHHHHC.TTEEEEEEEEC.GGGHHHHHHHH.HHCTT-SEEEEE.SCCHHHHH CS
                               Bmp   2 vkvavlvegtidDksfnessyeGirrlkkeq.nieliskesslltdedyiadlkn.lkeegsdlivat.gfalqdal 75 
                                        +++++  g+i+++ +      + +rlkk +   + ++ e + l+ +d i+++++ ++  + ++++++  +a    +
  gi|557693967|ref|YP_008797021.1|  86 IVLGMVLGGFIEGSTWDGRQVRAAERLKKFYpWFDYAYDEGVVLKGKDPISSARDlIATAKANIVFGSwEPAAIPGF 162
                                       57889999999999999999999999999999999999999999999999988762689999999975378888899 PP

                                       HHHHHH-TTS-EEEESS--TT-STTEEEEEE-HHHHHHHHHHHHHHHHHCTTTTEECSS-SCCCHHCHHHHHHHHHH CS
                               Bmp  76 qevssdfpkvkFliiDavvekeyknvlsvaFrseegaFLaGvaaAlmsktnkigfvgGveipvvksfingFeaGiky 152
                                        +++++fp+v+Fl i +       n + v+ r++++ +L G++a++++++nkig   G       + +++F +Gik+
  gi|557693967|ref|YP_008797021.1| 163 HTLANEFPNVYFLGIVGSDVSSERNFMRVFVRQYQAMYLEGLVAGAITQSNKIGIAVGPLAVQNLRRMAAFYLGIKD 239
                                       ************966666555558*******************************999999999999999******* PP

                                       H-TT-EEEEEE-SSSS-HHHHHHHHHHHHHCT--EEEEE-GGGHHHHHHHHHHHCHCTEEEEEES--....CGCSTT CS
                               Bmp 153 vnpdievvvkvagtfsDakkgkslAsslykegvdvifpaagkagkgvieaakelglsnyvIgvdkdq....sylape 225
                                       +npd+++++k++g + D+ k+++++ sl ++g+dv  +    ++   ++ a+e+++    +g d+d       ++++
  gi|557693967|ref|YP_008797021.1| 240 ANPDAKLYIKYVGEWFDPPKEREVSLSLLDQGIDVLTH--YTDSVEPLKVAEENKIW--FVGKDTDIvglyGWSTTD 312
                                       **************************************..55555557777777765..*******9776667899* PP

                                       CCEEEEEEEHHHHHHHHHHHHHCCT CS
                               Bmp 226 nvitsiiknvedlvvsiiekvakge 250
                                       +v++s  + +e +  +ii++++ g+
  gi|557693967|ref|YP_008797021.1| 313 TVAVSFDTRWEVMFDQIIKEYLAGT 337
                                       ********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (469 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 00:00:00.44
# Mc/sec: 3231.83
//
Query:       gi|557693968|ref|YP_008797022.1|  [L=340]
Description: basic membrane lipoprotein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-27   95.2   0.0    4.7e-27   94.8   0.0    1.1  1  Bmp       ABC transporter substrate-binding protein PnrA-like
  ------ inclusion threshold ------
      0.023   14.1   0.0        5.1    6.4   0.0    2.2  2  ZnuA      Zinc-uptake complex component A periplasmic


Domain annotation for each model (and alignments):
>> Bmp  ABC transporter substrate-binding protein PnrA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0   5.2e-31   4.7e-27      22     250 ..      38     275 ..      28     284 .. 0.84

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 5.2e-31
                                       HHHHHHHHHHCTTEEEEEEEEC.....GGGHHHHHHHHHHCTT-SEEEEESCCHHHHHHHHHHH-TTS-EEEESS-- CS
                               Bmp  22 yeGirrlkkeqnieliskessll....tdedyiadlknlkeegsdlivatgfalqdalqevssdfpkvkFliiDavv 94 
                                       + +i ++++e++ + i  ++++        dy+ +l+++++   d++++  f  +d+   v+++f++v F+  + + 
  gi|557693968|ref|YP_008797022.1|  38 HAAILAVADEFKTKGINVDYQFVdrkiDPRDYELALRDAAR-VADIVFLDAFLKEDIARRVAKEFKNVAFAAGSEFL 113
                                       55566666666555555555554444455677777777664.579******************************** PP

                                       TT-STTEEEEEE-HHHHHHHHHHHHHHHHHCTTTTEECSS-SCCCHHCHHHHHHHHHHH-TT-EEEEEE-.SS.... CS
                               Bmp  95 ekeyknvlsvaFrseegaFLaGvaaAlmsktnkigfvgGveipvvksfingFeaGikyvnpdievvvkva.gt.... 166
                                       +++  n + +     + a+LaG++a++++k++ ig+v+++ i++v++ +n+F aG+k vnpd++ +v  + g+    
  gi|557693968|ref|YP_008797022.1| 114 PAQP-NFSVFDNWLHQPAYLAGIIAGKITKSKRIGAVAAMDINEVNRIVNAFIAGAKSVNPDVKAKVVNLlGNippg 189
                                       ***5.9999999999*************************************************9876543545555 PP

                                       ...SS-HHHHHHHHHHHHHCT--EEEEE-GGGHHHHHHHHHHHCHCTEEEEEES--CGCSTTCCEEEEEEEHHHHHH CS
                               Bmp 167 ...fsDakkgkslAsslykegvdvifpaagkagkgvieaakelglsnyvIgvdkdqsylapenvitsiiknvedlvv 240
                                          ++ ++++k lA+ l++   dvif    +a ++++e ak +g++ ++Ig   dq+ +ap   its ++++  +v 
  gi|557693968|ref|YP_008797022.1| 190 espWYHPATAKRLAKALIDLNTDVIFAERVGAEEAAVE-AKAEGKDVWIIGNMADQYSRAPTVTITSLVWDMRPTVR 265
                                       566************************77777777765.56667777****************************** PP

                                       HHHHHHHCCT CS
                               Bmp 241 siiekvakge 250
                                       ++ ++v+ + 
  gi|557693968|ref|YP_008797022.1| 266 IAFQRVLANA 275
                                       **99999887 PP

>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0013        12      24      54 ..      58      86 ..      44     116 .. 0.78
   2 ?    6.4   0.0   0.00057       5.1     183     218 ..     188     231 ..     149     245 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0013
                                      ECS-TTSTTTT----HHHHHHHHHSSEEEES CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 24 vLvppgadpHsyeptprdvrklaeAdllvyn 54
                                        v+ ++dp +ye+ +rd++++  Ad+++  
  gi|557693968|ref|YP_008797022.1| 58 QFVDRKIDPRDYELALRDAARV--ADIVFLD 86
                                      578999*************998..5666655 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.00057
                                       S.......HHHHHHHHHHHHHTT-SEEEEETTS.-THHHHHHHH CS
                                       x.......xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                              ZnuA 183 e.......aaqiaalieeikeagvkaifvepla.spklaetlae 218
                                               +a+ ++l++++ ++++ +if+e +  +++++e+ ae
  gi|557693968|ref|YP_008797022.1| 188 PgespwyhPATAKRLAKALIDLNTDVIFAERVGaEEAAVEAKAE 231
                                       1467788999*********************6636666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); 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:                         2  (0.000111551); expected 0.2 (1e-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: 2528.14
//
Query:       gi|557693969|ref|YP_008797023.1|  [L=510]
Description: sugar ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-30  104.5   0.0    9.9e-17   61.7   0.0    2.6  3  ABC_tran     ABC transporter
    5.8e-05   23.7   0.0     0.0001   22.9   0.0    1.3  1  AAA_23       AAA domain
    0.00041   19.8   0.7       0.63    9.4   0.1    2.4  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00072   19.5   5.3     0.0066   16.3   0.0    2.4  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
      0.005   16.8   0.2      0.018   14.9   0.0    1.9  2  RsgA_GTPase  RsgA GTPase
     0.0065   16.2   0.0      0.014   15.2   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.015   15.6   1.2       0.67   10.2   0.3    2.3  2  AAA_22       AAA domain
      0.047   14.1   0.0       0.11   12.9   0.0    1.6  1  AAA_16       AAA ATPase domain
       0.06   13.1   0.0      0.096   12.4   0.0    1.2  1  AAA_15       AAA ATPase domain
       0.11   12.5   0.0       0.25   11.2   0.0    1.6  1  Rad17        Rad17 P-loop domain
       0.16   11.5   0.0       0.29   10.7   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 !   61.7   0.0   6.1e-20   9.9e-17       2     136 ..      26     176 ..      25     177 .. 0.87
   2 ?   -2.9   0.0       5.6   9.2e+03      28      51 ..     187     210 ..     186     259 .. 0.72
   3 !   40.2   0.0   2.8e-13   4.5e-10       2     132 ..     283     434 ..     282     439 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 6.1e-20
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + +s++l++ +++++vG+nGaGKSt+++l++g l p++Ge++++g ++++         +  ++q+p+l p lt +e
  gi|557693969|ref|YP_008797023.1|  26 DSISFELSPFRVYGFVGPNGAGKSTIMNLISGYLFPDSGEVWVNGIQVTDFHQALNVCGVVKVEQHPNLSPYLTPAE 102
                                       789***********************************************77777788899999**********999 PP

                                       H............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHT........SSEEEEEST CS
                                       x............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxx RF
                          ABC_tran  79 n............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkk........pkllllDEp 135
                                       +              +  ++++l++lg + + +++v    ++L  G+ +  ++++al++         +++l+lDE+
  gi|557693969|ref|YP_008797023.1| 103 HlsmllpkfiptkSLNHLAHELLRQLGVEVDLERRV----EELPIGHLRVFEIVKALIQCeilhkkglSPVLILDEA 175
                                       99*******998555666******************....9999999999999999886422222233578999999 PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                       t
  gi|557693969|ref|YP_008797023.1| 176 T 176
                                       8 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.6
                                       HHHHTTSS--SEEEEEETTCEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  28 lkllagllkpteGeilldgkdlke 51 
                                       lkl++++l+ ++ ++l+ ++dl+e
  gi|557693969|ref|YP_008797023.1| 187 LKLILRKLTSKQHTVLVVSHDLHE 210
                                       677788888888888777777776 PP

  == domain 3  score: 40.2 bits;  conditional E-value: 2.8e-13
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS...--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe...pqlfpel 74 
                                       +n +l++k ge+++i    G+G   L++ ++g  + + Geil+ g+ +k+ + ++  r+ ++vl+ +   + l  + 
  gi|557693969|ref|YP_008797023.1| 283 RNFNLSIKSGEVHGIAVIPGTGEKELVEGILGVRRIERGEILVYGHVVKNpTVTTMRRRGVAVLSDDrirDGLITDA 359
                                       799***********************************************777788888999999999988999999 PP

                                       BHHHH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEE CS
                                       xxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllll 132
                                       +v +n                 +s+ + e a s +++  +  + ++   ++LSgG  qrv +ar+l ++pk+ll+
  gi|557693969|ref|YP_008797023.1| 360 SVFDNltlglfdkyckakgffiDSRLRTELAKSLVRDFSIVVKDLRGPVTNLSGGNMQRVYIARVLGTEPKILLA 434
                                       99999*******9888888876555556666666666666666665556************************97 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   6.2e-08    0.0001      10      46 ..      25      62 ..      10      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.2e-08
                            AAA_23 10 frdqeidFsk.gltlItGpNGaGKTTildAiklaLyge 46
                                       +  ++++s+  ++ ++GpNGaGK+Ti++ i   L+ +
  gi|557693969|ref|YP_008797023.1| 25 VDSISFELSPfRVYGFVGPNGAGKSTIMNLISGYLFPD 62
                                      45556777777999****************99888765 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 !    9.4   0.1   0.00039      0.63      28      45 ..      39      56 ..      19      65 .. 0.83
   2 !    8.4   0.1   0.00082       1.3     153     208 ..     161     218 ..     151     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00039
                                      EEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnlldAil 45
                                        vGpNG+GKs +++ i+
  gi|557693969|ref|YP_008797023.1| 39 GFVGPNGAGKSTIMNLIS 56
                                      579**********98775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00082
                                       HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH.CTTSEEEEE-SS.HHHCCC-SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.xxxxxxxxxx RF
                             SMC_N 153 iqkvkpaplyllDeidaaLDeknvkkvaellkek.sknaQfivislr.eemlekadkl 208
                                       ++k   +p+ +lDe    L +++ + +  +l++  sk+  ++v+s++ +e++  ad++
  gi|557693969|ref|YP_008797023.1| 161 LHKKGLSPVLILDEATTFLPQHHKNTLKLILRKLtSKQHTVLVVSHDlHEIIDVADEI 218
                                       5788889************************97615668999**99835566666665 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 !   16.3   0.0   4.1e-06    0.0066       2      24 ..      38      60 ..      37      81 .. 0.79
   2 ?    3.6   2.5      0.03        49     220     300 ..     124     209 ..      88     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.1e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllar 24
                                       +++GpNg+GKS+++ ++++  +
  gi|557693969|ref|YP_008797023.1| 38 YGFVGPNGAGKSTIMNLISGYLF 60
                                      579***************88765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.03
                            AAA_21 220 gvvflengdgqelparelSdGtkrll...alltallralkkg..sllliDEpEngL..HPkllrrllellkelsrng 289
                                        +++l  + + e+ + el+ G++r++   + l  +  ++kkg  ++l++DE  ++L  H+k + +l+  l++l+++ 
  gi|557693969|ref|YP_008797023.1| 124 LLRQLGVEVDLERRVEELPIGHLRVFeivKALIQCEILHKKGlsPVLILDEATTFLpqHHKNTLKLI--LRKLTSKQ 198
                                       5566777888999999**********7777777777777777*********9999977665554444..56666678 PP

                            AAA_21 290 aQviltTHSpl 300
                                         v++++H+ +
  gi|557693969|ref|YP_008797023.1| 199 HTVLVVSHDLH 209
                                       89999999976 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05     0.018      88     121 ..      23      57 ..      10      74 .. 0.85
   2 ?   -1.4   0.1       1.1   1.9e+03      42      91 ..     161     209 ..     144     225 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       +++++++ +l+  ++  +vG+ G+GKSt++n + +
  gi|557693969|ref|YP_008797023.1|  23 RAVDSISFELSPfRVYGFVGPNGAGKSTIMNLISG 57 
                                       567889999999999****************9987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                                       HHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTT...SEEEE--TTTHTTHH CS
                       RsgA_GTPase  42 aeekgiepvivlnKiDlleeeeeleelkeelealg...yevllvsaktkegle 91 
                                       +++kg++pv++l  +     +++ ++lk  l++l     +vl+vs +    l+
  gi|557693969|ref|YP_008797023.1| 161 LHKKGLSPVLILDEATTFLPQHHKNTLKLILRKLTskqHTVLVVSHD----LH 209
                                       34678888888888777666664444444444444000444444443....33 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   8.3e-06     0.014      24      50 ..      37      63 ..      23      71 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.3e-06
                            AAA_29 24 atlltGpsGsGKSTllDAiqalLvpak 50
                                      ++ ++Gp+G+GKST++  i+  L p++
  gi|557693969|ref|YP_008797023.1| 37 VYGFVGPNGAGKSTIMNLISGYLFPDS 63
                                      55699***********88888887776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.039        64      11      24 ..      41      54 ..      37      59 .. 0.88
   2 ?   10.2   0.3   0.00041      0.67      52     135 ..     116     210 ..      85     212 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.039
                            AAA_22 11 tGesGtGKTtllrr 24
                                      +G+ G+GK+t ++ 
  gi|557693969|ref|YP_008797023.1| 41 VGPNGAGKSTIMNL 54
                                      8*********9975 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00041
                            AAA_22  52 sskdllrellralglelka.........erlsseell.ealeqalrarav.ielliiDEaqh.lrseealeeLrsll 116
                                       s+  l++ellr+lg+e +            l+  e++ ++++  + +++   ++li+DEa   l ++ + ++L+ +l
  gi|557693969|ref|YP_008797023.1| 116 SLNHLAHELLRQLGVEVDLerrveelpiGHLRVFEIVkALIQCEILHKKGlSPVLILDEATTfL-PQHHKNTLKLIL 191
                                       778899999999998877777885555544444444435555444444448***********66.777777776666 PP

                            AAA_22 117 nlsrkgvqliLvGtpelrk 135
                                          +++ + +Lv  ++l++
  gi|557693969|ref|YP_008797023.1| 192 RKLTSKQHTVLVVSHDLHE 210
                                       6544455555666666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.6e-05      0.11      29     168 ..      40     201 ..      31     242 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
                            AAA_16  29 lsGesGvGKsslvrellralekd..ggiflrgkcdqlesa...............ipy.......salaqalareel 81 
                                       ++G+ G GKs++++ +  +l  d  ++++   + +++++a                py       s           
  gi|557693969|ref|YP_008797023.1|  40 FVGPNGAGKSTIMNLISGYLFPDsgEVWVNGIQVTDFHQAlnvcgvvkveqhpnlSPYltpaehlS----------- 105
                                       68****************999998646666666666655544555555444444434422222222........... PP

                            AAA_16  82 lrqlldeaesaeleawrekleeala......avpelagaea.....srllellkrll..allsrderplvlvlDdlq 145
                                          l     +++l++ +++l+++l+         e     +      r++e +k+l+  + l++++   vl+lD++ 
  gi|557693969|ref|YP_008797023.1| 106 -MLLPKFIPTKSLNHLAHELLRQLGvevdleRRVE-----ElpighLRVFEIVKALIqcEILHKKGLSPVLILDEAT 176
                                       .2222223334556666666666664333332222.....1334447777777777766666665556777777777 PP

                            AAA_16 146 wadeaslql.laaLlrllesk.pll 168
                                        + ++ ++  l+++lr l+sk + +
  gi|557693969|ref|YP_008797023.1| 177 TFLPQHHKNtLKLILRKLTSKqHTV 201
                                       6555444444666666665543433 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.9e-05     0.096      17      43 ..      28      55 ..      23      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-05
                            AAA_15 17 veidlsee.ltvliGkNnsGKSsileal 43
                                      ++ +ls+  +  ++G+N++GKS+i++++
  gi|557693969|ref|YP_008797023.1| 28 ISFELSPFrVYGFVGPNGAGKSTIMNLI 55
                                      555666655667*************999 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016      0.25      35      99 ..      25      89 ..      13     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                             Rad17 35 lkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre.wlnpvslkepdn.qksdfkglteke 99
                                      +++ + e  + r+    GP G gkst+++ +s  l ++  e w+n+++   +d+ q  ++ g++++e
  gi|557693969|ref|YP_008797023.1| 25 VDSISFELSPFRVYGFVGPNGAGKSTIMNLISGYLFPDSGEvWVNGIQ--VTDFhQALNVCGVVKVE 89
                                      55666777788888899****************9999876559***99..56665666666666655 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00018      0.29      30      51 ..      39      60 ..      24      63 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00018
                            AAA_27 30 liyGpNEAGKstalrAisdllf 51
                                        +GpN AGKst+++ is  lf
  gi|557693969|ref|YP_008797023.1| 39 GFVGPNGAGKSTIMNLISGYLF 60
                                      568************9999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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 0.28s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3693.07
//
Query:       gi|557693970|ref|YP_008797024.1|  [L=715]
Description: sugar ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-55  188.2  75.0    7.6e-28   97.4  36.9    2.5  2  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
       0.19   11.9   0.0       0.38   10.9   0.0    1.4  1  HTH_28        Helix-turn-helix domain


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 !   96.4  30.1   1.7e-31   1.6e-27       4     260 ..      59     325 ..      56     340 .. 0.87
   2 !   97.4  36.9   8.5e-32   7.6e-28       4     250 ..     418     670 ..     415     692 .. 0.88

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 1.7e-31
                      BPD_transp_2   4 nlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl.....lllallvallvgaavglllgl 75 
                                       ++ ++a++l+++A ++ + f +a+ +n+g+ g++++G+ ++a+l + l+s      ++l++  + l+g av+l+  +
  gi|557693970|ref|YP_008797024.1|  59 EIFVTATPLTLLAFSILIAF-RARFWNIGAHGQFIIGGLMSAWLGVVLGSVpqyllIPLMFTCSWLAGSAVALISWW 134
                                       68899***************.****************9999888888888888888889999999999999999999 PP

                      BPD_transp_2  76 lvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv....llalllvlavlll 148
                                       l+++ + de+++t+l+ s+++++++ lltg+ + ++++  ++  + ++  l   +         +  ++++l++++l
  gi|557693970|ref|YP_008797024.1| 135 LKTKKGQDEVLTTILIWSAILLINAGLLTGPLRSPYTTYPQSQEISINAKLPVLIPDTRLhagvIAPFIIMLLLWFL 211
                                       9999999**************************99998876666666666666666555568889999********* PP

                      BPD_transp_2 149 lrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGg 224
                                       + rt fG+++ av+ n++aa + Gi+v rv +++ ++sg++AglaGa+  + + +  + ++g+++g+ a+a+++lG 
  gi|557693970|ref|YP_008797024.1| 212 MSRTTFGVKVTAVT-NPRAAILEGIDVSRVYFWVCFLSGGIAGLAGAIELMGILFYMTpFVGPNYGLVALAIAMLGN 287
                                       *************7.9********************************98877776666****************** PP

                      BPD_transp_2 225 agsllgtviGaliigvvksllltllgi....ptelarvll 260
                                       +  ++g+ i++l ++++ + + +++ +    p+ la++++
  gi|557693970|ref|YP_008797024.1| 288 L-DVIGATIASLFFSIIIN-GANAMAWstgvPSFLADLIQ 325
                                       *.**************999.77777664555444444444 PP

  == domain 2  score: 97.4 bits;  conditional E-value: 8.5e-32
                      BPD_transp_2   4 nlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrl 80 
                                        ++t ++++++a++G +l+  ++G +nlg+ g+m+ Ga   ++ ++++   +++++l+a++vga++glll++l++ l
  gi|557693970|ref|YP_008797024.1| 418 LTITITTPITLASVGETLSE-KGGSLNLGILGIMISGAAWGFMGAYFFND-IFVGILLAIAVGALLGLLLAFLIVTL 492
                                       5688899*************.****************************9.************************** PP

                      BPD_transp_2  81 kvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv.........llalllvlavlll 148
                                       + ++ i++++++++  +l++++++ +++ +   ++v+ +      ll  +  v v         + ++++ l+++l+
  gi|557693970|ref|YP_008797024.1| 493 GAQQHIAGIAVTFFSMNLAYFFHRILIGSPLVEPKVPLIPVLRIPLLESIPVVGVifkqnifvyFGIFIIPLIIYLV 569
                                       ***********************99999999888777666666666666655555669999998777788899**** PP

                      BPD_transp_2 149 lrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGg 224
                                       +++tr+G+ + avgen++ a+alG++v  ++ l+ +++g+l +l G +++l    +   n+g ++++ a+a vvlG 
  gi|557693970|ref|YP_008797024.1| 570 FTKTRWGLVITAVGENPKSADALGVRVHFTRYLAIMFGGILMALGGSFYSLVDIRAFNlNVGGEWSWIALALVVLGN 646
                                       **************************************************996666668****************** PP

                      BPD_transp_2 225 agsllgtviGaliigvvksllltllg 250
                                       +  + ++ +++l++g++++   t+l 
  gi|557693970|ref|YP_008797024.1| 647 W-KVQWVWVATLLFGLLNA-VQTWLV 670
                                       *.***************99.555443 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.2e-05      0.38      17      45 ..     228     255 ..     218     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.2e-05
                            HTH_28  17 eaArelgisrrtvyrWikryeegGiagLv 45 
                                        aA + gi+ ++vy W+ ++ +gGiagL+
  gi|557693970|ref|YP_008797024.1| 228 RAAILEGIDVSRVYFWV-CFLSGGIAGLA 255
                                       589999***********.*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (715 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 5046.96
//
Query:       gi|557693971|ref|YP_008797025.1|  [L=288]
Description: hypothetical protein CSUB_C0535 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.095   13.3   2.0       0.69   10.5   0.1    2.7  3  PrmC_N    PrmC N-terminal domain
       0.17   11.9   1.5       0.62   10.1   0.3    2.0  2  Cnd1      non-SMC mitotic condensation complex subunit 1


Domain annotation for each model (and alignments):
>> PrmC_N  PrmC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.054   4.9e+02      15      42 ..      88     119 ..      75     142 .. 0.66
   2 ?   -1.6   0.0      0.48   4.3e+03      20      20 ..     149     149 ..     128     177 .. 0.51
   3 ?   10.5   0.1   7.7e-05      0.69      14      67 ..     232     285 ..     221     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.054
                            PrmC_N  15 ieeaeldAelLla....hvlglsrsdlllrge 42 
                                       + +a++d+++L+a    +   ++ ++l++r +
  gi|557693971|ref|YP_008797025.1|  88 SKSARADVRVLMAieerWFKAVDETYLIMREK 119
                                       57899999999985543444566666666655 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.48
                            PrmC_N  20 l 20 
                                       l
  gi|557693971|ref|YP_008797025.1| 149 L 149
                                       1 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 7.7e-05
                            PrmC_N  14 gieeaeldAelLlahvlglsrsdlllrgerelteeqlerfeelierRaarePlq 67 
                                       +  +a+   + L  +v ++++ +l +++++ l ++ + + ++  ++R+a++P q
  gi|557693971|ref|YP_008797025.1| 232 YNGQARKALQRLTIAVYNIKPKELTAKMQKTLLRQIWLTIRREAQERLAGIPAQ 285
                                       557888888999999*************************************99 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3     7e-05      0.62      88     146 ..     117     175 ..      97     179 .. 0.89
   2 ?    0.4   0.0     0.065   5.9e+02     100     133 ..     239     277 ..     215     281 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 7e-05
                              Cnd1  88 ksenaiynllpdiisklsdalnecsewgqitilefLlsyipkdkqeaeslveklcprlq 146
                                       +++  ++++l+++i ++s++l+++se+++   l+++    +k +++a+ +ve    r +
  gi|557693971|ref|YP_008797025.1| 117 REKASTFRSLQKTIEQYSNRLDSASEDEREDLLDMVKIAEKKLHRQAKRIVEEAERRYS 175
                                       45567899999*****************************************9888865 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.065
                              Cnd1 100 iisklsd.....alnecsewgqitilefLlsyipkdkqe 133
                                        +++l       + +e++ + q+t l+ +   i +++qe
  gi|557693971|ref|YP_008797025.1| 239 ALQRLTIavyniKPKELTAKMQKTLLRQIWLTIRREAQE 277
                                       333333333333678999999999999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1305  (0.0727871); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2222.68
//
Query:       gi|557693972|ref|YP_008797026.1|  [L=411]
Description: glutamate dehydrogenase (NAD(P)+) [Candidatus Caldiarchaeum subterraneum]
Scores for 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-51  174.0   0.0    5.6e-51  173.6   0.0    1.1  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
    1.2e-26   93.1   0.0    2.9e-26   91.9   0.0    1.6  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
  ------ inclusion threshold ------
       0.01   15.2   0.0      0.022   14.1   0.0    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.029   14.7   0.2       0.54   10.6   0.1    2.4  2  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA


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 !  173.6   0.0   1.3e-54   5.6e-51       1     240 [.     146     378 ..     146     381 .. 0.93

  Alignments for each domain:
  == domain 1  score: 173.6 bits;  conditional E-value: 1.3e-54
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS.....-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETT CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkld.....slegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpe 72 
                                       GG+ ++ + Tg+Gv+++++  lk l+       + ++++vai+G+Gnvgs++a++l elg k+va+sD +G+iy+pe
  gi|557693972|ref|YP_008797026.1| 146 GGIPHELGTTGYGVAVATDLTLKMLNKFgslslDPHEAKVAIQGFGNVGSFTAKFLDELGYKIVAISDITGCIYNPE 222
                                       9**************99886666655444556778899*************************************** PP

                                       EE-HHHHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS- CS
                     ELFV_dehydrog  73 GldieellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlp 149
                                       Gldi  +++  +  +s++++      ++e + +e +++++k d+++P+At + i++e a +lik+g klv+E+AN+p
  gi|557693972|ref|YP_008797026.1| 223 GLDIPHIMRELQTAGSIERLS-----RYEIYHKE-KIFDVKSDVFIPAATSDTINSETAPKLIKAGTKLVIEAANIP 293
                                       ********************9.....45666665.9***************************************** PP

                                       B-HHHHHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHH CS
                     ELFV_dehydrog 150 ttqeAkeileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkg 226
                                       tt+eA+++l e+g +vvpd++ N+GGV+ S +E+         te+e  + ++ + ++ +k v++ a++++ + +k 
  gi|557693972|ref|YP_008797026.1| 294 TTSEAEKMLIEKGFWVVPDFVVNSGGVIGSFVEYKGG------TEKEAFDLINYKITTNVKLVITLAQQNGSTPRKI 364
                                       ***********************************98......788999999999********************** PP

                                       HHHHHHHHHHHHHH CS
                     ELFV_dehydrog 227 aniagfekvaeamk 240
                                       a  ++ ++v +am 
  gi|557693972|ref|YP_008797026.1| 365 AQEIAKTRVKRAML 378
                                       ************97 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 !   91.9   0.0   6.5e-30   2.9e-26       4     127 ..      20     131 ..      17     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 6.5e-30
                                       EEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES-GG CS
                   ELFV_dehydrog_N   4 vlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvkidpk 80 
                                       v++       d+G    ++g+ ++ ++a+gP kGGiRf+p+v+  ev +La+ mt+K+al++lpfGGakgg+ +dp+
  gi|557693972|ref|YP_008797026.1|  20 VVFAY---DPDTG----MRGVLVIDNTAIGPGKGGIRFTPTVTPVEVFRLARVMTWKCALAGLPFGGAKGGIMGDPS 89 
                                       44444...44899....9**********************************************************9 PP

                                       GS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHH CS
                   ELFV_dehydrog_N  81 klseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawlade 127
                                       k ++ +    +r+f++++  +++ p + v+A D+gt++ +ma++a e
  gi|557693972|ref|YP_008797026.1|  90 KVDRVA---WMRSFAKAIK-PYV-PLQYVAATDMGTTELDMAVFAHE 131
                                       998875...5678888888.887.88999*************99876 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 ?   14.1   0.0   4.9e-06     0.022      32      66 ..     178     212 ..     166     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.9e-06
                                       S-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEES CS
                      2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkafgmkviayd 66 
                                        + ++ +v+i G+G++G+ +ak l ++g k++a++
  gi|557693972|ref|YP_008797026.1| 178 LDPHEAKVAIQGFGNVGSFTAKFLDELGYKIVAIS 212
                                       567899*************************9986 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 ?   10.6   0.1   0.00012      0.54       2      36 ..     184     217 ..     183     259 .. 0.85
   2 ?    1.6   0.0     0.078   3.5e+02      44      97 ..     266     320 ..     243     324 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                                       EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-H CS
                           Gp_dh_N   2 kvainGfGRIGrlvlralleekelevvaindltdl 36 
                                       kvai GfG +G  +++ l +e   ++vai d+t  
  gi|557693972|ref|YP_008797026.1| 184 KVAIQGFGNVGSFTAKFL-DELGYKIVAISDITGC 217
                                       8**********9887655.56799*****998765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.078
                                       HEETTTEC-SS-EEEETTEEEETTEEEEEE--SSGGGS-CHHHTS.SEEEE-SSS CS
                           Gp_dh_N  44 kyDsvhgrfkgeveaeeealvvngkkikvlaekdpeelpwkelgv.dlVvestGv 97 
                                         D++  +   ++   +++lv++  +i +++e++   ++ + + v d+Vv+s Gv
  gi|557693972|ref|YP_008797026.1| 266 TSDTINSETAPKLIKAGTKLVIEAANIPTTSEAEKMLIEKGFWVVpDFVVNSGGV 320
                                       568888888888899999999*999999999998665554443333677777766 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:                      471  (0.0262703); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.36
# Mc/sec: 3393.77
//
Query:       gi|557693973|ref|YP_008797027.1|  [L=145]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  100.8   0.0    8.8e-29  100.6   0.0    1.1  1  DUF488    Protein of unknown function, DUF488


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 !  100.6   0.0   4.9e-33   8.8e-29       2     122 .]      31     139 ..      30     139 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 4.9e-33
                            DUF488   2 lervyd.llkkdgvrvlvDVRlwPrSrnpgfskealkedlkeagiaYvwlkelgpsrelrkwfkhdp.rweefferY 76 
                                        +rvy+ ++++dg rvlvD RlwPr    g+ k++++ d         wlke++ps  lrkwf+h+p rweef++r+
  gi|557693973|ref|YP_008797027.1|  31 TKRVYEpPSPEDGCRVLVD-RLWPR----GLGKNRAAVDV--------WLKEVAPSGSLRKWFGHKPeRWEEFKRRF 94 
                                       69*****************.*****....***********........*******************99******** PP

                            DUF488  77 aaeles.keaakealeelkelakkg..vaLlcaekdperchrvvlaeyl 122
                                         el + +    +++++l el +k+  v Ll+++kd+ ++++  l+ey+
  gi|557693973|ref|YP_008797027.1|  95 FMELSRqP----DGVRKLLELEEKHgtVSLLYSAKDTVHNNATALKEYI 139
                                       *****944....899**999998888*********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1071.22
//
Query:       gi|557693974|ref|YP_008797028.1|  [L=156]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  101.6   0.0    4.7e-29  101.0   0.0    1.2  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 !  101.0   0.0   2.6e-33   4.7e-29      10     117 ..      23     136 ..      18     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 2.6e-33
                                       -.-EEEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-..SS--E-TT-........SS-E.EGGGS--S-SSS CS
                              TrmO  10 eeaeaeielepeynseealegleefshlwllfvfhenaekk.lkakvrpprl.......ggnervGvfatRsphRpn 78 
                                        ++++++e+ pey  eeal+g+e+++hl+++ vfh+++ ++    kv+p+rl       ++   +Gvf+t sp Rpn
  gi|557693974|ref|YP_008797028.1|  23 GAVSGRVEILPEY--EEALDGVEKYTHLFIIAVFHKSKPEHrSLLKVKPRRLlrmglreDELPILGVFSTDSPVRPN 97 
                                       45789********..********************884444222344444433333322455678************ PP

                                       -EEEEEEEEEEEETTEEEEES----TT-EEEEEEE--HH CS
                              TrmO  79 piglsvvklekvegnvlevsgvDlldgtpvlDiKPYvpy 117
                                       pi+l++vkl + e+nvl v+g+Dl+dgtpv+DiKPY p+
  gi|557693974|ref|YP_008797028.1|  98 PIALTLVKLVRRERNVLFVEGLDLFDGTPVIDIKPYRPD 136
                                       ************************************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1153.69
//
Query:       gi|557693975|ref|YP_008797029.1|  [L=133]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-11   43.1  21.0    4.7e-11   43.0  21.0    1.0  1  EamA      EamA-like transporter family
  ------ inclusion threshold ------
        7.9    4.6   8.3        8.7    4.4   8.3    1.1  1  YfhO      Bacterial membrane protein YfhO


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 !   43.0  21.0   5.2e-15   4.7e-11       6     136 ..       2     132 ..       1     133 [] 0.95

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 5.2e-15
                              EamA   6 lallaalfwaiyfvlskil.lrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafll 81 
                                       +al+a l+ +++ ++ k++  +  ++++++ v +++  +ll i+a++  gkl  ls ++ + ++ll+ + +++a ++
  gi|557693975|ref|YP_008797029.1|   2 FALIAFLCLGLTDFFRKKGaAAGANSFSYLLVETVVLLALLPIVAMVYSGKL-TLSFSGAIPYALLSGVTITVALVA 77 
                                       89**************77658999**********999999999999999999.999999999999999********* PP

                              EamA  82 ffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       ++++l+ ++ s + +i++l  +++++ls ++l+e++tl+++lgi+l++++v+l++
  gi|557693975|ref|YP_008797029.1|  78 MLSGLSIGEGSLVIPISRLGLALATLLSLFFLNESITLTKVLGIGLAVAAVFLLS 132
                                       *****************************************************97 PP

>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   8.3   0.00097       8.7     219     318 ..      28     130 ..       1     132 [. 0.65

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.00097
                              YfhO 219 issllagllsavlllPtvlgllsskrasae.......atisltfdinpldllsklligtfdfeqmgslpniyvgllp 288
                                       +s+ll  ++ + +llP+v  + s k + +        + + +t  ++++ +ls l ig+ +      +p +++gl  
  gi|557693975|ref|YP_008797029.1|  28 FSYLLVETVVLLALLPIVAMVYSGKLTLSFsgaipyaLLSGVTITVALVAMLSGLSIGEGSLV----IPISRLGLAL 100
                                       555666666666666666666665555554221000034445556667777777777777766....********** PP

                              YfhO 289 llllilyFvlkkiklkeklafallllllil 318
                                       ++ll l+F++++i+l + l+++l ++ ++l
  gi|557693975|ref|YP_008797029.1| 101 ATLLSLFFLNESITLTKVLGIGLAVAAVFL 130
                                       *****************9999887666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1023.29
//
Query:       gi|557693976|ref|YP_008797030.1|  [L=410]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-81  273.7   0.0    2.9e-81  273.3   0.0    1.2  1  Nre_N     Archaeal Nre, N-terminal
    3.3e-30  104.2   0.0      6e-30  103.4   0.0    1.4  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 !  273.3   0.0   3.2e-85   2.9e-81       1     265 [.      25     290 ..      25     292 .. 0.97

  Alignments for each domain:
  == domain 1  score: 273.3 bits;  conditional E-value: 3.2e-85
                             Nre_N   1 LcglkkcpileklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppveg.dasvldspekwlglsledi 76 
                                       Lc+l++cp+++ l + + a k + +++l+G spP+++VG++gYP+V +g ++   ++ +++ l+sp+kwl++s++++
  gi|557693976|ref|YP_008797030.1|  25 LCKLSTCPFYRDLFKEALAAKLS-GRQLSGPSPPTFLVGEKGYPRVALGSALVYADDiNPALLESPSKWLDFSVNEL 100
                                       8***********99988877666.**************************99999999******************* PP

                             Nre_N  77 iklrlslvrgekkvkvkkak.edklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenp 152
                                       ++lrlsl+ g + ++vk++  + + ++ +qe+a s kpvd+e++ +  +k+   f+  +aP+Gpsa++ek+k+++n 
  gi|557693976|ref|YP_008797030.1| 101 LRLRLSLLLGLTITHVKTPIqRRDPFTALQESAASIKPVDFEITTAGAVKTMPGFSIRTAPYGPSARVEKVKLTGNV 177
                                       ******************996444469************************************************** PP

                             Nre_N 153 kvprkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlp 229
                                       ++prkv+ +++D  +kAee++++Ly++g d+y+++rl+S+GlLG +++r+lVPT WsITAvddi++k+l++++++++
  gi|557693976|ref|YP_008797030.1| 178 SIPRKVDSYLNDPYVKAEETLTSLYKTGHDEYYLTRLFSAGLLGIASQRKLVPTEWSITAVDDILSKQLYNQVRQYS 254
                                       ***************************************************************************** PP

                             Nre_N 230 eidevevfsgeylgNrflviLaPgkwsfelvEawap 265
                                        i+e++v+s+++++N+ +v+L+P++w++el+E w +
  gi|557693976|ref|YP_008797030.1| 255 IINEYRVHSYSAVENSATVVLTPTPWMYELLEGWLR 290
                                       **********************************86 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.4   0.0   6.7e-34     6e-30       3     108 ..     303     408 ..     301     409 .. 0.97

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 6.7e-34
                             Nre_C   3 yegrkeyse.iaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleeale 78 
                                       ++ rk+y+e ++GaYya r++ l +L++++ q+++iv+ ei+p+ w+P+GvW+ Re v+kale+++++f+sl+eal+
  gi|557693976|ref|YP_008797030.1| 303 IRPRKTYAEnTGGAYYAVRFSLLRHLADRREQSGAIVFFEIKPG-WVPLGVWRFREIVKKALEQRCERFQSLDEALA 378
                                       6789*****9**********************************.6******************************* PP

                             Nre_C  79 evseklklplkkllkkskllkelkkqktLd 108
                                       +v+ +l++pl+++lk+s+l+  l++q+++d
  gi|557693976|ref|YP_008797030.1| 379 HVRPRLSIPLHNYLKQSSLIPFLRRQQKID 408
                                       ***************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2914.09
//
Query:       gi|557693977|ref|YP_008797031.1|  [L=533]
Description: ATPase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   37.3   0.0    2.4e-09   36.7   0.0    1.2  1  T2SSE            Type II/IV secretion system protein
    7.3e-05   23.3   0.0    0.00075   20.0   0.0    2.5  2  AAA_18           AAA domain
    0.00072   19.6   0.0     0.0014   18.6   0.0    1.4  1  AAA_14           AAA domain
    0.00088   19.1   0.0      0.018   14.8   0.0    2.3  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.001   19.5   0.0     0.0019   18.6   0.0    1.4  1  AAA_16           AAA ATPase domain
     0.0034   17.8   0.0     0.0075   16.7   0.0    1.6  1  AAA              ATPase family associated with various cellul
     0.0041   16.9   0.0     0.0067   16.2   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
     0.0069   16.4   0.0      0.014   15.4   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
  ------ inclusion threshold ------
      0.023   14.9   0.0      0.069   13.3   0.0    1.8  1  AAA_33           AAA domain
      0.025   14.5   0.0      0.041   13.8   0.0    1.3  1  Rad17            Rad17 P-loop domain
      0.033   14.5   0.0       0.07   13.4   0.0    1.5  1  AAA_22           AAA domain
      0.035   13.9   0.0      0.055   13.2   0.0    1.3  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.046   14.0   0.0       0.11   12.7   0.0    1.7  1  AAA_28           AAA domain
      0.046   14.1   0.0      0.084   13.3   0.0    1.5  1  RNA_helicase     RNA helicase
      0.049   13.5   0.0       0.22   11.4   0.0    2.0  2  NTPase_1         NTPase
      0.054   13.6   0.0      0.091   12.9   0.0    1.3  1  Sigma54_activ_2  Sigma-54 interaction domain
      0.056   13.4   0.0        0.1   12.5   0.0    1.4  1  NACHT            NACHT domain
      0.072   12.8   0.0       0.16   11.7   0.0    1.6  1  AAA_24           AAA domain
      0.077   12.8   0.0       0.19   11.5   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
      0.087   12.3   0.0       0.16   11.4   0.0    1.4  1  KTI12            Chromatin associated protein KTI12
      0.099   12.0   0.0        0.2   11.0   0.0    1.4  1  DnaB_C           DnaB-like helicase C terminal domain
       0.12   12.9   0.0       0.27   11.8   0.0    1.6  1  ABC_tran         ABC transporter
       0.12   11.9   0.0       0.25   10.9   0.0    1.4  1  AAA_25           AAA domain
       0.14   11.3   0.0       0.26   10.4   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
       0.17   11.5   0.0       0.33   10.6   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
        0.2   10.9   0.0       0.49    9.6   0.0    1.6  1  Zeta_toxin       Zeta toxin


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 !   36.7   0.0   3.5e-12   2.4e-09      75     245 ..     226     385 ..     176     401 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 3.5e-12
                             T2SSE  75 ekgvrlrvvllPvvagealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallk 151
                                        ++ r+ +  +P++ g ++++ k+   +++ldd++  +++ e++    +k       il++G+ g GK+t++ al +
  gi|557693977|ref|YP_008797031.1| 226 LGQFRIVITRPPLSDGMEMTVVKPVL-RVRLDDYRLPPKVLERL----EKR---AEGILIAGPPGMGKSTFAQALAE 294
                                       45667777778888885555554544.45888888776655544....444...5789******************* PP

                             T2SSE 152 einksderivtvEDpvEiql.eganqvqlnakkakvtfadllraaLRlrPDrimvGEiRdketlei.lkAvnTGHlg 226
                                       +  +  + + tvE p+ ++l  ++ q +  a+ ++ +++++   +L  rPD  +  E+R++  +e+ +     G   
  gi|557693977|ref|YP_008797031.1| 295 YYRNMRKVVKTVESPRDLNLpPDITQYSKSAA-KDGEIHSV---LLLSRPDYTVFDEMREARDFEMyIDLRYAGIGM 367
                                       *****99999*********9444444444444.44444444...3678******************99888899777 PP

                             T2SSE 227 slsTlHansaagalerLeq 245
                                        ++ +Ha ++++al+r+++
  gi|557693977|ref|YP_008797031.1| 368 -IGVIHASTPIDALHRIAN 385
                                       .***************986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.1   1.5e+03      62      91 ..     164     192 ..     147     221 .. 0.80
   2 !   20.0   0.0   1.1e-06   0.00075       1      34 [.     275     305 ..     275     356 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.1
                            AAA_18  62 daleenssaleegknlvidghlaeleseaa 91 
                                       ++le  ++ +++++ +v++++++++ s   
  gi|557693977|ref|YP_008797031.1| 164 EGLEPKIK-RGHPGRWVFESIREKPMSRTE 192
                                       45555554.9999********999887655 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 1.1e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgfgvnlrdvake 34 
                                       Il++G+pG GK+t+a++L++     +n r+v+k 
  gi|557693977|ref|YP_008797031.1| 275 ILIAGPPGMGKSTFAQALAEY---YRNMRKVVKT 305
                                       99****************998...5555555544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     2e-06    0.0014       5      86 ..     275     361 ..     272     386 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke.........ekktylflDE 72 
                                       ++i G+  +GK+t+++ l++ +   + + +  +++++rd +l  p ++ ++ ++ +k+         ++  y ++DE
  gi|557693977|ref|YP_008797031.1| 275 ILIAGPPGMGKSTFAQALAEYYR--NMRKVVKTVESPRDLNLP-P-DITQYSKSAAKDgeihsvlllSRPDYTVFDE 347
                                       689***********999985555..556666678888886544.3.344444444333556677888899******* PP

                            AAA_14  73 iqevpewekalksl 86 
                                       + e++++e ++   
  gi|557693977|ref|YP_008797031.1| 348 MREARDFEMYIDLR 361
                                       ********998755 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 !   14.8   0.0   2.6e-05     0.018      31      59 ..     270     298 ..     263     325 .. 0.73
   2 ?    1.5   0.0      0.33   2.3e+02      90     130 ..     377     415 ..     372     432 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-05
                            RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgv 59 
                                       +  + +l++GpPG+Gk+t+a+ +a+    
  gi|557693977|ref|YP_008797031.1| 270 KRAEGILIAGPPGMGKSTFAQALAEYYRN 298
                                       456789*****************974332 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.33
                            RuvB_N  90 ideihrlsraveevlysamedfrldivigkGpsarsikldl 130
                                       id +hr++++v+  + +++ d    i ++kG+ a  ++l++
  gi|557693977|ref|YP_008797031.1| 377 IDALHRIANKVDIGILPSIVDTL--IFMDKGRVASIHTLEV 415
                                       899*********99999999986..5788998888887765 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   0.0   2.8e-06    0.0019      17      51 ..     266     299 ..     262     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.8e-06
                            AAA_16  17 ervrsgrpelvllsGesGvGKsslvrellralekd 51 
                                       er+   r e +l+ G++G+GKs+ +++l+++++  
  gi|557693977|ref|YP_008797031.1| 266 ERLE-KRAEGILIAGPPGMGKSTFAQALAEYYRNM 299
                                       5444.44599*******************877655 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   0.0   1.1e-05    0.0075       1      23 [.     275     297 ..     275     337 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                                       EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA   1 vllyGppGtGKTllakavakelg 23 
                                       +l+ GppG+GK+++a+a+a+   
  gi|557693977|ref|YP_008797031.1| 275 ILIAGPPGMGKSTFAQALAEYYR 297
                                       699****************9853 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 !   16.2   0.0   9.8e-06    0.0067      45      69 ..     270     294 ..     265     384 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.8e-06
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgv 69 
                                       +++e+i++ Gp+G+GKs +a al+ 
  gi|557693977|ref|YP_008797031.1| 270 KRAEGILIAGPPGMGKSTFAQALAE 294
                                       57899******************96 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     2e-05     0.014       2      34 ..     275     310 ..     274     353 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                                       EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--T CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltr 34 
                                       +l+ GppG gKs++a+ la+ +   ++ v +v  +r
  gi|557693977|ref|YP_008797031.1| 275 ILIAGPPGMGKSTFAQALAEYYrnmRKVVKTVESPR 310
                                       7999*****************985555555554444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0    0.0001     0.069       2      21 ..     275     294 ..     275     310 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                            AAA_33   2 vllvGlpGsGKstlaerllk 21 
                                       +l+ G+pG+GKst+a+ l++
  gi|557693977|ref|YP_008797031.1| 275 ILIAGPPGMGKSTFAQALAE 294
                                       5789************9985 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.9e-05     0.041      38      68 ..     263     295 ..     256     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.9e-05
                             Rad17  38 dvLesrkkr..iLLisGPsGCgkstvvkvLske 68 
                                       +vLe+ +kr   +Li+GP+G gkst  + L+  
  gi|557693977|ref|YP_008797031.1| 263 KVLERLEKRaeGILIAGPPGMGKSTFAQALAEY 295
                                       67888777766689***************9964 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    0.0001      0.07       4      30 ..     271     297 ..     267     319 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.0001
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqld 30 
                                       +a  +++ G++G+GK+t ++ l+e + 
  gi|557693977|ref|YP_008797031.1| 271 RAEGILIAGPPGMGKSTFAQALAEYYR 297
                                       566799****************99774 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 ?   13.2   0.0   7.9e-05     0.055       1      30 [.     277     306 ..     277     315 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.9e-05
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavv 30 
                                       ++Gp+G GK+tf +al+e++++  + v++v
  gi|557693977|ref|YP_008797031.1| 277 IAGPPGMGKSTFAQALAEYYRNMRKVVKTV 306
                                       79******************9997777766 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00017      0.11       2      24 ..     275     299 ..     274     312 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                            AAA_28   2 ivitGgestGKTtlleaLaar..gy 24 
                                       i i G+++ GK+t ++aLa+   ++
  gi|557693977|ref|YP_008797031.1| 275 ILIAGPPGMGKSTFAQALAEYyrNM 299
                                       789****************875543 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00012     0.084       1      23 [.     275     297 ..     275     357 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakall 23 
                                       i++ Gp+g GKSt+a+ La+   
  gi|557693977|ref|YP_008797031.1| 275 ILIAGPPGMGKSTFAQALAEYYR 297
                                       6899*************998655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00031      0.22       2      25 ..     275     298 ..     274     309 .. 0.85
   2 ?   -2.0   0.0       4.3   2.9e+03     127     150 ..     366     389 ..     360     393 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00031
                                       EEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellks 25 
                                       ++i GppG+GK+T+ + ++e  ++
  gi|557693977|ref|YP_008797031.1| 275 ILIAGPPGMGKSTFAQALAEYYRN 298
                                       78**************99998765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.3
                                       EEEEE--SS--SHHHHHHHT-TT- CS
                          NTPase_1 127 pvlavihrrkdlalveeirerkdv 150
                                        +++vih +++ + +++i ++ d+
  gi|557693977|ref|YP_008797031.1| 366 GMIGVIHASTPIDALHRIANKVDI 389
                                       5899*****999999999998665 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 ?   12.9   0.0   0.00013     0.091      14      50 ..     265     301 ..     262     327 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                                       HHHHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE- CS
                   Sigma54_activ_2  14 LeqaaqsklpvfltGekGsgkelvArlLhknsgpwle 50 
                                       Le ++++   ++++G++G gk+++A++L++   +  +
  gi|557693977|ref|YP_008797031.1| 265 LERLEKRAEGILIAGPPGMGKSTFAQALAEYYRNMRK 301
                                       8889999999******************986555444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00015       0.1       3      22 ..     275     294 ..     273     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       +++ G++G+GK+t++q la+
  gi|557693977|ref|YP_008797031.1| 275 ILIAGPPGMGKSTFAQALAE 294
                                       789**************996 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   0.00023      0.16       5      22 ..     275     292 ..     271     303 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       ili Gp+g+GK+t+a  l
  gi|557693977|ref|YP_008797031.1| 275 ILIAGPPGMGKSTFAQAL 292
                                       89*************877 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 ?   11.5   0.0   0.00028      0.19      21      42 ..     272     292 ..     265     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                            AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                        +g +l++Gp G GKST+  A+
  gi|557693977|ref|YP_008797031.1| 272 AEG-ILIAGPPGMGKSTFAQAL 292
                                       455.9************97776 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00023      0.16       4      36 ..     275     307 ..     274     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                       EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE- CS
                             KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvvid 36 
                                       +++ G P  GKst+a+ La++ ++  + v  ++
  gi|557693977|ref|YP_008797031.1| 275 ILIAGPPGMGKSTFAQALAEYYRNMRKVVKTVE 307
                                       799******************999766665554 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 ?   11.0   0.0   0.00029       0.2      20      45 ..     273     298 ..     266     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                                       XEEEEEEXTTSSHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  20 dliiiAarpsmGktalalniaenaav 45 
                                       + i+iA+ p+mGk+++a  +ae   +
  gi|557693977|ref|YP_008797031.1| 273 EGILIAGPPGMGKSTFAQALAEYYRN 298
                                       5589*****************97664 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00039      0.27      12      37 ..     273     298 ..     269     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00039
                                       SEEEEEESTTSSHHHHHHHHTTSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkp 37 
                                       e + i G+ G GKSt++++la+ +++
  gi|557693977|ref|YP_008797031.1| 273 EGILIAGPPGMGKSTFAQALAEYYRN 298
                                       66889***************998876 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00036      0.25      32      54 ..     271     293 ..     250     296 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                            AAA_25  32 agelallaGapgtGKttlaldla 54 
                                       + e +l+aG+pg GK+t+a  la
  gi|557693977|ref|YP_008797031.1| 271 RAEGILIAGPPGMGKSTFAQALA 293
                                       566789*************9987 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00038      0.26      51      88 ..     270     309 ..     266     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00038
                            DUF815  51 lpannvLLwGarGtGKSslvkallneyaeeg..Lrlieve 88 
                                       ++a+ +L+ G  G+GKS+  +al + y++    ++ +e  
  gi|557693977|ref|YP_008797031.1| 270 KRAEGILIAGPPGMGKSTFAQALAEYYRNMRkvVKTVESP 309
                                       67999******************99988765556666644 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00048      0.33      16      51 ..     266     301 ..     259     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                                       HHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS CS
                   Sigma54_activat  16 kkvaktdlsvlitGesGtGKellaraiheaskrkek 51 
                                       +++ k    +li G  G GK+++a+a+ e  ++ +k
  gi|557693977|ref|YP_008797031.1| 266 ERLEKRAEGILIAGPPGMGKSTFAQALAEYYRNMRK 301
                                       5556666789****************9886655444 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00071      0.49      18      47 ..     274     303 ..     263     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00071
                        Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvv 47 
                                        il++G pG GKs+ a++l+++ ++ ++vv
  gi|557693977|ref|YP_008797031.1| 274 GILIAGPPGMGKSTFAQALAEYYRNMRKVV 303
                                       69******************9987766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3660.18
//
Query:       gi|557693978|ref|YP_008797032.1|  [L=135]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   61.5   0.2    8.6e-17   60.9   0.2    1.3  1  PUA       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 !   60.9   0.2   4.8e-21   8.6e-17       2      73 ..      51     122 ..      50     123 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 4.8e-21
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETT.SCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivded.gelvavGlanysseelakikggksveierv 73 
                                        v+vd gAv  ++sga+++ pG+v+++  f+ gdvV + d    +++avG a++ssee+ +  +gk+v++ ++
  gi|557693978|ref|YP_008797032.1|  51 SVWVDMGAVPRVASGADVMRPGIVKMDV-FRTGDVVLVRDVThSKPLAVGQALMSSEEASTLSKGKVVKNLHH 122
                                       599************************9.***********9879**************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1027.60
//
Query:       gi|557693979|ref|YP_008797033.1|  [L=357]
Description: ATP-binding protein involved in chromosome partitioning [Candidatus Caldiarchaeum subterraneum]
Scores for 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-94  313.4   0.9    1.3e-93  313.0   0.9    1.2  1  ParA            NUBPL iron-transfer P-loop NTPase
    6.8e-23   80.6   1.9    1.9e-22   79.2   0.3    2.5  2  FeS_assembly_P  Iron-sulfur cluster assembly protein
    9.8e-15   54.7   0.0    6.7e-14   52.1   0.0    2.1  1  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
      2e-11   44.1   0.6      1e-09   38.5   0.7    2.2  2  AAA_31          AAA domain
    5.6e-07   29.3   0.1      0.015   14.8   0.0    2.2  2  Fer4_NifH       4Fe-4S iron sulfur cluster binding proteins, 
    3.3e-06   26.6   0.2    6.6e-06   25.6   0.2    1.6  1  MipZ            ATPase MipZ
    8.8e-05   21.9   0.2    0.00014   21.2   0.2    1.2  1  VirC1           VirC1 protein
    0.00012   21.4   2.7    0.00048   19.4   1.4    2.1  2  ArsA_ATPase     Anion-transporting ATPase
    0.00033   20.3   0.2    0.00093   18.8   0.2    1.7  1  AAA_25          AAA domain
     0.0027   17.5   0.9       0.12   12.1   0.0    2.4  2  AAA_26          AAA domain
  ------ inclusion threshold ------
      0.016   15.2   0.3       0.03   14.4   0.3    1.4  1  Sensor          Putative sensor
      0.019   14.4   0.9       0.43   10.0   0.7    2.1  2  CBP_BcsQ        Cellulose biosynthesis protein BcsQ
      0.023   14.3   0.4      0.067   12.8   0.2    1.9  2  SRP54           SRP54-type protein, GTPase domain
      0.044   13.5   0.2      0.076   12.8   0.2    1.3  1  A2L_zn_ribbon   A2L zinc ribbon domain
      0.055   13.3   0.0       0.11   12.3   0.0    1.5  1  CLP1_P          mRNA cleavage and polyadenylation factor CLP1
        0.2   11.3   0.1       0.37   10.4   0.1    1.5  1  zf_UBZ          Ubiquitin-Binding Zinc Finger
        5.5    6.7   6.6         20    4.8   0.3    2.9  3  AAA_30          AAA domain


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 !  313.0   0.9   1.2e-96   1.3e-93       2     245 ..      95     338 ..      94     339 .. 0.98

  Alignments for each domain:
  == domain 1  score: 313.0 bits;  conditional E-value: 1.2e-96
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPvea.kgikvmS 77 
                                       vk+v+av+SgKGGVGK+tva+nlA++La +g++vgl+DaDiyGp ip+++++ e    + +kk+ P ++  gikvmS
  gi|557693979|ref|YP_008797033.1|  95 VKNVVAVASGKGGVGKTTVAINLACSLALSGARVGLVDADIYGPTIPKIVKIVEPPRLRPDKKVEPAKMmLGIKVMS 171
                                       9***************************************************99755555889*****989****** PP

                              ParA  78 igfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvk 154
                                       +g++++ e +av+wrGp++++a+kqll++++wgelDyLi+DlPPGtgD++lt+aq++pl+g+viVttpq++a  ++ 
  gi|557693979|ref|YP_008797033.1| 172 LGLFVD-EGTAVIWRGPLVASAVKQLLTEAQWGELDYLIVDLPPGTGDASLTLAQTMPLTGVVIVTTPQQAASVIAA 247
                                       *****9.********************************************************************** PP

                              ParA 155 kaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlkepe 231
                                       ka++mf+++ v+++G+veNms++vcp+cg+++++fg+++++k+a+el+v++lg+ip++p+++ + d+g p+vl++p+
  gi|557693979|ref|YP_008797033.1| 248 KALSMFRRLGVTIIGIVENMSYYVCPECGKESSLFGQSHTDKMAAELDVEVLGRIPMSPDVSVNHDQGVPIVLAAPS 324
                                       ***************************************************************************** PP

                              ParA 232 seaakaleeiaekv 245
                                       s+aaka++e a+k+
  gi|557693979|ref|YP_008797033.1| 325 SPAAKAFDEAAKKI 338
                                       ***********998 PP

>> 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 !   79.2   0.3   1.8e-25   1.9e-22       1      72 [.       5      74 ..       5      78 .. 0.95
   2 ?   -0.9   0.1       1.9     2e+03      41      62 ..     322     343 ..     306     350 .. 0.72

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 1.8e-25
                                      HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEE CS
                    FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieggkVsvditltypacslaeairadaeaalralpgvevveV 72
                                      +++vl+aLr+V+DP l +d+v lg++++++i++g+Vs++++lt+pac+    i+++a+aa++++pg  v +V
  gi|557693979|ref|YP_008797033.1|  5 EQTVLNALRQVIDPDLKIDIVTLGMIKNLVIKDGDVSFTLELTTPACPYNKSIEDSARAAVESIPG--VRSV 74
                                      689***************************************************************..5555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                                       --SSTT-TTHHHHHHHHHHHHC CS
                    FeS_assembly_P  41 tltypacslaeairadaeaalr 62 
                                       ++ +pa  ++++ ++++ a++ 
  gi|557693979|ref|YP_008797033.1| 322 APSSPAAKAFDEAAKKIAAKIS 343
                                       5667777788888888888876 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 !   52.1   0.0   6.3e-17   6.7e-14       1     120 [.      99     310 ..      99     318 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 6.3e-17
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       +a+as+kGGvGKTt+a+nLa++la  g rV lvDaD  ++      + ++ +ep                       
  gi|557693979|ref|YP_008797033.1|  99 VAVASGKGGVGKTTVAINLACSLALSGARVGLVDADIYGPTIP---KIVKIVEPprlrpdkkvepakmmlgikvmsl 172
                                       69**************************************988...3333333368889999999999999999999 PP

                                       ........................................................................CCHCC CS
                                       ........................................................................xxxxx RF
                              CbiA  55 ........................................................................dlkrl 59 
                                                                                                                + + 
  gi|557693979|ref|YP_008797033.1| 173 glfvdegtaviwrgplvasavkqllteaqwgeldylivdlppgtgdasltlaqtmpltgvvivttpqqaasvIAAKA 249
                                       99999999999999999999999999999999999999999999999999999999999999998887777733344 PP

                                       CHHHHHHCHCHHHH..EEEEEEEEE.........SS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  60 lellealgkkkalllkiagvvlnrv.........dgeneetllkealeelkqrygvpvlgviprdeavae 120
                                       l ++++lg +      i+g+v n+          ++++  +++ + ++ ++    v+vlg ip + +v+ 
  gi|557693979|ref|YP_008797033.1| 250 LSMFRRLGVT------IIGIVENMSyyvcpecgkESSLFGQSHTDKMAAEL---DVEVLGRIPMSPDVSV 310
                                       6666666644......67777766422222221123344555555555555...8888888888888865 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.7   9.8e-13     1e-09       2      40 ..      97     135 ..      96     140 .. 0.95
   2 ?    3.2   0.0     0.068        72     110     151 ..     196     240 ..     172     256 .. 0.64

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 9.8e-13
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                                        v+a+a  KGGvGKTT ++nla++la +g +v lvD+D 
  gi|557693979|ref|YP_008797033.1|  97 NVVAVASGKGGVGKTTVAINLACSLALSGARVGLVDADI 135
                                       599**********************************95 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.068
                            AAA_31 110 llekvk.deYDyiiiDcpPsLg...lltenaLvasdsviipvqaea 151
                                       ll++ +  e Dy i+D pP  g   l + + +     vi+ + +++
  gi|557693979|ref|YP_008797033.1| 196 LLTEAQwGELDYLIVDLPPGTGdasLTLAQTMPLTGVVIV-TTPQQ 240
                                       5544442578*********876321333334444444444.44433 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 !   12.3   0.1   7.9e-05     0.083       6      37 ..     103     134 ..      98     143 .. 0.89
   2 !   14.8   0.0   1.4e-05     0.015     143     247 ..     231     341 ..     163     347 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.9e-05
                         Fer4_NifH   6 yGkGGiGksttsqnlsaalaemgkkvlivGCD 37 
                                        GkGG+Gk+t + nl+ +la  g +v +v  D
  gi|557693979|ref|YP_008797033.1| 103 SGKGGVGKTTVAINLACSLALSGARVGLVDAD 134
                                       59***********************9887665 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.4e-05
                         Fer4_NifH 143 evyivtsgelmalyaanniakgiekyaksggvrlgGliinsr.....kvdde.....reliekfaeelgtkvlevvP 209
                                        v+ivt+ +     aa  ia+    + ++ gv + G++ n       +  +e     +   +k+a+el+++vl  +P
  gi|557693979|ref|YP_008797033.1| 231 GVVIVTTPQQ----AASVIAAKALSMFRRLGVTIIGIVENMSyyvcpECGKEsslfgQSHTDKMAAELDVEVLGRIP 303
                                       4455554443....3444444344444555788888888854111111223311111556799************** PP

                         Fer4_NifH 210 rdeivrkaelrkktvieyapeseqakeyrelarkilen 247
                                       ++ +v  ++ +   ++  ap+s+ ak + e a+ki+ +
  gi|557693979|ref|YP_008797033.1| 304 MSPDVSVNHDQGVPIVLAAPSSPAAKAFDEAAKKIAAK 341
                                       **********************************9865 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.2   6.2e-09   6.6e-06       2      47 ..      98     143 ..      97     238 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.2e-09
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHH CS
                              MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlary 47 
                                       v+ ++  kGG Gk+t+a+ +a +L+ +Garv+ +d d+   t+ + 
  gi|557693979|ref|YP_008797033.1|  98 VVAVASGKGGVGKTTVAINLACSLALSGARVGLVDADIYGPTIPKI 143
                                       78899********************************987776655 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   1.3e-07   0.00014       2      40 ..      97     135 ..      96     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.3e-07
                             VirC1   2 klitfcslkGGaGkttalmglcsalasdgkrvalfeade 40 
                                       ++++++s kGG Gktt  + l ++la  g rv+l +ad 
  gi|557693979|ref|YP_008797033.1|  97 NVVAVASGKGGVGKTTVAINLACSLALSGARVGLVDADI 135
                                       67999********************************95 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.4   4.5e-07   0.00048       5      38 ..     101     134 ..      97     135 .. 0.88
   2 ?    0.8   0.0      0.21   2.2e+02     114     143 ..     194     225 ..     189     271 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4.5e-07
                                       EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase   5 lvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                                       + +GKGGVGKttv+  +a+ l+ +g +v l+  D
  gi|557693979|ref|YP_008797033.1| 101 VASGKGGVGKTTVAINLACSLALSGARVGLVDAD 134
                                       569*********************9999887665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.21
                                       HHHHHHHHCSSSSEEEEESBS.CCHT.CGGGG CS
                       ArsA_ATPase 114 eellkyvkeeeydvvvlDtaP.TGht.lrlls 143
                                       ++ll + +  e d++++D +P TG++ l l +
  gi|557693979|ref|YP_008797033.1| 194 KQLLTEAQWGELDYLIVDLPPgTGDAsLTLAQ 225
                                       566677778899*******9978864255544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   8.8e-07   0.00093      32      61 ..      96     126 ..      79     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8.8e-07
                            AAA_25  32 agelallaGapgtGKttlaldlalava.tGk 61 
                                       ++ +a+  G +g+GKtt+a++la+++a +G 
  gi|557693979|ref|YP_008797033.1|  96 KNVVAVASGKGGVGKTTVAINLACSLAlSGA 126
                                       688999********************96665 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.5     0.058        61       4      33 ..     100     129 ..      97     131 .. 0.85
   2 !   12.1   0.0   0.00012      0.12     131     195 ..     232     309 ..     215     312 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.058
                            AAA_26   4 fvtgtdtgvGKTvvslgLvralkrkgvkvg 33 
                                        v++   gvGKT+v+  L+ +l   g++vg
  gi|557693979|ref|YP_008797033.1| 100 AVASGKGGVGKTTVAINLACSLALSGARVG 129
                                       57888889***********99988888887 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00012
                            AAA_26 131 vilVargglgtinqllltiealrqknvrvlGvilNk....vrnp....e.......nvetlekksgipvlGvvPylp 192
                                       v++V+++++ +   ++ +++++r+ +v ++G++ N     +  p    e         +++ +   ++vlG++P++p
  gi|557693979|ref|YP_008797033.1| 232 VVIVTTPQQAASVIAAKALSMFRRLGVTIIGIVENMsyyvC--PecgkEsslfgqsHTDKMAAELDVEVLGRIPMSP 306
                                       7777777777777778899999*************844422..134431445555577777777779*********9 PP

                            AAA_26 193 dle 195
                                       d++
  gi|557693979|ref|YP_008797033.1| 307 DVS 309
                                       985 PP

>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   2.8e-05      0.03      73     138 ..     187     264 ..     168     284 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.8e-05
                            Sensor  73 gllarlrallrdpatwrdllylllhfplg..lvlfvvavvllalalalltaPl.wt.........lpeallvavlGl 137
                                       +l+a +++ l  +a w +l yl++ +p g   +++++a ++++++++ +t+P  ++         +++ l+v+++G+
  gi|557693979|ref|YP_008797033.1| 187 PLVASAVKQLLTEAQWGELDYLIVDLPPGtgDASLTLAQTMPLTGVVIVTTPQqAAsviaakalsMFRRLGVTIIGI 263
                                       566777777888899**************553466677777999999999999442455555555899999999998 PP

                            Sensor 138 l 138
                                       +
  gi|557693979|ref|YP_008797033.1| 264 V 264
                                       7 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.7   0.00041      0.43       3      38 ..      98     133 ..      96     135 .. 0.90
   2 ?    2.4   0.0     0.086        91     107     153 ..     195     244 ..     183     256 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00041
                          CBP_BcsQ   3 vlalqGvRGGvGttsllaaLawalhelgesvlviDl 38 
                                       v+a+   +GGvG+t+++  La +l   g +v ++D+
  gi|557693979|ref|YP_008797033.1|  98 VVAVASGKGGVGKTTVAINLACSLALSGARVGLVDA 133
                                       66777779*************************996 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.086
                          CBP_BcsQ 107 aalkelk.eqyrwillDlpagasaltrellala..dlvllvvepdanchv 153
                                       + l+e + ++ +++++Dlp g+ +   +l ++   + v+ v++p++++ v
  gi|557693979|ref|YP_008797033.1| 195 QLLTEAQwGELDYLIVDLPPGTGDASLTLAQTMplTGVVIVTTPQQAASV 244
                                       4444445678899*******887766665554411556778888877765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   6.3e-05     0.067       4      40 ..     100     136 ..      96     140 .. 0.89
   2 ?   -2.7   0.0       3.6   3.8e+03      72      90 ..     193     211 ..     189     255 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.3e-05
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTS CS
                             SRP54   4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtf 40 
                                        +  G  G+GKTt +  La  l  +g +v lv aD++
  gi|557693979|ref|YP_008797033.1| 100 AVASGKGGVGKTTVAINLACSLALSGARVGLVDADIY 136
                                       4556999****************************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHTTSSEEEEE CS
                             SRP54  72 akeavekakeekidvvlvD 90 
                                       +k+ + +a+  + d+++vD
  gi|557693979|ref|YP_008797033.1| 193 VKQLLTEAQWGELDYLIVD 211
                                       5556666666666666666 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 ?   12.8   0.2   7.2e-05     0.076      13      28 ..     262     276 ..     262     279 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-05
                     A2L_zn_ribbon  13 gilnseqgylvCieCg 28 
                                       gi+  + +y+vC+eCg
  gi|557693979|ref|YP_008797033.1| 262 GIV-ENMSYYVCPECG 276
                                       577.899********9 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 ?   12.3   0.0    0.0001      0.11       1      34 [.     104     137 ..     104     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGq 34 
                                       G+  +GK+T+a +L+  ++ +g ++ +vD+D+  
  gi|557693979|ref|YP_008797033.1| 104 GKGGVGKTTVAINLACSLALSGARVGLVDADIYG 137
                                       66789**************************965 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00035      0.37       2      15 ..     269     282 ..     268     288 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00035
                            zf_UBZ   2 tylCerCgkeipes 15 
                                       +y+C++Cgke +  
  gi|557693979|ref|YP_008797033.1| 269 YYVCPECGKESSLF 282
                                       7********98765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.019        20      18      40 ..      97     119 ..      89     131 .. 0.79
   2 ?   -0.9   0.0       1.1   1.2e+03     117     139 ..     230     252 ..     185     260 .. 0.65
   3 ?    4.1   0.3     0.033        35      42      77 ..     311     346 ..     304     356 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                            AAA_30  18 drvavltGpAGtGKttalkalre 40 
                                       + vav+ G  G GKtt+   l+ 
  gi|557693979|ref|YP_008797033.1|  97 NVVAVASGKGGVGKTTVAINLAC 119
                                       6799************9766655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                            AAA_30 117 akvilvGDerQlasVeaGgvlrd 139
                                       + v++v  ++Q asV a ++l++
  gi|557693979|ref|YP_008797033.1| 230 TGVVIVTTPQQAASVIAAKALSM 252
                                       44666666777777777666655 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.033
                            AAA_30  42 weaaggrviglAptgkaAkvLaeelgieastiakll 77 
                                        +++g +++++Ap++ aAk+  e++   a+ i  l 
  gi|557693979|ref|YP_008797033.1| 311 NHDQGVPIVLAAPSSPAAKAFDEAAKKIAAKISILA 346
                                       466799**************9998776666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2435.08
//
Query:       gi|557693980|ref|YP_008797034.1|  [L=387]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  153.3  13.7    1.2e-16   60.9   0.9    4.3  4  CBS            CBS domain
  ------ inclusion threshold ------
      0.048   13.4   0.4        0.5   10.1   0.1    2.6  2  Phage_Mu_Gp45  Bacteriophage Mu Gp45 protein


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 !   24.7   0.3   2.7e-09   2.4e-05       1      49 [.       5      54 ..       5      57 .. 0.87
   2 !   24.3   0.0   3.5e-09   3.1e-05      10      52 ..      76     117 ..      65     120 .. 0.93
   3 !   60.9   0.9   1.3e-20   1.2e-16       1      55 [.     129     182 ..     129     184 .. 0.94
   4 !   50.0   0.5   3.3e-17   2.9e-13       1      53 [.     206     257 ..     206     260 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 2.7e-09
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEE..ETTTBEEEEEEHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVV..dedgklvGivtlr 49
                                      +gdim  ++v+v  d++  +++ l+++++++ + VV    +g+lvG+vt+r
  gi|557693980|ref|YP_008797034.1|  5 AGDIMAAEFVSVGDDEPFTKVIGLFTDRKLDVV-VVkdSRSGRLVGVVTKR 54
                                      68***********************99778555.788766779******98 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 3.5e-09
                                       EEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS  10 vtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52 
                                       + ++p++tl  ++  m+ek++ ++PV+ e gk+vG+v   Dl+
  gi|557693980|ref|YP_008797034.1|  76 PKITPEDTLPHVASAMVEKNLKAMPVT-EAGKPVGLVAAADLI 117
                                       589************************.9*********99998 PP

  == domain 3  score: 60.9 bits;  conditional E-value: 1.3e-20
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       V  imt+dv+t++ d+t+++a+ +mr+ gvsrlPVV ++g lvGivt +D+++++
  gi|557693980|ref|YP_008797034.1| 129 VQKIMTKDVITINADDTIGKAISIMRDQGVSRLPVV-NNGYLVGIVTVTDVAEKI 182
                                       6689********************************.5*************9987 PP

  == domain 4  score: 50.0 bits;  conditional E-value: 3.3e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       V++imtr+vvt++ ++t+ ea+e+m+++g+s+l VV e +++vGivtl+D l+
  gi|557693980|ref|YP_008797034.1| 206 VKSIMTREVVTARGNETVVEAVERMKQYGFSSL-VVTERNRVVGIVTLMDALS 257
                                       899**********************9999****.9889************885 PP

>> Phage_Mu_Gp45  Bacteriophage Mu Gp45 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.44   3.9e+03      56      75 ..      31      50 ..      21      61 .. 0.71
   2 ?   10.1   0.1   5.6e-05       0.5      23      47 ..     220     244 ..     200     287 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.44
                                      XXXXXXXXXXXX--S---SS CS
                     Phage_Mu_Gp45 56 drshgvviavedrryRlkgl 75
                                      dr+  vv++ + r+ Rl g+
  gi|557693980|ref|YP_008797034.1| 31 DRKLDVVVVKDSRSGRLVGV 50
                                      66777777777777787765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 5.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXX CS
                     Phage_Mu_Gp45  23 agetlddverfqpyGftSvppaGae 47 
                                       +++++++ver+++yGf+S   +  +
  gi|557693980|ref|YP_008797034.1| 220 NETVVEAVERMKQYGFSSLVVTERN 244
                                       4567789***********7665543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2804.21
//
Query:       gi|557693981|ref|YP_008797035.1|  [L=215]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
       0.56   10.6   0.1       0.56   10.6   0.1    2.8  4  Phage_holin_5_1  Bacteriophage A118-like holin, Hol118


Domain annotation for each model (and alignments):
>> Phage_holin_5_1  Bacteriophage A118-like holin, Hol118
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2      0.47   8.3e+03      36      54 ..       3      21 ..       2      22 .. 0.77
   2 ?   -0.6   0.1       0.1   1.8e+03      34      56 ..      82     104 ..      61     120 .. 0.70
   3 ?   -0.7   0.2      0.11   1.9e+03      34      48 ..     138     152 ..     104     171 .. 0.57
   4 ?   10.6   0.1   3.1e-05      0.56       9      38 ..     175     204 ..     166     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.47
                   Phage_holin_5_1 36 lptvsilvgailgalatsl 54
                                      l t +i  ga + ala  l
  gi|557693981|ref|YP_008797035.1|  3 LSTKTITSGASMAALALIL 21
                                      5677888899999998765 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.1
                   Phage_holin_5_1  34 kwlptvsilvgailgalatsldg 56 
                                       k+l   s l+g  lg+   +  g
  gi|557693981|ref|YP_008797035.1|  82 KFLAVASSLLGFWLGSRMVYAKG 104
                                       77777788888888776665554 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.11
                   Phage_holin_5_1  34 kwlptvsilvgailg 48 
                                        +l   + l+ga lg
  gi|557693981|ref|YP_008797035.1| 138 DFLSLATSLLGAFLG 152
                                       344445555566555 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 3.1e-05
                   Phage_holin_5_1   9 vymtflvvvtpvfvqaikktelvpskwlpt 38 
                                       ++m f ++ t ++++ai+kt  + skw p 
  gi|557693981|ref|YP_008797035.1| 175 LHMGFSLIPTILLLKAIQKTRALGSKWTPW 204
                                       6899***********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); 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: 1539.06
//
Query:       gi|557693982|ref|YP_008797036.1|  [L=337]
Description: Zn-dependent alcohol dehydrogenases [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-25   88.8   2.2      6e-25   87.7   1.8    1.8  2  ADH_zinc_N      Zinc-binding dehydrogenase
      8e-25   86.8   1.5      8e-25   86.8   1.5    1.9  2  ADH_N           Alcohol dehydrogenase GroES-like domain
    2.7e-09   36.8   0.6    3.7e-09   36.4   0.6    1.2  1  Glu_dehyd_C     Glucose dehydrogenase C-terminus
    7.9e-08   33.4   0.1    1.8e-07   32.3   0.1    1.7  1  ADH_zinc_N_2    Zinc-binding dehydrogenase
    0.00064   20.0   0.4     0.0011   19.2   0.4    1.3  1  TrkA_N          TrkA-N domain
    0.00069   19.0   0.9    0.00069   19.0   0.9    1.9  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.037   13.6   0.3      0.068   12.7   0.3    1.4  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.039   13.3   0.2      0.091   12.1   0.1    1.6  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.45   11.1   3.1         24    5.6   1.2    2.7  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.3   6.5e+03      33      50 ..     114     140 ..     112     152 .. 0.69
   2 !   87.7   1.8     3e-28     6e-25       2     129 ..     171     299 ..     170     300 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.3
                                       TT.ESEEEET.......TTC.HHHHHH CS
                        ADH_zinc_N  33 lG.adeviny.......kea.dlveri 50 
                                       +G a++v+ y       +e+ d++e++
  gi|557693982|ref|YP_008797036.1| 114 FGfAEYVVAYpghvqrfRETiDFEEAV 140
                                       777888888877777776666777665 PP

  == domain 2  score: 87.7 bits;  conditional E-value: 3e-28
                                       HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHC CS
                        ADH_zinc_N   2 vGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkl 78 
                                       +Gl+ vql+k +Ga v+avd see+l+la+ lGad+v+++ ++++ve++++l ggegvd+v  +vG g+++e+ +++
  gi|557693982|ref|YP_008797036.1| 171 IGLMQVQLLKLMGAMVVAVDYSEERLRLAEMLGADVVVDAADKSVVEKVRSLAGGEGVDFVSLTVGEGKAVETGFRC 247
                                       8***************************************4449********************************* PP

                                       EEEEEEEEECSCTSSEEE..EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                        ADH_zinc_N  79 lkpgGrlvvvGggkgeee..fdlrnlllkeksilGsllgslreefkealdlla 129
                                       l+++G l +++ ++g+ +  ++l++l++ e +++G+  ++ r  + +a++l++
  gi|557693982|ref|YP_008797036.1| 248 LAKRGVLNIFASLHGDGVvgVNLNKLHFGEYTLTGTYAST-RGHINRAVQLIE 299
                                       ************77766679*******************9.999999999986 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 !   86.8   1.5     4e-28     8e-25       2     104 ..      25     125 ..      24     130 .. 0.91
   2 ?   -3.8   0.0       5.9   1.2e+04      58      71 ..     139     152 ..     136     156 .. 0.77

  Alignments for each domain:
  == domain 1  score: 86.8 bits;  conditional E-value: 4e-28
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSS..EE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklp..lilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkeg 76 
                                       + vl++vka+g+C  D+ +++g +++ v+lp   + GHE++G+ve+vg++v+ lk GdrV+     +cg+C++C +g
  gi|557693982|ref|YP_008797036.1|  25 DSVLVRVKACGVCPVDVRVYTG-ENVWVPLPsvGVSGHEVAGVVEKVGENVSALKPGDRVAGTLSKPCGTCRYCVKG 100
                                       68********************.7999999944579***************************************** PP

                                       -GGG-TTBEETTTSS-SSSBSEEEECGG CS
                             ADH_N  77 eenlCeeakllgvsldGgfaeyvvvpek 104
                                       +enlC++     v    gfaeyvv+   
  gi|557693982|ref|YP_008797036.1| 101 YENLCTNSLKPKVF---GFAEYVVAYPG 125
                                       *******9999999...99999998655 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.9
                                       EEEE-SEEE-SSSH CS
                             ADH_N  58 rVvvepliscgeCa 71 
                                        V+ epl +c +C 
  gi|557693982|ref|YP_008797036.1| 139 AVFTEPLAACINCV 152
                                       57788888888885 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 !   36.4   0.6   1.8e-12   3.7e-09      32     210 ..     161     335 ..     137     336 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.8e-12
                       Glu_dehyd_C  32 esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYv.dsr.etpvdeipea..seemdlv 104
                                       + alv+G G +GL+ + ll+++  g     v++  d+ + +++l e lGa  v d + ++ v+++ +    e +d+v
  gi|557693982|ref|YP_008797036.1| 161 DWALVVGVGQIGLMQVQLLKLM--GA---MVVA-VDYSEERLRLAEMLGADVVvDAAdKSVVEKVRSLagGEGVDFV 231
                                       569************9999973..44...3444.4788899*********76525441455677765422689**** PP

                       Glu_dehyd_C 105 vEaTGsakhafeaiealapnGvaaL.lGvpedsevevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpes 180
                                         + G+ k++    + la  Gv  + + +  d  v v+ ++lh         l G+  + r h + av+ +++    
  gi|557693982|ref|YP_008797036.1| 232 SLTVGEGKAVETGFRCLAKRGVLNIfASLHGDGVVGVNLNKLHFG----EYTLTGTYASTRGHINRAVQLIEKG-LV 303
                                       **********************86615567778888888888755....889****************987765.45 PP

                       Glu_dehyd_C 181 lldelvtkvvdldeleeAfe..dddetiKtvv 210
                                        ++ l+t++++l++l e fe  ++ + +K+vv
  gi|557693982|ref|YP_008797036.1| 304 KVRPLITHRLPLEKLVEGFEihRERKGVKVVV 335
                                       5899***************8446667899987 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 !   32.3   0.1   9.2e-11   1.8e-07       1     120 [.     202     323 ..     202     335 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 9.2e-11
                                       TT-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEE.EE----.S-EEE-CHHHCTTT-E CS
                      ADH_zinc_N_2   1 lGAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrl.vsiggpplsaallkpakkrkgrs 72 
                                       lGAd v+d  +++++    + +ggegvD v  tvg  +++e  +++l+++G l +  +     +++  +++  ++  
  gi|557693982|ref|YP_008797036.1| 202 LGADVVVDAADKSVVekvrSLAGGEGVDFVSLTVGEGKAVETGFRCLAKRGVLnIFASL--HGDGVVGVNL--NKLH 274
                                       8******99977777799788889***********55566*******888999755443..2344444444..3333 PP

                                       EEE--GGG...-.-HHHHHHHHHHHHHHH..----EEEEEEGGGHHHHHH CS
                      ADH_zinc_N_2  73 vkyeflfsmkasaqadileelaalieeGk..lrpvvdrvfpleeaaeAhr 120
                                       +   +l+ + as + + +++ ++lie+G   +rp +++++ple+++e ++
  gi|557693982|ref|YP_008797036.1| 275 FGEYTLTGTYASTRGH-INRAVQLIEKGLvkVRPLITHRLPLEKLVEGFE 323
                                       3333333333333777.***********7557899**99*****999876 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.4   5.5e-07    0.0011       2      57 ..     164     218 ..     163     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.5e-07
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHH CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeglevvvgdatdeevLee 57 
                                       +++G+G++G   ++ L+  g + vv++d +eer++ ++  g++vvv da+d++v+e+
  gi|557693982|ref|YP_008797036.1| 164 LVVGVGQIGLMQVQLLKLmGAM-VVAVDYSEERLRLAEMLGADVVV-DAADKSVVEK 218
                                       79****************7776.**************999998775.8899999887 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 ?   -2.6   0.1       1.4   2.7e+03      36      57 ..      56      77 ..      55      92 .. 0.83
   2 !   19.0   0.9   3.5e-07   0.00069      32      86 ..     164     217 ..     155     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.4
                                      TSHHHHHHHHHHHHTT-EEEEE CS
                       AlaDh_PNT_C 36 gGvaGlqAiatakglgakVtvl 57
                                      +Gv G + + +  ++g +V +l
  gi|557693982|ref|YP_008797036.1| 56 VGVSGHEVAGVVEKVGENVSAL 77
                                      6999999999999999999887 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 3.5e-07
                                       EEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHH CS
                       AlaDh_PNT_C  32 lviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeella 86 
                                       lv+G+G  Gl  ++  k +ga V+++D +++rl+  e lga  v v +++++ ++
  gi|557693982|ref|YP_008797036.1| 164 LVVGVGQIGLMQVQLLKLMGAMVVAVDYSEERLRLAEMLGAD-VVVDAADKSVVE 217
                                       8****************************************9.777666665555 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 ?   12.7   0.3   3.4e-05     0.068       5      38 ..     165     198 ..     163     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                                       EE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHH CS
                    UDPG_MGDP_dh_N   5 viGlGYvGlvtaavlaeighevigvDideekvdk 38 
                                       v+G G +Gl++  +l  +g  v+ vD +ee+ + 
  gi|557693982|ref|YP_008797036.1| 165 VVGVGQIGLMQVQLLKLMGAMVVAVDYSEERLRL 198
                                       9****************************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 ?   -2.9   0.0       1.9   3.8e+03      44      67 ..      56      79 ..      53      85 .. 0.83
   2 ?   12.1   0.1   4.6e-05     0.091      39      73 ..     163     197 ..     153     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.9
                                      -SHHHHHHHHHHHHTT-EEEEESS CS
                      2-Hacid_dh_C 44 lGrIGqavakrlkafgmkviaydr 67
                                      +G  G++va +++++g +v a ++
  gi|557693982|ref|YP_008797036.1| 56 VGVSGHEVAGVVEKVGENVSALKP 79
                                      577899999999999999998876 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.6e-05
                                       EEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C  39 vGiiGlGrIGqavakrlkafgmkviaydrskkkee 73 
                                         ++G+G+IG    ++lk +g+ v+a+d s+++ +
  gi|557693982|ref|YP_008797036.1| 163 ALVVGVGQIGLMQVQLLKLMGAMVVAVDYSEERLR 197
                                       579*************************9977544 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.024        47       8      35 ..      57      84 ..      56      93 .. 0.89
   2 ?    5.6   1.2     0.012        24       3      40 ..     164     201 ..     163     231 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.024
                                      SHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  8 GyiglElAgalaelgkkVtvversdkll 35
                                      G++g E+Ag+  + g +V+ +  +d++ 
  gi|557693982|ref|YP_008797036.1| 57 GVSGHEVAGVVEKVGENVSALKPGDRVA 84
                                      899****************999999986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.012
                                       EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSH CS
                         Pyr_redox   3 vvvGgGyiglElAgalaelgkkVtvversdkllrllDe 40 
                                       +vvG G igl+  + l+ +g+ V  v+ s++ lrl + 
  gi|557693982|ref|YP_008797036.1| 164 LVVGVGQIGLMQVQLLKLMGAMVVAVDYSEERLRLAEM 201
                                       8************************9999998865544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2525.71
//
Query:       gi|557693983|ref|YP_008797037.1|  [L=125]
Description: acylphosphatase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   0.0    1.8e-21   76.3   0.0    1.3  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 !   76.3   0.0     1e-25   1.8e-21       4      69 ..       7      72 ..       4      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 1e-25
                   Acylphosphatase  4 lvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdev 69
                                       v GrVQ+vg+R++v +l +el l+GyvrN++dg+V i a+g+ee++++f+e+lk+ pp+a++++ 
  gi|557693983|ref|YP_008797037.1|  7 KVVGRVQRVGYRRHVLELGQELELAGYVRNEKDGTVTIFAQGDEETLNRFMEALKTPPPPAKIKKN 72
                                      799************************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 00:00:00.40
# Mc/sec: 937.30
//
Query:       gi|557693984|ref|YP_008797038.1|  [L=278]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-51  174.6   0.0    3.4e-51  174.5   0.0    1.0  1  Methyltrn_RNA_3  Putative RNA methyltransferase
  ------ inclusion threshold ------
      0.012   15.7   0.0       0.15   12.2   0.0    2.3  2  SpoU_methylase   SpoU rRNA Methylase family
      0.099   12.7   0.0       0.23   11.6   0.0    1.5  1  APC_N_CC         Coiled-coil N-terminus of APC, dimerisation 


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 !  174.5   0.0   5.7e-55   3.4e-51       3     286 .]       5     270 ..       3     270 .. 0.92

  Alignments for each domain:
  == domain 1  score: 174.5 bits;  conditional E-value: 5.7e-55
                   Methyltrn_RNA_3   3 siaiPssiisnaqsleqktylagqIARaaaiFnVdeivvfddseseeekkekpseflarlLqYletPpYLrkelFpl 79 
                                        + +P s ++++ s +++t+++g + R +a F+Vde+v+++d+ ++ + +  ++ ++ +lL Yl+t pYLr +++pl
  gi|557693984|ref|YP_008797038.1|   5 AVFLPHSFTAEVPSFREATMKIGFVGRVLATFRVDELVLYPDEPGAPRLR--NALLIKELLDYLVTAPYLRSRVYPL 79 
                                       689******************************************99877..9************************ PP

                   Methyltrn_RNA_3  80 hkelkyaglLppldaphhl....rsseegeyreGvvvekskekkskkklVniGlkkevklelkqevpegtRVtVkls 152
                                       +++l+yaglLppl++p h      ++e ++yr+ +v+ + +  +s   l + G+ k++k+++  ++p++t Vt+++ 
  gi|557693984|ref|YP_008797038.1|  80 KPSLRYAGLLPPLNIPTHPeadaLKKEGTHYRQALVTASGQ--TS---LLEAGMGKPLKIPR--KLPKNTIVTLRV- 148
                                       *******************77765567899*******9977..44...9*************..************. PP

                   Methyltrn_RNA_3 153 seesveakvVspsepreeaglywGYsVrlakslsavftespfeggydlsigtsergekveeklaelekkk.efkhll 228
                                         + +e++v  +   ++  ++y G++ r++ksl+++++       y+++++ts+ ge+++++ a+++++  e  +  
  gi|557693984|ref|YP_008797038.1| 149 --RVKEGRVKYSVVGKKSGETYTGFRTRVVKSLEEALKP------YTFRLATSRLGEPINQVYATVAQRLkESTQTC 217
                                       ..334444444444445679****************985......899*********************988***** PP

                   Methyltrn_RNA_3 229 ivfGg.vrgleaaleadeelklegekaeelFdlwlntvpnqgsrtirtEEavliaLalL 286
                                       +vfG+  +gl ++++a+      g + + lF + +nt pnqg +tirtEEa+  +La L
  gi|557693984|ref|YP_008797038.1| 218 VVFGAaDKGLHEIARAH------GLEYNRLFTHTVNTAPNQGVKTIRTEEALAYTLAIL 270
                                       *****99*******888......899******************************976 PP

>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.085   5.1e+02      15      34 ..      26      45 ..      22      58 .. 0.85
   2 ?   12.2   0.0   2.6e-05      0.15      57     112 ..     172     231 ..     146     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.085
                                      HHHHHHHHHHTT-SEEEEES CS
                    SpoU_methylase 15 lGaiaRtakafgaselvlvk 34
                                      +G + R+ ++f ++elvl  
  gi|557693984|ref|YP_008797038.1| 26 IGFVGRVLATFRVDELVLYP 45
                                      7999*************965 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.6e-05
                                       HEEEESSHHHHHHHHCCCTEEEEEESTT-SEGCCS........HHHTTEEEEEEBTTTBS-HHH CS
                    SpoU_methylase  57 elkvvdsleealkelkeegfalvatslkgkslsei........dlkekvalvfGnEdkGlsnel 112
                                       + +vv+sleealk  + +    +ats+ g++++++        + + ++++vfG  dkGl++ +
  gi|557693984|ref|YP_008797038.1| 172 RTRVVKSLEEALKPYTFR----LATSRLGEPINQVyatvaqrlKESTQTCVVFGAADKGLHEIA 231
                                       56799************9....9999999999966555555445559*************9755 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 ?   11.6   0.0   3.8e-05      0.23      11      36 ..     101     126 ..      99     129 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.8e-05
                          APC_N_CC  11 EaLkkenthlrrELedNSshLskLEt 36 
                                        aLkke th+r+ L   S + s LE 
  gi|557693984|ref|YP_008797038.1| 101 DALKKEGTHYRQALVTASGQTSLLEA 126
                                       69********************9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2068.65
//
Query:       gi|557693985|ref|YP_008797039.1|  [L=140]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  118.1   0.3    3.5e-34  118.0   0.3    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 !  118.0   0.3     2e-38   3.5e-34       1     138 []       6     140 .]       6     140 .] 0.95

  Alignments for each domain:
  == domain 1  score: 118.0 bits;  conditional E-value: 2e-38
                                       EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S- CS
                          Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvf 77 
                                       +  l+h AD+ iea+G+sleeafe+a+lalf++++  +  e++ + ++e++++dl +lL+d+L++ll+ f+ +++v+
  gi|557693985|ref|YP_008797039.1|   6 FHQLPHMADIYIEAYGSSLEEAFEQAGLALFKTLVL-NASEKTVSLSVEARGQDLMELLYDWLEKLLHKFEIDNIVA 81 
                                       7889******************************97.666777788******************************* PP

                                       ---EEEE.E-SSSEEEEEEEE----.-TT--------B--S---EEEEETTEEEEEEEEE- CS
                          Archease  78 kevkvdeeeeeeeleleaeargekfdkekhevqtevKAvTyhelrieeeddgweayvvvDi 138
                                       +e+kv++  ++ e++lea+++ge++++ekh+++t vK  Ty  ++i  e+   ++++v+Di
  gi|557693985|ref|YP_008797039.1|  82 TEIKVNKIMRNGEYRLEATLWGENYNREKHQTGTAVKSPTYALMEIDTEK--NKVRFVLDI 140
                                       *****999999********************99*************9998..679999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1085.44
//
Query:       gi|557693986|ref|YP_008797040.1|  [L=122]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   72.8   1.7    2.8e-20   72.6   1.7    1.1  1  HEPN          HEPN domain
  ------ inclusion threshold ------
       0.01   15.8   0.2      0.011   15.7   0.2    1.3  1  NICE-3        NICE-3 protein
       0.16   10.5   0.0        0.2   10.1   0.0    1.1  1  Cytochrom_D1  Cytochrome D1 heme 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 !   72.6   1.7   4.7e-24   2.8e-20       4     116 ..       2     115 ..       1     117 [. 0.93

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 4.7e-24
                                       HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT.........-HHHH CS
                              HEPN   4 wlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke......seelr 74 
                                       + rr+ e+le Ae++l +++ d   f+ +qaa+++lK++llk+ ge+ +th+lr+L+ el++   +       ee r
  gi|557693986|ref|YP_008797040.1|   2 LRRRGVEFLEMAEKALADKKVD---FMLEQAAQLYLKSALLKLVGEYSRTHSLRRLVWELAEASRDdelrkfGEERR 75 
                                       679999**************99...89*******************************9999998777788777788 PP

                                       HHHHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHH CS
                              HEPN  75 eeleeLekayiesrYpdakeeyteedaeealkdaeevlelve 116
                                         l+ Le+ yi++rY + ++  +e da e l++++e+++lv 
  gi|557693986|ref|YP_008797040.1|  76 SVLSSLEDVYIMARYFPKEY--SEMDAAEFLEVVRELFRLVG 115
                                       888**************999..***************99875 PP

>> NICE-3  NICE-3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   0.2   1.9e-06     0.011     138     179 ..      69     110 ..      11     112 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-06
                            NICE-3 138 plksvrkslidqlldlyehARhgpeeFgeeeylkyqelleeL 179
                                       ++ + r+s + +l d+y  AR+ p+e+ e +  ++ e+++eL
  gi|557693986|ref|YP_008797040.1|  69 KFGEERRSVLSSLEDVYIMARYFPKEYSEMDAAEFLEVVREL 110
                                       5667788999****************************9998 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   3.4e-05       0.2      74     113 ..      69     108 ..      54     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.4e-05
                                       E-SSEEEEEEE--TTSEEEEEEEETTEEEEEETTT.--EEE CS
                      Cytochrom_D1  74 kiGlnarsvavSqddryvivgnYlPgqlvildaet.Lelvk 113
                                       k G + rsv +S +d y+++  Y P +++ +da + Le v+
  gi|557693986|ref|YP_008797040.1|  69 KFGEERRSVLSSLEDVYIMA-RYFPKEYSEMDAAEfLEVVR 108
                                       5799*************875.8**********854277766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 00:00:00.37
# Mc/sec: 999.19
//
Query:       gi|557693987|ref|YP_008797041.1|  [L=111]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-10   38.6   0.0    1.2e-09   38.4   0.0    1.1  1  NTP_transf_2  Nucleotidyltransferase domain
    4.9e-07   29.8   0.0    5.6e-07   29.6   0.0    1.1  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 !   38.4   0.0   1.3e-13   1.2e-09       4      74 ..      22      90 ..      19     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.3e-13
                                      HHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEE CS
                      NTP_transf_2  4 lleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlv 74
                                      l+e++++  ++a+v++fGS+++G+    SD+D+lvv+++  +   + e+   ++ei+++  +   ++  l+
  gi|557693987|ref|YP_008797041.1| 22 LAEAVRKVLGDADVYVFGSVVTGECVASSDVDVLVVSDRVPE--SMLERGALKVEIEDAAGLPVYHPFELH 90
                                      6789998888*****************************966..577777777777777666555555555 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   6.2e-11   5.6e-07      16      59 ..      35      82 ..      24     108 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 6.2e-11
                                      TTEEEEEE-S------EEEEEEEESS-.--HHHHHHHHHHHHHH.... CS
                           Polbeta 16 aylFGSrakgkareeSDiDlavllkek.ldleeelelaaeledi...k 59
                                      +y+FGS+++g+   +SD+D+ v+ ++  +++ e+  l+ e+ed+    
  gi|557693987|ref|YP_008797041.1| 35 VYVFGSVVTGECVASSDVDVLVVSDRVpESMLERGALKVEIEDAaglP 82
                                      8**************************9999999*******9996653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 832.28
//
Query:       gi|557693988|ref|YP_008797042.1|  [L=352]
Description: hypothetical protein CSUB_C0552 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.5   1.4      0.075   12.4   1.4    1.6  1  DUF5305       Family of unknown function (DUF5305)
      0.095   12.5   0.3       0.16   11.7   0.3    1.3  1  Collectrin    Renal amino acid transporter
       0.12   12.5   0.0        1.6    8.8   0.0    2.3  2  7TMR-DISMED2  7TMR-DISM extracellular 2


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 ?   12.4   1.4   1.3e-05     0.075      76     140 ..     279     342 ..     238     351 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                           DUF5305  76 srlpiplteqtyeikkdetdeengeitetvtvkespslae.gilliilgllaliglvvlirriift 140
                                       ++++++++e t++ ++++t +++ + te +t + s+++a+ +++++++g++ l++++++i r + +
  gi|557693988|ref|YP_008797042.1| 279 YTITLSINEATTSTTTTTT-TTPIT-TEITTPSLSHETAQlIVYGTVTGIAVLAVAATVIMRRRSQ 342
                                       5677777777777665444.33333.3333444555555578999999999999999988885544 PP

>> Collectrin  Renal amino acid transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   2.7e-05      0.16      95     148 ..     285     338 ..     281     343 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.7e-05
                        Collectrin  95 ineaflLddktLeflgilptLappveppvtiWlivfgvvmgvvvvgivlLivsg 148
                                       inea + + +t   + i++ +++p  ++ t  liv+g v g+ v+++ + +++ 
  gi|557693988|ref|YP_008797042.1| 285 INEATTSTTTTTTTTPITTEITTPSLSHETAQLIVYGTVTGIAVLAVAATVIMR 338
                                       88888888889999999999**************************99988875 PP

>> 7TMR-DISMED2  7TMR-DISM extracellular 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.071   4.3e+02      87     123 ..      38      79 ..      30      88 .. 0.61
   2 ?    8.8   0.0   0.00027       1.6      59     123 ..     186     271 ..     176     273 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.071
                                       ESTTS-..--SS-TTE...EEEEE--SSS-E.EEEEEEEESS CS
                      7TMR-DISMED2  87 lGdlrp..eRpvahrn...fvfplplppgetvtvylrvkseg 123
                                       +Gd +p  e  +a r    f+   +l+pge++ + + v++++
  gi|557693988|ref|YP_008797042.1|  38 AGDTLPpiEATLAGRLredFYRFENLRPGERLVLRVTVTTNT 79 
                                       78888855333332224534444588****955555555554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00027
                                       E..EEEE-TT-SEEEEEEEC...............TCEEEEEEESTTS-.............--SS-TTE...EEEE CS
                      7TMR-DISMED2  59 rwllelayplldevdlYvpd...............ggslrearlGdlrp.............eRpvahrn...fvfp 104
                                       + +l  ++  ld+vd Yv++               +        G+ ++             +R          +++
  gi|557693988|ref|YP_008797042.1| 186 SGYLTNSSEGLDYVDTYVLTavlgkgkqltatlttQ-------PGNIYElvildqtgyglrsNRTN---TsgeAAVS 252
                                       5678888999************99654433333330.......44444455554332221133333...25669999 PP

                                       E--SSS-E.EEEEEEEESS CS
                      7TMR-DISMED2 105 lplppgetvtvylrvkseg 123
                                       l+ + ++++t+y+rv+++g
  gi|557693988|ref|YP_008797042.1| 253 LETQDAAEKTYYIRVSNQG 271
                                       999999999******9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); 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:                         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 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2641.74
//
Query:       gi|557693989|ref|YP_008797043.1|  [L=2586]
Description: hypothetical protein CSUB_C0553 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   46.6  23.3    5.5e-07   29.8   1.9    7.0  8  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    1.2e-05   25.2  18.7      0.094   12.7   1.2    7.6  7  Big_1            Bacterial Ig-like domain (group 1)
     0.0083   16.3   3.1      0.054   13.7   0.1    3.3  3  SdrD_B           SdrD B-like domain
     0.0097   15.9   1.9       0.13   12.3   0.1    3.2  3  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
  ------ inclusion threshold ------
      0.051   13.4   3.3         12    5.9   0.1    5.0  4  DUF824           Salmonella repeat of unknown function (DUF82
      0.087   13.0   0.7        3.8    7.7   0.0    3.6  3  MG4              Macroglobulin domain MG4
       0.18   12.1   9.8        8.5    6.8   0.2    5.7  5  Invasin_D3       Invasin, domain 3


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 ?   -3.1   0.1       3.9   9.9e+03      10      33 ..     230     253 ..     229     266 .. 0.61
   2 ?   -2.2   0.0       2.1   5.3e+03      19      52 ..    1003    1036 ..     996    1037 .. 0.83
   3 ?   -2.7   0.0         3   7.7e+03       6      19 ..    1254    1267 ..    1253    1268 .. 0.91
   4 ?   -3.2   0.0       4.1   1.1e+04      11      29 ..    1516    1536 ..    1509    1552 .. 0.68
   5 ?    0.6   0.0      0.27   6.8e+02       2      27 ..    2045    2070 ..    2044    2083 .. 0.77
   6 !    9.7   0.1   0.00039         1       6      54 ..    2298    2346 ..    2294    2366 .. 0.74
   7 !   14.8   2.2   9.8e-06     0.025       2      73 ..    2380    2446 ..    2379    2453 .. 0.84
   8 !   29.8   1.9   2.1e-10   5.5e-07       4      63 ..    2460    2518 ..    2457    2533 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.9
                   CarboxypepD_reg  10 sgapiagatVtvtnadtgtvastt 33 
                                       ++ ++++at+ ++++d +  +st+
  gi|557693989|ref|YP_008797043.1| 230 TNDVLTYATIFIYDTDHTDASSTQ 253
                                       678899999999987755333333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                   CarboxypepD_reg   19 VtvtnadtgtvastttdadGafrlrglppgtysv 52  
                                        V v   +  t + t+ d++Ga  +  l+ g+y++
  gi|557693989|ref|YP_008797043.1| 1003 VKVVPPSPATPYVTQLDSTGALDFGYLAGGQYTI 1036
                                        6666666778889999*********9*99***97 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3
                   CarboxypepD_reg    6 VtdasgapiagatV 19  
                                        Vtd++ +pi +at+
  gi|557693989|ref|YP_008797043.1| 1254 VTDPNLNPIGNATL 1267
                                        9***********96 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 4.1
                   CarboxypepD_reg   11 gapiagatVtvtn..adtgtv 29  
                                         +pi++a V +    +d+gtv
  gi|557693989|ref|YP_008797043.1| 1516 ARPIPYAVVQLDVyyDDSGTV 1536
                                        689999999975322555654 PP

  == domain 5  score: 0.6 bits;  conditional E-value: 0.27
                   CarboxypepD_reg    2 isGrVtdasgapiagatVtvtnadtg 27  
                                        +s r+td +g+p++ga   + +a+tg
  gi|557693989|ref|YP_008797043.1| 2045 VSARITDFNGRPLPGAFYQIIDAQTG 2070
                                        7889***********97666665555 PP

  == domain 6  score: 9.7 bits;  conditional E-value: 0.00039
                   CarboxypepD_reg    6 VtdasgapiagatVtvtnadtgtvastttdadGafrlrglpp.gtysvtv 54  
                                        V+d +g+p+aga+V+v+  +   ++  +  +d  f++  +p   ty+ tv
  gi|557693989|ref|YP_008797043.1| 2298 VVDRQGRPVAGARVSVSP-NLVREQDIQLRPDSIFTILRVPDgRTYDFTV 2346
                                        9***************93.2234566777777777777777766677766 PP

  == domain 7  score: 14.8 bits;  conditional E-value: 9.8e-06
                   CarboxypepD_reg    2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglpp.gtysvtvsapGyatatreevtltagq 73  
                                        ++ +V+d +g+p+aga++++       ++   td++G   + ++p   +y+++vs++G      + v+ ta +
  gi|557693989|ref|YP_008797043.1| 2380 VTLTVVDFDGRPVAGAAIRFG-----GQQVGSTDSQGVVIIGQVPLdNEYQIEVSKDGTTIGGDR-VRFTASR 2446
                                        6679****************9.....6777799*************************8766643.6666555 PP

  == domain 8  score: 29.8 bits;  conditional E-value: 2.1e-10
                   CarboxypepD_reg    4 GrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatat 63  
                                          V+ a g+pi ga V++   +++t a++ tda+G+  ++ +   +ysv++s++ +  ++
  gi|557693989|ref|YP_008797043.1| 2460 VIVKGAAGQPIQGAIVELV-RGGTTIATAATDASGSAVFSKVVGADYSVRASYEQFSNSA 2518
                                        57999**************.477889*****************************98776 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 ?   -1.8   0.1       1.2   3.2e+03      12      35 ..     884     907 ..     878     916 .. 0.72
   2 ?   -2.9   0.0       2.9   7.4e+03      13      25 ..    1254    1266 ..    1253    1267 .. 0.90
   3 ?    0.8   0.0      0.19   4.9e+02       9      24 ..    2045    2060 ..    2042    2061 .. 0.91
   4 !    6.9   0.0    0.0023         6      10      30 ..    2295    2315 ..    2293    2324 .. 0.88
   5 !    9.3   0.5   0.00042       1.1       9      35 ..    2380    2407 ..    2377    2415 .. 0.78
   6 ?   -0.6   0.0      0.53   1.4e+03      16      37 ..    2430    2452 ..    2422    2457 .. 0.75
   7 !   12.7   1.2   3.7e-05     0.094       9      50 ..    2458    2497 ..    2456    2500 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.2
                             Big_1  12 tvkDangnpvagatVtfsvsggal 35 
                                       +++D+ gnp + a+  ++   g+ 
  gi|557693989|ref|YP_008797043.1| 884 RLVDNLGNPAPAANTAITLQRGNG 907
                                       68999***9998887777777665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
                             Big_1   13 vkDangnpvagat 25  
                                        v+D n np+ +at
  gi|557693989|ref|YP_008797043.1| 1254 VTDPNLNPIGNAT 1266
                                        9********9987 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.19
                             Big_1    9 ltatvkDangnpvaga 24  
                                        ++a+++D ng p++ga
  gi|557693989|ref|YP_008797043.1| 2045 VSARITDFNGRPLPGA 2060
                                        799***********97 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0023
                             Big_1   10 tatvkDangnpvagatVtfsv 30  
                                        +  v+D++g pvaga V++s 
  gi|557693989|ref|YP_008797043.1| 2295 SFNVVDRQGRPVAGARVSVSP 2315
                                        6789**************985 PP

  == domain 5  score: 9.3 bits;  conditional E-value: 0.00042
                             Big_1    9 ltatvkDangnpvagatVtfsvsg.gal 35  
                                        +t tv+D +g pvaga++ f   + g++
  gi|557693989|ref|YP_008797043.1| 2380 VTLTVVDFDGRPVAGAAIRFGGQQvGST 2407
                                        89******************87664444 PP

  == domain 6  score: -0.6 bits;  conditional E-value: 0.53
                             Big_1   16 angnpvagatVtfsvsg.galsa 37  
                                        ++g+ + g  V f++s  +a+++
  gi|557693989|ref|YP_008797043.1| 2430 KDGTTIGGDRVRFTASRtSATIQ 2452
                                        68999***********9544433 PP

  == domain 7  score: 12.7 bits;  conditional E-value: 3.7e-05
                             Big_1    9 ltatvkDangnpvagatVtfsvsggalsassgtTdanGkatv 50  
                                        + ++vk a g+p++ga V +   g++   +++ Tda+G a++
  gi|557693989|ref|YP_008797043.1| 2458 IAVIVKGAAGQPIQGAIVELVRGGTT--IATAATDASGSAVF 2497
                                        789*****************955544..489*********87 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.31   7.9e+02      42      80 ..    1016    1056 ..    1003    1075 .. 0.79
   2 ?   -0.9   0.2      0.72   1.8e+03      49      79 ..    1171    1202 ..    1162    1205 .. 0.79
   3 !   13.7   0.1   2.1e-05     0.054      21      69 ..    2467    2514 ..    2462    2528 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.31
                            SdrD_B   42 ttTdasGkYkFtnltpGeYkVeftapagy..tvtakkaGsd 80  
                                        t  d++G+  F  l+ G+Y++  +  +g+  ++t +  G+d
  gi|557693989|ref|YP_008797043.1| 1016 TQLDSTGALDFGYLAGGQYTIDGVWWKGVwvKFTDARIGDD 1056
                                        56689****************98776665345666655555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.72
                            SdrD_B   49 kYkFtnltpGeYkVefta.pagytvtakkaGs 79  
                                        +Y F ++ +  Y++++t+ ++g   t+++ G+
  gi|557693989|ref|YP_008797043.1| 1171 RYVFYKMPSALYNITVTTvTTGDPETQQTPGN 1202
                                        79**************9967776666666665 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 2.1e-05
                            SdrD_B   21 ekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapag 69  
                                         + i+g  V+L  + g+++at  TdasG+  F+++   +Y+V+ ++ + 
  gi|557693989|ref|YP_008797043.1| 2467 GQPIQGAIVEL-VRGGTTIATAATDASGSAVFSKVVGADYSVRASYEQF 2514
                                        578********.66788889**********************9987654 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 ?   -1.6   0.0       1.1   2.7e+03      24      36 ..    2302    2314 ..    2301    2316 .. 0.89
   2 ?    0.5   0.0      0.25   6.3e+02      24      55 ..    2388    2414 ..    2375    2430 .. 0.58
   3 !   12.3   0.1     5e-05      0.13      23      59 ..    2465    2500 ..    2450    2521 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                              bMG3   24 sgkPvagaeVrll 36  
                                        +g+Pvaga+V+++
  gi|557693989|ref|YP_008797043.1| 2302 QGRPVAGARVSVS 2314
                                        699*******997 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.25
                              bMG3   24 sgkPvagaeVrlldkkgevlaegtTDaqGvar 55  
                                        +g+Pvaga++r+    g+++  g TD+qGv+ 
  gi|557693989|ref|YP_008797043.1| 2388 DGRPVAGAAIRF---GGQQV--GSTDSQGVVI 2414
                                        345555555443...23333..4577777765 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 5e-05
                              bMG3   23 dsgkPvagaeVrlldkkgevlaegtTDaqGvarfaal 59  
                                        + g+P++ga V+l+   g ++a+++TDa+G a f++ 
  gi|557693989|ref|YP_008797043.1| 2465 AAGQPIQGAIVELVR-GGTTIATAATDASGSAVFSKV 2500
                                        579**********95.79**************99875 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0046        12      23      41 ..     887     907 ..     885     908 .. 0.86
   2 ?   -0.9   0.0      0.57   1.5e+03      21      37 ..    2298    2314 ..    2294    2315 .. 0.89
   3 ?    1.8   0.0     0.085   2.2e+02      17      36 ..    2380    2399 ..    2379    2400 .. 0.89
   4 ?    1.0   0.0      0.15   3.7e+02      19      39 ..    2460    2480 ..    2457    2482 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0046
                            DUF824  23 DasGn..PvpnapftltRgdg 41 
                                       D +Gn  P++n+++tl+Rg+g
  gi|557693989|ref|YP_008797043.1| 887 DNLGNpaPAANTAITLQRGNG 907
                                       7789977889*********97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.57
                            DUF824   21 vkDasGnPvpnapftlt 37  
                                        v+D +G Pv+ a ++++
  gi|557693989|ref|YP_008797043.1| 2298 VVDRQGRPVAGARVSVS 2314
                                        89**********99885 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.085
                            DUF824   17 ltitvkDasGnPvpnapftl 36  
                                        +t tv+D +G Pv+ a++++
  gi|557693989|ref|YP_008797043.1| 2380 VTLTVVDFDGRPVAGAAIRF 2399
                                        688*************9875 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.15
                            DUF824   19 itvkDasGnPvpnapftltRg 39  
                                        + vk a+G+P+  a + l Rg
  gi|557693989|ref|YP_008797043.1| 2460 VIVKGAAGQPIQGAIVELVRG 2480
                                        6799**********9999997 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.39   9.9e+02      19      40 ..    2295    2318 ..    2293    2347 .. 0.82
   2 ?   -0.4   0.1       0.5   1.3e+03      18      58 ..    2380    2413 ..    2379    2425 .. 0.82
   3 ?    7.7   0.0    0.0015       3.8       6      61 ..    2447    2498 ..    2442    2509 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.39
                               MG4   19 kVlvkdpdgspaknvpVkiea..l 40  
                                           v+d +g+p+++  V++++  +
  gi|557693989|ref|YP_008797043.1| 2295 SFNVVDRQGRPVAGARVSVSPnlV 2318
                                        5689***************99332 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.5
                               MG4   18 ikVlvkdpdgspaknvpVkiealkseteekeslttdedGta 58  
                                        +++ v+d dg+p+++  ++    +      +   td++G++
  gi|557693989|ref|YP_008797043.1| 2380 VTLTVVDFDGRPVAGAAIRFGG-Q------QVGSTDSQGVV 2413
                                        6889************999998.3......55567777776 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0015
                               MG4    6 tpkffKpGlPfsikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakfs 61  
                                        t+  +  G+ ++i V vk + g+p+++  V +   +   +   +  td++G a fs
  gi|557693989|ref|YP_008797043.1| 2447 TSATIQAGI-YDIAVIVKGAAGQPIQGAIVELVR-G--GTTIATAATDASGSAVFS 2498
                                        556666666.9********************998.4..445556678999999987 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.6   4.2e+03      24      49 ..     881     905 ..     874     915 .. 0.68
   2 ?    1.2   0.2      0.18   4.6e+02      21      54 ..    1894    1929 ..    1884    1934 .. 0.85
   3 ?    2.6   0.0     0.068   1.7e+02      24      45 ..    2294    2315 ..    2290    2327 .. 0.87
   4 ?    6.8   0.2    0.0033       8.5      24      50 ..    2380    2406 ..    2378    2452 .. 0.77
   5 ?    1.8   0.3      0.12     3e+02      24      60 ..    2458    2493 ..    2438    2512 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.6
                        Invasin_D3  24 ltvtlkDangnpvsgltvtfsttsag 49 
                                       l   l D+ gnp+  ++ +++ +  g
  gi|557693989|ref|YP_008797043.1| 881 LAYRLVDNLGNPAPAANTAITLQ-RG 905
                                       567899******77776666655.33 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.18
                        Invasin_D3   21 tstltvtlkDangnp.vsgltvtfsttsag.tlsav 54  
                                        t+  t+t+ D+  n  +sg+ v + t  +g t s+v
  gi|557693989|ref|YP_008797043.1| 1894 TTAGTITVGDKTVNIcISGKPVGLVTVTSGdTPSTV 1929
                                        6779******************99988788777765 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.068
                        Invasin_D3   24 ltvtlkDangnpvsgltvtfst 45  
                                        l++++ D +g pv+g+ v++s 
  gi|557693989|ref|YP_008797043.1| 2294 LSFNVVDRQGRPVAGARVSVSP 2315
                                        899***************9985 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0033
                        Invasin_D3   24 ltvtlkDangnpvsgltvtfsttsagt 50  
                                        +t+t+ D +g pv+g+++ f  ++ g+
  gi|557693989|ref|YP_008797043.1| 2380 VTLTVVDFDGRPVAGAAIRFGGQQVGS 2406
                                        8********************773331 PP

  == domain 5  score: 1.8 bits;  conditional E-value: 0.12
                        Invasin_D3   24 ltvtlkDangnpvsgltvtfsttsag.tlsavtdngdG 60  
                                        + v +k a+g+p++g+ v++     g t+ ++ ++++G
  gi|557693989|ref|YP_008797043.1| 2458 IAVIVKGAAGQPIQGAIVELVR--GGtTIATAATDASG 2493
                                        78999***********9**993..45466665565555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 1.24u 0.29s 00:00:01.53 Elapsed: 00:00:00.49
# Mc/sec: 15752.64
//
Query:       gi|557693990|ref|YP_008797044.1|  [L=150]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   46.2   0.1    6.7e-12   46.0   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 !   46.0   0.1   3.7e-16   6.7e-12       2     121 ..      13     139 ..      12     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 3.7e-16
                                       EE-HHHHHHHH.TTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHS..SCHCHHHHHHHHHHHHH.HHTSEE CS
                               PIN   2 vlDTsvliall.rgeekaeaarklleel....eelvtsalvlaEllyvlar..rkskrekaaelvellll.lsalki 70 
                                       v+D+sv ++++  ge+  e+ar l +++     + + + l+++El+ v+++  ++s   +++ + +l+ + + ++++
  gi|557693990|ref|YP_008797044.1|  13 VIDASVAVKWFiPGEPWEEEARVLKNSIaldrVKAYAPTLIIYELASVISKavKNSVLTLEDGVSALKSIgALGINM 89 
                                       89*********85555555555544444667*********************777777788888888888******* PP

                                       EEBCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  71 lpidaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrvak 121
                                       +p+ ++ a e++eia   gl+++D   + + ++ g kl+ t+D+d+r+ +k
  gi|557693990|ref|YP_008797044.1|  90 VPVLWNEASEVLEIAVTSGLTIYDSAYLWLSRKLGEKLV-TADKDLRQKGK 139
                                       ***************************************.*******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1104.53
//
Query:       gi|557693991|ref|YP_008797045.1|  [L=80]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   16.4   0.0      0.013   15.4   0.0    1.6  1  RHH_3     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> RHH_3  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.4e-07     0.013      15      38 ..      17      40 ..       9      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.4e-07
                             RHH_3 15 ekLkaLSekTrIprSklldeAiel 38
                                      e+L++L ++ ++  S++++ Aie 
  gi|557693991|ref|YP_008797045.1| 17 EELRQLMRRVKVDWSEYIRGAIEA 40
                                      89********************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 608.84
//
Query:       gi|557693992|ref|YP_008797046.1|  [L=74]
Description: hypothetical protein CSUB_C0556 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-21   74.3   0.3    1.1e-20   74.1   0.3    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 !   74.1   0.3   6.4e-25   1.1e-20       1      66 [.       3      66 ..       3      69 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 6.4e-25
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgilseeea.deiekaskelrk 66
                                      K Is+sde+Y +Lk++KregeSFsdv++rL++   + k + l e++g++  +++ + +e++++e ++
  gi|557693992|ref|YP_008797046.1|  3 KVISLSDEAYAALKRIKREGESFSDVVLRLVG---QAKYRPLSEFAGRWAGDDIdKVFEEILRERER 66
                                      89*****************************9...56688**************6667777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 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:                        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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 599.03
//
Query:       gi|557693993|ref|YP_008797047.1|  [L=130]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   59.4   0.5    5.1e-16   59.3   0.5    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 !   59.3   0.5   2.9e-20   5.1e-16       1     119 [.       2     122 ..       2     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.3 bits;  conditional E-value: 2.9e-20
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTS.SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBCHH CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleel.eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpidae 76 
                                       ++lDT +++allrg++ka +  + l+++     t++++++Ell ++a    +++ +++++ +++ll ++ il +d +
  gi|557693993|ref|YP_008797047.1|   2 VCLDTDIIVALLRGDNKAIETIEELQRMgMQFKTTIITVYELLKGAAI---SSKSSENIKTVKELLHNVTILGLDID 75 
                                       69****************999999999999999***************...************************** PP

                                       HHHHHHHHHHHHH.....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                               PIN  77 iaeeaaeialkyg.....llpnDaliaAtAkehgikliatfDedfrrv 119
                                       +  +a+ i++ ++     ++ +D liaA  ++++ +li t+D++f ++
  gi|557693993|ref|YP_008797047.1|  76 ACGKAGLIYSDLRrsgkmISEFDILIAAIVQHNRETLI-TRDKHFQEI 122
                                       **************************************.******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1076.15
//
Query:       gi|557693994|ref|YP_008797048.1|  [L=363]
Description: hypothetical protein CSUB_C0558 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2675.12
//
Query:       gi|557693995|ref|YP_008797049.1|  [L=398]
Description: site-specific DNA-methyltransferase (adenine-specific) [Candidatus Caldiarchaeum subterraneum]
Scores for 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   59.5   0.0    8.1e-07   29.0   0.0    2.6  3  N6_N4_Mtase      DNA methylase
    1.5e-07   31.3   0.0     0.0019   17.9   0.0    2.4  2  UPF0020          Putative RNA methylase family UPF0020
    1.4e-05   25.7   0.0      0.081   13.6   0.0    3.2  3  Methyltransf_11  Methyltransferase domain
     0.0029   18.3   0.0        6.3    7.6   0.0    3.3  3  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
       0.15   11.9   0.0       0.59   10.0   0.0    2.0  2  Methyltransf_23  Methyltransferase domain
       0.16   11.8   0.1         19    5.0   0.0    2.5  3  Methyltransf_8   Hypothetical methyltransferase
       0.17   11.7   0.0       0.46   10.3   0.0    1.7  2  Methyltransf_31  Methyltransferase domain
       0.23   11.1   0.0       0.38   10.4   0.0    1.3  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran


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 !   27.6   0.0   9.7e-10   2.2e-06     148     225 ..      26     100 ..      18     105 .. 0.83
   2 ?   -2.0   0.0       1.1   2.4e+03      34      59 ..     115     140 ..     111     176 .. 0.74
   3 !   29.0   0.0   3.6e-10   8.1e-07       1      66 [.     256     337 ..     256     370 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 9.7e-10
                                       -BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSHH CS
                       N6_N4_Mtase 148 iediWdlseiqsnekkskgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieieee 224
                                       ++d W  + + ++ ++s + +  + + ++P al++ ++  +++ gd+vlDpF G Gt   +a   gr  +G +  +e
  gi|557693995|ref|YP_008797049.1|  26 VSDSW--KGFGRSWGHSLHRIMSR-TGSFPPALARWVVTRFSERGDLVLDPFSGKGTAPLEACLTGRVGVGNDLAPE 99 
                                       56666..66666677777666555.899******************************9999999999999888877 PP

                                       H CS
                       N6_N4_Mtase 225 y 225
                                       +
  gi|557693995|ref|YP_008797049.1| 100 A 100
                                       6 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHEEEEEEEEEEE-CC CS
                       N6_N4_Mtase  34 flekvlkevrrvLkddgsifinidds 59 
                                         +++++++ rv+ +d + +  +d+ 
  gi|557693995|ref|YP_008797049.1| 115 DVRSWVEKASRVMRPDAVSVYDVDED 140
                                       56789999999999999988888765 PP

  == domain 3  score: 29.0 bits;  conditional E-value: 3.6e-10
                                       EEEEEE--SSSSSCS.....................GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy................endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddsei 61 
                                       vdlivt+pPY + + y                  ++ + + +s++ y+ef+ +vl+e  r+Lk++g  ++ ++d + 
  gi|557693995|ref|YP_008797049.1| 256 VDLIVTSPPYLNLQTYawdnwlrlwflghdyrVVGKRLFATQSVKRYVEFMGRVLDEFFRMLKPGGYCVLVVGDVKS 332
                                       89*****************************9999999***********************************9987 PP

                                       HTHHH CS
                       N6_N4_Mtase  62 kkelk 66 
                                         +++
  gi|557693995|ref|YP_008797049.1| 333 GGRRV 337
                                       76444 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   8.6e-07    0.0019      14      55 ..      53      93 ..      42     161 .. 0.70
   2 !   10.9   0.0   0.00012      0.27     109     132 ..     243     266 ..     220     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.6e-07
                                      HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--T CS
                           UPF0020 14 etLAaalvrlagwkpgepllDPmCGsGtilIEaallganiap 55
                                      ++LA+  v++   ++g+  lDP++G Gt ++Ea+l g+  + 
  gi|557693995|ref|YP_008797049.1| 53 PALARWVVTRFS-ERGDLVLDPFSGKGTAPLEACLTGRVGVG 93
                                      666666666543.578999****************9986654 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00012
                                       E--GGG--STTS---EEEE----- CS
                           UPF0020 109 qadaakLrlkegevdvivtnpPYG 132
                                       ++da +L+ ++++vd+ivt pPY 
  gi|557693995|ref|YP_008797049.1| 243 NMDASALPIADESVDLIVTSPPYL 266
                                       6899****8888***********7 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      0.72   1.6e+03      75      92 ..     114     131 ..      75     135 .. 0.72
   2 !    7.8   0.0    0.0023         5      48      67 ..     242     261 ..     204     272 .. 0.88
   3 !   13.6   0.0   3.6e-05     0.081      72      96 .]     301     325 ..     293     325 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.72
                                       CCHHHHHHHHHHHEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgG 92 
                                        d+++ ++++ Rv++p+ 
  gi|557693995|ref|YP_008797049.1| 114 RDVRSWVEKASRVMRPDA 131
                                       466677777778887775 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0023
                                       TTEECCCTSS-TT-EEEEEE CS
                   Methyltransf_11  48 vvadaeklpfednsfDlvvs 67 
                                         +da+ lp++d+s+Dl+v 
  gi|557693995|ref|YP_008797049.1| 242 FNMDASALPIADESVDLIVT 261
                                       5799*************996 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 3.6e-05
                                       CC-CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  72 hhvedpekalkeiaRvLkpgGllvi 96 
                                        +ve + ++l+e+ R+LkpgG++v+
  gi|557693995|ref|YP_008797049.1| 301 RYVEFMGRVLDEFFRMLKPGGYCVL 325
                                       55677889***************95 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0       0.2   4.5e+02       1      56 [.      70     124 ..      70     156 .. 0.68
   2 !    7.6   0.0    0.0028       6.3      47      72 ..     238     263 ..     218     281 .. 0.72
   3 ?    5.0   0.0     0.018        40      83      97 .]     307     321 ..     294     321 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.2
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCC CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdae 56 
                                       vLd   G+G+  l++    g    +g D+++e+   +r++++ + + +v+  + +a+
  gi|557693995|ref|YP_008797049.1|  70 VLDPFSGKGTAPLEACLT-G-RVGVGNDLAPEAYVVTRAKVKPAMFrDVRSWVEKAS 124
                                       566666777666655544.3.555889999999888888887665565555555544 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0028
                                       TEEEEESBCCGBSSSTTTEEEEEEES CS
                   Methyltransf_25  47 nvefvqgdaedlpfedgsfDlvvssg 72 
                                       +    ++da++lp +d+s+Dl+v s 
  gi|557693995|ref|YP_008797049.1| 238 RGAAFNMDASALPIADESVDLIVTSP 263
                                       6677899***************9964 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHEEEEE CS
                   Methyltransf_25  83 ekalkeiarvLkpgG 97 
                                        ++l+e++r+LkpgG
  gi|557693995|ref|YP_008797049.1| 307 GRVLDEFFRMLKPGG 321
                                       589***********9 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.88     2e+03      98     154 ..     116     153 ..      95     162 .. 0.56
   2 ?   10.0   0.0   0.00026      0.59      98     123 ..     306     331 ..     265     376 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.88
                   Methyltransf_23  98 ppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkel 154
                                       + +++ ++ + ++p+++ +                   +v++ +++ f+  ++lk++
  gi|557693995|ref|YP_008797049.1| 116 VRSWVEKASRVMRPDAVSVY------------------DVDE-DVRAFYHPQTLKQI 153
                                       44444444444444433222..................2222.44444444444444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00026
                   Methyltransf_23  98 ppellrqiatllkpgGylllseplas 123
                                       + ++l+ ++++lkpgGy++l + +++
  gi|557693995|ref|YP_008797049.1| 306 MGRVLDEFFRMLKPGGYCVLVVGDVK 331
                                       5589***************9986554 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.9   8.7e+03     133     150 ..     112     129 ..     111     139 .. 0.79
   2 ?    4.2   0.0     0.015        34     109     128 ..     242     261 ..     217     278 .. 0.78
   3 ?    5.0   0.0    0.0086        19     139     181 ..     308     355 ..     297     385 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.9
                                       -SS-HHHHHHHHHHHEEE CS
                    Methyltransf_8 133 mgtnladflkeanrvlkv 150
                                       m  ++++ ++ a rv+++
  gi|557693995|ref|YP_008797049.1| 112 MFRDVRSWVEKASRVMRP 129
                                       667889999999999886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.015
                                       EES-TTS-S--TT-EEEEEE CS
                    Methyltransf_8 109 vacdlakvPledesvdvavf 128
                                          d + +P++desvd++v 
  gi|557693995|ref|YP_008797049.1| 242 FNMDASALPIADESVDLIVT 261
                                       5678899*********9996 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.0086
                                       HHHHHHHHHEEEEE..EEEEEEEGG...G-S-HHHHHHHHHCTTEEEE CS
                    Methyltransf_8 139 dflkeanrvlkvGG..llkvaevks...rfesvklfaraltklGfevk 181
                                         l e  r+lk+GG  +l v +vks   r+   +l+++  +k Gf  +
  gi|557693995|ref|YP_008797049.1| 308 RVLDEFFRMLKPGGycVLVVGDVKSggrRVDLAELLVEPAEKSGFTAR 355
                                       568899********4448899***977667778889999999999865 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.9   6.4e+03       7      20 ..      70      83 ..      65      91 .. 0.79
   2 ?   10.3   0.0   0.00021      0.46      62     113 ..     245     329 ..     237     371 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.9
                   Methyltransf_31  7 vlDlGCGtGeltfe 20
                                      vlD+ +G+G+  +e
  gi|557693995|ref|YP_008797049.1| 70 VLDPFSGKGTAPLE 83
                                      99******987665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00021
                   Methyltransf_31  62 dieeleklledekfDlilsn...................................evlnaladpdkileeiervlkp 103
                                       d+ +l+  ++de++Dli++                                    +v  ++ ++  +l e +r lkp
  gi|557693995|ref|YP_008797049.1| 245 DASALP--IADESVDLIVTSppylnlqtyawdnwlrlwflghdyrvvgkrlfatqSVKRYVEFMGRVLDEFFRMLKP 319
                                       677788..999********999999999999999999999999999998888887777******************* PP

                   Methyltransf_31 104 ggilliedpr 113
                                       gg++++   +
  gi|557693995|ref|YP_008797049.1| 320 GGYCVLVVGD 329
                                       ****987655 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 ?   10.4   0.0   0.00017      0.38       8      71 ..      55     121 ..      53     162 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                                       THHHHHCCS-..--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCH....SHHHHHH CS
                   MethyltransfD12   8 llpeIkelipkdkgktfvepFaGggaVffeakkqgkkvlinDinedlinlykalikn....nveelik 71 
                                       l+++ ++ +++ +g+ + +pF+G g   +ea   g   + nD+ ++ +++ +a++k     +v++ ++
  gi|557693995|ref|YP_008797049.1|  55 LARWVVTRFSE-RGDLVLDPFSGKGTAPLEACLTGRVGVGNDLAPEAYVVTRAKVKPamfrDVRSWVE 121
                                       89999*****9.8899*******99999999889******************9999865544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2967.53
//
Query:       gi|557693996|ref|YP_008797050.1|  [L=190]
Description: phosphoribosyl transferase domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-07   30.9   0.2    2.7e-07   30.3   0.2    1.2  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 !   30.3   0.2   1.5e-11   2.7e-07       9     116 ..      45     159 ..      40     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 1.5e-11
                                       --EEEEEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-.EE-EEEEEE-TTT--EE............. CS
                      Pribosyltran   9 paildavarlaaeileeyngkpdvvvgiargGvpfakiladeLevp.layvrkvkyrpdgseeaargssdes..... 79 
                                       +++++ +a+++a++l++      ++v+ +++G+p+++++a+ L+ p + + rk+++   + + +++     +     
  gi|557693996|ref|YP_008797050.1|  45 REFIAYCAKILADHLRD----CEILVTSESKGIPLVHEIASTLGHPrYIVCRKERKAFMKDPIIVTYR-P-Itsakd 115
                                       56777899999999999....899*******************8883445555555555555444332.2.246889 PP

                                       .......EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BS CS
                      Pribosyltran  80 .......rlledpagkkVliVDDildtGgTllaalelLkekgpe 116
                                              r  + ++gkkV iVDDi++t +T++a+ +++  +g  
  gi|557693996|ref|YP_008797050.1| 116 lelvidgRYVPYIKGKKVGIVDDIVSTKNTMEAMEKIVNLAGGI 159
                                       99999999************************987677666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1464.13
//
Query:       gi|557693997|ref|YP_008797051.1|  [L=93]
Description: hypothetical protein CSUB_C0561 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 785.22
//
Query:       gi|557693998|ref|YP_008797052.1|  [L=71]
Description: PilT protein domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       321  (0.017904); 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: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 601.43
//
Query:       gi|557693999|ref|YP_008797053.1|  [L=320]
Description: 2-dehydro-3-deoxygluconokinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-52  177.3   0.0    4.8e-52  177.1   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 !  177.1   0.0   2.7e-56   4.8e-52       3     301 ..       4     303 ..       2     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 177.1 bits;  conditional E-value: 2.7e-56
                                       EEEEEEEEEEEEEEECSSHTTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEE CS
                              PfkB   3 kvvviGealidliavseklegelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdt 79 
                                        vv +Ge li+l+av+ +    l +v  +e++ +Ga   vAv++ r+g d+ +i++vGdD+fG+ ++++ + egvd+
  gi|557693999|ref|YP_008797053.1|   4 TVVTLGESLIQLNAVTRG---PLRHVTLFERHVAGAETTVAVCVRRQGLDSGLITRVGDDEFGKCIINWVRGEGVDI 77 
                                       6999************99...888***************************************************** PP

                                       TTEEEESSSEEEEEEEEETTT.SEEEEEE.EEGGGGGHHHHHHHHHHHHHGCTSEEEEES...EECTTSHHHHHHHH CS
                              PfkB  80 dyvkidedtrtglalivvded.gertivf.nrgaaadltkeeleededlleeadllyisg...llsselpeavleel 151
                                       ++vkid++++tg++++        r+ +f +r  +a  + ++ + d d++++a+++++ g   +ls+  ++a++++l
  gi|557693999|ref|YP_008797053.1|  78 SHVKIDPEAPTGIYFVQRGFPiPARSKMFyYRTGSAGSRLSPEDIDPDYIGSAKVFHVTGitpALSETAKNATYKAL 154
                                       *******************99955555550565566666666669******************************** PP

                                       HHHHHHTTE..EEEEECESSSHH...HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEE CS
                              PfkB 152 aeaaknggt..fdpnlldplgaq...fkeallellaladllkpneeElealtgekledieealaalhklkakgaktv 223
                                       ++a +n  t  fd n+++ l++    ++++l+ +++++++l++  +++++l+g    d++ +++   +    g++ v
  gi|557693999|ref|YP_008797053.1| 155 EAAVSNDVTisFDTNIRPVLWKTnerAVKTLMPIIEKTNILFTDPTDASILLGTM--DQDTIIKTFLN---MGVDIV 226
                                       *********************99********************************..99999999877...9***** PP

                                       EEEEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCSC CS
                              PfkB 224 vvtlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiaslp 300
                                       v ++G++Gal++++++  ++ ++p v v D++GAGD+f+g f+ ++l+g sl ++l++a+ ++ lvv+ +g  ++lp
  gi|557693999|ref|YP_008797053.1| 227 VLKMGERGALAADRNNRAFAAPLP-VYVEDPIGAGDAFAGTFITSILKGRSLNKSLQRATIAGTLVVTVRGDEEALP 302
                                       **********************88.***********************************************99998 PP

                                       C CS
                              PfkB 301 t 301
                                       t
  gi|557693999|ref|YP_008797053.1| 303 T 303
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2689.17
//
Query:       gi|557694000|ref|YP_008797054.1|  [L=295]
Description: dihydrodipicolinate synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  177.1   0.0    3.6e-52  176.9   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 !  176.9   0.0     2e-56   3.6e-52       1     286 [.       5     287 ..       5     290 .. 0.97

  Alignments for each domain:
  == domain 1  score: 176.9 bits;  conditional E-value: 2e-56
                                       --SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE- CS
                             DHDPS   1 kfsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagv 77 
                                       kf+gi++al+tp        +e++++lief++++gv+g +v+GttGE   l  + +++++e ave a+ r  vi++v
  gi|557694000|ref|YP_008797054.1|   5 KFEGIVSALLTPSTA----YREKMAELIEFHLKHGVNGFFVLGTTGEGVKLGPSARQEVAEAAVEYAGSRGLVIIHV 77 
                                       588999999999655....589******************************************************* PP

                                       --SSHHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHT. CS
                             DHDPS  78 GsnstseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLae. 153
                                       G+  +++  +l+++a + Ga++v+av P+Y++  +  l ++++ i+   + pv++Yn p+r g ++ +e ++++ e 
  gi|557694000|ref|YP_008797054.1|  78 GASDMDTVKQLTRHASRIGAHAVSAVAPFYYRYDPDSLTSFYQSIADISSVPVLVYNNPGRQGYSIPLEGLQKILEt 154
                                       ***********************************************************************998877 PP

                                       STTEEEEEE-SS-CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHH CS
                             DHDPS 154 lenivgvKeavgdleevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaa 230
                                       ++  vg+Ke +gd +++ ++ k+ + +  + +G d+l+   + +G +  +s+ s i +e+++q+++ +k+G+l+ea 
  gi|557694000|ref|YP_008797054.1| 155 VKPTVGLKESSGDPDTLLQVFKRFKGSRFLGAGGDHLMVYSFIIGYRVHVSSLSSIYPEIAKQVFDCVKNGKLDEAL 231
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHCCCC.SCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHH CS
                             DHDPS 231 elnekllplikilfae.pnvilvktalellGlvveatlrkPltpleeeekeeleall 286
                                        l++ l+++ ++l++  p ++  ++al+l G++ +    +P   l+ eek++le+ll
  gi|557694000|ref|YP_008797054.1| 232 RLQTILNKVRAALKKIgPDMASNRYALKLRGIDIGG-PIPPTRDLTPEEKNTLENLL 287
                                       *************99989******************.9***************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2191.63
//
Query:       gi|557694001|ref|YP_008797055.1|  [L=258]
Description: 3-oxoacyl-[acyl-carrier protein] reductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-54  182.9   0.0    7.8e-54  182.7   0.0    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    5.6e-50  169.5   0.1    6.4e-50  169.3   0.1    1.0  1  adh_short     short chain dehydrogenase
    7.7e-11   42.2   0.0      1e-10   41.9   0.0    1.1  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 !  182.7   0.0   1.3e-57   7.8e-54       1     234 []      16     254 ..      16     254 .. 0.94

  Alignments for each domain:
  == domain 1  score: 182.7 bits;  conditional E-value: 1.3e-57
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilv 74 
                                       Ga +g Gr iA  +a+eG +vv+++ + ++ + ++++  e++g ++  +++DVt+ ++v+++ve++ ++fg +D+lv
  gi|557694001|ref|YP_008797055.1|  16 GAGRGFGRLIALGFAREGGNVVVHYNKSAEsALQTAKEIEQMGVRAytVKADVTKWDEVKQAVEKTWREFGPIDVLV 92 
                                       889**************************9988888888899988447***************************** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaale 149
                                       nn+g + + + +  e+++e +d++l+v++++++ +++++   +++++ g ivn+ s   + + p    y+a+K ++ 
  gi|557694001|ref|YP_008797055.1|  93 NNVGDTAPGQMSWREITEERIDHVLAVDIKGTLFMTHEVGSrMLERKkGVIVNICSNVITTGSPRAPQYAASKYGVL 169
                                       ****99999999****************************96555557***************************** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT.HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SE CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgikg.fdelleelearaplgrlgtpeevaeaalfLasdeasyitGq 225
                                       +lt++ A+ ++p  +RvNav+pg+++T++  + ++ +   ++++ +++pl+r+++pe++  ++lfLasd++  +tG+
  gi|557694001|ref|YP_008797055.1| 170 GLTKSYANAFAP-YVRVNAVAPGYMETESLLSRPDwTAGRRKWVIEHTPLRRIAKPEDIVPVVLFLASDDSIHMTGN 245
                                       ************.8***************7777774777888899******************************** PP

                                       EEEESTTGG CS
                      adh_short_C2 226 tlvvDgGlt 234
                                       +++ DgG++
  gi|557694001|ref|YP_008797055.1| 246 VVICDGGFS 254
                                       *******96 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.3   0.1   1.1e-53   6.4e-50       3     187 ..      12     198 ..      10     206 .. 0.95

  Alignments for each domain:
  == domain 1  score: 169.3 bits;  conditional E-value: 1.1e-53
                                       EEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                       v+vtGa++G+Gr ia  +a+eG +vvv +++s+e + ++ake+++ g +a+++++Dvt+++ev+++vek   ++g++
  gi|557694001|ref|YP_008797055.1|  12 VFVTGAGRGFGRLIALGFAREGGNVVVhYNKSAESALQTAKEIEQMGVRAYTVKADVTKWDEVKQAVEKTWREFGPI 88 
                                       89*************************************************************************** PP

                                       SEEEE---S..S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  79 dvLvnNAGi..tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                       dvLvnN+G    g+ +  e++ee+++ v++v ++g++ +t++v   ml++++G Ivn++S++   +++  + Y+AsK
  gi|557694001|ref|YP_008797055.1|  89 DVLVNNVGDtaPGQMSWREITEERIDHVLAVDIKGTLFMTHEVGSRMLERKKGVIVNICSNVITTGSPRAPQYAASK 165
                                       *********544555667*********************************************************** PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHH CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdma 187
                                        +v glt+s a+ +ap+ +rvnavaPG+++T+  
  gi|557694001|ref|YP_008797055.1| 166 YGVLGLTKSYANAFAPY-VRVNAVAPGYMETESL 198
                                       ****************9.*************976 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   1.7e-14     1e-10       4     152 ..      13     164 ..      11     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 1.7e-14
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       ++tG+  g+G+ +a   a++g + +v   +s    e++ ++ +e+e++g++  +v+aDv++ d+v++++e+  +e++
  gi|557694001|ref|YP_008797055.1|  13 FVTGAGRGFGRLIALGFAREGGNVVVHYNKS---AESALQTAKEIEQMGVRAYTVKADVTKWDEVKQAVEKTWREFG 86 
                                       79**************************999...34556689*********************************** PP

                                       ---EEEE---------T..TT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHH CS
                                KR  81 pikGvihaAgvlrdkll..eemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaa 151
                                       pi   ++  g ++ +++   e t+e++++vla  +kG+  + + + +    ++  ++v + S   ++gs+   +Yaa
  gi|557694001|ref|YP_008797055.1|  87 PIDVLVNNVGDTAPGQMswREITEERIDHVLAVDIKGTLFMTHEVGSrmleRKKGVIVNICSNVITTGSPRAPQYAA 163
                                       *********999866652279*****************998766655355466678999999999999999999998 PP

                                       H CS
                                KR 152 a 152
                                        
  gi|557694001|ref|YP_008797055.1| 164 S 164
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1887.91
//
Query:       gi|557694002|ref|YP_008797056.1|  [L=429]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   43.8   0.1    5.8e-11   42.5   0.1    1.7  1  Peptidase_M20  Peptidase family M20/M25/M40
    7.5e-10   38.7   0.0    1.3e-09   37.9   0.0    1.4  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 !   42.5   0.1   6.5e-15   5.8e-11       2     180 ..      79     383 ..      78     407 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 6.5e-15
                                       EEEES-BSS.TTCG.GGSSS...TTSEE.....ETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEE CS
                                       xxxxxxxxx.xxxx.xxxxx...xxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVp.eeet.dgwtt...pfslt.....eedGklyGrGaddmkggvlaalealralkdegikpkgtivllfq 68 
                                       +++HlD+   + e  +  +     ++l+      e + lyG G+  mkg ++a++ a++al+ +g+++kg+i+++ +
  gi|557694002|ref|YP_008797056.1|  79 FNGHLDTSFsPREPaEILKAispVYRLEppwayREGDWLYGMGVFNMKGALAAYVSAVEALQNAGVELKGDIMIAGV 155
                                       6777777776555523333344233444667744556**************************************** PP

                                       STT.SSTT..............THHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE............... CS
                                       xxx.xxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                     Peptidase_M20  69 pdE.Eggr..............gGakallegleerekvdavfelhieepgileagklaigvv............... 115
                                       + E E                  G+++l+       +v   f ++++ep++l         +               
  gi|557694002|ref|YP_008797056.1| 156 VGEiEK-TqvdqyrgaqyrgygTGTAYLVT----HGGVTD-F-AILGEPTGLRLML-----Thfgsvwakmylkgqm 220
                                       ***554.24778866667666666677777....344444.3.4689999999433.....344566********** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|557694002|ref|YP_008797056.1| 221 vhtahstgvtnlilrmnrvlnvleewipkyqerfshqgvkptvnigsieggwpwrcsrtpwfcnlyvdlrypppysa 297
                                       ***************************************************************************** PP

                                       ....................EEEEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH..TTT CS
                                       ....................xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                     Peptidase_M20 116 ....................kvevelleggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff..agi 169
                                                           k  ++ + + a +t++ ds++vka+ e  +++fg   e++v +  ++da+ +  +g+
  gi|557694002|ref|YP_008797056.1| 298 vdvkealeemlnevekrygfKPMLDIYVSDAWATVPeDSAVVKAIDEGHKAVFGTPAERVVFS-WSSDANVLtrNGV 373
                                       ***************97777444444467777777789****************9999999**.********88888 PP

                                       EEEEEEESSGG CS
                                       xxxxxxxxxxx RF
                     Peptidase_M20 170 ptvmifgpgsg 180
                                         ++ +gp++g
  gi|557694002|ref|YP_008797056.1| 374 -VAVNYGPSGG 383
                                       .6667998743 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   1.5e-13   1.3e-09       2     108 ..     205     315 ..     204     316 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 1.5e-13
                                       EB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC........TCCTCCCCCEECCE-C..CCCEES CS
                         M20_dimer   2 ghkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia...eerslprttlnvtgiegGs..aknvip 73 
                                        h+G++++k+  kg+++H +    + N i  + r+l+ le+   ++     +++  ++t+n+++iegG       +p
  gi|557694002|ref|YP_008797056.1| 205 THFGSVWAKMYLKGQMVHTAHSTGVTNLILRMNRVLNVLEEW-IPKYqerFSHQGVKPTVNIGSIEGGWpwRCSRTP 280
                                       69******************888888*************997.33336888889999*************9999*** PP

                                       SEEEEEEEEEHHHHHHHHHHHHHHHHHHTSCCSTT CS
                         M20_dimer  74 deaeakidiRllpgedpeevleeieeilekeaped 108
                                         + +++d+R +p  ++ +v+e++ee+l+++ +++
  gi|557694002|ref|YP_008797056.1| 281 WFCNLYVDLRYPPPYSAVDVKEALEEMLNEVEKRY 315
                                       *****************************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3077.99
//
Query:       gi|557694003|ref|YP_008797057.1|  [L=779]
Description: molybdenum hydroxylase family protein, large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-184  612.5   0.0   7.3e-184  612.3   0.0    1.0  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    2.7e-20   72.8   0.0      5e-20   71.9   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 !  612.3   0.0  8.2e-188  7.3e-184       3     549 ..     148     710 ..     146     711 .. 0.95

  Alignments for each domain:
  == domain 1  score: 612.3 bits;  conditional E-value: 8.2e-188
                                       TT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHH CS
                     Ald_Xan_dh_C2   3 eeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvae 77 
                                       ee +dn+++  +++ Gdveaafa+ad v+++++ ++r +++++E ++++a++d++ geltv+ stq ph +++++++
  gi|557694003|ref|YP_008797057.1| 148 EEWGDNIIMnySFKAGDVEAAFASADLVLQRRYVNQRYAPTPIEGRGVVADFDKSRGELTVWDSTQFPHVLQTYLSQ 224
                                       668899999788889************************************************************** PP

                                       HHT--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-E CS
                     Ald_Xan_dh_C2  78 vlglpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGki 154
                                       +l+ pen++rvi+p+vGGGFG K+ ++p+ev    +A+k+grpVk+v++R+e+ml  g+++++ +++++++++dGk+
  gi|557694003|ref|YP_008797057.1| 225 ALNYPENRIRVIAPDVGGGFGPKSSVWPEEVSTIQLAMKLGRPVKWVETRSEHMLVCGHERQQVHYVEAAFKRDGKL 301
                                       ***************************************************************************** PP

                                       EEEEEEEEEEESST.HHHCHCC.HCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 155 taldvdlladaGay.adlspav.leralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelA 229
                                       +a++ +++ad G y a ++++  ++ +++ + gpY+++++++e+ +v tN++p ++ RGfG+p a+f++Erlm+++A
  gi|557694003|ref|YP_008797057.1| 302 LAIRDKVIADIGVYgAFWTETQpVMVTMAAIPGPYRFDAYQYEVFCVATNKAPYSPHRGFGRPVAAFVMERLMNDAA 378
                                       **************533333331346788888********************************************* PP

                                       HHHT--HHHHHHHHBCECGCC.SEEET...EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEE CS
                     Ald_Xan_dh_C2 230 eelgldplelRrrNlikpgeltpygqp...vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvveg 303
                                       + lg+dp+e+RrrNli ++++ p+++    vydsgd+p++l+++++ ++y+++r+ qae++++++ +Gig+a++ve 
  gi|557694003|ref|YP_008797057.1| 379 ANLGIDPVEIRRRNLIPAEAM-PFKNIhniVYDSGDYPKALEEALKLAQYDRLRRMQAEARKQGRLIGIGIAMYVEY 454
                                       ****************99999.*9997788*******************************98899*********** PP

                                       BS--S.EETTEE.........EEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS CS
                     Ald_Xan_dh_C2 304 iglgftakflnq.........egalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvp 371
                                       ++ ++  ++l++         ++a+vr++++G+v+v tg++++GqG++t++aq+aa+ Lgv+++dv+v egd++++p
  gi|557694003|ref|YP_008797057.1| 455 TTPSS--ERLDKglgwevggyDSATVRIEPEGKVVVLTGTASQGQGHYTVYAQLAADYLGVNMDDVTVFEGDSKTCP 529
                                       *5555..345555778999999******************************************************* PP

                                       ----S-TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH..... CS
                     Ald_Xan_dh_C2 372 ngsgtaaSrstdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl..... 440
                                       +g g++aSrst+ +g+A+ kA+e+l ++++ iaa++le+sped+e +dgk++vk   +k+v++a++a+ a++     
  gi|557694003|ref|YP_008797057.1| 530 YGFGAWASRSTVAVGGAIIKACETLLAKVKHIAAHMLEASPEDIEASDGKLYVKgspDKYVTFADVAKIAWRqptrl 606
                                       **********************************************************************99999** PP

                                       ...TTSSEEEEEEE...EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 441 ...ervslsatgfyktldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfv 514
                                          ++++l+at++y        + ++f + +y++++ +Ve+D+etg++kvl++ i +D G+++Np + +gQi+G+++
  gi|557694003|ref|YP_008797057.1| 607 ppdTEPGLEATAHY--------EPKAFTTCSYAVHIPVVEIDPETGQMKVLEYHIFDDSGRVLNPLTLYGQIHGALA 675
                                       **99**********........588999************************************************* PP

                                       HHHHHHHT---EEETTTEESS-STTTS----GGGS CS
                     Ald_Xan_dh_C2 515 qGiGlalmEelvydedGqlltasladYkiPtaadi 549
                                       +G+G a++Eelvyde+Gqllt+++adY+iP+a ++
  gi|557694003|ref|YP_008797057.1| 676 HGVGGAIYEELVYDENGQLLTSTFADYLIPSAVEM 710
                                       *******************************9886 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 !   71.9   0.0   5.5e-24     5e-20       1     110 []      20     130 ..      20     130 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 5.5e-24
                                       TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT.TSSS-EEEESS-SSE CS
                      Ald_Xan_dh_C   1 tGeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig.siledeedallaedk 76 
                                       tG+++YvdDi++p+++y+ fvrS++ah++ivsid s+a+++p +va +  ++ +   + ++ + l+d ++  la+ k
  gi|557694003|ref|YP_008797057.1|  20 TGRGRYVDDIKLPNMVYAGFVRSPYAHGRIVSIDLSEAQKHPDFVAALLPEEAAPLPSWMKyKGLRDVPRFSLARGK 96 
                                       8*******************************************9999999988887766667788888999***** PP

                                       ESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                      Ald_Xan_dh_C  77 vrsvgqavaavvAedeetArkAaklvkveYeelp 110
                                       vr+vg++v  v+ +d++  ++ ++lv+ve ++lp
  gi|557694003|ref|YP_008797057.1|  97 VRFVGEPVVGVAVKDRYSVEEVVSLVNVEIQPLP 130
                                       *****************************88875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 5268.14
//
Query:       gi|557694004|ref|YP_008797058.1|  [L=396]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   90.5   1.5    1.4e-25   89.3   0.2    2.0  2  PyrI          Aspartate carbamoyltransferase regulatory chain
    1.6e-09   37.5   0.0    2.9e-09   36.6   0.0    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
    2.3e-06   27.2   0.1    3.8e-06   26.5   0.1    1.2  1  PRTase_2      Phosphoribosyl transferase
     0.0064   16.4   0.5      0.013   15.4   0.5    1.5  1  PyrI_C        Aspartate carbamoyltransferase regulatory chain
  ------ inclusion threshold ------
      0.043   13.3   0.1       0.07   12.6   0.1    1.3  1  UPRTase       Uracil phosphoribosyltransferase


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 !   89.3   0.2   3.9e-29   1.4e-25       2      93 ..       9      97 ..       8      98 .. 0.95
   2 ?   -0.3   0.1      0.36   1.3e+03      19      50 ..     308     339 ..     297     354 .. 0.75

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 3.9e-29
                                      -----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EEE CS
                              PyrI  2 kvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnatin 80
                                       v+kie+G+ViDHI+  k++ ++++L+ d   s  + +i+knv+s+klg+Kd++kieg++++++ ++++ali+p+atin
  gi|557694004|ref|YP_008797058.1|  9 LVQKIERGVVIDHIAPCKGFLIYSILNPDP-GS--TAVIAKNVPSTKLGRKDLVKIEGEYITSSLVNVIALISPTATIN 84
                                      69***************************7.33..479***************************************** PP

                                      EEETTEEEEEE-- CS
                              PyrI 81 iIkdgevveKkkv 93
                                      iI d +v +K++v
  gi|557694004|ref|YP_008797058.1| 85 IIADWSVKSKERV 97
                                      **********998 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.36
                                       -HHHHHHHCT--T...TS-EEEEEEEEETTTE CS
                              PyrI  19 kalkvlklLkldklkseekvaiiknvkskklg 50 
                                         +kv ++ kld+l s++ va++  v+ +++ 
  gi|557694004|ref|YP_008797058.1| 308 GRTKVASIKKLDSLGSHRVVAVVVAVDRQETS 339
                                       45789999999999999999999998887765 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   8.1e-13   2.9e-09      19     141 ..     228     350 ..     216     356 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 8.1e-13
                                       TEEEEEE--GGGEEEEEEETTTHHHHHHHHHHS......TT-EE-EEEEEE-TTT--EE........EE----TTSE CS
                      Pribosyltran  19 aaeileeyngkpdvvvgiargGvpfakiladeL......evplayvrkvkyrpdgseeaargssdesrlledpagkk 89 
                                       ++e + e     d v+g+a++G+ +a+ +   L      + ++ y rk+ ++ ++       ++     +    g+k
  gi|557694004|ref|YP_008797058.1| 228 LKENILE---DFDFVFGPAYKGINLASLVCEGLkeyygiNKRFLYDRKEVKEYGDVRMDGS-IVG---SEYFQPGQK 297
                                       3333333...79*********************9999998889999887666666555532.232...456678*** PP

                                       EEEE-SEESSSHHHHHHHHHHHCC-BS.EEEEEEEEE-HHHHHHHHHH-TTS. CS
                      Pribosyltran  90 VliVDDildtGgTllaalelLkekgpe.evriavlvdkpateeevdknakrvf 141
                                       +liVDD ++tG+T  a ++ L + g + +v ++v vd+ +t ee+  +a++++
  gi|557694004|ref|YP_008797058.1| 298 ILIVDDTVTTGRTKVASIKKLDSLGSHrVVAVVVAVDRQETSEEEGISAVEYL 350
                                       ***************************77888888899999999887777665 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1   1.1e-09   3.8e-06     116     184 ..     290     361 ..     285     366 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.1e-09
                          PRTase_2 116 ellaaakelvLvDDEistGktalnliralqeklprkryvvvslvdwrseedea...afaaleeelgirievv 184
                                       e ++  +++++vDD ++tG+t ++ i++l +   ++ ++vv  vd +++++e+   a++ le+ lg+r++ +
  gi|557694004|ref|YP_008797058.1| 290 EYFQPGQKILIVDDTVTTGRTKVASIKKLDSLGSHRVVAVVVAVDRQETSEEEgisAVEYLEKTLGVRVHPI 361
                                       6788899****************************9999999999988776652226778899999999876 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 !   15.4   0.5   3.5e-06     0.013       1      45 [.     102     148 ..     102     151 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.5e-06
                                       EEESSS--S-TTBGGGTTS-.-EEEE....EETTTTEEEETTT--EEEH CS
                            PyrI_C   1 eiegvlkCpNpnCItnnepveskFkv....edkekvklkCkYCekeise 45 
                                       e+ gv+ C+Np C ++    +s+F+v    e+ e ++lkC  C+ ++ +
  gi|557694004|ref|YP_008797058.1| 102 EVVGVIDCRNPLCSSKGP--NSRFYVnlntENLELTTLKCGSCGYVYYY 148
                                       699**********88775..6899998544456678899*999987765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   1.9e-05      0.07     122     160 ..     296     332 ..     285     376 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                           UPRTase 122 rtvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvl 160
                                       +++l++D ++ TG++ +a i++L + g   ++++ + v 
  gi|557694004|ref|YP_008797058.1| 296 QKILIVDDTVTTGRTKVASIKKLDSLGS--HRVVAVVVA 332
                                       679**********************664..566655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2894.32
//
Query:       gi|557694005|ref|YP_008797059.1|  [L=262]
Description: orotidine-5'-phosphate decarboxylase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-22   79.6   0.0      3e-22   79.3   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 !   79.3   0.0   1.7e-26     3e-22       2     222 ..      19     243 ..      18     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.7e-26
                                       EEEEEE-SSSH.........HHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-H CS
                         OMPdecase   2 nLclalDvata.........relleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIG 69 
                                        +cl+lD+            r +l ++d v+p+i+ +K++ ++v +++ +    +l +++r  g   + D K++DI 
  gi|557694005|ref|YP_008797059.1|  19 VICLGLDPNPDlhpqtteklRFCLNMVDAVEPYIAAVKVNENFVRDFSLA-DHRRLTEKIRGVGLVSIYDCKMCDID 94 
                                       589****9999999999999999**********************99966.6799********************** PP

                                       HHHHHHHHSTCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH...H...SHHHHHH CS
                         OMPdecase  70 ntvekqatagsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqe...k...gytqacv 140
                                       ntv++ ++     ++ + d++t ++v+  ++++ +++   +++  g+++l   s++++ +  +   +   +++++++
  gi|557694005|ref|YP_008797059.1|  95 NTVKAGIK---LVSEMGYDFITFNPVM--GTLSTAVKHGSANN-VGIIVLLHPSNPESSKYFRaklDdgrKVYEKIL 165
                                       *******9...679*************..78999999999996.9*************998888552689******* PP

                                       HHHHHHHHHTTESEEECCCHTH...HHHHH.TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHH CS
                         OMPdecase 141 eaarehkaedfvmGfvaqetln...ateed.addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIl 213
                                       ++  e+ ae  v+G+    +++   a +e  +d  i+l pg+g+ qggd   +   t+ k+ g   a +i++GR+I+
  gi|557694005|ref|YP_008797059.1| 166 DEFVENDAEGVVVGLHPELNEAdvrAVREViGDGKIVLFPGVGA-QGGD---LA--TAVKAGG--SAILINIGRSII 234
                                       *********9999999888888886555559************8.4444...44..2333333..367899****** PP

                                       TSSSHHHHH CS
                         OMPdecase 214 kagdpveea 222
                                        +++p++++
  gi|557694005|ref|YP_008797059.1| 235 YSSNPRQAV 243
                                       ******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1869.47
//
Query:       gi|557694006|ref|YP_008797060.1|  [L=525]
Description: 1-pyrroline-5-carboxylate dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-141  470.2   0.0     7e-141  469.9   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
  ------ inclusion threshold ------
      0.017   14.7   1.6      0.041   13.5   1.6    1.6  1  SPW       SPW repeat


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 !  469.9   0.0  7.8e-145    7e-141       5     458 ..      49     516 ..      46     519 .. 0.96

  Alignments for each domain:
  == domain 1  score: 469.9 bits;  conditional E-value: 7.8e-145
                                       SSSEEEEEETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH- CS
                            Aldedh   5 esetievinPa.tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletG 80 
                                       e++++e+ +P+ t+ v++ +++++a ++++a+a+Ak+ f++wa+++++eR +++r+aa+l+ erk e+a+++t e+G
  gi|557694006|ref|YP_008797060.1|  49 EKGEFETRSPIdTSVVVGYFQKGDAGHMRQAIAEAKKRFREWADTDWRERVRVMRRAAQLIDERKFEIAAVITYEAG 125
                                       44679******8899999*********************************************************** PP

                                       --HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEE.C..TTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT CS
                            Aldedh  81 kplaearaeveeaidvlryyaelaeklegevlps.s..egklalvrrePlGvvgaItPWNfPlllaawklapalaaG 154
                                       k+  ea ae  eaid l+yya+ +ek +g  +++    +g+++ ++ +P+Gv+++I+P+NfP++la ++++ al++G
  gi|557694006|ref|YP_008797060.1| 126 KNRLEALAEAWEAIDALKYYAQVMEKNNGYEMEMgPggPGEQCRMVARPYGVWVVISPFNFPFMLANGMMLGALITG 202
                                       *****************************888885588*************************************** PP

                                       -EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTT.. CS
                            Aldedh 155 NtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknl.. 229
                                       Ntvv+KP++etpls l+l ++f +ag+P+g++n+vtg+gs + +++v++p+v+ ++ftGs +vg++++++ +++   
  gi|557694006|ref|YP_008797060.1| 203 NTVVFKPTSETPLSGLMLYRVFVDAGVPPGAINYVTGPGSAFEDEIVSNPDVAGIAFTGSKDVGMRLYRRFTSSQpy 279
                                       **********************************************************************6644334 PP

                                       .SEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT CS
                            Aldedh 230 .krvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdplded 305
                                        k+++lE+G+knp+iv+++aD+ kav ++v++afg+ GQ+C+a+sr++vq+++ ++f+++lv++++++k+gdp+ ++
  gi|557694006|ref|YP_008797060.1| 280 pKPILLEMGSKNPTIVTKNADIGKAVLGVVRAAFGYGGQKCSATSRVYVQREVKNRFLDELVKETSRIKIGDPRLRE 356
                                       5**************************************************************************** PP

                                       -SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEES CS
                            Aldedh 306 tdvGPliseaqlekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfk 381
                                       + +GP+i+++++e++++y+++a+ +g ++++Gge       +kgy+v+Pt++++++++++++++E+F P+l v +f+
  gi|557694006|ref|YP_008797060.1| 357 VFLGPVINKRAVENFRSYIDTARRDGGEIVYGGEvLGGGLFDKGYYVQPTIIDKLPRSHPLFKQELFLPILLVAEFD 433
                                       **********************************9778999************************************ PP

                                       SHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSS...ST--TTT.SEB--CGGGEES..-BSHHHH CS
                            Aldedh 382 deeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNds...ttgaaea.lpfgGvkqSglG..reggkeg 452
                                       ++eea++ aN+teyGL+ag+f++d++++e++ +++e+G  y N++   ttga    + f G+k+Sg      gg+++
  gi|557694006|ref|YP_008797060.1| 434 TLEEALREANNTEYGLTAGIFSEDPREVEYFFNNIEFGVTYANRKggaTTGAWPGaQTFVGWKASGATgkGVGGPHY 510
                                       ********************************************988899999999**********65344555998 PP

                                       HHHTEE CS
                            Aldedh 453 leeyte 458
                                       l  +++
  gi|557694006|ref|YP_008797060.1| 511 LLTFLR 516
                                       888875 PP

>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.6   4.6e-06     0.041       8      38 ..     176     206 ..     174     207 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.6e-06
                               SPW   8 GlwlivSPWvlGfsattgaawnnvivGavva 38 
                                       G+w+++SP+ + f    g+++ ++i+G  v+
  gi|557694006|ref|YP_008797060.1| 176 GVWVVISPFNFPFMLANGMMLGALITGNTVV 206
                                       9**************************8887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3712.18
//
Query:       gi|557694007|ref|YP_008797061.1|  [L=333]
Description: coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-54  185.2   0.0    2.4e-54  184.9   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
      0.035   14.2   0.0      0.079   13.0   0.0    1.5  1  Rsbr_N          Rsbr N terminal


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.9   0.0   2.7e-58   2.4e-54      18     312 ..      13     312 ..       5     314 .. 0.88

  Alignments for each domain:
  == domain 1  score: 184.9 bits;  conditional E-value: 2.7e-58
                    Bac_luciferase  18 asaslrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLd 94 
                                       +s+++r++  +a++aE+lGfd+v+++e+++ +   +da+t+l+  a   e+  lg + ++ + r+P+vlAq++atLd
  gi|557694007|ref|YP_008797061.1|  13 PSMTVREMTLYAKKAEQLGFDMVFFSETLQTF---RDAVTTLTSFALTVEKPLLGCTQVVRL-RSPLVLAQTFATLD 85 
                                       447899***********************987...***********9999999999999999.************** PP

                    Bac_luciferase  95 hlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsv..kgalllprpgqgpiPv 169
                                       +lsgGR++l lg+   ++  +++G++++++ + l E+++++++l++ e++++e ++f++   g+  +p      iPv
  gi|557694007|ref|YP_008797061.1|  86 ELSGGRVVLSLGACTKQHM-AKHGLEYADPAETLIEYITLFKKLLTNEKITYESKHFRLseSGLGFKPLR--SNIPV 159
                                       *******************.99***********************99************65555555544..559** PP

                    Bac_luciferase 170 yvaaaspaglelaarhadglllag.eppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearali 245
                                       +vaa+s +gl++a+++adg+ll+   + e  + +++ +r++a+e grdp++++++  + ++v++   +++  +r+  
  gi|557694007|ref|YP_008797061.1| 160 WVAATSAKGLRIAGEYADGVLLNAtTSVEYCRNAVKIVRKAAEEKGRDPDELQIAGLIVTAVDAEKPAVEYVRREVA 236
                                       ********************************************************999999965544444444444 PP

                    Bac_luciferase 246 agld.......fyaldsegagreaeaa..eiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagv 312
                                       ++l        +++   +g  + +++   +  e+++a+++ + ++ +p e+++++++vGt+e+v+ ++++y+eagv
  gi|557694007|ref|YP_008797061.1| 237 SKLSplmvdfaMKPRLKVGEPYITPQLieKMLEAYNAGGFGKLMSEIPVEVLKGLTAVGTAEEVRRKIDQYREAGV 312
                                       444456688888888888888777665435589999***************************************9 PP

>> Rsbr_N  Rsbr N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.8e-06     0.079      57      90 ..      18      51 ..      12      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.8e-06
                                      HHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHH CS
                            Rsbr_N 57 ekleefaerlvqlGwpLkyltkgLqefrkvvlel 90
                                      ++++ +a+++ qlG  + ++++ Lq+fr++v++l
  gi|557694007|ref|YP_008797061.1| 18 REMTLYAKKAEQLGFDMVFFSETLQTFRDAVTTL 51
                                      578899***********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2525.57
//
Query:       gi|557694008|ref|YP_008797062.1|  [L=415]
Description: branched-chain amino acid ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-61  208.0   0.0    3.8e-61  207.7   0.0    1.0  1  Peripla_BP_6  Periplasmic binding protein
    1.2e-15   57.4   0.2    3.6e-15   55.8   0.2    1.7  1  Peripla_BP_5  Periplasmic binding protein domain
    1.6e-12   47.2   0.0    2.3e-12   46.7   0.0    1.1  1  ANF_receptor  Receptor family ligand binding region
  ------ inclusion threshold ------
       0.11   12.2   0.0       0.11   12.2   0.0    1.7  2  PAP2          PAP2 superfamily


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.7   0.0   8.4e-65   3.8e-61       2     342 .]      42     394 ..      41     394 .. 0.93

  Alignments for each domain:
  == domain 1  score: 207.7 bits;  conditional E-value: 8.4e-65
                                       EEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEET....TE..EEEEEEEE-TTSHHHHHHHHHHHHHCT--SE CS
                      Peripla_BP_6   2 ikiGlltplsGpyassgksllagaqaafeeiNaaGGin....Gr..kielverDdaydpdraaeaarrlvdqdgvda 72 
                                       + iG+  + sG++a  g+ +l g++++ ++iN +GGi+     +  k+el  +Dd+++ d+ ++ +++l+++d+vd+
  gi|557694008|ref|YP_008797062.1|  42 LVIGFSISISGDFAVPGRKQLEGIELWKDWINSKGGIYvkdqNKyyKVELKYYDDKSSKDEVIRLYEKLINEDKVDI 118
                                       67************************************87552277******************************* PP

                                       EEE-BSHHHHHHHHHHHHHHT-EEEESS-HHC...CTTSTTEEESS--HHHHHHHHHHHHHHHTTSCEEEEEEESSH CS
                      Peripla_BP_6  73 lvgplssavaaavaevlakdgvpvigpagltg...ekcspyvfslgpsysaqasalveylakelggkkvalvyadya 146
                                       l+ p ss  a+ +a +++k g +++ ++++++   ++++ +++ ++  +s +++ +++ l++++ + +va++  d+a
  gi|557694008|ref|YP_008797062.1| 119 LLSPYSSTLALTAAGITEKYGRLMVVVGANSDtifKQGYKNIVGTYTPASKMLTQAIDILLEKVQNPSVAIIFKDDA 195
                                       ************************998877763336***************************************** PP

                                       HHHHHHHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEEEE CS
                      Peripla_BP_6 147 fgregiaalkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakrillv 223
                                       f +++++++ka+a+++G++vv+ e +p ++ d+s+++++ik  ++da+l++g  +d + l+++a+e G++ k + l+
  gi|557694008|ref|YP_008797062.1| 196 FAKSVAEGAKAYAEQKGVNVVAFEMYPRDAKDLSPILTKIKGLNVDAILGGGHYEDEVLLVRQAKELGINVKLMSLL 272
                                       **********************************************************************7755555 PP

                                       CCC-CHHHHHHHHHHHHTTEEEEESCSTC.....CCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHC CS
                      Peripla_BP_6 224 swsgseedlkalggeaaegvlavtpyfpd.....ldnpavrafvaayeaayggapppsqfaaggyiaadlllealka 295
                                        +   ++   al++   eg+la++ + p+     + +p+ ++f++++++++  +  ps+++a++++a++++++a+++
  gi|557694008|ref|YP_008797062.1| 273 VSPSLPAFYDALKE-TSEGILAPSHWEPQtkpkiTYGPTIDEFMTQFRQKWNSE--PSYHSAAAFAAGLYITAAIEK 346
                                       44455555566665.899**********96666656888**************8..********************* PP

                                       CTHCCHHHHHHHHHHS-BECCCTCCBEE.CTTSBEE--EEEEEE-TSS CS
                      Peripla_BP_6 296 agsltreavraaleslgfdgllgplkft.aedhqasrpvyvvqvdggk 342
                                       ag+l+ +++raa++ l++++++g+lk++ a+ +q+++ + ++q++ggk
  gi|557694008|ref|YP_008797062.1| 347 AGTLDNAKLRAAFNDLDITTFYGRLKIDpATGNQVGHELVLLQWQGGK 394
                                       ****************************677889***********996 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.2   7.9e-19   3.6e-15       3     350 ..      44     402 ..      42     413 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 7.9e-19
                      Peripla_BP_5   3 vGvLhSlsGtmaisekslkdaallaieeinaagGvlg......rkieavvvdpasdwelfaekaeklieedkvevvf 73 
                                       +G   S sG  a+  +++++++ l  + in++gG+         k+e   +d +s  +   +  ekli+edkv++++
  gi|557694008|ref|YP_008797062.1|  44 IGFSISISGDFAVPGRKQLEGIELWKDWINSKGGIYVkdqnkyYKVELKYYDDKSSKDEVIRLYEKLINEDKVDILL 120
                                       677789****************************98533333368******************************** PP

                      Peripla_BP_5  74 GcwtSasRkavlpvveelnalLfYpvqYEG...eEssknviYtGaapnqqaipavdyllselgakrvflvGsdyvyp 147
                                         + S+   +   + e+  +l+           +   kn++ t   + + +++a+d ll++  +  v+++  d  ++
  gi|557694008|ref|YP_008797062.1| 121 SPYSSTLALTAAGITEKYGRLMVVVGANSDtifKQGYKNIVGTYTPASKMLTQAIDILLEKVQNPSVAIIFKDDAFA 197
                                       *********************98754443311134568***99999999**************9************* PP

                      Peripla_BP_5 148 retnrilkallkakggevvgeeYlplgssdvqkivakikkakpdvvlstinGdsnvafykelkeagikaekipvvsl 224
                                       +++++ +ka+ ++kg++vv+ e  p +++d++ i++kik  + d++l     +  v + ++ ke gi+ + +  + +
  gi|557694008|ref|YP_008797062.1| 198 KSVAEGAKAYAEQKGVNVVAFEMYPRDAKDLSPILTKIKGLNVDAILGGGHYEDEVLLVRQAKELGINVKLMSLL-V 273
                                       ********************9999*******************************************98877654.3 PP

                      Peripla_BP_5 225 svaeeelaaidaealvGhlaawnYf.....qsvdtpenkafvakfkarvgedrvtndpmeaayiqvklwaqAvekag 296
                                       s +   + +  +e+ +G la + +      +    p+ ++f+++f+++ +++   + +  aa+ +   +++A+ekag
  gi|557694008|ref|YP_008797062.1| 274 SPSLPAFYDALKETSEGILAPSHWEpqtkpKITYGPTIDEFMTQFRQKWNSEP--SYHSAAAFAAGLYITAAIEKAG 348
                                       33344555555667777776666541011033446777888888888777765..4566788888888899****** PP

                      Peripla_BP_5 297 stdvekvreallgqelkapeGevkidpenhhlsktvrigkikadGqfeivwetk 350
                                       + d +k+r+a  +  +++  G++kidp++   +    +    + G+ ++vw  +
  gi|557694008|ref|YP_008797062.1| 349 TLDNAKLRAAFNDLDITTFYGRLKIDPATGNQVGHELVLLQWQGGKKQVVWPRE 402
                                       ***************************998888777777777888888888655 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 !   46.7   0.0     5e-16   2.3e-12      23     351 ..      87     391 ..      70     394 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 5e-16
                                       EEEEEEEEE-TT-HHHHHHHHHHHCCC.CEEEEEE-SSHHHHHHHHHHHCCTT-EEEESS---GG.GG-TTTTTTE. CS
                      ANF_receptor  23 iklgyeiidtccdfslaleaaldflkg.kvvaviGpssssvsdavaslanlfkiPvisygstspe.lsdknryptf. 96 
                                       +k++++  d++++   + +   ++++  kv++++ p+ss  + ++a +++++   ++ +g+ s++ ++    y+ + 
  gi|557694008|ref|YP_008797062.1|  87 YKVELKYYDDKSSKDEVIRLYEKLINEdKVDILLSPYSSTLALTAAGITEKYGRLMVVVGANSDTiFKQ--GYKNIv 161
                                       47788888999999999999999999856********************************99996655..555553 PP

                                       EESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEESTCHHHCHHHHHHHHHH CS
                      ANF_receptor  97 lrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqaleeeleergicvalkekipessnddevvrkllkei 173
                                        + +p ++++ qAi  +l++ +  +va+i  dd+  +s+++  +  +e++g++v+  e++p   +d ++++++l++i
  gi|557694008|ref|YP_008797062.1| 162 GTYTPASKMLTQAIDILLEKVQNPSVAIIFKDDAFAKSVAEGAKAYAEQKGVNVVAFEMYP---RDAKDLSPILTKI 235
                                       77789999*****************************************************...8999999999999 PP

                                       TT.T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC.......HHHHHTT-EEEEE..... CS
                      ANF_receptor 174 ks.karvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpe.....ltgleaaegvlgfrl..... 239
                                       k  + ++i+   + ed   l+++a++lg++ +    ++s            +     +   e+ eg+l  +      
  gi|557694008|ref|YP_008797062.1| 236 KGlNVDAILGGGHYEDEVLLVRQAKELGINVKLMSLLVSP-----------SlpafyDALKETSEGILAPSHwepqt 301
                                       999***************************9866666433...........22334433555688888888877777 PP

                                       ..--B-HHHHHHHHHST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSHCCB-HHHHCCHHH CS
                      ANF_receptor 240 ..kdpnspkfsefldkreklsdekqnyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgralscntlkpwegg 314
                                         k +  p  +ef+          q  ++  ++++sy++a+ + a   +  A++k++                + + 
  gi|557694008|ref|YP_008797062.1| 302 kpKITYGPTIDEFM---------TQ-FRQKWNSEPSYHSAAAFAAGLYITAAIEKAG----------------TLDN 352
                                       77777778888888.........44.4444555569999999999999999999999................4455 PP

                                       HHHHHHHHT-EEEETTSCEEB-T.TSBBE.-EEEEEEEE CS
                      ANF_receptor 315 qkllrylrnvnfeGltGdvkfde.ngdrv.ptydilnlq 351
                                       +kl  +  ++ ++ + G++k+d+  g+ v   + +l++q
  gi|557694008|ref|YP_008797062.1| 353 AKLRAAFNDLDITTFYGRLKIDPaTGNQVgHELVLLQWQ 391
                                       555556666666666677777541444445555555555 PP

>> PAP2  PAP2 superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   0.6       3.5   1.6e+04      88      91 ..      15      18 ..       6      28 .. 0.41
   2 ?   12.2   0.0   2.5e-05      0.11      28      77 ..     303     346 ..     278     366 .. 0.69

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 3.5
                              PAP2 88 alil 91
                                      ++i+
  gi|557694008|ref|YP_008797062.1| 15 LVIA 18
                                      1111 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.5e-05
                              PAP2  28 Pfflaeetkldtqvstletses...keakesfPSgHsafafalalllalllrr 77 
                                       P ++   t++ +         +   ++ ++s PS Hsa+afa+ l++++ + +
  gi|557694008|ref|YP_008797062.1| 303 PKITYGPTIDEF---------MtqfRQKWNSEPSYHSAAAFAAGLYITAAIEK 346
                                       222233333333.........23334556777**************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      783  (0.0436723); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.38
# Mc/sec: 3261.96
//
Query:       gi|557694009|ref|YP_008797063.1|  [L=284]
Description: branched-chain amino acid ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  113.9  44.2      8e-33  113.7  44.2    1.0  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 !  113.7  44.2   4.5e-37     8e-33       2     267 ..      11     275 ..      10     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 4.5e-37
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvl 78 
                                       ++n+l ++a+++iaA+Gl+l++g++Gv+nl+hg+f++l+ay+a +   + ++++ll+ ++a+++g+avg ll+  v 
  gi|557694009|ref|YP_008797063.1|  11 LVNGLLMGAVYGIAAVGLSLIWGVLGVVNLAHGSFIILAAYIAYVFFSAAGAPPLLTAPIAVAMGFAVGYLLYKGVG 87 
                                       789********************************************************************998888 PP

                      BPD_transp_2  79 rlkvdeliitllllsv..lvgltlllltgitsgvkgqssvkellgfagallsflsavivllalllvlavllllrrtr 153
                                       r  v    +t ll+++   +++ + +l+ +  +v g+++    l+  g+ ++ +     + +++  +++++ll++t 
  gi|557694009|ref|YP_008797063.1|  88 RKVVTLDPSTSLLFFFglSLLISNSILNIWGPDVRGIPWLIQSLELGGTRIPIARLIALVSTIISFMLLYMLLQHTY 164
                                       76555444444443330044444556666677889999****************99999****************** PP

                      BPD_transp_2 154 fGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGgagsllg 230
                                       +G a+rav  n+  a+ +Gi+v+ v ++++ i+ ++  ++G +++l   + p + g g+ ++++a+vvlGg+g+++g
  gi|557694009|ref|YP_008797063.1| 165 YGKAIRAVVANRVGAASVGIDVDNVFAISMGIALGVTFFSGTMISLVNPFTP-SSGDGYLMYSFASVVLGGVGNIIG 240
                                       ***********************************************88888.************************ PP

                      BPD_transp_2 231 tviGaliigvvksllltllgiptelarvllgallilv 267
                                       t+++++ +g+v+sl + ++++  + + ++ +++l++v
  gi|557694009|ref|YP_008797063.1| 241 TLLAGIFMGLVESLVGVYFSQ--SISPAVAFIILVIV 275
                                       *******************77..66666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       837  (0.0466841); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2301.91
//
Query:       gi|557694010|ref|YP_008797064.1|  [L=315]
Description: branched-chain amino acid ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-37  128.0  32.1    4.9e-37  127.5  32.1    1.2  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
       0.44   10.4   7.1          5    6.9   0.2    2.5  2  Pam17         Mitochondrial import protein Pam17


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 !  127.5  32.1   5.5e-41   4.9e-37       9     267 ..      40     290 ..      32     291 .. 0.89

  Alignments for each domain:
  == domain 1  score: 127.5 bits;  conditional E-value: 5.5e-41
                      BPD_transp_2   9 aailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlkvdel 85 
                                       +++ + ++++l+++ g++G +n+gh + +++Gay++a+l +     +++ +++a +++aav+ l+g+++lr + +++
  gi|557694010|ref|YP_008797064.1|  40 FLQMLALVMSLNFITGFTGYVNFGHIAYYGVGAYTVAYLTTTTRVDPYVFVPAAAITSAAVAYLIGRPILRIRGPYF 116
                                       556667889******************************************************************** PP

                      BPD_transp_2  86 iitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsavivllalllvlavllllrrtrfGralravg 162
                                       +it+l+l ++v+++        + ++ + s   +++   ++  ++s    +++++ +++++l lrrtrfG+ l+ ++
  gi|557694010|ref|YP_008797064.1| 117 AITTLGLGEAVRVII------VNIPAFNYSEGLPIAAYFTYNVTGSYIAMYTTVATLFILTLYLRRTRFGYMLESIR 187
                                       **************9......333333333334444444444555555669************************** PP

                      BPD_transp_2 163 eneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGgagsllgtviGalii 238
                                       e+e+aa+ +Gin+ + kl+++v+s+a+Ag+ G l a   + + p +++++l  +++a+ ++Gg g+llg+++Ga ++
  gi|557694010|ref|YP_008797064.1| 188 EDEDAAESMGINTAKAKLAAYVLSSACAGVIGGLTAITHVYAHPgFFSITLNVSVLASLLMGGGGTLLGPLVGAGLF 264
                                       **************************************************************************999 PP

                      BPD_transp_2 239 gvvksllltllgiptelarvllgallilv 267
                                        ++++ ll  +   + l+ v++ga+++ v
  gi|557694010|ref|YP_008797064.1| 265 FFISDALLIRF---PYLHLVIFGAVVMTV 290
                                       99999444444...89********99976 PP

>> Pam17  Mitochondrial import protein Pam17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.2   0.00056         5      57      92 ..      73     108 ..      37     114 .. 0.76
   2 ?    5.9   1.8    0.0012        11      42     101 ..     212     268 ..     198     275 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00056
                             Pam17  57 leidptqqilglDplvvlglatlasgalGwllGpvl 92 
                                        ++  +++ + +Dp+v++ +a ++s+a+ +l+G  +
  gi|557694010|ref|YP_008797064.1|  73 YTVAYLTTTTRVDPYVFVPAAAITSAAVAYLIGRPI 108
                                       445556777789*********************765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0012
                             Pam17  42 tallglllgaavlstleidp.tqqilglDplvvlglatlasgalGwllGpvlgsavfklln 101
                                       +a++g++ g++ ++++ + p    i    +l v +la l +g+ G llGp++g  +f +++
  gi|557694010|ref|YP_008797064.1| 212 SACAGVIGGLTAITHVYAHPgFFSI----TLNVSVLASLLMGGGGTLLGPLVGAGLFFFIS 268
                                       4566666667777776666633444....456777888999**************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2604.24
//
Query:       gi|557694011|ref|YP_008797065.1|  [L=231]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-34  117.3   0.0    8.6e-34  117.0   0.0    1.1  1  ABC_tran       ABC transporter
    3.4e-13   50.1   0.0    1.4e-06   28.3   0.1    2.1  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    0.00014   21.7   0.0     0.0031   17.3   0.0    2.0  2  AAA_15         AAA ATPase domain
    0.00016   21.3   0.1     0.0003   20.5   0.1    1.4  1  AAA_29         P-loop containing region of AAA domain
    0.00063   19.3   0.0     0.0026   17.3   0.0    1.8  1  SMC_N          RecF/RecN/SMC N terminal domain
    0.00068   19.9   0.1     0.0022   18.3   0.1    2.0  1  AAA_22         AAA domain
     0.0022   17.9   0.0     0.0035   17.3   0.0    1.3  1  RsgA_GTPase    RsgA GTPase
      0.004   17.6   0.0      0.006   17.0   0.0    1.4  1  AAA_16         AAA ATPase domain
     0.0042   17.6   0.1     0.0075   16.8   0.1    1.4  1  AAA_23         AAA domain
     0.0089   15.8   0.0      0.012   15.3   0.0    1.3  1  AAA_30         AAA domain
     0.0094   16.0   0.0       0.14   12.2   0.0    2.2  2  AAA_14         AAA domain
  ------ inclusion threshold ------
      0.012   15.7   0.2      0.034   14.2   0.2    1.9  1  MMR_HSR1       50S ribosome-binding GTPase
      0.014   15.0   0.1      0.065   12.8   0.0    1.8  2  AAA_27         AAA domain
      0.027   13.4   0.0       0.04   12.9   0.0    1.2  1  AAA_10         AAA-like domain
      0.037   13.4   0.0      0.056   12.8   0.0    1.3  1  Mg_chelatase   Magnesium chelatase, subunit ChlI
      0.041   13.6   0.1      0.079   12.7   0.1    1.5  1  AAA_24         AAA domain
      0.045   14.3   0.2       0.12   12.9   0.0    1.9  1  AAA_18         AAA domain
      0.049   13.8   0.1       0.12   12.5   0.1    1.8  2  AAA_33         AAA domain
      0.058   12.6   0.0      0.077   12.2   0.0    1.2  1  PIF1           PIF1-like helicase
      0.066   12.8   0.3       0.68    9.5   0.1    2.0  2  cobW           CobW/HypB/UreG, nucleotide-binding domain
       0.12   12.0   0.0        0.2   11.3   0.0    1.3  1  Guanylate_kin  Guanylate kinase
       0.13   12.2   0.1       0.52   10.2   0.1    2.0  2  NACHT          NACHT domain
       0.13   12.3   0.1       0.31   11.1   0.1    1.7  1  Dynamin_N      Dynamin family
       0.15   10.8   0.1       0.76    8.5   0.1    1.9  2  ABC_ATPase     Predicted ATPase of the ABC class


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 !  117.0   0.0   1.2e-36   8.6e-34       1     136 [.      18     164 ..      18     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 1.2e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l+ vs+++++g+++a++G+nGaGKStLlk+l g lkp++Geilldg+++++  ++e+ r  + ++pqe+ +f  +tv
  gi|557694011|ref|YP_008797065.1|  18 LDGVSVQVEQGKVYAVIGPNGAGKSTLLKTLFGFLKPKSGEILLDGRKITStAPHERIRMGVFYIPQESGIFGSMTV 94 
                                       789**********************************************99899*********************** PP

                                       HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +en               +e++e++l+++       +++++++ ++SgG+++ ++la+a++++p+ ll+DEpt
  gi|557694011|ref|YP_008797065.1|  95 KENlelaawlfrgnkaLVTERVEAVLNQFPRLR---ERLYTKAGKMSGGEQKFLELAKAMMNEPRYLLIDEPT 164
                                       ****99999999977666677888888887554...7777889*****************************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 !   28.3   0.1   1.9e-09   1.4e-06       2      92 ..      31     109 ..      30     114 .. 0.91
   2 !   19.7   0.0   8.4e-07   0.00063     234     294 ..     134     191 ..     128     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.9e-09
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                        ++iGpNg+GKS+LL++l ++             ++++g+i  + +++++++p ++++ ++     q++ + +++++
  gi|557694011|ref|YP_008797065.1|  31 YAVIGPNGAGKSTLLKTLFGF------------LKPKSGEILLDGRKITSTAPHERIRMGVF-YIPQESGIFGSMTV 94 
                                       689***************888............7899999**********************.99999999999999 PP

                            AAA_21  79 ersqv.eeklssvet 92 
                                       +++   +++l++ ++
  gi|557694011|ref|YP_008797065.1|  95 KENLElAAWLFRGNK 109
                                       999999999988766 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 8.4e-07
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                       a ++S G +++l l+ a+   +   + lliDEp  gL P++   ++e l++l+ +++ +++
  gi|557694011|ref|YP_008797065.1| 134 AGKMSGGEQKFLELAKAMMNEP---RYLLIDEPTVGLSPAMADMVYEELRKLTGKDIGILI 191
                                       679*****************99...88************9999999999999988887765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.2e-06    0.0031      23      56 ..      29      57 ..      19     110 .. 0.75
   2 ?    2.8   0.0       0.1        77     322     356 ..     153     187 ..      93     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.2e-06
                            AAA_15 23 eeltvliGkNnsGKSsilealdlFlnnkekknkk 56
                                      + +  +iG+N++GKS++l+ l  Fl+ k    + 
  gi|557694011|ref|YP_008797065.1| 29 K-VYAVIGPNGAGKSTLLKTLFGFLKPK----SG 57
                                      4.7899*******************988....23 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.1
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnk 356
                                       +++  lli+EP + L p +  ++++ l++l  ++ 
  gi|557694011|ref|YP_008797065.1| 153 NEPRYLLIDEPTVGLSPAMADMVYEELRKLTGKDI 187
                                       356779**********************9987765 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 !   20.5   0.1     4e-07    0.0003      13      42 ..      19      48 ..      16      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAi 42
                                      dg ++++++  ++ ++Gp+G+GKSTll  +
  gi|557694011|ref|YP_008797065.1| 19 DGVSVQVEQGKVYAVIGPNGAGKSTLLKTL 48
                                      67788888555***************9655 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 !   17.3   0.0   3.4e-06    0.0026      25     148 ..      29     148 ..      19     211 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.4e-06
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEE..EE..EETTEE....SSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx..xxxxxx....xxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaevei..tf..dnedkk....lkie 93 
                                       ++ a++GpNG+GKs ll  +   +G      l+ ++ + l+  +k  + + + ++ +  ++  ++   +    + + 
  gi|557694011|ref|YP_008797065.1|  29 KVYAVIGPNGAGKSTLLKTL---FG-----FLKPKSGEILLDGRKITSTAPHERIRMgvFYipQE---SgifgSMTV 94 
                                       5789**************99...67.....36666667677664333333333333310333222...223455566 PP

                                       SSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  94 keevsisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvala 148
                                       ke++++   ++r+++     ++ e+  ++  +l e+   +   +SgGe++ + la
  gi|557694011|ref|YP_008797065.1|  95 KENLELAAWLFRGNK-ALVTERVEAVLNQFPRLRERLYTKAGKMSGGEQKFLELA 148
                                       677777777777776.666677777778888888888888888888888877665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   2.9e-06    0.0022       4      30 ..      27      53 ..      24     195 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.9e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                                      + ++ +v+G+ G+GK+tll++l+  l+
  gi|557694011|ref|YP_008797065.1| 27 QGKVYAVIGPNGAGKSTLLKTLFGFLK 53
                                      67899*****************98874 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.6e-06    0.0035      98     130 ..      27      59 ..      14      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.6e-06
                                       TTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktgev 130
                                       ++k+ +++G+ G+GKStL+++l + l+ k ge+
  gi|557694011|ref|YP_008797065.1|  27 QGKVYAVIGPNGAGKSTLLKTLFGFLKPKSGEI 59 
                                       459*******************99888888777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     8e-06     0.006      25      52 ..      29      78 ..      18     185 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8e-06
                            AAA_16 25 elvllsGesGvGKsslvrellralekd......................g 52
                                       +  ++G+ G GKs+l+++l+  l+ +                      g
  gi|557694011|ref|YP_008797065.1| 29 KVYAVIGPNGAGKSTLLKTLFGFLKPKsgeilldgrkitstapherirmG 78
                                      6788*****************98888876666655444444444444331 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1     1e-05    0.0075      20      39 ..      29      48 ..      15      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-05
                            AAA_23 20 gltlItGpNGaGKTTildAi 39
                                      ++++++GpNGaGK+T+l  +
  gi|557694011|ref|YP_008797065.1| 29 KVYAVIGPNGAGKSTLLKTL 48
                                      68899***********9765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-05     0.012      17      78 ..      27      99 ..      21     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa.g......grviglAptgkaAkvLa...eelgi.eastiakllk 78
                                      + +v ++ Gp G+GK+t+lk+l   ++ + g      +++   Ap ++    +    +e+gi  ++t+++ l+
  gi|557694011|ref|YP_008797065.1| 27 QGKVYAVIGPNGAGKSTLLKTLFGFLKPKsGeilldgRKITSTAPHERIRMGVFyipQESGIfGSMTVKENLE 99
                                      446999****************999988866888888888888988887444334445556446666666654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00019      0.14       2      24 ..      28      50 ..      27      74 .. 0.84
   2 ?    1.6   0.0      0.35   2.6e+02      55      72 ..     143     162 ..     120     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                            AAA_14  2 rkilvitGaRrvGKTtllkqlik 24
                                      +k++++ G+  +GK+tllk+l+ 
  gi|557694011|ref|YP_008797065.1| 28 GKVYAVIGPNGAGKSTLLKTLFG 50
                                      6999****************985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.35
                            AAA_14  55 lileklke..ekktylflDE 72 
                                        +le++k+  ++ +yl++DE
  gi|557694011|ref|YP_008797065.1| 143 KFLELAKAmmNEPRYLLIDE 162
                                       34444222335899*****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 ?   14.2   0.2   4.5e-05     0.034       3      27 ..      32      57 ..      30     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.5e-05
                                      EEEESTTSSHHHHHHHHHTS.TEEES CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge.kaivs 27
                                      a++G   +GKStL+++l+g  k + +
  gi|557694011|ref|YP_008797065.1| 32 AVIGPNGAGKSTLLKTLFGFlKPKSG 57
                                      89***************985444444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.8e-05     0.065      24      47 ..      26      49 ..      17      66 .. 0.81
   2 ?   -0.3   0.0      0.93   6.9e+02     138     180 ..      94     138 ..      89     156 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.8e-05
                            AAA_27 24 eeadlhliyGpNEAGKstalrAis 47
                                      e+ ++  ++GpN AGKst+l+ + 
  gi|557694011|ref|YP_008797065.1| 26 EQGKVYAVIGPNGAGKSTLLKTLF 49
                                      56677889***********98754 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.93
                            AAA_27 138 leaegelgqlLfeasaGl..aslrevleaLeaeadelfkprkskk 180
                                       ++++ el+  Lf  + +l  +++++vl+++ + +++l+++ ++ +
  gi|557694011|ref|YP_008797065.1|  94 VKENLELAAWLFRGNKALvtERVEAVLNQFPRLRERLYTKAGKMS 138
                                       566678888888877665226789999999999999999988766 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   0.0   5.3e-05      0.04      17      53 ..      24      60 ..      11      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.3e-05
                            AAA_10 17 sktnasasliiGdlGnGKSvlakllvlyisllggkal 53
                                      ++++    ++iG+ G+GKS l k+l+ ++    g +l
  gi|557694011|ref|YP_008797065.1| 24 QVEQGKVYAVIGPNGAGKSTLLKTLFGFLKPKSGEIL 60
                                      555566679*****************99877666665 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.5e-05     0.056      27      66 ..      33      72 ..      20      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.5e-05
                      Mg_chelatase 27 lvGppGsGKtmlakrlpsllpplseeealevakiasvagk 66
                                      ++Gp G+GK+ l k l + l p s e  l+ +ki+s a +
  gi|557694011|ref|YP_008797065.1| 33 VIGPNGAGKSTLLKTLFGFLKPKSGEILLDGRKITSTAPH 72
                                      79*********************************98863 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00011     0.079       3      23 ..      29      53 ..      27      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                            AAA_24  3 lkiliyGpsgiGKTtlakel....g 23
                                      + ++++Gp+g+GK+tl+k+l    +
  gi|557694011|ref|YP_008797065.1| 29 KVYAVIGPNGAGKSTLLKTLfgflK 53
                                      6789***************966654 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   0.00017      0.12       3      45 ..      33      88 ..      32     162 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00017
                            AAA_18  3 ltGtpGvGKttlakeL.....skrlgf...gvnlrdvakenglllevdpe.....a 45
                                      + G+ G+GK+tl k L      k++++   g++++++a++++++ +v+        
  gi|557694011|ref|YP_008797065.1| 33 VIGPNGAGKSTLLKTLfgflkPKSGEIlldGRKITSTAPHERIRMGVFYIpqesgI 88
                                      89**************6666422224489999999999999999888877544440 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00016      0.12       3      20 ..      32      49 ..      30     130 .. 0.89
   2 ?   -1.5   0.0       3.3   2.5e+03      15      36 ..     147     173 ..     146     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                            AAA_33  3 llvGlpGsGKstlaerll 20
                                       ++G++G+GKstl++ l 
  gi|557694011|ref|YP_008797065.1| 32 AVIGPNGAGKSTLLKTLF 49
                                      689***********9995 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.3
                            AAA_33  15 laerllkklgavllssdt.....lrrr 36 
                                       la+ ++++  + l++++t     ++  
  gi|557694011|ref|YP_008797065.1| 147 LAKAMMNEPRYLLIDEPTvglspAMAD 173
                                       678888888899999999666663333 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001     0.077      13      54 ..      21      60 ..      15     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                      H......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEE CS
                              PIF1 13 iieavlnekgklfFvtGsgGtgKtflwkallkklrsegkivl 54
                                      +  +v+ e+gk+  v G  G+gK+ l+k+l  +l+++   +l
  gi|557694011|ref|YP_008797065.1| 21 V--SVQVEQGKVYAVIGPNGAGKSTLLKTLFGFLKPKSGEIL 60
                                      4..78889**************************99755444 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 ?    9.5   0.1   0.00091      0.68       2      21 ..      30      49 ..      29      60 .. 0.83
   2 ?    1.3   0.0       0.3   2.2e+02      74     121 ..     149     194 ..     113     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00091
                                      EEEEEESTTCCHHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhll 21
                                      v+ + G+ G+GK+tLl++l 
  gi|557694011|ref|YP_008797065.1| 30 VYAVIGPNGAGKSTLLKTLF 49
                                      67899************986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.3
                                       HHHHHHHTT-SEEEE.EECTTTTHHHHHTTSHHHHHCCCECEEEEEEET CS
                              cobW  74 ealeereerldvili.EttGlaePapvafteeelksdltldavvavvDa 121
                                       +a++   +++ ++li E t  ++Pa+  +  eel++ +  d+ + +vD 
  gi|557694011|ref|YP_008797065.1| 149 KAMM---NEPRYLLIdEPTVGLSPAMADMVYEELRKLTGKDIGILIVDQ 194
                                       3333...456788883444456788876779999999999999999996 PP

>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00027       0.2       2      31 ..      28      57 ..      27      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                                      SSEEEEESTTTSSHHHHHHHHHHHSTTTEE CS
                     Guanylate_kin  2 rrpvvlvgpsgaGksslkkaLlselpekfg 31
                                       + + ++gp+gaGks+l k+L+  l+ k g
  gi|557694011|ref|YP_008797065.1| 28 GKVYAVIGPNGAGKSTLLKTLFGFLKPKSG 57
                                      578899****************98887765 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   0.00069      0.52       2      21 ..      30      49 ..      29      58 .. 0.86
   2 ?   -1.1   0.0       2.1   1.6e+03     115     140 ..     102     127 ..      59     145 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00069
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      + ++ G++G GK+tLl+ l 
  gi|557694011|ref|YP_008797065.1| 30 VYAVIGPNGAGKSTLLKTLF 49
                                      56899***********9985 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.1
                                       TTTTT--EEEEEEECCCHHHHCTTSS CS
                             NACHT 115 kkllpeasllltvrpralrdleeqle 140
                                       + l+++++ l+t r +a+ +    l+
  gi|557694011|ref|YP_008797065.1| 102 AWLFRGNKALVTERVEAVLNQFPRLR 127
                                       44788888899988888877333333 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00041      0.31       2      22 ..      32      52 ..      32     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
                                      EEEEBTTTTHHHHHHHHHTS- CS
                         Dynamin_N  2 avvGsqSsGKSSvlnaLlged 22
                                      av+G   +GKS++l  L g  
  gi|557694011|ref|YP_008797065.1| 32 AVIGPNGAGKSTLLKTLFGFL 52
                                      79***************9974 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 ?    8.5   0.1     0.001      0.76     242     264 ..      25      48 ..      18      72 .. 0.84
   2 ?   -0.1   0.0       0.4     3e+02     318     350 ..     132     164 ..     111     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                                       E-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAl 264
                                       + +G v +++G++  GKsTLL+ l
  gi|557694011|ref|YP_008797065.1|  25 VEQGkVYAVIGPNGAGKSTLLKTL 48 
                                       56788****************998 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.4
                                       EEESS--HHHHHHHHHHHHHHTT-SEEEEEGGG CS
                        ABC_ATPase 318 fstedASGStsqAanimealeagakllLiDEDt 350
                                           + SG   +  ++++a+ ++ ++lLiDE t
  gi|557694011|ref|YP_008797065.1| 132 TKAGKMSGGEQKFLELAKAMMNEPRYLLIDEPT 164
                                       555666888888888999999999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 1650.75
//
Query:       gi|557694012|ref|YP_008797066.1|  [L=252]
Description: neutral amino acid ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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    2.1e-29  102.8   0.0    1.3  1  ABC_tran       ABC transporter
    2.9e-10   40.5   1.8    1.7e-05   24.8   0.0    2.1  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    1.3e-05   25.0   0.0    3.3e-05   23.7   0.0    1.7  1  BCA_ABC_TP_C   Branched-chain amino acid ATP-binding cassette
    0.00073   19.2   0.0      0.019   14.7   0.0    2.3  2  AAA_29         P-loop containing region of AAA domain
     0.0013   18.2   0.2       0.13   11.7   0.2    2.1  1  SMC_N          RecF/RecN/SMC N terminal domain
      0.006   17.1   0.0     0.0081   16.7   0.0    1.3  1  AAA_23         AAA domain
  ------ inclusion threshold ------
      0.013   16.0   0.0      0.061   13.7   0.0    2.2  1  AAA            ATPase family associated with various cellular
       0.03   14.0   0.0       0.75    9.4   0.0    2.0  2  AAA_15         AAA ATPase domain
      0.039   13.9   0.0      0.091   12.7   0.0    1.6  2  RsgA_GTPase    RsgA GTPase
      0.088   13.2   0.0       0.15   12.4   0.0    1.6  1  AAA_16         AAA ATPase domain
       0.11   12.4   0.0        0.2   11.5   0.0    1.6  1  ATPase_2       ATPase domain predominantly from Archaea
       0.12   12.5   0.0       0.28   11.4   0.0    1.6  1  Baculo_LEF-10  Baculovirus late expression factor 10 (LEF-10)
       0.15   11.8   0.0       0.25   11.0   0.0    1.5  1  AAA_30         AAA domain
       0.19   11.7   0.0       0.33   10.9   0.0    1.3  1  TsaE           Threonylcarbamoyl adenosine biosynthesis prote
        0.2   11.4   0.0       0.39   10.5   0.0    1.4  1  IRF-3          Interferon-regulatory factor 3


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 !  102.8   0.0   1.7e-32   2.1e-29       1     137 []      29     175 ..      29     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 1.7e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l+ +sl+++ege+++++G+nGaGK+t++++++gl +p++G++ + g+++ e +  e +r+ i    q p++f +lt+
  gi|557694012|ref|YP_008797066.1|  29 LDGLSLEMYEGEVLGLIGPNGAGKTTFINVVCGLIRPDSGKVYYYGENILEkNVYELARAGIVKTYQIPRVFGNLTA 105
                                       6899*****************************************999999688999******************** PP

                                       HHH........HHHTC..HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx........xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren........esdee..iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        +n        ++++e   ++a ++l+l++  d +++  +s+LSgG+++ ++ ara++ kp+llllDEp+a
  gi|557694012|ref|YP_008797066.1| 106 LDNlvasaswlKMSVEelRKAAYDSLRLVK-LDVKADLLGSQLSGGERKLLEFARAMMLKPRLLLLDEPFA 175
                                       *****9988873333344566666667666.566667779*****************************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 !   15.0   0.4   1.4e-05     0.017       3      19 ..      43      59 ..      41      88 .. 0.82
   2 !   24.8   0.0   1.4e-08   1.7e-05     235     300 ..     145     207 ..     115     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                            AAA_21  3 vliGpNgsGKSnLLdal 19
                                      +liGpNg+GK++++   
  gi|557694012|ref|YP_008797066.1| 43 GLIGPNGAGKTTFINVV 59
                                      79***********9766 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.4e-08
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                       ++lS G ++ll ++ a+   +   +lll+DEp +g +P l + l++ lk+ ++ g  +++++H+  
  gi|557694012|ref|YP_008797066.1| 145 SQLSGGERKLLEFARAMMLKP---RLLLLDEPFAGVNPVLKSILIDALKRVNTQGLSILVVSHDMA 207
                                       589********9999999877...**************8889999***999999*********964 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.7e-08   3.3e-05       2      23 .]     224     245 ..     223     245 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.7e-08
                      BCA_ABC_TP_C   2 vIAeGtPaEvrndPrVieAYLG 23 
                                       ++ eG+P+Ev ++++V++ YLG
  gi|557694012|ref|YP_008797066.1| 224 KLLEGSPDEVLRNEEVVRLYLG 245
                                       667******************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 !   14.7   0.0   1.6e-05     0.019      16      50 ..      33      67 ..      27      72 .. 0.74
   2 ?    1.9   0.0      0.15   1.8e+02      35      45 ..     182     192 ..     172     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++e+ + ++  l+Gp+G+GK+T++  +  l+ p++
  gi|557694012|ref|YP_008797066.1| 33 SLEMYEGEVLGLIGPNGAGKTTFINVVCGLIRPDS 67
                                      556654447789************88877777766 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.15
                            AAA_29  35 KSTllDAiqal 45 
                                       KS l+DA++ +
  gi|557694012|ref|YP_008797066.1| 182 KSILIDALKRV 192
                                       9******9876 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 !   11.7   0.2   0.00011      0.13      26     198 ..      41     205 ..      29     223 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrr 102
                                       +  ++GpNG+GK+ +++ ++ ++  +s    +   + + i + k+  ++ +a +  t++ +    + ++ +     +
  gi|557694012|ref|YP_008797066.1|  41 VLGLIGPNGAGKTTFINVVCGLIRPDSG---KVYYYGENILE-KNVYELARAGIVKTYQIPRVFGNLTALDNL-VAS 112
                                       5568999999999999888655554444...44444444444.455555555555555555544222222222.222 PP

                                       EETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkv 179
                                       ++  + s  ++ +    +  + +l  +a++  ++LSgGe++L+     fA  ++ +  l llDe  a       +++
  gi|557694012|ref|YP_008797066.1| 113 ASWLKMSVEELRKAAYDSLRLVKLDVKADLLGSQLSGGERKLLE----FARAMMLKPRLLLLDEPFAGVNPVLKSIL 185
                                       22222233445555555555666666677777788888888855....45444445557777887777777777777 PP

                                       HHHHHHHCTT.SEEEEE-SS CS
                                       xxxxxxxxxx.xxxxxxxxx RF
                             SMC_N 180 aellkekskn.aQfivislr 198
                                        + lk+ +++   ++v+s++
  gi|557694012|ref|YP_008797066.1| 186 IDALKRVNTQgLSILVVSHD 205
                                       77777655444667777765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.7e-06    0.0081      23      40 ..      43      60 ..      25     146 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.7e-06
                            AAA_23 23 lItGpNGaGKTTildAik 40
                                       ++GpNGaGKTT+++ ++
  gi|557694012|ref|YP_008797066.1| 43 GLIGPNGAGKTTFINVVC 60
                                      689***********9887 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 ?   13.7   0.0   5.1e-05     0.061       3      35 ..      44      86 ..      42     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.1e-05
                                      EESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCS CS
                               AAA  3 lyGppGtGKTllakavakel..........gvefleisgsell 35
                                      l+Gp G GKT++++ v+  +          g ++le ++ el 
  gi|557694012|ref|YP_008797066.1| 44 LIGPNGAGKTTFINVVCGLIrpdsgkvyyyGENILEKNVYELA 86
                                      89***************99644444333333444444444444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00063      0.75      25      42 ..      41      58 ..      26      85 .. 0.84
   2 ?    2.7   0.0     0.072        86     323     354 ..     164     195 ..     153     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00063
                            AAA_15 25 ltvliGkNnsGKSsilea 42
                                      +  liG+N++GK++++++
  gi|557694012|ref|YP_008797066.1| 41 VLGLIGPNGAGKTTFINV 58
                                      6679***********975 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.072
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkeland 354
                                       k+ +ll++EP a   p ++++li++lk++  +
  gi|557694012|ref|YP_008797066.1| 164 KPRLLLLDEPFAGVNPVLKSILIDALKRVNTQ 195
                                       57799*********************998655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.6e-05     0.091      95     121 ..      35      61 ..      12      72 .. 0.79
   2 ?   -3.0   0.0         5     6e+03     114     122 ..     184     192 ..     174     220 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.6e-05
                                       HHCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinallp 121
                                       e+ ++++  l+G+ G+GK+t+in++ +
  gi|557694012|ref|YP_008797066.1|  35 EMYEGEVLGLIGPNGAGKTTFINVVCG 61 
                                       345669999**************9876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5
                                       HHHHHHCTT CS
                       RsgA_GTPase 114 tLinallpe 122
                                        Li+al+  
  gi|557694012|ref|YP_008797066.1| 184 ILIDALKRV 192
                                       444444432 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00012      0.15       4     106 ..      21     124 ..      18     202 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            AAA_16   4 GReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd..ggif....lrgkcdqlesaipysalaq 74 
                                        R +el++L  +  ++ + ++e++ l+G+ G GK++ ++ +   ++ d  ++++    + +k++     ++++ +++
  gi|557694012|ref|YP_008797066.1|  21 KRYDELRALDGL--SLEMYEGEVLGLIGPNGAGKTTFINVVCGLIRPDsgKVYYygenILEKNVYE---LARAGIVK 92 
                                       566677666665..45666779999**************999888888432222333322222222...33333333 PP

                            AAA_16  75 alareellrqlldeaesaeleawrekleeala 106
                                       +    +++  l + ++  + + w +   e+l+
  gi|557694012|ref|YP_008797066.1|  93 TYQIPRVFGNLTALDNLVASASWLKMSVEELR 124
                                       33333444444444444444444444444444 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 ?   11.5   0.0   0.00017       0.2       4      54 ..      22      73 ..      19     144 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                          ATPase_2  4 Rekelkeleei.lerepneiyfiYGpegsGKtaLlkeiienledkdkyviyy 54
                                      R  el+ l  + le+ + e++ + Gp g GKt++++ +    +  + +v yy
  gi|557694012|ref|YP_008797066.1| 22 RYDELRALDGLsLEMYEGEVLGLIGPNGAGKTTFINVVCGLIRPDSGKVYYY 73
                                      777788887654788888999999*************999997655444444 PP

>> Baculo_LEF-10  Baculovirus late expression factor 10 (LEF-10)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00024      0.28       9      42 ..     180     213 ..     174     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                     Baculo_LEF-10   9 llngiLkDnlfLvdnkYlilnvldqetdelRrlC 42 
                                       +l +iL D l+ v+ + l + v+ ++  e+RrlC
  gi|557694012|ref|YP_008797066.1| 180 VLKSILIDALKRVNTQGLSILVVSHDMAEIRRLC 213
                                       7899****************************** PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00021      0.25      19      50 ..      40      71 ..      34     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00021
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                       v  l Gp G+GKtt ++++  +++ + g+v 
  gi|557694012|ref|YP_008797066.1| 40 EVLGLIGPNGAGKTTFINVVCGLIRPDSGKVY 71
                                      477899*************9999888866665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.33      18      40 ..      37      60 ..      20      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
                                      H.TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 18 l.gdvilLeGdLGaGKTtlvrgla 40
                                        g+v+ L G+ GaGKTt++  ++
  gi|557694012|ref|YP_008797066.1| 37 YeGEVLGLIGPNGAGKTTFINVVC 60
                                      2488999************98775 PP

>> IRF-3  Interferon-regulatory factor 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00032      0.39      76     116 ..     199     239 ..     182     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00032
                                       EEEEETTEEEEEE-SSB-EEEEEEBSSBSSS-SEE-SSS-E CS
                             IRF-3  76 lLevagqglyakRlcqsrvfwsgpealekdkPnkLerekev 116
                                       +L v+++   ++Rlc+  vf+++ ++l ++ P+++ r++ev
  gi|557694012|ref|YP_008797066.1| 199 ILVVSHDMAEIRRLCKRVVFMAAGSKLLEGSPDEVLRNEEV 239
                                       46666667779**********************99999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1727.88
//
Query:       gi|557694013|ref|YP_008797067.1|  [L=128]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   0.4    1.2e-20   73.8   0.4    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 !   73.8   0.4   6.8e-25   1.2e-20       2     117 ..       7     127 ..       6     128 .] 0.89

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 6.8e-25
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT.........-HH CS
                              HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke......see 72 
                                       e  + rA  +l++A +l+ee+++dla+f+ +q +++ lK+ ll + g +pkth+lr L++ l ++ +        ++
  gi|557694013|ref|YP_008797067.1|   7 ELMKARAIAFLRNADRLMEEHEWDLAMFNLEQYCQLMLKYKLLVQRGIYPKTHSLRTLIRILGENNPGlltmveDSS 83 
                                       677889******************************************************99888887777655555 PP

                                       HHHHHHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHH.HHH CS
                              HEPN  73 lreeleeLekayiesrYpdakeeyteedaeealkdaeevlel.vee 117
                                          ++ +Le+ayi srY ++++  +e++++++ +++ ev++  ve+
  gi|557694013|ref|YP_008797067.1|  84 KLHYVARLEEAYIVSRYMPYRF--EEKEVRDVYRFVVEVFKPfVEK 127
                                       55555*****************..9*************99976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 900.56
//
Query:       gi|557694014|ref|YP_008797068.1|  [L=106]
Description: DNA polymerase beta domain protein region [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   46.4   0.1    4.6e-12   46.1   0.1    1.2  1  NTP_transf_2    Nucleotidyltransferase domain
    2.2e-08   34.1   0.0    2.8e-08   33.7   0.0    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
    5.4e-06   26.6   0.1    6.7e-06   26.3   0.1    1.1  1  DNA_pol_B_palm  DNA polymerase beta palm


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 !   46.1   0.1   7.7e-16   4.6e-12       3      91 ..      22     102 ..      21     106 .] 0.77

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 7.7e-16
                                       HHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEEC CS
                      NTP_transf_2   3 klleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekl 79 
                                       +++++l++ +p+++v++fGS++rG ++  SDiD+lv++++ ++       +++ + + +  +e  ++e ++ t +k 
  gi|557694014|ref|YP_008797068.1|  22 EVKRILRKIDPDVRVFVFGSVVRGRYTAASDIDILVLTDDLSK-------KYEMMVEVYRSVE-APVELHITTPQKY 90 
                                       6899*************************************65.......3444444444444.6677777777777 PP

                                       CCCTEEEEEECE CS
                      NTP_transf_2  80 edpllvksilee 91 
                                       ++++ + + l+e
  gi|557694014|ref|YP_008797068.1|  91 RSWYSRFIPLDE 102
                                       767666666665 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0   4.8e-12   2.8e-08       3      56 ..      23      77 ..      21      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 4.8e-12
                                      TTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS-.--HHHHHHHHHHHH CS
                           Polbeta  3 ikeilekekeielaylFGSrakgkareeSDiDlavllkek.ldleeelelaaele 56
                                      +k il+k +    +++FGS+++g+++  SDiD+ vl+++  +++e  +e++  +e
  gi|557694014|ref|YP_008797068.1| 23 VKRILRKIDPDVRVFVFGSVVRGRYTAASDIDILVLTDDLsKKYEMMVEVYRSVE 77
                                      56777777555569*************************9777877888777665 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 !   26.3   0.1   1.1e-09   6.7e-06       8      62 ..      17      72 ..      14      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.1e-09
                                      HHHHHHHHHHHHHH-TT-EEEE-HHHHTT-SE.ESSEEEEEEBTTBSTTSS--HHH CS
                    DNA_pol_B_palm  8 ealealvkkaakeldpevevivcGSYRRgaes.sGDvDvlitkkdakseskklkkl 62
                                      +++ a vk+ ++++dp+v+v v GS  Rg+ + + D+D+l+  +d +++ +   ++
  gi|557694014|ref|YP_008797068.1| 17 REVGAEVKRILRKIDPDVRVFVFGSVVRGRYTaASDIDILVLTDDLSKKYEMMVEV 72
                                      567899**********************9865268**********99965544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 769.42
//
Query:       gi|557694015|ref|YP_008797069.1|  [L=55]
Description: hypothetical protein CSUB_C0579 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                      1301  (0.072564); expected 358.6 (0.02)
Passed bias filter:                      608  (0.0339115); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 404.54
//
Query:       gi|557694016|ref|YP_008797070.1|  [L=87]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   27.2   2.7    5.9e-06   26.8   2.7    1.2  1  ParE_toxin  ParE toxin of type II toxin-antitoxin system, par


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   2.7   3.3e-10   5.9e-06       1      90 []       5      87 .]       5      87 .] 0.76

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.3e-10
                                      EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEE..CTSTC...CTTEEEEEECTEEEEEEEETS CS
                        ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrp..rrelg...lkglrririgdyriiYridde 74
                                      v++++rA+k lk +++          ++  ++ e l  l enp +      +  +   l  ++r+rigd riiY++ ++
  gi|557694016|ref|YP_008797070.1|  5 VIISNRARKSLKSLVK----------QHRRRVLELLLILRENPVPTDYfdVK--KlkgLIYTYRVRIGDIRIIYEVSWN 71
                                      799***********76..........55555555556666666665553322..13478889**************999 PP

                                      TTEEEEEEEEEHHHHC CS
                        ParE_toxin 75 elvvvilrvlhrsedy 90
                                       ++++il +  r+++y
  gi|557694016|ref|YP_008797070.1| 72 AKTIKILLIEWRERAY 87
                                      9******999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 630.43
//
Query:       gi|557694017|ref|YP_008797071.1|  [L=100]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  102.8   0.6    9.2e-30  102.7   0.6    1.0  1  DUF211    Uncharacterized ArCR, COG1888
     0.0087   15.9   0.0     0.0093   15.8   0.0    1.0  1  RVT_3     Reverse transcriptase-like
  ------ inclusion threshold ------
      0.058   13.9   1.1       0.24   11.9   1.1    2.0  1  HMA       Heavy-metal-associated domain


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 !  102.7   0.6   1.5e-33   9.2e-30       2      80 ..      14      92 ..      13      99 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.7 bits;  conditional E-value: 1.5e-33
                                      EEEEEEEEEEESSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEEEE CS
                            DUF211  2 irrlvLDvlkphepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDevva 80
                                      + rlvLDvlkph+p +ve+a++l+ l+gv+ v+++++evD +te++k+t+eG+ni++e+i +++++lg+++hS+D+v  
  gi|557694017|ref|YP_008797071.1| 14 LTRLVLDVLKPHKPGMVEFAQALTGLRGVTKVEVSIIEVDADTETVKLTVEGNNINFEQIANTVKQLGAAVHSVDQVTY 92
                                      68***************************************************************************86 PP

>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-06    0.0093      39     109 ..      26      95 ..      11     100 .] 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-06
                             RVT_3  39 sveeAElqALlrGLqlalklgirrlvvegDsktvvqllngrekvksselanlldeirkllksfesvsvehi 109
                                       ++ ++E++  l GL+ + k +++ ++v  D +tv   + g++ ++ +++an++++  + ++s ++v+ +h 
  gi|557694017|ref|YP_008797071.1|  26 KPGMVEFAQALTGLRGVTKVEVSIIEVDADTETVKLTVEGNN-INFEQIANTVKQLGAAVHSVDQVTYSHP 95 
                                       57899999999*******************************.6***********************9995 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.1   4.1e-05      0.24      23      60 ..      39      81 ..      32      83 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                               HMA 23 lpgV.....esvkvdlatktvtVegdaestklrkiieaiekag 60
                                      l gV     + ++vd +t tv  +++   +++++i ++++++g
  gi|557694017|ref|YP_008797071.1| 39 LRGVtkvevSIIEVDADTETVKLTVEGNNINFEQIANTVKQLG 81
                                      5555333436678999999999999999999*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 708.57
//
Query:       gi|557694018|ref|YP_008797072.1|  [L=492]
Description: phytoene dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  114.9   0.0      7e-33  114.6   0.0    1.1  1  Amino_oxidase   Flavin containing amine oxidoreductase
    1.9e-14   53.6   1.1    3.8e-14   52.7   0.3    1.9  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      1e-10   41.8   0.0    1.3e-05   25.0   0.0    2.2  2  DAO             FAD dependent oxidoreductase
    1.8e-08   34.2   0.1    6.7e-07   29.0   0.0    2.1  2  FAD_oxidored    FAD dependent oxidoreductase
    4.9e-08   32.6   0.3    1.5e-05   24.4   0.0    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.6e-06   26.4   5.7     0.0026   16.5   2.7    2.2  2  HI0933_like     HI0933-like protein
    2.9e-06   27.7   6.3     0.0025   18.3   3.0    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    5.1e-06   25.8   6.6    1.6e-05   24.2   3.7    2.1  2  FAD_binding_2   FAD binding domain
     0.0011   18.2   0.4      0.002   17.4   0.4    1.3  1  Thi4            Thi4 family
     0.0019   17.5   1.6      0.003   16.9   1.6    1.2  1  FAD_binding_3   FAD binding domain
     0.0072   15.7   2.9      0.013   14.8   2.9    1.4  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
      0.028   14.0   0.1      0.056   13.0   0.1    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.037   13.9   1.9      0.074   12.9   1.9    1.5  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.057   11.8   0.1        0.1   11.0   0.1    1.3  1  FMO-like        Flavin-binding monooxygenase-like
      0.059   13.4   2.9       0.86    9.6   0.7    2.8  2  NAD_binding_9   FAD-NAD(P)-binding
      0.066   12.3   7.6      0.065   12.3   4.6    2.3  3  GIDA            Glucose inhibited division protein A
        0.1   11.3   0.4       0.31    9.8   0.0    1.8  2  MCRA            MCRA family
       0.28   10.0   2.0       0.45    9.3   2.0    1.3  1  Trp_halogenase  Tryptophan halogenase
       0.37   10.4   1.3       0.73    9.5   1.3    1.5  1  ApbA            Ketopantoate reductase PanE/ApbA
        1.6    7.9   4.3       0.56    9.4   0.9    1.8  2  Pyr_redox_3     Pyridine nucleotide-disulphide 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 !  114.6   0.0   7.8e-36     7e-33       2     444 ..      14     480 ..      13     482 .. 0.77

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 7.8e-36
                                       HHHHHHHHHHHTTEEEEEEESSSSSBTTS-EEEETTEEEESS--EEETTTHHHHHHHHH.TTCCCCEE..EESCCGC CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvGGRirtvrsdGylielGamwftgagnpllellke.lgledsls..lpdpgap 75 
                                        GLaaA  L++ G++Vtv E ++ vGGR+    +dG+++++G++w+ +  ++++  +   +g ++s++  l + ++ 
  gi|557694018|ref|YP_008797072.1|  14 GGLAAAALLAREGHEVTVAEKNNNVGGRAGVLSRDGFTFDMGPTWYLM--PEIFDRFYShFGKKTSDFynLLKLDPG 88 
                                       6***********************************************..555554444488888888554444578 PP

                                       EEEEETTEECC.............TTEECHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH CS
                     Amino_oxidase  76 krvlskggref.............pgdlspvpaewealleqgalsaellsleeklrlgleallqktldeldldsksl 139
                                       +rv + +g ++             +g+ +   ++++++l ++           +++++l + l++ +  l+++  s 
  gi|557694018|ref|YP_008797072.1|  89 YRVFFDDGVKVdisaeleenirlfDGLEPNGGEKLRRFLAKCEEL------YNSISKTLYLDLDSPFSFLNPEILSQ 159
                                       999999888888866666666665555555566666666633332......33444444444455555555555555 PP

                                       HHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTSTTTTCBHHHHTCCCCHHHHHTSCCCEETTHTHHHHHHH CS
                     Amino_oxidase 140 aesleelgrrepgdvevwdrliepelfaklefasglfagdpselsaklalpllwelegfggslllprgGlsqlpeal 216
                                        ++++ ++   + + +v   +  +++++ l ++ g+ +  p   s+  a+++ +++ +  +++++p++G++q++++l
  gi|557694018|ref|YP_008797072.1| 160 GIKINIFE---SVESYVKKWFQSDKARKLLLYSIGFIGTPP---SKAPAFYAILNYVKLVQGVYMPEHGIRQVVDTL 230
                                       55555555...555455666666778999999999988777...********************************* PP

                                       HH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHHSSEEESCC.SHHHHHHHHHSEEEEE CS
                     Amino_oxidase 217 ae..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlkailfsPpl.pdekaeairnlgfgsv 290
                                           ++ +++++l+++V++i+  +++    + + +++++DaVvv ++ +   +  ++P+    ++    +++ ++s+
  gi|557694018|ref|YP_008797072.1| 231 YGlaKQENVEFLLGHEVSKIEVTNSKAERVYLNDSSMKVDAVVVNADYAFFETRVLEPRYrTYDVDYWSKRMFTPSA 307
                                       ***9**********************999999**************************5534444444448899999 PP

                                       EEEEEEESSGG...SGCSTS..ECE.......CECCCEEETTTEEEEECC.....ECCCSTTTEEEEEEEEEC.HHH CS
                     Amino_oxidase 291 nkvilefdrkf...wednal..gqg.......vlvseltttlgeafissd.....fpsrappgkglvllvyvg.gda 349
                                         ++l  d+k+    ++n    +            ++  +++++a ++           appg    ++ +++ ++ 
  gi|557694018|ref|YP_008797072.1| 308 LIAYLGLDKKVeniIPHNVFleK-DwgenfyqIFDPRYAKWPEYASYYVHvpskiDKTAAPPGGEA-VFILIPvANG 382
                                       9**********776666665441.123566776667777777777777666677655666666655.7777775555 PP

                                       HHHHTTS-HHHHHHHHHHHHHHHHTGTSSTCSE....EEEEECCT..ETTTSSSEEE.BTTHHHHHHHHHHCHHCST CS
                     Amino_oxidase 350 aneleslsdeelvqavlrdLrklfgeevpepka....tlvtrWht..dplargsysyvsvgpghedydplakpegdp 420
                                       +++ +++ +e l++ vlrdL++  ge++ e +     + ++++++   ++++++  + ++  ++  ++p++++++++
  gi|557694018|ref|YP_008797072.1| 383 IED-DDKKRETLFNNVLRDLEQKTGENIHENIVfkqlFSIRDFSAryHAYRGSALGLAHTLGQTAFWRPVHRSKKVK 458
                                       555.788******************55555554566799999*9966677788888889999*************** PP

                                       TEEE.SGGGCTTTTTS.HHHHHHHH CS
                     Amino_oxidase 421 rlffAGehtsreypgt.vegAilSG 444
                                       +l+++G +t+   pg  v+  + S+
  gi|557694018|ref|YP_008797072.1| 459 NLYYTGQYTH---PGIgVPMVLISA 480
                                       **********...999999988886 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 !   52.7   0.3   4.2e-17   3.8e-14       1      59 [.       8      66 ..       8      73 .. 0.91
   2 ?   -2.7   0.0       8.2   7.4e+03      42      65 ..     437     461 ..     427     461 .. 0.67

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 4.2e-17
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECETTCEECTS---EEETTHHH CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyevpgvrvdygahifhgsgyyp 59
                                      +vGaG++Gl+aA+lLa++g++v++ ek++ +GGra   +++g+++d g++++  ++ ++
  gi|557694018|ref|YP_008797072.1|  8 VVGAGVGGLAAAALLAREGHEVTVAEKNNNVGGRAGVLSRDGFTFDMGPTWYLMPEIFD 66
                                      8***************************************************8865444 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.2
                                       TCEECTS---EEET.THHHHCHHHH CS
                     NAD_binding_8  42 gvrvdygahifhgs.gyypnvrrll 65 
                                       g ++ +g ++f+ + +++++v++l+
  gi|557694018|ref|YP_008797072.1| 437 GLAHTLGQTAFWRPvHRSKKVKNLY 461
                                       5778888888866437777777765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.4e-08   1.3e-05       1      35 [.       5      40 ..       5     145 .. 0.87
   2 !   14.8   0.0   1.8e-05     0.016     130     199 ..     211     276 ..     166     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.4e-08
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsg 35
                                      ++v++G+G+ Gl++A  Lar+g  Vt+ ek++ +g g
  gi|557694018|ref|YP_008797072.1|  5 RIVVVGAGVGGLAAAALLAREGheVTVAEKNNNVG-G 40
                                      59******************999********9999.4 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.8e-05
                                       TTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEE.EEE- CS
                               DAO 130 gllgalfypdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgve.rttpgendaada.vVna 199
                                       +l+ ++++p+ g+   ++++  l+  a++  ve+l+g+ev ++e ++ k+ +v+ ++++    ++da vVna
  gi|557694018|ref|YP_008797072.1| 211 KLVQGVYMPEHGI---RQVVDTLYGLAKQENVEFLLGHEVSKIEVTNSKAERVYlNDSS-M--KVDAvVVNA 276
                                       5778999999999...9**************************9999999999765443.2..379956665 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   7.5e-10   6.7e-07       2      70 ..       6      75 ..       5     111 .. 0.82
   2 ?    3.1   0.1     0.055        49      89     131 ..     223     271 ..     205     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 7.5e-10
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGG...lltsglvatdignkaeeqvvtgiareflerlrqr 70
                                      +vVvG+g++G+aAA   ar+G +v + e+++ +GG    l++ + + d+g++  + +   i+++f+++  ++
  gi|557694018|ref|YP_008797072.1|  6 IVVVGAGVGGLAAAALLAREGHEVTVAEKNNNVGGragVLSRDGFTFDMGPT--WYLMPEIFDRFYSHFGKK 75
                                      8*********************************822256888888888855..589999999999988664 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.055
                      FAD_oxidored  89 akavleeml...aeagvtvllntrlvevekegkriesvtveske.g..r 131
                                        ++v++ +    ++++v+ ll+++++++e+++ + e v +++++ +   
  gi|557694018|ref|YP_008797072.1| 223 IRQVVDTLYglaKQENVEFLLGHEVSKIEVTNSKAERVYLNDSSmKvdA 271
                                       455666666777899***************9999999999877655433 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 !   24.4   0.0   1.7e-08   1.5e-05       2      40 ..       5      43 ..       4      99 .. 0.90
   2 !    6.2   0.1    0.0057       5.1     191     233 ..     232     274 ..     202     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.7e-08
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggc 40
                                      ++vv+G+G++Glaaa  la+ g++vt+ e+++++ ++  
  gi|557694018|ref|YP_008797072.1|  5 RIVVVGAGVGGLAAAALLAREGHEVTVAEKNNNVGGRAG 43
                                      79**************************77776655555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0057
                                       HHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCEEEESEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 191 ealekeGvevklgtsvkeidgngekle.vvledgeeidadlvvv 233
                                          ++e+ve+ lg++v +i+  ++k+e v l+d + +++d vvv
  gi|557694018|ref|YP_008797072.1| 232 GLAKQENVEFLLGHEVSKIEVTNSKAErVYLNDSS-MKVDAVVV 274
                                       556888**************999988856666655.79999998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.7   2.9e-06    0.0026       2      36 ..       5      39 ..       4      44 .. 0.94
   2 !   10.5   0.1   0.00019      0.17     107     160 ..     222     274 ..     210     277 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.9e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      +++v+G+G  Gl aA+ +a++g++V++ ek++++g
  gi|557694018|ref|YP_008797072.1|  5 RIVVVGAGVGGLAAAALLAREGHEVTVAEKNNNVG 39
                                      68******************************998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00019
                                       -CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE CS
                       HI0933_like 107 kaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvl 160
                                         +++vd+l   +k+++v++ l +ev+++e +++++ rv + ++++++ d++v+
  gi|557694018|ref|YP_008797072.1| 222 GIRQVVDTLYGLAKQENVEFLLGHEVSKIEVTNSKAERVYL-NDSSMKVDAVVV 274
                                       5579*************************************.999******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 !   18.3   3.0   2.8e-06    0.0025       1      35 [.       5      39 ..       5      44 .. 0.93
   2 !    9.9   0.1    0.0012       1.1      50      79 ..     234     263 ..     222     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.8e-06
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      ++vvvG+G+ gl +A+ la+ g++Vtv e ++++ 
  gi|557694018|ref|YP_008797072.1|  5 RIVVVGAGVGGLAAAALLAREGHEVTVAEKNNNVG 39
                                      79***************************999886 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0012
                                       HHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                         Pyr_redox  50 lekngievllntkveeiegsedgvesvklk 79 
                                        +++++e+ll+++v +ie ++++ e+v l+
  gi|557694018|ref|YP_008797072.1| 234 AKQENVEFLLGHEVSKIEVTNSKAERVYLN 263
                                       5778**************999999999886 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   3.7   1.8e-08   1.6e-05       2      37 ..       6      41 ..       5      51 .. 0.92
   2 ?    2.3   0.0     0.081        73     139     182 ..     222     265 ..     209     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.8e-08
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                      ++V+G+G++GLaAA+ +a++G++v+v ek +++gg 
  gi|557694018|ref|YP_008797072.1|  6 IVVVGAGVGGLAAAALLAREGHEVTVAEKNNNVGGR 41
                                      79******************************9994 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.081
                                       HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEET CS
                     FAD_binding_2 139 tghallarlvesarkagvdfqerteadeLivedgrvtGavvenp 182
                                         ++++ +l+  a++ +v+f+  +e+ ++ v++ ++  ++++++
  gi|557694018|ref|YP_008797072.1| 222 GIRQVVDTLYGLAKQENVEFLLGHEVSKIEVTNSKAERVYLNDS 265
                                       67899**************************9998888877743 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.4   2.2e-06     0.002      20      57 ..       6      42 ..       2      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-06
                                      EEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                              Thi4 20 vvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                      +v+vGaG  GL+aa  la++ + +v++ e++  +GG a
  gi|557694018|ref|YP_008797072.1|  6 IVVVGAGVGGLAAAALLARE-GHEVTVAEKNNNVGGRA 42
                                      8*******************.*************9965 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.6   3.3e-06     0.003       3      43 ..       5      43 ..       3      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.3e-06
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS-- CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlprad 43
                                       +++VGaG  Gl +a lL++ G +v++ ek ++  v +ra+
  gi|557694018|ref|YP_008797072.1|  5 RIVVVGAGVGGLAAAALLAREGHEVTVAEKNNN--VGGRAG 43
                                      579**************************9864..455555 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   2.9   1.4e-05     0.013      29      62 ..       4      37 ..       1      45 [. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                                      -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHH CS
                       AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrpa 62
                                       +++v+G+Gv Gl+A+a  ++ g +Vtv +++ +
  gi|557694018|ref|YP_008797072.1|  4 LRIVVVGAGVGGLAAAALLAREGHEVTVAEKNNN 37
                                      589***************************9986 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 ?   13.0   0.1   6.2e-05     0.056       2      33 ..       5      36 ..       4      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-05
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-H CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDide 33
                                      +i+v+G+G  Gl  aa+la+ ghev++  +++
  gi|557694018|ref|YP_008797072.1|  5 RIVVVGAGVGGLAAAALLAREGHEVTVAEKNN 36
                                      89************************988875 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   1.9   8.3e-05     0.074       2      33 ..       6      37 ..       5      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.3e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                      + v+GaG+ G   aa++a++g+eV++ + +++
  gi|557694018|ref|YP_008797072.1|  6 IVVVGAGVGGLAAAALLAREGHEVTVAEKNNN 37
                                      78*************************99886 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00011       0.1       3      38 ..       5      40 ..       3      46 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
                          FMO-like  3 kvaviGaGvsGlasikccleegleptcfersddiGG 38
                                      ++ v+GaGv Gla+      eg e t  e+ +++GG
  gi|557694018|ref|YP_008797072.1|  5 RIVVVGAGVGGLAAAALLAREGHEVTVAEKNNNVGG 40
                                      899********************************9 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 ?    9.6   0.7   0.00096      0.86       1      40 [.       7      41 ..       7      49 .. 0.78
   2 ?    2.9   0.1      0.11        99     107     151 ..     226     274 ..     106     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00096
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgagr 40
                                      ++vGaG+ Gla+++ L+++      +e+t+ ++ ++ g gr
  gi|557694018|ref|YP_008797072.1|  7 VVVGAGVGGLAAAALLARE-----GHEVTVAEKnNNVG-GR 41
                                      69********999877777.....6999****955554.44 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                     NAD_binding_9 107 llarl...pegvtvevh.raevvdleeradgqavlladgaslaadaVvL 151
                                       ++++l    ++ +ve++  +ev ++e ++++++ +  +++s+++daVv+
  gi|557694018|ref|YP_008797072.1| 226 VVDTLyglAKQENVEFLlGHEVSKIEVTNSKAERVYLNDSSMKVDAVVV 274
                                       3333322245567787647799999999999988888899999999985 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.6   7.2e-05     0.065       2      32 ..       6      35 ..       5      44 .. 0.85
   2 ?   -1.0   0.1      0.78     7e+02     105     145 ..     233     274 ..     225     285 .. 0.79
   3 ?   -2.4   0.0       2.1   1.9e+03     351     365 ..     453     467 ..     450     467 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.2e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEES-G CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLithkl 32
                                      ++V+G+G  G++AA+ +ar G++v+    k 
  gi|557694018|ref|YP_008797072.1|  6 IVVVGAGVGGLAAAALLAREGHEVTVAE-KN 35
                                      89**********************9874.33 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.78
                                       HHTSTTEE.EEES-EEEEEECTTEEEEEEETTS-EEEECEEE CS
                              GIDA 105 lenepnle.iieeeveeliveekkvkgvvtedgetikakavv 145
                                       l +++n+e ++  ev++++v+++k + v+++d ++  + +vv
  gi|557694018|ref|YP_008797072.1| 233 LAKQENVEfLLGHEVSKIEVTNSKAERVYLNDSSMKVDAVVV 274
                                       5677888745678999***99999999999998876666666 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 2.1
                                       BBSSSBTEEE-CGGG CS
                              GIDA 351 etkkvkgLflAGqin 365
                                       ++kkvk+L+  Gq +
  gi|557694018|ref|YP_008797072.1| 453 RSKKVKNLYYTGQYT 467
                                       579**********75 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00034      0.31       5      45 ..       7      43 ..       4      70 .. 0.79
   2 ?   -1.2   0.1      0.71   6.4e+02     217     251 ..     235     264 ..     225     284 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00034
                                      EEE--SHHHHHHHHHHHHTT---GGGEEEE-SS-------- CS
                              MCRA  5 ylvGsGiasLaaAvyLirdakvpgenihileelkvaggsld 45
                                       +vG+G+++LaaA+ L r++    +++++ e+++ +gg   
  gi|557694018|ref|YP_008797072.1|  7 VVVGAGVGGLAAAALLAREG----HEVTVAEKNNNVGGRAG 43
                                      589**************986....58999999998888654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.71
                                       HHTT-EEE-SEEEEEEEEEEE.TTEEEEEEEEEEE CS
                              MCRA 217 keqgVdfqfntkVtdiefeeeeedkktvteielek 251
                                       k+++V+f ++ +V+ ie++++     +++++ l++
  gi|557694018|ref|YP_008797072.1| 235 KQENVEFLLGHEVSKIEVTNS-----KAERVYLND 264
                                       7899**************965.....345555554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.0   0.00051      0.45       1      34 [.       5      35 ..       5      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00051
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-S CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvese 34
                                      +iv+vG+G  G  aAa+la+ +   +evt+ e++
  gi|557694018|ref|YP_008797072.1|  5 RIVVVGAGVGGLAAAALLAREG---HEVTVAEKN 35
                                      69*******************9...899999986 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.3   0.00081      0.73       1      30 [.       6      35 ..       6      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00081
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SC CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrs 30
                                      i+++GaG  G   aa La+ g++vt+  ++
  gi|557694018|ref|YP_008797072.1|  6 IVVVGAGVGGLAAAALLAREGHEVTVAEKN 35
                                      89*****999999999999******86655 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 ?    9.4   0.9   0.00062      0.56       1      31 [.       7      36 ..       3      42 .. 0.74
   2 ?   -1.9   0.1       1.7   1.5e+03     221     261 ..     233     273 ..     223     279 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00062
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                                      +++GaG  Glaaa  l + g  ++++ Ek+n
  gi|557694018|ref|YP_008797072.1|  7 VVVGAGVGGLAAAALLAREGH-EVTVAEKNN 36
                                      578888888888888888887.577888874 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.7
                       Pyr_redox_3 221 lvkeekikvlfnaevkeikekeeeykvktedgkkvevkddv 261
                                       l k+e++++l  +ev +i+ ++++ +    + ++++v+  v
  gi|557694018|ref|YP_008797072.1| 233 LAKQENVEFLLGHEVSKIEVTNSKAERVYLNDSSMKVDAVV 273
                                       44556666666667777766655553333333455554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3331.83
//
Query:       gi|557694019|ref|YP_008797073.1|  [L=294]
Description: phytoene synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  147.6   0.0    5.5e-43  147.4   0.0    1.0  1  SQS_PSY       Squalene/phytoene synthase
  ------ inclusion threshold ------
       0.13   12.1   0.0        0.4   10.5   0.0    1.9  1  EF-hand_13    EF-hand domain
       0.15   11.6   0.0       0.23   11.0   0.0    1.2  1  Peptidase_C9  Peptidase family C9


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 !  147.4   0.0   9.1e-47   5.5e-43       3     263 .]      19     269 ..      17     269 .. 0.94

  Alignments for each domain:
  == domain 1  score: 147.4 bits;  conditional E-value: 9.1e-47
                                       HH-HHHHHHHTTS-HHHHHHHHHHHHHHHHHT-.-----........------------..---------THHHHHH CS
                           SQS_PSY   3 aasksfylaslllppelRdalgalYafcreaddlvDdvseplqararldwwrdavdavyaedklkpprepvlralaq 79 
                                       ++s +++ ++l++p  ++++++ lYaf r ad  vD    p++ +  + +++++++++     + ++ + v  ++ +
  gi|557694019|ref|YP_008797073.1|  19 KGSTTYFNSTLFFPDNVKKDVFKLYAFLRKADNYVDLI--PQDVEG-FYAFKEEYERAA---SGYQSSDIVINEFVE 89 
                                       7899999*****************************95..666666.78*********9...899************ PP

                                       HHHHHT--HHHHHHHHHHTS--SS-..--SHHHHHHHHHHHHHHHHHHHHHHH-S.S-HHHHHHHHHHHHHHHHHHH CS
                           SQS_PSY  80 lirtyklpkellleliegmeadleftryetlddLeeYcyrvagvVgelclrllgarrsdralaeaarrlGkalQltn 156
                                       l  ++k ++e+ ++++++me+dl++++y tld+L  Y+y +a vVg++++++l + +++   + +ar lG+a+Q++n
  gi|557694019|ref|YP_008797073.1|  90 LSNRKKFEQEWITAFLDAMESDLYRKTYYTLDELCVYMYGSAEVVGLFMAKILDLPEES---YIYARFLGRAMQYIN 163
                                       *******************************************************5555...9************** PP

                                       HHT---SHHHHTT..S-HHHHHHHT--HHHHHHT-.-SHHHHHHHHHHHHHHHHHHHHHHHTGGGS.-HHHHHHHHH CS
                           SQS_PSY 157 ilRdvpeDaergrvyLPadvlkefgvseedllrkgvrsaelrallrrlaerArelldearellkqlpdrrarpalll 233
                                       ++Rd++eD e+gr yLP + ++ +g++  + +r   +++++ + +r ++er  e+ + a+++ k + + r+  ++++
  gi|557694019|ref|YP_008797073.1| 164 FIRDIREDYELGRQYLPYEEMRMHGIEDFEPARFCGKHESFARFIRLQIERYLEWQRFAEQGYKYI-PYRYLIPIKT 239
                                       **************************99999887778888**************************.77788889** PP

                                       HHHHHHHHHHHHHHTTT-TTT------HHH CS
                           SQS_PSY 234 avalyrailerieaadydvlsrrvklsllr 263
                                       a+ +y  + + i++++  v+ r+vk +++r
  gi|557694019|ref|YP_008797073.1| 240 AADMYKWTAKIIHRHPSIVFMRKVKPRKRR 269
                                       *****************9999***999876 PP

>> EF-hand_13  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   6.7e-05       0.4      20      48 ..     240     268 ..     233     279 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.7e-05
                        EF-hand_13  20 redlkplvkelvetHPgLeFlreaeefqd 48 
                                       ++d+++++ +++++HP + F+r+ +  ++
  gi|557694019|ref|YP_008797073.1| 240 AADMYKWTAKIIHRHPSIVFMRKVKPRKR 268
                                       689*******************9876555 PP

>> Peptidase_C9  Peptidase family C9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.9e-05      0.23      68     114 ..      97     144 ..      84     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.9e-05
                                       HHHHHH.H-HHHHTT----HHHHHHHHHHHHHSS-GGG-TTBSS-EEE CS
                      Peptidase_C9  68 deqwse.iitafkedkaysavvalneicikfyGvdldsGlfskpkvsl 114
                                       +++w + +++a++ d    + ++l+e+c+ +yG     Glf ++ + l
  gi|557694019|ref|YP_008797073.1|  97 EQEWITaFLDAMESDLYRKTYYTLDELCVYMYGSAEVVGLFMAKILDL 144
                                       5677651456777788888999*******************9887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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 0.29s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2097.13
//
Query:       gi|557694020|ref|YP_008797074.1|  [L=288]
Description: UbiA prenyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-29  103.2  12.9    1.7e-29  102.9  12.9    1.1  1  UbiA       UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.078   13.3   3.1        1.6    9.0   0.1    2.3  2  Cornichon  Cornichon protein


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 !  102.9  12.9   1.9e-33   1.7e-29       4     223 ..      24     245 ..      21     260 .. 0.72

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 1.9e-33
                              UbiA   4 palvglalaaggspdl...llllllllgtllaaaaanalNdyfDreiDadmert..pnRPlv.sGrispkealifai 74 
                                       p++vg++l+a+g +d+      + l+ +++ a++ ++++NdyfD+e+Da+++ +  ++  +v + r+      +  +
  gi|557694020|ref|YP_008797074.1|  24 PYVVGYTLGATGFSDFlrpEYYIYLIYFFIPANILVYGVNDYFDVETDALNPKKssKELRIVgRDRVR-----LRRL 95 
                                       889*************99888888888888*********************97722333344455555.....3333 PP

                              UbiA  75 vllilgllllalllnpltallgllallly.vvYt.g.lrlKrrtllgtvvggiafglppllgwaavtgslsllalll 148
                                       +l++lg++++++l++  +a +++ ++l++ ++Y+ + lr+K  ++  ++     + +p ++g ++++gsl+ +++ll
  gi|557694020|ref|YP_008797074.1|  96 LLGVLGISFALMLFQDNVARILFGGFLFLsIFYSaPpLRFKSKPF-LDFASNYLYIMPGVFGHYIASGSLPDTLILL 171
                                       333333333333344444444444445555*****99********.89999999***************98777777 PP

                              UbiA 149 alavflltwaialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllallla 223
                                       a +  l++ a++++ +++d+e D++agikt+pvv+Grk+a+il  +++  +++la++l+++  l+ l+l++ ++ +
  gi|557694020|ref|YP_008797074.1| 172 AGF--LHISAMHIFSAVPDIEFDLAAGIKTTPVVIGRKNALILvTVFWAGLAYLAIMLTGFHPLSFLALIYPMVPL 245
                                       775..*************************************7433333333433334444444444444444333 PP

>> Cornichon  Cornichon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00018       1.6       7      73 ..      47     113 ..      43     131 .. 0.81
   2 ?    4.2   0.8    0.0057        51       8      74 ..     169     239 ..     167     257 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00018
                         Cornichon   7 aliltaallflsvyfiialsDleadyinpidlcsklNplvlpelilhafltllfllsgewilfllnl 73 
                                        li   +   + vy +  + D+e+d +np + +++l  + +  + l+ +l+ ++ +s+  +lf  n+
  gi|557694020|ref|YP_008797074.1|  47 YLIYFFIPANILVYGVNDYFDVETDALNPKKSSKELRIVGRDRVRLRRLLLGVLGISFALMLFQDNV 113
                                       455555556688999**********************999999999999988888888888886655 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0057
                         Cornichon   8 liltaallflsvyfiialsDleadyinpidlc....sklNplvlpelilhafltllfllsgewilfllnlp 74 
                                       ++l+++l + ++++  a+ D+e+d+   i+ +     + N l+l++++  ++  l+++l+g   l +l+l+
  gi|557694020|ref|YP_008797074.1| 169 ILLAGFLHISAMHIFSAVPDIEFDLAAGIKTTpvviGRKNALILVTVFWAGLAYLAIMLTGFHPLSFLALI 239
                                       45667777777777889999999999999876222257799****99999999886666654444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); 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 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1985.48
//
Query:       gi|557694021|ref|YP_008797075.1|  [L=175]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1372.67
//
Query:       gi|557694022|ref|YP_008797076.1|  [L=162]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-73  244.5   0.1    4.1e-73  244.3   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 !  244.3   0.1   2.3e-77   4.1e-73       1     154 []       8     161 ..       8     161 .. 0.99

  Alignments for each domain:
  == domain 1  score: 244.3 bits;  conditional E-value: 2.3e-77
                                       EEE---TTEEEEEEEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTEE CS
                     Adenosine_kin   1 vkiekpeevnvilgqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghvf 77 
                                       v +e+pe++nv++g shfiktved+yea+v++vpg+kfglaf+Easg++Lvr+eg+d+el+++a++++l+ig+gh+f
  gi|557694022|ref|YP_008797076.1|   8 VGVEIPEGCNVVFGVSHFIKTVEDIYEAVVNTVPGAKFGLAFMEASGECLVRHEGTDPELRKHAAETMLRIGCGHTF 84 
                                       6799************************************************************************* PP

                                       EEEEEST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS- CS
                     Adenosine_kin  78 villknafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigYk 154
                                       ++++k  +Pin+++++k+vpev++i aAtanpl++ivaeteqgrgvlgvvDG++pkg+e+e+++++rk++lrkigYk
  gi|557694022|ref|YP_008797076.1|  85 ILFIKGFYPINIMQRLKDVPEVCTILAATANPLQIIVAETEQGRGVLGVVDGHKPKGIETEQHIEARKQFLRKIGYK 161
                                       ****************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1283.89
//
Query:       gi|557694023|ref|YP_008797077.1|  [L=354]
Description: octaprenyl-diphosphate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-64  217.4   0.0      2e-64  217.1   0.0    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 !  217.1   0.0   1.1e-68     2e-64       4     255 ..      56     304 ..      53     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: 217.1 bits;  conditional E-value: 1.1e-68
                                       HHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCH CS
                   polyprenyl_synt   4 leealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGn 80 
                                       l +++  l+ +gGKr+Rp+l++ ++eal+  +      ++la++ e++h+a+L++DD+ D s +RRG+pc+hr++G 
  gi|557694023|ref|YP_008797077.1|  56 LAKPFWELFRRGGKRWRPALTVIVYEALGGGD---PGIYILAAVPEIIHNATLIVDDVEDGSLMRRGEPCIHRIYGI 129
                                       7889999**********************555...789*************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH.STT.HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHC CS
                   polyprenyl_synt  81 klAindgdfllarafellaklf.eks.lellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylf 155
                                       ++Ain+g++ + +  +l ak   ++  + +le + e+++++  Gq +d+ ++ +  +++ ++e+yl++   KT++l 
  gi|557694023|ref|YP_008797077.1| 130 DIAINAGNAYYYIPAYLAAKKLpKNMaTLFLEKYVETMTRLSLGQTMDIVWH-RGLVTDITEEHYLQMAAFKTGALS 205
                                       *******988776555555444344468999******************999.68888899**************** PP

                                       HHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHH CS
                   polyprenyl_synt 156 alpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqr 232
                                       + +v+laa++ag   + le+l ++g+ +G+aFQiqDDyl++fgd++  gK++g Di+egk tl++++al++ s+e++
  gi|557694023|ref|YP_008797077.1| 206 RFAVELAAIYAGR-GDLLEELGRFGEAVGTAFQIQDDYLNIFGDEARYGKEIGGDITEGKYTLMTVYALTHLSSEKA 281
                                       ************6.6779*********************************************************** PP

                                       HHHHHHTTSSHHHHHHHHHHHHH CS
                   polyprenyl_synt 233 kvlkeilgkkaekeedvkealel 255
                                       k+l++il +++++++++kea++l
  gi|557694023|ref|YP_008797077.1| 282 KRLRQILHSHTSDKQELKEAINL 304
                                       ********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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 0.20s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2902.94
//
Query:       gi|557694024|ref|YP_008797078.1|  [L=257]
Description: NADPH-flavin oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-11   42.9   0.9    4.2e-09   36.7   0.4    2.5  2  Nitroreductase  Nitroreductase 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 !   36.7   0.4   2.4e-13   4.2e-09       2     169 ..      14     167 ..      13     168 .. 0.84
   2 ?   -2.5   0.0      0.25   4.5e+03      91      91 ..     224     224 ..     184     250 .. 0.45

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.4e-13
                                       HH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGGGH CS
                    Nitroreductase   2 rkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrkee 78 
                                       ++RrSiR F++  +++e+l  i+e ++ aPs + +    ++ +++++l +++++ + +++ k   +  l+      +
  gi|557694024|ref|YP_008797078.1|  14 ASRRSIRRFRKSAMSEEVLGMIVESGQSAPSYFQA--YSIIWLRSDQLVEAVYDVCGSEAIKQASAVLLICLDF--N 86 
                                       79*****************************9988..678999999999********99999887777777633..2 PP

                                       HHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT CS
                    Nitroreductase  79 lklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllg 155
                                       +    ++ +             +  + ++ + ++  ++l++g++++n+++a +alG+gs  +    ++ e++ +ll 
  gi|557694024|ref|YP_008797078.1|  87 KLTVFAETVSPE----------HFLKLDTYPAETLLSVLELGLVVENMVIASEALGYGSLLLDCGIYECERLSALLK 153
                                       333333333333..........34456799999*********************************9999******* PP

                                       -S..SEEEEEEEEE CS
                    Nitroreductase 156 lpdeeeivvliavG 169
                                       lp +  +v l+ +G
  gi|557694024|ref|YP_008797078.1| 154 LPTGVVPVILLLIG 167
                                       **888888887777 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.25
                                       S CS
                    Nitroreductase  91 p 91 
                                       +
  gi|557694024|ref|YP_008797078.1| 224 T 224
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1862.34
//
Query:       gi|557694025|ref|YP_008797079.1|  [L=361]
Description: cell division protein FtsZ [Candidatus Caldiarchaeum subterraneum]
Scores for 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-41  140.2   0.1    2.6e-40  138.7   0.1    1.8  1  Tubulin         Tubulin/FtsZ family, GTPase domain
    2.3e-24   85.5   0.0    9.6e-24   83.5   0.0    2.1  1  FtsZ_C          FtsZ family, C-terminal domain
     0.0017   18.3   0.0     0.0031   17.4   0.0    1.5  1  NAD_binding_10  NAD(P)H-binding
  ------ inclusion threshold ------
       0.13   11.4   7.4       0.64    9.1   2.0    2.7  2  Tubulin_2       Tubulin like


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.7   0.1   5.8e-44   2.6e-40       1     196 [.      15     175 ..      15     176 .. 0.96

  Alignments for each domain:
  == domain 1  score: 138.7 bits;  conditional E-value: 5.8e-44
                                       EEEEEEEHHHHHHHHHHHHH...HHHCH....HHHT.....TTEEEEE....EEESBHHHHHTS-GS......EEEE CS
                           Tubulin   1 eiivigvGqcGnqignelwellakehgiqsdgdslesfFsesgkveyiprsvaidtdpqvlneikagselfnpnkll 77 
                                       +i+ igvG++G++++n+l        g+             +g v +    +a++td q+l+ ++a+      +k+l
  gi|557694025|ref|YP_008797079.1|  15 RIKLIGVGGAGCNTVNRLNA----L-GL-------------TG-VYT----IAANTDLQHLDMVRAD------KKIL 62 
                                       5999****************....4.88.............66.444....6***************......**** PP

                                       --CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEEEEEE CS
                           Tubulin  78 lgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalvvtvv 154
                                       lgk+ ++  gagg+p  g++aaee++eeir+++e++d    +f+ a+lgGGTG+G++pv+++v++ee  +a+vv+vv
  gi|557694025|ref|YP_008797079.1|  63 LGKSVTRLRGAGGDPVRGRKAAEESEEEIRRALEGADI---VFLAAGLGGGTGTGAAPVVARVAREE--GATVVGVV 134
                                       **************************************...**************************..******** PP

                                       EE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCS CS
                           Tubulin 155 vlPsefsevvvepynailalkelieesdavividNdaLlkil 196
                                        lP+ef e++v+ + a  +l+el+++ ++ +v+dN++Ll+++
  gi|557694025|ref|YP_008797079.1| 135 SLPFEF-EGMVRKRIAQAGLEELKNYTNTSVVVDNNKLLDLY 175
                                       ******.*******************************9975 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.0   2.1e-27   9.6e-24       3      94 ..     225     316 ..     223     317 .. 0.98

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 2.1e-27
                                       EEEEEEEEESTTHHHHHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE-T CS
                            FtsZ_C   3 AmmgvGeasgedraeeaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavide 79 
                                       A +gvG++s  +raeea+ +a++spLLd+++++ +g++v+++gg+d++l E+ + ae i+e + e+  vi+Ga+id+
  gi|557694025|ref|YP_008797079.1| 225 ASLGVGRSSTPNRAEEATFNALQSPLLDASYENLSGAIVHVCGGEDMQLAEAARPAEIISELMGEDGLVIWGARIDD 301
                                       899************************************************************************** PP

                                       T--SEEEEEEEEES- CS
                            FtsZ_C  80 eledeirvtvvatgl 94 
                                        ++ +++v+ ++tgl
  gi|557694025|ref|YP_008797079.1| 302 TFSSTMQVSLILTGL 316
                                       **************8 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 !   17.4   0.0   6.9e-07    0.0031      49      97 ..      86     135 ..      67     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.9e-07
                                       T-CCHHHHHHTT-SEEEES---TCCHHHHHHHHH.HHHHHCT--EEEEEE CS
                    NAD_binding_10  49 tdvedlaealkgadaVvsalggggkdeegakniv.daakeagvkRfvlvs 97 
                                       +++e++++al+gad+V+ a+g gg++ +ga+ +v ++a+e+g   + +vs
  gi|557694025|ref|YP_008797079.1|  86 ESEEEIRRALEGADIVFLAAGLGGGTGTGAAPVVaRVAREEGATVVGVVS 135
                                       6899****************988887777555551567777776666665 PP

>> Tubulin_2  Tubulin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.3    0.0047        21       2      18 ..      18      34 ..      18      62 .. 0.81
   2 ?    9.1   2.0   0.00014      0.64     115     183 ..      71     126 ..      58     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0047
                         Tubulin_2  2 viGLGGtGgkvlaelrr 18
                                      +iG+GG G++++++l  
  gi|557694025|ref|YP_008797079.1| 18 LIGVGGAGCNTVNRLNA 34
                                      6*************976 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00014
                         Tubulin_2 115 eGAGqiRtvGRlalfanleeirealrdaikrlrgsageeeglnvfVvgSLaGGTGSGiflDvayllrki 183
                                       +GAG+ +  GR a  ++ eeir+al+ a               vf++ +L GGTG G +  va + r++
  gi|557694025|ref|YP_008797079.1|  71 RGAGGDPVRGRKAAEESEEEIRRALEGA-------------DIVFLAAGLGGGTGTGAAPVVARVAREE 126
                                       7777777777777776666666666654.............37**************999888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); 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:                         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: 00:00:00.40
# Mc/sec: 2716.49
//
Query:       gi|557694026|ref|YP_008797080.1|  [L=102]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   32.5   0.0    7.2e-08   32.1   0.0    1.2  1  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.031   14.5   0.0      0.044   13.9   0.0    1.2  1  RHH_8     Ribbon-Helix-Helix transcriptional regulator 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 !   32.1   0.0   8.1e-12   7.2e-08       2      37 ..      58      94 ..      57      96 .. 0.96

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 8.1e-12
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelIReAlreyl 37
                                      v+++l+e +l ++del++rr  ++r e+IR Alr+++
  gi|557694026|ref|YP_008797080.1| 58 VTVHLPEPYLQAIDELVKRRLyPNRAEAIRMALRDFI 94
                                      9*********************************987 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 ?   13.9   0.0     5e-06     0.044       6      43 ..      58      95 ..      54     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5e-06
                             RHH_8  6 vtinlgvvDLgqiDlLveeGfYsnRtDlirtairaqLa 43
                                      vt+ l    L  iD Lv+   Y nR++ ir a+r+ ++
  gi|557694026|ref|YP_008797080.1| 58 VTVHLPEPYLQAIDELVKRRLYPNRAEAIRMALRDFIR 95
                                      7888988999***********************98665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 852.53
//
Query:       gi|557694027|ref|YP_008797081.1|  [L=122]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00043   20.7   0.0     0.0034   17.8   0.0    2.1  1  Toprim_4  Toprim domain
    0.00099   19.5   0.0     0.0014   19.0   0.0    1.3  1  Toprim_2  Toprim-like
      0.003   17.8   0.0      0.061   13.5   0.0    2.1  2  Toprim    Toprim domain


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 !   17.8   0.0   5.7e-07    0.0034       3      82 ..      26      91 ..      24      96 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.7e-07
                          Toprim_4  3 iiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerlaelllee 81
                                      +++VEg  D  al  ag++  +  +  ++   + ++   +++          +++il+ld D eG +t +r+++ll++ 
  gi|557694027|ref|YP_008797081.1| 26 VVLVEGARDEKALRLAGVRAKIVYVS-RF--REAVE--MMPR---------PRKIILLLDFDSEGMKTVKRVSRLLRQM 90
                                      67777777777777776655443222.34..56666..6666.........58*********************77666 PP

                          Toprim_4 82 g 82
                                      g
  gi|557694027|ref|YP_008797081.1| 91 G 91
                                      5 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.3e-07    0.0014       2      74 ..      18      93 ..      17     106 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.3e-07
                          Toprim_2  2 vfEgaiDalSlaqlgikektnvvalgGt....alteaalkllerype.kkvvlalDnDkaGrkaakrlaellreagvr 74
                                      v+E++ D+  l +     +++++ l+G+     +  +  + +e  p  +k++l lD D  G k +kr+++llr+ g++
  gi|557694027|ref|YP_008797081.1| 18 VAEAVEDVVVLVEGAR--DEKALRLAGVrakiVYVSRFREAVEMMPRpRKIILLLDFDSEGMKTVKRVSRLLRQMGYE 93
                                      6788888888888333..45899999995443333333333444444489***********************99943 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.026   1.5e+02       1      21 [.      25      44 ..      25      53 .. 0.74
   2 !   13.5   0.0     1e-05     0.061      62      88 ..      62      88 ..      42     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.026
                                      EEEEESSHHHHHHHHHTHTST CS
                            Toprim  1 elvivEgpsdaktiakalgsg 21
                                      ++v+vEg +d k+++ a g  
  gi|557694027|ref|YP_008797081.1| 25 VVVLVEGARDEKALRLA-GVR 44
                                      589*********99888.434 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1e-05
                                      HHSEEEEECSSSHHHHHHHHHHHHHHT CS
                            Toprim 62 radeiilatDpDreGeaiawellevlk 88
                                      r  +iil++D D eG ++ +++  +l+
  gi|557694027|ref|YP_008797081.1| 62 RPRKIILLLDFDSEGMKTVKRVSRLLR 88
                                      5569*****************997766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      670  (0.0373696); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 887.43
//
Query:       gi|557694028|ref|YP_008797082.1|  [L=681]
Description: glutamine amidotransferase class-II domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   93.1   7.2    2.6e-26   92.4   7.2    1.3  1  GXGXG       GXGXG motif
    2.7e-08   34.1   0.0    3.2e-07   30.6   0.0    2.5  2  GATase_6    Glutamine amidotransferase domain
    2.2e-07   30.0   0.1    0.00012   21.0   0.1    2.2  1  GATase_2    Glutamine amidotransferases class-II
     0.0021   17.0   0.0     0.0036   16.3   0.0    1.3  1  GATase_4    Glutamine amidotransferases class-II
  ------ inclusion threshold ------
      0.021   14.7   0.0       0.11   12.4   0.0    2.0  1  GATase_7    Glutamine amidotransferase domain
      0.095   12.6   0.2       0.23   11.3   0.2    1.6  1  Flavi_NS2B  Flavivirus non-structural protein NS2B


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 !   92.4   7.2   8.7e-30   2.6e-26      20     165 ..     406     552 ..     379     562 .. 0.90

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 8.7e-30
                                       HHHTTT---.-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEEEE--TT-SS-GGGSB-S-SSTT CS
                             GXGXG  20 krygeeglpedtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkivikpskeskfkaeeniivGnvvl 96 
                                       +ry   ++p ++  ++++G+aG+ l+ f+ +G  +++ G+a+d v++ + gG+++i++++            G+v++
  gi|557694028|ref|YP_008797082.1| 406 HRYLGVNVPPGR-FLNIYGTAGNCLANFN-RGGVITVYGNAEDDVADAMVGGRVIIHGNA------------GDVLA 468
                                       555555555443.489*************.8889**************************............***** PP

                                       TT--SEEEEESSB--SSTTTT-.....SS-EEEESEB.-SSTTTT-EEEEEEE-S-B.........-SSBTTT--EE CS
                             GXGXG  97 ygatgGklfirgkageRfavrn.....sgatavvegv.gdhgceYmtGGvvvvLgkt.........grnfaaGmsgG 158
                                       ++ ++G++f+rg+ag+R+a+++     +++ ++++g   d+++eYm+GGvv vLg           gr +a+Gm gG
  gi|557694028|ref|YP_008797082.1| 469 QAFQAGEIFVRGSAGNRVAIQMrefreHKPYLIIGGRvDDYLGEYMAGGVVAVLGVDsfdsdeclvGRCVATGMVGG 545
                                       **********************9999999*******9899***************999******************* PP

                                       EEEEE-S CS
                             GXGXG 159 iayvlde 165
                                       ++y++ +
  gi|557694028|ref|YP_008797082.1| 546 VIYIRGR 552
                                       ****844 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.9   1.2e+04      79     103 ..     105     129 ..     104     135 .. 0.79
   2 !   30.6   0.0   1.1e-10   3.2e-07      11     134 .]     166     318 ..     153     318 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.9
                          GATase_6  79 alleelGeevlerlrGmfafaiwdk 103
                                        ++ e+ ee+l++l+  + + +w++
  gi|557694028|ref|YP_008797082.1| 105 SAYVETSEETLRKLVDSINYELWNA 129
                                       5777888999999999999999987 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 1.1e-10
                          GATase_6  11 edevalaHvRlaivglaeeega.qPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall..... 81 
                                       e+++++aH+R  ++   +     +Pf  ++++++++hNG+i+ ++  + e+ + +g++    +D+e+++ ll     
  gi|557694028|ref|YP_008797082.1| 166 EADMWIAHTRQPTNSPGVYPIWsHPF--ASQEWAIAHNGDISSFG-ANMEFIRFRGYRSFVGTDSELIAYLLdyltn 239
                                       55699******999998777777***..****************8.78888888****889*********9989999 PP

                          GATase_6  82 .eelG............eevle...........rlrGmfafaiwdk.rentlila.rdrlgvkplyyavdesglafa 132
                                        ++l+            e+ l+            l+G f++++  +  e+ ++la +dr   +pl++++de+++++a
  gi|557694028|ref|YP_008797082.1| 240 iQRLPilhaaqllvsgfEDDLDkvdeyvrwrgaGLDGPFSVVAGYCdGEDIYMLAlADRSKFRPLVVGYDEERIYVA 316
                                       94444555545555566444423444444556689999999998887888888889999999999999999999999 PP

                          GATase_6 133 se 134
                                       se
  gi|557694028|ref|YP_008797082.1| 317 SE 318
                                       98 PP

>> GATase_2  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   3.9e-08   0.00012     177     405 ..     142     353 ..     114     368 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3.9e-08
                                       EEEEEESS-GGGHHHHBHGGGSTT--BSEEEEEE---SSS...S--GGG..SSS-SSEEEEE--TTHHHHHHHHHHH CS
                          GATase_2 177 tivYkglltseqlkefykdlkdeelesalalvHsRfstnt...fPsWel..aqPlRllaHnGEintlrGnknwmkar 248
                                       + v+kg+  + ++++ y  l++++le+ + + H+R  tn    +P W+   a     +aHnG+i     n+++++ r
  gi|557694028|ref|YP_008797082.1| 142 VEVFKGVGYPLDVSQMY-GLTEKNLEADMWIAHTRQPTNSpgvYPIWSHpfASQEWAIAHNGDISSFGANMEFIRFR 217
                                       569*************9.5********************644479996322666678***************99988 PP

                                       CTT--BT-HH.HHHTC--S--TTS-HHHHHHHHHHHHHHTT.--HHHHHHHHS----TT-GGGTHHHHHHHHHHTTT CS
                          GATase_2 249 eaelksellgdelekllPivneegsDsasldnvlellvlsg.rslaealmlliPeawennksldkekkafyeyasal 324
                                         +   ++               g Ds+ +   l++l+      + +a+ ll+         +++++ +  ey    
  gi|557694028|ref|YP_008797082.1| 218 GYR---SF--------------VGTDSELIAYLLDYLTNIQrLPILHAAQLLVS-------GFEDDLDKVDEYVRWR 270
                                       753...22..............35799999999999988763577889988885.......3455555666777777 PP

                                       -----SSEEEE..EE-SS..EEEEEE-TT--S--EEEEETT--EEEES.STTSS---GGGEEEEEE--TT-EEEEET CS
                          GATase_2 325 mepWDGPaliv..ftdGk..vvgavLDRnGLRPaRylvtkddlvvlas.EvGvldleeeevvekgrlqPGrmllvdl 396
                                           DGP ++v  ++dG+  ++ a  DR   RP       ++++++as E+ + + ++e vv  + ++PG ++l  l
  gi|557694028|ref|YP_008797082.1| 271 GAGLDGPFSVVagYCDGEdiYMLALADRSKFRPLVVGYD-EERIYVASeEAEIRQNSPEAVV--WPVKPGGIFLASL 344
                                       888899998874468998435678899999999765554.4555555515667777788887..6789999999999 PP

                                       TTTEEEEHH CS
                          GATase_2 397 eegrilede 405
                                       ++g i++ +
  gi|557694028|ref|YP_008797082.1| 345 KKGIIVSGR 353
                                       999998765 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-06    0.0036      65     143 ..     161     239 ..     133     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-06
                          GATase_4  65 reypiksknvvaHiRkatqG.evklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCe 136
                                        e ++++ + +aH R+ t+   v    +hpF    + +ew +AHnGd++++  ++       ++    TDsEl+  +
  gi|557694028|ref|YP_008797082.1| 161 TEKNLEADMWIAHTRQPTNSpGVYPIWSHPF----ASQEWAIAHNGDISSFGANMefirFRGYRSFVGTDSELI-AY 232
                                       455799999******9998413445556666....689***********99988876663445555569***97.57 PP

                          GATase_4 137 lleelas 143
                                       ll+ l++
  gi|557694028|ref|YP_008797082.1| 233 LLDYLTN 239
                                       7776655 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.6e-05      0.11      15     121 ..     190     322 ..     182     324 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.6e-05
                          GATase_7  15 PmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea........................... 64 
                                       P++   +++ +i++nG i  +    e ++ +g+r    +D+e+++ ll++                           
  gi|557694028|ref|YP_008797082.1| 190 PFA---SQEWAIAHNGDISSFGANMEFIRFRGYRSFVGTDSELIAYLLDYltniqrlpilhaaqllvsgfeddldkv 263
                                       444...57899*********************************999999999*****************9999766 PP

                          GATase_7  65 .ewgeealerlnGmfAfa..iwdeeekrlllaRDrlGikPLyygedkgdallfaSelkal 121
                                        e+++     l+G f+++  + d e+  +l+  Dr  ++PL +g+d+ +++++aSe   +
  gi|557694028|ref|YP_008797082.1| 264 dEYVRWRGAGLDGPFSVVagYCDGEDIYMLALADRSKFRPLVVGYDE-ERIYVASEEAEI 322
                                       6666666678******98334577777889999*************6.7******97665 PP

>> Flavi_NS2B  Flavivirus non-structural protein NS2B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   7.6e-05      0.23       6      47 ..     514     555 ..     511     560 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.6e-05
                        Flavi_NS2B   6 aavGlvsvllslllkedvnllGPlivGGllialvvvaGrvdd 47 
                                       +a G+v+vl    +  d+ l+G  ++ G++  ++ + Grvd 
  gi|557694028|ref|YP_008797082.1| 514 MAGGVVAVLGVDSFDSDECLVGRCVATGMVGGVIYIRGRVDR 555
                                       899************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); 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:                         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 0.31s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 4586.12
//
Query:       gi|557694029|ref|YP_008797083.1|  [L=316]
Description: glutamate synthase (NADPH/NADH) large chain [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   33.9   0.1     0.0059   16.1   0.0    2.1  2  Glu_syn_central  Glutamate synthase central domain
    0.00021   20.6   0.1     0.0051   16.0   0.2    2.6  3  Glu_synthase     Conserved region in glutamate synthase
  ------ inclusion threshold ------
      0.041   12.9   0.3      0.061   12.3   0.3    1.4  1  FMN_dh           FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> Glu_syn_central  Glutamate synthase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   9.8e-07    0.0059       7      74 ..       4      73 ..       1      85 [. 0.76
   2 !   15.8   0.1   1.3e-06    0.0076     173     262 ..     192     282 ..     188     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.8e-07
                                      T--HHHHHHTHHHHH.....HHSS--EE-S---S--TTT-SS---GGGGEEE----SSS----TTTTGGG-B- CS
                   Glu_syn_central  7 gyteedlelllepma.....kegkeaigsmGdDtplavLsekprllydYFkqlfAqVTNPpiDpiREelvmsl 74
                                      g+te+ +++ l++ma     + ++ +i smG+ +p  v  + p  + d++    AqVT P+iDp RE + + +
  gi|557694029|ref|YP_008797083.1|  4 GWTEDRVKH-LREMAgvigrQPAEPPIVSMGSTAPPYV--DAPFFIRDHIVIDGAQVTRPSIDPYREPVETHV 73
                                      777777774.4444422222345668******999876..9999***********************876655 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHHHHHTT-GGG-EEEEEESS--SHHHHHHHHHTT-SEEEEHHHHHHHHHHHTTTS-----HH.HHHHHHH CS
                   Glu_syn_central 173 LavgavhhhLvrkglrtkvslvvesgearevhhfavllgyGadavnPylaletieklveegalaeeele.knyrkav 248
                                       ++v+ ++++L r+g+r+ v+lv    ++r   ++  l+++Gadav    ++e + + v++++++  + + +n+  ++
  gi|557694029|ref|YP_008797083.1| 192 VVVALLDRELRRHGVRNTVGLVAGGWSVRGADDVFKLVALGADAVLLSACVEEALEPVKTQTVSIVQEKmENLLLGL 268
                                       578999***************************************99888888877777776633333337777777 PP

                                       HHHHHHHHHHTT-- CS
                   Glu_syn_central 249 ekGllKimskmGis 262
                                       ++ +       G+s
  gi|557694029|ref|YP_008797083.1| 269 QREIKLLAGAAGVS 282
                                       77776666666666 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 ?   -0.6   0.0     0.094   5.6e+02       8      43 ..      48      82 ..      46      97 .. 0.79
   2 !   16.0   0.2   8.6e-07    0.0051     256     303 ..     191     239 ..     185     245 .. 0.89
   3 ?    0.5   0.0     0.044   2.6e+02     336     367 ..     250     281 ..     240     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.094
                                      HHHHHHHHHH---HHHHHHHHHHHTS.-S-SGGGGE CS
                      Glu_synthase  8 ikllqkavqveskesidkyrekleerevlkakrdll 43
                                      ++++ + +qv +++sid yre++e++++l   r +l
  gi|557694029|ref|YP_008797083.1| 48 DHIVIDGAQV-TRPSIDPYREPVETHVYLRGGRLRL 82
                                      5778888888.99999****9999998776655555 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8.6e-07
                                       HHHHHHHHHHHHHTT-GGG-EEEEES.S--SHHHHHHHHHHT-SEEE-S CS
                      Glu_synthase 256 elalaevdqtlkeeglrdrvsliadG.glktgadvvkalalGAdavgig 303
                                       e+ +a  d+ l+++g+r+ v l a G  ++ ++dv+k +alGAdav ++
  gi|557694029|ref|YP_008797083.1| 191 EVVVALLDRELRRHGVRNTVGLVAGGwSVRGADDVFKLVALGADAVLLS 239
                                       566778899****************9679****************9876 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.044
                                       ..TT----HHHHHHHHHHHHHHHHHHHHHHT- CS
                      Glu_synthase 336 krlkveekaervvnyikalaeevrellaalgi 367
                                       k + v+ ++e++ n++  l++e++ l++a+g+
  gi|557694029|ref|YP_008797083.1| 250 KTQTVSIVQEKMENLLLGLQREIKLLAGAAGV 281
                                       67889999*******************99996 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3     1e-05     0.061     280     306 ..     219     245 ..     187     290 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1e-05
                                       --SHHHHHHHHHTT-SEEEESHHHHHH CS
                            FMN_dh 280 irrGsDvlkAlalGAdavllGRpflyg 306
                                       +r   Dv+k +alGAdavll   +  +
  gi|557694029|ref|YP_008797083.1| 219 VRGADDVFKLVALGADAVLLSACVEEA 245
                                       88889*************997655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2354.64
//
Query:       gi|557694030|ref|YP_008797084.1|  [L=275]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  134.6  40.7    4.9e-39  134.4  40.7    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 !  134.4  40.7   2.7e-43   4.9e-39       2     236 .]       8     268 ..       7     268 .. 0.92

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 2.7e-43
                              TauE   2 llagllaGfvagllGiGggliavPlLll.llppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGa 77 
                                       l++ +laG+v++++G+Gg+ i++PlL+l ++p+++a+a+ +++++ats ++a+++ r g  +++++++l +++++Ga
  gi|557694030|ref|YP_008797084.1|   8 LAISFLAGLVGSITGLGGASITTPLLTLaGVPIKYAIAAGIVSIIATSSGAAASYVRGGLSNVKAAMFLEMFTVVGA 84 
                                       6889************************669**************************9999**************** PP

                              TauE  78 llGallllllpsellkllfgvlllllallmllrkkr........................srakgrerrptaillvl 130
                                       ++Ga++  +++++ll +lf+ +ll + + + +  ++                        + +++++++ t++l++ 
  gi|557694030|ref|YP_008797084.1|  85 IIGAIITIYVSARLLYFLFAGFLLTSFIGIRRHLGEelptnvnqdraarwlslegvyydhALGREVSYKLTRPLAAG 161
                                       ***********************988887744333377899999999999888888877633336778888888888 PP

                              TauE 131 iggl.vGllsGllGiGgGfllvpllllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGa 206
                                        g++ +G+++G+lGiG+G++ v++  l++++p k++ ats+++i +++laga +y+++g ++++l++++++g+ lGa
  gi|557694030|ref|YP_008797084.1| 162 GGMFiAGVAAGMLGIGAGAFKVAVHELIMRMPSKVSSATSTFIIGMTALAGASVYFSSGLLYLTLAAPMVLGTTLGA 238
                                       88999************************************************************************ PP

                              TauE 207 llGarlarrlsertlrrlfallllvlgvkl 236
                                       ++G+r+  ++s+r+ r++f+++++vl +++
  gi|557694030|ref|YP_008797084.1| 239 VVGSRILGHISNRVTRLFFLAVVFVLFLQM 268
                                       **************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); 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:                         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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2067.15
//
Query:       gi|557694031|ref|YP_008797085.1|  [L=110]
Description: hypothetical protein CSUB_C0596 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   66.4   5.8    2.2e-18   66.2   5.8    1.0  1  DUF1634          Protein of unknown function (DUF1634)
  ------ inclusion threshold ------
        8.1    6.5   9.8         12    5.9   4.5    2.0  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


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 !   66.2   5.8   2.4e-22   2.2e-18       1     102 []       3     108 ..       3     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 2.4e-22
                           DUF1634   1 igklLriGvllsaavvllGlilllvkhgs....sesenseltslseilegllelkglaiiqlGllvLiatPvlrVvl 73 
                                       i+++L +Gv++s+av++++l+ +++++g     s + + +  s+ + l  ++++   + + +G+  L++tP +r ++
  gi|557694031|ref|YP_008797085.1|   3 ISWILVAGVAASLAVTTWALASYYLSNGPalalSDEYRVSSKSFFDYLLHIHKGGVAGAMAVGVAALMLTPYIRALA 79 
                                       89**************************7554432444555555555555677778899****************** PP

                           DUF1634  74 sliaFlkekdilyviitliVLliLllsll 102
                                       sli F++++di y++it++V++iL++sll
  gi|557694031|ref|YP_008797085.1|  80 SLIYFIAKRDIKYILITAFVFTILTISLL 108
                                       **************************985 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 ?    3.9   0.2    0.0057        51      39      58 ..       5      24 ..       1      44 [. 0.63
   2 ?    5.9   4.5    0.0014        12      32      81 ..      55     105 ..      52     109 .. 0.70

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0057
                   Phage_holin_3_6 39 llgaagvlallalllllval 58
                                      ++++agv a la++++ +a 
  gi|557694031|ref|YP_008797085.1|  5 WILVAGVAASLAVTTWALAS 24
                                      55666666666666665554 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0014
                   Phage_holin_3_6  32 ragsgagllgaagvlallalllllvalalala.alwlaalivaavllvlag 81 
                                       + g++++++++ ++l+l+  + +l+ l++++a       li+a v+ +l++
  gi|557694031|ref|YP_008797085.1|  55 KGGVAGAMAVGVAALMLTPYIRALASLIYFIAkRDIKYILITAFVFTILTI 105
                                       677888888888888888888888888999953365666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 876.25
//
Query:       gi|557694032|ref|YP_008797086.1|  [L=285]
Description: Rieske (2Fe-2S) domain-containing protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   37.3   0.0    3.4e-09   36.5   0.0    1.4  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 !   36.5   0.0   1.9e-13   3.4e-09      25      82 ..      89     145 ..      62     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.9e-13
                                       EEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE-TTH CS
                            Rieske  25 plvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikgPap 82 
                                       +++++    g+++A+s+vC H+ +    ++  +k +++CpcHg+ y+  +G +i gPa 
  gi|557694032|ref|YP_008797086.1|  89 QYILVHLPSGDLKAYSKVCVHLWCLY--DYFPDKRQFQCPCHGSIYNpDTGVAIRGPAA 145
                                       456666679***************94..4554677************999*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 2158.92
//
Query:       gi|557694033|ref|YP_008797087.1|  [L=213]
Description: hypothetical protein CSUB_C0598 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1658.75
//
Query:       gi|557694034|ref|YP_008797088.1|  [L=325]
Description: DNA methylase N-4/N-6 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-26   92.1   0.1    1.3e-12   48.0   0.0    2.1  2  N6_N4_Mtase      DNA methylase
    2.4e-07   30.7   0.1      0.003   17.3   0.0    2.2  2  UPF0020          Putative RNA methylase family UPF0020
    1.7e-05   25.4   0.0    0.00014   22.5   0.0    2.2  1  Methyltransf_11  Methyltransferase domain
      0.003   18.2   0.0      0.072   13.8   0.0    2.5  2  Methyltransf_25  Methyltransferase domain


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 !   48.0   0.0   2.8e-16   1.3e-12     147     226 ..      66     140 ..      28     145 .. 0.87
   2 !   42.3   0.1   1.5e-14   6.9e-11       1     114 [.     180     310 ..     180     320 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 2.8e-16
                                       --BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSH CS
                       N6_N4_Mtase 147 kiediWdlseiqsnekkskgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaakelgrkfiGieiee 223
                                       + +++W ++++ + + +s       +        ++ lI+ +tk+g++vlD   GSGtT+v+a  lgr++iG++i+ 
  gi|557694034|ref|YP_008797088.1|  66 EATTVWSFPDRGDWATHSGD-----YRGNWSPYVPRNLILKYTKPGELVLDQMVGSGTTLVEATLLGRNAIGVDINY 137
                                       56789989999999888874.....89999999*******************************************9 PP

                                       HHH CS
                       N6_N4_Mtase 224 eyv 226
                                       e++
  gi|557694034|ref|YP_008797088.1| 138 EAC 140
                                       987 PP

  == domain 2  score: 42.3 bits;  conditional E-value: 1.5e-14
                                       EEEEEE--SSSSSCS........GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT......HHHHH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy...endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk......elkal 68 
                                       vdli t pPY++   y   + + ++ +  + e+yl  + ++++e +rvLk++    i i+d + +k      + ++l
  gi|557694034|ref|YP_008797088.1| 180 VDLIATHPPYWNIIPYsrkRPEGDLSAYRKLEDYLGKMMQIARESYRVLKPGRYCAILIGDTRKHKhyvpisTYVML 256
                                       89*************9777778888888999***************************************9988888 PP

                                       HHHHTT-EEEEEEEEEEES......SSTTTSTCC..........S-B--EEEEEEEESSTT- CS
                       N6_N4_Mtase  69 adeifggffllnvivwkkp......nsmpesnkd..........rltsthEyilvfsknkky 114
                                          ++g f+l+++i++ +       +       +          + + +hE++++f+k++++
  gi|557694034|ref|YP_008797088.1| 257 KFLQAG-FVLAEDIIKLQHkmkttrE-------KwsgknfeqygFHKIAHEHLYIFRKPENE 310
                                       888888.*******997763344431.......335555567768899***********987 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   6.8e-07     0.003      26      54 ..     103     131 ..      98     159 .. 0.86
   2 !   11.2   0.0   4.8e-05      0.21     104     131 ..     161     189 ..     155     199 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.8e-07
                                       --TTS-EEETT-TTSHHHHHHHHHHTT-- CS
                           UPF0020  26 wkpgepllDPmCGsGtilIEaallgania 54 
                                        kpge  lD m GsGt l+Ea llg+n++
  gi|557694034|ref|YP_008797088.1| 103 TKPGELVLDQMVGSGTTLVEATLLGRNAI 131
                                       5899***********************98 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4.8e-05
                                       GEEEEE--GGG--.STTS---EEEE---- CS
                           UPF0020 104 liefsqadaakLr.lkegevdvivtnpPY 131
                                        i+++  daakL+  ++++vd+i+t pPY
  gi|557694034|ref|YP_008797088.1| 161 VIKVYHGDAAKLNiIEDESVDLIATHPPY 189
                                       689999*******96777*********** PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     3e-08   0.00014       5      96 .]     114     236 ..     110     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 3e-08
                                       -TTSHHHHHHHHTTSEEEEEES-HHHH..HHHHHHCCHHT-......EEEETTEECCCTS.S-TT-EEEEEEES-CC CS
                   Methyltransf_11   5 cGtGrlaealakrgarvvgvDlskeml..klakekaseegl......kvefvvadaeklp.fednsfDlvvssevlh 72 
                                       +G+G  + + +  g++ +gvD++ e+   +l + + +  +l       +++ ++da kl+ +ed+s+Dl+  +    
  gi|557694034|ref|YP_008797088.1| 114 VGSGTTLVEATLLGRNAIGVDINYEACilTLDRLNFEFHPLdeqqepVIKVYHGDAAKLNiIEDESVDLIATHPPYW 190
                                       56677777777779***********9955333444443333667777899*********559********9999777 PP

                                       C-.C.....................CHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  73 hv.e.....................dpekalkeiaRvLkpgGllvi 96 
                                       ++ +                     +++++ +e +RvLkpg +++i
  gi|557694034|ref|YP_008797088.1| 191 NIiPysrkrpegdlsayrkledylgKMMQIARESYRVLKPGRYCAI 236
                                       7753566788999999999999999****************99875 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   1.6e-05     0.072       1      70 [.     109     185 ..     109     199 .. 0.79
   2 ?    1.5   0.0      0.11   4.9e+02      82      96 ..     217     231 ..     205     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH........TTTTEEEEESBCCGBS.SSTTTEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee........eglnvefvqgdaedlp.fedgsfDlv 68 
                                       vLd   G+G+++ ++    g  + +gvDi+ e++  +  r++         +++ +++++gda +l+  ed+s+Dl+
  gi|557694034|ref|YP_008797088.1| 109 VLDQMVGSGTTLVEATLL-G-RNAIGVDINYEACILTLDRLNFefhpldeqQEPVIKVYHGDAAKLNiIEDESVDLI 183
                                       89999******9999977.5.9*******9888655444443334455544666************9569******9 PP

                                       EE CS
                   Methyltransf_25  69 vs 70 
                                         
  gi|557694034|ref|YP_008797088.1| 184 AT 185
                                       75 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHEEEE CS
                   Methyltransf_25  82 lekalkeiarvLkpg 96 
                                       + ++ +e +rvLkpg
  gi|557694034|ref|YP_008797088.1| 217 MMQIARESYRVLKPG 231
                                       567899********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); 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:                         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: 00:00:00.38
# Mc/sec: 2563.69
//
Query:       gi|557694035|ref|YP_008797089.1|  [L=93]
Description: thioredoxin [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   36.4   1.2    9.6e-09   35.2   1.2    1.7  1  Thioredoxin_3  Thioredoxin domain
      2e-06   27.9   0.0    2.8e-06   27.4   0.0    1.2  1  Glutaredoxin   Glutaredoxin
     0.0012   19.0   0.5     0.0087   16.2   0.0    2.0  2  Thioredoxin_4  Thioredoxin
     0.0049   16.8   0.3       0.41   10.7   0.1    2.2  2  Thioredoxin    Thioredoxin
     0.0053   17.1   0.0     0.0073   16.7   0.0    1.2  1  GST_N_3        Glutathione S-transferase, N-terminal domain
  ------ inclusion threshold ------
      0.012   16.1   1.6        0.6   10.6   1.8    2.7  2  Thioredoxin_2  Thioredoxin-like domain
       0.15   12.3   0.0       0.21   11.9   0.0    1.3  1  GST_N_2        Glutathione S-transferase, N-terminal domain


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 !   35.2   1.2   3.8e-12   9.6e-09       4      70 ..       6      75 ..       3      78 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 3.8e-12
                                      EEESSSSTTCHHHHHHHHHHCHCCTCEC...EEECC.TTHHHH.HHCT-SSSSEEECTTCEEEESS---CCH CS
                     Thioredoxin_3  4 kvlgpgCakCpklekavkeaaaekgika...evekv.tdfeei.ekygVmsvPalvidgkvvvsGkvpseee 70
                                      + + ++C+ C+k++++++   +  g ++   ++ k  + +ee+ +ky+++svP+l+idgk++++G vp+  +
  gi|557694035|ref|YP_008797089.1|  6 ELFISNCPLCRKTRAMIEL-GKCAGCSFtihDLSKNfYAVEELvKKYQIRSVPTLIIDGKIKIEG-VPTFTF 75
                                      556799*****99999863.3444555522455555588999***********************.*98665 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.1e-09   2.8e-06       7      58 ..      10      64 ..       5      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.1e-09
                                      TSSHHHHHHHHHH...HHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTE CS
                      Glutaredoxin  7 ptCpyCkkakrlL...kelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgk 58
                                      ++Cp C+k+++     k  g +f+++d++k+  + eel ++  +r+vP++ idgk
  gi|557694035|ref|YP_008797089.1| 10 SNCPLCRKTRAMIelgKCAGCSFTIHDLSKNFYAVEELVKKYQIRSVPTLIIDGK 64
                                      68***********777777799**********9999999999************8 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2     0.099   2.5e+02      22      32 ..      10      19 ..       2      28 .. 0.73
   2 !   16.2   0.0   3.4e-06    0.0087     120     155 ..      35      71 ..      17      76 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.099
                                      -TT-HHHHHHH CS
                     Thioredoxin_4 22 dlrCphCakfe 32
                                      + +Cp C+k  
  gi|557694035|ref|YP_008797089.1| 10 S-NCPLCRKTR 19
                                      3.8*****976 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.4e-06
                                       ---HHHHHHHHHHHHHHT--SS-EEEETTEE.E-TT- CS
                     Thioredoxin_4 120 ekldalveaeskeakkagiestPtfiingek.veepq 155
                                        +l++   a  + +kk +i s+Pt+ii+g++ +e+ +
  gi|557694035|ref|YP_008797089.1|  35 HDLSKNFYAVEELVKKYQIRSVPTLIIDGKIkIEGVP 71 
                                       45555555666666****************9566555 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00016      0.41      27      78 ..       9      61 ..       2      64 .. 0.71
   2 !    5.0   0.0    0.0095        24      67      83 ..      64      80 ..      61      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
                                      -TTSHHHHCHHHHHHHHHHHCTT.TSEEEEEETTTSHHHHHHTT-SSSSEEEE CS
                       Thioredoxin 27 ApwCghCkalaPeleklaeelkd.kvklakvdvdenedlakkyevegiPtlkl 78
                                       + C+ C++   ++e  + +    ++  +  +  + e+l+kky+++++Ptl++
  gi|557694035|ref|YP_008797089.1|  9 ISNCPLCRKTRAMIELGKCAGCSfTIHDLSKNFYAVEELVKKYQIRSVPTLII 61
                                      566888888887776544333323555556688899***************76 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0095
                                      HTT-SSSSEEEEEETTE CS
                       Thioredoxin 67 kyevegiPtlklfkngk 83
                                      k+++eg+Pt+ ++ +++
  gi|557694035|ref|YP_008797089.1| 64 KIKIEGVPTFTFICDEN 80
                                      789*********98876 PP

>> GST_N_3  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.8e-06    0.0073       4      59 ..      12      68 ..       9      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.8e-06
                                      -TTSHHHHHHHHHHHHHT--EEEE---TTTT.HHHHHHH-TT--SSEEETTS-EEES CS
                           GST_N_3  4 fpaSpyarrvrlaLnekglpvevvevtpgeh.deellaknplgkvPvLeddgealtd 59
                                      +p ++ +r + ++ ++ g +++++++++     eel +k+  + vP+L +dg++  +
  gi|557694035|ref|YP_008797089.1| 12 CPLCRKTRAMIELGKCAGCSFTIHDLSKNFYaVEELVKKYQIRSVPTLIIDGKIKIE 68
                                      34444444455555677778*******99988*******************997665 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.8   0.00024       0.6      68      90 ..      43      64 ..       8      74 .. 0.71
   2 ?    1.3   0.0      0.18   4.7e+02      76      90 ..      65      80 ..      62      87 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                     Thioredoxin_2 68 envelarkygvrgtPtivfldgk 90
                                      + +el++ky++r++Pt+++ dgk
  gi|557694035|ref|YP_008797089.1| 43 AVEELVKKYQIRSVPTLII-DGK 64
                                      457899**********986.444 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.18
                     Thioredoxin_2 76 ygvrgtPtiv.fldgk 90
                                       +++g+Pt+  + d++
  gi|557694035|ref|YP_008797089.1| 65 IKIEGVPTFTfICDEN 80
                                      6899****66155555 PP

>> GST_N_2  Glutathione S-transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.3e-05      0.21       2      55 ..      12      64 ..      11      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.3e-05
                                      -HHHHHHHHHHHHCT--EEEEEEH...-TTSHHHHHHHHCTTTSSSEEE-CTTE CS
                           GST_N_2  2 CPwahRvlialalkglediisvvvlepkgfekseefprlnprgtVPvLwdkdgq 55
                                      CP +++++ +++l +       +++  k f++ ee+ +     +VP+L++ dg+
  gi|557694035|ref|YP_008797089.1| 12 CPLCRKTRAMIELGKCAGCSFTIHDLSKNFYAVEELVKKYQIRSVPTLII-DGK 64
                                      *************988777555555578999999998888888******9.554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 717.08
//
Query:       gi|557694036|ref|YP_008797090.1|  [L=210]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-10   40.0  11.1    8.7e-08   32.7   8.8    3.0  2  SNARE_assoc  SNARE associated Golgi protein
  ------ inclusion threshold ------
       0.42   10.7   2.5       0.52   10.4   1.1    1.8  2  DUF1230      Conserved in the green lineage and diatoms 27


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 !   32.7   8.8   9.7e-12   8.7e-08       2     116 ..      40     149 ..       2     152 .. 0.90
   2 !    4.8   0.0    0.0044        39       9      40 ..     165     195 ..     157     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 9.7e-12
                       SNARE_assoc   2 PsevllvaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvka...lerlverygflallllr 75 
                                       P  +++v+aG l ++l + l++++ga  ++++ + + +      ++r l+s ++ ++   lerlv r+g++a+l + 
  gi|557694036|ref|YP_008797090.1|  40 PPIIIAVMAGRL-DPLPTALASAAGAASAKLVLFRFFK------GGRVLISDETRRRiqpLERLVARHGWFAVLAAA 109
                                       555777888888.8999999999999999999998863......5666677777676778***************** PP

                       SNARE_assoc  76 llpivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyay 116
                                        +p +P+d++ ++++++++s k F+ + f+G+++ +++ ay
  gi|557694036|ref|YP_008797090.1| 110 ATP-LPDDIIYILLAIANYSSKLFLPTVFAGKLLITTIAAY 149
                                       ***.79*******************************9998 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0044
                       SNARE_assoc   9 aaGvlfglllgtlvtslgallGaslayllgry 40 
                                       +aG l ++l ++l++++ a ++++l y++ r 
  gi|557694036|ref|YP_008797090.1| 165 TAGQL-NPLQTILLAAASAAAAMTLIYIITRL 195
                                       56666.89999*****************9986 PP

>> DUF1230  Conserved in the green lineage and diatoms 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.27   2.4e+03      50      85 ..      42      76 ..      10      81 .. 0.67
   2 ?   10.4   1.1   5.8e-05      0.52      31      95 ..     141     205 ..     118     208 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.27
                           DUF1230 50 vaaasfspekellelllssalgalvlvalvllrlyl 85
                                      + +a ++ + ++l + l+sa+ga  +  lvl r++ 
  gi|557694036|ref|YP_008797090.1| 42 IIIAVMAGRLDPLPTALASAAGAASA-KLVLFRFFK 76
                                      44445555556777777777777654.456666665 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 5.8e-05
                           DUF1230  31 eylrrlllvwlvlllvvgpvaaasfspekellelllssalgalvlvalvllrlylgWsYvgdRLl 95 
                                        +++++++  ++ +  ++   +  ++ + ++l+++l +a++a  +++l+ +   l W+ + ++L 
  gi|557694036|ref|YP_008797090.1| 141 LLITTIAAYTALYWSTLACTIIECTAGQLNPLQTILLAAASAAAAMTLIYIITRLDWQKILTKLG 205
                                       344444444444444333222223356678****************************9998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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: 00:00:00.42
# Mc/sec: 1514.32
//
Query:       gi|557694037|ref|YP_008797091.1|  [L=450]
Description: hydroxypyruvate reductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-68  228.5   0.0      1e-67  228.0   0.0    1.2  1  DUF4147   Domain of unknown function (DUF4147)
    2.4e-37  127.4   0.4    4.5e-37  126.6   0.4    1.5  1  MOFRL     MOFRL family
  ------ inclusion threshold ------
       0.12   12.9   0.4       0.12   12.9   0.4    2.2  2  NBD_C     Nucleotide-binding C-terminal domain


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 !  228.0   0.0   1.8e-71     1e-67       6     228 ..      23     254 ..      18     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: 228.0 bits;  conditional E-value: 1.8e-71
                                       HHHHHHTTSHHHHHHTTHHHH--..............-SEEEEEESTTHHHHHHHHH.HHHG....EEEEEEETT-- CS
                           DUF4147   6 feaaveavdpeklvkralslkee.......eldlskkkrvvvvgaGKAaaamaaaleeealk....sgvvvvkkgha 71 
                                       ++++++av+p +l++r+++++          ++l++++++v+vg GKAa +maa + +  l+    +gvvvv++g++
  gi|557694037|ref|YP_008797091.1|  23 LRSGLAAVEPGALIRRVVKRRGGclqiggkVVELRRFRDFVIVGGGKAAEGMAAEMLR-LLDgldvRGVVVVPRGYR 98 
                                       7899**************98333555555588999******************77773.4445559******86655 PP

                                       -..--TT-EEEEE-SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHHHHCT CS
                           DUF4147  72 e..ekerievleaahplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaLlasG 146
                                          + + +evl ++hplPd+ s ea r ile+a++++ d l +vl+SGG SAl a+Paeg++l+dk + t+aLl++G
  gi|557694037|ref|YP_008797091.1|  99 LrrRLKPLEVLYGGHPLPDSMSEEAGRLILEMASSCSGDSLAFVLVSGGFSALAAVPAEGVSLQDKVEATSALLRAG 175
                                       5336678********************************************************************** PP

                                       --HHHHHHHHHTTBSSTTTHHHHHHTTSEEEEEEE--STT--TTTGGG-TTS-----HHHHHHHHHHTT---..-HH CS
                           DUF4147 147 asIqelNtVRkhlsaikGGrLaraaaparvvsLilSDVvgddldvIASGPtvpdsstfadalailekykleeklpes 223
                                       asI+elNtVRkhlsa+kGG La+ ++  r +sLilSDVvgd++dvI+SGPt+pd++tf+dal++l++ ++e  ++e+
  gi|557694037|ref|YP_008797091.1| 176 ASIDELNTVRKHLSAFKGGWLAKSLRC-RAFSLILSDVVGDRVDVIGSGPTAPDPTTFRDALDVLRRRGVE--VSEN 249
                                       *************************98.******************************************9..99** PP

                                       HHHHH CS
                           DUF4147 224 vrelL 228
                                       v + L
  gi|557694037|ref|YP_008797091.1| 250 VWRRL 254
                                       99988 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.6   0.4   7.5e-41   4.5e-37       2     109 .]     339     443 ..     338     443 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 7.5e-41
                                       EEEEEE--B----S-----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EEEEETTHHHHHHHTT--H CS
                             MOFRL   2 vllsgGEttvtvkgkGkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGaivdaetleraeaaglda 78 
                                       +l++gGEttvtv+g+G+GGrnqel+la++  l+++   +++v++s+gtDG+DG tdaaGa+++++tl++a+++gld+
  gi|557694037|ref|YP_008797091.1| 339 ALVAGGETTVTVRGRGRGGRNQELVLATLHLLRDV---PRFVFASIGTDGVDGVTDAAGAVATPQTLRNAAKEGLDP 412
                                       799**************************966665...9************************************** PP

                                       HHHHHTT-HHHHHHHTT-EE-----S----E CS
                             MOFRL  79 keaLanndsyeffeklgallktgpTgtNVnD 109
                                         +L++ndsy+ff+++g l+ tgpTgtNV D
  gi|557694037|ref|YP_008797091.1| 413 LPFLEDNDSYTFFSRVGGLVLTGPTGTNVGD 443
                                       *****************************87 PP

>> NBD_C  Nucleotide-binding C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.36   2.2e+03     106     140 ..      56      85 ..      46     113 .. 0.62
   2 ?   12.9   0.4     2e-05      0.12      82     125 ..     303     350 ..     280     364 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.36
                                       HHHCTECEEEEESHHHHHHHHHHCT--EEEEEEEE CS
                             NBD_C 106 lvergvrrlviaGGdtssavlkaLgvkgleilgei 140
                                       l  r++r +vi GG   +++++++ ++ l++l+ +
  gi|557694037|ref|YP_008797091.1|  56 L--RRFRDFVIVGG---GKAAEGMAAEMLRLLDGL 85 
                                       3..35899888855...455556666666665555 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 2e-05
                                       HHCCC-HHHHHHHHHHHHHHHHHHHHHCT...ECE.EEEESHHHHHHH CS
                             NBD_C  82 lqaelglerageriaaalaeiarrlverg...vrr.lviaGGdtssav 125
                                       ++ + g+  +++++a+++a++ar++v++g     +  ++aGG+t+  v
  gi|557694037|ref|YP_008797091.1| 303 VALTSGVVGEARTVANLFAAVARDVVRHGvphAPPfALVAGGETTVTV 350
                                       555567777799**************776454566799*******988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3561.69
//
Query:       gi|557694038|ref|YP_008797092.1|  [L=345]
Description: deoxyhypusine synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-84  283.4   0.0    2.1e-84  283.2   0.0    1.0  1  DS        Deoxyhypusine synthase


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 !  283.2   0.0   1.2e-88   2.1e-84       1     287 [.      27     325 ..      27     326 .. 0.96

  Alignments for each domain:
  == domain 1  score: 283.2 bits;  conditional E-value: 1.2e-88
                                DS   1 ellesyekigfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlika 77 
                                       +ll++++ +gfq+++l+ a++ ++k+ +++++ i+lg++++l ++G  +i+++l+++++vdv+v+T+++i+eDli a
  gi|557694038|ref|YP_008797092.1|  27 QLLDQMKLTGFQGRNLALAAETWAKAAQAKDTVIMLGYAGSLSTTGQWKIVKWLIEKRFVDVVVSTGANISEDLIAA 103
                                       599************************************************************************** PP

                                DS  78 lgkktylgdfelddeeLrekginRignllvpnenyckfedwvreildkleeeqkvwspselikelGkeinde..eSi 152
                                       +g ++y+g+  +dd+ Lr+  i R+++++v++e+y k+e ++++++ +l++  + +s++e+++ +Gk+++++  ++i
  gi|557694038|ref|YP_008797092.1| 104 MGYNYYIGTSYIDDDLLRRLRIYRFHDVFVKEEDYIKMEGMLADFMLTLDN-MNPISSAEFLHLFGKWLDQRniHGI 179
                                       ************************************************997.5778**************55559** PP

                                DS 153 lywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanl 229
                                       +++Ay++++pvf+pa+ D+ +G ++++ ++ k   +l+ld +kD+++l +i  +++ ++a+++GGGvpK++i+ +++
  gi|557694038|ref|YP_008797092.1| 180 VQAAYRAGVPVFSPAIEDSGYGVAYIINRHRKPGYRLVLDHFKDYEQLVRIRGRHRDSAAVFIGGGVPKDFIQLSAV 256
                                       ***********************7777776668899*************************************9998 PP

                                DS 230 m...........rngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                       +            + + yav+itt+++++G+lsgatl+E++Swgk ++e   v++++DaTi+lPL++++
  gi|557694038|ref|YP_008797092.1| 257 AvdilekgdaltTRPHRYAVQITTDNPHWGGLSGATLEEGKSWGKETSEGVGVQCFCDATIALPLIAHY 325
                                       88*******998458***************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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 0.21s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2865.78
//
Query:       gi|557694039|ref|YP_008797093.1|  [L=184]
Description: oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-24   86.3   0.0    1.7e-24   86.2   0.0    1.1  1  LDcluster4       SLOG cluster4 family
    2.3e-05   24.5   0.0      5e-05   23.4   0.0    1.6  1  Lysine_decarbox  Possible lysine decarboxylase
     0.0055   16.0   0.1      0.023   13.9   0.0    1.9  2  LSDAT_prok       SLOG in TRPM, prokaryote
     0.0098   15.5   0.1       0.18   11.4   0.1    2.2  2  DAGK_cat         Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.018   14.4   0.0    1.3  1  LSDAT_euk        SLOG in TRPM


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 !   86.2   0.0   4.9e-28   1.7e-24       2     150 ..       2     160 ..       1     170 [. 0.84

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 4.9e-28
                        LDcluster4   2 lkigVmGsaeteakeealelaeelGrliA..kegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnk.. 74 
                                       l+igV  s++ e  + a+e+a++ +  +   + ++vlltGg +G+m+++++   ++gG+tvG++p ++e  ++ +  
  gi|557694039|ref|YP_008797093.1|   2 LQIGVGCSSDREPLPGAVEKARRFAARLGvyRDEVVLLTGGDGGLMRVVCEEFVRRGGITVGVIPYEDEFIDKTHpr 78 
                                       6788877777665555566666665554322899********************************88876666678 PP

                        LDcluster4  75 ...yvdiiiyTGlglagRnlilvlssdvviaiggrsGTlsEialaleegkpvivlkgt...dellseiiekkekder 145
                                          y +i+  +G  ++ R++ lv+ssd  +++gg+sGT+ E  la+ ++ p+i+l++t   +++l ++  + + d+r
  gi|557694039|ref|YP_008797093.1|  79 ynpYNTIVFRSGQTYQARSIGLVRSSDSFVILGGGSGTIIEAHLAYIYRIPLIILTETgypSDILAQMHPDGHLDHR 155
                                       89999***************************************************999998899999999999998 PP

                        LDcluster4 146 kviva 150
                                       k+  a
  gi|557694039|ref|YP_008797093.1| 156 KINAA 160
                                       66544 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.4e-08     5e-05       2     131 ..      48     172 ..      47     173 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.4e-08
                                       HHHHHHHHHTTS-EEEEEECCHHHHHCCTTT-SEE.....EEESSHHHHHHHHHHHESEEEE-S-SHHHHHHHHHHH CS
                   Lysine_decarbox   2 eavakgaleaggrviGiipkillaeeapneevnel.....vivedmeeRkealveladafvilPGGiGTleElleil 73 
                                        +v +  ++ gg ++G+ip        +++++n          ++ + R   lv+ +d fvil GG GT+ E+    
  gi|557694039|ref|YP_008797093.1|  48 RVVCEEFVRRGGITVGVIPYEDEFIDKTHPRYNPYntivfRSGQTYQARSIGLVRSSDSFVILGGGSGTIIEA---- 120
                                       556666677788888887754433333333333322212233468899*********************7664.... PP

                                       HHHHTTSS-S.EEEEEEGGGCCHHHHHHHHHHHHTTSS-GGGGGCEEEESSHHHHHHH CS
                   Lysine_decarbox  74 tliqlgkhqkvPiillnpkgyydkllefletlveegtisekareliivvddpeevlek 131
                                           l    ++P+i+l + gy + +l+ +      g +++ ++++++ ++dpe++++k
  gi|557694039|ref|YP_008797093.1| 121 ---HLAYIYRIPLIILTETGYPSDILAQM---HPDGHLDHRKINAAHYINDPEAAADK 172
                                       ...45566778999999999***999988...579******************99986 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.15   5.4e+02      37      55 ..      34      52 ..      17      77 .. 0.70
   2 !   13.9   0.0   6.5e-06     0.023     127     178 ..     107     159 ..      93     183 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.15
                        LSDAT_prok 37 gavvidgGtdtGvmkllgr 55
                                      + vv+ +G d G m+++ +
  gi|557694039|ref|YP_008797093.1| 34 DEVVLLTGGDGGLMRVVCE 52
                                      4566666677777777655 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.5e-06
                        LSDAT_prok 127 tvlvnGgeitlkdiresvkagrpilvvaGsgrladeiaaal.rgdseearlka 178
                                        v+++Gg+ t+ ++  +   + p+++++ +g   d +a+++ +g+ ++ + +a
  gi|557694039|ref|YP_008797093.1| 107 FVILGGGSGTIIEAHLAYIYRIPLIILTETGYPSDILAQMHpDGHLDHRKINA 159
                                       46789999*****************************9999866666533333 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.1   5.2e-05      0.18      42      89 ..      20      66 ..      14      67 .. 0.81
   2 ?    1.9   0.0     0.046   1.6e+02      53      71 ..     102     120 ..      69     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.2e-05
                                      THHHHHHHHHHHCC-SEEEEEESHHHHHHHH.HHHCTHHCTTSEEEEEE CS
                          DAGK_cat 42 gdakelakeakeegvdlivvaGGDGtvsevl.nglleelatkpplgiiP 89
                                      ++a+++a+++   + ++++  GGDG +  v+ + +++  +  + +g+iP
  gi|557694039|ref|YP_008797093.1| 20 EKARRFAARLGVYRDEVVLLTGGDGGLMRVVcEEFVR--RGGITVGVIP 66
                                      678999999999999*********8766665155555..999999*999 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.046
                                       HCC-SEEEEEESHHHHHHH CS
                          DAGK_cat  53 eegvdlivvaGGDGtvsev 71 
                                       +++ ++++  GG Gt+ e+
  gi|557694039|ref|YP_008797093.1| 102 RSSDSFVILGGGSGTIIEA 120
                                       335589*********9775 PP

>> LSDAT_euk  SLOG in TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.1e-06     0.018     183     228 ..     108     151 ..      84     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.1e-06
                         LSDAT_euk 183 vvveGGpntiktv.leyvrespkvPvvvvdgsGraaDllafahklle 228
                                       v++ GG  ti  + l y+    ++P++++  +G  +D+la +h   +
  gi|557694039|ref|YP_008797093.1| 108 VILGGGSGTIIEAhLAYIY---RIPLIILTETGYPSDILAQMHPDGH 151
                                       8999999987665155555...5*****************9997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1500.21
//
Query:       gi|557694040|ref|YP_008797094.1|  [L=1175]
Description: reverse gyrase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-75  253.8   0.0    4.2e-75  253.3   0.0    1.2  1  Topoisom_bac    DNA topoisomerase
    9.3e-21   74.0   0.0      4e-20   72.0   0.0    2.2  1  Toprim          Toprim domain
    9.1e-13   48.3   0.0    6.2e-12   45.6   0.0    2.3  2  DEAD            DEAD/DEAH box helicase
      2e-08   34.5   0.0      0.024   15.0   0.0    3.9  3  Helicase_C      Helicase conserved C-terminal domain
    4.1e-07   29.3   6.5    6.7e-07   28.6   0.8    3.1  3  zf_Rg           Reverse gyrase zinc finger
    6.3e-07   29.6   0.1    2.1e-06   27.9   0.0    1.8  2  ResIII          Type III restriction enzyme, res subunit
    0.00022   20.7   0.0    0.00043   19.8   0.0    1.4  1  PhoH            PhoH-like protein
     0.0017   18.8   0.8       0.45   11.0   0.2    2.5  2  zf-C4pol        C4-type zinc-finger of DNA polymerase delta
     0.0065   15.8   8.6      0.048   13.1   3.1    2.4  2  zf-ribbon_3     zinc-ribbon domain
     0.0099   15.7   5.2      0.015   15.2   1.0    2.5  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.032   14.2   5.1       0.51   10.4   0.7    2.4  2  DZR             Double zinc ribbon
      0.033   13.5   0.0       0.06   12.6   0.0    1.5  1  SecA_DEAD       SecA DEAD-like domain
      0.051   13.7   3.9        6.7    6.9   0.0    2.6  2  DUF1272         Protein of unknown function (DUF1272)
      0.099   12.7   4.1        1.2    9.2   0.5    2.7  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.11   12.8   0.0        3.6    7.9   0.0    3.0  2  DUF1400         Alpha/beta hydrolase of unknown function (DUF
       0.11   12.4   0.6       0.24   11.3   0.6    1.6  1  VATC            Vms1-associating treble clef domain
       0.15   11.7   0.0       0.42   10.3   0.0    1.8  1  AAA_30          AAA domain
       0.16   11.5   0.0         16    4.9   0.0    2.4  2  BRI3BP          Negative regulator of p53/TP53
       0.16   12.0   0.1        2.5    8.1   0.1    2.8  2  CbiA            CobQ/CobB/MinD/ParA nucleotide binding domain
       0.18   11.7   3.5       0.59   10.1   0.2    2.7  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
       0.22   11.5   5.3       0.21   11.6   1.2    2.3  2  zinc-ribbons_6  zinc-ribbons
       0.27   10.9   2.2       0.47   10.1   0.1    2.2  2  TackOD1         Thaumarchaeal output domain 1
       0.41   10.3  12.6      0.056   13.0   2.2    3.2  3  RecR            RecR protein
       0.47   10.6   5.0          5    7.3   2.7    2.7  2  Zn-ribbon_8     Zinc ribbon domain
        0.5   10.7   4.4       0.28   11.5   0.7    2.5  2  Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase


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 !  253.3   0.0   5.9e-78   4.2e-75       5     413 .]     772    1158 ..     768    1158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 253.3 bits;  conditional E-value: 5.9e-78
                      Topoisom_bac    5 nlvdaaeaRrelDwliGinlsrlltkklkgkkvlsaGRVqtptLaliveRereienFvpeeyweveatlkkekke 79  
                                         lv+a+ +Rr+ D+++G++lsr l++  +g+k lsaGRVqtp+L++i++R +e ++       ++ a++++e+++
  gi|557694040|ref|YP_008797094.1|  772 PLVEAQVVRRIEDRWVGFELSRRLWE-FFGEKHLSAGRVQTPVLGWIIQRMEEAKKK------RLVASMTFEDGS 839 
                                        589**********************7.8889***********************999......455555444433 PP

                      Topoisom_bac   80 kekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkL 154 
                                             +   ++i+d + +++++++   + ++v +v+  e+  p+ +p++t++L+++as  l+lsa++++++aq L
  gi|557694040|ref|YP_008797094.1|  840 -----ELMLDSIEDVDVVKRLYAEGVLN-VEVADVKYVETVVPAVKPYTTDSLLRDASIFLRLSAAEAMDAAQTL 908 
                                        .....45678899999999999998445.99*****999999********************************* PP

                      Topoisom_bac  155 YekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelp.k 228 
                                        +e+ glitY+RT st++s++  l+ ++++l++++   + +   +     +        + +aHe+IrPt+ l+ k
  gi|557694040|ref|YP_008797094.1|  909 FES-GLITYHRTGSTYVSSTG-LSVARNYLEENFPGLFVA---R-----H------HGEPGAHECIRPTKPLSrK 967 
                                        **7.*****************.9*********86543222...2.....2......22349********999944 PP

                      Topoisom_bac  229 lkels...............ddekklYelIvrrflaslmkdakyeettvkleveeeefkasgk.tilekGfkkvy 287 
                                          +l+               d e  lY+l++rrf+as+mkda ++++ +kl + +++++++    ++e+Gf+ +y
  gi|557694040|ref|YP_008797094.1|  968 --QLElylqsglirvpmrigDREFMLYDLVFRRFMASQMKDALVQRQICKLMILGKTYDIERIvDVIEPGFLHLY 1040
                                        ..555569999*********99999****************************8889988765169********* PP

                      Topoisom_bac  288 keekkeeeeeelpelkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverk 362 
                                        +  k+      +++l+ g    v  ++l+ k+ ++ + + e+++i++m ++giG+p+T+a++++ l++r+Y+ ++
  gi|557694040|ref|YP_008797094.1| 1041 QVIKT------VKALEPGVHR-V--LNLQIKSMQAVPFFREGDIIALMRERGIGRPSTYAQVLNLLYKRRYIFND 1106
                                        96654......4568999883.3..457889999****************************************9 PP

                      Topoisom_bac  363 kkslvptelGkalvell.ekfkdlvspelTaeleekLdeIaegkadakevld 413 
                                        ++++ +t+lGk+++  l ++f ++vs+ lT++lee ++ I++gk +++evl+
  gi|557694040|ref|YP_008797094.1| 1107 NGRVLATKLGKTIYGYLvSNFGSFVSEALTRRLEELMESIESGKVSYQEVLK 1158
                                        9****************999*****************************985 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   0.0   5.6e-23     4e-20       2     103 .]     600     754 ..     599     754 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 5.6e-23
                                       EEEESSHHHHHHHHHTHT..................STEEEEEEESSSSEEEHS............TTEEEEE.... CS
                            Toprim   2 lvivEgpsdaktiakalg..................sgfqavtaslGhildlet............efkpvye.... 44 
                                       l++vE+p++a+t+a ++g                  +     ta++Gh++d++t            ef p+y     
  gi|557694040|ref|YP_008797094.1| 600 LIVVESPTKARTLAYFFGkparrvvdgltvyesvgeGYVACLTACQGHLVDITTsqgfhgvwvhdgEFVPMYVdirr 676
                                       9*********************************99889999************************99999999999 PP

                                       ....................ECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEES CS
                            Toprim  45 ....................eiedkkkvlkalkelakradeiilatDpDreGeaiawellevlkellenkigrvefs 101
                                                           +  +k +++++l++la++ d++++atDpD+eGe+i+++l+  + +++++ i r+e +
  gi|557694040|ref|YP_008797094.1| 677 cskcgeqftdsevcpncrsdKYFTKLSIIESLRKLALEFDRVFIATDPDTEGEKIGYDLYVSIWPFNKR-IERLELH 752
                                       9999999999999999999999999999999*****************************9999*9999.******9 PP

                                       SS CS
                            Toprim 102 ei 103
                                       ei
  gi|557694040|ref|YP_008797094.1| 753 EI 754
                                       97 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   8.7e-15   6.2e-12       3     139 ..      70     204 ..      68     230 .. 0.80
   2 ?   -0.8   0.0       1.6   1.2e+03      51     109 ..     291     348 ..     283     364 .. 0.66

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 8.7e-15
                                       HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                              DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyid.... 75 
                                        Q+  i  +  g+++ +  +TG+GKT+ f+  ++ +      ++g+k  i++Pt  La+q+++++ ++  + +    
  gi|557694040|ref|YP_008797094.1|  70 LQRTWIRRTFLGRSFSIVSPTGTGKTTFFIAMAIYQA-----SKGKKSYIIVPTSLLAQQIHERALSMAAKHGekap 141
                                       5888888888899****************99999555.....678899*****************999998664443 PP

                                       ..SEEEEEETTSSHHHHHHHHH.TTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTH CS
                                       ..xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  76 ..lrvlliiggvaardqlskld.ngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfs 139
                                           + + +++++a++ l+k++ ++ +i+v+t   l   ++   l+ ++++f+ +D +d +l++   
  gi|557694040|ref|YP_008797094.1| 142 kiAGYFSGMKKSEAEEMLQKIRdEEFNILVTTDRFLNTRFE--LLRGKKFSFIFVDDVDSFLKS--A 204
                                       3222223355788899999996355*******999988664..67789*************997..3 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.6
                                       EEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  51 livePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvdivvgtpgrld 109
                                       +++ P++ + eq+++ +k+ +  + + v  + g ++a++  + l n+  i     +r+d
  gi|557694040|ref|YP_008797094.1| 291 MYLRPSKNMWEQVAELVKTHGGGCLIFVPQTAGVESAKELAKFL-NSQGISAYAYERMD 348
                                       688999*******9999999997654444444444444444444.66555555555555 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 !   13.0   0.1   0.00014     0.098      11      74 ..     104     174 ..      94     217 .. 0.79
   2 !   15.0   0.0   3.3e-05     0.024       6      96 ..     303     394 ..     298     405 .. 0.74
   3 ?    1.2   0.0      0.63   4.5e+02      96     110 ..     509     523 ..     491     524 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                                       HHTTTTSEEEEEESSHHHHHH..HHHH....HHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESG CS
                        Helicase_C  11 kleeeggkilifvntidrlek..vkll....lekk...gikvavlhgelpqnereeileqfnkgesdvLiatd 74 
                                        + ++g+k++i+v+t   +++   + l    +  +   + k+a + + ++++e ee+l++ +++e+++L++td
  gi|557694040|ref|YP_008797094.1| 104 YQASKGKKSYIIVPTSLLAQQihERALsmaaK--HgekAPKIAGYFSGMKKSEAEEMLQKIRDEEFNILVTTD 174
                                       46789999999999999665444222222221..23446777777778************************8 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHTTTTSEEEEEESSHHHHHH...HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG.... CS
                        Helicase_C   6 llellkleeeggkilifvntidrlek...vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdv.... 75 
                                       + el+  + +gg +lifv+++  +e+   +  +l+++gi++   + ++      ++l +f  ge+dvL+        
  gi|557694040|ref|YP_008797094.1| 303 VAELV--KTHGGGCLIFVPQTAGVESakeLAKFLNSQGISAY-AYERM----DAKMLGRFELGEYDVLVGVASrrsp 372
                                       55665..789999*********66664344444566667664.34435....5578************988887888 PP

                                       GTSSSTST.TESEEEESSSSSS CS
                        Helicase_C  76 aerGidip.kvnlVinfdlprn 96 
                                       ++rGid+p ++++Vi+ ++pr 
  gi|557694040|ref|YP_008797094.1| 373 LARGIDLPeRIRYVIFAGVPRR 394
                                       *******967999*99999954 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.63
                                       SHHHHHHHHTTSSST CS
                        Helicase_C  96 nvtsyiqriGRtgRa 110
                                       +++ yiq++GR  R+
  gi|557694040|ref|YP_008797094.1| 509 DIDGYIQASGRSSRM 523
                                       5799*******9997 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.8   9.4e-10   6.7e-07       3      35 ..       2      34 ..       1      44 [. 0.90
   2 ?   -0.8   0.0       1.5   1.1e+03      29      45 ..     435     451 ..     433     453 .. 0.89
   3 ?    1.9   0.1       0.2   1.4e+02       8      14 ..     688     694 ..     686     698 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.4e-10
                             zf_Rg  3 kavfeklCPNCgGdisdeRlekGLpCkrClPke 35
                                      k+++ +lCPNCgG+i+de l     C rC+ ++
  gi|557694040|ref|YP_008797094.1|  2 KSIYASLCPNCGGAITDEELIGNGVCSRCVSQD 34
                                      79******************99889****8765 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.5
                             zf_Rg  29 krClPkegdvckaLkeg 45 
                                       k+C+P + +v + + eg
  gi|557694040|ref|YP_008797094.1| 435 KKCVPTDREVLEIVREG 451
                                       79********9999886 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.2
                             zf_Rg   8 klCPNCg 14 
                                       + CPNC 
  gi|557694040|ref|YP_008797094.1| 688 EVCPNCR 694
                                       68****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 !   27.9   0.0   2.9e-09   2.1e-06      26     140 ..      83     196 ..      67     212 .. 0.81
   2 ?   -2.9   0.0       8.3   5.9e+03      67      90 ..     563     585 ..     559     604 .. 0.69

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.9e-09
                                       EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.......GEEEESSS-B--... CS
                            ResIII  26 rglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke...igkkvsgdkkka... 96 
                                        + i+ +TGtGKT   ++++ + ++kgk  k  ++vp+  l +q  e+  +++ ++ ++   i + +sg kk++   
  gi|557694040|ref|YP_008797094.1|  83 SFSIVSPTGTGKTTFFIAMAIYQASKGK--KSYIIVPTSLLAQQIHERALSMAAKHGEKapkIAGYFSGMKKSEaee 157
                                       56799********999766666666655..9***************9998888887776667555577777766677 PP

                                       .........-SEEEEEHHHHHHTH........HHHTTT-SEEEEET CS
                            ResIII  97 ..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDE 140
                                         +++++++ +ilvtt   l+ +        e l+ ++f +i++D 
  gi|557694040|ref|YP_008797094.1| 158 mlQKIRDEEFNILVTTDRFLNTRF-------ELLRGKKFSFIFVDD 196
                                       778999999*******99999999.......888888889999996 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.3
                                       HHHHHHHGGGGTGG....GEEEES CS
                            ResIII  67 leqtleefkkflseaykeigkkvs 90 
                                       leq++eefk++  + + +  ++ +
  gi|557694040|ref|YP_008797094.1| 563 LEQAREEFKQCDRDRQ-FLREIRT 585
                                       6899999998877653.3444444 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     6e-07   0.00043      23     131 ..      85     200 ..      71     221 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6e-07
                                       EEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--T.....T----SS---------TTTHHHH....HHHTTT CS
                              PhoH  23 faiGpaGtGKtylavalavealkkkkvkriiltrpavea.....geelGflpgdleekvdpylrply....daLkdl 90 
                                        ++ p+GtGKt + +a+a+ + +k+k + ii+    +         ++ +  g+ + k++ y++ +     +++ + 
  gi|557694040|ref|YP_008797094.1|  85 SIVSPTGTGKTTFFIAMAIYQASKGKKSYIIVPTSLLAQqiherALSMAAKHGEKAPKIAGYFSGMKkseaEEMLQK 161
                                       5789************************99987777644455224456778999999*****999962222456666 PP

                                       S-TTCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG- CS
                              PhoH  91 lgaekvekllekgkievaplaymRGrTlndafvilDEAQnt 131
                                       + +e+++ l+ +++   + ++ +RG+ +  +f+++D+  ++
  gi|557694040|ref|YP_008797094.1| 162 IRDEEFNILVTTDRFLNTRFELLRGKKF--SFIFVDDVDSF 200
                                       699***********************98..69999998765 PP

>> zf-C4pol  C4-type zinc-finger of DNA polymerase delta
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.032        23       1      41 [.       9      55 ..       9      65 .. 0.70
   2 !   11.0   0.2   0.00062      0.45       1      40 [.     677     717 ..     677     720 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.032
                          zf-C4pol  1 ClvCkeklk......kalCkkCrsdkqesllkllsrlkelekklnel 41
                                      C +C+  ++      + +C++C s++ +    + ++  ele++++e 
  gi|557694040|ref|YP_008797094.1|  9 CPNCGGAITdeeligNGVCSRCVSQDGRLKPGKYTKALELEERYREF 55
                                      999**44444556679******9777666666666666666666655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00062
                          zf-C4pol   1 ClvCkeklk.kalCkkCrsdkqesllkllsrlkelekklne 40 
                                       C  C+e+++ +++C +Crsdk  + l+++++l++l  ++++
  gi|557694040|ref|YP_008797094.1| 677 CSKCGEQFTdSEVCPNCRSDKYFTKLSIIESLRKLALEFDR 717
                                       999**877779*******99999988888888888777765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3     0.019        14      17      24 ..       7      14 ..       5      18 .. 0.79
   2 !   13.1   3.1   6.7e-05     0.048       3      22 ..     675     693 ..     675     696 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.019
                       zf-ribbon_3 17 nvCpyCGt 24
                                      + Cp+CG+
  gi|557694040|ref|YP_008797094.1|  7 SLCPNCGG 14
                                      67999986 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.7e-05
                       zf-ribbon_3   3 vrCPnCGaplssddnvCpyC 22 
                                       +rC++CG++  +d  vCp+C
  gi|557694040|ref|YP_008797094.1| 675 RRCSKCGEQ-FTDSEVCPNC 693
                                       59******8.7********* 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 ?    1.6   0.2      0.38   2.7e+02      27      33 ..       8      14 ..       6      18 .. 0.79
   2 !   15.2   1.0   2.1e-05     0.015      11      35 ..     674     697 ..     672     698 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.38
                           DUF35_N 27 vCphCgs 33
                                       Cp+Cg+
  gi|557694040|ref|YP_008797094.1|  8 LCPNCGG 14
                                      6999987 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2.1e-05
                           DUF35_N  11 gqrCpdCGtvqfPPravCphCgsdd 35 
                                       ++rC++CG   f    vCp+C+sd 
  gi|557694040|ref|YP_008797094.1| 674 IRRCSKCGEQ-FTDSEVCPNCRSDK 697
                                       58********.8999********85 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.3     0.031        22      14      35 ..       8      31 ..       4      38 .. 0.63
   2 ?   10.4   0.7   0.00071      0.51      13      36 ..     675     695 ..     663     698 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.031
                               DZR 14 fCseCgtklkavaa..edrCpsCg 35
                                       C++Cg ++  ++   + +C++C 
  gi|557694040|ref|YP_008797094.1|  8 LCPNCGGAITDEELigNGVCSRCV 31
                                      566666666543336666666664 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00071
                               DZR  13 rfCseCgtklkavaaedrCpsCge 36 
                                       r Cs+Cg++      +++Cp+C +
  gi|557694040|ref|YP_008797094.1| 675 RRCSKCGEQFTD---SEVCPNCRS 695
                                       668888888764...888888875 PP

>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.3e-05      0.06      99     215 ..      90     205 ..      48     462 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.3e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SecA_DEAD  99 TGEGKtlvatlpaylnaltgkgvhvvtvndYLakrdaewmgpvyeflGlsvgvieseleseerreaYeaditYgtnn 175
                                       TG GKt   +  a+++a +gk+  ++     La++ +e   ++   +G +   i   ++  ++ ea e  +     +
  gi|557694040|ref|YP_008797094.1|  90 TGTGKTTFFIAMAIYQASKGKKSYIIVPTSLLAQQIHERALSMAAKHGEKAPKIAGYFSGMKKSEA-EEMLQKIRDE 165
                                       9**************************************************999888776666665.4445667889 PP

                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                         SecA_DEAD 176 elgfdyLrDnlalskeelvq.rglnfaivDEvDsvLiDeAr 215
                                       e+      D++  ++ el++ ++++f  vD+vDs L  +Ar
  gi|557694040|ref|YP_008797094.1| 166 EFNILVTTDRFLNTRFELLRgKKFSFIFVDDVDSFL-KSAR 205
                                       99999999**666666666659************87.4454 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0093       6.7      39      51 ..       4      16 ..       1      19 [. 0.79
   2 ?    6.4   1.4     0.014       9.7      32      48 ..     677     694 ..     674     697 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0093
                           DUF1272 39 vlenvCPncgGel 51
                                      ++++ CPncgG +
  gi|557694040|ref|YP_008797094.1|  4 IYASLCPNCGGAI 16
                                      56789******87 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                           DUF1272  32 CaeCaeevl.envCPncg 48 
                                       C++C e+   ++vCPnc 
  gi|557694040|ref|YP_008797094.1| 677 CSKCGEQFTdSEVCPNCR 694
                                       9*****998679*****7 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 ?    3.6   0.2      0.09        65      72     103 ..       8      41 ..       3      49 .. 0.80
   2 ?    9.2   0.5    0.0016       1.2      72      96 ..     676     697 ..     666     703 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.09
                                       EETTTS-EEECHH.H.HHS-TTTSSS-EEEEESS CS
                              HypA  72 rCreCgkefelee.k.alrCpkCgsadveivsGe 103
                                        C +Cg  ++ ee   +  C +C s+d +++ G+
  gi|557694040|ref|YP_008797094.1|   8 LCPNCGGAITDEElIgNGVCSRCVSQDGRLKPGK 41 
                                       6*****9999776425679******999988887 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0016
                                       EETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  72 rCreCgkefeleekalrCpkCgsad 96 
                                       rC++Cg++f+ +   + Cp+C s +
  gi|557694040|ref|YP_008797094.1| 676 RCSKCGEQFTDS---EVCPNCRSDK 697
                                       8********955...46****9975 PP

>> DUF1400  Alpha/beta hydrolase of unknown function (DUF1400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0051       3.6       6      71 ..     115     180 ..     113     188 .. 0.86
   2 ?    0.9   0.0      0.75   5.4e+02      62      86 ..     470     494 ..     428     506 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0051
                           DUF1400   6 tlrygplersisvedLekfaktgevsseLatylkllskeqreelreaLqaeiklspvllsqllnsp 71 
                                       ++  + l ++i  ++L+  ak ge  +++a y++ ++k + ee+ +  + e     v+++++ln++
  gi|557694040|ref|YP_008797094.1| 115 IVPTSLLAQQIHERALSMAAKHGEKAPKIAGYFSGMKKSEAEEMLQKIRDEEFNILVTTDRFLNTR 180
                                       56677889999999********************9999988887777776666669999****997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.75
                           DUF1400  62 vllsqllnspigeklLerlgeviqt 86 
                                       + + qll++ ige+ L+r++e +  
  gi|557694040|ref|YP_008797094.1| 470 TRAHQLLKTYIGEEELRRVAENLDM 494
                                       56789*********99999987665 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   0.00033      0.24       1      23 [.     672     703 ..     672     705 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                              VATC   1 knvlrCsiCgesleg.........kvyFekfd 23 
                                       ++++rCs Cge++            +yF+k++
  gi|557694040|ref|YP_008797094.1| 672 VDIRRCSKCGEQFTDsevcpncrsDKYFTKLS 703
                                       689***********888999987777****97 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00059      0.42      21      66 ..      84     129 ..      69     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00059
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeel 66 
                                         ++ p GtGKtt   a++   +++g++  ++ pt+  A+++ e +
  gi|557694040|ref|YP_008797094.1|  84 FSIVSPTGTGKTTFFIAMAIYQASKGKKSYIIVPTSLLAQQIHERA 129
                                       568899*********9998888888***************998743 PP

>> BRI3BP  Negative regulator of p53/TP53
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.023        16       4      40 ..     471     507 ..     468     516 .. 0.88
   2 ?    4.0   0.0     0.044        32       2      52 ..    1116    1166 ..    1115    1170 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.023
                            BRI3BP   4 tvyqtlesllGeenvrallkfLskllellvsgvssal 40 
                                        ++q l+  +Gee++r ++++L   l++  +gvs  l
  gi|557694040|ref|YP_008797094.1| 471 RAHQLLKTYIGEEELRRVAENLDMRLRVDENGVSIIL 507
                                       57899**********************9999999887 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.044
                            BRI3BP    2 grtvyqtlesllGeenvrallkfLskllellvsgvssalevlarivtdlLd 52  
                                        g+t+y +l+s +G    +al + L++l+e + sg  s  evl ++  + L+
  gi|557694040|ref|YP_008797094.1| 1116 GKTIYGYLVSNFGSFVSEALTRRLEELMESIESGKVSYQEVLKELYRETLQ 1166
                                        789*******************************99999999999988886 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 ?    8.1   0.1    0.0035       2.5       8      30 ..      90     112 ..      85     330 .. 0.90
   2 ?    0.3   0.0      0.93   6.7e+02      72     125 ..     809     859 ..     642     863 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0035
                                       TTSSHHHHHHHHHHHHHHTT--E CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   8 GGvGKTtlaanLaralarrglrV 30 
                                        G+GKTt+ +++a++ a +g++ 
  gi|557694040|ref|YP_008797094.1|  90 TGTGKTTFFIAMAIYQASKGKKS 112
                                       59****************99985 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.93
                                       HH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  72 lllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparg 125
                                       ++  ++g+++ r ++   +++l  +++ +        l++i  ++ v +++a+g
  gi|557694040|ref|YP_008797094.1| 809 VQTPVLGWIIQRMEEA-KKKRLVASMTFEDG--SELMLDSIEDVDVVKRLYAEG 859
                                       3378999999999987.57777777877762..444556888888888888877 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 ?   10.1   0.2   0.00082      0.59       4      28 ..       9      31 ..       7      33 .. 0.90
   2 ?    1.5   0.3       0.4   2.8e+02       2       8 ..     688     694 ..     687     695 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00082
                                      -TTT--BBEEEECTTEEEEE-TTTT CS
                      zf-FPG_IleRS  4 CpRCwryiervgqagrstyfCprCq 28
                                      Cp C++ i+++++   ++ +C rC 
  gi|557694040|ref|YP_008797094.1|  9 CPNCGGAITDEEL--IGNGVCSRCV 31
                                      *************..8888999997 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.4
                                       SB-TTT- CS
                      zf-FPG_IleRS   2 epCpRCw 8  
                                       e+Cp C+
  gi|557694040|ref|YP_008797094.1| 688 EVCPNCR 694
                                       6777776 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.54   3.9e+02       2      24 ..       8      32 ..       7      39 .. 0.75
   2 ?   11.6   1.2   0.00029      0.21      15      37 ..     673     695 ..     640     701 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.54
                                      --SSS-S--EE-S..SEEE-TTT-- CS
                    zinc-ribbons_6  2 kCpeCqqelekrg..eqyhCeaCqe 24
                                       Cp+C  +++ ++   +  C+ C +
  gi|557694040|ref|YP_008797094.1|  8 LCPNCGGAITDEEliGNGVCSRCVS 32
                                      5999999988666567888888865 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00029
                                       SEEE-TTT--EEEEEEE-SSS-S CS
                    zinc-ribbons_6  15 eqyhCeaCqedlkkealCpeCeq 37 
                                       +  +C++C e+++   +Cp+C++
  gi|557694040|ref|YP_008797094.1| 673 DIRRCSKCGEQFTDSEVCPNCRS 695
                                       5579*****************87 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3       1.4     1e+03      75      95 ..       8      32 ..       3      38 .. 0.47
   2 ?   10.1   0.1   0.00066      0.47      71     100 ..     672     700 ..     608     706 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                           TackOD1 75 lCpsCksg....hlnvrevCpkCkS 95
                                      lCp+C ++    +l    vC+ C S
  gi|557694040|ref|YP_008797094.1|  8 LCPNCGGAitdeELIGNGVCSRCVS 32
                                      3444443211113444444444444 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00066
                           TackOD1  71 drirlCpsCksghlnvrevCpkCkSidiee 100
                                         ir C++C   +++  evCp+C+S +  +
  gi|557694040|ref|YP_008797094.1| 672 VDIRRCSKCG-EQFTDSEVCPNCRSDKYFT 700
                                       56899****6.689999********88655 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.1      0.15   1.1e+02      18      35 ..       8      31 ..       6      34 .. 0.78
   2 ?   -1.7   0.0       3.1   2.3e+03       9      21 ..     563     575 ..     562     575 .. 0.88
   3 ?   13.0   2.2   7.8e-05     0.056      15      37 ..     673     696 ..     670     697 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.15
                                      E-TTT--E.ESSS.....S-CCCC CS
                              RecR 18 hCsrCgnl.teed.....lCaICs 35
                                       C++Cg   t+e+     +C+ C 
  gi|557694040|ref|YP_008797094.1|  8 LCPNCGGAiTDEEligngVCSRCV 31
                                      7****8644999977777799996 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.1
                                       HHHHHHH-EE-TT CS
                              RecR   9 LqeakekvrhCsr 21 
                                       L++a+e+ ++C r
  gi|557694040|ref|YP_008797094.1| 563 LEQAREEFKQCDR 575
                                       89*********75 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 7.8e-05
                                       H-EE-TTT--.EESSSS-CCCCST CS
                              RecR  15 kvrhCsrCgn.lteedlCaICsdp 37 
                                       ++r+Cs+Cg  +t++++C+ C+++
  gi|557694040|ref|YP_008797094.1| 673 DIRRCSKCGEqFTDSEVCPNCRSD 696
                                       69*******626*********986 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.27     2e+02      29      35 ..       9      15 ..       3      22 .. 0.80
   2 ?    7.3   2.7     0.007         5       7      34 ..     676     695 ..     673     698 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.27
                       Zn-ribbon_8 29 CPeCgse 35
                                      CP+Cg++
  gi|557694040|ref|YP_008797094.1|  9 CPNCGGA 15
                                      9***985 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.007
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs 34 
                                       rC +Cg++f+      d   ++CP+C s
  gi|557694040|ref|YP_008797094.1| 676 RCSKCGEQFT------D--SEVCPNCRS 695
                                       8*****9999......2..456****98 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.7    0.0004      0.28       2      36 ..       5      34 ..       4      36 .. 0.86
   2 ?   -1.4   0.2       4.2     3e+03       6      11 ..     690     695 ..     688     700 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                                      EEE--TTTT-TTTEEETT....S-EEETTTTBXXX CS
                    Prim_Zn_Ribbon  2 khspCPvCGGrDrFrfddkdgrGtwfCrqCggggd 36
                                      ++s CP+CGG     ++d++  G ++C+ C  + d
  gi|557694040|ref|YP_008797094.1|  5 YASLCPNCGGA----ITDEELIGNGVCSRC-VSQD 34
                                      7899******7....99*9999********.5444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.2
                                       -TTTT- CS
                    Prim_Zn_Ribbon   6 CPvCGG 11 
                                       CP+C +
  gi|557694040|ref|YP_008797094.1| 690 CPNCRS 695
                                       9***54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      725  (0.0404373); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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):              25  [number of targets reported over threshold]
# CPU time: 0.87u 0.28s 00:00:01.14 Elapsed: 00:00:00.42
# Mc/sec: 8407.27
//
Query:       gi|557694041|ref|YP_008797095.1|  [L=475]
Description: 3-isopropylmalate/(R)-2-methylmalate dehydratase large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-151  504.4   0.0   3.7e-151  504.2   0.0    1.0  1  Aconitase  Aconitase family (aconitate hydratase)
    2.1e-05   23.4   0.0    3.9e-05   22.5   0.0    1.4  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 !  504.2   0.0  4.1e-155  3.7e-151       1     461 []      12     462 ..      12     462 .. 0.96

  Alignments for each domain:
  == domain 1  score: 504.2 bits;  conditional E-value: 4.1e-155
                         Aconitase   1 ekiwdahlvee..eg..iayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeeale 73 
                                       ekiw++h+ +e  +g  ++y+ dr+l+++vt++ a+++l+aa+++vrr++ t+a++dh+vp+    d++        
  gi|557694041|ref|YP_008797095.1|  12 EKIWNSHALAEreDGqtLLYI-DRHLTHEVTSPLAFEGLRAAGRRVRRPDLTFAVMDHNVPTG---DRLE------- 77 
                                       79*****88443344657888.*****************************************...6666....... PP

                         Aconitase  74 knledefernkeryefLksaakafgirvvppg...qGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGg 147
                                         ++d+++    ++++L+++a++fgi++++     qGIvH++++E g++ pg t+v++DSHT+++g++G+la+G+G+
  gi|557694041|ref|YP_008797095.1|  78 -PVRDPMSA--AQMQALSRNAREFGITLFDYFspfQGIVHVIGPELGFTIPGITLVCGDSHTSTHGAFGALAFGIGT 151
                                       .89999999..*************88665544444****************************************** PP

                         Aconitase 148 ieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMa 224
                                       +e e+v+++q+l+lk+pk ++++l Gkl+e vtakD++l++i+kl++ g  g+vvEf+G+ v+s+ +e+r+T++NM+
  gi|557694041|ref|YP_008797095.1| 152 SEGEHVFATQTLWLKKPKQMNIRLMGKLGENVTAKDVILYIIRKLGTGGCIGHVVEFTGDYVRSIGVEERMTLTNMS 228
                                       ***************************************************************************** PP

                         Aconitase 225 aEvGAttglfpvdektleYLkatgreeaavlveaydkaqalf.elaadedaeydkvleldlstlepsvagpkrPqda 300
                                       +E GA+t+++++dek++++Lk  + ++++ +++++d+a +++ +l++d++a+yd+v e+d+s +ep+v+++++P ++
  gi|557694041|ref|YP_008797095.1| 229 IEGGARTAIIEPDEKVFNFLK--DAPYSP-KGREWDEAMEYWrTLKTDPGAKYDTVHEFDVSRIEPQVTWGTNPAMT 302
                                       *********************..999999.7***********88********************************* PP

                         Aconitase 301 vplselvk.k.efkeelekeaaekaley.klkegtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkp 374
                                       v ++e+v+ + +f++  +++a+e+al+y +lk+g+k++d+kvd ++igSCTN++++d+  +a+l++     g+k ++
  gi|557694041|ref|YP_008797095.1| 303 VGVTENVPsPdDFDDPSDRKAVERALQYmGLKPGMKVSDIKVDTVFIGSCTNARLSDLIDVARLVK-----GRKKAE 374
                                       *******97669******************************************************.....****** PP

                         Aconitase 375 gvktsvaPGSevvkayleaeGlleiLekaGfevvgagCstCig.nsdrleegeaivsssNRNFegRqgpntrayLaS 450
                                       gv+++v+PGS+  k+++e+ Gl++i+++aGfe++++gCs+Ci+ n+drl++ge+++s+sNRNFe+Rqg ++r++LaS
  gi|557694041|ref|YP_008797095.1| 375 GVRVLVVPGSQLTKRRAERMGLHRIFMEAGFEWRNSGCSMCIAmNEDRLRPGERCLSTSNRNFENRQGVGGRTHLAS 451
                                       ***************************************************************************** PP

                         Aconitase 451 PelvvaaAlaG 461
                                       P +++a+Al+G
  gi|557694041|ref|YP_008797095.1| 452 PLVAAATALTG 462
                                       *********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 !   22.5   0.0   4.3e-09   3.9e-05     286     361 ..     339     417 ..     302     446 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 4.3e-09
                            DUF521 286 akeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvttsre.vkeeaerlglveklekaGvkvlsdtCmvv 360
                                        ++ kvd v++G c  + l++l ++a+l+kg+kk+++v+++v+ + + +k++aer+gl ++  +aG +  ++ C ++
  gi|557694041|ref|YP_008797095.1| 339 VSDIKVDTVFIGsCTNARLSDLIDVARLVKGRKKAEGVRVLVVPGSQlTKRRAERMGLHRIFMEAGFEWRNSGCSMC 415
                                       56779******97899*************************99988868999*****************99999655 PP

                            DUF521 361 .s 361
                                        +
  gi|557694041|ref|YP_008797095.1| 416 iA 417
                                       22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 00:00:00.41
# Mc/sec: 3471.00
//
Query:       gi|557694042|ref|YP_008797096.1|  [L=269]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.2    1.8e-15   57.0   0.2    1.4  1  ParBc      ParB-like nuclease domain
    0.00015   21.9   0.0    0.00036   20.7   0.0    1.6  1  HTH_17     Helix-turn-helix domain
    0.00028   21.1   0.1    0.00081   19.7   0.1    1.8  1  HTH_Tnp_1  Transposase
     0.0015   18.2   0.0     0.0047   16.7   0.0    1.8  1  HTH_23     Homeodomain-like domain
     0.0018   18.3   0.1      0.026   14.5   0.1    2.1  2  GPP34      Golgi phosphoprotein 3 (GPP34)
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.034   14.2   0.0    1.6  1  HTH_29     Winged helix-turn helix
      0.034   14.2   0.2          4    7.6   0.0    2.7  2  HTH_22     HTH domain
      0.056   13.4   0.1       0.13   12.2   0.1    1.6  1  DUF1778    Protein of unknown function (DUF1778)


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 !   57.0   0.2   7.9e-19   1.8e-15       2      85 ..       9      92 ..       8      94 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 7.9e-19
                             ParBc  2 evplseirpnplqprkd.spekieelvasIkkkGllqPiivrktrqgryeiiaGerRlrAakrlglkevpvivleidde 79
                                      ++++ ++r+++++pr   +pe+ + l +sI+ +G+ +P++v +++ + ye+++G rRl+Aa ++gl +vp+i+   ++ 
  gi|557694042|ref|YP_008797096.1|  9 YIETTRLRKSRYNPRMVhDPERHKILLESIRRNGVMEPLLVYQVD-DGYEVLDGSRRLEAAVEAGLDTVPCIIVRREEA 86
                                      68999***********9***************************7.***************************998877 PP

                             ParBc 80 eamals 85
                                       +++l+
  gi|557694042|ref|YP_008797096.1| 87 PRISLA 92
                                      777665 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.6e-07   0.00036       3      31 ..     120     148 ..     120     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.6e-07
                            HTH_17   3 tveEaAelLgvsrstvyrlirrgelpaak 31 
                                       +veE++++Lgvs+s  y l+r+ +l ++ 
  gi|557694042|ref|YP_008797096.1| 120 SVEEVCRFLGVSKSWFYTLRRAARLGPLD 148
                                       79*******************99997765 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   3.6e-07   0.00081      18      58 ..     115     153 ..     109     176 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.6e-07
                         HTH_Tnp_1  18 eslepgksvsevArrhgvspnqLykWrrqyregeeaspaef 58 
                                       e     ksv ev+r +gvs++ +y+ rr++r g + s a+ 
  gi|557694042|ref|YP_008797096.1| 115 EE--VFKSVEEVCRFLGVSKSWFYTLRRAARLGPLDSGASA 153
                                       43..689************************5555444442 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.1e-06    0.0047      17      41 ..     118     142 ..     111     153 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.1e-06
                            HTH_23  17 GlsvreIAreLgvsrrTvyrwlkry 41 
                                        +sv+e++r Lgvs+++ y  +++ 
  gi|557694042|ref|YP_008797096.1| 118 FKSVEEVCRFLGVSKSWFYTLRRAA 142
                                       589*****************99985 PP

>> GPP34  Golgi phosphoprotein 3 (GPP34)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.08   1.8e+02      71     118 ..      80     133 ..      33     144 .. 0.70
   2 !   14.5   0.1   1.2e-05     0.026      34      99 ..     154     234 ..     136     263 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.08
                             GPP34  71 ikaserprsvktwvdllsksvrer....vakgLvdkGilrtekrr..flglfdm 118
                                       i ++e++++++  +   + +++e+    ++++Lv++++ + ++    flg+ ++
  gi|557694042|ref|YP_008797096.1|  80 IVRREEAPRISLAIHFSQDDLTESelvlYVERLVAEEVFKSVEEVcrFLGVSKS 133
                                       334555567888888888889999999999********9999765568887443 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.2e-05
                             GPP34  34 iELalrgriavdk.eggrvv.vidsrptgdplldealklikaserprsvktwvdlls..............ksvrer 94 
                                       + La+ ++ +v+  +++r+v  +d  p   p+l+eal++i+ +++ ++++ ++++                 +v+e 
  gi|557694042|ref|YP_008797096.1| 154 TTLAMVEKTRVEPeKKKRIVeALDNYPLPRPMLREALREIE-EKPMEEPERVLERFYwasprrsgedaftaSGVYEY 229
                                       556666665665567999999*******************9.778899*****999975555555555554444444 PP

                             GPP34  95 vakgL 99 
                                       v+ +L
  gi|557694042|ref|YP_008797096.1| 230 VLRRL 234
                                       44333 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05     0.034       7      38 ..     112     144 ..     109     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                            HTH_29   7 llaeGvs.tvsqiAkllglsrrtvyrwlkrfee 38 
                                       l+ae+v  +v +++++lg+s++++y+ +++ + 
  gi|557694042|ref|YP_008797096.1| 112 LVAEEVFkSVEEVCRFLGVSKSWFYTLRRAARL 144
                                       5566655679****************9998765 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0018         4      28      56 ..     108     133 ..      92     138 .. 0.74
   2 ?    3.8   0.1     0.026        59      13      34 ..     159     178 ..     151     179 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0018
                            HTH_22  28 ivraLdekGiFllkgavekvAekLgiSra 56 
                                        v++L ++ +F   ++ve+v++ Lg+S+ 
  gi|557694042|ref|YP_008797096.1| 108 YVERLVAEEVF---KSVEEVCRFLGVSKS 133
                                       56666666666...69***********96 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.026
                            HTH_22  13 lgkpverltkeekieivraLde 34 
                                       + k+  r   e+k++iv+aLd+
  gi|557694042|ref|YP_008797096.1| 159 VEKT--RVEPEKKKRIVEALDN 178
                                       4455..8889**********85 PP

>> DUF1778  Protein of unknown function (DUF1778)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.7e-05      0.13      39      78 ..     154     193 ..     149     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.7e-05
                           DUF1778  39 kviedherieLseedfqafvaaLdeppkpnprLlkaarrl 78 
                                        +++  e  ++++e+ +++v+aLd+ p p p L++a+r+ 
  gi|557694042|ref|YP_008797096.1| 154 TTLAMVEKTRVEPEKKKRIVEALDNYPLPRPMLREALREI 193
                                       5667777889999************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2228.89
//
Query:       gi|557694043|ref|YP_008797097.1|  [L=315]
Description: hypothetical protein CSUB_C0608 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2335.68
//
Query:       gi|557694044|ref|YP_008797098.1|  [L=485]
Description: ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-07   32.2   0.0     0.0036   17.8   0.0    2.3  2  ABC_tran         ABC transporter
    2.7e-05   24.4   0.0    0.00014   22.1   0.0    2.2  2  Acetyltransf_1   Acetyltransferase (GNAT) family
     0.0002   21.7   0.0    0.00049   20.5   0.0    1.7  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00043   19.8   0.0    0.00087   18.8   0.0    1.4  1  DUF3798          Protein of unknown function (DUF3798)
    0.00049   20.4   0.0     0.0018   18.6   0.0    1.9  1  AAA_22           AAA domain
    0.00092   19.6   0.1     0.0044   17.4   0.1    2.1  2  AAA_16           AAA ATPase domain
     0.0016   18.5   0.0     0.0035   17.4   0.0    1.6  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
     0.0084   16.0   0.0      0.019   14.9   0.0    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.02   14.1   0.0       0.03   13.5   0.0    1.2  1  PIF1             PIF1-like helicase
      0.022   14.2   0.0      0.044   13.3   0.0    1.4  1  Acetyltransf_15  Putative acetyl-transferase
      0.027   14.4   0.0      0.063   13.2   0.0    1.6  1  NACHT            NACHT domain
      0.028   14.5   0.2       0.16   12.1   0.1    2.3  2  Acetyltransf_9   Acetyltransferase (GNAT) domain
       0.04   13.8   0.0      0.081   12.8   0.0    1.5  1  ATPase_2         ATPase domain predominantly from Archaea
      0.075   13.4   0.0       0.25   11.8   0.0    1.8  2  RNA_helicase     RNA helicase
      0.086   12.4   0.1       0.32   10.5   0.1    1.9  1  AAA_25           AAA domain
        0.1   12.3   0.0       0.22   11.2   0.0    1.6  1  AAA_30           AAA domain
       0.11   13.0   0.0       0.32   11.4   0.0    1.8  1  AAA              ATPase family associated with various cellul
       0.13   12.3   0.0       0.45   10.5   0.0    2.0  1  Acetyltransf_13  ESCO1/2 acetyl-transferase
       0.13   12.1   0.0       0.25   11.3   0.0    1.3  1  RsgA_GTPase      RsgA GTPase
       0.18   12.1   0.0       0.38   11.1   0.0    1.6  1  AAA_19           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 !   17.8   0.0     4e-06    0.0036       6      36 ..      69      99 ..      66     122 .. 0.92
   2 !   12.0   0.0   0.00025      0.23     105     135 ..     152     182 ..     115     184 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4e-06
                                      EEEETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  6 lklkegekvaivGenGaGKStLlkllagllk 36
                                      +++++g +v ++Ge+G GKS Ll+ la++++
  gi|557694044|ref|YP_008797098.1| 69 VEVEKGDVVYVTGESGGGKSLLLRHLAEEMS 99
                                      6899**********************99876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00025
                                       TSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 105 spssLSgGqkqrvalarallkkpkllllDEp 135
                                          +LS Gq+ r   a+al   +k ++lDE 
  gi|557694044|ref|YP_008797098.1| 152 CFDELSDGQRMRFIFAKALDAGAKTVVLDEF 182
                                       3489*************************95 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.6e-07   0.00014      34      84 ..     282     349 ..     249     355 .. 0.77
   2 ?   -2.8   0.0       8.1   7.3e+03      92     114 ..     373     394 ..     363     396 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.6e-07
                                       EEEEEEETTEEEEEEEEEEEET.................TSTTEEEEEEEEESGGGTTSSHHHHHHHH CS
                    Acetyltransf_1  34 gllvaeedgeliGfisllkipd.................ekggvayieslaVspeyrgkGlGsaLlea 84 
                                        ++ a  +g+++G + + k +                    ++v  i +++V+p++rg G++++Ll++
  gi|557694044|ref|YP_008797098.1| 282 KIFRAVLNGRVVGVVVYAKPYLqaagfaqffshdwyrreRMNHVLRIQRVVVHPSFRGIGVARKLLQE 349
                                       333377889999999999999988888888888889999778999999******************97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.1
                                       TTE.SEEEEEEETTEHHHHHHHHH CS
                    Acetyltransf_1  92 egi.kkivlaveedndaairlYek 114
                                       +gi +   ++v e+n+  ++l+e+
  gi|557694044|ref|YP_008797098.1| 373 RGImT--RWTVVEPNREKRALLEE 394
                                       45533..56788999998888876 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   5.4e-07   0.00049      16      48 ..     307     349 ..     277     393 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.4e-07
                                       EEEEEEEES..........TCTEEEEE-GGGTTSSHHHHHHHH CS
                    Acetyltransf_7  16 Gfialslld..........aeitrlaVdpeyrgkGiGraLlea 48 
                                       Gf+ +  +d            i r++V+p++rg G++r+Ll+ 
  gi|557694044|ref|YP_008797098.1| 307 GFAQFFSHDwyrrermnhvLRIQRVVVHPSFRGIGVARKLLQE 349
                                       555555555777766665566777*****************96 PP

>> DUF3798  Protein of unknown function (DUF3798)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   9.7e-07   0.00087      79     172 ..     117     218 ..     110     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 9.7e-07
                                       HHHH-TTSEEEESS--S-HHHHHHH..SSEEE...E--HHHHHH...HHHHHHHHTT-S-EEEEEETTGGGSHHHHH CS
                           DUF3798  79 vkekrpdilliagepeedpavlssa..aDlvl...eadaakrgk...liiekakelGaktfvhysfprhlsyellak 147
                                       +   rp i ++   ++e +++ls+a  +D+ +   + d+ ++g+    i +ka ++Gakt+v   f   l  e+ ++
  gi|557694044|ref|YP_008797098.1| 117 IPRRRPLIDCVGRDVKEAVEILSAAglSDVYTwfrCFDELSDGQrmrFIFAKALDAGAKTVVLDEFCSALDRETAKA 193
                                       556677777777777777777765433677653336788887762225899************************** PP

                                       HHHHHHHHHHHCT--EEEEEE---S CS
                           DUF3798 148 rreimektckelGlefvevtapdpt 172
                                          +m+k +   G++f+ +ta+d  
  gi|557694044|ref|YP_008797098.1| 194 TAYTMQKLARRRGITFIAATAVDDL 218
                                       **********************965 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0     2e-06    0.0018       5     102 ..      74     184 ..      70     222 .. 0.58

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..........................erpevvfvtlpsstsskd 55 
                                         +++vtGesG GK++llr l+e+  + ++ +                           e      v++ s  +++d
  gi|557694044|ref|YP_008797098.1|  74 GDVVYVTGESGGGKSLLLRHLAEEMSRLEEFAPvacswkimdniprrrplidcvgrdvkE-----AVEILSAAGLSD 145
                                       5689********************988877777888888887776333333333222220.....333333333333 PP

                            AAA_22  56 llrellralglelka...erlsseellealeqalraravielliiDEaqh 102
                                       +++++         +   e  + ++++  +++al+a a+   +++DE+  
  gi|557694044|ref|YP_008797098.1| 146 VYTWF---------RcfdELSDGQRMRFIFAKALDAGAK--TVVLDEFCS 184
                                       33332.........0222233445555555555555555..555555544 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   4.9e-06    0.0044      19      76 ..      71     127 ..      63     210 .. 0.64
   2 ?   -0.3   0.0       1.4   1.2e+03      37      79 ..     175     204 ..     172     242 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.9e-06
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysa.laqal 76 
                                       v +g   +v+++GesG GKs l+r+l++++++ + +  +++ ++    +ip+   l+++ 
  gi|557694044|ref|YP_008797098.1|  71 VEKG--DVVYVTGESGGGKSLLLRHLAEEMSRLEeFAPVACSWKIM-DNIPRRRpLIDCV 127
                                       5555..58********************988763222244444443.3455533355555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                            AAA_16  37 Ksslvrellralekdggiflrgkcdqlesaipysalaqalare 79 
                                       K+ +++e+  al ++     ++k++ +          q lar+
  gi|557694044|ref|YP_008797098.1| 175 KTVVLDEFCSALDRE-----TAKATAY--------TMQKLARR 204
                                       999999999888888.....3444444........22222222 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 !   17.4   0.0   3.9e-06    0.0035      18      50 ..     312     351 ..     284     354 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.9e-06
                   Acetyltransf_CG  18 e.......vrkegvldfthTeVpeelrGkGiAkkLvkaal 50 
                                               +r ++vl ++ ++V++++rG G+A+kL ++ +
  gi|557694044|ref|YP_008797098.1| 312 FshdwyrrERMNHVLRIQRVVVHPSFRGIGVARKLLQESM 351
                                       2455555678889**********************99866 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.1e-05     0.019      52      75 ..     322     349 ..     277     355 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                   Acetyltransf_10  52 s....hisllfVdpeyrgqGigkaLlea 75 
                                            +i++++V+p++rg G++++Ll++
  gi|557694044|ref|YP_008797098.1| 322 MnhvlRIQRVVVHPSFRGIGVARKLLQE 349
                                       1445689*******************98 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.3e-05      0.03      13      48 ..      64     100 ..      57     111 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                                       H.......HCTS-EEEEESTTSSCHHHHHHHHHHCHC CS
                              PIF1  13 iieavln.ekgklfFvtGsgGtgKtflwkallkklrs 48 
                                        +eav++ ekg +++vtG +G gK+ l+++l + +  
  gi|557694044|ref|YP_008797098.1|  64 FLEAVVEvEKGDVVYVTGESGGGKSLLLRHLAEEMSR 100
                                       467777769**********************988754 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.9e-05     0.044      68     100 ..     321     353 ..     267     361 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.9e-05
                   Acetyltransf_15  68 ieknvleiYtlyvsekyrgkGlakklLeeslke 100
                                         ++vl i  ++v++ +rg G+a+klL+es+ +
  gi|557694044|ref|YP_008797098.1| 321 RMNHVLRIQRVVVHPSFRGIGVARKLLQESMPR 353
                                       456899***********************9865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     7e-05     0.063       2      25 ..      76      99 ..      75     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawa 25
                                      +v ++Ge+G GK+ Ll++la+++ 
  gi|557694044|ref|YP_008797098.1| 76 VVYVTGESGGGKSLLLRHLAEEMS 99
                                      899*****************9876 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00017      0.16      54      99 ..     306     351 ..     268     358 .. 0.89
   2 ?   -1.3   0.0       2.4   2.1e+03      81     118 ..     382     419 ..     376     433 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00017
                                       EEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHHHHHHH CS
                    Acetyltransf_9  54 vgqlallplelnvpGktlkaagvtgVavapehrgrgvlskLlaral 99 
                                       +g +++++++++ +++  ++  +  V v+p  rg gv++kLl++++
  gi|557694044|ref|YP_008797098.1| 306 AGFAQFFSHDWYRRERMNHVLRIQRVVVHPSFRGIGVARKLLQESM 351
                                       6778999999*********************************987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                                       E-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--SSHH CS
                    Acetyltransf_9  81 vapehrgrgvlskLlaraleemreegqplsllfPssip 118
                                       v p+  +r +l+++ +r+  ++ ++g+  +ll++ +++
  gi|557694044|ref|YP_008797098.1| 382 VEPNREKRALLEEFSQRFGIDVMKHGVVDVLLYAEKRG 419
                                       55555555555555555555555555555555554444 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 ?   12.8   0.0     9e-05     0.081      11      47 ..      65     101 ..      63     107 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-05
                          ATPase_2  11 leeilerepneiyfiYGpegsGKtaLlkeiienledk 47 
                                       le ++e e+ ++++++G  g GK+ Ll++++e+ + +
  gi|557694044|ref|YP_008797098.1|  65 LEAVVEVEKGDVVYVTGESGGGKSLLLRHLAEEMSRL 101
                                       788999*************************998655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00028      0.25       1      23 [.      77      99 ..      77     116 .. 0.89
   2 ?   -2.1   0.0       5.6     5e+03      51      66 ..     175     191 ..     172     221 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakall 23
                                      ++++G+sg GKS+l ++La++++
  gi|557694044|ref|YP_008797098.1| 77 VYVTGESGGGKSLLLRHLAEEMS 99
                                      79*****************9997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.6
                      RNA_helicase  51 evvvidDfgqvkdee.n 66 
                                       + vv d+f++  d+e  
  gi|557694044|ref|YP_008797098.1| 175 KTVVLDEFCSALDREtA 191
                                       55666666665555422 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00036      0.32      31     160 ..      72     191 ..      68     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
                            AAA_25  31 pagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvld 107
                                        +g+++ ++G +g GK+ l+ +la ++++ +++       ++++ +   ++   + r+ + +vg+++  ++ + +l+
  gi|557694044|ref|YP_008797098.1|  72 EKGDVVYVTGESGGGKSLLLRHLAEEMSRLEEF------APVACSWKIMDNIP-RRRPLIDCVGRDV--KEAVEILS 139
                                       6899***********************987765......33455554444444.4556666666666..56666666 PP

                            AAA_25 108 lagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralggden 160
                                       +ag  ++  ++  +++    + ++ + a++ + +g++ vv+D + +al+ +  
  gi|557694044|ref|YP_008797098.1| 140 AAGLSDVYTWFRCFDELSDGQRMRFIFAKALD-AGAKTVVLDEFCSALDRETA 191
                                       65555555555555555555555556666666.57888888887777766544 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   0.00025      0.22      15     100 ..      72     185 ..      65     212 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                            AAA_30  15 tsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa..............eelgi.eastiakl 76 
                                       ++gd v+ +tG  G GK+ +l++l+e + + + + + +A + k  +++               e+++i  a+ +  +
  gi|557694044|ref|YP_008797098.1|  72 EKGD-VVYVTGESGGGKSLLLRHLAEEMSRLE-EFAPVACSWKIMDNIPrrrplidcvgrdvkEAVEIlSAAGLSDV 146
                                       3444.99*****************99999875.78888888888877774444444444333333333344445555 PP

                            AAA_30  77 lkrlk...............grarlepg.tllivDEagmv 100
                                        ++ +               + ++l++g + ++ DE   +
  gi|557694044|ref|YP_008797098.1| 147 YTWFRcfdelsdgqrmrfifA-KALDAGaKTVVLDEFCSA 185
                                       545556667777777777753.456666677777776555 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 ?   11.4   0.0   0.00036      0.32       1     109 [.      77     213 ..      77     230 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                                       EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS....................................ST CS
                               AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellsk....................................yv 39 
                                       v+++G  G GK+ll + +a+e++   ef  + +s  + +                                     +
  gi|557694044|ref|YP_008797098.1|  77 VYVTGESGGGKSLLLRHLAEEMSrlEEFAPVACSWKIMDniprrrplidcvgrdvkeaveilsaaglsdvytwfrCF 153
                                       6899*****************97554455555544442235556666664444444445555555555555666555 PP

                                       THHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS...........SSTEE CS
                               AAA  40 gesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk...........eskvi 104
                                        e ++  r+ f  ak+   + + +++DE+ +   ++                      + k           ++ ++
  gi|557694044|ref|YP_008797098.1| 154 DELSDGQRMRFIFAKALDaGAKTVVLDEFCSALDRE----------------------TAKataytmqklarRRGIT 208
                                       555555555555555544444566666665555444......................3333333333333223356 PP

                                       EEEEE CS
                               AAA 105 vigat 109
                                       +i+at
  gi|557694044|ref|YP_008797098.1| 209 FIAAT 213
                                       66655 PP

>> Acetyltransf_13  ESCO1/2 acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0005      0.45       4      27 ..     325     348 ..     322     354 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0005
                   Acetyltransf_13   4 lcGisriWvssshRrkgiAtkLld 27 
                                       ++ i+r+ v++s+R  g+A+kLl+
  gi|557694044|ref|YP_008797098.1| 325 VLRIQRVVVHPSFRGIGVARKLLQ 348
                                       5669******************97 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00027      0.25      91     123 ..      66      98 ..      55     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                                       HHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  91 eelkellkdktsvlvGqSGvGKStLinallpel 123
                                       e++ e+ k++++ + G+SG GKS L+ +l++e+
  gi|557694044|ref|YP_008797098.1|  66 EAVVEVEKGDVVYVTGESGGGKSLLLRHLAEEM 98 
                                       6777888899*******************9986 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   0.00042      0.38       4      43 ..      67     107 ..      65     203 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00042
                            AAA_19   4 ave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpe 43 
                                       av    k +v+ vt+  G GK+ +l+h  +++ +l++ +p 
  gi|557694044|ref|YP_008797098.1|  67 AVVeVEKGDVVYVTGESGGGKSLLLRHLAEEMSRLEEFAPV 107
                                       5543678899************************9988773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); 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: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3292.12
//
Query:       gi|557694045|ref|YP_008797099.1|  [L=126]
Description: hypothetical protein CSUB_C0610 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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: 928.66
//
Query:       gi|557694046|ref|YP_008797100.1|  [L=139]
Description: hypothetical protein CSUB_C0611 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   16.2   9.2     0.0045   16.0   9.2    1.0  1  TRC8_N    TRC8 N-terminal domain


Domain annotation for each model (and alignments):
>> TRC8_N  TRC8 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   9.2   2.5e-07    0.0045     152     284 ..      11     133 ..       2     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.5e-07
                            TRC8_N 152 llpelpsevlktlpvlaallplllvkvvllsslleliklvksayqelrnvievyglsalveneWkrlnvpsvlrvfw 228
                                       +   l +++++t++ l+ ll ++ + v+++   l++i+  k++ +e+r+++ + g+++  +   + +n  ++l +f+
  gi|557694046|ref|YP_008797100.1|  11 T--LLVATIIHTTSSLKLLLLIASATVFIIATTLTPIHYRKAGWTETRATYLTLGVQTAASFISTAINTANILDTFQ 85 
                                       3..3457899999**************************************************************** PP

                            TRC8_N 229 lirvleqlvllllskeeaeeseeellellkslliegCetllavlGmtsvvSyvahy 284
                                       +i++ +  ++ll+ + ++        +l  +  ++   t  ++lG++s ++yv   
  gi|557694046|ref|YP_008797100.1|  86 TILLFAANTYLLIRVIAE--------SLAVNKTSNAAATASTLLGLSSYITYVIST 133
                                       *99888888888877766........36677788999999************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1052.36
//
Query:       gi|557694047|ref|YP_008797101.1|  [L=378]
Description: hypothetical protein CSUB_C0612 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   61.0   0.0    1.3e-16   60.7   0.0    1.1  1  Phage_portal  Phage portal protein


Domain annotation for each model (and alignments):
>> Phage_portal  Phage portal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.0   7.4e-21   1.3e-16       3     314 .]      69     369 ..      67     369 .. 0.80

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 7.4e-21
                      Phage_portal   3 vraavrliaeaiAklplklyrggreevedhplyrlLnvrPNpymtayeflealvanlllygnayalivrdgrrvvel 79 
                                       vra+ + + +a+ +  + ++   +ee   + + + L+     +   + fl+ lv + l+  +ay++ v d       
  gi|557694047|ref|YP_008797101.1|  69 VRACLDAVVDAVTANGWYVV---GEENARKTVEEWLQ---RREDDFFFFLRNLVLTTLIFDEAYIECVSD------F 133
                                       67777777777777777765...23344455566666...45666788********************64......3 PP

                      Phage_portal  80 .yplppdrvt......grleydytddggg......vlpaddvlhirglpl.d.lkGlspleaareaielalaaeeya 141
                                         ++ p +++      g +  ++     +       +++d+++h+  +pl d  +G + l+ +++ +    +ae + 
  gi|557694047|ref|YP_008797101.1| 134 pRVIAPWTMQvvrddyGVVKEYV-----QqtsrvvRFSPDEIVHVVLHPLaDrTYGTPKLASLARILLAKREAELFL 205
                                       45788888887556552222222.....233344666*******999***99*99********************** PP

                      Phage_portal 142 akffkngarpsgilkikapgklseeqreklkeefeeaysgasnagkvavleggldykplslspkdaqflesrkfaae 218
                                        ++f ++++ s +++ k+    +e ++++lk+ +e+a  g       ++l g++d+k+ls + +d+  +e+ ++ ++
  gi|557694047|ref|YP_008797101.1| 206 FQVFMRKGVLSKAIVLKHG---DETTFNRLKAVLESARPGD-----NLLLMGEIDVKTLSQPVEDLRVVELLEEFRQ 274
                                       **********999989999...89999********988886.....6****************************** PP

                      Phage_portal 219 eIarafgvpphllgdlgkstysnieeanlafyentlepllkrieqelnrkLl....kkglylefdldgllrgdtktr 291
                                       +I ++++vpp ++g  +  + + +++++ +f ++ ++ l + +  +++  L          + f l +   +++++ 
  gi|557694047|ref|YP_008797101.1| 275 RILAVLRVPPIVYGVVQGLNLETSRNQMTTFAQY-IKSLQRIFGASVTLALKrimgI--DGFSFRLVEW--MNPEQE 346
                                       ***************9999999999999888855.9999999999999888777542..4566666666..555555 PP

                      Phage_portal 292 aeayaklvqagiltpNEvRelln 314
                                       +++  + v+agi t+ E+R++++
  gi|557694047|ref|YP_008797101.1| 347 TAMHVERVKAGIETVEEARRAMG 369
                                       555578899999*****999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2544.43
//
Query:       gi|557694048|ref|YP_008797102.1|  [L=83]
Description: hypothetical protein CSUB_C0613 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 610.62
//
Query:       gi|557694049|ref|YP_008797103.1|  [L=209]
Description: phage head maturation protease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-07   30.2   0.0    7.2e-07   29.5   0.0    1.2  1  Peptidase_S78    Caudovirus prohead serine protease
  ------ inclusion threshold ------
      0.015   15.4   0.1      0.068   13.3   0.0    2.1  2  Peptidase_S78_2  Putative phage serine protease XkdF


Domain annotation for each model (and alignments):
>> Peptidase_S78  Caudovirus prohead serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0     8e-11   7.2e-07      12     153 ..      22     158 ..      13     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 8e-11
                     Peptidase_S78  12 eetisGYasvfnevsellggfkeviapgafeetlke.kdvralfnHdtskvlGrtksgtL..elseDekGlrfelkl 85 
                                        e++ GY   +  +s  ++  ++ ++ + f+   ++    ++l++H +s+ +G+   g +    ++  kGl++++ +
  gi|557694049|ref|YP_008797103.1|  22 DEVFAGYLEGVAATSD-IDLEGDIFSEEVFKANAANlVGKPILLQHGRSQAIGEQAVGQIidAKHIPGKGLWIKAGI 97 
                                       3469999999988888.77666666666666666665556***************9997421223456899999999 PP

                     Peptidase_S78  86 pdttvardlyellkrgdldglSfgFrvvedeweereekvvvrtikkveLlEvSvVtvPAyddtsvevs 153
                                              d+ + +k+g l+ lS+g +v++  ++ +++    r+i+++e++EvS     A++ +++ ++
  gi|557694049|ref|YP_008797103.1|  98 YK--AFGDVWRMVKNGFLRFLSIGGYVKR--VRFHDK---YREIEEAEITEVSLTHRAANPRAQIITV 158
                                       54..567999******************6..999999...99*********************99854 PP

>> Peptidase_S78_2  Putative phage serine protease XkdF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.5e-06     0.068      21     118 ..      35     124 ..      16     126 .. 0.67
   2 ?   -0.9   0.0      0.19   1.7e+03      96     116 ..     128     148 ..     122     150 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.5e-06
                   Peptidase_S78_2  21 epdveDaqgDiltaeeiekaaheflkeyrevdkqHeferagegvvvesyiaptdeevgeeeik.kGtWv.vlvkvad 95 
                                       ++d  D +gDi ++e  +  a + +   + +  qH     +   + e+ +    + +++++i+ kG W+ +++ +a 
  gi|557694049|ref|YP_008797103.1|  35 TSD-IDLEGDIFSEEVFKANAANLVG--KPILLQHG----RSQAIGEQAVG---QIIDAKHIPgKGLWIkAGIYKAF 101
                                       443.5888888888888888877743..45666773....33334444333...3344555544899*734677777 PP

                   Peptidase_S78_2  96 devwekikkgeitgySiagtakk 118
                                        +vw  +k+g +  +Si+g  k+
  gi|557694049|ref|YP_008797103.1| 102 GDVWRMVKNGFLRFLSIGGYVKR 124
                                       *******************8776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.19
                   Peptidase_S78_2  96 devwekikkgeitgySiagta 116
                                        + + +i++ eit +S++ +a
  gi|557694049|ref|YP_008797103.1| 128 HDKYREIEEAEITEVSLTHRA 148
                                       577788999999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1604.62
//
Query:       gi|557694050|ref|YP_008797104.1|  [L=316]
Description: hypothetical protein CSUB_C0615 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   61.1   0.2    1.2e-16   60.9   0.2    1.0  1  Phage_capsid  Phage capsid family
  ------ inclusion threshold ------
      0.032   13.5   0.0      0.046   13.0   0.0    1.2  1  Linocin_M18   Encapsulating protein for peroxidase


Domain annotation for each model (and alignments):
>> Phage_capsid  Phage capsid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.9   0.2   1.3e-20   1.2e-16       5     278 ..      27     310 ..      26     312 .. 0.88

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.3e-20
                      Phage_capsid   5 vpeelsteiiellrerspirqlatvtrtsasgtvkilvqtgeaeaawvgeteaipetdsp.tfgq.itlsvkklaal 79 
                                       +p+ ++++++    e+s   ++ + ++   s+ vk+ v+ ++ +++  +e ++ p ++++ tf+  + l ++++ a 
  gi|557694050|ref|YP_008797104.1|  27 IPPAVASDVFDTFIEESIAAKVFRFITMG-SDVVKFYVKGAALNVYAPTE-AS-PVPETKlTFEPpVVLEAREVRAV 100
                                       79999**********************88.9*****99999677777777.55.7777777**963789******** PP

                      Phage_capsid  80 vpvsnelLddsavdleayiadelaeafarkedeaflnGdGdgng...qpkGilas.....tgavatgtaaavtatnt 148
                                        ++s+ + + s+vdl a+  +++a+++a ++d+ +++G Gdg+     ++G++ s     +++++++ a a     t
  gi|557694050|ref|YP_008797104.1| 101 SRISDVAEEESVVDLVAMTVEDMARSIADAVDKNVFRGAGDGSDaynLFTGLRRShtlpgSQTQTLDIAKAP---LT 174
                                       **************************************77655432579****98*9999888888888777...79 PP

                      Phage_capsid 149 addlidliy.slkaayra.nasfvmnpstlaalr.klkdadGnylwqpglqagqp.tLlGr.pvveseampd..... 215
                                        + +++++    +  yr+  + ++++p+t+  lr  l++++ + + +++l++g+   ++G+ +v+++++  +     
  gi|557694050|ref|YP_008797104.1| 175 VEHINKAVAaLGELGYRDdLV-MIIHPKTALHLRnDLAEKGLETISGDILRTGEVnAIFGLkKVYVTTHLEKrsysg 250
                                       9********88899***9555.************4455566677777888999999****73699*****99***99 PP

                      Phage_capsid 216 agaksageilfGDf.sayiivdregveikvlrdpysafekdqvafratervdgavvdpeAfkkl 278
                                       ++ ++++++++    +a + + r++++i+++rd  +  e + +++ a  r+++++ +++A+ ++
  gi|557694050|ref|YP_008797104.1| 251 SDGTKVSDVIVCSSrDAGVGGYRRALRIERDRD--V--EAGLTKVAASIRFAWRIAKTDAIFLI 310
                                       888889******9999999999******99999..7..**********************9876 PP

>> Linocin_M18  Encapsulating protein for peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.1e-06     0.046      91     179 ..     105     202 ..      73     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-06
                                       HHHHT-SS---..HHHHHHHHHHHHHHHHHHHT--TTTT.....---STT-GG...GBE---..SSHHHHHHHHHHH CS
                       Linocin_M18  91 avergaedldl..savaeAArklAlaEdrlifeGlaeag.....ieGlleakg..kkklklsdwakagnileavleA 158
                                       +v+ +++ +dl   +v++ Ar++A a d+ +f+G  + +     ++Gl+ + +   ++ +  d aka   +e + +A
  gi|557694050|ref|YP_008797104.1| 105 DVAEEESVVDLvaMTVEDMARSIADAVDKNVFRGAGDGSdaynlFTGLRRSHTlpGSQTQTLDIAKAPLTVEHINKA 181
                                       44444444444116899****************9876543444489**988752245556667999999******** PP

                                       HHHHHTT---SSEEEEEEHHH CS
                       Linocin_M18 159 lekLreaGvegpyalvlspel 179
                                       +++L e G+  ++ +++ p+ 
  gi|557694050|ref|YP_008797104.1| 182 VAALGELGYRDDLVMIIHPKT 202
                                       ****************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 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:                        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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2403.91
//
Query:       gi|557694051|ref|YP_008797105.1|  [L=273]
Description: hypothetical protein CSUB_C0616 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.063   12.8   0.0       0.11   11.9   0.0    1.3  1  DUF2460      Conserved hypothetical protein 2217 (DUF2460)
       0.17   12.2   0.0         24    5.3   0.0    2.6  3  La_HTH_kDCL  La HTH in kinetoplastid DICER domain


Domain annotation for each model (and alignments):
>> DUF2460  Conserved hypothetical protein 2217 (DUF2460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.3e-05      0.11     127     166 ..      53      90 ..      46      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                           DUF2460 127 vrvavdgvelaegafsvdtttGlvtfaaapaagasvtagf 166
                                       v v+++g +++ +  s+d  tGl+++  +p++g+sv a++
  gi|557694051|ref|YP_008797105.1|  53 VLVYLGGEHVEPE--SIDPSTGLISIHPPPSQGTSVEADY 90 
                                       6789999999996..************************9 PP

>> La_HTH_kDCL  La HTH in kinetoplastid DICER domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0027        24      27      48 ..       7      28 ..       2      43 .. 0.78
   2 ?    3.8   0.0    0.0078        70      62      81 ..     209     228 ..     189     236 .. 0.84
   3 ?   -2.8   0.0      0.88   7.9e+03       4      16 ..     249     261 ..     248     265 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0027
                       La_HTH_kDCL 27 esillasGWvPleevlselkad 48
                                      +++ l +GW+P+ee ++ lk+ 
  gi|557694051|ref|YP_008797105.1|  7 KDVRLYNGWLPIEEKKQPLKKI 28
                                      5666778*******99998875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.0078
                       La_HTH_kDCL  62 akillslLtqldllgrlqlg 81 
                                       +k+ +  L+ ++ll r+q +
  gi|557694051|ref|YP_008797105.1| 209 VKHAVLALSSHNLLTRFQQR 228
                                       6788889***********66 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.88
                       La_HTH_kDCL   4 eklvriLRlvsvy 16 
                                       ek +r+LR++  +
  gi|557694051|ref|YP_008797105.1| 249 EKRLRFLRNEVEK 261
                                       6778999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2160.10
//
Query:       gi|557694052|ref|YP_008797106.1|  [L=122]
Description: hypothetical protein CSUB_C0617 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 977.52
//
Query:       gi|557694053|ref|YP_008797107.1|  [L=307]
Description: serine protease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   87.5   1.9    1.9e-23   83.2   0.7    2.3  2  Peptidase_S8  Subtilase family


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 !    3.3   0.0    0.0022        40       1      19 [.      31      49 ..      31      71 .. 0.82
   2 !   83.2   0.7   1.1e-27   1.9e-23     108     284 ..      95     247 ..      67     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.0022
                                      -TT-EEEEECS-B-TT-TT CS
                                      xxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8  1 gkgvlvavlDtGvdpshpd 19
                                      g gv+v  +D+G++p+hp 
  gi|557694053|ref|YP_008797107.1| 31 GAGVKVVFIDSGCSPEHPL 49
                                      789**************97 PP

  == domain 2  score: 83.2 bits;  conditional E-value: 1.1e-27
                                       HHHHHHHHHHHHCT-SEEEE-EESCETTCHHCHHHHHHHHHHHH.CCT-EEEEE--SS-T-HHEEE-TTCEECTTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 108 teliraieeaaedkvdvinmslgestslpktgrsiealainravnkkgvlvviSaGNngktgsslqagspvgtpsts 184
                                         li a++ea +  ++vin+s++  +++p+ g++++   +n     ++++v ++aGN g      ++  ++g+p+ +
  gi|557694053|ref|YP_008797107.1|  95 NLLITALSEASRLSPHVINLSIT--SEVPSDGTDPASTYVNHVA--RRSVVAVAAGNGG------PKMMSIGSPAVA 161
                                       45899999***************..6666666666655666666..688999999****......9999******** PP

                                       TTCEEEEEESTTSSB-TT--B-TT.......-EEEE-S-CCCCCCCCCHHHTTTHHEEEE-SHHHCHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 185 knvitvgayttegkiapfSsrGpssdgklkpdivapGgnivstwsrqsnnsaglssyqsmsGTSmAsPnaagaaAll 261
                                       + ++tvga++t g +   SsrGp+ dg+ k +ivap g      + +s         + ++GTS+A+P aa++aA l
  gi|557694053|ref|YP_008797107.1| 162 EKALTVGAVDTRGRLWKRSSRGPTLDGRWKTEIVAPTGY----KPPKS--------SEEVWGTSFATPIAAAVAAHL 226
                                       **************************************9....34444........4689***************** PP

                                       HHHHTT--HHHHHHHHHCCS-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                      Peptidase_S8 262 lsalpkltpetvraallntAqdl 284
                                        ++l+  +p+t  ++++ tA ++
  gi|557694053|ref|YP_008797107.1| 227 NKRLN--NPYTATRVMMLTAAPV 247
                                       **999..7888899999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 00:00:00.38
# Mc/sec: 2416.53
//
Query:       gi|557694054|ref|YP_008797108.1|  [L=296]
Description: hypothetical protein CSUB_C0619 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   12.7   0.0         24    4.9   0.0    2.9  3  DUF2001   Phage tail tube protein


Domain annotation for each model (and alignments):
>> DUF2001  Phage tail tube protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0     0.034   6.1e+02      22      75 ..      25      79 ..      14     100 .. 0.79
   2 ?    3.5   0.0    0.0037        66     104     133 ..     121     149 ..     107     153 .. 0.86
   3 ?    4.9   0.0    0.0014        24      15      86 ..     174     245 ..     162     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.034
                           DUF2001 22 elaevkkleakvelekeevkvl.gklgkghKvtgwkgtgtltlykvtsrmrklla 75
                                      ++  v+++   ve   eev++l g+++ +  v g++++ ++++y  + r++k + 
  gi|557694054|ref|YP_008797108.1| 25 WIGGVTSFSGGVEPVSEEVPTLsGSRVFQTLVHGLDVSPNMEFYVQNPRILKYAF 79
                                      5666788888888888999875488999999999*********999999988764 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0037
                           DUF2001 104 vlknvnfdeltlakfeagklleeevpFtFe 133
                                       v +++ +d+l+l ++e+++ l+++++F  +
  gi|557694054|ref|YP_008797108.1| 121 VYNGCRVDKLSL-SWEEDNFLKTSMDFRAT 149
                                       6789******98.7*************765 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0014
                           DUF2001  15 klwidgeelaevkkleakvelekeevkvlgklgkghKvtgwkgtgtltlykvtsrmrkllaeyiktGkdprf 86 
                                       ++ i+g e+ +v +  ++++ +   +++ g+  ++h ++ ++ +  l+ly+ +s +  l++ + +  +++rf
  gi|557694054|ref|YP_008797108.1| 174 TVEINGVEIGYVVSGSVTLSNNIVAFPRQGDFHQKHVAGNAQLEAELELYYLDSSIVDLMIGKTRFDVKIRF 245
                                       455689999999999999999999**********************************99877666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2336.39
//
Query:       gi|557694055|ref|YP_008797109.1|  [L=118]
Description: hypothetical protein CSUB_C0620 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.2   0.2      0.017   15.0   0.2    1.0  1  DUF3323   Protein of unknown function N-terminus (DUF3323)
      0.071   13.8   0.0      0.081   13.6   0.0    1.2  1  DUF3750   Protein of unknown function (DUF3750)


Domain annotation for each model (and alignments):
>> DUF3323  Protein of unknown function N-terminus (DUF3323)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   1.9e-06     0.017      36     116 ..      24     102 ..      13     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-06
                           DUF3323  36 ladldaalrksrfarsdleevlealfgeplltrkeeraaeaeawaavfaaleaeaaarpelreWldklrgygllrrl 112
                                        ++++a  ++ r+ r++l+e le + ge     +e    +ae+ a+++++l ++++++p+l++ +d+l  +++l+rl
  gi|557694055|ref|YP_008797109.1|  24 FEEFEAFGHRFRIRRMTLAEELEWY-GERDKILAENGFSQAEKLAKIWERLLQRVVESPRLENYVDEL-PTPVLARL 98 
                                       578888889999***********99.****************************************87.56888888 PP

                           DUF3323 113 ykkd 116
                                       +++ 
  gi|557694055|ref|YP_008797109.1|  99 IQAI 102
                                       7765 PP

>> DUF3750  Protein of unknown function (DUF3750)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   9.1e-06     0.081      32      85 ..      22      75 ..      15     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.1e-06
                           DUF3750 32 esytryevvgwkeavrqkkelpdrsWfgnepelllelrgekaeeliekiekave 85
                                      ++++ +e  g++  +r+ + +++ +W+g+++++l+e   ++ae+l++  e+  +
  gi|557694055|ref|YP_008797109.1| 22 KKFEEFEAFGHRFRIRRMTLAEELEWYGERDKILAENGFSQAEKLAKIWERLLQ 75
                                      67899999999999**********************999999999887666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 952.33
//
Query:       gi|557694056|ref|YP_008797110.1|  [L=107]
Description: phage-related protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   55.3   0.2    2.2e-14   54.2   0.2    1.5  2  HK97-gp10_like  Bacteriophage HK97-gp10, putative tail-compon
    0.00035   20.8   0.0    0.00046   20.4   0.0    1.2  1  DUF5403         Family of unknown function (DUF5403)
  ------ inclusion threshold ------
      0.014   14.9   0.0      0.017   14.6   0.0    1.1  1  CbiJ            Precorrin-6x reductase CbiJ/CobK
       0.15   12.1   0.0       0.18   11.8   0.0    1.2  1  Minor_capsid_2  Minor capsid protein


Domain annotation for each model (and alignments):
>> 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 !   54.2   0.2   4.9e-18   2.2e-14       5      81 .]      12      80 ..       8      80 .. 0.93
   2 ?   -1.6   0.0       1.3   5.7e+03      16      35 ..      87     106 ..      83     107 .] 0.69

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 4.9e-18
                    HK97-gp10_like  5 kkleklserevekaikkalkkaAkevldkakkrtpsvdtggdLrdsitvqgkvkkkggeyrvevgnnaeyArlvEfG 81
                                      + lekl e ++ k ++k+l +aA+e    a++++p v+t g+Lr+si+v      + +++  +v ++a+yA +vEfG
  gi|557694056|ref|YP_008797110.1| 12 RGLEKLGE-DAVKHVEKVLAAAAEECMSRARENAP-VRT-GRLRESIAV-----SRQDKLAYVVEASAPYAGYVEFG 80
                                      779*****.5*************************.9**.*********.....5557899***************9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                    HK97-gp10_like  16 ekaikkalkkaAkevldkak 35 
                                       ++ +++al +  + +++ ++
  gi|557694056|ref|YP_008797110.1|  87 RRYMQTALLQTLQTLRRRLQ 106
                                       66777788777777777665 PP

>> DUF5403  Family of unknown function (DUF5403)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     1e-07   0.00046      11      83 ..      21      89 ..      12      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1e-07
                           DUF5403 11 lvahlpgvkaavaeelerraarvrAvvagHrdtGalaasievetg.rvdstvsleDPavlsieyGHlakegarw 83
                                       v h+++v   +a+++e+  +  rA+ ++ ++tG l+ si v ++ +  ++v  + P +  +e+G + +   r+
  gi|557694056|ref|YP_008797110.1| 21 AVKHVEKV---LAAAAEECMS--RARENAPVRTGRLRESIAVSRQdKLAYVVEASAPYAGYVEFGTSRQRPRRY 89
                                      45555554...4445555444..46678899***********9886899****************988777666 PP

>> CbiJ  Precorrin-6x reductase CbiJ/CobK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.7e-06     0.017      11      78 ..      10      77 ..       4      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-06
                                      HHHHHHHHHHTT--EEEEE---SSS----S....S-EEES--SHHHHHHHHHHHT--EEEE-S-TT-HHH CS
                              CbiJ 11 arelaeaLaeagievvvsvateygaellpe..kklevrvgrlgeeglaellreekidlvvDATHPfAaei 78
                                      a + +e+L e+ ++ v  v  + ++e ++   ++++vr+grl e   +++ r+ k+ +vv A+ P+A  +
  gi|557694056|ref|YP_008797110.1| 10 ASRGLEKLGEDAVKHVEKVLAAAAEECMSRarENAPVRTGRLRE--SIAVSRQDKLAYVVEASAPYAGYV 77
                                      5556677888877777777777777777755779********65..58899****************766 PP

>> Minor_capsid_2  Minor capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0     4e-05      0.18      19      72 ..      25      81 ..       6     103 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
                    Minor_capsid_2 19 lkrgqlalanqvladinryVPkkegsLrdsaevesdgskiiy....dtpYAkaqyeGg 72
                                      +++   a a++ +    +  P+++g Lr+s  v+ ++ k+ y    ++pYA +   G 
  gi|557694056|ref|YP_008797110.1| 25 VEKVLAAAAEECMSRARENAPVRTGRLRESIAVSRQD-KLAYvveaSAPYAGYVEFGT 81
                                      3445556677778888899**************9985.77763322667777655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 860.61
//
Query:       gi|557694057|ref|YP_008797111.1|  [L=187]
Description: nuclease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-12   48.2   0.0    1.9e-12   47.6   0.0    1.3  1  SNase     Staphylococcal nuclease homologue
  ------ inclusion threshold ------
      0.069   13.4   0.1       0.14   12.4   0.1    1.5  1  SepF      Cell division protein SepF
       0.17   12.1   0.5       0.39   10.9   0.5    1.6  1  DUF4731   Domain of unknown function (DUF4731)


Domain annotation for each model (and alignments):
>> SNase  Staphylococcal nuclease homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0   3.2e-16   1.9e-12       1      83 [.      92     174 ..      92     183 .. 0.89

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 3.2e-16
                                       EEEETTEE-STSSBTTTTTSTTHHHHHHHHHHHHHHCSSEEEEE-S.SBSTTSEEEEEEEET.....TEEHHHHHHH CS
                             SNase   1 kvrLvgidaPetakpkktvqpfgkeAkeflkklvlqkkvvvleldk.kkDkygrllayvyln.....kknineeLvk 71 
                                       +vrL++i++Pe++      +p  +eAke l++lv +k+v +++++   +D+y+rl+a vy++       n+n+ Lv 
  gi|557694057|ref|YP_008797111.1|  92 RVRLADINTPERN------EPGYNEAKEALRRLVEGKQVFLDVDNVnVMDSYQRLVAVVYVQhnsthVLNVNLWLVT 162
                                       79***********......55559*************99999999999**************9999888******** PP

                                       TTSSEE---BTT CS
                             SNase  72 eGlArvyevyek 83 
                                       +G+A+   + ++
  gi|557694057|ref|YP_008797111.1| 163 NGYAVFRDFNNE 174
                                       ****96656654 PP

>> SepF  Cell division protein SepF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.4e-05      0.14       9      41 ..     108     141 ..     105     145 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                                       GGGHHHHHHHHHTT-EEEEE-CCCTC.HHHHHHH CS
                              SepF   9 fedaqeiadalkegkiVilnledldk.eeakriv 41 
                                       +++a+e+ ++l egk V l++++++  ++++r+v
  gi|557694057|ref|YP_008797111.1| 108 YNEAKEALRRLVEGKQVFLDVDNVNVmDSYQRLV 141
                                       9*************************9*****98 PP

>> DUF4731  Domain of unknown function (DUF4731)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   6.6e-05      0.39      57      73 ..       7      23 ..       2      25 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.6e-05
                           DUF4731 57 lfwvvfilGYvtGyyvh 73
                                       +++vfi+G+ tGy+v+
  gi|557694057|ref|YP_008797111.1|  7 TILAVFIIGFFTGYLVY 23
                                      46789*********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1507.86
//
Query:       gi|557694058|ref|YP_008797112.1|  [L=787]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-28   98.4  12.0    4.6e-28   98.4  12.0    5.4  4  PhageMin_Tail  Phage-related minor tail protein
  ------ inclusion threshold ------
        0.1   12.5   2.0       0.53   10.2   0.5    3.1  2  MarR_2         MarR family
       0.67    9.7   6.9       0.44   10.3   0.9    2.9  2  DUF2520        Domain of unknown function (DUF2520)


Domain annotation for each model (and alignments):
>> PhageMin_Tail  Phage-related minor tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   2.5     0.057   3.4e+02      80     148 ..      50     119 ..      32     133 .. 0.66
   2 !   98.4  12.0   7.8e-32   4.6e-28       3     186 ..     138     312 ..     132     324 .. 0.94
   3 ?    0.8   0.3     0.063   3.8e+02      21     147 ..     348     366 ..     312     396 .. 0.60
   4 ?   -2.1  15.7      0.49   2.9e+03      28     176 ..     538     654 ..     436     676 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.057
                     PhageMin_Tail  80 Dvlaaaanngatsvedlaealkevg.avakaaGlsfeetaaalallaaagikgseAgtalknllsrl...tke 148
                                       ++l   +++g  +++ l++a+  +g a  +a+G+ f ++ a l+++    i   +A t + ++ +rl   t++
  gi|557694058|ref|YP_008797112.1|  50 SQLESFGDAGVREAGRLGSAFEVLGsALSRALGIAFYQAGAYLQNFLRGSI---QAFTEFEAAATRLaslTAS 119
                                       566677888888888899999886514567889999888888888887334...3555555555555333333 PP

  == domain 2  score: 98.4 bits;  conditional E-value: 7.8e-32
                     PhageMin_Tail   3 lakelgektkysatelaealeelasaGvsteeilnllegaaklataggaddleeaaeilstalnafglsaadaeeaa 79 
                                       +a+e++     s +e+ +ale+l++aG+s++++l++l+ +++la   g +d + aa+ l++++ +fg++ + a+ a+
  gi|557694058|ref|YP_008797112.1| 138 AAREMSV----SGAEAMKALEALVKAGLSGADALQALRYSLALARIEG-EDYGKAASNLVQVMAQFGVEGSRAAVAV 209
                                       5778888....*************************************.66******************88****** PP

                     PhageMin_Tail  80 DvlaaaanngatsvedlaealkevgavakaaGlsfeetaaalallaaagikgseAgtalknllsrltkeaaealkkl 156
                                       Dvl+ a+  g  s++d+a++l+ vg++a+a+G+s++et+a l +l     +++eAgt+l+ ll++l    +e + kl
  gi|557694058|ref|YP_008797112.1| 210 DVLVNASRLGIGSATDFAQGLANVGSTARAMGMSLQETTAWLVALERRLGSAEEAGTQLARLLINL----YEVAAKL 282
                                       ***********************************************778****************....******* PP

                     PhageMin_Tail 157 Gistkdaqgkmksldeiledlsealkkltd 186
                                       G+ ++d++++ ++++ei+ d+  ++ +l  
  gi|557694058|ref|YP_008797112.1| 283 GVPVRDSADHLRTASEIMLDIIARVRELGG 312
                                       *********************999888854 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.063
                     PhageMin_Tail  21 aleelasaGvsteeilnllegaaklataggaddleeaaeilstalnafglsaadaeeaaDvlaaaanngatsvedla 97 
                                       ++                                                                           
  gi|557694058|ref|YP_008797112.1| 348 GV--------------------------------------------------------------------------- 349
                                       33........................................................................... PP

                     PhageMin_Tail  98 ealkevgavakaaGlsfeetaaalallaaagikgseAgtalknllsrl.tk 147
                                                                         seAgtal+++   l t+
  gi|557694058|ref|YP_008797112.1| 350 ----------------------------------SEAGTALRTFEEYLgTA 366
                                       ..................................45666666655555322 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 0.49
                     PhageMin_Tail  28 aGvsteeilnllegaaklataggaddleeaaeilstalnafglsaadaeeaaDvlaaaanngatsvedlaealke.v 103
                                       aG++   +l+ +  a+ +a     ++ + + e+l++a +  + + +++  +  +  ++   gat+++++ +a+ + +
  gi|557694058|ref|YP_008797112.1| 538 AGLDFYNVLKQVHEALGVAEPLT-EEQAKSMEYLAAAQSVVNYT-SQLLSLQQQALQLYMMGATEAGNMLTAMMQgL 612
                                       35555555555544455554444.33666666666666666666.56777777777777777777777774443326 PP

                     PhageMin_Tail 104 gavakaaGlsfeetaaalallaaagikgseAgtalknllsrltkeaaealkklGistkdaqgkmksldeiled 176
                                       + + +  +++  e  a+l++l     ++  ++ +l  +l +                             le 
  gi|557694058|ref|YP_008797112.1| 613 SQALADGNITQSEFIALLGTLGV---NAGNVAGSLHGMLVKA----------------------------LET 654
                                       66666667777776666666644...4444444455554444............................333 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   8.8e-05      0.53      12      50 ..     114     161 ..     108     161 .. 0.83
   2 ?   -1.8   0.0      0.49   2.9e+03      36      51 ..     503     518 ..     502     524 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8.8e-05
                                       HHHHCTTTS.........EEEHHHHHHHHTSSHHHHHHHHHHHHHTTS CS
                            MarR_2  12 aaLgrrpgr.........dltvgelarrlglsksavsrilkrLvaaGL 50 
                                       a L ++ g+         + ++++ ar++ +s + + ++l+ Lv+aGL
  gi|557694058|ref|YP_008797112.1| 114 ASLTASAGEsvnmlayafRAAASAAAREMSVSGAEAMKALEALVKAGL 161
                                       556666666677777766789**************************8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.49
                                       HHHHHHHHHHHHTTSE CS
                            MarR_2  36 savsrilkrLvaaGLv 51 
                                       savs  + r+++  L 
  gi|557694058|ref|YP_008797112.1| 503 SAVSDSVSRMSELNLA 518
                                       89*********99885 PP

>> DUF2520  Domain of unknown function (DUF2520)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.6     0.054   3.2e+02      46      85 ..     125     165 ..     100     174 .. 0.71
   2 ?   10.3   0.9   7.4e-05      0.44      13      85 ..     544     617 ..     537     624 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.054
                                       CCHHHHH.HHHHHHHHCTT-S-..HHHHHHHHHHHHHHHHH CS
                           DUF2520  46 Nflvtlv.alaaellreagldekdaakallpLleatlenal 85 
                                       N+l + + a a  + re+ ++ ++a kal+ L++a l+ a 
  gi|557694058|ref|YP_008797112.1| 125 NMLAYAFrAAASAAAREMSVSGAEAMKALEALVKAGLSGAD 165
                                       44444441344455666688888899999999998887765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 7.4e-05
                                       HHHHHHHHCCS.S-EEE--HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCTT-S-..HHHHHHHHHHHHHHHHH CS
                           DUF2520  13 aiaeelaeelg.gevvvideedralyHaAavlasNflvtlvalaaellreagldekdaakallpLleatlenal 85 
                                       ++++++ e+lg +e+++ ++++ + y aAa  + N++  l++l +++l+   + +++a ++l+ ++++  + + 
  gi|557694058|ref|YP_008797112.1| 544 NVLKQVHEALGvAEPLTEEQAKSMEYLAAAQSVVNYTSQLLSLQQQALQLYMMGATEAGNMLTAMMQGLSQALA 617
                                       5666666666634566666677789**************************99999*********998766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (787 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 5476.24
//
Query:       gi|557694059|ref|YP_008797113.1|  [L=621]
Description: hypothetical protein CSUB_C0624 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      0.005   15.9   0.0        3.2    6.7   0.0    3.0  2  Sipho_Gp37  Siphovirus ReqiPepy6 Gp37-like protein


Domain annotation for each model (and alignments):
>> Sipho_Gp37  Siphovirus ReqiPepy6 Gp37-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.0   0.00056        10       8     118 ..      16     113 ..      12     209 .. 0.63
   2 !    6.7   0.0   0.00018       3.2     288     336 ..     244     289 ..     226     302 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.00056
                        Sipho_Gp37   8 dgyesltwtrryyevGtfeltipateenaall..qkgnlivvddvtkviltGiiesfeitedaekgetltvtgrdlk 82 
                                       d+++sl+w+ +  +    e+++ a+ e  ++   ++g  i          +G++ ++  + + ++ ++ ++t +++ 
  gi|557694059|ref|YP_008797113.1|  16 DTVTSLRWRLESRSLEALEVDVLAHVEVGERVrlRRGSTILF--------EGVVYEVGRKHQRGDIARCSFTSHSDL 84 
                                       778888888888777777777766666555433377877777........377888888888888899999999999 PP

                        Sipho_Gp37  83 vllarriiwpntttalkrdvqsgtaetvikalvnen 118
                                       +l++r ++++++ t++       ta  +i++l + +
  gi|557694059|ref|YP_008797113.1|  85 ILYDRHVVFREYPTGT-------TAGAIIRDLASLE 113
                                       9999999999998888.......8888888886654 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00018
                        Sipho_Gp37 288 eakasksfeaevktggdlkyek.dydlGDiVtveeekvgvtvdd.rItevt 336
                                       e+ +s  +++      ++ +++ + dlGD+Vtv  +++g+  ++  I e+ 
  gi|557694059|ref|YP_008797113.1| 244 EYGRSLRLQMH-----QQIFSTlGLDLGDTVTVNLPSLGIDNENlHILEIR 289
                                       44444444444.....666777899**************876665666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 4100.91
//
Query:       gi|557694060|ref|YP_008797114.1|  [L=222]
Description: hypothetical protein CSUB_C0625 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.1   0.9      0.071   13.1   0.1    1.9  2  DUF5038         Domain of unknown function (DUF5038)
      0.057   13.2   0.3       0.13   12.1   0.3    1.6  1  Ig_mannosidase  Ig-fold domain


Domain annotation for each model (and alignments):
>> DUF5038  Domain of unknown function (DUF5038)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   7.9e-06     0.071      79     127 ..      55     104 ..      16     110 .. 0.81
   2 ?   -1.4   0.1      0.24   2.2e+03      72      87 ..     179     194 ..     139     213 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.9e-06
                           DUF5038  79 stlpvfydtmtgafsfgedrtvlgtsgktyek..pvvdtlppvssseveqr 127
                                        tlp fydt+  ++sfg   +  g  g +y k   v  t   +ss  v q 
  gi|557694060|ref|YP_008797114.1|  55 NTLPNFYDTVRISYSFGHSVSSTGV-GEAYMKilGVNGTTFSISSGSVTQS 104
                                       69***************99887775.8888883346678888888888775 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.24
                           DUF5038  72 hfllsddstlpvfydt 87 
                                        +++s++st   + +t
  gi|557694060|ref|YP_008797114.1| 179 FYMFSNESTTDTLTET 194
                                       3344444443333332 PP

>> Ig_mannosidase  Ig-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   1.4e-05      0.13      35      60 ..     168     193 ..     158     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.4e-05
                    Ig_mannosidase  35 sgvdgrFsdNgFdLlpgesktvtftv 60 
                                       ++++ +F+dN+F ++ +es t t+t 
  gi|557694060|ref|YP_008797114.1| 168 PQTTFIFDDNAFYMFSNESTTDTLTE 193
                                       567889*************9987777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1654.16
//
Query:       gi|557694061|ref|YP_008797115.1|  [L=181]
Description: hypothetical protein CSUB_C0626 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00019   21.7   0.0    0.00032   20.9   0.0    1.4  1  Peptidase_S74  Chaperone of endosialidase
  ------ inclusion threshold ------
      0.046   13.8   3.0       0.11   12.7   3.0    1.7  1  bZIP_2         Basic region leucine zipper
      0.046   14.1   0.1      0.092   13.2   0.1    1.5  1  Chibby         Chibby family
      0.047   13.8   2.7        0.1   12.7   2.7    1.5  1  bZIP_1         bZIP transcription factor
      0.051   12.8   0.5      0.069   12.3   0.5    1.2  1  HAP1_N         HAP1 N-terminal conserved region
       0.19   10.9   0.0       0.23   10.6   0.0    1.1  1  BDV_G          Borna disease virus G protein
       0.31   10.9   1.9       0.55   10.0   1.9    1.4  1  DivIC          Septum formation initiator


Domain annotation for each model (and alignments):
>> Peptidase_S74  Chaperone of endosialidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.3e-07   0.00032       4      52 ..      96     135 ..      93     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.3e-07
                                       TTBSS-EC-.HHHHHHHCT---EEE-BCCHHHHHGGGGS-BEEE--HHHH CS
                     Peptidase_S74   4 RlKtnIrpl.edalakvlklrpvtYrykdesirkskdsgrrevGfIAQev 52 
                                        +Kt+I+++ e +la ++  +p++Yr           +gr+e+Gf+A+e+
  gi|557694061|ref|YP_008797115.1|  96 SDKTDITEIdEQELASLQLPKPKKYRR----------GGRWEIGFLAEEM 135
                                       57*******9999************99..........48*********97 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.0   4.1e-05      0.11      32      52 ..      15      35 ..      11      43 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                                      HHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2 32 ervkeLeeeNaqLrqkveqLe 52
                                      +++k Le+eN+ Lr+++++L+
  gi|557694061|ref|YP_008797115.1| 15 KKLKALESENQLLREENSMLR 35
                                      566666666666666666664 PP

>> Chibby  Chibby family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   3.6e-05     0.092      71      98 ..      14      41 ..       4      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                            Chibby 71 skeslrlkkenkqLeeEnnllklklevL 98
                                       k+ ++l+ en+ L+eEn +l+ ++e+L
  gi|557694061|ref|YP_008797115.1| 14 AKKLKALESENQLLREENSMLRARIELL 41
                                      4888999*******************98 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.7     4e-05       0.1      27      58 ..      16      47 ..      14      49 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 27 eieeLerrvkaLekeNksLkseleelkkevek 58
                                      + ++Le++ + L +eN++L+ ++e l+  v+k
  gi|557694061|ref|YP_008797115.1| 16 KLKALESENQLLREENSMLRARIELLESVVQK 47
                                      56789999999999999999999999887775 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 ?   12.3   0.5   2.7e-05     0.069     170     198 ..      15      43 ..      11      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                            HAP1_N 170 eklreLeeeNekLreeasqLktetdtlEe 198
                                       +kl+ Le eN+ Lree s L+   + lE 
  gi|557694061|ref|YP_008797115.1|  15 KKLKALESENQLLREENSMLRARIELLES 43 
                                       8*******************776666665 PP

>> BDV_G  Borna disease virus G protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     9e-05      0.23     164     240 ..      18      93 ..      11     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9e-05
                             BDV_G 164 qelesgkamlsdgstltytpyilqsevvnktlngtilcnssskivsfdefrrsysltngsyqsssinvtcanytssc 240
                                       + les + +l + +++  +   l   vv+kt++g++++n      +  e ++ y+lt gs ++ + ++  an t   
  gi|557694061|ref|YP_008797115.1|  18 KALESENQLLREENSMLRARIELLESVVQKTVDGALVANVKITP-TRIEAQQPYTLTIGSTENPAAEIVTANITIPS 93 
                                       56899999999888888888888889***********9975444.3458899*******************998543 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   1.9   0.00021      0.55      24      51 ..      15      42 ..      11      50 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00021
                                      HHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC 24 qeiaalqaelaklkaeneeLeaevkdLk 51
                                      ++++al+ e++ l++en  L a++++L+
  gi|557694061|ref|YP_008797115.1| 15 KKLKALESENQLLREENSMLRARIELLE 42
                                      6889999999999999999999999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1317.32
//
Query:       gi|557694062|ref|YP_008797116.1|  [L=70]
Description: hypothetical protein CSUB_C0627 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 539.91
//
Query:       gi|557694063|ref|YP_008797117.1|  [L=439]
Description: prophage MuMc02, terminase, ATPase subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   50.9   0.0    4.9e-13   49.2   0.0    1.9  2  Terminase_6    Terminase-like family
    1.3e-08   35.1   0.0    4.1e-08   33.5   0.0    1.8  2  Terminase_6C   Terminase RNaseH-like domain
     0.0012   18.7   0.1      0.004   17.0   0.0    1.8  2  Helicase_RecD  Helicase
     0.0013   17.4   0.0       0.88    8.0   0.0    2.1  2  Terminase_1    Phage Terminase


Domain annotation for each model (and alignments):
>> Terminase_6  Terminase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   1.1e-16   4.9e-13       1     211 [.      37     240 ..      37     243 .. 0.80
   2 ?   -3.2   0.0       1.2   5.5e+03      94     121 ..     281     308 ..     280     312 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 1.1e-16
                                       .EEE-SSS-HHHHHHHHHHHHHHSSSS.-EEEEE.ESSHHHHHHHHH........HHHHHHHTS-TTTS--EEEE-S CS
                       Terminase_6   1 lilggrqsGKTfagarellrhalgrgprnqvfls.asktqareeggq........fekgigelakeildiefeesak 68 
                                       +il+ r++G+Tf++a+e+++ al  +  + + l+  s +q  e++          ++k ++  ++ i+++  +    
  gi|557694063|ref|YP_008797117.1|  37 IILKHRGAGATFTIAAEACAEALTHPA-STILLIsYSLRQSLEIFRHvrtilsrlENKRLKHGHS-IYRLAAK-IGA 110
                                       57888*********************8.6666663666666665444889998764444443333.3444433.347 PP

                                       SEEEETTS-EEEEES....SHHHHHTS--SEEEEESGGGSTTHHHHHHHHHHHHCSTT--EEEEEE---SSSHHHHH CS
                       Terminase_6  69 nlvvlsnGaslhflslesetaggiqGaqidliyfDElteipksqelekvtrlratkgtdtktfattpptpdhgvydf 145
                                       ++v l nG++++ l+ +    ++ +G ++d++y+DE+++++ +++l+++  + +  +  ++t ++tp  +  ++++ 
  gi|557694063|ref|YP_008797117.1| 111 RTVELGNGSRIISLPNNP---ESLRGYRADAVYVDEAAFFRGDTNLKTAIMFTTVARNGRVTLVSTPKGKRGWFHEA 184
                                       79999**********555...78888888*******************99988888888999*************** PP

                                       HHHHHCTSS-EEEEE-GGGSGB-TTSBB-TTHHHHHHHHHTS-HHHHHHHHS---TTCTCESSXCH CS
                       Terminase_6 146 vtgwldeegpqsvtkiqavvevtiedakklgedlieeleaeysveerarllrGewidtsgsiFqrs 211
                                       +t +         t ++++v+    d ++ +    eel++  s+ e++++ ++e+ d+  + ++++
  gi|557694063|ref|YP_008797117.1| 185 WTTDN--------TWSKHLVK--LGDSPHITMHDLEELRKTMSPLEWRQEMMCEFLDEVNAFIPYE 240
                                       *9988........44567766..888999999999********************99877776665 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
                                       TS--SEEEEESGGGSTTHHHHHHHHHHH CS
                       Terminase_6  94 GaqidliyfDElteipksqelekvtrlr 121
                                       G ++++ y++El + p+ + le++ r++
  gi|557694063|ref|YP_008797117.1| 281 GERFRVCYVEELRQKPFAAQLEAINRAN 308
                                       7889999999999999999999888876 PP

>> Terminase_6C  Terminase RNaseH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.2     1e+04      22      50 ..      31      59 ..      28      63 .. 0.78
   2 !   33.5   0.0   9.1e-12   4.1e-08       1     151 [.     261     408 ..     261     411 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.2
                                      TTTCEEEEEEEEESSS-CCCHHHHHHHHH CS
                      Terminase_6C 22 kddkfellavlherglspalqaaaikkla 50
                                      +  +f+++ +++  g+++ ++a+a ++++
  gi|557694063|ref|YP_008797117.1| 31 DPSRFRIILKHRGAGATFTIAAEACAEAL 59
                                      56689999999999999999998877765 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 9.1e-12
                                       EEEE--SSCTTBEEEEEEEETTTTCEEEEEEEEESSS-CCCHHHHHHHHHHCTTCEEEEECCSCHHHHHHHHHHCCT CS
                      Terminase_6C   1 igvDpaegrggDyaalvvidvkddkfellavlherglspalqaaaikklaerynviyvyieitsaGesvaellkrdl 77 
                                       +gvD++  r  D+++++ +  ++++f++  v+  r + +a q +ai+++     ++ v ++ t++G  +ae+l++++
  gi|557694063|ref|YP_008797117.1| 261 VGVDFG--RFRDSTVIIAVVEDGERFRVCYVEELRQKPFAAQLEAINRANMVLHPAIVAVDSTGMGAPLAETLAKTI 335
                                       599***..****************************************999999*********************** PP

                                       --S-SCEESSH..HHHHHHHHHHHHHHHTTSEEEETHHCECCCCCCHCC-EEHCC....HHCHCSGCCTCHHHHHHH CS
                      Terminase_6C  78 esealavkpepaskdkatrvskvkdliesgrlkvdkgaecaksfealegfhtdlg....aerstsaehdDlvdAlsy 150
                                       + +  +++ ++   +k t+v+ ++  i +++l +++  + +++++ l+ + +        +     ehdD+v Al  
  gi|557694063|ref|YP_008797117.1| 336 P-HLQPITITS--STKQTLVNNLRNNILNKKLIIPA--DEKTLINQLRLYQEINTghsiKYEAPAGEHDDYVMALAL 407
                                       9.778999998..***********************..89999999999988666678888888999*****99987 PP

                                       H CS
                      Terminase_6C 151 a 151
                                       a
  gi|557694063|ref|YP_008797117.1| 408 A 408
                                       7 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   8.9e-07     0.004       3     125 ..      39     176 ..      37     180 .. 0.69
   2 ?   -1.6   0.0      0.48   2.1e+03      21      44 ..     330     356 ..     319     403 .. 0.46

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.9e-07
                     Helicase_RecD   3 tAdRGRGKSaal.Glalaaliaegksnilvtapskenvktlfeflakglealglkeeekkkkaekaelrvr...... 72 
                                         +RG G + ++ + a+a+++ +  s+il+ + s ++  ++f+++++ l++l+ k+ ++ ++  + + ++       
  gi|557694063|ref|YP_008797117.1|  39 LKHRGAGATFTIaAEACAEALTHPASTILLISYSLRQSLEIFRHVRTILSRLENKRLKHGHSIYRLAAKIGartvel 115
                                       5679999997661568999999999***************************9998444444444444444223333 PP

                     Helicase_RecD  73 ..kqrieyiapdellklkeqadllvvDEAAa......iplpllkkllekfkrvvlatTvhG 125
                                         ++ri  ++ +    +  +ad++ vDEAA       ++++++ + + ++ rv l +T +G
  gi|557694063|ref|YP_008797117.1| 116 gnGSRIISLPNNPESLRGYRADAVYVDEAAFfrgdtnLKTAIMFTTVARNGRVTLVSTPKG 176
                                       335555555555555555567*********7222222455566666778888888888666 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.48
                     Helicase_RecD  21 liaegk...snilvtapskenvktlfe 44 
                                        +a+     + i +t+ +k+++ + ++
  gi|557694063|ref|YP_008797117.1| 330 TLAKTIphlQPITITSSTKQTLVNNLR 356
                                       333333333577888777765443332 PP

>> Terminase_1  Phage Terminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0002      0.88      51     160 ..      61     174 ..      35     185 .. 0.76
   2 !    7.2   0.0   0.00035       1.6     269     303 ..     251     284 ..     236     306 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0002
                       Terminase_1  51 kansqifvaattkdqAekilkkvkrqvklskekikvkdekilksr.kke..ieislvdsvikplssneDavDGkdps 124
                                       +++s i +++    q   i+++v  ++ + ++k +   ++i +   k +  +++    s i +l +n++++ G +  
  gi|557694063|ref|YP_008797117.1|  61 HPASTILLISYSLRQSLEIFRHVRTILSRLENKRLKHGHSIYRLAaKIGarTVELGNGSRIISLPNNPESLRGYRAD 137
                                       5789999999999**************999999977777775542133311333334688999************** PP

                       Terminase_1 125 lvilDElaafkdde.lletikeglikrknpltllitt 160
                                        v +DE a f+ d  l   i  + ++r+ ++tl+ t 
  gi|557694063|ref|YP_008797117.1| 138 AVYVDEAAFFRGDTnLKTAIMFTTVARNGRVTLVSTP 174
                                       **********966505555777777777777776554 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00035
                       Terminase_1 269 prdlsGrdvyiGvDlSrkdDvtavvvafpedgkvy 303
                                       p  + G  vy+GvD+ r  D t v++a+ edg+ +
  gi|557694063|ref|YP_008797117.1| 251 PARVVGGRVYVGVDFGRFRDST-VIIAVVEDGERF 284
                                       34456667************88.567888888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3114.65
//
Query:       gi|557694064|ref|YP_008797118.1|  [L=281]
Description: oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-72  243.7   0.0    3.7e-72  243.0   0.0    1.3  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 !  243.0   0.0   2.1e-76   3.7e-72       2     292 ..      16     279 ..      15     281 .] 0.96

  Alignments for each domain:
  == domain 1  score: 243.0 bits;  conditional E-value: 2.1e-76
                                       EEEE-SSS-ST....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSS CS
                      Aldo_ket_red   2 lglGtwqlgsk...eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrda 75 
                                       +glGtw +g++   ++ ++++a+e++r+a+e G+n++DtAe+Yg g+seel+G+alk    +reev++atKv     
  gi|557694064|ref|YP_008797118.1|  16 IGLGTWGIGGRetpDYSQDDQAIEAIRYAVELGMNHIDTAEIYGGGHSEELVGKALKT--IPREEVFVATKV----- 85 
                                       9*********************************************************..************..... PP

                                       TTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HH CS
                      Aldo_ket_red  76 eiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.kk 151
                                        ++s+l+ +++ +++++sl+rL+++yvDl+ +H+p+p  p + e++ ale+lvk G++r+iGvSnf+v  l++a ++
  gi|557694064|ref|YP_008797118.1|  86 -WPSNLRYDDVLKACRRSLERLQLKYVDLYMIHWPNPRIP-VSETMHALEKLVKDGLVRYIGVSNFDVPLLQEAmEA 160
                                       .***************************************.*********************************777 PP

                                       TTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHH CS
                      Aldo_ket_red 152 kkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknlda 228
                                        +  +iv++q+ y+l ++++e++++++c+k+++ ++ay+plg+G +  + ++                     n ++
  gi|557694064|ref|YP_008797118.1| 161 CRSEEIVSNQIIYSLENRENEREVIPFCEKNKITVVAYTPLGKGRIAAEAEK---------------------NTER 216
                                       77788*****************************************955553.....................4467 PP

                                       HHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                      Aldo_ket_red 229 aeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                        ++l  lak++g++++q+al++++ +++ +i+ip+a + e+le+n++   ++l ee+++ l ++
  gi|557694064|ref|YP_008797118.1| 217 GRALATLAKKYGKTPTQVALNWVI-WKPHVITIPKAIRREHLEENAGGAGWRLAEEDYQLLSRA 279
                                       89**********************.99******************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 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:                        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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2020.78
//
Query:       gi|557694065|ref|YP_008797119.1|  [L=290]
Description: ABC-2 type transport system permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  111.7  24.2    3.2e-32  111.7  24.2    1.7  2  ABC2_membrane    ABC-2 type transporter
    4.2e-10   39.2  24.2    4.2e-10   39.2  24.2    1.6  2  ABC2_membrane_3  ABC-2 family transporter protein
    4.7e-07   29.4  20.3      7e-07   28.8  20.3    1.2  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.037   14.5   6.7       0.17   12.3   0.6    3.3  3  PNTB_4TM         4TM region of pyridine nucleotide transhydro
       0.35   10.8  12.2        1.8    8.5  12.1    2.3  1  ABC2_membrane_4  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 !  111.7  24.2   8.9e-36   3.2e-32       3     209 ..       8     250 ..       6     251 .. 0.90
   2 ?   -3.6   0.3       1.7   6.1e+03     105     118 ..     265     278 ..     258     286 .. 0.39

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 8.9e-36
                     ABC2_membrane   3 ikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlg..nsedgl.nr........................ 52 
                                       i++l++re+++++r+p+l  ++ l+qp++++ +fg +f  +g     +++ ++                        
  gi|557694065|ref|YP_008797119.1|   8 IGVLTMREVRKWLRSPFLM-FFTLVQPVIWMGLFGKAFNITGflRIPEEMlQNlppyvtsqlaeifnnvmtrffgta 83 
                                       899****************.99****************986665433333344899999999999999********* PP

                     ABC2_membrane  53 .........pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivy 120
                                                +g+l ++vlf +  + +++++ ++r+ g+l+++l++p+  + +++++kvl+ ++++++qa+++ll+++
  gi|557694065|ref|YP_008797119.1|  84 didyfsyiaVGMLSITVLFSS--MSSGMGIAWDRRLGFLNKLLAAPI-WRGSIIVSKVLSGVLRAIMQAALLLLVAL 157
                                       *******66666666666666..9999999*****************.***************************** PP

                     ABC2_membrane 121 flvgldls.....rfflflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwi 192
                                        + g +         + ++++l+++al ++sl+++++  ++s e  + +++l+ lpl++ s +++pi  mp+wlq++
  gi|557694065|ref|YP_008797119.1| 158 AF-GARFHvlfplGPLAAFAALFFLALGLTSLFIALGLRLKSWESQAAVMNLLNLPLMFASNALYPIALMPSWLQAV 233
                                       *8.888887555334************************************************************** PP

                     ABC2_membrane 193 aylnPltyavealrsnl 209
                                       a++nP++yav+a+r+++
  gi|557694065|ref|YP_008797119.1| 234 AQANPISYAVDAVRQSF 250
                                       **************986 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.7
                     ABC2_membrane 105 lpvsllqaliflli 118
                                       l+v++ +++ +l++
  gi|557694065|ref|YP_008797119.1| 265 LTVTTGFGIGLLML 278
                                       33333333333332 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 ?   -1.3   0.2      0.25   8.9e+02     214     233 ..      26      46 ..      24      69 .. 0.61
   2 !   39.2  24.2   1.2e-13   4.2e-10     158     345 .]      86     281 ..      53     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.25
                   ABC2_membrane_3 214 flvyllqlllilll...afglgi 233
                                       ++  l+q +++++l   af+  i
  gi|557694065|ref|YP_008797119.1|  26 MFFTLVQPVIWMGLfgkAFN--I 46 
                                       44555566666664344444..3 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 1.2e-13
                   ABC2_membrane_3 158 nvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill..lafgl. 231
                                       ++ s++++ +l i +++++++  ++i+ +++ + +  +l +++ + ++++sk+l+ +l ++ q++l+ll  lafg  
  gi|557694065|ref|YP_008797119.1|  86 DYFSYIAVGMLSITVLFSSMSSGMGIAWDRRLGFLNKLLAAPIWRGSIIVSKVLSGVLRAIMQAALLLLvaLAFGAr 162
                                       4555555555555555666667779***************************************9999833467768 PP

                   ABC2_membrane_3 232 ..gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPf 306
                                          ++  + ++++  +++ +l +++l+ +l+   k+ e+  +++ +++l+l++++ +l+p+  +ps+l+ ++  +P+
  gi|557694065|ref|YP_008797119.1| 163 fhVLFPLGPLAAFAALFFLALGLTSLFIALGLRLKSWESQAAVMNLLNLPLMFASNALYPIALMPSWLQAVAQANPI 239
                                       8766666999999888888888888888888888888887789********************************** PP

                   ABC2_membrane_3 307 fapglgllrl.itgd..plweillsliilalfavvylllall 345
                                       ++  ++  +  i g   + + +l++l++  +f++ +l+l+++
  gi|557694065|ref|YP_008797119.1| 240 SYAVDAVRQSfILGSaaNTAALLTDLTVTTGFGIGLLMLSAY 281
                                       *******9994555522335588***************9986 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 !   28.8  20.3     2e-10     7e-07       5     276 ..      13     282 ..      10     287 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2e-10
                   ABC2_membrane_2   5 kkEfrdlvrsrrfllltvllpli...........dvalaylkdlgsslqseakaikeatlaleyveaasasdeaedt 70 
                                        +E+r+ +rs+ +  +t++ p+i           +++l++ +++ ++l+ ++ ++ +   +  + ++   +  a+ +
  gi|557694065|ref|YP_008797119.1|  13 MREVRKWLRSPFLMFFTLVQPVIwmglfgkafniTGFLRIPEEMLQNLPPYVTSQLAEIFNNVMTRF---FGTADID 86 
                                       5799*******************99999998888666666666666666555544444433222222...1112222 PP

                   ABC2_membrane_2  71 dqdlkvvstimavlipviaalfgada.iagEkergTlkllLskPvsRdeillgKfigglaigla.iavallatvlla 145
                                       + +   + +   + i+v+   +++ + ia ++  g l  lL+ P+ R++i+++K+++g++ +++  a++ll++    
  gi|557694065|ref|YP_008797119.1|  87 YFS---YIAVGMLSITVLFSSMSSGMgIAWDRRLGFLNKLLAAPIWRGSIIVSKVLSGVLRAIMqAALLLLVA---- 156
                                       222...3345555555556666666669*********************************666666666666.... PP

                   ABC2_membrane_2 146 laiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellag 222
                                       la+ + + + ++l+ l  +++++ l +l   +++l+++l   ++s +++aa++  l + l ++ +++ly++a +++ 
  gi|557694065|ref|YP_008797119.1| 157 LAFGARFHVLFPLGPLAAFAALFFL-AL--GLTSLFIALGLRLKSWESQAAVMNLLNLPL-MFASNALYPIALMPSW 229
                                       999**********999988776662.22..249***********6666666666555555.7888999999999995 PP

                   ABC2_membrane_2 223 pavpqeindflsllsptsay.ntllneilagsdlna.....lgstatnllilllllavll 276
                                        ++       +   +p+s+  ++++++++ gs+ n+      +  +t ++i ll+l ++l
  gi|557694065|ref|YP_008797119.1| 230 LQA-------VAQANPISYAvDAVRQSFILGSAANTaalltDLTVTTGFGIGLLMLSAYL 282
                                       555.......99999999752677777778886666777665555566666666666665 PP

>> PNTB_4TM  4TM region of pyridine nucleotide transhydrogenase, mitoch
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.019        67      11      44 ..       8      41 ..       4     112 .. 0.85
   2 ?   -0.5   0.3       0.5   1.8e+03      16      40 ..     135     159 ..     120     195 .. 0.52
   3 ?   12.3   0.6   4.9e-05      0.17      18      80 ..     204     281 ..     199     282 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.019
                          PNTB_4TM 11 vGyeviwkVtpaLhtPLmsvtnaisgiiivgall 44
                                      +G+ ++ +V + L +P + +   ++ +i +g + 
  gi|557694065|ref|YP_008797119.1|  8 IGVLTMREVRKWLRSPFLMFFTLVQPVIWMGLFG 41
                                      7999999*********999999999999888665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.5
                          PNTB_4TM  16 iwkVtpaLhtPLmsvtnaisgiiiv 40 
                                       ++kV +    ++m  +  +    + 
  gi|557694065|ref|YP_008797119.1| 135 VSKVLSGVLRAIMQAALLLLVALAF 159
                                       3333333333333333333333333 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 4.9e-05
                          PNTB_4TM  18 kVtpaLhtPLmsvtnaisgiiivgallalg...............stlakvlgaiavvlasinvvGGFlvtqrmLkm 79 
                                        V + L+ PLm  +na+  i ++ + l++                s +    + +a++l+ + v+ GF +   mL+ 
  gi|557694065|ref|YP_008797119.1| 204 AVMNLLNLPLMFASNALYPIALMPSWLQAVaqanpisyavdavrqSFILGSAANTAALLTDLTVTTGFGIGLLMLSA 280
                                       68899******************999998878878877765544333333667777799999********9999987 PP

                          PNTB_4TM  80 F 80 
                                       +
  gi|557694065|ref|YP_008797119.1| 281 Y 281
                                       6 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 ?    8.5  12.1    0.0005       1.8      45     153 ..      86     192 ..      11     224 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0005
                   ABC2_membrane_4  45 efyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfa 121
                                        ++s+  + +++l + +l   + +++ i   +  + l++Ll  P+ r +++++K++  +l +++   +++l++++f+
  gi|557694065|ref|YP_008797119.1|  86 DYFSY--IAVGMLSITVLFSSMSSGMGIAWDRRLGFLNKLLAAPIWRGSIIVSKVLSGVLRAIMQAALLLLVALAFG 160
                                       23333..3334444555555667889999999*********************************999999999999 PP

                   ABC2_membrane_4 122 llsgfvgfsvklvlellk.kclelgllvffavl 153
                                         ++   f  ++++ +    +l lgl+++f+ l
  gi|557694065|ref|YP_008797119.1| 161 ARFHVL-FPLGPLAAFAAlFFLALGLTSLFIAL 192
                                       999954.55555443333034566666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); 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:                         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 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2129.31
//
Query:       gi|557694066|ref|YP_008797120.1|  [L=332]
Description: antibiotic ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-30  104.7   0.0    7.2e-30  104.3   0.0    1.2  1  ABC_tran  ABC transporter
    9.8e-12   45.3   1.7    6.2e-08   32.8   0.0    2.2  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.9e-11   44.5   0.0    4.4e-11   43.4   0.0    1.7  1  DUF4162   Domain of unknown function (DUF4162)
    0.00014   22.4   0.1    0.00022   21.8   0.1    1.3  1  AAA_23    AAA domain
     0.0079   15.9   0.2      0.015   15.0   0.2    1.4  1  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.011   15.4   0.2      0.019   14.6   0.2    1.3  1  SRP54     SRP54-type protein, GTPase domain
      0.015   14.9   0.2      0.028   14.0   0.2    1.4  1  AAA_27    AAA domain
      0.044   13.5   0.0       0.77    9.4   0.0    2.0  2  AAA_15    AAA ATPase domain
      0.064   13.3   0.0       0.16   12.1   0.0    1.8  2  MMR_HSR1  50S ribosome-binding GTPase
       0.08   13.4   0.3        1.1    9.7   0.3    2.6  1  AAA       ATPase family associated with various cellular acti
       0.18   11.3   0.0       0.34   10.4   0.0    1.3  1  GTP_EFTU  Elongation factor Tu GTP 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 !  104.3   0.0   4.4e-33   7.2e-30       2     136 ..      21     163 ..      20     164 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 4.4e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + vs+++ ege+ +++G+nGaGK+t +++l+ llkpt+G+ ++ g d+++   +++rk++g +pqe +++++lt  e
  gi|557694066|ref|YP_008797120.1|  21 NGVSFSVGEGELFGFLGPNGAGKTTTINILTTLLKPTAGKATVAGYDVST-HPHEVRKQVGLVPQELTVDDDLTGME 96 
                                       78***********************************************9.77889******************999 PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e+++++ ++l+ +gl e++d++v    +++SgG+++r+ l   ll +p++l+lDEpt
  gi|557694066|ref|YP_008797120.1|  97 NlmlqaglyhiprsEARRRALELLDLVGLREFADKRV----ETYSGGMRKRLDLITGLLHEPEVLFLDEPT 163
                                       99**********9999999******************....*****************************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 !   11.7   0.4   9.8e-05      0.16       2      22 ..      33      53 ..      32      70 .. 0.86
   2 !   32.8   0.0   3.8e-11   6.2e-08     237     297 ..     136     194 ..      88     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.8e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       ++ GpNg+GK++ + +l  l
  gi|557694066|ref|YP_008797120.1| 33 FGFLGPNGAGKTTTINILTTL 53
                                      5789*************9776 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 3.8e-11
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTH 297
                                        S G+++ l l+t ll  +    +l++DEp +gL+ +  + +++ +++l++ +g+ v+ltTH
  gi|557694066|ref|YP_008797120.1| 136 YSGGMRKRLDLITGLLHEP---EVLFLDEPTLGLDVATRAAIWDYIRRLRKeTGTTVFLTTH 194
                                       499*************999...9***********************99988899******** PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   2.7e-14   4.4e-11       6      80 ..     223     305 ..     219     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2.7e-14
                                       HHTTS-SSEEEEE.....--.-----..---EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---HH CS
                           DUF4162   6 iKrsygknrieve.....ad.aeelleepgveeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsLn 74 
                                       +K+++g+++ie+e      d +  l+ ++g++ v  +gg ++l++e  +++ +++l+ l ++gv++++++ ++PsL+
  gi|557694066|ref|YP_008797120.1| 223 LKARLGGDIIELElvengLDaVRLLEGVEGIRRVYLDGGVYRLTVERgDKTLPHVLEVLiQRGVSVKRVSMKRPSLD 299
                                       8************9986644244444567799999999********99***********99**************** PP

                                       HHHHHH CS
                           DUF4162  75 dIFiek 80 
                                       ++F+e 
  gi|557694066|ref|YP_008797120.1| 300 EVFLEF 305
                                       ***996 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.4e-07   0.00022       6      44 ..      13      55 ..      10      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.4e-07
                            AAA_23  6 nfrsfrdqe.idF...skgltlItGpNGaGKTTildAiklaLy 44
                                       f+ f  ++ + F   +  l+ + GpNGaGKTT ++ ++  L 
  gi|557694066|ref|YP_008797120.1| 13 KFGDFTAVNgVSFsvgEGELFGFLGPNGAGKTTTINILTTLLK 55
                                      5666655556677666667******************998885 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   0.2   9.3e-06     0.015      15      50 ..      23      58 ..      14      63 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.3e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                       ++++ + + + + Gp+G+GK+T +  +++lL p+ 
  gi|557694066|ref|YP_008797120.1| 23 VSFSVGEGELFGFLGPNGAGKTTTINILTTLLKPTA 58
                                      44455534477799******************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 ?   14.6   0.2   1.2e-05     0.019       6      39 ..      35      68 ..      31      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                      EEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      ++G++GaGKTtt+  L  llk  + k+ ++  D+
  gi|557694066|ref|YP_008797120.1| 35 FLGPNGAGKTTTINILTTLLKPTAGKATVAGYDV 68
                                      79*******************9999998888885 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   1.7e-05     0.028       9      50 ..      12      54 ..       9      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                            AAA_27  9 eryGkftdr.sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      +++G ft    ++fs +e +l   +GpN AGK+t+++ ++ ll
  gi|557694066|ref|YP_008797120.1| 12 KKFGDFTAVnGVSFSVGEGELFGFLGPNGAGKTTTINILTTLL 54
                                      79****98537*************************9999887 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00047      0.77      28      50 ..      35      57 ..      24      97 .. 0.83
   2 ?    2.0   0.0     0.086   1.4e+02     324     364 ..     154     194 ..     142     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00047
                            AAA_15 28 liGkNnsGKSsilealdlFlnnk 50
                                      + G+N++GK++ +++l  +l+ +
  gi|557694066|ref|YP_008797120.1| 35 FLGPNGAGKTTTINILTTLLKPT 57
                                      88***************999976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.086
                            AAA_15 324 nvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       + +l+++EP + L       +++++++l +++ t v++tTH
  gi|557694066|ref|YP_008797120.1| 154 PEVLFLDEPTLGLDVATRAAIWDYIRRLRKETGTTVFLTTH 194
                                       5689999999999999999********************** PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.8e-05      0.16       3      58 ..      34     127 ..      32     192 .. 0.68
   2 ?   -2.6   0.0       3.6   5.8e+03      27      45 ..     182     200 ..     171     227 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.8e-05
                                       EEEESTTSSHHHHHHHHHT.....S.TEEESSSTTSSSSEEEEEEE...ETTEE....................... CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg.....e.kaivsdkpgtTrdinegrvk...lkgke....................... 47 
                                       +++G   +GK+t in lt      + ka v+ +   T   + ++         +                       
  gi|557694066|ref|YP_008797120.1|  34 GFLGPNGAGKTTTINILTTllkptAgKATVAGYDVSTHPHEVRKQVglvP---Qeltvdddltgmenlmlqaglyhi 107
                                       799**************975544424677777776665553333222221...134444455556666666666666 PP

                                       .........EEEEECGGCSS CS
                          MMR_HSR1  48 .........ielvDtpGlie 58 
                                                +el+D++Gl e
  gi|557694066|ref|YP_008797120.1| 108 prsearrraLELLDLVGLRE 127
                                       66666666688888888533 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.6
                                       SSSTTSSSSEEEEEEEETT CS
                          MMR_HSR1  27 sdkpgtTrdinegrvklkg 45 
                                        ++ gtT   +++ +++ +
  gi|557694066|ref|YP_008797120.1| 182 RKETGTTVFLTTHYMDEAD 200
                                       4566777777777666222 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 ?    9.7   0.3   0.00065       1.1       3      26 ..      35      83 ..      33     211 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00065
                                      EESSTTSSHHHHHHHHHHHHTHE.........................E CS
                               AAA  3 lyGppGtGKTllakavakelgve.........................f 26
                                      + Gp G GKT++++ + + l+ +                          
  gi|557694066|ref|YP_008797120.1| 35 FLGPNGAGKTTTINILTTLLKPTagkatvagydvsthphevrkqvglvP 83
                                      68************99999863322223333333333333333333330 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 ?   10.4   0.0   0.00021      0.34       6      87 ..      33     132 ..      31     138 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00021
                                       EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.................. CS
                          GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.................. 64 
                                       +g++g   +GKtT++  L++ ++ ++ k+++a+++  + t+++E ++++    +  +++                  
  gi|557694066|ref|YP_008797120.1|  33 FGFLGPNGAGKTTTINILTTLLKPTAGKATVAGYD--VSTHPHEVRKQVGLVPQELTVDddltgmenlmlqaglyhi 107
                                       68899999*******************99999876..8888888888866666666666666666699999999998 PP

                                       ..TTCSSEEEEEEEESSSGGGHHHH CS
                          GTP_EFTU  65 ..ketkkylinliDtPGHvdFskev 87 
                                         +e +++ + l+D  G ++F ++ 
  gi|557694066|ref|YP_008797120.1| 108 prSEARRRALELLDLVGLREFADKR 132
                                       8558999999999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2521.94
//
Query:       gi|557694067|ref|YP_008797121.1|  [L=174]
Description: transcriptional regulator, PadR family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   68.1   0.0    7.4e-19   67.5   0.0    1.3  1  PadR          Transcriptional regulator PadR-like family
     0.0011   19.6   0.0     0.0025   18.4   0.0    1.7  2  RTP           Replication terminator protein
     0.0084   15.9   0.1      0.013   15.2   0.1    1.5  1  AphA_like     Putative AphA-like transcriptional regulator
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.018   15.2   0.0    1.2  1  FUR           Ferric uptake regulator family
      0.012   14.0   0.1       0.02   13.3   0.1    1.4  1  DUF505        Protein of unknown function (DUF505)
      0.037   13.8   0.0      0.047   13.4   0.0    1.3  1  DUF4364       Domain of unknown function (DUF4364)
      0.054   13.4   0.0       0.18   11.7   0.0    1.9  1  TrmB          Sugar-specific transcriptional regulator TrmB
      0.094   12.8   0.0       0.16   12.0   0.0    1.3  1  Replic_Relax  Replication-relaxation


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 !   67.5   0.0   3.3e-22   7.4e-19       1      75 []      39     108 ..      39     108 .. 0.96

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 3.3e-22
                                       HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHHH CS
                              PadR   1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrelae 75 
                                       iL  l+++p++Gy+++ke+++ ++gl+e+s+G++Yp+L+ Le+eg+v++e +       +++Y lT+aG r+l+e
  gi|557694067|ref|YP_008797121.1|  39 ILRALSQRPMHGYDVAKEISRMFGGLYEPSAGTIYPTLQWLEDEGMVATEVVG-----GKRVYSLTEAGARYLEE 108
                                       8999**********************************************874.....799***********986 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.1e-06    0.0025       3      63 ..      28      87 ..      26     117 .. 0.87
   2 ?   -2.3   0.0       3.1   6.9e+03      13      21 ..     142     150 ..     123     169 .. 0.57

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                                      S--HHHHHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEE CS
                               RTP  3 llkqrAFlklylitlvekkklyglklldelkkeFkelgykPnhseiyralhelvedgilkr 63
                                         +r  ++l +++ + +++++g+ ++ e+ + F  l y+P+  +iy +l+ l ++g++  
  gi|557694067|ref|YP_008797121.1| 28 FAMKRGGIRLLILRALSQRPMHGYDVAKEISRMFGGL-YEPSAGTIYPTLQWLEDEGMVAT 87
                                      555677899*********************9999765.*******************9865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.1
                                       HHHHHHHTT CS
                               RTP  13 ylitlvekk 21 
                                       ++i ++e++
  gi|557694067|ref|YP_008797121.1| 142 FMIVMAEND 150
                                       444444443 PP

>> AphA_like  Putative AphA-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   5.8e-06     0.013       7      87 ..      30     107 ..      27     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.8e-06
                         AphA_like   7 tpkeavrLvvLGlieraplryselagavrhlvsriagPsldLlgsslellreeGLveavdGeGmednalLaiteaGr 83 
                                       + +  +rL +L ++ + p+   ++a+ +  + + +  Ps   ++ +l+ l  eG+v +     +  +   ++teaG 
  gi|557694067|ref|YP_008797121.1|  30 MKRGGIRLLILRALSQRPMHGYDVAKEISRMFGGLYEPSAGTIYPTLQWLEDEGMVATE---VVGGKRVYSLTEAGA 103
                                       56788**************************************************9642...223334455566666 PP

                         AphA_like  84 relq 87 
                                       r l+
  gi|557694067|ref|YP_008797121.1| 104 RYLE 107
                                       5554 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     8e-06     0.018       9      74 ..      35     100 ..      29     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8e-06
                                       HHHHHHHHHHHHSS..SBEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS CS
                               FUR   9 qRekilevleksee..hlsaeevykelkeedpeislaTVYrtLklleeaglvkelefedgesryelak 74 
                                        R+ il+ l + +   +  a+e+ +++   ++  s  T+Y tL+ le++g+v +  + +g+++y l++
  gi|557694067|ref|YP_008797121.1|  35 IRLLILRALSQRPMhgYDVAKEISRMFGGLYE-PSAGTIYPTLQWLEDEGMVATEVV-GGKRVYSLTE 100
                                       58889999999888667788888888776665.599****************87555.5999998875 PP

>> DUF505  Protein of unknown function (DUF505)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   9.1e-06      0.02     366     409 ..      72     114 ..      41     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.1e-06
                            DUF505 366 lreaLysLesfeLieseveekgkevyvlTeyGekvledqekklr 409
                                       +   L  Le  +++++ev   gk+vy+lTe G + le+++ kl+
  gi|557694067|ref|YP_008797121.1|  72 IYPTLQWLEDEGMVATEV-VGGKRVYSLTEAGARYLEENRDKLE 114
                                       5667999**********8.59****************9987765 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    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      39      80 ..      75     116 ..      71     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                           DUF4364  39 alseLvesglieeeekenktlykiTekGketlelfenripks 80 
                                       +l+ L+++g++ +e   +k +y++Te+G++ le+  +++   
  gi|557694067|ref|YP_008797121.1|  75 TLQWLEDEGMVATEVVGGKRVYSLTEAGARYLEENRDKLEGL 116
                                       6888*****************************999998765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.8e-05      0.18      35      64 ..      68      98 ..      40     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.8e-05
                                      SCHCHHHHHHHHHHCTSEEEES.STTTEEEE CS
                              TrmB 35 prskvYevLrsLedkGlVerek.grpklYra 64
                                      +  ++Y +L+ Led G+V +e  g +++Y+ 
  gi|557694067|ref|YP_008797121.1| 68 SAGTIYPTLQWLEDEGMVATEVvGGKRVYSL 98
                                      5679***************998455888875 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     7e-05      0.16      26      75 ..      71     112 ..      54     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7e-05
                      Replic_Relax  26 tarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGarllaaqrae 75 
                                       t++  L+ L+++g++++   +v g  g   + vY Lt++Gar+l+++r++
  gi|557694067|ref|YP_008797121.1|  71 TIYPTLQWLEDEGMVAT---EVVG--G---KRVYSLTEAGARYLEENRDK 112
                                       58899999*******99...4333..3...449***********777763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1271.51
//
Query:       gi|557694068|ref|YP_008797122.1|  [L=102]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.1   0.1       0.11   13.0   0.1    1.6  1  DUF2274   Protein of unknown function (DUF2274)


Domain annotation for each model (and alignments):
>> DUF2274  Protein of unknown function (DUF2274)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1     6e-06      0.11      17      55 ..       3      41 ..       1      43 [. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6e-06
                           DUF2274 17 ltvelpaalhrdLaaYaellaretgeaadpakLiapMLe 55
                                       t+++  + ++ L+++a+ l++++g+ +d ++ i ++L 
  gi|557694068|ref|YP_008797122.1|  3 STIKVAKQTKEMLVRFAATLQKRYGRRVDLDEAIRHLLL 41
                                      6999*******************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.63
# Mc/sec: 488.20
//
Query:       gi|557694069|ref|YP_008797123.1|  [L=129]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   51.9   0.0    8.2e-14   51.6   0.0    1.1  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
     0.0024   17.9   0.1      0.003   17.5   0.1    1.1  1  Pyridox_ox_2    Pyridoxamine 5'-phosphate oxidase


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   0.0   9.2e-18   8.2e-14       1      82 [.       3      83 ..       3      89 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 9.2e-18
                                      HHHHHHHHHHHSSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETT.GSEEEEEE CS
                    Putative_PNPOx  1 ldeelreflaeskavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfldde.lgrgvrie 78
                                      lde +r +++++++++lATv+ dG+P+vspv+  + dg    ++ t+  + k rn +++prval + d++  +++  i 
  gi|557694069|ref|YP_008797123.1|  3 LDENVRRIVRGRNFGFLATVNGDGSPQVSPVWVDEADGY--VLVNTAVGRVKERNTRRDPRVALAVPDWQnPYEYAYIT 79
                                      68999****************************977777..*****************************988999899 PP

                                      EEEE CS
                    Putative_PNPOx 79 Gtae 82
                                      G++ 
  gi|557694069|ref|YP_008797123.1| 80 GRVV 83
                                      9875 PP

>> Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   3.4e-07     0.003       3     135 ..       5     124 ..       4     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.4e-07
                                       HHHHHHHHC-SEEEEEEEE.TTEEEEEEEEEEEETTEEEEEEETTSHCCHCCCT--.ECEEEEEEEEEEE-SEGGEE CS
                      Pyridox_ox_2   3 eeilalLdegevgrlafvd.dgepvilPvnyvvdgdslyfhgakgsrlaaalrgap.vcvvvtevdglvlarsfnsl 77 
                                       e + ++++   +g la+v  dg p + Pv +   ++ +++ +a+g  + + +r  p v+ +v + ++         +
  gi|557694069|ref|YP_008797123.1|   5 ENVRRIVRGRNFGFLATVNgDGSPQVSPVWVDEADGYVLVNTAVGRVKERNTRRDPrVALAVPDWQN--------PY 73 
                                       567889999999*****997777*****987777999****************44446665555444........33 PP

                                       EEEEEEEEEE.EEEE--HHHHHHHCCCHHHHHSTTT..GGCSB---CCCCCTEEEEEEEEE CS
                      Pyridox_ox_2  78 nyrSVvvrGr.aeevtdeeekaealellvekivpgr..wenlrpptrkelkatsvlrlkie 135
                                       +y  + ++Gr +e vt +e ++++++l++ k++ ++  w++          +  +l++k+e
  gi|557694069|ref|YP_008797123.1|  74 EY--AYITGRvVEWVTGPEAEEHIDKLAI-KYTGEKfkWRTPG-------VKRVILKIKPE 124
                                       46..9*****5566777777777777776.6777774566443.......34567777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 883.71
//
Query:       gi|557694070|ref|YP_008797124.1|  [L=497]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-07   28.7   2.9    1.8e-05   24.5   0.6    2.9  3  HTH_IclR   IclR helix-turn-helix domain
    0.00013   21.9   0.4      0.013   15.5   0.2    2.7  2  HTH_Crp_2  Crp-like helix-turn-helix domain
    0.00019   21.7   0.2        1.8    9.0   0.0    3.2  3  Rrf2       Transcriptional regulator
    0.00099   19.2   0.0     0.0032   17.5   0.0    1.9  1  HTH_9      RNA polymerase III subunit RPC82 helix-turn-helix 
     0.0021   18.0   0.2       0.29   11.2   0.1    2.9  3  HTH_29     Winged helix-turn helix
     0.0047   16.8   2.6       0.92    9.5   0.2    3.2  3  MarR_2     MarR family
     0.0056   16.5   0.0       0.48   10.3   0.0    3.2  3  TrmB       Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.011   15.7   0.0        9.2    6.3   0.0    3.2  3  HTH_36     Helix-turn-helix domain
      0.032   14.1   0.0        2.3    8.1   0.0    3.3  4  HTH_5      Bacterial regulatory protein, arsR family
      0.032   14.2   0.1       0.47   10.4   0.2    2.4  2  MarR       MarR family
      0.045   13.8   0.4       0.99    9.5   0.1    2.9  3  HTH_20     Helix-turn-helix domain
      0.085   13.2   0.0        0.4   11.1   0.0    2.1  2  FaeA       FaeA-like protein
       0.35   10.5   1.1        4.3    7.0   0.5    2.1  2  TEX13      Testis-expressed sequence 13 protein family


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 !   24.5   0.6   1.3e-08   1.8e-05      18      52 .]      43      77 ..      35      77 .. 0.92
   2 ?   -3.3   0.1         6   8.3e+03      36      43 ..      89      96 ..      87     103 .. 0.51
   3 ?    3.1   0.0     0.059        82      24      45 ..     473     494 ..     466     497 .] 0.87

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.3e-08
                                      S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                      + +l++lA+ tgl+ S+ +  L tL+e+G v+++g
  gi|557694070|ref|YP_008797124.1| 43 PTRLTDLAQLTGLSESALRKTLTTLMERGAVKREG 77
                                      468*****************************975 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6
                                      HHHHHHHH CS
                          HTH_IclR 36 hRlLqtLv 43
                                       Rl q L 
  gi|557694070|ref|YP_008797124.1| 89 QRLAQLLK 96
                                      45555555 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.059
                                       HHHHHTS-HHHHHHHHHHHHHT CS
                          HTH_IclR  24 lArrtglpkStvhRlLqtLvel 45 
                                       +Ar  g+++S v+R L+ L + 
  gi|557694070|ref|YP_008797124.1| 473 IARDMGVHPSYVRRKLAELRRK 494
                                       9**************9999775 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 !   15.5   0.2   9.2e-06     0.013      23      68 .]      45      91 ..      20     103 .. 0.89
   2 ?    3.8   0.0     0.041        56      27      48 ..     473     494 ..     445     497 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.2e-06
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE.TEEEEES-HHHHHHH CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisr.grririldleaLral 68
                                        ++lA++ Gl+ + + ++l+ L ++g ++r g + r+ d e L++l
  gi|557694070|ref|YP_008797124.1| 45 RLTDLAQLTGLSESALRKTLTTLMERGAVKReGWHYRLADDETLQRL 91
                                      5589**************************73634*******99985 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.041
                                       HHHHTTSSHHHHHHHHHHHHHT CS
                         HTH_Crp_2  27 lAsmlGltretvsrilseLkre 48 
                                       +A+ +G++++ v r l+eL+r+
  gi|557694070|ref|YP_008797124.1| 473 IARDMGVHPSYVRRKLAELRRK 494
                                       8999****************97 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0    0.0013       1.8      26      56 ..      44      74 ..      39      86 .. 0.89
   2 ?   -2.1   0.0       3.7   5.1e+03      16      41 ..     383     407 ..     378     414 .. 0.69
   3 !    8.8   0.0    0.0015       2.1      28      53 ..     470     495 ..     463     497 .] 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0013
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 26 vsseeiaerqnispsylekilakLrkaglvk 56
                                       +++++a+ +++s+s l+k l++L + g vk
  gi|557694070|ref|YP_008797124.1| 44 TRLTDLAQLTGLSESALRKTLTTLMERGAVK 74
                                      67899***********************998 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.7
                                       HHHHSSTCC-B-HHHHHHHHTS-HHH CS
                              Rrf2  16 yLakeeeeepvsseeiaerqnispsy 41 
                                        L+++e++    ++ei +r++i+ + 
  gi|557694070|ref|YP_008797124.1| 383 LLTTRERD-VSDAAEIIRRHGINWET 407
                                       34445554.49999999999998665 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0015
                                       HHHHHHHHTS-HHHHHHHHHHHHHTT CS
                              Rrf2  28 seeiaerqnispsylekilakLrkag 53 
                                       ++ ia+ ++++psy+++ la+Lr++ 
  gi|557694070|ref|YP_008797124.1| 470 ASIIARDMGVHPSYVRRKLAELRRKR 495
                                       5679*******************985 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 !   17.5   0.0   2.3e-06    0.0032       9      57 ..      27      73 ..      25      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.3e-06
                                      HCSTTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9  9 ehFGevvakVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                      +++G +++k+  +Ll+ +rlt  +l+++t+Ls +  +k+L +L+ ++ V
  gi|557694070|ref|YP_008797124.1| 27 TILGGLAEKILPHLLNPTRLT--DLAQLTGLSESALRKTLTTLMERGAV 73
                                      689****************87..********************988766 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.053        73      16      40 ..      47      71 ..      39      89 .. 0.80
   2 ?   -3.7   0.0       9.3   1.3e+04      16      30 ..     395     409 ..     391     409 .. 0.77
   3 !   11.2   0.1   0.00021      0.29       9      32 ..     464     487 ..     463     495 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.053
                            HTH_29 16 sqiAkllglsrrtvyrwlkrfeegG 40
                                       ++A+l+gls++  +++l    e G
  gi|557694070|ref|YP_008797124.1| 47 TDLAQLTGLSESALRKTLTTLMERG 71
                                      579*************998776666 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.3
                            HTH_29  16 sqiAkllglsrrtvy 30 
                                       ++i +++g+ + t++
  gi|557694070|ref|YP_008797124.1| 395 AEIIRRHGINWETFR 409
                                       678888999888876 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 0.00021
                            HTH_29   9 aeGvstvsqiAkllglsrrtvyrw 32 
                                       ++Gv++ s iA+ +g+++++v+r 
  gi|557694070|ref|YP_008797124.1| 464 KRGVDNASIIARDMGVHPSYVRRK 487
                                       58999*****************95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2   0.00066      0.92      23      54 ..      45      76 ..      39      86 .. 0.91
   2 ?   -1.2   0.0       1.4   1.9e+03      36      54 ..      86     104 ..      80     108 .. 0.83
   3 ?    5.5   0.1     0.011        16      24      48 ..     470     494 ..     464     497 .] 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00066
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + ++la+ +gls sa+ ++l  L ++G v r+
  gi|557694070|ref|YP_008797124.1| 45 RLTDLAQLTGLSESALRKTLTTLMERGAVKRE 76
                                      779**************************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                                       HHHHHHHHHHHHTTSEEEE CS
                            MarR_2  36 savsrilkrLvaaGLverr 54 
                                        +++r+ + L ++ L+ ++
  gi|557694070|ref|YP_008797124.1|  86 ETLQRLAQLLKEKNLLKKV 104
                                       57899*********99887 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.011
                                       HHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2  24 vgelarrlglsksavsrilkrLvaa 48 
                                       ++ +ar +g+ +s+v r l++L ++
  gi|557694070|ref|YP_008797124.1| 470 ASIIARDMGVHPSYVRRKLAELRRK 494
                                       6669***************999775 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00035      0.48      22      55 ..      43      76 ..      36      82 .. 0.90
   2 ?    1.0   0.0       0.3   4.1e+02      13      32 ..     379     398 ..     372     404 .. 0.77
   3 ?   -0.0   0.0      0.59   8.2e+02      20      49 ..     465     494 ..     463     497 .] 0.89

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVere 55
                                      p + +++a+ +g+++s   ++L  L+++G V+re
  gi|557694070|ref|YP_008797124.1| 43 PTRLTDLAQLTGLSESALRKTLTTLMERGAVKRE 76
                                      667899**************************98 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.3
                                       HCHHHHHHCCCHHCHHCCCT CS
                              TrmB  13 vYlaLlklgpatadeiaeel 32 
                                       +Y +Ll+  + ++++ ae++
  gi|557694070|ref|YP_008797124.1| 379 AYMKLLTTRERDVSDAAEII 398
                                       8*****88888888777765 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.59
                                       HCCCHHCHHCCCTTSSCHCHHHHHHHHHHC CS
                              TrmB  20 lgpatadeiaeelgvprskvYevLrsLedk 49 
                                       +g  +a+ ia++ gv  s v + L +L +k
  gi|557694070|ref|YP_008797124.1| 465 RGVDNASIIARDMGVHPSYVRRKLAELRRK 494
                                       67889999**************99999887 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0067       9.2      28      53 ..      46      71 ..      39      73 .. 0.89
   2 ?   -2.2   0.0       2.9   4.1e+03      28      40 ..     233     245 ..     229     256 .. 0.79
   3 ?    5.5   0.0     0.012        16      28      52 ..     470     494 ..     444     495 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0067
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlG 53
                                        +la+++gls++  ++ +  L++ G
  gi|557694070|ref|YP_008797124.1| 46 LTDLAQLTGLSESALRKTLTTLMERG 71
                                      679********************998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                            HTH_36  28 qetlakrlglskn 40 
                                       +++l++ +g++++
  gi|557694070|ref|YP_008797124.1| 233 FSDLCAVYGVKVE 245
                                       799******9975 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.012
                            HTH_36  28 qetlakrlglsknTvsraikeLeql 52 
                                        + +a+++g++ + v+r ++eL+++
  gi|557694070|ref|YP_008797124.1| 470 ASIIARDMGVHPSYVRRKLAELRRK 494
                                       678*******************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 ?    8.1   0.0    0.0017       2.3      14      45 ..      42      73 ..      35      75 .. 0.89
   2 ?   -2.7   0.0       4.1   5.7e+03       7      22 ..     117     132 ..     117     133 .. 0.88
   3 ?   -1.6   0.0       1.9   2.6e+03       8      24 ..     381     397 ..     381     399 .. 0.85
   4 ?    1.3   0.0      0.23   3.1e+02      21      41 ..     473     493 ..     466     495 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0017
                                      SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5 14 gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +++  ++la  +gls+s+++  L  L+e G V
  gi|557694070|ref|YP_008797124.1| 42 NPTRLTDLAQLTGLSESALRKTLTTLMERGAV 73
                                      577889***************99999998866 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.1
                                       HHHHHTTSSEEHHHHH CS
                             HTH_5   7 ILklLaegelcvcela 22 
                                       I+k++ +ge+  +el+
  gi|557694070|ref|YP_008797124.1| 117 IIKAVPKGEKALGELT 132
                                       8999999***999997 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.9
                                       HHHHTTSSEEHHHHHHH CS
                             HTH_5   8 LklLaegelcvcelaee 24 
                                       +klL  +e+ v++ ae+
  gi|557694070|ref|YP_008797124.1| 381 MKLLTTRERDVSDAAEI 397
                                       689999******98887 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.23
                                       HHHHHTS-HHHHHHHHHHHHH CS
                             HTH_5  21 laeelglsqstvShHLkkLre 41 
                                       +a+++g+ +s v++ L+ Lr 
  gi|557694070|ref|YP_008797124.1| 473 IARDMGVHPSYVRRKLAELRR 493
                                       99***************9996 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00034      0.47      16      50 ..      42      76 ..      39      77 .. 0.94
   2 ?    0.8   0.0      0.35   4.8e+02      21      41 ..     471     491 ..     463     494 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00034
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      +p ++++La   g+s s++ ++l++L ++G ++R+
  gi|557694070|ref|YP_008797124.1| 42 NPTRLTDLAQLTGLSESALRKTLTTLMERGAVKRE 76
                                      57899****************************96 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.35
                                       HHHHHHHTS-HHHHHHHHHHH CS
                              MarR  21 seLakklgvskstvtrvldrL 41 
                                       s +a+ +gv++s+v r l +L
  gi|557694070|ref|YP_008797124.1| 471 SIIARDMGVHPSYVRRKLAEL 491
                                       5699**********9999888 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00071      0.99      24      57 ..      43      76 ..      31      78 .. 0.87
   2 ?   -2.7   0.0       4.7   6.4e+03       7      17 ..     185     195 ..     182     196 .. 0.84
   3 ?    0.5   0.0      0.45   6.2e+02      14      50 ..     445     493 ..     442     495 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00071
                                      TB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 24 gltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +  +++la++ +ls + l++ L +L e g+v+++
  gi|557694070|ref|YP_008797124.1| 43 PTRLTDLAQLTGLSESALRKTLTTLMERGAVKRE 76
                                      566789*************************987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.7
                                       HS-HHHHHHHH CS
                            HTH_20   7 LahPvRrrilr 17 
                                       L +++R +i+ 
  gi|557694070|ref|YP_008797124.1| 185 LVNRTRIDIFE 195
                                       7899*****97 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.45
                                       HHHHHH............STCTTB-HHHHHHHHTS-HHHHHHHHHHHHH CS
                            HTH_20  14 rilraL............araegltaselaerldlskntlsyHLrvLee 50 
                                       +++++L            + ++   as +a+ ++++++ +++ L++L++
  gi|557694070|ref|YP_008797124.1| 445 KLYSWLrrmaidsgikefWKRGVDNASIIARDMGVHPSYVRRKLAELRR 493
                                       566666666666666666777777788899**************99986 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00029       0.4       3      47 ..      34      75 ..      32      78 .. 0.93
   2 ?   -2.4   0.0       4.8   6.6e+03      21      43 ..     473     495 ..     469     497 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00029
                                      HHHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEE CS
                              FaeA  3 eeIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikr 47
                                      e+Il +l +   p + +++A+ +gls    R  L +L   g +kr
  gi|557694070|ref|YP_008797124.1| 34 EKILPHLLN---PTRLTDLAQLTGLSESALRKTLTTLMERGAVKR 75
                                      788999887...*******************************99 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.8
                                       HHHHHTS-HHHHHHHHHHHHHHS CS
                              FaeA  21 iAdalglsaYQaRyYLeqLekeg 43 
                                       iA  +g+    +R  L  L+++ 
  gi|557694070|ref|YP_008797124.1| 473 IARDMGVHPSYVRRKLAELRRKR 495
                                       88899999888999999999876 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 ?    7.0   0.5    0.0032       4.3      88     144 ..      45     103 ..      41     107 .. 0.90
   2 ?    1.6   0.0      0.15   2.1e+02      60     105 ..     265     309 ..     252     317 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0032
                             TEX13  88 kLqdqveehksaaqaLaselkrlreqqemerkeaasqlq..laqaalaevqkerdlLrk 144
                                       +L d +++     +aL  +l++l+e+  + r+  +++l    + ++la++ ke++lL+k
  gi|557694070|ref|YP_008797124.1|  45 RLTDLAQLTGLSESALRKTLTTLMERGAVKREGWHYRLAddETLQRLAQLLKEKNLLKK 103
                                       8999999999*************************99963367899**********986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.15
                             TEX13  60 keacawsaLaLgvrvaarqrelqarrvqkLqdqveehksaaqaLas 105
                                       ke+ +   L  gv++  rq +  ++ +  L +  +e + +a+aL +
  gi|557694070|ref|YP_008797124.1| 265 KESVTA-YLLGGVNMVLRQIKSSTKDIDLLVENSREYELIAEALQA 309
                                       555543.34459******************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.59u 0.26s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3393.83
//
Query:       gi|557694071|ref|YP_008797125.1|  [L=243]
Description: nucleotidyl transferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   95.7   0.0    4.3e-27   95.3   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    9.3e-14   52.1   0.0    1.1e-13   51.9   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.074   13.0   0.1       0.13   12.2   0.1    1.5  1  Nre_C            Archaeal Nre, C-terminal


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 !   95.3   0.0   7.2e-31   4.3e-27       1     244 [.       2     229 ..       2     233 .. 0.92

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 7.2e-31
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTET.ETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgke.rliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevl 76 
                                       k+v+L+GG+G+RL+PLt   +k ++pv+ ++ +l+++ l  l + g+ e  v l  ++ + v +++++g+++g++++
  gi|557694071|ref|YP_008797125.1|   2 KPVVLCGGEGSRLRPLTYYFQKTMIPVGREQkPLLEYILMHLKAYGFSE-AVLLVGYKGEQVVNYFGDGERVGMRLT 77 
                                       79****************************99*****************.8889999******************** PP

                                       EEEESS--.BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEE CS
                   NTP_transferase  77 ialepegk.gtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvie 152
                                       ++  +e   gt +A++ a++  + +  d+++l+  gD+l++  ++e+v++++ ++a  t+t++++p+ +    Gv++
  gi|557694071|ref|YP_008797125.1|  78 YVWDREDAkGTCGALLNALREKAFTM-DDTLLIYYGDILTNLSLSELVEQHRREKA--TATLAVSPRYQ-LPVGVAT 150
                                       ***999877*********99998888.79***************************..88888888765.567**** PP

                                       ECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-E CS
                   NTP_transferase 153 adeegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyW 229
                                       +++ +r +++ EKP  +     +  G+ v +  +l ++       ++ +d ++d++p+++e++++ +a++ ++   W
  gi|557694071|ref|YP_008797125.1| 151 IEN-NRLTEMREKPFINI---NVTIGLLVLEARALAYA-------ENASDIMSDLIPRLIEKKEKVAAYITEA--FW 214
                                       *98.59********9977...699**999999999999.......67899*********************99..6* PP

                                       EEXSSHHHHHHHHHH CS
                   NTP_transferase 230 sDvGtldslleanek 244
                                        DvG+ + + + + +
  gi|557694071|ref|YP_008797125.1| 215 YDVGSTEKYEKLTHE 229
                                       ******999887665 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 !   51.9   0.0   1.8e-17   1.1e-13       2     130 ..       4     145 ..       3     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 1.8e-17
                                       EEEEESS-TTTTT.....THHHHCC..CCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTC.....TS-EEE CS
                      NTP_transf_3   2 viLAGGrSsRmgg.....dKallpl..ggkpllervldalraagvdevvvvggd..eevlaalarl.....gvrvve 64 
                                       v+L+GG++sR+        K ++p+   +kplle++l +l+a g++e v+ +g+  e+v +++ +      ++++v+
  gi|557694071|ref|YP_008797125.1|   4 VVLCGGEGSRLRPltyyfQKTMIPVgrEQKPLLEYILMHLKAYGFSEAVLLVGYkgEQVVNYFGDGervgmRLTYVW 80 
                                       9**********9445678*******87789***************99999988856677776644444444799*** PP

                                       -TTSS-SHHHHHHHHHHHH...SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEEC CS
                      NTP_transf_3  65 dedpgkgplaslaaalraaa..dadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghp 130
                                       d++  kg+ ++l+ alr+ a   +d +l+  +D+  lt   + +l++++++++a ++ +++  +++ p
  gi|557694071|ref|YP_008797125.1|  81 DREDAKGTCGALLNALREKAftMDDTLLIYYGDI--LTNLSLSELVEQHRREKATATLAVSP-RYQLP 145
                                       ****************99555599**********..89**********99888777666654.44444 PP

>> Nre_C  Archaeal Nre, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.1e-05      0.13      25      67 ..     121     163 ..     114     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                             Nre_C  25 eaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkp 67 
                                        +L +++r+ k+     ++p Y +PvGv  + ++  + +++kp
  gi|557694071|ref|YP_008797125.1| 121 SELVEQHRREKATATLAVSPRYQLPVGVATIENNRLTEMREKP 163
                                       568888999999*****************99998888887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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: 00:00:00.40
# Mc/sec: 1812.40
//
Query:       gi|557694072|ref|YP_008797126.1|  [L=403]
Description: iron ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-25   90.5   0.0    1.9e-25   89.9   0.0    1.3  1  ABC_tran     ABC transporter
    1.1e-12   48.5   5.4    9.5e-06   25.6   2.8    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.4e-05   25.0   0.5      0.016   14.9   0.0    2.1  2  AAA_15       AAA ATPase domain
      0.001   19.3   0.8      0.008   16.5   0.8    2.2  1  AAA_22       AAA domain
     0.0015   18.9   1.4     0.0057   17.0   1.4    1.9  1  AAA_16       AAA ATPase domain
     0.0076   16.4   0.2      0.024   14.8   0.2    1.9  1  AAA_33       AAA domain
  ------ inclusion threshold ------
      0.012   15.1   0.1        3.9    6.9   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
      0.017   15.1   0.0      0.068   13.2   0.0    1.9  2  AAA_14       AAA domain
      0.018   14.6   0.0      0.034   13.8   0.0    1.4  1  AAA_27       AAA domain
      0.027   14.1   1.9      0.067   12.8   1.9    1.8  1  AAA_25       AAA domain
      0.079   13.2   0.1       0.67   10.2   0.0    2.2  2  AAA_28       AAA domain
       0.11   13.0   0.4        2.7    8.4   0.1    2.2  2  AAA          ATPase family associated with various cellular a
       0.15   11.9   0.1        1.5    8.7   0.0    2.2  2  RsgA_GTPase  RsgA GTPase
       0.19   12.2   0.0       0.32   11.5   0.0    1.2  1  AAA_23       AAA domain
       0.21   11.3   0.1       0.46   10.2   0.1    1.5  1  AAA_24       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 !   89.9   0.0   1.6e-28   1.9e-25       2     136 ..      20     167 ..      19     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 1.6e-28
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEE.EE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeig.vlpqepqlfpeltvr 77 
                                       ++++l+l +ge v+++G+n aGK+t+lk+lagl kp  G i l g+d++   l++  ++++ vl+  p +   l v+
  gi|557694072|ref|YP_008797126.1|  20 SDIDLELLAGEFVVVIGPNAAGKTTFLKTLAGLAKPVTGVIYLAGEDMRVLGLRQRARNVAaVLTGRPDVSGML-VE 95 
                                       6899**********************************************666655555550555556666666.99 PP

                                       HH.................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       e                   +++ +++a++k g  +l+ ++v    s+LS Gq qrv +aral+++p++l+lDEpt
  gi|557694072|ref|YP_008797126.1|  96 EVvglgryawtgplhmlapVDKKVVDDAMAKTGVAHLRGRRV----STLSDGQLQRVLIARALAQHPRVLILDEPT 167
                                       99**************99888888******************....*****************************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 !   23.4   0.0   3.7e-08   4.5e-05       1      24 [.      31      54 ..      31      74 .. 0.88
   2 !   25.6   2.8     8e-09   9.5e-06     234     301 ..     137     202 ..     129     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.7e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      + v+iGpN++GK+++L++l +la 
  gi|557694072|ref|YP_008797126.1| 31 FVVVIGPNAAGKTTFLKTLAGLAK 54
                                      689****************99974 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 8e-09
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpll 301
                                       ++ lSdG+++   l++  l++++  ++l++DEp ++L+ k   ++++ll ++++r++  vi++TH  +l
  gi|557694072|ref|YP_008797126.1| 137 VSTLSDGQLQR-VLIARALAQHP--RVLILDEPTTHLDAKSRLEIITLLhSLAHRENLTVIASTHELEL 202
                                       5678****999.78888888887..************************999999**********8877 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.4e-05     0.016      23      48 ..      30      54 ..      19      78 .. 0.76
   2 !    8.0   0.7    0.0017         2     323     365 ..     157     199 ..     145     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                            AAA_15 23 eeltvliGkNnsGKSsilealdlFln 48
                                      e + v+iG+N++GK+++l+ l  + +
  gi|557694072|ref|YP_008797126.1| 30 E-FVVVIGPNAAGKTTFLKTLAGLAK 54
                                      3.99***************9976655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0017
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        + +l+++EP +hL  +   ++i ll +la  ++  vi +TH 
  gi|557694072|ref|YP_008797126.1| 157 HPRVLILDEPTTHLDAKSRLEIITLLHSLAHRENLTVIASTHE 199
                                       567899************************************6 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.8   6.7e-06     0.008       7     127 ..      31     195 ..      28     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.7e-06
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsst....sskdllrellralglelka...... 70 
                                       ++vv+G+  +GKTt l++l+  ++ +    +   e                 ++++ +r+++  l+ + +       
  gi|557694072|ref|YP_008797126.1|  31 FVVVIGPNAAGKTTFLKTLAGLAKPVTGVIYlagE------------DmrvlGLRQRARNVAAVLTGRPDVsgmlve 95 
                                       89********************9533222224442............323444444433333333333333566666 PP

                            AAA_22  71 .....................................erlsseell.ealeqalrarav...ielliiDEaqh.lr. 104
                                                                            ++ + + l   +l++ l ara    +++li+DE    l+ 
  gi|557694072|ref|YP_008797126.1|  96 evvglgryawtgplhmlapvdkkvvddamaktgvahlRGRRVSTLSdGQLQRVLIARALaqhPRVLILDEPTThLDa 172
                                       6666667789999999*************9******9888888888888888888888888889******8776998 PP

                            AAA_22 105 ..seealeeLrsllnlsrkgvqliL 127
                                         + e+++ L+sl+   r ++++i 
  gi|557694072|ref|YP_008797126.1| 173 ksRLEIITLLHSLAH--RENLTVIA 195
                                       744999999999999..88888874 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.4   4.8e-06    0.0057      25     170 .]      30     194 ..      24     194 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.8e-06
                            AAA_16  25 elvllsGesGvGKsslvrellralekd..ggiflrgkcdqlesaipysalaqalareellrqllde........... 88 
                                       e v+++G+ + GK++ +++l+  l k   g+i+l+g+  +       + l q + r  + + l  +           
  gi|557694072|ref|YP_008797126.1|  30 EFVVVIGPNAAGKTTFLKTLA-GLAKPvtGVIYLAGEDMRV------LGLRQRA-R-NVAAVLTGRpdvsgmlveev 97 
                                       789******************.5777745455555555555......3333333.2.22222222211111111122 PP

                            AAA_16  89 .....aesaeleawrekleeala.......................avpelagaea.srllellkrll.allsrder 135
                                                             a                        v++l+g    +    +l+r l a++   ++
  gi|557694072|ref|YP_008797126.1|  98 vglgrY----------------AwtgplhmlapvdkkvvddamaktGVAHLRGRRVsTLSDGQLQRVLiARALA-QH 157
                                       222220................1444444445466655555555776667777766544556899999888888.** PP

                            AAA_16 136 plvlvlDdlq.wadeaslqllaaLlrllesk.pllvv 170
                                       p vl+lD+    +d+ s+  + +Ll++l ++ +l+v+
  gi|557694072|ref|YP_008797126.1| 158 PRVLILDEPTtHLDAKSRLEIITLLHSLAHReNLTVI 194
                                       *******866466666666677777777776688876 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     2e-05     0.024       2      99 ..      32     189 ..      31     211 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg....avllssdt.......................................... 32 
                                       v+++G++++GK+t+++ l+   +    ++ l+  +                                          
  gi|557694072|ref|YP_008797126.1|  32 VVVIGPNAAGKTTFLKTLAGLAKpvtgVIYLAGEDmrvlglrqrarnvaavltgrpdvsgmlveevvglgryawtgp 108
                                       799**************964333445644455555577777777777777777777777777777777777777777 PP

                            AAA_33  33 ...........lrrrlfgtdqqsktdytrvldrlyqilne..larkalsagrnvildat..nlsrrerarflklarr 94 
                                                  + +++++t++ +++   rv++   ++l++  +ar  +++ r +ild +   l+++ r +++ l++ 
  gi|557694072|ref|YP_008797126.1| 109 lhmlapvdkkvVDDAMAKTGVAHLRG-RRVSTLSDGQLQRvlIARALAQHPRVLILDEPttHLDAKSRLEIITLLHS 184
                                       77777766665444555566655543.44444444444441134444455566777665335556666666666665 PP

                            AAA_33  95 lgvpv 99 
                                       l  ++
  gi|557694072|ref|YP_008797126.1| 185 LAHRE 189
                                       55444 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 ?    6.1   0.0    0.0056       6.7      24      44 ..      29      49 ..      21      52 .. 0.86
   2 ?    6.9   0.0    0.0033       3.9     148     200 ..     151     201 ..     114     219 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0056
                                      SSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlldAi 44
                                       +f +++GpN +GK+ +l  +
  gi|557694072|ref|YP_008797126.1| 29 GEFVVVIGPNAAGKTTFLKTL 49
                                      5799***********998765 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0033
                                       HHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                             SMC_N 148 aLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislree 200
                                       a  +A    +   + +lDe   +LD+k + ++ +ll+  ++++n  +i  +++ e
  gi|557694072|ref|YP_008797126.1| 151 ARALA----QHPRVLILDEPTTHLDAKSRLEIITLLHslAHRENLTVIASTHELE 201
                                       33333....3334679*********************333455555555555544 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.7e-05     0.068       3      49 ..      30      75 ..      28      93 .. 0.81
   2 ?   -1.2   0.0       1.7     2e+03      55      76 ..     148     169 ..     131     201 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.7e-05
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladp 49
                                      + +v+ G+  +GKTt+lk+l+     +   ++y++ +d r   l++ 
  gi|557694072|ref|YP_008797126.1| 30 EFVVVIGPNAAGKTTFLKTLAGLAK-PVTGVIYLAGEDMRVLGLRQR 75
                                      679*****************96666.889999999999998776654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.7
                            AAA_14  55 lilek.lkeekktylflDEiqev 76 
                                       ++ ++ l  ++ ++l+lDE    
  gi|557694072|ref|YP_008797126.1| 148 VLIARaLA-QHPRVLILDEPTTH 169
                                       44444233.47788999997665 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   2.8e-05     0.034      19      48 ..      22      51 ..       4      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.8e-05
                            AAA_27 19 ldfsaeeadlhliyGpNEAGKstalrAisd 48
                                      +d++  + ++ +++GpN AGK+t l+ +  
  gi|557694072|ref|YP_008797126.1| 22 IDLELLAGEFVVVIGPNAAGKTTFLKTLAG 51
                                      444445789****************98865 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.9   5.6e-05     0.067      31     149 ..      27     164 ..      17     199 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                            AAA_25  31 pagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsed.elrrRlravgeal......... 97 
                                        age+++++G+ ++GKtt++  la  +a  kp++g        V+y+++Ed +  +lr+R+r v + l         
  gi|557694072|ref|YP_008797126.1|  27 LAGEFVVVIGPNAAGKTTFLKTLA-GLA--KPVTG--------VIYLAGEDMRVlGLRQRARNVAAVLtgrpdvsgm 92 
                                       48*****************87776.455..57777........9*******98778888888877766666766766 PP

                            AAA_25  98 ....................rddarllvldlagv.eslpLfakdrggtlltadvda..leaaieevegvrlvviD 149
                                                           ++ ++  v d++ + +  +L+  +r +tl ++++++  +++a+ + + +r++++D
  gi|557694072|ref|YP_008797126.1|  93 lveevvglgryawtgplhmlAPVDKKVVDDAMAKtGVAHLRG-RRVSTLSDGQLQRvlIARALAQ-H-PRVLILD 164
                                       666666666666666666664444444555555545555543.3333333333333113333333.3.6777777 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00056      0.67       2      21 ..      32      51 ..      31      82 .. 0.79
   2 ?    0.4   0.0      0.57   6.9e+02      34      80 ..     119     165 ..     112     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00056
                            AAA_28  2 ivitGgestGKTtlleaLaa 21
                                      +v++G+  +GKTt l+ La 
  gi|557694072|ref|YP_008797126.1| 32 VVVIGPNAAGKTTFLKTLAG 51
                                      8*****************93 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.57
                            AAA_28  34 ileeklakge.dalpwvedllafaervleeqleeeaaaaankvlfcDr 80 
                                       ++++ +ak++  +l+  +++  + +++l+  l + a a+ ++vl++D 
  gi|557694072|ref|YP_008797126.1| 119 VVDDAMAKTGvAHLRG-RRVSTLSDGQLQRVLIARALAQHPRVLILDE 165
                                       6677776655144444.7999999999999999999999999999996 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 ?    8.4   0.1    0.0022       2.7       1      50 [.      32      83 ..      32      98 .. 0.82
   2 ?    2.5   0.0      0.15   1.8e+02      49     112 ..     149     200 ..     122     211 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0022
                                      EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakelg..vefleisgsellskyvgesekkirelf 50
                                      v+++Gp   GKT++ k +a  ++  + ++ + g +++   + ++++++++++
  gi|557694072|ref|YP_008797126.1| 32 VVVIGPNAAGKTTFLKTLAGLAKpvTGVIYLAGEDMRVLGLRQRARNVAAVL 83
                                      5799****************99876778888888888666667777776665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.15
                                       HHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSG CS
                               AAA  49 lfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrp 112
                                       l+++a   a +p +l++DE      ++       ++  + +Ll+ l   ++    ++vi+ t++ 
  gi|557694072|ref|YP_008797126.1| 149 LIARA--LAqHPRVLILDEPTTHLDAK-------SRLEIITLLHSLAHREN----LTVIASTHEL 200
                                       34444..44458999999987777777.......44445566666666655....7888888875 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    0.0012       1.5      95     126 ..      25      56 ..      17      66 .. 0.85
   2 ?    0.4   0.0      0.43   5.2e+02      13      47 ..     185     219 ..     139     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                                       HHCTTSEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  95 ellkdktsvlvGqSGvGKStLinallpelelk 126
                                       ell+++++v++G+  +GK+t++++l++ ++  
  gi|557694072|ref|YP_008797126.1|  25 ELLAGEFVVVIGPNAAGKTTFLKTLAGLAKPV 56 
                                       57899********************9866555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.43
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT- CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi 47 
                                        a  ++l ++ s++e el l++ dr++++a  k i
  gi|557694072|ref|YP_008797126.1| 185 LAHRENLTVIASTHELELALRFADRLILIADGKAI 219
                                       56667889999999999999999999998876655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00027      0.32      20      37 ..      30      47 ..      19      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                            AAA_23 20 gltlItGpNGaGKTTild 37
                                       +++++GpN aGKTT+l 
  gi|557694072|ref|YP_008797126.1| 30 EFVVVIGPNAAGKTTFLK 47
                                      57899**********996 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00039      0.46       5      23 ..      32      52 ..      29      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00039
                            AAA_24  5 iliyGpsgiGKTtlakel..g 23
                                      ++++Gp+ +GKTt++k+l   
  gi|557694072|ref|YP_008797126.1| 32 VVVIGPNAAGKTTFLKTLagL 52
                                      799**************9663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3076.99
//
Query:       gi|557694073|ref|YP_008797127.1|  [L=333]
Description: iron complex ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-76  255.7  38.4      6e-76  255.4  38.4    1.0  1  FecCD     FecCD transport family


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 !  255.4  38.4   3.3e-80     6e-76       2     312 .]      13     328 ..      12     328 .. 0.97

  Alignments for each domain:
  == domain 1  score: 255.4 bits;  conditional E-value: 3.3e-80
                             FecCD   2 lllllllslllgavkispsevfeallgka.dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpLadPsil 77 
                                       l++++l s++lg+v ++ps+v+ +llg   +     +v+++rl r +aa+l+Ga+L+vaGa+lQ+++rNpLadP +l
  gi|557694073|ref|YP_008797127.1|  13 LFASFLSSVFLGSVRVPPSDVLMYLLGWRgEVHVFDVVVDMRLVRGVAAVLTGASLGVAGAVLQSLFRNPLADPFVL 89 
                                       56789999******************9774555666***************************************** PP

                             FecCD  78 Gissgaalgavlallll.....lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsalts 149
                                       Gissg++l+++l+l+ +     +++   +al +aa +ga+l++l v++++  +  ++ + liLaG+++++l ++lt+
  gi|557694073|ref|YP_008797127.1|  90 GISSGSSLAIALTLVAGlgaglIQAYDPYALYMAAAAGAALTSLAVVIFS--TIAKTAIGLILAGVMLGYLNAGLTT 164
                                       ***************999**9999*************************9..888999******************* PP

                             FecCD 150 llllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrlllll 226
                                       ll++l+  e+++++ fw+lG++s a+ws v  +l+l++++l+++ll+a++l++la+g+e+A+s+G  v+  r+++++
  gi|557694073|ref|YP_008797127.1| 165 LLVTLSPVETMRAFSFWTLGTFSAAKWSLVEPVLPLFAVGLVASLLVAKPLNALAFGEEVAASMGAWVRGARVAAVA 241
                                       ***************************************************************************** PP

                             FecCD 227 lvalltavavalvGpigFvGLivPhiarllvg.adhrkllplsallGallllladllarlllsptelpvgivtaliG 302
                                       ++++++a+a++++GpigF+GL++Ph+arll++  d+r ++pls+l+Ga+l + ad++ar+++ p +lp+ ++t+l+G
  gi|557694073|ref|YP_008797127.1| 242 ASSAVVALATVVAGPIGFIGLAAPHVARLLAKsVDNRVVIPLSGLAGATLSITADIAARNIMPPLDLPLTAITSLFG 318
                                       ********************************9******************************************** PP

                             FecCD 303 apffiylllr 312
                                       ap+ ++lllr
  gi|557694073|ref|YP_008797127.1| 319 APIILLLLLR 328
                                       *******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       843  (0.0470188); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 2734.21
//
Query:       gi|557694074|ref|YP_008797128.1|  [L=412]
Description: iron complex ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   81.3   0.0    1.2e-22   80.7   0.0    1.2  1  Peripla_BP_2     Periplasmic binding protein
  ------ inclusion threshold ------
       0.12   12.8   0.1       0.36   11.2   0.1    1.8  2  Clathrin_propel  Clathrin propeller repeat
        0.5   10.9   2.4        4.2    7.9   0.4    2.3  2  FtsX             FtsX-like permease family


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 !   80.7   0.0   1.9e-26   1.2e-22      41     236 ..     174     373 ..     157     375 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 1.9e-26
                                       S-BSBESSSB-HHHHHHH--SEEEE-GGG.....GGGHHHHHHHS-EEE----TTSHHHHHHHHHHHHHTT-HHHHH CS
                      Peripla_BP_2  41 ivevgadgeidvEklaalkPDlvilskgl..gltdedeellksgiptvivessntgeslkeqiralgellgledeae 115
                                       i +vga +++d+E+l+al+PDlv   ++    ++++ eel  + + + ++ ++  + ++ e+i+ +   +gled a+
  gi|557694074|ref|YP_008797128.1| 174 ISDVGAAWSPDFERLVALQPDLVMIYTYPgdPVVSKLEELKLPYVVVSEYLEDD-LLGRFEWIKFVSVFFGLEDVAD 249
                                       5689*******************9999996445555544444444444555554.4********************* PP

                                       HHHHHHHHHHH....HHHHTS-TT.-EEEEEEEETTE..EEEE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHH CS
                      Peripla_BP_2 116 klvaeidskla....aaksaidsekpkpvlvfggadeggyvvagsnsyigdlldalgieniaaeskkseyeeisaEq 188
                                       k+++ +++ +     +ak+ ++   p p +v+ + ++g+++vag +sy+ + l +lg+ +++++ ++s+++++ +E+
  gi|557694074|ref|YP_008797128.1| 250 KVFSYVEQSVLltslRAKALVAHGVPAPKVVWFSVYRGTVYVAGGGSYVAKALKDLGASYVFSDIASSGSATVTPEE 326
                                       ********99722225566666669999999999******************************************* PP

                                       HHH..H--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT-EEEE-H CS
                      Peripla_BP_2 189 ila..sdpdvifvsgraeadnktgleflkenpllaelpAvkngrVyalds 236
                                       ++a   d+dvi+ s+      +t+ + lke p lae +A++++rVy++ s
  gi|557694074|ref|YP_008797128.1| 327 LVAraLDADVIVLSTD---LITTREDLLKELPQLAESKAFRENRVYRYSS 373
                                       ***999**********...9**************************9865 PP

>> Clathrin_propel  Clathrin propeller repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   5.9e-05      0.36       7      31 ..       1      28 [.       1      29 [. 0.94
   2 ?   -2.6   0.0       1.5   8.8e+03      20      33 ..      79      91 ..      78      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.9e-05
                                      EECCCEEEEECCEEEEEE...CETEEEE CS
                   Clathrin_propel  7 infptatneswlfiiain...gtkkGqv 31
                                      +++pt++++++  i+ i    g ++G++
  gi|557694074|ref|YP_008797128.1|  1 MDYPTNIMNKTTTILSILiiiGLVGGFL 28
                                      79********************9*9998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                                      EEEEECETEEEEEE CS
                   Clathrin_propel 20 iiaingtkkGqvql 33
                                      ++a+++ ++G+v+l
  gi|557694074|ref|YP_008797128.1| 79 LFALEN-RGGYVLL 91
                                      577775.99**986 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.4    0.0007       4.2      19      67 ..       9      57 ..       5      64 .. 0.67
   2 ?    2.4   0.1     0.037   2.2e+02      35      68 ..     290     326 ..     279     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0007
                              FtsX 19 llllteillitlvalviGlglgllaaqllsdvllssvfsselkisidli 67
                                         +t + ++++++lv G++lg  +aq++   +    + ++++ ++ + 
  gi|557694074|ref|YP_008797128.1|  9 NKTTTILSILIIIGLVGGFLLGQSIAQPVVRTVYVTSVETRVQTTVETR 57
                                      556777889999999999****999999665443333335555555555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.037
                              FtsX  35 iGlglgllaaqllsdvllssvfs...selkisidlit 68 
                                          g g+ +a++l d++ s+vfs   s+ + ++ ++ 
  gi|557694074|ref|YP_008797128.1| 290 YVAGGGSYVAKALKDLGASYVFSdiaSSGSATVTPEE 326
                                       445689****************888887777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2990.88
//
Query:       gi|557694075|ref|YP_008797129.1|  [L=278]
Description: molybdenum hydroxylase family protein, medium subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-34  117.9   0.2    5.6e-34  117.3   0.2    1.2  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
    2.5e-12   46.9   0.0    4.8e-12   46.0   0.0    1.4  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 !  117.3   0.2   6.3e-38   5.6e-34       5     168 ..       8     168 ..       2     171 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.3 bits;  conditional E-value: 6.3e-38
                                       EEE-SSHHHHHHHHHH.CTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHHHHH CS
                     FAD_binding_5   5 ylrpasleealallaa.epdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlselaae 80 
                                       +l p+++++al+l++  +++a +v+Ggt  ++l+++ +++p ++i+++++ +l++++++++ +eiGA++t +e++++
  gi|557694075|ref|YP_008797129.1|   8 FLVPETVNKALQLKRLyRDSALVVSGGTASVQLVTKMLVSPTAIISLEKL-PLNYVKKKGNTIEIGATTTAAEIIES 83 
                                       678************98899999***************************.9**********************988 PP

                                       HHHHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETTEESS CS
                     FAD_binding_5  81 alvrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkgpgktal 157
                                         v      l ea++ i + ++++ aTiGGN+ t +p +D+a+aLl ldA++ l+s++g r+vpl++f+kgp +  +
  gi|557694075|ref|YP_008797129.1|  84 GEVP---TCLLEAAKGIHGLALKQNATIGGNIFTPAPGGDMATALLSLDAQLILNSTQGMRTVPLAKFYKGPLTYNI 157
                                       7776...7789****************************************************************** PP

                                       -TT-EEEEEEE CS
                     FAD_binding_5 158 epgelitavei 168
                                       +++el+ta++i
  gi|557694075|ref|YP_008797129.1| 158 RSNELLTAIRI 168
                                       *********98 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 !   46.0   0.0   5.4e-16   4.8e-12      18     101 ..     191     272 ..     188     274 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 5.4e-16
                                       EEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHHHTCTTC-HHHHHHHHHH CS
                     CO_deh_flav_C  18 aAfrveleedgkiedariafggvaptpvraekaeaaLiGkplseelleeaakaleeelspasdprasaeYRrslavs 94 
                                       a ++v l++ +k++++ +a+gg  p+p ra+k+e++L+G+++s+el+e  a+++ ee+s       s eY ++la +
  gi|557694075|ref|YP_008797129.1| 191 ASVSVALDSVDKVKRVGVAVGGLTPHPYRASKVEKMLMGQKISKELIETTAQNIVEEASDTGL--VSGEYLSHLAGV 265
                                       56788888878******************************************9999987666..999********* PP

                                       HHHHHHH CS
                     CO_deh_flav_C  95 llfrfll 101
                                       l +r+l+
  gi|557694075|ref|YP_008797129.1| 266 LYKRILT 272
                                       ***9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2203.82
//
Query:       gi|557694076|ref|YP_008797130.1|  [L=151]
Description: molybdenum hydroxylase family protein, small subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-30  103.1   0.0    6.1e-30  103.1   0.0    1.5  2  Fer2_2           [2Fe-2S] binding domain
    2.8e-10   40.0   2.0    3.9e-10   39.5   0.1    2.0  2  Fer2             2Fe-2S iron-sulfur cluster binding domain
    7.5e-07   29.1   0.6    1.1e-06   28.5   0.1    1.5  1  Fer2_3           2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.012   15.6   0.5      0.072   13.2   0.5    2.2  1  Fer2_4           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 ?   -4.4   1.3         4   1.8e+04      27      34 ..      44      48 ..      36      52 .. 0.52
   2 !  103.1   0.0   1.4e-33   6.1e-30       1      76 []      73     146 ..      73     146 .. 0.96

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 4
                            Fer2_2 27 CGyCtpGf 34
                                      CG C   +
  gi|557694076|ref|YP_008797130.1| 44 CGAC---M 48
                                      3333...3 PP

  == domain 2  score: 103.1 bits;  conditional E-value: 1.4e-33
                            Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAvk 76 
                                       Tv+gl ++ +el+p+q++fve++a qCGyCtpG+v+ a+all++n p+p++eei +al+gnlCRCtgY piv+Avk
  gi|557694076|ref|YP_008797130.1|  73 TVAGLLSD-HELSPLQKKFVENNAAQCGYCTPGMVLVAKALLDKN-PSPSDEEIFDALAGNLCRCTGYVPIVKAVK 146
                                       89999988.89**********************************.88888***********************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 !   39.5   0.1   8.8e-14   3.9e-10       2      74 ..       6      60 ..       5      75 .. 0.80
   2 ?   -0.3   0.1      0.23     1e+03      38      44 ..      96     102 ..      92     135 .. 0.67

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 8.8e-14
                                      ETTTEEEEEEEETTTHBHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCE.CTTSSSSTHHHHHTTEEEEGGG CS
                              Fer2  2 tidgkevevevadgettlldaaee.nggidipysCggggCgtClvevlegev.qsdetelegeeldegklrlaCq 74
                                      ++dg+ vev+v++++t ll+++ +  g + ++y+Cg+g+Cg+C+v+v+ g+                     +C 
  gi|557694076|ref|YP_008797130.1|  6 YLDGQLVEVDVKPTDT-LLKVLVDkLGITSVHYGCGEGSCGACMVMVD-GKLrY------------------SCL 60
                                      689************9.88888877999*****************877.55433..................333 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.23
                                       SSSSTTE CS
                              Fer2  38 ggCgtCl 44 
                                       ++Cg C+
  gi|557694076|ref|YP_008797130.1|  96 AQCGYCT 102
                                       4599997 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 !   28.5   0.1   2.6e-10   1.1e-06      23      94 ..      14      89 ..       9      95 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.6e-10
                            Fer2_3 23 veaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlakqkse........ieleplpk 93
                                      v+++++dt+l++L           + ++ C+eg CG+c v+++Gk +  C +   +++++k +         el pl+k
  gi|557694076|ref|YP_008797130.1| 14 VDVKPTDTLLKVLVD----KLGITSVHYGCGEGSCGACMVMVDGKLRYSCLTFAASVNDKKITtvagllsdHELSPLQK 88
                                      555555555555532....2233456799***************************99887534677777777777766 PP

                            Fer2_3 94 f 94
                                       
  gi|557694076|ref|YP_008797130.1| 89 K 89
                                      5 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 ?   13.2   0.5   1.6e-05     0.072       3      69 ..       2      61 ..       1      68 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                            Fer2_4  3 pvtltfDGkevt..vpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracst 69
                                      ++++++DG+ v+  v++ dt++++l +     ++s +y       c  g+C  C+V v+g+    +c t
  gi|557694076|ref|YP_008797130.1|  2 MIRFYLDGQLVEvdVKPTDTLLKVLVDK--LGITSVHY------GCGEGSCGACMVMVDGKL-RYSCLT 61
                                      689*****96651167899999998753..23377777......4999***********986.567766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); 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:                         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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1210.92
//
Query:       gi|557694077|ref|YP_008797131.1|  [L=451]
Description: molybdenum hydroxylase family protein, large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-83  279.2   0.0    8.1e-83  278.7   0.0    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    2.2e-28   98.8   0.0    3.8e-28   98.0   0.0    1.4  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 !  278.7   0.0     9e-87   8.1e-83      11     276 ..     178     440 ..     169     443 .. 0.96

  Alignments for each domain:
  == domain 1  score: 278.7 bits;  conditional E-value: 9e-87
                                       EEEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHHT--GGGEE CS
                     Ald_Xan_dh_C2  11 akiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevlglpenkvr 87 
                                       + +++G+ve+afa+a  vveg++ ++ +eh++lE++ +++ p + +g+lt+y+ tq p++vr+ va +l++p++++r
  gi|557694077|ref|YP_008797131.1| 178 FLVKRGNVEQAFANAYEVVEGSYMIPPIEHAPLEPHICVVKP-EPSGKLTIYTPTQSPYFVRDNVATILNIPASNIR 253
                                       44679*************************************.77******************************** PP

                                       EE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEEEEEEEEE CS
                     Ald_Xan_dh_C2  88 vivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkitaldvdllad 164
                                       v++p vGGGFGgK  +   e+ +a+aA+ +grpVk++ +Ree+++ +++r ++ki++k +++++G+i++ +++ll+d
  gi|557694077|ref|YP_008797131.1| 254 VVSPHVGGGFGGK-VDPEFEMQVAVAAMVVGRPVKWRWTREEEFTVSTTRPAVKIELKDALSREGRILGRKARLLHD 329
                                       *************.999************************************************************ PP

                                       ESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT--HHHHHH CS
                     Ald_Xan_dh_C2 165 aGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgldplelRr 241
                                       aGaya  sp  + + +++l gpY+i+n+r+eg++v+tN+ p++a+RG+G  ++ +a+E +m+++A++lg+d +e+R 
  gi|557694077|ref|YP_008797131.1| 330 AGAYARTSPYGVIKSTVNLSGPYNIENLRYEGYCVFTNRQPSSAMRGYGVFEVSYAVELHMERAARKLGIDSWEFRF 406
                                       ***************************************************************************** PP

                                       HHBCECGCC.SEEETEESSS-HHHHHHHHHHHHTH CS
                     Ald_Xan_dh_C2 242 rNlikpgeltpygqpvydsgdlpelldklkessdy 276
                                       +N+++++++t +g p +d+  l e+++++++ +++
  gi|557694077|ref|YP_008797131.1| 407 INAYRNNQVTATGRP-VDDAYLIEVMKEAAALAGV 440
                                       ***************.6999999999999988875 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 !   98.0   0.0   4.2e-32   3.8e-28       1     110 []      23     134 ..      23     134 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 4.2e-32
                                       TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT...TSSS-EEEESS-S CS
                      Ald_Xan_dh_C   1 tGeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig...siledeedallae 74 
                                       tG  +Y+d i++pg+l+++ vrS+++++ki++id+s+a++lpGV+++itak++p++ +  +    +  ++ + +l e
  gi|557694077|ref|YP_008797131.1|  23 TGATQYIDSISFPGMLWIKAVRSPVPRGKIKKIDYSKAEKLPGVAKIITAKHVPNNYHVNLaglGVGPPD-EPVLPE 98 
                                       7999**************************************************9977666666444444.47**** PP

                                       SEESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                      Ald_Xan_dh_C  75 dkvrsvgqavaavvAedeetArkAaklvkveYeelp 110
                                       d+v+++g+a+++vvA+deetA+kAa+lv+v+ eelp
  gi|557694077|ref|YP_008797131.1|  99 DEVNYKGEAICLVVARDEETAAKAANLVEVDIEELP 134
                                       *******************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 3546.75
//
Query:       gi|557694078|ref|YP_008797132.1|  [L=336]
Description: molybdenum hydroxylase family protein, large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-72  244.1   2.8    2.9e-72  243.9   2.8    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd


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 !  243.9   2.8   1.6e-76   2.9e-72     291     550 .]       3     268 ..       1     268 [. 0.96

  Alignments for each domain:
  == domain 1  score: 243.9 bits;  conditional E-value: 1.6e-76
                                       CEEEEEEEEEEEEBS--S.EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBT CS
                     Ald_Xan_dh_C2 291 kkrGiglapvvegiglgftakflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdt 367
                                       k rG g+a++ +++g++ +    +++++ +  ++dG+ +v+++++e+GqG++t+laqia+e  gv++ed++v+ gdt
  gi|557694078|ref|YP_008797132.1|   3 KLRGRGIAAINYPTGMNLG---GDPSQVVIVAQPDGRLVVNVASVELGQGIKTVLAQIASEITGVSVEDIEVRFGDT 76 
                                       459***********87764...577889************************************************* PP

                                       TSSS----S-TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH. CS
                     Ald_Xan_dh_C2 368 dkvpngsgtaaSrstdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl. 440
                                       +++p+++gt+aSrst   gnAv kA e++re +l+ aa++levsp dle+++g+v vk   +ksv++++++++a + 
  gi|557694078|ref|YP_008797132.1|  77 ESAPHDTGTFASRSTHRMGNAVVKASEEIREIVLNTAAKMLEVSPRDLEIREGRVWVKgvsDKSVEVKQVISQAQFt 153
                                       ************************************************************************88665 PP

                                       TTSSEEEEEEE.......EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 441 ervslsatgfykt....ldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGf 513
                                        + ++  +gfy +    +d etg ++p++++a g++vaeVevDtetg v+vl+v++v+ vGk+iNp++ve Qi GG+
  gi|557694078|ref|YP_008797132.1| 154 YNTPVVGKGFYVKpkssVDPETGASDPHSTMAHGCTVAEVEVDTETGFVTVLKVYTVYEVGKAINPQLVESQIIGGI 230
                                       889********889*************************************************************** PP

                                       HHHHHHHHT---EEE.TTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 514 vqGiGlalmEelvyd.edGqlltasladYkiPtaadiP 550
                                       v+G+G+al+E +    +   ++t+s++dY +Pta diP
  gi|557694078|ref|YP_008797132.1| 231 VMGMGAALTETVYPRyPALDFQTTSFRDYILPTAGDIP 268
                                       ***********9776788999****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2686.32
//
Query:       gi|557694079|ref|YP_008797133.1|  [L=270]
Description: metal-dependent hydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-20   72.9   0.0    4.3e-20   72.2   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
    1.3e-16   60.7   0.0    1.8e-16   60.3   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    8.4e-05   22.7   0.1     0.0002   21.4   0.1    1.6  2  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.028   14.7   0.1       0.26   11.6   0.0    2.1  2  ATXN-1_C       Capicua transcriptional repressor modulator


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 !   72.2   0.0   9.6e-24   4.3e-20       2     163 .]       6     222 ..       5     222 .. 0.79

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 9.6e-24
                     Lactamase_B_3   2 ltwlghnsflletagarilvDPfka...nlgyeppa.............eeaDlvlisqaledHahletlkql.... 58 
                                       ++++gh+sf +++++ +i++DP+ +   + g    a             ++a +vl+s+++ dH  ++ ++ +    
  gi|557694079|ref|YP_008797133.1|   6 INFIGHASFSIKWRNEVIYIDPWLKtplESG----AgnspvspigledvKNATVVLVSHGHIDHLGHA-IEIVkktg 77 
                                       789********************74323333....23355889999999***************8654.44444446 PP

                     Lactamase_B_3  59 ..............................aenvkvlee.......geslevggleiravatsh.........davg 89 
                                                                     +               g+s +++++ ++av++ h          + +
  gi|557694079|ref|YP_008797133.1|  78 aclvctpevgmyadiygipydsepdekagrK-------YwmypinvGGSCTINKVTYTAVPAFHsssimhydyIKNK 147
                                       6666666666666666666555555554443.......044445559*****************8888887553333 PP

                     Lactamase_B_3  90 gsergenngflleq.dgltiyhlGhlahelsseelkelgrvDvvltPvggpltlgqeealelakrLkpklvlPmh 163
                                        + ++  +g++++  dg  iy+ G+++  +++  ++el  +++ ++  gg++ +g +e + ++k Lkpkl +P h
  gi|557694079|ref|YP_008797133.1| 148 TRYPDAPVGYIISPeDGPVIYFSGDTGVSMEMHMIQELYSPEICIMTAGGQYNMGVREFAYACKILKPKLAIPCH 222
                                       4444668*****9978*********************************************************98 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 !   60.3   0.0     4e-20   1.8e-16       3     201 .]      23     223 ..      22     223 .. 0.84

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 4e-20
                                       EEES--TT..HHHHHTCGG.S--S..SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTC CS
                     Lactamase_B_2   3 iLiDagpd..lrqqalral.qPve..lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanf 74 
                                       i iD+++   l    + a  +Pv+   +++++   +Vl++h+H+DHl  +  + +   + + l+++++v+ + +  +
  gi|557694079|ref|YP_008797133.1|  23 IYIDPWLKtpL--E-SGAGnSPVSpiGLEDVKNATVVLVSHGHIDHLGHAIEIVKK--TGACLVCTPEVGMYADIYG 94 
                                       66788888431..2.2222234443458999****************555555553..346799*********9999 PP

                                       GHHHCHTT....TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C.......TCCE-TTTSEEEEEE.CTTEEEEE CS
                     Lactamase_B_2  75 vylaleee....pavnvheldwgesfelgdggleitatparhksgr.......rldrnagdtlGlrie.gggkrvyy 139
                                       ++  +e++     +  + +++ g+s +++  +++ ta+pa h+s         +++r +   +G++i  ++g  +y+
  gi|557694079|ref|YP_008797133.1|  95 IPYDSEPDekagRKYWMYPINVGGSCTIN--KVTYTAVPAFHSSSImhydyikNKTRYPDAPVGYIISpEDGPVIYF 169
                                       999999988999899999**********9..689***************99999999999***************** PP

                                       ESS-S.---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 140 igDtg.yipeeigerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       +gDtg  ++ ++ ++l+ +++ ++ ++         + + + ++e + a++ l++k +++ H+
  gi|557694079|ref|YP_008797133.1| 170 SGDTGvSMEMHMIQELYSPEICIMTAG---------GQYNMGVREFAYACKILKPKLAIPCHY 223
                                       *****4455778889999999998888.........7899**********************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   4.5e-08    0.0002      43      79 ..      51      87 ..      47     119 .. 0.90
   2 ?   -2.4   0.0      0.91   4.1e+03     144     156 ..     166     178 ..     150     189 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.5e-08
                                      GGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                       Lactamase_B 43 kdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79
                                      k+ + v+++H+H+DH G + ++v++t+++ ++ +e++
  gi|557694079|ref|YP_008797133.1| 51 KNATVVLVSHGHIDHLGHAIEIVKKTGACLVCTPEVG 87
                                      56689***********************999888776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.91
                                       CEEEECTTTSSHH CS
                       Lactamase_B 144 kvlftGDallage 156
                                        + f+GD++ + e
  gi|557694079|ref|YP_008797133.1| 166 VIYFSGDTGVSME 178
                                       4568999887665 PP

>> ATXN-1_C  Capicua transcriptional repressor modulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       0.2   8.9e+02      19      38 ..      40      56 ..      30      65 .. 0.74
   2 ?   11.6   0.0   5.8e-05      0.26      21      43 ..     225     247 ..     220     250 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.2
                          ATXN-1_C 19 SfalpppalgadslKaaVat 38
                                      S   p +++g + +K a   
  gi|557694079|ref|YP_008797133.1| 40 S---PVSPIGLEDVKNATVV 56
                                      4...8889999****98444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.8e-05
                          ATXN-1_C  21 alpppalgadslKaaVatlsPht 43 
                                       ++p + l  + lK aV+ +sP t
  gi|557694079|ref|YP_008797133.1| 225 TFPRQRLDKEKLKQAVSVMSPST 247
                                       79*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1943.51
//
Query:       gi|557694080|ref|YP_008797134.1|  [L=126]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   36.6   0.3    9.2e-05   22.3   0.0    2.0  2  DUF3237   Protein of unknown function (DUF3237)


Domain annotation for each model (and alignments):
>> DUF3237  Protein of unknown function (DUF3237)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   7.1e-08    0.0013       2      74 ..       4      76 ..       3      78 .. 0.85
   2 !   22.3   0.0   5.1e-09   9.2e-05      65     137 ..      51     122 ..      47     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.1e-08
                                      -EEEEEEEEEEE---EEEEEET.EEEEEEEEEEEEEESTT--EEE-ST-EEEEEE-T...TS-EEEEEEEEEEETTS CS
                           DUF3237  2 slepaftlevkleapvpigegp.gkrnivpitgGtikgprldgevlpgGaDwiridp...ggtarldaryvlktddg 74
                                      +lep+++le+++    +ige+p g+r+ ++++ G +kg +++g+    G D+ +i +   g+++ + +r ++ td g
  gi|557694080|ref|YP_008797134.1|  4 ELEPFYELEAQIVRTEEIGETPyGRRSNFHMK-GVVKG-KINGTYE--GIDYGTIVKtevGDVVYVYVRETITTDRG 76
                                      69**********999*******9999999985.89***.6****66..******99966666667778877777776 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 5.1e-09
                                       EEEEEEETTS-EEEEEEEEEEE--GGGHHHHHHT-..---GGG-E..EEEEEEEEESSGGGGGGGSS-EEEEEEE CS
                           DUF3237  65 aryvlktddgaliyirytGvvtldeevlavlgggekkesspteyg..frthptfetgdekykwLnnavfvGsgrf 137
                                          ++kt+ g+++y+  + ++t d+ + + +++g    + pt+ g  +r+ ++f t+ ++y+ Ln+++ v++g+ 
  gi|557694080|ref|YP_008797134.1|  51 YGTIVKTEVGDVVYVYVRETITTDRGIISGIRQGY---AVPTQGGlaVRLFIFFHTQIPEYRFLNWTLGVAEGKA 122
                                       55689****************************88...347777777************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 944.32
//
Query:       gi|557694081|ref|YP_008797135.1|  [L=185]
Description: hypothetical protein CSUB_C0646 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1405.96
//
Query:       gi|557694082|ref|YP_008797136.1|  [L=363]
Description: maltooligosaccharide ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   92.0   0.0    7.7e-26   91.2   0.0    1.4  1  ABC_tran         ABC transporter
    1.4e-07   31.7   0.3    0.00071   19.5   0.0    2.5  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    5.7e-06   27.1   0.0    1.7e-05   25.5   0.0    1.9  1  OB_MalK          MalK OB fold domain
    0.00036   21.0   0.0    0.00083   19.9   0.0    1.7  1  CysA_C_terminal  CysA C-terminal regulatory domain
    0.00081   19.8   0.1     0.0034   17.8   0.0    2.1  2  AAA              ATPase family associated with various cellul
     0.0011   19.1   0.0     0.0024   18.0   0.0    1.6  1  TOBE_2           TOBE domain
      0.002   17.8   0.0     0.0037   17.0   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
     0.0024   18.4   0.3     0.0094   16.5   0.1    2.0  2  AAA_23           AAA domain
     0.0046   16.7   0.0     0.0091   15.7   0.0    1.5  1  AAA_30           AAA domain
     0.0046   17.1   0.6       0.04   14.1   0.6    2.1  1  AAA_33           AAA domain
     0.0051   17.1   0.0      0.016   15.5   0.0    1.8  2  AAA_22           AAA domain
     0.0071   16.7   0.0      0.015   15.7   0.0    1.6  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.047   13.6   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
      0.036   14.0   0.0      0.076   12.9   0.0    1.6  1  ATPase_2         ATPase domain predominantly from Archaea
      0.036   14.1   0.0      0.085   12.9   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
      0.039   13.7   0.0        0.2   11.3   0.0    1.8  2  AAA_15           AAA ATPase domain
      0.048   13.1   0.1        6.8    6.1   0.0    2.2  2  SMC_N            RecF/RecN/SMC N terminal domain
      0.054   12.6   0.0      0.081   12.1   0.0    1.3  1  G-alpha          G-protein alpha subunit
      0.065   13.1   0.0       0.12   12.3   0.0    1.4  1  NACHT            NACHT domain
      0.095   13.2   0.1       0.19   12.3   0.1    1.6  1  AAA_18           AAA domain
      0.098   12.9   0.0       0.18   12.0   0.0    1.6  1  AAA_28           AAA domain
       0.12   12.3   0.0       0.28   11.2   0.0    1.5  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.13   12.7   0.0       0.29   11.5   0.0    1.6  1  RNA_helicase     RNA helicase
       0.15   11.3   0.0        9.7    5.4   0.0    2.2  2  Zeta_toxin       Zeta toxin


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 !   91.2   0.0     1e-28   7.7e-26       1     136 [.      19     161 ..      19     162 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.2 bits;  conditional E-value: 1e-28
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+nvsl++  g+   ++G++G+GK+tL++++agl++p +G++ + g+d++e  l+ ++++i++++q p++ p l+++
  gi|557694082|ref|YP_008797136.1|  19 LDNVSLHVDDGSFFCLLGPSGSGKTTLMRIIAGLETPSSGSVYFGGEDVTE--LSPSERNIAMVFQFPSIYPSLNIY 93 
                                       79*************************************************..************************ PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +n             e +e++ +++s l+++e  +++     +++  G  qrv++a+a++++++++++DEp 
  gi|557694082|ref|YP_008797136.1|  94 DNialalrrettdrnEIRERVMQVASLLKIEEHLNKKS----HQIDFGILQRVSIAKAIVRRANVYIFDEPL 161
                                       ********998766666666777777777777666665....*****************************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 !   19.5   0.0   9.5e-07   0.00071       1      63 [.      31      86 ..      31     135 .. 0.60
   2 !    9.9   0.0   0.00078      0.58     250     299 ..     147     194 ..     138     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.5e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie 63
                                      + +l Gp gsGK++L++++ +l       e   + +  +gg+++ + ++ ++++ + f+f  +
  gi|557694082|ref|YP_008797136.1| 31 FFCLLGPSGSGKTTLMRIIAGL-------ETPSSGSVYFGGEDVTELSPSERNIAMVFQFPSI 86
                                      6789***************999.......3333333333355544444444444444444444 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00078
                            AAA_21 250 allralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSp 299
                                       a+ r++    ++++DEp ++L+ kl + l   + +++s+ ++ ++ +TH+ 
  gi|557694082|ref|YP_008797136.1| 147 AIVRRA---NVYIFDEPLSNLDTKLREALRSEFqRIHSEVRGTFLYVTHDQ 194
                                       556666...699******************77768888888********95 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   2.3e-08   1.7e-05       1      51 [.     235     288 ..     235     290 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 2.3e-08
                           OB_MalK   1 GSPaMNflpatveedg..vlvegggvtlplpeeq.klalklyagkevilGiRPE 51 
                                       GSP  N+++ +v+  +  v++  g+  + l +++ +l + +++ +++ilGiRP 
  gi|557694082|ref|YP_008797136.1| 235 GSPTINLIESEVKLVEniVYASVGDGHIHLGNKAlELFQTSREPRKIILGIRPH 288
                                       9**********996666999999999********999****************5 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 !   19.9   0.0   1.1e-06   0.00083       5      43 .]     255     292 ..     251     292 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.1e-06
                   CysA_C_terminal   5 GrvedGklriGglalpvPelagadgqevvayVRPhDlei 43 
                                       + v dG++++G+ al++  +  ++ ++ ++++RPh++++
  gi|557694082|ref|YP_008797136.1| 255 ASVGDGHIHLGNKALELF-QTSREPRKIILGIRPHEITL 292
                                       6789************99.567778************86 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 !   17.8   0.0   4.5e-06    0.0034       2      99 ..      33     130 ..      32     184 .. 0.71
   2 ?   -2.4   0.0       8.2   6.1e+03      84     119 ..     324     358 ..     308     362 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.5e-06
                                       EEESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTT CS
                               AAA   2 llyGppGtGKTllakavakel..gvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsg 76 
                                       +l Gp G GKT+l++ +a     ++  + + g +++   ++ se++i+++f+   +   ps  + D+i    +++++
  gi|557694082|ref|YP_008797136.1|  33 CLLGPSGSGKTTLMRIIAGLEtpSSGSVYFGGEDVT--ELSPSERNIAMVFQFP-SIY-PSLNIYDNIALALRRETT 105
                                       799***************984233556777777777..67799********873.444.899999999888888844 PP

                                       CCCHHHHHH..HHHHHHHHHHTTTS CS
                               AAA  77 seseeeerv..vnqLlteldgvkkk 99 
                                       + +e +erv  v+ Ll+  + ++kk
  gi|557694082|ref|YP_008797136.1| 106 DRNEIRERVmqVASLLKIEEHLNKK 130
                                       4444444441155677776666665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.2
                                       HHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHH CS
                               AAA  84 rvvnqLlteldgvkkkeskvivigatnrpdkldpal 119
                                       +v+   +  l+++++k +kv+ +  t +++ +dp+ 
  gi|557694082|ref|YP_008797136.1| 324 TVLRSYVDSLSDFREK-EKVFAVFNTESIHGFDPQT 358
                                       4444445556666664.5588888888888887765 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.2e-06    0.0024       1      76 []     283     354 ..     283     354 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.2e-06
                            TOBE_2   1 laiRPEklrlaaagg.anglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                       l+iRP  ++l ++++ +n+l+++++ +e lG+  ++ ++ ++  l + ++++ +   ++++ ++V   +++++++ +
  gi|557694082|ref|YP_008797136.1| 283 LGIRPHEITL-SREPvGNALPAEISFIESLGTAQVIELRNGSTVL-RSYVDSLS---DFREKEKVFAVFNTESIHGF 354
                                       79********.5666679***************997777555544.55666666...9***************9965 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 !   17.0   0.0   4.9e-06    0.0037      13      41 ..      20      48 ..      17      62 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.9e-06
                            AAA_29 13 dghtieidlkg.atlltGpsGsGKSTllDA 41
                                      d+ ++++d  g ++ l GpsGsGK+Tl+  
  gi|557694082|ref|YP_008797136.1| 20 DNVSLHVDD-GsFFCLLGPSGSGKTTLMRI 48
                                      567778884.4599*************955 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.3e-05    0.0094      10      39 ..      19      49 ..       4      54 .. 0.78
   2 ?   -0.9   0.0       2.6     2e+03     175     190 ..     113     132 ..      63     183 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                            AAA_23 10 frdqeidFsk.gltlItGpNGaGKTTildAi 39
                                      +++++++ ++  ++++ Gp G+GKTT+++ i
  gi|557694082|ref|YP_008797136.1| 19 LDNVSLHVDDgSFFCLLGPSGSGKTTLMRII 49
                                      46666666442689**************987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.6
                            AAA_23 175 l....eqekekekeleelee 190
                                       +      +++ e+ l+++  
  gi|557694082|ref|YP_008797136.1| 113 RvmqvASLLKIEEHLNKKSH 132
                                       22222333333333333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.2e-05    0.0091      18     112 ..      29     176 ..      20     197 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                            AAA_30  18 drvavltGpAGtGKttalkalreaweaa.g......grviglAptgkaAkv.La....................... 63 
                                         + +l Gp G+GKtt+++ ++ + + + g      ++v  l+p+++  +   +                       
  gi|557694082|ref|YP_008797136.1|  29 GSFFCLLGPSGSGKTTLMRIIAGLETPSsGsvyfggEDVTELSPSERNIAMvFQfpsiypslniydnialalrrett 105
                                       4578999**************99999886689988888888888877544414455555555555444444444333 PP

                            AAA_30  64 ..eelgieastiakllkrlk...................grarlepgtllivDE.agmvdtkqlaallkaa 112
                                         +e+  + + +a+llk  +                   ++a +++++++i DE  + +dtk  +al ++ 
  gi|557694082|ref|YP_008797136.1| 106 drNEIRERVMQVASLLKIEEhlnkkshqidfgilqrvsiAKAIVRRANVYIFDEpLSNLDTKLREALRSEF 176
                                       33244446666666665444777777777777777777654555666777777755667777766666655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.6   5.3e-05      0.04       4     109 ..      34     193 ..      32     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.3e-05
                            AAA_33   4 lvGlpGsGKstlaerllkklg.....avllssdt..........................................l 33 
                                       l G++GsGK+tl + ++  ++     +++  +d+                                          +
  gi|557694082|ref|YP_008797136.1|  34 LLGPSGSGKTTLMRIIAGLETpssgsVYFGGEDVtelspserniamvfqfpsiypslniydnialalrrettdrneI 110
                                       67************998555456665444444448888999999999999999999999999987766666666654 PP

                            AAA_33  34 rrrlfg.....tdqqskt......dytrvldrlyqilnelarkalsagrnvildat..nlsrrerarflklarrlgv 97 
                                       r+r+       +            ++ ++ + + q++  +a+   ++++ +i+d +  nl+ + r+++++ ++r+++
  gi|557694082|ref|YP_008797136.1| 111 RERVMQvasllK-----IeehlnkKSHQIDFGILQRV-SIAKAIVRRANVYIFDEPlsNLDTKLREALRSEFQRIHS 181
                                       444444444442.....03333334444667799998.788777788888999999888889999999999999999 PP

                            AAA_33  98 pvrivvvetdee 109
                                       +vr  ++ +  +
  gi|557694082|ref|YP_008797136.1| 182 EVRGTFLYVTHD 193
                                       988766666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.1e-05     0.016       4      70 ..      28     106 ..      25     159 .. 0.70
   2 ?   -1.4   0.0       3.5   2.6e+03      37      67 ..     146     179 ..     116     199 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee................erpevvfvtlpsstsskdllrellral 64 
                                       + ++ ++ G+sG+GKTtl+r ++   +                       er   + ++ ps   s +++ +++ al
  gi|557694082|ref|YP_008797136.1|  28 DGSFFCLLGPSGSGKTTLMRIIAGLETPS----SgsvyfggedvtelspsERNIAMVFQFPSIYPSLNIYDNIALAL 100
                                       578999**************988776322....13355777777777755555555666666667777777777777 PP

                            AAA_22  65 glelka 70 
                                        +e+ +
  gi|557694082|ref|YP_008797136.1| 101 RRETTD 106
                                       765555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.5
                            AAA_22  37 e...erpevvfvtlpsstsskdllrellralgle 67 
                                       +   +r+ v+ ++ p s+  ++l+++l +++++ 
  gi|557694082|ref|YP_008797136.1| 146 KaivRRANVYIFDEPLSNLDTKLREALRSEFQRI 179
                                       1444566666666666665666666666666654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     2e-05     0.015      24     125 ..      29     178 ..      15     204 .. 0.51

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-05
                            AAA_16  24 pelvllsGesGvGKsslvrellralekd..g.giflrgkcdql...esaipy.salaqalareellrqllde..aes 91 
                                       ++   l G+sG+GK++l+r ++  le+   g ++f  ++ ++l   e++i++  ++ ++     ++  ++ +   e+
  gi|557694082|ref|YP_008797136.1|  29 GSFFCLLGPSGSGKTTLMRIIAG-LETPssGsVYFGGEDVTELspsERNIAMvFQFPSIYPSLNIYDNIALAlrRET 104
                                       367889************99994.55553433555333333334445555553113333333333333333311122 PP

                            AAA_16  92 aeleawrekleeala............................................avpelagaeasrllellk 124
                                       +++++ re+                                                  + ++l+ +++++l+ +++
  gi|557694082|ref|YP_008797136.1| 105 TDRNEIRERV----MqvasllkieehlnkkshqidfgilqrvsiakaivrranvyifdePLSNLDTKLREALRSEFQ 177
                                       2233333322....222235555555555555666665555555555555555555555555555555555555555 PP

                            AAA_16 125 r 125
                                       r
  gi|557694082|ref|YP_008797136.1| 178 R 178
                                       5 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   6.3e-05     0.047      86     121 ..      15      51 ..       3      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.3e-05
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       t+++l++++ +++d ++ +l+G+SG GK+tL+  +++
  gi|557694082|ref|YP_008797136.1|  15 TTRALDNVSLHVDDgSFFCLLGPSGSGKTTLMRIIAG 51 
                                       567788888888888999**************99887 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    0.0001     0.076      21     136 ..      30     169 ..      12     183 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                          ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefie........................eee 73 
                                       ++  + Gp gsGKt+L++ i+      +   +y+      ++s  ++ i+                        e+ 
  gi|557694082|ref|YP_008797136.1|  30 SFFCLLGPSGSGKTTLMRIIAGLE-TPSSGSVYFGGEDVTELSPSERNIAmvfqfpsiypslniydnialalrrETT 105
                                       566678***********9666555.5455566654444444444444444455566688888888888888888888 PP

                          ATPase_2  74 ekkklekalgiavpkaeleeilkeksklvfkaiel...llekikkkgkkiiiiiDelqklidlgln 136
                                       +++++++ ++++    ++ee l++ks +++  i +   + ++i +++   + i+De     d +l+
  gi|557694082|ref|YP_008797136.1| 106 DRNEIRERVMQVASLLKIEEHLNKKSHQIDFGILQrvsIAKAIVRRA--NVYIFDEPLSNLDTKLR 169
                                       88888888888888888888888777766665543011223333333..46777776555555555 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 ?   12.9   0.0   0.00011     0.085       2      22 ..      32      52 ..      31      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                      EEEE--SSSSHHHHHHHGGGG CS
                             AAA_5  2 vlLvGppGtgKselaerlaaa 22
                                      ++L+Gp+G+gK++l++ +a +
  gi|557694082|ref|YP_008797136.1| 32 FCLLGPSGSGKTTLMRIIAGL 52
                                      69*************999865 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00026       0.2      12      50 ..      17      56 ..      17     136 .. 0.72
   2 ?   -0.6   0.1       1.1   8.6e+02     312     365 ..     145     193 ..     108     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                            AAA_15 12 Rslkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      R+l++v++++++  + +l G+ +sGK+++++++  + + +
  gi|557694082|ref|YP_008797136.1| 17 RALDNVSLHVDDGsFFCLLGPSGSGKTTLMRIIAGLETPS 56
                                      89999*******9999****************97666655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                            AAA_15 312 leaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       ++a+ +     + ++++++EP  +L +++ + l   ++++ ++ ++  ++ TH 
  gi|557694082|ref|YP_008797136.1| 145 AKAIVR-----RANVYIFDEPLSNLDTKLREALRSEFQRIHSEVRGTFLYVTHD 193
                                       333333.....6788888888888888888888888888888888888888885 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 ?    6.1   0.0    0.0091       6.8      24      42 ..      29      47 ..      11      52 .. 0.80
   2 ?    4.7   0.0     0.023        17     154     199 ..     147     194 ..     140     211 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0091
                                      SSEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlld 42
                                       sf +++Gp GSGK+ l+ 
  gi|557694082|ref|YP_008797136.1| 29 GSFFCLLGPSGSGKTTLMR 47
                                      46899**********9986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.023
                                       HCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
                             SMC_N 154 qkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislre 199
                                         v++a +y++De  ++LD k ++++ + +++ +++    f+ +++++
  gi|557694082|ref|YP_008797136.1| 147 AIVRRANVYIFDEPLSNLDTKLREALRSEFQRIHSEvrGTFLYVTHDQ 194
                                       5578999****************9998777654443125566666665 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00011     0.081      27     112 ..      33     131 ..      20     204 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                                       EEEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT.......H CS
                           G-alpha  27 lllGqseSGKsTilkqlkllykkg.............fseeelatwraviqlnivrsiktilealesleselsesfe 90 
                                        llG s+SGK+T+++ +  l++++              s +e+++   + +  i+ s++   ++   l  e +++ e
  gi|557694082|ref|YP_008797136.1|  33 CLLGPSGSGKTTLMRIIAGLETPSsgsvyfggedvteLSPSERNIAMVFQFPSIYPSLNIYDNIALALRRETTDRNE 109
                                       79*******************99999999777666554545444443444445555555554444455555555567 PP

                                       HHC-SS-SCCCS-HCHHHH... CS
                           G-alpha  91 lqelkerldplkkveasliakl 112
                                        +e+  +++ l+k+e+ l++k 
  gi|557694082|ref|YP_008797136.1| 110 IRERVMQVASLLKIEEHLNKKS 131
                                       8888888888899998876543 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00016      0.12       3      21 ..      32      50 ..      30      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00016
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                       +l G++GsGKTtL++ +a
  gi|557694082|ref|YP_008797136.1| 32 FCLLGPSGSGKTTLMRIIA 50
                                      5899***********9886 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00025      0.19       2      22 ..      33      53 ..      33     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00025
                            AAA_18  2 lltGtpGvGKttlakeLskrl 22
                                      +l G++G+GKttl + ++ ++
  gi|557694082|ref|YP_008797136.1| 33 CLLGPSGSGKTTLMRIIAGLE 53
                                      799************997654 PP

>> AAA_28  AAA domain
   #    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       2      23 ..      32      53 ..      31     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                            AAA_28  2 ivitGgestGKTtlleaLaarg 23
                                      ++++G++++GKTtl++ +a  +
  gi|557694082|ref|YP_008797136.1| 32 FCLLGPSGSGKTTLMRIIAGLE 53
                                      699*************999443 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00038      0.28      18      40 ..      26      50 ..       8      58 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00038
                                      H..TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrgla 40
                                      +  g++++L G+ G+GKTtl+r +a
  gi|557694082|ref|YP_008797136.1| 26 VddGSFFCLLGPSGSGKTTLMRIIA 50
                                      2457789**************9886 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00039      0.29       2      39 ..      33      65 ..      32      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00039
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkklklkkkdsvysrnp 39
                                      +l Gpsg GK+tl++  ++     l++++++svy+++ 
  gi|557694082|ref|YP_008797136.1| 33 CLLGPSGSGKTTLMRI-IA----GLETPSSGSVYFGGE 65
                                      789***********99.33....445777888888665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.013       9.7      22      60 ..      35      73 ..      29      80 .. 0.83
   2 ?    3.5   0.0     0.051        38      50     110 ..     106     167 ..     104     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.013
                        Zeta_toxin 22 gGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                       G +G+GK++l++ ++   ++ ++ v + + d+ el P 
  gi|557694082|ref|YP_008797136.1| 35 LGPSGSGKTTLMRIIAGLETPSSGSVYFGGEDVTELSPS 73
                                      5889**********9988888999999988888888886 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.051
                        Zeta_toxin  50 dpDdlRelhPeyeeilkadpkkaseltqkdaselvekllqeaiengyni.ivegtlrspdvv 110
                                       d+ ++Re+  +++++lk +++ + +  q d + l++  +++ai ++ n+ i++  l++ d+ 
  gi|557694082|ref|YP_008797136.1| 106 DRNEIRERVMQVASLLKIEEHLNKKSHQIDFGILQRVSIAKAIVRRANVyIFDEPLSNLDTK 167
                                       56789999999999999999****************************98999999999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 2669.26
//
Query:       gi|557694083|ref|YP_008797137.1|  [L=87]
Description: hypothetical protein CSUB_C0648 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.3   1.3      0.072   12.8   0.1    1.7  2  Neurensin  Neurensin
      0.054   13.2   1.1      0.059   13.1   1.1    1.1  1  CybS       CybS, succinate dehydrogenase cytochrome B small s
      0.084   13.0   3.8       0.16   12.1   3.8    1.4  1  YrhC       YrhC-like protein
        4.9    6.5   6.2        1.8    7.9   0.3    2.1  2  TMEM43     Transmembrane protein 43


Domain annotation for each model (and alignments):
>> Neurensin  Neurensin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.6e-05     0.072      85     126 ..      20      61 ..       8      67 .. 0.88
   2 ?   -0.5   0.5      0.21   9.3e+02      50      63 ..      64      77 ..      59      86 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.6e-05
                         Neurensin  85 aiefnnaLdtlklaGavllclGglllalsllvpalsksdkke 126
                                       a+ f+  +d l l G++++++Gg++ + +  +p  ++ ++++
  gi|557694083|ref|YP_008797137.1|  20 ALLFQPFMDKLLLYGFIIMSIGGFMYVYTTYIPDEANGKTMA 61 
                                       788999***********************9999988887766 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.21
                         Neurensin 50 lvlllGvtallvGy 63
                                      lv+l+G ++  v  
  gi|557694083|ref|YP_008797137.1| 64 LVVLVGTVVFFVAL 77
                                      66677766666653 PP

>> CybS  CybS, succinate dehydrogenase cytochrome B small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.1   1.3e-05     0.059      49     115 ..      14      80 ..       2      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                              CybS  49 ltvvplvagslspvlDavlavlllihshlgfesciiDYipkrvyg.klhklahylLalgtvlslvGlY 115
                                       l  ++l+    +p++D +l   ++i s  gf  + + Yip +  g +++k   +l+  + ++  + +Y
  gi|557694083|ref|YP_008797137.1|  14 LSFAGLAL-LFQPFMDKLLLYGFIIMSIGGFMYVYTTYIPDEANGkTMAKWLVVLVGTVVFFVALSIY 80 
                                       44444444.459*******************************9966667766666666666677777 PP

>> YrhC  YrhC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.8   3.6e-05      0.16      13      57 ..      33      81 ..      30      86 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                              YrhC 13 FafvLLalsaFLyi.GlviPseaketlkksillgai...vvfLllaflf 57
                                      ++f+ +++++F+y+  + iP+ea  ++ +++l++ +   v f++l++++
  gi|557694083|ref|YP_008797137.1| 33 YGFIIMSIGGFMYVyTTYIPDEANGKTMAKWLVVLVgtvVFFVALSIYL 81
                                      9************94467***9999888888765441104455566655 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.2     0.033   1.5e+02     192     218 ..      10      36 ..       3      52 .. 0.63
   2 ?    7.9   0.3   0.00041       1.8     177     209 ..      53      85 ..      47      87 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.033
                            TMEM43 192 lGfllmflglllllsplsvlvslipll 218
                                       +G+ l f gl+ll++p+   + l  ++
  gi|557694083|ref|YP_008797137.1|  10 IGLALSFAGLALLFQPFMDKLLLYGFI 36 
                                       677888888888888876555555553 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00041
                            TMEM43 177 keksenklltwllRllGfllmflglllllspls 209
                                       +e++ +++ +wl+ l+G +++f++l+++l p+ 
  gi|557694083|ref|YP_008797137.1|  53 DEANGKTMAKWLVVLVGTVVFFVALSIYLVPIL 85 
                                       6778899********************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 635.11
//
Query:       gi|557694084|ref|YP_008797138.1|  [L=360]
Description: sugar ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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    4.6e-34  117.9   0.0    1.4  1  ABC_tran      ABC transporter
    6.2e-07   29.5   0.2      0.027   14.3   0.0    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
      4e-05   23.7   0.0    9.4e-05   22.5   0.0    1.7  1  TOBE_2        TOBE domain
    0.00048   20.7   0.0      0.001   19.6   0.0    1.5  1  AAA_23        AAA domain
     0.0011   18.9   0.7      0.029   14.3   0.0    2.8  3  RsgA_GTPase   RsgA GTPase
     0.0023   18.3   0.2       0.09   13.2   0.0    2.1  2  AAA_16        AAA ATPase domain
     0.0026   16.7   0.0     0.0042   16.0   0.0    1.2  1  DLIC          Dynein light intermediate chain (DLIC)
      0.004   17.4   2.5      0.052   13.8   2.5    2.2  1  AAA_22        AAA domain
     0.0048   16.6   0.0      0.012   15.4   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
     0.0074   16.0   0.0      0.017   14.8   0.0    1.5  1  AAA_30        AAA domain
      0.009   16.0   0.1       0.02   14.9   0.1    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
  ------ inclusion threshold ------
      0.018   15.3   0.8      0.094   13.0   0.1    2.5  3  TOBE          TOBE domain
      0.027   13.7   0.0      0.055   12.6   0.0    1.5  1  NB-ARC        NB-ARC domain
      0.034   13.5   0.0      0.089   12.2   0.0    1.7  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.05   13.0   0.0        6.7    6.1   0.0    2.3  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.073   12.5   0.2       0.71    9.3   0.0    2.1  2  PhoH          PhoH-like protein
      0.075   12.8   0.0       0.16   11.6   0.0    1.5  1  IstB_IS21     IstB-like ATP binding protein
      0.079   13.4   0.1       0.48   10.9   0.0    2.2  2  AAA           ATPase family associated with various cellular 
       0.13   12.5   0.1       0.86    9.9   0.1    2.1  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.14   11.6   0.6        3.8    6.9   0.2    2.5  2  TniB          Bacterial TniB protein
       0.17   11.8   0.1       0.38   10.7   0.1    1.5  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 !  117.9   0.0   5.4e-37   4.6e-34       1     136 [.      19     162 ..      19     163 .. 0.91

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 5.4e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ v+++++ g +va++G++GaGK+tL+k++ag ++p++G+i +dg+++ +  ++ +++++++++q+  l p+++v+
  gi|557694084|ref|YP_008797138.1|  19 LRGVDVTVESGDIVALLGPTGAGKTTLMKCIAGVERPDKGDIMFDGESVVD--TPPWERNVAMFFQTYALYPHMSVY 93 
                                       6789**********************************************9..9*********************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +n             e ++ ++++++kl++++l  ++   +p++LSgG+ qrvalaral+++p++lllDEp 
  gi|557694084|ref|YP_008797138.1|  94 DNiayplrerkmaenEIKDIVHRVAEKLRISHLLSRK---EPATLSGGEMQRVALARALVREPRVLLLDEPI 162
                                       ******9999865555555588888888888877776...48*****************************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 !   14.3   0.0   3.2e-05     0.027       1      24 [.      31      54 ..      31     102 .. 0.81
   2 !   13.4   0.1     6e-05     0.051     241     297 ..     140     193 ..      97     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.2e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      + +l Gp g+GK++L++++ ++ r
  gi|557694084|ref|YP_008797138.1| 31 IVALLGPTGAGKTTLMKCIAGVER 54
                                      5789***************87744 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6e-05
                            AAA_21 241 tkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTH 297
                                       ++r+ al+ al r +   ++ll+DEp ++L+ kl ++    +k+l+r  +  +i +T 
  gi|557694084|ref|YP_008797138.1| 140 MQRV-ALARALVREP---RVLLLDEPISNLDAKLREEMRAEFKRLHReLKRTLIYATP 193
                                       4555.9999999988...*********************9998888878888888885 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.1e-07   9.4e-05       1      75 [.     280     350 ..     280     351 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.1e-07
                            TOBE_2   1 laiRPEklrlaaagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavv 75 
                                       +aiRP ++ l++  g+n l ++V++ e lG++t ++v++ g +  +v++       +++ G++V ++++  + ++
  gi|557694084|ref|YP_008797138.1| 280 VAIRPADVVLEPVHGQNLLIAKVVSSERLGTHTIVTVKVSGIEMKTVVKGMK----TYQYGEEVKIGINGNKPLL 350
                                       79********64444689************************9966666666....79*******9988776666 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-06     0.001      12      40 ..      21      50 ..      10      52 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-06
                            AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAik 40
                                      ++++   s  ++++ Gp+GaGKTT++ +i 
  gi|557694084|ref|YP_008797138.1| 21 GVDVTVeSGDIVALLGPTGAGKTTLMKCIA 50
                                      444444455799****************96 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   3.3e-05     0.029      88     123 ..      17      53 ..       1      71 [. 0.76
   2 ?    1.7   0.0      0.24   2.1e+02       8      66 ..     157     217 ..     150     242 .. 0.74
   3 ?   -1.5   0.1       2.5   2.1e+03     124     150 ..     296     322 ..     288     329 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.3e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                       ++l+ +   +++ ++++l+G++G+GK+tL++ +++ +
  gi|557694084|ref|YP_008797138.1|  17 QALRGVDVTVESgDIVALLGPTGAGKTTLMKCIAGVE 53 
                                       555556666666699****************998855 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.24
                                       ETTTTEES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH..HHH CS
                       RsgA_GTPase   8 lvrpkvaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee..ele 66 
                                       l++++++N+d  l     +e +  ++ l+r L+ a    +e   v  Ki l++e +  +++
  gi|557694084|ref|YP_008797138.1| 157 LLDEPISNLDAKLREEMRAEFKRLHRELKRTLIYATPDYLEAFAVAEKIALINEGQviQYD 217
                                       5556666666655544444455557889************************999944444 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.5
                                       ----S--------------SEEEEEET CS
                       RsgA_GTPase 124 elktgevseklgrGkhTTtavellela 150
                                       +l +++v ++ + G hT  +v++  ++
  gi|557694084|ref|YP_008797138.1| 296 NLLIAKVVSSERLGTHTIVTVKVSGIE 322
                                       566778888899999998877766555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00011      0.09      18      45 ..      25      50 ..      15      85 .. 0.83
   2 ?    3.1   0.2      0.13   1.1e+02      52     131 ..     131     192 ..     110     207 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrell 45
                                      +v sg   +v l G+ G GK++l+++++
  gi|557694084|ref|YP_008797138.1| 25 TVESG--DIVALLGPTGAGKTTLMKCIA 50
                                      45555..69***************9987 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.13
                            AAA_16  52 ggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrlla 128
                                       +  +l+g   q       +ala+al r e    llde+ s++ +  re+ +++++           rl+++lkr l 
  gi|557694084|ref|YP_008797138.1| 131 EPATLSGGEMQR------VALARALVR-EPRVLLLDEPISNLDAKLREEMRAEFK-----------RLHRELKRTLI 189
                                       445555555555......679999967.777778888788788888887777777...........88888888776 PP

                            AAA_16 129 lls 131
                                       +++
  gi|557694084|ref|YP_008797138.1| 190 YAT 192
                                       665 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   4.9e-06    0.0042      21      55 ..      25      59 ..       5      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.9e-06
                              DLIC 21 klPsgksvlvlGedgsGkttliaklqGveeekkGr 55
                                       + sg  v +lG  g+Gkttl+  + Gve + kG 
  gi|557694084|ref|YP_008797138.1| 25 TVESGDIVALLGPTGAGKTTLMKCIAGVERPDKGD 59
                                      5679999**************************96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   2.5   6.1e-05     0.052       4     115 ..      28     180 ..      25     197 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.1e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee............................erpevv...fvtlps 49 
                                       +  i+++ G++G+GKTtl++ ++      ++  +                            ++ +v+    + l +
  gi|557694084|ref|YP_008797138.1|  28 SGDIVALLGPTGAGKTTLMKCIAGVER--PDKGDimfdgesvvdtppwernvamffqtyalyPHMSVYdniAYPLRE 102
                                       567899**************9998653..222226688888999998855555555555555333333322222222 PP

                            AAA_22  50 st....sskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDE.aqhlr...seealeeLrs 114
                                        +    + kd+ ++++++l  ++  +r++   l    +++ + ara    +++l++DE + +l+   +ee+  e+++
  gi|557694084|ref|YP_008797138.1| 103 RKmaenEIKDIVHRVAEKLRISHLLSRKEPATLSgGEMQRVALARALvrePRVLLLDEpISNLDaklREEMRAEFKR 179
                                       22223355555555555555444446666666666777777766666777778888883333655434555555555 PP

                            AAA_22 115 l 115
                                       l
  gi|557694084|ref|YP_008797138.1| 180 L 180
                                       5 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 !   15.4   0.0   1.4e-05     0.012      14      44 ..      21      51 ..      10      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqa 44
                                      g +++++  +++ l Gp+G+GK+Tl+  i+ 
  gi|557694084|ref|YP_008797138.1| 21 GVDVTVESGDIVALLGPTGAGKTTLMKCIAG 51
                                      5567777556***************977665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     2e-05     0.017      13      42 ..      25      53 ..      16      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-05
                            AAA_30 13 lltsgdrvavltGpAGtGKttalkalreaw 42
                                      +++sgd +++l Gp G+GKtt++k ++ + 
  gi|557694084|ref|YP_008797138.1| 25 TVESGD-IVALLGPTGAGKTTLMKCIAGVE 53
                                      566776.99***************998765 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.4e-05      0.02      18      40 ..      25      50 ..       4      54 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.4e-05
                                      H...TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 18 l...gdvilLeGdLGaGKTtlvrgla 40
                                      +   gd+++L G+ GaGKTtl++ +a
  gi|557694084|ref|YP_008797138.1| 25 TvesGDIVALLGPTGAGKTTLMKCIA 50
                                      0344788***************9886 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       6.4   5.5e+03       3      12 ..     239     248 ..     237     249 .. 0.82
   2 ?   -1.8   0.0       4.8   4.1e+03      50      62 ..     275     287 ..     274     289 .. 0.83
   3 ?   13.0   0.1   0.00011     0.094       5      55 ..     296     341 ..     294     347 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 6.4
                              TOBE   3 arNqlpgtVv 12 
                                       + N+l+g ++
  gi|557694084|ref|YP_008797138.1| 239 TANILRGVIK 248
                                       78*****996 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.8
                              TOBE  50 GeeVfalikaakv 62 
                                       G+eV ++i +a+v
  gi|557694084|ref|YP_008797138.1| 275 GKEVEVAIRPADV 287
                                       8899999999887 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.00011
                              TOBE   5 NqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfa 55 
                                       N l ++Vv +e lg ++ V+v ++g + +  +v +    +     GeeV +
  gi|557694084|ref|YP_008797138.1| 296 NLLIAKVVSSERLGTHTIVTVKVSGIE-MKTVVKGMKTYQ----YGEEVKI 341
                                       77889********************99.999988877777....7777755 PP

>> NB-ARC  NB-ARC 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     0.055      19      58 ..      29      82 ..      17     166 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.5e-05
                                      CSEEEEEEESTTSSHHHHHHHHCCSH..CCCCCCBTEEEEE.............E CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakqilnks..devegrFdsvawv.............v 58
                                      + ++val G  G GKttl+k i      d+ +  Fd+   v             +
  gi|557694084|ref|YP_008797138.1| 29 G-DIVALLGPTGAGKTTLMKCIAGVErpDKGDIMFDGESVVdtppwernvamffQ 82
                                      4.69***************998643200333336666555555666666665551 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0001     0.089       7      45 ..      14      52 ..       9      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                      Mg_chelatase  7 GqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsl 45
                                      G+ +a r +++++  g  + l+Gp G+GKt l k+++++
  gi|557694084|ref|YP_008797138.1| 14 GKVQALRGVDVTVESGDIVALLGPTGAGKTTLMKCIAGV 52
                                      888999999**************************9886 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 ?    4.7   0.0     0.021        18      25      44 ..      30      49 ..       3      54 .. 0.81
   2 ?    6.1   0.0    0.0078       6.7     113     186 ..     113     180 ..      74     210 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.021
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                       + a++Gp G+GK+ l+  i
  gi|557694084|ref|YP_008797138.1| 30 DIVALLGPTGAGKTTLMKCI 49
                                      47899***********9988 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0078
                                       ETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 113 ingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                       i  + ++k  +s+ll+++  ++ +LSgGe + vala       v+   + llDe  ++LD+k ++++   +k+ 
  gi|557694084|ref|YP_008797138.1| 113 IVHRVAEKLRISHLLSRK--EPATLSGGEMQRVALARA----LVREPRVLLLDEPISNLDAKLREEMRAEFKRL 180
                                       334445555556666555..3559*****888777644....34555577999999999999988876666655 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00083      0.71      17      40 ..      27      50 ..      16      60 .. 0.80
   2 ?    0.8   0.0      0.34   2.9e+02      45      92 ..     136     192 ..     132     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00083
                                      HH-SEEEEE--TTSSTTHHHHHHH CS
                              PhoH 17 kkndivfaiGpaGtGKtylavala 40
                                      ++ div  +Gp+G+GKt l  ++a
  gi|557694084|ref|YP_008797138.1| 27 ESGDIVALLGPTGAGKTTLMKCIA 50
                                      5779************98865544 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.34
                                       HTTS-SEEEEEE-S--T......T----SS---------TTTHHHHHHHTTTS...- CS
                              PhoH  45 kkkkvkriiltrpavea......geelGflpgdleekvdpylrplydaLkdll...g 92 
                                       + ++++r+ l+r+ v        +e +  l+ +l+e ++  ++ l+ +Lk +l    
  gi|557694084|ref|YP_008797138.1| 136 SGGEMQRVALARALVREprvlllDEPISNLDAKLREEMRAEFKRLHRELKRTLiyaT 192
                                       557888999999888666778889999***********9999999999999884441 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 ?   11.6   0.0   0.00019      0.16      34      67 ..      15      49 ..      10      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                         IstB_IS21 34 kvkeLatlsf.iekkenivllGpsGvGKshlaial 67
                                      kv++L++ +  +e+ + ++llGp+G+GK+ l   +
  gi|557694084|ref|YP_008797138.1| 15 KVQALRGVDVtVESGDIVALLGPTGAGKTTLMKCI 49
                                      5788888876367889999**********997666 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 ?   10.9   0.0   0.00056      0.48       2      20 ..      33      51 ..      32      84 .. 0.91
   2 ?   -0.4   0.0       1.7   1.5e+03      50      66 ..     145     160 ..     109     192 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00056
                                      EEESSTTSSHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavak 20
                                       l Gp G GKT+l+k +a 
  gi|557694084|ref|YP_008797138.1| 33 ALLGPTGAGKTTLMKCIAG 51
                                      699************9995 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.7
                                       HHHHHHTSTSEEEEEET CS
                               AAA  50 fkeakekakpsilfiDE 66 
                                       +++a    +p +l++DE
  gi|557694084|ref|YP_008797138.1| 145 LARALVR-EPRVLLLDE 160
                                       3333333.478888888 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 ?    9.9   0.1     0.001      0.86      31      85 ..     133     174 ..     113     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.001
                           SbcCD_C  31 gtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatll 85 
                                       +tlSGGe q    +ala   +al++        +r+++LDE  s+lD++ ++++ 
  gi|557694084|ref|YP_008797138.1| 133 ATLSGGEMQ---RVALA---RALVR-------EPRVLLLDEPISNLDAKLREEMR 174
                                       566777763...23333...22223.......489**************999885 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.091        78      38      56 ..      32      50 ..      26     122 .. 0.88
   2 ?    6.9   0.2    0.0045       3.8     118     160 ..     151     191 ..     107     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.091
                              TniB 38 lllvGdsnnGKtmivekFa 56
                                      + l+G++  GKt++++  a
  gi|557694084|ref|YP_008797138.1| 32 VALLGPTGAGKTTLMKCIA 50
                                      5799*********998655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0045
                              TniB 118 lkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                        ++rvL++DE  + l   a+ ++e+ +  k+L++elk +++++
  gi|557694084|ref|YP_008797138.1| 151 REPRVLLLDEPISNL--DAKLREEMRAEFKRLHRELKRTLIYA 191
                                       479*******76666..688899**************999875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00044      0.38       2      21 ..      31      50 ..      30      54 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00044
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      +v+l G+ G GKTtL++ +a
  gi|557694084|ref|YP_008797138.1| 31 IVALLGPTGAGKTTLMKCIA 50
                                      689*************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2583.74
//
Query:       gi|557694085|ref|YP_008797139.1|  [L=302]
Description: multiple sugar ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-20   74.0  18.9    1.2e-20   74.0  18.9    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.025   15.0   1.4        3.6    8.0   0.0    2.7  2  DUF3981       Domain of unknown function (DUF3981)
        9.2    6.6  17.0      0.047   14.0   3.8    2.8  3  DUF4064       Protein of unknown function (DUF4064)


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 ?   -0.0   0.1      0.11   6.4e+02      54      72 ..      21      40 ..       3      60 .. 0.58
   2 !   74.0  18.9   2.1e-24   1.2e-20       1     184 [.     109     294 ..     109     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.11
                      BPD_transp_1 54 lp.viillllsaapyvrlir 72
                                      ++ ++i+++ +++++ ++++
  gi|557694085|ref|YP_008797139.1| 21 TYaAVIVTVGFFIFPLFWLI 40
                                      22233333333333333333 PP

  == domain 2  score: 74.0 bits;  conditional E-value: 2.1e-24
                      BPD_transp_1   1 gillGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirra 74 
                                       +i++G+laa    +++  +++ l+++i  +++lP +v+ai+++ +f+ + +l+++ l++i+l++++++p++++++++
  gi|557694085|ref|YP_008797139.1| 109 AIVIGVLAAysfSRYKPLGTNTLMFFILSTRMLPGIVVAIPIY-FFYRSIGLYNTYLGLILLYTMFNLPFAIWMMKS 184
                                       589********9999**************************98.67888889999999******************* PP

                      BPD_transp_1  75 alrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydys 151
                                       +++ +pkd ++aa ++G ++ ++frk++lP+++  + +++++ +++++++++++++l+  +  + ++l a+    + 
  gi|557694085|ref|YP_008797139.1| 185 FFDDIPKDIEQAAFVDGSPPLRVFRKIALPQVAVGLGATIGFLIINVWNEFLFALLLTERTTRTVPVLIASTRGEVG 261
                                       **********************************************************7766444444444444444 PP

                      BPD_transp_1 152 eisnggvlalviavlllnlvadilqrlldprvr 184
                                        +   ++++ ++++l+ ++++++lqr+l + ++
  gi|557694085|ref|YP_008797139.1| 262 INWGLIAAIETLYILPALVLIFLLQRYLLRGMT 294
                                       33356888999*****************99875 PP

>> DUF3981  Domain of unknown function (DUF3981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   0.00061       3.6      16      54 ..       5      43 ..       1      54 [. 0.87
   2 ?    4.9   0.6    0.0057        34      58      96 ..     100     136 ..      95     151 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00061
                           DUF3981 16 dkkgdkkvvkgkkssilvipvlfwigiaiyeyfwliddr 54
                                      +++g++k  k  ks      v++ +g  i+  fwli   
  gi|557694085|ref|YP_008797139.1|  5 NRRGNRKARKIIKSIATYAAVIVTVGFFIFPLFWLIATS 43
                                      679999********9999*****************9764 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0057
                           DUF3981  58 ilthysvavailiglvl.fsqdqigklegtlkgllmfvll 96 
                                       ++t +s+a+ai+ig++  +s  +  k  gt    lmf +l
  gi|557694085|ref|YP_008797139.1| 100 VVTSFSIALAIVIGVLAaYSFSR-YKPLGT--NTLMFFIL 136
                                       7899**********764144433.333344..34555544 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.8   7.8e-06     0.047       1      95 [.       9     135 ..       9     143 .. 0.78
   2 ?   -3.5   0.2       2.2   1.3e+04      19      29 ..     164     174 ..     157     184 .. 0.55
   3 ?    1.7   1.1     0.052   3.1e+02      19      82 ..     219     282 ..     207     288 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.8e-06
                           DUF4064   1 krkaeiiLglIGgilgillglllllf..lfllssgefsqeltee............................qalsg 47 
                                       +rka +i+  I+    ++ +++ ++f  ++l+ ++ ++ ++ ++                            + ++ 
  gi|557694085|ref|YP_008797139.1|   9 NRKARKIIKSIATYAAVIVTVGFFIFplFWLIATSLKTRAQAFStpplfiweptfrnfidiflkrqteieaiTGQEL 85 
                                       6888888888887777776666666532444444444444444477**************************9**** PP

                           DUF4064  48 edasavleflstllivlgvialiaivlgivgalllkknkk..vsGilfii 95 
                                       e a+ ++ f++++++v+ +   +aiv+g+++a+  ++ k   +  ++f+i
  gi|557694085|ref|YP_008797139.1|  86 ELATGAEIFFFNSFVVTSFSIALAIVIGVLAAYSFSRYKPlgTNTLMFFI 135
                                       ********************************998876664444555555 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.2
                           DUF4064  19 lglllllflfl 29 
                                       lgl+ll+++f+
  gi|557694085|ref|YP_008797139.1| 164 LGLILLYTMFN 174
                                       34444444443 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.052
                           DUF4064  19 lglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgivgalll 82 
                                       + +++++fl+++ ++ef ++l+ ++ ++ +++  +++  ++++i  g+ia i ++ ++ +++l+
  gi|557694085|ref|YP_008797139.1| 219 GLGATIGFLIINVWNEFLFALLLTERTTRTVPVLIASTRGEVGINWGLIAAIETLYILPALVLI 282
                                       4455666667777999999999988888888888888888888888777777666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2159.35
//
Query:       gi|557694086|ref|YP_008797140.1|  [L=291]
Description: multiple sugar ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   45.7  20.3      6e-12   45.7  20.3    2.1  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 ?    0.0   3.0     0.034   6.1e+02      19      43 ..       9      32 ..       1      71 [. 0.65
   2 !   45.7  20.3   3.4e-16     6e-12       3     181 ..      90     289 ..      88     291 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.034
                      BPD_transp_1 19 llrpliivllslPsfvlaillvlvf 43
                                      l+++ + v+l +P ++l+i+lv +f
  gi|557694086|ref|YP_008797140.1|  9 LSYRTFPVILITPAVALVIFLV-IF 32
                                      3444444555555555555555.22 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 3.4e-16
                      BPD_transp_1   3 llGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf.................vilsilghlilpviill 60 
                                       l+G+ +a  ++ ++k++++  +l+ ++l + +++++i++ ++                   +    ++ +l+v+++ 
  gi|557694086|ref|YP_008797140.1|  90 LVGFALAhlFYTKFKGRRIAITLVTTPLLIAPVAVGIFFRYIYdatfgvftyfaelltgqRVRMLSQQPMLAVVFMD 166
                                       68999999999999999999999999999999999999888889999999999*******7777899********** PP

                      BPD_transp_1  61 llsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGl 137
                                       ++++ p+++l++ a+l+++pk   e ++++ +s +  fr+vv P ++p ++  l+++ + ++  +  + +l+++++ 
  gi|557694086|ref|YP_008797140.1| 167 VWQWSPFMMLFILAGLEAIPKHMLESSEIDRLSWINKFRYVVWPKIKPLVALALLFRTMDAFRTFDTIFTLTGGGPG 243
                                       *****************************************************************999998877765 PP

                      BPD_transp_1 138 gtllleailgydyseis..nggvlalviavlllnlvadilqrlldp 181
                                       +++ + +i +y +++     g + al++++l++++++  l+  l++
  gi|557694086|ref|YP_008797140.1| 244 TLTEVLSITIYRTAFQFfrTGEATALAFIFLIIIILLTNLYLRLSR 289
                                       5555555555555555566555555555555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2149.32
//
Query:       gi|557694087|ref|YP_008797141.1|  [L=558]
Description: multiple sugar ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   62.1   0.0    1.2e-16   61.3   0.0    1.3  1  SBP_bac_8  Bacterial extracellular solute-binding protein
    2.1e-14   54.2   0.9    3.9e-14   53.3   0.0    1.9  2  SBP_bac_1  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0   1.4e-20   1.2e-16       7     274 ..     118     466 ..     113     471 .. 0.67

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 1.4e-20
                                       HHH-.T..EEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH........-H CS
                         SBP_bac_8   7 ekkt.g..vkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnldd........lt 72 
                                        k++ g  v+v+   ++++ + + l++ l a +  ++ +++ ++ +l+++ + g +  l+d+   d+        ++
  gi|557694087|ref|YP_008797141.1| 118 SKANiGkaVEVKMDLIPWDVIFERLSTTLIARSK-EPTLLISDSQWLGQFYVGGHIRRLNDYIARDPelqqllnrFD 193
                                       57777777999999999**********9999986.456888999****************88777778777888855 PP

                                       HHHHTT.......--TS.----EEEEEEE-EEEEEHHHHHH.....S........---BHHHHH............. CS
                         SBP_bac_8  73 dalaav.......gydgklygvPyasetpyvliynkdllek.....a.......edpktwdell............. 117
                                       +al ++        y+  + g+        +++y+ dl+ +     +       + p+ ++++              
  gi|557694087|ref|YP_008797141.1| 194 PALVYFymtfpqgNYNN-IVGFAHEGD-VLLFVYRHDLFTHptereNfkaeygyDLPANYEDWYpnqldwyqirdia 268
                                       54444455445435555.777776655.579********86554441444677767777777643444344443333 PP

                                       .....HHHHHHHHH-.........SEGG.---G....GGGGGTHH.......ETTEE---H........HHH.HHHH CS
                         SBP_bac_8 118 .....aaakklkgkf.........glpd.pasg....wlqaalla.......kdgksldddg......gkdglkeal 162
                                            +a ++l gk+           ++  a++     +  +l++        +       g      +++  ++al
  gi|557694087|ref|YP_008797141.1| 269 kfftrKAGDELAGKRleedfygiaV-HMsRAYDaiacPFGSMLYChgeywwdPET------GevdgyiNSERAVKAL 338
                                       3333333334456666666564421.22022222223334444445443333222......233333366666**** PP

                                       HHHHHHHHTT-..EE-.S..--SSTTTTTSBSEEEE-TTHHHHHH....-TTTSEEEE--S--...........EEE CS
                         SBP_bac_8 163 ellkklkdngk..tyd.tgadavsefanGevaftingswdiaaaq....kagkklgaivpkqg...........sfa 221
                                       e++++l+++     ++   ++ ++ ++ G+va+++n+ + + ++      +  +l  +vp++g           s +
  gi|557694087|ref|YP_008797141.1| 339 EFYASLVQYSPpnALEiWFDESNAVMQAGRVAMIYNWAGFLPSLFdpaaSKVHNLIRVVPPPGhrgddgifrrySGI 415
                                       **********77744423489999************997777655331133346554455443344555888879** PP

                                       EEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHHHH CS
                         SBP_bac_8 222 ggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnksaalspev 274
                                       gg+++++++ ++   + Al+F+k++ +p+nq+++ae +g + ++k+  +++++
  gi|557694087|ref|YP_008797141.1| 416 GGQPMCINAYSDRVVE-ALAFIKYWFQPQNQRKWAE-GGGGVCIKDIVQTEWF 466
                                       ***************7.*******************.6667777777777766 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 ?   -2.6   0.3      0.44     4e+03     153     189 ..      33      68 ..      14      85 .. 0.54
   2 !   53.3   0.0   4.4e-18   3.9e-14      19     314 ..     118     445 ..     104     446 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.44
                                       HCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHC CS
                         SBP_bac_1 153 iggarggsasgtayyfalalakslggkvfdkdgggld 189
                                        +g   g+ +++a+  + ++ ++ gg+ ++  + +++
  gi|557694087|ref|YP_008797141.1|  33 LAGYLAGTSGQQAATVTRTVTAGGGGQTVTVTN-TVT 68 
                                       345555666666666666666666644443332.333 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 4.4e-18
                                       HHHHTT..EEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEEEE CS
                         SBP_bac_1  19 ekehpg..ikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkdaadkl 93 
                                        k++ g  ++V+ + ++++   + l++ + a ++++ + ++d+ w++++  +g    l++y++ +  p+ ++   ++
  gi|557694087|ref|YP_008797141.1| 118 SKANIGkaVEVKMDLIPWDVIFERLSTTLIARSKEPTLLISDSQWLGQFYVGGHIRRLNDYIARD--PELQQLLNRF 192
                                       454444449999*********************9*******************************..5556667777 PP

                                       HHHHTHHHHCE.EE....ES.EEEEE.EEEEEEETTTHH..........CTTGGG..........SHBHHHHHHHHH CS
                         SBP_bac_1  94 sssvlpkilds.kv....ly.vPlya.argliYNkdlfe..........kagldp..........pwtWdelveaak 143
                                       ++  ++ ++++  +    ++ +   + + +++Y++dlf           ++g d+             W ++ + ak
  gi|557694087|ref|YP_008797141.1| 193 DPALVYFYMTFpQGnynnIVgFAHEGdVLLFVYRHDLFThpterenfkaEYGYDLpanyedwypnQLDWYQIRDIAK 269
                                       777777777755558987777777768********************8877777799***9**99999********* PP

                                       HHHHHCTCT...........HCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT....HHCSHHHHSHHHHHHHHHH CS
                         SBP_bac_1 144 klkekgkkp...........iggarggsasgtayyfalalakslggkvfdkdgg....gldnpegvtaatylvklya 205
                                        ++ k + +           ++ ++++ a +  +  +  ++   g +++d + g     ++++ +v+a++++  l+ 
  gi|557694087|ref|YP_008797141.1| 270 FFTRKAGDElagkrleedfyGIAVHMSRAYDAIACPFGSMLYCHGEYWWDPETGevdgYINSERAVKALEFYASLV- 345
                                       *****9999***********99********************************7775445555555999999999. PP

                                       HHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSE CS
                         SBP_bac_1 206 vanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpg 282
                                             ++++++a++   ++  a ++aG++am+++  wa        + + f+++++k+ + + v p+P+ +g+ + 
  gi|557694087|ref|YP_008797141.1| 346 ------QYSPPNALEIWFDESNAVMQAGRVAMIYN--WA------GFLPSLFDPAASKVHNLIRVVPPPGHRGDDGI 408
                                       ......99*****999999999**********655..55......569*******************9988888877 PP

                                       E.....EEEEEEEEBTTCSTHHHHHHHHHHHTSHHHH CS
                         SBP_bac_1 283 i.....lgayglaipkgsknpeaAkkFldfllspeaq 314
                                             +g++++ i++ s+  ++A +F+++ + p++q
  gi|557694087|ref|YP_008797141.1| 409 FrrysgIGGQPMCINAYSDRVVEALAFIKYWFQPQNQ 445
                                       7*********************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3888.63
//
Query:       gi|557694088|ref|YP_008797142.1|  [L=492]
Description: aldehyde dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-171  568.4   0.1   1.1e-170  568.1   0.1    1.0  1  Aldedh    Aldehyde dehydrogenase family
    0.00094   18.3   0.0     0.0025   16.9   0.0    1.6  2  LuxC      Acyl-CoA reductase (LuxC)
  ------ inclusion threshold ------
      0.029   14.3   0.2      0.049   13.6   0.2    1.3  1  Wtap      WTAP/Mum2p family
      0.088   12.1   0.0       0.13   11.5   0.0    1.1  1  M157      MHC class I-like protein M157
      0.091   12.2   0.0       0.16   11.4   0.0    1.3  1  SMP_LBD   Synaptotagmin-like mitochondrial-lipid-binding doma


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 !  568.1   0.1    3e-174  1.1e-170       9     462 .]      30     488 ..      22     488 .. 0.98

  Alignments for each domain:
  == domain 1  score: 568.1 bits;  conditional E-value: 3e-174
                                       EEEEETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HH CS
                            Aldedh   9 ievinPa.tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkpla 84 
                                       +e  nPa  +ev+a +p  ++ed+++a+++A++af++wa+l++ +R+++L kaa+++e+++eela+++t+e Gk+l+
  gi|557694088|ref|YP_008797142.1|  30 FEDRNPAdVEEVVAVFPLLSREDAKNAIDSAEKAFEKWAALSPLQRGKYLVKAAQIMENEAEELARILTREEGKTLN 106
                                       7899***88999***************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEE CS
                            Aldedh  85 earaeveeaidvlryyaelaeklegevlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlK 160
                                       e+raev++aid++r+y  + ++l+ge +ps +++++ ++ rePlGvv++ItPWNfP+++++wk+apal++GNtvv+K
  gi|557694088|ref|YP_008797142.1| 107 ESRAEVARAIDIFRFYGVMGSRLRGEFTPStDPRTHLFTLREPLGVVSIITPWNFPIAIPSWKIAPALICGNTVVFK 183
                                       ******************************88********************************************* PP

                                       E-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE- CS
                            Aldedh 161 PaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElG 237
                                       Pa+ tpl+ ++++e+++ ag+P+gv+n+vtgsg evg++l+ +++vd++sftGs evg++i + a ++  rv+lElG
  gi|557694088|ref|YP_008797142.1| 184 PASYTPLIGYKIVEALHSAGIPPGVVNFVTGSGGEVGAELIINDKVDAISFTGSAEVGEEIKQYACRSNIRVQLELG 260
                                       ****************************************************************98888******** PP

                                       --EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSH CS
                            Aldedh 238 GknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPlise 314
                                       Gknp +vledaDl kave + ++afg +GQ C+a+sr++v e+i+++f eklve++k+++vg++l++ +++GP++ e
  gi|557694088|ref|YP_008797142.1| 261 GKNPSVVLEDADLGKAVEMVTRAAFGLTGQACTATSRAIVVEKIAKQFEEKLVERVKQIRVGNGLADGVEMGPVVGE 337
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHH CS
                            Aldedh 315 aqlekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieia 390
                                       ++l+k+ +yv+ +  egakll+Gg+  ++++ +kg+f+ePt+++nvtpdm+iaqeEiFGPVls+i ++d++ea+e+a
  gi|557694088|ref|YP_008797142.1| 338 KELKKILSYVDIGLREGAKLLIGGKrLTSSEHAKGFFLEPTIFTNVTPDMKIAQEEIFGPVLSIIHVSDFDEAVEVA 414
                                       *************************98899*********************************************** PP

                                       HSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES..-BSHHHHHHHTEEEEEE CS
                            Aldedh 391 NdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglG..reggkegleeytevktv 462
                                       N+ +yGL+a+vft++l ra+++++r++aG v +N++ttg + ++pfgG+k+S++G  +e+g+ +l++y+++ktv
  gi|557694088|ref|YP_008797142.1| 415 NKIDYGLSASVFTTSLPRAFEFIHRVQAGVVKVNKPTTGLEFQVPFGGYKRSSYGdiKEQGETALDFYSKLKTV 488
                                       ************************************99999999****************************97 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0     7e-07    0.0025      82     261 ..     142     313 ..     128     323 .. 0.78
   2 ?   -2.4   0.0      0.51   1.8e+03     319     346 ..     391     418 ..     367     449 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7e-07
                              LuxC  82 ksyekaqprglvlhvlsgNvpl.lpvmsilqglLvknvnllkvSssdpflaaallksladvdenhtladslsvvyf. 156
                                       + +  + p g+v+ +++ N p+ +p + i+ +l+++n  ++k+ s  p + ++++  l    +         vv+f 
  gi|557694088|ref|YP_008797142.1| 142 HLFTLREPLGVVSIITPWNFPIaIPSWKIAPALICGNTVVFKPASYTPLIGYKIVEALHSAGIP------PGVVNFv 212
                                       6899999*************964899******************************99887774......4688886 PP

                              LuxC 157 ksgdtkleeeiv..qnaDvvvawGgeeaikaise.klkpgkql.ikfGakvSfavvdkealeeealdkaaeraAkDi 229
                                        ++  ++  e++  +++D+++  G+ e  + i++   + + ++ ++ G k    v++ ++     l ka+e +    
  gi|557694088|ref|YP_008797142.1| 213 TGSGGEVGAELIinDKVDAISFTGSAEVGEEIKQyACRSNIRVqLELGGKNPSVVLEDAD-----LGKAVEMVTRAA 284
                                       6666788777666799****************9965555555437888888766666555.....888888888888 PP

                              LuxC 230 ivfdQqACls.pqvvfvekddkieidefaeaLa 261
                                         +  qAC + ++++ vek     +++f e+L 
  gi|557694088|ref|YP_008797142.1| 285 FGLTGQACTAtSRAIVVEKI----AKQFEEKLV 313
                                       88999999764688888855....455555554 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.51
                              LuxC 319 qeelnePlnrtvnvkavdsledvvryvt 346
                                       qee++ P+  ++ v   d++ +v++ + 
  gi|557694088|ref|YP_008797142.1| 391 QEEIFGPVLSIIHVSDFDEAVEVANKID 418
                                       5788889999999999999999988776 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   1.4e-05     0.049      63     118 ..      51     106 ..      41     116 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.4e-05
                              Wtap  63 eeaenkleeaqeeLqalkftpdsqtGkrLmakcrvLeqENeELgkvleegrvakLe 118
                                       e+a+n++ +a++  +++      q+Gk L++  + +e+E eEL+++l+ ++ + L 
  gi|557694088|ref|YP_008797142.1|  51 EDAKNAIDSAEKAFEKWAALSPLQRGKYLVKAAQIMENEAEELARILTREEGKTLN 106
                                       688999999********999999***********************9988877775 PP

>> M157  MHC class I-like protein M157
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.7e-05      0.13     169     244 ..     248     319 ..     245     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                                       EESSSS-EEEEE---------EEE---SS-EEEEE--SS-----EEEEETTTEEEE--..S--SS---......B- CS
                              M157 169 ksrsnvpltvelsletdssaivkeestvdleavtvkapglnaklCtvesslGWkgvVtnipegryrtksvegdrRa 244
                                        +rsn+++++el  +  s+++   + +  +e vt  a gl  + Ct +s      vV +i   ++  k+ve  +  
  gi|557694088|ref|YP_008797142.1| 248 ACRSNIRVQLELGGKNPSVVLEDADLGKAVEMVTRAAFGLTGQACTATSR---AIVVEKI-AKQFEEKLVERVKQI 319
                                       59***********************************************9...7777755.569999999987665 PP

>> SMP_LBD  Synaptotagmin-like mitochondrial-lipid-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.6e-05      0.16      70     103 ..     220     255 ..     201     276 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.6e-05
                                       -TTSEEEEE..EEEEEEEEEEEEEECCCTEEEEEEE CS
                           SMP_LBD  70 dkrqiildl..qisfvgnceidleikryfcragvks 103
                                           ii d    isf g +e+  eik+y cr+ ++ 
  gi|557694088|ref|YP_008797142.1| 220 GAELIINDKvdAISFTGSAEVGEEIKQYACRSNIRV 255
                                       5555666642269******************99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3578.07
//
Query:       gi|557694089|ref|YP_008797143.1|  [L=308]
Description: fumarylacetoacetate (FAA) hydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-25   89.6   0.0    8.3e-25   87.7   0.0    1.8  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 !   87.7   0.0   4.6e-29   8.3e-25      25     218 .]     121     299 ..      91     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 4.6e-29
                                       EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HHHHHTTEEEEEEEEEEE-SBGGG CS
                     FAA_hydrolase  25 drhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsveeAedaiaGytllnDvsaRdlqa 101
                                       +  ++  ++ff +++s  vgpg++  +++ ++    E ELa++ig +             i+Gyt++nD+saRd+  
  gi|557694089|ref|YP_008797143.1| 121 E--AKRPEIFFKATPSRCVGPGEDAFIRSDTNWSVPEPELALIIGPRH-----------EILGYTIGNDLSARDIEG 184
                                       2..223346999999*********999999998999********9542...........268************975 PP

                                       ---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEE..TTEEEEEEEG..GGTTTSHHHHHHHHHHHH-B- CS
                     FAA_hydrolase 102 eekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrv..ngeevqdsnt..kdmifspaeliahlsagltLe 174
                                       e+  pl   ++k +++++ +Gp+i t ++++d ++l++++ +   ge+v +++t  + +  s++eli++++    ++
  gi|557694089|ref|YP_008797143.1| 185 EN--PLYLPQAKIYRGSCALGPVISTQESVGDAKNLTITMAIyrGGEKVYEGSTstARLKRSFEELIHYWVLDNVIP 259
                                       55..688999******************************999988888777765599******************* PP

                                       TT-EEEEEES.......S--EE--TT-EEEEEETTTEEEEEEE. CS
                     FAA_hydrolase 175 pGdliltGTpsgvgaeeeslkflkdgDeveveieglGelrnrVa 218
                                       +G+++ltGT          +  l+dgD+ve+eie++G lrnr++
  gi|557694089|ref|YP_008797143.1| 260 AGSVLLTGTGIV----PPDDFSLQDGDVVEIEIEKIGVLRNRIR 299
                                       *********943....677899*******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2348.00
//
Query:       gi|557694090|ref|YP_008797144.1|  [L=320]
Description: NAD-dependent epimerase/dehydratase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-33  115.5   0.0    3.1e-33  115.2   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.4e-31  109.4   0.0    2.8e-31  109.2   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.5e-16   60.3   0.0      2e-16   59.8   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
      2e-12   46.8   0.0    7.7e-12   44.9   0.0    1.9  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    4.5e-12   45.7   0.0    6.4e-12   45.2   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    2.4e-06   27.6   0.0    4.1e-06   26.8   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
    2.9e-06   26.6   0.0      0.017   14.3   0.0    2.3  2  NAD_binding_4    Male sterility protein
     0.0012   18.4   0.0      0.002   17.6   0.0    1.4  1  adh_short        short chain dehydrogenase
     0.0071   15.9   0.5      0.034   13.7   0.5    2.0  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.064   13.2   0.0       0.11   12.3   0.0    1.4  1  KR               KR domain


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 !  115.2   0.0   1.7e-36   3.1e-33       1     241 []       3     241 ..       3     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 1.7e-36
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAa 73 
                                       +lVtGatGfiG+ +v++l +kg++ i  d + ++s+ + l d      +++ldl+++s+l++++++++++ +ihlAa
  gi|557694090|ref|YP_008797144.1|   3 VLVTGATGFIGAWVVRNLHQKGVKFILSDIRFDTSRLKYLIDNpeslPFTTLDLRNASDLDKVLRKHDVERIIHLAA 79 
                                       79**********************99999995555555544448999****************************88 PP

                                       ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHH.TCTEEEEEEEGGGGTSCSS...SSBSTCSTTS----SSHHHHHH CS
                         Epimerase  74 vggvaassedpadfieknlqgtlnlleaarka.gvkrllflsSsevYGkdae...qpkeettltgplkpnspYaaaK 146
                                          +++   dp      n++g l+++eaa+k+ gvk+++++sS +vYG+++    +p +e++   plkp++ Y+a K
  gi|557694090|ref|YP_008797144.1|  80 -LQIPQCRADPVNGGLVNVVGFLKIFEAAKKYgGVKNIVYASSFAVYGPQELygeKPLNEDA---PLKPTTHYGAFK 152
                                       .568888999**********************99**************98887645888888...99********** PP

                                       HHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHH CS
                         Epimerase 147 lageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeail 223
                                       ++ e  + ay+ ++g++ + lr+ ++yG ++  g  s v +al + il +k ++++   g+  ++  y+ Dvae ++
  gi|557694090|ref|YP_008797144.1| 153 VCNELSAYAYWVENGIPSVGLRPHTVYGFGRDVGVTSDVTTALKAAIL-KK-PFKIRFGGKVSMQ--YAADVAESFV 225
                                       ******************************555556666665555555.56.7777777888665..89******99 PP

                                       HHHHHHTT-STTEEEEES CS
                         Epimerase 224 lvlehvdagdkgeiyniG 241
                                       +++ +  +g   ++yn+G
  gi|557694090|ref|YP_008797144.1| 226 AAAFANPSG--AKVYNLG 241
                                       998884444..3499987 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 !  109.2   0.0   1.6e-34   2.8e-31       1     261 [.       4     253 ..       4     295 .. 0.87

  Alignments for each domain:
  == domain 1  score: 109.2 bits;  conditional E-value: 1.6e-34
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG +GfiG+++++ L +kg +++     +  f+t+r++ l ++p+     +l +   Dl+++s l+++l++++++
  gi|557694090|ref|YP_008797144.1|   4 LVTGATGFIGAWVVRNLHQKGVKFIL---SDIRFDTSRLKYLIDNPE-----SLPFTTLDLRNASDLDKVLRKHDVE 72 
                                       9*******************998855...5778999*******9884.....699********************** PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S...SSSB-TTS-----S CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq...evpqtEttpfyPrs 151
                                       ++++LAA    +    +P     vnv+G l+++ea++++g    + ++ aS+  vYG ++   e p +E+ p++P+ 
  gi|557694090|ref|YP_008797144.1|  73 RIIHLAALQIPQ-CRADPVNGGLVNVVGFLKIFEAAKKYGGV--KNIVYASSFAVYGPQElygEKPLNEDAPLKPTT 146
                                       *******97655.5667**********************854..57899********996667************** PP

                                       HHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHH CS
                     GDP_Man_Dehyd 152 PYaaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkD 228
                                        Y+a K+  +  + +y+ + g++ v  +    ++  r    vt  +t+a+  + l+k  ++++G      + +++ D
  gi|557694090|ref|YP_008797144.1| 147 HYGAFKVCNELSAYAYWVENGIPSVGLRPHTVYGFGRDV-GVTSDVTTALKAAILKKPFKIRFGGK---VSMQYAAD 219
                                       ************************************955.7*********9999999889998765...47889999 PP

                                       HHHHHHHHH.HCSS---EEE-TT-EEECHHCHHC CS
                     GDP_Man_Dehyd 229 yveamwlml.qqdkpedyviatgethsvrefvel 261
                                       ++e ++++   + +  +++   g ++sv e+v+ 
  gi|557694090|ref|YP_008797144.1| 220 VAESFVAAAfANPSGAKVYNLGGPVVSVSEVVDT 253
                                       9999877651445555666677788888888874 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 !   59.8   0.0   1.1e-19     2e-16       1     229 [.       4     228 ..       4     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1.1e-19
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleels.kvnvkkviegDvtdkdkleealegvdv..vihla 74 
                                       +vtG++GF+G+ +v++L + +   +    D+r++++ l+ l  + +   + + D++++++l+++l++ dv  +ihla
  gi|557694090|ref|YP_008797144.1|   4 LVTGATGFIGAWVVRNLHQKGV--KFILSDIRFDTSRLKYLIdNPESLPFTTLDLRNASDLDKVLRKHDVerIIHLA 78 
                                       69****************9993..555789999988766554044444499**************97666559***9 PP

                         3Beta_HSD  75 slvdvagkltedeimkvnvkGTrnvleacvka.gvrvlvYtSsaevvgpns.lgeeilngdEeleyeslhqdaypes 149
                                       +l+  + +    +   vnv G  ++ ea++k  gv+ +vY Ss  v gp   +ge+ l  +E    + +++  y  +
  gi|557694090|ref|YP_008797144.1|  79 ALQIPQCRADPVNGGLVNVVGFLKIFEAAKKYgGVKNIVYASSFAVYGPQElYGEKPL--NE--DAPLKPTTHYGAF 151
                                       9998888788878899*************98637***************321444444..33..455668889**** PP

                         3Beta_HSD 150 KalaEklvlkaNgrtlknggrlyTcaLRpagiyGegdkllvpllkq.laklg.lalfkigdeevlsdrvYvgNvawa 224
                                       K   E   l+a    ++ng  +  + LRp ++yG g ++ v++ ++ ++k   l++        ++++ Y+  va  
  gi|557694090|ref|YP_008797144.1| 152 KVCNE---LSAYAYWVENG--IPSVGLRPHTVYGFGRDVGVTSDVTtALKAAiLKKPFKIRFGGKVSMQYAADVAES 223
                                       *9999...78888899***..9**************99877664440444331333334455566788999999999 PP

                         3Beta_HSD 225 hilAa 229
                                        + Aa
  gi|557694090|ref|YP_008797144.1| 224 FVAAA 228
                                       99887 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   4.3e-15   7.7e-12       1     140 [.       3     133 ..       3     143 .. 0.86
   2 ?   -0.5   0.0      0.29   5.2e+02     132     155 ..     142     165 ..     136     261 .. 0.70

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 4.3e-15
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlvtGa+G iG  +vr++ +k +k   +l+   +   +++  ++   + ++l ++      d+r+++ l+k+l++++
  gi|557694090|ref|YP_008797144.1|   3 VLVTGATGFIGAWVVRNLHQKGVKF--ILSDIRFDTSRLKYLID---NPESLPFT----TLDLRNASDLDKVLRKHD 70 
                                       8*****************9999985..45666677777776552...33456666....78**************** PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHT.T-SEEEEEEEGGGSS--SHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaiea.gvkkvvliStDKAvnPtnvmGa 140
                                       v+ ++h AAl ++P +   p+++   Nv+g  ++ eaa+++ gvk++v+ S+     P  ++G 
  gi|557694090|ref|YP_008797144.1|  71 VERIIHLAAL-QIPQCRADPVNGGLVNVVGFLKIFEAAKKYgGVKNIVYASSFAVYGPQELYGE 133
                                       *********9.8***************************9846*******99888889998885 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.29
                                       SS--SHHHHHHHHHHHHHHHGGG- CS
                   Polysacc_synt_2 132 vnPtnvmGatKrlaekllqalake 155
                                        +Pt  +Ga K + e+ + a+  e
  gi|557694090|ref|YP_008797144.1| 142 LKPTTHYGAFKVCNELSAYAYWVE 165
                                       678888888888888877665444 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 !   45.2   0.0   3.6e-15   6.4e-12       1     134 [.       1     157 [.       1     184 [. 0.93

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 3.6e-15
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...................T--TTSHHHHHHHHHHH--SEEEE- CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre...................eldltdaeavaellkeakpdvvvna 58 
                                       m++lvtGa+G +G  ++++l+++g++++  + +                   +ldl++a+ ++++l++++ + ++++
  gi|557694090|ref|YP_008797144.1|   1 MTVLVTGATGFIGAWVVRNLHQKGVKFILSDIRfdtsrlkylidnpeslpftTLDLRNASDLDKVLRKHDVERIIHL 77 
                                       89*************************9998888999**************************************** PP

                                       -----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-..EEEEEEEGGGS-S-...TTS-B-TTS----SSHHHHHHH CS
                     RmlD_sub_bind  59 AAytavDkaEseeeaayavnaeavealAeaaaavga..lLihvStDyVFdGe...kkrpYeeddetsPlnvYGrtKl 130
                                       AA  ++ ++  ++ +   vn+ +  ++ eaa+++g    +++ S+  V+  +    ++p +ed++ +P + YG+ K+
  gi|557694090|ref|YP_008797144.1|  78 AAL-QIPQCRADPVNGGLVNVVGFLKIFEAAKKYGGvkNIVYASSFAVYGPQelyGEKPLNEDAPLKPTTHYGAFKV 153
                                       **7.6789**************************96336**********999999999****************999 PP

                                       HHHH CS
                     RmlD_sub_bind 131 aGEq 134
                                         E 
  gi|557694090|ref|YP_008797144.1| 154 CNEL 157
                                       8775 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 !   26.8   0.0   2.3e-09   4.1e-06       1     103 [.       7     126 ..       7     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.3e-09
                                       TTTSHHHHHHHHHHHHC-.T-EEEEEETTHHHCHHHHCT.TTCEEEE--TT-CCHHHHHHTT-SE..EEES-..... CS
                    NAD_binding_10   1 GAtGkvGrllvkellarg.ghevtalvRnpeklaeleae.eglevvegdvtdvedlaealkgada..Vvsal..... 68 
                                       GAtG +G  +v+ l ++g ++ +  +  ++++l+ l ++ e l  +++d+ +++dl ++l+ +d+  + + l     
  gi|557694090|ref|YP_008797144.1|   7 GATGFIGAWVVRNLHQKGvKFILSDIRFDTSRLKYLIDNpESLPFTTLDLRNASDLDKVLRKHDVerI-IHLaalqi 82 
                                       9****************744444445668******9977589999*******************6533.33313565 PP

                                       ........--TCCHHHH.......HHHHHHHHHHCT.--EEEEEEETTTTS CS
                    NAD_binding_10  69 ........ggggkdeeg.......aknivdaakeag.vkRfvlvsaigvgd 103
                                               +       g         +i +aak+ g vk +v+ s++ v+ 
  gi|557694090|ref|YP_008797144.1|  83 pqcradpvN-------GglvnvvgFLKIFEAAKKYGgVKNIVYASSFAVYG 126
                                       554433322.......1344444599999****9655***********995 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00017      0.31       1      17 [.       5      21 ..       5      35 .. 0.88
   2 !   14.3   0.0   9.7e-06     0.017      86     209 ..      69     182 ..      58     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                                      EE-TTSHHHHHHHHHHH CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLL 17
                                      +TGaTGF+G+ ++++L 
  gi|557694090|ref|YP_008797144.1|  5 VTGATGFIGAWVVRNLH 21
                                      7*************995 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 9.7e-06
                                       HH--EEEE--SS-S.STTSSE..EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......H CS
                     NAD_binding_4  86 eevdviihsaAtvnfdepyke..llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeek 160
                                       + v+ iih aA    + + +      vNv G  +++e akk    k +++ S+ +v+g +e                
  gi|557694090|ref|YP_008797144.1|  69 HDVERIIHLAALQIPQCRADPvnGGLVNVVGFLKIFEAAKKYGGVKNIVYASSFAVYGPQELY-G------------ 132
                                       578899999998766655555115679**************************7777777733.2............ PP

                                       HH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.- CS
                     NAD_binding_4 161 ldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.e 209
                                       ++ ++++   + +++Y   K++ E    ++  ++g+p v +Rp +++g  
  gi|557694090|ref|YP_008797144.1| 133 EKPLNEDAPLKPTTHYGAFKVCNELSAYAYWVENGIPSVGLRPHTVYGfG 182
                                       55666777778888999999999999999999999999999999998852 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.1e-06     0.002       2      70 ..       2      68 ..       1      81 [. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.1e-06
                                      EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHH CS
                         adh_short  2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvek 70
                                      +vlvtGa++ IG  ++++l ++G+k ++ d++ ++    +k l ++ +++ + ++D++++++++++++k
  gi|557694090|ref|YP_008797144.1|  2 TVLVTGATGFIGAWVVRNLHQKGVKFILSDIRFDTS--RLKYLIDNPESLPFTTLDLRNASDLDKVLRK 68
                                      79**************************99997765..45555555678999*********99999876 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.5   1.9e-05     0.034       1     102 [.       3     121 ..       3     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                       EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S..-SHHHHHHHHSTTEEE..ES-TT-HHHHHHHHTT-SE..EEE- CS
                              NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdt..kselakslkeaGvelv..kgdlddkeslvealkgvdv..vfsv 71 
                                       +lv+GaTG +G+ vvr l ++g k   ++ d   ++ ++k l +++  l     dl + + l+++l++ dv  ++  
  gi|557694090|ref|YP_008797144.1|   3 VLVTGATGFIGAWVVRNLHQKGVK--FILSDIrfDTSRLKYLIDNPESLPftTLDLRNASDLDKVLRKHDVerIIHL 77 
                                       79******************9966..445555458888999999998886557899999999999998666325555 PP

                                       --GG............S-HHHHHHHHHHHHHHHS.-SEEEEEE- CS
                              NmrA  72 tgfy............skeiedgkklvdAakeaG.vkhfiySsl 102
                                        +++              ++    k+ +Aak+ G vk+++y+s 
  gi|557694090|ref|YP_008797144.1|  78 AALQipqcradpvnggLVNVVGFLKIFEAAKKYGgVKNIVYASS 121
                                       55558889977777655555556799999999999999999874 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.4e-05      0.11       2      75 ..       2      69 ..       1      85 [. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.4e-05
                                      EEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHH CS
                                KR  2 tylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleei 75
                                      t+l+tG++G +G  ++r l +kg + ++   R       ++++++ l ++  +  +  +D+ +++++ ++l++ 
  gi|557694090|ref|YP_008797144.1|  2 TVLVTGATGFIGAWVVRNLHQKGVKFILSDIRF------DTSRLKYLIDNPESLPFTTLDLRNASDLDKVLRKH 69
                                      78*********************9987755555......22345555555555666666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2342.04
//
Query:       gi|557694091|ref|YP_008797145.1|  [L=251]
Description: 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  133.1   0.9    9.2e-39  132.8   0.9    1.0  1  HpcH_HpaI  HpcH/HpaI aldolase/citrate lyase family


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 !  132.8   0.9   5.2e-43   9.2e-39       3     218 ..      13     236 ..      11     239 .. 0.94

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 5.2e-43
                                       EEEEESTSHHHHHHHCTC--SEEEEESSTSSSHHHHHHHHHHHHHHHHHHHHCTTTS.SEEEEE-SSTTHHHHHHHG CS
                         HpcH_HpaI   3 glflpganaalaekaaiagaDsvliDlEdavalaeKdaARvlvsealkqldalaaaa.sevvVRvnsldselikqdl 78 
                                       glf+   ++a++e aa+ag+D v+iDlE++v          + +++ + ++a a+++  ++vVRv++  +  + +  
  gi|557694091|ref|YP_008797145.1|  13 GLFATIPSPAIVELAAVAGFDFVIIDLEHGV---------IDYETMENMVRA-ADVHgLTAVVRVPESFEDAVLK-- 77 
                                       8999***************************.........666555555555.5555589******998888888.. PP

                                       GHHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---.....................HCCC-EEEEEE-SHHHHHT CS
                         HpcH_HpaI  79 evldlgaqvvlvPkvetaeealevvsalrepekgirg.....................anketrllaqiEsaegvkn 134
                                        +l++ga +v +P + +a+ea+++v+a++++++g+rg                     +n et ++ qiE  egv+n
  gi|557694091|ref|YP_008797145.1|  78 -ALEAGAHGVEIPHIGSAAEAEKAVKAVKYAPEGMRGvspytraawyssvsprehfatSNRETMVVLQIEGVEGVEN 153
                                       .9*************************************************************************** PP

                                       HHHHHTSTTEEEEEE-HHHHHHHTT-TTSTTSHHHHHHHHHHHHTTHCEEEEEEE.E-SSHHHHHHHHHTTHCEEEE CS
                         HpcH_HpaI 135 aeeIaavegldgvflGaeDlsadlgtkrspegtevldareriltaaraagiaaldtvasdiddaegflaegalfval 211
                                       +e+Ia+v+g+d++f+G+ Dls +lg  ++ + ++vl+a +++++ + ++++   +++a  i++a++++ +g   va 
  gi|557694091|ref|YP_008797145.1| 154 MEAIASVKGVDVLFVGPYDLSQALGVPGDVDNEKVLAALKKLVQICMQKDV-SAGSFAPTIEKARQLISQGVKYVAY 229
                                       ***************************************************.889********************** PP

                                       EEHHHHH CS
                         HpcH_HpaI 212 Gfdgkll 218
                                        +d+  +
  gi|557694091|ref|YP_008797145.1| 230 SVDTGII 236
                                       ***9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1859.16
//
Query:       gi|557694092|ref|YP_008797146.1|  [L=254]
Description: hypothetical protein CSUB_C0657 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-27   96.2   0.1    3.1e-27   96.0   0.1    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 !   96.0   0.1   1.7e-31   3.1e-27       1     212 [.      20     230 ..      20     231 .. 0.86

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 1.7e-31
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT..EEE-SEEEEEETTT.SEEEEEEE. CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg..relepprlyakdsgsrdllvlqg. 74 
                                       +i+G p +G +g lav++L e ++a+ vgei s++ +p     ++ +++++   ++++ +ly+ + ++ +ll+l   
  gi|557694092|ref|YP_008797146.1|  20 FIEGSPTAGAAGILAVNYLREVFDAVLVGEIVSPH-FP-----QISIIDDDgiASRPKLELYLVNLKGLRLLLLSRv 90 
                                       69*********************************.**.....9999999978888888889997789********7 PP

                                       ...E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHH.HCT........- CS
                              PAC2  75 ...repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleel.ees........e 139
                                           + ++ ye +a++l +++++++v+e +vL++               +v++  t+ ++ + l + +        e
  gi|557694092|ref|YP_008797146.1|  91 fpvESNEGSYE-LASKLYQFLSRHNVNEYLVLASGRVTGD--------GSVFVSTTSLDQSKALlD-AgakrspslE 157
                                       77666666666.****************999999885544........478888888888877733.2234567764 PP

                                       CEEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 140 yggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                          +  ++g L+  +++ g ++ +l+  +  y+pd  aa++lle++s++lg+evd + L+ + e+ +++++e+
  gi|557694092|ref|YP_008797146.1| 158 TLPVDRVSGFLMLFFARDGKKVSMLFSDSASYIPDHLAARRLLEVVSRYLGIEVDFKALDTEIEKQAKAMQEV 230
                                       444477888888888******************************************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1807.34
//
Query:       gi|557694093|ref|YP_008797147.1|  [L=79]
Description: hypothetical protein CSUB_C0658 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   33.4   0.3      6e-08   32.7   0.3    1.5  1  DUF350         Domain of Unknown Function (DUF350)
     0.0092   15.2   1.3       0.01   15.1   1.3    1.2  1  DUF2232        Predicted membrane protein (DUF2232)
  ------ inclusion threshold ------
      0.071   12.9   1.2      0.076   12.8   0.4    1.5  1  Brr6_like_C_C  Di-sulfide bridge nucleocytoplasmic transport 


Domain annotation for each model (and alignments):
>> DUF350  Domain of Unknown Function (DUF350)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.3     1e-11     6e-08       3      51 ..      11      60 ..       3      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1e-11
                            DUF350  3 vvGivllllgffvfdllTp.gklgelIkqgnnAaaivlagviiglaiiva 51
                                      ++++   ++++ ++ ++T+ ++++e+I+++n+A a +l+g++++++++++
  gi|557694093|ref|YP_008797147.1| 11 ALALFSITVAINILNRVTKdVNEFEEIRKKNLAGAYMLFGTFVAISLVIS 60
                                      5677778999999*****88****************************97 PP

>> DUF2232  Predicted membrane protein (DUF2232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.3   1.7e-06      0.01     166     221 ..       6      61 ..       1      79 [] 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-06
                           DUF2232 166 viasllaaflnyllakkilkrlklkvpklppfrewklPe.sliwlliiilllllllk 221
                                       +++++++a++++ +a +il+r++++v+++ ++r+  l   +++ ++++++ l+ + +
  gi|557694093|ref|YP_008797147.1|   6 LVFAVALALFSITVAINILNRVTKDVNEFEEIRKKNLAGaYMLFGTFVAISLV-ISQ 61 
                                       6789999***************************9998625566666655555.333 PP

>> Brr6_like_C_C  Di-sulfide bridge nucleocytoplasmic transport domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   1.3e-05     0.076       3      42 ..       3      42 ..       1      48 [. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                     Brr6_like_C_C  3 ylqllfnlllvllllylvisfvltikkDiekkleekkael 42
                                       +ql+f + l+l+ ++++i+++  + kD+++  e +k++l
  gi|557694093|ref|YP_008797147.1|  3 LIQLVFAVALALFSITVAINILNRVTKDVNEFEEIRKKNL 42
                                      68****************************9988888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 571.81
//
Query:       gi|557694094|ref|YP_008797148.1|  [L=738]
Description: hypothetical protein CSUB_C0659 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (738 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); 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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 5115.63
//
Query:       gi|557694095|ref|YP_008797149.1|  [L=703]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  157.5  17.8    7.9e-46  157.0  17.8    1.2  1  STT3      Oligosaccharyl transferase STT3 subunit
  ------ inclusion threshold ------
      0.038   12.2   4.7       0.73    8.0   0.0    2.2  2  Dpy19     Q-cell neuroblast polarisation
       0.99    9.6  25.7      0.024   14.9  12.6    3.4  3  PMT_2     Dolichyl-phosphate-mannose-protein mannosyltransfer


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 !  157.0  17.8   1.3e-49   7.9e-46      26     487 ..      51     556 ..      48     557 .. 0.87

  Alignments for each domain:
  == domain 1  score: 157.0 bits;  conditional E-value: 1.3e-49
                                       T--S--SSCHHHHHHHCCCHHHT-C.....CCHHSSEETTSSTTT-EEESTTCCHCCC.CHHHHHHCCHHC.....H CS
                              STT3  26 glsylsefDpYYnyRltenllnnGfpGdvvikkknwfdhsqyyPpGsrvdygplivlLamlasaiinhsld.....v 97 
                                       +   lsefDp+  y+   +++++G+      ++ nw d  ++yP G r  + +  +++   a+a+i++ l+     v
  gi|557694095|ref|YP_008797149.1|  51 WGVALSEFDPWVQYKEALFVIERGW--GGFSEFFNWHDTMSWYPWG-RDMGRTAFPGI-PFAMAFIYLTLKslgitV 123
                                       55679********************..4478999************.99999999999.77777777777777799* PP

                                       HHHHHHHCCHHHHHHHHCHHHHHHHHHHS-CCCHHHHHHHCCC-CCCCCTTSTT--STCCCCHHHHHHHHHHHHHHH CS
                              STT3  98 sirevclwlpallgsLlaIpiyflvrelksdiaGllAAlllaiaPgYlsrtvaGfyDtdmfeivlllfvlffflkai 174
                                       + +e + +lp + g L++++iyfl +++ +   Gl+AAl++ai+   + rt +G++D + + + l+l  ++f l ai
  gi|557694095|ref|YP_008797149.1| 124 DTLELAAVLPVVYGVLTVVAIYFLGKRVGGTSTGLAAALFMAISTAHIGRTHLGWFDDESLSLPLMLGGYIFYLAAI 200
                                       ***************************************************************************** PP

                                       HCCS...TTCHHHHHHHHHHHHHHTTSCCGGHHHHCCHHHHHHHHHCTTTS-CCHHHHHHHHHHHHHHH..CCCCCC CS
                              STT3 175 ktks...nkislaviaaliiflivlaWggyailiyallllfilalLiigrfelklkiavtfsviiaflviaiivllf 248
                                        +k    + ++++++++l++  + ++Wg+   + +a+++lf + l +igr+   l++a   +v+ a++   +i++++
  gi|557694095|ref|YP_008797149.1| 201 SEKRslrGTVVFSLLSGLFLGFMAASWGAH-KFPLAFIPLFSVFLAVIGRYRRSLLVAT--AVAFAIYT--SIAVSV 272
                                       *9999************************9.9*******************88777665..45555555..667777 PP

                                       CTTCHHHSTTTCHHCCCCHHHHHHHHCCCHHC..CCCCCHHCCCHHTT.HHHHTT--GGGHHHHHHHHHHHHCCCCC CS
                              STT3 249 lgfqvvavseiigalgifgllqlvafgsvvvlvaelkfyqfislfqpgilsevlgligevvtalavlglialwlgil 325
                                        ++ +   ++i  ++++ g + l+++g + +  +++k ++++ l+ ++ +  + +++  ++  l+vlg++ l   ++
  gi|557694095|ref|YP_008797149.1| 273 PKLGP---GYIREITIFSGFIALFILGVFEAA-SRIKQPETRRLTIFT-VLLLSAVGFFALLGLGVLGVPGL---KF 341
                                       77777...566666666666666666666666.677888888876666.44444444456666666666654...34 PP

                                       CTS-----TTHHHHHHHHHS---S--CCHHHCCSSSTTTTCCCHHHCHHCCHHCTCHHHHHHHHHHHHHCCC-SCHC CS
                              STT3 326 yslldleyaklkikiiilvsvwlpvgllaltkglrfliftvPlgiifvgllleflavfvkiysvsqilfsgvvvill 402
                                       +s++    +  +++i+ +v++ ++ +++ ++ +  +++++vP+g++ +++  ++  +f+  + + + +f+  +v+ l
  gi|557694095|ref|YP_008797149.1| 342 LSVIL-PGLRDALPIVESVAENQVPTWSIMFSDFGLTLALVPIGVYQLIKTRRDPDLFIVLFLLFSAYFASSMVR-L 416
                                       44443.3455689**************************************************************.8 PP

                                       CCCCHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHHHHH....................................... CS
                              STT3 403 mltllpvlallaavkiskifstykdekeakikvaakav....................................... 440
                                        l+ +p++al+a+   +++fs   d +++  +v++k +                                       
  gi|557694095|ref|YP_008797149.1| 417 SLLASPAVALIAGHGYAFVFSRLGDLIAQ-RRVSKKRGeevniglaaftpvllvllllisivpsvygglgsrvtlsp 492
                                       9999*****************99988655.555344445667788889999************************** PP

                                       ................HHHHCT.TTTTHHH.TTHHHCHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                              STT3 441 ................aptksnglkeslew.kantnrdsvvitwwdyghilaveadrpVtfdgg 487
                                                       a      + ++l w + n ++d+vv +wwdyg+ ++   +r +++d g
  gi|557694095|ref|YP_008797149.1| 493 idqgyqpativtssfpARQSVPDWVRALAWmRDNLPKDAVVASWWDYGYWITILGERITLIDNG 556
                                       **************888888889***********************************999965 PP

>> Dpy19  Q-cell neuroblast polarisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   4.3    0.0063        38     118     313 ..     137     328 ..     130     340 .. 0.72
   2 ?    8.0   0.0   0.00012      0.73     424     525 ..     398     535 ..     383     539 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.0063
                             Dpy19 118 qgvtvlvLflystllsesvlgGllavllflfnhsevtrveftppLREnFalPflllqmllltiilkrkikeqkksls 194
                                       + +tv+++++++  ++++  +Gl a+l+  +   ++ r +      E+ +lP++l   ++    +++k     +sl+
  gi|557694095|ref|YP_008797149.1| 137 GVLTVVAIYFLGKRVGGTS-TGLAAALFMAISTAHIGRTHLGWFDDESLSLPLMLGGYIFYLAAISEK-----RSLR 207
                                       4567778888888887774.5777788888888889999999999************99999999996.....3333 PP

                             Dpy19 195 ellkiillslstv.lflltWqFsqFvl.ltqilslfaldllglipteklalillihllslllafvlqfgnsmlllsl 269
                                         +++ lls   + ++  +W   +F l ++ ++s+f+  + ++  +  +a+ + + +   ++++v + g+ ++    
  gi|557694095|ref|YP_008797149.1| 208 GTVVFSLLSGLFLgFMAASWGAHKFPLaFIPLFSVFLAVIGRYRRSLLVATAVAFAIYTSIAVSVPKLGPGYIREIT 284
                                       4445556655554044569******6626788888888888877777777777777777777888999********* PP

                             Dpy19 270 llsvllslllilvlqrkvkskrlllklillllklllsialtlil 313
                                       ++s  ++l++  v+++  + k+  ++ + +++ llls +++++l
  gi|557694095|ref|YP_008797149.1| 285 IFSGFIALFILGVFEAASRIKQPETRRLTIFTVLLLSAVGFFAL 328
                                       **********9999955555553344444444444444444433 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00012
                             Dpy19 424 YhllqllvftllallimrLklLwtphlcviaslvl...........skklfkfllk..................... 468
                                       + +l ll+    a ++ rL lL++p +++ia+ +                     +                     
  gi|557694095|ref|YP_008797149.1| 398 FIVLFLLFSAYFASSMVRLSLLASPAVALIAGHGYafvfsrlgdliA--------Qrrvskkrgeevniglaaftpv 466
                                       777888999999*******************9999455433332220........1334446778888889999999 PP

                             Dpy19 469 ...........kifisavlavlllsmsvkgvpnleeelselrefsnpdt.eeLleWIksntekdavfaG 525
                                                    +   +   ++ls++++g++  +  +s     +++++ ++ l W++ n +kdav a+
  gi|557694095|ref|YP_008797149.1| 467 llvllllisivPSVYGGLGSRVTLSPIDQGYQPATIVTSSFPARQSVPDwVRALAWMRDNLPKDAVVAS 535
                                       99997776444334444556688999999999999999999999999999****************997 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9  12.6   3.9e-06     0.024      20     140 ..     125     257 ..     103     276 .. 0.64
   2 ?   -2.4   0.2      0.82   4.9e+03      34      65 ..     292     326 ..     282     343 .. 0.53
   3 ?    2.6   0.8     0.023   1.4e+02      58      97 ..     377     418 ..     368     437 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-06
                             PMT_2  20 selairlvsalagvltilllyllarrlfgkraallaalllavvplfvalsalftp.daplvllwalalylllralek 95 
                                       +   + +++++ gvlt++++y+l +r+ g++++l+aal++a+++  +  ++l+   d  l l ++l  y+++ a+ +
  gi|557694095|ref|YP_008797149.1| 125 TLELAAVLPVVYGVLTVVAIYFLGKRVGGTSTGLAAALFMAISTAHIGRTHLGWFdDESLSLPLMLGGYIFYLAAIS 201
                                       5555677889********************************88777777755554555555556666666666654 PP

                             PMT_2  96 nk..lkyw....llagvlfGlgfls....Kytaallliaall.yllisarrilkek 140
                                       +k  l+      ll+g+++G++  s    K+  a++++  ++ +++ + rr l   
  gi|557694095|ref|YP_008797149.1| 202 EKrsLRGTvvfsLLSGLFLGFMAASwgahKFPLAFIPLFSVFlAVIGRYRRSLLVA 257
                                       44126555777777777777776655555888888877433324444444433322 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.82
                             PMT_2  34 ltilllyllarrlfg...kraallaalllavvplf 65 
                                       l il+++  a r+ +   +r  ++++lll++v +f
  gi|557694095|ref|YP_008797149.1| 292 LFILGVFEAASRIKQpetRRLTIFTVLLLSAVGFF 326
                                       44444444444444321133444444444444433 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.023
                             PMT_2  58 llavvplfvalsa..lftpdaplvllwalalylllraleknk 97 
                                        la+vp+ v+ +      pd + vl++++++y+   ++    
  gi|557694095|ref|YP_008797149.1| 377 TLALVPIGVYQLIktRRDPDLFIVLFLLFSAYFASSMVRLSL 418
                                       555666555555544566788888888888888777665543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (703 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 4925.87
//
Query:       gi|557694096|ref|YP_008797150.1|  [L=571]
Description: hypothetical protein CSUB_C0661 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   17.5   2.4          1    9.7   0.2    3.9  3  DUF5122   Domain of unknown function (DUF5122) beta-propeller
  ------ inclusion threshold ------
        5.2    6.9  12.1        9.5    6.0  12.1    1.4  1  RIFIN     Rifin


Domain annotation for each model (and alignments):
>> DUF5122  Domain of unknown function (DUF5122) beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.019   1.7e+02       4      17 ..     199     210 ..     199     215 .. 0.81
   2 ?    2.1   0.0     0.028   2.5e+02       4      28 ..     248     272 ..     248     276 .. 0.61
   3 !    9.7   0.2   0.00011         1       4      32 ..     299     326 ..     299     330 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.019
                           DUF5122   4 GKIlVaGsftsyng 17 
                                       G+++VaG+++ + g
  gi|557694096|ref|YP_008797150.1| 199 GRVYVAGTSN-D-G 210
                                       99******99.3.3 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.028
                           DUF5122   4 GKIlVaGsftsyngss.dfalvRLna 28 
                                       G I++aG++  ++g   +  l+RL++
  gi|557694096|ref|YP_008797150.1| 248 GNIYLAGKTV-IAGRMdEAVLARLDS 272
                                       5677777777.655540456677776 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00011
                           DUF5122   4 GKIlVaGsftsyngssdfalvRLnaDGsl 32 
                                       G I++aG++t   g +d  l+ + +DG++
  gi|557694096|ref|YP_008797150.1| 299 GTIYLAGYTT-GYGTRDVLLAAFAPDGTF 326
                                       89********.77**************97 PP

>> RIFIN  Rifin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  12.1    0.0011       9.5     183     293 ..     444     552 ..     405     563 .. 0.38

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0011
                             RIFIN 183 tnyknvtslvkaikeeyeescllklkkskaaltsakekekkeasskekikkkvekive.kaekkaaaaaaeaaaeat 258
                                       t+ + +++ +++ ++     +++ +++s+ +l+s+++++++   +++++++++++ ++  +++++a+++++a +++t
  gi|557694096|ref|YP_008797150.1| 444 TTATATATTTTTAYAI---ATTTITQTSSVILVSTATSTTTIPVTTTQTQTQTTTNTQtVTTTTTATTTSTALTTQT 517
                                       1111111111111111...1111222222222222222222222222222222222220222222222223333333 PP

                             RIFIN 259 aeaekaetaaveattaslqtaiiasivaivvIvLi 293
                                       ++++++ t+ ++ ++ +  ++ i  ++ i++ vLi
  gi|557694096|ref|YP_008797150.1| 518 QSTTQTLTQITTVAFPEPVSTYILPMLLILIAVLI 552
                                       33333333333444444444455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2195  (0.122427); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); 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):               2  [number of targets reported over threshold]
# CPU time: 0.80u 0.31s 00:00:01.11 Elapsed: 00:00:00.43
# Mc/sec: 3951.92
//
Query:       gi|557694097|ref|YP_008797151.1|  [L=133]
Description: translation initiation inhibitor [Candidatus Caldiarchaeum subterraneum]
Scores for 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-37  126.5   0.0    6.2e-37  126.3   0.0    1.0  1  Ribonuc_L-PSP  Endoribonuclease L-PSP
  ------ inclusion threshold ------
       0.13   11.4   0.0       0.15   11.2   0.0    1.1  1  DUF844         Baculovirus protein of unknown function (DUF84


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 !  126.3   0.0     7e-41   6.2e-37       2     120 ..      13     129 ..      12     130 .. 0.96

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 7e-41
                                       TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGG CS
                     Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelvegdveeqtrqalenlkavLaaagaslsdvVkvtvFladied 78 
                                       ++ap ++++Ysqavkag+++++sGq++++petg++ e+dv+ qtr++l+n+ka+++++g slsdvVkvtv+l   ed
  gi|557694097|ref|YP_008797151.1|  13 NKAPRPMGQYSQAVKAGGFLFISGQVAINPETGKIEEKDVRGQTRRILQNVKAIVESQGGSLSDVVKVTVYLSRPED 89 
                                       789************************************************************************** PP

                                       HHHHHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEEE CS
                     Ribonuc_L-PSP  79 faevnevyaeafdelkeaParsaveVaaLpkgakvEIeaiav 120
                                       f+++nevy e+f+++   Par++v+++   +ga++EI++ia+
  gi|557694097|ref|YP_008797151.1|  90 FQDMNEVYSEFFTQDP--PARATVAATIPGEGALLEIDVIAY 129
                                       ***************5..******887666**********97 PP

>> DUF844  Baculovirus protein of unknown function (DUF844)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   1.7e-05      0.15     110     170 ..      43     102 ..      32     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.7e-05
                            DUF844 110 aeelldtkryrsaaeklinyyvlasvssteykvkdvvklylyllriekykslyklleetld 170
                                        +  ++ k  r  ++++++  v a v+s    ++dvvk+ +yl+r e ++ + ++  e + 
  gi|557694097|ref|YP_008797151.1|  43 ETGKIEEKDVRGQTRRILQ-NVKAIVESQGGSLSDVVKVTVYLSRPEDFQDMNEVYSEFFT 102
                                       5666777777888887776.4789999**********************999888887774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1006.36
//
Query:       gi|557694098|ref|YP_008797152.1|  [L=377]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  145.9   0.0    1.7e-42  145.5   0.0    1.1  1  Peptidase_M24  Metallopeptidase family M24
    7.3e-17   62.3   0.0    5.7e-16   59.4   0.0    2.0  2  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 !  145.5   0.0   1.9e-46   1.7e-42       2     208 ..     161     363 ..     160     364 .. 0.95

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 1.9e-46
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvl 78 
                                       ++r+aa++ + a++ ++e+   g +e+el  +i+ + l ++ ++ + f++   sge++  + + p++r+l+ g+ ++
  gi|557694098|ref|YP_008797152.1| 161 NLREAAKLNDYAYRVAKENTTVGRSEAELYTIIHSE-LVKKKSGFQFFSGDFVSGERCLQIGGPPTNRRLQMGETLI 236
                                       68********************************99.7888999999*999************************** PP

                                       EEEEEEETTEEEEEEEEEECS.SGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSE CS
                     Peptidase_M24  79 idagaeydgyasDitrTvlvG.kftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglG 154
                                       +d+++ +++y sD++rT++vG  +++ q++++e+++ea++a+ +a+kpG+t+s++++a+   + ++g++k+fph+ G
  gi|557694098|ref|YP_008797152.1| 237 LDLWVTHQEYWSDTCRTFVVGsVPSALQKKVFEVLKEALKAGEAALKPGATGSDVYRAVYGAIDRHGYGKYFPHHAG 313
                                       *********************666668************************************************** PP

                                       EEESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                     Peptidase_M24 155 HgvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                       H +Gle  +  p+    ++d+  ++e+ v ++Epgiy   ++ggvr+e+ ++v+
  gi|557694098|ref|YP_008797152.1| 314 HALGLEAWEP-PYFI--PGDKNIITENTVCALEPGIY-FGDVGGVRLENNYVVK 363
                                       ********98.9977..689*****************.57999*********97 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 !   59.4   0.0   6.3e-20   5.7e-16       1     130 [.      10     151 ..      10     152 .. 0.87
   2 ?    0.3   0.0      0.11     1e+03      51      92 ..     235     278 ..     194     298 .. 0.67

  Alignments for each domain:
  == domain 1  score: 59.4 bits;  conditional E-value: 6.3e-20
                                       HHHHHHHHHHHTT-SEEEEECCHHHHHHHSS...-SSSEEEEEEESSCE.EEEEECTTHHHHHHHH.TTSEEEEEST CS
                      Creatinase_N   1 RlerlralmeekgldallvtspenlrYltGfatetgsrglalvvtadga.lllvdalryteaaeesatveevveydd 76 
                                       R +rl ++me+++ld++++ s++n++Y+tG+ t     ++ l+++ dg+ ll++      e+a+++   +e+vey  
  gi|557694098|ref|YP_008797152.1|  10 RWRRLLQWMERQQLDMVVLGSQKNIYYITGYITARIFMPAFLFIPIDGEpLLVTG-KSDSEQAAKT-FGGEIVEYVN 84 
                                       789****************************999999999999******777777.7788888888.7888888877 PP

                                       .............HSSHHHHHHHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHH CS
                      Creatinase_N  77 .............pvealadllkellesekrvgveldaltvafyealkealpdaelvdaselieelR 130
                                                     vea ++ l+++ ++ k++g e +al +  ++++ +  p ae++d+se i  +R
  gi|557694098|ref|YP_008797152.1|  85 ynldnvmrpypihGVEAAVKTLRSRQPKIKKLGYEGWALDAVILHEMLKMYPTAEFTDVSENILLMR 151
                                       88889999996676777777777776777********************************887777 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                                       EEEECTTHHHHHHHH...TTSEEEEEST.HSSHHHHHHHHHHHHT CS
                      Creatinase_N  51 llvdalryteaaees..atveevveydd.pvealadllkellese 92 
                                       l++d l +t++ + s  ++ + v ++++  +++++++lke+l+++
  gi|557694098|ref|YP_008797152.1| 235 LILD-LWVTHQEYWSdtCRTFVVGSVPSaLQKKVFEVLKEALKAG 278
                                       4444.4444444444334445555555567889999999987764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); 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:                         2  (0.000111551); expected 0.2 (1e-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: 2897.75
//
Query:       gi|557694099|ref|YP_008797153.1|  [L=363]
Description: maltooligosaccharide ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-30  106.6   0.0    2.1e-30  106.0   0.0    1.3  1  ABC_tran         ABC transporter
    7.6e-10   39.5   0.0    2.7e-09   37.7   0.0    2.0  1  OB_MalK          MalK OB fold domain
      6e-09   35.9   0.0    1.7e-08   34.5   0.0    1.8  1  TOBE_2           TOBE domain
    4.3e-05   23.5   0.0       0.16   11.7   0.0    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
    4.7e-05   23.4   0.0    6.9e-05   22.8   0.0    1.2  1  Rad17            Rad17 P-loop domain
    0.00012   21.6   0.0     0.0019   17.7   0.0    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
    0.00062   19.7   0.0     0.0014   18.6   0.0    1.5  1  RsgA_GTPase      RsgA GTPase
     0.0019   18.5   0.0     0.0043   17.3   0.0    1.6  1  TOBE             TOBE domain
     0.0045   16.7   0.1      0.012   15.4   0.1    1.6  1  AAA_29           P-loop containing region of AAA domain
     0.0053   17.3   0.0      0.021   15.4   0.0    2.2  1  CysA_C_terminal  CysA C-terminal regulatory domain
  ------ inclusion threshold ------
       0.02   15.2   0.0      0.036   14.3   0.0    1.6  1  AAA_22           AAA domain
      0.026   15.0   0.1      0.046   14.2   0.1    1.3  1  AAA_23           AAA domain
      0.069   13.5   0.0       0.13   12.6   0.0    1.4  1  AAA_16           AAA ATPase domain
      0.075   12.4   0.0       0.14   11.4   0.0    1.4  1  AIG1             AIG1 family
      0.097   13.1   0.0       0.64   10.4   0.0    2.3  2  RNA_helicase     RNA helicase
       0.14   12.2   0.0       0.28   11.2   0.0    1.4  1  MIT_C            Phospholipase D-like domain at C-terminus of
       0.15   12.3   0.1        1.8    8.8   0.1    2.3  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
       0.17   12.1   0.2       0.44   10.8   0.1    1.7  2  AAA_28           AAA domain
       0.25   11.0   0.0       0.49   10.1   0.0    1.4  2  AAA_15           AAA ATPase 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 !  106.0   0.0   2.2e-33   2.1e-30       2     136 ..      20     161 ..      19     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 2.2e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       + v+l++k  e  +++G++G+GKSt l+++agl++  +G+i +d++ +++   +  ++ +++++q   l p++tv +
  gi|557694099|ref|YP_008797153.1|  20 DGVDLEIKDKEFFVLLGPSGCGKSTTLNMIAGLETVSSGNIYFDDQLVND--VPPEKRDVAMVFQSFALYPTMTVFQ 94 
                                       789*****************************************999999..9999********************* PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e  +++ + ++ l++++l +++     ++LSgG+kqrvalara+++ pkl+llDEp 
  gi|557694099|ref|YP_008797153.1|  95 NiafplrirgydkvEIMRRVRETAEMLRIVHLLEKKP----HELSGGEKQRVALARAVVRSPKLFLLDEPL 161
                                       **********877777777888999999999887777....*****************************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 !   37.7   0.0   2.9e-12   2.7e-09       1      53 []     235     289 ..     235     289 .. 0.93

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 2.9e-12
                           OB_MalK   1 GSPaMNflpatveedg..vlvegggvtlplpeeqklalklyagkevilGiRPEhi 53 
                                       GSP+MNf+++  + +g  ++++ g ++++l+ + + al+   g e++lGiRP hi
  gi|557694099|ref|YP_008797153.1| 235 GSPPMNFFECSARIEGtnAVLDCGFFEVRLDSQYAEALSRLSGSELVLGIRPHHI 289
                                       9**********998888899999*******9998779999************998 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   1.8e-11   1.7e-08       1      76 []     282     354 ..     282     354 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.8e-11
                            TOBE_2   1 laiRPEklrla.aagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                       l+iRP ++++  ++++++++ G+V  ve lG++t++ ++++++   ++++++       ++Gd++ +++d+ +++v+
  gi|557694099|ref|YP_008797153.1| 282 LGIRPHHIKIFkNKEPNTTFDGEVFAVEPLGTETVVDIRVGDNIY-KAVTDPYF---SARIGDRIYVWLDINQIHVF 354
                                       79*********6556566************************976.66677776...789****************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 !    9.8   0.0   0.00066      0.62       1      25 [.      31      55 ..      31      84 .. 0.77
   2 !   11.7   0.0   0.00017      0.16     234     299 ..     131     194 ..     106     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00066
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                      + vl Gp g+GKS+ L  + +l  +
  gi|557694099|ref|YP_008797153.1| 31 FFVLLGPSGCGKSTTLNMIAGLETV 55
                                      68***************99999443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00017
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHSp 299
                                       ++elS G k+  al+ a+ r +   +l+l+DEp ++++ kl      el+++ ++ ++  i +TH+ 
  gi|557694099|ref|YP_008797153.1| 131 PHELSGGEKQRVALARAVVRSP---KLFLLDEPLSNIDAKLRVYMRaELIRLQKDLKTTTIYVTHDQ 194
                                       578899**99999999999999...9*************999666666666666667799*****86 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   7.4e-08   6.9e-05      38     123 ..      22     109 ..      11     165 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.4e-08
                             Rad17  38 dvLesrkkriLLisGPsGCgkstvvkvLsk.elgiklrewlnpvslkepdnqksdfkgltekesrflsqiesfke.. 111
                                         Le + k+  ++ GPsGCgkst++++++  e + + + + +  ++++ + +k d+  +++ +  + + + +f++  
  gi|557694099|ref|YP_008797153.1|  22 VDLEIKDKEFFVLLGPSGCGKSTTLNMIAGlETVSSGNIYFDDQLVNDVPPEKRDVAMVFQSFA-LYPTMTVFQNia 97 
                                       5689999999****************99972455556667788888888888899888888887.789999998733 PP

                             Rad17 112 leLkdakylklq 123
                                       + L+   y k++
  gi|557694099|ref|YP_008797153.1|  98 FPLRIRGYDKVE 109
                                       445555555443 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 !   17.7   0.0     2e-06    0.0019      23     205 ..      28     200 ..      18     213 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2e-06
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                       +k+f +++Gp G+GKs  l+ i    G ++ ++      ++l++        +k +v+++f+      ++ +   +i
  gi|557694099|ref|YP_008797153.1|  28 DKEFFVLLGPSGCGKSTTLNMI---AGLETVSSGNIYFDDQLVND----VPPEKRDVAMVFQSFALY-PTMTVFQNI 96 
                                       5789999999999999999999...56655544444444566665....444555555555554444.333333445 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                          +   g  +++i ++  + +e+ ++++  + ++++LSgGek+ vala       v+   l+llDe  +++D+k +
  gi|557694099|ref|YP_008797153.1|  97 AFPLRIRGYDKVEIMRRVRETAEMLRIVHLLEKKPHELSGGEKQRVALAR----AVVRSPKLFLLDEPLSNIDAKLR 169
                                       555555566677788888888888888888888999********988764....4567777******9999999865 PP

                                       H.HHHHHHH.HHCTTSEEEEE-SSHHHCCC- CS
                                       x.xxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 177 k.kvaellk.eksknaQfivislreemleka 205
                                           ael++ +k  ++  i +++++     +
  gi|557694099|ref|YP_008797153.1| 170 VyMRAELIRlQKDLKTTTIYVTHDQVEAMTM 200
                                       5055677763333345566666665444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.5e-06    0.0014      95     130 ..      24      60 ..       6      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                                       HHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  95 ellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                        ++kd ++ vl+G+SG GKSt +n++++ ++++ g++
  gi|557694099|ref|YP_008797153.1|  24 LEIKDkEFFVLLGPSGCGKSTTLNMIAGLETVSSGNI 60 
                                       556666899*****************99777766665 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.6e-06    0.0043       5      64 .]     299     353 ..     296     353 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.6e-06
                              TOBE   5 NqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                        ++ g+V +veplg e++V++++g+     A+ ++   ++    +G+++++ ++ +++h+
  gi|557694099|ref|YP_008797153.1| 299 TTFDGEVFAVEPLGTETVVDIRVGDNI-YKAVTDPYFSAR----IGDRIYVWLDINQIHV 353
                                       5899**********************9.899999999999....9999998888888875 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 !   15.4   0.1   1.2e-05     0.012      12      39 ..      19      46 ..      14      57 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                                       dg ++ei+ k++++l GpsG GKST l
  gi|557694099|ref|YP_008797153.1| 19 VDGVDLEIKDKEFFVLLGPSGCGKSTTL 46
                                      578899999999**************87 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 !   15.4   0.0   2.2e-05     0.021      20      43 .]     263     291 ..     240     291 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.2e-05
                   CysA_C_terminal  20 pvP.....elagadgqevvayVRPhDlei 43 
                                        +      +l    g+e v+++RPh++ i
  gi|557694099|ref|YP_008797153.1| 263 RLDsqyaeALSRLSGSELVLGIRPHHIKI 291
                                       44442432334449*************87 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   3.8e-05     0.036       4      27 ..      28      51 ..      24     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.8e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlle 27
                                      ++ + v+ G+sG+GK+t+l++++ 
  gi|557694099|ref|YP_008797153.1| 28 DKEFFVLLGPSGCGKSTTLNMIAG 51
                                      78899**************99875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   4.9e-05     0.046      15      39 ..      24      49 ..      11      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.9e-05
                            AAA_23 15 idF.skgltlItGpNGaGKTTildAi 39
                                      ++  +k ++++ Gp G+GK+T l+ i
  gi|557694099|ref|YP_008797153.1| 24 LEIkDKEFFVLLGPSGCGKSTTLNMI 49
                                      44468899***************988 PP

>> AAA_16  AAA ATPase domain
   #    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      25      45 ..      30      50 ..      21      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                            AAA_16 25 elvllsGesGvGKsslvrell 45
                                      e  +l G+sG+GKs+ +++++
  gi|557694099|ref|YP_008797153.1| 30 EFFVLLGPSGCGKSTTLNMIA 50
                                      6789*************9987 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.14       4      25 ..      33      54 ..      31      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                      EEESSTTSSHHHHHHHHHTS-- CS
                              AIG1  4 vlvGktgnGkSaTgNsilgkka 25
                                      vl+G +g+GkS+T N i g + 
  gi|557694099|ref|YP_008797153.1| 33 VLLGPSGCGKSTTLNMIAGLET 54
                                      9****************88665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00068      0.64       2      19 ..      33      50 ..      32      70 .. 0.81
   2 ?   -1.0   0.0       2.4   2.2e+03      32      62 ..     323     352 ..     308     360 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00068
                      RNA_helicase  2 wlyGpsgeGKStlakeLa 19
                                      +l Gpsg+GKSt+ + +a
  gi|557694099|ref|YP_008797153.1| 33 VLLGPSGCGKSTTLNMIA 50
                                      689**********99844 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.4
                      RNA_helicase  32 dsvysrnpeddfwdgYtgqevvvidDfgqvk 62 
                                       d++y ++++d +++   g  + v+ D++q++
  gi|557694099|ref|YP_008797153.1| 323 DNIY-KAVTDPYFSARIGDRIYVWLDINQIH 352
                                       4554.68899999999999*******99976 PP

>> MIT_C  Phospholipase D-like domain at C-terminus of MIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00029      0.28      66     124 ..     173     233 ..     159     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                             MIT_C  66 kenleelkesleklgielevef..sstihdreirldngwiikigrGLdifkkseskfslgs 124
                                       +++l +l+++l+++ i ++ +     t+ dr  +++ g i+++g  +++fkk+ + f  g 
  gi|557694099|ref|YP_008797153.1| 173 RAELIRLQKDLKTTTIYVTHDQveAMTMGDRIAVMNAGKIMQVGEPMEVFKKPANLFVAGF 233
                                       678999**********9999876678999************************99998654 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 ?    8.8   0.1    0.0019       1.8      26      81 ..     127     169 ..     100     177 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0019
                           SbcCD_C  26 lsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesi 81 
                                       l+++  +lSGGekq    +ala   +a+++       +++l++LDE  s++D++ +
  gi|557694099|ref|YP_008797153.1| 127 LEKKPHELSGGEKQR---VALA---RAVVR-------SPKLFLLDEPLSNIDAKLR 169
                                       677778899999953...4444...33334.......4899999999999998865 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00046      0.44       2      20 ..      32      50 ..      31      62 .. 0.86
   2 ?   -2.0   0.0       3.9   3.7e+03      63      90 ..     140     169 ..     112     197 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      +v++G++++GK+t+l+ +a
  gi|557694099|ref|YP_008797153.1| 32 FVLLGPSGCGKSTTLNMIA 50
                                      79*************9988 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.9
                            AAA_28  63 qleeeaaa..aankvlfcDrglldtlaYar 90 
                                       q+ ++a+a  +++k++++D  l ++ a +r
  gi|557694099|ref|YP_008797153.1| 140 QRVALARAvvRSPKLFLLDEPLSNIDAKLR 169
                                       333444446677777777766655443333 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00052      0.49      18      50 ..      23      56 ..      19     102 .. 0.79
   2 ?   -3.5   0.0       6.7   6.3e+03     328     365 ..     156     193 ..     150     195 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00052
                            AAA_15 18 eidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      +++++++ + vl G+ ++GKS+ l+++  + + +
  gi|557694099|ref|YP_008797153.1| 23 DLEIKDKeFFVLLGPSGCGKSTTLNMIAGLETVS 56
                                      45555556******************97666655 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6.7
                            AAA_15 328 liEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       l++EP  ++  ++   +   l++l +d kt +i+ TH 
  gi|557694099|ref|YP_008797153.1| 156 LLDEPLSNIDAKLRVYMRAELIRLQKDLKTTTIYVTHD 193
                                       55555555555555566666777777777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2896.15
//
Query:       gi|557694100|ref|YP_008797154.1|  [L=291]
Description: multiple sugar ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   74.2  17.5    1.1e-20   74.2  17.5    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
        4.9    8.1   9.2       0.48   11.4   0.9    2.9  3  PIG-Y         Phosphatidylinositol N-acetylglucosaminyltransf


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 ?   -0.4   1.1      0.09     8e+02     144     144 ..      41      41 ..       3     101 .. 0.45
   2 !   74.2  17.5   1.2e-24   1.1e-20       1     180 [.     100     277 ..     100     281 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.09
                      BPD_transp_1 144 a 144
                                       a
  gi|557694100|ref|YP_008797154.1|  41 A 41 
                                       0 PP

  == domain 2  score: 74.2 bits;  conditional E-value: 1.2e-24
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalr 77 
                                       ++++G+ ++ + + k + +l  +  + +slP++ +a++ +++ + +++l  + l++ii+ l+ ++p+v++i  +++ 
  gi|557694100|ref|YP_008797154.1| 100 AVPAGYALG-RLKVKARSILILFLLASRSLPPVSVALPYFFL-FSQTGLRATLLGMIIIHLTITIPIVTWILMGFFA 174
                                       5899*****.999***********************997743.7788****************************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                       +lp+dl++aar++G+sr   f++vvlP+a+p i++++++af ++++++++  +l   +G    + +a+l+  +++ +
  gi|557694100|ref|YP_008797154.1| 175 ALPRDLEKAARLDGCSRLGAFYRVVLPMAAPGIAATAVIAFLFSWNDFFFSWLLS--QGTPAATYNAQLSGFFNFQN 249
                                       ************************************************9876666..56899999999999999999 PP

                      BPD_transp_1 155 ..nggvlalviavlllnlvadilqrlld 180
                                         +  ++a+ + + l  +va +lq+++ 
  gi|557694100|ref|YP_008797154.1| 250 epAMFAAAVMLQISLAAVVAIALQKYIV 277
                                       7544555555556666677777777776 PP

>> PIG-Y  Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.2     1e+04      10      18 ..      91      99 ..      84     124 .. 0.63
   2 ?    1.5   0.1     0.067     6e+02       1      51 [.     152     204 ..     148     207 .. 0.45
   3 ?   11.4   0.9   5.3e-05      0.48       4      59 ..     207     270 ..     205     272 .. 0.66

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                             PIG-Y 10 llfivgmya 18
                                      +++++++ +
  gi|557694100|ref|YP_008797154.1| 91 IVMVITITT 99
                                      333333333 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.067
                             PIG-Y   1 Gyallltsvllfivgmyavlfskll.r.lgeaplsppvladd....ryYcylvplli 51 
                                       G++++ +++++ iv+   + f ++l r l++     + l+       +Y +++p+ +
  gi|557694100|ref|YP_008797154.1| 152 GMIIIHLTITIPIVTWILMGFFAALpRdLEK----AARLDGCsrlgAFYRVVLPMAA 204
                                       4555555665555544444422222111111....1112222334447777777765 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 5.3e-05
                             PIG-Y   4 llltsvllfivgmyavlfskll.r.lgeaplsppv.....ladd.ryYcylvpllipvtlvfvi 59 
                                       +++t+v++f+++ + ++fs+ll + ++ a+++ +      ++++   +   v+l+i  + v++i
  gi|557694100|ref|YP_008797154.1| 207 IAATAVIAFLFSWNDFFFSWLLsQgTPAATYNAQLsgffnFQNEpAMFAAAVMLQISLAAVVAI 270
                                       7899*****************9323444444433355544333345777777777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2365.41
//
Query:       gi|557694101|ref|YP_008797155.1|  [L=288]
Description: multiple sugar ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-07   30.6  24.6    2.6e-07   30.6  24.6    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.24   11.3   0.1       0.52   10.2   0.1    1.6  1  PIP49_N       N-term cysteine-rich ER, FAM69


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 ?   -3.2   3.6      0.64   5.8e+03      21      35 ..      14      28 ..       2      85 .. 0.59
   2 !   30.6  24.6   2.9e-11   2.6e-07       4     172 ..      86     280 ..      81     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.64
                      BPD_transp_1 21 rpliivllslPsfvl 35
                                       plii+++s+ ++ +
  gi|557694101|ref|YP_008797155.1| 14 VPLIILVFSINIYPI 28
                                      233333333333333 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 2.9e-11
                      BPD_transp_1   4 lGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.....................vilsilghlilpviil 59 
                                       +Gi + ln +  l+ +l +l+i++++l  f++ai   +++                     ++l    +++ +++i 
  gi|557694101|ref|YP_008797155.1|  86 IGIALVLNEKTALTPVLKVLVILPWALSEFAVAIAGRFFLdrnygflnalllhlglvdkpiYFL-NPVNAVDWLAIF 161
                                       44444478999999*********************88766999999999999999999995444.555566667899 PP

                      BPD_transp_1  60 lllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalp.piitglilafggllggavlleflgswp 135
                                       +++ ++p+  +++ +al+++p+dl++ a ++Gas + +fr +++P +   ++it+++ ++ ++    ++  ++g++p
  gi|557694101|ref|YP_008797155.1| 162 YAWNITPIGAYFILSALQTIPEDLYRQAQVDGASAFWRFRIITFPFIRYaVLITTVLATILSASSLVLAFALTGGGP 238
                                       ***********************************************8615566666666666788888899999** PP

                      BPD_transp_1 136 Glgtllleailgydyseis.....nggvlalviavlllnlva 172
                                       G+ ++  + ++ + + +++     +++++ l+i+v++ ++++
  gi|557694101|ref|YP_008797155.1| 239 GFASTPATLYSFRVFFNAQdfgygAAMSWLLLIFVMIGSIFY 280
                                       *99999999999999999995555555555555555555554 PP

>> PIP49_N  N-term cysteine-rich ER, FAM69
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   5.8e-05      0.52       2      36 ..       2      37 ..       1      65 [. 0.84

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.8e-05
                           PIP49_N  2 RlsalrvkYlllvllavavlswvvY.vqyssyselC 36
                                      Rls   v  ll+v l+++v+s+ +Y + ys++  l 
  gi|557694101|ref|YP_008797155.1|  2 RLSDTGVALLLVVPLIILVFSINIYpIAYSFWLSLN 37
                                      9999999*************************7664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); 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 0.21s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2352.58
//
Query:       gi|557694102|ref|YP_008797156.1|  [L=507]
Description: hypothetical protein CSUB_C0667 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   64.1   1.9      3e-17   63.4   1.9    1.3  1  SBP_bac_8  Bacterial extracellular solute-binding protein
    4.6e-08   33.4   4.0    7.5e-08   32.7   4.0    1.3  1  SBP_bac_1  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   1.9   3.3e-21     3e-17       2     260 ..     107     410 ..     106     430 .. 0.76

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 3.3e-21
                                       HHHHHHHH-TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH.....-HH CS
                         SBP_bac_8   2 lakefekktgvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnldd.....ltd 73 
                                       ++k+fe+  g kv+ +  a + +++ l a+ +ag+   id+ +an   +a+l++ g + d+++++++++     +++
  gi|557694102|ref|YP_008797156.1| 107 YVKKFEEYFGEKVTEIHLANENYNPLLEAKFQAGDI--IDMCYANFFEAARLIQLGFTRDVESFPEIKQiksemYPS 181
                                       699*******************************98..566666666799************999999977786677 PP

                                       HHHTT.--TS.----EEEEEEE-EEEEEHHHHHHS.....---BHHHHHHHHHHHH..HH-...SEGG---G..... CS
                         SBP_bac_8  74 alaav.gydgklygvPyasetpyvliynkdlleka....edpktwdellaaakklk..gkf...glpdpasg..... 135
                                        ++a+ ++dgkl+g+Py ++   + ++n+++leka    e p twdel+++a ++k  g++    +p + +      
  gi|557694102|ref|YP_008797156.1| 182 IVEAYsTVDGKLAGLPYFWSARSAPVVNDSILEKAgmagERPGTWDELWDMARDIKaaGAAdtpVMPHWFNAnygit 258
                                       99999777************988***********9999***************997434446664444433211232 PP

                                       GGGGGTHH.................ETTEE---H..HHH.HHHHHHHHHHHHTT-EE......-S..--SSTTTTTS CS
                         SBP_bac_8 136 wlqaalla.................kdgksldddggkdglkealellkklkdngkty......dtgadavsefanGe 189
                                       w +    a                 k  +++ d   + ++ e l+ +++  + g +         ++d vs++ +G+
  gi|557694102|ref|YP_008797156.1| 259 WDFL---AemsnvyndpdltqtlfnKKFEPVFDA--NTEVGELLRTWQQVFKEGLVDptvlaqAGDSDHVSAIVTGK 330
                                       2122...133455444433333333333333333..5555777777777778887445558866778999******* PP

                                       BSEEEE-TTHHHHHH-TTT.SEEEE....--..S--.EEEEEEEEEEBTTS-HHHHHHHHHHHHH..TTSHHHHHHH CS
                         SBP_bac_8 190 vaftingswdiaaaqkagk.klgai....vp..kqg.sfaggkglavpknaknedlaAldFlkwl..tspenqaala 256
                                       +aft++    +  +++ ++ ++ ++    vp  k+g  ++++  ++ p+++++  + +++++k+l   +p++ + +a
  gi|557694102|ref|YP_008797156.1| 331 YAFTPTALYYFKVLNDPSQsRIPVGkanlVPvtKSGwGVIDTGLYCWPNKTTDDFR-SQRLIKFLgwRTPDGERLTA 406
                                       ***************88655555554366677788899****************98.*******9545888888777 PP

                                       HHH- CS
                         SBP_bac_8 257 ektg 260
                                       +++ 
  gi|557694102|ref|YP_008797156.1| 407 TAWA 410
                                       7665 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 !   32.7   4.0   8.4e-12   7.5e-08      12     249 ..     106     345 ..      99     372 .. 0.67

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 8.4e-12
                                       HHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTCC CS
                         SBP_bac_1  12 alvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvkd 88 
                                        +v k+fe+ + g kV+ +     ++   l + ++aGd  +D+ +        + +a+ l+ l+   + +  p+ k+
  gi|557694102|ref|YP_008797156.1| 106 SYV-KKFEE-YFGEKVTEIHLANENYNPLLEAKFQAGD-IIDMCYA------NFFEAARLIQLGFTRDVESFPEIKQ 173
                                       566.77777.7788888777777777776777777777.5555555......3333455555555555555555555 PP

                                       TEEEEHHHHTHHHHC.E.EE...ES.EEEE.E.EEEEEEETTTHHCTTGGG..SHBHHHHHHHHHHHHHHCTCT..H CS
                         SBP_bac_1  89 aadklsssvlpkild.s.kv...ly.vPly.a.argliYNkdlfekagldp..pwtWdelveaakklkekgkkp..i 153
                                        ++      +p+i + + +v   l  +P+  +  ++ ++N +++ekag+++  p tWdel + a+ +k++g ++  +
  gi|557694102|ref|YP_008797156.1| 174 IKSE----MYPSIVEaYsTVdgkLAgLPYFwSaRSAPVVNDSILEKAGMAGerPGTWDELWDMARDIKAAGAADtpV 246
                                       4444....566666644444789999*************************************************55 PP

                                       CCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCT.HHCSHHHHSHHHHHHHHHHHHHHHHHHHTTEEECSSHHHH..H CS
                         SBP_bac_1 154 ggarggsasgtayyfalalakslggkvfdkdgg.gldnpegvtaatylvklyavanltkelkgkgaenkdgaaa..l 227
                                          ++ ++ g ++ f+ +++++++ +  ++    ++  p++  +++ ++ l  ++ ++ke   +++  ++  +   +
  gi|557694102|ref|YP_008797156.1| 247 MPHWFNANYGITWDFLAEMSNVYNDPDLTQTLFnKKFEPVFDANTEVGELLRTWQQVFKEGLVDPTVLAQAGDSdhV 323
                                       555555678999999999******66666666565555555555555555555555544444433333332222003 PP

                                       HHHHTTSCSEEEEEHHHHHHHH CS
                         SBP_bac_1 228 alfeaGeaamaivglwaalaam 249
                                       +++ +G+ a++   l++ ++ +
  gi|557694102|ref|YP_008797156.1| 324 SAIVTGKYAFTPTALYYFKVLN 345
                                       3333788888877777755554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.37
# Mc/sec: 4135.51
//
Query:       gi|557694103|ref|YP_008797157.1|  [L=366]
Description: alanine racemase domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-31  108.6   0.1    4.5e-31  108.2   0.1    1.1  1  Ala_racemase_N  Alanine racemase, N-terminal domain
    2.4e-22   79.4   0.1    5.4e-22   78.3   0.1    1.6  1  D-ser_dehydrat  Putative serine dehydratase domain
  ------ inclusion threshold ------
      0.018   14.3   0.1      0.026   13.8   0.1    1.2  1  DUF3834         Protein of unknown function (DUF3834)


Domain annotation for each model (and alignments):
>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.2   0.1   7.5e-35   4.5e-31       1     216 [.      19     243 ..      19     245 .. 0.85

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 7.5e-35
                                       EEHHHHHHHHHHHHHHSCT.TSEEEEE-HHHHHTTHHHHHHHHHHHTTESEEEESSHHHHHHHHHTTSCSEEEEESC CS
                    Ala_racemase_N   1 idldalrhNlrrlralagp.gaklmavvKanayghgavevaralaeggadgfgvatleEalelreagitapilvleg 76 
                                       +d + l++N+  +++ a++ g+kl+++vK+ ++  ++   a ++ e+gadg++v++l Ea+ ++eag++  ilv + 
  gi|557694103|ref|YP_008797157.1|  19 VDVKVLKRNITEMADFARSlGKKLRPHVKT-HKTPEI---AWMQMEAGADGICVQKLGEAEVMAEAGLDD-ILVSNE 90 
                                       578889***********556**********.555555...55555678*******************665.888888 PP

                                       ....STGGGHHHHHHT.TEEEEESSHHHHHHHHHHHHHTTS-EEEEEEBESSSSSSSBSCHHHHHHHHHHHHTTTEE CS
                    Ala_racemase_N  77 ....fspeelaalaey.dltvtvdsleqlealaaaareagkplrvhlkidtgmgRlGftpeeleellealaalpglr 148
                                            +  +l +lae  +l+v+vd+ e++ +l ++ re+g  + v + +d+gm+R G++pe++  l+e++++ +g+ 
  gi|557694103|ref|YP_008797157.1|  91 vvgvQKMHRLVKLAEKvKLSVAVDDVENVSELGRFCRENGVEVGVYVDVDCGMHRTGVPPEKAWLLAEKVTRTEGVY 167
                                       74433555566666677*******************************************9999************* PP

                                       EEEEE-S-SST......TSTS.HHHHHHHHHHHHHHHHHHHTTGGGSEEEEESHHHHHHSG.GG.TTEEEESGGGGT CS
                    Ala_racemase_N 149 leglmtHfasa......depd.eeteaqlarfeealeelekaglrppvvslanSaaillaa.ah.fdmvRpGialyG 216
                                       l+glm + ++a      +e + + +e+ +++  +a++ ++++g++p  vs+++Sa++     ++ +++++pG++++ 
  gi|557694103|ref|YP_008797157.1| 168 LVGLMGYEGHAgsptsrEE-RhKLIEEAVKATLHAAKLMKNNGIEPGEVSMGSSATVRVSGrYEgVTELQPGMYVFN 243
                                       ***********66665333.24677778888899999999999***************9954667********9986 PP

>> D-ser_dehydrat  Putative serine dehydratase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.1     9e-26   5.4e-22       1      94 [.     259     346 ..     259     348 .. 0.88

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 9e-26
                                       -EEEEEEEEEEETTTTEEES--HHHH-S-S.S--BT-EEE-TTSEEEEB-..EE-SS-EEEE--TT-GGGS-TT-EE CS
                    D-ser_dehydrat   1 AlavlatVvSrptarralvdaGskalslds.sgpgfgkvvagleegwvvsvrrlsdEhgiltleeesaddlrvGdvv 76 
                                       Al+vl+tV+S+  ++r++vdaGska+ ld  ++p +  v         v++ +ls+Ehg+++l+ ++ d++++Gd++
  gi|557694103|ref|YP_008797157.1| 259 ALHVLTTVMSKTSPERCVVDAGSKAFHLDMgRYPVCVGVE-------GVEIYKLSEEHGWVKLSGKAVDKVKLGDRL 328
                                       89***************************64444433333.......56688************999********** PP

                                       EEE-S-HHHHHTT-SEEE CS
                    D-ser_dehydrat  77 rlipnHaCptvnlhdayv 94 
                                       ++ip H+Cp+vn++d ++
  gi|557694103|ref|YP_008797157.1| 329 EFIPYHVCPCVNQFDIMY 346
                                       ***************987 PP

>> DUF3834  Protein of unknown function (DUF3834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.3e-06     0.026      66     149 ..      61     145 ..       2     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.3e-06
                           DUF3834  66 igkekIavwrkGsaaDvllrilldlkkikaevvyaddpeevlkllnegevdsav..vaselkkgeafedllkklgvy 140
                                        g + I v + G  a v++ + ld   +++evv  +++++++kl+++ +++ av  v+++ + g +  +   ++gvy
  gi|557694103|ref|YP_008797157.1|  61 AGADGICVQKLGE-AEVMAEAGLDDILVSNEVVGVQKMHRLVKLAEKVKLSVAVddVENVSELGRFCRENGVEVGVY 136
                                       5555676666665.789*********************************98885566889999999777667**** PP

                           DUF3834 141 vpGsCgaav 149
                                       v   Cg++ 
  gi|557694103|ref|YP_008797157.1| 137 VDVDCGMHR 145
                                       *****9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2563.81
//
Query:       gi|557694104|ref|YP_008797158.1|  [L=332]
Description: F420-dependent alcohol dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-52  176.6   0.0    1.2e-51  176.0   0.0    1.2  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.0   0.0   6.7e-56   1.2e-51      28     314 .]      24     304 ..      10     304 .. 0.92

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 6.7e-56
                    Bac_luciferase  28 laraaEelGfdavwvaehhggpgga....ldaftllaalaaaTerirlgtavtply..trhPavlAqqaatLdhlsg 98 
                                       +  + E++Gfd++w+++h ++++++    +  + +laa+a++T++i lg+ vt++   ++hPa++Aq+  tLd++++
  gi|557694104|ref|YP_008797158.1|  24 FLGLCEKAGFDSLWFGDHFLPWHHSfkhnFFVWPVLAAAAERTKKILLGVDVTVPIggRYHPAIIAQAMGTLDNMYP 100
                                       55678************************99*******************99999889******************* PP

                    Bac_luciferase  99 GRfglglgtggpaveerrfGv..dhderyarlrEfvevlrrlwrgeev.dfeGeffsvkgalllprpgqgpiPvyva 172
                                        Rf lg+gtg++++e r +G+  +++er +rl E+++++++lw++++  df+G++fs+ +++l  +p++  iP+y+ 
  gi|557694104|ref|YP_008797158.1| 101 SRFLLGVGTGEAMSEKRFMGRwpPWRERMERLVEALDLIKKLWSSRDYfDFDGKYFSMSKVYLHLKPKKS-IPIYFS 176
                                       *******************************************887777**************9999888.****** PP

                    Bac_luciferase 173 aaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearaliagld 249
                                       a +++++ +a++++d l++a+  +    + ++ ++++aaeagr p +i+ ++ l  +v d ++  ++ ++++     
  gi|557694104|ref|YP_008797158.1| 177 AIGEKAATYAGKYGDRLITANTLENCRDKIFPAFEKAAAEAGRNPRRIEKAVLLEGAVVDIDKTIKR-IKRIH---- 248
                                       *********************9999999999***************999999888888754444444.44444.... PP

                    Bac_luciferase 250 fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatal.vGtpeqvaerlaayaeagvde 314
                                                 ++a+  e+++eed+++ ++ +  ++de +++ +l   + ++ ++ l+++++ g+++
  gi|557694104|ref|YP_008797158.1| 249 ----------AGATIMENFNEEDPRKIEESGLRLSDEAIRNYYLlYEDVDDLIDHLDQFRKIGANH 304
                                       ..........5667789*************************99999**************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2596.15
//
Query:       gi|557694105|ref|YP_008797159.1|  [L=300]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  101.6  32.5    1.1e-15   58.0  10.4    2.1  2  EamA           EamA-like transporter family
  ------ inclusion threshold ------
      0.034   13.3  12.3       0.16   11.0   2.9    3.1  3  Mg_trans_NIPA  Magnesium transporter NIPA
       0.12   12.1   0.2       0.32   10.8   0.2    1.7  1  DUF4748        Domain of unknown function (DUF4748)


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 !   58.0  10.4   1.8e-19   1.1e-15       4     136 ..       6     144 ..       3     145 .. 0.92
   2 !   49.9  14.1     6e-17   3.6e-13       2     135 ..     155     289 ..     154     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 1.8e-19
                              EamA   4 illallaalfwaiyfvlskillrkv....spltltfvrfliagillliiallkegkl..aklslkdwllllllgllg 74 
                                       +l++ +a+++w+++ ++++++l++v    ++l+++f++++++ ++l+++++ + g +  + l ++++++   +g+l 
  gi|557694105|ref|YP_008797159.1|   6 YLYLAIASILWGSGHPVIRYILADVnsqmNSLHVAFLSTVVGMVILSVVLASRHGLKrlKMLGRRGLAIAGAVGCLQ 82 
                                       78999****************988855557779*************999888888887888889999999******* PP

                              EamA  75 tvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                         l+++l ++al++++as  ++i+  +P+++++ls ++l+e+l+   + gi+l+++++++++
  gi|557694105|ref|YP_008797159.1|  83 YGLYPILSYTALSYIPASLNAIIVGSSPMLIALLSRAVLREQLKMVGYGGILLAFASLFILV 144
                                       **********************************************************9986 PP

  == domain 2  score: 49.9 bits;  conditional E-value: 6e-17
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl..aklslkdwllllllgllgtv 76 
                                       lg++l  ++al+ +iy+v+ ++l+r+++ ++++ + + ++ ++l  ++  + g     + ++ d+ll+ + g ++++
  gi|557694105|ref|YP_008797159.1| 155 LGLVLSSAGALVASIYAVAGRYLMRSHDAFAVSQFGTSVGLLVLTSVTYSQSGLGglLNSDVMDLLLVTYWG-IAVT 230
                                       578888999***************************999999998888888888866666666777778888.6999 PP

                              EamA  77 lafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                        ++llf+ alkk++a++a+ +++++P+ ++ lsv++lge+lt++ +lg+v  l+G+ l+
  gi|557694105|ref|YP_008797159.1| 231 TGNLLFYLALKKLDAARAGSFFFVSPMAAATLSVIFLGEPLTVLMVLGMVATLMGIRLT 289
                                       999****************************************************9875 PP

>> Mg_trans_NIPA  Magnesium transporter NIPA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.2      0.05     3e+02      85     109 ..      48      72 ..       8      87 .. 0.69
   2 ?   11.0   2.9   2.7e-05      0.16      60     120 ..      84     144 ..      73     148 .. 0.88
   3 ?    6.9   0.2   0.00049       2.9      85     116 ..     255     286 ..     245     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.05
                     Mg_trans_NIPA  85 svivsavlasllLkekLkllgllGc 109
                                        vi+s vlas+    +Lk+lg  G+
  gi|557694105|ref|YP_008797159.1|  48 MVILSVVLASRHGLKRLKMLGRRGL 72 
                                       2677777777777777777777664 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 2.7e-05
                     Mg_trans_NIPA  60 avGeaanfaayafaPatLvtPLGalsvivsavlasllLkekLkllgllGcllailGstvlv 120
                                       ++  +  ++a ++ Pa+L + +   s ++ a+l+  +L+e+Lk++g  G+lla++   +lv
  gi|557694105|ref|YP_008797159.1|  84 GLYPILSYTALSYIPASLNAIIVGSSPMLIALLSRAVLREQLKMVGYGGILLAFASLFILV 144
                                       55556678999*********9999999999************************9988887 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.00049
                     Mg_trans_NIPA  85 svivsavlasllLkekLkllgllGcllailGs 116
                                       s + +a l++++L e L +l +lG++ +++G 
  gi|557694105|ref|YP_008797159.1| 255 SPMAAATLSVIFLGEPLTVLMVLGMVATLMGI 286
                                       556789***********************996 PP

>> DUF4748  Domain of unknown function (DUF4748)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   5.3e-05      0.32       9      33 ..     225     249 ..     222     253 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.3e-05
                           DUF4748   9 WgslcvaGigayyfAKrsidadRaa 33 
                                       Wg+ + +G +++y+A ++ da Ra 
  gi|557694105|ref|YP_008797159.1| 225 WGIAVTTGNLLFYLALKKLDAARAG 249
                                       ***********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); 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:                         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 0.22s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2342.43
//
Query:       gi|557694106|ref|YP_008797160.1|  [L=357]
Description: N5,N10-methylenetetrahydromethanopterin reductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  194.7   0.0    2.9e-57  194.5   0.0    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.5   0.0   1.6e-61   2.9e-57      15     313 ..      11     324 ..       4     325 .. 0.91

  Alignments for each domain:
  == domain 1  score: 194.5 bits;  conditional E-value: 1.6e-61
                    Bac_luciferase  15 lgaasaslrylvelaraaEelGfdavwvaehhggpgga...ldaftllaalaaaTerirlgtavtplytrhPavlAq 88 
                                         +++++++++++la +a++l +d v +++h  +p  +   ++a tllaa    T+++r+ tavt  y+rhP+ +Aq
  gi|557694106|ref|YP_008797160.1|  11 IITSQHTIDEILRLAILADKLSYDHVRIGDHVIVPNAEvsyPNAQTLLAAFGVLTKHVRISTAVTDCYRRHPVEIAQ 87 
                                       5566789***************************9999*************************************** PP

                    Bac_luciferase  89 qaatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrg..eev.dfeGeffsvkgalllprp 162
                                       ++atLd l++GR++lg+g+g+ ++    fG+++ ++++rlrE+vev++ l+++  + + ++eGe fs+k+a+l+ +p
  gi|557694106|ref|YP_008797160.1|  88 AIATLDVLTHGRAVLGIGAGEMMNL-SPFGIEWTKPVKRLREAVEVINLLLAStpKSPaTYEGEIFSLKKAYLQIKP 163
                                       ************************9.*************************77887777****************** PP

                    Bac_luciferase 163 gqgpiP.vyvaaaspaglelaarhadglllag.eppeeaaelierlragaaeagrdpadirvgisltvivadteeeA 237
                                       +q+p+P +y++aa+ +++el + ++dg+l++g e+p+ +++++ +++ ga++ +r+ ++i++ + + ++v+++ e A
  gi|557694106|ref|YP_008797160.1| 164 VQKPRPpIYIGAAGCKTRELVGMVGDGWLPVGvESPQTLKKHLLDVKNGAERTSRQISNIDIDVTVYTAVDEDIENA 240
                                       ****656********************************************************************** PP

                    Bac_luciferase 238 raearaliagld........fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaa 306
                                        + +   ++++              ++  +   ++   +++e+ ++++++ ++vp+  v+  a+ G+ + v+ +l++
  gi|557694106|ref|YP_008797160.1| 241 YRVVSPAVKSMLvqqrevlrELTGLEVPENLSLQRIDPTDKERLMSFEEMVKQVPRSAVEDVAAFGPIDSVIGKLEE 317
                                       ****88885555886677643333333333344444669999999******************************** PP

                    Bac_luciferase 307 yaeagvd 313
                                       + +ag++
  gi|557694106|ref|YP_008797160.1| 318 FLGAGAT 324
                                       ***9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.50
# Mc/sec: 2151.91
//
Query:       gi|557694107|ref|YP_008797161.1|  [L=528]
Description: thermosome alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-112  374.7   0.0   7.2e-112  374.5   0.0    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 !  374.5   0.0    4e-116  7.2e-112       1     487 [.      20     504 ..      20     508 .. 0.96

  Alignments for each domain:
  == domain 1  score: 374.5 bits;  conditional E-value: 4e-116
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +ad++++++GP Gm K+l  ++g+ +vT+D++ i +e+ + hP+akll ea +++ +e GDG  t+v+La+ L+e++
  gi|557694107|ref|YP_008797161.1|  20 VADLFSSSFGPAGMAKLLLMDNGDFKVTRDAEIISSEVAFVHPVAKLLMEAGTTCRKEGGDGFITTVVLAALLVERG 96 
                                       6899************************************************************************* PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCH CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.kli 153
                                        +l ++g+hp     gy+ al++al++++    + +++  d ++L+k+a+  l +kl  ++ae+l+ +vv A+  + 
  gi|557694107|ref|YP_008797161.1|  97 WRLANNGIHPALTATGYQLALKEALKIIDIE--SSHIDFHDYSTLKKIAKNHLATKLPLSWAEHLAPIVVSALiGVS 171
                                       ****************************644..555566788*******************************8777 PP

                                       CCCS..EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                        Cpn60_TCP1 154 eene..keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                       e+ +  +++dl++ikv    g s+edselv+G++l k+ + + mpk++++ak++ ++ +L i+++++ t+vvls+++
  gi|557694107|ref|YP_008797161.1| 172 ESVNgyTKFDLDMIKVDGRRGASVEDSELVDGVILHKKGVDRLMPKTITDAKIAFIQEKLGIKRPDMFTKVVLSTPN 248
                                       77779************************************************************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGG CS
                        Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledlt 305
                                       +++++ ++   +l++ l+ + + gvnvv+c ++i +++   la  gila+r+v  +d++rl  a+G+++v+++ dl+
  gi|557694107|ref|YP_008797161.1| 249 KIKDFYSERLSYLRDFLDPLLRIGVNVVLCGGDIAEELRRPLANCGILAVRNVALEDMKRLRMAVGGELVMRPWDLN 325
                                       ***************************************************************************** PP

                                       CGC-EEEEEE.EECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHH CS
                        Cpn60_TCP1 306 peelGtakkv.eeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatel 381
                                       +++lG+++++ ++     +++++++++++++  +il+rg  d v+de++rai ++l+ ++++++++ vv+GGG +e 
  gi|557694107|ref|YP_008797161.1| 326 SQSLGYCGRIdQRIVAAHDEWLFFKNCRNPHFKSILVRGTGDFVVDEVKRAIINCLKLLQSLLKNGAVVAGGGFIEY 402
                                       **********555555669********************************************************** PP

                                       HHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCT CS
                        Cpn60_TCP1 382 elakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveag 458
                                       ++a++l++ a s++++ q  +++fa+ALe++p  L +N G dp +v  klr++ +++     id  +ge+   +++ 
  gi|557694107|ref|YP_008797161.1| 403 KIAHMLRKLALSYPSKIQQTVQVFADALEELPLWLVRNTGGDPANVKGKLRSGIAANM-LCSIDGYTGEV---IKSS 475
                                       ****************************************************999999.99999999986...788* PP

                                       XEEEHHHHHHHHHHHHHHHHHHHCEEEEE CS
                        Cpn60_TCP1 459 vvDplkvkrqalksAteaastiLrideii 487
                                       + +p+ vk q+lksAte+a tiLrid + 
  gi|557694107|ref|YP_008797161.1| 476 ITEPAIVKIQCLKSATETAVTILRIDHVF 504
                                       **************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3387.91
//
Query:       gi|557694108|ref|YP_008797162.1|  [L=432]
Description: enolase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-90  303.6   0.0    1.7e-90  303.2   0.0    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
    1.5e-47  161.0   0.0    2.5e-47  160.3   0.0    1.4  1  Enolase_N  Enolase, N-terminal domain
    1.1e-05   25.1   0.0    1.8e-05   24.4   0.0    1.3  1  MR_MLE_C   Enolase C-terminal domain-like
     0.0024   17.1   0.3       0.01   15.0   0.0    2.0  2  MAAL_C     Methylaspartate ammonia-lyase C-terminus


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 !  303.2   0.0   3.9e-94   1.7e-90       3     293 ..     142     424 ..     140     427 .. 0.98

  Alignments for each domain:
  == domain 1  score: 303.2 bits;  conditional E-value: 3.9e-94
                                       EE-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSH CS
                         Enolase_C   3 vlPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsn 79 
                                       ++P P++n+i GG+ha  +l++q+++i+P+ga++f eal     vyh+lk++l kk+   +t + deGGf+P+ ++ 
  gi|557694108|ref|YP_008797162.1| 142 IIPTPMVNIISGGHHAAWNLDIQDLLIIPIGAKNFVEALENVGAVYHNLKQLLMKKG--LTTLLADEGGFSPDCRNH 216
                                       89***************************************99**************..99**************** PP

                                       HHHHHHHHHHHHHCT-TC..TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEE CS
                         Enolase_C  80 kealdliveaiekaGykg..kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsi 154
                                       +ea++li +a+e++G ++  ++ +aldva+s ++  kd+ y l+ ++       +l+s++l+d++++l++ yPivs+
  gi|557694108|ref|YP_008797162.1| 217 REAIELILAAVEETGLTPktDIALALDVAASHLF--KDGSYMLSREG------LTLSSHELVDFLVDLCETYPIVSV 285
                                       ****************98778999**********..889******99......89********************** PP

                                       ES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EE CS
                         Enolase_C 155 edpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygv 231
                                       ed+  edd ++w++l+++l  kvqivGddl+ tn+kr++ +     a a l+k nq+G+lte+lea++l+k+ g   
  gi|557694108|ref|YP_008797162.1| 286 EDGCGEDDLDGWQYLFQKLSGKVQIVGDDLFATNVKRIRMCSSLSLATASLIKPNQVGTLTETLEAIRLCKQLGIKP 362
                                       ***************************************************************************** PP

                                       EEE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHHGCC-EE-GGGCT CS
                         Enolase_C 232 vvshrsGetedttiadlavglsaGqiktGaparserlakynqllrieeelgekakyaGkkvr 293
                                       +vs rsG+ted++iadlavg ++ qik G++arser  kyn+ll ie e   ka+y G+k+ 
  gi|557694108|ref|YP_008797162.1| 363 IVSARSGDTEDSFIADLAVGAACPQIKIGSIARSERTVKYNRLLEIEREQMGKAVYMGEKAL 424
                                       ***********************************************99999******9875 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.3   0.0   5.5e-51   2.5e-47       1     129 [.       4     130 ..       4     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 160.3 bits;  conditional E-value: 5.5e-51
                                       EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHT CS
                         Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapali 77 
                                       I++v+++e+ldSrG pT++ +v+++++ +g+a+vp+GaS g++ea+elrDg  +r++gkgv++avenv+++iapali
  gi|557694108|ref|YP_008797162.1|   4 ITRVDTYEVLDSRGLPTLKTRVWVDHEFMGEAMVPAGASRGRHEAVELRDG-GARWMGKGVSRAVENVKSVIAPALI 79 
                                       899***********************************************9.8************************ PP

                                       TSBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHH CS
                         Enolase_N  78 gldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyr 129
                                       +++ +d +++D++l++lDgtenksklGaNail+vSlA+a+a A+++++ply 
  gi|557694108|ref|YP_008797162.1|  80 NVE-ADVAKVDNILLDLDGTENKSKLGANAILSVSLATARAIAAYEKIPLYY 130
                                       999.799********************************************6 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 !   24.4   0.0   4.1e-09   1.8e-05      30     186 ..     219     398 ..     188     415 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.1e-09
                                       HHHHHHHHHHHHT..TTSTSEEEEE-TTTS................BHHHHHHHHHHHGG.GTESEEESSSSTTTHH CS
                          MR_MLE_C  30 dvervravreavg..pgddvdlmvDanqaw................dlatAirvarelee.ldllwlEEPvppeddl 87 
                                        +e + a+ e++g  p++d+ l++D+ ++                 +  + + ++  l e + +  +E+ +   ddl
  gi|557694108|ref|YP_008797162.1| 219 AIELILAAVEETGltPKTDIALALDVAASHlfkdgsymlsregltlSSHELVDFLVDLCEtYPIVSVEDGCGE-DDL 294
                                       444444444443322567777777777775556666677777776677788888888855599*********9.78* PP

                                       HHHHHHHH.HH.SSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSC.S.S CS
                          MR_MLE_C  88 eglaelra.ra.sipiaagEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsg.s.g 159
                                       +g + l +  + +++i+++   ++ ++++r + +   +++  +++++vg +te+++ ++l+++ g++ ++ +  + +
  gi|557694108|ref|YP_008797162.1| 295 DGWQYLFQkLSgKVQIVGDDLFATnVKRIRMCSSLSLATASLIKPNQVGTLTETLEAIRLCKQLGIKPIVSARsGdT 371
                                       *******863379*******998879999999***********************************6666631336 PP

                                       HHHHHHHHHHHHTTTTBEEEEEEGGGG CS
                          MR_MLE_C 160 glglaaslhlaaaipnllileyfldae 186
                                         +++a l + aa p+++i ++  ++ 
  gi|557694108|ref|YP_008797162.1| 372 EDSFIADLAVGAACPQIKIGSIARSER 398
                                       99**************99988877665 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.18   8.1e+02     189     217 ..      89     117 ..      80     122 .. 0.82
   2 !   15.0   0.0   2.3e-06      0.01     132     215 ..     300     384 ..     279     391 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.18
                            MAAL_C 189 kgvgaylGGscnetdvsarvsvhvalatr 217
                                        ++   l G+ n  + +a+++  v+lat 
  gi|557694108|ref|YP_008797162.1|  89 DNILLDLDGTENKSKLGANAILSVSLATA 117
                                       556667889******************96 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.3e-06
                            MAAL_C 132 klkekgikvelvaDe.WcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvsar 207
                                        +++ + kv++v D+ ++ +++ ir     + a +  ik   +G++++t+ea+  ck+ g++  +   + +t+ s  
  gi|557694108|ref|YP_008797162.1| 300 LFQKLSGKVQIVGDDlFATNVKRIRMCSSLSLATASLIKPNQVGTLTETLEAIRLCKQLGIKPIVSARSGDTEDSFI 376
                                       56778889****99845777999***************************************999999999998866 PP

                            MAAL_C 208 vsvhvala 215
                                       +   v+ a
  gi|557694108|ref|YP_008797162.1| 377 ADLAVGAA 384
                                       66666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3283.03
//
Query:       gi|557694109|ref|YP_008797163.1|  [L=326]
Description: aminoglycoside phosphotransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   61.4   0.0    2.6e-16   60.3   0.0    1.4  1  APH              Phosphotransferase enzyme family
    8.2e-05   22.3   0.2     0.0019   17.8   0.0    2.6  2  Choline_kinase   Choline/ethanolamine kinase
    0.00021   20.8   0.0     0.0012   18.3   0.0    2.3  1  APH_6_hur        Aminoglycoside/hydroxyurea antibiotic resist
  ------ inclusion threshold ------
      0.052   13.1   0.1        0.1   12.2   0.1    1.4  1  RIO1             RIO1 family
       0.12   11.6   0.1       0.19   11.0   0.1    1.3  1  EcKinase         Ecdysteroid kinase
       0.19   11.7   3.1       0.11   12.4   1.0    1.6  2  Coatomer_b_Cpla  Coatomer beta subunit appendage platform


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   8.6e-20   2.6e-16       2     211 ..      23     231 ..      22     237 .. 0.75

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 8.6e-20
                                       EEEE--.SSCEEEEEEETT--EEEEEE-TT......S-HHHHH..HHHHHHHHHHHTT-...B--B-CTTBS-EEET CS
                               APH   2 vrelsggasnrtylvttpagryvlrrnppa......raaeeir..revallrlLakagv...pvPevlagdtddeei 67 
                                       +++l+gg s +++lvt+++g++v++ + p+      ++a + r  re  +l++++++ v    +P+vl      e++
  gi|557694109|ref|YP_008797163.1|  23 LKPLGGGVSCHVVLVTSSKGKWVVKKALPRlmvkdeWLADRWRifRETGCLKVIREL-VdknAAPRVLL-----EDR 93 
                                       799***********************8888665554555555533555566666666.55777******.....888 PP

                                       TEEEEEEE----EE-SS..HHHHHHHHHHHHHHHHHHCCHHCH.-STTTB-SHHC..HTCCHHHHHHCHHHCCCGCC CS
                               APH  68 gllfalieyvpgrsllr..klsaaqlpellealgeflaalhqvdpaalpladfla..qdlellrqlesatarllase 140
                                       + ++ ++ey +g + +    ++  ++ e+  ++++ la++h    ++++ +  ++  +d ++ +++ +   ++la +
  gi|557694109|ref|YP_008797163.1|  94 ESYSCVLEYGEGGVTWKklLMDGVVDNEVTIRVASILAKIHTK--TSNRSEIVSDfwDDTNFIQLRIDPYINHLAKK 168
                                       888****************99********************99..43444433331112334444444444556666 PP

                                       TCCHHHHHHHHHHHHHHHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-EEEECCHHHHCCHHH CS
                               APH 141 lldlleeleeqvlaalaallpgelptvllHgDlhpgNllvdpddgrvtGviDfedaglgpplyDlavllrs 211
                                        ld ++     + + l  +       +l+HgD++p N+l+ pd      v+D+e a++g+p++D+a++ ++
  gi|557694109|ref|YP_008797163.1| 169 HLD-IAPHLYKISQILTSRK-----LSLVHGDYSPKNILILPDSRI--WVLDCEPAHYGNPVFDIAFCTNH 231
                                       666.4444443455555444.....59**************87555..5******************9877 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.3e-07    0.0019      55     186 ..     110     228 ..      66     255 .. 0.64
   2 ?   -0.9   0.1      0.33   9.9e+02     103     140 ..     284     321 ..     233     325 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.3e-07
                                       EE--TTGGGCHHHHHHHHHHHHHHTTCHH.TTSSSS-HHHHHHHHHHHCCS.TT..ECHHGGCCHCCCTHHHHHHHH CS
                    Choline_kinase  55 rtlstedlrepeiskkiAkklaelHsleleseskespslwktmqkwllnkeaqtkakkekkkkqlklinledlekel 131
                                       ++l  + + ++e+  ++A+ la++H+    + s+  +  w+  +          + + +++ ++l + +l d+   l
  gi|557694109|ref|YP_008797163.1| 110 KKLLMDGVVDNEVTIRVASILAKIHTKTS-NRSEIVSDFWDDTNFI--------QLRIDPYINHLAKKHL-DIAPHL 176
                                       45666777788888888888888888777.3333333344433322........3333333344433332.344455 PP

                                       HTHHHHHHCHGG-EEEE-S--SGGGEEE.-CTTEEEE--GTT-EEEEHHHHHHHH CS
                    Choline_kinase 132 ekleklleelespvvfcHnDlqegNillnkeekklvlIDFEYagynyrgfDlanh 186
                                        k+ ++l  +  ++ + H D  ++Nil    ++++++ D E a y   +fD+a  
  gi|557694109|ref|YP_008797163.1| 177 YKISQIL--TSRKLSLVHGDYSPKNILI-LPDSRIWVLDCEPAHYGNPVFDIAFC 228
                                       5566666..55568889***********.99*********************943 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.33
                                       CCS.TT..ECHHGGCCHCCCTHHHHHHHHHTHHHHHHC CS
                    Choline_kinase 103 nkeaqtkakkekkkkqlklinledlekeleklekllee 140
                                       ++++  ++ +e+k+ +++ ++ + + k ++++ekl+ee
  gi|557694109|ref|YP_008797163.1| 284 DGKSPVEYLNEEKRAKVRILSKNMIIKAVNEFEKLCEE 321
                                       45555666677777777777777777777777777765 PP

>> APH_6_hur  Aminoglycoside/hydroxyurea antibiotic resistance kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.1e-07    0.0012      56     196 ..      83     226 ..      13     244 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.1e-07
                         APH_6_hur  56 dGavrvleedeeesalLLErlsgersltslvaeg.dDdeAtrilaellarLhapspgplPp.Llpleevfealfrea 130
                                       + a rvl ed e+ +  LE+ +g ++ ++l+ +g  D+e t  +a +la++h++  +   + +  + +  + +  + 
  gi|557694109|ref|YP_008797163.1|  83 NAAPRVLLEDRESYSCVLEYGEGGVTWKKLLMDGvVDNEVTIRVASILAKIHTKTSNRS-EiVSDFWDDTNFIQLRI 158
                                       56789***********************99866536*****************997766.33555544443333333 PP

                         APH_6_hur 131 asdagagasrlyveaaaiaaeLle.....epselrpLHgdlhhenvLagerrgWlaidPkgl.vGergfdla 196
                                           +   ++l ++ + ia +L +     +++ l + Hgd   +n+L  ++    ++d ++  +G++ fd a
  gi|557694109|ref|YP_008797163.1| 159 ----DPYINHLAKKHLDIAPHLYKisqilTSRKLSLVHGDYSPKNILILPDSRIWVLDCEPAhYGNPVFDIA 226
                                       ....333333444444444444221111155778999**********99986555888888637******98 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.4e-05       0.1     121     149 ..     184     213 ..     143     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.4e-05
                                       HHHTSTEEESS-STTSEEEETT.EEEE--G CS
                              RIO1 121 lykeaglvHaDLSeyNvlvded.kvviIDv 149
                                         ++  lvH+D S  N+l+  d +++++D 
  gi|557694109|ref|YP_008797163.1| 184 TSRKLSLVHGDYSPKNILILPDsRIWVLDC 213
                                       345678**************999****996 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   6.4e-05      0.19     173     265 ..     139     233 ..     110     247 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.4e-05
                          EcKinase 173 aalealreelpelekea.......ekleklkenlferllelveekeeefnvlnHGDlwvnNimfkydeegepedvil 242
                                       +  e++++ +++++  +       ++l k + ++  +l ++ +  +++   l+HGD+  +Ni++  d++     +  
  gi|557694109|ref|YP_008797163.1| 139 NRSEIVSDFWDDTNFIQlridpyiNHLAKKHLDIAPHLYKISQILTSRKLSLVHGDYSPKNILILPDSR-----IWV 210
                                       445566666666665555556333445555555555555555578888889*************99855.....9** PP

                          EcKinase 243 vDFQlsrygSpalDLlyflytst 265
                                       +D   + yg p++D+++  +  +
  gi|557694109|ref|YP_008797163.1| 211 LDCEPAHYGNPVFDIAFCTNHLV 233
                                       ***************99766555 PP

>> Coatomer_b_Cpla  Coatomer beta subunit appendage platform
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.4   4.2e+03      42      62 ..     132     152 ..     117     169 .. 0.59
   2 ?   12.4   1.0   3.8e-05      0.11       4      88 ..     231     312 ..     229     320 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.4
                   Coatomer_b_Cpla  42 avktkltdlkeyleelvkktn 62 
                                       +++tk+++ +e+++ + + tn
  gi|557694109|ref|YP_008797163.1| 132 KIHTKTSNRSEIVSDFWDDTN 152
                                       344555555555555555554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.8e-05
                   Coatomer_b_Cpla   4 vvilndikidimdyikpakiseeeFremWaefeWEnkiavktkltd..lkeyleelvkktnmklltpeeeleeeaef 78 
                                        ++l+ i+++    ++ ak+    ++  W++  WEn  +++ + t     ++l ++  k  ++ l+  ee++ + ++
  gi|557694109|ref|YP_008797163.1| 231 HLVLKAIHLNSEAHLNAAKLL---WKVYWSTARWENFHTLEEEATLtlTAHMLARIDGKSPVEYLN--EEKRAKVRI 302
                                       678888888888888877764...6777***********998855433789999***********9..5667889** PP

                   Coatomer_b_Cpla  79 lsanlyaksv 88 
                                       ls+n+  k+v
  gi|557694109|ref|YP_008797163.1| 303 LSKNMIIKAV 312
                                       *****98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); 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: 00:00:00.41
# Mc/sec: 2403.57
//
Query:       gi|557694110|ref|YP_008797164.1|  [L=333]
Description: oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-30  106.8   0.1    2.1e-30  106.0   0.1    1.4  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
     0.0082   16.1   0.0      0.015   15.3   0.0    1.5  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
  ------ inclusion threshold ------
      0.018   14.9   0.4      0.031   14.1   0.4    1.3  1  NAD_binding_10  NAD(P)H-binding
      0.022   14.3   0.0      0.044   13.4   0.0    1.4  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
      0.081   13.6   0.6       0.17   12.5   0.6    1.6  1  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain


Domain annotation for each model (and alignments):
>> 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 !  106.0   0.1   5.8e-34   2.1e-30       1     120 []       4     122 ..       4     122 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 5.8e-34
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHH CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngthee 77 
                                       lr ++iG+G +g  h+++++++ +l+e+va+ d+d  r  +va ++gv +ysd+ ++l+ ++ d+v+vatp ++h e
  gi|557694110|ref|YP_008797164.1|   4 LRAGVIGVGSFGVLHAEAYRDN-PLTELVAVADIDIGRVSEVASKLGVRSYSDFHDMLRREKLDVVSVATPDDKHTE 79 
                                       589*************999999.****************************************************** PP

                                       HHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  78 lakaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                        a aa+eag+++llEKP+at+++eak++++++ek++++++v++
  gi|557694110|ref|YP_008797164.1|  80 PAVAATEAGVNILLEKPIATDLQEAKKIIAAVEKNNVKLMVNF 122
                                       *****************************************86 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.3e-06     0.015       2      84 ..     135     209 ..     135     256 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.3e-06
                                       HHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCTC CS
                    GFO_IDH_MocA_C   2 elIengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaeaa 78 
                                       el+ + ++Ge+v++  w ++      akk +k      + +l+d  iHdiD+ ++++ ++p +v+  g ++++ e++
  gi|557694110|ref|YP_008797164.1| 135 ELVSEREIGEIVTI--WARRSTLLETAKKYGK-----FSNLLYDVIIHDIDMCNLFTMSEPKKVYCVG-VKKVLEKT 203
                                       7899999*******..8888888888888888.....459************************9986.57777777 PP

                                       CSCSEE CS
                    GFO_IDH_MocA_C  79 ededaa 84 
                                       + eda 
  gi|557694110|ref|YP_008797164.1| 204 GLEDAY 209
                                       777766 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 ?   14.1   0.4   8.8e-06     0.031      21      93 ..      45     119 ..      40     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.8e-06
                                       EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SE.EEES---TCC.HHHHHHHHHHHHHHCT--EE CS
                    NAD_binding_10  21 evtalvRnpeklaeleaeeglevvegdvtdvedlaealkgada.Vvsalggggk.deegaknivdaakeagvkRf 93 
                                       + ++ vR+ ++++++ ++e+l+vv++   d +  + a++ ++a V + l +    d + ak+i++a+++++vk +
  gi|557694110|ref|YP_008797164.1|  45 ASKLGVRSYSDFHDMLRREKLDVVSVATPDDKHTEPAVAATEAgVNILLEKPIAtDLQEAKKIIAAVEKNNVKLM 119
                                       56789********99999************************96777775554448888*************965 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 ?   13.4   0.0   1.2e-05     0.044       8      75 ..       7      79 ..       2      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                                      EEES-SHHHHHHHHHHHHTT--EEEEE-..TT-HHHHHHHHTT-EEEE.HHHHH..HT-SEEEE-S-HHHHHH CS
                              IlvN  8 aviGyGsqGhaqalnlrdsgldvvvglr..egsksvkkAkeegfevlt.vaeav..kkadvvmiliPDelqke 75
                                       viG Gs G  +a+  rd+ l   v++   + ++  + A++ g++ ++  +++   +k dvv + +PD  ++e
  gi|557694110|ref|YP_008797164.1|  7 GVIGVGSFGVLHAEAYRDNPLTELVAVAdiDIGRVSEVASKLGVRSYSdFHDMLrrEKLDVVSVATPDDKHTE 79
                                      69*******************75555550055689999999999987526676522578*********98865 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 ?   12.5   0.6   4.8e-05      0.17       3     116 ..       7     120 ..       6     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.8e-05
                                       SHHHHHHHHHHHH---S..SEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHH CS
                     NAD_binding_3   3 GaiGsavleqlkrqqse..ielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvl 77 
                                       G+iG + +  l +++ +     elvavad d   +    a     + ++d+ d++++++ dvv  +++++   e ++
  gi|557694110|ref|YP_008797164.1|   7 GVIGVGSFGVLHAEAYRdnPLTELVAVADID-IGRVSEVASKLGVRSYSDFHDMLRREKLDVVSVATPDDKHTEPAV 82 
                                       6666666666666665554456999999999.555555566778999*********99***99999*********** PP

                                       HHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE- CS
                     NAD_binding_3  78 kaLkagkdvvtankgaladealyeeLreaaeangakiyv 116
                                       +a +ag++++   k   +d++  +++++a e+n++k++v
  gi|557694110|ref|YP_008797164.1|  83 AATEAGVNILL-EKPIATDLQEAKKIIAAVEKNNVKLMV 120
                                       ********986.4555569****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2456.08
//
Query:       gi|557694111|ref|YP_008797165.1|  [L=289]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-18   64.0   0.1    1.6e-09   37.0   0.1    2.0  2  DUF4432   Domain of unknown function (DUF4432)


Domain annotation for each model (and alignments):
>> DUF4432  Domain of unknown function (DUF4432)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.1   9.1e-14   1.6e-09      39     183 ..       2     142 ..       1     175 [. 0.77
   2 !   25.4   0.0     3e-10   5.3e-06     228     301 ..     202     282 ..     180     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 9.1e-14
                                       ---S-----GGG--...HHHHTG.GGGT--.-SEEEEEES--SS-EEETTEEE-TTBSGGGS--SEEEEEEESSTT- CS
                           DUF4432  39 wdspvgvvapalve...sreglg.wlrgFnggllttCGlenvgapeedegeelgLHGrisnipAeevsveaeeegkl 111
                                       w+sp g ++p  v+   +++  g +l+ ++ g       +  g+p++  g ++g+HG+ s +p   +  e++++   
  gi|557694111|ref|YP_008797165.1|   2 WQSPLGWRNPL-VDtmpNPNHEGaFLDYYG-GGWQDIVPSAGGHPTTHRGASMGVHGESSMLPWTCILEEESDD--- 73 
                                       55555555554.222444444440555555.55566667888*********************87766655433... PP

                                       -EEEEEEEEEEETTTEEEEEEEEEEE-TT-SEEEEEEEEEE-SSS-EEEEEEEEEEE-TTT-STT-EEE--E CS
                           DUF4432 112 eievtGevkeaalfgenlelereislelgeaeleveDevtNegsepaplmllYHvNfGtPlldegaellapv 183
                                         +vt+ ++    ++  ++le++i+++ +e+ + +  ++tN +++p ++++l H  fG P++++g ++++ +
  gi|557694111|ref|YP_008797165.1|  74 --KVTAYMRTD-GVRYPFKLEKRITITKTENMIYFWEKLTNTANQPLEYSWLQHPAFGEPFIEPGVKIELSG 142
                                       ..567777654.45677*************************************************999876 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 3e-10
                                       EEEEE-SSSS-EEEEEEETTTS-EEEEEEEES-.......T-EEEEEEEESS-SS-HHHHHHTT--EEE-TT-EEEE CS
                           DUF4432 228 laalvnkklglgvavkfdkdqLPvltlWkntga.......geYvlGlEPstnfllgrsaereqgelitlepgesksf 297
                                       +  + n++lglg+++ +d + + +l  W+n+++       +++ ++lEP+t++++g  ++ ++g+ +tl  g+s ++
  gi|557694111|ref|YP_008797165.1| 202 RYLIWNRRLGLGFEMIWDVSIFRYLWFWQNYNTpdypwygRAWNIALEPCTSYPAGLPEQVKHGTHVTLDGGASLET 278
                                       56789***************************99999999999***************************9999887 PP

                                       EEEE CS
                           DUF4432 298 rlel 301
                                       + ++
  gi|557694111|ref|YP_008797165.1| 279 KYSV 282
                                       7655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 2130.53
//
Query:       gi|557694112|ref|YP_008797166.1|  [L=255]
Description: creatinine amidohydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-64  216.6   0.0    3.8e-64  216.4   0.0    1.0  1  Creatininase  Creatinine amidohydrolase


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 !  216.4   0.0   2.1e-68   3.8e-64       2     240 ..       7     248 ..       6     249 .. 0.90

  Alignments for each domain:
  == domain 1  score: 216.4 bits;  conditional E-value: 2.1e-68
                      Creatininase   2 eltwpeveealkeddvailPvGstEqHGphlplgtDtliaealaervaeklgakalvlPtlpyGvseehlgfpGTis 78 
                                       e ++pe+ e+  +++vai P+GstEqHGphlp+gtD++ia +l+++v e+++  al+lP lpyG s+ h  +pGTis
  gi|557694112|ref|YP_008797166.1|   7 EKSSPELGELCSQKRVAIFPIGSTEQHGPHLPTGTDHIIAWELSKKVVEDVD--ALLLPLLPYGFSDDHFPMPGTIS 81 
                                       56899******************************************99999..9********************** PP

                      Creatininase  79 lspetliavlrdileslarhGfrrivlvngHggnsaalkeaarelraehdaaavrvtaaekelaaalkleeaaeaae 155
                                       +s etl+a++rd+++sl+r G+r++v+v+gH g+   +  +  +l+  ++++ +rv++ + ++ +         ++ 
  gi|557694112|ref|YP_008797166.1|  82 ISSETLKAIIRDVADSLSRYGIRHLVIVSGHAGHLGQISDITYRLNLSYPVQSLRVHNISPYNTV-------PVERL 151
                                       *************************************************9998887733333333.......22333 PP

                      Creatininase 156 eseeee.gggHAgelEtSlmlalrpelVrmdraedpeeaklakeg...........vstaedaeelspsGvlGdpsk 220
                                        +  ee   +HA elEtS+ml+l+p+lV+m++a++++++  +k             v+t++   +  ++Gv+Gd++ 
  gi|557694112|ref|YP_008797166.1| 152 ATVLEEdMFIHAEELETSIMLYLHPHLVDMSKAVKEHPPFIPKGLttpnfleairiVTTSKFLGRDFKTGVCGDATL 228
                                       444444599****************************99998888**********866666666657********** PP

                      Creatininase 221 ataekGealleaaveelael 240
                                       a++ekGe+l++ +ve l+e 
  gi|557694112|ref|YP_008797166.1| 229 ASREKGEKLFKILVEGLVET 248
                                       *****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1941.08
//
Query:       gi|557694113|ref|YP_008797167.1|  [L=344]
Description: microsomal peptidase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-84  284.0   0.0    1.7e-84  283.7   0.0    1.0  1  Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
    3.5e-05   23.8   0.0    4.8e-05   23.3   0.0    1.2  1  Amidohydro_2   Amidohydrolase


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 !  283.7   0.0   1.9e-88   1.7e-84       7     319 .]       4     338 ..       2     338 .. 0.94

  Alignments for each domain:
  == domain 1  score: 283.7 bits;  conditional E-value: 1.9e-88
                                       .EEEEEE-HHHHHHHCTTTTT.....-TTTHCTSSS-HHHHHHHTEEEEEEEEE--C.................... CS
                     Peptidase_M19   7 iviDghndlplklrqekkesl.....llekdselqtdlerlraggvsavlfaifvpe.................... 58 
                                       +++D h d++l+  +++   +     +  + s  + d++++r++ v++v+ +i++ +                    
  gi|557694113|ref|YP_008797167.1|   4 PLVDLHEDISLYYVHAGAGLKfkpmgFDVDLSGRHGDIPKYRRANVKLVFSSIAPLTptisrmrveqlargyggfyg 80 
                                       67999999999988888877788998888999**********************44458****************97 PP

                                       CCCCCCHHHHHHHHHHHHHHHHHHGTTTEEE-SSHHHHHHHHHTT-EEEEEEEESCGGGTT-HHHHHHHHHTTEEEE CS
                     Peptidase_M19  59 dasyeeavkatleqidlirrlvrknpeqlklvrtaddierakkegkiavllgiegaealgddlallrafyalGvrvl 135
                                       +  ++    +tle i  +++l+r+++++l+ v t++d+++  k+g+i++l+ iegae+l +d++ l+ fy+lGvr+l
  gi|557694113|ref|YP_008797167.1|  81 AYRTRAPTLTTLEHIVTYNNLLRQHSKDLRPVLTTSDVDELGKDGRIGFLIAIEGAEPL-EDVEDLEIFYKLGVRSL 156
                                       55666777789************************************************.9**************** PP

                                       ES-SSS-BSSB-BCCGTT.SSSSB-HHHHHHHHHHHHHT-EEE-TTB-HHHHHHHHHH-SSE.EECCEEBTTTS--T CS
                     Peptidase_M19 136 gltynrnnkfAdgaleekdedgGLsefGkelVrelNrlgiliDlShlsektfldvlelSkaPvvaSHSnaralcdhp 212
                                       +lt+n +nk++  ++++  +d GL+  G++lVr +N++g+++DlSh+s++t+ ++l+ Sk P+++SH+na+++ +h+
  gi|557694113|ref|YP_008797167.1| 157 QLTWNFDNKYGATCMSK--KDYGLTGDGEDLVRLCNEMGVIVDLSHASKRTTVEALSASKLPAIVSHANAKSVRNHA 231
                                       ****************9..********************************************************** PP

                                       TSB-HHHHHHHHHTT-EEEE-SSHHHCTTTS--BHHHHHHHHHHHHHHT-GGGEEE---TTTTSS-..BBTBSSGGG CS
                     Peptidase_M19 213 RNltDeqlkaiaesgGvvgvtfvpaflkekaeatledvvdhidyivelaGidhVGlGsDfdgggel..pegledvsk 287
                                       RNl+De+l+a++++gGvvg tf+p ++++   a+l+ ++dhi yi e++G d  ++G+Df g  ++  p+gled++k
  gi|557694113|ref|YP_008797167.1| 232 RNLDDEELEALKNNGGVVGATFIPPTISD--HASLKGLADHIMYIYEKFGPDILAIGTDFFGLLNVdePDGLEDITK 306
                                       ***************************97..9****************************55444444********* PP

                                       HHHHHHHHHHTTS-HHHHHHHHTHHHHHHHHH CS
                     Peptidase_M19 288 lpnltaeLlrrgyseadiekilggNflrvlee 319
                                       + nl +eLl+rg +e+d+eki++ N+lrv++e
  gi|557694113|ref|YP_008797167.1| 307 IVNLWNELLNRGVKESDVEKIAYLNALRVVRE 338
                                       *****************************985 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   5.4e-09   4.8e-05     130     289 ..     183     336 ..     122     337 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.4e-09
                                       GHHHHHHHHHHHT-EEEEE....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHH CS
                      Amidohydro_2 130 ldrpifealeelglpvdihtGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarr 206
                                           ++++++e+g+ vd+          + +  tt + ++     +++ + n k v +H+ +      ++le+l++ 
  gi|557694113|ref|YP_008797167.1| 183 E--DLVRLCNEMGVIVDLS---------HASKRTTVEALSASKLPAIVSHANAKSVRNHARNL---DDEELEALKNN 245
                                       3..4899**********99.........889999*****************************...99********* PP

                                       HHCCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHCHHHHH.........SSH CS
                      Amidohydro_2 207 pnvyvklsglytellyfdspladppalarlieavgpdrilfGsDyPhptleaepealalldlval.........lsd 274
                                        +v   + +++t  ++  s++  + ++  + e +gpd +  G+D++     +ep+ l ++ ++            ++
  gi|557694113|ref|YP_008797167.1| 246 GGVVGATFIPPTI-SDHASLKGLADHIMYIYEKFGPDILAIGTDFFGLLNVDEPDGLEDITKIVNlwnellnrgVKE 321
                                       ****999888888.**********************************************99999************ PP

                                       HHHHHHHTHHHHHHC CS
                      Amidohydro_2 275 eerekilggNAarly 289
                                        ++eki++ NA r+ 
  gi|557694113|ref|YP_008797167.1| 322 SDVEKIAYLNALRVV 336
                                       *************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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 0.27s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2428.40
//
Query:       gi|557694114|ref|YP_008797168.1|  [L=522]
Description: hypothetical protein CSUB_C0679 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-17   62.2   6.5    1.5e-16   61.3   6.5    1.4  1  SBP_bac_1     Bacterial extracellular solute-binding protein
    5.9e-14   52.5   1.9    1.1e-13   51.6   1.9    1.4  1  SBP_bac_8     Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.035   14.1   0.3      0.082   12.9   0.3    1.6  1  CytB6-F_Fe-S  Cytochrome B6-F complex Fe-S subunit
      0.064   13.3   0.0        1.1    9.3   0.0    2.2  2  CEL_III_C     CEL-III C-terminal
       0.15   12.0   2.1        0.3   11.1   2.1    1.4  1  EspB          Enterobacterial EspB protein


Domain annotation for each model (and alignments):
>> 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 !   61.3   6.5   4.1e-20   1.5e-16      14     308 ..     103     392 ..      93     395 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 4.1e-20
                                       HHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEECGGHHH.HHHHTTSBECCHHHHHHTTECTTCCT CS
                         SBP_bac_1  14 vakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviavdndwia.rlakaglllpldpyvkaylapgvkda 89 
                                       + ++f++ + ++ +++++ g +++   +++a  aG++p  + ++ + +++  + ++g+++++  y+ +       ++
  gi|557694114|ref|YP_008797168.1| 103 A-NKFNQWNDDVYIKVVDYGLDTFFSGISAAYTAGNPP-TIHYS-TPDVTyIYQQNGWAIDMEQYFPEI-----RRY 171
                                       4.668888889999999999****************66.66555.55555346666************9.....566 PP

                                       EEEEHHHHTHHHHCE.EE.ES.EEEEE.EEEEEEETTTHHCTTGGG.SHBHHHHHHHHHHHHHHCTCT.....HCCH CS
                         SBP_bac_1  90 adklsssvlpkilds.kv.ly.vPlya.argliYNkdlfekagldp.pwtWdelveaakklkekgkkp.....igga 156
                                        d+ ++ +  + ++  ++    + +y+ a++++YN   +e+ag+d+ p+tW+el e a+k+k  g ++      +g+
  gi|557694114|ref|YP_008797168.1| 172 LDDIFPGFRTGFINPdTGlMSgLAYYGgAQPFMYNQRHLEEAGIDEpPKTWEELEEQARKIKQRGVNDdpigiWYGS 248
                                       6666677777777776779888999977*****************************************99999999 PP

                                       CCEEHHHHHHHHHHHHHHHHTGGGEECCCT.HHCSHHHHS..HHHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHH CS
                         SBP_bac_1 157 rggsasgtayyfalalakslggkvfdkdgg.gldnpegvt..aatylvklyavanltkelkgkgaenkdgaaalalf 230
                                       +g+   g  +  +    ++ g++ +d+d +  +++ +     ++ ++ +++    ++++l+  +   +d+a+a+++f
  gi|557694114|ref|YP_008797168.1| 249 WGFVEVGIYDFMLGMAENDRGPYMWDEDLNpIFNDKNSPLfrSLRWQLDMI----HKEKLASTKGVLYDEAQAVNAF 321
                                       999999999999999999999*********977777777788*********....999******************* PP

                                       HTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE...EEEEEEEEBTTCSTHHHHHHH CS
                         SBP_bac_1 231 eaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi...lgayglaipkgsknpeaAkkF 304
                                        +G   ++++  ++          + ++++ +k  ++l + + P++ +    i     +++ +  kg k+ eaA+ +
  gi|557694114|ref|YP_008797168.1| 322 GSGAHTFFWMPDYD---------LAFANTPPSKEAGNLRMGMNPGTGKVSA-IyrtYLVSKATADKGMKHLEAAWRV 388
                                       ***********999.........999999999999*******886544433.257777777888888888999***9 PP

                                       HHHH CS
                         SBP_bac_1 305 ldfl 308
                                       ++f+
  gi|557694114|ref|YP_008797168.1| 389 MQFV 392
                                       9997 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   1.9   3.1e-17   1.1e-13       3     246 ..     103     392 ..     101     408 .. 0.71

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 3.1e-17
                                       HHHHHHH-.TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGS.TTHHH.-HHHHH CS
                         SBP_bac_8   3 akefekkt.gvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdl.dnldd.ltdala 76 
                                       a++f++ + +v ++vv ++ ++  + ++aa  ag+ p+i   +   d  + + ++g+  d++++ +++   l+d + 
  gi|557694114|ref|YP_008797168.1| 103 ANKFNQWNdDVYIKVVDYGLDTFFSGISAAYTAGNPPTI--HYSTPDVTYIYQQNGWAIDMEQYfPEIRRyLDDIFP 177
                                       689*****89***************************95..677778888888999999***555777773477777 PP

                                       TT......--TS.----EEEEEEE-EEEEEHHHHHHS....---BHHHHHHHHHHHHHH-SEGG---G..GGGGGTH CS
                         SBP_bac_8  77 av......gydgklygvPyasetpyvliynkdlleka...edpktwdellaaakklkgkfglpdpasg..wlqaall 142
                                       ++         g   g+ y  +  + ++yn+  le+a   e+pktw+el + a k+ +++g  d+++g  ++ ++++
  gi|557694114|ref|YP_008797168.1| 178 GFrtgfinPDTGLMSGLAYYGGA-QPFMYNQRHLEEAgidEPPKTWEELEEQARKI-KQRGVNDDPIGiwYGSWGFV 252
                                       77776684334558888888776.9***********9**************99999.56666666666643355555 PP

                                       H......................ETTEE---H..HHH.HHHHHHHHHHHHTT-......EE-S..--SSTTTTTSBS CS
                         SBP_bac_8 143 a......................kdgksldddggkdglkealellkklkdngk......tydtgadavsefanGeva 191
                                                              +++  ++d+  +  l + l++  ++  + k      ++ + a+av++f +G   
  gi|557694114|ref|YP_008797168.1| 253 EvgiydfmlgmaendrgpymwdeDLNPIFNDK--NSPLFRSLRWQLDMIHKEKlastkgVLYDEAQAVNAFGSGAHT 327
                                       55565676777888665555553333333333..3333555555555555555455554447789*********999 PP

                                       EEEE-TTHHHHHH....-TTTSEEEE-.-S--EEEEEE.EEEEBTTS-HH...HH.HHHHHHHHH CS
                         SBP_bac_8 192 ftingswdiaaaq....kagkklgaiv.pkqgsfaggk.glavpknakne...dl.aAldFlkwl 246
                                       f+  ++ d+a a+    k+  +l++++ p +g ++ +  +++v+k + ++    l aA++ ++++
  gi|557694114|ref|YP_008797168.1| 328 FFWMPDYDLAFANtppsKEAGNLRMGMnPGTGKVSAIYrTYLVSKATADKgmkHLeAAWRVMQFV 392
                                       99998888887777798888899999647666444443145555543333332446899888887 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 ?   12.9   0.3   2.3e-05     0.082       6      36 ..      22      52 ..      21      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                      CytB6-F_Fe-S  6 msrRqllNlllvGaialtaaaaLyPvvkFFi 36
                                      m+rR   +++ ++ai+++a+a + +++ F+ 
  gi|557694114|ref|YP_008797168.1| 22 MTRRHAISKVGAAAIGAVAGAVIGGAGGFLA 52
                                      9**************************9985 PP

>> CEL_III_C  CEL-III C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00031       1.1      60     120 ..      54     115 ..      34     124 .. 0.85
   2 ?    1.5   0.0      0.08   2.9e+02      94     127 ..     385     417 ..     359     423 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00031
                         CEL_III_C  60 saeasvavadsvtkslsksvtttitatcakkdkekvalyQwslkgqe.egeeevsvddenfi 120
                                       s +a+ a  ++vt++++++vt t+t+t a+k +++  ++ w ++  + + ++  +++d  +i
  gi|557694114|ref|YP_008797168.1|  54 SSQAGPARTETVTRTVTQTVTGTVTQTAAEKIEVTWGIWSWGVELVQdNANKFNQWNDDVYI 115
                                       55677778899******************************999766155555689998887 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.08
                         CEL_III_C  94 kvalyQwslkgqeegeeevsvddenficrygana 127
                                          + Q++   +++g+ +++ + e ++cr ++n+
  gi|557694114|ref|YP_008797168.1| 385 AWRVMQFVGGRTRNGKPDFE-NGEYYVCRRLNNE 417
                                       44567999999999999998.6789****97665 PP

>> EspB  Enterobacterial EspB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.1   8.3e-05       0.3      40     103 ..      22      85 ..       6      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.3e-05
                              EspB  40 qtqkkaIeekkAgAtaallegvlsivlGilgsaaaiasgaieelatkGasvvvdkatsasaksV 103
                                        t++ aI++  A A  a++++v++ ++G l     +  +  e ++    + v +  t+++a ++
  gi|557694114|ref|YP_008797168.1|  22 MTRRHAISKVGAAAIGAVAGAVIGGAGGFLAGSSQAGPARTETVTRTVTQTVTGTVTQTAAEKI 85 
                                       588999**99988888888888888888777666667788899999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3810.71
//
Query:       gi|557694115|ref|YP_008797169.1|  [L=295]
Description: multiple sugar ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   31.0  32.4    1.9e-07   31.0  32.4    2.2  3  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.39   11.2   0.1       0.39   11.2   0.1    3.2  3  Arc_PepC_II   Archaeal Peptidase A24 C-terminus Type II


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 ?   -3.5   0.3      0.79   7.1e+03      61      71 ..      17      27 ..       9      39 .. 0.42
   2 !    2.9   1.7    0.0088        79      20     178 ..      69      92 ..      47      99 .. 0.53
   3 !   31.0  32.4   2.2e-11   1.9e-07       5     174 ..      86     280 ..      64     290 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.79
                      BPD_transp_1 61 llsaapyvrli 71
                                      l +++p++++ 
  gi|557694115|ref|YP_008797169.1| 17 LSFIFPFTFYP 27
                                      22233332222 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.0088
                      BPD_transp_1  20 lrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwq 96 
                                         ++i+v  ++P++vl+ l +                                                        
  gi|557694115|ref|YP_008797169.1|  69 QATVIFVAIAVPIVVLLSLGL-------------------------------------------------------- 89 
                                       334555555555555555544........................................................ PP

                      BPD_transp_1  97 ifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlvad 173
                                                                                                                    
  gi|557694115|ref|YP_008797169.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                      BPD_transp_1 174 ilqrl 178
                                         + l
  gi|557694115|ref|YP_008797169.1|  90 --AIL 92 
                                       ..333 PP

  == domain 3  score: 31.0 bits;  conditional E-value: 2.2e-11
                      BPD_transp_1   5 Gilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf.....................vilsilghlilpvii 58 
                                       ++ +a  ln+n+++  +l++l+ v++++P +  + ++ ++f                      +l+  + ++l +++
  gi|557694115|ref|YP_008797169.1|  86 SLGLAilLNQNFRGVGFLQWLVLVPWAVPLVDSGAIWKWIFdanygifnaalkalglidsyvPWLNLRWPAMLVLVM 162
                                       34444446678888888888888888888888888888888******************9977776666666669** PP

                      BPD_transp_1  59 llllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswp 135
                                       ++++ ++p+ +l++ a+++s+p++l+eaa ++Ga+ w  f+++++  + p ++  +++++  ++  + l++ +++++
  gi|557694115|ref|YP_008797169.1| 163 AFIWVQLPLPTLLFLAGMQSIPQELYEAAVIDGAGAWAKFKTITVTWLRPFMLIVAVYTSLMAIWTFDLVYVITAGG 239
                                       ****************************************************9999999999999999998888766 PP

                      BPD_transp_1 136 G..lgtllleailgydyseis...nggvlalviavlllnlvadi 174
                                       +  ++ ++   +++ ++++ +   +    al ++v+l+++ + i
  gi|557694115|ref|YP_008797169.1| 240 PgnFTAVISYYTWSEMFTFLNfgrA---SALSVLVVLVSIGLII 280
                                       67999999*************5552...3333333333322222 PP

>> 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 ?   11.2   0.1   4.4e-05      0.39      48      86 ..      53      92 ..      19      94 .. 0.87
   2 ?   -0.2   0.3      0.16   1.4e+03      66      76 ..     164     174 ..     135     179 .. 0.57
   3 ?    0.1   0.3      0.14   1.2e+03      65      80 ..     203     218 ..     190     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.4e-05
                       Arc_PepC_II 48 eelrkelkkykkkglieet.vWvtygvPflipitaGfiia 86
                                      +++++ l++y  ++ ++ t ++v+ +vP ++++ +G+ i 
  gi|557694115|ref|YP_008797169.1| 53 DNFIEVLTSYYMADSVQATvIFVAIAVPIVVLLSLGLAIL 92
                                      678999*************9****************9876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.16
                       Arc_PepC_II  66 tvWvtygvPfl 76 
                                        +Wv   +P l
  gi|557694115|ref|YP_008797169.1| 164 FIWVQLPLPTL 174
                                       25555555555 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.14
                       Arc_PepC_II  65 etvWvtygvPflipit 80 
                                       +t+ vt+  Pf++ + 
  gi|557694115|ref|YP_008797169.1| 203 KTITVTWLRPFMLIVA 218
                                       46889******98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2090.31
//
Query:       gi|557694116|ref|YP_008797170.1|  [L=300]
Description: multiple sugar ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   52.0  21.7    6.8e-14   52.0  21.7    2.6  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.036   13.7   0.6      0.036   13.7   0.6    2.2  2  DUF5336       Family of unknown function (DUF5336)


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 ?   -4.4   7.8       1.5   1.3e+04      43     172 ..      60     109 ..       3     114 .. 0.47
   2 !   52.0  21.7   7.6e-18   6.8e-14       7     178 ..     111     289 ..     106     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 1.5
                      BPD_transp_1  43 f......................vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqi 97 
                                       f                      ++  ++ ++                                             
  gi|557694116|ref|YP_008797170.1|  60 FifdtssaiearlqesgrlsflpAVARWFPNAL-------------------------------------------- 92 
                                       033333333333333333333332222222222............................................ PP

                      BPD_transp_1  98 frkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlva 172
                                                                                                 + +++++++v ++n++a
  gi|557694116|ref|YP_008797170.1|  93 ----------------------------------------------------------VNSVIIGLVVTVINIIA 109
                                       ..........................................................22444444444444444 PP

  == domain 2  score: 52.0 bits;  conditional E-value: 7.6e-18
                      BPD_transp_1   7 laa....lnrnkkldkllrpliivllslPsfvlaillvlvf..vilsilghlilpviillllsaapyvrlirraalr 77 
                                        +a    ++ ++k++ ll  ++ +++ +P+++++++ + ++  ++   l ++ ++vi++ + +++p++++i + +l+
  gi|557694116|ref|YP_008797170.1| 111 TLAsytfTRIRFKGSGLLFYMSVAGRLIPPVAIVVPYYIIIqnFFGLNLLDTLFAVILVHAAFTLPINIWILNTYLS 187
                                       3334666899999*******************99998877788777789999999********************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                       ++p+d + aar++G +r ++++kvvlP +lp i++  i++f+ ++g+++++ ++++ +  ++++l +i g++ ++ +
  gi|557694116|ref|YP_008797170.1| 188 AIPSDIEDAARVDGYGRLETLFKVVLPVILPGIVAIGIISFMVSWGEFFFAFMVTQTQ--QSRTLPVIVGFMAAQPY 262
                                       *******************************************************886..66666666666666555 PP

                      BPD_transp_1 155 ...nggvlalviavlllnlvadilqrl 178
                                           ++++ +++a+l+ ++ + ++ r+
  gi|557694116|ref|YP_008797170.1| 263 kpvGILMAGGLVAMLPALVMIAVFRRY 289
                                       777445555555555555555555555 PP

>> DUF5336  Family of unknown function (DUF5336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2      0.18   1.6e+03     133     149 ..      95     111 ..      74     117 .. 0.51
   2 ?   13.7   0.6     4e-06     0.036      34      93 ..     213     277 ..     200     282 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.18
                           DUF5336 133 glwvvlvlallqaaaAv 149
                                        +++ lv++++  +aA+
  gi|557694116|ref|YP_008797170.1|  95 SVIIGLVVTVINIIAAT 111
                                       34444555555555544 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4e-06
                           DUF5336  34 LplyLsiavaaLGliayllgFgplltvsass..adlee....asatsgglglavvllLlagLlAgv 93 
                                       Lp++L  +++a+G+i++++++g+++ +   +  +++++    + +++ ++  +v +l+++gL+A +
  gi|557694116|ref|YP_008797170.1| 213 LPVIL-PGIVAIGIISFMVSWGEFFFAFMVTqtQQSRTlpviVGFMAAQPYKPVGILMAGGLVAML 277
                                       66666.4899**********998765544443333333011134455556666*********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); 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:                         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 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2016.72
//
Query:       gi|557694117|ref|YP_008797171.1|  [L=362]
Description: maltooligosaccharide ABC transportor ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  112.4   0.0    3.7e-32  111.7   0.0    1.3  1  ABC_tran         ABC transporter
    5.6e-10   39.2   0.0    1.3e-09   38.1   0.0    1.6  1  TOBE_2           TOBE domain
    9.6e-06   26.3   0.0    4.1e-05   24.3   0.0    2.2  1  OB_MalK          MalK OB fold domain
    0.00011   22.4   0.0    0.00028   21.1   0.0    1.7  1  TOBE             TOBE domain
     0.0025   17.3   0.0     0.0051   16.3   0.0    1.4  1  SMC_N            RecF/RecN/SMC N terminal domain
      0.003   17.8   0.0     0.0056   17.0   0.0    1.6  1  AAA_22           AAA domain
     0.0042   17.5   0.0     0.0097   16.3   0.0    1.6  1  AAA              ATPase family associated with various cellul
     0.0055   16.4   0.0       0.01   15.6   0.0    1.5  1  AAA_30           AAA domain
  ------ inclusion threshold ------
      0.012   15.2   0.0      0.026   14.1   0.0    1.6  1  AAA_25           AAA domain
      0.013   15.2   0.1       0.14   11.9   0.1    2.2  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
      0.013   15.3   0.1       0.46   10.3   0.0    2.1  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      0.014   15.4   0.0       0.02   14.8   0.0    1.2  1  Rad17            Rad17 P-loop domain
      0.021   15.4   0.0      0.036   14.6   0.0    1.4  1  AAA_23           AAA domain
      0.021   15.2   0.0      0.032   14.6   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.022   15.3   0.0      0.041   14.4   0.0    1.5  1  AAA_18           AAA domain
      0.032   14.8   0.0       0.19   12.3   0.0    2.3  2  CysA_C_terminal  CysA C-terminal regulatory domain
      0.048   13.9   0.0       0.15   12.3   0.0    1.8  2  AAA_28           AAA domain
       0.05   13.6   0.1       0.11   12.5   0.1    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.056   13.0   0.0      0.099   12.2   0.0    1.4  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
      0.067   13.5   0.2       0.12   12.7   0.1    1.6  1  AAA_19           AAA domain
      0.085   12.8   0.0       0.16   11.9   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
      0.088   12.6   0.0       0.21   11.3   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
       0.14   11.3   0.0        0.2   10.8   0.0    1.3  1  NB-ARC           NB-ARC 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 !  111.7   0.0   4.8e-35   3.7e-32       2     136 ..      20     161 ..      19     162 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 4.8e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++++l++k+ge va++G+ GaGK+t+l+++agl++ t+G+i++ ++ +++  l+ +++ +++++q+  l p++tv+e
  gi|557694117|ref|YP_008797171.1|  20 DDITLEVKHGEFVALFGPPGAGKTTILRMIAGLEEVTSGKIWIGDRVVND--LSPAERDVAMVFQTFALYPTMTVYE 94 
                                       89***************************************999999999..************************* PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n             e d++++++++ l++++l +++      +LSgG++qrval ra++++p+l+++DEp 
  gi|557694117|ref|YP_008797171.1|  95 NlafplrkrrlandEIDRRVKEVATILNISHLLEKKP----GTLSGGERQRVALGRAMVRNPQLFIFDEPL 161
                                       **********999999999999999999999888887....*****************************6 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   1.6e-12   1.3e-09       1      76 []     281     353 ..     281     353 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.6e-12
                            TOBE_2   1 laiRPEklrlaaagg.an.glsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavv 75 
                                       l+ RP  +++ +++g ++ +++G Ve vey+Gs++   v+l++ +   v  p++    +++pG++V+l +++ ++++
  gi|557694117|ref|YP_008797171.1| 281 LGFRPHYVEI-SKEGlGGlSIKGSVEAVEYMGSESYAIVSLGSSEA-SVLLPPNM---RVEPGSEVWLNINTSRMHL 352
                                       578*******.5666578899***********************99.66666666...8*****************9 PP

                            TOBE_2  76 l 76 
                                       +
  gi|557694117|ref|YP_008797171.1| 353 F 353
                                       8 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   5.2e-08   4.1e-05       1      50 [.     235     285 ..     235     288 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.2e-08
                           OB_MalK   1 GSPaMNflpatveedg..vlvegggvtlplpeeqklalklyagkevilGiRP 50 
                                       GSP+ N ++++++ dg  +l++ g ++l+l+      l +  gk+v+lG+RP
  gi|557694117|ref|YP_008797171.1| 235 GSPQINTVKGELSVDGgkTLLDLGFAKLDLSFLS-DVLTKFSGKKVVLGFRP 285
                                       9************777665555555555554433.389************** PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.5e-07   0.00028       7      64 .]     300     352 ..     299     352 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.5e-07
                              TOBE   7 lpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       ++g V++ve  gse++  v lg  +   + ++++ ++e    pG+eV++ i+ +++hl
  gi|557694117|ref|YP_008797171.1| 300 IKGSVEAVEYMGSESYAIVSLGSSE-ASVLLPPNMRVE----PGSEVWLNINTSRMHL 352
                                       79***********************.999999999999....**************97 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 !   16.3   0.0   6.6e-06    0.0051      23     197 ..      28     191 ..       8     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.6e-06
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                       + +f a+ Gp G+GK+ +l  i    G ++ ++ +    +++++   + a+ + a v  tf      ++ e+  + +
  gi|557694117|ref|YP_008797171.1|  28 HGEFVALFGPPGAGKTTILRMI---AGLEEVTSGKIWIGDRVVND-LSPAERDVAMVFQTFALYPTMTVYENLAFPL 100
                                       45799**************999...79889988999999999998.8999999999999999988888888889999 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                       ++r   ++e + +++ + +t  ++s+lle+   ++ +LSgGe++ val       +v+   l+++De   +LD+k +
  gi|557694117|ref|YP_008797171.1| 101 RKRRLANDEIDRRVK-EVATILNISHLLEK---KPGTLSGGERQRVALG----RAMVRNPQLFIFDEPLTNLDAKLR 169
                                       999998888444443.34445556666665...6889******988875....45788889*************999 PP

                                       HHHHHHHHHHCTT.SEEEEE-S CS
                                       xxxxxxxxxxxxx.xxxxxxxx RF
                             SMC_N 177 kkvaellkekskn.aQfivisl 197
                                         +   l++ +k+  Q  + s 
  gi|557694117|ref|YP_008797171.1| 170 LHMRVELRKIQKEmGQTAIFST 191
                                       8888777776666357666654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.1e-06    0.0056       4      29 ..      28      53 ..      23     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.1e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      +  +++++G++G+GKTt lr+++   
  gi|557694117|ref|YP_008797171.1| 28 HGEFVALFGPPGAGKTTILRMIAGLE 53
                                      78899***************987654 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 !   16.3   0.0   1.2e-05    0.0097       2      22 ..      33      53 ..      32      89 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                                      EEESSTTSSHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavakel 22
                                       l+GppG GKT++ + +a   
  gi|557694117|ref|YP_008797171.1| 33 ALFGPPGAGKTTILRMIAGLE 53
                                      69***************9764 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.3e-05      0.01      19      47 ..      30      65 ..      22     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g......g 47
                                       +++l Gp+G+GKtt+l+ ++ + e   g      +
  gi|557694117|ref|YP_008797171.1| 30 EFVALFGPPGAGKTTILRMIAGLEEVTsGkiwigdR 65
                                      478999**************9988877445555542 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.3e-05     0.026      32      65 ..      28      63 ..      16      80 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                            AAA_25 32 agelallaGapgtGKttlaldlal..avatGkpwlg 65
                                       ge+++l+G+pg+GKtt++  +a   +v++Gk w g
  gi|557694117|ref|YP_008797171.1| 28 HGEFVALFGPPGAGKTTILRMIAGleEVTSGKIWIG 63
                                      699**************9976664336778888877 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 ?   11.9   0.1   0.00018      0.14      34      55 ..      30      51 ..      15      61 .. 0.85
   2 ?    0.6   0.0      0.55   4.3e+02     120     152 ..      71     103 ..      60     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                            RuvB_N 34 dhvllyGpPGlGkttlakiiak 55
                                      + v l+GpPG Gktt+ ++ia 
  gi|557694117|ref|YP_008797171.1| 30 EFVALFGPPGAGKTTILRMIAG 51
                                      5789************999984 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.55
                            RuvB_N 120 GpsarsikldlpkftlvgattragllssPlrdr 152
                                        p+ r + + ++ f+l  + t    l+ Plr+r
  gi|557694117|ref|YP_008797171.1|  71 SPAERDVAMVFQTFALYPTMTVYENLAFPLRKR 103
                                       6788999999*********************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 ?   10.3   0.0   0.00058      0.46       1      25 [.      31      55 ..      31      80 .. 0.71
   2 ?    2.8   0.0      0.11        83     236     274 ..     133     168 ..      92     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00058
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl 25
                                      + +l Gp g+GK+++L+ + +l  +
  gi|557694117|ref|YP_008797171.1| 31 FVALFGPPGAGKTTILRMIAGLEEV 55
                                      6799***************999443 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.11
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkl 274
                                        lS G ++  al  a+ r +    l+++DEp ++L+ kl
  gi|557694117|ref|YP_008797171.1| 133 TLSGGERQRVALGRAMVRNP---QLFIFDEPLTNLDAKL 168
                                       45777777777777777777...99**********9877 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   0.0   2.5e-05      0.02      37     114 ..      21      98 ..      10     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.5e-05
                             Rad17  37 advLesrkkriLLisGPsGCgkstvvkvLsk.elgiklrewlnpvslkepdnqksdfkgltekesrflsqiesfkel 112
                                         +Le ++ + + + GP+G gk+t++++++  e +++ + w+    +++ +  + d+  +++++  + + + ++++l
  gi|557694117|ref|YP_008797171.1|  21 DITLEVKHGEFVALFGPPGAGKTTILRMIAGlEEVTSGKIWIGDRVVNDLSPAERDVAMVFQTFA-LYPTMTVYENL 96 
                                       55678887789999*************9986378999999***999999999*****99999999.88999999987 PP

                             Rad17 113 eL 114
                                         
  gi|557694117|ref|YP_008797171.1|  97 AF 98 
                                       43 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   4.6e-05     0.036      11      39 ..      20      49 ..       3      52 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.6e-05
                            AAA_23 11 rdqeidFsk.gltlItGpNGaGKTTildAi 39
                                      +d +++ ++  +++++Gp GaGKTTil+ i
  gi|557694117|ref|YP_008797171.1| 20 DDITLEVKHgEFVALFGPPGAGKTTILRMI 49
                                      45555665525889*************988 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   4.1e-05     0.032      21      45 ..      28      50 ..      11     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.1e-05
                            AAA_16 21 sgrpelvllsGesGvGKsslvrell 45
                                       g  e v l G++G GK++++r+++
  gi|557694117|ref|YP_008797171.1| 28 HG--EFVALFGPPGAGKTTILRMIA 50
                                      44..789***************998 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.3e-05     0.041       1      38 [.      32      67 ..      32     116 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.3e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakengll 38
                                      ++l G+pG+GKtt+ + ++ ++   v +++++  ++ +
  gi|557694117|ref|YP_008797171.1| 32 VALFGPPGAGKTTILRMIAGLE--EVTSGKIWIGDRVV 67
                                      6899************998887..44444444444444 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 ?   -1.2   0.0       4.1   3.2e+03       7      16 ..      55      64 ..      54      78 .. 0.76
   2 ?   12.3   0.0   0.00024      0.19       8      43 .]     249     290 ..     240     290 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.1
                   CysA_C_terminal  7 vedGklriGg 16
                                      v  Gk+ iG+
  gi|557694117|ref|YP_008797171.1| 55 VTSGKIWIGD 64
                                      789*****99 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00024
                   CysA_C_terminal   8 edGk..lriGglalpvP....elagadgqevvayVRPhDlei 43 
                                       ++Gk  l +G + l++      l    g++vv++ RPh +ei
  gi|557694117|ref|YP_008797171.1| 249 DGGKtlLDLGFAKLDLSflsdVLTKFSGKKVVLGFRPHYVEI 290
                                       444455666667777777766777779************998 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00019      0.15       2      21 ..      32      51 ..      31      83 .. 0.77
   2 ?   -1.7   0.0         4   3.1e+03      72     119 ..     151     195 ..     135     234 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                            AAA_28  2 ivitGgestGKTtlleaLaa 21
                                      ++++G++++GKTt+l+ +a 
  gi|557694117|ref|YP_008797171.1| 32 VALFGPPGAGKTTILRMIAG 51
                                      899************99983 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4
                            AAA_28  72 ankvlfcDrglldtlaYarayggeaeaeleaaarekrydlvfllppap 119
                                       +++++++D  l +  a +r ++     el ++ +e+  +++f +p ++
  gi|557694117|ref|YP_008797171.1| 151 NPQLFIFDEPLTNLDAKLRLHMRV---ELRKIQKEMGQTAIFSTPDDA 195
                                       556666665555544444444443...455555555555555555555 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   0.1   0.00015      0.11      18      41 ..      26      51 ..       9      60 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00015
                                      H..TEEEEEEESTTSSHHHHHHHHHH CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrglak 41
                                      +  g++++L G+ GaGKTt+ r +a 
  gi|557694117|ref|YP_008797171.1| 26 VkhGEFVALFGPPGAGKTTILRMIAG 51
                                      233788****************9974 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   0.0   0.00013     0.099       4      46 ..      33      80 ..      30      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                      EEEESTTCCHHHHHHHHH..CT--SS-EEE...EESS-SSCHCCCCCC CS
                              cobW  4 vltGflGsGKTtLlnhll..enraglklav...ivNefgevsiDaell 46
                                       l G++G+GKTt+l+ +   e+  + k+ +   +vN+++  + D +++
  gi|557694117|ref|YP_008797171.1| 33 ALFGPPGAGKTTILRMIAglEEVTSGKIWIgdrVVNDLSPAERDVAMV 80
                                      688************998765555555544455777777666666665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00015      0.12      10      32 ..      29      51 ..      20     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhiva 32
                                       + +++ ++pG GKT++l++i  
  gi|557694117|ref|YP_008797171.1| 29 GEFVALFGPPGAGKTTILRMIAG 51
                                      57899************998754 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.16      89     129 ..      18      59 ..       8      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                        +++++ ++k+ ++++l G+ G+GK+t++ ++++ +e+  g+
  gi|557694117|ref|YP_008797171.1|  18 VVDDITLEVKHgEFVALFGPPGAGKTTILRMIAGLEEVTSGK 59 
                                       5667777777669*******************9977766555 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 ?   11.3   0.0   0.00027      0.21      15      39 ..      22      46 ..      17      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                       t+e++  +++ l Gp G+GK+T+l
  gi|557694117|ref|YP_008797171.1| 22 ITLEVKHGEFVALFGPPGAGKTTIL 46
                                      56778855699************98 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00026       0.2      21      42 ..      30      51 ..      14     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00026
                                      EEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqiln 42
                                       +val G +G GKtt+++ i  
  gi|557694117|ref|YP_008797171.1| 30 EFVALFGPPGAGKTTILRMIAG 51
                                      49**************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2395.93
//
Query:       gi|557694118|ref|YP_008797172.1|  [L=364]
Description: maltooligosaccharide ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  100.9   0.0    1.3e-28  100.2   0.0    1.3  1  ABC_tran         ABC transporter
    4.1e-08   33.9   0.0    1.4e-07   32.2   0.0    2.0  1  OB_MalK          MalK OB fold domain
    1.9e-05   24.8   0.0    5.4e-05   23.3   0.0    1.8  2  TOBE_2           TOBE domain
      3e-05   24.2   0.0    0.00043   20.5   0.0    2.5  2  TOBE             TOBE domain
    0.00028   20.8   0.1        0.6    9.9   0.0    2.3  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0031   17.4   0.0     0.0048   16.8   0.0    1.3  1  Rad17            Rad17 P-loop domain
  ------ inclusion threshold ------
      0.012   15.9   1.4      0.098   12.9   1.4    2.2  1  AAA_22           AAA domain
      0.039   14.4   0.6        0.1   13.0   0.6    2.0  1  AAA              ATPase family associated with various cellul
      0.043   14.2   0.1       0.11   12.9   0.1    1.4  1  AAA_16           AAA ATPase domain
      0.046   13.6   0.0      0.096   12.6   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
      0.075   13.6   0.0       0.42   11.2   0.0    2.4  2  CysA_C_terminal  CysA C-terminal regulatory domain
       0.17   11.0   0.0       0.22   10.7   0.0    1.2  1  G-alpha          G-protein alpha 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 !  100.2   0.0   8.9e-32   1.3e-28       1     136 [.      19     161 ..      19     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 8.9e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       +kn+s+++  g+   ++G++G+GK+t l+++agl+kp++G+il+dg  +++   +  ++ i++++q   + p++tv 
  gi|557694118|ref|YP_008797172.1|  19 VKNLSFEVPDGSFASLLGPSGCGKTTTLRMIAGLEKPDKGDILIDGVRVND--VPPHKRDIAMVFQFYAIYPGMTVF 93 
                                       58************************************************9..999********************* PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +n             + +++++++++ l +++l d+ +      L  G+kqrval ra++++pk++l+DEp 
  gi|557694118|ref|YP_008797172.1|  94 DNmafplrqrkmskqDIQRRVKEIAEILHISHLLDKDA----MGLTVGEKQRVALGRAMVREPKVFLFDEPL 161
                                       *********98776666666888888888888888888....*****************************6 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   9.5e-11   1.4e-07       1      53 []     235     289 ..     235     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 9.5e-11
                           OB_MalK   1 GSPaMNflpatveedg..vlvegggvtlplpeeq..klalklyagkevilGiRPEhi 53 
                                       G+P MN+++++v+++g  v+++++g++l    e   k   +l +g e+++G+RP +i
  gi|557694118|ref|YP_008797172.1| 235 GTPTMNLIDCRVSNSGqkVFLQFDGFSLSE--EFlgKNLRALPDGMELVFGVRPTDI 289
                                       99***********************88863..3323559999************887 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       7.1   1.1e+04      60      69 ..     249     258 ..     245     259 .. 0.82
   2 !   23.3   0.0   3.6e-08   5.4e-05       2      76 .]     283     352 ..     282     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 7.1
                            TOBE_2  60 pGdtVelswd 69 
                                        G++V l++d
  gi|557694118|ref|YP_008797172.1| 249 SGQKVFLQFD 258
                                       6999999997 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 3.6e-08
                            TOBE_2   2 aiRPEklrla.aagganglsGtVedveylGsstryvvelaggqlvvvrqpnadrdsalapGdtVelswdpddavvl 76 
                                       ++RP +++ + ++ g + l+G++  +e lG+ +   ++l  g+ ++ +++ ++   a ++Gd+ ++ +dpd+++++
  gi|557694118|ref|YP_008797172.1| 283 GVRPTDIEAElGEKG-GVLRGKINVIESLGDRYI--LDLSVGNTIFRVVSREA---AATIGDEMAIYIDPDKIHLF 352
                                       79******9643333.699************655..56666666666666666...669***************98 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.44   6.6e+02      49      58 ..     249     258 ..     245     262 .. 0.87
   2 !   20.5   0.0   2.9e-07   0.00043       5      64 .]     298     351 ..     295     351 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.44
                              TOBE  49 pGeeVfalik 58 
                                        G++Vf++++
  gi|557694118|ref|YP_008797172.1| 249 SGQKVFLQFD 258
                                       59*******9 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.9e-07
                              TOBE   5 NqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakvhl 64 
                                       ++l+g+++v+e lg ++ +++ +g       +v+r++a+     +G+e+ + i++ k+hl
  gi|557694118|ref|YP_008797172.1| 298 GVLRGKINVIESLGDRYILDLSVGNTI-F-RVVSREAAAT----IGDEMAIYIDPDKIHL 351
                                       78*********************9988.4.4455777777....**************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 !    8.9   0.0   0.00082       1.2       2      22 ..      32      52 ..      31      93 .. 0.82
   2 !    9.9   0.0    0.0004       0.6     254     298 ..     151     193 ..     114     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00082
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                      + l Gp g+GK++ L+ + +l
  gi|557694118|ref|YP_008797172.1| 32 ASLLGPSGCGKTTTLRMIAGL 52
                                      6799**************998 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0004
                            AAA_21 254 alkkgsllliDEpEngLHPkllrrllellkelsrngaQv..iltTHS 298
                                        +   +++l+DEp ++L+ +l ++    lk+l++ ++++  i +TH+
  gi|557694118|ref|YP_008797172.1| 151 EP---KVFLFDEPLTNLDARLRAKMRVELKKLHN-RIKIttIYVTHD 193
                                       22...9********************99988888.555555999998 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.2e-06    0.0048      50     114 ..      34      98 ..       9     129 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.2e-06
                             Rad17  50 isGPsGCgkstvvkvLskelgiklre.wlnpvslkepdnqksdfkgltekesrflsqiesfkeleL 114
                                       + GPsGCgk+t++++++    ++  +  +++v +++ + +k d+  +++    + + + +f ++  
  gi|557694118|ref|YP_008797172.1|  34 LLGPSGCGKTTTLRMIAGLEKPDKGDiLIDGVRVNDVPPHKRDIAMVFQFYA-IYPGMTVFDNMAF 98 
                                       77*************9987766555416789999998888888876666555.7888888887632 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   6.6e-05     0.098       6      29 ..      30      53 ..      27     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleql 29
                                      ++  + G+sG+GKTt+lr+++   
  gi|557694118|ref|YP_008797172.1| 30 SFASLLGPSGCGKTTTLRMIAGLE 53
                                      678899************998665 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 ?   13.0   0.6     7e-05       0.1       3      20 ..      34      51 ..      32     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7e-05
                                      EESSTTSSHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavak 20
                                      l Gp G+GKT++ + +a 
  gi|557694118|ref|YP_008797172.1| 34 LLGPSGCGKTTTLRMIAG 51
                                      88**************96 PP

>> AAA_16  AAA ATPase 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      25      45 ..      30      50 ..      16      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.1e-05
                            AAA_16 25 elvllsGesGvGKsslvrell 45
                                      +   l G+sG+GK++ +r+++
  gi|557694118|ref|YP_008797172.1| 30 SFASLLGPSGCGKTTTLRMIA 50
                                      66789*************997 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.4e-05     0.096      85     123 ..      14      53 ..       3      66 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.4e-05
                                       TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                        ++e++++l+ ++ d +++ l+G+SG GK+t + ++++ +
  gi|557694118|ref|YP_008797172.1|  14 GKQEAVKNLSFEVPDgSFASLLGPSGCGKTTTLRMIAGLE 53 
                                       357899999999988899*************999998754 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 ?   11.2   0.0   0.00028      0.42       1      42 [.     240     290 ..     240     291 .. 0.71
   2 ?   -2.5   0.0       5.5   8.3e+03      14      38 ..     320     346 ..     318     351 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
                   CysA_C_terminal   1 NlFhGrve.dGk...lriGglalpvP....elaga..dgqevvayVRPhDle 42 
                                       Nl++ rv+  G+   l+++g++l  +     l  a  dg e v +VRP D+e
  gi|557694118|ref|YP_008797172.1| 240 NLIDCRVSnSGQkvfLQFDGFSLSEEflgkNLR-AlpDGMELVFGVRPTDIE 290
                                       777777865676677777777777776654222.24699************9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.5
                   CysA_C_terminal  14 iGglalpvP..elagadgqevvayVRP 38 
                                       +G++ + v   e+a++ g+e   y+ P
  gi|557694118|ref|YP_008797172.1| 320 VGNTIFRVVsrEAAATIGDEMAIYIDP 346
                                       566556633356666678888888755 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015      0.22      28     109 ..      34     128 ..      30     223 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
                                       EEESTTSSHHHHHHHHHHHCS--.............--HHHHHCCHHHHHHHHHHHHHHHHHHHHHT.T.......H CS
                           G-alpha  28 llGqseSGKsTilkqlkllykkg.............fseeelatwraviqlnivrsiktilealesl.eselsesfe 90 
                                       llG s++GK+T+l+ +  l+k+              +    ++ +  v q+  +    t+++++ ++  ++ +++ +
  gi|557694118|ref|YP_008797172.1|  34 LLGPSGCGKTTTLRMIAGLEKPDkgdilidgvrvndVPPH-KRDIAMVFQFYAIYPGMTVFDNMAFPlRQRKMSKQD 109
                                       8****************99988877888888554432222.233455777777777777777777752233333334 PP

                                       HHC-SS-SCCCS-HCHHHH CS
                           G-alpha  91 lqelkerldplkkveasli 109
                                        q + +++++++++++ l 
  gi|557694118|ref|YP_008797172.1| 110 IQRRVKEIAEILHISHLLD 128
                                       4444444555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2623.92
//
Query:       gi|557694119|ref|YP_008797173.1|  [L=363]
Description: oxidoreductase domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   88.7   1.3      8e-25   88.0   1.3    1.3  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    3.3e-07   30.9   0.6    5.5e-07   30.2   0.6    1.4  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
      8e-06   26.0   0.2    1.2e-05   25.3   0.2    1.3  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    7.1e-05   23.2   0.1    0.00018   21.9   0.1    1.6  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0002   21.3   0.0    0.00046   20.2   0.0    1.7  1  GFO_IDH_MocA_C   Oxidoreductase family, C-terminal alpha/beta
     0.0081   16.8   0.1      0.017   15.7   0.1    1.5  1  G6PD_N           Glucose-6-phosphate dehydrogenase, NAD bindi
  ------ inclusion threshold ------
       0.01   16.4   1.0      0.032   14.8   0.3    2.1  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.032   14.4   0.1        4.3    7.5   0.0    2.4  2  Response_reg     Response regulator receiver domain
       0.04   13.5   0.1      0.071   12.7   0.1    1.3  1  MTS              Methyltransferase small domain
       0.11   13.3   0.0       0.27   12.0   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
       0.11   11.8   0.0       0.16   11.3   0.0    1.3  1  CMAS             Mycolic acid cyclopropane synthetase
       0.27   10.7   1.9        1.9    8.0   0.3    2.0  2  HMGL-like        HMGL-like


Domain annotation for each model (and alignments):
>> 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 !   88.0   1.3   5.4e-28     8e-25       2     118 ..       6     124 ..       5     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 5.4e-28
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE...EESSHHHHHTCTTESEEEE-S-GGGH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve...aysdleelladpeidavivatpngth 75 
                                        v++ GaG++ ++h+++++++ ++++vva+ +++ e+a++ ae+ g++    y+dl + l++pe+d+v+v+tp + h
  gi|557694119|ref|YP_008797173.1|   6 GVLVHGAGWVSTQHIKAFQNN-PHTKVVAISSRKIESARKRAEEAGLKdvkLYDDLHKALENPEVDIVSVCTPQHVH 81 
                                       68999**********999999.************************99999************************** PP

                                       HHHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEE CS
                      GFO_IDH_MocA  76 eelakaaleagkhvllEKPlattveeakelvelaekkgklvsv 118
                                       +e ++aa++agkh+++EKP+  ++ee+k++ ++++k++++  v
  gi|557694119|ref|YP_008797173.1|  82 AENTIAAAKAGKHIVIEKPIGNSLEEIKNMRDAVRKAKVKTVV 124
                                       *************************************998766 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 !   30.2   0.6   3.7e-10   5.5e-07       1     114 [.      11     122 ..      11     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.7e-10
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESS.EEE-TT.HHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTT CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrd.sllskd.rkallasealtldlddliahldpdvvVEcasseavael 75 
                                       G+G + ++ ++++++++ +   ++va+  r+   ++k+  +a l++ +l++dl + ++++++d+v  c+++   ae 
  gi|557694119|ref|YP_008797173.1|  11 GAGWVSTQHIKAFQNNPHT---KVVAISSRKiESARKRaEEAGLKDVKLYDDLHKALENPEVDIVSVCTPQHVHAEN 84 
                                       89999999*******9975...*********866666668899********************************** PP

                                       HHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.E CS
                     NAD_binding_3  76 vlkaLkagkdvvtankgaladealyeeLreaaeangaki 114
                                         +a kagk++v+     ++ ++  +++r+a +++++k 
  gi|557694119|ref|YP_008797173.1|  85 TIAAAKAGKHIVIEKPIGNS-LEEIKNMRDAVRKAKVKT 122
                                       ************98888888.888888888888887775 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   8.3e-09   1.2e-05      13     100 ..       5      91 ..       1     112 [. 0.88

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8.3e-09
                                       -EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS- CS
                      Shikimate_DH  13 kkvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisataseep 88 
                                         vl+ GaG ++++ +k++ ++ + k v++  R +e a++ aee + +   ++ +++l+++l++ +v i+++ ++++
  gi|557694119|ref|YP_008797173.1|   5 LGVLVHGAGWVSTQHIKAFQNNpHTKVVAISSRKIESARKRAEEAGLK--DVKLYDDLHKALENPEVDIVSVCTPQH 79 
                                       569999**************996788889****************888..8999*******************9999 PP

                                       SB-HHHHHCCHH CS
                      Shikimate_DH  89 ilekeeveealk 100
                                       +  ++ + +a++
  gi|557694119|ref|YP_008797173.1|  80 VHAENTIAAAKA 91 
                                       999888887764 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 !   21.9   0.1   1.2e-07   0.00018       8      94 ..      12      96 ..       7      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
                                      TSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEE..GGGGGCTT-SEEEE-SCHHHHHHHHH CS
                    Semialdhyde_dh  8 tGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkved..vdeeelkevdivflalpagvskelap 84
                                       G v ++ ++  +++p+ ++v+++s++ +  +k ae ++     kd+k+ d   ++ e  evdiv  ++p+ v++e + 
  gi|557694119|ref|YP_008797173.1| 12 AGWVSTQHIKAFQNNPHTKVVAISSRKIESARKRAEEAG----LKDVKLYDdlHKALENPEVDIVSVCTPQHVHAENTI 86
                                      699999****************99999955555555544....89999888544455559******************* PP

                                      HHHHTTSEEE CS
                    Semialdhyde_dh 85 klaeagvkvi 94
                                      ++a+ag +++
  gi|557694119|ref|YP_008797173.1| 87 AAAKAGKHIV 96
                                      *****99554 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0     3e-07   0.00046       1      61 [.     138     198 ..     138     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3e-07
                                       HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSE CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqp 61 
                                       K  I++g+lG++++v+ ++    a+ ++ +   r k ++  ++   g+H iD ++w++ + 
  gi|557694119|ref|YP_008797173.1| 138 KRIIADGMLGNIYYVEADYQSAIAAWWSGYEDARKKSTGVSAFLVGGCHAIDAVRWFAEKQ 198
                                       6789***********9888888888888888777778888899*************99875 PP

>> G6PD_N  Glucose-6-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.2e-05     0.017     107     156 ..      75     117 ..      17     123 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                            G6PD_N 107 avppslfeevaeklkkaglakeeewkrvvvEKPfGkdlesarelneelkk 156
                                        +p ++ +e +       +a++++ k +v+EKP+G++le  +++ ++++k
  gi|557694119|ref|YP_008797173.1|  75 CTPQHVHAENT-------IAAAKAGKHIVIEKPIGNSLEEIKNMRDAVRK 117
                                       44444433322.......222356789******************99987 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 ?   14.8   0.3   2.1e-05     0.032       4      92 ..       7      97 ..       4      99 .. 0.76
   2 ?   -1.2   0.0       2.1   3.2e+03      54      75 ..     333     354 ..     324     358 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                                      EE..TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...-EEECECHHHHHHH-SEEEE-S-HHHHHHH CS
                     F420_oxidored  4 ii..GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...vkvtavdneeaaeeadvvvlavkpedveev 77
                                      ++  GaG +    ++ ++++  + +++v ++sr+ e+a++ aee+g   vk+   d  +a+e+ +v +++v + ++  +
  gi|557694119|ref|YP_008797173.1|  7 VLvhGAGWVSTQHIKAFQNN--PHTKVVAISSRKIESARKRAEEAGlkdVKLYD-DLHKALENPEVDIVSVCTPQHVHA 82
                                      55567777777778877777..58999999****************98888888.99*****88888888876666666 PP

                                      HHHCGHHHHTTSEEE CS
                     F420_oxidored 78 lselakdalkgklvi 92
                                       + +a+++  +++vi
  gi|557694119|ref|YP_008797173.1| 83 ENTIAAAKAGKHIVI 97
                                      666644555555665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.1
                                       CHHHHHHH-SEEEE-S-HHHHH CS
                     F420_oxidored  54 dneeaaeeadvvvlavkpedve 75 
                                       + e+a++  ++ + a+  ++++
  gi|557694119|ref|YP_008797173.1| 333 NLEDAIKTHEIAFAALECYKTA 354
                                       578999*******999888765 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0029       4.3      60      96 ..      15      53 ..       8      56 .. 0.84
   2 ?    4.7   0.0     0.022        33      70     104 ..      67     103 ..      54     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0029
                                      HHHHHHHHCT..TTSEEEEEESSTSHHHHHHHHHCTESE CS
                      Response_reg 60 ellkeireed..pelpviiltahseeedavealkagadd 96
                                        +++i++ +  p+++v+++++++ e+ +++a +ag +d
  gi|557694119|ref|YP_008797173.1| 15 VSTQHIKAFQnnPHTKVVAISSRKIESARKRAEEAGLKD 53
                                      5667777665569***********************988 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.022
                                       TTSEEE.EEE.SSTSHHHHHHHHHCTESEEEESSG-H CS
                      Response_reg  70 pelpvi.ilt.ahseeedavealkagaddflsKpfdp 104
                                       pe+ ++ ++t +h   e++++a kag + ++ Kp+  
  gi|557694119|ref|YP_008797173.1|  67 PEVDIVsVCTpQHVHAENTIAAAKAGKHIVIEKPIGN 103
                                       555555256688999*******************954 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.7e-05     0.071      41     117 ..      11      88 ..       4      95 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
                                       TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---STTTCHCHHH CS
                               MTS  41 GaGvlgaalakespeae.vtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPfhagkatela 116
                                       GaG ++++  k+ +++   ++v ++ r +esa++ +e+ +l+   +  d+ +++e+ ++d++    P h + + + a
  gi|557694119|ref|YP_008797173.1|  11 GAGWVSTQHIKAFQNNPhTKVVAISSRKIESARKRAEEAGLKDVKLYDDLHKALENPEVDIVSVCTPQHVHAENTIA 87 
                                       89999987666555444399**********************888899**************999999988886655 PP

                                       H CS
                               MTS 117 v 117
                                       +
  gi|557694119|ref|YP_008797173.1|  88 A 88 
                                       5 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   0.00018      0.27       7      84 ..      11      87 ..       8      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                                      TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHH CS
                   Methyltransf_25  7 GtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsdedle 83
                                      G G ++ +  k++ ++ +   v is++ +e ar+raee+gl +v+++    ++l+ ++  +D+v ++ + +h++ e++ 
  gi|557694119|ref|YP_008797173.1| 11 GAGWVSTQHIKAFqNNPHTKVVAISSRKIESARKRAEEAGLkDVKLYDDLHKALENPE--VDIVSVC-TPQHVHAENTI 86
                                      888888888889865888899999*****************99999888778887665..9999994.55777766654 PP

                                      H CS
                   Methyltransf_25 84 k 84
                                      +
  gi|557694119|ref|YP_008797173.1| 87 A 87
                                      4 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00011      0.16      68     152 ..       9      92 ..       4     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                                       EES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGG CS
                              CMAS  68 diGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgken 144
                                         G+GW s+ +  + + + +   + +S+ + + a+kr +e++l++ v+++   ++ l+++   +vsv   +hv  en
  gi|557694119|ref|YP_008797173.1|   9 VHGAGWVSTQHIKAFQNNPHTKVVAISSRKIESARKRAEEAGLKD-VKLYDDLHKALENPEVDIVSVCTPQHVHAEN 84 
                                       569*****9998888889************************765.455555578888866679*********9998 PP

                                       HHHHHHHH CS
                              CMAS 145 ydtffkkl 152
                                         +  k+ 
  gi|557694119|ref|YP_008797173.1|  85 TIAAAKAG 92 
                                       76655555 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1     0.076   1.1e+02      50      97 ..      12      58 ..       4      61 .. 0.69
   2 ?    8.0   0.3    0.0012       1.9      29      96 ..      61     126 ..      58     139 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.076
                                      THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEE CS
                         HMGL-like 50 ddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvfi 97
                                        + +++ i+++ +++  + +v    + i+ a +++++ag k v++++
  gi|557694119|ref|YP_008797173.1| 12 AGWVSTQHIKAFQNNP-HTKVVAISSRKIESARKRAEEAGLKDVKLYD 58
                                      4466666666666655.445566667788999999999**99999875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0012
                                       HHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEE CS
                         HMGL-like  29 akaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvf 96 
                                        kaL++  vd + v+ p++   + e + a+aka+k+  i  ++    + ik   +a+++a++k+v  f
  gi|557694119|ref|YP_008797173.1|  61 HKALENPEVDIVSVCTPQHV--HAENTIAAAKAGKHIVIEKPIGNSLEEIKNMRDAVRKAKVKTVVSF 126
                                       5899****************..9****************************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2740.62
//
Query:       gi|557694120|ref|YP_008797174.1|  [L=339]
Description: oxidoreductase domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  103.1   0.0    2.4e-29  102.6   0.0    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    2.4e-11   43.7   0.0    4.2e-11   42.9   0.0    1.4  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
    5.2e-08   33.5   0.0    7.4e-08   33.1   0.0    1.2  1  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain
     0.0061   17.1   0.0      0.011   16.3   0.0    1.4  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0075   16.4   0.0      0.012   15.7   0.0    1.4  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
       0.16   12.4   0.0       0.28   11.6   0.0    1.3  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai


Domain annotation for each model (and alignments):
>> 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 !  102.6   0.0     8e-33   2.4e-29       2     120 .]       5     122 ..       4     122 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 8e-33
                                       EEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHH CS
                      GFO_IDH_MocA   2 rvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngtheel 78 
                                        va+ G+G++g+ hl +++   ++ evv+++ ++ ++ ++ a +++v+   +le++++d +id+v ++tp++th+el
  gi|557694120|ref|YP_008797174.1|   5 GVAVLGYGFMGTTHLSAWKLV-EGCEVVGVWGRNRKKLDETALHYEVKPIYELEDVFRDNRIDIVDICTPTYTHHEL 80 
                                       69******************9.999**************************************************** PP

                                       HHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE- CS
                      GFO_IDH_MocA  79 akaaleagkhvllEKPlattveeakelvelaekkgklvsvgy 120
                                       a +aleagkhv++EKP+a+++e+a++++++ +k+g +++v++
  gi|557694120|ref|YP_008797174.1|  81 AVKALEAGKHVIIEKPMALSLEAADAMIKASRKTGGKLMVAH 122
                                       ***************************************986 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   1.4e-14   4.2e-11       1     108 [.     134     236 ..     134     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.4e-14
                                       HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEEEEE.SEEESCT CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvvaalgrmrqnaea 77 
                                       KelI+ g++G++ s+   +++ +a+ ++++  +r+  +sgG+++dl+iHd D+++w  G  ps+v+a     +++ +
  gi|557694120|ref|YP_008797174.1| 134 KELIDMGMVGDIASIR-MWRGGPAPEWSPWFMNRE--MSGGIAVDLAIHDVDYAIWVNGGLPSRVYAKV--ENLV-H 204
                                       9**************9.999999999999999965..8****************************994..5555.5 PP

                                       CCSCSEE.EEEEEEEEETTEEEEEEEECCTSS CS
                    GFO_IDH_MocA_C  78 aededaa.vmsvlnlekgsgevitlesgvskg 108
                                       ++++     ++ l++ +g +++i ++++  k+
  gi|557694120|ref|YP_008797174.1| 205 GKYNVEDfALITLRFPTGCIAIIEANWALPKT 236
                                       55554440345555555555566666665555 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 !   33.1   0.0   2.5e-11   7.4e-08       1     116 [.      10     120 ..      10     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.5e-11
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHHTTHH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseavaelvl 77 
                                       G+G  G++ l++ k  +   ++e+v+v+ r+ +++ d  al  + +   +l+d++++ ++d+v  c++    +el++
  gi|557694120|ref|YP_008797174.1|  10 GYGFMGTTHLSAWKLVE---GCEVVGVWGRN-RKKLDETALHYEVKPIYELEDVFRDNRIDIVDICTPTYTHHELAV 82 
                                       56666666666555555...79*********.55555667888889999*******8889987777*********** PP

                                       HHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE- CS
                     NAD_binding_3  78 kaLkagkdvvtankgaladealyeeLreaaeangakiyv 116
                                       kaL+agk+v++    al+ ++  +++++a++++g k++v
  gi|557694120|ref|YP_008797174.1|  83 KALEAGKHVIIEKPMALS-LEAADAMIKASRKTGGKLMV 120
                                       ******************.9999999*****99998876 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 !   16.3   0.0   3.8e-06     0.011       2      92 ..       6      92 ..       5      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.8e-06
                                      EEEETTSHHHHHHHHHH.HHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH..H-SEEEE-S-HHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgl.laagaqpheivvansrnpekaeelaeelgvkvtavdneeaae..eadvvvlavkpedveev 77
                                      ++++G+G mg + +s + l +g    e+v +  rn +k++e+a +++vk +  + e++ +  + d+v ++ +++ ++e+
  gi|557694120|ref|YP_008797174.1|  6 VAVLGYGFMGTTHLSAWkLVEG---CEVVGVWGRNRKKLDETALHYEVKPIY-ELEDVFRdnRIDIVDICTPTYTHHEL 80
                                      79**********9999944566...8888888********************.******9778899********99999 PP

                                      HHHCGHHHHTTSEEE CS
                     F420_oxidored 78 lselakdalkgklvi 92
                                      + ++   + +gk vi
  gi|557694120|ref|YP_008797174.1| 81 AVKA---LEAGKHVI 92
                                      8666...56666555 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0     4e-06     0.012       3      96 ..       6      93 ..       4     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4e-06
                                      EEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SE.EEE-S-HHHH CS
                            DapB_N  3 vavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadv.liDFTtpeav 80
                                      vav+G+ G mG++ ++a +  e++e+v++  r++++l+++ +       + +v+   +le+v++++ + ++D  tp+ +
  gi|557694120|ref|YP_008797174.1|  6 VAVLGY-GFMGTTHLSAWKLVEGCEVVGVWGRNRKKLDETAL-------HYEVKPIYELEDVFRDNRIdIVDICTPTYT 76
                                      99****.**************************955554333.......456666699*******554489******99 PP

                                      HHHHH.HHHHTT-EEEE CS
                            DapB_N 81 lenlk.lalekgvklVi 96
                                       + l+  ale+g++++i
  gi|557694120|ref|YP_008797174.1| 77 HHELAvKALEAGKHVII 93
                                      87665157888999887 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 ?   11.6   0.0   9.3e-05      0.28       2      94 ..       6      92 ..       5      95 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.3e-05
                                      EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHH CS
                    Semialdhyde_dh  2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvsk 80
                                      va++G  G +G+  l   +    +e+v + +++r   kkl+e + + e +  +++   d    +++div  ++p  +++
  gi|557694120|ref|YP_008797174.1|  6 VAVLG-YGFMGTTHLSAWKLVEGCEVVGVWGRNR---KKLDETALHYEVKPIYEL--EDVFRDNRIDIVDICTPTYTHH 78
                                      77888.7888888888888888888888888888...788887554333333444..44666689************** PP

                                      HHHHHHHHTTSEEE CS
                    Semialdhyde_dh 81 elapklaeagvkvi 94
                                      ela k++eag +vi
  gi|557694120|ref|YP_008797174.1| 79 ELAVKALEAGKHVI 92
                                      ***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2472.09
//
Query:       gi|557694121|ref|YP_008797175.1|  [L=335]
Description: oxidoreductase domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-22   79.8   0.3      4e-22   79.3   0.3    1.3  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    1.2e-06   28.5   0.1    2.3e-06   27.6   0.1    1.5  1  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
    0.00055   20.6   0.3    0.00097   19.8   0.3    1.3  1  NAD_binding_3   Homoserine dehydrogenase, NAD binding domain
  ------ inclusion threshold ------
      0.066   12.9   0.0      0.098   12.3   0.0    1.2  1  Oxidoreduct_C   Putative oxidoreductase C terminal domain
       0.12   12.5   0.1       0.24   11.5   0.1    1.5  1  DapB_N          Dihydrodipicolinate reductase, N-terminus
       0.13   12.8   0.1        6.2    7.4   0.0    2.4  2  Elf-1_N         Transcription factor protein N terminal


Domain annotation for each model (and alignments):
>> 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 !   79.3   0.3   1.3e-25     4e-22       1     118 [.       5     120 ..       5     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.3e-25
                                       EEEEEETTSHH.HHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHH CS
                      GFO_IDH_MocA   1 lrvaiiGaGki.gskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladpeidavivatpngthe 76 
                                       +rv++ G+  + ++ +++ ++   ++ evv++++++ e a +++++fg +  ++l++ll+  ++dav+va+ n  h+
  gi|557694121|ref|YP_008797175.1|   5 IRVGFAGVAHFhADSYVQCFKMI-PNVEVVGAFERNRELAIQFSDRFGTQLHESLQALLR--DVDAVVVASENAFHF 78 
                                       58888888777666666555555.888*********************************..9************** PP

                                       HHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEE CS
                      GFO_IDH_MocA  77 elakaaleagkhvllEKPlattveeakelvelaekkgklvsv 118
                                       e+a +a+e++khvl+EKP++ ++e+a++lv+l+ek+g+++++
  gi|557694121|ref|YP_008797175.1|  79 EYAAEAVENKKHVLCEKPMTIDLEQADKLVKLVEKNGVKFQM 120
                                       **************************************9987 PP

>> GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.1   7.7e-10   2.3e-06       1     101 [.     134     230 ..     134     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 7.7e-10
                                       HHHHHTTTTSSEEEEEEEEECBEEECHHHHCCGGSHHCSTSHHHHTCHHHHHHHHHHHTSEEEEEE.EEE.SEEESC CS
                    GFO_IDH_MocA_C   1 KelIengklGevvsvdvwtldtragaeakkrwkrrkkksgGvlgdlgiHdiDllqwLfGqppsvva.algrmrqnae 76 
                                       K l+++gk+G+ +s+ ++   +r+    + +  + +  +gG+++d+ +H  Dl +w  G+++++v+  +g  r+++e
  gi|557694121|ref|YP_008797175.1| 134 KGLVDEGKIGKLLSIIGTNKLNRYLVLLRNWFTDKRLSGGGAVMDHTVHLSDLIRWYSGSEIEEVYtEIG--RNVNE 208
                                       77999**********666666666665555555555***************************9995666..9**** PP

                                       TCCSCSEEEEEEEEEEETTEEEEEE CS
                    GFO_IDH_MocA_C  77 aaededaavmsvlnlekgsgevitl 101
                                       +  +ed++   + +  +++  + ++
  gi|557694121|ref|YP_008797175.1| 209 NLSVEDNF---LTTVRTQNRVIGHI 230
                                       ********...66666655554444 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 !   19.8   0.3   3.3e-07   0.00097      21     115 ..      29     119 ..      10     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.3e-07
                                       EEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHHS-EEEEE-S--HHHH.TTHHHHHHTTEEEE-S--CGGG- CS
                     NAD_binding_3  21 elelvavadrdsllskdrkallasealtldlddliahldpdvvVEcasseava.elvlkaLkagkdvvtankgalad 96 
                                       ++e+v+  +r+ ++ +   +++  ++l+++l++l++  d+d vV +as +a + e++++a++++k+v+ + k    d
  gi|557694121|ref|YP_008797175.1|  29 NVEVVGAFERN-RELAIQFSDRFGTQLHESLQALLR--DVDAVV-VASENAFHfEYAAEAVENKKHVL-CEKPMTID 100
                                       57888888888.66666778899999**********..988888.67777777478899****99987.56666669 PP

                                       HHHHHHHTSSSTTS--.EE CS
                     NAD_binding_3  97 ealyeeLreaaeangakiy 115
                                       +++ ++L+++ e+ng+k++
  gi|557694121|ref|YP_008797175.1| 101 LEQADKLVKLVEKNGVKFQ 119
                                       ****************985 PP

>> Oxidoreduct_C  Putative oxidoreductase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05     0.098      44      74 ..     162     192 ..     124     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                     Oxidoreduct_C  44 rPaWffDveqqGeG.ivDvtthLvDlvqweaf 74 
                                       r +Wf D    G G ++D t+hL Dl++w + 
  gi|557694121|ref|YP_008797175.1| 162 R-NWFTDKRLSGGGaVMDHTVHLSDLIRWYSG 192
                                       4.7******99988577************765 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   8.1e-05      0.24      18      95 ..      22      92 ..       8     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.1e-05
                                      HHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS.--S-BEBSSHHHHHHH-SEEEE-S-HHHHHHHHHHHHHTT-EEE CS
                            DapB_N 18 kaveeaedlelvaavdrkeselegkdagellglg.klgvavtddleevlekadvliDFTtpeavlenlklalekgvklV 95
                                      ++ +  +++e+v+a++r++          +++++ + g ++ ++l+++l+++d ++  +  +   e+++ a+e+++++ 
  gi|557694121|ref|YP_008797175.1| 22 QCFKMIPNVEVVGAFERNR--------ELAIQFSdRFGTQLHESLQALLRDVDAVVVASENAFHFEYAAEAVENKKHVL 92
                                      66677789*********98........2345555689************************************999875 PP

>> Elf-1_N  Transcription factor protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.065   1.9e+02       2      28 ..      69      96 ..      67     101 .. 0.71
   2 ?    7.4   0.0    0.0021       6.2      33      86 ..     175     222 ..     167     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.065
                           Elf-1_N  2 vvvqsgelvfefasnvmedeq.qledkp 28
                                      vv  ++   fe+a +++e+++  l++kp
  gi|557694121|ref|YP_008797175.1| 69 VVASENAFHFEYAAEAVENKKhVLCEKP 96
                                      4555677789*******99873555555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0021
                           Elf-1_N  33 aViveevPsadllqgysglelvyddetdlmqdrsldvaeeqeietedvelavea 86 
                                       aV+   v   dl++ ysg e + +++t++ ++    v+e+ ++e++ +++ v +
  gi|557694121|ref|YP_008797175.1| 175 AVMDHTVHLSDLIRWYSGSE-IEEVYTEIGRN----VNENLSVEDNFLTT-VRT 222
                                       67777888899*********.***********....99999999998877.543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2485.99
//
Query:       gi|557694122|ref|YP_008797176.1|  [L=219]
Description: dimethylmenaquinone methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-33  115.6   0.5    2.5e-33  115.4   0.5    1.1  1  RraA-like  Aldolase/RraA


Domain annotation for each model (and alignments):
>> RraA-like  Aldolase/RraA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.4   0.5   1.4e-37   2.5e-33       3     150 .]      15     176 ..      13     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 1.4e-37
                                       HHHHHCEE-SSBST....B.TT.EES..EEEEEEEEEESS.........BGHHHHHHHTS--TTEEEEEESTT.SSS CS
                         RraA-like   3 dvsDalkklggrsg....girplers..fvGpavTvkvvea........dnslvkealeeagpgdvlVvdgggdesl 65 
                                        v+D l+++g++++      rpl+++  ++GpavTv+++ +        d + + ++ + + +g v+Vv +gg++  
  gi|557694122|ref|YP_008797176.1|  15 AVADVLDDMGYTNQvlncMPRPLYPDvkLAGPAVTVSTYWYssyksgerDVESLASIFDVCYDGCVVVVATGGRK-D 90 
                                       578888888888887766667777745699********8888899999888999****************99955.3 PP

                                       SSECE-HHHHHHHHHTTBSEEEEEEEES-HHHHTTS..SSEEEEEEE-SSB-B-S.STSEESS-EEETTEEE-TTSE CS
                         RraA-like  66 raallGgllataakangvaGvvvdGavRDvaelrel..dfpvfargvtprkkpkkkgkgevnvpveiggvtvkpgdl 140
                                       +a++ G+l+++aa+a+g+ G+v+dGa+RDv ++ e+  +f+vf++g tp+ ++ + + ge ++++ +ggv+v+pgd+
  gi|557694122|ref|YP_008797176.1|  91 AACW-GELMSNAARAKGAVGAVLDGAIRDVPKIYEIapPFQVFSTGFTPADSKGRVEFGEKQIEIVVGGVRVRPGDI 166
                                       6666.******************************9889***********988888899****************** PP

                                       EEEETTEEEE CS
                         RraA-like 141 ivaDedGvvv 150
                                       +++D dGvv+
  gi|557694122|ref|YP_008797176.1| 167 VFGDFDGVVI 176
                                       ********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); 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 0.28s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1619.59
//
Query:       gi|557694123|ref|YP_008797177.1|  [L=325]
Description: ornithine cyclodeaminase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-86  289.1   6.1    4.1e-86  288.8   6.1    1.1  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    4.7e-05   23.5   0.1    9.3e-05   22.5   0.1    1.5  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0031   16.8   0.6     0.0059   15.9   0.6    1.4  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
       0.12   13.3   0.1       0.59   11.1   0.0    2.1  2  DUF2624          Protein of unknown function (DUF2624)


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 !  288.8   6.1   9.2e-90   4.1e-86       4     317 ..      10     316 ..       7     317 .. 0.97

  Alignments for each domain:
  == domain 1  score: 288.8 bits;  conditional E-value: 9.2e-90
                                       EEE-HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCC CS
                   OCD_Mu_crystall   4 avltaveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkks 80 
                                        vl++ ++e+ +++++ ++ave+af+ la+g+v +p     ev++++g+  v+ a +++++ ++vKl+ ++++n+++
  gi|557694123|ref|YP_008797177.1|  10 LVLSKTDLEKVMSMKETIDAVEKAFKGLALGEVVMPMPYIIEVHKHNGVWGVKSALINTQDVVAVKLSSGYFDNPAK 86 
                                       588999*****************************99999************************************* PP

                                       .TSSSEEEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SE CS
                   OCD_Mu_crystall  81 .glptvtalvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldike 156
                                         lp+ t++vv +d   Gvpla+mda ++ta+RT+Av++vaakyLarkd++ +ai+GaGvq +tql+a+ +vl+++e
  gi|557694123|ref|YP_008797177.1|  87 yNLPSITGVVVVADARYGVPLAVMDASIITAYRTGAVAGVAAKYLARKDSEIAAIFGAGVQGRTQLLAIAEVLKLSE 163
                                       9**************************************************************************** PP

                                       EEEE-SSHHHHHHHHHHCCS..CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB CS
                   OCD_Mu_crystall 157 vriydrdeeaaekfaenlqe.fefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteL 232
                                       v++yd+ +  aekf+++++e  +++++ ++s+e+a +++d+v t+T++k p++  ewv+ G+hi+ vg+d +gk+eL
  gi|557694123|ref|YP_008797177.1| 164 VKVYDVAPAYAEKFVKEMKEkTGLDIRKASSVEDALKEVDVVSTATPSKTPYINLEWVSKGTHITTVGSDHKGKQEL 240
                                       ********************78******************************************************* PP

                                       -HHHHHCCEEEESHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHH CS
                   OCD_Mu_crystall 233 dddilkradifvdseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaakl 309
                                       +++i  +a+++vd+ + a          ek+ l++ ++ aelge++aG+k GRts eeit+ ds Gl+++D aa  +
  gi|557694123|ref|YP_008797177.1| 241 ENKIYDVAKVVVDKREVAL---------EKDYLKPHQIYAELGEIVAGVKVGRTSPEEITVMDSSGLGIQDAAAGLV 308
                                       ************9987654.........5566999****************************************** PP

                                       HHHHHCCC CS
                   OCD_Mu_crystall 310 vyeraeek 317
                                       +y+ a++k
  gi|557694123|ref|YP_008797177.1| 309 AYQLAKKK 316
                                       **999887 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.1   2.1e-08   9.3e-05       7      99 ..     131     225 ..     125     232 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.1e-08
                                       HS..TT-EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.E.T-EEEEGCGHHHHHHT-SEEEE CS
                      Shikimate_DH   7 leslkekkvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkge.eiealkleelkellaeadvvis 81 
                                       l + +++ + + GaG  ++  + ++++  ++ +v v     + a+++++e+k++  + ++k ++++++l+e+dvv +
  gi|557694123|ref|YP_008797177.1| 131 LARKDSEIAAIFGAGVQGRTQLLAIAEVlKLSEVKVYDVAPAYAEKFVKEMKEKtGLDIRKASSVEDALKEVDVVST 207
                                       555566677899**999999888888877899999****************655158899***************** PP

                                       -SSSSS-SB-HHHHHCCH CS
                      Shikimate_DH  82 ataseepilekeeveeal 99 
                                       at s++p ++ e+v++  
  gi|557694123|ref|YP_008797177.1| 208 ATPSKTPYINLEWVSKGT 225
                                       ***********9998865 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 !   15.9   0.6   1.3e-06    0.0059      32      98 ..     140     208 ..     113     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-06
                                       EEESTSHHH.HHHHHHHHHTT.-EEEEEESSHHHHHHHHH.TTTCECEEHCHHHHHHHHHHHH-SEEEE- CS
                       AlaDh_PNT_C  32 lviGgGvaG.lqAiatakglg.akVtvlDvrparleqles.lgakfvevlksqeellaeavkeadvvigt 98 
                                        ++G+Gv G +q +a+a  l+  +V+v+Dv pa +e++ + +++k   +  ++++++++a+ke+dvv ++
  gi|557694123|ref|YP_008797177.1| 140 AIFGAGVQGrTQLLAIAEVLKlSEVKVYDVAPAYAEKFVKeMKEK-TGLDIRKASSVEDALKEVDVVSTA 208
                                       699******656677888776468*********999977759999.999****************99776 PP

>> DUF2624  Protein of unknown function (DUF2624)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.98   4.4e+03      26      42 ..     102     118 ..      87     122 .. 0.82
   2 ?   11.1   0.0   0.00013      0.59      11      65 ..     149     204 ..     140     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.98
                           DUF2624  26 qygveltksqAekivki 42 
                                        ygv+l   +A+ i  +
  gi|557694123|ref|YP_008797177.1| 102 RYGVPLAVMDASIITAY 118
                                       59*********999765 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00013
                           DUF2624  11 klnsiTaeellkyakqygveltksqAekivkilrekk.idifnkeerkkllkelak 65 
                                       + + +   e+lk+++   +++ ++ Aek+vk ++ek+ +di +++ ++  lke+  
  gi|557694123|ref|YP_008797177.1| 149 RTQLLAIAEVLKLSEVKVYDVAPAYAEKFVKEMKEKTgLDIRKASSVEDALKEVDV 204
                                       55667889**************************99759************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); 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:                         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: 2494.47
//
Query:       gi|557694124|ref|YP_008797178.1|  [L=130]
Description: hypothetical protein CSUB_C0689 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   17.9   3.5     0.0018   17.7   3.5    1.1  1  OST3_OST6  OST3 / OST6 family, transporter family
  ------ inclusion threshold ------
        2.3    8.3  11.3         11    6.0  11.3    1.9  1  MARVEL     Membrane-associating domain


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 !   17.7   3.5     2e-07    0.0018     181     274 ..      23     115 ..      12     129 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2e-07
                         OST3_OST6 181 tlwavlslliillftsGymfnqIrgvpfvakdekggisyfaggsqnQfgaEtqivallygllallvilLiklvprik 257
                                        l+a +++++  ++ +G ++n    v        +++  f++ ++ Q +aE+++va +y+ l+++ +lL  ++ + +
  gi|557694124|ref|YP_008797178.1|  23 ELVAWVAVVVSSVVLAGVVYNVASRVVIGVAFIGDSVRVFYPDTRVQTVAEMMVVATFYI-LGFVGLLLYGVAFSKR 98 
                                       578999999999*********999888877777777**********************85.6776777775655555 PP

                         OST3_OST6 258 nakvqrvlvivllvlif 274
                                        + + +  ++++++l++
  gi|557694124|ref|YP_008797178.1|  99 FSPRASRYMLLFSTLLI 115
                                       43333333333333333 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.3    0.0012        11      29      91 ..      46     120 ..      15     127 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0012
                            MARVEL  29 a.............kldqllgspssalnfavfvavfsflyalfllvlylfknsaftsilwplidlivdalaallwl 91 
                                       +             +++ + ++  +++  +++va+f +l +++ll+  + +++ f +++ ++++l+ ++l++l  l
  gi|557694124|ref|YP_008797178.1|  46 SrvvigvafigdsvRVF-YPDTRVQTVAEMMVVATFYILGFVGLLLYGVAFSKRFSPRASRYMLLFSTLLITLAAL 120
                                       15555555554443222.223334556668888888888888888888888********************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1060  (0.0591221); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); 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):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 951.32
//
Query:       gi|557694125|ref|YP_008797179.1|  [L=214]
Description: DNA repair protein RadB [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-07   30.2   0.0    3.8e-07   29.9   0.0    1.2  1  RecA      recA bacterial DNA recombination protein
    0.00018   21.5   0.0    0.00029   20.8   0.0    1.4  1  ATPase_2  ATPase domain predominantly from Archaea
    0.00041   20.8   0.0    0.00053   20.4   0.0    1.3  1  AAA_16    AAA ATPase domain
    0.00069   19.0   0.0     0.0016   17.7   0.0    1.5  1  Rad51     Rad51
     0.0011   18.6   0.0     0.0017   18.0   0.0    1.4  1  AAA_25    AAA domain
     0.0026   17.5   0.0     0.0086   15.8   0.0    1.7  2  AAA_24    AAA domain
  ------ inclusion threshold ------
      0.046   13.1   0.0        2.6    7.4   0.0    2.4  2  TniB      Bacterial TniB protein
      0.065   12.4   0.0      0.092   11.9   0.0    1.2  1  DAP3      Mitochondrial ribosomal death-associated protein 3
       0.12   12.4   0.0       0.15   12.2   0.0    1.3  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain
       0.16   12.2   0.0       0.36   11.1   0.0    1.6  1  AAA_22    AAA domain


Domain annotation for each model (and alignments):
>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   2.1e-10   3.8e-07      58     187 ..      22     152 ..      18     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 2.1e-10
                                       EEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHHT.T--.GGG-EEE--SSHHHHHHHHHHHHT..TT CS
                              RecA  58 iyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakkl.Gvd.idellvsqpdtGeqaleiadalvr..sg 130
                                       +yG e sGkt+l l a a++ +kgg +++id+   l p+  +++  v+ + +l++sqp t  + +e +  + +   +
  gi|557694125|ref|YP_008797179.1|  22 LYGEEKSGKTALLLTAAAKIAEKGGKVVWIDCGARLHPARLRQIfPVErLSQLYISQPRTFREQFETLLNVHDfpPS 98 
                                       7*************************************99888636764899******9987777665555441134 PP

                                       --SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT--EEEEEE CS
                              RecA 131 aidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksntvvifin 187
                                          liv d  + l  k e+ G+ +      +a  +  al k  +  +k  +  +++ 
  gi|557694125|ref|YP_008797179.1|  99 DASLIVCDDFTYL-HKLELSGKPSTDLPVYRALSLQAALLKNLAIARKISV--VLVG 152
                                       4568999998776.6899999998888888888788887776665555443..3333 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 !   20.8   0.0   1.6e-07   0.00029      17      68 ..      14      65 ..      11     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.6e-07
                          ATPase_2 17 repneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68
                                       +p   y++YG e+sGKtaLl  ++ +  +k+ +v++++   +   ++l++ 
  gi|557694125|ref|YP_008797179.1| 14 FKPTASYLLYGEEKSGKTALLLTAAAKIAEKGGKVVWIDCGARLHPARLRQI 65
                                      5678889******************************998888777777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0     3e-07   0.00053      25     129 ..      18     142 ..       6     191 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3e-07
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrekl 101
                                        + ll+Ge  +GK++l+ +++  + ++gg +++ +c      ++ + l q++   e l ql       +++ +re++
  gi|557694125|ref|YP_008797179.1|  18 ASYLLYGEEKSGKTALLLTAAAKIAEKGGKVVWIDCGAR---LHPARLRQIFPV-ERLSQLYIS----QPRTFREQF 86 
                                       5789*************9999999999888877777777...444447777744.444444433....677788888 PP

                            AAA_16 102 eeala............................avpelagaeasrllellkrllal 129
                                       e+ l+                            ++ +l+   a +l ++l + la 
  gi|557694125|ref|YP_008797179.1|  87 ETLLNvhdfppsdaslivcddftylhklelsgkPSTDLPVYRALSLQAALLKNLAI 142
                                       88888666777666666666666666666666544444444445555555544444 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   9.2e-07    0.0016      42     251 ..      22     208 ..      17     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.2e-07
                                       EEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHH CS
                             Rad51  42 ifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaerykldkeevlenvayaRaytiehqe 118
                                       ++Ge +sGkt l  t +   +  +      gk+v+id  + ++p rl +i   + +++ + l  ++  R +  e+ e
  gi|557694125|ref|YP_008797179.1|  22 LYGEEKSGKTALLLTAAA--K--IAE--KGGKVVWIDCGARLHPARLRQI---FPVERLSQL-YISQPRTFR-EQFE 87 
                                       69********88655443..3..333..3469****************99...555544443.356667664.5666 PP

                                       HHHHHTHHHHHHS-EEEEEEETTTGGGCH-------THH.HHHHHHHHHHHHHHHHHHH--EEEEEEE-------.- CS
                             Rad51 119 ellqqaaallaedkfallivDsvtalyRtdfsgrgelak.RqqklgkllrtLrkladefevavvitnqvvaqvdgqa 194
                                        ll+   + +  +  +l++ D  t l++ + sg+        + l+  +  L++la   +++vv+   v + +    
  gi|557694125|ref|YP_008797179.1|  88 TLLNV--HDFPPSDASLIVCDDFTYLHKLELSGKPSTDLpVYRALSLQAALLKNLAIARKISVVLVGLVHSIPAI-- 160
                                       66653..5799999*******************9765531345677778889*************9999988877.. PP

                                       -----------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-EEEEEEETTE CS
                             Rad51 195 alfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpeleavfaigeeG 251
                                            d++ P+  ++++  s +  +++kg++ + +++  + P    + + f i e+G
  gi|557694125|ref|YP_008797179.1| 161 -----DAQEPVAARIVTYWSDVVAKVQKGRDASVVMQ--EKPVA--QKIYFKIVEKG 208
                                       .....8999********************99876643..33432..33455555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   9.3e-07    0.0017      35      92 ..      19      64 ..      10     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.3e-07
                            AAA_25 35 lallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlra 92
                                        ll+G +++GKt+l+l  a+++a+          + gkV+++++ +++   + Rlr+
  gi|557694125|ref|YP_008797179.1| 19 SYLLYGEEKSGKTALLLTAAAKIAE----------KGGKVVWIDC-GAR-LHPARLRQ 64
                                      569*********************5..........4567777774.333.23345554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.8e-06    0.0086       4      68 ..      19      88 ..      17     116 .. 0.78
   2 ?   -1.1   0.0      0.75   1.3e+03     157     171 ..     168     182 ..     159     200 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.8e-06
                            AAA_24  4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvel.aaeladykt 68
                                      ++l+yG++++GKT l++++       g k++ id+ +   +l ++++ +i  +e + + + +  ++  ++++t
  gi|557694125|ref|YP_008797179.1| 19 SYLLYGEEKSGKTALLLTAaakiaekGGKVVWIDCGA---RLHPARLRQIFPVERLSQLYISQpRTFREQFET 88
                                      689********************************99...778888888886666666655554444444444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.75
                            AAA_24 157 anelkeevDlvlran 171
                                       a+ +++++D+v+ ++
  gi|557694125|ref|YP_008797179.1| 168 ARIVTYWSDVVAKVQ 182
                                       567999999999876 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.031        56      36      52 ..      18      34 ..      11      44 .. 0.86
   2 ?    7.4   0.0    0.0015       2.6     144     179 ..     135     170 ..     127     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.031
                              TniB 36 pnlllvGdsnnGKtmiv 52
                                       ++ll+G+ + GKt+++
  gi|557694125|ref|YP_008797179.1| 18 ASYLLYGEEKSGKTALL 34
                                      689***********986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0015
                              TniB 144 nalksLgnelkipivlvGteealralrtDpqlasRF 179
                                       ++lk+L    ki++vlvG  + + a+++ + +a R 
  gi|557694125|ref|YP_008797179.1| 135 ALLKNLAIARKISVVLVGLVHSIPAIDAQEPVAARI 170
                                       789***********************9999888885 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 ?   11.9   0.0   5.2e-05     0.092      21      55 ..      15      49 ..       9      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.2e-05
                                      S---EEEEE-SSSSSTTTTHHHHHHHGGGS--EEE CS
                              DAP3 21 kkvkrlvltGekgsGKSvlLlqalayAlekgwvvl 55
                                      k++  ++l+Ge+ sGK+ lLl a a  +ekg  v+
  gi|557694125|ref|YP_008797179.1| 15 KPTASYLLYGEEKSGKTALLLTAAAKIAEKGGKVV 49
                                      78999****************99998888865555 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 ?   12.2   0.0   8.1e-05      0.15      10      38 ..      28      56 ..      22     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.1e-05
                                      SSHHHHHHHHHHHHHHTT--EEEEEEEES CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA 10 vGKTtlaanLaralarrglrVllvDaDpq 38
                                      +GKT l+++ a+ +a++g +V+ +D++  
  gi|557694125|ref|YP_008797179.1| 28 SGKTALLLTAAAKIAEKGGKVVWIDCGAR 56
                                      8*************************976 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    0.0002      0.36       7     129 ..      19     152 ..      13     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                       + +++Ge  +GKT ll + + +  e      ++ +vv +++ +   ++ l++ +  +  ++l     + + ++e++e
  gi|557694125|ref|YP_008797179.1|  19 SYLLYGEEKSGKTALLLTAAAKIAE------KGGKVVWIDCGARLHPARLRQIFPVERLSQLYI--SQPRTFREQFE 87 
                                       689***************9999855......499999999999999999977766555555555..68889999999 PP

                            AAA_22  84 qalrarav....ielliiDEaqhlr....s.............eealeeLrsllnlsrkgvqliLvG 129
                                         l+ ++      +l++ D++ +l     s               +   L++l+     +++++LvG
  gi|557694125|ref|YP_008797179.1|  88 TLLNVHDFppsdASLIVCDDFTYLHklelSgkpstdlpvyralSLQAALLKNLAI--ARKISVVLVG 152
                                       9999999999999999999999996665524555675554444333333344444..7778888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1528.00
//
Query:       gi|557694126|ref|YP_008797180.1|  [L=102]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   38.3   0.0    1.9e-09   38.1   0.0    1.1  1  ASCH      ASCH domain
  ------ inclusion threshold ------
       0.09   12.4   0.0       0.16   11.5   0.0    1.4  1  LRR_11    Leucine-rich repeat


Domain annotation for each model (and alignments):
>> ASCH  ASCH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   2.1e-13   1.9e-09       2     105 ..       6     100 ..       5     102 .] 0.85

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.1e-13
                                       EE-TTHHHHHHTTS--EEEESSTTTGGGT-CEEEEEECCCCTSEEEEEEEEEEEEEEHHHHHHHHHCHCC--.-HCH CS
                              ASCH   2 sfhqelaslivsGkKtaeirvwdeelpkvrgdllilaalkptgralgivevtkvevkpfeevteehalkege.slee 77 
                                        f++e+++li++G Kt +ir +d    ++  + lil  ++  g   + +e+  vev++++e  +    +eg  s ee
  gi|557694126|ref|YP_008797180.1|   6 RFKPEYLDLILKGLKTSTIRPGDGG--EY-AKELIL--TD--GNRRIAAELLAVEVMTLREAVNTRYRLEGYsSPEE 75 
                                       6899******************999..44.688899..66..7777778888888898877766666679999**** PP

                                       HHHHHHCCHHHHHCCEEEEEEEEEEEEE CS
                              ASCH  78 wrevheefyeeeseeyedelvvveefel 105
                                       +++ ++++y ++    +d++v++++f++
  gi|557694126|ref|YP_008797180.1|  76 LYQSIKKIYNSLG---PDDPVTIIHFDP 100
                                       *********9985...6*********86 PP

>> LRR_11  Leucine-rich repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   1.8e-05      0.16      17      28 ..      14      25 ..      12      26 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.8e-05
                                      HHHHHTTT-EEE CS
                            LRR_11 17 VIlkGLqNSTiq 28
                                       IlkGL+ STi+
  gi|557694126|ref|YP_008797180.1| 14 LILKGLKTSTIR 25
                                      5*********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 793.06
//
Query:       gi|557694127|ref|YP_008797181.1|  [L=82]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-21   76.2   0.0    1.4e-21   76.0   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 !   76.0   0.0     8e-26   1.4e-21       2      70 .]       9      80 ..       8      80 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 8e-26
                                      EEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-...GCC-EEEEEEE CS
                              TusA  2 elDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelvevee...edgeyrivirk 70
                                      ++D+rG +CP P+lk+++a+ +++ gev+evla+dpa++ d++++a+k+g+++++vee   +  +yr++i++
  gi|557694127|ref|YP_008797181.1|  9 TVDVRGAMCPWPVLKTREAVQRINVGEVIEVLATDPASKPDLEAWARKTGNRILSVEEsgsDPVVYRFLIER 80
                                      79********************************************************88555999**9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 608.22
//
Query:       gi|557694128|ref|YP_008797182.1|  [L=140]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   96.8   0.9    1.5e-14   54.2   0.1    2.0  2  DrsE_2    DsrE/DsrF/DrsH-like family
    2.9e-11   43.8   0.0      4e-11   43.3   0.0    1.2  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 !   41.7   0.1   1.1e-14     1e-10       2      56 ..       5      59 ..       4      62 .. 0.93
   2 !   54.2   0.1   1.6e-18   1.5e-14      80     148 ..      64     133 ..      60     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 1.1e-14
                                      T-EEEEEE----H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GGG---TT CS
                            DrsE_2  2 kkklaiifskgtldkalaalilAsgAaalglevtiFftFwGLnilrkeekkkvkk 56
                                      k +l+i++s gt d  ++alilA++A a g+e +++ftF G+++l k+  +++k 
  gi|557694128|ref|YP_008797182.1|  5 KTRLVIVASRGTADGLYPALILATTAVAQGKEAAVYFTFGGMKLLTKQMAETIKP 59
                                      6799*******************************************99888875 PP

  == domain 2  score: 54.2 bits;  conditional E-value: 1.6e-18
                                       GHHHHHHHHHHHHCT---HHHHHHHHHHTT-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHHHC- CS
                            DrsE_2  80 gigtkmmkkvmkekgvasleeLleaakeagvklvaCqmtmdlmglkkeelidgv.eiagaatylkeaeea 148
                                       g+ ++ +++++ + g++sl ++l++ak++gvk++aC  tm+l+gl+ke+l+d v  i+ga t+l+ a++ 
  gi|557694128|ref|YP_008797182.1|  64 GVSKEQLEQLLAKGGMPSLVDMLKMAKQSGVKIYACSPTMNLFGLRKEDLVDVVdDIIGASTFLEIASDP 133
                                       56788899999******************************************************99875 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   4.4e-15     4e-11      15     107 ..      18     129 ..       6     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 4.4e-15
                                       SHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS...................---TGGGTS---GGGGGGCGGGT- CS
                              DrsE  15 eaarealelalaaaalghevsvffygdGvllllk...................gqtanpadeknlaellkalkeygv 72 
                                       +  + al la+ a a+g e +v f+  G +ll+k                   +q  ++ ++++l+++lk++k+ gv
  gi|557694128|ref|YP_008797182.1|  18 DGLYPALILATTAVAQGKEAAVYFTFGGMKLLTKqmaetikpsldlgvskeqlEQLLAKGGMPSLVDMLKMAKQSGV 94 
                                       446889***********************************************999********************* PP

                                       EEEEEHHHHHHTT--GGGE-.T--EEEE-HHHHHHH CS
                              DrsE  73 klyvCgqaakargldededl.gvgvevsglgelael 107
                                       k+y+C  +++ +gl  +edl +v   + g++++ e+
  gi|557694128|ref|YP_008797182.1|  95 KIYACSPTMNLFGLR-KEDLvDVVDDIIGASTFLEI 129
                                       ***************.56774556666666676665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1021.40
//
Query:       gi|557694129|ref|YP_008797183.1|  [L=146]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.3   0.0      0.022   14.8   0.0    1.3  1  BsuPI     Intracellular proteinase inhibitor


Domain annotation for each model (and alignments):
>> BsuPI  Intracellular proteinase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.2e-06     0.022      15      95 ..      55     129 ..      43     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-06
                                       EEEEEEEE-SSS-EEEEESSS--EEEEEE-TT--EEEETTTT-------EEEEE-TT-EEEEEEEE.S---SEEEEE CS
                             BsuPI  15 elaltvtNesdeavtlqFssgqkydlvvkdeegeevwrysegrmFtqalssetlepgesatyeetwdedlepGeYtl 91 
                                        l++t+ N++ e++ +    g  yd+  k++++ +  ++ ++r+++  l+  +lepg+s++ + +++ d+epG+Y+l
  gi|557694129|ref|YP_008797183.1|  55 TLTYTIINNTPETIGF----GEPYDIQKKQDGEWVSVEWMKDRAWI--LIYYNLEPGKSLSKRVELPVDIEPGDYRL 125
                                       5677777777655544....788999998888888899*****985..77789*************99********9 PP

                                       EEEE CS
                             BsuPI  92 eael 95 
                                       + e+
  gi|557694129|ref|YP_008797183.1| 126 VKEV 129
                                       9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 00:00:00.42
# Mc/sec: 1036.79
//
Query:       gi|557694130|ref|YP_008797184.1|  [L=316]
Description: hypothetical protein CSUB_C0695 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   33.3   0.0    7.7e-08   32.7   0.0    1.2  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    0.00058   19.2   0.8     0.0016   17.8   0.8    1.7  1  Peptidase_M50    Peptidase family M50
      0.002   18.3   0.0     0.0029   17.8   0.0    1.2  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
       0.49   10.0   8.5        5.2    6.7   8.5    2.1  1  Peptidase_M50B   Peptidase M50B-like


Domain annotation for each model (and alignments):
>> 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 !   32.7   0.0   1.7e-11   7.7e-08       9     132 ..      10     122 ..       3     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.7e-11
                                       EESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCS.SEEEEEEEEEET.TTTEEEEEEE.SS CS
                   Polyketide_cyc2   9 viaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggr.gtvreelvevdp.egrllsyrivkpv 83 
                                       v+++p+e+V++++++ en+ +  p  + ++l++++ +  +    +r  g   ++r +++e++  e+ + + +    +
  gi|557694130|ref|YP_008797184.1|  10 VVPRPVEEVYEFFRNVENMGKVWPTELGMKLVSQDKD--VYTVSFRLLGQlYQTRFRIIERSStEQYHETLD----F 80 
                                       79******************9888888899**97888..777888877777669******996244444444....6 PP

                                       S-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHH CS
                   Polyketide_cyc2  84 pvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavkgdle 132
                                       p+++   t+t tp++ggt+++ ++ ++        ++p+a +++k++l+
  gi|557694130|ref|YP_008797184.1|  81 PFGKLYHTITTTPADGGTKIVEDMVLES-------SNPFAGRFFKKILT 122
                                       9***********************8885.......44555555555544 PP

>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.8   3.5e-07    0.0016       3     108 ..     183     272 ..     181     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.5e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....X CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   3 illlgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaf 79 
                                       i  l++  + H l+H++v +l g+++ ++ +g+  ++++ +    +++   + LG  ++ a+++             
  gi|557694130|ref|YP_008797184.1| 183 ISFLLLWFFTHDLAHYVVGRLVGIRFSNYYVGL-SNIVRLNILPKPFKTLPVALGIKIDRANTQ------------- 245
                                       55688899*************************.888888877888877777788655555544............. PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  80 lkkspwqrllivlAGplanfilailvfvv 108
                                         +sp   +++ +AGp+a +++++ v v+
  gi|557694130|ref|YP_008797184.1| 246 --ASPRGYAATYAAGPIASMLFPLTVPVI 272
                                       ..889999************999987665 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 !   17.8   0.0   6.5e-07    0.0029       1     117 [.      11     120 ..      11     130 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.5e-07
                                       ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...EEEECSTTSSCEEEEEEEEEEETTTEEECTTCCCCCEE CS
                    Polyketide_cyc   1 vpapadqvyalvadvesypeflphcssvevleeaesglsadlevgfggltesftarvtldppeeitfklvegdfksl 77 
                                       vp p+++vy++ ++ve++ + +p    +++++++ +      +v+f  l++ + +r +  +  +++   +  df   
  gi|557694130|ref|YP_008797184.1|  11 VPRPVEEVYEFFRNVENMGKVWPTELGMKLVSQDKD----VYTVSFRLLGQLYQTRFRIIERSSTEQYHETLDFPFG 83 
                                       799********************************8....5556666666666666644444445555556666666 PP

                                       EEEEEECTECCEEECEEEEEEEEEEEE-SSCHHHHHHHHH CS
                    Polyketide_cyc  78 egkWtieslppnsggtrtkvalevdfkfaspllgalvgqv 117
                                       +  +ti+  p    + +tk++ +  ++ + p+ g + +++
  gi|557694130|ref|YP_008797184.1|  84 KLYHTITTTPA---DGGTKIVEDMVLESSNPFAGRFFKKI 120
                                       66677766776...67788888888888888888777766 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   8.5    0.0012       5.2       2     110 ..     157     296 ..     156     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0012
                    Peptidase_M50B   2 laivlalvvlwnkpllrp..........fkllvvffHElGHalaalLtGgrvkgielhsd................. 51 
                                       l i++a v+lw +pl  p          f ll  f+H l+H ++  L+G r+++  +  +                 
  gi|557694130|ref|YP_008797184.1| 157 LGIAAAYVLLWLQPLQIPggrlitglisFLLLWFFTHDLAHYVVGRLVGIRFSNYYVGLSnivrlnilpkpfktlpv 233
                                       6789999999999888777777778888**************************999988899999**********9 PP

                    Peptidase_M50B  52 ....esGvtvtrg.pgglgqiltllaGYlgpallGlllillsasgkarlllv.llvllllvllll 110
                                           +   + t+  p+g   ++t +aG++++ l+ l++ ++  +++ + l++ +l+l+ ++ +++
  gi|557694130|ref|YP_008797184.1| 234 algiKIDRANTQAsPRGY--AATYAAGPIASMLFPLTVPVIMLANNFTSLAGqILLLIAVANIIF 296
                                       666655556666656664..689**********99998777766666555553554544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); 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:                         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: 00:00:00.43
# Mc/sec: 2190.72
//
Query:       gi|557694131|ref|YP_008797185.1|  [L=437]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-16   60.4   0.0    5.5e-10   39.4   0.0    2.3  2  Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
  ------ inclusion threshold ------
       0.35   11.1   3.9         13    6.1   0.2    3.3  3  Osmo_CC    Osmosensory transporter coiled coil


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 !   39.4   0.0   6.1e-14   5.5e-10       5     138 ..       9     163 ..       6     178 .. 0.80
   2 !   18.8   0.2   1.1e-07     0.001     252     359 .]     195     405 ..     168     405 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 6.1e-14
                         Cas_DxTHG   5 flGt.gnykevkYelkeeeeeeketsfvqeallellaekedpdkvvilltdtlad.....keaeek.........ee 66 
                                        +G  +nyk+++Y+   +e++  e  +++ a++++    +   + ++l++++l++     +    +         e 
  gi|557694131|ref|YP_008797185.1|   9 VIGEpKNYKKARYV---YENQAREALLAATAVADIT---GG--EAILLAPESLVTslesdR----DearkllekpEM 73 
                                       6889899*******...889999**********988...66..799*********965442....323446655533 PP

                         Cas_DxTHG  67 aak.lkeeleelleiekvd.veiipgggte..ee.lwe.............ifekllekleendeiilDiThGfryl 125
                                       +++ + e+le++ e ++++ v+i+p++g++  +e  w              +f  + + ++e++ i + +T+G++++
  gi|557694131|ref|YP_008797185.1|  74 LEQkVLEQLERMGENHPKPmVKILPSIGSFsqHEkGWRinaqgsfavieaaLFLIMRKLVNEGKNITMVVTSGLNIY 150
                                       33334444455555999*************88444566777777888889999999999****************** PP

                         Cas_DxTHG 126 Pvlallalaylrn 138
                                       P lal +l+++ +
  gi|557694131|ref|YP_008797185.1| 151 PALALRTLNHILT 163
                                       ****999998865 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.1e-07
                         Cas_DxTHG 252 eei.esleeeesakplellldeikkklekflkkq....ikwclekgliqqaltllreliisl.llegedilnkkkrr 322
                                        +i +++ e+  + ++ l +dei+k+++k+++ +    ++w+l++g+  +a+  +  ++  l l++++ i++++ r 
  gi|557694131|ref|YP_008797185.1| 195 IQIeTHTIETRVFNIFPLTIDEIDKEICKLYQHEmrsnLRWHLSNGM--RAFNCITRNT-PLpLYYEKIINKIDPR- 267
                                       222233334455666666************433356669****9997..6775455554.2545556666666666. PP

                         Cas_DxTHG 323 eeieeelknlskvekksseekeek..................................................... 346
                                        ei+      +kv+ + +++++++                                                     
  gi|557694131|ref|YP_008797185.1| 268 -EISFLE---EKVAEDLKNRYKPEihvvnneilikrpselglslirrammslaltrvlmrlvdearrevdddgwvpl 340
                                       .554433...34444444444445677888899999999************************************** PP

                         Cas_DxTHG 347 ....................................................lsniRNdiaHaGl 359
                                                                                            +++RN++aH+G+
  gi|557694131|ref|YP_008797185.1| 341 eaiekmfidkiyddkrefklnkflleselykiregggdvygssinghrvggsSNEKRNFFAHSGF 405
                                       ************************************************99999***********8 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2    0.0014        13       1      21 [.      59      78 ..      59      91 .. 0.82
   2 ?    4.3   0.0    0.0052        47      20      33 ..     213     226 ..     211     235 .. 0.82
   3 ?   -1.2   0.2      0.29   2.6e+03      18      34 ..     258     275 ..     256     283 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0014
                                      XXXXXXXXXXXXXXTHHHHHH CS
                           Osmo_CC  1 SdreEAkelLqehYdnIEqkv 21
                                      Sdr EA++lL+ + +  Eqkv
  gi|557694131|ref|YP_008797185.1| 59 SDRDEARKLLE-KPEMLEQKV 78
                                      9********95.558888887 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0052
                                       HHHHHHHHHHHHHH CS
                           Osmo_CC  20 kvedideeIaaLee 33 
                                       ++++id+eI +L +
  gi|557694131|ref|YP_008797185.1| 213 TIDEIDKEICKLYQ 226
                                       69********9965 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.29
                                       HHHHHHHH.HHHHHHHHH CS
                           Osmo_CC  18 Eqkvedid.eeIaaLeek 34 
                                       E+ ++ id  eI  Leek
  gi|557694131|ref|YP_008797185.1| 258 EKIINKIDpREISFLEEK 275
                                       566777775689999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3024.71
//
Query:       gi|557694132|ref|YP_008797186.1|  [L=189]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-12   48.0   0.9    2.1e-11   44.0   0.9    2.0  1  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 !   44.0   0.9   1.2e-15   2.1e-11       7     205 ..       6     175 ..       1     180 [. 0.78

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.2e-15
                            DUF429   7 crtgwaavaledgrlrlvdv..eae.eivaalaallaaaeeaavvaiDaPiglpe........retggRaaDraark 72 
                                        r+ ++av+  d++lr+ +     + ei+a++++l      +++v+iDaP+glp          +   R +D+++r 
  gi|557694132|ref|YP_008797186.1|   6 TRPSGMAVL--DEELRVRTWvrFLDaEILADVDEL-----RPVAVGIDAPLGLPRgrasletrGPPHFRICDNELR- 74 
                                       677788888..888888666753347*********.....9******************999888899*******7. PP

                            DUF429  73 llarrgasvfpvparaalaagkglserafgllpklrevdelldarpelrgrvvEvhPeaafvalnggaplakkkkta 149
                                          rrg++ fp+       a+++l++r+++l++++r+++            v+E++P  +   l g+ +  ++ k  
  gi|557694132|ref|YP_008797186.1|  75 ---RRGIRFFPITIG----AMRKLTARGIRLAEEIRRRN----------IPVYETFPGGVQDLL-GLPRKHHSLK-- 131
                                       ...56*******999....3345589**********664..........579********9999.7766665553.. PP

                            DUF429 150 eg..raeRrellaraiaellleseakkeklvaadDvlDAvacaltArraarGraeslp 205
                                        g     R+  ++++               + + D  DAv ca++ + ++rG +e + 
  gi|557694132|ref|YP_008797186.1| 132 -GlvKGLRKLGVKNL-------------PPKISADEADAVTCAYAVYLWWRGLCEEVG 175
                                       .42234444444433.............245688999***************997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1345.75
//
Query:       gi|557694133|ref|YP_008797187.1|  [L=341]
Description: glyoxalase/bleomycin resistance protein/dioxygenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-26   91.2   0.0      2e-14   53.9   0.0    2.1  2  Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygena


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 !   53.9   0.0   1.1e-18     2e-14       1     128 []       7     130 ..       7     130 .. 0.89
   2 !   35.4   0.0   5.8e-13     1e-08      37     128 .]     151     277 ..     140     277 .. 0.74

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 1.1e-18
                                       EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEE..EESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC.TS CS
                        Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdn..teeteglriaffhaggghielvlneapsgaakhvkkiee.tv 74 
                                       g++h++l++g +  + +FYt+vLG++ vk ++n   + +  l +a ++  +g++  + ++++ ++  +       + 
  gi|557694133|ref|YP_008797187.1|   7 GLHHITLVTGSYLVNNRFYTEVLGLRRVKLSVNqdDIYHRHLFYANLDKPTGSAITFFEWPELPRGYPG----YgSP 79 
                                       79******************************9865566999999999999988777777777766555....2389 PP

                                       EEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  75 hhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       hh+a ++ + e ++k++  l+e+     a  g +++g+l+s+y rDpdG+lle+
  gi|557694133|ref|YP_008797187.1|  80 HHLAYRVGSAEALAKWFHFLRERN---IAAKGPYVYGGLVSIYLRDPDGVLLEL 130
                                       **********************99...666688*******************96 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 5.8e-13
                                       TEEEEEEEEETTTSEEEEEEEECCTTSCTHHCC.....................................BSC..TS CS
                        Glyoxalase  37 teglriaffhaggghielvlneapsgaakhvkk.....................................iee..tv 74 
                                       t+++ +  ++     +++++ + p+    + +k                                     +    +v
  gi|557694133|ref|YP_008797187.1| 151 TPTAISQDMRLTAFDHASPIISDPGLTSRFLEKfldivdveisngvlrilnmdgdvylrcivdplnldgyV-ArgSV 226
                                       55555555555556666666666666666666677777777777777777766666666666655544442.0459* PP

                                       EEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  75 hhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                       hh+a+ + ++e +    +rl + g +++++++r  f++ly   frDpdG+lle+
  gi|557694133|ref|YP_008797187.1| 227 HHIALCVESEETQRLVMRRLNSVGWSNSGIVDRFWFKSLY---FRDPDGNLLEL 277
                                       ****************************************...*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2501.65
//
Query:       gi|557694134|ref|YP_008797188.1|  [L=170]
Description: hypothetical protein CSUB_C0699 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   35.3   2.3    1.2e-08   35.1   1.2    1.6  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    0.00032   20.6   0.3    0.00066   19.6   0.1    1.6  2  CarbopepD_reg_2  CarboxypepD_reg-like domain
     0.0018   18.3   0.2      0.011   15.7   1.1    1.8  2  Big_1            Bacterial Ig-like domain (group 1)
  ------ inclusion threshold ------
      0.074   13.3   0.1       0.13   12.5   0.1    1.3  1  SdrD_B           SdrD B-like domain


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 !   35.1   1.2   2.7e-12   1.2e-08       9      62 ..       5      56 ..       2      69 .. 0.91
   2 ?   -2.2   0.0       1.2   5.3e+03      38      69 ..     111     145 ..     109     151 .. 0.48

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.7e-12
                   CarboxypepD_reg  9 asgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyata 62
                                      +sg+pi gatVtv+  +++++ st+t+a+G+ +++ ++pgty  +v + Gy  +
  gi|557694134|ref|YP_008797188.1|  5 SSGRPIVGATVTVQ-LSDTASVSTVTNATGYAAFS-IAPGTYGYVVDMMGYWIR 56
                                      69************.789999*************7.***************865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                   CarboxypepD_reg  38 Gafrlrglpp...gtysvtvsapGyatatreevtl 69 
                                       G f+++ l+    g  + ++ ++G     + +vt+
  gi|557694134|ref|YP_008797188.1| 111 GVFNITRLKMhvaGYDKPVAVYQGVVLEKVFNVTV 145
                                       55555555433334444445555544444444555 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 !   19.6   0.1   1.5e-07   0.00066       9      55 ..       5      53 ..       1      59 [. 0.83
   2 ?   -2.3   0.0      0.99   4.4e+03      47      56 ..     117     126 ..     105     145 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.5e-07
                   CarbopepD_reg_2  9 etkeplpgatVyv..kgt.kkgtvTdenGnFelknlpagkytLvvsyvGy 55
                                      ++++p+ gatV+v   +t ++ tvT++ G+  ++ + +g+y  vv ++Gy
  gi|557694134|ref|YP_008797188.1|  5 SSGRPIVGATVTVqlSDTaSVSTVTNATGYAAFS-IAPGTYGYVVDMMGY 53
                                      6789****98888323333799********9996.889***********9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.99
                   CarbopepD_reg_2  47 tLvvsyvGyk 56 
                                       +L++ + Gy+
  gi|557694134|ref|YP_008797188.1| 117 RLKMHVAGYD 126
                                       4445555554 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 !   15.7   1.1   2.4e-06     0.011      17      52 ..       6      39 ..       5      46 .. 0.87
   2 ?   -1.8   0.0      0.71   3.2e+03      46      63 ..      99     116 ..      96     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.4e-06
                             Big_1 17 ngnpvagatVtfsvsggalsassgtTdanGkatvtl 52
                                      +g p+ gatVt++ s++a  + s++T+a G a +++
  gi|557694134|ref|YP_008797188.1|  6 SGRPIVGATVTVQLSDTA--SVSTVTNATGYAAFSI 39
                                      79*************944..4799********9987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.71
                             Big_1  46 Gkatvtltstkagtvtvt 63 
                                       G a   l++ + g +++t
  gi|557694134|ref|YP_008797188.1|  99 GWAMLRLKNLEEGVFNIT 116
                                       889999999999999997 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.9e-05      0.13      23      61 ..       9      45 ..       4      56 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                            SdrD_B 23 gisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYk 61
                                       i g tVt++ +++ +  +t+T+a+G+ +F+ ++pG+Y 
  gi|557694134|ref|YP_008797188.1|  9 PIVGATVTVQLSDTAS-VSTVTNATGYAAFS-IAPGTYG 45
                                      6778888885555555.599*******9998.8999964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); 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:                         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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1240.89
//
Query:       gi|557694135|ref|YP_008797189.1|  [L=661]
Description: hypothetical protein CSUB_C0700 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   16.0   1.5     0.0054   16.0   1.5    1.7  2  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.5     3e-07    0.0054       6      31 ..       9      34 ..       7      35 .. 0.90
   2 ?   -3.2   0.0      0.31   5.5e+03      32      38 ..     270     276 ..     269     277 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3e-07
                        UCR_Fe-S_N  6 sdeptRRDFLyiATgavgaVGaaaaa 31
                                      s +  RR+FL ++ + v++V+a+aa+
  gi|557694135|ref|YP_008797189.1|  9 SAKIGRREFLALTSAQVAGVAAGAAL 34
                                      56778*******************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.31
                        UCR_Fe-S_N  32 wPfidqm 38 
                                        Pfi+++
  gi|557694135|ref|YP_008797189.1| 270 APFISSL 276
                                       6****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 4771.02
//
Query:       gi|557694136|ref|YP_008797190.1|  [L=231]
Description: hypothetical protein CSUB_C0701 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.5   1.9      0.019   15.5   1.9    2.0  2  DUF1218    Protein of unknown function (DUF1218)
        1.9    7.2   8.4        2.7    6.7   8.4    1.2  1  Otopetrin  Otopetrin
        7.1    4.8  19.5        9.8    4.3  19.5    1.3  1  DUF2070    Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF1218  Protein of unknown function (DUF1218)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   1.9   3.1e-06     0.019       9      62 ..      92     144 ..      81     151 .. 0.69
   2 ?   -3.0   0.1       1.9   1.1e+04      48      48 ..     212     212 ..     188     225 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.1e-06
                           DUF1218   9 qiiasvasgclccrk..ekspssakrtlavvlfvlswivfaiAvalllvGaavnae 62 
                                       q+ + +    +++++    s+++ ++++ v++ ++ w++f +A+a l++G+  + +
  gi|557694136|ref|YP_008797190.1|  92 QAFIGL---LFILGPaqTLSTNQRSNIFLVFFTLFIWFAFYVAIAALATGVKAEEK 144
                                       333333...22444411345556699************************988875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.9
                           DUF1218  48 i 48 
                                       +
  gi|557694136|ref|YP_008797190.1| 212 V 212
                                       2 PP

>> Otopetrin  Otopetrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   8.4   0.00046       2.7     245     346 ..      53     177 ..      48     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00046
                         Otopetrin 245 kGLflglLllvltiislilFfvlvrkpklsslailladlselv.......................llalaiiavii 298
                                        GL++++L l++ i+++ + +v ++ + + ++  +l++   ++                       +++l i   ++
  gi|557694136|ref|YP_008797190.1|  53 SGLVGAVLRLIVVISTVSVSYVAINPKGVIQVLAMLLSSQAFIgllfilgpaqtlstnqrsniflvFFTLFIWFAFY 129
                                       69999999999999999999999998877776666666666668999999999999999999954444444444444 PP

                         Otopetrin 299 gfirvrklkfrreeqleLddiLllisafGlfvysvfsiiaaslkaees 346
                                        +i +    ++ ee+ +L ++Ll i ++G ++  +f ++a +++   +
  gi|557694136|ref|YP_008797190.1| 130 VAIAALATGVKAEEKVSLAEVLLSINLMGGVLLILFLLVARVYSLLPK 177
                                       4455555667888999************************99887665 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  19.5    0.0016       9.8      21     174 ..      62     223 ..      36     230 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0016
                           DUF2070  21 iillalligllaflssk..lfgillfglp..alvaflltlpvlrilggrltykrs.lflalltelivviisllaill 92 
                                       +i+++  +++ ++ +++  ++++l+++l+  a++ +l+ l   ++     t +rs +fl ++t++i+++++++ ++l
  gi|557694136|ref|YP_008797190.1|  62 LIVVISTVSVSYVAINPkgVIQVLAMLLSsqAFIGLLFILGPAQT---LSTNQRSnIFLVFFTLFIWFAFYVAIAAL 135
                                       222222223322233324566666666653433333333333322...26666778**************9999998 PP

                           DUF2070  93 sall...qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly..........fspesfll 156
                                       ++ +   ++++l  ++ls+ l+ ++ l+++++v++     ++lp  ++p+ + + ++l+                 l
  gi|557694136|ref|YP_008797190.1| 136 ATGVkaeEKVSLAEVLLSINLMGGVLLILFLLVARV---YSLLPKHATPAQVDFWSTLFskcvygsicwQ----GSL 205
                                       887789866666666677666655555555555554...3444444444444444444444445874442....333 PP

                           DUF2070 157 llllslifalavylfivv 174
                                        ++++l+ +++ ++f ++
  gi|557694136|ref|YP_008797190.1| 206 PFIYLLVAGVMTLIFARL 223
                                       344555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 1880.97
//
Query:       gi|557694137|ref|YP_008797191.1|  [L=180]
Description: thiamine S protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   56.5   0.0    6.4e-15   55.6   0.0    1.5  1  ThiS             ThiS family
    1.2e-07   31.6   0.1     0.0088   16.0   0.0    3.2  3  MraZ             MraZ protein, putative antitoxin-like
    1.9e-05   24.9   0.3    4.3e-05   23.8   0.1    1.6  2  Urm1             Urm1 (Ubiquitin related modifier)
  ------ inclusion threshold ------
      0.081   11.8   0.1        4.2    6.1   0.0    2.0  2  Transposase_mut  Transposase, Mutator family
       0.12   12.6   0.0        3.1    8.1   0.0    2.3  2  Poly_export      Polysaccharide biosynthesis/export protein


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 !   55.6   0.0   1.8e-18   6.4e-15       1      77 []       5      91 ..       5      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 1.8e-18
                                      EEETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHG.........TTTTEEEEETTEEEGC.CTTTSB--TTCEEE CS
                              ThiS  1 vllfaelrelageeelelaegstvaelleaLgerypela.........lerrvavavNgeivpr.lwldtelkdgDeva 69
                                      v l++ lr+ a  +  ++ +gstv+e+l++L  ry +l+          + +v+v vN+e++++ ++ +t++kdgD+v 
  gi|557694137|ref|YP_008797191.1|  5 VYLPTPLRQYADGRDMVELDGSTVGEVLNKLVSRYTALQkhlfnengaIRSFVNVFVNNEDIRFlEGVNTKIKDGDVVY 83
                                      56888999999999999*********************9*********99**************99************* PP

                                      EEESTTC- CS
                              ThiS 70 ilppVaGG 77
                                      i+p +aGG
  gi|557694137|ref|YP_008797191.1| 84 IIPSIAGG 91
                                      *******9 PP

>> MraZ  MraZ protein, putative antitoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.027        97      16      31 ..       5      20 ..       2      27 .. 0.80
   2 !   16.0   0.0   2.5e-06    0.0088      13      36 ..     111     133 ..     107     140 .. 0.88
   3 !    8.9   0.0   0.00041       1.5       9      27 ..     141     159 ..     137     163 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.027
                                      EE--CHHHHHTTSCSE CS
                              MraZ 16 lllPaklreeakleke 31
                                      + lP+ lr++a +   
  gi|557694137|ref|YP_008797191.1|  5 VYLPTPLRQYADGRDM 20
                                      679********98744 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 2.5e-06
                                       TSEEE--CHHHHHTTSCSEEEEEE CS
                              MraZ  13 kGRlllPaklreeaklekevvviG 36 
                                        GR+++Pakl+++ak + ev+vi+
  gi|557694137|ref|YP_008797191.1| 111 HGRITVPAKLLKKAKKN-EVTVII 133
                                       7****************.888776 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.00041
                                       EB-TTSEEE--CHHHHHTT CS
                              MraZ   9 elDakGRlllPaklreeak 27 
                                       e D+ +R+ lP++lre+++
  gi|557694137|ref|YP_008797191.1| 141 EPDRYNRIYLPPTLREKIA 159
                                       78*************9875 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   1.2e-08   4.3e-05      31      96 .]      26      91 ..      14      91 .. 0.91
   2 ?   -2.2   0.0       1.5   5.4e+03      13      28 ..     120     135 ..     117     141 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.2e-08
                                      -BHHHHHHHHCCCC-SSGHHHCBSTTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
                              Urm1 31 vnleeliayikknlikerkevFlekdkvrPGilvLindaDwellgekdyelkdkDkivFistlhGG 96
                                       ++ e+++ ++++    +k++F e++ +r  + v +n+ D+  l+  ++++kd+D++  i ++ GG
  gi|557694137|ref|YP_008797191.1| 26 STVGEVLNKLVSRYTALQKHLFNENGAIRSFVNVFVNNEDIRFLEGVNTKIKDGDVVYIIPSIAGG 91
                                      577888888888888889******************************************999998 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                       GCTT-SEEEEEE-SSS CS
                              Urm1  13 llekkkkhkveleies 28 
                                       ll+k kk++v++ i++
  gi|557694137|ref|YP_008797191.1| 120 LLKKAKKNEVTVIIDD 135
                                       6677777877776554 PP

>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0    0.0065        23     341     375 ..      30      64 ..      22      70 .. 0.89
   2 ?    6.1   0.0    0.0012       4.2     240     285 ..      97     142 ..      83     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0065
                   Transposase_mut 341 ErLNkeirRrtrvvgiFPneesilrlvgavlaeah 375
                                       E LNk + R t  +++  ne+ ++r  + v+++ +
  gi|557694137|ref|YP_008797191.1|  30 EVLNKLVSRYTALQKHLFNENGAIRSFVNVFVNNE 64 
                                       89************************999999866 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0012
                   Transposase_mut 240 vkaisavfpeaavQrCrvHllrnllakvpkkkadkvaealksiyka 285
                                       ++a+ + +  +  Q  r+ + ++ll+k++k++ +++ +++k i++ 
  gi|557694137|ref|YP_008797191.1|  97 PAAVAKKLGRTVKQHGRITVPAKLLKKAKKNEVTVIIDDVKYIFEP 142
                                       57999999************************************85 PP

>> Poly_export  Polysaccharide biosynthesis/export protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.056     2e+02      50      69 ..      21      43 ..      18      61 .. 0.81
   2 ?    8.1   0.0   0.00086       3.1       6      45 ..      73     117 ..      70     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.056
                       Poly_export 50 ikvaGltveelreeieekl...s 69
                                      +++ G tv e+ +++ +++   +
  gi|557694137|ref|YP_008797191.1| 21 VELDGSTVGEVLNKLVSRYtalQ 43
                                      7899************9995432 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00086
                       Poly_export   6 eyrigpgDvLsItvwehpels.....ssqalqgylVdpdGtIslP 45 
                                       + +i+ gDv+ I  +    ls     + +++ g +V+++G+I++P
  gi|557694137|ref|YP_008797191.1|  73 NTKIKDGDVVYIIPSIAGGLSiaapaAVAKKLGRTVKQHGRITVP 117
                                       56899999999977555666699999777899***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1407.09
//
Query:       gi|557694138|ref|YP_008797192.1|  [L=140]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   71.7   0.0    4.7e-20   71.5   0.0    1.0  1  Prok-JAB  Prokaryotic homologs of the JAB domain
    1.4e-07   31.5   0.0    1.9e-07   31.1   0.0    1.2  1  JAB       JAB1/Mov34/MPN/PAD-1 ubiquitin protease


Domain annotation for each model (and alignments):
>> 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 !   71.5   0.0   5.2e-24   4.7e-20       4     116 ..       9     122 ..       6     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 5.2e-24
                          Prok-JAB   4 vlsalvaharrahpeEtcGlllgkeseseevivvplvnewsn....rfeipdpedslarlkfearerglevvgiwHS 76 
                                       v+++++++  + +p Et+Gl++g+  ++ +  ++p++n+ ++    r++i dp +  ++ k  a+e+g+++vg++HS
  gi|557694138|ref|YP_008797192.1|   9 VFEEIAKRCIEGYPYETAGLMFGDLGNRLVLDIYPVQNIHEQdrrvRYRI-DPMEYYRAEK-TAEEKGMTIVGVYHS 83 
                                       67899999999**************999*********98888********.**********.*************** PP

                          Prok-JAB  77 HpggsarPSetDrrdaaalarvkalliivgdkaeel...rawr 116
                                       Hp+ +arPS+ D+++a +    + +++i++ + e +   ++wr
  gi|557694138|ref|YP_008797192.1|  84 HPNVAARPSAYDLEYALP----PWSYLILSINHEKVleyTSWR 122
                                       ******************....899999988222224556776 PP

>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   2.1e-11   1.9e-07       7     107 ..       4      97 ..       1      99 [. 0.82

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 2.1e-11
                                       EEEHHHHHHHHHHHHHHHHHTS--EEEEEEEESSSEEEEEEEEEEESEEEESSECEEEEEHHHHHHHHHHHHHHHCT CS
                               JAB   7 hleslvllkildhalrtekeeeevmGlliGelnddttveitnvfalpfeetekdvdavsldqeylekksellkklrg 83 
                                        ++ lv+ +i +   ++     e++Gl+ G l ++    + +++ ++   ++++++  ++d +   ++++  k  ++
  gi|557694138|ref|YP_008797192.1|   4 VVKRLVFEEIAKRCIEGYPY--ETAGLMFGDLGNR---LVLDIYPVQNIHEQDRRVRYRIDPM---EYYRAEKTAEE 72 
                                       57778888888888888888..*************...4677777777777777777899888...55566666666 PP

                                       T.SEEEEEEEESSSS-SS--HHHHH CS
                               JAB  84 r.ervvGWYhshpditvwlsevdvr 107
                                       + + +vG Yhshp++ + +s+ d++
  gi|557694138|ref|YP_008797192.1|  73 KgMTIVGVYHSHPNVAARPSAYDLE 97 
                                       77*******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1040.82
//
Query:       gi|557694139|ref|YP_008797193.1|  [L=302]
Description: cysteine synthase B [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-61  207.8   0.0      3e-61  207.4   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 !  207.4   0.0   1.7e-65     3e-61       3     294 .]      18     295 ..      16     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 207.4 bits;  conditional E-value: 1.7e-65
                                       GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHH.HHTT..TTTSEEEEEBSSHHHHHHHHHHHH CS
                              PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllar.lkeg..tgaktvveassGNhgralAaaaal 76 
                                         +g+TPl+rl++++ + gv+l++K+E +np+gS+KdR a ++l++ ++ g   ++k ++ a+sGN+g++ ++ aa 
  gi|557694139|ref|YP_008797193.1|  18 HLVGKTPLLRLRSFE-KPGVKLYAKCEMFNPGGSVKDRPALSILLDgIRSGrlSPGKSILDATSGNMGVSYSMLAAS 93 
                                       6789*********95.99****************************87777999*********************** PP

                                       HT-EEEEEEETTS-HHHHHHHHHTT-EEEEE..CCHHHHHHHHHHHHHHH.STTCEE--TTTSHHHHHH.HHTHHHH CS
                              PALP  77 lGlkvtivvpadaspekvallrllGaevvev..ggdydeavaaaaelaae.gegaylvsqfdnptvieg.ygtiglE 149
                                       lG++++ v p++ s+ k+++++++Ga+v+++   ++ d a ++++e+ ++  e++++++q++np++  + y+t+g+E
  gi|557694139|ref|YP_008797193.1|  94 LGYRAVMVSPSNISSIKLRKMKAFGAQVILTdaLEGIDGAIRKVREIYEQePEKYFYADQYSNPANPRAhYETTGPE 170
                                       *******************************77444**********999989************************* PP

                                       HHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGT CS
                              PALP 150 ileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgsps 226
                                       ++ q+ggk++++v++vG+ g++ G+a +lke++p ++v+ v+pe  d +++                  gl+   +s
  gi|557694139|ref|YP_008797193.1| 171 VWMQTGGKLTHFVAGVGTSGTLQGTASFLKEKNPRIKVVEVQPE--DEFHGIE----------------GLKHM-AS 228
                                       ********************************************..5555555................77777.55 PP

                                       TCCHHHH.SEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 227 elafell.drlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       +l  +l+ ++  d  + + +e+a+e+ r+la+ eg++ + s++aal a+  +  +el+eg +vvv+l++
  gi|557694139|ref|YP_008797193.1| 229 ALRPSLYrEDIADNRYFIRTEDAAETSRRLAQSEGLLSGYSGGAALRAA-VELMEELDEG-VVVVVLPD 295
                                       566666636666799**********************************.**********.99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2137.55
//
Query:       gi|557694140|ref|YP_008797194.1|  [L=71]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       607  (0.0338558); 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:                         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: 00:00:00.38
# Mc/sec: 555.14
//
Query:       gi|557694141|ref|YP_008797195.1|  [L=202]
Description: DNA-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   65.6   0.0      4e-18   64.9   0.0    1.3  1  HTH_10         HTH DNA binding domain
    3.6e-11   42.4   0.0    7.1e-11   41.5   0.0    1.4  1  Sigma70_r4     Sigma-70, region 4
    3.2e-07   29.8   0.0    5.3e-06   25.9   0.1    2.1  2  GerE           Bacterial regulatory proteins, luxR family
    4.2e-07   29.7   0.7    1.5e-06   27.9   0.2    2.1  2  HTH_IclR       IclR helix-turn-helix domain
    1.8e-06   27.7   0.1    8.5e-06   25.5   0.0    2.1  2  HTH_5          Bacterial regulatory protein, arsR family
    2.8e-05   24.1   0.2    0.00012   22.0   0.2    2.1  1  HTH_20         Helix-turn-helix domain
    3.4e-05   23.3   1.0    4.7e-05   22.9   0.4    1.6  1  HTH_24         Winged helix-turn-helix DNA-binding
    4.5e-05   23.3   0.2    0.00013   21.8   0.2    1.8  1  MarR_2         MarR family
      6e-05   22.6   2.0    0.00026   20.6   0.5    2.4  2  Sigma70_r4_2   Sigma-70, region 4
    7.9e-05   22.3   0.8    0.00019   21.1   0.8    1.6  1  HTH_38         Helix-turn-helix domain
    0.00081   19.3   0.0     0.0015   18.5   0.0    1.4  1  Sigma70_ECF    ECF sigma factor
     0.0018   18.1   0.1     0.0061   16.5   0.1    1.9  2  MarR           MarR family
     0.0024   17.8   0.0     0.0042   17.0   0.0    1.3  1  HTH_36         Helix-turn-helix domain
     0.0025   17.6   0.1      0.007   16.1   0.1    1.7  1  HTH_23         Homeodomain-like domain
     0.0047   16.7   0.2      0.011   15.5   0.2    1.6  1  LacI           Bacterial regulatory proteins, lacI family
     0.0071   16.8   0.0       0.02   15.4   0.0    1.7  1  HTH_40         Helix-turn-helix domain
     0.0092   15.9   0.1      0.023   14.6   0.1    1.6  1  HTH_11         HTH domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.024   14.4   0.0    1.5  1  TetR_N         Bacterial regulatory proteins, tetR family
      0.018   14.9   1.0      0.026   14.3   0.2    1.7  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain
      0.022   14.6   0.0      0.055   13.3   0.0    1.7  1  Homeodomain    Homeodomain
      0.029   14.3   1.4      0.056   13.4   0.3    2.0  2  HTH_1          Bacterial regulatory helix-turn-helix protein,
      0.047   13.1   0.2      0.098   12.1   0.2    1.5  1  HTH_Tnp_ISL3   Helix-turn-helix domain of transposase family 
      0.056   13.5   0.1        0.7   10.0   0.0    2.5  2  HTH_22         HTH domain
      0.063   13.3   0.1       0.24   11.5   0.0    1.9  2  HTH_29         Winged helix-turn helix
      0.085   12.8   0.0       0.17   11.8   0.0    1.5  1  PuR_N          Bacterial purine repressor, N-terminal
      0.085   13.0   0.1        0.2   11.8   0.1    1.6  1  HTH_28         Helix-turn-helix domain
      0.089   13.0   0.1       0.32   11.2   0.1    1.9  2  HTH_17         Helix-turn-helix domain
      0.093   12.4   0.1       0.19   11.4   0.1    1.6  1  Sigma54_DBD    Sigma-54, DNA binding domain
      0.099   12.7   0.3       0.18   11.8   0.3    1.4  1  HTH_35         Winged helix-turn-helix DNA-binding
        0.1   12.8   0.0       0.18   12.0   0.0    1.4  1  UPF0122        Putative helix-turn-helix protein, YlxM / p13 
       0.11   12.6   0.1       0.23   11.6   0.1    1.5  1  HTH_3          Helix-turn-helix
       0.11   12.2   1.0       0.56   10.0   1.0    2.1  1  LexA_DNA_bind  LexA DNA binding domain
       0.12   12.2   0.1       0.37   10.6   0.0    1.8  2  HTH_Tnp_4      Helix-turn-helix of DDE superfamily endonuclea
       0.13   12.3   4.0       0.14   12.2   0.2    2.7  3  HTH_Crp_2      Crp-like helix-turn-helix domain
       0.15   11.9   0.7        1.5    8.8   0.1    2.2  2  HTH_Tnp_Tc3_1  Tc3 transposase
       0.16   12.1   0.2       0.64   10.2   0.1    2.0  1  SoPB_HTH       Centromere-binding protein 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 !   64.9   0.0   8.1e-21     4e-18       1      52 [.     143     194 ..     143     195 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 8.1e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT+kq +vl +A+ mGYF  +R+++l+e+A +lG+skst+s hLr a++kl+
  gi|557694141|ref|YP_008797195.1| 143 LTPKQQQVLYTAFMMGYFSPSRETSLSEIATRLGLSKSTVSRHLRTAMRKLA 194
                                       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 !   41.5   0.0   1.4e-13   7.1e-11       4      48 ..     142     193 ..     141     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.4e-13
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       +L++++++vl+  f        ++ +l+EI+ rlg+S+++V+++++ A+rkL
  gi|557694141|ref|YP_008797195.1| 142 VLTPKQQQVLYTAFmmgyfspSRETSLSEIATRLGLSKSTVSRHLRTAMRKL 193
                                       7********************9*****************************9 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.39     2e+02       2      11 ..     142     151 ..     141     159 .. 0.88
   2 !   25.9   0.1   1.1e-08   5.3e-06      21      48 ..     169     196 ..     164     202 .] 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.39
                                       SS-HHHHHHH CS
                              GerE   2 sLskRErevL 11 
                                       +L++++++vL
  gi|557694141|ref|YP_008797195.1| 142 VLTPKQQQVL 151
                                       8********9 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 1.1e-08
                                       HHHHHHHTS-HHHHHHHHHHHHHHHT-S CS
                              GerE  21 keIAeelniSekTVkvhksnimkKLnvk 48 
                                        eIA +l++S+ TV+ h++ +m+KL v+
  gi|557694141|ref|YP_008797195.1| 169 SEIATRLGLSKSTVSRHLRTAMRKLAVT 196
                                       69***********************997 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 ?   -1.4   0.0       4.2   2.1e+03      32      46 ..      13      27 ..       7      28 .. 0.81
   2 !   27.9   0.2   3.1e-09   1.5e-06      11      41 ..     159     188 ..     156     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.2
                                      HHHHHHHHHHHHHTT CS
                          HTH_IclR 32 kStvhRlLqtLvelG 46
                                      + ++ R +qtL + G
  gi|557694141|ref|YP_008797195.1| 13 RNSTCRVVQTLFQKG 27
                                      6789999***97766 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 3.1e-09
                                       T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHH CS
                          HTH_IclR  11 alaeapqeltlselArrtglpkStvhRlLqt 41 
                                       +++  ++  +lse+A r+gl+kStv+R+L+t
  gi|557694141|ref|YP_008797195.1| 159 YFSPSRET-SLSEIATRLGLSKSTVSRHLRT 188
                                       66667775.9*******************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 ?   -1.9   0.0       6.4   3.2e+03       6      15 ..     117     126 ..     116     130 .. 0.67
   2 !   25.5   0.0   1.7e-08   8.5e-06      14      37 ..     164     187 ..     159     192 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.4
                                       HHHHHHTTSS CS
                             HTH_5   6 kILklLaege 15 
                                       kIL +++e+ 
  gi|557694141|ref|YP_008797195.1| 117 KILDQMRERG 126
                                       7888887754 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 1.7e-08
                                       SSEEHHHHHHHHTS-HHHHHHHHH CS
                             HTH_5  14 gelcvcelaeelglsqstvShHLk 37 
                                       +e++ +e+a  lgls+stvS+HL+
  gi|557694141|ref|YP_008797195.1| 164 RETSLSEIATRLGLSKSTVSRHLR 187
                                       78999******************9 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.2   2.5e-07   0.00012      20      46 ..     161     187 ..     114     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.5e-07
                                       STCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  20 araegltaselaerldlskntlsyHLr 46 
                                       ++ ++ ++se+a rl+lsk+t+s+HLr
  gi|557694141|ref|YP_008797195.1| 161 SPSRETSLSEIATRLGLSKSTVSRHLR 187
                                       566789********************8 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 !   22.9   0.4   9.5e-08   4.7e-05      18      41 ..     166     189 ..     163     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 9.5e-08
                            HTH_24  18 isqreLAerlglSpstvnrrlkrL 41 
                                       +s +e+A rlglS+stv+r+l+  
  gi|557694141|ref|YP_008797195.1| 166 TSLSEIATRLGLSKSTVSRHLRTA 189
                                       6899*****************965 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.2   2.5e-07   0.00013      18      45 ..     162     189 ..     143     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.5e-07
                                       TTSEEEHHHHHHHHTSSHHHHHHHHHHH CS
                            MarR_2  18 pgrdltvgelarrlglsksavsrilkrL 45 
                                       p r+ + +e+a rlglsks+vsr+l+ +
  gi|557694141|ref|YP_008797195.1| 162 PSRETSLSEIATRLGLSKSTVSRHLRTA 189
                                       4457799******************976 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       0.9   4.5e+02      10      20 ..     142     152 ..     133     159 .. 0.70
   2 !   20.6   0.5   5.2e-07   0.00026      28      54 .]     167     193 ..     164     193 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.9
                                       TS-HHHHHHHH CS
                      Sigma70_r4_2  10 eLperqreifl 20 
                                        L+++q++++ 
  gi|557694141|ref|YP_008797195.1| 142 VLTPKQQQVLY 152
                                       47888888876 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 5.2e-07
                                       -HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  28 sykEIAellgisegtVksrlsRArkkL 54 
                                       s  EIA +lg+s +tV ++l+ A++kL
  gi|557694141|ref|YP_008797195.1| 167 SLSEIATRLGLSKSTVSRHLRTAMRKL 193
                                       789**********************98 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.8   3.8e-07   0.00019      21      42 ..     166     187 ..     163     188 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.8e-07
                            HTH_38  21 lslreIArrLgrspsTIsRElk 42 
                                        sl+eIA rLg s+sT+sR+l+
  gi|557694141|ref|YP_008797195.1| 166 TSLSEIATRLGLSKSTVSRHLR 187
                                       699*****************98 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.9e-06    0.0015     123     179 ..     129     193 ..     110     198 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.9e-06
                       Sigma70_ECF 123 lleLdealerlls.ldpeqarlvelrkleGl.......sveEiAeklgvskrtverrlalaRawl 179
                                       ++ L+  + +l + l p+q +++  +++ G+       s  EiA++lg+sk+tv r+l+ a  +l
  gi|557694141|ref|YP_008797195.1| 129 VEVLNRKVFNLRAvLTPKQQQVLYTAFMMGYfspsretSLSEIATRLGLSKSTVSRHLRTAMRKL 193
                                       5567778888988899**************96666666789*****************9987776 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       9.2   4.6e+03      33      45 ..      15      27 ..      11      28 .. 0.80
   2 !   16.5   0.1   1.2e-05    0.0061      18      40 ..     166     188 ..     143     190 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 9.2
                                      HHHHHHHHHHHTT CS
                              MarR 33 tvtrvldrLekkG 45
                                      ++ rv+ +L +kG
  gi|557694141|ref|YP_008797195.1| 15 STCRVVQTLFQKG 27
                                      5679999999998 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.2e-05
                                       EEHHHHHHHHTS-HHHHHHHHHH CS
                              MarR  18 lsvseLakklgvskstvtrvldr 40 
                                        s+se+a +lg+skstv+r l++
  gi|557694141|ref|YP_008797195.1| 166 TSLSEIATRLGLSKSTVSRHLRT 188
                                       5788****************985 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   8.4e-06    0.0042      27      50 ..     167     190 ..     156     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.4e-06
                            HTH_36  27 sqetlakrlglsknTvsraikeLe 50 
                                       s + +a+rlglsk+Tvsr+++  +
  gi|557694141|ref|YP_008797195.1| 167 SLSEIATRLGLSKSTVSRHLRTAM 190
                                       7899***************98765 PP

>> HTH_23  Homeodomain-like 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     0.007      19      40 ..     167     188 ..     165     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                            HTH_23  19 svreIAreLgvsrrTvyrwlkr 40 
                                       s +eIA++Lg s++Tv+r l++
  gi|557694141|ref|YP_008797195.1| 167 SLSEIATRLGLSKSTVSRHLRT 188
                                       679***************8876 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   2.3e-05     0.011       2      23 ..     168     189 ..     167     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHCTS-HHHHHHHCTTS CS
                              LacI   2 ikDVArlAGVSkaTVSrvLnnk 23 
                                       + ++A++ G Sk+TVSr L+ +
  gi|557694141|ref|YP_008797195.1| 168 LSEIATRLGLSKSTVSRHLRTA 189
                                       789***************9875 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     4e-05      0.02      13      38 ..     166     191 ..     163     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 4e-05
                            HTH_40  13 lsieeIAkerglkesTIegHLaelie 38 
                                        s+ eIA++ gl++sT+ +HL  +++
  gi|557694141|ref|YP_008797195.1| 166 TSLSEIATRLGLSKSTVSRHLRTAMR 191
                                       5899*****************88776 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   4.7e-05     0.023      16      38 ..     166     188 ..     160     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.7e-05
                            HTH_11  16 isgeeLAeeLnvSrrtvrrdIka 38 
                                        s +e+A +L++S++tv r++++
  gi|557694141|ref|YP_008797195.1| 166 TSLSEIATRLGLSKSTVSRHLRT 188
                                       699*****************976 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 ?   14.4   0.0   4.8e-05     0.024      16      36 ..     165     185 ..     163     194 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.8e-05
                                       T--HHHHHHHHTSSHHHHHHH CS
                            TetR_N  16 attvreIAkrAGvskgalYry 36 
                                       +t+++eIA r+G+sk+++ r+
  gi|557694141|ref|YP_008797195.1| 165 ETSLSEIATRLGLSKSTVSRH 185
                                       79****************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 ?   14.3   0.2   5.2e-05     0.026      18      36 ..     166     184 ..     165     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.2e-05
                     HTH_AsnC-type  18 isyaeLAervGlSestvlr 36 
                                       +s +e+A r+GlS stv r
  gi|557694141|ref|YP_008797195.1| 166 TSLSEIATRLGLSKSTVSR 184
                                       699**************98 PP

>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00011     0.055       4      44 ..     140     182 ..     138     184 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                       SSSS-HHHHHHHHHHHHH.SSS-SHHH.HHHHHHHHTS-HHHH CS
                       Homeodomain   4 RttftkeqleeLeklFee.nrypsaee.reeLAkklgLeerqV 44 
                                       R  +t++q ++L ++F +    ps+e+   e+A++lgL+++ V
  gi|557694141|ref|YP_008797195.1| 140 RAVLTPKQQQVLYTAFMMgYFSPSRETsLSEIATRLGLSKSTV 182
                                       8899*************98999*9986379**********999 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 ?   -1.9   0.0       6.9   3.4e+03      38      57 ..     124     145 ..     119     146 .. 0.66
   2 ?   13.4   0.3   0.00011     0.056      12      41 ..     164     193 ..     163     196 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.9
                                       HHHHTS-SEEESSS..EEEE-H CS
                             HTH_1  38 EeelgvpLfeRtgr..glrLTe 57 
                                       E+ l+v+ ++R+    +++LT+
  gi|557694141|ref|YP_008797195.1| 124 ERGLDVEVLNRKVFnlRAVLTP 145
                                       5567888888843323478886 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00011
                                       HHSSHHHHHHHHTS-HHHHHHHHHHHHHHH CS
                             HTH_1  12 eegsftrAAeeLglsqpavsrqikrLEeel 41 
                                       +e s+++ A +Lgls ++vsr++++  + l
  gi|557694141|ref|YP_008797195.1| 164 RETSLSEIATRLGLSKSTVSRHLRTAMRKL 193
                                       67899999***************9866655 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 ?   12.1   0.2    0.0002     0.098      25      46 ..     164     184 ..     163     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                      HTH_Tnp_ISL3  25 lesrsvkavArqlgvSwtTVwr 46 
                                       +e+ s +++A +lg+S +TV r
  gi|557694141|ref|YP_008797195.1| 164 RET-SLSEIATRLGLSKSTVSR 184
                                       567.9***************99 PP

>> HTH_22  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       1.6     8e+02      24      37 ..      15      28 ..       6      28 .. 0.84
   2 ?   10.0   0.0    0.0014       0.7      43      63 .]     167     187 ..     162     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.6
                            HTH_22 24 ekieivraLdekGi 37
                                         ++v+ L +kG+
  gi|557694141|ref|YP_008797195.1| 15 STCRVVQTLFQKGV 28
                                      56789*******97 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0014
                            HTH_22  43 avekvAekLgiSraTvYryLr 63 
                                       + +++A +Lg S+ Tv r+Lr
  gi|557694141|ref|YP_008797195.1| 167 SLSEIATRLGLSKSTVSRHLR 187
                                       6789************99997 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       5.6   2.8e+03      31      62 ..     117     148 ..     115     149 .. 0.63
   2 ?   11.5   0.0   0.00048      0.24      13      34 ..     167     187 ..     163     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 5.6
                            HTH_29  31 rwlkrfeegGlaa.lldrrrsgrprnrlseeqe 62 
                                       ++l+ ++e Gl+   l+r+   ++r +l++ q+
  gi|557694141|ref|YP_008797195.1| 117 KILDQMRERGLDVeVLNRK-VFNLRAVLTPKQQ 148
                                       6677777777776655544.3667777777776 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00048
                            HTH_29  13 stvsqiAkllglsrrtvyrwlk 34 
                                       s  s+iA +lgls++tv r+l+
  gi|557694141|ref|YP_008797195.1| 167 S-LSEIATRLGLSKSTVSRHLR 187
                                       5.89***************986 PP

>> PuR_N  Bacterial purine repressor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00034      0.17      16      44 ..     161     189 ..     150     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                             PuR_N  16 nPnklisltyfaerfeaAKSsiSeDlaii 44 
                                       +P++ +sl+++a r++ +KS++S  l++ 
  gi|557694141|ref|YP_008797195.1| 161 SPSRETSLSEIATRLGLSKSTVSRHLRTA 189
                                       699********************888765 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0004       0.2      13      34 ..     166     187 ..     163     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0004
                            HTH_28  13 hsvreaArelgisrrtvyrWik 34 
                                        s +e+A +lg+s +tv+r ++
  gi|557694141|ref|YP_008797195.1| 166 TSLSEIATRLGLSKSTVSRHLR 187
                                       4899**************9987 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       9.3   4.7e+03       8      21 ..      54      67 ..      54      70 .. 0.82
   2 ?   11.2   0.1   0.00064      0.32       4      23 ..     168     187 ..     167     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 9.3
                            HTH_17  8 AelLgvsrstvyrl 21
                                      +elL++ +s vy +
  gi|557694141|ref|YP_008797195.1| 54 QELLHIPDSIVYTM 67
                                      699**999988876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00064
                            HTH_17   4 veEaAelLgvsrstvyrlir 23 
                                        +E+A  Lg+s+stv r +r
  gi|557694141|ref|YP_008797195.1| 168 LSEIATRLGLSKSTVSRHLR 187
                                       689*************9887 PP

>> Sigma54_DBD  Sigma-54, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00038      0.19      48      71 ..     164     187 ..     116     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                                       XXXXHHHHHTTSSSXHHHHHHHHH CS
                       Sigma54_DBD  48 rpltlrevaealelhesTvSRvvs 71 
                                       r  +l+e+a+ l+l++sTvSR   
  gi|557694141|ref|YP_008797195.1| 164 RETSLSEIATRLGLSKSTVSRHLR 187
                                       56689****************765 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 ?   11.8   0.3   0.00037      0.18      14      42 ..     164     192 ..     162     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00037
                            HTH_35  14 rgttLaalsreaglssstlsnaltrpwpk 42 
                                       r+t+L++++ ++gls+st+s+ l++ ++k
  gi|557694141|ref|YP_008797195.1| 164 RETSLSEIATRLGLSKSTVSRHLRTAMRK 192
                                       89******************999987765 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 ?   12.0   0.0   0.00037      0.18      16      59 ..     141     191 ..     131     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00037
                           UPF0122  16 sLLTekqany.....lelyy..adDlSlsEiAeefnvsrqavydnikrtek 59 
                                       ++LT kq+++     +  y+    + SlsEiA +  +s+++v+ +++++ +
  gi|557694141|ref|YP_008797195.1| 141 AVLTPKQQQVlytafMMGYFspSRETSLSEIATRLGLSKSTVSRHLRTAMR 191
                                       56888887751111134455223688******************9998765 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00045      0.23      10      28 ..     166     184 ..     163     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHHTSSHHHHHH CS
                             HTH_3  10 lsqeeLAeklGvsrstisr 28 
                                        s+ e+A +lG+s+st+sr
  gi|557694141|ref|YP_008797195.1| 166 TSLSEIATRLGLSKSTVSR 184
                                       6899**************8 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 ?   10.0   1.0    0.0011      0.56      26      53 ..     166     192 ..     141     200 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0011
                                       --HHHHHHHHTS-.HHHHHHHHHHHHHT CS
                     LexA_DNA_bind  26 PsireiaralglkSpsaveehLkaLerK 53 
                                        s  eia +lgl+  s+v  hL++  rK
  gi|557694141|ref|YP_008797195.1| 166 TSLSEIATRLGLS-KSTVSRHLRTAMRK 192
                                       2668********7.9********98888 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 ?   -2.1   0.0       6.5   3.3e+03       4      13 ..     145     154 ..     142     155 .. 0.73
   2 ?   10.6   0.0   0.00074      0.37      23      50 ..     169     196 ..     166     199 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6.5
                         HTH_Tnp_4   4 sledqllltL 13 
                                       ++++q+l+t 
  gi|557694141|ref|YP_008797195.1| 145 PKQQQVLYTA 154
                                       6789999885 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00074
                         HTH_Tnp_4  23 qdLayrFgvsestvsrifhkwvdlLaer 50 
                                       + +a r g s stvsr  ++ +  La  
  gi|557694141|ref|YP_008797195.1| 169 SEIATRLGLSKSTVSRHLRTAMRKLAVT 196
                                       6799**************9999888765 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 ?   -0.7   0.0         3   1.5e+03      34      59 ..      12      37 ..       8      55 .. 0.76
   2 ?   -0.6   0.1       2.7   1.4e+03      40      60 ..     117     132 ..     111     139 .. 0.53
   3 ?   12.2   0.2   0.00028      0.14      24      43 ..     168     187 ..     162     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 3
                                      SHHHHHHHHHHHHHTTSEE.ETEEEEE CS
                         HTH_Crp_2 34 tretvsrilseLkreglis.rgrriri 59
                                       r ++ r+ + L ++g+    +  ir+
  gi|557694141|ref|YP_008797195.1| 12 VRNSTCRVVQTLFQKGVEGsFRS-IRV 37
                                      57888899999888887553343.555 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.7
                                       HHHHHHHHTTSEEETEEEEES CS
                         HTH_Crp_2  40 rilseLkreglisrgrriril 60 
                                       +il +++++gl      +++l
  gi|557694141|ref|YP_008797195.1| 117 KILDQMRERGLD-----VEVL 132
                                       345555555541.....4444 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00028
                                       HHHHHHHTTSSHHHHHHHHH CS
                         HTH_Crp_2  24 qeelAsmlGltretvsrils 43 
                                         e+A +lGl+ +tvsr l+
  gi|557694141|ref|YP_008797195.1| 168 LSEIATRLGLSKSTVSRHLR 187
                                       579**************998 PP

>> HTH_Tnp_Tc3_1  Tc3 transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.75   3.8e+02      10      30 ..     116     136 ..     114     142 .. 0.84
   2 ?    8.8   0.1    0.0029       1.5      21      42 ..     166     187 ..     163     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.75
                                       HHHHHHHHHTT--HHHHHHHH CS
                     HTH_Tnp_Tc3_1  10 raillvmkllnvklsEiarkl 30 
                                       r il+ m++ +  +  + rk+
  gi|557694141|ref|YP_008797195.1| 116 RKILDQMRERGLDVEVLNRKV 136
                                       779*******99998888886 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0029
                                       --HHHHHHHHT--HHHHHHHHH CS
                     HTH_Tnp_Tc3_1  21 vklsEiarklsRsRnCIrryLK 42 
                                        +lsEia++l  s+  ++r+L+
  gi|557694141|ref|YP_008797195.1| 166 TSLSEIATRLGLSKSTVSRHLR 187
                                       69*****************997 PP

>> SoPB_HTH  Centromere-binding protein HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0013      0.64      21      51 ..     167     197 ..     163     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0013
                          SoPB_HTH  21 nlsalaeaeklskkilskmlrvaklPdavva 51 
                                        ls +a ++ lsk  +s+ lr+a    av a
  gi|557694141|ref|YP_008797195.1| 167 SLSEIATRLGLSKSTVSRHLRTAMRKLAVTA 197
                                       6899*******************87666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); 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):              36  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1460.38
//
Query:       gi|557694142|ref|YP_008797196.1|  [L=485]
Description: nitrite reductase (NO-forming) [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   0.2    6.1e-10   39.1   0.0    2.6  2  Cu-oxidase_3  Multicopper oxidase
    4.6e-11   42.8   0.0      2e-05   24.6   0.0    2.7  2  Cupredoxin_1  Cupredoxin-like domain
    5.1e-11   42.5   0.1    1.1e-06   28.4   0.1    3.5  2  Cu-oxidase_2  Multicopper oxidase
    4.4e-07   30.3   0.2     0.0011   19.4   0.0    2.8  2  Copper-bind   Copper binding proteins, plastocyanin/azurin fa


Domain annotation for each model (and alignments):
>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   1.4e-13   6.1e-10       6     118 ..      51     159 ..      47     160 .. 0.89
   2 ?    2.7   0.0     0.026   1.2e+02      71     112 ..     259     300 ..     194     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.4e-13
                                       EEECTTEESEEEEEECTSSBS-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSCSGGG-B-TT-EEE CS
                      Cu-oxidase_3   6 tvsplggterevitvNgqfpgptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpgvtqcpiqpgesft 82 
                                       +v +++g+  ++ ++Ng+ pgp i v+egd v++ v+N  +++  +++h  + +++      ++     i+pg + +
  gi|557694142|ref|YP_008797196.1|  51 DVVIDDGVVFRAFVFNGTSPGPLIVVEEGDVVEIIVKNVGQYTHGLSFHAANTQTS------KF--IGNIPPGGEGR 119
                                       5666777778899************************************9999988......44..468******** PP

                                       EEEE--S-SEEEEEEE--TT.....HHHTT-EEEEEEE-HH CS
                      Cu-oxidase_3  83 yrftvkqqagtlwYhshlsl.....qqaaGlaGaiiiedke 118
                                         f+++   g ++Yh    +     +  aG++G++++e+k+
  gi|557694142|ref|YP_008797196.1| 120 LVFKADF-PGVYMYHCAPGGhgiltHTLAGMYGMVVVEPKK 159
                                       *******.*******9998888996666**********986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.026
                                       GGG-B-TT-EEEEEEE--S-SEEEEEEE--TTHHH.TT-EEEE CS
                      Cu-oxidase_3  71 tqcpiqpgesftyrftvkqqagtlwYhshlslqqa.aGlaGai 112
                                       ++   +p es++ +++v   +g ++  sh+ + qa +G aG i
  gi|557694142|ref|YP_008797196.1| 259 QTVNAAPTESYVIEWRVPA-EGNFLIVSHAFGTQAiKGAAGYI 300
                                       455668999**********.9999999999996666**99987 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   4.2e-06     0.019      37      93 ..      74     135 ..      41     144 .. 0.87
   2 !   24.6   0.0   4.5e-09     2e-05      22     104 .]     348     438 ..     336     438 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-06
                      Cupredoxin_1  37 ievkagekvklkiknkdktpeefesed.....lgeekvlapgktttitiaplkpGeYeftcd 93 
                                       i v++g  v++ +kn ++ ++ ++++       ++  +++pg + ++ ++++ pG Y ++c 
  gi|557694142|ref|YP_008797196.1|  74 IVVEEGDVVEIIVKNVGQYTHGLSFHAantqtSKFIGNIPPGGEGRLVFKADFPGVYMYHCA 135
                                       7899****************999999966554455569***********************5 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 4.5e-09
                      Cupredoxin_1  22 tveitvkdggfePskievkagekvklkiknkdkt.........peefesed..lgeekvlapg.ktttitiaplkpG 86 
                                       +v i++  ++f+P+   v+ g   ++++ n+d            +++ + +  +++  +l ++ ++++++i  +k+G
  gi|557694142|ref|YP_008797196.1| 348 KVMIQIVGNSFYPKIARVPVGS--TVTWINEDVLsigsgeitgQHNVAAIQgpVSFASQLLKNaEQFSFKI--EKEG 420
                                       578999999************9..66777777766667777655777777778777766555505555555..**** PP

                      Cupredoxin_1  87 eYeftcdmhmdakGkliV 104
                                       eY+++c++h+++kG+l++
  gi|557694142|ref|YP_008797196.1| 421 EYNYICGIHPYMKGTLVA 438
                                       ****************95 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.1   2.4e-10   1.1e-06      32     136 ..      71     158 ..      47     159 .. 0.80
   2 !    7.2   0.0   0.00085       3.8      23     118 ..     197     286 ..     177     289 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2.4e-10
                                       SEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEEEEEES. CS
                      Cu-oxidase_2  32 tnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwvairfkad 108
                                        + i++++g+vvei+++n ++       HG +f   ++++++                    ++ppgg+ ++ fkad
  gi|557694142|ref|YP_008797196.1|  71 GPLIVVEEGDVVEIIVKNVGQY-----THGLSFHAANTQTSK-----------------FIGNIPPGGEGRLVFKAD 125
                                       5677788888888888888887.....477777776444444.................6789************** PP

                                       S-EEEEEEES.....SHHHHHTT-EEEEEEECH CS
                      Cu-oxidase_2 109 npGvwllHCH.....ilwHldqGmalqfvvrpd 136
                                        pGv+++HC      il H+ +Gm++ +vv+p+
  gi|557694142|ref|YP_008797196.1| 126 FPGVYMYHCApgghgILTHTLAGMYGMVVVEPK 158
                                       *********64444588************9986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00085
                                       E...ETCCTTTSSEEEEEETTEEEEEEEEE-SSS.-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE CS
                      Cu-oxidase_2  23 t...ngeefsentnvitlpkgevveiviqnntkl.pHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqv 95 
                                       +   ng+ f+  t +i+++ g++v++++ n ++    +fH  G  ++   r++++           +  v   tv+ 
  gi|557694142|ref|YP_008797196.1| 197 YvmfNGRVFRYLTEPIQARPGDYVRFYFLNIGPSlVSSFHAVGGIWEYAYRNGNP----------ENVEVGLQTVNA 263
                                       04449999**********************9999999***999888888777777..........233556699999 PP

                                       -TTEEEEEEEES.S-EEEEEEES CS
                      Cu-oxidase_2  96 ppggwvairfkadnpGvwllHCH 118
                                        p +  +i++++   G +l+ +H
  gi|557694142|ref|YP_008797196.1| 264 APTESYVIEWRVPAEGNFLIVSH 286
                                       99999999999999999998777 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 !    7.8   0.1   0.00098       4.4      71      99 .]     121     156 ..      73     156 .. 0.69
   2 !   19.4   0.0   2.5e-07    0.0011      13      96 ..     357     436 ..     348     438 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00098
                                       EEEEESSEEEEEEETT..TTT.....TTSEEEEEEE CS
                       Copper-bind  71 svtfdeagtYkffCsP..Haa.....agMkgkvtve 99 
                                         + d +g Y ++C+P  H       agM+g v+ve
  gi|557694142|ref|YP_008797196.1| 121 VFKADFPGVYMYHCAPggHGIlthtlAGMYGMVVVE 156
                                       334558999******998864222226999999986 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 2.5e-07
                                       EEESSEEEEETTEEEEEEEE.........SSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEE CS
                       Copper-bind  13 qFetkeitvkkgekvtfvnl.........avmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtY 80 
                                       +F +k  +v  g++vt++n              HNv   ++ v   ++++ +k           e++s +++++g+Y
  gi|557694142|ref|YP_008797196.1| 357 SFYPKIARVPVGSTVTWINEdvlsigsgeITGQHNVAAIQGPV--SFASQLLKN---------AEQFSFKIEKEGEY 422
                                       6899999************988888888656669998888887..456666666.........499*********** PP

                                       EEEETTTTTTTSEEEE CS
                       Copper-bind  81 kffCsPHaaagMkgkv 96 
                                       +++C  H    Mkg++
  gi|557694142|ref|YP_008797196.1| 423 NYICGIHP--YMKGTL 436
                                       ********..69*997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3426.45
//
Query:       gi|557694143|ref|YP_008797197.1|  [L=196]
Description: electron transport protein SCO1/SenC [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-31  108.6   0.0    2.9e-31  108.1   0.0    1.1  1  SCO1-SenC      SCO1/SenC
    7.9e-07   29.0   0.0      1e-06   28.7   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
    1.5e-06   28.0   0.0    1.7e-06   27.8   0.0    1.1  1  Redoxin        Redoxin
     0.0067   16.7   0.0     0.0099   16.2   0.0    1.3  1  Thioredoxin_8  Thioredoxin-like
  ------ inclusion threshold ------
      0.018   14.9   0.0      0.033   14.1   0.0    1.4  1  NACHT          NACHT domain
      0.086   12.4   0.0       0.32   10.6   0.0    1.8  2  GSHPx          Glutathione peroxidase


Domain annotation for each model (and alignments):
>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.1   0.0   9.9e-35   2.9e-31       3     130 ..      46     171 ..      44     173 .. 0.94

  Alignments for each domain:
  == domain 1  score: 108.1 bits;  conditional E-value: 9.9e-35
                         SCO1-SenC   3 pFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyl 79 
                                       +F l++  ge+   e+++gk++l+ffg+++CpdvCp +l + ae+ + lg++a +v ++fiT DP rD+pe+l++ +
  gi|557694143|ref|YP_008797197.1|  46 RFILTNIYGERTALESFRGKVVLIFFGYANCPDVCPQALRKYAELEQLLGPKASEVVLIFITTDPFRDSPETLAHLV 122
                                       6999************************************************************************* PP

                         SCO1-SenC  80 eafdpriigltGskeeiakaakefrvyvekvedeesdytvdHsssvyLvdp 130
                                       e++++ri++ltG+ +e+a++ +++++   + +++     + Hs+ +y+ d+
  gi|557694143|ref|YP_008797197.1| 123 EKYSSRIVALTGEWDELAEVWQKYHIRPLERDEQ--AAFITHSAVIYVGDR 171
                                       *************************995555444..459********8776 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   3.4e-10     1e-06       2     101 ..      41     149 ..      40     174 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.4e-10
                                       TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-C.CHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH...... CS
                          AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcp.vCttelpalaklyeefkergvevigvsvdspe...... 71 
                                       g++ p f l+n  ge   l+ ++gk+v++ff  + +cp vC++ l+++a+l + +  +  ev+ + +++        
  gi|557694143|ref|YP_008797197.1|  41 GRALPRFILTNIYGERTALESFRGKVVLIFFGYA-NCPdVCPQALRKYAELEQLLGPKASEVVLIFITTDPfrdspe 116
                                       7889********************7777777555.78768********99999998766666555443222234444 PP

                                       HHHHHHHH-H....SSEEEE-TTSHHHHHTT-E CS
                          AhpC-TSA  72 shkkfiekes...lnfpllsDeegkvakaygvl 101
                                       +++  +ek+s   + ++  +De  +v ++y + 
  gi|557694143|ref|YP_008797197.1| 117 TLAHLVEKYSsriVALTGEWDELAEVWQKYHIR 149
                                       999999999966666666667777777777765 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   5.8e-10   1.7e-06       3     104 ..      41     149 ..      39     193 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 5.8e-10
                                       TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-H.HHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH... CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcP.tCsaehpyleklaellkekgvdvvavvadndaf... 75 
                                       g ++P f l  ++  g+ + l++f+gk+v+++f  +  cP +C + +++ ++l++ll+ k+ +vv + + +d+f   
  gi|557694143|ref|YP_008797197.1|  41 GRALPRFIL--TNIYGERTALESFRGKVVLIFFGYA-NCPdVCPQALRKYAELEQLLGPKASEVVLIFITTDPFrds 114
                                       778999998..569**************88888887.9*944666666**************************886 PP

                                       ...HHHHHHHTT-TSEEEE-...TTSHHHHHTT-T CS
                           Redoxin  76 ...vkefwgkeglkfpvlsD...gsaaftkalGlr 104
                                              ++k++  ++ l+    + a++ +++ +r
  gi|557694143|ref|YP_008797197.1| 115 petLAHLVEKYSSRIVALTGewdELAEVWQKYHIR 149
                                       66545555556666666665332555555555554 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.3e-06    0.0099       1      54 [.      64     121 ..      64     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.3e-06
                                       .SEEEEEE--SSSHH.HHHHHHHHHHHHHHHHH.TTSEEEEEEE-S..S-HHHHHHHG CS
                     Thioredoxin_8   1 gkvvlLyfgaswcpp.ckaftpklkelyeklkk.kkkveivyvsld..kkeeefekyl 54 
                                       gkvvl++fg  +cp+ c + ++k  el++ l   +  v+++++  d  ++  e+ ++l
  gi|557694143|ref|YP_008797197.1|  64 GKVVLIFFGYANCPDvCPQALRKYAELEQLLGPkASEVVLIFITTDpfRDSPETLAHL 121
                                       79************99***************9559**********9554544444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.1e-05     0.033      33     159 ..      17     160 ..      13     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                       C-SEEEEEETTTTTTS-.........-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEEEEEE-STT-SS-TCH.... CS
                             NACHT  33 afklvFflslrelsrsgna......rsladllfsqlpepaapvsevwavllelperlLlilDglDelvtdlgqkekq 103
                                       af l+F++s+re+++  +       r l +++  +   +          l + + +++li+ g+  +++  +q  + 
  gi|557694143|ref|YP_008797197.1|  17 AFLLSFYFSQRETPETLQPdvlmsgRALPRFILTNIYGERT-------ALESFRGKVVLIFFGYANCPDVCPQ--AL 84 
                                       58999999999999987666666665566665555554444.......45579****************9999..99 PP

                                       .....HHHHHCTTTTT--EEEEEEECCCHHHHCTTSSCE........................EEEE--TCCHHHHH CS
                             NACHT 104 pvrtlLselirkkllpeasllltvrpralrdleeqleea......................ivlevegfsesrrkql 158
                                       +    L++l+  k    + +++t+ p +    +e+l++                       + ++++++++++ +++
  gi|557694143|ref|YP_008797197.1|  85 RKYAELEQLLGPKASEVVLIFITTDPFRD--SPETLAHLvekyssrivaltgewdelaevwQKYHIRPLERDEQAAF 159
                                       99999*******99999999999998655..4444444444458878888888888888888888888888887777 PP

                                       H CS
                             NACHT 159 v 159
                                       +
  gi|557694143|ref|YP_008797197.1| 160 I 160
                                       6 PP

>> GSHPx  Glutathione peroxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.32       7      46 ..      50      94 ..      45     109 .. 0.74
   2 ?   -0.9   0.0       0.4   1.2e+03      33      50 ..     130     147 ..     116     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                                      EBTTSSEEEGGGGTTSEEEE....EEEESSSTTHH.HHHHHHHHH CS
                             GSHPx  7 kdidgekvkleklrgkvvli....vnvaskCglte.qykeleelq 46
                                      ++i ge + le++rgkvvli     n    C  +  +y ele+l 
  gi|557694143|ref|YP_008797197.1| 50 TNIYGERTALESFRGKVVLIffgyANCPDVCPQALrKYAELEQLL 94
                                      67889**************93333366666666656899988875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.4
                                       STTHHHHHHHHHHHHHHG CS
                             GSHPx  33 Cglteqykeleelqkryk 50 
                                        +lt ++ el e+ ++y+
  gi|557694143|ref|YP_008797197.1| 130 VALTGEWDELAEVWQKYH 147
                                       467889999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1374.65
//
Query:       gi|557694144|ref|YP_008797198.1|  [L=216]
Description: hypothetical protein CSUB_C0709 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       425  (0.0237046); 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:                         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: 00:00:00.41
# Mc/sec: 1595.08
//
Query:       gi|557694145|ref|YP_008797199.1|  [L=261]
Description: hypothetical protein CSUB_C0710 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1899.88
//
Query:       gi|557694146|ref|YP_008797200.1|  [L=257]
Description: ABC-2 type transport system permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-10   40.9  17.4    1.5e-10   40.9  17.4    1.5  2  ABC2_membrane    ABC-2 type transporter
    0.00067   18.9  18.3    0.00067   18.9  18.3    1.7  2  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 !   40.9  17.4   1.7e-14   1.5e-10       2     208 ..       6     215 ..       5     217 .. 0.79
   2 ?   -1.3   0.1      0.14   1.2e+03     122     143 ..     217     237 ..     214     243 .. 0.46

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.7e-14
                     ABC2_membrane   2 qikallkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr..pgllffsvlflafsaltsvapvfe 76 
                                       q+ a++  e+++++r    ++++ ++  ++ +l +g     +g  e + +r    +++f v+++++++++s+a +f 
  gi|557694146|ref|YP_008797200.1|   6 QFAAVFEAELKSYLREVGPLVFVAVFPLFFSTLTYGMGTVLTG--EAAPERwlYQVIGFGVMTVSIVLTSSTAWYFR 80 
                                       8889999999999999977766666666666666666666444..22224466555566666666555555555555 PP

                     ABC2_membrane  77 r..ergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv.gldls.rfflflllllltalaasslgl 149
                                       r    g le  +++p+  + ++++a+ l++++ sll+ +   l++ ++v gl     f+l+ +++++ +l ++++ l
  gi|557694146|ref|YP_008797200.1|  81 RgmSSGRLEYVMAAPV-NPLVILTAHSLANVLTSLLAFVFTGLVATYIVyGLSKIpGFLLAAAVTFFALLPVVGVNL 156
                                       51155668999*****.******************99999999666654255554778******************* PP

                     ABC2_membrane 150 lisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                       ++++ +  ++    +a+ v  +   +sGf +pi+ +p +lq i  ++P+ ++ve  r++
  gi|557694146|ref|YP_008797200.1| 157 VVGVATIVAKEPEPVANTVAAVVAATSGFAYPITLLPPVLQLIGMILPFHHVVETARAA 215
                                       ************************************77*****************9987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.14
                     ABC2_membrane 122 lvgldlsrfflflllllltala 143
                                       +++l ++  + +lll++l+++a
  gi|557694146|ref|YP_008797200.1| 217 MTNLSPT-QLPILLLMMLYLVA 237
                                       5555554.33333444443333 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   0.2     0.077   6.9e+02      11      25 ..      24      38 ..      22      52 .. 0.64
   2 !   18.9  18.3   7.4e-08   0.00067     159     335 ..      55     236 ..      36     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.077
                   ABC2_membrane_3 11 Piilvlllglifsns 25
                                      P+++v+++ l+fs+ 
  gi|557694146|ref|YP_008797200.1| 24 PLVFVAVFPLFFSTL 38
                                      666666666666543 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 7.4e-08
                   ABC2_membrane_3 159 vasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllill....lafgl 231
                                         ++++g+ ++ ++++  s++a ++ +  +s+ +e  + ++v+pl +++++ l+ +l +ll ++++ l    +++g 
  gi|557694146|ref|YP_008797200.1|  55 WLYQVIGFGVMTVSIVLTSSTAWYFRRGMSSGRLEYVMAAPVNPLVILTAHSLANVLTSLLAFVFTGLvatyIVYG- 130
                                       56788888888888888888998888899999999999******99888888888888888877776633336888. PP

                   ABC2_membrane_3 232 gipfg.nlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPff 307
                                        ++   +++l+  + ++ +l ++ + +++++++  +++   ++  v  +  + +g+ +p+  lp  l+ i++i+Pf+
  gi|557694146|ref|YP_008797200.1| 131 -LSKIpGFLLAAAVTFFALLPVVGVNLVVGVATIVAKEPEPVANTVAAVVAATSGFAYPITLLPPVLQLIGMILPFH 206
                                       .444446666666666666666666666666666666666777777777888999999999999************* PP

                   ABC2_membrane_3 308 apglgllrlitgd.plweil.lsliilalf 335
                                       ++ +     ++++ ++ ++  l l++l+l 
  gi|557694146|ref|YP_008797200.1| 207 HVVETARAAVMTNlSPTQLPiLLLMMLYLV 236
                                       *********999956656432333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1766.48
//
Query:       gi|557694147|ref|YP_008797201.1|  [L=314]
Description: ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-24   87.1   0.0      3e-24   86.1   0.0    1.5  1  ABC_tran  ABC transporter
    1.2e-13   51.6   0.5    1.3e-07   31.8   0.0    2.3  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    9.2e-06   26.3   0.2    2.1e-05   25.1   0.2    1.7  1  DUF4162   Domain of unknown function (DUF4162)
      1e-05   25.5   0.0    2.1e-05   24.5   0.0    1.4  1  Rad17     Rad17 P-loop domain
    0.00041   20.0   0.1    0.00085   19.0   0.1    1.5  1  AAA_29    P-loop containing region of AAA domain
     0.0011   18.8   0.0        0.3   10.8   0.0    2.2  2  AAA_15    AAA ATPase domain
     0.0021   18.6   0.0     0.0039   17.7   0.0    1.4  1  AAA_23    AAA domain
     0.0031   17.4   0.0     0.0053   16.6   0.0    1.3  1  MukB      MukB N-terminal
  ------ inclusion threshold ------
      0.014   15.1   0.1      0.028   14.2   0.1    1.6  1  AAA_30    AAA domain
      0.025   14.2   0.1       0.04   13.5   0.1    1.3  1  SRP54     SRP54-type protein, GTPase domain
      0.033   14.5   0.1       0.34   11.2   0.0    2.3  2  AAA_22    AAA domain
      0.053   13.2   0.1       0.43   10.3   0.0    2.1  2  AAA_24    AAA domain
      0.062   13.2   0.3        7.5    6.5   0.1    2.8  3  MobB      Molybdopterin guanine dinucleotide synthesis protei
      0.062   13.8   0.0       0.25   11.9   0.0    1.9  2  AAA_18    AAA domain
       0.11   12.9   0.2       0.68   10.4   0.0    2.3  3  AAA       ATPase family associated with various cellular acti
       0.16   12.2   0.0       0.38   11.0   0.0    1.6  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 !   86.1   0.0   2.7e-27     3e-24       2     136 ..      31     174 ..      30     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 2.7e-27
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvr 77 
                                       + vslk+++g++ ++vG+nGaGK+t +k+l+ ll p++G+ +++g d+ + e  s+r+ ig +    + + p+l+ +
  gi|557694147|ref|YP_008797201.1|  31 DGVSLKVRRGSVFGLVGPNGAGKTTTIKILTTLLIPDAGQAWVNGFDVVK-EADSVREVIGLVLAPdKGFYPRLSGY 106
                                       78**********************************************99.899999999987665599******** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             e+ ++++++l+++gl ++  +      +++S G+k ++++a+al+++p+ ++lDEpt
  gi|557694147|ref|YP_008797201.1| 107 ENlvyygrlygfdkgEAGRRAAELLETVGLGKDGYRFY----EEYSLGMKAKLSIAKALINDPETVFLDEPT 174
                                       ********************************999998....*****************************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 !   18.1   0.4   1.6e-06    0.0018       2      23 ..      43      64 ..      42     131 .. 0.89
   2 !   31.8   0.0   1.2e-10   1.3e-07     234     298 ..     144     205 ..      97     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.6e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       +l+GpNg+GK++ +++l  l 
  gi|557694147|ref|YP_008797201.1| 43 FGLVGPNGAGKTTTIKILTTLL 64
                                      68****************8774 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 1.2e-10
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       + e S G+k  l ++ al+ ++    ++++DEp  gL+P   +++  l+++l+r g  v+lt+H+
  gi|557694147|ref|YP_008797201.1| 144 YEEYSLGMKAKLSIAKALINDP---ETVFLDEPTIGLDPLSAKKIRALISDLARQGKTVLLTSHN 205
                                       4566****************99...89***************************9*********8 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.2   1.9e-08   2.1e-05       1      81 []     228     312 ..     228     312 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.9e-08
                                       E-HHHHHTTS.-SSEEEEE-------..--.-EEEE-TTS-EEEEE--.-----------.----EEEEEEEE---H CS
                           DUF4162   1 GtleeiKrsy.gknrieveadaeelleepg.veeveeeggelelkled.eeaanellkal.tsgveirsFeeeePsL 73 
                                       Gt++e+K+++  + ++eve    + ++++  ve  e+ ++ +++  ++ +++  e+l++l +++++i  ++++ePsL
  gi|557694147|ref|YP_008797201.1| 228 GTPRELKEKLnLSYIVEVEIIGNSPQDISYpVENGERGNKVIKMVSNSpSDTLIEILDELrSHDIRIGYVKVHEPSL 304
                                       9999*****955556669966666677878788888888778888888899*********88*************** PP

                                       HHHHHHHH CS
                           DUF4162  74 ndIFiekv 81 
                                       +++F ++v
  gi|557694147|ref|YP_008797201.1| 305 EEVFAQVV 312
                                       *****998 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   1.9e-08   2.1e-05      29     112 ..      24     109 ..      21     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.9e-08
                             Rad17  29 eevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdnqksdfkgltekesr.fl 103
                                       ++v ++++  +L+ r+  +  + GP G gk+t++k+L+  l ++  + w+n+  + +    + ++ gl+   ++ f 
  gi|557694147|ref|YP_008797201.1|  24 KQVVKAVDGVSLKVRRGSVFGLVGPNGAGKTTTIKILTTLLIPDAgQAWVNGFDVVKEADSVREVIGLVLAPDKgFY 100
                                       578889999999999999************************987477****9988877788888888776554378 PP

                             Rad17 104 sqiesfkel 112
                                       +++  +++l
  gi|557694147|ref|YP_008797201.1| 101 PRLSGYENL 109
                                       888777776 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 !   19.0   0.1   7.6e-07   0.00085      13      50 ..      31      68 ..      28      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.6e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      dg ++++++ +++ l+Gp+G+GK+T +  +++lL+p+ 
  gi|557694147|ref|YP_008797201.1| 31 DGVSLKVRRGSVFGLVGPNGAGKTTTIKILTTLLIPDA 68
                                      67788888656999**********************97 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00027       0.3      28      47 ..      45      64 ..      33      85 .. 0.85
   2 !    5.7   0.0    0.0094        11     321     365 ..     162     205 ..     146     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                            AAA_15 28 liGkNnsGKSsilealdlFl 47
                                      l+G+N++GK++ +++l  +l
  gi|557694147|ref|YP_008797201.1| 45 LVGPNGAGKTTTIKILTTLL 64
                                      8***************8877 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0094
                            AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        +++ +++++EP + L p   k +  l+ +la+++k  v++t+H+
  gi|557694147|ref|YP_008797201.1| 162 INDPETVFLDEPTIGLDPLSAKKIRALISDLARQGK-TVLLTSHN 205
                                       578999*****************************9.9******8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.5e-06    0.0039      21      44 ..      42      65 ..      23      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.5e-06
                            AAA_23 21 ltlItGpNGaGKTTildAiklaLy 44
                                      ++ ++GpNGaGKTT +  ++  L 
  gi|557694147|ref|YP_008797201.1| 42 VFGLVGPNGAGKTTTIKILTTLLI 65
                                      7899************99998886 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   4.7e-06    0.0053      28      56 ..      42      70 ..      37     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.7e-06
                                      HHHHHS--SHHHHHHHHHHHHHHS--TTT CS
                              MukB 28 vttlsGgnGaGksttmaafvtaliPdlsl 56
                                      v  l G nGaGk+tt+  + t liPd   
  gi|557694147|ref|YP_008797201.1| 42 VFGLVGPNGAGKTTTIKILTTLLIPDAGQ 70
                                      66799*********************764 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   2.5e-05     0.028      19      50 ..      41      89 ..      33     206 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaa.g................grvi 50
                                       v  l+Gp G+GKtt++k l+ ++  + g                ++vi
  gi|557694147|ref|YP_008797201.1| 41 SVFGLVGPNGAGKTTTIKILTTLLIPDaGqawvngfdvvkeadsvREVI 89
                                      47789***************77665543666666655555555555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.6e-05      0.04       3      32 ..      42      71 ..      40      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.6e-05
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkv 32
                                      v+ lvG++GaGKTtt+  L  ll  ++ ++
  gi|557694147|ref|YP_008797201.1| 42 VFGLVGPNGAGKTTTIKILTTLLIPDAGQA 71
                                      5669************99988876665555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0003      0.34       9      35 ..      44      70 ..      37     103 .. 0.75
   2 ?    0.6   0.0      0.58   6.5e+02      16      63 ..     195     240 ..     187     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                            AAA_22  9 vvtGesGtGKTtllrrlleqldeeaka 35
                                       ++G+ G+GKTt+++ l+  l  +a +
  gi|557694147|ref|YP_008797201.1| 44 GLVGPNGAGKTTTIKILTTLLIPDAGQ 70
                                      589************999887555555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.58
                            AAA_22  16 tGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellra 63 
                                        GKT+ll    ++ +e     ee +  + + ++++s+++++l ++l   
  gi|557694147|ref|YP_008797201.1| 195 QGKTVLLTSHNMWEVE--TLSEEVAL-InRGKVAASGTPRELKEKLNLS 240
                                       5999999999999743..33333333.3477777777888777777655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00038      0.43       5      28 ..      43      65 ..      39      92 .. 0.80
   2 ?    0.8   0.0      0.31   3.5e+02     108     142 ..     182     216 ..     180     275 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00038
                            AAA_24  5 iliyGpsgiGKTtlakelgpkplf 28
                                      + ++Gp+g+GKTt++k l  + l+
  gi|557694147|ref|YP_008797201.1| 43 FGLVGPNGAGKTTTIKIL-TTLLI 65
                                      6799************99.44333 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.31
                            AAA_24 108 aeefrrllkklqelrknvifiahektrkdedpege 142
                                       a+++r l+ +l   +k+v +++h   +  +  e+ 
  gi|557694147|ref|YP_008797201.1| 182 AKKIRALISDLARQGKTVLLTSHNMWEVETLSEEV 216
                                       5788999999999999*******988777776665 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 ?    6.5   0.1    0.0067       7.5       1      23 [.      42      64 ..      42      70 .. 0.88
   2 ?   -1.9   0.0       2.5   2.8e+03       8      17 ..     193     202 ..     186     215 .. 0.75
   3 ?    3.5   0.0     0.054        61      14      37 ..     279     301 ..     268     307 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0067
                              MobB  1 vlgivgksgsGKTtLleklipel 23
                                      v+g+vg +g+GKTt ++ l + l
  gi|557694147|ref|YP_008797201.1| 42 VFGLVGPNGAGKTTTIKILTTLL 64
                                      689************99988776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                              MobB   8 sgsGKTtLle 17 
                                         +GKT Ll+
  gi|557694147|ref|YP_008797201.1| 193 ARQGKTVLLT 202
                                       4678888876 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.054
                              MobB  14 tLleklipelkarglrvgtiKhah 37 
                                       tL+e ++ el+++++r+g++K ++
  gi|557694147|ref|YP_008797201.1| 279 TLIE-ILDELRSHDIRIGYVKVHE 301
                                       5554.789*************776 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00022      0.25       3      41 ..      45      88 ..      44      97 .. 0.86
   2 ?   -2.4   0.0       5.8   6.5e+03      71      88 ..     193     210 ..     178     219 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf......gvnlrdvakenglllev 41
                                      l G+ G+GKtt  k L  +l +      +vn  dv+ke +++ ev
  gi|557694147|ref|YP_008797201.1| 45 LVGPNGAGKTTTIKILTTLL-IpdagqaWVNGFDVVKEADSVREV 88
                                      89**************8886.577888999999999999988765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.8
                            AAA_18  71 leegknlvidghlaeles 88 
                                        ++gk++++ +h  + ++
  gi|557694147|ref|YP_008797201.1| 193 ARQGKTVLLTSHNMWEVE 210
                                       356777777777766655 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 ?   10.4   0.0   0.00061      0.68       3      21 ..      45      63 ..      43      92 .. 0.82
   2 ?   -1.8   0.0       3.6     4e+03      42      54 ..     181     193 ..     152     212 .. 0.62
   3 ?   -1.4   0.0       2.6   2.9e+03      80      98 ..     271     289 ..     231     310 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00061
                                      EESSTTSSHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavake 21
                                      l+Gp G GKT+++k + + 
  gi|557694147|ref|YP_008797201.1| 45 LVGPNGAGKTTTIKILTTL 63
                                      89************98765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.6
                                       HHHHHHHHHHHHH CS
                               AAA  42 sekkirelfkeak 54 
                                       s+kkir+l++++ 
  gi|557694147|ref|YP_008797201.1| 181 SAKKIRALISDLA 193
                                       4555555555533 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHHHHHTTT CS
                               AAA  80 eeeervvnqLlteldgvkk 98 
                                        ++++  ++L++ ld++++
  gi|557694147|ref|YP_008797201.1| 271 MVSNSPSDTLIEILDELRS 289
                                       3444445555555555444 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   0.00034      0.38       4      30 ..      45      82 ..      43     101 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                            AAA_28  4 itGgestGKTtlleaLa........ar...gypvvpEa 30
                                      ++G+ ++GKTt+++ L+        +    g+ vv+Ea
  gi|557694147|ref|YP_008797201.1| 45 LVGPNGAGKTTTIKILTtllipdagQAwvnGFDVVKEA 82
                                      78**************9666665441156677788443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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 0.29s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2271.28
//
Query:       gi|557694148|ref|YP_008797202.1|  [L=204]
Description: HTH DNA binding domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-17   60.6   0.0    1.4e-16   60.0   0.0    1.3  1  HTH_10          HTH DNA binding domain
  ------ inclusion threshold ------
      0.019   15.3   0.0       0.34   11.3   0.0    2.5  3  GHMP_kinases_C  GHMP kinases C terminal
      0.081   12.9   0.1       0.17   11.9   0.1    1.7  1  Lig_C           Ligase Pab1020 C-terminal region


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 !   60.0   0.0   2.3e-20   1.4e-16       1      52 [.     148     199 ..     148     200 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 2.3e-20
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT++q +vl + y +GYFd PR + l++LAk+lGI++++++e Lrka +k++
  gi|557694148|ref|YP_008797202.1| 148 LTPRQEQVLLHSYLNGYFDNPRPIPLSKLAKDLGITPPSYLELLRKALKKVV 199
                                       9*************************************************97 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 ?   11.3   0.0   5.7e-05      0.34      28      82 ..       7      61 ..       1      64 [. 0.89
   2 ?    0.7   0.0      0.11   6.8e+02      65      83 ..     113     131 ..     106     133 .. 0.77
   3 ?   -1.7   0.0      0.65   3.9e+03      28      44 ..     179     195 ..     165     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.7e-05
                    GHMP_kinases_C 28 vvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvaralree 82
                                      +v + +p++ el+++ s++ + + +    G+G++ f+ f+++ +a  +  +++++
  gi|557694148|ref|YP_008797202.1|  7 RVHVTCPWISELVKESSDVEIVSCRPVFKGSGASAFVRFRSQVDARILSTRVSSH 61
                                      77899***************************************99999888765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.11
                    GHMP_kinases_C  65 lfkdkdeaeqvaralreef 83 
                                       l++d+ e++++++ lr+ +
  gi|557694148|ref|YP_008797202.1| 113 LVQDEKEVQEIVDGLRRSG 131
                                       5689999999999988776 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.65
                    GHMP_kinases_C  28 vvgilppeleelleals 44 
                                        +gi pp+  ell++++
  gi|557694148|ref|YP_008797202.1| 179 DLGITPPSYLELLRKAL 195
                                       67888999989888885 PP

>> Lig_C  Ligase Pab1020 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.8e-05      0.17      67     104 ..     110     147 ..      62     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.8e-05
                                       EEEE-SSHHHHHHHHHHHHCTT--EEEEEEE..TTEEE CS
                             Lig_C  67 frvrfkdeenieellehLrrlgvkaeveekekedgelv 104
                                       fr+ ++de++++e+++ Lrr gv+++ve+ +++  ++ 
  gi|557694148|ref|YP_008797202.1| 110 FRLLVQDEKEVQEIVDGLRRSGVRFRVENIRRIRAKHF 147
                                       8999*************************999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1461.00
//
Query:       gi|557694149|ref|YP_008797203.1|  [L=337]
Description: copper-containing oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-22   78.4   0.6    2.6e-16   59.7   0.2    2.3  2  Cu-oxidase_3  Multicopper oxidase
    4.8e-18   65.2   4.8    3.4e-10   39.8   0.6    3.2  2  Cu-oxidase_2  Multicopper oxidase


Domain annotation for each model (and alignments):
>> Cu-oxidase_3  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.2   2.9e-20   2.6e-16       9     116 ..      56     173 ..      49     176 .. 0.83
   2 !   16.8   0.0   5.6e-07    0.0051      26     115 ..     247     336 ..     229     337 .] 0.85

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.9e-20
                                       CTTEESEEEEEECTSSBS-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSC......SGGG-B-TT- CS
                      Cu-oxidase_3   9 plggterevitvNgqfpgptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpg......vtqcpiqpge 79 
                                       ++ g+  +++t+Ng++pgpt+ ++ gd ++v+ +Nkl+ + s+h h    + +  +DG +       +   +i+pg 
  gi|557694149|ref|YP_008797203.1|  56 LAPGVVWHAWTYNGTIPGPTLYAKVGDLIRVRAINKLNLTHSLHPHLPYYDLQ--HDGSQVniitgvGKGSMIPPGG 130
                                       555566789*************************************8877777..88855311111134689***** PP

                                       EEEEEEE--S-SEEEEEEE--TT.......HHHTT-EEEEEEE- CS
                      Cu-oxidase_3  80 sftyrftvkqqagtlwYhshlsl.......qqaaGlaGaiiied 116
                                       +++y++++++ ag  +Yh h++        +  +Gl+Gaii+++
  gi|557694149|ref|YP_008797203.1| 131 EWVYEWPATK-AGIWYYHCHSADgglrivdHMLMGLYGAIIVDE 173
                                       **********.**********999999995555*********86 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 5.6e-07
                                       S-EEEEETT-EEEEEEEE-SSS-B-EEEET--S-GG.....GSCSGG.G-B-TT-EEEEEEE--S-SEEEEEEE--T CS
                      Cu-oxidase_3  26 gptievregdtvvvnvtNkldentsihwhGlqqrktswmDGvpgvtq.cpiqpgesftyrftvkqqagtlwYhshls 101
                                        p ++++ g++++ +++N  d   s h h  ++r++ +  G +  +q  p+ pg+  t  +  ++  g +++h h+ 
  gi|557694149|ref|YP_008797203.1| 247 MPVFKAKLGERLRFHIINIGDLYHSFHAHVGDHRSQYVLGGRSWPAQiVPLVPGAADTVILVYNK-PGVYLFHCHVV 322
                                       478999************************9*999977766665444246779999999998888.*********** PP

                                       THHHTT-EEEEEEE CS
                      Cu-oxidase_3 102 lqqaaGlaGaiiie 115
                                       ++  aG+ G+iiie
  gi|557694149|ref|YP_008797203.1| 323 SHADAGMIGLIIIE 336
                                       **99*********8 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.3   1.4e-09   1.2e-05      35     135 ..      76     173 ..      60     175 .. 0.82
   2 !   39.8   0.6   3.8e-14   3.4e-10      26     133 ..     241     335 ..     216     337 .] 0.78

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.4e-09
                                       EEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEEEEEES.S-E CS
                      Cu-oxidase_2  35 itlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwvairfkadnpG 111
                                       + ++ g+ +++   n+ +l+H++H H    ++  +++++        +n  + v +   ++ppgg+ ++++ a+ +G
  gi|557694149|ref|YP_008797203.1|  76 LYAKVGDLIRVRAINKLNLTHSLHPHLPYYDLQ-HDGSQ--------VNIITGVGK-GSMIPPGGEWVYEWPATKAG 142
                                       556779999999999999999999999866664.55555........577556655.5689**************** PP

                                       EEEEEESSH.......HHHHTT-EEEEEEEC CS
                      Cu-oxidase_2 112 vwllHCHil.......wHldqGmalqfvvrp 135
                                        w++HCH +        H+ +G++++++v++
  gi|557694149|ref|YP_008797203.1| 143 IWYYHCHSAdgglrivDHMLMGLYGAIIVDE 173
                                       *******9999999999********999985 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 3.8e-14
                                       CCTTTSSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSSGCCGSSCBSEEEE-TTEEEE CS
                      Cu-oxidase_2  26 eefsentnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksynlenpvrrdtvqvppggwva 102
                                       + f+++ +v++++ ge++++ i n ++l H+fH H  d +     +g        s+     + + +  vp+ + ++
  gi|557694149|ref|YP_008797203.1| 241 QLFNKSMPVFKAKLGERLRFHIINIGDLYHSFHAHVGDHRSQYVLGGR-------SW-----PAQIVPLVPGAADTV 305
                                       57889999***************************8555444334444.......12.....444555566566666 PP

                                       EEEES.S-EEEEEEESSHHHHHTT-EEEEEE CS
                      Cu-oxidase_2 103 irfkadnpGvwllHCHilwHldqGmalqfvv 133
                                       i +  + pGv+l+HCH+  H+d+Gm + +++
  gi|557694149|ref|YP_008797203.1| 306 ILVY-NKPGVYLFHCHVVSHADAGMIGLIII 335
                                       6555.5*******************987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2569.99
//
Query:       gi|557694150|ref|YP_008797204.1|  [L=144]
Description: blue (type 1) copper domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-10   39.2   0.0    7.4e-10   38.9   0.0    1.3  1  Cupredoxin_1  Cupredoxin-like domain
    6.8e-10   39.3   0.1    1.1e-07   32.1   0.1    2.2  1  Copper-bind   Copper binding proteins, plastocyanin/azurin fa
  ------ inclusion threshold ------
       0.25   11.6   1.7       0.54   10.6   0.9    1.7  2  DUF948        Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   1.2e-13   7.4e-10      14     102 ..      45     140 ..       6     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.2e-13
                      Cupredoxin_1  14 kaaaaaektveitvkdg.........gfePskievkagekvklkiknkdktpeefesedlgeekvlapgktttitia 81 
                                       ++  +  +t e++v +          +f+P ++ v  g + +++++n+d  p++++s d +++  l+pg++ + t+ 
  gi|557694150|ref|YP_008797204.1|  45 TTTRETMATEEVVVVNPlgsgsdtslSFKPPRVRVVIGVNNTVTWVNEDLVPHKVTSMDRDFDFLLQPGEKISYTF- 120
                                       334555566666666556778888889*************************************************. PP

                      Cupredoxin_1  82 plkpGeYeftcdmhmdakGkl 102
                                         +pG+Ye++c +h+ + G++
  gi|557694150|ref|YP_008797204.1| 121 -TSPGTYEYFCTLHPWMNGVV 140
                                       .*************9889986 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 !   32.1   0.1   1.9e-11   1.1e-07       8      98 ..      66     142 ..      59     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.9e-11
                                       TTETSEEESSEEEEETT..EEEEEEEESSSSBEEEEETTSSTTTGGGTTSCTTCEEEEBSTTEEEEEEEESSEEEEE CS
                       Copper-bind   8 esgdlqFetkeitvkkg..ekvtfvnlavmgHNvvldkdgvpagvdkdkvkaedetkliggGekdsvtfdeagtYkf 82 
                                       ++++l+F++ +++v  g  ++vt+vn + ++H v                   d + l  +Gek s tf+ +gtY++
  gi|557694150|ref|YP_008797204.1|  66 SDTSLSFKPPRVRVVIGvnNTVTWVNEDLVPHKVTSMDR--------------DFDFLLQPGEKISYTFTSPGTYEY 128
                                       566799999988876553267888888888887754332..............24567779**************** PP

                                       EETTTTTTTSEEEEEE CS
                       Copper-bind  83 fCsPHaaagMkgkvtv 98 
                                       fC+ H    M+g v+v
  gi|557694150|ref|YP_008797204.1| 129 FCTLHP--WMNGVVEV 142
                                       ******..68**9987 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 ?   10.6   0.9     9e-05      0.54       3      40 ..       4      42 ..       4      60 .. 0.85
   2 ?   -0.9   0.0      0.34     2e+03      49      72 ..      83     104 ..      77     118 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9e-05
                            DUF948  3 glIaAiAFvvLviflivvllkl.kktldeaaatieelek 40
                                      ++IaA AF++ +++ + ++ ++ ++ l+ a+ati+++  
  gi|557694150|ref|YP_008797204.1|  4 VIIAAAAFAFFAAVTFNFFSRIeSRPLSTATATIHTVST 42
                                      69********************77889999999999874 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.34
                            DUF948  49 vedllakvnelledvneklekvdp 72 
                                       v+++++ vne  + v +k+ ++d+
  gi|557694150|ref|YP_008797204.1|  83 VNNTVTWVNE--DLVPHKVTSMDR 104
                                       5666666666..556666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1023.62
//
Query:       gi|557694151|ref|YP_008797205.1|  [L=314]
Description: hypothetical protein CSUB_C0716 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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    3.8e-11   43.4   0.0    1.5  1  NosL           NosL
    1.4e-10   41.1   0.0    3.3e-10   39.9   0.0    1.6  1  AhpC-TSA       AhpC/TSA family
    1.7e-09   37.6   0.1    3.4e-09   36.6   0.1    1.5  1  Redoxin        Redoxin
    3.4e-05   24.1   0.0    6.1e-05   23.3   0.0    1.4  1  Thioredoxin_8  Thioredoxin-like
    0.00012   22.2   0.0    0.00026   21.1   0.0    1.5  1  Thioredoxin_7  Thioredoxin-like
    0.00039   20.4   0.0     0.0007   19.6   0.0    1.4  1  Thioredoxin    Thioredoxin
    0.00076   19.4   0.0     0.0012   18.7   0.0    1.3  1  SCO1-SenC      SCO1/SenC
     0.0029   18.0   0.0      0.005   17.3   0.0    1.5  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.087   12.6   0.0       0.14   11.9   0.0    1.3  1  IBP39          Initiator binding protein 39 kDa


Domain annotation for each model (and alignments):
>> NosL  NosL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.0   1.9e-14   3.8e-11       8     124 ..      37     152 ..      35     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 1.9e-14
                              NosL   8 aecdvCgMliaehpgpkgqifyededepakFcstrdlfafllepee..........rkeikaiyvtDmsavdwespd 74 
                                       + c++CgM i +    ++ +++++  e ++++++ +++ ++l+ e            +++++i+v D++        
  gi|557694151|ref|YP_008797205.1|  37 RRCSYCGMEIRDR-RFAAVLVVNG--EKLFYDDVGCMMIHYLSVEGvippvsnapvLGKVEKIHVYDFG-------- 102
                                       68********995.5677777777..999****************977777777656688888888888........ PP

                              NosL  75 aeafidakkalyVvgsdveGaMGpelvpFsdeadAeaFaaehgGkvlrfe 124
                                       ++  +d  +a+yV+gs+ve +M + +++F++ +dA +Fa+++gG+v+ ++
  gi|557694151|ref|YP_008797205.1| 103 SSDEVDGFSAWYVLGSRVETPMRRGVIAFKSFSDAVQFARSEGGEVVGWD 152
                                       66779999**************************************9875 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   1.7e-13   3.3e-10       8     119 ..     180     289 ..     175     294 .. 0.69

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.7e-13
                                       -EEESTTCEEEECHHH..TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEES..SSCHHHHHHHHH- CS
                          AhpC-TSA   8 felknadgetvslsdy..kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsv..dspeshkkfieke 80 
                                       + l++ dg+tv++s++  +gkpv+l+f+++ wcp C +  + l+ +y +f+ + + ++   +  d+ e++++f + +
  gi|557694151|ref|YP_008797205.1| 180 IPLTTVDGKTVTVSEIlrQGKPVLLVFFAT-WCPTCSKNTSTLSTAYRKFRGKALVLLSSFDprDTSEKIQQFLKIH 255
                                       557799***********999**********.********************66554444333345555777777766 PP

                                       H..SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTS CS
                          AhpC-TSA  81 s.lnfpllsDeegkvakaygvlkeekglalratfvidkeg 119
                                       +  +  ++  ++ ++  a+ v+      ++ + f i ++g
  gi|557694151|ref|YP_008797205.1| 256 GaSEEWIVTQPNLDFLVALRVI------TQETIFAIAPNG 289
                                       6433333344444444444444......444555555555 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.1   1.7e-12   3.4e-09       9      62 ..     178     232 ..     170     297 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.7e-12
                                       -ECCEETTCEEEEEHHH..HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCST CS
                           Redoxin   9 ftlplaatdgnsvslse..fkgkkvvvnfvpgafcPtCsaehpyleklaellkekg 62 
                                       f  pl++ dg++v++se   +gk+v+++f+++ +cPtCs+++  l + +++++ k+
  gi|557694151|ref|YP_008797205.1| 178 FHIPLTTVDGKTVTVSEilRQGKPVLLVFFAT-WCPTCSKNTSTLSTAYRKFRGKA 232
                                       5567788***********999***********.*********88888877765554 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0     3e-08   6.1e-05       1      44 [.     199     243 ..     199     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 3e-08
                                       .SEEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-....S CS
                     Thioredoxin_8   1 gkvvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsl....d 44 
                                       gk vlL+f+a+wcp c + t++l+  y+k++   +  +v +s+    d
  gi|557694151|ref|YP_008797205.1| 199 GKPVLLVFFATWCPTCSKNTSTLSTAYRKFR---GKALVLLSSfdprD 243
                                       699***************************8...66677777654432 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   1.3e-07   0.00026      11      52 ..     193     231 ..     190     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.3e-07
                                       HHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT CS
                     Thioredoxin_7  11 akaaergkpvlvffgaswcftCqalerdflsdeevkaalaek 52 
                                       ++  ++gkpvl++f a+wc+tC ++  ++ ++   ++ +++k
  gi|557694151|ref|YP_008797205.1| 193 SEILRQGKPVLLVFFATWCPTCSKNTSTLSTA--YRK-FRGK 231
                                       56789*******************98877666..445.5644 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.5e-07    0.0007      13      53 ..     194     236 ..     185     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.5e-07
                                       HHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTT..TSEE CS
                       Thioredoxin  13 evakekklvlveFyApwCghCkalaPeleklaeelkd..kvkl 53 
                                       e+  + k+vl+ F+A+wC+ C + +++l ++ +++++   v l
  gi|557694151|ref|YP_008797205.1| 194 EILRQGKPVLLVFFATWCPTCSKNTSTLSTAYRKFRGkaLVLL 236
                                       4555699******************999999999998433444 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   6.1e-07    0.0012       6      83 ..     182     256 ..     175     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.1e-07
                         SCO1-SenC   6 lvdqdgeavteedl..egkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyle 80 
                                       l++ dg++vt +++  +gkp+l+ f+ t Cp+ C +++++++ +++++  +     +l  + DP rDt e+++++l+
  gi|557694151|ref|YP_008797205.1| 182 LTTVDGKTVTVSEIlrQGKPVLLVFFATWCPT-CSKNTSTLSTAYRKFRGK---ALVLLSSFDP-RDTSEKIQQFLK 253
                                       56667777776665348**************7.9999***********998...6788889***.5*********98 PP

                         SCO1-SenC  81 afd 83 
                                        ++
  gi|557694151|ref|YP_008797205.1| 254 IHG 256
                                       665 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.5e-06     0.005       4      30 ..     198     224 ..     195     292 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.5e-06
                     Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkel 30 
                                       +gkpvl+vf +++Cp C k   +l++ 
  gi|557694151|ref|YP_008797205.1| 198 QGKPVLLVFFATWCPTCSKNTSTLSTA 224
                                       89*****************87777665 PP

>> IBP39  Initiator binding protein 39 kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.3e-05      0.14      83     118 ..     235     269 ..     228     282 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.3e-05
                                       HHHHSSSGGGHHHHHHHHHHHHHTTTS-B-SSSSTT CS
                             IBP39  83 FlarFgPeetvliKiaslLevskekkqwlllkPdae 118
                                        l  F+P +t  +Ki+++L++  ++++w+  +P+  
  gi|557694151|ref|YP_008797205.1| 235 LLSSFDPRDT-SEKIQQFLKIHGASEEWIVTQPNLD 269
                                       5789*****9.79****************99**764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2381.43
//
Query:       gi|557694152|ref|YP_008797206.1|  [L=151]
Description: hypothetical protein CSUB_C0717 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   24.1   1.7      4e-05   23.4   1.7    1.3  1  MarR_2       MarR family
    5.1e-05   23.1   0.3      8e-05   22.4   0.3    1.3  1  TrmB         Sugar-specific transcriptional regulator TrmB
    0.00039   19.9   0.5    0.00056   19.4   0.5    1.2  1  HTH_24       Winged helix-turn-helix DNA-binding
    0.00051   19.8   0.1    0.00087   19.1   0.1    1.3  1  HTH_IclR     IclR helix-turn-helix domain
    0.00052   19.9   0.3    0.00084   19.3   0.3    1.5  1  HTH_Crp_2    Crp-like helix-turn-helix domain
     0.0046   17.4   1.0     0.0071   16.8   1.0    1.3  1  HTH_27       Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.014   14.0   2.8      0.018   13.7   2.8    1.0  1  AA_permease  Amino acid permease
      0.028   14.7   0.2      0.053   13.9   0.2    1.4  1  Rrf2         Transcriptional regulator
       0.07   11.9   0.0      0.092   11.6   0.0    1.1  1  HTH_micro    HTH-like


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 !   23.4   1.7     2e-08     4e-05       2      55 ..      84     136 ..      83     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2e-08
                                       T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2   2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       glt  ++ v   L+r+ g  + ++++ r+lg+s+  ++ri++ L ++  ve ++
  gi|557694152|ref|YP_008797206.1|  84 GLTSEERAVVDLLRRSNGV-VEQRDISRALGISRIKTHRIVASLRRREVVEVTR 136
                                       9*****************6.7*****************************9774 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.3     4e-08     8e-05      10      58 ..      88     138 ..      82     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4e-08
                                       CCCHCHHHH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  10 EakvYlaLl..klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       E ++ + Ll  ++g  + ++i+++lg++r k  +++ sL ++ +Ve+ ++ 
  gi|557694152|ref|YP_008797206.1|  88 EERAVVDLLrrSNGVVEQRDISRALGISRIKTHRIVASLRRREVVEVTRRG 138
                                       4456688998999*********************************99854 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 !   19.4   0.5   2.8e-07   0.00056       7      48 .]      91     133 ..      89     133 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.8e-07
                            HTH_24   7 kILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       ++  lL++ n+   qr+++++lg+S+  ++r +  L + ++++
  gi|557694152|ref|YP_008797206.1|  91 AVVDLLRRsNGVVEQRDISRALGISRIKTHRIVASLRRREVVE 133
                                       56677888788899*************************9996 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 !   19.1   0.1   4.3e-07   0.00087       8      49 ..      92     133 ..      91     136 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.3e-07
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                       + d+l++ ++ +  ++++r++g+++ ++hR++++L ++  ve
  gi|557694152|ref|YP_008797206.1|  92 VVDLLRRSNGVVEQRDISRALGISRIKTHRIVASLRRREVVE 133
                                       7899********************************999887 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 !   19.3   0.3   4.2e-07   0.00084      22      55 ..     103     137 ..      62     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.2e-07
                                       HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ETE CS
                         HTH_Crp_2  22 ltqeelAsmlGltretvsrilseLkreglis.rgr 55 
                                       + q+++++ lG++r  + ri + L+r+ +++ ++r
  gi|557694152|ref|YP_008797206.1| 103 VEQRDISRALGISRIKTHRIVASLRRREVVEvTRR 137
                                       689****************************8443 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 !   16.8   1.0   3.6e-06    0.0071       1      53 [.      85     137 ..      85     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.6e-06
                            HTH_27   1 ltrqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgd 53 
                                       lt  +++v+ l+r+ ++ ++++d++++l ++ + ++ ++  L ++++ve t+ 
  gi|557694152|ref|YP_008797206.1|  85 LTSEERAVVDLLRRSNGVVEQRDISRALGISRIKTHRIVASLRRREVVEVTRR 137
                                       6889999******89999999***************************65543 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   2.8   8.9e-06     0.018     367     442 ..       8      81 ..       3      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.9e-06
                       AA_permease 367 fllaisaliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpk 442
                                       +ll +sa++g+++++++++s   +      +g+  e +g+ + +++++v+l l+a  ++l++l +++yl +++ p+
  gi|557694152|ref|YP_008797206.1|   8 VLLVFSAVSGVLLLTVVLVSV--WQHDVAMSGMMREMMGMSMLGMMWWVYLPLLAGALLLIALPVVLYLSARDVPV 81 
                                       6899******99999999986..599999***************************************99777765 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   2.7e-05     0.053      12      59 ..      90     136 ..      87     148 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2  12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59 
                                       +a+++L +++++  v+ ++i++  +is+    +i+a Lr+ ++v+++r
  gi|557694152|ref|YP_008797206.1|  90 RAVVDLLRRSNGV-VEQRDISRALGISRIKTHRIVASLRRREVVEVTR 136
                                       5778888888876.******************************9654 PP

>> HTH_micro  HTH-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.6e-05     0.092      95     152 ..      91     147 ..      84     150 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.6e-05
                         HTH_micro  95 kivdflvkakdyvkaaelraklnidpKklfYvikkLakkglieqktkeeakivikink 152
                                        +vd+l +++  v++ ++   l i   k++ ++  L++++++e  t  +   ++k+++
  gi|557694152|ref|YP_008797206.1|  91 AVVDLLRRSNGVVEQRDISRALGISRIKTHRIVASLRRREVVE-VTRRGRTNLVKLKA 147
                                       699****************************************.77777777778876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1230.46
//
Query:       gi|557694153|ref|YP_008797207.1|  [L=228]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.2   0.0         12    6.5   0.1    2.6  2  PepSY     Peptidase propeptide and YPEB domain


Domain annotation for each model (and alignments):
>> PepSY  Peptidase propeptide and YPEB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1   0.00068        12       2      59 ..      64     121 ..      63     121 .. 0.71
   2 ?    6.0   0.0     0.001        18       1      15 [.     153     167 ..     153     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00068
                                       S-HHHHHHHHHHHSTTE.EEEEEEEEEETTEEEEEEEEE.EE.TTEEEEEEEETTT--E CS
                             PepSY   2 iseeqAlaiAlaavpgk.iieielededdgrlvYevelstaepegpeyevfiDAkTGkv 59 
                                       is +qA +i ++ v g  +     e  +  +  Y + ++ a+ + + +e +++++TG+v
  gi|557694153|ref|YP_008797207.1|  64 ISMQQAEEILERYVAGLgQGFKLKEVMEFQQNFYAIVVE-ADTGIGAFELLVNPYTGTV 121
                                       788888888888887663333333333377788888888.57788889*********98 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.001
                                       SS-HHHHHHHHHHHS CS
                             PepSY   1 kiseeqAlaiAlaav 15 
                                       +i++eqA +iAl  +
  gi|557694153|ref|YP_008797207.1| 153 PITPEQAEEIALNYL 167
                                       69*********8663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1700.89
//
Query:       gi|557694154|ref|YP_008797208.1|  [L=130]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  21.6    0.00018   21.7  12.2    3.0  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 !   21.7  12.2     1e-08   0.00018       1     102 [.       6     105 ..       6     106 .. 0.84
   2 !    3.0   1.9    0.0068   1.2e+02      68      81 ..     110     123 ..     107     128 .. 0.60

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1e-08
                           DUF4064   1 krkaeiiLglIGgilgillglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgiv 77 
                                       k +a+++L+l++g+l +l+g++++++ +++ +g  +   +  + + +  + ++  ++   l ++ v++l++++++++
  gi|557694154|ref|YP_008797208.1|   6 KPTAAFVLSLVAGVLILLGGVFGMVA-WMM-WGGAA---YWGGGWGMMGPMMMGWWMPMWLSAFSVLGLVSGIVIVA 77 
                                       689*********************99.444.44422...33378888888888888888889*************** PP

                           DUF4064  78 galllkknkk...vsGilfiiaailslf 102
                                       +al+l + +    ++G l+++++++slf
  gi|557694154|ref|YP_008797208.1|  78 SALMLQNRPSeakTWGTLILVFSVVSLF 105
                                       ******7776777**************9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0068
                           DUF4064  68 aliaivlgivgall 81 
                                       +li ++lgivg +l
  gi|557694154|ref|YP_008797208.1| 110 LLIGALLGIVGGIL 123
                                       56666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 970.63
//
Query:       gi|557694155|ref|YP_008797209.1|  [L=150]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   91.2   0.2    4.3e-26   90.6   0.2    1.2  1  DUF411        Protein of unknown function, DUF
    0.00032   20.8   0.1    0.00061   19.9   0.1    1.5  1  Glutaredoxin  Glutaredoxin
  ------ inclusion threshold ------
       0.11   12.9   0.1       0.18   12.3   0.1    1.4  1  DUF836        Glutaredoxin-like domain (DUF836)
       0.19   11.5   0.3       0.31   10.8   0.3    1.3  1  Redoxin       Redoxin


Domain annotation for each model (and alignments):
>> DUF411  Protein of unknown function, DUF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.6   0.2   9.5e-30   4.3e-26       8      69 .]      64     125 ..      58     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.6 bits;  conditional E-value: 9.5e-30
                            DUF411   8 dlaavkkklgvpeelaSchtavvggyvieGHVPaadikrlLaekpkaaGlavPgmPvgspGm 69 
                                       +l++v+kklgvp+el Schta   +y+ieGH Pa+++k+lL+ekp ++G+avPgmP gspGm
  gi|557694155|ref|YP_008797209.1|  64 ELENVRKKLGVPRELYSCHTASAMQYFIEGHTPAEALKKLLEEKPLLKGIAVPGMPPGSPGM 125
                                       7899*********************************************************9 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   1.4e-07   0.00061       2      44 ..      31      71 ..      30      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.4e-07
                                      EEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHH CS
                      Glutaredoxin  2 vlftkptCpyCkkakrlLkelgvkfeeidvdkdeeireelkel 44
                                      +++ + +Cp Ck   ++L++ g++f+++ v+  e   e ++++
  gi|557694155|ref|YP_008797209.1| 31 TIYRTEQCPCCKEYEAYLRNSGIPFRTVVVSGVE--LENVRKK 71
                                      79****************************9854..3333333 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1     4e-05      0.18       1      23 [.      29      51 ..      29      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4e-05
                                      -EEEEE-TT-HHHHHHHHHHHHH CS
                            DUF836  1 kltLyskpgChlCeqakekLkel 23
                                      +lt+y +++C+ C++ ++ L++ 
  gi|557694155|ref|YP_008797209.1| 29 QLTIYRTEQCPCCKEYEAYLRNS 51
                                      59****************99974 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   6.8e-05      0.31      11      53 ..       9      50 ..       4      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.8e-05
                                      CCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHT CS
                           Redoxin 11 lplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpylek 53
                                      l ++a +  +v++s  ++ +v ++++++ +cP C++   yl++
  gi|557694155|ref|YP_008797209.1|  9 LVTMAVNSWTVNTST-TETTVQLTIYRTEQCPCCKEYEAYLRN 50
                                      566777777888888.88999**************98888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1164.99
//
Query:       gi|557694156|ref|YP_008797210.1|  [L=310]
Description: hypothetical protein CSUB_C0721 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.088   12.9   0.0       0.22   11.6   0.0    1.6  1  HTH_20    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 ?   11.6   0.0   1.3e-05      0.22       9      49 ..      31      71 ..      24      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.3e-05
                                      -HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHH CS
                            HTH_20  9 hPvRrrilraLaraegltaselaerldlskntlsyHLrvLe 49
                                      h+vR +i  a  +++   a++l++ l++s  +l+y+Lr+++
  gi|557694156|ref|YP_008797210.1| 31 HKVRKAIILAVGEEGRIGATALKQKLGISTGSLYYNLRQMS 71
                                      899********7777788********************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2558.41
//
Query:       gi|557694157|ref|YP_008797211.1|  [L=101]
Description: hypothetical protein CSUB_C0722 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 00:00:00.39
# Mc/sec: 774.33
//
Query:       gi|557694158|ref|YP_008797212.1|  [L=288]
Description: hypothetical protein CSUB_C0723 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.7      0.029   14.4   0.7    1.9  1  CRISPR_Cas9_WED  CRISPR-Cas9 WED domain
      0.023   15.3   2.1       0.17   12.5   0.1    2.8  3  PrmC_N           PrmC N-terminal domain


Domain annotation for each model (and alignments):
>> CRISPR_Cas9_WED  CRISPR-Cas9 WED domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.7   3.3e-06     0.029      36      74 ..      95     140 ..      67     172 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-06
                   CRISPR_Cas9_WED  36 vkkll.......kkdkekflmakkdpktfeklkkilkeysdkkeks 74 
                                       vk l+       kk +e +l+ +k   tf +l+k l++y++  e  
  gi|557694158|ref|YP_008797212.1|  95 VKTLMaieekwfKKVDETYLIMRKKASTFRSLQKTLEQYKNRLEAA 140
                                       3333334444459999************************987654 PP

>> PrmC_N  PrmC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1     0.072   6.5e+02      16      58 ..      89     135 ..      76     144 .. 0.64
   2 ?    0.1   0.1      0.14   1.3e+03       3      20 ..     130     146 ..     128     179 .. 0.65
   3 ?   12.5   0.1   1.9e-05      0.17      15      67 ..     233     285 ..     222     286 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.072
                            PrmC_N  16 eeaeldAelLla....hvlglsrsdlllrgerelteeqlerfeelie 58 
                                        +a++d++ L+a    +  +++ ++l++r++    ++ ++++e++ +
  gi|557694158|ref|YP_008797212.1|  89 KSARADVKTLMAieekWFKKVDETYLIMRKKASTFRSLQKTLEQYKN 135
                                       56777777777755544556788888887776554444444444444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
                            PrmC_N   3 LreaearLkaagieeael 20 
                                       L++ ++rL+aa   +++ 
  gi|557694158|ref|YP_008797212.1| 130 LEQYKNRLEAAS-GDERE 146
                                       677888888873.33332 PP

  == domain 3  score: 12.5 bits;  conditional E-value: 1.9e-05
                            PrmC_N  15 ieeaeldAelLlahvlglsrsdlllrgerelteeqlerfeelierRaarePlq 67 
                                         +a+   + L  +v ++++ +l +++++ l ++ + ++++  ++R+a++P q
  gi|557694158|ref|YP_008797212.1| 233 NGQARKALQRLTIAVYNIKPKELTAKMQKTLLRQIWLTVRQEAQKRLAGIPAQ 285
                                       56788888999999*************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1331  (0.0742373); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2068.57
//
Query:       gi|557694159|ref|YP_008797213.1|  [L=134]
Description: hypothetical protein CSUB_C0724 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 1016.34
//
Query:       gi|557694160|ref|YP_008797214.1|  [L=127]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1002.56
//
Query:       gi|557694161|ref|YP_008797215.1|  [L=299]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-17   64.1   0.1      1e-14   54.6   0.1    2.5  2  LAGLIDADG_3  LAGLIDADG-like domain
  ------ inclusion threshold ------
      0.019   15.1   0.0      0.064   13.4   0.0    1.8  3  Hom_end      Homing endonuclease
      0.024   15.6   0.5       0.25   12.3   0.1    2.2  2  LAGLIDADG_1  LAGLIDADG endonuclease
       0.14   12.2   0.7       0.27   11.3   0.7    1.4  1  Imm43        Immunity protein 43


Domain annotation for each model (and alignments):
>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0015       6.7       3      46 ..      93     133 ..      91     164 .. 0.90
   2 !   54.6   0.1   2.2e-18     1e-14       2      83 .]     182     275 ..     181     275 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHH CS
                       LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlr 46 
                                        +a+L G  ++D +v++++     ++l  ++k++++ ++  L+r
  gi|557694161|ref|YP_008797215.1|  93 DLAYLIGVHAGDAYVTGEQFF---LRLEVKDKDFADAYSISLSR 133
                                       689****************99...************99988876 PP

  == domain 2  score: 54.6 bits;  conditional E-value: 2.2e-18
                                       HHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCC............. CS
                       LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvy............. 65 
                                       ++a+fLrG+fd++Gsvsk ++    i++++++++ll +v +lL++lGIe+t y  k ++  g +             
  gi|557694161|ref|YP_008797215.1| 182 CVAMFLRGFFDSEGSVSKLGT----ITVYNTDYQLLVYVIYLLKKLGIETTSYAPKTKQLAGGPfrnprtgktyhyn 254
                                       689*****************7....******************************6666666668999********* PP

                                       ...ECCCHCHCTTCGGGTTTX CS
                       LAGLIDADG_3  66 ...rlliisgenlkrFlekig 83 
                                          ++l+i++++ + +++ +g
  gi|557694161|ref|YP_008797215.1| 255 kdyYYLRIRRSSNESYYNLVG 275
                                       ***999999999999998886 PP

>> Hom_end  Homing endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.1   9.2e+03      49      61 ..      50      62 ..      44      65 .. 0.75
   2 ?   -3.9   0.0       3.4   1.5e+04      17      31 ..      96     110 ..      95     120 .. 0.75
   3 ?   13.4   0.0   1.4e-05     0.064      16      64 ..     185     231 ..     177     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.1
                           Hom_end 49 ivklarsLGikas 61
                                      i ++ + LGik++
  gi|557694161|ref|YP_008797215.1| 50 INEVEKTLGIKIT 62
                                      5567788999986 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3.4
                           Hom_end  17 FlaGLvdsdgyvkke 31 
                                       +l G   +d yv+ e
  gi|557694161|ref|YP_008797215.1|  96 YLIGVHAGDAYVTGE 110
                                       788888888888766 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 1.4e-05
                           Hom_end  16 aFlaGLvdsdgyvkkekedsatvktedksvmegivklarsLGikasvkt 64 
                                       +Fl G+ ds+g+v+k   +++tv  +d +++  ++ l ++LGi+++  +
  gi|557694161|ref|YP_008797215.1| 185 MFLRGFFDSEGSVSKL--GTITVYNTDYQLLVYVIYLLKKLGIETTSYA 231
                                       7**************9..9************************988655 PP

>> LAGLIDADG_1  LAGLIDADG endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.18   8.2e+02      25      60 ..      31      67 ..      18      82 .. 0.71
   2 ?   12.3   0.1   5.5e-05      0.25       1      79 [.     187     274 ..     187     278 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.18
                                      EEEEEEEEEEEE.GGGHHHHHHHHHHHTECEEEEETT CS
                       LAGLIDADG_1 25 lkvqlefqielk.kkdesllekikeylglgsikkrkk 60
                                        + l +q+ ++     ++++++ + lg+++ k +++
  gi|557694161|ref|YP_008797215.1| 31 KAYDLVIQLRQQgLTYKQIINEVEKTLGIKITKSHCS 67
                                      4466777888888888899999999999666655544 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHEEEEEEEEETTTTTTSEE..EEEEEEEEEE...GGGHHHHHHHHHHHT.......ECEEEEETTTEEEE CS
                       LAGLIDADG_1   1 laGFiDgdGsfsitvtkskskktslk..vqlefqielk...kkdesllekikeylg.......lgsikkrkkdkyvs 65 
                                       l GF+D++Gs s   t +  ++t ++  v   +   lk    +  s   k k++ g        g+ + ++kd y++
  gi|557694161|ref|YP_008797215.1| 187 LRGFFDSEGSVSKLGTITV-YNTDYQllV--YVIYLLKklgIETTSYAPKTKQLAGgpfrnprTGKTYHYNKD-YYY 259
                                       67*********99999999.899999642..333333335777888888888888888889999999999999.*** PP

                                       EEE-S.HHHHHHTHH CS
                       LAGLIDADG_1  66 yiisn.sskslkili 79 
                                       ++i++ s++s+ +l+
  gi|557694161|ref|YP_008797215.1| 260 LRIRRsSNESYYNLV 274
                                       ***996777777766 PP

>> Imm43  Immunity protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7     6e-05      0.27      79     112 ..     247     280 ..     243     292 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6e-05
                             Imm43  79 kgeslksdknYyalRvkkldndlFldlknsdlee 112
                                        g++ + +k+Yy+lR++++ n+++++l   + e+
  gi|557694161|ref|YP_008797215.1| 247 TGKTYHYNKDYYYLRIRRSSNESYYNLVGFSIER 280
                                       67888899****************8876654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2449.08
//
Query:       gi|557694162|ref|YP_008797216.1|  [L=119]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   45.3   0.9    1.3e-11   44.4   0.9    1.5  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
  ------ inclusion threshold ------
      0.078   13.0   0.1       0.12   12.4   0.1    1.2  1  DZR             Double zinc ribbon
       0.13   12.1   3.1        6.6    6.7   0.8    2.3  2  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
       0.15   12.1   6.7       0.87    9.7   3.0    2.4  2  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 !   44.4   0.9   2.9e-15   1.3e-11       1      40 []       7      44 ..       7      44 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 2.9e-15
                     Auto_anti-p27  1 kkmgelLlkGwtMLaetCpvCgvPLmrdrkggkvyCvaCd 40
                                      k+m++ L  G++ML+e+CpvC++PL++   gg++ C +Cd
  gi|557694162|ref|YP_008797216.1|  7 KRMSDALRSGAKMLSEVCPVCSSPLFE--IGGEMRCLRCD 44
                                      79*************************..68********7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.6e-05      0.12      12      38 ..      21      47 ..      13      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.6e-05
                               DZR 12 arfCseCgtklkavaaedrCpsCgekv 38
                                      +++C+ C ++l +   e rC +C+++v
  gi|557694162|ref|YP_008797216.1| 21 SEVCPVCSSPLFEIGGEMRCLRCDKPV 47
                                      568*********9999********985 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 ?    5.4   0.1    0.0038        17       2       8 ..      22      28 ..      20      33 .. 0.72
   2 ?    6.7   0.8    0.0015       6.6       3      16 ..      39      52 ..      39      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0038
                                      SB-TTT- CS
                      zf-FPG_IleRS  2 epCpRCw 8 
                                      e+Cp+C 
  gi|557694162|ref|YP_008797216.1| 22 EVCPVCS 28
                                      6777775 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0015
                                      B-TTT--BBEEEEC CS
                      zf-FPG_IleRS  3 pCpRCwryiervgq 16
                                      +C RC  +++rv+ 
  gi|557694162|ref|YP_008797216.1| 39 RCLRCDKPVVRVRE 52
                                      5***********97 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 ?    9.7   3.0   0.00019      0.87       2      20 ..      24      43 ..      23      43 .. 0.86
   2 ?    4.8   1.3    0.0064        29       2      17 ..      40      55 ..      39      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00019
                    DNA_ligase_ZBD  2 CPvCGsavvReegeai.yRC 20
                                      CPvC s++    ge   +RC
  gi|557694162|ref|YP_008797216.1| 24 CPVCSSPLFEIGGEMRcLRC 43
                                      ********988888777777 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0064
                    DNA_ligase_ZBD  2 CPvCGsavvReegeai 17
                                      C  C+ +vvR  +e+ 
  gi|557694162|ref|YP_008797216.1| 40 CLRCDKPVVRVREESE 55
                                      889******9777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1200  (0.0669307); expected 358.6 (0.02)
Passed bias filter:                      784  (0.043728); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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 0.27s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 895.28
//
Query:       gi|557694163|ref|YP_008797217.1|  [L=421]
Description: archaeal cell division control protein 6 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   67.8   0.3    3.2e-18   65.5   0.1    2.3  2  Cdc6_C           CDC6, C terminal winged helix domain
    1.3e-11   45.0   0.0    2.9e-11   43.8   0.0    1.5  1  AAA_22           AAA domain
    1.3e-08   35.4   1.8    2.8e-07   31.1   0.1    3.0  2  AAA_16           AAA ATPase domain
      2e-08   34.7   0.0    4.1e-08   33.7   0.0    1.5  1  AAA              ATPase family associated with various cellul
    6.6e-05   22.7   0.0    0.00011   21.9   0.0    1.3  1  Sigma54_activat  Sigma-54 interaction domain
     0.0039   16.6   0.0     0.0069   15.8   0.0    1.3  1  TniB             Bacterial TniB protein
     0.0065   16.4   0.0      0.017   15.0   0.0    1.8  1  ATPase_2         ATPase domain predominantly from Archaea
     0.0068   16.5   0.1      0.018   15.2   0.1    1.7  1  TIP49_C          TIP49 AAA-lid domain
  ------ inclusion threshold ------
      0.015   15.7   0.4      0.031   14.6   0.4    1.5  1  AAA_assoc_2      AAA C-terminal domain
      0.022   14.7   0.0       0.12   12.3   0.0    2.2  2  AAA_5            AAA domain (dynein-related subfamily)
       0.04   12.7   1.3        4.1    6.1   0.0    2.1  2  AAA_32           AAA domain
       0.04   13.4   0.1       0.23   10.9   0.1    1.8  1  ORC5_C           Origin recognition complex (ORC) subunit 5 C
      0.045   14.3   0.0       0.16   12.5   0.0    1.9  1  AAA_18           AAA domain
      0.056   12.6   0.0       0.08   12.1   0.0    1.3  1  PIF1             PIF1-like helicase
      0.059   13.4   0.0       0.11   12.5   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.07   12.3   0.0        0.1   11.7   0.0    1.3  1  NB-ARC           NB-ARC domain
       0.11   12.9   0.0        0.2   12.0   0.0    1.4  1  RNA_helicase     RNA helicase
       0.14   11.6   0.0       0.27   10.7   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
       0.15   11.3   0.0       0.19   10.9   0.0    1.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.18   12.4   0.0       0.44   11.1   0.0    1.6  1  Pox_D5           Poxvirus D5 protein-like
       0.29    9.7   0.0       0.42    9.2   0.0    1.1  1  AAA_13           AAA 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 ?   -2.2   0.0       4.8   4.1e+03      28      48 ..     221     242 ..     217     245 .. 0.75
   2 !   65.5   0.1   3.7e-21   3.2e-18       2      83 ..     327     405 ..     326     406 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.8
                                       HHHHT.T-----HHHHHHHHHH CS
                            Cdc6_C  28 lCese.gvdpltqrevsdllse 48 
                                       l e+e  ++p t +e  d+l+e
  gi|557694163|ref|YP_008797217.1| 221 LSEEEvVFQPYTATELADILRE 242
                                       5555534589999999999987 PP

  == domain 2  score: 65.5 bits;  conditional E-value: 3.7e-21
                                       HHHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSC CS
                            Cdc6_C   2 calvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdp 78 
                                       +a+  +   +++ e+t+g +y++Y++ C s+g+dplt r+vs l+seL+mlgi+ +  +s Gr +grtr+i+ +++ 
  gi|557694163|ref|YP_008797217.1| 327 LAVYMVS--RKSSETTSGTLYNTYREYCVSLGLDPLTDRRVSTLVSELDMLGIVACDLVSYGR-HGRTRRIKPTIPF 400
                                       5655554..5999*************************************************9.8***********9 PP

                                       HHHHH CS
                            Cdc6_C  79 ddvle 83 
                                       d+v e
  gi|557694163|ref|YP_008797217.1| 401 DEVVE 405
                                       99976 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   3.4e-14   2.9e-11       6     113 ..      79     189 ..      76     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 3.4e-14
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleal 82 
                                       + l+++G +GtGKT ++r ++++l  + + +  + ++v++++   ++   +l+el+ a g+     + s+ el++++
  gi|557694163|ref|YP_008797217.1|  79 SNLFIYGKTGTGKTAVCRYVFNRLSSAVAEKGFDIRFVYINCRLAGTEYRVLSELCAAAGVAVPFTGVSKGELFRRF 155
                                       5689********************76655555******************************99999********** PP

                            AAA_22  83 eqalraravielliiDEaqhlr...seealeeLr 113
                                       + a+++     ++ +DE++ l     +++l eL 
  gi|557694163|ref|YP_008797217.1| 156 QTAASRLNSSFVVCLDEVDALVkafGDDLLYELT 189
                                       *********778889*****97544488888883 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.1   3.3e-10   2.8e-07       2     145 ..      55     174 ..      54     201 .. 0.63
   2 ?   -0.1   0.2       1.2   1.1e+03      72     115 ..     248     292 ..     207     327 .. 0.47

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 3.3e-10
                            AAA_16   2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipysa 71 
                                       l+ R e ++++ ++l +v ++   ++++++G  G+GK+++ r ++++l+ +      ++ f++ +c+    +++y +
  gi|557694163|ref|YP_008797217.1|  55 LPHRTEHIKAVGNVLATVLRPVKpSNLFIYGKTGTGKTAVCRYVFNRLSSAvaekgfDIRFVYINCRLA--GTEYRV 129
                                       7889************99988778*************************99555555555566666555..444433 PP

                            AAA_16  72 laqalareellrqlldeaesaeleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlq 145
                                       l +++a+ ++                              +g ++  l++ ++ ++++l +    +v++lD+++
  gi|557694163|ref|YP_008797217.1| 130 LSELCAAAGVAVP--------------------------FTGVSKGELFRRFQTAASRLNS---SFVVCLDEVD 174
                                       3333333222222..........................2233334455555555522222...2555555555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                            AAA_16  72 laqalareellrqlldeaesaeleawrekleeala....avpelagae 115
                                       l   +   e +  l++++++ae++++r++++        +v+e +gae
  gi|557694163|ref|YP_008797217.1| 248 LRPGAVG-EDVVRLCAALAAAEHGDARRAIDL--LrvsaEVAEREGAE 292
                                       2222222.222233333333333333333322..02333444444444 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 !   33.7   0.0   4.8e-11   4.1e-08       2     120 ..      82     218 ..      81     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 4.8e-11
                                       EEESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS................STTHHHHHHHHHHHHH CS
                               AAA   2 llyGppGtGKTllakavakel.........gvefleisgsellsk................yvgesekkirelfkea 53 
                                        +yG  GtGKT++++ v + l         +++f+ i++     +                + g s+ ++   f++a
  gi|557694163|ref|YP_008797217.1|  82 FIYGKTGTGKTAVCRYVFNRLssavaekgfDIRFVYINCRLAGTEyrvlselcaaagvavpFTGVSKGELFRRFQTA 158
                                       68******************8444444433477999999877766899999************************98 PP

                                       HHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHH CS
                               AAA  54 keka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pdkldpall 120
                                        +   +  ++ +DE+dal+k+             + Ll el + +  ++ v ++g++n+    ++ldp +l
  gi|557694163|ref|YP_008797217.1| 159 ASRLnSSFVVCLDEVDALVKAF-----------GDDLLYELTRSSIGSGWVSLVGISNDllfKEQLDPRVL 218
                                       6666566***********9998...........77888888888888788888888888777777887777 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.3e-07   0.00011      21     120 ..      77     191 ..      56     196 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-07
                                       SSS-EEEECSTTSSHHHHHHHHHH......HSTTTTS-EEEEETT.TS-TTCHHHHHHEBSSSS..STTTSS-BE.H CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraihe......askrkekpfvavnca.aipeelleseLFGhekGa..FtGAekekk.G 87 
                                       ++++++i G++GtGK+ + r +++      a+k  + +fv +nc  a +e  + seL   +  a  FtG +k +   
  gi|557694163|ref|YP_008797217.1|  77 KPSNLFIYGKTGTGKTAVCRYVFNrlssavAEKGFDIRFVYINCRlAGTEYRVLSELCAAAGVAvpFTGVSKGELfR 153
                                       45899******************977443333334559******95567788999999876655559**99988778 PP

                                       HHHHTTTS.....EEEEETGGGS-HHHHHHHHHHHHHS CS
                   Sigma54_activat  88 lfekadgG.....tlfLDeigelplelQekLlrvlqeg 120
                                       +f++a        ++ LDe+  l  ++   Ll+ l + 
  gi|557694163|ref|YP_008797217.1| 154 RFQTAASRlnssfVVCLDEVDALVKAFGDDLLYELTRS 191
                                       88887543222226889999999999999988877665 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     8e-06    0.0069      26     100 ..      69     143 ..      54     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8e-06
                              TniB  26 LleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplka 100
                                       L ++ +  +++nl ++G++ +GKt++++   ++ +++  e+   ++ ++++++   +e r  +++ +a g+ +  
  gi|557694163|ref|YP_008797217.1|  69 LATVLRPVKPSNLFIYGKTGTGKTAVCRYVFNRLSSAVAEKGFDIRFVYINCRLAGTEYRVLSELCAAAGVAVPF 143
                                       45556778899*****************99988888889999999********9999999999998887766544 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 !   15.0   0.0     2e-05     0.017      20      50 ..      78     108 ..      57     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdky 50 
                                        + +fiYG  g GKta+ + + ++l++   +
  gi|557694163|ref|YP_008797217.1|  78 PSNLFIYGKTGTGKTAVCRYVFNRLSSAVAE 108
                                       4558********************9765544 PP

>> TIP49_C  TIP49 AAA-lid 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     0.018      31      63 ..     273     305 ..     268     306 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                           TIP49_C  31 RYaiqLltpasilakkrkkkevevedveeveeL 63 
                                       R ai Ll ++  +a++++++++e ++v+++++L
  gi|557694163|ref|YP_008797217.1| 273 RRAIDLLRVSAEVAEREGAERIEEQHVRRAQSL 305
                                       669***************************998 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 ?   14.6   0.4   3.6e-05     0.031      12      54 ..     261     302 ..     254     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXX CS
                       AAA_assoc_2  12 lealaeladGDaRkaLnlLElaaeaaeakegkieitledleea 54 
                                       ++ala++ +GDaR+a+ lL + ae ae+ eg ++i+++++++a
  gi|557694163|ref|YP_008797217.1| 261 CAALAAAEHGDARRAIDLLRVSAEVAER-EGAERIEEQHVRRA 302
                                       56899999*****************986.99999999999865 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 ?   12.3   0.0   0.00015      0.12       1      77 [.      80     176 ..      80     193 .. 0.75
   2 ?   -2.4   0.0         5   4.3e+03      64      92 ..     277     309 ..     217     314 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                                       EEEEE--SSSSHHHHHHHGGGGB.........S--EEEEE--TT--HHHHH--B--.............-------- CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.........nreveyvqltrdtteedlkgrreik....ngttslvdsplvraar 64 
                                       ++++ G++GtgK+ + +++  +l           +++y++++   te  ++ ++  +       t  ++++l r ++
  gi|557694163|ref|YP_008797217.1|  80 NLFIYGKTGTGKTAVCRYVFNRLssavaekgfDIRFVYINCRLAGTEYRVLSELCAAagvaVPFTGVSKGELFRRFQ 156
                                       6899***********99988888777788877778888888877777666666666644443334566677777777 PP

                                       .......G-SEEEEESGGG- CS
                             AAA_5  65 .......egeilvlDEvera 77 
                                              ++ +++lDEv+ +
  gi|557694163|ref|YP_008797217.1| 157 taasrlnSSFVVCLDEVDAL 176
                                       8888888999******9965 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5
                                       -....G-SEEEEESGGG--HHHHHHHHHHHHSS CS
                             AAA_5  64 r....egeilvlDEveraesevlnsLlslleer 92 
                                            ++e++  ++ er+e + + + +sl+e+ 
  gi|557694163|ref|YP_008797217.1| 277 DllrvSAEVAEREGAERIEEQHVRRAQSLIEKG 309
                                       255555556666666666666666666666665 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0048       4.1      32      57 ..      80     105 ..      75     119 .. 0.76
   2 ?    5.3   0.5    0.0081       6.9     478     508 ..     273     303 ..     253     308 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0048
                            AAA_32  32 NifvlGesgtGrttlvkrlleeiakk 57 
                                       N+f+ G++gtG+t + + + ++ ++ 
  gi|557694163|ref|YP_008797217.1|  80 NLFIYGKTGTGKTAVCRYVFNRLSSA 105
                                       9*************999998887654 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0081
                            AAA_32 478 seiadllrEAdywakkegaevveaehVekAl 508
                                       ++ +dllr ++ +a++egae +e++hV++A 
  gi|557694163|ref|YP_008797217.1| 273 RRAIDLLRVSAEVAEREGAERIEEQHVRRAQ 303
                                       56789************************96 PP

>> ORC5_C  Origin recognition complex (ORC) subunit 5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00027      0.23     106     150 ..     289     338 ..     229     347 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                            ORC5_C 106 v.....ektaasssassasskssssklpeLpylaklLLiAAYLASynppr 150
                                       +     e+++ ++++s  ++ + ++   +Lp++++l+L+A Y+ S+ +++
  gi|557694163|ref|YP_008797217.1| 289 EgaeriEEQHVRRAQSLIEKGRVKEVISSLPLHSRLVLLAVYMVSRKSSE 338
                                       02333344555555555566667777899****************98765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00019      0.16       2      30 ..      82     115 ..      81     135 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf.....gvnlrd 30 
                                       ++ G+ G+GKt +++++ +rl +     g+ +r+
  gi|557694163|ref|YP_008797217.1|  82 FIYGKTGTGKTAVCRYVFNRLSSavaekGFDIRF 115
                                       699**************77763345555555554 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.4e-05      0.08       9      48 ..      64     104 ..      58     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.4e-05
                                       HHHHH.......HCTS-EEEEESTTSSCHHHHHHHHHHCHC CS
                              PIF1   9 vfdaiieavln.ekgklfFvtGsgGtgKtflwkallkklrs 48 
                                       ++ +++++vl+  k+ ++F++G  GtgKt + + + + l s
  gi|557694163|ref|YP_008797217.1|  64 AVGNVLATVLRpVKPSNLFIYGKTGTGKTAVCRYVFNRLSS 104
                                       455666666665899**************777666666655 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   0.00013      0.11       4      44 ..      59     103 ..      56     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHCH....TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE   4 eeetealgkklakal....gdvilLeGdLGaGKTtlvrglakalg 44 
                                       +e+++a+g+ la++l     + ++++G+ G+GKT+ +r + + l 
  gi|557694163|ref|YP_008797217.1|  59 TEHIKAVGNVLATVLrpvkPSNLFIYGKTGTGKTAVCRYVFNRLS 103
                                       6788999999999886655456*****************999885 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00012       0.1      18      56 ..      78     117 ..      58     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                                       SCSEEEEEEESTTSSHHHHHHHHCCSHCC..CCCCBT.EEEE CS
                            NB-ARC  18 lqslvvalvGmgGvGKttlakqilnksde..vegrFd.svaw 56 
                                       +    ++++G+ G GKt + + ++n +++   e+ Fd ++++
  gi|557694163|ref|YP_008797217.1|  78 PS--NLFIYGKTGTGKTAVCRYVFNRLSSavAEKGFDiRFVY 117
                                       33..799******************97652134589844454 PP

>> RNA_helicase  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       0.2       1      26 [.      81     106 ..      81     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                                       +++yG++g+GK+ +++++ ++l++++
  gi|557694163|ref|YP_008797217.1|  81 LFIYGKTGTGKTAVCRYVFNRLSSAV 106
                                       589**************999999776 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 ?   10.7   0.0   0.00031      0.27      35      59 ..      80     104 ..      61     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                             AAA_7  35 pvllvGptGtGKtviikdllkkldk 59 
                                       +++++G+tGtGKt++++ ++++l++
  gi|557694163|ref|YP_008797217.1|  80 NLFIYGKTGTGKTAVCRYVFNRLSS 104
                                       67899************99999884 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00022      0.19       3      26 ..      80     105 ..      78     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                           DUF2075   3 vvlVtGvaGtGKtvvllnllael..e 26 
                                        +++ G++GtGKt v   ++++l   
  gi|557694163|ref|YP_008797217.1|  80 NLFIYGKTGTGKTAVCRYVFNRLssA 105
                                       68*******************99422 PP

>> Pox_D5  Poxvirus D5 protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00051      0.44      15      48 ..     332     364 ..     325     371 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00051
                            Pox_D5  15 eeekstrvpsdvlYeaYkafcekngykpvlskrt 48 
                                       +  ks  + s  lY++Y+++c + g++p l++r 
  gi|557694163|ref|YP_008797217.1| 332 VSRKSSETTSGTLYNTYREYCVSLGLDP-LTDRR 364
                                       4568889999******************.98875 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00049      0.42      20      36 ..      82      98 ..      70     120 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00049
                            AAA_13 20 liYGwNGaGKTtLSrll 36
                                      +iYG+ G+GKT ++r+ 
  gi|557694163|ref|YP_008797217.1| 82 FIYGKTGTGKTAVCRYV 98
                                      79*************74 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2960.49
//
Query:       gi|557694164|ref|YP_008797218.1|  [L=207]
Description: deoxyribonuclease V [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-36  125.4   0.1    2.8e-36  125.1   0.1    1.1  1  Endonuclease_5  Endonuclease V
      0.003   17.0   0.3      0.012   15.0   0.0    1.9  2  DUF99           Protein of unknown function DUF99


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 !  125.1   0.1   3.1e-40   2.8e-36      17     197 .]      32     198 ..      16     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 3.1e-40
                                       -SEEEEEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEE.E--S-SSTT-CHHHCHHHHHHHHCC-SS--SEEEE CS
                    Endonuclease_5  17 lklvaGvDvsfvkeekkeavaalvvldlpslevvekavavv.klsfpYipgfLaFRElpvllkaleklkqkpdvllv 92 
                                       +++v GvD+++   ++ +  aa+vv+d+ + +vve  v+v+   ++pYipgfL  RE p++l+al++ k++ dvl+ 
  gi|557694164|ref|YP_008797218.1|  32 VERVCGVDAAY---RRGRVAAAAVVYDVGERRVVEDVVEVIaGKTTPYIPGFLVLREGPAMLRALQRTKTDYDVLVA 105
                                       699********...4445589*****************99835699******************************* PP

                                       EC-SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE----SSTTEEEEEEETTEEEEEEEESSTTS--EEEEEECS CS
                    Endonuclease_5  93 DGnGiaHprrlGlAshlGvlldlptiGvaKsllvgkveepekekgsvvplvsegevigaalrtkknvkpiyvSvGhr 169
                                       DG+G aHprr+GlA+ lG+++d p+iGvaKs+l+g+ +     ++s+ ++v+ +evig+a       k +y S+G  
  gi|557694164|ref|YP_008797218.1| 106 DGHGRAHPRRCGLATLLGFAVDKPSIGVAKSILIGTRQP----SNSHDKIVEGDEVIGVAKG-----KTVY-SQGYG 172
                                       ***********************************5443....3456688987899998743.....6677.9**** PP

                                       S-HHHHHHHHHHCS-T-SS-HHHHHHHH CS
                    Endonuclease_5 170 isletalelvlallkkyrlPepirqAdl 197
                                       +s+++ l++   +      Pep+r Ad+
  gi|557694164|ref|YP_008797218.1| 173 VSFNDLLKVFDLFG--GAYPEPLRVADR 198
                                       *******9998886..556*******95 PP

>> DUF99  Protein of unknown function DUF99
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.5     0.097   8.7e+02       4      32 ..      34      57 ..      32      68 .. 0.69
   2 !   15.0   0.0   1.4e-06     0.012     137     182 ..     161     203 ..     132     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.097
                                      EEEEEEEEE.....-SS-EEEEEEEEETT CS
                             DUF99  4 rvlGiddsfferkkkdgksvlvGvvmrad 32
                                      rv G+d ++  r   +g+++ ++vv++ +
  gi|557694164|ref|YP_008797218.1| 34 RVCGVDAAY--R---RGRVAAAAVVYDVG 57
                                      899999999..3...57888888886543 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.4e-06
                                       TT....EEEEEESS-HHHHHHHHHHC-SSSSS-HHHHHHHHHHHHH CS
                             DUF99 137 ektgeelyvravGieleeaaklvrkltlegriPEPlRvAhliAsal 182
                                         +g+++y + +G++ ++  k+ + +   g  PEPlRvA+ +++++
  gi|557694164|ref|YP_008797218.1| 161 A-KGKTVYSQGYGVSFNDLLKVFDLF--GGAYPEPLRVADRLSREA 203
                                       3.5899************99999976..689**********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1646.59
//
Query:       gi|557694165|ref|YP_008797219.1|  [L=170]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   51.0   0.1    2.5e-13   50.5   0.1    1.2  1  Methyltransf_25  Methyltransferase domain
    4.1e-13   49.8   0.1    6.2e-13   49.2   0.1    1.2  1  Methyltransf_11  Methyltransferase domain
    1.5e-08   34.5   0.0    2.1e-08   34.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
      3e-07   31.1   0.0    5.2e-07   30.3   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
    5.5e-06   26.3   0.0    6.6e-06   26.1   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
     0.0032   17.1   0.0     0.0039   16.8   0.0    1.1  1  MetW             Methionine biosynthesis protein MetW
  ------ inclusion threshold ------
      0.086   12.8   0.0       0.11   12.5   0.0    1.3  1  Methyltransf_32  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 !   50.5   0.1   9.8e-17   2.5e-13       1      93 [.      46     132 ..      46     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 9.8e-17
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       v d+GcGt  +++ +  rlg  +++g+D +++ml++a++ra+   +  ++vq+da+++pf  + f   ++  ++hhl
  gi|557694165|ref|YP_008797219.1|  46 VCDAGCGTALFLETIRSRLGPVDYVGFDTAANMLAKAASRAD---AYTHLVQADANHMPFRCKVFSHLFCLTVIHHL 119
                                       78*****************99********************4...679**********************877***9 PP

                                       SHHHHHHHHHHHHHHE CS
                   Methyltransf_25  78 sdedlekalkeiarvL 93 
                                       ++   +++++e++r +
  gi|557694165|ref|YP_008797219.1| 120 NP---QQFIREAHRTT 132
                                       85...479****9976 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.1   2.4e-16   6.2e-13       2      87 ..      48     131 ..      47     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 2.4e-16
                                       EET-TTSHHHHHHH.HTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CC CS
                   Methyltransf_11   2 dvGcGtGrlaeala.krg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhved 76 
                                       d+GcGt +++e +  + g  ++vg+D++++ml+ a ++a        +v+ada ++pf+ + f   ++  v+hh+ +
  gi|557694165|ref|YP_008797219.1|  48 DAGCGTALFLETIRsRLGpVDYVGFDTAANMLAKAASRADAYT---HLVQADANHMPFRCKVFSHLFCLTVIHHL-N 120
                                       89************6666**************88877777664...57***************************.6 PP

                                       HHHHHHHHHHH CS
                   Methyltransf_11  77 pekalkeiaRv 87 
                                       p+++++e++R 
  gi|557694165|ref|YP_008797219.1| 121 PQQFIREAHRT 131
                                       **********7 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0   8.3e-12   2.1e-08       6     113 ..      45     142 ..      41     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 8.3e-12
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       rv+D+GCGt  ++  + ++lgp  ++vG+D  ++++ +A ++a+   ++  ++ q+d+++++  +  + f  +++  
  gi|557694165|ref|YP_008797219.1|  45 RVCDAGCGTALFLETIRSRLGP-VDYVGFDTAANMLAKAASRAD--AYT--HLVQADANHMP--FRCKVFSHLFCLT 114
                                       89*******999999999*999.******************988..666..99*********..99999******66 PP

                   Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr 113
                                       v+ +  +p+++++e++r  +  + ++i++++
  gi|557694165|ref|YP_008797219.1| 115 VI-HHLNPQQFIREAHRTTT--TKIIISQHK 142
                                       66.6668**********988..444444444 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.3   0.0     2e-10   5.2e-07       2      91 ..      48     130 ..      47     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 2e-10
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       + GcGt+ +l+ ++ +l +++y+g D  ++++++a+ +  ++       v+ +a++   +   + f   +++ v+hh
  gi|557694165|ref|YP_008797219.1|  48 DAGCGTALFLETIRSRLGPVDYVGFDTAANMLAKAASRADAYTH----LVQADANHMPFRC--KVFSHLFCLTVIHH 118
                                       78******************************999999999996....6666666654433..59************ PP

                   Methyltransf_12  79 lkdirevldnirk 91 
                                       l +++++++++++
  gi|557694165|ref|YP_008797219.1| 119 L-NPQQFIREAHR 130
                                       9.88888888776 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   2.6e-09   6.6e-06      15     100 ..      34     123 ..      16     151 .. 0.67

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.6e-09
                   Methyltransf_23  15 rllpk.lraggrvLdiGcGtGillevlren.gf.svtgvDlspeaveiae...............kakkaqkdqfde 73 
                                        ++++ +++ +rv+d GcGt  +le +r + g  +++g+D   ++ ++a+                           
  gi|557694165|ref|YP_008797219.1|  34 HAVDRvREPVSRVCDAGCGTALFLETIRSRlGPvDYVGFDTAANMLAKAAsradaythlvqadanH----------- 99 
                                       44444478889****************6665556**************998855554444444440........... PP

                   Methyltransf_23  74 qeaaepqgkfdlIvlrevlehvpdppe 100
                                          ++  + f    +  v++h+  p  
  gi|557694165|ref|YP_008797219.1| 100 --MPFRCKVFSHLFCLTVIHHLN-PQQ 123
                                       ..444444444444444444442.233 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.5e-06    0.0039       4     107 ..      33     137 ..      29     142 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                              MetW   4 feliaelikpgsrvldlGcGdGellellkeekq.vdgrGleldeegvaecvakG.lsviqgdldkdlenfedksfdy 78 
                                       ++++ ++ +p srv d GcG   +le ++ + + vd  G ++ ++ +a++ ++   + +  ++d +   f+ k f  
  gi|557694165|ref|YP_008797219.1|  33 HHAVDRVREPVSRVCDAGCGTALFLETIRSRLGpVDYVGFDTAANMLAKAASRAdAYTHLVQADANHMPFRCKVFSH 109
                                       678889999*******************9987659999**********99999724455567888888999999987 PP

                              MetW  79 vvlsqtlqatrnpkevldellrigrraiv 107
                                         +  t+    np++ ++e  r +   i+
  gi|557694165|ref|YP_008797219.1| 110 L-FCLTVIHHLNPQQFIREAHRTTTTKII 137
                                       5.456667777999999999997654443 PP

>> Methyltransf_32  Methyltransferase domain
   #    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      23      82 ..      40      97 ..      30     148 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.2e-05
                   Methyltransf_32 23 esgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrl 82
                                      +++  +v+D+G+G +    ++ +  +  ++  vg+d+ +++ +ka  ra+++ + ++++ 
  gi|557694165|ref|YP_008797219.1| 40 REPVSRVCDAGCGTALFLETIRS--RLGPVDYVGFDTAANMLAKAASRADAYTHLVQADA 97
                                      456789********977777777..358*********************99986665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1243.01
//
Query:       gi|557694166|ref|YP_008797220.1|  [L=218]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   27.1   0.0    7.7e-06   26.1   0.0    1.5  1  NTP_transf_2  Nucleotidyltransferase domain
     0.0013   18.7   0.0     0.0026   17.8   0.0    1.4  1  Polbeta       Polymerase beta, Nucleotidyltransferase
     0.0092   15.8   0.0      0.015   15.1   0.0    1.3  1  DUF294        Putative nucleotidyltransferase DUF294


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 !   26.1   0.0   1.3e-09   7.7e-06       3      55 ..      20      68 ..      18     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.3e-09
                                      HHHHHHHHHTT.TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHH CS
                      NTP_transf_2  3 klleelkelep.vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeeglek 55
                                      ++l+ ++ le+ + + +++GS+arG+ +  SD+D+++  p + +     + +++
  gi|557694166|ref|YP_008797220.1| 20 RALTVMSHLEQhGFSSIVYGSVARGDVTLSSDLDIFIPIPVPMY-----KLEYA 68
                                      6777888888889999*************************954.....33333 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   4.4e-07    0.0026      17      57 ..      36      77 ..      28      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.4e-07
                                      TEEEEEE-S------EEEEEEEESS-.--HHHHHHHHHHHHH CS
                           Polbeta 17 ylFGSrakgkareeSDiDlavllkek.ldleeelelaaeled 57
                                      +++GS+a+g+ + +SD+D+++ +     +le+ l+l + +++
  gi|557694166|ref|YP_008797220.1| 36 IVYGSVARGDVTLSSDLDIFIPIPVPmYKLEYALSLLQPIHK 77
                                      79******************9877666677777777766665 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.6e-06     0.015      31      73 ..      13      56 ..       8      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-06
                            DUF294 31 llrrlielaeeelgk.ppvpfallvmGSeGReEqtlktDqDnal 73
                                      llrrl + a++ + + ++  f+ +v GS +R++ tl++D D ++
  gi|557694166|ref|YP_008797220.1| 13 LLRRLRDRALTVMSHlEQHGFSSIVYGSVARGDVTLSSDLDIFI 56
                                      67888888888888856999*********************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
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: 1710.53
//
Query:       gi|557694167|ref|YP_008797221.1|  [L=492]
Description: inosine monophosphate dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-149  495.7   6.0   7.1e-149  495.5   6.0    1.0  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    1.4e-23   83.1   0.1    4.2e-11   43.1   0.0    2.9  2  CBS           CBS domain
    2.5e-11   43.5  13.9    1.9e-07   30.8   0.7    3.3  3  NMO           Nitronate monooxygenase
    3.4e-09   36.2  12.5      2e-08   33.6   9.4    2.9  3  FMN_dh        FMN-dependent dehydrogenase
      5e-05   22.7   4.4    0.00073   18.8   1.1    2.3  2  DHO_dh        Dihydroorotate dehydrogenase
    8.4e-05   22.1   6.9     0.0003   20.3   0.1    2.7  3  His_biosynth  Histidine biosynthesis protein
      9e-05   22.0   2.9     0.0001   21.9   0.8    2.2  2  PEP_mutase    Phosphoenolpyruvate phosphomutase
     0.0012   18.0   6.4     0.0022   17.2   5.9    1.7  1  Glu_synthase  Conserved region in glutamate synthase
     0.0035   16.5   1.0     0.0082   15.3   0.0    2.0  2  Dus           Dihydrouridine synthase (Dus)
  ------ inclusion threshold ------
      0.018   14.5   2.5       0.16   11.4   0.1    2.9  3  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
      0.043   13.1   7.1      0.031   13.6   2.4    2.5  3  ThiG          Thiazole biosynthesis protein ThiG
       0.82    9.1   7.8      0.079   12.4   1.8    2.2  2  Aldolase      KDPG and KHG aldolase


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.5   6.0  4.8e-152  7.1e-149       1     345 []      18     487 ..      18     487 .. 0.97

  Alignments for each domain:
  == domain 1  score: 495.5 bits;  conditional E-value: 4.8e-152
                                       E--GGGEEEE---B-S-GG.GSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH   1 gltfddvllvpaksevlpk.evdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeev 76 
                                       gltfddvll+p++s++ ++ +v++++++t++i+l++P+vsaamdtvte+emA+a+areGgigvih+  ++e+q+e+v
  gi|557694167|ref|YP_008797221.1|  18 GLTFDDVLLLPRRSSIRSRrDVSTRSRFTRRIELEVPIVSAAMDTVTEAEMAVAMAREGGIGVIHRFNTVEQQVEQV 94 
                                       79***************998********************************************************* PP

                                       HHHHTS....................................................................... CS
                                       xxxxxx....................................................................... RF
                             IMPDH  77 kkvkrs....................................................................... 82 
                                       k vkr+                                                                       
  gi|557694167|ref|YP_008797221.1|  95 KLVKRAeniaveepytiepeatvaeaealmrrknvsgllvtkssrklvgilsrrdilfapreakvseymtpreklit 171
                                       ***************************************************************************** PP

                                       ..............................................TTSXBXTTSXB-EEEEE-SSTTHHHHHHHHH CS
                                       ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  83 ..............................................pnaakdekgrllvgaavgvkedalervkalv 113
                                                                                     pna++d++grl+v+aa+gv+e+a++r++al+
  gi|557694167|ref|YP_008797221.1| 172 appsisleeakqifmkhkveklplvdsewnikglitsadivkklmhPNASRDSRGRLMVAAAIGVREEAMDRAEALL 248
                                       ***************************************************************************** PP

                                       HTT-SEEEEE-STSSSHHHHHHHHHHHHHTTT.SEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 114 eagvdvlvvdsahghsekvleavkeikkkvee.veviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvG 189
                                       +ag+d+lv+d+ahgh+++v++ +k++++++ e  e++aGnvataeg+++L++aga +vkvG+GpGs+CttrvvagvG
  gi|557694167|ref|YP_008797221.1| 249 AAGADCLVIDVAHGHTDMVINLIKQLRRSFGEdFELVAGNVATAEGVEDLAAAGASGVKVGVGPGSVCTTRVVAGVG 325
                                       ******************************988******************************************** PP

                                       --HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 190 vpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgeviliegrkyKeyrGmgsl 266
                                       vpqltA++++ae+a+ +gvp+iaDGGi++s d+vkAlaaGa++vm+G+llagt+Espg v++ +grk+K+yrGm+s+
  gi|557694167|ref|YP_008797221.1| 326 VPQLTAIMDCAETAEAMGVPIIADGGIRSSADLVKALAAGASTVMIGRLLAGTDESPGAVVVKNGRKMKVYRGMASF 402
                                       ***************************************************************************** PP

                                       HHH..HH.-SS-.TTS-...-.-SS-SBEEEEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEEE-HH CS
                                       xxx..xx.xxxx.xxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 267 gam..kk.gskd.ryfqk.ke.klvpeGvegrvpykgsvkevveqlvgglrsgmgylGaktieelkekakfvritaa 337
                                        am  k+ ++ d  + q+ +e ++++eGve++vpykgs ++vv+qlv+glrsg++ylGa++i+el+++a f+r+t+a
  gi|557694167|ref|YP_008797221.1| 403 YAMlaKEsRAGDeDFLQDaSEySFIAEGVEAYVPYKGSASDVVKQLVAGLRSGLSYLGASNIKELQRNAVFIRMTEA 479
                                       ***7422333331555643335******************************************************* PP

                                       HHHHHS-- CS
                                       xxxxxxxx RF
                             IMPDH 338 glkeshvH 345
                                       glkesh+H
  gi|557694167|ref|YP_008797221.1| 480 GLKESHPH 487
                                       *******9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   2.8e-14   4.2e-11       7      54 ..     106     153 ..      97     156 .. 0.91
   2 !   36.9   0.0   2.4e-12   3.6e-09       1      57 []     159     217 ..     159     217 .. 0.91

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 2.8e-14
                                       SSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   7 rdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       +++ t+ p++t++ea  lmr+k+vs+l+V+ ++ klvGi+++rD+l a
  gi|557694167|ref|YP_008797221.1| 106 EEPYTIEPEATVAEAEALMRRKNVSGLLVTKSSRKLVGILSRRDILFA 153
                                       6788***********************9999999***********976 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 2.4e-12
                                       HHHHSBS..SCEEEETTSBHHHHHHH.HHHHTSSEEEEEETTTBEEEEEEHHHHHHHHHC CS
                               CBS   1 Vgdimtr..dvvtvppdttleealel.mrekgvsrlPVVdedgklvGivtlrDllralle 57 
                                       V+++mt+  +++t+pp+ +leea ++ m +++v  lP Vd++ ++ G++t  D++++l++
  gi|557694167|ref|YP_008797221.1| 159 VSEYMTPreKLITAPPSISLEEAKQIfM-KHKVEKLPLVDSEWNIKGLITSADIVKKLMH 217
                                       78898887799***************55.999*******9888*************9985 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     1e-06    0.0015       3      59 ..      44      99 ..      42     127 .. 0.83
   2 ?   -0.3   4.6      0.36   5.4e+02     146     222 ..     241     309 ..     151     311 .. 0.73
   3 !   30.8   0.7   1.3e-10   1.9e-07     187     273 ..     337     423 ..     318     479 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1e-06
                               NMO  3 lltellkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvka 59
                                      + t  ++ + p+v + m  +++a++a a + +Gg+Gv+     t  +  ++++ vk+
  gi|557694167|ref|YP_008797221.1| 44 RFTRRIELEVPIVSAAMDTVTEAEMAVAMAREGGIGVIH-RFNTVEQQVEQVKLVKR 99
                                      5566778899****************************9.77787666666666655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.36
                               NMO 146 vkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqig 222
                                       ++ a ++ a+GaD l+++   a Gh+  + ++     +L  +  +  +   + aG + +++gv+   a+GAsgv++g
  gi|557694167|ref|YP_008797221.1| 241 MDRAEALLAAGADCLVID--VAHGHTD-MVIN--LIKQLRRSFGEDFE---LVAGNVATAEGVEDLAAAGASGVKVG 309
                                       555666777777777775..4456766.4332..23333333333333...458999*****************998 PP

  == domain 3  score: 30.8 bits;  conditional E-value: 1.3e-10
                               NMO 187 qvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakdahkkklleaklddteltsavsGrpaRal 263
                                       + ++a+ +P+iA GGi    ++  aLa+GAs v ig  + +t+es+  +++k+  + +   ++    a+  ++ Ra 
  gi|557694167|ref|YP_008797221.1| 337 ETAEAMGVPIIADGGIRSSADLVKALAAGASTVMIGRLLAGTDESPGAVVVKNGRKMKVYRGMASFYAMLAKESRAG 413
                                       3456777*****************************9999*********9998877777766665555555777777 PP

                               NMO 264 atelleelee 273
                                         ++l+   e
  gi|557694167|ref|YP_008797221.1| 414 DEDFLQDASE 423
                                       7777776665 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.17   2.5e+02      30     105 ..      21      95 ..      16     138 .. 0.69
   2 !   33.6   9.4   1.4e-11     2e-08     202     303 ..     265     375 ..     199     384 .. 0.74
   3 ?    0.6   0.0      0.15   2.2e+02     316     346 ..     442     472 ..     437     474 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.17
                                       GGGEEE---SSSS-SS-B--EE.ETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT-SS-HHHHH CS
                            FMN_dh  30 ferirlrprvlrdvskvdlstt.llGqklslPvliaPvglaklahpdgelalaraaakagipfvlstvastsleeva 105
                                       f+++ l pr     s++d+st+  + ++++l v i ++++ ++ +++  +a+ar+    g++  + tv ++++e+v+
  gi|557694167|ref|YP_008797221.1|  21 FDDVLLLPRRSSIRSRRDVSTRsRFTRRIELEVPIVSAAMDTVTEAEMAVAMAREG-GIGVIHRFNTV-EQQVEQVK 95 
                                       88888999998888999988752688888888888888999998877777777763.35666666666.55666664 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 1.4e-11
                                       C--HHHHHHHHHHHS..SEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT-.--HHHCHHHHHHHH.. CS
                            FMN_dh 202 sltwddikwlreqtk..lplvvKGvltaedakraveaGvdgivvSNHGG.....Rqldga.patidvLpeiveavgg 270
                                       ++  + ik+lr+      +lv   v tae ++ +++aG++g+ v    G     R + g+ ++ + ++ +++e ++ 
  gi|557694167|ref|YP_008797221.1| 265 DMVINLIKQLRRSFGedFELVAGNVATAEGVEDLAAAGASGVKVGVGPGsvcttRVVAGVgVPQLTAIMDCAETAEA 341
                                       5556668888887764478888899*******************988885555565555423334444444554444 PP

                                       .SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 271 .rievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                         +++++DgGir+ +D +kAla GA+ v++GR +
  gi|557694167|ref|YP_008797221.1| 342 mGVPIIADGGIRSSADLVKALAAGASTVMIGRLL 375
                                       35******************************76 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHT-SBHHHHHCGGE CS
                            FMN_dh 316 ervleilraelertmallGvksvaeldrsll 346
                                       ++v++ l a l++ +  lG+++++el+r+++
  gi|557694167|ref|YP_008797221.1| 442 SDVVKQLVAGLRSGLSYLGASNIKELQRNAV 472
                                       6789999********************9876 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.011        16     228     275 ..     265     311 ..     263     325 .. 0.89
   2 !   18.8   1.1   4.9e-07   0.00073     240     275 ..     341     374 ..     321     382 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHH CS
                            DHO_dh 228 dialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvyta 275
                                       d+ +++i +l++ + ++  +++ G + ++e + + + aGAs v+v+ +
  gi|557694167|ref|YP_008797221.1| 265 DMVINLIKQLRRSFGEDFELVA-GNVATAEGVEDLAAAGASGVKVGVG 311
                                       5678999***********9996.9*******************99865 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4.9e-07
                                       HTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHH CS
                            DHO_dh 240 rlkkeipiIgvGGiesgeDalekieaGAslvqvyta 275
                                        +   +piI+ GGi s+ D +  + aGAs v ++  
  gi|557694167|ref|YP_008797221.1| 341 AMG--VPIIADGGIRSSADLVKALAAGASTVMIGRL 374
                                       444..9*************************99865 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.8   2.7e+03     114     161 ..      58     105 ..      52     107 .. 0.64
   2 !    5.0   0.2    0.0098        15      32     102 ..     241     309 ..     233     322 .. 0.84
   3 !   20.3   0.1     2e-07    0.0003      66     103 ..     336     373 ..     325     381 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.8
                                       HHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHHHHHTT- CS
                      His_biosynth 114 elaekfgsqkivvaiDarrgykvaikgwreetgldavelakkleelga 161
                                        +++ + + +++va   + g  v  +  + e++++ v+l+k++e+  +
  gi|557694167|ref|YP_008797221.1|  58 AAMDTVTEAEMAVAMAREGGIGVIHRFNTVEQQVEQVKLVKRAENIAV 105
                                       556666666666666633346666666777778888888888877666 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0098
                                       HHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESS.SSSHHHHHHHHHCT-SEEEES CS
                      His_biosynth  32 velakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGG.Irsledveelleagadkviig 102
                                       ++ a+++ ++gad l+ +D+  a+ +++  ++l++++++++  ++++  G + + e ve+l  aga+ v +g
  gi|557694167|ref|YP_008797221.1| 241 MDRAEALLAAGADCLV-IDV--AHGHTDMVINLIKQLRRSFGEDFELVAGnVATAEGVEDLAAAGASGVKVG 309
                                       5667777788888875.466..889999999**************987777***************977665 PP

  == domain 3  score: 20.3 bits;  conditional E-value: 2e-07
                                       HHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESH CS
                      His_biosynth  66 eeiaeevfipvqvGGGIrsledveelleagadkviigt 103
                                       +e+ae++ +p+  +GGIrs  d+ ++l aga+ v+ig 
  gi|557694167|ref|YP_008797221.1| 336 AETAEAMGVPIIADGGIRSSADLVKALAAGASTVMIGR 373
                                       46777777777777777777777777777777777764 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.8   6.8e-08    0.0001     155     225 ..     237     314 ..     204     325 .. 0.80
   2 ?   -2.5   0.0       1.9   2.8e+03     165     175 ..     361     371 ..     356     380 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 6.8e-08
                        PEP_mutase 155 leeaieRaraYaeAGAdgvfvpglqkdae.iaelvaavd......vplnvvp.l.kgtlsvaelaelGvarislgnh 222
                                        eea++Ra+a ++AGAd++++  ++   + + +l+++++          +v+ +  ++  v++la++G++ + +g  
  gi|557694167|ref|YP_008797221.1| 237 REEAMDRAEALLAAGADCLVIDVAHGHTDmVINLIKQLRrsfgedF--ELVAgNvATAEGVEDLAAAGASGVKVGVG 311
                                       589*********************9998889999999955887552..333322244689*********99999877 PP

                        PEP_mutase 223 llr 225
                                       +  
  gi|557694167|ref|YP_008797221.1| 312 PGS 314
                                       655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                        PEP_mutase 165 YaeAGAdgvfv 175
                                        ++AGA++v++
  gi|557694167|ref|YP_008797221.1| 361 ALAAGASTVMI 371
                                       57899999998 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 !   17.2   5.9   1.4e-06    0.0022     243     304 ..     316     373 ..     264     376 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                                       EEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SH CS
                      Glu_synthase 243 spkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgigt 304
                                         + ++  +G+P ++a+    +t  + g    v +iadGg++++ad+vkala GA +v ig+
  gi|557694167|ref|YP_008797221.1| 316 CTTRVVAGVGVPQLTAIMDCAETAEAMG----VPIIADGGIRSSADLVKALAAGASTVMIGR 373
                                       345678889**********999988876....89**************************97 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.58   8.7e+02     138     183 ..     238     279 ..     230     311 .. 0.60
   2 !   15.3   0.0   5.5e-06    0.0082     179     217 ..     339     376 ..     327     419 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.58
                                       C.HHHHHHHHHHCT-SEEEE...ESSECCCTT-CG--CHHHHHHHHH-S CS
                               Dus 138 enalelakiveaaGaqaltv...HgRtraqnyegtadweaIkevkqavs 183
                                       e+a++ a+++ aaGa+ l++   Hg t +        ++ Ik++++++ 
  gi|557694167|ref|YP_008797221.1| 238 EEAMDRAEALLAAGADCLVIdvaHGHTDM-------VINLIKQLRRSFG 279
                                       56788888899999998887444555544.......3444555555555 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 5.5e-06
                                       HHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC CS
                               Dus 179 kqavsipviaNGdIkdaedaqaileetGadgvmigrgal 217
                                        +a+ +p+ia G+I++  d+ ++l+  Ga  vmigr   
  gi|557694167|ref|YP_008797221.1| 339 AEAMGVPIIADGGIRSSADLVKALAA-GASTVMIGRLLA 376
                                       56777********************9.*********654 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 ?   -1.3   0.0      0.86   1.3e+03      77     104 ..      64      91 ..      59     135 .. 0.75
   2 ?    1.5   0.1      0.11   1.7e+02     128     166 ..     268     307 ..     241     310 .. 0.80
   3 ?   11.4   0.1   0.00011      0.16     132     167 ..     336     371 ..     326     374 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.86
                                       ES-HHHHHHHHHTT--EEEEEE--SHHH CS
                      G3P_antiterm  77 stksslikkakklglltiqrlfliDssa 104
                                       +  +  + +a++ g+ +i+r+  + ++ 
  gi|557694167|ref|YP_008797221.1|  64 TEAEMAVAMAREGGIGVIHRFNTVEQQV 91 
                                       5566778899999999999998776654 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
                                       HHHHCTSTTS.....EEEEESS--SHHHHHHHCTT.SSEEE CS
                      G3P_antiterm 128 pkvikeikkel..kipiiaGGLietkedveealkaGaiavs 166
                                        ++ik++++++  +++ + +G + t e ve++ +aGa++v 
  gi|557694167|ref|YP_008797221.1| 268 INLIKQLRRSFgeDFE-LVAGNVATAEGVEDLAAAGASGVK 307
                                       5677777777632333.5568899*************9996 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00011
                                       CTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                      G3P_antiterm 132 keikkelkipiiaGGLietkedveealkaGaiavst 167
                                       +e+ +++ +piia G i+++ d+ +al+aGa+ v+ 
  gi|557694167|ref|YP_008797221.1| 336 AETAEAMGVPIIADGGIRSSADLVKALAAGASTVMI 371
                                       4667889*************************9986 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.23   3.5e+02     136     198 ..      10      74 ..       3     107 .. 0.69
   2 ?   -2.0   0.1       1.2   1.7e+03     196     227 ..     278     309 ..     230     323 .. 0.77
   3 ?   13.6   2.4     2e-05     0.031     171     213 ..     339     381 ..     322     414 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.23
                                       HHHHHHHTT-S....EBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT- CS
                              ThiG 136 larrleevGca....avmPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGa 198
                                       la+ le+vG +     ++P  + i s + ++++  ++  i e++vP+ v A + + ++a +a+ +  
  gi|557694167|ref|YP_008797221.1|  10 LAKILEKVGLTfddvLLLPRRSSIRSRRDVSTRSRFTRRI-ELEVPI-VSAAMDTVTEAEMAVAMAR 74 
                                       5677777776422224778888888888888888776654.578886.5666777777766666544 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                                       TT-SEEEESHHHHTSSSHHHHHHHHHHHHHHH CS
                              ThiG 196 lGadavllntavaeakdpvamArafklaveaG 227
                                       +G d  l++  va+a+    +A+a + +v+ G
  gi|557694167|ref|YP_008797221.1| 278 FGEDFELVAGNVATAEGVEDLAAAGASGVKVG 309
                                       46666778888888888888888877777766 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 2e-05
                                       HHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSH CS
                              ThiG 171 ieeakvPvivDAGigspsdaaqamelGadavllntavaeakdp 213
                                        e + vP+i D Gi+s+ d ++a+  Ga++v++   +a +++ 
  gi|557694167|ref|YP_008797221.1| 339 AEAMGVPIIADGGIRSSADLVKALAAGASTVMIGRLLAGTDES 381
                                       45679****************************9988877653 PP

>> Aldolase  KDPG and KHG aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.7     4e+03      31      49 ..      75      93 ..      50     121 .. 0.55
   2 ?   12.4   1.8   5.3e-05     0.079       8      84 ..     226     306 ..     221     344 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.7
                                      HTT--EEEEETTSTTHHHH CS
                          Aldolase 31 agGlrvlevtlrteaalda 49
                                      +gG+ v+    + e+ ++ 
  gi|557694167|ref|YP_008797221.1| 75 EGGIGVIHRFNTVEQQVEQ 93
                                      3444444444444444444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.3e-05
                                       HSEEEEE--SSGGGHHHHHHHHHHTT--EEEEET...TSTTHHHHHHHHHHH-.TTSEEEEES--SHHHHHHHHHCT CS
                          Aldolase   8 akvvpvivikdkedalplaeaLvagGlrvlevtl...rteaaldairvlrker.pdllvgaGtvlnaeqlaeakeaG 80 
                                       ++++   +i   e+a++ aeaL+a G   l + +    t++ ++ i+ lr+   +d+ + aG v +ae +++ ++aG
  gi|557694167|ref|YP_008797221.1| 226 GRLMVAAAIGVREEAMDRAEALLAAGADCLVIDVahgHTDMVINLIKQLRRSFgEDFELVAGNVATAEGVEDLAAAG 302
                                       5677777888899*************98776665113466677777777666448999**********999988888 PP

                                       -SEE CS
                          Aldolase  81 aqfv 84 
                                       a  v
  gi|557694167|ref|YP_008797221.1| 303 ASGV 306
                                       8644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3347.98
//
Query:       gi|557694168|ref|YP_008797222.1|  [L=413]
Description: adenylosuccinate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-139  465.2   0.0   2.2e-139  465.0   0.0    1.0  1  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 !  465.0   0.0  1.2e-143  2.2e-139       2     416 ..       5     407 ..       4     410 .. 0.95

  Alignments for each domain:
  == domain 1  score: 465.0 bits;  conditional E-value: 1.2e-143
                                       EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHH CS
                   Adenylsucc_synt   2 vvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealle 78 
                                       vvvG+qwGDEGKGki  +l++ a++v+RfqGGanAGHt+ +++++yk+++lp+G+l +g + vi++g+++dpea+ +
  gi|557694168|ref|YP_008797222.1|   5 VVVGLQWGDEGKGKISYVLSRGAEAVARFQGGANAGHTIKIGETRYKFNMLPAGCL-AGPRPVIASGCLLDPEAFEK 80 
                                       8*******************************************************.59999*************** PP

                                       HHTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHHH CS
                   Adenylsucc_synt  79 EieeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeeel 155
                                       E++ l+ +g +   ++ l+s  ah+v+p+h++lD+  e+ +g++++GtT++GiGpayadk+ r girvgdll++++l
  gi|557694168|ref|YP_008797222.1|  81 ELQLLQTSGHR---HQPLVSMGAHIVFPMHRELDGRLESLRGSSAVGTTRRGIGPAYADKMLRVGIRVGDLLSHSSL 154
                                       *******9984...599*********************************************************9** PP

                                       HHHHHHHHHHTHHHHHHT...T-----HHHHHHHHHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSST CS
                   Adenylsucc_synt 156 eeklekllelknkllekldkeeleveelleellkyaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtY 232
                                        ek++ l +l+  + e      ++       ++k+ + l+p+  +++ +lne +++g +vL+EGaqgtllDidhGtY
  gi|557694168|ref|YP_008797222.1| 155 GEKVKFLRRLHG-V-E----PGVD-------FEKLEKLLRPFAGNVSGFLNEVVESGGRVLLEGAQGTLLDIDHGTY 218
                                       ***999887776.3.2....3455.......3467889*************************************** PP

                                       TSS-SS--SHHHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHHHHHHHHHTT-B-TTT--B-EEE-EEH CS
                   Adenylsucc_synt 233 PfvTsSnttaggaltglglapkkidevlgvvKAyttrvGeGpfptelkdevgeklrekGkEfgtttgrpRrcGwlDl 309
                                       P+vTsSnt++++ ++ +gl+ ++ ++++gv+KAyttrvG+Gpfpte+++ ++e++rekG+EfgtttgrpRr+GwlD+
  gi|557694168|ref|YP_008797222.1| 219 PYVTSSNTISANGFVSTGLPISRKGQIIGVTKAYTTRVGAGPFPTEITGPTAETIREKGGEFGTTTGRPRRIGWLDI 295
                                       ***************************************************************************** PP

                                       HHHHHHHHHHT-SEEEEE-GGGGTT-SEEEEEEEEEETTEEESS--S.....-GEEEEEEEEE--.S--TT-..... CS
                   Adenylsucc_synt 310 vllryavrvngvtelaltklDvldgldeikvcvaYkldgkeldefpasleelekvepvyeelpgWkedisgv..... 381
                                       ++lrya+++ngv+++a+tk Dvl+gl+++k cv+Y +dg e+++f   l++l++v+pvyee++gW+ d +g+     
  gi|557694168|ref|YP_008797222.1| 296 PALRYACMINGVDTVAVTKSDVLSGLPTVKACVRYMVDGVETTRFGDFLHRLDEVQPVYEEFHGWNMDEAGLrrvve 372
                                       ****************************************999***99******************88777655588 PP

                                       --GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT CS
                   Adenylsucc_synt 382 rsfedlpenakkyvefieellgvpvkiisvGpere 416
                                       + +++lp n+++y+e++e+ l v+++i svG+e +
  gi|557694168|ref|YP_008797222.1| 373 KGWDELPPNLREYLEWLEKQLRVNISIASVGEEAS 407
                                       89*****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       346  (0.0192983); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 00:00:00.39
# Mc/sec: 3143.09
//
Query:       gi|557694169|ref|YP_008797223.1|  [L=454]
Description: adenylosuccinate lyase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-35  121.1   0.0    9.2e-35  120.5   0.0    1.2  1  Lyase_1   Lyase
    1.1e-15   57.8   0.0    3.3e-15   56.2   0.0    1.8  1  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 !  120.5   0.0     1e-38   9.2e-35       1     304 [.      11     303 ..      11     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 120.5 bits;  conditional E-value: 1e-38
                                       CEEEEETCHHHHHHHHHHHHHGGGHHHHHCHHHHHHHH.HHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSS CS
                           Lyase_1   1 grftvkadklmgiftersrenfrlseedikalaalkka.aakanvdlkeeaaaiikaldevleegklddqfvlkviq 76 
                                       gr+  k ++    f+e+++ ++rl      ++a + +a +a  ++      a ++++l++ l e+  ++++++k i+
  gi|557694169|ref|YP_008797223.1|  11 GRYREKLEECSRFFSEYALIRYRLV-----VEACYLRAfLAAIGKGS---EAHAVEGLEKELWELPMEEAVEVKNIE 79 
                                       6777777777788888888888888.....56666665245555555...45667778888888************* PP

                                       SSHHHHHHHHHHHHHHHHTT..HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT CS
                           Lyase_1  77 egsgtavnmnlnevigellg..ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkd 151
                                       +  g++v + ++ ++ ++l+   + + + ++h+g +s+D+++ a+ +al++ +++ L p l +L++ ++  a+ +++
  gi|557694169|ref|YP_008797223.1|  80 RRVGHDVVA-VTLFLEKKLEerGHAALKPFIHFGLTSEDINNIAYGMALRDFIQTSLTPVLANLVKEITSLAETHAS 155
                                       ********9.******7777666889999************************************************ PP

                                       -EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHH..HHH CS
                           Lyase_1 152 vvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakela..kvt 226
                                       ++ + rTh+q+A+P+t+g  l+ y   l +   +lk+l+    + +lgg+++   +++++++  ++ +  +a  +v+
  gi|557694169|ref|YP_008797223.1| 156 TPYLARTHGQPAVPTTFGSYLANYGYRLAKLTAKLKNLR---PQAKLGGAVGDLSAHKTAYP--QVDWVSFAekFVE 227
                                       ***************************************...78899**999*******999..8999999886788 PP

                                       CSTEESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHH CS
                           Lyase_1 227 glpvkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlEll 303
                                        ++   ++  ++v+++ +  e+l++++ +a     +++D +l+ +  +glve   + +   SS+MP+K NP  +E+ 
  gi|557694169|ref|YP_008797223.1| 228 QMGLEYMPAATQVAPHERFSEILQTVAAIASVAANLCRDFWLFGA--LGLVEFGKPSEHRHSSTMPQKHNPLLFENA 302
                                       88888888889**********************************..***************************997 PP

                                       H CS
                           Lyase_1 304 t 304
                                        
  gi|557694169|ref|YP_008797223.1| 303 E 303
                                       6 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   3.7e-19   3.3e-15       1      74 [.     323     396 ..     323     413 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 3.7e-19
                                       -STT--TCHHHHHTTCHHHHHHHHHHHHHHHHHHCCEEE-HHHHHHHHHT-GGGGHHHHHHHHHHTT-TTHHHH CS
                             ASL_C   1 SrlQRDLtdStvlRnlgvalahslialksllkglsklevneealaedLdenwevlaEaiqtvlrregiekpYek 74 
                                       Srl RDL+dS ++R  g+ala +l+++k+l+++l++ +v++++++e++++++e  aE +q +lr++g+e+ Y  
  gi|557694169|ref|YP_008797223.1| 323 SRLHRDLSDSVIKRFYGTALALTLLGVKNLIQALGQTHVKTDKMREEVEKTPEASAEILQLILRKHGVEDGYSL 396
                                       9**********************************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3495.81
//
Query:       gi|557694170|ref|YP_008797224.1|  [L=444]
Description: zinc-dependent protease, TldD/PmbA family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-45  154.9   0.2    4.6e-45  154.6   0.2    1.1  1  PmbA_TldD  Putative modulator of DNA gyrase
  ------ inclusion threshold ------
       0.09   13.3   0.1       0.21   12.1   0.1    1.5  1  HtaA       Htaa


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 !  154.6   0.2   5.1e-49   4.6e-45       7     279 .]      28     306 ..      22     306 .. 0.87

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 5.1e-49
                                       EEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-........ CS
                         PmbA_TldD   7 eesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea........ 75 
                                       ++++ + +rf+n++++ +++ ++ ++ v v ++gr ++ st+d s e++ee+v++ v++ak++pe + +        
  gi|557694170|ref|YP_008797224.1|  28 HQTQWQMIRFSNNKITVSKNGSTVSVDVYVSVKGRRAVQSTTDVSPESVEELVRKTVAAAKSSPETDVYaplpkgpf 104
                                       6678899*******************************888888889*************************99999 PP

                                       ...........GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEE CS
                         PmbA_TldD  76 ...........eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrvs 141
                                                  +ev++e+ +e++ e+ +   +  +        + + v +sl  ++++ l+ ++ G++++ ++t ++
  gi|557694170|ref|YP_008797224.1| 105 kydkkllkpvsAEVPPEQLVEYVGEAVNGGLD--N--------GGKRVAGSLVYTRGKMLLTTTGGVEASASSTGIE 171
                                       99999998888888888888885555533222..2........4444557788887888888888************ PP

                                       EEEEEEE..S.TCSETEEEEEEEE....SSHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGH CS
                         PmbA_TldD 142 lslsvia.dd.ggsgdgmgggsgy....edleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllhea 212
                                       +s+ + a dd  g          +     d++++ +++++++a e a+ +l++++ ++g y+ +l+p+ ++ +l+  
  gi|557694170|ref|YP_008797224.1| 172 ISVRAFAaDDaTGH---------FvsvaADPKQFTPYQAGAKAGEIAKMALNPVDGEAGVYEGLLGPMTFAHILE-Q 238
                                       *******6652222.........22345567779999*************************************7.7 PP

                                       HHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE--- CS
                         PmbA_TldD 213 vghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkny 279
                                       vg+ ++a  v+  +Sfl++ lG+k +s+ ++++ddpt  g +g +pfDdEG+pt+r++l enGvLk+y
  gi|557694170|ref|YP_008797224.1| 239 VGSWASAFYVDGEMSFLTGLLGQKAGSDVFSLYDDPTLaGTYGATPFDDEGLPTRRNTLFENGVLKTY 306
                                       999**************778*****************99****************************9 PP

>> HtaA  Htaa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   2.3e-05      0.21      62     110 ..      21      71 ..      12      95 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                              HtaA  62 s.vhftghngaLdl.tlsnpkievsgetgtLladvsskdkeggekvtkedv 110
                                       s v+ft+h+ + ++ ++sn ki+vs+++ t+++dv  + k   ++++++dv
  gi|557694170|ref|YP_008797224.1|  21 SdVVFTSHQTQWQMiRFSNNKITVSKNGSTVSVDVYVSVKGRRAVQSTTDV 71 
                                       459*****77776539******************87543333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); 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:                         2  (0.000111551); expected 0.2 (1e-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: 3496.34
//
Query:       gi|557694171|ref|YP_008797225.1|  [L=505]
Description: hypothetical protein CSUB_C0737 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   26.7   0.0    1.3e-05   25.2   0.0    1.8  1  APH        Phosphotransferase enzyme family
  ------ inclusion threshold ------
       0.18   11.7   0.0       0.36   10.8   0.0    1.4  1  Gemini_C4  Geminivirus C4 protein


Domain annotation for each model (and alignments):
>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.5e-09   1.3e-05       8     116 ..     280     407 ..     274     458 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.5e-09
                                       .SSCEEEEEEETT--EEEEE.....................E-TT.S-HHHHHHHHHHHHHHHHTT-B--B-CTTBS CS
                               APH   8 gasnrtylvttpagryvlrr.....................nppa.raaeeirrevallrlLakagvpvPevlagdt 62 
                                       g+ n ty ++ ++ +++ +r                     +  +  +  ++++e  +l++L+++g+++Pe+++   
  gi|557694171|ref|YP_008797225.1| 280 GLFNSTYVIEVGSEKLFAKRymswtdvkwvaariwtawiknF--SiNPSTRLAKEIYFLDFLRGHGFHTPEIIH--- 351
                                       466778888888888888888888888888888888888541..3446689***********************... PP

                                       -EEETTE.EEEEEE----EE-SS..HHHHHHHHHHHHHHHHHHCCHHCH.-S..TTTB- CS
                               APH  63 ddeeigl.lfalieyvpgrsllr..klsaaqlpellealgeflaalhqvdpa..alpla 116
                                          ++++   +  +yv+g++ll+      +++  +++++g++la +h+v+++  +++++
  gi|557694171|ref|YP_008797225.1| 352 ---VNWRdKILYTTYVEGETLLDawLSKKPDRAVFADKVGQVLASVHRVGGRlgDCKPE 407
                                       ...3444357789***********96678899999**************5442233333 PP

>> Gemini_C4  Geminivirus C4 protein
   #    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      11      45 ..     225     255 ..     211     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4e-05
                         Gemini_C4  11 nskenssakikdsstWyPqPGqhisirtfrelnpa 45 
                                       +     +++++  s   P P qhi +rt r l p 
  gi|557694171|ref|YP_008797225.1| 225 E----ATTNLSSQSPPLPDPEQHIHLRTSRGLQPL 255
                                       3....345566678899*************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.39
# Mc/sec: 3859.16
//
Query:       gi|557694172|ref|YP_008797226.1|  [L=341]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.3   0.0      0.018   14.5   0.0    1.3  1  NeuB          NeuB family
       0.05   13.9   0.0       0.11   12.8   0.0    1.6  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     2e-06     0.018      43     114 ..     193     263 ..     167     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2e-06
                                       -HHHHHHHH---HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHHT-S-EEE-GGGTT-HHHHHHHHTT-S CS
                              NeuB  43 sqlellkklelseeehkelkeyceekgieflstpfdlesvdlleslgveayKiaSgeltnlpllekiaktgk 114
                                        + ++++k+ +++e+ +el+++c+++gi +  tp++l++v+ l++ + ++  + S  +   + + +i +t +
  gi|557694172|ref|YP_008797226.1| 193 LVKNYMTKYPITQEDAEELAKRCRTRGI-YNGTPYSLHAVKTLRENKRNYGEVVSRYIGVEKTILRITDTSE 263
                                       4557789999*****************9.679***********99998888888888777777777766665 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    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      18      80 ..     144     204 ..     125     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                                       EEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECEEECC CS
                      NTP_transf_2  18 vlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtrekle 80 
                                        + GS    ++++  DiDl+v++ e++   k+ e  ++l  +    e    l    +t++++ 
  gi|557694172|ref|YP_008797226.1| 144 GVSGSLLLRLFNPAADIDLVVYGGENFL--KVVEASYRLQTEKTLAENHAILVKNYMTKYPIT 204
                                       5789999******************987..466666666666666666666666666777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2734.57
//
Query:       gi|557694173|ref|YP_008797227.1|  [L=299]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   25.3   0.0    2.7e-05   24.4   0.0    1.5  1  NTP_transf_2  Nucleotidyltransferase domain
     0.0088   15.8   0.0      0.014   15.2   0.0    1.3  1  MdcG          Phosphoribosyl-dephospho-CoA transferase MdcG
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.028   14.5   0.0    1.4  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 !   24.4   0.0   4.5e-09   2.7e-05      13      50 ..     104     143 ..      91     189 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 4.5e-09
                                       T..TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHH CS
                      NTP_transf_2  13 p..vakvvlfGSyarGtalkgSDiDllvvlpeevsrekke 50 
                                       +  +++   +GS   Gta ++SDiD+++++ +  +r  k+
  gi|557694173|ref|YP_008797227.1| 104 SqaGVEHGFTGSLLLGTADSDSDIDIVIYGGSREYRKLKT 143
                                       2357888899********************9998874222 PP

>> MdcG  Phosphoribosyl-dephospho-CoA transferase MdcG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.4e-06     0.014      61     141 ..      66     136 ..      53     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.4e-06
                              MdcG  61 RlalavapsaiarvveplaLaaalaaaplaaraalaalaallaalglawgvyGSlgwqlatglpylhesSDLDLlir 137
                                       R  +av++++i++v++p +      + p+++ +++++l + l+++g++ g +GSl +       ++ ++SD+D++i+
  gi|557694173|ref|YP_008797227.1|  66 RRVIAVPRRNIKQVITPSKNI----KGPPRLVETAKKLSQVLSQAGVEHGFTGSLLLG------TADSDSDIDIVIY 132
                                       566889999999999999555....57999*************************965......56899******98 PP

                              MdcG 138 vasa 141
                                         s 
  gi|557694173|ref|YP_008797227.1| 133 GGSR 136
                                       6554 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.6e-06     0.028      20      53 ..     114     148 ..      97     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-06
                                       EEEE-S------EEEEEEEESS-.--HHHHHHHHH CS
                           Polbeta  20 GSrakgkareeSDiDlavllkek.ldleeelelaa 53 
                                       GS + g+a ++SDiD+ ++  ++  ++ + l+l++
  gi|557694173|ref|YP_008797227.1| 114 GSLLLGTADSDSDIDIVIYGGSReYRKLKTLRLKN 148
                                       9******************9988544444555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); 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:                         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 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2363.11
//
Query:       gi|557694174|ref|YP_008797228.1|  [L=186]
Description: pyruvate ferredoxin oxidoreductase, gamma subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-31  108.3   0.0    5.9e-31  107.9   0.0    1.1  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 !  107.9   0.0   3.3e-35   5.9e-31       1     174 [.      17     174 ..      17     179 .. 0.91

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 3.3e-35
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHH..HHGGG CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetls..ehldg 75 
                                       GGqGvvta+++la+aa  +G+ vq+++e+g+e++G+++ ++ r+s++pi  + +v++ad +v ++ ++    e  + 
  gi|557694174|ref|YP_008797228.1|  17 GGQGVVTASRMLAEAALLEGKFVQSFPEFGPERSGAPVKAYARVSNTPIEIRAPVEKADTVVYFEGKLTRvyEPTTL 93 
                                       9**********************************************99999999***********888666***** PP

                                       EEEEEEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHT.S-HHHHH CS
                               POR  76 lkpggiiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallg.lpleale 151
                                        +p+g++++     +p+ l++ +           ++v++vd + +++ +++ ++ +N+vmlGa++a+++ ++le+l+
  gi|557694174|ref|YP_008797228.1|  94 TRPNGVVVVSCR--EPSALPRMDG----------LHVFTVDGQHVVESLKR-PLSLNMVMLGATVAATKiVSLETLK 157
                                       ***********6..4677777664..........58**********99999.************************* PP

                                       HHHHCCS-CH.HHHHHHHHHHHH CS
                               POR 152 eaikkrfpkkkeviekNlkafra 174
                                         ++krf   +      +ka+++
  gi|557694174|ref|YP_008797228.1| 158 SLVAKRFSSAD------VKALEK 174
                                       *******9744......444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1481.29
//
Query:       gi|557694175|ref|YP_008797229.1|  [L=86]
Description: pyruvate ferredoxin oxidoreductase, delta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   40.7  20.9    2.3e-05   24.0   8.4    2.1  2  Fer4      4Fe-4S binding domain
      2e-07   30.7  11.9     0.0005   20.0   1.8    2.4  2  Fer4_2    4Fe-4S binding domain
    2.1e-07   31.0  13.3    2.8e-07   30.5  13.3    1.2  1  Fer4_21   4Fe-4S dicluster domain
    2.2e-06   27.7  10.5    3.6e-06   27.0  10.5    1.4  1  Fer4_10   4Fe-4S dicluster domain
    3.1e-06   27.2  13.5    4.4e-06   26.8  13.5    1.2  1  Fer4_9    4Fe-4S dicluster domain
    7.2e-06   26.5  38.3    0.00033   21.2  14.9    2.0  3  Fer4_7    4Fe-4S dicluster domain
    3.5e-05   24.6  11.4      0.064   14.2   0.1    2.2  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00018   21.5  17.7      0.015   15.4   3.4    2.3  2  Fer4_6    4Fe-4S binding domain
     0.0092   16.7  11.1       0.15   12.8   4.9    2.5  2  Fer4_15   4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.02   15.3  10.5        1.1    9.7   0.2    2.2  2  Fer4_8    4Fe-4S dicluster domain
      0.078   13.5  14.4        1.4    9.5   1.6    2.2  2  Fer4_17   4Fe-4S dicluster domain
       0.18   12.4  14.5       0.44   11.1   2.8    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.23   11.3   0.0       0.29   10.9   0.0    1.1  1  REC104    Meiotic recombination protein REC104
       0.46   11.1  14.7        1.7    9.4   1.3    2.4  2  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 !   22.9   4.6     4e-08   5.1e-05       1      23 [.      29      51 ..      29      52 .. 0.94
   2 !   24.0   8.4   1.8e-08   2.3e-05       1      24 []      59      82 ..      59      82 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4e-08
                                      EEEETTTSSS-THHHHHSTTTEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAI 23
                                      +v++++kC++C +C   CP  AI
  gi|557694175|ref|YP_008797229.1| 29 PVVHYDKCTNCLICWIYCPEPAI 51
                                      689*****************999 PP

  == domain 2  score: 24.0 bits;  conditional E-value: 1.8e-08
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      +vid+  C gCG+C+  CP  +I+
  gi|557694175|ref|YP_008797229.1| 59 IVIDYMHCKGCGICAAECPRKCIE 82
                                      69*******************996 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   2.9   8.7e-06     0.011       2      22 .]      28      48 ..      27      48 .. 0.87
   2 !   20.0   1.8   3.9e-07    0.0005       2      21 ..      58      77 ..      57      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.7e-06
                            Fer4_2  2 pvvvdtdrCigCgaCvsa.CPa 22
                                      ++vv  d+C++C +C +  CP+
  gi|557694175|ref|YP_008797229.1| 28 KPVVHYDKCTNCLIC-WIyCPE 48
                                      689999*********.887995 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.9e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      ++v+d  +C gCg+C   CP
  gi|557694175|ref|YP_008797229.1| 58 KIVIDYMHCKGCGICAAECP 77
                                      6899***********999*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 !   30.5  13.3   2.2e-10   2.8e-07       2      59 .]      30      83 ..      29      83 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.2e-10
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedciem 59
                                      +++ dkC +C  C i C++    ai  d++ ++ +   +C GC +C++ CP  +ciem
  gi|557694175|ref|YP_008797229.1| 30 VVHYDKCTNCLICWIYCPE---PAIIRDPSGKIVIDYMHCKGCGICAAECP-RKCIEM 83
                                      6899**************7...89999*****999****************.7****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 !   27.0  10.5   2.8e-09   3.6e-06       2      56 .]      29      77 ..      28      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 2.8e-09
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +v+  d+C++C  C   CP          ++++++++ +++ +C gcg C+++CP
  gi|557694175|ref|YP_008797229.1| 29 PVVHYDKCTNCLICWIYCPE------PAIIRDPSGKIVIDYMHCKGCGICAAECP 77
                                      57789***************......8899999*********************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 !   26.8  13.5   3.4e-09   4.4e-06       1      51 []      35      81 ..      35      81 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.4e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      kCt+C  C   Cp  ++++d +++++   +     C gCg C++ Cp+++i
  gi|557694175|ref|YP_008797229.1| 35 KCTNCLICWIYCPEPAIIRDPSGKIVIDYM----HCKGCGICAAECPRKCI 81
                                      7*******999****************988....5*************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 !   13.8   1.6   5.1e-05     0.065      29      50 ..      27      48 ..       9      50 .. 0.78
   2 !   21.2  14.9   2.6e-07   0.00033       1      51 [.      35      79 ..      35      80 .. 0.94
   3 !   14.1   6.4   4.1e-05     0.053       1      20 [.      65      84 ..      65      86 .] 0.91

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.1e-05
                            Fer4_7 29 ekveidpekClgCgaCvavCPt 50
                                      +k++++++kC++C  C   CP 
  gi|557694175|ref|YP_008797229.1| 27 RKPVVHYDKCTNCLICWIYCPE 48
                                      788999**************96 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 2.6e-07
                            Fer4_7  1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51
                                      +C++C  C  +Cp  ai  d++       k++id++ C gCg C+a+CP +
  gi|557694175|ref|YP_008797229.1| 35 KCTNCLICWIYCPEPAIIRDPS------GKIVIDYMHCKGCGICAAECPRK 79
                                      7******************997......59*******************75 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 4.1e-05
                            Fer4_7  1 rCigCgaCvaaCpvkaield 20
                                      +C gCg C+a Cp k+ie+ 
  gi|557694175|ref|YP_008797229.1| 65 HCKGCGICAAECPRKCIEMV 84
                                      6****************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 !   14.2   0.1     5e-05     0.064       1      23 [.      35      57 ..       7      63 .. 0.85
   2 !   13.5   6.8   8.5e-05      0.11       1      20 [.      65      84 ..      65      86 .] 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkek 23
                                      +C++C  C   CP+ ai  + + 
  gi|557694175|ref|YP_008797229.1| 35 KCTNCLICWIYCPEPAIIRDPSG 57
                                      59999999999999998777554 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 8.5e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C++Cg Ca  CP ++i++ 
  gi|557694175|ref|YP_008797229.1| 65 HCKGCGICAAECPRKCIEMV 84
                                      7****************975 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.4   1.2e-05     0.015       1      24 []      28      51 ..      28      52 .. 0.92
   2 !   11.9   6.5   0.00014      0.18       2      21 ..      59      78 ..      58      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      ++++ +dkC+ C  C + CPe ai
  gi|557694175|ref|YP_008797229.1| 28 KPVVHYDKCTNCLICWIYCPEPAI 51
                                      699*****************9776 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00014
                            Fer4_6  2 veidpdkCigCgdCvrvCPe 21
                                      ++id+  C gCg C++ CP 
  gi|557694175|ref|YP_008797229.1| 59 IVIDYMHCKGCGICAAECPR 78
                                      6666777************6 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 !    7.4   0.4    0.0059       7.5       3      20 ..      31      48 ..      30      58 .. 0.84
   2 !   12.8   4.9   0.00012      0.15       1      20 [.      59      78 ..      59      83 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0059
                           Fer4_15  3 vDrdaCigcglCvaeape 20
                                      v  d+C+ c  C+  +pe
  gi|557694175|ref|YP_008797229.1| 31 VHYDKCTNCLICWIYCPE 48
                                      5579***********986 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00012
                           Fer4_15  1 VvvDrdaCigcglCvaeape 20
                                      +v+D   C gcg C+ae+p+
  gi|557694175|ref|YP_008797229.1| 59 IVIDYMHCKGCGICAAECPR 78
                                      79****************95 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00087       1.1      46      63 ..      31      48 ..       5      50 .. 0.73
   2 ?    9.1   5.1    0.0014       1.8       3      16 ..      64      77 ..      62      85 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00087
                            Fer4_8 46 ealwsCttcgaCtevCpv 63
                                         ++Ct+c  C   Cp+
  gi|557694175|ref|YP_008797229.1| 31 VHYDKCTNCLICWIYCPE 48
                                      457899999999999996 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0014
                            Fer4_8  3 ekCieCgaCqsaCp 16
                                      ++C +Cg C ++Cp
  gi|557694175|ref|YP_008797229.1| 64 MHCKGCGICAAECP 77
                                      56777777777776 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.6    0.0011       1.4      42      58 ..      32      48 ..       6      50 .. 0.78
   2 ?    8.7   6.0     0.002       2.6       2      14 ..      66      78 ..      65      84 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                           Fer4_17 42 kaslCieCgeCerkCPq 58
                                        ++C++C  C  +CP+
  gi|557694175|ref|YP_008797229.1| 32 HYDKCTNCLICWIYCPE 48
                                      56899999999999996 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                           Fer4_17  2 CiqCgyClpeCps 14
                                      C +Cg C++eCp+
  gi|557694175|ref|YP_008797229.1| 66 CKGCGICAAECPR 78
                                      8999999999987 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 ?   11.1   2.8   0.00034      0.44       4      18 ..      34      48 ..      31      61 .. 0.89
   2 ?    7.8   3.1    0.0037       4.8       1      17 [.      61      77 ..      61      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00034
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      d+C++c +C+  +P+
  gi|557694175|ref|YP_008797229.1| 34 DKCTNCLICWIYCPE 48
                                      89************8 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0037
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      +D   C +cg+C++ +P
  gi|557694175|ref|YP_008797229.1| 61 IDYMHCKGCGICAAECP 77
                                      67778************ PP

>> REC104  Meiotic recombination protein REC104
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00022      0.29      45      74 ..      32      61 ..      26      71 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                            REC104 45 efdkaanciltetsypepelkrtastyllk 74
                                       +dk +nc+++++  pep + r+ s  ++ 
  gi|557694175|ref|YP_008797229.1| 32 HYDKCTNCLICWIYCPEPAIIRDPSGKIVI 61
                                      58*********************9998875 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.3    0.0013       1.7       1      15 [.      33      47 ..      33      57 .. 0.91
   2 ?    6.8   6.2    0.0085        11       4      16 ..      66      78 ..      62      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      +++C++C  C ++CP
  gi|557694175|ref|YP_008797229.1| 33 YDKCTNCLICWIYCP 47
                                      59************9 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0085
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C gCg C a CP 
  gi|557694175|ref|YP_008797229.1| 66 CKGCGICAAECPR 78
                                      9***********5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); 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: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 693.31
//
Query:       gi|557694176|ref|YP_008797230.1|  [L=390]
Description: pyruvate ferredoxin oxidoreductase, alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-70  236.2   1.3    5.2e-70  235.8   1.3    1.1  1  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
    1.4e-13   51.0   0.0    3.3e-13   49.8   0.0    1.6  1  PFOR_II       Pyruvate:ferredoxin oxidoreductase core domain 
  ------ inclusion threshold ------
      0.014   15.0   0.8      0.022   14.4   0.8    1.4  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
      0.084   13.4   0.0       0.68   10.5   0.0    2.3  3  Reprolysin_3  Metallo-peptidase family M12B Reprolysin-like


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 !  235.8   1.3   1.2e-73   5.2e-70       1     230 [.      18     241 ..      18     242 .. 0.96

  Alignments for each domain:
  == domain 1  score: 235.8 bits;  conditional E-value: 1.2e-73
                                       .HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCC CS
                             POR_N   1 eaaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmie 77 
                                       +a++ a+vdv+aaYPITP+++i+e+l+e++a+g + d+e+v +esE++a s+++GA+++Gar++TaTS+qGl+Lm+e
  gi|557694176|ref|YP_008797230.1|  18 HAVMDADVDVVAAYPITPQTTIVEKLSEYVASGML-DAEFVPVESEHSALSVCLGASLTGARVFTATSSQGLALMHE 93 
                                       58899*****************************9.9**************************************** PP

                                       CHHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHH..CTSEEEEE CS
                             POR_N  78 nlglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAek..vrvPvivl 152
                                        l++a+g ++P+v+++++Ral+++ ++i++d+sD+m  rd g+i+l++en q+a+d++l+A+++Ae+  v++Pv v 
  gi|557694176|ref|YP_008797230.1|  94 ILYIASGLRTPIVMAIANRALSAP-INIHGDHSDIMGSRDAGWIQLFAENPQQAYDFTLIAYRVAEDnrVMLPVAVN 169
                                       ************************.******************************************99******** PP

                                       EEHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXXSXXXBXXTXXTSSXXEEESBXBXTTSXBXXXXHHHHHHHH CS
                             POR_N 153 fDgfllshevekvelpdeedelklikekleeyerkeyaldpekpiargtaanpdtglehrekgneaedaaekvveev 229
                                       +Dgf++sh +e v+++ +e     ++ +l++  r    l+ e pi++g+ +  +++  ++ ++ +a ++  +vv+ev
  gi|557694176|ref|YP_008797230.1| 170 VDGFTVSHCYEGVRVLGKE----DARAFLPRTPRP--RLEYETPITVGAMFSSMHYHVAKTEQAKALESSLNVVKEV 240
                                       *******************....677777777665..5***************************999999999887 PP

                                       H CS
                             POR_N 230 e 230
                                       +
  gi|557694176|ref|YP_008797230.1| 241 F 241
                                       5 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 !   49.8   0.0   7.5e-17   3.3e-13       3      99 ..     263     357 ..     261     359 .. 0.91

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 7.5e-17
                                       EEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G.-HHHHHHHHHT CS
                           PFOR_II   3 vvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgse.Gqlveevkaal 78 
                                       v++v++G v+gt ++  +      ++vG+  lr++rPFP+++l   l++++ ++vldr++s g++  +l+ ++k+ l
  gi|557694176|ref|YP_008797230.1| 263 VMVVGLGGVMGTFRHLGR-----RMNVGVASLRLYRPFPAADLLPSLREAELIIVLDRAYSPGAPaPPLAADIKTLL 334
                                       578888888888887654.....369***************************************9*********** PP

                                       GGG..TSEEEEEE--GGG----H CS
                           PFOR_II  79 kks..kvkvvnfvaglgGrditv 99 
                                       +    + +v ++v glgG++i++
  gi|557694176|ref|YP_008797230.1| 335 HTAglQTPVWSVVCGLGGHEIRL 357
                                       99999**************9986 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 ?   14.4   0.8   4.9e-06     0.022       1     103 [.      10     115 ..      10     171 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.9e-06
                                       EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT......TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-C CS
                      TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeq.....girvvlarhEqgaafaAdgyaratgkpgvvlvts 72 
                                       m++ ea+++a  +++v++v ++p +  + ++++lse       + ++v + +E +a     g + +tg ++  +++s
  gi|557694176|ref|YP_008797230.1|  10 MSGNEAIAHAVMDADVDVVAAYPITPQTTIVEKLSEYVasgmlDAEFVPVESEHSALSVCLGAS-LTGARVFTATSS 85 
                                       6899********************************9999999*******************75.566555555555 PP

                                       HHHHHHCHHHHHHHHHHT--EEEEEEE--CC CS
                      TPP_enzyme_N  73 gpGatnaltalaeAkvdriPllvlsgdrpts 103
                                         G++ +   l+ A+  r+P+++  ++r+ s
  gi|557694176|ref|YP_008797230.1|  86 -QGLALMHEILYIASGLRTPIVMAIANRALS 115
                                       .589999999999999999999988887665 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 ?   -0.4   0.0      0.36   1.6e+03      59      86 ..      63      93 ..      14     111 .. 0.70
   2 ?   10.5   0.0   0.00015      0.68      44      86 ..     231     273 ..     211     289 .. 0.73
   3 ?   -3.3   0.0       2.7   1.2e+04      64      83 ..     328     352 ..     327     373 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.36
                      Reprolysin_3 59 rgqagyDlvhlftarde...sgvgGlAyvgs 86
                                          +++l++ +t+  +    +++GlA +  
  gi|557694176|ref|YP_008797230.1| 63 HSALSVCLGASLTGARVftaTSSQGLALMHE 93
                                      3566788888888877788888888887754 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00015
                      Reprolysin_3  44 tealdelaevtaeaergqagyDlvhlftardesgvgGlAyvgs 86 
                                       +++l+  +ev++ + ++++gyD+vh+++++    v Gl +v +
  gi|557694176|ref|YP_008797230.1| 231 ESSLNVVKEVFRSYPMREEGYDVVHAVNTDSPVMVVGLGGVMG 273
                                       55566667777778889************99988888877743 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.7
                      Reprolysin_3  64 yDlvhlftarde.....sgvgGlAy 83 
                                       +D+ +l+++        s v+Gl +
  gi|557694176|ref|YP_008797230.1| 328 ADIKTLLHTAGLqtpvwSVVCGLGG 352
                                       6888888887767788888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3096.41
//
Query:       gi|557694177|ref|YP_008797231.1|  [L=311]
Description: pyruvate ferredoxin oxidoreductase, beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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   95.8   0.0    2.7e-27   95.4   0.0    1.2  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


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 !   95.4   0.0   1.5e-31   2.7e-27       2     153 .]      47     208 ..      46     208 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 1.5e-31
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHH.........STTSEEEEEEEHHHHHHT.GGGHHH CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGakla.........kpdrevvaivGDGgflmi.lqelat 67 
                                       +Gcl++++  +     p++ ++ + +++++ ++ +aA+G+++a          +++++++++GDGg+++i lq l+ 
  gi|557694177|ref|YP_008797231.1|  47 TGCLEVVTTPY-----PYTAWNvPWLHVAFENAAAAASGVEAAlkvlerkglGRRHNIIVFAGDGGTFDIgLQSLSG 118
                                       79999966666.....788777699****************944555554433357********************* PP

                                       HHHTT-SEEEEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHH CS
                      TPP_enzyme_C  68 avrrnlpitvvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealk 140
                                       a +r++ +++v+++Ne+y++tg q    +p g++++++pagk++ ++d+  ++ a+G+k +a+ ++  +++l ++++
  gi|557694177|ref|YP_008797231.1| 119 ALERGHRLLFVCYDNEAYMNTGIQrsaATPPGAWSSTTPAGKQESKKDIMSIVIAHGVKyAATATPFLWKDLVNKVA 195
                                       *******************************************9***************888*9************* PP

                                       HHHCSSSEEEEEE CS
                      TPP_enzyme_C 141 ealekkgpaliev 153
                                       +a++ +gpa+++v
  gi|557694177|ref|YP_008797231.1| 196 KAFTFDGPAFLHV 208
                                       ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      732  (0.0408277); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2283.82
//
Query:       gi|557694178|ref|YP_008797232.1|  [L=127]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-21   76.0   0.4    1.7e-21   75.7   0.4    1.2  1  Cupin_2          Cupin domain
    2.1e-09   37.1   0.0    2.9e-09   36.7   0.0    1.2  1  Cupin_1          Cupin
    1.1e-08   35.1   0.1    1.3e-08   34.8   0.1    1.2  1  AraC_binding     AraC-like ligand binding domain
    1.3e-06   28.4   0.0    1.5e-06   28.2   0.0    1.2  1  MannoseP_isomer  Mannose-6-phosphate isomerase
    3.3e-05   23.5   0.1    4.9e-05   22.9   0.1    1.3  1  Cupin_3          Protein of unknown function (DUF861)
    0.00025   20.8   0.0     0.0004   20.2   0.0    1.3  1  EutQ             Ethanolamine utilisation protein EutQ
     0.0014   18.1   0.0      0.012   15.1   0.0    1.9  2  PCO_ADO          PCO_ADO
     0.0021   18.0   0.0     0.0025   17.8   0.0    1.2  1  Pirin            Pirin
      0.004   16.8   0.0      0.026   14.2   0.0    1.9  1  Auxin_BP         Auxin binding protein
     0.0064   16.7   0.0      0.011   15.9   0.0    1.4  1  CENP-C_C         Mif2/CENP-C like
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.018   14.9   0.1    1.4  1  Cupin_7          ChrR Cupin-like domain
      0.086   13.0   0.0      0.094   12.9   0.0    1.1  1  Ectoine_synth    Ectoine synthase
       0.13   12.7   0.0       0.19   12.2   0.0    1.3  1  JmjC             JmjC domain, hydroxylase
       0.14   11.8   0.0       0.16   11.6   0.0    1.2  1  Cupin_6          Cupin


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 !   75.7   0.4   1.4e-24   1.7e-21       3      70 ..      42     109 ..      40     110 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 1.4e-24
                                       EEEETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SSS-EEEEEE CS
                           Cupin_2   3 velppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgdeparllvv 70 
                                       ++++pG+++p+h+Hp+ +++ yVl+Ge e+ +dg +++++ Gd++++pa+t H +rNtg+e+a++l+v
  gi|557694178|ref|YP_008797232.1|  42 FVIKPGGEIPAHSHPDIEHVQYVLRGEYEVVLDGVVHKVKSGDVLFIPAKTVHSYRNTGKEDAEFLCV 109
                                       789****************************************************************9 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   2.3e-12   2.9e-09      33     111 ..      37     107 ..      26     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 2.3e-12
                                       EEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEESSSSEEE CS
                           Cupin_1  33 isaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsgdepava 109
                                       i++ r++++pgg ++ h hp  + ++yvl Ge    +v  g        k++ Gdv+ +Pa  vh   n+g+e+a +
  gi|557694178|ref|YP_008797232.1|  37 IFLRRFVIKPGGEIPAHSHPDIEHVQYVLRGEYE--VVLDG-----VVHKVKSGDVLFIPAKTVHSYRNTGKEDA-E 105
                                       45556666************************99..66666.....56779********************6554.4 PP

                                       EE CS
                           Cupin_1 110 iv 111
                                       + 
  gi|557694178|ref|YP_008797232.1| 106 FL 107
                                       44 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 !   34.8   0.1     1e-11   1.3e-08      12      73 ..      46     108 ..      37     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1e-11
                                       TT-SEEEETT-.SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE-TTSEEEEEE CS
                      AraC_binding  12 pdhsfpphvhd.eyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyesdsedgweyrw 73 
                                       p+ + p h h+   +++yv++G+  + l+g  + +++Gd++++p  ++H+y+  + ++ e+ +
  gi|557694178|ref|YP_008797232.1|  46 PGGEIPAHSHPdIEHVQYVLRGEYEVVLDGVVHKVKSGDVLFIPAKTVHSYRNTGKEDAEFLC 108
                                       666778999998889*************************************99977666554 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.2   0.0   1.1e-09   1.5e-06      61     138 ..      35     112 ..       4     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.1e-09
                   MannoseP_isomer  61 eryqvkritvkPgeklslqkhhhraehWvvvkGtakvtvddevlllkenestyiplgaihrlenpGkiplelievqs 137
                                        +  ++r ++kPg ++  + h        v++G  +v  d  v ++k+ +  +ip+ ++h+  n Gk + e++ v  
  gi|557694178|ref|YP_008797232.1|  35 ANIFLRRFVIKPGGEIPAHSHPDIEHVQYVLRGEYEVVLDGVVHKVKSGDVLFIPAKTVHSYRNTGKEDAEFLCVIR 111
                                       5566899*********99999877666789**************************************999876644 PP

                   MannoseP_isomer 138 G 138
                                       G
  gi|557694178|ref|YP_008797232.1| 112 G 112
                                       4 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 !   22.9   0.1   3.9e-08   4.9e-05      17      66 ..      48     104 ..      42     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.9e-08
                                       EEEEECESS.EEEE.EEEECEEEEEETTTEEEEEETTEEEEE-TTE......EECCCE CS
                           Cupin_3  17 Gkfrltyee.dEfc.yileGevkvtpeggetvelraGDlvvlpkgl......sgtwdv 66 
                                       G+ + +     E++ y+l+Ge +v+  +g  ++++ GD++++p+++      +g+ d+
  gi|557694178|ref|YP_008797232.1|  48 GEIPAHSHPdIEHVqYVLRGEYEVVL-DGVVHKVKSGDVLFIPAKTvhsyrnTGKEDA 104
                                       556666666578888***********.*****************99777766666655 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   3.1e-07    0.0004      96     144 ..      59     109 ..      55     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.1e-07
                              EutQ  96 deidyvieGrldvlidGrkvvaeaGdviliPkgskiefsvt..deakflyv 144
                                       + + yv+ G+ +v+ dG     ++Gdv++iP  +   +  t  ++a fl v
  gi|557694178|ref|YP_008797232.1|  59 EHVQYVLRGEYEVVLDGVVHKVKSGDVLFIPAKTVHSYRNTgkEDAEFLCV 109
                                       6799***************************88766665441145667665 PP

>> PCO_ADO  PCO_ADO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     9e-06     0.012      44      78 ..      37      71 ..      32      83 .. 0.88
   2 ?    2.2   0.0     0.082   1.1e+02     101     147 ..      70     117 ..      67     123 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9e-06
                           PCO_ADO 44 fslgvFvlppgaviPLHdHPgMtvlskllyGslhi 78
                                      + l  Fv++pg  iP H HP    ++ +l G+ ++
  gi|557694178|ref|YP_008797232.1| 37 IFLRRFVIKPGGEIPAHSHPDIEHVQYVLRGEYEV 71
                                      55677************************998765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.082
                           PCO_ADO 101 klvsdeeltapsetsvL.tPteGgnlHeitait.gpaaflDil.sPPYse 147
                                       ++v d+ +++  + +vL  P++   +H  ++   + a fl ++ + PY++
  gi|557694178|ref|YP_008797232.1|  70 EVVLDGVVHKVKSGDVLfIPAK--TVHSYRNTGkEDAEFLCVIrGGPYET 117
                                       6788888777666677768998..99*****9989999999985678875 PP

>> Pirin  Pirin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0     2e-06    0.0025      38      91 ..      43      95 ..       6     109 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2e-06
                                      EE..T-EEEEEEEBSEEEEEEEECSEEEEEETTS-EEEEETT-EEEEE-TT-EEEE CS
                             Pirin 38 vi..gagfpphphrgletvtylleGevehrDslGnkgvirpGdvqwmtAgsGivhs 91
                                      vi  g ++p h h ++e v y+l+Ge e     G  +++++Gdv  + A +  vhs
  gi|557694178|ref|YP_008797232.1| 43 VIkpGGEIPAHSHPDIEHVQYVLRGEYEVV-LDGVVHKVKSGDVLFIPAKT--VHS 95
                                      44667789******************9875.67999999999999988875..444 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0     2e-05     0.026      10     130 ..       3     114 ..       1     122 [. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                                       -SEEEGGGS--B-TT-TTEEEEEEE-HHHH--SSEEEEEEEE-TT-B--EEEE.SS-EEEEEEE--EEEEE--SSSS CS
                          Auxin_BP  10 sivrniselpqdnygreglshitvagsvlhgmkevevwlqtlapgsrtpihrh.sceevfvvlkgkgtlylassssk 85 
                                       ++v+n+ ++   +  ++  + i v      g  ++ +    + pg + p h h   e v  vl+g+  ++l     k
  gi|557694178|ref|YP_008797232.1|   3 AVVKNVVNVEARAVDKSRDAFIQVLVDSRDGSANIFLRRFVIKPGGEIPAHSHpDIEHVQYVLRGEYEVVLDGVVHK 79 
                                       678888888888888888888888888888988888888899***********55899********99999765544 PP

                                       S--S-EEEEE-TTEEEEE-TT--EEEE---SSS-EEEEEEEESSS CS
                          Auxin_BP  86 ypgkpqelpifanstlsipvndahqvkntgehedlqvlviisrpp 130
                                                  +   l ip + +h  +ntg +ed + l +i   p
  gi|557694178|ref|YP_008797232.1|  80 V---------KSGDVLFIPAKTVHSYRNTG-KEDAEFLCVIRGGP 114
                                       3.........34456779999999999999.89999999887666 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 !   15.9   0.0   8.6e-06     0.011      31      81 ..      56     106 ..      41     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.6e-06
                                       -SEEEEEEEEESEEEEEETTEEEEEETT-EEEE-TT-EEEEEE-SSS-EEE CS
                          CENP-C_C  31 kkatlvFyViqGrvevtvsktsfvigkgsvFqvPagneysieNklnkeakl 81 
                                        +   v yV++G+ ev + +  + + +g+v  +Pa    s +N+++++a+ 
  gi|557694178|ref|YP_008797232.1|  56 PDIEHVQYVLRGEYEVVLDGVVHKVKSGDVLFIPAKTVHSYRNTGKEDAEF 106
                                       4556788**************************************999975 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   1.4e-05     0.018      31      57 ..      44      71 ..      23     110 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                      E-TTEE---EE-TT-EEE.EEEEEEEEE CS
                           Cupin_7 31 yapgsafsahkHpggeei.lVLeGvfsd 57
                                      ++pg + +ah+Hp  e++ +VL+G+++ 
  gi|557694178|ref|YP_008797232.1| 44 IKPGGEIPAHSHPDIEHVqYVLRGEYEV 71
                                      69**************9769*****985 PP

>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.3e-05     0.094      38     107 ..      40     110 ..       2     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-05
                                       EEEEE-TT--EEEE-TT-EEEE.EEEE--EEEEETTT--EEEE-TTEEEEETTT-EEEEEESS..-EEEEEEE CS
                     Ectoine_synth  38 hettikagtetelkYknHleav.ycieGegeveeledgevyeikpgtlYlldkhdkHllrakk..elrlvcvF 107
                                        + +ik g e   + +  +e v y+++Ge ev    dg v+++k g++  +  +  H  r +   + + +cv 
  gi|557694178|ref|YP_008797232.1|  40 RRFVIKPGGEIPAHSHPDIEHVqYVLRGEYEVVL--DGVVHKVKSGDVLFIPAKTVHSYRNTGkeDAEFLCVI 110
                                       5567888888888888899987799999998875..8************999999999886433499999985 PP

>> JmjC  JmjC domain, hydroxylase
   #    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      84     105 ..      79     100 ..      62     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                                       EE-TT-EEEE-TT-EEEEEESS CS
                              JmjC  84 vqkpgefVfvfpgayHsvfnlg 105
                                       + k+g+++f++++++Hs  n+g
  gi|557694178|ref|YP_008797232.1|  79 KVKSGDVLFIPAKTVHSYRNTG 100
                                       5799****************98 PP

>> Cupin_6  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.16      34      73 ..      59      96 ..      35     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                           Cupin_6 34 lalhvvlrGscwlidpasgepvrLsagdvvllpggephvl 73
                                       ++  vlrG+  +++++     +++ gdv+++p ++ h  
  gi|557694178|ref|YP_008797232.1| 59 EHVQYVLRGEYEVVLDG--VVHKVKSGDVLFIPAKTVHSY 96
                                      68899*********888..679************998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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):              14  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 847.66
//
Query:       gi|557694179|ref|YP_008797233.1|  [L=119]
Description: hypothetical protein CSUB_C0745 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 837.18
//
Query:       gi|557694180|ref|YP_008797234.1|  [L=130]
Description: hypothetical protein CSUB_C0746 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   37.0   0.1    5.5e-09   36.4   0.1    1.3  1  HTH_27          Winged helix DNA-binding domain
    6.7e-06   25.9   0.1    1.1e-05   25.2   0.1    1.3  1  TrmB            Sugar-specific transcriptional regulator TrmB
    8.3e-06   25.5   0.3    1.6e-05   24.6   0.3    1.5  1  HTH_IclR        IclR helix-turn-helix domain
    1.6e-05   24.7   0.0    2.5e-05   24.1   0.0    1.3  1  MarR            MarR family
    4.1e-05   23.5   0.0    6.2e-05   22.9   0.0    1.3  1  HTH_45          Winged helix-turn-helix
    0.00029   20.7   0.1    0.00072   19.4   0.1    1.6  1  MarR_2          MarR family
     0.0008   19.3   0.1     0.0016   18.4   0.1    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00095   19.5   0.0     0.0017   18.6   0.0    1.4  1  Rrf2            Transcriptional regulator
     0.0076   16.4   0.0      0.016   15.4   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.009   15.6   0.0      0.015   14.8   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.015   15.2   0.3      0.036   14.0   0.3    1.7  1  HTH_12          Ribonuclease R winged-helix domain
       0.02   15.0   0.0      0.035   14.2   0.0    1.4  1  S10_plectin     Plectin/S10 domain
       0.11   12.9   0.3       0.21   11.9   0.0    1.6  2  ANT             Phage antirepressor protein KilAC domain
       0.12   12.3   0.1       0.19   11.6   0.1    1.3  1  TFIIE_alpha     TFIIE alpha subunit


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 !   36.4   0.1   4.3e-12   5.5e-09       5      68 .]      65     122 ..      61     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 4.3e-12
                            HTH_27   5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                         + L+li+ +r+++  +d++++ln++  h++  lk L+ +G+v+r+g++      r+ lT+kG
  gi|557694180|ref|YP_008797234.1|  65 ALAALRLIE-ERGEVMSSDVSKALNLSREHTARLLKSLHDRGYVKREGKP-----FRYMLTEKG 122
                                       556799***.**********************************888888.....********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 !   25.2   0.1   8.6e-09   1.1e-05      18      63 ..      72     117 ..      65     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 8.6e-09
                                       H.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEE CS
                              TrmB  18 l.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYr 63 
                                       + ++g+   ++++++l+++r    + L+sL d+G+V+re g+p +Y 
  gi|557694180|ref|YP_008797234.1|  72 IeERGEVMSSDVSKALNLSREHTARLLKSLHDRGYVKRE-GKPFRYM 117
                                       457899999*****************************9.8888885 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 !   24.6   0.3   1.3e-08   1.6e-05       5      52 .]      65     111 ..      65     111 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-08
                                       HHHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR   5 alaiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52 
                                       ala L++++e+++    s++++++ l++  + RlL++L+ +Gyv+++g
  gi|557694180|ref|YP_008797234.1|  65 ALAALRLIEERGEV-MSSDVSKALNLSREHTARLLKSLHDRGYVKREG 111
                                       68889999999995.69****************************975 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0     2e-08   2.5e-05       4      52 ..      64     112 ..      61     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2e-08
                                       HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR   4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                                       + + +Lr+++e+g+   s+  k+l++s+ ++ r+l+ L ++G+++R+ +
  gi|557694180|ref|YP_008797234.1|  64 SALAALRLIEERGEVMSSDVSKALNLSREHTARLLKSLHDRGYVKREGK 112
                                       67889*****************************************865 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.8e-08   6.2e-05      12      67 ..      69     127 ..      65     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.8e-08
                            HTH_45  12 Leais.egeakkTkimykanLsykllnkYLdmLvekglikkske..kYvlTekGlelle 67 
                                       L+ i+ +ge   + + ++ nLs + + + L+ L ++g++k +++   Y+lTekGl  ++
  gi|557694180|ref|YP_008797234.1|  69 LRLIEeRGEVMSSDVSKALNLSREHTARLLKSLHDRGYVKREGKpfRYMLTEKGLAAVK 127
                                       56666456677788999**********************775553389******98765 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   5.6e-07   0.00072       3      54 ..      61     110 ..      59     113 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.6e-07
                                       --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       l p+ + +L  +  r++  +  +++ ++l+ls+  + r+lk L ++G+v r+
  gi|557694180|ref|YP_008797234.1|  61 LHPSALAALRLIEERGE--VMSSDVSKALNLSREHTARLLKSLHDRGYVKRE 110
                                       67888899999999999..9*****************************998 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 !   18.4   0.1   1.2e-06    0.0016      25      55 ..      81     111 ..      64     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.2e-06
                                       HHHHHHTTSSHHHHHHHHHHHHHTTSEEETE CS
                         HTH_Crp_2  25 eelAsmlGltretvsrilseLkreglisrgr 55 
                                        + +  l+l+re++ r+l+ L ++g+++r++
  gi|557694180|ref|YP_008797234.1|  81 SDVSKALNLSREHTARLLKSLHDRGYVKREG 111
                                       578899**********************643 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.4e-06    0.0017      13      59 ..      65     110 ..      59     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                                       HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2  13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59 
                                       al+ L + ee++ v s+++++  n+s+++ +++l+ L   g+vk ++
  gi|557694180|ref|YP_008797234.1|  65 ALAALRLIEERGEVMSSDVSKALNLSREHTARLLKSLHDRGYVK-RE 110
                                       6788888888888******************************8.44 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 !   15.4   0.0   1.3e-05     0.016      14      56 ..      69     111 ..      66     113 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                                       HHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                    Fe_dep_repress  14 YtlseekkvvktkdlaerLnvspssVsemlkkLekdGyveyek 56 
                                       ++l ee++ v  +d++++Ln s       lk L++ Gyv+ e+
  gi|557694180|ref|YP_008797234.1|  69 LRLIEERGEVMSSDVSKALNLSREHTARLLKSLHDRGYVKREG 111
                                       5899***********************************9876 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 !   14.8   0.0   1.2e-05     0.015       9      48 .]      69     108 ..      62     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                            HTH_24   9 LelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       L+l+++ +    ++++++l+lS+  + r lk L + G++k
  gi|557694180|ref|YP_008797234.1|  69 LRLIEERGEVMSSDVSKALNLSREHTARLLKSLHDRGYVK 108
                                       8888999999999*************************97 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 ?   14.0   0.3   2.8e-05     0.036       4      64 ..      69     124 ..      66     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.8e-05
                            HTH_12   4 LkilaesdkpigakeiaeeLkkrgydigeravRyrLrkleergltrrvgya.greltEkGle 64 
                                       L++++e+ +++++  + + L++  +        + L++l +rg+++r g+     ltEkGl 
  gi|557694180|ref|YP_008797234.1|  69 LRLIEERGEVMSS-DVSKALNLSREHT-----ARLLKSLHDRGYVKREGKPfRYMLTEKGLA 124
                                       7888999997776.5788888875555.....478***************96668*****96 PP

>> S10_plectin  Plectin/S10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-05     0.035      31      78 ..      85     130 .]      71     130 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-05
                                       SSS---HHHHHHHHHHCCCCTSEEEEEETTEEEEEE-HHHHHHHHHHH CS
                       S10_plectin  31 eelnvpnlqvikalqSLksrgyvkeqfaWrhyYytLtneGieylreyl 78 
                                       + ln++  +  ++l+SL++rgyvk++   + + y+Lt++G++ ++++l
  gi|557694180|ref|YP_008797234.1|  85 KALNLSREHTARLLKSLHDRGYVKREG--KPFRYMLTEKGLAAVKSKL 130
                                       566888889999************985..68899******99998876 PP

>> ANT  Phage antirepressor protein KilAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       4.2   5.4e+03      67      77 ..      29      39 ..      21      49 .. 0.52
   2 ?   11.9   0.0   0.00017      0.21       4      63 ..      58     120 ..      56     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.2
                               ANT 67 dkglfevktqt 77
                                      + g+++ k q 
  gi|557694180|ref|YP_008797234.1| 29 HHGVTQQKSQQ 39
                                      33444444444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00017
                               ANT   4 laelaPkaeyaDrvlesdgsititeiAkllg...igenrlfelLrekgilyrqkgsgqnlpyq 63 
                                       l++l P a +a r++e  g +   ++ k l+       rl + L+++g++ r+ +  +++++ 
  gi|557694180|ref|YP_008797234.1|  58 LEALHPSALAALRLIEERGEVMSSDVSKALNlsrEHTARLLKSLHDRGYVKREGKPFRYMLTE 120
                                       7999***************************444445689999999***99974444666655 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00015      0.19      14      58 ..      64     108 ..      56     112 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha  14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58 
                                       +a  +l  + e+gev   d++k l++ ++   +lL  L + + vk
  gi|557694180|ref|YP_008797234.1|  64 SALAALRLIEERGEVMSSDVSKALNLSREHTARLLKSLHDRGYVK 108
                                       6778899999******************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      728  (0.0406046); 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: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 945.48
//
Query:       gi|557694181|ref|YP_008797235.1|  [L=428]
Description: hydroxymethylpyrimidine transporter [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-27   96.2  37.4    2.2e-27   95.9  37.4    1.0  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 !   95.9  37.4   1.2e-31   2.2e-27       1     417 [.      13     398 ..      13     418 .. 0.86

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 1.2e-31
                    Transp_cyt_pur   1 pvpeeeRtwktlnlfsiWlganlnintwvigalglalgLnwwqsvlviivgnligaifvallglaGakyGlpfpils 77 
                                       pvpe+ R  + +++f++W   +l + ++v++a+ +   L+++++++v ++g++ig  ++a++g++G++yG+p++++ 
  gi|557694181|ref|YP_008797235.1|  13 PVPENTRILRFFDYFVLWS--SLGVGLLVMVAGSFLSSLSFFEVLAVSLAGSVIGSLMLASAGVVGSRYGVPTMVSL 87 
                                       8*****************6..57889999999998889*************************************** PP

                    Transp_cyt_pur  78 RasfGirgsllplllrvviaivwfgvqawiGsealllmlgkifgkwleiggailgtsltelvtffifwvvslvivll 154
                                       R + G rgs +p +l +v  i+w+g   +i ++a  ++ g +fg           +s   +v +f  w + l ++  
  gi|557694181|ref|YP_008797235.1|  88 RPVLGLRGSYIPTVLNIVQLIGWTGFEIMIMAQAAGVLTGWLFG----------DLSFPLWVVVFSLWCLLL-ALGG 153
                                       *******************************************9..........688889999999998755.5667 PP

                    Transp_cyt_pur 155 gvskirk.ffviaallvpvaafgfliwalvkaegGpvldkavklgkselflsavagvlagfatlilnapDFtryakt 230
                                       +   +rk ++ +a+ lv++ ++ +   ++  +++G+ l  ++k+ +   +l a+  v+a ++++ ++++D+ r+a +
  gi|557694181|ref|YP_008797235.1| 154 PLAVVRKwLERYAIWLVYISSIWITYLVATSPGVGQWLT-GGKPDA-MPLLLALDIVVAMPVSWWPLVSDYNRFAAR 228
                                       777787746789999999999888888888888899998.556663.3799************************** PP

                    Transp_cyt_pur 231 kkssvkiqlvavpllftlllligilvaaaakaayganawspldilakfdetagvllililvalaqlgvnisanllsa 307
                                         ss ++ l+++ +++t ++l+g+  +a+  + +  +a  +l     f+ +     +++++ l     n +a ++s+
  gi|557694181|ref|YP_008797235.1| 229 SSSSFWGTLSGYTVANTWFYLLGAGLVAVLGINDIISAIGTL-----FLGN-----AALILILVDETDNGFADIYSS 295
                                       ***********************9999999999999999999.....9999.....3334444445568899***** PP

                    Transp_cyt_pur 308 gldlaallPkkinikrgsliaavialvivpwkllssssklftaflsllavflspvagviiadyfvvrrgylklaaly 384
                                       +  +++++Pk+     +++ +a+ al+   + ll+ + +     l l++ ++ p  g + a++f++rr +    + +
  gi|557694181|ref|YP_008797235.1| 296 AVSFQNIFPKTPQWVFAAFTTAAGALLALTVPLLQYEWF-----LLLIGSLFVPLLGAMTAEFFINRRNNPPTVDEF 367
                                       *********999999999999999999999999977666.....99**********************998877777 PP

                    Transp_cyt_pur 385 trrrgsaYwyrkgvNwravaayivGiaaglvgv 417
                                       +  + s+ ++r+ v+w a + + v+i+   + +
  gi|557694181|ref|YP_008797235.1| 368 Y--QPSRVKIRGFVSWIAGIMVYVAIVQLAPNI 398
                                       7..799989888888888666655554433332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); 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:                         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 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 3009.09
//
Query:       gi|557694182|ref|YP_008797236.1|  [L=250]
Description: DNA primase large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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   85.1   0.2    1.1e-23   84.1   0.2    1.5  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
  ------ inclusion threshold ------
      0.089   12.7   0.1        0.8    9.6   0.0    2.1  2  Phage_integr_3   Archaeal phage integrase


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 !   84.1   0.2   1.2e-27   1.1e-23       2     219 ..      51     240 ..      50     250 .] 0.80

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 1.2e-27
                                       EEEEEHHHHHHHTT..-G.......GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---H CS
                   DNA_primase_lrg   2 fykvpfedvldlvk..rr.......rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikedere 69 
                                       +y+++f+d+l+l++  +r       ++ l +G++yl+++ l +ll++   ++l +++e t++  +          ++
  gi|557694182|ref|YP_008797236.1|  51 EYMIRFTDYLRLAQdlTRelswklvNQKLSRGWVYLTRTRLTRLLRQYLYQELVRSFETTRRLAKPP--------EK 119
                                       89************88668**************************************9977764443........33 PP

                                       HHHHHHCT--.............TTSSTTGGSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CHH CS
                   DNA_primase_lrg  70 kleellealsesyvaedvqeeedskisaknidklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglslde 146
                                       + +++ e ++                + ++ +  +k+ +PpCm +++e+l   +  +h++ + l++ l + g++++e
  gi|557694182|ref|YP_008797236.1| 120 IAQAMAEVVK----------------NWQRQAPATKGILPPCMIAIHERL---SDTSHTENFILAAHLLSSGYTVEE 177
                                       3344444444................2223367899**************...77889999**************** PP

                                       HHCCCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S..-HHHH.HHHHHHHHH CS
                   DNA_primase_lrg 147 ilelwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg..CpfrhdpdklktlLq 219
                                       ++++++        +F +   ry+++h++G  g+r++y p+sC+++ + +      ++g  Cp      ++++ Lq
  gi|557694182|ref|YP_008797236.1| 178 VVNIFRIR-----SDFREdIARYQVEHIAGLRGSRVKYRPPSCQRMRELN---LCVQNGrlCP-----PNIRNPLQ 240
                                       *******7.....9****9999************************3222...2233333364.....55555555 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1     0.055   4.9e+02      74     114 ..      83     133 ..      59     143 .. 0.68
   2 ?    9.6   0.0   8.9e-05       0.8      21      88 ..     159     221 ..     144     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.055
                                       EEEESS---....--B--HHHHHHHHHT-T..........--GHHHHHHHH CS
                    Phage_integr_3  74 yiylptelakelerlelseeavkefeakkk..........vkakyiRkwva 114
                                       ++yl +   ++l r +l +e v++fe  +             a+++++w  
  gi|557694182|ref|YP_008797236.1|  83 WVYLTRTRLTRLLRQYLYQELVRSFETTRRlakppekiaqAMAEVVKNWQR 133
                                       777766555455555888888887777665556666665555666666665 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 8.9e-05
                                       HHHHHHHHHHHHH---HHHHHHHHHS..GGG-EEETTEEEEEEEE-SSS-EEEEEEESS---....-- CS
                    Phage_integr_3  21 eevelvykllvfsGiRLkevlklLreyDpekliveddiarYpialekgeKkafyiylptelakelerl 88 
                                        e  +++  l+ sG   +ev++++r     +    +diarY++++  g + +   y p + + ++++l
  gi|557694182|ref|YP_008797236.1| 159 TENFILAAHLLSSGYTVEEVVNIFRI----RSDFREDIARYQVEHIAGLRGSRVKYRPPSCQ-RMREL 221
                                       35557788899**************9....677789***********999999999988777.55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1891.22
//
Query:       gi|557694183|ref|YP_008797237.1|  [L=1030]
Description: type II restriction enzyme, methylase subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-07   32.3   0.0    3.5e-07   30.7   0.0    1.8  1  Eco57I    Eco57I restriction-modification methylase
    4.2e-07   29.5   0.0      0.061   12.6   0.0    3.2  3  N6_Mtase  N-6 DNA Methylase
  ------ inclusion threshold ------
      0.027   14.4   0.5      0.062   13.2   0.5    1.5  1  TMEM239   Transmembrane protein 239 family
       0.13   12.4   0.0       0.39   10.8   0.0    1.9  1  DUF5343   Family of unknown function (DUF5343)


Domain annotation for each model (and alignments):
>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   7.9e-11   3.5e-07       4      63 ..     564     632 ..     561     666 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 7.9e-11
                            Eco57I   4 dviiGNPPYqeseak.kelkaleek.........akdiyqkFvekalkle.dkylaliip.arflasgkglk 63 
                                       d+++ NPPY ++e++ k++k+   +         ++diy +F+ +alkl  ++  a+ii+  ++l+ g glk
  gi|557694183|ref|YP_008797237.1| 564 DIVVMNPPYVRQEKIpKNVKE---HyvksygldrTSDIYAYFMVRALKLLnERGAAVIISsDKWLEVGYGLK 632
                                       9**********9954233443...3456899999**************99755555555559***7766554 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.018        80       6      40 ..     311     342 ..     307     365 .. 0.73
   2 !   12.6   0.0   1.4e-05     0.061      49     102 ..     393     462 ..     381     471 .. 0.83
   3 !   10.4   0.0   6.1e-05      0.28     124     188 ..     561     625 ..     548     698 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.018
                          N6_Mtase   6 lGdvYEyllrkfaeeegksgGeffTPrevsklive 40 
                                       lG v E +l +    e  ++G f+TP + +++i +
  gi|557694183|ref|YP_008797237.1| 311 LGTVLENMLPEH---ERGEKGTFYTPVSEISFICR 342
                                       666777776665...66777******887777765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.4e-05
                          N6_Mtase  49 svyDpacGsggllvqaekvlkee................dgktkelsiyGqeknettyrLakmNlllhgi 102
                                       +v Dpa+Gsgg+lv + + + +                  +++   ++yG +++++++++a++ l l  i
  gi|557694183|ref|YP_008797237.1| 393 KVCDPAVGSGGFLVVMMQTILSLvqeveealgwradpaiYKSRILPNLYGFDIEPEAVEIARLRLWLSLI 462
                                       699***********99998876567789999999988887888888999999999999999998887655 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 6.1e-05
                          N6_Mtase 124 kkfdvvvaNppfnqkewkektlekderfrea.vapksnadla.fllhiieslkpkGraavvlangvL 188
                                       ++ d+vv Npp+  +e   k + k+++ +++ +  +s   +a f+  +++ l++ G a ++  +  L
  gi|557694183|ref|YP_008797237.1| 561 SRPDIVVMNPPYVRQEKIPK-NVKEHYVKSYgLDRTSDI-YAyFMVRALKLLNERGAAVIISSDKWL 625
                                       5679*********9954333.334443444435555544.555999**********77777666555 PP

>> TMEM239  Transmembrane protein 239 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   1.4e-05     0.062      18     101 ..     837     919 ..     832     931 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                           TMEM239  18 glrqawrawvlrrawvrwwvspnss.rrrwitwcsssnwrvplqrllwllesilylllalglchalfttgshllrsl 93 
                                       g +q ++   + ra + ww  p+    +  +t+ s + ++vpl r   l + +ly l +  +     tt   l ++l
  gi|557694183|ref|YP_008797237.1| 837 GEQQGYHQRPTCRARNPWWALPQFQpAHILLTYLSQARYFVPLARESVLCDHLLYALYTKNINE--TTTWVFLNSTL 911
                                       7899999999***********98651466789*************************9998876..58999999999 PP

                           TMEM239  94 wpvvaavw 101
                                       + vva ++
  gi|557694183|ref|YP_008797237.1| 912 FYVVAELF 919
                                       99999876 PP

>> DUF5343  Family of unknown function (DUF5343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   8.8e-05      0.39      16      68 ..     573     625 ..     570     676 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8.8e-05
                           DUF5343  16 irkanlPekvtqdflktlglkssnasliiplLkflGfldedGkptelykelrn 68 
                                       +r++++P++v++  +k++gl  +++ ++  + ++l +l+e G++  + ++  +
  gi|557694183|ref|YP_008797237.1| 573 VRQEKIPKNVKEHYVKSYGLDRTSDIYAYFMVRALKLLNERGAAVIISSDKWL 625
                                       6899**************************************98666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1030 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.71u 0.31s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 6850.10
//
Query:       gi|557694184|ref|YP_008797238.1|  [L=1017]
Description: DNA/RNA helicase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   61.7   0.0    2.9e-16   59.8   0.0    2.1  1  Helicase_C       Helicase conserved C-terminal domain
    5.1e-13   49.1   0.2    3.7e-11   43.0   0.0    3.0  3  PLDc_2           PLD-like domain
    6.8e-13   48.1   5.9    2.5e-08   33.0   0.3    2.7  3  SNF2_N           SNF2 family N-terminal domain
    1.2e-12   48.2   2.2    6.4e-06   26.3   0.1    3.3  3  ResIII           Type III restriction enzyme, res subunit
    1.1e-06   29.0   0.7    4.9e-06   26.9   0.0    2.5  2  AAA_22           AAA domain
    4.1e-05   23.4   0.4     0.0061   16.4   0.4    2.7  1  DEAD             DEAD/DEAH box helicase
     0.0016   18.2   0.0      0.004   16.9   0.0    1.6  1  AAA_30           AAA domain
     0.0018   18.3   0.1     0.0063   16.5   0.1    1.9  1  Flavi_DEAD       Flavivirus DEAD domain
  ------ inclusion threshold ------
      0.012   14.9   0.2       0.07   12.4   0.0    2.2  2  RE_NgoFVII       NgoFVII restriction endonuclease
      0.014   14.7   0.0      0.073   12.3   0.0    2.2  1  DUF2075          Uncharacterized conserved protein (DUF2075)
      0.018   15.5   0.6       0.21   12.0   0.0    3.1  3  AAA              ATPase family associated with various cellul
      0.023   14.7   0.6       0.15   12.1   0.6    2.5  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.024   14.4   0.2        1.6    8.4   0.2    2.9  1  IstB_IS21        IstB-like ATP binding protein
      0.033   14.0   0.5       0.77    9.5   0.5    2.7  1  AAA_26           AAA domain
       0.11   12.1   0.5       0.36   10.4   0.1    2.1  2  SRP54            SRP54-type protein, GTPase domain
       0.13   12.4   0.5        2.7    8.2   0.1    3.1  2  Tae4             Type VI secretion system (T6SS), amidase eff
        1.3    8.9   5.9         13    5.8   0.2    4.3  4  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   2.7e-19   2.9e-16       4     111 .]     614     730 ..     611     730 .. 0.74

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 2.7e-19
                                       HHHHHHH....HHTTTTSEEEEEESSHHHHHHHHHH...HHHTTSTEEEESTTSTHHHHH......HHHHHHHTTSS CS
                        Helicase_C   4 eallell....kleeeggkilifvntidrlekvkll...lekkgikvavlhgelpqnere......eileqfnkges 67 
                                       eall +l    k+  +++ i+if++++d+++   +l   l++ + +++ ++g+   n+        e++e f +++ 
  gi|557694184|ref|YP_008797238.1| 614 EALLTELktlaKKLTNNNGIIIFTQYVDTAS---YLfnhLKTIHQQTLLVTGRGGENSSGkrldeaEAVELF-QKNG 686
                                       5555555566688899999*********994...44232233367777777775555555222444555555.5566 PP

                                       SEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  68 dvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        ++++tdv++ G +++++++Vin+d+p+n+ ++iqr+GR+ R+g
  gi|557694184|ref|YP_008797238.1| 687 GIMVSTDVLSAGQNLQNAQHVINYDFPWNPVTLIQRAGRIDRIG 730
                                       7***************************************9986 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   3.5e-14   3.7e-11       3     133 .]      18     166 ..      16     166 .. 0.69
   2 ?   -2.6   0.0       4.4   4.7e+03      79      87 ..     643     653 ..     597     710 .. 0.64
   3 ?    2.4   0.1      0.12   1.3e+02      22      61 ..     939     977 ..     917    1006 .. 0.75

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 3.5e-14
                            PLDc_2   3 qliksAkksidiatyyfvsdreildallk.aakrgvkvrilldskkd.........dagavdeaslkelkellleag 69 
                                       +++++  ++i iat yf  + + + ++ + +a++   +r+ll++  +          + +++++   ++ +l l+  
  gi|557694184|ref|YP_008797238.1|  18 KELQE-ASEIAIATAYF--NITGFGDIEQgLADK--PLRLLLGRPPTeqieweeevLHELEEYEDDPHYFKL-LQRA 88 
                                       56666.57899999999..333345555545544..599999984337777777774455555555555555.3344 PP

                            PLDc_2  70 vevrvfet..ll......gslHaKlyli.dgk.......tvivGSsNltkrgldlnlElnvviedkelakeleeeFe 130
                                       ++  +fe+  ++      +++H K++l  + +        +ivGSsN+t+ gl+ n+Eln++++ ++ ++el+e+F+
  gi|557694184|ref|YP_008797238.1|  89 IQ--FFEQpsRQvrivdgKFFHGKAFLGvHPSfkevrrgFAIVGSSNFTHGGLTTNRELNMFTTERQTVQELAEWFQ 163
                                       55..33322311344557899***999736446667778************************************** PP

                            PLDc_2 131 rlw 133
                                       + w
  gi|557694184|ref|YP_008797238.1| 164 QQW 166
                                       999 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.4
                            PLDc_2  79 l..gslHaKly 87 
                                           ++H K++
  gi|557694184|ref|YP_008797238.1| 643 AsyLFNHLKTI 653
                                       12334455543 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.12
                            PLDc_2  22 dreildallkaakrgvkvrilldskkddagavdeaslkel 61 
                                        rei+dal k+ ++g k+  ++ ++++++++v+ + +k l
  gi|557694184|ref|YP_008797238.1| 939 IREIYDALEKTGEEGIKLAAIFKKHANNPNIVK-QLKKAL 977
                                       4789********************888666655.333333 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 !   17.4   0.1   1.3e-06    0.0014      57     117 ..     238     286 ..     228     288 .. 0.78
   2 !   33.0   0.3   2.4e-11   2.5e-08     174     308 ..     313     459 ..     286     499 .. 0.77
   3 ?   -3.4   0.1       2.8   2.9e+03     284     340 ..     572     623 ..     566     633 .. 0.60

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                       -EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHH.HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                            SNF2_N  57 GGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslld.qWeneier 117
                                       G ++aD +GLGKT+++lal +   + ++ +          + tL+++P+s+ld  W++e+e+
  gi|557694184|ref|YP_008797238.1| 238 GVVIADSTGLGKTLTALALAH---Y-YKGQG---------VRTLLIAPKSILDtTWKTEMEK 286
                                       5579***************99...3.22222.........349******999746***9986 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 2.4e-11
                                       -S-S-SEEEES-GGGT--TTSHHHHHHHH--...-S-EEEE-S--SSS-HHHHH.HHHHHH-TT.TT--.HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxx.xxxxxxx RF
                            SNF2_N 174 kqvewkrvvlDEghtlknstskaaeavskLs...tsnrwiltGTPiqnsledly.gLlkfLree.pfge.kqtfdkl 244
                                       +q+++  +++DE+h ++  +++ ++a+ +L+   + + +++t+TP+  sl dly  +  +L+e+ +++e ++t ++ 
  gi|557694184|ref|YP_008797238.1| 313 NQKKIGLIIVDEAHYFRHPATNRYNALYRLVkmtNAKLVLMTATPVNTSLMDLYhIMALYLNEDaIYDEyRTTLRDY 389
                                       5778999************9888888888766636666778*************66667798873688855599999 PP

                                       THHHHHHHHHHHHHHHHTT-STTEE---GGGT.......--S---EEEEEEEEE--HHHHHHHH....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 245 lqrpieaqaekgrsrLlqllqrlmlrrakkdv.......eknlPpkteeiiflklskverksYnrllevlr 308
                                       + ++ ++  ++    + ++l+++++r++ +          + +P++  ++i+ +l    +k+Yn +l++l 
  gi|557694184|ref|YP_008797238.1| 390 FIQNQKKWLNNEPVDMDDILRKFVVRHSRQLAkaldregRIRFPERLLHTIHYDLPIDVEKLYN-ILDSLN 459
                                       99999999999999************99875555566545579999999999999999999999.554444 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.8
                                       EEEEEEEE--HHHHHHHH....................HHHHHH-HHH-HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 284 teeiiflklskverksYnrllevlrkkalakllkrseaalkssskskekilelllel 340
                                       +  ++++kls++e++ + +  +   kk+   l +  +   k +      +l  l  l
  gi|557694184|ref|YP_008797238.1| 572 IHLLRRCKLSEEEARQFIEKNQEDLKKINEILAMLPKQDPKLEA-----LLTELKTL 623
                                       55678899999999999876666666665555444333333333.....44444444 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 !   26.3   0.1   6.1e-09   6.4e-06       3      79 ..     217     289 ..     215     307 .. 0.83
   2 !   20.9   0.1   2.7e-07   0.00028     110     169 ..     296     357 ..     286     359 .. 0.65
   3 ?   -3.4   0.1       8.2   8.6e+03     102     115 ..     611     624 ..     572     650 .. 0.43

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 6.1e-09
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                       +l+++Q+    + l+k+  +    ++i+  TG GKTl+a++l+ +++ +g   ++l+++p+ +l   +++e++k+  
  gi|557694184|ref|YP_008797238.1| 217 DLYPHQQLTFVDALDKI--ETYGGVVIADSTGLGKTLTALALAHYYKGQGV--RTLLIAPKSILDTTWKTEMEKTDI 289
                                       57888888888888888..4777889*********************9877..9****************9988765 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.7e-07
                                       EHHHHHHTH........HHHTTT-S..EEEEETGGGTTS...TTTHHH..HHT---SEEEEEESS- CS
                            ResIII 110 tiqsldadseeeeeeseellrdrfd..viiiDEaHrlgak..kswrei..lekfkeavllglTATp 169
                                       + ++l+ad    e+ ++ l+ ++++  +ii+DEaH ++    + ++++  l k+ +a+l+ +TATp
  gi|557694184|ref|YP_008797238.1| 296 NSEKLSADP---ESINHYLD-NQKKigLIIVDEAHYFRHPatNRYNALyrLVKMTNAKLVLMTATP 357
                                       333333333...44444444.333347**********99754477777776677889********9 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 8.2
                                       ..-SEEEEEHHHHH CS
                            ResIII 102 tnkkilvttiqsld 115
                                        + + l+t+ ++l 
  gi|557694184|ref|YP_008797238.1| 611 PKLEALLTELKTLA 624
                                       22222222222222 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   4.6e-09   4.9e-06      14     129 ..     245     354 ..     234     361 .. 0.83
   2 ?   -2.6   0.0       5.7     6e+03      76      76 ..     967     967 ..     905    1011 .. 0.50

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.6e-09
                            AAA_22  14 sGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst..sskdllrellralglelkaerlsseellealeqalra 88 
                                       +G GKT+++  l++ ++ +      +++++++ ++s    ++k+ +++    + +  ++   ++++  e ++++l++
  gi|557694184|ref|YP_008797238.1| 245 TGLGKTLTALALAHYYKGQ------GVRTLLIAPKSILdtTWKTEMEKTDITIINTINS--EKLSADPESINHYLDN 313
                                       7*************99655......8888877777633448888888888877777777..7888999********* PP

                            AAA_22  89 ravielliiDEaqhlr.s.eealeeLrsllnlsrkgvqliLvG 129
                                       +++i+l+i+DEa+++r +  + ++ L +l++   ++ +l+L+ 
  gi|557694184|ref|YP_008797238.1| 314 QKKIGLIIVDEAHYFRhPaTNRYNALYRLVK--MTNAKLVLMT 354
                                       ***************8625999999999999..******9985 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.7
                            AAA_22  76 e 76 
                                        
  gi|557694184|ref|YP_008797238.1| 967 P 967
                                       2 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   5.7e-06    0.0061       9     170 ..     231     358 ..     219     365 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.7e-06
                                       HHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   9 plilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggv 85 
                                       + i + g v++a  TG GKTl +l  +    y   + +g ++l+++P   L     ++++k   +    +  +i+  
  gi|557694184|ref|YP_008797238.1| 231 DKIETYGGVVIADSTGLGKTLTALALAH--YY---KGQGVRTLLIAPKSILDTTWKTEMEKTDIT----IINTIN-- 296
                                       3344557899***********9876665..55...58999********99988777777665553....322222.. PP

                                       SHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  86 aardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqv 162
                                             +kl        + p+ + + l+++    +++ ++++DEa+ +      + +n++ + +    + ++   ++
  gi|557694184|ref|YP_008797238.1| 297 -----SEKL-------SADPESINHYLDNQ----KKIGLIIVDEAHYFRHP-ATNRYNALYRLV----KMTN--AKL 350
                                       .....2344.......66788888888644....599*********99998.566666655555....2223..449 PP

                                       EEEESSBS CS
                                       xxxxxxxx RF
                              DEAD 163 ivlSATlp 170
                                       ++++AT+ 
  gi|557694184|ref|YP_008797238.1| 351 VLMTATPV 358
                                       999**986 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.8e-06     0.004      21     122 ..     239     353 ..     220     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.8e-06
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk.........grarlep 88 
                                       +v+    G GKt +  al++ ++ +g r +++Ap++    + ++e++ +  ti + +++ k         +  + ++
  gi|557694184|ref|YP_008797238.1| 239 VVIADSTGLGKTLTALALAHYYKGQGVRTLLIAPKSILDTTWKTEMEKTDITIINTINSEKlsadpesinHYLDNQK 315
                                       455556899*****************************999998888666666666666556677889985555667 PP

                            AAA_30  89 g.tllivDEagmv...dtkqlaallkaaekagakvilv 122
                                       +  l+ivDEa      +t+  +al + ++ ++ak++l+
  gi|557694184|ref|YP_008797238.1| 316 KiGLIIVDEAHYFrhpATNRYNALYRLVKMTNAKLVLM 353
                                       779********9999999*****************996 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   5.9e-06    0.0063      93     138 ..     314     359 ..     240     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.9e-06
                                       ----SEEEEETTT--SHHHHHHHHHHHHHHHTTS-EEEEEESS-TT CS
                        Flavi_DEAD  93 kknyeliimDeahflDPasiaarGyletkaeegeaalilltatPPG 138
                                       +k+  lii+Deah+    +      l +++++ +a+l+l+tatP  
  gi|557694184|ref|YP_008797238.1| 314 QKKIGLIIVDEAHYFRHPATNRYNALYRLVKMTNAKLVLMTATPVN 359
                                       567889*******9987778888999******************65 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.6e-05      0.07      71     143 ..      98     173 ..      77     196 .. 0.73
   2 ?   -1.4   0.1       1.1   1.1e+03      45      82 ..     927     964 ..     911     965 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                                       EEEEXSSSXBXXXEEE.....EEET.TEEEEEEESXXSXXTTSXXXSBXEEEEEE.HHHHHHHHHHHHHHHHH.HXE CS
                        RE_NgoFVII  71 evkvsysvkvHsKlYi.....wkkdgkplsAliGSANlssnglrtrqrEtlvdldtedafkeldeyiqsllsksisk 142
                                       +v+++    +H+K ++     +k+  +   A++GS N++  gl+t++ E+ + ++++++++el+e +q+  s++ s+
  gi|557694184|ref|YP_008797238.1|  98 QVRIVDGKFFHGKAFLgvhpsFKEV-RRGFAIVGSSNFTHGGLTTNR-ELNMFTTERQTVQELAEWFQQQWSDTASR 172
                                       5556666666666553222214433.6778************98765.55555577************999987666 PP

                                       E CS
                        RE_NgoFVII 143 n 143
                                       +
  gi|557694184|ref|YP_008797238.1| 173 E 173
                                       5 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.1
                                       HHHXXXHHHHHHHHHHHHHHHHCTSEEEEEXSSSXBXX CS
                        RE_NgoFVII  45 pleglskrlheallklnkklseegigevkvsysvkvHs 82 
                                        +eg++  + ++++++ + l+++g + +k+  ++k H+
  gi|557694184|ref|YP_008797238.1| 927 TIEGMPIHSNKTIREIYDALEKTGEEGIKLAAIFKKHA 964
                                       579*****************************999997 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     7e-05     0.073       9     103 ..     244     331 ..     239     355 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7e-05
                           DUF2075   9 vaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke...ekkkkkeafeklssfinnlsefkkaee 82 
                                        +G GKt+ +l+l++ +  + ++ ++ ++     l  + + +++k++    ++  +e+++   + in +        
  gi|557694184|ref|YP_008797238.1| 244 STGLGKTLTALALAHYY--KGQGVRTLLIAPKSILDTTWKTEMEKTDitiINTINSEKLSADPESINHYL------- 311
                                       6799*************..888888888888888888999999999999956666666666566666666....... PP

                           DUF2075  83 kkeepkedvvivDEAhrlltk 103
                                        ++++k+ ++ivDEAh  ++ 
  gi|557694184|ref|YP_008797238.1| 312 -DNQKKIGLIIVDEAHYFRHP 331
                                       .69*************98883 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 ?   12.0   0.0   0.00019      0.21       7      93 ..     245     343 ..     239     364 .. 0.63
   2 ?   -2.4   0.0       5.8   6.1e+03      19      55 ..     455     501 ..     452     516 .. 0.75
   3 ?   -1.2   0.1       2.4   2.5e+03      64     112 ..     599     640 ..     571     648 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                                       TTSSHHHHHHHHHHHHT...HEEEEEETTTCSSS....................STTHHHHHHHHHHHHHHHTSTSE CS
                               AAA   7 pGtGKTllakavakelg...vefleisgsellsk....................yvgesekkirelfkeakekakps 60 
                                        G GKTl+a a+a+  +   v+ l i  +++l+                      +++ +++i++++++ k+     
  gi|557694184|ref|YP_008797238.1| 245 TGLGKTLTALALAHYYKgqgVRTLLIAPKSILDTtwktemektditiintinseKLSADPESINHYLDNQKK---IG 318
                                       69*************843447766666666664444444444444444444444556777777777766433...48 PP

                                       EEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                               AAA  61 ilfiDEidalaksrsgseseeeervvnqLltel 93 
                                        +++DE++ +            ++  n+L++ +
  gi|557694184|ref|YP_008797238.1| 319 LIIVDEAHYFRHPA--------TNRYNALYRLV 343
                                       999***99874333........34455555555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.8
                                       HHHHTHEEEEEETTTCSSS..........STTHHHHHHHHHHHHHHH CS
                               AAA  19 akelgvefleisgsellsk..........yvgesekkirelfkeake 55 
                                         +l+ +f+e+s+ +l  +          +  e++k++++l+ke+ +
  gi|557694184|ref|YP_008797238.1| 455 LDSLNLSFYELSVDKLSTEfklpngrpasTYIEQAKNLKNLVKEIHK 501
                                       56778888888888888776777777777777777888887777654 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.4
                                       EETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.SSTEEEEEEESSG CS
                               AAA  64 iDEidalaksrsgseseeeervvnqLlteldgvkkk.eskvivigatnrp 112
                                       i Ei a+ +++        +  +++Lltel+ + kk +++  +i+ t+++
  gi|557694184|ref|YP_008797238.1| 599 INEILAMLPKQ--------DPKLEALLTELKTLAKKlTNNNGIIIFTQYV 640
                                       67777777777........3345555555555555442333455566555 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 ?   12.1   0.6   0.00015      0.15       3      55 ..     240     425 ..     239     659 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH..HTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx....................... RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai..leglendiep....................... 54 
                                       +++ + G GKT +a++La + + +g r+ll+   p + ++++       ++                          
  gi|557694184|ref|YP_008797238.1| 240 VIADSTGLGKTLTALALAHYYKGQGVRTLLIA--PKSILDTTwkT--EMEKT-Ditiintinseklsadpesinhyl 311
                                       677789************************95..44444443221..11111.123344555555555555555555 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|557694184|ref|YP_008797238.1| 312 dnqkkigliivdeahyfrhpatnrynalyrlvkmtnaklvlmtatpvntslmdlyhimalylnedaiydeyrttlrd 388
                                       55555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                                       ....................................C CS
                                       ....................................x RF
                              CbiA  55 ....................................d 55 
                                                                           d
  gi|557694184|ref|YP_008797238.1| 389 yfiqnqkkwlnnepvdmddilrkfvvrhsrqlakalD 425
                                       5555555555555555555555555555555555550 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   0.2    0.0016       1.6      34      87 ..     223     276 ..     204     361 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                         IstB_IS21  34 kvkeLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLv 87 
                                       +++ + +l+ ie+  ++v+   +G GK+  a al++    +g+++l +  + ++
  gi|557694184|ref|YP_008797238.1| 223 QLTFVDALDKIETYGGVVIADSTGLGKTLTALALAHYYKGQGVRTLLIAPKSIL 276
                                       55556678889999999******************9888888887766555444 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.5   0.00073      0.77       5      36 ..     240     271 ..     238     378 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00073
                            AAA_26   5 vtgtdtgvGKTvvslgLvralkrkgvkvgyfK 36 
                                       v++ +tg GKT+++l+L++++k +gv++  + 
  gi|557694184|ref|YP_008797238.1| 240 VIADSTGLGKTLTALALAHYYKGQGVRTLLIA 271
                                       778899***************99999876554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00034      0.36       7      60 ..     242     292 ..     238     359 .. 0.60
   2 ?   -3.2   0.0       5.1   5.3e+03      63     119 ..     637     690 ..     615     706 .. 0.51

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00034
                                       EESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEE CS
                             SRP54   7 vGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvi 60 
                                       +  +G GKT t+  La+++k +g ++ll+a            kt  ek+++++i
  gi|557694184|ref|YP_008797238.1| 242 ADSTGLGKTLTALALAHYYKGQGVRTLLIAPKSILDTTW---KTEMEKTDITII 292
                                       5579************************99654433332...344444444444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.1
                                       STTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEE CS
                             SRP54  63 keeadpaavakeavekakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevll 119
                                       ++  d+a+++++ +++ ++   +++lv   G  ++  + ++e ++++ + k+  +++
  gi|557694184|ref|YP_008797238.1| 637 TQYVDTASYLFNHLKTIHQ---QTLLVTGRGGENSSGKRLDEAEAVELFQKNGGIMV 690
                                       3334444455444444444...44666666666666666666666665555555555 PP

>> Tae4  Type VI secretion system (T6SS), amidase effector protein 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.2   1.2e+03      40      63 ..     154     175 ..     127     188 .. 0.77
   2 ?    8.2   0.1    0.0026       2.7      37      89 ..     485     640 ..     454     658 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                              Tae4  40 rvkelanwLkekeafgklekpeiv 63 
                                        v+ela+w +++  + ++  +e +
  gi|557694184|ref|YP_008797238.1| 154 TVQELAEWFQQQ--WSDTASREYK 175
                                       699******888..9886665554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0026
                              Tae4  37 yiirvkelanwLkekeafgklek...................................................... 59 
                                       yi ++k+l+n++ke +++g l+                                                       
  gi|557694184|ref|YP_008797238.1| 485 YIEQAKNLKNLVKEIHKIGLLKRlessihafkesinrmktyieyanryatennifipprlkgelfallddeeepeel 561
                                       66667777777766666666666666666666666666667777777777777777777777777777777777777 PP

                              Tae4  60 .................................................peivaeiekkklkkkklkgkkGIivfkd 87 
                                                                                        p+  a  ++ k+ +kkl +++GIi+f++
  gi|557694184|ref|YP_008797238.1| 562 pkiedlfskhihllrrcklseeearqfieknqedlkkineilamlpkqdPKLEALLTELKTLAKKLTNNNGIIIFTQ 638
                                       7777777777777777777777777777777777777777888887777666677777788899************9 PP

                              Tae4  88 ew 89 
                                       + 
  gi|557694184|ref|YP_008797238.1| 639 YV 640
                                       96 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 ?   -1.8   0.0       2.7   2.9e+03      24      42 ..     415     433 ..     405     434 .. 0.82
   2 ?    2.6   0.0      0.12   1.2e+02      12      31 ..     579     598 ..     573     599 .. 0.87
   3 ?    5.8   0.2     0.012        13       9      40 ..     894     925 ..     892     927 .. 0.92
   4 ?   -2.6   0.1       4.8     5e+03      25      37 ..     969     981 ..     968     984 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.7
                   HU-CCDC81_bac_2  24 keveelkqeLeeegrvele 42 
                                        + ++l ++L++egr+ ++
  gi|557694184|ref|YP_008797238.1| 415 RHSRQLAKALDREGRIRFP 433
                                       56789999*******9986 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.12
                   HU-CCDC81_bac_2  12 gisyeeAlqkiekeveelkq 31 
                                       ++s eeA+q iek  e+lk+
  gi|557694184|ref|YP_008797238.1| 579 KLSEEEARQFIEKNQEDLKK 598
                                       799*************9997 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.012
                   HU-CCDC81_bac_2   9 eaegisyeeAlqkiekeveelkqeLeeegrve 40 
                                       + e i+y++ + k+++  eelk eL++++ +e
  gi|557694184|ref|YP_008797238.1| 894 KGERINYDTLVDKLKQLKEELKTELDKKHAIE 925
                                       5689***********************99886 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 4.8
                   HU-CCDC81_bac_2  25 eveelkqeLeeeg 37 
                                        v++lk++L++++
  gi|557694184|ref|YP_008797238.1| 969 IVKQLKKALNQGN 981
                                       599******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1017 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1470  (0.0819901); expected 358.6 (0.02)
Passed bias filter:                      794  (0.0442858); 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):              17  [number of targets reported over threshold]
# CPU time: 0.93u 0.33s 00:00:01.26 Elapsed: 00:00:00.47
# Mc/sec: 6461.36
//
Query:       gi|557694185|ref|YP_008797239.1|  [L=132]
Description: hypothetical protein CSUB_C0751 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   16.5   0.0      0.008   16.3   0.0    1.3  1  DUF2096   Uncharacterized protein conserved in archaea (DUF20


Domain annotation for each model (and alignments):
>> DUF2096  Uncharacterized protein conserved in archaea (DUF2096)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.5e-07     0.008      11      79 ..      28      94 ..      10     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.5e-07
                           DUF2096 11 llsdLkkrgkevpkevlenlrlaktiinfYkldphapdlikelkkaekelneiqeaLldlaekvdeeya 79
                                      l++d  k+ +++pk++ ++l++     + Y +dp++    ++l+ +e  +n++ e   +l+e+ d+++ 
  gi|557694185|ref|YP_008797239.1| 28 LVEDALKELRNLPKNLSKRLGCDEHFWQQYLSDPNNA--SQKLNAIEGAVNYVGERAHSLSEQHDKDLC 94
                                      66677788899*************************9..9*********************99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 994.97
//
Query:       gi|557694186|ref|YP_008797240.1|  [L=266]
Description: hypothetical protein CSUB_C0752 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-30  104.2   0.2    9.8e-30  103.2   0.1    1.5  2  Cas_APE2256     CRISPR-associated protein (Cas_APE2256)
      0.003   17.9   0.7      0.034   14.5   0.1    2.3  2  DUF3734         Patatin phospholipase
     0.0071   15.2   0.0      0.018   13.8   0.0    1.5  1  Cas_Cas02710    CRISPR-associated protein (Cas_Cas02710)
  ------ inclusion threshold ------
      0.041   13.2   0.2       0.21   10.9   0.0    2.0  2  DUF5630         Family of unknown function (DUF5630)
      0.066   13.6   0.3       0.14   12.6   0.1    1.6  2  DUF3486         Protein of unknown function (DUF3486)
      0.069   13.2   0.6       0.15   12.1   0.2    1.9  2  CompInhib_SCIN  Staphylococcal complement inhibitor SCIN
       0.11   12.2   0.1       0.19   11.4   0.1    1.4  1  Band_7_1        SPFH domain-Band 7 family


Domain annotation for each model (and alignments):
>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.1   3.8e-33   9.8e-30       2     135 ..      66     193 ..      65     194 .. 0.91
   2 ?   -3.3   0.0         3   7.7e+03      69      81 ..     207     219 ..     202     240 .. 0.55

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 3.8e-33
                       Cas_APE2256   2 kasAElnallkllekkkkeqkeelvllssdTaaGklvaeilkeyleeegaevevveieklsdlgreeFre.glrnLv 77 
                                       +asAEl+++ ++++kkk +    ++ll++dT+ G+++a++l++ + ++g++ + ++ie+ ++  ++eF+e gl+nL+
  gi|557694186|ref|YP_008797240.1|  66 EASAELSSISEYMQKKKVD---IVHLLHTDTEVGEVCATALQQHFWQKGINASKERIEGFRT--EQEFYErGLQNLL 137
                                       79***************99...69***********************999988877655555..4557777****** PP

                       Cas_APE2256  78 eklarevknkkregekvlinaTgGfKpeiavltlvallladevyYihEsfsevvelPk 135
                                        k ++ +k  k + e+vl+naTgG+Kpe+++l lva +++++vyY hE+f+  ++l +
  gi|557694186|ref|YP_008797240.1| 138 LKTHDLIK--KYRDERVLLNATGGYKPETTALSLVAFIMGKPVYYRHETFKTTITLSP 193
                                       ********..677789**************************************9965 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3
                       Cas_APE2256  69 FreglrnLvekla 81 
                                       ++++l +L++  +
  gi|557694186|ref|YP_008797240.1| 207 YKSALLDLIKLNT 219
                                       5556666665433 PP

>> DUF3734  Patatin phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.011        29      26      57 ..      23      54 ..      15      65 .. 0.83
   2 !   14.5   0.1   1.3e-05     0.034      20      64 ..      49      94 ..      44      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                           DUF3734 26 elleklpeelredpevkeleelgcekrvnvvh 57
                                      + l  lp++l+++p+v+++ + g+ ++ n+v+
  gi|557694186|ref|YP_008797240.1| 23 KTLTSLPQHLQNQPDVENALKKGEINKQNIVK 54
                                      56789**********************99997 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.3e-05
                           DUF3734 20 lrrairelleklpeelre.dpevkeleelgcekrvnvvhLiyreke 64
                                       +++++ell  + ++ +e ++e+  ++e+ ++k+v++vhL++ ++e
  gi|557694186|ref|YP_008797240.1| 49 KQNIVKELLTYIEKKGQEaSAELSSISEYMQKKKVDIVHLLHTDTE 94
                                      5789********8888887**********************98876 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 !   13.8   0.0   7.1e-06     0.018      57      99 ..     139     180 ..     123     189 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.1e-06
                                       HHHHHHHHS.TTS-EEEE-SSS-HHHHHHHHHHHHHHTEEEEE CS
                      Cas_Cas02710  57 kikevlekaleeeevivDlTgGtkeMtaglalagillrvklsy 99 
                                       k +++++k+ ++e v +++TgG k  t +l+l+++++++++ y
  gi|557694186|ref|YP_008797240.1| 139 KTHDLIKKY-RDERVLLNATGGYKPETTALSLVAFIMGKPVYY 180
                                       677889999.*****************************9998 PP

>> DUF5630  Family of unknown function (DUF5630)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.18   4.7e+02       3      33 ..      18      48 ..      16      73 .. 0.77
   2 ?   10.9   0.0   8.4e-05      0.21       8      53 ..      80     124 ..      74     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.18
                                      HHHHHS-HHHHHHHHHH-HHHHHHHTSGGGH CS
                           DUF5630  3 sllkslslesLaklalkspeirellkspefd 33
                                      + l++ +l+sL + ++++p++++ lk+ e +
  gi|557694186|ref|YP_008797240.1| 18 NALREKTLTSLPQHLQNQPDVENALKKGEIN 48
                                      6788888888888888888888888887765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.4e-05
                                       S-HHHHHHHHHH-HHHHHHHTSGGGHHHHHHHHHHH--S...S--- CS
                           DUF5630   8 lslesLaklalkspeirellkspefdkfWeklreklrkpgepefef 53 
                                        +  +++ l++++ e+ e++  + ++ fW+k +++ +++  + f++
  gi|557694186|ref|YP_008797240.1|  80 KKKVDIVHLLHTDTEVGEVCATALQQHFWQKGINASKER-IEGFRT 124
                                       4567899*************************9777665.666665 PP

>> DUF3486  Protein of unknown function (DUF3486)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.3e-05      0.14       6      60 ..      24      81 ..      20     119 .. 0.78
   2 ?   -2.5   0.0       2.4   6.1e+03     143     154 ..     227     238 ..     214     249 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.3e-05
                           DUF3486  6 kvdlLPeevree..LdeaLrekgftqdeIyeelnallaerG.eykiSkSalnryaqrl 60
                                      ++  LP+ ++ +  +++aL + ++ +++I++el + ++++G e+    S++  y+q+ 
  gi|557694186|ref|YP_008797240.1| 24 TLTSLPQHLQNQpdVENALKKGEINKQNIVKELLTYIEKKGqEASAELSSISEYMQKK 81
                                      677899999875337**************************8788888*******983 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                           DUF3486 143 aeirkeaaeaaa 154
                                       +++ ke+aea+ 
  gi|557694186|ref|YP_008797240.1| 227 KRYGKEVAEAMS 238
                                       444444444433 PP

>> CompInhib_SCIN  Staphylococcal complement inhibitor SCIN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   5.9e-05      0.15      20      79 ..      56     116 ..      41     146 .. 0.89
   2 ?   -2.9   0.0       2.6   6.7e+03      15      28 ..     211     224 ..     202     239 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.9e-05
                    CompInhib_SCIN  20 gikllekneadassldktsseyqdkklaeeLkeLldesnvnkLaagsLna.yykrtiliae 79 
                                       +++ +ek+  +as+ +   sey +kk ++ ++ L  +++v +++a +L+  + ++ i +++
  gi|557694186|ref|YP_008797240.1|  56 LLTYIEKKGQEASAELSSISEYMQKKKVDIVHLLHTDTEVGEVCATALQQhFWQKGINASK 116
                                       67899***************************************99997526677777765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.6
                    CompInhib_SCIN  15 lLsstgikllekne 28 
                                       lL+   +++++k e
  gi|557694186|ref|YP_008797240.1| 211 LLDLIKLNTIDKTE 224
                                       44444444444443 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 ?   11.4   0.1   7.6e-05      0.19     135     198 ..      54     127 ..      41     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.6e-05
                          Band_7_1 135 eqlkslivtr..........lsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpee 198
                                       ++l + i ++          +s+ ++++k+ +++l  + +e++e ++ al++++ + G++ +k  ie    ++e
  gi|557694186|ref|YP_008797240.1|  54 KELLTYIEKKgqeasaelssISEYMQKKKVDIVHLLHTDTEVGEVCATALQQHFWQKGINASKERIEGFRTEQE 127
                                       5555555544445555555599**************************************99988887766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1292  (0.072062); expected 358.6 (0.02)
Passed bias filter:                      747  (0.0416643); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); 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 0.24s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 1977.40
//
Query:       gi|557694187|ref|YP_008797241.1|  [L=59]
Description: hypothetical protein CSUB_C0753 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.0       0.12   12.3   0.0    1.1  1  Mesd      Chaperone for wingless signalling and trafficking o


Domain annotation for each model (and alignments):
>> Mesd  Chaperone for wingless signalling and trafficking of LDL receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.8e-06      0.12      13      46 ..      13      46 ..       8      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.8e-06
                                      HHHHHHHHHHHH.HHCTXXSSSXXSXSSTHCCHC CS
                              Mesd 13 erlldqWeeddepleedelpehkrpspkidlskl 46
                                       +lldq   +  p+ +   pe++r sp+id++ +
  gi|557694187|ref|YP_008797241.1| 13 HHLLDQKTGKATPMTNVHCPEKQRASPQIDTTII 46
                                      79****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); 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: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 451.69
//
Query:       gi|557694188|ref|YP_008797242.1|  [L=252]
Description: hypothetical protein CSUB_C0754 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.027   14.7   0.2      0.043   14.0   0.2    1.2  1  Condensin2nSMC  Condensin II non structural maintenance of ch
        0.2   10.6   0.1       0.27   10.2   0.1    1.1  1  DuoxA           Dual oxidase maturation factor


Domain annotation for each model (and alignments):
>> Condensin2nSMC  Condensin II non structural maintenance of chromosomes subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   4.7e-06     0.043       3      82 ..      72     154 ..      71     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.7e-06
                    Condensin2nSMC   3 vispaflkteeGrkflafvltldtklikeilkaiksqipkleksvleaygeilfraWkkasge...lkeeieesciq 76 
                                       +i+p  l +e+ ++f  +v++  ++l+ +ilkaik++  kl+  +++ + +i  + W+  ++e    +++i ++++ 
  gi|557694188|ref|YP_008797242.1|  72 IINPPTLLHENTIQFRLTVFGHANQLMPHILKAIKKEHDKLQLLEATIVNDITGEKWEANNQEektQQQSITYQMLL 148
                                       678888999999*********999**********************************8777733333444444443 PP

                    Condensin2nSMC  77 dlmeaa 82 
                                       + +++ 
  gi|557694188|ref|YP_008797242.1| 149 QNVKQH 154
                                       333333 PP

>> DuoxA  Dual oxidase maturation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   3.1e-05      0.27      56     106 ..     117     168 ..     112     185 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 3.1e-05
                             DuoxA  56 avilvvnfgseWevaevkakttykafsneeieakiglkiGL.egvNiTLkge 106
                                       a+i+    g++We  +++ kt+ ++ + +++  +++ +i   e++NiTL+  
  gi|557694188|ref|YP_008797242.1| 117 ATIVNDITGEKWEANNQEEKTQQQSITYQMLLQNVKQHIENkEKINITLTLL 168
                                       788888999******************************75268*****865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1729  (0.0964359); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 1971.30
//
Query:       gi|557694189|ref|YP_008797243.1|  [L=544]
Description: hypothetical protein CSUB_C0755 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-10   40.0   0.0    1.9e-09   37.4   0.0    2.0  1  Cellulase     Cellulase (glycosyl hydrolase family 5)
    4.6e-05   23.7   0.8    7.5e-05   23.0   0.8    1.2  1  HMMR_C        Hyaluronan mediated motility receptor C-termina
  ------ inclusion threshold ------
      0.094   13.3   2.4       0.18   12.4   0.2    2.5  2  Syntaxin-6_N  Syntaxin 6, N-terminal
      0.094   12.1   7.8       0.17   11.2   7.8    1.4  1  GAS           Growth-arrest specific micro-tubule binding
          1    9.4  11.6        1.9    8.6   2.1    2.6  2  DHR10         Designed helical repeat protein 10 domain
        2.3    8.5   7.4         12    6.2   0.2    2.7  3  Spc24         Spc24 subunit of Ndc80
        9.5    5.8   9.5       0.78    9.4   0.2    2.5  3  Med4          Vitamin-D-receptor interacting Mediator subunit


Domain annotation for each model (and alignments):
>> Cellulase  Cellulase (glycosyl hydrolase family 5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   7.5e-13   1.9e-09      10     279 ..     219     501 ..     212     503 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 7.5e-13
                                       GEEECET.....TSCGGSHHHHHHHH...HHHT-SEEEEEEECTGGTTSSTTTGCTHHHHHHHHHHHHHHHHTT-EE CS
                         Cellulase  10 lkglsts.....wgnpyttkalidev...kdagfntvRlpvswgelvenapdykvdenslerveevvkyakenglyv 78 
                                       ++g +++     w+++ t+++li ++   +++  n++R+ + + ++ ++       +++l  + evv+   ++glyv
  gi|557694189|ref|YP_008797243.1| 219 FFGANMRsgldaWSKK-TENELILQIlsaREMELNVIRIVIDVWKYAQPY--QHLPSDALRAIMEVVDMLWRAGLYV 292
                                       5666666677778886.6677665542328899*********77888433..356999******************* PP

                                       EEEEESSTTTCSSSSTTTTHHHHHHHHHHHHHHHHHHHTTTTTTEEEESSSS--STTCT............CCTCHH CS
                         Cellulase  79 ildiHseegwltkadgnssedtaeeffkklwtqiAerykkndevvifelmNEPhgnntg............aewtse 143
                                       i+   +   w  + d+++       ++k+++  + + +   + vv+++l NEP    +             +ew   
  gi|557694189|ref|YP_008797243.1| 293 IVTFDK-VMW-MDSDSTKFWVG-YRQYKEAIMDVVNMLRLHPAVVAYDLSNEPVLAIEAgvtegkisrreaDEW--- 363
                                       ****99.688.44444444444.6668999999*****99**************97666776555555555555... PP

                                       HTTHHHHHHHHHHHHHHHHTTSSEEEEECHHHHTBHHHHHCTSGSSSSTTEEEEEEE...ETTTHHHTGCGSHSCTH CS
                         Cellulase 144 eadevkayaeeaikaIRavgpnrliivegnswsgnldgavlndPndsqdnliysvHf...Ygpsdfaqtefgkdltd 217
                                         + +++++  + + I + +p  ++ v+     + +d +  ++    +   ++s+H+    +p+  ++t+     ++
  gi|557694189|ref|YP_008797243.1| 364 -IKGLTNVYRVMRNDIVSRDPFVTVTVGD----AEPDYS--KYFI--DVIDFVSFHNtgiWSPYPEEDTWD----GT 427
                                       .5556666666666666777778888888....444442..2222..345699999944455888888888....88 PP

                                       HHHHHHHHHHHHHHHHHTTSEEEEEEEESS...TTSSH............HHHHHHHHHHHHHHHTTTEEEEEEESS CS
                         Cellulase 218 ktnlaqrledaakylvekgipviigEfGgs...nadgd............lakeeaekwldylkekgiswiyWslnp 279
                                         +l+ rl+  +++++  g+pv+++E+G++                       ++   +ld + ++gi+ ++W +n 
  gi|557694189|ref|YP_008797243.1| 428 LEDLRRRLSFRIERAKALGKPVVLEEYGVDpnfV---YgrqlermgkvvyHPLDYYRVILDEVYSHGIGALFWVINI 501
                                       999*************************975440...2433223333444444444444999999********9986 PP

>> HMMR_C  Hyaluronan mediated motility receptor C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.8   2.9e-08   7.5e-05      13     142 ..      79     222 ..      71     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.9e-08
                            HMMR_C  13 ekeetldelkeevkkWrklyeellnkvkPfq...eqldafeaekn.all...nekGaaqeelnklsdayakllGhqn 82 
                                       e +++ld l + +k  +  +ee+ n+v  ++   e ld++e+e   al+   ++  aa + +nk+ d y kl+G  n
  gi|557694189|ref|YP_008797243.1|  79 EASNKLDRLSSVLKDKNVESEEMANRVAELElklENLDKLESESYlALFqieSDVDAAIAGMNKILDRYQKLVGEEN 155
                                       55666777767666677778999999999883335577888887524543334568999****************** PP

                            HMMR_C  83 q...kqkikhvvklkeenselkq...evsklrsqlakekqeekklkeqlkea.kgvrrfdpskafkh 142
                                           ++ +  +  l++  +el +   +++  r+++a  ++ ++ l+e lk++ ++ r + ps  f  
  gi|557694189|ref|YP_008797243.1| 156 LafeRKTVEIMENLRDTKTELAStlkDLASYRARMAELQRIKDYLEEDLKSVmRTARGLSPSDFFGA 222
                                       73324445555579999999986122667779999999999********987256677888887765 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 ?   -0.9   0.2      0.93   2.4e+03      35      61 ..      97     116 ..      71     119 .. 0.53
   2 ?   12.4   0.2   7.1e-05      0.18       4      54 ..     127     184 ..     125     212 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.93
                      Syntaxin-6_N  35 tseeldetrteLrkalrsiewdledLe 61 
                                       +see+ +   eL+ +l       e+L+
  gi|557694189|ref|YP_008797243.1|  97 ESEEMANRVAELELKL-------ENLD 116
                                       3455555555555444.......4444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.1e-05
                      Syntaxin-6_N   4 fevkeeVqkslnkaeslyrrwerlledtsss.......tseeldetrteLrkalrsie 54 
                                       f+++++V  ++  ++++++r+++l  +++ +         e+l++t+teL ++l+++ 
  gi|557694189|ref|YP_008797243.1| 127 FQIESDVDAAIAGMNKILDRYQKLVGEENLAferktveIMENLRDTKTELASTLKDLA 184
                                       8999*****************9988777665345555566666666666666665543 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 ?   11.2   7.8   6.7e-05      0.17      68     179 ..      82     190 ..      73     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.7e-05
                               GAS  68 eeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiqevqqktglkn 144
                                       +++++L   lk+ + + +++    +r+ ele +l++l          + ++e++ d+  +  ++ ++ +q+ +g +n
  gi|557694189|ref|YP_008797243.1|  82 NKLDRLSSVLKDKNVESEEM---ANRVAELELKLENLDKLESESYLALFQIESDVDAAIAGMNKILDRYQKLVGEEN 155
                                       55666666666666655555...5577777777777777777777788899************************** PP

                               GAS 145 llLekklkalqeelEkkeaqleevlaaanldpaal 179
                                       l  e+k  ++ e+l   + +l+++l+      a +
  gi|557694189|ref|YP_008797243.1| 156 LAFERKTVEIMENLRDTKTELASTLKDLASYRARM 190
                                       ***********************998655443433 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 ?    8.6   2.1   0.00073       1.9      41      90 ..      66     115 ..      65     122 .. 0.90
   2 ?    5.3   2.3    0.0077        20      27     115 ..     125     211 ..     120     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00073
                             DHR10  41 lleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlena 90 
                                       l+ e+   + ++ ea+ kl++l+  l++k+ e++e+ ++ + l+ +len 
  gi|557694189|ref|YP_008797243.1|  66 LMRELLLCMDRYIEASNKLDRLSSVLKDKNVESEEMANRVAELELKLENL 115
                                       6778888899999********************************99996 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0077
                             DHR10  27 alqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaee 103
                                       al ++e d+ ++i+ +++i +  +kl  ++ +l+  r+++e +e+ lr+ +++ +   + l++ + +++ l++  + 
  gi|557694189|ref|YP_008797243.1| 125 ALFQIESDVDAAIAGMNKILDRYQKLVGEE-NLAFERKTVEIMEN-LRDTKTELASTLKDLASYRARMAELQRIKDY 199
                                       667899999999999999999999998765.56777778888877.8999999999999999999999999998888 PP

                             DHR10 104 kreaakarleel 115
                                        +e+ k+ +  +
  gi|557694189|ref|YP_008797243.1| 200 LEEDLKSVMRTA 211
                                       888777777666 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.0    0.0073        19       7      44 ..      78     120 ..      74     150 .. 0.76
   2 ?    6.2   0.2    0.0045        12       3      43 ..     159     199 ..     157     251 .. 0.87
   3 ?   -3.0   0.0       3.5   8.9e+03      83      98 ..     386     401 ..     373     401 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0073
                             Spc24   7 friakelsdleselesleselaelkeeleeleeesee.....k 44 
                                       ++++++l+ l s l++ + e +e+ ++++ele + e+     +
  gi|557694189|ref|YP_008797243.1|  78 IEASNKLDRLSSVLKDKNVESEEMANRVAELELKLENldkleS 120
                                       6778999999999999999999999999999999998544322 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0045
                             Spc24   3 dnekfriakelsdleselesleselaelkeeleeleeesee 43 
                                       +++ ++i ++l+d+++el s  + la+ +++++el++ +  
  gi|557694189|ref|YP_008797243.1| 159 ERKTVEIMENLRDTKTELASTLKDLASYRARMAELQRIKDY 199
                                       678899*****************************997765 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.5
                             Spc24  83 dvnvlnlddklseffi 98 
                                       +v+v + ++++s++fi
  gi|557694189|ref|YP_008797243.1| 386 TVTVGDAEPDYSKYFI 401
                                       56777789999*9997 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 ?    2.3   0.6     0.045   1.2e+02      25      64 ..      99     138 ..      81     157 .. 0.82
   2 ?    9.4   0.2    0.0003      0.78       2      39 ..     164     201 ..     163     214 .. 0.83
   3 ?   -3.9   0.2       3.6   9.1e+03     127     134 ..     415     422 ..     413     423 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.045
                              Med4  25 qknearilqLraeveslDekikeivksLkeyekeLkavpd 64 
                                       ++  +r+ +L+ + e+lD+  +e   +L ++e+ + a++ 
  gi|557694189|ref|YP_008797243.1|  99 EEMANRVAELELKLENLDKLESESYLALFQIESDVDAAIA 138
                                       56778999***************************99984 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0003
                              Med4   2 klaekLlaaddelskslkeleehqknearilqLraeve 39 
                                       +++e+L +  +el+++lk l  + ++ a++++++   e
  gi|557694189|ref|YP_008797243.1| 164 EIMENLRDTKTELASTLKDLASYRARMAELQRIKDYLE 201
                                       689**********************9999999986544 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3.6
                              Med4 127 frPwPtEd 134
                                       + P+P Ed
  gi|557694189|ref|YP_008797243.1| 415 WSPYPEED 422
                                       78*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (544 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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):               7  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3735.38
//
Query:       gi|557694190|ref|YP_008797244.1|  [L=207]
Description: hypothetical protein CSUB_C0756 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   0.3    2.9e-12   46.4   0.3    1.5  1  DUF559     Protein of unknown function (DUF559)
    1.7e-09   37.7   0.6    9.5e-09   35.3   0.2    2.0  2  MTES_1575  REase_MTES_1575
    0.00085   19.2   0.5     0.0017   18.2   0.5    1.6  1  DUF2726    Protein of unknown function (DUF2726)
  ------ inclusion threshold ------
      0.016   15.3   0.0      0.061   13.4   0.0    1.9  2  RAP        RAP domain
      0.051   13.1   0.1      0.078   12.5   0.1    1.2  1  NLBH       Neuraminyllactose-binding hemagglutinin precursor 


Domain annotation for each model (and alignments):
>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.3     8e-16   2.9e-12      17     107 ..     107     196 ..      97     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 8e-16
                                       HHHHHHHHHGGGTTTT--EEEEEEETTEEEEEEETTTTEEEEEE-------..----HHHHHHHHHTT-EEEEEEHH CS
                            DUF559  17 aekkLWqllrnrrlsglkfrRqkpigsYivDfvclkaklivelDGaqhdee..eeyDaeRtelLeslGftvlRfknd 91 
                                       +e+ L + l +rr+   +  R +  g Y vD +  + ++ive+DG qh++e  +++D e+ +lL++ G+ v+R +  
  gi|557694190|ref|YP_008797244.1| 107 EEHMLSRELWRRRI---RHLRNVFCGGYNVDILIPEPRIIVEIDGLQHYQErvQAKDLEKLNLLKKKGYDVFRIQAA 180
                                       56666666666665...57799**************************9988899********************** PP

                                       HHHH-HHHHHHHHHHH CS
                            DUF559  92 evlknieevleeilka 107
                                       +v++++ +++e i  a
  gi|557694190|ref|YP_008797244.1| 181 DVRRDTASIAEMIRDA 196
                                       *********9999765 PP

>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.23   8.1e+02       4      43 ..      47      86 ..      45      98 .. 0.84
   2 !   35.3   0.2   2.6e-12   9.5e-09       6      93 ..     112     195 ..     108     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.23
                         MTES_1575  4 eVaeaLrergykvkpqvgvggfriDlvvedpgkyllaIec 43
                                      +V + L++  ++++p++  +g+ + ++ve+ +  ++a+e 
  gi|557694190|ref|YP_008797244.1| 47 AVRRLLEHAPVRLVPRHVGKGYAVFFIVESDEAVRAAVEK 86
                                      6788888889999999999999999999999889999885 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 2.6e-12
                         MTES_1575   6 aeaLrergykvkpqvgvggfriDlvvedpgkyllaIecdgdkyhsskeardrdierqevLerlGWkilRiwssdwyr 82 
                                        ++L +r ++  ++v +gg+++D+ + +p   ++ +e+dg ++ + ++  ++d+e+ + L++ G++++Ri   d  r
  gi|557694190|ref|YP_008797244.1| 112 SRELWRRRIRHLRNVFCGGYNVDILIPEP---RIIVEIDGLQHYQ-ERVQAKDLEKLNLLKKKGYDVFRIQAADVRR 184
                                       5678888999999****************...*********8877.889999************************* PP

                         MTES_1575  83 npeeeleklve 93 
                                       + ++  e +++
  gi|557694190|ref|YP_008797244.1| 185 DTASIAEMIRD 195
                                       99988887765 PP

>> DUF2726  Protein of unknown function (DUF2726)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.5   4.8e-07    0.0017       8     118 ..      76     187 ..      69     197 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.8e-07
                           DUF2726   8 eEraflsaLkkavgd.elrvlakVslsdvlkvekgtsksqsqealnrisakrvDfllcdkadl.....kpvavIeld 78 
                                       +++a+ +a++kav + + ++  +V++  v   e+  s++ +++  + +++       c   +      +p++++e+d
  gi|557694190|ref|YP_008797244.1|  76 SDEAVRAAVEKAVAEgSAKLGVRVKMLGVSMEEHMLSRELWRRRIRHLRNV-----FCGGYNVdilipEPRIIVEID 147
                                       556777777777777555777777777775544555555555444444433.....3332222223336******** PP

                           DUF2726  79 gakhkqgkarkrDalkraalaaAgipllrvkakksytvee 118
                                       g +h+q++++++D  k ++l++ g  + r++a++  ++++
  gi|557694190|ref|YP_008797244.1| 148 GLQHYQERVQAKDLEKLNLLKKKGYDVFRIQAADVRRDTA 187
                                       ******************************9988766544 PP

>> RAP  RAP 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      20      38 ..     116     138 ..     107     139 .. 0.62
   2 ?   13.4   0.0   1.7e-05     0.061       1      39 [.     144     179 ..     144     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.81
                               RAP  20 tklKkriLsk...lGykv.inIp 38 
                                       ++ + r+L++    Gy+v i Ip
  gi|557694190|ref|YP_008797244.1| 116 WRRRIRHLRNvfcGGYNVdILIP 138
                                       55667777763323677766666 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.7e-05
                               RAP   1 IevdGpshyyknsknltgktklKkriLsklGykvinIpy 39 
                                       +e+dG +hy ++ ++   k   K ++L+k+Gy v +I  
  gi|557694190|ref|YP_008797244.1| 144 VEIDGLQHYQERVQA---KDLEKLNLLKKKGYDVFRIQA 179
                                       79******9999877...7899*************9975 PP

>> NLBH  Neuraminyllactose-binding hemagglutinin precursor (NLBH)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.2e-05     0.078      60     107 ..     134     181 ..     130     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                                       EEEEEEEEEEE-.CCCHHHHHHHHHHHHHHHHHHHHCTT-EEEEESSCC CS
                              NLBH  60 vvallePkiqvs.dnikpYidkFqnalvkqvqeilekkGYkvirlkdaq 107
                                        +++ eP+i v+ d ++ Y+++ q + +++++ +l+kkGY+v r++ a+
  gi|557694190|ref|YP_008797244.1| 134 DILIPEPRIIVEiDGLQHYQERVQAKDLEKLN-LLKKKGYDVFRIQAAD 181
                                       5788899998875788**************95.89*********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); 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:                         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 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1596.23
//
Query:       gi|557694191|ref|YP_008797245.1|  [L=65]
Description: hypothetical protein CSUB_C0757 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      185  (0.0103185); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 512.76
//
Query:       gi|557694192|ref|YP_008797246.1|  [L=134]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0013   18.4   0.0     0.0022   17.7   0.0    1.4  1  DUF1627   Protein of unknown function (DUF1627)
  ------ inclusion threshold ------
      0.018   14.7   0.9       0.19   11.4   0.0    2.3  2  HTH_33    Winged helix-turn helix
       0.11   12.9   0.2       0.17   12.4   0.2    1.4  1  DUF406    Protein of unknown function (DUF406)


Domain annotation for each model (and alignments):
>> DUF1627  Protein of unknown function (DUF1627)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   3.6e-07    0.0022      10      50 ..      89     131 ..      80     134 .] 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.6e-07
                           DUF1627  10 delallfgv..tsrkvastlavaiskgrlirvnqngkfrycis 50 
                                       +++  +fg+   srkv+ +l +   kg l rv q+g +r+ ++
  gi|557694192|ref|YP_008797246.1|  89 QKIIEQFGLpfQSRKVSQALGILYDKGVLTRVGQKGNYRWILP 131
                                       5566778863379***************************987 PP

>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.4     0.043   2.6e+02      39      49 ..      46      56 ..      44      64 .. 0.85
   2 ?   11.4   0.0   3.2e-05      0.19       5      31 ..      82     108 ..      79     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.043
                            HTH_33 39 qkPrprapkqd 49
                                       kP+p+apk+ 
  gi|557694192|ref|YP_008797246.1| 46 TKPQPKAPKRR 56
                                      69******995 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.2e-05
                            HTH_33   5 WtlarlaqlieerfgvsysvsgvyrlL 31 
                                        t+a+++q i e+fg+ + ++ v++ L
  gi|557694192|ref|YP_008797246.1|  82 RTTAEVRQKIIEQFGLPFQSRKVSQAL 108
                                       69*******************999765 PP

>> DUF406  Protein of unknown function (DUF406)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   2.9e-05      0.17      21      60 ..       9      47 ..       2      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.9e-05
                                      -STTEEEEEEE-SSHHHHHHHHHHHHHHHHHH.STT-.EE CS
                            DUF406 21 nsdcvaeveivaaseaeaeaalakltekAkavesepveis 60
                                      ++++ +ev+ +a+s++ea a+l++l+++ +av  e  + +
  gi|557694192|ref|YP_008797246.1|  9 ETEDDVEVSLEASSKEEALANLDELLALTRAV-AERLKTK 47
                                      78999***************************.6666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1063.76
//
Query:       gi|557694193|ref|YP_008797247.1|  [L=290]
Description: protoheme IX farnesyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-41  142.9  24.7    1.3e-41  142.6  24.7    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 !  142.6  24.7   7.2e-46   1.3e-41       2     246 ..      23     270 ..      22     282 .. 0.91

  Alignments for each domain:
  == domain 1  score: 142.6 bits;  conditional E-value: 7.2e-46
                              UbiA   2 lipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGris.pkealifaivll 77 
                                        ++ ++g+++a++g pd+ l+ +++l ++l  a++ a  +y++   D+ m+rt +R l++G+i+ p++al+f++vl+
  gi|557694193|ref|YP_008797247.1|  23 AFTGAAGIVAASNGLPDPYLFTVAILSITLGVAGTEAASNYLELSLDSVMKRTSKRVLPRGLINpPWKALVFGLVLM 99 
                                       5788999*********************************************************899********** PP

                              UbiA  78 ilgllllalllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavf 153
                                        ++l+l+ +l+np+t+++++ +++ y vvY  ++ Krrt+l++++g+ a+g p+++g++av+ + +++a++la+++ 
  gi|557694193|ref|YP_008797247.1| 100 TISLILA-YLINPVTFFFMATGMFDYlVVYV-MWSKRRTPLNIILGSYAGGAPLMAGYTAVSYWPTAEAFILAALIV 174
                                       *******.***********************.5******************************************** PP

                              UbiA 154 lltwaialandlrdregDrkagiktlpvvlGrkaaril..lalllavllla.llllllalllllylllalllaalal 227
                                       l++ ++++  +l  +e++ +a++++lpvv  +++a+++  ++ ++ vl+ + l++l++  ++l+yl++a+l++++++
  gi|557694193|ref|YP_008797247.1| 175 LWIPPHIWSLALIYKEDYMRAHVPMLPVVTSEATAIRCisSTTIISVLFTFlLYFLYPEKYGLIYLVAAALSGLMIV 251
                                       *********99999***********************8663334444444467788888999999999999999999 PP

                              UbiA 228 lraarlvrrrdakkaakff 246
                                       l aa l+ + ++k+a  +f
  gi|557694193|ref|YP_008797247.1| 252 LPAAALMVKPNRKTAYLLF 270
                                       9999999999999987766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       756  (0.0421663); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2201.11
//
Query:       gi|557694194|ref|YP_008797248.1|  [L=441]
Description: dihydroorotase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-27   94.6   0.0    8.6e-27   94.3   0.0    1.1  1  Amidohydro_1  Amidohydrolase family
    1.7e-18   67.4   0.1    2.1e-08   34.1   0.0    2.3  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
       0.13   12.6   0.2       0.69   10.3   0.1    2.2  3  Urease_alpha  Urease alpha-subunit, N-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 !   94.3   0.0   1.4e-30   8.6e-27       1     322 [.      50     392 ..      50     423 .. 0.74

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 1.4e-30
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH..HHHHHHHHHHT... CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst..giealleaaee... 72 
                                       +v+PG++D HvH++             +p+ +++e + +g ++a  +G+ttv++m++t ++   ++ l++ ae    
  gi|557694194|ref|YP_008797248.1|  50 YVFPGFVDEHVHFR-------------EPGYEWKEDFSTGSAAAAAGGVTTVLEMPNTVPPvaDASTLRKKAELvrg 113
                                       69***********9.............******************************8777*977777777777556 PP

                                       .SSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTE CS
                      Amidohydro_1  73 .lplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlp 147
                                         +++++++g        ++++  ++ e l+aga  ++      ++  +++++ e+p+ +  ++ eal + ++++  
  gi|557694194|ref|YP_008797248.1| 114 kSWVDYGLYGV------LTDQSLNNLEEMLEAGAVGFK------AFLgPTTGDIEQPSDP--TIIEALTLSREKGFT 176
                                       88888888876......555555555555555553333......3444999999999998..*************** PP

                                       EEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCC...HHTTTHCCEE.........EHCTCEEE.HHHHHHHHHHHH CS
                      Amidohydro_1 148 vaiHaletkgevedaeaafgetiehgthlevaes...lglldeikli.........lahgvhlt.pteaellkerlk 211
                                       +a+H+ e+++ v + e++     e  ++l+ ++s   ++  d++  i         +a +vhl+  + + +l+ +  
  gi|557694194|ref|YP_008797248.1| 177 IAFHC-ENRHLVHHYEQKTR--REPVSPLSHLHSrpaICEVDSVIKInyyaaktggRALIVHLSsGEAVDYLRGN-- 248
                                       *****.55555544444444..44456666666655545544433335666666669999999975544443333.. PP

                                       HHCEE..........HHHHHHHH..............SEHHHHHHHHHHHHTSCEEEEEECT............... CS
                      Amidohydro_1 212 eagva..........hcpfsnsi..............lrsgrealrkaldeGvkvglgtDga............... 249
                                         + +          ++ +sn++                ++re+l + l+++v+  +g+D+a               
  gi|557694194|ref|YP_008797248.1| 249 --KAPsvfvetcpqyLLLDSNDYqrfgnlikvnppirFPEDREKLLQGLRANVITNIGSDHAphtleekrknvfeap 323
                                       ..3333456899999888899999999999********************************999888554444444 PP

                                       TSSCCGGHHHHHHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC.CT... CS
                      Amidohydro_1 250 asgnslnlleelrlalklqrgllye.deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl.di... 321
                                       a          + ++++l  +l  +   +g++ l+++ ++ ++n+Ak +gl+ ++G +  G dAD++++d+ ++   
  gi|557694194|ref|YP_008797248.1| 324 A----------GMFGVELLGPLMVDmALRGHIHLEKVAEVLSTNPAKTFGLYPRKGGLLIGSDADFAIFDPrTPtki 390
                                       2..........33333222222222334999**************************************99733333 PP

                                       .C CS
                      Amidohydro_1 322 .l 322
                                         
  gi|557694194|ref|YP_008797248.1| 391 qA 392
                                       41 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   2.5e-11   1.5e-07       1      92 [.      42     142 ..      42     152 .. 0.75
   2 !   34.1   0.0   3.4e-12   2.1e-08     407     472 ..     344     423 ..     296     424 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.5e-11
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrdqagtt.........pkgrwivgeGwd 67 
                                       +v+Da+G++v+PGFvD H H  + g+++   ++ +   + ++ gv+t+++    +          +k +++ g  w 
  gi|557694194|ref|YP_008797248.1|  42 DVVDASGMYVFPGFVDEHVHFREPGYEWkEDFSTGS-AAAAAGGVTTVLEMPNTVPpvadastlrKKAELVRGKSWV 117
                                       69**************************88888777.6778889999987666555666666666666666777776 PP

                      Amidohydro_3  68 eaqfaeerfpyalaeldevledapv 92 
                                       +  ++    +++l++l+e le+++v
  gi|557694194|ref|YP_008797248.1| 118 DYGLYGVLTDQSLNNLEEMLEAGAV 142
                                       6666666666666666666666665 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 3.4e-12
                      Amidohydro_3 407 elsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear.............vrltvvdG 469
                                        + le+++  ++++pAk++gl  rkG+L +G dAD++++d + p ++++++l+++               r+tv +G
  gi|557694194|ref|YP_008797248.1| 344 HIHLEKVAEVLSTNPAKTFGLYPRKGGLLIGSDADFAIFDpRTPTKIQAAKLHSKHrftpfdgreilakHRYTVLRG 420
                                       57799999***********************************************9********************* PP

                      Amidohydro_3 470 rvv 472
                                       +++
  gi|557694194|ref|YP_008797248.1| 421 KII 423
                                       *97 PP

>> Urease_alpha  Urease alpha-subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00012      0.69      66     101 ..       2      37 ..       1      53 [. 0.85
   2 ?   -3.0   0.0       1.4   8.5e+03      10      19 ..     146     155 ..     143     164 .. 0.77
   3 ?   -1.5   0.0      0.52   3.1e+03      87     112 ..     294     319 ..     292     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                      Urease_alpha  66 lDlvitnavilDatgivkadigikdgrivaiGkagn 101
                                        Dl+i +  i+  +g+++a i +  g+i+a G   +
  gi|557694194|ref|YP_008797248.1|   2 SDLIIRDGYIVSPQGVTRASIYVSGGKIAAFGEKFD 37 
                                       69*****************************98765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.4
                      Urease_alpha  10 elyGptvgDr 19 
                                       +  Gpt+gD 
  gi|557694194|ref|YP_008797248.1| 146 AFLGPTTGDI 155
                                       567*****95 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.52
                      Urease_alpha  87 gikdgrivaiGkagnpdvmdgvdeel 112
                                       g++   i++iG    p++ ++  +++
  gi|557694194|ref|YP_008797248.1| 294 GLRANVITNIGSDHAPHTLEEKRKNV 319
                                       789999**********9998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
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: 00:00:00.42
# Mc/sec: 3125.36
//
Query:       gi|557694195|ref|YP_008797249.1|  [L=770]
Description: molybdenum hydroxylase family protein, large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-168  559.9   0.1   6.5e-168  559.6   0.1    1.1  1  Ald_Xan_dh_C2    Molybdopterin-binding domain of aldehyde deh
    1.2e-15   57.8   0.0    2.8e-15   56.6   0.0    1.7  1  Ald_Xan_dh_C     Aldehyde oxidase and xanthine dehydrogenase,
  ------ inclusion threshold ------
      0.046   13.7   0.0      0.097   12.6   0.0    1.5  1  Gram_pos_anchor  LPXTG cell wall anchor motif


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 !  559.6   0.1  1.1e-171  6.5e-168       1     550 []     160     707 ..     160     707 .. 0.97

  Alignments for each domain:
  == domain 1  score: 559.6 bits;  conditional E-value: 1.1e-171
                                       STTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHH CS
                     Ald_Xan_dh_C2   1 vheeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlv 75 
                                       vhee+++n++   +++kGdv  + +e+d vve+++ ++ q+h+y+Et+aala+p  + + +tv s+ q ph  +++v
  gi|557694195|ref|YP_008797249.1| 160 VHEEKGSNIAVtaQVRKGDVTVGERESDEVVEKTYVLSPQDHVYMETEAALAIP--SIDGVTVISQAQYPHLAQKTV 234
                                       6999999999988999**************************************..6788***************** PP

                                       HHHHT--GGGEEEE-SB-S--TTTT.SS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TT CS
                     Ald_Xan_dh_C2  76 aevlglpenkvrvivprvGGGFGgK.tqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkd 151
                                       a+vlg+p +kv +i+p +GG+FGgK     ++++ aala++k+g+pV l+++Ree++++++kr p  ik+++ga++d
  gi|557694195|ref|YP_008797249.1| 235 ARVLGIPYSKVAIIQPAIGGAFGGKdDMGPIVSAQAALACWKLGKPVYLQYSREESFTSHCKRDPAVIKCRTGASRD 311
                                       *************************99999*********************************************** PP

                                       S-EEEEEEEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 152 GkitaldvdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdel 228
                                       G ++ ld++++ d Gaya+ +p +l+ra++h+ gpY+ip+v+v g++vytN++ ++ fRGfG+pqa fa+Er+mdel
  gi|557694195|ref|YP_008797249.1| 312 GLLKFLDAEVIFDSGAYANRGPYTLWRACVHVSGPYRIPHVNVVGKLVYTNKVYQGSFRGFGNPQAEFAAERQMDEL 388
                                       ***************************************************************************** PP

                                       HHHHT--HHHHHHHHBCECGCC.SEEETEESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS CS
                     Ald_Xan_dh_C2 229 AeelgldplelRrrNlikpgeltpygqpvydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegig 305
                                       A++lg+dp+e+R +Nl++pg+l  + qp+ ++ +++ l++k+++++++ ++r+e       + ++G g+a++++gi+
  gi|557694195|ref|YP_008797249.1| 389 ARRLGIDPIEFRLKNLLRPGDLSATSQPMPEDTGIAPLVEKMRNQLHIPKKRREN------GYQYGYGFAVAWHGIS 459
                                       **********************99****99****************998776653......3569***********5 PP

                                       --S.EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HH CS
                     Ald_Xan_dh_C2 306 lgftakflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrst 382
                                       ++  +  ++ ++a+++v  dGsv+vs+g +e+GqG++t++ q++ae+Lg+p+e v+++ g t+ +p++++t +Sr+ 
  gi|557694195|ref|YP_008797249.1| 460 TS--RGVPDWGSATLTVLRDGSVVVSSGIVEFGQGTHTAIKQVVAEVLGIPYEWVKLEGG-TSYAPDTGATHGSRGL 533
                                       55..467999**********************************************9876.667799999******* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHHTTSSEEEEEEE..... CS
                     Ald_Xan_dh_C2 383 dlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaaylervslsatgfykt... 453
                                       +l+g+A++ Aa ++r+r+ k+aae+le++p+d+e++dgkv+v+   +k +++++++aa+y+++v+l+++g++     
  gi|557694195|ref|YP_008797249.1| 534 TLGGSAALVAAGRVRKRVVKVAAEMLEANPDDIEIADGKVFVRgveNKMLDWRDVVAACYSKGVDLTSSGYFFLkkd 610
                                       *******************************************9977777*********************85689* PP

                                       ..EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEET CS
                     Ald_Xan_dh_C2 454 .ldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvyde 529
                                        +de++g+g+++ ++++ a+++eV vDtetg+v+v +v+    +G++iNp i+ gQi+G++vq +G+ l+E++v+ e
  gi|557694195|ref|YP_008797249.1| 611 kFDESRGQGHAYTVYSFSAVLVEVRVDTETGKVEVTNVWPGAACGRIINPGIALGQIHGSVVQSLGYSLTERMVF-E 686
                                       ***************************************************************************.8 PP

                                       TTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 530 dGqlltasladYkiPtaadiP 550
                                       +G+lltasl+dY+iP+aa++P
  gi|557694195|ref|YP_008797249.1| 687 EGRLLTASLMDYLIPSAAETP 707
                                       *******************98 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 !   56.6   0.0   4.8e-19   2.8e-15       2     110 .]      45     145 ..      44     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 4.8e-19
                                       T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEES CS
                      Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkvr 78 
                                       G  +Yv+D+    +l++++vrS ++h+ ++si+ ++++ +      +ta d+p+en+ +  + +d++  +lae+kvr
  gi|557694195|ref|YP_008797249.1|  45 GMLRYVEDYVDGRCLHARIVRSMVPHGLLKSIKLNDSRGH-----LVTARDVPGENQVGY-AVADQP--VLAEKKVR 113
                                       7789*****988888********************99875.....6*********98885.566665..******** PP

                                       STT-EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                      Ald_Xan_dh_C  79 svgqavaavvAedeetArkAaklvkveYeelp 110
                                       ++g++va+vv  + + A++ +++v+ve e+lp
  gi|557694195|ref|YP_008797249.1| 114 FYGEPVALVVSGNGYSAEDLLEKVEVEVEPLP 145
                                       ***************************99875 PP

>> Gram_pos_anchor  LPXTG cell wall anchor motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.6e-05     0.097      10      32 ..     522     545 ..     522     552 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                                       XXXX.XXXXXXXXXXXXXXXXXXX CS
                   Gram_pos_anchor  10 PkTG.engnifltaaGllallggl 32 
                                       P+TG ++g+ +lt++G++al++++
  gi|557694195|ref|YP_008797249.1| 522 PDTGaTHGSRGLTLGGSAALVAAG 545
                                       9***77**************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (770 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 5328.49
//
Query:       gi|557694196|ref|YP_008797250.1|  [L=764]
Description: molybdenum hydroxylase family protein, large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-141  470.5   6.8   8.3e-141  470.1   6.8    1.1  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    5.8e-24   84.6   0.1    1.3e-23   83.4   0.1    1.7  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 !  470.1   6.8  9.3e-145  8.3e-141       6     549 ..     161     701 ..     157     702 .. 0.92

  Alignments for each domain:
  == domain 1  score: 470.1 bits;  conditional E-value: 9.3e-145
                                       STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHHT CS
                     Ald_Xan_dh_C2   6 pdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevlg 80 
                                       ++n+ +  ++e G  e+a ++   + e++frt+  + +++E++a+++ p + dg+l+vy++tq +h +r  +a++l+
  gi|557694196|ref|YP_008797250.1| 161 ESNIGFmdTVEIGSREDAYSRVVKTYEDSFRTQILYNAAIEPRAMIVSP-RPDGTLDVYCTTQSIHGTRYWLAKALQ 236
                                       566666678999***********99************************.77************************* PP

                                       --GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEE CS
                     Ald_Xan_dh_C2  81 lpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkital 157
                                       lp+nkv+v+   +GGGFG K++ +++e+++a++A+ tgr Vk+v +R++d+  t+ r++ ++++++g++++G+i a+
  gi|557694196|ref|YP_008797250.1| 237 LPMNKVVVHGMTLGGGFGAKYNLAIHEPVIAYLAQVTGRTVKFVSTRQQDFY-TTARRAAYMDVRLGVSREGRIEAM 312
                                       ***************************************************8.66788999**************** PP

                                       EEEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT- CS
                     Ald_Xan_dh_C2 158 dvdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgl 234
                                       +++ + + Gayad+    ++ + + + + Y      +eg++vytN p ++a+RGfG+pq +falE+l+de+Ae lg+
  gi|557694196|ref|YP_008797250.1| 313 EMRAVLQSGAYADHMLEAVTCTGGWFISSYAAGYRYFEGKGVYTNLPVCGAMRGFGNPQQNFALESLVDEIAEDLGM 389
                                       ***************************************************************************** PP

                                       -HHHHHHHHBCECGCC.SEEET.....EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS- CS
                     Ald_Xan_dh_C2 235 dplelRrrNlikpgeltpygqp.....vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegigl 306
                                       dple+R +Nl + g++  ygq      v  s  l+++ +k++e++++   r+ ++   ++    G+++   + g+g 
  gi|557694196|ref|YP_008797250.1| 390 DPLEFRLKNLPRVGDI-YYGQGptvttVIRSMALEQVARKTAEAFGWTTERRVVDGVARA---CGVAVGHHTSGTGG 462
                                       ****************.9999667777889*****************9998888877754...77777777777776 PP

                                       -S...EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-H CS
                     Ald_Xan_dh_C2 307 gf..takflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrs 381
                                        +  ++++++ +g+ +++n+dG+ +++t+++emG G + +la i+ae+Lg+++edv+v+ g+t+ +p+++gt aSr+
  gi|557694196|ref|YP_008797250.1| 463 EMseQQDRQEGAGVVLKLNEDGTLSLNTAMVEMGPGEHETLAAICAEALGTRPEDVYVEIGNTQYTPFDMGTHASRG 539
                                       66533344444789999************************************************************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHHTTS..SEEEEEEE.. CS
                     Ald_Xan_dh_C2 382 tdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaaylerv..slsatgfykt 453
                                       t+++g Av  Aaeklre++l  aae+le+sp+dl++edg v++    +k++sl+ +a++  +++   +++ +g    
  gi|557694196|ref|YP_008797250.1| 540 TYVGGLAVVSAAEKLREQILTQAAEMLECSPKDLRIEDGWVMHVedtDKRLSLSAVAMRFKTRKGflPIAVSGL--- 613
                                       *****************************************999998889999999996633332235555555... PP

                                       .EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETT CS
                     Ald_Xan_dh_C2 454 ldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvyded 530
                                               p  a  + ++ +a+V+vD etg+vkv+++   +D+G ++Np  + gQ +GG++ GiG+al+Ee+v+ +d
  gi|557694196|ref|YP_008797250.1| 614 -------RPNAAPPSWAVIFAQVAVDLETGAVKVEKIAGGYDIGVVVNPSEAAGQAHGGIATGIGYALLEEVVV-QD 682
                                       .......3333445789*********************************************************.8* PP

                                       TEESS-STTTS----GGGS CS
                     Ald_Xan_dh_C2 531 GqlltasladYkiPtaadi 549
                                       G++++ s++dY++P+a+d+
  gi|557694196|ref|YP_008797250.1| 683 GKYINPSFMDYLLPSATDA 701
                                       ****************995 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 !   83.4   0.1   1.5e-27   1.3e-23       1     109 [.      19     130 ..      19     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 1.5e-27
                                       TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT.....TSSS-EE...E CS
                      Ald_Xan_dh_C   1 tGeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig.....siledee...d 69 
                                       tG+ +Y+ Di+ +++l++a++ S+++hA +++idvs+al++pGV+av+t  ++p+++         +     +   d
  gi|557694196|ref|YP_008797250.1|  19 TGRLKYTADIQPAKTLHAALLHSPYPHAVVKQIDVSKALKTPGVAAVLTPFNVPQHRFGRTfspvpW-----KvicD 90 
                                       89******************************************************88876443221.....12345 PP

                                       ESS-SSEESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                      Ald_Xan_dh_C  70 allaedkvrsvgqavaavvAedeetArkAaklvkveYeel 109
                                       + ++++  r++g++vaav+A++ etA +A+++++v+Ye l
  gi|557694196|ref|YP_008797250.1|  91 RKIIDRVQRFAGDIVAAVAADSPETAYDAVEKIEVDYEVL 130
                                       567777889*****************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (764 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 00:00:00.43
# Mc/sec: 5356.02
//
Query:       gi|557694197|ref|YP_008797251.1|  [L=345]
Description: isocitrate dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-90  301.6   0.0    8.5e-90  301.4   0.0    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


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 !  301.4   0.0   4.8e-94   8.5e-90       3     347 ..       5     335 ..       3     336 .. 0.96

  Alignments for each domain:
  == domain 1  score: 301.4 bits;  conditional E-value: 4.8e-94
                                       EEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHS..SSS-HHHHHHHHHSSEEEEEE---CS.S CS
                            Iso_dh   3 allegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetg..eplpeetleaikeadvvllgavgtpk.e 76 
                                       +l++gdg+Gpe  +a +kvl+a++  ++  le+ e+++G +   ++g  +++p+et eai+++d+  + +++tp  +
  gi|557694197|ref|YP_008797251.1|   5 VLIKGDGTGPELAAALKKVLEAVS--PP--LEIIECEAGSEWWMKHGgnSMIPAETWEAIRSSDACFKSPTTTPPdP 77 
                                       789********************9..66..99**********99999889***********************9856 PP

                                       SSSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEE CS
                            Iso_dh  77 kevrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavd 153
                                       +  r+    +++r+ +dl+an+rp+k f   +++spl + + + +d+v+vRe+t+g+Y+g e+  ++      v + 
  gi|557694197|ref|YP_008797251.1|  78 NAPRSVA--VSIRQAMDLYANIRPIKTF--KGAESPLSS-IFGPFDFVCVREATEGLYSGLEHRLSDD-----VSIA 144
                                       6667777..9******************..899*****6.9999********************9997.....8*** PP

                                       EEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSG CS
                            Iso_dh 154 tklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaeeeypdielehqlvDsaamqlvksp 229
                                       + +++++++er+ar af++A +r+ +kv++++K+n+l++++  + + ve va+ e+p+i +e+ ++D++ +ql+k+p
  gi|557694197|ref|YP_008797251.1| 145 IRKITRRGSERVARWAFKIAAERNWSKVIVITKRNILRVTDgVFWEAVETVAK-EFPGISYEEYYIDNMSQQLIKNP 220
                                       *****************************************999999999999.*********************** PP

                                       GGGS..EEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHT CS
                            Iso_dh 230 kqfd..VivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLrys 304
                                       ++f+  V++ +Nlf D+lS +aa lvG +G++  a++g ++ a+fE++HGsap++ g d +Np+a+il+ a mL+y 
  gi|557694197|ref|YP_008797251.1| 221 DRFNqnVLLSTNLFMDVLSEAAAGLVGNIGMVYAANIG-DRYAMFEPAHGSAPKYKGMDRVNPTATILAGAWMLKY- 295
                                       999889********************************.79***********************************. PP

                                       TT-HHHHHHHHHHHHHHHHH.TSCCHHHCTTSTCCCHHHHHHHH CS
                            Iso_dh 305 lgleeaAdkiekAvekvlea.givTkDlageaakevstsefgda 347
                                       lgl++  ++iekA e+v+++ ++vT Dl+g+a    +tse+  +
  gi|557694197|ref|YP_008797251.1| 296 LGLNKYGEAIEKATEQVIAEhKVVTVDLGGTA----KTSEMAAE 335
                                       *******************999**********....99999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 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:                        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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2399.28
//
Query:       gi|557694198|ref|YP_008797252.1|  [L=571]
Description: succinate dehydrogenase flavoprotein subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-106  355.2   0.6   6.4e-106  354.9   0.6    1.1  1  FAD_binding_2   FAD binding domain
    2.8e-36  124.3   0.2    4.2e-36  123.8   0.2    1.3  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    1.9e-06   27.3   2.6     0.0002   20.7   1.1    3.0  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    6.2e-05   22.2   0.6    0.00016   20.9   0.3    1.8  2  GIDA            Glucose inhibited division protein A
     0.0038   16.6   3.9      0.022   14.1   3.8    2.2  3  FAD_oxidored    FAD dependent oxidoreductase
     0.0083   15.7   0.3      0.016   14.8   0.1    1.6  2  DAO             FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.057   12.1   2.7        0.2   10.3   0.9    2.4  3  HI0933_like     HI0933-like protein
      0.065   12.5   0.9       0.12   11.6   0.9    1.4  1  FAD_binding_3   FAD binding domain
      0.091   12.0   0.4       0.23   10.7   0.4    1.6  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain


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 !  354.9   0.6  3.2e-109  6.4e-106       1     416 [.       8     390 ..       8     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 354.9 bits;  conditional E-value: 3.2e-109
                                       SEEEE--SHHHHHHHHHHHHTTT.-EE..EEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTT CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGl.kva..vvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkald 74 
                                       Dv ViGsGlAGL+AA+eaa+ G+ kv+  v +k+q+++++++ ++Gg +avl+pe      +ds+++h++dt+k++d
  gi|557694198|ref|YP_008797252.1|   8 DVAVIGSGLAGLRAAIEAARVGRdKVVvgVFTKTQVMRSHSVSAEGGTAAVLYPEE-----GDSLQSHMYDTVKGSD 79 
                                       9*******************99988773358*********************9998.....8*************** PP

                                       T-S-HHHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHH CS
                     FAD_binding_2  75 eladqplveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesa 151
                                        ladq++ve+fv++ape++ +Le++g+p+ r+edg++++r +Gg+s + r ++ a d+       g+  + +l+++a
  gi|557694198|ref|YP_008797252.1|  80 FLADQDAVELFVKKAPEEILQLERWGMPWARREDGKIAQRFFGGQSFP-RACY-AEDK------VGFFEMSTLYDTA 148
                                       ************************************************.****.9999......999999******* PP

                                       HTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S- CS
                     FAD_binding_2 152 rkag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtG 227
                                       +k + ++f+++++a++L+ve+g+  G v+ ++++g+++++ aka vlatgG+gr           +  +t     t 
  gi|557694198|ref|YP_008797252.1| 149 LKFDnIHFYPEWAAVSLLVENGKFKGLVALELKTGKIHTVSAKAGVLATGGAGR----------LYSFATFGYSSTP 215
                                       99999*************************************************..........************* PP

                                       HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH.......GGGS-HHHHHH CS
                     FAD_binding_2 228 dglalalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm.......nelasrdvvsr 297
                                       dgl +a+raga+l+d  me+vqfhPt+lv    +sgiLitea+rgeGgil +++G+rFm       +ela+rd+vsr
  gi|557694198|ref|YP_008797252.1| 216 DGLYIAYRAGAPLKD--MEFVQFHPTGLV----PSGILITEAARGEGGILTNANGERFMkryapekMELAPRDIVSR 286
                                       ***************..************....******************************************** PP

                                       HHH.HHHHTTTS......CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEE CS
                     FAD_binding_2 298 ailekeiaeggs......eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpa 368
                                       a+  +ei e ++       ++ yld++  l+ae+++++l++i+e +++ ++      idp ++pip       v+p 
  gi|557694198|ref|YP_008797252.1| 287 AMY-NEITEDRGvegpggVKCLYLDLTV-LGAEKIKKKLAGIREYCMRLAG------IDPINEPIP-------VRPV 348
                                       ***.****99999***9988********.*******************999......*********.......**** PP

                                       EEEES-EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHH CS
                     FAD_binding_2 369 qhytmgGvetdengrvldadgqpipGLYAaGevaaggvhganrlgGns 416
                                       +hy mgGv t+  g +      +++GL+AaGeva+++++ganrlg+ns
  gi|557694198|ref|YP_008797252.1| 349 AHYYMGGVDTNIGGAT------AVKGLWAAGEVACVSINGANRLGSNS 390
                                       ****************......*************************8 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 !  123.8   0.2   2.1e-39   4.2e-36       1     128 []     447     571 .]     447     571 .] 0.94

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 2.1e-39
                                       .HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHH.HTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S CS
                    Succ_DH_flav_C   1 rkeLgkimqkkvgvfRteegLkealkelkelrer.lknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkE 76 
                                       r+eL+++m++ + ++R+e++L ++++ ++++r++ ++  +v d+s+ +N++l+++le++ ++e+Ae+i+ sAl+RkE
  gi|557694198|ref|YP_008797252.1| 447 RQELQTTMEQTCHIYREEKSLLQGIDAVRKIRQKlFR--GVVDSSRYYNTNLMNVLEIEMMIEVAEVILISALNRKE 521
                                       79********************************666..999*********************************** PP

                                       -BTTBEBTTS-SEETTT-SEEEEE...TT-SS-EEEEEE--GGG--S---SS CS
                    Succ_DH_flav_C  77 SrGaHaredfperdDenwlkhtlasldaakeeveleyepveletlkpkeRsY 128
                                       SrGaHar d+p+rdD n+lkhtla++++  + +++ey    +++ +p+eR Y
  gi|557694198|ref|YP_008797252.1| 522 SRGAHARLDYPKRDDINFLKHTLAYYTE--DGPRIEYISPVITEYAPTERRY 571
                                       ************************8775..59*****777777799****99 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 !   20.7   1.1   9.8e-08    0.0002       2      58 ..       8      97 ..       7     214 .. 0.59
   2 ?    4.0   0.0     0.012        24     256     279 ..     354     381 ..     342     394 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.8e-08
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH....................... CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias....................... 57
                                      dv+viG+G AGl+aa+++a+ g + ++v   g +   +++ s+ + + ++ a ++                        
  gi|557694198|ref|YP_008797252.1|  8 DVAVIGSGLAGLRAAIEAARVGRDKVVV---GVFTKTQVMRSHSVSAEGGTAAVLYpeegdslqshmydtvkgsdflad 83
                                      8*******************98888888...555555555555555555555444453333344555555555555555 PP

                                      .............H CS
                                      .............x RF
                       Pyr_redox_2 58 .............e 58
                                                   e
  gi|557694198|ref|YP_008797252.1| 84 qdavelfvkkapeE 97
                                      55555555555550 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.012
                                       TEEE--TTSBESSTTEEE-GGGC....T CS
                                       xxxxxxxxxxxxxxxxxxxxxxx....x RF
                       Pyr_redox_2 256 ggivvdeflrtnvpgiyaiGDva....g 279
                                       gg+ ++  ++t v+g++a+G va    +
  gi|557694198|ref|YP_008797252.1| 354 GGVDTNIGGATAVKGLWAAGEVAcvsiN 381
                                       677777788**************66553 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.3   8.1e-08   0.00016       1      66 [.       8      74 ..       8      82 .. 0.80
   2 ?   -2.6   0.0       1.1   2.2e+03     121     150 ..     165     199 ..     160     213 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8.1e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEE.E-TTHHHHHHHHHHHT-SHHHH CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsi.ggiakgllvrEidalggliika 66
                                      dv ViG G+AG+ AA++aar G + + +   ++t +  s + s  gg+a+ l  +E d l++ +  +
  gi|557694198|ref|YP_008797252.1|  8 DVAVIGSGLAGLRAAIEAARVGRDKVVVGVFTKTQVMRSHSVSAeGGTAAVLYPEEGDSLQSHMYDT 74
                                      79********************998888666666666666555516668888889999999999776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.1
                                       EEECTTEEEE.EE....ETTS-EEEECEEEE--TT CS
                              GIDA 121 liveekkvkg.vv....tedgetikakavviatGt 150
                                       l+ve++k kg v     t + +t++aka v+atG 
  gi|557694198|ref|YP_008797252.1| 165 LLVENGKFKGlVAlelkTGKIHTVSAKAGVLATGG 199
                                       44666666663221111334457889999999997 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   3.8   1.1e-05     0.022       1      28 [.       8      35 ..       8      39 .. 0.93
   2 ?   -1.5   0.0      0.62   1.2e+03      90     145 ..     142     199 ..     128     211 .. 0.84
   3 ?   -3.2   0.0         2   4.1e+03      26      54 ..     247     283 ..     246     298 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLv 28
                                      Dv V+G+g+aG+ AAi Aar G+  ++v
  gi|557694198|ref|YP_008797252.1|  8 DVAVIGSGLAGLRAAIEAARVGRDKVVV 35
                                      9*********************987766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.62
                      FAD_oxidored  90 kavleemlaeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDATgd 145
                                        ++++  l+ ++++ + +  +v+  +e+++ +++++ + + g  +t++Ak  + ATg 
  gi|557694198|ref|YP_008797252.1| 142 STLYDTALKFDNIHFYPEWAAVSLLVENGKFKGLVALELKtGkIHTVSAKAGVLATGG 199
                                       567888889999999999999999999989999888888878899****999999874 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2
                      FAD_oxidored  26 lLveergvlGGlltsglvatdignkaee........q 54 
                                       l++e  +  GG lt++ +  +++ +a+e         
  gi|557694198|ref|YP_008797252.1| 247 LITEAARGEGGILTNANGERFMKRYAPEkmelaprdI 283
                                       5777788889999999999999999877665544433 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   8.1e-06     0.016       1      85 [.       8     114 ..       8     125 .. 0.68
   2 ?   -3.8   0.0       3.7   7.3e+03     176     202 ..     182     199 ..     162     209 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.1e-06
                                       EEEEECTSHHHHHHHHHHHHTT.....EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTH................. CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg.....VtllekgdiagsgaSgrnsgllhsglrylpeas................. 55 
                                       dv++iG+G +Gl +A e+ar g     V ++ k     s++ ++ +g  +  +  ++e+                  
  gi|557694198|ref|YP_008797252.1|   8 DVAVIGSGLAGLRAAIEAARVGrdkvvVGVFTKTQVMRSHSVSAEGGTAAVLY--PEEGDslqshmydtvkgsdfla 82 
                                       8*****************99788899999999996666566666666665533..4444334555666666666666 PP

                                       ...HHHHHHHHHHHHHHHHHHHHSSTTSEEEEE CS
                               DAO  56 ...elarlslealeelreleeelgididyrrtG 85 
                                          ++  +++ a ee+ +le+  g+++  r+ G
  gi|557694198|ref|YP_008797252.1|  83 dqdAVELFVKKAPEEILQLERW-GMPWARREDG 114
                                       6653334555666666666653.6666666555 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.7
                                       ETCEEEEEEECTEEEEEEEEEEE--GG CS
                               DAO 176 dgkvwgverttpgendaadavVnaaGa 202
                                        gk+++v         +a+a V+a+G 
  gi|557694198|ref|YP_008797252.1| 182 TGKIHTV---------SAKAGVLATGG 199
                                       2222222.........46888888885 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.9    0.0001       0.2       2      28 ..       8      34 ..       7      54 .. 0.85
   2 ?    0.3   0.0      0.11   2.1e+02     143     186 ..     178     227 ..     153     236 .. 0.78
   3 ?   -2.9   0.0         1     2e+03     372     384 ..     363     375 ..     353     394 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0001
                                      SEEEE--SHHHHHHHHHHHHTT--EEE CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVll 28
                                      dv+viG G AGl aAi+aa+ g++ ++
  gi|557694198|ref|YP_008797252.1|  8 DVAVIGSGLAGLRAAIEAARVGRDKVV 34
                                      89****************998876444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                                       EEEEE.TTEEEEESEEEE----S....S-GGGT..--SHHHHHHHHTT-- CS
                       HI0933_like 143 frvktkseeeleadklvlAtGGl....SiPklG..stgkgyklaeqfght 186
                                       +++kt + ++++a++ vlAtGG+    S+++ G  st++g  +a  +g  
  gi|557694198|ref|YP_008797252.1| 178 LELKTGKIHTVSAKAGVLATGGAgrlySFATFGysSTPDGLYIAYRAGAP 227
                                       45666677899***********7555578888777788888887777765 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1
                                       BTTSTTEEE-GGG CS
                       HI0933_like 372 skkvpgLffaGEv 384
                                       + +v+gL+ aGEv
  gi|557694198|ref|YP_008797252.1| 363 ATAVKGLWAAGEV 375
                                       56799*******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 ?   11.6   0.9   5.8e-05      0.12       1      33 [.       6      38 ..       6      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.8e-05
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                      ++dV+++G+G+aGl +a + ++ G + v+v   
  gi|557694198|ref|YP_008797252.1|  6 DVDVAVIGSGLAGLRAAIEAARVGRDKVVVGVF 38
                                      689*********************999998654 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 ?   10.7   0.4   0.00011      0.23      30      56 ..       8      34 ..       4      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                                      EEEEESTSHHHHHHHHHHHHTT-EEEE CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtv 56
                                       v viG G aGl A+  a+++g + +v
  gi|557694198|ref|YP_008797252.1|  8 DVAVIGSGLAGLRAAIEAARVGRDKVV 34
                                      699*****************9976444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (571 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3977.44
//
Query:       gi|557694199|ref|YP_008797253.1|  [L=156]
Description: succinate dehydrogenase cytochrome b-556 subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   48.7   1.1    1.2e-12   47.9   1.1    1.4  1  Sdh_cyt       Succinate dehydrogenase/Fumarate reductase tran
  ------ inclusion threshold ------
      0.071   13.1   0.1      0.071   13.1   0.1    2.7  3  OppC_N        N-terminal TM domain of oligopeptide transport 
      0.092   12.3   4.6        4.5    6.8   1.3    2.3  2  Ni_hydr_CYTB  Prokaryotic cytochrome b561


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 !   47.9   1.1     2e-16   1.2e-12      14     117 ..      15     140 ..       3     145 .. 0.74

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 2e-16
                           Sdh_cyt  14 yrlplgawlsilhritGvallvglllllvwlllalslsspesfarv............vallaspiklillllllla 78 
                                       +r+ l+ w + l+r++Gva+++ +++++++ + ++ +++p ++a               ++la+pi+ i l+ll++ 
  gi|557694199|ref|YP_008797253.1|  15 VRYGLERWSYTLQRVSGVAIIL-FFVMHIAETGNV-VGGPTVWAIPpyeyarqvwnetKEFLANPIFDIGLVLLAFM 89 
                                       567799****************.999998555443.455554444455555667777799**99************* PP

                           Sdh_cyt  79 llyHllnGiRhllwDlglgl.elesa...........rksalavlalaval 117
                                        ++H++nGiR+ l  +gl l ++++             ++ l+++ +++a+
  gi|557694199|ref|YP_008797253.1|  90 IFFHTFNGIRLTLAHFGLLLeKPKRPeypyhpgsmskAQRLLFWISIVLAT 140
                                       **************9999995544437888888876555555555555544 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 ?    1.0   0.8     0.071   4.2e+02      18      41 ..      29      62 ..      28      70 .. 0.48
   2 ?   13.1   0.1   1.2e-05     0.071       3      33 ..      63      96 ..      61     130 .. 0.80
   3 ?   -1.0   0.5       0.3   1.8e+03      20      32 ..     132     144 ..     125     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.071
                            OppC_N 18 vglvilllllli.......aifaPlia...Pydp 41
                                      v+ v ++l++++       ++ +P ++   Py +
  gi|557694199|ref|YP_008797253.1| 29 VSGVAIILFFVMhiaetgnVVGGPTVWaipPYEY 62
                                      4555566666663333333233455533445554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.2e-05
                            OppC_N  3 wqdaw...rrFkrNklAvvglvilllllliaifa 33
                                       +++w   + F+ N++  +glv+l++++++  f+
  gi|557694199|ref|YP_008797253.1| 63 ARQVWnetKEFLANPIFDIGLVLLAFMIFFHTFN 96
                                      578887767*******************995554 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.3
                            OppC_N  20 lvilllllliaif 32 
                                       ++i ++l+ +ai+
  gi|557694199|ref|YP_008797253.1| 132 FWISIVLATAAII 144
                                       6677777777776 PP

>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1   0.00096       5.8     137     163 ..      17      43 ..       6      46 .. 0.89
   2 ?    6.8   1.3   0.00076       4.5      49     122 ..      81     145 ..      63     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00096
                                       TS-THHHHHHH.HHHHHHHHHHHHHHH CS
                      Ni_hydr_CYTB 137 kggaqlarelHellaaallafvvlHia 163
                                        g++++  +l  ++++a+++f+v+Hia
  gi|557694199|ref|YP_008797253.1|  17 YGLERWSYTLQRVSGVAIILFFVMHIA 43 
                                       588999999**9**************8 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00076
                                       HHHHHHHHH.HHHHHHH------------STTTSSSSS----------------TTTHHHHHHHHHHHHHHHHHH CS
                      Ni_hydr_CYTB  49 aGlvllall.lfrllwlkkakkpspriifrqikrdltlllrgrkpeagknnplqklvhlllyvllvvliltGlll 122
                                       +Glvlla + +f  +            i+  + +   ll + + pe+++++     ++ ll+   +vl+   +++
  gi|557694199|ref|YP_008797253.1|  81 IGLVLLAFMiFFHTFN----------GIRLTLAHFGLLLEKPKRPEYPYHPGSMSKAQRLLFWISIVLATAAIIY 145
                                       5666666663333333..........5888888888888888888888888887776666666666555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1202.34
//
Query:       gi|557694200|ref|YP_008797254.1|  [L=117]
Description: succinate dehydrogenase subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-07   29.0   7.5    1.1e-06   28.7   7.5    1.2  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 !   28.7   7.5   6.2e-11   1.1e-06      24     119 ..       8     102 ..       3     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 6.2e-11
                           Sdh_cyt  24 ilhritGvallv.glllllvwlllalslsspesfarv....vallaspiklilllllllallyHllnGiRhllwD.l 94 
                                       +lh itG+++lv g ++l  ++ll++    + +f+      +a++ ++  ++ l +ll+ +++H++nG+R +l   +
  gi|557694200|ref|YP_008797254.1|   8 LLHYITGIGILVaGAIHLATVFLLSPY-EASMAFDGHpfsvIAVYRNILLAASLQALLIFVAFHGFNGVRTILSElY 83 
                                       69**********999999988887773.55556666688888889885555555777777777***********933 PP

                           Sdh_cyt  95 glglelesarksalavlalavalvl 119
                                             + ++  +++ +a++va+ +
  gi|557694200|ref|YP_008797254.1|  84 ------QGKTYLRVVNIAVTVAALA 102
                                       ......3333333444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 876.31
//
Query:       gi|557694201|ref|YP_008797255.1|  [L=237]
Description: succinate dehydrogenase iron-sulfur protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  116.8   0.1    9.6e-34  115.7   0.0    1.6  2  Fer2_3      2Fe-2S iron-sulfur cluster binding domain
    2.9e-09   37.3   0.9    2.9e-09   37.3   0.9    2.0  2  Fer4_8      4Fe-4S dicluster domain
      1e-08   35.6   7.5    3.6e-07   30.6   0.8    2.3  3  Fer4_17     4Fe-4S dicluster domain
    2.2e-08   34.5  13.3    3.6e-06   27.5   5.1    2.7  3  Fer4_7      4Fe-4S dicluster domain
    2.7e-07   30.6  11.2    5.4e-06   26.5   2.5    2.6  3  Fer4_9      4Fe-4S dicluster domain
    1.2e-06   28.5   3.9    1.2e-06   28.5   3.9    2.5  3  Fer4_10     4Fe-4S dicluster domain
    7.1e-05   22.5   2.1    7.1e-05   22.5   2.1    3.1  3  Fer4        4Fe-4S binding domain
    9.1e-05   23.3   2.9    9.1e-05   23.3   2.9    2.3  2  Fer4_16     4Fe-4S double cluster binding domain
    0.00037   20.7   1.9       0.14   12.3   0.0    2.6  3  Fer4_18     4Fe-4S dicluster domain
    0.00086   19.4   0.2    0.00086   19.4   0.2    2.8  3  Fer4_21     4Fe-4S dicluster domain
     0.0018   18.7   0.6     0.0018   18.7   0.6    3.2  3  Fer4_4      4Fe-4S binding domain
     0.0019   18.2   1.9     0.0019   18.2   1.9    3.0  2  Fer4_6      4Fe-4S binding domain
     0.0026   17.7   0.8     0.0083   16.1   0.1    2.1  2  Fer2        2Fe-2S iron-sulfur cluster binding domain
      0.006   16.3   2.0        1.2    9.0   0.0    2.3  2  Fer4_20     Dihydroprymidine dehydrogenase domain II, 4Fe-4S 
  ------ inclusion threshold ------
      0.032   12.8   0.0      0.042   12.4   0.0    1.1  1  RdRP_1      RNA dependent RNA polymerase
       0.06   14.2   4.8       0.17   12.7   0.6    2.6  2  Fer4_22     4Fe-4S dicluster domain
      0.064   13.4   1.7      0.064   13.4   1.7    3.5  3  Fer4_2      4Fe-4S binding domain
        3.6    8.7  23.1       0.25   12.4   4.9    3.0  2  Fer4_3      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 !  115.7   0.0   9.6e-37   9.6e-34       2     108 ..       6     109 ..       5     110 .. 0.95
   2 ?   -2.4   0.0       4.7   4.7e+03      41      57 ..     140     156 ..     112     170 .. 0.60

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 9.6e-37
                            Fer2_3   2 lkvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikd 78 
                                       ++v+R+dp++ +g++ +q+y+v++ +++tvl+ Ll+ike++dptl+ r sCr + CGsc+++inG p+laC + i++
  gi|557694201|ref|YP_008797255.1|   6 FRVFRYDPDK-DGRRSYQTYTVPTFKGMTVLQGLLHIKEKIDPTLSIRFSCRMATCGSCGMMINGLPRLACYTLIEE 81 
                                       89******65.459*************************************************************** PP

                            Fer2_3  79 lakqkseieleplpkfpvirDLvvDideml 108
                                       l++++  i++epl+++p+i+DLv+D +e++
  gi|557694201|ref|YP_008797255.1|  82 LKTRT--ITVEPLRNLPIIKDLVTDFEEFF 109
                                       *9886..*******************9987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.7
                            Fer2_3  41 evdptlafrasCregiC 57 
                                       e+++ ++f +  + g C
  gi|557694201|ref|YP_008797255.1| 140 ELERYIQFAYCIKCGLC 156
                                       34444555544333333 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.5       2.9   2.9e+03       4       8 ..      59      63 ..      49      79 .. 0.76
   2 !   37.3   0.9   2.9e-12   2.9e-09       2      65 .]     147     220 ..     146     220 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.9
                            Fer4_8  4 kCieC 8 
                                       C+ C
  gi|557694201|ref|YP_008797255.1| 59 TCGSC 63
                                      33333 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 2.9e-12
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaae.....dvqeeqvlee...........eealwsCttcgaCtevCp 62 
                                       + +Ci+Cg+C +aCpv  + k++l  +    ++     d  +++   e              l +C+  g+C++vCp
  gi|557694201|ref|YP_008797255.1| 147 FAYCIKCGLCYAACPVTATDKEFLGPQALA-QAyryyaD--SRD---EggvdrlrplaeGSRLLRCHFAGSCSKVCP 217
                                       679************877766665444444.33355321..222...233456777877899*************** PP

                            Fer4_8  63 vgi 65 
                                       +g+
  gi|557694201|ref|YP_008797255.1| 218 KGV 220
                                       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 ?   -0.5   0.1       1.9   1.9e+03      42      50 ..      56      64 ..      34      67 .. 0.71
   2 !   15.7   1.0   1.6e-05     0.016      30      57 ..     134     161 ..     117     165 .. 0.72
   3 !   30.6   0.8   3.6e-10   3.6e-07       2      61 .]     150     221 ..     149     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.9
                           Fer4_17 42 kaslCieCg 50
                                      ++ +C +Cg
  gi|557694201|ref|YP_008797255.1| 56 RMATCGSCG 64
                                      455555554 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.6e-05
                           Fer4_17  30 klglleeaekeekaslCieCgeCerkCP 57 
                                       +l++ ee e+  ++  Ci+Cg+C ++CP
  gi|557694201|ref|YP_008797255.1| 134 YLQSDEELERYIQFAYCIKCGLCYAACP 161
                                       335667777888999************9 PP

  == domain 3  score: 30.6 bits;  conditional E-value: 3.6e-10
                           Fer4_17   2 CiqCgyClpeCpsyeaydn..epkkllraakl..........glleeaekeekaslCieCgeCerkCPqgld 61 
                                       Ci+Cg C ++Cp  +  ++   p+ l++a+++           +l+   + ++  +C+  g C+++CP+g+d
  gi|557694201|ref|YP_008797255.1| 150 CIKCGLCYAACPVTATDKEflGPQALAQAYRYyadsrdeggvDRLRPLAEGSRLLRCHFAGSCSKVCPKGVD 221
                                       *************999887455888877776666666665444444466669*****************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 ?    0.4   0.0         1     1e+03      34      42 ..      56      64 ..       8      78 .. 0.75
   2 !   19.1   1.1   1.5e-06    0.0015      29      52 .]     141     164 ..     116     164 .. 0.63
   3 !   27.5   5.1   3.6e-09   3.6e-06       2      52 .]     150     220 ..     149     220 .. 0.62

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1
                            Fer4_7 34 dpekClgCg 42
                                      ++ +C +Cg
  gi|557694201|ref|YP_008797255.1| 56 RMATCGSCG 64
                                      445555554 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 1.5e-06
                            Fer4_7  29 ekveidpekClgCgaCvavCPtga 52 
                                        + +i+  +C+ Cg C a+CP+ a
  gi|557694201|ref|YP_008797255.1| 141 LERYIQFAYCIKCGLCYAACPVTA 164
                                       334889999999999999999876 PP

  == domain 3  score: 27.5 bits;  conditional E-value: 3.6e-09
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenek...............gtekv....ei.dpekClgCgaCvavCPtga 52 
                                       Ci+Cg C aaCpv a + +    ++               g++++    e+ +  +C + g+C +vCP+g+
  gi|557694201|ref|YP_008797255.1| 150 CIKCGLCYAACPVTATDKEFLGPQAlaqayryyadsrdegGVDRLrplaEGsRLLRCHFAGSCSKVCPKGV 220
                                       ************99999775322222222222222223333333344444414679************996 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.63   6.3e+02      36      42 ..      55      63 ..      20      76 .. 0.75
   2 !   16.3   1.6     8e-06     0.008      33      49 ..     143     163 ..     124     165 .. 0.68
   3 !   26.5   2.5   5.5e-09   5.4e-06       1      49 [.     149     219 ..     149     220 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.63
                            Fer4_9 36 C..igCgaC 42
                                      C   +Cg+C
  gi|557694201|ref|YP_008797255.1| 55 CrmATCGSC 63
                                      433346665 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 8e-06
                            Fer4_9  33 e....eaCigCgaCveaCpkg 49 
                                              Ci+Cg C++aCp +
  gi|557694201|ref|YP_008797255.1| 143 RyiqfAYCIKCGLCYAACPVT 163
                                       0333446***********986 PP

  == domain 3  score: 26.5 bits;  conditional E-value: 5.5e-09
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpkg 49 
                                       +C++Cg C +aCp +++ ++  +  a  +a+++                       +C++ g+C ++Cpkg
  gi|557694201|ref|YP_008797255.1| 149 YCIKCGLCYAACPVTATDKEFLGPQALAQAYRYyadsrdeggvdrlrplaegsrlLRCHFAGSCSKVCPKG 219
                                       6***************9999999888888888899999*****************99************98 PP

>> Fer4_10  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       1.8   1.8e+03       8      51 ..      59      63 ..      42      68 .. 0.67
   2 !   28.5   3.9   1.2e-09   1.2e-06       4      56 .]     145     217 ..     142     217 .. 0.93
   3 !    8.6   0.5    0.0019       1.9       8      21 ..     205     218 ..     201     228 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.8
                           Fer4_10  8 tCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaC 51
                                      t                                       cg+C
  gi|557694201|ref|YP_008797255.1| 59 T---------------------------------------CGSC 63
                                      2.......................................3333 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 1.2e-09
                           Fer4_10   4 idddtCirCgkCvkaCPadl....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       i+   Ci+Cg C +aCP+++                    +++++   + +  a+   + +C++ g+C ++CP
  gi|557694201|ref|YP_008797255.1| 145 IQFAYCIKCGLCYAACPVTAtdkeflgpqalaqayryyadSRDEGGVDRLRPLAEGSRLLRCHFAGSCSKVCP 217
                                       77789*************99******************99888888888888888899**************9 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0019
                           Fer4_10   8 tCirCgkCvkaCPa 21 
                                       +C   g C k+CP 
  gi|557694201|ref|YP_008797255.1| 205 RCHFAGSCSKVCPK 218
                                       57777777777776 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   1.1       3.3   3.3e+03      11      14 ..      60      63 ..      59      65 .. 0.67
   2 !   22.5   2.1   7.1e-08   7.1e-05       3      20 ..     145     162 ..     143     164 .. 0.85
   3 !    7.6   0.6    0.0036       3.6      12      21 ..     210     219 ..     204     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.3
                                      -THH CS
                              Fer4 11 CGaC 14
                                      CG C
  gi|557694201|ref|YP_008797255.1| 60 CGSC 63
                                      7777 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 7.1e-08
                                       EETTTSSS-THHHHHSTT CS
                              Fer4   3 ideekCigCGaCvevCPv 20 
                                       i    Ci+CG+C+ +CPv
  gi|557694201|ref|YP_008797255.1| 145 IQFAYCIKCGLCYAACPV 162
                                       56678************8 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0036
                                       THHHHHSTTT CS
                              Fer4  12 GaCvevCPvg 21 
                                       G C +vCP g
  gi|557694201|ref|YP_008797255.1| 210 GSCSKVCPKG 219
                                       99******88 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   0.2         4     4e+03      56      60 ..      59      63 ..      42      66 .. 0.70
   2 !   23.3   2.9   9.2e-08   9.1e-05       2      66 ..     150     218 ..     149     219 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4
                           Fer4_16 56 gCdiC 60
                                       C+ C
  gi|557694201|ref|YP_008797255.1| 59 TCGSC 63
                                      45555 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 9.2e-08
                           Fer4_16   2 CgtCgkCaevCPtnaikek.kekeiearecisy....ntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       C++Cg C  +CP+ a +++   +++ a++   y     + + ++l++ +e      ++++ + C +vCP 
  gi|557694201|ref|YP_008797255.1| 150 CIKCGLCYAACPVTATDKEfLGPQALAQAYRYYadsrDEGGVDRLRPLAEGSR-LLRCHFAGSCSKVCPK 218
                                       ***************99985333333333333344422333344444444444.67889999*******6 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       6.9   6.9e+03      84      93 ..      59      68 ..      48      86 .. 0.57
   2 !   12.3   0.0   0.00014      0.14      40      74 ..     129     163 ..     115     171 .. 0.76
   3 !    7.3   0.0    0.0052       5.2      60      81 ..     205     226 ..     184     230 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.9
                           Fer4_18 84 eciscllcid 93
                                       c sc+  i+
  gi|557694201|ref|YP_008797255.1| 59 TCGSCGMMIN 68
                                      3555555444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00014
                           Fer4_18  40 rkkekkalkekeerkekgagdcidcescvkvcPtg 74 
                                       +++ +  ++++e+++  + + ci+c+ c + cP+ 
  gi|557694201|ref|YP_008797255.1| 129 KSNVSYLQSDEELERYIQFAYCIKCGLCYAACPVT 163
                                       3444455666777888899**************85 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0052
                           Fer4_18  60 dcidcescvkvcPtgidirkGl 81 
                                        c   +sc kvcP g+d    +
  gi|557694201|ref|YP_008797255.1| 205 RCHFAGSCSKVCPKGVDPALAI 226
                                       5777899*********965555 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.4       7.5   7.5e+03      10      15 ..      59      64 ..      54      71 .. 0.67
   2 !   19.4   0.2   8.6e-07   0.00086       3      24 ..     145     166 ..     143     179 .. 0.87
   3 ?    3.3   0.2      0.09        90      44      52 ..     209     217 ..     202     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.5
                           Fer4_21 10 gCgkCl 15
                                       Cg+C 
  gi|557694201|ref|YP_008797255.1| 59 TCGSCG 64
                                      355554 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 8.6e-07
                           Fer4_21   3 idedkCigCgkCliaCedtshq 24 
                                       i+ + Ci+Cg+C+ aC+ t+++
  gi|557694201|ref|YP_008797255.1| 145 IQFAYCIKCGLCYAACPVTATD 166
                                       66678***********998876 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.09
                           Fer4_21  44 CnlCssvCP 52 
                                          Cs+vCP
  gi|557694201|ref|YP_008797255.1| 209 AGSCSKVCP 217
                                       557999999 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   2.3         5     5e+03       6      10 ..      59      63 ..      54      63 .. 0.71
   2 !   18.7   0.6   1.8e-06    0.0018       3      16 ..     149     162 ..     141     173 .. 0.90
   3 ?    1.5   0.6      0.55   5.5e+02       8      16 ..     210     218 ..     204     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5
                            Fer4_4  6 gCgsC 10
                                       CgsC
  gi|557694201|ref|YP_008797255.1| 59 TCGSC 63
                                      79999 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.8e-06
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                        Ci Cg C+aaCP+
  gi|557694201|ref|YP_008797255.1| 149 YCIKCGLCYAACPV 162
                                       5************5 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.55
                            Fer4_4   8 gsCvaaCPq 16 
                                       gsC  +CP 
  gi|557694201|ref|YP_008797255.1| 210 GSCSKVCPK 218
                                       58*9***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 !   18.2   1.9   1.9e-06    0.0019       9      21 ..     150     162 ..     148     171 .. 0.91
   2 ?    4.5   0.5      0.04        40      13      22 ..     210     219 ..     206     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-06
                            Fer4_6   9 CigCgdCvrvCPe 21 
                                       Ci Cg C+++CP 
  gi|557694201|ref|YP_008797255.1| 150 CIKCGLCYAACPV 162
                                       ************5 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.04
                            Fer4_6  13 gdCvrvCPeg 22 
                                       g C +vCP g
  gi|557694201|ref|YP_008797255.1| 210 GSCSKVCPKG 219
                                       56******87 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 !   16.1   0.1   8.3e-06    0.0083      19      76 ..      38      78 ..      21      80 .. 0.74
   2 ?   -0.9   0.1       1.7   1.7e+03      39      47 ..     152     160 ..     130     183 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.3e-06
                                      HHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSE CS
                              Fer2 19 lldaaee.nggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaCqti 76
                                      ll + e+ ++ + i++sC++++Cg+C  +++            g +      rlaC t+
  gi|557694201|ref|YP_008797255.1| 38 LLHIKEKiDPTLSIRFSCRMATCGSCGMMIN------------GLP------RLACYTL 78
                                      4455555566789**************9999............555......6777665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                                       SSSTTEEEE CS
                              Fer2  39 gCgtClvev 47 
                                       +Cg C + +
  gi|557694201|ref|YP_008797255.1| 152 KCGLCYAAC 160
                                       488887654 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 !    6.4   0.7    0.0072       7.1      22      46 ..     148     170 ..     124     185 .. 0.78
   2 !    9.0   0.0    0.0012       1.2      17      50 ..     196     230 ..     182     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0072
                                       TT----TT-HHHHCSTT---HHHHH CS
                           Fer4_20  22 sRClqCkkapcvkgCPveidipefi 46 
                                       + C++C    c ++CPv+ + +ef+
  gi|557694201|ref|YP_008797255.1| 148 AYCIKC--GLCYAACPVTATDKEFL 170
                                       569999..79********9999997 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0012
                                       HHHHHTT----T.T-HHHHCSTT---HHHHHHHHH CS
                           Fer4_20  17 aleeAsRClqCk.kapcvkgCPveidipefikkia 50 
                                        l+e sR l+C+    c+k CP  +d    i+ ++
  gi|557694201|ref|YP_008797255.1| 196 PLAEGSRLLRCHfAGSCSKVCPKGVDPALAIQMLR 230
                                       57899******95667********99887777766 PP

>> RdRP_1  RNA dependent RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.2e-05     0.042     169     220 ..      79     130 ..      73     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.2e-05
                                       HCCCEEEEEEEE-HHHHHHHHHHHHHHHHHHHHTCCCCSBSTCHHCCCCHHC CS
                            RdRP_1 169 vekeKtRlftglPlelnlviravfqpfnnkiysnalklgitvGinkesrewe 220
                                       +e+ KtR++t+ Pl  +  i+ ++ +f +++  ++   +  ++++++++e++
  gi|557694201|ref|YP_008797255.1|  79 IEELKTRTITVEPLRNLPIIKDLVTDFEEFFSKHRWVKPYLIRLDTYEQEKS 130
                                       5788******************************************999998 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   0.00017      0.17       5      94 ..      60     162 ..      55     164 .. 0.60
   2 ?    2.2   0.2      0.32   3.2e+02       1      13 [.     205     217 ..     197     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                           Fer4_22   5 CgaCtlv...CptCsCfdvedetkeeskegervrvwd..sClleeftkvaggenvrkekkerlrqrllhklsefkek 76 
                                       Cg+C ++    p   C+++ +e k+++ ++e +r+      l+++f++  ++++  k    rl +   +k +    +
  gi|557694201|ref|YP_008797255.1|  60 CGSCGMMingLPRLACYTLIEELKTRTITVEPLRNLPiiKDLVTDFEEFFSKHRWVKPYLIRLDTYEQEKSNVSYLQ 136
                                       55555551115788899998888767777777776541145677788877777665555555444444443322211 PP

                           Fer4_22  77 f........gesgCvGCgRCieacpv 94 
                                                +   C+ Cg C +acpv
  gi|557694201|ref|YP_008797255.1| 137 SdeeleryiQFAYCIKCGLCYAACPV 162
                                       1122333348899***********97 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.32
                           Fer4_22   1 rClsCgaCtlvCp 13 
                                       rC   g+C+ vCp
  gi|557694201|ref|YP_008797255.1| 205 RCHFAGSCSKVCP 217
                                       5666777777777 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   1.5       1.3   1.3e+03       9      13 ..      59      63 ..      53      77 .. 0.70
   2 ?   13.4   1.7   6.5e-05     0.064      10      21 ..     150     161 ..     144     162 .. 0.93
   3 ?    5.8   0.9     0.017        16      12      21 ..     205     217 ..     204     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                            Fer4_2  9 rCigC 13
                                      +C +C
  gi|557694201|ref|YP_008797255.1| 59 TCGSC 63
                                      45555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.5e-05
                            Fer4_2  10 CigCgaCvsaCP 21 
                                       Ci Cg C+ aCP
  gi|557694201|ref|YP_008797255.1| 150 CIKCGLCYAACP 161
                                       ************ PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.017
                            Fer4_2  12 gC...gaCvsaCP 21 
                                       +C   g+C ++CP
  gi|557694201|ref|YP_008797255.1| 205 RChfaGSCSKVCP 217
                                       675557******9 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   4.9   0.00025      0.25       1      14 [.     150     163 ..     150     164 .. 0.92
   2 ?    9.6   1.2    0.0019       1.9       5      14 ..     210     219 ..     204     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00025
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+ Cg+C  +CPv 
  gi|557694201|ref|YP_008797255.1| 150 CIKCGLCYAACPVT 163
                                       ************85 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0019
                            Fer4_3   5 gaCvevCPvg 14 
                                       g C +vCP+g
  gi|557694201|ref|YP_008797255.1| 210 GSCSKVCPKG 219
                                       58******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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):              18  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.79
# Mc/sec: 900.10
//
Query:       gi|557694202|ref|YP_008797256.1|  [L=307]
Description: hypothetical protein CSUB_C0768 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
        3.2    7.1  13.7       0.43   10.0   5.3    2.1  2  DUF373    Domain of unknown function (DUF373)


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 ?   10.0   5.3   2.4e-05      0.43     218     317 ..      24     126 ..       8     154 .. 0.61
   2 ?    2.3   1.2    0.0051        92     249     310 ..     247     303 ..     233     307 .] 0.59

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 2.4e-05
                            DUF373 218 ritfvtyvvalll....lligiisgyislesvss...asvssglltlilafiygavewlalailtaslgkiideylk 287
                                       +  +v++++al      ++i+ ++++++   +     + v+ +l++l   +++++++++++ ++++ +g+i+ ++l 
  gi|557694202|ref|YP_008797256.1|  24 KALIVFTLAALSQaavaIYIYRFKTVYE---IALgpySIVELELFQLDYLLMASLTTVFIALVIIVGVGRILGRLLG 97 
                                       3333333433333100133333444444...333444566777777777778889999999999999*********5 PP

                            DUF373 288 reekdiarllllpflvlaiglvlygasayl 317
                                       ++ +   r +l++fl+l + + +++++ + 
  gi|557694202|ref|YP_008797256.1|  98 KN-HASMRDFLTVFLYLFTVFAMVNVAIFA 126
                                       55.555666666666666666666665555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.0051
                            DUF373 249 svssglltlilafiygavewlalailtaslgkiideylkreekdiarllllpflvlaiglvl 310
                                       s ++g ++ i++    +v+ +a  il+++ + ++ +yl++  ++ +++l++++++la+++++
  gi|557694202|ref|YP_008797256.1| 247 SEQPGAFIPIIS----VVKNFAWRILMSIYTGLFVMYLHN-TSRKSAFLVMLLTYLAVANLV 303
                                       445555555555....555555555555556666666633.345556777888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2316.59
//
Query:       gi|557694203|ref|YP_008797257.1|  [L=170]
Description: phosphopantetheine adenylyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   54.1   0.0    2.4e-14   53.7   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.11   11.7   0.0       0.39    9.9   0.0    1.8  2  Pantoate_ligase  Pantoate-beta-alanine ligase


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 !   53.7   0.0   2.7e-18   2.4e-14       2     140 ..      18     152 ..      17     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 2.7e-18
                                       EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST.-.SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHH.. CS
                   CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkk.k.kplasaeeRlemlelakevdevisvdpweltr.. 74 
                                       +gGtF  iH GH++ll +a+ + e+ +ivgv+sd  + k  k  p+ s+e+R+++l+++ ++  +++ + ++     
  gi|557694203|ref|YP_008797257.1|  18 LGGTFSVIHVGHMALLAEAFTKAEK-VIVGVTSDSFAAKLgKkYPIPSYEQRVRQLREFLSKYGWLERARITALEdp 93 
                                       69***********************.**************657889999*****************99999999889 PP

                                       ..HHHHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHH CS
                   CTP_transf_like  75 ..evlkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstki 140
                                          +l++ +++   +v +  +   +se +  ++    ++l ++  p       l  +++ +++Sst++
  gi|557694203|ref|YP_008797257.1|  94 ygPTLEDPAVE--LIVTSPATAYRASEINMKRTERNLNTLDIRICP-------LVVAEDGQPVSSTRV 152
                                       99999999999..777777777777777777777777777777667.......999999999***997 PP

>> Pantoate_ligase  Pantoate-beta-alanine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   4.3e-05      0.39      27      54 ..      20      47 ..       3      78 .. 0.87
   2 ?   -0.5   0.0     0.065   5.8e+02     162     185 ..     130     153 ..     120     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.3e-05
                                      EE-SS-GHHHHHHHHHHHHHSSEEEEEE CS
                   Pantoate_ligase 27 pTmGaLHeGHlsLvkaakeendvvvvSi 54
                                       T   +H GH++L+ +a +++++v+v +
  gi|557694203|ref|YP_008797257.1| 20 GTFSVIHVGHMALLAEAFTKAEKVIVGV 47
                                      677889*******************987 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.065
                                       SSEEEEEEEEBETTSEBTTGGGGG CS
                   Pantoate_ligase 162 pveivavpivReedgLAlSSRNky 185
                                        ++i+++p v +edg  +SS  + 
  gi|557694203|ref|YP_008797257.1| 130 TLDIRICPLVVAEDGQPVSSTRVM 153
                                       47899***********99997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1268.56
//
Query:       gi|557694204|ref|YP_008797258.1|  [L=104]
Description: hypothetical protein CSUB_C0770 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   12.6   0.3       0.15   12.4   0.3    1.1  1  DUF4199   Protein of unknown function (DUF4199)


Domain annotation for each model (and alignments):
>> DUF4199  Protein of unknown function (DUF4199)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   8.4e-06      0.15      96     133 ..      24      62 ..      21      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.4e-06
                           DUF4199  96 dpdfienyiaeilekleeakeesae.eenaemseeeike 133
                                       d d++e+++ae+le+ e++ e++a  + + +m ee i+e
  gi|557694204|ref|YP_008797258.1|  24 DTDYMEKALAEQLEYCEKMLEMEARlDLVVAMLEEIINE 62 
                                       89*****************99999988777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 793.80
//
Query:       gi|557694205|ref|YP_008797259.1|  [L=272]
Description: hypothetical protein CSUB_C0771 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00063   18.0  16.8    0.00085   17.6  16.8    1.2  1  HOOK             HOOK protein
     0.0069   14.6   6.0     0.0084   14.3   6.0    1.1  1  RHD3             Root hair defective 3 GTP-binding protein (R
  ------ inclusion threshold ------
      0.027   14.6   2.4      0.027   14.6   2.4    2.0  2  Caudo_TAP        Caudovirales tail fibre assembly protein, la
      0.028   14.5   3.0      0.028   14.5   3.0    2.3  2  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
      0.028   13.4   1.3      0.042   12.8   1.3    1.3  1  DUF913           Domain of Unknown Function (DUF913)
      0.029   14.4   8.1        1.4    9.0   2.8    2.3  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.036   13.7  11.4      0.052   13.1  11.4    1.3  1  HAUS-augmin3     HAUS augmin-like complex subunit 3
      0.041   13.6  10.7      0.059   13.1  10.7    1.2  1  SHE3             SWI5-dependent HO expression protein 3
      0.054   13.5   4.1       0.88    9.6   0.9    2.6  2  Taeniidae_ag     Taeniidae antigen
      0.057   12.3  17.4      0.083   11.8  17.4    1.3  1  Spc7             Spc7 kinetochore protein
      0.057   12.9   4.8      0.063   12.8   3.5    1.7  1  CAP_N            Adenylate cyclase associated (CAP) N termina
      0.075   11.0  10.6       0.24    9.3  10.6    1.6  1  Prominin         Prominin
       0.12   12.9  12.3       0.15   12.7  10.3    1.9  2  AF0941-like      AF0941-like
       0.14   12.0  21.4       0.33   10.8  20.9    1.7  1  Apolipoprotein   Apolipoprotein A1/A4/E domain
       0.29   11.5  11.1      0.067   13.6   4.1    2.3  2  Gp-FAR-1         Nematode fatty acid retinoid binding protein
       0.33   10.2   4.0       0.48    9.7   4.0    1.2  1  CmlA_N           Diiron non-heme beta-hydroxylase N-terminal 
       0.38    9.2   4.6       0.57    8.6   4.6    1.3  1  FUSC             Fusaric acid resistance protein family
       0.38   10.7  20.9       0.61   10.0   6.6    2.7  2  PLC-beta_C       PLC-beta C terminal
       0.44   11.0   3.3        3.5    8.1   0.3    2.6  2  Asp23            Asp23 family, cell envelope-related function
       0.45   10.9   4.8       0.85   10.0   0.6    2.4  2  MADF_DNA_bdg     Alcohol dehydrogenase transcription factor M
       0.51   10.6   6.8        9.9    6.5   0.2    2.9  2  Retrotrans_gag   Retrotransposon gag protein
       0.67    9.9  13.1        2.8    7.9   2.2    2.2  2  PhaP_Bmeg        Polyhydroxyalkanoic acid inclusion protein (
       0.69   10.4  17.0        2.4    8.6   1.5    3.1  3  Snapin_Pallidin  Snapin/Pallidin
       0.71    9.7  18.4        1.1    9.1  16.0    2.1  2  CdvA             CdvA-like coiled-coil domain
       0.76    9.2   8.1        1.2    8.6   8.1    1.4  1  FAP206           Domain of unknown function
       0.77    9.7  10.1       0.75    9.7   1.1    2.7  2  Shugoshin_N      Shugoshin N-terminal coiled-coil region
       0.89   10.2  14.1       0.19   12.4   3.9    2.6  2  DUF883           Bacterial protein of unknown function (DUF88
       0.94    9.6   4.9          5    7.3   2.4    2.3  2  Arch_flagellin   Archaebacterial flagellin
        1.1    9.1  14.5        0.1   12.4   3.1    2.5  2  SKA2             Spindle and kinetochore-associated protein 2
        1.2    7.8  15.2        2.1    7.0  15.1    1.4  1  AAA_32           AAA domain
        1.4    9.5  11.8        2.8    8.6   5.6    2.9  2  YtxH             YtxH-like protein
        1.5    9.2  22.2        6.8    7.0  20.6    2.1  2  OmpH             Outer membrane protein (OmpH-like)
        1.6    9.1   7.8         20    5.5   7.8    2.6  1  DUF948           Bacterial protein of unknown function (DUF94
        1.6    8.7  16.0        4.2    7.3  15.3    1.9  1  Rootletin        Ciliary rootlet component, centrosome cohesi
        1.7    8.5  10.0          4    7.3   1.6    2.2  2  Mt_ATP-synt_D    ATP synthase D chain, mitochondrial (ATP5H)
          2    7.8  19.5        1.6    8.1  17.1    1.6  1  Golgin_A5        Golgin subfamily A member 5
        2.4    7.7  14.0        3.9    7.0  14.0    1.4  1  Exonuc_VII_L     Exonuclease VII, large subunit
        3.7    7.9  16.8        1.9    8.8   9.7    2.1  2  Muted            Organelle biogenesis, Muted-like protein
        4.7    7.7  10.0        7.7    7.0   8.1    1.9  2  IZUMO            Izumo sperm-egg fusion, Ig domain-associated
        7.5    6.6  19.7        4.3    7.4  11.1    2.9  3  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        7.6    5.5  15.1         14    4.6  15.2    1.4  1  Atg14            Vacuolar sorting 38 and autophagy-related su
        9.8    6.5   8.4        5.1    7.4   1.7    2.4  2  DUF3135          Protein of unknown function (DUF3135)


Domain annotation for each model (and alignments):
>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6  16.8     2e-06   0.00085     404     531 ..      44     185 ..      20     220 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                              HOOK 404 llaerdaLketneE..Lkcaqlqqkelsqadalaskssssgenlaae............llpaevreklirLqhENK 466
                                       +++ r+a +e+  E  Lk+ q+++++ +   +  +++++ +e++ ae            ++  e+   l  Lq E K
  gi|557694205|ref|YP_008797259.1|  44 VVEHREAVREALLEfkLKLEQIKENKTELIAQFLEERQNRMEQIRAEienlrqqylagnITKDEYVASLKVLQTELK 120
                                       45556666666665333445565555555555555555566666666666666666666****************** PP

                              HOOK 467 mLklkqegseeekltelqe.lledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaed 531
                                       +L  + e+   +k++el +  +e  ++++++L++ nr   qr+ e  +++ +l+++ +e+++  + 
  gi|557694205|ref|YP_008797259.1| 121 ALAKSSEKL-GQKMQELVKdIKEAVKEKVERLREINREFGQRVAEEAKKLGDLAREEAENQGTDNG 185
                                       **6666666.6666666551666678999*************************998876665543 PP

>> RHD3  Root hair defective 3 GTP-binding protein (RHD3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   6.0     2e-05    0.0084     327     472 ..      32     177 ..      25     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HCT.TT....THHHHHHHHHHHHHHHHHHHH.HTTSTTTTS-- CS
                              RHD3 327 Leekvdsklkalfqavlealrkellekfkeavekalkage....dFaesvkekkkklvekfdeeaeslvveqakwda 399
                                       L +++ ++l++++ ++ ea+r++ll +fk ++e+  ++ +    +F e  ++ ++++ +++++  ++    +++ d+
  gi|557694205|ref|YP_008797259.1|  32 LGQRITEELRSIVVEHREAVREALL-EFKLKLEQIKENKTeliaQFLEERQNRMEQIRAEIENLRQQYLAGNITKDE 107
                                       6788999999999999999988777.588888855554445666777777777777777777777777888888888 PP

                                       .HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS--TTCHHHHHHHHTTSSS...... CS
                              RHD3 400 sdkiilklekdieaviaklrkeelkelvervekkleselseavellleklskevWdrvlkefkseveeavskl 472
                                       +   ++ l+ +++a  ++  +e+l +++++++k ++++++e+ve  l + + e+ +rv +e k+  + a ++ 
  gi|557694205|ref|YP_008797259.1| 108 YVASLKVLQTELKALAKS--SEKLGQKMQELVKDIKEAVKEKVER-LREINREFGQRVAEEAKKLGDLAREEA 177
                                       888888899999887765..78999999**************995.788899999999888887766665555 PP

>> Caudo_TAP  Caudovirales tail fibre assembly protein, lambda gpK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.4   6.4e-05     0.027      59      99 ..      66     108 ..      39     124 .. 0.86
   2 ?   -0.8   0.8       3.7   1.6e+03      60      98 ..     136     176 ..     110     179 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 6.4e-05
                         Caudo_TAP  59 k..keeqiqqAeqekqqllaqAseqiaplqdavdlgiatdeEk 99 
                                       k  k e+i+q  +e+q++++q +++i+ l+++   g +t++E 
  gi|557694205|ref|YP_008797259.1|  66 KenKTELIAQFLEERQNRMEQIRAEIENLRQQYLAGNITKDEY 108
                                       24599**********************************9995 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.7
                         Caudo_TAP  60 keeqiqqAeqekqqllaqAseqiaplq..davdlgiatdeE 98 
                                         + i++A +ek ++l++ + +  +    +a +lg +  eE
  gi|557694205|ref|YP_008797259.1| 136 LVKDIKEAVKEKVERLREINREFGQRVaeEAKKLGDLAREE 176
                                       55677888888888888877776655433566666666665 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 ?    2.8   4.6      0.27   1.1e+02      58     144 ..      35     120 ..      26     121 .. 0.78
   2 ?   14.5   3.0   6.5e-05     0.028      20      76 ..     115     171 ..      99     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.27
                         ApoLp-III  58 ealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslkensqeakek.lakaikqayddav 133
                                       ++ +e+++ ++e ++ ++e+  e k k+++ +e+  + + + ++e q+  e++ +++++  ++ la  i +  d+ v
  gi|557694205|ref|YP_008797259.1|  35 RITEELRSIVVEHREAVREALLEFKLKLEQIKENKTELIAQFLEERQNRMEQIRAEIENLRQQyLAGNITK--DEYV 109
                                       56788999999999999999999999999999999999999999999999999999988755436666554..6666 PP

                         ApoLp-III 134 eaaqklakqLk 144
                                        +++ l+++Lk
  gi|557694205|ref|YP_008797259.1| 110 ASLKVLQTELK 120
                                       66666666665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.5e-05
                         ApoLp-III  20 qeevvetiKensenlvdqlkqvikslqeelkkksdeleealkevkkkieetadklse 76 
                                        ++ ++++ ++se+l ++++++ k ++e++k+k + l e+ +e+ + ++e a+kl  
  gi|557694205|ref|YP_008797259.1| 115 LQTELKALAKSSEKLGQKMQELVKDIKEAVKEKVERLREINREFGQRVAEEAKKLGD 171
                                       556677888888888888888888888888888888888888888888888888755 PP

>> DUF913  Domain of Unknown Function (DUF913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.3   9.8e-05     0.042     202     314 ..     104     218 ..      97     262 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.8e-05
                            DUF913 202 espehvkamesdgdlasnlGssfdELvRhhpsLktaiikavikmlarvvelgkekaakllvedassasskseassss 278
                                       ++ e+v  ++  +   ++l++s + L     +L ++i +av + ++r++e+ +e+  ++  e+++  + ++e+++++
  gi|557694205|ref|YP_008797259.1| 104 TKDEYVASLKVLQTELKALAKSSEKLGQKMQELVKDIKEAVKEKVERLREINREFGQRVAEEAKKLGDLAREEAENQ 180
                                       677899999988888888888888888888888899999****************9777777744444444444444 PP

                            DUF913 279 sssetkeeek.......ssededvemedaeeetesesdesees 314
                                        +++ +++++       s+e ++v+++d       +++ ++e+
  gi|557694205|ref|YP_008797259.1| 181 GTDNGRGRGQgnphrdnSTETNSVNNSDR-----GQNNTADER 218
                                       44444444443332221111111222222.....111111111 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 ?    9.0   2.8    0.0033       1.4      38      99 ..      35      96 ..      10     106 .. 0.78
   2 ?    8.3   0.2     0.005       2.2      25      76 ..     112     155 ..     106     176 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0033
                      Baculo_PEP_C 38 tlldaietqLnalsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLls 99
                                      ++ +++ + + +  e+++++l e++ +l++  +n t+ ++++ ++ +n+++ + +++ nL  
  gi|557694205|ref|YP_008797259.1| 35 RITEELRSIVVEHREAVREALLEFKLKLEQIKENKTELIAQFLEERQNRMEQIRAEIENLRQ 96
                                      45566677777778899999999999*******************************99975 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.005
                      Baculo_PEP_C  25 irlqnvqilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdal 76 
                                       ++ +        +t l+a++++ ++l +++++l++++++++++ +++L +  
  gi|557694205|ref|YP_008797259.1| 112 LKVL--------QTELKALAKSSEKLGQKMQELVKDIKEAVKEKVERLREIN 155
                                       4444........4444455555555555555555555555555555554433 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 ?   13.1  11.4   0.00012     0.052      46     166 ..      53     178 ..      27     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00012
                      HAUS-augmin3  46 geaLeeaLk..tiepsdlkq..edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkl 118
                                       ++ Le++Lk  +i++++ +   +  e+ +  +e++++ +e+L+q+  +   +k+     l+ Lq    +l++ ++kl
  gi|557694205|ref|YP_008797259.1|  53 EALLEFKLKleQIKENKTELiaQFLEERQNRMEQIRAEIENLRQQYLAGNITKDEYVASLKVLQTELKALAKSSEKL 129
                                       45555555411444222222345555555566666666666666666666789999999999*************** PP

                      HAUS-augmin3 119 eeeekeakkklkeaqeelraenaetnavLqq.lteeakqlaeyfeeaek 166
                                        ++ +e  k++kea +e  ++  e+n+++ q ++eeak+l    +e+ +
  gi|557694205|ref|YP_008797259.1| 130 GQKMQELVKDIKEAVKEKVERLREINREFGQrVAEEAKKLGDLAREEAE 178
                                       ******************9**********65278899999988877765 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  10.7   0.00014     0.059      74     193 ..      54     170 ..      38     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHHHHHHHHHH.HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  74 elselkesveelklekkqlkkr.lenssaseteleeelerlkvqYdalvdsqkeYkehYqqeieeLkesleklklen 149
                                        l e+k + e++k++k++l  + le+ +++ ++ ++e+e+l+ qY a     +  k+ Y   ++ L+++l++l +  
  gi|557694205|ref|YP_008797259.1|  54 ALLEFKLKLEQIKENKTELIAQfLEERQNRMEQIRAEIENLRQQYLA----GNITKDEYVASLKVLQTELKALAKSS 126
                                       577899999****99999877637899999999************65....6889********************** PP

                                       HSSSXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SHE3 150 ekqleelqerissndkdidtkldsynnkkknlesieeeknkkll 193
                                       ek  +++qe + + ++++++k++ + +  +++ +   e+ kkl 
  gi|557694205|ref|YP_008797259.1| 127 EKLGQKMQELVKDIKEAVKEKVERLREINREFGQRVAEEAKKLG 170
                                       *9999999999999999999999888887777776666666665 PP

>> Taeniidae_ag  Taeniidae antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.092        39      29      60 ..      33      61 ..      31      64 .. 0.80
   2 ?    9.6   0.9    0.0021      0.88      27      62 ..     128     163 ..     105     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.092
                      Taeniidae_ag 29 GqKlvdllkeltaicqklrkKvreaLkeYvkk 60
                                      Gq++    +el +i+   r+ vreaL e+  k
  gi|557694205|ref|YP_008797259.1| 33 GQRI---TEELRSIVVEHREAVREALLEFKLK 61
                                      6665...5799***************988555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0021
                      Taeniidae_ag  27 PlGqKlvdllkeltaicqklrkKvreaLkeYvkkLv 62 
                                        lGqK+++l+k++++ ++   +++re  +e+ ++  
  gi|557694205|ref|YP_008797259.1| 128 KLGQKMQELVKDIKEAVKEKVERLREINREFGQRVA 163
                                       59***************9999999998888766655 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8  17.4   0.00019     0.083     157     257 ..      43     147 ..      29     178 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                              Spc7 157 lLekqeeeldellpeleeekaeleeeleklqe.....aaeelesidkeeLeelreelaelkaeieekkkelaelqeq 228
                                        + +++e + e+l e++ + ++++e+ ++l +     +++ +e+i ++e+e+lr++  + + + +e  + l+ lq++
  gi|557694205|ref|YP_008797259.1|  43 IVVEHREAVREALLEFKLKLEQIKENKTELIAqfleeRQNRMEQI-RAEIENLRQQYLAGNITKDEYVASLKVLQTE 118
                                       566778888888888888888888887777666555466666665.6899999999999999999999999999999 PP

                              Spc7 229 leeleekieelkeqkseleeeiaeaervl 257
                                       l++l+++ e+l ++++el ++i+ea + +
  gi|557694205|ref|YP_008797259.1| 119 LKALAKSSEKLGQKMQELVKDIKEAVKEK 147
                                       99999999999999999999999884432 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 ?   12.8   3.5   0.00015     0.063       7      95 ..      77     175 ..      70     179 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                                       XXXXXXXXXXX....................XXXXXXXXXXXXXXXXXXXXXXXSXH.HHHHHHHHHHHHHHHHHHH CS
                             CAP_N   7 LEaatsrLEdiais..........essssasskasssssaaaaaaaaaakaaaaaaaaksveaFdelisgsvkefve 73 
                                       LE+  +r+E+i ++           + ++ +  as +  +++ +a a+++++  ++ ++ v++ +e ++++v+++ e
  gi|557694205|ref|YP_008797259.1|  77 LEERQNRMEQIRAEienlrqqylaGNITKDEYVASLKVLQTELKALAKSSEKLGQKMQELVKDIKEAVKEKVERLRE 153
                                       6667777777765566665567763333333333334444444444444445555556******************* PP

                                       HHHHH-HHHHHHHHHHHHHHHH CS
                             CAP_N  74 lskkiggevaeqaelvkkafea 95 
                                       + +++g+ vae a+++ +  ++
  gi|557694205|ref|YP_008797259.1| 154 INREFGQRVAEEAKKLGDLARE 175
                                       *************998776655 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  10.6   0.00056      0.24     220     362 ..      30     167 ..      17     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00056
                          Prominin 220 khlgldladtlesnvlpaLaelerllenlkeakeqLeqvnklekeL.rksgsqLrdglrgvkrdlnqalsn.lCqse 294
                                        +lg+++ ++l+s    ++++ e++ e+l e k +Leq++++++eL  +  ++ ++ +++++ +++++ ++ l ++ 
  gi|557694205|ref|YP_008797259.1|  30 MSLGQRITEELRSI---VVEHREAVREALLEFKLKLEQIKENKTELiAQFLEERQNRMEQIRAEIENLRQQyLAGNI 103
                                       46899999999999...889999999999999999999999999873456778888899999999999999666644 PP

                          Prominin 295 eCskilssleiekldtskcldqlpnvdevl.ealeevletnlssivkeglarlneipekvknqtaevvp 362
                                       + ++   sl++  l  +++l++l + +e l ++++e+  ++++++vke+++rl+ei++   + +ae  +
  gi|557694205|ref|YP_008797259.1| 104 TKDEYVASLKV--L--QTELKALAKSSEKLgQKMQEL-VKDIKEAVKEKVERLREINREFGQRVAEEAK 167
                                       44445555555..3..334455655544441555555.6788888888888888888877766665554 PP

>> AF0941-like  AF0941-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  10.3   0.00034      0.15      20     105 ..      62     151 ..      30     157 .. 0.65
   2 ?    5.3   2.3     0.065        28      11      62 ..     129     178 ..     122     180 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00034
                                       TSS-GGGHHHHT-...HHHHHHH..HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHCTT CS
                       AF0941-like  20 iddiekvldelld...keeieel..frsdvedvleklkagdieeeeakknlklLkvyvvsqLdehykrvlelledke 91 
                                       +++i++   el+    +e+ + +  +r+++e++ +++ ag+i+++e   +lk+L++  +  L +  +++ + +++  
  gi|557694205|ref|YP_008797259.1|  62 LEQIKENKTELIAqflEERQNRMeqIRAEIENLRQQYLAGNITKDEYVASLKVLQT-ELKALAKSSEKLGQKMQELV 137
                                       33444444444447776666777779********************9978777765.45566666666666666666 PP

                                       -----HHHHHHHHH CS
                       AF0941-like  92 kkiekevvdeIvea 105
                                       k+i++ v++++ + 
  gi|557694205|ref|YP_008797259.1| 138 KDIKEAVKEKVERL 151
                                       66666666655544 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.065
                                       HHHHHT...TSS-GGGHHHHT-HHHHHHHHHHHHHHHHHHHHT.TSS-HHHHH CS
                       AF0941-like  11 lgellkkeviddiekvldelldkeeieelfrsdvedvleklka.gdieeeeak 62 
                                       lg+ + +e ++di+++++e +  e++ e+ r+  + v e+ k+ gd++ eea+
  gi|557694205|ref|YP_008797259.1| 129 LGQKM-QELVKDIKEAVKEKV--ERLREINREFGQRVAEEAKKlGDLAREEAE 178
                                       44444.355557777776644..456666677777777776544788888877 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  20.9   0.00076      0.33      35     176 ..      37     175 ..      30     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00076
                                       HHHHHHHHHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHH CS
                    Apolipoprotein  35 leelrarlraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaeelrerlerh 111
                                       +eelr  + ++ e+vr++l +    + eq+++n  el ++  +  ++++e+++a++e+l++q  + ++  +++  ++
  gi|557694205|ref|YP_008797259.1|  37 TEELRSIVVEHREAVREALLEFKLKL-EQIKENKTELIAQFLEERQNRMEQIRAEIENLRQQYLA-GNITKDEYVAS 111
                                       56666666777777777777777777.77888888888888888888888999999999999887.88889999999 PP

                                       HHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..-----SSSHHHHHHHTS-TTSHHHHHS--X CS
                    Apolipoprotein 112 vealkarlapyveelrqklaerleelkeslaphaeeveerlssrveelrekleeqaeelrerlea 176
                                       ++ l++ l++++ +  + l+++++el + ++++++e  erl++  +e+ ++++e+a++l + +++
  gi|557694205|ref|YP_008797259.1| 112 LKVLQTELKALAKSSEK-LGQKMQELVKDIKEAVKEKVERLREINREFGQRVAEEAKKLGDLARE 175
                                       99999988888877764.88888888888888888888888888888888888888887665554 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 ?    1.7   1.1      0.69   2.9e+02      56      98 ..      61     103 ..      34     113 .. 0.71
   2 ?   13.6   4.1   0.00016     0.067      38      91 ..     114     171 ..     103     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.69
                          Gp-FAR-1  56 kaeklqaklkekvdkLspeakeFvkkliakgrkleaqvlagek 98 
                                       k+e+++++ +e +++  +e ++ ++++ a++ +l++q+lag+ 
  gi|557694205|ref|YP_008797259.1|  61 KLEQIKENKTELIAQFLEERQNRMEQIRAEIENLRQQYLAGNI 103
                                       4555556666666666677777777777888888888887764 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00016
                          Gp-FAR-1  38 nedellaalKkkspaLyekaekl....qaklkekvdkLspeakeFvkkliakgrklea 91 
                                         +  l+al k+s++L++k+++l    ++ +kekv+ L++  +eF + + ++++kl +
  gi|557694205|ref|YP_008797259.1| 114 VLQTELKALAKSSEKLGQKMQELvkdiKEAVKEKVERLREINREFGQRVAEEAKKLGD 171
                                       55666899999*******999873333677899****************999999864 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 ?    9.7   4.0    0.0011      0.48      58     143 ..      71     165 ..      46     177 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                            CmlA_N  58 llGgpfvdleeerveevrallektkkeq.adll...elaeaikeleklLk.....eeakGasLeplYaklpeaLkGy 125
                                        l ++f++ +++r+e++ra +e+++++  a ++   e+ + +k l++ Lk     +e+ G+++++l + + ea+k +
  gi|557694205|ref|YP_008797259.1|  71 ELIAQFLEERQNRMEQIRAEIENLRQQYlAGNItkdEYVASLKVLQTELKalaksSEKLGQKMQELVKDIKEAVKEK 147
                                       45577888888888777776666655431344411156666666666665222224566****************** PP

                            CmlA_N 126 vElvydlnnrpslrliEs 143
                                       vE + ++n + + r+ E+
  gi|557694205|ref|YP_008797259.1| 148 VERLREINREFGQRVAEE 165
                                       **********99999997 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   4.6    0.0013      0.57     219     343 ..      75     197 ..       5     200 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0013
                              FUSC 219 ralrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrrale. 294
                                       + l + ++rm  + a +  l+++  + + ++++ v++l+ l  el+a   a+++e+l +++++l ++++++ ++   
  gi|557694205|ref|YP_008797259.1|  75 QFLEERQNRMEQIRAEIENLRQQYLAGNITKDEYVASLKVLQTELKA--LAKSSEKLGQKMQELVKDIKEAVKEKVe 149
                                       44556666777777777777777777777777777777777777777..4667777777777777777555444444 PP

                              FUSC 295 adadtaalllarlaellaelaqllaslraleaaiaaarraerlarhrdh 343
                                         ++ ++++ +r+ae+ ++l +l ++ ++ +  +   r +++  +hrd+
  gi|557694205|ref|YP_008797259.1| 150 RLREINREFGQRVAEEAKKLGDLAREEAENQGTDNG-RGRGQGNPHRDN 197
                                       777777777777777777777776665555555554.666666677765 PP

>> PLC-beta_C  PLC-beta C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   6.6    0.0014      0.61     130     171 ..      60     101 ..      34     107 .. 0.81
   2 ?    6.1   6.4     0.023        10      53     119 ..     113     175 ..     101     182 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                        PLC-beta_C 130 eilqqikeeekqlqeeldeeyeeklkrLpaevkelvkeelke 171
                                         l+qike+++ l ++  ee +++++++ ae+++l +++l+ 
  gi|557694205|ref|YP_008797259.1|  60 LKLEQIKENKTELIAQFLEERQNRMEQIRAEIENLRQQYLAG 101
                                       359******************************998888765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.023
                        PLC-beta_C  53 KkLkeisekekKelkKkleakrleriqeakkktkdkakqeklkkeinnshiqevVqvikrleekqkr 119
                                       K L+       K    kl +k +e ++  k++ k+k   e+l +ein+++ q v +  k+l +   +
  gi|557694205|ref|YP_008797259.1| 113 KVLQTELKALAKSSE-KLGQKMQELVKDIKEAVKEK--VERL-REINREFGQRVAEEAKKLGDLARE 175
                                       544444433333322.35555555555555555444..5777.488888888888888877765544 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 ?    3.0   0.2      0.32   1.4e+02       7      41 ..      11      44 ..       7      94 .. 0.83
   2 ?    8.1   0.3    0.0083       3.5      70      95 ..     129     154 ..     104     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.32
                             Asp23  7 isdeViakiagiaaeeveGvvgmagklkdglaell 41
                                      ++++V+a++a  aa+e +   +++++++++l++++
  gi|557694205|ref|YP_008797259.1| 11 LTTAVLATVALAAAQELSDM-SLGQRITEELRSIV 44
                                      67899*********999876.55666677776666 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0083
                             Asp23  70 YGvkipevaenvqekVkeaveemtgl 95 
                                        G k++e++++++e+Vke+ve++ ++
  gi|557694205|ref|YP_008797259.1| 129 LGQKMQELVKDIKEAVKEKVERLREI 154
                                       699******************98776 PP

>> MADF_DNA_bdg  Alcohol dehydrogenase transcription factor Myb/SANT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.6     0.002      0.85      23      57 ..      64      99 ..      57     117 .. 0.83
   2 ?    2.2   0.3      0.53   2.3e+02      31      54 ..     128     153 ..     116     178 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.002
                      MADF_DNA_bdg 23 ekrekaweeiaeelnekvd.veeckkkwknLRdryr 57
                                      + +e+  e ia+ l+e+ + +e++++ ++nLR++y 
  gi|557694205|ref|YP_008797259.1| 64 QIKENKTELIAQFLEERQNrMEQIRAEIENLRQQYL 99
                                      558899999*****666655899************6 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.53
                      MADF_DNA_bdg  31 eiaeelnekvd..veeckkkwknLRd 54 
                                       ++ ++++e v+  +e++k+k++ LR+
  gi|557694205|ref|YP_008797259.1| 128 KLGQKMQELVKdiKEAVKEKVERLRE 153
                                       33444433333445668888888886 PP

>> Retrotrans_gag  Retrotransposon gag protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.023       9.9      49      91 ..      36      77 ..      28      79 .. 0.89
   2 ?    5.8   3.5     0.038        16      35      83 ..      71     127 ..      69     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.023
                    Retrotrans_gag 49 leeelsslrQ.gtesvreYvtrfktladqldevlteeakiekfl 91
                                       +eel+s+   + e vre++ +fk  + q++  +++ ++i +fl
  gi|557694205|ref|YP_008797259.1| 36 ITEELRSIVVeHREAVREALLEFKLKLEQIK--ENKTELIAQFL 77
                                      567899999989*******************..89999999998 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.038
                    Retrotrans_gag  35 aflktflp..serkdqleeelsslrQ....gtesvreYvtrfktladqlde..vlte 83 
                                       ++ ++fl+  ++r++q ++e+ +lrQ    g+ + +eYv+ +k l ++l+   +++e
  gi|557694205|ref|YP_008797259.1|  71 ELIAQFLEerQNRMEQIRAEIENLRQqylaGNITKDEYVASLKVLQTELKAlaKSSE 127
                                       4555555411358899999******954333778899******99999998643333 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 ?    7.9   2.2    0.0065       2.8      32      83 ..      41      92 ..      25     100 .. 0.81
   2 ?    6.6   4.3     0.016       6.7      32      95 ..     105     171 ..      92     180 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0065
                         PhaP_Bmeg 32 EqltLkalkqqqdlvkeltkalselekeskqltaeledqlqktvenlrskaG 83
                                           +  + +++++ e++ +l+++++++ +l a+++++ q+ +e++r +  
  gi|557694205|ref|YP_008797259.1| 41 RSIVVEHREAVREALLEFKLKLEQIKENKTELIAQFLEERQNRMEQIRAEIE 92
                                      45556666788999999****************************9988765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.016
                         PhaP_Bmeg  32 EqltLkalkqqqdlvkeltkalselekeskqltaeledqlqktvenlr...skaGnkvednieEwtd 95 
                                        + +  +lk  q  +k l k+ ++l ++ ++l  ++++  ++ ve+lr   +++G++v+++ + + d
  gi|557694205|ref|YP_008797259.1| 105 KDEYVASLKVLQTELKALAKSSEKLGQKMQELVKDIKEAVKEKVERLReinREFGQRVAEEAKKLGD 171
                                       5666677777777777779999999999999999999999888888762225778877776665555 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   4.5     0.015       6.4      27      78 ..      46      97 ..      34     100 .. 0.87
   2 ?    5.9   0.8      0.04        17      11      45 ..     108     142 ..     104     144 .. 0.89
   3 ?    8.6   1.5    0.0057       2.4       2      51 ..     128     177 ..     127     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.015
                   Snapin_Pallidin 27 qsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslner 78
                                      ++ e+++e l + + kL++++e++ + + ++l+e ++++ +i+ ++++l ++
  gi|557694205|ref|YP_008797259.1| 46 EHREAVREALLEFKLKLEQIKENKTELIAQFLEERQNRMEQIRAEIENLRQQ 97
                                      56678899999999********999999********************9875 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.04
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLke 45 
                                       ++ +l+ l+++lk+l +s e+L +++++l +++ke
  gi|557694205|ref|YP_008797259.1| 108 YVASLKVLQTELKALAKSSEKLGQKMQELVKDIKE 142
                                       67889999********************9998886 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0057
                   Snapin_Pallidin   2 aLaegllellepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe 51 
                                       +L++ ++el++   ++++ek++ lr+  +e  +++ ++++kL +l++++ 
  gi|557694205|ref|YP_008797259.1| 128 KLGQKMQELVKDIKEAVKEKVERLREINREFGQRVAEEAKKLGDLAREEA 177
                                       789999999999999****************************9998876 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1  16.0    0.0026       1.1      19     119 ..      43     148 ..      36     151 .. 0.82
   2 ?    4.0   2.5     0.096        41      15      48 ..     132     165 ..     127     178 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0026
                              CdvA  19 tyeeikekleealkklkekakelkek....lkkrlkeledqikslekalanlkisyasGEidEeaYksaieairell 91 
                                        + e +e ++eal + k k +++ke+    + + l+e ++ ++++   + nl+ +y +G i  ++Y ++ + ++++l
  gi|557694205|ref|YP_008797259.1|  43 IVVEHREAVREALLEFKLKLEQIKENktelIAQFLEERQNRMEQIRAEIENLRQQYLAGNITKDEYVASLKVLQTEL 119
                                       55566777888888888888888876333356667777888999999999*************************** PP

                              CdvA  92 esaleekeeikkllekl.skleleeeeve 119
                                       + + ++ e + + +++l ++++++ +e+ 
  gi|557694205|ref|YP_008797259.1| 120 KALAKSSEKLGQKMQELvKDIKEAVKEKV 148
                                       **********9999999888888877765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.096
                              CdvA  15 ipkstyeeikekleealkklkekakelkeklkkr 48 
                                        +++ +++ike ++e++++l+e   e  +++ ++
  gi|557694205|ref|YP_008797259.1| 132 KMQELVKDIKEAVKEKVERLREINREFGQRVAEE 165
                                       3445555555555555555555444444444444 PP

>> FAP206  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   8.1    0.0029       1.2       7     100 ..      52     148 ..      25     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                            FAP206   7 patreaiekeleeaqelasrytallekl..veeseaevaeeqlerlkqal....invrqyeaylrilledveksaee 77 
                                       +++  +++ +le+++e   + t+l+ +   ++++  e+  +++e+l+q+     i+   y a l++l+++++ +a+ 
  gi|557694205|ref|YP_008797259.1|  52 REALLEFKLKLEQIKE---NKTELIAQFleERQNRMEQIRAEIENLRQQYlagnITKDEYVASLKVLQTELKALAKS 125
                                       3333344444444444...445555555554566666666677766666511115566899**************** PP

                            FAP206  78 veellkrfeaeleklketvkskt 100
                                        e+l +++++ ++++ke vk+k 
  gi|557694205|ref|YP_008797259.1| 126 SEKLGQKMQELVKDIKEAVKEKV 148
                                       *******************9986 PP

>> Shugoshin_N  Shugoshin N-terminal coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.3       0.1        44      27      43 ..      81      97 ..      58      99 .. 0.90
   2 ?    9.7   1.1    0.0017      0.75       9      38 ..     119     148 ..     117     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.1
                       Shugoshin_N 27 ekevseLlsENlnLRel 43
                                       ++++++++E+ nLR++
  gi|557694205|ref|YP_008797259.1| 81 QNRMEQIRAEIENLRQQ 97
                                      699************98 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0017
                       Shugoshin_N   9 NreLAKsNsalslkirelekevseLlsENl 38 
                                       ++ LAKs+ +l +k++el k + e ++E++
  gi|557694205|ref|YP_008797259.1| 119 LKALAKSSEKLGQKMQELVKDIKEAVKEKV 148
                                       689*******************99888876 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 ?    2.9   2.4      0.39   1.7e+02       3      59 ..      36      92 ..      34     100 .. 0.69
   2 ?   12.4   3.9   0.00044      0.19       6      67 ..     111     175 ..     106     182 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.39
                            DUF883  3 leaeleslladleellkeaadeageeaeelRerleerlerarerlrdaeeavaerak 59
                                      +++el+s++ + +e ++ea  e + ++e+++e+ +e +++  e+ ++ +e+++++++
  gi|557694205|ref|YP_008797259.1| 36 ITEELRSIVVEHREAVREALLEFKLKLEQIKENKTELIAQFLEERQNRMEQIRAEIE 92
                                      567777777777777777777777777777777777777777777777666666554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00044
                            DUF883   6 eleslladleellkeaadea...geeaeelRerleerlerarerlrdaeeavaerakeaaeaadd 67 
                                        l+ l ++l++l+k++++ +   +e +++++e ++e++er+re  r+  ++vae+ak+  + a++
  gi|557694205|ref|YP_008797259.1| 111 SLKVLQTELKALAKSSEKLGqkmQELVKDIKEAVKEKVERLREINREFGQRVAEEAKKLGDLARE 175
                                       55666666666666665544111345667777777777777777777777777777777665554 PP

>> Arch_flagellin  Archaebacterial flagellin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.4     0.012         5      10      44 ..       5      37 ..       3      45 .. 0.81
   2 ?    2.3   0.0       0.4   1.7e+02      24      52 ..     121     149 ..     114     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.012
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                    Arch_flagellin 10 vfIAmVlVAAvaagvlintagflqqkaqstgeest 44
                                      vf+A++l  Av+a+v++ +a+ l++   s g+++t
  gi|557694205|ref|YP_008797259.1|  5 VFMAVLLTTAVLATVALAAAQELSDM--SLGQRIT 37
                                      9********************99974..4555555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHHHHHHHHHHHHHHHT--E CS
                    Arch_flagellin  24 vlintagflqqkaqstgeesteqvssgle 52 
                                       +l++++ +l qk+q+ ++ + e v++++e
  gi|557694205|ref|YP_008797259.1| 121 ALAKSSEKLGQKMQELVKDIKEAVKEKVE 149
                                       5788999*****************99988 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   3.7      0.64   2.7e+02      47      81 ..      62      93 ..      29     100 .. 0.50
   2 ?   12.4   3.1   0.00024       0.1      44      97 ..     109     162 ..     107     169 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.64
                              SKA2 47 lkkvkeelqaLkeqceellaekkelidkirttlva 81
                                      l+++ke  ++L   + + l+e+++ +++ir+ + +
  gi|557694205|ref|YP_008797259.1| 62 LEQIKENKTEL---IAQFLEERQNRMEQIRAEIEN 93
                                      22222222222...222344555555555555444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00024
                              SKA2  44 lerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasaelpp 97 
                                       +++lk +++el+aL +  e+l ++ +el++ i+  + +  e l++++++ +   
  gi|557694205|ref|YP_008797259.1| 109 VASLKVLQTELKALAKSSEKLGQKMQELVKDIKEAVKEKVERLREINREFGQRV 162
                                       5789***************************************99998876555 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  15.1     0.005       2.1      88     224 ..      35     166 ..      29     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.005
                            AAA_32  88 elkkdmeelveelkkeipkafeseeYeerkeeieeefeekeeelleelekeaeekgfalkrtpegivlvPlkdgkpl 164
                                       +  ++++++v e ++++++a+   e++ + e+i+e+  e   ++lee ++++e+   ++ +  +++    +++++ +
  gi|557694205|ref|YP_008797259.1|  35 RITEELRSIVVEHREAVREAL--LEFKLKLEQIKENKTELIAQFLEERQNRMEQIRAEIENLRQQYLAGNITKDEYV 109
                                       555555555555555555554..356666666666666666666666666666666666666666655555555444 PP

                            AAA_32 165 seeefeal..peeerkeleekseeleeeleeilrelrelekeakeklkelerevakeavepl 224
                                       +     +l   + e k+l ++se+l ++++e++++++e  ke  e+l+e++re+ +++ e++
  gi|557694205|ref|YP_008797259.1| 110 A-----SLkvLQTELKALAKSSEKLGQKMQELVKDIKEAVKEKVERLREINREFGQRVAEEA 166
                                       4.....44324689999*************************************99988765 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.4      0.23        98      31      68 ..      59      92 ..      33      98 .. 0.50
   2 ?    8.6   5.6    0.0064       2.8      21      51 ..     124     154 ..     100     184 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.23
                              YtxH 31 kekaddlkekakelleeakekakekaedlkekvkekad 68
                                      k k++++ke+ +el+ ++     e+ ++ +e+++ +++
  gi|557694205|ref|YP_008797259.1| 59 KLKLEQIKENKTELIAQF----LEERQNRMEQIRAEIE 92
                                      222344444444444333....5555555555555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0064
                              YtxH  21 ksGketRkdlkekaddlkekakelleeakek 51 
                                       ks +++ ++++e ++d+ke +ke +e+++e 
  gi|557694205|ref|YP_008797259.1| 124 KSSEKLGQKMQELVKDIKEAVKEKVERLREI 154
                                       2333333333333333333333333333333 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   7.2      0.08        34      11      79 ..      27      98 ..      20     107 .. 0.72
   2 ?    7.0  20.6     0.016       6.8      15     104 ..      63     150 ..      60     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.08
                                      HHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS....-HHHHHHHHHHHHHHHHHHHHH CS
                              OmpH 11 leespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.e..keekeqelqkkeqelqqkqqqk 79
                                      l+++  g+++ e+l +   + ++++++   e++ + e++++++ +l +   ee+++ +++ ++e+++++qq 
  gi|557694205|ref|YP_008797259.1| 27 LSDMSLGQRITEELRSIVVEHREAVREALLEFKLKLEQIKENKTELiAqfLEERQNRMEQIRAEIENLRQQY 98
                                      567888999999999999999999999999999999999866666554885566666666666666644444 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.016
                                       HHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  15 pegkaaqeqlekkf.kklqaeleakekelqklqeelqkkakklekeekeqe.lqkkeqelqqkqqqkaqelqkkqqe 89 
                                       ++ k+ +++l ++f +++q+ +e+ ++e+++l++++    + + +++++ + l+ +++el++ +++  ++l +k qe
  gi|557694205|ref|YP_008797259.1|  63 EQIKENKTELIAQFlEERQNRMEQIRAEIENLRQQYL---AGNITKDEYVAsLKVLQTELKA-LAKSSEKLGQKMQE 135
                                       5677788888888779********************7...33324455555699999***99.99999********* PP

                                       HHHHHHHHHHHHHHH CS
                              OmpH  90 llkpildkinkaike 104
                                       l+k i + +++ ++ 
  gi|557694205|ref|YP_008797259.1| 136 LVKDIKEAVKEKVER 150
                                       999999999998865 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 ?    5.5   7.8     0.046        20      27      73 ..     104     154 ..       5     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.046
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvnelledvne....klekvdpl 73 
                                       t de  a++++l+ +++++ k +e+l +k++el++d++e    k+e++ ++
  gi|557694205|ref|YP_008797259.1| 104 TKDEYVASLKVLQTELKALAKSSEKLGQKMQELVKDIKEavkeKVERLREI 154
                                       557788889999999999999999999999999999888433344444443 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  15.3    0.0099       4.2      57     157 ..      58     158 ..      23     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0099
                         Rootletin  57 sareleeeesadleealakLeeErqrseklaqvnslLreqleearqaneaLtedlqkltkdwerlreeleqkekewr 133
                                        + +le+ +++++e + + Lee ++r e++ ++ + Lr+q  + + + ++   +l+ l+++++ l++++e+  ++++
  gi|557694205|ref|YP_008797259.1|  58 FKLKLEQIKENKTELIAQFLEERQNRMEQIRAEIENLRQQYLAGNITKDEYVASLKVLQTELKALAKSSEKLGQKMQ 134
                                       334566666777777888899999999**9999999****9999999999999999999999999999999999999 PP

                         Rootletin 134 eeeeafneylssehsrllsLWrev 157
                                       e  + ++e +++  +rl ++ re+
  gi|557694205|ref|YP_008797259.1| 135 ELVKDIKEAVKEKVERLREINREF 158
                                       999999999999999999888776 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 ?    7.3   1.6    0.0094         4      87     134 ..      61     108 ..      56     112 .. 0.84
   2 ?    6.6   1.4     0.015       6.3      75     117 ..     112     158 ..      98     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0094
                                       HHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXX CS
                     Mt_ATP-synt_D  87 evdaeekevkkeikefkeeskkrieelekeleklksllpfeemtmedf 134
                                       ++++ +++ ++ i++f ee ++r+e+++ e+e+l++     ++t +++
  gi|557694205|ref|YP_008797259.1|  61 KLEQIKENKTELIAQFLEERQNRMEQIRAEIENLRQQYLAGNITKDEY 108
                                       567777888899**********************99887777777776 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                                       -------....-TTTTHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHH CS
                     Mt_ATP-synt_D  75 lkipype....dkyteevdaeekevkkeikefkeeskkrieelekel 117
                                       lk++ +e     k++e++ ++++e +k+ike ++e  +r++e++ e 
  gi|557694205|ref|YP_008797259.1| 112 LKVLQTElkalAKSSEKLGQKMQELVKDIKEAVKEKVERLREINREF 158
                                       44444444445677799999999999999999999999999998775 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 ?    8.1  17.1    0.0038       1.6      43     151 ..      34     143 ..      20     164 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0038
                         Golgin_A5  43 talsaeldel.kqerdllreelqklnqqieqlrtelqdleaqqqaeaeslreqlqeleeqleeerkakeeveaeler 118
                                       ++ + el ++  + r+++re l +++ ++eq++ +  +l aq+ +e ++ +eq++   e+l+++  a + +++e   
  gi|557694205|ref|YP_008797259.1|  34 QRITEELRSIvVEHREAVREALLEFKLKLEQIKENKTELIAQFLEERQNRMEQIRAEIENLRQQYLAGNITKDEYVA 110
                                       45555665553677999999999999999999988888887777777766666666666665555555444444444 PP

                         Golgin_A5 119 lkeelryleeelvrskatlqsrikdrekeiekl 151
                                         + l++  + l +s ++l +++++  k+i++ 
  gi|557694205|ref|YP_008797259.1| 111 SLKVLQTELKALAKSSEKLGQKMQELVKDIKEA 143
                                       444444444444444444444444444444332 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  14.0    0.0091       3.9     142     231 ..      55     168 ..      17     213 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0091
                      Exonuc_VII_L 142 kaeleeqleelerrlekaikrlleekkqrleklasrlks........................peellerkrqrlde 194
                                         e++ +le+++++ ++ i++ lee+++r+e+++ ++++                          + l++++++l +
  gi|557694205|ref|YP_008797259.1|  55 LLEFKLKLEQIKENKTELIAQFLEERQNRMEQIRAEIENlrqqylagnitkdeyvaslkvlqtELKALAKSSEKLGQ 131
                                       22334444444444444444444555555554444443211122222222222222111111112222222222222 PP

                      Exonuc_VII_L 195 leerleralkkqlkkkrerleelkerlkekleekker 231
                                         ++l + +k+++k+k erl+e+++++ ++++e++++
  gi|557694205|ref|YP_008797259.1| 132 KMQELVKDIKEAVKEKVERLREINREFGQRVAEEAKK 168
                                       2222222222223333333333332222233333333 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   4.4     0.036        15      55     109 ..      43      97 ..      22     101 .. 0.74
   2 ?    8.8   9.7    0.0045       1.9      39     126 ..      82     171 ..      79     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.036
                             Muted  55 llpkclesmkenLselnkkleaalekverllqkeleeekrkseqlqekeeerkae 109
                                       +  +  e++ e L e++ kle+ +e+ ++l  + lee++++ eq+ ++ e+++++
  gi|557694205|ref|YP_008797259.1|  43 IVVEHREAVREALLEFKLKLEQIKENKTELIAQFLEERQNRMEQIRAEIENLRQQ 97 
                                       3455667788899999999999999999999999999999999998887776665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0045
                             Muted  39 elLenikklvnelkeqllpkcles..mkenLselnkkleaalekverllqkeleeekrkseqlqekeeerkaeweef 113
                                       +++e+i+  +++l++q+l  ++++     +L+ l+++l+a+ +++e+l qk +e  k  +e ++ek e++++   ef
  gi|557694205|ref|YP_008797259.1|  82 NRMEQIRAEIENLRQQYLAGNITKdeYVASLKVLQTELKALAKSSEKLGQKMQELVKDIKEAVKEKVERLREINREF 158
                                       589***************999888667789*********************9999999999***********999*9 PP

                             Muted 114 lkelqekkeevDe 126
                                        + ++e+ +++ +
  gi|557694205|ref|YP_008797259.1| 159 GQRVAEEAKKLGD 171
                                       9999888877655 PP

>> IZUMO  Izumo sperm-egg fusion, Ig domain-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   2.0      0.31   1.3e+02      36     104 ..      24      91 ..      12      98 .. 0.55
   2 ?    7.0   8.1     0.018       7.7      11     110 ..      63     157 ..      57     168 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.31
                                       HHHHHTTT.---SGGGGGGSEEE.HHHHHHHHHHHHHHHHHHHHS---HHHHHHHHHHHHHHHHHHHHHHH CS
                             IZUMO  36 ealledls.ekelaenkflgvvd.eetlekvasslkkelkrltdsdlkgelllkeLlwllqkqkkklkeal 104
                                        ++l+d+s  + + e+    vv+ +e + ++  ++k +l+++++++ +   l+ + l+ +q+  +++   +
  gi|557694205|ref|YP_008797259.1|  24 AQELSDMSlGQRITEELRSIVVEhREAVREALLEFKLKLEQIKENKTE---LIAQFLEERQNRMEQIRAEI 91 
                                       566677776455555544444441445677777788888888877654...33333344444443333333 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.018
                                       HHHHHHHHTHHHHHSGGHHHHHHHHHHHHHTTT---SGGGGGGSEEEHHHHHHHHHHHHHHHHHHHHS---HHHHHH CS
                             IZUMO  11 ealksLeedllpselehreklleraealledlsekelaenkflgvvdeetlekvasslkkelkrltdsdlkgelllk 87 
                                       e++k+ +++l+ + le+r++ +e+++a++e+l ++ la     g +++++     + l+ elk l +s+ k  + ++
  gi|557694205|ref|YP_008797259.1|  63 EQIKENKTELIAQFLEERQNRMEQIRAEIENLRQQYLA-----GNITKDEYVASLKVLQTELKALAKSSEKLGQKMQ 134
                                       66677777777777777777777777777777766555.....5677777777777777777777777777666666 PP

                                       HHHHHHHHHHHHHHHHHHHHHHT CS
                             IZUMO  88 eLlwllqkqkkklkealkefqke 110
                                       eL++ +++++k+  e l+e+++e
  gi|557694205|ref|YP_008797259.1| 135 ELVKDIKEAVKEKVERLREINRE 157
                                       66665555554444444444333 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 ?    2.3   1.7       0.4   1.7e+02      10      28 ..      69      87 ..      61      99 .. 0.55
   2 ?    7.4  11.1      0.01       4.3       7      72 ..      77     142 ..      71     143 .. 0.90
   3 ?    7.3  11.0     0.011       4.6      15      66 ..     113     172 ..     104     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.4
                        TMF_DNA_bd 10 KDeqIaqLmeEGekLskke 28
                                      K e Iaq +eE ++   + 
  gi|557694205|ref|YP_008797259.1| 69 KTELIAQFLEERQNRMEQI 87
                                      6666666666666554443 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.01
                        TMF_DNA_bd   7 lkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                       l+e++ + +q ++E e+L+ + l+ n t ++  + +k l +e+k l k  ekl ++++el +  ke
  gi|557694205|ref|YP_008797259.1|  77 LEERQNRMEQIRAEIENLRQQYLAGNITKDEYVASLKVLQTELKALAKSSEKLGQKMQELVKDIKE 142
                                       7999**********************9999999999999999999999999999999999888776 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.011
                        TMF_DNA_bd  15 aqLmeEGekLskkelklnntikkLrkknkele.keikelk.......kkleklekeleel 66 
                                       + L++E+++L+k+  kl +++ +L k++ke+  +++++l        ++++++ k+l  l
  gi|557694205|ref|YP_008797259.1| 113 KVLQTELKALAKSSEKLGQKMQELVKDIKEAVkEKVERLReinrefgQRVAEEAKKLGDL 172
                                       5699***************************95566666655555556666666665555 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 ?    4.6  15.2     0.034        14      40     173 ..      31     174 ..      20     192 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.034
                             Atg14  40 slkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk.... 112
                                       sl+++i+++l +       e ++  + a le + +l ++++++++++ + l++++ ++e+ +++++ l+++      
  gi|557694205|ref|YP_008797259.1|  31 SLGQRITEELRSIV----VEHREAVREALLEFKLKLEQIKENKTELIAQFLEERQNRMEQIRAEIENLRQQYLagni 103
                                       56666666666665....55556666666666666666666677777777777777777777777777766555666 PP

                             Atg14 113 .............kRrsdleslqneleerrkkqiaklqdaikrieqklsslssktlesrsslcselaklyglrr 173
                                                    +  + l++ +++l ++ +++++ + +a+k++ + l +++++  +     ++e+ kl +l r
  gi|557694205|ref|YP_008797259.1| 104 tkdeyvaslkvlqTELKALAKSSEKLGQKMQELVKDIKEAVKEKVERLREINREFGQ---RVAEEAKKLGDLAR 174
                                       666555555554433333344445555555555555555555555555555555555...34444444444444 PP

>> DUF3135  Protein of unknown function (DUF3135)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.7     0.012       5.1      19      56 ..      62      98 ..      59     102 .. 0.84
   2 ?    2.6   0.7      0.39   1.7e+02       7      45 ..     118     154 ..     115     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.012
                           DUF3135 19 lealrqelieelIesapeemqrrLrglqfqiDmqlsra 56
                                      le+++++   elI++  ee q+r+++++ +i+  ++++
  gi|557694205|ref|YP_008797259.1| 62 LEQIKEN-KTELIAQFLEERQNRMEQIRAEIENLRQQY 98
                                      5555544.5689********************999875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.39
                           DUF3135   7 eLvaLakedPealealrqelieelIesapeemqrrLrgl 45 
                                       eL+aLak+  e+l +  qel++++ ++a +e  +rLr++
  gi|557694205|ref|YP_008797259.1| 118 ELKALAKSS-EKLGQKMQELVKDI-KEAVKEKVERLREI 154
                                       788999887.99999999999985.55556666788876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2622  (0.146244); expected 358.6 (0.02)
Passed bias filter:                      888  (0.0495287); expected 358.6 (0.02)
Passed Vit filter:                       170  (0.00948185); expected 17.9 (0.001)
Passed Fwd filter:                        66  (0.00368119); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              42  [number of targets reported over threshold]
# CPU time: 0.94u 0.33s 00:00:01.27 Elapsed: 00:00:00.50
# Mc/sec: 1641.93
//
Query:       gi|557694206|ref|YP_008797260.1|  [L=290]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   35.0   0.1    1.9e-08   34.0   0.1    1.6  1  HTH_IclR         IclR helix-turn-helix domain
    1.7e-08   34.2   0.4    4.1e-08   33.0   0.4    1.6  1  MarR_2           MarR family
    2.8e-07   30.0   0.0    5.7e-07   29.0   0.0    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    3.9e-06   26.7   0.0    8.1e-06   25.7   0.0    1.5  1  MarR             MarR family
    1.4e-05   24.8   0.3    3.3e-05   23.7   0.3    1.6  1  TrmB             Sugar-specific transcriptional regulator Trm
    1.7e-05   24.6   0.0    3.1e-05   23.7   0.0    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
    2.7e-05   24.1   0.3    5.5e-05   23.1   0.3    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    7.5e-05   22.7   0.3    0.00014   21.8   0.3    1.5  1  HTH_20           Helix-turn-helix domain
    0.00024   21.0   0.0    0.00032   20.5   0.0    1.2  1  DUF4897          Domain of unknown function (DUF4897)
     0.0003   21.1   0.3    0.00059   20.2   0.3    1.4  1  Penicillinase_R  Penicillinase repressor
    0.00052   20.1   0.3     0.0011   19.0   0.1    1.7  1  HTH_28           Helix-turn-helix domain
    0.00053   19.5   0.2     0.0011   18.4   0.2    1.5  1  Sigma70_r4       Sigma-70, region 4
     0.0014   18.3   0.1     0.0034   17.1   0.1    1.6  1  HTH_23           Homeodomain-like domain
     0.0046   16.7   0.1      0.012   15.4   0.1    1.8  1  HTH_8            Bacterial regulatory protein, Fis family
     0.0047   16.9   0.0     0.0085   16.0   0.0    1.3  1  HTH_11           HTH domain
     0.0071   15.9   0.0      0.012   15.2   0.0    1.4  1  CENP-B_N         CENP-B N-terminal DNA-binding domain
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.021   14.5   0.0    1.4  1  Sigma70_r4_2     Sigma-70, region 4
      0.029   14.6   0.2      0.061   13.5   0.2    1.5  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.032   14.3   0.1      0.077   13.0   0.1    1.6  1  HTH_29           Winged helix-turn helix
      0.032   14.0   0.0      0.057   13.2   0.0    1.4  1  HTH_38           Helix-turn-helix domain
      0.035   14.5   0.1      0.087   13.2   0.1    1.6  1  Rrf2             Transcriptional regulator
      0.038   13.7   1.7       0.12   12.0   0.8    2.1  2  GntR             Bacterial regulatory proteins, gntR family
      0.039   14.0   0.0        0.1   12.7   0.0    1.8  1  HTH_7            Helix-turn-helix domain of resolvase
      0.073   12.9   0.1        0.4   10.6   0.0    2.3  3  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.084   12.6   0.5       0.59    9.8   0.0    2.3  2  Crp              Bacterial regulatory proteins, crp family
       0.15   11.4   0.0       0.21   10.9   0.0    1.2  1  RNA_pol_Rpc34    RNA polymerase Rpc34 subunit


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 !   34.0   0.1   2.7e-11   1.9e-08       8      50 ..     236     278 ..     233     280 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2.7e-11
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       +   l+++++e++ s++Ar++glp+Stv+  ++ L+e+G v +
  gi|557694206|ref|YP_008797260.1| 236 VVAVLRRHGGEMKQSQIARELGLPRSTVSTVMKVLEEQGRVSR 278
                                       556799*********************************8876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.4     6e-11   4.1e-08       9      54 ..     235     279 ..     231     284 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 6e-11
                                       HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2   9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       rv a+L+r++g+ + ++++ar+lgl++s+vs + k L+++G v r+
  gi|557694206|ref|YP_008797260.1| 235 RVVAVLRRHGGE-MKQSQIARELGLPRSTVSTVMKVLEEQGRVSRV 279
                                       79999*****96.9***************************99887 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 !   29.0   0.0   8.2e-10   5.7e-07       7      47 ..     235     276 ..     232     277 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 8.2e-10
                            HTH_24   7 kILelLqknpr.isqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       ++  +L+++++ + q+++A++lgl++stv++ +k Lee+G +
  gi|557694206|ref|YP_008797260.1| 235 RVVAVLRRHGGeMKQSQIARELGLPRSTVSTVMKVLEEQGRV 276
                                       567789999999***************************965 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.2e-08   8.1e-06       8      51 ..     236     280 ..     235     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.2e-08
                                       HHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR   8 iLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                       +++ l+++g+ +++s++a+ lg+ +stv++v + Le++G ++R k
  gi|557694206|ref|YP_008797260.1| 236 VVAVLRRHGGeMKQSQIARELGLPRSTVSTVMKVLEEQGRVSRVK 280
                                       56778999988*******************************976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3   4.8e-08   3.3e-05      21      58 ..     245     282 ..     237     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.8e-08
                                       CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       g+++ ++ia+elg+prs+v  v++ Le+ G V r+k  
  gi|557694206|ref|YP_008797260.1| 245 GEMKQSQIARELGLPRSTVSTVMKVLEEQGRVSRVKMG 282
                                       79999*****************************9965 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 !   23.7   0.0   4.5e-08   3.1e-05      11      45 ..     240     276 ..     235     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.5e-08
                                       HTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  11 Lae..gelcvcelaeelglsqstvShHLkkLreaGLV 45 
                                       L++  ge++ +++a+elgl++stvS   k+L+e+G V
  gi|557694206|ref|YP_008797260.1| 240 LRRhgGEMKQSQIARELGLPRSTVSTVMKVLEEQGRV 276
                                       666779****************************966 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 !   23.1   0.3     8e-08   5.5e-05      21      59 ..     246     287 ..     232     290 .] 0.80

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 8e-08
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..TEE.EEE CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglis.r..grr.iri 59 
                                        + q ++A+ lGl r+tvs +++ L+++g +s    g r +++
  gi|557694206|ref|YP_008797260.1| 246 EMKQSQIARELGLPRSTVSTVMKVLEEQGRVSrVkmG-RdVVV 287
                                       589*****************************52234.33665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.3   2.1e-07   0.00014      21      61 .]     243     283 ..     217     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 2.1e-07
                                       TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  21 raegltaselaerldlskntlsyHLrvLeeagLvevvregr 61 
                                        ++++  s++a++l+l+++t+s  ++vLee g v +v+ gr
  gi|557694206|ref|YP_008797260.1| 243 HGGEMKQSQIARELGLPRSTVSTVMKVLEEQGRVSRVKMGR 283
                                       56666679************************999999886 PP

>> DUF4897  Domain of unknown function (DUF4897)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   4.7e-07   0.00032      50     147 ..      71     173 ..      25     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.7e-07
                           DUF4897  50 ekylsqlseevgreikvvslessate...regileveEka.vlkglvkvengvve.tslgdiklnlagdselvvslP 121
                                       e+ +s+ +  +gre+ v+++++  +     +g+l v+ ++ + +g++k  ++ +e  ++    + l +  +l +s P
  gi|557694206|ref|YP_008797260.1|  71 ERLVSDAAAATGREMMVEDFHVEHEVvetVSGMLGVVKVVfRWSGFAKRLDNGLEaGDVFVGGMVLLDGETLRISFP 147
                                       5667888899*********9876543224789**9998763689*****9665541466666777777777****** PP

                           DUF4897 122 kdaklisvePtPtkivenellWkges 147
                                           + +v PtP  i + ++ W+g  
  gi|557694206|ref|YP_008797260.1| 148 SSYRVAEVRPTPDGIGDGFVEWRGRR 173
                                       **********************9864 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.3   8.5e-07   0.00059       8      60 ..     236     285 ..     233     287 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.5e-07
                                       HHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEE CS
                   Penicillinase_R   8 vmeilwekge.atvkevveeleeekelaysTVktllrrLvkKgllsrekegraf 60 
                                       v  +l+++g  ++ +++  el  +    +sTV t+++ L+++g +sr k gr  
  gi|557694206|ref|YP_008797260.1| 236 VVAVLRRHGGeMKQSQIARELGLP----RSTVSTVMKVLEEQGRVSRVKMGRDV 285
                                       777888887778888888888877....***********************975 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1   1.6e-06    0.0011       4      41 ..     237     275 ..     234     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.6e-06
                            HTH_28   4 eiikllaaGh.svreaArelgisrrtvyrWikryeegGi 41 
                                        ++++   G+  ++++Arelg+ r+tv+  +k +ee+G+
  gi|557694206|ref|YP_008797260.1| 237 VAVLRRHGGEmKQSQIARELGLPRSTVSTVMKVLEEQGR 275
                                       566666667789************************996 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   1.6e-06    0.0011      14      41 ..     239     267 ..     234     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                                       HHHH.TTT--HHHHHHHHTS-HHHHHHHH CS
                        Sigma70_r4  14 elrf.geglTleEIgerlgiSrerVrqie 41 
                                       +lr+ g ++ +++I+++lg++r++V+  +
  gi|557694206|ref|YP_008797260.1| 239 VLRRhGGEMKQSQIARELGLPRSTVSTVM 267
                                       56667********************9876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1     5e-06    0.0034      17      43 ..     246     272 ..     231     279 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5e-06
                            HTH_23  17 GlsvreIAreLgvsrrTvyrwlkryre 43 
                                        + +++IAreLg +r+Tv+ + k  +e
  gi|557694206|ref|YP_008797260.1| 246 EMKQSQIARELGLPRSTVSTVMKVLEE 272
                                       5789***************99886655 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 !   15.4   0.1   1.7e-05     0.012      10      35 ..     236     263 ..     233     270 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHTTT-..HHHHHHHHTS-HHHH CS
                             HTH_8  10 IeaALertgGn..kskAArlLGisRrtL 35 
                                        +a+L+r+gG   +s+ Ar+LG+ R+t+
  gi|557694206|ref|YP_008797260.1| 236 VVAVLRRHGGEmkQSQIARELGLPRSTV 263
                                       6799******722679***********7 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   1.2e-05    0.0085       4      43 ..     235     274 ..     233     283 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                            HTH_11   4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                        ++  L+++ g +  +++A+eL++ r+tv   +k Lee+g
  gi|557694206|ref|YP_008797260.1| 235 RVVAVLRRHGGEMKQSQIARELGLPRSTVSTVMKVLEEQG 274
                                       578899999999**************************99 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 !   15.2   0.0   1.8e-05     0.012      18      44 ..     241     268 ..     232     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-05
                                       HHHCTT.-HHHHHHHHT--CCHHHHHHH CS
                          CENP-B_N  18 rleege.Skaelarrfnvpestlsdilk 44 
                                       r + ge     +ar++++p+st+s+++k
  gi|557694206|ref|YP_008797260.1| 241 RRHGGEmKQSQIARELGLPRSTVSTVMK 268
                                       55778878889**************997 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 ?   14.5   0.0   3.1e-05     0.021      18      44 ..     238     264 ..     229     267 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-05
                                       HHHHHHTS---HHHHHHHHT--HHHHH CS
                      Sigma70_r4_2  18 ifllryleglsykEIAellgisegtVk 44 
                                       ++l r+  ++++ +IA++lg++ +tV 
  gi|557694206|ref|YP_008797260.1| 238 AVLRRHGGEMKQSQIARELGLPRSTVS 264
                                       78999999*****************96 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 ?   13.5   0.2   8.8e-05     0.061      23      53 ..     247     277 ..     236     282 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.8e-05
                                       B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress  23 vktkdlaerLnvspssVsemlkkLekdGyve 53 
                                        k++++a++L+   s+Vs  +k Le++G v 
  gi|557694206|ref|YP_008797260.1| 247 MKQSQIARELGLPRSTVSTVMKVLEEQGRVS 277
                                       789*************************876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   0.00011     0.077       3      40 ..     238     274 ..     236     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                            HTH_29   3 qallllaeGvstvsqiAkllglsrrtvyrwlkrfeegG 40 
                                       ++l+ +  +++  sqiA+ lgl r+tv ++ k  ee G
  gi|557694206|ref|YP_008797260.1| 238 AVLRRHGGEMK-QSQIARELGLPRSTVSTVMKVLEEQG 274
                                       57888888998.***************99988777776 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.3e-05     0.057      21      41 ..     247     267 ..     233     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.3e-05
                            HTH_38  21 lslreIArrLgrspsTIsREl 41 
                                       + +++IAr+Lg  +sT+s  +
  gi|557694206|ref|YP_008797260.1| 247 MKQSQIARELGLPRSTVSTVM 267
                                       7789**************876 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   0.00013     0.087      13      56 ..     236     277 ..     232     283 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                                       HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2  13 allyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56 
                                       ++++L ++ +e  ++ ++ia++ ++++s ++ +++ L+++g v 
  gi|557694206|ref|YP_008797260.1| 236 VVAVLRRHGGE--MKQSQIARELGLPRSTVSTVMKVLEEQGRVS 277
                                       66677777774..89**************************886 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.7   1.1e+03      31      59 ..      87     115 ..      81     117 .. 0.87
   2 ?   12.0   0.8   0.00018      0.12       9      60 ..     232     282 ..     225     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.7
                                       HHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR  31 aaefgVsrttvReALrrLeaeglverrqg 59 
                                       ++ f+V + +v  +  +L   ++v r++g
  gi|557694206|ref|YP_008797260.1|  87 VEDFHVEHEVVETVSGMLGVVKVVFRWSG 115
                                       67899999999999999999999999887 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00018
                                       HHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                              GntR   9 LredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgr 60 
                                       L e++++   r+G  + +++++a e+g  r+tv  +++ Le++g v r +++
  gi|557694206|ref|YP_008797260.1| 232 LVERVVAVLRRHGGEM-KQSQIARELGLPRSTVSTVMKVLEEQGRVSRVKMG 282
                                       5566666666899999.******************************98865 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 ?   12.7   0.0   0.00015       0.1      14      38 ..     239     263 ..     223     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                                       GGSSTTTT.--STTTSSSS---SSSS CS
                             HTH_7  14 vvkLleeG.isiskIAkevnisRsTv 38 
                                       v  ++  G ++ s+IA+e+++ RsTv
  gi|557694206|ref|YP_008797260.1| 239 V-LRRHGGeMKQSQIARELGLPRSTV 263
                                       3.3445566************99998 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 ?   -2.1   0.0       5.2   3.6e+03      29      41 ..      61      73 ..      51      74 .. 0.68
   2 ?   10.6   0.0   0.00058       0.4      10      35 ..     238     264 ..     234     271 .. 0.84
   3 ?   -1.9   0.0       4.6   3.2e+03      10      26 ..     268     284 ..     265     286 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.2
                     HTH_AsnC-type 29 lSestvlrRvrrL 41
                                      l     l+Rv+rL
  gi|557694206|ref|YP_008797260.1| 61 LQSGDYLARVERL 73
                                      5555567999999 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00058
                     HTH_AsnC-type  10 eaLqed.aRisyaeLAervGlSestvl 35 
                                       + L++  + +  +++A+++Gl +stv 
  gi|557694206|ref|YP_008797260.1| 238 AVLRRHgGEMKQSQIARELGLPRSTVS 264
                                       667777799999*************96 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.6
                     HTH_AsnC-type  10 eaLqedaRisyaeLAer 26 
                                       + L+e++R s  ++++ 
  gi|557694206|ref|YP_008797260.1| 268 KVLEEQGRVSRVKMGRD 284
                                       57999999998888875 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.2   8.1e+02      16      24 ..      97     105 ..      97     106 .. 0.87
   2 ?    9.8   0.0   0.00085      0.59       7      30 ..     251     274 ..     247     275 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.2
                                       HHHHHHHHH CS
                               Crp  16 rETVSRlLt 24 
                                       +ETVS +L+
  gi|557694206|ref|YP_008797260.1|  97 VETVSGMLG 105
                                       7****9987 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00085
                                       HHHHHHTS-HHHHHHHHHHHHHTT CS
                               Crp   7 dIAdylGlTrETVSRlLtrLrekG 30 
                                       +IA+ lGl r TVS +++ L+e+G
  gi|557694206|ref|YP_008797260.1| 251 QIARELGLPRSTVSTVMKVLEEQG 274
                                       8*********************98 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 ?   10.9   0.0    0.0003      0.21     104     136 ..     248     280 ..     219     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                                       EHHHHHHTTGXXHHHHHHHHHHHHHTTXXEEEE CS
                     RNA_pol_Rpc34 104 wsrtiksklnLhksvvkkcLksLeskkyiksvk 136
                                        + +i + l+L+ s v  ++k+Le ++++  vk
  gi|557694206|ref|YP_008797260.1| 248 KQSQIARELGLPRSTVSTVMKVLEEQGRVSRVK 280
                                       5789*************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2127.89
//
Query:       gi|557694207|ref|YP_008797261.1|  [L=422]
Description: actin/actin family protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-16   60.2   0.0    2.1e-14   53.0   0.0    2.2  1  Actin     Actin


Domain annotation for each model (and alignments):
>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   1.2e-18   2.1e-14     124     378 ..     150     399 ..     146     403 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.2e-18
                             Actin 124 palylaksavlsafasgkstglvvDsGasvtsvvpVldGyvLkkairrsdlgGkaLteqlkellssknvevtpryli 200
                                       ++  +  ++  +a a+ +++ +vv+sG+++t v+p+    ++++a+  ++ gG a +   +e+l++           
  gi|557694207|ref|YP_008797261.1| 150 HSSTIIPQPLAVAIAHKQTSCVVVESGHGNTQVSPISR-APIREAVIALNRGGGAANAITAEILKDA---------- 215
                                       667788899999************************87.69*************************6.......... PP

                             Actin 201 kkkkvveaessaekeelekltesyktleeeevleeiKesvcevsedpeg...deeksssspeksYeLPDgs.eiklg 273
                                                               + ++ee +++++Ke++     +  +    +++  ++ +++Y  P  + +i+lg
  gi|557694207|ref|YP_008797261.1| 216 ---------------------GYGDLVKEEALVRKVKENIGLLPLELDKalaFAKNYPDELKTVYQPPGTRiKIDLG 271
                                       .....................234678999**********9999888885545555558899999988777889999 PP

                             Actin 274 ee...RfkvpEiLFdpsligsesaleee.............kskllgiselivaainacdvdlrpeLlanivvtGGn 334
                                       ++   Rf + E  F+p+    es +++                 +l+i++ i++a+++c+++l+p L+++++++GGn
  gi|557694207|ref|YP_008797261.1| 272 KDswmRFLIGEYVFNPNHEIFESYHRRGmpkpadtkvgdvvFYGTLSIADTIIQAVEKCPTELQPLLYSQVILSGGN 348
                                       86666************999988866669999*******999999******************************** PP

                             Actin 335 sllp......gl....teRlekelaqlaskgvkvkiiapeeerkysaWiGGSiL 378
                                        + +      g+    + Rl +el+q+  ++  vk  a++   +y++W G  ++
  gi|557694207|ref|YP_008797261.1| 349 FSWQapqrlrGVavdsETRLTHELRQRGVENPVVKLSAEP---QYAVWRGCIVF 399
                                       886522222233222268********99999999998876...9*****97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3138.01
//
Query:       gi|557694208|ref|YP_008797262.1|  [L=188]
Description: hypothetical protein CSUB_C0774 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.1   1.4       0.74    9.7   0.1    2.4  2  HSBP1     Heat shock factor binding protein 1
      0.069   13.0   0.0       0.23   11.2   0.0    1.7  2  DUF1819   Putative inner membrane protein (DUF1819)
       0.13   11.7   0.1       0.17   11.3   0.1    1.2  1  Cupin_4   Cupin superfamily protein


Domain annotation for each model (and alignments):
>> HSBP1  Heat shock factor binding protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.016        95      22      49 ..      17      44 ..      15      46 .. 0.89
   2 ?    9.7   0.1   0.00012      0.74      17      39 ..     115     137 ..     113     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.016
                             HSBP1 22 sdqilsriDdMssriDdLEksiadlmtq 49
                                      s++i+  +D++ sr + L + i+  m++
  gi|557694208|ref|YP_008797262.1| 17 SESIVRVVDELASRDEMLATIIQAAMES 44
                                      899***********99999999999986 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00012
                             HSBP1  17 kFqtmsdqilsriDdMssriDdL 39 
                                       + ++m  ++l r++d+++r++++
  gi|557694208|ref|YP_008797262.1| 115 RLENMLAEVLRRVEDLERRVEEM 137
                                       78899999999999999999986 PP

>> DUF1819  Putative inner membrane protein (DUF1819)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0       0.2   1.2e+03      12      38 ..      12      38 ..      10      41 .. 0.85
   2 ?   11.2   0.0   3.9e-05      0.23       3      74 ..      65     139 ..      63     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.2
                                      --HHHHHHHHHHHHH---HHHHHHHHH CS
                           DUF1819 12 fllaEsrkvaelllegkseaeirekal 38
                                      fl  Es  +++++ e  s++e+ + ++
  gi|557694208|ref|YP_008797262.1| 12 FLCGESESIVRVVDELASRDEMLATII 38
                                      888999999999999999999888776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.9e-05
                                       --SGGGG----HHHHHHHHHHHHH...---HHHHHHHHHTS-TT--------HHHHHHHHHHHTTS-HHHHHHHH CS
                           DUF1819   3 YsasltkgsfllaEsrkvaellle...gkseaeirekaleeNifqkrtesrakriasevirRlklLdeellella 74 
                                       Y ++ +k ++l+++ r v+e+++    gk+++e ++ + e+  + +    r+++++ ev+rR++ L + + e+ +
  gi|557694208|ref|YP_008797262.1|  65 YAFRVNKIGVLVYDERDVVEIVEAglvGKTSDEEKSTISEKPSIDVGRVERLENMLAEVLRRVEDLERRVEEMAR 139
                                       8888999999999999999999887779************************************99777666655 PP

>> Cupin_4  Cupin superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.8e-05      0.17     235     292 ..      93     151 ..      66     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.8e-05
                                       HCTSCHHCTCGTTTGGGTTS-HHHHHHHHHHHHHHHHHHHCS-HHHHCCHHHHH.HHHS CS
                           Cupin_4 235 rlrdallravqargeidsdsidalaaqlsellrdpalleeflgqlltsssrekd.iaqs 292
                                       + +d++++++ ++  id   +++l+++l+e+lr++++le+  +++++++ +  + i q 
  gi|557694208|ref|YP_008797262.1|  93 KTSDEEKSTISEKPSIDVGRVERLENMLAEVLRRVEDLERRVEEMARQPIQPTQsIPQP 151
                                       5667777888999***********************************94333323332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
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: 00:00:00.42
# Mc/sec: 1357.11
//
Query:       gi|557694209|ref|YP_008797263.1|  [L=309]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-31  107.1   0.4    1.4e-30  106.4   0.4    1.3  1  MS_channel  Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.017   15.2   0.1      0.029   14.5   0.1    1.3  1  SseB_C      SseB protein C-terminal domain
       0.11   12.5   0.0        1.5    8.9   0.0    2.3  2  DUF2647     Protein of unknown function (DUF2647)
       0.22   12.2   0.0       0.36   11.5   0.0    1.4  1  DUF2470     Protein of unknown function (DUF2470)


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 !  106.4   0.4   3.1e-34   1.4e-30       3     201 ..      90     302 ..      88     306 .. 0.91

  Alignments for each domain:
  == domain 1  score: 106.4 bits;  conditional E-value: 3.1e-34
                                       HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS......... CS
                        MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig......... 70 
                                       i+ i+ ++++ + vls+lg+++ + la+  ++gl++g+a ++++sn++aGiill+++pfk+GD++ +          
  gi|557694209|ref|YP_008797263.1|  90 IIQIIGYILIAVFVLSTLGIPPETALAGGTVTGLVIGFAGQTTLSNVIAGIILLTSRPFKLGDRIAVVtssvpyqwa 166
                                       789999*************************************************************99******** PP

                                       ...............SEEEEEEEE-SSEEEEEETTSEEEEEEHHHHH.TS-EEESSS.SSEEEEEEEEEE-TTS-.. CS
                        MS_channel  71 ...............dieGtVediglrttkirtfdgrivtiPnsslv.tsnieNlsresgtrrikvsigvtyssdvk 131
                                                        +G Ve+++l  t++ t dg ++ iPn+ ++ +s+i+N+s+  ++r  k++ +++ + +  
  gi|557694209|ref|YP_008797263.1| 167 flpgykffsrdyvipAYTGVVENMSLMYTTLVTDDGLVIKIPNNLILaNSAIANYSE-VTERERKLRYEFPIDIS-- 240
                                       ********************************************9873678******.66666666666666666.. PP

                                       .HHHHHHHHHHHHHH-TTB-TTS-EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHH CS
                        MS_channel 132 klekvleelkealkekpevlkdkellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkilee 201
                                        +e vl +l+eal+e pe+++      +l+e +d++  + v  f  +  + ++ +++s +  +++++ +e
  gi|557694209|ref|YP_008797263.1| 241 -PETVLNNLREALSEFPEIKD-----IYLEEQSDKTHYIVVVTFEAP--VTQWRELKSRLLAKVIEVHRE 302
                                       .78****************95.....899999999999999999999..899999999999998887766 PP

>> SseB_C  SseB protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   6.5e-06     0.029      12      66 ..     236     291 ..     226     306 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.5e-06
                            SseB_C  12 p.aeepvdllaalseyfakrkeVkaAylalmrkenekpslligvdleg...dteklfkd 66 
                                       p +  p+++l++l+e +++ +e+k  yl + ++++   +++++v +e    ++++l + 
  gi|557694209|ref|YP_008797263.1| 236 PiDISPETVLNNLREALSEFPEIKDIYLEEQSDKT---HYIVVVTFEApvtQWRELKSR 291
                                       546689**********************9888777...*********977755555444 PP

>> DUF2647  Protein of unknown function (DUF2647)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00034       1.5      27      49 ..      69      91 ..      62     106 .. 0.82
   2 ?    0.7   0.0      0.12   5.4e+02      30      65 ..     267     302 ..     260     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00034
                           DUF2647 27 rshvdltfyslvGsGrsGGGtta 49
                                       shv +tf  lvG    GGG   
  gi|557694209|ref|YP_008797263.1| 69 SSHVVKTFRPLVGQQAVGGGLII 91
                                      59*****************9755 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.12
                           DUF2647  30 vdltfyslvGsGrsGGGttallssrisisllsvyre 65 
                                        d+t y +v +  +     + l sr   +++ v+re
  gi|557694209|ref|YP_008797263.1| 267 SDKTHYIVVVTFEAPVTQWRELKSRLLAKVIEVHRE 302
                                       6889999998888888899999****9999999998 PP

>> DUF2470  Protein of unknown function (DUF2470)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0     8e-05      0.36      50      75 ..     270     293 ..     220     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8e-05
                                       ...CEEEEEE-SS---SCCHHHHHHH CS
                           DUF2470  50 agsektvripFdpplkswaearerLv 75 
                                       +  +  v ++F+ p+++w+e+++rL 
  gi|557694209|ref|YP_008797263.1| 270 T--HYIVVVTFEAPVTQWRELKSRLL 293
                                       3..66799****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2171.09
//
Query:       gi|557694210|ref|YP_008797264.1|  [L=206]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   29.9  17.1    3.2e-05   23.9   4.3    2.0  2  VIT1             VIT family
  ------ inclusion threshold ------
       0.67    9.8   0.0       0.67    9.8   0.0    3.7  4  LapA_dom         Lipopolysaccharide assembly protein A domain


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 !   14.6   3.3   2.4e-06     0.022      10      62 ..      39      91 ..      35     107 .. 0.85
   2 !   23.9   4.3   3.6e-09   3.2e-05     115     209 ..      97     196 ..      89     200 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-06
                              VIT1 10 DGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdl 62
                                      DG++++++l +G ++a   + +tv++aGl   +A  +S   G Y+  ++e   
  gi|557694210|ref|YP_008797264.1| 39 DGVLTVTGLCLGAAVAPGTRVSTVVFAGLGASIAMLVSGFTGIYVTESAETRR 91
                                      9*************997779*************************88877543 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 3.6e-09
                              VIT1 115 lelmlreelgpsa.seelasplkaAlssalsfliGgliPllpylfve....svglalvvsiavtllalllfGavkal 186
                                       +e mlr+ ++    +  l+ pl a l+ +ls ++ ++  llpy+        +  a+++s av +l l+++G++ ++
  gi|557694210|ref|YP_008797264.1|  97 EESMLRDVSDTIIgRAGLVGPLIASLIGGLSTFLLSITVLLPYIASLyideLQPYAMFLSPAVGMLLLFVLGMFLGK 173
                                       55566666664441444488999********************8644455458899********************* PP

                              VIT1 187 ltgssklvsalrmlliGalAaaa 209
                                       +++ ++++ +l+ml +G+++a++
  gi|557694210|ref|YP_008797264.1| 174 FSKIEMVKTGLKMLGMGIVTAVM 196
                                       *******************9986 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 ?    9.8   0.0   7.5e-05      0.67      24      58 ..      62      98 ..      59     104 .. 0.82
   2 ?   -0.2   0.8     0.097   8.7e+02      24      40 ..     118     134 ..     115     140 .. 0.85
   3 ?   -0.7   1.3      0.14   1.3e+03      23      34 ..     161     172 ..     152     185 .. 0.68
   4 ?   -1.3   0.5      0.22     2e+03      27      41 ..     187     201 ..     183     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 7.5e-05
                          LapA_dom 24 lvafgiGallgwllslwsyl..rlrrelrrlkkkikk 58
                                      +v++g+Ga +++l+s ++ +      e rr  ++i++
  gi|557694210|ref|YP_008797264.1| 62 VVFAGLGASIAMLVSGFTGIyvTESAETRRRVREIEE 98
                                      799*************755544888888888888876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.097
                          LapA_dom  24 lvafgiGallgwllslw 40 
                                       l+a +iG l ++lls+ 
  gi|557694210|ref|YP_008797264.1| 118 LIASLIGGLSTFLLSIT 134
                                       68899999999999985 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.14
                          LapA_dom  23 llvafgiGallg 34 
                                       +l+ f++G++lg
  gi|557694210|ref|YP_008797264.1| 161 MLLLFVLGMFLG 172
                                       455555555554 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.22
                          LapA_dom  27 fgiGallgwllslws 41 
                                       +g+G++ ++ + l+ 
  gi|557694210|ref|YP_008797264.1| 187 LGMGIVTAVMILLME 201
                                       788999998888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1458.51
//
Query:       gi|557694211|ref|YP_008797265.1|  [L=345]
Description: methylthioribose-1-phosphate isomerase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-85  284.2   0.1    1.1e-84  284.0   0.1    1.0  1  IF-2B     Initiation factor 2 subunit 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 !  284.0   0.1     6e-89   1.1e-84       2     282 .]      48     336 ..      47     336 .. 0.96

  Alignments for each domain:
  == domain 1  score: 284.0 bits;  conditional E-value: 6e-89
                                       S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHH CS
                             IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakks 78 
                                       vrG+pai++aa+++++ ++ ++++ + ++L ++lrka+++L ++rPtav+l++a++r++k+  + + + +  e+ ++
  gi|557694211|ref|YP_008797265.1|  48 VRGAPAIGVAAAYGMALAALRSRARTREQLLTKLRKAAKTLGSTRPTAVNLFWALDRMMKK--AENIDGSPAEIAEE 122
                                       89**********************************************************5..556667778999** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH CS
                             IF-2B  79 liekikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG 147
                                       l+++++++++e++e ++ ig+ +aeli d+ +ilT+cn+++        +l+v+r a++++k++ V++ E+rPrlqG
  gi|557694211|ref|YP_008797265.1| 123 LLNEAQKIHREDVEMNKTIGRLGAELIPDNSRILTHCNAGAlatagygtALGVIRYAHESGKQILVYASETRPRLQG 199
                                       ***************************************************************************** PP

                                       .HTHHHHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEET.TSEEEEETTHHHHHHHHHHTTXEEEEEXXGGG CS
                             IF-2B 148 .rltakeLvqagipvtlitdsavayvmse.evdkvivGAdrile.nGaiankiGTsslAvlAkefnipvlvvaeslk 221
                                        +lta eL+  +ip+ +++d+ava++ms+ ++d+v+vGAdril+  G ++nkiGT+s Av A++fnip++v+a++++
  gi|557694211|ref|YP_008797265.1| 200 aKLTAFELKTLKIPFYVVPDTAVAFLMSRgMIDCVVVGADRILAkTGHVINKIGTLSAAVNAHHFNIPFYVAAPTST 276
                                       ******************************************872577***************************** PP

                                       BESTSSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 222 fservqldedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       ++   ++ ++++ieer ++e+ ++  eri++  ++ +n+afD+tPp+l+t++ITe+Gv++p
  gi|557694211|ref|YP_008797265.1| 277 IDLH-KTVDEVVIEERSEDEVHYVGRERITPPGTRAINYAFDITPPQLVTAVITEKGVFKP 336
                                       ***9.55555888**********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2461.70
//
Query:       gi|557694212|ref|YP_008797266.1|  [L=380]
Description: FAD-dependent pyridine nucleotide-disulphide oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-18   66.1   0.0    2.1e-09   37.0   0.0    2.1  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.8e-07   29.7   0.1     0.0016   18.1   0.0    2.4  2  DAO             FAD dependent oxidoreductase
    4.1e-06   27.3   0.2     0.0092   16.5   0.0    3.2  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    8.5e-05   22.7   0.0    0.00028   21.0   0.0    1.9  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0014   18.7   0.6       0.35   10.8   0.0    2.4  2  NAD_binding_9   FAD-NAD(P)-binding
     0.0023   17.1   0.0      0.015   14.4   0.0    2.1  2  FAD_binding_2   FAD binding domain
     0.0074   15.6   0.0        7.1    5.8   0.0    3.0  3  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
       0.24   10.2   0.0       0.34    9.7   0.0    1.2  1  Trp_halogenase  Tryptophan halogenase


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 !   37.0   0.0   9.4e-13   2.1e-09       2     137 ..       3     133 ..       2     147 .. 0.80
   2 !   27.2   0.0   9.3e-10   2.1e-06     184     279 ..     196     289 ..     169     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 9.4e-13
                                       SEEEE--SHHHHHHHHHHHH...HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.......HHHHCHHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq...agakvtlvelegtclnggcllskallgvaedaeias.......evvkklnqgie 68 
                                       +v+v+G+G++Glaaa +l++    ++ vt+v +++ ++  g +    ++g ++ +++++       ++      g++
  gi|557694212|ref|YP_008797266.1|   3 EVLVLGAGFGGLAAAVELRRllpPEHSVTVV-DRRDMFSMGFMNLWLMVGEKSMPRECLfpvrgveKH------GVR 72 
                                       699*****************8777*******.777777777888789999999999999877765444......799 PP

                                       CCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  69 lllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealk 137
                                       ++++ ev++i p +++v+ +         +  d +v+A G++     +pG  e+++ +   l+ a a +
  gi|557694212|ref|YP_008797266.1|  73 FVNE-EVLEINPVSRRVVTSG------GVYNPDVVVVALGAEYAFDAVPGFREHAHNF-YDLMGAYAAQ 133
                                       9999.*********9999943......36999********9766557****9999877.5555555444 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 9.3e-10
                                       HHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                       Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelle.eklglelderggiv 259
                                        +++++e+ l+++G+ ++ +++vk+i ++      v edge  + dl++   Gv p ++ ++ +++ l +de+g+i 
  gi|557694212|ref|YP_008797266.1| 196 PVGKRVEQFLTERGIGFHPRKQVKQIVDRR----IVFEDGEA-PFDLLL---GVPPHRAPKPvRDSPL-VDETGWIP 263
                                       68999**********************776....69999995.999997...8888887777555555.89****** PP

                                       --TTS.BESSTTEEE-GGGC.....T CS
                                       xxxxx.xxxxxxxxxxxxxx.....x RF
                       Pyr_redox_2 260 vdefl.rtnvpgiyaiGDva.....g 279
                                       v+++  +t   ++yaiGD++     +
  gi|557694212|ref|YP_008797266.1| 264 VNPQTtETRFRNVYAIGDITsvklpN 289
                                       ***997899**********9554443 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   7.2e-07    0.0016       2      33 ..       4      40 ..       3      42 .. 0.85
   2 !    9.1   0.0   0.00039      0.87     154     203 ..      64     107 ..      59     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.2e-07
                                      EEEECTSHHHHHHHHHHHHT..T....EEEEESSSSTT CS
                               DAO  2 vviiGGGiiGlstAyeLarr..g....Vtllekgdiag 33
                                      v++ G+G  Gl++A eL rr  +    Vt+++++d ++
  gi|557694212|ref|YP_008797266.1|  4 VLVLGAGFGGLAAAVEL-RRllPpehsVTVVDRRDMFS 40
                                      99***************.665735789*******8876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00039
                                       HHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGG CS
                               DAO 154 raaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGaw 203
                                       r +e++Gv+++++ ev +++       +v  +t+ g     d vV+a Ga 
  gi|557694212|ref|YP_008797266.1|  64 RGVEKHGVRFVNE-EVLEINPV---SRRV--VTSgGVYNP-DVVVVALGAE 107
                                       56899*******9.*****443...3455..677565467.99******97 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.1e-06    0.0092       2      35 ..       4      40 ..       3      45 .. 0.90
   2 ?   -1.5   0.1       1.7   3.8e+03      50      67 ..      66      82 ..      63      91 .. 0.67
   3 ?   -3.8   0.0         8   1.8e+04      37      57 ..     126     146 ..     120     148 .. 0.75
   4 !    7.0   0.0    0.0038       8.5      26      67 ..     182     222 ..     161     231 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.1e-06
                                      EEEECSSHHHHHHHHHHHHTT...SEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg...kkVtvversdkll 35
                                      v+v+G+G+ gl +A +l++l    ++Vtvv+r+d++ 
  gi|557694212|ref|YP_008797266.1|  4 VLVLGAGFGGLAAAVELRRLLppeHSVTVVDRRDMFS 40
                                      89*****************977889*********986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                                      HHHTTEEEECSEEEEEEE CS
                         Pyr_redox 50 lekngievllntkveeie 67
                                      +ek+g++++ + +v ei+
  gi|557694212|ref|YP_008797266.1| 66 VEKHGVRFVNE-EVLEIN 82
                                      68999999855.455555 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 8
                                       TSSHHHHHHHHHHHHHTTEEE CS
                         Pyr_redox  37 llDeeaskilqeklekngiev 57 
                                       l+++ a++++ + +++ +i +
  gi|557694212|ref|YP_008797266.1| 126 LMGAYAAQNMLKDFTHGHIAI 146
                                       567888999999888877766 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0038
                                       EEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEE CS
                         Pyr_redox  26 tvversdkllrllDeeaskilqeklekngievllntkveeie 67 
                                        v   +++++++ ++ ++k++++ l+++gi ++  ++v++i+
  gi|557694212|ref|YP_008797266.1| 182 DVYTPEPQPMPAAGP-VGKRVEQFLTERGIGFHPRKQVKQIV 222
                                       555556666655555.699*********************98 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 !   21.0   0.0   1.3e-07   0.00028       1      30 [.       6      38 ..       6      43 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.3e-07
                                      EE--SHHHHHHHHHHHCC...TEEEEEE-SSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka...gfdvlllekrdr 30
                                      ++GaG++Gl+aA +L++     ++v+++++rd 
  gi|557694212|ref|YP_008797266.1|  6 VLGAGFGGLAAAVELRRLlppEHSVTVVDRRDM 38
                                      89***************76789********985 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 !   10.8   0.0   0.00016      0.35       2      37 ..       6      39 ..       5      45 .. 0.88
   2 !    5.7   0.1    0.0059        13     114     155 ..      68     106 ..      63     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                                      + GaG+ Gla++ +L +    + ++++t++d++ + 
  gi|557694212|ref|YP_008797266.1|  6 VLGAGFGGLAAAVELRRLL--PPEHSVTVVDRRDMF 39
                                      67****************8..9*********98775 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0059
                     NAD_binding_9 114 gvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       +  v+++++ev+++++  +++    ++g  +  d Vv+AlG 
  gi|557694212|ref|YP_008797266.1|  68 KHGVRFVNEEVLEINPVSRRV---VTSGGVYNPDVVVVALGA 106
                                       5579************98874...689*************95 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   6.5e-06     0.015       2      41 ..       4      40 ..       3      58 .. 0.79
   2 ?   -0.1   0.0      0.17   3.9e+02     278     342 ..      66     125 ..      63     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.5e-06
                                      EEEE--SHHHHHHHHHHHH...TTT-EEEEESSSGGGSGGGG- CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaae...aGlkvavvekeqefggataws 41
                                      v+V G+G++GLaAA+e+++     ++v+vv+  +       +s
  gi|557694212|ref|YP_008797266.1|  4 VLVLGAGFGGLAAAVELRRllpPEHSVTVVDRRDM------FS 40
                                      9****************997755669999988775......45 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.17
                                       E-TTSSBTH.GGGS-HHHHHHHHH.HHHHTTTSCCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT CS
                     FAD_binding_2 278 vdkdGrrFm.nelasrdvvsrailekeiaeggseanvyldashgldaegleatleaineeaangld 342
                                       v k G rF+ +e+ + + vsr+++      gg   n+++++ + l+ae     +++++e+a+n++d
  gi|557694212|ref|YP_008797266.1|  66 VEKHGVRFVnEEVLEINPVSRRVV----TSGGV-YNPDVVVVA-LGAEYAFDAVPGFREHAHNFYD 125
                                       678899999666778888888888....23333.677777777.7899999999999999999999 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 ?    3.3   0.0     0.018        39       1      19 [.       5      23 ..       2      43 .. 0.68
   2 ?    2.8   0.0     0.025        57     101     147 ..      75     117 ..      68     136 .. 0.71
   3 !    5.8   0.0    0.0032       7.1     281     305 .]     256     280 ..     197     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.018
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkka 19
                                      ++ GaG  Glaaa+el+++
  gi|557694212|ref|YP_008797266.1|  5 LVLGAGFGGLAAAVELRRL 23
                                      4778899999999888876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.025
                       Pyr_redox_3 101 feeVesvkkedegfevetsketyeAkkviiAtGe.fdkPnklnipGee 147
                                       +eeV ++++ +   +v ts ++y+ + v++A G  + +     +pG  
  gi|557694212|ref|YP_008797266.1|  75 NEEVLEINPVS--RRVVTSGGVYNPDVVVVALGAeYAFDA---VPGFR 117
                                       67788887765..5799****************5144444...45554 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0032
                       Pyr_redox_3 281 ldedgrpvlteeteetnvpglflaG 305
                                        de+g++ ++++t et + +++ +G
  gi|557694212|ref|YP_008797266.1| 256 VDETGWIPVNPQTTETRFRNVYAIG 280
                                       479*******************999 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   0.00015      0.34       2      40 ..       4      42 ..       3      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00015
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---S CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigtvg 40
                                      ++++G+G  G  aA  l++ l  +++vt+v+  +++ +g
  gi|557694212|ref|YP_008797266.1|  4 VLVLGAGFGGLAAAVELRRLLPPEHSVTVVDRRDMFSMG 42
                                      89*******************999*******99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2850.43
//
Query:       gi|557694213|ref|YP_008797267.1|  [L=909]
Description: aconitate hydratase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-178  593.8   0.0   3.4e-178  593.4   0.0    1.1  1  Aconitase    Aconitase family (aconitate hydratase)
    8.8e-43  145.8   0.0    1.4e-42  145.1   0.0    1.3  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 !  593.4   0.0  3.8e-182  3.4e-178      12     461 .]      73     577 ..      58     577 .. 0.92

  Alignments for each domain:
  == domain 1  score: 593.4 bits;  conditional E-value: 3.8e-182
                         Aconitase  12 egiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsv.....gaeealeknledefern 83 
                                       +++++ p+rvllqd+tgv+alvdlaa+r+av+r+g++++++++ +pvdlvidhs+     g+ ea++ nl+ ef+rn
  gi|557694213|ref|YP_008797267.1|  73 REVPFFPSRVLLQDFTGVPALVDLAAMRSAVKRVGQDPSKVNPSIPVDLVIDHSIqvdffGTPEAFSLNLDYEFRRN 149
                                       3499************************************************************************* PP

                         Aconitase  84 keryefLksaakaf.girvvppgqGIvHqvnlEy............g.lalpgktvvgtDSHTtmigglGvlaiGvG 146
                                       +ery fLk+a++af ++rv+ppg+GIvHqvnlEy            g +a+p+ tv+gtDSHT+m++glGv+++GvG
  gi|557694213|ref|YP_008797267.1| 150 TERYVFLKWAQNAFrNFRVIPPGRGIVHQVNLEYlakvvdvrsfggGlTAFPD-TVLGTDSHTPMVNGLGVVGWGVG 225
                                       ******************************************99864688999.*********************** PP

                         Aconitase 147 gieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNM 223
                                       gieaeav+lgqp+++++p+vvgv+l G+l+eg+ta+Dlvl+++++lrk+gvvgk+vEffG+ +++Ls+ draTiaNM
  gi|557694213|ref|YP_008797267.1| 226 GIEAEAVMLGQPYYMTTPEVVGVRLVGELREGTTATDLVLTITEMLRKHGVVGKFVEFFGPSLSKLSVPDRATIANM 302
                                       ***************************************************************************** PP

                         Aconitase 224 aaEvGAttglfpvdektleYLkatgreeaav.lveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqd 299
                                       a+E+GAt+g+fp+d++t++YL++tgr+e+++  ve+y+k q+lf  +  e ++y++vleldlst+eps++gp +P+d
  gi|557694213|ref|YP_008797267.1| 303 APEYGATIGYFPIDRETINYLRMTGRPEEHIrVVEEYAKIQGLF-YNPLETPVYNTVLELDLSTVEPSISGPANPED 378
                                       *******************************999**********.6678899************************* PP

                         Aconitase 300 avplselvkkefkeele..........................keaaekaley.klkegtklkdgkvdiaaigSCTN 349
                                       ++pl+e +++ ++e +                           + a  ++++  + +    l++g+v+i ai+SCTN
  gi|557694213|ref|YP_008797267.1| 379 RIPLREAKRR-TRE-IMlaylkqagiavddvnerewsyeggaaR-ASVATVQKkTGSVVDGLSHGSVVISAITSCTN 452
                                       ****777763.232.2246778999************9976431.222222221223356789************** PP

                         Aconitase 350 ssnedvraaaglla.kavekglkvkpgvktsvaPGSevvkayleaeGlleiLekaGfevvgagCstCignsdrle.. 423
                                       +sn++v++ aglla kavekgl++ ++vkts+aPGS +v++yle++Gl ++Lek+G+ +vg+gC+tCigns++l+  
  gi|557694213|ref|YP_008797267.1| 453 TSNPSVMIGAGLLAkKAVEKGLRTPSYVKTSLAPGSMAVTEYLEKAGLAPYLEKLGYSLVGYGCTTCIGNSGPLPeh 529
                                       **************************************************************************977 PP

                         Aconitase 424 ......ege...aivsssNRNFegRqgpntra.yLaSPelvvaaAlaG 461
                                             e++   ++v+s+NRNFegR++p++ra yL+SP lvva+ laG
  gi|557694213|ref|YP_008797267.1| 530 ivqqikERNlytVAVLSGNRNFEGRINPHVRAsYLMSPMLVVAYGLAG 577
                                       777664333999**********************************98 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.1   0.0   1.6e-46   1.4e-42       3     130 ..     707     834 ..     705     835 .. 0.98

  Alignments for each domain:
  == domain 1  score: 145.1 bits;  conditional E-value: 1.6e-46
                                       CCCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE CS
                       Aconitase_C   3 kllklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvvi 79 
                                       k+l ++G+++ d++ +++++++++++++gt+ani+l+n lve+k+   t + ++ge + v+daa+ry+++g +l+v+
  gi|557694213|ref|YP_008797267.1| 707 KYLIEQGVDPVDFNTYGARRGNHEVMIRGTFANIRLKNLLVEGKEGWWTVYHPTGEVTTVYDAAMRYREAGVPLIVL 783
                                       7999************************************************************************* PP

                                       --SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEEST CS
                       Aconitase_C  80 agknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefke 130
                                       agk +G+GSSR++AAk++rllG++aviaeS+erI+++nl+++g+Lpl+f e
  gi|557694213|ref|YP_008797267.1| 784 AGKMYGAGSSRDWAAKGTRLLGVRAVIAESYERIHRSNLVGMGVLPLQFME 834
                                       ************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (909 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 6312.44
//
Query:       gi|557694214|ref|YP_008797268.1|  [L=747]
Description: hypothetical protein CSUB_C0780 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   25.4   5.1    9.3e-06   24.7   5.1    1.3  1  Spc7             Spc7 kinetochore protein
    0.00017   21.6  12.6    0.00031   20.8  12.6    1.3  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    0.00036   20.7   0.0      0.001   19.3   0.0    1.8  1  Reprolysin_5     Metallo-peptidase family M12
    0.00051   20.6   0.1     0.0031   18.0   0.0    2.1  2  Reprolysin_3     Metallo-peptidase family M12B Reprolysin-lik
    0.00066   19.7   2.7     0.0015   18.6   1.3    2.2  1  DUF2730          Protein of unknown function (DUF2730)
    0.00069   19.7  17.6      0.023   14.7   8.1    2.5  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
    0.00072   18.3   1.8    0.00096   17.9   1.8    1.1  1  AAA_13           AAA domain
     0.0014   18.9   3.5     0.0014   18.9   3.5    3.0  3  CCDC-167         Coiled-coil domain-containing protein 167
     0.0014   18.2   0.9     0.0022   17.6   0.9    1.3  1  Exonuc_VII_L     Exonuclease VII, large subunit
     0.0016   18.1   0.6      0.023   14.3   0.2    2.3  2  Reprolysin_4     Metallo-peptidase family M12B Reprolysin-lik
     0.0019   16.5   4.1     0.0026   16.1   4.1    1.1  1  FPP              Filament-like plant protein, long coiled-coi
     0.0025   17.5   7.7     0.0047   16.6   7.7    1.4  1  Filament         Intermediate filament protein
     0.0026   17.2   4.9     0.0042   16.5   4.9    1.3  1  DUF4407          Domain of unknown function (DUF4407)
     0.0038   17.4  15.7     0.0067   16.6  15.7    1.3  1  Tropomyosin_1    Tropomyosin like
     0.0042   17.4   3.9      0.011   16.0   3.9    1.7  1  OmpH             Outer membrane protein (OmpH-like)
     0.0043   16.2   4.4     0.0064   15.7   4.4    1.1  1  CCDC144C         CCDC144C protein coiled-coil region
     0.0045   15.4   5.8     0.0068   14.8   5.8    1.1  1  MAD              Mitotic checkpoint protein
     0.0057   14.9   2.9      0.012   13.8   2.9    1.5  1  EzrA             Septation ring formation regulator, EzrA
     0.0084   14.3   4.7      0.012   13.8   4.7    1.1  1  HOOK             HOOK protein
  ------ inclusion threshold ------
       0.01   14.8   9.1      0.018   14.0   9.1    1.3  1  DUF812           Protein of unknown function (DUF812)
      0.021   14.1   0.2      0.045   13.0   0.2    1.5  1  DUF4953          Met-zincin
      0.025   14.6   3.7       0.16   12.0   3.7    2.2  1  DUF1664          Protein of unknown function (DUF1664)
      0.039   13.5   4.6      0.063   12.8   4.6    1.2  1  Leu_zip          Leucine zipper
       0.04   14.1  16.9        0.1   12.8  17.0    1.5  1  ATG16            Autophagy protein 16 (ATG16)
      0.047   14.1   4.4       0.86   10.1   0.3    3.2  2  FlaC_arch        Flagella accessory protein C (FlaC)
      0.051   12.4  10.8      0.077   11.9  10.8    1.1  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
      0.065   12.2   3.6       0.12   11.3   3.6    1.4  1  IFT57            Intra-flagellar transport protein 57
      0.068   12.2   4.3       0.14   11.2   4.3    1.4  1  Atg14            Vacuolar sorting 38 and autophagy-related su
      0.077   12.9   1.4       0.17   11.7   0.3    1.9  2  Reprolysin_2     Metallo-peptidase family M12B Reprolysin-lik
       0.08   13.0   5.0       0.21   11.6   5.0    1.6  1  Laminin_II       Laminin Domain II
      0.088   13.3   4.8       0.15   12.5   4.8    1.3  1  T3SSipB          Type III cell invasion protein SipB
      0.089   13.0  13.0       0.51   10.6   8.2    2.4  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
      0.089   13.2   7.2       0.16   12.4   7.2    1.3  1  Fez1             Fez1
      0.092   13.1   5.6       0.27   11.6   5.6    1.9  1  V-SNARE          Vesicle transport v-SNARE protein N-terminus
      0.093   10.2  11.0       0.13    9.7  11.0    1.1  1  DUF3584          Protein of unknown function (DUF3584)
        0.1   12.8   8.0        0.2   11.9   8.0    1.4  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
        0.1   10.5   1.1        0.2    9.5   1.1    1.3  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.11   11.7   0.3        0.2   10.9   0.3    1.4  1  TMPIT            TMPIT-like protein
       0.11   11.0   0.8        0.2   10.3   0.8    1.3  1  FapA             Flagellar Assembly Protein A
       0.13   11.9   3.9       0.27   10.8   3.9    1.5  1  PEARLI-4         Arabidopsis phospholipase-like protein (PEAR
       0.14   12.5   5.0       0.65   10.3   5.0    2.1  1  BLOC1_2          Biogenesis of lysosome-related organelles co
       0.15   11.4  15.4      0.037   13.4  11.2    1.9  2  GAS              Growth-arrest specific micro-tubule binding
       0.15   12.4  17.9      0.094   13.1  14.0    1.9  2  HrpB7            Bacterial type III secretion protein (HrpB7)
       0.23   11.5  19.1        1.7    8.7  16.9    2.4  2  DHR10            Designed helical repeat protein 10 domain
       0.24   11.5   8.0          3    8.0   1.0    2.9  2  bZIP_1           bZIP transcription factor
       0.32   10.4   9.1       0.52    9.7   9.1    1.2  1  HMMR_N           Hyaluronan mediated motility receptor N-term
       0.33   10.8  13.8        1.2    9.0   9.7    2.5  3  DASH_Spc19       Spc19
       0.41   10.9   5.5       0.82    9.9   5.5    1.4  1  zf-C4H2          Zinc finger-containing protein
       0.43   10.8  10.0        4.4    7.6   4.0    2.4  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.43    9.9   3.3       0.65    9.3   3.3    1.1  1  FAM76            FAM76 protein
       0.43   10.0   8.7       0.85    9.0   8.7    1.4  1  Golgin_A5        Golgin subfamily A member 5
       0.43   11.0   4.9         24    5.4   0.0    3.4  3  LPP              Lipoprotein leucine-zipper
       0.46   10.3   5.0       0.87    9.4   5.0    1.4  1  DUF724           Protein of unknown function (DUF724)
       0.47   10.0   3.2        1.1    8.8   3.2    1.6  1  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
       0.48    8.9   4.8       0.74    8.3   4.8    1.2  1  FUSC             Fusaric acid resistance protein family
       0.49    9.9   5.2       0.82    9.2   1.9    2.3  2  Fzo_mitofusin    fzo-like conserved region
       0.57   10.3   8.8       0.18   11.9   5.1    2.0  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
       0.57    9.8   5.3        1.4    8.5   5.3    1.6  1  YkyA             Putative cell-wall binding lipoprotein
       0.64   10.3  14.3         13    6.1  13.5    2.8  1  ABC_tran_CTD     ABC transporter C-terminal domain
       0.72    8.5  11.4        1.1    7.9  11.4    1.2  1  HAUS5            HAUS augmin-like complex subunit 5
       0.74   10.2  12.3       0.75   10.2   1.4    3.4  3  CLZ              C-terminal leucine zipper domain of cyclic n
       0.91   10.0  16.6        1.3    9.5   3.9    2.4  2  DUF4140          N-terminal domain of unknown function (DUF41
       0.97    9.4  11.1        5.9    6.9   0.1    3.5  3  Prefoldin_2      Prefoldin subunit
        1.1    9.4   9.8       0.34   11.0   1.2    2.8  2  TolA_bind_tri    TolA binding protein trimerisation
        1.1    9.3   8.9        4.2    7.5   8.9    2.0  1  BRE1             BRE1 E3 ubiquitin ligase
        1.2   10.1   9.6        3.2    8.7   9.6    1.7  1  PRKG1_interact   cGMP-dependent protein kinase interacting do
        1.2    8.6   6.9        1.5    8.3   4.4    2.0  2  Vps5             Vps5 C terminal like
        1.8    8.8   4.4        1.3    9.3   0.9    2.6  1  XhlA             Haemolysin XhlA
        1.9    8.3   5.2        2.9    7.7   3.1    1.9  1  Phage_GP20       Phage minor structural protein GP20
        2.1    7.6  11.2        5.7    6.2   3.6    2.0  2  DUF3450          Protein of unknown function (DUF3450)
        2.3    8.9   7.3         22    5.8   7.3    2.4  1  DUF2203          Uncharacterized conserved protein (DUF2203)
        2.5    8.6   6.9       0.34   11.4   1.2    2.4  1  NPV_P10          Nucleopolyhedrovirus P10 protein
        3.2    8.2   5.6        1.1    9.7   3.0    1.7  1  AAA_23           AAA domain
        3.7    8.0   8.6        2.6    8.5   1.5    2.8  2  Snapin_Pallidin  Snapin/Pallidin
        4.5    7.5  15.8        2.6    8.3   2.9    2.7  2  FliJ             Flagellar FliJ protein
        4.6    7.6  13.3         13    6.2  13.2    1.8  1  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
        4.9    7.3   7.8         55    3.8   7.5    2.5  1  COG2             COG (conserved oligomeric Golgi) complex com
        6.4    6.9  10.0         12    6.0  10.0    1.4  1  DivIVA           DivIVA protein
        6.7    6.9   6.6        1.8    8.8   2.9    1.8  1  Fib_alpha        Fibrinogen alpha/beta chain family
        6.8    6.0  11.2        8.2    5.8   2.6    2.7  3  DUF4618          Domain of unknown function (DUF4618)
        7.4    6.7  13.7         10    6.2   6.4    2.4  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding


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 !   24.7   5.1   4.2e-08   9.3e-06     166     283 ..     595     707 ..     589     720 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.2e-08
                              Spc7 166 dellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeq 242
                                       + +lp l+ e ++l  e+ +l   +e+l    + e+e++++el+e+ a +ee+k+ela  +e++ +le+++++++++
  gi|557694214|ref|YP_008797268.1| 595 NYVLPGLVDEVKRLGGEVSRLTGIREQL----RSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETR 667
                                       5567778888888888888888766654....458888888888888888888888888888888888888888888 PP

                              Spc7 243 kseleeeiaeaervleeckgwsesevsrlkeevkaleeltg 283
                                        ++++++ +e  ++le++ +  + +v++l +++ +l e+ +
  gi|557694214|ref|YP_008797268.1| 668 VANARAAREEV-KTLENRLQQLSADVDALDKRLVSLREQNN 707
                                       88887776644.45555556666788888888888887765 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 !   20.8  12.6   1.4e-06   0.00031      18     108 ..     611     704 ..     601     707 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.4e-06
                    CENP-F_leu_zip  18 kadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr...sekeeLekelqk 91 
                                       + + L +  e+L +e+e +++++e++    E+ k e+ + +ee+++l+++ ++ e+ +++ r   +e ++Le+ lq+
  gi|557694214|ref|YP_008797268.1| 611 EVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARaarEEVKTLENRLQQ 687
                                       55666666799***********************************************9988555788899****** PP

                    CENP-F_leu_zip  92 kqervseLeslnsslen 108
                                           v+ L+++ +sl++
  gi|557694214|ref|YP_008797268.1| 688 LSADVDALDKRLVSLRE 704
                                       ************99986 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.6e-06     0.001     133     189 ..     419     475 ..     321     486 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.6e-06
                      Reprolysin_5 133 nsvvvstatevqvvaHElGHnfGavHDcdsss...esqsCslsnstepaggryiMapsss 189
                                       ++ ++        v+HE+GH fG +H +d+     +s s+++         ++iM++s s
  gi|557694214|ref|YP_008797268.1| 419 YYEHMIEEGMTVLVTHEAGHIFGLRHPHDDYDeyrQSESSFF---PLTYFTETIMSYSKS 475
                                       44455566777889************8776655544444444...245557788888765 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 !   18.0   0.0   1.4e-05    0.0031      75     123 ..     390     444 ..     342     445 .. 0.72
   2 ?   -0.6   0.0       8.3   1.8e+03      37      86 ..     678     728 ..     658     734 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-05
                      Reprolysin_3  75 e....sgvgGlAyv...gsvcnsskkagvnsgssvlgkvgadtvaHEiGHnfganH 123
                                       +     gv+G A         +   +a+v++++ ++ +++   v+HE GH fg++H
  gi|557694214|ref|YP_008797268.1| 390 SfieePGVLGRASPdprDPTQPHHASAAVYYEH-MIEEGMTVLVTHEAGHIFGLRH 444
                                       346666677777765532223333335666666.6888999*************** PP

  == domain 2  score: -0.6 bits;  conditional E-value: 8.3
                      Reprolysin_3  37 pytkkdatealdelaevtae...aergqagyDlvhlftardesgvgGlAyvgs 86 
                                        +t +++ + l++ ++  ++   + r+q++  +++++ +     v+G A +g 
  gi|557694214|ref|YP_008797268.1| 678 VKTLENRLQQLSADVDALDKrlvSLREQNNLFIGVAVVGA--VAVAGAAVIGR 728
                                       4555566777777777777777767788999998888885..36888888765 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.3   6.8e-06    0.0015      32      97 ..     644     710 ..     642     714 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.8e-06
                           DUF2730  32 redleklaekveendkrlteletkvenLP.takdlekLkllladlrgelkaleaevrqlshqvdLLL 97 
                                       + +l+  +e+v++ + r++++et+v+n    ++++++L+  l++l ++++al++++ +l+ q +L +
  gi|557694214|ref|YP_008797268.1| 644 KRELAGAEEEVRQLEARVSDAETRVANARaAREEVKTLENRLQQLSADVDALDKRLVSLREQNNLFI 710
                                       78999999*****************998616789****************************99986 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 !   14.7   8.1   0.00011     0.023      58     116 ..     604     665 ..     601     667 .. 0.88
   2 !   13.5   7.2   0.00025     0.055      58     121 ..     646     708 ..     645     711 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00011
                        TPR_MLP1_2  58 elqalreelnelkaeiaelkaeaesakaeleeseesweeqkeel...ekelselekriedln 116
                                       e+++l  e+++l+  +++l++e+e+a+ elee+++++ee+k el   e+e+++le+r+ d +
  gi|557694214|ref|YP_008797268.1| 604 EVKRLGGEVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELagaEEEVRQLEARVSDAE 665
                                       5666777899999999***************************977789*********9976 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00025
                        TPR_MLP1_2  58 elqalreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneqNkl 121
                                       el+ + ee+ +l+a+++++++++ +a+a+ ee  + +e++ ++l  +++ l kr+  l eqN+l
  gi|557694214|ref|YP_008797268.1| 646 ELAGAEEEVRQLEARVSDAETRVANARAAREEV-KTLENRLQQLSADVDALDKRLVSLREQNNL 708
                                       6788999********************998776.589*************************98 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.8   4.3e-06   0.00096     367     470 ..     601     702 ..     470     712 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.3e-06
                            AAA_13 367 ikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykklekaieklekelkeeeae...lk 440
                                       + ++v+++   +++   + ++l +e+e+a+ +le     e++++l+e k++++++e+++ +le++++++e++   ++
  gi|557694214|ref|YP_008797268.1| 601 LVDEVKRLGGEVSRLTGIREQLRSEVEKAQRELE-----EARAALEERKRELAGAEEEVRQLEARVSDAETRvanAR 672
                                       4444555555555555555555555666655555.....55555666666666666666666666666555411145 PP

                            AAA_13 441 kleeeikeLekqlrdekpaaeeinkeLkaf 470
                                       +++ee+k Le++l++    ++ + k L + 
  gi|557694214|ref|YP_008797268.1| 673 AAREEVKTLENRLQQLSADVDALDKRLVSL 702
                                       67899********************99876 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 ?    0.6   0.0       3.2     7e+02      14      47 ..     514     547 ..     511     565 .. 0.84
   2 ?    0.1   1.0       4.7     1e+03      13      37 ..     619     643 ..     604     648 .. 0.52
   3 !   18.9   3.5   6.3e-06    0.0014       5      66 ..     646     707 ..     644     721 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 3.2
                          CCDC-167  14 ascrerLeaverrlrkeelseeeResleeEeasl 47 
                                       ++++++++++ + lr++++ +++  +l+e ++s 
  gi|557694214|ref|YP_008797268.1| 514 QNYEQNMQTILSTLRQNNINPNDIPELNEVLNSA 547
                                       6899999999999999999999988888776665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 4.7
                          CCDC-167  13 lascrerLeaverrlrkeelseeeR 37 
                                        +++r ++e+  r+l++++   eeR
  gi|557694214|ref|YP_008797268.1| 619 REQLRSEVEKAQRELEEARAALEER 643
                                       4444444444444444444333333 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 6.3e-06
                          CCDC-167   5 eIdkleeklascrerLeaverrlrkeelseeeResleeEeaslkeqleenekeLksLrkeNr 66 
                                       e+ + ee++ +++ r+ + e+r+ +++   ee + le+ +++l+ +++  +k+L sLr++N 
  gi|557694214|ref|YP_008797268.1| 646 ELAGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVDALDKRLVSLREQNN 707
                                       77899******************************************************995 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 !   17.6   0.9   9.9e-06    0.0022     180     268 ..     621     711 ..     509     723 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 9.9e-06
                      Exonuc_VII_L 180 speellerkrqrldeleerleralkkqlkkkrerleelkerl.k.....ekleekkerlkklkerlelleekkerle 250
                                       + ++ +e+++++l+e+++ le+  k++l+ ++e++++l++r+       ++ ++++e++k+l++   +l++ + +++
  gi|557694214|ref|YP_008797268.1| 621 QLRSEVEKAQRELEEARAALEE-RKRELAGAEEEVRQLEARVsDaetrvANARAAREEVKTLEN---RLQQLSADVD 693
                                       2222333333333333333333.33333333333333333331122111111122222222222...2334445555 PP

                      Exonuc_VII_L 251 eleeklealsplkvLkrG 268
                                       +l ++l +l  ++ L  G
  gi|557694214|ref|YP_008797268.1| 694 ALDKRLVSLREQNNLFIG 711
                                       555555555555555555 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 !   14.3   0.2   0.00011     0.023     132     177 ..     422     474 ..     402     482 .. 0.68
   2 ?    1.3   0.0         1   2.3e+02      59     117 ..     662     719 ..     654     731 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00011
                      Reprolysin_4 132 s..rdeydi.fAHEiGHtfGaaHdlsdegegl.sskt...eegsgqtIMsyas 177
                                           ++  + + HE GH fG+ H  +d  e   s++     +   +tIMsy +
  gi|557694214|ref|YP_008797268.1| 422 HmiEEGMTVlVTHEAGHIFGLRHPHDDYDEYRqSESSffpLTYFTETIMSYSK 474
                                       24455777889************999554422222224456667789999975 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1
                      Reprolysin_4  59 tdsetdsfaadisgedlgn..sslatltstrdskdyDlaallrdtrasqqnvgvawvgalc 117
                                       +d et  ++a    e++ +   +l +l +  d +d+ l+ l  +    +   gva vga+ 
  gi|557694214|ref|YP_008797268.1| 662 SDAETRVANARAAREEVKTleNRLQQLSADVDALDKRLVSLREQN---NLFIGVAVVGAVA 719
                                       788888888888888886522578888888888888888887666...6669*****9987 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 !   16.1   4.1   1.2e-05    0.0026     686     785 ..     592     703 ..     511     707 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                               FPP 686 k.........keenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetql 753
                                       +          +e k+l  e+ +l+  +e+l  e+++a+ +le++ a l+e  + la  ++e+ +l+   s aet +
  gi|557694214|ref|YP_008797268.1| 592 NtknyvlpglVDEVKRLGGEVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRV 668
                                       244456666678999999**********************************************************9 PP

                               FPP 754 kcmk...esyesletrateleaelnelkqkieaLe 785
                                        +     e  ++le r+++l a++  l +++ +L 
  gi|557694214|ref|YP_008797268.1| 669 ANARaarEEVKTLENRLQQLSADVDALDKRLVSLR 703
                                       98761115567899999999999999999887775 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   7.7   2.1e-05    0.0047     205     279 ..     620     693 ..     609     704 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-05
                                       XXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 205 eknsealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireema 279
                                       e+  +++++a++e++e+r  +++++ el+  +++ ++lea+++++e r+++++  ++e+++ le+ l+++ ++++
  gi|557694214|ref|YP_008797268.1| 620 EQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANAR-AAREEVKTLENRLQQLSADVD 693
                                       56678999****************************************99876.58999**********988876 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   4.9   1.9e-05    0.0042     131     232 ..     608     698 ..     575     713 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-05
                           DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld 207
                                       l  e+++l+  +++l++e+++a+++l+++ra++++             aG +++ ++ +a   +a++++a+++a   
  gi|557694214|ref|YP_008797268.1| 608 LGGEVSRLTGIREQLRSEVEKAQRELEEARAALEERKR--------ELAGAEEEVRQLEARVSDAETRVANARAA-- 674
                                       56788899999999999999999999999999984433........27888899999999999999999998888.. PP

                           DUF4407 208 atarlaalraelaeleaerakeraa 232
                                        ++++++l+++l++l a+ ++  ++
  gi|557694214|ref|YP_008797268.1| 675 -REEVKTLENRLQQLSADVDALDKR 698
                                       .444555555555555444444333 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  15.7     3e-05    0.0067       3      88 ..     620     705 ..     618     707 .. 0.97

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3e-05
                     Tropomyosin_1   3 nsLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekleeklkeakekaeesekkktnnealt 79 
                                       ++L+ e e+aq   ee+++++ e   e    e+e+++L+ +++ +e  v ++ ++ +e+k+  +  ++++++ +al 
  gi|557694214|ref|YP_008797268.1| 620 EQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVDALD 696
                                       589************************************************************************** PP

                     Tropomyosin_1  80 rkiqlLEee 88 
                                       +++  L e+
  gi|557694214|ref|YP_008797268.1| 697 KRLVSLREQ 705
                                       **9999886 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   3.9   5.1e-05     0.011      20      93 ..     618     691 ..     603     716 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHH CS
                              OmpH  20 aqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqka......qelqkkqqel 90 
                                       ++eql ++ +k q ele+ +++l++ ++el         ee+ ++l++++ + +++ ++++      + l+++ q+l
  gi|557694214|ref|YP_008797268.1| 618 IREQLRSEVEKAQRELEEARAALEERKRELAG------AEEEVRQLEARVSDAETRVANARaareevKTLENRLQQL 688
                                       55666666666666666666666666666642......333333333333333332222222322334455555555 PP

                                       HHH CS
                              OmpH  91 lkp 93 
                                        + 
  gi|557694214|ref|YP_008797268.1| 689 SAD 691
                                       443 PP

>> CCDC144C  CCDC144C protein coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   4.4   2.9e-05    0.0064     117     240 ..     576     702 ..     572     708 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.9e-05
                          CCDC144C 117 lelalqrerdewlrlqdklnfdvsnlkdknevLsqqLskaeskansLenelhetrdaLrektlllesvqrdlsqaqc 193
                                       ++ a+  +   wl   +  n+ +  l d+++ L  ++s+     ++L  e+++++ +L e   +le+ +r+l  a+ 
  gi|557694214|ref|YP_008797268.1| 576 VNTAFDAAFSAWLYTENTKNYVLPGLVDEVKRLGGEVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAEE 652
                                       66778888888999999999999999999999999999999999********************************* PP

                          CCDC144C 194 qikeleqmyqneeekvnkyiakqe...sleerlaqlqsenmlLrqqLeda 240
                                       ++++le+    +e +v +  a +e   +le+rl+ql  +   L + L   
  gi|557694214|ref|YP_008797268.1| 653 EVRQLEARVSDAETRVANARAAREevkTLENRLQQLSADVDALDKRLVSL 702
                                       *******99999988877766555233689******99988888887655 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   5.8   3.1e-05    0.0068     104     180 ..     617     693 ..     605     709 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                               MAD 104 evisalknelaelkrqiekqelelsekeseleelqerldllkkklseleqliqqlekkqkelaeaeqrikeLefeiq 180
                                        + ++l+ e+++ +r++e++  +l+e++ el   +e+   l++++s++e ++++  ++ +e ++ e+r+++L+  + 
  gi|557694214|ref|YP_008797268.1| 617 GIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVD 693
                                       56677888888888888888888888888888888888888888888888888888888888888888888877665 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   2.9   5.5e-05     0.012     116     218 ..     604     700 ..     590     707 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT--TTTTHHHHHHHHHHHHHHHH----------------HHH CS
                              EzrA 116 kikkileelkelteseeknreeieklkekYrelrkkllanrfsygealeelekqleniekefsefeeltengdyvea 192
                                       ++k++  e++ lt   e+ r+e+ek++ + +e r  l++++ ++  a+    +++ ++e + s+ e+   n    +a
  gi|557694214|ref|YP_008797268.1| 604 EVKRLGGEVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAE----EEVRQLEARVSDAETRVANA--RAA 674
                                       678888999********************************9998875....56788999999999988765..699 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHT CS
                              EzrA 193 keilkkleeeideleevieeiPelle 218
                                       +e +k+le+++++l+++++ + + l 
  gi|557694214|ref|YP_008797268.1| 675 REEVKTLENRLQQLSADVDALDKRLV 700
                                       **************999998876655 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   4.7   5.4e-05     0.012     453     560 ..     600     706 ..     575     709 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.4e-05
                              HOOK 453 evreklirLqhENKmLklkqegseeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgska 529
                                        + +++ rL  E  +L +  +++ + ++++ q++le+a+  ++e + e   a++ + +Lea+v + +++ ++  +  
  gi|557694214|ref|YP_008797268.1| 600 GLVDEVKRLGGEVSRL-TGIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAR 675
                                       4567788999999999.777777799999*********************************************999 PP

                              HOOK 530 edssllkkkleehleklkevqeelqkkkeql 560
                                       e+  +l+++l+++   +  +++ l + +eq 
  gi|557694214|ref|YP_008797268.1| 676 EEVKTLENRLQQLSADVDALDKRLVSLREQN 706
                                       99999*********99999999999988886 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   9.1     8e-05     0.018     333     418 ..     620     705 ..     612     707 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8e-05
                            DUF812 333 eelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalveasa 409
                                       e+l++++e++++++ee ++ +++ + ++  +eee++++++  +  e  v++++ + e +++ e+ +++L a+v+a  
  gi|557694214|ref|YP_008797268.1| 620 EQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVDALD 696
                                       589************************************************************************** PP

                            DUF812 410 qrlvelakq 418
                                       +rlv+l +q
  gi|557694214|ref|YP_008797268.1| 697 KRLVSLREQ 705
                                       ******987 PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2    0.0002     0.045       6      29 ..     421     444 ..     417     452 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0002
                           DUF4953   6 delmgallrfvvaHEvGhtLGLrh 29 
                                       + ++++ ++ +v+HE Gh++GLrh
  gi|557694214|ref|YP_008797268.1| 421 EHMIEEGMTVLVTHEAGHIFGLRH 444
                                       67999******************* PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   3.7   0.00073      0.16      36     120 ..     619     702 ..     601     707 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00073
                           DUF1664  36 krslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveg 112
                                       +  l++ ve+  ++le+  ++l++ kr+L+   ++v  +l++    ++   ++  ++re+++++++ ++++++ v  
  gi|557694214|ref|YP_008797268.1| 619 REQLRSEVEKAQRELEEARAALEERKRELAGAEEEVR-QLEARVSDAETRVANARAAREEVKTLENRLQQLSADVDA 694
                                       5667777888888888888888888888876555443.333333333333334455555555555555555555555 PP

                           DUF1664 113 leskleri 120
                                       l+++l ++
  gi|557694214|ref|YP_008797268.1| 695 LDKRLVSL 702
                                       55555554 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   4.6   0.00028     0.063     131     235 ..     601     705 ..     594     709 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00028
                           Leu_zip 131 LkkeierLkeenekLkerlkelEkqatsaleeksklekalkelqkelg.ekkdekenskeiskleeklaelkldlek 206
                                       L  e++rL  e ++L    ++l +++++a +e ++ ++al+e ++el  +++++++ ++++s+ e+++a+ ++  e 
  gi|557694214|ref|YP_008797268.1| 601 LVDEVKRLGGEVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAgAEEEVRQLEARVSDAETRVANARAARE- 676
                                       56799************************************9998876155666778999*********9987655. PP

                           Leu_zip 207 tleektasaksleedlastkhelLkvqeq 235
                                       ++++ +++ ++l++d+    ++l++++eq
  gi|557694214|ref|YP_008797268.1| 677 EVKTLENRLQQLSADVDALDKRLVSLREQ 705
                                       56778889999999999999999999998 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  17.0   0.00047       0.1      77     182 ..     599     707 ..     589     710 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00047
                             ATG16  77 qsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklv 153
                                       + l +++++l  e++ l   r++l + + +++ el++ ++ l+e++++la +e+e+++le +++d e +++  +++ 
  gi|557694214|ref|YP_008797268.1| 599 PGLVDEVKRLGGEVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAR 675
                                       567789999999*****************************************************999998877776 PP

                             ATG16 154 q...dlqDElsaLqlqlnqaEeklrklekENk 182
                                       +   +l   l++L   +  ++++l  l++ N+
  gi|557694214|ref|YP_008797268.1| 676 EevkTLENRLQQLSADVDALDKRLVSLREQNN 707
                                       62226667889999999999999888888875 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 ?    4.7   0.7      0.18        40       4      40 ..     621     657 ..     619     657 .. 0.84
   2 ?   10.1   0.3    0.0039      0.86       3      42 ..     655     701 ..     653     705 .. 0.52

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.18
                         FlaC_arch   4 elEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       +l ++++k + ele +++ +ee + ++   +e+V++l
  gi|557694214|ref|YP_008797268.1| 621 QLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQL 657
                                       5778999999999999999999999999999998876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0039
                         FlaC_arch   3 delEnklsklsteletvkkeneels...ksveelkenV....kdlls 42 
                                        +lE ++s+ +t+++++++  ee++   + +++l  +V    k+l+s
  gi|557694214|ref|YP_008797268.1| 655 RQLEARVSDAETRVANARAAREEVKtleNRLQQLSADVdaldKRLVS 701
                                       57888888888855555444444331114444444444444445554 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 ?   11.9  10.8   0.00035     0.077     181     265 ..     620     704 ..     602     708 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00035
                          CALCOCO1 181 eqseeelrslskelqelrnslaerdtqvlqLqdtittltqkLttAqrkeaenEallkelrslqerlaaSerkvegLk 257
                                       eq ++e+++  +el+e+r  l+er+ ++   ++++ +l+ ++++A+ ++a+  a+++e+++l +rl+     v++L 
  gi|557694214|ref|YP_008797268.1| 620 EQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVDALD 696
                                       566788899999********************************************************99******9 PP

                          CALCOCO1 258 eeLssvaa 265
                                       + L s+  
  gi|557694214|ref|YP_008797268.1| 697 KRLVSLRE 704
                                       99988755 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.6   0.00056      0.12     281     353 ..     621     697 ..     606     707 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00056
                             IFT57 281 eaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDgsp....lvkikkaltklkkEikqmdv 353
                                       +++ e+++++++++++ + ++e++rela  +ee+++++ ++ + ++++++++     + ++ + l++l  ++  +d 
  gi|557694214|ref|YP_008797268.1| 621 QLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAareeVKTLENRLQQLSADVDALDK 697
                                       66778888888888888888888888888888888888888888888888865111133344455555555555554 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 ?   11.2   4.3   0.00062      0.14      91     167 ..     620     707 ..     600     710 .. 0.38

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00062
                             Atg14  91 sqlkkeieekkkklaklsdklkkRrsdleslqneleerrkk..qiaklqdaik.........rieqklsslssktle 156
                                       +ql++e+e+++++l++ +++l +R+++l+ +++e+++ +++    ++ + + +         + + ++ s   + l+
  gi|557694214|ref|YP_008797268.1| 620 EQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARvsDAETRVANARaareevktlENRLQQLSADVDALD 696
                                       33333444444444444444444444433333333322221001111111111222222211111111122233344 PP

                             Atg14 157 srsslcselak 167
                                       +r+++++e ++
  gi|557694214|ref|YP_008797268.1| 697 KRLVSLREQNN 707
                                       45555555555 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00078      0.17     125     149 ..     427     451 ..     409     485 .. 0.68
   2 ?   -1.1   0.0       6.6   1.5e+03      50      97 ..     671     719 ..     650     727 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00078
                      Reprolysin_2 125 eidv.vaHEvGHaFGatHdndgssas 149
                                        + v v HE+GH+FG  H  d ++++
  gi|557694214|ref|YP_008797268.1| 427 GMTVlVTHEAGHIFGLRHPHD-DYDE 451
                                       444559**********99887.4444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 6.6
                      Reprolysin_2  50 cnssttevrr.lnllsqlegekdydlahlvllgtfsggvlGLayvgqic 97 
                                       +  +  ev+  +n l+ql+ + d     lv l++ ++  +G a+vg + 
  gi|557694214|ref|YP_008797268.1| 671 ARAAREEVKTlENRLQQLSADVDALDKRLVSLREQNNLFIGVAVVGAVA 719
                                       3444455666578888888888888888888999999999999999875 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   5.0   0.00094      0.21      10      83 ..     624     700 ..     616     709 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00094
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXX--TTTTTGGGHHHHHHHHH CS
                        Laminin_II  10 etakevleqlaplsqnlentkeklseinrsveetnekvkdankaird...ArrsvkkLeklapqLldklkelkqlee 83 
                                       + +++ ++ l++  + le+ k +l +++++v++ ++ v+da + ++    Ar++vk+Le+ ++qL + +  l+++ +
  gi|557694214|ref|YP_008797268.1| 624 SEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANaraAREEVKTLENRLQQLSADVDALDKRLV 700
                                       45677788888889999999999999999999999999988887755111567899999999999888777777655 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 ?   12.5   4.8   0.00069      0.15      43     119 ..     621     697 ..     616     704 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00069
                                       ---STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHHHHHHHHH..HHHHHH CS
                           T3SSipB  43 klSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakleaaeqQagaaadalqa 119
                                       +l  e+++a  e ++a  +le+   ++  a+ ++ +++++v++a +r+ +   +  e + le+  qQ+ a  dal +
  gi|557694214|ref|YP_008797268.1| 621 QLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVDALDK 697
                                       67788999*************************************************************88999865 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 ?    5.6   1.5     0.083        18      27      63 ..     604     640 ..     600     644 .. 0.78
   2 ?   10.6   8.2    0.0023      0.51      17      84 ..     636     703 ..     633     705 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.083
                       TMF_TATA_bd  27 Elaslkeelerleaerdeareeivklmkeneelkelk 63 
                                       E++ l  e++rl+  r+++r+e+ k  +e ee +++ 
  gi|557694214|ref|YP_008797268.1| 604 EVKRLGGEVSRLTGIREQLRSEVEKAQRELEEARAAL 640
                                       6777778888999999999999999888888887765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0023
                       TMF_TATA_bd  17 lsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlL 84 
                                         +++ ++  Ela ++ee+ +lea  ++a+  +++  +  ee+k+l+++l++l++ +++l++r+ +l 
  gi|557694214|ref|YP_008797268.1| 636 ARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVDALDKRLVSLR 703
                                       56889999*******************************************************98765 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   7.2   0.00074      0.16      31     146 ..     610     701 ..     600     711 .. 0.35

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00074
                              Fez1  31 seivalkaqlrelrakleekeeeikeleesleektlelevcenelqrk.................kseaellrekve 90 
                                       +e+  l +   +lr+++e+ ++e++e++++lee+++el   e+e+++                  ++e+++l     
  gi|557694214|ref|YP_008797268.1| 610 GEVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLearvsdaetrvanaraaREEVKTL----- 681
                                       333333333334444444444444444444444444444444444333222222222211111111222222..... PP

                              Fez1  91 kleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLke 146
                                                                           +++l++l+++v+ l ++L  
  gi|557694214|ref|YP_008797268.1| 682 ------------------------------------ENRLQQLSADVDALDKRLVS 701
                                       ....................................22333333333333333333 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 ?   11.6   5.6    0.0012      0.27       5      72 ..     619     687 ..     601     700 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0012
                           V-SNARE   5 laeiksklarlsslageerkaalreiekkldeaeelldqMelEvrnlps......serasykaklreykselkk 72 
                                        ++++s++++++ +  ee +aal e +++l  aee ++q+e  v+++ +      +      + ++   ++l++
  gi|557694214|ref|YP_008797268.1| 619 REQLRSEVEKAQRE-LEEARAALEERKRELAGAEEEVRQLEARVSDAETrvanarA----AREEVKTLENRLQQ 687
                                       68999999999977.79****************************99765653331....23333333333333 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  11.0   0.00059      0.13     623     702 ..     620     701 ..     604     708 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00059
                           DUF3584 623 kqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaiaerk..qqaeeqlqkldaqlkqle 697
                                       +q+ +e+++++ eleea++a++e++++l  a++++++l+     ++ ++ +a+a+r   ++ e++lq+l a+ ++l+
  gi|557694214|ref|YP_008797268.1| 620 EQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREevKTLENRLQQLSADVDALD 696
                                       67777888888888888888888888888888888888887777777777766665522566788888888888888 PP

                           DUF3584 698 eqqka 702
                                       +   +
  gi|557694214|ref|YP_008797268.1| 697 KRLVS 701
                                       76655 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 ?   11.9   8.0   0.00091       0.2      51     139 ..     604     690 ..     596     708 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00091
                     Jnk-SapK_ap_N  51 eleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekea 127
                                       e+++l  e+++L+  +e+ +++ ++a++elee+  ++ee+++el       eee+r+le+++++a++++++     +
  gi|557694214|ref|YP_008797268.1| 604 EVKRLGGEVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELA----GAEEEVRQLEARVSDAETRVANARAARE 676
                                       667777788888888888888888888888888888888887763....3455555555555555555555555555 PP

                     Jnk-SapK_ap_N 128 elkkeysklhe..r 139
                                       e+k+ +++l++   
  gi|557694214|ref|YP_008797268.1| 677 EVKTLENRLQQlsA 690
                                       55555555554331 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 ?    9.5   1.1    0.0009       0.2      14     102 ..     622     709 ..     606     720 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0009
                        V_ATPase_I  14 lnedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelne 90 
                                       l ++v++ qr+  +    ++e +r+l   eee+++le  v  +e+    ++++ ++e+++le++l++l +++  l++
  gi|557694214|ref|YP_008797268.1| 622 LRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAET-RVANARAAREEVKTLENRLQQLSADVDALDK 697
                                       677888999999999999999999999999999996666655554.6666667777888888888888888888888 PP

                        V_ATPase_I  91 nleklkkelnel 102
                                        l +l+++ n  
  gi|557694214|ref|YP_008797268.1| 698 RLVSLREQNNLF 709
                                       888888887755 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.3   0.00089       0.2       4     106 ..     612     720 ..     602     725 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00089
                             TMPIT   4 weelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk..eeeeeeveelkeelker 78 
                                       +++l+   ++l+++ ++ +++lee  +  ++ ++e++  ++++++l++++++ +++v   +  +eev++l+++l++ 
  gi|557694214|ref|YP_008797268.1| 612 VSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVAnaRAAREEVKTLENRLQQL 688
                                       33444444455555555555555555555555555555555555555555555555436677788999999999998 PP

                             TMPIT  79 kkvlkeves...llpkknglylkl.vlGnvnv 106
                                       ++ ++ +++   +l ++n l++ + v+G v v
  gi|557694214|ref|YP_008797268.1| 689 SADVDALDKrlvSLREQNNLFIGVaVVGAVAV 720
                                       88888555511145566888886535667666 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.8   0.00089       0.2     330     415 ..     618     706 ..     600     721 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00089
                              FapA 330 ldepelkeklkeleeeleeleeeleklkkk....ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelk 402
                                       ++  +l++++++ ++elee ++ le+ k++     +++++l+a+    +++      ++e+ + l+++l++l ++ +
  gi|557694214|ref|YP_008797268.1| 618 IR-EQLRSEVEKAQRELEEARAALEERKRElagaEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVD 693
                                       44.44444444444444444444444444433334555555556666666667777777777777777777777777 PP

                              FapA 403 elkeeleskkeea 415
                                       +l+++l s +e++
  gi|557694214|ref|YP_008797268.1| 694 ALDKRLVSLREQN 706
                                       7777766664444 PP

>> PEARLI-4  Arabidopsis phospholipase-like protein (PEARLI 4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   3.9    0.0012      0.27     189     260 ..     620     694 ..     608     715 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0012
                          PEARLI-4 189 etavvEKevkerdvllkkqEmekqekelaekEKeikevrekvtemaaklgelemkra...rlekrlaflssKvek 260
                                       e+  +E e+ +r++  ++  +e+ ++ela  E e++++ ++v + ++++++  + r     le+rl+ ls  v+ 
  gi|557694214|ref|YP_008797268.1| 620 EQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREevkTLENRLQQLSADVDA 694
                                       455566667777778888888888888888888888888888888888777776664111466777777766664 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 ?   10.3   5.0    0.0029      0.65       7      91 ..     618     702 ..     613     706 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0029
                           BLOC1_2   7 vskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavse 83 
                                       +++ l++e+e ++ +++   +  e+  ++ +  ++++ +le+ +++ + + ++ +   ++++ +e+++++L + v++
  gi|557694214|ref|YP_008797268.1| 618 IREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVDA 694
                                       56778888888888998889999999999999999****************************************** PP

                           BLOC1_2  84 LDeyskeL 91 
                                       LD+   +L
  gi|557694214|ref|YP_008797268.1| 695 LDKRLVSL 702
                                       **988777 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 ?   -1.1   0.1       4.4   9.8e+02     154     187 ..     512     545 ..     509     548 .. 0.84
   2 ?   13.4  11.2   0.00017     0.037      36     120 ..     620     704 ..     614     708 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 4.4
                               GAS 154 lqeelEkkeaqleevlaaanldpaalsavsekle 187
                                       l ++ E++ + + ++l+++n++p+++ +++e l+
  gi|557694214|ref|YP_008797268.1| 512 LLQNYEQNMQTILSTLRQNNINPNDIPELNEVLN 545
                                       5678899999999999999999999999888776 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00017
                               GAS  36 eelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevle 112
                                       e+l+ + e++++el+e+ +  ++ k +L  aeeev +L++++ + e   +  +++++++k+le+ l++l+ + + l 
  gi|557694214|ref|YP_008797268.1| 620 EQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVDALD 696
                                       57888889999**************************************************************9999 PP

                               GAS 113 qrfekvek 120
                                       +r+ ++ +
  gi|557694214|ref|YP_008797268.1| 697 KRLVSLRE 704
                                       99877765 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1  14.0   0.00042     0.094      80     139 ..     618     677 ..     610     679 .. 0.89
   2 ?    7.2   6.2     0.027         6      84     136 ..     650     705 ..     649     707 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00042
                             HrpB7  80 yrdvlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraaer 139
                                        r++l+ +v++a++el+ ar+al+++++++a  +++++ ++a++   + r++ +r+a e+
  gi|557694214|ref|YP_008797268.1| 618 IREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREE 677
                                       68899999******************************************9999998775 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.027
                             HrpB7  84 legrvraaeaelaaarqald...aaedavaatarkiaRndaqidacrerierlrra 136
                                       +e++vr++ea++  a+ +++   aa+++v++ + ++  + a +da ++r+  lr++
  gi|557694214|ref|YP_008797268.1| 650 AEEEVRQLEARVSDAETRVAnarAAREEVKTLENRLQQLSADVDALDKRLVSLREQ 705
                                       689999999999999998861115567899999*****************999875 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 ?    8.7  16.9    0.0077       1.7      50     104 ..     624     678 ..     605     690 .. 0.83
   2 ?    4.4   1.1      0.17        38      70     100 ..     675     705 ..     673     708 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0077
                             DHR10  50 akleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeek 104
                                        ++e+a+++l+e+r+alee+++el+  e + ++l+ +++ ae + + +r  +ee 
  gi|557694214|ref|YP_008797268.1| 624 SEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREEV 678
                                       5678999***************************************999877764 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.17
                             DHR10  70 eielrelerkeerlqrqlenaeeklerlreq 100
                                       ++e++ le++ ++l   ++   ++l  lreq
  gi|557694214|ref|YP_008797268.1| 675 REEVKTLENRLQQLSADVDALDKRLVSLREQ 705
                                       4567777777777777777777777777766 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1     0.033       7.4      27      58 ..     604     635 ..     602     641 .. 0.88
   2 ?    8.0   1.0     0.013         3      25      56 ..     675     706 ..     671     708 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  27 eieeLerrvkaLekeNksLkseleelkkevek 58 
                                       e+++L  +v+ L++  ++L+se+e+ + e e+
  gi|557694214|ref|YP_008797268.1| 604 EVKRLGGEVSRLTGIREQLRSEVEKAQRELEE 635
                                       799*********************99888776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  25 qaeieeLerrvkaLekeNksLkseleelkkev 56 
                                       ++e++ Le+r ++L++   +L ++l +l++++
  gi|557694214|ref|YP_008797268.1| 675 REEVKTLENRLQQLSADVDALDKRLVSLREQN 706
                                       58999999999999999999999999999876 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 ?    9.7   9.1    0.0024      0.52     225     326 ..     604     704 ..     602     708 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0024
                            HMMR_N 225 eteklleyieelsnvseqlekykldiaqleellkekndeiesLkssL...eekeqelskqvkdlnekckllekekee 298
                                       e+++l  ++++l  ++eql   + ++++++  l+e+   +e+ k +L   ee+  +l+++v+d+++++    + +e 
  gi|557694214|ref|YP_008797268.1| 604 EVKRLGGEVSRLTGIREQL---RSEVEKAQRELEEARAALEERKRELagaEEEVRQLEARVSDAETRVANARAARE- 676
                                       5677888899999999999...999999999999999999999999944446666799999999999999999999. PP

                            HMMR_N 299 lvreeeekeqtlsaEleelkeklklkeq 326
                                       +v+  e++ q+lsa ++ l ++l + ++
  gi|557694214|ref|YP_008797268.1| 677 EVKTLENRLQQLSADVDALDKRLVSLRE 704
                                       8999999999999999999988765443 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.35        78       8      43 ..     513     551 ..     510     556 .. 0.79
   2 ?    9.0   9.7    0.0056       1.2      57     156 ..     593     694 ..     589     695 .. 0.74
   3 ?    4.9   0.4     0.097        21      70     103 ..     672     705 ..     668     707 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHHHHHHHHT...THHHHHHHHHHH---- CS
                        DASH_Spc19   8 LrssvslLqssietLdsgvs...dfprlkkvLkttrvFe 43 
                                       L++  +++q+ ++tL+++     d+p l++vL++ + F 
  gi|557694214|ref|YP_008797268.1| 513 LQNYEQNMQTILSTLRQNNInpnDIPELNEVLNSAKTFA 551
                                       67777889999999988652244*************996 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0056
                                       HHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXX.. CS
                        DASH_Spc19  57 laeeiePqieellekaekeleklerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkk.. 131
                                        ++ + P + + ++++  e+++l+  +e+L++++e+ +  l++a++  +e + +   +eee ++ + + ++++++  
  gi|557694214|ref|YP_008797268.1| 593 TKNYVLPGLVDEVKRLGGEVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRva 669
                                       5666778888999******************************8777666665555555544444444444444455 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXX CS
                        DASH_Spc19 132 ltkeelerlkkLkqkKerLkytler 156
                                        +++  e++k L ++ ++L+  ++ 
  gi|557694214|ref|YP_008797268.1| 670 NARAAREEVKTLENRLQQLSADVDA 694
                                       5555569999999999999988876 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.097
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.... CS
                        DASH_Spc19  70 ekaekeleklerreetLkaklelqegrlsnaess 103
                                       + a++e++ le+r ++L a ++ +++rl + +++
  gi|557694214|ref|YP_008797268.1| 672 RAAREEVKTLENRLQQLSADVDALDKRLVSLREQ 705
                                       568899*********************9986554 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   5.5    0.0037      0.82       5     102 ..     608     705 ..     604     710 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0037
                           zf-C4H2   5 irektleleklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekeks... 78 
                                       +  ++++l+ ++++l++eve  +   + lee ++ le+ ++E     ee+r+++a +++ E+ + +a+ ++e+    
  gi|557694214|ref|YP_008797268.1| 608 LGGEVSRLTGIREQLRSEVEKAQ---RELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREEVktl 681
                                       55567889999999999998665...669**********************************99987766543001 PP

                           zf-C4H2  79 lekakklyeeykklkeevnelrse 102
                                       +++ ++l++++++l +++ +lr++
  gi|557694214|ref|YP_008797268.1| 682 ENRLQQLSADVDALDKRLVSLREQ 705
                                       445666677777777766666665 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 ?    7.6   4.0      0.02       4.4      36     106 ..     603     670 ..     591     672 .. 0.61
   2 ?    6.8   0.6     0.035       7.8      68      97 ..     670     699 ..     664     709 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS-- CS
                      Seryl_tRNA_N  36 ekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllaiPN 106
                                       ++ ++l  e+  l   r +l  e++ka ++    ee +a  +e k el+ +e+e+++lea++ ++ +++ N
  gi|557694214|ref|YP_008797268.1| 603 DEVKRLGGEVSRLTGIREQLRSEVEKAQRE---LEEARAALEERKRELAGAEEEVRQLEARVSDAETRVAN 670
                                       445555555555666666666666666654...35555666666677777777777777766666555554 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.035
                                       -TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  68 daeeliaevkelkeelkaleaelkeleael 97 
                                       +a + ++evk+l ++l++l+a++++l+++l
  gi|557694214|ref|YP_008797268.1| 670 NARAAREEVKTLENRLQQLSADVDALDKRL 699
                                       566777777777777777777777777766 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.3    0.0029      0.65     222     297 ..     620     697 ..     607     699 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0029
                             FAM76 222 tqLkeeiaslkkqleqkdqellekdkkitelkaellekekel...reklkelekeakekieklekkirellkevael 295
                                       +qL+ e+++ +++le+   +l e++++++ +  e  + e+++   ++++ +  + a+e++++le++ ++l  +v +l
  gi|557694214|ref|YP_008797268.1| 620 EQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVsdaETRVAN-ARAAREEVKTLENRLQQLSADVDAL 695
                                       69***************************9999998888765111455544.5678899************999988 PP

                             FAM76 296 sk 297
                                        k
  gi|557694214|ref|YP_008797268.1| 696 DK 697
                                       77 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 ?    9.0   8.7    0.0038      0.85      56     175 ..     619     688 ..     602     708 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0038
                         Golgin_A5  56 rdllreelqklnqqieqlrtelqdleaq...qqaeaeslreqlqeleeqleeerkakeeveaelerlkeelryleee 129
                                       r++lr+e++k++ ++e+ r+ l++ +++   +++e+++l+ +++++e+++++ r+a+eev++               
  gi|557694214|ref|YP_008797268.1| 619 REQLRSEVEKAQRELEEARAALEERKRElagAEEEVRQLEARVSDAETRVANARAAREEVKT--------------- 680
                                       44444444444444444444444433221113445555555555555555555555554432............... PP

                         Golgin_A5 130 lvrskatlqsrikdrekeieklrnqlttkslsssseselesRlkqL 175
                                                                             le+Rl+qL
  gi|557694214|ref|YP_008797268.1| 681 --------------------------------------LENRLQQL 688
                                       ......................................22222222 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0      0.11        24       2      34 ..     605     637 ..     601     645 .. 0.72
   2 ?    0.4   0.1       4.1   9.1e+02       8      32 ..     653     677 ..     650     684 .. 0.61
   3 ?    4.7   0.4      0.18        41       5      21 ..     681     697 ..     677     708 .. 0.46

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.11
                               LPP   2 ldeLssqVsqLkskvdqlssdvnsakaaaqaak 34 
                                       ++ L  +Vs+L    +ql s+v++a+ ++++a+
  gi|557694214|ref|YP_008797268.1| 605 VKRLGGEVSRLTGIREQLRSEVEKAQRELEEAR 637
                                       456667777787777888888888777776664 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 4.1
                               LPP   8 qVsqLkskvdqlssdvnsakaaaqa 32 
                                       +V qL++ v+  +  v++a+aa ++
  gi|557694214|ref|YP_008797268.1| 653 EVRQLEARVSDAETRVANARAAREE 677
                                       5566666666666666665555554 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.18
                               LPP   5 LssqVsqLkskvdqlss 21 
                                       L + ++qL+++vd+l +
  gi|557694214|ref|YP_008797268.1| 681 LENRLQQLSADVDALDK 697
                                       34444444444444433 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   5.0    0.0039      0.87      99     179 ..     621     704 ..     605     709 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0039
                            DUF724  99 slkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk...ekkeaadkeiarlkseaeklee 172
                                       +l++e +k+++e++++   +ee + e + +eee+++le ++++ e++ a ++   e+ ++ ++++ +l++++++l++
  gi|557694214|ref|YP_008797268.1| 621 QLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARaarEEVKTLENRLQQLSADVDALDK 697
                                       57889999999999999999999999999999999999999999999888887667777888888999999988888 PP

                            DUF724 173 eledveq 179
                                       +l + ++
  gi|557694214|ref|YP_008797268.1| 698 RLVSLRE 704
                                       8877665 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.2    0.0051       1.1     191     250 ..     642     701 ..     606     709 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0051
                         Phage_GPO 191 sddarfadveeavelvAeevkelsekveallaleaelaalkkeveklkaeleaLkekLsk 250
                                       + + + a  ee v ++ ++v++++++v+++ a+++e+++l++++++l+a+++aL ++L +
  gi|557694214|ref|YP_008797268.1| 642 ERKRELAGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVDALDKRLVS 701
                                       22345566667777777888889999998889999999***************9999755 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.8    0.0033      0.74     241     330 ..     618     701 ..     599     727 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0033
                              FUSC 241 llarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaql 317
                                         ++lr+e ++a++el++  a+l++  +++  ++ e+++++l+ar+ +++++ +     a+++ +++++l  +l+ql
  gi|557694214|ref|YP_008797268.1| 618 IREQLRSEVEKAQRELEEARAALEE--RKRELAGAEEEVRQLEARVSDAETRVA----NARAAREEVKTLENRLQQL 688
                                       3345555555555556666666666..445566667777777777766666666....6777777777777777777 PP

                              FUSC 318 laslraleaaiaa 330
                                        a+++al+++ ++
  gi|557694214|ref|YP_008797268.1| 689 SADVDALDKRLVS 701
                                       7777777776665 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.9    0.0037      0.82      98     154 ..     614     670 ..     610     674 .. 0.90
   2 ?    5.9   3.8      0.04       8.8      95     156 ..     629     689 ..     627     701 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0037
                     Fzo_mitofusin  98 elsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLek 154
                                       +l+   ++l+++v+++++elee  ++le++ ++l+ ++++ ++l  + s  e+++++
  gi|557694214|ref|YP_008797268.1| 614 RLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVAN 670
                                       6889999*************************************9999888877765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.04
                     Fzo_mitofusin  95 vqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfe 156
                                        q+el+++ a l+++ +e  +  eee+++le++++  e+   +a++ r++ ++le++L++ +
  gi|557694214|ref|YP_008797268.1| 629 AQRELEEARAALEERKREL-AGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLS 689
                                       6788888888887765544.345677777777777777777777777777777777777654 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 ?   11.9   5.1   0.00081      0.18      26     107 ..     603     692 ..     590     708 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00081
                             Mod_r  26 pevkqlkeekeellaeneslaeknlsl.epeleelrselqekleelkelekefeekeqeldell........qkfsp 93 
                                       +evk+l  e + l + +++ +++  ++ + elee r+ l+e+  el+ +e+e++++e++ +++          +   
  gi|557694214|ref|YP_008797268.1| 603 DEVKRLGGEVSRL-TGIREQLRSEVEKaQRELEEARAALEERKRELAGAEEEVRQLEARVSDAEtrvanaraAREEV 678
                                       5666666666666.555555566666656666666666666666666666666666666655543222222344444 PP

                             Mod_r  94 dallarLqtavaea 107
                                       ++l +rLq+  a+ 
  gi|557694214|ref|YP_008797268.1| 679 KTLENRLQQLSADV 692
                                       45555555555444 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.3    0.0065       1.4      47     122 ..     624     697 ..     614     710 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0065
                              YkyA  47 defdkikklsdealenveeReellekekesieeakeefekikeeieeiedeelkkeaeelieameeryeaydklyk 122
                                       +e +k + + +ea + +eeR+ +l+  +e + + +  ++++++ + +    ++++e+++l++ +++  +  d+l k
  gi|557694214|ref|YP_008797268.1| 624 SEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANAR--AAREEVKTLENRLQQLSADVDALDK 697
                                       5677888888888888888888888888888888888888888888884..5699999999988888877777655 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 ?    6.1  13.5     0.058        13       6      60 ..     643     695 ..     619     704 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.058
                      ABC_tran_CTD   6 eqreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeel 60 
                                        +rel+  e+e  +LE++ ++ e+++a++   +  e+++ l ++l++l a+ ++l
  gi|557694214|ref|YP_008797268.1| 643 RKRELAGAEEEVRQLEARVSDAETRVANAR--AAREEVKTLENRLQQLSADVDAL 695
                                       577777888888888888888888888887..56688888888888888888876 PP

>> HAUS5  HAUS augmin-like complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  11.4    0.0051       1.1      81     163 ..     618     696 ..     609     706 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0051
                             HAUS5  81 ereelekeverLraeirrldkeleareeelsreeaevkraldeisdsrhrqvlLeaydqqceeaakilaedtkrlqe 157
                                        re+l +eve+ + e+++ +  le r++el+  e+ev +  + +sd+ +r +     +++ +e+ k+l +  ++l++
  gi|557694214|ref|YP_008797268.1| 618 IREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVAN----ARAAREEVKTLENRLQQLSA 690
                                       59************************************************755....55555666779999999998 PP

                             HAUS5 158 qvqqlr 163
                                        v++l+
  gi|557694214|ref|YP_008797268.1| 691 DVDALD 696
                                       888775 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 ?    4.2   1.5      0.26        57      31      70 ..     603     642 ..     600     647 .. 0.87
   2 ?    2.8   1.0      0.68   1.5e+02      19      48 ..     640     669 ..     633     674 .. 0.76
   3 ?   10.2   1.4    0.0034      0.75      19      53 ..     671     705 ..     663     708 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.26
                               CLZ  31 ekverLessLeaLqtrlarLlaeyessqrkLkqRitkLEk 70 
                                       + v+rL +++  L+   ++L +e+e++qr+L++  ++LE+
  gi|557694214|ref|YP_008797268.1| 603 DEVKRLGGEVSRLTGIREQLRSEVEKAQRELEEARAALEE 642
                                       5789999999999999999999999999999999888887 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.68
                               CLZ  19 aakagaeqkeleekverLessLeaLqtrla 48 
                                        ++++ e   +ee v++Le+++   +tr+a
  gi|557694214|ref|YP_008797268.1| 640 LEERKRELAGAEEEVRQLEARVSDAETRVA 669
                                       3455577788999******99999999988 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0034
                               CLZ  19 aakagaeqkeleekverLessLeaLqtrlarLlae 53 
                                       a++a++e k+le+++++L + ++aL++rl  L ++
  gi|557694214|ref|YP_008797268.1| 671 ARAAREEVKTLENRLQQLSADVDALDKRLVSLREQ 705
                                       4566799*********************9888665 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 ?    6.3   6.0     0.059        13      48      95 ..     614     661 ..     604     662 .. 0.86
   2 ?    9.5   3.9     0.006       1.3      47      96 ..     659     707 ..     658     709 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.059
                           DUF4140  48 tildvqvervpnreaeeeelkalraeleeledelaaledelaaaearl 95 
                                       ++++++ + + + e+++ el+++ra+lee ++ela +e+e + +ear 
  gi|557694214|ref|YP_008797268.1| 614 RLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARV 661
                                       6788888888888888889************************99986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.006
                           DUF4140  47 atildvqvervpnreaeeeelkalraeleeledelaaledelaaaearla 96 
                                       a+++d +++  +n +a++ee+k+l+++l++l ++ +al+++l +++++ +
  gi|557694214|ref|YP_008797268.1| 659 ARVSDAETRV-ANARAAREEVKTLENRLQQLSADVDALDKRLVSLREQNN 707
                                       5677777776.555555556***********************9999976 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.027       5.9      57     101 ..     591     635 ..     588     637 .. 0.93
   2 ?    6.3   2.0     0.041         9      58      97 ..     631     673 ..     629     678 .. 0.82
   3 ?    4.6   0.2      0.14        31      70      97 ..     677     704 ..     669     709 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.027
                                       EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                       Prefoldin_2  57 kqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqk 101
                                       +++k+ v++ L ++ ++l  e+++l+   e+l+ e+e+ + el +
  gi|557694214|ref|YP_008797268.1| 591 ENTKNYVLPGLVDEVKRLGGEVSRLTGIREQLRSEVEKAQRELEE 635
                                       78999************************************9986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.041
                                       E-HHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  58 qdkeevkeeLeerketl...ekeiktlekqleklekeleelke 97 
                                       +++ee+++ Leerk +l   e+e+++le + ++ e+++++ ++
  gi|557694214|ref|YP_008797268.1| 631 RELEEARAALEERKRELagaEEEVRQLEARVSDAETRVANARA 673
                                       78999999999998764444999*********99999999876 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  70 rketlekeiktlekqleklekeleelke 97 
                                       + +tle ++++l+   + l k+l  l+e
  gi|557694214|ref|YP_008797268.1| 677 EVKTLENRLQQLSADVDALDKRLVSLRE 704
                                       3344444444444444444444444444 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 ?   11.0   1.2    0.0015      0.34      23      73 ..     601     651 ..     592     654 .. 0.90
   2 ?    1.8   2.3       1.2   2.6e+02      17      39 ..     672     704 ..     650     709 .. 0.49

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0015
                     TolA_bind_tri  23 lqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkleagg 73 
                                       l  ++++l  e+++L G  E+l+ ++e++++   +    l+er r+l +++
  gi|557694214|ref|YP_008797268.1| 601 LVDEVKRLGGEVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAE 651
                                       677899999*************************************99876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 1.2
                     TolA_bind_tri  17 s..........qlllelqqqlealqqelreLRG 39 
                                                  + l +l   ++al + l +LR 
  gi|557694214|ref|YP_008797268.1| 672 RaareevktleNRLQQLSADVDALDKRLVSLRE 704
                                       344433333334444455555555555555554 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   8.9     0.019       4.2       1      68 [.     622     689 ..     622     708 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.019
                              BRE1   1 lqkELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkll 68 
                                       l +E++k +++ ee++++l++ + el+  ee++ +lea  + a+    +a+ +++ +++  ++L++l 
  gi|557694214|ref|YP_008797268.1| 622 LRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLS 689
                                       578********************************************999988887776666666654 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 ?    8.7   9.6     0.014       3.2      14      83 ..     620     706 ..     613     709 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.014
                    PRKG1_interact  14 erLkreLeelekelselkseleklkqq...rqe...........svskrssllelekrerrslerkiseleeel... 73 
                                       e+L++e+e++++el+e+++ le+ k++     e             ++r + + + ++e ++le+++++l+ ++   
  gi|557694214|ref|YP_008797268.1| 620 EQLRSEVEKAQRELEEARAALEERKRElagA-EeevrqlearvsDAETRVANARAAREEVKTLENRLQQLSADVdal 695
                                       6777777777777777777777765443221.023333344332334444444555666666666666655444444 PP

                    PRKG1_interact  74 .keleeLraen 83 
                                        k l  Lr++n
  gi|557694214|ref|YP_008797268.1| 696 dKRLVSLREQN 706
                                       46666666665 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.4    0.0067       1.5     123     185 ..     612     674 ..     590     684 .. 0.60
   2 ?    1.6   0.2      0.75   1.7e+02      29      53 ..     674     698 ..     671     709 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0067
                              Vps5 123 vksvfeqRvklwqkwqsaeqelskkkeqleKlekaaksqqdklqqlkkeveelerkvqeaeke 185
                                       v  +   R +l  ++++a++el+  +++le  +++   +++ ++ql++ v ++e++v++a+  
  gi|557694214|ref|YP_008797268.1| 612 VSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANARAA 674
                                       555555566666666666666666666666666666666666666666666666666666544 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.75
                              Vps5  29 kkqeldslesqLkkLykaiellvsq 53 
                                       +++e+ +le++L++L+  +++l++ 
  gi|557694214|ref|YP_008797268.1| 674 AREEVKTLENRLQQLSADVDALDKR 698
                                       4678888888888888888887765 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.9    0.0058       1.3       3      65 ..     658     723 ..     642     725 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0058
                              XhlA   3 kerlerietkldnlee...rvdkleekaaeaeekiknleedlkklesnqkWlirtiiGalisaviy 65 
                                       + r+   et++ n      +v++le++     + ++ l ++l +l ++++ +i++ + + ++++++
  gi|557694214|ref|YP_008797268.1| 658 EARVSDAETRVANARAareEVKTLENRLQQLSADVDALDKRLVSLREQNNLFIGVAVVGAVAVAGA 723
                                       567777778887777777788888888888888888888888888888888888776666666665 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 ?    7.7   3.1     0.013       2.9      17      70 ..     644     697 ..     633     707 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.013
                        Phage_GP20  17 kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkaka 70 
                                       k +l+ +eee+ +l+ ++ d+++ + +  ++ +++++L++ +++l a++++ ++
  gi|557694214|ref|YP_008797268.1| 644 KRELAGAEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVDALDK 697
                                       7889999*****************************************998776 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   3.6     0.026       5.7      38      92 ..     611     665 ..     601     668 .. 0.82
   2 ?    5.3   1.4     0.048        11      47      88 ..     665     706 ..     662     709 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.026
                           DUF3450  38 kidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                       ++++l+  +++l +e++++++ele++++  e+ +r +a +e+e+ +le + +++e
  gi|557694214|ref|YP_008797268.1| 611 EVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAE 665
                                       5677888889999999999999999999999999999999999999998888776 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.048
                           DUF3450  47 qellaeyralkeeleslevyneqlerlvasqeqeiasleeqi 88 
                                       ++ +a+ ra++ee++ le   +ql++ v+++++++ sl+eq 
  gi|557694214|ref|YP_008797268.1| 665 ETRVANARAAREEVKTLENRLQQLSADVDALDKRLVSLREQN 706
                                       566788899999999999999999999999999999999986 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   7.3     0.097        22      15      81 ..     626     697 ..     588     709 .. 0.50

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.097
                           DUF2203  15 lkelleelralrkeleeleeeleeakaeaekse.....aaeleaeleeleaeieelveeieelGvevkdlea 81 
                                       +++  +el ++r+ lee+++el+ a++e ++ e     a+++ a+ +++++e++ l +++++l ++v  l++
  gi|557694214|ref|YP_008797268.1| 626 VEKAQRELEEARAALEERKRELAGAEEEVRQLEarvsdAETRVANARAAREEVKTLENRLQQLSADVDALDK 697
                                       222333333333333333333333333333333343334444444444455555555555555555555554 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.2    0.0015      0.34      11      58 ..     652     699 ..     647     708 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0015
                           NPV_P10  11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkv 58 
                                       +++++++ +V+  +++v++ ++  ++v+ l+++L+++sa +++l++ +
  gi|557694214|ref|YP_008797268.1| 652 EEVRQLEARVSDAETRVANARAAREEVKTLENRLQQLSADVDALDKRL 699
                                       67999***************************************9876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.0    0.0051       1.1     114     198 ..     605     691 ..     501     693 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0051
                            AAA_23 114 ideleqfisellgskki.ilnlilflgqerfeefelkdkkerleelekeleeledekkllekl.eqekekekeleel 188
                                       ++ l  ++s+l g++++ ++++   + + ++++ +l+++k +l+ +e+e ++le++ +  e++  ++   ++e ++l
  gi|557694214|ref|YP_008797268.1| 605 VKRLGGEVSRLTGIREQlRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRvANARAAREEVKTL 681
                                       3566666666666665545566666666667777777777788888888888777554444445899999******* PP

                            AAA_23 189 eeeleeilke 198
                                       e++l+++  +
  gi|557694214|ref|YP_008797268.1| 682 ENRLQQLSAD 691
                                       ******9765 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.5     0.012       2.6      12      88 ..     602     670 ..     597     672 .. 0.80
   2 ?    4.0   7.4      0.31        69      24      88 ..     625     694 ..     620     704 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.012
                   Snapin_Pallidin  12 epkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRaek 88 
                                       + ++++l  +++ l+   e+L++++++ +++L+e++ a        l+e ++ L+ ++ ++ +l+ r++ ++ R+ +
  gi|557694214|ref|YP_008797268.1| 602 VDEVKRLGGEVSRLTGIREQLRSEVEKAQRELEEARAA--------LEERKRELAGAEEEVRQLEARVSDAETRVAN 670
                                       56788888899999999999999999999999855554........5588888888888888888888888888765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.31
                   Snapin_Pallidin  24 elrqsQeeL...leqldrlnekLkeleea.qe.aevlpdlkeyakKLvnikkrmsslnerlqklkkRaek 88 
                                       e+++ Q+eL   ++ l++ +++L+ +ee+  + ++ ++d+++ ++  ++++ ++++l++rlq+l + ++ 
  gi|557694214|ref|YP_008797268.1| 625 EVEKAQRELeeaRAALEERKRELAGAEEEvRQlEARVSDAETRVANARAAREEVKTLENRLQQLSADVDA 694
                                       4555555551114578888888887765415578899999999999****************99876665 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.9     0.012       2.6      56      91 ..     614     649 ..     603     652 .. 0.80
   2 ?    6.0   3.1     0.061        14      64     101 ..     650     687 ..     646     698 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.012
                              FliJ  56 aldeaiaqqkqelaqaekqvekareewqearqerkk 91 
                                       +l    +q+++e+++a++++e+ar+++ e ++e+  
  gi|557694214|ref|YP_008797268.1| 614 RLTGIREQLRSEVEKAQRELEEARAALEERKRELAG 649
                                       566677889999999999999999999999988765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.061
                              FliJ  64 qkqelaqaekqvekareewqearqerkklekLkerekk 101
                                       +++e+ q+e++v+ a+ +   ar  r+ +++L+ r ++
  gi|557694214|ref|YP_008797268.1| 650 AEEEVRQLEARVSDAETRVANARAAREEVKTLENRLQQ 687
                                       789*****************************998665 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 ?    6.2  13.2     0.058        13       4      75 ..     627     699 ..     617     712 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.058
                       Uso1_p115_C   4 seleseaaslkdeneklkaelqslskalesleqk.eakkaaesqakeleaenkklekeleklraelkeekeke 75 
                                       +++++e ++++   e+ k el  +++++++le   +  +   ++a+ +++e+k le++l++l+a +++  ++ 
  gi|557694214|ref|YP_008797268.1| 627 EKAQRELEEARAALEERKRELAGAEEEVRQLEARvSDAETRVANARAAREEVKTLENRLQQLSADVDALDKRL 699
                                       3444444444445555555555555555555555766666677888999999999999999999998876654 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 ?    3.8   7.5      0.25        55      75     112 ..     623     660 ..     598     699 .. 0.53

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.25
                              COG2  75 esplaaarkkvesvreklsereeeveskleeakeleek 112
                                       +s++++a++++e++r++l+er++e+ +  ee ++le+ 
  gi|557694214|ref|YP_008797268.1| 623 RSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEAR 660
                                       44444444444444444444444444444443333322 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  10.0     0.056        12      33     128 ..     611     704 ..     602     707 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  33 dyeallkeneelkekvkeleeklkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeea 109
                                       ++ +l   +e+l+++v++++++l+e + + e+ k+ l  a+e   ++ a     ae+ +++A+++ e++ ++ e+++
  gi|557694214|ref|YP_008797268.1| 611 EVSRLTGIREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARV-SDAETRVANARAAREEV-KTLENRL 685
                                       5677888899*****************999999*************98876.56899999999988887.899**** PP

                                       XXXXXXXXXXXXXXXXXXX CS
                            DivIVA 110 kkiaeeieelkrqarlfrq 128
                                       ++++++++ l ++  + r+
  gi|557694214|ref|YP_008797268.1| 686 QQLSADVDALDKRLVSLRE 704
                                       **********998877775 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 ?    8.8   2.9     0.008       1.8      22     109 ..     618     704 ..     615     708 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.008
                                       HHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH CS
                         Fib_alpha  22 lqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketid 98 
                                       +++ l +  ++ +++le+ +  lee +++   aee v++++  + ++++  + n ++ ++  k+le++ ++l + +d
  gi|557694214|ref|YP_008797268.1| 618 IREQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVA-NARAAREEVKTLENRLQQLSADVD 693
                                       6677777778888888888999999999999999999999999888888888.788888888889989999999998 PP

                                       CCHHHHHHHHH CS
                         Fib_alpha  99 aqesnirvLqn 109
                                       a  +++  L++
  gi|557694214|ref|YP_008797268.1| 694 ALDKRLVSLRE 704
                                       88888888876 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       6.6   1.5e+03      37      77 ..     506     549 ..     496     568 .. 0.60
   2 ?    5.8   2.6     0.037       8.2      58     104 ..     619     668 ..     612     672 .. 0.74
   3 ?    5.0   0.3     0.065        14     197     228 ..     673     704 ..     667     712 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 6.6
                           DUF4618  37 akkvrklLqqyek.lktvisilekss..kkqleqakaeLqewee 77 
                                          +  lLq ye+ ++t+ s+l +++   +++ ++++ L++ ++
  gi|557694214|ref|YP_008797268.1| 506 RATIILLLQNYEQnMQTILSTLRQNNinPNDIPELNEVLNSAKT 549
                                       45555678888753667777777665113456666666655555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.037
                           DUF4618  58 eksskkqleqakaeLqeweekeek...klekLeqqleqlnakvqklqeel 104
                                        ++ ++++e+a++eL+e    +e+   +l+  e++++ql+a+v  +++ +
  gi|557694214|ref|YP_008797268.1| 619 REQLRSEVEKAQRELEEARAALEErkrELAGAEEEVRQLEARVSDAETRV 668
                                       556678999999999999877665111555668999****9999887665 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.065
                           DUF4618 197 kfrefieeleeeipeLkaeveqLqaqaeepre 228
                                         re++++le+++++L a+v++L ++    re
  gi|557694214|ref|YP_008797268.1| 673 AAREEVKTLENRLQQLSADVDALDKRLVSLRE 704
                                       679999****************9998887776 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 ?    6.2   6.4     0.047        10      15      66 ..     620     671 ..     618     674 .. 0.80
   2 ?    4.9   0.6      0.12        26      39      66 ..     675     702 ..     667     707 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.047
                        TMF_DNA_bd  15 aqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleel 66 
                                       +qL++E ek + +  + ++++ + + +++ +e+e+++l+ ++++ e  +++ 
  gi|557694214|ref|YP_008797268.1| 620 EQLRSEVEKAQRELEEARAALEERKRELAGAEEEVRQLEARVSDAETRVANA 671
                                       5888888888888888888888888888888888888888888888777765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.12
                        TMF_DNA_bd  39 rkknkelekeikelkkkleklekeleel 66 
                                       r+++k le+ +++l+  ++ l+k l +l
  gi|557694214|ref|YP_008797268.1| 675 REEVKTLENRLQQLSADVDALDKRLVSL 702
                                       4555555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (747 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1564  (0.087233); expected 358.6 (0.02)
Passed bias filter:                     1099  (0.0612973); expected 358.6 (0.02)
Passed Vit filter:                       287  (0.0160076); 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):              81  [number of targets reported over threshold]
# CPU time: 1.26u 0.34s 00:00:01.60 Elapsed: 00:00:00.51
# Mc/sec: 4447.25
//
Query:       gi|557694215|ref|YP_008797269.1|  [L=716]
Description: hypothetical protein CSUB_C0781 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-05   23.3   0.0    6.9e-05   22.6   0.0    1.3  1  Reprolysin_4     Metallo-peptidase family M12B Reprolysin-lik
    4.6e-05   22.8  18.7     0.0011   18.3  16.6    2.2  2  GAS              Growth-arrest specific micro-tubule binding
    6.2e-05   22.7   4.2    6.2e-05   22.7   4.2    1.4  1  Exonuc_VII_L     Exonuclease VII, large subunit
    9.5e-05   22.6   0.5    0.00038   20.7   0.0    2.0  1  Reprolysin_5     Metallo-peptidase family M12
    9.7e-05   21.8   4.8    0.00013   21.3   4.8    1.2  1  TMPIT            TMPIT-like protein
    0.00022   21.5  15.8    0.00056   20.2  15.8    1.6  1  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
    0.00067   20.0  11.2     0.0014   19.0  11.2    1.5  1  CENP-H           Centromere protein H (CENP-H)
     0.0011   19.0  11.0     0.0021   18.1  11.0    1.3  1  Laminin_II       Laminin Domain II
     0.0013   18.0   0.3     0.0013   18.0   0.3    2.0  2  DUF4953          Met-zincin
     0.0014   19.1   0.6     0.0029   18.1   0.0    1.8  1  Reprolysin_3     Metallo-peptidase family M12B Reprolysin-lik
     0.0022   17.2  10.5     0.0035   16.5  10.5    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
     0.0024   17.7  18.3     0.0041   17.0  18.3    1.2  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
     0.0027   18.2  17.9     0.0079   16.7  17.9    1.8  1  APG6_N           Apg6 coiled-coil region
      0.003   16.5   8.3     0.0041   16.1   8.3    1.1  1  DUF812           Protein of unknown function (DUF812)
     0.0034   17.0  11.7     0.0064   16.1  11.7    1.3  1  Filament         Intermediate filament protein
     0.0071   16.2   0.0      0.015   15.1   0.0    1.5  1  Peptidase_M10    Matrixin
     0.0076   16.6  10.8      0.021   15.2  10.8    1.7  1  OmpH             Outer membrane protein (OmpH-like)
  ------ inclusion threshold ------
      0.014   14.1   6.3       0.02   13.5   6.3    1.2  1  FapA             Flagellar Assembly Protein A
      0.021   13.4  14.5       0.03   12.9  14.5    1.1  1  Macoilin         Macoilin family
      0.022   13.7   1.0      0.033   13.1   1.0    1.2  1  LMBR1            LMBR1-like membrane protein
      0.022   14.4  13.6      0.017   14.7  12.2    1.4  1  DUF4795          Domain of unknown function (DUF4795)
      0.027   14.7  16.2      0.051   13.8  16.2    1.4  1  ATG16            Autophagy protein 16 (ATG16)
      0.028   14.3   0.0      0.054   13.4   0.0    1.4  1  Reprolysin       Reprolysin (M12B) family zinc metalloproteas
      0.029   13.1  12.2      0.042   12.6  12.2    1.1  1  WEMBL            Weak chloroplast movement under blue light
      0.031   13.9   0.1      0.056   13.1   0.1    1.3  1  Astacin          Astacin (Peptidase family M12A)
      0.034   13.4   8.7      0.059   12.7   8.7    1.3  1  CorA             CorA-like Mg2+ transporter protein
      0.036   12.6   4.0      0.073   11.6   4.0    1.4  1  FUSC             Fusaric acid resistance protein family
      0.048   13.7   0.1       0.17   11.9   0.0    1.9  1  Peptidase_M54    Peptidase family M54
      0.058   13.0   0.0       0.13   11.8   0.0    1.5  1  Peptidase_M57    Dual-action HEIGH metallo-peptidase
      0.058   12.3  12.3        0.1   11.6  12.3    1.3  1  IFT57            Intra-flagellar transport protein 57
      0.064   13.3  21.1       0.47   10.5  21.1    2.1  1  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
      0.068   13.5  13.0        1.1    9.6   4.3    2.6  2  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.077   12.9   5.7       0.12   12.3   5.7    1.3  1  FTA4             Kinetochore complex Fta4 of Sim4 subunit, or
      0.087   12.2  10.1       0.15   11.4  10.1    1.3  1  DUF4407          Domain of unknown function (DUF4407)
      0.087   12.5   7.4       0.22   11.2   7.4    1.6  1  SHE3             SWI5-dependent HO expression protein 3
      0.098   12.1   7.6       0.22   10.9   7.6    1.5  1  Not3             Not1 N-terminal domain, CCR4-Not complex com
      0.099   12.9  15.5        0.8   10.0   3.6    2.4  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.12   12.2   9.0       0.29   10.9   9.0    1.7  1  She9_MDM33       She9 / Mdm33 family
       0.12   12.8  16.5       0.29   11.5  16.5    1.6  1  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
       0.14   11.3   6.7       0.38    9.8   6.7    1.7  1  Effector_1       Effector from type III secretion system
       0.15   12.9  16.2       0.26   12.2  13.9    2.2  2  PRKG1_interact   cGMP-dependent protein kinase interacting do
       0.19   11.2  12.0       0.37   10.3  12.0    1.4  1  DegS             Sensor protein DegS
        0.2   11.5   7.9        0.4   10.5   7.9    1.4  1  PCRF             PCRF domain
       0.21   11.3  13.1       0.48   10.1  13.1    1.5  1  DUF4201          Domain of unknown function (DUF4201)
       0.22   11.6  23.3        0.6   10.2  23.3    1.6  1  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.27   11.6  11.5        4.3    7.8   2.2    3.0  2  FlaC_arch        Flagella accessory protein C (FlaC)
       0.27   10.3  10.2        0.4    9.7  10.2    1.1  1  AIP3             Actin interacting protein 3
       0.28   11.5  18.3        0.9    9.9  18.3    1.7  1  HrpB7            Bacterial type III secretion protein (HrpB7)
       0.29    9.4  11.4       0.41    8.9  11.4    1.1  1  CCD48            Coiled-coil domain-containing protein 48
       0.29   11.5  15.9        0.3   11.4   6.5    2.6  2  Tup_N            Tup N-terminal
       0.31   11.5  15.0        6.2    7.3   3.3    3.8  4  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
       0.32   10.7   5.2        1.5    8.6   0.3    2.5  2  3-PAP            Myotubularin-associated protein
       0.32   10.0  11.7        0.5    9.3  11.7    1.2  1  Perilipin        Perilipin family
       0.34   10.5   9.6       0.55    9.8   9.6    1.2  1  Phage_GPO        Phage capsid scaffolding protein (GPO) serin
       0.35   11.0  17.5        1.1    9.3  17.2    1.9  1  BRE1             BRE1 E3 ubiquitin ligase
       0.35   10.6  14.4       0.67    9.6  14.4    1.4  1  DUF745           Protein of unknown function (DUF745)
       0.36   10.9  11.5       0.64   10.1   3.9    2.4  2  DUF1664          Protein of unknown function (DUF1664)
       0.38   10.2  16.4       0.67    9.4  16.4    1.3  1  HMMR_N           Hyaluronan mediated motility receptor N-term
       0.39   10.5  12.0       0.72    9.6  12.0    1.4  1  DUF724           Protein of unknown function (DUF724)
       0.39   10.9   2.5       0.89    9.7   2.4    1.7  1  CwsA             Cell wall synthesis protein CwsA
        0.4   10.7   4.2         10    6.1   4.2    2.5  1  ApoO             Apolipoprotein O
       0.43   10.0  16.4       0.83    9.1  16.4    1.4  1  Golgin_A5        Golgin subfamily A member 5
       0.46   10.4  19.7         31    4.6  19.9    2.8  1  Prefoldin_2      Prefoldin subunit
       0.47    8.5  15.0       0.67    8.0  15.0    1.1  1  HOOK             HOOK protein
       0.48   10.2   5.3       0.76    9.5   5.3    1.2  1  AAA_11           AAA domain
       0.51    7.8  15.0       0.79    7.2  15.0    1.2  1  DUF3584          Protein of unknown function (DUF3584)
       0.74    8.5  19.4        2.6    6.7  19.4    1.7  1  HAUS5            HAUS augmin-like complex subunit 5
       0.74   10.1   7.2        3.8    7.8   0.8    2.7  2  XhlA             Haemolysin XhlA
       0.76    7.9  12.7        2.3    6.3  12.6    1.5  1  EzrA             Septation ring formation regulator, EzrA
       0.77    8.6  20.3        2.9    6.7  20.3    1.8  1  Spc7             Spc7 kinetochore protein
       0.78    9.9  14.8      0.072   13.3   2.9    2.6  2  JIP_LZII         JNK-interacting protein  leucine zipper II
        0.9    9.1   7.2          2    8.0   7.2    1.6  1  PEARLI-4         Arabidopsis phospholipase-like protein (PEAR
       0.99    9.5  19.5        0.6   10.2   8.3    2.2  2  Tropomyosin_1    Tropomyosin like
          1    9.5   5.3          2    8.5   5.3    1.4  1  DUF4337          Domain of unknown function (DUF4337)
        1.2    9.0  16.4       0.78    9.6  12.6    2.4  1  DASH_Spc19       Spc19
        1.2    9.1  22.4        2.5    8.2  10.9    2.4  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
        1.5    9.0  13.2        3.3    7.9  13.2    1.6  1  Fib_alpha        Fibrinogen alpha/beta chain family
        1.5    8.9  12.0        3.1    7.9  12.0    1.5  1  UPF0242          Uncharacterised protein family (UPF0242) N-t
        1.5    7.3  11.6        5.5    5.5  11.4    1.6  1  AAA_13           AAA domain
        1.8    7.7  17.0        7.2    5.8  17.0    1.7  1  DUF2046          Uncharacterized conserved protein H4 (DUF204
        2.1    8.5  25.1        3.5    7.8   5.0    3.7  3  bZIP_2           Basic region leucine zipper
        2.2    8.5  17.7        4.1    7.6   0.6    2.7  2  Cnn_1N           Centrosomin N-terminal motif 1
        2.3    8.1  16.8       0.22   11.5   9.2    2.2  2  Wtap             WTAP/Mum2p family
        2.5    7.4   9.3        4.3    6.6   9.3    1.3  1  FAM76            FAM76 protein
        2.5    8.2  20.8         33    4.5  20.3    2.1  1  ADIP             Afadin- and alpha -actinin-Binding
        2.6    8.8  13.6         62    4.3  12.4    2.6  1  DUF2203          Uncharacterized conserved protein (DUF2203)
        2.6    8.5  12.5         15    6.0   6.7    2.3  2  T3SSipB          Type III cell invasion protein SipB
        2.7    5.9   6.9          4    5.3   6.9    1.1  1  Prominin         Prominin
        2.7    8.1  16.2        4.2    7.5   0.7    3.0  2  Cep57_CLD_2      Centrosome localisation domain of PPC89
        2.8    8.2  18.8        2.2    8.5  14.1    2.3  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
        3.1    7.9  15.2        1.1    9.5   1.0    2.7  2  Med9             RNA polymerase II transcription mediator com
        3.5    7.8   9.4        3.8    7.6   5.7    2.4  2  DUF2730          Protein of unknown function (DUF2730)
        3.6    5.3  11.7        5.5    4.7  11.7    1.2  1  Nup88            Nuclear pore component
        3.6    8.0  11.3        7.3    7.0  11.3    1.5  1  Syntaxin_2       Syntaxin-like protein
        3.8    7.6  21.7          2    8.5  18.5    2.1  1  Mod_r            Modifier of rudimentary (Mod(r)) protein
        4.3    7.5  15.2          2    8.6   7.1    2.2  2  Uds1             Up-regulated During Septation
        4.5    6.2   5.7          8    5.4   5.7    1.3  1  ArAE_2_N         Putative ER transporter, 6TM, N-terminal
        4.5    6.6   9.3        9.6    5.5   9.3    1.4  1  Phlebovirus_NSM  Phlebovirus nonstructural protein NS-M
        4.6    6.4  20.2       0.29   10.4   8.0    2.3  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
        5.3    7.0  13.7         21    5.1  13.7    1.8  1  DUF1640          Protein of unknown function (DUF1640)
        5.4    6.2   7.3          4    6.6   5.6    1.5  1  ISG65-75         Invariant surface glycoprotein
        5.5    7.2  12.7       0.61   10.2   3.1    3.1  2  Myc-LZ           Myc leucine zipper domain
        6.1    6.7  14.7       0.28   11.0   3.3    2.5  2  betaPIX_CC       betaPIX coiled coil
        6.4    6.0  18.8       0.68    9.2   9.4    2.2  2  DUF4763          Domain of unknown function (DUF4763)
        6.8    6.7  10.5       0.87    9.6   1.0    3.2  2  Nas2_N           Nas2 N_terminal domain
        7.2    5.9  14.3         12    5.3  14.3    1.2  1  Cluap1           Clusterin-associated protein-1
        7.5    4.3   7.6         12    3.7   7.6    1.2  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        7.8    6.4  26.0         10    6.1  15.4    2.6  2  YscO             Type III secretion protein YscO
        8.9    7.0  18.9         18    6.0  12.1    2.4  2  BST2             Bone marrow stromal antigen 2
         10    6.3  18.5         10    6.3   9.9    2.5  2  DUF3847          Protein of unknown function (DUF3847)


Domain annotation for each model (and alignments):
>> 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 !   22.6   0.0   4.2e-07   6.9e-05     125     177 ..     403     461 ..     371     466 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.2e-07
                      Reprolysin_4 125 kasgvaasrdeydi.fAHEiGHtfGaaHdlsdegegl.sskt....eegsgqtIMsyas 177
                                        as ++   ++  + +AHEiGHt+G+ H  +d  e + s+k      ++s +t M y  
  gi|557694215|ref|YP_008797269.1| 403 AASYYSLLYEGLAVtVAHEIGHTLGLRHPHDDFDESTeSEKWyrwiYTDSMETFMVYST 461
                                       334444445677777*************9986555553555467779999999999976 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 ?    4.2   0.0      0.15        24     151     186 ..     496     531 ..     493     543 .. 0.87
   2 !   18.3  16.6   6.9e-06    0.0011      27     119 ..     597     689 ..     580     695 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.15
                               GAS 151 lkalqeelEkkeaqleevlaaanldpaalsavsekl 186
                                       ++ l ++ Ek+ aq+ e+l++a+l+p++l +++  l
  gi|557694215|ref|YP_008797269.1| 496 ISLLLQDYEKNYAQILETLSNAGLRPDDLPQLKTVL 531
                                       5678899*********************98887665 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 6.9e-06
                               GAS  27 lIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkd 103
                                        I++l++e+e l +  e++++   e++++ ++ ++++ +a++  ++Lr +l++ ek+ ++l +l +r +ele+e+ +
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELESEVDK 673
                                       47788888888888888888888888888888888888888888888888888888888888888888888888888 PP

                               GAS 104 lkwehevleqrfekve 119
                                       l+++  + + +++++e
  gi|557694215|ref|YP_008797269.1| 674 LEQKLSQARNEVTQLE 689
                                       8877777777777666 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 !   22.7   4.2   3.8e-07   6.2e-05     164     273 ..     580     702 ..     505     709 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 3.8e-07
                      Exonuc_VII_L 164 l...........eekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerlkekleekk 229
                                       +           ++   ++e+l+++++s ++ le++rq+ +e+ee++++ +++q+ ++r+r  +l++rl  +le+++
  gi|557694215|ref|YP_008797269.1| 580 MklyveavllgnKRLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQ-VTQQIVEARNRAAQLRDRLA-QLEKEA 654
                                       0444444444444444678999999999999999999999999999999.89999999999999999994.477777 PP

                      Exonuc_VII_L 230 erlkklkerle....lleekkerleeleeklealsplkvLkrGyaivr 273
                                       ++l +l +r +    ++++ +++l+++ +++++l+ +++   G a+v 
  gi|557694215|ref|YP_008797269.1| 655 ADLPQLMQRKTelesEVDKLEQKLSQARNEVTQLETMNMVMMGVAVVL 702
                                       777555444444447799999999999999999999999999999885 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.3e-06   0.00038     143     189 ..     415     462 ..     373     483 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-06
                      Reprolysin_5 143 vqvvaHElGHnfGavHDcdsssesqsCslsn...stepaggryiMapsss 189
                                       + +vaHE+GH++G +H +d+   + s+  ++       ++ ++ M +s++
  gi|557694215|ref|YP_008797269.1| 415 AVTVAHEIGHTLGLRHPHDDF--DESTESEKwyrWIYTDSMETFMVYSTT 462
                                       679*************66665..233322223345566666666666665 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   4.8   8.1e-07   0.00013       3     109 ..     597     712 ..     595     716 .] 0.84

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.1e-07
                             TMPIT   3 eweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk.........eeeeeevee 70 
                                       e+e+l++e+++l+++ ++ +q   e ++++++++++i + ++r+ +l+++l +l+k++          +e e+ev++
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAAdlpqlmqrkTELESEVDK 673
                                       78889999999999999999999999999999999999999999999999999998866677777777888999*** PP

                             TMPIT  71 lkeelkerkkvlkevesllpkknglylklvlGnvnvsll 109
                                       l+++l+++++ + ++e +     g+ + l+ G   v ll
  gi|557694215|ref|YP_008797269.1| 674 LEQKLSQARNEVTQLETMNMVMMGVAVVLFAGAGGVFLL 712
                                       ************999999888888888888887776666 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 !   20.2  15.8   3.4e-06   0.00056      39     145 ..     585     687 ..     583     697 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 3.4e-06
                     Jnk-SapK_ap_N  39 eslasrneeeeaeleelreeleqLeteyerekelrkraeeeleeiedqw...eeerkelqekveqleeenrelelka 112
                                       e+++  n++   e+e+lr+e+e+L + +e+ ++++ +aee++ ++ +q+   ++++ +l+++++qle+e   l    
  gi|557694215|ref|YP_008797269.1| 585 EAVLLGNKRLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIveaRNRAAQLRDRLAQLEKEAADLP--- 658
                                       67778899999************************************973335556678888888888877666... PP

                     Jnk-SapK_ap_N 113 knaadqlsrleekeaelkkeysklheretellk 145
                                           + ++r  e e+e+ k ++kl++  +e+ +
  gi|557694215|ref|YP_008797269.1| 659 ----QLMQRKTELESEVDKLEQKLSQARNEVTQ 687
                                       ....33444444444444444444444444433 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 !   19.0  11.2   8.9e-06    0.0014       3      83 ..     600     686 ..     594     705 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.9e-06
                            CENP-H   3 plieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek......eklkeeleklea 73 
                                       +l ++ + ls++l++  q+ +e++e++++v++++++++++ ++l  +l++l+ke++         ++l++e++kle+
  gi|557694215|ref|YP_008797269.1| 600 QLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPqlmqrkTELESEVDKLEQ 676
                                       45567889****************************************99999999988898888778999999999 PP

                            CENP-H  74 elkksrqrwr 83 
                                       +l ++r++++
  gi|557694215|ref|YP_008797269.1| 677 KLSQARNEVT 686
                                       9999988776 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1  11.0   1.3e-05    0.0021      19     104 ..     598     683 ..     582     689 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHHHHH CS
                        Laminin_II  19 laplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdnisei 95 
                                       +++l q++e ++++l+++++   e +e++++ +++i++Ar+   +L   + qL++    l ql + +  l  +++++
  gi|557694215|ref|YP_008797269.1| 598 IEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELESEVDKL 674
                                       68999****************9********************************************999******** PP

                                       HHHHHHHHH CS
                        Laminin_II  96 kelIaqARk 104
                                        +  +qAR+
  gi|557694215|ref|YP_008797269.1| 675 EQKLSQARN 683
                                       ********7 PP

>> DUF4953  Met-zincin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.3   8.1e-06    0.0013       8      29 ..     409     430 ..     405     433 .. 0.89
   2 ?   -1.8   1.1       8.3   1.4e+03     209     286 ..     618     641 ..     573     694 .. 0.51

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.1e-06
                           DUF4953   8 lmgallrfvvaHEvGhtLGLrh 29 
                                       l+ + l+  vaHE+GhtLGLrh
  gi|557694215|ref|YP_008797269.1| 409 LLYEGLAVTVAHEIGHTLGLRH 430
                                       567889999************* PP

  == domain 2  score: -1.8 bits;  conditional E-value: 8.3
                           DUF4953 209 nrkkkgdegrpyepvpkekQkeAldfllkevfepdalatpewllnllektgldydpvdrvealqssvlseLlsperl 285
                                       +++++                                                    ++++++ +++++   +++r+
  gi|557694215|ref|YP_008797269.1| 618 AKTEA---------------------------------------------------EEQINQVTQQIVE---ARNRA 640
                                       11111...................................................1111111111111...12222 PP

                           DUF4953 286 a 286
                                       a
  gi|557694215|ref|YP_008797269.1| 641 A 641
                                       2 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 !   18.1   0.0   1.8e-05    0.0029      99     123 ..     408     430 ..     367     431 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.8e-05
                      Reprolysin_3  99 gssvlgkvgadtvaHEiGHnfganH 123
                                       +   l ++ a tvaHEiGH +g++H
  gi|557694215|ref|YP_008797269.1| 408 SL--LYEGLAVTVAHEIGHTLGLRH 430
                                       22..3344569************** 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  10.5   2.1e-05    0.0035      53     131 ..     593     680 ..     575     693 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-05
                             Atg14  53 e...eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk......kRrsdles 120
                                       +   e eql++++++++++le+ ++ + + +e+++++ +++ + + + ++ + +la+l ++ +      +R+ +les
  gi|557694215|ref|YP_008797269.1| 593 RlmpEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAAdlpqlmQRKTELES 669
                                       2555668999999*********************************************99999******88888888 PP

                             Atg14 121 lqneleerrkk 131
                                         ++le++  +
  gi|557694215|ref|YP_008797269.1| 670 EVDKLEQKLSQ 680
                                       88888776444 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 !   17.0  18.3   2.5e-05    0.0041      28     132 ..     581     692 ..     577     699 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.5e-05
                          KASH_CCD  28 kkavetaeetnakLteeieeLkkklkstQqalqkaklleeElee.lkalvkeleEkra...rlkaqnkqlekenqsL 100
                                       k  ve++   n++L+ eie+L++ + s+ q+l++a+  + E ee + ++++++ E r+   +l  +  qleke   L
  gi|557694215|ref|YP_008797269.1| 581 KLYVEAVLLGNKRLMPEIEQLRQEVESLSQSLEQARQAKTEAEEqINQVTQQIVEARNraaQLRDRLAQLEKEAADL 657
                                       5678888889*******************************9983455556666655511155667789****9865 PP

                          KASH_CCD 101 ...iakiesLqeenikllaekdelkkklkeLlkek 132
                                          +++ ++L+ e  kl +  ++ ++ + +L +++
  gi|557694215|ref|YP_008797269.1| 658 pqlMQRKTELESEVDKLEQKLSQARNEVTQLETMN 692
                                       11155556899999999999999999999998776 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7  17.9   4.9e-05    0.0079      16     114 ..     596     692 ..     589     695 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.9e-05
                            APG6_N  16 kqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeele 92 
                                        ++eq+++e +++++ l++ ++ k+e+e   e++++  +++ + ++  ++l   L++leke ++l + ++  +e ++
  gi|557694215|ref|YP_008797269.1| 596 PEIEQLRQEVESLSQSLEQARQAKTEAE---EQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELES 669
                                       5899*****************9988866...8********************************************* PP

                            APG6_N  93 aleeeeerfwreyne.lqlelle 114
                                       ++++ e++  + +ne  qle ++
  gi|557694215|ref|YP_008797269.1| 670 EVDKLEQKLSQARNEvTQLETMN 692
                                       **************988888775 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   8.3   2.5e-05    0.0041     331     418 ..     597     684 ..     533     691 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.5e-05
                            DUF812 331 eleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalvea 407
                                       e+e+l++++e+l++++e+ ++   + e++i+qv++++ e ++  ++l + ++  +k ++ lp+  +   +L+++v++
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELESEVDK 673
                                       67777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                            DUF812 408 saqrlvelakq 418
                                        +q+l +  ++
  gi|557694215|ref|YP_008797269.1| 674 LEQKLSQARNE 684
                                       77777665544 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1  11.7   3.9e-05    0.0064      63     160 ..     584     686 ..     574     698 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.9e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......X CS
                          Filament  63 ldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdldeatlarvdLekkvesLkee......l 133
                                       ++++   ++rl  e+++lr+e+e l +++e+  + ++e+E++++++ +++ ea  + ++L  ++ +L++e      l
  gi|557694215|ref|YP_008797269.1| 584 VEAVLLGNKRLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEaadlpqL 660
                                       66667778999999999999999999999999999999999999999888888888888888888888763333335 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament 134 aflkkvheeEvkelqkqvseqvlvevd 160
                                       + +k+  e Ev++l++++s q+  ev 
  gi|557694215|ref|YP_008797269.1| 661 MQRKTELESEVDKLEQKLS-QARNEVT 686
                                       5667788888888888884.3333444 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.5e-05     0.015     109     128 ..     414     433 ..     338     437 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.5e-05
                                       HHHHHHHHHHHHTTBESXSS CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 109 lflVaaHEiGHalGLeHssd 128
                                       l + +aHEiGH+lGL+H +d
  gi|557694215|ref|YP_008797269.1| 414 LAVTVAHEIGHTLGLRHPHD 433
                                       556789***********776 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2  10.8   0.00013     0.021      22     124 ..     599     704 ..     571     708 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHH CS
                              OmpH  22 eqlekkfkklqaeleakekelqklqeelqkkakkl.ekeekeqelqkkeqelqqkqqqkaqelqkkqqe...llkpi 94 
                                       eql ++ ++l + le+ +++ ++++e++++ +++  e ++++ +l+++ ++l++  +++  +l++++ e   +++++
  gi|557694215|ref|YP_008797269.1| 599 EQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIvEARNRAAQLRDRLAQLEK-EAADLPQLMQRKTElesEVDKL 674
                                       233333344444444444444444444443334443366666667777777777.5555555666666633344489 PP

                                       HHHHHHHHHHHHHHTT-SEEEE.GGG-S-- CS
                              OmpH  95 ldkinkaikevakekgydlvldsrgavlya 124
                                        +k+ +a +ev + +  ++v+ + ++vl+a
  gi|557694215|ref|YP_008797269.1| 675 EQKLSQARNEVTQLETMNMVMMGVAVVLFA 704
                                       999999999999999999999844555554 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   6.3   0.00013      0.02     314     429 ..     587     700 ..     579     705 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00013
                              FapA 314 kklGselgtkteievgldepelkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkekl 390
                                       + lG++       ++  +  +l ++l++ ++   e ee++++++++i + ++   + ++  +++ ql+k   ++ +l
  gi|557694215|ref|YP_008797269.1| 587 VLLGNKRLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARN---RAAQLRDRLAQLEKEAADLPQL 660
                                       5555544433333335555666777777777777777777777777665555...7788899999999999999999 PP

                              FapA 391 keeleeleeelkelkeeleskkeea.kikvnkeiypgvki 429
                                       +++ +ele e ++l+++l + ++e  ++++ ++++ gv +
  gi|557694215|ref|YP_008797269.1| 661 MQRKTELESEVDKLEQKLSQARNEVtQLETMNMVMMGVAV 700
                                       9999999999999999999997766688888888877765 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9  14.5   0.00018      0.03     460     551 ..     597     690 ..     577     696 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00018
                          Macoilin 460 akqkdkqtlqqlekrLkeekearaslekqLaeekkrkkeeeetaaravalaaasrsecte..slkskkreleaeikk 534
                                       +  + +q++++l + L++ ++a++++e+q+++  ++  e+ ++aa+ +   a+  +e ++   l ++k+ele+e++k
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADlpQLMQRKTELESEVDK 673
                                       556789****************************************99999999999999445899*********** PP

                          Macoilin 535 Lekelklkeeqirelel 551
                                       Le++l  + +++ +le+
  gi|557694215|ref|YP_008797269.1| 674 LEQKLSQARNEVTQLET 690
                                       ************99994 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   1.0    0.0002     0.033     199     332 ..     576     688 ..     500     712 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0002
                             LMBR1 199 deelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklksnenkteeslak 275
                                         +l+kly+ea+ l +++     e+e+l +ev+ l++s+++                        + ++++ee++++
  gi|557694215|ref|YP_008797269.1| 576 ATDLMKLYVEAVLLGNKRLM--PEIEQLRQEVESLSQSLEQAR----------------------QAKTEAEEQINQ 628
                                       55555555555555533322..334433444444444443333......................356678888888 PP

                             LMBR1 276 lekqlikalqkrertekqwkrllekalelediiknksskekefksses...srrgefakq 332
                                        ++q+ +a+++ ++ ++++ +l ++a++l ++++ k++ e e+ ++e+   + r+e+ + 
  gi|557694215|ref|YP_008797269.1| 629 VTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELESEVDKLEQklsQARNEVTQL 688
                                       888888888888888888888888888888888888888888888877664344444332 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7  12.2    0.0001     0.017      11     109 ..     593     690 ..     577     697 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.0001
                           DUF4795  11 klqeaieklqeelekleekvkelekrledkekklealkkqieelekvk.adkeeveeelaekadkeaLatkvsrdqf 86 
                                        l  +ie+l +e+e+l+++ ++  + + + e++++ +++qi e +++  + ++ +++ ++e+ad  +L +    +++
  gi|557694215|ref|YP_008797269.1| 593 RLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAaQLRDRLAQLEKEAADLPQLMQRK--TEL 667
                                       556789**********************************9887766626799************9997654..79* PP

                           DUF4795  87 DeakkeLekmleellekleeqee 109
                                       ++ +++Le++l+++++ +++ e 
  gi|557694215|ref|YP_008797269.1| 668 ESEVDKLEQKLSQARNEVTQLET 690
                                       *****************998775 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8  16.2   0.00031     0.051      25     131 ..     592     691 ..     577     696 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00031
                             ATG16  25 nrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrg... 98 
                                       +rL+  +++l++e ++l+++ ++a++       ++e e++ +q     +++i +  ++ aqlr+ la+l k+ +   
  gi|557694215|ref|YP_008797269.1| 592 KRLMPEIEQLRQEVESLSQSLEQARQ------AKTEAEEQINQ----VTQQIVEARNRAAQLRDRLAQLEKEAAdlp 658
                                       56666777777777777555554443......22222222222....455555666666666666666666555222 PP

                             ATG16  99 elaqrllelneelqkleeklkedeerlaeleae 131
                                       +l qr +el++e++kle+kl++ ++++ +le++
  gi|557694215|ref|YP_008797269.1| 659 QLMQRKTELESEVDKLEQKLSQARNEVTQLETM 691
                                       334455556666666666666666666666655 PP

>> Reprolysin  Reprolysin (M12B) family zinc metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00033     0.054     116     150 ..     399     433 ..     363     462 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00033
                                       TSEEEEE--SSSHHHHHHHHHHHHHHHCT---GHH CS
                        Reprolysin 116 ksggvaedkkknlealavilaqeLghnlGlthdee 150
                                        +++ a++ +   e+lav++a+e+gh lGl+h ++
  gi|557694215|ref|YP_008797269.1| 399 AATAAASYYSLLYEGLAVTVAHEIGHTLGLRHPHD 433
                                       5677788888899*****************98554 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 ?   12.6  12.2   0.00025     0.042     175     268 ..     591     687 ..     568     696 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00025
                             WEMBL 175 skevekaveeltielialkesLesahaahleaeEkrlgaa..l.areqdklnwekeLkqaeeelqrLneellsakdl 248
                                        k    ++e+l  e+ +l +sLe a+ a +eaeE+  ++   +   ++  +++++ L q e+e   L + ++ +++l
  gi|557694215|ref|YP_008797269.1| 591 NKRLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTqqIvEARNRAAQLRDRLAQLEKEAADLPQLMQRKTEL 667
                                       555666899*************************9655431140445556788999********************* PP

                             WEMBL 249 kskletasallldLkaeLaa 268
                                       +s++++ +++l + ++e++ 
  gi|557694215|ref|YP_008797269.1| 668 ESEVDKLEQKLSQARNEVTQ 687
                                       *************9999876 PP

>> Astacin  Astacin (Peptidase family M12A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00034     0.056      82     126 ..     417     461 ..     412     470 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00034
                                       HHHHHHHHHHTB--GGGSTTGGGTEEE-GGGB-TT-GGGC----C CS
                           Astacin  82 iivHElmHalGffHeqsRtdrdeyvsinkeniekgqeenfekvds 126
                                       +++HE++H+lG+ H +  +d     + +++ i ++++e f ++++
  gi|557694215|ref|YP_008797269.1| 417 TVAHEIGHTLGLRHPHDDFDESTESEKWYRWIYTDSMETFMVYST 461
                                       799**************9999988888888888888888887775 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   8.7   0.00036     0.059     120     224 ..     591     694 ..     577     699 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00036
                              CorA 120 vdrlfellekleeeldeledel..edstkkeilrelaqlrrrlvklrralapnrevlkrlla.kaddkllddedkey 193
                                       ++rl +++e+l +e++ l++ l   ++ k e  +++ q+ +++v+ r  +a++r+ l +l +  ad ++l +    +
  gi|557694215|ref|YP_008797269.1| 591 NKRLMPEIEQLRQEVESLSQSLeqARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKeAADLPQLMQ----R 663
                                       789999****************8666667777788999999****************777775444444444....4 PP

                              CorA 194 lrdlldelerllemlealrerleslqdtyss 224
                                         +l++e+++l+++l++ r+ +++l    + 
  gi|557694215|ref|YP_008797269.1| 664 KTELESEVDKLEQKLSQARNEVTQLETMNMV 694
                                       4899999999999999999999999766655 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.0   0.00045     0.073     252     363 ..     594     710 ..     576     713 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00045
                              FUSC 252 avpelaallaelaaleaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslraleaai 328
                                        +pe+++l +e+++l  +++ e+ ++a ++ +++++++ ++  +++++aa l  rla+l +e+a+l + +++ ++  
  gi|557694215|ref|YP_008797269.1| 594 LMPEIEQLRQEVESL--SQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELE 668
                                       445566666666663..445666666666666666666666666666666666666666666666666666666666 PP

                              FUSC 329 aa.......arraerlarhrdhlaallnglraalaillaglf 363
                                       ++         +a+  +++ +++ +++ g+ ++l + ++g+f
  gi|557694215|ref|YP_008797269.1| 669 SEvdkleqkLSQARNEVTQLETMNMVMMGVAVVLFAGAGGVF 710
                                       666556554333344578888888888888888888888777 PP

>> Peptidase_M54  Peptidase family M54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     0.001      0.17     143     165 ..     412     434 ..     358     443 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.001
                                       HHHHHHHHHHHHHHTT----S-T CS
                     Peptidase_M54 143 ervvkevlhelGhlyGLshCked 165
                                       e     v he+Gh++GL h ++d
  gi|557694215|ref|YP_008797269.1| 412 EGLAVTVAHEIGHTLGLRHPHDD 434
                                       5566689************9987 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 ?   11.8   0.0   0.00081      0.13     137     150 ..     418     431 ..     394     441 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00081
                     Peptidase_M57 137 ithelGhtvGlRhs 150
                                       + he+Ght+GlRh 
  gi|557694215|ref|YP_008797269.1| 418 VAHEIGHTLGLRHP 431
                                       78**********94 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6  12.3   0.00062       0.1     267     353 ..     600     690 ..     593     697 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00062
                             IFT57 267 ylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemeergssmtDg....splvkikk 339
                                       +l +++e+l q +++a++  +e++e+++q+++++ e ++  a++ ++l ++++e  +  + m       s + k+ +
  gi|557694215|ref|YP_008797269.1| 600 QLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKteleSEVDKLEQ 676
                                       5788999999999999999999999999999999999999999999999999999998887766611124567999* PP

                             IFT57 340 altklkkEikqmdv 353
                                        l++ ++E+ q++ 
  gi|557694215|ref|YP_008797269.1| 677 KLSQARNEVTQLET 690
                                       **********9986 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 ?   10.5  21.1    0.0029      0.47      24     104 ..     596     693 ..     590     698 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0029
                    CENP-F_leu_zip  24 dkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr.................seke 83 
                                         +e+L +e+e + +++e++   + ++ ++++++ ++i e +++  +l+  L++l                  se +
  gi|557694215|ref|YP_008797269.1| 596 PEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEkeaadlpqlmqrkteleSEVD 672
                                       56777777777777777777777777777777777777777777777777777777222222244455555555555 PP

                    CENP-F_leu_zip  84 eLekelqkkqervseLeslns 104
                                       +Le++l + +++v +Le++n+
  gi|557694215|ref|YP_008797269.1| 673 KLEQKLSQARNEVTQLETMNM 693
                                       555555555555555555554 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   2.1     0.029       4.7      29      69 ..     591     631 ..     590     635 .. 0.89
   2 ?    9.6   4.3    0.0068       1.1      29      79 ..     638     690 ..     631     694 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.029
                           BLOC1_2  29 Neaasekykklkdvaaslekkleklnekyeelqpylqqidq 69 
                                       N++ + ++++l+++++sl+++le+ ++ + e +++++q+ q
  gi|557694215|ref|YP_008797269.1| 591 NKRLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQ 631
                                       777788999******************99999999998865 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0068
                           BLOC1_2  29 Neaase..kykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                       N+aa+   + ++l+++aa+l + +++  e++ e++++ q++ q  ++vt+Le+
  gi|557694215|ref|YP_008797269.1| 638 NRAAQLrdRLAQLEKEAADLPQLMQRKTELESEVDKLEQKLSQARNEVTQLET 690
                                       33333211345555555555555555555555555555555555555555554 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   5.7   0.00073      0.12      99     197 ..     596     697 ..     503     700 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00073
                              FTA4  99 k.....eelIkeLPesweveekeaeeepleallerYaelrarLielserrqqlqarlarlrklkallepflgs.... 166
                                             ++ +++L +s e    +a+++++ea  e+ +++ ++++e ++r  ql++rla+l+k  a l ++++     
  gi|557694215|ref|YP_008797269.1| 596 PeieqlRQEVESLSQSLE----QARQAKTEA-EEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRktel 667
                                       133333566777777776....333333344.6889**************************999999998887887 PP

                              FTA4 167 edpqesvqenlvtrdgeleaElermRvLlar 197
                                       e++ ++ +++l   ++e++ +le m++ +  
  gi|557694215|ref|YP_008797269.1| 668 ESEVDKLEQKLSQARNEVT-QLETMNMVMMG 697
                                       8888888888888888875.68888887765 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  10.1   0.00092      0.15     138     239 ..     594     684 ..     585     699 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00092
                           DUF4407 138 leaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakldatarlaa 214
                                       l  +i++l++e++++++ l+++r++ ++  ++     +++v        e+++ +++++ +la+l+++   +a+l++
  gi|557694215|ref|YP_008797269.1| 594 LMPEIEQLRQEVESLSQSLEQARQAKTEAEEQ-----INQVTQ---QIVEARNRAAQLRDRLAQLEKE---AADLPQ 659
                                       55678899999999999999998877744333.....232333...4444555666666666666666...666666 PP

                           DUF4407 215 lraelaeleaerakeraasqaaaaa 239
                                       l ++++ele+e +k +++  +a+++
  gi|557694215|ref|YP_008797269.1| 660 LMQRKTELESEVDKLEQKLSQARNE 684
                                       6666666666666666666665554 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   7.4    0.0013      0.22       5      91 ..     605     694 ..     582     699 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHH CS
                              SHE3   5 IesLHeqiDaLtktnlqLtqqsqeLleklelaqkkeskflenlaslkhENdnLsslLkRKer...rlkdlekelsel 78 
                                       +esL + + +  +  ++  +q ++ +++   a ++ +++ + la+l +E   L  l++RK+     +  le++ls+ 
  gi|557694215|ref|YP_008797269.1| 605 VESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTElesEVDKLEQKLSQA 681
                                       34444444444444555566778888888889999999999999999999999999999974222677777777777 PP

                                       HHHHHHHHHHHHH CS
                              SHE3  79 kesveelklekkq 91 
                                       +++v +l++ +  
  gi|557694215|ref|YP_008797269.1| 682 RNEVTQLETMNMV 694
                                       7777777666655 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 ?   10.9   7.6    0.0013      0.22     135     216 ..     594     677 ..     583     694 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0013
                              Not3 135 Lneqvekleaeieklsskkkkkkk.skeka.rveeleklierhkfhieklelllrlleneelepeevekikedieyy 209
                                       L  ++e+l++e+e+ls++ ++ ++ ++e + ++++++++i + +   ++l++ l +le+e+ +  ++++ k ++e  
  gi|557694215|ref|YP_008797269.1| 594 LMPEIEQLRQEVESLSQSLEQARQaKTEAEeQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELESE 670
                                       5566788888888887777555543333334999****************************999999999999999 PP

                              Not3 210 vesnqde 216
                                       v++ +++
  gi|557694215|ref|YP_008797269.1| 671 VDKLEQK 677
                                       9887765 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 ?   10.0   3.6    0.0049       0.8      67     104 ..     596     633 ..     588     636 .. 0.77
   2 ?    7.5   5.7     0.028       4.6      43     100 ..     631     688 ..     628     691 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0049
                                       S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                      Seryl_tRNA_N  67 edaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                        ++e+l++ev++l++ l+++ ++ +e+e+++++++++i
  gi|557694215|ref|YP_008797269.1| 596 PEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQI 633
                                       57888888888888888888888888888888888877 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  43 veleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                       +++ e++++  +l    +++ k+ +d  +l+++  el  e+++le++l+++++e+++l
  gi|557694215|ref|YP_008797269.1| 631 QQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELESEVDKLEQKLSQARNEVTQL 688
                                       5666777888888899999999999**************************9999875 PP

>> She9_MDM33  She9 / Mdm33 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   9.0    0.0018      0.29      31     125 ..     597     690 ..     592     703 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0018
                        She9_MDM33  31 eieklkksieeleeeleeakeevreakeayeeaiekrsksqrevneLLqRkssWspedlerftelyrkdhanekeee 107
                                       eie+l++++e+l ++le+a+++ +ea e+ ++++++  ++     +L +R  +  +++ +   +l+++ +++e+e++
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQL-EKEAADLPQLMQRKTELESEVD 672
                                       7************************************99999999999998876.5667788999999999999999 PP

                        She9_MDM33 108 eakeklkeaeakeeelse 125
                                       ++++kl++a +++ +l++
  gi|557694215|ref|YP_008797269.1| 673 KLEQKLSQARNEVTQLET 690
                                       999999999988887654 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 ?   11.5  16.5    0.0018      0.29      16     112 ..     597     687 ..     589     692 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0018
                       Uso1_p115_C  16 eneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelkeekekekekqkEldDLLlllgDl 92 
                                       e e+l +e++sls++le+++q+  k +ae+q +++ +++ + +++  +lr +l++ ++++    ++l  L+   + l
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQA--KTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEA----ADLPQLMQRKTEL 667
                                       4566777777777777777777..999999999999999999999999999999988888....69999******** PP

                       Uso1_p115_C  93 eeKvekykarLkelGeevsd 112
                                       e+ v+k++++L++   ev++
  gi|557694215|ref|YP_008797269.1| 668 ESEVDKLEQKLSQARNEVTQ 687
                                       ***********998888855 PP

>> Effector_1  Effector from type III secretion system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   6.7    0.0023      0.38     189     274 ..     599     687 ..     593     699 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0023
                        Effector_1 189 dklakEkeqvrkdlksaekAkekvkellkrveadkkltteqkaklkdelngY...adeleaiveqLaelkvllrkls 262
                                       ++l +E e + + l++a++Ak+  +e++++v+ + + + +++a+l+d l++    a  l  +++  +el++ + kl+
  gi|557694215|ref|YP_008797269.1| 599 EQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLekeAADLPQLMQRKTELESEVDKLE 675
                                       68999*****************************************9888762225668889999999********9 PP

                        Effector_1 263 vsvvegddeyde 274
                                        +  + ++e+ +
  gi|557694215|ref|YP_008797269.1| 676 QKLSQARNEVTQ 687
                                       999999999877 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 ?   12.2  13.9    0.0016      0.26       3      89 ..     580     670 ..     578     680 .. 0.78
   2 ?    2.9   1.9       1.3   2.1e+02      11      38 ..     662     689 ..     659     696 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0016
                    PRKG1_interact   3 kkLY.eeekeenerLkreLeelekelselkseleklkqqrqe...svskrssllelekrerrslerkiseleeelke 75 
                                        kLY e+ +  n+rL+ e+e+l++e+++l ++le+++q ++e   ++++ ++ +   ++   +l  ++++le+e+  
  gi|557694215|ref|YP_008797269.1| 580 MKLYvEAVLLGNKRLMPEIEQLRQEVESLSQSLEQARQAKTEaeeQINQVTQQIVEARNRAAQLRDRLAQLEKEAAD 656
                                       578834557789***********************9988776333444444444445666677889999******** PP

                    PRKG1_interact  76 leeLraenqrLkdE 89 
                                       l +L + +  L  E
  gi|557694215|ref|YP_008797269.1| 657 LPQLMQRKTELESE 670
                                       *****999999988 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 1.3
                    PRKG1_interact  11 eenerLkreLeelekelselkseleklk 38 
                                       + + +L +e+++le++ls++++e+++l+
  gi|557694215|ref|YP_008797269.1| 662 QRKTELESEVDKLEQKLSQARNEVTQLE 689
                                       5677888888888888888888887765 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  12.0    0.0023      0.37      38     133 ..     593     690 ..     581     698 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0023
                              DegS  38 elkeevsevikevdklekkerkarkrLaeVskdFkkyseeeikeaYeeakelqvelallrekEk...qlrerRdele 111
                                       +l  e++++ +ev++l++   +ar+  +e + + ++ + ++i ea ++a +l+ +la l ++ +   ql +r+ ele
  gi|557694215|ref|YP_008797269.1| 593 RLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVT-QQIVEARNRAAQLRDRLAQLEKEAAdlpQLMQRKTELE 668
                                       56778999999***********************9876.5799999********99988776654447899****** PP

                              DegS 112 rrLkklketierAeklvsqvgv 133
                                        ++ kl++ + +A + v+q+++
  gi|557694215|ref|YP_008797269.1| 669 SEVDKLEQKLSQARNEVTQLET 690
                                       *************999999875 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.9    0.0025       0.4       2     111 ..     602     708 ..     597     709 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0025
                                       HHHHTTTTTST.-GGGTTT..GGGSSSTTHHHHHTHHHHHHHH.HHHHHTTTHHH...HT....-S-..-GGGTHHH CS
                              PCRF   2 eeeleelekklsdpevwed..qekakklskelaeleeiveale.eleealedleeakelleedeelaelaeeeleel 75 
                                       ++e+e+l+++l++ + ++   +e+++++++++ e ++ +++l+ +l +++++++++ +l+    + + + e+e+++l
  gi|557694215|ref|YP_008797269.1| 602 RQEVESLSQSLEQARQAKTeaEEQINQVTQQIVEARNRAAQLRdRLAQLEKEAADLPQLM----QRKTELESEVDKL 674
                                       677888888887766554311344444444444444443333213444444444444444....2223335689999 PP

                                       HHHHHHH..HHHHHT-..SSSTTSEEEEEEEE-SST CS
                              PCRF  76 ekeleeleeelkklLlpkdendeknaileiraGaGG 111
                                       e++l+++++e+++l +   +   +++ + + aGaGG
  gi|557694215|ref|YP_008797269.1| 675 EQKLSQARNEVTQLET--MNMVMMGVAVVLFAGAGG 708
                                       9999999999998877..88899999999999*999 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  13.1    0.0029      0.48      78     172 ..     597     689 ..     589     693 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0029
                           DUF4201  78 althlkeklhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekv 154
                                       ++++l++    l++ l+++++   e ee+++++ +++ +++++ ++lr++ ++l+++ ++   P+L++   + +++v
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAAD--LPQLMQRKTELESEV 671
                                       667788888888888888888888888888888888888888888888888888888877..688888555555666 PP

                           DUF4201 155 eekrksvkkLrrkvkile 172
                                       +++++++ + r +v +le
  gi|557694215|ref|YP_008797269.1| 672 DKLEQKLSQARNEVTQLE 689
                                       666666666666666555 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 ?   10.2  23.3    0.0037       0.6      20     120 ..     594     693 ..     584     696 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0037
                        TPR_MLP1_2  20 aeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseeswee 96 
                                       +  ++++l++++e+ ++++++a q   +   + ++ ++++ ++r+++++l++++a+l++ea ++ + l + + ++e+
  gi|557694215|ref|YP_008797269.1| 594 LMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQ-LMQRKTELES 669
                                       445667777777777777777766555555577889999**********************99975.66778899** PP

                        TPR_MLP1_2  97 qkeelekelselekriedlneqNk 120
                                       + ++le++ls++++ ++ l++ N 
  gi|557694215|ref|YP_008797269.1| 670 EVDKLEQKLSQARNEVTQLETMNM 693
                                       *****************9999986 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 ?    7.7   2.1     0.028       4.5       2      37 ..     598     633 ..     597     657 .. 0.93
   2 ?    7.8   2.2     0.026       4.3       3      28 ..     665     690 ..     663     696 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.028
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelkenV 37 
                                       i++l +++++ls +le +++   e +++++++ +++
  gi|557694215|ref|YP_008797269.1| 598 IEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQI 633
                                       78999***************************9998 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.026
                         FlaC_arch   3 delEnklsklsteletvkkeneelsk 28 
                                        elE++++kl+ +l+ +++e  +l++
  gi|557694215|ref|YP_008797269.1| 665 TELESEVDKLEQKLSQARNEVTQLET 690
                                       69*****************9999865 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  10.2    0.0025       0.4      70     176 ..     583     689 ..     575     699 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXX CS
                              AIP3  70 niepldevkkhideslaslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLav 146
                                        +e++   +k++  ++++l++e+++l++s+e+ +++++e++e+ ++ +++  +  +++++l+++l+++++   dL  
  gi|557694215|ref|YP_008797269.1| 583 YVEAVLLGNKRLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQ 659
                                       555555556788889999*************9999999988888888888888888889999999999999999999 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              AIP3 147 lrqlysefkseikeslselrekakkvkeas 176
                                       l q ++e +se+++  ++l++  ++v +++
  gi|557694215|ref|YP_008797269.1| 660 LMQRKTELESEVDKLEQKLSQARNEVTQLE 689
                                       999999888877666555555555555332 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  18.3    0.0055       0.9      14     105 ..     602     688 ..     597     691 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0055
                             HrpB7  14 arreerlraeleaaraalaaaeaalaaaqaqveaardavraheerlddlttgsspfsiadylacrayrdvlegrvra 90 
                                       +++ e l   le+ar+a  +ae+++++  +q+ +ar+++++ ++rl++l   +     ad+ +++   ++le +v +
  gi|557694215|ref|YP_008797269.1| 602 RQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEA-----ADLPQLMQRKTELESEVDK 673
                                       567788999****************************************8755.....699999999********** PP

                             HrpB7  91 aeaelaaarqaldaa 105
                                       +e++l +ar+++ + 
  gi|557694215|ref|YP_008797269.1| 674 LEQKLSQARNEVTQL 688
                                       *********999875 PP

>> CCD48  Coiled-coil domain-containing protein 48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  11.4    0.0025      0.41     230     320 ..     602     692 ..     586     696 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0025
                             CCD48 230 rgepeaaarelrqaqgalaaaeararrlrrgqaevrrraeearqavlrslkrvrelealarqvpslqrlvrrleael 306
                                       r e e++++ l qa++a ++ae++ +++ ++ +e+r+ra + r+   +  k   +l  l ++   l+  v +le +l
  gi|557694215|ref|YP_008797269.1| 602 RQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELESEVDKLEQKL 678
                                       56788999***********************************99888888899*********************** PP

                             CCD48 307 rryrsegsqlptpa 320
                                        + r+e +ql t++
  gi|557694215|ref|YP_008797269.1| 679 SQARNEVTQLETMN 692
                                       *********99865 PP

>> Tup_N  Tup N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   6.5    0.0018       0.3       5      54 ..     597     646 ..     593     654 .. 0.87
   2 ?    3.3   4.0      0.64     1e+02      18      54 ..     655     691 ..     642     696 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0018
                             Tup_N   5 lLdavkqEfdalsqeasslkaqkdeyelkiqsqiqElqqirqtlyeLeea 54 
                                        +++++qE ++lsq +++ ++ k e e +i++ +q +   r+   +L  +
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDR 646
                                       579*****************************999999999998888765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.64
                             Tup_N  18 qeasslkaqkdeyelkiqsqiqElqqirqtlyeLeea 54 
                                        ++ +l ++k e+e+ + +  q l q r+++ +Le+ 
  gi|557694215|ref|YP_008797269.1| 655 ADLPQLMQRKTELESEVDKLEQKLSQARNEVTQLETM 691
                                       4555677899999999999999999999999999975 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       2.1   3.5e+02      25      63 ..     496     533 ..     494     540 .. 0.77
   2 ?    6.7   1.9      0.06       9.7      42      70 ..     593     621 ..     589     628 .. 0.88
   3 ?    0.5   1.5       5.2   8.4e+02      36      71 ..     622     657 ..     609     662 .. 0.65
   4 ?    7.3   3.3     0.038       6.2      39      71 ..     656     688 ..     651     692 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 2.1
                       Fungal_TACC  25 VkllkkgyeakyqkkldklelenkslkqeieqLkkqlea 63 
                                       ++ll + ye+ y + l+ l++      +++ qLk  l++
  gi|557694215|ref|YP_008797269.1| 496 ISLLLQDYEKNYAQILETLSNA-GLRPDDLPQLKTVLST 533
                                       578999***********99865.3334677777777766 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.06
                       Fungal_TACC  42 klelenkslkqeieqLkkqleaerkEKqe 70 
                                       +l  e ++l+qe+e+L++ le +r+ K+e
  gi|557694215|ref|YP_008797269.1| 593 RLMPEIEQLRQEVESLSQSLEQARQAKTE 621
                                       6777889*****************99986 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 5.2
                       Fungal_TACC  36 yqkkldklelenkslkqeieqLkkqleaerkEKqeL 71 
                                        ++++++++++  + ++   qL+++l+  +kE  +L
  gi|557694215|ref|YP_008797269.1| 622 AEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADL 657
                                       356677777777777777777777777777776666 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.038
                       Fungal_TACC  39 kldklelenkslkqeieqLkkqleaerkEKqeL 71 
                                       +l +l + + +l++e+++L+++l+ +r+E ++L
  gi|557694215|ref|YP_008797269.1| 656 DLPQLMQRKTELESEVDKLEQKLSQARNEVTQL 688
                                       67899999*********************9887 PP

>> 3-PAP  Myotubularin-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.3     0.009       1.5     101     129 ..     590     618 ..     582     621 .. 0.84
   2 ?    3.9   0.7      0.26        42     105     129 ..     660     684 ..     625     687 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.009
                             3-PAP 101 gpvtaahklseLadeveaLqraLrqkrss 129
                                       g  +++ ++++L++eve+L+++L+q r+ 
  gi|557694215|ref|YP_008797269.1| 590 GNKRLMPEIEQLRQEVESLSQSLEQARQA 618
                                       55578999*****************9986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.26
                             3-PAP 105 aahklseLadeveaLqraLrqkrss 129
                                       ++++  eL++ev++L+++L q r++
  gi|557694215|ref|YP_008797269.1| 660 LMQRKTELESEVDKLEQKLSQARNE 684
                                       5677789**************9976 PP

>> Perilipin  Perilipin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  11.7    0.0031       0.5     252     358 ..     578     683 ..     573     695 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0031
                                       HHHHHHH--...---------------------------------..SHHHHH..HHHHHHHHHHHHHHHHHHHHHH CS
                         Perilipin 252 dLielakkglsaanqklseaqekllqswlewkkkqqeeseeeeeeeeeeqvEs..rtLsllrsltqqLqttcqslvs 326
                                       dL++l  +++   n++l+ + e+l+q + + +++ +++++ ++e+  eeq+ +  +++  +r+ ++qL++ + +l  
  gi|557694215|ref|YP_008797269.1| 578 DLMKLYVEAVLLGNKRLMPEIEQLRQEVESLSQSLEQARQAKTEA--EEQINQvtQQIVEARNRAAQLRDRLAQLEK 652
                                       556555556666678889999************999999988888..566665115566789*************** PP

                                       TTTTS-HHHHHHHHHHHHHHHHHHHHGGG--S CS
                         Perilipin 327 siqglPssvqekvqqarrsaeelqaslskass 358
                                       ++  lP+ +q k +++++++++l++ ls+a++
  gi|557694215|ref|YP_008797269.1| 653 EAADLPQLMQRK-TELESEVDKLEQKLSQARN 683
                                       ******777766.56*************9974 PP

>> Phage_GPO  Phage capsid scaffolding protein (GPO) serine peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   9.6    0.0034      0.55     172     257 ..     603     687 ..     583     692 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0034
                         Phage_GPO 172 eegeslferikallskkkksddarfadveeavelvAeevkelsekveallaleaelaalkkeveklkaeleaLkekL 248
                                       +e esl +++++  ++ k++ ++++++v++ + +  +++++l++++++l++++a+l +l ++ ++l++e+++L++kL
  gi|557694215|ref|YP_008797269.1| 603 QEVESLSQSLEQA-RQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELESEVDKLEQKL 678
                                       3334455555443.33444457788888888888888899999****99999************************* PP

                         Phage_GPO 249 sktdakekq 257
                                       s+  ++ +q
  gi|557694215|ref|YP_008797269.1| 679 SQARNEVTQ 687
                                       *98876655 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3  17.2     0.007       1.1       3      87 ..     596     680 ..     594     687 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.007
                              BRE1   3 kELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLk 79 
                                        E+++l ++ e ls++l++  +  t  ee+++++++++ +a++   +++    +le+e   L +l+++++el ++  
  gi|557694215|ref|YP_008797269.1| 596 PEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELESEVD 672
                                       69*************************************************************************** PP

                              BRE1  80 elekefvr 87 
                                        le ++ +
  gi|557694215|ref|YP_008797269.1| 673 KLEQKLSQ 680
                                       *9999877 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  14.4    0.0041      0.67      54     165 ..     585     688 ..     574     693 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0041
                            DUF745  54 eAaLaGKqqlv...eqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqva 127
                                       eA+L G + l+   eql qe++  ++ +++  ++ +++e++++ +++   +a++ +++l++ l++ +       + a
  gi|557694215|ref|YP_008797269.1| 585 EAVLLGNKRLMpeiEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLE-------KEA 654
                                       5666666655411134444444444444444444444444444444444444444444444433333.......333 PP

                            DUF745 128 agaqqelaektqlleaAkkRveeLkkqlkearkdlekt 165
                                       a   q ++ kt+l    ++ v++L+++l++ar++ ++ 
  gi|557694215|ref|YP_008797269.1| 655 ADLPQLMQRKTEL----ESEVDKLEQKLSQARNEVTQL 688
                                       3333333333333....445666666666666665544 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   3.9    0.0039      0.64      62     115 ..     599     652 ..     575     658 .. 0.63
   2 ?    6.9   5.6     0.038       6.3      44     110 ..     627     692 ..     625     698 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0039
                           DUF1664  62 rhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       ++L ++++++ ++l++  ++++e +e++++v +++ e ++   ++++   +le+
  gi|557694215|ref|YP_008797269.1| 599 EQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEK 652
                                       456666666666666666666666666666666666666666666666666665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.038
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav 110
                                       ++v++q+ +  +  a+ +++L++ +++  + l + ++ ++e+++ev++++++ls+ +++v++++++ 
  gi|557694215|ref|YP_008797269.1| 627 NQVTQQIVEARNRAAQLRDRLAQ-LEKEAADLPQLMQRKTELESEVDKLEQKLSQARNEVTQLETMN 692
                                       45555555555555555555543.455556788889999999********************99875 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 ?    9.4  16.4    0.0041      0.67     229     332 ..     594     689 ..     582     692 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0041
                            HMMR_N 229 lleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekekeelvreeee 305
                                       l+ +ie+l   ++++e  ++ ++q+++   e++++i+++ +++ e  +    ++ +l  ++ +leke    + +  +
  gi|557694215|ref|YP_008797269.1| 594 LMPEIEQL---RQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARN----RAAQLRDRLAQLEKEAA-DLPQLMQ 662
                                       44444444...4444444777777777777777777777777766655....77778888888888877.6677777 PP

                            HMMR_N 306 keqtlsaEleelkeklklkeqeaqklq 332
                                       ++ +l++E+++l++kl + ++e+++l+
  gi|557694215|ref|YP_008797269.1| 663 RKTELESEVDKLEQKLSQARNEVTQLE 689
                                       778888888888888888888887764 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  12.0    0.0044      0.72     103     183 ..     597     680 ..     591     691 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0044
                            DUF724 103 eqtklleerkklekkieeeesekrkleeeidelekkilelerqlallk...ekkeaadkeiarlkseaekleeeled 176
                                       e ++l++e + l +++e+++++k+++ee+i+++ ++i+e ++++a+l+   ++ e++++++ +l + + +le e+++
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRdrlAQLEKEAADLPQLMQRKTELESEVDK 673
                                       5789999*****************************************99966666666666666666666666666 PP

                            DUF724 177 veqeFea 183
                                        eq+ ++
  gi|557694215|ref|YP_008797269.1| 674 LEQKLSQ 680
                                       6655443 PP

>> CwsA  Cell wall synthesis protein CwsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.4    0.0054      0.89      30     113 ..     633     715 ..     605     716 .] 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0054
                              CwsA  30 vesaqstaeelrrryresrlarelaaaqeaiaqelaaaqevvaglPqaledarkk..rrrkrplllagvavavlaGG 104
                                       +  a++ a++lr r +  +l++e a+  + +    +  +  v  l q l +ar++  + +  ++++ gvav+++aG 
  gi|557694215|ref|YP_008797269.1| 633 IVEARNRAAQLRDRLA--QLEKEAADLPQLMQ-RKTELESEVDKLEQKLSQARNEvtQLETMNMVMMGVAVVLFAGA 706
                                       4567778888887764..68888777766554.5555666689999*99999766114556679************9 PP

                              CwsA 105 avafsivrr 113
                                          f ++rr
  gi|557694215|ref|YP_008797269.1| 707 GGVFLLSRR 715
                                       999999998 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   4.2     0.062        10      19      87 ..     614     715 ..     590     716 .] 0.65

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.062
                              ApoO  19 gvrslRkslepytsavqdel..................................nkvkskvetaeqsvtdtiasLke 61 
                                       + r++  ++e+++++v++++                                  ++  +k+e++ ++ ++++ +L  
  gi|557694215|ref|YP_008797269.1| 614 QARQAKTEAEEQINQVTQQIvearnraaqlrdrlaqlekeaadlpqlmqrktelESEVDKLEQKLSQARNEVTQLET 690
                                       44555555555555555555555555555555556666666888888888844455555555555566666666666 PP

                              ApoO  62 ppedllPrlgyilvagLaGsilarrr 87 
                                           ++ +++++l+ag  G++l  rr
  gi|557694215|ref|YP_008797269.1| 691 M-NMVMMGVAVVLFAGAGGVFLLSRR 715
                                       5.99999********99999986655 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 ?    9.1  16.4    0.0051      0.83      47     132 ..     596     687 ..     581     696 .. 0.40

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0051
                         Golgin_A5  47 aeldelkqerdllreelqklnqqieqlrtelqdleaqqq...aeaeslreqlqeleeqle...eerkakeeveaele 117
                                        e+++l+qe + l ++l++++q+  +   +++++ +q     + a +lr++l++le++ +   +  ++k e+e+e+ 
  gi|557694215|ref|YP_008797269.1| 596 PEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVearNRAAQLRDRLAQLEKEAAdlpQLMQRKTELESEVD 672
                                       33333333333333333333333333333333333332200012233333333333332211122334444444444 PP

                         Golgin_A5 118 rlkeelryleeelvr 132
                                       +l+++l+ +++e+++
  gi|557694215|ref|YP_008797269.1| 673 KLEQKLSQARNEVTQ 687
                                       444444444444443 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  19.9      0.19        31       8     103 ..     599     696 ..     597     698 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHS-TT--EEEEETTEEEEE-HHHH.HHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   8 qqlqqqlqqlaqqikqletqlkelelvleel.elldedtkvyklvGdvlvkqdkeev.keeLeerketlekeiktle 82 
                                       +ql+q+++ l q ++q+++ ++e+e+ ++ + +++ e ++   +  d l + +ke + +++L +rk +le e+++le
  gi|557694215|ref|YP_008797269.1| 599 EQLRQEVESLSQSLEQARQAKTEAEEQINQVtQQIVEARNRAAQLRDRLAQLEKEAAdLPQLMQRKTELESEVDKLE 675
                                       79**********************98777652778888999999999999999999846****************** PP

                                       HHHHHHHHHHHHHHHHHHCCT CS
                       Prefoldin_2  83 kqleklekeleelkeelqkkl 103
                                       ++l++ ++e+++l+++++ ++
  gi|557694215|ref|YP_008797269.1| 676 QKLSQARNEVTQLETMNMVMM 696
                                       **************9988765 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0  15.0    0.0041      0.67     464     564 ..     590     689 ..     575     697 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0041
                              HOOK 464 ENKmLklkqegseeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkle 540
                                        NK+L +   ++ ++++++l++ le+a++ k e e++  + +q+i e +++  +l+ +l++ + +a d  +l ++ +
  gi|557694215|ref|YP_008797269.1| 590 GNKRL-MPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKT 665
                                       59999.55555559999999999999999999999999999999999999999999999988888888434333333 PP

                              HOOK 541 ehleklkevqeelqkkkeqleele 564
                                       e+  ++ +++++l++ ++ + +le
  gi|557694215|ref|YP_008797269.1| 666 ELESEVDKLEQKLSQARNEVTQLE 689
                                       444444444444444444333333 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   5.3    0.0047      0.76      96     190 ..     592     687 ..     574     701 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0047
                            AAA_11  96 ee.....eriseavksvsleekvekrlekeekaqlakeiskeleklakelrafeeeeekeklkkskekskskleqer 167
                                       +      e+ +++v+s+s  +++e+ +++  k++  ++i++ ++++ ++ +  ++   + ++++++  +  +l q++
  gi|557694215|ref|YP_008797269.1| 592 KRlmpeiEQLRQEVESLS--QSLEQARQA--KTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRK 664
                                       444444455555665555..344444433..3455555555555555555555555555667788888888888888 PP

                            AAA_11 168 rklkkerkelskeleeaeeslee 190
                                       ++l++e+++l+++l +a++++++
  gi|557694215|ref|YP_008797269.1| 665 TELESEVDKLEQKLSQARNEVTQ 687
                                       99999999999999888888754 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  15.0    0.0049      0.79     602     690 ..     599     689 ..     578     695 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0049
                           DUF3584 602 eeLrerlqaleealqsaeakqkqaeeelkqlnaeleeakr...avaeaatalknardtlerlqnekesekdklekai 675
                                       e+Lr++++ l++ l++a++ +++aee+++q+ +++ ea++   ++ ++ ++l+++  +l +l + k +++ +++k +
  gi|557694215|ref|YP_008797269.1| 599 EQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNraaQLRDRLAQLEKEAADLPQLMQRKTELESEVDK-L 674
                                       588888888888888888888888888888888765544311144456666666667777776666665555554.4 PP

                           DUF3584 676 aerkqqaeeqlqkld 690
                                       +++ +qa++++++l+
  gi|557694215|ref|YP_008797269.1| 675 EQKLSQARNEVTQLE 689
                                       444455555555554 PP

>> HAUS5  HAUS augmin-like complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  19.4     0.016       2.6      83     165 ..     592     677 ..     585     691 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.016
                             HAUS5  83 eelekeverLraeirrldkeleareeelsreeaevkraldeisdsrhrqvlLeaydqqceeaakilaedtkr...lq 156
                                       + l  e+e+Lr+e++ l ++le++ +  ++ e++++++ ++i ++r r++ L+   +q e++a  l + ++r   l+
  gi|557694215|ref|YP_008797269.1| 592 KRLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRkteLE 668
                                       56788******************99999999**********************999999999987777666522266 PP

                             HAUS5 157 eqvqqlrda 165
                                       + v++l++ 
  gi|557694215|ref|YP_008797269.1| 669 SEVDKLEQK 677
                                       666666554 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.9       0.2        32       6      41 ..     598     633 ..     595     637 .. 0.79
   2 ?    7.8   0.8     0.023       3.8       3      48 ..     644     692 ..     642     701 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.2
                              XhlA   6 lerietkldnleervdkleekaaeaeekiknleedl 41 
                                       +e++ +++++l++ +++  + ++eaee+i +++ ++
  gi|557694215|ref|YP_008797269.1| 598 IEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQI 633
                                       667777888888888888888888888888888877 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.023
                              XhlA   3 kerlerietkldnlee...rvdkleekaaeaeekiknleedlkklesnq 48 
                                       ++rl+++e++  +l +   r ++le   ++ e+k+ ++ +++ +le ++
  gi|557694215|ref|YP_008797269.1| 644 RDRLAQLEKEAADLPQlmqRKTELESEVDKLEQKLSQARNEVTQLETMN 692
                                       6778888877666666666889999999999999999999999998876 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  12.6     0.014       2.3      98     182 ..     600     690 ..     595     693 .. 0.55

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                                       HTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT......--TTTTHHHHHHHHHHH CS
                              EzrA  98 kakkklaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkk......llanrfsygealeelek 168
                                       ++++++++l + l+++++   +  e+++++t++  + r++  +l+++  +l+k+      l +++ ++++ +++le+
  gi|557694215|ref|YP_008797269.1| 600 QLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEaadlpqLMQRKTELESEVDKLEQ 676
                                       45556666666666666666666666666666666666666666666666665411111144566666666666666 PP

                                       HHHHH--------- CS
                              EzrA 169 qleniekefsefee 182
                                       +l++  +e +++e+
  gi|557694215|ref|YP_008797269.1| 677 KLSQARNEVTQLET 690
                                       66666666666665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7  20.3     0.018       2.9     182     278 ..     597     681 ..     576     696 .. 0.34

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.018
                              Spc7 182 eleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervle 258
                                       e+e+l++++e+l    +++Le++r++ +e++++i++  +++ e +++ ++l++++++l+++ ++l + ++       
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESL----SQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQ------- 662
                                       333333322211....112333333333333333322222222222222222222222222222222111....... PP

                              Spc7 259 eckgwsesevsrlkeevkal 278
                                        +k   esev++l++++++ 
  gi|557694215|ref|YP_008797269.1| 663 -RKTELESEVDKLEQKLSQA 681
                                       .2222222222222222221 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 ?   13.3   2.9   0.00044     0.072      29      69 ..     592     632 ..     585     634 .. 0.92
   2 ?    1.6   4.2         2   3.2e+02      37      67 ..     659     689 ..     638     692 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00044
                          JIP_LZII  29 ddLIarvdeLtsereiLreEleslqkakerlesrikelEee 69 
                                       + L+ ++++L +e e+L++ le+ ++ak++ e++i+++ ++
  gi|557694215|ref|YP_008797269.1| 592 KRLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQ 632
                                       67999******************************999876 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 2
                          JIP_LZII  37 eLtsereiLreEleslqkakerlesrikelE 67 
                                       +L ++++ L++E+++l++ +++ ++++++lE
  gi|557694215|ref|YP_008797269.1| 659 QLMQRKTELESEVDKLEQKLSQARNEVTQLE 689
                                       5666667777777777777777777777776 PP

>> PEARLI-4  Arabidopsis phospholipase-like protein (PEARLI 4)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   7.2     0.012         2     187     261 ..     597     674 ..     580     690 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.012
                          PEARLI-4 187 eqetavvEKevkerdvllkkqEmekqekelaekEKeikevrekvtemaaklgelemkrarlek...rlaflssKvek 260
                                       e e+   E e   + +  ++q   + e+++ +  ++i+e+r++  +++ +l++le + a l +   r + l+s v+k
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQlmqRKTELESEVDK 673
                                       667788899999999******************************************99876511144566777776 PP

                          PEARLI-4 261 f 261
                                       +
  gi|557694215|ref|YP_008797269.1| 674 L 674
                                       6 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   9.5      0.68   1.1e+02       2      55 ..     598     651 ..     589     654 .. 0.51
   2 ?   10.2   8.3    0.0037       0.6      17      69 ..     634     689 ..     626     694 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.68
                     Tropomyosin_1   2 lnsLkleaeeaqekaeeleekvKeleqenlekeqeiksLtkknqqleeevekle 55 
                                       +++L+ e e+  +  e++++++ e+e++  +  q+i +  ++  ql + + +le
  gi|557694215|ref|YP_008797269.1| 598 IEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLE 651
                                       344555555555555555555555555555555555555555555555554444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0037
                     Tropomyosin_1  17 eeleekvKeleqenlekeqeik...sLtkknqqleeevekleeklkeakekaeese 69 
                                        e+++++ +l ++  + e+e +   +L ++  +le+ev+kle+kl++a++++ + e
  gi|557694215|ref|YP_008797269.1| 634 VEARNRAAQLRDRLAQLEKEAAdlpQLMQRKTELESEVDKLEQKLSQARNEVTQLE 689
                                       455555555555555555555411167788899*************9998877655 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.3     0.012         2      44     132 ..     614     704 ..     597     715 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.012
                           DUF4337  44 QAksikehlaeleleqlelllkak.aeelaaavdkkiakykkkiarykke...kkeikkkAkeleaerdeaneasdk 116
                                       QA++ k++  e   +q++ +     a++ aa+ +++ a+++k++a   +    k+e++ + ++le++  +a  +  +
  gi|557694215|ref|YP_008797269.1| 614 QARQAKTEAEEQ-INQVTQQ--IVeARNRAAQLRDRLAQLEKEAADLPQLmqrKTELESEVDKLEQKLSQARNEVTQ 687
                                       444444444443.3333322..2223333444444444444444433222444888888888888888888877777 PP

                           DUF4337 117 fd.lasalLqiaIvlaa 132
                                        + + ++++ +a+vl a
  gi|557694215|ref|YP_008797269.1| 688 LEtMNMVMMGVAVVLFA 704
                                       54278888999999876 PP

>> DASH_Spc19  Spc19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6  12.6    0.0048      0.78      78     157 .]     593     674 ..     589     674 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0048
                                       HHHHHHHHHHHHHHHHHHHHHH......HHHHT-XXXXXXXXXXXX....XXXX..XXXXXXXXXXXXXXXXXXXXX CS
                        DASH_Spc19  78 klerreetLkaklelqegrlsnaesskkeeeeseeskeeeeeeenkeeekskkk..ltkeelerlkkLkqkKerLky 152
                                       +l  + e+L++++e +++ l++a++ k+e+ee+ ++ +++  e+++++++ +++    ++e++ l +L q+K++L+ 
  gi|557694215|ref|YP_008797269.1| 593 RLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRlaQLEKEAADLPQLMQRKTELES 669
                                       56678899999999999999997776666666666655555555444444444477667788*************** PP

                                       XXXXX CS
                        DASH_Spc19 153 tlerL 157
                                       ++++L
  gi|557694215|ref|YP_008797269.1| 670 EVDKL 674
                                       **987 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 ?    8.2  10.9     0.015       2.5      13      70 ..     597     654 ..     592     657 .. 0.74
   2 ?    6.2   3.7     0.064        10      38      67 ..     660     689 ..     657     692 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.015
                        TMF_DNA_bd  13 qIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerl 70 
                                       +I+qL++E e Ls +  + +++  +  +++++ +++i e  ++ ++l   l++le+++
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEA 654
                                       5778888888888777777777777777777777777777777777777777777776 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.064
                        TMF_DNA_bd  38 Lrkknkelekeikelkkkleklekeleele 67 
                                       L +   ele+e+++l++kl++   e+++le
  gi|557694215|ref|YP_008797269.1| 660 LMQRKTELESEVDKLEQKLSQARNEVTQLE 689
                                       566778999999999999999999999998 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 ?    7.9  13.2      0.02       3.3      31     123 ..     599     690 ..     591     696 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.02
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvL 107
                                       +++++++e+l ++le++++ ++eaee ++++++++ e+ + +++    + +++ke   +  +l ++ ++ es++ +L
  gi|557694215|ref|YP_008797269.1| 599 EQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAA-DLPQLMQRKTELESEVDKL 674
                                       467888999999999999999999999999999888888888877777777777777.7777777777778889999 PP

                                       HHHHHHHHHHHHHHHH CS
                         Fib_alpha 108 qnvlesneqkiqkLeq 123
                                        + l++ ++++++Le+
  gi|557694215|ref|YP_008797269.1| 675 EQKLSQARNEVTQLET 690
                                       9999999999999887 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 ?    7.9  12.0     0.019       3.1      76     162 ..     597     689 ..     566     693 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.019
                           UPF0242  76 klteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiae......dfeelkleleeqLae 146
                                        + +l+++++   ++le++++ + e +e++++ ++++ + +++ +qL+ +l +  +      +  + k ele+++++
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKeaadlpQLMQRKTELESEVDK 673
                                       34445577788899999999999999999*******************99999988777777777788899999999 PP

                           UPF0242 147 kqellqeyqetieeqr 162
                                        +++l++ +++++++ 
  gi|557694215|ref|YP_008797269.1| 674 LEQKLSQARNEVTQLE 689
                                       9999998888888765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  11.4     0.034       5.5     403     470 ..     597     664 ..     592     687 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.034
                            AAA_13 403 lveeleseldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                       ++e+l++e++ + + ++++ +a +++e+++++ ++++ ++++++++L+ +l + ++ a+++ +++++ 
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRK 664
                                       57788888888888888888888888888888888888888888888888888888888888888764 PP

>> DUF2046  Uncharacterized conserved protein H4 (DUF2046)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  17.0     0.044       7.2      83     171 ..     594     690 ..     589     694 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.044
                           DUF2046  83 llkkiqalkkeketlalnyeq......eeefltndlsrklsqlrqekveleqtlek.eqe.vqvnklmrkiekleae 151
                                       l+  i++l++e e l++  eq      e e   n++ +++ + r+  ++l   l + e+e   + +lm++  +le e
  gi|557694215|ref|YP_008797269.1| 594 LMPEIEQLRQEVESLSQSLEQarqaktEAEEQINQVTQQIVEARNRAAQLRDRLAQlEKEaADLPQLMQRKTELESE 670
                                       788999999999999998887444444566677999999999999999999988774333257889*********** PP

                           DUF2046 152 vlakqtkleqlrrekvelen 171
                                       v + ++kl+q r e  +le 
  gi|557694215|ref|YP_008797269.1| 671 VDKLEQKLSQARNEVTQLET 690
                                       *9999******999999985 PP

>> bZIP_2  Basic region leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.3     0.027       4.4      34      53 ..     591     610 ..     581     611 .. 0.87
   2 ?    1.8   7.1       1.5   2.5e+02      28      54 .]     627     653 ..     610     653 .. 0.64
   3 ?    7.8   5.0     0.022       3.5      25      53 ..     662     690 ..     659     691 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.027
                                       HHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  34 vkeLeeeNaqLrqkveqLek 53 
                                       +k+L+ e++qLrq+ve+L +
  gi|557694215|ref|YP_008797269.1| 591 NKRLMPEIEQLRQEVESLSQ 610
                                       689**************976 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  28 eeleervkeLeeeNaqLrqkveqLeke 54 
                                       ++  +++ e +++ aqLr++++qLeke
  gi|557694215|ref|YP_008797269.1| 627 NQVTQQIVEARNRAAQLRDRLAQLEKE 653
                                       344455666666667888888888887 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.022
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_2  25 akeeeleervkeLeeeNaqLrqkveqLek 53 
                                       +++ ele++v +Le++ +q r++v qLe+
  gi|557694215|ref|YP_008797269.1| 662 QRKTELESEVDKLEQKLSQARNEVTQLET 690
                                       67889999999999999999999999986 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 ?    7.6   0.6     0.025       4.1      39      71 ..     585     617 ..     570     619 .. 0.85
   2 ?    4.2  10.8      0.29        47       4      71 ..     621     690 ..     620     692 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.025
                            Cnn_1N  39 eellkenielkveveslqkelkekkkllreaek 71 
                                       e++l  n  l  e+e+l++e++++ ++l++a +
  gi|557694215|ref|YP_008797269.1| 585 EAVLLGNKRLMPEIEQLRQEVESLSQSLEQARQ 617
                                       667777899999*****************9977 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.29
                            Cnn_1N   4 EqeeqidkLkKENFdLKLriyfLeerleklse..eqkeellkenielkveveslqkelkekkkllreaek 71 
                                       E eeqi++++      + r + L++rl +l++   +  +l++  +el+ ev +l+++l + +++++++e+
  gi|557694215|ref|YP_008797269.1| 621 EAEEQINQVTQQIVEARNRAAQLRDRLAQLEKeaADLPQLMQRKTELESEVDKLEQKLSQARNEVTQLET 690
                                       789999999999999999*************94445559**************************99986 PP

>> Wtap  WTAP/Mum2p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   9.2    0.0013      0.22      89     152 ..     592     657 ..     589     661 .. 0.90
   2 ?    0.3   1.1       3.7     6e+02      96     113 ..     665     682 ..     659     692 .. 0.37

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0013
                              Wtap  89 krLmakcrvLeqENeELgkvleegrvakLe..selalqkkfveelkkaleeleelleeleeevevl 152
                                       krLm  + +L qE e L ++le++r ak e  ++++  ++++ e +++ ++l++ l++le+e+ +l
  gi|557694215|ref|YP_008797269.1| 592 KRLMPEIEQLRQEVESLSQSLEQARQAKTEaeEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADL 657
                                       9*************************99751166888899**********************9776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 3.7
                              Wtap  96 rvLeqENeELgkvleegr 113
                                         Le+E + L++ l+++r
  gi|557694215|ref|YP_008797269.1| 665 TELESEVDKLEQKLSQAR 682
                                       333333333333333322 PP

>> FAM76  FAM76 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   9.3     0.027       4.3     218     297 ..     595     676 ..     578     691 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.027
                             FAM76 218 lvavtqLkeeiaslkkqleqkdqellekdkkitelkaellekek...elreklkelekeakekieklekkirellke 291
                                       + +++qL++e++sl + leq  q+  e + +i +++ + +e ++   +lr++l +lekea +   +l ++ +el  e
  gi|557694215|ref|YP_008797269.1| 595 MPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNraaQLRDRLAQLEKEAADLP-QLMQRKTELESE 670
                                       55799***************9999999999999888877766542227999***9999987654.455555677777 PP

                             FAM76 292 vaelsk 297
                                       v +l++
  gi|557694215|ref|YP_008797269.1| 671 VDKLEQ 676
                                       766655 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  20.3       0.2        33      63     150 ..     592     685 ..     583     687 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.2
                              ADIP  63 rkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalq......qiktqya 133
                                       ++l  eie+l++++e+l+++leq ++  + ++++ +q ++++ ++ + + ++++ l+ l++ ++      q+kt ++
  gi|557694215|ref|YP_008797269.1| 592 KRLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAAdlpqlmQRKTELE 668
                                       56667888888888888888888888888888888888888888888888888888888776552222225666666 PP

                              ADIP 134 helkkkdreiekLkekl 150
                                        e+ k ++++++ ++ +
  gi|557694215|ref|YP_008797269.1| 669 SEVDKLEQKLSQARNEV 685
                                       66666666666666655 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3  12.4      0.38        62      13      73 ..     624     689 ..     582     704 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.38
                           DUF2203  13 pllkelleelralrkeleeleeeleeakaeaekse.....aaeleaeleeleaeieelveeieelG 73 
                                        ++++++++++++r+++++l+++l++ ++ea+        ++ele+e+++le++++++ +e+++l 
  gi|557694215|ref|YP_008797269.1| 624 EQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPqlmqrKTELESEVDKLEQKLSQARNEVTQLE 689
                                       356666666777777777777777777776655446677777888888888877777666666553 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 ?    6.0   6.7     0.092        15      42     104 ..     592     651 ..     581     657 .. 0.78
   2 ?    5.0   2.9      0.19        31      48      93 ..     643     688 ..     640     693 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.092
                                       ----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---------CHH CS
                           T3SSipB  42 sklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePekakle 104
                                       ++l  e++++ +e + + + le+a ++  +a+ +++++t+++ ea +r  +L       a+le
  gi|557694215|ref|YP_008797269.1| 592 KRLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQL---RDRLAQLE 651
                                       5667788999999999999999999999999999999999999999988887...33334444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  48 lqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                       l++ l + ++ + dl + +++  +++s++d++++k+++a + + +L
  gi|557694215|ref|YP_008797269.1| 643 LRDRLAQLEKEAADLPQLMQRKTELESEVDKLEQKLSQARNEVTQL 688
                                       556666777777788888999999*****************99998 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   6.9     0.024         4     626     710 ..     598     687 ..     582     701 .. 0.51

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.024
                          Prominin 626 letlaekleelanelsngkknlkqslkneaqdlraiqqelvlp......lessvkklkksvkklde...ensdlqes 693
                                       +e+l +++e+l+++l+++    +q+ +++ ++++++ q++v+       l+  +++l+k+  +l +   ++++l+++
  gi|557694215|ref|YP_008797269.1| 598 IEQLRQEVESLSQSLEQA----RQAKTEAEEQINQVTQQIVEArnraaqLRDRLAQLEKEAADLPQlmqRKTELESE 670
                                       566667777777777544....3333333334444433333221111114444444444444444444444555555 PP

                          Prominin 694 ikkllaaveraenflkk 710
                                       ++kl +++++a n++++
  gi|557694215|ref|YP_008797269.1| 671 VDKLEQKLSQARNEVTQ 687
                                       55555555555555443 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 ?    7.5   0.7     0.026       4.2      44      66 ..     595     617 ..     589     619 .. 0.85
   2 ?    3.2   8.8      0.59        96       7      51 ..     642     689 ..     634     694 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.026
                       Cep57_CLD_2  44 yeelneLkaevealrkELkeqra 66 
                                        +e+++L++eve+l + L+  r+
  gi|557694215|ref|YP_008797269.1| 595 MPEIEQLRQEVESLSQSLEQARQ 617
                                       689*************9998775 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.59
                       Cep57_CLD_2   7 tLqnrLdsltrklqvhe...eelkrLnkERdsalrqLgvAyeelneLk 51 
                                       +L++rL +l+ +++        + +L +E d  +++L++A+ e+ +L 
  gi|557694215|ref|YP_008797269.1| 642 QLRDRLAQLEKEAADLPqlmQRKTELESEVDKLEQKLSQARNEVTQLE 689
                                       7999999999999988767677788999*****************996 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 ?    8.5  14.1     0.013       2.2      16      96 ..     593     670 ..     588     673 .. 0.87
   2 ?    6.8  10.5     0.048       7.8      25      83 ..     623     681 ..     620     697 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.013
                       TMF_TATA_bd  16 rlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGeksE 92 
                                       rl  ei +l  E++sl ++le+  + + ea+e+i +++   ++  e+ ++ ++l+ +l++l+++   l +l++ k+E
  gi|557694215|ref|YP_008797269.1| 593 RLMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVT---QQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTE 666
                                       67778999999999999999999999999999999999...56667778889999********************** PP

                       TMF_TATA_bd  93 eveE 96 
                                          E
  gi|557694215|ref|YP_008797269.1| 667 LESE 670
                                       8877 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.048
                       TMF_TATA_bd  25 EgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetl 83 
                                       E +++++ +++ +  +   ++r+ +++l ke  +l +l ++ +ele+e+++l+++++++
  gi|557694215|ref|YP_008797269.1| 623 EEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELESEVDKLEQKLSQA 681
                                       66777777777777777777777777777777777777777777777777777777665 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 ?    1.3   9.2       2.2   3.7e+02      20      78 ..     597     652 ..     592     654 .. 0.89
   2 ?    9.5   1.0    0.0064       1.1      17      49 ..     654     692 ..     647     695 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 2.2
                              Med9  20 sskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrelLkkykn 78 
                                       ++++l +++ +l + L++ar++  e    ++ + +  ++i e +++ a+ r+ L+++ +
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTE---AEEQINQVTQQIVEARNRAAQLRDRLAQLEK 652
                                       5688999999999999999999998...8999999999999999999999999999876 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0064
                              Med9  17 p......nlsskdletktgelrhkLkkarelirelpgid 49 
                                               +  ++le+++++l +kL++ar+ + +l+ ++
  gi|557694215|ref|YP_008797269.1| 654 AadlpqlMQRKTELESEVDKLEQKLSQARNEVTQLETMN 692
                                       4445555567899**********************9876 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.4       2.6   4.2e+02      62      90 ..     602     630 ..     593     635 .. 0.58
   2 ?    7.6   5.7     0.023       3.8      40      90 ..     638     689 ..     622     697 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 2.6
                           DUF2730  62 akdlekLkllladlrgelkaleaevrqls 90 
                                       ++++e+L+  l++ r    ++e++++q+ 
  gi|557694215|ref|YP_008797269.1| 602 RQEVESLSQSLEQARQAKTEAEEQINQVT 630
                                       34555555555555555555555555554 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.023
                           DUF2730  40 ekveendkrlteletkvenLPtakd.lekLkllladlrgelkaleaevrqls 90 
                                       + +++ + rl++le + ++LP   +   +L+ ++ +l+ +l+++++ev+ql+
  gi|557694215|ref|YP_008797269.1| 638 NRAAQLRDRLAQLEKEAADLPQLMQrKTELESEVDKLEQKLSQARNEVTQLE 689
                                       3344555566666666666665433134566666666666666666666665 PP

>> Nup88  Nuclear pore component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  11.7     0.034       5.5     558     653 ..     596     690 ..     570     698 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.034
                             Nup88 558 krvkllkkqkeqqleelqsleeerkslseraeklAekyeeikdkQeklvrrvkkvlkrlnsklpvlseaeremkkel 634
                                         +++l+++ e   + l++ ++++ + +e+ +++ ++  e++++  +l  r+ ++ ++  + lp+l++ + e+++e+
  gi|557694215|ref|YP_008797269.1| 596 PEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQL-EKEAADLPQLMQRKTELESEV 671
                                       56889999999999999999*******************************9996.5566889************** PP

                             Nup88 635 ekikeklkslknalkqvkk 653
                                        k+++kl++  n++ q+++
  gi|557694215|ref|YP_008797269.1| 672 DKLEQKLSQARNEVTQLET 690
                                       **********999999864 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  11.3     0.045       7.3       8      98 ..     598     690 ..     594     693 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.045
                        Syntaxin_2   8 insnvstleklvkqLgtkk.dteelreklhelieeinelikktnellkklsqldnsssdsqqkl.qkekLkkdfkea 82 
                                       i ++ ++ e+l ++L+ ++   +e  e++++++++i e  ++  +l  +l+ql++   d  q +  k  L +++ ++
  gi|557694215|ref|YP_008797269.1| 598 IEQLRQEVESLSQSLEQARqAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMqRKTELESEVDKL 674
                                       44444455555555555542478999*******************************999888856789******** PP

                        Syntaxin_2  83 lqeFqkiqrqyaekek 98 
                                        q++ ++ +++++ e 
  gi|557694215|ref|YP_008797269.1| 675 EQKLSQARNEVTQLET 690
                                       *****99999998876 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 ?    8.5  18.5     0.013         2      24     115 ..     594     689 ..     578     694 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.013
                             Mod_r  24 tlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldell....qkfspdal 96 
                                        +pe++ql++e e+l ++ e+  +++ + e++++++ +++ e+++ +++l++++ ++e+e  +l     +k+ +++ 
  gi|557694215|ref|YP_008797269.1| 594 LMPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPqlmqRKTELESE 670
                                       4599***********99998888888888******************************997666666889999999 PP

                             Mod_r  97 larLqtavaeaeeeSeala 115
                                        ++L++++++a +e  +l+
  gi|557694215|ref|YP_008797269.1| 671 VDKLEQKLSQARNEVTQLE 689
                                       9999999999999887776 PP

>> Uds1  Up-regulated During Septation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   7.1     0.012         2      73     119 ..     601     647 ..     572     659 .. 0.73
   2 ?    4.7  15.2      0.19        31      22     116 ..     597     689 ..     595     695 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.012
                              Uds1  73 arsnskssreslakaeeelaeserkvdelaselekleeraaevrrrL 119
                                        r++ +s ++sl++a ++ +e+e++++++++++ ++++raa++r rL
  gi|557694215|ref|YP_008797269.1| 601 LRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRL 647
                                       34455556789**********************************99 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.19
                              Uds1  22 eVeelkkelkaLeerlealrk.kLaletklrdaarsLsrlyssskksakssaarsnskssreslakaeeelaeserk 97 
                                       e+e+l++e+++L++ le++r+ k + e ++ + ++++ ++  + ++ +++ a   + +++ + l + ++  +e+e+ 
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQaKTEAEEQINQVTQQIVEARNRAAQLRDRLA---QLEKEAADLPQLMQRKTELESE 670
                                       89**************999864789999999999999999844444433333...2333345677788888888888 PP

                              Uds1  98 vdelaselekleeraaevr 116
                                       vd+l+++l +++++ ++++
  gi|557694215|ref|YP_008797269.1| 671 VDKLEQKLSQARNEVTQLE 689
                                       8888888888888877765 PP

>> ArAE_2_N  Putative ER transporter, 6TM, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   5.7     0.049         8     376     468 ..     600     695 ..     587     697 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.049
                          ArAE_2_N 376 qrsltlsdldeviealrelsgeileaveegletivewleaanefR.iyslalpwnak..khkekqkeaaaeleeake 449
                                       q ++ +++l++  e+ r+  +e  e+++++ ++ive  + a + R   + +++++a   +  ++++e++ e++++++
  gi|557694215|ref|YP_008797269.1| 600 QLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRdRLAQLEKEAADlpQLMQRKTELESEVDKLEQ 676
                                       6688899999999********************************43444444444333678999************ PP

                          ArAE_2_N 450 tlekaledfakakrlklla 468
                                       +l++a+++ ++ +++++++
  gi|557694215|ref|YP_008797269.1| 677 KLSQARNEVTQLETMNMVM 695
                                       *********9999988776 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 ?    5.5   9.3     0.059       9.6     144     248 ..     599     701 ..     580     710 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.059
                   Phlebovirus_NSM 144 eklkkkaeekdktisr..ktkesEediknqvlhseieqlknelqkkRndikrgqekrdakklveesmArvkdlkeel 218
                                       e+l+++ e   + +++  ++k   e+  nqv  ++i   +n+  ++R  +  +q  ++a     ++m r ++l  e 
  gi|557694215|ref|YP_008797269.1| 599 EQLRQEVESLSQSLEQarQAKTEAEEQINQVT-QQIVEARNRAAQLRDRL--AQLEKEAAD-LPQLMQRKTELESEV 671
                                       55555554444444332122222222344443.34555556666666552..232222222.345677777788888 PP

                   Phlebovirus_NSM 219 kiltdelsqikseiqilrkkikdfetvvpA 248
                                        +l   lsq+++e++ l   ++ ++ v   
  gi|557694215|ref|YP_008797269.1| 672 DKLEQKLSQARNEVTQLETMNMVMMGVAVV 701
                                       888888888888888887777777776544 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 ?    2.2   8.3      0.54        88      60     102 ..     597     639 ..     585     642 .. 0.69
   2 ?   10.4   8.0    0.0018      0.29      28      86 ..     631     689 ..     629     694 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.54
                              HemX  60 qkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga 102
                                       + ++l ++++ l+++le++++++++ ++q+++++qq+ +  ++
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNR 639
                                       4566777777777777777777777777777777777665554 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0018
                              HemX  28 qqvqeltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlq 86 
                                       qq  e++ ++a+l+++la+le+++a + ++ ++k+ele+++++l++kl+++++e++ql+
  gi|557694215|ref|YP_008797269.1| 631 QQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTELESEVDKLEQKLSQARNEVTQLE 689
                                       7888999999*********************************************9986 PP

>> DUF1640  Protein of unknown function (DUF1640)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1  13.7      0.13        21      74     166 ..     598     698 ..     583     704 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.13
                           DUF1640  74 faalrseteklqreleklkq...kLreeidklkadirldlnleKgrireelakleaki......qelnnkidrevsa 141
                                       +++lr+e e+l + le+ +q   + +e+i++++++  ++  ++ ++ r+ la+le++       ++ ++ ++ ev +
  gi|557694215|ref|YP_008797269.1| 598 IEQLRQEVESLSQSLEQARQaktEAEEQINQVTQQ-IVEARNRAAQLRDRLAQLEKEAadlpqlMQRKTELESEVDK 673
                                       45555555555555555444222344445555544.45555555566666666666553333222225556677777 PP

                           DUF1640 142 lrteiEsvKldvikyliglvvgila 166
                                       l +++ +++++v++   + +v++ +
  gi|557694215|ref|YP_008797269.1| 674 LEQKLSQARNEVTQLETMNMVMMGV 698
                                       7777777777777665555555544 PP

>> ISG65-75  Invariant surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   5.6     0.025         4      69     128 ..     597     656 ..     592     666 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.025
                          ISG65-75  69 akekvdyyvekleslleeakekgtltesdaeklkkaceeAkaknkkarekakkalekaek 128
                                       ++e+++++ve l + le+a++ +t  e++++++++++ eA + +++ r++ ++  ++a++
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAAD 656
                                       678999*****************************************9999999988876 PP

>> Myc-LZ  Myc leucine zipper domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.1    0.0038      0.61       4      28 ..     592     616 ..     591     617 .. 0.93
   2 ?    2.2   0.2       1.2     2e+02      14      27 ..     637     650 ..     636     651 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0038
                            Myc-LZ   4 qrLlSekEqLRkrrEqLKhkLeQLr 28 
                                       +rL+ e+EqLR + E L + LeQ r
  gi|557694215|ref|YP_008797269.1| 592 KRLMPEIEQLRQEVESLSQSLEQAR 616
                                       79*********************65 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 1.2
                            Myc-LZ  14 RkrrEqLKhkLeQL 27 
                                       R r  qL  +L+QL
  gi|557694215|ref|YP_008797269.1| 637 RNRAAQLRDRLAQL 650
                                       67889********9 PP

>> betaPIX_CC  betaPIX coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.3    0.0017      0.28      42      82 ..     596     636 ..     592     641 .. 0.91
   2 ?    0.8   3.7       2.8   4.5e+02      39      84 ..     642     683 ..     639     691 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0017
                        betaPIX_CC  42 devqelkqenkklkksleeEqkaRkdLEkvvrkllksinde 82 
                                        e+++l+qe  +l +sle+ ++a+ + E+ +++++++i + 
  gi|557694215|ref|YP_008797269.1| 596 PEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEA 636
                                       689*********************************99765 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 2.8
                        betaPIX_CC  39 aLkdevqelkqenkklkksleeEqkaRkdLEkvvrkllksindetw 84 
                                       +L+d +++l++e   l + +++      +LE+ v kl +++++   
  gi|557694215|ref|YP_008797269.1| 642 QLRDRLAQLEKEAADLPQLMQRKT----ELESEVDKLEQKLSQARN 683
                                       69***********99999987655....566666655555554433 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   9.4    0.0042      0.68      99     156 ..     595     652 ..     585     653 .. 0.93
   2 ?    1.4   3.5         1   1.6e+02      98     136 ..     653     691 ..     649     696 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0042
                           DUF4763  99 qpeileLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlnelds 156
                                        pei +L+++   L q l+++ q +++ +++++++++++ + ++r+++l+ rl +l++
  gi|557694215|ref|YP_008797269.1| 595 MPEIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEK 652
                                       69***************************************************99986 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 1
                           DUF4763  98 eqpeileLqrnnhkLrqqlaelqqhlkasrkslkelres 136
                                       e  ++ +L +++  L  ++++l+q+l + r+++++l+++
  gi|557694215|ref|YP_008797269.1| 653 EAADLPQLMQRKTELESEVDKLEQKLSQARNEVTQLETM 691
                                       667888999999999999999999999999999999875 PP

>> Nas2_N  Nas2 N_terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   2.8       4.8   7.8e+02       3      25 ..     593     615 ..     591     654 .. 0.76
   2 ?    9.6   1.0    0.0053      0.87       2      26 ..     658     682 ..     657     691 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 4.8
                            Nas2_N   3 eLekkkdeiekeieelsevLesq 25 
                                       +L+ + +++ +e+e+ls+ Le++
  gi|557694215|ref|YP_008797269.1| 593 RLMPEIEQLRQEVESLSQSLEQA 615
                                       67778888888888888888733 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0053
                            Nas2_N   2 keLekkkdeiekeieelsevLesqn 26 
                                        +L+++k+e+e+e+++l++ L++++
  gi|557694215|ref|YP_008797269.1| 658 PQLMQRKTELESEVDKLEQKLSQAR 682
                                       69*******************9654 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  14.3     0.071        12     141     218 ..     599     680 ..     593     689 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.071
                            Cluap1 141 dlLekeve.lreartkalsrqleleeiekalkeaikkvkeelektkkalenlesdeanLeakiekkk...qeleraq 213
                                       ++L++eve l ++ ++a ++++e ee  ++++++i ++++++++++++l++le++ a L + +++k+   +e+++ +
  gi|557694215|ref|YP_008797269.1| 599 EQLRQEVEsLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAADLPQLMQRKTeleSEVDKLE 675
                                       57888887677888888889999999999999999999999999999999999999999887777642224666666 PP

                            Cluap1 214 krLqs 218
                                       ++L++
  gi|557694215|ref|YP_008797269.1| 676 QKLSQ 680
                                       66655 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 ?    3.7   7.6     0.073        12      15     105 ..     602     691 ..     588     704 .. 0.38

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.073
                        V_ATPase_I  15 nedvnafqrkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnen 91 
                                        ++v++++++  +  +   e e++++ ++++i ++++  ++ ++    + ++e+++l +l ++ ++le+e+ +l+++
  gi|557694215|ref|YP_008797269.1| 602 RQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRD-RLAQLEKEAADLPQLMQRKTELESEVDKLEQK 677
                                       22233333333222233333333333333333333333333322.22222222333333333333333333333333 PP

                        V_ATPase_I  92 leklkkelnelvel 105
                                       l++ ++e+++l+ +
  gi|557694215|ref|YP_008797269.1| 678 LSQARNEVTQLETM 691
                                       33333333333333 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  15.4     0.063        10      74     132 ..     597     655 ..     591     662 .. 0.84
   2 ?    4.0   6.1      0.27        44      67     109 ..     649     691 ..     646     693 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.063
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  74 qvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvraeas 132
                                       ++  Lr+++++l + +e+a+q  ++++e+ +q  +++ ear   + +    +++++ea+
  gi|557694215|ref|YP_008797269.1| 597 EIEQLRQEVESLSQSLEQARQAKTEAEEQINQVTQQIVEARNRAAQLRDRLAQLEKEAA 655
                                       68899999999999999999999999999999999999999888888887777777775 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  67 elekvkqqvalLrekeaelekqveeakqqleaerealrqarke 109
                                       +lek  + +  L ++  ele++v++++q+l ++r++++q++ +
  gi|557694215|ref|YP_008797269.1| 649 QLEKEAADLPQLMQRKTELESEVDKLEQKLSQARNEVTQLETM 691
                                       677777788889999*********************9998765 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   8.3       6.4     1e+03      44      89 ..     602     650 ..     580     651 .. 0.68
   2 ?    6.0  12.1      0.11        18      27      90 ..     620     686 ..     617     687 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 6.4
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHC CS
                              BST2  44 nqtvvtLkasLekekaqsqkqqakvqelqgei...kkLnqkLqdaeaev 89 
                                        q v++L++sLe+ +  + ++++++++  ++i   ++ + +L+d +a++
  gi|557694215|ref|YP_008797269.1| 602 RQEVESLSQSLEQARQAKTEAEEQINQVTQQIveaRNRAAQLRDRLAQL 650
                                       5667888888888777777777777666665511144556666666665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                              BST2  27 tqaqeslreaeaqaatcnqtvvtLka...sLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                       t+a+e++++  +q+    +   +L++    Leke a   +  ++  el+ e+ kL+qkL +a+ ev 
  gi|557694215|ref|YP_008797269.1| 620 TEAEEQINQVTQQIVEARNRAAQLRDrlaQLEKEAADLPQLMQRKTELESEVDKLEQKLSQARNEVT 686
                                       6778888888888888888888887611156777777666778889*****************9997 PP

>> DUF3847  Protein of unknown function (DUF3847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   9.9     0.063        10       2      59 ..     598     660 ..     597     665 .. 0.88
   2 ?    4.6   1.6      0.21        35       4      27 ..     666     689 ..     663     694 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.063
                           DUF3847   2 leeLkaelekaekklrqaehkekiLenrlkyle.....RkeRtHrLitrGaalEsilpeakeL 59 
                                       +e+L++e+e   + l+qa++ ++  e ++ +++      ++R+ +L +r a+lE+ +  + +L
  gi|557694215|ref|YP_008797269.1| 598 IEQLRQEVESLSQSLEQARQAKTEAEEQINQVTqqiveARNRAAQLRDRLAQLEKEAADLPQL 660
                                       8******************************99999999999999999999999866655555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.21
                           DUF3847   4 eLkaelekaekklrqaehkekiLe 27 
                                       eL  e++k e+kl qa+++ + Le
  gi|557694215|ref|YP_008797269.1| 666 ELESEVDKLEQKLSQARNEVTQLE 689
                                       7999****************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (716 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2174  (0.121256); expected 358.6 (0.02)
Passed bias filter:                     1229  (0.0685482); expected 358.6 (0.02)
Passed Vit filter:                       355  (0.0198003); expected 17.9 (0.001)
Passed Fwd filter:                       164  (0.00914719); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             110  [number of targets reported over threshold]
# CPU time: 1.46u 0.36s 00:00:01.81 Elapsed: 00:00:00.56
# Mc/sec: 3875.57
//
Query:       gi|557694216|ref|YP_008797270.1|  [L=108]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   41.2   0.6    1.9e-10   40.6   0.6    1.3  1  HTH_3           Helix-turn-helix
    1.2e-08   35.2   0.0    1.5e-08   34.8   0.0    1.2  1  HTH_31          Helix-turn-helix domain
      3e-08   33.6   0.1    4.5e-08   33.0   0.1    1.3  1  HTH_19          Helix-turn-helix domain
    8.5e-05   22.3   0.2    0.00018   21.3   0.2    1.5  1  HTH_25          Helix-turn-helix domain
     0.0033   17.5   0.1     0.0045   17.1   0.1    1.2  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.062   13.3   0.0    1.5  1  HTH_37          Helix-turn-helix domain


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 !   40.6   0.6   6.3e-14   1.9e-10       1      52 [.      25      76 ..      25      79 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 6.3e-14
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsl 52
                                      +++ R++lglsq+eLA ++  + + i +iE +e nP l+ +k+l+k+L++sl
  gi|557694216|ref|YP_008797270.1| 25 VRREREKLGLSQAELASLVKTKETIIKKIEQNEFNPPLDLVKRLEKVLKTSL 76
                                      5899*********************************************998 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   0.0   5.2e-12   1.5e-08       1      57 [.      20      75 ..      20      83 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 5.2e-12
                            HTH_31  1 aLGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgld 57
                                      +LG+ +r+ Re+ GLsq+e+A ++   e+ + ++Eq +  +p+++ + +l  +l ++
  gi|557694216|ref|YP_008797270.1| 20 DLGQVVRREREKLGLSQAELASLVKTKETIIKKIEQNEF-NPPLDLVKRLEKVLKTS 75
                                      69*************************************.6*********9999886 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.1   1.5e-11   4.5e-08       1      55 [.      22      75 ..      22      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.5e-11
                            HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid 55
                                      G+ +++ Re+lgl+q+ela+ +++  + i +iE +++ +p+ +l++++ + l+ +
  gi|557694216|ref|YP_008797270.1| 22 GQVVRREREKLGLSQAELASLVKTKETIIKKIEQNEF-NPPLDLVKRLEKVLKTS 75
                                      78899********************************.***9**99998877766 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.2     6e-08   0.00018       3      36 ..      26      59 ..      24      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 6e-08
                                      HHHHHTTT--HHHHHHHSS--HHHHHHHHCT--T CS
                            HTH_25  3 raaRearglsleevaketkIrkdylealEeddfd 36
                                      r++Re++gls  e+a   k ++ +++++E+++f+
  gi|557694216|ref|YP_008797270.1| 26 RREREKLGLSQAELASLVKTKETIIKKIEQNEFN 59
                                      89*****************************996 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 !   17.1   0.1   1.5e-06    0.0045      71     118 ..      22      69 ..       5      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.5e-06
                    MqsA_antitoxin  71 pafiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalvkllk 118
                                       ++ ++r r+kl+l+q+e+a++  +      + e+ + +ppl lvk l+
  gi|557694216|ref|YP_008797270.1|  22 GQVVRREREKLGLSQAELASLVKTKETIIKKIEQNEFNPPLDLVKRLE 69 
                                       678999**************************************9775 PP

>> HTH_37  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   2.1e-05     0.062      21      56 ..      23      58 ..      16      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                                      HHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT-- CS
                            HTH_37 21 laiaeliekrelsqseaaqllgiaqPkvsrllrgkl 56
                                      + +++ +ek++lsq+e+a l ++++  + ++++ ++
  gi|557694216|ref|YP_008797270.1| 23 QVVRREREKLGLSQAELASLVKTKETIIKKIEQNEF 58
                                      568999********************9999997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); 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 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 763.81
//
Query:       gi|557694217|ref|YP_008797271.1|  [L=221]
Description: ribosome biogenesis protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  163.6   0.0    4.7e-48  163.4   0.0    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 !  163.4   0.0   2.6e-52   4.7e-48       4     194 .]       2     215 ..       1     215 [. 0.90

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 2.6e-52
                                       EEES--B--GG................SCGGSB--HHHHCGG.TTSTTGGGSS-CHHHHHHHHHHHCSCHHCTT.EE CS
                              EMG1   4 eeasLelvkvk................kkseqLLnsddhkkilkklkreakeaRpDIvHqcLlalldspLnkagllq 64 
                                       +ea+Le+v+ +                k+s+ LL+ ++h+ ++kkl +++k++RpDIvH+cLl +l spLn+a++l+
  gi|557694217|ref|YP_008797271.1|   2 AEAALETVPPEiqghpavvkdaerrgkKPSQILLDRSYHHFAMKKLPDAEKRGRPDIVHFCLLEALGSPLNQANKLE 78 
                                       789*******999*************9************************************************** PP

                                       EEEEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS-HHHHCCC...SEEEEE-TTSEE CS
                              EMG1  65 vyihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkviknpitdhlpp..gskiillsesaek 139
                                        y+ t+ + +I+vnp++R+Pr ++rF+g++++L+ +++ir+++ge +Ll+  k++++ + ++   s++ill+e++e+
  gi|557694217|ref|YP_008797271.1|  79 TYVATRGGLVIYVNPRVRLPRVYERFKGVVEKLFAEGEIRSETGE-TLLRCEKKSLKTLAESlnPSTKILLTERGEP 154
                                       ********************************************9.*********999988877789999999***7 PP

                                       -................EEEE-SSSS....---HH.......EEESSSS---HHHHHHHHHHHCH CS
                              EMG1 140 klvdleefv...vkpvvfvigamskgsvkidykee.......eisisnypLsaavvcskiltafE 194
                                       + ++ ++ +   ++   +++g++++g    d+++e       +++i + pL+a++v+s++l+ +E
  gi|557694217|ref|YP_008797271.1| 155 VNARGFSAAlagHTRPLIMVGCFPHG----DFTSEtksladkTLAIHQTPLEAWTVISRVLCYIE 215
                                       766666655888556669********....444333333444******************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1500.65
//
Query:       gi|557694218|ref|YP_008797272.1|  [L=109]
Description: ribonuclease P subunit RPR2 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   40.5   0.2    3.2e-10   40.1   0.2    1.2  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
    0.00094   19.2   0.2     0.0015   18.5   0.2    1.3  1  DZR             Double zinc ribbon
      0.009   16.0   0.3       0.02   14.9   0.3    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.026   14.3   5.7       0.22   11.3   0.2    2.3  2  zinc_ribbon_2   zinc-ribbon domain
      0.039   14.3   1.6       0.18   12.2   0.0    2.1  2  GFA             Glutathione-dependent formaldehyde-activating
       0.04   13.9   8.8      0.044   13.7   1.3    2.4  2  zinc_ribbon_4   zinc-ribbon domain
      0.044   13.7   2.4       0.21   11.6   2.3    1.9  2  RNHCP           RNHCP domain
      0.068   12.9   0.9      0.068   12.9   0.9    2.5  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.12   12.5   2.8        1.2    9.4   2.8    2.2  1  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
        0.2   11.1   2.4        4.3    6.9   0.1    2.2  2  zf-ribbon_3     zinc-ribbon domain
        0.3   11.2   3.2        3.6    7.8   0.4    2.3  2  UPF0547         Uncharacterised protein family UPF0547
       0.38   10.4   1.5        3.3    7.4   0.2    2.2  2  zf_C2H2_13      Zinc finger domain
       0.81    9.6   5.2        1.6    8.7   0.2    2.2  2  TFIIS_C         Transcription factor S-II (TFIIS)
        1.3    9.0   7.6        5.8    6.9   1.0    2.4  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
        1.4    8.9  10.2        5.5    7.0   6.8    2.8  3  Nudix_N_2       Nudix N-terminal
        2.3    8.4   6.4        2.9    8.0   5.8    1.4  1  PknG_rubred     Protein kinase G rubredoxin domain
          7    6.7   9.4        1.5    8.9   1.6    2.3  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


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 !   40.1   0.2     3e-13   3.2e-10      18      90 .]      27      90 ..      13      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 3e-13
                                      HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E.........EEEEETTTT CS
                              Rpr2 18 palsrylakqlrevskkaqlrlppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlvvtClaCg 90
                                      ++ +   ++ + ++++k++lrlp+ ++r++C+kCg+ ++  +t+svrv+  ++         + +vv+C++Cg
  gi|557694218|ref|YP_008797272.1| 27 SEKAVEAVRIAMRIAQKTRLRLPTYLRRRFCRKCGTPWTGPSTVSVRVRG-NRA--------THVVVRCKKCG 90
                                      5555566677789***********************************74.332........2368******7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   1.5e-06    0.0015      11      36 ..      53      91 ..      48      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                               DZR 11 darfCseCgtklkavaa.............edrCpsCge 36
                                      + rfC +Cgt+   +++               rC +Cg+
  gi|557694218|ref|YP_008797272.1| 53 RRRFCRKCGTPWTGPSTvsvrvrgnrathvVVRCKKCGH 91
                                      679********9988889999****************97 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 !   14.9   0.3   1.9e-05      0.02      38      95 ..      21      92 ..       2     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                                      T--HHHHHHHHHHHHCC.T.TTT-EEEEEEE--EEEETTTS-EEECHHH.HH............S-TTTSSS CS
                              HypA 38 gvepeaLefafellaegtv.legaeLeieevpvkvrCreCgkefeleek.al............rCpkCgsa 95
                                      +++pe  e a e+++     +++++L++ +   +  Cr+Cg+ ++  ++ ++            rC+kCg++
  gi|557694218|ref|YP_008797272.1| 21 TIHPEDSEKAVEAVRIAMRiAQKTRLRLPTYLRRRFCRKCGTPWTGPSTvSVrvrgnrathvvvRCKKCGHT 92
                                      5677777777777765555489999*******************955432336789999**********986 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00021      0.22      14      22 ..      55      63 ..      53      64 .. 0.87
   2 ?    4.9   1.4     0.022        23       1       7 [.      85      91 ..      85      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
                     zinc_ribbon_2 14 kFCpyCGtp 22
                                      +FC +CGtp
  gi|557694218|ref|YP_008797272.1| 55 RFCRKCGTP 63
                                      79*****98 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.022
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +C++CG+
  gi|557694218|ref|YP_008797272.1| 85 RCKKCGH 91
                                      6999997 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00017      0.18      41      61 ..      46      66 ..      27      77 .. 0.70
   2 ?    2.1   0.3      0.24   2.6e+02      44      58 ..      76      92 ..      64     104 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                               GFA 41 adsgnkvtrsfCpeCgsplys 61
                                          + ++r+fC++Cg+p + 
  gi|557694218|ref|YP_008797272.1| 46 LRLPTYLRRRFCRKCGTPWTG 66
                                      455678899********9875 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.24
                               GFA 44 gnkvtr..sfCpeCgsp 58
                                      gn++t+    C++Cg +
  gi|557694218|ref|YP_008797272.1| 76 GNRATHvvVRCKKCGHT 92
                                      44555544789999964 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.1     0.039        41      28      36 .]      57      65 ..      55      65 .. 0.93
   2 ?   13.7   1.3   4.1e-05     0.044      20      34 ..      78      92 ..      71      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.039
                     zinc_ribbon_4 28 CskCghvFr 36
                                      C kCg+ ++
  gi|557694218|ref|YP_008797272.1| 57 CRKCGTPWT 65
                                      ******996 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.1e-05
                     zinc_ribbon_4 20 pakgvkvrCskCghv 34
                                      +a++v vrC+kCgh+
  gi|557694218|ref|YP_008797272.1| 78 RATHVVVRCKKCGHT 92
                                      578899********7 PP

>> RNHCP  RNHCP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.63   6.7e+02      25      73 ..      56      61 ..      20      66 .. 0.53
   2 ?   11.6   2.3    0.0002      0.21      52      77 ..      69      94 ..      57     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.63
                             RNHCP 25 HCpsCLlskHvdeepgdraseCkglmepiavevkkkkewvivhrCekCg 73
                                                                                  C+kCg
  gi|557694218|ref|YP_008797272.1| 56 F-------------------------------------------CRKCG 61
                                      2...........................................55554 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0002
                             RNHCP 52 piavevkkkkewvivhrCekCgelkk 77
                                       ++v+v+ ++ + +v rC+kCg++++
  gi|557694218|ref|YP_008797272.1| 69 TVSVRVRGNRATHVVVRCKKCGHTRR 94
                                      6899999***************9986 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 ?    1.9   0.7      0.17   1.8e+02      20      24 ..      57      61 ..      54      63 .. 0.90
   2 ?   12.9   0.9   6.4e-05     0.068      17      25 ..      83      91 ..      78     101 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.17
                                      -SSS- CS
                    DNA_RNApol_7kD 20 CkeCG 24
                                      C++CG
  gi|557694218|ref|YP_008797272.1| 57 CRKCG 61
                                      99**9 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6.4e-05
                                      ----SSS-- CS
                    DNA_RNApol_7kD 17 piRCkeCGh 25
                                      ++RCk+CGh
  gi|557694218|ref|YP_008797272.1| 83 VVRCKKCGH 91
                                      79******9 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 ?    9.4   2.8    0.0011       1.2      30      49 ..      78      97 ..      56     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                    zinc_ribbon_13 30 nkkfitvsCknCgYtelYka 49
                                      + ++++v Ck+Cg+t  + a
  gi|557694218|ref|YP_008797272.1| 78 RATHVVVRCKKCGHTRRFYA 97
                                      67889*********975444 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1     0.004       4.3      17      25 ..      55      63 ..      53      63 .. 0.86
   2 ?    3.9   0.3     0.035        37       4      10 ..      85      91 ..      83      92 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.004
                       zf-ribbon_3 17 nvCpyCGtk 25
                                      ++C +CGt+
  gi|557694218|ref|YP_008797272.1| 55 RFCRKCGTP 63
                                      69*****96 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.035
                       zf-ribbon_3  4 rCPnCGa 10
                                      rC +CG+
  gi|557694218|ref|YP_008797272.1| 85 RCKKCGH 91
                                      5555554 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.4    0.0034       3.6      15      24 ..      55      64 ..      54      65 .. 0.91
   2 ?    3.8   0.2      0.06        63      15      22 ..      84      91 ..      82      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0034
                           UPF0547 15 qfCphCGyvF 24
                                      +fC+ CG+ +
  gi|557694218|ref|YP_008797272.1| 55 RFCRKCGTPW 64
                                      79******98 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.06
                           UPF0547 15 qfCphCGy 22
                                      ++C  CG+
  gi|557694218|ref|YP_008797272.1| 84 VRCKKCGH 91
                                      57999998 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.2    0.0031       3.3      17      26 ..      54      63 ..      47      69 .. 0.84
   2 ?    2.0   0.1      0.15   1.6e+02      20      25 ..      86      91 ..      84      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0031
                        zf_C2H2_13 17 YRvCnkCGkP 26
                                       R C kCG P
  gi|557694218|ref|YP_008797272.1| 54 RRFCRKCGTP 63
                                      599*****99 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.15
                        zf_C2H2_13 20 CnkCGk 25
                                      C+kCG 
  gi|557694218|ref|YP_008797272.1| 86 CKKCGH 91
                                      *****6 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 ?    2.7   1.0      0.11   1.2e+02      31      39 .]      57      65 ..      53      65 .. 0.83
   2 ?    8.7   0.2    0.0015       1.6      27      37 ..      82      92 ..      78      98 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                           TFIIS_C 31 CtkCghrWr 39
                                      C kCg  W+
  gi|557694218|ref|YP_008797272.1| 57 CRKCGTPWT 65
                                      889998885 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0015
                           TFIIS_C 27 vfykCtkCghr 37
                                      v ++C+kCgh+
  gi|557694218|ref|YP_008797272.1| 82 VVVRCKKCGHT 92
                                      56677777775 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 ?    5.7   0.8     0.013        13      22      33 ..      51      62 ..      49      65 .. 0.78
   2 ?    6.9   1.0    0.0055       5.8      11      21 ..      83      93 ..      82      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.013
                           DUF35_N 22 fPPravCphCgs 33
                                      + +r++C++Cg 
  gi|557694218|ref|YP_008797272.1| 51 YLRRRFCRKCGT 62
                                      567899999985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0055
                           DUF35_N 11 gqrCpdCGtvq 21
                                      + rC++CG+ +
  gi|557694218|ref|YP_008797272.1| 83 VVRCKKCGHTR 93
                                      56******986 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1         9   9.5e+03      18      23 ..       3       8 ..       3       9 .. 0.79
   2 ?    7.0   6.8    0.0052       5.5       1      30 [.      55      91 ..      55      93 .. 0.68
   3 ?    3.9   0.4      0.05        53       3       9 ..      86      92 ..      85     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9
                                      -SS-EE CS
                         Nudix_N_2 18 DnreRl 23
                                      ++r+R+
  gi|557694218|ref|YP_008797272.1|  3 EERQRA 8 
                                      689997 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0052
                                      -B-TTT--B-E....EE--TT-SS-EEE...ETTTTE CS
                         Nudix_N_2  1 kFCsqCGtpve....lripdgDnreRlv...CpaCgt 30
                                      +FC++CGtp +      +   +nr  +v   C++Cg+
  gi|557694218|ref|YP_008797272.1| 55 RFCRKCGTPWTgpstVSVRVRGNRATHVvvrCKKCGH 91
                                      8*******97656665555566666665555777777 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.05
                                      -TTT--B CS
                         Nudix_N_2  3 CsqCGtp 9 
                                      C++CG++
  gi|557694218|ref|YP_008797272.1| 86 CKKCGHT 92
                                      6666654 PP

>> PknG_rubred  Protein kinase G rubredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.8    0.0028       2.9      91     127 ..      53      96 ..      49     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0028
                                       GG-B-TTT--B.-S......---SS----SEEE-TTT--EEE-S CS
                       PknG_rubred  91 skRfCwrCGrp.vG......RsekerkgaseGtCpkCgspysFl 127
                                       ++RfC +CG+p  G      R +++r+++    C+kCg++  F 
  gi|557694218|ref|YP_008797272.1|  53 RRRFCRKCGTPwTGpstvsvRVRGNRATHVVVRCKKCGHTRRFY 96 
                                       69*******995352233336667778888889*****987775 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 ?    2.1   1.6      0.18   1.9e+02      18      25 ..      54      61 ..      28      78 .. 0.76
   2 ?    8.9   1.6    0.0014       1.5      19      37 ..      84     103 ..      73     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.18
                     Zn_Tnp_IS1595 18 gfvCPhCg 25
                                      ++ C +Cg
  gi|557694218|ref|YP_008797272.1| 54 RRFCRKCG 61
                                      24477777 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0014
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrgl 37 
                                       ++C +Cg++ ++y +k+rg+
  gi|557694218|ref|YP_008797272.1|  84 VRCKKCGHTrRFYALKKRGK 103
                                       56**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 808.99
//
Query:       gi|557694219|ref|YP_008797273.1|  [L=143]
Description: small subunit ribosomal protein S19e [Candidatus Caldiarchaeum subterraneum]
Scores for 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-51  172.7   0.0    3.7e-51  172.4   0.0    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
     0.0055   16.6   0.0      0.014   15.3   0.0    1.6  2  HTH_12          Ribonuclease R winged-helix domain
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.21   11.6   0.0    1.3  1  HTH_45          Winged helix-turn-helix


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 !  172.4   0.0   6.1e-55   3.7e-51       2     134 ..       5     137 ..       4     139 .. 0.98

  Alignments for each domain:
  == domain 1  score: 172.4 bits;  conditional E-value: 6.1e-55
                                       SSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS- CS
                    Ribosomal_S19e   2 vkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGgk 78 
                                       v+ V++e+li+++a++Lk+++ +++P wa +vKt++a+e +p ++dW++vRaAsilRk+yl gpvGv+r+rk+YGg+
  gi|557694219|ref|YP_008797273.1|   5 VRAVEPEKLINRVAAYLKNNQVVTPPPWAMFVKTSVAREEPPRNPDWWFVRAASILRKLYLYGPVGVSRMRKFYGGR 81 
                                       789************************************************************************** PP

                                       ------THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXX CS
                    Ribosomal_S19e  79 krrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeev 134
                                       +r g++p  f+k+ g+++rki+qqLek++lv++  +kgr +t+kG +ll++ a+++
  gi|557694219|ref|YP_008797273.1|  82 HRVGMAPPYFAKGGGAIVRKIMQQLEKAELVSTVPRKGRAITPKGVKLLQQAAKSI 137
                                       *******************************999999****************998 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 ?   -2.5   0.0      0.85   5.1e+03      40      51 ..       6      17 ..       5      20 .. 0.81
   2 !   15.3   0.0   2.4e-06     0.014      35      66 .]      99     130 ..      93     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.85
                            HTH_12 40 rkleergltrrv 51
                                      r+ e ++l++rv
  gi|557694219|ref|YP_008797273.1|  6 RAVEPEKLINRV 17
                                      788899999998 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.4e-06
                            HTH_12  35 vRyrLrkleergltrrvgyagreltEkGleeL 66 
                                       vR  ++ le+ +l+  v + gr +t kG+++L
  gi|557694219|ref|YP_008797273.1|  99 VRKIMQQLEKAELVSTVPRKGRAITPKGVKLL 130
                                       8999*************************987 PP

>> HTH_45  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   3.5e-05      0.21      36      72 ..      99     136 ..      97     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
                            HTH_45  36 lnkYLdmLvekglikk.skekYvlTekGlelleklkel 72 
                                       ++k +++L + +l+++   +   +T kG +ll++  + 
  gi|557694219|ref|YP_008797273.1|  99 VRKIMQQLEKAELVSTvPRKGRAITPKGVKLLQQAAKS 136
                                       678899********7779999***********998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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 0.22s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1156.73
//
Query:       gi|557694220|ref|YP_008797274.1|  [L=214]
Description: phosphoribosyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-29  101.6   0.6    4.2e-29  101.1   0.6    1.2  1  Pribosyltran  Phosphoribosyl transferase domain
     0.0054   16.2   0.1     0.0079   15.7   0.1    1.3  1  UPRTase       Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.017   14.6   0.0       0.11   12.0   0.0    2.3  3  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 !  101.1   0.6   7.1e-33   4.2e-29      16     158 ..      14     194 ..       4     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 101.1 bits;  conditional E-value: 7.1e-33
                                       EETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE..................... CS
                      Pribosyltran  16 arlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes............. 79 
                                        ++++++++       vv+gi+rgGv++++++a+eL++pl++v  +k  ++g++e a g+++e              
  gi|557694220|ref|YP_008797274.1|  14 GKYLKRLYQG----TCVVLGIPRGGVVIGYEVAKELKCPLDVVVTRKIGAPGQPELAVGAVAEDgtvfvdeeiaaiv 86 
                                       5555555555....78************************************************************* PP

                                       ............................EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HH CS
                      Pribosyltran  80 ............................rlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpa 128
                                                                   ++   + +++V+iVDD+l+tG T++aa++  +++++ +v++av+v++++
  gi|557694220|ref|YP_008797274.1|  87 gvsreyvekkaeeemrevrrrailyrggKPMQPLIDMRVVIVDDGLATGLTMKAAVHMARNQRAGKVIVAVPVAPSE 163
                                       ****************************99999999***************************************** PP

                                       HHHHHHHH-TTS......EEEEEEE-SEE-T CS
                      Pribosyltran 129 teeevdknakrvfsls.pdnfvavvgfelds 158
                                       t+e+ +k a+ v+ l+ p+nf a+ +f+ ++
  gi|557694220|ref|YP_008797274.1| 164 TVEKLKKIADDVVVLEtPTNFFAIGQFYERF 194
                                       ***************************9776 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   1.3e-06    0.0079     121     178 ..     122     177 ..      80     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-06
                           UPRTase 121 ertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeefpkvkv 178
                                       + +v+++D  +aTG ++ aa+++ ++   +  k++v+  +a +e v++l +   +v v
  gi|557694220|ref|YP_008797274.1| 122 DMRVVIVDDGLATGLTMKAAVHMARN--QRAGKVIVAVPVAPSETVEKLKKIADDVVV 177
                                       5679*********************9..55679**************99998888766 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.13   7.8e+02      34      77 ..       8      47 ..       5      66 .. 0.75
   2 ?   -3.0   0.0      0.75   4.5e+03     124     133 ..      75      84 ..      69     104 .. 0.71
   3 ?   12.0   0.0   1.8e-05      0.11     122     165 ..     123     166 ..     106     189 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.13
                          PRTase_2 34 eagaaLaellaeakkeelpepvlvigfAEtAtaLghgvadalee 77
                                      +ag++L++ l+    +  +++++v+g+    + +g  va++l+ 
  gi|557694220|ref|YP_008797274.1|  8 DAGQKLGKYLK----RLYQGTCVVLGIPRGGVVIGYEVAKELKC 47
                                      56777777777....56789999999999999999999999844 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.75
                          PRTase_2 124 lvLvDDEist 133
                                        v+vD Ei++
  gi|557694220|ref|YP_008797274.1|  75 TVFVDEEIAA 84 
                                       5888888864 PP

  == domain 3  score: 12.0 bits;  conditional E-value: 1.8e-05
                          PRTase_2 122 kelvLvDDEistGktalnliralqeklprkryvvvslvdwrsee 165
                                        ++v+vDD ++tG t+ + ++  +++   k +v v +    + e
  gi|557694220|ref|YP_008797274.1| 123 MRVVIVDDGLATGLTMKAAVHMARNQRAGKVIVAVPVAPSETVE 166
                                       679***************99999999888888877665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1609.63
//
Query:       gi|557694221|ref|YP_008797275.1|  [L=545]
Description: spermine synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   50.2   0.0    3.1e-13   49.5   0.0    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
    0.00024   21.0   0.0    0.00044   20.1   0.0    1.4  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
     0.0031   18.2   0.0     0.0064   17.2   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.048   14.4   0.0      0.092   13.5   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
      0.066   12.5   0.0       0.13   11.6   0.0    1.4  1  Methyltransf_2   O-methyltransferase domain
        0.2   11.1   0.0       0.31   10.5   0.0    1.1  1  Methyltransf_5   MraW methylase family


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 !   49.5   0.0     1e-16   3.1e-13      11     132 ..     279     395 ..     274     427 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 1e-16
                                       HHHCCSSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEEESTCHHHHC CS
                    Spermine_synth  11 vplmlhknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklvlgdgfkflk 87 
                                       ++l l++  ++ L iGGg     +  +k     ++++v+iD +v+d  ++f+        +d+r+ ++++d+ +fl+
  gi|557694221|ref|YP_008797275.1| 279 LGLALKPDAEKTLFIGGGGLSGPKYFLKNYPEVRVDVVEIDPDVVDTARRFFHV---P--EDSRLRVFVDDARMFLT 350
                                       678899999*******999877776666443679*****************964...4..677************** PP

                                       TCSS-EEEEEEECCSTTCSSCGCSSHHHHHHHHHTEEEEEEEEEE CS
                    Spermine_synth  88 ayekkfdvvivdsldpvgpaenlFskeffdllkkvlkedGviilq 132
                                       ++ +k+dvvi+d         +l + ef++ll +++  dGv+++ 
  gi|557694221|ref|YP_008797275.1| 351 KTDEKYDVVIMDAYSKTYVPFHLMTLEFYQLLRQKISSDGVVVSN 395
                                       ***************77777779******************9975 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 !   20.1   0.0   1.5e-07   0.00044      26      88 ..     331     394 ..     312     400 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.5e-07
                                       ETTTTEEEEEEES-HHHHHHHC-T-EEEEEE-SS-TTTSG.GGCSHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_30  26 laaeevtlklligdarealkeldekadawFlDgFsPaknP.elwseellkelarllkkkgtlat 88 
                                          e+ +l++ + dar +l + dek+d++ +D++s +  P  l + e++++l +++++ g++++
  gi|557694221|ref|YP_008797275.1| 331 HVPEDSRLRVFVDDARMFLTKTDEKYDVVIMDAYSKTYVPfHLMTLEFYQLLRQKISSDGVVVS 394
                                       446899******************************999978***************9999876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.1e-06    0.0064      12      73 ..     301     363 ..     291     385 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                                       HHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH.TTTTEEEEESBCCG.BSSSTTTEEEEEEEST CS
                   Methyltransf_25  12 tlalakrlgkakvtgvDiseemleaareraee.eglnvefvqgdaed.lpfedgsfDlvvssga 73 
                                        ++++k++++ +v  v+i+++ +++ar+ ++  e+ ++++ + da+  l   d+++D+v++  a
  gi|557694221|ref|YP_008797275.1| 301 PKYFLKNYPEVRVDVVEIDPDVVDTARRFFHVpEDSRLRVFVDDARMfLTKTDEKYDVVIM-DA 363
                                       4678888889******************99664555*********885789*********9.34 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.1e-05     0.092       3      72 ..     293     361 ..     291     399 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.1e-05
                   Methyltransf_12   3 iGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvva 72 
                                       iG+G  s  +++l++ p++++ +v+i+p+++ d+++++ +  +++  +v +++   + ++  +++D+v++
  gi|557694221|ref|YP_008797275.1| 293 IGGGGLSGPKYFLKNYPEVRVDVVEIDPDVV-DTARRFFHVPEDSRLRVFVDDARMFLTKTDEKYDVVIM 361
                                       899999999**********************.9999999999888888888888888777779******9 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.3e-05      0.13      69     119 ..     293     344 ..     287     384 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.3e-05
                                       ET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS-----TTEEEEES- CS
                    Methyltransf_2  69 vGGGtGalakaivsayPtikvivfDl.peVveaAkehlsageeervefvgGd 119
                                       +GGG     k   ++yP+++v v ++ p+Vv +A+++++++e++r+++   d
  gi|557694221|ref|YP_008797275.1| 293 IGGGGLSGPKYFLKNYPEVRVDVVEIdPDVVDTARRFFHVPEDSRLRVFVDD 344
                                       6788778889999***********9989**********99999988876544 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0001      0.31      29      99 ..     293     362 ..     284     364 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                       -TTSHHH..HHHHTT--TTEEEEEES-HHHHHHHTT.....---.EEEEES-GGGHHHHHHHTTTT-EEEEEEE CS
                    Methyltransf_5  29 lGaggHs..ealLeqlselrligidrDksalarakerLkefekr.ltlvkgnfkelkealaeanvtkvdgillD 99 
                                       +G+gg s  +++L++++e r+  +++D++++++a+++++  e+  l+++ +  + + ++++e+    +d +++D
  gi|557694221|ref|YP_008797275.1| 293 IGGGGLSgpKYFLKNYPEVRVDVVEIDPDVVDTARRFFHVPEDSrLRVFVDDARMFLTKTDEK----YDVVIMD 362
                                       5777776558**************************998776544999988887777766644....5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); 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):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.21s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 4196.91
//
Query:       gi|557694222|ref|YP_008797276.1|  [L=74]
Description: DNA-directed RNA polymerase subunit P [Candidatus Caldiarchaeum subterraneum]
Scores for 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-05   24.1   0.8    4.1e-05   23.6   0.8    1.3  1  Zn-ribbon_8     Zinc ribbon domain
    0.00013   21.8   1.0    0.00017   21.4   1.0    1.2  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
     0.0049   16.4   2.4       0.13   11.8   0.1    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0079   15.9   0.1     0.0097   15.6   0.1    1.1  1  TackOD1         Thaumarchaeal output domain 1
     0.0097   16.3   3.0       0.28   11.7   0.2    2.3  2  zf-C2H2         Zinc finger, C2H2 type
  ------ inclusion threshold ------
      0.022   14.7   0.1      0.028   14.4   0.1    1.2  1  zf-C2HC5        Putative zinc finger motif, C2HC5-type
      0.033   14.2   0.2      0.036   14.1   0.2    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.035   14.9   2.3        1.7    9.7   0.2    2.3  2  zf-C2H2_4       C2H2-type zinc finger
       0.43   10.6   0.2       0.43   10.6   0.2    2.1  2  zf-C2HC_2       zinc-finger of a C2HC-type
        3.8    8.1   5.6        3.1    8.4   0.2    2.2  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 !   23.6   0.8   2.3e-08   4.1e-05       6      32 ..      12      37 ..       5      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.3e-08
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeC 32
                                      Y+C +Cg++fe+   + + p+t CP C
  gi|557694222|ref|YP_008797276.1| 12 YQCVKCGRVFEKEKLV-KGPDTRCPYC 37
                                      99*********66644.488999**** 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 !   21.4   1.0   9.6e-08   0.00017       5      33 ..      12      40 ..      11      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.6e-08
                    Zn_ribbon_SprT  5 YrCtgCgreythhlsirrhnYrCrrCkgt 33
                                      Y+C+ Cgr ++ +  ++    rC++C  +
  gi|557694222|ref|YP_008797276.1| 12 YQCVKCGRVFEKEKLVKGPDTRCPYCTPV 40
                                      **************************865 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   7.2e-05      0.13      22      40 ..      14      32 ..       9      33 .. 0.91
   2 !    6.3   0.3    0.0038       6.7      19      29 ..      31      41 ..      30      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.2e-05
                                      ESSSSBEEEECCCCCCCHH CS
                      TF_Zn_Ribbon 22 CtdCGlVlednsidegpew 40
                                      C +CG V e +  ++gp+ 
  gi|557694222|ref|YP_008797276.1| 14 CVKCGRVFEKEKLVKGPDT 32
                                      ****************986 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0038
                                      CEEESSSSBEE CS
                      TF_Zn_Ribbon 19 elvCtdCGlVl 29
                                      +++C+ C++V+
  gi|557694222|ref|YP_008797276.1| 31 DTRCPYCTPVV 41
                                      689****9997 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   5.4e-06    0.0097     100     130 ..       8      38 ..       3      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.4e-06
                           TackOD1 100 eqelihhftCgnvgpeeeflkegkleCpkCk 130
                                       ++ l ++++Cg+v ++e+ +k+ +  Cp C 
  gi|557694222|ref|YP_008797276.1|   8 SRPLYQCVKCGRVFEKEKLVKGPDTRCPYCT 38 
                                       567789************************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 !   11.7   0.2   0.00015      0.28       1      12 [.      12      23 ..      12      28 .. 0.82
   2 ?    5.2   0.2     0.018        33       2       9 ..      33      40 ..      32      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                                      EEETTTTEEESS CS
                           zf-C2H2  1 ykCpdCgksFkr 12
                                      y+C +Cg++F  
  gi|557694222|ref|YP_008797276.1| 12 YQCVKCGRVFEK 23
                                      9*********64 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.018
                                      EETTTTEE CS
                           zf-C2H2  2 kCpdCgks 9 
                                      +Cp+C+ +
  gi|557694222|ref|YP_008797276.1| 33 RCPYCTPV 40
                                      8****975 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 ?   14.4   0.1   1.6e-05     0.028      18      43 ..      12      40 ..       4      50 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                          zf-C2HC5 18 pnClnCGkiiCakegls...kpCsfCgsp 43
                                       +C++CG +  + + ++    +C++C   
  gi|557694222|ref|YP_008797276.1| 12 YQCVKCGRVFEKEKLVKgpdTRCPYCTPV 40
                                      57*******977666668889*****854 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 ?   14.1   0.2     2e-05     0.036      69      95 ..      10      40 ..       4      56 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                                      -EEEETTTS-EEECHH..H..HHS-TTTSSS CS
                              HypA 69 vkvrCreCgkefelee..k..alrCpkCgsa 95
                                        ++C +Cg+ fe+e+  k  ++rCp C   
  gi|557694222|ref|YP_008797276.1| 10 PLYQCVKCGRVFEKEKlvKgpDTRCPYCTPV 40
                                      5679*********8876635678*****865 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 ?    9.7   0.2   0.00096       1.7       1      16 [.      12      26 ..      12      28 .. 0.80
   2 ?    5.4   0.1     0.023        41       2       8 ..      33      39 ..      32      47 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00096
                         zf-C2H2_4  1 fkCpiCgksFsskkaL 16
                                      ++C  Cg++F  k++L
  gi|557694222|ref|YP_008797276.1| 12 YQCVKCGRVF-EKEKL 26
                                      89********.66554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.023
                         zf-C2H2_4  2 kCpiCgk 8 
                                      +Cp+C+ 
  gi|557694222|ref|YP_008797276.1| 33 RCPYCTP 39
                                      7****54 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 ?   10.6   0.2   0.00024      0.43       1      19 [.      10      28 ..      10      28 .. 0.89
   2 ?    1.2   1.3       0.2   3.5e+02       4       8 ..      33      37 ..      32      37 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                         zf-C2HC_2  1 elvpCpkCgRsFnpdrlek 19
                                      +l +C kCgR F  + l+k
  gi|557694222|ref|YP_008797276.1| 10 PLYQCVKCGRVFEKEKLVK 28
                                      688*********9999987 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.2
                         zf-C2HC_2  4 pCpkC 8 
                                       Cp+C
  gi|557694222|ref|YP_008797276.1| 33 RCPYC 37
                                      6**** 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 ?    8.4   0.2    0.0017       3.1      13      25 ..       9      22 ..       7      23 .. 0.83
   2 ?    1.9   1.3      0.19   3.5e+02      16      20 ..      33      37 ..      22      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0017
                         zf-H2C2_2 13 kp.yeCplCdkaFk 25
                                      +p y+C +C+ +F 
  gi|557694222|ref|YP_008797276.1|  9 RPlYQCVKCGRVFE 22
                                      467********996 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.19
                         zf-H2C2_2 16 eCplC 20
                                       Cp+C
  gi|557694222|ref|YP_008797276.1| 33 RCPYC 37
                                      7**** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 593.81
//
Query:       gi|557694223|ref|YP_008797277.1|  [L=317]
Description: resolvase related protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   2.2    4.8e-13   49.1   0.4    2.6  2  HTH_17        Helix-turn-helix domain
    1.7e-06   28.0   0.2    4.1e-06   26.8   0.2    1.7  1  MerR_1        MerR HTH family regulatory protein
    2.5e-05   23.9   0.2    5.4e-05   22.9   0.2    1.6  1  MerR          MerR family regulatory protein
     0.0016   18.1   0.2     0.0057   16.4   0.2    1.9  1  HTH_23        Homeodomain-like domain
     0.0063   16.2   0.0      0.071   12.8   0.0    2.6  2  Sigma70_r4_2  Sigma-70, region 4
  ------ inclusion threshold ------
      0.011   15.8   0.2      0.041   14.0   0.2    1.9  1  HTH_28        Helix-turn-helix domain
      0.017   14.6   2.7       0.54    9.8   0.1    3.0  3  Sigma70_r4    Sigma-70, region 4
      0.023   14.9   0.0      0.064   13.4   0.0    1.8  1  DUF3853       Protein of unknown function (DUF3853)
      0.032   13.8   0.0      0.056   13.0   0.0    1.3  1  DDRGK         DDRGK domain
      0.059   13.4   0.0       0.16   12.0   0.0    1.7  1  HTH_29        Winged helix-turn helix
      0.096   13.1   0.0       0.15   12.4   0.0    1.5  1  DUF1323       Putative transcription regulator (DUF1323)


Domain annotation for each model (and alignments):
>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.4   2.9e-16   4.8e-13       1      46 [.      10      56 ..      10      59 .. 0.97
   2 ?    0.3   0.0       0.5   8.2e+02      22      41 ..     104     124 ..      98     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 2.9e-16
                            HTH_17  1 lltveEaAelLgvsrstvyrlirrgelpaak.iGrrwriprsdleew 46
                                      ++t+ E+A++Lgvs +tv r+i +g++ a+k  G+++ri+r+ le+ 
  gi|557694223|ref|YP_008797277.1| 10 WYTTGEVAKILGVSFRTVKRWIYSGKIEATKtAGGHYRISREVLERL 56
                                      9*******************************************996 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.5
                            HTH_17  22 irrgelpaak.iGrrwriprs 41 
                                       i +++  a    Grrw +p +
  gi|557694223|ref|YP_008797277.1| 104 ITQKRVNAIFeYGRRWFFPLN 124
                                       6666666664489*****976 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 !   26.8   0.2   2.5e-09   4.1e-06       1      47 [.      11      57 ..      11      58 .. 0.97

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.5e-09
                                      EEHHHHHHHHTS-HHHHHHHHHHTT-S-EE-TTS-EEEEHHHHHHHH CS
                            MerR_1  1 ysigevakilgvtthtlrywekegllkpkrteggrryYtdedierLk 47
                                      y+ gevakilgv+ +t++ w   g++   +t gg+++ ++e +erL+
  gi|557694223|ref|YP_008797277.1| 11 YTTGEVAKILGVSFRTVKRWIYSGKIEATKTAGGHYRISREVLERLR 57
                                      89******************************************998 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.2   3.3e-08   5.4e-05       1      37 [.      12      47 ..      12      48 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.3e-08
                                      EHHHHHHHHTTTHHHHHHHHHTTSSTSEEETTTSSEE CS
                              MerR  1 tIgevAeltGvsprtLRyYEreGLipppeRtegGyRl 37
                                      t+gevA+++Gvs rt+ ++   G+i ++++t+gG+ +
  gi|557694223|ref|YP_008797277.1| 12 TTGEVAKILGVSFRTVKRWIYSGKI-EATKTAGGHYR 47
                                      89***********************.********965 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   3.5e-06    0.0057      18      38 ..      11      31 ..       6      33 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.5e-06
                            HTH_23 18 lsvreIAreLgvsrrTvyrwl 38
                                      +++ e+A++Lgvs rTv rw+
  gi|557694223|ref|YP_008797277.1| 11 YTTGEVAKILGVSFRTVKRWI 31
                                      57789***************8 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 !   12.8   0.0   4.4e-05     0.071      27      49 ..      11      33 ..       6      36 .. 0.86
   2 ?   -0.2   0.0      0.49     8e+02      14      25 ..      73      84 ..      72     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.4e-05
                                      --HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 27 lsykEIAellgisegtVksrlsR 49
                                      +++ E+A++lg+s +tVk++++ 
  gi|557694223|ref|YP_008797277.1| 11 YTTGEVAKILGVSFRTVKRWIYS 33
                                      7889****************985 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.49
                                      HHHHHHHHHHTS CS
                      Sigma70_r4_2 14 rqreifllryle 25
                                      ++rei+ lr+++
  gi|557694223|ref|YP_008797277.1| 73 DEREIVYLREVQ 84
                                      689999999876 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.5e-05     0.041      14      33 ..      12      31 ..       5      32 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                            HTH_28 14 svreaArelgisrrtvyrWi 33
                                      +  e+A++lg+s rtv+rWi
  gi|557694223|ref|YP_008797277.1| 12 TTGEVAKILGVSFRTVKRWI 31
                                      5579***************8 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00033      0.54      16      39 ..       6      29 ..       4      31 .. 0.91
   2 ?   -2.8   0.1         3   4.9e+03      40      49 ..      48      57 ..      46      58 .. 0.75
   3 ?    3.8   0.1     0.025        40       9      37 ..      74     109 ..      73     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00033
                                      HHTTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 16 rfgeglTleEIgerlgiSrerVrq 39
                                      r+ e +T  E++++lg+S  +V++
  gi|557694223|ref|YP_008797277.1|  6 RYREWYTTGEVAKILGVSFRTVKR 29
                                      888999****************97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3
                                      HHHHHHHHHH CS
                        Sigma70_r4 40 iekrAlrkLR 49
                                      i ++ l++LR
  gi|557694223|ref|YP_008797277.1| 48 ISREVLERLR 57
                                      6778888888 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.025
                                       HHHHHHHHH.....TTT--HHHHHHHHT..S-HHHH CS
                        Sigma70_r4   9 erevlelrf.....geglTleEIgerlg..iSrerV 37 
                                       ere+++lr      ++++++ E++++l+  i++ rV
  gi|557694223|ref|YP_008797277.1|  74 EREIVYLREvqlnfEDKYPHYETSNKLNllITQKRV 109
                                       9*******9999999999999999999844466666 PP

>> DUF3853  Protein of unknown function (DUF3853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.9e-05     0.064      45      79 ..      10      44 ..       2      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.9e-05
                           DUF3853 45 vyGikglarllGislptanrikksGkiDkaitqiG 79
                                       y   ++a++lG+s  t++r   sGki+   t  G
  gi|557694223|ref|YP_008797277.1| 10 WYTTGEVAKILGVSFRTVKRWIYSGKIEATKTAGG 44
                                      466789*********************98766655 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.4e-05     0.056      87     146 ..      51     112 ..      44     121 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.4e-05
                                       XXXXXXXXXXXXXHHHHHHHHHHH-SEE-HHHHHHHH-S-..HHHHHHHHHHHHHHSSS-EE CS
                             DDRGK  87 egtekesaeeeeklleefinyikekKvvlleelavkfklk..tqevierikeLeeqgsltGv 146
                                       e  e+ ++e+ e+  e++i++i e+ +v l e+  +f+ k  + e  ++++ L +q++++ +
  gi|557694223|ref|YP_008797277.1|  51 EVLERLRSEVGERSAEDIIKFIDEREIVYLREVQLNFEDKypHYETSNKLNLLITQKRVNAI 112
                                       55667778888999***********************755338899***********99976 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   9.8e-05      0.16      11      33 ..       9      31 ..       4      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 9.8e-05
                            HTH_29 11 GvstvsqiAkllglsrrtvyrwl 33
                                      +++t+ ++Ak+lg+s rtv rw+
  gi|557694223|ref|YP_008797277.1|  9 EWYTTGEVAKILGVSFRTVKRWI 31
                                      577999****************9 PP

>> DUF1323  Putative transcription regulator (DUF1323)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.3e-05      0.15       2      33 ..      12      43 ..      11     101 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.3e-05
                           DUF1323  2 tpeelaellGyarqtinrWvRkegWkteplpG 33
                                      t++e+a++lG++  t+ rW+     + +++ G
  gi|557694223|ref|YP_008797277.1| 12 TTGEVAKILGVSFRTVKRWIYSGKIEATKTAG 43
                                      99******************877666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2298.00
//
Query:       gi|557694224|ref|YP_008797278.1|  [L=247]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   46.2   0.1      5e-12   45.8   0.1    1.2  1  MS_channel  Mechanosensitive ion channel


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 !   45.8   0.1   2.8e-16     5e-12       3     202 ..      44     241 ..      42     245 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.8e-16
                                       HHHHHHHHHHHHHHHHTTT--SCCHH.HHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEE CS
                        MS_channel   3 ilkiliivvgilivlsllgvnvsall.avlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVed 78 
                                       +l+i+++v + +i+   +  +v + + a++Ga+ +  + ++ ++++ +v G ++ +   ++ GD+v + +   +V++
  gi|557694224|ref|YP_008797278.1|  44 ALRIGALVSAYVIAVVKVVEQVDTWVaAAAGAGLILFTAVSFKPLRLMVLGDVMKAVGVLREGDYVSVRGRVARVTE 120
                                       56777777777777766666666655055666666667778899999999999************************ PP

                                       E-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-....HHHHHHHHHHHHHH-TTB-TTS CS
                        MS_channel  79 iglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkk.lekvleelkealkekpevlkdk 154
                                       ++ + t ++t d r ++iPn  l++++i+N+++ sg+  + v+i+v+   +    ++ +l +  + + +  e  ++ 
  gi|557694224|ref|YP_008797278.1| 121 VKATHTILTTSDLRKLYIPNDRLLSEKIVNFTK-SGAGVLFVRIKVDGRRISIPdAKLILLKTGTDIAK-AEAAPNR 195
                                       *********************************.99999999999998887333034444444444444.4455589 PP

                                       -EEEEEEEE-SSSEEEEEEEEEET...TTHHHHHHHHHHHHHHHHHHH CS
                        MS_channel 155 ellvvldefgdsslnfevrvfvktvvpeeylsvqseinlrikkileee 202
                                       +++v++++++d +++++++ +v +  p++ + + s i++r+  +l e+
  gi|557694224|ref|YP_008797278.1| 196 APEVRVEKIEDPYVTLRLTLYVIN--PAKAEPLASHIMERVYTKLAEA 241
                                       ************************..**************99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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 0.23s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1777.65
//
Query:       gi|557694225|ref|YP_008797279.1|  [L=227]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
       0.18   11.9   2.9       0.32   11.1   1.4    2.1  2  Nucleoporin2  Nucleoporin autopeptidase


Domain annotation for each model (and alignments):
>> Nucleoporin2  Nucleoporin autopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.4   1.8e-05      0.32      19      72 ..      18      70 ..       2     105 .. 0.74
   2 ?   -3.7   0.0      0.65   1.2e+04     120     131 ..     207     218 ..     202     221 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.8e-05
                                      HHHTSBSS-EE.EETTTEEEEESS-B--GGG-HHHHBTTTEEEETTEEEESSSCC CS
                      Nucleoporin2 19 eelsavkdFtv.grkgvGsveFlepvdlssldldeiagkivklekkevtVYpdee 72
                                      e  ++++dF+v ++++ G v F+  +d+s+ldl++    +  l ++  ++Y +++
  gi|557694225|ref|YP_008797279.1| 18 EIAAKLRDFKVvEHQKHGDVDFELVTDVSKLDLRNG--MLFGLFSRDKVIYVNQR 70
                                      3567899**76267789***************9886..56666666666666664 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.65
                                       HH-SSSEEEEEE CS
                      Nucleoporin2 120 kkvegteFvsyd 131
                                       +++++++F++y 
  gi|557694225|ref|YP_008797279.1| 207 SRMSEAQFIEYV 218
                                       577889999995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1668.91
//
Query:       gi|557694226|ref|YP_008797280.1|  [L=82]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-20   72.0   4.5    3.3e-20   71.7   4.5    1.1  1  Biotin_lipoyl    Biotin-requiring enzyme
    9.3e-10   38.2   1.8      4e-05   23.3   0.2    2.1  2  Biotin_lipoyl_2  Biotin-lipoyl like
    3.2e-06   27.8   2.0     0.0088   16.7   0.2    2.1  2  HlyD_3           HlyD family secretion protein
    4.1e-05   23.5   6.5      6e-05   22.9   2.4    2.0  2  GCV_H            Glycine cleavage H-protein
     0.0002   21.3   2.5     0.0034   17.3   0.7    2.0  2  RnfC_N           RnfC Barrel sandwich hybrid domain
    0.00039   20.0   1.3       0.16   11.6   0.1    2.2  2  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin
    0.00059   19.1   2.2     0.0049   16.1   0.8    2.0  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
     0.0054   16.7   2.3      0.015   15.3   1.0    1.9  2  DUF2118          Uncharacterized protein conserved in archaea
  ------ inclusion threshold ------
      0.022   15.0   0.9          1    9.6   0.9    2.1  1  Peptidase_M23    Peptidase family M23
       0.03   14.2   2.2      0.035   14.0   2.2    1.1  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens


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 !   71.7   4.5   1.8e-23   3.3e-20       4      73 .]       8      78 ..       6      78 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.7 bits;  conditional E-value: 1.8e-23
                                      EESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl  4 ksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73
                                       +P i + +e+g + e+ +kvGd V+ g+v+a+ve+ K+ +ei+++++Gv+++il+++G++v+vg+ +a+i
  gi|557694226|ref|YP_008797280.1|  8 ILPRIDVAMESGrISEWVKKVGDRVSRGEVVAIVETEKAAVEITSEVDGVITKILHNVGEEVKVGEAIAEI 78
                                      57999999*************************************************************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 !   16.0   0.1   4.4e-06    0.0079      10      39 ..      18      47 ..       8      50 .. 0.86
   2 !   23.3   0.2   2.2e-08     4e-05       3      36 ..      48      81 ..      42      82 .] 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.4e-06
                   Biotin_lipoyl_2 10 sGrVaqlnVkdGqrVkaGdvLaelDsralq 39
                                      sGr++++  k G+rV  G v a+ ++++ +
  gi|557694226|ref|YP_008797280.1| 18 SGRISEWVKKVGDRVSRGEVVAIVETEKAA 47
                                      9**********************9998755 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 2.2e-08
                   Biotin_lipoyl_2  3 vsIaapvsGrVaqlnVkdGqrVkaGdvLaelDsr 36
                                      v+I++ v+G++++++   G +Vk G  +ae++ +
  gi|557694226|ref|YP_008797280.1| 48 VEITSEVDGVITKILHNVGEEVKVGEAIAEIEVE 81
                                      89*****************************865 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.1   0.00013      0.22       4      39 ..      15      49 ..      14      51 .. 0.84
   2 !   16.7   0.2   4.9e-06    0.0088       2      31 ..      50      79 ..      49      82 .] 0.94

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            HlyD_3  4 ApvdGvvvelnveegevvqagdelleiippdtllve 39
                                      A  +G+++e+  ++g+ v++g++++ +  +++++ve
  gi|557694226|ref|YP_008797280.1| 15 AMESGRISEWVKKVGDRVSRGEVVAIVE-TEKAAVE 49
                                      789*******************999777.6666665 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 4.9e-06
                            HlyD_3  2 lrApvdGvvvelnveegevvqagdelleii 31
                                      +++ vdGv++++ +++ge v  g++++ei 
  gi|557694226|ref|YP_008797280.1| 50 ITSEVDGVITKILHNVGEEVKVGEAIAEIE 79
                                      89**************************95 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   2.4   3.3e-08     6e-05      37      79 ..      24      66 ..       2      68 .. 0.85
   2 ?    5.2   0.5      0.01        18      38      58 ..      62      82 .]      57      82 .] 0.85

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.3e-08
                                      E---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGGT CS
                             GCV_H 37 elpevgtkvkkgeslaavEsvKaasevyapvsGevvevNekle 79
                                       +++vg++v+ ge +a+vE+ Kaa e+ ++v+G ++++ +++ 
  gi|557694226|ref|YP_008797280.1| 24 WVKKVGDRVSRGEVVAIVETEKAAVEITSEVDGVITKILHNVG 66
                                      589********************************99877665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.01
                                      ---TT-EE-TT-EEEEEEESS CS
                             GCV_H 38 lpevgtkvkkgeslaavEsvK 58
                                      l +vg++vk ge++a +E  K
  gi|557694226|ref|YP_008797280.1| 62 LHNVGEEVKVGEAIAEIEVEK 82
                                      789**************9755 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 !   17.3   0.7   1.9e-06    0.0034      37      81 ..      17      62 ..       8      66 .. 0.85
   2 !    7.1   0.2    0.0028       5.1      41      61 ..      58      78 ..      56      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.9e-06
                            RnfC_N 37 hiGapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaie 81
                                        G   + + kvgd+V +G+++a  e+   ++++ + v G +++i 
  gi|557694226|ref|YP_008797280.1| 17 ESGRISEWVKKVGDRVSRGEVVAIVETeKAAVEITSEVDGVITKIL 62
                                      568889999************99876656699***********995 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0028
                            RnfC_N 41 pakplvkvgdkVlkGqkiaea 61
                                       +k+l +vg++V+ G+ iae 
  gi|557694226|ref|YP_008797280.1| 58 ITKILHNVGEEVKVGEAIAEI 78
                                      578899*************96 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 !   11.6   0.1   9.2e-05      0.16      37      57 ..      25      45 ..      23      59 .. 0.80
   2 !    7.7   0.1    0.0015       2.8      38      53 ..      63      78 ..      56      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.2e-05
                                      S--TT-EEBTTSEEEEEEESS CS
                            PYNP_C 37 hkklGdkVkkGeplatiYank 57
                                       kk+Gd+V++Ge++a + ++k
  gi|557694226|ref|YP_008797280.1| 25 VKKVGDRVSRGEVVAIVETEK 45
                                      69************9985555 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0015
                                      --TT-EEBTTSEEEEE CS
                            PYNP_C 38 kklGdkVkkGeplati 53
                                        +G++Vk Ge++a i
  gi|557694226|ref|YP_008797280.1| 63 HNVGEEVKVGEAIAEI 78
                                      679**********987 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 ?    4.4   0.1      0.01        18      27      52 ..      18      42 ..      11      47 .. 0.81
   2 !   16.1   0.8   2.7e-06    0.0049      15      53 ..      43      80 ..      36      82 .] 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.01
                                      XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 27 eGwveklyvnatgdkVkkGqpLaely 52
                                      +G++++   + +gd+V++G+ +a ++
  gi|557694226|ref|YP_008797280.1| 18 SGRISEWVKK-VGDRVSRGEVVAIVE 42
                                      6888887666.*********998776 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.7e-06
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 15 derrlarvsarveGwveklyvnatgdkVkkGqpLaelys 53
                                       e+  ++++++v+G ++k+  n +g++Vk G+++ae++ 
  gi|557694226|ref|YP_008797280.1| 43 TEKAAVEITSEVDGVITKILHN-VGEEVKVGEAIAEIEV 80
                                      47788899*************9.************9986 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 !   15.3   1.0   8.3e-06     0.015      96     134 ..      25      62 ..      12      68 .. 0.84
   2 ?    5.2   0.1     0.011        19      87     113 ..      53      79 ..      50      82 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.3e-06
                           DUF2118  96 ivdvGdrveegdtlaavttrkgevrylrapvegvVvfik 134
                                       + +vGdrv  g+++a v t k  v  + + v+gv+  i 
  gi|557694226|ref|YP_008797280.1|  25 VKKVGDRVSRGEVVAIVETEKAAVE-ITSEVDGVITKIL 62 
                                       4589******************996.7899999998765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.011
                           DUF2118  87 pvegvkvtlivdvGdrveegdtlaavt 113
                                       +v+gv   +  +vG++v+ g+++a + 
  gi|557694226|ref|YP_008797280.1|  53 EVDGVITKILHNVGEEVKVGEAIAEIE 79 
                                       789999999**************9876 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.9   0.00058         1      57      76 ..      26      45 ..      15      82 .] 0.52

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00058
                                      S-TTEEE-TTCEEEEEBSTS CS
                     Peptidase_M23 57 vkegqkVkaGqvIGtvgstg 76
                                       k+g++V++G+v++ v +++
  gi|557694226|ref|YP_008797280.1| 26 KKVGDRVSRGEVVAIVETEK 45
                                      34566666666665555333 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 ?   14.0   2.2   1.9e-05     0.035      40      96 ..      26      81 ..      15      82 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                                      S-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEEE--EE..EE-TTSECEEECET CS
                   ATP-synt_ab_Xtn 40 vkvgdkvsggdilGtvqeteliehkimvppkvegkvkeiaeeg..eytvedtiaevete 96
                                       kvgd+vs g+++++v+ +++    + +  +v+g +++i ++   e +v + iae+e e
  gi|557694226|ref|YP_008797280.1| 26 KKVGDRVSRGEVVAIVETEKA---AVEITSEVDGVITKILHNVgeEVKVGEAIAEIEVE 81
                                      589*************87776...56667889*****9987643569*********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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):              10  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 591.27
//
Query:       gi|557694227|ref|YP_008797281.1|  [L=332]
Description: pyruvate dehydrogenase E1 component subunit beta [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-44  150.9   0.0      4e-44  150.4   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    7.3e-39  132.5   1.9    1.1e-38  131.8   0.7    1.9  3  Transketolase_C  Transketolase, C-terminal domain
    8.7e-06   26.0   0.2    1.9e-05   24.9   0.2    1.6  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
     0.0099   15.8   0.8      0.025   14.5   0.8    1.6  1  Thiamine_BP      Thiamine-binding protein
  ------ inclusion threshold ------
      0.013   14.9   0.1      0.093   12.2   0.1    2.3  2  DUF3343          Protein of unknown function (DUF3343)


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 !  150.4   0.0   1.1e-47     4e-44       2     175 ..       5     179 ..       4     182 .. 0.97

  Alignments for each domain:
  == domain 1  score: 150.4 bits;  conditional E-value: 1.1e-47
                                       EEEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEE CS
                      Transket_pyr   2 kiawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllvi 76 
                                       ++++ +a++eal e++++d++v+++g++va  gg+++v+k+ll+++g++rv+d++isE a++g+a+Gaalag l+++
  gi|557694227|ref|YP_008797281.1|   5 ELTYVEALNEALREEMRRDDSVIVFGEEVAaaGGVYKVTKDLLKEFGPKRVMDTPISEIAIVGAAIGAALAG-LRPV 80 
                                       67899*************************99****************************************.9*** PP

                                       EEEEEHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHH CS
                      Transket_pyr  77 veaqFgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetk 151
                                       +e++F+dF+  A  q+++++ +++ +++g++k ++v+r+ +++g +  +++ ++l a+l   pglk+v+P++p+++k
  gi|557694227|ref|YP_008797281.1|  81 AEIMFFDFVGIAfdQLVTHASKMRFMSGGQVKLPLVVRTQYSLGRSYGSQHTQFLAASLLQAPGLKIVAPATPYDAK 157
                                       ***************************************************************************** PP

                                       HHHHHHHHSSS.SEEEEEE-SSEE CS
                      Transket_pyr 152 hllrrairredrkPvvlrlpksll 175
                                       +ll+  ir  d++Pv ++++  l+
  gi|557694227|ref|YP_008797281.1| 158 GLLKSSIR--DDDPVLFVESGALY 179
                                       ********..899*****997776 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.2   4.3e+03      60      76 ..      23      39 ..       7      65 .. 0.61
   2 ?   -3.0   0.0       1.7   6.2e+03      84     116 ..     135     162 ..     126     170 .. 0.63
   3 !  131.8   0.7   3.2e-42   1.1e-38       1     124 []     201     323 ..     201     323 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                                      HHSEEEEEEEEESTTSH CS
                   Transketolase_C 60 ktgrlvvveeavkrgGi 76
                                          +v+ ee +  gG+
  gi|557694227|ref|YP_008797281.1| 23 DDSVIVFGEEVAAAGGV 39
                                      44445555555555555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                                       HHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHH CS
                   Transketolase_C  84 laeeafdgldapvkrvggpdviepgsaeeleka 116
                                       la      l+ap +++++p +  p+ a+ l+k 
  gi|557694227|ref|YP_008797281.1| 135 LAA---SLLQAPGLKIVAPAT--PYDAKGLLKS 162
                                       444...557777777777755..7776666665 PP

  == domain 3  score: 131.8 bits;  conditional E-value: 3.2e-42
                                       TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       gka+++r g+dvt+va++++v+ea++Aa +Le++g++aeV+dlrt+ p+D eti +svkkt+rlvv e+ vk+gGi+
  gi|557694227|ref|YP_008797281.1| 201 GKADVKRVGDDVTIVAVSRTVSEAMAAASQLEEKGVKAEVIDLRTIMPMDYETIINSVKKTNRLVVAEDSVKTGGIS 277
                                       89*************************************************************************** PP

                                       HHHHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                       +eva+ + e af++l+ap++r+  p ++ p +  elek f+++aeki
  gi|557694227|ref|YP_008797281.1| 278 AEVASHVCEYAFEYLEAPIVRLNSPPMPAPQA-SELEKKFMVSAEKI 323
                                       *************************6655555.59**********98 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 !   24.9   0.2   5.3e-09   1.9e-05       2      81 ..     211     287 ..     210     299 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 5.3e-09
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHHT CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaal 78 
                                       +v iva+  ++++a +a+ +l e+g+k+ ++ lrt+ P  +e + + +kk++++vv + ++    +G +  ev++++
  gi|557694227|ref|YP_008797281.1| 211 DVTIVAVSRTVSEAMAAASQLEEKGVKAEVIDLRTIMPMDYETIINSVKKTNRLVVAEDSV---KTGGISAEVASHV 284
                                       789**********************************************************...4688999999999 PP

                                       GGG CS
                           PFOR_II  79 kks 81 
                                       +++
  gi|557694227|ref|YP_008797281.1| 285 CEY 287
                                       877 PP

>> Thiamine_BP  Thiamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.8     7e-06     0.025      12      65 ..     218     270 ..     210     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7e-06
                                       SSGHHHHHHHHHHHHHTTSSEEEEETTEEEEEEEHHHHHHHHHHHHHHHHCTTS CS
                       Thiamine_BP  12 gesvskyVakvvevlkesglkyeltpmgTtiegeldevmevvkkahealfeaGa 65 
                                       +  vs++ a++   l+e+g+k e+    T++  +++++++ vkk ++ ++++++
  gi|557694227|ref|YP_008797281.1| 218 SRTVSEAMAAA-SQLEEKGVKAEVIDLRTIMPMDYETIINSVKKTNRLVVAEDS 270
                                       33444444444.347********************************9998865 PP

>> DUF3343  Protein of unknown function (DUF3343)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.6e-05     0.093       3      30 ..     215     242 ..     213     245 .. 0.90
   2 ?   -0.5   0.0      0.25   8.9e+02       8      29 ..     260     281 ..     255     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                           DUF3343   3 vitFssthhAiaaekalkeggiearlip 30 
                                       v++ +++++A+aa + l+e+g++a++i 
  gi|557694227|ref|YP_008797281.1| 215 VAVSRTVSEAMAAASQLEEKGVKAEVID 242
                                       6777899*******************97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.25
                           DUF3343   8 sthhAiaaekalkeggiearli 29 
                                        t+    ae+ +k ggi+a++ 
  gi|557694227|ref|YP_008797281.1| 260 KTNRLVVAEDSVKTGGISAEVA 281
                                       57777889999*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2512.61
//
Query:       gi|557694228|ref|YP_008797282.1|  [L=327]
Description: pyruvate dehydrogenase E1 component subunit alpha [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-77  261.0   0.0    1.2e-77  260.8   0.0    1.0  1  E1_dh            Dehydrogenase E1 component
      3e-07   30.3   0.1    2.2e-06   27.6   0.1    2.2  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    0.00071   18.6   0.0     0.0012   17.9   0.0    1.3  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    0.00087   18.6   0.0     0.0022   17.3   0.0    1.7  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  260.8   0.0   2.8e-81   1.2e-77       2     296 ..      17     312 ..      16     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: 260.8 bits;  conditional E-value: 2.8e-81
                                       HHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-T. CS
                             E1_dh   2 klvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkv. 77 
                                       k+  +r +e++++ ly + k+ig  hl+ gqea++vg+  al+k+D++i++YR++g+ +arg+++++il e+ g++ 
  gi|557694228|ref|YP_008797282.1|  17 KMIEIRLFEERVEKLYREGKIIGPTHLYFGQEAVAVGVIEALDKDDVVISTYRGHGHGVARGVPMKAILGEILGRAv 93 
                                       78889999********************************************************************* PP

                                       ...TTSSGTT-..-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHT CS
                             E1_dh  78 ...kgkggsrh.elmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalw 150
                                          kg ggs+h +++    e +i  +  ivg+  p++ G+ la k+++k +va +++GDgA n G ++ealnlaa+w
  gi|557694228|ref|YP_008797282.1|  94 gtcKGLGGSMHaPIS---VEHNIPLATAIVGSGIPIAVGVGLAFKYREKRSVATVFFGDGAVNTGAFHEALNLAAVW 167
                                       ***********7777...33469****************************************************** PP

                                       T--EEEEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--S CS
                             E1_dh 151 klpvifvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRy 227
                                       +lpv+fv+eNN y++ T+ ++  a++++a+ra g+gip+    gnD+l+vye +  A e  r+++gp+ ie+ tYR 
  gi|557694228|ref|YP_008797282.1| 168 RLPVLFVCENNLYAMYTSLKNVLAAESIAARASGYGIPSYVAFGNDVLEVYETTSKALEKIRNESGPVFIECRTYRQ 244
                                       ***************************************************************************** PP

                                       S-SSTTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS-- CS
                             E1_dh 228 ggHsesDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskke 296
                                       +gH   D ++ yr++ee+ee+    dpi+ l e++++kg++++ee k+ie+ev++e +  v+++ +++ 
  gi|557694228|ref|YP_008797282.1| 245 KGHGGYDFGTWYRSKEEIEEWMRR-DPINMLTERMKTKGFITDEERKKIEEEVAAELDKVVEEVLNSPV 312
                                       *************99999998877.**********************************9999987765 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 !   27.6   0.1   4.8e-10   2.2e-06      27     153 .]     117     239 ..     101     239 .. 0.70

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.8e-10
                                       TS-TTTHHHHHHHHHHH...STTS.EEEEEEEHHHHHHT..GGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTC CS
                      TPP_enzyme_C  27 lgtmGyglpaAiGakla...kpdr.evvaivGDGgflmi..lqelatavrrnlpitvvvlnNegygmtggqqepfgg 97 
                                       ++  G g+p+A+G+ la   +++r    ++ GDG+      +++l  a+  +lp+++v+ nN + + t  +   + +
  gi|557694228|ref|YP_008797282.1| 117 TAIVGSGIPIAVGVGLAfkyREKRsVATVFFGDGAVNTGafHEALNLAAVWRLPVLFVCENNLYAMYTSLKNVLAAE 193
                                       5678************765434441555899****766662566667777789999999887666555555444443 PP

                                       CTTTTSBB.BS----HHHHHHHTTSEEE......EESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  98 krksgpagkdlkpvdfaklaealGakga......rvekadveeleealkealekkgpaliev 153
                                                     ++a+ a ++G++ +      ++e++  e + +al++ +++ gp++ie+
  gi|557694228|ref|YP_008797282.1| 194 --------------SIAARASGYGIPSYvafgndVLEVY--ETTSKALEKIRNESGPVFIEC 239
                                       ..............3555555555553323444456688..99999999999********96 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.6e-07    0.0012     147     244 ..     143     242 ..     102     252 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.6e-07
                                       EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEESSEETTEEGG.GT--S-HHHHHHHTT-EEEEETTTT-H... CS
                   Transketolase_N 147 tyvilgDgclmeGvsseasslagtlkLgkLivlyDdnkisidGete.isftedvakrfeaygWhvievedgedv... 219
                                         v+ gDg ++ G  +ea +la++ +L  L v  ++n  ++  + + +  +e++a+r + yg        g+dv   
  gi|557694228|ref|YP_008797282.1| 143 ATVFFGDGAVNTGAFHEALNLAAVWRLPVLFVC-ENNLYAMYTSLKnVLAAESIAARASGYGIPSYV-AFGNDVlev 217
                                       5699***********************998775.666667766665156689999998888876544.334444111 PP

                                       .HHHHHHHHHHHH-TTS-EEEEEE-- CS
                   Transketolase_N 220 .eaikaaieeakaekdkPsliklrtv 244
                                        e+ ++a+e+ ++e   P +i++rt 
  gi|557694228|ref|YP_008797282.1| 218 yETTSKALEKIRNE-SGPVFIECRTY 242
                                       15567888888887.88*******96 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 !   17.3   0.0   4.9e-07    0.0022     115     176 ..     122     183 ..      97     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.9e-07
                    DXP_synthase_N 115 tsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsis 176
                                       + i +a+G+  a +++++++ +    GDga+ +G  +ealn ++  +  +l +  +N  ++ 
  gi|557694228|ref|YP_008797282.1| 122 SGIPIAVGVGLAFKYREKRSVATVFFGDGAVNTGAFHEALNLAAVWRLPVLFVCENNLYAMY 183
                                       56788999999999998877777789************************999999976654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      799  (0.0445647); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2260.23
//
Query:       gi|557694229|ref|YP_008797283.1|  [L=306]
Description: UDP-glucose 4-epimerase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-52  177.2   0.0    4.5e-52  176.9   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.3e-45  156.3   0.0    3.3e-45  154.9   0.0    1.5  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    5.3e-28   97.8   0.0    6.5e-28   97.5   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.5e-25   90.0   0.1    5.1e-25   88.2   0.1    1.8  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.8e-24   86.4   0.0    2.5e-24   85.9   0.0    1.2  1  RmlD_sub_bind    RmlD substrate binding domain
    1.6e-17   63.5   0.5      4e-12   45.9   0.0    3.1  3  NAD_binding_4    Male sterility protein
    2.2e-10   40.7   0.0    1.8e-09   37.7   0.0    2.3  2  NAD_binding_10   NAD(P)H-binding
    4.8e-08   32.7   0.2    1.5e-07   31.0   0.2    1.8  1  adh_short        short chain dehydrogenase
    0.00079   19.0   0.1      0.027   14.1   0.1    2.3  2  NmrA             NmrA-like family
     0.0011   19.0   1.1       0.69    9.8   0.1    2.7  3  KR               KR domain


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 !  176.9   0.0   2.5e-55   4.5e-52       1     241 []       6     238 ..       6     238 .. 0.93

  Alignments for each domain:
  == domain 1  score: 176.9 bits;  conditional E-value: 2.5e-55
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHHT-SEEEE--S- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfkeeqpdavihlAav 74 
                                       +lVtG++GfiG  lvk+lle+g++v ++d  s+++ +++l++    ++   d+  +  l ++f+  ++dav+hlAa+
  gi|557694229|ref|YP_008797283.1|   6 VLVTGGAGFIGGVLVKRLLENGVHVRVVDDFSTGR-WENLPNSpdlKVFVHDVAVKHGLPDFFD--KVDAVVHLAAI 79 
                                       79*****************************6654.444444446799999*************..9********** PP

                                       --HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHH CS
                         Epimerase  75 ggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlagek 151
                                        +v+    + ++ +e n++g  n+le + ++gv +++f sS++vYG+ + +  +e++   +++p s Y+ +Kl+ge 
  gi|557694229|ref|YP_008797283.1|  80 PSVPMCERNVQRAFEVNVIGLENVLETCVEKGVGKIVFTSSAAVYGDAEGM-LNEDA---ETRPFSVYGWTKLLGEA 152
                                       **********************************************99997.89999...66777************ PP

                                       HHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHH CS
                         Epimerase 152 lveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvleh 228
                                       +++++ +++g++a++lr+fn+yG    ++   +v+ ++i+ ++egk ++ + gdg ++Rdf++v+D+a+aill+le+
  gi|557694229|ref|YP_008797283.1| 153 ILRSFGEKHGVEAVALRIFNVYGRK-SMSGFLGVVDQFIADAAEGK-PLHIHGDGGQVRDFIHVDDIANAILLALEK 227
                                       ************************9.555567899***********.****************************** PP

                                       HTT-STTEEEEES CS
                         Epimerase 229 vdagdkgeiyniG 241
                                         + ++ e++niG
  gi|557694229|ref|YP_008797283.1| 228 --TLKNFEVINIG 238
                                       ..667889****9 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 !  154.9   0.0   1.8e-48   3.3e-45       1     329 [.       7     299 ..       7     301 .. 0.90

  Alignments for each domain:
  == domain 1  score: 154.9 bits;  conditional E-value: 1.8e-48
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiG  l+++Lle+g +v ++    + f+tgr e+l ++      ++lk++ +D+  ++ l + +++v  d
  gi|557694229|ref|YP_008797283.1|   7 LVTGGAGFIGGVLVKRLLENGVHVRVV----DDFSTGRWENLPNS------PDLKVFVHDVAVKHGLPDFFDKV--D 71 
                                       9********************999776....578899****9764......46889999**************9..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                       +v++LAA   V+    + ++ +evnv+G  ++Le + + g+    +++++S++ vYG++ e   +E+  ++P s Y+
  gi|557694229|ref|YP_008797283.1|  72 AVVHLAAIPSVPMCERNVQRAFEVNVIGLENVLETCVEKGVG---KIVFTSSAAVYGDA-EGMLNEDAETRPFSVYG 144
                                       ************************************999875...8999*********9.5899************* PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                        +Kl  + i +++ e++g+ av  ++fn ++ +    f    + +++a +a+gk +  + G++ ++Rd+ hv+D+++
  gi|557694229|ref|YP_008797283.1| 145 WTKLLGEAILRSFGEKHGVEAVALRIFNVYGRKSMSGFL-GVVDQFIADAAEGK-PLHIHGDGGQVRDFIHVDDIAN 219
                                       *******************************99766655.99***********9.77778***************** PP

                                       HHHHHHHC..SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB- CS
                     GDP_Man_Dehyd 232 amwlmlqq..dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdll 306
                                       a+ l+l++  ++ e ++i+tg+ +s+++++e+ + + g +                    v  + +++ r g+ +  
  gi|557694229|ref|YP_008797283.1| 220 AILLALEKtlKNFEVINIGTGQPTSIKNLAEKVLTAFGHS--------------------VSAIVYEPARVGDIRYS 276
                                       ******9944445667788888888888888777777753....................44566788999****** PP

                                       -B-THHHHHHH----SS-HHHHH CS
                     GDP_Man_Dehyd 307 lgdaskakeeLgWkpkvsfeelv 329
                                       ++d+ska++ Lg++p++s+++ +
  gi|557694229|ref|YP_008797283.1| 277 VADISKARQLLGFSPTTSLDTYL 299
                                       *******************9865 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 !   97.5   0.0   3.6e-31   6.5e-28       1     235 [.       7     231 ..       7     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 3.6e-31
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G  lvk+L++ +   +vrv+D     ++ e+l ++   kv   Dv  k+ l +  ++vd+v+hla++ 
  gi|557694229|ref|YP_008797283.1|   7 LVTGGAGFIGGVLVKRLLENG--VHVRVVDDFSTGRW-ENLPNSPDLKVFVHDVAVKHGLPDFFDKVDAVVHLAAIP 80 
                                       69****************999..69*****8888888.77777777779***************************9 PP

                         3Beta_HSD  78 dvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                        v   + + ++  +vnv G +nvle+cv++gv ++v+tSsa v g+   +e +ln d     e+ + ++y  +K l 
  gi|557694229|ref|YP_008797283.1|  81 SVPMcERNVQRAFEVNVIGLENVLETCVEKGVGKIVFTSSAAVYGD---AEGMLNED----AETRPFSVYGWTKLLG 150
                                       9976588999************************************...99999444....45567889*******9 PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyGegdkl....lvpllkqlaklglalfkigdeevlsdrvYvgNvawahi 226
                                       E+ +l++ g   k g  +  +aLR   +yG ++      +v ++   a  g+ l   gd  ++ d++ v+ +a a++
  gi|557694229|ref|YP_008797283.1| 151 EA-ILRSFG--EKHG--VEAVALRIFNVYGRKSMSgflgVVDQFIADAAEGKPLHIHGDGGQVRDFIHVDDIANAIL 222
                                       96.666666..2566..99***********9987521222233333455677999********************** PP

                         3Beta_HSD 227 lAaralqdp 235
                                       lA  + +++
  gi|557694229|ref|YP_008797283.1| 223 LALEKTLKN 231
                                       **9887766 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   0.1   2.9e-28   5.1e-25       1     252 [.       6     261 ..       6     276 .. 0.84

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 2.9e-28
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       vlvtG++G iG  lv+++l++ ++  ++ + +  +  ++ +       + +lkv+    + dv+ k+ l + ++  k
  gi|557694229|ref|YP_008797283.1|   6 VLVTGGAGFIGGVLVKRLLENGVHVRVVDDFSTGRWENLPN-------SPDLKVF----VHDVAVKHGLPDFFD--K 69 
                                       89******************988654444434333333333.......3457667....9**************..* PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE.............GGGSS--SHHHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt.............DKAvnPtnvmGat 141
                                       vd+v+h AA+  VP++e+n+  a++ Nv+g env+e+++e+gv k+v+ S+             D   +P +v+G t
  gi|557694229|ref|YP_008797283.1|  70 VDAVVHLAAIPSVPMCERNVQRAFEVNVIGLENVLETCVEKGVGKIVFTSSaavygdaegmlneDAETRPFSVYGWT 146
                                       ***********************************************9997555555555555577899******** PP

                                       HHHHHHHHHHGGG--SSS--EEEEEEE-EETTGT...T..SSHHHHHHHHHTTSSEEES.-TT-EEEEE-HHHHHHH CS
                   Polysacc_synt_2 142 KrlaekllqalakeseekktkfvvvRfGNVlgSr...G..SviplFkkqikeggpvtvT.dpemtRyfmtieeavqL 212
                                       K+l e +l ++ +++     + v+ R  NV g +   G   v+  F +  +eg+p+ +  d   +R f+ +++ ++ 
  gi|557694229|ref|YP_008797283.1| 147 KLLGEAILRSFGEKH---GVEAVALRIFNVYGRKsmsGflGVVDQFIADAAEGKPLHIHgDGGQVRDFIHVDDIANA 220
                                       ************999...788999999999985411244469****************637789***********99 PP

                                       HHHHHHH.--SS-EEEE--.-EEEHHHHHHHH......... CS
                   Polysacc_synt_2 213 vlqalal.akggeifvldmGepvkivdlakalielsgleek 252
                                       +l al++  k+ e+     G+p++i++la+++++ +g++++
  gi|557694229|ref|YP_008797283.1| 221 ILLALEKtLKNFEVINIGTGQPTSIKNLAEKVLTAFGHSVS 261
                                       9999965167889999****************999997765 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 !   85.9   0.0   1.4e-27   2.5e-24       2     268 ..       5     288 ..       4     299 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.4e-27
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.................T--TTSHHHHHHHHHHH--SEEEE---- CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre.................eldltdaeavaellkeakpdvvvnaAAy 61 
                                       ++lvtG+ G +G  L+k+l e+g++v  ++                     d++ ++ + +++++   d+vv++AA 
  gi|557694229|ref|YP_008797283.1|   5 NVLVTGGAGFIGGVLVKRLLENGVHVRVVDDFstgrwenlpnspdlkvfVHDVAVKHGLPDFFDK--VDAVVHLAAI 79 
                                       68************************99966568999*******999988899999999999998..889******* PP

                                       --HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-.EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHH CS
                     RmlD_sub_bind  62 tavDkaEseeeaayavnaeavealAeaaaavga.lLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavl 137
                                         v  +E + ++a++vn+ + e++ e + + g+ ++++ S+  V+ G+++   +ed+et P +vYG tKl+GE   +
  gi|557694229|ref|YP_008797283.1|  80 PSVPMCERNVQRAFEVNVIGLENVLETCVEKGVgKIVFTSSAAVY-GDAEGMLNEDAETRPFSVYGWTKLLGEAILR 155
                                       ********************************96799*******9.777888************************* PP

                                       H....H-SSEEEEEE-SEESS.SSS-H...HHHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHHHHCHH.G CS
                     RmlD_sub_bind 138 a....agkkalivRtswvyge.kgknf...vktmlrlakereelkvvaD..qlgsPTsardlAevllqllekaaeek 204
                                       +    +g +a+ +R+  vyg+ +   f   v +++  a+e ++l++  D  q++   +++d+A+++l +lek ++  
  gi|557694229|ref|YP_008797283.1| 156 SfgekHGVEAVALRIFNVYGRkSMSGFlgvVDQFIADAAEGKPLHIHGDggQVRDFIHVDDIANAILLALEKTLK-- 230
                                       955545556788*******9954455522266778889*********9999**********************98.. PP

                                       GG-EEEE---BS-EEHHHHHHHHHHHHCHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT CS
                     RmlD_sub_bind 205 elagvyHlanegetswlefArailkeagadseevkpistaeyptpAkRPanSvLdtekleatfg 268
                                         ++v  ++  + ts  ++A+++l ++g     v++i     p++    ++Sv d +k+++  g
  gi|557694229|ref|YP_008797283.1| 231 -NFEVINIGTGQPTSIKNLAEKVLTAFGH---SVSAI--VYEPARVGDIRYSVADISKARQLLG 288
                                       .789999999999***********99998...55555..3335555555566666666666555 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.3   1.5e-05     0.026       1      25 [.       8      32 ..       8      34 .. 0.87
   2 !   45.9   0.0   2.2e-15     4e-12      85     257 .]      67     221 ..      60     221 .. 0.85
   3 ?   -0.5   0.0      0.31   5.6e+02     180     207 ..     246     271 ..     243     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.5e-05
                                      EE-TTSHHHHHHHHHHHHHS-.TEE CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevki 25
                                      +TG+ GF+G vL+++LL++  +v++
  gi|557694229|ref|YP_008797283.1|  8 VTGGAGFIGGVLVKRLLENGVHVRV 32
                                      7****************99776654 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 2.2e-15
                                       HHH--EEEE--SS-S....STTSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H..... CS
                     NAD_binding_4  85 aeevdviihsaAtvnf...depykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegeke 158
                                        ++vd+++h aA  ++   +++++++++vNv G ++vle + +      +++ S+a+v+g+ eg             
  gi|557694229|ref|YP_008797283.1|  67 FDKVDAVVHLAAIPSVpmcERNVQRAFEVNVIGLENVLETCVEKGVG-KIVFTSSAAVYGDAEGM------------ 130
                                       689*********65432225699******************977666.89*************74............ PP

                                       .HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST---TTSHHHHHHHHHHHH-EE CS
                     NAD_binding_4 159 ekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwingsdlgirgllgliakgvl 234
                                         l+ed++++       Y ++K l+E ++r+ ++++g+ +v +R+ +++g +s++G +   d     +++ +a+g+ 
  gi|557694229|ref|YP_008797283.1| 131 --LNEDAETRPF---SVYGWTKLLGEAILRSFGEKHGVEAVALRIFNVYGrKSMSGFLGVVD----QFIADAAEGKP 198
                                       ..4555555555...57*********************************888888888777....77777788888 PP

                                       ES-SB---TT--EEEHHHHHHHH CS
                     NAD_binding_4 235 peilgdkeavldlvpvDyvanai 257
                                        +i+gd  +v d++ vD +anai
  gi|557694229|ref|YP_008797283.1| 199 LHIHGDGGQVRDFIHVDDIANAI 221
                                       88******************997 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHHH---EEEEEE-EEE CS
                     NAD_binding_4 180 KalaEklvrearrrsglpvvivRpsiit 207
                                       K laEk++ + +  + + ++++ p  + 
  gi|557694229|ref|YP_008797283.1| 246 KNLAEKVLTAFG--HSVSAIVYEPARVG 271
                                       8999****9999..89999999998886 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 !   37.7   0.0     1e-12   1.8e-09       1     133 [.      10     156 ..      10     228 .. 0.84
   2 ?    0.1   0.0      0.36   6.4e+02      10      36 ..     248     274 ..     244     285 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 1e-12
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETT..HHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCC.. CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRn..peklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggk.. 73 
                                       G+ G +G  lvk+ll++g ++v+++  +  + + ++l++++ l+v++ dv  +  l + ++ +daVv  ++  +   
  gi|557694229|ref|YP_008797283.1|  10 GGAGFIGGVLVKRLLENG-VHVRVV-DDfsTGRWENLPNSPDLKVFVHDVAVKHGLPDFFDKVDAVVHLAAIPSVpm 84 
                                       99***************5.999866.553477889******************************999987666667 PP

                                       ...HHHH..........HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHHHHCCHHHHHH.HHHHHHHHHH CS
                    NAD_binding_10  74 ...deeg..........aknivdaakeagvkRfvlvsaigvgdevpgefgewnkellkaylaa.kraaeellra 133
                                          +  +           +n+++ + e+gv ++v+ s++ v+ +++g ++e +++   +++ + k   e++lr+
  gi|557694229|ref|YP_008797283.1|  85 cerN--VqrafevnvigLENVLETCVEKGVGKIVFTSSAAVYGDAEGMLNEDAETRPFSVYGWtKLLGEAILRS 156
                                       6431..23457778889******************************999988876667666535566666665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.36
                                       HHHHHHHC-T-EEEEEETTHHHCHHHH CS
                    NAD_binding_10  10 lvkellargghevtalvRnpeklaele 36 
                                       l+++ l + gh+v a+v +p+++ +++
  gi|557694229|ref|YP_008797283.1| 248 LAEKVLTAFGHSVSAIVYEPARVGDIR 274
                                       6677777779***********998875 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.2   8.6e-11   1.5e-07       2     138 ..       5     122 ..       4     130 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 8.6e-11
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                        vlvtG+++ IG  ++k+l+++G++v vvd  +       ++l + + ++ ++  Dv+ ++ + ++++k+       
  gi|557694229|ref|YP_008797283.1|   5 NVLVTGGAGFIGGVLVKRLLENGVHVRVVDDFSTGR---WENLPN-SPDLKVFVHDVAVKHGLPDFFDKV------- 70 
                                       69**************************98876655...556665.57799*******888888887665....... PP

                                       SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGG CS
                         adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSva 138
                                       d++v+ A+i    p   ++e++++r +evN+ g+ ++ +++++    +  G+Iv++sS a
  gi|557694229|ref|YP_008797283.1|  71 DAVVHLAAI----PSVPMCERNVQRAFEVNVIGLENVLETCVE----KGVGKIVFTSSAA 122
                                       *********....788899*************99777766655....599********87 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   1.5e-05     0.027       1      70 [.       6      75 ..       6     122 .. 0.84
   2 ?    2.7   0.0     0.044        80     138     199 ..     172     230 ..     151     261 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEE.ES-TT-HHHHHHHHTT-SEEEE CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelv.kgdlddkeslvealkgvdvvfs 70
                                      +lv+G++G +G+ +v+ ll++g +vr+ v d ++ + ++l +++   v   d+  k  l   +++vd+v  
  gi|557694229|ref|YP_008797283.1|  6 VLVTGGAGFIGGVLVKRLLENGVHVRV-VDDFSTGRWENLPNSPDLKVfVHDVAVKHGLPDFFDKVDAVVH 75
                                      79************************7.7888888999999998877778888888888888888888865 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.044
                                       EEEE-EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHH CS
                              NmrA 138 fvyagffmenflsllaqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprk 199
                                        vy    m+ fl+++ q ++ d a+++  + ++g+g     ++ +++Di+++++ +l++  k
  gi|557694229|ref|YP_008797283.1| 172 NVYGRKSMSGFLGVVDQ-FIADAAEGK-PLHIHGDGGQVRDFI-HVDDIANAILLALEKTLK 230
                                       45555667788887777.666666665.899****99777777.*********999987544 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00039      0.69       3      25 ..       6      28 ..       5      40 .. 0.90
   2 !    6.9   0.0    0.0031       5.5      80     140 ..      68     124 ..      49     135 .. 0.80
   3 ?   -1.7   0.0       1.3   2.3e+03      43      87 ..     220     265 ..     209     287 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00039
                                      EEEETTTSHHHHHHHHHHHHHHS CS
                                KR  3 ylitGGlGgLGlelarwlaekga 25
                                      +l+tGG+G +G +l++ l+e+g 
  gi|557694229|ref|YP_008797283.1|  6 VLVTGGAGFIGGVLVKRLLENGV 28
                                      69******************995 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0031
                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTTS--SEEEEEEEHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelledesldffvlfSSiagl 140
                                       +++  v+h A +        m + +++++++  v G++n+ e++ ++ +  +v++SS+a  
  gi|557694229|ref|YP_008797283.1|  68 DKVDAVVHLAAIPSV----PMCERNVQRAFEVNVIGLENVLETCVEKGVGKIVFTSSAAVY 124
                                       567788888877654....5667799*************************9999998754 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.3
                                       HHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS.S---EEEE CS
                                KR  43 aliaelealgaevevvaaDvsdkdavealleeikaee.ppikGvih 87 
                                       a + +le++  + ev+++   +++++++l e++ + + ++++ ++ 
  gi|557694229|ref|YP_008797283.1| 220 AILLALEKTLKNFEVINIGTGQPTSIKNLAEKVLTAFgHSVSAIVY 265
                                       5566677777777777777777777777777777777666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1987.67
//
Query:       gi|557694230|ref|YP_008797284.1|  [L=343]
Description: glycosyl transferase family 1 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  128.9   0.2    2.2e-37  128.2   0.2    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
      2e-34  118.9   2.7    2.9e-34  118.4   0.4    2.2  3  Glyco_trans_1_4  Glycosyl transferases group 1
    5.8e-16   58.9   5.4    3.8e-15   56.3   4.6    2.6  2  Glyco_transf_4   Glycosyltransferase Family 4
    2.5e-15   56.6   0.1      1e-14   54.7   0.0    2.0  2  Glyco_trans_1_2  Glycosyl transferases group 1
    8.3e-13   49.1  10.0    2.7e-09   37.7   2.6    3.1  3  Glyco_trans_4_4  Glycosyl transferase 4-like domain
    0.00061   18.6   0.0      0.001   17.8   0.0    1.3  1  Glyco_transf_20  Glycosyltransferase family 20
     0.0024   17.6   1.8       0.58    9.8   0.5    2.4  2  Glyco_transf_5   Starch synthase catalytic domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.028   14.2   0.0    1.5  1  PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin 
      0.018   15.1   0.1       0.65   10.0   0.1    2.7  1  Glyco_trans_4_2  Glycosyl transferase 4-like
       0.19   10.6   0.0       0.29   10.0   0.0    1.2  1  Glyco_transf_90  Glycosyl transferase family 90


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 !  128.2   0.2   1.2e-40   2.2e-37      15     171 ..     173     321 ..     166     322 .. 0.95

  Alignments for each domain:
  == domain 1  score: 128.2 bits;  conditional E-value: 1.2e-40
                                       -EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHHHH CS
                   Glycos_transf_1  15 kkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleellk 91 
                                        + +++vgrl++eK+v++l++a+++l     p++k+vi+G+g+++  l+k a++  +   v f+g v++e+   ++ 
  gi|557694230|ref|YP_008797284.1| 173 HPQVVYVGRLSREKNVSTLVEAARRL-----PEAKFVIVGDGPDKPFLEKAAQNISN---VVFTGAVEHEKALGYIA 241
                                       5789********************98.....789************99999887766...**********9****** PP

                                       CESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHHHH CS
                   Glycos_transf_1  92 nadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlgen 168
                                        +d++vlps  Eg+ +vllEAma+++pv+a+++gg+ e+v++getGllv++++ e+l eai+ ll+++ +++rl e+
  gi|557694230|ref|YP_008797284.1| 242 GSDVLVLPSVAEGMSTVLLEAMALKTPVVATAVGGNTELVQHGETGLLVDAGDLEQLTEAIAYLLNNSAEAKRLAEK 318
                                       ****************************************************************************9 PP

                                       HHH CS
                   Glycos_transf_1 169 ark 171
                                       a++
  gi|557694230|ref|YP_008797284.1| 319 AYQ 321
                                       986 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 ?   -0.4   0.0      0.79   1.4e+03      88     102 ..      34      48 ..      11      69 .. 0.78
   2 ?   -2.7   0.0       4.2   7.5e+03      59      79 ..     116     138 ..      89     155 .. 0.59
   3 !  118.4   0.4   1.6e-37   2.9e-34       2     134 .]     174     308 ..     173     308 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.79
                                       HHHHHTT-EEEE-TG CS
                   Glyco_trans_1_4  88 lEamaaglpvVatdv 102
                                       lEa+ + ++vV+++ 
  gi|557694230|ref|YP_008797284.1|  34 LEAAGYHVAVVSSEN 48 
                                       788888888888865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.2
                                       EE---.TH.HHHHHHH-SEEEE- CS
                   Glyco_trans_1_4  59 ftGfv.ed.laellaaadvfvaP 79 
                                       ++G+v +   +++l+ ad + a 
  gi|557694230|ref|YP_008797284.1| 116 LVGWVaSRlEKAALKWADAVTAV 138
                                       44555322233335555554444 PP

  == domain 3  score: 118.4 bits;  conditional E-value: 1.6e-37
                                       EEEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SE CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaadv 75 
                                       p +++vGrl  ++k+v  l+ea+ +l   ++++vivGdgp +p  le+ a+++ ++v+ftG v  e+   ++a +dv
  gi|557694230|ref|YP_008797284.1| 174 PQVVYVGRL-SREKNVSTLVEAARRLP--EAKFVIVGDGPdKP-FLEKAAQNI-SNVVFTGAVehEKALGYIAGSDV 245
                                       789******.566**************..46*********665.999777799.6********8667999******* PP

                                       EEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHHH- CS
                   Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLled 134
                                       +v+Ps  eg++ +llEama+++pvVat+vgg  e+v  ge+gllv++gd e+l+eai+ Ll++
  gi|557694230|ref|YP_008797284.1| 246 LVLPSvaEGMSTVLLEAMALKTPVVATAVGGNTELVqhGETGLLVDAGDLEQLTEAIAYLLNN 308
                                       *************************************************************87 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   4.6   2.1e-18   3.8e-15       2     168 ..      21     162 ..      20     164 .. 0.82
   2 ?   -2.2   0.0         2   3.5e+03      84     102 ..     254     272 ..     190     273 .. 0.62

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 2.1e-18
                    Glyco_transf_4   2 GGverhvleLaraLarrGheVtvvtpgddgpleeevelvvrvprvplpllkrllrslaflrrlrrllkrekpDvvHa 78 
                                       GGv+rhv  La +L ++G++V vv+++  +                  +lk++ ++l++++    l++  +  vvHa
  gi|557694230|ref|YP_008797284.1|  21 GGVARHVSGLAARLEAAGYHVAVVSSENTPIVNV-------------KGLKNPTFMLSSMF--STLFR--RASVVHA 80 
                                       9***********************9654444333.............35555555555443..44444..899**** PP

                    Glyco_transf_4  79 hspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrviavSeatadelrerygvp 155
                                       h+ ++ +a+ +a+      + +lt+Hg y+      + ++   ++ +le+ +l++ad+v+avS  ta+ +r   gv+
  gi|557694230|ref|YP_008797284.1|  81 HNVPSSLAM-RAAS---AGRRILTMHGVYAEQVNLLHGSLVGWVASRLEKAALKWADAVTAVSMRTAEFYRL-KGVD 152
                                       **8887555.4444...3478********9888999999999999***************************.**** PP

                    Glyco_transf_4 156 pekitVipnGvDl 168
                                       +   + ipn+vD+
  gi|557694230|ref|YP_008797284.1| 153 A---VYIPNAVDV 162
                                       8...9*******7 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                    Glyco_transf_4  84 lgaallalrrrlgiplVlt 102
                                       ++  +l  +++l+ p+V+t
  gi|557694230|ref|YP_008797284.1| 254 GMSTVLLEAMALKTPVVAT 272
                                       3333333333477777776 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 ?   -2.1   0.0         3   5.3e+03      61      81 ..      82     102 ..      75     108 .. 0.76
   2 !   54.7   0.0   5.8e-18     1e-14       4      91 ..     248     337 ..     245     338 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3
                   Glyco_trans_1_2  61 anpeerraiaeaarervlaeh 81 
                                       + p   + +a+ a +r+l+ h
  gi|557694230|ref|YP_008797284.1|  82 NVPSSLAMRAASAGRRILTMH 102
                                       556667778999999999988 PP

  == domain 2  score: 54.7 bits;  conditional E-value: 5.8e-18
                   Glyco_trans_1_2   4 npsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarervl 78 
                                        ps +e+++++l+Ea+a  +++++++  g  el++ g++++l++  dle+l e+i+yll+n +e++++ae+a++ v 
  gi|557694230|ref|YP_008797284.1| 248 LPSVAEGMSTVLLEAMALKTPVVATAVGGNTELVQHGETGLLVDagDLEQLTEAIAYLLNNSAEAKRLAEKAYQNVV 324
                                       58999********************99************************************************** PP

                   Glyco_trans_1_2  79 aehtydhraeqll 91 
                                       ++++++  + q+l
  gi|557694230|ref|YP_008797284.1| 325 NHFSWEAVFPQYL 337
                                       *******999887 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 !   14.1   0.5   2.6e-05     0.047       1      30 [.      21      50 ..      21      59 .. 0.92
   2 !   37.7   2.6   1.5e-12   2.7e-09      71     159 ..      72     158 ..      54     159 .. 0.86
   3 ?   -0.3   0.0      0.73   1.3e+03      75     107 ..     244     279 ..     235     321 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                   Glyco_trans_4_4  1 gGigryvaelaraLaarGheVtvltpapap 30
                                      gG++r+v  la++L+a+G++V v+ ++ +p
  gi|557694230|ref|YP_008797284.1| 21 GGVARHVSGLAARLEAAGYHVAVVSSENTP 50
                                      8***********************988776 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 1.5e-12
                   Glyco_trans_4_4  71 rerpdvvhahsptaglaarlarrrrgiplvvtlhglllrrg.sgavrrlyralerrllrradavlvvseaeaeelra 146
                                        +r  vvhah+ +++la+r+a+++r+i  ++ +++  ++   ++ v++++ +le+++l+ adav++vs   ae +r 
  gi|557694230|ref|YP_008797284.1|  72 FRRASVVHAHNVPSSLAMRAASAGRRILTMHGVYAEQVNLLhGSLVGWVASRLEKAALKWADAVTAVSMRTAEFYRL 148
                                       5799******************998988888888766655557899******************************* PP

                   Glyco_trans_4_4 147 lgvpadrvvvvpn 159
                                       +gv+a   v++pn
  gi|557694230|ref|YP_008797284.1| 149 KGVDA---VYIPN 158
                                       ***95...77777 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.73
                   Glyco_trans_4_4  75 dvvhahsptaglaarlar.rrrgiplvvtlhg..ll 107
                                       dv+++ s   g+  +l+  ++ ++p+v t+ g  ++
  gi|557694230|ref|YP_008797284.1| 244 DVLVLPSVAEGMSTVLLEaMALKTPVVATAVGgnTE 279
                                       666666654344444443267799999999742222 PP

>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.7e-07     0.001     358     459 ..     228     326 ..     218     338 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.7e-07
                                       ES---HHHHHHHHHH-SEEEE--SSBSS-CHHHHHHHCSTTT--EEEEETTBGGGGT-TTT...SEEE-TT-HHHHH CS
                   Glyco_transf_20 358 ersldfeeliallaaadvllvtslRdGmnlvakeyvvcqqekkgvLiLSeFaGaaqsLkda...ailvNPwdieeva 431
                                       +  ++ e+ + ++a +dvl+  s+ +Gm++v +e ++ ++      ++   +G   +L ++    +lv   d+e+++
  gi|557694230|ref|YP_008797284.1| 228 TGAVEHEKALGYIAGSDVLVLPSVAEGMSTVLLEAMALKTP-----VVATAVGGNTELVQHgetGLLVDAGDLEQLT 299
                                       45699999******************************999.....67777777777754312259*********** PP

                                       HHHHHHHC--HHHHHHHHHHHHHHHHHT CS
                   Glyco_transf_20 432 eaikeaLkmseeerkkrekkllkqvskh 459
                                       eai + L+ s e ++   +k +++v +h
  gi|557694230|ref|YP_008797284.1| 300 EAIAYLLNNSAEAKRL-AEKAYQNVVNH 326
                                       ********99988765.56667777765 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 !    9.8   0.5   0.00032      0.58       5      40 ..      13      45 ..       9      55 .. 0.83
   2 !    6.6   0.0    0.0031       5.6     163     226 ..      74     143 ..      60     147 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00032
                    Glyco_transf_5  5 vasEvaplaktGGLadvvgaLpkaLaklghdvrvil 40
                                      v++ +      GG+a++v++L+  L+++g++v v++
  gi|557694230|ref|YP_008797284.1| 13 VSPTAKG---LGGVARHVSGLAARLEAAGYHVAVVS 45
                                      5555544...8***********************97 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0031
                    Glyco_transf_5 163 iktvftiHN....layqgrfpkdel.aalglpaedfekldglefyg......kvnflkagivyadavttVSptya 226
                                        ++v++ HN    la++       +  ++g+ ae+ + l+     g      +  + ka+++ adavt+VS  +a
  gi|557694230|ref|YP_008797284.1|  74 RASVVHAHNvpssLAMRAASAGRRIlTMHGVYAEQVNLLH-----GslvgwvASRLEKAALKWADAVTAVSMRTA 143
                                       5566666665555444444443333355555544443333.....1233333555667*************9887 PP

>> PhdYeFM_antitox  Antitoxin Phd_YefM, type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05     0.028      31      68 ..     282     318 ..     269     321 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                       ETTEEEEEEEEHHHHHHHHH.HHHHHCSHHHHHHHHHH CS
                   PhdYeFM_antitox  31 rrGkpvaVlvsleeyerlqeltekllslplnaerlaes 68 
                                       ++G+ +  lv++ ++e+l+e++++ll + + a+rlae+
  gi|557694230|ref|YP_008797284.1| 282 QHGE-TGLLVDAGDLEQLTEAIAYLLNNSAEAKRLAEK 318
                                       6676.789****************************95 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 ?   10.0   0.1   0.00036      0.65      16     137 ..      30     137 ..       9     139 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00036
                   Glyco_trans_4_2  16 lakeLakrgyeVhvitpkkgakdeleaegihvhrlkvd...rkg.pleylkafklkklikkikPDvvhahyakpygl 88 
                                       la  L ++gy V+v+++++                  +   +kg +  ++++ ++++ ++++   vvhah++++   
  gi|557694230|ref|YP_008797284.1|  30 LAARLEAAGYHVAVVSSENT-----------------PivnVKGlKNPTFMLSSMFSTLFRRA-SVVHAHNVPSS-- 86 
                                       45555555555555555444.................02224455677777777766666554.79*****9884.. PP

                   Glyco_trans_4_2  89 lgslaarlsgvipvvlsvwGldvlkfpkksk...lkkl......llklalkkatkvis 137
                                       l+  aa      + +l+++  +v++++ +     l  +      l+k+alk a++v++
  gi|557694230|ref|YP_008797284.1|  87 LAMRAASA---GRRILTMH--GVYAEQVNLLhgsL--VgwvasrLEKAALKWADAVTA 137
                                       33334333...56899999..77888776643441..144566799999999998887 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 ?   10.0   0.0   0.00016      0.29     269     313 ..     293     337 ..     289     340 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00016
                   Glyco_transf_90 269 dklrdlkeavdwgnahdekaqeiaeegseFireeLkmddvydYmf 313
                                        +l++l ea+ ++ +++++a+++ae++ + + ++++ + v+  ++
  gi|557694230|ref|YP_008797284.1| 293 GDLEQLTEAIAYLLNNSAEAKRLAEKAYQNVVNHFSWEAVFPQYL 337
                                       6899***********************************996655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 2147.38
//
Query:       gi|557694231|ref|YP_008797285.1|  [L=71]
Description: small subunit ribosomal protein S17e [Candidatus Caldiarchaeum subterraneum]
Scores for 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   24.5   0.1    2.1e-05   24.4   0.1    1.1  1  Ribosomal_S17e  Ribosomal S17


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 !   24.4   0.1   1.2e-09   2.1e-05      18      60 ..       3      46 ..       1      70 [. 0.80

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.2e-09
                                      HS-TTT--S-HHHHHHHHHHHS---.-SHHHHHHHHHHHHHHHH CS
                    Ribosomal_S17e 18 ekyyskltndFhtnkkvceevaiip.skklrnkiaGyvthlmkr 60
                                      e y  ++++ F++nkk+++ev   + skkl n+iaGy  +l k 
  gi|557694231|ref|YP_008797285.1|  3 ELYGDRVSTSFEENKKLVREVLEGRfSKKLANRIAGYLVTLKKL 46
                                      66889999************987554***********9988553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       960  (0.0535445); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 524.17
//
Query:       gi|557694232|ref|YP_008797286.1|  [L=325]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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    8.3   9.2       0.19   11.6   0.2    2.1  2  RIFIN     Rifin


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 ?   -0.6   4.3     0.055   9.9e+02     254     291 ..      28      65 ..      25      72 .. 0.83
   2 ?   11.6   0.2   1.1e-05      0.19     213     305 ..     236     325 .]     179     325 .] 0.49

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.055
                             RIFIN 254 aaeataeaekaetaaveattaslqtaiiasivaivvIv 291
                                       aa++++ +++++t+ v+ + ++++t i++s ++iv  +
  gi|557694232|ref|YP_008797286.1|  28 AAQTQSVITTTTTRVVTISPTTYTTVITVSATTIVATI 65 
                                       56667778888899999999999999****99999755 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 1.1e-05
                             RIFIN 213 altsakekekkeasskekikkkvekivekaekkaaaaaaeaaaeataeaekaetaaveattaslqtaiiasivaivv 289
                                       +++++  ++ + +s  ++i+++ +++++    +++++ a++ +++t ++ +++ta +++t a +  +++   +   v
  gi|557694232|ref|YP_008797286.1| 236 QTITEGRTTATIVSPGTTITETYTTVITL---QQQTTPAQTMTTTTPTVATTTTAVTTQTQAPSGPSLTDVLIPAAV 309
                                       22222223333333333333333333332...222333333444444444444444444444444444444443344 PP

                             RIFIN 290 IvLimvIIYLiLRYrR 305
                                       Iv+ + ++ + LR rR
  gi|557694232|ref|YP_008797286.1| 310 IVVLLAVVVFALRLRR 325
                                       4444555555677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1347  (0.0751297); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2307.83
//
Query:       gi|557694233|ref|YP_008797287.1|  [L=344]
Description: flap endonuclease 1 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-27   94.2   0.0    8.2e-27   93.4   0.0    1.4  1  XPG_I       XPG I-region
    5.5e-17   62.1   0.0    9.5e-17   61.3   0.0    1.4  1  XPG_N       XPG N-terminal domain
    1.4e-06   28.8   0.0    3.2e-06   27.6   0.0    1.7  1  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
     0.0043   17.6   0.0      0.012   16.2   0.0    1.7  1  HHH_5       Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.032   14.3   0.1       0.26   11.4   0.0    2.4  2  HHH_2       Helix-hairpin-helix motif
       0.29   11.3   2.8       0.64   10.2   2.8    1.5  1  HemY_N      HemY protein N-terminus


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 !   93.4   0.0   2.8e-30   8.2e-27       2      94 .]     144     239 ..     143     239 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 2.8e-30
                                       HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHH CS
                             XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlk 75 
                                       +mg+pyv Ap+E+EAq+ay+++kg v+a+ s+D+D+llFG+p+++rnls  +++k    ke++++ +e+i l+k+l 
  gi|557694233|ref|YP_008797287.1| 144 AMGVPYVMAPSEGEAQAAYMAAKGSVYAAGSQDMDSLLFGSPRLVRNLSiVGRRKLPgrKEYVEVVPEIIYLDKLLA 220
                                       7************************************************755555557799999************* PP

                                       HHT--HHHHHHHHHHHCET CS
                             XPG_I  76 elgltreqlidlaillgcD 94 
                                        lgltreqlid+ +l+g+D
  gi|557694233|ref|YP_008797287.1| 221 SLGLTREQLIDIGLLVGTD 239
                                       *****************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 !   61.3   0.0   3.2e-20   9.5e-17       9     100 ..       8     103 ..       1     104 [. 0.92

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 3.2e-20
                                       HHHHH-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE- CS
                             XPG_N   9 llkevaairsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFd 80 
                                       ++    a+++ s+++l+gk +a Da+  ly+fl ++r ++g  l+      tshl glf r++ +l+ g  P++VFd
  gi|557694233|ref|YP_008797287.1|   8 IIPGE-AVEQTSLKRLSGKAIAFDAYNILYQFLATIRGPDGRPLMDrrgrvTSHLSGLFFRTINFLQEGLLPVYVFD 83 
                                       44444.59*************************************99****************************** PP

                                       -S--GGGHHHHHHHHHHHHH CS
                             XPG_N  81 gkapdlkkeelekrserrqe 100
                                       g +p+ k  ++ekr  +r+e
  gi|557694233|ref|YP_008797287.1|  84 GRPPEEKYRTIEKRAVAREE 103
                                       **************999987 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 !   27.6   0.0   1.1e-09   3.2e-06       4      47 ..     227     268 ..     224     298 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.1e-09
                        5_3_exonuc   4 eqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilen 47 
                                       eq+id+  LvG  +D  p v+g+G+ktA k++keygsle+ +e 
  gi|557694233|ref|YP_008797287.1| 227 EQLIDIGLLVG--TDYSPQVRGVGPKTALKIVKEYGSLEKAVET 268
                                       79999999999..5889***********************9985 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.1e-06     0.012       7      28 ..     244     264 ..     242     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.1e-06
                                       STT--HHHHHHHHTTT--SHHH CS
                             HHH_5   7 vsGiGpktAlallsaGiesved 28 
                                       v G+GpktAl++++  ++s+e+
  gi|557694233|ref|YP_008797287.1| 244 VRGVGPKTALKIVKE-YGSLEK 264
                                       89*************.999985 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.59   1.8e+03      15      48 ..     119     152 ..     118     154 .. 0.80
   2 ?   11.4   0.0   8.6e-05      0.26       8      28 ..     244     264 ..     243     274 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.59
                             HHH_2  15 tAklLakrFksldaLkkasleeLlevddiGeeiA 48 
                                       +A+  a+r  sl++ +  s+ +Ll+  ++  ++A
  gi|557694233|ref|YP_008797287.1| 119 AARRYAQRAASLEKYMVESAADLLKAMGVPYVMA 152
                                       6888899999999999999999998888876666 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8.6e-05
                             HHH_2   8 IrhVGektAklLakrFkslda 28 
                                       +r VG ktA +++k+++sl++
  gi|557694233|ref|YP_008797287.1| 244 VRGVGPKTALKIVKEYGSLEK 264
                                       699****************97 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   2.8   0.00021      0.64      68     100 ..     110     144 ..      89     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00021
                            HemY_N  68 ialaeGdfarAekaaakaaklsea..pllayllaA 100
                                        alaeGd ++A++ a++aa+l++   +  a ll+A
  gi|557694233|ref|YP_008797287.1| 110 AALAEGDLEAARRYAQRAASLEKYmvESAADLLKA 144
                                       589*******************9988668888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2464.87
//
Query:       gi|557694234|ref|YP_008797288.1|  [L=726]
Description: AAA family ATPase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-100  330.4   0.0    1.3e-49  168.0   0.0    2.6  2  AAA              ATPase family associated with various cellul
    2.6e-36  123.2   3.2      2e-18   65.9   1.2    2.9  2  AAA_lid_3        AAA+ lid domain
    1.5e-28   98.8   1.0    6.3e-28   96.8   1.0    2.2  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    1.5e-16   61.2   0.1    7.3e-07   29.7   0.0    3.2  2  AAA_16           AAA ATPase domain
    2.4e-16   59.9   0.0    1.2e-07   31.6   0.0    3.1  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.4e-16   59.8   0.0    2.2e-08   34.4   0.0    2.4  2  AAA_2            AAA domain (Cdc48 subfamily)
    8.2e-13   48.5   0.0      7e-06   26.1   0.0    2.4  2  AAA_14           AAA domain
    1.8e-12   47.5   0.2    0.00019   21.5   0.1    3.9  2  AAA_5            AAA domain (dynein-related subfamily)
    9.8e-12   44.7   0.0      5e-05   22.7   0.0    2.6  2  TIP49            TIP49 P-loop domain
    1.2e-10   41.8   0.4      0.015   15.6   0.0    4.1  4  AAA_22           AAA domain
    1.1e-09   38.5   0.0    0.00069   19.8   0.0    2.5  2  AAA_33           AAA domain
    8.3e-09   35.8   0.0     0.0081   16.5   0.0    2.8  2  RNA_helicase     RNA helicase
    1.3e-07   32.2   0.0     0.0095   16.5   0.0    2.5  2  ABC_tran         ABC transporter
      2e-07   30.9   0.0      0.015   15.0   0.0    2.9  3  IstB_IS21        IstB-like ATP binding protein
      3e-07   30.0   0.2       0.03   13.7   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    5.4e-07   29.8   0.3      0.045   13.6   0.0    3.3  3  ATPase_2         ATPase domain predominantly from Archaea
    5.6e-07   30.0   0.0       0.03   14.6   0.0    2.7  2  AAA_28           AAA domain
    1.2e-06   28.0   0.0      0.033   13.5   0.0    2.4  2  Zeta_toxin       Zeta toxin
    2.1e-06   28.3   0.0        0.1   13.2   0.0    3.0  2  AAA_18           AAA domain
    2.5e-06   27.4   0.1     0.0058   16.6   0.1    3.0  2  Vps4_C           Vps4 C terminal oligomerisation domain
      3e-06   27.2   0.0       0.12   12.3   0.0    3.1  3  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    3.6e-06   27.0   0.1       0.15   12.0   0.0    3.1  2  NACHT            NACHT domain
    3.8e-06   27.0   0.6       0.33   10.9   0.0    3.4  3  Rad17            Rad17 P-loop domain
    8.4e-06   25.5   0.5    2.5e-05   24.0   0.5    1.8  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    9.3e-06   25.2   0.1       0.22   10.9   0.0    3.2  3  ATPase           KaiC
    9.5e-06   25.5   0.0      0.095   12.4   0.0    2.6  2  AAA_24           AAA domain
    1.2e-05   25.0   0.0        0.4   10.4   0.0    3.4  2  Sigma54_activat  Sigma-54 interaction domain
    1.6e-05   24.5   5.7       0.51    9.9   0.5    4.4  4  AAA_25           AAA domain
      2e-05   25.0   0.0       0.22   12.0   0.0    3.2  3  AAA_17           AAA domain
      2e-05   23.9   0.0       0.11   11.6   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
    7.5e-05   22.3   0.0       0.47    9.9   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
    7.7e-05   22.5   0.0      0.049   13.4   0.0    2.3  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    9.2e-05   21.8   0.0       0.21   10.7   0.0    2.7  3  DAP3             Mitochondrial ribosomal death-associated pro
    0.00012   21.4   0.0       0.56    9.3   0.0    2.5  2  NB-ARC           NB-ARC domain
    0.00014   21.7   0.0       0.14   12.0   0.0    2.6  2  Bac_DnaA         Bacterial dnaA  protein
    0.00028   20.4   0.2       0.75    9.2   0.0    2.5  2  PhoH             PhoH-like protein
    0.00035   20.4   0.0        1.2    9.0   0.0    2.5  2  AAA_3            ATPase family associated with various cellul
     0.0012   18.2   0.0       0.14   11.4   0.0    2.3  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0012   18.0   0.0        1.3    8.1   0.0    2.2  2  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0015   18.0   0.0     0.0029   17.1   0.0    1.5  1  UFD1             Ubiquitin fusion degradation protein UFD1
     0.0017   18.5   0.0        2.2    8.4   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.012   15.1   0.0        5.9    6.3   0.0    3.1  3  TniB             Bacterial TniB protein
      0.014   15.3   2.3         17    5.3   0.0    4.1  4  NTPase_1         NTPase
      0.016   15.4   0.0        5.9    7.0   0.0    2.5  2  SKI              Shikimate kinase
      0.026   14.8   1.4         15    5.9   0.1    3.2  3  AAA_19           AAA domain
      0.032   14.0   0.0        9.9    5.9   0.0    2.5  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.038   13.7   0.0         13    5.5   0.0    2.6  2  AAA_30           AAA domain
      0.038   13.4   0.0        8.7    5.7   0.0    2.4  2  SRPRB            Signal recognition particle receptor beta su
       0.04   12.8   0.0        7.5    5.3   0.0    2.4  2  AFG1_ATPase      AFG1-like ATPase
      0.063   13.1   0.0         14    5.3   0.0    2.3  2  AAA_11           AAA domain
       0.13   12.0   0.0         26    4.6   0.0    2.4  2  AAA_29           P-loop containing region of 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 !  168.0   0.0   3.8e-52   1.3e-49       1     131 [.     218     347 ..     218     348 .. 0.98
   2 !  159.9   0.0   1.2e-49   4.2e-47       1     131 [.     491     622 ..     491     623 .. 0.97

  Alignments for each domain:
  == domain 1  score: 168.0 bits;  conditional E-value: 3.8e-52
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vllyGppG+GKTllakava+e++++f+ i+g+e+++ky ge+e+++re+f++a+e+a psi+fiDEida+a++rs+ 
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAEANFILINGPEIMNKYYGETEARLREIFRKAEEEA-PSIIFIDEIDAIAPKRSEV 293
                                       79******************************************************9.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLl+ +dg++ + s vivigatnrp+ ldpal+r gRfdr+iei+
  gi|557694234|ref|YP_008797288.1| 294 TGEVEKRVVAQLLALMDGLEGRGS-VIVIGATNRPNALDPALRRpGRFDREIEIG 347
                                       *********************866.***************************986 PP

  == domain 2  score: 159.9 bits;  conditional E-value: 1.2e-49
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..T CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr..s 75 
                                       vllyGppG+GKTllakava+e++++f++i+g+e++sk+vgesek ire+f++a++ a p ++f+DEi+a+a+++   
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESEANFITIKGPEIFSKWVGESEKAIREIFRKARQAA-PAVIFFDEIEAIAPRKdlA 566
                                       79******************************************************9.****************999 PP

                                       TCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       +++s++++rv++qLl+e+dg ++  ++++vigatnrpd+ldpallr gRfdr + i+
  gi|557694234|ref|YP_008797288.1| 567 EDSSGVTNRVASQLLAEIDGIEEL-NDIVVIGATNRPDMLDPALLRpGRFDRLLLIP 622
                                       99*********************7.66************************988775 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   5.7e-18     2e-15       1      43 [.     370     429 ..     370     431 .. 0.82
   2 !   65.9   1.2   5.7e-21     2e-18       1      45 []     645     691 ..     645     691 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 5.7e-18
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrr.................gikeitmedf 43 
                                       dv++++L e+T Gy+GADlaalcreAa+ A+rr                 +  e+tm+df
  gi|557694234|ref|YP_008797288.1| 370 DVQVDKLGEMTRGYTGADLAALCREAAMKAIRRilpsidfsserispeilNSLEVTMKDF 429
                                       8********************************777776666666666544556777777 PP

  == domain 2  score: 65.9 bits;  conditional E-value: 5.7e-21
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedfee 45 
                                       dv+++ LA+r+eGySGAD++++c+eAal+Alrr+i   ++t++dfee
  gi|557694234|ref|YP_008797288.1| 645 DVNIEVLASRCEGYSGADIESVCKEAALAALRRDINadKVTKRDFEE 691
                                       9*********************************99656******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 !   96.8   1.0   1.8e-30   6.3e-28       1      85 []       7      92 ..       7      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 1.8e-30
                                      CEEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTST.TTTEEEE-HHHHHHHT--TTEEE CS
                           CDC48_N  1 rLrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepede.gkgiIrmdgvtRknagvsiGdkV 78
                                      rLrVaea+q+dvg gi+rid+++ +e gl++gd++ei+gk+ T+a vw ++ ede +k+iIr+dg +R+nagvs++d V
  gi|557694234|ref|YP_008797288.1|  7 RLRVAEAKQRDVGYGIARIDRSVGAEAGLSTGDIIEIRGKKLTAATVWLGYMEDEkEKDIIRIDGHIRNNAGVSLNDYV 85
                                      79***************************************************************************** PP

                                      EEEEE-- CS
                           CDC48_N 79 tVrkaev 85
                                      +Vrka+v
  gi|557694234|ref|YP_008797288.1| 86 IVRKANV 92
                                      ****985 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   2.1e-09   7.3e-07      22     140 ..     213     320 ..     185     322 .. 0.77
   2 !   27.5   0.1     1e-08   3.6e-06      24     133 ..     488     590 ..     479     596 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 2.1e-09
                            AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawr 98 
                                       + p  vll+G++G+GK+ l++++++++e++ +i+++g    +     y+  ++a  r e++r+ ++e   a    + 
  gi|557694234|ref|YP_008797288.1| 213 DPPKGVLLYGPPGCGKTLLAKAVATEAEAN-FILINGPEIMN----KYYGETEARLR-EIFRKAEEE---APSIIFI 280
                                       44599***********************99.66666666666....56565555536.888888888...4556677 PP

                            AAA_16  99 ekleealaavpelagaeasrllellkrllallsrderplvlv 140
                                       +++++ +   +e++g+ ++r+ ++l +l++ l+ +++  v+v
  gi|557694234|ref|YP_008797288.1| 281 DEIDAIAPKRSEVTGEVEKRVVAQLLALMDGLEGRGS--VIV 320
                                       778888888999999999**********999987665..443 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 1e-08
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                                       p+ vll+G++G+GK+ l+++++++ e++   f++ k  +      +s ++    + + +r++ ++a++a+++     
  gi|557694234|ref|YP_008797288.1| 488 PRGVLLYGPPGCGKTLLAKAVATESEAN---FITIKGPEI-----FSKWVGES-E-KAIREIFRKARQAAPAVIFFD 554
                                       699*******************988888...999999999.....77777777.4.899999999888888888888 PP

                            AAA_16 101 leealaavpelagaea...srllellkrllallsrd 133
                                         ea+a+ ++la +++   +r++ +l + ++ +++ 
  gi|557694234|ref|YP_008797288.1| 555 EIEAIAPRKDLAEDSSgvtNRVASQLLAEIDGIEEL 590
                                       888888888888888888888888888777766665 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 !   31.6   0.0   3.4e-10   1.2e-07      35     103 ..     217     293 ..     208     341 .. 0.80
   2 !   24.4   0.0   5.6e-08     2e-05      36      98 ..     491     561 ..     485     616 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.4e-10
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvleka..gdlaalltnl....eek..dvlfideihrlsraveev 103
                                        vllyGpPG Gkt lak +a+e ++++    gP + ++  g+  a l ++    ee+   ++fidei  ++++  ev
  gi|557694234|ref|YP_008797288.1| 217 GVLLYGPPGCGKTLLAKAVATEAEANFILINGPEIMNKyyGETEARLREIfrkaEEEapSIIFIDEIDAIAPKRSEV 293
                                       69*******************************996543355555555442221443337********999988876 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 5.6e-08
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleek..dvlfideihrlsr 98 
                                       vllyGpPG Gkt lak +a+e ++++ +  gP +      e ++ +  ++ + ++    v+f dei  +++
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESEANFITIKGPEIfskwvgESEKAIREIFRKARQAapAVIFFDEIEAIAP 561
                                       9*******************************884433334455666676665544226888888877665 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   6.3e-11   2.2e-08       6     105 ..     218     311 ..     213     315 .. 0.89
   2 !   23.0   0.0   2.1e-07   7.2e-05       6      92 ..     491     571 ..     486     587 .. 0.80

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 6.3e-11
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a   ++    ++i ++  e++     + + + +   ++   +aee+   i+++DEid i
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAEA----NFILINGPEIMN----KYYGETEARLREIFRKAEEEApsIIFIDEIDAI 286
                                       6899****************9985....************....9999****************99*********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk ++ + +v +  V+  LL +++g
  gi|557694234|ref|YP_008797288.1| 287 APKrSEVTGEVEK-RVVAQLLALMDG 311
                                       **96666666655.677889999987 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 2.1e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a   ++    ++i++   e+      + + ++++  ++   +a +    ++++DEi+ i
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESEA----NFITIKGPEIFS----KWVGESEKAIREIFRKARQAApaVIFFDEIEAI 559
                                       6899***************99985....**********99....66666666666666666666689********** PP

                                       ------------ CS
                             AAA_2  81 hpkessgadvSr 92 
                                       +p++   +d S+
  gi|557694234|ref|YP_008797288.1| 560 APRKDLAEDSSG 571
                                       **9888888875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0     2e-08     7e-06       5      99 ..     218     322 ..     215     340 .. 0.76
   2 !   19.9   0.0   1.6e-06   0.00057       5      76 ..     491     559 ..     488     601 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2e-08
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT l+k ++ e      +++ in  +  +k + ++e  l++i++k++ee  +++f+DEi  +     
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAE---ANFILINGPEIMNKYYGETEARLREIFRKAEEEAPSIIFIDEIDAIapkrs 291
                                       7899***************8888...**********9999988777555555555556699********99966666 PP

                            AAA_14  77 .......pewekalkslvd..egknldvivtG 99 
                                              +++   l  l+d  eg ++ viv G
  gi|557694234|ref|YP_008797288.1| 292 evtgeveKRVVAQLLALMDglEG-RGSVIVIG 322
                                       66666665666666666664333.55555555 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.6e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       +++ G+  +GKT l+k ++ e+     +++ i+  +   k   ++ek +++i++k+++    ++f+DEi  +
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESE---ANFITIKGPEIFSKWVGESEKAIREIFRKARQAAPAVIFFDEIEAI 559
                                       7899***************9988...999999999988888877777777777775556899*******987 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 !   21.5   0.1   5.3e-07   0.00019       1     135 [.     217     335 ..     217     337 .. 0.68
   2 !   21.0   0.0   7.2e-07   0.00025       1     135 [.     490     610 ..     490     612 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 5.3e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppG+gK+ la+ +a   ++++  +++++ +++      +    g+t+ +  ++ r+a+   ++i+++DE++
  gi|557694234|ref|YP_008797288.1| 217 GVLLYGPPGCGKTLLAKAVATEAEANFILINGPEIMNK------YY---GETEARLREIFRKAEeeAPSIIFIDEID 284
                                       59*******************99999999999996654......33...55666678888888877899******** PP

                                       G--...HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  76 rae...sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                        +    sev++++ +    + l l++g e  +         + vi+++n+++     l+palr
  gi|557694234|ref|YP_008797288.1| 285 AIApkrSEVTGEVEKRVVAQLLALMDGLEGRGS--------VIVIGATNRPN----ALDPALR 335
                                       987222344444433333333333333333322........66666666666....5666665 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 7.2e-07
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppG+gK+ la+ +a   ++++ ++ +++      ++ ++    g+ +    ++ r+ar   ++++++DE+e
  gi|557694234|ref|YP_008797288.1| 490 GVLLYGPPGCGKTLLAKAVATESEANFITIKGPE------IFSKWV---GESEKAIREIFRKARqaAPAVIFFDEIE 557
                                       59*******************99****9999997......999999...66777777777788878999******** PP

                                       G--..HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  76 rae..sevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                        +   ++ ++    + ++   +l      + + nd     + vi+++n++d     l+pal+
  gi|557694234|ref|YP_008797288.1| 558 AIAprKDLAEDSSGVTNRVASQLLAEIDGIEELND-----IVVIGATNRPD----MLDPALL 610
                                       98765667776666666666665555555544443.....88888888888....6677765 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.7e-06   0.00062      51     106 ..     216     270 ..     207     284 .. 0.92
   2 !   22.7   0.0   1.4e-07     5e-05      51     106 ..     489     543 ..     482     546 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.7e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltqalrks 106
                                       ++vLl Gp+g Gkt la a++ e      f+ ++g e+       te+ l + +rk+
  gi|557694234|ref|YP_008797288.1| 216 KGVLLYGPPGCGKTLLAKAVATEAE--ANFILINGPEIMNKYYGETEArLREIFRKA 270
                                       89*******************9965..89******************8678899997 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.4e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrks 106
                                       r+vLl Gp+g Gkt la a++ e  ++  f++++g e++s  v  +e ++ + +rk+
  gi|557694234|ref|YP_008797288.1| 489 RGVLLYGPPGCGKTLLAKAVATE--SEANFITIKGPEIFSKWVGESEkAIREIFRKA 543
                                       89*******************98..5689**************99985688999997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.1e-05     0.015       8      43 ..     218     244 ..     213     256 .. 0.80
   2 ?    5.4   0.0     0.059        21      74     132 ..     259     325 ..     249     330 .. 0.71
   3 !   14.9   0.1     7e-05     0.025       8      30 ..     491     513 ..     486     545 .. 0.78
   4 ?    0.3   0.0       2.3     8e+02      82     106 ..     536     563 ..     523     581 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.1e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43 
                                       ++++G++G+GKT+l++ ++ ++         ++ ++
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEA---------EANFI 244
                                       689****************998.........44444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.059
                            AAA_22  74 sseellealeqalraravielliiDEaqhlr...s.......eealeeLrsllnlsrkgvqliLvGtpe 132
                                       ++ +l+e +++a +++   +++ iDE++ +    s       ++++ +L  l++  +   ++i++G ++
  gi|557694234|ref|YP_008797288.1| 259 TEARLREIFRKAEEEAP--SIIFIDEIDAIApkrSevtgeveKRVVAQLLALMDGLEGRGSVIVIGATN 325
                                       44555555555555554..5**********887626667777888899988888877888888888776 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 7e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                       ++++G++G+GKT+l++ ++ + +
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESE 513
                                       689***************99873 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 2.3
                            AAA_22  82 leqalrarav..ielliiDEaqhlr.se 106
                                       +++ +r+++   ++++  DE++ +  ++
  gi|557694234|ref|YP_008797288.1| 536 IREIFRKARQaaPAVIFFDEIEAIApRK 563
                                       33333333334458********986433 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0     2e-06   0.00069       2      46 ..     218     264 ..     218     343 .. 0.74
   2 !   16.3   0.0   2.4e-05    0.0083       2      46 ..     491     537 ..     491     601 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                       vll G+pG+GK+ la+ ++ +    ++l++ ++++++++g+ + +++
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAEanFILINGPEIMNKYYGETEARLR 264
                                       7899**************9999899*************997666665 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.4e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt 46 
                                       vll G+pG+GK+ la+ ++ +    ++++  ++++++ +g+ ++ ++
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESEanFITIKGPEIFSKWVGESEKAIR 537
                                       7899***************9999999999999988888886666555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.3e-05    0.0081       1      60 [.     218     268 ..     218     295 .. 0.67
   2 !   16.3   0.0   2.8e-05    0.0098       1      36 [.     491     526 ..     491     568 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.3e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgq 60 
                                       ++lyGp+g+GK++lak +a++ + ++            +  +++++Y g++     ++ +
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAEANFI---------LINGPEIMNKYYGETEARLREIFR 268
                                       689**************7776664442.........233445555555555555555555 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.8e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                       ++lyGp+g+GK++lak +a++ + ++ ++k ++++s
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESEANFITIKGPEIFS 526
                                       689**************8888877764444444444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00029       0.1       7      54 ..     211     256 ..     208     310 .. 0.76
   2 !   16.5   0.0   2.7e-05    0.0095       6      75 ..     483     551 ..     481     599 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00029
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqel 54 
                                        + + + v + G+ G+GK+ L+k++a + +  +  il++g ++ ++  
  gi|557694234|ref|YP_008797288.1| 211 GIDPPKGVLLYGPPGCGKTLLAKAVATEAE--ANFILINGPEIMNKYY 256
                                       566777899*****************9975..6777788777776333 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.7e-05
                                       EEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                          ABC_tran   6 lklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpelt 75 
                                       l +k+ + v + G+ G+GK+ L+k++a +++  +  i+++g ++ ++   +++k i+ ++ +  q  p + 
  gi|557694234|ref|YP_008797288.1| 483 LGIKPPRGVLLYGPPGCGKTLLAKAVATESE--ANFITIKGPEIFSKWVGESEKAIREIFRKaRQAAPAVI 551
                                       6678888899******************986..68899999999998888888888888887555555554 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 !   15.0   0.0   4.3e-05     0.015      44      71 ..     212     239 ..     188     283 .. 0.89
   2 ?   -2.1   0.0       7.7   2.7e+03       4      45 ..     388     431 ..     386     436 .. 0.69
   3 !   12.3   0.0    0.0003      0.11      49      71 ..     490     512 ..     485     520 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-05
                         IstB_IS21  44 iekkenivllGpsGvGKshlaialgvea 71 
                                       i+  ++++l Gp+G GK+ la a+++ea
  gi|557694234|ref|YP_008797288.1| 212 IDPPKGVLLYGPPGCGKTLLAKAVATEA 239
                                       6667899******************998 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.7
                         IstB_IS21   4 letrlrlaklp.aqktledidfraarsldkrkvkeL..atlsfie 45 
                                       l++  r+a+++  ++ l +idf+++r ++++++++L     +f++
  gi|557694234|ref|YP_008797288.1| 388 LAALCREAAMKaIRRILPSIDFSSER-ISPEILNSLevTMKDFLD 431
                                       567789999997789999****9996.455555544225556665 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.0003
                         IstB_IS21  49 nivllGpsGvGKshlaialgvea 71 
                                       +++l Gp+G GK+ la a+++e 
  gi|557694234|ref|YP_008797288.1| 490 GVLLYGPPGCGKTLLAKAVATES 512
                                       799***************99875 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   8.6e-05      0.03      25      43 ..     218     236 ..     215     240 .. 0.90
   2 !   13.7   0.0   8.7e-05     0.031      25      43 ..     491     509 ..     486     513 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.6e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+++
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVA 236
                                       79*************9875 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.7e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt+lak+++
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVA 509
                                       79*************9875 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 !   13.6   0.0   0.00013     0.045      19      68 ..     214     259 ..     204     323 .. 0.58
   2 !   11.4   0.0   0.00061      0.21      23      45 ..     491     513 ..     481     520 .. 0.83
   3 ?   -0.6   0.0       2.8     1e+03     107     130 ..     533     559 ..     516     565 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00013
                          ATPase_2  19 pneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldef 68 
                                       p + +++YGp g+GKt L k ++++ e      + +i+  e+ ++++ e+
  gi|557694234|ref|YP_008797288.1| 214 PPKGVLLYGPPGCGKTLLAKAVATEAEA----NFILINGPEIMNKYYGET 259
                                       5566899************999998844....334455555555555555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00061
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienle 45 
                                       +++YGp g+GKt L k +++++e
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESE 513
                                       789************99998774 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.8
                          ATPase_2 107 elllekikkkgkk...iiiiiDelqkl 130
                                       e+++++i +k+++    +i++De+  +
  gi|557694234|ref|YP_008797288.1| 533 EKAIREIFRKARQaapAVIFFDEIEAI 559
                                       344555555555566578899999776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.4e-05      0.03       2      49 ..     218     270 ..     217     296 .. 0.82
   2 !   12.5   0.0   0.00037      0.13       2      37 ..     491     531 ..     490     583 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.4e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareileeklakgedalpwv 49 
                                       + + G++++GKT l++a a +   ++  +  pE++ +++ e  a+ +++ +++
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEaeaNFILIngPEIMNKYYGETEARLREIFRKA 270
                                       6799***************5444577777899999999999888888776665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00037
                            AAA_28   2 ivitGgestGKTtlleaLaar...gypvv..pEaareilee 37 
                                       + + G++++GKT l++a a +   ++ ++  pE++ + + e
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATEseaNFITIkgPEIFSKWVGE 531
                                       6799***************5544566666667766665544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   9.4e-05     0.033      15      51 ..     214     248 ..     206     270 .. 0.89
   2 !   11.9   0.0   0.00029       0.1      15      51 ..     487     521 ..     478     524 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.4e-05
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                        Pk +ll G pG+GK+ la+++++e   + n++ +++
  gi|557694234|ref|YP_008797288.1| 214 PPKGVLLYGPPGCGKTLLAKAVATEA--EANFILING 248
                                       5999*********************8..899999987 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00029
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrldp 51 
                                        P  +ll G pG+GK+ la+++++e   + n++++++
  gi|557694234|ref|YP_008797288.1| 487 PPRGVLLYGPPGCGKTLLAKAVATES--EANFITIKG 521
                                       58889********************8..899999875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00029       0.1       1      25 [.     218     260 ..     218     327 .. 0.59
   2 !   11.7   0.0   0.00082      0.29       1      22 [.     491     512 ..     491     558 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00029
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................g 25 
                                       +ll G+pG+GKt lak+++ +  ++                  
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAeANfilingpeimnkyygetE 260
                                       799***************7765333476776666666666663 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00082
                            AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                       +ll G+pG+GKt lak+++ + 
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATES 512
                                       799**************96553 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 ?    7.6   0.0     0.011       3.8      20      44 ..     415     439 ..     392     459 .. 0.80
   2 !   16.6   0.1   1.7e-05    0.0058      24      55 ..     679     710 ..     665     711 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.011
                            Vps4_C  20 psdklleP.pvtlkDflkalkkarpt 44 
                                          ++l+  +vt+kDfl+a k+  p+
  gi|557694234|ref|YP_008797288.1| 415 S-PEILNSlEVTMKDFLDAYKEITPS 439
                                       4.4455554***********999987 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.7e-05
                            Vps4_C  24 llePpvtlkDflkalkkarptVskeDLekhee 55 
                                       + + +vt +Df++al +++p+++++ ++++e+
  gi|557694234|ref|YP_008797288.1| 679 INADKVTKRDFEEALMNVKPSITPQMMKEYEK 710
                                       55669*********************999986 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00035      0.12      19      61 ..     215     257 ..     187     284 .. 0.75
   2 ?    1.1   0.1       1.1   3.8e+02      79     104 ..     452     477 ..     431     486 .. 0.81
   3 !   10.2   0.1    0.0016      0.57      20      50 ..     489     521 ..     460     526 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00035
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEEE CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYel 61 
                                        + +lL+G+ G+GKT l++++a + + +   ++ P   ++++Y  
  gi|557694234|ref|YP_008797288.1| 215 PKGVLLYGPPGCGKTLLAKAVATEAEANfiLINGP--EIMNKYYG 257
                                       3449*******************999987677777..67777755 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.1
                                       HHHHCTTCCCCSTSCEEEEETGGGGC CS
                              TsaE  79 eleelgleeyleeeavvlvEWpekle 104
                                       ++e++g  e ++++ + +vEWp k+ 
  gi|557694234|ref|YP_008797288.1| 452 RWEDIGGLEQVKQKLIEMVEWPLKYP 477
                                       5788888888887789******8854 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0016
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..---- CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkS 50 
                                       + +lL+G+ G+GKT l++++a + + +  ++k 
  gi|557694234|ref|YP_008797288.1| 489 RGVLLYGPPGCGKTLLAKAVATESEANfiTIKG 521
                                       349******************998776656665 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   0.00042      0.15       3      25 ..     218     240 ..     216     243 .. 0.90
   2 !   11.4   0.0   0.00062      0.22       3      23 ..     491     511 ..     489     517 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00042
                                       EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                       v+l G++G+GKT L++ +a+++ 
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAE 240
                                       799***************99875 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00062
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       v+l G++G+GKT L++ +a++
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATE 511
                                       899*************99986 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2     0.012       4.2      48      68 ..     218     238 ..     207     242 .. 0.81
   2 ?    6.1   0.0     0.028       9.8     131     178 ..     239     286 ..     230     292 .. 0.77
   3 !   10.9   0.0   0.00094      0.33      42     111 ..     485     555 ..     461     571 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.012
                             Rad17  48 LLisGPsGCgkstvvkvLske 68 
                                       +L+ GP+GCgk+   k ++ e
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATE 238
                                       6899********988877765 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.028
                             Rad17 131 tdkklilve..dlPnkfyrds.dalrevirkylrssealplilviteiesl 178
                                       ++ ++il++  ++ nk+y+++  +lre+ rk+   +ea p i+ i ei+ +
  gi|557694234|ref|YP_008797288.1| 239 AEANFILINgpEIMNKYYGETeARLREIFRKAE--EEA-PSIIFIDEIDAI 286
                                       56788999755899*******889******984..455.567778888765 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00094
                             Rad17  42 srkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn.qksdfkgltekesrflsqiesfke 111
                                        ++ r +L+ GP+GCgk+   k ++ e   +++    p  + +     ++ ++ ++ k  +  + +  f e
  gi|557694234|ref|YP_008797288.1| 485 IKPPRGVLLYGPPGCGKTLLAKAVATESEANFITIKGPEIFSKWVGeSEKAIREIFRKARQAAPAVIFFDE 555
                                       556667899**********9999999988888777766665443222455555555555555555555555 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 !   24.0   0.5     7e-08   2.5e-05       3      60 ..     110     167 ..     108     171 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7e-08
                                       SCCCCHHHHCCCTTEEE-TTEEEEECCTCCCEEEEEEEECCCCSCEEECTSCCEEEST CS
                           CDC48_2   3 dgdemaylkrqFlgrpvtkGdlvvfefkgqeiklvVvstePkgpvgitetTeielgtk 60 
                                       d+++   +k+++   pv+   ++++ f+g+ ++++Vv   P g+++it+ T+  ++ +
  gi|557694234|ref|YP_008797288.1| 110 DENFTKLVKSRLIEYPVVHRNIIPVLFFGNLFTFAVVQMRPTGVAKITPRTKLVIQSR 167
                                       67877799********************************************988766 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0013      0.45      10      38 ..     205     234 ..     201     243 .. 0.82
   2 ?   -0.9   0.0       2.4   8.6e+02     108     152 ..     260     310 ..     252     326 .. 0.63
   3 !   10.9   0.0   0.00061      0.22      14      42 ..     483     511 ..     470     523 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0013
                            ATPase  10 eil.kgGipegrvvlitGepGtGKtifalq 38 
                                       e++ k Gi   + vl++G pG+GKt++a+ 
  gi|557694234|ref|YP_008797288.1| 205 ELFqKLGIDPPKGVLLYGPPGCGKTLLAKA 234
                                       5665668888899**************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.4
                            ATPase 108 ieelaeaikeika...krvviDsitgl...ayeekeavaReilrqlvrvlk 152
                                        ++l+e+ ++ ++   + + iD i+++     e + +v ++ + ql+  + 
  gi|557694234|ref|YP_008797288.1| 260 EARLREIFRKAEEeapSIIFIDEIDAIapkRSEVTGEVEKRVVAQLLALMD 310
                                       566777777776644577889999999321122233445566666766664 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00061
                            ATPase  14 gGipegrvvlitGepGtGKtifalqFlik 42 
                                        Gi   r vl++G pG+GKt++a+  + +
  gi|557694234|ref|YP_008797288.1| 483 LGIKPPRGVLLYGPPGCGKTLLAKAVATE 511
                                       58888999**************9876655 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   0.00027     0.095       5      33 ..     218     250 ..     215     297 .. 0.62
   2 !   10.2   0.0    0.0013      0.45       5      22 ..     491     508 ..     488     555 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00027
                            AAA_24   5 iliyGpsgiGKTtlakel....gpkplfidtek 33 
                                       +l+yGp+g GKT lak      + ++++i+  +
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVateaEANFILINGPE 250
                                       89**************99886666666665444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       +l+yGp+g GKT lak  
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAV 508
                                       79*************987 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    0.0011       0.4      23      61 ..     216     251 ..     204     294 .. 0.85
   2 !   10.2   0.0    0.0013      0.44      23      56 ..     489     519 ..     475     564 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0011
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                         vl+ G  G+GK+lla+a+ ++   +e++f+ +n  +i
  gi|557694234|ref|YP_008797288.1| 216 KGVLLYGPPGCGKTLLAKAVATE---AEANFILINGPEI 251
                                       679***************99765...5578888887665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEE CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvav 56 
                                         vl+ G  G+GK+lla+a+ ++s+   ++f+++
  gi|557694234|ref|YP_008797288.1| 489 RGVLLYGPPGCGKTLLAKAVATESE---ANFITI 519
                                       679****************998876...556655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.1   2.2e+03     135     166 ..      88     119 ..      53     123 .. 0.74
   2 !    8.9   0.0    0.0029         1      36      54 ..     218     236 ..     212     240 .. 0.87
   3 ?    4.3   0.0     0.077        27     128     177 ..     261     310 ..     251     325 .. 0.85
   4 !    9.9   0.5    0.0015      0.51      36      56 ..     491     511 ..     485     601 .. 0.52

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.1
                            AAA_25 135 aaieevegvrlvviDplsralggdensnsdv.g 166
                                       ++++ v++++lvv+ p +    +den  + v +
  gi|557694234|ref|YP_008797288.1|  88 RKAN-VKEAQLVVLAPYNTSIKADENFTKLVkS 119
                                       4444.47899******99999999997766655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0029
                            AAA_25  36 allaGapgtGKttlaldla 54 
                                       +ll+G+pg+GKt la  +a
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVA 236
                                       69************97766 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.077
                            AAA_25 128 advdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                       a ++++ +++ee e +  + iD ++++ +  ++   +v +++v++l  + +
  gi|557694234|ref|YP_008797288.1| 261 ARLREIFRKAEE-EAPSIIFIDEIDAIAPKRSEVTGEVeKRVVAQLLALMD 310
                                       567899999***.99***************888888888999999987765 PP

  == domain 4  score: 9.9 bits;  conditional E-value: 0.0015
                            AAA_25  36 allaGapgtGKttlaldlala 56 
                                       +ll+G+pg+GKt la  +a +
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATE 511
                                       69**********998665543 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       4.7   1.7e+03      66      83 ..      59      76 ..      31     100 .. 0.73
   2 !   12.0   0.0   0.00062      0.22       1      57 [.     221     278 ..     221     303 .. 0.75
   3 !    8.8   0.0    0.0059       2.1       1      25 [.     494     518 ..     494     570 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 4.7
                                      HHHHHSSEEEEEE-SEEE CS
                            AAA_17 66 aeeakkkgvlvdghprik 83
                                      ++e++k+ + +dgh r++
  gi|557694234|ref|YP_008797288.1| 59 EDEKEKDIIRIDGHIRNN 76
                                      455667778899999863 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00062
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeakrgglakardemrklpleekkel 57 
                                       +G+PG+GK+ +++ ++ +   +f  ++  +++ +   + ++ + r+ +rk+++e    +
  gi|557694234|ref|YP_008797288.1| 221 YGPPGCGKTLLAKAVATEAeaNFILINGPEIMNKYYGETEA-RLREIFRKAEEEAPSII 278
                                       7***********99997654499999988888877776665.67888888887776655 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0059
                                       EE-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                       +G+PG+GK+ +++ ++ + +  +++
  gi|557694234|ref|YP_008797288.1| 494 YGPPGCGKTLLAKAVATESEANFIT 518
                                       7***********9999776444433 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0012      0.42      52      92 ..     214     256 ..     176     324 .. 0.77
   2 !   11.6   0.0   0.00033      0.11      22      83 ..     448     518 ..     431     557 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0012
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrli..evekedl 92 
                                       p + vLL+G  G+GK  l ka+ +e++++ + +   e+ ++  
  gi|557694234|ref|YP_008797288.1| 214 PPKGVLLYGPPGCGKTLLAKAVATEAEANFILINgpEIMNKYY 256
                                       56789******************99887764321225554444 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00033
                            DUF815  22 vdevklddLvgidkqkealvente.......qfle..glpannvLLwGarGtGKSslvkallneyaeegLr 83 
                                       + +v+++d+ g+++ k++l+e +e       +f +   +p + vLL+G  G+GK  l ka+ +e +++ + 
  gi|557694234|ref|YP_008797288.1| 448 TPTVRWEDIGGLEQVKQKLIEMVEwplkypeKFEKlgIKPPRGVLLYGPPGCGKTLLAKAVATESEANFIT 518
                                       4568888999999999998887752222222343221478899*******************998887644 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 !    9.9   0.0    0.0013      0.47      32      60 ..     214     241 ..     204     255 .. 0.81
   2 !    9.5   0.0    0.0019      0.66      32      61 ..     487     515 ..     478     523 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0013
                             AAA_7  32 nkkpvllvGptGtGKtviikdllkkldke 60 
                                         k vll+Gp G+GKt+++k + ++ +  
  gi|557694234|ref|YP_008797288.1| 214 PPKGVLLYGPPGCGKTLLAKAVATEAE-A 241
                                       5688****************9888777.3 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0019
                             AAA_7  32 nkkpvllvGptGtGKtviikdllkkldkek 61 
                                         + vll+Gp G+GKt+++k + ++ +  +
  gi|557694234|ref|YP_008797288.1| 487 PPRGVLLYGPPGCGKTLLAKAVATESE-AN 515
                                       56789**************99877766.44 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 ?    6.9   0.0     0.013       4.6       5      71 ..     222     283 ..     218     288 .. 0.67
   2 !   13.4   0.0   0.00014     0.049       5      71 ..     495     556 ..     491     569 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.013
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pGcGK+ l + ++ +   ++  ++   e+ ++   +++++  + ++++++ +       i+++DE+
  gi|557694234|ref|YP_008797288.1| 222 GPPGCGKTLLAKAVATEAeANFILING-PEIMNKYYGETEARLREIFRKAEEEAP-----SIIFIDEI 283
                                       78*******999999886644444444.455555556666666666666666543.....48888886 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00014
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pGcGK+ l + ++ +s  ++ +++   e++++++ ++++   + ++++ +a+ +     ++++DE+
  gi|557694234|ref|YP_008797288.1| 495 GPPGCGKTLLAKAVATESeANFITIKG-PEIFSKWVGESEKAIREIFRKARQAAPA-----VIFFDEI 556
                                       78*************999*88888888.8*******99999999999999998764.....8999998 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 !   10.7   0.0    0.0006      0.21      23      62 ..     215     253 ..     203     270 .. 0.83
   2 ?   -1.3   0.0       2.6   9.3e+02     144     192 ..     261     310 ..     252     312 .. 0.85
   3 !    7.8   0.0    0.0045       1.6      25      60 ..     490     524 ..     479     541 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0006
                                       --EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES-GGG CS
                              DAP3  23 vkrlvltGekgsGKSvlLlqalayAlekgwvvlhvpeaed 62 
                                        k ++l+G +g+GK+ lL++a+a  +e+++++++ pe  +
  gi|557694234|ref|YP_008797288.1| 215 PKGVLLYGPPGCGKT-LLAKAVATEAEANFILINGPEIMN 253
                                       56689*********8.68***************9988766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.6
                                       HHHHHHHHHTTSS--EEEEEE-GGGGSS-.BS---TTS--B-GGGBHHHH CS
                              DAP3 144 allkeLkaqskgrvpvlvtvDglnallkn.tkyksadkkpihahdLtlvk 192
                                       a l+e+ ++++++ p ++ +D+++a++ + ++ + +  k++ a+ L+l++
  gi|557694234|ref|YP_008797288.1| 261 ARLREIFRKAEEEAPSIIFIDEIDAIAPKrSEVTGEVEKRVVAQLLALMD 310
                                       5567777777788999***********999**999999999999999875 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0045
                                       EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES-G CS
                              DAP3  25 rlvltGekgsGKSvlLlqalayAlekgwvvlhvpea 60 
                                        ++l+G +g+GK+ lL++a+a   e++++ ++ pe 
  gi|557694234|ref|YP_008797288.1| 490 GVLLYGPPGCGKT-LLAKAVATESEANFITIKGPEI 524
                                       578*********8.5899998888889988887765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0016      0.56      22      43 ..     217     238 ..     204     243 .. 0.80
   2 !    9.3   0.0    0.0016      0.57      23      44 ..     491     512 ..     480     518 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0016
                                       EEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnk 43 
                                        v l+G +G+GKt lak +  +
  gi|557694234|ref|YP_008797288.1| 217 GVLLYGPPGCGKTLLAKAVATE 238
                                       4789*************99876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0016
                                       EEEEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  23 valvGmgGvGKttlakqilnks 44 
                                       v l+G +G+GKt lak +  +s
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATES 512
                                       779*************998874 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00039      0.14      37     176 ..     218     359 ..     213     374 .. 0.73
   2 ?    6.8   0.0     0.015       5.4      37      63 ..     491     517 ..     486     569 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00039
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagk 112
                                       +++yg+ G Gkt L ka++ e+++n+     + +++ e +n+     + +  e f++    +  ++ iD+i  +a k
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAEANF-----ILINGPEIMNKYYGETEARLREIFRKAEEeAPSIIFIDEIDAIAPK 289
                                       79****************99887765.....7899999999999999999999999987724578899***999988 PP

                                       HH.........HHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHH CS
                          Bac_DnaA 113 ek.........tqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailk 176
                                        +         +  +l+ +++ l + g  +v+ +   P++l+    r   rf++ +  +i  pd++ r++il 
  gi|557694234|ref|YP_008797288.1| 290 RSevtgevekrVVAQLLALMDGLEGRGSVIVIGATNRPNALDPAL-RRPGRFDREI--EIGIPDKKGRVEILT 359
                                       642222211113345666667777788889999999998876543.3356777654..455578888888875 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.015
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSS CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenap 63 
                                       +++yg+ G Gkt L ka++ e ++n+ 
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESEANFI 517
                                       79*****************99887765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0021      0.75      22      43 ..     218     239 ..     211     245 .. 0.87
   2 !    8.5   0.0    0.0036       1.3      22      42 ..     491     511 ..     484     518 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                                       EEEE--TTSSTTHHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalavea 43 
                                       v   Gp G+GKt+la a+a ea
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEA 239
                                       6789*************99876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0036
                                       EEEE--TTSSTTHHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalave 42 
                                       v   Gp G+GKt+la a+a e
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATE 511
                                       6789************99976 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 !    9.0   0.0    0.0034       1.2       2      30 ..     218     246 ..     217     294 .. 0.88
   2 !    9.0   0.0    0.0035       1.2       2      30 ..     491     519 ..     490     566 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0034
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG +ktll+ka+a+  +++f  i
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAEANFILI 246
                                       7999****************999998655 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0035
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkri 30 
                                       vll g PG +ktll+ka+a+  +++f  i
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESEANFITI 519
                                       7999****************999999776 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   0.00039      0.14       4      75 ..     218     284 ..     215     302 .. 0.72
   2 ?    4.6   0.0     0.044        15       4      25 ..     491     512 ..     488     550 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00039
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkkeafekls.sfinnls 75 
                                       vl  G +G GKt+++ ++++e+       +a++++ N+p+++ +++ + + + ++  +k++ e +s  fi +++
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEA-------EANFILINGPEIMnKYYGETEARLREIFRKAEEEAPSiIFIDEID 284
                                       6789****************99.......999999999986538888887777444444433333313555555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.044
                           DUF2075   4 vlVtGvaGtGKtvvllnllael 25 
                                       vl  G +G GKt+++ ++++e 
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATES 512
                                       6789***********9999987 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 !    7.6   0.0    0.0052       1.8     117     136 ..     218     237 ..     213     244 .. 0.91
   2 !    8.1   0.0    0.0037       1.3     117     136 ..     491     510 ..     485     515 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0052
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v++yGp+ +Gkt la+a a+
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVAT 237
                                       89***************986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0037
                         Parvo_NS1 117 vwfyGpantGktnlaeaIak 136
                                       v++yGp+ +Gkt la+a a+
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVAT 510
                                       89***************997 PP

>> UFD1  Ubiquitin fusion degradation protein UFD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.2e-06    0.0029      57     159 ..      53     154 ..      32     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.2e-06
                              UFD1  57 thagVleFtaeegtvylPewmmenlgleegdlveiesvslpkgkfvklqpqsedfldisdpkavLekaLrnfatLtk 133
                                       +  g +e   e++ + +   + +n g++ +d+v +++++++++++v l p ++++   ++  ++ +++L ++ ++ +
  gi|557694234|ref|YP_008797288.1|  53 VWLGYMEDEKEKDIIRIDGHIRNNAGVSLNDYVIVRKANVKEAQLVVLAPYNTSIKADENFTKLVKSRLIEYPVVHR 129
                                       455667777788899999999****************************************************9876 PP

                              UFD1 134 gdvieikyndkvyelkvlevkpesav 159
                                        ++i++ +  + ++++v++++p+   
  gi|557694234|ref|YP_008797288.1| 130 -NIIPVLFFGNLFTFAVVQMRPTGVA 154
                                       .69999999*************8754 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 ?    7.3   0.0     0.013       4.6      24      50 ..     218     244 ..     213     291 .. 0.68
   2 !    8.4   0.0    0.0063       2.2      24      48 ..     491     515 ..     479     566 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.013
                                       EEEEEETT--HHHHHHCC--TTS-EE- CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwle 50 
                                       v+l G++G+gk+l A++ + +++ +  
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAEANFI 244
                                       9****************9998877654 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0063
                                       EEEEEETT--HHHHHHCC--TTS-E CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpw 48 
                                       v+l G++G+gk+l A++ + +s+ +
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESEAN 515
                                       9*****************9988764 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.017       5.9      22      57 ..     202     237 ..     188     245 .. 0.82
   2 ?   -1.8   0.0       4.9   1.7e+03     117     133 ..     272     288 ..     250     341 .. 0.63
   3 ?    4.8   0.0     0.048        17      34      58 ..     487     511 ..     455     522 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.017
                              TniB  22 rLeeLleypkrkrmpnlllvGdsnnGKtmivekFar 57 
                                       r+ eL+++   + ++ +ll+G++ +GKt +++  a 
  gi|557694234|ref|YP_008797288.1| 202 RFPELFQKLGIDPPKGVLLYGPPGCGKTLLAKAVAT 237
                                       677899999999999**************9987665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.9
                              TniB 117 elkvrvLiiDEihnlla 133
                                       e  + ++ iDEi+ +  
  gi|557694234|ref|YP_008797288.1| 272 EEAPSIIFIDEIDAIAP 288
                                       44567899999998863 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.048
                              TniB  34 rmpnlllvGdsnnGKtmivekFarl 58 
                                        ++ +ll+G++ +GKt +++  a +
  gi|557694234|ref|YP_008797288.1| 487 PPRGVLLYGPPGCGKTLLAKAVATE 511
                                       35789************99987765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.063        22       2      25 ..     218     241 ..     217     250 .. 0.81
   2 ?    1.4   0.1      0.77   2.7e+02      82     107 ..     260     286 ..     250     307 .. 0.71
   3 ?   -1.7   0.0       6.7   2.4e+03      87     123 ..     439     475 ..     427     480 .. 0.69
   4 ?    5.3   0.0     0.048        17       2      32 ..     491     521 ..     490     526 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.063
                                       EEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellks 25 
                                       v++ GppG GKt l k v+ + + 
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAEA 241
                                       6788********999999987754 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.77
                                       HHHHHHHHHHHH.HHH-EEEE---STT CS
                          NTPase_1  82 eelalealrkal.seadviviDEiGkm 107
                                       e    e++rka  + + +i iDEi  +
  gi|557694234|ref|YP_008797288.1| 260 EARLREIFRKAEeEAPSIIFIDEIDAI 286
                                       55667788888844556******9665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 6.7
                                       HHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHT CS
                          NTPase_1  87 ealrkalseadviviDEiGkmElkskkfkeaveevLk 123
                                       +alr+   e+  +    iG +E   +k++e+ve  Lk
  gi|557694234|ref|YP_008797288.1| 439 SALREVEIETPTVRWEDIGGLEQVKQKLIEMVEWPLK 475
                                       555555544445555679************9997776 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.048
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       v++ GppG GKt l k v+ + + + ++++G
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESEANFITIKG 521
                                       6788*********999999887766666665 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0      0.04        14       1      22 [.     224     245 ..     224     274 .. 0.67
   2 ?    7.0   0.0     0.017       5.9       1      40 [.     497     541 ..     497     547 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.04
                                       TTSSHHHHHHHHHHHHTSEEEE CS
                               SKI   1 mGaGKstvGkllAkklglefiD 22 
                                       +G+GK+ ++k++A + + +fi 
  gi|557694234|ref|YP_008797288.1| 224 PGCGKTLLAKAVATEAEANFIL 245
                                       6**************9999974 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.017
                                       TTSSHHHHHHHHHHHHTSEEEEH..HHHHHHHHT...S-HHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl..Deliekrtg...ksiaeife 40 
                                       +G+GK+ ++k++A + + +fi +   e+++k +g   k i+eif+
  gi|557694234|ref|YP_008797288.1| 497 PGCGKTLLAKAVATESEANFITIkgPEIFSKWVGeseKAIREIFR 541
                                       6*******************9873234555554432344555555 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     0.042        15      11      32 ..     216     237 ..     212     247 .. 0.81
   2 ?   -1.0   0.0       5.9   2.1e+03      99     132 ..     271     305 ..     251     311 .. 0.67
   3 ?    5.7   0.0      0.05        18      12      31 ..     490     509 ..     485     526 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.042
                            AAA_19  11 kvllvtaGpGtGKTrvlkhiva 32 
                                       k +l+ ++pG+GKT + k++ +
  gi|557694234|ref|YP_008797288.1| 216 KGVLLYGPPGCGKTLLAKAVAT 237
                                       56899*********98777665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 5.9
                            AAA_19  99 klqeeellivDEfqdvdelqyrLlkallgek.kkl 132
                                       + ++  ++++DE+  + +   ++  ++ ++  ++l
  gi|557694234|ref|YP_008797288.1| 271 EEEAPSIIFIDEIDAIAPKRSEVTGEVEKRVvAQL 305
                                       33344599*****9999888877777765555555 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.05
                            AAA_19  12 vllvtaGpGtGKTrvlkhiv 31 
                                        +l+ ++pG+GKT + k++ 
  gi|557694234|ref|YP_008797288.1| 490 GVLLYGPPGCGKTLLAKAVA 509
                                       5899*********8877655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.028       9.9       2      24 ..     216     238 ..     215     241 .. 0.88
   2 ?    5.4   0.0     0.039        14       4      24 ..     491     511 ..     488     516 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.028
                         PduV-EutP   2 kkilliGkvgsGKttLtqalkge 24 
                                       k +ll G+ g+GKt L++a+  e
  gi|557694234|ref|YP_008797288.1| 216 KGVLLYGPPGCGKTLLAKAVATE 238
                                       5699**************98765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.039
                         PduV-EutP   4 illiGkvgsGKttLtqalkge 24 
                                       +ll G+ g+GKt L++a+  e
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATE 511
                                       89**************98765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.036        13      21      44 ..     218     241 ..     206     248 .. 0.85
   2 ?    5.2   0.0     0.044        16      21      43 ..     491     513 ..     480     523 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.036
                            AAA_30  21 avltGpAGtGKttalkalreawea 44 
                                       ++l Gp+G GKt + ka++  +ea
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAEA 241
                                       6789************99876665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.044
                            AAA_30  21 avltGpAGtGKttalkalreawe 43 
                                       ++l Gp+G GKt + ka++   e
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVATESE 513
                                       6899***********99987655 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 ?    5.1   0.0     0.039        14       6      32 ..     218     244 ..     215     266 .. 0.74
   2 ?    5.7   0.0     0.025       8.7       5      33 ..     490     518 ..     486     538 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.039
                                       EEEE-STTSSHHHHHHHHHHSS---B- CS
                             SRPRB   6 vllvGlsdsGKTslftrLttdsvkktv 32 
                                       vll G+  +GKT+l + + t++  +  
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAVATEAEANFI 244
                                       99************9999888766555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.025
                                       EEEEE-STTSSHHHHHHHHHHSS---B-- CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvt 33 
                                        vll G+  +GKT+l + + t+s  +  t
  gi|557694234|ref|YP_008797288.1| 490 GVLLYGPPGCGKTLLAKAVATESEANFIT 518
                                       69*************99999987666555 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.021       7.5      51      79 ..     206     232 ..     157     242 .. 0.79
   2 ?    5.0   0.0     0.027       9.6      59      79 ..     485     505 ..     454     512 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.021
                       AFG1_ATPase  51 lfgrkrksvepvrglYlwGgvGrGKtylm 79 
                                       lf++      p++g+ l+G+ G GKt l 
  gi|557694234|ref|YP_008797288.1| 206 LFQKL--GIDPPKGVLLYGPPGCGKTLLA 232
                                       44432..568****************985 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.027
                       AFG1_ATPase  59 vepvrglYlwGgvGrGKtylm 79 
                                        +p+rg+ l+G+ G GKt l 
  gi|557694234|ref|YP_008797288.1| 485 IKPPRGVLLYGPPGCGKTLLA 505
                                       579***************985 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.043        15      20      37 ..     218     235 ..     207     273 .. 0.81
   2 ?    5.3   0.0     0.041        14      20      38 ..     491     509 ..     482     548 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.043
                            AAA_11  20 tliqGPPGtgKTktivel 37 
                                       +l+ GPPG+gKT    ++
  gi|557694234|ref|YP_008797288.1| 218 VLLYGPPGCGKTLLAKAV 235
                                       6999********655444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.041
                            AAA_11  20 tliqGPPGtgKTktivell 38 
                                       +l+ GPPG+gKT    ++ 
  gi|557694234|ref|YP_008797288.1| 491 VLLYGPPGCGKTLLAKAVA 509
                                       6899********6655554 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 ?    4.6   0.0     0.075        26      21      42 ..     215     235 ..     205     239 .. 0.74
   2 ?    4.6   0.0     0.074        26      21      42 ..     488     508 ..     466     510 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.075
                            AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                       +kg +ll Gp G GK+ l  A+
  gi|557694234|ref|YP_008797288.1| 215 PKG-VLLYGPPGCGKTLLAKAV 235
                                       355.9**********8776665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.074
                            AAA_29  21 lkgatlltGpsGsGKSTllDAi 42 
                                       ++g +ll Gp G GK+ l  A+
  gi|557694234|ref|YP_008797288.1| 488 PRG-VLLYGPPGCGKTLLAKAV 508
                                       345.9**********8776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (726 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        51  (0.00284455); 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: 0.77u 0.33s 00:00:01.10 Elapsed: 00:00:00.47
# Mc/sec: 4675.67
//
Query:       gi|557694235|ref|YP_008797289.1|  [L=109]
Description: ArsR family transcriptional regulator [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   36.1   0.0    8.4e-09   35.4   0.0    1.4  1  HTH_20    Helix-turn-helix domain
    2.8e-05   23.9   0.1    4.5e-05   23.2   0.1    1.3  1  HTH_5     Bacterial regulatory protein, arsR family
     0.0064   16.3   0.1     0.0096   15.8   0.1    1.2  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.051   13.6   0.0    1.8  2  NCD1      NAB conserved region 1 (NCD1)
      0.023   14.6   0.0      0.027   14.4   0.0    1.1  1  PAX       'Paired box' domain
      0.037   13.8   1.2      0.056   13.3   0.5    1.5  2  HTH_IclR  IclR helix-turn-helix domain
      0.096   13.0   0.1       0.15   12.4   0.1    1.3  1  Rrf2      Transcriptional regulator


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 !   35.4   0.0   3.3e-12   8.4e-09       2      61 .]      22      82 ..      21      82 .. 0.92

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 3.3e-12
                                      HHHHHHS-HHHHHHHHHH.STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20  2 qiaeALahPvRrrilraL.araegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                      +i+ AL++PvR+ril++  ++ ++l    +a++l ++ +  ++H+++L+eagLv+  ++gr
  gi|557694235|ref|YP_008797289.1| 22 RIFMALGNPVRLRILSLVsSSQRPLHIRGVARLLKTRYAITYKHVKTLQEAGLVTIYEVGR 82
                                      699*******************************666666**************9888876 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 !   23.2   0.1   1.8e-08   4.5e-05       1      46 [.      29      76 ..      29      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1.8e-08
                                      SHHHHHHHHHHTT..SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLae..gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +p Rl+IL+l+++  ++l +   a+ l+   +++  H k L eaGLV+
  gi|557694235|ref|YP_008797289.1| 29 NPVRLRILSLVSSsqRPLHIRGVARLLKTRYAITYKHVKTLQEAGLVT 76
                                      699***********9********************************5 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   3.8e-06    0.0096      17      68 .]      38      92 ..      36      96 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.8e-06
                                      HH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE--HH CS
                              TrmB 17 Ll..klgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravdpe 68
                                      L+  ++ p+ ++ +a+ l+  ++  Y+ ++ L ++GlV++ + gr ++  + +pe
  gi|557694235|ref|YP_008797289.1| 38 LVssSQRPLHIRGVARLLKTRYAITYKHVKTLQEAGLVTIYEvGRSRVVAPKHPE 92
                                      6666788999*****************************9985556677777765 PP

>> NCD1  NAB conserved region 1 (NCD1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     2e-05     0.051      39      69 ..      26      56 ..       2      67 .. 0.76
   2 ?   -1.0   0.0       0.7   1.8e+03      11      24 ..      66      79 ..      58      80 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-05
                              NCD1 39 eaeeeefleimelvGmaskPLhvrRlqkaLq 69
                                      ++++   l i++lv  + +PLh+r + + L+
  gi|557694235|ref|YP_008797289.1| 26 ALGNPVRLRILSLVSSSQRPLHIRGVARLLK 56
                                      445555689***************9998886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.7
                              NCD1 11 yrvLqranLlqYyd 24
                                       + Lq a L++ y+
  gi|557694235|ref|YP_008797289.1| 66 VKTLQEAGLVTIYE 79
                                      46677777777775 PP

>> PAX  'Paired box' domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     1e-05     0.027      17      94 ..      26     107 ..      15     109 .] 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                               PAX  17 plpdsirqkivelahsgvrpcvi...srqlrvshgcvskilgryqetgsirpgviggskpk.vatpevvkkieeykr 89 
                                        l + +r +i+ l  s  rp  i   +r l+       k +   qe+g +    +g s+      pe+  k++ + +
  gi|557694235|ref|YP_008797289.1|  26 ALGNPVRLRILSLVSSSQRPLHIrgvARLLKTRYAITYKHVKTLQEAGLVTIYEVGRSRVVaPKHPELFRKVALFGK 102
                                       47899***************9874447999**************************998763467999999999999 PP

                               PAX  90 enpsi 94 
                                       e  s+
  gi|557694235|ref|YP_008797289.1| 103 EITSM 107
                                       98877 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 ?   -2.4   0.0       1.7   4.3e+03       7      15 ..       2      10 ..       1      27 [. 0.66
   2 ?   13.3   0.5   2.2e-05     0.056       6      49 ..      33      76 ..      32      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.7
                                      HHHCT-CTT CS
                          HTH_IclR  7 aiLdalaea 15
                                      +iL ++a++
  gi|557694235|ref|YP_008797289.1|  2 DILSYVAAQ 10
                                      677777665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.2e-05
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      l+iL ++++ +++l ++ +Ar +    + ++ +++tL+e G+v+
  gi|557694235|ref|YP_008797289.1| 33 LRILSLVSSSQRPLHIRGVARLLKTRYAITYKHVKTLQEAGLVT 76
                                      79****************************************95 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.9e-05      0.15      18      56 ..      40      76 ..      30      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.9e-05
                                      HHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 18 akeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      +  ++++p+ ++ +a+  ++   +  k +++L++aglv+
  gi|557694235|ref|YP_008797289.1| 40 S--SSQRPLHIRGVARLLKTRYAITYKHVKTLQEAGLVT 76
                                      3..34458******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 815.37
//
Query:       gi|557694236|ref|YP_008797290.1|  [L=208]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  15.6    1.3e-07   31.8  15.6    1.1  1  ECF_trnsprt  ECF transporter, substrate-specific component


Domain annotation for each model (and alignments):
>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8  15.6   7.5e-12   1.3e-07       2     170 ..       7     186 ..       6     187 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 7.5e-12
                                       HHHHHHHHHHHHHHHHH...H.HEEE.STSEEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHH. CS
                       ECF_trnsprt   2 klvitglliAisivlsl...l.gyiplpnikitiihipvllggllfGpikGailgiitsvlkailtggtgalssfv. 73 
                                       +l++++ ++A++ v++l      ++ lp + +++  ip +l+ ll+G+ +G++ ++  +++++++   tg+++ +  
  gi|557694236|ref|YP_008797290.1|   7 RLALASSFAALAYVMGLapaSvPFPLLPFLRFDLAEIPDMLSFLLLGWRYGLVTAL-AHWYALVI-TATGVFAPPPi 81 
                                       7899999***********9755666667779********************99988.99999999.45566766668 PP

                                       ....HHHHHHHHCHHHHHHHHH..HCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCC....HHHHS.......... CS
                       ECF_trnsprt  74 ....piaflsriligliaglly..kkgkkknlkeivvsfilagvlgtivatllvllii....lplylklktakaiai 140
                                              ++ ++++g+ agl    + g+ k     v ++++ + +++ v + l +l++    lp+    k  +a ++
  gi|557694236|ref|YP_008797290.1|  82 pqlmKLTAVLSMFLGVYAGLWAarRLGRGKVVLSTVGGVLMRAGVMAPVTFALYYLLFpqiyLPFG--KKALSAVGF 156
                                       999966777777888888833300222222222236666666666777777777777777644444..466777888 PP

                                       ...--HHHHHHHHHCCTTCCHHHHHHHHHH CS
                       ECF_trnsprt 141 agkallaailgpiivkglieaiiaaiivvl 170
                                       +  + la++l++  +++l++ai aa++++l
  gi|557694236|ref|YP_008797290.1| 157 VAETDLAVALLITGLTALFNAISAAYLIPL 186
                                       888899999999999**********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1615.86
//
Query:       gi|557694237|ref|YP_008797291.1|  [L=333]
Description: DNA repair protein RadA [Candidatus Caldiarchaeum subterraneum]
Scores for 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-91  304.2   0.0    7.6e-91  303.9   0.0    1.0  1  Rad51            Rad51
    1.9e-12   47.2   0.0    2.9e-12   46.6   0.0    1.3  1  RecA             recA bacterial DNA recombination protein
    4.7e-10   39.9   0.6    1.4e-09   38.4   0.6    1.8  1  HHH_5            Helix-hairpin-helix domain
    1.1e-09   38.0   0.0      2e-09   37.2   0.0    1.5  1  ATPase           KaiC
    0.00045   20.5   0.1    0.00099   19.4   0.1    1.5  1  AAA_22           AAA domain
    0.00083   19.6   0.0     0.0017   18.6   0.0    1.5  1  Cdd1             Pathogenicity locus
     0.0022   18.5   0.0     0.0034   17.9   0.0    1.4  1  ABC_tran         ABC transporter
     0.0075   16.5   0.1      0.033   14.4   0.0    2.1  2  DUF4332          Domain of unknown function (DUF4332)
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.23   11.3   0.0    1.6  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
       0.13   12.7   0.1       0.43   11.0   0.1    1.8  1  AAA              ATPase family associated with various cellul
       0.14   12.5   0.0       0.43   11.0   0.0    1.8  1  IMS_HHH          IMS family HHH motif
       0.24   11.3   0.6       0.59   10.1   0.1    1.8  2  INCENP_ARK-bind  Inner centromere protein, ARK binding region


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 !  303.9   0.0   5.1e-94   7.6e-91       2     254 ..      79     328 ..      78     329 .. 0.98

  Alignments for each domain:
  == domain 1  score: 303.9 bits;  conditional E-value: 5.1e-94
                                       S-EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEE CS
                             Rad51   2 gfvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyid 78 
                                        fv a+e+le+r+ + +lttGs++lD++LgGG+et++ite++Gef+sGktq+chtlcv++qlp e+gG eg a+yid
  gi|557694237|ref|YP_008797291.1|  79 EFVPATEVLERRKAMQRLTTGSRALDAMLGGGVETQAITELIGEFGSGKTQVCHTLCVMAQLPREQGGLEGSAIYID 155
                                       5899************************************************************************* PP

                                       SSS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------T CS
                             Rad51  79 tegtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgel 155
                                       te+tfrper+ +iae  +ld++++len+  a +y++ h +  ++++   + + k +l+i+Ds+++++R++f grg l
  gi|557694237|ref|YP_008797291.1| 156 TEATFRPERISQIAEARGLDPQKILENIIFASVYNSSHLQLTVKELGRYVEKYKARLVIIDSIISHFRAEFIGRGTL 232
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEE CS
                             Rad51 156 akRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkv 232
                                       a+Rqq+l+ ll++L + a+ +++avv+tnqv+a++d+    f +dp+kP+gG+vlah+st R+ +r+  +++R++++
  gi|557694237|ref|YP_008797291.1| 233 AERQQRLNDLLHRLLRTAQVHNIAVVLTNQVQANPDQ----FFGDPNKPSGGHVLAHSSTYRIFIRRAANNTRLARI 305
                                       *************************************....99********************************** PP

                                       ES-SSS.-S-EEEEEEETTEEE- CS
                             Rad51 233 vdsPnl.peleavfaigeeGied 254
                                       +dsP   p +ea f i+e+G+ed
  gi|557694237|ref|YP_008797291.1| 306 IDSPYHpPTAEAYFKITEKGVED 328
                                       ****872689***********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 !   46.6   0.0     2e-15   2.9e-12      26     226 ..      88     300 ..      38     310 .. 0.78

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 2e-15
                                       -.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHH..HHHHHHHHHHT.T...--EEEEESS----H. CS
                              RecA  26 keklkvetissGslaldialGiGGlpkGriieiyGpessGkttl..alhaiaeaqkk.g...gvaafidaehaldp. 95 
                                       ++++ ++ +++Gs ald  lG GG+    i+e+ G   sGkt +  +l ++a+  ++ g   g a +id+e ++ p 
  gi|557694237|ref|YP_008797291.1|  88 ERRKAMQRLTTGSRALDAMLG-GGVETQAITELIGEFGSGKTQVchTLCVMAQLPREqGgleGSAIYIDTEATFRPe 163
                                       34578999*************.********************984568899998665242225799********993 PP

                                       ...HHHHHTT--GGG-E....E.E--SSHHHHHHHHH..HHHTTT--SEEEEE-TTT---STT-----------HHH CS
                              RecA  96 ...kyakklGvdidell....v.sqpdtGeqaleiad..alvrsgaidlivvdsvaalvpkaeieGemgdskvglqa 162
                                          + a++ G+d +++l      s  ++    l + +    v+     l+++ds+ +   +ae  G    +    q 
  gi|557694237|ref|YP_008797291.1| 164 risQIAEARGLDPQKILeniiFaSVYNSSHLQLTVKElgRYVEKYKARLVIIDSIISHF-RAEFIGR--GTLAERQQ 237
                                       3334678889996554322213145556666676665226899999*********9865.7887664..33445566 PP

                                       HHHHHHHHHHHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES--- CS
                              RecA 163 rlmsqalrkltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrrieeik 226
                                       rl    l +l  + +  n++v++ nq++      fg+p+  +GG+ l   ++ r+ +rr+++ +
  gi|557694237|ref|YP_008797291.1| 238 RL-NDLLHRLLRTAQVHNIAVVLTNQVQANPDQFFGDPNKPSGGHVLAHSSTYRIFIRRAANNT 300
                                       66.566777777788899*****************************************98765 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.6   9.2e-13   1.4e-09       3      56 ..      15      67 ..      13      68 .. 0.97

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 9.2e-13
                                      HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56
                                      +L+s++G+G++t  +l saGi+sv dlaaa++ eL ++ Gi++++Ae ++l ++
  gi|557694237|ref|YP_008797291.1| 15 DLQSIEGVGKATEEKLNSAGITSVLDLAAATPRELVEL-GISAEKAEELCLKAR 67
                                      89************************************.**********99887 PP

>> ATPase  KaiC
   #    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       2     201 ..      97     307 ..      96     332 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.3e-12
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikg.aek..yge..pgvfvtveepa..edlrenakslG 71 
                                        tg   lD +l gG+  ++++ + Ge G+GKt ++ +  +   + +   g     +++ +e +   e + + a++ G
  gi|557694237|ref|YP_008797291.1|  97 TTGSRALDAMLGGGVETQAITELIGEFGSGKTQVCHTLCVMAqLPReqGGLegSAIYIDTEATFrpERISQIAEARG 173
                                       589999***************************999987654133311233114578888886566*********** PP

                            ATPase  72 wdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.a........yeekeav 139
                                        d +k+ e+  +++  +++s          + l+  ++el ++++++ka+ v+iDsi ++            e+++ 
  gi|557694237|ref|YP_008797291.1| 174 LDPQKILEN--IIFASVYNS----------SHLQLTVKELGRYVEKYKARLVIIDSIISHfRaefigrgtLAERQQR 238
                                       *********..555555554..........356778999*****************987643122222113466777 PP

                            ATPase 140 aReilrqlvrvlkklgvTailvsekss........seeaaggygveefivdgvivLdlkeieeelvRtle 201
                                       + + l++l+r+ +  ++  +l+++++          ++  gg+ +++ +++  i +++  ++++l R+++
  gi|557694237|ref|YP_008797291.1| 239 LNDLLHRLLRTAQVHNIAVVLTNQVQAnpdqffgdPNKPSGGHVLAH-SSTYRIFIRRAANNTRLARIID 307
                                       888999999999999999******99999999987667778888888.8888899998888888888876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   6.6e-07   0.00099       4     127 ..     113     259 ..     111     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.6e-07
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.......... 70 
                                       t+ i+ ++Ge G+GKT ++ +l   ++   ++   + + ++++  +   ++ + +++++a gl+  +          
  gi|557694237|ref|YP_008797291.1| 113 TQAITELIGEFGSGKTQVCHTLCVMAQLPREQGGLEGSAIYIDTEATFRPERI-SQIAEARGLDPQKileniifasv 188
                                       788999***************99988766666668888888888888866666.88888888888888888888888 PP

                            AAA_22  71 erlsseell.ealeqalraravielliiDEaqh.lr.....s......eealeeL.rsllnl.srkgvqliL 127
                                       ++ s  +l  + l ++++++++ +l+iiD +   +r     +      ++ l++L ++ll   + ++++++L
  gi|557694237|ref|YP_008797291.1| 189 YNSSHLQLTvKELGRYVEKYKA-RLVIIDSIIShFRaefigRgtlaerQQRLNDLlHRLLRTaQVHNIAVVL 259
                                       6667777777************.******8765476655541445555666666643334334566666665 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.1e-06    0.0017       5      43 ..      13      51 ..       9      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                              Cdd1  5 lkelqdiPniGkalaedlvelGirsveelkgedpeelye 43
                                      + +lq+i ++Gka+ e+l + Gi+sv +l+  +p el+e
  gi|557694237|ref|YP_008797291.1| 13 IFDLQSIEGVGKATEEKLNSAGITSVLDLAAATPRELVE 51
                                      5689********************************987 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.3e-06    0.0034       8      95 ..     111     225 ..     107     309 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.3e-06
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren.... 79 
                                       ++   ++ ++Ge G+GK+ ++ +l+ + +   ++  l+g  +   +e ++  ++i+ + +   l+p++ + en    
  gi|557694237|ref|YP_008797291.1| 111 VETQAITELIGEFGSGKTQVCHTLCVMAQLPREQGGLEGSAIYIdTEATFRPERISQIAEARGLDPQK-ILENiifa 186
                                       67788999*****************9999866666668888777578899999***************.99999*** PP

                                       ...........................HHHTCHHHHHHHSTTG CS
                                       ...........................xxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...........................esdeeiekalsklglk 95 
                                                                       i+ ++s+++ +
  gi|557694237|ref|YP_008797291.1| 187 svynsshlqltvkelgryvekykarlvI----IDSIISHFRAE 225
                                       9988888888887776666644433330....33333333333 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.2e-05     0.033      53      90 ..      14      51 ..       8      68 .. 0.86
   2 ?   -2.3   0.0       3.4   5.1e+03      32      50 ..     165     183 ..     158     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.2e-05
                           DUF4332 53 AdLarikgigeeyaeLLeaaGvdsvaeLaqrnpanLhq 90
                                       dL  i+g+g++  e L  aG++sv +La  +p +L++
  gi|557694237|ref|YP_008797291.1| 14 FDLQSIEGVGKATEEKLNSAGITSVLDLAAATPRELVE 51
                                      589999999***99*******************99987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.4
                           DUF4332  32 rkalaeklgisernvlkla 50 
                                         ++ae++g++ +++l+ +
  gi|557694237|ref|YP_008797291.1| 165 ISQIAEARGLDPQKILENI 183
                                       3458999999999998755 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 ?   11.3   0.0   0.00015      0.23       3      30 ..      16      43 ..      15      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                   DNA_pol_lambd_f  3 FtkvyGVGpktAkkwyakGirtledlra 30
                                      ++++ GVG +t +k+ ++Gi+++ dl a
  gi|557694237|ref|YP_008797291.1| 16 LQSIEGVGKATEEKLNSAGITSVLDLAA 43
                                      78999*********************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 ?   11.0   0.1   0.00029      0.43       3     113 ..     119     264 ..     118     272 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                                       EESSTTSSHHHHHHHHHHHHTHE.......................EEEEETTTCSSS................... CS
                               AAA   3 lyGppGtGKTllakavakelgve.......................fleisgsellsk................... 37 
                                       l+G  G GKT +++ ++  ++ +                       +          +                   
  gi|557694237|ref|YP_008797291.1| 119 LIGEFGSGKTQVCHTLCVMAQLPreqgglegsaiyidteatfrperI----------Sqiaeargldpqkileniif 185
                                       78999************998644445555555444444444444440..........04444455555556666665 PP

                                       .......STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCCCHHHHHHHHHHHHHHHHTTTSSSTEEE CS
                               AAA  38 .......yvgesekkirelfkeakekakpsilfiDEidalaksr..sgseseeeervvnqLlteldgvkkkeskviv 105
                                              +++ + k++  ++++     k   ++iD i + ++++   +++  e+++ +n Ll+ l +  + ++  i 
  gi|557694237|ref|YP_008797291.1| 186 asvynssHLQLTVKELGRYVEKY----KARLVIIDSIISHFRAEfiGRGTLAERQQRLNDLLHRLLRTAQVHN--IA 256
                                       44432224444444444444443....3578*************99777777777777777777777777555..77 PP

                                       EEEESSGG CS
                               AAA 106 igatnrpd 113
                                       ++ tn+++
  gi|557694237|ref|YP_008797291.1| 257 VVLTNQVQ 264
                                       77788765 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00029      0.43      12      32 .]      15      35 ..      12      35 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00029
                           IMS_HHH 12 pitkipGiGgklgekLeklGi 32
                                      ++ +i G+G+ ++ekL++ Gi
  gi|557694237|ref|YP_008797291.1| 15 DLQSIEGVGKATEEKLNSAGI 35
                                      788888*************98 PP

>> INCENP_ARK-bind  Inner centromere protein, ARK binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.7   4.1e+03      29      43 ..     166     180 ..     161     183 .. 0.77
   2 ?   10.1   0.1    0.0004      0.59      22      49 ..     250     277 ..     250     278 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.7
                   INCENP_ARK-bind  29 qaLikqepiDpdeiF 43 
                                        ++ + + +Dp++i 
  gi|557694237|ref|YP_008797291.1| 166 SQIAEARGLDPQKIL 180
                                       677888999**9995 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0004
                   INCENP_ARK-bind  22 AqspeLrqaLikqepiDpdeiFGpikpl 49 
                                       Aq ++++  L++q + +pd++FG + ++
  gi|557694237|ref|YP_008797291.1| 250 AQVHNIAVVLTNQVQANPDQFFGDPNKP 277
                                       677899999*************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); 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: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2503.57
//
Query:       gi|557694238|ref|YP_008797292.1|  [L=453]
Description: pyruvate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-80  270.0   0.0      3e-80  269.7   0.0    1.1  1  PK         Pyruvate kinase, barrel domain
    2.1e-17   63.4   0.0    6.5e-17   61.8   0.0    1.8  1  PK_C       Pyruvate kinase, alpha/beta domain
      2e-05   23.8   0.2    5.3e-05   22.4   0.1    1.6  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 !  269.7   0.0     5e-84     3e-80       3     343 ..       2     329 ..       1     334 [. 0.97

  Alignments for each domain:
  == domain 1  score: 269.7 bits;  conditional E-value: 5e-84
                                       -SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BTT CS
                                PK   3 rtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllkd 79 
                                       rtki ctlGP+ ++v  +ek i+ G  + r+nfshG+    ++  +n+rea++k g+k+ ++ D++Gp ir++ l+ 
  gi|557694238|ref|YP_008797292.1|   2 RTKIACTLGPSLQEVVDIEKAISLGCRIYRINFSHGNPILWRQLADNAREAAEKRGEKIVLIGDLRGPSIRVSGLET 78 
                                       8************************************************************************9998 PP

                                       CSSSEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EEE CS
                                PK  80 gkkdielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgvl 156
                                          +i+l++g++ k+sld  l         +l y+  ++ vevG+t+l+dDG+  lkv ++de + ++ e+   +++
  gi|557694238|ref|YP_008797292.1|  79 ---SISLRAGERAKFSLDGPL---------SLPYPRFFETVEVGDTLLLDDGRGMLKVVAKDETS-IAAEAIRPATI 142
                                       ...69**********999765.........589***************************99988.*********** PP

                                       -SS-BEE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHHTH CS
                                PK 157 gskkgvnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegvenl 233
                                       + +k++ + g +v++p      +++l+ +++ ++d + +sfv ka+Dv ++++ l+e+g    +iakie   gv+n+
  gi|557694238|ref|YP_008797292.1| 143 SPNKSIVIRGKEVQVPDYLATCREQLQAAADMELDYVGLSFVTKAADVDAAKTFLHEKGLATGVIAKIETPSGVKNV 219
                                       ***************************************************************************** PP

                                       HHHHHHSSEEEEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT-S CS
                                PK 234 deileasDgimvarGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDGtD 310
                                       dei e sD++++arGDlG+  p e v+ +qk++i  + +a kpvi+atq+l  m+++P ptr+e+ Dv+  v DG D
  gi|557694238|ref|YP_008797292.1| 220 DEISERSDAVLIARGDLGMHFPLEYVPRLQKTIIDAAYNACKPVIVATQLLGTMVNEPVPTRSEIVDVMTCVEDGVD 296
                                       ***************************************************************************** PP

                                       EEEESHHHHTSS-HHHHHHHHHHHHHHHHHTS- CS
                                PK 311 avmLsgetakGkyPveavkamaevaleaekalk 343
                                        +mL +eta G+yP e+++ + ++a + ek ++
  gi|557694238|ref|YP_008797292.1| 297 VLMLTAETAVGRYPLESIQWLVNIAETYEKGIE 329
                                       *************************99998876 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 !   61.8   0.0   1.1e-20   6.5e-17       3     105 ..     344     441 ..     342     445 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1.1e-20
                                       HHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSHHH CS
                              PK_C   3 iakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdellr 79 
                                        a a+v++ae l ak I ++t  G+ Ar+i++++p   iia tpn+++  +l l++Gv+p+l+e    a+s  e l+
  gi|557694238|ref|YP_008797292.1| 344 FALAVVNLAESLAAK-IAIFTINGNMARRIARFKPVSGIIAATPNHDVVPRLMLLWGVTPLLLE----AQSYAEGLE 415
                                       6899******99665.**********************************************97....5778889** PP

                                       HHHHHHHHTTSS-STSEEEEEE-SSS CS
                              PK_C  80 eavkvakeaglvkkgdevvvtaGtpk 105
                                       ++ k + e++l+++gd+ v+t G  k
  gi|557694238|ref|YP_008797292.1| 416 KLEKKLEEERLAEPGDTYVLTYGLVK 441
                                       *********************99765 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 !   22.4   0.1   8.9e-09   5.3e-05      72     169 ..     163     251 ..     133     278 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.9e-09
                                       HHHHHHGG.HHHTTSSEEEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHHTSTTEEEE CS
                         HpcH_HpaI  72 elikqdle.vldlgaqvvlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIaavegldgv 147
                                       ++ +q l+ ++d +++ v + +v++a+++ ++++ l e           t ++a iE+  gvkn++eI  +e+ d+v
  gi|557694238|ref|YP_008797292.1| 163 TCREQ-LQaAADMELDYVGLSFVTKAADVDAAKTFLHEKG-------LATGVIAKIETPSGVKNVDEI--SERSDAV 229
                                       44455.77799999999***************99999988.......99*******************..68999** PP

                                       EE-HHHHHHHTT-TTSTTSHHH CS
                         HpcH_HpaI 148 flGaeDlsadlgtkrspegtev 169
                                        ++  Dl +   ++  p  +++
  gi|557694238|ref|YP_008797292.1| 230 LIARGDLGMHFPLEYVPRLQKT 251
                                       ******9998766665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); 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:                         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: 00:00:00.43
# Mc/sec: 3199.43
//
Query:       gi|557694239|ref|YP_008797293.1|  [L=317]
Description: 3-hydroxybutyryl-CoA dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-46  157.9   0.0    3.5e-46  157.3   0.0    1.3  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
    4.2e-23   81.8   0.1    1.6e-22   79.9   0.1    2.0  2  3HCDH          3-hydroxyacyl-CoA dehydrogenase, C-terminal do
    0.00011   22.5   0.0    0.00025   21.4   0.0    1.6  1  3HCDH_RFF      3-hydroxybutyryl-CoA dehydrogenase reduced Ros
     0.0059   16.8   0.0      0.031   14.4   0.0    2.1  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
  ------ inclusion threshold ------
      0.032   14.8   0.0      0.082   13.5   0.0    1.6  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
      0.082   12.3   0.0       0.14   11.5   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
       0.16   12.8   2.2       0.29   11.9   0.4    2.4  2  TetR_C_33      Tetracyclin repressor-like, C-terminal 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 !  157.3   0.0   1.4e-49   3.5e-46       2     179 ..       4     187 ..       3     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 157.3 bits;  conditional E-value: 1.4e-49
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-......HHHHCCCHHCEEEES- CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk......eeeveaalarisfttd 72 
                                       v viGaG +G+gia  +a +g++V+l d+++++ ++ +   ek +++  e+ +l       +e+ve+++ ri f + 
  gi|557694239|ref|YP_008797293.1|   4 VDVIGAGRIGHGIALCVAMHGFRVRLRDVKHRTPDERKMLQEKIFSQIRESLRLFeecefiHESVEEVVRRIVFVDG 80 
                                       67***************************666665555555555555555544444555557*************** PP

                                       HHHHHC-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEE CS
                           3HCDH_N  73 leeavdadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEv 149
                                       ++ + da  v+Eav+E+ ++K++v+  +++ +  d++las++Ss+++s+la+++k+per++++H++nP++l++LvEv
  gi|557694239|ref|YP_008797293.1|  81 YDGLEDAFHVVEAVPEDAAVKKQVYGMVSERIGGDVLLASTSSSMRPSALAKHVKHPERFLVTHWINPAELIPLVEV 157
                                       ***************************************************************************** PP

                                       EE-TT--HHHHHHHHHHHHHTT-EEEEECS CS
                           3HCDH_N 150 vrgekTseetvatvvelakkigktpvvvkd 179
                                        ++++Ts etv+++ve++++ gk pvv+ d
  gi|557694239|ref|YP_008797293.1| 158 APSPQTSRETVEEAVEFLRRCGKRPVVCGD 187
                                       ****************************87 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 ?   -1.7   0.0       1.8   4.6e+03      10      35 ..      49      74 ..      43      77 .. 0.83
   2 !   79.9   0.1   6.3e-26   1.6e-22       1      97 []     190     289 ..     190     289 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.8
                                      HHHHHHHHHHHTTSS-HHHHHHHHHH CS
                             3HCDH 10 pllneavrlveegvaspediDaamrl 35
                                      + ++e +rl+ee     e++++++r+
  gi|557694239|ref|YP_008797293.1| 49 SQIRESLRLFEECEFIHESVEEVVRR 74
                                      56889999999999999999998875 PP

  == domain 2  score: 79.9 bits;  conditional E-value: 6.3e-26
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHS...SCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH- CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlp...mGpfelldlvgldvakkilevlaeelgerayaps 74 
                                       G+v  R++a+l+nea+rlveegvasp+d+D+a+++g+G++    G +e +d  g+d+ +++ e+la+el+ ++++p+
  gi|557694239|ref|YP_008797293.1| 190 GYVSARLQAALMNEALRLVEEGVASPRDVDEALMAGIGFRlsvHGLLEFVDWGGVDILYRVDEYLAAELKAERFKPP 266
                                       9***************************************6666888999999************************ PP

                                       HHHHHHHHTT--BGGGTBSSSBC CS
                             3HCDH  75 plleklveagrlgrktgkgfyky 97 
                                        ll+klve+g lg   g+g+++y
  gi|557694239|ref|YP_008797293.1| 267 ALLRKLVEKGCLGMHVGRGVFDY 289
                                       ********************998 PP

>> 3HCDH_RFF  3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   9.9e-08   0.00025      34      69 .]     154     189 ..     140     189 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.9e-08
                         3HCDH_RFF  34 rlAlAaaaqaspqalaqavalLqalGkkvlvlaDaP 69 
                                        + +A+++q+s++++++av++L+++Gk+++v +D P
  gi|557694239|ref|YP_008797293.1| 154 LVEVAPSPQTSRETVEEAVEFLRRCGKRPVVCGDSP 189
                                       5669******************************99 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 !   14.4   0.0   1.2e-05     0.031       4      95 ..       6     126 ..       4     140 .. 0.76
   2 ?   -2.6   0.0       2.1   5.5e+03      70     115 ..     165     211 ..     157     214 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
                                       EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHH..HHHHTT...............EEE-SSHHHHHHHC....... CS
                     NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekve..elvaeg...............akaaesieelvasl....... 56 
                                       +iG G +G+ +al ++ +g++v + ++++   +  ++++e+                 ++es+ee+v+++       
  gi|557694239|ref|YP_008797293.1|   6 VIGAGRIGHGIALCVAMHGFRVRLRDVKHRTPDerKMLQEKifsqireslrlfeecEFIHESVEEVVRRIvfvdgyd 82 
                                       8**********************999665444311344444688999999996665445666666666669999999 PP

                                       .....SEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HH CS
                     NAD_binding_2  57 .....dvvitmvkagkavdeviegllealkkgdilidgstsspe 95 
                                              v+  v++++av++ + g++++   gd+l+ +++ss++
  gi|557694239|ref|YP_008797293.1|  83 gledaFHVVEAVPEDAAVKKQVYGMVSERIGGDVLLASTSSSMR 126
                                       99866668888999999999999988888889998888877765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.1
                                       HHHHHSHCCC-.-TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEE CS
                     NAD_binding_2  70 devieglleal.kkgdilidgstsspedtrelakelkekglkfldaP 115
                                       +e++e+ +e l + g+  + ++ s    + +l+++l ++ l++++ +
  gi|557694239|ref|YP_008797293.1| 165 RETVEEAVEFLrRCGKRPVVCGDSPGYVSARLQAALMNEALRLVEEG 211
                                       44455544444233555555555555555566666666666655555 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 ?   13.5   0.0   3.2e-05     0.082       4      65 ..       6      64 ..       4      72 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
                                      EETTSHHHHHHHHHHHHTTS..-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEE CS
                     F420_oxidored  4 iiGaGnmgealasgllaaga..qpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvv 65
                                      +iGaG++g+++a+ ++ +g+  + +++    +r+p++++ l+e++  ++ +     + ee++++
  gi|557694239|ref|YP_008797293.1|  6 VIGAGRIGHGIALCVAMHGFrvRLRDVK---HRTPDERKMLQEKIFSQIRE--SLRLFEECEFI 64
                                      8******************988888888...8*****99999998766665..66666666665 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 ?   11.5   0.0   5.6e-05      0.14      41      77 ..       6      42 ..       3      69 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.6e-05
                                      EES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C 41 iiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77
                                      +iG+GrIG+ +a +++  g++v   d+++++ +e + 
  gi|557694239|ref|YP_008797293.1|  6 VIGAGRIGHGIALCVAMHGFRVRLRDVKHRTPDERKM 42
                                      8************************999886662222 PP

>> TetR_C_33  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1         1   2.7e+03      33      33 ..      37      37 ..       8     122 .. 0.60
   2 ?   11.9   0.4   0.00011      0.29      59     101 ..     187     258 ..     133     260 .. 0.63

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1
                                      H CS
                         TetR_C_33 33 p 33
                                      p
  gi|557694239|ref|YP_008797293.1| 37 P 37
                                      1 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                                       H.............................--CCHHHHHHHHHHHHHHHHHHHHCTTTTSSS-HHHHHHHHH CS
                         TetR_C_33  59 l.............................ppadavaaaralwaalhGlvsLelfghfglpadpdalferlv 101
                                                                     + ++a+ a + ++ ++hGl+ +   g+ ++   +d+++ +++
  gi|557694239|ref|YP_008797293.1| 187 DspgyvsarlqaalmnealrlveegvasprDVDEALMAGIGFRLSVHGLLEFVDWGGVDILYRVDEYLAAEL 258
                                       0444444444444455555555555555325444*****************999999988888888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2240.26
//
Query:       gi|557694240|ref|YP_008797294.1|  [L=292]
Description: F420-dependent N5,N10-methenyltetrahydromethanopterin reductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   53.6   0.3    4.4e-13   49.3   0.3    2.0  1  Bac_luciferase   Luciferase-like monooxygenase
  ------ inclusion threshold ------
      0.095   11.5   0.0       0.13   11.1   0.0    1.1  1  Phage_stabilise  Phage stabilisation protein


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.3   4.9e-17   4.4e-13      21     314 .]      11     261 ..       3     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 4.9e-17
                    Bac_luciferase  21 slrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhls 97 
                                       +++  +++a++++   f ++ + eh+  +   + a++l +a+a+  +r+r+g  ++p+ +++Pav A+  a L+ l+
  gi|557694240|ref|YP_008797294.1|  11 DFETCLAVAKTIDGNHFYSLHFYEHLP-W---RPAWSLSTAVAPYLKRLRVGPVTVPANLYSPAVNARFLAHLNTLA 83 
                                       677778889999999999999999984.5...99******************************************* PP

                    Bac_luciferase  98 gGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiP.vyvaa 173
                                       +G ++lg+ +g ++ e            a   E ve ++ +  +       e+ s     ++ r+ ++  P vyv+ 
  gi|557694240|ref|YP_008797294.1|  84 PG-AVLGVSRGAYMGE----------KRAKISEVVEKVKMIV-D-------EY-SR----ISWRSSSE--PeVYVGT 134
                                       **.99********999..........7789************.4.......44.32....22233223..55***** PP

                    Bac_luciferase 174 aspaglelaar..hadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearaliagl 248
                                       ++p+ ++ aa+  ++ g+++ +     +a++++++     e gr   d++++++++++++++ ++ ++ +  ++   
  gi|557694240|ref|YP_008797294.1| 135 SGPKLARAAASldYVKGIVVDNLANPRYAQYLRNIID---ETGRK--DLQLIARPFTSIGEDMDKLLEALWSYV--- 203
                                       *******999633688999999777788888888886...9***5..*******************99996666... PP

                    Bac_luciferase 249 dfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvde 314
                                            + +g   + +aa i ++    ++ g+++     +++++al G+ ++++e+ a++ +agv++
  gi|557694240|ref|YP_008797294.1| 204 ----PELVGDSPMLAAAGINYRDLLAHEPGVEEK----MIENLALGGDVDTIVEKAAQLIRAGVSH 261
                                       ....777888888788777777776666666555....79999********************986 PP

>> Phage_stabilise  Phage stabilisation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.5e-05      0.13     215     286 ..      85     158 ..      72     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.5e-05
                   Phage_stabilise 215 gaalyvaqpsymvqk..giagtfcktey.adkyaiishpatgapsvylvgsgqaskiatasiekiirsytadela 286
                                       ga l v++ +ym +k   i+    k+++ +d+y+ is +++ +p vy+ +sg +   a+as++  +++   d+la
  gi|557694240|ref|YP_008797294.1|  85 GAVLGVSRGAYMGEKraKISEVVEKVKMiVDEYSRISWRSSSEPEVYVGTSGPKLARAAASLDY-VKGIVVDNLA 158
                                       778888899999765225777777877527******************************9986.4666667666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); 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):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2103.12
//
Query:       gi|557694241|ref|YP_008797295.1|  [L=414]
Description: ABC-2 type transport system permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  102.3  22.1    4.4e-29  101.7  22.1    1.3  1  ABC2_membrane_3  ABC-2 family transporter protein
    6.3e-29  100.9  22.5      5e-25   88.2  19.1    2.3  2  ABC2_membrane    ABC-2 type transporter


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 !  101.7  22.1   4.9e-33   4.4e-29       1     344 [.      19     406 ..      19     407 .. 0.79

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 4.9e-33
                   ABC2_membrane_3   1 ksfliitlllPiilvlllglifsnsveddentpiavvdedn......sslsqqlvealeaspsvelvyevdseeeak 71 
                                       ks+l++ + lPi ++l++g+if+    +++n ++++ ++d+       +l+  +++al++s+ ++  +++ +  +  
  gi|557694241|ref|YP_008797295.1|  19 KSSLFFGFALPIMFLLVFGTIFGGP--APPNYSLYIRNLDTdpqgnpEPLADAFIQALNSSQVFD--IKLLNPGDP- 90 
                                       799******************9854..599999999999999999**9*****************..555555544. PP

                   ABC2_membrane_3  72 kalkngdidg..ilvipkgfskdll.....................kgesatvtvlinssnlnss.......kailn 118
                                        a +++++ +  il+ipkgfs +ll                                   + n+        ++ l+
  gi|557694241|ref|YP_008797295.1|  91 -APRSTGFAAirILTIPKGFSASLLnntianriditvdtinrliqmA-------------GENIPettraniTQGLS 153
                                       .567777666447889*******999999999955555555555443.............44444333333322222 PP

                   ABC2_membrane_3 119 alnsllqqlnasalv.........................lqseatstsaninvestqleeelsnvasflvg.lili 169
                                       ++n++ q ++++++                               +++s +i++++ q++  +  +++++++ ++++
  gi|557694241|ref|YP_008797295.1| 154 QMNTFKQLFKTEKKTlilegspddrllqpieaiintvadrFELALLNSSSTIDLNTVQTSVRQLRAVDYYLPgYVAA 230
                                       23322222222222244444444555555555555555555678999************99996666666665999* PP

                   ABC2_membrane_3 170 ilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll...afglgipfgnlgllll 243
                                       ++++ +++ ++++ +e +++++++l+ ++++s+++ ++s +l+  +v+l+ +++++++   +f   i     ++ ll
  gi|557694241|ref|YP_008797295.1| 231 FIMTNGLIGVSSFTAEMRRNGVMKLIASTPLSRFSWIVSLVLMQTIVSLILTAVMIAVgwmVFR--IAAVPDLFSLL 305
                                       ********************************************************95544888..88887788999 PP

                   ABC2_membrane_3 244 lfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiPffapglgllrlitgd 320
                                        +ll+ la++ lg +++ + k+ e++ +l   +++++++++g+++ple +p+++++i+++ P++++ ++l   +   
  gi|557694241|ref|YP_008797295.1| 306 IILLGTLAFTGLGSFIGGVLKSVEAVTALGNTLSFPMMFLSGAFWPLELMPTFMQQIARFTPLYYFHVALRESLIAG 382
                                       99********************************************************************9997544 PP

                   ABC2_membrane_3 321 plweillsliilalfavvylllal 344
                                       + ++ l++ ++ a +a++ ++la 
  gi|557694241|ref|YP_008797295.1| 383 SVSTALTPTAVVASMALAGIILAT 406
                                       477777888888888888888876 PP

>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.1     3e-06     0.027       6      42 ..       7      42 ..       3      80 .. 0.86
   2 !   88.2  19.1   5.6e-29     5e-25      52     209 ..     217     379 ..     182     380 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3e-06
                     ABC2_membrane  6 llkreflqrwrdpslgllwrliqplllalvfgtvfgn 42
                                      +++  f+++ rd+s++ ++ ++ p++++lvfgt+fg+
  gi|557694241|ref|YP_008797295.1|  7 IVWLLFRSWMRDKSSL-FFGFALPIMFLLVFGTIFGG 42
                                      567779999****999.99****************95 PP

  == domain 2  score: 88.2 bits;  conditional E-value: 5.6e-29
                     ABC2_membrane  52 r.......pgllffsvlflafsaltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyf 121
                                               pg ++ +++++++++++s  +  +r++gv++   ++pl s+++ +++ vl++ +vsl+++++++++ + 
  gi|557694241|ref|YP_008797295.1| 217 LravdyylPGYVAAFIMTNGLIGVSSF-TAEMRRNGVMKLIASTPL-SRFSWIVSLVLMQTIVSLILTAVMIAVGWM 291
                                       14555578************7777777.888888888888888888.****************************** PP

                     ABC2_membrane 122 lvgldlsrf..flflllllltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiayln 196
                                       ++ +    +  ++ ll++ll +la+++lg +i+ +++s+e ++ l++ + +p+++lsG+f+p++ mp ++q ia++ 
  gi|557694241|ref|YP_008797295.1| 292 VFRIAA--VpdLFSLLIILLGTLAFTGLGSFIGGVLKSVEAVTALGNTLSFPMMFLSGAFWPLELMPTFMQQIARFT 366
                                       *98888..558999*************************************************************** PP

                     ABC2_membrane 197 Pltyavealrsnl 209
                                       Pl+y+  alr +l
  gi|557694241|ref|YP_008797295.1| 367 PLYYFHVALRESL 379
                                       *******999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3029.95
//
Query:       gi|557694242|ref|YP_008797296.1|  [L=316]
Description: ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  111.6   0.0      6e-32  111.0   0.0    1.3  1  ABC_tran  ABC transporter
    1.1e-14   54.9   0.0      1e-08   35.4   0.0    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    1.4e-05   25.0   0.0       0.11   12.2   0.0    2.1  2  AAA_15    AAA ATPase domain
    3.9e-05   23.2   0.0      0.008   15.6   0.0    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain
     0.0023   18.6   0.1     0.0075   17.0   0.0    2.0  2  DUF4162   Domain of unknown function (DUF4162)
  ------ inclusion threshold ------
      0.018   14.8   0.6        2.8    7.6   0.1    2.8  3  AAA_24    AAA domain
      0.024   15.1   0.5      0.039   14.5   0.5    1.5  1  AAA_23    AAA domain
      0.043   14.4   0.4       0.48   11.0   0.4    2.3  1  AAA_18    AAA domain
      0.066   13.0   0.0       0.13   12.0   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain
      0.088   13.1   0.0       0.98    9.7   0.0    2.3  1  SbcCD_C   Putative exonuclease SbcCD, C subunit
      0.089   12.7   0.0       0.16   11.9   0.0    1.4  1  YcaO_C    YcaO cyclodehydratase C-terminal domain
      0.091   11.4   0.0       0.37    9.4   0.0    1.8  2  AAA_13    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 !  111.0   0.0     4e-35     6e-32       2     136 ..      29     167 ..      28     168 .. 0.98

  Alignments for each domain:
  == domain 1  score: 111.0 bits;  conditional E-value: 4e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       ++vs+k++ ge+  ++G+nGaGK+t +++l  l +pt+G+  ++g ++k+  ++++ ++ igvlpqe +  ++ltv 
  gi|557694242|ref|YP_008797296.1|  29 DDVSFKVYVGEVFSLLGPNGAGKTTTVEILECLRTPTSGDAYIKGLSVKNlGDIKKIKQIIGVLPQEFNAVDNLTVL 105
                                       89************************************************99************************* PP

                                       HH.......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en       ++ +++ ++l++lgl +++++      s+LSgGqk+rv +a+al+ +p++++lDEpt
  gi|557694242|ref|YP_008797296.1| 106 ENvqlaavaKQANNVRDVLEQLGLWQIRNKLF----SKLSGGQKRRVGIAMALVGNPEIVFLDEPT 167
                                       ******99888889*****************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 !   17.4   0.0   2.1e-06    0.0031       3      36 ..      42      78 ..      40     109 .. 0.70
   2 !   35.4   0.0   6.9e-12     1e-08     234     298 ..     137     198 ..     131     201 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.1e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl...drdvegltdel 36
                                       l GpNg+GK++  ++l++l+     d++++gl  ++
  gi|557694242|ref|YP_008797296.1| 42 SLLGPNGAGKTTTVEILECLRTPtsgDAYIKGLSVKN 78
                                      589*****************76566644444444444 PP

  == domain 2  score: 35.4 bits;  conditional E-value: 6.9e-12
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       +++lS G+kr  +++ al   +    ++++DEp +gL+P++ r+ +  +k+l++ ga viltTH 
  gi|557694242|ref|YP_008797296.1| 137 FSKLSGGQKRRVGIAMALVGNP---EIVFLDEPTTGLDPEARRETWLYIKNLRKSGATVILTTHY 198
                                       5789***************999...9**************************************5 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   7.1e-05      0.11      17      55 ..      33      86 ..      30     141 .. 0.72
   2 !   11.3   0.0   0.00013       0.2     323     364 ..     157     197 ..      82     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-05
                            AAA_15 17 veidlseeltvliGkNnsGKSsilealdlFlnnkekkn...................k 55
                                      +++ + e +  l G+N++GK++ +e+l+ + + +   +                   k
  gi|557694242|ref|YP_008797296.1| 33 FKVYVGE-VFSLLGPNGAGKTTTVEILECLRTPT---SgdayikglsvknlgdikkiK 86
                                      5667777.88999***************998877...222344444444444444332 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00013
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++ i++++EP + L p+a ++ + ++k+l +++   vi+tTH
  gi|557694242|ref|YP_008797296.1| 157 NPEIVFLDEPTTGLDPEARRETWLYIKNLRKSGA-TVILTTH 197
                                       5678*****************************8.9****** 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    0.0068        10      26      42 ..      40      56 ..      20      63 .. 0.83
   2 !   15.6   0.0   5.3e-06     0.008     118     211 ..     118     211 ..      72     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0068
                                      EEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlld 42
                                      + +++GpNG+GK+  ++
  gi|557694242|ref|YP_008797296.1| 40 VFSLLGPNGAGKTTTVE 56
                                      55789*******98776 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.3e-06
                                       E-HHHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.S CS
                                       xxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                             SMC_N 118 vtkkevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.a 190
                                        + ++v e+l   +i  +    LSgG+k  v +a+ +    v    +++lDe    LD + +++   ++k+ +k+ a
  gi|557694242|ref|YP_008797296.1| 118 NNVRDVLEQLGLWQIRNKlfsKLSGGQKRRVGIAMAL----VGNPEIVFLDEPTTGLDPEARRETWLYIKNLRKSgA 190
                                       34455555555555554444489******99998874....45556889**********************999878 PP

                                       EEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 191 Qfivislreemlekadklvgv 211
                                        +i +++  e  e+ +  v v
  gi|557694242|ref|YP_008797296.1| 191 TVILTTHYMEEAERLSDRVAV 211
                                       889898887777776555555 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       4.2   6.3e+03      39      39 ..     108     108 ..      76     141 .. 0.54
   2 !   17.0   0.0     5e-06    0.0075       1      80 [.     221     304 ..     221     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 4.2
                                       - CS
                           DUF4162  39 e 39 
                                        
  gi|557694242|ref|YP_008797296.1| 108 V 108
                                       1 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5e-06
                                       E-HHHHHTTS.-SSEEEEE...-------..---EEEE-TTS-EEEEE-----------------EEEEEEEE---H CS
                           DUF4162   1 GtleeiKrsy.gknrieve...adaeelleepgveeveeeggelelkledeeaanellkaltsgveirsFeeeePsL 73 
                                       G ++e+ +s+ gk+r++     +da e+l+ +g  +   ++g++++k+++e++  ++ + l++ +     e+++P L
  gi|557694242|ref|YP_008797296.1| 221 GRVRELVASHgGKTRLVFDfldEDAVEILRGKGYAVEYVQDGRVVVKVDKESDVFDVVALLRNSGFEAYPEVRQPGL 297
                                       8899999999555556666977778888888887777777899******************888888889******* PP

                                       HHHHHHH CS
                           DUF4162  74 ndIFiek 80 
                                       +d+F+ +
  gi|557694242|ref|YP_008797296.1| 298 EDVFLSV 304
                                       ****986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0019       2.8       6      57 ..      42      90 ..      38     141 .. 0.58
   2 ?    4.5   0.0     0.017        25     107     141 ..     174     208 ..     172     231 .. 0.78
   3 ?   -2.3   0.0       2.1   3.2e+03      14      43 ..     232     262 ..     226     279 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0019
                            AAA_24  6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevv 57
                                       + Gp+g+GKTt++  l  + l   t  G + +++  ++++  ++++++ + 
  gi|557694242|ref|YP_008797296.1| 42 SLLGPNGAGKTTTVEIL--ECLRTPTS-GDAYIKGLSVKNLGDIKKIKQIIG 90
                                      589**********9988..33333332.344444444444444444444444 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.017
                            AAA_24 107 laeefrrllkklqelrknvifiahektrkdedpeg 141
                                       +++e + ++k+l++ + +vi++ h  ++     ++
  gi|557694242|ref|YP_008797296.1| 174 ARRETWLYIKNLRKSGATVILTTHYMEEAERLSDR 208
                                       578899999***************99988776644 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.1
                            AAA_24  14 GKTtlakel.gpkplfidtekGlksldadkf 43 
                                       GKT l+  +  ++++ i   kG++  ++ ++
  gi|557694242|ref|YP_008797296.1| 232 GKTRLVFDFlDEDAVEILRGKGYAVEYVQDG 262
                                       8999999888888888888777766666555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.5   2.6e-05     0.039      21      39 ..      40      58 ..      21     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.6e-05
                            AAA_23 21 ltlItGpNGaGKTTildAi 39
                                      ++ + GpNGaGKTT ++ +
  gi|557694242|ref|YP_008797296.1| 40 VFSLLGPNGAGKTTTVEIL 58
                                      78899*********66544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.4   0.00032      0.48       3     117 ..      43     212 ..      42     226 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00032
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf............gvnlrdvakenglllevdpe..aldeskrldedkldklldale 65 
                                       l G+ G+GKtt  + L+ +               + nl+d+ k +++     +e  a+d+  +l+  +l+++ ++ +
  gi|557694242|ref|YP_008797296.1|  43 LLGPNGAGKTTTVEILECLR-TptsgdayikglsVKNLGDIKKIKQIIGVLPQEfnAVDNLTVLENVQLAAVAKQAN 118
                                       689*************5543.24566666777786677776666665555555565455544444444444444444 PP

                            AAA_18  66 enss...............................aleegknlvidghlaeleseaakdikk.............vv 98 
                                       + ++                                 ++++ + +d     l +ea+++  +             v+
  gi|557694242|ref|YP_008797296.1| 119 NVRDvleqlglwqirnklfsklsggqkrrvgiamaLVGNPEIVFLDEPTTGLDPEARRE--TwlyiknlrksgatVI 193
                                       44445555555666666666666666666666666555566666665555555444443..1446777888888899 PP

                            AAA_18  99 LtaspeelleRlekRgyee 117
                                       Lt+++ e +eRl++R    
  gi|557694242|ref|YP_008797296.1| 194 LTTHYMEEAERLSDRVAVM 212
                                       9999988899998887655 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 ?   12.0   0.0   8.7e-05      0.13      14      49 ..      30      65 ..      26      70 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.7e-05
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                      + ++++ + +++ l Gp+G+GK+T +  +  l +p+
  gi|557694242|ref|YP_008797296.1| 30 DVSFKVYVGEVFSLLGPNGAGKTTTVEILECLRTPT 65
                                      5667777677999***********987766666665 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 ?    9.7   0.0   0.00066      0.98      63      85 ..     157     179 ..     118     184 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00066
                           SbcCD_C  63 alrlvfLDEAFsklDeesiatll 85 
                                       ++++vfLDE   +lD+e +++  
  gi|557694242|ref|YP_008797296.1| 157 NPEIVFLDEPTTGLDPEARRETW 179
                                       489**************999876 PP

>> YcaO_C  YcaO cyclodehydratase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.16      21      68 ..      69     116 ..      58     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                            YcaO_C  21 ellerLeeeelddytrvaeLiGiefdentvWgqLrigELklliaLalg 68 
                                       ++++ L  ++l d  +++++iG+ ++e ++  +L+++E   l a+a +
  gi|557694242|ref|YP_008797296.1|  69 AYIKGLSVKNLGDIKKIKQIIGVLPQEFNAVDNLTVLENVQLAAVAKQ 116
                                       5678899999****************************7777777655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00025      0.37      23      51 ..      45      73 ..      39     122 .. 0.83
   2 ?   -0.6   0.0      0.27     4e+02     525     571 ..     156     199 ..     151     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00025
                            AAA_13 23 GwNGaGKTtLSrllrslelgetepkfang 51
                                      G NGaGKTt  ++l++l +    +++ +g
  gi|557694242|ref|YP_008797296.1| 45 GPNGAGKTTTVEILECLRTPTSGDAYIKG 73
                                      99***************887776666655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.27
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnl 571
                                       g+ +iv++D P   LD ++      +ik+     k+ + +++ TH +
  gi|557694242|ref|YP_008797296.1| 156 GNPEIVFLDEPTTGLDPEARRETWLYIKNLR---KSGATVILTTHYM 199
                                       6789***************999999999997...7888899999966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2211.02
//
Query:       gi|557694243|ref|YP_008797297.1|  [L=143]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-34  118.9   0.0    1.5e-34  118.6   0.0    1.0  1  HEPN      HEPN domain
    0.00011   22.2   0.9    0.00051   19.9   0.9    2.1  1  PaREP1    Archaeal PaREP1/PaREP8 family


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 !  118.6   0.0   1.7e-38   1.5e-34       2     115 ..      11     127 ..      10     131 .. 0.97

  Alignments for each domain:
  == domain 1  score: 118.6 bits;  conditional E-value: 1.7e-38
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHH CS
                              HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreele 78 
                                       ++wl +A+++l++A+ +le+gdy++acf+++qaae+a+KAll   g + +++h+++ L+++l++ +  ++e+ e+++
  gi|557694243|ref|YP_008797297.1|  11 SRWLMMARRTLDSARGDLERGDYSWACFKSHQAAEYAVKALLRGVGET-AHGHSISNLVKRLSTVD--FSEILEQAK 84 
                                       58*********************************************8.**************988..9******** PP

                                       HHHCCCHHCCCTSS--S......--HHHHHHHHHHHHHHHHHH CS
                              HEPN  79 eLekayiesrYpdakee......yteedaeealkdaeevlelv 115
                                        L+k+y+++rYpda++e      yte+da eal+ ae++l++v
  gi|557694243|ref|YP_008797297.1|  85 ALDKFYVPTRYPDAWPEgipvdyYTEKDAIEALRSAEKILDWV 127
                                       ******************************************5 PP

>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.9   5.7e-08   0.00051       3      43 ..      14      54 ..      12     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.7e-08
                            PaREP1  3 leeaekeleeAeellekGdlrqAaeKaykAvkalvkalaek 43
                                      l +a++ l+ A+  le+Gd+  A+ K  +A++ +vkal+  
  gi|557694243|ref|YP_008797297.1| 14 LMMARRTLDSARGDLERGDYSWACFKSHQAAEYAVKALLRG 54
                                      5689999*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1043.44
//
Query:       gi|557694244|ref|YP_008797298.1|  [L=102]
Description: DNA polymerase beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-08   34.1   0.0    2.5e-08   34.1   0.0    1.2  1  NTP_transf_2  Nucleotidyltransferase domain
     0.0024   17.9   0.1     0.0029   17.7   0.1    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 !   34.1   0.0   2.8e-12   2.5e-08      14      47 ..      15      48 ..       2      97 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 2.8e-12
                                      TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH CS
                      NTP_transf_2 14 vakvvlfGSyarGtalkgSDiDllvvlpeevsre 47
                                       ++++l+GSyarG+++  SD+D+++v++ ++  +
  gi|557694244|ref|YP_008797298.1| 15 EVSAFLVGSYARGDFNLWSDVDIVLVSDVFSGNP 48
                                      7899************************997643 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   3.2e-07    0.0029      16      42 ..      18      44 ..      15      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.2e-07
                                      TTEEEEEE-S------EEEEEEEESS- CS
                           Polbeta 16 aylFGSrakgkareeSDiDlavllkek 42
                                      a+l GS+a+g+++  SD+D+ ++ +  
  gi|557694244|ref|YP_008797298.1| 18 AFLVGSYARGDFNLWSDVDIVLVSDVF 44
                                      7999****************9987755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 777.16
//
Query:       gi|557694245|ref|YP_008797299.1|  [L=214]
Description: 3-isopropylmalate/(R)-2-methylmalate dehydratase small subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-31  108.7   0.0    3.4e-31  108.3   0.0    1.2  1  Aconitase_C  Aconitase C-terminal domain


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 !  108.3   0.0   1.9e-35   3.4e-31       4     130 ..      11     130 ..       8     131 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.9e-35
                                       CCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE- CS
                       Aconitase_C   4 llklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvvia 80 
                                       + +++G+++++e++ vdtd++ip +f++ i++ glg+ l++ +r++++  l    k d+v+  ++y+  +ak++v++
  gi|557694245|ref|YP_008797299.1|  11 VVRVVGKAAPLEADDVDTDQIIPAEFLKVIERRGLGKYLFYRWRYDEQGRL----KGDFVLDRPEYR--DAKILVAG 81 
                                       67889*****************************************99998....569*********..99***999 PP

                                       -SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEEST CS
                       Aconitase_C  81 gknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplefke 130
                                         nfG GSSRe A +al ++Gi+ via SF++If++n+ kngl+ +++++
  gi|557694245|ref|YP_008797299.1|  82 -RNFGIGSSRENAVWALTDFGIRCVIASSFGDIFYTNASKNGLVCIKLPD 130
                                       .*********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1759.69
//
Query:       gi|557694246|ref|YP_008797300.1|  [L=154]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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    4.1e-10   40.2   0.0    1.1  1  Methyltransf_25  Methyltransferase domain
    1.1e-08   34.7   0.0    1.4e-08   34.4   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    2.6e-08   33.8   0.0    2.9e-08   33.6   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    2.8e-07   31.1   0.0    3.9e-07   30.6   0.0    1.1  1  Methyltransf_11  Methyltransferase domain
    1.8e-05   24.7   0.0      2e-05   24.5   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.8e-05   24.3   0.0    2.3e-05   23.9   0.0    1.0  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00012   21.3   0.0    0.00015   21.0   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    0.00034   20.3   0.0    0.00045   19.9   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.001   18.8   0.0     0.0014   18.4   0.0    1.1  1  N6_N4_Mtase      DNA methylase
     0.0011   19.6   0.0     0.0014   19.3   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
     0.0024   17.2   0.0     0.0029   17.0   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
     0.0024   17.7   0.0     0.0028   17.4   0.0    1.1  1  Met_10           Met-10+ like-protein
     0.0031   17.1   0.0      0.004   16.7   0.0    1.1  1  MTS              Methyltransferase small domain
     0.0036   16.9   0.0     0.0056   16.2   0.0    1.3  1  DOT1             Histone methylation protein DOT1
     0.0051   16.8   0.0     0.0054   16.7   0.0    1.1  1  Methyltransf_32  Methyltransferase domain
  ------ inclusion threshold ------
      0.021   14.3   0.0      0.025   14.0   0.0    1.2  1  Methyltransf_4   Putative methyltransferase
      0.024   14.3   0.1       0.31   10.7   0.1    2.1  1  UPF0020          Putative RNA methylase family UPF0020
      0.056   13.4   0.0      0.074   13.0   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
      0.093   12.3   0.0       0.11   12.1   0.0    1.1  1  FmrO             Ribosomal RNA methyltransferase (FmrO)
       0.11   12.2   0.0       0.15   11.8   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.12   11.3   0.0       0.13   11.1   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
       0.14   11.5   0.0       0.16   11.4   0.0    1.2  1  TehB             Tellurite resistance protein TehB
       0.16   11.6   0.1       0.28   10.8   0.0    1.4  1  Cons_hypoth95    Conserved hypothetical protein 95


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 !   40.2   0.0   5.2e-13   4.1e-10       1      95 [.      30     125 ..      30     126 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 5.2e-13
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEEST.G CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssga.l 74 
                                       vLdlGcG Gr+++ +a+++g ak +g ++ +++++ +re+a+  +l   v+++++d+++ p++d+ +   +++   l
  gi|557694246|ref|YP_008797300.1|  30 VLDLGCGDGRILFTAAEEYG-AKAIGYELRPSLVNFIREKAKLMRLdeMVHVIKQDFTASPLPDADVITLYLTRDvL 105
                                       9******************8.********************98878989*************998777777777767 PP

                                       GGSSHHHHHHHHHHHHHHEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkp 95 
                                       ++++ ++le+al++ ar++  
  gi|557694246|ref|YP_008797300.1| 106 SLIK-PRLEAALSRGARIVSH 125
                                       7776.8899999999998765 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   1.8e-11   1.4e-08      52     122 ..      16      86 ..      12     102 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.8e-11
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GG CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldye 122
                                       +++l+ +++++G+t+Ld+GcG G ++ +a+e+y++k +g  l     +  +++ + + l++ v+v  +d+ 
  gi|557694246|ref|YP_008797300.1|  16 RRMLDLAGVDEGETVLDLGCGDGRILFTAAEEYGAKAIGYELRPSLVNFIREKAKLMRLDEMVHVIKQDFT 86 
                                       6789999************************************************9999999999999986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0   3.8e-11   2.9e-08       3      80 ..      26      98 ..      24     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 3.8e-11
                   Methyltransf_31  3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlils 80
                                      +g +vlDlGCG G+++f +aee   +a+ +G +  +  +++ re+a+   ld  v++ ++d+++ +  l d   D+i+ 
  gi|557694246|ref|YP_008797300.1| 26 EGETVLDLGCGDGRILFTAAEEY--GAKAIGYELRPSLVNFIREKAKLMRLDeMVHVIKQDFTASP--LPD--ADVITL 98
                                      6889****************876..589************************8899999****988..776..777654 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0     5e-10   3.9e-07       1      90 [.      31     125 ..      31     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 5e-10
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES...-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvsse...vl 71 
                                       Ld+GcG Gr++   a+ + a+ +g +l + +++  +eka+  +l   v ++++d++  p++d   D+++++    vl
  gi|557694246|ref|YP_008797300.1|  31 LDLGCGDGRILFTAAEEYgAKAIGYELRPSLVNFIREKAKLMRLdeMVHVIKQDFTASPLPD--ADVITLYLtrdVL 105
                                       8**************5555*********************999999999*************..6777666622256 PP

                                       CC-.CCHHHHHHHHHHHEEE CS
                   Methyltransf_11  72 hhv.edpekalkeiaRvLkp 90 
                                         + +++e+al+  aR++  
  gi|557694246|ref|YP_008797300.1| 106 SLIkPRLEAALSRGARIVSH 125
                                       55588999999999998876 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   2.6e-08     2e-05      21      69 ..      25      83 ..      11     128 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.6e-08
                   Methyltransf_23 21 raggrvLdiGcGtG.illevlrengfsvtgvDlspeaveiae.........kakkaqkd 69
                                      ++g  vLd+GcG+G il   ++e+g++ +g++l+p +v+ ++         +    +k+
  gi|557694246|ref|YP_008797300.1| 25 DEGETVLDLGCGDGrILFTAAEEYGAKAIGYELRPSLVNFIRekaklmrldEMVHVIKQ 83
                                      56789*********7788888999**************999876666655433333333 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   2.9e-08   2.3e-05     159     260 ..      24     126 ..      16     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.9e-08
                              PrmA 159 vkegeevlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk..eekadviva 232
                                       v ege+vlD+G+G G iL  aa   gak ++++ + +  v+  +e a+l ++++ ++v ++++ ++     advi  
  gi|557694246|ref|YP_008797300.1|  24 VDEGETVLDLGCGDGrILFTAAEEYGAK-AIGYELRPSLVNFIREKAKLMRLDEMVHV-IKQDFTAspLPDADVITL 98 
                                       6789**********999*********97.57************************999.4555554344679***99 PP

                              PrmA 233 NILaevlielaedikklvkeggllilSG 260
                                           +vl  + +++ +++  g++++  G
  gi|557694246|ref|YP_008797300.1|  99 YLTRDVLSLIKPRLEAALSRGARIVSHG 126
                                       9999999999999999999999988766 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.9e-07   0.00015      20      88 ..      16      88 ..      13     108 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.9e-07
                                      HHHHHHH-GGTTSEEEEES-TTT.CCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGH CS
                            RrnaAD 20 neIldklnleekltvleigpGkG.ilTeeLakrakqvvvlElderLakllqkkls...kdeklkvvhqDflkf 88
                                       + ld + + e  tvl++g G G il +   ++  +   +El+++L+++ ++k +   +de + v++qDf   
  gi|557694246|ref|YP_008797300.1| 16 RRMLDLAGVDEGETVLDLGCGDGrILFTAAEEYGAKAIGYELRPSLVNFIREKAKlmrLDEMVHVIKQDFTAS 88
                                      5667778888*************44555556777******************999999***********9765 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   5.8e-07   0.00045      11      50 ..      24      63 ..      16      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.8e-07
                              MetW 11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegva 50
                                      +++g +vldlGcGdG +l   +ee + ++ G el  + v+
  gi|557694246|ref|YP_008797300.1| 24 VDEGETVLDLGCGDGRILFTAAEEYGAKAIGYELRPSLVN 63
                                      77899***************************99877766 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   1.8e-06    0.0014     175     227 ..       9      63 ..       6      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.8e-06
                                       ---HHHHHHHH.HHHS-TT-EEEETT-TTTHHH.HHHHHTT-EEEEEESSHHHHH CS
                       N6_N4_Mtase 175 qkPvallerlI.klstkkgdivlDpFaGSGtTa.vaakelgrkfiGieieeeyve 227
                                       + P  +++r++ ++  ++g++vlD  +G G ++ +aa+e g k+iG+e  ++ v+
  gi|557694246|ref|YP_008797300.1|   9 PTPYPIVRRMLdLAGVDEGETVLDLGCGDGRILfTAAEEYGAKAIGYELRPSLVN 63 
                                       6788999999977899***************974799999*********999887 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.8e-06    0.0014       1      87 [.      31     117 ..      31     126 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.8e-06
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvv...asn 74 
                                       L++GcG+G++l+  +e+  +++ +g+++ ps ++  +ek +  + +    v++ ++d   ++ +   D+++     +
  gi|557694246|ref|YP_008797300.1|  31 LDLGCGDGRILFTAAEE-YGAKAIGYELRPSLVNFIREKAKLMRLDE--MVHVIKQDFTASPLP-DADVITlylTRD 103
                                       8****************.9**************88888888777655..444444444444444.889988544557 PP

                   Methyltransf_12  75 vlhhl.kdirevld 87 
                                       vl+ + + ++++l+
  gi|557694246|ref|YP_008797300.1| 104 VLSLIkPRLEAALS 117
                                       77777555556665 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.7e-06    0.0029      53     133 ..      17      98 ..      13     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.7e-06
                                       HHHHSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-.HHHHHHHHHHS.-----TTEEEEES-TTTS---- CS
                    Methyltransf_2  53 kvleafdleglkslvDvGGGtGalakaivsayPtikvivfDl.peVveaAkehl.sageeervefvgGdffkdslPe 127
                                       ++l    + + ++++D+G G G ++ ++++ y + k+i ++l p+ v+  +e+   + ++e v++++ df  ++lP+
  gi|557694246|ref|YP_008797300.1|  17 RMLDLAGVDEGETVLDLGCGDGRILFTAAEEY-GAKAIGYELrPSLVNFIREKAkLMRLDEMVHVIKQDFTASPLPD 92 
                                       55555556666899******************.579999999889999988887567899***************** PP

                                       -SEEEE CS
                    Methyltransf_2 128 aDaill 133
                                       aD+i l
  gi|557694246|ref|YP_008797300.1|  93 ADVITL 98 
                                       ***987 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.6e-06    0.0028      93     161 ..      17      86 ..      15     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.6e-06
                                       HHHTT..--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GG CS
                            Met_10  93 rlakl..veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgr 161
                                       r+  l  v+ege+V+d+  G G    ++a    + + ++ +l P+ v++++e  kl +++++v++i++D  
  gi|557694246|ref|YP_008797300.1|  17 RMLDLagVDEGETVLDLGCGDGRILFTAAE-EYGAKAIGYELRPSLVNFIREKAKLMRLDEMVHVIKQDFT 86 
                                       555554589**************9999997.5666689*****************************9975 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   5.1e-06     0.004      31      98 ..      26      93 ..      16      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.1e-06
                                      TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-E CS
                               MTS 31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkf 98
                                      + ++vlDlGcG G +  ++a+e+   +   ++     +++ +e ++  +l+  v+v+++d ++     + 
  gi|557694246|ref|YP_008797300.1| 26 EGETVLDLGCGDGRILFTAAEEYGA-KAIGYELRPSLVNFIREKAKLMRLDemVHVIKQDFTASPL-PDA 93
                                      5678************999999988.6678999999**********99999999999999987765.445 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.2e-06    0.0056      28      88 ..      12      71 ..       9      89 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.2e-06
                                      HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHH CS
                              DOT1 28 peflsevldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkee 88
                                      ++++ ++ld   +++ ++ +DLG G G++ + aa e+g k ++G E+  +  ++ +++++ 
  gi|557694246|ref|YP_008797300.1| 12 YPIVRRMLDLAGVDEGETVLDLGCGDGRILFTAAEEYGAK-AIGYELRPSLVNFIREKAKL 71
                                      5678899999****************************99.9****999988887776665 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   6.9e-06    0.0054      13      86 ..      15      82 ..       8     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.9e-06
                   Methyltransf_32 13 vakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfae 86
                                      v+++l+  a  ++ +tv+D+G+G g   f+ a    ey+ k +g +++ +lv+ +++ a+ ++  +++ ++ ++
  gi|557694246|ref|YP_008797300.1| 15 VRRMLDL-AGVDEGETVLDLGCGDGRILFTAAE---EYGAKAIGYELRPSLVNFIREKAKLMR--LDEMVHVIK 82
                                      5555555.3456679***************999...*****************9999998877..655544444 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.3e-05     0.025       4      52 ..      29      76 ..      26     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.3e-05
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSS CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkN 52
                                      +vl++GcG G++l + A++    + +G E+r ++v+ + +k++  +l  
  gi|557694246|ref|YP_008797300.1| 29 TVLDLGCGDGRILFTAAEEYGA-KAIGYELRPSLVNFIREKAKLMRLDE 76
                                      79************99998876.579**********9999998877654 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1    0.0004      0.31      18      64 ..      16      63 ..      13      98 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                                      HHHHHHTT--TTS-EEETT-TTSHHHHHHHHH.HTT--TTTT----SS CS
                           UPF0020 18 aalvrlagwkpgepllDPmCGsGtilIEaall.ganiapgllrefvle 64
                                      + ++ lag+++ge+ lD  CG G il  aa   ga+++   lr+  ++
  gi|557694246|ref|YP_008797300.1| 16 RRMLDLAGVDEGETVLDLGCGDGRILFTAAEEyGAKAIGYELRPSLVN 63
                                      56999********************99999751444444444444443 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.5e-05     0.074      12      77 ..      24      88 ..      15      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.5e-05
                   Methyltransf_18 12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlek 77
                                      v++g++v+D G+  g + + +++e    k+i  +++++ ++  +e+++  +l++ ++v+ +d  ++
  gi|557694246|ref|YP_008797300.1| 24 VDEGETVLDLGCGDGRILFTAAEEYG-AKAIGYELRPSLVNFIREKAKLMRLDEMVHVIKQDFTAS 88
                                      889***************99997665.59***************************9998875554 PP

>> FmrO  Ribosomal RNA methyltransferase (FmrO)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00014      0.11     106     186 ..      26     106 ..       6     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00014
                              FmrO 106 apasvlDvaCgLnpLavpwlllaadatylasDidsdlvefldrflalvevegrvevrDl.vadvpapraDlaLvLkt 181
                                         ++vlD++Cg   + +    +   a  +++++   lv+f+     l+ +++ v v  +  + +p p aD+  +  t
  gi|557694246|ref|YP_008797300.1|  26 EGETVLDLGCGDGRILFTAA-EEYGAKAIGYELRPSLVNFIREKAKLMRLDEMVHVIKQdFTASPLPDADVITLYLT 101
                                       5689*******999988765.56778889*********************999987554145688999998777667 PP

                              FmrO 182 lpvLe 186
                                         vL 
  gi|557694246|ref|YP_008797300.1| 102 RDVLS 106
                                       77665 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 ?   11.8   0.0    0.0002      0.15      62     128 ..      15      80 ..       9      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                       HHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEE CS
                              PCMT  62 valalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nviv 128
                                       v ++l+l  +++g+ vL++G+G G      a+  g+k+  ++ e  ++lv+  +++ k   l+  v+v
  gi|557694246|ref|YP_008797300.1|  15 VRRMLDLAGVDEGETVLDLGCGDGRILFTAAEEYGAKA--IGYELRPSLVNFIREKAKLMRLDeMVHV 80 
                                       567999999***************87777777766666..9999999999876666655555434444 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 ?   11.1   0.0   0.00017      0.13     115     170 ..      26      81 ..      16     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                                       TT-EEEEET-TTSHHHHHHHHCT-SEEEEE-..--HHHHHHHHHHHCCTTTTSSEEEE CS
                    Methyltransf_9 115 kgrtildvGcgnGyhlwrmvgegaklvvGid..Pselfliqfeavrkllgedqrahll 170
                                       +g t+ld+Gcg+G  l+  + e  + ++G +  Ps + +i  +a  kl+  d+ +h++
  gi|557694246|ref|YP_008797300.1|  26 EGETVLDLGCGDGRILFTAAEEYGAKAIGYElrPSLVNFIREKA--KLMRLDEMVHVI 81 
                                       5789******************9999999772255555554444..666666666655 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021      0.16      33      77 ..      29      71 ..      14     114 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                      EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT- CS
                              TehB 33 kvldlgcgqgrnslylsllgydvtawdknensiafleeikekenl 77
                                       vldlgcg+gr  l+ ++  y  +a+  +    + ++ i+ek +l
  gi|557694246|ref|YP_008797300.1| 29 TVLDLGCGDGR-ILFTAAEEYGAKAIGYELR-PSLVNFIREKAKL 71
                                      69********9.5999999999888765432.2233334444443 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00036      0.28      41     101 ..      26      86 ..      17      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                                       CC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-H CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedal 101
                                       eg++vLDl +G G + + A+  + +ka+  e  ++ v+ ++e+ + ++l+e ++++k+d +
  gi|557694246|ref|YP_008797300.1|  26 EGETVLDLGCGDGRILFTAAEEYGAKAIGYELRPSLVNFIREKAKLMRLDEMVHVIKQDFT 86 
                                       6789**********************************************98888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1279.65
//
Query:       gi|557694247|ref|YP_008797301.1|  [L=325]
Description: ketol-acid reductoisomerase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  232.4   0.0    3.6e-69  231.6   0.0    1.4  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
    6.5e-55  185.4   0.1    8.7e-55  185.0   0.1    1.2  1  IlvC           Acetohydroxy acid isomeroreductase, catalytic 
    0.00039   20.6   0.0     0.0023   18.1   0.0    2.1  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
    0.00057   20.4   0.0     0.0013   19.2   0.0    1.6  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
    0.00072   19.0   0.0     0.0013   18.1   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
     0.0022   18.1   0.0     0.0079   16.3   0.0    1.8  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi


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 !  231.6   0.0   1.2e-72   3.6e-69       1     165 []      13     177 ..      13     177 .. 0.99

  Alignments for each domain:
  == domain 1  score: 231.6 bits;  conditional E-value: 1.2e-72
                                       HHHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHH CS
                              IlvN   1 llkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevy 77 
                                       +l+gkkiaviGyGsqG+aqaln+rdsgldvvvglreg++s+kkA e+gf+ l ++ea+k  dv++iliPD  q  +y
  gi|557694247|ref|YP_008797301.1|  13 VLRGKKIAVIGYGSQGRAQALNMRDSGLDVVVGLREGGSSWKKAVEDGFNPLPIEEAAKIGDVIHILIPDPEQPMLY 89 
                                       589************************************************************************** PP

                                       HHHTGGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHH CS
                              IlvN  78 eeeiepnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelala 154
                                       +e+i+ ++k+gk+l f+hG+nihf++i+pp +vdvvl+APk+pG  +re y +gkGvpal++v q+++g+a e+ala
  gi|557694247|ref|YP_008797301.1|  90 KEKIHRHMKAGKTLGFSHGYNIHFRQIVPPPNVDVVLMAPKAPGPRMRELYLQGKGVPALVGVGQNYTGHALETALA 166
                                       ***************************************************************************** PP

                                       HHHHTTHHHH- CS
                              IlvN 155 yakgiGatraG 165
                                       +ak++G++raG
  gi|557694247|ref|YP_008797301.1| 167 MAKACGCSRAG 177
                                       **********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 !  185.0   0.1   2.9e-58   8.7e-55       1     142 [.     183     323 ..     183     325 .] 0.98

  Alignments for each domain:
  == domain 1  score: 185.0 bits;  conditional E-value: 2.9e-58
                                       HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHH CS
                              IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdl 77 
                                       Fk+EtetDlfgEqavL+Ggv+el+++gFe+lve+Gy+pelAyfe+l+elklivdliy+gGi++m++++Sdta+yg+l
  gi|557694247|ref|YP_008797301.1| 183 FKDETETDLFGEQAVLVGGVMELIRNGFEVLVENGYPPELAYFEVLNELKLIVDLIYQGGITHMLKAVSDTAKYGGL 259
                                       9**************************************************************************** PP

                                       HHHHHHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHCH CS
                              IlvC  78 tagprviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklralm 142
                                       t+gp++++++v+++m++ l++i+sGef+++++ +  + ++ l++l+k+ a+h+iekvg+k+r++ 
  gi|557694247|ref|YP_008797301.1| 260 TVGPQIVDSHVRKNMEKALARIKSGEFVETWTGNP-RSYEILNDLMKKMADHQIEKVGEKIRKMA 323
                                       *******************************9998.56999**********************96 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 !   18.1   0.0   7.7e-07    0.0023       1      85 [.      18     102 ..      18     109 .. 0.89
   2 ?   -0.5   0.0      0.42   1.2e+03     132     152 ..     290     310 ..     267     316 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.7e-07
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SS.HHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrt.kekveelvaegakaaesieelvasldvvitmvkagkavdeviegl 76 
                                       ki++iG G  G+  aln+ ++g +v+v  r+  ++ +++v++g++++  iee+++  dv+ +++++ ++     e++
  gi|557694247|ref|YP_008797301.1|  18 KIAVIGYGSQGRAQALNMRDSGLDVVVGLREgGSSWKKAVEDGFNPLP-IEEAAKIGDVIHILIPDPEQPMLYKEKI 93 
                                       79************************9988835899********9986.67788888*********99988888889 PP

                                       CCC--TT-E CS
                     NAD_binding_2  77 lealkkgdi 85 
                                        +++k+g++
  gi|557694247|ref|YP_008797301.1|  94 HRHMKAGKT 102
                                       999999986 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.42
                                       EEE-HHHHHHHHHHHHHHEEE CS
                     NAD_binding_2 132 vGGseeafervkpvleaigak 152
                                         G+  ++e +++++++++ +
  gi|557694247|ref|YP_008797301.1| 290 WTGNPRSYEILNDLMKKMADH 310
                                       568888999999999999974 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 !   19.2   0.0   4.5e-07    0.0013       1      70 [.      18      81 ..      18     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.5e-07
                                      EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S- CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavk 70
                                      ki++iG+G++g+a a+++  +g    ++vv+     e   +++++++ +  + + eeaa+  dv+ + ++
  gi|557694247|ref|YP_008797301.1| 18 KIAVIGYGSQGRAQALNMRDSG---LDVVVG---LREGGSSWKKAVEDGFNPLPIEEAAKIGDVIHILIP 81
                                      7*********************...****99...344445666666667888889*********988777 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 !   18.1   0.0   4.4e-07    0.0013      30     120 ..      10     100 ..       3     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.4e-07
                                       SBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S--STTT CS
                      2-Hacid_dh_C  30 lgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlpltpet 105
                                       +   l+gk++++iG+G+ G+a a  ++  g++v++  r   ++  ++ e g++   +ee+ +  D++ + +p  pe 
  gi|557694247|ref|YP_008797301.1|  10 SLDVLRGKKIAVIGYGSQGRAQALNMRDSGLDVVVGLREGGSSWkKAVEDGFNPLPIEEAAKIGDVIHILIP-DPEQ 85 
                                       556799*************************998877776654458889999*******************9.6777 PP

                                       TTSBSHHHHHCSTTT CS
                      2-Hacid_dh_C 106 rhlinaeelakmkkg 120
                                         l +++  ++mk g
  gi|557694247|ref|YP_008797301.1|  86 PMLYKEKIHRHMKAG 100
                                       777777777777776 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 !   16.3   0.0   2.6e-06    0.0079      20      82 ..      13      76 ..       8      99 .. 0.87
   2 ?   -1.6   0.0      0.86   2.6e+03      76     105 ..     281     312 ..     269     317 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-06
                                      --TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHH.HHHCTT-EE--HHHCTTT-SEE CS
                     AdoHcyase_NAD 20 llaGkvavvaGyGdvGkGcaaslkglGarvivtevdPical.qaameGfevvtleevvkkadiv 82
                                      +l Gk++ v+GyG  G+  a  ++  G  v+v   +  ++  +a+ +Gf+   +ee++k +d++
  gi|557694247|ref|YP_008797301.1| 13 VLRGKKIAVIGYGSQGRAQALNMRDSGLDVVVGLREGGSSWkKAVEDGFNPLPIEEAAKIGDVI 76
                                      46799999************************988877665268889**********9999986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.86
                                       TTT-SEEEE-SSSSS..SB-HHHHCCS-TTEE CS
                     AdoHcyase_NAD  76 vkkadivvtttGnkd..iitlehlkkmkddai 105
                                       +k++++v t tGn     i ++ +kkm d+ i
  gi|557694247|ref|YP_008797301.1| 281 IKSGEFVETWTGNPRsyEILNDLMKKMADHQI 312
                                       56778888999985411477899999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 2696.08
//
Query:       gi|557694248|ref|YP_008797302.1|  [L=79]
Description: hypothetical protein CSUB_C0815 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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 0.23s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 599.26
//
Query:       gi|557694249|ref|YP_008797303.1|  [L=576]
Description: acetolactate synthase I/II/III large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-57  192.5   0.2    8.8e-55  184.9   0.1    2.4  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    1.2e-45  154.6   0.4    2.6e-45  153.5   0.2    1.7  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    1.9e-45  154.3   0.2    2.6e-44  150.7   0.0    2.6  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b


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 !  184.9   0.1   1.5e-58   8.8e-55       1     170 [.       1     168 [.       1     170 [. 0.99
   2 !    5.3   0.0    0.0022        13     112     147 ..     493     528 ..     450     539 .. 0.81

  Alignments for each domain:
  == domain 1  score: 184.9 bits;  conditional E-value: 1.5e-58
                                       EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHH CS
                      TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGat 77 
                                       m++a+alv+++++ gve+vfg+pG+ ++p++dal++++ i+ +l+rhEq aa+aA+gy r++++pg++  tsgpGat
  gi|557694249|ref|YP_008797303.1|   1 MRAADALVKMMEKKGVEYVFGIPGGANMPFYDALRDSD-IKSILMRHEQQAAHAAEGYGRVKRRPGICSGTSGPGAT 76 
                                       789**********************************6.************************************** PP

                                       HCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--E CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgP 154
                                       n++t+l++A+ d++P+++++g++ +s  g++++q e d+++l+ p+ kya++v++p+++ +++  A+ +a+++rpgP
  gi|557694249|ref|YP_008797303.1|  77 NLITGLVDAYMDSSPVVAITGQVVRSFMGTDAFQ-EADIVGLVLPHIKYAVTVKDPHRVLQEFVNAYHIAAHHRPGP 152
                                       **********************************.****************************************** PP

                                       EEEEEEHHHCC-EEEH CS
                      TPP_enzyme_N 155 vylelpkdvlleevde 170
                                       ++l+lp+dv++eev+e
  gi|557694249|ref|YP_008797303.1| 153 TLLDLPRDVFMEEVEE 168
                                       *************997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0022
                                       --T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHH CS
                      TPP_enzyme_N 112 qeldqlalfrpvtkyaervtspeelpealrrAirta 147
                                       + +d ++l + +  +a+rv+s +el +++ rA+rt 
  gi|557694249|ref|YP_008797303.1| 493 DRTDLVKLSEAFGVEAVRVESYDELLKVVMRAVRTN 528
                                       25589999999**********************985 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 ?   -3.4   0.0       1.2   7.3e+03      42      56 ..      99     113 ..      94     118 .. 0.68
   2 !  153.5   0.2   4.3e-49   2.6e-45       1     137 []     190     325 ..     190     325 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.2
                                       EEEEGGGTTSS-TTS CS
                      TPP_enzyme_M  42 vvttlmgkgvipedh 56 
                                       vv ++mg ++++e +
  gi|557694249|ref|YP_008797303.1|  99 VVRSFMGTDAFQEAD 113
                                       677777777776654 PP

  == domain 2  score: 153.5 bits;  conditional E-value: 4.3e-49
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealee 77 
                                       i++aa+l+++a++pv+lvGgg+ +s a +e+ elae++ +P+vtt mgkg++pedhpl lg++g+hg  +a+ a+ e
  gi|557694249|ref|YP_008797303.1| 190 IKQAAKLIAEAEKPVLLVGGGAVYSMAGKEILELAEHIAAPIVTTTMGKGAVPEDHPLVLGVVGMHGRVEADLAIVE 266
                                       799************************************************************************** PP

                                       -SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  78 aDlvlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketleaL 137
                                       +Dlv+++G+r++d r  g+ +ef ++ k ihidid++e+gkn+++++++ gd++++l +L
  gi|557694249|ref|YP_008797303.1| 267 SDLVICIGSRLSD-RAIGPAKEFEKNRKTIHIDIDASEFGKNVRPTVSLPGDARKVLAEL 325
                                       *************.99*********99******************************987 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 ?    0.5   0.0     0.079   4.7e+02      39      76 ..     193     232 ..     189     236 .. 0.65
   2 !  150.7   0.0   4.3e-48   2.6e-44       1     153 []     387     535 ..     387     535 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.079
                                       HHHH.HSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-.SEE CS
                      TPP_enzyme_C  39 Gakl.akpdrevvaivGDGgflmi.lqelatavrrnl.pit 76 
                                       +akl a+ + + v +vG G+ + + + e+   +++ + pi+
  gi|557694249|ref|YP_008797303.1| 193 AAKLiAEAE-KPVLLVGGGAVYSMaGKEILELAEHIAaPIV 232
                                       678855445.555556666655555***9999998555665 PP

  == domain 2  score: 150.7 bits;  conditional E-value: 4.3e-48
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitv 77 
                                       ++G++++wa+ ++k ++p+++ltsgglgtmG+glpaA Gak+a+pdr v+ + GDG+flm++q la ++ ++lp+++
  gi|557694249|ref|YP_008797303.1| 387 GVGQHQMWAQLFWKNRTPGTWLTSGGLGTMGFGLPAAFGAKAAAPDRIVMNLDGDGSFLMTCQTLACVADYDLPVIT 463
                                       69**********99999************************************************************ PP

                                       EEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  78 vvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       v+++N+++gm++++q++f++kr+  +++   + +d++kl ea+G++++rve++  +el +++ +a++++    ++v
  gi|557694249|ref|YP_008797303.1| 464 VIFDNRSLGMVKQWQDMFYNKRYKDVEY--NDRTDLVKLSEAFGVEAVRVESY--DELLKVVMRAVRTNSALTVDV 535
                                       ***********************99986..8899*************9*****..***********8888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3774.42
//
Query:       gi|557694250|ref|YP_008797304.1|  [L=507]
Description: 2-isopropylmalate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  280.7   1.5    1.2e-83  280.7   1.5    1.5  2  HMGL-like   HMGL-like
    6.4e-12   45.5   0.4    1.3e-11   44.6   0.4    1.5  1  LeuA_dimer  LeuA allosteric (dimerisation) 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 !  280.7   1.5   1.4e-87   1.2e-83       2     264 .]      15     272 ..      14     272 .. 0.99
   2 ?   -3.9   0.1      0.88   7.9e+03     215     228 ..     421     434 ..     415     441 .. 0.66

  Alignments for each domain:
  == domain 1  score: 280.7 bits;  conditional E-value: 1.4e-87
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       v ++dttLRDGeq+++aal+ ++k+++a+aL+++gvd+iE+gfp  s ++  ++++i   +  a++++l r+++ di
  gi|557694250|ref|YP_008797304.1|  15 VLVFDTTLRDGEQTAGAALRPADKVRLAEALADLGVDVIEAGFPPVSLGESSAIKEITGMGLGAKVCVLSRCEKADI 91 
                                       6689************************************************************************* PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       +aa++     + + +hvfiats++hl++kl+ +re++ +ka+ av++a+s+g  v +s+eda+rt+l fl++v +a+
  gi|557694250|ref|YP_008797304.1|  92 DAAAK----VEPEWIHVFIATSDIHLQHKLRLTREQAYEKAVSAVEYAKSYGFTVHFSAEDATRTELPFLLRVFKAV 164
                                       *****....9******************************************************************* PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                       eeaGa ++ i+DtvG + P ++++++ ++++ vk  ++++vHcH+d+GlAvan+la+veaGa+ v +tvnG+GeraG
  gi|557694250|ref|YP_008797304.1| 165 EEAGAHSVDIPDTVGTAIPLAMKKIVTEVRNTVK--IPVAVHCHDDFGLAVANSLAGVEAGAEIVHATVNGIGERAG 239
                                       **********************************..***************************************** PP

                                       B-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealg.vdtgldlqklrsiaalv 264
                                       na+lee+vaal+ l  v+tg++++k+ ++++lv
  gi|557694250|ref|YP_008797304.1| 240 NASLEEIVAALRFLYgVETGIKFEKIFRVSRLV 272
                                       ************9866**************997 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.88
                                       TT--EEEEBTTS-- CS
                         HMGL-like 215 aGadrvdgtvnGlG 228
                                       +Ga+ v++++n + 
  gi|557694250|ref|YP_008797304.1| 421 EGASAVEAALNAVT 434
                                       56777777766554 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.4   1.4e-15   1.3e-11       8     132 ..     374     497 ..     367     498 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.4e-15
                                       XXXXXXXXXXXX.--EEEEEEEEEEETTCEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH..T-EEEEE CS
                        LeuA_dimer   8 ealvkdelleae.erlkleklqvssgedelstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv..dikLldY 81 
                                          +++++++++ +r  +++l  + + + + +a+v+l v  ge ++  +eG  +v+A+lnA+++a ++  d++++dY
  gi|557694250|ref|YP_008797304.1| 374 LNYAEEVYGRRSqQRSYVKNLFLMLAGN-VFKAQVDLMV-AGELVTGDGEGASAVEAALNAVTNAAQRitDFQIIDY 448
                                       5567788888877999999999999987.999*******.9**************************99999***** PP

                                       EEE--TT-TT--EEEEEEEE--GGGEEEEEEEESSHHHHHHHHHHHHHHHH CS
                        LeuA_dimer  82 svhaitegtdaqaevrVelevddgkkvsgvGvdsdiveASlkAlisalnrl 132
                                       ++ha  +g + ++e+ V l  ++g ++ g+G+ +d   A + A+ sa+ +l
  gi|557694250|ref|YP_008797304.1| 449 KIHAPFAG-GQSSEAEVVLA-SGGVEFVGRGIGPDPSLAVVSAFTSAVHQL 497
                                       *****999.77888899999.89999*********************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); 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 0.26s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3784.68
//
Query:       gi|557694251|ref|YP_008797305.1|  [L=520]
Description: DNA topoisomerase VI subunit B [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-59  199.8   0.0    3.5e-59  199.2   0.0    1.3  1  Topo-VIb_trans  Topoisomerase VI B subunit, transducer
    1.1e-06   28.5   0.0    4.2e-06   26.6   0.0    1.8  2  HATPase_c_3     Histidine kinase-, DNA gyrase B-, and HSP90-l
    1.6e-06   28.6   0.0    3.1e-06   27.7   0.0    1.4  1  HATPase_c       Histidine kinase-, DNA gyrase B-, and HSP90-l
    6.9e-06   25.1   0.0    1.1e-05   24.4   0.0    1.2  1  FbpA            Fibronectin-binding protein A N-terminus (Fbp
  ------ inclusion threshold ------
       0.14   12.6   0.0       0.28   11.6   0.0    1.4  1  Ribosomal_S13   Ribosomal protein S13/S18


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 !  199.2   0.0   9.9e-63   3.5e-59       1     158 [.     316     473 ..     316     474 .. 0.97

  Alignments for each domain:
  == domain 1  score: 199.2 bits;  conditional E-value: 9.9e-63
                    Topo-VIb_trans   1 PstdclspigeeliekglkkelkpefvaavtrkpkvyeghpfivEvgiayGGelekeekaeilRfaNrvPLlydega 77 
                                       P+ + lsp+g++++e+g++++++p+fv +v+r+p++y+ghpfivE+++ayGG+++ +e++ ++RfaN++PLlyde+a
  gi|557694251|ref|YP_008797305.1| 316 PDPTPLSPVGKDFLEAGIRRIFNPDFVYVVQREPSSYSGHPFIVEAAVAYGGTIPVTETIMLFRFANKIPLLYDERA 392
                                       88999************************************************************************ PP

                    Topo-VIb_trans  78 dvitkav.ksinwkrYkleqpedpvvvlvhvastkvPfksegKeaiadveeiekeiklalqevarkLkkylskkeke 153
                                       dv++k+v ++i+w++Yk+ +p+ p++v+ +++stkvP+k++gKeaiad +eie+e+++al+e++r+Lk yls+ ek+
  gi|557694251|ref|YP_008797305.1| 393 DVAWKVVeEKIDWSNYKVPKPA-PLAVFTSICSTKVPYKTVGKEAIADRPEIERELTMALRECGRNLKLYLSRIEKR 468
                                       *******559*********999.****************************************************99 PP

                    Topo-VIb_trans 154 keeke 158
                                       + +++
  gi|557694251|ref|YP_008797305.1| 469 EAAAK 473
                                       98776 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 !   26.6   0.0   1.2e-09   4.2e-06       4     112 ..      42     161 ..      39     173 .. 0.77
   2 ?   -1.5   0.0      0.55     2e+03      84     120 ..     248     284 ..     246     299 .. 0.77

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.2e-09
                       HATPase_c_3   4 ekAlaelvdNsldAdaen.....vkievnknr..gktgeivieDdGkGmseeelknal.rlatsskeakrkstslGk 72 
                                       + ++ elv+NsldA         v ie+ +++    + ++++ D+G G++ +++ +a+ ++   sk+    ++s+G 
  gi|557694251|ref|YP_008797305.1|  42 YMSIRELVENSLDAAEMGrilpeVLIELGEEDseRGVYRLRVVDNGVGVPGDKIPSAFaTVLYGSKYG--FKQSRGT 116
                                       56789********765556898988888776622445899****************885799999994..6999*** PP

                       HATPase_c_3  73 kGiGlklAsl....slgkkltvitkkegess.tltldvdkidken 112
                                       +G+G  +A l       k ++++++++g++   ++l +d+++++ 
  gi|557694251|ref|YP_008797305.1| 117 FGLGGTMALLygqiTTNKPAKIMSSTDGKTLhIYELMIDVVENRP 161
                                       ***967776522224567889999999999867999999998765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.55
                       HATPase_c_3  84 lgkkltvitkkegesstltldvdkidkenekvleelt 120
                                       + +++ ++tk+++  + lt + +ki  + +k++ el+
  gi|557694251|ref|YP_008797305.1| 248 MMSRMLLETKARNLLTFLTTSFQKIGPKTAKEVLELA 284
                                       5678999999999999999999999988877776654 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 !   27.7   0.0   8.5e-10   3.1e-06       5      82 ..      40     136 ..      37     187 .. 0.59

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 8.5e-10
                                       HHHHHHHHHHHHHHHHHSTTTEE..EEEEEE..EE...TEEEEEEEESSSSSTTHHHTGTCS.TTCH.HCSTCHTST CS
                         HATPase_c   5 rLrqiisnlvdNavkfatkagei..eveika..se...ddlvisveDnGiGipkedlkklfe.kfsq.ddstkrggg 72 
                                        L+  i++lv+N++++ +++g+i  ev i+   ++   + ++++v DnG G+p ++++  f+  ++  + + k++ g
  gi|557694251|ref|YP_008797305.1|  40 SLYMSIRELVENSLDA-AEMGRIlpEVLIELgeEDserGVYRLRVVDNGVGVPGDKIPSAFAtVLYGsKYGFKQSRG 115
                                       677889*********8.999988664444444422567999*****************8887755553333444445 PP

                                       SSSHHHHHH...........H CS
                         HATPase_c  73 gtGlGlsiv...........k 82 
                                        +GlG +++            
  gi|557694251|ref|YP_008797305.1| 116 TFGLGGTMAllygqittnkpA 136
                                       555544444334444444332 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 !   24.4   0.0   3.1e-09   1.1e-05     161     238 ..     233     310 ..     228     330 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.1e-09
                                       SXXXSXBXTTSXXH.HHHHHHHHH.S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHH CS
                              FbpA 161 PpsqdklnPleaeeleefkellsk.kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealq 236
                                       Pp  + + P  ++  e ++  l + k+++l  +L ++fq ++p +a+e+le agl++ets ++ls e++++l +a++
  gi|557694251|ref|YP_008797305.1| 233 PPRETLPHPVGVDV-EMMSRMLLEtKARNLLTFLTTSFQKIGPKTAKEVLELAGLKPETSPRKLSHEQVTALVDAFK 308
                                       77777777886666.666666656699************************************************99 PP

                                       HH CS
                              FbpA 237 el 238
                                       ++
  gi|557694251|ref|YP_008797305.1| 309 RY 310
                                       75 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.8e-05      0.28      17      67 ..     266     316 ..     254     328 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.8e-05
                     Ribosomal_S13  17 ltaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykip 67 
                                        t+ + iG ++ak++l+ a+++ ++  ++l++e++  +++  ++  ++++p
  gi|557694251|ref|YP_008797305.1| 266 TTSFQKIGPKTAKEVLELAGLKPETSPRKLSHEQVTALVDAFKRYDKFRPP 316
                                       578899**********************************99997777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); 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:                         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: 00:00:00.43
# Mc/sec: 3646.49
//
Query:       gi|557694252|ref|YP_008797306.1|  [L=324]
Description: AAA family ATPase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-11   44.8   0.0    1.6e-10   41.3   0.0    2.2  1  ATPase_2  ATPase domain predominantly from Archaea
    1.8e-08   34.5   0.0      1e-07   32.1   0.0    2.2  1  AAA_14    AAA domain
    4.5e-05   23.9   0.7    0.00028   21.3   0.4    2.2  2  AAA_16    AAA ATPase domain
     0.0004   20.7   0.2     0.0015   18.8   0.0    2.1  3  AAA_22    AAA domain
  ------ inclusion threshold ------
      0.065   13.3   0.5        0.4   10.8   0.2    2.4  2  GIIM      Group II intron, maturase-specific 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 !   41.3   0.0   4.5e-14   1.6e-10       2     228 ..      15     214 ..      14     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 4.5e-14
                          ATPase_2   2 fdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkkl 78 
                                       f Re e +el +++e+++   + + G +  GKt+L+k ++ ++       +y++ l  + ++++            +
  gi|557694252|ref|YP_008797306.1|  15 FGRESEYSELVRLVENGS--WVAVLGKRMTGKTSLVKTLARER-----AGVYVNLLGARGLDSVMAR---------I 75 
                                       78*************955..56789****************99.....67*******9999998876.........5 PP

                          ATPase_2  79 ekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltke 155
                                         a g ++++ +l      +   v+ +++++ +++ +k     +++De+q +    +     ++k L n+++     
  gi|557694252|ref|YP_008797306.1|  76 LSASGLRLEELAL------TLGPVNVKWSNVAANVLEKIGDKPLVLDEVQDVA--SV----HFLKILKNVWDT---Y 137
                                       5566666666666......445667777777666555544434678*******..44....489*******99...8 PP

                          ATPase_2 156 khlcvviclsSeglfie..rvyneselegrhky.ilvddldketalnflkegfkel.eelskedfeeiyryvGGkPk 228
                                        +l++v+ +s  gl+++  + +  s+l+gr+   i+++++ ke++ +fl++gfk+     ++++++e+++ + G ++
  gi|557694252|ref|YP_008797306.1| 138 GRLRLVFTGSYIGLMRNilEPSAGSPLYGRRPAvITLNPFSKEKSIEFLRKGFKQAgFTTQENELNEVVEQLNGYVG 214
                                       99***************44445678******999**********************655589999999988888665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   2.8e-11     1e-07       4     126 ..      33     178 ..      30     182 .. 0.64

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2.8e-11
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd................kkladpe.............k 51 
                                        +++ G R +GKT l+k+l++e+       +y+nl   r                 +     e             +
  gi|557694252|ref|YP_008797306.1|  33 WVAVLGKRMTGKTSLVKTLARERA-----GVYVNLLGARGldsvmarilsasglrlE-----ElaltlgpvnvkwsN 99 
                                       6899****************9999.....5556555554444444444444333322.....122223333343334 PP

                            AAA_14  52 llelileklkeekktylflDEiqev..pewekalkslvdegknldvivtGSnskllskeiatslagrva......ei 120
                                       +   +lek+   +++ l+lDE+q v   ++ k+lk++ d++ +l++++tGS  +l+ + i +  ag         +i
  gi|557694252|ref|YP_008797306.1| 100 VAANVLEKI---GDKPLVLDEVQDVasVHFLKILKNVWDTYGRLRLVFTGSYIGLMRN-ILEPSAGSPLygrrpaVI 172
                                       555555554...6688********9444699*********99*********9998855.544444332222222366 PP

                            AAA_14 121 elypls 126
                                       +l+p+s
  gi|557694252|ref|YP_008797306.1| 173 TLNPFS 178
                                       777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.4   7.9e-08   0.00028       2      59 ..      14      66 ..      13     133 .. 0.76
   2 ?    0.4   0.0      0.22   7.7e+02      89     135 ..     197     260 ..     165     300 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 7.9e-08
                            AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggif..lrgk 59
                                      l+GRe e ++L +++e+      + v + G + +GK+slv++l+r  e++g+++  l ++
  gi|557694252|ref|YP_008797306.1| 14 LFGRESEYSELVRLVENG-----SWVAVLGKRMTGKTSLVKTLAR--ERAGVYVnlLGAR 66
                                      89******9999999933.....8********************8..7778888533333 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.22
                            AAA_16  89 aesaeleawrekleeala..................avpelagaea...srllellkrllallsrder 135
                                       ++++el++  e+l + ++                  a ++     +   + +l++l+++l+  +r e+
  gi|557694252|ref|YP_008797306.1| 197 TQENELNEVVEQLNGYVGwltyyghfrciqrkdhreALDSTL---RegeKIILAELRNFLRNRKR-EH 260
                                       455555555565655555666666666644444322222222...14447777777777766555.55 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   4.2e-07    0.0015       6     131 ..      32     148 ..      26     156 .. 0.76
   2 ?   -2.7   0.0       1.9   6.7e+03      38      65 ..     167     194 ..     157     213 .. 0.64
   3 ?   -2.0   0.0       1.1   4.1e+03      71      71 ..     275     275 ..     227     307 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.2e-07
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka..erlsseell. 79 
                                       + ++v G   tGKT l+++l+++          r++ v+v+l +  ++++++ ++l+a gl+l++   +l    +  
  gi|557694252|ref|YP_008797306.1|  32 SWVAVLGKRMTGKTSLVKTLARE----------RAG-VYVNLLGARGLDSVMARILSASGLRLEElaLTLGPVNVKw 97 
                                       5678899999************8..........455.99**************************884444444444 PP

                            AAA_22  80 eale.qalraravielliiDEaqhlrseealeeLrsllnlsrkgvqliLvGtp 131
                                       + ++ + l++ ++ + l++DE+q + s   l+ L++ ++     ++l++ G +
  gi|557694252|ref|YP_008797306.1|  98 SNVAaNVLEKIGD-KPLVLDEVQDVASVHFLKILKNVWD-TYGRLRLVFTGSY 148
                                       4444044455555.99********956666666666666.5567888888876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.9
                            AAA_22  38 erpevvfvtlpsstsskdllrellralg 65 
                                       +rp v++ ++ s+++s ++lr+ +++ g
  gi|557694252|ref|YP_008797306.1| 167 RRPAVITLNPFSKEKSIEFLRKGFKQAG 194
                                       5666777777777777777666555544 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.1
                            AAA_22  71 e 71 
                                       +
  gi|557694252|ref|YP_008797306.1| 275 S 275
                                       0 PP

>> GIIM  Group II intron, maturase-specific domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.48   1.7e+03      15      37 ..      77      99 ..      68      99 .. 0.81
   2 ?   10.8   0.2   0.00011       0.4      20      45 ..     201     226 ..     194     263 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.48
                              GIIM 15 sskgvsleelirklnpilrGWan 37
                                      s +g+ leel+  l p+   W n
  gi|557694252|ref|YP_008797306.1| 77 SASGLRLEELALTLGPVNVKWSN 99
                                      347899**********9999987 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00011
                              GIIM  20 sleelirklnpilrGWanYyrlg.vak 45 
                                        l e++++ln ++ GW  Yy+++ + +
  gi|557694252|ref|YP_008797306.1| 201 ELNEVVEQLNGYV-GWLTYYGHFrCIQ 226
                                       6889999***997.********95433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); 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:                         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: 00:00:00.43
# Mc/sec: 2267.20
//
Query:       gi|557694253|ref|YP_008797307.1|  [L=466]
Description: 6-phosphogluconate dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-105  352.5   0.0   2.2e-105  352.2   0.0    1.1  1  6PGD             6-phosphogluconate dehydrogenase, C-terminal
    3.8e-49  166.9   0.1    8.1e-49  165.8   0.1    1.6  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
    9.9e-08   32.1   0.3    4.3e-07   30.1   0.1    2.1  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    9.2e-07   29.4   0.0    2.9e-06   27.8   0.0    1.9  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
    2.6e-06   27.4   0.8    1.1e-05   25.4   0.0    2.4  3  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
    0.00013   21.7   0.0    0.00023   20.8   0.0    1.4  1  ApbA             Ketopantoate reductase PanE/ApbA
    0.00096   19.4   0.0     0.0031   17.8   0.0    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0015   17.9   0.0     0.0033   16.8   0.0    1.5  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
     0.0048   16.2   0.1     0.0094   15.3   0.1    1.5  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0073   16.3   0.0      0.037   14.0   0.0    2.1  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
  ------ inclusion threshold ------
      0.065   13.4   0.0       0.24   11.5   0.0    1.9  2  Mannitol_dh      Mannitol dehydrogenase Rossmann domain
       0.14   11.6   0.0       0.24   10.8   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> 6PGD  6-phosphogluconate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.2   0.0  1.5e-108  2.2e-105       1     289 []     178     464 ..     178     464 .. 0.98

  Alignments for each domain:
  == domain 1  score: 352.2 bits;  conditional E-value: 1.5e-108
                              6PGD   1 GhyVKmvHNGieygdmqliaEaydllkkvlglsneeiaevFeeWnkgelesyLieitakilrkkdeedgkplvdkil 77 
                                       Gh+VKmvHNGiey+ +qliaE+yd+++++lg s++ei+e+F++W+kg l+syL+ei+a+ l  kdee+g plv+ +l
  gi|557694253|ref|YP_008797307.1| 178 GHFVKMVHNGIEYALLQLIAETYDIMSRGLGKSAAEIGEIFRKWSKGLLSSYLLEIAADALMVKDEETGLPLVELVL 254
                                       9**************************************************************************** PP

                              6PGD  78 DkagqkGTgkwtvqealelgvpvptiaeavfaRllSslkeervkaskllkeeeekeeedkeefiedlrkAlyaskiv 154
                                       DkagqkGTg+wtvq+a+elgvp+p+i++av+aR++S+ ke r++++++      +++ ++++++e l++A+++s iv
  gi|557694253|ref|YP_008797307.1| 255 DKAGQKGTGRWTVQTAAELGVPTPSIDAAVAARNISAFKELRQRVAEKTG--PLTSRINAANVVEMLHDAYLCSAIV 329
                                       **********************************************9993..346777789**************** PP

                              6PGD 155 sYaqglellkaaskeygwnlnlaeiariWrgGCiIrakfldkikeafeknpelenllldpefakelkealealrrvv 231
                                       sY+qg++l+++ sk+yg++  l+++a++Wr+GCiIra++l+++++af++ +e e+lll++++++ +++++e +++++
  gi|557694253|ref|YP_008797307.1| 330 SYIQGFALISHGSKTYGYGTVLEDVAKVWRNGCIIRAALLKNFSDAFREGAEDESLLLTNTIHQLIQTRVEPWKQTL 406
                                       ***************************************************************************** PP

                              6PGD 232 alaveagipvpalsaalaYldslrserlpanliqaqrDyFGahtyervdkegkfhteW 289
                                       a++  agip+p++ a+l+Y+ s+ s++lpan+iqa rD FG+hty+r+dk g++h +W
  gi|557694253|ref|YP_008797307.1| 407 AHTHLAGIPTPVHDASLNYYLSIASAKLPANIIQALRDRFGSHTYQRIDKPGTYHSNW 464
                                       ********************************************************** 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 !  165.8   0.1   5.4e-52   8.1e-49       2     152 ..       5     162 ..       4     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 165.8 bits;  conditional E-value: 5.4e-52
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.....EEE-SSHHHHHHHC...SEEEE-SSSHHHHH CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.....akaaesieelvasl...dvvitmvkagkavd 70 
                                       +g+iGlGvMG+n+a+n++++gy v+vynrt+ek+e+lv++      +++ +s++elv++l   +++i+mv+agkavd
  gi|557694253|ref|YP_008797307.1|   5 VGLIGLGVMGENLARNIASKGYGVTVYNRTREKTERLVESVknildIRPSYSLAELVSKLekpRIIILMVEAGKAVD 81 
                                       8**************************************9889999******************************* PP

                                       HHHHSHCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-EEEEEEEESHHHHHHHT-EEEEEEE-HHHHHHHHHHHH CS
                     NAD_binding_2  71 eviegllealkkgdilidgstsspedtrelakelkekglkfldaPVSGGeegAekGtLsimvGGseeafervkpvle 147
                                       +v+e+l++ l++gd++ d+++s ++dt++++k ++ekg+ +++++VSGGeegA kG+ simvGG+ e +++++++ +
  gi|557694253|ref|YP_008797307.1|  82 SVLEELVPLLSPGDVVCDCGNSFFRDTERRQKTAAEKGVLLMGVGVSGGEEGALKGP-SIMVGGPFEGYHATEKLWK 157
                                       *********************************************************.******************* PP

                                       HHEEE CS
                     NAD_binding_2 148 aigak 152
                                       ai+ak
  gi|557694253|ref|YP_008797307.1| 158 AIAAK 162
                                       ***95 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   2.8e-10   4.3e-07      14      83 ..       4      74 ..       1      87 [. 0.80
   2 ?   -0.9   0.0       1.1   1.6e+03      39      59 ..     282     302 ..     261     320 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.8e-10
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EE...EEGCGHHHHHHT-SEEEE-S CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiea...lkleelkellaeadvvisat 83
                                      +v liG G m+e +a+++++kg+  v+v NRt+e+ ++l+e++k+  + +    +l el + l++  ++i  +
  gi|557694253|ref|YP_008797307.1|  4 EVGLIGLGVMGENLARNIASKGYG-VTVYNRTREKTERLVESVKNI-LDIrpsYSLAELVSKLEKPRIIILMV 74
                                      689********************9.******************776.54411145667777777777777655 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                                       EEEEESSHHHHHHHHHHHT.E CS
                      Shikimate_DH  39 vvvaNRtlerakelaeelkge 59 
                                        +va R+++  kel++++ ++
  gi|557694253|ref|YP_008797307.1| 282 AAVAARNISAFKELRQRVAEK 302
                                       579999999999999999655 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 !   27.8   0.0   1.9e-09   2.9e-06       2      96 ..       5     102 ..       4     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.9e-09
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC......-EEECECHHHHHHH-SEEEE-S-H. CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg......vkvtavdneeaaeeadvvvlavkp. 71 
                                       +g+iG G mge la++++++g   + ++v  +r+ ek e l e+++      ++ +  +    +e+  +++l v   
  gi|557694253|ref|YP_008797307.1|   5 VGLIGLGVMGENLARNIASKG---YGVTVY-NRTREKTERLVESVKnildirPSYSLAELVSKLEKPRIIILMVEAg 77 
                                       89*******************...****55.*************999988543333334444555899******973 PP

                                       HHHHHHHHHCGHHHHTTSEEEEESS CS
                     F420_oxidored  72 edveevlselakdalkgklvisvla 96 
                                       ++v++vl+el + ++ g +v ++ +
  gi|557694253|ref|YP_008797307.1|  78 KAVDSVLEELVPLLSPGDVVCDCGN 102
                                       67899*****999999999999876 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 !   25.4   0.0   7.4e-09   1.1e-05       2      47 ..       5      50 ..       4      86 .. 0.90
   2 ?   -1.2   0.1       1.1   1.6e+03       7      21 ..     169     183 ..     168     226 .. 0.71
   3 ?   -2.2   0.0       2.2   3.4e+03     171     171 ..     274     274 ..     247     324 .. 0.54

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 7.4e-09
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksle 47
                                      v+ iG G+mG+ +a  +as+g+ V+++++++e+ e+  e++++ l+
  gi|557694253|ref|YP_008797307.1|  5 VGLIGLGVMGENLARNIASKGYGVTVYNRTREKTERLVESVKNILD 50
                                      999************************************9998665 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                                       -SCCHHHHHHHHHHT CS
                           3HCDH_N   7 aGtmGagiaavfasa 21 
                                       aG mG+g a  f++ 
  gi|557694253|ref|YP_008797307.1| 169 AGYMGSGGAGHFVKM 183
                                       799999999888754 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.2
                                       T CS
                           3HCDH_N 171 g 171
                                       g
  gi|557694253|ref|YP_008797307.1| 274 G 274
                                       2 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.6e-07   0.00023       2     124 ..       6     125 ..       5     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.6e-07
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SS CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvK 77 
                                         +G+G +G  la ++a +g+ vt+++r+r + e+l++   ++ + +      p+ +l++   s+le+  ++i+ v 
  gi|557694253|ref|YP_008797307.1|   6 GLIGLGVMGENLARNIASKGYGVTVYNRTReKTERLVESVKNILDIR------PSYSLAEL-VSKLEKPRIIILMVE 75 
                                       579***************************77777777777777766......88888877.899************ PP

                                       GGGHHH.HHHHHGGGECTCEEEEEESSS.SCHHHHHTTTS.TTSEEEEEE CS
                              ApbA  78 ayqtee.aleeikplldpntvvlllqNG.lgheeelreal.pkprvlggv 124
                                       a  +++ +lee+ pll p  vv+ + N  ++  e+ ++    k  +l+gv
  gi|557694253|ref|YP_008797307.1|  76 AGKAVDsVLEELVPLLSPGDVVCDCGNSfFRDTERRQKTAaEKGVLLMGV 125
                                       *9988758999***********9999984333344444431333555555 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 !   17.8   0.0   2.1e-06    0.0031       1      98 [.       5     124 ..       5     165 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.1e-06
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...................TTTCEEEEE--T.. CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka...................lgvrfeaialda.. 56 
                                       v +iG G +G+ +a+ +a ++ +   +tv  r++ek e+l++++                    ++r+++  + a  
  gi|557694253|ref|YP_008797307.1|   5 VGLIGLGVMGENLARNIASKG-Y--GVTVYNRTREKTERLVESVknildirpsyslaelvsklEKPRIIILMVEAgk 78 
                                       6789**************997.5..7*****************9*******************99999999998722 PP

                                       ..TTHHHHHHHHHTTSSEEEE-SSGG..GHHHHHHHHHHHT-EEEE CS
                   Sacchrp_dh_NADP  57 ..enyeavLaallkegdlvvnlsppi..ssldvlkaCietgvhyvd 98 
                                         + + + L++ll+ gd+v ++  ++   ++   k+++e+gv+ + 
  gi|557694253|ref|YP_008797307.1|  79 avDSVLEELVPLLSPGDVVCDCGNSFfrDTERRQKTAAEKGVLLMG 124
                                       224455669999**********999988888999999999998875 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 !   16.8   0.0   2.2e-06    0.0033      38      77 ..       4      43 ..       2      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-06
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77
                                      +vG+iGlG +G+++a+ +++ g  v++y+r+++k+e+  e
  gi|557694253|ref|YP_008797307.1|  4 EVGLIGLGVMGENLARNIASKGYGVTVYNRTREKTERLVE 43
                                      69*****************************998874433 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 !   15.3   0.1   6.3e-06    0.0094      29     158 ..       3     125 ..       1     130 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.3e-06
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCH.HHHHHHHHHHH-SEEEE---BTTS CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqleslgakfvevlks.qeellaeavkeadvvigtvlipGk 104
                                       ++v  iG Gv G + +++ ++ g  Vtv++   ++ e+l +  +++++++ s + ++l +++++  ++i    + + 
  gi|557694253|ref|YP_008797307.1|   3 GEVGLIGLGVMGENLARNIASKGYGVTVYNRTREKTERLVESVKNILDIRPSySLAELVSKLEKPRIIIL--MVEAG 77 
                                       67889*************************9888887777655555888544144667777888899995..57888 PP

                                       S---SC-HHHHHTS-TTEEEEETTGGGT-SBTT--TBBTTSEEEEETTEEEEEB CS
                       AlaDh_PNT_C 105 kaPkLvteemvksMkpgsVivDvAidqGGnvetsrltthgepvveekgvvhygv 158
                                       ka   v ee v  + pg V+ D     G ++   r t+  +++  ekgv+++gv
  gi|557694253|ref|YP_008797307.1|  78 KAVDSVLEELVPLLSPGDVVCD----CGNSFF--RDTERRQKTAAEKGVLLMGV 125
                                       9999999**********77766....577777..99999999999999999997 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   2.5e-05     0.037       2     114 ..       5     112 ..       4     139 .. 0.73
   2 ?   -1.3   0.0       1.3   1.9e+03      63      96 ..     376     409 ..     369     440 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                                       EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE--. CS
                    NAD_Gly3P_dh_N   2 iavlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvv. 77 
                                       ++++G G  G  lA+ +a++g  v+++ r +e +e++ e+ +n   +   + + +l   ++l + l++ +ii+l v 
  gi|557694253|ref|YP_008797307.1|   5 VGLIGLGVMGENLARNIASKGYGVTVYNRTREKTERLVESVKNILDI---RPSYSL---AELVSKLEKPRIIILMVe 75 
                                       899**********************************9998887533...223222...344555555555555442 PP

                                       -HHHHHHHHHHHCCC--TT-EEEE---SEET.TTEEH CS
                    NAD_Gly3P_dh_N  78 PsqalrevlkklkgllkkkailvsliKGieegtlkll 114
                                         +a+ +vl++l +ll++  ++  +   + ++t ++ 
  gi|557694253|ref|YP_008797307.1|  76 AGKAVDSVLEELVPLLSPGDVVCDCGNSFFRDTERRQ 112
                                       5677888888888888777777776666655555555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                                       HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT CS
                    NAD_Gly3P_dh_N  63 laealkgadiivlvvPsqalrevlkklkgllkkk 96 
                                       ++e +++ ++++ +  +q +++ ++ +k++l++ 
  gi|557694253|ref|YP_008797307.1| 376 FREGAEDESLLLTNTIHQLIQTRVEPWKQTLAHT 409
                                       5678888999999999999999999999998654 PP

>> Mannitol_dh  Mannitol dehydrogenase Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00016      0.24      31     102 ..       6      78 ..       2     116 .. 0.77
   2 ?   -1.7   0.0         2   2.9e+03      93     143 ..     250     306 ..     243     307 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                                       EEEEEE-STTHHHHHHHTTTT-EEEEE-SSS---EEEE--EEEEEEGGG-..HHHHHHHHTSTT--EEEE---T CS
                       Mannitol_dh  31 givevnlrevdareaLkaqdelyvviekgeeskearlvgsvnavlsveed..lealieamaePeirivsltvte 102
                                       g+++++ + ++   +++ +    +v+ + + +k++rlv+sv+++l +  +  l++l+ ++++P+i i  +  ++
  gi|557694253|ref|YP_008797307.1|   6 GLIGLGVMGENLARNIASKGYGVTVYNR-TREKTERLVESVKNILDIRPSysLAELVSKLEKPRIIILMVEAGK 78 
                                       6666667777776667666555555555.9999************999876789********988776665554 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2
                                       --EEEE---TTT.....BETTTEB-TTSHHHHHHHH-TT.HHHHHHHHHHHTT---- CS
                       Mannitol_dh  93 irivsltvtekG.....idatgeletdlpaiaadlakpe.llvealkrrraaglkpl 143
                                       +++v    ++kG     ++++ el    p+i a +a  +   ++ l++r a++  pl
  gi|557694253|ref|YP_008797307.1| 250 VELVLDKAGQKGtgrwtVQTAAELGVPTPSIDAAVAARNiSAFKELRQRVAEKTGPL 306
                                       566666667777777655678888888999999888877566777888888877776 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00016      0.24       8      73 ..      11      75 ..       7      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                                      SHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHH.T-SEEEE--S CS
                         Epimerase  8 GfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkee.qpdavihlAa 73
                                      G +G +l++++++kgy v++ +r   +++t+rl +     ld++ + +l++l+++  +p ++i++  
  gi|557694253|ref|YP_008797307.1| 11 GVMGENLARNIASKGYGVTVYNRT--REKTERLVESVKNILDIRPSYSLAELVSKLeKPRIIILMVE 75
                                      99*************999988888..555666666667799999999*****999889999998855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3404.60
//
Query:       gi|557694254|ref|YP_008797308.1|  [L=105]
Description: transcriptional regulator, ArsR family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   57.7   0.2    1.2e-15   57.1   0.2    1.3  1  HTH_5            Bacterial regulatory protein, arsR family
    1.1e-10   41.4   0.0      2e-10   40.6   0.0    1.4  1  HTH_20           Helix-turn-helix domain
    5.4e-05   23.0   0.0     0.0001   22.1   0.0    1.4  1  MarR_2           MarR family
    5.5e-05   23.6   0.0    8.1e-05   23.0   0.0    1.3  1  HTH_27           Winged helix DNA-binding domain
    7.2e-05   22.5   0.1    0.00011   22.0   0.1    1.3  1  HTH_IclR         IclR helix-turn-helix domain
    0.00011   22.0   0.0    0.00018   21.3   0.0    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
    0.00014   22.0   0.0    0.00024   21.3   0.0    1.4  1  PaaX             PaaX-like protein
    0.00015   21.2   0.1    0.00037   20.0   0.0    1.7  2  HTH_24           Winged helix-turn-helix DNA-binding
     0.0018   18.6   0.2     0.0028   18.0   0.2    1.4  1  Rrf2             Transcriptional regulator
     0.0027   17.5   0.1     0.0037   17.1   0.1    1.3  1  HxlR             HxlR-like helix-turn-helix
     0.0062   17.0   0.1     0.0087   16.5   0.1    1.3  1  HTH_40           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.017   15.4   0.0    1.4  1  DUF223           Domain of unknown function DUF223
      0.012   15.3   0.0      0.014   15.1   0.0    1.1  1  DUF4423          Domain of unknown function (DUF4423)
      0.013   15.7   0.1       0.02   15.0   0.1    1.3  1  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
      0.021   14.8   0.1      0.033   14.1   0.1    1.3  1  HTH_11           HTH domain
      0.022   14.8   0.1      0.038   14.0   0.1    1.4  1  HTH_29           Winged helix-turn helix
      0.035   14.4   0.1      0.059   13.7   0.1    1.5  1  Penicillinase_R  Penicillinase repressor
      0.045   13.3   0.1      0.092   12.3   0.1    1.5  1  GerE             Bacterial regulatory proteins, luxR family
      0.048   13.7   0.0      0.075   13.0   0.0    1.3  1  HTH_45           Winged helix-turn-helix
      0.048   13.6   0.1      0.083   12.8   0.1    1.3  1  MarR             MarR family
       0.12   12.3   0.0       0.17   11.8   0.0    1.4  1  TFIIE_alpha      TFIIE alpha subunit
       0.17   12.2   0.0        4.8    7.5   0.0    2.4  2  Mnd1             Mnd1 HTH 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 !   57.1   0.2   1.4e-18   1.2e-15       1      47 []      24      70 ..      24      70 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 1.4e-18
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      +p+Rl IL++Laege++v+el+e+l + qstvS+HL++++  G+V++
  gi|557694254|ref|YP_008797308.1| 24 HPKRLMILHILAEGEKSVGELVEQLAIKQSTVSQHLAFMKRTGVVKS 70
                                      69*******************************************86 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   2.4e-13     2e-10       2      60 ..      17      74 ..      16      75 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.4e-13
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      +  +A ahP R++il  L  +++ +++el e+l ++++t+s+HL+ + + g v+++r+g
  gi|557694254|ref|YP_008797308.1| 17 EFCKAQAHPKRLMILHIL-AEGEKSVGELVEQLAIKQSTVSQHLAFMKRTGVVKSRRVG 74
                                      567899************.**************************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.2e-07    0.0001       7      55 ..      27      72 ..      24      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.2e-07
                                      HHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  7 qarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                       +++L+ L+ ++    +vgel++ l +++s+vs++l+ + + G v  r+
  gi|557694254|ref|YP_008797308.1| 27 RLMILHILAEGEK---SVGELVEQLAIKQSTVSQHLAFMKRTGVVKSRR 72
                                      5788999999998...***************************998775 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     1e-07   8.1e-05       7      66 ..      29      83 ..      24      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1e-07
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrre...krvrlTd 66
                                      ++Lh ++  +++k+  +l++ l + +s++s  l  + + G+v      ++rr    ++++lTd
  gi|557694254|ref|YP_008797308.1| 29 MILHILA--EGEKSVGELVEQLAIKQSTVSQHLAFMKRTGVV------KSRRVgntVFYSLTD 83
                                      89*****..*********************************......66666666******8 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 !   22.0   0.1   1.3e-07   0.00011       6      50 ..      28      70 ..      26      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.3e-07
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      l+iL +lae+     + el +++++  Stv+ +L+ + + G v+ 
  gi|557694254|ref|YP_008797308.1| 28 LMILHILAEGEKS--VGELVEQLAIKQSTVSQHLAFMKRTGVVKS 70
                                      89**********6..**************************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 !   21.3   0.0   2.2e-07   0.00018      17      67 ..      33      84 ..      30      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.2e-07
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE--H CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravdp 67
                                      +l++g++++ e+ e+l + +s+v + L  +++ G+V+ ++ g++ +Y+ +dp
  gi|557694254|ref|YP_008797308.1| 33 ILAEGEKSVGELVEQLAIKQSTVSQHLAFMKRTGVVKSRRvGNTVFYSLTDP 84
                                      799**********************************999677889999998 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   2.9e-07   0.00024      28      68 ..      43      83 ..      34      85 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 2.9e-07
                              PaaX 28 rllaelGiseslvRaalsRlakaGwlvrekegrrsfYrLsd 68
                                      +l+++l i++s+v   l  +++ G +++ ++g+ +fY+L+d
  gi|557694254|ref|YP_008797308.1| 43 ELVEQLAIKQSTVSQHLAFMKRTGVVKSRRVGNTVFYSLTD 83
                                      688999**********************************9 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 !   20.0   0.0   4.5e-07   0.00037       5      48 .]      27      69 ..      24      69 .. 0.89
   2 ?   -2.1   0.0       3.6   2.9e+03      23      37 ..      86     100 ..      81     102 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.5e-07
                            HTH_24  5 drkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ++ IL +L + +  s  eL e+l + +stv+++l  +++ G++k
  gi|557694254|ref|YP_008797308.1| 27 RLMILHILAE-GEKSVGELVEQLAIKQSTVSQHLAFMKRTGVVK 69
                                      5667777777.*******************************97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.6
                            HTH_24  23 LAerlglSpstvnrr 37 
                                       +Ae++ + ++ v++r
  gi|557694254|ref|YP_008797308.1|  86 IAEACSIISQVVRER 100
                                       777777766666666 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   3.4e-06    0.0028      15      59 ..      29      72 ..      23      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.4e-06
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      ++L   +e+e  s+ e+ e+  i++s +++ la +++ g+vks+r
  gi|557694254|ref|YP_008797308.1| 29 MILHILAEGE-KSVGELVEQLAIKQSTVSQHLAFMKRTGVVKSRR 72
                                      4454444544.689*****************************98 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   4.6e-06    0.0037       8      67 ..      28      83 ..      26     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.6e-06
                                      HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-T CS
                              HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYslte 67
                                      l+il+ l +g+k  +el ++l  i q++ +q+L  +++ g+++ +   +v++ v Yslt+
  gi|557694254|ref|YP_008797308.1| 28 LMILHILAEGEKSVGELVEQL-AIKQSTVSQHLAFMKRTGVVKSR---RVGNTVFYSLTD 83
                                      689******************.9*******************975...566778899997 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.1e-05    0.0087      10      49 ..      36      74 ..      29     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.1e-05
                            HTH_40 10 eeglsieeIAkerglkesTIegHLaelieegeeidlerlv 49
                                      e  +s+ e  ++  +k+sT+ +HLa + ++g  ++ +r+ 
  gi|557694254|ref|YP_008797308.1| 36 EGEKSVGELVEQLAIKQSTVSQHLAFMKRTGV-VKSRRVG 74
                                      6789*************************996.7777663 PP

>> DUF223  Domain of unknown function DUF223
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   2.1e-05     0.017      47      81 ..      49      83 ..      38     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-05
                            DUF223 47 siritkheyrilFmeqTeVtssktretvlfnnltp 81
                                      +i+ ++++  ++Fm++T V +s  + +++f++lt+
  gi|557694254|ref|YP_008797308.1| 49 AIKQSTVSQHLAFMKRTGVVKSRRVGNTVFYSLTD 83
                                      5788899999***********************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 ?   15.1   0.0   1.7e-05     0.014      27      95 ..      31      98 ..       5     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                           DUF4423 27 rellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgk...yrqtekslttssevkseavr 95
                                      +    l ++++++ el ++l   i+++ v++ l f++++g++k  + g+   y  t+  ++   ++ s++vr
  gi|557694254|ref|YP_008797308.1| 31 L--HILAEGEKSVGELVEQLA--IKQSTVSQHLAFMKRTGVVKSRRVGNtvfYSLTDPRIAEACSIISQVVR 98
                                      3..45677789**********..********************99886522266666666666666666665 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   0.1   2.5e-05      0.02      24      53 ..      40      69 ..      30      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.5e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 24 ktkdlaerLnvspssVsemlkkLekdGyve 53
                                      ++ +l e L+++ s+Vs+ l  +++ G v+
  gi|557694254|ref|YP_008797308.1| 40 SVGELVEQLAIKQSTVSQHLAFMKRTGVVK 69
                                      578999*********************987 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   4.1e-05     0.033       3      44 ..      28      67 ..      26      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      l il++L e +   s  eL e+L +  +tv ++++ ++ +gv
  gi|557694254|ref|YP_008797308.1| 28 LMILHILAEGE--KSVGELVEQLAIKQSTVSQHLAFMKRTGV 67
                                      56889994444..4**************************93 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   0.1   4.6e-05     0.038       1      49 [.      27      72 ..      27      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-05
                            HTH_29  1 RaqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrr 49
                                      R+++l  laeG+++v +++++l +  +tv  +l  +  +G+    ++rr
  gi|557694254|ref|YP_008797308.1| 27 RLMILHILAEGEKSVGELVEQLAIKQSTVSQHLAFMKRTGV---VKSRR 72
                                      899******************************99999994...44444 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   7.3e-05     0.059      12      65 ..      33      82 ..      26     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-05
                                      HHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE-- CS
                   Penicillinase_R 12 lwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYspl 65
                                      + ++ge +v+e+ve+l+ +    +sTV   l  + + g++++++ g++  Ys +
  gi|557694254|ref|YP_008797308.1| 33 ILAEGEKSVGELVEQLAIK----QSTVSQHLAFMKRTGVVKSRRVGNTVFYSLT 82
                                      5678889999999999988....****************************855 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00011     0.092       9      42 ..      29      63 ..      25      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                      HHHHHHCTT.S-HHHHHHHHTS-HHHHHHHHHHHH CS
                              GerE  9 evLrllaeG.ksnkeIAeelniSekTVkvhksnim 42
                                       +L+ laeG ks+ e  e+l i++ TV+ h++ + 
  gi|557694254|ref|YP_008797308.1| 29 MILHILAEGeKSVGELVEQLAIKQSTVSQHLAFMK 63
                                      69999****56889****************98765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.3e-05     0.075      11      60 ..      30      83 ..      27      84 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.3e-05
                            HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTe 60
                                      IL+++ ege++  +++ +  ++ +++++ L ++   g++      ++  Y+lT+
  gi|557694254|ref|YP_008797308.1| 30 ILHILAEGEKSVGELVEQLAIKQSTVSQHLAFMKRTGVVksrrVGNTVFYSLTD 83
                                      9**************************************554444666777775 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1    0.0001     0.083       6      50 ..      28      71 ..      25      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      ++iL+il+e g+ sv eL ++l +++stv+  l  + + G ++++
  gi|557694254|ref|YP_008797308.1| 28 LMILHILAE-GEKSVGELVEQLAIKQSTVSQHLAFMKRTGVVKSR 71
                                      567777765.999******************99988888877765 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0002      0.17      14      62 ..      26      73 ..      13     104 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                      HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                       TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrr 62
                                      +   +l++L+ +ge +  +l ++l i++  + + L+ ++  ++vk +r 
  gi|557694254|ref|YP_008797308.1| 26 KRLMILHILA-EGEKSVGELVEQLAIKQSTVSQHLAFMKRTGVVKSRRV 73
                                      5567788887.9*********************************9985 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0059       4.8      25      56 ..      48      79 ..      37      81 .. 0.87
   2 ?    2.1   0.0       0.3   2.4e+02      22      36 ..      87     101 ..      84     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0059
                              Mnd1 25 kgivsqsVkdvlqsLvdDglveveKiGssnvy 56
                                        i++ +V  +l  +   g+v++ ++G++ +y
  gi|557694254|ref|YP_008797308.1| 48 LAIKQSTVSQHLAFMKRTGVVKSRRVGNTVFY 79
                                      57899999999*99***************998 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.3
                              Mnd1  22 pkekgivsqsVkdvl 36 
                                       + +++i+sq V++ l
  gi|557694254|ref|YP_008797308.1|  87 AEACSIISQVVRERL 101
                                       4569********977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 847.00
//
Query:       gi|557694255|ref|YP_008797309.1|  [L=397]
Description: FAD-dependent pyridine nucleotide-disulphide oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   72.9   0.0      4e-19   68.9   0.0    2.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0083   16.1   0.1        4.6    7.2   0.0    2.3  2  NAD_binding_9   FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.011   16.3   0.0        9.8    6.8   0.0    3.3  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
       0.17   10.7   0.0       0.95    8.2   0.1    2.0  2  Trp_halogenase  Tryptophan halogenase


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 !   68.9   0.0     9e-23     4e-19       1     284 [.       2     302 ..       2     310 .. 0.73

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 9e-23
                                       CSEEEE--SHHHHHHHHHHHH........HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq........agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgiel 69 
                                       k+v+v+GgG +G+ +a  la          ++ vtlv ++  ++ +++   +++ + a++++ ++++ + l+  i++
  gi|557694255|ref|YP_008797309.1|   2 KRVAVVGGGTGGTLLANLLASklhreidsGKIAVTLV-SDSPHHVFQPANLEIAFHGAQPQKYIRKQNTLLSRRIQF 77 
                                       58*****************99999999866999****.888888888888777777777777777665677888999 PP

                                       CHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBE.ECCSECHHHHHHCCSS-T..S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx..x RF
                       Pyr_redox_2  70 llgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvg.klvrtldsaealklkllp..k 143
                                       l++  v ki  + +++       +++++++yd+lv+AtGs +    +pG+ae  + ++ +++d a+ ++   +    
  gi|557694255|ref|YP_008797309.1|  78 LNE-GVEKINIADRHLIT-----SSGNELDYDYLVIATGSVADPSLTPGLAEASVnFHTSPWDAAKVWQALSTFerG 148
                                       988.67777666666666.....56779***********99988899**9665540444667777666655554785 PP

                                       EEEEES-SH.....HHHHHHHHH.....HHHT-....EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEE CS
                                       xxxxxxxxx.....xxxxxxxxx.....xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGy.....iGvElAaal.....aklgk....evtlveardrllraldkelsaaleealekeGvevklgtsv 206
                                       ++v v +G+      +   A++l     +k g     e t +   ++ +    k ++++++  le++Gv+++   s+
  gi|557694255|ref|YP_008797309.1| 149 KVVLVIAGVphkcpPAPTEAMFLldeyfRKRGIrdrvELTFLTPYPHAY--PAKTIADIVQPMLEERGVNIVPFFSI 223
                                       5555556642222246677777444444555555544566666666666..4699********************** PP

                                       EEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EE.EETTEEE--TTSBE.S.STTEEE-GGGC.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.x.xxxxxxxxxxx.. RF
                       Pyr_redox_2 207 keidgngeklevvledgeeidadlvvvavGvrpstelleeklglel.derggivvdeflrt.n.vpgiyaiGDva.. 278
                                         +d+ g+  +vv  +gee+++dl++        ++++  ++  e+ d++g+i  d+++ t n  +++yaiGD +  
  gi|557694255|ref|YP_008797309.1| 224 DHVDSAGK--RVVSLEGEEVPYDLLIAVP----PHRGARVAIVSEIgDKDGWIPADKHYMTvNgYDDVYAIGDATni 294
                                       *******9..9*************98754....3334325555566799******998865578*********9944 PP

                                       ..TECCSS CS
                                       ..xxxxxx RF
                       Pyr_redox_2 279 ..ggkggp 284
                                         ++ g++
  gi|557694255|ref|YP_008797309.1| 295 piSKSGVV 302
                                       44333333 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 !    7.2   0.0     0.001       4.6       1      35 [.       5      42 ..       5      52 .. 0.77
   2 !    6.8   0.0    0.0014       6.1     116     155 ..      74     111 ..      61     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.001
                     NAD_binding_9  1 aivGaGprGlavlerLlara...kkkspleitlfdpse 35
                                      a+vG+G  G+++++ L+++     ++ ++ +tl+ +s+
  gi|557694255|ref|YP_008797309.1|  5 AVVGGGTGGTLLANLLASKLhreIDSGKIAVTLVSDSP 42
                                      89********9999998888765556667788776655 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0014
                     NAD_binding_9 116 tvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       +++++++ v++++ +++  ++++++g++l++d++v+A+G 
  gi|557694255|ref|YP_008797309.1|  74 RIQFLNEGVEKINIADR--HLITSSGNELDYDYLVIATGS 111
                                       67788888888887655..4899***************95 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0062        28       1      20 [.       3      22 ..       3      54 .. 0.73
   2 ?   -2.6   0.0       1.9   8.6e+03      21      35 ..      64      78 ..      58      86 .. 0.74
   3 ?   -1.0   0.0      0.59   2.6e+03      25      56 ..     151     182 ..     136     189 .. 0.74
   4 ?    6.8   0.0    0.0022       9.8      40      75 ..     200     235 ..     174     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0062
                                      EEEEECSSHHHHHHHHHHHH CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalae 20
                                      +v+vvGgG+ g  lA+ la 
  gi|557694255|ref|YP_008797309.1|  3 RVAVVGGGTGGTLLANLLAS 22
                                      79**********99999943 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.9
                                      TTSEEEEEESSSSSS CS
                         Pyr_redox 21 lgkkVtvversdkll 35
                                      ++k+ t++ r+ ++l
  gi|557694255|ref|YP_008797309.1| 64 IRKQNTLLSRRIQFL 78
                                      678889999999888 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.59
                                       EEEEESSSSSSTTSSHHHHHHHHHHHHHTTEE CS
                         Pyr_redox  25 VtvversdkllrllDeeaskilqeklekngie 56 
                                       V v+   ++ ++  + ea  +l e+++k+gi+
  gi|557694255|ref|YP_008797309.1| 151 VLVIAGVPHKCPPAPTEAMFLLDEYFRKRGIR 182
                                       44555555555677788888999999999996 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0022
                                       HHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEE CS
                         Pyr_redox  40 eeaskilqeklekngievllntkveeiegsedgves 75 
                                       +++++i+q  le++g++++   ++  ++  ++ v s
  gi|557694255|ref|YP_008797309.1| 200 KTIADIVQPMLEERGVNIVPFFSIDHVDSAGKRVVS 235
                                       789**********************99988776544 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.1   0.00021      0.95       1      26 [.       3      28 ..       3      46 .. 0.76
   2 ?   -0.5   0.0     0.098   4.4e+02     152     233 ..     198     274 ..     177     286 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00021
                                      EEEEE--SHHHHHHHHHHHHHTTTSS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgkl 26
                                      ++ +vGGGt G l A++la  l++++
  gi|557694255|ref|YP_008797309.1|  3 RVAVVGGGTGGTLLANLLASKLHREI 28
                                      689**************999886542 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.098
                                       -HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EEE-TTT CS
                    Trp_halogenase 152 daalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqaLktgfedwsdv 228
                                        a+  a++ + + e+rGv++v   + + +  +  rv sl   +g+ev +dl i    +rg  ++ +  +++ d   +
  gi|557694255|ref|YP_008797309.1| 198 PAKTIADIVQPMLEERGVNIVPFFSIDHVDSAGKRVVSL---EGEEVPYDLLIAVPPHRGARVAIV--SEIGDKDGW 269
                                       577888999999999999999888877777777777666...579999999999888888877777..777777777 PP

                                       ----E CS
                    Trp_halogenase 229 Lltdr 233
                                       ++ d+
  gi|557694255|ref|YP_008797309.1| 270 IPADK 274
                                       77775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3066.88
//
Query:       gi|557694256|ref|YP_008797310.1|  [L=81]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   69.2   0.0    2.1e-19   69.1   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 !   69.1   0.0   1.2e-23   2.1e-19       2      69 ..       8      75 ..       7      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1.2e-23
                                      EEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-EEEEEE CS
                              TusA  2 elDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelveveeedgeyrivir 69
                                      ++D rG  CP+Pl  l ka ++++ g+vle+la+dpaa+ d++++a+k+g+ ++ + ee+g++riv+r
  gi|557694256|ref|YP_008797310.1|  8 VIDSRGSFCPGPLTDLFKAYREAKNGDVLELLATDPAAKSDVQAWARKTGNVIEQIVEEQGYIRIVVR 75
                                      79**************************************************999999*********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 591.29
//
Query:       gi|557694257|ref|YP_008797311.1|  [L=166]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-49  165.6   1.1      8e-49  165.5   1.1    1.0  1  DrsE_2          DsrE/DsrF/DrsH-like family
      2e-14   54.0   0.0    6.1e-14   52.4   0.0    1.7  1  DrsE            DsrE/DsrF-like family
  ------ inclusion threshold ------
      0.016   14.6   0.0      0.018   14.4   0.0    1.2  1  Far-17a_AIG1    FAR-17a/AIG1-like protein
       0.08   12.8   0.1       0.15   11.9   0.0    1.5  2  SfsA            Sugar fermentation stimulation protein RE dom
       0.23   11.4   0.0       0.35   10.9   0.0    1.3  1  Glyco_transf_4  Glycosyltransferase Family 4


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 !  165.5   1.1   2.2e-52     8e-49       2     149 ..      16     162 ..      15     166 .] 0.94

  Alignments for each domain:
  == domain 1  score: 165.5 bits;  conditional E-value: 2.2e-52
                                       T-EEEEEE----H.HHHHHHHHHHHHHHTT-EEEEEE-GGGGGGGB-GGG---TT--HHHHHHHHHS-SS--SSS-G CS
                            DrsE_2   2 kkklaiifskgtldkalaalilAsgAaalglevtiFftFwGLnilrkeekkkvkkkslekmamkmvtrksklskmnm 78 
                                       + kl ii+skgtld+a++a++lA++Aaa+g+ev+iFftFwG+n++ k++ +++k +s++++a++m++     + + m
  gi|557694257|ref|YP_008797311.1|  16 TSKLCIILSKGTLDMAYPAFMLANAAAAMGYEVHIFFTFWGMNVIDKRKIDNLKVSSVGNPALPMPNL--LGALPGM 90 
                                       6799************************************************************9865..3467899 PP

                                       GGHHHHHHHHHHHHCT---HHHHHHHHHHTT-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHHHC-S CS
                            DrsE_2  79 agigtkmmkkvmkekgvasleeLleaakeagvklvaCqmtmdlmglkkeelidgv.eiagaatylkeaeead 149
                                       + + tkm+k++m ++ v++++eL+++akeagvkl aC  tmd+mgl+ke++i++v  i+gaa++++  e ++
  gi|557694257|ref|YP_008797311.1|  91 TAMVTKMLKNKMAKQRVPTIRELIKTAKEAGVKLHACSTTMDVMGLRKEDFIPEVdDIVGAASFIQMSEGGQ 162
                                       9****************************************************************9776655 PP

>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   1.7e-17   6.1e-14       2     107 ..      18     157 ..      17     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 1.7e-17
                                       EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT-EEEEEE-GGGGGGGBS.............................. CS
                              DrsE   2 kvfilvtggpygseaarealelalaaaalghevsvffygdGvllllk.............................. 48 
                                       k++i+ ++g  + ++a+ a++la+aaaa+g+ev++ff+  G +++ k                              
  gi|557694257|ref|YP_008797311.1|  18 KLCIILSKG--TLDMAYPAFMLANAAAAMGYEVHIFFTFWGMNVIDKrkidnlkvssvgnpalpmpnllgalpgmta 92 
                                       678888866..8899************************************************************** PP

                                       ......---TGGGTS---GGGGGGCGGGT-EEEEEHHHHHHTT--GGGE-.T--EEEE-HHHHHHH CS
                              DrsE  49 ......gqtanpadeknlaellkalkeygvklyvCgqaakargldededl.gvgvevsglgelael 107
                                             +++ ++++ + + el+k++ke+gvkl++C ++++ +gl +++ + +    ++g+++++++
  gi|557694257|ref|YP_008797311.1|  93 mvtkmlKNKMAKQRVPTIRELIKTAKEAGVKLHACSTTMDVMGLRKEDFIpE-VDDIVGAASFIQM 157
                                       ******88899999*******************************7665543.4556666666665 PP

>> Far-17a_AIG1  FAR-17a/AIG1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     5e-06     0.018      72     111 ..      36      83 ..      17     126 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5e-06
                      Far-17a_AIG1  72 llavlafPv..evlvsvlFWgLyliDrelvypklldel......ipdW 111
                                       +la +a+ +  ev ++++FWg+ +iD++ + +  ++++      +p++
  gi|557694257|ref|YP_008797311.1|  36 MLANAAAAMgyEVHIFFTFWGMNVIDKRKIDNLKVSSVgnpalpMPNL 83 
                                       55555555522799**************99777776665555554444 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 ?   -3.5   0.0       2.5     9e+03      82      94 ..      41      53 ..      39      58 .. 0.79
   2 ?   11.9   0.0   4.3e-05      0.15     101     135 ..      98     132 ..      89     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.5
                                      HHHTT-EEEEEEE CS
                              SfsA 82 lvkegyravvlfv 94
                                      ++++gy+  ++f 
  gi|557694257|ref|YP_008797311.1| 41 AAAMGYEVHIFFT 53
                                      6788999999886 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.3e-05
                                       -EEEE-TTT-HHHHHHHHHHHHHT-EEEEEEEEE- CS
                              SfsA 101 refkpnkeidpefaealreaaeaGVevlaydckvt 135
                                        + k++k+  p + e++++a+eaGV+++a++++++
  gi|557694257|ref|YP_008797311.1|  98 LKNKMAKQRVPTIRELIKTAKEAGVKLHACSTTMD 132
                                       5668899999********************99987 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.7e-05      0.35       9      59 ..      35      89 ..      33     118 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.7e-05
                    Glyco_transf_4  9 leLaraLarrGheVtvv.tpgddgpleeev...elvvrvprvplpllkrllrsla 59
                                      + La+a a++G+eV+++ t+++   ++++      v +v+ + lp ++ l+  + 
  gi|557694257|ref|YP_008797311.1| 35 FMLANAAAAMGYEVHIFfTFWGMNVIDKRKidnLKVSSVGNPALPMPNLLGALPG 89
                                      579**************55555555555546654444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      668  (0.0372581); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1285.70
//
Query:       gi|557694258|ref|YP_008797312.1|  [L=539]
Description: DNA topoisomerase I [Candidatus Caldiarchaeum subterraneum]
Scores for 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  232.6   3.3    5.3e-69  232.0   3.3    1.3  1  Topoisom_I       Eukaryotic DNA topoisomerase I, catalytic co
    1.2e-68  230.8   0.5    1.2e-68  230.8   0.5    2.8  2  Topoisom_I_N     Eukaryotic DNA topoisomerase I, DNA binding 
    7.1e-17   61.1   0.4    7.1e-17   61.1   0.4    2.9  3  Topo_C_assoc     C-terminal topoisomerase domain
  ------ inclusion threshold ------
      0.025   14.2   1.4        2.7    7.6   0.0    2.4  2  DCB              Dimerisation and cyclophilin-binding domain 
      0.033   14.1   0.3      0.077   12.9   0.3    1.6  1  Armet            Degradation arginine-rich protein for mis-fo
      0.087   12.7   0.0       0.19   11.6   0.0    1.5  1  DUF2631          Protein of unknown function (DUF2631)
       0.23   10.8   0.0       0.23   10.8   0.0    3.3  4  PIN_5            PINc domain ribonuclease
        1.1    9.5   8.4          3    8.2   3.4    3.2  3  NES_C_h          Nicking enzyme C-terminal middle helical dom
        1.4    9.5   6.6       0.29   11.7   0.4    2.9  3  BST2             Bone marrow stromal antigen 2
        5.5    7.4  16.3       0.61   10.5   6.4    2.7  3  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
        8.4    6.9  14.2        9.4    6.8   8.8    2.6  2  APG6_N           Apg6 coiled-coil region
          9    6.9   7.8         59    4.3   4.3    2.9  2  Glycohydro_20b2  beta-acetyl hexosaminidase like


Domain annotation for each model (and alignments):
>> Topoisom_I  Eukaryotic DNA topoisomerase I, catalytic core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.0   3.3   3.6e-72   5.3e-69       3     230 ..     215     441 ..     213     443 .. 0.97

  Alignments for each domain:
  == domain 1  score: 232.0 bits;  conditional E-value: 3.6e-72
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHHHHHHHH---------TTS-----GGG-BGGG CS
                        Topoisom_I   3 klkgekdfkKYekarkLkkvvekiredykkklkskeilekqlatavylidklaLrvGnekeeeeadtvGccsLrveh 79 
                                       ++k+++d++KY+ka+ L+++++++re++ k l+ske + +++a+a+ylid+la+rvG+ek+ +eadtvG ++Lrveh
  gi|557694258|ref|YP_008797312.1| 215 DIKQKRDKSKYDKAEMLESHIDRVREKIFKGLRSKEPKMREIALACYLIDRLAMRVGDEKDPDEADTVGATTLRVEH 291
                                       79*************************************************************************** PP

                                       EEE-TT.SEEEEEEE-GGG-EEEEEEE--H...HHHHHHHHHHTT--TTSBTTTT--HHHHHHHHTTTSTT--TTHH CS
                        Topoisom_I  80 vklsekektitldFlGKdsiryfntvkvdk...qvyknlkifckkkkkgeevFdkintsklNkyLkelmegLsAKvF 153
                                       vkl e+  +i++dFlGKds+r++++++++k   +v ++++++ + kk+g+++F++in++++N++L ++++gL+AKvF
  gi|557694258|ref|YP_008797312.1| 292 VKLLED--RIEFDFLGKDSVRWQKSIDLRKeppEVRQVFEELLEGKKEGDQIFQNINSRHVNRFLGKIVKGLTAKVF 366
                                       **9997..*********************9888999999************************************** PP

                                       HHHHHHHHHHHHHHH..--------TTHHHHHHHHHHHHHHHHHT-EE-XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Topoisom_I 154 RTYnASitlqeqLkklekievdesnvaekikayneAnreVAilcnhqrsvpkqheksmeklkkkiealkedikelkk 230
                                       RTY A+ ++++ L ++   +++++++++ i   + An + A  +nh+r+ pk+ e+s++k ++++++l ++++e+++
  gi|557694258|ref|YP_008797312.1| 367 RTYIATKIVKDFLAAI--PREKVTSQERFIYYAKLANLKAAEALNHKRAPPKNWEQSIQKKEERVKKLMQQLREAES 441
                                       ***************9..6889999***********************************************99875 PP

>> Topoisom_I_N  Eukaryotic DNA topoisomerase I, DNA binding fragment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.8   0.5   8.3e-72   1.2e-68       1     213 []       2     210 ..       2     210 .. 0.95
   2 ?   -2.3   4.0       1.7   2.6e+03      81      81 ..     391     391 ..     309     468 .. 0.52

  Alignments for each domain:
  == domain 1  score: 230.8 bits;  conditional E-value: 8.3e-72
                                       ---S-EE----B---------TT--EEETTEEE---HHHHHHHHHHHHTTTSSGGG-HHHHHHHHHHHHHHHHHTT- CS
                      Topoisom_I_N   1 vkWktLehnGvlfppeYeplpknvklkydgkpvkLspeaEEvatfyaamletdyakkevFqknffkdfkkvlkekek 77 
                                       vkW+tL hnGv++pp+Y+  pk++++k++g++vkL+p +EE+a+ +a +++t y++++vFqknf++df k+++ + +
  gi|557694258|ref|YP_008797312.1|   2 VKWRTLVHNGVALPPPYQ--PKGLSIKIRGETVKLDPLQEEMAYAWALKKDTPYVQDPVFQKNFLTDFLKTFNGRFQ 76 
                                       69****************..********************************************************* PP

                                       ---GGGEE-HHHHHHHHHHHHHHT..T-----HHHHHHHHHHHHHHHHEEEETTEEEEEE--B----EE----TT-T CS
                      Topoisom_I_N  78 ikelekcdFskikeylekekekkk..altkeekkklkeekekleekygyalldgrkekvgnfrvepPgLfrgrGehp 152
                                         +++++dFs+++ey+e+e++ k   +  k+   + k+ +e+l+++yg+a +dg++ +++n++vepPg+f+grG+hp
  gi|557694258|ref|YP_008797312.1|  77 DVTINEIDFSEVYEYVERERQLKAdkEYRKKISAERKRLREELKARYGWAEMDGKRFEIANWMVEPPGIFMGRGNHP 153
                                       *******************9988611334444455689999************************************ PP

                                       TTT-EE----GGG-EEE--SSS-----STT---SEEE--TT---SEEEE-TTT--EEEEEE CS
                      Topoisom_I_N 153 ktGklkkrvlpedvtiNigkdakvPeppaghkWkevvhdntvtwlaswkeningqvkyvmL 213
                                        +G++k rv+ ed+t+N+g+da+vP+     +W+++vhd++++wla w+++++g+ kyv+L
  gi|557694258|ref|YP_008797312.1| 154 LRGRWKPRVYEEDITLNLGEDAPVPPG----NWGQIVHDHDSMWLARWDDKLTGKEKYVWL 210
                                       *************************97....9***************************98 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                                       G CS
                      Topoisom_I_N  81 l 81 
                                        
  gi|557694258|ref|YP_008797312.1| 391 E 391
                                       2 PP

>> Topo_C_assoc  C-terminal topoisomerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.8   8.6e+03      58      66 ..      43      51 ..      33      65 .. 0.66
   2 ?   -3.0   1.3       4.8   7.1e+03       1      19 [.     426     444 ..     426     446 .. 0.86
   3 !   61.1   0.4   4.8e-20   7.1e-17       2      64 ..     450     512 ..     449     517 .. 0.96

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.8
                      Topo_C_assoc 58 faWAmevde 66
                                      +aWA++ d+
  gi|557694258|ref|YP_008797312.1| 43 YAWALKKDT 51
                                      445555443 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.8
                      Topo_C_assoc   1 kekikklklqlkdkeenke 19 
                                       +e++kkl  ql++ e+ k+
  gi|557694258|ref|YP_008797312.1| 426 EERVKKLMQQLREAESEKK 444
                                       5899*******99999886 PP

  == domain 3  score: 61.1 bits;  conditional E-value: 4.8e-20
                      Topo_C_assoc   2 ekikklklqlkdkeenkevaLgtSkinYlDPRitvawckkhdvpiekiFsktlleKfaWAmev 64 
                                       e+++k++l+l+   ++++++L+tS  nY+DPR+  aw + ++ ++ ki++++ll+Kf+W+ ++
  gi|557694258|ref|YP_008797312.1| 450 ERLEKAELNLDLAVKVRDYNLATSLRNYIDPRVYKAWGRYTGYEWRKIYTASLLRKFKWVEKA 512
                                       89*********************************************************9875 PP

>> DCB  Dimerisation and cyclophilin-binding domain of Mon2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0018       2.7      40      82 ..     217     260 ..     204     275 .. 0.80
   2 ?    4.3   0.9     0.018        27       7      63 ..     429     480 ..     422     485 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0018
                               DCB  40 ktikssseee.eqslaeaseeilkPlllacetknpkivqiaLgs 82 
                                       k+ +++s+ +  + l ++++ + + ++++  +k+pk+ +iaL++
  gi|557694258|ref|YP_008797312.1| 217 KQKRDKSKYDkAEMLESHIDRVREKIFKGLRSKEPKMREIALAC 260
                                       45555554444778888899**********************99 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.018
                               DCB   7 lealqsdlkalsseskrkhskvkeasekgilkLktikssseeeeqslaeaseeilkP 63 
                                       +++l ++l+   +es++k+++++e  ek+ l+L  + +     +++la +  +++ P
  gi|557694258|ref|YP_008797312.1| 429 VKKLMQQLR--EAESEKKKARIAERLEKAELNLDLAVKVR---DYNLATSLRNYIDP 480
                                       445555555..47999******************999999...88888888888877 PP

>> Armet  Degradation arginine-rich protein for mis-folding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   5.2e-05     0.077       7      95 ..     352     444 ..     347     467 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                             Armet   7 kflerllkslkekeke...sekkiekelkkvCkeakgkenrlCyylgale.daatkilsevskplsvsvPvekiCek 79 
                                       +fl +++k l++k  +    +k +++ l+ + +e+   ++r+ yy    + +aa  + ++ + p +++  ++k  e+
  gi|557694258|ref|YP_008797312.1| 352 RFLGKIVKGLTAKVFRtyiATKIVKDFLAAIPREKVTSQERFIYYAKLANlKAAEALNHKRAPPKNWEQSIQKKEER 428
                                       67888888888887664435677788888888999999*******98766155555666778899************ PP

                             Armet  80 lkkkdsqicelkyekk 95 
                                       +kk  +q+ e   ekk
  gi|557694258|ref|YP_008797312.1| 429 VKKLMQQLREAESEKK 444
                                       *********9998887 PP

>> DUF2631  Protein of unknown function (DUF2631)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.19      20      52 ..     120     152 ..     100     156 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                           DUF2631  20 SaaWGWsgespkttriaGlisvlallamliGnh 52 
                                        a++GW ++  k ++ia +++    ++m +Gnh
  gi|557694258|ref|YP_008797312.1| 120 KARYGWAEMDGKRFEIANWMVEPPGIFMGRGNH 152
                                       599*****************************9 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       1.5   2.2e+03     116     149 ..      89     119 ..      41     124 .. 0.55
   2 ?   10.8   0.0   0.00015      0.23      89     125 ..     227     263 ..     208     290 .. 0.83
   3 ?    0.8   0.8      0.19   2.8e+02      79     143 ..     361     438 ..     320     451 .. 0.49
   4 ?   -0.5   0.1      0.45   6.7e+02      26      59 ..     444     478 ..     429     537 .. 0.43

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                             PIN_5 116 reaaeeseklekeeeeeevgelikklRekYreal 149
                                       +e +e++    + + ++e  + i+  R++ re l
  gi|557694258|ref|YP_008797312.1|  89 YEYVERER---QLKADKEYRKKISAERKRLREEL 119
                                       33333333...33345555555555555555544 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00015
                             PIN_5  89 paeilyeyveevrerinkGlrvaEeavreaaeesekl 125
                                        ae+l  +++ vre+i kGlr  E ++re a +++ +
  gi|557694258|ref|YP_008797312.1| 227 KAEMLESHIDRVREKIFKGLRSKEPKMREIALACYLI 263
                                       589**************************99988866 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.19
                             PIN_5  79 kspdryevkipaeilyeyveev.rerinkGlrvaEeavreaaeesekl....ekee..............eeeevge 136
                                        + + + + i ++i++++++ + re+++   r     ++ a+ ++ k+    +  +              +ee v++
  gi|557694258|ref|YP_008797312.1| 361 LTAKVFRTYIATKIVKDFLAAIpREKVTSQER----FIYYAKLANLKAaealN--HkrappknweqsiqkKEERVKK 431
                                       34455555566666666655554444443322....22222222222211111..0122333444444445666666 PP

                             PIN_5 137 likklRe 143
                                       l+++lRe
  gi|557694258|ref|YP_008797312.1| 432 LMQQLRE 438
                                       6666665 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.45
                             PIN_5  26 avkklldliaearlklgiscyip.psvykElkefl 59 
                                         +++ + +++a+l+l++ + +      + l++++
  gi|557694258|ref|YP_008797312.1| 444 KKARIAERLEKAELNLDLAVKVRdYNLATSLRNYI 478
                                       55555555555555555544443333333333333 PP

>> NES_C_h  Nicking enzyme C-terminal middle helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.5   2.2e+03      66      90 ..     226     250 ..     203     271 .. 0.70
   2 ?    1.8   0.0       0.2   2.9e+02      35     100 ..     310     375 ..     305     380 .. 0.64
   3 ?    8.2   3.4     0.002         3      24      74 ..     406     456 ..     398     467 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.5
                           NES_C_h  66 eAdellnkeadrlveklYpelDiee 90 
                                          e+l+   dr+ ek ++ l  +e
  gi|557694258|ref|YP_008797312.1| 226 DKAEMLESHIDRVREKIFKGLRSKE 250
                                       3346777778888887777665544 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.2
                           NES_C_h  35 nWknStlikkavgedktkql.eeiekqeelleeAdellnkeadrlveklYpelDieeltkaekreli 100
                                       +W++S+ ++k+   ++ + + e +e ++e  +  +++ ++ ++r++ k  + l  + + ++   +++
  gi|557694258|ref|YP_008797312.1| 310 RWQKSIDLRKEPP-EVRQVFeELLEGKKEGDQIFQNINSRHVNRFLGKIVKGLTAKVFRTYIATKIV 375
                                       6999999999843.33333313345555555666677777888888888777766666666555555 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.002
                           NES_C_h  24 esieekkrmLknWknStlikkavgedktkqleeiekqeelleeAdellnke 74 
                                       e ++ k+   knW++S++ k++  ++ ++ql+e e++++  + A+ l + e
  gi|557694258|ref|YP_008797312.1| 406 EALNHKRAPPKNWEQSIQKKEERVKKLMQQLREAESEKKKARIAERLEKAE 456
                                       7789999999************99999************999999876555 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       1.6   2.4e+03      50      82 ..      98     119 ..      80     123 .. 0.51
   2 ?   -1.0   0.1       1.8   2.7e+03      45      82 ..     205     242 ..     194     250 .. 0.77
   3 ?   11.7   0.4   0.00019      0.29      52      90 ..     406     444 ..     348     445 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  50 LkasLekekaqsqkqqakvqelqgeikkLnqkL 82 
                                       Lka+ e  k  s ++           k+L ++L
  gi|557694258|ref|YP_008797312.1|  98 LKADKEYRKKISAER-----------KRLREEL 119
                                       333333333333333...........3333333 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  45 qtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkL 82 
                                       +  v L++  + ++ + + +  k++ l+  i +  +k+
  gi|557694258|ref|YP_008797312.1| 205 EKYVWLSDTADIKQKRDKSKYDKAEMLESHIDRVREKI 242
                                       55666777788888888888899999999999988887 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                              BST2  52 asLekekaqsqkqqakvqelqgeikkLnqkLqdaeaeve 90 
                                       ++L++++a  +++++ +q+ ++ +kkL q+L++ae e +
  gi|557694258|ref|YP_008797312.1| 406 EALNHKRAPPKNWEQSIQKKEERVKKLMQQLREAESEKK 444
                                       5799999999************************99976 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 ?    3.2   0.3     0.073   1.1e+02      34      63 ..      92     121 ..      84     127 .. 0.76
   2 ?   -2.9   0.1       5.8   8.6e+03      40      59 ..     221     240 ..     210     251 .. 0.56
   3 ?   10.5   6.4   0.00041      0.61      33      83 ..     401     458 ..     389     467 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.073
                       Uso1_p115_C  34 leqkeakkaaesqakeleaenkklekelek 63 
                                        e++ ++ka ++  k+++ae+k+l++el++
  gi|557694258|ref|YP_008797312.1|  92 VERERQLKADKEYRKKISAERKRLREELKA 121
                                       344444777888899999999999999986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.8
                       Uso1_p115_C  40 kkaaesqakeleaenkklek 59 
                                        k+   +a++le+ ++++++
  gi|557694258|ref|YP_008797312.1| 221 DKSKYDKAEMLESHIDRVRE 240
                                       33344455555555555554 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00041
                       Uso1_p115_C  33 sleqkeakkaaesqakeleaenkklekeleklraelkeekekekek.......qkEld 83 
                                       +l+ +ea+++ ++  k++e++++k e++++kl ++l+e+++++k++       ++El+
  gi|557694258|ref|YP_008797312.1| 401 NLKAAEALNHKRAPPKNWEQSIQKKEERVKKLMQQLREAESEKKKAriaerleKAELN 458
                                       45555789999999************************99988866899888888887 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.2      0.15   2.3e+02      48      71 ..      97     120 ..      64     124 .. 0.55
   2 ?    6.8   8.8    0.0063       9.4      22      93 ..     389     456 ..     384     474 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.15
                            APG6_N  48 eleeleeeleklekeeeelleeLk 71 
                                       +l++ +e  +k+++e+++l eeLk
  gi|557694258|ref|YP_008797312.1|  97 QLKADKEYRKKISAERKRLREELK 120
                                       222222223333333333333333 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0063
                            APG6_N  22 ekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelea 93 
                                        +er  Y + l++lk+ +  + +++   ++ e++++k e+  ++l+++L+e+e+e+++ + +    + e+++
  gi|557694258|ref|YP_008797312.1| 389 SQERFIYYAKLANLKAAEALN-HKRAPPKNWEQSIQKKEERVKKLMQQLREAESEKKKARIA---ERLEKAE 456
                                       678888999999999996665.478999999********************99998765432...2233333 PP

>> Glycohydro_20b2  beta-acetyl hexosaminidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       4.5   6.7e+03      82     112 ..      76     109 ..      35     120 .. 0.61
   2 ?    4.3   4.3     0.039        59      14      59 ..     207     312 ..     197     493 .. 0.53

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.5
                   Glycohydro_20b2  82 ktvevsltsekse...ae.eltlevdEsYtLsvks 112
                                       + v ++  + +++    e e +l+ d++Y+ ++ s
  gi|557694258|ref|YP_008797312.1|  76 QDVTINEIDFSEVyeyVErERQLKADKEYRKKI-S 109
                                       444444433332222234455777777777666.3 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.039
                   Glycohydro_20b2  14 tlrlspsnfrlkvesaaseaveellheafdrtlkelfkskvvpwa................................ 58 
                                        ++ls      + +++++ +++e+l++++dr+++++fk  +++ +                                
  gi|557694258|ref|YP_008797312.1| 207 YVWLSDTADIKQKRDKSKYDKAEMLESHIDRVREKIFKGLRSKEPkmreialacylidrlamrvgdekdpdeadtvg 283
                                       55555433222223333566789999999999999999999888855555555555555555555555555555555 PP

                   Glycohydro_20b2  59 ............................k 59 
                                                                   +
  gi|557694258|ref|YP_008797312.1| 284 attlrvehvklledriefdflgkdsvrwQ 312
                                       55555555555444444444444444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2254  (0.125718); expected 358.6 (0.02)
Passed bias filter:                      921  (0.0513693); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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):              12  [number of targets reported over threshold]
# CPU time: 0.74u 0.30s 00:00:01.04 Elapsed: 00:00:00.45
# Mc/sec: 3572.74
//
Query:       gi|557694259|ref|YP_008797313.1|  [L=143]
Description: nuclear ribonucleoprotein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-23   81.8   0.6    6.1e-23   80.4   0.1    1.8  2  Lsm_C     Lsm C-terminal


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 ?   -0.9   0.0      0.08   1.4e+03      30      41 ..      17      30 ..      11      34 .. 0.52
   2 !   80.4   0.1   3.4e-27   6.1e-23       4      63 .]      80     139 ..      78     139 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.08
                                      ETTTE.E.EETTEE CS
                             Lsm_C 30 vldri.k.VsekGV 41
                                      ++dr+ k V+ +GV
  gi|557694259|ref|YP_008797313.1| 17 IMDRVvKvVTSSGV 30
                                      34443222455555 PP

  == domain 2  score: 80.4 bits;  conditional E-value: 3.4e-27
                                       HHHHHHHHS...TTTEEEETTTTEEEETTTEEEETTEEE--SHHHHHHHHHHHHHHH-.. CS
                             Lsm_C   4 FaelvekelnlrpglVkvieeanvvvvldrikVsekGVeGsGplAervyelyeeYiekkk 63 
                                       +++lve+ ++l+p+lV +++e++++vv+dri+Vs++GV G+Gp+Aerv+++yee+++++k
  gi|557694259|ref|YP_008797313.1|  80 MSALVERLNRLFPNLVVYHKESDTIVVMDRIRVSREGVFGEGPAAERVRKVYEEFMREQK 139
                                       6799*****************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 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:                        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 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1097.09
//
Query:       gi|557694260|ref|YP_008797314.1|  [L=434]
Description: citrate transporter [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  111.3  29.5    4.8e-32  111.3  29.5    1.7  2  CitMHS         Citrate transporter
    5.6e-09   35.6  19.1     0.0012   18.0   8.6    3.1  3  Na_sulph_symp  Sodium:sulfate symporter transmembrane region


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 !  111.3  29.5   5.4e-36   4.8e-32      11     298 ..      41     376 ..      29     382 .. 0.79
   2 ?   -0.3   0.9     0.054   4.9e+02     121     168 ..     377     433 ..     366     434 .] 0.46

  Alignments for each domain:
  == domain 1  score: 111.3 bits;  conditional E-value: 5.4e-36
                                       xxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  11 ldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrdllvllvllta 83 
                                       +  v++l ++l+    +++++eal+ i+ ++i+ll+g++ ++++ e++Gl d+++  +l+++++ r++l++ +ll +
  gi|557694260|ref|YP_008797314.1|  41 IWSVMILSASLTlllgLVGMDEALQLIDMDVIMLLIGMFALVGMAEHSGLLDFISSYFLSKVRRTRTMLIMASLLFG 117
                                       44555555555566679**********************************************99999999****** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                            CitMHS  84 llsafvsndgvvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnlll....... 153
                                       l+saf+ nd+v+l+  pi++ ++k+l+++  +++++l l+  ig+++tpiG+p            +n+l+       
  gi|557694260|ref|YP_008797314.1| 118 LMSAFFVNDTVALMGPPIAVLIGKSLGGRYEAAILLLCLSITIGSVMTPIGNP------------QNILIalqsgmk 182
                                       *****************************************************............666666666666 PP

                                       ....................xxxxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 154 ....................lalllvgl.......................lplvllfmfgvalalpvnapkvkkqk 187
                                                           ++l+++ l                       ++l+l++   ++ al+vn    +   
  gi|557694260|ref|YP_008797314.1| 183 spfiefltrlaaptllsliiTPLIITKLykipkedvvvpidpwetvrsrreFYLALFGGSVTVAALIVNDVLAAL-- 257
                                       666666665555444333335555555577777777777788888888888888888877777777777543333.. PP

                                       xxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x.xxxxxxx RF
                            CitMHS 188 aiieaiarsllpvatillla.........ykkveWsvlllfaGvfllvgaleqtGilealadllga..g.gplvala 252
                                             +r+l+p +++ +l+         + +v+++++l+f G+f+ v+++ ++ +l  l +++++  + gp + l+
  gi|557694260|ref|YP_008797314.1| 258 GQPHITSRGLIPFVSAAALWiltdtpreiLSRVDFGTILFFLGMFITVEGVWRSQVLSPLFSMMNSgnPaGP-MGLL 333
                                       23334568888888888888999*****************************************77542466.4456 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 253 lvlgliallsafisnvavaalmapialgmapalgllspsplalala 298
                                        +++++ ++s++isnv+++ l +  + gm  +    + ++++l+la
  gi|557694260|ref|YP_008797314.1| 334 QLTIISLVMSQLISNVPFTKLAIQQLTGMGVG---GHDVEVWLTLA 376
                                       66888888**********86666666665554...23444666665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.054
                                       xxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxx.....xxxxxxxxxxxxxxx RF
                            CitMHS 121 alaaniggaltpiGtpttraa...........arpglslpnlll.....lalllvgllplvllf 168
                                       a         t+ G++t+++a            r g+++p+l +     ++ ++ + ++l +l+
  gi|557694260|ref|YP_008797314.1| 377 AS-------STLAGGITVLGAasnvivlevleSRYGQTIPYLRFakigfIVTVVSLCIYLPFLM 433
                                       33.......3444444444444444444555533333333333366665555555555555554 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 !   18.0   8.6   1.3e-07    0.0012     274     432 ..      19     175 ..       5     178 .. 0.71
   2 !    9.7   0.0   4.2e-05      0.38     205     304 ..     175     303 ..     173     315 .. 0.84
   3 !   12.1   3.7     8e-06     0.071     401     460 ..     366     430 ..     308     434 .] 0.67

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.3e-07
                     Na_sulph_symp 274 ilfvlllll..Wifge.slnidattvaivvlvillllrvldWkDivkqktaWntllllgglialakllersgliewl 347
                                       +l+vl lll   + ++ ++++    v i+  ++ lll ++  +    q    ++++ll g+ al  + e+sgl++++
  gi|557694260|ref|YP_008797314.1|  19 GLVVLGLLLggVVLRGrFPKVPIWSVMILSASLTLLLGLVGMD-EALQLIDMDVIMLLIGMFALVGMAEHSGLLDFI 94 
                                       4444433331133333356677778888999999999999988.555677889************************ PP

                     Na_sulph_symp 348 gnklttslsglspavaiiiilslfvlvhylfaSatAttaall.pillavaqaipgappllvalllalatslagfllp 423
                                       +  + +++  +  ++ ++ +l+ +  +  +f     t+a +  pi + +++++ g   + ++lll l++ ++++++p
  gi|557694260|ref|YP_008797314.1|  95 SSYFLSKVRRTRTMLIMASLLFGL--MSAFFVND--TVALMGpPIAVLIGKSL-GGRYEAAILLLCLSITIGSVMTP 166
                                       ****99999444444444433333..33333332..35555426777788888.55599****************** PP

                     Na_sulph_symp 424 yatgpnpiv 432
                                       ++ ++n ++
  gi|557694260|ref|YP_008797314.1| 167 IGNPQNILI 175
                                       *****9875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 4.2e-05
                     Na_sulph_symp 205 insilgveitwasWflaaiptgvillllvplllyvlyppeikkke.........................eakavak 256
                                       i+ ++g++  +++ +  + ++ +++l+++pl++ +ly+   + +                           a+ +++
  gi|557694260|ref|YP_008797314.1| 175 IALQSGMKSPFIEFLTRLAAPTLLSLIITPLIITKLYKIPKEDVVvpidpwetvrsrrefylalfggsvtVAALIVN 251
                                       56688999999**************************865555556899*****************99988889999 PP

                     Na_sulph_symp 257 telkelGpltarekallilfvlllllWifgesln.....idattvaivvlvil 304
                                       + l++lG   +  + l+  fv +  lWi  + +      +d +t+ ++ ++ +
  gi|557694260|ref|YP_008797314.1| 252 DVLAALGQPHITSRGLI-PFVSAAALWILTDTPReilsrVDFGTILFFLGMFI 303
                                       99*****9999998875.58888999**9998777777788888888776554 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 8e-06
                     Na_sulph_symp 401 gappllvalllalatslagfllpyatgpnpivfga......gylkvkdywrlGfilsiigllilll 460
                                       g+  + v l+la ++ lag ++ ++++ n+iv+ +      ++++   ++++Gfi+++++l i+l 
  gi|557694260|ref|YP_008797314.1| 366 GH-DVEVWLTLAASSTLAGGITVLGAASNVIVLEVlesrygQTIPYLRFAKIGFIVTVVSLCIYLP 430
                                       34.567778888888888888888888888887653333334677788888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (434 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 3059.74
//
Query:       gi|557694261|ref|YP_008797315.1|  [L=318]
Description: methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-60  202.1   0.0    1.1e-59  201.5   0.0    1.2  1  Met_10           Met-10+ like-protein
    1.6e-14   53.5   0.0      3e-14   52.6   0.0    1.5  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    4.4e-09   36.1   0.0    1.1e-08   34.8   0.0    1.6  2  MTS              Methyltransferase small domain
      5e-08   32.8   0.0    7.7e-08   32.2   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    3.8e-06   26.6   0.0    5.8e-06   26.0   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    2.3e-05   25.0   0.0    9.4e-05   23.0   0.0    1.9  2  Methyltransf_25  Methyltransferase domain
    0.00024   20.4   0.0    0.00032   20.0   0.0    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    0.00059   19.7   0.0     0.0021   17.9   0.0    1.7  2  Methyltransf_31  Methyltransferase domain
    0.00074   19.0   0.0     0.0016   17.9   0.0    1.5  2  Methyltransf_4   Putative methyltransferase
     0.0012   18.3   0.0     0.0017   17.8   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0017   18.0   0.0     0.0029   17.3   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0028   17.6   0.0     0.0052   16.7   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
     0.0069   16.3   0.0     0.0099   15.7   0.0    1.2  1  PRMT5            PRMT5 arginine-N-methyltransferase
  ------ inclusion threshold ------
      0.055   12.7   0.0      0.079   12.2   0.0    1.1  1  N6_Mtase         N-6 DNA Methylase
      0.086   12.2   0.0       0.13   11.6   0.0    1.2  1  DNA_methylase    C-5 cytosine-specific DNA methylase
       0.12   12.2   0.0       0.45   10.3   0.0    1.8  2  Methyltransf_23  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 !  201.5   0.0     1e-62   1.1e-59       2     198 ..      70     269 ..      69     270 .. 0.98

  Alignments for each domain:
  == domain 1  score: 201.5 bits;  conditional E-value: 1e-62
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEE CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklD 77 
                                       +++++G v+iln  + + e ++ ++e+i+ ++  v+tvl+kv+ev+g+ R+++++vlaG++ tet+ +E gc +klD
  gi|557694261|ref|YP_008797315.1|  70 SYDVVGSVAILNDMDLAVEEARRLAELIMARHrGVRTVLQKVGEVSGVERVASFRVLAGDGVTETVYRETGCVYKLD 146
                                       79**********999999999**********99******************************************** PP

                                       TTTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEE CS
                            Met_10  78 vskvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvk 154
                                       v++v+fs++l++Er r+a++v e+e+V+d+fAG+Gpf+i ia+     +++a+++nP++  yl eniklNkvek vk
  gi|557694261|ref|YP_008797315.1| 147 VARVFFSPRLSTERLRVAAQVGENETVLDMFAGVGPFSILIARKHPSTTIYAVEKNPAACSYLLENIKLNKVEKQVK 223
                                       *******************************************9999****************************** PP

                                       EEES-GGG---..TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEE CS
                            Met_10 155 pileDgrevir..eqladrvvmnlpksaieFldkvlaalkdggvih 198
                                       p+++D++e+++  +++++rv+mnlp+++ ++l  +l++   g+vih
  gi|557694261|ref|YP_008797315.1| 224 PFCGDAAEIVPqlDKQFNRVIMNLPYQSLKYLPMALSKCLLGAVIH 269
                                       **********98999********************99999999998 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 !   52.6   0.0   2.6e-17     3e-14       1      44 [.       4      47 ..       4      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 2.6e-17
                                      EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S--H CS
                            Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeepe 44
                                      ++kVp++ +E++R++L+ +glLdr+++I +d++++yIPv+  ++
  gi|557694261|ref|YP_008797315.1|  4 AVKVPRSGAEEARRRLAGLGLLDRGRRIMRDGEFVYIPVTGPVD 47
                                      79**************************************9876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.4   2.7e+03     138     168 ..      97     126 ..      95     127 .. 0.79
   2 !   34.8   0.0   9.7e-12   1.1e-08      31     110 ..     169     252 ..     142     270 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.4
                                       EEETTSCHHHHHHHHHS--EEEEEESSEEEE CS
                               MTS 138 Vanrklgyeslleelfgnvevvaktkkfkvl 168
                                       ++ r+ g++++l+ ++g+v  v++ + f+vl
  gi|557694261|ref|YP_008797315.1|  97 IMARHRGVRTVLQ-KVGEVSGVERVASFRVL 126
                                       6678888888876.57999999999999997 PP

  == domain 2  score: 34.8 bits;  conditional E-value: 9.7e-12
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST..TS-EEEEEE CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve..ekkfdlivs 103
                                       ++++vlD+ +G+G+ ++ +a+++p++++ +v+++ +A     en++ nk+e  v+ +  d+ e v+  +k+f+ +++
  gi|557694261|ref|YP_008797315.1| 169 ENETVLDMFAGVGPFSILIARKHPSTTIYAVEKNPAACSYLLENIKLNKVEkqVKPFCGDAAEIVPqlDKQFNRVIM 245
                                       6778***********************************************888889999999887678******** PP

                                       ---STTT CS
                               MTS 104 NPPfhag 110
                                       N P+++ 
  gi|557694261|ref|YP_008797315.1| 246 NLPYQSL 252
                                       *999765 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   6.8e-11   7.7e-08      37     134 ..     165     260 ..     159     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 6.8e-11
                                       CCCHCC-EEEETT-TTSHHHHHHHHTT-..SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS CS
                     Cons_hypoth95  37 aaeiegarvLDlfaGsGalglEAlSRga..kkavlvekdkeavkilkenleelkleeetaelkedaleallklakkk 111
                                       a+ +e+++vLD+faG G  ++  + R+     +++vek+++a++ l en++  k+e++++ +  da+e +++l   +
  gi|557694261|ref|YP_008797315.1| 165 AQVGENETVLDMFAGVGPFSIL-IARKHpsTTIYAVEKNPAACSYLLENIKLNKVEKQVKPFCGDAAEIVPQL---D 237
                                       4568999*************95.666651145678**************************************...6 PP

                                       -EEEEEEE--SSSTTCH.HHHHH CS
                     Cons_hypoth95 112 eefdivflDPPyakellieevle 134
                                       ++f+ v ++ Py++ +++  +l+
  gi|557694261|ref|YP_008797315.1| 238 KQFNRVIMNLPYQSLKYLPMALS 260
                                       78***********9887655554 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 !   26.0   0.0   5.2e-09   5.8e-06       2      68 ..     171     239 ..     170     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 5.2e-09
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkle 68 
                                       +++lD+f+G G  +i +a++   ++++a+e+n+  +    +N ++  v++++++ +gd  e++ +l  +
  gi|557694261|ref|YP_008797315.1| 171 ETVLDMFAGVGPFSILIARKhpSTTIYAVEKNPAACSYLLENIKLNKVEKQVKPFCGDAAEIVPQLDKQ 239
                                       679***************99555679***********************************99886543 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.7   4.1e+03      61      92 ..      67      93 ..      51      95 .. 0.68
   2 !   23.0   0.0   8.4e-08   9.4e-05       1      86 [.     173     259 ..     173     264 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.7
                                      STTTEEEEEEESTGGGSSHHHHHHHHHHHHHH CS
                   Methyltransf_25 61 edgsfDlvvssgalhhlsdedlekalkeiarv 92
                                        +s+D+v s+ a  +l+  d++ a++e++r+
  gi|557694261|ref|YP_008797315.1| 67 FRASYDVVGSV-A--ILN--DMDLAVEEARRL 93
                                      45689999885.3..444..455667777775 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 8.4e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCG.BSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaed.lpfedgsfDlvvssgal 74 
                                       vLd+ +G G +++ +a++ ++ ++++v+ +++++ +  e+++ +++  +v+  +gda + +p+ d++f+ v+++  l
  gi|557694261|ref|YP_008797315.1| 173 VLDMFAGVGPFSILIARKHPSTTIYAVEKNPAACSYLLENIKLNKVekQVKPFCGDAAEiVPQLDKQFNRVIMN--L 247
                                       8*****************989********************9999999*********884799**********5..4 PP

                                       GGSSHHHHHHHH CS
                   Methyltransf_25  75 hhlsdedlekal 86 
                                        + s + l+ al
  gi|557694261|ref|YP_008797315.1| 248 PYQSLKYLPMAL 259
                                       454444555555 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   2.8e-07   0.00032      19     131 ..     149     251 ..     132     317 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.8e-07
                                       -SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHH CS
                               TRM  19 eVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvk 95 
                                        VF+ P+  + R l v++    ++ +     + +vld +++ G  +i  a   +   +++a + ++ A   + eN+k
  gi|557694261|ref|YP_008797315.1| 149 RVFFSPRLSTER-LRVAA----QVGE-----NETVLDMFAGVGPFSILIARK-HPSTTIYAVEKNPAACSYLLENIK 214
                                       577777777776.66666....4444.....448****************99.78899******************* PP

                                       HTT--GGEEEE-S-HHHHHC--SS-EEEEEE-.-SS- CS
                               TRM  96 lneveeivvineddAnvllaekkkrfdviDlD.PfGs 131
                                       ln+ve+ v++  +dA+ ++ + +k+f+ + +  P+ s
  gi|557694261|ref|YP_008797315.1| 215 LNKVEKQVKPFCGDAAEIVPQLDKQFNRVIMNlPYQS 251
                                       **************************98766546654 PP

>> Methyltransf_31  Methyltransferase domain
   #    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      72     113 ..      68     102 ..      48     133 .. 0.62
   2 !   17.9   0.0   1.9e-06    0.0021       3      85 ..     169     254 ..     168     288 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                   Methyltransf_31  72 dekfDlilsnevlnaladpdkileeiervlkpggilliedpr 113
                                       ++++D++ s ++l   +d+d + ee+ r+ +    l+++ +r
  gi|557694261|ref|YP_008797315.1|  68 RASYDVVGSVAIL---NDMDLAVEEARRLAE----LIMARHR 102
                                       3778887776555...444555555444443....4444444 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.9e-06
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDl 77 
                                       ++ +vlD  +G G +++ +a +  p  +++ ++ ++ a ++  en + ++++  v+   gd+ e  ++l  d++f+ 
  gi|557694261|ref|YP_008797315.1| 169 ENETVLDMFAGVGPFSILIA-RKHPSTTIYAVEKNPAACSYLLENIKLNKVEkQVKPFCGDAAEiVPQL--DKQFNR 242
                                       5789****************.88999**************************99**999*****99977..899*** PP

                   Methyltransf_31  78 ilsnevl....n 85 
                                       ++ n +     +
  gi|557694261|ref|YP_008797315.1| 243 VIMNLPYqslkY 254
                                       **9965533331 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         4   4.5e+03      34      60 ..     100     130 ..      89     135 .. 0.74
   2 !   17.9   0.0   1.4e-06    0.0016       3      81 ..     171     248 ..     169     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 4
                                       -HHHHHHHHHHHHHC....TTSSEEEEES-C CS
                    Methyltransf_4  34 rvkvvakvlkkieal....elkNlrilrgda 60 
                                       r ++v++vl+k+++     ++  +r+l gd 
  gi|557694261|ref|YP_008797315.1| 100 RHRGVRTVLQKVGEVsgveRVASFRVLAGDG 130
                                       6678888888888876666666677776665 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.4e-06
                                       EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTT.SSEEEEES-CCCHHHHCS-TTSEEEEEE CS
                    Methyltransf_4   3 pvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealel.kNlrilrgdalkvllelledgslekifi 78 
                                        +vl++  G G f + +A k+P++++ ++E++     ++l++i+ +++ k ++ ++gda +++++l  d++++++ +
  gi|557694261|ref|YP_008797315.1| 171 ETVLDMFAGVGPFSILIARKHPSTTIYAVEKNPAACSYLLENIKLNKVeKQVKPFCGDAAEIVPQL--DKQFNRVIM 245
                                       67899999************************************9977368********9999775..567888888 PP

                                       ES- CS
                    Methyltransf_4  79 lFP 81 
                                       + P
  gi|557694261|ref|YP_008797315.1| 246 NLP 248
                                       766 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.5e-06    0.0017     158     234 ..     166     247 ..     155     265 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.5e-06
                              PrmA 158 lvkegeevlDvGtGSGiLaia.aakLgakkvvavDiDevAvkvakeNaelNkveakleval..seell.k.eekadv 229
                                       +v e+e+vlD+ +G G  +i  a k    +++av  ++ A +   eN++lNkve++++ +   ++e++ + +++++ 
  gi|557694261|ref|YP_008797315.1| 166 QVGENETVLDMFAGVGPFSILiARKHPSTTIYAVEKNPAACSYLLENIKLNKVEKQVKPFCgdAAEIVpQlDKQFNR 242
                                       466789*************96256778899*************************9986431123332236678888 PP

                              PrmA 230 ivaNI 234
                                       ++ N 
  gi|557694261|ref|YP_008797315.1| 243 VIMNL 247
                                       88886 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 !   17.3   0.0   2.6e-06    0.0029       7      88 ..     168     248 ..     163     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.6e-06
                                       -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTCCHHHHCC..EEE CS
                   Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkidkvlggelfDr 82 
                                        e+et+lD+ a+ G    +ia   +++ t++Av++n    + + en+k   v+ +++ +++Da +i   l  ++f r
  gi|557694261|ref|YP_008797315.1| 168 GENETVLDMFAGVGPFSILIARK-HPSTTIYAVEKNPAACSYLLENIKLNKVEkQVKPFCGDAAEIVPQLD-KQFNR 242
                                       589***********999999987.9999*******************9777775678899*****977777.59*** PP

                                       EEEEE- CS
                   Methyltr_RsmB-F  83 iLlDaP 88 
                                       +++  P
  gi|557694261|ref|YP_008797315.1| 243 VIMNLP 248
                                       **9988 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.7e-06    0.0052       3      78 ..     159     233 ..     155     245 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.7e-06
                   Methyltransf_18   3 kRLkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlekl 78 
                                       +RL ++a+ v ++++v+D  +  g  +i +++++  ++++a++ n+ +++   eni+ +++e++++  ++d  e +
  gi|557694261|ref|YP_008797315.1| 159 ERL-RVAAQVGENETVLDMFAGVGPFSILIARKHPSTTIYAVEKNPAACSYLLENIKLNKVEKQVKPFCGDAAEIV 233
                                       677.57778899**********************************************************988766 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   8.8e-06    0.0099      90     125 ..     190     225 ..     156     246 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 8.8e-06
                                       CCCEEEEEEEES-HHHHHHHHHHHHHHTTCCGCEEE CS
                             PRMT5  90 kvtkvkivavEKnpnavvtLqkkvneekWeekvevi 125
                                       k+ +++i+avEKnp+a+ +L ++++ +k e++v+ +
  gi|557694261|ref|YP_008797315.1| 190 KHPSTTIYAVEKNPAACSYLLENIKLNKVEKQVKPF 225
                                       334689**********************99999865 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.1e-05     0.079      28     140 ..     151     254 ..     148     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.1e-05
                          N6_Mtase  28 ffTPrevsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgiey 104
                                       ff Pr  ++ +   ++  ++e+v+D+ +G g + +  ++       k+ + +iy +ekn+ +      N+ l  +e+
  gi|557694261|ref|YP_008797315.1| 151 FFSPRLSTERLRVAAQVGENETVLDMFAGVGPFSILIAR-------KHPSTTIYAVEKNPAACSYLLENIKLNKVEK 220
                                       7778777777777778889999*********99888777.......57899************99999999999999 PP

                          N6_Mtase 105 kkvkirlgdtlekpkfekdkkfdvvvaNppfnqkew 140
                                       + vk   gd+ e   +  dk+f+ v+ N p+ + ++
  gi|557694261|ref|YP_008797315.1| 221 Q-VKPFCGDAAEIVPQL-DKQFNRVIMNLPYQSLKY 254
                                       9.899999987765555.8************98666 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 ?   11.6   0.0   0.00012      0.13       3      48 ..     173     220 ..     172     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                       EEEES-TT-HHHHHHHHTT.-EEEEEEE--TTTHHHHHHH-..-SEEE CS
                     DNA_methylase   3 fidLfaGiGGfrlgleaag.fecvaaseidkkaaktYeanfk.kvsig 48 
                                       ++d+faG+G f++  +++   ++++a+e+++ a+  +  n+k +++++
  gi|557694261|ref|YP_008797315.1| 173 VLDMFAGVGPFSILIARKHpSTTIYAVEKNPAACSYLLENIKlNKVEK 220
                                       79**************99999**************9999998755544 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.5   1.7e+03      70     107 ..      58      95 ..      36     100 .. 0.76
   2 ?   10.3   0.0    0.0004      0.45       8     102 ..     155     259 ..     147     266 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.5
                   Methyltransf_23  70 qfdeqeaaepqgkfdlIvlrevlehvpdppellrqiat 107
                                       ++ e +a+e  +++d++ +   l+ ++   e  r++a+
  gi|557694261|ref|YP_008797315.1|  58 PASEPKAPEFRASYDVVGSVAILNDMDLAVEEARRLAE 95 
                                       45566777788899999999999888876666776666 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0004
                   Methyltransf_23   8 elsdklerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae........kakkaqkdqfdeq 74 
                                       +ls +++r+++   ++  vLd+ +G+G ++ +++++    ++++v+ +p+a + +         +++  ++    ++
  gi|557694261|ref|YP_008797315.1| 155 RLSTERLRVAAQVGENETVLDMFAGVGPFSILIARKHPstTIYAVEKNPAACSYLLeniklnkvEKQVKPFCGDAAE 231
                                       67788999999889999****************6663336999****998665544454444322222222222222 PP

                   Methyltransf_23  75 eaaepqgkfdlIvlrevlehvpdppell 102
                                         ++ +++f+ ++++    +++++p++l
  gi|557694261|ref|YP_008797315.1| 232 IVPQLDKQFNRVIMNLPYQSLKYLPMAL 259
                                       2333555777777777666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2265.78
//
Query:       gi|557694262|ref|YP_008797316.1|  [L=127]
Description: hypothetical protein CSUB_C0829 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); 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: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 980.48
//
Query:       gi|557694263|ref|YP_008797317.1|  [L=170]
Description: hypothetical protein CSUB_C0830 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.8   0.0      0.021   14.9   0.0    1.6  1  Cupredoxin_1  Cupredoxin-like domain
      0.014   15.2   0.3      0.018   14.9   0.3    1.1  1  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr
      0.039   14.9   0.9      0.065   14.2   0.8    1.5  1  Pilin_N       Archaeal Type IV pilin, N-terminal
      0.053   13.3   0.0       0.33   10.7   0.0    2.1  1  Cu-oxidase_2  Multicopper oxidase


Domain annotation for each model (and alignments):
>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.6e-06     0.021      36      94 ..      82     148 ..      19     153 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.6e-06
                      Cupredoxin_1  36 kievkagekvklkiknkdktp..eefesed......lgeekvlapgktttitiaplkpGeYeftcdm 94 
                                       +i++  g  +++++  +++ p  + f+ ++        ++  l  g+t++i++++  pGe++++c  
  gi|557694263|ref|YP_008797317.1|  82 TITAYVGDIIRITLIGNSTGPivHDFVLDEkspspyNVKSNRLSRGQTQVIEFTANIPGEFKYYCSV 148
                                       477777888888888888886669999988888885335589***********************86 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.3     4e-06     0.018      66     114 ..       9      56 ..       6      93 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4e-06
                      Trp_oprn_chp  66 grrvvgvllalagagaavaalsll..tdpadaaraaaaaatgvasaaaave 114
                                       +r vv+v+l++a+ag+++  + l     p++  +++++++t   ++ a+ +
  gi|557694263|ref|YP_008797317.1|   9 VRLVVAVVLVVAAAGVGALLIGLQpaQPPQTNTTTTKTETT---QTPATTK 56 
                                       68999998877777666555555400444333333333333...3333333 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 ?   14.2   0.8   1.4e-05     0.065      10      53 ..      10      56 ..       6      90 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-05
                           Pilin_N 10 iLmvait.vIlaAviaafvlglasneekapqasievk....idssastg 53
                                       L va++ v++aA ++a  +gl  ++ + pq++ +++    +++ a+t+
  gi|557694263|ref|YP_008797317.1| 10 RLVVAVVlVVAAAGVGALLIGL--QPAQPPQTNTTTTktetTQTPATTK 56
                                      56777662566778********..4444555554333212244444433 PP

>> Cu-oxidase_2  Multicopper oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   7.5e-05      0.33      23     120 ..      57     149 ..      32     167 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.5e-05
                                       E............ETCCTT..TSSEEEEEETTEEEEEEEEE-SSS-EEEEESS-EEEEEEEEECCCCCCTCCSSGCC CS
                      Cu-oxidase_2  23 t............ngeefs..entnvitlpkgevveiviqnntklpHPfHlHGhdfqvlgrgpgndpeedpksynle 85 
                                                    n+  ++  ++ ++it+  g++++i++ +n+++  P+    hdf + +++p++        yn+ 
  gi|557694263|ref|YP_008797317.1|  57 PstqnivsltlylNDYGYNasRGGPTITAYVGDIIRITLIGNSTG--PI---VHDFVLDEKSPSP--------YNV- 119
                                       033444566666644444433666777777788888888888877..55...6777777777776........776. PP

                                       GSSCBSEEEE-TTEEEEEEEES.S-EEEEEEESSH CS
                      Cu-oxidase_2  86 npvrrdtvqvppggwvairfkadnpGvwllHCHil 120
                                               ++  g++ +i+f+a+ pG + + C ++
  gi|557694263|ref|YP_008797317.1| 120 -----KSNRLSRGQTQVIEFTANIPGEFKYYCSVA 149
                                       .....667889999******************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 1407.63
//
Query:       gi|557694264|ref|YP_008797318.1|  [L=456]
Description: histidinol dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-133  445.0   4.5   3.4e-133  444.6   4.5    1.0  1  Histidinol_dh   Histidinol dehydrogenase
  ------ inclusion threshold ------
        2.6    8.0   4.5        4.7    7.2   0.0    3.1  4  VapB_antitoxin  Bacterial antitoxin of type II TA system, Vap


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 !  444.6   4.5  3.8e-137  3.4e-133       7     406 ..      52     452 ..      48     454 .. 0.97

  Alignments for each domain:
  == domain 1  score: 444.6 bits;  conditional E-value: 3.8e-137
                                       --HHHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSS.SGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC CS
                     Histidinol_dh   7 dseeveetvkeiledvreeGdealleytekFDkvk.kleslrvseeeieealekldeelkealeeaaenirkfheaq 82 
                                       +++++ e+v++++edvr++Gdeal+ey +kFD+   +le+lrv+ e++++a+++ld+++k+al+ + eni ++ ++q
  gi|557694264|ref|YP_008797318.1|  52 SVDHYVEAVRRVVEDVRARGDEALIEYVKKFDSPAmDLERLRVPVEKLADAYARLDDATKKALKISSENIARVCKSQ 128
                                       5678999*************************775478*************************************** PP

                                       ----EEEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SS.GG.--HHHHHHHH CS
                     Histidinol_dh  83 keseeevketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpq.dgkvnpavlaaak 158
                                       +++  + ++ e+gv + q+  p+++vG+YvPgG aaypStvlm++vpAkvA+v++i+v tPp+ +g++   v aa+ 
  gi|557694264|ref|YP_008797318.1| 129 LRRLFSSVRVEEGVLVVQRPSPLSSVGCYVPGGGAAYPSTVLMTVVPAKVAQVPRIAVFTPPTrEGNIPTVVAAALY 205
                                       *965556699******************************************************************* PP

                                       HCT-SEEEE--HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHHH CS
                     Histidinol_dh 159 lagvdeiykvGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvAa 235
                                       l+gv+e+y +GG +Aiaa+AyGtesi++v ki+GPG  yV+aAK+lvs +v++Dm+aGP+E++v aD+ ad+e vA+
  gi|557694264|ref|YP_008797318.1| 206 LTGVKEVYCAGGPHAIAAMAYGTESIKPVAKIIGPGGPYVTAAKKLVSRDVAVDMLAGPTELCVYADDVADAENVAL 282
                                       ***************************************************************************** PP

                                       HHHHHHTT-TT-EEEEEES-HHHHHHHHHHHHHHHCC-TTHHHHHHHHCCH-EEEE-SSHHHHHHHHHHH--SEEEE CS
                     Histidinol_dh 236 DLlsqaEHdedaqavlvttseelaeaveeevekqleelprkeiaekslekqsaiilvedleeaielaneyApEHlel 312
                                       ++ +qaEH +d+ + lvtts+el+++v + ++  +++l+r ei++++l+k+++++++++ ++a++l+ ++ApEHl +
  gi|557694264|ref|YP_008797318.1| 283 EMCAQAEHSTDTLVGLVTTSDELVNEVLKFLKLITPRLERGEIVNEALQKNGYAVVCDKPATAAALIQALAPEHLYI 359
                                       ***************************************************************************** PP

                                       ESTTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTGGGT---S-GGGGEEEEEEEEE-HHHHHHHHHHH CS
                     Histidinol_dh 313 qvedpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgtArfssglsvedFlkkisvqelskealkelaeav 389
                                        ++  e+ll++++naG i +G+y++ +l DY+ G nhvLPT g A   +gls+ d++k ++ +++ k a+k+l++++
  gi|557694264|ref|YP_008797318.1| 360 VTK-HEKLLQSVTNAGLISIGRYTSPALCDYVVGVNHVLPTMGQAALRGGLSILDYVKIVTEVRMLKGAAKRLGRHA 435
                                       665.678********************************************************************** PP

                                       HHHHHHTT-HHHHHHHH CS
                     Histidinol_dh 390 etlAeaEgLeaHaeavk 406
                                       + lA+aEgL+aHa+a++
  gi|557694264|ref|YP_008797318.1| 436 ALLARAEGLTAHAAAAS 452
                                       *************9975 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 ?    0.9   0.0     0.048   4.3e+02      30      42 ..      73      85 ..      72      92 .. 0.74
   2 ?   -1.8   0.1      0.33     3e+03      11      27 ..      98     114 ..      97     114 .. 0.86
   3 ?   -3.3   0.1         1   9.2e+03      12      23 ..     200     211 ..     199     211 .. 0.85
   4 ?    7.2   0.0   0.00053       4.7       9      33 ..     303     331 ..     302     332 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.048
                                      XXXXX-------H CS
                    VapB_antitoxin 30 lALreLiqrrkre 42
                                      +AL e++++ ++ 
  gi|557694264|ref|YP_008797318.1| 73 EALIEYVKKFDSP 85
                                      8*******99976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.33
                                       XXXXXXXXXXXXXXXXX CS
                    VapB_antitoxin  11 LlaeAirltglktKrEa 27 
                                        la+A+++   +tK+++
  gi|557694264|ref|YP_008797318.1|  98 KLADAYARLDDATKKAL 114
                                       68999999999999986 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1
                                       XXXXXXXXXXXX CS
                    VapB_antitoxin  12 laeAirltglkt 23 
                                       +a A+ ltg+k+
  gi|557694264|ref|YP_008797318.1| 200 VAAALYLTGVKE 211
                                       789999999996 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.00053
                                       XXXXXXXXXXXXXXXXX....XXXXXXXX CS
                    VapB_antitoxin   9 DeLlaeAirltglktKr....EaVnlALr 33 
                                       DeL++e+++  +l t r    E+Vn+AL+
  gi|557694264|ref|YP_008797318.1| 303 DELVNEVLKFLKLITPRlergEIVNEALQ 331
                                       9************99988888*******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3273.93
//
Query:       gi|557694265|ref|YP_008797319.1|  [L=187]
Description: DNA-3-methyladenine glycosylase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-52  174.9   0.0    1.2e-51  174.6   0.0    1.1  1  Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)


Domain annotation for each model (and alignments):
>> Pur_DNA_glyco  Methylpurine-DNA glycosylase (MPG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.6   0.0   6.6e-56   1.2e-51       2     175 .]      10     172 ..       9     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 174.6 bits;  conditional E-value: 6.6e-56
                     Pur_DNA_glyco   2 ffdrdalevAkeLLGkvlvreleegkvagrivEtEAYlgeeDpAshayrgrternavmFgppgtlYvYliygihhcl 78 
                                       f+drd++e+Ak LLGkvl+++  +  +++rivEtEAY+ ++D+A hay+g+t+rn++mFgppgtlYvY++++ h+c+
  gi|557694265|ref|YP_008797319.1|  10 FYDRDTVELAKLLLGKVLCVRRGDIVMSCRIVETEAYV-KNDKANHAYKGMTRRNKSMFGPPGTLYVYIVHT-HYCM 84 
                                       9********************8878*************.*********************************.**** PP

                     Pur_DNA_glyco  79 nvvteeegeasaVLiRalevveglelmrarrglanGPgkLcqaLgidkelngadlleseelvlekeeaeeeeivagp 155
                                       nvv    g ++aVL+Ra+e+++++      r  ++GPg+Lc+aLg+d++++g+dl+ se+++l ++  + ++i+ ++
  gi|557694265|ref|YP_008797319.1|  85 NVVR---GGGEAVLLRAAEPLANVV----GR--LDGPGRLCRALGVDRSFDGEDLCVSERVWLWDDGYRFAKIAVTR 152
                                       ***8...889**********87763....33..68****************************************** PP

                     Pur_DNA_glyco 156 RiGiskaaelpwRfyikgnp 175
                                       RiG++++a++++Rfyi+g+p
  gi|557694265|ref|YP_008797319.1| 153 RIGVTADAHRLLRFYIAGSP 172
                                       *****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1424.68
//
Query:       gi|557694266|ref|YP_008797320.1|  [L=200]
Description: DNA polymerase bacteriophage-type [Candidatus Caldiarchaeum subterraneum]
Scores for 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-45  152.5   0.0      1e-44  152.2   0.0    1.1  1  UDG       Uracil DNA glycosylase superfamily


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 !  152.2   0.0   5.8e-49     1e-44       1     153 [.      33     177 ..      33     189 .. 0.92

  Alignments for each domain:
  == domain 1  score: 152.2 bits;  conditional E-value: 5.8e-49
                                       HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCC CS
                               UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaei 77 
                                       pgeg+p a+++++Ge Pg+eed +g+pF+gr+g+ll ++l++ag+ r     ++v+itnvvkcrpp+nr +pt++e 
  gi|557694266|ref|YP_008797320.1|  33 PGEGNPRAELMFIGEGPGEEEDLQGRPFVGRSGRLLTEALEKAGIRR-----EDVFITNVVKCRPPENR-EPTPEER 103
                                       79*********************************************.....*****************.******* PP

                                       TCCHH.HHHHHHHHHHSSEEEEESHHHHHH..HH.HHSCESCCCSCT..SEEEEES-SSTTTTTTTTSHHHHHHHHH CS
                               UDG  78 kacap.lleeeiellkprlivllGktaakallge.klgklrgklleak.irvlplphPsplnrnffksnpelkaeaw 151
                                       + c + +l ++ie+++prlivllG  a ++llg  +++ +rgk +e+   r++ ++hP+++++n     p ++++++
  gi|557694266|ref|YP_008797320.1| 104 QTCTNkYLFRQIEAVNPRLIVLLGSVAVQTLLGIsSVTAVRGKAFEKMgRRFFCTYHPAAALYN-----PGNRETFF 175
                                       ***888*************************95559***********99***************.....44444444 PP

                                       HH CS
                               UDG 152 ed 153
                                        d
  gi|557694266|ref|YP_008797320.1| 176 SD 177
                                       43 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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: 1531.97
//
Query:       gi|557694267|ref|YP_008797321.1|  [L=156]
Description: peroxiredoxin Q/BCP [Candidatus Caldiarchaeum subterraneum]
Scores for 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  119.7   0.0    8.5e-35  119.4   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    2.2e-19   69.6   0.0    2.6e-19   69.4   0.0    1.0  1  Redoxin        Redoxin
     0.0023   17.8   0.0      0.014   15.4   0.0    2.1  1  SCO1-SenC      SCO1/SenC
     0.0056   16.8   0.0     0.0068   16.5   0.0    1.2  1  AhpC-TSA_2     AhpC/TSA antioxidant enzyme
  ------ inclusion threshold ------
      0.064   13.6   0.0      0.091   13.1   0.0    1.3  1  Thioredoxin_8  Thioredoxin-like


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 !  119.4   0.0   2.4e-38   8.5e-35       1     122 [.       4     124 ..       4     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 119.4 bits;  conditional E-value: 2.4e-38
                                       TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfi 77 
                                       vgd ap fel  + ge ++l++++g++vvlffypkd +p+Ct+e + l++++e+f+++g+  +g+s ds+eshk+f+
  gi|557694267|ref|YP_008797321.1|   4 VGDVAPGFELISHTGERINLEKLRGRYVVLFFYPKDGSPGCTRENCLLRDNFEKFEKLGAVTLGISRDSVESHKRFA 80 
                                       79*************************************************************************** PP

                                       HH-H.SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEE CS
                          AhpC-TSA  78 ekeslnfpllsDeegkvakaygvlkeekglalratfvidkegkir 122
                                       ek++++  llsD++g+v+kayg+     g++ r t+vid+eg ++
  gi|557694267|ref|YP_008797321.1|  81 EKHGFTHHLLSDPSGEVVKAYGAA-GLFGITKRITYVIDPEGRVA 124
                                       ************************.557**************997 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   7.3e-23   2.6e-19       2     144 ..       4     140 ..       3     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 7.3e-23
                                       TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHHHH CS
                           Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndafvk 77 
                                       +gd aP f+l  +   g+ ++l++++g+ vv++f+p   +P C++e +   ++++++ ++ g   ++++ d+ +  k
  gi|557694267|ref|YP_008797321.1|   4 VGDVAPGFEL--ISHTGERINLEKLRGRYVVLFFYPKDGSPGCTRENClLRDNFEKF-EKLGAVTLGISRDSVESHK 77 
                                       79999****8..66**********************************666666666.99999999*********** PP

                                       HHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.EEE-EEEEEEETTEEEEEEESSSCHTSTTSHH CS
                           Redoxin  78 efwgkeglkfpvlsDgsaaftkalGlrleedaseg.lrtpryavidedgkvvylevepepeteesnae 144
                                       +f++k+g ++++lsD+s++++ka+G++       + +  + + vid +g+v  +++  +p t +++a 
  gi|557694267|ref|YP_008797321.1|  78 RFAEKHGFTHHLLSDPSGEVVKAYGAAGL-----FgITKRITYVIDPEGRVARIIQSINPSTHVAEAL 140
                                       *************************7744.....3477777899************999955555554 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.8e-06     0.014       3      98 ..      10      99 ..       8     114 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.8e-06
                         SCO1-SenC  3 pFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeylea 81
                                       Fel++++ge+++ e+l+g+++++ff        C+ +   +++  +++++         +T+   rD++e  k+++e+
  gi|557694267|ref|YP_008797321.1| 10 GFELISHTGERINLEKLRGRYVVLFFYPKDGSPGCTRENCLLRDNFEKFEKL------GAVTLGISRDSVESHKRFAEK 82
                                      5**********************99965555555555555555555555444......345666677777777777777 PP

                         SCO1-SenC 82 fdpriigltGskeeiak 98
                                      ++   + l++++ e+ k
  gi|557694267|ref|YP_008797321.1| 83 HGFTHHLLSDPSGEVVK 99
                                      77766666665555554 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 !   16.5   0.0   1.9e-06    0.0068       2      54 ..      51     104 ..      50     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.9e-06
                        AhpC-TSA_2   2 Lsrdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalglk 54 
                                       L++  +++++ g    +i+ +++ s k+F++  gf   l+ Dps+++ +a g  
  gi|557694267|ref|YP_008797321.1|  51 LRDNFEKFEKLGAVTLGISRDSVeSHKRFAEKHGFTHHLLSDPSGEVVKAYGAA 104
                                       67779******************77*********************99999877 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.5e-05     0.091       1      81 [.      28     104 ..      28     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.5e-05
                                       .SEEEEEE--S.SSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT CS
                     Thioredoxin_8   1 gkvvlLyfgas.wcppckaftpklkelyeklkkkkkveivyvsldkkeeefekylkknkkpwlsvpfddkkrnklkk 76 
                                       g++v+L+f+ +  +p c++ +  l + +ek++   k+  v + + ++  e +k +++    ++++  +d++  ++ k
  gi|557694267|ref|YP_008797321.1|  28 GRYVVLFFYPKdGSPGCTRENCLLRDNFEKFE---KLGAVTLGISRDSVESHKRFAEK-HGFTHHLLSDPS-GEVVK 99 
                                       6788998886516667***************8...77777777777777777777766.588888888885.44444 PP

                                       -S--T CS
                     Thioredoxin_8  77 kynvk 81 
                                        y+  
  gi|557694267|ref|YP_008797321.1| 100 AYGAA 104
                                       45544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1309.74
//
Query:       gi|557694268|ref|YP_008797322.1|  [L=134]
Description: sterol-binding domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   49.9   0.0    4.2e-13   49.6   0.0    1.2  1  SCP2          SCP-2 sterol transfer family
    2.5e-05   24.5   0.0    3.1e-05   24.3   0.0    1.2  1  Alkyl_sulf_C  Alkyl sulfatase C-terminal
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.021   15.2   0.0    1.3  1  SCP2_2        Sterol carrier protein domain


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 !   49.6   0.0   7.1e-17   4.2e-13      10     100 ..      39     128 ..      26     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 7.1e-17
                                       HHHHHHHHCCH-EEEEEEECTC.TEEEEEETTSTEEESSCTTBS-SEEEEEEHHHHHHHHCTSS-HHHHHHTTSSEE CS
                              SCP2  10 dpekkealkklagvlrfdltdlkgsltldlkegqldvaakdegkadvtlslsledllelaegklnpqkafmqgkLki 86 
                                        pe + +++ ++ v++f+ +d+ +++++  ++ +l+v ++    + +t+  s +dl+++++g+l++ kaf++g++ki
  gi|557694268|ref|YP_008797322.1|  39 HPEVSRKAAGWSKVVQFKPSDG-NPFYIHSTGSGLTVTEGLHPNPSATVESSHQDLVSILRGELDAVKAFFSGRIKI 114
                                       4577888889999*********.77************777778********************************** PP

                                       EC-HHHHHHHHHHH CS
                              SCP2  87 eGDielaqkleall 100
                                       +GD++ aq+l +l+
  gi|557694268|ref|YP_008797322.1| 115 KGDVFAAQELNSLF 128
                                       ***********998 PP

>> Alkyl_sulf_C  Alkyl sulfatase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   5.1e-09   3.1e-05      61     115 ..      75     129 ..      43     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.1e-09
                                       CT---TTSSEEEEE-HHHHHHHHTTSS-HHHHHHTTTEEEEE-TCHHHHHHCTB- CS
                      Alkyl_sulf_C  61 kaaqaddadltvtltreqLvalllgkatlgkevaagklkieGdaealakllslld 115
                                       ++  ++++ +tv  ++++Lv++l g+  + k++ +g++ki+Gd+ a ++l sl+ 
  gi|557694268|ref|YP_008797322.1|  75 TEGLHPNPSATVESSHQDLVSILRGELDAVKAFFSGRIKIKGDVFAAQELNSLFS 129
                                       3455699*******************************************99986 PP

>> SCP2_2  Sterol carrier protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   3.6e-06     0.021      34      97 ..      63     129 ..      32     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3.6e-06
                                       EEEEEETTSEEEECSCE-.SCE..EEEEHHHHHHHHTTSS-HHHHHHTTSSB..SSHHHHHHHHHHS- CS
                            SCP2_2  34 frltiedgkgeevgkeee.ada.dltldiqtLaqlllGyrsaseLarlgrie..gaeealatldalfp 97 
                                       f ++ + g+g +v+++   +++ +++ + q+L+++l G  +a ++ + gri+  g+  a ++l++lf+
  gi|557694268|ref|YP_008797322.1|  63 FYIH-STGSGLTVTEGLHpNPSaTVESSHQDLVSILRGELDAVKAFFSGRIKikGDVFAAQELNSLFS 129
                                       5566.3444443332222466669****************************8777777799999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1001.64
//
Query:       gi|557694269|ref|YP_008797323.1|  [L=199]
Description: CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   51.3   1.9    1.4e-13   51.3   1.9    2.8  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


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 !   51.3   1.9     8e-18   1.4e-13       1      66 []      27      96 ..      27      96 .. 0.89
   2 ?    0.5   3.8     0.061   1.1e+03      11      39 ..     154     184 ..     101     196 .. 0.62

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 8e-18
                                      S-HHHHHHHHHHHHHHHHHGGGS-H.......HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  1 nlPnaiTllrlllsvlailllltyyp.....lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      ++Pn++T ++l+l+ +a+ + ++++      +++  +ll + s++D+lDG lAR l+++s++G++lDs+ D
  gi|557694269|ref|YP_008797323.1| 27 VTPNMLTAAGLILTAMAT-PCYYLSRadpvyFLVSGALLAAGSFLDGLDGSLARLLGSQSNFGAFLDSFTD 96
                                      58***********99999.77555558999888888888889999***********************998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.061
                                       HHHHHHHHHGGGS-H...........HHHHHHHHHHHH CS
                   CDP-OH_P_transf  11 lllsvlailllltyyp.........lvlailllliasl 39 
                                       ll++++a+                 + +ai++ +++++
  gi|557694269|ref|YP_008797323.1| 154 LLAAIAAT-------FtayinsltlFAAAIFITVVSII 184
                                       33333333.......02223345422333333334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1546.12
//
Query:       gi|557694270|ref|YP_008797324.1|  [L=155]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   96.2   0.0    1.8e-27   95.9   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 !   95.9   0.0     1e-31   1.8e-27      14     114 ..      29     125 ..      15     129 .. 0.91

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 1e-31
                                       EEEEE-HHH..HGGGTTGGG-SEEEEEEE-TTS...-.SS--E-TT-.SS-E.EGGGS--S-SSS-EEEEEEEEEEE CS
                              TrmO  14 aeielepeynseealegleefshlwllfvfhenaekklkakvrpprlggnervGvfatRsphRpnpiglsvvklekv 90 
                                       + ie+ pey  +e+l+gl e+sh+++++ +h +  ++++  +rp+   +  +vGvfa R p+Rpnpigl+++kl +v
  gi|557694270|ref|YP_008797324.1|  29 SFIEVYPEY--REGLRGLGEYSHIYVIYFMHLE--RRVQLVIRPRGRADMPEVGVFAFRGPTRPNPIGLTLCKLIEV 101
                                       67999****..********************87..4656777777777889************************** PP

                                       ETTEEEEES----TT-EEEEEEE- CS
                              TrmO  91 egnvlevsgvDlldgtpvlDiKPY 114
                                       + n l+v g+D++ gtpvlDiKPY
  gi|557694270|ref|YP_008797324.1| 102 TTNGLRVLGLDAFPGTPVLDIKPY 125
                                       ************************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 1138.89
//
Query:       gi|557694271|ref|YP_008797325.1|  [L=117]
Description: hypothetical protein CSUB_C0838 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-38  129.5   2.0    5.9e-38  129.4   2.0    1.0  1  Arcadin_1  Arcadin 1
  ------ inclusion threshold ------
      0.085   12.5   0.1       0.18   11.5   0.1    1.6  1  Tudor_2    Jumonji domain-containing protein 2A Tudor domain


Domain annotation for each model (and alignments):
>> Arcadin_1  Arcadin 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.4   2.0   6.5e-42   5.9e-38       1     110 [.       2     112 ..       2     113 .. 0.94

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 6.5e-42
                                       EEEEEEEEEEEEEE-TT-.-EEEEEEEEEEE------------------------------------....--EEEE CS
                         Arcadin_1   1 vlvrvkvssitlvkdPeg.ekgvkielvEerelpgpvlvasdeedaeiaRevapivqqivrslpllsl...nkvkvp 73 
                                       ++v vkv++it+++dPe+ ++g++ielvE+r+++g+++v ++ee+a+++R++++++ q+ +s++l+++   n++  p
  gi|557694271|ref|YP_008797325.1|   2 EMVLVKVQRITSYTDPETmRPGKIIELVEVRRSSGFQAVGMGEESAMVQRMLQTAMLQL-QSMGLMPItreNLF--P 75 
                                       589***************99***************************************.88888877633555..* PP

                                       EEEEEE-HHHHHHH-.---TT-EEEEEEETTEEEEEE CS
                         Arcadin_1  74 ritLvlteeEleklevklevgdvyeieisegkisikr 110
                                       +i+L++te+E+++l+v+lev++vye+++s+g+i++kr
  gi|557694271|ref|YP_008797325.1|  76 KIILYVTEQEYDMLNVRLEVNEVYEVTFSDGSIVFKR 112
                                       ************************************9 PP

>> Tudor_2  Jumonji domain-containing protein 2A Tudor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     2e-05      0.18      24      35 .]      96     107 ..      91     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2e-05
                           Tudor_2  24 qtfYeVeFEDgS 35 
                                        + YeV+F+DgS
  gi|557694271|ref|YP_008797325.1|  96 NEVYEVTFSDGS 107
                                       679********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 852.03
//
Query:       gi|557694272|ref|YP_008797326.1|  [L=140]
Description: glycine cleavage system H protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-41  140.5   0.1    2.7e-41  140.3   0.1    1.0  1  GCV_H          Glycine cleavage H-protein
     0.0058   16.4   0.0      0.011   15.5   0.0    1.4  1  Biotin_lipoyl  Biotin-requiring enzyme
  ------ inclusion threshold ------
      0.013   15.4   0.1      0.019   14.9   0.1    1.4  1  RnfC_N         RnfC Barrel sandwich hybrid domain
       0.13   12.6   0.0       0.26   11.7   0.0    1.5  1  MKT1_N         Temperature dependent protein affecting M2 dsR


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 !  140.3   0.1   6.1e-45   2.7e-41       1     121 [.      11     130 ..      11     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 140.3 bits;  conditional E-value: 6.1e-45
                                       -EE-TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GG CS
                             GCV_H   1 lyytkehewvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNek 77 
                                       l ytk+hewv  e++  a vGitd+aq++l ++++velp+ +t+v++ e l++vEsvK++++v apvsG vvevN+k
  gi|557694272|ref|YP_008797326.1|  11 LLYTKDHEWVLPEKK-HAVVGITDYAQKKLREIIYVELPHINTRVHAREVLGTVESVKSTADVLAPVSGRVVEVNSK 86 
                                       57**********987.9************************************************************ PP

                                       GTT-TTHHHH-TTTTT--EEEEES-GGGGGGSEEHHHHHHHHHH CS
                             GCV_H  78 leeepeliNkdpyeegWliklklsnleeleeLlsaeeyekllke 121
                                       l ++pe++N++py egW++k++ls+++ele+Ll+a+ey+++l+e
  gi|557694272|ref|YP_008797326.1|  87 LLDHPEILNESPYTEGWIAKIELSDPSELEKLLDADEYRRFLEE 130
                                       ****************************************9986 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.6e-06     0.011      26      57 ..      53      84 ..      47      88 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.6e-06
                                      EE-TTSEEEEEECTTEEEEEEBSSSEEEEEES CS
                     Biotin_lipoyl 26 kVkagqvlaeveamKmemeieapkaGvvkeil 57
                                       V a +vl +ve+ K + ++ ap++G+v+e+ 
  gi|557694272|ref|YP_008797326.1| 53 RVHAREVLGTVESVKSTADVLAPVSGRVVEVN 84
                                      69999************************996 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 ?   14.9   0.1   4.3e-06     0.019      51      89 ..      53      92 ..      22      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.3e-06
                            RnfC_N 51 kVlkGqkiaeaeg.fvsapvhasvsGtVkaiekrlvahgs 89
                                      +V   +++++ e+   +a v a+vsG+V+++++ l  h++
  gi|557694272|ref|YP_008797326.1| 53 RVHAREVLGTVESvKSTADVLAPVSGRVVEVNSKLLDHPE 92
                                      7788888999988455799*************99998886 PP

>> MKT1_N  Temperature dependent protein affecting M2 dsRNA replication
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   5.7e-05      0.26      31      63 ..     102     135 ..      97     140 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                            MKT1_N  31 naltsgelieeppldg.gdseeYrklvtdlltei 63 
                                       +++++ el+++  l++ +d++eYr+++++l++e 
  gi|557694272|ref|YP_008797326.1| 102 GWIAKIELSDPSELEKlLDADEYRRFLEELEEEK 135
                                       699999********999************99543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); 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:                         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 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1026.17
//
Query:       gi|557694273|ref|YP_008797327.1|  [L=65]
Description: hypothetical protein CSUB_C0840 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   16.6   0.4     0.0055   16.2   0.4    1.2  1  RecR           RecR protein
  ------ inclusion threshold ------
       0.02   14.6   2.3        3.1    7.6   0.2    2.2  2  zinc_ribbon_2  zinc-ribbon domain
      0.025   14.6   1.2      0.037   14.1   1.2    1.4  1  Nop10p         Nucleolar RNA-binding protein, Nop10p family
      0.032   14.7   0.6      0.032   14.7   0.6    1.5  2  CBM_10         Cellulose or protein binding domain
      0.036   14.1   0.7      0.058   13.4   0.7    1.4  1  DZR            Double zinc ribbon
       0.49   10.4   5.4       0.53   10.3   0.3    2.2  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
       0.61    9.6   6.3        5.4    6.6   6.4    2.1  1  zf-ribbon_3    zinc-ribbon domain
        1.6    8.5   6.7        1.8    8.3   1.1    2.2  2  zf-RRN7        Zinc-finger of RNA-polymerase I-specific TFIIB


Domain annotation for each model (and alignments):
>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   2.5e-06    0.0055      15      34 ..      20      41 ..      15      47 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-06
                                      H-EE-TTT--E..ESSSS-CCC CS
                              RecR 15 kvrhCsrCgnl..teedlCaIC 34
                                      + ++CsrC+ +  t+   C+ C
  gi|557694273|ref|YP_008797327.1| 20 GYKYCSRCRVYhlTDGVRCPYC 41
                                      679*****977669999***** 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   0.2    0.0022       4.9      11      20 ..      19      28 ..      15      29 .. 0.83
   2 ?    7.6   0.2    0.0014       3.1      16      20 ..      38      42 ..      36      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0022
                     zinc_ribbon_2 11 dnakFCpyCG 20
                                      ++ k+C++C+
  gi|557694273|ref|YP_008797327.1| 19 NGYKYCSRCR 28
                                      7899*****6 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0014
                     zinc_ribbon_2 16 CpyCG 20
                                      CpyCG
  gi|557694273|ref|YP_008797327.1| 38 CPYCG 42
                                      89998 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 ?   14.1   1.2   1.6e-05     0.037       6      29 ..      22      47 ..      19      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                                      EE-TTT--EESS..SB-TTT-SB-B- CS
                            Nop10p  6 rkcgkcrvYTLk..kvcpecggptks 29
                                      ++c++crvY L    +cp+cg  +++
  gi|557694273|ref|YP_008797327.1| 22 KYCSRCRVYHLTdgVRCPYCGILLRN 47
                                      79**********5559****975555 PP

>> CBM_10  Cellulose or protein binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.6   1.4e-05     0.032       4      18 ..      16      30 ..      15      35 .. 0.86
   2 ?   -3.1   0.1       5.1   1.1e+04      33      36 .]      40      43 ..      39      43 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                                      TTTTCCEB-STS..S CS
                            CBM_10  4 seglgYpcCsnckvv 18
                                      s+++gY++Cs c+v+
  gi|557694273|ref|YP_008797327.1| 16 SYANGYKYCSRCRVY 30
                                      799*********887 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.1
                                      EEEE CS
                            CBM_10 33 WCgi 36
                                      +Cgi
  gi|557694273|ref|YP_008797327.1| 40 YCGI 43
                                      4665 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   2.6e-05     0.058       9      38 ..      18      45 ..      12      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                               DZR  9 ppdarfCseCgtk.lkavaaedrCpsCgekv 38
                                       ++ ++Cs+C+   l   ++  rCp Cg  +
  gi|557694273|ref|YP_008797327.1| 18 ANGYKYCSRCRVYhL---TDGVRCPYCGILL 45
                                      688999****98744...4599999999665 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 ?    3.3   0.7     0.036        81      16      26 ..      18      29 ..       9      34 .. 0.62
   2 ?   10.3   0.3   0.00024      0.53      17      27 ..      34      44 ..      30      54 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.036
                     Zn_Tnp_IS1595 16 pngfv.CPhCgs 26
                                      +ng   C +C +
  gi|557694273|ref|YP_008797327.1| 18 ANGYKyCSRCRV 29
                                      455333666664 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00024
                     Zn_Tnp_IS1595 17 ngfvCPhCgsr 27
                                      +g++CP+Cg+ 
  gi|557694273|ref|YP_008797327.1| 34 DGVRCPYCGIL 44
                                      799******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 ?    6.6   6.4    0.0024       5.4       3      25 ..      22      44 ..      20      45 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0024
                       zf-ribbon_3  3 vrCPnCGa.plssddnvCpyCGtk 25
                                      ++C++C   +l+++++ CpyCG  
  gi|557694273|ref|YP_008797327.1| 22 KYCSRCRVyHLTDGVR-CPYCGIL 44
                                      6777777777777776.8888875 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 ?    8.3   1.1   0.00082       1.8      17      27 ..      16      27 ..      15      27 .. 0.86
   2 ?    3.3   0.4     0.029        65       3      11 ..      34      42 ..      33      42 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00082
                           zf-RRN7 17 l.ddGfyyCrrC 27
                                      + ++G+ yC rC
  gi|557694273|ref|YP_008797327.1| 16 SyANGYKYCSRC 27
                                      5579******** PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.029
                           zf-RRN7  3 kgppCgvCg 11
                                      +g +C+ Cg
  gi|557694273|ref|YP_008797327.1| 34 DGVRCPYCG 42
                                      6889*9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 470.61
//
Query:       gi|557694274|ref|YP_008797328.1|  [L=373]
Description: acetylornithine deacetylase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-36  126.5   0.1    3.4e-36  124.9   0.1    1.7  1  Peptidase_M20  Peptidase family M20/M25/M40
    6.8e-14   51.7   0.0    1.3e-13   50.8   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain
     0.0012   18.6   0.0      0.002   17.8   0.0    1.3  1  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 !  124.9   0.1   5.7e-40   3.4e-36       2     206 ..      68     369 ..      67     370 .. 0.93

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 5.7e-40
                                       EEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTH CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgG 77 
                                       ++sHlD+Vp ++ ++w++ pfs+ + dG+l GrG++d kg ++a+l+a+ +l+ e +   g +vl++++dEE+++ G
  gi|557694274|ref|YP_008797328.1|  68 FNSHLDTVPVGPIERWSFhPFSTGVSDGYLCGRGSVDAKGVLAAMLAAVSTLRSERF--VGRVVLMAVADEEVSGLG 142
                                       89*******99999*****************************************86..89***********988** PP

                                       HHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE....................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................... RF
                     Peptidase_M20  78 akallegleerekvdavfelhieepgileagklaigvv....................................... 115
                                       + +l++  +  ++vd+   ++++ep+ l+       ++                                       
  gi|557694274|ref|YP_008797328.1| 143 SLSLIKL-L--DRVDY---MVVGEPTSLK-------ICvasrgrtevsvnfygrpahaskplegvnavtasaracvk 206
                                       ******3.3..59999...66********.......44458999********************************* PP

                                       ......................................................................EEEEEEE CS
                                       ......................................................................xxxxxxx RF
                     Peptidase_M20 116 ......................................................................kvevell 122
                                                                                                             ++e +  
  gi|557694274|ref|YP_008797328.1| 207 laqlekgfgkrhrymgrssaavtvmrgglkpnvipdssnividvrttvekpaetlrfikqfikpalprkaSFEATIT 283
                                       ********************************************************************874666666 PP

                                       EEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEES.SSBHTHHHHTTT.E.EEEEEESSG.GCTTSTTTEEEHHHH CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.x.xxxxxxxxx.xxxxxxxxxxxxxxx RF
                     Peptidase_M20 123 eggapvtln.dsplvkalaeaaeelfgekvelivsg.pggtdarffagi.p.tvmifgpgs.glaHspnEyvdledl 194
                                       ++ +p++++  + lv+a+++a++++ g+k+ l   g  ++td + ++++ p   +i+gpg+  laHs  E+v +++l
  gi|557694274|ref|YP_008797328.1| 284 SHIPPYMTKlGGTLVNACQQACRAA-GVKPVLA--GfDAATDLNRIHKVrPvEGVIIGPGDlRLAHSFREKVAVKEL 357
                                       ************************8.*665555..555********9998877799****99*************** PP

                                       HHHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                     Peptidase_M20 195 ekgikvlarlle 206
                                       +k++ +++ l+e
  gi|557694274|ref|YP_008797328.1| 358 VKAATIYKTLAE 369
                                       *******99987 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   2.1e-17   1.3e-13       2     106 ..     169     273 ..     168     277 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.1e-17
                                       EB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC......TCCTCCCCCEECCE-CCCCEESSEEE CS
                         M20_dimer   2 ghkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia.eerslprttlnvtgiegGsaknvipdeae 77 
                                       + +G  ++ + + g+ +H++ p  g+NA+++ ar+  +l ++e+  +   r+++r++ +vt+ +gG ++nvipd+  
  gi|557694274|ref|YP_008797328.1| 169 ASRGRTEVSVNFYGRPAHASKPLEGVNAVTASARACVKLAQLEKGFGkRHRYMGRSSAAVTVMRGGLKPNVIPDSSN 245
                                       789***************************************77766999*************************** PP

                                       EEEEEEHHHHHHHHHHHHHHHHHHTSCCS CS
                         M20_dimer  78 akidiRllpgedpeevleeieeilekeap 106
                                         id+R+   e+p+e l  i+++++ ++p
  gi|557694274|ref|YP_008797328.1| 246 IVIDVRTTV-EKPAETLRFIKQFIKPALP 273
                                       ******544.5666666666666665554 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.4e-07     0.002      14      83 ..      65     148 ..      59     180 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.4e-07
                                       EEEEEEE--B-TTT...............TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGS CS
                     Peptidase_M28  14 vlllgAHyDsvgvg...............rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEag 74 
                                       vl++++H+D+v+vg               +g     G  D     aa+L  + +l +  +r   +v+++++  EE +
  gi|557694274|ref|YP_008797328.1|  65 VLVFNSHLDTVPVGpierwsfhpfstgvsDGYlCGRGSVDAKGVLAAMLAAVSTLRS--ERFVGRVVLMAVADEEVS 139
                                       89******************9999988764547777999999999***********7..599*************** PP

                                       SHHHHHHHH CS
                     Peptidase_M28  75 llGSkafak 83 
                                        lGS  ++k
  gi|557694274|ref|YP_008797328.1| 140 GLGSLSLIK 148
                                       ****98884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2670.43
//
Query:       gi|557694275|ref|YP_008797329.1|  [L=219]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1587.35
//
Query:       gi|557694276|ref|YP_008797330.1|  [L=398]
Description: glutamine--scyllo-inositol transaminase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-111  371.3   0.0   7.2e-111  371.0   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    6.6e-06   25.5   0.0    1.7e-05   24.2   0.0    1.9  1  Aminotran_1_2    Aminotransferase class I and II
     0.0013   17.4   0.0     0.0019   16.8   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0035   16.3   0.0      0.013   14.4   0.0    1.7  2  Aminotran_5      Aminotransferase class-V
     0.0098   15.2   0.0      0.016   14.5   0.0    1.5  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
      0.033   14.5   0.1       0.28   11.5   0.0    2.5  2  Glyoxalase_4     Glyoxalase/Bleomycin resistance protein/Diox
       0.06   12.8   0.0       0.14   11.6   0.0    1.6  2  PEP_mutase       Phosphoenolpyruvate phosphomutase
       0.13   12.1   0.0         22    4.9   0.0    2.5  2  OST-HTH          OST-HTH/LOTUS domain


Domain annotation for each model (and alignments):
>> 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 !  371.0   0.0  3.2e-114  7.2e-111       3     360 ..      31     389 ..      30     390 .. 0.95

  Alignments for each domain:
  == domain 1  score: 371.0 bits;  conditional E-value: 3.2e-114
                                       HHHHHHHHHHHHTSS-SSS.SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHH CS
                   DegT_DnrJ_EryC1   3 keeeleaveevlksgwlts.gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatan 78 
                                       ++ee ++v evl+ g ++   ++++ FE++fa ++++ + ++++sG+ Al ++L+alg+gpgde Ivp++tF+ata 
  gi|557694276|ref|YP_008797330.1|  31 DDEEVREVLEVLREGPWSAgSSKIRLFEEEFASFHHAGYGVSCTSGSVALFVSLKALGLGPGDEAIVPAYTFLATAT 107
                                       68999**********77775889****************************************************** PP

                                       HHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT CS
                   DegT_DnrJ_EryC1  79 avlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg 155
                                       av+ +ga+pv vD+dp+tyni+p+a+ +a+te+t+ I+pVhl+G +admd++ + a+khgl v+eDaA+A+Ga+++g
  gi|557694276|ref|YP_008797330.1| 108 AVIDTGATPVIVDIDPTTYNISPEAVSKAVTEKTRCIIPVHLAGCPADMDKILETAEKHGLRVLEDAAQAHGAEWRG 184
                                       ***************************************************************************** PP

                                       EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHHH CS
                   DegT_DnrJ_EryC1 156 kkvGalgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAigla 232
                                       ++vG+lgd+a fSFy++Kn+++GeGG+++tn eelae ar l n G+++   + ++++v+ G n+r+t +qAA+++a
  gi|557694276|ref|YP_008797330.1| 185 RRVGSLGDMAGFSFYQSKNMAAGEGGIITTNIEELAELARSLVNVGRDV--RRGWYEHVRYGWNFRMTAFQAAVLRA 259
                                       **********************************************996..334444448***************** PP

                                       HHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHH.HC.HHHHHHHHHHCCEE-B-S CS
                   DegT_DnrJ_EryC1 233 qLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeae.vk.rdelvealkeegigtrvh 307
                                       qL+rl el+ +R++ ae ++e L+ ++g+++l+ p++ ++h++hly+v+v+ ++   + ++e+v+al++egi +++ 
  gi|557694276|ref|YP_008797330.1| 260 QLRRLPELNRKRTRSAEFLDESLRAIDGVEPLEKPPQVTAHSYHLYIVRVDVKKFgFSaKEEFVKALNAEGIPCNAG 336
                                       **************************************99***********99988666****************** PP

                                       GSCHGGGSCCHHHHHHCCCHC-HHHHHHHH.HEEEEEGGTTGS.HHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 308 ypnplhrqpvyaerkeeasgdlpnaerlae.rvlsLplypelt.eedvdrVveal 360
                                       y +pl+++ + ae+  + +  l+n+e++++ +++++p y+ l  +ed+ +Vvea+
  gi|557694276|ref|YP_008797330.1| 337 Y-RPLSSYWFIAEKS-RVPMPLKNTEKACQyEAVWIPQYVLLGeREDLMDVVEAF 389
                                       *.7***888888886.66889******997589*********9799******997 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 !   24.2   0.0   7.4e-09   1.7e-05      49     192 ..      57     178 ..      48     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7.4e-09
                                       HHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEET CS
                     Aminotran_1_2  49 leealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyse 125
                                       +ee+ a+f++        +   v ++sG+ al + l++l  l pgde +vp+ t+    +++   g++ v + ++ +
  gi|557694276|ref|YP_008797330.1|  57 FEEEFASFHH--------AGYGVSCTSGSVALFVSLKALG-LGPGDEAIVPAYTFLATATAVIDTGATPVIVDID-P 123
                                       999*******........888*******************.********************************66.9 PP

                                       TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTT CS
                     Aminotran_1_2 126 edfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYag 192
                                        ++++  ea+ +a++e      kt++i+   p +  G    +++  k+l++a+k++l+++ D a a+
  gi|557694276|ref|YP_008797330.1| 124 TTYNISPEAVSKAVTE------KTRCII---PVHLAG---CPADMDKILETAEKHGLRVLEDAAQAH 178
                                       9***************......777776...333333...345555556667777777777766555 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 !   16.8   0.0   8.4e-07    0.0019      55     175 ..      55     175 ..      49     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 8.4e-07
                                       HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHHHHH.HHHHTHHHTTCEEEEEST.TSHH CS
                   Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYggtqr.llkkvlkklgievkfvdt.sdle 128
                                       + +ee+ a  +++  ++ ++sG  A+++++ al l  Gde +v  + +  t   ++++ ++ + ++++ +    ++e
  gi|557694276|ref|YP_008797330.1|  55 RLFEEEFASFHHAGYGVSCTSGSVALFVSLKALgLGPGDEAIVPAYTFLATATaVIDTGATPVIVDIDPTTYnISPE 131
                                       5799***************************996678**********999876166777777777776655424799 PP

                                       HHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 129 elekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDnt 175
                                       ++ ka++e+t+++    p       +D+ ki+++a k+g+ v+ D++
  gi|557694276|ref|YP_008797330.1| 132 AVSKAVTEKTRCII---PVHLAGCPADMDKILETAEKHGLRVLEDAA 175
                                       ************96...444444557999999999999998887766 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   5.9e-06     0.013      49     181 ..      58     179 ..      49     182 .. 0.76
   2 ?   -0.9   0.0      0.28   6.2e+02     272     339 ..     263     337 ..     247     363 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.9e-06
                                       HHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBET.T CS
                       Aminotran_5  49 rekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkviplde.e 124
                                       +e++a +++a     +  tsG   +++l++   a  l pgde++v +    a+  +   +  +tga+ +++ +d+ +
  gi|557694276|ref|YP_008797330.1|  58 EEEFASFHHAGY--GVSCTSG---SVALFVSLKALGLGPGDEAIVPAYTFLATATAV--I--DTGATPVIVDIDPtT 125
                                       677777777774..4444444...4444444333359***********999988333..3..566666666666515 PP

                                       SCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTT CS
                       Aminotran_5 125 geldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavg 181
                                        ++ ++++ k+++ekt+ ++  h     G   ++++i + a k+g  vl Daaqa g
  gi|557694276|ref|YP_008797330.1| 126 YNISPEAVSKAVTEKTRCIIPVHL---AGCPADMDKILETAEKHGLRVLEDAAQAHG 179
                                       6899****************9996...7**************************976 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBS....EEEEEETTCSH...HHHHHHHHHTTEEEEEE- CS
                       Aminotran_5 272 gleaiekhekelaeyllerlkslpgvrlygpdkaerras....ivsfnfkgvha...edvatlLdeegIavrsGh 339
                                        l + +++ ++ ae l e l++++gv+ +++ ++   +s    iv + +k++     e+++++L+ egI   +G 
  gi|557694276|ref|YP_008797330.1| 263 RLPELNRKRTRSAEFLDESLRAIDGVEPLEKPPQVTAHSyhlyIVRVDVKKFGFsakEEFVKALNAEGIPCNAGY 337
                                       556677888999999999999999999987433332222112234444443322344666777777777666665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   7.3e-06     0.016      32     216 ..      52     238 ..      29     340 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.3e-06
                                       HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT. CS
                   Beta_elim_lyase  32 ktvnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkea. 106
                                       ++++ +e+++a    + +++ +++G  A  ++lk+l   +g+e iv  pa ++  ++ a+    g++++ ++++ + 
  gi|557694276|ref|YP_008797330.1|  52 SKIRLFEEEFASFHHAGYGVSCTSGSVALFVSLKALGlGPGDEAIV--PAYTFLATATAVID-TGATPVIVDIDPTt 125
                                       4444455555555555566668888888888888887788888876..55666666655544.45556666655544 PP

                                       TBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CH CS
                   Beta_elim_lyase 107 GkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivk 183
                                        ++++e++ +a++e      k+++i+     +  +G +   + ++++ ++a+k+g++++ D+A    a        +
  gi|557694276|ref|YP_008797330.1| 126 YNISPEAVSKAVTE------KTRCIIPV---HL-AGCP---ADMDKILETAEKHGLRVLEDAAQAHGAE----WRGR 185
                                       78888888888888......35566533...32.3555...55667788999***********877765....4456 PP

                                       HHHTTSSE..EEEESSSTT--SS-EEEEE-HH..................... CS
                   Beta_elim_lyase 184 emfsyvDs..vtmslkKdllanvGgvlafrddel..................e 216
                                       ++ s  D+  +++  +K++ a  Gg++ ++ +el                   
  gi|557694276|ref|YP_008797330.1| 186 RVGSLGDMagFSFYQSKNMAAGEGGIITTNIEELaelarslvnvgrdvrrgwY 238
                                       667777761156667*************9999776666666666544444441 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 ?   11.5   0.0   0.00013      0.28      38     103 ..     107     180 ..      65     187 .. 0.66
   2 ?   -0.2   0.0      0.54   1.2e+03      48      48 ..     265     265 ..     210     345 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                       EEEEEEEETTEEEEEEEESSTT-THHH.........TS-EEEEEEEEES-HHHHHHHHCTTTEEEEEEEE-GGGT CS
                      Glyoxalase_4  38 lafallgsgsvqieLieplegpeflae.........hgeglhhlaywvddldaavarleeqGfevvqkgvragaa 103
                                       +a+ ++g + + i  i p  ++ + ++         +     hla    d+d++++++e++G++v++ + +a++a
  gi|557694276|ref|YP_008797330.1| 107 TAVIDTGAT-PVIVDIDPTTYNISPEAvskavtektRCIIPVHLAGCPADMDKILETAEKHGLRVLEDAAQAHGA 180
                                       455555554.44444666666633333333555566667778999999******************877666554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.54
                                       E CS
                      Glyoxalase_4  48 v 48 
                                       +
  gi|557694276|ref|YP_008797330.1| 265 P 265
                                       0 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.4e-05      0.14      42      93 ..      87     139 ..      47     152 .. 0.88
   2 ?   -3.0   0.0       1.8     4e+03     204     232 ..     214     242 ..     204     245 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.4e-05
                        PEP_mutase  42 aslGvpDgeelpleellaavraiaevvslPlivDle.dGygespeevaetvrr 93 
                                         lG  D+ ++p+ + la++ a++++   P+ivD++ + y  spe v+++v++
  gi|557694276|ref|YP_008797330.1|  87 LGLGPGDEAIVPAYTFLATATAVIDTGATPVIVDIDpTTYNISPEAVSKAVTE 139
                                       45788999***************************977899999999999976 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.8
                        PEP_mutase 204 lsvaelaelGvarislgnhllraalaalr 232
                                       ++++elael  +++ +g  + r +++ +r
  gi|557694276|ref|YP_008797330.1| 214 TNIEELAELARSLVNVGRDVRRGWYEHVR 242
                                       56788888888888888888777777766 PP

>> OST-HTH  OST-HTH/LOTUS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0099        22       6      47 ..      31      72 ..      26      75 .. 0.84
   2 ?    4.5   0.0     0.014        31      39      57 ..     309     327 ..     302     328 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0099
                                      HHHHHHHHHHH.TTTT.SBEHHHHHHHHHHHHSST-STCCCTSS CS
                           OST-HTH  6 lkkeirelLrs.dpdg.wvslsrlgslykkkygksfdprkyGfs 47
                                       ++e+re+L   ++ g w + s+  +l+ +++  sf +  yG s
  gi|557694276|ref|YP_008797330.1| 31 DDEEVREVLEVlRE-GpWSAGSSKIRLFEEEFA-SFHHAGYGVS 72
                                      68889999988555.66****************.********85 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.014
                                       -STCCCTSSSHHHHHHTST CS
                           OST-HTH  39 fdprkyGfskLseLlkalp 57 
                                        d++k+Gfs  +e++kal+
  gi|557694276|ref|YP_008797330.1| 309 VDVKKFGFSAKEEFVKALN 327
                                       69***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2922.31
//
Query:       gi|557694277|ref|YP_008797331.1|  [L=185]
Description: hypothetical protein CSUB_C0844 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.7   0.0      0.025   14.5   0.0    1.6  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
       0.18   10.8   0.0       0.24   10.3   0.0    1.1  1  Glucokinase     Glucokinase


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   2.8e-06     0.025       1      29 [.      15      43 ..      15      44 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.8e-06
                                      EEETTEEEEEE-CCCHHHCCEECTCEEEE CS
                    MazE_antitoxin  1 fkvGnsgavriPkevrfelgireGdevel 29
                                      +++Gns++ +iP e+ +   ireG e ++
  gi|557694277|ref|YP_008797331.1| 15 RRSGNSLIATIPPELSQRFLIREGQEYTI 43
                                      689**********************9877 PP

>> Glucokinase  Glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   2.7e-05      0.24      30      75 ..      77     124 ..      65     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.7e-05
                       Glucokinase  30 yasadyasleealqaflaea..eaevkrpksavlAvAgpvegdevelt 75 
                                       +++ d++sle++l+++ a++   ++ ++ ++a+ Av ++ve+++v+l 
  gi|557694277|ref|YP_008797331.1|  77 VEGVDFQSLENLLKKYDATNvvLKKSENNSVACYAVFTAVEKNRVKLP 124
                                       6789************998766556666788*************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 1500.66
//
Query:       gi|557694278|ref|YP_008797332.1|  [L=195]
Description: transcriptional regulator, HxlR family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-28   97.2   0.1    7.8e-15   54.5   0.0    2.6  2  HxlR            HxlR-like helix-turn-helix
      6e-08   32.4   0.2    0.00014   21.7   0.1    2.5  2  HTH_5           Bacterial regulatory protein, arsR family
      1e-07   31.9   0.0     0.0018   18.2   0.0    2.2  2  HTH_45          Winged helix-turn-helix
    1.7e-05   24.8   0.0      0.084   12.9   0.0    2.3  2  HTH_20          Helix-turn-helix domain
    0.00055   19.8   0.0      0.008   16.1   0.0    2.7  2  PadR            Transcriptional regulator PadR-like family
    0.00096   19.6   0.0      0.041   14.4   0.0    2.4  2  HTH_27          Winged helix DNA-binding domain
     0.0066   16.8   0.0       0.19   12.1   0.0    2.3  2  Rrf2            Transcriptional regulator
      0.007   16.6   0.0        2.7    8.3   0.0    2.3  2  Rio2_N          Rio2, N-terminal
  ------ inclusion threshold ------
      0.017   15.2   0.0         21    5.3   0.0    3.3  3  Mrr_N           Mrr N-terminal domain
      0.019   14.8   0.0        6.9    6.6   0.0    2.5  2  MarR_2          MarR family
      0.047   13.8   0.1       0.47   10.5   0.0    2.5  3  HemN_C          HemN C-terminal domain
      0.071   12.7   0.1        5.1    6.7   0.0    2.5  2  HTH_24          Winged helix-turn-helix DNA-binding
      0.073   13.0   0.0         10    6.1   0.0    2.3  2  MarR            MarR family
      0.096   12.7   0.0       0.19   11.8   0.0    1.5  1  Replic_Relax    Replication-relaxation
       0.12   12.5   0.3          9    6.5   0.1    2.2  2  B-block_TFIIIC  B-block binding subunit of TFIIIC


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 !   40.2   0.0     2e-13   2.3e-10       5      79 ..      23      89 ..      19     101 .. 0.90
   2 !   54.5   0.0   6.5e-18   7.8e-15       2      85 ..     102     186 ..     101     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2e-13
                                      TTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHH CS
                              HxlR  5 kWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqel 79
                                      kW++ i+v++++g++Rf +l++ l +isqk+La++L +L +++l++ +v         Y ltekGr++ ++++ l
  gi|557694278|ref|YP_008797332.1| 23 KWTVPIIVSMVDGPRRFADLAKSL-GISQKVLAHKLSNLMKHQLVSMDVS-------GYILTEKGREIGELVKPL 89
                                      9***********************.9*******************98875.......49********99998876 PP

  == domain 2  score: 54.5 bits;  conditional E-value: 6.5e-18
                                       HHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEES.SSS-EEEEEE-TCGGGGHHHHH CS
                              HxlR   2 iggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevyp.evPpkveYsltekGrslepvlq 77 
                                       +  kW+  il +l +g+    el + lp++s k+ + rLr+L ++gl+er v   e P +v+Yslt++Gr l++ l+
  gi|557694278|ref|YP_008797332.1| 102 LKCKWSKEILQTLGDGPLHSAELVDSLPGLSWKIASDRLRKLCRHGLVERMVQTcESPIRVQYSLTPRGRLLAAWLN 178
                                       677***********************************************9865389******************** PP

                                       HHHHHHHH CS
                              HxlR  78 elkkwgee 85 
                                       +++k g++
  gi|557694278|ref|YP_008797332.1| 179 AFHKPGTQ 186
                                       99987776 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 !   21.7   0.1   1.2e-07   0.00014       7      46 ..      28      67 ..      26      68 .. 0.94
   2 !    8.5   0.0    0.0015       1.8       6      46 ..     109     150 ..     108     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.2e-07
                                      HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      I+ ++ +g++ + +la+ lg+sq  + h L+ L++  LV+
  gi|557694278|ref|YP_008797332.1| 28 IIVSMVDGPRRFADLAKSLGISQKVLAHKLSNLMKHQLVS 67
                                      889999*****************************99986 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0015
                                       HHHHHHTTSSEEHHHHHHHH.TS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   6 kILklLaegelcvcelaeel.glsqstvShHLkkLreaGLVe 46 
                                       +IL+ L +g+l + el++ l gls  + S  L+kL   GLVe
  gi|557694278|ref|YP_008797332.1| 109 EILQTLGDGPLHSAELVDSLpGLSWKIASDRLRKLCRHGLVE 150
                                       79******************99*******************7 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.5e-06    0.0018      18      68 ..      35      85 ..      24      90 .. 0.84
   2 !   11.6   0.0   0.00017      0.21      10      73 ..     109     181 ..     103     183 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                            HTH_45 18 geakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlellek 68
                                      g  +   + ++  +s k+l   L+ L++ +l++ + + Y lTekG+e+ e 
  gi|557694278|ref|YP_008797332.1| 35 GPRRFADLAKSLGISQKVLAHKLSNLMKHQLVSMDVSGYILTEKGREIGEL 85
                                      555666777888999999*****************************9766 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00017
                            HTH_45  10 dILeaisegeakkTkimyka.nLsykllnkYLdmLvekgli........kkskekYvlTekGlelleklkele 73 
                                       +IL+ + +g  +  +++ +   Ls+k+++  L +L   gl+        +    +Y+lT +G+ l   l+ ++
  gi|557694278|ref|YP_008797332.1| 109 EILQTLGDGPLHSAELVDSLpGLSWKIASDRLRKLCRHGLVermvqtceSPIRVQYSLTPRGRLLAAWLNAFH 181
                                       6788887888888888877647******************999988875557899*******99988777765 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00072      0.86      19      57 ..      23      69 ..       3      73 .. 0.74
   2 !   12.9   0.0   7.1e-05     0.084      14      56 ..     109     151 ..     105     152 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00072
                                      H........STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 19 L........araegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                               + ++++ +++la+ l++s++ l + L  L ++ Lv   
  gi|557694278|ref|YP_008797332.1| 23 KwtvpiivsMVDGPRRFADLAKSLGISQKVLAHKLSNLMKHQLVSMD 69
                                      1555555666699*************************999999765 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 7.1e-05
                                       HHHHHHSTCTTB-HHHHHHHH.TS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  14 rilraLaraegltaselaerl.dlskntlsyHLrvLeeagLvev 56 
                                       +il+ L ++++l  +el + l +ls + +s++Lr+L ++gLve+
  gi|557694278|ref|YP_008797332.1| 109 EILQTL-GDGPLHSAELVDSLpGLSWKIASDRLRKLCRHGLVER 151
                                       79****.**************99*******************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 ?   -0.4   0.0      0.95   1.1e+03      63      71 ..      73      81 ..      55      83 .. 0.71
   2 !   16.1   0.0   6.7e-06     0.008       1      71 [.     110     172 ..     110     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.95
                                      EEESHCCCH CS
                              PadR 63 YrlTdaGrr 71
                                      Y lT++Gr+
  gi|557694278|ref|YP_008797332.1| 73 YILTEKGRE 81
                                      778888875 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 6.7e-06
                                       HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                              PadR   1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71 
                                       iL+ l+++p++  e+++ l  l    +++      + L++L ++glve+  ++  e+p r  Y lT++Gr 
  gi|557694278|ref|YP_008797332.1| 110 ILQTLGDGPLHSAELVDSLPGL--S-WKIAS----DRLRKLCRHGLVERMVQT-CESPIRVQYSLTPRGRL 172
                                       6788888888888888888888..4.66655....689************998.59*************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 ?    2.9   0.0      0.13   1.6e+02      14      68 .]      32      79 ..      24      79 .. 0.79
   2 !   14.4   0.0   3.5e-05     0.041      11      68 .]     113     170 ..     109     170 .. 0.67

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.13
                            HTH_27 14 hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      + +++ + adl++ l +++   +  l+ L ++ Lv +  +        + lT+kG
  gi|557694278|ref|YP_008797332.1| 32 MVDGPRRFADLAKSLGISQKVLAHKLSNLMKHQLVSMDVSG-------YILTEKG 79
                                      446666779**********9999999999999999666655.......8888887 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.5e-05
                            HTH_27  11 lirhrrrrkkladlcgrlnvedshis.yslkkLtekGLv..ertgdeadrrekrvrlTdkG 68 
                                       +++  +++ + a+l++ l   +  i+   l+kL+++GLv  + +++e +  +++++lT+ G
  gi|557694278|ref|YP_008797332.1| 113 TLG--DGPLHSAELVDSLPGLSWKIAsDRLRKLCRHGLVerMVQTCE-SPIRVQYSLTPRG 170
                                       555..666666666666655555566699**********53223444.445599****998 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00016      0.19      26      57 ..      37      68 ..      26      83 .. 0.82
   2 ?    2.1   0.0      0.21   2.5e+02      23      56 ..     116     150 ..     109     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 26 vsseeiaerqnispsylekilakLrkaglvks 57
                                       + +++a++ +is+++l++ l++L k+ lv  
  gi|557694278|ref|YP_008797332.1| 37 RRFADLAKSLGISQKVLAHKLSNLMKHQLVSM 68
                                      56789************************975 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.21
                                       CC-B-HHHHHHHH.TS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2  23 eepvsseeiaerq.nispsylekilakLrkaglvk 56 
                                       ++p+ s+e+ ++  ++s ++++  l+kL ++glv+
  gi|557694278|ref|YP_008797332.1| 116 DGPLHSAELVDSLpGLSWKIASDRLRKLCRHGLVE 150
                                       45677888888776899999999999999999997 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0022       2.7      33      70 ..      45      79 ..      39      82 .. 0.83
   2 ?    6.0   0.0     0.012        14      27      57 ..     122     152 ..     119     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0022
                            Rio2_N 33 isrlkeeevkkrlsrllkaklisrktakydGYkLtyeG 70
                                        +++++ + ++ls+l+k++l+s +     GY Lt +G
  gi|557694278|ref|YP_008797332.1| 45 SLGISQKVLAHKLSNLMKHQLVSMD---VSGYILTEKG 79
                                      55678888999***********987...6999999887 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.012
                            Rio2_N  27 telieeisrlkeeevkkrlsrllkaklisrk 57 
                                        el+ ++ +l+ +  ++rl++l++++l++r 
  gi|557694278|ref|YP_008797332.1| 122 AELVDSLPGLSWKIASDRLRKLCRHGLVERM 152
                                       6788899999999999*************93 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.16   1.9e+02      59      84 ..      58      82 ..      47      84 .. 0.76
   2 ?    5.3   0.0     0.018        21       6      27 ..     108     128 ..     105     148 .. 0.85
   3 ?    3.6   0.0     0.059        71      67      83 ..     156     172 ..     150     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.16
                             Mrr_N 59 tyLkkagllespkrgvwkiTekGrev 84
                                      ++L k +l++ +  + + +TekGre+
  gi|557694278|ref|YP_008797332.1| 58 SNLMKHQLVSMD-VSGYILTEKGREI 82
                                      566666666666.56689******86 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.018
                             Mrr_N   6 lplLealadgsehrlkeirerv 27 
                                       +++L++l dg +h+ +e+++ +
  gi|557694278|ref|YP_008797332.1| 108 KEILQTLGDGPLHS-AELVDSL 128
                                       789**********9.**99976 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.059
                             Mrr_N  67 lespkrgvwkiTekGre 83 
                                        esp r ++++T++Gr 
  gi|557694278|ref|YP_008797332.1| 156 CESPIRVQYSLTPRGRL 172
                                       68999**********95 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0      0.01        12      18      51 ..      34      66 ..      28      81 .. 0.84
   2 ?    6.6   0.0    0.0057       6.9      38      53 ..     136     151 ..     110     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.01
                                      TTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2 18 pgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                      +g++ + ++la+ lg+s+  +   l  L ++ Lv
  gi|557694278|ref|YP_008797332.1| 34 DGPR-RFADLAKSLGISQKVLAHKLSNLMKHQLV 66
                                      4554.99***********9998888888888887 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0057
                                       HHHHHHHHHHTTSEEE CS
                            MarR_2  38 vsrilkrLvaaGLver 53 
                                       +s +l++L ++GLver
  gi|557694278|ref|YP_008797332.1| 136 ASDRLRKLCRHGLVER 151
                                       7999***********8 PP

>> HemN_C  HemN C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00039      0.47      23      65 ..      39      80 ..      38      81 .. 0.94
   2 ?   -1.2   0.0       1.9   2.3e+03      36      52 ..     134     150 ..     123     151 .. 0.75
   3 ?   -0.9   0.0       1.4   1.7e+03      58      66 .]     164     172 ..     163     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00039
                            HemN_C 23 laafeqrfgldleellaaaleklqeqGLLeldggrlrltprGr 65
                                      +a+++   g++ +++la +l  l+++ L+++d +++ lt++Gr
  gi|557694278|ref|YP_008797332.1| 39 FADLAKSLGIS-QKVLAHKLSNLMKHQLVSMDVSGYILTEKGR 80
                                      68899999999.9999**************************8 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                            HemN_C  36 ellaaaleklqeqGLLe 52 
                                       ++  + l+kl ++GL+e
  gi|557694278|ref|YP_008797332.1| 134 KIASDRLRKLCRHGLVE 150
                                       44467799999999997 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.4
                            HemN_C  58 lrltprGrl 66 
                                       ++ltprGrl
  gi|557694278|ref|YP_008797332.1| 164 YSLTPRGRL 172
                                       589****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 ?    6.7   0.0    0.0043       5.1      21      43 ..      40      62 ..      34      66 .. 0.87
   2 ?    3.3   0.0     0.049        59      34      48 .]     136     150 ..     130     150 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0043
                            HTH_24 21 reLAerlglSpstvnrrlkrLee 43
                                      ++LA+ lg+S+  +   l +L++
  gi|557694278|ref|YP_008797332.1| 40 ADLAKSLGISQKVLAHKLSNLMK 62
                                      79*********999999999987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.049
                            HTH_24  34 vnrrlkrLeeeGlIk 48 
                                        + rl++L++ Gl++
  gi|557694278|ref|YP_008797332.1| 136 ASDRLRKLCRHGLVE 150
                                       578*********996 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.023        27      17      48 ..      36      67 ..      33      68 .. 0.88
   2 ?    6.1   0.0    0.0087        10      34      50 ..     136     152 ..     111     155 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.023
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 17 plsvseLakklgvskstvtrvldrLekkGlie 48
                                      p + ++Lak lg+s+  +   l  L k+ l++
  gi|557694278|ref|YP_008797332.1| 36 PRRFADLAKSLGISQKVLAHKLSNLMKHQLVS 67
                                      55788*************99999999999985 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0087
                                       HHHHHHHHHHTTSEEEE CS
                              MarR  34 vtrvldrLekkGlieRs 50 
                                       ++  l++L ++Gl+eR+
  gi|557694278|ref|YP_008797332.1| 136 ASDRLRKLCRHGLVERM 152
                                       7889************7 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.19      27      70 ..     136     174 ..     119     192 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                      Replic_Relax  27 arrrLarLrelgllsr.lrkrvggarggsepyvYaLtpkGarlla 70 
                                       a++rL++L+++gl++r ++    +      +  Y Ltp G rlla
  gi|557694278|ref|YP_008797332.1| 136 ASDRLRKLCRHGLVERmVQTC--ESPI---RVQYSLTPRG-RLLA 174
                                       789*************55544..3333...579*******.5553 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 ?    6.5   0.1    0.0075         9      23      50 ..      41      68 ..      39      71 .. 0.94
   2 ?    3.9   0.0     0.051        61      38      50 ..     139     151 ..     134     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0075
                    B-block_TFIIIC 23 dLakeskqdprslfyrlksLekkgLIvk 50
                                      dLak+++++ + l + l  L+k++L+ +
  gi|557694278|ref|YP_008797332.1| 41 DLAKSLGISQKVLAHKLSNLMKHQLVSM 68
                                      9*************************87 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.051
                    B-block_TFIIIC  38 rlksLekkgLIvk 50 
                                       rl++L+++gL+++
  gi|557694278|ref|YP_008797332.1| 139 RLRKLCRHGLVER 151
                                       899********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1391.61
//
Query:       gi|557694279|ref|YP_008797333.1|  [L=207]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  115.1   0.1    3.6e-33  114.7   0.1    1.2  1  Protoglobin  Protoglobin


Domain annotation for each model (and alignments):
>> Protoglobin  Protoglobin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.7   0.1     2e-37   3.6e-33       2     157 ..      33     206 ..      32     207 .] 0.98

  Alignments for each domain:
  == domain 1  score: 114.7 bits;  conditional E-value: 2e-37
                                       GHHHHHHHHHTT-SHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSHHHHHHHCH.......HCHHHHHHHHHHHHH CS
                       Protoglobin   2 earlayllsflglteedlaaLralapliealipavvdafYekllsfpetarifet.......ssqierlkdflksyl 71 
                                       +++++ l+ ++ +t+ed+++Lr++++++ +++++v+d +Y ++ s+++++++f +        ++++ +++++ +++
  gi|557694279|ref|YP_008797333.1|  33 DEEFRLLKTTVLMTDEDIRYLRMAGEVLRDQVDDVLDLWYGWVGSHKHLVYYFGDrksgqpiGEYLQAVRKRFGQWI 109
                                       6899************************************************************************* PP

                                       HHCCCSSCCHHHHHHHHHHHHHHC............HCT--HHHHHHCHHHHHHHHHHHHCCCS.-SHHHHHHHHHH CS
                       Protoglobin  72 lklfsgpfdsayveyldkvGkmht............rlgleprwyiaalglvqevlleallekeklsaaektalvka 136
                                       l+++ +++d+++++y+ ++G +h+              ++++r++ia++ ++++++ ++l++k+ +s+++++++++a
  gi|557694279|ref|YP_008797333.1| 110 LDTCFREYDRDWLNYQYEIGLRHHrskknktdkvdsVDHIPLRYLIAFIVPITATIKPFLAKKG-HSQEDVEKMYAA 185
                                       ****************************************************************.************ PP

                                       HHHHHHHHHHHHCGGGBXTTX CS
                       Protoglobin 137 lnKliwldndlaleaYvrege 157
                                       ++K+++l ++l++ +Y ++ge
  gi|557694279|ref|YP_008797333.1| 186 WFKAVTLSVALWSIPYANKGE 206
                                       *****************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1571.12
//
Query:       gi|557694280|ref|YP_008797334.1|  [L=110]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   22.3   0.0    0.00015   22.0   0.0    1.2  1  dsDNA_bind  Double-stranded DNA-binding domain


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 !   22.0   0.0   8.4e-09   0.00015      23     108 ..       9      95 ..       1      98 [. 0.85

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.4e-09
                                       .XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH--SS-----HHHHHHHHHHHS- CS
                        dsDNA_bind  23 seqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaqsGqlrskvteeqLkeLLeqvae 99 
                                       + + eqq + + +e   +++++ L p+  e L+      p +++a+ ++L ql+++Gq+++ ++  +L +L++++  
  gi|557694280|ref|YP_008797334.1|   9 QVKAEQQPKPAPAETPLEVVKKHLGPRGDEVLQAAYEQYPVETAAIVEKLAQLIKMGQISEPLDGGELYNLFRSLGL 85 
                                       34455556666999999********************************************************9988 PP

                                       .--XXXXX.. CS
                        dsDNA_bind 100 .kkketkivi 108
                                         + etki++
  gi|557694280|ref|YP_008797334.1|  86 rVRLETKITY 95 
                                       6666688876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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: 00:00:00.41
# Mc/sec: 813.35
//
Query:       gi|557694281|ref|YP_008797335.1|  [L=430]
Description: zinc-dependent protease, TldD/PmbA family [Candidatus Caldiarchaeum subterraneum]
Scores for 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  142.1   0.0      4e-41  141.7   0.0    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 !  141.7   0.0   2.2e-45     4e-41      33     278 ..       2     278 ..       1     278 [. 0.89

  Alignments for each domain:
  == domain 1  score: 141.7 bits;  conditional E-value: 2.2e-45
                                       EEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-.....................GGS-HHHHHHHHH CS
                         PmbA_TldD  33 gvrvikggrlgfastldtsdealeeaveraveiaklapedpea.....................eevsaeekielle 88 
                                       g+r+++ g+lgf++ +++++++l++av +a  +ak a    +                      ++v+  +kiell+
  gi|557694281|ref|YP_008797335.1|   2 GIRLLYRGSLGFSYVNQLDRASLRKAVAAAFGMAKAAVTRSQDvrmseeklvkasdikkpriryDDVDNRDKIELLK 78 
                                       9**9999*****999999999*************88777777799******************************** PP

                                       HHHHH.CHCSTTEEEEE..EEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEEEEEEE...S.TCS..ET.EE CS
                         PmbA_TldD  89 elekalrsadpkiensk..garisgvsaslsaskeeklianSeGldveqtrtrvslslsvia.d.d.ggs..gd.gm 157
                                       e+++a  +a       +  g++++++ ++l  + +ek+++nS+G dv+    r+++++ ++a   + g       ++
  gi|557694281|ref|YP_008797335.1|  79 EADAAGVEAA------DklGVKLVSRFIELGKWGTEKHVVNSDGGDVRFMVERATANYIITAyHpQrG-VvqRFeNL 148
                                       ***8744333......33688*****************************************887742.35645567 PP

                                       EEEEEESSHHH.S..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHHHHTBHHHHH......TT-- CS
                         PmbA_TldD 158 gggsgyedlee.edleeiaeeaaekalasleakplppgkypVvlspeavgsllheavghaleadavl......egrS 227
                                       g  sg+e +e+ + + ++aeea++  +a+l+ +++p    +Vvl++e vg+  he++gh+ ead++l      +g +
  gi|557694281|ref|YP_008797335.1| 149 GESSGWEAVERwDLPGRLAEEARDISKALLKGVEPPREPVDVVLGSEIVGLVCHESCGHPGEADRMLgreaaqAGET 225
                                       77888844444444779*************989988889****************************9988888999 PP

                                       TTTT-.TTSB-S-TT--EEEETT-......-SB-TTSBB---EEEEETTEE-- CS
                         PmbA_TldD 228 flkdk.lGekvaselltivddpts.gglgsypfDdEGvptqrtvlIenGvLkn 278
                                         k+  +G++++se++t+vddp+   ++g+y +DdE v+t+++vlI++GvL +
  gi|557694281|ref|YP_008797335.1| 226 YVKPElFGTRIGSEHVTVVDDPRLpRSFGYYLYDDECVATSERVLIDRGVLSG 278
                                       998846*****************99**************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 3160.24
//
Query:       gi|557694282|ref|YP_008797336.1|  [L=167]
Description: large subunit ribosomal protein L10e [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   96.7   0.1    1.2e-27   96.5   0.1    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e


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 !   96.5   0.1   6.7e-32   1.2e-27       4     132 .]      12     159 ..       1     159 [. 0.87

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 6.7e-32
                                       SXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC..EEXXSXXX CS
                     Ribosomal_L16   4 kkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk..klwirvfp 69 
                                         y +   +yi+g + +++tk++ g         + L+ + + q+++ a+e+ari++n+yl++k ++   l + ++p
  gi|557694282|ref|YP_008797336.1|  12 MTYARV--EYIHGPPpSRITKYNAGVyrsdytheLLLIPETDLQIRDVAIESARITVNKYLTEKLNDrfYLEVTAHP 86 
                                       344444..5*****************77777655559999**********************87777789999**** PP

                                       XEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE...TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                     Ribosomal_L16  70 hhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei...kagvneeiakealrraasKlpiktkiv 132
                                       hh+++++     a +dR+++G+    Gkp g +arv++g+++f +    +      a+eal++aa+Klp k+ iv
  gi|557694282|ref|YP_008797336.1|  87 HHVLRENkmifgAHADRLQEGMrrafGKPIGRAARVEMGEPVFRLltyAD--GVRAAREALELAAKKLPKKYYIV 159
                                       *********************************************87655..45567**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 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:                        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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1294.05
//
Query:       gi|557694283|ref|YP_008797337.1|  [L=134]
Description: ribonuclease HI [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   87.1   0.1      1e-24   86.7   0.1    1.2  1  RVT_3     Reverse transcriptase-like
    2.2e-18   66.8   0.1    2.9e-18   66.4   0.1    1.2  1  RNase_H   RNase H
  ------ inclusion threshold ------
       0.22   11.8   1.1        2.1    8.6   0.2    2.2  2  DUF3970   Protein of unknown function (DUF3970)


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 !   86.7   0.1   1.7e-28     1e-24       2     124 .]       9     128 ..       8     128 .. 0.93

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 1.7e-28
                             RVT_3   2 fdgafkkksgaggagvvirdsnGevllagaeklqgkasveeAElqALlrGLqlalklgirrlvvegDsktvvqllng 78 
                                       +dga + + g +g+g++i   +  + +  +    g a++ +AE+ AL+  L++al+lg+++ +v +Ds+ +v+++ng
  gi|557694283|ref|YP_008797337.1|   9 VDGASRGNPGPAGIGYIIKIGDQSFKHREH---IGVATNNQAEYHALIKSLEKALQLGVKKAHVYSDSELLVKQVNG 82 
                                       7999999***********866664444333...8899**************************************** PP

                             RVT_3  79 rekvksselanlldeirkllksfesvsvehipReqNrvAdalAkra 124
                                         k++++ l  l+++ ++l+++fe+++++h+ Re+Nr Ad lA++a
  gi|557694283|ref|YP_008797337.1|  83 AYKIRNNTLTILHQKLQQLITRFEEFHITHVDREKNREADRLANQA 128
                                       ********************************************86 PP

>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.1   4.9e-22   2.9e-18       4     142 ..       5     129 ..       2     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 4.9e-22
                                       EEEEEEEEEECTTTCEEEEEEECTT..EEEEEEEC.CCCHHHHHHHHHHHHHHH.TT.SC.SEEEEEES-HHHHHHH CS
                           RNase_H   4 vvvYtDGsclgnpgeggagavlykegarnisaple.eaqtnnraELsAvieaLk.alksd.ekvniytDSkYvvkgi 77 
                                         +Y+DG+++gnpg++g+g++++ + ++ ++++ + +  tnn+aE +A+i++L+ al+ + +k ++y+DS+ +vk +
  gi|557694283|ref|YP_008797337.1|   5 AEIYVDGASRGNPGPAGIGYIIKIG-DQSFKHREHiGVATNNQAEYHALIKSLEkALQLGvKKAHVYSDSELLVKQV 80 
                                       679*****************99544.47888888889*****************88888889999**********77 PP

                                       HCCCHHHHHTTSSSETTSSBHTTHHHHHHHHHCHCSSEEEEEE-SCCSSSTHHHHHHHHHHHHHH CS
                           RNase_H  78 tqwvhrwkknawkttseqkpvknkdlaellkelakkkkvqlkwvkgHaGvpkgNemaDrlAkeaa 142
                                       +   +     + ++++    +  ++l++l+   ++ +++++++v       ++N++aDrlA++a+
  gi|557694283|ref|YP_008797337.1|  81 NG-AY-----KIRNNTLT--ILHQKLQQLI---TRFEEFHITHVD----R-EKNREADRLANQAI 129
                                       76.22.....22222222..4555788887...777889999995....4.69*********986 PP

>> DUF3970  Protein of unknown function (DUF3970)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.04   2.4e+02      10      30 ..      46      70 ..      39      98 .. 0.64
   2 ?    8.6   0.2   0.00035       2.1      13      36 ..      98     120 ..      94     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.04
                           DUF3970 10 qeEieeflkslek....nyevtytS 30
                                      q E   ++kslek    + ++ ++ 
  gi|557694283|ref|YP_008797337.1| 46 QAEYHALIKSLEKalqlGVKKAHVY 70
                                      7888999999999665555555554 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00035
                           DUF3970  13 ieeflksleknyevtytSkeytrt 36 
                                       +++++  +e ++++t++ +e  r 
  gi|557694283|ref|YP_008797337.1|  98 LQQLITRFE-EFHITHVDREKNRE 120
                                       678888887.5*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1006.47
//
Query:       gi|557694284|ref|YP_008797338.1|  [L=258]
Description: pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [Candidatus Caldiarchaeum subterraneum]
Scores for 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-58  196.5   0.0    5.9e-58  196.1   0.0    1.1  1  2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catal
  ------ inclusion threshold ------
      0.019   14.8   0.1      0.039   13.8   0.1    1.5  1  VbhA          Antitoxin VbhA


Domain annotation for each model (and alignments):
>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.1   0.0   6.5e-62   5.9e-58       5     227 ..      45     254 ..      42     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 196.1 bits;  conditional E-value: 6.5e-62
                                       XXXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GGGG CS
                      2-oxoacid_dh   5 ervplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPeln 81 
                                       + v+lsg+rka+a+rl  s ++   + l+ e+d+  l+ + +  +ek+ + +   ++++++++k+va Al  + e+n
  gi|557694284|ref|YP_008797338.1|  45 RVVKLSGLRKAVAERLGYSFRNSLPVALMTEYDAGPLMMVYRGAREKFGE-K--SPSITAYVVKCVASALTVHGEFN 118
                                       679*******************************************9973.3..79********************* PP

                                       -EE.EESEEEE--SS--EEEE--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE---- CS
                      2-oxoacid_dh  82 asvdeeekeivvkkhvniGvAvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNlGm 158
                                       a ++++e  i+v ++vni+vAv+tprGL+ P i+n+dkk+ +e+++el++laeka +g+++ ++l g  ft+sNlG 
  gi|557694284|ref|YP_008797338.1| 119 ANIEGDE--IRVLDEVNIAVAVDTPRGLYAPTIRNVDKKTAVEVEAELRALAEKAVKGTITLNELAGHGFTVSNLGH 193
                                       *******..******************************************************************** PP

                                       -----------TT-SEEEEE---.B--TTSTT-HT---EEEEEEEEETTT--HHHHHHHHHHHHHTT-H CS
                      2-oxoacid_dh 159 lGvtsftPiinppqvaIlgvgrikerpvvkegelvvrkvmtlslsaDHRvidGaeaarFlntlkkllen 227
                                       lGvt+ftPiinpp+ aIlgvg+ik        +   r++ +l+l +DHR+ dGa aarFl+++++ le+
  gi|557694284|ref|YP_008797338.1| 194 LGVTHFTPIINPPDIAILGVGAIK--------NTGDRHRGYLTLVFDHRAADGAPAARFLEEIRHQLES 254
                                       ***********************4........45678999*************************9997 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   4.4e-06     0.039      17      40 ..     158     181 ..     157     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.4e-06
                              VbhA  17 lepsaetvadleayvrGeIdadEl 40 
                                       +e+ ae++a++e+ v+G+I+++El
  gi|557694284|ref|YP_008797338.1| 158 VEVEAELRALAEKAVKGTITLNEL 181
                                       699*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2000.19
//
Query:       gi|557694285|ref|YP_008797339.1|  [L=341]
Description: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-78  261.2   0.0    5.3e-78  260.9   0.0    1.1  1  DUF1297   Domain of unknown function (DUF1297)
    5.3e-44  149.1   0.0    7.8e-44  148.6   0.0    1.3  1  DUF1246   Protein of unknown function (DUF1246)


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 !  260.9   0.0   5.9e-82   5.3e-78       2     188 .]     154     341 .]     153     341 .] 0.99

  Alignments for each domain:
  == domain 1  score: 260.9 bits;  conditional E-value: 5.9e-82
                                       HHHHHHHHHCTTSSSHHHHCCEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT--- CS
                           DUF1297   2 feekleellekglieeedlkkasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelevep 78 
                                       +e+kl e+++kgl++e++l+++s+ee+v+Ga+fn+n+f+s +k+++el++idrR++snldg+ rl a eqlel+  +
  gi|557694285|ref|YP_008797339.1| 154 LEKKLGEMIAKGLVDEKSLERVSVEELVLGAHFNANFFHSVVKGRLELHSIDRRIQSNLDGVIRLAAAEQLELNPLI 230
                                       6899************************************************************************* PP

                                       -EEEEEEEEEEE-GGGHHHHHHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT.--C CS
                           DUF1297  79 eyvvvGnipvvlREsllekvfelgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvyme.gsp 154
                                       +y++vG++p+++REsllekvf++gekfvea+++lv+pG+iGpF+Lq +vt++l+lvv+dv++Ri+ggtnvy++ g++
  gi|557694285|ref|YP_008797339.1| 231 RYIEVGHEPATIRESLLEKVFTIGEKFVEACSRLVSPGVIGPFTLQFLVTPELDLVVYDVAPRIGGGTNVYLGfGGQ 307
                                       ***************************************************************************** PP

                                       CHHHTTSS---HHHHHHHHHHHHHHCT-GGGCEE CS
                           DUF1297 155 yskllfgeplsmGrrialEikeaiekdrleeivt 188
                                       yskl++g+p++mGrria+Ei+ea+e+++l++++t
  gi|557694285|ref|YP_008797339.1| 308 YSKLYHGRPVTMGRRIAMEIREAVEQNMLSRVTT 341
                                       *******************************987 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.6   0.0   8.7e-48   7.8e-44       3     122 .]       1     121 [.       1     121 [. 0.98

  Alignments for each domain:
  == domain 1  score: 148.6 bits;  conditional E-value: 8.7e-48
                                       EESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHHHC CS
                           DUF1246   3 tlaSHsalqilkgAkkegfrtlavcekgreklYekfkvidevivldkfkdilkeevqeklreenailvPhgsfveYv 79 
                                       +laSHsal++l+gA++egfrt+av+++grek+Y+ f+v+de++++d+f++i++++v ekl+  ++++vP++sf++Yv
  gi|557694285|ref|YP_008797339.1|   1 MLASHSALDVLDGAREEGFRTVAVAKRGREKAYRMFPVVDELVLVDEFHEIIEDHVLEKLA--DSVFVPNRSFAVYV 75 
                                       58*********************************************************98..78************ PP

                                       -HHHHH.C-SS-EES-TTHHHHHCSHHHHHHH..HHHTT-BB--BE CS
                           DUF1246  80 giekie.elkvpifGnrkllrwEerrekkrky..LekAgiriPkki 122
                                       g+++ie ++++p+fGnr llrwEer  ++++y  L+ Agir+P+++
  gi|557694285|ref|YP_008797339.1|  76 GYDAIEkQFRIPVFGNRFLLRWEERVGETSYYrlLDAAGIRRPRTY 121
                                       *********************************9*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2881.88
//
Query:       gi|557694286|ref|YP_008797340.1|  [L=330]
Description: 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  184.1   0.1    3.2e-54  183.3   0.1    1.4  1  DUF1297      Domain of unknown function (DUF1297)
    2.1e-39  134.3   0.0    4.4e-39  133.2   0.0    1.6  1  DUF1246      Protein of unknown function (DUF1246)
     0.0049   16.9   0.0     0.0098   16.0   0.0    1.4  1  ATP-grasp_3  ATP-grasp domain
  ------ inclusion threshold ------
       0.02   14.4   0.0      0.035   13.6   0.0    1.3  1  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin


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 !  183.3   0.1   7.2e-58   3.2e-54      22     187 ..     171     329 ..     158     330 .] 0.96

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 7.2e-58
                                       CEEEEE---SEEEEEEEEEETTTTEEEEEEEEEEEEEECCCHCCS-HHHHHCCT----EEEEEEEEEEE-GGGHHHH CS
                           DUF1297  22 kasieeyvvGanfnlnyfysplkeevellgidrRyesnldglvrlpakeqlelevepeyvvvGnipvvlREsllekv 98 
                                         +i++y++G+ ++++yf+sp+ ++ve++g d+Rye+n+dg v   a+        p++vvvGn p+v+REsll++ 
  gi|557694286|ref|YP_008797340.1| 171 PHIIQRYIIGVGVYMHYFSSPMFGRVEVFGADTRYETNVDGRVFGLAE--------PSFVVVGNRPLVVRESLLPRY 239
                                       4689*************************************9887775........9******************** PP

                                       HHHHHHHHHHHHHHSTT---EEEEEEEEE-TTS-EEEEEEESSB-GGGGGGTT.--CCHHHTTSS---HHHHHHHHH CS
                           DUF1297  99 felgekfveaakklvppGiiGpFcLqsvvtkdlelvvfdvsaRivggtnvyme.gspyskllfgeplsmGrrialEi 174
                                       +++ge+f +a+++++   +iGpFcL++++t++ e+ +f++s Riv+gtnvym+ gspys l+f++p+ mG ria E+
  gi|557694286|ref|YP_008797340.1| 240 MRYGEQFASAVEQTLGTPMIGPFCLETIITDTFEIKCFEFSGRIVAGTNVYMGtGSPYSVLYFDKPMDMGERIAHEL 316
                                       ***************************************************************************** PP

                                       HHHHHCT-GGGCE CS
                           DUF1297 175 keaiekdrleeiv 187
                                       + a+ek++le+i+
  gi|557694286|ref|YP_008797340.1| 317 RAAAEKNCLEKIT 329
                                       ***********96 PP

>> DUF1246  Protein of unknown function (DUF1246)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.2   0.0   9.8e-43   4.4e-39       1     122 []      11     129 ..      11     129 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.2 bits;  conditional E-value: 9.8e-43
                                       EEEESSTTHHHHHHHHHHTT--EEEEC-CCCHHHHHTTTT-SEEEE.S.S..TTSS--HHHHHHTTCEE--BTTHHH CS
                           DUF1246   1 iatlaSHsalqilkgAkkegfrtlavcekgreklYekfkvidevivldkfkdilkeevqeklreenailvPhgsfve 77 
                                       +at+aSH+alq+l++Akk+gfrt+a+c ++++ +Yekf++ide+++++   d l ++++ kl+e+n++++Phgsfve
  gi|557694286|ref|YP_008797340.1|  11 VATVASHTALQLLRAAKKTGFRTAAICLTDNKPFYEKFGFIDEIYTASV--DTL-DKLAPKLTEHNTVFIPHGSFVE 84 
                                       79*****************************************998543..445.56799***************** PP

                                       HC-HHHHHC-SS-EES-TTHHHHHCSHHHHHHHHHHTT-BB--BE CS
                           DUF1246  78 YvgiekieelkvpifGnrkllrwEerrekkrkyLekAgiriPkki 122
                                       Y+g ek++++kvp+fG+r+l+++E+++++k+ +L++A i++P+++
  gi|557694286|ref|YP_008797340.1|  85 YCGPEKAQSFKVPFFGTRQLIEVEADQRRKMMLLREASIPTPEEY 129
                                       ******************************************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 !   16.0   0.0   2.2e-06    0.0098       6      73 ..     113     181 ..     109     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-06
                                       HHHHHHTTT.S---....-EESS--SSSEEEEESS-------B--SS--TTE..........EEEE---SE CS
                       ATP-grasp_3   6 ktykkLkeagvkvPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve...lvqefieGk 73 
                                       + +  L+ea++++P   e +++ee+e ++++K + + gg + +++  kee+ea+  +++   ++q++i G 
  gi|557694286|ref|YP_008797340.1| 113 RKMMLLREASIPTP--EEYSSPEEAEPPVIIKLAGAKGGAGYSLAFTKEELEAKTRNLSqphIIQRYIIGV 181
                                       55667999999999..66678899999******99999999998888888887777666777******986 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 ?   13.6   0.0   7.9e-06     0.035      35      67 ..     133     165 ..     120     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.9e-06
                                       HHH-SSEEEEETTCCTTTTEEEESSHHHHHHHH CS
                       CPSase_L_D2  35 keigyPviikaafglGGkGmrvarneeelaelv 67 
                                       +e   Pviik a + GG G  +a ++eel++ +
  gi|557694286|ref|YP_008797340.1| 133 EEAEPPVIIKLAGAKGGAGYSLAFTKEELEAKT 165
                                       67778************************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); 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:                         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: 00:00:00.36
# Mc/sec: 2731.14
//
Query:       gi|557694287|ref|YP_008797341.1|  [L=495]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   60.5   0.3      5e-16   59.5   0.3    1.4  1  DUF87          Helicase HerA, central domain
    4.1e-06   26.0   0.0    7.4e-06   25.1   0.0    1.3  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
  ------ inclusion threshold ------
      0.022   14.4   0.0       0.28   10.8   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
       0.21   10.5   0.0       0.28   10.1   0.0    1.1  1  DUF5427        Family of unknown function (DUF5427)


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 !   59.5   0.3   1.1e-19     5e-16      18     219 ..     156     347 ..     140     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.1e-19
                             DUF87  18 lnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHG.EYgkalekllsekvkvitpspsakdkelkin 93 
                                       l++++t+H++++g TGsGKS+++++ l  ll++ g  +li+D+ G +Y++++    s+ +++ +             
  gi|557694287|ref|YP_008797341.1| 156 LKEYITHHIGVFGVTGSGKSYLTRYQLIPLLRQSGFDVLIFDWKGsDYAPYY----SDVINMDD------------- 215
                                       4899***************************9********************....66554444............. PP

                             DUF87  94 pwsldpeelldllee.....ddkpaaavqrsvleealdqakakeekeklssdepveklleelk........kekeel 157
                                         +ld e +l++l e      +  +a+++ ++l++++++ +        +++e +e++ +el+        +++ + 
  gi|557694287|ref|YP_008797341.1| 216 -ILLDDESILSFLLErlnyfGGGGSAEKLAEYLDQVITEGR----WRGKTAAEALETITNELYriisedntDKSGKP 287
                                       .4666666666666665555558888999999999999775....56667777788888999899999986666699 PP

                             DUF87 158 rklknqaiarlldkledllrkggsf...snsstdliallleklekegkitiidlsgvdelaqqlv 219
                                       ++ +n ++++ ++ l++l+++  +    + + ++++++l     +e+++ +idls  +++++ ++
  gi|557694287|ref|YP_008797341.1| 288 SHWANIYMRKAQRYLSKLDEDDVKPllgTLTAEEIVEKL-----REKHLIVIDLSYGSKEQKLSI 347
                                       99999999999*******999999888889999999999.....***********9998888764 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 !   25.1   0.0   1.6e-09   7.4e-06       6      68 ..     152     218 ..     149     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.6e-09
                     TrwB_AAD_bind   6 gvplpkeretqhilivGttGsGKtqale.kllrairargdraivlDltGafvsrfyd...egkdill 68 
                                       ++p+ ke  t+hi ++G tGsGK+  ++ +l+  +r+ g  ++++D +G  ++ +y+   + +dill
  gi|557694287|ref|YP_008797341.1| 152 KIPVLKEYITHHIGVFGVTGSGKSYLTRyQLIPLLRQSGFDVLIFDWKGSDYAPYYSdviNMDDILL 218
                                       699999******************988659**************************94444568887 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.3e-05      0.28      16      48 ..     179     209 ..     166     251 .. 0.75
   2 ?    1.3   0.0     0.048   2.2e+02      84     148 ..     258     322 ..     256     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.3e-05
                                       GTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTT CS
                     Abhydrolase_1  16 waerglapaLakdgfdvillDlrGvgySspapa 48 
                                        ++  l+p L ++gfdv+++D+ G++y +  ++
  gi|557694287|ref|YP_008797341.1| 179 RYQ--LIPLLRQSGFDVLIFDWKGSDYAPYYSD 209
                                       566..88899989************99875555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.048
                                       HHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCS CS
                     Abhydrolase_1  84 GmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladel 148
                                       G +a+++++   +   ++++ +  d + ++++++  ++ + ++++ +  +d+ ++ +g+l a e 
  gi|557694287|ref|YP_008797341.1| 258 GKTAAEALETITNELYRIISEDNTDKSGKPSHWANIYMRKAQRYLSKLDEDDVKPLLGTLTAEEI 322
                                       5677777777788888888888899999*****************************99998765 PP

>> DUF5427  Family of unknown function (DUF5427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   6.3e-05      0.28     128     220 ..     279     372 ..     255     374 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.3e-05
                           DUF5427 128 eeadpiasgsgWWgsilatasaavkqaea.avkeiqtneeAkkwaeqvrgnvgalrglgdelrtralptltellktl 203
                                       +++d+ ++ s W +  + +a+  ++++ +  vk +  +  A+++ e++r++   + +l+   +++ l+ + +++  l
  gi|557694287|ref|YP_008797341.1| 279 DNTDKSGKPSHWANIYMRKAQRYLSKLDEdDVKPLLGTLTAEEIVEKLREKHLIVIDLSYGSKEQKLSIFLSIVGYL 355
                                       455666666777777779********98769********************************************** PP

                           DUF5427 204 appisshEvLqIhithD 220
                                        + ++++ +L+I ++ D
  gi|557694287|ref|YP_008797341.1| 356 KRLMEEKNRLNIALVVD 372
                                       **************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); 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 0.24s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 3834.08
//
Query:       gi|557694288|ref|YP_008797342.1|  [L=426]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00072   19.3   0.1     0.0027   17.4   0.1    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 !   17.4   0.1   1.5e-07    0.0027       3     163 ..      68     251 ..      66     320 .. 0.82
   2 ?   -1.7   0.0       0.1   1.8e+03     210     241 ..     354     385 ..     331     386 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-07
                                       EEEEEEEEEEE.EETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHH.......HHH CS
                              NurA   3 vaAvDGSngvv.rlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElk.......lga 71 
                                       v+ vDGS     + + g+ y l a+a+    +++  e+++    d+ + +     r++ ++++l+l+       ++ 
  gi|557694288|ref|YP_008797342.1|  68 VCVVDGSDVPAlDDRIGVRYGLYAVAYKMFRGIDAVEDGEGYFGDKLPGKI--STRRETFLKLLDLLttyyerlVAK 142
                                       888999988888888888888888887666666666666666666655333..444444444444445555555*** PP

                                       HHCGGCCSCEEEEECSHHCCCH.................HHHHHHHHHHHHHHHHHHHHHTT-TTCEEEEESS-SCT CS
                              NurA  72 llleekgedllllDGsligslv.................efdelheeleyeeylyslsrlleaglnlvgvaKsfrsk 131
                                        ll+  ++dll++DGs++g+                    +    + +   e+++  + lle+  + vgv+K++ + 
  gi|557694288|ref|YP_008797342.1| 143 TLLDSMKPDLLMVDGSFFGYRAgcsmvkkdplnwrdpvtGKRFDTVFDLIDEINSLTMALLES-GKAVGVIKRVPTA 218
                                       **************************************95555566667789**********9.**********999 PP

                                       CCHCCC........S--HHHHCCHHCCHCH---S CS
                              NurA 132 ellnll..letlligesisDiallgallrkpgyt 163
                                        +  +l     l+ g+++sD+ +l+ l  k g++
  gi|557694288|ref|YP_008797342.1| 219 AIDGYLcyRHGLEMGLELSDRSILSHLM-KRGEV 251
                                       9888887777899999999999999998.66665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.1
                                       CHHHHHHHHHH..TTB-SSSBCCHHHHHHHHC CS
                              NurA 210 akdedvlsllasqrlsisGYprpLalAhelak 241
                                       + +edvl  +++++  ++G p  L+l++ l++
  gi|557694288|ref|YP_008797342.1| 354 EVAEDVLGYIYATANPATGLPIVLDLVDDLVS 385
                                       667788888888889999**********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3061.63
//
Query:       gi|557694289|ref|YP_008797343.1|  [L=629]
Description: glutamyl-tRNA(Gln) amidotransferase subunit E [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-67  228.1   0.0    2.2e-67  227.3   0.0    1.4  1  GatB_N           GatB/GatE catalytic domain
    1.4e-20   73.7   0.0      4e-20   72.2   0.0    1.8  1  GatB_Yqey        GatB domain
    1.5e-15   57.2   0.5    4.6e-14   52.4   0.3    2.5  2  GAD              GAD domain
    0.00079   19.0   0.5       0.39   10.4   0.0    4.2  4  DUF3562          Protein of unknown function (DUF3562)
  ------ inclusion threshold ------
      0.012   15.6   0.1      0.043   13.9   0.1    1.9  1  YqeY             Yqey-like protein
      0.018   15.1   4.6      0.032   14.3   0.2    3.2  3  DprA_WH          DprA winged helix domain
        0.1   12.3   0.0       0.38   10.4   0.0    1.9  1  Prok-E2_B        Prokaryotic E2 family B
       0.14   12.1   0.2       0.34   10.9   0.2    1.5  1  Antimicrobial_3  Spider antimicrobial peptide


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 !  227.3   0.0   9.9e-71   2.2e-67       2     273 .]       8     444 ..       7     444 .. 0.96

  Alignments for each domain:
  == domain 1  score: 227.3 bits;  conditional E-value: 9.9e-71
                                       EEEEEEEEEB--SB-SSSSSBSSSSCE...........STTSS--TTTTTS.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxxxx.......................... RF
                            GatB_N   2 viGlEiHaqlktksKlFssasteeege...........epnsevsevdlal.......................... 41 
                                       ++GlE+H ql+t++KlF++++te   e           e++se++evd a+                          
  gi|557694289|ref|YP_008797343.1|   8 KVGLEVHRQLDTRRKLFCDCPTEPA-EgpvikitrylrEAQSELGEVDPAAvfeskkrkkiiyhinpsnvclvemde 83 
                                       89*******************8732.2246667777768************************************99 PP

                                       .TT..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEEEEEEE.TEEEEEEEEEE CS
                                       .xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                            GatB_N  42 .PGtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplakeGslel.ekkvrierihl 115
                                        P   P+ ln eave+a+++a  l+++  +e++++RK+++++++++g+Q+t     +a +G+l +  kk+ i+++ l
  gi|557694289|ref|YP_008797343.1|  84 eP---PHdLNPEAVETALQIAALLKATPVDEIHVMRKIVIDGSNTSGFQRTC---IVALGGELVVdGKKIPIQTVTL 154
                                       99...9**********************************************...56699999886899******** PP

                                       EE---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 116 EeDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvre 192
                                       EeDaak v++++  + +dl R+G+pLiEi+t+p ++sp+ea++v+++++++lra++ +++++  G++R+D+NvS++ 
  gi|557694289|ref|YP_008797343.1| 155 EEDAAKIVSTSRGVVEYDLSRLGIPLIEIATAPVISSPQEAARVAQAIGKVLRATRRVKRGI--GTVRQDLNVSISG 229
                                       *********9999*************************************************..************4 PP

                                       SETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                            GatB_N 193 eekgeeegtrvEiKnlnslksiekaieyeierqiell........................................ 229
                                              g+ +EiK++++l+ i  ++e e++rq++ll                                        
  gi|557694289|ref|YP_008797343.1| 230 -------GAVTEIKGVQELELIPLVVELEVKRQLHLLevaeelrkrlgsqplpppeyidvthvfqntkssmvrkkle 299
                                       .......489******************************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                            GatB_N 230 ............................................................................. 229
                                                                                                                    
  gi|557694289|ref|YP_008797343.1| 300 tggrayalklvkfagllskepvkgirlgselaghakawaevegilhtdelpaygitaeevkmlreavgageqdavvm 376
                                       ***************************************************************************** PP

                                       ...........................-EEEEEETTTTEEEEECC--.--...-EEE-TTS--EE--HHHHH CS
                                       ...........................xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 230 ...........................qeTrkfdedkgetvslRske.eaedYryfpepdlppleiseelie 273
                                                                   eTr++++d g tv++R+++ +a   r++pe+d+ppl i++e++e
  gi|557694289|ref|YP_008797343.1| 377 vvdeearalealravyeraaqavegvpGETRAAKPD-GLTVYMRPRPgSA---RMYPETDIPPLPITREYVE 444
                                       ************************************.**********555...****************986 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.0   1.8e-23     4e-20       2     148 .]     483     622 ..     482     622 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1.8e-23
                                       HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH.TXXHH CS
                         GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleellee.gkspe 77 
                                       +fe++v+++  ++++++ +l+e++++l++eg ++++  l++  lae+l  +a+g  sk+++ +++  + ++ g s+e
  gi|557694289|ref|YP_008797343.1| 483 LFEQIVRATGLPATVVAATLTETMRNLRREGYPVQN--LSDHMLAEILHSLASGLFSKEAVPDIIGWMSKNpGASVE 557
                                       8***********************************..9************************************** PP

                                       HHHHHCTXXXXXXSSXHHHHHHHHHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
                         GatB_Yqey  78 eiieekgLkqisdeeeleklveeviaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                                       ++++  gL  +s+ +elek vee ++++       ++g  ++++ l+G +M+k +Gk+d+kl+  +l ek+
  gi|557694289|ref|YP_008797343.1| 558 DAVKSLGLSHVSS-KELEKEVEELVQRH-----AAEAGDPRLVNRLMGDLMRKYRGKVDGKLLHSILVEKI 622
                                       ************8.**************.....7789999**************************99986 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.3     2e-17   4.6e-14       2      95 .]     295     388 ..     294     388 .. 0.96
   2 ?    2.2   0.0     0.094   2.1e+02      62      79 ..     573     590 ..     560     594 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2e-17
                                       HHHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--T CS
                               GAD   2 sealksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaee 77 
                                       ++ l+ gg+  al++ + +a+l  ke  ++ +++ el+ +++aw+ veg  +t++++++ +t+eevk l+eavga e
  gi|557694289|ref|YP_008797343.1| 295 RKKLETGGRAYALKLVK-FAGLLSKEPVKGIRLGSELAGHAKAWAEVEGILHTDELPAYgITAEEVKMLREAVGAGE 370
                                       577999***********.7999999999************************************************* PP

                                       TEEEEEEEEEHHHHHHHH CS
                               GAD  78 gDillfvAdkkktvnkal 95 
                                       +D++++v+d+++ + +al
  gi|557694289|ref|YP_008797343.1| 371 QDAVVMVVDEEARALEAL 388
                                       ************999987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.094
                                       -HHHHHHHHHHCT--TTE CS
                               GAD  62 teeevkklleavgaeegD 79 
                                        e+ev++l+++  ae+gD
  gi|557694289|ref|YP_008797343.1| 573 LEKEVEELVQRHAAEAGD 590
                                       599**************9 PP

>> DUF3562  Protein of unknown function (DUF3562)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.29   6.4e+02      15      39 ..     352     375 ..     350     376 .. 0.87
   2 ?   -2.0   0.0       1.2   2.8e+03       3      29 ..     453     479 ..     452     483 .. 0.79
   3 !   10.4   0.0   0.00017      0.39       3      36 ..     479     512 ..     477     513 .. 0.92
   4 ?    2.7   0.0     0.043        97       2      34 ..     575     606 ..     574     608 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.29
                           DUF3562  15 tdaPeelVsrlyedavaalaedARv 39 
                                       +++++e+V +++ +av a ++dA v
  gi|557694289|ref|YP_008797343.1| 352 YGITAEEV-KMLREAVGAGEQDAVV 375
                                       7999***9.6999999999999976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.2
                           DUF3562   3 dvdeiiqaiAeetdaPeelVsrlyeda 29 
                                       ++d+  ++ A+ ++  ++lV+ l +++
  gi|557694289|ref|YP_008797343.1| 453 TLDQTAERLAKTYSLSTQLVQALIDEE 479
                                       567778899999999999999887765 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00017
                           DUF3562   3 dvdeiiqaiAeetdaPeelVsrlyedavaalaed 36 
                                       + +e+ ++i + t+ P+ +V   +++++++l+++
  gi|557694289|ref|YP_008797343.1| 479 EKEELFEQIVRATGLPATVVAATLTETMRNLRRE 512
                                       678999*************************986 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.043
                           DUF3562   2 ddvdeiiqaiAeetdaPeelVsrlyedavaala 34 
                                       ++v+e++q+ A e + P+ lV+rl  d +++++
  gi|557694289|ref|YP_008797343.1| 575 KEVEELVQRHAAEAGDPR-LVNRLMGDLMRKYR 606
                                       5799*************7.9*********9997 PP

>> YqeY  Yqey-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.9e-05     0.043      91     141 ..     568     620 ..     566     622 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-05
                                       --HHHHHHHHHHHHHHTT--..BGGGHHHHHHHHHHHHTTTS-HHHHHHHHHH CS
                              YqeY  91 lseeeiealvkeaiaevgae..smkdmGkvmkalkpkvkGkaDgkkvsalvke 141
                                       +s +e+e+ v+e +++  ae  +++ + ++m+ l+ k++Gk+Dgk + +++ e
  gi|557694289|ref|YP_008797343.1| 568 VSSKELEKEVEELVQRHAAEagDPRLVNRLMGDLMRKYRGKVDGKLLHSILVE 620
                                       577888888888888876665578999******************99887655 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.23   5.2e+02       5      28 ..      88     111 ..      83     122 .. 0.76
   2 ?   -3.6   0.1       5.6   1.2e+04       5      22 ..     186     203 ..     184     204 .. 0.72
   3 ?   14.3   0.2   1.4e-05     0.032      28      48 ..     484     504 ..     449     504 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.23
                           DprA_WH   5 paepplddlerrvLaaLgpePvhv 28 
                                          p++ +++ ++ a+L ++Pv +
  gi|557694289|ref|YP_008797343.1|  88 DLNPEAVETALQIAALLKATPVDE 111
                                       445677788999999**9999865 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.6
                           DprA_WH   5 paepplddlerrvLaaLg 22 
                                       ++  ++ ++++rv +a+g
  gi|557694289|ref|YP_008797343.1| 186 APVISSPQEAARVAQAIG 203
                                       555667788899999887 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 1.4e-05
                           DprA_WH  28 vDqLvrrtglpaaevsaaLle 48 
                                       ++q+vr+tglpa +v+a+L+e
  gi|557694289|ref|YP_008797343.1| 484 FEQIVRATGLPATVVAATLTE 504
                                       79*****************98 PP

>> Prok-E2_B  Prokaryotic E2 family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00017      0.38      53     100 ..      56      99 ..      53     113 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                         Prok-E2_B  53 pavflqdpeqlkllpHintfggaLCllee.eldldewdpngsvadvleq 100
                                       +avf  +   +k+ +Hin+  + +Cl+e  e ++   +p+++ +++  q
  gi|557694289|ref|YP_008797343.1|  56 AAVFESKKR-KKIIYHINP--SNVCLVEMdEEPPHDLNPEAVETAL--Q 99 
                                       455555444.449******..99****9888888888888776655..4 PP

>> Antimicrobial_3  Spider antimicrobial peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00015      0.34       5      25 ..     201     221 ..     200     224 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                   Antimicrobial_3   5 visKvLRaIAKvFKGVGKvRK 25 
                                        i+KvLRa  +v +G+G vR 
  gi|557694289|ref|YP_008797343.1| 201 AIGKVLRATRRVKRGIGTVRQ 221
                                       59*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (629 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); 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: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 4486.41
//
Query:       gi|557694290|ref|YP_008797344.1|  [L=451]
Description: glutamyl-tRNA(Gln) amidotransferase subunit D [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-60  204.2   0.8    2.1e-60  203.6   0.8    1.2  1  Asparaginase     Asparaginase, N-terminal
    1.2e-31  109.3   0.4    8.4e-31  106.5   0.1    2.2  2  Asparaginase_C   Glutaminase/Asparaginase C-terminal domain
    4.3e-18   64.4   0.1      8e-18   63.5   0.1    1.5  1  GatD_N           GatD N-terminal domain
  ------ inclusion threshold ------
      0.043   13.4   0.1      0.091   12.4   0.1    1.5  1  DMA              DMRTA motif
       0.22   11.5   0.0         24    4.9   0.0    2.3  2  T3SS_needle_reg  YopR, type III needle-polymerisation regulat


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 !  203.6   0.8   5.9e-64   2.1e-60       1     180 [.      96     282 ..      96     290 .. 0.96

  Alignments for each domain:
  == domain 1  score: 203.6 bits;  conditional E-value: 5.9e-64
                                       EEEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHC.CT- CS
                      Asparaginase   1 kvlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieeal.eey 76 
                                       +v++++tGGTias+ d+++g ++pal+a++l++ +pe+++ a++++e+l+++ S+nmt a+w  +a++++e + +++
  gi|557694290|ref|YP_008797344.1|  96 RVMIVNTGGTIASRIDYRTGGVKPALTASDLVSIVPEIAEKANVSTEVLMQVVSENMTSAHWTAIARKVDELFrKGF 172
                                       79***********************************************************************555* PP

                                       SEEEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE.... CS
                      Asparaginase  77 dgfVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk.... 149
                                       dg+V++hGTDT+ ytA+aLs++l+n + pvvl+G+qr++++++sD++ Nll+A+ vaa   ++a+v+v+++g     
  gi|557694290|ref|YP_008797344.1| 173 DGIVITHGTDTMGYTAAALSFALQNPPAPVVLVGAQRSSDRPSSDAALNLLTAVEVAAWA-PFAEVVVAMHGWhgdd 248
                                       ***********************************************************9.**************** PP

                                       ...EEETTTEEE-BSSSSS-EEETTT--SEEEET CS
                      Asparaginase 150 ...llranrvtKvhtssldaFespnlgplaeveg 180
                                          ++r++rv K+htss+ aF+s+n++p+a  + 
  gi|557694290|ref|YP_008797344.1| 249 nvlIHRGTRVVKLHTSSRGAFQSINASPIAVKTP 282
                                       ****************************995544 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 ?    0.4   0.0      0.21   7.6e+02      16      30 ..     164     178 ..     136     196 .. 0.78
   2 !  106.5   0.1   2.4e-34   8.4e-31       1     114 []     309     426 ..     309     426 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.21
                                       HHHHHHTT--EEEEE CS
                    Asparaginase_C  16 lkallkkgakGvvle 30 
                                       +++l++kg +G+v+ 
  gi|557694290|ref|YP_008797344.1| 164 VDELFRKGFDGIVIT 178
                                       567789999***997 PP

  == domain 2  score: 106.5 bits;  conditional E-value: 2.4e-34
                                       -EEEEE--TT--HHHHHHHHHT.T--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....H CS
                    Asparaginase_C   1 rVvvlklhpgmdtkvlkallkk.gakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagke 76 
                                       rV+++k++pgm+++vl+ l+++ g++GvvlegtG G++ s+++++lk ++++g+ v +tsqc +g+v++++ye+g++
  gi|557694290|ref|YP_008797344.1| 309 RVMLVKFFPGMKPEVLELLVERmGLRGVVLEGTGLGHVASSFVPVLKGLREKGVFVGMTSQCRFGRVNMNVYENGRD 385
                                       8*********************9****************************************************** PP

                                       HHHHTEEE-TT--HHHHHHHHHHHCTT...---HHHHHHHH CS
                    Asparaginase_C  77 lerlgvisaddmtpeaarikLmlllgk...gldpaevrklf 114
                                       l r+g++  d+m pe+a++kLm++lgk   + + ++v++l+
  gi|557694290|ref|YP_008797344.1| 386 LMRAGAVPLDNMLPETAMVKLMWVLGKlgeKASYETVKNLM 426
                                       **************************976555888888877 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.1   2.2e-21     8e-18       3      55 .]      22      74 ..      20      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 2.2e-21
                                      TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.---EE CS
                            GatD_N  3 vGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekiell 55
                                       GD ++v+++g +++G++m r+e++++d++vlKL nGYNiG++i+ +++i++l
  gi|557694290|ref|YP_008797344.1| 22 LGDEVEVVRNGLRLRGFVMARYEYGAPDVLVLKLPNGYNIGVRIDVSTQIRKL 74
                                      69************************************************986 PP

>> DMA  DMRTA motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.5e-05     0.091       6      25 ..     311     330 ..     306     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                               DMA   6 iLarvFPnhkrsvLelvLqr 25 
                                       +L++ FP +k++vLel+++r
  gi|557694290|ref|YP_008797344.1| 311 MLVKFFPGMKPEVLELLVER 330
                                       9***************9876 PP

>> T3SS_needle_reg  YopR, type III needle-polymerisation regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.011        41      58     104 ..     104     150 ..      79     171 .. 0.83
   2 ?    4.9   0.0    0.0067        24      37      67 ..     208     237 ..     204     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.011
                                       HHHHHHHTT--S---HHHHHHHHHHHHHHHS-SSHHHHHHHHHHHHT CS
                   T3SS_needle_reg  58 eeLladfgglqgsvkPplDlpeLrkvlrqfaplGkqkeavLlevlee 104
                                         + ++     g vkP+l  ++L +++ + a   +   +vL++v++e
  gi|557694290|ref|YP_008797344.1| 104 GTIASRIDYRTGGVKPALTASDLVSIVPEIAEKANVSTEVLMQVVSE 150
                                       5566777778899******************************9876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0067
                                       H...-SS--HHHHHHHHHHHHHHHHHHHTT- CS
                   T3SS_needle_reg  37 alkskkpsddavlevLlapvkeeLladfggl 67 
                                       + +s +ps da l+ Ll+ v  + +a f++ 
  gi|557694290|ref|YP_008797344.1| 208 QRSSDRPSSDAALN-LLTAVEVAAWAPFAEV 237
                                       45789*********.*************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); 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:                         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: 00:00:00.37
# Mc/sec: 3674.35
//
Query:       gi|557694291|ref|YP_008797345.1|  [L=94]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-07   29.4   0.1    8.8e-07   28.7   0.1    1.3  1  MarR_2         MarR family
    1.9e-06   27.6   0.0    4.2e-06   26.5   0.0    1.6  2  HTH_IclR       IclR helix-turn-helix domain
    0.00012   21.5   0.0    0.00033   20.1   0.0    1.7  1  HTH_24         Winged helix-turn-helix DNA-binding
     0.0015   18.4   0.0      0.011   15.6   0.0    2.0  2  PuR_N          Bacterial purine repressor, N-terminal
     0.0064   16.4   0.0     0.0092   15.9   0.0    1.3  1  HTH_Crp_2      Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.025   14.5   0.0      0.086   12.8   0.0    1.8  2  HTH_11         HTH domain
       0.05   13.4   0.0       0.09   12.6   0.0    1.4  1  DUF1495        Winged helix DNA-binding domain (DUF1495)
      0.078   12.8   0.0        0.2   11.5   0.0    1.7  1  HTH_AsnC-type  AsnC-type 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 !   28.7   0.1   3.9e-10   8.8e-07       6      55 ..      11      60 ..       8      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.9e-10
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      a+  +L +L  +pg+ ++ + lar++gl +s+v  +++ +++ GLv +r+
  gi|557694291|ref|YP_008797345.1| 11 AHSKILQFLLENPGKAFSLRYLARATGLAPSTVIIVVNNFERLGLVYQRR 60
                                      56779*****************************************8875 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 !   26.5   0.0   1.9e-09   4.2e-06       7      51 ..      14      59 ..      13      60 .. 0.95
   2 ?   -2.4   0.0         2   4.5e+03       6      14 ..      80      88 ..      76      92 .. 0.60

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.9e-09
                                      HHHCT-CTTBSS-.BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  7 aiLdalaeapqel.tlselArrtglpkStvhRlLqtLvelGyveqd 51
                                       iL++l e p+   +l+ lAr+tgl++Stv   ++ +++lG+v q 
  gi|557694291|ref|YP_008797345.1| 14 KILQFLLENPGKAfSLRYLARATGLAPSTVIIVVNNFERLGLVYQR 59
                                      599*********88*****************************996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2
                                      HHHHCT-CT CS
                          HTH_IclR  6 laiLdalae 14
                                      +++ ++l++
  gi|557694291|ref|YP_008797345.1| 80 MQLVELLRR 88
                                      455555555 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 !   20.1   0.0   1.5e-07   0.00033       6      47 ..      13      56 ..       9      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.5e-07
                            HTH_24  6 rkILelLqknpr..isqreLAerlglSpstvnrrlkrLeeeGlI 47
                                       kIL+ L +np+   s r LA+++gl pstv   ++++e+ Gl+
  gi|557694291|ref|YP_008797345.1| 13 SKILQFLLENPGkaFSLRYLARATGLAPSTVIIVVNNFERLGLV 56
                                      69**********8779**************************98 PP

>> PuR_N  Bacterial purine repressor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.1e-06     0.011       8      37 ..      14      43 ..      11      56 .. 0.91
   2 ?    0.9   0.0       0.2   4.5e+02       7      33 ..      64      92 ..      57      94 .] 0.50

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.1e-06
                             PuR_N  8 aitkiLlenPnklisltyfaerfeaAKSsi 37
                                      +i+++LlenP k +sl+y+a+  + A S++
  gi|557694291|ref|YP_008797345.1| 14 KILQFLLENPGKAFSLRYLARATGLAPSTV 43
                                      689***********************9997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.2
                             PuR_N  7 vaitkiLlenP..nklisltyfaerfeaA 33
                                      v+++ +  enP   +l++l ++ +r+e A
  gi|557694291|ref|YP_008797345.1| 64 VKMIMLNPENPvaGNLMQLVELLRRYEPA 92
                                      33333333444222567777777777766 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 !   15.9   0.0   4.1e-06    0.0092      22      62 ..      27      71 ..      13      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.1e-06
                                      HHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET.EE..EEES-H CS
                         HTH_Crp_2 22 ltqeelAsmlGltretvsrilseLkreglis.rg.rr..irildl 62
                                      ++ + lA+  Gl ++tv  + + ++r gl+  r+ r   ++ l++
  gi|557694291|ref|YP_008797345.1| 27 FSLRYLARATGLAPSTVIIVVNNFERLGLVYqRRlRSvkMIMLNP 71
                                      56788**************************54433334555555 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.8e-05     0.086       3      33 ..      13      44 ..      12      58 .. 0.87
   2 ?   -1.6   0.0       1.2   2.7e+03       2      13 ..      79      90 ..      78      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-05
                            HTH_11  3 lqilelLleargp.isgeeLAeeLnvSrrtvr 33
                                      ++il++Lle+ g+ +s  +LA+ +++  +tv 
  gi|557694291|ref|YP_008797345.1| 13 SKILQFLLENPGKaFSLRYLARATGLAPSTVI 44
                                      69*********************999888875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                            HTH_11  2 llqilelLlear 13
                                      l q++elL++ +
  gi|557694291|ref|YP_008797345.1| 79 LMQLVELLRRYE 90
                                      578999998766 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 ?   12.6   0.0     4e-05      0.09       5      42 ..       6      43 ..       3      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                           DUF1495  5 lnkSkvRkkvllyLysiypeksnlqeisrrvrskpsnv 42
                                      l  Sk+ +k+l +L+++  ++  l  ++r+++ +ps v
  gi|557694291|ref|YP_008797345.1|  6 LFASKAHSKILQFLLENPGKAFSLRYLARATGLAPSTV 43
                                      67899*****************************9988 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 ?   11.5   0.0   9.1e-05       0.2       7      34 ..      14      43 ..      13      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.1e-05
                     HTH_AsnC-type  7 kILeaLqed..aRisyaeLAervGlSestv 34
                                      kIL+ L e+     s + LA+++Gl++stv
  gi|557694291|ref|YP_008797345.1| 14 KILQFLLENpgKAFSLRYLARATGLAPSTV 43
                                      788999999755669999***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 798.17
//
Query:       gi|557694292|ref|YP_008797346.1|  [L=226]
Description: uridylate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-24   84.9   1.0    1.5e-23   83.6   1.0    1.6  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 !   83.6   1.0   8.6e-28   1.5e-23       3     212 ..       4     174 ..       3     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 8.6e-28
                                       EEEEE-TT.CCC.CTCC.HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHH CS
                         AA_kinase   3 vVvKlGGs.slt.dkee.aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagev 76 
                                       vV+KlGG+ +++ +  + + l+ +++ ++++  +g + vvV+Ggg ++++++a+++++  +e++             
  gi|557694292|ref|YP_008797346.1|   4 VVLKLGGHvVFGeNV-DtELLKGYVKLLREA-FDGGRWVVVVGGGEQARRYIAAARKIGLDEATC------------ 66 
                                       7*******5555444.36*************.777788****************77777777663............ PP

                                       HHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTT CS
                         AA_kinase  77 atrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeeg 153
                                          d++a+  +r+ a+l+a +l +v ++  +++                   ++i+ l   g+++v +g++     g
  gi|557694292|ref|YP_008797346.1|  67 ---DEAAIKVTRVHAYLFARALGDVAVQTVPTT------------------VDEIRYLTGFGKIVVSGGMQ----AG 118
                                       ...9************************99998..................689999************99....66 PP

                                       EEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSS CS
                         AA_kinase 154 elgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..sas 212
                                       +    s+  ++ + A  +gA++++i++dVdGVy++dpkk+p a+llp+is+ +++e  + +
  gi|557694292|ref|YP_008797346.1| 119 Q----STMAVSIHAASVIGAERVVIASDVDGVYTDDPKKNPEAKLLPRISFTQLAEisQ-K 174
                                       6....677799999******************************************742.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1694.17
//
Query:       gi|557694293|ref|YP_008797347.1|  [L=128]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-11   43.6   0.0    2.9e-11   42.9   0.0    1.5  1  UPF0175   Uncharacterised protein family (UPF0175)
    0.00018   21.3   0.3    0.00047   20.0   0.3    1.7  1  RHH_1     Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.016   15.0   0.2      0.043   13.6   0.1    1.8  2  HTH_23    Homeodomain-like domain
      0.078   13.1   0.2       0.25   11.5   0.1    1.8  2  HTH_28    Helix-turn-helix domain
      0.098   12.5   0.1       0.33   10.8   0.0    1.9  2  IF2_N     Translation initiation factor IF-2, N-terminal regi


Domain annotation for each model (and alignments):
>> UPF0175  Uncharacterised protein family (UPF0175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   8.2e-15   2.9e-11      25      66 ..      53      93 ..      33     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 8.2e-15
                           UPF0175 25 AvklYeegrlSlgkAaelaglsrveflelLarrgiplinyde 66
                                      +v lY++++l+ g+Aae++g+s  efle+L ++g+p +n d 
  gi|557694293|ref|YP_008797347.1| 53 VVDLYRQEKLTVGRAAEILGVSLREFLEILEKEGVP-VNWDI 93
                                      89**********************************.57765 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 !   20.0   0.3   1.3e-07   0.00047       2      30 ..      14      42 ..      14      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.3e-07
                                      EEEEEEHHHHHHHHHHHHHHTSSHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrgrSrSelIR 30
                                      v++rl++ +l+r++el+r +++ rS lI+
  gi|557694293|ref|YP_008797347.1| 14 VTVRLSKPDLKRIEELRRVENVDRSTLIK 42
                                      89************************997 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5   5.5e+03      21      33 ..      27      39 ..      18      42 .. 0.64
   2 ?   13.6   0.1   1.2e-05     0.043       7      32 ..      50      76 ..      45      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                            HTH_23 21 reIAreLgvsrrT 33
                                      +e  r  +v r+T
  gi|557694293|ref|YP_008797347.1| 27 EELRRVENVDRST 39
                                      4444555667777 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.2e-05
                            HTH_23  7 Rlrillllae.GlsvreIAreLgvsrr 32
                                      R r++ l+++ +l+v ++A++Lgvs r
  gi|557694293|ref|YP_008797347.1| 50 RKRVVDLYRQeKLTVGRAAEILGVSLR 76
                                      789******99**************87 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0         1   3.8e+03      15      29 ..      26      40 ..      22      40 .. 0.75
   2 ?   11.5   0.1   6.9e-05      0.25       2      25 ..      50      74 ..      49      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                            HTH_28 15 vreaArelgisrrtv 29
                                      + e+ r  +++r+t+
  gi|557694293|ref|YP_008797347.1| 26 IEELRRVENVDRSTL 40
                                      667778888999886 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.9e-05
                            HTH_28  2 RleiikllaaGh.svreaArelgis 25
                                      R++++ l+ + + +v  aA++lg+s
  gi|557694293|ref|YP_008797347.1| 50 RKRVVDLYRQEKlTVGRAAEILGVS 74
                                      99********999***********9 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 ?   -1.6   0.0       0.7   2.5e+03      14      31 ..      34      50 ..      22      54 .. 0.61
   2 ?   10.8   0.0   9.2e-05      0.33       2      32 ..      60      89 ..      59      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.7
                             IF2_N 14 gvkskevikkLfkelGie 31
                                      +v+   +ik +    G+ 
  gi|557694293|ref|YP_008797347.1| 34 NVDRSTLIKMFID-EGVR 50
                                      6666777777744.6665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.2e-05
                             IF2_N  2 skirVyeLAkeLgvkskevikkLfkelGiev 32
                                      +k++V   A+ Lgv+  e ++ L+k  G++v
  gi|557694293|ref|YP_008797347.1| 60 EKLTVGRAAEILGVSLREFLEILEK-EGVPV 89
                                      68999999***************76.9*994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 953.54
//
Query:       gi|557694294|ref|YP_008797348.1|  [L=175]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.2   0.1      0.055   12.9   0.1    1.7  2  PIN_5      PINc domain ribonuclease
      0.077   13.5   0.5       0.59   10.6   0.1    2.1  2  EF-hand_7  EF-hand domain pair


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 ?   -2.8   0.0       0.4   3.6e+03      47      71 ..      32      56 ..      21      73 .. 0.66
   2 ?   12.9   0.1   6.1e-06     0.055     156     201 ..      86     131 ..      84     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.4
                             PIN_5 47 ippsvykElkeflkreeveeeviak 71
                                      i+p v +E  ++  +++ ++ +i k
  gi|557694294|ref|YP_008797348.1| 32 ITPRVKREAYDMGAKHGHADATIGK 56
                                      5677777777776666665555544 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6.1e-06
                             PIN_5 156 saeDldvllLAkELdaavvssDeGikkwaeklGlrlveakkfpkvl 201
                                       s+ D + llLAkE +a+++ +++ ++++a+  Glr+ +++ + + l
  gi|557694294|ref|YP_008797348.1|  86 SQADAETLLLAKEKKAEILVDEKALSNIARLHGLRVWSTSILLEAL 131
                                       789********************************98887766655 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.073   6.5e+02      16      37 ..      60      81 ..      59     107 .. 0.65
   2 ?   10.6   0.1   6.6e-05      0.59      16      50 ..     133     164 ..     128     170 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.073
                         EF-hand_7 16 dgyldkeellrllrkifqgage 37
                                      dg++ +e l++ l + + +   
  gi|557694294|ref|YP_008797348.1| 60 DGWIKVEKLQKQLISSSKKLAS 81
                                      8999999999855543333222 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 6.6e-05
                         EF-hand_7  16 dgyldkeellrllrkifqgagegsklsdeelellf 50 
                                       +gy+++++++ ++r+++   +   kl +e++e+++
  gi|557694294|ref|YP_008797348.1| 133 RGYIEVSDIEAAIRQLD---EKRHKLKREHVEQIL 164
                                       7**************99...888888889998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1221.31
//
Query:       gi|557694295|ref|YP_008797349.1|  [L=891]
Description: Ca2+-transporting ATPase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-48  164.3   4.7    1.9e-48  164.3   4.7    3.2  4  E1-E2_ATPase     E1-E2 ATPase
    2.7e-31  108.7   3.9    2.7e-31  108.7   3.9    2.7  3  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    1.9e-25   90.4   0.8      8e-25   88.4   0.8    2.2  1  Hydrolase        haloacid dehalogenase-like hydrolase
    5.7e-24   83.6   0.0    1.4e-23   82.3   0.0    1.7  1  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
      2e-21   75.9   0.0    3.9e-21   74.9   0.0    1.5  1  Cation_ATPase    Cation transport ATPase (P-type)
    6.3e-06   26.7   0.1    3.3e-05   24.4   0.1    2.2  2  HAD              haloacid dehalogenase-like hydrolase
    9.7e-05   22.2   0.3      0.021   14.6   0.4    2.5  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
        6.1    7.1   7.8        3.4    7.9   1.9    2.6  2  YtpI             YtpI-like protein


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 !    4.8   1.2    0.0079        18     115     158 ..      57      99 ..      46     103 .. 0.61
   2 !  164.3   4.7   8.7e-52   1.9e-48       2     181 .]     119     319 ..     118     319 .. 0.97
   3 ?   -3.1   0.0       2.2   4.9e+03      49      73 ..     546     579 ..     539     582 .. 0.74
   4 ?   -3.1   0.1       2.1   4.7e+03     121     137 ..     692     709 ..     664     726 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0079
                                       HHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHH CS
                      E1-E2_ATPase 115 ldklgkvlvpvvlliallvflialllgkslaeallralallvaa 158
                                       ++ + k+++ + + i+l++++i  + g+++ ++l+ a+ ++ +a
  gi|557694295|ref|YP_008797349.1|  57 IKIFLKQFANILIGILLIAIVISAFFGEWV-DSLVIAVIVFFVA 99 
                                       455667777777777777777777777776.5555544443333 PP

  == domain 2  score: 164.3 bits;  conditional E-value: 8.7e-52
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-............G CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek............e 65 
                                       +l ++++v+rdg+e+e+  kelvpGDiv+l +g +++aD r++e+ + + +e+aLTGEs pv+k            +
  gi|557694295|ref|YP_008797349.1| 119 MLTQSVTVVRDGREREVSYKELVPGDIVILTTGTKIAADLRVIESINlQTNEAALTGESSPVQKkidplprdlalgD 195
                                       67789************************************************************************ PP

                                       -TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTS CS
                      E1-E2_ATPase  66 kgdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgk 142
                                       + +m+f+Gt+v+ g+ k+vV+atg+ te+gkia+++   +++ktpl++ +d++gk +++++ ++++++f++ l+++ 
  gi|557694295|ref|YP_008797349.1| 196 RVNMAFAGTIVTYGRGKGVVVATGQRTEFGKIAAATTVIEEEKTPLERRMDEIGKKFAVIAAAAIVVIFAVELFREL 272
                                       **************************************************************************887 PP

                                       STT........HHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 143 sla........eallralallvaaiPcaLplavplalalgarrlakk 181
                                                  e ll+a+al+va++P+aLp +v+ +la+g++ +a++
  gi|557694295|ref|YP_008797349.1| 273 ASGdfslnfiiEVLLFAVALAVAVVPEALPGIVTGTLAIGTGIMARR 319
                                       77688899999*********************************996 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.2
                                       EEE-TTTS---S-EE-.........G-TTEE-TT CS
                      E1-E2_ATPase  49 evdesaLTGEslpvek.........ekgdmvfsG 73 
                                        + + ++TG+++   +         ++gdmv +G
  gi|557694295|ref|YP_008797349.1| 546 GIRTVMVTGDHKLTAVavarevgimKEGDMVLTG 579
                                       5677788888887777777788887888888777 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 2.1
                                       H.HHHHHHHHHHHHHHS- CS
                      E1-E2_ATPase 121 v.lvpvvlliallvflia 137
                                         lv v+++ a+++f++ 
  gi|557694295|ref|YP_008797349.1| 692 AnLVEVIVITAVALFIAE 709
                                       335556666666666554 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   2.5       1.3     3e+03      57      72 ..      69      84 ..      48     127 .. 0.57
   2 ?   -3.3   0.7       2.8   6.2e+03     163     180 ..     253     270 ..     248     297 .. 0.61
   3 !  108.7   3.9   1.2e-34   2.7e-31       2     182 .]     719     886 ..     718     886 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.3
                   Cation_ATPase_C 57 qgllqalvtllvfflt 72
                                      +g+l++++++ +ff  
  gi|557694295|ref|YP_008797349.1| 69 IGILLIAIVISAFFGE 84
                                      3333333333333322 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.8
                   Cation_ATPase_C 163 lialllalvvllvdelvK 180
                                       +++++ a+vv++ +el++
  gi|557694295|ref|YP_008797349.1| 253 AVIAAAAIVVIFAVELFR 270
                                       444444555555555543 PP

  == domain 3  score: 108.7 bits;  conditional E-value: 1.2e-34
                   Cation_ATPase_C   2 lplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfgi 78 
                                       lpl +++iL+inL tD+lpa+aL++ pp++dimkr+P +k+ep+++++++ + ++  ++++ + l+ + +++   g+
  gi|557694295|ref|YP_008797349.1| 719 LPLLPVHILYINLATDGLPAIALGFAPPDPDIMKRKPTPKNEPVFNREVVAMLVTAVAVTTPLYLIGYVAAVP-EGV 794
                                       8****************************************************88888888888888855554.566 PP

                   Cation_ATPase_C  79 sekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgta 155
                                       ++         a+t  F++++  +++ al++rs+  + f     +  k+ll++i+ +++l+++i+ +pg +++++++
  gi|557694295|ref|YP_008797349.1| 795 EH---------ARTRLFLMFIANELVLALSCRSLVYTNF---EAKPHKWLLISIAWEITLIMAILTIPGAAQLLSLT 859
                                       66.........**********************333333...344679***************************** PP

                   Cation_ATPase_C 156 plsleewlialllalvvllvdelvKll 182
                                        ++  +++++++ al+v l +e  K++
  gi|557694295|ref|YP_008797349.1| 860 TPTTADLVWIIGGALFVYLTVETSKII 886
                                       **********************99975 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.8   3.6e-28     8e-25       2     210 .]     336     639 ..     335     639 .. 0.75

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 3.6e-28
                                       SEEEEESBTTTBCHHHHHHHHHHHH......................CHHHHHHHHHH......HHCHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx......................xxxxxxxxxxx......xxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa......................alalaaaletg......sehpigkalvaaa 50 
                                        +++fDk+GTLtt ++ v++v+v                         l+  a+ e++         p   al+  a
  gi|557694295|ref|YP_008797349.1| 336 QVICFDKTGTLTTNQMTVRKVYVDDqlidvdtlekpsttlkllmdtsVLCNDAVVEIVngretvRGDPTEGALILLA 412
                                       589*********************99999999999977666666666555555555558888888899999999999 PP

                                       HHHHHHHHHHHHETTTE........................................HHHHTHHHHHHHHHCHHHHH CS
                                       xxxxxxxxxxxxxxxxx........................................xxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  51 karsgaltgfatfigrg........................................ayaigkpewltaldippdlg 87 
                                       k ++++ +  ++   r                                         +y  g++  l++++    l 
  gi|557694295|ref|YP_008797349.1| 413 KRLGWDFEALRKTHPRLheipftserkmmttfhktqsgdvagymkgavevvlpkcdiVYNNGEKHSLDEQTRARILS 489
                                       99966665555533333454455555566666666777888444555555555555555555555555553333333 PP

                                       HHHHHHHHHCHHHHHH..........................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEE CS
                                       xxxxxxxxxxxxxxxx..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  88 aaigsaqsqgrtvall..........................qaralavftiadplkvkpeaaeavasLkaagievv 138
                                                                                     l+++ + dp  ++pe+ +av++ ++agi++v
  gi|557694295|ref|YP_008797349.1| 490 V--------------AeqmassglrvlalahkpdadndfeekGFVFLGLVGMMDP--PRPEVYDAVKKAHEAGIRTV 550
                                       3..............24555555556666699988877655433788888888**..******************** PP

                                       EEESSEHHHHHHHHHHTT.............GGGE.SEEEEHHCES...STTTSHHHHHHHHHHHTSTGGGEEEEES CS
                                       xxxxxxxxxxxxxxxxxx.............xxxx.xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 139 lltgdnpetaeraanqlG.............ddyf.daviasdiet...vakpspegkvaaireLqgkpeevamVGD 198
                                       ++tgd++ ta ++a+++G              d++ d +++ ++e     a  sp +k+++++  + k+  vam GD
  gi|557694295|ref|YP_008797349.1| 551 MVTGDHKLTAVAVAREVGimkegdmvltgeeLDKLsDKELDNIVEHvvvYARISPLHKLRIVEAWKRKGYVVAMTGD 627
                                       *******************9999998888884444477777777778889999************************ PP

                                       SHHHHHHHHHTT CS
                                       xxxxxxxxxxxx RF
                         Hydrolase 199 gvnDaaalaaAg 210
                                       gvnDa+al++A+
  gi|557694295|ref|YP_008797349.1| 628 GVNDAPALKRAD 639
                                       **********98 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0   6.3e-27   1.4e-23       1      69 []      11      79 ..      11      79 .. 0.99

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 6.3e-27
                   Cation_ATPase_N  1 ehalsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalvs 69
                                      +h+ls+eev ++L+td+ nGL+++ea++rl+ +GpNel+++kk+s ++++lkqf n l+ +Ll+a ++s
  gi|557694295|ref|YP_008797349.1| 11 WHSLSVEEVVARLGTDPVNGLSSEEAQRRLRIFGPNELEPPKKTSPIKIFLKQFANILIGILLIAIVIS 79
                                      9******************************************************************98 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   1.7e-24   3.9e-21       1      89 [.     383     468 ..     383     470 .. 0.96

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1.7e-24
                     Cation_ATPase   1 ilcNsaafsensekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyv 77 
                                       +lcN+a +  +  ++++++ G++tE AL+ la++lg d e lr+ +++++eipF+s+rK+m++ +k+ +++ v  y+
  gi|557694295|ref|YP_008797349.1| 383 VLCNDAVV--EIVNGRETVRGDPTEGALILLAKRLGWDFEALRKTHPRLHEIPFTSERKMMTTFHKT-QSGDVAGYM 456
                                       59******..88899999************************************************9.7******** PP

                     Cation_ATPase  78 KGApeiilkrCt 89 
                                       KGA e++l +C+
  gi|557694295|ref|YP_008797349.1| 457 KGAVEVVLPKCD 468
                                       ***********7 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   1.5e-08   3.3e-05      87     188 .]     532     636 ..     473     636 .. 0.68
   2 ?   -1.7   0.0       1.4   3.2e+03      73     116 ..     665     709 ..     659     718 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.5e-08
                               HAD  87 dpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.rltgelglegkpvrgegkv....... 155
                                       +p+++++++++++aG+r+v+v+g ++  + ++++e+g    +     + d +ltge    +k++ +e +        
  gi|557694295|ref|YP_008797349.1| 532 RPEVYDAVKKAHEAGIRTVMVTGDHKLTAVAVAREVG----IMK---EGDmVLTGE--ELDKLSDKELDNivehvvv 599
                                       36*******999*************************....444...244566666..4444444444443444434 PP

                               HAD 156 ....aalre..wlaaegegidleevvay.GDspsDlpllr 188
                                           +      +l   ++  +   vva  GD+++D p+l+
  gi|557694295|ref|YP_008797349.1| 600 yariS---PlhKLRIVEAWKRKGYVVAMtGDGVNDAPALK 636
                                       42222...233222222333333377778********996 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.4
                               HAD  73 lerfvaevirpklldpgalellaahraaGd.rvvvvSgglrplve 116
                                       ++ +v +v + ++++  ++++l   ++a+  +v+v+++   +++e
  gi|557694295|ref|YP_008797349.1| 665 FATIVKAVELGRWIYGNVRKYLTYLLKANLvEVIVITAVALFIAE 709
                                       5555666666676779999999955555554******97777766 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0091        20      19      54 ..     534     569 ..     529     596 .. 0.87
   2 !   14.6   0.4   9.4e-06     0.021     203     253 ..     619     670 ..     609     672 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0091
                                       HHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCC CS
                       Hydrolase_3  19 ktkeaikklkekgikvviATGRslravlpvleelgl 54 
                                       +  +a+kk++e+gi  v  TG +  ++  v++e+g+
  gi|557694295|ref|YP_008797349.1| 534 EVYDAVKKAHEAGIRTVMVTGDHKLTAVAVAREVGI 569
                                       6779******************99999999999986 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 9.4e-06
                                       GGGEEEEESSGGGHHHHHHSSEEEEET.TS-HHHHHHSSEEE--GGGTHHHH CS
                       Hydrolase_3 203 leeviafGDgeNDieMLeaaglgvAmg.naseevkkaAdyvtksnnedGVak 253
                                          v+  GDg ND + L++a++gv mg  +++ +k+a+d + ++ n   ++k
  gi|557694295|ref|YP_008797349.1| 619 GYVVAMTGDGVNDAPALKRADIGVSMGiTGTDVAKEASDIMLADDNFATIVK 670
                                       5567888********************6688888888888777777666666 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.9    0.0015       3.4      33      82 ..      64     112 ..      53     117 .. 0.69
   2 ?    1.4   0.4      0.16   3.5e+02      34      72 ..     253     294 ..     237     298 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0015
                              YtpI  33 kasialGlflilfginqllllestvalvvgavflvlGlanlfaGiraykh 82 
                                        a+i++G++li++ i +++    + +lv++++   ++++ + + +ra k+
  gi|557694295|ref|YP_008797349.1|  64 FANILIGILLIAIVISAFFGE-WVDSLVIAVIVFFVAVVGFAQEYRAEKT 112
                                       59********99999988763.3334566666666666666666766665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                              YtpI  34 asialGlflilfginqlllles...tvalvvgavflvlGlan 72 
                                       a ia ++++++f++ ++  l s    +++++++++ +++la 
  gi|557694295|ref|YP_008797349.1| 253 AVIAAAAIVVIFAVELFRELASgdfSLNFIIEVLLFAVALAV 294
                                       568889999999999776644322378999999988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (891 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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):               8  [number of targets reported over threshold]
# CPU time: 0.77u 0.31s 00:00:01.08 Elapsed: 00:00:00.49
# Mc/sec: 5491.19
//
Query:       gi|557694296|ref|YP_008797350.1|  [L=75]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1109  (0.0618551); expected 358.6 (0.02)
Passed bias filter:                      712  (0.0397122); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 543.36
//
Query:       gi|557694297|ref|YP_008797351.1|  [L=137]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-09   37.9   0.7    2.4e-09   37.7   0.7    1.0  1  PIN        PIN domain
  ------ inclusion threshold ------
      0.029   14.5   0.7      0.077   13.1   0.2    1.8  2  LPD7       Large polyvalent protein-associated domain 7
      0.076   12.3   0.3      0.087   12.1   0.3    1.1  1  TcdA_TcdB  TcdA/TcdB catalytic glycosyltransferase 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 !   37.7   0.7   4.1e-13   2.4e-09       2     120 ..       3     123 ..       2     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 4.1e-13
                                       EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS.....SCHCHHHHHHHHHHHHH.HHTSEEEE CS
                               PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar.....rkskrekaaelvellll.lsalkilp 72 
                                        +D+s+l  +l +ee+ +++ ++l   e  ++++lvl E+ + + +       sk+e +a+l +l  l  +alk+ +
  gi|557694297|ref|YP_008797351.1|   3 AIDASALACFLLKEEGWREVGEALK--EGALSPDLVLKEVSNAILKrfrrgEMSKEEVDAALQALSALtGRALKVEE 77 
                                       69***************99999998..9**********************988999999999999999788888888 PP

                                       BCHHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  73 idaeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                         ++ +eea ++a  +gl+++Da+ ++  k  +++l  t+D++ +++a
  gi|557694297|ref|YP_008797351.1|  78 -ETKYVEEAIKVAMDRGLTVFDAVYIVFSKGKNLRLM-TADDRQAKAA 123
                                       .7777777777777778******************99.*****99987 PP

>> LPD7  Large polyvalent protein-associated domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   1.3e-05     0.077      35      77 ..      53      96 ..      39     101 .. 0.88
   2 ?   -0.9   0.0       0.3   1.8e+03      67      78 ..     120     131 ..     105     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                              LPD7 35 dddeavaaalelAqakw.gsltvsGseeFkreaweaaaerglev 77
                                       ++e v aal++ +a   ++l+v+ + ++++ea+++a +rgl+v
  gi|557694297|ref|YP_008797351.1| 53 MSKEEVDAALQALSALTgRALKVEEETKYVEEAIKVAMDRGLTV 96
                                      56799********999746***********************98 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.3
                              LPD7  67 weaaaerglevt 78 
                                       ++aa+e+g+ev+
  gi|557694297|ref|YP_008797351.1| 120 AKAASEEGVEVR 131
                                       567777777776 PP

>> TcdA_TcdB  TcdA/TcdB catalytic glycosyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   1.5e-05     0.087      49     137 ..      52     133 ..      40     137 .] 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHHHCCCCCT--HHHHHHHHHHHHHHH.................HHHHHHHHHHHTTSTT-HHHHHHH CS
                         TcdA_TcdB  49 ilvesasdaalqdlreaidedtkkfvkkrdeliekraekdqlkdlldtlvivaqkafinflkakgnkntkDeirkey 125
                                        + ++ +daalq+l   ++      +k ++e ++ +   + +k ++d+   v++  +i f k k+++ +  + r+ +
  gi|557694297|ref|YP_008797351.1|  52 EMSKEEVDAALQALSALTGR----ALKVEEETKYVE---EAIKVAMDRGLTVFDAVYIVFSKGKNLRLMTADDRQAK 121
                                       57788899***********4....445555555555...56********99***********877765554445666 PP

                                       HHHHS---HHHH CS
                         TcdA_TcdB 126 Lekeysldteel 137
                                         +e + ++  +
  gi|557694297|ref|YP_008797351.1| 122 AASEEGVEVRLI 133
                                       666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 982.52
//
Query:       gi|557694298|ref|YP_008797352.1|  [L=421]
Description: peptide chain release factor eRF subunit 1 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  133.6   0.0    1.3e-38  132.3   0.0    1.7  1  eRF1_2          eRF1 domain 2
    6.3e-27   94.3   0.6    4.1e-26   91.7   0.3    2.3  2  eRF1_3          eRF1 domain 3
    3.1e-19   69.6   0.1    1.2e-18   67.7   0.0    2.0  2  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
    3.5e-17   62.9   0.7    6.5e-16   58.8   0.0    2.4  2  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
      4e-15   55.9   0.0    7.3e-15   55.1   0.0    1.4  1  eRF1_1          eRF1 domain 1
  ------ inclusion threshold ------
      0.015   15.3   0.1       0.03   14.3   0.1    1.5  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.015   15.4   3.4        2.2    8.4   0.1    3.6  3  Resolvase       Resolvase, N terminal domain
      0.017   14.8   0.1       0.05   13.3   0.1    1.8  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
      0.017   15.2   0.3       0.11   12.5   0.0    2.2  2  baeRF_family2   Bacterial archaeo-eukaryotic release factor f
       0.31   10.8   1.3        7.8    6.3   0.1    2.3  2  Ribosomal_S27e  Ribosomal protein S27
       0.33   10.9   2.2       0.89    9.5   2.2    1.7  1  zf-trcl         Probable zinc-ribbon domain
       0.76    9.8   3.2        3.9    7.5   3.4    2.1  2  zinc_ribbon_4   zinc-ribbon domain
        1.7    8.8   3.7        1.5    9.0   0.8    2.4  3  Zn-ribbon_8     Zinc ribbon domain


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 !  132.3   0.0   9.4e-42   1.3e-38       2     133 .]     146     274 ..     145     274 .. 0.97

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 9.4e-42
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTES CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklk 78 
                                       +g+iv+d++eA ++++kg++++ lk+ ++ vP+Kh++GgqsarrfeRlre  l+ f+k+vae+an+ fl  +  +lk
  gi|557694298|ref|YP_008797352.1| 146 YGVIVIDNEEAAVAVVKGRSISELKTYTSGVPGKHHAGGQSARRFERLREMTLNDFYKRVAEKANEIFL--QYPELK 220
                                       8******************************************************************99..69**** PP

                                       EEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
                            eRF1_2  79 giilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                                       g+ilagpg++ke f ++++l++ l++k i +vd+sy gesg++e++ k+a+ lk+
  gi|557694298|ref|YP_008797352.1| 221 GVILAGPGPTKEVFAQGEYLHYSLRDK-IHIVDTSYSGESGVREAVAKSADFLKE 274
                                       ************************986.789******************999985 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.9   1.2e+03      30      59 ..     137     181 ..     131     214 .. 0.60
   2 !   91.7   0.3   2.9e-29   4.1e-26       2     112 ..     278     418 ..     277     419 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.9
                                       HHHHHTT-EEEEEEEHCHHTSSSHHHHHS...............- CS
                            eRF1_3  30 lkalemgAvetLLvseelersrdtlkekv...............k 59 
                                       ++ l+ +Av  ++v+++ e    ++k +                +
  gi|557694298|ref|YP_008797352.1| 137 KELLREKAVYGVIVIDNEEAAVAVVKGRSiselktytsgvpgkhH 181
                                       566777888888888887777665554444455555554444441 PP

  == domain 2  score: 91.7 bits;  conditional E-value: 2.9e-29
                                       HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS.................... CS
                            eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekv.................... 58 
                                       ++e++l++++++e  + +g+avYG+++v++al+ ++ve LL+se+l+r ++++k++                     
  gi|557694298|ref|YP_008797352.1| 278 VEEQRLIQRLMSEATRADGLAVYGEKQVREALRKNMVELLLISEDLDRLEVKIKCQNcgyetvftidsgelqtevpk 354
                                       79**************99********************************99777777******************* PP

                                       .........-HHH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                            eRF1_3  59 .........ketgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                                +  +++l l e   li++l+ ++e++g +ve+isse+eeGe++ kafgG+a++LR +
  gi|557694298|ref|YP_008797352.1| 355 klaekcpvcQ--NQTLALAEttpLIDKLIAEAENMGVRVELISSEHEEGEMFRKAFGGVAGFLRHR 418
                                       ***9997443..44444444669*****************************************76 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 !   67.7   0.0   8.9e-22   1.2e-18       2     116 ..     132     248 ..     132     271 .. 0.88
   2 ?   -1.8   0.0       2.5   3.4e+03      82     107 ..     286     312 ..     277     317 .. 0.68

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 8.9e-22
                    baeRF_family10   2 ylapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAe 78 
                                       +++pL e+l+e   ygv+++d+e+a++++v ++++ e ++ ++ vpg++++gg+ s +rf+r +e++   ++k+vAe
  gi|557694298|ref|YP_008797352.1| 132 HTEPLKELLREKAVYGVIVIDNEEAAVAVVKGRSISELKTYTSGVPGKHHAGGQ-SARRFERLREMTLNDFYKRVAE 207
                                       578***************************************************.********************** PP

                    baeRF_family10  79 llaklleerg.verlvlgGdeeetaall..drlpkalrarv 116
                                        +++++ + + ++ ++l+G+   +++++  + l+ +lr+++
  gi|557694298|ref|YP_008797352.1| 208 KANEIFLQYPeLKGVILAGPGPTKEVFAqgEYLHYSLRDKI 248
                                       *********99*********888888762246777777776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.5
                    baeRF_family10  82 klleerg.verlvlgGdeeetaalldr 107
                                       +l++e   ++ l + G +++++al+++
  gi|557694298|ref|YP_008797352.1| 286 RLMSEATrADGLAVYGEKQVREALRKN 312
                                       444444447778888888888888776 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.0   4.7e-19   6.5e-16       3     104 ..     146     246 ..     144     277 .. 0.80
   2 ?    2.3   0.4      0.14   1.9e+02      66      92 ..     284     312 ..     258     329 .. 0.65

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 4.7e-19
                           acVLRF1   3 lgvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarll..aeesaev 77 
                                       +gv+++     av+vv+g+ + + k+ t+ v g++ aGG+S +Rf+R re + ++ +++vae+a++++   +e + v
  gi|557694298|ref|YP_008797352.1| 146 YGVIVIDNEEAAVAVVKGRSISELKTYTSGVPGKHHAGGQSARRFERLREMTLNDFYKRVAEKANEIFlqYPELKGV 222
                                       68899999999*********************************************************44366666* PP

                           acVLRF1  78 vlgGdrslvaevledarlaplatlare 104
                                       +l+G+  + + +++ +    l+   r+
  gi|557694298|ref|YP_008797352.1| 223 ILAGPGPTKEVFAQGEY---LHYSLRD 246
                                       ****9998888887754...5555555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.14
                           acVLRF1  66 aarllaeesae..vvlgGdrslvaevled 92 
                                       ++rl+ e++++  +++ G+++++++++++
  gi|557694298|ref|YP_008797352.1| 284 IQRLMSEATRAdgLAVYGEKQVREALRKN 312
                                       3344433333357***********99987 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0   5.3e-18   7.3e-15       3     128 ..      19     139 ..      17     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 5.3e-18
                                       EEEE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTT CS
                            eRF1_1   3 llkr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkd 77 
                                       ll+    le++g+++vtL++++d+ ++++ n++++++ ++a++++k +r         ++v+ ++++ ++++++  +
  gi|557694298|ref|YP_008797352.1|  19 LLETieRLEGRGTELVTLYVPPDKSISDVINYLRQEYATAANIKSKQTR---------KNVQDAIESAIQRLKLFDN 86 
                                       556555899*************************************999.........9**************9999 PP

                                       ...SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHHH CS
                            eRF1_1  78 ...agvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLkea 128
                                          +g++ +sG + ++++  ++ +   + + +++p+t++ ++ +++f++e+Lke+
  gi|557694298|ref|YP_008797352.1|  87 pgpTGLVIFSGAIPQNSG--QTSKIEVYHVIPPEPITTFLYRcDSRFHTEPLKEL 139
                                       9999***********999..68889999999*********999**********97 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 ?   14.3   0.1   2.2e-05      0.03      64     101 ..     323     372 ..     270     379 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                                       EEEE--EEEETTTS-EEECHHH..HH..........S-TTTSSS-EEEEE CS
                              HypA  64 ieevpvkvrCreCgkefeleek..al..........rCpkCgsadveivs 101
                                       +++ +vk++C++Cg+e+  + +  +l          +Cp C+++ + + +
  gi|557694298|ref|YP_008797352.1| 323 LDRLEVKIKCQNCGYETVFTIDsgELqtevpkklaeKCPVCQNQTLALAE 372
                                       67889*********9988544323336789999999******99887765 PP

>> Resolvase  Resolvase, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0016       2.2      81     142 ..      17      79 ..      15      82 .. 0.84
   2 ?    4.4   0.3     0.027        37      53     106 ..     284     339 ..     235     359 .. 0.77
   3 ?    0.2   0.0      0.52   7.2e+02      84     125 ..     378     415 ..     369     418 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                                       .S-HHHHHHHHHTT-EEEESS..SS----H.HHHHHHHHHHHHHHHHHHHHCT-TTHHHHHHH CS
                         Resolvase  81 rdlltlleelrekgvslvsldegidtstpm.grlllqilaalaeferelirertkeglaaaka 142
                                       r ll+++e l+ +g +lv+l  + d+s +   + l+q +a+ a ++++++r++++++++ a +
  gi|557694298|ref|YP_008797352.1|  17 RRLLETIERLEGRGTELVTLYVPPDKSISDvINYLRQEYATAANIKSKQTRKNVQDAIESAIQ 79 
                                       6799*****************7544433333677***********************998865 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.027
                                       HHHHHHHHTT-EE.EEEESSCCC..C-S...S-HHHHHHHHHTT-EEEESS..SS- CS
                         Resolvase  53 lkrllaalregkgdvlvvekldR..LaRsvrdlltlleelrekgvslvsldegidt 106
                                       ++rl++++++  g +++ ek  R  L  ++ +ll + e+l++ +v++++ + g++t
  gi|557694298|ref|YP_008797352.1| 284 IQRLMSEATRADGLAVYGEKQVReaLRKNMVELLLISEDLDRLEVKIKCQNCGYET 339
                                       57777777774444555555554436677999999999999999999999966766 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.52
                                       HHHHHHHHHTT-EEEESS..SS----HHHHHHHHHHHHHHHH CS
                         Resolvase  84 ltlleelrekgvslvsldegidtstpmgrlllqilaalaefe 125
                                        +l+ e ++ gv++  +++    ++++g+++++ ++ +a f 
  gi|557694298|ref|YP_008797352.1| 378 DKLIAEAENMGVRVELISS----EHEEGEMFRKAFGGVAGFL 415
                                       5678888888899988885....6788999999999998775 PP

>> 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 ?   13.3   0.1   3.6e-05      0.05       4      47 ..     285     329 ..     283     366 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.6e-05
                                       HHHHHHHHHHTE.EEESHHHHHHHHHTTTESEEEEETTSSSGGHH CS
                    Ribosomal_L7Ae   4 eevlkkakkagk.lvlGlkevtkalergeaklvilAedvepeekk 47 
                                       ++++++a +a++  v+G k+v  al+++ ++l +++ed +  e k
  gi|557694298|ref|YP_008797352.1| 285 QRLMSEATRADGlAVYGEKQVREALRKNMVELLLISEDLDRLEVK 329
                                       6778899999995689***********************998876 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 ?   12.5   0.0     8e-05      0.11       3     146 ..     147     290 ..     145     293 .. 0.77
   2 ?    1.0   0.1      0.29     4e+02      72      95 ..     290     313 ..     282     318 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8e-05
                     baeRF_family2   3 lvvevDrtGadltlvdaggeeeeetveGghdpvhkvraggwshrryqrraeeswerNaeavAeevdrlvres.gael 78 
                                        v+++D + a + +v+++   e +t + g     k +agg s rr++r  e + +   ++vAe+ +++  +  + + 
  gi|557694298|ref|YP_008797352.1| 147 GVIVIDNEEAAVAVVKGRSISELKTYTSGVPG--KHHAGGQSARRFERLREMTLNDFYKRVAEKANEIFLQYpELKG 221
                                       5899************8855555555555443..44468899*************************9865426677 PP

                     baeRF_family2  79 VvlaGDvrarsllr..deLpervrelvvevegggraagadrealaeevaealaerrarrreevlerfrae 146
                                       V+laG     +  +  + L+  +r+ ++ v+    +++  rea+a++ +  l+e+r  +++++ +r+  e
  gi|557694298|ref|YP_008797352.1| 222 VILAGPGPTKEVFAqgEYLHYSLRDKIHIVDTSYSGESGVREAVAKSAD-FLKEVRMVEEQRLIQRLMSE 290
                                       ****976666666522689999999999999999999999999988765.67777777777777777665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.29
                     baeRF_family2  72 resgaelVvlaGDvrarsllrdeL 95 
                                       + ++a+ + + G+ + r++lr+++
  gi|557694298|ref|YP_008797352.1| 290 EATRADGLAVYGEKQVREALRKNM 313
                                       457899999***********9876 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0057       7.8       6      18 ..     328     340 ..     327     346 .. 0.86
   2 ?    3.0   0.1     0.061        84       9      18 ..     359     368 ..     355     377 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0057
                                       EEEE-TTTS-EEE CS
                    Ribosomal_S27e   6 ldvkCpdCenetv 18 
                                       +++kC++C+ etv
  gi|557694298|ref|YP_008797352.1| 328 VKIKCQNCGYETV 340
                                       689******9986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.061
                                       E-TTTS-EEE CS
                    Ribosomal_S27e   9 kCpdCenetv 18 
                                       kCp C+n+t 
  gi|557694298|ref|YP_008797352.1| 359 KCPVCQNQTL 368
                                       9******996 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.2   0.00064      0.89       4      41 ..     329     365 ..     327     369 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00064
                           zf-trcl   4 tltCkdCgaefvFtageQeFyaekgfdnepkRCkaCRk 41 
                                       +++C++Cg e vFt    e   e   +  + +C+ C +
  gi|557694298|ref|YP_008797352.1| 329 KIKCQNCGYETVFTIDSGELQTE-VPKKLAEKCPVCQN 365
                                       689***********998886444.45677888888876 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.4     0.015        20      24      32 ..     328     336 ..     321     338 .. 0.83
   2 ?    7.5   3.4    0.0028       3.9       2      33 ..     329     365 ..     329     366 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.015
                     zinc_ribbon_4  24 vkvrCskCg 32 
                                       vk++C +Cg
  gi|557694298|ref|YP_008797352.1| 328 VKIKCQNCG 336
                                       899999998 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0028
                     zinc_ribbon_4   2 kitCpsCk..akyeiddeklp...akgvkvrCskCgh 33 
                                       ki C++C+  ++++id+  l+   +k+   +C+ C++
  gi|557694298|ref|YP_008797352.1| 329 KIKCQNCGyeTVFTIDSGELQtevPKKLAEKCPVCQN 365
                                       79*****6559*******9987555666679****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 ?   -2.0   0.0         3   4.1e+03       5      10 ..     124     129 ..     122     139 .. 0.70
   2 ?   -2.6   0.0       4.7   6.5e+03      13      22 ..     188     197 ..     185     200 .. 0.80
   3 ?    9.0   0.8    0.0011       1.5       7      34 ..     331     365 ..     329     369 .. 0.69

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3
                       Zn-ribbon_8   5 eYrCee 10 
                                        YrC++
  gi|557694298|ref|YP_008797352.1| 124 LYRCDS 129
                                       599987 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.7
                       Zn-ribbon_8  13 hefevlqsis 22 
                                       ++fe+l++++
  gi|557694298|ref|YP_008797352.1| 188 RRFERLREMT 197
                                       68***99986 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0011
                       Zn-ribbon_8   7 rCeeCghefe......vlqsisdaplta.CPeCgs 34 
                                       +C++Cg e        +lq+   ++l + CP C+ 
  gi|557694298|ref|YP_008797352.1| 331 KCQNCGYETVftidsgELQTEVPKKLAEkCPVCQN 365
                                       8*****66556677777775443446666****87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1266  (0.0706119); expected 358.6 (0.02)
Passed bias filter:                     1069  (0.0596241); 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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 2887.80
//
Query:       gi|557694299|ref|YP_008797353.1|  [L=116]
Description: hypothetical protein CSUB_C0866 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.7   0.1      0.036   13.6   0.1    1.2  1  DUF4908   Domain of unknown function (DUF4908)


Domain annotation for each model (and alignments):
>> DUF4908  Domain of unknown function (DUF4908)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     2e-06     0.036     113     181 ..      37     100 ..      11     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2e-06
                           DUF4908 113 svnallqrlvqasarasraaqrkiefeaddatPatsvlvadaatvtaeavvrmarkkdgrkllakvarv 181
                                        + +ll+ l+qa  ras+a+  + efea +  Pa  vl  d a      +v++ r+k g +l  + +++
  gi|557694299|ref|YP_008797353.1|  37 KFPQLLESLRQARDRASAAVYPR-EFEALNPSPAVAVLSRDDAG----KFVELIRRKTGASLYERAVKI 100
                                       4679*************998765.9***************9875....677777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); 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: 00:00:00.37
# Mc/sec: 933.94
//
Query:       gi|557694300|ref|YP_008797354.1|  [L=247]
Description: fructose-bisphosphate aldolase, class I [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-37  128.8   0.1    2.9e-37  128.6   0.1    1.0  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.6   0.1   1.6e-41   2.9e-37       2     235 .]      21     225 ..      20     225 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.6 bits;  conditional E-value: 1.6e-41
                                       EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCT.TSEEEEETECSSCCTTSTT CS
                              DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyak.diallvkldkgtyllkskq 77 
                                       +i+a+D++  ++++++       e++ ++ ++++++ga+av++++g++  ++  +a+ d + ++ l    + ++++ 
  gi|557694300|ref|YP_008797354.1|  21 LIFAIDHGFFMGPVKGV------EKPLEVLEKVVEAGADAVMTTYGIMKNYASSLARkDLGWILTLL---DTSPTT- 87 
                                       79***************......8*******************************999*******98...444444. PP

                                       EEEETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHH CS
                              DeoC  78 rdvdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlva 154
                                           ++ sv+ a+alGAdavkv v+y   gse+ ++ l+ + +v+ ac+e+glp+++e+y+          +p+ va
  gi|557694300|ref|YP_008797354.1|  88 ----VEKSVASAVALGADAVKVFVSY---GSENMKRDLDILWAVNMACREYGLPVLAEMYPVSRP------SPEEVA 151
                                       ....578*******************...*******************************99999......8***** PP

                                       HHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEE CS
                              DeoC 155 eAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvls 228
                                       + ar++ae G D++K+ ++        +da++f+ v++ +pvp vv+ GG    se+++le+v+d+v   g++G+++
  gi|557694300|ref|YP_008797354.1| 152 KMARIGAEYGGDFVKTVYT--------GDAASFRYVVETCPVP-VVVLGGEkieSEQQVLEMVRDSV-SVGGAGAAI 218
                                       *******************........****************.9999**999**************.********* PP

                                       SHHHHTT CS
                              DeoC 229 GRaifqk 235
                                       GR+ifq+
  gi|557694300|ref|YP_008797354.1| 219 GRNIFQH 225
                                       *****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 00:00:00.40
# Mc/sec: 1846.75
//
Query:       gi|557694301|ref|YP_008797355.1|  [L=378]
Description: pyruvate formate-lyase activating enzyme [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   52.8   0.0    1.3e-13   51.6   0.0    1.6  1  Radical_SAM  Radical SAM superfamily
    4.6e-05   23.7   0.1    8.6e-05   22.8   0.1    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 !   51.6   0.0   1.5e-17   1.3e-13       3     139 ..     147     282 ..     146     317 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.5e-17
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla...vp 76 
                                       ++ gC+l+C fC+++++ +   r+   sv+e++e+   +k   ++    ++gg p  + +f++++ r++ +    ++
  gi|557694301|ref|YP_008797355.1| 147 FFYGCSLNCLFCQNWTH-KLISRAPQTSVDELVELTLNNK---RISCWCWFGGSPEPQLPFAVEASRRIVETkpsNR 219
                                       678************97.9999999999999999997774...4**************************99***** PP

                                       TEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpd...eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklre 139
                                        +ri++e ng       ++ +e+ +e g   v ++l+a+++  v+k +  g ++ ++le++e+  +
  gi|557694301|ref|YP_008797355.1| 220 VMRICYEWNGDGNPalvKKAVETVAESG-GNVKFDLKAFTPA-VHKAL-TGLDNRRILENFEMVYR 282
                                       **********996589999999999999.*************.*****.99**********98655 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 !   22.8   0.1   9.6e-09   8.6e-05       7     102 ..     143     238 ..     134     251 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 9.6e-09
                           Fer4_12   7 rlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiied.lkkesiegltllGG..EPllpenaeallelvkevk 80 
                                        l+lf+ gC+l+C +C n   w  k     +++  +e++e  l++++i+    +GG  EP lp+ +ea  ++v+   
  gi|557694301|ref|YP_008797355.1| 143 NLALFFYGCSLNCLFCQN---WTHKLISRAPQTSVDELVELtLNNKRISCWCWFGGspEPQLPFAVEASRRIVETKP 216
                                       579************886...555555666666666666651567888999*****888999999999999999999 PP

                           Fer4_12  81 eekpekdiwlytgytleelskk 102
                                       ++ +   + +++g  + +l kk
  gi|557694301|ref|YP_008797355.1| 217 SNRVMRICYEWNGDGNPALVKK 238
                                       9988889*****9988777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2917.98
//
Query:       gi|557694302|ref|YP_008797356.1|  [L=232]
Description: 2-haloacid dehalogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-27   96.0   0.0    3.4e-27   95.7   0.0    1.1  1  HAD_2            Haloacid dehalogenase-like hydrolase
      4e-15   56.7   0.0    5.2e-14   53.0   0.0    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.7e-12   47.2   0.0    3.6e-12   46.2   0.0    1.5  1  Hydrolase_like   HAD-hyrolase-like
      0.005   16.5   0.1       0.21   11.2   0.0    2.5  3  PGP_phosphatase  Mitochondrial PGP phosphatase


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 !   95.7   0.0   7.7e-31   3.4e-27       1     176 [.       7     202 ..       7     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 7.7e-31
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleey..............glselseeelrkliglslrellrklgeseeeee... 60 
                                       ++FD+D+Tl+d+  ++  a ++++ee               ++   + e++++  gl +r+l+++  + + + +   
  gi|557694302|ref|YP_008797356.1|   7 VLFDFDNTLVDSAAVLPLARRRVAEEIvayygnsldveevaQV-VAWVEHVAERQGLLDRDLIWEHVIHNLKVDslp 82 
                                       79**********************999********99975433.7899********999999877665544444585 PP

                             HAD_2  61 kieellrkyneekkk..kevkpydgvkelLeeLkeagyklgivTsk..sreaveekleqlgiesyFdviv.tsedve 132
                                          e lr++ +   +   +  ++++  ++Le+L  ++y lg+vT+   +  + ++ le+ g+ ++F+ +v  +edv 
  gi|557694302|ref|YP_008797356.1|  83 P-SETLRRWSNIYWTeyAMGPLFPDTVSVLENL-GRRYVLGVVTNTdgMPGMKMRRLEKSGLLKFFKAVViAGEDVP 157
                                       3.34445555544443557899***********.99********98557899**************97651689*** PP

                             HAD_2 133 kkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikvi 176
                                       + KP+p++++ a + l++k+ee+i+vGD p +D+ +ak ag+ ++
  gi|557694302|ref|YP_008797356.1| 158 ETKPSPRPFLHAAKLLNVKPEECIMVGDDPiNDVLGAKSAGMYSV 202
                                       ******************************************987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   1.2e-17   5.2e-14       2     210 .]       5     198 ..       4     198 .. 0.72

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.2e-17
                                       SEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHH.........HHHHHHHHHETTTEHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakar.........sgaltgfatfigrgay 69 
                                       k+v+fD+d+TL+++      v++ a            ++  ++ +va++ +             ++ +a+     + 
  gi|557694302|ref|YP_008797356.1|   5 KAVLFDFDNTLVDSA----AVLPLA------------RRRVAEEIVAYYGNSldveevaqvVAWVEHVAE-----RQ 60 
                                       99**********999....344444............333455555555554332221110333344444.....44 PP

                                       HHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTE.EEEEEESSEH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                         Hydrolase  70 aigkpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagi.evvlltgdnp 145
                                           ++++ ++      + +++s+        +   ++++   +  p  ++p+++ +++ L ++ +  vv  t + p
  gi|557694302|ref|YP_008797356.1|  61 GLLDRDLIWEH---VIHNLKVDSLPPSETLRRWS--NIYWTEYAMGP--LFPDTVSVLENLGRRYVlGVVTNTDGMP 130
                                       44444444444...23334444455555555555..67777777788..***************7768888889999 PP

                                       HHHHHHHHHTT.GGGE.SEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHTT CS
                                       xxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                         Hydrolase 146 etaeraanqlG.ddyf.daviasdietvakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaAg 210
                                        + +r +++ G  ++f ++via++++   kpsp+ +++a++ L++kpee++mVGD +  D+ +++ Ag
  gi|557694302|ref|YP_008797356.1| 131 GMKMRRLEKSGlLKFFkAVVIAGEDVPETKPSPRPFLHAAKLLNVKPEECIMVGDDPInDVLGAKSAG 198
                                       9999********999999999999999***************************99655*******98 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0     8e-16   3.6e-12       4      75 .]     160     226 ..     158     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 8e-16
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES- CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlaea 75 
                                       KP+p  +  a++ l+++pee++m+GD++  D++gA+ aG+ svL      +p      + kp++++++l+e+
  gi|557694302|ref|YP_008797356.1| 160 KPSPRPFLHAAKLLNVKPEECIMVGDDPINDVLGAKSAGMYSVLLDKQGGKP-----YPVKPDHIVKSLREL 226
                                       9*******************************************97655555.....3489*******9986 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.019        87      41      54 ..       4      17 ..       2      43 .. 0.78
   2 ?   -1.8   0.0      0.46     2e+03     120     140 ..      30      50 ..      20      53 .. 0.83
   3 !   11.2   0.0   4.8e-05      0.21     134     164 ..     175     205 ..     117     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.019
                   PGP_phosphatase 41 ikavvlDKDnclaa 54
                                      +kav++D Dn+l  
  gi|557694302|ref|YP_008797356.1|  4 LKAVLFDFDNTLVD 17
                                      79*********975 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.46
                   PGP_phosphatase 120 aeevleyfkerkvveeadeia 140
                                       aee+++y+ ++  vee  +++
  gi|557694302|ref|YP_008797356.1|  30 AEEIVAYYGNSLDVEEVAQVV 50 
                                       7999****9999999888775 PP

  == domain 3  score: 11.2 bits;  conditional E-value: 4.8e-05
                   PGP_phosphatase 134 eeadeiavvgDRllTdvllanmmGslgvwlr 164
                                        +++e ++vgD  + dvl a+  G ++v+l 
  gi|557694302|ref|YP_008797356.1| 175 VKPEECIMVGDDPINDVLGAKSAGMYSVLLD 205
                                       479************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1904.37
//
Query:       gi|557694303|ref|YP_008797357.1|  [L=514]
Description: methionyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-134  447.7   0.0   3.6e-134  447.4   0.0    1.1  1  tRNA-synt_1g    tRNA synthetases class I (M)
    7.9e-09   35.7   0.0    1.3e-08   34.9   0.0    1.4  1  Anticodon_1     Anticodon-binding domain of tRNA
    2.1e-05   23.0   0.6    0.00086   17.7   0.0    3.1  3  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    0.00062   19.7   6.1      0.062   13.3   5.6    2.4  2  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.023   14.7   6.0       0.18   11.8   0.4    2.3  2  zf-C2HC5        Putative zinc finger motif, C2HC5-type
       0.03   14.4   8.6       0.81    9.9   1.1    2.5  2  Zn-ribbon_8     Zinc ribbon domain
       0.11   11.3   0.0        0.2   10.5   0.0    1.3  1  tRNA-synt_1f    tRNA synthetases class I (K)
       0.19   11.1   0.0       0.68    9.2   0.0    1.8  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
       0.19   11.8   2.7       0.39   10.8   2.7    1.6  1  zf-CRD          Cysteine rich domain with multizinc binding r
       0.33   11.0   4.3       0.45   10.5   2.0    1.7  2  zinc-ribbons_6  zinc-ribbons
       0.34   10.9   3.8        2.9    8.0   0.4    2.3  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.72    9.4  14.8         15    5.1   0.2    4.1  3  zf-ribbon_3     zinc-ribbon domain
       0.83    9.5   2.7        1.6    8.6   2.7    1.4  1  DUF2797         Protein of unknown function (DUF2797)
       0.98    9.2  13.4       0.14   11.9   3.7    3.2  2  zinc_ribbon_2   zinc-ribbon domain
        2.1    9.2   6.9       0.37   11.6   1.1    2.3  2  zinc_ribbon_15  zinc-ribbon family


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 !  447.4   0.0    3e-137  3.6e-134      40     391 .]       1     354 [.       1     354 [. 0.99

  Alignments for each domain:
  == domain 1  score: 447.4 bits;  conditional E-value: 3e-137
                                       EEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1g  40 lfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdkygrttseehkelvqeifkklkekgliyek 116
                                       +fv+g+DehGtpie++A+k+gv+p+e+++k+h+ + elf+k+++sfd+y+rt++ +h  ++q++f k++e+g+iye+
  gi|557694303|ref|YP_008797357.1|   1 MFVSGSDEHGTPIEVEAAKRGVDPREITDKNHALVVELFNKFHLSFDNYTRTHNPTHIAFCQNFFMKIYENGYIYEQ 77 
                                       69*************************************************************************** PP

                                       EEEEEEETTTTEEE-GGG-EE........-TTS-EE-TTSSB-E................EEE.EEEEEE-GGGGHH CS
                      tRNA-synt_1g 117 eieqlycpkderflpdryvegtCPkckseeargdqceecgkkleptelinpksaisgskpevketehlffklskfek 193
                                       +++qlyc++++rflpdr+v+g CP c++++argdqce+cgk l+p +l +p+++i+g+kp+v++++h+ff+l++f++
  gi|557694303|ref|YP_008797357.1|  78 DVNQLYCKNCGRFLPDRFVTGVCPSCGYQRARGDQCEACGKVLDPLDLLEPRCSICGEKPVVESSRHWFFDLPQFSD 154
                                       ***************************************************************************** PP

                                       HHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET..TECCEEE-HHHHHHHHHHHTTTTT-...TT CS
                      tRNA-synt_1g 194 klkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP..gaekkvlYVWldAligYisatkelakkkge 268
                                       kl++w+ +++++l+e+v++++++w++egLk++a++rd  wGip P  ga +k++YVW++A++gY sat e+a+kkge
  gi|557694303|ref|YP_008797357.1| 155 KLRTWL-TTNTTLSEKVRNFSLSWIREGLKPRAVTRDNLWGIPAPfpGAGNKTIYVWFEAVLGYPSATVEWAEKKGE 230
                                       ******.88889*******************************9988****************************** PP

                                       SGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHH CS
                      tRNA-synt_1g 269 eekwkeyWakdkevelvhfigkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakeale 343
                                       +  w+e+W   ++++  +figkd+i+FHt+++Pa+ll+  + + lp+ v+a+eylt+egkK+SkS gv+++ ++a+ 
  gi|557694303|ref|YP_008797357.1| 231 PALWREFW-LSPDTKSAYFIGKDNIPFHTVILPALLLAthEPYILPHIVSATEYLTFEGKKFSKSLGVGIWLDQAIA 306
                                       ********.77***************************989999********************************* PP

                                       HH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH. CS
                      tRNA-synt_1g 344 rldadllRYylaaeapekkDldfswedfvervNseLadklgnlvnRvl 391
                                        l+ad++RYyl++ +pe+ D++fs + +++ vNs+L+++lgn+++Rvl
  gi|557694303|ref|YP_008797357.1| 307 LLEADIWRYYLVKIRPETGDTNFSYDGLMAVVNSDLNNDLGNFIHRVL 354
                                       **********************************************85 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 !   34.9   0.0   1.1e-11   1.3e-08       1     101 [.     375     470 ..     375     508 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.1e-11
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       dr++l+ ++k+  ev+  + e r ++a+  + ++      ++y++  +p+   +  +++ a + +v + vl++l  l
  gi|557694303|ref|YP_008797357.1| 375 DREMLAAIEKTFTEVDSLLSEAREKQALETVIQL--AREGNVYFNRREPWRLVKARKEEAAtVLYVAAQVLKALALL 449
                                       89*******************************8..4447**********99988777666577************* PP

                       Anticodon_1  77 laPfmPfitEelwqreeeelgkkes 101
                                       laPf+P +t  +     e++g+ e+
  gi|557694303|ref|YP_008797357.1| 450 LAPFTPATTRRIL----ELIGQGEE 470
                                       *************....99977755 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 ?    1.4   0.0     0.062        74     127     169 ..      45      87 ..       1      94 [. 0.72
   2 ?   -0.2   0.1      0.18   2.2e+02     365     433 ..     130     199 ..     119     204 .. 0.79
   3 !   17.7   0.0   7.2e-07   0.00086     488     602 .]     208     330 ..     202     330 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.062
                       tRNA-synt_1 127 DfdreylTldkeleeavkevfvrladkgliyrgkklvnwstkl 169
                                        fd+   T ++   +  ++ f++++++g iy+      ++ ++
  gi|557694303|ref|YP_008797357.1|  45 SFDNYTRTHNPTHIAFCQNFFMKIYENGYIYEQDVNQLYCKNC 87 
                                       4667777777777777888889999999999877666666665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.18
                       tRNA-synt_1 365 cerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswlen.iqdWciSRqrwWGhripl 433
                                       c+  ++  ++ ++  Wf  + ++ d++   ++  +   ++ ++   sw+++  +  ++ R+  WG + p+
  gi|557694303|ref|YP_008797357.1| 130 CSICGEKPVVESSRHWFFDLPQFSDKLRTWLTTNTTLSEKVRNFSLSWIREgLKPRAVTRDNLWGIPAPF 199
                                       555555555677889999999999999999987777888888888999987468899********99885 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 7.2e-07
                       tRNA-synt_1 488 DvWFsSgs.wpfstlgypee.dteelkkff.....padmlleGlDiirgWvarlillslaltgsePfk..evlvhgl 555
                                        vWF+  +  p++t+++ e+  ++ l + f       + +  G D i +  +++il +l l  +eP+   +++    
  gi|557694303|ref|YP_008797357.1| 208 YVWFEAVLgYPSATVEWAEKkGEPALWREFwlspdTKSAYFIGKDNIPF--HTVILPALLLATHEPYIlpHIVSATE 282
                                       68999998568999***9983344554444344334688999***9986..7999************5326777777 PP

                       tRNA-synt_1 556 vrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinls 602
                                        +  eG+K SKslg  i  ++ i  + ad+ R++l+   + + d+n+s
  gi|557694303|ref|YP_008797357.1| 283 YLTFEGKKFSKSLGVGIWLDQAIALLEADIWRYYLVkIRPETGDTNFS 330
                                       7899********************************888899998875 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   5.6   5.2e-05     0.062      12      49 .]      81     117 ..      75     117 .. 0.83
   2 !   12.8   4.1   7.7e-05     0.092       1      37 [.     100     136 ..     100     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.2e-05
                               DZR  12 arfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49 
                                       + +C++Cg  l+      +CpsCg++   +   C +CG
  gi|557694303|ref|YP_008797357.1|  81 QLYCKNCGRFLPDRFVTGVCPSCGYQRARG-DQCEACG 117
                                       569********97777*********97666.5699998 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.7e-05
                               DZR   1 CpqCgeelppdarfCseCgtklkavaa.edrCpsCgek 37 
                                       Cp+Cg +   +   C++Cg+ l++    e rC+ Cgek
  gi|557694303|ref|YP_008797357.1| 100 CPSCGYQRARG-DQCEACGKVLDPLDLlEPRCSICGEK 136
                                       *******6665.57********8555599*******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 ?    5.5   0.8     0.015        17      19      42 ..      83     105 ..      79     112 .. 0.88
   2 ?   11.8   0.4   0.00015      0.18      19      47 ..     112     141 ..     109     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                          zf-C2HC5  19 nClnCGkiiCakeglskpCsfCgs 42 
                                        C nCG  +  +    + C++Cg 
  gi|557694303|ref|YP_008797357.1|  83 YCKNCGRFLPDRFVT-GVCPSCGY 105
                                       6********999988.******95 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00015
                          zf-C2HC5  19 nClnCGkiiCakeglskpCsfCg.spllss 47 
                                       +C +CGk++   + l+ +Cs Cg +p+++s
  gi|557694303|ref|YP_008797357.1| 112 QCEACGKVLDPLDLLEPRCSICGeKPVVES 141
                                       6**********************6666654 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.2    0.0023       2.8       7      35 ..      76     107 ..      72     110 .. 0.67
   2 ?    9.9   1.1   0.00068      0.81       7      36 ..     112     138 ..     112     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0023
                       Zn-ribbon_8   7 r.......CeeCghefevlqsisdaplta.CPeCgs.e 35 
                                       +       C++Cg +f + +       t  CP+Cg  +
  gi|557694303|ref|YP_008797357.1|  76 EqdvnqlyCKNCG-RFLPDRF-----VTGvCPSCGYqR 107
                                       55555555*****.9996664.....3444****9644 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00068
                       Zn-ribbon_8   7 rCeeCghefevlqsisdapltaCPeCgs.ev 36 
                                       +Ce+Cg++ ++l       ++ C  Cg+ +v
  gi|557694303|ref|YP_008797357.1| 112 QCEACGKVLDPLDL-L---EPRCSICGEkPV 138
                                       6***********74.3...566*****9776 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 ?   10.5   0.0   0.00017       0.2     276     316 ..     286     325 ..     274     344 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00017
                      tRNA-synt_1f 276 lkggekmssSkGnvltledwlevaepevlrflilrrkPkka 316
                                        +g +k s+S G+++ l++++ ++e ++ r+++++ +P++ 
  gi|557694303|ref|YP_008797357.1| 286 FEG-KKFSKSLGVGIWLDQAIALLEADIWRYYLVKIRPETG 325
                                       444.5*********************************873 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 ?   -1.3   0.0      0.93   1.1e+03     100     130 ..      53      83 ..      16      87 .. 0.74
   2 ?    9.2   0.0   0.00057      0.68     244     283 ..     281     320 ..     263     339 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.93
                                       BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EE CS
                      tRNA-synt_1e 100 rvsekvdeiielvekliekgyaYavsdgdvy 130
                                       +   +++   ++  k+ e+gy Y+++ +++y
  gi|557694303|ref|YP_008797357.1|  53 HNPTHIAFCQNFFMKIYENGYIYEQDVNQLY 83 
                                       44567788889999999*****999876665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00057
                                       E--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS CS
                      tRNA-synt_1e 244 nghlkiegekmsksLknfitikdvlkkfdprqlRllllsa 283
                                       +++l++eg+k sksL+  i + +++   ++ + R++l++ 
  gi|557694303|ref|YP_008797357.1| 281 TEYLTFEGKKFSKSLGVGIWLDQAIALLEADIWRYYLVKI 320
                                       679*********************************9875 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 ?   10.8   2.7   0.00033      0.39      10      47 ..      71     118 ..      51     165 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                            zf-CRD  10 dgfqCspqtaHltCtaCgqlmPkr......peagvp....qqCelCkr 47 
                                       +g+  +++ + l C++Cg+ +P+r      p++g++     qCe C +
  gi|557694303|ref|YP_008797357.1|  71 NGYIYEQDVNQLYCKNCGRFLPDRfvtgvcPSCGYQrargDQCEACGK 118
                                       677777888889*************99999888888888889****87 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.0   0.00038      0.45       2      37 ..      83     118 ..      61     120 .. 0.65
   2 ?    9.4   4.1   0.00085         1       2      41 ..      83     122 ..      82     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00038
                                       --SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S CS
                    zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlkkealCpeCeq 37 
                                       +C++C + l  r  +  C +C  +  +   C+ C++
  gi|557694303|ref|YP_008797357.1|  83 YCKNCGRFLPDRFVTGVCPSCGYQRARGDQCEACGK 118
                                       466666666666666666666666666666666654 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00085
                                       --SSS-S--EE-SSEEE-TTT--EEEEEEE-SSS-S---E CS
                    zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqedlkkealCpeCeqelev 41 
                                       +C++C + l  r  +  C +C  +  +   C+ C++ l+ 
  gi|557694303|ref|YP_008797357.1|  83 YCKNCGRFLPDRFVTGVCPSCGYQRARGDQCEACGKVLDP 122
                                       7*********************************998865 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 ?    8.0   0.4    0.0024       2.9      65      96 ..      76     107 ..      50     112 .. 0.76
   2 ?    3.8   0.2     0.048        58      72      97 ..     112     138 ..     109     143 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0024
                                       EEE--EEEETTTS-EEECHHH.HHS-TTTSSS- CS
                              HypA  65 eevpvkvrCreCgkefeleek.alrCpkCgsad 96 
                                       e+   +++C++Cg+    ++  +  Cp+Cg ++
  gi|557694303|ref|YP_008797357.1|  76 EQDVNQLYCKNCGRFLP-DRFvTGVCPSCGYQR 107
                                       55566899*****5555.5444679****9875 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.048
                                       EETTTS-EEECHHH.HHS-TTTSSS-E CS
                              HypA  72 rCreCgkefeleek.alrCpkCgsadv 97 
                                       +C+ Cgk  +  +  + rC  Cg++ v
  gi|557694303|ref|YP_008797357.1| 112 QCEACGKVLDPLDLlEPRCSICGEKPV 138
                                       6*****99995544588******9754 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   6.6      0.22   2.6e+02       4      25 ..      83     106 ..      82     107 .. 0.63
   2 ?    4.6   0.1     0.019        23       4      16 ..     112     124 ..     109     126 .. 0.84
   3 ?    5.1   0.2     0.013        15       4      12 ..     129     138 ..     127     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.22
                       zf-ribbon_3   4 rCPnCGa.plssddn.vCpyCGtk 25 
                                       +C nCG  +++  ++ vCp+CG++
  gi|557694303|ref|YP_008797357.1|  83 YCKNCGRfLPDRFVTgVCPSCGYQ 106
                                       566777744333333589999985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.019
                       zf-ribbon_3   4 rCPnCGaplssdd 16 
                                       +C +CG++l++ d
  gi|557694303|ref|YP_008797357.1| 112 QCEACGKVLDPLD 124
                                       7999***999977 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.013
                       zf-ribbon_3   4 rCPnCGa.pl 12 
                                       rC+ CG+ p+
  gi|557694303|ref|YP_008797357.1| 129 RCSICGEkPV 138
                                       8******884 PP

>> DUF2797  Protein of unknown function (DUF2797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.7    0.0013       1.6      10      43 ..      80     113 ..      74     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0013
                           DUF2797  10 gerrCvnCgrktkksfsqgvCakCfkklaeadec 43 
                                       ++ +C nCgr   + f +gvC +C  ++a+ d+c
  gi|557694303|ref|YP_008797357.1|  80 NQLYCKNCGRFLPDRFVTGVCPSCGYQRARGDQC 113
                                       5778*************************99999 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   3.7   0.00012      0.14       1      21 [.      83     105 ..      83     106 .. 0.96
   2 ?    0.6   2.2      0.43   5.1e+02       2      20 ..     113     134 ..     112     136 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                     zinc_ribbon_2   1 fCpnCGaelqdnakF..CpyCGt 21 
                                       +C+nCG+ l+d+ +   Cp CG+
  gi|557694303|ref|YP_008797357.1|  83 YCKNCGRFLPDRFVTgvCPSCGY 105
                                       8*********************8 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.43
                     zinc_ribbon_2   2 CpnCGaelqdnakF...CpyCG 20 
                                       C  CG+ l++ +     C+ CG
  gi|557694303|ref|YP_008797357.1| 113 CEACGKVLDPLDLLeprCSICG 134
                                       5555555554333333355555 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.1   0.00031      0.37      21      86 .]      42     104 ..      28     104 .. 0.66
   2 ?    0.0   0.5       1.2   1.5e+03      66      79 ..     111     124 ..     105     134 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                    zinc_ribbon_15  21 lklffipvfkwkkkkpylacskCkslleaskelgkeiekkessekkeCknCgkeveeef..kyCpkCg 86 
                                       ++l f +  ++++     ++  C++++++  e+g     ++++++ +CknCg+ + ++f    Cp+Cg
  gi|557694303|ref|YP_008797357.1|  42 FHLSFDNYTRTHN---PTHIAFCQNFFMKIYENGY--IYEQDVNQLYCKNCGRFLPDRFvtGVCPSCG 104
                                       4444444444444...5566677777777774444..44577889***********9972268****9 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.2
                    zinc_ribbon_15  66 keCknCgkeveeef 79 
                                        +C+ Cgk++++  
  gi|557694303|ref|YP_008797357.1| 111 DQCEACGKVLDPLD 124
                                       68999999888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      747  (0.0416643); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); 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):              15  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 3470.76
//
Query:       gi|557694304|ref|YP_008797358.1|  [L=87]
Description: hypothetical protein CSUB_C0871 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); 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: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 655.80
//
Query:       gi|557694305|ref|YP_008797359.1|  [L=239]
Description: Biotin operon repressor BirA [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.5   0.1      0.079   12.7   0.1    1.4  1  LSM       LSM 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 ?   12.7   0.1   4.4e-06     0.079       2      36 ..     185     219 ..     184     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-06
                                       HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEE CS
                               LSM   2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvL 36 
                                       ++ ++++  v v+l  g++l+G L+g D+   l+L
  gi|557694305|ref|YP_008797359.1| 185 DMMEYVRTVVSVNLSQGTQLIGFLEGLDELGRLIL 219
                                       67899999********************9765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1589.48
//
Query:       gi|557694306|ref|YP_008797360.1|  [L=237]
Description: 5'-methylthioadenosine phosphorylase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-35  120.7   0.1    6.8e-35  120.4   0.1    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 !  120.4   0.1   3.8e-39   6.8e-35       1     221 [.      14     227 ..      14     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 3.8e-39
                                       CEEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEE CS
                         PNP_UDP_1   1 kiaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriG 77 
                                       k+++ +g+p +v +l++  le+ +  +e+rgf  +tG+++g+ v+++++G+G p++a+v+e  ++   g+k iir G
  gi|557694306|ref|YP_008797360.1|  14 KRVVAAGDPARVVQLSKM-LEKPRLVNENRGFIAYTGKYEGEDVTVICHGVGGPSSAIVFEETVML--GAKLIIRLG 87 
                                       57999*************.999999999*****************************777777777..7******** PP

                                       EEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESES CS
                         PNP_UDP_1  78 taGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgf 154
                                       ++G++ +++k+G  vip++a +  g+ + y p        + +++ ++ + +++l+ + +++g k+ +G+v ++d f
  gi|557694306|ref|YP_008797360.1|  88 SCGAFLKGMKIGEAVIPTAASYIGGTLQQYIP------DTHITPV-PSYDVLTTLVDEFRRSGLKTYVGPVFSSDAF 157
                                       ********************999999997754......4455555.666777777777******************* PP

                                       S-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTB...ETTCTCH.HCCCHHHHHH CS
                         PNP_UDP_1 155 yaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaag...gadaeatheeveefaqea 221
                                       yae ++ ++ ++ lg  aveME+a ++ l  +++ + ++  ++sd++a+     dae+ ++ ve+++q+ 
  gi|557694306|ref|YP_008797360.1| 158 YAEDPNFVAKWSGLGYIAVEMECATLFGLGMLRKFKTGSALLISDNLAEmtpMVDAEQLKTYVEKAGQAT 227
                                       *********************************************9999555455555545555444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1705.65
//
Query:       gi|557694307|ref|YP_008797361.1|  [L=273]
Description: hypothetical protein CSUB_C0874 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.092   12.5   0.7       0.38   10.5   0.7    2.1  1  Ysc84        Las17-binding protein actin regulator
      0.098   12.5   0.1       0.18   11.7   0.1    1.3  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
        4.6    7.3   8.9        1.7    8.7   4.2    2.1  2  DUF3568      Protein of unknown function (DUF3568)
        8.6    6.4   6.2        3.8    7.6   0.3    2.3  2  OppC_N       N-terminal TM domain of oligopeptide transport p


Domain annotation for each model (and alignments):
>> Ysc84  Las17-binding protein actin regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.7   8.4e-05      0.38      36      88 ..      94     182 ..      34     192 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.4e-05
                             Ysc84  36 slGgdlsvaaGpvg....aggeaeaaaaak................................lkapvysysksrGly 76 
                                       ++ ++++++ Gp+     ++ e++++++++                                 +a++y++ ++ G+ 
  gi|557694307|ref|YP_008797361.1|  94 TVTAEAALVTGPITvqpsRTLELSWKSNKTidiyiavgsylnasswrlvgrgvvgsaatpfnDEAEIYVITRTDGAA 170
                                       45555566666655444444444444444477777777777777777777777777777777*************** PP

                             Ysc84  77 aGvsldgtvite 88 
                                       a vs+    +++
  gi|557694307|ref|YP_008797361.1| 171 ASVSVTVVETWP 182
                                       ****98776655 PP

>> 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 ?   11.7   0.1   3.9e-05      0.18      37      81 ..      78     132 ..      49     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.9e-05
                                       H..........HHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESH CS
                       Oxidored_q6  37 e..........eieakekeadvlvveGavtrkpkealellkelaekakaviavGt 81 
                                                  e+ ++   a+ ++v+G++t +p  +lel ++  +  ++ iavG+
  gi|557694307|ref|YP_008797361.1|  78 VttntlrhvaaEVVNQTVTAEAALVTGPITVQPSRTLELSWKSNKTIDIYIAVGS 132
                                       1222234455678888899***********************************6 PP

>> DUF3568  Protein of unknown function (DUF3568)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.2   0.00038       1.7      11     108 ..      35     132 ..      27     138 .. 0.91
   2 ?    0.6   0.1      0.12   5.5e+02      59      90 ..     194     226 ..     169     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00038
                           DUF3568  11 slillasCaalvagaaagagtvayvnGelkae.yeanlkkvykAtlkaiedlnvlsvvekskdsssatieakaaedk 86 
                                       ++i ++s+  +v   a+   t    +  ++++ ++++l +   +t ++++     +vv+++ ++  a +++     +
  gi|557694307|ref|YP_008797361.1|  35 VAIQTSSVTTVVETDAIVRTTTMELTEAFETSvVSTTLSTETAVTTNTLRHVA-AEVVNQTVTAEAALVTGPITVQP 110
                                       4588999999******9999999999999999788999999999*********.*********************99 PP

                           DUF3568  87 tvfiklekldknstkvsIrvGs 108
                                         + +l+ ++++++ + I vGs
  gi|557694307|ref|YP_008797361.1| 111 SRTLELSWKSNKTIDIYIAVGS 132
                                       999*****************97 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.12
                           DUF3568  59 edlnvlsvvekskdsssatieakaaedktvf.i 90 
                                         + + ++++ ++ +s++t++a++ ++k+v+ +
  gi|557694307|ref|YP_008797361.1| 194 STSLITTFTSTRYLTSETTYTASYTTEKPVYyV 226
                                       455567788889999999999999999999753 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 ?    7.6   0.3   0.00085       3.8      15      41 ..       5      33 ..       1      44 [. 0.75
   2 ?    1.2   1.2     0.084   3.8e+02      17      32 ..     247     262 ..     245     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00085
                            OppC_N 15 lAvvglvilllllliaifa..PliaPydp 41
                                      lAv +l+i+ ++l+   fa  P+++ yd 
  gi|557694307|ref|YP_008797361.1|  5 LAVSSLIIFGIILVGLGFAglPYVITYDE 33
                                      8*********9888544444899988875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.084
                            OppC_N  17 vvglvilllllliaif 32 
                                       + +++i++ +l+++++
  gi|557694307|ref|YP_008797361.1| 247 MGSFIIFVGILFMVLL 262
                                       7799999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2050.11
//
Query:       gi|557694308|ref|YP_008797362.1|  [L=336]
Description: simple sugar transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  113.1  34.5    1.3e-32  113.1  34.5    1.5  2  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 ?   -3.0   0.3      0.18   3.3e+03     138     150 ..      17      29 ..       6      36 .. 0.45
   2 !  113.1  34.5     7e-37   1.3e-32       2     266 ..      41     306 ..      40     308 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.18
                      BPD_transp_2 138 alllvlavllllr 150
                                       ++ +v++++ + +
  gi|557694308|ref|YP_008797362.1|  17 LIGFVAVAVTIYT 29 
                                       2222222222222 PP

  == domain 2  score: 113.1 bits;  conditional E-value: 7e-37
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvl 78 
                                       i++ l   ++la+aA+G  +   ++G+in+g++g+++++a++   ++  ++s  ll+ll++ ++ga++g +lgll +
  gi|557694308|ref|YP_008797362.1|  41 IEFALLALTPLAFAAVGECINE-KSGQINIGIEGIFLISAVAGVFWAEVFES-GLLGLLMGGVFGALIGGVLGLLNV 115
                                       667889999*************.*****************************.************************ PP

                      BPD_transp_2  79 rlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv.....llalllvlavllllr 150
                                       + + +++i++ +l+++++gl+++ l  +++   g+  ++++l +++ +++ +s+ ++     l a+++++a++lll+
  gi|557694308|ref|YP_008797362.1| 116 YGRAEQVIAGMGLNILAIGLFQY-LLMAIWAFPGIHIFPRTLVVPRISIPLVSEELAvspisLAAIAAAFAAYLLLN 191
                                       *********************95.55555555555555555555555555555555555666*************** PP

                      BPD_transp_2 151 rtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGgag 226
                                       +t +G +lra+ge +e ++++G++v rv++++ +++g+lAg+ Ga++ l   ++ +  i  g gf a+aavv  g+ 
  gi|557694308|ref|YP_008797362.1| 192 KTLLGIRLRAAGEKPESVDVAGLSVYRVRIFASIVGGFLAGVGGAFMPLGWFGGLVkEITAGRGFIALAAVVFSGL- 267
                                       ***********************************************9999999999*******************. PP

                      BPD_transp_2 227 sllgtviGaliigvvksllltllgiptelarvllgallil 266
                                       ++l ++++++i+g+++ l+ +++   ++++ ++ +  ++ 
  gi|557694308|ref|YP_008797362.1| 268 NPLTALAATFIFGFAEGLAFAVVVT-PSVKEAVPFHFIMM 306
                                       *****************66666655.99999998876664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); 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:                         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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2536.00
//
Query:       gi|557694309|ref|YP_008797363.1|  [L=358]
Description: ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-37  127.9  34.1    3.7e-37  127.9  34.1    2.0  2  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
       0.33   11.5   3.5        0.2   12.2   0.4    2.2  3  DUF1240       Protein of unknown function (DUF1240)


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 !    2.4   0.3    0.0082        74      56      75 ..      21      40 ..      12      48 .. 0.84
   2 !  127.9  34.1   4.2e-41   3.7e-37       2     267 ..      60     336 ..      59     337 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0082
                      BPD_transp_2 56 llallvallvgaavglllgl 75
                                       la++v+l++gaa+++++g+
  gi|557694309|ref|YP_008797363.1| 21 MLAVAVGLVGGAALMAAYGY 40
                                      799*************9997 PP

  == domain 2  score: 127.9 bits;  conditional E-value: 4.2e-41
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl....lllallvallvgaavglllg 74 
                                       +l++l+ a++l+++Al +a+ + ++G++n+g++g+m +Ga+ aa +  +l  +    l++a ++++l+ga++ l  +
  gi|557694309|ref|YP_008797363.1|  60 FLETLAFATPLIMTALTFAIGV-RSGLFNIGAEGQMYIGAIGAAFVGGALNLPpiihLIFATVFGMLAGAVWSLPAA 135
                                       578999****************.****************998888877777667899******************** PP

                      BPD_transp_2  75 llvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv.llalllvlavllllr 150
                                       ll++  +v+e+++t++l++++++l+ +l t    ++++ +   ++ ++a++l++ +s   v +l++++ l++++ll 
  gi|557694309|ref|YP_008797363.1| 136 LLKISRGVHEVVSTIMLNWIAFWLVTYLITYHVADPARAERAIPAQETARYLVIGSSLTTVfILVIAFSLIAYFLLW 212
                                       **************************************999999988888887766655555999************ PP

                      BPD_transp_2 151 rtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.....nigvglgfnaiaavvl 222
                                       rt +G+ lr+vg n+eaar++Gin+ ++++++f+++g+ AglaG+ ++l     ++        ++lgf++i ++++
  gi|557694309|ref|YP_008797363.1| 213 RTTLGYELRVVGHNQEAARYAGINISKTIVMSFFMGGLAAGLAGVSQVLGRPPHWTvfatmGNLINLGFEGIGVALV 289
                                       *************************************************96555555443466667*********** PP

                      BPD_transp_2 223 GgagsllgtviGaliigvvksllltllgi....ptelarvllgallilv 267
                                       G + +++g++++++ +g +   ++ ++ +    ++e  r++ g++++++
  gi|557694309|ref|YP_008797363.1| 290 GRN-HPVGIIFASIFYGGLLH-GGRFMEFeagvASEIVRAINGIIILAL 336
                                       ***.*****************.777777767777999999999999875 PP

>> DUF1240  Protein of unknown function (DUF1240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.73   6.5e+03       5      27 ..      57      79 ..      56      84 .. 0.76
   2 ?   -3.6   0.0       1.9   1.7e+04      10      24 ..     151     165 ..     144     173 .. 0.54
   3 ?   12.2   0.4   2.2e-05       0.2       8      60 ..     195     247 ..     188     249 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.73
                           DUF1240  5 FsskvvlllfssPlllYfsvlvv 27
                                      Fs     l f++Pl++ ++++++
  gi|557694309|ref|YP_008797363.1| 57 FSGFLETLAFATPLIMTALTFAI 79
                                      77777788899999987776655 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.9
                           DUF1240  10 vlllfssPlllYfsv 24 
                                       +l  +++ l+ Y+++
  gi|557694309|ref|YP_008797363.1| 151 MLNWIAFWLVTYLIT 165
                                       333444445555443 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 2.2e-05
                           DUF1240   8 kvvlllfssPlllYfsvlvvlvaitnklakvndklvkllaiiailsfvlslfl 60 
                                       +v++l++++ l+ Yf++  +++ ++ +++ +n++ +++  i    ++v+s+f+
  gi|557694309|ref|YP_008797363.1| 195 TVFILVIAFSLIAYFLLWRTTLGYELRVVGHNQEAARYAGINISKTIVMSFFM 247
                                       7999**********************************9999999999***97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       768  (0.0428356); 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:                         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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2518.34
//
Query:       gi|557694310|ref|YP_008797364.1|  [L=495]
Description: basic membrane protein A [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-28   98.7   0.2    1.4e-15   57.1   0.0    2.1  2  Bmp       ABC transporter substrate-binding protein PnrA-like


Domain annotation for each model (and alignments):
>> Bmp  ABC transporter substrate-binding protein PnrA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   7.6e-20   1.4e-15       3     149 ..      75     236 ..      73     238 .. 0.87
   2 !   39.6   0.1   1.6e-14   2.8e-10     159     244 ..     285     377 ..     282     420 .. 0.84

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 7.6e-20
                                       EEEEECSS-TTTSCHHHHHHHHHHHHHHHCTTEEEEEEEEC.GGGHHHHHHHHHHCT.T-SEEEEESCCHHHHHHHH CS
                               Bmp   3 kvavlvegtidDksfnessyeGirrlkkeqnieliskesslltdedyiadlknlkee.gsdlivatgfalqdalqev 78 
                                        ++v + g + D sfn ++ +G  +++k+ +++++++ s++  ++dy+ +l+ ++++  + liv++gf l++al ev
  gi|557694310|ref|YP_008797364.1|  75 IAVVSDIGGRGDLSFNDMAFKGGDEAEKDLGVQMVELISKT--EADYVPNLETAARDpDVKLIVGVGFLLSEALLEV 149
                                       5678889**************************99988887..8********99987369***************** PP

                                       HHH-TTS-EEEESS--TT-S........TTEEEEEE-HHHHHHHHH....HHHHHHHHCTTTT.EEC...SS-SCCC CS
                               Bmp  79 ssdfpkvkFliiDavvekey........knvlsvaFrseegaFLaG....vaaAlmsktnkig.fvg...Gveipvv 139
                                       ++++p+ +F+ iD + ++           n+l +++ +  g+ ++G    ++aA + +++  + ++g   G+eipv+
  gi|557694310|ref|YP_008797364.1| 150 AAKYPDKNFAGIDTFTQALAvqktgkplPNMLDIVYEEHKGSAMVGalgcLLAAYYNEQGGNYpYIGgvfGIEIPVL 226
                                       ***************999999999*********************9333335666666665553344888******* PP

                                       HHCHHHHHHH CS
                               Bmp 140 ksfingFeaG 149
                                        +f++g++ G
  gi|557694310|ref|YP_008797364.1| 227 WKFEIGYKWG 236
                                       *******998 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 1.6e-14
                                       EEEEE-SSSS-HHHHHHHHHHHHHCT--EEEEE-GGGHHHHHHHHHHHCHCT.......EEEEEES--CGCSTTCCE CS
                               Bmp 159 vvvkvagtfsDakkgkslAsslykegvdvifpaagkagkgvieaakelglsn.......yvIgvdkdqsylapenvi 228
                                       v   ++gtfsD +kg ++A+s+y++++  ++ +ag+ g g+ +a++e   ++       y Igvd +q  ++p  vi
  gi|557694310|ref|YP_008797364.1| 285 VLWTYTGTFSDITKGYAAAKSMYEQQAIAVYNIAGPLGLGINQAVQEIATEKklksgppYWIGVDANQDWINPGFVI 361
                                       56689*********************************999999998888888888********************* PP

                                       EEEEEEHHHHHHHHHH CS
                               Bmp 229 tsiiknvedlvvsiie 244
                                        s +k v++ v++++ 
  gi|557694310|ref|YP_008797364.1| 362 ASMMKRVDRGVYYAAL 377
                                       ********98877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); 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: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3549.84
//
Query:       gi|557694311|ref|YP_008797365.1|  [L=279]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-68  230.8   0.0      2e-68  230.6   0.0    1.0  1  BtpA          BtpA family
      2e-05   23.6   0.0    6.4e-05   21.9   0.0    1.8  2  Trp_syntA     Tryptophan synthase alpha chain
  ------ inclusion threshold ------
       0.12   11.8   0.0       0.21   11.0   0.0    1.3  1  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.6   0.0   3.3e-72     2e-68       2     253 ..      20     276 ..      19     277 .. 0.96

  Alignments for each domain:
  == domain 1  score: 230.6 bits;  conditional E-value: 3.3e-72
                              BtpA   2 ekpvigvvHLkpLPgsaeyka.nleevidkAvkeakaleegGvDavilenygdaPflke..vdpetvaamtvivkev 75 
                                       +kp+i+++HL+pLPg ++y++ ++e++i++ +++a++l+   vD++ +en gd P+lk   ++ et + ++v+++ev
  gi|557694311|ref|YP_008797365.1|  20 TKPIIAMIHLPPLPGAPRYSGmSVEDIIEYGLRDAEVLKSNDVDGLQVENIGDYPYLKPddIGHETSSILAVMAREV 96 
                                       69*****************9989*********************************99756999************* PP

                              BtpA  76 ksdvsiplGvnvLrndavaalaiAkavgakFiRvnvltgvalsdeGilegkaaellrykkllesr.vkiladvavkh 151
                                       ++  ++p+G+  L n+ + a+a   a g+k++R    ++++++deG +e+ a++ lry+++l +  v+++adv+vkh
  gi|557694311|ref|YP_008797365.1|  97 RKTTGLPVGICCLANGVIPAIAACVASGGKWVRAAEWANAYIADEGFVEAIAHRALRYRANLRAYdVRVFADVNVKH 173
                                       **************************************************************7755*********** PP

                              BtpA 152 avplv..erdlesavkdtvergladavilsGkatGgevdleelklaketvkvkvlvgsGvseenlekllsiadGviv 226
                                         +++  +r +e+ v d+ e   ada+i+sG +tG e+ le++++ak++ +++vl+gsG +++n+e+ll++adG iv
  gi|557694311|ref|YP_008797365.1| 174 GSHFIisDRPFEEQVADA-EFFDADAIIVSGTRTGAETPLEKVVRAKQATSLPVLIGSGLNADNAENLLKVADGAIV 249
                                       ***9744677********.999******************************************************* PP

                              BtpA 227 gtsikkdGkianaiDkervrkivelae 253
                                       g+++++dGk++n+++ erv+k+++ ++
  gi|557694311|ref|YP_008797365.1| 250 GSYLRRDGKFWNPVEPERVKKLMSVVK 276
                                       ***********************9987 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.42   2.5e+03      77      99 ..      92     113 ..      82     131 .. 0.63
   2 !   21.9   0.0   1.1e-08   6.4e-05     175     229 ..     201     253 ..     196     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.42
                                       HHHHHHHHCSSS-EEEEE-CHHH CS
                         Trp_syntA  77 lveevrkkevevPivlltylnlv 99 
                                       + +evr k++ +P+ +   +n v
  gi|557694311|ref|YP_008797365.1|  92 MAREVR-KTTGLPVGICCLANGV 113
                                       345555.6666666665555544 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 1.1e-08
                                       -SSTTSSB-TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHH CS
                         Trp_syntA 175 vTgaenavaaevdelverlkkltavPvavGFGistkeqvkqvakvadGvivGSal 229
                                       v g+++ +++ ++++v r k++t +Pv++G G++ +++++++ kvadG+ivGS l
  gi|557694311|ref|YP_008797365.1| 201 VSGTRTGAETPLEKVV-RAKQATSLPVLIGSGLN-ADNAENLLKVADGAIVGSYL 253
                                       5677777788888776.5699999********96.6899**************87 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   3.6e-05      0.21      52     108 ..     202     256 ..     184     267 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.6e-05
                                       HHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH- CS
                      His_biosynth  52 daakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavkn 108
                                       +++++g e+ l+ v +  +++++pv +G+G +  + +e+ll+  ad  i+g+   ++
  gi|557694311|ref|YP_008797365.1| 202 SGTRTGAETPLEKVVRAKQATSLPVLIGSGLNADN-AENLLKV-ADGAIVGSYLRRD 256
                                       6788999999999******************9887.9999999.9*****9976665 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:                      316  (0.0176251); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2090.83
//
Query:       gi|557694312|ref|YP_008797366.1|  [L=294]
Description: ribokinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-53  181.9   0.1      2e-53  181.7   0.1    1.0  1  PfkB        pfkB family carbohydrate kinase
  ------ inclusion threshold ------
      0.059   11.9   0.0          2    6.9   0.0    2.2  2  ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase cons


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 !  181.7   0.1   2.3e-57     2e-53       2     296 ..       4     290 ..       3     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 2.3e-57
                                       EEEEEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTT CS
                              PfkB   2 tkvvviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkeg 76 
                                       ++++v+G+++ d+ia+ +k+  eg    +++   + GG++aNvA+ la lg +v+++g+vG D++Ge+ll+ l+++g
  gi|557694312|ref|YP_008797366.1|   4 RRIMVLGDINLDIIAFHQKFpvEGYEDMAERAYIRHGGSAANVAHTLALLGTSVVMVGCVGVDPLGEMLLKGLADAG 80 
                                       579*****************98777789999999******************************************* PP

                                       EEETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEES..EECTTSHHHHHHHH CS
                              PfkB  77 vdtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisg..llsselpeavleel 151
                                       vdt++v+ ++   tg+++ivv+++gert+ ++rga+ +l+ ++l  + ++l+  ++l++sg  +l  + +e++++ l
  gi|557694312|ref|YP_008797366.1|  81 VDTAHVQKTAADITGITYIVVSKNGERTMFAYRGANKHLSHTHL--SSNILSDTAILHFSGysFLEGPQRETAFRFL 155
                                       *******************************************9..999*************999999999999999 PP

                                       HHHHHHTTEEEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCT.HSHHHHHHHHHHHHHTTSSEEEEEE CS
                              PfkB 152 aeaaknggtfdpnlldplgaqfkeallellaladllkpneeElealtgekl.edieealaalhklkakgaktvvvtl 227
                                       ++a +  +  d+++  ++ +   + l++++ ++d +++n +E + ++g  +  ++ ++ ++          +vv+++
  gi|557694312|ref|YP_008797366.1| 156 EKADNTVT-LDLCIPLASQP---SLLENIVKHVDCVFLNSAEYSVVSGYFGvGSVSDLSRRWG-------CMVVFKK 221
                                       99988888.67777777776...7899999********************9989999999865.......59***** PP

                                       GGGEEEEEE.TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSS CS
                              PfkB 228 GkeGalvve.kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgai 296
                                       G eG+ +++  ++++k pa  +v+ vD tGAGD+f++gfl   l+g ++ ++  fa++++al+v++ g +
  gi|557694312|ref|YP_008797366.1| 222 GGEGCEIAKtDGEVVKLPA-EPVETVDGTGAGDAFIAGFLHEMLKGSPITTCGLFATRLGALAVKTIGGR 290
                                       *****99997888888888.77******************************************998865 PP

>> ADP_PFK_GK  ADP-specific Phosphofructokinase/Glucokinase conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0   0.00022         2      82     122 ..      34      75 ..      25     115 .. 0.73
   2 ?    2.8   0.0     0.004        36     244     272 ..     175     203 ..     172     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00022
                                       -SEEEEESHHHHHHHHHCCTT-EEEEE----H.HHHTTS-SS CS
                        ADP_PFK_GK  82 kaelrmGGnagimanrlakegakvllgaklsk.klkellsek 122
                                       +a +r GG a+ +a+ la +g++v++++ ++   l e+l + 
  gi|557694312|ref|YP_008797366.1|  34 RAYIRHGGSAANVAHTLALLGTSVVMVGCVGVdPLGEMLLKG 75 
                                       567899****************99988844432677777666 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.004
                                       HHHHHCGGG-SEEEE-HHHHHHHHHHTT- CS
                        ADP_PFK_GK 244 eilekilpyvdslGlnEqElanllsvlgg 272
                                       ++le+i+++vd++ ln  E + ++ ++g 
  gi|557694312|ref|YP_008797366.1| 175 SLLENIVKHVDCVFLNSAEYSVVSGYFGV 203
                                       689****************9999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2280.83
//
Query:       gi|557694313|ref|YP_008797367.1|  [L=132]
Description: cytidine deaminase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-17   62.8   0.1    2.4e-17   62.6   0.1    1.0  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    2.9e-13   50.2   1.3    3.6e-12   46.6   0.5    2.0  2  dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-
    2.8e-05   23.8   1.8     0.0078   15.8   0.1    2.1  2  LmjF365940-deam  A distinct subfamily of CDD/CDA-like deamina


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.1     4e-21   2.4e-17       4      99 ..       3     103 ..       1     105 [. 0.91

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 4e-21
                                       HHHHHHHHHHHHHHHH.TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEE.. CS
                   dCMP_cyt_deam_1   4 dekllelalkaakeaq.kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyv.. 77 
                                       +  lle a ka k+++ ++s+f+VGa+++ ++  ++tg+n e+a++   ++AE++A+ ka+++g  k+ +a+ +v  
  gi|557694313|ref|YP_008797367.1|   3 YAALLEYAFKALKNSYaPYSRFRVGAALLLDDGEVVTGCNVENASYGLSMCAERTAVFKAVSQGVKKF-DAIAVVss 78 
                                       567899************************99*****************************9965466.88888889 PP

                                       ...EE--BHHHHHHHHHHT-SEEEE CS
                   dCMP_cyt_deam_1  78 ...tlePCsmCakaiiqsgikkvvv 99 
                                           + PC+ C++++ +++++  v+
  gi|557694313|ref|YP_008797367.1|  79 kvnPVYPCGACRQVLREFNPRLTVI 103
                                       9999**************9887776 PP

>> dCMP_cyt_deam_2  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.5     6e-16   3.6e-12      47     114 ..       6      74 ..       2      84 .. 0.87
   2 ?    2.5   0.0     0.026   1.6e+02       1      15 [.     116     130 ..     116     132 .] 0.87

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 6e-16
                                       HHHHHHHHHTT-B-TTT---EEEEEEETTS-EEEEE-B--TTSTT-B-HHHHHHHHHHH.TT--GGGEE CS
                   dCMP_cyt_deam_2  47 lkeaAlaaanasyapyskcpsGvaLvtkdgkvyaGsyiEsaAfNpsLpPlqaAlvalvl.ggkefeeie 114
                                       l e A++a ++syapys+   G aL ++dg+v++G  +E+a +  s+ + ++A+ ++v  g k+f+ i 
  gi|557694313|ref|YP_008797367.1|   6 LLEYAFKALKNSYAPYSRFRVGAALLLDDGEVVTGCNVENASYGLSMCAERTAVFKAVSqGVKKFDAIA 74 
                                       7789******************************************************94444555543 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.026
                                       HHHHSTT--SGGGGT CS
                   dCMP_cyt_deam_2   1 LsslLPhsFgPkdLl 15 
                                       L++lLP+sFg ++L 
  gi|557694313|ref|YP_008797367.1| 116 LDKLLPKSFGKESLR 130
                                       789*******99996 PP

>> 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 !    8.3   0.1   0.00027       1.6      59     101 ..      36      74 ..      30      78 .. 0.77
   2 !   15.8   0.1   1.3e-06    0.0078     148     177 ..      77     103 ..      64     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00027
                   LmjF365940-deam  59 elvrgvNlEvSmPtGSlCsErnaigkalasdpslrRrdlkaiA 101
                                       e+v g N+E      S+C+Er a+ ka++       +++ aiA
  gi|557694313|ref|YP_008797367.1|  36 EVVTGCNVENASYGLSMCAERTAVFKAVSQGV----KKFDAIA 74 
                                       68999****999999***********776533....3444555 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.3e-06
                   LmjF365940-deam 148 arksnPLkPCGaCeewLkkiaevnpdfkvl 177
                                       + k nP+ PCGaC++ L+   e np ++v+
  gi|557694313|ref|YP_008797367.1|  77 SSKVNPVYPCGACRQVLR---EFNPRLTVI 103
                                       4566************98...677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1103.16
//
Query:       gi|557694314|ref|YP_008797368.1|  [L=311]
Description: inosine/uridine-preferring nucleoside hydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  269.7   0.0    4.3e-80  269.5   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 !  269.5   0.0   2.4e-84   4.3e-80       2     304 ..       3     301 ..       2     302 .. 0.92

  Alignments for each domain:
  == domain 1  score: 269.5 bits;  conditional E-value: 2.4e-84
                                       EEEEEE--SHHHHHHHHHHHCTHTTEEEEEEEE-SSSS-HHHHHHHHHHHHHHHCTTT.S-EEEE-SS-SSSS.S-S CS
                      IU_nuc_hydro   2 kvilDtDpGiDDalAlllalaespeiellgittvaGnvsleqatrnalrvlealggrddipvyaGaekpllre.kaa 77 
                                       ++i+DtD+  DD + ll+al+  p ++l ++t+v+Gnv+ +q+++nal+++e+++++  +pvy+G+++p+lr+ k a
  gi|557694314|ref|YP_008797368.1|   3 RLIIDTDTAGDDTISLLMALK-WPGVRLEAVTVVCGNVEFSQQVENALYTVEKFADHY-VPVYPGCDRPFLRTwKYA 77 
                                       58******************9.6****************************9999666.**************8888 PP

                                       HHHHTTTSSTSS-.--SSHCSCSSHHHHHHHHHHHHCHHTTTTEEEEECS-SHHHHHHHHHTCCHHHHEEEEEEE-- CS
                      IU_nuc_hydro  78 aeihGedGlgdvllpeperkaesesavdalidaveaareypgevtlvatGplTNiAlalrldpelakkvkrlviMGG 154
                                       +++hG+dG+g+ + p++ +++e+++av+al ++v   ++ pge t++a GplTNiA+a+ ld++++kkv+rl+iMGG
  gi|557694314|ref|YP_008797368.1|  78 DYVHGKDGMGENYFPKARQRPENKHAVQALLELV---NSSPGEYTIIAQGPLTNIATAIMLDKNFVKKVRRLYIMGG 151
                                       88***************99***********9999...888889********************************** PP

                                       -SSS--SSSSSS-HHHHHSHHHHHHHHHT..S-E.EEEE-HHHHTTSCHEECHHHHHHHHCSTCBHHH..HHHHHHH CS
                      IU_nuc_hydro 155 aftarGNvtpvaEfNifvDPeAAkiVles..apvkitlvpldvthkvqalltseeveelaalekglga..fladlle 227
                                         ++ GNvtp+aE+N++vDPeAAkiVl+s  +p    +v++d+  k + +++++ ++e+a+ ++   +  f+ ++ +
  gi|557694314|ref|YP_008797368.1| 152 YADGYGNVTPAAEYNFWVDPEAAKIVLHSgiNP---FIVGWDIAVKYS-VVEEDMHREIAKWGTR--EadFFVKVNR 222
                                       ***************************987555...9*******9555.5555555554443233..23599***** PP

                                       HHHHHHHHHHHSSEEE-HHHHHHHHHH-GGGEEE.EEEEEEEESSSSTTTTEEEEETSTT.TTS--EEEEEEE-HHH CS
                      IU_nuc_hydro 228 fyikaykeaegsdgaplhDplavavaldpelvtt.krlavdveleggltrGrtvvdlrrl.kkaknvkvatevdver 302
                                        + +++k++ g+ g    D +++a+a++p++ ++ +r +vdve++++ltrG++vvd+r+  +k++n+ v+ e d++ 
  gi|557694314|ref|YP_008797368.1| 223 KVVEFEKKVMGIPGSTHPDTITTAIAIEPRIARKvERRYVDVETQSELTRGMSVVDHRGVlGKEPNADVCYEADAQL 299
                                       ********************************999999*********************9***************99 PP

                                       HH CS
                      IU_nuc_hydro 303 fl 304
                                       f 
  gi|557694314|ref|YP_008797368.1| 300 FR 301
                                       96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       449  (0.0250432); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2602.83
//
Query:       gi|557694315|ref|YP_008797369.1|  [L=229]
Description: deoxyribose-phosphate aldolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   48.2   2.0    1.4e-12   47.8   2.0    1.1  1  DeoC      DeoC/LacD family aldolase
  ------ inclusion threshold ------
      0.014   15.6   0.3       0.26   11.6   0.0    2.8  3  DUF4777   Domain of unknown function (DUF4777)
       0.13   11.3   4.1       0.18   10.8   4.1    1.6  1  FMN_dh    FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   2.0   2.3e-16   1.4e-12      15     224 ..      21     209 ..       9     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2.3e-16
                                       HHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCT...TSEEEEETECSSCCTTSTTEEEETTCHHHH CS
                              DeoC  15 dtasaqneqledlkalvkealtpgasavlldpgviasaskeyak...diallvkldkgtyllkskqrdvdevasvee 88 
                                       d      +   d+++l++ea++ g sav+++p  + +as  ++    ++ +++++++ +    +k      + +++e
  gi|557694315|ref|YP_008797369.1|  21 D------ATKRDIEKLCSEAVKYGFSAVVINPIWVKHASELLKGtgvKVCVALNYPMAGSKQLTK------AVEIRE 85 
                                       3......4558****************************99998888888899998777666666......9***** PP

                                       HHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEE.EEE-CTTBSSTTCHHHHHHHHHHHHTCCT CS
                              DeoC  89 akalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplile.lylrdeaikdekvdpdlvaeAarvsaelG 164
                                       a+a+G +++++++++ +++s+   +  +++++v ea++    + ile + l +e+          v+ Aa++  e+G
  gi|557694315|ref|YP_008797369.1|  86 AIADGCEEIDFMINVGYLKSGMVDEFRRDVEMVVEAADGRIVKAILEtAILSEEE----------VRLAAKICEEAG 152
                                       ***********************************************55555555..........************ PP

                                       -SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTE.EEEETTSSHHHHHHHHHHHHHHHTH..C CS
                              DeoC 165 aDiiKvevpkevvnateedaevfkdvikaapvpg.vvlsGGvseedfletvedAvkeaga..s 224
                                       +  +K + +    + ++  +e+ k + +++   + v+ sGG+  +df+ +v+  v eaga   
  gi|557694315|ref|YP_008797369.1| 153 VNYVKNSSG--WGKGGPATVEIVKLLRSSVSKKVgVKASGGI--RDFATAVKL-V-EAGAdlL 209
                                       *********..677888888888888887766646*******..888777764.2.5666554 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.3e-05      0.26      20      56 ..       4      39 ..       2      41 .. 0.94
   2 ?   -0.7   0.0      0.29   1.8e+03      38      51 ..     109     122 ..     107     124 .. 0.89
   3 ?   -0.1   0.1       0.2   1.2e+03      24      45 ..     125     146 ..     121     155 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.3e-05
                           DUF4777 20 aTldEivervaerydlseeelkkvVkntLeaAvrhGF 56
                                      ++++Ei+ r+ +++++s++  k++++++ ++Av +GF
  gi|557694315|ref|YP_008797369.1|  4 ISVKEIASRI-QHTNVSPDATKRDIEKLCSEAVKYGF 39
                                      6889999999.899**********************9 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.29
                           DUF4777  38 eelkkvVkntLeaA 51 
                                       +e++++V+ + eaA
  gi|557694315|ref|YP_008797369.1| 109 DEFRRDVEMVVEAA 122
                                       799******99998 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.2
                           DUF4777  24 EivervaerydlseeelkkvVk 45 
                                       +iv+++ e   lseee++   k
  gi|557694315|ref|YP_008797369.1| 125 RIVKAILETAILSEEEVRLAAK 146
                                       6899999999999999987655 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   4.1   3.1e-05      0.18     233     304 ..     148     216 ..       1     228 [. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.1e-05
                                       HHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
                            FMN_dh 233 aveaGvdgivvSNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                                       + eaGv+ +   N  G    g pat+++   ++  v +++ v ++gGir  + ++k +  GAd+ +  R + 
  gi|557694315|ref|YP_008797369.1| 148 CEEAGVNYV--KNSSG-WGKGGPATVEIVKLLRSSVSKKVGVKASGGIRDFATAVKLVEAGADLLGTSRGVQ 216
                                       334555544..44444.23689********************************************999883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); 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:                         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: 00:00:00.43
# Mc/sec: 1588.71
//
Query:       gi|557694316|ref|YP_008797370.1|  [L=307]
Description: ribokinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  192.3   2.8    1.4e-56  192.0   2.8    1.1  1  PfkB          pfkB family carbohydrate kinase
    7.2e-14   51.7   0.1    1.1e-13   51.1   0.1    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    2.6e-09   36.9   0.0    4.7e-09   36.1   0.0    1.4  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 !  192.0   2.8   2.3e-60   1.4e-56       3     292 ..       4     282 ..       2     291 .. 0.91

  Alignments for each domain:
  == domain 1  score: 192.0 bits;  conditional E-value: 2.3e-60
                                       EEEEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTE CS
                              PfkB   3 kvvviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegv 77 
                                       kv v+G+ +  ++ ++++l  ege+ +++ ++   GG+g N+A  +arlg++++ i +vG D fGe+ l+++++e++
  gi|557694316|ref|YP_008797370.1|   4 KVGVVGSYNTGFVVYVKRLpiEGETLKGHGFRIEHGGKGSNQAIQAARLGCQTFIIARVGADIFGERALNKWRAEKI 80 
                                       67799*************9********************************************************** PP

                                       EETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEES.EECTTSHHHHHHHHHH CS
                              PfkB  78 dtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisg.llsselpeavleelae 153
                                       dt +v++d + +tg  l++v  +g++ i++++ga+ +ltk++       +++a+    s+ ++ ++l     + l +
  gi|557694316|ref|YP_008797370.1|  81 DTTHVVVDRENPTGAGLVIVGPAGKNMIIVDLGANMHLTKTD-------VSNAAARIRSAdVVLTQLEIPFETSLHA 150
                                       ****************************************85.......5555555555545555566666666666 PP

                                       HHHHTTEEEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGG CS
                              PfkB 154 aaknggtfdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGke 230
                                       ++ ++g   + +l+p++a  +++  e l ++++++pne E +a++g +  + +++ +a++k  ak++++vvvtlG++
  gi|557694316|ref|YP_008797370.1| 151 LRTAEG---MKILNPAPA--QPTPPETLKGINIITPNEVEMAAMAGYTPGEDADLENAAKK-YAKYVDNVVVTLGER 221
                                       666666...5699****6..799**************************999******999.789************ PP

                                       EEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTS CS
                              PfkB 231 GalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqk 292
                                       Ga vv+k+++ +v+a p v++vD+tGAGD+f+g+++ al++g ++ ea+++a++++a+ + +
  gi|557694316|ref|YP_008797370.1| 222 GAMVVDKNDVKHVKA-PRVNAVDSTGAGDAFNGALATALARGYTVLEAVEYACHAGAFLAAR 282
                                       ***************.*****************************************97765 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.1   1.9e-17   1.1e-13      99     224 ..     155     272 ..     150     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.9e-17
                                       TSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEE CS
                      Phos_pyr_kin  99 sgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtd 175
                                       +g ++l++   +    e l+  ++itPN  E++a++g +  + +d+++aakk +k+ +++V+++ g+          
  gi|557694316|ref|YP_008797370.1| 155 EGMKILNPAPAQPTPPETLKGINIITPNEVEMAAMAGYTPGEDADLENAAKKYAKY-VDNVVVTLGER----G---A 223
                                       6777777777777778889999*********************************8.66777777652....2...3 PP

                                       EEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHH CS
                      Phos_pyr_kin 176 vlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkA 224
                                       +++d+++v++++a+r++  +  G+G+++  a+a+ la+g+++ eAv+ A
  gi|557694316|ref|YP_008797370.1| 224 MVVDKNDVKHVKAPRVNAVDSTGAGDAFNGALATALARGYTVLEAVEYA 272
                                       688*******************************************976 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   7.8e-13   4.7e-09     117     222 ..     174     280 ..     154     298 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 7.8e-13
                                       TSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG.-STTHHHH CS
                       Carb_kinase 117 kaeviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvllkgekdvivspegevlinstgssal.akGGsGDv 192
                                       k+  i+TP+ +E + +++   +++ d  ++a++ a+ +  vv+  ge   +v  +++v+++++  +++  + G GD 
  gi|557694316|ref|YP_008797370.1| 174 KGINIITPNEVEMAAMAGYTPGEDADLENAAKKYAKYVDNVVVTLGERGAMVVDKNDVKHVKAPRVNAvDSTGAGDA 250
                                       5667*****************9*****************************************998762689***** PP

                                       HHHHHHHHHHCTSSHHHHHHHHHHHHHHHH CS
                       Carb_kinase 193 LaGligalLaqneasyeaaiaaawlhgaas 222
                                         G+++  La  ++ +ea+  a+ + +  +
  gi|557694316|ref|YP_008797370.1| 251 FNGALATALARGYTVLEAVEYACHAGAFLA 280
                                       *************99999877777666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2200.12
//
Query:       gi|557694317|ref|YP_008797371.1|  [L=272]
Description: uridine phosphorylase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-38  130.2   0.1    8.6e-38  129.9   0.1    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 !  129.9   0.1   4.8e-42   8.6e-38       2     226 ..      25     248 ..      24     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 4.8e-42
                                       EEEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEE CS
                         PNP_UDP_1   2 iaiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGt 78 
                                       ++++ g+p++v  +a+   +e ++++ +r+++++ G+++++ + ++stGiG+p++a +a+ +l  ++ + ++ir+G+
  gi|557694317|ref|YP_008797371.1|  25 YVLMPGDPDRVLKIAQF-WDEGREISFHREYRVWNGRVGEVGIAACSTGIGAPSTA-IAVEELARAG-CHTFIRVGS 98 
                                       7899*************.**************************************.9999999966.********* PP

                                       EEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS CS
                         PNP_UDP_1  79 aGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfy 155
                                       +G+++p++++GD +i+ +a++++g+s         qy+++sy+a a+ e + +l eaae lg+++h Gv+a++d+fy
  gi|557694317|ref|YP_008797371.1|  99 CGAIQPGIEIGDQIISVAAVRLEGTSH--------QYALPSYPAYAHYEVVLALIEAAETLGARYHLGVTASTDSFY 167
                                       ***************************........****************************************** PP

                                       -CH.............HHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHH CS
                         PNP_UDP_1 156 aet.............eaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaq 219
                                         +             ++ +  lr +++ ++eME++a++++A ++g++ +a+++v   +a++ d++  ++ +e + +
  gi|557694317|ref|YP_008797371.1| 168 PGQgrpgyrgywwsysKNIIDDLRAMNVLNIEMEASALFVIAGLYGLRSGAVCSV---FANRVDDKFGVKGEETTSK 241
                                       ************988766666**********************************...5555555555454454444 PP

                                       HHHHHHH CS
                         PNP_UDP_1 220 eaaknaa 226
                                       +a ++++
  gi|557694317|ref|YP_008797371.1| 242 IATEAVK 248
                                       4444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       305  (0.0170115); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2095.97
//
Query:       gi|557694318|ref|YP_008797372.1|  [L=273]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-74  248.2   0.0    9.9e-74  248.0   0.0    1.0  1  BtpA       BtpA family
  ------ inclusion threshold ------
      0.016   14.0   0.1      0.035   13.0   0.0    1.6  2  Trp_syntA  Tryptophan synthase alpha chain


Domain annotation for each model (and alignments):
>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.0   0.0   1.1e-77   9.9e-74       3     253 ..       9     263 ..       7     264 .. 0.96

  Alignments for each domain:
  == domain 1  score: 248.0 bits;  conditional E-value: 1.1e-77
                              BtpA   3 kpvigvvHLkpLPgsaeyka.nleevidkAvkeakaleegGvDavilenygdaPflke..vdpetvaamtvivkevk 76 
                                       kpvig+vHL+pLPgs+ y + ++++v++ A+++a al +gGvD++ +en gd+Pf k+  v+petv+ ++vi++ev+
  gi|557694318|ref|YP_008797372.1|   9 KPVIGMVHLRPLPGSPGYGEwSVDDVLELALRDAVALRDGGVDGIQVENLGDKPFMKQgeVGPETVSLVSVIAREVR 85 
                                       9******************99************************************988***************** PP

                              BtpA  77 sdvsiplGvnvLrndavaalaiAkavgakFiRvnvltgvalsdeGilegkaaellrykkllesrvkiladvavkhav 153
                                       ++v++p+Gv vL n   +++  A a ga+++R n++  ++++deG +e+ a    r++++l  +vk++adv vkh  
  gi|557694318|ref|YP_008797372.1|  86 KEVGLPVGVFVLANAVPESITAAAACGASWVRANMYNLAYVADEGYVESAAPASERLRNKLAPGVKVFADVLVKHGS 162
                                       ***************************************************************************99 PP

                              BtpA 154 plverdlesavk.dtvergladavilsGkatGgevdleelklaketvkvkvlvgsGvseenlekllsiadGvivgts 229
                                       ++  +d   + +   +e   ada+++sG +tGge+ le++  +k++++ +v++gsG + en+ kll++adG ivgt+
  gi|557694318|ref|YP_008797372.1| 163 HFLVSDTPVYYQvARLEEIGADAIVVSGFRTGGETPLERVLEVKQIASKPVFIGSGLNLENVGKLLDVADGAIVGTY 239
                                       98876665544414578899********************************************************* PP

                              BtpA 230 ikkdGkianaiDkervrkivelae 253
                                       +kk+Gk+ n++D ervrk+++ ++
  gi|557694318|ref|YP_008797372.1| 240 FKKEGKTLNPVDVERVRKFMDVVR 263
                                       ********************9876 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.37   3.3e+03      78      99 ..      81     101 ..      69     103 .. 0.75
   2 ?   13.0   0.0   3.9e-06     0.035     189     229 ..     201     240 ..     174     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.37
                                       HHHHHHHCSSS-EEEEE-CHHH CS
                         Trp_syntA  78 veevrkkevevPivlltylnlv 99 
                                        +evr kev +P+ ++  +n v
  gi|557694318|ref|YP_008797372.1|  81 AREVR-KEVGLPVGVFVLANAV 101
                                       46777.8889999998888876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.9e-06
                                       HHHHHHHCTSS-EEEESSS-SHHHHHHHHTT-SEEEE-HHH CS
                         Trp_syntA 189 lverlkkltavPvavGFGistkeqvkqvakvadGvivGSal 229
                                        v ++k++  +Pv +G G++  e+v ++  vadG+ivG   
  gi|557694318|ref|YP_008797372.1| 201 RVLEVKQIASKPVFIGSGLN-LENVGKLLDVADGAIVGTYF 240
                                       45689*************95.799**************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 1750.18
//
Query:       gi|557694319|ref|YP_008797373.1|  [L=511]
Description: simple sugar ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-49  166.0   0.0    1.9e-29  102.9   0.0    2.4  2  ABC_tran     ABC transporter
     0.0013   18.6   3.4       0.75    9.5   0.2    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
  ------ inclusion threshold ------
      0.014   15.9   0.0      0.023   15.2   0.0    1.3  1  AAA_23       AAA domain
      0.032   14.2   0.2       0.69    9.8   0.0    2.3  2  RsgA_GTPase  RsgA GTPase
      0.095   12.3   0.1       0.69    9.5   0.0    2.3  2  AAA_25       AAA domain
       0.23   10.9   0.3        5.3    6.4   0.3    2.3  1  SMC_N        RecF/RecN/SMC N terminal domain
       0.27   10.9   2.1        8.7    6.0   0.0    2.8  3  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 !  102.9   0.0   7.6e-33   1.9e-29       1     137 []      25     174 ..      25     174 .. 0.96
   2 !   60.8   0.0   7.6e-20   1.9e-16       1     132 [.     279     432 ..     279     437 .. 0.84

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 7.6e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l+++++++++ge++a++GenGaGK+ L+++l+g ++  +Ge+ ++gk+++   +    r+ ig+++qe +l   ltv
  gi|557694319|ref|YP_008797373.1|  25 LDHIDFDVRAGEVHALLGENGAGKTVLANILSGFYTLSSGELIVKGKNVRFkSPADAIRHGIGMVHQEFTLAAPLTV 101
                                       789**********************************************998999********************** PP

                                       HHH................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        en                + +e+i ++ +++glk  ++++v    ++LS G++qrv++ ++l  +p++l+lDEpt+
  gi|557694319|ref|YP_008797373.1| 102 VENvaltlrrnnplsyplkKIEEKIRELSQRYGLKVEPHEKV----ENLSLGERQRVEIIKVLYWEPSILILDEPTS 174
                                       ***************999988999999999999999999999....*****************************96 PP

  == domain 2  score: 60.8 bits;  conditional E-value: 7.6e-20
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS...--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx...xxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe...pqlfpe 73 
                                       +knv+l++ ege+++i G +G G   L+++l+gl k  +G+i ++g dl++  ++++++  ++ +p++   + + +e
  gi|557694319|ref|YP_008797373.1| 279 VKNVNLEVGEGEILGIAGVSGNGQKELVEALTGLRKVVSGKIVINGVDLTNgSPRRFAQTGVRHIPEDrrrTGVVEE 355
                                       58*************************************************999**************777677777 PP

                                       SBHHHH....................HHHTC...HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTS CS
                                       xxxxxx....................xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren....................esdee...iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkp 127
                                       +  +en                    +       ++k+++++g      + ++++ + LSgG  qr+ lar l+k+p
  gi|557694319|ref|YP_008797373.1| 356 MVTAENimlreyrekpfsvfgvinkrA---VtelAQKLVASFGVLT--PDLWDTEVRILSGGNIQRLILARELWKEP 427
                                       777777999988888888888754322...1333666666666544..66677777********************* PP

                                       SEEEE CS
                                       xxxxx RF
                          ABC_tran 128 kllll 132
                                       kll++
  gi|557694319|ref|YP_008797373.1| 428 KLLIA 432
                                       ***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 !    9.4   0.3   0.00033      0.84       2      25 ..      38      61 ..      37      98 .. 0.72
   2 !    9.5   0.2   0.00029      0.75     246     298 ..     155     204 ..     127     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00033
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl 25
                                       +l G Ng+GK+ L  +l+++  l
  gi|557694319|ref|YP_008797373.1| 38 HALLGENGAGKTVLANILSGFYTL 61
                                      689***************998654 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00029
                            AAA_21 246 alltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                        ++  l+  +   s+l++DEp + L  +  ++l+++l++ +++g  +++ TH 
  gi|557694319|ref|YP_008797373.1| 155 EIIKVLYWEP---SILILDEPTSVLTLEESKELFQILRKMAEEGKGIVFITHR 204
                                       5555555555...9***********************888888*********5 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   8.9e-06     0.023      14     126 ..      27     149 ..      22     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.9e-06
                            AAA_23  14 eidF...skgltlItGpNGaGKTTildAiklaLygetprlsrks..............grgfeksdveiesegkvka 73 
                                       +idF      + ++ G+NGaGKT + + +    +  +++l  k               g g+++++++++   +v +
  gi|557694319|ref|YP_008797373.1|  27 HIDFdvrAGEVHALLGENGAGKTVLANILSGFYTLSSGELIVKGknvrfkspadairhGIGMVHQEFTLAAPLTVVE 103
                                       57776655578999*************99966666555553333457788999999999999999999999999999 PP

                            AAA_23  74 yveltfenkdgrytrsiererelskkkgkttkkaklelleideleqfisellg 126
                                        v lt+++++      +++  +++++k ++ ++  + ++e+ e+ +++s   g
  gi|557694319|ref|YP_008797373.1| 104 NVALTLRRNNP-----LSYPLKKIEEKIRELSQRYGLKVEPHEKVENLSL--G 149
                                       99999*99999.....9999999999999999999999999998888873..3 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00027      0.69      92     129 ..      27      65 ..      20      73 .. 0.79
   2 ?    1.7   0.1     0.083   2.1e+02      88     124 ..     277     314 ..     247     328 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00027
                                       HHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                       ++   ++  ++ +l+G+ G+GK+ L n l +  +l+ ge
  gi|557694319|ref|YP_008797373.1|  27 HIDFDVRAgEVHALLGENGAGKTVLANILSGFYTLSSGE 65 
                                       55555655599******************9876666555 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.083
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpele 124
                                       +++++++ ++ + ++  ++G SG G   L++al++  +
  gi|557694319|ref|YP_008797373.1| 277 AAVKNVNLEVGEgEILGIAGVSGNGQKELVEALTGLRK 314
                                       455555555555599999*************9998655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00027      0.69      31      58 ..      33      60 ..      25     136 .. 0.84
   2 ?   -0.4   0.0      0.28   7.2e+02      67     117 ..     313     365 ..     304     390 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00027
                            AAA_25 31 pagelallaGapgtGKttlaldlalava 58
                                      +age+++l G  g+GKt+la  l+  ++
  gi|557694319|ref|YP_008797373.1| 33 RAGEVHALLGENGAGKTVLANILSGFYT 60
                                      69*****************987777666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.28
                            AAA_25  67 vapeqgkVlyvsaEdsedelrrRlravg.ealrddarl.lvldlagv.eslpLf 117
                                       +++  gk ++   + ++ + +rR++++g +++++d+r   v+  +   e+++L+
  gi|557694319|ref|YP_008797373.1| 313 RKVVSGKIVINGVDLTN-GSPRRFAQTGvRHIPEDRRRtGVVEEMVTaENIMLR 365
                                       45678889999988898.999*****9966665554441555544444555554 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 ?    6.4   0.3    0.0021       5.3      26      50 ..      37      63 ..      26     226 .. 0.42

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0021
                                      EEEEEESTTSSHHHHHHHHH..HHCTT CS
                                      xxxxxxxxxxxxxxxxxxxx..xxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAil..FvLGe 50
                                      + a++G+NG+GK+ l + ++  ++L+ 
  gi|557694319|ref|YP_008797373.1| 37 VHALLGENGAGKTVLANILSgfYTLSS 63
                                      567788888888744443322155543 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 ?    6.0   0.0    0.0034       8.7      44      68 ..      32      56 ..      23     107 .. 0.77
   2 ?    3.8   0.0     0.017        44     106     143 ..     161     197 ..     142     217 .. 0.73
   3 ?   -3.7   0.1       3.4   8.7e+03      48      68 ..     290     310 ..     286     319 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0034
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg 68
                                      +++ e  +llG  G+GK+ la  l+
  gi|557694319|ref|YP_008797373.1| 32 VRAGEVHALLGENGAGKTVLANILS 56
                                      56778889*************8764 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.017
                         IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekryerrsi 143
                                       + ++++lilD+     l  +e+++lf+++ k  e    
  gi|557694319|ref|YP_008797373.1| 161 YWEPSILILDEPT-SVLTLEESKELFQILRKMAEEGKG 197
                                       456799****965.4466678899*****998876544 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3.4
                         IstB_IS21  48 enivllGpsGvGKshlaialg 68 
                                       e + + G sG G   l  al 
  gi|557694319|ref|YP_008797373.1| 290 EILGIAGVSGNGQKELVEALT 310
                                       566789999999999999884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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 0.30s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3389.39
//
Query:       gi|557694320|ref|YP_008797374.1|  [L=454]
Description: 2-methylcitrate dehydratase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-135  451.3   0.2   3.1e-135  451.1   0.2    1.0  1  MmgE_PrpD  MmgE/PrpD family


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 !  451.1   0.2  1.7e-139  3.1e-135      15     438 ..      18     439 ..       6     440 .. 0.97

  Alignments for each domain:
  == domain 1  score: 451.1 bits;  conditional E-value: 1.7e-139
                                       -H..HHHHHHHHHHHHHHHHHHHHTT-HHHHTT-SSSTT-B-.TT-EE-TTSS-EE-HHHHHHHHHHHHHCTS-S-B CS
                         MmgE_PrpD  15 dlpeevverakrlilDtlGvalaglrepavkkaleavkgtgg.pggatvigtgerlspvkAAfvnGaaihalDfdDt 90 
                                       dl+e+v+++akr++lD+lG+ +++  e+av + ++av+++   +gga+v+gt  ++sp++AAfvnG+ ++alDf+Dt
  gi|557694320|ref|YP_008797374.1|  18 DLDEDVLAEAKRRVLDSLGCFFGAWGEEAVVASRRAVQRFAQrDGGASVWGTAVKTSPEWAAFVNGVGVRALDFNDT 94 
                                       7889*******************************9999876166******************************** PP

                                       EESSSEE-GGGGHHHHHHHHHHHHHHBHHHHHHHHHHHHHHHHHCCC--SCCCT.B-THHHHHHHHHHHHHHHTT-- CS
                         MmgE_PrpD  91 hlaaelhhpsdvlpaalAvAealgasgkdlLtAivvGyEvqgrlglalsfnhygfhdtvtlgtfgaaaaaakLlgLd 167
                                       +l++e  hpsd++pa+lA+ e +ga g d+L+Aiv+GyEv++rl++a+ ++++g +d+v ++ +ga a+++k ++L+
  gi|557694320|ref|YP_008797374.1|  95 YLSKEPLHPSDMIPAVLAAGEVVGAGGMDVLKAIVTGYEVGCRLCDAATLRKRG-WDHVNFTMIGAVAGVSKVMKLS 170
                                       ******************************************************.********************** PP

                                       HHHHHHHHHHHHCT-B-BSGGGSTTT--CHHCHHHHHHHHHHHHHHHHHTT---TTTTT-TTTSHHHHHSTT----- CS
                         MmgE_PrpD 168 aeqianAlgiaatqaaglrqyrhagtkskklwaaGdAarnGveaallAkrGftGpsdilegewGflavlsggkdlel 244
                                        e++anA+++a++ +a++rq+r+++ +++k  aa++A+rn+v+a+llA+ G+tGps+ + ge+Gf+++++g+ +++l
  gi|557694320|ref|YP_008797374.1| 171 FEETANAVSLAVVPHAAMRQTRAGELSMWKGAAAANACRNAVFACLLASSGMTGPSQPFNGEMGFFKQVAGT-SFTL 246
                                       **********************************************************************99.8998 PP

                                       S.S-SS...SHHHHC-B---SSS-CCCHHHHHHHHHHHHHHCCTCCCEEEEEEEE-HHHHHHC---S...---SHHH CS
                         MmgE_PrpD 245 evkplgegesweienvlfKpypaerhthaaidaalklraelklkpddIesieirtseaalriigkkg...ppenrad 318
                                       +    + +   +i+++++K++p+e+h+ +a+daalk  ++ +  +++Ie+++++t+ea + i+ k++   +p++r++
  gi|557694320|ref|YP_008797374.1| 247 K-GLSETKRPRKILETYIKFHPVEYHAMTAVDAALKALQRAGS-AENIEKVVVETFEASYTILAKDPekwRPSTRET 321
                                       8.4444489*********************************7.**********************9********** PP

                                       HCT-CCHHHHHHHHCS---CCCCSCCCCTSCHHCCHHCCEEEEE-HHHHHHHTTT---EEEEETTS-B---EEESS- CS
                         MmgE_PrpD 319 adhSlqyvvAvalldgrvtledfederladpevqaLrekvevvedpeltadypekrsivvvvlkdggrtleerveyp 395
                                       adhSl+y+vA+ lldg + l++f+ er+ +p++ +L+++vevve+pelta+yp + + + +  +++g++  ++   p
  gi|557694320|ref|YP_008797374.1| 322 ADHSLPYIVAATLLDGGIWLNSFSRERISSPDIAELMKRVEVVENPELTARYPMELPNRIILKLRNGEEIAVEEAIP 398
                                       ***************************************************************************** PP

                                       TTSGGHHHHHHHHHHHHHHHHHCCS-HHHHHHHHHHHHHHSHH CS
                         MmgE_PrpD 396 kGhprnplsreeleeKfrrlaegvlseeeaereeileevlele 438
                                       +Gh +np+++ee+e+Kf+rl+++ l+  e +r+ i+e+v+ +e
  gi|557694320|ref|YP_008797374.1| 399 RGHYKNPMTNEEVEKKFHRLTSPLLD--EGRRRMIVEKVWSME 439
                                       **************************..999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3330.85
//
Query:       gi|557694321|ref|YP_008797375.1|  [L=364]
Description: citrate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-110  369.2   0.1   2.4e-110  369.0   0.1    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain


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 !  369.0   0.1  1.3e-114  2.4e-110       1     361 []       7     355 ..       7     355 .. 0.95

  Alignments for each domain:
  == domain 1  score: 369.0 bits;  conditional E-value: 1.3e-114
                                       GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHH CS
                      Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlea 77 
                                       gl+gv+a+e++i+++d e+ +++ RG ++e++a +++sfeeva+lL++g+lP+++e k+f++ +a +r++p +v++ 
  gi|557694321|ref|YP_008797375.1|   7 GLEGVPAVESRICTIDVENRRIIIRGKSLEKIA-QEHSFEEVAHLLIHGHLPDADESKQFTRLIAVERRVPSAVVDV 82 
                                       89*****************99************.799**************************************** PP

                                       HHCSSTTS-HHHHHHHHHHHHHHHSTTCTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.--.---TTSSHHH CS
                      Citrate_synt  78 lealpkdahpmavlraavsalsaddeeseakeeseeaalrdalkliAklptiaaaiyrarlgrepl.epddklsyae 153
                                       +++lp+++hpm++lr++vsal+ +d++   +++s ea  r+a++l+Ak  +++a+  +  + r  + e d+   +ae
  gi|557694321|ref|YP_008797375.1|  83 VKSLPAETHPMDALRTGVSALAPFDPD--LDDTSLEANKRKAARLVAKTGLLVANLDNLLTRR-TFaEADETRGHAE 156
                                       *************************95..444455777888889**********999999976.56589999***** PP

                                       HHHHHHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHH CS
                      Citrate_synt 154 nflymlrgkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmlee 230
                                       n+l+++rg   ++ ++k ++++++l+++Hel+aSTf+arv+aStlad+y a+++g++alkGplhggane++ +++e 
  gi|557694321|ref|YP_008797375.1| 157 NILRLIRGGGVEDWMIKPFEILFILYVEHELAASTFTARVIASTLADMYGAVVGGLAALKGPLHGGANEKATEIFEF 233
                                       *******988999**************************************************************95 PP

                                       HSSGG.GHHHHHHHHHHTTTS--TTBC-SSSSS-.-HHHHHHHHHHHHHHTCHTHHHHHHHHHHHHHHHHHHHHCHH CS
                      Citrate_synt 231 igsaeveveeylekvlakekerlpGfGHrvykks.DpRakilkelaeelaeekgkdpllklaeeleevapevlkeke 306
                                          a   +e+y++++l++ ker++GfGHrvy+++ DpRa++ k+l+e+ ++++g+d+l+++ae++e+++++     e
  gi|557694321|ref|YP_008797375.1| 234 D-VA--GAEKYVRERLER-KERIMGFGHRVYRRGiDPRAELTKRLLEQACAKVGDDRLYRVAEHVERLMEK-----E 301
                                       5.45..589********8.6***********9655************************************.....8 PP

                                       GCT-EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHHHT------E CS
                      Citrate_synt 307 eknlypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileqladnkiiRPr 361
                                        k+lypN+Dfy+++ly+ ++ip++++t++fa+sRvaGw Ah++eq+a+n+++RPr
  gi|557694321|ref|YP_008797375.1| 302 -KSLYPNLDFYAAALYKLMKIPPRFYTPIFAASRVAGWAAHVIEQQAENRLFRPR 355
                                       .9****************************************************8 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:                      369  (0.0205812); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2575.45
//
Query:       gi|557694322|ref|YP_008797376.1|  [L=386]
Description: tryptophanyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-22   78.6   0.0    8.5e-22   77.8   0.0    1.4  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 !   77.8   0.0   4.7e-26   8.5e-22       5     292 ..      76     351 ..      72     352 .. 0.84

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 4.7e-26
                                       --EEEEEEETSSS-BGGGHHHHHHHHHHHH.TTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHH..HHHHHHH CS
                      tRNA-synt_1b   5 plrvysGidPTgklHlGylvplkklvelqk.aghevffliaDlhAiigdpskaeerklrkreevlena..ikaqlak 78 
                                        + +y+G  P+g++H+G+++p+    +lq+  g +v++   D + ++ + +      l  +++ +  +  + ++ a+
  gi|557694322|ref|YP_008797376.1|  76 GFYLYTGRGPSGPMHVGHIIPFFFTKWLQErFGANVYIQMTDDEKFLEETR-----GLTLEDTAYWSLdnMVNIAAV 147
                                       5679*************************7667788887777666666666.....444333333333345779*** PP

                                       TCHTTTEEEEETHHHHTTH.HHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS.E CS
                      tRNA-synt_1b  79 gldpekaevvlqsewlehl.elaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad.l 153
                                       g+dp+k+ ++ ++e ++ +      +++  ++ +++ +  f +         + ++g   +p  q    ++ k + l
  gi|557694322|ref|YP_008797376.1| 148 GFDPDKTFIFRNTEFMARMyRPVLKVARKINFSWVRAVFGFNE---------QTNIGMVFFPAIQIVPTMFEKRRcL 215
                                       **************99877544444555556677777777777.........4478999*********999999999 PP

                                       EEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET.-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCST CS
                      tRNA-synt_1b 154 vpgGsDQkqnielgrdlarrfnkkevfkkpegltvp.lltgldGekKmSKSagnsaIfLddekesvkkkiqkavtds 229
                                        p   DQ+   ++ rd+a++++      k  ++  + l++++ ++ KmS S++++a+fL+d+ ++v+kki +a++  
  gi|557694322|ref|YP_008797376.1| 216 IPAAIDQDPYWRIQRDIAESLGFY----KAAAIHSRfLMPLTGPTGKMSASQPEAAVFLTDDDKTVRKKIWQAFSGG 288
                                       *********************655....666666666**************************************88 PP

                                       TC..SHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 230 de..evekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                       +   e+++ l +++ ++   ++ l ++ ++++ r++e+l +e+v++++  g+lk+ l e+++++l
  gi|557694322|ref|YP_008797376.1| 289 QPtvELHRKLGGNPDIDV-AFQWLYYFFEEDD-RKVEQLREEYVSGRLLTGELKEILIEKVQMFL 351
                                       7777**************.9999999999999.****************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2909.31
//
Query:       gi|557694323|ref|YP_008797377.1|  [L=223]
Description: sulfate ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-22   77.9   0.0    1.6e-21   77.3   0.0    1.3  1  ABC_tran     ABC transporter
    1.1e-09   38.5   5.2    0.00021   21.2   0.3    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.6e-07   29.5   0.1      0.016   14.7   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00021   21.8   0.3    0.00039   21.0   0.3    1.3  1  AAA_23       AAA domain
     0.0012   18.6   0.0     0.0024   17.6   0.0    1.4  1  AAA_30       AAA domain
     0.0031   17.9   0.0     0.0036   17.7   0.0    1.3  1  AAA_16       AAA ATPase domain
     0.0042   15.8   0.2      0.078   11.6   0.2    2.1  2  AAA_13       AAA domain
     0.0042   16.8   0.1     0.0071   16.1   0.1    1.3  1  AAA_29       P-loop containing region of AAA domain
     0.0056   16.9   0.2      0.011   16.0   0.2    1.7  1  AAA_22       AAA domain
     0.0061   16.3   0.7      0.016   15.0   0.3    1.7  2  AAA_15       AAA ATPase domain
     0.0077   16.7   0.0      0.012   16.0   0.0    1.3  1  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.015   15.6   0.0    1.3  1  AAA_19       AAA domain
      0.014   15.3   0.0      0.025   14.5   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
       0.02   14.9   0.3       0.14   12.2   0.2    2.0  2  AAA_14       AAA domain
      0.029   13.7   0.0      0.043   13.1   0.0    1.2  1  Zeta_toxin   Zeta toxin
      0.037   12.9   0.1      0.054   12.3   0.1    1.1  1  DLIC         Dynein light intermediate chain (DLIC)
      0.051   13.6   0.1       0.12   12.3   0.1    1.6  2  AAA_5        AAA domain (dynein-related subfamily)
       0.06   13.3   1.6      0.063   13.2   0.5    1.6  2  NACHT        NACHT domain
      0.075   12.9   0.1       0.16   11.9   0.1    1.5  1  NTPase_1     NTPase
      0.086   12.6   0.0       0.11   12.1   0.0    1.2  1  AAA_24       AAA domain
       0.12   11.5   0.0       0.17   11.0   0.0    1.1  1  DUF815       Protein of unknown function (DUF815)
       0.13   11.3   0.1       0.21   10.6   0.1    1.3  1  T2SSE        Type II/IV secretion system protein
        0.2   11.3   0.2       0.35   10.5   0.2    1.4  1  SRP54        SRP54-type protein, GTPase domain
       0.26   10.9   1.1       0.75    9.4   0.6    1.8  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.37    9.5   2.2       0.39    9.4   0.5    1.7  2  ABC_ATPase   Predicted ATPase of the ABC class


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 !   77.3   0.0   2.2e-24   1.6e-21      10     137 .]      23     147 ..      17     147 .. 0.89

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 2.2e-24
                                       TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH......H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......x RF
                          ABC_tran  10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren......e 80 
                                        ++++ i+G+nG+GK+tLlk++ag  kp +G i+l+g+d+++  l+ ++++ig++pq+p   p +  r+        
  gi|557694323|ref|YP_008797377.1|  23 SSKITIILGRNGTGKTTLLKTVAGFIKPRKGVIRLNGRDITN--LPPSERRIGYMPQQPIKLPYK-PRDAihyfakI 96 
                                       578999************************************..**************7776666.66767777777 PP

                                       HHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  81 sdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        +++++ +++k++l+ +  +      ++LS G+ q +al  +ll+k +llllDEpt+
  gi|557694323|ref|YP_008797377.1|  97 FRADPQPVIEKMRLEPILRK------EKLSTGEAQILALSILLLRKTELLLLDEPTS 147
                                       88889999999999984444......68***************************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 !   21.2   0.3   2.9e-07   0.00021       1      37 [.      26      62 ..      26      81 .. 0.70
   2 !   20.1   0.4   6.6e-07   0.00047     235     299 ..     117     175 ..      74     177 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.9e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdels 37
                                      ++++ G+Ng+GK++LL++  ++   ++ v++l+  + 
  gi|557694323|ref|YP_008797377.1| 26 ITIILGRNGTGKTTLLKTVAGFIKPRKGVIRLNGRDI 62
                                      79*****************877433444444444444 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.6e-07
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                        +lS G  ++lal  +llr      lll+DEp ++L+      ++ l+++l+   +  + +TH+p
  gi|557694323|ref|YP_008797377.1| 117 EKLSTGEAQILALSILLLRKT---ELLLLDEPTSSLDFPNSVNFWSLIRSLN---IPMVYVTHNP 175
                                       467*******99999999855...9************988888888887773...3666666665 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 !   12.9   0.0   7.5e-05     0.054      18      44 ..      18      44 ..       7      52 .. 0.85
   2 !   14.7   0.0   2.2e-05     0.016     132     187 ..     114     165 ..      87     192 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.5e-05
                                      EEEETTSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 18 vilpfsksftaivGpNGSGKsnlldAi 44
                                      v+  +s+++t+i+G+NG GK+ ll  +
  gi|557694323|ref|YP_008797377.1| 18 VERFVSSKITIILGRNGTGKTTLLKTV 44
                                      56678899**************99876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.2e-05
                                       -STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 132 iskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeks 187
                                       + ke LS Ge +++al++l+     +++ l llDe  + LD+ n  ++ +l+++ +
  gi|557694323|ref|YP_008797377.1| 114 LRKEKLSTGEAQILALSILL----LRKTELLLLDEPTSSLDFPNSVNFWSLIRSLN 165
                                       56889**********99985....88999**********************99876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.3   5.4e-07   0.00039      17      37 ..      21      42 ..      11      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.4e-07
                            AAA_23 17 F.skgltlItGpNGaGKTTild 37
                                      F s+++t+I G NG+GKTT+l 
  gi|557694323|ref|YP_008797377.1| 21 FvSSKITIILGRNGTGKTTLLK 42
                                      3799****************95 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.3e-06    0.0024      10      45 ..      18      51 ..      15      72 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.3e-06
                            AAA_30 10 vealltsgdrvavltGpAGtGKttalkalreaweaa 45
                                      ve++++s+  ++++ G+ GtGKtt+lk+++  ++ +
  gi|557694323|ref|YP_008797377.1| 18 VERFVSSK--ITIILGRNGTGKTTLLKTVAGFIKPR 51
                                      56677777..9******************9988766 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   0.0     5e-06    0.0036      21      63 ..      23      64 ..       6     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5e-06
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                      s+   ++++ G  G+GK++l+++++  ++ ++g+  l+g+   +
  gi|557694323|ref|YP_008797377.1| 23 SS--KITIILGRNGTGKTTLLKTVAGFIKPRKGVIrLNGRDITN 64
                                      44..799******************9999996544477776666 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.2   0.00011     0.078      16      38 ..      24      46 ..      14      59 .. 0.84
   2 ?    2.2   0.0     0.075        54     525     554 ..     135     164 ..     108     174 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                            AAA_13 16 kriNliYGwNGaGKTtLSrllrs 38
                                      ++i +i G+NG+GKTtL +  + 
  gi|557694323|ref|YP_008797377.1| 24 SKITIILGRNGTGKTTLLKTVAG 46
                                      57889************777665 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.075
                            AAA_13 525 gkdkivviDDPvSSLDsnslfivfsliksr 554
                                        k +   +D P SSLD   +    sli+s 
  gi|557694323|ref|YP_008797377.1| 135 RKTELLLLDEPTSSLDFPNSVNFWSLIRSL 164
                                       4667789*********98888888888875 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 !   16.1   0.1   9.9e-06    0.0071      21      50 ..      23      52 ..      12      59 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.9e-06
                            AAA_29 21 lkgatlltGpsGsGKSTllDAiqalLvpak 50
                                       + +t++ G++G+GK+Tll  ++  + p+k
  gi|557694323|ref|YP_008797377.1| 23 SSKITIILGRNGTGKTTLLKTVAGFIKPRK 52
                                      3458**************987776666666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.6e-05     0.011       5      32 ..      24      51 ..      19     178 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.6e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldee 32
                                       +i+++ G  GtGKTtll++++   + +
  gi|557694323|ref|YP_008797377.1| 24 SKITIILGRNGTGKTTLLKTVAGFIKPR 51
                                      5799****************98776544 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   2.2e-05     0.016      22      49 ..      23      50 ..      12      72 .. 0.80
   2 ?   -0.5   0.0       1.1     8e+02     292     333 ..     114     146 ..      72     175 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                            AAA_15 22 seeltvliGkNnsGKSsilealdlFlnn 49
                                      s+++t++ G+N++GK+++l+    F++ 
  gi|557694323|ref|YP_008797377.1| 23 SSKITIILGRNGTGKTTLLKTVAGFIKP 50
                                      444****************988777765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.1
                            AAA_15 292 lplnknGsGvqrllllillileaekkdekeeknvilliEEPE 333
                                       l  +k ++G  ++l l++l+l++ +          ll++EP 
  gi|557694323|ref|YP_008797377.1| 114 LRKEKLSTGEAQILALSILLLRKTEL---------LLLDEPT 146
                                       55678899999999999998887776.........6667765 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 !   16.0   0.0   1.7e-05     0.012       2      36 ..      28      64 ..      27      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.7e-05
                                      EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSS CS
                               AAA  2 llyGppGtGKTllakavakelg..vefleisgsells 36
                                      ++ G  GtGKT+l k va  ++    +++++g ++++
  gi|557694323|ref|YP_008797377.1| 28 IILGRNGTGKTTLLKTVAGFIKprKGVIRLNGRDITN 64
                                      5789****************98545599999999984 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   2.1e-05     0.015       8      90 ..      22     126 ..      15     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.1e-05
                            AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkp...eeillvaftgrAakelrerlaal.gaeatTiHrlal... 77 
                                       +++k+ ++++  GtGKT++lk++   ++ ++gv     ++i+ + + +r    + ++  +l  ++ + iH++a    
  gi|557694323|ref|YP_008797377.1|  22 VSSKITIILGRNGTGKTTLLKTVAGFIKPRKGVIRlngRDITNLPPSERRIGYMPQQPIKLpYKPRDAIHYFAKifr 98 
                                       68899*****************9999888887643555888888888888888877553331445777888877666 PP

                            AAA_19  78 ...............ldfddlltealel 90 
                                                      l  ++l t ++++
  gi|557694323|ref|YP_008797377.1|  99 adpqpviekmrlepiLRKEKLSTGEAQI 126
                                       6666666666666654444444444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.4e-05     0.025      92     125 ..      17      50 ..       4      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                                       HHHHHCTTSEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  92 elkellkdktsvlvGqSGvGKStLinallpelel 125
                                       ++++ +++k+++++G  G GK+tL++++++  + 
  gi|557694323|ref|YP_008797377.1|  17 NVERFVSSKITIILGRNGTGKTTLLKTVAGFIKP 50 
                                       56778899******************99876555 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00019      0.14       2      43 ..      24      64 ..      23      85 .. 0.82
   2 ?    0.1   0.0         1   7.4e+02      61      84 ..     134     156 ..     104     166 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderd 43
                                      +ki +i G   +GKTtllk+++     +++ ++ +n  d ++
  gi|557694323|ref|YP_008797377.1| 24 SKITIILGRNGTGKTTLLKTVAGFI-KPRKGVIRLNGRDITN 64
                                      699****************998444.4788888888777655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1
                            AAA_14  61 keekktylflDEiqevpewekalk 84 
                                         +k+++l+lDE   + ++ + ++
  gi|557694323|ref|YP_008797377.1| 134 L-RKTELLLLDEPTSSLDFPNSVN 156
                                       2.478999***9888777766665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.1e-05     0.043      17      60 ..      25      68 ..      13      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.1e-05
                        Zeta_toxin 17 klillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPe 60
                                      k+ ++ G  G GK++l++ ++  ++++++v+rl++ d+ +l P 
  gi|557694323|ref|YP_008797377.1| 25 KITIILGRNGTGKTTLLKTVAGFIKPRKGVIRLNGRDITNLPPS 68
                                      6778889***************************9998887775 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   7.5e-05     0.054      23      54 ..      22      53 ..      16      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.5e-05
                              DLIC 23 PsgksvlvlGedgsGkttliaklqGveeekkG 54
                                       s+k  ++lG +g+Gkttl+  + G  +++kG
  gi|557694323|ref|YP_008797377.1| 22 VSSKITIILGRNGTGKTTLLKTVAGFIKPRKG 53
                                      688999********************999999 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 ?   12.3   0.1   0.00017      0.12       3      37 ..      28      63 ..      26      65 .. 0.88
   2 ?   -2.4   0.0       6.1   4.4e+03      78      78 ..     123     123 ..      86     167 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                                      EEE--SSSSHHHHHHHGGGGB.S--EEEEE--TT-- CS
                             AAA_5  3 lLvGppGtgKselaerlaaal.nreveyvqltrdtt 37
                                      +++G  GtgK++l + +a ++  r+ ++ ++ rd+t
  gi|557694323|ref|YP_008797377.1| 28 IILGRNGTGKTTLLKTVAGFIkPRKGVIRLNGRDIT 63
                                      899******************988888888888876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.1
                                       - CS
                             AAA_5  78 e 78 
                                       e
  gi|557694323|ref|YP_008797377.1| 123 E 123
                                       3 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   8.7e-05     0.063       3      21 ..      27      45 ..      25      53 .. 0.86
   2 ?   -2.6   0.0       6.4   4.6e+03      60      85 ..     116     141 ..      93     156 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.7e-05
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                       i+ G++G GKTtLl+ +a
  gi|557694323|ref|YP_008797377.1| 27 TIILGRNGTGKTTLLKTVA 45
                                      799*************998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.4
                                       CCCTS--SSS-CCHHHHCCSCCCEEE CS
                             NACHT  60 sqlpepaapvsevwavllelperlLl 85 
                                       ++ +  ++++    ++ll +++ lLl
  gi|557694323|ref|YP_008797377.1| 116 KEKLSTGEAQILALSILLLRKTELLL 141
                                       44444444444444455555555544 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00022      0.16       3      47 ..      28      74 ..      26      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                                      EEE--TTSSHHHHHHHHHHHH....G.GGEEEEEEEEE-------EE CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkss.g.vkvgGfyteevreggrrigF 47
                                      +i G+ G+GKtTl+k v+  +k + g ++++G    +    +rrig+
  gi|557694323|ref|YP_008797377.1| 28 IILGRNGTGKTTLLKTVAGFIKPRkGvIRLNGRDITNLPPSERRIGY 74
                                      678****************9986534246677777777777777776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00016      0.11       5      39 ..      27      58 ..      23      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                            AAA_24  5 iliyGpsgiGKTtlakelgpkplfidtekGlksld 39
                                       +i G +g+GKTtl+k+    + fi   kG+ +l+
  gi|557694323|ref|YP_008797377.1| 27 TIILGRNGTGKTTLLKTV---AGFIKPRKGVIRLN 58
                                      6799*************9...44444444444444 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   0.0   0.00023      0.17      31     102 ..       5      72 ..       2      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                            DUF815  31 vgidkqkealventeqfleglpannvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklvell 102
                                        g++ +++ +  n+e+f++ +     ++ G  GtGK +l+k++   ++ ++  +i ++ +d+++lp   + +
  gi|557694323|ref|YP_008797377.1|   5 EGLEVERNGFRINVERFVSSKI---TIILGRNGTGKTTLLKTVAGFIKPRK-GVIRLNGRDITNLPPSERRI 72 
                                       5888899999999999998665...6899************9987666554.78888888888888665555 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   0.00029      0.21     127     157 ..      23      52 ..       9      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                             T2SSE 127 rerglilvsGgTgsGKttllyallkeinksd 157
                                       ++ ++ ++ G  g+GKttll ++  +i+ ++
  gi|557694323|ref|YP_008797377.1|  23 SS-KITIILGRNGTGKTTLLKTVAGFIKPRK 52 
                                       34.455667***************9999885 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   0.2   0.00048      0.35       2      30 ..      25      53 ..      24      64 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00048
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegk 30
                                      ++++++G +G+GKTt l  +a  +k ++ 
  gi|557694323|ref|YP_008797377.1| 25 KITIILGRNGTGKTTLLKTVAGFIKPRKG 53
                                      57899************999988887665 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 ?    9.4   0.6     0.001      0.75       2      21 ..      26      45 ..      25      55 .. 0.85
   2 ?   -0.9   0.0       1.5   1.1e+03     131     153 ..     118     140 ..     105     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.001
                                      EEEEEESTTCCHHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhll 21
                                      +t++ G  G+GKTtLl+++ 
  gi|557694323|ref|YP_008797377.1| 26 ITIILGRNGTGKTTLLKTVA 45
                                      6999************9985 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHTSSEEEEE-HHHH CS
                              cobW 131 ieekaedqlaaadllvlnKtDll 153
                                       + +++e q+ a ++l+l Kt+ll
  gi|557694323|ref|YP_008797377.1| 118 KLSTGEAQILALSILLLRKTELL 140
                                       5567889999999******9986 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 ?    9.4   0.5   0.00055      0.39     244     264 ..      24      44 ..      21      50 .. 0.89
   2 ?   -1.3   0.1      0.98     7e+02     337     352 ..     133     148 ..     120     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00055
                                       SSEEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 244 kGvtlIvGggfhGKsTLLeAl 264
                                        ++t+I G++  GK+TLL+ +
  gi|557694323|ref|YP_008797377.1|  24 SKITIILGRNGTGKTTLLKTV 44 
                                       68****************986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.98
                                       HHTT-SEEEEEGGGS- CS
                        ABC_ATPase 337 leagakllLiDEDtsA 352
                                       l ++++llL+DE ts 
  gi|557694323|ref|YP_008797377.1| 133 LLRKTELLLLDEPTSS 148
                                       55789*******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); 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: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1536.94
//
Query:       gi|557694324|ref|YP_008797378.1|  [L=231]
Description: sulfate ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.036   14.0   1.6       0.68    9.9   0.2    2.8  2  DUF4514       Domain of unknown function (DUF4514)
       0.17   11.6  31.8      0.013   15.3  25.5    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> DUF4514  Domain of unknown function (DUF4514)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1     0.019   1.7e+02      23      42 ..      82     101 ..      77     104 .. 0.87
   2 ?    9.9   0.2   7.6e-05      0.68      13      34 ..     199     220 ..     190     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.019
                           DUF4514  23 aiiGtalGvaisAgFLALKi 42 
                                       ai  ta+G ++   FLAL i
  gi|557694324|ref|YP_008797378.1|  82 AIPHTAIGLMVLPLFLALNI 101
                                       66679*************98 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 7.6e-05
                           DUF4514  13 sagaeidiKYaiiGtalGvais 34 
                                       + gae+ + Ya+i +alG++ s
  gi|557694324|ref|YP_008797378.1| 199 TGGAEVAVPYAVIVAALGMVFS 220
                                       679***************9987 PP

>> 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 ?   -0.1   0.4     0.075   6.7e+02     157     178 ..       8      29 ..       3      31 .. 0.75
   2 ?   15.3  25.5   1.4e-06     0.013       2     179 ..      55     226 ..      54     229 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.075
                      BPD_transp_1 157 gvlalviavlllnlvadilqrl 178
                                       +vla++i++++++++  +l++ 
  gi|557694324|ref|YP_008797378.1|   8 IVLAAAIMYVAVLFLPPLLYQR 29 
                                       6788888888888888888775 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.4e-06
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrs 78 
                                       ++l++l++++ + ++  +++p+  +  ++P+ +++++++ +f +   + +++l+vii++++ ++p+ +  ++++l++
  gi|557694324|ref|YP_008797378.1|  55 FPLAVLLGFYVSARGLAVVLPFLMFATAIPHTAIGLMVLPLF-LALNIVDTWLAVIITMMIVSLPLGVGSVASGLSA 130
                                       6999*****************************999988655.4457778*************************** PP

                      BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgydysei 153
                                         k l e+  +lG+++ + ++ + ++++   ++ +++l + +++ +  +l+++  +++  +g  ++e  +       
  gi|557694324|ref|YP_008797378.1| 131 TVKALDEFLSVLGVGELRNIW-IHMRAMGLGWAVSFMLMWLRAFSELGALLIVS-YTPstVGVYMFELFQT------ 199
                                       *********************.999********************999999888.2222333333333332...... PP

                      BPD_transp_1 154 s.nggvlalviavlllnlvadilqrll 179
                                         + +++ ++++v++l  v+  l  ++
  gi|557694324|ref|YP_008797378.1| 200 GgAEVAVPYAVIVAALGMVFSGLLYII 226
                                       244566666666666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); 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):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1608.79
//
Query:       gi|557694325|ref|YP_008797379.1|  [L=295]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   28.3   0.0    1.4e-05   25.0   0.0    2.1  1  SBP_bac_11  Bacterial extracellular solute-binding protein


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 !   25.0   0.0   7.6e-10   1.4e-05      24     198 ..      62     249 ..      43     268 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 7.6e-10
                                       H---EEEEESSHHHHHHHHHHH..-SEEEESSH.HHHHHHHHGGGGGGG-EEEEEEEEEEEESTT-TT---SHHHHH CS
                        SBP_bac_11  24 tgvkvevsaggsgklarqiadgarpDvwipassawlellaaaglvqaesavplassplviavpkgnpkkikgwadLl 100
                                       t   ++++  gs ++a+ i++g+ pD+++  +s+      ++gl    ++ +l + +l ++ +kg      ++++++
  gi|557694325|ref|YP_008797379.1|  62 TTEPLNIQVYGSVAAANLIKSGRTPDLYLTVDSEL-----KHGLNY-RKELTLGYFRLTFVCQKGI----NSLDAVK 128
                                       56667888899999999999999999999999854.....555555.6788899999999999986....5555555 PP

                                       HSS--EEEE--T-TTTTHH.HHHHG..GG--.HHHHHHHHHTEEEEESSH.......................HHHH CS
                        SBP_bac_11 101 kpglklavadPttspsGlaalalle..aaga.qellkalekkvvklgess.......................rqll 151
                                          +k+++adP+++p G++ala+l   a+++ +el+++l+++     + s                       + + 
  gi|557694325|ref|YP_008797379.1| 129 --TVKIGLADPNQAPIGYRALAALYllASERfPELIDELQQSLNIRYQESgdtlvmelseisasgrfylrpnlDGAG 203
                                       ..57********************95444559667777777644222222235688888888887777777777777 PP

                                       HHHHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--....EEEEEE CS
                        SBP_bac_11 152 taveageadagivyeseakaaengdkleavylpeglnl.dpldypaav 198
                                       t +eag +d +++    ++ +  ++   +++ p+ ln+ +  d p+++
  gi|557694325|ref|YP_008797379.1| 204 TLLEAGGVDCIFAHSPFIIVRNYSQTYNIIEMPPHLNFeN--DPPITI 249
                                       7799999999999888887777788888888888888744..444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2102.51
//
Query:       gi|557694326|ref|YP_008797380.1|  [L=182]
Description: molybdate transport system regulatory protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   55.0   0.2    1.7e-14   53.9   0.1    1.7  2  TOBE          TOBE domain
    1.7e-05   24.7   0.1    3.3e-05   23.8   0.1    1.5  1  HTH_29        Winged helix-turn helix
    0.00011   22.1   0.0     0.0002   21.3   0.0    1.5  1  HTH_1         Bacterial regulatory helix-turn-helix protein, 
     0.0054   16.3   0.0     0.0076   15.8   0.0    1.2  1  DUF2764       Protein of unknown function (DUF2764)
  ------ inclusion threshold ------
      0.037   13.5   0.0      0.067   12.6   0.0    1.4  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I
      0.038   14.2   0.0      0.072   13.3   0.0    1.4  1  TOBE_2        TOBE domain
       0.12   12.6   0.0       0.18   11.9   0.0    1.4  1  HTH_28        Helix-turn-helix domain
       0.14   11.3   0.0       0.18   10.9   0.0    1.2  1  LCAT          Lecithin:cholesterol acyltransferase


Domain annotation for each model (and alignments):
>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.4   5.4e+03      21      31 ..      11      21 ..      10      24 .. 0.78
   2 !   53.9   0.1   7.5e-18   1.7e-14       2      62 ..     117     177 ..     116     179 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.4
                              TOBE 21 veVrvdlggga 31
                                      ++V+v l+g++
  gi|557694326|ref|YP_008797380.1| 11 ALVTVNLEGKT 21
                                      67999999987 PP

  == domain 2  score: 53.9 bits;  conditional E-value: 7.5e-18
                              TOBE   2 sarNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaakv 62 
                                       sarN+l+g+V++v+++++ ++V vdl+g++++ + +t++s  +L+++pG++Vf+ +ka+++
  gi|557694326|ref|YP_008797380.1| 117 SARNILTGHVKHVTEGDVISMVSVDLDGHQEVKSIITTDSLKRLKISPGDPVFIILKATET 177
                                       9*********************************************************987 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   1.5e-08   3.3e-05       3      55 ..      30      81 ..      28      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.5e-08
                            HTH_29  3 qallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsgrprn 55
                                      + l +++++ s +s ++ ++g+s+rt  +wlk+ e +  ++   + r+gr++ 
  gi|557694326|ref|YP_008797380.1| 30 ELLENINRASS-ISSACLQMGISYRTAVNWLKDIERKAGGKPVQSIRGGRNKG 81
                                      56789999997.*********************99776445555666777665 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 !   21.3   0.0   8.9e-08    0.0002       2      59 ..      27      89 ..      26      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.9e-08
                                      HHHHHHHHHHHHSSHHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEE..ESSSE...EEE-HHH CS
                             HTH_1  2 rqlrlfvavaeegsftrAAeeLglsqpavsrqikrLEeelgvpLfe..Rtgrg...lrLTeaG 59
                                      ++++l++ + ++ s++ A+ ++g+s+ ++   +k+ E+  g + ++  R gr+   + LTe G
  gi|557694326|ref|YP_008797380.1| 27 ERFELLENINRASSISSACLQMGISYRTAVNWLKDIERKAGGKPVQsiRGGRNkglTLLTELG 89
                                      6899*************************************9988877766645578888877 PP

>> DUF2764  Protein of unknown function (DUF2764)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   3.4e-06    0.0076     121     181 ..      91     155 ..      80     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.4e-06
                           DUF2764 121 rLaalyyeyamkcgnkFlsewFelnlnlrnilaaitarklgldvsnvi....vgenevaealrts 181
                                       +L+  yy      +  F++++ el l  rnil++    + + dv++++     g++ev+  + t 
  gi|557694326|ref|YP_008797380.1|  91 KLLEAYYSAQSIHRPGFIKSFIELRLSARNILTGHVKHVTEGDVISMVsvdlDGHQEVKSIITTD 155
                                       78999**9999999********************************9987777999999888775 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 ?   12.6   0.0     3e-05     0.067      27      51 ..      39      62 ..      35      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                      HTH_Tnp_ISL3 27 srsvkavArqlgvSwtTVwrildry 51
                                      s s+++++ q+g+S +T  ++l+++
  gi|557694326|ref|YP_008797380.1| 39 S-SISSACLQMGISYRTAVNWLKDI 62
                                      5.********************985 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-05     0.072       8      72 ..     114     176 ..     110     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                            TOBE_2   8 lrlaaagganglsGtVedveylGsstryv.velaggqlvvvrqpnadr.dsalapGdtVelswdpdd 72 
                                       lrl   +++n l+G+V++v+  G+ + +v v+l+g q+v+      +  +  + pGd V + +++  
  gi|557694326|ref|YP_008797380.1| 114 LRL---SARNILTGHVKHVT-EGDVISMVsVDLDGHQEVKSIITTDSLkRLKISPGDPVFIILKATE 176
                                       566...67789*******98.699999999*********9988888887899*******99777665 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.3e-05      0.18      14      37 ..      40      63 ..      27      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.3e-05
                            HTH_28 14 svreaArelgisrrtvyrWikrye 37
                                      s++ a+ ++gis+rt   W+k  e
  gi|557694326|ref|YP_008797380.1| 40 SISSACLQMGISYRTAVNWLKDIE 63
                                      8999****************9866 PP

>> LCAT  Lecithin:cholesterol acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     8e-05      0.18     167     235 ..      69     148 ..      66     171 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8e-05
                              LCAT 167 kavkallsGenkgipvlseltlrvlsksfssslsllP...........kgeevlwkdvawpsdeiliqtpsinlteg 232
                                       k+v+++  G nkg+ +l el  ++l+++ s+ +   P            + ++l ++v++ ++  +i+  s+ l+ +
  gi|557694326|ref|YP_008797380.1|  69 KPVQSIRGGRNKGLTLLTELGHKLLEAYYSAQSIHRPgfiksfielrlSARNILTGHVKHVTEGDVISMVSVDLDGH 145
                                       799****************************9777775555555566677888888888887777777777666655 PP

                              LCAT 233 alv 235
                                       + v
  gi|557694326|ref|YP_008797380.1| 146 QEV 148
                                       544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1316.77
//
Query:       gi|557694327|ref|YP_008797381.1|  [L=350]
Description: aspartate-semialdehyde dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-34  119.9   0.0    2.1e-34  119.2   0.0    1.4  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    1.5e-31  109.3   0.0    3.2e-31  108.3   0.0    1.6  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
     0.0012   18.5   0.2       0.03   13.9   0.0    2.4  2  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
     0.0048   17.7   0.0      0.013   16.3   0.0    1.7  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
  ------ inclusion threshold ------
      0.024   15.4   0.0      0.045   14.5   0.0    1.4  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.0   5.8e-38   2.1e-34       1     183 [.     156     328 ..     156     329 .. 0.91

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 5.8e-38
                                       HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHH CS
                   Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetree 77 
                                       L+PL ++ +++++viv+t+qavSGaG+                    pgv ++ i+gN+ipyi +ee k e+et+++
  gi|557694327|ref|YP_008797381.1| 156 LQPLKQH-LGVKKVIVTTMQAVSGAGY--------------------PGVASLSILGNVIPYISGEERKVETETAKI 211
                                       89****8.88*****************....................9***************************** PP

                                       HHHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCS............TTEEEEESSH CS
                   Semialdhyde_dhC  78 lkavaetkkileftekvsatcvrVPvlrGhseavtiklklkdveveeveellaaa............pevkvvvnee 142
                                       l+ + + +  ++  e v atc+rVP l+Gh+e+++++++ k+++ e+v ella+             p   +vv+ e
  gi|557694327|ref|YP_008797381.1| 212 LGRYGDGRFTHDSVE-VHATCTRVPTLDGHMESIYLETA-KPADEETVAELLAEYvslpqelnlptaPARPIVVRRE 286
                                       ******999999887.**********************7.555555555555555555*********9999999999 PP

                                       CHHSSHHHHTTC....SSSEEEEEEEEETTCTTEEEEEEEEETTT CS
                   Semialdhyde_dhC 143 edrPtpaavagg....tnsvsVGRirkdemgdeglklvvvgDNll 183
                                        drP+++ +++     ++svsVGRir++   + ++ ++++++Nl+
  gi|557694327|ref|YP_008797381.1| 287 LDRPQTRIDVDAgtvpGMSVSVGRIRVNG--E-KVRFISLSHNLI 328
                                       *********9988999***********99..4.499********8 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 !  108.3   0.0     9e-35   3.2e-31       2     119 ..       6     126 ..       5     128 .. 0.97
   2 ?   -3.2   0.0       3.1   1.1e+04      11      38 ..     150     178 ..     149     192 .. 0.68

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 9e-35
                                       EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG.....GGTTTECEBEEEGGGGGCTT-SEEEE- CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk.....aleegkdlkvedvdeeelkevdivfla 73 
                                       vai+GatG+vGq  +r+L +hp++ +++l+++++  G+k+ eav+      ++e+++++v ++d++++ ++d+vf++
  gi|557694327|ref|YP_008797381.1|   6 VAILGATGMVGQHYIRMLYRHPWFRITALTGKES-VGRKYVEAVRgeapePPKEIAEMEVLPTDPKKV-DADFVFSC 80 
                                       9******************************999.*********99*99999**************99.9******* PP

                                       SCHHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                    Semialdhyde_dh  74 lpagvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                       lp ++++e +pk+aeag+ v++ ++++R+++d+++++pe+n ++++
  gi|557694327|ref|YP_008797381.1|  81 LPTEAAREAEPKFAEAGFPVFSDAAAYRMEEDVPLIVPEINHDHLN 126
                                       *******************************************986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.1
                                       HHHHH.HHHHHCTSSEEEEEEEESTTTTT CS
                    Semialdhyde_dh  11 vGqel.lrlLeehpevelvvllsssrsaG 38 
                                       vG +l l+ L++h  v+ v +++ +   G
  gi|557694327|ref|YP_008797381.1| 150 VGLVLpLQPLKQHLGVKKVIVTTMQAVSG 178
                                       56666677788888888887777666444 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 ?    2.2   0.0     0.034   1.2e+02       5      25 ..     156     176 ..     152     179 .. 0.87
   2 !   13.9   0.0   8.5e-06      0.03      71     110 ..     226     265 ..     222     314 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.034
                                       HHHHHHHHEEEEEEEEEEEEC CS
                           Gp_dh_C   5 akvlndkfgikkglmttvhay 25 
                                       ++ l++++g+kk+++tt  a+
  gi|557694327|ref|YP_008797381.1| 156 LQPLKQHLGVKKVIVTTMQAV 176
                                       5789*************9887 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 8.5e-06
                                       TEEEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHH CS
                           Gp_dh_C  71 kldglAvrVPtpnvsvvdlvvelekevtveevnaalkeaa 110
                                       +++++  rVPt ++++ ++ +e++k++  e v ++l e  
  gi|557694327|ref|YP_008797381.1| 226 EVHATCTRVPTLDGHMESIYLETAKPADEETVAELLAEYV 265
                                       678999****************************998875 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 !   16.3   0.0   3.6e-06     0.013       3      91 ..       6     102 ..       4     104 .. 0.82
   2 ?   -2.5   0.0       2.4   8.8e+03      64      81 ..     138     155 ..     125     176 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.6e-06
                                       EEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH.HHHTTHE....EESSHHHHHTCT...TESEEEE-S CS
                      GFO_IDH_MocA   3 vaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeav.aesfgve....aysdleelladp...eidavivat 70 
                                       vai Ga G++g++++r l ++ ++ +++al  +++   + v a + +++      +++e l++dp   ++d+v+ + 
  gi|557694327|ref|YP_008797381.1|   6 VAILGAtGMVGQHYIRMLYRH-PWFRITALTGKESVGRKYVeAVRGEAPeppkEIAEMEVLPTDPkkvDADFVFSCL 81 
                                       89****8888*****888888.***99999998887777664222233355788999********8777999999** PP

                                       -GGGHHHHHHHHHHTT-EEEE CS
                      GFO_IDH_MocA  71 pngtheelakaaleagkhvll 91 
                                       p++  +e + +++eag  v+ 
  gi|557694327|ref|YP_008797381.1|  82 PTEAAREAEPKFAEAGFPVFS 102
                                       ******************997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                                       SEEEE-S-GGGHHHHHHH CS
                      GFO_IDH_MocA  64 davivatpngtheelaka 81 
                                       + +iv+tpn+t   l++ 
  gi|557694327|ref|YP_008797381.1| 138 EGYIVTTPNCTTVGLVLP 155
                                       557889999876666654 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 ?   14.5   0.0   1.3e-05     0.045       1      37 [.       6      41 ..       6      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                                      EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEESSTHH CS
                   DXP_reductoisom  1 vviLGsTGSIGtqtLdvieenpdkfevvalaagsnve 37
                                      v+iLG+TG +G+  + ++ ++p  f+++al+++++v 
  gi|557694327|ref|YP_008797381.1|  6 VAILGATGMVGQHYIRMLYRHP-WFRITALTGKESVG 41
                                      79********************.9*******988775 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:                      291  (0.0162307); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2598.98
//
Query:       gi|557694328|ref|YP_008797382.1|  [L=262]
Description: fructose-bisphosphate aldolase, class I [Candidatus Caldiarchaeum subterraneum]
Scores for 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-42  143.5   0.0      9e-42  143.3   0.0    1.0  1  DeoC      DeoC/LacD family aldolase
     0.0018   17.6   0.0        1.1    8.6   0.0    2.3  2  TMP-TENI  Thiamine monophosphate synthase
  ------ inclusion threshold ------
       0.13   11.9   0.0       0.19   11.4   0.0    1.2  1  DUF4038   Protein of unknown function (DUF4038)


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.3   0.0   1.5e-45     9e-42       3     235 .]      20     233 ..      18     233 .. 0.95

  Alignments for each domain:
  == domain 1  score: 143.3 bits;  conditional E-value: 1.5e-45
                                       EEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEE CS
                              DeoC   3 ilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrd 79 
                                        +++D++++++++++       e+++ lv ++ ++g  a l ++gv +s ++ ++  ++++++++++t+l++  +r+
  gi|557694328|ref|YP_008797382.1|  20 CIPLDHGTSLGPVKGL------ENIEDLVYRLESAGVTALLAHKGVFRSLKRPLK--TGTIMHMSASTQLSTHYNRK 88 
                                       5899************......8*******************************9..******************** PP

                                       EETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTTCHHHHHHHH CS
                              DeoC  80 vdevasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdekvdpdlvaeA 156
                                       v+  asveea++lG dav+v++++   g  ++  +l+ ++ v+ ac+e++ pli+++y+r+e+ik+ + dp ++ + 
  gi|557694328|ref|YP_008797382.1|  89 VL-IASVEEALRLGVDAVSVHINI---GGVDDDIMLEHLGLVADACDEWQVPLIAMMYPRGENIKNAS-DPAVISHV 160
                                       **.*********************...99999************************************.******** PP

                                       HHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSSTEEEEETTS...SHHHHHHHHHHHHHHHTHCEEEESH CS
                              DeoC 157 arvsaelGaDiiKvevpkevvnateedaevfkdvikaapvpgvvlsGGv...seedfletvedAvkeagasGvlsGR 230
                                       arv+aelGaDi+K+++p       +  +++++ v++++pvp vv +GG+    +ed+l+ +  +v + g +G+  GR
  gi|557694328|ref|YP_008797382.1| 161 ARVGAELGADIVKTPMP-------SANVQEIEVVTRSCPVP-VVAAGGPkmeRDEDVLRLAYASV-AGGCMGITFGR 228
                                       *****************.......889999***********.*******7777777777777777.6666******* PP

                                       HHHTT CS
                              DeoC 231 aifqk 235
                                       ++fq+
  gi|557694328|ref|YP_008797382.1| 229 NVFQH 233
                                       ***97 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    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      12      61 ..      87     138 ..      78     140 .. 0.89
   2 !    6.8   0.1   0.00065       3.9     135     176 ..     177     218 ..     158     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00018
                          TMP-TENI  12 neellevveealkggvtlvqlRek..eldarellelaeklaalcrkygvpli 61 
                                       ++ l++ veeal+ gv++v +       d+  +le+   +a++c++ +vpli
  gi|557694328|ref|YP_008797382.1|  87 RKVLIASVEEALRLGVDAVSVHINigGVDDDIMLEHLGLVADACDEWQVPLI 138
                                       567899**********999998887789**********************98 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00065
                          TMP-TENI 135 eplgleglkelaealeiPvvaiGGitlenvaevleagadgva 176
                                       + ++++ ++ + +++ +Pvva GG ++e+ ++vl+   ++va
  gi|557694328|ref|YP_008797382.1| 177 PSANVQEIEVVTRSCPVPVVAAGGPKMERDEDVLRLAYASVA 218
                                       6778889999999999***********999999876655555 PP

>> DUF4038  Protein of unknown function (DUF4038)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.1e-05      0.19     244     276 ..     205     236 ..     196     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.1e-05
                                       -HHHHHHHHHHHHHCT-SEEEE-BHHHHTT-BT CS
                           DUF4038 244 taedvRraaywavlaGaaGvtYGangiwqmyee 276
                                        +edv r ay +v +G +G+t+G n ++q +++
  gi|557694328|ref|YP_008797382.1| 205 RDEDVLRLAYASVAGGCMGITFGRN-VFQHRSP 236
                                       589999*****************98.6665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2063.54
//
Query:       gi|557694329|ref|YP_008797383.1|  [L=333]
Description: 3-dehydroquinate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-105  351.0   2.5   7.2e-105  350.8   2.5    1.0  1  DHQS      3-dehydroquinate synthase II
  ------ inclusion threshold ------
      0.017   14.7   0.0      0.032   13.7   0.0    1.4  1  Hint      Hint module


Domain annotation for each model (and alignments):
>> DHQS  3-dehydroquinate synthase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  350.8   2.5    8e-109  7.2e-105      46     352 .]      35     333 .]       2     333 .] 0.91

  Alignments for each domain:
  == domain 1  score: 350.8 bits;  conditional E-value: 8e-109
                              DHQS  46 ikviakeeddavlvgkddleklkkakkvaalveikskeeeeeaaeaake.adyvivelkdwtvIPlEnliAalqgee 121
                                       +        ++++ ++d + +  ++k+++  v iks++++e++ae+a++ ad v++ + dw++IP+Enl+A ++g+ 
  gi|557694329|ref|YP_008797383.1|  35 V--------ETYVPTQDGYVRHGEKKATVPRVVIKSPKDLEHVAELARSgADEVVIATGDWKIIPVENLLAMIEGTG 103
                                       3........3344444433344445899999***********999998879************************** PP

                              DHQS 122 tkiiaavksaeeAklaletLEkGadgvllktedveeikelaelleeaeeekleLkeaevtkveevgmgdRvcvDtcs 198
                                        +i+a+v++++eA++++++LEkG++g++ k+ + +e++ l el+++ +  ++ L+ea v++v++vg+gdR+cvDt++
  gi|557694329|ref|YP_008797383.1| 104 CRILAEVSNVSEAEIFINILEKGVNGIVAKPANEQELRILLELVKKPA--EIPLVEAVVEEVRPVGVGDRACVDTVT 178
                                       ********************************************8886..79************************* PP

                              DHQS 199 lmkegeGmLvGsssrglfLvhsEtlespYvasRPFRVNAGavhaYvlvpggkTkYLseLkaGdevlvvdkkGktrea 275
                                       +m+ geG+LvGs+++ +fL+h E++ s++ ++RPFRVNAGavh+Yvl+p+g+T+YLseL+aGd+vl+v+++G+tr a
  gi|557694329|ref|YP_008797383.1| 179 MMEIGEGLLVGSHASMFFLIHNEAVGSSFTSPRPFRVNAGAVHSYVLMPDGNTRYLSELEAGDRVLIVSRTGRTRIA 255
                                       ***************************************************************************** PP

                              DHQS 276 vvGRvKiEkRPlllveaeaegkkvstilQnaetirlvtedgkaisvteLkeGdevlvylee.kaRHfGikieEtiiE 351
                                        +GRvKiE+RPl lv+a++++    + +Q+aetir +t++g+ ++vteLk+ d++l ++++ ++RHfG+++eEt++E
  gi|557694329|ref|YP_008797383.1| 256 SIGRVKIERRPLRLVKARYNDMVGAVTVQDAETIRFITPSGELVPVTELKKNDKILCHISQtRGRHFGMAVEETVVE 332
                                       *********************************************************9865389************* PP

                              DHQS 352 k 352
                                       k
  gi|557694329|ref|YP_008797383.1| 333 K 333
                                       8 PP

>> Hint  Hint module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.5e-06     0.032      17      47 ..     222     252 ..     219     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.5e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              Hint  17 stvtvedgeqkslseLepGdkVlavdesgev 47 
                                       s v + dg+++ lseLe Gd+Vl v+ +g++
  gi|557694329|ref|YP_008797383.1| 222 SYVLMPDGNTRYLSELEAGDRVLIVSRTGRT 252
                                       789***********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2697.70
//
Query:       gi|557694330|ref|YP_008797384.1|  [L=230]
Description: 3-dehydroquinate dehydratase I [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-47  162.2   0.0    2.7e-47  162.0   0.0    1.0  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 !  162.0   0.0   1.5e-51   2.7e-47       1     226 [.       7     217 ..       7     219 .. 0.93

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 1.5e-51
                                       EEEE--SSHHHHHHHHHHHTT.S-SEEEEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HH CS
                       DHquinase_I   1 cvpitgktleeilaelesgke.kaDlvElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrksee 76 
                                       cv++ g++ e++la +++g e +aDl+E+RlDl       ++v++ +++lr   +  l++tlr+  egg+  +   e
  gi|557694330|ref|YP_008797384.1|   7 CVSVYGENEENLLANIRRGFEkGADLAEVRLDLS-GY---SSVESLVAKLRPF-TDRLVLTLRPVGEGGKS-SLPAE 77 
                                       9******************999**********55.44...67999*****996.558*************5.9**** PP

                                       HHHHHHHHHHHCT-SEEEEEGG-.HHGHHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEE CS
                       DHquinase_I  77 eylellrtaielgadyvDvElteapeeskkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKia 153
                                       +++++lr++++ g++y+D+El+ +    k+  +++ r +g+kvI+S+h fe+tp++ +l +  e++ + g D++K++
  gi|557694330|ref|YP_008797384.1|  78 QRVKILRRLADIGPAYIDLELS-TL---KQHPADDFRVAGVKVIASWHSFESTPDDGSLNNFCEECLKQG-DVAKVV 149
                                       *********************4.55...3678899999********************************.****** PP

                                       E--SSHHHHHHHHHHHHHHHHHT-SS-EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHH CS
                       DHquinase_I 154 vmaksieDvlrllsltseakeekdeaplIamamGelGkiSRilgevfGspvtfasleeakasapGqltarelr 226
                                       +  +  +D++r+ sl+     +++++ lIa++mGe+G i+Ril+ +  +p+ +a+l++a ++apGqlt++e+ 
  gi|557694330|ref|YP_008797384.1| 150 TFSNGPRDNIRVISLYA----RYPSTRLIAFCMGEQGWITRILSMAADAPIAYAALGDA-KTAPGQLTVEEML 217
                                       ****************4....46779*******************************99.899********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1693.97
//
Query:       gi|557694331|ref|YP_008797385.1|  [L=260]
Description: shikimate 5-dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   61.6   0.0    3.6e-16   59.2   0.0    2.0  2  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
    1.1e-10   41.1   0.2    2.2e-10   40.1   0.2    1.5  1  SDH_C            Shikimate 5'-dehydrogenase C-terminal domain
  ------ inclusion threshold ------
      0.091   13.0   0.0       0.89    9.8   0.0    2.2  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


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 !   59.2   0.0     6e-20   3.6e-16      14      83 .]       1      71 [.       1      71 [. 0.97
   2 ?   -0.4   0.0      0.23   1.4e+03      11      38 ..     183     208 ..     179     225 .. 0.65

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 6e-20
                                      HHHHHHHHCTS.SEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT--SEE CS
                    Shikimate_dh_N 14 ihnaafkalgl.ngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigAvNti 83
                                      + naa++++g+ n+ y+a++v++ +l+ +v++++  ++ G+nvTiP+K ++i++ld+l+++A+ ++AvN++
  gi|557694331|ref|YP_008797385.1|  1 MMNAALQKQGIdNILYIAVDVHPRDLRGFVSSAHLMNFIGFNVTIPHKVSIIKHLDRLDRSAELVEAVNVV 71
                                      6799*******7789******************************************************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHCTS.SEEEEEEE-SCCTH CS
                    Shikimate_dh_N  11 SPaihnaafkalgl.ngsyeafeveedel 38 
                                       SP+  + + k+l + +++y+++e++   l
  gi|557694331|ref|YP_008797385.1| 183 SPLSAKLLHKKLTVfDMVYNPVETK---L 208
                                       6666666666655449999999998...3 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 !   40.1   0.2   3.6e-14   2.2e-10       1      31 []     222     252 ..     222     252 .. 0.98

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 3.6e-14
                                       HHHHHHHHHHHHHHHHHS----HHHHHHHHH CS
                             SDH_C   1 GLgMLveQgaeqFelWTGrepPvevMreall 31 
                                       GL+MLv Qgae+ ++W G+e +++ M++a+l
  gi|557694331|ref|YP_008797385.1| 222 GLDMLVAQGAEALKIWLGIEGDRKTMKKAAL 252
                                       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 ?    9.8   0.0   0.00015      0.89       2      78 ..     101     173 ..     100     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00015
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-SS CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnlsp 78 
                                       +++G G+ ++a+a  l+r++    e++ a+r k+ +++    a+++ + ++ +    ++   a++++ ++l+vn++p
  gi|557694331|ref|YP_008797385.1| 101 VVLGVGGAARAAAVALHRKGYG--ELVFAGRRKSTMDEFMRFARRKGLPTRVVKLGSKPF--AEAVERAELLVNATP 173
                                       79****************9865..****************99988888888888888775..777888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1963.67
//
Query:       gi|557694332|ref|YP_008797386.1|  [L=287]
Description: shikimate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   41.1   3.2    1.6e-10   41.1   3.2    3.0  3  GHMP_kinases_N  GHMP kinases N terminal domain
    0.00036   20.8   0.3     0.0011   19.3   0.3    1.8  1  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
       0.45   10.8   5.0       0.47   10.8   0.1    2.9  3  DUF1269         Protein of unknown function (DUF1269)


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 ?    0.0   0.0      0.17     1e+03      19      46 ..      12      40 ..       7      52 .. 0.56
   2 !   41.1   3.2   2.6e-14   1.6e-10       2      66 .]      77     145 ..      76     145 .. 0.82
   3 ?   -3.3   2.6       1.8   1.1e+04      20      20 ..     221     221 ..     194     254 .. 0.61

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.17
                                      HHHHHHHHHHHHHTTEHHHH.HHHHHHHH CS
                    GHMP_kinases_N 19 AlavalvaAllallglslee.aklaleae 46
                                      +++ a+ + + a+lg++l++ a+l  + e
  gi|557694332|ref|YP_008797386.1| 12 SIVNAISTGFGAALGIDLQTeAELETTDE 40
                                      45556666666666766633355554444 PP

  == domain 2  score: 41.1 bits;  conditional E-value: 2.6e-14
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH...HHHHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl...eeaklaleaerlaqggngsggDv.aasvyGg 66 
                                       i+++s+iPv+ GL SS+++ava++ A+l++lg ++   e+++  +ea  l ++  ++  D+ aa+++Gg
  gi|557694332|ref|YP_008797386.1|  77 IRTYSNIPVAVGLKSSSSAAVAIANAFLDALGEKMsadEMLRNVAEASILSGTSITGALDDaAACMLGG 145
                                       6789***************************98874323366677777777777788777769999998 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.8
                                       H CS
                    GHMP_kinases_N  20 l 20 
                                       l
  gi|557694332|ref|YP_008797386.1| 221 L 221
                                       2 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 !   19.3   0.3   1.8e-07    0.0011      36      76 ..     225     261 ..     208     269 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.8e-07
                    GHMP_kinases_C  36 leellealselGalgaklsGaGgGptvfalfkdkdeaeqva 76 
                                       +e +++al ++Ga++a+lsG+  Gp+v+a++  ++ +++va
  gi|557694332|ref|YP_008797386.1| 225 IEPAVNAL-RAGACAAGLSGT--GPAVAAIV-AEEWVDNVA 261
                                       66677776.9***********..*******9.555555555 PP

>> DUF1269  Protein of unknown function (DUF1269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2       2.4   1.4e+04      23      33 ..      16      26 ..       8      34 .. 0.61
   2 ?    1.6   0.1     0.055   3.3e+02      28      56 ..      87     115 ..      70     139 .. 0.74
   3 ?   10.8   0.1   7.9e-05      0.47      52      89 ..     241     278 ..     186     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.4
                           DUF1269 23 avGAaaGAlvg 33
                                      a+ +++GA+ g
  gi|557694332|ref|YP_008797386.1| 16 AISTGFGAALG 26
                                      34445555444 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.055
                           DUF1269  28 aGAlvgalsdvgidddflkelgeklkpgt 56 
                                       +G  +++ + v+i + fl+ lgek+++++
  gi|557694332|ref|YP_008797386.1|  87 VGLKSSSSAAVAIANAFLDALGEKMSADE 115
                                       45455566677777777777777776654 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 7.9e-05
                           DUF1269  52 lkpgtsalfllvekatvdkvlealaklggkvlrtslsk 89 
                                       l+    a+ ++v + +vd+v++ ++ ++gk+++ts+++
  gi|557694332|ref|YP_008797386.1| 241 LSGTGPAVAAIVAEEWVDNVADVFSAYEGKIVKTSVNR 278
                                       5556679999************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2237.64
//
Query:       gi|557694333|ref|YP_008797387.1|  [L=429]
Description: 3-phosphoshikimate 1-carboxyvinyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-107  358.5   0.1   4.9e-107  358.2   0.1    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 !  358.2   0.1  2.7e-111  4.9e-107       4     417 .]       8     418 ..       6     418 .. 0.93

  Alignments for each domain:
  == domain 1  score: 358.2 bits;  conditional E-value: 2.7e-111
                                       SS--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE CS
                     EPSP_synthase   4 gkrlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfea 80 
                                       ++rl+g v++p+sks+++r + lA+L ++++ti  +L s+D++++++a ++Lgaei++      +++  g  ++f++
  gi|557694333|ref|YP_008797387.1|   8 PSRLKGVVEAPPSKSYTHRVFSLASLCTEKTTIHTPLISRDTQATINAAKMLGAEIVEK---PGAYTALG-RRQFKT 80 
                                       789**************************************************987555...55666777.78**** PP

                                       -HHHHTT-GGGGGGHHHHHHHHSE.ESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEET..SS- CS
                     EPSP_synthase  81 peelvldlgnsgtalrlLtallal.asgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkg..lkl 154
                                       p ++++d+ nsgt+lr+ t+l++l  +g++vLtGdesir RP+++ll+aL q+Gae+++ +g+++ap++vkg  +  
  gi|557694333|ref|YP_008797387.1|  81 P-DNIIDVMNSGTTLRIYTGLATLvEKGYTVLTGDESIRRRPMAQLLEALHQIGAECWSTRGNGSAPIIVKGgnRIT 156
                                       *.8*********************555*********************************************97778 PP

                                       BEEEEETSSTTHHHHHHHHHHHTTSBS..EEEEES.-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--E CS
                     EPSP_synthase 155 kgveikaevsSqqvtsllllaallaeg..ttelee.lasepsiddtlkmlkkfgikietsgteesitvkGkeklpgt 228
                                       ++++ik++ sSq+vtslll     a g  +++++e l+s+p++d t+km + fg++i+  g e  ++v + ++l+g+
  gi|557694333|ref|YP_008797387.1| 157 GTAKIKGDESSQYVTSLLLTGL-AAHGdiEIQVTEeLVSKPYVDATVKMVEVFGGEIRRRGYEW-FRVSP-QELHGV 230
                                       999*************998776.667769999999************************77765.*****.889*** PP

                                       EEE--B-HHHHHHHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEEEEEETTS--BEEEEEB CS
                     EPSP_synthase 229 eyvvegDassAayflvaAaitggevtvenvginslqGdiealdeilekmgaeitqeedasivvgpsglklkdvdiet 305
                                       e++v+gD ssAa+ ++aA +t+g vt++n+ +   q+d ++++ i++  g e t + +   v+g  +    +v +++
  gi|557694333|ref|YP_008797387.1| 231 EFTVPGDFSSAAFIIAAAHLTQGHVTIKNLSTRYPQADEKIVE-IIKLYGSEATFTSEGLVVEGGRNHADAEVVLRD 306
                                       **************************************88888.******99999997788888878888999**** PP

                                       GSTTSBHGGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB.-EEEE-TTST CS
                     EPSP_synthase 306 lpdeaptlavlaafaegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlk.gaevesydDh 381
                                       +pd++p++av aa+ +g+t+i g+a+ r ke+dr+a +a+eLrklG+evee+ dgl i++   ++k g+ v+ ++Dh
  gi|557694333|ref|YP_008797387.1| 307 APDLLPVTAVIAAVNDGQTRIHGVAHARLKESDRIALTAAELRKLGVEVEELADGLLIHGN-PRIKgGVAVDGHGDH 382
                                       ********************************************************96665.55661578******* PP

                                       TTTHHHHHHHHHSBSEEEEETTHHHHHHSSSHHHHH CS
                     EPSP_synthase 382 RiamalalaglvaegeveiddiectdksfpefeekL 417
                                       R+ ma++++gl +e+  +++ +e +d+s+p f ++L
  gi|557694333|ref|YP_008797387.1| 383 RLFMAFTVLGLTLEKGLIVKGAESADVSYPAFLQDL 418
                                       ********************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3195.13
//
Query:       gi|557694334|ref|YP_008797388.1|  [L=76]
Description: hypothetical protein CSUB_C0901 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   4.4     0.0061   16.5   4.4    1.0  1  DUF4271    Domain of unknown function (DUF4271)
  ------ inclusion threshold ------
      0.052   12.4   6.8      0.063   12.1   6.8    1.0  1  TraG_N     TraG-like protein, N-terminal region
       0.12   11.7   2.1       0.13   11.6   2.1    1.0  1  OST3_OST6  OST3 / OST6 family, transporter family


Domain annotation for each model (and alignments):
>> DUF4271  Domain of unknown function (DUF4271)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   4.4     1e-06    0.0061     113     172 ..       3      62 ..       1      73 [. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-06
                           DUF4271 113 Ffdkkkirqwifsylsylsllglllfplvlllvyfplssqillililiilllikllllly 172
                                       F++++++r++++s++  +++ +l +++l++l ++ +l + +l+i++++ l+++ l++++y
  gi|557694334|ref|YP_008797388.1|   3 FKLSRQTRFMLESLVLAILYTALPILLLIILQTFRSLTALNLVIWLAFTLGWTALITYIY 62 
                                       8999*****************************************************777 PP

>> TraG_N  TraG-like protein, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   6.8   1.1e-05     0.063     326     381 ..       4      62 ..       2      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.1e-05
                            TraG_N 326 dlarqalpmmqaflemliyalfPlvlllslyplk...glkilkgylfllvwlqlWwpla 381
                                       +l rq+  m+ ++ ++++y+ +P++ll++l  ++   +l  + +++f+l w++l   ++
  gi|557694334|ref|YP_008797388.1|   4 KLSRQTRFMLESLVLAILYTALPILLLIILQTFRsltALNLVIWLAFTLGWTALITYIY 62 
                                       78899999**********************99988889999999999999999977776 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 ?   11.6   2.1   2.2e-05      0.13     222     285 ..       5      63 ..       1      69 [. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.2e-05
                         OST3_OST6 222 ggsqnQfgaEtqivallygllallvilLiklvpriknakvqrvlvivllvlifllfslllslfr 285
                                        + q+ f++E+ + a+ly++l +l++++ +   +++  +        +l++++    l+++++ 
  gi|557694334|ref|YP_008797388.1|   5 LSRQTRFMLESLVLAILYTALPILLLIILQTFRSLTALNLVI-----WLAFTLGWTALITYIYV 63 
                                       56799*****************98888887766666544444.....44444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); 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 0.24s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 602.67
//
Query:       gi|557694335|ref|YP_008797389.1|  [L=165]
Description: hypothetical protein CSUB_C0902 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.7   2.3       0.11   12.8   1.8    1.7  2  VirB3     Type IV secretory pathway, VirB3-like protein
       0.35   11.1   2.1        2.5    8.4   2.1    2.0  1  DUF3119   Protein of unknown function (DUF3119)


Domain annotation for each model (and alignments):
>> 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 ?   12.8   1.8   1.2e-05      0.11       9      61 ..      18      70 ..      16      90 .. 0.92
   2 ?   -1.6   0.0      0.38   3.4e+03       4      25 ..      77      98 ..      74     101 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                             VirB3  9 ltRpamllGvplelvllnllvsvilflvglslwillllvplhlvlrliakrDp 61
                                      l R+ m + + lel+++++++ + lfl  +s+w+ ll+ ++  ++ +++ rD 
  gi|557694335|ref|YP_008797389.1| 18 LQRDKMAFLLKLELLVISAAALFALFLTNQSPWLRLLFTISTCLALIVVLRDR 70
                                      57999999999****************************99999999999995 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.38
                             VirB3  4 plfkaltRpamllGvplelvll 25
                                      +l++a  R     G+++ ++l 
  gi|557694335|ref|YP_008797389.1| 77 RLRRAVVRSVKTRGGEWFFFLP 98
                                      6899999999999998888775 PP

>> DUF3119  Protein of unknown function (DUF3119)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.1   0.00028       2.5      24      60 ..      30      72 ..       6     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00028
                           DUF3119 24 qlvlgllvallglfllvQtvrlrlqftee.alevvrv.....d 60
                                      +l++  + al++lfl+ Q+  lrl ft +  l ++ v     +
  gi|557694335|ref|YP_008797389.1| 30 ELLVISAAALFALFLTNQSPWLRLLFTIStCLALIVVlrdrlE 72
                                      455666789*****************96646776666444442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1313.05
//
Query:       gi|557694336|ref|YP_008797390.1|  [L=246]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   20.6  10.8    0.00034   20.6  10.8    2.2  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 !   20.6  10.8   1.9e-08   0.00034       4     109 ..       7     113 ..       4     121 .. 0.79
   2 ?   -3.9   8.5      0.65   1.2e+04      57     171 ..     122     237 ..     118     238 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.9e-08
                                       TTHHHHHHHHHHHHHHHHH..H---B-S..SS-B--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS-GGGHH CS
                   ECF-ribofla_trS   4 tkkvvatailaAlvvvltl..fisIplp.antegsinlgdavlalaallfGpvvGflvGaiGsalaDllsgYgiwap 77 
                                       t ++v++a  aAl++ +++  f+ I  p ++t   + ++ ++ a++a+l+ p++G+l ++iG +++D+l    + ++
  gi|557694336|ref|YP_008797390.1|   7 TLELVLIAANAALYAGVGYltFLGIFAPvVGT-VRFWPAVVIPAVFAVLYSPKIGALGAGIGIFISDMLIHGDPVLS 82 
                                       568999********988874468888874444.5888899999*************************987556665 PP

                                       HHH.HHHHHHH.HHHHHH--S-S-SSH...HHHH CS
                   ECF-ribofla_trS  78 ftl.iikgliG.livGliakklkknkengvfkil 109
                                       +++ +++ + G +i+G++a+kl+ +++   +++l
  gi|557694336|ref|YP_008797390.1|  83 ISVgVTSNVAGfYILGVLARKLASSQR---VSVL 113
                                       555499999994589******988777...4444 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHHHSS-GGGHHHHHHHHHHHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHH..HHHHHHHHHH.. CS
                   ECF-ribofla_trS  57 lvGaiGsalaDllsgYgiwapftliikgliGlivGliakklkknkengvfkilalvlfaivmv..igyviaegll.p 130
                                       l++a+    aD++ g+   a++ +i  g++ l+++++   ++      v+   + ++ +++m+  +  + ++++  p
  gi|557694336|ref|YP_008797390.1| 122 LAAALAGSWADIFGGWE-TASI-FIGAGVLSLVISVAYSFYRPGYAGLVAASSTGLIIGAAMIgiGVWLYSQFFSlP 196
                                       66777777799988895.4555.699999999999888777444443333333333333333300333333333355 PP

                                       .........S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ECF-ribofla_trS 131 ildiiiysepaekvalqsipaniiqavvgaiialpLlkala 171
                                       +        p  ++a++ + + ++ + + +i+  pL++a++
  gi|557694336|ref|YP_008797390.1| 197 AAAGGGHGLPLYAAAIWFLWTYLTEIPFLMILLPPLVAAVR 237
                                       55555556677777777777777777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1810.83
//
Query:       gi|557694337|ref|YP_008797391.1|  [L=306]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   24.8   0.2    3.5e-05   24.0   0.2    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 !   24.0   0.2   1.9e-09   3.5e-05       8      48 ..      98     141 ..      89     154 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.9e-09
                                       SHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHH CS
                    GHMP_kinases_N   8 iPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerl 48 
                                       +P++ G+G SAA+a+++++Al +l g +l  +e +k + + e l
  gi|557694337|ref|YP_008797391.1|  98 VPIAMGFGTSAAAALGVLMALSRLVGRPLtlREaLKHTHRVEVL 141
                                       6*************************996443355555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2157.00
//
Query:       gi|557694338|ref|YP_008797392.1|  [L=256]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-23   83.5   0.0    2.2e-23   82.8   0.0    1.2  1  MAF_flag10  Protein of unknown function DUF115


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 !   82.8   0.0   1.2e-27   2.2e-23      13     167 ..      43     190 ..      29     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 1.2e-27
                        MAF_flag10  13 pslkellnkfkgnkpaiivgaGPSLeknlellkelr..dkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevf 86 
                                       ++l++ll+  +g   a ++gaGPSLe +l++  ++   ++av ia+d+a++  l  gI P ivv+ lD+     +v+
  gi|557694338|ref|YP_008797392.1|  43 QELSDLLH--RG-AFAAVFGAGPSLETDLKQYLQVFdpERAVTIAVDGAVRCFLTWGILPKIVVTdLDG---GDDVL 113
                                       34555555..67.99*************99985555599******************************...55555 PP

                        MAF_flag10  87 keaekkgdiplvfasgvnpellkkykgpkiflvtgstqa..lelleeekneilfgGgsvantaldlAvklgfkeIil 161
                                        +a ++g  ++v+a+g+n+e+++++ +     v g+tq+  +  l      ++fgG++++++a+ +  +lg+++I++
  gi|557694338|ref|YP_008797392.1| 114 VKAAENGCFMVVHAHGDNIEKIRRLVPLMRGRVLGTTQTepIGVL------ENFGGFTDGDRAVYMCEELGVEKIVV 184
                                       5666667********************999777777775455555......9************************* PP

                        MAF_flag10 162 iGqDla 167
                                       +G+D+ 
  gi|557694338|ref|YP_008797392.1| 185 AGMDFD 190
                                       ****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1965.21
//
Query:       gi|557694339|ref|YP_008797393.1|  [L=297]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-59  201.1   0.1    2.7e-59  200.8   0.1    1.0  1  GCHY-1    Type I GTP cyclohydrolase folE2
  ------ inclusion threshold ------
       0.21   11.9   0.1       0.58   10.4   0.0    1.7  2  RICTOR_V  Rapamycin-insensitive companion of mTOR, domain 5


Domain annotation for each model (and alignments):
>> GCHY-1  Type I GTP cyclohydrolase folE2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.8   0.1   3.1e-63   2.7e-59       3     256 ..       6     275 ..       5     278 .. 0.92

  Alignments for each domain:
  == domain 1  score: 200.8 bits;  conditional E-value: 3.1e-63
                                       XXXXXXXXX----SEEEEEEEEEEEEE--TTTS-EEEEEEEEEEEES-SS--GGGGGHHHHHHHHS-SSEEGGGHHH CS
                            GCHY-1   3 DvqsekderkipldrVGvkgvklpvkvkdkekkaqtlvaevdlfvdLpaekkGihmSRlvevleeaeeeleekslee 79 
                                       Dvqse+++++i+ld+V v++v  pv+ +  e+     +  v++ v+Lp++++Gih SR++e++++  + l+ +++  
  gi|557694339|ref|YP_008797393.1|   6 DVQSEPAATPIELDWVAVSDVLFPVDEEFLEGYRLASTPVVEAAVNLPQTQRGIHASRTYEAVKQGISGLKYRDVYG 82 
                                       9****************************999999*****************************6656666644443 PP

                                       ....HHHHHHHHTT.-SEEEEEEEEEEEEEEE-TTT--EEEEEEEEEEEEEE...TTE..EEEEEEEEEEEEEE-HH CS
                            GCHY-1  80 ....ileellekleyaeraevelkfeyfiekkapvsgkeglesyevtleaeler.kee..vkltvgvevpvttlCPC 149
                                           i+++llek+ y++ra+  l+ ++f  +++pv+++e++e+++ ++++ ++r +    ++  vgv+ +++t+CPC
  gi|557694339|ref|YP_008797393.1|  83 itaqIVKTLLEKHVYSTRAKAVLRLSLFEVERTPVTKSESMEYFDAVFKSYAHRvNGGlvLRNLVGVRGVGITACPC 159
                                       4558************************************************99544367***************** PP

                                       HHHHS............SS---EEEEEEEEEEEE......--HHHHHHHHHHHSSEE--S---HHHHHHHHHHHHTS CS
                            GCHY-1 150 skeisrell........eagaHnQRsvvtvkvelaeeekeveiedlielvessassevyellKReDEkavtekayen 218
                                       +ke++re++        ++++H QR+++++ ve+   + +v+i++l++++++s+ss++ ellKR DE++v+ +a+++
  gi|557694339|ref|YP_008797393.1| 160 AKEVIREVYlngdghkePIPTHIQRAYAEIVVES---DGNVTISQLLNILKESFSSRTIELLKRLDEAEVVVSAIQR 233
                                       ******999************************4...578************************************* PP

                                       ---HHHHHHHHHHHHHS-TTEEEE.........EEEEEEE-TTTSSE CS
                            GCHY-1 219 pkFvEDvvRevaaaleeeerveef.........sveveneESiHnHn 256
                                       p+FvEDv+R++a+ +     v++f         s++v++ ESiH+Hn
  gi|557694339|ref|YP_008797393.1| 234 PRFVEDVARTAAYLV-----VKQFpklpnshqvSIRVKSLESIHRHN 275
                                       **********99988.....4555555666666*************9 PP

>> RICTOR_V  Rapamycin-insensitive companion of mTOR, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   6.4e-05      0.58      18      55 ..      73     110 ..      67     115 .. 0.89
   2 ?   -3.3   0.0       1.3   1.1e+04      56      68 ..     212     224 ..     209     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.4e-05
                          RICTOR_V  18 lGielldeydivedivelaeespvlslRGtafyvLgli 55 
                                       +G+++ d y i  +iv++  e +v+s R+ a++ L+l+
  gi|557694339|ref|YP_008797393.1|  73 SGLKYRDVYGITAQIVKTLLEKHVYSTRAKAVLRLSLF 110
                                       577788889**************************997 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.3
                          RICTOR_V  56 ssteegaeiLdel 68 
                                       s+t e  + Lde+
  gi|557694339|ref|YP_008797393.1| 212 SRTIELLKRLDEA 224
                                       8899999988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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 0.27s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2151.74
//
Query:       gi|557694340|ref|YP_008797394.1|  [L=584]
Description: ATP-dependent DNA ligase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  209.0   0.1    8.9e-62  208.4   0.1    1.3  1  DNA_ligase_A_M  ATP dependent DNA ligase domain
    2.2e-36  125.8   0.0    3.4e-36  125.1   0.0    1.3  1  DNA_ligase_A_N  DNA ligase N terminus
    1.6e-22   79.9   0.1    4.6e-22   78.5   0.0    1.8  2  DNA_ligase_A_C  ATP dependent DNA ligase C terminal region
    2.1e-05   24.9   0.1      4e-05   24.0   0.1    1.4  1  RNA_ligase      RNA ligase
  ------ inclusion threshold ------
      0.049   13.1   0.5        8.8    5.9   0.0    3.1  3  Lipid_DES       Sphingolipid Delta4-desaturase (DES)
      0.097   13.0   0.0        0.3   11.4   0.0    1.8  1  PucR            Purine catabolism regulatory protein-like fam


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 !  208.4   0.1     3e-65   8.9e-62       2     204 .]     225     424 ..     224     424 .. 0.96

  Alignments for each domain:
  == domain 1  score: 208.4 bits;  conditional E-value: 3e-65
                                       EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEE CS
                    DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDG 78 
                                       mLAe+l s e++l+k++++ f +E+KyDGeR+q+hk+g++v +fSRr+++it+++p++v+++ + + ++  ++il++
  gi|557694340|ref|YP_008797394.1| 225 MLAERLASAEEILEKVGGRGF-AEYKYDGERMQIHKSGQTVVIFSRRQENITSQYPDVVEMVTRGVSAK--EAILEC 298
                                       9***************87777.****************************************9999886..8***** PP

                                       EEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE CS
                    DNA_ligase_A_M  79 ElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvel 155
                                       E+v +d+etge lpfq+l++rk +kk++e++++e+++ l++FDiLy+dge+lt +pl  Rrk Leei+  +++r++l
  gi|557694340|ref|YP_008797394.1| 299 EAVPLDPETGETLPFQELMHRK-RKKEIEKAAEEYPVALYFFDILYVDGEDLTTQPLPIRRKRLEEIV-VESERMKL 373
                                       *********************5.55569****************************************.9999**** PP

                                       --EEEESSHHHHHHHHHHHHHTTECEEEEEE..TT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 156 aeslevkdveeleelleeaiseglEGlvvKn..pdskYepgkrsknwlKvK 204
                                       ++ + v++ ee+e++++ea+++g+EGl++K+   +s+Y++g r+++w+K+K
  gi|557694340|ref|YP_008797394.1| 374 STGRMVETPEEVEKFFAEAVEAGCEGLMIKSvdEESVYRAGARGWQWIKLK 424
                                       ******************************97788**************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 !  125.1   0.0   1.2e-39   3.4e-36       2     173 .]       3     176 ..       2     176 .. 0.97

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 1.2e-39
                                       CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT- CS
                    DNA_ligase_A_N   2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealgl 74 
                                       F+ela+++e++e+ t+krle+++ila++++k+   +p+ + +++++    ++P+y+g e+g+ e+l  +++ +++g 
  gi|557694340|ref|YP_008797394.1|   3 FRELADFYERLEA-TTKRLEMTDILAELLSKT---PPDIIDKVVYMtlgeIYPAYRGLELGVAEKLALRVVKQVTGA 75 
                                       9************.999************764...7999************************************** PP

                                       -HHHHHHHHHHHS-HHHHHHHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHH CS
                    DNA_ligase_A_N  75 skkkikdalakvgDlgevaeevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEak 149
                                        +k++++a+a++gD+g +a+ +l+k++++   +++lt+++v+  ++k+a++ g g  d k+ il++ll++asp Eak
  gi|557694340|ref|YP_008797394.1|  76 HEKEVDEAYARHGDVGNAAMVLLRKKPQTtLFAQELTVQDVYTAFEKIARStGPGAVDVKMSILAGLLAQASPVEAK 152
                                       ***********************999999899*****************8889999********************* PP

                                       HHHHHHCT---SS--HHHHHHHHH CS
                    DNA_ligase_A_N 150 yliriilkdlriglsektvldala 173
                                        + r++++++r+g+++ t+ldala
  gi|557694340|ref|YP_008797394.1| 153 HILRMVTGNMRLGVADMTILDALA 176
                                       **********************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 ?   -3.1   0.0       4.2   1.3e+04       8      39 ..      56      86 ..      52     105 .. 0.66
   2 !   78.5   0.0   1.5e-25   4.6e-22       1      99 []     449     559 ..     449     559 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.2
                                      EEEEEEETTEEEEEEEE-SS--HHHHHHHHHH CS
                    DNA_ligase_A_C  8 lllgvyddgkleyvgkvgtGfsdaeleelrkk 39
                                      l lgv ++  l+ v k  tG  ++e++e +++
  gi|557694340|ref|YP_008797394.1| 56 LELGVAEKLALRVV-KQVTGAHEKEVDEAYAR 86
                                      56777776666666.55577777777776665 PP

  == domain 2  score: 78.5 bits;  conditional E-value: 1.5e-25
                                       GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHG..GGEECTTCESS---HHHHTTEEE-TT-EEEEE CS
                    DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklk..elerkkppfaekvpeeekrdvWvePelvveVk 73 
                                       r+g++g+ll++vy+  ++ +++v+kvg+Gf+d +le+l+++++  +l+ k+p++++  +    +d Wv+P+lv+e+ 
  gi|557694340|ref|YP_008797394.1| 449 RKGRYGALLMAVYNpeKDVFQTVCKVGSGFKDVDLETLTERVNrlRLDAKHPRVEALME----PDIWVQPSLVLEII 521
                                       6899**********97788***********************96777777777744444....459*********** PP

                                       ESEEECTSSSTT...........EECT-EEE.EE-TTS CS
                    DNA_ligase_A_C  74 faeitasgkyka...........slRfPrfk.rlReDk 99 
                                       +ae+t s+ +++            +RfPrf+ r+R+Dk
  gi|557694340|ref|YP_008797394.1| 522 GAEVTLSPVHTCawdvvkqgyglGIRFPRFTgRVRDDK 559
                                       *****************************9989****8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   1.3e-08     4e-05       5     160 ..     246     423 ..     244     424 .. 0.54

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.3e-08
                                       EEEE-SSEEEEEEEETT.EEEEETTCEB.CTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES.......... CS
                        RNA_ligase   5 vtEKlDGtnfriylvke.vgvasRsqil.pfgeekfkefkrwaaalrkklkeklaneelilyGElig.......... 69 
                                       ++ K DG++++i+++ + v ++sR+q+  + +++++ e  +  +            +e il +E +           
  gi|557694340|ref|YP_008797394.1| 246 AEYKYDGERMQIHKSGQtVVIFSRRQENiTSQYPDVVEMVTRGVS----------AKEAILECEAVPldpetgetlp 312
                                       577***********9445999999999963344444333333333..........3344444444444433333333 PP

                                       ...........SS....TT..SS.EEEEEEEEEEE.CTTBECE--HHHHHHHHHCCT.......B..EEEEE.SS.H CS
                        RNA_ligase  70 ..........hsi..kygg..lpkefyvFdifdir.dkeeqrylspdevealakglg.......tvpvlyegkfl.a 123
                                                 + i     +  +p  +y Fdi+ ++ +      l+++ +++ +k+l+         + l +g++  +
  gi|557694340|ref|YP_008797394.1| 313 fqelmhrkrkKEIekA--AeeYPVALYFFDILYVDgE-----DLTTQPLPIRRKRLEeivveseRMK-LSTGRMVeT 381
                                       4444425444333421..235677*********9853.....3333333333333322111121111.233333346 PP

                                       HHHHCCC..HHHHTC--EEEEEESSSSBE.TTE...BSEEEE CS
                        RNA_ligase 124 aeellell.lskgnkrEGlVikpeselyk.nkg...raifKv 160
                                        ee+++++ +  +  +EGl ik+++e    + g    +++K+
  gi|557694340|ref|YP_008797394.1| 382 PEEVEKFFaEAVEAGCEGLMIKSVDEESVyRAGargWQWIKL 423
                                       667777743456779********9876666555546666766 PP

>> Lipid_DES  Sphingolipid Delta4-desaturase (DES)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.38   1.1e+03      16      30 ..     269     283 ..     268     286 .. 0.74
   2 ?    3.2   0.3      0.02        61      11      21 ..     315     325 ..     313     328 .. 0.84
   3 ?    5.9   0.0     0.003       8.8      23      37 .]     497     511 ..     496     511 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.38
                         Lipid_DES  16 sRRkeILkkhPeikk 30 
                                       +R   I  ++P++ +
  gi|557694340|ref|YP_008797394.1| 269 RRQENITSQYPDVVE 283
                                       35566999***9965 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.02
                         Lipid_DES  11 dePHasRRkeI 21 
                                       + +H++R+keI
  gi|557694340|ref|YP_008797394.1| 315 ELMHRKRKKEI 325
                                       558*******9 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.003
                         Lipid_DES  23 kkhPeikkLmGpdpl 37 
                                       +khP ++ Lm pd +
  gi|557694340|ref|YP_008797394.1| 497 AKHPRVEALMEPDIW 511
                                       69**********975 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 ?   11.4   0.0    0.0001       0.3      40      94 ..     367     417 ..     358     434 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
                              PucR  40 rggeLllttglalkddpealaelvrelaeagvaaLviklgreipeelieaadelg 94 
                                       + + + l+tg  ++ +pe+++++ +e +eag+ +L+ik    ++ee +  a ++g
  gi|557694340|ref|YP_008797394.1| 367 ESERMKLSTGRMVE-TPEEVEKFFAEAVEAGCEGLMIKS---VDEESVYRAGARG 417
                                       45558899**9997.9**********************9...5666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 4266.97
//
Query:       gi|557694341|ref|YP_008797395.1|  [L=75]
Description: hypothetical protein CSUB_C0908 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00037   20.1   0.6    0.00037   20.1   0.6    2.1  2  DUF131           Protein of unknown function DUF131
  ------ inclusion threshold ------
       0.13   11.9   6.6       0.21   11.2   0.2    2.1  2  Baculo_11_kDa    Baculovirus 11 kDa family
       0.18   10.6   4.8       0.19   10.5   4.8    1.0  1  Herpes_LMP2      Gammaherpesvirus latent membrane protein (LM
       0.83   10.0   5.5        2.7    8.3   0.4    2.1  2  Sigma_reg_N      Sigma factor regulator N-terminal
        2.3    7.4   8.0        2.9    7.1   8.0    1.1  1  ABC2_membrane_2  ABC-2 family transporter protein
        6.3    7.0   5.7          1    9.5   0.2    2.1  2  Antimicrobial10  Metchnikowin family


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 ?    1.2   5.5       0.1     3e+02      42      61 ..       3      22 ..       1      23 [. 0.87
   2 !   20.1   0.6   1.2e-07   0.00037      16      59 ..      30      73 ..      24      75 .] 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.1
                            DUF131 42 rlaktaiiLaIilmilllil 61
                                      +++ t +iL I++++l+li+
  gi|557694341|ref|YP_008797395.1|  3 NMLSTPLILIIVFVLLVLII 22
                                      78999999*9**99999998 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.2e-07
                            DUF131 16 ekeesrvkgGGVvliGPIPIiFGsdkrlaktaiiLaIilmilll 59
                                      e e++r +g +++liGP+PI +   + +a +a  L + l+++++
  gi|557694341|ref|YP_008797395.1| 30 EGERTRGEGFAFILIGPLPILLRGKPWIALVAAALIVFLLLVVM 73
                                      6789999***************9999888888877666655554 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 ?   11.2   0.2   7.1e-05      0.21      46      71 ..       9      34 ..       7      41 .. 0.78
   2 ?    3.6   1.8     0.017        49      38      52 ..      59      73 ..      55      75 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.1e-05
                     Baculo_11_kDa 46 fvvivlfilLlvvilknaeaeeaeke 71
                                      +++i++f+lL++ il+ + a+e e++
  gi|557694341|ref|YP_008797395.1|  9 LILIIVFVLLVLIILTAVVAAEGERT 34
                                      58899999999999888877776664 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.017
                     Baculo_11_kDa 38 Lvicglvvfvvivlf 52
                                      Lv ++l+vf+++v++
  gi|557694341|ref|YP_008797395.1| 59 LVAAALIVFLLLVVM 73
                                      788999999888876 PP

>> Herpes_LMP2  Gammaherpesvirus latent membrane protein (LMP2) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   4.8   6.2e-05      0.19     395     453 ..       8      70 ..       1      74 [. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 6.2e-05
                                       XXXXXXXXXXXXXXXXXXX..XXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Herpes_LMP2 395 mlllivagilfilailtew..gsgnrtygp..vfmclgglltmvagavwltvmsntllsawil 453
                                        l+li+  +l++l ilt      g+rt g    f+ +g l  ++ g  w+++++ +l+   +l
  gi|557694341|ref|YP_008797395.1|   8 PLILIIVFVLLVLIILTAVvaAEGERTRGEgfAFILIGPLPILLRGKPWIALVAAALIVFLLL 70 
                                       5788999999999999975224577777642278899***************99999876555 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 ?    8.3   0.4   0.00092       2.7      13      33 ..       5      24 ..       2      37 .. 0.55
   2 ?    4.3   0.7     0.017        50      10      29 ..      54      73 ..      51      74 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00092
                       Sigma_reg_N 13 lrivlislivlllifvilvvt 33
                                      l++ li +iv++l+++i++ t
  gi|557694341|ref|YP_008797395.1|  5 LSTPLILIIVFVLLVLIIL-T 24
                                      5555555555555544442.2 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.017
                       Sigma_reg_N 10 ksilrivlislivlllifvi 29
                                      k ++  v ++liv+ll++v+
  gi|557694341|ref|YP_008797395.1| 54 KPWIALVAAALIVFLLLVVM 73
                                      56788888889999888875 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 ?    7.1   8.0   0.00096       2.9     130     177 ..      12      73 ..       2      74 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00096
                   ABC2_membrane_2 130 igla.iavallatvll..............alaiilalgivlaledllllvvasvlllllv.vf 177
                                       i+++ ++v+++ t  +              a+++i  l i l+++ ++ lv+a+++++ll+ v+
  gi|557694341|ref|YP_008797395.1|  12 IIVFvLLVLIILT--AvvaaegertrgegfAFILIGPLPILLRGKPWIALVAAALIVFLLLvVM 73 
                                       2222222222222..13367999*****9999999999999******************98444 PP

>> Antimicrobial10  Metchnikowin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2   0.00034         1       8      32 ..      13      37 ..       8      41 .. 0.83
   2 ?   -0.7   1.3      0.51   1.5e+03       8      17 ..      65      74 ..      57      75 .] 0.55

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00034
                   Antimicrobial10  8 lfllLLgllllltvvlaEasRrqGP 32
                                      ++ +LL l++l +vv aE +R  G 
  gi|557694341|ref|YP_008797395.1| 13 IVFVLLVLIILTAVVAAEGERTRGE 37
                                      5668888999999999*****9985 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.51
                   Antimicrobial10  8 lfllLLglll 17
                                      ++ lLL ++l
  gi|557694341|ref|YP_008797395.1| 65 IVFLLLVVML 74
                                      4445555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1229  (0.0685482); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 581.19
//
Query:       gi|557694342|ref|YP_008797396.1|  [L=263]
Description: transcriptional regulator, TrmB-like [Candidatus Caldiarchaeum subterraneum]
Scores for 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-24   83.7   0.4    2.8e-23   81.6   0.0    2.0  2  TrmB             Sugar-specific transcriptional regulator Trm
    9.2e-09   34.8   0.2    1.3e-08   34.3   0.2    1.2  1  Regulator_TrmB   Archaeal transcriptional regulator TrmB
    0.00093   19.5   0.0     0.0027   18.0   0.0    1.8  1  Rrf2             Transcriptional regulator
     0.0025   18.1   0.0      0.008   16.5   0.0    1.9  1  Penicillinase_R  Penicillinase repressor
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.031   14.1   0.0    1.7  1  HTH_IclR         IclR helix-turn-helix domain
      0.018   15.6   0.0      0.048   14.2   0.0    1.7  1  HTH_27           Winged helix DNA-binding domain
       0.12   12.3   0.0       0.27   11.2   0.0    1.6  1  PadR             Transcriptional regulator PadR-like 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 !   81.6   0.0   1.1e-26   2.8e-23       1      67 [.      17      83 ..      17      84 .. 0.98
   2 ?   -0.5   0.1      0.45   1.2e+03      17      40 ..      90     113 ..      88     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 1.1e-26
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                      Lq+lGL++yE+++Y+aL+++gp+ta+ei+    +p+sk+YevL sLe+kG++ ++ grp +Y++ +p
  gi|557694342|ref|YP_008797396.1| 17 LQDLGLTDYEVRAYIALVEHGPMTASEISDLKMIPYSKIYEVLGSLEEKGFIVTQSGRPARYVPKSP 83
                                      899*************************************************************998 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.45
                                       HHHHCCCHHCHHCCCTTSSCHCHH CS
                              TrmB  17 LlklgpatadeiaeelgvprskvY 40 
                                       L+k+ ++++++++e + ++   vY
  gi|557694342|ref|YP_008797396.1|  90 LVKKIEKNMRQLSETVVRELMPVY 113
                                       899999999999999877766666 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.2   5.2e-12   1.3e-08       2     137 ..     124     258 ..     123     263 .] 0.89

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 5.2e-12
                                       EEEESSHHHHHHHHHHHHHH-SSEEEEEE-...GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAenelivslp...selLeelreeliaaaergvtVllliypdedleeldleevatevr 75 
                                       +w+ ++ e++ e+i+e++   enel+v++p    e  e lr+ + + + r+ +V ++ +++ +++ l+ + +++evr
  gi|557694342|ref|YP_008797396.1| 124 IWILRGSESIAEKIREVVLRCENELLVAAPtlsRETAENLRKLILSVRARDGKVQVMASNNVNPSLLKVLAEVAEVR 200
                                       8**************************987333699999************************************** PP

                                       -S---S.EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEEE CS
                    Regulator_TrmB  76 vrrsgapllvivDrkrgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktsevikt 137
                                       vr++     +i+D +++v++ +   +d+e   ai+ +   l+ +    ++++lW++s+ +k+
  gi|557694342|ref|YP_008797396.1| 201 VREQMFGGGIISDNREVVIVFA---EDDESMIAIWSDHIGLAKFA-KNYFEYLWRESTPFKP 258
                                       ***9998889********9988...68999999998888888766.7778888*****9995 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.1e-06    0.0027      12      65 ..      28      78 ..      21      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCE CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGy 65
                                      +a  y+a+ e++ p++++ei++   i+ s +  +l  L+++g++ ++ G+   y
  gi|557694342|ref|YP_008797396.1| 28 RA--YIALVEHG-PMTASEISDLKMIPYSKIYEVLGSLEEKGFIVTQSGRPARY 78
                                      44..55555554.49**********************************97766 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.1e-06     0.008       1      84 [.      22      99 ..      22     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.1e-06
                                      ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXXXXXXXXXXX CS
                   Penicillinase_R  1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplvseeeavasavkql 79
                                      l++ E   + +l e+g++t++e+ +         ys +  +l+ L++Kg++ ++  gr  +Y p    + av++ vk++
  gi|557694342|ref|YP_008797396.1| 22 LTDYEVRAYIALVEHGPMTASEISDLKM----IPYSKIYEVLGSLEEKGFIVTQS-GRPARYVPKS-PDTAVENLVKKI 94
                                      57788888899999*****999977544....46*****************8876.********85.456667777766 PP

                                      XXXXX CS
                   Penicillinase_R 80 ldklf 84
                                       +++ 
  gi|557694342|ref|YP_008797396.1| 95 EKNMR 99
                                      66655 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   1.2e-05     0.031      17      50 ..      37      70 ..      32      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +++t se+++   +p S+ +  L +L+e G++ +
  gi|557694342|ref|YP_008797396.1| 37 GPMTASEISDLKMIPYSKIYEVLGSLEEKGFIVT 70
                                      67*****************************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 ?   14.2   0.0   1.9e-05     0.048      15      58 ..      35      77 ..      27      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.9e-05
                            HTH_27 15 rrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrr 58
                                      ++++++++++++  ++ +s i ++l  L+ekG+++++   ++ r
  gi|557694342|ref|YP_008797396.1| 35 EHGPMTASEISDLKMIPYSKIYEVLGSLEEKGFIVTQSG-RPAR 77
                                      4899******************************77655.4555 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.27      28      53 ..      49      74 ..      33      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                      CTTHHHHHHHHHHHHHTTSEEEEEE- CS
                              PadR 28 elseGslYpaLkrLekeglvesewee 53
                                       + ++++Y +L +Le++g+++++  +
  gi|557694342|ref|YP_008797396.1| 49 MIPYSKIYEVLGSLEEKGFIVTQSGR 74
                                      567899***************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      751  (0.0418874); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2067.95
//
Query:       gi|557694343|ref|YP_008797397.1|  [L=170]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-30  105.9  19.1    2.4e-30  105.7  19.1    1.1  1  QueT      QueT transporter


Domain annotation for each model (and alignments):
>> QueT  QueT transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7  19.1   1.3e-34   2.4e-30       3     138 ..       3     159 ..       1     160 [. 0.90

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 1.3e-34
                              QueT   3 raaviaAlYvvltlvlapisfgaiqvRiseaLtlLpv.ftpaailGltiGcliaNllsplgllDvifGslatliaal 78 
                                        a v a+lY++ +++l +isf +iqvR+s+aL+ L++ f++ a++G+t+G++iaNl+sp+g+lD++ G+l++l+a++
  gi|557694343|ref|YP_008797397.1|   3 AAIVFAGLYAAGVIALPGISFEIIQVRVSDALLPLAIvFGMPAVVGVTVGTFIANLFSPFGPLDLLGGTLTNLVATY 79 
                                       566889*********************************************************************** PP

                              QueT  79 ltyllkkkr......llaalppvlvnalivgav...........l...lelpflltvltvglgelivlyvlGlpllk 135
                                       + ++++++       +++a++++lv+++ivg++           +   +   +++++l v+ g +i+++v+G+pl k
  gi|557694343|ref|YP_008797397.1|  80 VGWKMARNFvfrgswMFVAVFQTLVVTFIVGSYlyvligvpptpVlgvVVPGIVFSWLGVLGGSVISIIVIGYPLTK 156
                                       *****99989999955899************8877777766655155545579***********************9 PP

                              QueT 136 ale 138
                                       a+ 
  gi|557694343|ref|YP_008797397.1| 157 AVA 159
                                       986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1229.14
//
Query:       gi|557694344|ref|YP_008797398.1|  [L=448]
Description: hypothetical protein CSUB_C0911 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   67.5   0.0    1.3e-18   67.2   0.0    1.1  1  ATPase       KaiC
      0.001   19.5   0.1      0.002   18.6   0.1    1.4  1  AAA_16       AAA ATPase domain
     0.0025   17.4   0.0     0.0042   16.7   0.0    1.3  1  AAA_25       AAA domain
     0.0037   17.8   0.0     0.0054   17.3   0.0    1.3  1  ABC_tran     ABC transporter
  ------ inclusion threshold ------
      0.023   14.6   0.1       0.34   10.8   0.1    2.2  1  NACHT        NACHT domain
      0.049   13.8   0.0      0.077   13.2   0.0    1.3  1  AAA_33       AAA domain
      0.064   13.5   0.0       0.13   12.6   0.0    1.4  1  AAA_22       AAA domain
      0.076   12.8   0.0        0.2   11.4   0.0    1.7  1  AAA_29       P-loop containing region of AAA domain
       0.12   12.1   0.0       0.21   11.3   0.0    1.3  1  IstB_IS21    IstB-like ATP binding protein
       0.14   11.8   0.0       0.23   11.1   0.0    1.3  1  SRP54        SRP54-type protein, GTPase domain
       0.14   12.0   0.1       0.25   11.2   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
       0.15   11.7   0.0       0.23   11.1   0.0    1.2  1  AAA_30       AAA domain
       0.16   12.2   0.0       0.32   11.2   0.0    1.5  1  AAA_28       AAA 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 !   67.2   0.0   9.2e-22   1.3e-18       2     212 ..     237     443 ..     236     448 .] 0.88

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 9.2e-22
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                        tg+eg+D+ +  G++  +vv ++G +G+G +++ ++   + ++  g+ +v+ ++  + e+lr + + lG d+e+le
  gi|557694344|ref|YP_008797398.1| 237 LTGVEGIDREI--GLMYPSVVAVVGPSGSGRSTLLARLSAHRLSA-GDGVVMLSLHDTVEELRSRLAGLGCDVERLE 310
                                       59*******99..*************************9999888.******************************* PP

                            ATPase  79 eegklaiidasesaeesaeekdkedleelieelaeaikeika..krvviDsitglayeekeavaReilrqlvrvlkk 153
                                       +egkl+++    s+++ +++   ++++e+   ++++++++    k  ++Dsit++++++  + a   l +l+   +k
  gi|557694344|ref|YP_008797398.1| 311 QEGKLVLLTSIPSSDN-TRHYVASEPNEINIAFTRVLSRLATarKWFILDSITPVMESHGVE-AGLKLLNLLVAKSK 385
                                       *********9999876.6678999999*********99998766889********5555555.55555555555555 PP

                            ATPase 154 lgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhsk 212
                                          +++ v+  +  + ++ +  v   +vdgv+   lke++++l R++++  m   k+s 
  gi|557694344|ref|YP_008797398.1| 386 AAGVSLWVAYNNLAYPQNVTAMVMD-SVDGVVETVLKEENGRLSRMVRVFTMKDVKVSG 443
                                       556689999989999**********.**************************9999875 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   1.4e-06     0.002      24     145 ..     252     362 ..     248     393 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdg.giflrgkcdqlesaipysalaqalareellrqlldeaesaeleawre 99 
                                       p++v ++G+sG+G s+l+ +l  +   +g g+++    d            + l r++l    +d   +++ ++ + 
  gi|557694344|ref|YP_008797398.1| 252 PSVVAVVGPSGSGRSTLLARLSAHRLSAGdGVVMLSLHDTV----------EEL-RSRLAGLGCDV--ERLEQEGKL 315
                                       5789**************88886555554377744444444..........445.54444444444..223444444 PP

                            AAA_16 100 kleeala...avpelagaeasrllellkrllallsrderplvlvlDdlq 145
                                        l++++     +++  ++e++ ++ +++r l++l++ +r   ++lD + 
  gi|557694344|ref|YP_008797398.1| 316 VLLTSIPssdNTRHYVASEPNEINIAFTRVLSRLAT-AR-KWFILDSIT 362
                                       444444444445555566669999999999977777.44.356666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     3e-06    0.0042      34     125 ..     253     338 ..     247     373 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3e-06
                            AAA_25  34 elallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal...rddarllvl 106
                                       ++++++G++g+G +tl+  l+++ +  G+            V+++s+ d+ +elr Rl+ +g ++   ++ ++l +l
  gi|557694344|ref|YP_008797398.1| 253 SVVAVVGPSGSGRSTLLARLSAHRLsAGD-----------GVVMLSLHDTVEELRSRLAGLGCDVerlEQEGKLVLL 318
                                       6899*********************4555...........7*********************777666555566555 PP

                            AAA_25 107 dlagv.eslpLfakdrggtl 125
                                       +   + ++++ + +   +++
  gi|557694344|ref|YP_008797398.1| 319 TSIPSsDNTRHYVASEPNEI 338
                                       53333344444433434444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   3.9e-06    0.0054      12      42 ..     253     284 ..     245     383 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3.9e-06
                                       SEEEEEESTTSSHHHHHHHHTTSS--.SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkp.teGei 42 
                                       ++va+vG++G+G StLl+ l+ +      G +
  gi|557694344|ref|YP_008797398.1| 253 SVVAVVGPSGSGRSTLLARLSAHRLSaGDGVV 284
                                       789**************999876443144444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00024      0.34       2      23 ..     254     275 ..     253     412 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00024
                                       CEEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   2 lvilqGeaGsGKTtLlqklala 23 
                                       +v++ G++GsG +tLl++l   
  gi|557694344|ref|YP_008797398.1| 254 VVAVVGPSGSGRSTLLARLSAH 275
                                       799**************99643 PP

>> AAA_33  AAA 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     0.077       1      39 [.     254     301 ..     254     371 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.5e-05
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.....avllssdt....lrrrlfg 39 
                                       +v +vG++GsG stl+ rl +++      +v ls  +    lr+rl+g
  gi|557694344|ref|YP_008797398.1| 254 VVAVVGPSGSGRSTLLARLSAHRLsagdgVVMLSLHDtveeLRSRLAG 301
                                       799***************953332356667777776655554445555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.2e-05      0.13       6      28 ..     253     275 ..     249     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.2e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleq 28 
                                       ++++v+G+sG+G++tll+rl   
  gi|557694344|ref|YP_008797398.1| 253 SVVAVVGPSGSGRSTLLARLSAH 275
                                       6899**************99765 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 ?   11.4   0.0   0.00015       0.2      24      39 ..     254     269 ..     244     274 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                            AAA_29  24 atlltGpsGsGKSTll 39 
                                       ++ ++GpsGsG STll
  gi|557694344|ref|YP_008797398.1| 254 VVAVVGPSGSGRSTLL 269
                                       5789***********8 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   0.00015      0.21      50      92 ..     255     297 ..     250     318 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                         IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkr 92 
                                       ++++GpsG G+s l + l+ +   ag  v+ ++++d veel+ 
  gi|557694344|ref|YP_008797398.1| 255 VAVVGPSGSGRSTLLARLSAHRLSAGDGVVMLSLHDTVEELRS 297
                                       799*************************************986 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00016      0.23       1      36 [.     252     287 ..     252     294 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                       SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE CS
                             SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllva 36 
                                       p+v+++vG+ G+G+ t la+L+a+  + g  v++ +
  gi|557694344|ref|YP_008797398.1| 252 PSVVAVVGPSGSGRSTLLARLSAHRLSAGDGVVMLS 287
                                       5799*****************988888877666654 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     122 ..     252     275 ..     234     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                                       TSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpe 122
                                        +++++vG+SG G+StL+ +l  +
  gi|557694344|ref|YP_008797398.1| 252 PSVVAVVGPSGSGRSTLLARLSAH 275
                                       57899**************99876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00017      0.23      20      61 ..     254     294 ..     249     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv 61 
                                       v++++Gp G+G +t+l+ l ++  +ag  v++l+   ++ ++
  gi|557694344|ref|YP_008797398.1| 254 VVAVVGPSGSGRSTLLARLSAHRLSAGDGVVMLSLHDTV-EE 294
                                       789******************999999999999876554.44 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00023      0.32       2      23 ..     255     280 ..     254     315 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00023
                            AAA_28   2 ivitGgestGKTtlleaLaar....g 23 
                                       ++++G++++G +tll++L+a+    g
  gi|557694344|ref|YP_008797398.1| 255 VAVVGPSGSGRSTLLARLSAHrlsaG 280
                                       899****************9945441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1087  (0.060628); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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):              13  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 2923.72
//
Query:       gi|557694345|ref|YP_008797399.1|  [L=134]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   90.0   0.1    1.4e-25   89.8   0.1    1.0  1  HEPN      HEPN domain
  ------ inclusion threshold ------
      0.067   13.3   0.1        0.4   10.9   0.0    2.3  3  TPR_2     Tetratricopeptide repeat


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 !   89.8   0.1   1.5e-29   1.4e-25       1     116 [.       6     126 ..       6     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 1.5e-29
                                       HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT..........- CS
                              HEPN   1 aeewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke.......s 70 
                                       ae++l+r++++ +aAe  + +gdydl++f+++qa+++ lKA+llk+g ++pkth++ +L+  l + l++       s
  gi|557694345|ref|YP_008797399.1|   6 AEKLLSRSRKFADAAEFHFMRGDYDLSVFNIEQALQLFLKAMLLKNGVDFPKTHSVGKLFIILGECLGKeqqftefS 82 
                                       689**********************************************************9999999866666666 PP

                                       HHHHHHHHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHH CS
                              HEPN  71 eelreeleeLekayiesrYpdakeeyteedaeealkdaeevlelve 116
                                       e+ + e+  Le+ayi srY ++++  t+++ae++  +  ev ++v+
  gi|557694345|ref|YP_008797399.1|  83 EKHALEFASLEDAYISSRYFPREF--TRKEAESLGTFFSEVKKFVQ 126
                                       6666666****************9..*******9999999988876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.47   4.2e+03      18      27 ..       4      13 ..       2      19 .. 0.68
   2 ?   10.9   0.0   4.5e-05       0.4       1      30 [.      20      49 ..      20      52 .. 0.81
   3 ?   -2.1   0.0      0.67   6.1e+03       6      18 ..      67      79 ..      63      80 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.47
                             TPR_2 18 eeAleafekA 27
                                      +eA++++ ++
  gi|557694345|ref|YP_008797399.1|  4 AEAEKLLSRS 13
                                      6788777665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.5e-05
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAlel 30
                                      ae ++++G+  +   + e+Al++f kA  l
  gi|557694345|ref|YP_008797399.1| 20 AEFHFMRGDYDLSVFNIEQALQLFLKAMLL 49
                                      678888888889999999999999988765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.67
                             TPR_2  6 nlGlayyklgdye 18
                                       lG+++ k +++ 
  gi|557694345|ref|YP_008797399.1| 67 ILGECLGKEQQFT 79
                                      5899998888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); 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 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 929.42
//
Query:       gi|557694346|ref|YP_008797400.1|  [L=100]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   45.7   0.0    6.9e-12   45.5   0.0    1.1  1  NTP_transf_2    Nucleotidyltransferase domain
    1.2e-07   31.7   0.0    1.4e-07   31.5   0.0    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
    0.00095   19.0   0.0     0.0014   18.5   0.0    1.3  1  DUF294          Putative nucleotidyltransferase DUF294
     0.0074   16.5   0.0     0.0088   16.2   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
      0.036   13.6   0.0      0.052   13.1   0.0    1.2  1  Peripla_BP_2    Periplasmic binding protein
      0.063   12.8   0.0      0.066   12.7   0.0    1.1  1  SieB            Super-infection exclusion protein B
       0.11   12.8   0.9       0.21   12.0   0.2    1.7  2  V-SNARE         Vesicle transport v-SNARE protein N-terminus


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 !   45.5   0.0   2.7e-15   6.9e-12       1      71 [.      18      81 ..      18      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2.7e-15
                                      HHHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEE CS
                      NTP_transf_2  1 lkklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglev 71
                                      l k++e++k+l+  a+++lfGS+arG++   SD+D+l+v++ +        +  ++ ++  f+e+ +  +v
  gi|557694346|ref|YP_008797400.1| 18 LQKIKEAVKQLDNEARLYLFGSAARGDHIYASDVDILIVTKLHP------AHVIAYLRELGFDEP-FEFHV 81
                                      579**************************************994......556666666666666.55555 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   5.4e-11   1.4e-07       1      42 [.      19      60 ..      19      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 5.4e-11
                                      -STTTTHHHHHHHHSTTEEEEEE-S------EEEEEEEESS- CS
                           Polbeta  1 ekikeilekekeielaylFGSrakgkareeSDiDlavllkek 42
                                      +kike +++ ++ + +ylFGS a+g++   SD+D+ +++k +
  gi|557694346|ref|YP_008797400.1| 19 QKIKEAVKQLDNEARLYLFGSAARGDHIYASDVDILIVTKLH 60
                                      79***********************************99866 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   5.3e-07    0.0014      36      88 ..      18      69 ..       5      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.3e-07
                            DUF294 36 ielaeeelgkppvpfallvmGSeGReEqtlktDqDnalvledeeeeaareyfa 88
                                      ++ ++e +++ + +  l+ +GS++R+++++++D D  +v +  + +++ +y++
  gi|557694346|ref|YP_008797400.1| 18 LQKIKEAVKQLDNEARLYLFGSAARGDHIYASDVDILIVTKL-HPAHVIAYLR 69
                                      4555555555688999**********************9987.6666666665 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 !   16.2   0.0   3.4e-06    0.0088       8      50 ..      15      58 ..       7      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.4e-06
                                      HHHHHHHHHHHHHH-TT-EEEE-HHHHTT-S.EESSEEEEEEBT CS
                    DNA_pol_B_palm  8 ealealvkkaakeldpevevivcGSYRRgae.ssGDvDvlitkk 50
                                      ++  + +k+a+k+ld+e++++  GS  Rg +  + DvD+li  k
  gi|557694346|ref|YP_008797400.1| 15 QHYLQKIKEAVKQLDNEARLYLFGSAARGDHiYASDVDILIVTK 58
                                      55667899******************999873699*****9865 PP

>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     2e-05     0.052     112     156 ..       5      50 ..       2      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHHHHHHHHHHTS-TT..-EEEEEEEETTE..EEEE-T CS
                      Peripla_BP_2 112 deaeklvaeidsklaaaksaidse.kpkpvlvfggadeggyvvags 156
                                       ++ +++++ +++ l+++k+a++++ ++  + +fg+a++g++++a++
  gi|557694346|ref|YP_008797400.1|   5 RRRREIFQNLQHYLQKIKEAVKQLdNEARLYLFGSAARGDHIYASD 50 
                                       67899*******************99999999*********99975 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.6e-05     0.066      66     120 ..      16      70 ..       4      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                              SieB  66 reqkkvekklknLteeekavLreflnqgksvltlplndpavkeLlekgiltkasn 120
                                       +  +k+++ +k+L++e + +L+   + g ++   +++  +v +L  + ++ ++ +
  gi|557694346|ref|YP_008797400.1|  16 HYLQKIKEAVKQLDNEARLYLFGSAARGDHIYASDVDILIVTKLHPAHVIAYLRE 70 
                                       56799*********************************************99876 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 ?   12.0   0.2   8.1e-05      0.21      22      49 ..       6      33 ..       2      42 .. 0.90
   2 ?   -1.3   0.0       1.2     3e+03      29      41 ..      86      98 ..      85      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.1e-05
                           V-SNARE 22 erkaalreiekkldeaeelldqMelEvr 49
                                       r++  ++++ +l+ ++e ++q++ E+r
  gi|557694346|ref|YP_008797400.1|  6 RRREIFQNLQHYLQKIKEAVKQLDNEAR 33
                                      689999********************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                           V-SNARE 29 eiekkldeaeell 41
                                      ++e +l++a++++
  gi|557694346|ref|YP_008797400.1| 86 RAEMYLKSADKIV 98
                                      5799999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1506  (0.083998); expected 358.6 (0.02)
Passed bias filter:                     1230  (0.0686039); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 768.62
//
Query:       gi|557694347|ref|YP_008797401.1|  [L=564]
Description: Fe-S oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   88.0   0.1    2.2e-24   86.7   0.1    1.7  1  Radical_SAM  Radical SAM superfamily
    4.6e-07   30.0   0.0    1.4e-06   28.5   0.0    1.8  1  Fer4_14      4Fe-4S single cluster domain
    1.6e-06   28.4   0.0    3.4e-06   27.4   0.0    1.6  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 !   86.7   0.1   3.7e-28   2.2e-24       2     166 ..     110     267 ..     109     268 .. 0.94

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 3.7e-28
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekg.vkevilgggepllypdfvellerlaklavp 76 
                                       v+t+ C l C++C ++   ++ g+ ++ ++++i e vk+lk +++  ++ v ++ggep l++d+ e+++ l+++   
  gi|557694347|ref|YP_008797401.1| 110 VITNRCDLHCWYCFFYA--EKAGYIYEPTLDQIREMVKQLKaERPVpGNSVQITGGEPCLRDDLPEIIRILKEE--G 182
                                       799*************9..5*********************777769***************************..9 PP

                                       TEEEEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEE CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  77 giritvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivg 151
                                         +i + tng+++    e+ +r +e+gv  ++++ + ++++     +n+++ +e   ++le++r++g+  vv + ++
  gi|557694347|ref|YP_008797401.1| 183 VDHIQLNTNGIRLAhdFEFFKRVKEAGVSNLYMSFDGVTPR-----TNPKNHWEVP-KTLENARKLGVG-VVLVPTV 252
                                       ****************************************9.....8775556555.************.******* PP

                                       BTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM 152 lpGendeeleellel 166
                                       ++ +nd+el +++++
  gi|557694347|ref|YP_008797401.1| 253 IKSVNDHELGDIIRF 267
                                       *********999987 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 !   28.5   0.0   2.3e-10   1.4e-06       4      99 ..     111     203 ..     109     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 2.3e-10
                           Fer4_14   4 rlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkse.ikiqglvltGGePLhyenkkellklvkrlkeeyp 79 
                                        +++C l+C  C+  ++++    +p t +++ +++k+lk+++ +  + + +tGGeP +    ++l ++++ lkee+ 
  gi|557694347|ref|YP_008797401.1| 111 ITNRCDLHCWYCFFYAEKAGYIYEP-TLDQIREMVKQLKAERpVPGNSVQITGGEPCLR---DDLPEIIRILKEEG- 182
                                       499**********888555544444.5555556777666665155688********955...78999999999999. PP

                           Fer4_14  80 ekkiwletngt.leielektp 99 
                                         +i+l+tng  l+ ++e ++
  gi|557694347|ref|YP_008797401.1| 183 VDHIQLNTNGIrLAHDFEFFK 203
                                       567******962455555444 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 !   27.4   0.0   5.8e-10   3.4e-06       3      98 ..     103     197 ..     101     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 5.8e-10
                           Fer4_12   3 GeGvrlslfvsgCnlsCkgCfnketwsfksgkef..tkelleeiiedlkkesi...egltllGGEPllpenaealle 74 
                                       ++G+  ++ +++C+l+C +Cf       k+g  +  t + ++e++++lk e+    + + ++GGEP l   +++l e
  gi|557694347|ref|YP_008797401.1| 103 HTGLSNLVITNRCDLHCWYCF---FYAEKAGYIYepTLDQIREMVKQLKAERPvpgNSVQITGGEPCL---RDDLPE 173
                                       6788888999***********...3444444444226777888888887766567799**********...999999 PP

                           Fer4_12  75 lvkevkeekpekdiwlytgytlee 98 
                                       +++ +kee+++   + ++g  l +
  gi|557694347|ref|YP_008797401.1| 174 IIRILKEEGVDHIQLNTNGIRLAH 197
                                       999999999988888899887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 4128.92
//
Query:       gi|557694348|ref|YP_008797402.1|  [L=377]
Description: DNA repair protein RadA/Sms [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   30.5   0.0      4e-07   29.6   0.0    1.4  1  ATPase          KaiC
    4.5e-05   23.3   0.0     0.0001   22.1   0.0    1.6  1  ChlI            Subunit ChlI of Mg-chelatase
  ------ inclusion threshold ------
      0.057   13.0   0.0       0.11   12.1   0.0    1.4  1  AAA_25          AAA domain
        0.4   11.2   3.1        2.1    8.9   2.0    2.3  2  EF-1_beta_acid  Eukaryotic elongation factor 1 beta central a


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 !   29.6   0.0     9e-11     4e-07     118     224 ..      60     161 ..      50     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 9e-11
                            ATPase 118 ikakrvviDsitglayeekeavaReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeiee 194
                                        ++k vviDs+++   +  + ++ + + ++++ lk++++T+ l+s ++++ + ag  ++e+  vd+v++ +    + 
  gi|557694348|ref|YP_008797402.1|  60 SGIKLVVIDSVQAGGVSPAARKMYTRVNKFTTALKNRKITTFLTSHVTKKGDIAGPKDLEH-HVDCVLQFR----RA 131
                                       46799*******996777777788889********************9999999999****.*****9988....56 PP

                            ATPase 195 elvRtleivkmRgtkhskkehpfeIteegi 224
                                          R l + k R  + + + +++eI ++g 
  gi|557694348|ref|YP_008797402.1| 132 FKLRPLFVPKNRFGPAKLDPFVLEIGNNGL 161
                                       779***********************9986 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   2.3e-08    0.0001      58     103 ..     247     292 ..     211     302 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.3e-08
                              ChlI  58 GsafDLpiAigilaaleqieaeeetlflGeLsldGslrpvkgvlpi 103
                                          fDL++ i++l+++ q+  +e ++f Ge++l+G +r+ +   ++
  gi|557694348|ref|YP_008797402.1| 247 DHGFDLAVVIALLSSYVQKGINEGCCFYGEVDLQGAVRSASAFKEA 292
                                       567***********************************98876554 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.4e-05      0.11     135     193 ..      54     110 ..      44     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                            AAA_25 135 aaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhHvgKes 193
                                       +++ e+ g++lvviD++++  gg + +++++   v+++    ++ +++++l+ Hv K++
  gi|557694348|ref|YP_008797402.1|  54 KRVAEYSGIKLVVIDSVQA--GGVSPAARKMYTRVNKFTTALKNRKITTFLTSHVTKKG 110
                                       66778899*********96..7788888888777777777778899***********87 PP

>> EF-1_beta_acid  Eukaryotic elongation factor 1 beta central acidic region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.18   7.9e+02      18      24 ..      53      59 ..      51      61 .. 0.89
   2 ?    8.9   2.0   0.00046       2.1       6      17 ..     302     313 ..     302     314 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                    EF-1_beta_acid 18 eeRLaaY 24
                                      e+R+a+Y
  gi|557694348|ref|YP_008797402.1| 53 EKRVAEY 59
                                      9****** PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00046
                    EF-1_beta_acid   6 DEEEDeEaerlr 17 
                                       DEEED+Ea +lr
  gi|557694348|ref|YP_008797402.1| 302 DEEEDDEAVQLR 313
                                       7888******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2670.52
//
Query:       gi|557694349|ref|YP_008797403.1|  [L=89]
Description: hypothetical protein CSUB_C0916 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 00:00:00.41
# Mc/sec: 644.83
//
Query:       gi|557694350|ref|YP_008797404.1|  [L=422]
Description: hypothetical protein CSUB_C0917 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.1     0.0041   17.4   0.1    2.8  2  LAGLIDADG_3      LAGLIDADG-like domain
  ------ inclusion threshold ------
        0.1   13.1   0.0       0.76   10.3   0.0    2.3  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain


Domain annotation for each model (and alignments):
>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.054   4.8e+02       5      49 ..     131     175 ..     127     189 .. 0.76
   2 !   17.4   0.1   4.6e-07    0.0041       2      80 ..     222     323 ..     221     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.054
                                       HHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT. CS
                       LAGLIDADG_3   5 afLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGI 49 
                                       a+ ++l ++D  v++++++ v++ l +  + +++ v++l +  G 
  gi|557694350|ref|YP_008797404.1| 131 AMAAALAQGDAAVRVKGRTMVEMILNTPYEGFAKTVAKLFEGHGT 175
                                       666788888888888888888888888888888888888776554 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 4.6e-07
                                       HHHHHHHHHHHHCCECCECSTTTTS..........EEEEES-HHHHHHHHHHHHHCT.HSCEEEE..EEE-SCCCC. CS
                       LAGLIDADG_3   2 vkaafLrGlfdaDGsvskskkkgvs..........isltssskelledvqrlLlrlGIestiyek..kkakgrgvy. 65 
                                       + +a+L+ + +++G++++s +++ +          + lt++++ l+ +v  +L r G + + +      +  r+ y 
  gi|557694350|ref|YP_008797404.1| 222 ELRAYLAMMLACEGYITWSARNKEKtdkpttefdvVILTNTNEILVSEVEDVLRRYGYVPSKTLYsdMGNVARDRYg 298
                                       689****************999888999*****************************98765554223333444446 PP

                                       ..........ECCCHCHCTTCGGGT CS
                       LAGLIDADG_3  66 ..........rlliisgenlkrFle 80 
                                                 rll+ ++e++++ l+
  gi|557694350|ref|YP_008797404.1| 299 rryvttkrayRLLVGRREEVQKVLR 323
                                       6666777776777777777777666 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 ?   -0.8   0.0      0.24   2.1e+03      42      54 ..     219     231 ..     202     244 .. 0.80
   2 ?   10.3   0.0   8.5e-05      0.76      20      65 ..     334     378 ..     321     391 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.24
                   Phage_int_SAM_4  42 tkedieaYlnyLa 54 
                                       t+e+++aYl++++
  gi|557694350|ref|YP_008797404.1| 219 TDEELRAYLAMML 231
                                       7899*****9987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.5e-05
                   Phage_int_SAM_4  20 ksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqk 65 
                                       ++Y  +  r+l++ ++++++ ++ + i++Yl  L  e+ +   +++
  gi|557694350|ref|YP_008797404.1| 334 EVYRIWALRLLEQANGRPIRWVEAQKIKDYLDELY-EKSVETGRCR 378
                                       78********************************9.6665555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2815.56
//
Query:       gi|557694351|ref|YP_008797405.1|  [L=338]
Description: hypothetical protein CSUB_C0918 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2516.67
//
Query:       gi|557694352|ref|YP_008797406.1|  [L=215]
Description: hypothetical protein CSUB_C0919 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   17.2   0.0     0.0097   16.2   0.0    1.4  1  GD_N      Serine protease gd N-terminus


Domain annotation for each model (and alignments):
>> GD_N  Serine protease gd N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.4e-07    0.0097      21      93 ..     122     198 ..     115     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.4e-07
                              GD_N  21 vvtlpsdpklkelkldvelsqkgellanyvgsleledskeeaienl....lngepvkyrvefpyqtelPkltsirlN 93 
                                       ++ l+s+  +++ +++v  + k+++++++ g+++l++  e a+ ++    +  +p +y ++f  ++  P+l+ ++ N
  gi|557694352|ref|YP_008797406.1| 122 YLYLRSNGIYRKWEIKVAVDGKTSVEGSFNGNITLKEIMEWALAKIysssVYRKPENYLIYFGNKQLSPQLRLYQTN 198
                                       577899999999**********************************998667*******************988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1718.92
//
Query:       gi|557694353|ref|YP_008797407.1|  [L=74]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-22   79.4   0.5    2.8e-22   79.2   0.5    1.0  1  VAPB_antitox  Putative antitoxin
  ------ inclusion threshold ------
       0.54    9.6   4.7       0.16   11.3   0.7    2.2  2  SeqA_N        SeqA protein N-terminal 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 !   79.2   0.5   3.2e-26   2.8e-22       1      69 []       6      71 ..       6      71 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 3.2e-26
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgilseeea.deiekaskelrkefk 69
                                      KtI+I+d++Y +L+k+Kr+geSFsdvI rLl++++++    + e+fg+++++ + +e+e+++++lr++++
  gi|557694353|ref|YP_008797407.1|  6 KTITIRDDIYLELVKRKRDGESFSDVIGRLLKRSRVN----IGEFFGCMKDSPLlEELESSTRRLREMAR 71
                                      9*******************************99999....**************************976 PP

>> SeqA_N  SeqA protein N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7   1.8e-05      0.16       2      34 ..       6      37 ..       5      39 .. 0.84
   2 ?   -3.1   0.2      0.55   4.9e+03      27      29 ..      64      66 ..      60      70 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.8e-05
                            SeqA_N  2 KtIevDeeLYrYIasntqaiGESaSdILRRLLn 34
                                      KtI + ++ Y     + ++ GES Sd+  RLL+
  gi|557694353|ref|YP_008797407.1|  6 KTITIRDDIYLEL-VKRKRDGESFSDVIGRLLK 37
                                      9999999999765.466788***********97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.55
                            SeqA_N 27 dIL 29
                                        L
  gi|557694353|ref|YP_008797407.1| 64 RRL 66
                                      334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 632.72
//
Query:       gi|557694354|ref|YP_008797408.1|  [L=71]
Description: hypothetical protein CSUB_C0921 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   28.4   0.1    1.9e-06   28.4   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 !   28.4   0.1     1e-10   1.9e-06      67     118 ..      17      69 ..       2      71 .] 0.79

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1e-10
                                       TSEEEEBCHHHHHHHHHHHHHHH.SBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                               PIN  67 alkilpidaeiaeeaaeialkyg.llpnDaliaAtAkehgikliatfDedfrr 118
                                        l++l   +e  e+aa++ +  + ++++D lia  A ++gi++iat+D+df +
  gi|557694354|ref|YP_008797408.1|  17 PLQYLRAAEESSEIAARLLASGKeVNALDILIAGIAVANGIEKIATRDKDFLE 69 
                                       566666666666666666666667**************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 528.83
//
Query:       gi|557694355|ref|YP_008797409.1|  [L=120]
Description: 4a-hydroxytetrahydrobiopterin dehydratase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-30  103.1   0.3    7.8e-30  102.9   0.3    1.1  1  Pterin_4a  Pterin 4 alpha carbinolamine dehydratase
     0.0084   15.2   0.0     0.0095   15.0   0.0    1.1  1  PAG        Phosphoprotein associated with glycosphingolipid-e


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 !  102.9   0.3   8.7e-34   7.8e-30       2      91 .]      18     110 ..      17     110 .. 0.93

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 8.7e-34
                         Pterin_4a   2 klseeeiqkllaelpgWr...leeaeelerefkfkdfeeaiafvnrvaalaeeenHhpdilvsynkvtvrltThdag 75 
                                        l++eei++l ++ p+W+   ++  ++ler+f+f++f ea+af+n+v+++ eee+Hhp i++++++v+v ++Th+++
  gi|557694355|ref|YP_008797409.1|  18 TLTDEEISALHSQVPDWQvveKDGIKRLERSFRFSNFVEALAFTNKVGEIVEEEGHHPVIMTEWGRVKVAWWTHKIK 94 
                                       699*******9777****875325568************************************************** PP

                         Pterin_4a  76 gltenDfklAakidel 91 
                                       gl++nDf++Aak+d++
  gi|557694355|ref|YP_008797409.1|  95 GLHRNDFIMAAKTDKI 110
                                       **************86 PP

>> PAG  Phosphoprotein associated with glycosphingolipid-enriched
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-06    0.0095     299     322 ..       9      32 ..       1      50 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-06
                               PAG 299 syksreddptLteeeisamYssvn 322
                                         + r d+ptLt+eeisa+ s v 
  gi|557694355|ref|YP_008797409.1|   9 CVACRGDEPTLTDEEISALHSQVP 32 
                                       567899***************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 900.47
//
Query:       gi|557694356|ref|YP_008797410.1|  [L=358]
Description: anthranilate phosphoribosyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-71  238.6   0.0    1.1e-70  238.2   0.0    1.1  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    3.3e-13   49.3   0.1    1.6e-12   47.1   0.0    2.3  3  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 !  238.2   0.0   1.2e-74   1.1e-70       2     252 ..      82     334 ..      81     335 .. 0.96

  Alignments for each domain:
  == domain 1  score: 238.2 bits;  conditional E-value: 1.2e-74
                                       TTBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEE CS
                   Glycos_transf_3   2 kdlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgf 78 
                                       ++++D++gTGG g  t+N+Sta++++ ++  v+v+khg rs+s ksGsaDv ealg+n+++t   ve+++++v+ gf
  gi|557694356|ref|YP_008797410.1|  82 PKVIDTCGTGG-GLHTYNVSTASSLLSSS-VVPVCKHGSRSISGKSGSADVQEALGINIHMTGRGVEEMIKRVNYGF 156
                                       679*******9.78899*****9987666.5********************************************** PP

                                       EEHHSSSSHHHHHHHHHHHHTT.-SS.HHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCS.TSHH CS
                   Glycos_transf_3  79 lfapeyhkamkhvapvrrelgirTvf.nlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhg.dGld 153
                                       + ap yh+ m  v+++  elgi+T+f  ++GPLi+pa +k++llgv++ke ++++ae+l+++g e+alvvhg dG d
  gi|557694356|ref|YP_008797410.1| 157 MYAPYYHPIMGRVVKPEFELGIKTIFyTIIGPLISPADIKRHLLGVFKKEYVQPVAEILAKIGYEHALVVHGlDGFD 233
                                       *************************96699*********************************************** PP

                                       HHHHHHHHHHHHHHTTEEE.EEEEEEGSSTSSSEEESHHHHSSH.HHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHH CS
                   Glycos_transf_3 154 evsllakttvaelkdgeit.eytlepedfglkraelealeggep.kenaeilkavlegkksaakrdlvllnagaalv 228
                                       e+s++++t+vae+ +g+++ +y+++p+++gl ++ l+ +  ++p + na+i+k++++g+++  ++dl+l+n +  l+
  gi|557694356|ref|YP_008797410.1| 234 EISITGETLVAEVVNGKVKdTYKITPSELGLPTSPLDRIIENNPpDVNAQIIKRLFNGEEKGPRLDLLLANSAGHLY 310
                                       **************99986389***************987666549******************************* PP

                                       HTTSSSSHHHHHHHHHHHHHTSHH CS
                   Glycos_transf_3 229 lagkadslkegvakaeevidsGkA 252
                                       + + + slk+gv+ a+++i++GkA
  gi|557694356|ref|YP_008797410.1| 311 VGDVVRSLKDGVELAKQIIEEGKA 334
                                       ***********************9 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 !   47.1   0.0   1.8e-16   1.6e-12       3      61 ..      14      72 ..      12      74 .. 0.96
   2 ?   -3.3   0.0      0.96   8.6e+03      21      32 ..     242     253 ..     240     257 .. 0.78
   3 ?   -2.5   0.0      0.52   4.6e+03       2      12 ..     283     293 ..     282     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.8e-16
                                      HHHHHHTT.---HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHH CS
                   Glycos_trans_3N  3 iikklrdgeeLtaeeirfaihgilkgevtdaqiaAfLmAlrlkGetaeEiaalaeAmre 61
                                      +i kl+ +e+L++e i  ++ +i +g++tdaqi+ fL+Al  kG t++Eia  a  mr+
  gi|557694356|ref|YP_008797410.1| 14 AISKLVLRENLNDEIINCLLGEIKDGKATDAQIGGFLVALTSKGPTPDEIASIALTMRK 72
                                      799******************************************************97 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.96
                                       HHHHHHTTSS-H CS
                   Glycos_trans_3N  21 aihgilkgevtd 32 
                                       ++ ++++g+v+d
  gi|557694356|ref|YP_008797410.1| 242 LVAEVVNGKVKD 253
                                       677899999998 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.52
                                       HHHHHHHTT.- CS
                   Glycos_trans_3N   2 diikklrdgee 12 
                                       +iik+l +gee
  gi|557694356|ref|YP_008797410.1| 283 QIIKRLFNGEE 293
                                       699***99975 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:                      309  (0.0172346); 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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2808.48
//
Query:       gi|557694357|ref|YP_008797411.1|  [L=232]
Description: indole-3-glycerol-phosphate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-47  160.2   0.0    5.4e-47  160.1   0.0    1.0  1  IGPS      Indole-3-glycerol phosphate synthase
      0.005   17.0   0.0     0.0078   16.4   0.0    1.3  1  DUF2787   Protein of unknown function (DUF2787)


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 !  160.1   0.0   6.1e-51   5.4e-47      35     252 ..       3     223 ..       1     225 [. 0.94

  Alignments for each domain:
  == domain 1  score: 160.1 bits;  conditional E-value: 6.1e-51
                                       S-HHHHCHCHTTS-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT.-SEEEEE--CCCC---CCHHHHHHHH-SS- CS
                              IGPS  35 rsfaeaLresekklaliaEvKkaSPskgliredfdpaeiAkkyeeagAsaiSVLteekyFqGsledLrevrqavslp 111
                                       + f ++L+  +k  ++iaEvK  SPs g +    +p eiA +ye+agA+a+S +te + ++G++  Lre  ++++lp
  gi|557694357|ref|YP_008797411.1|   3 KRFLNSLKA-AKGNRIIAEVKTYSPSYGDLLRGRNPIEIALAYERAGAAALSYITERENYRGNMLILRELCRSIRLP 78 
                                       679999999.8999*************************************************************** PP

                                       EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEE CS
                              IGPS 112 vlrKdFiideyqieearalgadaiLLivkvledeeleelaeaakslglevLvEvhdeeeleralklgakiiGvNnRn 188
                                       vlrKdFi ++  +e++  + a aiLLi ++l+ ++l ela++a + ++e++vEvh+e +l+ +      iiG+Nn++
  gi|557694357|ref|YP_008797411.1|  79 VLRKDFIHSKFDVEKTAEADASAILLITQFLKSKTL-ELADVALEHDIEPVVEVHSERDLTYIGG-YRGIIGINNKD 153
                                       ********************************9995.7**********************98765.467******** PP

                                       TTTTEE-...CHHHHHHCHCC-....TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHH CS
                              IGPS 189 Lktlevd...lntteeLaklvp....kdvllvaeSGiktredveklkeegvnafLvGeslmrqedvekair 252
                                       + +le+d   ++ t +La+ ++    +d+++++eSGi++ +d++   ++ ++a L+G+++m +++ e+ +r
  gi|557694357|ref|YP_008797411.1| 154 ISKLETDeggVKLTARLAPRIRelhgRDIFIISESGISNLNDLSIALKH-ADAALIGTAFMLSDNPEELVR 223
                                       ******955567899***9999888889****************99999.*************99998776 PP

>> DUF2787  Protein of unknown function (DUF2787)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.7e-07    0.0078      33     117 ..      25     110 ..       3     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.7e-07
                                       -TT-BTTTB----EEEEEEE-SSS-EEEEEEEEE.EEE---..--EEEEEEEEETTTTEEEETTTEEEE-T-HHHHH CS
                           DUF2787  33 dksYsaeegGlhPvEirleresseewslvyitdF.aYvgep..ypelekeldfdfqkkevyqadlgalelekaeake 106
                                        +sY     G  P+Ei+l+ e+ +   l yit+   Y g+     el++++ +   +k++ ++++   +++  ea+ 
  gi|557694357|ref|YP_008797411.1|  25 SPSYGDLLRGRNPIEIALAYERAGAAALSYITEReNYRGNMliLRELCRSIRLPVLRKDFIHSKFDVEKTA--EADA 99 
                                       578999999***********************9637999862258*********99999999999888877..4444 PP

                                       HHHHHHHHHHH CS
                           DUF2787 107 llqlweknFle 117
                                          l+++ Fl+
  gi|557694357|ref|YP_008797411.1| 100 SAILLITQFLK 110
                                       44455566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1696.11
//
Query:       gi|557694358|ref|YP_008797412.1|  [L=207]
Description: phosphoribosylanthranilate isomerase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   93.6   0.0    1.7e-26   93.2   0.0    1.1  1  PRAI      N-(5'phosphoribosyl)anthranilate (PRA) isomerase
  ------ inclusion threshold ------
        0.1   12.6   0.1       0.22   11.5   0.1    1.5  1  DUF1307   Protein of unknown function (DUF1307)


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 !   93.2   0.0   1.8e-30   1.7e-26       2     193 ..       4     199 ..       3     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 93.2 bits;  conditional E-value: 1.8e-30
                                       CE----SHHHHHHHHHHTSSEEEEE--TTBTTB--HHHHHHHCCCS--EEEEEESSS-HHHHHHHHHHCTECEEEE- CS
                              PRAI   2 kicgltrasdvkaavkagadelglifaesskrevseeqaqellekvpaklVGVfvNqpieevlriaqelgldvvQLH 78 
                                       k+c +t+ +++ka+  a+   +g+++ +s k++vs + ++el++++++ +V V    ++++  +i+  l+  ++Q+H
  gi|557694358|ref|YP_008797412.1|   4 KVCCNTDVEEIKASQIAD--LIGVVTMSSHKKAVSLKRVRELMKHSEKPVVLVSDSMKLQDWIEIIL-LEPPAIQIH 77 
                                       778888888887765555..5999999999*****************99******999999888875.679****** PP

                                       CGG.-HHHHHHHH.HHS-TTSEEEEEE.E-S...SS--S-SSTT-...SEEEEESSS-SSSXXXXGGGGTTSXX..T CS
                              PRAI  79 Gdedeqeyeellk.telpvikalkvae.svd...evkearradhv...dllllDsgaGGtGelldwsliskllks.l 146
                                       Gd +  ++++ ++ ++  vik + v+  s d   +++++ ++ +    d +llDsg++ +G+l d    s + +s +
  gi|557694358|ref|YP_008797412.1|  78 GDIPLPDFKKIQSiYGGLVIKSITVPTiSSDplrDAEKILHKIKLyeaDYYLLDSGKA-SGKLHDIRI-SRIVASrH 152
                                       **95544444443146778999988862333555333322222222349********9.**9999865.55554559 PP

                                       TEEEESSXXTTTHHHHHT.TXXSEEEEXGGGEEETEEXHHHHHHHHH CS
                              PRAI 147 kviLAGGLtpeNvaeaiklegvlgvDvssGVEtnGvkDlekirkfvq 193
                                       +v+LAGGLtpeNv+e+i++ +++gvD ssG E nG k +eki++fv+
  gi|557694358|ref|YP_008797412.1| 153 PVMLAGGLTPENVVEVIRFVRPIGVDASSGLEINGRKSQEKIKRFVE 199
                                       *********************************************98 PP

>> DUF1307  Protein of unknown function (DUF1307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   2.5e-05      0.22      81     120 ..       9      47 ..       4      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.5e-05
                                       EETTS--HHHHTTTT--TT-HHHHHH--BHHHHHHHHHHT CS
                           DUF1307  81 idyekadldelkkldgvttqkekkkkkislkktekllekq 120
                                        d e+++ ++++ l gv t + ++kk +slk++ +l++++
  gi|557694358|ref|YP_008797412.1|   9 TDVEEIKASQIADLIGVVTMS-SHKKAVSLKRVRELMKHS 47 
                                       5999***************99.7999***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1533.70
//
Query:       gi|557694359|ref|YP_008797413.1|  [L=425]
Description: tryptophan synthase beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  151.9   0.1    3.2e-44  151.5   0.1    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 !  151.5   0.1   1.8e-48   3.2e-44       5     294 .]      72     411 ..      68     411 .. 0.84

  Alignments for each domain:
  == domain 1  score: 151.5 bits;  conditional E-value: 1.8e-48
                                       SSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT- CS
                              PALP   5 igpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGl 79 
                                        +pTPl+++ +l+k l +p  +++K+E+l ptgS+K+++a+   +++k +  ++ v+e+++G++g +lA+a++l+G+
  gi|557694359|ref|YP_008797413.1|  72 GRPTPLRQAVNLEKMLSTParIYFKREDLSPTGSHKTNTAVAQAYYAKSEGVRELVTETGAGQWGSSLALACSLYGI 148
                                       69********************************************999856777777777**************** PP

                                       EEEEEEETTS-...HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHH.....................STTCEE-- CS
                              PALP  80 kvtivvpadas...pekvallrllGaevvevggdydeavaaaaelaae.....................gegaylvs 132
                                       k+ +++ +++    p+++ l+++lGaev+ ++++++e+ ++   l ++                      e++y + 
  gi|557694359|ref|YP_008797413.1| 149 KCKVFMTRSSYehkPYRRVLMQMLGAEVIPSPSSVTETGRR--VLSSNpnhvgslgvaisealevvlksPESRYAIG 223
                                       *******99987778****************6664444444..2222222233333333333344444478888888 PP

                                       TTTSHHHHHHHHTHHHHHH...HHTTTTEEEEEEE-SSSHHHHHHHHHHHH....HSTT....-EEEEEEECTTCGG CS
                              PALP 133 qfdnptviegygtiglEil...eqlggkpdavvvpvGgGgliaGiaaglke....rrpd....vrvigvepegsdal 198
                                       +     v+  ++ iglE +   e++g  pd v+ +vGgG++++G+ +++      +  +    +r+i+ve+  +++l
  gi|557694359|ref|YP_008797413.1| 224 SVM-NFVMIHQSVIGLEAIwqlEEIGVTPDIVIGCVGGGSNFCGLTFPMIGlksrG--EgyreTRFIAVESLAAPKL 297
                                       885.566666*******97688***********************98877755340..24666************** PP

                                       TTCCS..S.SS..B...................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHH CS
                              PALP 199 arslragrrvtvpvs..................dtiadglavgspselafelldrlvdeivtvsdeealeamrllar 257
                                       +r+    r++  +++                  +  a gl+ +++++    l+++ + e  +  ++e+lea+  +a+
  gi|557694359|ref|YP_008797413.1| 298 TRGE--YRYDYPDTAcilplmkmysigkdyvppPIHAAGLRYHAAAPTLSLLVKEGLVEPRAYGQDEVLEAAMMFAK 372
                                       ****..55555555588999999********************8888888899999999****************** PP

                                       HHSB-B-HHHHHHHHHH..HHHHHHCCTTCEEEEEEE-B CS
                              PALP 258 regivvepssaaalaal..klreagelkegdrvvviltg 294
                                       +egivv p +a+a+  +  ++ +++e +e+ ++++ l+g
  gi|557694359|ref|YP_008797413.1| 373 AEGIVVAPETAHAVKCVidEAIKCRETGEKLNILFCLSG 411
                                       ***************999****************99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3154.02
//
Query:       gi|557694360|ref|YP_008797414.1|  [L=254]
Description: tryptophan synthase alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-35  122.5   0.0    1.7e-35  122.2   0.0    1.0  1  Trp_syntA  Tryptophan synthase alpha chain
     0.0059   15.9   0.5     0.0096   15.2   0.5    1.2  1  ThiG       Thiazole biosynthesis protein ThiG
  ------ inclusion threshold ------
      0.049   13.2   0.0       0.12   11.9   0.0    1.7  1  HMGL-like  HMGL-like


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 !  122.2   0.0   2.8e-39   1.7e-35       9     235 ..      10     234 ..       2     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 2.8e-39
                                       B-EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHHC CS
                         Trp_syntA   9 raafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkke 85 
                                       ++ +  y+t+g+p+ +++lei+++l + g+d++E G+p+  P  dGPvI+++++  L++g    ++l l++e++ ++
  gi|557694360|ref|YP_008797414.1|  10 NKSLTIYLTLGYPSRDEMLEIVDELMRMGVDLLEFGIPYEAPKYDGPVIRRTHKTVLSNGFGYGEALGLLKEIKIEN 86 
                                       567888********************************************************************443 PP

                                       SSS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSBCCCHHHH...HHHHHHTT-EEEEEE-TTS-HHHHHHH CS
                         Trp_syntA  86 vevPivlltylnlvlsygeerflaelkeagvdglivpDlPleeaeel...veaakkkglelvflvapttsderlkev 159
                                            +llty++l  + g e+f++el e+gv +++ pDl  e  e+l    ++ ++++ e v  v+ + + + ++ +
  gi|557694360|ref|YP_008797414.1|  87 ----QFLLTYFELAQKIGVEKFFRELSETGVRAVLFPDLLIEYPEKLssyDKLSDQYQFEKVYFVSSSFPHRMIAGL 159
                                       ....389********************************877666551115678899******************** PP

                                       HHH--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHC.TSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHH CS
                         Trp_syntA 160 veqaegfvYvvsraGvTgaenavaaevdelverlkkl.tavPvavGFGistkeqvkqva.kvadGvivGSalvkkie 234
                                       v +  +f+Y+   +  Tg+  a+   v + ++ +k l ++vP+  GF ++t+eqv+q +  + +Gv++GSa+  +i+
  gi|557694360|ref|YP_008797414.1| 160 VDREPSFIYM-GLMASTGV--ALPIAVRRNIAIIKGLlNDVPIIGGFAVRTAEQVRQYVdGGISGVVIGSAVASIID 233
                                       *********7.34455665..5677899999999986269*****************998999*********99998 PP

                                       C CS
                         Trp_syntA 235 e 235
                                       +
  gi|557694360|ref|YP_008797414.1| 234 N 234
                                       5 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.5   1.6e-06    0.0096     149     210 ..     169     231 ..     160     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-06
                                       EEBSSSTTS----S-HHHHHHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTS CS
                              ThiG 149 mPlaapiGsglGllnkealkiiieea.kvPvivDAGigspsdaaqamelGadavllntavaea 210
                                       m l a  G +l ++ + ++ ii   + +vP+i    +++++++ q ++ G+++v++ +ava+ 
  gi|557694360|ref|YP_008797414.1| 169 MGLMASTGVALPIAVRRNIAIIKGLLnDVPIIGGFAVRTAEQVRQYVDGGISGVVIGSAVASI 231
                                       8899999****************9999*********************************985 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.12      21      49 ..      23      51 ..      21     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                                      -HHHHHHHHHHHHHHT-SEE--TSGGGT. CS
                         HMGL-like 21 sveeklaiakaLdeagvdeiEvgfpaase 49
                                      s +e+l+i+++L ++gvd +E g+p   +
  gi|557694360|ref|YP_008797414.1| 23 SRDEMLEIVDELMRMGVDLLEFGIPYEAP 51
                                      679*********************98654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1806.18
//
Query:       gi|557694361|ref|YP_008797415.1|  [L=553]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); 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 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3857.82
//
Query:       gi|557694362|ref|YP_008797416.1|  [L=88]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00029   21.4   0.0    0.00039   21.0   0.0    1.2  1  RHH_6     Ribbon-helix-helix domain


Domain annotation for each model (and alignments):
>> RHH_6  Ribbon-helix-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.2e-08   0.00039       6      48 ..       8      50 ..       3      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.2e-08
                             RHH_6  6 nvavspetdqavrafLAsqGggrkGdLSrfieeAVrayllela 48
                                       + +s+ + +  r ++A++ g+r+G+LS+ +e+ + + + e+ 
  gi|557694362|ref|YP_008797416.1|  8 KIEISKPIAEKFRRWVAERYGMRRGALSKAVEDLIAKAVNEPE 50
                                      68899999*************************9999888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 622.86
//
Query:       gi|557694363|ref|YP_008797417.1|  [L=126]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   37.7   0.3    2.9e-09   37.5   0.3    1.1  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.093   12.5   0.2       0.25   11.1   0.1    1.9  2  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 !   37.5   0.3   3.2e-13   2.9e-09       1     120 [.       2     120 ..       2     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 3.2e-13
                                       EEE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHH CS
                               PIN   1 ivlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidae 76 
                                       +++D++v++++l ++ek  +a+  le++ +  t+a +l  +l++++   +++ ++   +  ++  +++l ++ ++ +
  gi|557694363|ref|YP_008797417.1|   2 YLIDANVILEVLYKREKWQKAASFLERVKKGETTAYILHFTLHGISV-ILGKPELVSKLIIEISsWRGLGVIATSLD 77 
                                       68**************************8888888888888888888.66667777777777777999999999999 PP

                                       HHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  77 iaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                         + aae a + gl+  D l + +Ak++g+++  ++D+df++++
  gi|557694363|ref|YP_008797417.1|  78 EELAAAEKAIHIGLDFDDGLQYYVAKKRGLTIM-SYDSDFDNTD 120
                                       9999999999999*****************766.*******987 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      0.68   6.1e+03       4      12 ..       3      11 ..       2      18 .. 0.72
   2 ?   11.1   0.1   2.8e-05      0.25      30      61 ..      89     119 ..      70     126 .] 0.77

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.68
                           DUF5615  4 llDenlspr 12
                                      l+D+n+  +
  gi|557694363|ref|YP_008797417.1|  3 LIDANVILE 11
                                      899998655 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 2.8e-05
                           DUF5615  30 lglegasDeeileyAkeedriivTkDkDFgel 61 
                                       +gl+  +D     +Ak+++++i++ D+DF + 
  gi|557694363|ref|YP_008797417.1|  89 IGLD-FDDGLQYYVAKKRGLTIMSYDSDFDNT 119
                                       4555.788888899***************886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); 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:                         2  (0.000111551); expected 0.2 (1e-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: 951.03
//
Query:       gi|557694364|ref|YP_008797418.1|  [L=614]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 4547.30
//
Query:       gi|557694365|ref|YP_008797419.1|  [L=249]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   68.8   0.0    7.2e-19   68.3   0.0    1.4  1  Cas_NE0113    CRISPR-associated protein NE0113 (Cas_NE0113)
    0.00046   20.1   0.1    0.00089   19.2   0.1    1.6  1  Cas_APE2256   CRISPR-associated protein (Cas_APE2256)
     0.0016   17.4   0.0     0.0021   16.9   0.0    1.2  1  Cas_Cas02710  CRISPR-associated protein (Cas_Cas02710)
  ------ inclusion threshold ------
      0.092   11.4   0.1       0.14   10.8   0.1    1.2  1  AXE1          Acetyl xylan esterase (AXE1)


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 !   68.3   0.0   1.6e-22   7.2e-19       1     143 [.      11     140 ..      11     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 1.6e-22
                        Cas_NE0113   1 sPqVvTetldaLlqegepvdevvvittkdgkvrealelLleeflkdygakikldesaihviedvsgeelaDirteed 77 
                                       sP+VvTe +d +++  e ++ + +++t+  +v + + l           + +++ +++ + + v+  +l D+  e++
  gi|557694365|ref|YP_008797419.1|  11 SPAVVTEFVDYIEK-REKITTLRIVATRADQVVSGALLA----------AEAVRYRYPWIKASVDTLPLSDVTNEDE 76 
                                       7***********99.7789**********9998876555..........556677777778899************* PP

                        Cas_NE0113  78 neallqlivrlvrelrenegerlhlsiaGGRKtmsillalaaqLygreqDrlyHvlveeefesnre 143
                                       n ++++ +v+++++ ++++ er++l++aGGRK m++ + l+aq+ g   + +yHvl  +  ++n e
  gi|557694365|ref|YP_008797419.1|  77 NYVFMEELVNVIKSIKSSDAERIYLCLAGGRKEMAVAAVLVAQIMG--LNAVYHVLSHNIRKANVE 140
                                       ******************99**************************..9******76655444333 PP

>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1     2e-07   0.00089      49     123 ..      59     128 ..      18     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2e-07
                       Cas_APE2256  49 egaevevveieklsdlgree.FreglrnLveklarevknkkregekvlinaTgGfKpeiavltlvallladevyYi 123
                                        +a v++    ++++++++  F+e l+n ++ ++        ++e++++ + gG K  +++++lva++++ +++Y 
  gi|557694365|ref|YP_008797419.1|  59 IKASVDTLPLSDVTNEDENYvFMEELVNVIKSIK------SSDAERIYLCLAGGRKEMAVAAVLVAQIMGLNAVYH 128
                                       4566777777778777755447666666666655......4699************************98888884 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 !   16.9   0.0   4.8e-07    0.0021      53     130 ..      76     163 ..      45     175 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.8e-07
                                       HHHHHHHHHHHHS......TTS-EEEE-SSS-HHHHHHHHHHHHHHTEEEEE.EE--B....-----SB-GGG-EEE CS
                      Cas_Cas02710  53 elykkikevleka.....leeeevivDlTgGtkeMtaglalagillrvklsy.Vggea....dkelgrvepGteklr 119
                                       e y  ++e+++         +e +++ l gG keM+++++l++ +++++++y V +++    + el r++     l+
  gi|557694365|ref|YP_008797419.1|  76 ENYVFMEELVNVIksiksSDAERIYLCLAGGRKEMAVAAVLVAQIMGLNAVYhVLSHNirkaNVELERIRDKIKELA 152
                                       44444444444444446668899**********************99877764777666433445667777777777 PP

                                       EE--HHHH-TT CS
                      Cas_Cas02710 120 iledpyavfae 130
                                       +++dp + +a+
  gi|557694365|ref|YP_008797419.1| 153 SSKDPGEYYAR 163
                                       77777777776 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   3.1e-05      0.14     159     247 ..      82     172 ..      75     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHH.H-SS-SEEEEES-SSSSHHHHHHH-SSTTCHHHHHHHH.HS CS
                              AXE1 159 vrlveivaslpevDeeRvavlGasqGGalalavaa.lekrikavvadyPfLsdfkRvvelaleeaYdEitrylk.ld 233
                                        +lv++++s++  D eR+  + a  GG   +avaa l  +i  + a y  Ls+  R  +++le   d i++     d
  gi|557694365|ref|YP_008797419.1|  82 EELVNVIKSIKSSDAERIYLCLA--GGRKEMAVAAvLVAQIMGLNAVYHVLSHNIRKANVELERIRDKIKELASsKD 156
                                       579***************99865..88888887764799*****************999998777776666555444 PP

                                       H..-CCHHHHHHHHHH CS
                              AXE1 234 p..erekeeevletLs 247
                                       p    ++++e++e++ 
  gi|557694365|ref|YP_008797419.1| 157 PgeYYARNAELFEKVM 172
                                       3113355666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       910  (0.0507558); expected 358.6 (0.02)
Passed bias filter:                      755  (0.0421105); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1784.05
//
Query:       gi|557694366|ref|YP_008797420.1|  [L=687]
Description: hypothetical protein CSUB_C0935 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.9   0.3      0.062   13.0   0.3    1.3  1  ADP_ribosyl_GH  ADP-ribosylglycohydrolase
       0.11   12.6   0.0         17    5.6   0.0    2.5  2  Importin_rep_3  Importin 13 repeat
       0.14   12.6   0.2       0.33   11.4   0.2    1.5  1  FRB_dom         FKBP12-rapamycin binding domain
        0.2   11.8   2.4       0.36   11.0   2.4    1.4  1  MnmE_helical    MnmE helical domain


Domain annotation for each model (and alignments):
>> ADP_ribosyl_GH  ADP-ribosylglycohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   1.4e-05     0.062     135     219 ..     437     537 ..     432     571 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                                       HHHTSS.-HHHHHHHHHHHHHTTB--HHHHHHHHHHHHHHHHHHTT--STHHHHHH......HHHHTTT-HHHHHHH CS
                    ADP_ribosyl_GH 135 gllyag.dpeeaaelaeeaarlTHnhpeavagaaayaaliaaalrgksleealdaa....eeelavapaeeelaaal 206
                                        l+ +g  pee  el+ ++a+ TH h   ++ + ++ ++++a+l   ++ + +++     + ++ v++a+e+l+   
  gi|557694366|ref|YP_008797420.1| 437 TLALHGtRPEERWELVDRTASQTHVHLSKMELCSLLGYAVYALLSSFENITKVEEEkladALKEMVKEARERLEHGR 513
                                       56677779***************************************999999999555534444444444444444 PP

                                       GGGGG---HHH............. CS
                    ADP_ribosyl_GH 207 rkalaladsdkd...........v 219
                                       r ++a ++++ +           +
  gi|557694366|ref|YP_008797420.1| 514 RSVEATQRRQVSlldeassslkeA 537
                                       444444443333555544444431 PP

>> Importin_rep_3  Importin 13 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0    0.0099        44      32      59 ..     184     211 ..     169     218 .. 0.86
   2 ?    5.6   0.0    0.0037        17      22      55 ..     391     424 ..     387     426 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0099
                    Importin_rep_3  32 vvqedGklLvetvLeaiggesprslleh 59 
                                        ++++ k+++  +L ai g spr  +e 
  gi|557694366|ref|YP_008797420.1| 184 PLTQQDKVMLLLLLAAIVGFSPRYWIEA 211
                                       588999*****************99986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0037
                    Importin_rep_3  22 qceeipelkqvvqedGklLvetvLeaiggesprs 55 
                                        ++e   +++ ++++G++  ++vL+a g  ++r 
  gi|557694366|ref|YP_008797420.1| 391 ASAETIRVRELLTSEGESVFNQVLNALGVRATRA 424
                                       57788899********************999985 PP

>> FRB_dom  FKBP12-rapamycin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   7.4e-05      0.33      28      97 ..     493     571 ..     480     572 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.4e-05
                           FRB_dom  28 knveamlklleplhellek.....gpetlreasFaqafgreLkeaeewlkkykkteneed....lnqawdiyyevfr 95 
                                       k ++a+ +++++  e le+     +++  r++s + + +++Lkeaeewl+k k++ ++++    l+ +  ++y++ +
  gi|557694366|ref|YP_008797420.1| 493 KLADALKEMVKEARERLEHgrrsvEATQRRQVSLLDEASSSLKEAEEWLEKAKSSTSRREaatcLETVVILCYKIVE 569
                                       44455555566666666662222233456788999*****************6665555534448888888888888 PP

                           FRB_dom  96 ri 97 
                                       ++
  gi|557694366|ref|YP_008797420.1| 570 KL 571
                                       76 PP

>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.4   8.1e-05      0.36     117     169 ..     491     545 ..     329     562 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.1e-05
                                       xxxxxxxxxxxxxxxx.x.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      MnmE_helical 117 tgegieeLeeaikele.l.eei.eeeplltnaRhkealekalealeeakealeagl 169
                                       +++  ++L+e +ke++ + e +   ++ +t++R+ ++l +a ++l+ea+e le++ 
  gi|557694366|ref|YP_008797420.1| 491 EEKLADALKEMVKEAReRlE-HgRRSVEATQRRQVSLLDEASSSLKEAEEWLEKAK 545
                                       22224555555555332322.2355899**********************999874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (687 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       977  (0.0544927); expected 358.6 (0.02)
Passed bias filter:                      690  (0.0384851); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 4536.29
//
Query:       gi|557694367|ref|YP_008797421.1|  [L=131]
Description: hypothetical protein CSUB_C0936 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 992.62
//
Query:       gi|557694368|ref|YP_008797422.1|  [L=330]
Description: DNA primase large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-23   83.5   0.1    2.9e-23   82.6   0.1    1.4  1  DNA_primase_lrg  Eukaryotic and archaeal DNA primase, large s
  ------ inclusion threshold ------
      0.016   13.4   0.1      0.024   12.9   0.1    1.4  1  COG6             Conserved oligomeric complex COG6
      0.068   13.1   0.2       0.15   12.1   0.2    1.5  1  Hep_core_N       Hepatitis core protein, putative zinc finger


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 !   82.6   0.1   4.8e-27   2.9e-23       2     219 ..     122     315 ..     121     328 .. 0.82

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 4.8e-27
                                       EEEEEHHHHHHHTT..-G.......GS-EETTEEEE-HHHHHHHHHHHHHHHHHH..........HHGGGSSS---H CS
                   DNA_primase_lrg   2 fykvpfedvldlvk..rr.......rvllkkGyaylpkeeleslllekfrkrlekalestkeslpeleeeikedere 69 
                                        y+++f+d+l+l++  +        ++ l +Gy+ l+++e+ +l +e+  + +  ++  + ++l+       e++ +
  gi|557694368|ref|YP_008797422.1| 122 HYMIHFTDYLRLAErlTSntrwklvNRTLSRGYVHLTRSEVCRLAREAAYN-IFSDFSALPKNLKPP-----EKILN 192
                                       699***********6622678***********************9999888.888888888887766.....22222 PP

                                       HHHHHHCT--.............TTSSTTGG.SHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--CH CS
                   DNA_primase_lrg  70 kleellealsesyvaedvqeeedskisakni.dklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsld 145
                                       +l e+++ l                 +ak+i +   k+  PpC+ ++ +++   +  +h + ++l++Fl + g++++
  gi|557694368|ref|YP_008797422.1| 193 QLNEINQILA---------------AKAKTItTPSNKNEWPPCIHAIANRI---SDASHFECFTLAAFLTNKGYTVE 251
                                       3556666666...............6667877888999*************...788999***************** PP

                                       HHHCCCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S.-HHHH...HHHHHHHH CS
                   DNA_primase_lrg 146 eilelwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahg.Cpfrh..dpdklktlL 218
                                       +++++++        +Fd+   ry+++h++Gk g++t y p+sC ++         +ah  C  +    p+++k+ L
  gi|557694368|ref|YP_008797422.1| 252 QVVDIFRAR-----ADFDEkIARYQVEHIAGKRGSGTIYRPPSCPTM---------QAHNlCIEKGklCPKNIKNPL 314
                                       ********7.....9****8888************************.........666667554466677787777 PP

                                       H CS
                   DNA_primase_lrg 219 q 219
                                       q
  gi|557694368|ref|YP_008797422.1| 315 Q 315
                                       7 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     4e-06     0.024     386     487 ..     175     263 ..      94     276 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-06
                              COG6 386 kdklakllpelp..psdLspPewlsealskllelletyesslaseaserekdfeevlsalldpllqacersakklek 460
                                       +d+        +  p++L+pPe + + l++++++l++  +++++   +++++  + ++a+ + + +a     +++e 
  gi|557694368|ref|YP_008797422.1| 175 SDF--------SalPKNLKPPEKILNQLNEINQILAAKAKTITT--PSNKNEWPPCIHAIANRISDA-----SHFEC 236
                                       222........222689******************999998887..345777777777544444443.....46677 PP

                              COG6 461 kdkaifliNcldliqstLspysfaskk 487
                                          a+fl+N  +++++++  +   ++ 
  gi|557694368|ref|YP_008797422.1| 237 FTLAAFLTNKGYTVEQVVDIFRARADF 263
                                       777777777777777776666555555 PP

>> Hep_core_N  Hepatitis core protein, putative zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   2.4e-05      0.15      13      24 ..     289     300 ..     287     302 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                        Hep_core_N  13 sCPtvqAsKLCL 24 
                                       sCPt+qA  LC+
  gi|557694368|ref|YP_008797422.1| 289 SCPTMQAHNLCI 300
                                       9**********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); 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: 00:00:00.40
# Mc/sec: 2472.64
//
Query:       gi|557694369|ref|YP_008797423.1|  [L=467]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   40.3   0.0    8.5e-10   39.1   0.0    1.6  1  DUF87          Helicase HerA, central domain
    1.7e-07   30.5   0.0    3.4e-07   29.5   0.0    1.4  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
    3.2e-06   27.6   0.1      7e-06   26.5   0.1    1.6  1  AAA_16         AAA ATPase domain
    1.5e-05   23.8   0.0    0.00015   20.5   0.0    2.1  2  DUF853         Bacterial protein of unknown function (DUF853)
    2.5e-05   24.6   0.0      0.012   15.9   0.0    2.5  2  AAA_22         AAA domain
    0.00023   20.2   0.0    0.00042   19.3   0.0    1.3  1  AAA_10         AAA-like domain
    0.00038   19.6   0.0    0.00065   18.8   0.0    1.3  1  T2SSE          Type II/IV secretion system protein
    0.00062   19.7   0.0     0.0011   18.8   0.0    1.4  1  MobB           Molybdopterin guanine dinucleotide synthesis p
    0.00074   18.8   0.0     0.0011   18.2   0.0    1.2  1  DUF815         Protein of unknown function (DUF815)
     0.0017   17.9   0.0     0.0032   17.0   0.0    1.4  1  AAA_7          P-loop containing dynein motor region
     0.0019   18.1   0.1     0.0056   16.6   0.0    1.9  2  NTPase_1       NTPase
     0.0093   15.3   0.0      0.016   14.6   0.0    1.3  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
  ------ inclusion threshold ------
       0.02   14.9   0.0      0.049   13.6   0.0    1.6  1  AAA_5          AAA domain (dynein-related subfamily)
      0.029   13.5   0.0      0.045   12.8   0.0    1.2  1  LpxK           Tetraacyldisaccharide-1-P 4'-kinase
      0.029   13.6   0.0      0.054   12.8   0.0    1.3  1  Zeta_toxin     Zeta toxin
      0.035   13.8   0.0      0.087   12.5   0.0    1.6  2  AAA_30         AAA domain
      0.047   13.1   0.0        0.6    9.5   0.0    2.1  2  PhoH           PhoH-like protein
       0.05   13.7   0.0      0.097   12.7   0.0    1.6  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
      0.057   13.0   0.0        0.1   12.2   0.0    1.4  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
      0.062   13.5   0.0        0.1   12.8   0.0    1.3  1  RMP            Retinal Maintenance
      0.068   12.9   0.0       0.11   12.2   0.0    1.3  1  ATP_bind_1     Conserved hypothetical ATP binding protein
      0.068   13.1   0.0       0.16   11.9   0.0    1.8  1  ATPase_2       ATPase domain predominantly from Archaea
      0.076   13.4   0.0        3.1    8.2   0.0    2.5  2  AAA            ATPase family associated with various cellular
      0.087   11.8   0.0       0.16   10.9   0.0    1.3  1  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
        0.1   12.3   0.0       0.18   11.5   0.0    1.3  1  AAA_24         AAA domain
       0.14   11.9   0.0       0.24   11.1   0.0    1.4  1  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
       0.17   11.5   0.0       0.32   10.6   0.0    1.4  1  SRP54          SRP54-type protein, GTPase domain
       0.18   11.7   0.0       0.35   10.8   0.0    1.5  1  NACHT          NACHT 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 !   39.1   0.0   1.3e-12   8.5e-10      20     127 ..      67     163 ..      61     221 .. 0.75

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 1.3e-12
                             DUF87  20 klvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvkvitpspsakdkelkinpws 96 
                                         +++H++++g+TGsGK+ +v+  l+ l  ++g++++++D+ GEY         ++++ +++        +k+  ++
  gi|557694369|ref|YP_008797423.1|  67 D-FNKHVLVVGRTGSGKTSLVRKALDFLR-RRGVRVVVIDWKGEYDLNG----VPRIRGFDV--------FKVFGDR 129
                                       4.49*********************9999.***************8777....777777776........5677777 PP

                             DUF87  97 ldpeelldllee...ddkpaaavqrsvleealdq 127
                                       l+p  l++ l e     +p+a v  +vl++++++
  gi|557694369|ref|YP_008797423.1| 130 LTPLVLAEALREafnLSEPQAYVMLNVLQQFYEK 163
                                       7777777777776666666666666666666664 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 !   29.5   0.0   5.3e-10   3.4e-07      15      55 ..      69     109 ..      63     111 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 5.3e-10
                     TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairargdraivlDltGaf 55 
                                       ++h+l+vG tGsGKt  ++k l+ +r+rg r++v+D +G++
  gi|557694369|ref|YP_008797423.1|  69 NKHVLVVGRTGSGKTSLVRKALDFLRRRGVRVVVIDWKGEY 109
                                       68*************************************97 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   0.1   1.1e-08     7e-06      25     107 ..      70     175 ..      54     261 .. 0.64

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.1e-08
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggif....lrgkcdqlesaipysalaqalareellrqlldeaesaeleaw 97 
                                         vl++G  G+GK+slvr++l+ l+++g+ +     +g++d +  ++p+   ++ ++  +++ + l+++  ae+ + 
  gi|557694369|ref|YP_008797423.1|  70 KHVLVVGRTGSGKTSLVRKALDFLRRRGVRVvvidWKGEYDLN--GVPR---IRGFDVFKVFGDRLTPLVLAEALRE 141
                                       78*************************7666445555666666..6665...4444444566666666333222222 PP

                            AAA_16  98 rekleeala........................a 107
                                       +  l e  a                        +
  gi|557694369|ref|YP_008797423.1| 142 AFNLSEPQAyvmlnvlqqfyekgldnaeallklI 175
                                       2222222112333344444444444444555551 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 !   20.5   0.0   2.4e-07   0.00015      15      65 ..      63     115 ..      52     138 .. 0.90
   2 ?    0.7   0.0      0.24   1.5e+02     278     320 ..     270     312 ..     211     334 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.4e-07
                            DUF853  15 lalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkG..dLsgia 65 
                                       l+l+  n+h l+ G tG Gkt  +++  + l + Gv v++ d kG  dL g+ 
  gi|557694369|ref|YP_008797423.1|  63 LSLDDFNKHVLVVGRTGSGKTSLVRKALDFLRRRGVRVVVIDWKGeyDLNGVP 115
                                       567788***************************************66777775 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.24
                            DUF853 278 lekveqvvrLirskGvGvyfvtqnPldlPdtvLaqLGnrvqha 320
                                       +   e++v   r+ GvG   v+ +P  lP +  + +G+ +  +
  gi|557694369|ref|YP_008797423.1| 270 VSIGERMVNECRAFGVGCIIVAPDPFQLPLHLESDVGAVISFG 312
                                       55558899999******************99999999887765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.9e-05     0.012       6      46 ..      70     104 ..      67     119 .. 0.83
   2 ?    6.1   0.0      0.02        13      84     115 ..     240     283 ..     212     320 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.9e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvt 46 
                                       ++++v+G +G+GKT l+r+ l+ l ++      +++vv ++
  gi|557694369|ref|YP_008797423.1|  70 KHVLVVGRTGSGKTSLVRKALDFLRRR------GVRVVVID 104
                                       6899******************99654......66666555 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
                            AAA_22  84 qalrarav..ielliiDEaqhlr...s.......eealeeLrsl 115
                                       + ++  a+  + +++i+Eaq++    +       e++++e+r +
  gi|557694369|ref|YP_008797423.1| 240 ESVHGGARsfHTIVVIEEAQNIVrrgKnndvsigERMVNECRAF 283
                                       444444447789*********65566145566778888888776 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   6.6e-07   0.00042      21     135 ..      69     179 ..      65     197 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.6e-07
                            AAA_10  21 asasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpeiakkinvvtLdseeenegvLdPlvllk 97 
                                       + ++l++G +G GK  l++ +  +++ +g ++++iD k e     + +p   + ++v ++    +    L Plvl++
  gi|557694369|ref|YP_008797423.1|  69 NKHVLVVGRTGSGKTSLVRKALDFLRRRGVRVVVIDWKGEYD--LNGVPR-IRGFDVFKVF--GD---RLTPLVLAE 137
                                       7899************************************22..223344.3446666665..33...488888888 PP

                            AAA_10  98 eekeaesl....aedilelllgvkkkesekkaalseaveavl 135
                                         +ea +l    a  +l++l+++ +k  ++ +al + ++ ++
  gi|557694369|ref|YP_008797423.1| 138 ALREAFNLsepqAYVMLNVLQQFYEKGLDNAEALLKLIKDKV 179
                                       777765542222567888888888888888888888887766 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 !   18.8   0.0     1e-06   0.00065     129     175 ..      69     115 ..      41     121 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1e-06
                             T2SSE 129 rglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqlegan 175
                                       ++ +lv G TgsGKt l+  +l ++  +  r+v++    E++l+g+ 
  gi|557694369|ref|YP_008797423.1|  69 NKHVLVVGRTGSGKTSLVRKALDFLRRRGVRVVVIDWKGEYDLNGVP 115
                                       6789*******************************999999998865 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 !   18.8   0.0   1.7e-06    0.0011       2      33 ..      72     103 ..      71     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                              MobB   2 lgivgksgsGKTtLleklipelkarglrvgti 33 
                                       + +vg+ gsGKT+L+ k +  l++rg+rv +i
  gi|557694369|ref|YP_008797423.1|  72 VLVVGRTGSGKTSLVRKALDFLRRRGVRVVVI 103
                                       5689*************************998 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.7e-06    0.0011      53      90 ..      69     106 ..      52     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.7e-06
                            DUF815  53 annvLLwGarGtGKSslvkallneyaeegLrlieveke 90 
                                        ++vL++G  G+GK slv+ +l  ++++g+r++ ++ +
  gi|557694369|ref|YP_008797423.1|  69 NKHVLVVGRTGSGKTSLVRKALDFLRRRGVRVVVIDWK 106
                                       579******************************99854 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 !   17.0   0.0     5e-06    0.0032      32      67 ..      68     103 ..      53     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5e-06
                             AAA_7  32 nkkpvllvGptGtGKtviikdllkkldkekylslti 67 
                                        +k+vl+vG tG+GKt+++++ l+ l ++ + +++i
  gi|557694369|ref|YP_008797423.1|  68 FNKHVLVVGRTGSGKTSLVRKALDFLRRRGVRVVVI 103
                                       589******************999998877777666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   8.8e-06    0.0056       1      31 [.      71     101 ..      71     167 .. 0.87
   2 ?   -2.0   0.1       4.6     3e+03      39      77 ..     242     278 ..     237     285 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.8e-06
                                       EEEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                       +v++ G+ G+GKt lv+k+l+ l+++gv+v 
  gi|557694369|ref|YP_008797423.1|  71 HVLVVGRTGSGKTSLVRKALDFLRRRGVRVV 101
                                       7999************************995 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.6
                                       -------EEEEEET.T--EEEEEETT---SSEETTEEE- CS
                          NTPase_1  39 reggrrigFkivdlasgeegiLarveakreprvgkyvvd 77 
                                        +gg r+  +iv +  +e +++ r+++++ +++g+ +v+
  gi|557694369|ref|YP_008797423.1| 242 VHGGARSFHTIVVI--EEAQNIVRRGKNNDVSIGERMVN 278
                                       46788888888888..66666667777888888887776 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.5e-05     0.016      40      58 ..      70      88 ..      47     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.5e-05
                                      .SEEEE--TTSSHHHHHHH CS
                      FtsK_SpoIIIE 40 shllvaGatgsGKStalnt 58
                                       h+lv+G+tgsGK+  ++ 
  gi|557694369|ref|YP_008797423.1| 70 KHVLVVGRTGSGKTSLVRK 88
                                      6*************99875 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 ?   13.6   0.0   7.7e-05     0.049       1      31 [.      71     102 ..      71     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.7e-05
                                       EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaal.nreveyvq 31 
                                       +vl+vG +G+gK++l+++ + +l +r v +v 
  gi|557694369|ref|YP_008797423.1|  71 HVLVVGRTGSGKTSLVRKALDFLrRRGVRVVV 102
                                       79*********************666666555 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.1e-05     0.045      16      71 ..      52     103 ..      37     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.1e-05
                                       HHHHHHHHHTTSS--B--SS-EEEEEESBSS-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK  16 valrralyragllkserlpvpVivVGNitvGGtGKTPlvialvkllqarglkvgvl 71 
                                       v +r +++  +ll+   ++  V+vVG     G+GKT+lv   +++l++rg++v+v+
  gi|557694369|ref|YP_008797423.1|  52 VMRRSRRF-LNLLSLDDFNKHVLVVGRT---GSGKTSLVRKALDFLRRRGVRVVVI 103
                                       33344444.789999999********74...9**********************98 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.5e-05     0.054      17      50 ..      70     104 ..      66     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.5e-05
                        Zeta_toxin  17 klillgGqpGAGKselaellkdele.rqgnvvrld 50 
                                       k +l++G +G+GK++l +++ d l+ r+ +vv++d
  gi|557694369|ref|YP_008797423.1|  70 KHVLVVGRTGSGKTSLVRKALDFLRrRGVRVVVID 104
                                       5699********************85555666665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00014     0.087      19      52 ..      70     103 ..      64     108 .. 0.90
   2 ?   -3.1   0.0       8.4   5.4e+03      89     114 ..     250     282 ..     223     298 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrvigl 52 
                                       + ++++G+ G+GKt +++++ + ++++g rv+++
  gi|557694369|ref|YP_008797423.1|  70 KHVLVVGRTGSGKTSLVRKALDFLRRRGVRVVVI 103
                                       46899*************************9975 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.4
                            AAA_30  89 gtllivDEagmv.......dtkqlaallkaaek 114
                                       +t++++ Ea  +       d +  +++++++++
  gi|557694369|ref|YP_008797423.1| 250 HTIVVIEEAQNIvrrgknnDVSIGERMVNECRA 282
                                       477777777665444444444444555555555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00094       0.6      15      54 ..      62     103 ..      53     105 .. 0.79
   2 ?    1.0   0.0      0.37   2.4e+02     121     133 ..     251     263 ..     245     302 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00094
                                       HHH...H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEE CS
                              PhoH  15 alk...kndivfaiGpaGtGKtylavalavealkkkkvkriil 54 
                                        l+    n+ v ++G++G+GKt l v  a++ l+++ v+ +++
  gi|557694369|ref|YP_008797423.1|  62 LLSlddFNKHVLVVGRTGSGKTSL-VRKALDFLRRRGVRVVVI 103
                                       554445788999***********9.789999999998887775 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.37
                                       EEEEE-SGGG--H CS
                              PhoH 121 afvilDEAQnttk 133
                                       ++v++ EAQn+ +
  gi|557694369|ref|YP_008797423.1| 251 TIVVIEEAQNIVR 263
                                       6899******965 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 ?   12.7   0.0   0.00015     0.097       6      34 ..      76     104 ..      72     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                                       SSTTSSHHHHHHHHHHHHHHTT--EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   6 tkGGvGKTtlaanLaralarrglrVllvD 34 
                                       +  G+GKT+l+ + +  l rrg rV+++D
  gi|557694369|ref|YP_008797423.1|  76 GRTGSGKTSLVRKALDFLRRRGVRVVVID 104
                                       678*************************9 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   0.0   0.00016       0.1       3      32 ..      72     103 ..      70     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEE CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavi 32 
                                       ++++G  GsGKT+L+++ l   +r+g ++ vi
  gi|557694369|ref|YP_008797423.1|  72 VLVVGRTGSGKTSLVRKALdfLRRRGVRVVVI 103
                                       5799***************8777778877777 PP

>> RMP  Retinal Maintenance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00016       0.1      69      90 ..     428     449 ..     363     457 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                               RMP  69 sskkraCdqLrCtsCdfrvvsf 90 
                                        s+  +C++LrC+sC f+v  +
  gi|557694369|ref|YP_008797423.1| 428 VSSGGSCSSLRCISCGFTVPLL 449
                                       334489************9655 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 ?   12.2   0.0   0.00018      0.11       1      30 [.      74     103 ..      74     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavv 30 
                                       vvG  GsGKt++v++  ++l+ rg +v v+
  gi|557694369|ref|YP_008797423.1|  74 VVGRTGSGKTSLVRKALDFLRRRGVRVVVI 103
                                       89*******************998888776 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   0.00025      0.16      20      62 ..      69     111 ..      58     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesi 62 
                                       n+ +++ G+ gsGKt+L+++++  l+  + +v+ ++   e+++
  gi|557694369|ref|YP_008797423.1|  69 NKHVLVVGRTGSGKTSLVRKALDFLRRRGVRVVVIDWKGEYDL 111
                                       5667899****************99999998887766666555 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 ?    8.2   0.0    0.0048       3.1       1      23 [.      72      94 ..      72     148 .. 0.83
   2 ?    2.5   0.0      0.28   1.8e+02      59      88 ..     250     279 ..     234     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0048
                                      EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA  1 vllyGppGtGKTllakavakelg 23
                                      vl++G  G GKT+l++     l 
  gi|557694369|ref|YP_008797423.1| 72 VLVVGRTGSGKTSLVRKALDFLR 94
                                      799************99887774 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.28
                                       SEEEEEETGGGHHHHHTTCCCHHHHHHHHH CS
                               AAA  59 psilfiDEidalaksrsgseseeeervvnq 88 
                                       ++i++i+E+ +++++ ++++ + +er+vn+
  gi|557694369|ref|YP_008797423.1| 250 HTIVVIEEAQNIVRRGKNNDVSIGERMVNE 279
                                       48************9988888888888875 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   0.00025      0.16      31      63 ..      71     103 ..      47     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                                       EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB  31 vvGltGvPGaGkstlvealglelrrrGkrvavl 63 
                                        v + G  G+Gk  lv +    lrrrG rv v+
  gi|557694369|ref|YP_008797423.1|  71 HVLVVGRTGSGKTSLVRKALDFLRRRGVRVVVI 103
                                       45578999**********************998 PP

>> AAA_24  AAA domain
   #    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       3      53 ..      70     124 ..      69     164 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfl 53 
                                       + +l++G  g+GKT+l++++       g ++++id  +   + d + +p+i++++ f+
  gi|557694369|ref|YP_008797423.1|  70 KHVLVVGRTGSGKTSLVRKAldflrrrGVRVVVIDWKG---EYDLNGVPRIRGFDVFK 124
                                       6799****************9****99999***99887...55666666777777666 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00038      0.24       2      20 ..      70      88 ..      69     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00038
                         PduV-EutP  2 kkilliGkvgsGKttLtqa 20
                                      k++l++G++gsGKt+L ++
  gi|557694369|ref|YP_008797423.1| 70 KHVLVVGRTGSGKTSLVRK 88
                                      89**************875 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   0.0    0.0005      0.32       3      35 ..      71     103 ..      69     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0005
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEE CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllv 35 
                                        +l+vG +G+GKT+ + K  + l+++g +v+++
  gi|557694369|ref|YP_008797423.1|  71 HVLVVGRTGSGKTSLVRKALDFLRRRGVRVVVI 103
                                       689**********************99999875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00054      0.35       3      25 ..      72      94 ..      70     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00054
                                      EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                                      v++ G+ GsGKT L++k  + ++
  gi|557694369|ref|YP_008797423.1| 72 VLVVGRTGSGKTSLVRKALDFLR 94
                                      89**************9776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); expected 358.6 (0.02)
Passed Vit filter:                       139  (0.0077528); 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: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.44
# Mc/sec: 3197.07
//
Query:       gi|557694370|ref|YP_008797424.1|  [L=87]
Description: hypothetical protein CSUB_C0940 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0069   16.6   1.7     0.0069   16.6   1.7    1.8  2  DUF3082   Protein of unknown function (DUF3082)
  ------ inclusion threshold ------
       0.33   11.1   3.6       0.52   10.4   3.3    1.6  1  BTP       Chlorhexidine efflux transporter


Domain annotation for each model (and alignments):
>> DUF3082  Protein of unknown function (DUF3082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.7   7.7e-07    0.0069      45      78 ..      19      52 ..      16      58 .. 0.92
   2 ?   -2.1   0.1      0.53   4.7e+03      68      75 ..      66      73 ..      62      79 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 7.7e-07
                           DUF3082 45 riavavRtlvvGlcyLatfvfgivalGLfllaiq 78
                                      +ia++vR +++ ++ +at v  ++++G++ l++ 
  gi|557694370|ref|YP_008797424.1| 19 QIAALVREIILQIFQIATPVIHVISIGMIGLGLM 52
                                      8**************************9999875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.53
                           DUF3082 68 valGLfll 75
                                      v+ G++ l
  gi|557694370|ref|YP_008797424.1| 66 VSAGIVGL 73
                                      44444444 PP

>> BTP  Chlorhexidine efflux transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   3.3   5.8e-05      0.52       7      54 ..      38      86 ..      33      87 .] 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 5.8e-05
                               BTP  7 vlHallFElgll.lllvpllawllgvslleagvldiglslfalvwnfvy 54
                                      v+H++   +++l l+lv l   +lg+ +++ag+++++++ +++++++ y
  gi|557694370|ref|YP_008797424.1| 38 VIHVISIGMIGLgLMLVALKQEYLGYRMVSAGIVGLVMIHLVIPYALGY 86
                                      67888877777625556666789**********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 616.37
//
Query:       gi|557694371|ref|YP_008797425.1|  [L=253]
Description: hypothetical protein CSUB_C0941 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   16.1   0.0     0.0047   15.7   0.0    1.1  1  DUF1887   Domain of unknown function (DUF1887)


Domain annotation for each model (and alignments):
>> DUF1887  Domain of unknown function (DUF1887)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.6e-07    0.0047      13     121 ..     118     224 ..     110     249 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-07
                           DUF1887  13 apnLlpalldkelkpehlvlivteaq.kekanrlekvlkekgidveifeledevdleeleeslk.glleelkaaeev 87 
                                       a+n+l a   ++++ e++v+  t++   + a  +++  +++ id +++ +e+  d+e + + +  +++e  + +   
  gi|557694371|ref|YP_008797425.1| 118 AVNMLEA---QGFRLERIVIATTKEAySDWAFDIQRYRRYAIIDWKLVSVEQMNDIETMVNIMEpKVYELCR-EYVP 190
                                       5566666...89*******99999887899999************************998877625666666.6667 PP

                           DUF1887  88 vlNvtgGtklmalgayevfRskhkrIfyvetasd 121
                                       ++  t Gt++  +++ e+  +  ++++yv t+++
  gi|557694371|ref|YP_008797425.1| 191 IIDCTSGTRPAGIAFSEIADQLMAPLIYVYTNKE 224
                                       99***************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1937.86
//
Query:       gi|557694372|ref|YP_008797426.1|  [L=168]
Description: hypothetical protein CSUB_C0942 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1322.41
//
Query:       gi|557694373|ref|YP_008797427.1|  [L=758]
Description: exonuclease SbcC [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   93.4   0.0    5.3e-15   55.5   0.0    2.2  2  SMC_N           RecF/RecN/SMC N terminal domain
      6e-22   79.1  28.7    4.4e-17   63.3  28.7    3.7  1  AAA_23          AAA domain
    2.6e-17   63.6   0.1    3.3e-10   40.3   0.0    2.6  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    4.2e-16   59.6   0.0    8.8e-10   38.8   0.0    2.7  3  AAA_15          AAA ATPase domain
    3.7e-08   33.0   0.0    6.6e-08   32.2   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
    5.8e-06   26.0   0.3    5.8e-06   26.0   0.3    3.7  3  AAA_27          AAA domain
    7.8e-06   26.0   0.0    1.9e-05   24.8   0.0    1.7  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
    1.8e-05   25.2   0.2      0.052   14.1   0.4    3.6  2  ABC_tran        ABC transporter
    0.00028   21.1  34.3       0.21   11.8   2.4    5.4  5  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
    0.00066   20.0   8.4       0.14   12.6   0.0    4.7  4  Syntaxin_2      Syntaxin-like protein
     0.0014   17.6  41.6     0.0041   16.0   4.8    4.1  4  Spc7            Spc7 kinetochore protein
     0.0052   17.1   0.5     0.0052   17.1   0.5    4.4  3  OmpH            Outer membrane protein (OmpH-like)
  ------ inclusion threshold ------
       0.01   15.6   2.9       0.01   15.6   2.9    5.9  6  DivIC           Septum formation initiator
      0.013   15.9   2.9      0.013   15.9   2.9    6.0  5  ZapB            Cell division protein ZapB
      0.015   15.2   0.1       0.17   11.8   0.0    2.4  2  RsgA_GTPase     RsgA GTPase
       0.03   14.3   7.1       0.36   10.8   1.1    2.9  2  Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis 
      0.039   13.1   9.2          1    8.4   3.0    3.2  1  PLU-1           PLU-1-like protein
        0.1   12.3   3.1        1.1    9.0   0.1    3.2  2  TFA2_Winged_2   TFA2 Winged helix domain 2
       0.46    9.8  33.2       0.65    9.3   4.4    4.5  4  GAS             Growth-arrest specific micro-tubule binding
       0.76    9.8   8.2        1.2    9.1   0.4    3.2  3  DUF489          Protein of unknown function (DUF489)
        0.8    8.3  23.7       0.25    9.9   3.9    4.0  4  AAA_13          AAA domain
        1.5    8.8   4.4        1.6    8.7   1.1    2.8  3  DUF1045         Protein of unknown function (DUF1045)
        1.5    9.3  19.8         26    5.3   2.2    5.7  4  FlaC_arch       Flagella accessory protein C (FlaC)
        2.1    8.6  19.7        8.6    6.7   0.4    4.9  4  DUF5082         Domain of unknown function (DUF5082)
        2.8    7.8  11.3        1.5    8.7   2.8    3.8  3  Nsp1_C          Nsp1-like C-terminal region
        4.1    7.3   7.9         19    5.1   0.2    3.1  2  STAT_alpha      STAT protein, all-alpha domain
        6.4    6.6  19.2        2.9    7.7   3.7    3.9  4  PCRF            PCRF domain
          8    4.2  12.6        0.6    8.0   0.0    2.9  3  V_ATPase_I      V-type ATPase 116kDa subunit family
        8.7    7.0  22.3        1.9    9.1   3.2    4.5  4  Com_YlbF        Control of competence regulator ComK, YlbF/Ym


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 !   35.8   0.1   8.8e-12   5.4e-09       1     108 [.       1      92 [.       1     121 [. 0.82
   2 !   55.5   0.0   8.6e-18   5.3e-15      48     207 ..     367     729 ..     183     737 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 8.8e-12
                                       EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkka 77 
                                       +++r+++ nF s   + +++ + +++t+ +G+NG+GKs+++dAi + L  r++   r ++  +++h    +  ++++
  gi|557694373|ref|YP_008797427.1|   1 MIRRVRLFNFLSH--RDTEISLGDGLTVFIGRNGAGKSSVVDAIVYALYGRHT---RGQN-ANIVHD---GGGAQEG 68 
                                       6899********9..6899999**************************86666...6655.568887...7888999 PP

                                       EEEEEEEETTEESSSSSSCEEEEEEEETTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  78 eveitfdnedkklkiekeevsisrrvkrkge 108
                                       +ve+ f+ + k        ++++rr  +kg+
  gi|557694373|ref|YP_008797427.1|  69 RVELDFELNRKL-------YKVMRRFDNKGN 92 
                                       999998777666.......566666655555 PP

  == domain 2  score: 55.5 bits;  conditional E-value: 8.6e-18
                                       CTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSE.EEEEETTEEE-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N  48 LGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrrvkrkge.seykingkevtkkev 123
                                       LG ++  +l  + + +l+++ ++++++ +   e+ +++ d+  k e ee++ +rr  +k+     +ing++v++   
  gi|557694373|ref|YP_008797427.1| 367 LGLANRVELDVKGVVELVSE-AHGSALASRAAEL-VTKRDAI-KAEIEETNRRRREANKEIyELGTINGQDVQRLRN 440
                                       55555555666666666665.3333333333333.3444443.3344444433333333332334678888877654 PP

                                       HHHHHCTT-STT................................................................. CS
                                       xxxxxxxxxxxx................................................................. RF
                             SMC_N 124 sellesagiske................................................................. 135
                                       +  l+ +++ +e                                                                 
  gi|557694373|ref|YP_008797427.1| 441 KV-LAAEQLLREvggepgvaalkarleglreraaklekvkvpieldvaelqgvaevlpadvaellsrirtgikrlrd 516
                                       44.44444444459999999999999999999999999999999999999999999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|557694373|ref|YP_008797427.1| 517 dgysagdvvqlerlklrkdklsreigskekeleklredmqkaekeigelervrevlrkarefrdlmrkmrelvyhre 593
                                       999999999999999999999999999999999999999999999******************************** PP

                                       ............................................................CS-HHHHHHHHHHHHHH CS
                                       ............................................................xxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ............................................................lLSgGektLvalaLlfA 152
                                                                                                    LSgGek ++alaL++A
  gi|557694373|ref|YP_008797427.1| 594 gpvlmslrswvyervserageyldtfespvsdirieeertgrgsrvvfrcfyqgrevsweRLSGGEKVVLALALRLA 670
                                       ***************************************************************************** PP

                                       ...HHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SC CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                             SMC_N 153 ...iqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislreemlekadk 207
                                             +++  +++lDe   +LD+++++++ e+l +   +  Q+ivi+++ee++e a++
  gi|557694373|ref|YP_008797427.1| 671 igdALGAQRLGFFVLDEPTVHLDAEKRRRLREVLTRLGRKmPQVIVITHDEEVFEGAEA 729
                                       4444668999************************98876648*************9976 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3  28.7   7.1e-20   4.4e-17       1     200 []       4     238 ..       4     577 .. 0.87

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 7.1e-20
                            AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvel 77 
                                       ++++ nf s+rd+ei +++glt+++G NGaGK++++dAi +aLyg+ +r  +        + v+   +g +++ vel
  gi|557694373|ref|YP_008797427.1|   4 RVRLFNFLSHRDTEISLGDGLTVFIGRNGAGKSSVVDAIVYALYGRHTRGQNA-------NIVH-DGGGAQEGRVEL 72 
                                       68999****************************************76554443.......3333.234567777888 PP

                            AAA_23  78 tfenkdgrytrsiererelskkkgkttkkaklellei......deleqfisellgskkiilnlilflgqerfeefel 148
                                       +fe +++   +++ r++ ++ + ++    ++++ll +      +   +++s llg ++++++ ++ ++q++ + +++
  gi|557694373|ref|YP_008797427.1|  73 DFELNRKL--YKVMRRFDNKGNLKEASIREDGKLLATsergvdRRVSDIVSGLLGMNYERMRSSVVIQQGEVDAILR 147
                                       88888885..566555555555555555666666666565555666788888*******************888888 PP

                            AAA_23 149 kdkke..............................rleelekeleeledekkllekl.................... 175
                                       +d+ke                              r                    +                    
  gi|557694373|ref|YP_008797427.1| 148 ADPKElkelfddllglsafeqayarmkevlecfeeR--------------------Vrlmvrrsvdelllveqelek 204
                                       877777788889996666666666666666666662....................033333333333333333333 PP

                            AAA_23 176 .........eqekekekeleeleeeleeilkele 200
                                                e+e e ekele l++e +e+ + +e
  gi|557694373|ref|YP_008797427.1| 205 lrrlltegkEKEVELEKELERLRNEHQELSEGIE 238
                                       3666666667777777788888888777777664 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 !   20.8   0.0   4.7e-07   0.00029       1      79 [.      24      88 ..      24     110 .. 0.64
   2 !   40.3   0.0   5.3e-13   3.3e-10     144     301 ..     571     723 ..     518     725 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.7e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrle 79
                                      l+v+iG+Ng+GKS++ da+ ++             l g+ + +  ++    +   ++++ e++ f+++ + y+   r++
  gi|557694373|ref|YP_008797427.1| 24 LTVFIGRNGAGKSSVVDAIVYA-------------LYGRHTRGQNANIVHDGGGAQEGRVELD-FELNRKLYKVMRRFD 88
                                      79*****************776.............3444555555555555555555555555.555555555555555 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 5.3e-13
                            AAA_21 144 ltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrerg 220
                                        ++  +++++l   +++l ++r g+  ++ +   + ++ ++++++++ +  + + ++ ++e+               
  gi|557694373|ref|YP_008797427.1| 571 VLRKAREFRDLMRKMRELVYHREGPVLMSLRSWVYERVSERAGEYLDTFESPVSDIRIEEERTGRGS---------R 638
                                       4444444444444444444444444444444444444444444444444333333333333333333.........6 PP

                            AAA_21 221 vvflengdgqelparelSdGtkrllalltallralkkg....sllliDEpEngLHPkllrrllellkelsrngaQvi 293
                                       vvf    +g+e+++  lS G k +lal++ l+  +  g    +++++DEp  +L+ +  rrl e+l +l r+  Qvi
  gi|557694373|ref|YP_008797427.1| 639 VVFRCFYQGREVSWERLSGGEKVVLALALRLAIGDALGaqrlGFFVLDEPTVHLDAEKRRRLREVLTRLGRKMPQVI 715
                                       77777789****************99999999999888****************************999999***** PP

                            AAA_21 294 ltTHSpll 301
                                       + TH+ ++
  gi|557694373|ref|YP_008797427.1| 716 VITHDEEV 723
                                       ****9776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   1.4e-12   8.8e-10       1      44 [.       1      43 [.       1     107 [. 0.89
   2 ?   -1.7   0.1       2.9   1.8e+03     241     263 ..     204     232 ..     153     299 .. 0.67
   3 !   17.7   0.0   3.8e-06    0.0023     238     367 ..     544     722 ..     522     724 .. 0.70

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.4e-12
                            AAA_15  1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsileald 44
                                      M I+++++ NF s++d+ei+l + ltv+iG+N++GKSs+++a+ 
  gi|557694373|ref|YP_008797427.1|  1 M-IRRVRLFNFLSHRDTEISLGDGLTVFIGRNGAGKSSVVDAIV 43
                                      7.9***************************************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.9
                            AAA_15 241 klkeiqeklkeidkklaeelk......ki 263
                                       kl +++++ ke++ +l++el+      ++
  gi|557694373|ref|YP_008797427.1| 204 KLRRLLTEGKEKEVELEKELErlrnehQE 232
                                       33333333333333333333322222211 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 3.8e-06
                            AAA_15 238 lteklkeiqeklkeidkklaeelk.................................................kilk 265
                                       ++++l+++ e+ ++++k+++e +                                                  ++++
  gi|557694373|ref|YP_008797427.1| 544 KEKELEKLREDMQKAEKEIGELERvrevlrkarefrdlmrkmrelvyhregpvlmslrswvyervserageylDTFE 620
                                       33333333333333333332222233333344444444444555666677799999996666666666666666666 PP

                            AAA_15 266 kkidkikkfnykgkkneeieik...ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpq 339
                                       +++++i  ++        + ++    + e++ ++ + G +  l l+l ++         ++  +++++EP +hL  +
  gi|557694373|ref|YP_008797427.1| 621 SPVSDIRIEEERTGRGSRVVFRcfyQGREVSWERLSGGEKVVLALALRLAIGDAL--GAQRLGFFVLDEPTVHLDAE 695
                                       666666555555555555444499*********************9999999999..99****************** PP

                            AAA_15 340 aqkvlikllkelandnktQviitTHSph 367
                                         + l + l +l ++   Qvi+ TH + 
  gi|557694373|ref|YP_008797427.1| 696 KRRRLREVLTRLGRKMP-QVIVITHDEE 722
                                       ****************9.*******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 !   32.2   0.0   1.1e-10   6.6e-08       2      52 ..       3      52 ..       2      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.1e-10
                            AAA_29  2 krlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpakkv 52
                                      +r++l+N  + ++++i++  +g t+++G++G+GKS+++DAi + L++++++
  gi|557694373|ref|YP_008797427.1|  3 RRVRLFNFLSHRDTEISLG-DGLTVFIGRNGAGKSSVVDAIVYALYGRHTR 52
                                      6788888888888878887.669************************9855 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.3   9.4e-09   5.8e-06       3     119 ..       2     117 ..       1     175 [. 0.77
   2 ?    1.1   0.2       0.4   2.5e+02     165     199 ..     392     426 ..     379     448 .. 0.56
   3 ?    1.1   0.1      0.41   2.5e+02     162     199 ..     527     564 ..     499     572 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 9.4e-09
                            AAA_27   3 lerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipertk.dnflhd...akkLrigavle 75 
                                       ++r +L  + +  d++++++   ++l++ +G N AGKs++++Ai   l+G ++r +  n +hd   a++ r++  + 
  gi|557694373|ref|YP_008797427.1|   2 IRRVRLFNFLSHRDTEISLG---DGLTVFIGRNGAGKSSVVDAIVYALYGRHTRGQnANIVHDgggAQEGRVELDF- 74 
                                       78888999999999999998...8****************************996516899984445777888888. PP

                            AAA_27  76 eadgeelefaRrkgrkktlldaddqalpeevlaallggldretF 119
                                       e + +  ++ Rr  +k +l +a+ +  + ++la+  +g+dr+  
  gi|557694373|ref|YP_008797427.1|  75 ELNRKLYKVMRRFDNKGNLKEASIR-EDGKLLATSERGVDRRVS 117
                                       5566699999999999999877665.567777777777777654 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.4
                            AAA_27 165 Leaeadelfkprkskkrainealeeleeakkelre 199
                                       L ++a el ++r + k++i e++++ +ea+ke+ e
  gi|557694373|ref|YP_008797427.1| 392 LASRAAELVTKRDAIKAEIEETNRRRREANKEIYE 426
                                       45555555555555555555555555555555433 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.41
                            AAA_27 162 leaLeaeadelfkprkskkrainealeeleeakkelre 199
                                       le+L+ ++d+l ++ +sk++++ + +e++++a+ke+ e
  gi|557694373|ref|YP_008797427.1| 527 LERLKLRKDKLSREIGSKEKELEKLREDMQKAEKEIGE 564
                                       67778888888888888888888888888888887765 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 !   24.8   0.0   3.1e-08   1.9e-05      31      89 ..     653     705 ..     644     706 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.1e-08
                           SbcCD_C  31 gtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       ++lSGGek ++++lal +a+ ++++      ++l++++LDE    lD+e++++l e+l+
  gi|557694373|ref|YP_008797427.1| 653 ERLSGGEK-VVLALALRLAIGDALGA-----QRLGFFVLDEPTVHLDAEKRRRLREVLT 705
                                       789*****.66667777777776666.....69********************999876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.4   8.4e-05     0.052      13      34 ..      24      45 ..      14     252 .. 0.86
   2 ?    6.5   0.0     0.018        11      96     136 ..     630     689 ..     524     690 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.4e-05
                                      EEEEEESTTSSHHHHHHHHTTS CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagl 34
                                      +++++G+nGaGKS+++ ++   
  gi|557694373|ref|YP_008797427.1| 24 LTVFIGRNGAGKSSVVDAIVYA 45
                                      5789************998654 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
                                       G..............TTCBGESTTSGGS-HHHHHHHHHHHHHH.......HTSSEEEEESTT CS
                                       x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxx RF
                          ABC_tran  96 e..............lkdtvvksspssLSgGqkqrvalarall.......kkpkllllDEpt 136
                                       e               + + v  s + LSgG+k+ +ala  l+       ++  +++lDEpt
  gi|557694373|ref|YP_008797427.1| 630 EertgrgsrvvfrcfYQGREV--SWERLSGGEKVVLALALRLAigdalgaQRLGFFVLDEPT 689
                                       155555555555544444444..5599*******9999976641111111444567888887 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 !   10.6   3.2   0.00084      0.52      31     100 ..     209     282 ..     184     285 .. 0.84
   2 ?    6.9   0.9     0.011       6.9      66     100 ..     279     319 ..     269     327 .. 0.80
   3 ?   -1.7   0.0       5.3   3.3e+03      34      60 ..     335     361 ..     332     387 .. 0.77
   4 !   11.8   2.4   0.00034      0.21      26      82 ..     391     448 ..     376     468 .. 0.85
   5 !   10.0   3.4    0.0013      0.78      43      90 ..     525     569 ..     524     586 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00084
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT....S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  31 lleldekrrelqveleelqaerNelskeIgkakkkk....edaeeliaevkelkeelkaleaelkeleaelekl 100
                                       l e  ek  el++ele l++e+ els+ I+k+   +    e +++l a    +  el++le+e+  +e + + l
  gi|557694373|ref|YP_008797427.1| 209 LTEGKEKEVELEKELERLRNEHQELSEGIEKLEGLHrlfgEVRSSLEALKGLVRRELADLEEEVGRIERATKVL 282
                                       5566789999*********************9999899988888888888889999999999999998877655 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                                       T......S-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  66 k......edaeeliaevkelkeelkaleaelkeleaelekl 100
                                              e++e+ i +v+el  e+++l++++++l+ +l ++
  gi|557694373|ref|YP_008797427.1| 279 TkvlvlrEEIEKRITRVDELRVEISRLDEKERALQRQLREI 319
                                       334466689999***********************999886 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5.3
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                      Seryl_tRNA_N  34 ldekrrelqveleelqaerNelskeIg 60 
                                       l+e r e+++++e l+    el+k+++
  gi|557694373|ref|YP_008797427.1| 335 LEELRNEARTRAERLRDDAVELGKAVA 361
                                       677788888888888887777777665 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT.S-TCCCCCCCHHHHHH CS
                      Seryl_tRNA_N  26 advdelleldekrrelqveleelqaerNelskeIgkakkkk.edaeeliaevkelkee 82 
                                       a+  +  el +kr ++++e+ee +++r e++keI ++   + +d ++l+++v +  + 
  gi|557694373|ref|YP_008797427.1| 391 ALASRAAELVTKRDAIKAEIEETNRRRREANKEIYELGTINgQDVQRLRNKVLAAEQL 448
                                       5667788999**************************9988879999999998766655 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  43 veleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleael 90 
                                       v+le l+ ++ +ls+eIg++ k+    e+l++++++  +e+ +le   
  gi|557694373|ref|YP_008797427.1| 525 VQLERLKLRKDKLSREIGSKEKE---LEKLREDMQKAEKEIGELERVR 569
                                       6899***************9986...5778888888888887777543 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.5      0.77   4.8e+02      14      51 ..     201     239 ..     196     263 .. 0.77
   2 ?    2.5   0.2       0.3   1.9e+02      15      58 ..     268     311 ..     257     359 .. 0.55
   3 ?    4.9   0.0     0.056        34      32      79 ..     403     452 ..     389     457 .. 0.82
   4 !   12.6   0.0   0.00022      0.14      40     100 ..     498     562 ..     481     563 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.77
                        Syntaxin_2  14 tleklvkqLgtkk.dteelreklhelieeinelikktne 51 
                                       +lekl++ L   k    el ++l+ l++e +el++ +++
  gi|557694373|ref|YP_008797427.1| 201 ELEKLRRLLTEGKeKEVELEKELERLRNEHQELSEGIEK 239
                                       677888886666525788888888888888888776654 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.3
                        Syntaxin_2  15 leklvkqLgtkkdteelreklhelieeinelikktnellkklsq 58 
                                       le+ v  ++ ++    lre++++ i+++ el  ++++l +k  +
  gi|557694373|ref|YP_008797427.1| 268 LEEEVGRIERATKVLVLREEIEKRITRVDELRVEISRLDEKERA 311
                                       44444444444444555555555555555554444444333333 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.056
                        Syntaxin_2  32 reklhelieeinelikktnellkklsqldnsssds..qqklqkekLkkdf 79 
                                       r+ ++  iee+n+  ++ n+ + +l ++  ++ ++  ++ l++e L +++
  gi|557694373|ref|YP_008797427.1| 403 RDAIKAEIEETNRRRREANKEIYELGTINGQDVQRlrNKVLAAEQLLREV 452
                                       78889999999999999999999999987777666866667888888876 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00022
                        Syntaxin_2  40 eeinelikktnellkklsqldnsssds....qqklqkekLkkdfkealqeFqkiqrqyaekekqi 100
                                        ++ el++++   +k+l  +  s  d     + kl k+kL++++ +  +e++k+ ++ +++ek+i
  gi|557694373|ref|YP_008797427.1| 498 ADVAELLSRIRTGIKRLRDDGYSAGDVvqleRLKLRKDKLSREIGSKEKELEKLREDMQKAEKEI 562
                                       4567788888888888888777665559999999****************************986 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1  12.4   0.00088      0.54     195     287 ..     194     284 ..     141     293 .. 0.61
   2 !    5.9   4.6     0.008       4.9     165     246 ..     247     326 ..     239     363 .. 0.65
   3 ?    4.2   4.1     0.026        16     221     281 ..     388     448 ..     331     452 .. 0.72
   4 !   16.0   4.8   6.7e-06    0.0041     150     263 ..     460     575 ..     452     589 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00088
                              Spc7 195 s..idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevs 269
                                       +  + ++eLe+lr+ l+e k++  e++kel++l+++ +el+e ie+l+      +    e ++ le+ kg  + e+ 
  gi|557694373|ref|YP_008797427.1| 194 EllLVEQELEKLRRLLTEGKEKEVELEKELERLRNEHQELSEGIEKLEGL----HRLFGEVRSSLEALKGLVRRELA 266
                                       23234667777777777777777777777777777777777777776333....33333444677777788888888 PP

                              Spc7 270 rlkeevkaleeltgwkiv 287
                                        l+eev ++e+ t++ ++
  gi|557694373|ref|YP_008797427.1| 267 DLEEEVGRIERATKVLVL 284
                                       888888888888777654 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.008
                              Spc7 165 ldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelke 241
                                       + e+  +le+ k  +++el++l+e++  +e    +++  lree+++  + ++e++ e+++l e+  +l+ ++ e+  
  gi|557694373|ref|YP_008797427.1| 247 FGEVRSSLEALKGLVRRELADLEEEVGRIER--ATKVLVLREEIEKRITRVDELRVEISRLDEKERALQRQLREIGG 321
                                       5567778888888899999999997766665..56666677777777777777777777777777777777766665 PP

                              Spc7 242 qksel 246
                                       + ++l
  gi|557694373|ref|YP_008797427.1| 322 ELARL 326
                                       55544 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.026
                              Spc7 221 elaelqeqleeleekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleel 281
                                         + l ++ +el +k +++k++++e++ + +ea++ + e   ++ ++v+rl+++v a e+l
  gi|557694373|ref|YP_008797427.1| 388 HGSALASRAAELVTKRDAIKAEIEETNRRRREANKEIYELGTINGQDVQRLRNKVLAAEQL 448
                                       4456777788888888888999999999999999999999999999999999999888876 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 6.7e-06
                              Spc7 150 gleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelk..aeieekkkelae 224
                                       +l++  e L ++ ++l++++  +e   ael+  +e l + ++el s  ++ ++ lr++  ++   +++e++k + ++
  gi|557694373|ref|YP_008797427.1| 460 ALKARLEGLRERAAKLEKVKVPIELDVAELQGVAEVLPADVAELLSRIRTGIKRLRDDGYSAGdvVQLERLKLRKDK 536
                                       56666677778888888888888888888888888888888888887788888888777776622466777777777 PP

                              Spc7 225 lqeqleeleekieelkeqkseleeeiaeaervleeckgw 263
                                       l +++ ++e+++e+l+e ++++e+ei e erv+e  ++ 
  gi|557694373|ref|YP_008797427.1| 537 LSREIGSKEKELEKLREDMQKAEKEIGELERVREVLRKA 575
                                       778888888888888888888888888888887766654 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   8.5       6.9   4.3e+03      25      50 ..     213     238 ..     168     389 .. 0.68
   2 ?    1.9   2.8      0.42   2.6e+02      34      88 ..     391     440 ..     330     460 .. 0.66
   3 !   17.1   0.5   8.5e-06    0.0052      23      84 ..     529     590 ..     519     615 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.9
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  25 ekkfkklqaeleakekelqklqeelq 50 
                                       ++k+ +l++ele++++e q+l e ++
  gi|557694373|ref|YP_008797427.1| 213 KEKEVELEKELERLRNEHQELSEGIE 238
                                       23333333333333333333333332 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHH.HHHHHHHH CS
                              OmpH  34 eleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqka.qelqkkqq 88 
                                       +l+++++el +++++++++ ++  ++++++e +k+  el +     + q++q+ ++
  gi|557694373|ref|YP_008797427.1| 391 ALASRAAELVTKRDAIKAEIEE--TNRRRREANKEIYELGT----INgQDVQRLRN 440
                                       5556666666666666544444..33333333333333333....11122333332 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 8.5e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  23 qlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelq 84 
                                       +l+  + kl  e+ +kekel+kl+e++qk++k+  + e+ +e+ +k +e+++++++ ++ + 
  gi|557694373|ref|YP_008797427.1| 529 RLKLRKDKLSREIGSKEKELEKLREDMQKAEKEIGELERVREVLRKAREFRDLMRKMRELVY 590
                                       5666778999*****************97776652577888888888888886666555444 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       9.6   5.9e+03      18      50 ..     127     160 ..     126     172 .. 0.76
   2 ?    7.8   1.6    0.0046       2.8      23      55 ..     199     231 ..     187     247 .. 0.61
   3 ?    3.1   1.8      0.13        82      28      61 ..     283     316 ..     262     347 .. 0.76
   4 ?    3.2   0.3      0.12        75      25      50 ..     402     427 ..     389     439 .. 0.85
   5 ?    1.1   0.0      0.56   3.5e+02      26      45 ..     458     477 ..     456     479 .. 0.90
   6 ?   15.6   2.9   1.6e-05      0.01       9      64 ..     524     578 ..     518     591 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 9.6
                                       HHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHCC- CS
                             DivIC  18 aykqlkqeiaalqaelak.lkaeneeLeaevkdL 50 
                                       +y ++++ ++ +q e+++ l+a+ +eL++  +dL
  gi|557694373|ref|YP_008797427.1| 127 NYERMRSSVVIQQGEVDAiLRADPKELKELFDDL 160
                                       6777888888888888775688888888888777 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0046
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXX CS
                             DivIC  23 kqeiaalqaelaklkaeneeLeaevkdLksded 55 
                                       +qe+++l + l + k+++ eLe+e+++L+++  
  gi|557694373|ref|YP_008797427.1| 199 EQELEKLRRLLTEGKEKEVELEKELERLRNEHQ 231
                                       566666666666666666666666666655433 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXX CS
                             DivIC  28 alqaelaklkaeneeLeaevkdLksdedyieerA 61 
                                        l +e++k   + +eL  e+++L   e +++++ 
  gi|557694373|ref|YP_008797427.1| 283 VLREEIEKRITRVDELRVEISRLDEKERALQRQL 316
                                       5667777777777777777777754555555554 PP

  == domain 4  score: 3.2 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC  25 eiaalqaelaklkaeneeLeaevkdL 50 
                                       +++a++ae+++ + +++e ++e+ +L
  gi|557694373|ref|YP_008797427.1| 402 KRDAIKAEIEETNRRRREANKEIYEL 427
                                       67889999999999999999999888 PP

  == domain 5  score: 1.1 bits;  conditional E-value: 0.56
                                       HHHHHHHHHHHHHHHHHHHH CS
                             DivIC  26 iaalqaelaklkaeneeLea 45 
                                       +aal+a l+ l+++ ++Le+
  gi|557694373|ref|YP_008797427.1| 458 VAALKARLEGLRERAAKLEK 477
                                       6899**********999996 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 1.6e-05
                                       XXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXXXXXXXXXX CS
                             DivIC   9 lifgkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedyieerARse 64 
                                       ++++++  l+  +l +ei  +++el+kl+++ ++ e+e+ +L      + ++AR+ 
  gi|557694373|ref|YP_008797427.1| 524 VVQLERLKLRKDKLSREIGSKEKELEKLREDMQKAEKEIGEL-ERVREVLRKAREF 578
                                       678899999999******************************.7**********64 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8  11.1   0.00083      0.51      13      65 ..     188     240 ..     172     246 .. 0.84
   2 ?   15.9   2.9   2.1e-05     0.013      11      63 ..     286     350 ..     281     351 .. 0.86
   3 ?    5.1   1.6     0.052        32       9      56 ..     392     443 ..     390     454 .. 0.83
   4 ?    0.8   0.0       1.1   6.8e+02      22      64 ..     460     509 ..     457     516 .. 0.47
   5 ?    2.0   6.6      0.46   2.8e+02      27      63 ..     527     563 ..     525     589 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00083
                              ZapB  13 iqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                       +   +d++ l  +e+e+L++   e ke+  ele+e+e+l++e++++ e ++kL
  gi|557694373|ref|YP_008797427.1| 188 VRRSVDELLLVEQELEKLRRLLTEGKEKEVELEKELERLRNEHQELSEGIEKL 240
                                       34568999999****************************************98 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.1e-05
                              ZapB  11 skiqkaidtitlLqmeieeLkeeneelkeenrele............eeneqlkeereawqerlk 63 
                                       + i+k i+++++L+ ei++L e+ ++l+++ re+             + +e+l++e     erl+
  gi|557694373|ref|YP_008797427.1| 286 EEIEKRITRVDELRVEISRLDEKERALQRQLREIGgelarlptgagaRTLEELRNEARTRAERLR 350
                                       678999*****************************888899999888778888887777777775 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.052
                              ZapB   9 LEskiqkaidtitlLqmeieeLkeeneelkeenrele....eeneqlkeere 56 
                                       L s+  +++++ ++ + eiee  ++ +e ++e+ el     + +++l++   
  gi|557694373|ref|YP_008797427.1| 392 LASRAAELVTKRDAIKAEIEETNRRRREANKEIYELGtingQDVQRLRNKVL 443
                                       67888999****************************9888888888876554 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 1.1
                              ZapB  22 lLqmeieeLkeeneelkeenreleeeneqlk.......eereawqerlkk 64 
                                       +L+ ++e L+e+ ++l++ +  +e  + +l+       ++ +++ +r+++
  gi|557694373|ref|YP_008797427.1| 460 ALKARLEGLRERAAKLEKVKVPIELDVAELQgvaevlpADVAELLSRIRT 509
                                       55555555555555555544444433333332223333555555555555 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.46
                              ZapB  27 ieeLkeeneelkeenreleeeneqlkeereawqerlk 63 
                                       +e+Lk ++ +l++e+   e+e+e+l+e+ ++ ++ + 
  gi|557694373|ref|YP_008797427.1| 527 LERLKLRKDKLSREIGSKEKELEKLREDMQKAEKEIG 563
                                       5677777777777777777777777766666655443 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00027      0.17      96     120 ..      19      43 ..      11      57 .. 0.86
   2 ?    0.1   0.0       1.1   6.8e+02      53      97 ..     400     442 ..     393     458 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                                       HCTTSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinall 120
                                        l d ++v++G  G+GKS++++a++
  gi|557694373|ref|YP_008797427.1|  19 SLGDGLTVFIGRNGAGKSSVVDAIV 43 
                                       677899***************9986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.1
                                       EE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHC CS
                       RsgA_GTPase  53 lnKiDlleeeeeleelkeelealgyevllvsaktkegleelkell 97 
                                       ++K D ++ e   ee++ + ++++ e++ + + +++++++l++++
  gi|557694373|ref|YP_008797427.1| 400 VTKRDAIKAEI--EETNRRRREANKEIYELGTINGQDVQRLRNKV 442
                                       68888887765..999999999999***99999999999999875 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.4     0.022        14      60     111 ..     199     251 ..     189     262 .. 0.79
   2 ?   10.8   1.1   0.00058      0.36      46      99 ..     531     585 ..     502     590 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.022
                    Halogen_Hydrol  60 rkelkyiretlkeakekikrlekalkrvrs.levikqvreilriarrifkale 111
                                       ++el+ +r+ l e+kek  +lek+l r+r+ ++ +++  e l+  +r+f +++
  gi|557694373|ref|YP_008797427.1| 199 EQELEKLRRLLTEGKEKEVELEKELERLRNeHQELSEGIEKLEGLHRLFGEVR 251
                                       689999**********************9735666666666666666666665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00058
                    Halogen_Hydrol  46 knkkkkhlkksglsrkelkyiretlkeakekikrlekalkrvrslevi.kqvrei 99 
                                       k +k k+ ++ g ++kel+ +re +++a+++i +le+ +  +r+ + + +++r++
  gi|557694373|ref|YP_008797427.1| 531 KLRKDKLSREIGSKEKELEKLREDMQKAEKEIGELERVREVLRKAREFrDLMRKM 585
                                       5678888999****************************99999866440444444 PP

>> PLU-1  PLU-1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   3.0    0.0017         1      17      56 ..     201     240 ..     189     252 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0017
                             PLU-1  17 sLkelrallneaekikfplkellekLktfvkdaekwveka 56 
                                       +L++lr ll+e++++  +l++ le+L++++++  + +ek 
  gi|557694373|ref|YP_008797427.1| 201 ELEKLRRLLTEGKEKEVELEKELERLRNEHQELSEGIEKL 240
                                       79****************98888********998888876 PP

>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4      0.26   1.6e+02      30      53 ..     267     290 ..     255     298 .. 0.82
   2 ?    9.0   0.1    0.0018       1.1      20      45 ..     547     572 ..     533     641 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.26
                     TFA2_Winged_2  30 dveealeeLeaegeilvlrtkkdg 53 
                                       d ee++   e+  ++lvlr + ++
  gi|557694373|ref|YP_008797427.1| 267 DLEEEVGRIERATKVLVLREEIEK 290
                                       77888888899*******886554 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                     TFA2_Winged_2  20 kvkdLkdswpdveealeeLeaegeil 45 
                                       ++++L++ + ++e+++ eLe+ +e+l
  gi|557694373|ref|YP_008797427.1| 547 ELEKLREDMQKAEKEIGELERVREVL 572
                                       579*******************9976 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 ?    5.0   7.4     0.022        14      68     119 ..     190     241 ..     162     256 .. 0.82
   2 ?    3.4   0.5     0.068        42      23      74 ..     290     339 ..     285     356 .. 0.75
   3 ?    6.1   0.3      0.01       6.3      28     133 ..     403     511 ..     397     518 .. 0.76
   4 ?    9.3   4.4    0.0011      0.65      49      97 ..     527     575 ..     520     590 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.022
                               GAS  68 eeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekve 119
                                       + v+eL    ++ ek +  l++ k++  elekel++l+ eh+ l++ +ek+e
  gi|557694373|ref|YP_008797427.1| 190 RSVDELLLVEQELEKLRRLLTEGKEKEVELEKELERLRNEHQELSEGIEKLE 241
                                       5566677777788888888999999999999999999999999999999887 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.068
                               GAS  23 nNLelIkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLr 74 
                                       + ++ +++l+ ei +l++ke++ +++l ei  e  rl  p  +  + +eeLr
  gi|557694373|ref|YP_008797427.1| 290 KRITRVDELRVEISRLDEKERALQRQLREIGGELARL--PTGAGARTLEELR 339
                                       5567788999999999999999999999999888887..3344444555555 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.01
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlk...nyekdkqslknlkarlkelekel 101
                                        +  K eiee +++ ++++ke++e+ + n + ++ L++     e+L +++         k++l+ l++r  +lek  
  gi|557694373|ref|YP_008797427.1| 403 RDAIKAEIEETNRRRREANKEIYELGTINGQDVQRLRNKVLAAEQLLREVGgepGVAALKARLEGLRERAAKLEKVK 479
                                       5678*********************9999999998888888888888877511146788888888888888888877 PP

                               GAS 102 kdlkwehevleqrfekvekerdelykkfeaai 133
                                         ++++   l+   e + ++  el ++ ++ i
  gi|557694373|ref|YP_008797427.1| 480 VPIELDVAELQGVAEVLPADVAELLSRIRTGI 511
                                       77777777777666666666666666666555 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.0011
                               GAS  49 lseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkel 97 
                                       l+ ++ ++ +l+ ++   e+e+e+Lr+++++ ek+  +l+++++ l+++
  gi|557694373|ref|YP_008797427.1| 527 LERLKLRKDKLSREIGSKEKELEKLREDMQKAEKEIGELERVREVLRKA 575
                                       4555556666666666666666666666666666666666666666654 PP

>> DUF489  Protein of unknown function (DUF489)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.4     0.002       1.2      34     124 ..     142     235 ..     136     244 .. 0.90
   2 ?    2.2   0.2      0.26   1.6e+02      55     126 ..     250     323 ..     238     327 .. 0.73
   3 ?    1.5   0.1      0.41   2.5e+02      52     115 ..     504     565 ..     487     576 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.002
                                       HHHHH--S-SSHHHHTTS...GGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHT CS
                            DUF489  34 lkslletdpestedvygg...lanlklGletlleqlekekkkkdaeltryalsllalerkLsknkealaklgerieq 107
                                       ++++l+ dp+++++++++   l+++++++  ++e+le  +++ ++ + r + +ll +e++L+k +++l++ +e+  +
  gi|557694373|ref|YP_008797427.1| 142 VDAILRADPKELKELFDDllgLSAFEQAYARMKEVLECFEERVRLMVRRSVDELLLVEQELEKLRRLLTEGKEKEVE 218
                                       789**************977788999***************9999************************99999999 PP

                                       THHHHTTS-TTSHHHHH CS
                            DUF489 108 ierqlehfdllhenvla 124
                                       +e++le  +  h+++ +
  gi|557694373|ref|YP_008797427.1| 219 LEKELERLRNEHQELSE 235
                                       99999998888887765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.26
                                       GHHHHHHHHHHHHT--SCHHHHH..HHHHHHHHHHHHHHHHSTTHHHHHHHHHHTTHHHHTTS-TTSHHHHHHH CS
                            DUF489  55 lklGletlleqlekekkkkdael..tryalsllalerkLsknkealaklgerieqierqlehfdllhenvlanl 126
                                       ++  le+l+  +++e    + e+  +  a ++l l ++++k+ + +++l+ +i++++++ +  + + +++  +l
  gi|557694373|ref|YP_008797427.1| 250 VRSSLEALKGLVRRELADLEEEVgrIERATKVLVLREEIEKRITRVDELRVEISRLDEKERALQRQLREIGGEL 323
                                       5556666666666666654555522556899*************************999877666666655555 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.41
                                       GGGGHHHHHHHHHHHHT--SCHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHTTHHHHTTS CS
                            DUF489  52 lanlklGletlleqlekekkkkdaeltryalsllalerkLsknkealaklgerieqierqlehf 115
                                       l+++++G++ l++   +  +   ++l r+ l   +l+r++ ++++ l+kl+e ++++e++  + 
  gi|557694373|ref|YP_008797427.1| 504 LSRIRTGIKRLRDDGYSAGD--VVQLERLKLRKDKLSREIGSKEKELEKLREDMQKAEKEIGEL 565
                                       45677777777776655554..578888889999999999999999999999999999987655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.31   1.9e+02      21      36 ..      27      42 ..      22      70 .. 0.79
   2 ?    9.9   3.9   0.00041      0.25     286     456 ..     151     319 ..     143     353 .. 0.76
   3 ?   -0.7   0.4      0.65     4e+02     357     449 ..     403     503 ..     373     516 .. 0.49
   4 ?    7.9   2.6    0.0017         1     411     470 ..     527     585 ..     524     590 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.31
                            AAA_13 21 iYGwNGaGKTtLSrll 36
                                      + G+NGaGK+++  ++
  gi|557694373|ref|YP_008797427.1| 27 FIGRNGAGKSSVVDAI 42
                                      56********997776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00041
                            AAA_13 286 erLekliekveskk..selleklkavsdeasensafeedkeelkaeaealeeqLkglqralea.Krkepfksveles 359
                                       ++L++l +++++ +  +++ +++k+v   + ++++ +  +    +e+  +e++L++l+r l++ K ke+  + ele+
  gi|557694373|ref|YP_008797427.1| 151 KELKELFDDLLGLSafEQAYARMKEVL--ECFEERVRLMVRRSVDELLLVEQELEKLRRLLTEgKEKEVELEKELER 225
                                       678888888855540034444444444..45566778888888899999***********9764889999999**** PP

                            AAA_13 360 vkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeyk..kkykklekaieklekelke 434
                                       + ++ +++++ +++++ l + + e  ++le+ k  ++ +l       le+e+ + +  +k+  l ++iek  ++++e
  gi|557694373|ref|YP_008797427.1| 226 LRNEHQELSEGIEKLEGLHRLFGEVRSSLEALKGLVRRELAD-----LEEEVGRIEraTKVLVLREEIEKRITRVDE 297
                                       *****************9999999999999888877777766.....455555444113455567788888888888 PP

                            AAA_13 435 eeaelkkleeeikeLekqlrde 456
                                          e+  l+e+ ++L++qlr++
  gi|557694373|ref|YP_008797427.1| 298 LRVEISRLDEKERALQRQLREI 319
                                       8888888888888888888765 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.65
                            AAA_13 357 lesvkakiesikklvaeineli....akhNekvanleeekeeakkklelhlv....eeleseldeykkkykklekai 425
                                        + +ka+ie+ +    e+n+ i    + + + v++l +++ +a++ l+        + l++ l+ + +  +klek  
  gi|557694373|ref|YP_008797427.1| 403 RDAIKAEIEETNRRRREANKEIyelgTINGQDVQRLRNKVLAAEQLLREVGGepgvAALKARLEGLRERAAKLEKVK 479
                                       23333333333333333333331111223344555555555555544443323333455555555555555555555 PP

                            AAA_13 426 eklekelkeeeaelkkleeeikeL 449
                                          e +++e +  ++ l ++++eL
  gi|557694373|ref|YP_008797427.1| 480 VPIELDVAELQGVAEVLPADVAEL 503
                                       555555555555555555555555 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0017
                            AAA_13 411 ldeykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLkaf 470
                                       l+++k  ++kl+++i + ekel++  ++++k+e+ei eLe+ +r++ + a e+ ++++++
  gi|557694373|ref|YP_008797427.1| 527 LERLKLRKDKLSREIGSKEKELEKLREDMQKAEKEIGELER-VREVLRKAREFRDLMRKM 585
                                       567888899******************************96.799999999999998875 PP

>> DUF1045  Protein of unknown function (DUF1045)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       3.5   2.2e+03      36      72 ..     314     351 ..     291     359 .. 0.65
   2 ?    8.7   1.1    0.0025       1.6      35      85 ..     371     421 ..     330     424 .. 0.80
   3 ?   -2.6   0.0       7.6   4.7e+03      21      56 ..     468     504 ..     459     511 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.5
                           DUF1045  36 levarlggflALvpa.apsealqalAaacvraldefra 72 
                                        +++++gg lA  p+ a + +l++l +++ ++ +++r 
  gi|557694373|ref|YP_008797427.1| 314 RQLREIGGELARLPTgAGARTLEELRNEARTRAERLRD 351
                                       34777777777777756677777777777777777765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0025
                           DUF1045  35 elevarlggflALvpaapsealqalAaacvraldefraplseaelarrrae 85 
                                       +    +++g++ Lv +a+ +al++ Aa+ v++ d+ +a ++e+++ rr+a+
  gi|557694373|ref|YP_008797427.1| 371 NRVELDVKGVVELVSEAHGSALASRAAELVTKRDAIKAEIEETNRRRREAN 421
                                       444456789999*****************************9999999875 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.6
                           DUF1045  21 laalaarlapfalp.elevarlggflALvpaapseal 56 
                                       l++ aa+l+ +++p el+va+l+g+  + pa  +e l
  gi|557694373|ref|YP_008797427.1| 468 LRERAAKLEKVKVPiELDVAELQGVAEVLPADVAELL 504
                                       4555666666666656778888888877777666555 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 ?    5.3   2.2     0.042        26      11      34 ..     218     241 ..     192     243 .. 0.85
   2 ?    0.6   0.1       1.2   7.5e+02      19      37 ..     261     279 ..     247     293 .. 0.68
   3 ?    4.7   0.1     0.067        41       1      32 [.     294     325 ..     294     328 .. 0.92
   4 ?    5.3   2.5     0.042        26       3      40 ..     535     571 ..     533     573 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.042
                         FlaC_arch  11 klsteletvkkeneelsksveelk 34 
                                       +l+ ele +++e +els+ +e+l+
  gi|557694373|ref|YP_008797427.1| 218 ELEKELERLRNEHQELSEGIEKLE 241
                                       467799999999999999999987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.2
                         FlaC_arch  19 vkkeneelsksveelkenV 37 
                                       v++e+ +l+++v ++++  
  gi|557694373|ref|YP_008797427.1| 261 VRRELADLEEEVGRIERAT 279
                                       5666666666666666544 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.067
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksvee 32 
                                       r+del  ++s+l+ +   +++++ e+  ++ +
  gi|557694373|ref|YP_008797427.1| 294 RVDELRVEISRLDEKERALQRQLREIGGELAR 325
                                       8*************************988765 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.042
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkdl 40 
                                       d+l  ++++ + ele +++++++ +k++ el+ +V+++
  gi|557694373|ref|YP_008797427.1| 535 DKLSREIGSKEKELEKLREDMQKAEKEIGELE-RVREV 571
                                       56777777777788888888888888887775.45666 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   4.1     0.022        13       6     117 ..     217     322 ..     204     328 .. 0.50
   2 ?    2.3   0.9      0.31   1.9e+02       2      36 ..     400     434 ..     399     450 .. 0.86
   3 ?   -1.3   0.0       4.2   2.6e+03      85     107 ..     499     521 ..     469     531 .. 0.80
   4 ?    6.7   0.4     0.014       8.6       2      39 ..     538     575 ..     537     595 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.022
                           DUF5082   6 sklqaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkklekplnssesWkGk..eennydgirsnlessyq 80 
                                        +l+++ + lr+e + l+e Ie+L+   +   ++ +sl++ k  ++  l++ e+  G+  ++ ++   r+++e+ ++
  gi|557694373|ref|YP_008797427.1| 217 VELEKELERLRNEHQELSEGIEKLEGLHRLFGEVRSSLEALKGLVRRELADLEEEVGRieRATKVLVLREEIEKRIT 293
                                       45556666666666666666666665555555555555555555555555554333333222233333334443333 PP

                           DUF5082  81 tyvdkldelidaieeEIerLenqiseaqgvldtlqsq 117
                                       +        +d++  EI+rL ++   +q+ l  +  +
  gi|557694373|ref|YP_008797427.1| 294 R--------VDELRVEISRLDEKERALQRQLREIGGE 322
                                       3........2334445555555555555555554444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.31
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktkl 36 
                                        tk+ + +a+i+e+  +++  ++ I +L +   ++
  gi|557694373|ref|YP_008797427.1| 400 VTKRDAIKAEIEETNRRRREANKEIYELGTINGQD 434
                                       589999**********************9876655 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.2
                           DUF5082  85 kldelidaieeEIerLenqisea 107
                                       ++ el ++i + I+rL+ + ++a
  gi|557694373|ref|YP_008797427.1| 499 DVAELLSRIRTGIKRLRDDGYSA 521
                                       46678888888888888777666 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.014
                           DUF5082   2 ktkisklqaqiaelrseiaaleekIerLkeaktklsde 39 
                                       +++i + +++ ++lr+++++ e+ I +L+++++ l ++
  gi|557694373|ref|YP_008797427.1| 538 SREIGSKEKELEKLREDMQKAEKEIGELERVREVLRKA 575
                                       6889999************************9988765 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 ?    8.7   2.8    0.0024       1.5      57      99 ..     200     242 ..     190     256 .. 0.86
   2 ?    1.4   0.0      0.42   2.6e+02      55      76 ..     431     452 ..     427     494 .. 0.85
   3 ?   -0.2   0.4       1.3   8.2e+02      56      78 ..     545     567 ..     525     587 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0024
                            Nsp1_C  57 ekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdnyEk 99 
                                       ++++kL++ + e ++++ ++++eLe + ++++eL++ ++++E 
  gi|557694373|ref|YP_008797427.1| 200 QELEKLRRLLTEGKEKEVELEKELERLRNEHQELSEGIEKLEG 242
                                       6789999999*****************************9995 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.42
                            Nsp1_C  55 ngekIskLysevleaeqeqnki 76 
                                       ng+ +++L+++vl+aeq  +++
  gi|557694373|ref|YP_008797427.1| 431 NGQDVQRLRNKVLAAEQLLREV 452
                                       99**************987665 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.3
                            Nsp1_C  56 gekIskLysevleaeqeqnkidq 78 
                                        ++++kL++++ +ae+e  ++++
  gi|557694373|ref|YP_008797427.1| 545 EKELEKLREDMQKAEKEIGELER 567
                                       34455556666666655555554 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 ?    3.5   2.7     0.098        61       2      42 ..     217     257 ..     197     341 .. 0.59
   2 ?    5.1   0.2      0.03        19       5      32 ..     545     572 ..     542     592 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.098
                        STAT_alpha   2 qeieqrleelrskvqeteqdirkLedeqeeFdfqyqelqkl 42 
                                        e+e++le lr++ qe+ + i+kLe +   F    ++l+ l
  gi|557694373|ref|YP_008797427.1| 217 VELEKELERLRNEHQELSEGIEKLEGLHRLFGEVRSSLEAL 257
                                       46777777777777777777777776665554333333333 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.03
                        STAT_alpha   5 eqrleelrskvqeteqdirkLedeqeeF 32 
                                       e++le+lr+ +q+ e++i +Le + e +
  gi|557694373|ref|YP_008797427.1| 545 EKELEKLREDMQKAEKEIGELERVREVL 572
                                       6789******************998865 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.6      0.22   1.4e+02      19      81 ..     148     211 ..     131     220 .. 0.53
   2 ?    7.7   3.7    0.0047       2.9       3      95 ..     200     287 ..     198     305 .. 0.73
   3 ?   -0.7   0.2       1.8   1.1e+03      16      37 ..     409     430 ..     376     483 .. 0.44
   4 ?    7.2   0.6    0.0067       4.1      14      67 ..     538     588 ..     526     621 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.22
                                       TTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT......-S-..-GGGTHHHHHHHHH CS
                              PCRF  19 edqekakklskelaeleeivealeeleealedleeakell.e.edeelaelaeeeleelekelee 81 
                                       +d++++k+l  +l  l++  +a+ +++e+le  ee  +l+ + + +el  l+e+ele+l++ l e
  gi|557694373|ref|YP_008797427.1| 148 ADPKELKELFDDLLGLSAFEQAYARMKEVLECFEERVRLMvRrSVDELL-LVEQELEKLRRLLTE 211
                                       4555666666666666666666666666666666655544222222333.344555555444433 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0047
                                       HHHTTTTTST.-GG..GTTTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT....-S-..-GGGTHHHHH CS
                              PCRF   3 eeleelekklsdpe..vwedqekakklskelaeleeivealeeleealedleeakelleedeelaelaeeeleelek 77 
                                       +ele+l++ l++ +   +e ++++++l +e++el+e +e+le l+++  ++++    l   e l+ l++ el++le+
  gi|557694373|ref|YP_008797427.1| 200 QELEKLRRLLTEGKekEVELEKELERLRNEHQELSEGIEKLEGLHRLFGEVRS---SL---EALKGLVRRELADLEE 270
                                       66677777665443003445789999999999999999999999999999999...44...4567777888888888 PP

                                       HHHHH..HHHHHT-..SS CS
                              PCRF  78 eleeleeelkklLlpkde 95 
                                       e+ ++e+  k l l ++e
  gi|557694373|ref|YP_008797427.1| 271 EVGRIERATKVLVL-REE 287
                                       88888777766666.333 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.8
                                       GGTTTGGGSSSTTHHHHHTHHH CS
                              PCRF  16 evwedqekakklskelaeleei 37 
                                       e+ e +++ ++ +ke+ el +i
  gi|557694373|ref|YP_008797427.1| 409 EIEETNRRRREANKEIYELGTI 430
                                       1122222222222222222222 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0067
                                       -GGGTTTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT....-S-.. CS
                              PCRF  14 dpevwedqekakklskelaeleeivealeeleealedleeakelleedeelael 67 
                                       + e+ +++++++kl +++++ e+ + +le+++e+l++++e ++l+   ++++el
  gi|557694373|ref|YP_008797427.1| 538 SREIGSKEKELEKLREDMQKAEKEIGELERVREVLRKAREFRDLM---RKMREL 588
                                       334444555555555555555555555555555555555555555...334433 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 ?   -4.4   9.5       5.3   3.3e+03      23     120 ..     168     266 ..     153     447 .. 0.67
   2 ?   -1.6   0.2      0.75   4.6e+02      31     111 ..     395     477 ..     365     486 .. 0.70
   3 ?    8.0   0.0   0.00097       0.6      70     119 ..     533     582 ..     499     644 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 5.3
                        V_ATPase_I  23 rkfvkevrrcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnenleklkkel 99 
                                       +++++    ++  e+++r++ +   ++   v +e e+ ++l ++ +++  ele+ele+l +e +el+e  ekl+  +
  gi|557694373|ref|YP_008797427.1| 168 QAYARMKEVLECFEERVRLMVRRSVDELLLVEQELEKLRRLLTEGKEKEVELEKELERLRNEHQELSEGIEKLEGLH 244
                                       55544444444445555554444444333333333334444455555555555555555555555555555555555 PP

                        V_ATPase_I 100 nelvelkavlekakefleee.e 120
                                       +   e ++ le  k ++++e +
  gi|557694373|ref|YP_008797427.1| 245 RLFGEVRSSLEALKGLVRRElA 266
                                       5555555555555555554422 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.75
                        V_ATPase_I  31 rcdemerklrfleeeieklekavikeeeaeesleapeekeldeleeelekleeelkelnen..leklkkelnelvel 105
                                       r  e+  k + +++eie+++   ++++++  +l + + +++++l +++  +e+ l+e+  +    +lk++l+ l e 
  gi|557694373|ref|YP_008797427.1| 395 RAAELVTKRDAIKAEIEETNRRRREANKEIYELGTINGQDVQRLRNKVLAAEQLLREVGGEpgVAALKARLEGLRER 471
                                       55666667777777777777777777777777777777777777777777777777775432255666666666666 PP

                        V_ATPase_I 106 kavlek 111
                                        a lek
  gi|557694373|ref|YP_008797427.1| 472 AAKLEK 477
                                       555555 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00097
                        V_ATPase_I  70 eldeleeelekleeelkelnenleklkkelnelvelkavlekakefleee 119
                                       + d+l++e+ ++e+el++l+e ++k +ke  el+  ++vl+ka+ef +  
  gi|557694373|ref|YP_008797427.1| 533 RKDKLSREIGSKEKELEKLREDMQKAEKEIGELERVREVLRKAREFRDLM 582
                                       45789999************************************998644 PP

>> Com_YlbF  Control of competence regulator ComK, YlbF/YmcA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   2.1      0.11        71      35     100 ..     189     254 ..     151     258 .. 0.77
   2 ?    2.5   0.2      0.35   2.1e+02      16      72 ..     270     322 ..     263     342 .. 0.77
   3 ?    1.6   0.1      0.66   4.1e+02      24      73 ..     396     442 ..     393     470 .. 0.67
   4 ?    9.1   3.2    0.0031       1.9      41      98 ..     530     587 ..     525     591 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHH.HTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Com_YlbF  35 qklikefkklqkelqekqmkgeelkeeekkelqelkeel.dknplvkeyleaeqelnellqevnkii 100
                                       ++ ++e+   ++el++ ++   e ke+e  el+++ e+l +++++++e +e+ + l +l+ ev + +
  gi|557694373|ref|YP_008797427.1| 189 RRSVDELLLVEQELEKLRRLLTEGKEKEV-ELEKELERLrNEHQELSEGIEKLEGLHRLFGEVRSSL 254
                                       56778888888999998888888888888.8885555444999999999999999999999998776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHH CS
                          Com_YlbF  16 eeykeykeaeealeedeelqklikefkklqkelqekqmkgeelkeeekkelqelkee 72 
                                       ee+ + ++a + l   ee+ k i+++ +l+ e+++  +k  +l+    ++l+e+  e
  gi|557694373|ref|YP_008797427.1| 270 EEVGRIERATKVLVLREEIEKRITRVDELRVEISRLDEKERALQ----RQLREIGGE 322
                                       78889999999999999*************99988664443322....255555554 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.66
                                       HHHHHHCSHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHHHHH CS
                          Com_YlbF  24 aeealeedeelqklikefkklqkelqekqmkgeelkeeekkelqelkeel 73 
                                       a e + + +++++ i+e ++++ e++++     el   + + +q+l +++
  gi|557694373|ref|YP_008797427.1| 396 AAELVTKRDAIKAEIEETNRRRREANKEI---YELGTINGQDVQRLRNKV 442
                                       66778888899999999999999887743...244444444555555544 PP

  == domain 4  score: 9.1 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHHHHTT----HHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHH CS
                          Com_YlbF  41 fkklqkelqekqmkgeelkeeekkelqelkeeldknplvkeyleaeqelnellqevnk 98 
                                       +k ++++l+++  ++e++ e+ ++ +q++++e+ + + v+e l + +e+ +l+ ++ +
  gi|557694373|ref|YP_008797427.1| 530 LKLRKDKLSREIGSKEKELEKLREDMQKAEKEIGELERVREVLRKAREFRDLMRKMRE 587
                                       5555555655444444444444449****************************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (758 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1571  (0.0876234); expected 358.6 (0.02)
Passed bias filter:                      790  (0.0440627); expected 358.6 (0.02)
Passed Vit filter:                       163  (0.00909142); expected 17.9 (0.001)
Passed Fwd filter:                        89  (0.00496402); 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: 1.46u 0.34s 00:00:01.80 Elapsed: 00:00:00.50
# Mc/sec: 4553.43
//
Query:       gi|557694374|ref|YP_008797428.1|  [L=377]
Description: metallophosphoesterase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   43.2   3.1    9.2e-10   39.0   1.9    2.8  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.3e-09   38.1   1.2    2.3e-09   38.1   1.2    1.7  2  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 !   39.0   1.9     1e-13   9.2e-10       1     160 [.       1     226 [.       1     231 [. 0.70
   2 ?    0.8   0.0     0.057   5.1e+02      89     121 ..     302     337 ..     254     350 .. 0.72

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1e-13
                     Metallophos_2   1 MklaiiSDlH................snldaleavlealkevgvdaiihaGDl.eeeep.....evleellela... 52 
                                       M +++iSD+H                +  +   +++e++ +++vd +ih+GD+  e  p      vl+e  +++   
  gi|557694374|ref|YP_008797428.1|   1 MMIGHISDTHlgafigrdeelrevgeDVHASFLEAIEIFVREDVDIVIHSGDIlDEPRPygdamRVLMEGAKRLndr 77 
                                       99**********99977776666665555555566*****************9755555554443333333333599 PP

                     Metallophos_2  53 ..pvlaVrGNnD..eev..veedvlreaaelgtdlpeeaelelagekvlliHgdpl..................... 102
                                          +l   G +D  + +    +   ++ a+l++++ + + +e++g +v  +H+++l                     
  gi|557694374|ref|YP_008797428.1|  78 giHMLFTLGEHDisS-IpsTPHPYVAKLAGLAEYVGNGEAHEVKGLTVIGLHKHKLveagvlcerleeigrrvrgls 153
                                       89999999****863.2466777778888888888888888888888888888877888888888888888887777 PP

                     Metallophos_2 103 .............gvkdalaellkeaeegsd.vvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe..tyail 160
                                                    +   + +  ++e   g + ++++GH+H+++  + g  l+ +PG   +   +dp   +++++
  gi|557694374|ref|YP_008797428.1| 154 gkkvlvlhqgmreAFGPGSELSISEIPHG-FdYYAMGHIHKRYEVRMGRGLLAYPGPSHWVDVDDPDdcGVLLV 226
                                       77777666644452222223333332233.35**********99999999******988876666664455555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.057
                     Metallophos_2  89 l...agekvlliHgdplgvkdalaellkeaeegsdv 121
                                       +   +g++v l H+ +l+v+++l+el+ e+ +++d+
  gi|557694374|ref|YP_008797428.1| 302 VkpdKGKTVELRHERQLSVEERLRELALEQIKDKDL 337
                                       233466668889999889999999998887777764 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   1.2   2.5e-13   2.3e-09       3     203 ..       3     193 ..       1     194 [. 0.71
   2 ?   -3.3   0.0       1.2     1e+04      25      47 ..     329     352 ..     320     369 .. 0.55

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 2.5e-13
                                       EEEEESBTB...........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH....T CS
                       Metallophos   3 ilvigDlHl...........algggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky....p 64 
                                       i +i+D+Hl           + g+  ++++l++++ + re ++d+v++ GD+ d+  +  + ++ l +  k+    +
  gi|557694374|ref|YP_008797428.1|   3 IGHISDTHLgafigrdeelrEVGEDVHASFLEAIEIFVRE-DVDIVIHSGDILDEPRPYGDAMRVLMEGAKRlndrG 78 
                                       89***************99988999999999999999999.**************988888999976666666888* PP

                                       SEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE....EEEEEEESE...CEEE...THHH CS
                       Metallophos  65 ipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgs....lkvlllhGg...spel...lvsl 131
                                       i+  ++lG H+  +   +         ++p+  +    +    ++ g+ +    l+v+ lh +   +      ++ l
  gi|557694374|ref|YP_008797428.1|  79 IHMLFTLGEHD-ISSIPST--------PHPYVAK--LAGLAEYVGNGEAHevkgLTVIGLHKHklvE--AgvlCERL 142
                                       ***********.2222222........2333222..1122222222222232344666666663222..13355556 PP

                                       HHHHHHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHH.HHHTTESEEEEESSSS CS
                       Metallophos 132 dklgslnleleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedl.lkkygvdlvisGHtHv 203
                                       +++g++++ l                     ++++ H ++       fg+ +   + +  +g d++ +GH+H+
  gi|557694374|ref|YP_008797428.1| 143 EEIGRRVRGLS----------G--------KKVLVLHQGMR----EAFGPGSELSIsEIPHGFDYYAMGHIHK 193
                                       66666666644..........3........67888899999....99999999999899999**********7 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.2
                                       HHHHHHHTTESEEEEEST...SSSSS CS
                       Metallophos  25 lddllreekpdlvllaGD...lvdrg 47 
                                       l++++++  +d+ l  GD   l   g
  gi|557694374|ref|YP_008797428.1| 329 LEQIKDKDLIDFAL--GDllkLLSSG 352
                                       45555555555555..8855544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2783.12
//
Query:       gi|557694375|ref|YP_008797429.1|  [L=496]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-34  120.3   0.8    1.8e-34  119.8   0.8    1.2  1  DUF87          Helicase HerA, central domain
    0.00037   19.2   0.0      0.035   12.7   0.0    2.2  2  DUF853         Bacterial protein of unknown function (DUF853)
    0.00057   18.9   0.5        1.5    7.6   0.0    3.0  3  AAA_10         AAA-like domain
     0.0015   17.5   0.2      0.079   11.9   0.0    2.6  3  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-
     0.0027   17.1   0.2        0.7    9.2   0.0    2.4  2  FtsK_SpoIIIE   FtsK/SpoIIIE family
     0.0029   17.7   0.8      0.021   14.9   0.5    2.8  2  HAS-barrel     HAS barrel domain
     0.0083   16.6   0.0      0.015   15.8   0.0    1.5  1  ABC_tran       ABC transporter
  ------ inclusion threshold ------
      0.028   14.1   0.0      0.076   12.7   0.0    1.6  1  DUF188         Uncharacterized BCR, YaiI/YqxD family COG1671


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 !  119.8   0.8   8.2e-38   1.8e-34       1     226 [.     129     329 ..     129     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 8.2e-38
                             DUF87   1 ieiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkalekllsekvk 77 
                                       +e+G+ll + +v+v +dln + +rHlAil+ TG GKSn+ a+L ++++ +k++t++i+D H EY  ++     + +k
  gi|557694375|ref|YP_008797429.1| 129 VEVGSLLRRPGVRVNIDLNAVASRHLAILAITGRGKSNLLALLAKRVA-EKNGTMVIVDYHAEYEGLR----IKGIK 200
                                       79**********************************************.*******************....88888 PP

                             DUF87  78 vitpspsakdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqaka......keekeklssdepveklle 148
                                       +i p         k+np++l +eel+d+l++  +++a++qr++l +++d+ ++      +         e  +kl e
  gi|557694375|ref|YP_008797429.1| 201 HIIP---------KLNPSRLPVEELADVLGV--REKAEKQRALLHKVVDEDVRegqdfwG---------EVKKKLSE 257
                                       8888.........8*****************..****************88742332322.........33333333 PP

                             DUF87 149 elkkekeelrklknqaiarlldkledllrkggsf.snsstdliallleklekegkitiidlsgvdelaqqlvvsvil 224
                                         k  +e++ ++++  ++rll+ +++ lr +g++ ++  ++li+++      +++i+++d+sg+ e ++q++v+++l
  gi|557694375|ref|YP_008797429.1| 258 IAK--NEKIISQDRAVASRLLEIINRALRVRGQIfDTNAKRLIDSI-----YPNRINVLDVSGYTEIQAQILVAHLL 327
                                       333..44566666666666666666666666666666666699999.....*************************9 PP

                             DUF87 225 rr 226
                                       ++
  gi|557694375|ref|YP_008797429.1| 328 EE 329
                                       87 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 !    4.5   0.0    0.0047        10      18      68 ..     148     198 ..     136     206 .. 0.84
   2 !   12.7   0.0   1.6e-05     0.035     239     336 ..     329     426 ..     226     445 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0047
                            DUF853  18 klanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiakaG 68 
                                       ++a rh  i   tG Gk   L +la+ ++e   +++++d   +  g+   G
  gi|557694375|ref|YP_008797429.1| 148 AVASRHLAILAITGRGKSNLLALLAKRVAEKNGTMVIVDYHAEYEGLRIKG 198
                                       5789************************99988888889888777776665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.6e-05
                            DUF853 239 WllseLfeeLPevGdld..kPklvfffdeahLLfndapkal.lekveqvvrLirskGvGvyfvtqnPldlPdtvLaq 312
                                        ll +  + +   Gd+    P +++ ++eah++      +l  + ve++ r  r  G  + +v+q P+ l  +v++q
  gi|557694375|ref|YP_008797429.1| 329 ELLEDRKDAVRGEGDVRlrSP-VIVALEEAHVFIPSEGGSLcSDIVERIAREGRKFGLSLILVSQRPSRLDADVVSQ 404
                                       455555555566677542134.445689***998776666615889******************************* PP

                            DUF853 313 LGnrvqhalraftpkdqkavkaaa 336
                                       +G+    +l    p+dq  v+ ++
  gi|557694375|ref|YP_008797429.1| 405 IGSFAISGLT--HPRDQTFVQEVT 426
                                       **86555543..377777766665 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00068       1.5      21      63 ..     151     193 ..     142     220 .. 0.80
   2 ?    1.0   0.3     0.073   1.6e+02     111     169 ..     217     280 ..     209     315 .. 0.65
   3 !    6.8   0.0    0.0012       2.7     243     287 ..     351     398 ..     347     411 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00068
                            AAA_10  21 asasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerek 63 
                                       + + +i+  +G GKS l  ll   ++  +g ++i+D  +e e 
  gi|557694375|ref|YP_008797429.1| 151 SRHLAILAITGRGKSNLLALLAKRVAEKNGTMVIVDYHAEYEG 193
                                       567899999****************************999544 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.073
                            AAA_10 111 elllgvkkkesekkaalseaveavle.gkq..rgllavieelrkedekvarei..arhlesvvk 169
                                         +lgv++k+++++a+l+++v++ ++ g++   ++ + + e+ k+++ ++++   a  l ++++
  gi|557694375|ref|YP_008797429.1| 217 ADVLGVREKAEKQRALLHKVVDEDVReGQDfwGEVKKKLSEIAKNEKIISQDRavASRLLEIIN 280
                                       5589999**************9877515544444555555665555544443212555555554 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0012
                            AAA_10 243 vvifDEawiftssaeGk...kllkelvRiGRsynaavylvtqsadDvl 287
                                       +v + Ea +f  s+ G     +++ + R GR++   ++lv+q ++ ++
  gi|557694375|ref|YP_008797429.1| 351 IVALEEAHVFIPSEGGSlcsDIVERIAREGRKFGLSLILVSQRPSRLD 398
                                       5678999999999999533378999*****************987665 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 !   11.9   0.0   3.5e-05     0.079      15      55 ..     151     191 ..     142     203 .. 0.92
   2 ?   -1.3   0.0      0.35   7.9e+02     125     183 ..     222     280 ..     206     292 .. 0.73
   3 ?    2.3   0.0     0.028        63     261     287 ..     373     399 ..     371     435 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                     TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrairargdraivlDltGaf 55 
                                        +h++i+  tG GK++ l  l + + +++ +++++D + ++
  gi|557694375|ref|YP_008797429.1| 151 SRHLAILAITGRGKSNLLALLAKRVAEKNGTMVIVDYHAEY 191
                                       68**********************************98776 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.35
                     TrwB_AAD_bind 125 vrekkksnaallralltadleeLkellagteaaalvaeeaertaasiratlatnlevle 183
                                       vrek ++++all++++++d++e +++  + + +     ++e++ ++ ra+ ++ le+++
  gi|557694375|ref|YP_008797429.1| 222 VREKAEKQRALLHKVVDEDVREGQDFWGEVKKKLSEIAKNEKIISQDRAVASRLLEIIN 280
                                       45566666999999999999999999888877766668888888888888887777774 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.028
                     TrwB_AAD_bind 261 lksllaegRkfGgavvlglqsiaqlre 287
                                       +++++ egRkfG  ++l  q  ++l +
  gi|557694375|ref|YP_008797429.1| 373 VERIAREGRKFGLSLILVSQRPSRLDA 399
                                       678899***************999964 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00031       0.7      30     152 ..     141     265 ..     131     301 .. 0.72
   2 !    5.5   0.0    0.0043       9.6     166     211 ..     373     418 ..     307     435 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00031
                                       EEEEEGGGS-..SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSS.SCGGGTT-TTBSS...S-B-SH CS
                      FtsK_SpoIIIE  30 plvldlkkma.shllvaGatgsGKStalntLilSlatthtPeeVqliliDykgv.elsalediphlls..vavatdp 102
                                        + +dl+ +a  hl ++  tg+GKS+ l  L    a + + ++ +++++Dy    e   +++i h++    +++  +
  gi|557694375|ref|YP_008797429.1| 141 RVNIDLNAVAsRHLAILAITGRGKSNLLALL----AKRVAEKNGTMVIVDYHAEyEGLRIKGIKHIIPklNPSRLPV 213
                                       566788888888*************977544....444444677888999987778888888888887677888888 PP

                                       HHHHHHHHHHHHHHHHHH..HHHHHTT-SSHHHHHHHHHHHHHTT---B-TT CS
                      FtsK_SpoIIIE 103 eralraleeLvkemeery..alfreagvrsiaaydgeiaedpldifgdvflv 152
                                       e+ + +l   +k+ ++r+   +  ++ vr+ +++ ge++++  +i +   ++
  gi|557694375|ref|YP_008797429.1| 214 EELADVLGVREKAEKQRAllHKVVDEDVREGQDFWGEVKKKLSEIAKNEKII 265
                                       8888888888888888887877788888888887777777776665544444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0043
                                       ..........-----------B-----EEEEEEC-HHHHHHHHHHH CS
                      FtsK_SpoIIIE 166 itsLsnqgpsygvhvlvtagrelekrpslvvivderieLrlaapkd 211
                                       +  ++ +g ++g  +++ ++r ++    +v+++++++   l++p+d
  gi|557694375|ref|YP_008797429.1| 373 VERIAREGRKFGLSLILVSQRPSRLDADVVSQIGSFAISGLTHPRD 418
                                       3345555666666666666666666666666666666666666666 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.5   9.6e-06     0.021       1      45 [.       4      45 ..       4      97 .. 0.70
   2 ?   -2.6   0.0       2.7   6.1e+03      18      32 ..     441     455 ..     424     486 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.6e-06
                        HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvtd 45
                                      +G+v ges + +  f+ +    v+vG++V +e++ ++ vl mv++
  gi|557694375|ref|YP_008797429.1|  4 VGIVCGESRPEGIAFTGPK--SVRVGDFVTVETE-DGPVLYMVES 45
                                      7999999999777666665..9************.5555556665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.7
                        HAS-barrel  18 egskdvkvGeyVeie 32 
                                       ++++++ vG +V+++
  gi|557694375|ref|YP_008797429.1| 441 NPGEMILVGNFVRAP 455
                                       444477777777766 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   6.9e-06     0.015       3      51 ..     143     191 ..     142     294 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.9e-06
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51 
                                       n++l+  +++ +ai+  +G GKS Ll+lla+ +  ++G++ + + + ++
  gi|557694375|ref|YP_008797429.1| 143 NIDLNAVASRHLAILAITGRGKSNLLALLAKRVAEKNGTMVIVDYHAEY 191
                                       67888889999****************************9554433333 PP

>> DUF188  Uncharacterized BCR, YaiI/YqxD family COG1671
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.4e-05     0.076      48      84 ..     257     293 ..     251     300 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                            DUF188  48 raeagDlvvTqDipLAarvlekgaaalsprGevytee 84 
                                       ++++++ +++qD  +A+r+le   +al+ rG++++++
  gi|557694375|ref|YP_008797429.1| 257 EIAKNEKIISQDRAVASRLLEIINRALRVRGQIFDTN 293
                                       56778889**************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 3629.38
//
Query:       gi|557694376|ref|YP_008797430.1|  [L=290]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   86.4   0.8    3.2e-24   86.0   0.8    1.2  1  NurA           NurA domain
  ------ inclusion threshold ------
       0.12   12.6   0.0        0.4   11.0   0.0    1.9  1  SWIRM-assoc_3  SWIRM-associated domain at the C-terminal


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 !   86.0   0.8   3.6e-28   3.2e-24       2     242 .]      48     264 ..      47     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 3.6e-28
                                       EEEEEEEEEEEEEETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEE...HHHHHHHHHHHHHHHHHHHCG CS
                              NurA   2 rvaAvDGSngvvrlsggilyilsayavvgggkerleealslasvdsispsdel...errirllmetlElklgallle 75 
                                       +v++vD++ + + ++g+ +y+  a+a      er+e    + ++d+ s++  +   e+ ++l  e+ E+   +  + 
  gi|557694376|ref|YP_008797430.1|  48 EVYGVDSGWNIRLYDGFYVYAEMAAA----VNERQETCHHVIKFDLMSKDQGGltpENAVKLAAENDEHY--IAERA 118
                                       69************************....44555555555555554433333666**************..***** PP

                                       GCCSCEEEEECSHHCCCH.HHHHHHHHHHHHHHHHHHHHHTT-TTCEEEEESS-SCTCCHCCC......S--HHHHC CS
                              NurA  76 ekgedllllDGsligslv.efdelheeleyeeylyslsrlleaglnlvgvaKsfrskellnllletlligesisDia 151
                                        +++dl+l+DGsl++ l  +++ l +++ y+eyly  ++l+++ +n+v+ +K ++ + ll+           + Di 
  gi|557694376|ref|YP_008797430.1| 119 SHEADLVLVDGSLLARLRsAENLLRIGPTYAEYLYLAKSLMDR-ENVVFFSKYSQDSSLLKGE---------LGDIY 185
                                       ******************9999********************6.*****************99.........***** PP

                                       CHHCCHCH---STTS-HHHHTT-HCCHHHHHH-EEEEEEESSTTTTEEEEEHHHHHHCCHHHHHHHHHH..TTB-SS CS
                              NurA 152 llgallrkpgytspllkilrekpllrealidkeiyfaYvrlegggsilrleipaevstakdedvlsllasqrlsisG 228
                                       ++g  +  pgy                ++++ +i++aYvrl ++  +l++e+pa v+ +++  + ++ a   +  +G
  gi|557694376|ref|YP_008797430.1| 186 YFGLATSGPGYA----------LGPTLMRDNIPITIAYVRLTEYAAPLKIEVPANVGEDHIRRIMEAQA--LRTVKG 250
                                       ******99***7..........88999******************************************..****** PP

                                       SBCCHHHHHHHHCC CS
                              NurA 229 YprpLalAhelaki 242
                                       Yp+ L lAh+ +++
  gi|557694376|ref|YP_008797430.1| 251 YPYVLYLAHRTVSV 264
                                       ***********986 PP

>> SWIRM-assoc_3  SWIRM-associated domain at the C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.4e-05       0.4      14      41 ..     216     244 ..     203     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.4e-05
                     SWIRM-assoc_3  14 leeFsk.ikdevPaalveaHvknveaaae 41 
                                       l+e+++ +k evPa + e+H++++ +a++
  gi|557694376|ref|YP_008797430.1| 216 LTEYAApLKIEVPANVGEDHIRRIMEAQA 244
                                       6788654899*************998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 2329.83
//
Query:       gi|557694377|ref|YP_008797431.1|  [L=163]
Description: hypothetical protein CSUB_C0948 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1189.52
//
Query:       gi|557694378|ref|YP_008797432.1|  [L=111]
Description: hypothetical protein CSUB_C0949 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       341  (0.0190195); 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:                         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: 00:00:00.40
# Mc/sec: 836.97
//
Query:       gi|557694379|ref|YP_008797433.1|  [L=275]
Description: hypothetical protein CSUB_C0950 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2055.74
//
Query:       gi|557694380|ref|YP_008797434.1|  [L=694]
Description: helicase-associated endonuclease for fork-structured DNA [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-21   77.0   0.1    6.1e-21   74.9   0.1    2.1  2  Helicase_C       Helicase conserved C-terminal domain
    7.9e-17   61.6   0.0    6.1e-16   58.7   0.0    2.3  3  DEAD             DEAD/DEAH box helicase
      3e-15   56.6   0.0    8.9e-15   55.1   0.0    1.9  1  ResIII           Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.029   14.1   0.0      0.066   12.9   0.0    1.6  1  SWI2_SNF2        SWI2/SNF2 ATPase
      0.045   12.9   0.0      0.085   12.0   0.0    1.4  1  ERCC3_RAD25_C    ERCC3/RAD25/XPB C-terminal helicase
      0.054   13.1   0.4       0.46   10.1   0.2    2.7  2  Zot              Zonular occludens toxin (Zot)
      0.056   14.5   0.0         18    6.4   0.0    2.7  2  Methyltransf_24  Methyltransferase domain
       0.19   12.3   1.8          1    9.9   0.4    2.6  2  FeoB_Cyto        FeoB cytosolic helical domain


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         5   1.1e+04       8      34 ..      51      78 ..      46     102 .. 0.60
   2 !   74.9   0.1   2.7e-24   6.1e-21       4     109 ..     352     464 ..     346     465 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5
                                      HHHHHTTTTSEEEEEESSHH.HHHH.HHH CS
                        Helicase_C  8 ellkleeeggkilifvntid.rlek.vkl 34
                                      ell +++ g +il++++t+   l++  ++
  gi|557694380|ref|YP_008797434.1| 51 ELL-HRHPGCRILVMAPTKPlVLQHrQSF 78
                                      445.7888889999998887422223233 PP

  == domain 2  score: 74.9 bits;  conditional E-value: 2.7e-24
                                       HHHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTT........STHHHHHHHHHHHHTTSSSEEE CS
                        Helicase_C   4 eallellkleeeggkilifvntidrlek.vklllekkgikvavlhge........lpqnereeileqfnkgesdvLi 71 
                                       +++ + l +e+ +++i++f+n ++++e  v+ l ++ g+++ ++ g+        ++q+e+++ l++f++g +++L+
  gi|557694380|ref|YP_008797434.1| 352 QRISQHL-SEKPDDRIMVFANIRNTAEViVSRL-TELGYRARMFIGKgegktgpkMTQQEQIRLLKEFREGVFNILV 426
                                       4555666.899*************998665555.34477777777777799************************** PP

                                       ESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  72 atdvaerGidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       at+++e+G+dip++ +Vi++++  +  +yiqr+GRtgR
  gi|557694380|ref|YP_008797434.1| 427 ATSIGEEGLDIPECGYVIFYEPAISGIRYIQRRGRTGR 464
                                       *************************************9 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.0   2.7e-19   6.1e-16       2     169 ..      17     174 ..      16     181 .. 0.82
   2 ?   -0.6   0.0      0.44   9.8e+02      36     104 ..     351     428 ..     341     433 .. 0.57
   3 ?   -3.9   0.0       4.5     1e+04      82     109 ..     574     601 ..     557     610 .. 0.74

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 2.7e-19
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       ++Q+++++++l+g + lv  +T+ GKT ++ + + + +   ++ +g ++l+++Pt+ L+ q+ + + k ++  + + 
  gi|557694380|ref|YP_008797434.1|  17 EYQRSMVEEALRG-NTLVVLPTALGKTVIAELVAAELL---HRHPGCRILVMAPTKPLVLQHRQSFLKHLNISEDEG 89 
                                       6899*******55.*********************999...47***********************99999655455 PP

                                       EEEETTSSHHHHHHHHHTT..CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHT.TTHHHHHHHHHHSHHH CS
                                       xxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldng..vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldq.gfsdfinrilnqlpqi 152
                                        +i+g+v+++  + +   +  v+iv++tp+  ++  ++g ++l+++ +lV+DE++r  +   + +  ++ ++++   
  gi|557694380|ref|YP_008797434.1|  90 IAITGEVSESVRKMAW-GSpsVRIVFSTPQTAFNDYRRGWIRLEEFALLVFDECHRSRSRyAYTRLASEYVRRC--- 162
                                       5677776665555555.2246*************9***********************9977777777777777... PP

                                       CTTST.TTSEEEEEESSB CS
                                       xxxxx.xxxxxxxxxxxx RF
                              DEAD 153 tcdgk.lqrqvivlSATl 169
                                           +    +v+ l+A +
  gi|557694380|ref|YP_008797434.1| 163 ----PwP--RVLGLTASP 174
                                       ....322..366666665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.44
                                       HHHHHHS.TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET........TSSHHHHHHHH...HTT.CS CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxx...xxx.xx RF
                              DEAD  36 lqivyet.kgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig........gvaardqlskl...dng.vd 99 
                                       +q+++++  +k+  ++++ +  r  ae ++++l++++  ++    ++ig        + ++++q++ l   ++g  +
  gi|557694380|ref|YP_008797434.1| 351 VQRISQHlSEKPDDRIMVFANIRNTAEVIVSRLTELGYRAR----MFIGkgegktgpKMTQQEQIRLLkefREGvFN 423
                                       44554445567888888888888888888888888888433....22332122221223333333333211344566 PP

                                       EEEEE CS
                                       xxxxx RF
                              DEAD 100 ivvgt 104
                                       i+v+t
  gi|557694380|ref|YP_008797434.1| 424 ILVAT 428
                                       66666 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 4.5
                                       ETTSSHHHHHHHHHTTCSEEEEEHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  82 iggvaardqlskldngvdivvgtpgrld 109
                                       ++g +  + ls+l+ ++d+v +   rl+
  gi|557694380|ref|YP_008797434.1| 574 VKGLSMAEALSQLSYSPDVVRMSMNRLV 601
                                       5667777788888777888888888776 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 !   55.1   0.0     4e-18   8.9e-15       5     169 ..      16     174 ..      12     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 4e-18
                                       -HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG. CS
                            ResIII   5 reyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflsea 81 
                                       reyQ +++e+ l       + + l++++T  GKT++a  ++++ll+ ++  ++l+++p+k l+ q ++ f k l+  
  gi|557694380|ref|YP_008797434.1|  16 REYQRSMVEEAL-------RGNTLVVLPTALGKTVIAELVAAELLHRHPGCRILVMAPTKPLVLQHRQSFLKHLNIS 85 
                                       666666666665.......55789*************88888898888999*******************9999888 PP

                                       ......GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHH.H CS
                            ResIII  82 yke...igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswrei.l 154
                                        +e   i+++vs+  +k  +  s + +i+++t q++ +d       +   + ++f ++++DE+Hr+++  +++++  
  gi|557694380|ref|YP_008797434.1|  86 EDEgiaITGEVSESVRKM-AWGSPSVRIVFSTPQTAFNDY-----RRGWIRLEEFALLVFDECHRSRSRYAYTRLaS 156
                                       776777444444444444.58999****************.....788899999**************999999647 PP

                                       HT---...SEEEEEESS- CS
                            ResIII 155 ekfke...avllglTATp 169
                                       e++++     +lglTA p
  gi|557694380|ref|YP_008797434.1| 157 EYVRRcpwPRVLGLTASP 174
                                       777666779*******98 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.9e-05     0.066      30     163 ..      40     180 ..      23     200 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                         SWI2_SNF2  30 GKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfaka....geek.pkqaesrkeLkell.ekesekiift 100
                                       GK++   ++a++ll+ +   ++++v+   k L  Q  + f k     ++e  + + e +++++++   + s +i+f+
  gi|557694380|ref|YP_008797434.1|  40 GKTVIAELVAAELLH-RHPGCRILVMAPTKPLVLQHRQSFLKHlnisEDEGiAITGEVSESVRKMAwGSPSVRIVFS 115
                                       899999999999999.8889999999999999999999998864332111102233333444444444568999999 PP

                         SWI2_SNF2 101 tiqKfeeeekeklevlsereniivlvDEaHRsqyg....elakklrkalpnaafigFTGTPilkkdk 163
                                       t q   ++ +     ++ +e  ++++DE+HRs++     +la++  +  p   ++g+T  P ++++k
  gi|557694380|ref|YP_008797434.1| 116 TPQTAFNDYR--RGWIRLEEFALLVFDECHRSRSRyaytRLASEYVRRCPWPRVLGLTASPGSEEEK 180
                                       9997655433..4667777778999*******97765667888888888999999999999887765 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 ?   12.0   0.0   3.8e-05     0.085      88     148 ..     404     465 ..     340     485 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.8e-05
                     ERCC3_RAD25_C  88 etseaerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrr..qeaqrlGri 148
                                       +++++e++++l++f++   +n ++   +g++ +D+Pe   +i  +  ++  r  q   r Gr 
  gi|557694380|ref|YP_008797434.1| 404 KMTQQEQIRLLKEFREG-VFNILVATSIGEEGLDIPECGYVIFYEPAISGIRyiQRRGRTGRK 465
                                       35799*********986.89*******************999888776655523444444444 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   0.00021      0.46      56     147 ..     111     243 ..      91     327 .. 0.77
   2 ?   -1.8   0.0      0.89     2e+03      49      88 ..     610     647 ..     597     650 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                               Zot  56 rliridnpegaetlkefakwatidkgallviDEcqeifpvrakegrkd............................. 103
                                       r+++  +  +    ++ + w + ++ allv+DEc++  +  a   r                               
  gi|557694380|ref|YP_008797434.1| 111 RIVF--STPQTAFNDYRRGWIRLEEFALLVFDECHRSRSRYAYT-R-Laseyvrrcpwprvlgltaspgseeekvle 183
                                       4444..344455567888899999***********987666653.3.245678888888888888888888888888 PP

                               Zot 104 ................pevinaftehRhlgwDivlltqdiskihkevralaekavklkrk 147
                                                       +e +  +    +  w  v +  +  +++k++r+++e  v++ ++
  gi|557694380|ref|YP_008797434.1| 184 vvknlwvekivwrteeDEEVSSYIPGVKVDWVRVEIPHEYEEVRKAIREAIENRVRHLQR 243
                                       888888888888888877778888888888888888888888888888888888877665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.89
                               Zot  49 gekvstarliridnpegaetlkefakwatidkgallviDE 88 
                                       gek  ++ +ir +  +++ +++e+++ ++++  a++v+DE
  gi|557694380|ref|YP_008797434.1| 610 GEKYVAKAVIRAS--KKPDKIHEIRIEKVYPGFAIVVVDE 647
                                       4444456688855..7788888999999999999999999 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0079        18      54      97 ..     117     161 ..      29     164 .. 0.78
   2 ?    5.1   0.0      0.02        45      60      92 ..     201     234 ..     169     249 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0079
                   Methyltransf_24  54 ikadseealasla.agsiDllfiDgghaaeavledleallprlap 97 
                                        +  ++++++++   +++ ll++D +h  ++++++ +++ +++++
  gi|557694380|ref|YP_008797434.1| 117 PQTAFNDYRRGWIrLEEFALLVFDECHRSRSRYAYTRLASEYVRR 161
                                       45555666665557789********************99999875 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.02
                   Methyltransf_24  60 ealasla.agsiDllfiDgghaaeavledleall 92 
                                       e+++s     ++D++ +  +h++e+v+++++ + 
  gi|557694380|ref|YP_008797434.1| 201 EEVSSYIpGVKVDWVRVEIPHEYEEVRKAIREAI 234
                                       33443334789************99888875553 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.59   1.3e+03      36      60 ..     198     235 ..     197     244 .. 0.55
   2 ?    9.9   0.4   0.00046         1       7      75 ..     301     367 ..     295     379 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.59
                         FeoB_Cyto  36 egDeelleelk.............edpelraeveeark 60 
                                       e+Dee+ +++              e++e+r++++ea++
  gi|557694380|ref|YP_008797434.1| 198 EEDEEVSSYIPgvkvdwvrveiphEYEEVRKAIREAIE 235
                                       67777777777777777655444433333333333333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00046
                         FeoB_Cyto   7 kaiekleellkesnlkaklppRwlAlklLegDeelleelk...edpelraeveearkeleaelgedledvIv 75 
                                       ++i++l e l+e      +++   + ++L g e++++ ++   +++++  ++e++++++ ++l+e+++d I 
  gi|557694380|ref|YP_008797434.1| 301 QHIHSLREYLREV-----MHSELRSHRMLSGSEDFRKIIQlaaKSQADHPKIEALVQRISQHLSEKPDDRIM 367
                                       5666666666664.....6677777899999999999999777779999*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (694 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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 0.29s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 4311.11
//
Query:       gi|557694381|ref|YP_008797435.1|  [L=96]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   36.8   0.3    3.3e-09   36.6   0.3    1.1  1  Hjc        Archaeal holliday junction resolvase (hjc)
      0.003   18.0   0.0     0.0036   17.7   0.0    1.1  1  NERD       Nuclease-related domain
     0.0046   17.0   0.1     0.0053   16.8   0.1    1.1  1  VRR_NUC    VRR-NUC domain
     0.0064   16.5   0.2      0.093   12.8   0.0    1.9  2  Mrr_cat    Restriction endonuclease
  ------ inclusion threshold ------
      0.042   14.0   0.1       0.14   12.3   0.0    1.7  2  MTES_1575  REase_MTES_1575
      0.068   13.4   0.0      0.078   13.2   0.0    1.1  1  DUF4263    Domain of unknown function (DUF4263)


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 !   36.6   0.3   1.1e-12   3.3e-09       2      85 ..       9      84 ..       8      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.1e-12
                                      HHHHHHHHHHHTT-EEEEBSCSSSSSSSS-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHHTCEEEEEEE CS
                               Hjc  2 yERelvkiLrergfavvRsagSggatkplpDviAirgdvvlviEvKsskkeriylkkeqvekllefarkaggelllavk 80
                                      +E e+++++++rg+ v+R+a S+ +     D++ i+ + v+++E+K++      l ke+ + l +  ++ g + ++a +
  gi|557694381|ref|YP_008797435.1|  9 FEYEVRDFFEDRGWLVIRAARSKPV-----DLVCIKDGRVMLVECKYAG---GRLLKEERKALEKIGKRYGVDVVVARR 79
                                      799**********************.....******************9...556678888888889999999999988 PP

                                      ETTTE CS
                               Hjc 81 lqgke 85
                                       ++ e
  gi|557694381|ref|YP_008797435.1| 80 KKRGE 84
                                      65554 PP

>> NERD  Nuclease-related 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    0.0036       2      75 ..       6      71 ..       5      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                              NERD  2 gaegEravakeLkelkedeylvlhdvrlrpgtgeiDhlvispkgifviEvKnwsGwifgdkegrwtqkikkgfk 75
                                      g++ E +v ++ +   ++++lv++  r +p    +D++ i  ++++++E+K+  G++ ++ e++  +ki+k++ 
  gi|557694381|ref|YP_008797435.1|  6 GRRFEYEVRDFFE---DRGWLVIRAARSKP----VDLVCIKDGRVMLVECKYAGGRLLKE-ERKALEKIGKRYG 71
                                      6777888888888...56899999988844....6*****************99988877.6667777766663 PP

>> VRR_NUC  VRR-NUC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.8e-06    0.0053      58     105 ..      34      78 ..      14      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-06
                                       SEEEEETTTTE..EEEEEEE-TT----HHHHHHHHHHHHT.T-EEEEEE CS
                           VRR_NUC  58 DLilwieeqkryvflliEvKgpgdrlsdnQrkwldelars.gvrvevcr 105
                                       DL++ ++  +   ++l+E K  g rl ++ rk l+++ ++ gv+v v+r
  gi|557694381|ref|YP_008797435.1|  34 DLVCIKDG-R---VMLVECKYAGGRLLKEERKALEKIGKRyGVDVVVAR 78 
                                       66665543.3...8***********************999899999987 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   3.1e-05     0.093       6      57 ..       6      51 ..       3      66 .. 0.83
   2 ?    2.3   0.0     0.055   1.7e+02      31      46 ..      67      83 ..      53      92 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                                      TTCHHHHHHHHHHHHSSSEEE---B-TTSSB--EEEETTEEEEEEEEEEE-- CS
                           Mrr_cat  6 pkeFeklvaellealGykeveltgrsgDggiDliakkdplgserilvqaKry 57
                                      +++Fe+ v++++e  G+  v ++  ++ + +Dl+  kd+   + +lv++K  
  gi|557694381|ref|YP_008797435.1|  6 GRRFEYEVRDFFEDRGWL-VIRA--ARSKPVDLVCIKDG---RVMLVECKYA 51
                                      789**************9.6655..57899****99987...789****975 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.055
                                      -TTSSB--E.EEETTEE CS
                           Mrr_cat 31 sgDggiDli.akkdplg 46
                                      ++ +g+D++ a++++ g
  gi|557694381|ref|YP_008797435.1| 67 GKRYGVDVVvARRKKRG 83
                                      46789999834444444 PP

>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.8e-05      0.14       1      51 [.       9      56 ..       9      66 .. 0.85
   2 ?   -0.7   0.0      0.55   1.6e+03      24      34 ..      69      79 ..      61      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.8e-05
                         MTES_1575  1 FeeeVaeaLrergykvkpqvgvggfriDlvvedpgkyllaIecdgdkyhss 51
                                      Fe+eV +  ++rg+ v +  + +   +Dlv+++  ++++ +ec  +     
  gi|557694381|ref|YP_008797435.1|  9 FEYEVRDFFEDRGWLVIRAARSK--PVDLVCIKD-GRVMLVECKYAGGRLL 56
                                      9****************998877..79******9.9999****87755555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.55
                         MTES_1575 24 gfriDlvvedp 34
                                      ++ +D+vv ++
  gi|557694381|ref|YP_008797435.1| 69 RYGVDVVVARR 79
                                      57888888877 PP

>> DUF4263  Domain of unknown function (DUF4263)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.6e-05     0.078       5      65 ..      11      62 ..       8      80 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                           DUF4263  5 kkwqkffeknpwllypiisefpikevdfksDfllidslngnivlvEikkpdknlltkekkk 65
                                       ++++ffe++ wl    i+ +  k v    D++ i++  g ++lvE k +  +ll++e+k 
  gi|557694381|ref|YP_008797435.1| 11 YEVRDFFEDRGWLV---IRAARSKPV----DLVCIKD--GRVMLVECKYAGGRLLKEERKA 62
                                      57899*********...777777777....*****96..****************987776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); 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:                         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 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 694.12
//
Query:       gi|557694382|ref|YP_008797436.1|  [L=105]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); 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: 828.38
//
Query:       gi|557694383|ref|YP_008797437.1|  [L=164]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-31  107.1  13.9    9.9e-31  106.8  13.9    1.1  1  DUF996           Protein of unknown function (DUF996)
  ------ inclusion threshold ------
      0.084   12.3   2.8      0.053   13.0   1.2    1.4  1  DUF4481          Domain of unknown function (DUF4481)
       0.34    9.9  13.7       0.54    9.2  13.7    1.5  1  DUF973           Protein of unknown function (DUF973)
       0.37   10.1   8.1       0.59    9.5   8.1    1.4  1  ThrE             Putative threonine/serine exporter
       0.94    9.0  13.9          2    7.9  13.9    1.6  1  ABC2_membrane_5  ABC-2 family transporter protein
        1.1    9.5   4.0       0.29   11.3   1.0    1.6  2  DUF2371          Uncharacterised conserved protein (DUF2371)
        4.2    6.4   7.4       0.21   10.6   0.8    1.9  2  7tm_6            7tm Odorant receptor


Domain annotation for each model (and alignments):
>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8  13.9   3.9e-34   9.9e-31       4     135 .]      12     148 ..       9     148 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 3.9e-34
                            DUF996   4 vGliLvlvalkeiskavndekifsnaliafilsiialvvailalllvlgalatalelpgleeaas.....lilllll 75 
                                       +G+i +++alk+is+a++++k+++ a++++ ++++++++a+l++l++  a+a++l++p+++ +a+     ++l++++
  gi|557694383|ref|YP_008797437.1|  12 AGTIAIVIALKRISEAIKQPKVYRFAFYSVAATVAGVAAAVLLMLAWPPAYASMLGNPDPYVYAFtfpwyYLLGTIA 88 
                                       8*************************************************************9999*********** PP

                            DUF996  76 vliiayvlliisavflkksyellgkrtgvklFetagllyfiGaiLtivlvGliilliaei 135
                                       v ++ ++++iisa+flkks++ +g+r+++k+F+t+gll+++Ga+L+iv+vG++i++ ++i
  gi|557694383|ref|YP_008797437.1|  89 VAVTSTIFAIISALFLKKSLDIVGDRLSIKTFKTSGLLLVLGAVLAIVIVGIYISIAGYI 148
                                       ********************************************************9998 PP

>> DUF4481  Domain of unknown function (DUF4481)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.2   2.1e-05     0.053      44     115 ..      23      99 ..      14     115 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                           DUF4481  44 lieeallepevRRyllynSrl.frlilavvlYvvlWanlystlqly......slgeywvlvllvsLvsvlltvalil 113
                                        i+ea+++p+v R+ +y+ ++ +  + a+vl +  W   y+++         +++  w    l+  ++v++t ++ +
  gi|557694383|ref|YP_008797437.1|  23 RISEAIKQPKVYRFAFYSVAAtVAGVAAAVLLMLAWPPAYASMLGNpdpyvyAFTFPWYY--LLGTIAVAVTSTIFA 97 
                                       699**************976516678899***********99743222222244444443..333444444444444 PP

                           DUF4481 114 il 115
                                       i+
  gi|557694383|ref|YP_008797437.1|  98 II 99 
                                       43 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  13.7   0.00021      0.54     124     194 ..      77     147 ..       4     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00021
                            DUF973 124 slilslillgviilligiilaliGqillglsfyklGevYnnglikigGiliiipvidilsfIGyilsyigl 194
                                             +l  +++++++ i+a+i  + l  s   +G++ + ++ k++G+l++++ +  + ++G+++s+ g 
  gi|557694383|ref|YP_008797437.1|  77 TFPWYYLLGTIAVAVTSTIFAIISALFLKKSLDIVGDRLSIKTFKTSGLLLVLGAVLAIVIVGIYISIAGY 147
                                       445556667778889999************************************99877888888887775 PP

>> ThrE  Putative threonine/serine exporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   8.1   0.00023      0.59      83     194 ..      11     134 ..       9     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00023
                              ThrE  83 aageisleeaeerLdeIerskpryprwlvvlaaglaaaafallfggdwidflvaflagllggllrlllakrglnsfv 159
                                       +ag+i +  a +r+ e  ++++ y+  +  +aa +a++a a+l+   w+ + +++l+    ++  + ++ + l   +
  gi|557694383|ref|YP_008797437.1|  11 TAGTIAIVIALKRISEAIKQPKVYRFAFYSVAATVAGVAAAVLLMLAWPPAYASMLGNPDPYVYAFTFPWYYLLGTI 87 
                                       5677777778899999999********************************************************** PP

                              ThrE 160 leavaaflasllallavs.........l...glglnpdaiiigsill 194
                                       + av++ + +++++l+++         l   +++ +   +++g++l 
  gi|557694383|ref|YP_008797437.1|  88 AVAVTSTIFAIISALFLKksldivgdrLsikTFKTSGLLLVLGAVLA 134
                                       ****************9955443322212221111123444444443 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 ?    7.9  13.9   0.00078         2      91     205 ..      12     147 ..       5     149 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00078
                   ABC2_membrane_5  91 liailitlllliiavlikgn....vtisevllsiliglvialif..................laivlPlyfkfgvek 145
                                       + +i i+++l  i++ ik++    + + +v  +++ + + +l++                  +a+++P y+++g+  
  gi|557694383|ref|YP_008797437.1|  12 AGTIAIVIALKRISEAIKQPkvyrFAFYSVAATVAGVAAAVLLMlawppayasmlgnpdpyvYAFTFPWYYLLGTIA 88 
                                       445555555556667777666766555555555555555555556667777888888888889***********544 PP

                   ABC2_membrane_5 146 grivliiiifgiifllvaifslskl.....elslidlsnyilliillviillliivSyfiSikiy 205
                                       + +        i+++++a+f +++l      ls+ ++ +  ll+ +l+ +l++ iv + iSi  y
  gi|557694383|ref|YP_008797437.1|  89 VAV-----TSTIFAIISALFLKKSLdivgdRLSIKTFKTSGLLL-VLGAVLAIVIVGIYISIAGY 147
                                       443.....333333334444443333334355555555554333.44556677777777777655 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1         4     1e+04      48      60 ..      41      53 ..      36      61 .. 0.63
   2 ?   11.3   1.0   0.00011      0.29      23      64 ..     106     149 ..     100     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4
                           DUF2371 48 llvllvGiamavl 60
                                      +   + G+a avl
  gi|557694383|ref|YP_008797437.1| 41 VAATVAGVAAAVL 53
                                      4455667777665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                           DUF2371  23 rkadvvvvkGklkLlsvsglvlllGll..vllvGiamavlgywp 64 
                                       +  d+v  +  +k + +sgl+l+lG +  +++vGi +++ gy  
  gi|557694383|ref|YP_008797437.1| 106 KSLDIVGDRLSIKTFKTSGLLLVLGAVlaIVIVGIYISIAGYIV 149
                                       566777778889999**********65337889*********75 PP

>> 7tm_6  7tm Odorant receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.8   8.3e-05      0.21     106     157 ..      64     115 ..      23     120 .. 0.73
   2 ?   -1.1   1.3       0.3   7.6e+02     204     240 ..     120     153 ..     115     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.3e-05
                             7tm_6 106 dwnasegmyyisyafqilgvlfsvlqnillDvlfcslllflclhlqlLkgrl 157
                                        +  ++ +y++++ f ++++l ++  ++++ +++++  lfl+  l++  +rl
  gi|557694383|ref|YP_008797437.1|  64 SMLGNPDPYVYAFTFPWYYLLGTIAVAVTSTIFAIISALFLKKSLDIVGDRL 115
                                       22345667777*******************************9999998887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.3
                             7tm_6 204 fllsalvlclllfqllfisgenvqaitvvlYllaall 240
                                       f +s+l l l ++ +++i+g    +i +++Y++ a++
  gi|557694383|ref|YP_008797437.1| 120 FKTSGLLLVLGAVLAIVIVG---IYISIAGYIVLATA 153
                                       56788888888888888888...66777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1282  (0.0715043); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 1166.31
//
Query:       gi|557694384|ref|YP_008797438.1|  [L=205]
Description: probable transcription initiation factor IIB [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   45.1   2.1    8.1e-10   38.6   0.0    3.1  2  TFIIB     Transcription factor TFIIB repeat
     0.0033   17.1   0.1      0.094   12.5   0.0    2.2  2  Cyclin_N  Cyclin, N-terminal domain
  ------ inclusion threshold ------
      0.012   15.3   3.2       0.72    9.6   0.4    3.0  3  HD_4      HD 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 !   38.6   0.0   1.4e-13   8.1e-10       3      63 ..       9      69 ..       7      73 .. 0.93
   2 ?    2.8   1.4      0.02   1.2e+02       3      21 ..     102     120 ..     100     150 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 1.4e-13
                                      HHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHH CS
                             TFIIB  3 rfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissv 63
                                      + a+a  Lp+ V d A e++++  ++++ +Gr  ++++AA+lyiAc+++++   +k++ ++
  gi|557694384|ref|YP_008797438.1|  9 SYANAFSLPNHVVDLAREMLERLRRMGLSQGRNGETLVAAVLYIACKQSQHPVQLKDMLQR 69
                                      5688999********************************************9999988775 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.02
                                       HHHHHTT--HHHHHHHHHH CS
                             TFIIB   3 rfadaleLpekVadaAkel 21 
                                       ++a++l+L  +V++aA  l
  gi|557694384|ref|YP_008797438.1| 102 MVANKLGLEPYVEEAASIL 120
                                       7888899988988888644 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   1.6e-05     0.094      37      99 ..       6      67 ..       2      76 .. 0.89
   2 ?    2.1   0.0     0.025   1.5e+02      30      78 ..      92     139 ..      85     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHH CS
                          Cyclin_N 37 wlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlv 99
                                       l+  a+ f+l + ++ la ++l+R+ +    + ++ ++++a+ L++A+K  +  p++l+d+ 
  gi|557694384|ref|YP_008797438.1|  6 LLTSYANAFSLPNHVVDLAREMLERLRRMGLSQGRNGETLVAAVLYIACKQSQH-PVQLKDML 67
                                      67888999********************9999999999************9655.99999975 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHH CS
                          Cyclin_N  30 mRailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvga 78 
                                        R+++  +l  va+k+ l+p +   a+++l+R+ ++  v  + +  v+a
  gi|557694384|ref|YP_008797438.1|  92 QRQSAQIFLRMVANKLGLEPYVE-EAASILHRYGEHTHVAATAALYVAA 139
                                       67888888888888888887654.5677889988866665554444443 PP

>> HD_4  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.014        84      35      55 ..      39      59 ..      11      72 .. 0.65
   2 ?    2.1   0.0     0.025   1.5e+02     121     155 ..      74     109 ..      72     110 .. 0.88
   3 ?    9.6   0.4   0.00012      0.72      26      79 ..     115     168 ..     110     204 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.014
                              HD_4 35 gldaetviAalLhdvvedals 55
                                      g + et++Aa+L+ ++++ ++
  gi|557694384|ref|YP_008797438.1| 39 GRNGETLVAAVLYIACKQSQH 59
                                      36678*******999986433 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.025
                              HD_4 121 lqtlrslaaakeekrrdvaretldiyapl.AnrlGi 155
                                       l+tlr +++a     ++ +r++ +i+ ++ An+lG+
  gi|557694384|ref|YP_008797438.1|  74 LKTLRKVSEALGYSTVADQRQSAQIFLRMvANKLGL 109
                                       6789999888888888999********999****96 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00012
                              HD_4  26 evAailaelgldaetviAalLhdvvedalsleeirerfGeevarLvegvsklkr 79 
                                       e+A+il++ g    ++++a+L+ + +   sl+e++++ G +v+++ + ++ +++
  gi|557694384|ref|YP_008797438.1| 115 EAASILHRYGEHTHVAATAALYVAAAPSCSLTEVTKASGFSVVAICRRAKAIRE 168
                                       6799****98665555555555555544699************99888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1409.99
//
Query:       gi|557694385|ref|YP_008797439.1|  [L=141]
Description: hypothetical protein CSUB_C0956 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.9   4.5      0.011   15.7   4.5    1.2  1  YqhR           Conserved membrane protein YqhR
  ------ inclusion threshold ------
        1.3    8.7   4.6       0.57    9.8   2.5    1.5  2  RTX            N-terminal domain in RTX protein
        5.7    6.8   7.3       0.78    9.6   2.7    1.8  2  PMP22_Claudin  PMP-22/EMP/MP20/Claudin family


Domain annotation for each model (and alignments):
>> YqhR  Conserved membrane protein YqhR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   4.5   1.8e-06     0.011      24     123 ..       1     100 [.       1     128 [. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-06
                              YqhR  24 iGfvGGvlWsllaylaylfnfsevsp.nlilepwvlgdWkkkalGtvisivligvvsigvallyyvllkkikslwag 99 
                                       +Gf  G++ s+ + l+ ++ ++ v+  + +l +  +gd   + lG  i++++ +v ++  a++y + +   ++l a+
  gi|557694385|ref|YP_008797439.1|   1 MGFKAGIVLSTFGLLISFLVLAAVQEaARLLASPPTGDIL-SGLGAGIAVFIAAVSALISAIFYGAAYLTTRGLRAA 76 
                                       59**********************9735677777788876.579********************************* PP

                              YqhR 100 ilyGvvlwllvfyvlnPlfPdvka 123
                                       ++ G+++   ++ v+ Pl    + 
  gi|557694385|ref|YP_008797439.1|  77 VVGGLMILGGLLLVVSPLILAPQI 100
                                       *******99999999998754444 PP

>> RTX  N-terminal domain in RTX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.5   9.5e-05      0.57      97     124 ..      40      67 ..      20      71 .. 0.89
   2 ?   -1.7   0.0      0.31   1.8e+03       5      31 ..      69      95 ..      65      98 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.5e-05
                               RTX  97 asgVGaPvallvalitglisgileaskq 124
                                        sg Ga +a+ +a++ +lis+i+ ++ +
  gi|557694385|ref|YP_008797439.1|  40 LSGLGAGIAVFIAAVSALISAIFYGAAY 67 
                                       599*******************988765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.31
                               RTX  5 vaaglattgaaaaliaasvalAisPle 31
                                       ++gl +++  + +i +++ l +sPl 
  gi|557694385|ref|YP_008797439.1| 69 TTRGLRAAVVGGLMILGGLLLVVSPLI 95
                                      567775555556788999999999985 PP

>> PMP22_Claudin  PMP-22/EMP/MP20/Claudin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.7   0.00013      0.78      80     131 ..       6      69 ..       3      77 .. 0.87
   2 ?   -0.9   0.1      0.22   1.3e+03      94      94 ..      99      99 ..      71     134 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHHHHHHHHTGGGTTTSS............HHHHHHHHHHHHHHHHHHHHHHHHH CS
                     PMP22_Claudin  80 siilgilslivavlqlkclkkgerfkl............aGiiflvsgLcvlvgasiYtsriae 131
                                       +i+l+ ++l++ +l l  +++  r  +            aGi ++++++++l+ a+ Y+ ++ +
  gi|557694385|ref|YP_008797439.1|   6 GIVLSTFGLLISFLVLAAVQEAARLLAspptgdilsglgAGIAVFIAAVSALISAIFYGAAYLT 69 
                                       6788888888888888888888888888889***************************998866 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.22
                                      H CS
                     PMP22_Claudin 94 q 94
                                      q
  gi|557694385|ref|YP_008797439.1| 99 Q 99
                                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 967.57
//
Query:       gi|557694386|ref|YP_008797440.1|  [L=493]
Description: hypothetical protein CSUB_C0957 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   33.7   0.4    7.3e-08   32.8   0.4    1.5  1  DUF87            Helicase HerA, central domain
    2.5e-05   24.7   0.0       0.01   16.3   0.0    2.4  2  AAA              ATPase family associated with various cellul
     0.0024   16.9   0.0     0.0068   15.4   0.0    1.6  2  AAA_10           AAA-like domain
     0.0025   17.8   0.1        2.3    8.2   0.0    2.2  2  ResIII           Type III restriction enzyme, res subunit
     0.0027   16.7   0.0     0.0045   16.0   0.0    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
     0.0051   16.9   0.0        0.8    9.7   0.0    2.4  2  AAA_14           AAA domain
      0.006   16.0   0.1      0.019   14.3   0.1    1.8  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
  ------ inclusion threshold ------
      0.012   16.0   0.4       0.11   12.9   0.4    2.1  1  AAA_16           AAA ATPase domain
      0.021   14.4   0.1       0.36   10.4   0.0    2.2  2  AAA_25           AAA domain
      0.054   13.8   0.2        1.6    9.0   0.2    2.5  1  AAA_22           AAA domain
      0.056   12.5   0.0      0.099   11.7   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
      0.057   12.7   0.0       0.12   11.6   0.0    1.5  2  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.08   12.7   0.7       0.19   11.5   0.7    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.083   12.4   0.1       0.18   11.3   0.1    1.5  1  AAA_7            P-loop containing dynein motor region
      0.095   12.8   0.0       0.12   12.5   0.0    1.3  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.12   12.1   0.0       0.19   11.4   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.12   11.8   0.2       0.25   10.8   0.2    1.4  1  Pox_A32          Poxvirus A32 protein
       0.13   12.6   0.0        0.4   11.0   0.0    1.8  1  AAA_19           AAA domain
       0.16   11.5   1.4        1.1    8.7   0.7    2.0  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
       0.16   12.4   0.1       0.32   11.5   0.1    1.5  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 !   32.8   0.4   8.2e-11   7.3e-08       2      69 ..     134     206 ..     133     328 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 8.2e-11
                             DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleelle.kkgatililDpHGEYgkal.....e 69 
                                        iG++   ++v+++l l+ l+++  +++g  G+GKS++  +L+ ++l+  ++a+il++D++GE+ +       +
  gi|557694386|ref|YP_008797440.1| 134 SIGTI-YPTDVRLRLSLKILFRQGALVVGGVGTGKSTLLMSLMLKILKtVRNAHILLIDWDGEFRSKVleenaR 206
                                       68988.577899*****99*******************9999999999899*************8766555442 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 ?    6.0   0.0     0.016        15       2      41 ..     158     203 ..     157     224 .. 0.68
   2 !   16.3   0.0   1.1e-05      0.01      38     122 ..     332     417 ..     293     426 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.016
                                       EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCS.SSSTTH CS
                               AAA   2 llyGppGtGKTllakavakel.....gvefleisgsell.skyvge 41 
                                       l++G  GtGK++l  +++ ++     ++++l i+    + sk+++e
  gi|557694386|ref|YP_008797440.1| 158 LVVGGVGTGKSTLLMSLMLKIlktvrNAHILLIDWDGEFrSKVLEE 203
                                       899*******999999887754544456666666554442444444 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.1e-05
                                       STTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..SSTEEEEEEESS CS
                               AAA  38 yvgesekkirelfkeakekakp.silfiDEidalaksrsgseseeeervvnqLlteldgvkkk..eskvivigatnr 111
                                       ++  s + ++ +  +a++  +  + +fiDE++++a+++  +e   ++++ + ++++++   +   ++ v + +at+r
  gi|557694386|ref|YP_008797440.1| 332 IINRSREILETCYLQARADPTFgVAVFIDEVHNFAPQS-PHEGAASREAYDMMIPVMKLIATTgpRNGVPLFLATQR 407
                                       4444444444444445544444588************9.66777778888888888877666666677********* PP

                                       GGGSTHHHHST CS
                               AAA 112 pdkldpallrg 122
                                        +++d+ +   
  gi|557694386|ref|YP_008797440.1| 408 LSEVDKFIS-T 417
                                       *99998776.4 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.6e-06    0.0068      23     181 ..     156     327 ..     153     347 .. 0.60
   2 ?   -2.0   0.0       1.4   1.3e+03     278     351 ..     403     470 ..     393     476 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.6e-06
                            AAA_10  23 asliiGdlGnGKSvlakllvlyi..sllggkaliiDpkke.rekfketlpeiakkinvvtLdse.eenegvLdPlvl 95 
                                       ++l++G++G GKS l   l+l i  ++++ ++l+iD   e r k  e+     + ++++t +    ++e +L P + 
  gi|557694386|ref|YP_008797440.1| 156 GALVVGGVGTGKSTLLMSLMLKIlkTVRNAHILLIDWDGEfRSKVLEENARQHGGYQRITSSTRlARKEKSLSPASW 232
                                       5799*********9877666655236899***********8777554444446678888876444888889****** PP

                            AAA_10  96 lkeekeaeslaedilel...llgvkkkesekkaalsea...veavle.gkqrgllavieelrkedekvarei..... 160
                                        ++ +  + l  +  e    +  +kk e+++++ ++ +    e+ l   +  ++ + +ee+ +       +i     
  gi|557694386|ref|YP_008797440.1| 233 YNSFRTRAGLSGSAREArtlYAITKKLEEDGVNSIEWSqqgLEKILSiVEADDVRKRLEEIGR-------NIfkhas 302
                                       998877776654444332214444444555554333222223333332333444444444444.......4422222 PP

                            AAA_10 161 ....arhlesvvkkslaklvfsdgs 181
                                            + +e v+ + l ++ fsd s
  gi|557694386|ref|YP_008797440.1| 303 eengVDIVETVRTNALVHVDFSDAS 327
                                       2223566677777777777777776 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.4
                            AAA_10 278 lvtqsadDvlkeelknniglklaFretdkeeikkvLeflgldvedednkkelrelesGqCLmkDllgrvgkiki 351
                                       l+tq  + v+k    +     +aFr +d    ++    +g d          r l  G C++k ++ ++++ +i
  gi|557694386|ref|YP_008797440.1| 403 LATQRLSEVDKFISTQMGQNIFAFRVEDVDL-ERLRSIMGSDIA-----YSARLLPRGYCIYKGHALKIQRPVI 470
                                       6677777776654444444457777555444.555556666662.....3457788888888888888777666 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 !    7.5   0.0    0.0042       3.8      26      60 ..     156     190 ..     144     238 .. 0.84
   2 !    8.2   0.0    0.0025       2.3      52     155 ..     272     381 ..     249     395 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0042
                                       EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                            ResIII  26 rglikmaTGtGKTlvaaklierllkkgkeekflfl 60 
                                        +l++   GtGK+ ++++l+ ++lk  ++ ++l++
  gi|557694386|ref|YP_008797440.1| 156 GALVVGGVGTGKSTLLMSLMLKILKTVRNAHILLI 190
                                       56778889******************999999987 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0025
                                       ....-EEEEESSHHHHHHHHHHGGGGTGG........GEEEESSS-B--........-SEEEEEHHHHHHTH..... CS
                            ResIII  52 gkeekflflvprkslleqtleefkkflseayke....igkkvsgdkkka.kekdstnkkilvttiqsldadseeeee 123
                                       ++ ek+l +v   ++ ++++e  +++++ a +e    i + v+ +   +   +d++n++ ++    ++ +      +
  gi|557694386|ref|YP_008797440.1| 272 QGLEKILSIVEADDVRKRLEEIGRNIFKHASEEngvdIVETVRTNALVHvDFSDASNWDEIINRSREILETC----Y 344
                                       344499999999999999996666666666555333333333333333344445555555555555555555....6 PP

                                       ...HHHTTT-SEEEEETGGGTTS.T.....TTHHHHH CS
                            ResIII 124 eseellrdrfdviiiDEaHrlgakk.....swreile 155
                                        + ++++++   ++iDE+H+++ ++     + re+ +
  gi|557694386|ref|YP_008797440.1| 345 LQARADPTFGVAVFIDEVHNFAPQSphegaASREAYD 381
                                       77777777788*********99874333334444444 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 !   16.0   0.0     5e-06    0.0045      16      60 ..     155     201 ..     150     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5e-06
                     TrwB_AAD_bind  16 qhilivGttGsGKtqalekllraira..rgdraivlDltGafvsrfy 60 
                                       q +l+vG++G+GK++ l +l+ +i +  r+  ++ +D  G+f s+  
  gi|557694386|ref|YP_008797440.1| 155 QGALVVGGVGTGKSTLLMSLMLKILKtvRNAHILLIDWDGEFRSKVL 201
                                       6789****************9999764477889999*****988765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00089       0.8       6      46 ..     158     200 ..     154     225 .. 0.80
   2 ?    4.7   0.0     0.032        29      30      76 ..     315     365 ..     297     395 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00089
                            AAA_14   6 vitGaRrvGKTtllkqlikell..vkkesilyinldderdkkl 46 
                                       +++G   +GK+tll  l+ + l  v++ +il i++d e  +k 
  gi|557694386|ref|YP_008797440.1| 158 LVVGGVGTGKSTLLMSLMLKILktVRNAHILLIDWDGEFRSKV 200
                                       56677789**********99999************98766544 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.032
                            AAA_14  30 kesilyinldderd....kkladpekllelilek.lkeekktylflDEiqev 76 
                                        +  + +++ d ++      ++  e l++ +l+  + +     +f+DE+++ 
  gi|557694386|ref|YP_008797440.1| 315 TNALVHVDFSDASNwdeiI-NRSREILETCYLQArADPTFGVAVFIDEVHNF 365
                                       5667778888877753321.22223455666665444466778*******97 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   2.1e-05     0.019      43      68 ..     158     183 ..     143     198 .. 0.84
   2 ?   -2.8   0.0       3.6   3.2e+03     222     242 ..     389     409 ..     357     420 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.1e-05
                                       EEE--TTSSHHHHHHHHHHHHHTT-- CS
                      FtsK_SpoIIIE  43 lvaGatgsGKStalntLilSlattht 68 
                                       lv+G+ g+GKSt l++L+l ++ t  
  gi|557694386|ref|YP_008797440.1| 158 LVVGGVGTGKSTLLMSLMLKILKTVR 183
                                       9******************9987655 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.6
                                       HHHHHCGGGTEEEEEEES--- CS
                      FtsK_SpoIIIE 222 RlarkgraaglHlllatqrls 242
                                        +a  g ++g+ l latqrls
  gi|557694386|ref|YP_008797440.1| 389 LIATTGPRNGVPLFLATQRLS 409
                                       222224477777777777776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.4   0.00012      0.11      26     150 ..     156     368 ..     152     378 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            AAA_16  26 lvllsGesGvGKsslvrellralekd...............ggiflrgkcdqlesaipysalaqalareellrqlld 87 
                                         l++G  G+GKs+l+ +l+  + k+               +  +l+++++q+          q ++     + l++
  gi|557694386|ref|YP_008797440.1| 156 GALVVGGVGTGKSTLLMSLMLKILKTvrnahillidwdgefRSKVLEENARQH-------GGYQRITS---STRLAR 222
                                       579*************9999999999886666666665555444455555555.......22222211...112222 PP

                            AAA_16  88 eaesaeleawrekleeala.......................................................... 106
                                       +++s +++ w   ++++++                                                          
  gi|557694386|ref|YP_008797440.1| 223 KEKSLSPASWYNSFRTRAGlsgsareartlyaitkkleedgvnsiewsqqglekilsiveaddvrkrleeigrnifk 299
                                       22223444444444444444444444444444444444555555556556666666666666666666666666666 PP

                            AAA_16 107 .................avpelagaea.......srllellkrllallsrderp.lvlvlDdlqwadea 150
                                                        a  +++ ++a       +r +e l  +  +++ d    + +++D+++ + ++
  gi|557694386|ref|YP_008797440.1| 300 haseengvdivetvrtnALVHVDFSDAsnwdeiiNRSREILETCYLQARADPTFgVAVFIDEVHNFAPQ 368
                                       666666666555555443333333333556555566666666666444443333577777777776665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0004      0.36      36      59 ..     157     180 ..     150     232 .. 0.84
   2 ?    1.7   0.0      0.19   1.7e+02      83     139 ..     283     338 ..     280     384 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0004
                            AAA_25  36 allaGapgtGKttlaldlalavat 59 
                                       al++G  gtGK+tl+++l+l++++
  gi|557694386|ref|YP_008797440.1| 157 ALVVGGVGTGKSTLLMSLMLKILK 180
                                       6889999**************984 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.19
                            AAA_25  83 edelrrRlravgeal.rddarllvldlagv.eslpLfakdrggtlltadvdaleaaiee 139
                                       +d++r+Rl+++g+++ ++ +++  +d+++    + L++ d+ ++     +d+++++ +e
  gi|557694386|ref|YP_008797440.1| 283 ADDVRKRLEEIGRNIfKHASEENGVDIVETvRTNALVHVDFSDAS---NWDEIINRSRE 338
                                       678999999999999855555555555555566778777766654...44444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.2    0.0017       1.6       8      30 ..     157     179 ..     154     407 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0017
                            AAA_22   8 lvvtGesGtGKTtllrrlleqld 30 
                                        +v+G +GtGK+tll  l+ +  
  gi|557694386|ref|YP_008797440.1| 157 ALVVGGVGTGKSTLLMSLMLKIL 179
                                       5899*********9998887753 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 ?   11.7   0.0   0.00011     0.099     128     163 ..     153     190 ..     138     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                             T2SSE 128 erglilvsGgTgsGKttllyallkeinks..derivtv 163
                                        r+  lv Gg g+GK+tll +l+ +i k+  + +i+++
  gi|557694386|ref|YP_008797440.1| 153 FRQGALVVGGVGTGKSTLLMSLMLKILKTvrNAHILLI 190
                                       56667999***********7766555554367777776 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    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      67 ..     157     229 ..     154     252 .. 0.57
   2 ?   -3.3   0.0       4.6   4.1e+03      66     106 ..     328     371 ..     313     385 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00014
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke.........ekkkkkeafekl 67 
                                        lV G+ GtGK+ +l++l+ ++ ++ ++ +  ++   ++++ ++ e+ a++          ++  +ke+   +
  gi|557694386|ref|YP_008797440.1| 157 ALVVGGVGTGKSTLLMSLMLKILKTVRNAHILLIDWDGEFRSKVLEENARQHggyqritssTRLARKEKSLSP 229
                                       6899******************555544444444444444444444433333222111111134444444444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.6
                           DUF2075  66 klssfinnlsef..kkaeekkeepkedvvi.vDEAhrlltksdq 106
                                       + +++in+ +e    +  + +++p++ v++ +DE h    +s +
  gi|557694386|ref|YP_008797440.1| 328 NWDEIINRSREIleTCYLQARADPTFGVAVfIDEVHNFAPQSPH 371
                                       55666777776676566666777777776525888877665544 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 ?   11.5   0.7   0.00021      0.19      22      39 ..     155     171 ..     148     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                            AAA_29  22 kgatlltGpsGsGKSTll 39 
                                       +g  l++G  G+GKSTll
  gi|557694386|ref|YP_008797440.1| 155 QG-ALVVGGVGTGKSTLL 171
                                       55.9*************9 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   0.1    0.0002      0.18      25      58 ..     148     180 ..     133     192 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                             AAA_7  25 llelllknkkpvllvGptGtGKtviikd.llkkld 58 
                                        l+ l+  ++  l+vG +GtGK++++++ +lk l+
  gi|557694386|ref|YP_008797440.1| 148 SLKILF--RQGALVVGGVGTGKSTLLMSlMLKILK 180
                                       444444..55679***************5555444 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 ?   12.5   0.0   0.00013      0.12       9      55 ..     164     273 ..     157     435 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                                       TSSHHHHHHHHHHHHHH..TT--EEEEEEEESSCCCCHHTTEB-HHHH............................. CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................. RF
                              CbiA   9 GvGKTtlaanLaralar..rglrVllvDaDpqannlaileglendiep............................. 54 
                                       G+GK+tl+ +L+  + +  r+ ++ll+D D +  +      le++ ++                             
  gi|557694386|ref|YP_008797440.1| 164 GTGKSTLLMSLMLKILKtvRNAHILLIDWDGEFRSKV----LEENARQhggyqritsstrlarkekslspaswynsf 236
                                       9*********9977666589**********9955543....333333356666666677777777777777777777 PP

                                       ....................................C CS
                                       ....................................x RF
                              CbiA  55 ....................................d 55 
                                                                           +
  gi|557694386|ref|YP_008797440.1| 237 rtraglsgsareartlyaitkkleedgvnsiewsqqG 273
                                       7666666666666666666666666666666665553 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 ?   11.4   0.0   0.00022      0.19       3      44 ..     159     202 ..     157     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                   Viral_helicase1   3 vhGvpGcGKStlirkllrtsliltvnrptaelltegk....pklpn 44 
                                       v G  G GKStl+ +l+ +  il+++r++ +ll ++     +k+  
  gi|557694386|ref|YP_008797440.1| 159 VVGGVGTGKSTLLMSLMLK--ILKTVRNAHILLIDWDgefrSKVLE 202
                                       55666**************..***************9766544444 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00027      0.25      18      47 ..     159     190 ..     148     197 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00027
                           Pox_A32  18 lvGgsGsGktvyLlsLlrtlvkky..khifLl 47 
                                       +vGg G Gk + L+sL+ ++ k     hi+L+
  gi|557694386|ref|YP_008797440.1| 159 VVGGVGTGKSTLLMSLMLKILKTVrnAHILLI 190
                                       79******************998833477776 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   0.00044       0.4      13      78 ..     157     321 ..     150     369 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00044
                            AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelre.rlaalgae.................... 68 
                                        lv++G GtGK+++l+  +  ++++ +   ++ill+   g   +++ e + ++ g+                     
  gi|557694386|ref|YP_008797440.1| 157 ALVVGGVGTGKSTLLMSLMLKILKTVRN--AHILLIDWDGEFRSKVLEeNARQHGGYqritsstrlarkekslspas 231
                                       699************9987666665533..67887777766554433313322222244333333333334444444 PP

                            AAA_19  69 .................atTiHrlal................................................... 77 
                                                        a                                                           
  gi|557694386|ref|YP_008797440.1| 232 wynsfrtraglsgsareA-------Rtlyaitkkleedgvnsiewsqqglekilsiveaddvrkrleeigrnifkha 301
                                       444433333333333333.......0333333466666666666666666666666555555555555555555555 PP

                            AAA_19  78 ...................l 78 
                                                          +
  gi|557694386|ref|YP_008797440.1| 302 seengvdivetvrtnalvhV 321
                                       55555555555555555552 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.7    0.0012       1.1      13      49 ..     154     188 ..     148     232 .. 0.85
   2 ?    1.9   0.0      0.15   1.3e+02     169     234 ..     239     325 ..     184     361 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                                       SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEE CS
                     UvrD-helicase  13 ggpilveAsAGsGKTfvlaerilrlikeeeiepdril 49 
                                       ++  lv+ + G+GK++ l++++l+ +k+    + +il
  gi|557694386|ref|YP_008797440.1| 154 RQGALVVGGVGTGKSTLLMSLMLKILKTV--RNAHIL 188
                                       6788*******************999876..555555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.15
                                       HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS.......TSCSHHHHHHHHHHHHHHHHHHHHTC......... CS
                     UvrD-helicase 169 keelslskskaeelrelvskakekqlspkelkkaf.......ekasdlqkkiaeflkeyqeqkkeena......... 229
                                          ls+s++ a  l ++++k++e+ +++ e  ++         +a+d +k ++e+ ++++++ +een          
  gi|557694386|ref|YP_008797440.1| 239 RAGLSGSAREARTLYAITKKLEEDGVNSIEWSQQGlekilsiVEADDVRKRLEEIGRNIFKHASEENGvdivetvrt 315
                                       33566677777777777788888888877777766778888889999999999999999999999999777777777 PP

                                       .....EEHHH CS
                     UvrD-helicase 230 .....lDfsd 234
                                            +Dfsd
  gi|557694386|ref|YP_008797440.1| 316 nalvhVDFSD 325
                                       7777744444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00036      0.32       9      42 ..     152     185 ..     146     298 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00036
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGei 42 
                                          +   +vG  G+GKStLl+ l+ +  +t  + 
  gi|557694386|ref|YP_008797440.1| 152 LFRQGALVVGGVGTGKSTLLMSLMLKILKTVRNA 185
                                       555667799***********98876655543333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 3048.98
//
Query:       gi|557694387|ref|YP_008797441.1|  [L=315]
Description: hypothetical protein CSUB_C0958 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-21   76.2   0.0    4.8e-21   75.6   0.0    1.2  1  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 !   75.6   0.0   2.7e-25   4.8e-21       2     242 .]      58     280 ..      58     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 2.7e-25
                                       EEEEEEEEEEEEEETTCEEEEEEEEEEECCE..EECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGG CS
                              NurA   2 rvaAvDGSngvvrlsggilyilsayavvggg..kerleealslasvdsispsdelerrirllmetlElklgalllee 76 
                                       rvaAvDG++g  +++++ + ++ a+av++ g  ++r+    +l +++  + + e+ +r++  +et+ l+l+++    
  gi|557694387|ref|YP_008797441.1|  58 RVAAVDGGSGILSFADIDIGFATALAVIQDGaeYRRQLLQPKLLVQEYGEADGEFGDRVDVERETMLLMLAQKVVRD 134
                                       69**************************877224566666677777666666666********************** PP

                                       CCSCEEEEECSHHCCCHHHHHHHHHHHHHHHHHHHHHHTT-....TTCEEEEESS-SCTCCHCCC......S--HHH CS
                              NurA  77 kgedllllDGsligslvefdelheeleyeeylyslsrllea....glnlvgvaKsfrskellnllletlligesisD 149
                                        + +ll++DG+li+ +            +ey+y+l++l+e     g+  +g +K+ +s++l++l          ++D
  gi|557694387|ref|YP_008797441.1| 135 NDLELLIVDGPLIPRPK---------YVGEYVYQLRTLIELcrerGILAAGFVKRPQSRYLSELG---------FTD 193
                                       *****************.........666666666666666666*******************88.........*** PP

                                       HCCHHCCHCH---STTS-HHHHTT-HCCHHHHHH-EEEEEEES..STTTTEEEEEHHHHHHCCHHHHHHHHHH..TT CS
                              NurA 150 iallgallrkpgytspllkilrekpllrealidkeiyfaYvrl..egggsilrleipaevstakdedvlsllasqrl 224
                                       +all+a+l+k    +  ++     p+     ++ +++++Y++l  e++  ++r+++p +v++ ++ ++l+  a    
  gi|557694387|ref|YP_008797441.1| 194 RALLSAVLEK---MEAAPW-----PPTAPPTEKTDVRYTYIKLlnEPEAGVFRIDFPPFVDDRQALETLEYFAYSSD 262
                                       ********66...445565.....999********************************999999999999993333 PP

                                       B-SSSBCCHHHHHHHHCC CS
                              NurA 225 sisGYprpLalAhelaki 242
                                          G p +L +A+e++k+
  gi|557694387|ref|YP_008797441.1| 263 PVHGPPAILMKADEEVKV 280
                                       34588888*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2211.09
//
Query:       gi|557694388|ref|YP_008797442.1|  [L=508]
Description: hypothetical protein CSUB_C0959 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-22   79.0   0.4    3.4e-22   78.3   0.4    1.4  1  DnaJ            DnaJ domain
    5.5e-18   65.0   2.0    1.7e-17   63.4   2.0    1.9  1  DUF1294         Protein of unknown function (DUF1294)
  ------ inclusion threshold ------
      0.067   13.6   7.1        4.6    7.7   0.1    3.5  3  Romo1           Reactive mitochondrial oxygen species modulat
       0.14   12.2   2.3        0.4   10.8   2.3    1.7  1  YqzM            YqzM-like protein
       0.89    7.9   5.4      0.063   11.7   0.3    1.6  2  SID-1_RNA_chan  dsRNA-gated channel SID-1
        1.3    8.7   8.7         12    5.5   4.6    2.8  3  CPP1-like       Protein CHAPERONE-LIKE PROTEIN OF POR1-like


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.4   1.1e-25   3.4e-22       1      63 []       9      70 ..       9      70 .. 0.99

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 1.1e-25
                                      HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                              DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                      dyY+iLgv ++as++eIk+aYr+l++kyHPD +  +p aee  k +neAy vL dp kR+ YD
  gi|557694388|ref|YP_008797442.1|  9 DYYSILGVGRHASQEEIKRAYRNLVKKYHPDIS-PHPHAEEIMKIVNEAYRVLGDPAKRRLYD 70
                                      8******************************99.999*************************9 PP

>> DUF1294  Protein of unknown function (DUF1294)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   2.0   5.7e-21   1.7e-17       1      55 []     252     306 ..     252     306 .. 0.99

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 5.7e-21
                           DUF1294   1 nlitfllygiDKrkAkkkkwRipEktLlllallgGslGallgmrlfrHKtkkksF 55 
                                       n+++fl++++DK++A+ ++wRi+E +L  +allg +lG+++g   frHK++k+sF
  gi|557694388|ref|YP_008797442.1| 252 NIAAFLAMAWDKKQAQARQWRIRETVLKRFALLGAGLGIMMGAIAFRHKIRKASF 306
                                       99****************************************************9 PP

>> Romo1  Reactive mitochondrial oxygen species modulator 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.14   4.3e+02      41      66 .]     116     141 ..     110     141 .. 0.87
   2 ?    6.4   0.3     0.004        12      15      43 ..     283     310 ..     281     316 .. 0.81
   3 ?    7.7   0.1    0.0015       4.6       5      50 ..     332     377 ..     329     390 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.14
                             Romo1  41 rtlgksmlgsaatFGfFmsiGsviRc 66 
                                        ++ +++ +s  +F + ++i+ +iR+
  gi|557694388|ref|YP_008797442.1| 116 ANMYTYVTTSFTFFVILFAIAGLIRS 141
                                       5677899999999************7 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.004
                             Romo1  15 aVGlaiGllfGtfsalryglrgrgllrtl 43 
                                       ++G+ +G+++G + a+r+++r+ ++++++
  gi|557694388|ref|YP_008797442.1| 283 LLGAGLGIMMGAI-AFRHKIRKASFMSYI 310
                                       5688888888766.79*********9987 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0015
                             Romo1   5 kikmGalmGaaVGlaiGllfGtfsalryglrgrgllrtlgksmlgs 50 
                                       k  + +++G ++Gla+G+++G   +       + + + + ++ l+ 
  gi|557694388|ref|YP_008797442.1| 332 KAAAAVAVGLLIGLALGVFLGHPPVTFTTTKHTTITEAVTTTSLKT 377
                                       5556677777777777777776544444444445555555555554 PP

>> YqzM  YqzM-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.3   0.00013       0.4      23      38 ..     124     139 ..     119     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                              YqzM  23 vsFgFFavlFiIAtvi 38 
                                        sF FF++lF+IA +i
  gi|557694388|ref|YP_008797442.1| 124 TSFTFFVILFAIAGLI 139
                                       69***********887 PP

>> SID-1_RNA_chan  dsRNA-gated channel SID-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.9       1.1   3.2e+03     381     421 ..     120     167 ..     113     177 .. 0.52
   2 ?   11.7   0.3   2.1e-05     0.063     409     507 ..     225     324 ..     197     351 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 1.1
                    SID-1_RNA_chan 381 aysafallavvillgvigvle..gknkfw.....ilfsiihllatlll 421
                                        y +  +  +vil+++ g++    ++++w      + ++ +++a++ll
  gi|557694388|ref|YP_008797442.1| 120 TYVTTSFTFFVILFAIAGLIRspASDAVWwdgfiGTYVAPYITAIALL 167
                                       566666667778888888877443334444654322233333344444 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.1e-05
                    SID-1_RNA_chan 409 lfsiihllatlllslqiyymgrwkldvgilrrilevlkkeviqq...csrplyksrmvllvlgnlvnvslavlglvl 482
                                        f +ih l++ +ls +i   ++   + +i+  +++ + k+ +q     +r++  +r++ll  g  + ++++++   +
  gi|557694388|ref|YP_008797442.1| 225 PFRFIHDLLVTSLSNNIEVAAVALSALNIAAFLAMAWDKKQAQArqwRIRETVLKRFALLGAGLGIMMGAIAFRHKI 301
                                       58899999999999999887766667777777777776666665558889999************************ PP

                    SID-1_RNA_chan 483 kpkdfasylLaifivnlllYlvfYi 507
                                       ++ +f sy+  i+ + + lY+++ i
  gi|557694388|ref|YP_008797442.1| 302 RKASFMSYI--ILSLAINLYFTYMI 324
                                       *********..66666667877765 PP

>> CPP1-like  Protein CHAPERONE-LIKE PROTEIN OF POR1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.011        32       2      22 ..      19      39 ..      18      55 .. 0.91
   2 ?   -2.4   0.0         1   3.1e+03     148     158 ..     125     135 ..      69     174 .. 0.61
   3 ?    5.5   4.6     0.004        12     101     187 ..     287     372 ..     240     389 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.011
                         CPP1-like  2 dAsfeeiqeArnrlleeyagd 22
                                       As eei++A  +l+++y  d
  gi|557694388|ref|YP_008797442.1| 19 HASQEEIKRAYRNLVKKYHPD 39
                                      69***************9877 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                         CPP1-like 148 tlvgLvvGlll 158
                                       ++ ++v+ +++
  gi|557694388|ref|YP_008797442.1| 125 SFTFFVILFAI 135
                                       33333333333 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.004
                         CPP1-like 101 avflvlavltlvapaes.vpalllalglgasiyf..lnrKekklgravlltlvgLvvGlllGsllasllqvdvalsg 174
                                       ++ ++++++++  +  + +    ++l+l++++yf  +    + l +a++   vgL++Gl+lG +l       v+++ 
  gi|557694388|ref|YP_008797442.1| 287 GLGIMMGAIAFRHKIRKaSFMSYIILSLAINLYFtyMIFGGGLLAKAAAAVAVGLLIGLALGVFLGHPP---VTFTT 360
                                       344444444444433336333345566666666611556788999*****************9998743...44553 PP

                         CPP1-like 175 lsseellvslvtl 187
                                       + +  +++ +vt 
  gi|557694388|ref|YP_008797442.1| 361 T-KHTTITEAVTT 372
                                       2.33334444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1229  (0.0685482); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 3642.76
//
Query:       gi|557694389|ref|YP_008797443.1|  [L=127]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   33.9   0.0    4.3e-08   32.8   0.0    1.7  2  DUF4325   STAS-like domain of unknown function (DUF4325)
  ------ inclusion threshold ------
      0.021   15.2   0.0      0.058   13.7   0.0    1.7  1  STAS_2    STAS domain


Domain annotation for each model (and alignments):
>> 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 !   32.8   0.0   4.8e-12   4.3e-08       2      62 ..      19      70 ..      18      80 .. 0.85
   2 ?   -2.5   0.0      0.49   4.4e+03       8      24 ..      88     101 ..      87     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4.8e-12
                           DUF4325  2 GerfrdkilkpllkegekvelDFdgvesigssFldeaFgglirefgeeeiskklkiknlne 62
                                      +  ++d i+k+     +kv++DF+gv+si+ +F+++ +  l ++ ++    kk++ +n+ e
  gi|557694389|ref|YP_008797443.1| 19 ANTLFDMIEKAQ---DKKVVIDFEGVRSITGAFAHQYI--LRKRASR----KKVIEQNMPE 70
                                      6679******66...*********************99..7777777....6666666655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.49
                           DUF4325   8 kilkpllkegekvelDF 24 
                                       ++l+p+   ++ + l+ 
  gi|557694389|ref|YP_008797443.1|  88 HVLPPA---NKPIQLSI 101
                                       678888...89888875 PP

>> STAS_2  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.5e-06     0.058       7      76 ..      14      78 ..      12      80 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-06
                            STAS_2  7 ldldtaaelreqllealaagaevvvDlsgvervDsaal.alLlalartarargrrlvlrglppalrrlldl 76
                                      l +dta +l +  ++a ++  +vv+D+ gv+++  a++ + +l+ ++    +++++  +++p+a+rr+l +
  gi|557694389|ref|YP_008797443.1| 14 LLRDTANTLFDMIEKA-QDK-KVVIDFEGVRSITGAFAhQYILRKRA----SRKKVIEQNMPEAVRRMLKI 78
                                      5689999999999998.555.***********988854133333333....45666668999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 976.72
//
Query:       gi|557694390|ref|YP_008797444.1|  [L=101]
Description: hypothetical protein CSUB_C0961 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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: 00:00:00.39
# Mc/sec: 776.23
//
Query:       gi|557694391|ref|YP_008797445.1|  [L=157]
Description: hypothetical protein CSUB_C0962 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.6   0.5      0.029   14.2   0.5    1.1  1  DUF2157   Predicted membrane protein (DUF2157)


Domain annotation for each model (and alignments):
>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   1.6e-06     0.029      32      93 ..      78     142 ..      64     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-06
                           DUF2157  32 rsf.leallvlGalllgl.GlilfvAanWqglsrlvkfllllvllllslllg.avlwrdrrvppr 93 
                                        +  + + +v ++l+l l +++l  Aa+ ++l+ +++++  +++ ll++++g + ++  ++++++
  gi|557694391|ref|YP_008797445.1|  78 GRVaRAIASVAAVLALSLaAIVLQQAAFIEELPVEARLAATAGPPLLAIAAGvYGAYTATQEQRV 142
                                       33325555666666665515556678999********************9995555544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1229.68
//
Query:       gi|557694392|ref|YP_008797446.1|  [L=158]
Description: hypothetical protein CSUB_C0963 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00047   19.8   1.2     0.0038   16.9   1.2    2.1  1  zinc_ribbon_2   zinc-ribbon domain
    0.00056   19.5   1.1     0.0023   17.6   1.2    1.8  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
      0.003   17.0   1.4      0.006   16.1   1.4    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0035   17.2   0.0      0.007   16.3   0.0    1.5  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
     0.0064   16.5   0.4      0.011   15.8   0.4    1.4  1  DZR             Double zinc ribbon
     0.0094   15.3   5.0      0.035   13.5   5.0    1.8  1  zf-ribbon_3     zinc-ribbon domain
  ------ inclusion threshold ------
      0.013   15.4   0.9      0.027   14.4   0.9    1.5  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.025   14.3   0.4        0.3   10.8   0.7    2.2  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.032   14.5   0.2      0.051   13.8   0.2    1.3  1  IBR             IBR domain, a half RING-finger domain
      0.035   14.0   1.0       0.59   10.1   0.1    2.4  2  Nudix_N_2       Nudix N-terminal
      0.061   13.3   0.5       0.11   12.5   0.5    1.4  1  Prok-RING_1     Prokaryotic RING finger family 1
       0.17   12.0   3.2       0.22   11.6   1.2    2.1  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


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 !   16.9   1.2   2.5e-06    0.0038       2      22 ..       8      32 ..       8      33 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-06
                     zinc_ribbon_2  2 CpnCGaelq.dnakF...CpyCGtp 22
                                      CpnCGa+++   ++    C yCGt 
  gi|557694392|ref|YP_008797446.1|  8 CPNCGAPVElSPDTVvliCGYCGTA 32
                                      *******9655555558******96 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 !   17.6   1.2   1.5e-06    0.0023       5      30 ..       7      32 ..       6      33 .. 0.93
   2 !    5.6   0.2    0.0081        12       6      14 ..      26      34 ..      23      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.5e-06
                     zf-NADH-PPase  5 FCgrCGaptepaeggwarvCpaCgle 30
                                      +C+ CGap+e++++   + C  Cg+ 
  gi|557694392|ref|YP_008797446.1|  7 WCPNCGAPVELSPDTVVLICGYCGTA 32
                                      7**********************985 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0081
                     zf-NADH-PPase  6 CgrCGapte 14
                                      Cg CG+++ 
  gi|557694392|ref|YP_008797446.1| 26 CGYCGTAVS 34
                                      ******975 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.4     4e-06     0.006       3      27 ..       8      31 ..       7      34 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4e-06
                                      ETTTTCEECHEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGl 27
                                      CPnCg + +++ p++  l+C+ CG+
  gi|557694392|ref|YP_008797446.1|  8 CPNCGAP-VELSPDTVVLICGYCGT 31
                                      *****97.8**************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 !   16.3   0.0   4.7e-06     0.007       7      34 ..       8      33 ..       7      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.7e-06
                    Zn_ribbon_SprT  7 CtgCgreythhlsirrhnYrCrrCkgtL 34
                                      C++Cg   +++ls ++   +C++C+   
  gi|557694392|ref|YP_008797446.1|  8 CPNCG--APVELSPDTVVLICGYCGTAV 33
                                      *****..7****************9765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   7.1e-06     0.011      15      42 ..       8      37 ..       1      49 [. 0.64

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.1e-06
                               DZR 15 CseCgtklkavaa..edrCpsCgekvdpea 42
                                      C++Cg++++  ++     C  Cg++v+++ 
  gi|557694392|ref|YP_008797446.1|  8 CPNCGAPVELSPDtvVLICGYCGTAVSLTG 37
                                      666666655444455666666666666654 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   5.0   2.3e-05     0.035       5      24 ..       8      31 ..       7      32 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                       zf-ribbon_3  5 CPnCGa.p.lssd..dnvCpyCGt 24
                                      CPnCGa + ls+d  + +C yCGt
  gi|557694392|ref|YP_008797446.1|  8 CPNCGApVeLSPDtvVLICGYCGT 31
                                      ******889999944557*****7 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.9   1.8e-05     0.027       4      26 ..       7      30 ..       3      31 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                    PhnA_Zn_Ribbon  4 kCplCaSeytY.edgallvCpeCa 26
                                       Cp+C++ +++  d+ +l+C  C+
  gi|557694392|ref|YP_008797446.1|  7 WCPNCGAPVELsPDTVVLICGYCG 30
                                      6*******************9997 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 ?   10.8   0.7    0.0002       0.3       3      25 ..       8      31 ..       7      33 .. 0.87
   2 ?    6.1   0.1    0.0059       8.8       2      13 ..      25      36 ..      24      40 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                                      -SSS--B----SSS--.--SSS-- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgdpi.RCkeCGh 25
                                      C +Cga+v+l++  ++  C +CG 
  gi|557694392|ref|YP_008797446.1|  8 CPNCGAPVELSPDTVVlICGYCGT 31
                                      99********99987648****95 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0059
                                      B-SSS--B---- CS
                    DNA_RNApol_7kD  2 iCgeCgaevslk 13
                                      iCg Cg+ vsl 
  gi|557694392|ref|YP_008797446.1| 25 ICGYCGTAVSLT 36
                                      8********986 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 ?   13.8   0.2   3.4e-05     0.051      19      47 ..       6      32 ..       1      36 [. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.4e-05
                               IBR 19 kwCprpdCeaiieksegcksvtCskCgfe 47
                                       wCp  +C+a++e s ++  + C  Cg++
  gi|557694392|ref|YP_008797446.1|  6 SWCP--NCGAPVELSPDTVVLICGYCGTA 32
                                      7***..***********99999****976 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0004      0.59       2      12 ..       7      17 ..       6      21 .. 0.89
   2 ?    2.1   0.1      0.13   1.9e+02       3      11 ..      26      34 ..      24      36 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0004
                                      B-TTT--B-EE CS
                         Nudix_N_2  2 FCsqCGtpvel 12
                                       C++CG+pvel
  gi|557694392|ref|YP_008797446.1|  7 WCPNCGAPVEL 17
                                      5********97 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.13
                                      -TTT--B-E CS
                         Nudix_N_2  3 CsqCGtpve 11
                                      C  CGt+v+
  gi|557694392|ref|YP_008797446.1| 26 CGYCGTAVS 34
                                      666777776 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 ?   12.5   0.5   7.3e-05      0.11       3      29 ..       4      32 ..       2      34 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.3e-05
                       Prok-RING_1  3 tgkkCpvCgkelkeedDiVv..CpeCgtp 29
                                      +g+ Cp Cg +++   D Vv  C  Cgt 
  gi|557694392|ref|YP_008797446.1|  4 EGSWCPNCGAPVELSPDTVVliCGYCGTA 32
                                      6788*****9988887766444*****95 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 ?   11.6   1.2   0.00015      0.22       2      20 ..       8      26 ..       8      27 .. 0.94
   2 ?   -1.2   0.0       1.4   2.1e+03       5       9 ..      29      33 ..      28      36 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                    DNA_ligase_ZBD  2 CPvCGsavvReegeaiyRC 20
                                      CP CG++v+  ++ +++ C
  gi|557694392|ref|YP_008797446.1|  8 CPNCGAPVELSPDTVVLIC 26
                                      *********9999999988 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.4
                    DNA_ligase_ZBD  5 CGsav 9 
                                      CG+av
  gi|557694392|ref|YP_008797446.1| 29 CGTAV 33
                                      ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1150.47
//
Query:       gi|557694393|ref|YP_008797447.1|  [L=128]
Description: hypothetical protein CSUB_C0964 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1022.42
//
Query:       gi|557694394|ref|YP_008797448.1|  [L=265]
Description: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   49.8   1.8    7.8e-13   49.5   1.8    1.0  1  Abhydrolase_6  Alpha/beta hydrolase family
    4.9e-05   23.1   0.0    8.2e-05   22.4   0.0    1.4  1  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.081   12.4   0.0       0.12   11.9   0.0    1.2  1  ANAPC4         Anaphase-promoting complex, cyclosome, subunit


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 !   49.5   1.8   1.3e-16   7.8e-13       1     218 [.      26     257 ..      26     259 .. 0.64

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 1.3e-16
                                       EEEE--GC.....G....C.HHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHH.HHHHCCTT...TTSEEEE CS
                     Abhydrolase_6   1 vlllHGagssassW....l.vapLaallaagvhvlapDlpGhGrsdpppldledladl.aalldelaa.gggpvvlv 70 
                                       +l+++G       W      ++ L+++ +++ ++l++D+pGhG+sd+p+ d+ +  +l aa++  +   g++++v v
  gi|557694394|ref|YP_008797448.1|  26 LLFMPG-------WcdnrTqYRDLVPFCSSRSRCLVIDWPGHGESDTPAADFGE-KELvAAAISVIERsGARRIVTV 94 
                                       79****.......877652578*********666********************.7775554444444678999999 PP

                                       EETCHHHHHHHHHHCC.........EE.EEES-..----TTTS----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHH CS
                     Abhydrolase_6  71 GHSlGGalalaaapla.......lvvg.vlldppptalpagllaaalelllallallrllawlsreplprlfladed 139
                                          + G++a ++++++       ++   ++l+pp ++l a+ +   +e++++++ +l +  wls+  ++ ++l  + 
  gi|557694394|ref|YP_008797448.1|  95 STAHAGWVAIELRRQLleknqklVLLDwLVLEPPQPFLEALRGLQSREHWEQVRESLFS-MWLSGVVDD-RILQHVR 169
                                       999********999999988864333378888855666666688888888888887776.888764222.4444222 PP

                                       ..C....CCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEEC....TT-C.HHHHCHHCCCH..STTEEETCE.. CS
                     Abhydrolase_6 140 ..a....daawrarlarlaallaglgllpaaawadlpvpllvlg....geDp.lvprllerlla..qagarlpvvlp 203
                                         +     + w+++ ++ +a+   +g  p+ a+  l +p +vl+     +D+  ++  ++   a   + + +   l 
  gi|557694394|ref|YP_008797448.1| 170 reMgshgFEMWARAGREISASYERFG-SPLKALSELEPPPHVLHlfslPKDEaYLR--AQNEFAknHQWFSV-YRLD 242
                                       22122233444444444444444333.23334444444445543334755552666..55444444334444.6666 PP

                                       .SSS-HHHHSHHHHH CS
                     Abhydrolase_6 204 gaGHlphleepdeva 218
                                        + H+p le+p+ v 
  gi|557694394|ref|YP_008797448.1| 243 ANTHFPALEDPKTVS 257
                                       888*******98775 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.4e-08   8.2e-05       1      54 [.      24      70 ..      24     118 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.4e-08
                                      SEEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHH CS
                     Abhydrolase_1  1 pvlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddy 54
                                      pvl++ +G++++   ++   l+p ++  + +++++D++G+g+S+++ a     +
  gi|557694394|ref|YP_008797448.1| 24 PVLLFMPGWCDNRTQYRD--LVPFCSS-RSRCLVIDWPGHGESDTPAAD----F 70
                                      79****************..******9.******************964....4 PP

>> ANAPC4  Anaphase-promoting complex, cyclosome, subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.12      48     111 ..     124     185 ..     110     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                            ANAPC4  48 alelldrklrnledelkeegeeeksisaeLldllltGlispalkdfLvnqlgerglkkwekave 111
                                       +le+++ +l++l  ++++e+   +++++ L+++ l+G++ + + ++   ++g +g++ w +a+ 
  gi|557694394|ref|YP_008797448.1| 124 VLEPPQPFLEALRGLQSREH--WEQVRESLFSMWLSGVVDDRILQHVRREMGSHGFEMWARAGR 185
                                       678999*********99999..4699999******************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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: 00:00:00.40
# Mc/sec: 1997.66
//
Query:       gi|557694395|ref|YP_008797449.1|  [L=91]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
       0.39   10.7   8.0       0.28   11.2   0.9    3.3  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   0.9   1.5e-05      0.28       2      36 ..       4      35 ..       3      38 .. 0.77
   2 ?    1.6   0.5     0.016   2.9e+02      28      35 ..      51      58 ..      49      59 .. 0.87
   3 ?   -0.3   0.3     0.067   1.2e+03       9      17 ..      57      65 ..      54      70 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.5e-05
                                      EEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrgrSrSelIReAlrey 36
                                      +s+r+d+ l++r+d+l   r+ + Sel+R++++  
  gi|557694395|ref|YP_008797449.1|  4 ISFRVDKRLKARIDRL---RHINWSELLRRYVETI 35
                                      7888888888888887...4699999999988765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.016
                                      HHHHHHHH CS
                             RHH_1 28 lIReAlre 35
                                      +IR+A++e
  gi|557694395|ref|YP_008797449.1| 51 AIRRAIEE 58
                                      79****97 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.067
                                      HHHHHHHHH CS
                             RHH_1  9 ellerLdel 17
                                      e+++rL +l
  gi|557694395|ref|YP_008797449.1| 57 EEMDRLAKL 65
                                      344455444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 666.29
//
Query:       gi|557694396|ref|YP_008797450.1|  [L=140]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   41.5   0.5      2e-10   41.2   0.5    1.0  1  PIN       PIN domain
     0.0022   18.2   0.0     0.0027   17.9   0.0    1.2  1  PIN_2     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 !   41.2   0.5   2.3e-14     2e-10       2     116 ..       8     125 ..       7     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 2.3e-14
                                       EE-HHHHHHHHTTSHHHHHHHHHHHTS....SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHHHHTSEEEEBC CS
                               PIN   2 vlDTsvliallrgeekaeaarklleel....eelvtsalvlaEllyvlarrkskrekaaelvelllllsalkilpid 74 
                                       vlD+sv +++++ e  +++a+ +  ++     +l+ ++l  +E+++ l+++++   ++ +  +  l+  ++   ++ 
  gi|557694396|ref|YP_008797450.1|   8 VLDASVAVKWFNVESLRKEALTIRSKYangeIDLIAPDLLHYEVANALRYNPRFGIEDVKTALKALQDMSITTYEFK 84 
                                       89*********55555555555555555559*******************5555555555555555578888888** PP

                                       HHHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHH CS
                               PIN  75 aeiaeeaaeialkygllpnDaliaAtAkehgikliatfDedf 116
                                        e++e+a e+a k g+ ++Da+ +++A+ ++++ ++t+D++ 
  gi|557694396|ref|YP_008797450.1|  85 GELLERAVELAYKFGIPLYDAVYVSLALLQNAT-LYTADKEV 125
                                       ********************************5.56***984 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     3e-07    0.0027      17     116 ..      29     126 ..       8     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3e-07
                             PIN_2  17 kkrlilvekaleliapeeaveeiekhkealvkksklseeeleellelletkikiveeslyeskikeAkeriarvDp. 92 
                                         r   ++ +++liap+ ++ e+++       + ++  e ++++l++l + + i + + + + ++ A e++ ++   
  gi|557694396|ref|YP_008797450.1|  29 TIRSKYANGEIDLIAPDLLHYEVANALR---YNPRFGIEDVKTALKAL-QDMSITTYEFKGELLERAVELAYKFGIp 101
                                       4455667889999999999999987666...67889999999998876.5678888888889999999999988653 PP

                             PIN_2  93 .dDtpfvAlaLlleapiWTeDkdli 116
                                         D+ +v laLl +a + T Dk+ +
  gi|557694396|ref|YP_008797450.1| 102 lYDAVYVSLALLQNATLYTADKEVV 126
                                       37********************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1092.20
//
Query:       gi|557694397|ref|YP_008797451.1|  [L=128]
Description: hypothetical protein CSUB_C0968 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-09   37.7   0.0    1.5e-09   37.6   0.0    1.1  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
  ------ inclusion threshold ------
      0.019   15.0   0.0      0.021   14.8   0.0    1.0  1  S_layer_C    S-layer like family, C-terminal region


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 !   37.6   0.0   1.7e-13   1.5e-09       1      88 [.       5      91 ..       5     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 1.7e-13
                                      S-BB--SB---SS-----------------HHHHHHHHHHHHHHHHHHTT--SCBE-B-TT-SSTTHHHHTTSTTE.E- CS
                       Meth_synt_2  1 lpTttiGSfPqtaevrearaevkkgelseeeyekaireeiekvvrrqeelgvDvlvhgepeRgdmveyfgealdgf.af 78
                                      +pTt++GS+P  + + +  ++ ++ge+s +e  + + e++  +v+ qe++g+D++ +ge  R d   + + +ldg+ ++
  gi|557694397|ref|YP_008797451.1|  5 FPTTVVGSWPRPSWLLAELKRKNRGEISYDEFSSVADEAVLLAVKYQEDAGIDIITDGEQ-RRDNF-FVADKLDGLkLM 81
                                      8**********************************************************7.66654.568999999888 PP

                                      -SS--EEEET CS
                       Meth_synt_2 79 tkngwvqsyg 88
                                      t ++ ++  +
  gi|557694397|ref|YP_008797451.1| 82 TVAEVIDYVE 91
                                      8888887554 PP

>> S_layer_C  S-layer like family, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.4e-06     0.021      33     105 ..      22      99 ..      16     121 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-06
                         S_layer_C  33 kvvidsgitleykdeekledkvvglalkykgdkladikdkdkvd.ianyaklkfdD...klsvyfkid..eekevel 103
                                       +++ ++ +++ y + +++ d+ v la+ky++d  +di ++ ++  ++ ++  k  D    ++v   id  e+k   +
  gi|557694397|ref|YP_008797451.1|  22 ELKRKNRGEISYDEFSSVADEAVLLAVKYQEDAGIDIITDGEQRrDNFFVADKL-DglkLMTVAEVIDyvEDKSRYE 97 
                                       667788899*************************99988777773555553333.4464444444444333333333 PP

                         S_layer_C 104 iv 105
                                       ++
  gi|557694397|ref|YP_008797451.1|  98 QM 99 
                                       33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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 0.23s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1051.72
//
Query:       gi|557694398|ref|YP_008797452.1|  [L=73]
Description: hypothetical protein CSUB_C0969 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   20.9   0.0     0.0004   20.8   0.0    1.1  1  OsmC      OsmC-like protein


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 !   20.8   0.0   2.2e-08    0.0004      50      97 ..      20      65 ..       2      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.2e-08
                                      ECTCEEEEEEEEEEE-SS-H..HHHHHHHHHHHHHSHHHHHHCT-SSS CS
                              OsmC 50 gakgiteirlkvevkipgadseeklkkllekaekrCpvsntlkngvkv 97
                                      g+ g+ e + k++v++p ++  ++++++  k+ +++pv ntl ++vk+
  gi|557694398|ref|YP_008797452.1| 20 GHLGYRETKAKLYVRSPADP--KTIQDIWSKTLETSPVGNTLSRNVKI 65
                                      3337999999****999887..************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       255  (0.0142228); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 542.75
//
Query:       gi|557694399|ref|YP_008797453.1|  [L=128]
Description: HEPN domain-containing protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-31  106.6   0.1    8.9e-31  106.5   0.1    1.0  1  HEPN      HEPN domain
  ------ inclusion threshold ------
      0.047   13.0   0.7       0.32   10.3   0.1    1.9  2  TAtT      TRAP transporter T-component
        0.2   10.5   0.0       0.22   10.3   0.0    1.1  1  DUF1679   Protein of unknown function (DUF1679)


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 !  106.5   0.1   1.5e-34   8.9e-31       2     115 ..       5     123 ..       4     127 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 1.5e-34
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHH CS
                              HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreele 78 
                                       +++l  Ae++l +A++l+e+g+++ +cf+aqqaae+alKA+l + g e  +th+l +Ll+el ++l+es ++ ++++
  gi|557694399|ref|YP_008797453.1|   5 RDLLIDAEDFLGTARDLMEKGRWSKVCFNAQQAAELALKAVLQRMGVE-RRTHSLVDLLRELVTHLPESGRFWDDVK 80 
                                       678889*****************************************9.**************************** PP

                                       HHHCCCHHCCCTSS--S......--HHHHHHHHHHHHHHHHHH CS
                              HEPN  79 eLekayiesrYpdakee......yteedaeealkdaeevlelv 115
                                        L+++yi++rY +a+        yte++a++a+++a++++e++
  gi|557694399|ref|YP_008797453.1|  81 ILDQYYIPTRYANAFASgpakdkYTENQARDAVERAKRIIEWA 123
                                       ***************99*************************6 PP

>> TAtT  TRAP transporter T-component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.026   1.5e+02      47      78 ..      14      45 ..      10      70 .. 0.83
   2 ?   10.3   0.1   5.3e-05      0.32      41      81 ..      89     127 ..      80     128 .] 0.81

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.026
                                      HTHHHHHTS-GGGHHHHHHHHHHHHHHHHHHH CS
                              TAtT 47 FvqaeaelleddeldakeaareRAkkLylrar 78
                                      F  +  +l+e+ +  + + +++ A++L+l+a 
  gi|557694399|ref|YP_008797453.1| 14 FLGTARDLMEKGRWSKVCFNAQQAAELALKAV 45
                                      67777899999999999999999*99999996 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHTHHHHHTS-GGGHHHHHHHHHHHHHHHHHHHHHH CS
                              TAtT  41 taYanaFvqaeaelleddeldakeaareRAkkLylrareya 81 
                                       t YanaF+ ++a+  ++ + ++++ a eRAk++ + a +++
  gi|557694399|ref|YP_008797453.1|  89 TRYANAFASGPAK--DKYTENQARDAVERAKRIIEWAGKHV 127
                                       57*********65..555666778899*****998887765 PP

>> DUF1679  Protein of unknown function (DUF1679)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   3.7e-05      0.22     261     342 ..      12      95 ..       4     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3.7e-05
                           DUF1679 261 skvlGikkvlvhgDlwsaNiLfseeeegklklkkviDyQlvslg.npaeDlvrlllscLsgedRrarkeelLeqyy. 335
                                       +++lG    l+    ws  + f++++ ++l lk+v+    v +      Dl r l++ L ++ R     ++L+qyy 
  gi|557694399|ref|YP_008797453.1|  12 EDFLGTARDLMEKGRWS-KVCFNAQQAAELALKAVLQRMGVERRtHSLVDLLRELVTHLPESGRFWDDVKILDQYYi 87 
                                       67899988899999995.788999999*********9888876515668***************************4 PP

                           DUF1679 336 .etflkal 342
                                        + + +a+
  gi|557694399|ref|YP_008797453.1|  88 pTRYANAF 95 
                                       44455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); 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:                         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: 997.74
//
Query:       gi|557694400|ref|YP_008797454.1|  [L=142]
Description: DNA polymerase beta domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-10   41.2   0.1    1.9e-10   40.9   0.1    1.2  1  NTP_transf_2  Nucleotidyltransferase domain
    1.8e-08   34.3   0.1    2.3e-08   34.0   0.1    1.4  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.036   13.6   0.1          3    7.5   0.0    2.5  2  HTH_24        Winged helix-turn-helix DNA-binding
       0.16   11.7   0.0       0.21   11.4   0.0    1.2  1  DUF294        Putative nucleotidyltransferase DUF294


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 !   40.9   0.1   4.1e-14   1.9e-10      13      74 ..      24     102 ..      12     127 .. 0.74

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 4.1e-14
                                       T....TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH.............HHHEHHHHHHHHCCCEEECTTEEEE CS
                      NTP_transf_2  13 p....vakvvlfGSyarGtalkgSDiDllvvlpeevsre.............kkeegleklaeiikfleellglevd 72 
                                            + +v+lfGSya++ ++++SDiD++v+ ++  ++e              ++ + +  +e+ + le+l+ +   
  gi|557694400|ref|YP_008797454.1|  24 DagikPHSVILFGSYAKDSFTEESDIDICVIAENLPEEEsarrslsshlphkGVQAISYFPHEFLELLEKLNIMVLE 100
                                       44446789***************************998899999999999774555556666666677776666666 PP

                                       EE CS
                      NTP_transf_2  73 lv 74 
                                       +v
  gi|557694400|ref|YP_008797454.1| 101 IV 102
                                       66 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.1   5.2e-12   2.3e-08      11      55 ..      27      72 ..      13     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 5.2e-12
                                      HHHHSTTEEEEEE-S------EEEEEEEESS-.--HHHHHHHHHHH CS
                           Polbeta 11 keielaylFGSrakgkareeSDiDlavllkek.ldleeelelaael 55
                                       +   ++lFGS+ak+ ++eeSDiD++v+ ++  ++ + + +l++ l
  gi|557694400|ref|YP_008797454.1| 27 IKPHSVILFGSYAKDSFTEESDIDICVIAENLpEEESARRSLSSHL 72
                                      577889************************9954444455555555 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 ?    7.5   0.0   0.00067         3      31      46 ..      12      27 ..      11      27 .. 0.91
   2 ?    3.5   0.1     0.011        51      37      48 .]     120     131 ..     115     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00067
                            HTH_24 31 pstvnrrlkrLeeeGl 46
                                      ++ vn+++++L+++G+
  gi|557694400|ref|YP_008797454.1| 12 LQRVNEYIDKLVDAGI 27
                                      689************7 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.011
                            HTH_24  37 rlkrLeeeGlIk 48 
                                        l+rL++eG+Ik
  gi|557694400|ref|YP_008797454.1| 120 ILERLKSEGVIK 131
                                       799********8 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.7e-05      0.21      25      86 ..       5      67 ..       1      82 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.7e-05
                            DUF294 25 selndallrrlielaeeelgkppvpfallvmGSeGReEqtlktDqDnalvled.eeeeaarey 86
                                      sel++a+l+r+ e + + ++    p +++ +GS + +  t ++D D + + e+ +eee+ar+ 
  gi|557694400|ref|YP_008797454.1|  5 SELKAAALQRVNEYIDKLVDAGIKPHSVILFGSYAKDSFTEESDIDICVIAENlPEEESARRS 67
                                      7899999******999999889*******************************8454444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1147.81
//
Query:       gi|557694401|ref|YP_008797455.1|  [L=640]
Description: D-alanine-D-alanine ligase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-26   90.3   0.0    7.9e-25   87.4   0.0    2.2  2  Methyltransf_25  Methyltransferase domain
    1.1e-23   83.8   0.0    1.6e-23   83.3   0.0    1.3  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    1.8e-20   73.4   0.0    3.8e-20   72.3   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
      1e-17   64.3   0.0    1.7e-17   63.6   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    2.8e-14   53.0   0.0    5.8e-14   52.0   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.9e-11   43.5   0.0    7.8e-11   42.1   0.0    1.7  1  Methyltransf_23  Methyltransferase domain
    3.2e-09   37.4   0.0      8e-09   36.2   0.0    1.7  1  Methyltransf_12  Methyltransferase domain
    2.4e-07   30.5   0.0      4e-07   29.7   0.0    1.3  1  MTS              Methyltransferase small domain
    4.4e-06   26.8   0.0    1.1e-05   25.6   0.0    1.7  1  ATP-grasp_3      ATP-grasp domain
    6.3e-05   22.5   0.0    0.00011   21.6   0.0    1.3  1  TehB             Tellurite resistance protein TehB
    0.00011   21.9   0.0    0.00021   21.0   0.0    1.5  1  ATP-grasp_4      ATP-grasp domain
    0.00066   18.7   0.0     0.0011   18.0   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
     0.0018   17.6   0.0     0.0028   17.0   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0058   16.3   0.0      0.014   15.1   0.0    1.5  2  Cons_hypoth95    Conserved hypothetical protein 95
     0.0079   15.8   0.0      0.013   15.0   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.023   14.5   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.046   13.5   0.0        2.8    7.7   0.0    2.9  3  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
      0.052   13.3   0.0       0.11   12.2   0.0    1.5  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
      0.057   12.9   0.0       0.11   11.9   0.0    1.5  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
      0.097   11.6   0.0       0.15   11.0   0.0    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
        0.1   12.3   0.0       0.87    9.2   0.0    2.2  1  UPF0020          Putative RNA methylase family UPF0020
       0.11   11.9   0.0       0.19   11.1   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.16   11.4   0.0       0.32   10.4   0.0    1.5  1  Methyltransf_4   Putative methyltransferase


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 !   87.4   0.0     1e-27   7.9e-25       1      97 []      67     164 ..      67     164 .. 0.95
   2 ?   -0.1   0.0         2   1.6e+03      20      48 ..     330     356 ..     318     379 .. 0.73

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 1e-27
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh 76 
                                       +Ldl+cG+Gr++l+la+r g  +vtg+D+see+l++are+ae+e+l+v+f +gda++lpf+++sfD+vv++g+ + +
  gi|557694401|ref|YP_008797455.1|  67 ILDLCCGNGRHSLELARR-GFRNVTGLDYSEELLKIAREKAEAEHLKVRFARGDARSLPFQANSFDAVVMMGNsFGY 142
                                       8*****************.69******************************************************** PP

                                       SSHH.HHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  77 lsde.dlekalkeiarvLkpgG 97 
                                       ++++ d   +lk+++r+L+p G
  gi|557694401|ref|YP_008797455.1| 143 FHNPlDDLIVLKQVHRILRPYG 164
                                       8876455669**********87 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2
                                       TSSEEEEEESSHHHHHHHHHHHHHTTTTE CS
                   Methyltransf_25  20 gkakvtgvDiseemleaareraeeeglnv 48 
                                        ++k++ vD  ++m+e   ++   +g+++
  gi|557694401|ref|YP_008797455.1| 330 REYKFIFVDDHSKMIEFLTKNR--AGIHM 356
                                       37999***********999887..34444 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 !   83.3   0.0   2.1e-26   1.6e-23      33     203 ..     429     615 ..     406     616 .. 0.84

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 2.1e-26
                                       HHC-SSEEEEESSSSTTTTEEE...ESSGGGHHHHHHHHH...TT-SCEEEEE--ESEEEEEEEEETSSCE.EEEEE CS
                   Dala_Dala_lig_C  33 eelgypvfVKpareGSSvGvsk...veseeelkeaieeaf...kydekvlvEeaiegreievavlgnekle.vsevg 102
                                       ++++ypv+VKp     S G+++   v++++el +ai+e      y   +lvEe++eg +++v++lgn  +  v+++ 
  gi|557694401|ref|YP_008797455.1| 429 KHVKYPVIVKPNYGDNSWGITErnvVRNRDELISAIKEIRvkwGYSGPILVEEFVEGMDLTVSILGNPPQDvVLPIL 505
                                       4899****************855559**********997522258899******************98755155555 PP

                                       EEE-SS......SSS-HHHHH...C.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEE CS
                   Dala_Dala_lig_C 103 eivvkk......gfydyeaky...sddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivln 170
                                          ++k      ++  y+ak+   s  +    +p++l++  +e++     k +++l++r+ aR D  l ++g + l 
  gi|557694401|ref|YP_008797455.1| 506 TEDYSKlpdglpKILTYAAKWcpdSPYRFVNSIPVELPHRLREQLIWWCRKLFAMLECRDYARFDWRLGSDGVPRLL 582
                                       5566668899***********632224555679******************************************** PP

                                       EEESS---STTSHHHHHHHCTT--HHHHHHHHH CS
                   Dala_Dala_lig_C 171 EvNtlPGfTeiSlfpklakasGlefkkLvdqli 203
                                       EvN+ PG      f+k++   G++++ ++++++
  gi|557694401|ref|YP_008797455.1| 583 EVNPNPGWVWDGHFAKACLVLGWSYRRMLHEIL 615
                                       *****************************9997 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.0   4.9e-23   3.8e-20       1      96 []      68     168 ..      68     168 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 4.9e-23
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES.-CCC-. CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvsse.vlhhv. 74 
                                       Ld+ cG+Gr++ +la+rg ++v+g+D+s+e+lk+a+eka+ e+lkv+f ++da++lpf+ nsfD+vv+   ++ ++ 
  gi|557694401|ref|YP_008797455.1|  68 LDLCCGNGRHSLELARRGfRNVTGLDYSEELLKIAREKAEAEHLKVRFARGDARSLPFQANSFDAVVMMGnSFGYFh 144
                                       89****************************************************************99886555553 PP

                                       ..CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 ..edpekalkeiaRvLkpgGllvi 96 
                                          d   +lk+++R+L+p G+++i
  gi|557694401|ref|YP_008797455.1| 145 npLDDLIVLKQVHRILRPYGKFMI 168
                                       2357888*************9986 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   0.0   2.2e-20   1.7e-17       2     113 ..      62     172 ..      61     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 2.2e-20
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDli 78 
                                       +k+ ++lDl CG+G+ ++ela++ +   +v+G+D+see ++ Are+a+   l+ v+F +gd+ +l+  ++ ++fD +
  gi|557694401|ref|YP_008797455.1|  62 EKDDSILDLCCGNGRHSLELARRGF--RNVTGLDYSEELLKIAREKAEAEHLK-VRFARGDARSLP--FQANSFDAV 133
                                       57889****************6533..5799*********************8.************..********9 PP

                   Methyltransf_31  79 lsnevl....naladpdkileeiervlkpggilliedpr 113
                                       +  +      +   d   +l++++r l+p g ++i+ ++
  gi|557694401|ref|YP_008797455.1| 134 VMMGNSfgyfHNPLDDLIVLKQVHRILRPYGKFMIDIAD 172
                                       9874334454777777789***************99888 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   7.4e-17   5.8e-14      40     151 ..      56     168 ..      39     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 7.4e-17
                                       HHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T- CS
                   Ubie_methyltran  40 eklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfedds 116
                                       ++l +  +  ++lD+++G g  +++l++      +v++lD++e++Lk++++k++ e   +++f  ++a  Lpf+ +s
  gi|557694401|ref|YP_008797455.1|  56 IQLLGFEKDDSILDLCCGNGRHSLELARRG--FRNVTGLDYSEELLKIAREKAEAE-HLKVRFARGDARSLPFQANS 129
                                       56667778889*************998753..4489****************9877.568***************** PP

                                       EEEEEE...ES-.GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran 117 fDvvtv...sfG.lrnvtDklkaLkeayrvlkpGGrlvv 151
                                       fD v +   sfG + n  D l +Lk+++r+l+p G++++
  gi|557694401|ref|YP_008797455.1| 130 FDAVVMmgnSFGyFHNPLDDLIVLKQVHRILRPYGKFMI 168
                                       **98765669**558999*****************9875 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0     1e-13   7.8e-11      20     163 ..      61     248 ..      44     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 1e-13
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqgkfdlIvlr. 89 
                                        +++ ++Ld+ cG G+ + +l+++gf +vtg D s+e+ +ia+     +  k ++   d+ + ++++++fd +v++ 
  gi|557694401|ref|YP_008797455.1|  61 FEKDDSILDLCCGNGRHSLELARRGFrNVTGLDYSEELLKIARekaeaEHLKVRFARGDARSLPFQANSFDAVVMMg 137
                                       578899********************9****************9998988888888888889999******999884 PP

                   Methyltransf_23  90 evlehvpdpp...ellrqiatllkpgGylllseplasl..........................kedrllld..... 132
                                       ++++ +++p     +l+q++++l+p G +++   + +                                  d     
  gi|557694401|ref|YP_008797455.1| 138 NSFGYFHNPLddlIVLKQVHRILRPYGKFMIDIADGEYlrhnyqpvstesktdgtliirerelsR------Drgrlv 208
                                       69*****9988889*******************76554466666655555555555543333320......133333 PP

                   Methyltransf_23 133 ........wlyl.vpag..rhisffsarslkelleeaGlevv 163
                                                    v a+    ++++  +++k lle+aG++ v
  gi|557694401|ref|YP_008797455.1| 209 trelvigrD--GsVVADnlYAVRLYGFEDIKALLERAGFTGV 248
                                       344443331..0333331255699999999999999999876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0     1e-11     8e-09       1      99 []      68     166 ..      68     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1e-11
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvvas.nv 75 
                                       L++ cG+G+ + +l+++  + ++tg+D+s++ ++ a+ek  +++  ++ + + +a++l     + +sfD+vv+  n 
  gi|557694401|ref|YP_008797455.1|  68 LDLCCGNGRHSLELARR-GFRNVTGLDYSEELLKIAREKAEAEHL-KVRFARGDARSLPF---QaNSFDAVVMMgNS 139
                                       8999***********99.999999*********888888777775.55666666666554...447******88799 PP

                   Methyltransf_12  76 lhhl...kdirevldnirklLkpgGrl 99 
                                       + ++    d   vl+++++ L+p G++
  gi|557694401|ref|YP_008797455.1| 140 FGYFhnpLDDLIVLKQVHRILRPYGKF 166
                                       99998555555899*********9975 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   5.2e-10     4e-07      21     103 ..      53     135 ..      37     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 5.2e-10
                                       HHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTT.TSTTS CS
                               MTS  21 klLletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvle.eveek 96 
                                       +l+++ l  e+++++lDl+cG+G  +++la++  + +vt +d + + l++a+e +ea++l+v++   d+ +  ++ +
  gi|557694401|ref|YP_008797455.1|  53 DLMIQLLGFEKDDSILDLCCGNGRHSLELARRGFR-NVTGLDYSEELLKIAREKAEAEHLKVRFARGDARSlPFQAN 128
                                       58889999899999*****************9888.7********************************98346689 PP

                                       -EEEEEE CS
                               MTS  97 kfdlivs 103
                                       +fd++v+
  gi|557694401|ref|YP_008797455.1| 129 SFDAVVM 135
                                       9**9997 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.4e-08   1.1e-05       2     156 ..     398     586 ..     397     589 .. 0.75

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.4e-08
                                       TSHHHHHHHHTTT.S---.........-EESS--SSSEEEEESS-------B...--SS--TTE............. CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvP.....tkleaeeleeeekklvvKprdGaggesvr...vveekeeaeaaieeve...... 64 
                                        dK k+    +  g++vP      +  + +l+ ++++++vKp +G  + +++   vv++++e+ +ai+e+       
  gi|557694401|ref|YP_008797455.1| 398 YDKAKVKAIASSMGIPVPhhtilFNGDNGSLKHVKYPVIVKPNYGDNSWGITernVVRNRDELISAIKEIRvkwgys 474
                                       5787777666777999997766656677788889***********99988872225667777777777766****** PP

                                       ...EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET....................TEEEEEE..ES----HHHHH CS
                       ATP-grasp_3  65 ...lvqefieGkplSvsllsdgekvlvlavnrqliekaeke................fvyaGnv..tpietelkeev 120
                                          lv ef+eG +l+vs+l++  + +vl +  +   k  ++                ++++ n+  ++ +++l+e++
  gi|557694401|ref|YP_008797455.1| 475 gpiLVEEFVEGMDLTVSILGNPPQDVVLPILTEDYSKLPDGlpkiltyaakwcpdspYRFV-NSipVELPHRLREQL 550
                                       *********************9999999888777766555578888888888888764433.340145556668888 PP

                                       HHHHHHHHTTSTT--EEEEEEEEESS..SEEEEEEES CS
                       ATP-grasp_3 121 velaeevvekleglaGyvGvDlvlkd.eepyviEvNP 156
                                       +  ++++ + l +++ y+  D  l   + p ++EvNP
  gi|557694401|ref|YP_008797455.1| 551 IWWCRKLFAML-ECRDYARFDWRLGSdGVPRLLEVNP 586
                                       88888888888.8888888887654437788888888 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.5e-07   0.00011      33      94 ..      66     127 ..      48     141 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.5e-07
                                       EEEEES-TTSHHHHHHHHTT-.EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S CS
                              TehB  33 kvldlgcgqgrnslylsllgy.dvtawdknensiafleeikekenlknistalydineaklde 94 
                                        +ldl cg+gr sl l+  g+ +vt +d  e+ ++  +e +e e lk ++ a  d  ++ ++ 
  gi|557694401|ref|YP_008797455.1|  66 SILDLCCGNGRHSLELARRGFrNVTGLDYSEELLKIAREKAEAEHLK-VRFARGDARSLPFQA 127
                                       58******************978***********************9.777777777766664 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.6e-07   0.00021       2      91 ..     432     512 ..     431     536 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.6e-07
                       ATP-grasp_4   2 slPvviKPsvgffSlGVy...kinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfavdayfdee 75 
                                       ++Pv++KP+ g  S G++   +++n++e+ +a+++i+ ++      y      ++ +lvEe++eG    v ++ +  
  gi|557694401|ref|YP_008797455.1| 432 KYPVIVKPNYGDNSWGITernVVRNRDELISAIKEIRVKW-----GY------SGPILVEEFVEGMDLTVSILGNPP 497
                                       89***************83335778888888887777442.....33......4679************99988544 PP

                       ATP-grasp_4  76 Gepvilnilkkefase 91 
                                        + v+l il+ ++++ 
  gi|557694401|ref|YP_008797455.1| 498 -QDVVLPILTEDYSKL 512
                                       .888888888777665 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 !   18.0   0.0   1.4e-06    0.0011     115     208 ..      63     156 ..      45     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.4e-06
                                       TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T.---EEEEEEES CS
                    Methyltransf_9 115 kgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe.leafdtvfsmG 190
                                       k+ +ild+ cgnG h   ++ +g + v G+d se  l    a +k  +e+ ++         lp   ++fd+v  mG
  gi|557694401|ref|YP_008797455.1|  63 KDDSILDLCCGNGRHSLELARRGFRNVTGLDYSEELLKI--AREKAEAEHLKVRFARGDARSLPFqANSFDAVVMMG 137
                                       7889*****************************988754..334444444444444455788997799********* PP

                                       -GG.G-S-HHHHHHHHHCT CS
                    Methyltransf_9 191 vly.hrrsPldhllqlkdq 208
                                         + + + Pld l+ lk+ 
  gi|557694401|ref|YP_008797455.1| 138 NSFgYFHNPLDDLIVLKQV 156
                                       86635689****9988764 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.6e-06    0.0028      49     164 ..      50     168 ..      35     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.6e-06
                                       HHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-- CS
                              CMAS  49 aKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedld 125
                                         +dl+++ l+ ++ + +Ld+ cG G    + ++r   +v gl  S+e  k a+++ +++ l+  v+    d + l+
  gi|557694401|ref|YP_008797455.1|  50 YEVDLMIQLLGFEKDDSILDLCCGNGRHSLELARRGFRNVTGLDYSEELLKIAREKAEAEHLK--VRFARGDARSLP 124
                                       468999*****************************8889*****************9999865..444555555554 PP

                                       -...--SEEEEES-GGGTSGGGHHHH..HHHHHHHS-TT-EEEE CS
                              CMAS 126 e...kvdrvvsvgafehvgkenydtf..fkklkkllkedGllll 164
                                            +d+vv +g      ++ +d+    k+++++l++ G +++
  gi|557694401|ref|YP_008797455.1| 125 FqanSFDAVVMMGNSFGYFHNPLDDLivLKQVHRILRPYGKFMI 168
                                       32358999988875444445555554225777777777777776 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.8e-05     0.014      43     105 ..      65     124 ..      55     135 .. 0.78
   2 ?   -3.5   0.0       9.1   7.1e+03      66      87 ..     333     354 ..     330     359 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                                       -EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHC CS
                     Cons_hypoth95  43 arvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleall 105
                                        ++LDl++G+G  +lE + Rg ++++ ++ ++e +ki +e+ e+ +l+     + + ++++l+
  gi|557694401|ref|YP_008797455.1|  65 DSILDLCCGNGRHSLELARRGFRNVTGLDYSEELLKIAREKAEAEHLK---VRFARGDARSLP 124
                                       579************************************999887766...344444444444 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.1
                                       EEEEEES-HHHHHHHHHHHCCC CS
                     Cons_hypoth95  66 kavlvekdkeavkilkenleel 87 
                                       k ++v+ ++++++ l +n + +
  gi|557694401|ref|YP_008797455.1| 333 KFIFVDDHSKMIEFLTKNRAGI 354
                                       5789999999999999997655 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 !   15.0   0.0   1.7e-05     0.013       3      60 ..      66     122 ..      64     152 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60 
                                        ilDl++G G  + ++a+  f++v ++++++e l++a + ae+   + k+ +  gd  +
  gi|557694401|ref|YP_008797455.1|  66 SILDLCCGNGRHSLELARRgFRNVTGLDYSEELLKIAREKAEAE--HLKVRFARGDARS 122
                                       58***************999*******************99987..6677788888765 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 ?   14.5   0.0   2.9e-05     0.023      62     146 ..      52     133 ..      38     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTG CS
                              PCMT  62 valalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGye 138
                                       v l+++ll ++k +++L++ +G G ++  lar   +  +v ++++++el + a+++ ++++l +v +  gD r    
  gi|557694401|ref|YP_008797455.1|  52 VDLMIQLLGFEKDDSILDLCCGNGRHSLELARRGFR--NVTGLDYSEELLKIAREKAEAEHL-KVRFARGDARSLPF 125
                                       5689**********************9988875333..357**************9998877.69999999886555 PP

                                       GG-SEEEE CS
                              PCMT 139 ekaPYdai 146
                                       ++  +da+
  gi|557694401|ref|YP_008797455.1| 126 QANSFDAV 133
                                       55556665 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 ?    2.1   0.0      0.19   1.5e+02      18      63 ..      68     112 ..      54     116 .. 0.87
   2 ?   -3.2   0.0       8.3   6.4e+03       4      23 ..     476     495 ..     475     502 .. 0.82
   3 ?    7.7   0.0    0.0036       2.8      46      84 ..     547     586 ..     543     589 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.19
                      ATPgrasp_Ter  18 vDvlaekgevlaavpRrKekgglqelekdeelielaerlaeefgld 63 
                                        D ++++g+    ++Rr    +++ l+++eel+++a++ ae+ +l+
  gi|557694401|ref|YP_008797455.1|  68 LDLCCGNGRHSLELARRGF-RNVTGLDYSEELLKIAREKAEAEHLK 112
                                       5889999999999999988.999**************999987776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.3
                      ATPgrasp_Ter   4 allvmeyLegpEySvDvlae 23 
                                       ++lv e+ eg   +v +l +
  gi|557694401|ref|YP_008797455.1| 476 PILVEEFVEGMDLTVSILGN 495
                                       68999*******99999865 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0036
                      ATPgrasp_Ter  46 deelielaerlaeefgldglvnvQvrededg.pkLLEiNp 84 
                                       +e+li  +++l   +++  +  +  r + dg p+LLE+Np
  gi|557694401|ref|YP_008797455.1| 547 REQLIWWCRKLFAMLECRDYARFDWRLGSDGvPRLLEVNP 586
                                       57889999*******************************9 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 ?   12.2   0.0   0.00014      0.11      34     120 ..     429     515 ..     399     521 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                       HHHSSSEEEEEESC-GGGT-EE...EESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE---SEEEEEEEEECTTEEEE CS
                            GARS_A  34 eeatakalVvKadglaagKgvi...vakseeealkavkeilekkkfGeagekvviEelleGeEvsllalvdgktvkp 107
                                       ++++ ++ +vK++      g++   v+++++e ++a+kei +  k+G  +  +++Ee++eG ++++  l +  + + 
  gi|557694401|ref|YP_008797455.1| 429 KHVKYPV-IVKPNYGDNSWGITernVVRNRDELISAIKEIRV--KWGY-SGPILVEEFVEGMDLTVSILGNPPQDVV 501
                                       5555555.5665555555554333399*************98..8884.468**************99987655444 PP

                                       --.-BEEEEEEECC CS
                            GARS_A 108 lp.laqdhkrvleg 120
                                       lp l+ d+ ++ +g
  gi|557694401|ref|YP_008797455.1| 502 LPiLTEDYSKLPDG 515
                                       44156788777665 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 ?   11.9   0.0   0.00015      0.11       1      91 [.     399     485 ..     399     501 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTT...EEEESSHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkG...mrvarneeelaelvkkalaea 74 
                                       Dk + k++++ +++pv + ++   +         k+++yPvi+k+ +g    G     v+rn++el+ ++k+ + + 
  gi|557694401|ref|YP_008797455.1| 399 DKAKVKAIASSMGIPVPHHTIL-FNGD---NGSLKHVKYPVIVKPNYGDNSWGiteRNVVRNRDELISAIKEIRVKW 471
                                       5666666666666666666666.2222...23457899*********97666622268********99998877666 PP

                                       HHHHSTS-EEEEE--SS CS
                       CPSase_L_D2  75 kaafgnkqvlvekslkg 91 
                                            +  +lve++++g
  gi|557694401|ref|YP_008797455.1| 472 G---YSGPILVEEFVEG 485
                                       3...3467888888876 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0002      0.15     200     248 ..      62     111 ..      36     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                   tRNA_U5-meth_tr 200 eskgdllelycGnGnfslalarn.fekvlateiakssveaaqyniaanki 248
                                       e+++ +l+l cGnG  sl lar+ f++v   + +   ++ a+   +a+++
  gi|557694401|ref|YP_008797455.1|  62 EKDDSILDLCCGNGRHSLELARRgFRNVTGLDYSEELLKIAREKAEAEHL 111
                                       345579***************86588898888888888888777776655 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0    0.0011      0.87      76     126 ..      86     134 ..      43     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                                       H--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEE CS
                           UPF0020  76 elklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdviv 126
                                         ++ g+D  +++++ are+ae+  +  ++ f   da++L+ + +++d++v
  gi|557694401|ref|YP_008797455.1|  86 FRNVTGLDYSEELLKIAREKAEAEHL--KVRFARGDARSLPFQANSFDAVV 134
                                       33478****************98876..688999999***977779*9998 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00024      0.19     160     231 ..      62     134 ..      50     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                              PrmA 160 kegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell.keekadviv 231
                                       ++++++lD+ +G G  ++  a+ g ++v+++D+ e  +k+a+e ae  +++ ++    +++l+ +++++d +v
  gi|557694401|ref|YP_008797455.1|  62 EKDDSILDLCCGNGRHSLELARRGFRNVTGLDYSEELLKIAREKAEAEHLKVRFARGDARSLPfQANSFDAVV 134
                                       57899******************************************99999885433344444456677766 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00041      0.32       4      64 ..      66     123 ..      63     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00041
                                       EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHH CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvl 64 
                                        +l+++cG+G++ ++lA +    n+ G++ ++++++ + +k+ea++lk +r  rgda + l
  gi|557694401|ref|YP_008797455.1|  66 SILDLCCGNGRHSLELARR-GFRNVTGLDYSEELLKIAREKAEAEHLK-VRFARGDA-RSL 123
                                       689**************86.567999*********9999999999997.88888888.555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (640 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); 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: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.40
# Mc/sec: 4778.36
//
Query:       gi|557694402|ref|YP_008797456.1|  [L=118]
Description: DNA polymerase beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   43.6   0.1    3.8e-11   43.1   0.1    1.3  1  NTP_transf_2    Nucleotidyltransferase domain
    2.2e-07   30.9   0.0    2.8e-07   30.5   0.0    1.3  1  Polbeta         Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.083   13.1   0.0      0.098   12.9   0.0    1.2  1  DNA_pol_B_palm  DNA polymerase beta palm


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 !   43.1   0.1   6.3e-15   3.8e-11       1      78 [.      25      98 ..      25     114 .. 0.68

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 6.3e-15
                                      HHHHHHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH............HHHEHHHHHHHHCCCEEECT CS
                      NTP_transf_2  1 lkklleelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsre............kkeegleklaeiikfleell 67
                                      l+kl++ + +l+p+a+v+lfGS+a + +l  SDiD+lvv+++   +             +                e++
  gi|557694402|ref|YP_008797456.1| 25 LEKLATVVAKLDPDAEVYLFGSVAENRHLLSSDIDILVVTEKKPGEVlaelwregirdpF----------------EIH 87
                                      579999*************************************76313333333333220................333 PP

                                      TEEEEEECEEE CS
                      NTP_transf_2 68 glevdlvtrek 78
                                      ++  d+++ + 
  gi|557694402|ref|YP_008797456.1| 88 VVTDDVLEVYR 98
                                      34444444433 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   4.8e-11   2.8e-07      14      53 ..      39      77 ..      20     112 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 4.8e-11
                                      HSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHH CS
                           Polbeta 14 elaylFGSrakgkareeSDiDlavllkekldleeelelaa 53
                                      + +ylFGS+a++++  +SDiD+ v++++k   e  +el+ 
  gi|557694402|ref|YP_008797456.1| 39 AEVYLFGSVAENRHLLSSDIDILVVTEKK-PGEVLAELWR 77
                                      459*************************9.3444444433 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 ?   12.9   0.0   1.6e-05     0.098      12      79 ..      26      92 ..      14     112 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
                                      HHHHHHHHHH-TT-EEEE-HHHHTT-S.EESSEEEEEEBTTBSTTSS--HHHHHHHHHHHHHTTSEEEE CS
                    DNA_pol_B_palm 12 alvkkaakeldpevevivcGSYRRgae.ssGDvDvlitkkdakseskklkklleklvkklkkkgfltds 79
                                      + + + +++ldp++ev+  GS   +++  s D+D+l+  +++  e   l +l ++ ++   + +++td+
  gi|557694402|ref|YP_008797456.1| 26 EKLATVVAKLDPDAEVYLFGSVAENRHlLSSDIDILVVTEKKPGE--VLAELWREGIRDPFEIHVVTDD 92
                                      45667899*************9866542699******99887773..3566666666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 853.14
//
Query:       gi|557694403|ref|YP_008797457.1|  [L=130]
Description: HEPN domain-containing protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   83.5   0.1    1.4e-23   83.2   0.1    1.1  1  HEPN      HEPN domain
  ------ inclusion threshold ------
       0.02   14.5   0.0      0.025   14.2   0.0    1.1  1  DUF884    Nucleopolyhedrovirus protein of unknown function (D
       0.12   12.4   0.4       0.67   10.0   0.0    2.2  2  DUF2384   Protein of unknown function (DUF2384)


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 !   83.2   0.1   2.4e-27   1.4e-23       2     116 ..       8     126 ..       7     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 2.4e-27
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT.........-HH CS
                              HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke......see 72 
                                        ++l+r+  ++e+A     +g+ydla+f  +q+++++lKA+ll++g+++p+th++r+ le++++ +++       ++
  gi|557694403|ref|YP_008797457.1|   8 ARLLERSMWFFETALMQVGRGFYDLAVFSLEQSLQLYLKACLLRLGIDYPRTHSVRKPLELIRDVTGHrdieeiLSR 84 
                                       579*************************************************************9996665444444 PP

                                       HHHHHHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHHHH CS
                              HEPN  73 lreeleeLekayiesrYpdakeeyteedaeealkdaeevlelve 116
                                       ++ el  Le+ayi+srY  + +     ++e++ +++eev ++v 
  gi|557694403|ref|YP_008797457.1|  85 YAVELGSLEDAYITSRYVTRTY--AAVEVEKLKNTVEEVRNVVG 126
                                       444559***************9..9**************99875 PP

>> DUF884  Nucleopolyhedrovirus protein of unknown function (DUF884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   4.1e-06     0.025      29      87 ..      47     105 ..      32     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.1e-06
                            DUF884  29 vylfkldieePrtynvnaktklvsGlenskPinivvrsitvelngtrqayvismirarr 87 
                                         l +l i+ Prt+ v     l+  +   + i+  +   +vel + ++ay+ s + +r 
  gi|557694403|ref|YP_008797457.1|  47 ACLLRLGIDYPRTHSVRKPLELIRDVTGHRDIEEILSRYAVELGSLEDAYITSRYVTRT 105
                                       45789************************************************887765 PP

>> DUF2384  Protein of unknown function (DUF2384)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00011      0.67      26      48 ..      63      85 ..      62      87 .. 0.93
   2 ?   -0.5   0.1      0.22   1.3e+03      39      48 ..     119     128 ..     118     130 .] 0.85

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00011
                           DUF2384 26 rtPldlldteaGarlVedyLdri 48
                                      r+Pl+l++ ++G r +e++L r 
  gi|557694403|ref|YP_008797457.1| 63 RKPLELIRDVTGHRDIEEILSRY 85
                                      79******************996 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.22
                           DUF2384  39 rlVedyLdri 48 
                                       ++V+++++ri
  gi|557694403|ref|YP_008797457.1| 119 EEVRNVVGRI 128
                                       68*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 955.41
//
Query:       gi|557694404|ref|YP_008797458.1|  [L=226]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  123.2   0.0    1.3e-35  122.9   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase


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 !  122.9   0.0   7.3e-40   1.3e-35       2     205 ..       4     209 ..       2     220 .. 0.89

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 7.3e-40
                   Diphthami_syn_2   2 kvavlysGGkDsilaLykalke..sevesLvsvisenkesymfhvvnvhlvellaesvGiplikle..taGeeekev 74 
                                       +va  +sGGkDs++a +  + +    +e+L++  +e ++   +h+v ++l+e++ae +G  l k     +  +e + 
  gi|557694404|ref|YP_008797458.1|   4 RVALSWSGGKDSAMAYHTLAAQedLLIEFLITTYNESNNRSSMHGVRLDLIEMQAEKLGARLLKIPlpPNCSNETYS 80 
                                       67888**********998554414679*********999999********************98651157889**** PP

                   Diphthami_syn_2  75 edLkgtlkkld...veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegld 148
                                       e++k  l++l    ++ v +G+i +e  +++ e+    + ++ ++PLW++d++el+ e++  +f++i+  v  +   
  gi|557694404|ref|YP_008797458.1|  81 ERMKTALQTLAsegINDVAFGDIFLEDVRRYREENLASVNFRGIFPLWGRDTKELAHEFLRLGFKAIICCVDTQQAP 157
                                       **********966677789**********9999999*************************************9997 PP

                   Diphthami_syn_2 149 eslLGrridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkw 205
                                         l+Gr    +l+++l +      +d++ge Ge++t+v D+P+fk  +++++ e+  
  gi|557694404|ref|YP_008797458.1| 158 SWLIGREYSWELLENLPRE-----VDPCGERGEFHTFVYDGPIFKEPIRIEKGEMVL 209
                                       7778************998.....**********************99999877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1635.66
//
Query:       gi|557694405|ref|YP_008797459.1|  [L=199]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   68.6   0.2    5.7e-18   65.2   0.2    1.9  2  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 ?    1.3   0.0     0.018   3.3e+02      47      88 ..      17      53 ..       8      60 .. 0.82
   2 !   65.2   0.2   3.2e-22   5.7e-18      27     136 ..      63     169 ..      59     170 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.018
                   Nitrate_red_del 47 PyesvYlsekkgllfgestlevrefyrqaglevaeefneppD 88
                                      +  s ++s ++ ++ ++s   +re++ ++g+++++++   +D
  gi|557694405|ref|YP_008797459.1| 17 LLSSSFTS-DP-KTIQKSVNSLREIFDKLGMTEESNL---AD 53
                                      55667777.66.79999999************99998...55 PP

  == domain 2  score: 65.2 bits;  conditional E-value: 3.2e-22
                   Nitrate_red_del  27 lelaaeYtrLFlgpgrrsasPyesvYlsekkgllfgest...levrefyrqaglevaeefneppDHlaveLeflahL 100
                                       ++  aeY+rLF     ++a+P+e++Y+     + ++ +t   ++++ fyr++ +++ +++   pDH+ +eLef+a  
  gi|557694405|ref|YP_008797459.1|  63 ENASAEYVRLFE---MGAAPPCETAYTCA---ENMEHRTyelADIAGFYRAFNVKQSTGT---PDHIKAELEFMALI 130
                                       67789******8...8************4...557777756699****************...************99 PP

                   Nitrate_red_del 101 aereaeaeea...eeaealleaqkafleehllpWlpefa 136
                                       + +e  a e+   e+ae + +a ++f++ehl++W++e++
  gi|557694405|ref|YP_008797459.1| 131 MVKELLAHENsntEAAEICRDARRKFYREHLSRWVGEWV 169
                                       9999999988999999999*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      634  (0.0353617); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1419.87
//
Query:       gi|557694406|ref|YP_008797460.1|  [L=329]
Description: molybdopterin oxidoreductase subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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   72.7   0.5    2.8e-19   70.1   0.5    2.0  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 !   70.1   0.5   1.5e-23   2.8e-19       2     248 ..      79     318 ..      78     319 .. 0.75

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.5e-23
                                       HHHHTS-EEEEE-EE--GGGG--S-----EEEEEEEE-SSEEEEEEEEE----.......-S--STT----EEEEEE CS
                             EB_dh   2 adWskappveislsgqklvipvpgkeevkpvtVkAaydgeniyfrleWkdptksalpsevgegkeddeyedkvAvmf 78 
                                       ++W+++p ++isl  q ++ p++ +  ++++ V+Aa+dge i f+leW d+ +      +  + + +e+ d+ Avm+
  gi|557694406|ref|YP_008797460.1|  79 PIWDNVPLSRISLADQSIIRPLKLSVPKETLNVRAAHDGEFIGFLLEWRDDIA------NTSAIKVPEFRDACAVML 149
                                       89***************************************************......888999************ PP

                                       ES............STT--GGG..........T-BTTB-EEEEEEETT-SS..-EEEEESSTTSEE-GGGGG..... CS
                             EB_dh  79 dddqaGcwgtchegarglpgapakeeatgskymgtagsfvdlwqWkagrse..plglvddgyvleerqndkgktnyt 153
                                        +            +++ ++            mgt+  ++ + +Wka  +   ++g+ d ++          + n++
  gi|557694406|ref|YP_008797460.1| 150 TS-----------YPAPPEARF----------MGTQTIPATILHWKADWQVdiEEGFQDLEKA---------FPNVS 196
                                       **...........555555555..........*****************96333333332222.........22233 PP

                                       ..................................................................---EEEEEEET CS
                             EB_dh 154 ynvenekdepaamf.skegfradd...................enesvpfdpewkegdt.......advkaeakykd 203
                                        ++ +  +e    +  k+ +++d                     ++++p  +++ +g         +d+ + +++++
  gi|557694406|ref|YP_008797460.1| 197 ADMYPLLKES--ITgGKPPKTIDLpdfarirlpgtwvgnpisqPKKEKPVEKIIAKGPAtvttlptQDAVGWGRWRN 271
                                       3322222222..112333333333444555556666666666544444444444444335778888*********** PP

                                       TEEEEEEEEES---TTS....---TTEEEEEEEEEE-GGGT--TT-S CS
                             EB_dh 204 GkWtVelvRpLkagnpldv..alepgkvydvafAvwdgkagershhk 248
                                       G W V+l  ++ka++++    ++e g++y+vaf vw g +g+r+ +k
  gi|557694406|ref|YP_008797460.1| 272 GVWRVVLAKKMKASDQTAGeiNIERGNTYSVAFTVWFGDQGDRGARK 318
                                       *************99985567**********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2330.49
//
Query:       gi|557694407|ref|YP_008797461.1|  [L=384]
Description: molybdopterin oxidoreductase Fe-S binding subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-31  105.9   5.9    9.6e-31  105.9   5.9    1.9  2  Fer4_11   4Fe-4S dicluster domain
    3.9e-05   24.2  18.8      0.023   15.3   0.2    3.4  3  Fer4_7    4Fe-4S dicluster domain
    5.8e-05   23.2  17.9      0.016   15.4   0.6    3.2  3  Fer4_9    4Fe-4S dicluster domain
    9.5e-05   22.4  23.1     0.0081   16.2   0.8    3.4  4  Fer4_10   4Fe-4S dicluster domain
    0.00049   20.0  29.1    0.00078   19.4   4.1    4.5  4  Fer4_2    4Fe-4S binding domain
     0.0018   18.3   0.7     0.0018   18.3   0.7    3.3  3  Fer4_21   4Fe-4S dicluster domain
     0.0054   16.5   2.5     0.0054   16.5   2.5    4.3  4  Fer4      4Fe-4S binding domain
      0.007   16.4  27.4      0.015   15.4   3.0    4.7  4  Fer4_6    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.015   16.0   5.9        1.2    9.9   0.9    2.7  2  Fer4_15   4Fe-4S single cluster domain
       0.13   12.8   0.6       0.13   12.8   0.6    3.0  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
       0.17   12.3   0.1       0.17   12.3   0.1    3.6  1  Fer4_8    4Fe-4S dicluster domain
       0.24   12.0  20.5       0.46   11.1   0.2    3.5  2  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 ?   -1.5   0.6       1.8   2.7e+03       8      49 ..      33      40 ..      22      52 .. 0.51
   2 !  105.9   5.9   6.4e-34   9.6e-31       2      98 ..     150     245 ..     149     247 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.8
                           Fer4_11  8 eqCrhCleppCvasapseaivkdeetGaVlldektkkeevre 49
                                      ++C  C+                                  +
  gi|557694407|ref|YP_008797461.1| 33 NKCIACQ----------------------------------T 40
                                      3333332..................................2 PP

  == domain 2  score: 105.9 bits;  conditional E-value: 6.4e-34
                           Fer4_11   2 ewlflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrv 78 
                                       ++++lp++C+hC+ p+C+as+p+ +i+k++e+G+Vl+d+ +++ ++re+v+ac yk+v++n+ t  +ekC +c++ v
  gi|557694407|ref|YP_008797461.1| 150 WFFYLPRICNHCTYPACLASCPRLSIYKRPEDGIVLVDQARCR-GYRECVQACSYKKVFYNHVTRISEKCVLCYPAV 225
                                       579***************************************9.********************************* PP

                           Fer4_11  79 eaGllpacvescptgalnfg 98 
                                       e+G  p c+++c +++++fg
  gi|557694407|ref|YP_008797461.1| 226 EKGIWPRCMRTCIGKIRMFG 245
                                       *******************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.5e-05     0.023       1      20 [.      34      53 ..      15      78 .. 0.79
   2 !   14.9   5.6     2e-05     0.029       2      50 ..     158     203 ..     157     205 .. 0.88
   3 ?    3.2   8.7     0.093   1.4e+02       1      48 [.     190     237 ..     190     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                            Fer4_7  1 rCigCgaCvaaCpvkaield 20
                                      +Ci C+ C++aC++ + + +
  gi|557694407|ref|YP_008797461.1| 34 KCIACQTCTVACKTTWTSGK 53
                                      68888888888877776654 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2e-05
                            Fer4_7   2 CigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPt 50 
                                       C +C   aC a Cp   i+ ++e   +    v +d+ +C g ++Cv++C +
  gi|557694407|ref|YP_008797461.1| 158 CNHCTypACLASCPRLSIYKRPE---D--GIVLVDQARCRGYRECVQACSY 203
                                       9***8789******999999887...3..58999***************75 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.093
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCg.........aCvavC 48 
                                       rC g + Cv+aC++k + ++ +         +  +ekC+ C+         +C+++C
  gi|557694407|ref|YP_008797461.1| 190 RCRGYRECVQACSYKKVFYNHV---------TRISEKCVLCYpavekgiwpRCMRTC 237
                                       799999***********99775.........55677888885444444444677777 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.6   1.1e-05     0.016      34      48 ..      33      47 ..      11      61 .. 0.70
   2 !   14.1   5.7   2.6e-05     0.038       2      48 ..     158     203 ..     157     206 .. 0.91
   3 ?    0.9   0.2      0.36   5.3e+02       1      13 [.     217     238 ..     208     256 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                            Fer4_9 34 eaCigCgaCveaCpk 48
                                      ++Ci C++C+ aC++
  gi|557694407|ref|YP_008797461.1| 33 NKCIACQTCTVACKT 47
                                      567777777777775 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.6e-05
                            Fer4_9   2 CtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                       C+ C++  C ++Cp   + ++   +++ +++a   +C g ++Cv+aC  
  gi|557694407|ref|YP_008797461.1| 158 CNHCTYpaCLASCPRLSIYKRPEDGIVLVDQA---RCRGYRECVQACSY 203
                                       ****9778*************99999999886...8***********86 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.36
                            Fer4_9   1 kCtgC.........gaCveaCp 13 
                                       kC+ C          +C++ C 
  gi|557694407|ref|YP_008797461.1| 217 KCVLCypavekgiwPRCMRTCI 238
                                       4555544444433334666664 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.8   5.4e-06    0.0081       2      37 ..      28      62 ..      27      69 .. 0.66
   2 !   15.6   7.0   8.8e-06     0.013       6      55 ..     155     201 ..     152     202 .. 0.95
   3 ?    5.7   7.4     0.011        16       2      55 ..     184     237 ..     183     238 .. 0.71
   4 ?   -0.2   1.5      0.75   1.1e+03       6      19 ..     215     237 ..     210     256 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.4e-06
                           Fer4_10  2 vvidddtCirCgkCvkaCPadltsvgakgeaseeea 37
                                      +v+d+++Ci C++C+ aC +  +++g+ +e+++ + 
  gi|557694407|ref|YP_008797461.1| 28 AVFDTNKCIACQTCTVACKT-TWTSGKGQEYMYWNN 62
                                      6899**************33.344444444444444 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 8.8e-06
                           Fer4_10   6 ddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaC 55 
                                       +  C +C+  +C ++CP        ++++ e++ v ++  +C g  +Cv+aC
  gi|557694407|ref|YP_008797461.1| 155 PRICNHCTypACLASCPR-----LSIYKRPEDGIVLVDQARCRGYRECVQAC 201
                                       578*****999*******.....99*************************** PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.011
                           Fer4_10   2 vvidddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgc......g...aCveaC 55 
                                       v +d+ +C + ++Cv+aC +        +++   ++v   +ekC  c      g    C++ C
  gi|557694407|ref|YP_008797461.1| 184 VLVDQARCRGYRECVQAC-S--------YKKVFYNHVTRISEKCVLCypavekGiwpRCMRTC 237
                                       568999************.4........66666666666699****94444331445676666 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.75
                           Fer4_10   6 ddtCirCg.........kCvkaC 19 
                                       +++C+ C          +C++ C
  gi|557694407|ref|YP_008797461.1| 215 SEKCVLCYpavekgiwpRCMRTC 237
                                       44555554333333333444444 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   4.1   5.2e-07   0.00078       2      21 ..      27      46 ..      26      47 .. 0.90
   2 !   10.1   2.3   0.00047      0.71       4      21 ..     152     171 ..     151     172 .. 0.89
   3 ?    5.0   0.4      0.02        30       3      20 ..     184     201 ..     182     203 .. 0.82
   4 ?    0.7   1.4      0.48   7.2e+02       6      14 ..     214     222 ..     210     238 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.2e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                                      ++v+dt++Ci+C +C+ aC 
  gi|557694407|ref|YP_008797461.1| 27 AAVFDTNKCIACQTCTVACK 46
                                      579****************7 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00047
                            Fer4_2   4 vvdtdrCigCg..aCvsaCP 21 
                                       ++ +++C++C   aC+ +CP
  gi|557694407|ref|YP_008797461.1| 152 FYLPRICNHCTypACLASCP 171
                                       68899*****889******* PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.02
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       v vd +rC g + Cv+aC
  gi|557694407|ref|YP_008797461.1| 184 VLVDQARCRGYRECVQAC 201
                                       678999999977999999 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.48
                            Fer4_2   6 dtdrCigCg 14 
                                        +++C+ C 
  gi|557694407|ref|YP_008797461.1| 214 ISEKCVLCY 222
                                       5799**996 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.7   1.2e-06    0.0018       1      21 [.      28      48 ..      28      63 .. 0.90
   2 ?    2.6   6.0       0.1   1.6e+02       8      52 ..     158     202 ..     155     207 .. 0.70
   3 ?    3.8   3.4     0.041        62       3      44 ..     186     221 ..     184     227 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                           Fer4_21  1 AridedkCigCgkCliaCedt 21
                                      A++d +kCi C+ C++aC++t
  gi|557694407|ref|YP_008797461.1| 28 AVFDTNKCIACQTCTVACKTT 48
                                      7899**************975 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.1
                           Fer4_21   8 CigCg..kCliaCedtshqaieidakt.vlkvvedeCvGCnlCssvCP 52 
                                       C +C+   Cl +C+      i + ++  ++ v + +C G   C++ C 
  gi|557694407|ref|YP_008797461.1| 158 CNHCTypACLASCPR---LSIYKRPEDgIVLVDQARCRGYRECVQACS 202
                                       667764458888884...556666655155566899*******99995 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.041
                           Fer4_21   3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGC 44 
                                       +d+++C g  +C++aC+   ++ +     ++++ ++++Cv C
  gi|557694407|ref|YP_008797461.1| 186 VDQARCRGYRECVQACS---YKKVF---YNHVTRISEKCVLC 221
                                       79999999999*****9...44443...45777789999988 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.5   3.6e-06    0.0054       2      19 ..      29      46 ..      28      47 .. 0.91
   2 ?   -0.6   0.1      0.89   1.3e+03      13      20 ..     165     172 ..     165     176 .. 0.79
   3 ?    1.5   0.5       0.2   2.9e+02       3      18 ..     186     201 ..     184     203 .. 0.73
   4 ?    2.5   0.1     0.095   1.4e+02       4      11 ..     214     221 ..     211     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.6e-06
                                      EEETTTSSS-THHHHHST CS
                              Fer4  2 videekCigCGaCvevCP 19
                                      v+d++kCi+C +C  +C 
  gi|557694407|ref|YP_008797461.1| 29 VFDTNKCIACQTCTVACK 46
                                      89***************6 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.89
                                       HHHHHSTT CS
                              Fer4  13 aCvevCPv 20 
                                       aC   CP 
  gi|557694407|ref|YP_008797461.1| 165 ACLASCPR 172
                                       7999***7 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.2
                                       EETTTSSS-THHHHHS CS
                              Fer4   3 ideekCigCGaCvevC 18 
                                       +d+ +C g  +Cv++C
  gi|557694407|ref|YP_008797461.1| 186 VDQARCRGYRECVQAC 201
                                       56666666678***** PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.095
                                       ETTTSSS- CS
                              Fer4   4 deekCigC 11 
                                       + ekC+ C
  gi|557694407|ref|YP_008797461.1| 214 ISEKCVLC 221
                                       689***** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   3.0   9.7e-06     0.015       2      20 ..      28      46 ..      27      48 .. 0.93
   2 ?    5.3   1.7     0.015        22       8      20 ..     157     171 ..     153     176 .. 0.86
   3 !    7.1   0.2     0.004       5.9       1      21 [.     183     203 ..     183     207 .. 0.90
   4 ?    2.7   2.3       0.1   1.5e+02       2      14 ..     211     223 ..     210     238 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.7e-06
                            Fer4_6  2 veidpdkCigCgdCvrvCP 20
                                      +++d +kCi C  C+++C 
  gi|557694407|ref|YP_008797461.1| 28 AVFDTNKCIACQTCTVACK 46
                                      79****************7 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
                            Fer4_6   8 kCigC.gd.CvrvCP 20 
                                        C++C ++ C + CP
  gi|557694407|ref|YP_008797461.1| 157 ICNHCtYPaCLASCP 171
                                       7****666******9 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.004
                            Fer4_6   1 vveidpdkCigCgdCvrvCPe 21 
                                       +v +d+ +C g ++Cv +C +
  gi|557694407|ref|YP_008797461.1| 183 IVLVDQARCRGYRECVQACSY 203
                                       5789***************97 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.1
                            Fer4_6   2 veidpdkCigCgd 14 
                                       v+   +kC+ C++
  gi|557694407|ref|YP_008797461.1| 211 VTRISEKCVLCYP 223
                                       677889*****97 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 ?    7.7   0.3    0.0038       5.7       2      21 ..      29      48 ..      29      66 .. 0.81
   2 ?    9.9   0.9   0.00079       1.2       1      24 [.     184     209 ..     184     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0038
                           Fer4_15  2 vvDrdaCigcglCvaeapev 21
                                      v+D ++Ci c  C  ++++ 
  gi|557694407|ref|YP_008797461.1| 29 VFDTNKCIACQTCTVACKTT 48
                                      589**************865 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00079
                           Fer4_15   1 VvvDrdaCigcglCvaea..pevfel 24 
                                       V vD+ +C g   Cv+++  ++vf +
  gi|557694407|ref|YP_008797461.1| 184 VLVDQARCRGYRECVQACsyKKVFYN 209
                                       78****************77777765 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 ?   12.8   0.6     9e-05      0.13       2      30 ..      31      59 ..      30      68 .. 0.81
   2 ?   -2.0   0.6       3.6   5.4e+03      48      56 ..     167     175 ..     158     182 .. 0.71
   3 ?    3.6   0.2     0.064        96       1      16 [.     186     201 ..     186     209 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-05
                           Fer4_13  2 DrdtCiacgaCvelaPdvFeeddeggasv 30
                                      D ++Ciac++C  ++  +    + +++++
  gi|557694407|ref|YP_008797461.1| 31 DTNKCIACQTCTVACKTTWTSGKGQEYMY 59
                                      789************99888777766665 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.6
                           Fer4_13  48 adaCPvesI 56 
                                       +++CP  sI
  gi|557694407|ref|YP_008797461.1| 167 LASCPRLSI 175
                                       456666655 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.064
                           Fer4_13   1 VDrdtCiacgaCvela 16 
                                       VD+ +C +   Cv+++
  gi|557694407|ref|YP_008797461.1| 186 VDQARCRGYRECVQAC 201
                                       9**************9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00012      0.17       3      62 ..      33      46 ..      11      79 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00012
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCp 62
                                      +kCi C+ C+ aC                                              +
  gi|557694407|ref|YP_008797461.1| 33 NKCIACQTCTVAC----------------------------------------------K 46
                                      4555555555555..............................................4 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00031      0.46      42      57 ..      31      46 ..       4      68 .. 0.75
   2 ?   -1.0  15.6       1.9   2.8e+03       2      31 ..     158     191 ..     157     241 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                           Fer4_17 42 kaslCieCgeCerkCP 57
                                        ++Ci C+ C+ +C 
  gi|557694407|ref|YP_008797461.1| 31 DTNKCIACQTCTVACK 46
                                      5677888888887774 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.9
                           Fer4_17   2 CiqCgy..ClpeCpsyeaydnepk..kllraakl 31 
                                       C++C y  Cl++Cp++ +y+  ++   l+ +a++
  gi|557694407|ref|YP_008797461.1| 158 CNHCTYpaCLASCPRLSIYKRPEDgiVLVDQARC 191
                                       *****999**********9997773224444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2876.28
//
Query:       gi|557694408|ref|YP_008797462.1|  [L=707]
Description: molybdopterin oxidoreductase molybdopterin binding subunit, C-terminal [Candidatus Caldiarchaeum subterraneum]
Scores for 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-17   61.0   0.0    1.5e-16   60.4   0.0    1.2  1  Molybdopterin    Molybdopterin oxidoreductase
    0.00091   19.2   0.1      0.052   13.6   0.0    2.7  3  Molydop_binding  Molydopterin dinucleotide 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 !   60.4   0.0   1.7e-20   1.5e-16     195     432 .]      48     300 ..      12     300 .. 0.78

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.7e-20
                                       EECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSS CS
                     Molybdopterin 195 tygkeetdmpllvtleeetgkkkevvariarelarnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgq 271
                                       + +++  +++l++  +  +++++ ++ + + elar +a+++++ +++ G+g nh +++d   r++i +a l++n+g 
  gi|557694408|ref|YP_008797462.1|  48 RPVFDLIKQYLEAFDPYTVSEITWAPPESIEELARLIAANKTRTLFVEGMGPNHFYHSDLKDRGIILVASLTNNIGH 124
                                       556777788888888888999******************************************************** PP

                                       TTCEEEEESS...........CTTHHHCHHHHTCCTTCCCCCCCTT.............HHHHHCCCTTTCSTSS.- CS
                     Molybdopterin 272 pgGgwahlnG...........qlilagaaekvgalpvllsvkslke.............ekikfaaeqpgnlgnf.p 323
                                        gG ++++ G           q         v + p  +      e             +++ + +   ++ ++   
  gi|557694408|ref|YP_008797462.1| 125 FGGTVGSYAGnyrmellngvlQ--------WVTEDPFNP------EldpskparqkkywKEESAHYYAYDDRPLRiG 187
                                       *********9554444433332........222222222......13344446666777444444444455555405 PP

                                       -ECGGCHHHHHHTTSSSEEEEESH.HHH...HSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSEEEEBE-CCG..S CS
                     Molybdopterin 324 rnlfversnllkssgkkvlyllgnnpev...dhadenevekalekldlvvvldgrltstalyaDiiLPaatwyE..k 395
                                       + lf+ + ++++    k+ +++++n +    ++a +  v ++l k +++vv d  +t t++yaD+++   +w E  k
  gi|557694408|ref|YP_008797462.1| 188 GRLFTGKTHMPS--PTKATFWANTNSILgnsKWAHNIMV-NTLPKIEMIVVNDWLWTATCEYADVVFGVDSWAErkK 261
                                       667777777776..6999999999776422267777766.7888******************************888 PP

                                       EEEEE-TTSEEEE..EEESSS-STT-BEHHHHHHHHHHH CS
                     Molybdopterin 396 edlytndegrfqh..lkqavsppgeaksdwkIlkaLakk 432
                                        d+y +   +f +   +   +  ++ ++d ++l  +a+k
  gi|557694408|ref|YP_008797462.1| 262 PDMYGSVTNPFLQawPRTPLPRIYDTRDDLEVLAGIAEK 300
                                       8********999965555566679999999999999886 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.92   8.3e+03       2      19 ..     471     488 ..     471     492 .. 0.83
   2 !   13.6   0.0   5.8e-06     0.052      30      52 ..     514     536 ..     502     540 .. 0.83
   3 ?    2.4   0.0     0.017   1.6e+02      59      82 ..     560     583 ..     556     606 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.92
                                       EEEEE-BTTBSTTTTTCG CS
                   Molydop_binding   2 rLitgrsldqlhsqtrtr 19 
                                       +L+t+++++ +hs+ +++
  gi|557694408|ref|YP_008797462.1| 471 ILVTPKYRHACHSMGAST 488
                                       599**********98766 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 5.8e-06
                                       -EEEEEHHHHHHHT--TT-EEEE CS
                   Molydop_binding  30 evveinpedAaalGikdGdlVev 52 
                                        ++ inp  A++lGi+dGd V++
  gi|557694408|ref|YP_008797462.1| 514 GYIDINPIVAKKLGIEDGDYVWC 536
                                       499******************96 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.017
                                       EEEEEEEESSB-TTEEEEESSHCC CS
                   Molydop_binding  59 vevrakvtervrpGvvfmpfgwwe 82 
                                         vra+  ++++pGv+ + f+++ 
  gi|557694408|ref|YP_008797462.1| 560 WLVRARHYPNIAPGVARAWFHFYV 583
                                       5799*****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (707 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 4813.10
//
Query:       gi|557694409|ref|YP_008797463.1|  [L=446]
Description: molybdopterin oxidoreductase molybdopterin binding subunit, N-terminal [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-21   77.1   0.0    1.4e-18   67.1   0.0    2.1  2  Molybdopterin  Molybdopterin oxidoreductase


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 !    7.9   0.0   7.2e-05       1.3      10      41 ..     170     201 ..     131     210 .. 0.78
   2 !   67.1   0.0   7.6e-23   1.4e-18      75     196 ..     276     390 ..     268     428 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 7.2e-05
                                       TTTTTSEEEE--HHHHHHHHHHHHHHHHHHCS CS
                     Molybdopterin  10 qargeGkFvrvsWdeAleliaaslkytikkyg 41 
                                       + rg+ +Fv+v  +eA++++a+ l++++ +y 
  gi|557694409|ref|YP_008797463.1| 170 SGRGKEEFVKVPFEEAFKIVAQTLLNIVATYS 201
                                       6799***********************99985 PP

  == domain 2  score: 67.1 bits;  conditional E-value: 7.6e-23
                                       -BEECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB CS
                     Molybdopterin  75 sfydwyadlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpry 151
                                        +y w  dlpp+++      + + n  +  +l+  en+++iilwG N   + +++ ++ + +a+ k+ak++ i p+y
  gi|557694409|ref|YP_008797463.1| 276 DNYAWHTDLPPGHP------MVTGNKTLDFDLYTAENAKVIILWGKNWIATKMPD-GHWLTEAKLKGAKIVTIAPEY 345
                                       6899********98......334455677889999********************.89999888889********** PP

                                       -HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEE CS
                     Molybdopterin 152 aellkfadewlaikpgtdaalalamghvilqelkvdkeflrkyty 196
                                       ++++++ad  + i++gtd+a+al+++hv+++  ++d++f+++ t 
  gi|557694409|ref|YP_008797463.1| 346 QSSSSKADYVIVIRAGTDQAFALGLAHVLIRDRLYDEKFVKSFTD 390
                                       **99*********************************99776553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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 0.27s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 3032.35
//
Query:       gi|557694410|ref|YP_008797464.1|  [L=225]
Description: bacterio-opsin activator HTH domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-17   62.3   0.1    4.1e-17   61.7   0.1    1.3  1  HTH_10    HTH DNA binding domain
  ------ inclusion threshold ------
       0.12   11.9   0.0       0.48   10.0   0.0    2.0  2  HTH_24    Winged helix-turn-helix DNA-binding
       0.13   12.1   0.0       0.32   10.8   0.0    1.7  1  HTH_DeoR  DeoR-like helix-turn-helix 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 !   61.7   0.1   6.9e-21   4.1e-17       1      53 []     154     206 ..     154     206 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 6.9e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LT +q  ++k+A+e+G+FdyP+++++keLA+ +GI+++tl+e +rka++++++
  gi|557694410|ref|YP_008797464.1| 154 LTSRQELIIKAALELGFFDYPKKIHVKELAQLFGITPATLTETMRKAMKRIVK 206
                                       9*************************************************985 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 ?   -1.6   0.0      0.35   2.1e+03      35      46 ..     127     138 ..     124     138 .. 0.85
   2 ?   10.0   0.0     8e-05      0.48      18      43 ..     177     202 ..     174     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.35
                            HTH_24  35 nrrlkrLeeeGl 46 
                                       +r ++rL e G+
  gi|557694410|ref|YP_008797464.1| 127 RRFMQRLSERGI 138
                                       68899**99997 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 8e-05
                            HTH_24  18 isqreLAerlglSpstvnrrlkrLee 43 
                                       i  +eLA+  g++p+t+++ +++ ++
  gi|557694410|ref|YP_008797464.1| 177 IHVKELAQLFGITPATLTETMRKAMK 202
                                       6789*****************99776 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 ?   10.8   0.0   5.3e-05      0.32      14      30 ..     176     192 ..     172     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.3e-05
                          HTH_DeoR  14 klsveelvellgvSeaT 30 
                                       k++v+el++l+g+++aT
  gi|557694410|ref|YP_008797464.1| 176 KIHVKELAQLFGITPAT 192
                                       89*************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
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: 1592.39
//
Query:       gi|557694411|ref|YP_008797465.1|  [L=506]
Description: mercuric reductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-62  209.0   0.1    1.2e-61  208.6   0.1    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    8.2e-20   71.1   0.0      2e-19   69.9   0.0    1.7  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    6.7e-16   58.6   3.0    1.8e-14   54.0   0.2    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.3e-12   46.8   1.4    2.6e-10   40.0   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      3e-08   33.2   0.6    2.8e-06   26.7   0.0    3.4  4  GIDA            Glucose inhibited division protein A
     0.0002   21.5   0.2        1.1    9.5   0.0    2.6  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00071   18.4   4.6       0.22   10.2   0.1    2.9  4  HI0933_like     HI0933-like protein
     0.0038   17.2   0.5       0.77    9.7   0.0    2.8  3  NAD_binding_9   FAD-NAD(P)-binding
     0.0047   16.3   0.1       0.07   12.5   0.0    2.1  2  FAD_oxidored    FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.014   15.0   0.1        2.8    7.4   0.0    2.5  2  DAO             FAD dependent oxidoreductase
      0.044   13.1   0.2        8.3    5.6   0.0    2.4  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.046   12.8   6.6       0.15   11.1   1.1    3.4  4  FAD_binding_2   FAD binding domain
       0.05   13.7   0.0        0.1   12.7   0.0    1.4  1  P2              P2 response regulator binding domain
      0.057   13.3   0.2       0.13   12.1   0.1    1.6  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      0.059   12.2   0.4      0.098   11.5   0.4    1.3  1  Trp_halogenase  Tryptophan halogenase
       0.28   10.2   4.5        8.3    5.3   0.4    2.9  3  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 !  208.6   0.1     1e-64   1.2e-61       2     279 ..       5     317 ..       4     338 .. 0.87

  Alignments for each domain:
  == domain 1  score: 208.6 bits;  conditional E-value: 1e-64
                                       SEEEE--SHHHHHHHHHHHH...HTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH............... CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq...agakvtlve...legtclnggcllskallgvaedaeias............... 57 
                                       ++v+iGgG+A+++aa+++++   +++ +++++   l+gtc+n+gc++sk l ++a++++  +               
  gi|557694411|ref|YP_008797465.1|   5 ELVIIGGGAAAFSAAIKASElteNKLSILMISagkLGGTCVNVGCVPSKYLIEAAKHYHSSHtplfdgvtpkgadld 81 
                                       68******************9989*******8889************************999*************** PP

                                       ..HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC.............TCEEEEEESEEEE---EEE-BCTCTTC CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ..evvkklnqgielllgeevvkidpgkkkvklekkke.............gdeekiaydklvlAtGssprdlgipGv 119
                                         + +++l+  ++++ ge++ ++ +   +v+l + ++             +  ++++++k ++AtGs+p +++ipG+
  gi|557694411|ref|YP_008797465.1|  82 fgKLMESLRRFVDVMRGEKYADVLKHYPNVELIEGRGsftsphtiavetrDGVREVEFEKALIATGSRPAIPNIPGL 158
                                       **5555555555555554444554444455544444445555555599998889*********************** PP

                                       .TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 120 aenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealeke 196
                                       ++n+     +++++  +  + lp++++ vG G++G+E+ +a+ +lg++vtlve +dr+l+++++e+s +l + l +e
  gi|557694411|ref|YP_008797465.1| 159 EKNG-----YYTTDTIWDMDTLPENTLLVGRGAVGLEIGQAMQRLGSQVTLVELLDRILPNMESEISSTLSKILADE 230
                                       7777.....5789999999999******************************************************* PP

                                       TEEEEESCEEEEEEETTE..EEEEEETTSCE.EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESST CS
                                       xxxxxxxxxxxxxxxxxx..xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 197 Gvevklgtsvkeidgnge..klevvledgee.idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvp 269
                                       G +++++++v+e+ ++g+  ++e v+++g++ i+ d v++a+G++p+t+  + ek+ +++d+rg+i+vde++rt+ p
  gi|557694411|ref|YP_008797465.1| 231 GMRIMTKARVVEFSRHGDlgQAEIVTNEGRQtIEFDAVLIATGRKPNTDRMGlEKSSVAVDNRGFIKVDETMRTSSP 307
                                       ******************98888666666666********************************************* PP

                                       TEEE-GGGCT CS
                                       xxxxxxxxxx RF
                       Pyr_redox_2 270 giyaiGDvag 279
                                       +iya+GD++ 
  gi|557694411|ref|YP_008797465.1| 308 NIYAAGDCIA 317
                                       ********92 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 !   69.9   0.0   1.8e-22     2e-19       1      90 [.     350     438 ..     350     452 .. 0.94

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 1.8e-22
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       +p vvft+p+vasvGlte e+ +  +++++  +++k++++a++ +  +g++Klv++ ++g+vlG+hiv+p+a+e i 
  gi|557694411|ref|YP_008797465.1| 350 VPLVVFTEPQVASVGLTEREVVKRFGACSCRVVSLKNVAKARMTG-GRGLAKLVINPNDGRVLGVHIVSPNAAEYIT 425
                                       799***************************************997.89***************************** PP

                                       HHHHHHHTTSBHH CS
                     Pyr_redox_dim  78 elavaikagltve 90 
                                       e+a+ ik+g +++
  gi|557694411|ref|YP_008797465.1| 426 EAALYIKYGKKTH 438
                                       ********98765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.047        53       2      22 ..       6      26 ..       5      39 .. 0.85
   2 !   54.0   0.2   1.6e-17   1.8e-14       3      71 ..     180     248 ..     178     259 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.047
                                      EEEECSSHHHHHHHHHHHHTT CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg 22
                                      +v++GgG  +  +A  ++el 
  gi|557694411|ref|YP_008797465.1|  6 LVIIGGGAAAFSAAIKASELT 26
                                      79************9998875 PP

  == domain 2  score: 54.0 bits;  conditional E-value: 1.6e-17
                                       EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox   3 vvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsed 71 
                                       + vG G +glE ++a+++lg++Vt+ve  d++l++++ e+s+ l + l ++g++++++++v+e+  ++d
  gi|557694411|ref|YP_008797465.1| 180 LLVGRGAVGLEIGQAMQRLGSQVTLVELLDRILPNMESEISSTLSKILADEGMRIMTKARVVEFSRHGD 248
                                       679*************************************************************98887 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 !    5.1   1.0    0.0099        11       1      27 [.       7      33 ..       7      46 .. 0.79
   2 !   40.0   0.0   2.4e-13   2.6e-10     115     305 .]     127     313 ..     119     313 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0099
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylil 27
                                      +IiG+G+a  +aai++ ++  +++ il
  gi|557694411|ref|YP_008797465.1|  7 VIIGGGAAAFSAAIKASELTENKLSIL 33
                                      7*************9998887666554 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 2.4e-13
                       Pyr_redox_3 115 evetske..tyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefh.kyagqkvvViGgknSavDaAlelvrkga 188
                                        vet+ +  ++e +k +iAtG   +P  +nipG e +   y +++ ++ ++  ++ + +G +  + ++   + r g+
  gi|557694411|ref|YP_008797465.1| 127 AVETRDGvrEVEFEKALIATGS--RPAIPNIPGLE-KNGYYTTDTIWDmDTLPENTLLVGRGAVGLEIGQAMQRLGS 200
                                       6788887667888999*****9..**********9.566666666553145589*********************** PP

                       Pyr_redox_3 189 eVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikeke..eeykvktedgkkvevkddvvl 263
                                       +Vt+v   + i  +   ++ +++ +  + l    + e ++++++a+v e +++    + ++ t++g+++ + d v++
  gi|557694411|ref|YP_008797465.1| 201 QVTLVELLDRILPN---MESEISSTLSKIL----ADEGMRIMTKARVVEFSRHGdlGQAEIVTNEGRQTIEFDAVLI 270
                                       *****998766554...4444554444444....4466999999999999987622477899*************** PP

                       Pyr_redox_3 264 atGykpdlsf..lkkslfeldedgrpvlteeteetnvpglflaG 305
                                       atG kp+++   l+ks ++ d+ g+++++ et+ t  p+++ aG
  gi|557694411|ref|YP_008797465.1| 271 ATGRKPNTDRmgLEKSSVAVDNRGFIKVD-ETMRTSSPNIYAAG 313
                                       *******9875688899999999999997.699*********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 !   26.7   0.0   2.5e-09   2.8e-06       2     150 ..       6     148 ..       5     169 .. 0.84
   2 ?   -0.2   0.1      0.37   4.2e+02       4      33 ..     181     209 ..     178     219 .. 0.85
   3 ?    0.7   0.0       0.2   2.2e+02     113     150 ..     226     274 ..     213     292 .. 0.70
   4 ?    0.2   0.0      0.27     3e+02     345     385 ..     297     338 ..     280     342 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.5e-09
                                       EEEE-SSHHHHHHHHHHHHT...T--EEEE..ES-GGGTT--SSSSEEE-T..THHHHHHHHHHHT-SHHHHHHHHE CS
                              GIDA   2 viViGgGhAGceAAlaaarl...GakvlLi..thkldtiaelsCnpsiggi..akgllvrEidalggliikaadkag 71 
                                       +++iGgG A + AA++a++l    +++l+i   +  +t+++++C ps + i  ak         ++g+  k ad   
  gi|557694411|ref|YP_008797465.1|   6 LVIIGGGAAAFSAAIKASELtenKLSILMIsaGKLGGTCVNVGCVPSKYLIeaAKHYHSSHTPLFDGVTPKGADLDF 82 
                                       69**************997622156666669778889**************966666777788889********998 PP

                                       EEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS.-EEEECEEEE- CS
                              GIDA  72 iqfrilNrskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedg.etikakavvia 147
                                                 G+ +++lr  vd  +  +++ ++l+++pn+e+ie++ +  ++   ++ +v t+dg ++++ ++  ia
  gi|557694411|ref|YP_008797465.1|  83 ----------GKLMESLRRFVDVMRG-EKYADVLKHYPNVELIEGRGSFTSP---HTIAVETRDGvREVEFEKALIA 145
                                       ..........799*********9875.56789****************9988...66667776663689999***** PP

                                       -TT CS
                              GIDA 148 tGt 150
                                       tG+
  gi|557694411|ref|YP_008797465.1| 146 TGS 148
                                       **9 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.37
                                       EE-SSHHHHHHHHHHHHTT--EEEEES-GG CS
                              GIDA   4 ViGgGhAGceAAlaaarlGakvlLithkld 33 
                                        +G G  G+e   a+ rlG +v+L+ + ld
  gi|557694411|ref|YP_008797465.1| 181 LVGRGAVGLEIGQAMQRLGSQVTLV-ELLD 209
                                       6999********************9.4444 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.2
                                       EEES-EEEEEECT...........TEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 113 iieeeveelivee...........kkvkgvvtedgetikakavviatGt 150
                                       i+ +e ++++++            ++ + v+ e  +ti+ +av iatG 
  gi|557694411|ref|YP_008797465.1| 226 ILADEGMRIMTKArvvefsrhgdlGQAEIVTNEGRQTIEFDAVLIATGR 274
                                       5555555554444555555666777888888899999999999999996 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.27
                                       GB-TTSBBSSSBTEEE-CGGGTB-SHHHHHH..HHHHHHHHHH CS
                              GIDA 345 qllntLetkkvkgLflAGqinGteGYeEaaa..qGllAGinaa 385
                                       ++ +t++t+  +++++AG+       +E  +   G++A+ n++
  gi|557694411|ref|YP_008797465.1| 297 KVDETMRTS-SPNIYAAGDCIAKPLMLETLSarEGVVAASNIV 338
                                       346799998.9*******9988777777554457888877775 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 !    9.4   0.1    0.0011       1.2       1      35 [.       8      44 ..       8      69 .. 0.80
   2 !    9.5   0.0   0.00099       1.1       2      54 ..     182     237 ..     181     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                                      EE--SHHHHHHHHHHHC...CTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLak...agfdvlllekrdrlGGra 35
                                      I+G+G+++ +aA  +++   +++++l + ++ +lGG +
  gi|557694411|ref|YP_008797465.1|  8 IIGGGAAAFSAAIKASElteNKLSILMISAG-KLGGTC 44
                                      9***********9987633258899999665.888877 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00099
                                       E--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE...TTCEECTS---EEE CS
                     NAD_binding_8   2 vGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev...pgvrvdygahifhg 54 
                                       vG G+ Gl + +++++ g +v+l+e  dr+  ++ s+      ++ +d g++i+++
  gi|557694411|ref|YP_008797465.1| 182 VGRGAVGLEIGQAMQRLGSQVTLVELLDRILPNMESEISstlSKILADEGMRIMTK 237
                                       99****************************99999997744466999999999876 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.5   0.00056      0.63       2      28 ..       5      34 ..       4      45 .. 0.73
   2 ?   -3.7   0.0       3.2   3.6e+03     143     165 ..     126     149 ..     122     155 .. 0.77
   3 ?   -0.9   0.0      0.44     5e+02       3      31 ..     179     207 ..     177     213 .. 0.87
   4 !   10.2   0.1    0.0002      0.22      99     165 ..     209     275 ..     191     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00056
                                      SEEEE--SHHHHHHHHHH...HHTT--EEE CS
                       HI0933_like  2 dviviGgGaAGlmaAisa...akrgkrVll 28
                                      ++++iGgGaA + aAi+a    +++ ++l+
  gi|557694411|ref|YP_008797465.1|  5 ELVIIGGGAAAFSAAIKAselTENKLSILM 34
                                      689**************9433344445555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.2
                                       EEEEE..TTEEEEESEEEE----S CS
                       HI0933_like 143 frvkt.kseeeleadklvlAtGGl 165
                                       + v+t ++ +e+e +k ++AtG+ 
  gi|557694411|ref|YP_008797465.1| 126 IAVETrDGVREVEFEKALIATGSR 149
                                       56777677889999******9975 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.44
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllek 31 
                                       ++ +G Ga Gl    ++++ g++V+l+e 
  gi|557694411|ref|YP_008797465.1| 179 TLLVGRGAVGLEIGQAMQRLGSQVTLVEL 207
                                       6789**********************996 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0002
                                       TEEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETT.E.EEEEE..TTEEEEESEEEE----S CS
                       HI0933_like  99 grlFpvsdkaedivdallkelkeagvklrletevksvekeed.gkfrvkt.kseeeleadklvlAtGGl 165
                                       +r+ p+    ++i ++l k l ++g++++++ +v +++++ d g+ ++ t ++++++e d++++AtG +
  gi|557694411|ref|YP_008797465.1| 209 DRILPNM--ESEISSTLSKILADEGMRIMTKARVVEFSRHGDlGQAEIVTnEGRQTIEFDAVLIATGRK 275
                                       5666665..468999**********************877653667777768999************65 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 ?    4.7   0.1     0.024        27       1      39 [.       7      42 ..       7      60 .. 0.87
   2 ?   -2.5   0.0       4.1   4.5e+03     133     154 ..     125     147 ..     116     148 .. 0.82
   3 !    9.7   0.0   0.00068      0.77     120     155 ..     236     274 ..     218     275 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.024
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgag 39
                                      +i+G+G+++ +++ +  +    +++l+i ++   ++g g
  gi|557694411|ref|YP_008797465.1|  7 VIIGGGAAAFSAAIKASELT--ENKLSILMISAGKLG-G 42
                                      7**************99996..999999999887776.4 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.1
                     NAD_binding_9 133 gqavlladg.aslaadaVvLAlG 154
                                       + av ++dg +++++++  +A+G
  gi|557694411|ref|YP_008797465.1| 125 TIAVETRDGvREVEFEKALIATG 147
                                       5578898996779********99 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00068
                     NAD_binding_9 120 hraevvdleeradg.q.avlladg.aslaadaVvLAlGh 155
                                        +a+vv+ ++++d  q ++++++g +++++daV +A+G 
  gi|557694411|ref|YP_008797465.1| 236 TKARVVEFSRHGDLgQaEIVTNEGrQTIEFDAVLIATGR 274
                                       4789999999886434488888773568**********6 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   6.3e-05      0.07       2      43 ..       6      49 ..       5     141 .. 0.84
   2 ?    1.9   0.0       0.1   1.1e+02      90     144 ..     220     273 ..     183     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-05
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAar..aGakvlLveergvlGGlltsglv 43
                                      +v++GGg+a + AAi A +  + +  +L    g lGG+  + + 
  gi|557694411|ref|YP_008797465.1|  6 LVIIGGGAAAFSAAIKASEltENKLSILMISAGKLGGTCVNVGC 49
                                      79***************872256678888889999999887665 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.1
                      FAD_oxidored  90 kavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDATg 144
                                        ++l ++la++g+++++++r+ve  + g ++ + ++ ++egr+ti+ + ++ ATg
  gi|557694411|ref|YP_008797465.1| 220 SSTLSKILADEGMRIMTKARVVEFSRHG-DLGQAEIVTNEGRQTIEFDAVLIATG 273
                                       56788899999***************98.88888888999999998777777765 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.013        15       2      39 ..       6      45 ..       5     113 .. 0.73
   2 ?    7.4   0.0    0.0025       2.8     154     201 ..     225     273 ..     218     298 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                                      EEEECTSHHHHHHHHHHHHTT.....EEEEESSSSTTSSGGGS CS
                               DAO  2 vviiGGGiiGlstAyeLarrg.....VtllekgdiagsgaSgr 39
                                      +viiGGG +  s+A  +++       ++ + +g  +g g +  
  gi|557694411|ref|YP_008797465.1|  6 LVIIGGGAAAFSAAIKASELTenklsILMISAG-KLG-G-TCV 45
                                      69***************7752246899999999.665.3.444 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0025
                                       HHHHHTT-EEEESECEEEEEEEE..TCEEEEEEECTEEE.EEEEEEEE--G CS
                               DAO 154 raaealGveilegtevtgleeed..gkvwgverttpgen.daadavVnaaG 201
                                       + +++ G +i ++++v+++++++  g++  v  t++g++  ++dav +a+G
  gi|557694411|ref|YP_008797465.1| 225 KILADEGMRIMTKARVVEFSRHGdlGQAEIV--TNEGRQtIEFDAVLIATG 273
                                       5578899************887666665555..5558776688*******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 ?    5.1   0.0     0.011        12      30      51 ..       5      26 ..       1      33 [. 0.87
   2 ?    5.6   0.0    0.0074       8.3      29      72 ..     177     221 ..     172     259 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.011
                                      EEEEESTSHHHHHHHHHHHHTT CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglg 51
                                      + ++iGgG a  +A+  a++l 
  gi|557694411|ref|YP_008797465.1|  5 ELVIIGGGAAAFSAAIKASELT 26
                                      679*************999886 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0074
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTT CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lga 72 
                                        ++l +G G +Gl+  ++ ++lg +Vt++++  + l ++es + +
  gi|557694411|ref|YP_008797465.1| 177 ENTLLVGRGAVGLEIGQAMQRLGSQVTLVELLDRILPNMESeISS 221
                                       57899************************9988888888875444 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.1   0.00013      0.15       2      32 ..       6      39 ..       5      46 .. 0.74
   2 ?   -1.4   0.1      0.84   9.4e+02       3      31 ..     180     208 ..     178     233 .. 0.90
   3 ?   -0.6   0.0      0.49   5.5e+02     147     204 ..     223     277 ..     212     292 .. 0.73
   4 ?    2.0   0.0     0.077        87     376     403 ..     296     317 ..     288     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                      EEEE--SHHHHHHHHHHHH...TTT-EEEEESSS CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaae...aGlkvavvekeq 32
                                      +++iG+G+A  +AA++a+e   + l++++++ ++
  gi|557694411|ref|YP_008797465.1|  6 LVIIGGGAAAFSAAIKASElteNKLSILMISAGK 39
                                      79*************9987552344666666655 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.84
                                       EEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                     FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavveke 31 
                                       + +G G+ GL  + ++++ G +v++ve  
  gi|557694411|ref|YP_008797465.1| 180 LLVGRGAVGLEIGQAMQRLGSQVTLVELL 208
                                       679***********************976 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.49
                                       HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                       l + + + g++++++++++e+ +  g+   a++   +++++++i+ +av++atg  ++
  gi|557694411|ref|YP_008797465.1| 223 LSKILADEGMRIMTKARVVEFSR-HGDLGQAEIV--TNEGRQTIEFDAVLIATGRKPN 277
                                       55556666788888899999977.5555556666..7888888999999999996665 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 0.077
                                       EEBETTSBESTTEEESSBTEEE-STCEE CS
                     FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaa 403
                                       +++de++r+        p+ YAaG ++a
  gi|557694411|ref|YP_008797465.1| 296 IKVDETMRT------SSPNIYAAGDCIA 317
                                       789999999......*********9985 PP

>> P2  P2 response regulator binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   8.9e-05       0.1       8      63 ..      80     136 ..      78     143 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.9e-05
                                       --TT-SSHHHHHHHHHHHHHHTTEEEEEES-HHHHHT.T-SSSEEEEEEEESS-HHH CS
                                P2   8 ldedclmksvRaflvfkaLeelgeiiksiPsvediee.ekfdegfevvlltkeskee 63 
                                       ld + lm+s+R f+ + + e++++++k +P+ve ie  + f +  ++ + t     e
  gi|557694411|ref|YP_008797465.1|  80 LDFGKLMESLRRFVDVMRGEKYADVLKHYPNVELIEGrGSFTSPHTIAVETRDGVRE 136
                                       566789******************************977777777777766655555 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 ?   12.1   0.1   0.00012      0.13       5      56 ..     182     233 ..     179     255 .. 0.87
   2 ?   -3.8   0.0       9.1     1e+04     129     140 ..     407     418 ..     404     421 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                       E--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS- CS
                           3HCDH_N   5 iGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk 56 
                                       +G G +G +i +++ + g +V+lv+  +++l + +++i+++l+k  +++ + 
  gi|557694411|ref|YP_008797465.1| 182 VGRGAVGLEIGQAMQRLGSQVTLVELLDRILPNMESEISSTLSKILADEGMR 233
                                       9*****************************************9988776655 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 9.1
                                       GGGEEEEEE-SS CS
                           3HCDH_N 129 perviglHFfnP 140
                                       + rv+g+H ++P
  gi|557694411|ref|YP_008797465.1| 407 DGRVLGVHIVSP 418
                                       679******999 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   8.8e-05     0.098       2      47 ..       6      51 ..       5      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.8e-05
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--T CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatip 47
                                      +vi+GGG a++ aA+  ++ +++kl+++++ + ++g   v  + +p
  gi|557694411|ref|YP_008797465.1|  6 LVIIGGGAAAFSAAIKASELTENKLSILMISAGKLGGTCVNVGCVP 51
                                      79*******************999********99997766655555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.4    0.0074       8.3       2      33 ..       6      38 ..       5      43 .. 0.76
   2 ?    0.6   0.1      0.21   2.3e+02       4      35 ..     181     210 ..     179     217 .. 0.87
   3 ?    4.0   0.0     0.019        21      90     147 ..     220     278 ..     215     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0074
                     Lycopene_cycl  2 vvviGaGpAglslAarlte.akpglkvvlieas 33
                                      +v+iG+G+A  s A +  e  + +l++++i a+
  gi|557694411|ref|YP_008797465.1|  6 LVIIGGGAAAFSAAIKASElTENKLSILMISAG 38
                                      89**********987763325667778877665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.21
                     Lycopene_cycl   4 viGaGpAglslAarlteakpglkvvlieasps 35 
                                       ++G G+ gl + + +  ++ g +v+l+e  + 
  gi|557694411|ref|YP_008797465.1| 181 LVGRGAVGLEIGQAM--QRLGSQVTLVELLDR 210
                                       79*************..**********96655 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.019
                     Lycopene_cycl  90 keellerlv.engvklleakvesveeeea.geslvvleggr.kirarlvvdarglaslkka 147
                                        + l + l+ e+ +++++a+v +   + + g+  +v+++gr +i+  +v+ a+g  ++++ 
  gi|557694411|ref|YP_008797465.1| 220 SSTLSKILAdEGMRIMTKARVVEFSRHGDlGQAEIVTNEGRqTIEFDAVLIATG--RKPNT 278
                                       566777788566678999***999988888*******999999**********9..44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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 0.26s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3470.47
//
Query:       gi|557694412|ref|YP_008797466.1|  [L=128]
Description: transcriptional regulator, HxlR family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-22   77.1   0.2    1.1e-21   76.5   0.2    1.3  1  HxlR      HxlR-like helix-turn-helix
     0.0086   16.2   0.1      0.025   14.7   0.0    1.8  2  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d
  ------ inclusion threshold ------
      0.018   15.0   0.1      0.027   14.4   0.1    1.4  1  PadR      Transcriptional regulator PadR-like family
      0.033   13.6   0.0      0.042   13.3   0.0    1.2  1  RepL      Firmicute plasmid replication protein (RepL)
      0.039   13.9   0.0      0.062   13.2   0.0    1.3  1  MarR      MarR family


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 !   76.5   0.2     3e-25   1.1e-21       1      86 [.      20     106 ..      20     110 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 3e-25
                                       HHHSTTHHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHH CS
                              HxlR   1 liggkWkllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvl 76 
                                       li++kW+lli+ e+ + g+ R++ l ++l +is k+L+ +L++L +++l++re+y+e+Pp+veY+lt++G +l+++ 
  gi|557694412|ref|YP_008797466.1|  20 LISKKWSLLIVNEIGNhGRIRYNMLMKELDGISPKILSDTLKALIKHNLVKREAYNEIPPRVEYTLTKEGDELRAAT 96 
                                       699***********999************************************************************ PP

                                       HHHHHHHHHH CS
                              HxlR  77 qelkkwgeey 86 
                                         + +w+ ++
  gi|557694412|ref|YP_008797466.1|  97 IPILQWALKQ 106
                                       ******8765 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 !   14.7   0.0   6.9e-06     0.025      24      58 ..      35      70 ..      28      70 .. 0.90
   2 ?   -2.9   0.0       2.1   7.7e+03      13      27 ..     109     123 ..     108     124 .. 0.64

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.9e-06
                                      HHSSBEHHHHHHHHS.STHHHHHHHHHHHHHTTSEE CS
                             HTH_9 24 rkgrltlrelvkktk.LsldqVkksLvvLiqhrlVq 58
                                      ++gr   ++l k+++ +s++   ++L +Li+h+lV+
  gi|557694412|ref|YP_008797466.1| 35 NHGRIRYNMLMKELDgISPKILSDTLKALIKHNLVK 70
                                      688888999*************************96 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                                       THHHHHHHHHHHHSS CS
                             HTH_9  13 evvakVvetLlrkgr 27 
                                       +v a    tL++kg+
  gi|557694412|ref|YP_008797466.1| 109 TVIAHCSCTLIEKGK 123
                                       555666667888876 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   7.4e-06     0.027      36      72 ..      58      92 ..      27      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.4e-06
                                      HHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                              PadR 36 paLkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                      ++Lk L k++lv++e  +  e ppr  Y+lT++G++ 
  gi|557694412|ref|YP_008797466.1| 58 DTLKALIKHNLVKREAYN--EIPPRVEYTLTKEGDEL 92
                                      689***********9887..69************875 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.2e-05     0.042      65     109 ..      30      73 ..       8      88 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                              RepL  65 idnlnsnntliatnRelaeetgislktvsetlkileeanilkkka 109
                                       ++++  n   i  n ++ e  gis k  s tlk+l + n++k++a
  gi|557694412|ref|YP_008797466.1|  30 VNEIG-NHGRIRYNMLMKELDGISPKILSDTLKALIKHNLVKREA 73 
                                       44443.44557888899999***********************87 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.7e-05     0.062       8      51 ..      29      73 ..      26      76 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHSTTEEHHHHH.HHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  8 iLrilyeqgplsvseLa.kklgvskstvtrvldrLekkGlieRsk 51
                                      i+  + ++g ++   L  +  g+s+  ++ +l++L+k++l++R+ 
  gi|557694412|ref|YP_008797466.1| 29 IVNEIGNHGRIRYNMLMkELDGISPKILSDTLKALIKHNLVKREA 73
                                      5566777788777755404558*********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1015.06
//
Query:       gi|557694413|ref|YP_008797467.1|  [L=472]
Description: hypothetical protein CSUB_C0984 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   59.8   0.1    4.8e-16   59.2   0.1    1.3  1  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 !   59.2   0.1   2.7e-20   4.8e-16       2     241 ..      88     436 ..      87     437 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 2.7e-20
                                       EEEEEEEEEEEE.EETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGG. CS
                              NurA   2 rvaAvDGSngvv.rlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgalllee. 76 
                                       +v+++DGS+  +  + gg+ly+++a++v g++++r+ e  +  s  s  + d+  r + + me lE+++++ +le+ 
  gi|557694413|ref|YP_008797467.1|  88 KVVGIDGSRALRlYVVGGVLYVVRAVGVYGKHRIRELEVDAFTSASS--SRDI-NRFVNRKMEWLEHRAALHALEKf 161
                                       699******9999999*****************99988755555555..4455.99999999999999888877775 PP

                                       CCSCEEEEECSHHCCCH....HHHHHHHHHHHHHHHHHHHHHTT-....TTCEEEEESS-SCTCCHCCC........ CS
                              NurA  77 kgedllllDGsligslv....efdelheeleyeeylyslsrllea....glnlvgvaKsfrskellnll........ 137
                                       ++++ +l+DG+l+g  +    +++++   + ++ y++ +   le+    ++ ++gv+K++rs+ ++ +         
  gi|557694413|ref|YP_008797467.1| 162 DDVECVLIDGTLHGRMMavprDSAAEGQKDFMLQYFQDYTAFLEEcrrrNVVPIGVSKDSRSTHFKTYFlslileny 238
                                       89*******************999***************************************************** PP

                                       ............................................S--HHHHCCHHCCHCH---STTS-HHHHTT... CS
                              NurA 138 ......................................letlligesisDiallgallrkpgytspllkilrek... 173
                                                                             +   + + s++D++++  ++++ g+t+pl  + ++    
  gi|557694413|ref|YP_008797467.1| 239 fdvsktgsqqlekllsmlfemadeevkkqfttnsvvlaNVFREATSSVTDHQIIRNYAEEAGFTQPLEIGVYGRgar 315
                                       ************************************99999999********************9999999998999 PP

                                       ..................................-HCCHHHHHH-.EEEEEEESSTTTTEEEEEHHHHHH.C..... CS
                              NurA 174 ..................................pllrealidke.iyfaYvrlegggsilrleipaevs.t..... 209
                                                                          +  ++   ++ i+++ + l++ +s+lr+++p ++        
  gi|557694413|ref|YP_008797467.1| 316 lvgqfiespihyihrnfpeafeeagdkasflewgRRVLSKILRLPtIVSFHILLDRRDSPLRIDVPSWYFgLdntls 392
                                       9****************9999999999999988855555555666699999999**************764388899 PP

                                       ............CHHHHHHHHHH..TTB-SS....SBCCHHHHHHHHC CS
                              NurA 210 ............akdedvlsllasqrlsisG....YprpLalAhelak 241
                                                   ++ e ++ +l      + G    Y+++L  A++++k
  gi|557694413|ref|YP_008797467.1| 393 dkigvspmnvrpDLLERIVATLM----RGYGglrnYNVWLVQADKEVK 436
                                       99999999555555555555555....444434447777999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3506.34
//
Query:       gi|557694414|ref|YP_008797468.1|  [L=495]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  134.2   0.0    1.3e-38  133.4   0.0    1.3  1  DUF87            Helicase HerA, central domain
    2.4e-07   30.0   0.0    3.9e-05   22.7   0.0    2.1  2  AAA_10           AAA-like domain
    0.00012   21.1   0.0     0.0085   15.0   0.0    2.3  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
    0.00019   21.7   0.0      0.036   14.3   0.0    2.7  2  AAA_22           AAA domain
    0.00021   20.0   0.0      0.048   12.3   0.0    2.1  2  DUF853           Bacterial protein of unknown function (DUF85
    0.00031   20.4   0.0    0.00074   19.2   0.0    1.6  1  Zot              Zonular occludens toxin (Zot)
     0.0023   16.8   0.0     0.0031   16.4   0.0    1.2  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
  ------ inclusion threshold ------
      0.015   15.3   0.0       0.17   11.9   0.0    2.2  2  ResIII           Type III restriction enzyme, res subunit
      0.029   13.7   0.0       0.78    9.0   0.0    2.6  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.11   12.3   0.0       0.22   11.3   0.0    1.6  1  Helicase_RecD    Helicase


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 !  133.4   0.0     7e-42   1.3e-38       1     227 []     102     324 ..     102     324 .. 0.93

  Alignments for each domain:
  == domain 1  score: 133.4 bits;  conditional E-value: 7e-42
                             DUF87   1 ieiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal......ekl 71 
                                       +++G+l+++ +vpv l +  + +rHlAi+++TG+GKS++++vLleell +kgatil+lDpH++Y++++        +
  gi|557694414|ref|YP_008797468.1| 102 LHVGHLITRPDVPVHLSVRGF-RRHLAIIAQTGAGKSYLAGVLLEELL-SKGATILVLDPHSDYVRLTmtpdgrLHE 176
                                       58****************555.**************************.**********************999889 PP

                             DUF87  72 lsekvkvitpspsa.......kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssde 141
                                       l++++ v++   ++         ++++i + +l  ++++d++++  +++a++qr+++++al+++     ++ ++ ++
  gi|557694414|ref|YP_008797468.1| 177 LADRITVYRHTAATgryqklfHLRRYEIAFTELYADDICDIAGI--REEATRQRAAVRKALEKL----ADTAYTPQD 247
                                       999999999976669999999999********************..****************66....59******* PP

                             DUF87 142 pveklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqql 218
                                       +++ l++  +   ++++k+  +a+++  + +++l   + +   sstd+ +ll     k+ + +iidlsg+ ++ +++
  gi|557694414|ref|YP_008797468.1| 248 LLKMLENPPW---TDEDKELADAARAAARYIRRLAHLNVFG-LSSTDVSELL-----KPAHASIIDLSGLRDDSMNY 315
                                       ***9999999...8888888888888888888888888877.999*******.....******************** PP

                             DUF87 219 vvsvilrri 227
                                       ++  il ++
  gi|557694414|ref|YP_008797468.1| 316 IAYTILSKV 324
                                       ***999875 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   2.2e-08   3.9e-05      23     172 ..     125     283 ..     118     309 .. 0.75
   2 !    5.2   0.0    0.0047       8.4     259     296 ..     357     394 ..     337     412 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.2e-08
                            AAA_10  23 asliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketlpe..iakkinvvtLdseeenegvLdPlvllk 97 
                                       + +ii ++G+GKS+la +l   ++  g  +l++Dp  +  +   t     + +  +++t+ +++ + g    l  l 
  gi|557694414|ref|YP_008797468.1| 125 HLAIIAQTGAGKSYLAGVLLEELLSKGATILVLDPHSDYVRLTMTP-DgrLHELADRITVYRHTAATGRYQKLFHLR 200
                                       789***********************************66654444.2347778999999999*******9999888 PP

                            AAA_10  98 eekea..eslaedilelllgvkkkesekkaalseaveavlegkq..rgllavieel.....rkedekvareiarhle 165
                                       + ++a  e  a di + + g++++++ ++aa+++a e+ ++ +   ++ll+++e+       ke   +ar +ar+++
  gi|557694414|ref|YP_008797468.1| 201 RYEIAftELYADDICD-IAGIREEATRQRAAVRKALEKLADTAYtpQDLLKMLENPpwtdeDKELADAARAAARYIR 276
                                       7655421445555554.689*****************9998443348999999998654333555567777899987 PP

                            AAA_10 166 svvkksl 172
                                        +++ ++
  gi|557694414|ref|YP_008797468.1| 277 RLAHLNV 283
                                       7665544 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0047
                            AAA_10 259 kkllkelvRiGRsynaavylvtqsadDvlkeelknnig 296
                                        ++++ +   GR++  +++lvtq ++ +++++l++  +
  gi|557694414|ref|YP_008797468.1| 357 SAIINRIAAEGRKFGLFLILVTQRPSKIDDDSLSQCNS 394
                                       5688889999******************9998776544 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 !   15.0   0.0   4.8e-06    0.0085       9      57 ..     117     165 ..     108     171 .. 0.89
   2 ?    3.7   0.0     0.013        24     261     310 ..     360     401 ..     357     419 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-06
                     TrwB_AAD_bind   9 lpkeretqhilivGttGsGKtqalekllrairargdraivlDltGafvs 57 
                                       l+++  ++h++i+  tG+GK+  +  ll+++ ++g +++vlD++ ++v+
  gi|557694414|ref|YP_008797468.1| 117 LSVRGFRRHLAIIAQTGAGKSYLAGVLLEELLSKGATILVLDPHSDYVR 165
                                       45666789************************************99985 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.013
                     TrwB_AAD_bind 261 lksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvs 310
                                       +++++aegRkfG  ++l  q  +++ +          ls +n+++i+r +
  gi|557694414|ref|YP_008797468.1| 360 INRIAAEGRKFGLFLILVTQRPSKIDD--------DSLSQCNSQIIMRLT 401
                                       67889*****************99975........234555555555544 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     2e-05     0.036       5      60 ..     123     181 ..     120     249 .. 0.80
   2 ?    4.3   0.0     0.025        46      91     128 ..     333     377 ..     302     384 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllrel 60 
                                       +++l++++++G+GK++l+  lle+l    +      +++++v+ t++ ++ + +l+ ++
  gi|557694414|ref|YP_008797468.1| 123 RRHLAIIAQTGAGKSYLAGVLLEELLSKGATILvldPHSDYVRLTMTPDGRLHELADRI 181
                                       689*********************97654444488888888888888877666665554 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.025
                            AAA_22  91 v..ielliiDEaqhlr..seealeeLrsllnl.....srkgvqliLv 128
                                          +++++i+Ea+++   +ee +     + n      +++g+ liLv
  gi|557694414|ref|YP_008797468.1| 333 FgyPVFIVIEEAHRFVpyREETYASA--IINRiaaegRKFGLFLILV 377
                                       256679********875533333332..1111123334555555554 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 !    5.6   0.0    0.0028         5       9      67 ..     111     169 ..     106     192 .. 0.82
   2 !   12.3   0.0   2.7e-05     0.048     292     361 ..     371     434 ..     337     459 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0028
                            DUF853   9 aeqelalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGdLsgiaka 67 
                                       ++ +++l+++   rh  i   tG+Gk     vl e+l + G ++++ d   d   ++ +
  gi|557694414|ref|YP_008797468.1| 111 PDVPVHLSVRGFRRHLAIIAQTGAGKSYLAGVLLEELLSKGATILVLDPHSDYVRLTMT 169
                                       5678889999999***********************************99998877653 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 2.7e-05
                            DUF853 292 GvGvyfvtqnPldlPdtvLaqLGnrvqhalraftpkdqkavkaaadtfranpefdveeaiteLgvGealv 361
                                       G  + +vtq P+ + d+ L+q  +++   +r   p+dq+av  +++ + +    d+ + + +L+ Gea+v
  gi|557694414|ref|YP_008797468.1| 371 GLFLILVTQRPSKIDDDSLSQCNSQI--IMRLTNPEDQNAVARSSERMSQ----DLLNDLPSLNQGEAVV 434
                                       5555689**************98866..68999********999988865....7788899999999998 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.1e-07   0.00074      31     133 ..     277     387 ..     261     397 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.1e-07
                               Zot  31 kiit.nidGlrlerieqvlgekvstarlirid..npegaetlkefakwatid..kga......llviDEcqeifpvr 96 
                                       +++  n+ Gl    +  +l+ +     +i+++    ++   +++    +++d   ++      ++vi E++++ p r
  gi|557694414|ref|YP_008797468.1| 277 RLAHlNVFGLSSTDVSELLKPAHA--SIIDLSglRDDSMNYIAYTILSKVYDrvSNGlfgypvFIVIEEAHRFVPYR 351
                                       444448888887777776665554..69999888888888888888888877763332333338*********9999 PP

                               Zot  97 akegrkdpevi.naftehRhlgwDivlltqdiskihke 133
                                        +      ++i    +e R++g  ++l+tq +ski+++
  gi|557694414|ref|YP_008797468.1| 352 EET--YASAIInRIAAEGRKFGLFLILVTQRPSKIDDD 387
                                       997..5699995566799*****************986 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 !   16.4   0.0   1.7e-06    0.0031      44      87 ..     122     168 ..      56     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-06
                   T4SS-DNA_transf  44 f.ehvlvvAptrsgKg..vgvviPnllkwkqsiVvlDpkgElaelts 87 
                                       f  h  ++A t++gK+  +gv +  ll+++ +i vlDp ++ + lt 
  gi|557694414|ref|YP_008797468.1| 122 FrRHLAIIAQTGAGKSylAGVLLEELLSKGATILVLDPHSDYVRLTM 168
                                       3689***********9777**********************998875 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 ?   11.9   0.0   9.4e-05      0.17      25      62 ..     124     159 ..      88     195 .. 0.88
   2 ?    0.7   0.0      0.26   4.6e+02     134     147 ..     334     350 ..     296     373 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.4e-05
                                       SEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEES CS
                            ResIII  25 krglikmaTGtGKTlvaaklierllkkgkeekflflvp 62 
                                       +++ i + TG+GK+++a  l e+ll+kg    +l+l p
  gi|557694414|ref|YP_008797468.1| 124 RHLAIIAQTGAGKSYLAGVLLEELLSKGA--TILVLDP 159
                                       57779*********************987..7777765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.26
                                       S...EEEEETGGGTTS. CS
                            ResIII 134 d...viiiDEaHrlgak 147
                                           +i+i EaHr+   
  gi|557694414|ref|YP_008797468.1| 334 GypvFIVIEEAHRFVPY 350
                                       3555899******9754 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.091   1.6e+02      29      64 ..     113     148 ..     100     156 .. 0.77
   2 ?    9.0   0.0   0.00044      0.78     215     242 ..     355     382 ..     347     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.091
                                       -EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHH CS
                      FtsK_SpoIIIE  29 nplvldlkkmashllvaGatgsGKStalntLilSla 64 
                                        p+ l  ++   hl ++  tg GKS    +L+  l+
  gi|557694414|ref|YP_008797468.1| 113 VPVHLSVRGFRRHLAIIAQTGAGKSYLAGVLLEELL 148
                                       555566666668*************88777766555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00044
                                       .HHHHHHHHHHHCGGGTEEEEEEES--- CS
                      FtsK_SpoIIIE 215 lvedaivRlarkgraaglHlllatqrls 242
                                        +  +i R+a+ gr+ gl+l+l tqr+s
  gi|557694414|ref|YP_008797468.1| 355 YASAIINRIAAEGRKFGLFLILVTQRPS 382
                                       56789*********************98 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012      0.22       2      41 ..     128     166 ..     127     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                     Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvkt 41 
                                       ++A+ G GKS ++G++l++l+++g  +ilv  p+ + v+ 
  gi|557694414|ref|YP_008797468.1| 128 IIAQTGAGKSYLAGVLLEELLSKGA-TILVLDPHSDYVRL 166
                                       89*********************97.89998888776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); 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: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 3647.51
//
Query:       gi|557694415|ref|YP_008797469.1|  [L=383]
Description: exonuclease SbcCD, D subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-13   51.7   0.5    3.3e-13   50.2   0.5    2.0  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    8.4e-12   46.0   0.2    1.6e-11   45.1   0.2    1.4  1  Metallophos    Calcineurin-like phosphoesterase
     0.0016   17.8   0.3        2.9    7.2   0.0    3.6  4  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
  ------ inclusion threshold ------
      0.011   15.6   1.0      0.083   12.8   0.4    2.4  2  Homeodomain    Homeodomain
      0.013   15.1   0.0      0.048   13.2   0.0    1.8  2  DUF4088        Protein of unknown function (DUF4088)


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 !   50.2   0.5   9.1e-17   3.3e-13       5     160 ..       7     238 ..       3     243 .. 0.69

  Alignments for each domain:
  == domain 1  score: 50.2 bits;  conditional E-value: 9.1e-17
                     Metallophos_2   5 iiSDlH.................snldaleavlealkevgvdaiihaGDl.eeeep.........evleellela.. 52 
                                       i +D H                 ++l+  e+v+e++k++++d++++aGD+  +++p         + +++l      
  gi|557694415|ref|YP_008797469.1|   7 ITADNHldppatmfgakrferkrDHLRCFEEVMEHAKREKPDLLLMAGDIfDTVKPsnfvrarlmQHMKQL---Her 80 
                                       55666666666666666666666889999********************9877777555654333333344...366 PP

                     Metallophos_2  53 ..pvlaVrGNnD...................................eevveedvlreaaelgtdl........... 81 
                                         +v++V G +D                                   e   ++ +    a+    l           
  gi|557694415|ref|YP_008797469.1|  81 gvKVVMVSGHHDtpksaeegvsplavyghsgyayfiqdpnsmdyfslE---VDGCEVVVAG----Lghnpllhpadd 150
                                       6***********999999999999888888888888777665333330...3333333333....133446664444 PP

                     Metallophos_2  82 p.eeaele.lagekvlliHgdpl.....gvkdalaellkeaeegsd..vvvcGHtHvpevekeggvlvvnPGsvgep 149
                                       p ++ ++e  +++++ll+H+            + +++++ ++ +++  +v++GH H+++v++ g++ +v+PGs ++ 
  gi|557694415|ref|YP_008797469.1| 151 PlSSVKMEkRGDVNILLLHYPVEgfvgvY---GEEPVIRLNSIPKTcqLVAVGHLHRHQVKRLGDTAIVYPGSTERV 224
                                       44666666337777******865996532...4444444444444447***************************** PP

                     Metallophos_2 150 rdgdpe...tyail 160
                                       +++++e   +++  
  gi|557694415|ref|YP_008797469.1| 225 SFAEEEepkGFVWA 238
                                       99998766666555 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.2   4.4e-15   1.6e-11       4     203 ..       6     204 ..       4     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 4.4e-15
                                       EEEESBTB............TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHH.... CS
                       Metallophos   4 lvigDlHl............algggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvky.... 63 
                                       ++++D Hl            ++   +l+ +++++++++re kpdl+l+aGD++d+  +++ +++  l +  k+    
  gi|557694415|ref|YP_008797469.1|   6 IITADNHLdppatmfgakrfERKRDHLRCFEEVMEHAKRE-KPDLLLMAGDIFDTVKPSN-FVRArLMQHMKQlher 80 
                                       5899*********999777777777777777777887777.***************9999.5555465555556999 PP

                                       TSEEEEEC-TTS...CHHHHHHHHHHHHHHH.HHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEETHHHHHHH CS
                       Metallophos  64 pipvylllGNHe...gfeeellnkygylgif.sepwrsdaevfnnlplaslgsgs.lkvlllhGgspellvsldklg 135
                                       +++v+++ G H+         ++    l+ +   ++ ++ +  n +  +sl  +    v+   G+            
  gi|557694415|ref|YP_008797469.1|  81 GVKVVMVSGHHDtpkS----AEEGVSPLAVYgHSGYAYFIQDPNSMDYFSLEVDGcEVVVAGLGH------------ 141
                                       ************5441....344434444443334444433334444444333433345555555............ PP

                                       HHHHSCHHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHHHHHTT.ESEEEEESSSS CS
                       Metallophos 136 slnleleapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdealedllkkyg.vdlvisGHtHv 203
                                         +l  +a++p    l+  + ++++d+ i+l H p++ g   ++g+e + +l  +++  +lv  GH H+
  gi|557694415|ref|YP_008797469.1| 142 -NPLLHPADDP----LSSVKMEKRGDVNILLLHYPVE-GFVGVYGEEPVIRLNSIPKtCQLVAVGHLHR 204
                                       .3333333333....333355779*************.**************666666**********6 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.0    0.0089        32      12      55 ..      23      68 ..      16      73 .. 0.67
   2 ?    2.0   0.0      0.03   1.1e+02      80     103 ..      72      95 ..      63      98 .. 0.87
   3 !    7.2   0.0    0.0008       2.9     207     243 ..     192     227 ..     155     230 .. 0.80
   4 ?   -0.7   0.0      0.19     7e+02      16      54 ..     266     306 ..     257     316 .. 0.61

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0089
                                      E--TT-GGGH...HHHHHHHHHH--SEEEEES-----HHHHHHHHHH CS
                     Metallophos_3 12 sdlkgevell...erlveviedkdpDllvlvGdlvkaeakadeyesa 55
                                      ++++ + + l   e+++e ++  +pDll++ Gd+     k  ++ +a
  gi|557694415|ref|YP_008797469.1| 23 KRFERKRDHLrcfEEVMEHAKREKPDLLLMAGDIF-DTVKPSNFVRA 68
                                      55655555541126777778888***********5.44555556555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.03
                                       HHHHHHHTT-SEEEEE--TTS--H CS
                     Metallophos_3  80 klfrelgeldvpafvvPGkrDaPl 103
                                       + +++l e +v++++v G++D P 
  gi|557694415|ref|YP_008797469.1|  72 QHMKQLHERGVKVVMVSGHHDTPK 95 
                                       567999****************97 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0008
                                       HHH--SEEEE-SS--EE.EEETTEEEEE--BGGGTEEE CS
                     Metallophos_3 207 ktlnPevvvvghavkeh.eelgktlvvnPGaleeGdfa 243
                                       kt   ++v vgh ++++   lg+t +v PG+ e   fa
  gi|557694415|ref|YP_008797469.1| 192 KT--CQLVAVGHLHRHQvKRLGDTAIVYPGSTERVSFA 227
                                       44..4699*******999*************9887776 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.19
                                       T-GGGHHHHHHHHHHH.--SEEE..EES-----HHHHHHHHH CS
                     Metallophos_3  16 gevellerlveviedk.dpDllv..lvGdlvkaeakadeyes 54 
                                        e + +erl+++i+++ dp l++  ++  +v+ae k  ey++
  gi|557694415|ref|YP_008797469.1| 266 PEKDAIERLKQLIDQHaDPQLVLrlVIKGVVEAE-KLTEYRR 306
                                       5678899999999877556554221233333333.4456665 PP

>> Homeodomain  Homeodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.2   7.3e+02      24      46 ..      61      84 ..      58      84 .. 0.89
   2 ?   12.8   0.4   2.3e-05     0.083      10      41 ..     342     374 ..     334     378 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.2
                                      S-SHHHHHHHHHHH.TS-HHHHHH CS
                       Homeodomain 24 ypsaeereeLAkkl.gLeerqVkv 46
                                      +ps   r++L +++ +L er Vkv
  gi|557694415|ref|YP_008797469.1| 61 KPSNFVRARLMQHMkQLHERGVKV 84
                                      799999********99****9997 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHHHHH.SSS-SHHHHHHHHHHHTS-H CS
                       Homeodomain  10 eqleeLeklFee.nrypsaeereeLAkklgLee 41 
                                       + leeL ++F   +++ saeere LA+ l+L+e
  gi|557694415|ref|YP_008797469.1| 342 TPLEELRRYFSTlMQTASAEEREILAEALRLSE 374
                                       5689*******99******************98 PP

>> DUF4088  Protein of unknown function (DUF4088)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.34   1.2e+03     192     215 ..      36      58 ..      32      62 .. 0.81
   2 ?   13.2   0.0   1.3e-05     0.048      25      54 ..      63      92 ..      55     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.34
                           DUF4088 192 qqvleklrrlkPelfreePkdvfe 215
                                       ++v+e+ +r+kP l+  +  d+f+
  gi|557694415|ref|YP_008797469.1|  36 EEVMEHAKREKPDLLLMAG-DIFD 58 
                                       689**********987766.6666 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.3e-05
                           DUF4088 25 ddflraklldnsvplteeavqrllasGeya 54
                                       +f+ra+l+++++ l e+ v+ ++ sG++ 
  gi|557694415|ref|YP_008797469.1| 63 SNFVRARLMQHMKQLHERGVKVVMVSGHHD 92
                                      59*************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); 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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2726.48
//
Query:       gi|557694416|ref|YP_008797470.1|  [L=767]
Description: exonuclease SbcCD, C subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-13   50.8  56.5    1.1e-12   48.8  35.3    4.2  2  AAA_23           AAA domain
    1.1e-12   47.9   0.0    5.8e-12   45.5   0.0    2.0  1  SMC_N            RecF/RecN/SMC N terminal domain
    1.1e-06   28.2   0.0    2.1e-06   27.4   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
    2.8e-05   24.2   0.1    0.00012   22.3   0.0    2.1  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
    0.00014   21.5   0.0    0.00014   21.5   0.0    4.1  6  AAA_27           AAA domain
     0.0063   16.6   1.4      0.017   15.2   1.4    1.7  1  DUF1290          Protein of unknown function (DUF1290)
  ------ inclusion threshold ------
      0.023   14.4  24.8       0.02   14.6  20.6    2.7  2  AAA_15           AAA ATPase domain
       0.13   12.5   1.4        8.3    6.7   0.0    2.6  2  Egg_lysin        Egg lysin (Sperm-lysin)
       0.33   11.4  23.3         11    6.5   0.0    7.5  7  FlaC_arch        Flagella accessory protein C (FlaC)
       0.38   11.6   8.8       0.13   13.2   0.6    3.5  3  DUF5339          Family of unknown function (DUF5339)
       0.67   10.2   4.0       0.29   11.4   0.5    2.1  2  RskA             Anti-sigma-K factor rskA
        1.2    8.9   7.1       0.34   10.7   0.3    3.0  3  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
        1.3    9.0   3.4        2.5    8.1   3.4    1.4  1  MSA-2c           Merozoite surface antigen 2c
        1.7    8.8  30.7       0.52   10.5   0.6    4.2  3  Fib_alpha        Fibrinogen alpha/beta chain family
        3.5    6.4  54.5     0.0087   15.0   9.3    3.4  4  Spc7             Spc7 kinetochore protein
        3.6    7.8  15.2         13    6.0   0.3    5.0  5  FAA_hydrolase_N  Fumarylacetoacetase N-terminal
        3.8    7.9  12.6         34    4.8   0.0    5.2  5  V-SNARE_C        Snare region anchored in the vesicle membran
        4.4    5.8  22.8        1.9    7.0  11.3    2.9  3  Peptidase_S46    Peptidase S46
        4.9    7.1   6.8        2.4    8.1   0.2    3.3  3  Phage_tail_APC   Phage tail assembly chaperone protein
        8.5    6.8  16.5        1.1    9.7   0.3    4.0  3  T3SSipB          Type III cell invasion protein SipB


Domain annotation for each model (and alignments):
>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8  35.3   1.3e-15   1.1e-12       6     199 ..      11     292 ..       6     350 .. 0.59
   2 ?   -2.3  13.2         6   5.4e+03     137     200 .]     481     530 ..     403     618 .. 0.66

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.3e-15
                            AAA_23   6 nfrsfr.dqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfen 81 
                                       nf+++r d+ + Fs+g+tlI+G N+aGK++ildAi +aLy ++ r ++++g +  ++d+  +  g  ka v l+f  
  gi|557694416|ref|YP_008797470.1|  11 NFKKLRfDEPLRFSDGVTLISGLNEAGKSSILDAILYALYARVIRPPPEKG-KTRNEDII-AY-GASKATVVLEFAV 84 
                                       9999975777*******************************9988777654.33344443.33.4566777777777 PP

                            AAA_23  82 kdgry...............................trsiererelskkkgkttkkaklelleideleqfisellgs 127
                                        d+ry                               ++++               ++++ +l+  + ++++s+ +  
  gi|557694416|ref|YP_008797470.1|  85 GDKRYrvsreikrsgkpranldeiladnslkplavgQEKV--------------TEQIEAILGGITFNELVSSTVVA 147
                                       7776544333322232334444333333333333331111..............22222222223333444444444 PP

                            AAA_23 128 kkiilnlilflgqer.....................feefelkdkke...................rleelekelee 164
                                       +k+ ++li + +++r                     +         +                   +le+l++elee
  gi|557694416|ref|YP_008797470.1| 148 QKELNKLIELRKEDRkkiinvflnlesfnivlenleE---------QkrelegtkerpgrlrvekeKLESLREELEE 215
                                       4444455555555555554444444444455443331.........0222334444555555555555555555555 PP

                            AAA_23 165 ledekkllekl..........................................eqekekekeleeleeeleeilkel 199
                                         ++kk+ e+l                                          ++++ k+k+le+l+++ e++lk++
  gi|557694416|ref|YP_008797470.1| 216 YLKKKKEREDLveermkllkniekteaeyaeaeklykmlqeydeflnrrqkleLEIEGKRKQLETLRKQRETLLKNI 292
                                       55544444444433365565555555555555555555555555555544444444444446666666666666655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6
                            AAA_23 137 flgqerfeefelkdkkerleelekeleeledekkllekleqekekekeleeleeeleeilkele 200
                                        l+q +++++el+d k++l++++++l+ l +e               el+++e+e+ ++ ++le
  gi|557694416|ref|YP_008797470.1| 481 VLQQAEKDRQELNDLKSKLDAYREQLKNLPAEH--------------ELNQVESEIHSLGEQLE 530
                                       234444555555666666666666665544433..............33333333333333332 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 !   45.5   0.0   6.5e-15   5.8e-12       4     212 ..       6     759 ..       3     765 .. 0.94

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 6.5e-15
                                       EEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTT...TTTCHCCCCCC--BTTCSSTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   4 rleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersak...klrseklsdlihkskekasvkka 77 
                                       +l   nFk ++     l+fs+++t i G N +GKs++ldAil+ L  r  +   +  +++ +d+i +      ++ka
  gi|557694416|ref|YP_008797470.1|   6 SLYAYNFKKLR-FDEPLRFSDGVTLISGLNEAGKSSILDAILYALYARVIRpppEKGKTRNEDIIAY-----GASKA 76 
                                       56778999997.88899****************************9765552223446778899998.....8899* PP

                                       EEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................... RF
                             SMC_N  78 eveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske................... 135
                                       +v + f   dk+       + +sr++kr+g+ +  +++  + ++     + +++++++                   
  gi|557694416|ref|YP_008797470.1|  77 TVVLEFAVGDKR-------YRVSREIKRSGKPRANLDEILADNSLKPLAVGQEKVTEQieailggitfnelvsstvv 146
                                       *****9999999.......9999999999999999988776665555555666666667788999999999****** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|557694416|ref|YP_008797470.1| 147 aqkelnklielrkedrkkiinvflnlesfnivlenleeqkrelegtkerpgrlrvekekleslreeleeylkkkker 223
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|557694416|ref|YP_008797470.1| 224 edlveermkllkniekteaeyaeaeklykmlqeydeflnrrqkleleiegkrkqletlrkqretllknientesdmh 300
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|557694416|ref|YP_008797470.1| 301 ryrdlhlvekeleslskeyqqlvtlehqigeareaetrlgiqvrsleqqlppsakatalrrpsirpfaagaaasiii 377
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|557694416|ref|YP_008797470.1| 378 afillfigsvlpallflaagvvfliivfqrvsrlsrmmvlqetlarleqaremhataratlrnliqnhsvktsylkn 454
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|557694416|ref|YP_008797470.1| 455 afsslprygelfqqklveglpkaveavlqqaekdrqelndlkskldayreqlknlpaehelnqveseihslgeqleg 531
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|557694416|ref|YP_008797470.1| 532 vrlptlspglefsrdvleearkrvqqlaeniqayrtrtellsqlvleleewlrahgdveqryseqlavvanlerela 608
                                       ***************************************************************************** PP

                                       .................................................................CS-HH..HHHHH CS
                                       .................................................................xxxxx..xxxxx RF
                             SMC_N 136 .................................................................lLSgG..ektLv 145
                                                                                                        ++SgG  ++ L+
  gi|557694416|ref|YP_008797470.1| 609 vvrkaveaiqataealrnrvkplvaahmgiilpaltnnrykaaildddyrlqvwdpdagqyrvkeVFSGGteDQMLL 685
                                       **********************************************************************4446788 PP

                                       HHHHHHH.....HHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCCC-SCEEEEE CS
                                       xxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 146 alaLlfA.....iqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemlekadklvgvt 212
                                       a+ L fA       k ++  +++lDe     De +++ + e++    ++k +Q+++is+  ++ e++++++++ 
  gi|557694416|ref|YP_008797470.1| 686 AMRLAFAlallpEAKGQKPEFVFLDEPLGSSDEVRRSGIIEYIAidLAKKFSQIFIISHVGGLEEHVNHIIRLH 759
                                       88888887775423334445999*******************986344555********999999998888765 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 !   27.4   0.0   2.4e-09   2.1e-06       7      49 ..      10      52 ..       4      55 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.4e-09
                            AAA_29  7 vNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalLvpa 49
                                      +N   ++  + ++++ +g+tl++G +++GKS++lDAi + L+++
  gi|557694416|ref|YP_008797470.1| 10 YNFKKLRFdEPLRFS-DGVTLISGLNEAGKSSILDAILYALYAR 52
                                      555555555677887.779**********************985 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 !   22.3   0.0   1.3e-07   0.00012      14      88 ..     659     728 ..     647     729 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.3e-07
                           SbcCD_C  14 vevrdedgkekelsrssgtlSGG.ekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllell 88 
                                       ++v d+d      +r  +  SGG e q+l+++ la+ala l + +    +++++vfLDE  ++ De +++ ++e++
  gi|557694416|ref|YP_008797470.1| 659 LQVWDPDAG---QYRVKEVFSGGtEDQMLLAMRLAFALALLPEAK---GQKPEFVFLDEPLGSSDEVRRSGIIEYI 728
                                       455544444...488899999995678888888888888777774...89*****************999998876 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.6e-07   0.00014      16      52 ..      18      51 ..       2     125 .. 0.78
   2 ?   -1.5   0.2       1.7   1.6e+03     157     200 ..     174     216 ..     152     224 .. 0.76
   3 ?   -1.1   1.0       1.4   1.2e+03     160     188 ..     204     232 ..     174     252 .. 0.62
   4 ?   -2.0   1.5       2.5   2.2e+03     155     195 ..     244     283 ..     218     294 .. 0.52
   5 ?   -0.5   0.1      0.89     8e+02     160     199 ..     469     508 ..     456     525 .. 0.81
   6 ?   -2.4   0.4       3.3     3e+03     143     197 ..     553     607 ..     542     616 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.6e-07
                            AAA_27 16 drsldfsaeeadlhliyGpNEAGKstalrAisdllfG 52
                                      d+ l+fs   ++++li G NEAGKs++l+Ai   l+ 
  gi|557694416|ref|YP_008797470.1| 18 DEPLRFS---DGVTLISGLNEAGKSSILDAILYALYA 51
                                      4455555...89*******************999986 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.7
                            AAA_27 157 slrevleaLeaeadelfkprkskkrainealeeleeakkelrea 200
                                       s + vle+Le++++el  ++++   +++ ++e+le++++el+e 
  gi|557694416|ref|YP_008797470.1| 174 SFNIVLENLEEQKRELEGTKERPG-RLRVEKEKLESLREELEEY 216
                                       566678888888888877777777.8888888888888887764 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.4
                            AAA_27 160 evleaLeaeadelfkprkskkraineale 188
                                       e le+L++e +e+ k++k+++  + e ++
  gi|557694416|ref|YP_008797470.1| 204 EKLESLREELEEYLKKKKEREDLVEERMK 232
                                       45666666666666666666633333333 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.5
                            AAA_27 155 laslrevleaLeaeadelfkprkskkrainealeeleeakk 195
                                       +a+ +++++ L +e de+ ++r++ + +i  ++++le+++k
  gi|557694416|ref|YP_008797470.1| 244 YAEAEKLYKML-QEYDEFLNRRQKLELEIEGKRKQLETLRK 283
                                       33434433333.34455555555555555555555555555 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.89
                            AAA_27 160 evleaLeaeadelfkprkskkrainealeeleeakkelre 199
                                       +++e L +  +++ ++ ++ ++++n+ +++l++ +++l++
  gi|557694416|ref|YP_008797470.1| 469 KLVEGLPKAVEAVLQQAEKDRQELNDLKSKLDAYREQLKN 508
                                       5677788888888888888888888888888888888776 PP

  == domain 6  score: -2.4 bits;  conditional E-value: 3.3
                            AAA_27 143 elgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkel 197
                                       +  q L e   ++++ +e+l +L  e +e+ + ++  ++++ e+l+ ++++++el
  gi|557694416|ref|YP_008797470.1| 553 KRVQQLAENIQAYRTRTELLSQLVLELEEWLRAHGDVEQRYSEQLAVVANLEREL 607
                                       4455566666666777778888888888888888888888888877777777665 PP

>> DUF1290  Protein of unknown function (DUF1290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.4   1.9e-05     0.017      36      85 ..     366     415 ..     352     416 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                           DUF1290  36 vfisgffsnvllAalLvylGdklgvdlylaavvvfgirifqnlaiirrll 85 
                                        f  g  + +++A +L ++G+ l   l+laa vvf i +fq ++ + r++
  gi|557694416|ref|YP_008797470.1| 366 PFAAGAAASIIIAFILLFIGSVLPALLFLAAGVVFLIIVFQRVSRLSRMM 415
                                       5788889999*********************************9998876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6  20.6   2.2e-05      0.02       5     277 ..       6     270 ..       3     346 .. 0.42
   2 ?   -0.7   0.1         1   9.3e+02     234     259 ..     474     509 ..     416     537 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                            AAA_15   5 kikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn.......................... 54 
                                       ++   NF++l+    + +s+ +t++ G N +GKSsil+a+ + l                                 
  gi|557694416|ref|YP_008797470.1|   6 SLYAYNFKKLRFdEPLRFSDGVTLISGLNEAGKSSILDAILYALYAR--VIrpppekgktrnediiaygaskatvvl 80 
                                       55667*****96699999999******************96655533..2245655444555555555555555544 PP

                            AAA_15  55 .......................................................kkvikiekedleifeniseskd 76 
                                                                                                                    
  gi|557694416|ref|YP_008797470.1|  81 efavgdkryrvsreikrsgkpranldeiladnslkplavgqekvteqieailggiT--------------------- 136
                                       44444444444444444444444333333333333333333333333333333330..................... PP

                            AAA_15  77 ikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekee 153
                                                                                                           +el +++  
  gi|557694416|ref|YP_008797470.1| 137 -------------------------------------------------------------------FNELVSSTVV 146
                                       ...................................................................4444444444 PP

                            AAA_15 154 klekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsd.....edsekkssllgklkeki 225
                                        +++ ++ +++ ked kk+i+     l+ e+ ++ vl++      l + kR+ +       +  ++++ l++l e++
  gi|557694416|ref|YP_008797470.1| 147 AQKELNKLIELRKEDRKKIIN---VFLNLES-FNIVLEN------LEEQKRELEGtkerpGRLRVEKEKLESLREEL 213
                                       444444444444444444444...1111111.1111111......22222222221111122222222223333333 PP

                            AAA_15 226 leealqekleeelteklkeiqeklkeidkklaeelk.....kilkkkidkikkfnyk 277
                                        e+ +++k +e+l e+  ++++++++++ ++ae +k     ++++++++  +k++  
  gi|557694416|ref|YP_008797470.1| 214 EEYLKKKKEREDLVEERMKLLKNIEKTEAEYAEAEKlykmlQEYDEFLNRRQKLELE 270
                                       222222222333333333333333333333333333322221111111111111111 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1
                            AAA_15 234 l..........eeelteklkeiqeklkeidkklaee 259
                                       l           e+++++l+++++kl+   ++l++ 
  gi|557694416|ref|YP_008797470.1| 474 LpkaveavlqqAEKDRQELNDLKSKLDAYREQLKNL 509
                                       133335533334455555555555555555555333 PP

>> Egg_lysin  Egg lysin (Sperm-lysin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.5      0.07        63      21      66 ..     213     267 ..     201     277 .. 0.69
   2 ?    6.7   0.0    0.0093       8.3      10      71 ..     568     629 ..     562     652 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.07
                                       HHHHHHHHHCCC..........-HHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCC CS
                         Egg_lysin  21 lakwlrrhgsrl..........skvqkktlrfvnrrrmqtlwqnYaewvskkirkL 66 
                                       l+++l++ ++r           ++++k+++ +   ++++++ q+Y e+ ++  +kL
  gi|557694416|ref|YP_008797470.1| 213 LEEYLKKKKEREdlveermkllKNIEKTEAEYAEAEKLYKMLQEYDEFLNR-RQKL 267
                                       333333333333333455577899************************554.4555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0093
                                       HHHHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCTS--S CS
                         Egg_lysin  10 kvgiiagldkklakwlrrhgsrlskvqkktlrfvnrrrmqtlwqnYaewvskkirkLgrkpn 71 
                                       +++++++l  +l++wlr hg++ ++  ++++   n +r +++ ++ +e ++   ++L +++ 
  gi|557694416|ref|YP_008797470.1| 568 RTELLSQLVLELEEWLRAHGDVEQRYSEQLAVVANLERELAVVRKAVEAIQATAEALRNRVK 629
                                       67778888889**********778888888888888**999999999999998888876655 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 ?   -1.2   0.8       3.2   2.8e+03      15      32 ..     205     222 ..     197     244 .. 0.65
   2 ?    6.3   1.1     0.015        13      10      38 ..     265     293 ..     258     305 .. 0.64
   3 ?    0.7   0.9      0.79   7.1e+02      14      33 ..     301     322 ..     286     331 .. 0.65
   4 ?    0.5   0.2      0.94   8.4e+02       5      25 ..     308     331 ..     305     349 .. 0.61
   5 ?    3.3   0.4      0.13   1.1e+02       6      18 ..     512     524 ..     489     534 .. 0.46
   6 ?    4.1   0.0     0.069        62       9      38 ..     534     563 ..     527     573 .. 0.87
   7 ?    6.5   0.0     0.012        11       9      41 ..     600     632 ..     595     634 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.2
                         FlaC_arch  15 eletvkkeneelsksvee 32 
                                       +le++++e+ee  k+ +e
  gi|557694416|ref|YP_008797470.1| 205 KLESLREELEEYLKKKKE 222
                                       567777777765555444 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.015
                         FlaC_arch  10 sklsteletvkkeneelsksveelkenVk 38 
                                       +kl+ e+e  +k++e l+k+ e+l +n++
  gi|557694416|ref|YP_008797470.1| 265 QKLELEIEGKRKQLETLRKQRETLLKNIE 293
                                       45666666666666666666666655553 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.79
                         FlaC_arch  14 t..eletvkkeneelsksveel 33 
                                           l  v+ke+e+lsk+ ++l
  gi|557694416|ref|YP_008797470.1| 301 RyrDLHLVEKELESLSKEYQQL 322
                                       2446777888888888776654 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.94
                         FlaC_arch   5 lEnklsklst...eletvkkenee 25 
                                       +E++l++ls    +l t++ ++ e
  gi|557694416|ref|YP_008797470.1| 308 VEKELESLSKeyqQLVTLEHQIGE 331
                                       466666666655555555555555 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.13
                         FlaC_arch   6 Enklsklstelet 18 
                                       E +l+++++e+ +
  gi|557694416|ref|YP_008797470.1| 512 EHELNQVESEIHS 524
                                       2333333333333 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.069
                         FlaC_arch   9 lsklsteletvkkeneelsksveelkenVk 38 
                                       l+ ls  le  ++ +ee +k v++l en++
  gi|557694416|ref|YP_008797470.1| 534 LPTLSPGLEFSRDVLEEARKRVQQLAENIQ 563
                                       7788888999999***************96 PP

  == domain 7  score: 6.5 bits;  conditional E-value: 0.012
                         FlaC_arch   9 lsklsteletvkkeneelsksveelkenVkdll 41 
                                       + +l+ el+ v+k  e ++ + e l  +Vk l+
  gi|557694416|ref|YP_008797470.1| 600 VANLERELAVVRKAVEAIQATAEALRNRVKPLV 632
                                       678999999999999999999999999999887 PP

>> DUF5339  Family of unknown function (DUF5339)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       5.1   4.6e+03      13      32 ..     231     250 ..     207     262 .. 0.59
   2 ?    1.4   0.7      0.65   5.9e+02       8      47 ..     253     296 ..     247     300 .. 0.78
   3 ?   13.2   0.6   0.00014      0.13      10      50 ..     476     513 ..     472     517 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.1
                           DUF5339  13 dkliakaekqpgtktqadai 32 
                                        kl++++ek+++  + a+++
  gi|557694416|ref|YP_008797470.1| 231 MKLLKNIEKTEAEYAEAEKL 250
                                       34555555554444444444 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.65
                           DUF5339   8 YFkevdkliakaekq....pgtktqadaikkqleqsKkqilalp 47 
                                       + +e+d+++   +k     +g+ +q+++++kq e+  k i   +
  gi|557694416|ref|YP_008797470.1| 253 MLQEYDEFLNRRQKLeleiEGKRKQLETLRKQRETLLKNIENTE 296
                                       55788888888855577789999999999999998888777655 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 0.00014
                           DUF5339  10 kevdkliakaekqpgtktqadaikkqleqsKkqilalpkeq 50 
                                       k+v++ +++aek   + + ++ +k++l++ ++q++ lp+e+
  gi|557694416|ref|YP_008797470.1| 476 KAVEAVLQQAEK---DRQELNDLKSKLDAYREQLKNLPAEH 513
                                       789999999966...***********************996 PP

>> RskA  Anti-sigma-K factor rskA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   0.00032      0.29      18      85 ..     348     441 ..     333     457 .. 0.62
   2 ?   -1.8   0.2       3.7   3.3e+03     100     105 ..     605     610 ..     548     689 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                                       ....................................XXXXXXXXXXXXXX........................... CS
                              RskA  18 qaaaaaaaaaaapppaaapaararr...........laaaaAaalllvlg........................... 56 
                                       q+ ++ a a+a ++p+ +p a++++           +            g                           
  gi|557694416|ref|YP_008797470.1| 348 QQLPPSAKATALRRPSIRPFAAGAAasiiiafillfI------------Gsvlpallflaagvvfliivfqrvsrls 412
                                       3333333333333333334332222233333333330............3555555555555666677799****** PP

                                       ..........XXXXXXXXXXXXXXXXXXX CS
                              RskA  57 qlavasaaldplrqsaaqaeavvavlaap 85 
                                       +  v++++l++l+q+++  +++ a+l++ 
  gi|557694416|ref|YP_008797470.1| 413 RMMVLQETLARLEQAREMHATARATLRNL 441
                                       999************99999999998875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.7
                                       XXXXXX CS
                              RskA 100 ggalvl 105
                                       ++++v+
  gi|557694416|ref|YP_008797470.1| 605 RELAVV 610
                                       222222 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   0.3   0.00038      0.34       1     123 [.      27     125 ..      27     188 .. 0.75
   2 ?   -1.0   2.0       1.4   1.2e+03     113     188 ..     203     267 ..     130     327 .. 0.48
   3 ?   -0.7   0.0       1.1     1e+03     244     266 ..     689     712 ..     686     744 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                       ++++ G N +GKS++Lda+ ++                   ++ +++ ++++ ++    +  +   +  v+ ++ + 
  gi|557694416|ref|YP_008797470.1|  27 VTLISGLNEAGKSSILDAILYA------------------LYARVIRPPPEKGKTRNEDIIAYGASKATVVLEFAVG 85 
                                       6889999************999..................7777777777777777777777777777777777777 PP

                            AAA_21  78 lersqveeklssvetllesgllldkrsleeedvfnpeargirggvs 123
                                        +r +v      +++ ++sg  + +++++  d++        + v+
  gi|557694416|ref|YP_008797470.1|  86 DKRYRV------SREIKRSGKPRANLDEILADNSLKPLAVGQEKVT 125
                                       777777......6666666666666666666665555555555555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                            AAA_21 113 peargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrl 188
                                        e+ ++   + +++lk +   e+  ++++k+l +i ++ ++           +     + +++  +++ ++++q+l
  gi|557694416|ref|YP_008797470.1| 203 KEKLESLREELEEYLKKKKEREDLVEERMKLLKNIEKTEAE-----------YAEAEKLYKMLQEYDEFLNRRQKL 267
                                       22222222222222222222222223333333333333332...........333333333333333333333333 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.1
                            AAA_21 244 llalltallralkkg..sllliDEp 266
                                       l a+++all  +k     ++++DEp
  gi|557694416|ref|YP_008797470.1| 689 L-AFALALLPEAKGQkpEFVFLDEP 712
                                       5.66666666554446688999988 PP

>> MSA-2c  Merozoite surface antigen 2c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   3.4    0.0028       2.5      47     147 ..     173     290 ..     159     303 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0028
                            MSA-2c  47 ellkallesikgmkiileklnkflkelrknsdkleeDkekvvkYykkhiyakenvkdvtglvkvck....eflddes 119
                                       e ++ +le+++  k  le + +  + lr + +kle+ +e++ +Y kk+   ++ v +   l k  +    e+ + e 
  gi|557694416|ref|YP_008797470.1| 173 ESFNIVLENLEEQKRELEGTKERPGRLRVEKEKLESLREELEEYLKKKKEREDLVEERMKLLKNIEkteaEYAEAE- 248
                                       78999*******************************************9988877776655554431111343332. PP

                            MSA-2c 120 efyklvelykafa..............tdiaalkdvteeLlk 147
                                       + yk+ + y+ f                +  +l++  e Llk
  gi|557694416|ref|YP_008797470.1| 249 KLYKMLQEYDEFLnrrqkleleiegkrKQLETLRKQRETLLK 290
                                       334566667777678888775555555455555555555555 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 ?    7.7  11.6    0.0042       3.7      34     125 ..     203     299 ..     199     305 .. 0.85
   2 ?    0.7   2.5      0.59   5.3e+02      76     107 ..     479     509 ..     416     530 .. 0.42
   3 ?   10.5   0.6   0.00058      0.52      31     112 ..     549     629 ..     544     634 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0042
                                       CHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHHHCCCHHHHHHHCCHHHH CS
                         Fib_alpha  34 kkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn......dnvikksskeleeeilrlketidaqesni 104
                                       k++le+l++elee+ +++ke e+lv+e ++ l++ +k++++        ++++++ + l+ + ++l+ +i  + +++
  gi|557694416|ref|YP_008797470.1| 203 KEKLESLREELEEYLKKKKEREDLVEERMKLLKNIEKTEAEYaeaeklYKMLQEYDEFLN-RRQKLELEIEGKRKQL 278
                                       689999********9999999999999888888887777764333345677889999999.9*************** PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 105 rvLqnvlesneqkiqkLeqdi 125
                                       + L++  e++ ++i++ e+d+
  gi|557694416|ref|YP_008797470.1| 279 ETLRKQRETLLKNIENTESDM 299
                                       **************9999886 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.59
                                       HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  76 dnvikksskeleeeilrlketidaqesnirvL 107
                                       + v+++ +k+ + e ++lk ++da  +++++L
  gi|557694416|ref|YP_008797470.1| 479 EAVLQQAEKDRQ-ELNDLKSKLDAYREQLKNL 509
                                       233333333322.4444444444444444444 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00058
                                       CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvL 107
                                       ++ +k++++l ++++ ++ +t+  ++lv e+++ lr++   ++  ++ +  +  +le+e + +++ + a   + ++L
  gi|557694416|ref|YP_008797470.1| 549 EEARKRVQQLAENIQAYRTRTELLSQLVLELEEWLRAHGDVEQRYSEQL-AVVANLERELAVVRKAVEAIQATAEAL 624
                                       56789***********************************999755554.566789999999999999999999999 PP

                                       HHHHH CS
                         Fib_alpha 108 qnvle 112
                                       +n ++
  gi|557694416|ref|YP_008797470.1| 625 RNRVK 629
                                       99987 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9  11.0      0.64   5.8e+02     176     255 ..     144     225 ..     114     230 .. 0.42
   2 ?    2.6  29.2     0.059        53     146     278 ..     194     322 ..     178     330 .. 0.71
   3 ?   -2.9   0.1       2.8   2.5e+03     179     204 ..     417     441 ..     412     456 .. 0.60
   4 ?   15.0   9.3   9.7e-06    0.0087     133     260 ..     467     610 ..     465     637 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.64
                              Spc7 176 kaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkk......elaelqeqleeleekieelkeqksel 246
                                           ++el+kl e ++e    d++++ ++  +l++ +  +e++++       ++e+  +l   +ek+e+l+e+ +e+
  gi|557694416|ref|YP_008797470.1| 144 TVVAQKELNKLIELRKE----DRKKIINVFLNLESFNIVLENLEEqkreleGTKERPGRLRVEKEKLESLREELEEY 216
                                       44445555555552222....33333333333333333222111100000022222223333333333333333333 PP

                              Spc7 247 eeeiaeaer 255
                                        ++ +e e+
  gi|557694416|ref|YP_008797470.1| 217 LKKKKERED 225
                                       333333333 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.059
                              Spc7 146 enlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelr.eelaelkaeieekkke 221
                                       e+   l+ +ke+Le+ +eel+e+l++ +e+++ +ee+++ l++       i+k+e e +  e+l +  +e++e+ ++
  gi|557694416|ref|YP_008797470.1| 194 ERPGRLRVEKEKLESLREELEEYLKKKKEREDLVEERMKLLKN-------IEKTEAEYAEaEKLYKMLQEYDEFLNR 263
                                       3333455566666666666666666666666666666666666.......444444444315677778888888889 PP

                              Spc7 222 laelqeqleeleekieelkeqkseleeeiaeaervleeckgws..esevsrlkeevkal 278
                                        ++l+ ++e +++++e+l++q+++l ++i++ e+ +++ ++    e+e+++l +e+++l
  gi|557694416|ref|YP_008797470.1| 264 RQKLELEIEGKRKQLETLRKQRETLLKNIENTESDMHRYRDLHlvEKELESLSKEYQQL 322
                                       999********************************999998654489999999999987 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.8
                              Spc7 179 leeeleklqeaaeelesidkeeLeel 204
                                       l+e+l++l++ a+e+ +  ++ L++l
  gi|557694416|ref|YP_008797470.1| 417 LQETLARLEQ-AREMHATARATLRNL 441
                                       6666666666.445555555555554 PP

  == domain 4  score: 15.0 bits;  conditional E-value: 9.7e-06
                              Spc7 133 RmqllegLkegleenlegleedkelLekqeeeldellpelee.....ekaeleeeleklqeaaeeles........i 196
                                         +l+egL + +e  l++ e+d+++L++ +++ld++ ++l++     e +++e+e+++l e+ e +           
  gi|557694416|ref|YP_008797470.1| 467 QQKLVEGLPKAVEAVLQQAEKDRQELNDLKSKLDAYREQLKNlpaehELNQVESEIHSLGEQLEGVRLptlspgleF 543
                                       579***********************************998622222455888888888885554444667778778 PP

                              Spc7 197 dkeeLeelreelaelkaeieekk...kelaelqeqleeleekieelkeqkseleeeiaeaervleec 260
                                        ++ Lee+r+++++l ++i++ +   + l++l  +lee   +  ++++++se  + +a+ er l   
  gi|557694416|ref|YP_008797470.1| 544 SRDVLEEARKRVQQLAENIQAYRtrtELLSQLVLELEEWLRAHGDVEQRYSEQLAVVANLERELAVV 610
                                       8999999999888888887765511155666666777777777777777777777777777665543 PP

>> FAA_hydrolase_N  Fumarylacetoacetase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.056        51      48      71 ..     142     165 ..     109     192 .. 0.80
   2 ?    0.7   0.5      0.63   5.7e+02      64     102 ..     202     240 ..     198     244 .. 0.75
   3 ?   -2.0   0.1       4.4   3.9e+03      55      92 ..     265     303 ..     241     313 .. 0.60
   4 ?    3.8   0.1     0.072        65      48      83 ..     412     446 ..     386     462 .. 0.76
   5 ?    6.0   0.3     0.015        13      41     101 ..     521     581 ..     499     586 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.056
                                       SSGTTSSSSSHHHHHT-HHHHHHH CS
                   FAA_hydrolase_N  48 kesvfsqptLnafaalgrevwrav 71 
                                        ++v++q++Ln++++l +e ++++
  gi|557694416|ref|YP_008797470.1| 142 SSTVVAQKELNKLIELRKEDRKKI 165
                                       56788***********99877654 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.63
                                       -HHHHHHHHHHHHHHHBTSHHHHT-HHHHHHHEEEGGGE CS
                   FAA_hydrolase_N  64 grevwravRaalqelLsaeeelrdneelreealvpleev 102
                                       ++e  +++R++l e L++++e +d  e r ++l ++e+ 
  gi|557694416|ref|YP_008797470.1| 202 EKEKLESLREELEEYLKKKKEREDLVEERMKLLKNIEKT 240
                                       57778899********77777777777777777776665 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4.4
                                       SSSHHHHHT-HHHHHHHHHHHHHHHBT.SHHHHT-HHHH CS
                   FAA_hydrolase_N  55 ptLnafaalgrevwravRaalqelLsa.eeelrdneelr 92 
                                       ++L+  ++ +r+  +++R++  +lL++ e++ +d ++ r
  gi|557694416|ref|YP_008797470.1| 265 QKLELEIEGKRKQLETLRKQRETLLKNiENTESDMHRYR 303
                                       556666666677777777777777765544444444444 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.072
                                       SSGTTSSSSSHHHHHT-HHHHHHHHHHHHHHHBTSH CS
                   FAA_hydrolase_N  48 kesvfsqptLnafaalgrevwravRaalqelLsaee 83 
                                        + ++ q+tL ++ ++ re++ ++Ra+l +l+++++
  gi|557694416|ref|YP_008797470.1| 412 SRMMVLQETLARL-EQAREMHATARATLRNLIQNHS 446
                                       4556688888876.7789*************95533 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.015
                                       TGG...SSSGTTSSSSSHHHHHT-HHHHHHHHHHHHHHHBTSHHHHT-HHHHHHHEEEGGG CS
                   FAA_hydrolase_N  41 leedaeekesvfsqptLnafaalgrevwravRaalqelLsaeeelrdneelreealvplee 101
                                        +++  e+ + ++ ptL   ++  r+v +++R+++q+l ++ ++ r+ +el ++++++lee
  gi|557694416|ref|YP_008797470.1| 521 EIHSLGEQLEGVRLPTLSPGLEFSRDVLEEARKRVQQLAENIQAYRTRTELLSQLVLELEE 581
                                       34445556666677999999*******************8888999999999999888876 PP

>> V-SNARE_C  Snare region anchored in the vesicle membrane C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.051        46      27      44 ..     178     195 ..     176     199 .. 0.93
   2 ?    1.7   0.2      0.37   3.3e+02      28      39 ..     278     289 ..     275     295 .. 0.87
   3 ?   -0.4   0.2       1.6   1.4e+03      16      34 ..     426     444 ..     418     447 .. 0.74
   4 ?    0.1   0.2       1.2     1e+03      26      49 ..     480     503 ..     477     508 .. 0.82
   5 ?    4.8   0.0     0.038        34      33      53 ..     543     563 ..     540     567 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.051
                         V-SNARE_C  27 iledLhsQretLkrarsk 44 
                                       +le+L +Q+  L++++++
  gi|557694416|ref|YP_008797470.1| 178 VLENLEEQKRELEGTKER 195
                                       79*************988 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.37
                         V-SNARE_C  28 ledLhsQretLk 39 
                                       le+L++QretL 
  gi|557694416|ref|YP_008797470.1| 278 LETLRKQRETLL 289
                                       799*******95 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.6
                         V-SNARE_C  16 ivdetisiGaailedLhsQ 34 
                                       ++ e+ + + a+l++L + 
  gi|557694416|ref|YP_008797470.1| 426 QAREMHATARATLRNLIQN 444
                                       5678888888888888765 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 1.2
                         V-SNARE_C  26 ailedLhsQretLkrarsklhnva 49 
                                       a+l++  ++r+ L++ +skl    
  gi|557694416|ref|YP_008797470.1| 480 AVLQQAEKDRQELNDLKSKLDAYR 503
                                       678888999*********997655 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.038
                         V-SNARE_C  33 sQretLkrarsklhnvanrlg 53 
                                         r++L+ ar++++++a+++ 
  gi|557694416|ref|YP_008797470.1| 543 FSRDVLEEARKRVQQLAENIQ 563
                                       5699*************9986 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  11.3    0.0021       1.9     326     517 ..     142     335 ..     118     371 .. 0.52
   2 ?    5.4   0.1    0.0066       5.9      68     155 ..     439     524 ..     429     531 .. 0.86
   3 ?   -0.0   0.7      0.29   2.6e+02     327     414 ..     550     615 ..     536     636 .. 0.43

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHCT-H.HHHTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHHHH.... CS
                     Peptidase_S46 326 ekkqaeeaalrawlkkdpekkekygkalselealvkekrklaersalleeaessgsellslarklvrlaeerekpda 402
                                        +   ++++l++ ++ ++e ++k+ +++ +le+     ++l+e+++ le ++ +  +l    +kl++l ee e  + 
  gi|557694416|ref|YP_008797470.1| 142 SSTVVAQKELNKLIELRKEDRKKIINVFLNLESFNIVLENLEEQKRELEGTKERPGRLRVEKEKLESLREELE--EY 216
                                       5555555555555555555555555555555555555555555555555555555555555555555555555..44 PP

                                       HH-HHHHHHHHHHHHHHCHHHHCS--HHHHHHHHHHHHHHHHHHS-GGG--S----SS...........-S-SHHCC CS
                     Peptidase_S46 403 ereeeyqeralealekeleridkdldaevdkavlaallkeyreklkaerlpavdkvlgkes.....kgdlealvdrl 474
                                        ++++ +e+ +e+ +k l++i+k+  + ++ + l ++l+ey e l++ +  +++  ++ ++      ++ ++++ + 
  gi|557694416|ref|YP_008797470.1| 217 LKKKKEREDLVEERMKLLKNIEKTEAEYAEAEKLYKMLQEYDEFLNRRQ--KLELEIEGKRkqletLRKQRETLLKN 291
                                       4555555555555555555555555555555555555555555555333..22222222222233322222333333 PP

                                       CCC-TTSSCHHHH.HHT-SHHCHHHHCC-HHHHHHHHHHHHHHH CS
                     Peptidase_S46 475 vakskladeakrk.alleeakaaveaskDplielavaladaraa 517
                                       +++++ + ++ r+ +l+e++ ++++++  +l+ l  ++ +ar+a
  gi|557694416|ref|YP_008797470.1| 292 IENTESDMHRYRDlHLVEKELESLSKEYQQLVTLEHQIGEAREA 335
                                       44444444443321444445555555555555555554444444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0066
                                       HHHHHHT--SSS-HHHH-EE-SSGGGSBE-TT--EEEEEEEEE-HHHHTTTTTTSS-CHHHHHHHHHHHHHHHHHS- CS
                     Peptidase_S46  68 ygaiqqhssaekdylkdGFlAksreeElpapglrvtvleritdVTkrvkaalkaeeeeeerakaieaelkalakece 144
                                       ++ iq+hs +   ylk++F +  r  El  ++l     ++++ V ++ +++ ++ ++ ++  +a +++lk+l +e e
  gi|557694416|ref|YP_008797470.1| 439 RNLIQNHSVK-TSYLKNAFSSLPRYGELFQQKLVEGLPKAVEAVLQQAEKDRQELNDLKSKLDAYREQLKNLPAEHE 514
                                       6778888865.99****************************************999999999999999999999966 PP

                                       --TT-EEEEEE CS
                     Peptidase_S46 145 eedglrcevas 155
                                        + +++ e++s
  gi|557694416|ref|YP_008797470.1| 515 LN-QVESEIHS 524
                                       55.66666665 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHCT-H.HHHTTHHHHHHHHHHHHHHHHHHHHHHHHHTTTTSHHHHHHHHHHHHHHHHH....H CS
                     Peptidase_S46 327 kkqaeeaalrawlkkdpekkekygkalselealvkekrklaersalleeaessgsellslarklvrlaeerekpdae 403
                                       + +++ ++l++ +++  +++e + +++ ele+ ++++ ++++r+    ++                       ++ e
  gi|557694416|ref|YP_008797470.1| 550 EARKRVQQLAENIQAYRTRTELLSQLVLELEEWLRAHGDVEQRYSEQLAV----------------------VANLE 604
                                       44444444444444444444444444444444444443333332211111......................12222 PP

                                       H-HHHHHHHHH CS
                     Peptidase_S46 404 reeeyqerale 414
                                       re  + ++a+e
  gi|557694416|ref|YP_008797470.1| 605 RELAVVRKAVE 615
                                       22222222222 PP

>> Phage_tail_APC  Phage tail assembly chaperone protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.45   4.1e+02       2      40 ..     279     322 ..     278     336 .. 0.66
   2 ?   -2.7   0.2       6.2   5.6e+03      25      43 ..     423     441 ..     405     445 .. 0.54
   3 ?    8.1   0.2    0.0026       2.4      22      47 ..     488     513 ..     476     519 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHH.....HTHHHHSTTS---HHHHHHHHHHHHHH CS
                    Phage_tail_APC   2 aevRaeRdrrLa.....asDwvqlpDspldeeerqalkaYrqaL 40 
                                       +++R++R  +L+     +sD+ + +D +l e+e + l +  q L
  gi|557694416|ref|YP_008797470.1| 279 ETLRKQRETLLKnientESDMHRYRDLHLVEKELESLSKEYQQL 322
                                       57899999999722222455688888888888877776655555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.2
                                       --HHHHHHHHHHHHHHHHS CS
                    Phage_tail_APC  25 ldeeerqalkaYrqaLRDl 43 
                                       + e++r+  ++ r  LR+l
  gi|557694416|ref|YP_008797470.1| 423 RLEQAREMHATARATLRNL 441
                                       3344566667778888877 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0026
                                       TS---HHHHHHHHHHHHHHHHS---S CS
                    Phage_tail_APC  22 DspldeeerqalkaYrqaLRDlPeqe 47 
                                       D++  ++ +++l+aYr  L +lP+  
  gi|557694416|ref|YP_008797470.1| 488 DRQELNDLKSKLDAYREQLKNLPAEH 513
                                       333334449**************875 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 ?   -1.1   5.2       2.6   2.3e+03      38      89 ..     203     263 ..     198     340 .. 0.55
   2 ?    9.7   0.3    0.0012       1.1      19     108 ..     437     523 ..     429     539 .. 0.80
   3 ?    3.4   0.2      0.11     1e+02      20      93 ..     555     624 ..     541     669 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.6
                                       TTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHH......H CS
                           T3SSipB  38 qeaasklSdelqtalseakgatddleaaiekadqaks...aadaatkkvdeaqk......r 89 
                                       +e+++ l +el++ l++ k+  d +e+ ++ ++++++   ++ +a+k  +  q+      r
  gi|557694416|ref|YP_008797470.1| 203 KEKLESLREELEEYLKKKKEREDLVEERMKLLKNIEKteaEYAEAEKLYKMLQEydeflnR 263
                                       5666777777777777777777777777666666543000222333222222222223332 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                                       CHHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--- CS
                           T3SSipB  19 SLsqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaP 95 
                                        L +L ++  +  +  k +   + +  + +q+ l   +g+ +++ea  ++a++  ++ ++++ k+d+  ++lk+L P
  gi|557694416|ref|YP_008797470.1| 437 TLRNLIQNHSVKTSYLKNAFSSLPRYGELFQQKL--VEGLPKAVEAVLQQAEKDRQELNDLKSKLDAYREQLKNL-P 510
                                       5666666666666666777777777777777766..5699999********************************.9 PP

                                       ------CHHHHHH CS
                           T3SSipB  96 dePekakleaaeq 108
                                       +e e  ++e + +
  gi|557694416|ref|YP_008797470.1| 511 AEHELNQVESEIH 523
                                       9999999988765 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  20 LsqLenrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                        +qL ++++a++       e +s+l  el++ l +  ++ + + ++ + + +++ +   + k+v+++q+  + L
  gi|557694416|ref|YP_008797470.1| 555 VQQLAENIQAYRTR----TELLSQLVLELEEWLRAHGDVEQRYSEQLAVVANLERELAVVRKAVEAIQATAEAL 624
                                       67888888888764....45666777777777788888888888888888888888888888888888744444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (767 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2624  (0.146355); expected 358.6 (0.02)
Passed bias filter:                      801  (0.0446762); expected 358.6 (0.02)
Passed Vit filter:                       140  (0.00780858); expected 17.9 (0.001)
Passed Fwd filter:                        74  (0.00412739); 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: 1.52u 0.35s 00:00:01.87 Elapsed: 00:00:00.56
# Mc/sec: 4138.53
//
Query:       gi|557694417|ref|YP_008797471.1|  [L=239]
Description: phosphohydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   26.8   2.2      7e-06   26.3   2.2    1.6  1  HD        HD domain
    0.00016   21.8   0.3     0.0002   21.6   0.3    1.2  1  HD_6      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 !   26.3   2.2   7.8e-10     7e-06       3      93 ..      13     112 ..      11     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 7.8e-10
                                       HHHHHHHHHHHHHHHHHHH............HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHH CS
                                HD   3 eHsleVaklarrlaedlge............eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeil 67 
                                       eH +  ++++    +d+g+             e++  l++a ++HD Gk    d+ +kke ++ +f++He ++a+ +
  gi|557694417|ref|YP_008797471.1|  13 EHLITCLRFLDSHFIDRGYavhvaycfgideAEAVKALKTAVIFHDYGKAA--DEYQKKESKKLSFPKHEYFSATAA 87 
                                       677777777777777777777777777777779******************..65566666699**********999 PP

                                       HHHHHHHHHHHHHHHHHHHTTCCHHH CS
                                HD  68 revekrlgldledvaklirehheswe 93 
                                       +++ k   +  ++ + +i +hh  + 
  gi|557694417|ref|YP_008797471.1|  88 HKSIKETVW-RDECLMAIGWHHMAMK 112
                                       999888844.8888889988887665 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.3   2.2e-08    0.0002      42     121 ..      39     109 ..      14     182 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.2e-08
                                       C.TS-HHHHHHHHHHHHHCCCGGGSSHHHHTTS----TTS-.....-GGGT----HHHHHHHHHHHHHHHHHHHHHT CS
                              HD_6  42 lrgleeealrrllaflaalHDlGKaspaFqakvpelaekleeaglelekelekarHdslgaalleevarslaaavgg 118
                                       + g++e+++ + l   ++ HD+GKa++++q+k +++++  +++   ++    +a H+s+   +    +++ + a+g 
  gi|557694417|ref|YP_008797471.1|  39 F-GIDEAEAVKALKTAVIFHDYGKAADEYQKKESKKLSFPKHE--YFS---ATAAHKSIKETVW---RDECLMAIGW 106
                                       3.899999*************************7666644433..222...7899*99999994...7899999999 PP

                                       TTS CS
                              HD_6 119 HHG 121
                                       HH 
  gi|557694417|ref|YP_008797471.1| 107 HHM 109
                                       996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1798.80
//
Query:       gi|557694418|ref|YP_008797472.1|  [L=537]
Description: CRISPR-associated helicase Cas3 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   49.9   0.0    6.5e-13   49.0   0.0    1.5  1  Helicase_C       Helicase conserved C-terminal domain
      2e-05   24.5   0.7     0.0013   18.5   0.0    3.3  3  DEAD             DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.036   14.1   0.2      0.066   13.2   0.2    1.4  1  CagS             Cag pathogenicity island protein S of Helico
       0.15   11.5   0.1        0.4   10.1   0.1    1.6  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   1.5e-16   6.5e-13      15     110 ..     269     359 ..     257     360 .. 0.87

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.5e-16
                                       TTSEEEEEESSHHHHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEE CS
                        Helicase_C  15 eggkilifvntidrlek.vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVin 90 
                                       + +++li++nt++++++  +ll   ++  ++ lhg+l++++r+ +l++ ++g+  v+++t+v+e G++i   +l+i 
  gi|557694418|ref|YP_008797472.1| 269 VWDRVLIMANTVEKAKHlYRLL---SDADAVLLHGRLTKKDRQNVLDNLKNGKKWVVVSTQVVEAGVNIS-SELMIT 341
                                       56799********997444444...6799****************************************5.888888 PP

                                       SSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  91 fdlprnvtsyiqriGRtgRa 110
                                         +p   +s++qr+GR++R+
  gi|557694418|ref|YP_008797472.1| 342 ELAPA--SSLVQRAGRVARY 359
                                       88884..69**********6 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.9e-07    0.0013      15     112 ..      35     130 ..      21     213 .. 0.72
   2 ?   -1.0   0.1      0.29   1.3e+03      62     106 ..     278     326 ..     271     342 .. 0.55
   3 ?    2.1   0.0     0.032   1.4e+02     102     157 ..     438     489 ..     380     495 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.9e-07
                                       CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE.EEETTSSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
                              DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl.liiggvaardq 90 
                                       g  +v+ +TG+GKT   +   l++++e   ++  + + v P+r+++ + ++ + k ++ i+++    i+ ++     
  gi|557694418|ref|YP_008797472.1|  35 GVNVVQLPTGYGKTSLSIACGLKSIVE--PREYLRSIHVLPLRSIIDDAYKSTVKNLQRIGITNPeEIVAEQMMGAP 109
                                       56689********************98..99999*****************99999998884433244444444444 PP

                                       HHHHHTTCSEEEEEHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  91 lskldngvdivvgtpgrlddll 112
                                        s +  + div+ t + +  ++
  gi|557694418|ref|YP_008797472.1| 110 GSPF-LNKDIVFVTYETFKFHM 130
                                       4444.56677777776666544 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.29
                                       HHHHHHHHHTTT.STSEEEEEET...TSSHHHHHHHHHTTCSEEEEEHH CS
                                       xxxxxxxxxxxx.xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  62 qtlnnlkkfkky.idlrvlliig...gvaardqlskldngvdivvgtpg 106
                                       +t++++k +     d  ++l+ g   ++++++ l++l+ng + vv  ++
  gi|557694418|ref|YP_008797472.1| 278 NTVEKAKHLYRLlSDADAVLLHGrltKKDRQNVLDNLKNGKKWVVVSTQ 326
                                       4444455444442334444444411155555556666677666666554 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.032
                                       EEEHHHHHHHHHCTSSHCTTE.EEEEEETHHHHHHT.TTHHHHHHHHHHSHHHCTTST CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 102 vgtpgrlddllstgklnlsqv.rflVlDEadrlldq.gfsdfinrilnqlpqitcdgk 157
                                       v+tp + ++l++      + v ++ V D +d+l ++ +f  ++++++ ++pq+t+  +
  gi|557694418|ref|YP_008797472.1| 438 VSTPHQAQNLIR------DTVtTVYVADDIDKLEKDnSFTTDLQQLAYKFPQATAIIQ 489
                                       444444444443......33326789*******98889********999999987665 PP

>> CagS  Cag pathogenicity island protein S of Helicobacter pylori
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   1.5e-05     0.066      47     101 ..     243     300 ..     232     311 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHCC-HHHHHHHHHHHSSSH...HHHHHHT-HHHHHHHHHHHHHHHHHHHHH CS
                              CagS  47 mhdffkqmhtnkgaldkvlrnymkdy...raviksigvdkfkkvyrllesetmellha 101
                                       m+    + + + g+l+ v+rn ++d    r +i +  v+k k++yrll      llh 
  gi|557694418|ref|YP_008797472.1| 243 MKSKKIETYLEEGSLEDVVRNRLRDAvwdRVLIMANTVEKAKHLYRLLSDADAVLLHG 300
                                       554444556689************95455999****************9999999995 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 ?   10.1   0.1   8.9e-05       0.4      18      93 ..     272     352 ..     258     366 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 8.9e-05
                   Glyco_transf_21  18 KvnnllqaleaakydllvisDsdvrvkpdyL.....eellaaledpkvglVtslpvgsdakglaaaleaaflntlag 89 
                                       +v  +++++e+ak+ + ++sD+d+++    L     +++l +l+  k ++V+s+ v+ +  ++ ++l    l++ + 
  gi|557694418|ref|YP_008797472.1| 272 RVLIMANTVEKAKHLYRLLSDADAVLLHGRLtkkdrQNVLDNLKNGKKWVVVSTQVVEAGVNISSELMITELAPASS 348
                                       677799******************98877773333358*****************************9999988888 PP

                   Glyco_transf_21  90 vlqa 93 
                                       ++q+
  gi|557694418|ref|YP_008797472.1| 349 LVQR 352
                                       8877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3563.57
//
Query:       gi|557694419|ref|YP_008797473.1|  [L=220]
Description: hypothetical protein CSUB_C0990 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1526.93
//
Query:       gi|557694420|ref|YP_008797474.1|  [L=153]
Description: hypothetical protein CSUB_C0991 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   12.9   0.0      0.061   12.8   0.0    1.1  1  Sulfotransfer_1  Sulfotransferase domain
      0.075   12.2   0.0       0.09   11.9   0.0    1.0  1  Melibiase_2      Alpha galactosidase A


Domain annotation for each model (and alignments):
>> Sulfotransfer_1  Sulfotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.8e-06     0.061      68     133 ..      56     122 ..      12     146 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-06
                                       HTTTEEHHHHHHHSTSS.EEEE...GGGS..CHHHHTT-EEEEEE--HHHHHHHHHHHHHHBTTSTT CS
                   Sulfotransfer_1  68 yshvaekvvrlralesprllktHlplkllp.kslldsnlKiiylvRnpkdvavSryhfsrslkklke 133
                                       ++ +++  + l++ +++ ++k+H++   +  k + ++nlKi   +R   d++ S+     ++++ k+
  gi|557694420|ref|YP_008797474.1|  56 AQVFQNAQQLLANKNELPPIKPHFNDRQVMaKIMRKLNLKINDTYREYVDALCSWAIKDLQKNPDKW 122
                                       4566778888999999********9866550556678*****************9887777765554 PP

>> Melibiase_2  Alpha galactosidase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     1e-05      0.09      90     173 ..      34     118 ..      21     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1e-05
                                       T-EEEEEEESSSB-TTSSB--TTTHHHHHHHHHHHT--EEEEE-TSSSHHHHHHHHHHHHHHHHHTTS--EEE.E-H CS
                       Melibiase_2  90 glklgiyadlgtktcagypgslkyleidaktfadwgvdllkldgcysnleelaegykelslalnktgrsivys.cew 165
                                       g  l iy+d  + + ag  gsl ++ ++a+ +     +l  +   +++ + +a+  ++l+l +n t r+ v + c+w
  gi|557694420|ref|YP_008797474.1|  34 GTTLDIYEDEAVVSGAGAIGSLAQVFQNAQQLLANKNELPPIKPHFNDRQVMAKIMRKLNLKINDTYREYVDAlCSW 110
                                       67899*************************9999999*******************************998655*** PP

                                       HHHH.TTT CS
                       Melibiase_2 166 plyavvkk 173
                                        +   +k+
  gi|557694420|ref|YP_008797474.1| 111 AIKDLQKN 118
                                       98775554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1126.43
//
Query:       gi|557694421|ref|YP_008797475.1|  [L=252]
Description: CRISPR-associated protein, Cas5 family [Candidatus Caldiarchaeum subterraneum]
Scores for 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   21.2   0.1     0.0016   18.4   0.0    2.1  2  DUF3764    Protein of unknown function (DUF3764)
    0.00084   19.3   0.0     0.0017   18.3   0.0    1.5  1  Cas_Cas5d  CRISPR-associated protein (Cas_Cas5)


Domain annotation for each model (and alignments):
>> DUF3764  Protein of unknown function (DUF3764)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.11   9.8e+02      23      41 ..      52      70 ..      47      75 .. 0.79
   2 !   18.4   0.0   1.8e-07    0.0016      19      65 ..      89     134 ..      81     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.11
                           DUF3764 23 eeakkmhkevgikslyrGv 41
                                      e+++   ++  i++l++G+
  gi|557694421|ref|YP_008797475.1| 52 ENSESNSSAEKIRTLFKGI 70
                                      56667778999******97 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.8e-07
                           DUF3764  19 ifdseeakkmhkevgikslyrGvsk.dDpkkvivifqapegvaekife 65 
                                        +d +e++ + +++++  +yrGvs+ dD+ k++ +f+     ++k+f+
  gi|557694421|ref|YP_008797475.1|  89 SYDVDEKQIRTDAAAVSKIYRGVSSaDDSVKIVYLFEE--QDVRKFFD 134
                                       5899******************9753888888888764..44566665 PP

>> Cas_Cas5d  CRISPR-associated protein (Cas_Cas5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.9e-07    0.0017      19     154 ..      22     165 ..      12     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.9e-07
                                       CSCCCBESS--HHHHHHHHHHHHT--TTS--CCCCTTEEEEEEE............EEEEEEEE.TEEEEECT..-G CS
                         Cas_Cas5d  19 kveretydvPtkSavlGllaaalGirrdddleelkpalrwgvrv............drrgellr.gdyhtvag..rt 80 
                                        + r++++ +++++++G la++++++       ++++   +  +             ++ +l++ +d++++ +  + 
  gi|557694421|ref|YP_008797475.1|  22 TKSRPALKTIPPTTLIGALAQPIALKNH-----WAENSESNSSAekirtlfkgiylSQNLPLIEyNDLSKIFSydVD 93 
                                       678999*****************66665.....44444444444444446667776777777776666666546444 PP

                                       GGS--BSSS----CCEEEEEEEEEEEECEEEEEECCSCCH.HHHHHH.HHHHHHTTSSSSE.SSSTTSEEEECESET CS
                         Cas_Cas5d  81 lperrkektadrkkraatvlseraYladahfevalegeee.gkllee.laralrkpvwply.LGrkecivpvepvea 154
                                       +++ r+++   +  ++++ +s  +   d + +v l  e + +k +++  +++l + +w ++ LG +e+iv+v+ v  
  gi|557694421|ref|YP_008797475.1|  94 EKQIRTDA--AAVSKIYRGVSSAD---DSVKIVYLFEEQDvRKFFDVgWEEMLLEAAWSITrLGARESIVSVDKVSI 165
                                       44444444..33445555555554...6666666666666756666538************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1939.20
//
Query:       gi|557694422|ref|YP_008797476.1|  [L=360]
Description: CRISPR-associated autoregulator, DevR family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-66  222.8   0.0    6.1e-66  222.2   0.0    1.2  1  DevR      CRISPR-associated negative auto-regulator DevR/Csa2


Domain annotation for each model (and alignments):
>> DevR  CRISPR-associated negative auto-regulator DevR/Csa2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.2   0.0   3.4e-70   6.1e-66       1     268 [.       5     303 ..       5     304 .. 0.95

  Alignments for each domain:
  == domain 1  score: 222.2 bits;  conditional E-value: 3.4e-70
                                       EEEEEE-------------------EEEEEE--T..T--EEEEEE-THHHHHHHHHHHHHHHHTS...TTSSBHHHH CS
                              DevR   1 isgrvvvnveaLNmdesvGNytehrkvpvvlkee..ykvrtvpaiSgeslkHayfetlvklaken...nlpvcelck 72 
                                       +++r++ nveaLNm+es+GN+ +hrk+p+v++++  +k+ +vpaiSgesl Hay++++v+ a++    ++p++e  k
  gi|557694422|ref|YP_008797476.1|   5 MGVRFLCNVEALNMVESIGNLSKHRKAPIVIPTTdgFKLLYVPAISGESLGHAYQQAIVEEAINFygeKAPLDEWSK 81 
                                       579*****************************999************************99987666689******* PP

                                       TT------TT--EEEBTTS...................EESS-HHHHHHH-HHHHHH-EEEGGGT..EEE--SEEE- CS
                              DevR  73 rvegdggvikfatekklke...................kelkvekeiikecvveDvfGfLitekeksvkRkspvkfs 130
                                       r    g++ikf + k++ +                   ++ +vek++ik ++v+D++GfL +e   +vkR+s ++++
  gi|557694422|ref|YP_008797476.1|  82 R----GEFIKFGDLKHMPSelssiikpksgkkedetvdQKHQVEKTAIKLSIVADIGGFLVAEGV-PVKRTSCFQIG 153
                                       *....*******99999999*****************999*********************9666.5********** PP

                                       -BEE-TTTTTTT.-----------.............------------------HHHHHSSEEEEEEEEEGGGTTS CS
                              DevR 131 yavpveesekav.vdaqfharydl.............lenrarkkgeeeekqnifqvEehsalYalsfvlDldriGk 193
                                       yavpv ++  ++ +++qfh+ry               +e+++ k  +e ++q+i++vE +sa+Y+++f+++ld+iG+
  gi|557694422|ref|YP_008797476.1| 154 YAVPVFDALDSTaMESQFHVRYVAsetvkqeesqeggEEKNQAKTVKERQGQAIYYVELASAVYGFTFNINLDSIGR 230
                                       *********9999**********99**********997777777888****************************** PP

                                       -TTS--EE---S-HHHHHHHHHHHHHTHHHHHH--.------------EEEEEEEE--S.SS------TTTTHHHHH CS
                              DevR 194 pevkkskieyvleeeerkkRikaalkallnlLsgs.fgakrarllPvfeveslvaavsk.kpfpvfpirledyveee 268
                                       +++     +++  + +r +R+k al a ++l++g+ fgakr+r+lP+ +v+sl a+vs+  pf+ +p+++ d+ve++
  gi|557694422|ref|YP_008797476.1| 231 TSM----VKVEDAVTDRLDRMKIALLAAARLFTGHsFGAKRSRFLPIEDVLSLGAVVSRqRPFVISPPQFPDFVENT 303
                                       ***....677777799*******************************************99*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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 0.21s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2886.30
//
Query:       gi|557694423|ref|YP_008797477.1|  [L=131]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   33.0   1.3     0.0021   18.3   0.2    2.2  2  Cas_Csa5  CRISPR-associated protein (Cas_Csa5)


Domain annotation for each model (and alignments):
>> Cas_Csa5  CRISPR-associated protein (Cas_Csa5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.2   1.2e-07    0.0021       4      41 ..      53      90 ..      50      93 .. 0.88
   2 !   14.1   0.1   2.4e-06     0.043      73     105 ..      94     126 ..      91     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-07
                          Cas_Csa5  4 sesptlvDRianaLskeavakvlydaqRivqmglerge 41
                                        +  +vDR+ana ++  +++++++a R  ++  + ge
  gi|557694423|ref|YP_008797477.1| 53 ESKYGYVDRLANAFNHRIAEVAVMEALREARSAADAGE 90
                                      55678*************************99999887 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.4e-06
                          Cas_Csa5  73 lpsdedvedFlelverDiyvarkvgalalaian 105
                                       +ps+  v + +el+++D+  a+  +alala+++
  gi|557694423|ref|YP_008797477.1|  94 IPSETHVIKVVELMKKDLSAAKVLAALALAFPE 126
                                       799***************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1070.25
//
Query:       gi|557694424|ref|YP_008797478.1|  [L=218]
Description: CRISPR-associated protein, Cas3 family [Candidatus Caldiarchaeum subterraneum]
Scores for 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   17.6   0.2     0.0063   16.3   0.2    1.8  1  HTH_IclR     IclR helix-turn-helix domain
     0.0075   15.0   0.0     0.0097   14.6   0.0    1.1  1  DUF1887      Domain of unknown function (DUF1887)
  ------ inclusion threshold ------
       0.01   15.9   0.1      0.019   15.0   0.1    1.5  1  HTH_20       Helix-turn-helix domain
      0.012   15.3   0.0      0.016   14.9   0.0    1.2  1  Cas_NE0113   CRISPR-associated protein NE0113 (Cas_NE0113)
       0.05   14.1   0.2       0.16   12.5   0.2    1.9  1  HTH_27       Winged helix DNA-binding domain
       0.13   12.2   0.1       0.26   11.2   0.1    1.7  2  Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
       0.13   12.1   0.9       0.45   10.4   0.2    2.2  2  TrmB         Sugar-specific transcriptional regulator TrmB


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 !   16.3   0.2   2.5e-06    0.0063      12      49 ..     155     192 ..     152     195 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.5e-06
                                       -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  12 laeapqeltlselArrtglpkStvhRlLqtLvelGyve 49 
                                       l++a    ++  lA+ + lp +t++R +  L+++G++ 
  gi|557694424|ref|YP_008797478.1| 155 LEAAKNSESVVALAKTARLPLATAYRRVVALEKMGLLS 192
                                       66666667999*************************97 PP

>> DUF1887  Domain of unknown function (DUF1887)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   3.8e-06    0.0097      29     106 ..      30     113 ..      14     131 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.8e-06
                           DUF1887  29 hlvlivteaq....kekanrlekvlke..kgidveifeledevdleeleeslkglleelkaaeevvlNvtgGtklma 99 
                                       ++v iv  +       + + +++ l +   g++ e++ ++     +++   lk l++e k   +v++N++gG++   
  gi|557694424|ref|YP_008797478.1|  30 RIVTIVPSKSdarsSAAIQEIRNFLSKfsPGVSLEVLTVDVVKFEQAVATVLKRLFKEKKEGRNVIVNLSGGMRILI 106
                                       555555433334334455666666654225777788887766666788999999****9*9**************** PP

                           DUF1887 100 lgayevf 106
                                       l ay ++
  gi|557694424|ref|YP_008797478.1| 107 LEAYTAL 113
                                       ***9876 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   0.1   7.4e-06     0.019      24      58 ..     161     195 ..     141     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.4e-06
                                       TB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20  24 gltaselaerldlskntlsyHLrvLeeagLvevvr 58 
                                         ++ +la++ +l+ +t+++++ +Le+ gL+ +v+
  gi|557694424|ref|YP_008797478.1| 161 SESVVALAKTARLPLATAYRRVVALEKMGLLSTVK 195
                                       557889**************************998 PP

>> 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 ?   14.9   0.0   6.2e-06     0.016      79     144 ..      74     137 ..      66     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.2e-06
                        Cas_NE0113  79 eallqlivrlvrelrenegerlhlsiaGGRKtmsillalaaqLygreqDrlyHvlveeefesnref 144
                                       e++++++++++++ +++ g+ + ++++GG +++ + + +a+ L+g     ++ +++e++ e    +
  gi|557694424|ref|YP_008797478.1|  74 EQAVATVLKRLFKEKKE-GRNVIVNLSGGMRILILEAYTALVLWG-AGAAVSEIVTEDKQELVLPT 137
                                       67888999999999999.9**************999999999999.77789999998887764433 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 ?   12.5   0.2   6.3e-05      0.16      24      68 .]     167     208 ..     152     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.3e-05
                            HTH_27  24 lcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       l+++  +  +++   + +L+++GL+ + + +   r ++v+lT+ G
  gi|557694424|ref|YP_008797478.1| 167 LAKTARLPLATAYRRVVALEKMGLLSTVKRD---RVRTVSLTALG 208
                                       6667777788888999*********777665...********977 PP

>> Cas_APE2256  CRISPR-associated protein (Cas_APE2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1    0.0001      0.26      69     110 ..      73     110 ..      19     138 .. 0.72
   2 ?   -1.0   0.0      0.59   1.5e+03      52     103 ..     121     174 ..     106     186 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                       Cas_APE2256  69 FreglrnLveklarevknkkregekvlinaTgGfKpeiavlt 110
                                       F++++   +++l     ++k+eg++v++n++gG+   i  ++
  gi|557694424|ref|YP_008797478.1|  73 FEQAVATVLKRLF----KEKKEGRNVIVNLSGGMRILILEAY 110
                                       5555444444443....4589*************98765444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.59
                       Cas_APE2256  52 evevveieklsdlgreeFre.glrnLveklarevknkkregek.vlinaTgGfK 103
                                       +v+ + +e+ ++l   ++++ g+  L+++ +  v ++ +++e+ v+++ T+ + 
  gi|557694424|ref|YP_008797478.1| 121 AVSEIVTEDKQELVLPTLSTvGVFSLLKESDFRVLEAAKNSESvVALAKTARLP 174
                                       444444455555555566777888888888877777777777745666666555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.85   2.2e+03      12      27 ..     108     124 ..     107     128 .. 0.63
   2 ?   10.4   0.2   0.00018      0.45      19      58 ..     158     197 ..     147     205 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.85
                                       CHCHHHH.HHCCCHHCH CS
                              TrmB  12 kvYlaLl.klgpatade 27 
                                       ++Y+aL+     a ++e
  gi|557694424|ref|YP_008797478.1| 108 EAYTALVlWGAGAAVSE 124
                                       79****94344455555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00018
                                       HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       ++ + ++  +a+ + +p +++Y+ +  Le++Gl  ++k+ 
  gi|557694424|ref|YP_008797478.1| 158 AKNSESVVALAKTARLPLATAYRRVVALEKMGLLSTVKRD 197
                                       456677889************************9888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1578.25
//
Query:       gi|557694425|ref|YP_008797479.1|  [L=293]
Description: CRISPR-associated protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-13   50.6   2.1    1.2e-12   48.2   1.5    2.4  2  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 ?   -0.5   0.0      0.11   2.1e+03      10      31 ..      56      85 ..      17     112 .. 0.62
   2 !   48.2   1.5   6.9e-17   1.2e-12       1      85 [.     137     279 ..     137     280 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.11
                                      E........TEEESS..--HHHHHHHHHHHHH CS
                       CRISPR_Cas6 10 k........krkgll..psprlvfssllrrwn 31
                                               + +  +  ++p+ vf+  ++++n
  gi|557694425|ref|YP_008797479.1| 56 SpvetlagrGIF--YgvIQPGFVFQMRMNALN 85
                                      333333322222..233555555555555544 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 6.9e-17
                                       EEEEEEE-EE........................TEEESS--HHHHHHHHHHHHHHHTSS................. CS
                       CRISPR_Cas6   1 lrfltPtrfk........................krkgllpsprlvfssllrrwnalaglkgk.............. 39 
                                       +rf++Pt f+                         r+++lp+p l+f++l+r ++++ +                  
  gi|557694425|ref|YP_008797479.1| 137 VRFRSPTFFRstqkgptffmrllprrlrkpvrpvYRYMILPDPYLFFRTLARLYRQFGEPGFPyksysewlleggva 213
                                       699*************9999****9999999998899999*************999999875566666666555544 PP

                                       ......EECHHHHHH.............EEEEEEEE.....--HHHECCC........HHHHHHHH-SSSTGGGTTT CS
                       CRISPR_Cas6  40 ......ptveeeleg.............GfvGevky.....sgeleelek........llrfaeylgvGkktafGlG 84 
                                                                   GfvG+v +           + +        ll+fa +++vG ++++G+G
  gi|557694425|ref|YP_008797479.1| 214 letfsrL-------RvskvyddrgrwsrGFVGHVVFtiprdL-----FDRrmasitvnLLEFARFSNVGGNRTAGFG 278
                                       4333331.......03333344444455********544331.....33344455556******************* PP

                                       - CS
                       CRISPR_Cas6  85 k 85 
                                        
  gi|557694425|ref|YP_008797479.1| 279 V 279
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       238  (0.0132746); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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: 00:00:00.42
# Mc/sec: 2116.02
//
Query:       gi|557694426|ref|YP_008797480.1|  [L=320]
Description: CRISPR-associated protein Cas1 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  190.1   0.0    5.7e-56  189.7   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 !  189.7   0.0   3.2e-60   5.7e-56       1     250 [.       4     259 ..       4     265 .. 0.94

  Alignments for each domain:
  == domain 1  score: 189.7 bits;  conditional E-value: 3.2e-60
                                       EEEESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEEST.EEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE. CS
                          Cas_Cas1   1 lyvteqgaylrkkgerlvvekegeekkeiplediesivifge.vslstkalrllaekgipvvflsengkylgrlep. 75 
                                       l+++++g+yl+++++ +vv+++g  + e++  ++++i i  + v +s +alrl+++ gi+v+++s +g+++g++++ 
  gi|557694426|ref|YP_008797480.1|   4 LVIDKPGTYLGVRKGLFVVRTKGGGRSEFSPVELSHISIRCRgVGVSVDALRLACRFGIEVSVYS-RGRPVGKVVGa 79 
                                       6899***********************************9999*******************997.589*******8 PP

                                       SSSSTHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHC.TT.....HHHHCHCHHHHHHHHHHHH-H CS
                          Cas_Cas1  76 eesgnvelrraQyraaddeekrlelakkivagklenqrkvlrrlkrdr.ee.....eeleeaieeleelleklekae 146
                                          g + +rraQ++a  +e+ +l++a++iv++kl+nqr v+r+ ++++  +     + l +  +e+ ++++ l+ a 
  gi|557694426|ref|YP_008797480.1|  80 FLGGGAVTRRAQLEAWGTER-GLAVAREIVSAKLYNQRLVVRQRAKEYlAKglavgQTLMKLEQEIGDCMNLLNGAG 155
                                       88999999*******99877.***********************99996447667777777777788888888888* PP

                                       SHHHHHHHHHHHHHHHHHHHHHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--T CS
                          Cas_Cas1 147 sleeLrgiEGeaakaYfeafdkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedr 223
                                       +++++r +E++ a+ Y++a++ ll+ e+ f+gR +  p+Dp+N  L+ gY++l s+v+sa+  + LdP iGfLH++r
  gi|557694426|ref|YP_008797480.1| 156 DVDSVRAYEARGAASYWKAVSLLLPSELGFTGRVTWSPQDPFNKALNIGYGVLRSRVWSAVLGANLDPFIGFLHQPR 232
                                       ***************************************************************************** PP

                                       TSS-HHHHHHHHHHHHHHCHHHHHHHH CS
                          Cas_Cas1 224 pgrpsLalDLmEefRpllvDrlvlsli 250
                                        ++  L+ DLmEefRp +vDr ++ l 
  gi|557694426|ref|YP_008797480.1| 233 GRHMCLVSDLMEEFRPGVVDRPLIGLA 259
                                       *********************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2307.43
//
Query:       gi|557694427|ref|YP_008797481.1|  [L=100]
Description: CRISPR-associated protein Cas2 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   52.7   0.0    4.2e-14   52.5   0.0    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 !   52.5   0.0   2.3e-18   4.2e-14       3      74 ..       8      78 ..       6      80 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 2.3e-18
                                      EEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHHH CS
                       CRISPR_Cas2  3 vlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqfe 74
                                      +lv+YD+ +d+ rr ++a  lk+ G++rvQ S F+g  + a + ++k+  ++iid ++d++ iy+lt  +++
  gi|557694427|ref|YP_008797481.1|  8 ILVIYDV-SDDGRRFELAAALKRLGLTRVQRSAFVGPCTVALISDVKNVSRRIIDFSTDNVQIYPLTPASYR 78
                                      89*****.************************************************99*********98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 788.20
//
Query:       gi|557694428|ref|YP_008797482.1|  [L=198]
Description: CRISPR-associated protein Cas4 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   52.4   0.0    8.1e-14   52.0   0.0    1.1  1  Cas_Cas4  Domain of unknown function DUF83
    6.8e-07   29.4   0.0    8.2e-07   29.2   0.0    1.1  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 !   52.0   0.0   9.1e-18   8.1e-14       5     161 ..      13     190 ..      10     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 9.1e-18
                          Cas_Cas4   5 iqyyliCkrklwlisheitleensetvelGkllheesyer.ek...kevel.se..........sikiDvve.keke 65 
                                       ++ +++C++  ++  +   +e + e++  G+  h + +++      + v++ ++          s+++D +     +
  gi|557694428|ref|YP_008797482.1|  13 VKNFYFCQQIPYINLVLHVFEPETESMVYGRERHLRFHAQyLPrgiRVVRVeTDvwlvgrrlglSGVLDALVhAVFG 89 
                                       6789999999888877555555555666699999855554311234666663337888889999999**98856678 PP

                          Cas_Cas4  66 klvvvEvKkskkk....eeaaklQllyYlllLe.kkgveikeGvleypkekkreevelteelreelekaikeieeii 137
                                       +lv+ E+K s         ++ +Ql++Y++l+e   g ++k+Gvl+y     +  v + + lr  +++a++ +++++
  gi|557694428|ref|YP_008797482.1|  90 ELVPCELKVSALGrggaPLKDLVQLTAYAMLVEeVYGKTVKRGVLYYADDGGKHVVYFRDSLRGLVRRAVEAMRRMV 166
                                       9999****998773332234489**********99****************************************** PP

                          Cas_Cas4 138 ssekppkvkkkkiCkkCayaelCl 161
                                       ++e+pp + +  +C  C y+ +C+
  gi|557694428|ref|YP_008797482.1| 167 ETEEPPAARSLDKCAGCWYSRVCW 190
                                       ***********************9 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 !   29.2   0.0   9.1e-11   8.2e-07     103     254 ..      49     189 ..      23     190 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 9.1e-11
                          PDDEXK_1 103 rlaeeleakrgfrpvalelefg..gekvrLkGriDrvd.dkegelriiDyKtgsappkskelaelkeglQlllYlla 176
                                         a+    +rg+r+v++e ++   g+++ L G +D +     gel+  + K ++   +  +   lk+ +Ql++Y+++
  gi|557694428|ref|YP_008797482.1|  49 FHAQ--YLPRGIRVVRVETDVWlvGRRLGLSGVLDALVhAVFGELVPCELKVSA-LGRGGA--PLKDLVQLTAYAML 120
                                       3333..56667999999965556679999*******8879999********555.555555..899999******** PP

                          PDDEXK_1 177 laegeelkeegepagalylrleepkvkdeevvkkmalteeeleallqeleelaeeilagefparpskk..CeyCpyk 251
                                       ++e   +++   + g+ly+             k++++ ++ l+ l +++ e ++++ + e p++      C+ C y+
  gi|557694428|ref|YP_008797482.1| 121 VEEV--YGKTV-KRGVLYYAD--------DGGKHVVYFRDSLRGLVRRAVEAMRRMVETEEPPAARSLdkCAGCWYS 186
                                       ****..55332.556666655........23344445688898888888899999997755555553356******* PP

                          PDDEXK_1 252 svC 254
                                       +vC
  gi|557694428|ref|YP_008797482.1| 187 RVC 189
                                       *** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1556.00
//
Query:       gi|557694429|ref|YP_008797483.1|  [L=302]
Description: CRISPR-associated RAMP family protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   45.5   0.0    1.8e-11   44.5   0.0    1.5  1  RAMPs            RAMP superfamily
  ------ inclusion threshold ------
       0.11   12.1   0.0        0.2   11.2   0.0    1.4  1  MaoC_dehydratas  MaoC like domain


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 !   44.5   0.0     2e-15   1.8e-11       2     213 .]      11     256 ..      10     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 2e-15
                                       EEESS-EE----..............---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H............ CS
                             RAMPs   2 letltPlhiGdgkisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd... 75 
                                       +e  tPlh+G+g             ++gg+ +IP+S++kGa+R+ +e +++s  +    + +  +++ +++ +    
  gi|557694429|ref|YP_008797483.1|  11 FELETPLHVGAG----GFGAMRSMLRVGGRVVIPASTFKGAFRWVAEVVAKSMMGSLHGYERVALKCYQETDKGivy 83 
                                       7899********....55555556679********************777744444443333333333333333444 PP

                                       .....................................................................HHHHHH-- CS
                             RAMPs  76 .....................................................................leeaiFGn 83 
                                                                                                             + +++Gn
  gi|557694429|ref|YP_008797483.1|  84 akrsgdpdyeegyrsfvkalreqvrvgdlrgvelatlldlgygedelredvlesdvgyelfgdflaancPVGRLMGN 160
                                       44455555556788888888888888889999999999999999999999999999999999988888888888899 PP

                                       S...SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-TT-EEEE CS
                             RAMPs  84 eeeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktngkkkgglftl 160
                                             ag++++ D                                l+   + +r++v i+r+t+++++  + l   
  gi|557694429|ref|YP_008797483.1| 161 G---VLAGKFRVFDV------------------------------FLDVLAVHIRPGVGIERSTGKAKG--DVLRFT 202
                                       9...**********9..............................67999*****************99..9999** PP

                                       EEEESS...............HHHHHHHHHHHHHH.HHH---STTTTBTTT-EE CS
                             RAMPs 161 eaipae.rikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsve 213
                                       e++p++ ri+ ++        +++ + +  +L+ +    l+lG+gk+ G+G+++
  gi|557694429|ref|YP_008797483.1| 203 EVVPPGeRIRMRVVADNLLPGESDSRVFAGVLEWVGKLGLQLGAGKSTGLGLLR 256
                                       ******555555555555557899999************************986 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   2.3e-05       0.2      77     101 ..     193     217 ..     183     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.3e-05
                                       GEEEEEEEE-S--BTTCEEEEEEEE CS
                   MaoC_dehydratas  77 rvgeikvrFtkpVlpgdtlkvelev 101
                                       + +++ +rFt++V+pg++++++++ 
  gi|557694429|ref|YP_008797483.1| 193 KAKGDVLRFTEVVPPGERIRMRVVA 217
                                       5678889***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       258  (0.0143901); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2174.53
//
Query:       gi|557694430|ref|YP_008797484.1|  [L=371]
Description: hypothetical protein CSUB_C1001 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00029   20.9   0.0     0.0033   17.5   0.0    2.0  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 !   17.5   0.0   1.8e-07    0.0033      33     213 .]      31     232 ..      28     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-07
                                       ---HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.........HHHHHH--S...SS--SEEEEE............ CS
                             RAMPs  33 yIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgdleeaiFGneeeskiagrvffeDarpvkipgqile 109
                                       yIP+++l+Gal +al ++                         l +a +  e   k    +  + a+pv++ ++++ 
  gi|557694430|ref|YP_008797484.1|  31 YIPSTTLRGALVTALYREGY-----------------------LDAAQLKRE---KLSPEIVSSPAYPVSGGARTVP 81 
                                       9**************96655.......................444444444...4444444444666666666666 PP

                                       .......................................................................EEEEEE CS
                             RAMPs 110 eskqikstpsp............................................................klsgse 126
                                         + i +++                                                              k +gs+
  gi|557694430|ref|YP_008797484.1|  82 AHPFISKCKQCgeivgeksirdlerrlvdgdgfgwsvecdkghralrplhpnefltvvngefradkkmlgeKREGSS 158
                                       66555555555666666666666666777777777788888899999999999999999****************** PP

                                       EEEEEEEEEEE--SSS-EEEEEE...-TT-EEEEEEEESS..............HHHHHHHHHHHHHH.HHH---ST CS
                             RAMPs 127 lrelldhsterrtrvaidrktktngkkkgglftleaipaerikfsgrirlenlsdeelgallklLdlldlhflglGg 203
                                         +++ ++   +  vai ++  +  k  g l+ +ea+ ++         + +++  + g +++  +++    l++G 
  gi|557694430|ref|YP_008797484.1| 159 ADDDRVPRELYSVSVAISKSRASGVK--GLLYHYEALSPG--------LEYWATVAVPGSIDFPRSKF---VLHVGR 222
                                       ******************99887777..999*********........66667777777777777777...999*** PP

                                       TTTBTTT-EE CS
                             RAMPs 204 gkplGfGsve 213
                                       g ++GfG ve
  gi|557694430|ref|YP_008797484.1| 223 GVSRGFGMVE 232
                                       *****99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2969.26
//
Query:       gi|557694431|ref|YP_008797485.1|  [L=213]
Description: CRISPR-associated RAMP family protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   35.2   0.0    2.6e-08   34.2   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 !   34.2   0.0   1.4e-12   2.6e-08      24     120 ..      33     129 ..      22     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.4e-12
                                       ....---S----HHHHHHHHHHHHHHHHH.............HHHTT-HHHHH.H..............HHHHHH-- CS
                             RAMPs  24 efrdkgglPyIPGSSlkGalRsalekllg............sekkekkdeysrkkekqrvkkgd.....leeaiFGn 83 
                                        + + g++ yIPG S+kG+lRsa+ ++++            ++ + +                       ++++FG+
  gi|557694431|ref|YP_008797485.1|  33 IYGKGGRSLYIPGASFKGVLRSAASRVARsygfsscgqvrpDLISRA----------------HgdglcDVCKLFGS 93 
                                       567889999********************444444444422222222................133455******** PP

                                       S...SS--SEEEEE....................... CS
                             RAMPs  84 eeeskiagrvffeDarpvkipgqileeskqikstpsp 120
                                       + +++    vff+D +p ++ +++ + +  i+ +++ 
  gi|557694431|ref|YP_008797485.1|  94 P-SRSYLPVVFFSDLVPAAKAAPWAVTRVHIEDSTLR 129
                                       *.*************9988877766666555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      189  (0.0105416); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1585.15
//
Query:       gi|557694432|ref|YP_008797486.1|  [L=861]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   36.3   0.3    1.2e-08   35.2   0.3    1.5  1  HD        HD domain
     0.0042   17.3   0.0      0.022   14.9   0.0    2.3  1  DUF3692   CRISPR-associated protein


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 !   35.2   0.3   1.3e-12   1.2e-08       2     121 ..     161     256 ..     160     262 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 1.3e-12
                                       HHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHH CS
                                HD   2 leHsleVaklarrlaedlge.eedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgld 77 
                                       l H l +  +a  +a + ++ +ed  +l+laa +HDi k++  d        fek++ +++v +++l+ ++ +++l 
  gi|557694432|ref|YP_008797486.1| 161 LSHLLLTSTIAWSYAVENEYsREDGAKLRLAAMFHDISKPY--D--------FEKHYQNTEVVEKVLSGILRDNQL- 226
                                       68****************99*********************..4........3477889***************77. PP

                                       HHHHHHHHHTTCCHHHHHHHHHHHHCCTSCHHHHHHHHHHHHHH CS
                                HD  78 ledvaklirehheswegkkrprglaerqlslearivklaDrlaa 121
                                         d+++ +rehh+                + ++ i+ +aDrlaa
  gi|557694432|ref|YP_008797486.1| 227 -NDLVEFVREHHFEGA-------------TGLSSILNRADRLAA 256
                                       .8*************9.............779999999999987 PP

>> DUF3692  CRISPR-associated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.5e-06     0.022       2      42 ..     336     376 ..     335     420 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-06
                                       EEEEEEESHHHHHS-SSHHHHHHHHHHHHHHHHHHHHHHHH CS
                           DUF3692   2 lvvsigpVqefIaaaRktrDlWagSyllSylawkaikelve 42 
                                        +++ig++qefI + R +r   a+S ++ +++   +  l++
  gi|557694432|ref|YP_008797486.1| 336 CQIDIGGIQEFIMRTRDLRSVAASSLVIDMVTSTQLPILIQ 376
                                       689*************************9998877666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (861 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 5370.21
//
Query:       gi|557694433|ref|YP_008797487.1|  [L=316]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   34.6   0.0    4.2e-08   33.5   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 !   33.5   0.0   2.4e-12   4.2e-08       2      99 ..      31     181 ..      30     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.4e-12
                                       EEESS-EE----.........................................---S----HHHHHHHHHHHHH... CS
                             RAMPs   2 letltPlhiGdg...........................kisdekeespefrdkgglPyIPGSSlkGalRsale... 48 
                                       + t + lh+G+g                            +   + +++    ++++P IPGSS+kG +Rs +e   
  gi|557694433|ref|YP_008797487.1|  31 INTESYLHVGSGiahyeapnpdeilkslektgwektieaQAAKIGLDYLDMVIVDDKPCIPGSSVKGNVRSRIElsl 107
                                       67889999999999999999999999999999999999999999999***************************876 PP

                                       .............................HHHH.HHHTT-HHHHH.H.............................. CS
                             RAMPs  49 .............................kllgsekkekkdeysrkkekqrvkkgd..................... 75 
                                                                    k                                               
  gi|557694433|ref|YP_008797487.1| 108 tnnngktpscfikasppqfardrrayrhrK-------------------------Vwgnvldedrgfpcdytksqnv 159
                                       555555555555555555555555555551.........................0444444444444444445555 PP

                                       .HHHHHH--S...SS--SEEEEE.. CS
                             RAMPs  76 .leeaiFGneeeskiagrvffeDar 99 
                                         ++ +FG +   +  g v f D++
  gi|557694433|ref|YP_008797487.1| 160 cMVCDMFGTA---GLSGLVAFTDFV 181
                                       59********...**********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2317.29
//
Query:       gi|557694434|ref|YP_008797488.1|  [L=296]
Description: CRISPR-associated RAMP family protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   87.4   0.0    2.3e-24   86.6   0.0    1.3  1  RAMPs     RAMP superfamily
  ------ inclusion threshold ------
      0.083   12.3   0.0       0.11   11.8   0.0    1.2  1  Cas_Cmr3  CRISPR-associated protein (Cas_Cmr3)


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 !   86.6   0.0   2.6e-28   2.3e-24       5     212 ..      24     230 ..      21     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 2.6e-28
                                       SS-EE----...................---S----HHHHHHHHHHHHH.....................HHHH.HH CS
                             RAMPs   5 ltPlhiGdg.....kisdekeespefrdkgglPyIPGSSlkGalRsale.....................kllgsek 55 
                                       +tP+++G+g     ++     +   +r+  ++ y+PGSSlkG +Rsa+e                           +
  gi|557694434|ref|YP_008797488.1|  24 ITPIRVGAGkeaplGSLVDLAVVRIRRNGREETYVPGSSLKGLFRSAAEpfvrmknprvqpcsgiardncM----ML 96 
                                       79*******9999999999999999************************7777777777777766633331....33 PP

                                       HTT-HHHHH.H.....................HHHHHH--S...SS--SEEEEE....................... CS
                             RAMPs  56 kekkdeysrkkekqrvkkgd............leeaiFGneeeskiagrvffeDarpvkipgqileeskqikstpsp 120
                                       +e +++++++++  +++ +             l+++iFG +   + agrv+f Da++                    
  gi|557694434|ref|YP_008797488.1|  97 GERGEYLLNEIQYLQRTEKSaeamklffektcLLCKIFGAP---SYAGRVIFQDAYLK------------------- 151
                                       34444444443333333333666777999999*********...***********984................... PP

                                       EEEEEEEEEEEEEEEEE--SSS-EEEEEE...-TT-EEEEEEEESS..............HHHHHHHHHHHHHH.HH CS
                             RAMPs 121 klsgselrelldhsterrtrvaidrktktngkkkgglftleaipaerikfsgrirlenlsdeelgallklLdlldlh 197
                                                 +  s  +rt++aidr+t+ ++   g+++++e+++++ + f +  r  nl++ +lg+l kl+  + + 
  gi|557694434|ref|YP_008797488.1| 152 ----------SEASYGVRTGIAIDRRTGAVFR--GQFYQVEYVEPD-ACFGFTLRARNLPNYALGLLSKLIFMMRDG 215
                                       ..........57899****************9..************.****************************** PP

                                       H---STTTTBTTT-E CS
                             RAMPs 198 flglGggkplGfGsv 212
                                        l++Gg k++GfG v
  gi|557694434|ref|YP_008797488.1| 216 ELKVGGFKTRGFGTV 230
                                       *************87 PP

>> Cas_Cmr3  CRISPR-associated protein (Cas_Cmr3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.3e-05      0.11     176     208 ..     158     190 ..     141     220 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.3e-05
                          Cas_Cmr3 176 eRigialdpetrtaeegalyqteglrlkedvrl 208
                                        R+gia+d++t ++  g++yq+e++++   +++
  gi|557694434|ref|YP_008797488.1| 158 VRTGIAIDRRTGAVFRGQFYQVEYVEPDACFGF 190
                                       7*************************9833333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2207.65
//
Query:       gi|557694435|ref|YP_008797489.1|  [L=239]
Description: CRISPR-associated RAMP family protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-23   84.2   0.0    2.4e-23   83.3   0.0    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 !   83.3   0.0   1.3e-27   2.4e-23       5     213 .]      28     215 ..      24     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 1.3e-27
                                       SS-EE----...................---S----HHHHHHHHHHHHHHHHH.HHHTT-HHHHH.H.......... CS
                             RAMPs   5 ltPlhiGdg.....kisdekeespefrdkgglPyIPGSSlkGalRsalekllgsekkekkdeysrkkekqrvkkgd. 75 
                                       ltP+++G g     ++   + +++ +++  + PyIPGSSlkG++Rs +e l++s++++  d    ++ kq++k++  
  gi|557694435|ref|YP_008797489.1|  28 LTPIRVGVGresplGAAADIAVLKIRHNGREAPYIPGSSLKGVFRSFVEMLARSRNHNIHDPWEFEIMKQEAKNCSp 104
                                       8********************************************************9999999999999999999* PP

                                       .HHHHHH--S...SS--SEEEEE.......................EEEEEEEEEEEEEEEEE--SSS-EEEEEE.. CS
                             RAMPs  76 .leeaiFGneeeskiagrvffeDarpvkipgqileeskqikstpspklsgselrelldhsterrtrvaidrktktng 151
                                        +++ iFG++     a+ +++ Da p ++  +i                            + +t+v idr+++ + 
  gi|557694435|ref|YP_008797489.1| 105 cIVCSIFGST---ELASHIRIYDALPASNTEPI---------------------------IRLKTGVVIDREFRGAR 151
                                       **********...***********998887666...........................5689***********99 PP

                                       .-TT-EEEEEEEESS..................HHHHHHHHHHHHHH.HHH---STTTTBTTT-EE CS
                             RAMPs 152 kkkgglftleaipae....rikfsgrirlenlsdeelgallklLdlldlhflglGggkplGfGsve 213
                                       +  g l+t+e+i+++           i + + +d+  ++l +l++ l+   l++G+++++G+G+++
  gi|557694435|ref|YP_008797489.1| 152 P--GLLYTEEIIEPGyeweFRMDIINIPFPDENDDRSKLLMELFKTLKTLGLQVGARRSIGMGLMK 215
                                       9..999*********96653333334556677888889999999999****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); 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 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1777.55
//
Query:       gi|557694436|ref|YP_008797490.1|  [L=124]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 961.93
//
Query:       gi|557694437|ref|YP_008797491.1|  [L=515]
Description: hypothetical protein CSUB_C1008 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   38.2   0.0    1.6e-09   37.8   0.0    1.2  1  Cas_DxTHG  CRISPR-associated (Cas) DxTHG family
  ------ inclusion threshold ------
      0.073   12.6   0.1       0.19   11.3   0.1    1.6  2  PSY3       Shu complex component Psy3, DNA-binding descriptio


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 !   37.8   0.0   1.8e-13   1.6e-09       2     183 ..      18     274 ..      17     351 .. 0.66

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.8e-13
                         Cas_DxTHG   2 lisflGt.gnykevkYelkeeeeeeketsfvqeallell...aekedpdkvvilltdtlad................ 58 
                                       +i+++G+ ++++ + Y     ++    ++f++++ + ll   a+  +   + + + d                    
  gi|557694437|ref|YP_008797491.1|  18 IIAPIGDpSTWRLASYWI---NG---DSCFTCCSAIALLfhyARSCKRIHLQLYALD---Slgcsslmgvwsqgqql 85 
                                       8******999*******3...34...6777777777777444444443444444444...24558888888888887 PP

                         Cas_DxTHG  59 ..keaeek.......eeaaklkeeleelle....................iekvdveiipgggte........eelw 98 
                                         +e+  k       ee+ k         +                    + +v vei+  +g++            
  gi|557694437|ref|YP_008797491.1|  86 ltRESFRKrveslfrEEVVKAA-------KrmnvktaaqddgslilddrcVVTVAVEICQASGEYavnrtgapW--- 152
                                       7744444433334442222222.......02223445567777888899899999**********998875550... PP

                         Cas_DxTHG  99 e..........ifekllek...leendeiilDiThGfrylPvlallalaylrnvkn..ltikgi.yYgaf....... 152
                                                  if k++ +   l +   iilD+ThG++y+  + + a+  l+n+    +++ ++ +Y+a+       
  gi|557694437|ref|YP_008797491.1| 153 StvtfsghptsIFTKIIANvstLSDTANIILDLTHGVNYMQSMSIYAVEALKNLLPasVQVFNAsPYPATvyqtqrc 229
                                       35555688999***99999454455577************9999999999998884459999998999988777777 PP

                         Cas_DxTHG 153 ..........keeeedPil...dlteflelsdwltave.rflktg 183
                                                 +  e+ P l   +++++ +l + + ++    l+++
  gi|557694437|ref|YP_008797491.1| 230 fasnertvklRTIENLPSLkmfNISDLPQLWKLTAGLAgMMLTSE 274
                                       765554444433333343355544444444444444444444444 PP

>> PSY3  Shu complex component Psy3, DNA-binding description
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.1e-05      0.19      72     157 ..     171     262 ..     162     268 .. 0.74
   2 ?   -3.7   0.0      0.81   7.2e+03      96     112 ..     393     409 ..     384     420 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.1e-05
                              PSY3  72 ivsiwkqllesqaeskksvsylnslsilnvdgLinfL....eqlldspleALk.rcqq.edsldkqLsgilidNlSy 142
                                        vs+ +++++   + +++v+y++s+si+ v+ L n L    + +++sp  A   ++q+  +s ++ ++   i+Nl  
  gi|557694437|ref|YP_008797491.1| 171 NVSTLSDTANIILDLTHGVNYMQSMSIYAVEALKNLLpasvQVFNASPYPATVyQTQRcFASNERTVKLRTIENLPS 247
                                       4677777777778899*******************995443457888887753233323456666666666899999 PP

                              PSY3 143 lssepksklklLlkl 157
                                       l++ + s+l +L kl
  gi|557694437|ref|YP_008797491.1| 248 LKMFNISDLPQLWKL 262
                                       999999988888776 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.81
                              PSY3  96 lsilnvdgLinfLeqll 112
                                        + +++d+L  fL+ + 
  gi|557694437|ref|YP_008797491.1| 393 RTTVRMDDLAYFLSSFS 409
                                       56688999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.37
# Mc/sec: 4129.89
//
Query:       gi|557694438|ref|YP_008797492.1|  [L=80]
Description: hydrogenase maturation protein HypF [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00078   19.0   0.0    0.00093   18.7   0.0    1.1  1  Sua5_yciO_yrdC  Telomere recombination


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 !   18.7   0.0   5.2e-08   0.00093      15      58 ..      31      73 ..      22      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.2e-08
                                      SSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC CS
                    Sua5_yciO_yrdC 15 tvYgLacdatneeaverlreiKgrpsdkplavlvasledlkkla 58
                                        Y + + a +++ v rlr++K+ p ++p+a+++ +    ++l+
  gi|557694438|ref|YP_008797492.1| 31 NRYLFTAPAVDDQGVVRLRRRKNKP-TEPFAIMCLNEYVSSRLL 73
                                      56889999*****************.********8866666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 598.01
//
Query:       gi|557694439|ref|YP_008797493.1|  [L=209]
Description: thiamine-phosphate pyrophosphorylase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  157.2   0.1      3e-46  157.0   0.1    1.0  1  TMP-TENI      Thiamine monophosphate synthase
    0.00078   18.9   1.4      0.001   18.5   1.4    1.3  1  NMO           Nitronate monooxygenase
     0.0011   18.1   0.1     0.0022   17.2   0.1    1.5  1  NanE          Putative N-acetylmannosamine-6-phosphate epimer
      0.004   16.7   0.1     0.0052   16.3   0.1    1.3  1  His_biosynth  Histidine biosynthesis protein
     0.0042   16.3   0.1      0.011   14.9   0.1    1.7  2  DUF561        Protein of unknown function (DUF561)
  ------ inclusion threshold ------
      0.023   13.9   0.1      0.031   13.5   0.1    1.3  1  DHO_dh        Dihydroorotate dehydrogenase
      0.034   13.2   0.0        0.1   11.6   0.0    1.7  2  Dus           Dihydrouridine synthase (Dus)
      0.036   13.1   0.6      0.055   12.5   0.6    1.4  1  FMN_dh        FMN-dependent dehydrogenase
       0.15   12.0   0.0        1.6    8.8   0.0    2.3  3  DUF1422       Protein of unknown function (DUF1422)


Domain annotation for each model (and alignments):
>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.0   0.1   1.5e-49     3e-46       2     180 ..      10     187 ..       9     188 .. 0.98

  Alignments for each domain:
  == domain 1  score: 157.0 bits;  conditional E-value: 1.5e-49
                          TMP-TENI   2 ylvtdskldkneellevveealkggvtlvqlRekeldarellelaeklaalcrkygvpliindrvdlalavgadgvH 78 
                                        ++tds+l  + +ll++vee+l++g++++ +Rek++  ++l++l   +a++++ky++++++n + ++  + ga gvH
  gi|557694439|ref|YP_008797493.1|  10 LVITDSGLA-EGRLLAIVEECLAAGCRWFMVREKNMPLESLIKLTISIAKMAEKYSAAVVVNGYPEIVNQTGAAGVH 85 
                                       689999999.99***************************************************************** PP

                          TMP-TENI  79 lgqddlpvaearellgpdliiGlSvhsleeaeeaealgadYigvGpifpTdtKkda.eplgleglkelaealeiPvv 154
                                       l   +++++ ar+++g d+++G+S+hs e+a eae++gadY++++pifp+ +K++  +p+gl+ lk+++++l+iPv+
  gi|557694439|ref|YP_008797493.1|  86 LPW-SMDIKAARRVVGGDKLLGVSTHSTEQAVEAEKMGADYVTLSPIFPSVSKPGYqNPAGLQMLKDIVRRLTIPVI 161
                                       *96.7************************************************************************ PP

                          TMP-TENI 155 aiGGitlenvaevleagadgvavvsa 180
                                       a+GGi++ n++++++ ga+gvav  a
  gi|557694439|ref|YP_008797493.1| 162 ALGGIKPGNAKTCIANGAAGVAVLGA 187
                                       ***********************866 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.4   5.2e-07     0.001     138     226 ..     104     189 ..      53     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.2e-07
                               NMO 138 vliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLal 214
                                       +l +++ s ++a ++e++GaD + +        ++   +++   +++++ ++  + iPviA GGi  + + ++ +a 
  gi|557694439|ref|YP_008797493.1| 104 LLGVSTHSTEQAVEAEKMGADYVTLSPIFPSVSKP--GYQNPAGLQMLKDIVRRLTIPVIALGGIKPG-NAKTCIAN 177
                                       55677888899999999999998777655444444..333334588899999999*********9765.68****** PP

                               NMO 215 GAsgvqigtrfL 226
                                       GA+gv++  +++
  gi|557694439|ref|YP_008797493.1| 178 GAAGVAVLGAMM 189
                                       *****9876665 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 !   17.2   0.1   1.1e-06    0.0022      98     180 ..     108     192 ..      90     206 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.1e-06
                                       E-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-.....SS--HHHHHHHHHT.T--EEEES---SHHHHHHHHTT--SE CS
                              NanE  98 DistleeglvakklGvdivGttlsGytkeeek....aepDfalvkalsea.glkviaeGrintPekakkaieiGvda 169
                                          + e+++ a+k+G+d+v  tls    + +k    +   ++++k+++    + via G i+ P +ak++i  G++ 
  gi|557694439|ref|YP_008797493.1| 108 STHSTEQAVEAEKMGADYV--TLSPIFPSVSKpgyqNPAGLQMLKDIVRRlTIPVIALGGIK-PGNAKTCIANGAAG 181
                                       4556899***********9..66665444443355356689*****98753788******96.9************* PP

                                       EEE-HHHH-HH CS
                              NanE 170 vvvGsaitrle 180
                                       v v +a+ + +
  gi|557694439|ref|YP_008797493.1| 182 VAVLGAMMKAQ 192
                                       ***99998765 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   2.6e-06    0.0052     147     219 ..     109     184 ..      50     193 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.6e-06
                                       EEHHHHHHHHHHTT-SEE....EEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEE CS
                      His_biosynth 147 ldavelakkleelgagei....lltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdaviv 219
                                        + +e a ++e++ga  +    ++ ++++ G ++   l+++k++ ++++ipvia GG+ ++   k+  ++g+++v v
  gi|557694439|ref|YP_008797493.1| 109 THSTEQAVEAEKMGADYVtlspIFPSVSKPGYQNPAGLQMLKDIVRRLTIPVIALGGI-KPGNAKTCIANGAAGVAV 184
                                       33445555566666555433338889********************************.566666666666666554 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.7   3.4e+03      66      85 ..     107     126 ..     104     132 .. 0.81
   2 !   14.9   0.1   5.6e-06     0.011     178     234 ..     149     206 ..     133     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.7
                            DUF561  66 vsaveakllleavkaGadlv 85 
                                       vs+  +++ +ea k Gad v
  gi|557694439|ref|YP_008797493.1| 107 VSTHSTEQAVEAEKMGADYV 126
                                       77788888999999999987 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 5.6e-06
                            DUF561 178 tyeiskkvslPvicasGlsdvtvplalslgasGiGigsavsklndeeemv.allseik 234
                                          i++++++Pvi+  G++   ++  ++ ga+G+ +  a+ k ++  +++ ++++eik
  gi|557694439|ref|YP_008797493.1| 149 LKDIVRRLTIPVIALGGIKPGNAKTCIANGAAGVAVLGAMMKAQKPYDVIlSIINEIK 206
                                       56799*******************************9999888887765427788876 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.5e-05     0.031     228     291 ..     143     205 ..      91     208 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHG..TCHHHHHHHHH CS
                            DHO_dh 228 dialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfeg..pkiakkikkel 291
                                       + +l+++ ++ +rl   ip+I+ GGi+ g+ a   i  GA+ v+v  a++++   + ++  i++e+
  gi|557694439|ref|YP_008797493.1| 143 PAGLQMLKDIVRRLT--IPVIALGGIKPGN-AKTCIANGAAGVAVLGAMMKAQkpYDVILSIINEI 205
                                       678999999999999..**********996.88899999999999888876541134556666665 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.43   8.6e+02     142     190 ..      24      71 ..      18      84 .. 0.64
   2 ?   11.6   0.0   5.2e-05       0.1     144     212 ..     115     184 ..     105     194 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.43
                                       HHHHHHHHCT-SEEEEESSECCCTT-CG--C.HHHHHHHHH-SS-EEEES CS
                               Dus 142 elakiveaaGaqaltvHgRtraqnyegtadw.eaIkevkqavsipviaNG 190
                                        +++   aaG+ +++v  R ++   e  +++  +I+++ ++ s  v++NG
  gi|557694439|ref|YP_008797493.1|  24 AIVEECLAAGCRWFMV--REKNMPLESLIKLtISIAKMAEKYSAAVVVNG 71 
                                       5666666777777776..54444444433331357777777777777777 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.2e-05
                                       HHHHHHCT-SEEEEESS...ECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEE CS
                               Dus 144 akiveaaGaqaltvHgR...traqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmi 212
                                       a  +e+ Ga+ +t+      + + +y+ +a ++  k++ ++++ipvia G+Ik + +a+ ++++ Ga gv +
  gi|557694439|ref|YP_008797493.1| 115 AVEAEKMGADYVTLSPIfpsVSKPGYQNPAGLQMLKDIVRRLTIPVIALGGIK-PGNAKTCIAN-GAAGVAV 184
                                       5566777777777655455578889999************************6.7889999998.9999865 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.6   2.8e-05     0.055     202     304 ..      85     189 ..      29     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                                       C--HH.HHHHHHHHHSSEEEEEEE..-SHHHHHHHHHTTESEEEE--...GGGTSSTT---HHHCHHHHHHHH..SS CS
                            FMN_dh 202 sltwd.dikwlreqtklplvvKGv..ltaedakraveaGvdgivvSN...HGGRqldgapatidvLpeiveavggri 272
                                       +l w+ dik  r+ + +  ++ Gv   + e a +a ++G+d + +S       +   + pa +++L +iv+++   i
  gi|557694439|ref|YP_008797493.1|  85 HLPWSmDIKAARRVVGGDKLL-GVstHSTEQAVEAEKMGADYVTLSPifpSVSKPGYQNPAGLQMLKDIVRRLT--I 158
                                       456776777777777776555.6744667899999999999999996222456777789**************7..* PP

                                       -EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
                            FMN_dh 273 evlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                                       +v++ gGi+ G+ +   +a GA +v++  +++
  gi|557694439|ref|YP_008797493.1| 159 PVIALGGIKPGN-AKTCIANGAAGVAVLGAMM 189
                                       ***********7.6789********9877766 PP

>> DUF1422  Protein of unknown function (DUF1422)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00079       1.6      16      74 ..      26      84 ..      19     102 .. 0.82
   2 ?    0.5   0.0       0.3   5.9e+02      71      94 ..     104     127 ..      89     132 .. 0.87
   3 ?   -3.0   0.0       3.6   7.2e+03      73      86 ..     181     194 ..     171     197 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00079
                           DUF1422 16 aGlslngtlsalfsslvpfsifplialvlavyclyqrYlnksleeglPllalacfllGv 74
                                      +  +l + + ++++ + +  + +li l++++  + ++Y    + +g+P ++  +   Gv
  gi|557694439|ref|YP_008797493.1| 26 VEECLAAGCRWFMVREKNMPLESLIKLTISIAKMAEKYSAAVVVNGYPEIVNQTGAAGV 84
                                      44577888888888888899999***************************988777776 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.3
                           DUF1422  71 llGvlgysalvraeyPeiGsnfls 94 
                                       llGv ++s+   +e  ++G+++++
  gi|557694439|ref|YP_008797493.1| 104 LLGVSTHSTEQAVEAEKMGADYVT 127
                                       89*****************99986 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.6
                           DUF1422  73 GvlgysalvraeyP 86 
                                       Gv +  a+++a+ P
  gi|557694439|ref|YP_008797493.1| 181 GVAVLGAMMKAQKP 194
                                       66677788888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1540.47
//
Query:       gi|557694440|ref|YP_008797494.1|  [L=232]
Description: thiamine biosynthesis protein ThiG [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-101  339.0   0.7   1.5e-101  338.8   0.7    1.0  1  ThiG            Thiazole biosynthesis protein ThiG
     0.0011   18.4   0.1      0.002   17.7   0.1    1.3  1  His_biosynth    Histidine biosynthesis protein
     0.0033   16.5   0.6     0.0049   16.0   0.6    1.3  1  FMN_dh          FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.015   14.5   0.5      0.027   13.7   0.5    1.3  1  DUF561          Protein of unknown function (DUF561)
      0.017   14.1   1.3      0.026   13.5   1.3    1.2  1  IMPDH           IMP dehydrogenase / GMP reductase domain
       0.04   13.0   0.6      0.086   11.9   0.6    1.5  1  Dus             Dihydrouridine synthase (Dus)
      0.095   12.1   1.5       0.14   11.6   1.5    1.2  1  NMO             Nitronate monooxygenase
      0.098   11.8   1.1        1.4    8.1   0.4    2.1  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
       0.11   12.6   0.1       0.44   10.6   0.1    2.0  2  Hydrolase_like  HAD-hyrolase-like


Domain annotation for each model (and alignments):
>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  338.8   0.7  7.6e-105  1.5e-101      25     247 .]       3     222 ..       1     222 [. 0.98

  Alignments for each domain:
  == domain 1  score: 338.8 bits;  conditional E-value: 7.6e-105
                                       HHHHHHHT-SEEEEECCGSTTTS.TTS--CCCCCHCCTSEEEEE-TT-SSHHHHHHHHHHHHHTTS-SEEEE--BCE CS
                              ThiG  25 keaveasgaeivtvalrRvnleekaseeellelleekevtllPntaGaktaeeAvriarlarevletdliklEviad 101
                                        +a+easgae+vtva+rR++l ek  + ++l++l+ +++ +lPntaG++ta+eAv +a+lare+l+t+++klEvi+d
  gi|557694440|ref|YP_008797494.1|   3 LDALEASGAEVVTVAIRRISLAEK--GYSILDFLR-NKYFILPNTAGCYTAREAVLTAKLAREALGTNWVKLEVIGD 76 
                                       589*******************95..79******9.8999************************************* PP

                                       TTTTEB-HHHHHHHHHHHHHTT-EEEEEE-S-HHHHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-B CS
                              ThiG 102 ektLlPdvvetlkaaeiLvkeGFevlpYvsdDlvlarrleevGcaavmPlaapiGsglGllnkealkiiieeakvPv 178
                                       ++tL+Pd+v++l+aa++Lv+eGF+vlpY++dD+v++ +le++Gc+avmPl+apiGsg+G+ln+++++ii ++a vPv
  gi|557694440|ref|YP_008797494.1|  77 DETLYPDTVQLLEAAKQLVDEGFVVLPYCNDDPVVCGKLEKIGCEAVMPLGAPIGSGMGILNPYNIRIIKKNAGVPV 153
                                       ***************************************************************************** PP

                                       EEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHHHHHHHHHH------SS-XTTST CS
                              ThiG 179 ivDAGigspsdaaqamelGadavllntavaeakdpvamArafklaveaGrlaylagriekrevasassp 247
                                       ivDAG+g++sd+a amelG+d+vl+nta+a+ak+pvamA+a++l+veaGrlaylagri+++ +a++ssp
  gi|557694440|ref|YP_008797494.1| 154 IVDAGVGTASDVAVAMELGCDGVLVNTAIAQAKNPVAMAKAIRLSVEAGRLAYLAGRIPRKLYAEPSSP 222
                                       ********************************************************************8 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   9.9e-07     0.002      65     110 ..     142     187 ..     137     198 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.9e-07
                                       HHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-TH CS
                      His_biosynth  65 veeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpe 110
                                       ++ i ++  +pv v+ G+ + +dv+ ++e+g+d v ++ta ++ ++
  gi|557694440|ref|YP_008797494.1| 142 IRIIKKNAGVPVIVDAGVGTASDVAVAMELGCDGVLVNTAIAQAKN 187
                                       5557778889*****************************9775544 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.6   2.4e-06    0.0049     271     302 ..     150     181 ..     115     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.4e-06
                                       SS-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                            FMN_dh 271 rievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                        ++v+vD G+ + sDv+ A+ lG d+vl+  +
  gi|557694440|ref|YP_008797494.1| 150 GVPVIVDAGVGTASDVAVAMELGCDGVLVNTA 181
                                       4999*********************9998655 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   1.3e-05     0.027     181     231 ..     145     196 ..     140     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.3e-05
                            DUF561 181 iskkvslPvicasGlsd.vtvplalslgasGiGigsavsklndeeemvalls 231
                                       i k+  +Pvi  +G+ + + v +a++lg  G+ +  a+ + ++ ++m ++++
  gi|557694440|ref|YP_008797494.1| 145 IKKNAGVPVIVDAGVGTaSDVAVAMELGCDGVLVNTAIAQAKNPVAMAKAIR 196
                                       788999*********7615699*************************99886 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.3   1.3e-05     0.026     202     243 ..     145     186 ..     127     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.3e-05
                                       HHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 202 aakkagvpviaDGGikysgdivkAlaaGadavmlGsllagte 243
                                       + k+agvpvi D G+ +  d++ A+ +G d v++   +a  +
  gi|557694440|ref|YP_008797494.1| 145 IKKNAGVPVIVDAGVGTASDVAVAMELGCDGVLVNTAIAQAK 186
                                       67889*****************************99999776 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.6   4.3e-05     0.086     174     224 ..     141     192 ..     133     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.3e-05
                                       HHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHH..CCSTTHHH CS
                               Dus 174 aIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrga..lgnPwlfa 224
                                       +I+ +k++  +pvi+  ++ +a+d+  ++e  G+dgv++  +    +nP  +a
  gi|557694440|ref|YP_008797494.1| 141 NIRIIKKNAGVPVIVDAGVGTASDVAVAMEL-GCDGVLVNTAIaqAKNPVAMA 192
                                       79999***********************999.******976541145777666 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.5   6.8e-05      0.14     190     234 ..     147     191 ..     116     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.8e-05
                               NMO 190 davdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdak 234
                                       +   +Pvi   G+ ++ +va a+ lG  gv + t+   +k+  a 
  gi|557694440|ref|YP_008797494.1| 147 KNAGVPVIVDAGVGTASDVAVAMELGCDGVLVNTAIAQAKNPVAM 191
                                       4455*******************************9888775554 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 ?    2.8   0.0      0.03        59      58     168 ..       4     121 ..       2     146 .. 0.64
   2 ?    8.1   0.4   0.00068       1.4     141     180 ..     147     186 ..     137     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.03
                                       HHHHTTT-SEEEEE--SS--T--HHHHHHHHHHH--EE..EEE-SSHHHHHHHHHTT-SEEE-TTTT..SSTTS-.S CS
                              NanE  58 deLaaagadiialDatdrerpvtieelikkikekyqll..maDistleeglvakklGvdivGttlsG..ytkeeeka 130
                                       d+L a ga+++ +     +  ++  +++  +++ky +l   a + t  e++ + kl  + +Gt       +++ e  
  gi|557694440|ref|YP_008797494.1|   4 DALEASGAEVVTVAIRRISLAEKGYSILDFLRNKYFILpnTAGCYTAREAVLTAKLAREALGTNWVKleVIGDDETL 80 
                                       778888888888766555555777889999999995542379999999*9999999999999975431123333333 PP

                                       S--.HHHH...HHHHHTT--EEEES---SHHHHHHHHTT--S CS
                              NanE 131 epD.falv...kalseaglkviaeGrintPekakkaieiGvd 168
                                        pD ++l+   k+l+++g+ v+     + P    k  +iG +
  gi|557694440|ref|YP_008797494.1|  81 YPDtVQLLeaaKQLVDEGFVVLPYC-NDDPVVCGKLEKIGCE 121
                                       4442455422245666666555433.3445555555555555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00068
                                       HHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HH CS
                              NanE 141 seaglkviaeGrintPekakkaieiGvdavvvGsaitrle 180
                                       ++ag+ vi++  + t    + a+e+G d v v +ai++ +
  gi|557694440|ref|YP_008797494.1| 147 KNAGVPVIVDAGVGTASDVAVAMELGCDGVLVNTAIAQAK 186
                                       5899********************************9876 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.4   2.8e+03      11      30 ..      58      77 ..      54      79 .. 0.77
   2 ?   10.6   0.1   0.00022      0.44      32      55 ..     162     185 ..     159     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                                      HHHHHHH---GGGEEEEES- CS
                    Hydrolase_like 11 dfalevlgsdpeevlmiGDr 30
                                      + a+e+lg +  +  +iGD+
  gi|557694440|ref|YP_008797494.1| 58 KLAREALGTNWVKLEVIGDD 77
                                      56888888888888899998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00022
                                       TTHHHHHHHCT-EEEEESSSSS-T CS
                    Hydrolase_like  32 atDiagAnnaGwksvLVltGvtrp 55 
                                       a+D+a A + G+++vLV t + ++
  gi|557694440|ref|YP_008797494.1| 162 ASDVAVAMELGCDGVLVNTAIAQA 185
                                       79*****************88776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1766.07
//
Query:       gi|557694441|ref|YP_008797495.1|  [L=71]
Description: thiamine biosynthesis protein ThiS [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   52.5   0.3    7.1e-14   52.2   0.3    1.1  1  ThiS           ThiS family
    0.00014   22.1   1.4    0.00042   20.6   1.4    1.7  1  Lambda_tail_I  Bacteriophage lambda tail assembly protein I
     0.0091   15.7   0.0      0.014   15.1   0.0    1.3  1  DUF2635        Protein of unknown function (DUF2635)
  ------ inclusion threshold ------
      0.023   12.4   0.2      0.024   12.4   0.2    1.0  1  CobN-Mg_chel   CobN/Magnesium Chelatase
      0.076   13.1   0.1       0.12   12.4   0.1    1.5  1  TGS            TGS domain


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 !   52.2   0.3     2e-17   7.1e-14       1      77 []       7      71 .]       7      71 .] 0.92

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2e-17
                                      EEETTCCHHHHTCEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEESTTC- CS
                              ThiS  1 vllfaelrelageeelelaegstvaelleaLgerypelalerrvavavNgeivpr.lwldtelkdgDevailppVaGG 77
                                      v+++++ + ++         g+t++++l ++g +     +++++avavNge+vpr  w   +lk+gD v+i+++VaGG
  gi|557694441|ref|YP_008797495.1|  7 VKINGRDMVCV---------GKTISQVLVSVGVDP----ARQGIAVAVNGEVVPRsMWGRVRLKAGDIVEIVTAVAGG 71
                                      67777777777.........6************99....89**************88********************9 PP

>> Lambda_tail_I  Bacteriophage lambda tail assembly protein I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.4   1.2e-07   0.00042      18      86 .]      13      71 .]       4      71 .] 0.76

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                     Lambda_tail_I 18 dvveavktleeairalssqldafkellqrskfavrvagvdVgesvpvdrya.etlkdgkvvtivpvpaGg 86
                                      d+v ++kt  ++++  +           +  +++    v+ ge vp+  +  + lk+g  v iv  +aGg
  gi|557694441|ref|YP_008797495.1| 13 DMVCVGKTISQVLVSVGV----------DPARQGIAVAVN-GEVVPRSMWGrVRLKAGDIVEIVTAVAGG 71
                                      455555555555544432..........34478888899*.****************************8 PP

>> DUF2635  Protein of unknown function (DUF2635)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.8e-06     0.014      17      44 ..      38      65 ..      31      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.8e-06
                           DUF2635 17 lLpaeGeevprtlyWlRRlkdGDvvevk 44
                                       +   Ge vpr+ + + Rlk GD+ve+ 
  gi|557694441|ref|YP_008797495.1| 38 AVAVNGEVVPRSMWGRVRLKAGDIVEIV 65
                                      56789********************985 PP

>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   6.6e-06     0.024     764     805 ..      14      55 ..       4      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 764 mrteGediAqiLallGvrPvwdaagrvvdlelipleeLgRPR 805
                                       m   G++i+q+L  +Gv P +++    v+ e++p +  gR R
  gi|557694441|ref|YP_008797495.1|  14 MVCVGKTISQVLVSVGVDPARQGIAVAVNGEVVPRSMWGRVR 55 
                                       55679*******************999999********9998 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.4e-05      0.12      25      60 .]      27      66 ..       8      66 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                                      HHSTTHHHHEEEEEECSEEEETTS....BB-SSEEEEEEE CS
                               TGS 25 kIhrslakkfiyAlVnGqrvgldh....vLedgdvveIvt 60
                                      +++ + a++ i+  VnG+ v+ +     +L+ gd+veIvt
  gi|557694441|ref|YP_008797495.1| 27 SVGVDPARQGIAVAVNGEVVPRSMwgrvRLKAGDIVEIVT 66
                                      55666678889999***888887444449**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 544.76
//
Query:       gi|557694442|ref|YP_008797496.1|  [L=299]
Description: DsbA oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-36  125.4   0.0    2.8e-36  124.9   0.0    1.1  1  Thioredoxin_5    Thioredoxin
    3.3e-15   56.4   0.7    3.6e-14   53.0   0.1    2.5  2  DSBA             DSBA-like thioredoxin domain
    4.4e-05   23.7   0.0     0.0053   16.9   0.0    2.3  1  Thioredoxin_4    Thioredoxin
     0.0016   18.3   0.0     0.0042   16.9   0.0    1.7  1  TrmB             Sugar-specific transcriptional regulator Trm
  ------ inclusion threshold ------
      0.011   15.7   0.0       0.89    9.6   0.1    2.4  2  Thioredoxin      Thioredoxin
      0.014   15.8   0.1      0.035   14.5   0.1    1.6  1  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.9   0.0   9.4e-40   2.8e-36       3     184 ..      10     207 ..       9     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 9.4e-40
                     Thioredoxin_5   3 FidPlcseCweiEpelkklkveygekiklrfilllnlktlnksskkkkkas...............asrtgmsidgd 64 
                                       ++dP c  Cw+ Ep l+k+k+ yge++++ + + + + ++ ++ +  ++                 ++r gm++d +
  gi|557694442|ref|YP_008797496.1|  10 YTDPYCTWCWGSEPVLRKIKEVYGEQVEISYKMGGLVRDIRDFYDPVNEIGgeswyeqvavhwedaSRRHGMPVDSR 86 
                                       89****************************************999976666999***********99********** PP

                     Thioredoxin_5  65 vl..leellsssYlaslaiKAAelQgkkkgrkFLrklqealflekkniskeellleiaekaglDveefkeDleskla 139
                                       v+   +++++s+Y+a +a+KAAe+Q+++ ++++Lr+l+e    e+k+i + e+ +e+ae++gl+  ++  D+ s  a
  gi|557694442|ref|YP_008797496.1|  87 VFyeIKDSFTSTYPANIAVKAAEFQDRELAKRYLRRLREGAAAERKHIHRLEVQAELAEEVGLEAGKLVDDIRSGRA 163
                                       **8999*********************************************************************** PP

                     Thioredoxin_5 140 kkafqcDlklakemgvtevPtlvffneneeeeglkveglksyevy 184
                                       ++af +Dl   + mg+t +Pt+ + n  +++   +v+g+ +y+ +
  gi|557694442|ref|YP_008797496.1| 164 EEAFLKDLSECRAMGITGFPTFLVKN-LKTGRTHLVYGYRRYSYF 207
                                       **************************.778888899999999876 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.1   1.2e-17   3.6e-14       2     189 ..       7     208 ..       6     212 .. 0.77
   2 ?   -0.6   0.1      0.31   9.3e+02     126     153 ..     243     270 ..     239     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.2e-17
                                       EEEEEBTTBHHHHHHHHHHHHHHHHC.CTEEEEEEE-SSSCHHHHCT.S.GGG...SHHHHHHHHHHHHHHHHHHT. CS
                              DSBA   2 vdeffDvlCPyCylgkerleklaars.pdvkvvlrpfelagakkasgnvgpse...lpeklkylledlkrlaeaegi 74 
                                       ++e+ D +C +C+  +++l+k+ + + ++v++ ++   l ++ ++   ++p +    +  +++++ + +    + g 
  gi|557694442|ref|YP_008797496.1|   7 IVEYTDPYCTWCWGSEPVLRKIKEVYgEQVEISYKMGGLVRDIRDF--YDPVNeigGESWYEQVAVHWEDASRRHGM 81 
                                       89************************777*************7754..34444457445556666666666666666 PP

                                       ...GGSS...HHH.HHHH.HHHHHHHHHHHH..GHHHHHHHHHHHHHTSSS-TSSHHHHHHHHHHTTS.HHHHHHHH CS
                              DSBA  75 plrfpkd...klk.nstr.aarlllaagaeg..laekvvrelfealwsegqaitddqellevaekaGldaeeldeal 144
                                       p         k +  st+ a+ ++ aa+ ++  la++++r+l e +  e++ i + ++ +e+ae++Gl+a +l  ++
  gi|557694442|ref|YP_008797496.1|  82 PVDSRVFyeiKDSfTSTYpANIAVKAAEFQDreLAKRYLRRLREGAAAERKHIHRLEVQAELAEEVGLEAGKLVDDI 158
                                       664332232344445555155555566666699******************************************** PP

                                       TSHHHHHHHHHHHHHHHHTT-SSSSEEEETT.C....EEEESSSSHHHHH CS
                              DSBA 145 eseavkeavrentaaaqslgvtGvPtvvvdg.k....rmvfGadrldtla 189
                                        s++++ea+ ++  + +++g+tG Pt++v + k    + v G  r+  ++
  gi|557694442|ref|YP_008797496.1| 159 RSGRAEEAFLKDLSECRAMGITGFPTFLVKNlKtgrtHLVYGYRRYSYFE 208
                                       *****************************553233356777776666655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.31
                                       HHHHHHHTTS.HHHHHHHHTSHHHHHHH CS
                              DSBA 126 llevaekaGldaeeldealeseavkeav 153
                                       ++eva+ + ++ +++ e+l+s   k++v
  gi|557694442|ref|YP_008797496.1| 243 TQEVATLLDISKNQAFEMLKSMSDKNMV 270
                                       57899999999**********9999988 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.8e-06    0.0053      56     148 ..      89     189 ..       4     213 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.8e-06
                                       ..---S.TTTHHHHHHHTT--TT.HHHHHHHHHHHHTHHHHTTS-......HHHHH.....HHHHHTS-------HH CS
                     Thioredoxin_4  56 pldkek.eslkaamaarcagees.peaflaikallysqqeewaes......lkelaaealdkdekfeacleeeklda 124
                                       +  k++  s+  a++a  a+e +  e  + + + l++  ++ +++      ++ela+e + +  k+ ++++++++++
  gi|557694442|ref|YP_008797496.1|  89 YEIKDSfTSTYPANIAVKAAEFQdRELAKRYLRRLREGAAAERKHihrlevQAELAEEVGLEAGKLVDDIRSGRAEE 165
                                       333333344445555544444431222222222223322222222554454555666688999************** PP

                                       HHHHHHHHHHHHT--SS-EEEETT CS
                     Thioredoxin_4 125 lveaeskeakkagiestPtfiing 148
                                       +  +++ e +++gi++ Ptf+++ 
  gi|557694442|ref|YP_008797496.1| 166 AFLKDLSECRAMGITGFPTFLVKN 189
                                       *********************965 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   1.4e-06    0.0042      21      58 ..     239     276 ..     228     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.4e-06
                                       CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  21 gpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58 
                                       g+  ++e+a  l+++++++ e+L+s++dk +V+ ++  
  gi|557694442|ref|YP_008797496.1| 239 GKVATQEVATLLDISKNQAFEMLKSMSDKNMVYAKRTG 276
                                       567789**************************998743 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1    0.0003      0.89      22      53 ..       7      38 ..       3      42 .. 0.92
   2 ?    3.5   0.0     0.023        68      63      81 ..     172     189 ..     164     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0003
                                      EEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEE CS
                       Thioredoxin 22 lveFyApwCghCkalaPeleklaeelkdkvkl 53
                                      +ve++ p+C+ C   +P+l k++e + ++v +
  gi|557694442|ref|YP_008797496.1|  7 IVEYTDPYCTWCWGSEPVLRKIKEVYGEQVEI 38
                                      89************************999877 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.023
                                       HHHHHTT-SSSSEEEEEET CS
                       Thioredoxin  63 dlakkyevegiPtlklfkn 81 
                                       + ++ ++++g+Pt+ l+kn
  gi|557694442|ref|YP_008797496.1| 172 SECRAMGITGFPTF-LVKN 189
                                       67999*********.5555 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.2e-05     0.035       4      66 ..     227     285 ..     224     288 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                       S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETTEEEEE--- CS
                   Penicillinase_R   4 lEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegrafiYsplv 66 
                                       +E+ev+  +++ g++ ++ev + l+      ++    +l+ + +K+++ ++++g+ + + p++
  gi|557694442|ref|YP_008797496.1| 227 SEEEVLGFVRRWGKVATQEVATLLDIS----KNQAFEMLKSMSDKNMVYAKRTGNDYFWLPRM 285
                                       89********************99877....566678***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); 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:                         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 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2162.13
//
Query:       gi|557694443|ref|YP_008797497.1|  [L=244]
Description: dithiol-disulfide isomerase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   77.4   0.4    3.9e-21   75.7   0.4    1.7  1  DSBA           DSBA-like thioredoxin domain
    1.1e-17   64.4   0.0    1.6e-17   63.8   0.0    1.2  1  Thioredoxin_5  Thioredoxin
    1.3e-07   32.0   0.1    0.00012   22.3   0.0    2.3  2  Thioredoxin_4  Thioredoxin
    0.00078   19.5   0.1     0.0023   18.0   0.0    1.9  2  Thioredoxin_3  Thioredoxin domain
  ------ inclusion threshold ------
       0.13   12.4   0.1       0.25   11.5   0.1    1.4  1  DUF1525        Protein of unknown function (DUF1525)


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   0.4   1.1e-24   3.9e-21       2     189 ..      17     212 ..      16     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 75.7 bits;  conditional E-value: 1.1e-24
                                       EEEEEBTTBHHHHHHHHHHHHHHHHCCTEEEEEEE-SSSCHHHHCT.S.GGG.SHHHHHHHHHHHHHHHH......H CS
                              DSBA   2 vdeffDvlCPyCylgkerleklaarspdvkvvlrpfelagakkasgnvgpse.lpeklkylledlkrlae......a 71 
                                       v++f DvlC +Cy  ++r++++++++p+++vv+r f la+          +e   +k k  +e l+ +++      +
  gi|557694443|ref|YP_008797497.1|  17 VEFFHDVLCAWCYCLSPRMRRMVSKYPELEVVHRCFALAPRPES-----IEEiFGNKAKGKHEILNHWRAanlnddE 88 
                                       99***************************************332.....2335555566666666666541111113 PP

                                       HT....GGSS..HHHHHHHHHHHHHHHHHHH..GHHHHHHHHHHHH....HTSSS-TSSHHHHHHHHHHTTS.HHHH CS
                              DSBA  72 egiplrfpkd..klknstraarlllaagaeg..laekvvrelfeal....wsegqaitddqellevaekaGldaeel 140
                                        +i+  + +   +  +  + +  l a +a++  + +   +++f+++    ++e ++i d+++l ++a++ Glda+ +
  gi|557694443|ref|YP_008797497.1|  89 HRINADLMAArdF--DYPYSMPGLRACKAAElqRGQSGHWDMFDRVqkahLTECRNIADENVLIDCAKDIGLDADRF 163
                                       4555555554333..5556666666666666333334445556555111167889********************** PP

                                       HHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHHH CS
                              DSBA 141 dealeseavkeavrentaaaqslgvtGvPtvvvdgkrmvfGadrldtla 189
                                         ++ s+ v + v ++ ++a++lgv  vPt v++ +++v+Ga + d l 
  gi|557694443|ref|YP_008797497.1| 164 VSDFMSQTVLDLVWKDLREAAKLGVHAVPTLVINRRYAVVGAVQEDVLD 212
                                       *******************************************999875 PP

>> Thioredoxin_5  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   4.5e-21   1.6e-17       3     163 ..      20     196 ..      19     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 4.5e-21
                     Thioredoxin_5   3 FidPlcseCweiEpelkklkveyge..kiklrfilllnlktlnksskkkkkas...........asrtgmsidgdvl 66 
                                       F d lc+ C+ + p +++++ +y e   ++  f l+ + +++++  ++k+k +            +  +  i+ d +
  gi|557694443|ref|YP_008797497.1|  20 FHDVLCAWCYCLSPRMRRMVSKYPEleVVHRCFALAPRPESIEEIFGNKAKGKheilnhwraanLNDDEHRINADLM 96 
                                       7889*****************98752256667778888888888887766655789999998766667788999999 PP

                     Thioredoxin_5  67 leellsssYla..slaiKAAelQgkkkgr.kFLrklqealflekkniskeellleiaekaglDveefkeDlesklak 140
                                         + ++ +Y+     a+KAAelQ  + g+ +   ++q+a   e +ni++e++l+++a+++glD ++f  D+ s+++ 
  gi|557694443|ref|YP_008797497.1|  97 AARDFDYPYSMpgLRACKAAELQRGQSGHwDMFDRVQKAHLTECRNIADENVLIDCAKDIGLDADRFVSDFMSQTVL 173
                                       9999999997532459*******99999757899******************************************* PP

                     Thioredoxin_5 141 kafqcDlklakemgvtevPtlvf 163
                                       +   +Dl+ a+ +gv+ vPtlv+
  gi|557694443|ref|YP_008797497.1| 174 DLVWKDLREAAKLGVHAVPTLVI 196
                                       *********************98 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.3    0.0017       6.1      14      64 ..      14      61 ..      11      74 .. 0.90
   2 !   22.3   0.0   3.3e-08   0.00012      62     149 ..     105     199 ..      95     216 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0017
                                      SEEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-..---STTT CS
                     Thioredoxin_4 14 pvtvieyedlrCphCakfeeeveklleeyidtGkvkfiirdfpldkekesl 64
                                      +v+v+ ++d+ C  C  ++  +  ++++y    ++++++r f+l ++ es+
  gi|557694443|ref|YP_008797497.1| 14 KVSVEFFHDVLCAWCYCLSPRMRRMVSKY---PELEVVHRCFALAPRPESI 61
                                      7899*************************...9999999999998887776 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 3.3e-08
                                       TTTHHHHHHHTT--TT..HHHHHHHHHHHHTHHHHTTS-HHHHH..............HHHHHTS-------HHHHH CS
                     Thioredoxin_4  62 eslkaamaarcagees..peaflaikallysqqeewaeslkelaae.........aldkdekfeacleeekldalve 127
                                       +s+ ++ a ++a+ ++     + +++++   q+++ +e   ++a e          + +  +f +++ ++++ +lv 
  gi|557694443|ref|YP_008797497.1| 105 YSMPGLRACKAAELQRgqSGHWDMFDRV---QKAHLTEC-RNIADEnvlidcakdIGLDADRFVSDFMSQTVLDLVW 177
                                       5677777777777775322345555554...33333333.4444333444443326666888*************** PP

                                       HHHHHHHHHT--SS-EEEETTE CS
                     Thioredoxin_4 128 aeskeakkagiestPtfiinge 149
                                       ++++ea k+g+ ++Pt++in +
  gi|557694443|ref|YP_008797497.1| 178 KDLREAAKLGVHAVPTLVINRR 199
                                       ********************86 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       1.5   5.5e+03       9      25 ..      24      40 ..      13      47 .. 0.60
   2 !   18.0   0.0   6.3e-07    0.0023      36      66 ..     176     207 ..     146     215 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.5
                                      SSTTCHHHHHHHHHHCH CS
                     Thioredoxin_3  9 gCakCpklekavkeaaa 25
                                       Ca C+ l+  +++++ 
  gi|557694443|ref|YP_008797497.1| 24 LCAWCYCLSPRMRRMVS 40
                                      38888866666665554 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 6.3e-07
                                       C.TTHHHHHHCT-SSSSEEECTTCEEEESS-- CS
                     Thioredoxin_3  36 v.tdfeeiekygVmsvPalvidgkvvvsGkvp 66 
                                       v +d++e +k gV++vP+lvi+ +  v+G+v 
  gi|557694443|ref|YP_008797497.1| 176 VwKDLREAAKLGVHAVPTLVINRRYAVVGAVQ 207
                                       558999***********************664 PP

>> DUF1525  Protein of unknown function (DUF1525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   6.9e-05      0.25      71      98 ..     178     205 ..     167     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.9e-05
                           DUF1525  71 qgvadawqlgikkiPAVvvdrraVvYGe 98 
                                       + + +a++lg++ +P  v++rr+ v G 
  gi|557694443|ref|YP_008797497.1| 178 KDLREAAKLGVHAVPTLVINRRYAVVGA 205
                                       56889******************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1806.14
//
Query:       gi|557694444|ref|YP_008797498.1|  [L=263]
Description: hypothetical protein CSUB_C1016 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1913.67
//
Query:       gi|557694445|ref|YP_008797499.1|  [L=142]
Description: hydrogenase nickel incorporation protein HypA [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   0.1    2.6e-18   66.1   0.1    1.0  1  HypA             Hydrogenase/urease nickel incorporation, met
    0.00031   20.2   0.9      0.033   13.7   0.3    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
      0.017   15.0   1.2      0.027   14.4   0.3    1.7  2  DUF5402          Family of unknown function (DUF5402)
      0.029   14.7   0.0        1.7    9.1   0.0    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar
      0.075   13.0   2.3       0.25   11.3   0.2    2.2  2  Nudix_N_2        Nudix N-terminal


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 !   66.1   0.1   7.1e-22   2.6e-18       1     110 [.      10     139 ..      10     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 7.1e-22
                                       XCHHHHHHHHHHHHHHHHCCTT..EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS CS
                              HypA   1 MHElsiaesivevveeeakeaaarkvtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreCg 77 
                                       MHE+ +a  +v+ +++  ++ ++r+v++ +v vGels+++ e+L+ a+e l +++ +++a++++e ++++v C +Cg
  gi|557694445|ref|YP_008797499.1|  10 MHEYVVAVGVVDSLQNFSRS-SGRRVKSFRVFVGELSMLNLEVLREALEKLIRQSEVADAVFSVEVERARVICGSCG 85 
                                       **************999965.569***************************************************** PP

                                       -EEECHH..HHH...................S-TTTSSS-EEEEESSSEEEEEE CS
                              HypA  78 kefelee..kal...................rCpkCgsadveivsGeellvksi 110
                                       + ++  e  ++l                    C  Cgs+d++i sG+++ v+++
  gi|557694445|ref|YP_008797499.1|  86 YVMSFGEvvEDLddqekevihflpeliasygACRICGSKDLRIESGRGVSVRDV 139
                                       *9996653323377899*********************************9876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.3   9.1e-06     0.033      16      42 ..      75     101 ..      68     102 .. 0.85
   2 !    5.1   0.0    0.0046        17       3      14 ..     118     129 ..     116     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.1e-06
                                       STTCEEESSSSBEEEECCCCCCCHHHH CS
                      TF_Zn_Ribbon  16 ergelvCtdCGlVlednsidegpewre 42 
                                       er+ ++C++CG+V+    ++e  + +e
  gi|557694445|ref|YP_008797499.1|  75 ERARVICGSCGYVMSFGEVVEDLDDQE 101
                                       78899**********999999888776 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0046
                                       ETTTTCEECHEE CS
                      TF_Zn_Ribbon   3 CPnCgstnlveD 14 
                                       C +Cgs++l  +
  gi|557694445|ref|YP_008797499.1| 118 CRICGSKDLRIE 129
                                       ******996444 PP

>> DUF5402  Family of unknown function (DUF5402)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   7.5e-06     0.027       8      71 ..      52     115 ..      45     120 .. 0.83
   2 ?   -1.4   0.0      0.61   2.2e+03      36      53 ..     121     139 ..     115     141 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.5e-06
                           DUF5402   8 dreklekklqn.llgkevfvsevdifalrcGcvGilievrGlevddveifkekileklkelakdl 71 
                                        re lek +++  +++ vf  ev+   + cG +G +++  G  v+d++  ++++ + l el  ++
  gi|557694445|ref|YP_008797499.1|  52 LREALEKLIRQsEVADAVFSVEVERARVICGSCGYVMSF-GEVVEDLDDQEKEVIHFLPELIASY 115
                                       48889998876258999*****************98875.88899*9999999999998876665 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.61
                           DUF5402  36 cGcvGilie.vrGlevddv 53 
                                       cG   + ie  rG+ v+dv
  gi|557694445|ref|YP_008797499.1| 121 CGSKDLRIEsGRGVSVRDV 139
                                       6666666651599999997 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 ?    9.1   0.0   0.00048       1.7      27      56 ..      71     106 ..      33     107 .. 0.80
   2 ?    3.7   0.0     0.022        80       6      23 ..     118     135 ..     115     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00048
                   Lar_restr_allev  27 q......cvyCadCgastpwfkiaedeaeaekeaie 56 
                                               v+C  Cg++ +  +  ed  + eke+i+
  gi|557694445|ref|YP_008797499.1|  71 SveveraRVICGSCGYVMSFGEVVEDLDDQEKEVIH 106
                                       15555668********88888889999999999886 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.022
                   Lar_restr_allev   6 CPfCggravlersqrvva 23 
                                       C  Cg+++  ++s+r+v+
  gi|557694445|ref|YP_008797499.1| 118 CRICGSKDLRIESGRGVS 135
                                       889*********999986 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2     7e-05      0.25      19      31 ..      75      87 ..      72      88 .. 0.92
   2 ?    1.0   0.1      0.11   4.1e+02       3      14 ..     118     128 ..     118     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7e-05
                                      SS-EEEETTTTEE CS
                         Nudix_N_2 19 nreRlvCpaCgti 31
                                      +r R +C +Cg++
  gi|557694445|ref|YP_008797499.1| 75 ERARVICGSCGYV 87
                                      799*********9 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.11
                                       -TTT--B-EEE- CS
                         Nudix_N_2   3 CsqCGtpvelri 14 
                                       C+ CG++  lri
  gi|557694445|ref|YP_008797499.1| 118 CRICGSK-DLRI 128
                                       999**98.5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1100.15
//
Query:       gi|557694446|ref|YP_008797500.1|  [L=254]
Description: ATP-binding protein involved in chromosome partitioning [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-52  177.6   0.3    1.5e-51  175.2   0.3    1.8  1  ParA         NUBPL iron-transfer P-loop NTPase
    4.1e-12   46.3   0.1      7e-12   45.5   0.1    1.4  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    6.2e-07   28.9   0.9    2.3e-05   23.8   0.4    2.1  2  ArsA_ATPase  Anion-transporting ATPase
    2.3e-05   24.4   0.4     0.0013   18.7   0.1    2.2  2  AAA_31       AAA domain
    5.8e-05   22.5   0.1    0.00018   20.9   0.1    1.8  1  MipZ         ATPase MipZ
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.021   15.0   0.0    1.4  1  YopE_N       YopE, N terminal
      0.075   12.6   0.3       0.13   11.8   0.3    1.5  1  AAA_25       AAA domain
      0.091   12.2   0.1        3.1    7.2   0.0    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
       0.12   12.2   0.8        2.1    8.1   0.0    2.1  2  AAA_26       AAA domain
       0.22   10.7   0.1       0.35   10.0   0.1    1.2  1  NB-ARC       NB-ARC domain


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 !  175.2   0.3   8.3e-55   1.5e-51       2     223 ..      21     229 ..      20     249 .. 0.92

  Alignments for each domain:
  == domain 1  score: 175.2 bits;  conditional E-value: 8.3e-55
                              ParA   2 vkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSi 78 
                                       +++v++v+ gKGGVGKStva++ Al L+++  ++gllD+D+ Gps   llgv+e+ p ++e++liP ++ g+kvmS+
  gi|557694446|ref|YP_008797500.1|  21 ISRVLLVTGGKGGVGKSTVASTAALILSQSSNRTGLLDLDLNGPSACLLLGVDES-PVETEEGLIPPSVGGLKVMSV 96 
                                       789**************************************************97.5566669************** PP

                              ParA  79 gfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevaladvk 154
                                       +++ +   +++   G  k++++k++++ +++g lDyL++D+PPGt De lt++    ++ ga++Vtt   +++++++
  gi|557694446|ref|YP_008797500.1|  97 DLFAR--GRPLPLTGGAKEEVVKEMMALTSFGRLDYLVVDTPPGTDDELLTITRLTkQVGGALVVTTSSPLSISVAR 171
                                       **998..99*********************************************998899***************** PP

                              ParA 155 kaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegk 223
                                       + ie++ +++ +++G+veNms+ + +           +  ++la+e++v++lg+ip+d ei++ + +  
  gi|557694446|ref|YP_008797500.1| 172 RVIEILGSMNYRIVGLVENMSTGAGD-----------SPSRHLAAETEVEFLGAIPFDAEIMTGGGKTG 229
                                       *********************87655...........456789******************98876655 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 !   45.5   0.1   3.9e-15     7e-12       1     119 [.      25     222 ..      25     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.9e-15
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       ++++++kGGvGK+t+a + a +l++  +r+ l+D+D  ++++ +l g+ +   +                       
  gi|557694446|ref|YP_008797500.1|  25 LLVTGGKGGVGKSTVASTAALILSQSSNRTGLLDLDLNGPSACLLLGVDESPVEteeglippsvgglkvmsvdlfar 101
                                       589**************************************9986666666666899******************** PP

                                       ................................................................CCHCCCHHHHHHC CS
                                       ................................................................xxxxxxxxxxxxx RF
                              CbiA  55 ................................................................dlkrllellealg 67 
                                                                                                       +++   +++e lg
  gi|557694446|ref|YP_008797500.1| 102 grplpltggakeevvkemmaltsfgrldylvvdtppgtddelltitrltkqvggalvvttssplSISVARRVIEILG 178
                                       ****************************************************9999999999984444444444444 PP

                                       HCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  68 kkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeava 119
                                            + +i+g+v n+  g     + + +l+ +    +v++lg ip+d +++
  gi|557694446|ref|YP_008797500.1| 179 SM---NYRIVGLVENMSTGA--GDSPSRHLAAET---EVEFLGAIPFDAEIM 222
                                       32...389**********99..999*****9998...***********9986 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.4   1.3e-08   2.3e-05       4      38 ..      26      60 ..      22      64 .. 0.86
   2 ?    3.5   0.0     0.019        34     114     187 ..     117     191 ..     109     197 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.3e-08
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      ++ gGKGGVGK+tv+++ a+ ls++ +++ l+ +D
  gi|557694446|ref|YP_008797500.1| 26 LVTGGKGGVGKSTVASTAALILSQSSNRTGLLDLD 60
                                      45689********************9999887666 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.019
                                       HHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHHHHHHH..HHHHHHHHHCCCSHCHHHHHHHHHHHH CS
                       ArsA_ATPase 114 eellkyvkeeeydvvvlDtaPTGhtlrllslpevleklleklvklke..klsplakqlvkllglggvsieealeel 187
                                       +e++ +++    d++v+Dt+P G+   ll + +  +++   lv ++      ++a+ + ++lg +++ i   +e++
  gi|557694446|ref|YP_008797500.1| 117 KEMMALTSFGRLDYLVVDTPP-GTDDELLTITRLTKQVGGALVVTTSspLSISVARRVIEILGSMNYRIVGLVENM 191
                                       567777778899*******98.566667777666666655555444433344556666666666666666555555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   7.2e-07    0.0013       2      43 ..      23      64 ..      22      94 .. 0.86
   2 ?    4.1   0.0     0.021        38     116     166 ..     126     179 ..      74     190 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.2e-07
                            AAA_31  2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQan 43
                                      +v+ ++  KGGvGK+T +   a  l+++ +++ l DlD  + 
  gi|557694446|ref|YP_008797500.1| 23 RVLLVTGGKGGVGKSTVASTAALILSQSSNRTGLLDLDLNGP 64
                                      67778889******************************7664 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.021
                            AAA_31 116 deYDyiiiDcpPsL..glltenaLvas.dsviipvqaeayaleGleqllktiee 166
                                        + Dy ++D+pP    +llt++ L+      ++++ +++++++ ++++++ + +
  gi|557694446|ref|YP_008797500.1| 126 GRLDYLVVDTPPGTddELLTITRLTKQvGGALVVTTSSPLSISVARRVIEILGS 179
                                       568*********762257888888754145566666667777777777766655 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   9.8e-08   0.00018       2     116 ..      24     145 ..      23     168 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 9.8e-08
                                       EEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHHHHH.HHHHHT-......-----EEE-SS CS
                              MipZ   2 vivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylenraa.taerkgl......sLplpealals 71 
                                       v+ ++  kGG Gkst+a   a  L+++  r + +dldl   +    l+     +++++gl       L++ ++  ++
  gi|557694446|ref|YP_008797500.1|  24 VLLVTGGKGGVGKSTVASTAALILSQSSNRTGLLDLDLNGPSACLLLGVDESpVETEEGLippsvgGLKVMSVDLFA 100
                                       6678889*********************************9999999866551444555622211123333333344 PP

                                       S-HHHHTTS-HHHHHHHHHHHHHHHHHH-SEEEEE--.SS--HHHH CS
                              MipZ  72 eaeeaeveeeeeaevaeleelvadleaeldfividtP.Gsdsalsr 116
                                        +    +++++++ev++ + +++++  +ld++v+dtP G+d++l  
  gi|557694446|ref|YP_008797500.1| 101 RGRPLPLTGGAKEEVVKEMMALTSF-GRLDYLVVDTPpGTDDELLT 145
                                       5566677777777765544455444.579******95488887643 PP

>> YopE_N  YopE, N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.2e-05     0.021      38      83 ..     152     197 ..     145     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            YopE_N  38 qyannlagrtespqgsslasriierlssvahsvigfiqrmfsegsh 83 
                                       q    l   t sp   s+a r+ie l s+ + ++g+++ m +    
  gi|557694446|ref|YP_008797500.1| 152 QVGGALVVTTSSPLSISVARRVIEILGSMNYRIVGLVENMSTGAGD 197
                                       666778889*****************************99766555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   7.3e-05      0.13      34      83 ..      24      76 ..       3     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.3e-05
                            AAA_25 34 elallaGapgtGKttlaldlalavatGkpwlg....pvapeqgkVlyvsaEdse 83
                                       l +  G +g+GK+t+a+  al +++ ++ +g    ++ + + ++l++  ++s 
  gi|557694446|ref|YP_008797500.1| 24 VLLVTGGKGGVGKSTVASTAALILSQSSNRTGlldlDL-NGPSACLLLGVDESP 76
                                      455667***************99986665555554433.355666666666655 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 ?    7.2   0.0    0.0017       3.1       7      43 ..      30      66 ..      25      78 .. 0.76
   2 ?    2.9   0.0     0.035        63     161     215 ..     169     222 ..     150     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0017
                         Fer4_NifH  7 GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDst 43
                                      GkGG+Gkst ++  +  l++  ++  ++  D    s+
  gi|557694446|ref|YP_008797500.1| 30 GKGGVGKSTVASTAALILSQSSNRTGLLDLDLNGPSA 66
                                      9********9999999998888776666655555555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.035
                         Fer4_NifH 161 iakgiekyaksggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeivr 215
                                       +a+ + +   s + r+ Gl+ n  ++  ++   +++a+e +++ l ++P d ++ 
  gi|557694446|ref|YP_008797500.1| 169 VARRVIEILGSMNYRIVGLVEN-MSTGAGDSPSRHLAAETEVEFLGAIPFDAEIM 222
                                       444455556677889*******.6689999999****************998875 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.6     0.069   1.2e+02       1      30 [.      23      52 ..      23      57 .. 0.77
   2 ?    8.1   0.0    0.0012       2.1     136     195 ..     161     222 ..     129     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.069
                            AAA_26  1 rtifvtgtdtgvGKTvvslgLvralkrkgv 30
                                      r ++vtg   gvGK++v+   + +l++   
  gi|557694446|ref|YP_008797500.1| 23 RVLLVTGGKGGVGKSTVASTAALILSQSSN 52
                                      5699************98776666666555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0012
                            AAA_26 136 rgglgtinqllltiealrqknvrvlGvilNkvrnp..envetlekksgipvlGvvPylpdle 195
                                       ++   +i  +   ie+l + n r++G++ N  + +   + + l + ++++ lG++P +++++
  gi|557694446|ref|YP_008797500.1| 161 TSSPLSISVARRVIEILGSMNYRIVGLVENMSTGAgdSPSRHLAAETEVEFLGAIPFDAEIM 222
                                       44445666666678888899**********9766654699*****************99876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00019      0.35       9      40 ..      15      43 ..       9      54 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00019
                                      HHHHHCTTTSCSEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC  9 iekLlekdelqslvvalvGmgGvGKttlakqi 40
                                      +++L+   e+ ++++   G+gGvGK+t+a+ +
  gi|557694446|ref|YP_008797500.1| 15 MKRLS---EISRVLLVTGGKGGVGKSTVASTA 43
                                      45555...7888889999**********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1800.91
//
Query:       gi|557694447|ref|YP_008797501.1|  [L=375]
Description: 4Fe-4S ferredoxin, iron-sulfur binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  117.5   7.8    3.6e-34  117.5   7.8    2.2  3  Fer4_22     4Fe-4S dicluster domain
    2.5e-07   31.1   5.5     0.0079   16.7   0.1    2.6  2  Fer4_17     4Fe-4S dicluster domain
    2.8e-07   31.0   9.3     0.0069   17.0   0.1    2.7  2  Fer4_7      4Fe-4S dicluster domain
    2.9e-07   30.2  12.7    0.00078   19.4   4.1    2.7  2  Fer4_2      4Fe-4S binding domain
    4.2e-07   30.3  18.5    2.4e-06   27.9   7.6    2.2  2  Fer4_8      4Fe-4S dicluster domain
      1e-06   28.8   8.0     0.0082   16.3   0.1    2.6  2  Fer4_9      4Fe-4S dicluster domain
    1.7e-06   28.0  11.6     0.0051   16.9   0.4    2.6  2  Fer4_10     4Fe-4S dicluster domain
    2.4e-05   24.5   5.0     0.0038   17.4   0.0    2.6  2  Fer4_18     4Fe-4S dicluster domain
    0.00011   23.0   9.3      0.058   14.3   1.1    2.6  2  Fer4_16     4Fe-4S double cluster binding domain
    0.00039   20.5  13.2      0.036   14.2   0.7    2.5  2  Fer4_21     4Fe-4S dicluster domain
    0.00057   19.6  18.8      0.008   16.0   3.7    2.5  2  Fer4        4Fe-4S binding domain
     0.0049   16.9  19.6        0.3   11.2   4.2    2.5  2  Fer4_6      4Fe-4S binding domain
     0.0093   16.4  17.0       0.31   11.7   1.3    2.9  2  Fer4_4      4Fe-4S binding domain
  ------ inclusion threshold ------
      0.027   15.4   4.2      0.027   15.4   4.2    2.9  2  Fer4_3      4Fe-4S binding domain
      0.058   13.5   0.4       0.13   12.4   0.4    1.5  1  Sigma70_r3  Sigma-70 region 3
       0.16   12.5  12.4        1.6    9.4   5.5    2.8  2  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
        1.2    8.9  11.2          2    8.2   0.3    2.5  2  Fer4_20     Dihydroprymidine dehydrogenase domain II, 4Fe-4S 
        6.7    7.5  10.2         33    5.3   3.1    2.9  2  Fer4_15     4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       3.7   3.7e+03       7      21 ..     157     171 ..     153     188 .. 0.83
   2 ?   -1.8   0.1         6     6e+03      45      82 ..     207     244 ..     192     245 .. 0.65
   3 !  117.5   7.8   3.7e-37   3.6e-34       1      96 []     263     357 ..     263     357 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.7
                           Fer4_22   7 aCtlvCptCsCfdve 21 
                                       +Ct     C+C ++ 
  gi|557694447|ref|YP_008797501.1| 157 NCTEPGENCFCSSMG 171
                                       79999999***9875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6
                           Fer4_22  45 ftkvaggenvrkekkerlrqrllhklsefkekfgesgC 82 
                                       f +  g +++ +e+ ++  + + +    fk++f+++gC
  gi|557694447|ref|YP_008797501.1| 207 FLEQVGARKATEEEVAKAASLMERSRMLFKKRFEAKGC 244
                                       55555555555556666665555666677777777777 PP

  == domain 3  score: 117.5 bits;  conditional E-value: 3.7e-37
                           Fer4_22   1 rClsCgaCtlvCptCsCfdvedetkeeskegervrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekf 77 
                                       rCl+Cg+CtlvCptC+C+++ ++t+ + +++er+r+wdsC+ ++f++++gg  +r+++ +r+rq+++hkls+++++f
  gi|557694447|ref|YP_008797501.1| 263 RCLACGNCTLVCPTCFCTSTDEVTDLSGEKAERWRRWDSCFNADFSYIHGG-PIRASRLSRYRQWITHKLSTWVDQF 338
                                       7***********************9999***********************.9************************ PP

                           Fer4_22  78 gesgCvGCgRCieacpvki 96 
                                       g+ gCvGCgRCi++cpv+i
  gi|557694447|ref|YP_008797501.1| 339 GMLGCVGCGRCITWCPVGI 357
                                       ****************987 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.3   3.1e-05     0.031      30      58 ..     248     276 ..     215     278 .. 0.68
   2 !   16.7   0.1   7.9e-06    0.0079       2      29 ..     343     370 ..     318     374 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-05
                           Fer4_17  30 klglleeaekeekaslCieCgeCerkCPq 58 
                                        ++ le     e+a++C+ Cg+C+ +CP 
  gi|557694447|ref|YP_008797501.1| 248 LYNNLESPVYAEVAERCLACGNCTLVCPT 276
                                       223344444459****************5 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 7.9e-06
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraa 29 
                                       C +Cg C+  Cp ++++ +e +k++++a
  gi|557694447|ref|YP_008797501.1| 343 CVGCGRCITWCPVGIDITEEAAKIMQRA 370
                                       9999999999999999999999888875 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   5.1   1.9e-05     0.019      20      50 ..     236     276 ..     155     277 .. 0.78
   2 !   17.0   0.1   6.9e-06    0.0069      33      52 .]     338     357 ..     291     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.9e-05
                            Fer4_7  20 deeenekgt..........ekveidpekClgCgaCvavCPt 50 
                                       +++ ++kg+          + ++ ++e+Cl Cg+C  vCPt
  gi|557694447|ref|YP_008797501.1| 236 KKRFEAKGCrealynnlesPVYAEVAERCLACGNCTLVCPT 276
                                       44444554432333333336668899**************8 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 6.9e-06
                            Fer4_7  33 idpekClgCgaCvavCPtga 52 
                                       + +  C+gCg+C++ CP+g+
  gi|557694447|ref|YP_008797501.1| 338 FGMLGCVGCGRCITWCPVGI 357
                                       56778999999999999986 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   4.1   7.8e-07   0.00078       3      22 .]     257     276 ..     255     276 .. 0.84
   2 !   15.2   1.3   1.7e-05     0.017       9      21 ..     342     354 ..     334     355 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.8e-07
                            Fer4_2   3 vvvdtdrCigCgaCvsaCPa 22 
                                       ++ +++rC++Cg C+ +CP+
  gi|557694447|ref|YP_008797501.1| 257 YAEVAERCLACGNCTLVCPT 276
                                       455689*************7 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.7e-05
                            Fer4_2   9 rCigCgaCvsaCP 21 
                                        C+gCg C++ CP
  gi|557694447|ref|YP_008797501.1| 342 GCVGCGRCITWCP 354
                                       6************ PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   3.1   1.3e-05     0.013      27      63 ..     236     276 ..     195     278 .. 0.69
   2 !   27.9   7.6   2.4e-09   2.4e-06       2      65 .]     261     357 ..     260     357 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                            Fer4_8  27 dargeaaedvqeeqvlee.............eealwsCttcgaCtevCpv 63 
                                       ++r ea++                       +e +++C++cg+Ct vCp+
  gi|557694447|ref|YP_008797501.1| 236 KKRFEAKG---------CrealynnlespvyAEVAERCLACGNCTLVCPT 276
                                       33333333.........03333334466778999***************6 PP

  == domain 2  score: 27.9 bits;  conditional E-value: 2.4e-09
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtk.khlldargeaae..........dvqeeqvlee....................... 44 
                                       +e+C  Cg C+  Cp++ +t  ++  d  ge+ae                   +                       
  gi|557694447|ref|YP_008797501.1| 261 AERCLACGNCTLVCPTCFCTStDEVTDLSGEKAErwrrwdscfnA--------Dfsyihggpirasrlsryrqwith 329
                                       589************999999888888888877756444444440........155666666666666666667778 PP

                            Fer4_8  45 .......eealwsCttcgaCtevCpvgi 65 
                                              + ++  C++cg+C + Cpvgi
  gi|557694447|ref|YP_008797501.1| 330 klstwvdQFGMLGCVGCGRCITWCPVGI 357
                                       888899899*****************97 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   3.8   4.2e-05     0.042      12      48 ..     244     276 ..     224     304 .. 0.77
   2 !   16.3   0.1   8.2e-06    0.0082       2      26 ..     343     367 ..     318     373 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-05
                            Fer4_9  12 CpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                       C   ++++ +++ +a++     e+C+ Cg C+ +Cp+
  gi|557694447|ref|YP_008797501.1| 244 CREALYNNLESPVYAEVA----ERCLACGNCTLVCPT 276
                                       555555555555555554....468888888888886 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 8.2e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerka 26 
                                       C+gCg+C++ Cp g+ + ++a++++
  gi|557694447|ref|YP_008797501.1| 343 CVGCGRCITWCPVGIDITEEAAKIM 367
                                       8888888888888887777777666 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   5.3     4e-05      0.04       6      40 ..     261     296 ..     258     306 .. 0.71
   2 !   16.9   0.4   5.1e-06    0.0051       9      31 ..     343     365 ..     337     374 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4e-05
                           Fer4_10   6 ddtCirCgkCvkaCPadl.tsvgakgeaseeeavrk 40 
                                       +++C+ Cg+C+ +CP+++ ts +     s+e+a+r 
  gi|557694447|ref|YP_008797501.1| 261 AERCLACGNCTLVCPTCFcTSTDEVTDLSGEKAERW 296
                                       589*************98855555555555555554 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5.1e-06
                           Fer4_10   9 CirCgkCvkaCPadltsvgakge 31 
                                       C++Cg+C + CP+ ++  +  ++
  gi|557694447|ref|YP_008797501.1| 343 CVGCGRCITWCPVGIDITEEAAK 365
                                       *************6644443333 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   2.3    0.0063       6.2      56      74 ..     259     277 ..     236     281 .. 0.80
   2 !   17.4   0.0   3.8e-06    0.0038      47      79 ..     329     361 ..     300     367 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0063
                           Fer4_18  56 kgagdcidcescvkvcPtg 74 
                                       + a  c++c+ c  vcPt 
  gi|557694447|ref|YP_008797501.1| 259 EVAERCLACGNCTLVCPTC 277
                                       55667************95 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 3.8e-06
                           Fer4_18  47 lkekeerkekgagdcidcescvkvcPtgidirk 79 
                                       +k +    + g+  c+ c+ c++ cP+gidi +
  gi|557694447|ref|YP_008797501.1| 329 HKLSTWVDQFGMLGCVGCGRCITWCPVGIDITE 361
                                       44455556667789*****************75 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 !   12.7   1.7   0.00018      0.18      52      65 ..     262     275 ..     213     296 .. 0.73
   2 !   14.3   1.1   5.8e-05     0.058       2      20 ..     343     362 ..     342     373 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
                           Fer4_16  52 eaitgCdiCqdvCP 65 
                                       e++  C++C+ vCP
  gi|557694447|ref|YP_008797501.1| 262 ERCLACGNCTLVCP 275
                                       55667777777776 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 5.8e-05
                           Fer4_16   2 CgtCgkCaevCPtna.ikek 20 
                                       C++Cg+C+  CP++  i+e+
  gi|557694447|ref|YP_008797501.1| 343 CVGCGRCITWCPVGIdITEE 362
                                       *************9866666 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   5.8    0.0006       0.6      34      54 ..     257     277 ..     241     282 .. 0.75
   2 !   14.2   0.7   3.6e-05     0.036      41      53 ..     343     355 ..     328     361 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0006
                           Fer4_21  34 lkvvedeCvGCnlCssvCPve 54 
                                       ++ v+++C +C  C+ vCP+ 
  gi|557694447|ref|YP_008797501.1| 257 YAEVAERCLACGNCTLVCPTC 277
                                       4567899************74 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.6e-05
                           Fer4_21  41 CvGCnlCssvCPv 53 
                                       CvGC  C++ CPv
  gi|557694447|ref|YP_008797501.1| 343 CVGCGRCITWCPV 355
                                       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 !   16.0   3.7     8e-06     0.008       5      20 ..     261     276 ..     259     276 .. 0.93
   2 !    8.8   7.2    0.0014       1.4       8      21 ..     343     356 ..     342     357 .. 0.95

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8e-06
                                       TTTSSS-THHHHHSTT CS
                              Fer4   5 eekCigCGaCvevCPv 20 
                                        e+C +CG+C  vCP+
  gi|557694447|ref|YP_008797501.1| 261 AERCLACGNCTLVCPT 276
                                       59*************7 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0014
                                       SSS-THHHHHSTTT CS
                              Fer4   8 CigCGaCvevCPvg 21 
                                       C+gCG+C+  CPvg
  gi|557694447|ref|YP_008797501.1| 343 CVGCGRCITWCPVG 356
                                       ************98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   7.4   0.00039      0.39       7      21 ..     262     276 ..     260     277 .. 0.93
   2 !   11.2   4.2    0.0003       0.3       9      22 ..     343     356 ..     343     359 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00039
                            Fer4_6   7 dkCigCgdCvrvCPe 21 
                                       ++C+ Cg+C+ vCP+
  gi|557694447|ref|YP_008797501.1| 262 ERCLACGNCTLVCPT 276
                                       89************7 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0003
                            Fer4_6   9 CigCgdCvrvCPeg 22 
                                       C+gCg+C++ CP g
  gi|557694447|ref|YP_008797501.1| 343 CVGCGRCITWCPVG 356
                                       ************97 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   8.4    0.0029       2.9       2      16 ..     262     276 ..     261     283 .. 0.93
   2 !   11.7   1.3   0.00031      0.31       4      17 .]     343     356 ..     334     356 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       erC+ Cg C+ +CP+
  gi|557694447|ref|YP_008797501.1| 262 ERCLACGNCTLVCPT 276
                                       9*************6 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00031
                            Fer4_4   4 CigCgsCvaaCPqg 17 
                                       C+gCg+C+  CP+g
  gi|557694447|ref|YP_008797501.1| 343 CVGCGRCITWCPVG 356
                                       ************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 ?    2.9  10.0      0.27   2.7e+02       1      13 [.     264     276 ..     264     277 .. 0.94
   2 ?   15.4   4.2   2.7e-05     0.027       1      15 []     343     357 ..     343     357 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.27
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+ Cg C  vCP+
  gi|557694447|ref|YP_008797501.1| 264 CLACGNCTLVCPT 276
                                       999*********6 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.7e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+gCg+C  +CPvg+
  gi|557694447|ref|YP_008797501.1| 343 CVGCGRCITWCPVGI 357
                                       *************95 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   0.00013      0.13       7      30 ..     202     225 ..     201     230 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHSSXXXHHHHHHHH CS
                        Sigma70_r3   7 kraqreLeqelgrePtpeEiAeeL 30 
                                       k+aqr Leq   r +t+eE+A++ 
  gi|557694447|ref|YP_008797501.1| 202 KNAQRFLEQVGARKATEEEVAKAA 225
                                       78*******************985 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 ?    9.4   5.5    0.0016       1.6       4      25 ..     262     283 ..     260     288 .. 0.88
   2 ?    6.3   0.6     0.014        14       5      24 ..     342     361 ..     341     373 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                           Fer4_13   4 dtCiacgaCvelaPdvFeedde 25 
                                       ++C acg+C  ++P +F    +
  gi|557694447|ref|YP_008797501.1| 262 ERCLACGNCTLVCPTCFCTSTD 283
                                       79***************87655 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.014
                           Fer4_13   5 tCiacgaCvelaPdvFeedd 24 
                                        C++cg C   +P   ++ +
  gi|557694447|ref|YP_008797501.1| 342 GCVGCGRCITWCPVGIDITE 361
                                       5************6655555 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 ?    3.4   5.6     0.063        63      16      38 ..     256     276 ..     242     282 .. 0.78
   2 ?    8.2   0.3     0.002         2      24      55 ..     343     372 ..     340     375 .] 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.063
                                       HHHHHHTT----TT-HHHHCSTT CS
                           Fer4_20  16 ealeeAsRClqCkkapcvkgCPv 38 
                                         +e A+RCl C   +c+  CP+
  gi|557694447|ref|YP_008797501.1| 256 VYAEVAERCLAC--GNCTLVCPT 276
                                       45677*******..679999997 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.002
                                       ----TT-HHHHCSTT---HHHHHHHHHTT-HH CS
                           Fer4_20  24 ClqCkkapcvkgCPveidipefikkiaegnle 55 
                                       C+ C    c++ CPv idi e   ki ++ +e
  gi|557694447|ref|YP_008797501.1| 343 CVGC--GRCITWCPVGIDITEEAAKIMQRAVE 372
                                       8889..78***********9988888877665 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 ?    5.3   3.1     0.033        33       6      32 ..     262     288 ..     259     298 .. 0.82
   2 ?    5.2   0.7     0.035        35       8      23 ..     343     358 ..     340     373 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.033
                           Fer4_15   6 daCigcglCvaeapevfeldedglasv 32 
                                       ++C  cg+C  ++p+ f    d + ++
  gi|557694447|ref|YP_008797501.1| 262 ERCLACGNCTLVCPTCFCTSTDEVTDL 288
                                       79***************9888877644 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.035
                           Fer4_15   8 CigcglCvaeapevfe 23 
                                       C gcg+C++ +p  + 
  gi|557694447|ref|YP_008797501.1| 343 CVGCGRCITWCPVGID 358
                                       **********996554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); 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:                        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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2704.57
//
Query:       gi|557694448|ref|YP_008797502.1|  [L=162]
Description: transcriptional regulator, Crp/Fnr family [Candidatus Caldiarchaeum subterraneum]
Scores for 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   49.4   0.0    5.3e-13   48.8   0.0    1.3  1  cNMP_binding  Cyclic nucleotide-binding domain


Domain annotation for each model (and alignments):
>> cNMP_binding  Cyclic nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0     3e-17   5.3e-13       2      88 ..      37     123 ..      36     124 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 3e-17
                                       EEE-TT-EEE-TTSB-SEEEEEEES-EEEEEEETTS.EEEEEEE-TTEEESHHHHHHTS--SSEEEESSTEEEEEEE CS
                      cNMP_binding   2 rsfkagevifrqGdpadslyivlsGevrvyrlsedgkevvlavlgpGdlfGelalltgeprtatvvAltdsellalp 78 
                                       ++f+ag+ if++G+  ++ly+++ G v++y + +   e  ++++g+G+++G  +l++  + t  +vA++++  +a++
  gi|557694448|ref|YP_008797502.1|  37 VRFSAGQKIFEEGEVHKRLYLIVYGLVALYFQIPTRGEFRFETIGSGEVLGWSSLMEPFKKTSGAVAVENTLAIAVD 113
                                       79****************************999999999*****************98999999************* PP

                                       HHHHHHHHHH CS
                      cNMP_binding  79 rddflellqq 88 
                                        +++l+++++
  gi|557694448|ref|YP_008797502.1| 114 SEKLLRMMRD 123
                                       *******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1173.41
//
Query:       gi|557694449|ref|YP_008797503.1|  [L=284]
Description: oxidoreductase FAD/NAD(P)-binding subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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   64.9   0.0    1.6e-17   64.1   0.0    1.3  1  NAD_binding_1    Oxidoreductase NAD-binding domain
    1.6e-10   40.6   2.1    3.5e-10   39.5   2.1    1.6  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
     0.0038   17.4   0.4       0.01   16.0   0.0    1.9  3  NAD_binding_6    Ferric reductase NAD binding domain
     0.0056   17.0   0.0      0.016   15.5   0.0    1.8  2  FAD_binding_6    Oxidoreductase FAD-binding domain


Domain annotation for each model (and alignments):
>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   3.6e-21   1.6e-17       2     107 ..     123     224 ..     122     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 3.6e-21
                                       EEEGGGGHHHHHHHHHHHHHCTTCSEEEEEEEESSGCGSTTHHHHHHHHHHCTTEEEEEEEESSCTTTSSSEESSHH CS
                     NAD_binding_1   2 iagGtGiaPvrsvlraileeakdktkvvlvyGnrteedllyreeleelakklpgrlkvvavvsreeagweggkgrvq 78 
                                       +agG G+aP+r ++r++l+  ++ +k++++yG+r+  +l+y+ el++++k+l  r  +++v ++ +++w+g  g v+
  gi|557694449|ref|YP_008797503.1| 123 VAGGIGLAPLRPLIRHFLRSREKIGKLYILYGARSPGELVYKRELQAWKKRLGAR-LLITV-DKGDEKWRGHIGVVT 197
                                       8*******************9999************************9999997.46666.9************** PP

                                       HHHHHHHHHHSSTTEEEEEECSHHHHHHH CS
                     NAD_binding_1  79 dalleellslkkeethvyvCGppgMikav 107
                                       + +   +l+   e+t +y+CGp+ M++++
  gi|557694449|ref|YP_008797503.1| 198 TLFKYVTLD--PENTYAYICGPEIMMRFT 224
                                       999666666..9**************985 PP

>> 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 !   39.5   2.1   7.7e-14   3.5e-10       1      41 [.     243     275 ..     243     276 .. 0.95

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 7.7e-14
                                       ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       e+ M+CGvG+C++C             +vCkdGPvF ++ev
  gi|557694449|ref|YP_008797503.1| 243 ERNMKCGVGLCGHCQFGP--------YFVCKDGPVFSYSEV 275
                                       899**************9........8***********998 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.2e-06      0.01       3      49 ..     119     161 ..     117     177 .. 0.83
   2 ?   -2.4   0.0         1   4.6e+03     140     148 ..     213     221 ..     201     224 .. 0.82
   3 ?   -3.9   0.4       2.9   1.3e+04     132     144 ..     243     255 ..     239     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_6   3 nvllvagGiGitpfisilkdllkkskkealktkkikliwvvresssl 49 
                                        v+ vagGiG++p+ ++++++l+  +    k+ k+++    r+ ++l
  gi|557694449|ref|YP_008797503.1| 119 DVVVVAGGIGLAPLRPLIRHFLRSRE----KIGKLYILYGARSPGEL 161
                                       5999*******************998....88888877777777766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1
                                       xxxxxxxxx RF
                     NAD_binding_6 140 fvCGppklv 148
                                       ++CGp++++
  gi|557694449|ref|YP_008797503.1| 213 YICGPEIMM 221
                                       68***9996 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 2.9
                                       xxxxxxxxxxxxx RF
                     NAD_binding_6 132 hknssvgvfvCGp 144
                                       + n + gv  CG+
  gi|557694449|ref|YP_008797503.1| 243 ERNMKCGVGLCGH 255
                                       5677899999997 PP

>> FAD_binding_6  Oxidoreductase FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.6e-06     0.016       3      96 ..      22     108 ..      20     110 .. 0.73
   2 ?   -2.6   0.0       1.7   7.4e+03      17      43 ..     200     226 ..     194     230 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                                       EEEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHH CS
                     FAD_binding_6   3 kltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaL 79 
                                       +++++++ ++dt ++++k    + ++++ +Gq+ +l+    gea   + ++  ++++  ++e   + +  G ++ aL
  gi|557694449|ref|YP_008797503.1|  22 RVVSRRRETPDTYTLKIK--PLNGSVNYSPGQFSMLYRYGVGEA---PISFSGDSDNGEQVEHTLRAV--GGVTRAL 91 
                                       566667777777655554..457788999999999998877773...445334444555677777765..889**** PP

                                       HCS-TT-EEEEEEEE-S CS
                     FAD_binding_6  80 delkigdtleikGPlGk 96 
                                        ++++gdt+ ++GP+G+
  gi|557694449|ref|YP_008797503.1|  92 ASAQPGDTVGMRGPFGN 108
                                       ***************97 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                                       EEEEESTTTS-----TT-EEEEEECET CS
                     FAD_binding_6  17 frfklpsekqklglpvGqhvflrlkik 43 
                                       f+  + +++++  +  G  +++r++i 
  gi|557694449|ref|YP_008797503.1| 200 FKYVTLDPENTYAYICGPEIMMRFTIA 226
                                       555455578888899999999988864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2051.69
//
Query:       gi|557694450|ref|YP_008797504.1|  [L=253]
Description: NADH ubiquinone oxidoreductase 20 kDa subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   85.5   0.0    3.8e-24   85.0   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 !   85.0   0.0   2.1e-28   3.8e-24       1     130 [.      15     151 ..      15     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 2.1e-28
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakavi 77 
                                       C+Gc++s+l+le++ll++ e +e++y   +l++s+  ++ +     d+++veG++  ++ ++  l+ke++++++++i
  gi|557694450|ref|YP_008797504.1|  15 CDGCQLSVLDLEDELLAIGEKFEIAY---FLEASR--AVVK--GPYDIALVEGSI--TTPHDAALIKEVRKNSRILI 82 
                                       ******************99999999...667777..3444..59**********..9999**************** PP

                                       EESHHHHH-TGGGSTT-T.EE...............-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                       Oxidored_q6  78 avGtCAafGGipaaannp.sv...............geevgellevvpvdinipGCPphpeailetlla 130
                                        +G+CA+ GGi+a++n   s                +++++++ ++vpvd+++ GCP+++ ++le+++a
  gi|557694450|ref|YP_008797504.1|  83 TIGACATAGGIQALRNWRgSAefmkyvyarpeyietLDKSTPVADHVPVDFELRGCPINKYQLLEVMSA 151
                                       **************996663367778888777765548999***********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1825.38
//
Query:       gi|557694451|ref|YP_008797505.1|  [L=428]
Description: nickel-dependent hydrogenase large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-27   95.5   0.2    1.1e-14   54.3   0.1    3.3  3  NiFeSe_Hases  Nickel-dependent hydrogenase
  ------ inclusion threshold ------
        0.2   11.4   0.0       0.53   10.0   0.0    1.7  2  DUF3236       Protein of unknown function (DUF3236)


Domain annotation for each model (and alignments):
>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.1   1.2e-18   1.1e-14       1      87 [.      40     126 ..      40     136 .. 0.94
   2 !    7.1   0.0   0.00024       2.2     155     200 ..     136     178 ..     134     266 .. 0.77
   3 !   30.8   0.0   1.5e-11   1.4e-07     396     505 .]     314     419 ..     261     419 .. 0.73

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 1.2e-18
                                       --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHHTTGGG CS
                      NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhFYhLhalD 77 
                                       R +E +l gr   da  ++ RiCG+C+++ +++s++a+e+ +g+ +    r +r l+   +++++h++h + Lha D
  gi|557694451|ref|YP_008797505.1|  40 RLFEAFLIGRMYYDAPDITARICGICPVAYQMSSIHAMENLFGVVVEPAVRELRRLLYCGEWIESHMLHAFLLHAPD 116
                                       6689************************************************************************* PP

                                       TS-THGGGGS CS
                      NiFeSe_Hases  78 wvdvvsalka 87 
                                       ++   +alk 
  gi|557694451|ref|YP_008797505.1| 117 FLGYDDALKM 126
                                       **99999987 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHTHHHHHHHSSSSS--.EBTTBESSGBGSBSHHHHHHH CS
                      NiFeSe_Hases 155 eaLelqrkaakivaifggknPhpqslvvGGvtcaidllnaerlaev 200
                                       +aL++++  + +va +gg++ hp s +vGG   + +    ++lae+
  gi|557694451|ref|YP_008797505.1| 136 KALKAKKIGNDVVARLGGREIHPVSACVGGFYRVPSK---RELAEL 178
                                       689999999*********************9887443...333333 PP

  == domain 3  score: 30.8 bits;  conditional E-value: 1.5e-11
                                       HHHHHHTTB---B--TT-SGGGS-.SEEEEEEEEEETTEEEEEEEEE.ETTEEEEEEEE-HHHHHH--S-TT----H CS
                      NiFeSe_Hases 396 lvenikkgdtetaneekldkkevp.keakGvglveapRGaLsHwiki.kdgkienYqavvPsTWnasPrdakgqkga 470
                                       ++e ++    +t++e ++++ e+  +  +G+g++eapRG L H  ++ + g+i   ++v P+  n    +++     
  gi|557694451|ref|YP_008797505.1| 314 FEEALRIV--DTYSEPRVARVELSvRAGRGCGCTEAPRGILYHRYDVdEHGRILSAKIVPPTAQNQKSIEED--LRK 386
                                       44444444..445556666666665679*******************55789*9999999998887555444..444 PP

                                       HHHHHTT-B-SSTTS-HHHHHHHHHT--BHHHHH- CS
                      NiFeSe_Hases 471 yEaaLigtpvadpekPleilrtihSfDPClACavH 505
                                       +   +i  p +++       + i+ +DPC++Ca+H
  gi|557694451|ref|YP_008797505.1| 387 LAPKIIKLPRSQA--VWRFEQAIRNYDPCISCATH 419
                                       5556666555444..4555589************9 PP

>> DUF3236  Protein of unknown function (DUF3236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0      0.84   7.6e+03     142     153 .]     281     292 ..     277     292 .. 0.75
   2 ?   10.0   0.0   5.9e-05      0.53     114     142 ..     358     386 ..     356     393 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.84
                                       HHHHHHHHTTT- CS
                           DUF3236 142 kelleaLkriGl 153
                                       + + +aL+riG+
  gi|557694451|ref|YP_008797505.1| 281 DLTKTALERIGF 292
                                       456789****97 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 5.9e-05
                                       EETTS-EEEEEEE--TTTS---HHHHHHH CS
                           DUF3236 114 ldekgriltaalsPshvihkksveeavkk 142
                                       +de+gril+a + P+ + ++ks+ee ++k
  gi|557694451|ref|YP_008797505.1| 358 VDEHGRILSAKIVPPTAQNQKSIEEDLRK 386
                                       79**********************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3019.58
//
Query:       gi|557694452|ref|YP_008797506.1|  [L=160]
Description: hydrogenase maturation protease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   40.7   0.0    2.3e-10   40.4   0.0    1.1  1  HycI      Hydrogenase maturation protease


Domain annotation for each model (and alignments):
>> HycI  Hydrogenase maturation protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.4   0.0   1.3e-14   2.3e-10      33     128 ..      60     153 ..      50     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.3e-14
                                       HCC-SEEEEEEE--SSS-TT-EEEEEC.CHHHHHHTTC.CGCCCHCHHHHHHHHHHCCS--SEEEEEEE--S-BST. CS
                              HycI  33 leeadkliivDavdfglepGevkiikd.devpkklkakkmsaHqlplaevlklleekgeipkevillgvqpesledv 108
                                       l + ++l++vDa +     Ge+ +++  +++      +  s+H++ + e+lkl++    +p+++++ g++ es ++ 
  gi|557694452|ref|YP_008797506.1|  60 LDDVSHLVVVDALEKVSRSGEIHRFQSvENLS-TAVPW-RSTHTMSVPEALKLMKLLTTFPEKITIYGIEGESFQP- 133
                                       56699******************998615666.56777.9************************************. PP

                                       CCS--HHHHCCHHHHHHHCC CS
                              HycI 109 gielseevkkavekavelil 128
                                       g+++se v+ka   ++++i 
  gi|557694452|ref|YP_008797506.1| 134 GVGISEGVEKACRIVAKEIA 153
                                       ***********999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1159.75
//
Query:       gi|557694453|ref|YP_008797507.1|  [L=771]
Description: hydrogenase maturation protein HypF [Candidatus Caldiarchaeum subterraneum]
Scores for 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-45  152.7   0.0    1.1e-44  152.1   0.0    1.3  1  Sua5_yciO_yrdC   Telomere recombination
    1.3e-25   88.8   9.3    1.6e-15   56.5   1.3    2.5  2  zf-HYPF          HypF finger
    1.9e-24   86.3   0.0    3.7e-24   85.4   0.0    1.5  1  HypF_C           HypF Kae1-like domain
    2.4e-23   82.3   0.1    4.4e-23   81.5   0.1    1.5  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
       0.16   11.9   0.1          8    6.5   0.0    2.5  2  DUF4428          Domain of unknown function (DUF4428)
       0.64   10.1   3.4        9.7    6.3   0.1    2.4  2  DZR              Double zinc ribbon
        1.1    9.1   6.7        3.2    7.6   0.8    2.5  2  zf-RING_4        RING/Ubox like zinc-binding domain
        2.3    8.3   6.2        3.9    7.5   0.9    2.5  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain


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 !  152.1   0.0   4.8e-48   1.1e-44       2     179 .]     213     388 ..     212     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 152.1 bits;  conditional E-value: 4.8e-48
                                       HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-.TC--HHHHHHHHCT-SSS CS
                    Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklae.seveeealkllerfwPGp 77 
                                       ++++G iva++++++Y++a++a ++++v+ lr++K+rp +kp+a+++ + + ++ l+e ++ + e+l+++ r    p
  gi|557694453|ref|YP_008797507.1| 213 LIDDGCIVAVKGLGGYHIAASAVDDDVVALLRRRKNRP-TKPFAIMCLNADVASLLVElTSPTLELLESPMR----P 284
                                       799***********************************.*******************9999999999****....* PP

                                       CEEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-.EEEEES-STTS-S-SSHHHHHHHC-TTSECB-S CS
                    Sua5_yciO_yrdC  78 itlllkrskeklpkevapglktvGvrlPdtplarlLlealgep.lvaTSanlsgepsitdaeeveeelgeivdlild 153
                                       i ll  r + ++++ vap+lk++Gv+lP+t l++lLl+ +++   ++TS+n+ +ep++t+ +e+ e+l++ivd++l 
  gi|557694453|ref|YP_008797507.1| 285 ILLLPMRGDVPVSPLVAPNLKKLGVFLPYTGLHYLLLSFTKQRyTIMTSGNIYNEPMCTRDDEALEKLADIVDFFLM 361
                                       ******99999***************************997655********************************* PP

                                       S-.--SSS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 154 gg.eiavgvdstVvdltegkpkilRrG 179
                                       ++ ei ++vd++Vv++t++kp++lRrG
  gi|557694453|ref|YP_008797507.1| 362 HNrEIVNRVDDSVVRFTDQKPTMLRRG 388
                                       **************************8 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   1.5   1.3e-12   2.9e-09       1      33 [.     110     141 ..     110     142 .. 0.95
   2 !   56.5   1.3   7.2e-19   1.6e-15       1      34 []     159     193 ..     159     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.3e-12
                                       --HHHHHHHC-TTSTTTT-TT---TTTS--EEE CS
                           zf-HYPF   1 lCedClrEykdpldRRfhaqfisCtnCGPrlsl 33 
                                       +C dCl+E+   + R+ +++f+sC nCGPr+s+
  gi|557694453|ref|YP_008797507.1| 110 ICGDCLNEILSDT-RWRNYPFNSCANCGPRYSM 141
                                       7**********88.*****************98 PP

  == domain 2  score: 56.5 bits;  conditional E-value: 7.2e-19
                                       --HHHHHHHC-TTS.TTTT-TT---TTTS--EEEE CS
                           zf-HYPF   1 lCedClrEykdpld.RRfhaqfisCtnCGPrlsli 34 
                                       +C dClr+y dp + RRfhaq+isC+ CGP ++l+
  gi|557694453|ref|YP_008797507.1| 159 MCNDCLRDYSDPDNvRRFHAQGISCPACGPSVYLV 193
                                       9******************************9985 PP

>> HypF_C  HypF Kae1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0   1.6e-27   3.7e-24       2     102 .]     402     504 ..     401     504 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 1.6e-27
                            HypF_C   2 aekevLAlGaelkntfalakggqallsqhlGdlenletleayeealeeleklleik..pevivcDlhpdylstklae 76 
                                       +e+ev+A+Ga l+++ a+a +++++l+q++Gd++ + +++++e+ l++l + ++i+   +v vcDlhp y st lae
  gi|557694453|ref|YP_008797507.1| 402 TEREVVAFGAMLQTAGAVAFDDKIVLTQFIGDVDGYTSFTDLEKYLNTLVTSYGITleSAVNVCDLHPLYPSTLLAE 478
                                       7899*************************************************9862266999************** PP

                            HypF_C  77 elaekeklelievqHHhAHllavlae 102
                                       e++++ ++el++vqHH AH +av+ae
  gi|557694453|ref|YP_008797507.1| 479 EWSRRFGSELLRVQHHWAHTAAVMAE 504
                                       *************************8 PP

>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.5   0.1     2e-26   4.4e-23       1      85 []       7      91 ..       7      91 .. 0.94

  Alignments for each domain:
  == domain 1  score: 81.5 bits;  conditional E-value: 2e-26
                   Acylphosphatase  1 vrllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppk.arvdeveveeleeee 78
                                      vrl+v+G VQgvgFR+fv+r+A+e g++GyvrN     Vei +ege ekv++f++ l++++p+ ar+d+++++ +e ++
  gi|557694453|ref|YP_008797507.1|  7 VRLWVSGVVQGVGFRPFVYRIARETGVSGYVRNVGGSGVEIIVEGEAEKVDEFIHLLQTRKPEkARIDKFSATSIEPRG 85
                                      5789*******************************999*********************76666************999 PP

                   Acylphosphatase 79 efkdFei 85
                                        + Fei
  gi|557694453|ref|YP_008797507.1| 86 Y-TCFEI 91
                                      8.88887 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0036         8      19      31 ..     107     120 ..     100     129 .. 0.83
   2 ?    2.6   0.1     0.059   1.3e+02      15      28 ..     152     165 ..     131     173 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0036
                           DUF4428  19 DgyvCkdClkKl.s 31 
                                       D+ +C dCl+++ s
  gi|557694453|ref|YP_008797507.1| 107 DFAICGDCLNEIlS 120
                                       889********943 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.059
                           DUF4428  15 lkleDgyvCkdClk 28 
                                       +   D+ +C+dCl 
  gi|557694453|ref|YP_008797507.1| 152 TSMRDFPMCNDCLR 165
                                       6678999*****95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1    0.0043       9.7       8      36 ..     104     137 ..      92     145 .. 0.85
   2 ?    3.5   1.0     0.033        73      14      37 ..     159     189 ..     149     195 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0043
                               DZR   8 lppdarfCseCgtklkavaa.....edrCpsCge 36 
                                       +ppd   C++C +++ + ++      + C +Cg 
  gi|557694453|ref|YP_008797507.1| 104 IPPDFAICGDCLNEILSDTRwrnypFNSCANCGP 137
                                       89999*******997655558999999*****96 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.033
                               DZR  14 fCseCgtklkavaa.......edrCpsCgek 37 
                                       +C++C  + + + +        + Cp+Cg +
  gi|557694453|ref|YP_008797507.1| 159 MCNDCLRDYSDPDNvrrfhaqGISCPACGPS 189
                                       6777777766555577787788888888865 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 ?    7.6   0.8    0.0014       3.2      21      47 ..     107     139 ..      88     140 .. 0.84
   2 ?    4.2   0.6     0.016        37      21      43 ..     156     186 ..     155     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0014
                         zf-RING_4  21 gyqiClfCyhrileee......egrCPaCreeY 47 
                                       ++ iC +C+++il+++       + C +C  +Y
  gi|557694453|ref|YP_008797507.1| 107 DFAICGDCLNEILSDTrwrnypFNSCANCGPRY 139
                                       799***********7766666678899997777 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.016
                         zf-RING_4  21 gyqiClfCyhrile........eeegrCPaC 43 
                                       ++ +C +C+++  +        +++  CPaC
  gi|557694453|ref|YP_008797507.1| 156 DFPMCNDCLRDYSDpdnvrrfhAQGISCPAC 186
                                       5889*****999987766666555889**** 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 ?    7.5   0.9    0.0018       3.9       8      43 ..     117     163 ..     113     166 .. 0.77
   2 ?    3.1   0.4     0.043        96      16      26 ..     178     188 ..     173     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                     Zn_Tnp_IS1595   8 alLealrWpng.fv.CPhCgsr..kayrikt.......rglfqCkeC 43 
                                       ++L + rW+n  f  C +Cg r   +yr+         r   +C++C
  gi|557694453|ref|YP_008797507.1| 117 EILSDTRWRNYpFNsCANCGPRysMLYRVPYdrentsmRDFPMCNDC 163
                                       68999******7667*****998777776556667777777777777 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.043
                     Zn_Tnp_IS1595  16 pngfvCPhCgs 26 
                                       ++g  CP+Cg 
  gi|557694453|ref|YP_008797507.1| 178 AQGISCPACGP 188
                                       67789****95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (771 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 5193.17
//
Query:       gi|557694454|ref|YP_008797508.1|  [L=384]
Description: hydrogenase expression/formation protein HypD [Candidatus Caldiarchaeum subterraneum]
Scores for 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-120  400.5   0.0   7.3e-120  400.2   0.0    1.0  1  HypD       Hydrogenase formation hypA family
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.26   11.2   0.0    1.6  1  zf-RING_6  zf-RING of BARD1-type protein
       0.51   10.0   2.2       0.91    9.2   2.2    1.3  1  MTHFR_C    Methylene-tetrahydrofolate reductase C terminal


Domain annotation for each model (and alignments):
>> HypD  Hydrogenase formation hypA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.2   0.0  1.2e-123  7.3e-120      17     349 ..      36     373 ..      17     375 .. 0.95

  Alignments for each domain:
  == domain 1  score: 400.2 bits;  conditional E-value: 1.2e-123
                                       SS-EEEEE--HHHHHHHHHTTHHHHS-TTEEEEE-S--TTTTS-HHHHHHHHHHHHH--EEEEE-CCHHG---T... CS
                              HypD  17 erelkimevCGghthaivryglrslLpenielisGPGCpVCvtpeeeidkaielaekeevilatfgDmlrvpgs... 90 
                                        +e+kim++CG+h+ + ++yg+r++Lp+ ++l++GPGCpVC+tp+ ++++a+ela + +++ +t+gD++r+p+    
  gi|557694454|ref|YP_008797508.1|  36 VEEVKIMNFCGTHEYTSTHYGIRNILPQGVSLVAGPGCPVCITPSYYVETAVELALE-GFTAYTYGDAYRLPAVrev 111
                                       689*****************************************************9.**************99777 PP

                                       ..T--HHHHHHTT-EEEE-SSHHHHHHHHHH-TTSEEEEEEEE-HHHHHHHHHHHHHHHHHT-SSEEEEEEEE-HHH CS
                              HypD  91 ..kksLleakaegadvrivyspldalkiakenpdkevvflavGFEttapatalalleakkeglknfsvlsshklvpp 165
                                          +sL +a+ +gadvr+vys+lda++ a+++  k  vflavGFEtt pa+a a+++  +  ++n++++s+ +l+pp
  gi|557694454|ref|YP_008797508.1| 112 kgCRSLSDARMAGADVRVVYSFLDAVRDAASH-GKPAVFLAVGFETTCPAYASAIAS--EMVPSNLTLISAGRLTPP 185
                                       6668**************************99.9*********************99..99**************** PP

                                       HHHHHHHTT.---SEEEEEHHHHHHHTTHHHHHHHHHH---EEEE-SSHHHHHHHHHHHHHHHHTT---EEETTTTT CS
                              HypD 166 alealleseelkidgfiapghvstviGlkayeelaeeykvpvvvaGFepldilqailmlvkqleegeaeveneYkrv 242
                                       a ++ +e+   +++g+iapghvst++G+  +++l eey++p+vv+GFep+d+l a+++++kql+e+++ +  eY+r+
  gi|557694454|ref|YP_008797508.1| 186 AARYAVERV-GTVSGVIAPGHVSTITGAGVWRFLPEEYGIPTVVTGFEPVDVLIAVATILKQLAENKPGLVVEYSRT 261
                                       ******986.69***************************************************************** PP

                                       --TT--HHHHHHHHHHEEEEEEEETTTEEEEEEEEEE-GGGGGGBGGGT---.....-S---SS-TT--HHHHHTTS CS
                              HypD 243 vkeegnkkaqklieevfevrdaewRglgvipksglklreeyaefdaekkfel.....ekeeekekkackcgevlkGk 314
                                       v+ +gn++a+k++++vf+v+d++wRg+g i+ksg++lr++++++d+ k+f l     ++ +++  ++c+cg+v+ G 
  gi|557694454|ref|YP_008797508.1| 262 VTMDGNQRAKKFLSQVFDVVDSAWRGIGFIEKSGYSLRKQFEQYDVVKTFGLrepgkDDWKNDLMPGCICGQVILGA 338
                                       **************************************************9977776677888899*********** PP

                                       --GGGSTTBTTTB-SSS-SSHHHHSTT-HHHHHHH CS
                              HypD 315 akPedCklFgkaCtpenpvGacmvSsEGaCaayyk 349
                                       akP+dC+lF+k+Ctp +p+G+cmvS EGaC+++ +
  gi|557694454|ref|YP_008797508.1| 339 AKPTDCPLFMKRCTPGTPYGPCMVSAEGACSIWAR 373
                                       *********************************87 PP

>> zf-RING_6  zf-RING of BARD1-type protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.3e-05      0.26      35      56 ..      65      86 ..      56      94 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.3e-05
                         zf-RING_6 35 isdcfgsgcpvcytpawiqdvk 56
                                      +s   g gcpvc tp++  +  
  gi|557694454|ref|YP_008797508.1| 65 VSLVAGPGCPVCITPSYYVETA 86
                                      6667899********9976655 PP

>> MTHFR_C  Methylene-tetrahydrofolate reductase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.2   0.00015      0.91      24      61 ..     330     370 ..     317     374 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00015
                           MTHFR_C  24 aCgdCvlaetg.giCp..vsrCakkllnGpCggskngkCev 61 
                                        Cg+ +l+    + Cp  ++rC+    +GpC  s++g C +
  gi|557694454|ref|YP_008797508.1| 330 ICGQVILGAAKpTDCPlfMKRCTPGTPYGPCMVSAEGACSI 370
                                       59999998765256996679*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2668.81
//
Query:       gi|557694455|ref|YP_008797509.1|  [L=102]
Description: hydrogenase expression/formation protein HypC [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   58.2   0.7    9.5e-16   57.7   0.7    1.3  1  HupF_HypC  HupF/HypC family
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.028   14.8   0.0    1.6  1  FhuF       Ferric iron reductase FhuF-like transporter


Domain annotation for each model (and alignments):
>> HupF_HypC  HupF/HypC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.7   1.1e-19   9.5e-16       1      62 [.       1      62 [.       1      65 [. 0.90

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 1.1e-19
                                      CCEEEEEEEEEEETTEEEEECT.TEEEEEEGTTCTTB-TT-EEEEETTEEEEEE-HHHHHHHH CS
                         HupF_HypC  1 MCLaiPgkvveiedelAlvdvg.GvrrevslalveevkvGdyVLvhvGfAiekideeeaeetl 62
                                      MCL++ gkv+++e++lA+vd++ G  +ev ++ veevk GdyV+vh+G+ +++++e+e +e+ 
  gi|557694455|ref|YP_008797509.1|  1 MCLGVYGKVLKVEGDLAVVDFSgGLVKEVLVG-VEEVKAGDYVVVHAGVIVSRLNENEFAEVF 62
                                      **********************6667777666.578**********************99975 PP

>> FhuF  Ferric iron reductase FhuF-like transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   3.1e-06     0.028      21     127 ..       5      97 ..       1     102 [] 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.1e-06
                                       HH-EE---STTTEEEEEETTEEEEEEE---...TTT-EES-TT----TTSGGGB----GGGSHHHHIIIIIIIHHHH CS
                              FhuF  21 eygialeahlqNvllvlddgrpvrlllrdfegvslkaellpelpalpeevkrlltddpeelreevfyglfvnhlapl 97 
                                       +yg +l + ++  ++ ++ g+++ +l+      + ka+++  ++a       ++++  e+++     + ++nh+ + 
  gi|557694455|ref|YP_008797509.1|   5 VYGKVLKVEGDLAVVDFSGGLVKEVLVGVE---EVKAGDYVVVHAGV-----IVSRLNENEF-----AEVFNHVSEA 68 
                                       688888888888888888888888888877...23333333333333.....5555556666.....7788****** PP

                                       HHHHHHTTSS-HHHHHHHHHHHHHHHHHHS CS
                              FhuF  98 iealaaagglsekllWsnvaellewylael 127
                                       +++l   +g++ +++W+n++ +l+++l++ 
  gi|557694455|ref|YP_008797509.1|  69 VQTL-VSSGADVADYWQNIKTRLAELLTQK 97 
                                       ****.999******************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      751  (0.0418874); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 714.72
//
Query:       gi|557694456|ref|YP_008797510.1|  [L=341]
Description: hydrogenase expression/formation protein HypE [Candidatus Caldiarchaeum subterraneum]
Scores for 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-22   79.0   0.1    6.1e-22   78.4   0.1    1.2  1  AIRS_C    AIR synthase related protein, C-terminal domain
    2.6e-13   50.4   1.8    5.1e-13   49.5   1.8    1.5  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 !   78.4   0.1   6.9e-26   6.1e-22       1     149 [.     166     311 ..     166     317 .. 0.86

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 6.9e-26
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                       kpGd+++ tg+lG +ga+++++++ + +++       ++dv  + + +    +     ++++aa+D T+GG +  l+
  gi|557694456|ref|YP_008797510.1| 166 KPGDKIMATGPLGEHGAAILAAQQKIFSQQF------KSDVKPLTKILLPIIERYV--EDIHAARDPTRGGAAMVLN 234
                                       79****************8888877777776......5888888455544444444..7****************** PP

                                       HHHHTTTEEEEEECGTHHHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
                            AIRS_C  78 emapasgvgaeidldkvpifdele.....splemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                                        +a++s+v ++++++++p+++++      ++ ++l  +++G  l+av+pe+ + vl++l++ g+ ea+vIGe+ +k 
  gi|557694456|ref|YP_008797510.1| 235 DWAKGSDVLLVVYESELPLREPVVnlcemLGVDPLTLASEGSALLAVSPESVEDVLNMLHDNGCGEARVIGEAREKT 311
                                       ***************9999999986666677888888***************************88******99986 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 !   49.5   1.8   5.7e-17   5.1e-13       1      93 [.      44     155 ..      44     156 .. 0.92

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 5.7e-17
                                       SSSE........EEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHH CS
                              AIRS   1 dDaa........vvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevv 59 
                                       dDaa        +v t+d    ++ v+pv f    +G++a+a++++Dl++ GArPla+++++ ++      +l ++v
  gi|557694456|ref|YP_008797510.1|  44 DDAAaipvkdgyLVCTID----SYTVSPVFFpggdLGKLAAAGTINDLLMLGARPLAVMDAVVVEegmaidDLTRLV 116
                                       788866666655699999....889999999********************************************** PP

                                       HHHHHHHHHTT-EEEEEEEEEESS.....EEEEEEEEEE CS
                              AIRS  60 rglaeaaeelgvplvgGdtsfsne.....ptisvtavGl 93 
                                       +++ + ++  g  l+gGd++++++     ++i+++ +G 
  gi|557694456|ref|YP_008797510.1| 117 DSMIAVLRDEGLCLIGGDVKVMPKgqldgVLITTAGLGF 155
                                       **********************88899999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2488.22
//
Query:       gi|557694457|ref|YP_008797511.1|  [L=292]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2124.58
//
Query:       gi|557694458|ref|YP_008797512.1|  [L=308]
Description: purine nucleosidase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-88  295.8   0.1      5e-88  295.6   0.1    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 !  295.6   0.1   2.8e-92     5e-88       2     305 .]       4     299 ..       3     299 .. 0.88

  Alignments for each domain:
  == domain 1  score: 295.6 bits;  conditional E-value: 2.8e-92
                                       EEEEEE--SHHHHHHHHHHHCTHTTEEEEEEEE-SSSS-HHHHHHHHHHHHHHHCTTT.S-EEEE-SS-SSSS.S-S CS
                      IU_nuc_hydro   2 kvilDtDpGiDDalAlllalaespeiellgittvaGnvsleqatrnalrvlealggrddipvyaGaekpllre.kaa 77 
                                        v+lD+DpGiDDalA++lal++ pe+e+lgit+v+Gnv+++++  nalrvle++g   dipvy+Ga++pl++e  +a
  gi|557694458|ref|YP_008797512.1|   4 AVVLDMDPGIDDALAIMLALNS-PELEVLGITAVSGNVHVDKSSVNALRVLETMG-DMDIPVYRGAATPLVKElVTA 78 
                                       599*****************95.****************************8888.666**************7777 PP

                                       HHHHTTTSSTSS-.--SSHCSCSSHHHHHHHHHHHHCHHTTTTEEEEECS-SHHHHHHHHHTCCHHHHEEEEEEE-- CS
                      IU_nuc_hydro  78 aeihGedGlgdvllpeperkaesesavdalidaveaareypgevtlvatGplTNiAlalrldpelakkvkrlviMGG 154
                                       + +hGedGlgd+ lp p rk+ +  av++l+d++   +++ ++vt+vatGplTNiA  l  +p lak++k+l+iMGG
  gi|557694458|ref|YP_008797512.1|  79 EWVHGEDGLGDAGLPMPMRKPLE-GAVKFLVDTL---TSE-RNVTIVATGPLTNIAHTLLIEPTLAKHLKQLIIMGG 150
                                       77*************99666654.69*******9...433.36********************************** PP

                                       -SS....S--SSSSSS-HHHHHSHHHHHHHHHT..S-E.EEEE-HHHHTTSCHEECHHHHHHHHCSTCBHHHHHHHH CS
                      IU_nuc_hydro 155 aft....arGNvtpvaEfNifvDPeAAkiVles..apvkitlvpldvthkvqalltseeveelaalekglgafladl 225
                                       a++    + GN tpv+EfNi+vDPeAAki+++s  +     +++ldvt++ +a l++++ve++a+  +++ ++ a++
  gi|557694458|ref|YP_008797512.1| 151 AYGltpyGYGNETPVSEFNIYVDPEAAKIIFQSgvK---PLCIGLDVTTDPKATLSKKDVEKMASSSSKTARTAAKI 224
                                       *******************************97633...49********88899********877654555445554 PP

                                       HHHHHHHHHHHHHSSEEE-HHHHHHHHHH-GGGEEEEEEEEEEESSSSTTTTEEEEETSTT.TTS--EEEEEEE-HH CS
                      IU_nuc_hydro 226 lefyikaykeaegsdgaplhDplavavaldpelvttkrlavdveleggltrGrtvvdlrrl.kkaknvkvatevdve 301
                                       +  +++       +  ++lhDp+ava+ ++p+l++t++ +v v +eg+ltrG+t+v+ r   +k++n++v+++vd +
  gi|557694458|ref|YP_008797512.1| 225 VWNFAE------RFGFVQLHDPMAVAASIKPDLFKTSQHHVYVVCEGELTRGQTIVEKRFWvRKEPNAEVCEQVDGP 295
                                       443333......255678*************************************9665559*************** PP

                                       HHHH CS
                      IU_nuc_hydro 302 rfle 305
                                       rfle
  gi|557694458|ref|YP_008797512.1| 296 RFLE 299
                                       **85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2366.00
//
Query:       gi|557694459|ref|YP_008797513.1|  [L=203]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1618.54
//
Query:       gi|557694460|ref|YP_008797514.1|  [L=269]
Description: cobalt/nickel ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-26   93.8  17.2    1.6e-26   93.3  17.2    1.2  1  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 !   93.3  17.2     9e-31   1.6e-26       2     211 ..       5     219 ..       4     227 .. 0.90

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 9e-31
                                       SCCCCS-HHHHHHHHHHHH.HHHHHS-HHHHHHHHHHHHHHHHHTTS---..HHHHHHHCCCHCHHHHHHHHHHE.. CS
                              CbiQ   2 ksvlhrldprvkliwlfll.llalvlapnlvtlliiiallllllllvilp..rvlaqalilpllflllgllillf.q 74 
                                       +++lh  d r+k i ++ + lla +++  ++tl+++++ ++l++ +++ +  +++++ ++lp++ + + +l l + +
  gi|557694460|ref|YP_008797514.1|   5 RTPLHLADGRTKFIYFIWVsLLAYIFYDYILTLVFLVVNVTLAFIGRVARqvILPLILVVLPWMGFAIPILSLPLgF 81 
                                       6899********9988765156778999999*****999999999999998999999****************9963 PP

                                       ......EECTTEEE....E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHH CS
                              CbiQ  75 littegefvfaggg.qisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfi 150
                                         +++    ++++g ++ ++ eGl  g +  lRi + +s++ll+ lTT+   l++ l r +vP +++++++ ++ fi
  gi|557694460|ref|YP_008797514.1|  82 PWNQTVVYRLTIFGlELPVYLEGLAWGFTWPLRIGVTISAALLFYLTTQQTALIAMLFRFRVPFKFIYMVAATLQFI 158
                                       3333333444555577************************************************************* PP

                                       HHHHHHHHHHHHHHHHTTTTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS CS
                              CbiQ 151 flLleevqrikqAqklRlgdsklgirrslrslgkliaalflralkraervalAmeaRGYtg 211
                                       +l+++ev++i+qAq +R++++  +++++l+   +l+++l l++l + ++ a+A+e+RG++ 
  gi|557694460|ref|YP_008797514.1| 159 PLMADEVRSIYQAQLARGLRTDVNLVKKLSNFVRLLVPLTLSSLGKVQTRAIALESRGFSA 219
                                       ***********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 2138.54
//
Query:       gi|557694461|ref|YP_008797515.1|  [L=295]
Description: cobalt/nickel ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-30  104.1   0.0    1.4e-29  103.4   0.0    1.3  1  ABC_tran      ABC transporter
    6.7e-12   45.8   0.7    4.7e-05   23.4   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.7e-07   30.3   0.0      1e-05   25.1   0.0    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00046   19.9   0.0    0.00088   19.0   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0011   18.7   0.3       0.55    9.9   0.1    2.2  2  IstB_IS21     IstB-like ATP binding protein
     0.0024   18.2   0.2      0.016   15.5   0.2    2.2  1  AAA_22        AAA domain
     0.0041   16.1   0.0     0.0081   15.2   0.0    1.5  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
     0.0042   16.6   0.0     0.0059   16.1   0.0    1.3  1  KdpD          Osmosensitive K+ channel His kinase sensor doma
     0.0043   17.6   0.0     0.0064   17.0   0.0    1.2  1  AAA_23        AAA domain
     0.0048   17.4   0.1     0.0092   16.5   0.1    1.5  1  AAA_18        AAA domain
     0.0056   16.1   0.1       0.11   11.9   0.0    2.1  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.007   16.8   0.3      0.026   14.9   0.3    1.8  1  AAA_16        AAA ATPase domain
  ------ inclusion threshold ------
      0.038   13.6   0.0      0.079   12.5   0.0    1.4  1  AAA_27        AAA domain
      0.039   14.4   0.1       0.21   12.0   0.0    2.0  2  AAA           ATPase family associated with various cellular 
      0.046   13.6   0.0      0.084   12.8   0.0    1.4  1  RsgA_GTPase   RsgA GTPase
      0.067   13.3   0.1       0.14   12.3   0.1    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
      0.071   12.9   0.1       0.16   11.7   0.0    1.6  2  ATP_bind_1    Conserved hypothetical ATP binding protein
      0.071   12.8   0.3        0.6    9.8   0.1    2.1  2  AAA_30        AAA domain
      0.079   12.7   0.0       0.15   11.8   0.0    1.4  1  AAA_15        AAA ATPase domain
      0.084   11.5   0.0        0.2   10.3   0.0    1.5  2  AAA_13        AAA domain
       0.11   12.7   0.1       0.21   11.8   0.1    1.6  1  AAA_28        AAA domain
       0.15    9.6   0.3       0.23    8.9   0.3    1.2  1  DUF3584       Protein of unknown function (DUF3584)
       0.15   12.3   0.0        2.5    8.4   0.0    2.2  1  SbcCD_C       Putative exonuclease SbcCD, C subunit
       0.17   12.0   0.1        5.1    7.1   0.1    2.5  2  AAA_14        AAA domain
       0.22   10.3   0.4       0.58    8.9   0.3    1.7  2  ABC_ATPase    Predicted ATPase of the ABC class


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 !  103.4   0.0   1.9e-32   1.4e-29       1     137 []      28     181 ..      28     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 103.4 bits;  conditional E-value: 1.9e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqe..pql 70 
                                       lknv+lk+++ge v+i+G+nGaGKStL+k+l gl+        +G++ + g d+ +++  +l  ++g ++qe  +ql
  gi|557694461|ref|YP_008797515.1|  28 LKNVTLKVERGEAVGIIGPNGAGKSTLCKALNGLVPHfyggrISGRVYVAGMDTLKHTVAELATKVGLVFQEpeTQL 104
                                       79*********************************999999999999***9999999***************64333 PP

                                       -T.TSBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xx.xxxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fp.eltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                           ltv+++               + + ++a++++gl++l+ +       +LSgGq+qr+a+a +l+ +p++++lD
  gi|557694461|ref|YP_008797515.1| 105 SGlALTVEDEisfglamlgypkdVIKTRTAEAIKRVGLQGLERRSP----FELSGGQQQRLAIATVLAMRPEVIVLD 177
                                       3213456666*********998888888************998888....*************************** PP

                                       STTT CS
                                       xxxx RF
                          ABC_tran 134 Epta 137
                                       Ept+
  gi|557694461|ref|YP_008797515.1| 178 EPTS 181
                                       **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 !   21.1   0.1   3.2e-07   0.00023       3      32 ..      42      68 ..      41      82 .. 0.81
   2 !   23.4   0.0   6.5e-08   4.7e-05     188     283 ..     104     200 ..      96     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.2e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegl 32
                                      ++iGpNg+GKS+L +al +l    +++ g+
  gi|557694461|ref|YP_008797515.1| 42 GIIGPNGAGKSTLCKALNGL---VPHFYGG 68
                                      69***************999...6666555 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 6.5e-08
                            AAA_21 188 lvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliD 264
                                       l++  ++ve+e+s+ +++   +++v+     + +  +   +   ++++elS G+++ la++t l+ ++    ++++D
  gi|557694461|ref|YP_008797515.1| 104 LSGLALTVEDEISFGLAMLGYPKDVIKTRTAEAIKRVGLQGLERRSPFELSGGQQQRLAIATVLAMRP---EVIVLD 177
                                       5555566666666666666666666655555566666666777899********************99...9***** PP

                            AAA_21 265 EpEngLHP.......kllrrllellk 283
                                       Ep + L+P            l ell+
  gi|557694461|ref|YP_008797515.1| 178 EPTSQLDPigkaqvfD---VLRELLR 200
                                       ********88663333...3334443 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 !   25.1   0.0   1.4e-08     1e-05      26     196 ..      40     208 ..      26     224 .. 0.65

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.4e-08
                                       EEEEEESTTSSHHHHHHHHH....HHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE....SSSSS CS
                                       xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAil....FvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk....lkiek 94 
                                          i+GpNG+GKs l+ A+     +  G r +  +  + ++ l h      +    +v ++f++++ +    + + +
  gi|557694461|ref|YP_008797515.1|  40 AVGIIGPNGAGKSTLCKALNglvpHFYGGRISGRVYVAGMDTLKHT----VAELATKVGLVFQEPETQlsglALTVE 112
                                       457***************9533333334444445555556555554....455567899999999999333222222 PP

                                       SCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT...CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  95 eevsisrrvkrkgeseykingkevtkkevsellesagiske...lLSgGektLvalaLlfAiqkvkpaplyllDeid 168
                                       +e+s        g  +  i+ ++   +e  + +  +g+++    +LSgG+++ +a+a ++A+   +p+ + +lDe  
  gi|557694461|ref|YP_008797515.1| 113 DEISFGLA--MLGYPKDVIKTRT---AEAIKRVGLQGLERRspfELSGGQQQRLAIATVLAM---RPE-VIVLDEPT 180
                                       22222222..2222223333333...3333444444443334449**************997...455.679***** PP

                                       TTS-HHHHHHHHHHHHHHCTTSEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 169 aaLDeknvkkvaellkeksknaQfivis 196
                                       ++LD    ++v ++l+e   +   iv++
  gi|557694461|ref|YP_008797515.1| 181 SQLDPIGKAQVFDVLRELLRDGTTIVVA 208
                                       *****************99998888876 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 !   19.0   0.0   1.2e-06   0.00088      14      43 ..      30      59 ..      26      64 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.2e-06
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiq 43
                                      + t+++++ +a+ ++Gp+G+GKSTl  A++
  gi|557694461|ref|YP_008797515.1| 30 NVTLKVERGEAVGIIGPNGAGKSTLCKALN 59
                                      5678888666999************98876 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 !    9.9   0.1   0.00077      0.55      44      67 ..      35      58 ..      24      62 .. 0.91
   2 !    6.7   0.0    0.0076       5.5      96     154 ..     158     215 ..     152     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00077
                         IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                      +e+ e++ ++Gp G+GKs l  al
  gi|557694461|ref|YP_008797515.1| 35 VERGEAVGIIGPNGAGKSTLCKAL 58
                                      78999***************9998 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0076
                         IstB_IS21  96 dgklaralkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlpfaew 154
                                       +++la a    +++++++lD+  + +ld   ++++f+v+ +     ++i+ ++ +++e 
  gi|557694461|ref|YP_008797515.1| 158 QQRLAIATVLAMRPEVIVLDEP-TSQLDPIGKAQVFDVLRELLRDGTTIVVAEHEIEEL 215
                                       45555566667889*******7.5789***********************999988775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   2.2e-05     0.016      10     117 ..      43     200 ..      35     216 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.2e-05
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaeeerpevv......fvtlpsstsskdllrellralglelka.......... 70 
                                       ++G+ G+GK+tl++ l    +          +++      +v++++  ++k    el+ ++gl   +          
  gi|557694461|ref|YP_008797515.1|  43 IIGPNGAGKSTLCKALNGLVP----------HFYggrisgRVYVAGMDTLKHTVAELATKVGLVFQEpetqlsglal 109
                                       99*************999863..........3333333456666666666666666666655544444444666666 PP

                            AAA_22  71 ....................................erlsseellealeqalrarav...............ielli 96 
                                                                           er s  el                            +e+++
  gi|557694461|ref|YP_008797515.1| 110 tvedeisfglamlgypkdviktrtaeaikrvglqglERRSPFELS-----------GgqqqrlaiatvlamrPEVIV 175
                                       666677777777777777765555555555555444333333333...........022222222223466666777 PP

                            AAA_22  97 iDEaqh.lr...seealeeLrslln 117
                                       +DE    l+   +++++  Lr+ll 
  gi|557694461|ref|YP_008797515.1| 176 LDEPTSqLDpigKAQVFDVLRELLR 200
                                       7766666655433555555555555 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 !   15.2   0.0   1.1e-05    0.0081       7      50 ..      13      59 ..       7      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                                      HHH-...-SHHHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHH CS
                              MeaB  7 lves...erpeakellerllakaGraqvvGltGvPGaGkstlvealg 50
                                      lve+   ++p+  ++l++++ k  r + vG+ G  GaGkstl +al 
  gi|557694461|ref|YP_008797515.1| 13 LVENlsySYPSKPNVLKNVTLKVERGEAVGIIGPNGAGKSTLCKALN 59
                                      56652224568889****************************99985 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 !   16.1   0.0   8.2e-06    0.0059      54     130 ..     141     218 ..     120     259 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.2e-06
                              KdpD  54 gleviprk.eveykgkeleeldldailarkpevvlvDelahtnapgsrhekryqdveelLeagidVi.ttvnvqhle 128
                                       gl+ ++r+  +e +g + ++l + ++la++pev+++De   +  +   +++ ++  +elL+ g  ++ +  ++++l 
  gi|557694461|ref|YP_008797515.1| 141 GLQGLERRsPFELSGGQQQRLAIATVLAMRPEVIVLDEPTSQ-LDPIGKAQVFDVLRELLRDGTTIVvAEHEIEELA 216
                                       4444444314788999**********************7665.567788999**********988650445566655 PP

                              KdpD 129 sl 130
                                        +
  gi|557694461|ref|YP_008797515.1| 217 TF 218
                                       54 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     9e-06    0.0064      22      40 ..      41      59 ..      26      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 9e-06
                            AAA_23 22 tlItGpNGaGKTTildAik 40
                                      + I+GpNGaGK+T+  A+ 
  gi|557694461|ref|YP_008797515.1| 41 VGIIGPNGAGKSTLCKALN 59
                                      57************99986 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   1.3e-05    0.0092       1      25 [.      41      68 ..      41     101 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf..g 25
                                      +++ G+ G+GK+tl+k+L+ +  +f  g
  gi|557694461|ref|YP_008797515.1| 41 VGIIGPNGAGKSTLCKALNGLVpHFygG 68
                                      689***************7665555642 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00015      0.11      26      51 ..      42      67 ..      29     113 .. 0.75
   2 ?    2.2   0.0      0.14     1e+02      90     143 ..     153     211 ..     142     242 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                      Mg_chelatase 26 llvGppGsGKtmlakrlpsllpplse 51
                                       ++Gp G+GK+ l k+l++l+p+   
  gi|557694461|ref|YP_008797515.1| 42 GIIGPNGAGKSTLCKALNGLVPHFYG 67
                                      579*******************8765 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                      Mg_chelatase  90 lvGggskpkpGeislahn.GvLfLDElpef.....krkvlevLRePledgevtisrakak 143
                                       l Gg+++    +  la +  v++LDE +       k++v++vLRe l dg+  +   + +
  gi|557694461|ref|YP_008797515.1| 153 LSGGQQQRLAIATVLAMRpEVIVLDEPTSQldpigKAQVFDVLRELLRDGTTIVVAEH-E 211
                                       56666655555555555425888888543222223689*********99875443322.2 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   0.3   3.6e-05     0.026      21     129 ..      37     201 ..      27     223 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.6e-05
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekd.ggiflrgkcdqlesaipysalaqalareellrqlldeaesaelea 96 
                                       +  +e+v ++G+ G GKs+l ++l   l  + +g  ++g+    ++++   ++a+++++ +l+ q+ +     +l+ 
  gi|557694461|ref|YP_008797515.1|  37 R--GEAVGIIGPNGAGKSTLCKALN-GLVPHfYGGRISGRVYVAGMDTLKHTVAELATKVGLVFQEPET----QLSG 106
                                       3..48999*************9999.5666644444777777776665555677777664444444444....3333 PP

                            AAA_16  97 wrekleeala..............................................................avpel 111
                                        + + e++++                                                              ++++l
  gi|557694461|ref|YP_008797515.1| 107 LALTVEDEISfglamlgypkdviktrtaeaikrvglqglerrspfelsggqqqrlaiatvlamrpevivldePTSQL 183
                                       33434444445566777777777777778888888888888888888888888888888888888888888888888 PP

                            AAA_16 112 agaeasrllellkrllal 129
                                       ++ ++ +++++l++ll+ 
  gi|557694461|ref|YP_008797515.1| 184 DPIGKAQVFDVLRELLRD 201
                                       888888888888888843 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011     0.079      31      49 ..      43      61 ..      29      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                            AAA_27 31 iyGpNEAGKstalrAisdl 49
                                      i+GpN AGKst+ +A++ l
  gi|557694461|ref|YP_008797515.1| 43 IIGPNGAGKSTLCKALNGL 61
                                      89*************9877 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 ?   12.0   0.0    0.0003      0.21       3      54 ..      43     101 ..      41     115 .. 0.74
   2 ?   -0.0   0.0       1.6   1.1e+03      45      66 ..     158     178 ..     128     223 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0003
                                       EESSTTSSHHHHHHHHHHHH....T...HEEEEEETTTCSSSSTTHHHHHHHHHHHHHH CS
                               AAA   3 lyGppGtGKTllakavakel....g...vefleisgsellskyvgesekkirelfkeak 54 
                                       ++Gp G GK++l+ka+   +    g   +  + + g++ l+++v e + k+  +f+e +
  gi|557694461|ref|YP_008797515.1|  43 IIGPNGAGKSTLCKALNGLVphfyGgriSGRVYVAGMDTLKHTVAELATKVGLVFQEPE 101
                                       78*************99886544423333357788888888888888888888888754 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  45 kirelfkeakeka.kpsilfiDE 66 
                                       + r  ++++   a +p ++++DE
  gi|557694461|ref|YP_008797515.1| 158 QQRLAIATV--LAmRPEVIVLDE 178
                                       444444444..444589999998 PP

>> RsgA_GTPase  RsgA GTPase
   #    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      96     122 ..      34      61 ..      14     100 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                                       HCTT.SEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpe 122
                                       +++  + + ++G+ G+GKStL +al++ 
  gi|557694461|ref|YP_008797515.1|  34 KVERgEAVGIIGPNGAGKSTLCKALNGL 61 
                                       4444478889************999873 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00019      0.14       2      21 ..      41      60 ..      40      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      v+i+G   +GKStL +al g
  gi|557694461|ref|YP_008797515.1| 41 VGIIGPNGAGKSTLCKALNG 60
                                      89***************965 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 ?   11.7   0.0   0.00023      0.16       1      19 [.      43      61 ..      43      66 .. 0.88
   2 ?   -3.0   0.0       7.2   5.2e+03     126     170 ..     203     247 ..     189     265 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                        ATP_bind_1  1 vvGpaGsGKttfvgalsei 19
                                      ++Gp G+GK+t+++al+ +
  gi|557694461|ref|YP_008797515.1| 43 IIGPNGAGKSTLCKALNGL 61
                                      79*************9865 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.2
                        ATP_bind_1 126 vvyLvDsqrltdptkfisgllsalsamlrlelPhvvvlnkfDllk 170
                                       ++ +v  + +++ ++f +++l+  +  + +e     vln+++llk
  gi|557694461|ref|YP_008797515.1| 203 TTIVVAEHEIEELATFTNRMLLLNNGRVLCEGSAKDVLNQVELLK 247
                                       444555555555566666666555555555555555555555554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00084       0.6      20      49 ..      40      70 ..      30     114 .. 0.82
   2 ?    1.0   0.0      0.43     3e+02     125     142 ..     180     197 ..     154     237 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00084
                            AAA_30 20 vavltGpAGtGKttalkalreaweaa.ggrv 49
                                       + + Gp G+GK+t+ kal+ ++ +  ggr+
  gi|557694461|ref|YP_008797515.1| 40 AVGIIGPNGAGKSTLCKALNGLVPHFyGGRI 70
                                      67799**************998877666444 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.43
                            AAA_30 125 erQlasVeaGgvlrdlve 142
                                       + Ql+++++ +v++ l e
  gi|557694461|ref|YP_008797515.1| 180 TSQLDPIGKAQVFDVLRE 197
                                       579999999998888843 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0002      0.15      24      44 ..      38      59 ..      27      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                            AAA_15 24 e.ltvliGkNnsGKSsileald 44
                                           +iG+N++GKS++ +al+
  gi|557694461|ref|YP_008797515.1| 38 GeAVGIIGPNGAGKSTLCKALN 59
                                      446679**************97 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00027       0.2      21      39 ..      43      61 ..      42      93 .. 0.84
   2 ?   -2.4   0.0       1.9   1.3e+03     527     542 ..     171     186 ..     167     219 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00027
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      i G NGaGK+tL+++l+ l
  gi|557694461|ref|YP_008797515.1| 43 IIGPNGAGKSTLCKALNGL 61
                                      569*************987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
                            AAA_13 527 dkivviDDPvSSLDsn 542
                                        +++v+D P S LD  
  gi|557694461|ref|YP_008797515.1| 171 PEVIVLDEPTSQLDPI 186
                                       6799******999965 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0003      0.21       2      20 ..      41      59 ..      40     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      + i+G+ ++GK+tl++aL+
  gi|557694461|ref|YP_008797515.1| 41 VGIIGPNGAGKSTLCKALN 59
                                      569**************97 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.3   0.00032      0.23      16      44 ..      37      69 ..      25      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00032
                           DUF3584 16 ldghtnieGtNaaGKTtLlr....LiPlFYGee 44
                                        + + i G N+aGK tL +    L+P FYG +
  gi|557694461|ref|YP_008797515.1| 37 RGEAVGIIGPNGAGKSTLCKalngLVPHFYGGR 69
                                      5577899**********98655569******76 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 ?    8.4   0.0    0.0035       2.5      33      89 ..     153     196 ..     130     197 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0035
                           SbcCD_C  33 lSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       lSGG++q la  +       ++        ++++++LDE  s+lD+   a+++++l+
  gi|557694461|ref|YP_008797515.1| 153 LSGGQQQRLAIAT-------VLAM------RPEVIVLDEPTSQLDPIGKAQVFDVLR 196
                                       6666664433222.......2223......578999999999999999999998887 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0071       5.1       3      22 ..      39      58 ..      37      98 .. 0.91
   2 ?    2.3   0.0      0.22   1.6e+02      74     107 ..     210     242 ..     159     250 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0071
                            AAA_14  3 kilvitGaRrvGKTtllkql 22
                                      +++ i G+  +GK+tl+k l
  gi|557694461|ref|YP_008797515.1| 39 EAVGIIGPNGAGKSTLCKAL 58
                                      6899************9876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.22
                            AAA_14  74 qevpewekalkslvdegknldvivtGSnskllsk 107
                                       +e++e+ ++ ++++  + n++v++ GS++ +l +
  gi|557694461|ref|YP_008797515.1| 210 HEIEELATFTNRMLLLN-NGRVLCEGSAKDVLNQ 242
                                       56688888888888877.8999999999988754 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 ?    8.9   0.3   0.00082      0.58     244     291 ..      37      87 ..      25      96 .. 0.75
   2 ?   -1.6   0.0       1.3   9.1e+02     324     351 ..     154     181 ..     152     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00082
                                       SS.EEEEEE-TTSSHHHHHHHHHHCCSEE-TT...SS-TTEEE-TT-EEE-- CS
                        ABC_ATPase 244 kG.vtlIvGggfhGKsTLLeAlekGvynhvpg...DGRefvvtdktavkira 291
                                       +G  + I+G++  GKsTL +Al+ G  +h  g    GR +v   +t+ +  a
  gi|557694461|ref|YP_008797515.1|  37 RGeAVGIIGPNGAGKSTLCKALN-GLVPHFYGgriSGRVYVAGMDTLKHTVA 87 
                                       5555679***************6.7888888844448888776666655555 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDts 351
                                       SG   q  +i+  l ++ +++++DE ts
  gi|557694461|ref|YP_008797515.1| 154 SGGQQQRLAIATVLAMRPEVIVLDEPTS 181
                                       889999999****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 2257.62
//
Query:       gi|557694462|ref|YP_008797516.1|  [L=277]
Description: cobalt/nickel ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-28   98.0   0.0    1.1e-27   97.2   0.0    1.4  1  ABC_tran      ABC transporter
    4.2e-08   33.4   0.0    0.00045   20.1   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    3.3e-07   30.0   0.0    5.1e-07   29.4   0.0    1.3  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00033   20.5   0.2       0.31   10.7   0.0    2.2  2  AAA_24        AAA domain
     0.0006   19.6   0.0      0.028   14.1   0.0    2.1  2  AAA_15        AAA ATPase domain
    0.00095   19.1   0.1       0.12   12.3   0.0    2.2  2  RsgA_GTPase   RsgA GTPase
     0.0017   17.7   0.1      0.025   13.9   0.0    2.3  2  Zeta_toxin    Zeta toxin
     0.0087   15.4   0.8        1.6    8.0   0.1    2.2  2  ATPase        KaiC
     0.0088   14.8   0.1          1    8.0   0.0    2.0  2  AAA_13        AAA domain
     0.0094   15.7   0.2       0.02   14.7   0.2    1.5  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.018   15.4   0.0    1.6  1  AAA_16        AAA ATPase domain
      0.017   14.5   0.0      0.029   13.7   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.033   14.1   0.3      0.055   13.4   0.3    1.3  1  NACHT         NACHT domain
       0.04   14.2   0.0       0.12   12.7   0.0    1.8  2  AAA_22        AAA domain
       0.04   14.1   1.0        0.2   11.8   1.0    2.1  1  AAA_33        AAA domain
      0.048   13.5   0.5          1    9.3   0.1    2.5  2  APS_kinase    Adenylylsulphate kinase
      0.051   13.2   1.0       0.54    9.9   0.1    2.2  2  SRP54         SRP54-type protein, GTPase domain
      0.052   12.4   0.1      0.084   11.7   0.1    1.2  1  DLIC          Dynein light intermediate chain (DLIC)
      0.068   13.2   0.3       0.45   10.5   0.1    2.3  2  AAA_5         AAA domain (dynein-related subfamily)
      0.082   13.4   0.1       0.15   12.6   0.1    1.4  1  AAA_23        AAA domain
      0.087   12.7   1.6        3.6    7.5   0.2    2.2  2  NTPase_1      NTPase
      0.091   12.5   0.2        6.5    6.5   0.0    2.1  2  ATP_bind_1    Conserved hypothetical ATP binding protein
       0.12   12.1   0.4        5.7    6.6   0.1    2.5  2  IstB_IS21     IstB-like ATP binding protein
       0.12   11.9   0.4        2.3    7.8   0.0    2.3  2  AAA_25        AAA domain
       0.15   12.3   0.4       0.44   10.8   0.1    2.0  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 !   97.2   0.0   1.6e-30   1.1e-27       1     136 [.      19     165 ..      19     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 97.2 bits;  conditional E-value: 1.6e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.v 76 
                                       l+ vsl++  ge+v i+G+nG GK+tL+k l gllkp +G +l+dg+d++e+++++l + +++++q+p+++  ++ v
  gi|557694462|ref|YP_008797516.1|  19 LRGVSLSIDSGEVVSIIGQNGGGKTTLAKHLNGLLKPSKGAVLVDGRDTRETPTHILASTVAYVFQNPSHQIFMStV 95 
                                       678****************************************************************5555554448 PP

                                       HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +++             + d+++++al+ +gl  +++++   +p+ L +Gq + + +a a++ +p++++lDEpt
  gi|557694462|ref|YP_008797516.1|  96 YDEvaygplqqnlpksAIDNRVATALEMVGLGAVDTKI---HPYDLDYGQMKLLTIASAIAMNPDVIVLDEPT 165
                                       8889**********9999999*********99965555...59*****************************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 !   11.3   0.0    0.0003      0.22       3      23 ..      33      53 ..      31      82 .. 0.80
   2 !   20.1   0.0   6.2e-07   0.00045     239     299 ..     140     197 ..     101     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                            AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                       +iG Ng GK++L + l +l 
  gi|557694462|ref|YP_008797516.1| 33 SIIGQNGGGKTTLAKHLNGLL 53
                                      59***********99999985 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 6.2e-07
                            AAA_21 239 dGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                        G+ +ll +++a++  +   +++++DEp +g +++  r+++e++k+l++ g  +i+ TH+ 
  gi|557694462|ref|YP_008797516.1| 140 YGQMKLLTIASAIAMNP---DVIVLDEPTTGQDHRGRRKVAEVVKRLNNMGKTIIIITHDM 197
                                       69999999999999988...9**************************************95 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 !   29.4   0.0   7.1e-10   5.1e-07      25     211 ..      30     209 ..      20     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 7.1e-10
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--...BTTCSSTTEEEEEEEEEETTEESSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk...skekasvkkaeveitfdnedkklkiekeevs 98 
                                       ++ +i+G+NG GK+ l   +    G      l+ +k   l+     +++  ++   +v+ +f+n+++++ +++   +
  gi|557694462|ref|YP_008797516.1|  30 EVVSIIGQNGGGKTTLAKHL---NG-----LLKPSKGAVLVDGrdtRETPTHILASTVAYVFQNPSHQIFMSTVYDE 98 
                                       5789************9988...23.....588899999999866566667778899***********999999999 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHH.HHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsel.lesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                       +     +++  + +i+++ +t  e+  l   +++i++  L  G+ +L+ +a  +A++   p  + +lDe     D++
  gi|557694462|ref|YP_008797516.1|  99 VAYGPLQQNLPKSAIDNRVATALEMVGLgAVDTKIHPYDLDYGQMKLLTIASAIAMN---PD-VIVLDEPTTGQDHR 171
                                       9999999999***********97766653789*****************99887764...54.679*********** PP

                                       HHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 175 nvkkvaellkekskn.aQfivislreemlekadklvgv 211
                                        ++kvae++k+ ++    +i+i+++ +++++  +   v
  gi|557694462|ref|YP_008797516.1| 172 GRRKVAEVVKRLNNMgKTIIIITHDMKFVTETARRTVV 209
                                       **********999885778999**99998887555444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   0.00043      0.31       4      23 ..      31      54 ..      28      98 .. 0.85
   2 !    8.0   0.0    0.0031       2.2     108     173 ..     173     237 ..     166     270 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00043
                            AAA_24  4 kiliyGpsgiGKTtlakel....g 23
                                       + i+G++g GKTtlak+l    +
  gi|557694462|ref|YP_008797516.1| 31 VVSIIGQNGGGKTTLAKHLngllK 54
                                      5779**************965552 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0031
                            AAA_24 108 aeefrrllkklqelrknvifiahektrkdedpegeakytrlepklgkktanelkeevDlvlranlk 173
                                       ++++ +++k+l++++k++i+i h  +   e+ +++   +   + + ++   ++ + v l++ra +k
  gi|557694462|ref|YP_008797516.1| 173 RRKVAEVVKRLNNMGKTIIIITHDMKFVTETARRT-VVMANGQIIADGPTSAIMSDVELLARAAIK 237
                                       678999****************9765444444444.444444555555556777777777777776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.9e-05     0.028      18      62 ..      23      64 ..      18      83 .. 0.77
   2 ?    3.3   0.0     0.077        55     321     367 ..     153     198 ..     130     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.9e-05
                            AAA_15 18 eidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiek 62
                                      ++++++  +  +iG N+ GK+++++ l+ +l+ +    k ++ ++ 
  gi|557694462|ref|YP_008797516.1| 23 SLSIDSGeVVSIIGQNGGGKTTLAKHLNGLLKPS----KGAVLVDG 64
                                      4445544599********************9988....55555555 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.077
                            AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                         ++++++++EP + +     + +++  k+l n +k  +ii TH   
  gi|557694462|ref|YP_008797516.1| 153 AMNPDVIVLDEPTTGQDHRGRRKVAEVVKRLNNMGK-TIIIITHDMK 198
                                       446889*****************************9.99999**865 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   0.00017      0.12      99     143 ..      28      73 ..       8      87 .. 0.78
   2 ?    4.8   0.0     0.033        23      12      99 ..     182     273 ..     170     275 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00017
                                       T.SEEEEECSTTSSHHHHHHHHCTT-----S--------------S CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTta 143
                                       + +++ ++Gq G GK+tL ++l++ l+ + g+v  + +  + T t+
  gi|557694462|ref|YP_008797516.1|  28 SgEVVSIIGQNGGGKTTLAKHLNGLLKPSKGAVLVDGRDTRETPTH 73 
                                       448999*****************99888888887776666666665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.033
                                       TEES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-...EEEEEEE-GGG--HHH....HHHHHHHHHHHTTSEEEE CS
                       RsgA_GTPase  12 kvaNvdqllivvslkepelslnlldrfLvlaeekgi...epvivlnKiDlleeee....eleelkeelealgyevll 81 
                                       +  N+ + +i+++ +  ++ +++  r +v+a+ + i   +   +++ ++ll ++     ++ +l+++l++ gy++ +
  gi|557694462|ref|YP_008797516.1| 182 RLNNMGKTIIIITHD-MKFVTETARRTVVMANGQIIadgPTSAIMSDVELLARAAikppQTVQLAHALNERGYRLRM 257
                                       567999999999999.9**************9998866567889999999999998898899999999999999999 PP

                                       --TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  82 vsaktkegleelkellkd 99 
                                       +  +  e+leel ++lk 
  gi|557694462|ref|YP_008797516.1| 258 LTIS--EALEELGKMLKR 273
                                       9777..888888888875 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   3.4e-05     0.025      19      57 ..      32      70 ..      25     100 .. 0.86
   2 ?    1.3   0.0      0.24   1.7e+02     100     129 ..     232     260 ..     185     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.4e-05
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrldpDdlRel 57
                                      + + Gq G GK++la+ l+  l++ +++v +d+ d Re 
  gi|557694462|ref|YP_008797516.1| 32 VSIIGQNGGGKTTLAKHLNGLLKPSKGAVLVDGRDTRET 70
                                      6677*****************************999986 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.24
                        Zeta_toxin 100 vegtlrspdvvkklaealkkaGYevevvvv 129
                                          +++ p++v+ la al ++GY+++ + +
  gi|557694462|ref|YP_008797516.1| 232 ARAAIKPPQTVQ-LAHALNERGYRLRMLTI 260
                                       555566667766.99999999999987765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1    0.0022       1.6      17      38 ..      27      48 ..      23      62 .. 0.89
   2 !    5.9   0.0    0.0099       7.1     121     167 ..     157     199 ..     134     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0022
                            ATPase 17 pegrvvlitGepGtGKtifalq 38
                                       +g+vv i G+ G GKt++a++
  gi|557694462|ref|YP_008797516.1| 27 DSGEVVSIIGQNGGGKTTLAKH 48
                                      6799***************987 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0099
                            ATPase 121 krvviDsitglayeekeavaReilrqlvrvlkklgvTailvseksss 167
                                         +v+D  t+     +++  R+ + ++v++l+++g T i+++   + 
  gi|557694462|ref|YP_008797516.1| 157 DVIVLDEPTTG----QDHRGRRKVAEVVKRLNNMGKTIIIITHDMKF 199
                                       55566655444....78889*******************99986553 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0014         1      21      39 ..      34      52 ..      27      73 .. 0.87
   2 ?    4.9   0.0     0.012       8.4     526     581 ..     155     207 ..     143     222 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0014
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      i G+NG GKTtL++ l+ l
  gi|557694462|ref|YP_008797516.1| 34 IIGQNGGGKTTLAKHLNGL 52
                                      77************99987 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.012
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkknt 581
                                       +  ++v+D P    D      v+  +k      +  k ++i TH ++f  e  ++t
  gi|557694462|ref|YP_008797516.1| 155 NPDVIVLDEPTTGQDHRGRRKVAEVVKRLN---NMGKTIIIITHDMKFVTETARRT 207
                                       678999999999999999999999999986...999************99987765 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   0.2   2.7e-05      0.02      14      50 ..      21      57 ..      15      60 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      g +++id  +++ ++G++G GK+Tl   ++ lL p+k
  gi|557694462|ref|YP_008797516.1| 21 GVSLSIDSGEVVSIIGQNGGGKTTLAKHLNGLLKPSK 57
                                      5678899666***************888887777776 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   2.5e-05     0.018      21      73 ..      26      76 ..      18     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysala 73
                                       +++e+v ++G+ G GK++l+++l   l+ ++g + + g+ ++    +p  +la
  gi|557694462|ref|YP_008797516.1| 26 IDSGEVVSIIGQNGGGKTTLAKHLNGLLKPSKGAVlVDGRDTRE---TPTHILA 76
                                      456699*******************9999997555377776666...4443333 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   4.1e-05     0.029       7      52 ..      14      59 ..      10      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                      Mg_chelatase  7 GqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplsee 52
                                      G+e a r + +++  g  + ++G  G GKt lak l++ll p + +
  gi|557694462|ref|YP_008797516.1| 14 GDEPALRGVSLSIDSGEVVSIIGQNGGGKTTLAKHLNGLLKPSKGA 59
                                      67778888888888889999********************998765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   7.7e-05     0.055       2      26 ..      31      55 ..      30      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.7e-05
                                      CEEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                      +v + G++G GKTtL+++l  +++ 
  gi|557694462|ref|YP_008797516.1| 31 VVSIIGQNGGGKTTLAKHLNGLLKP 55
                                      7889**************9877765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00016      0.12       6      55 ..      30      73 ..      26     130 .. 0.77
   2 ?   -1.8   0.0       4.9   3.5e+03      92      99 ..     156     163 ..     134     199 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskd 55
                                       ++ ++G+ G GKTtl++ l   l+       ++++ v+v+      +++ 
  gi|557694462|ref|YP_008797516.1| 30 EVVSIIGQNGGGKTTLAKHLNGLLK-------PSKGAVLVDGRDTReTPTH 73
                                      6788***************998885.......3555555555555555555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.9
                            AAA_22  92 ielliiDE 99 
                                       + ++++DE
  gi|557694462|ref|YP_008797516.1| 156 PDVIVLDE 163
                                       56666666 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.0   0.00028       0.2       1      33 [.      31      95 ..      31     226 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                            AAA_33  1 lvllvGlpGsGKstlaerl...lkklg.avllssdt............................l 33
                                      +v ++G +G GK+tla++l   lk+ + avl++  +                            +
  gi|557694462|ref|YP_008797516.1| 31 VVSIIGQNGGGKTTLAKHLnglLKPSKgAVLVDGRDtretpthilastvayvfqnpshqifmstV 95
                                      68899*************96666666689999876656666666655555555555555544441 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1    0.0014         1       2      43 ..      29      69 ..      28      81 .. 0.80
   2 ?    1.9   0.1      0.26   1.9e+02      60      79 ..     173     192 ..     165     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                                      -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTT CS
                        APS_kinase  2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRh 43
                                      g vv + G  g GK+t+a++l+  L+   + ++l+dG   R+
  gi|557694462|ref|YP_008797516.1| 29 GEVVSIIGQNGGGKTTLAKHLNGLLK-PSKGAVLVDGRDTRE 69
                                      6689999**************96655.556677889988776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHTT-EEEE CS
                        APS_kinase  60 irrvaevaklladaglivlv 79 
                                        r+vaev k+l++ g  +++
  gi|557694462|ref|YP_008797516.1| 173 RRKVAEVVKRLNNMGKTIII 192
                                       58999999999999875553 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00075      0.54       3      39 ..      31      67 ..      29      71 .. 0.87
   2 ?    1.9   0.1       0.2   1.5e+02      74     121 ..     146     195 ..     112     217 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00075
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      v+ ++G +G GKTt +  L  llk ++  vl+   Dt
  gi|557694462|ref|YP_008797516.1| 31 VVSIIGQNGGGKTTLAKHLNGLLKPSKGAVLVDGRDT 67
                                      7889***********9999999999988888877776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.2
                                       HHHHHHHHTTSSEEEEE..E--SSTTHHHHHHHHHHHHHHHSSSEEEEEE CS
                             SRP54  74 eavekakeekidvvlvD..TaGrlqndkelmeelkkikkvvkpdevllvl 121
                                        ++ +a + + dv+++D  T+G+ +  ++ ++e+ k  + + ++ ++++ 
  gi|557694462|ref|YP_008797516.1| 146 LTIASAIAMNPDVIVLDepTTGQDHRGRRKVAEVVKRLNNMGKTIIIITH 195
                                       56777888889999999889999999888888876655555444444444 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00012     0.084      22      56 ..      26      60 ..      15      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                              DLIC 22 lPsgksvlvlGedgsGkttliaklqGveeekkGrG 56
                                      + sg  v ++G++g Gkttl   l G+ ++ kG  
  gi|557694462|ref|YP_008797516.1| 26 IDSGEVVSIIGQNGGGKTTLAKHLNGLLKPSKGAV 60
                                      6789999*************************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 ?   10.5   0.1   0.00063      0.45       4      26 ..      34      57 ..      31      72 .. 0.75
   2 ?   -0.1   0.0       1.2   8.4e+02      47      47 ..     176     176 ..     141     251 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00063
                                      EE--SSSSHHHHHHHGGGGB.S-- CS
                             AAA_5  4 LvGppGtgKselaerlaaal.nre 26
                                      ++G+ G gK++la++l  +l  ++
  gi|557694462|ref|YP_008797516.1| 34 IIGQNGGGKTTLAKHLNGLLkPSK 57
                                      89***************9995333 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                                       - CS
                             AAA_5  47 i 47 
                                       +
  gi|557694462|ref|YP_008797516.1| 176 V 176
                                       2 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1    0.0002      0.15      20      39 ..      30      49 ..      18      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                            AAA_23 20 gltlItGpNGaGKTTildAi 39
                                       ++ I+G+NG GKTT+   +
  gi|557694462|ref|YP_008797516.1| 30 EVVSIIGQNGGGKTTLAKHL 49
                                      5788***********98655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2     0.005       3.6       2      36 ..      32      68 ..      31      74 .. 0.76
   2 ?    4.5   0.1     0.041        29      88     145 ..     147     204 ..     113     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.005
                                      EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfyte 36
                                      v i G+ G GKtTl k +  llk s   v v+G  t+
  gi|557694462|ref|YP_008797516.1| 32 VSIIGQNGGGKTTLAKHLNGLLKPSkgAVLVDGRDTR 68
                                      6688**************9999866323556665555 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.041
                                       HHHHHH.HHH-EEEE--..-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHH CS
                          NTPase_1  88 alrkal.seadviviDE..iGkmElkskkfkeaveevLksekpvlavihrrkdlalveeir 145
                                        +  a+  ++dviv+DE   G+     +k++e v+++ + +k ++++ h  k   +v e  
  gi|557694462|ref|YP_008797516.1| 147 TIASAIaMNPDVIVLDEptTGQDHRGRRKVAEVVKRLNNMGKTIIIITHDMK---FVTETA 204
                                       3444444799*******77799999999999999999998888888888773...444444 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 ?    4.2   0.1     0.043        31       1      23 [.      34      56 ..      34      62 .. 0.83
   2 ?    6.5   0.0    0.0091       6.5      73     214 ..     139     270 ..     118     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.043
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelr 23
                                      ++G  G GKtt+ + l+ +l+ +
  gi|557694462|ref|YP_008797516.1| 34 IIGQNGGGKTTLAKHLNGLLKPS 56
                                      79***********9999887766 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0091
                        ATP_bind_1  73 eflresldwldeelekeeddyllfDtP..GQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisglls 147
                                       ++++ +l  +++++   + d +++D P  GQ+     + + a++v++L++ ++++++   D +++t+++        
  gi|557694462|ref|YP_008797516.1| 139 DYGQMKLLTIASAI-AMNPDVIVLDEPttGQD--HRGRRKVAEVVKRLNNMGKTIIIITHDMKFVTETARRTVV--- 209
                                       56666665556666.44667777777744555..4566778889**********************96655444... PP

                        ATP_bind_1 148 alsamlrlelPhvvvlnkfDllkeklekeleffedvealslllekeeekykklaeaiaelleefalv 214
                                         +  + ++ P+  +++ ++ll+         ++ +++++l+  ++e+ y+  + +i+e+lee + +
  gi|557694462|ref|YP_008797516.1| 210 MANGQIIADGPTSAIMSDVELLA------RAAIKPPQTVQLAHALNERGYRLRMLTISEALEELGKM 270
                                       45667778899999999999998......44556677788888888888888999999999987665 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 ?    6.6   0.1    0.0079       5.7      44      67 ..      26      49 ..      17      53 .. 0.86
   2 ?    2.9   0.0      0.11        81     106     151 ..     153     199 ..     137     207 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0079
                         IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                      i++ e + ++G+ G GK+ la  l
  gi|557694462|ref|YP_008797516.1| 26 IDSGEVVSIIGQNGGGKTTLAKHL 49
                                      788999**************9765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.11
                         IstB_IS21 106 llkvdllilDdlgllpldqaeaellfeviekr..yerrsiiitsnlpf 151
                                        +++d+++lD+  +   d+  ++++ ev+++    +++ iiit +++f
  gi|557694462|ref|YP_008797516.1| 153 AMNPDVIVLDEPTT-GQDHRGRRKVAEVVKRLnnMGKTIIIITHDMKF 199
                                       34569*****9865.568889999999999752267888888888776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0031       2.3      30      53 ..      26      49 ..      16      51 .. 0.89
   2 ?    2.0   0.1      0.19   1.3e+02     138     188 ..     152     195 ..     110     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0031
                            AAA_25 30 lpagelallaGapgtGKttlaldl 53
                                      +  ge++ ++G+ g GKttla +l
  gi|557694462|ref|YP_008797516.1| 26 IDSGEVVSIIGQNGGGKTTLAKHL 49
                                      56799***************9665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.19
                            AAA_25 138 eevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhH 188
                                        +  +++++v+D    ++g d    ++v+++v++l+++    g +++++ H
  gi|557694462|ref|YP_008797516.1| 152 IA-MNPDVIVLDE--PTTGQDHRGRRKVAEVVKRLNNM----GKTIIIITH 195
                                       33.2599999995..67888999999999999999997....777777777 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00061      0.44       2      20 ..      32      50 ..      31      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00061
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      + i+G  ++GKTtl+++L+
  gi|557694462|ref|YP_008797516.1| 32 VSIIGQNGGGKTTLAKHLN 50
                                      679**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1994.56
//
Query:       gi|557694463|ref|YP_008797517.1|  [L=320]
Description: ribokinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-68  230.7   7.3    2.7e-68  230.5   7.3    1.0  1  PfkB          pfkB family carbohydrate kinase
    2.4e-11   43.5   0.3    3.5e-11   42.9   0.3    1.2  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
  ------ inclusion threshold ------
       0.12   12.1   2.3        4.8    6.9   0.7    2.3  2  AAA_26        AAA 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 !  230.5   7.3   4.6e-72   2.7e-68       3     301 ..       5     296 ..       3     297 .. 0.97

  Alignments for each domain:
  == domain 1  score: 230.5 bits;  conditional E-value: 4.6e-72
                                       EEEEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTE CS
                              PfkB   3 kvvviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegv 77 
                                       +vvv+G++ +dli +  ++  +ge+v +++++ s+GG+gaN+Ava+arlga+va +g+vG D fG+ lle l+ke+v
  gi|557694463|ref|YP_008797517.1|   5 EVVVVGSLHMDLIVKLARIpaKGETVIGGSFQLSPGGKGANQAVAAARLGASVAIVGRVGSDLFGDLLLERLRKENV 81 
                                       69*************************************************************************** PP

                                       EETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEES...EECTTSHHHHHHHH CS
                              PfkB  78 dtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisg...llsselpeavleel 151
                                        tdyv+ d +t+ g+ali+vd+dg++ i +  ga a  +++       ++ +a+++  s+   l + e+p a++e+ 
  gi|557694463|ref|YP_008797517.1|  82 ATDYVVKDVETHSGVALIMVDKDGNNLIAVASGADARCSPS-------DVDAAENVIASSkaiLTQLEIPLAAVERG 151
                                       ****************************************5.......778888888888888999*********** PP

                                       HHHHHHTTEEEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEG CS
                              PfkB 152 aeaaknggtfdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlG 228
                                        ++a+ +   +p++l++++a  +   ++ll+++d++ +n+ E++ ltg   +d+ +a++a++ l+a g+k  vvtlG
  gi|557694463|ref|YP_008797517.1| 152 VAIARRHE--VPVILNAAPA--QRLPRRLLEMVDVVVANRIEASVLTGVRVNDVVSAVRAGKRLLAMGVKYAVVTLG 224
                                       ********..*********6..799999************************************************* PP

                                       GGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCSCC CS
                              PfkB 229 keGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiaslpt 301
                                        +Ga+ v+++++++   v kvk+vD tGAGD+f+g+++ +l++g ++ +a+++an++Aal+++k ga++++pt
  gi|557694463|ref|YP_008797517.1| 225 RRGAVTVDRKETVYLRGV-KVKAVDATGAGDAFCGALAFGLVRGIKIHDAAELANNAAALATTKLGAQEAMPT 296
                                       *****************5.7*************************************************9998 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.3   5.9e-15   3.5e-11     104     226 ..     164     279 ..     134     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 5.9e-15
                                       SSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETS CS
                      Phos_pyr_kin 104 leeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydg 180
                                       l++   + l ++Ll++++v++ N  Ea++L+g +++++ ++ +a+k+ll++g+k+ +++ g+          v +d+
  gi|557694463|ref|YP_008797517.1| 164 LNAAPAQRLPRRLLEMVDVVVANRIEASVLTGVRVNDVVSAVRAGKRLLAMGVKYAVVTLGRR----G---AVTVDR 233
                                       556667888999***********************************************9983....2...36889* PP

                                       SEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHH CS
                      Phos_pyr_kin 181 eeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAke 226
                                       +e++ l++ +++  ++ G+G+++  a+a  l +g ++++A + A++
  gi|557694463|ref|YP_008797517.1| 234 KETVYLRGVKVKAVDATGAGDAFCGALAFGLVRGIKIHDAAELANN 279
                                       ****************************************999976 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0045        27     110     147 ..      36      73 ..      11      99 .. 0.81
   2 ?    6.9   0.7    0.0008       4.8     121     176 ..     152     205 ..     140     231 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0045
                            AAA_26 110 lgvpiteellnadiaknlgapvilVargglgtinqlll 147
                                        ++p  +++ +a  a++lga v +V+r+g++ + +lll
  gi|557694463|ref|YP_008797517.1|  36 QLSPGGKGANQAVAAARLGASVAIVGRVGSDLFGDLLL 73 
                                       5555666667777899****************999986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0008
                            AAA_26 121 adiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNkvrnpenvetl 176
                                       + ia++  +pvil a++ ++ + +ll +++++  +   + + +l +vr  + v ++
  gi|557694463|ref|YP_008797517.1| 152 VAIARRHEVPVILNAAPAQRLPRRLLEMVDVVVANR--IEASVLTGVRVNDVVSAV 205
                                       689*****************************9964..444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); 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:                         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 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2368.32
//
Query:       gi|557694464|ref|YP_008797518.1|  [L=524]
Description: 2-isopropylmalate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-51  175.8   0.0    3.3e-51  174.4   0.0    1.7  2  HMGL-like   HMGL-like
    4.8e-24   84.8   0.7    1.5e-22   79.9   0.8    2.2  2  LeuA_dimer  LeuA allosteric (dimerisation) domain
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.26   11.1   0.0    1.5  1  SurA_N_3    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 !  174.4   0.0   5.6e-55   3.3e-51       5     247 ..       1     249 [.       1     270 [. 0.89
   2 ?   -2.4   0.1      0.48   2.8e+03      84     101 ..     460     477 ..     430     500 .. 0.73

  Alignments for each domain:
  == domain 1  score: 174.4 bits;  conditional E-value: 5.6e-55
                                       EE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---T.T-B..--EE-SSHHHHHH CS
                         HMGL-like   5 vdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakav.kkarilalvrarekdika 80 
                                       +dttLRDG q+ ++++++ +kl+ia++Lde+gvd iE g p + ++d ++ r++ k    ++r+ a    r   +k 
  gi|557694464|ref|YP_008797518.1|   1 MDTTLRDGAQTRGVTFTLHDKLRIAEKLDELGVDIIEGGWPGSNPKDEDFFREARKLSfSHSRLGAFGSTRRPNVKP 77 
                                       69****************************************************99761566677777777766664 PP

                                       ....HHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTB...S--HHHHHH CS
                         HMGL-like  81 ....avealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledas...rtdleflae 150
                                            v+al +a + +  vf     lh+  +l+ + ee ++++++ v++ r++g +v++ +e +    r ++e++++
  gi|557694464|ref|YP_008797518.1|  78 sqdpSVNALLKADVPVAIVFGKSWILHVIDVLRTTPEENLRMVADTVEYLREHGLEVVFDAEHFFdgyRESPEYALQ 154
                                       1112678999***************************************************987533389******* PP

                                       HHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS- CS
                         HMGL-like 151 vveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGl 227
                                       v+++a++aGa +i + Dt G + P+ ++e++++++++++  + l +H+Hnd G+Avan+l+Av +G+++v gt+ Gl
  gi|557694464|ref|YP_008797518.1| 155 VLKQARDAGASTIVLCDTNGGTLPFRVGEVVRRVRREID--TRLGIHAHNDCGVAVANSLVAVTEGVRHVQGTMIGL 229
                                       ***************************************..************************************ PP

                                       -SSBBB-BHHHHHHHHHHTT CS
                         HMGL-like 228 GeraGnaaleelvaalealg 247
                                       Ger Gna+l +++ +l+ + 
  gi|557694464|ref|YP_008797518.1| 230 GERCGNADLTQIIPNLALKM 249
                                       ************99987655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.48
                                       ....TT-SEEEEEEES-H CS
                         HMGL-like  84 alkgagakrvhvfiatse 101
                                         k a a+ v+vfi  s+
  gi|557694464|ref|YP_008797518.1| 460 DTKDATAAAVRVFIEFSD 477
                                       456788888999998887 PP

>> LeuA_dimer  LeuA allosteric (dimerisation) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.025   1.5e+02      80     105 ..     150     175 ..     142     187 .. 0.89
   2 !   79.9   0.8   2.5e-26   1.5e-22       6     132 ..     372     506 ..     367     507 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.025
                                       EEEEE--TT-TT--EEEEEEEE--GG CS
                        LeuA_dimer  80 dYsvhaitegtdaqaevrVelevddg 105
                                       +Y ++++++  da a++ V + +++g
  gi|557694464|ref|YP_008797518.1| 150 EYALQVLKQARDAGASTIVLCDTNGG 175
                                       8********************96555 PP

  == domain 2  score: 79.9 bits;  conditional E-value: 2.5e-26
                                       XXXXXXXXXXXXXX--EEEEEEEEEEETT..CEEEEEEEEEE.TTEEEEEEEE-SSHHHHHHHHHHHHHHH...... CS
                        LeuA_dimer   6 dlealvkdelleaeerlkleklqvssged..elstatvklevkdgeekeasaeGnGpvdAllnAlrkalgv...... 74 
                                        +  ++ + ++   erl++  + v        ++ a+v +++ dge +++ aeG+Gpv+Al+ A+r a+ +      
  gi|557694464|ref|YP_008797518.1| 372 TVSLMILEAVGYDVERLRVRTWWVEVLMAgrITARAVVSMDI-DGEAVTEMAEGVGPVHALDAAIRAAVLKrypqle 447
                                       555566666666667788877765544443389999******.*************************999787665 PP

                                       T-EEEEEEEE--TT-TT--EEEEEEEE-.-GGGEEEEEEEESSHHHHHHHHHHHHHHHH CS
                        LeuA_dimer  75 dikLldYsvhaitegtdaqaevrVelev.ddgkkvsgvGvdsdiveASlkAlisalnrl 132
                                       +++L +Y+v +i   + + a+vrV +e+ d+g+++ ++Gv+++iveASlkA+++++ + 
  gi|557694464|ref|YP_008797518.1| 448 STQLVNYKVSVIDTKDATAAAVRVFIEFsDNGNRWATTGVSKNIVEASLKAIVDGYSYK 506
                                       56*************************9455999********************99875 PP

>> SurA_N_3  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.3e-05      0.26      88     127 ..     324     363 ..     306     373 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.3e-05
                          SurA_N_3  88 ldqlidealllqeakklglsvsdeevakeiasipaFqedG 127
                                       +++l  +a+l ++a+klgl  ++e+va+ +++i+ + ++G
  gi|557694464|ref|YP_008797518.1| 324 VSELAGRAALVNHAAKLGLVLTKEQVASILEKIKRLEAEG 363
                                       6789999***************************999666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); 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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 3932.08
//
Query:       gi|557694465|ref|YP_008797519.1|  [L=130]
Description: translation initiation factor eIF-5A [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   31.6   0.1    3.2e-06   27.1   0.0    2.2  2  EFP_N     Elongation factor P (EF-P) KOW-like domain
    1.3e-06   28.4   0.1    2.1e-06   27.7   0.1    1.3  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.013   15.1   0.1    1.2  1  DUF1609   Protein of unknown function (DUF1609)


Domain annotation for each model (and alignments):
>> 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 !   27.1   0.0   5.4e-10   3.2e-06       4      35 ..       9      41 ..       6      44 .. 0.85
   2 ?    2.4   0.0     0.027   1.6e+02       6      24 ..      72      90 ..      69      93 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 5.4e-10
                                      G--TT-EEEETTEEEEEEEEEEEEETT.S--EE CS
                             EFP_N  4 elkkGlvieidgklyvVlefehvkpGk.Gqafv 35
                                      +lk G  i idg++++++e+e +kpGk G+a v
  gi|557694465|ref|YP_008797519.1|  9 SLKEGHNIVIDGEPCRIVEVEKSKPGKhGSAKV 41
                                      79************************7245555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.027
                                      -TT-EEEETTEEEEEEEEE CS
                             EFP_N  6 kkGlvieidgklyvVlefe 24
                                      ++G+v+ + g+ ++V++++
  gi|557694465|ref|YP_008797519.1| 72 RTGQVVALSGDSVSVMDNQ 90
                                      89**************998 PP

>> 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 !   27.7   0.1   3.5e-10   2.1e-06       1      69 []      68     130 .]      68     130 .] 0.91

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.5e-10
                                       --EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEEEEEE- CS
                            eIF-5a   1 nVkrkeyqLidIqdDgflsLmd.ddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeekiiavK 69 
                                       +V++++ q+++ ++D  +s md ++ e+ e ++lp    ++++++k e+g +  V+++s+m++   ++vK
  gi|557694465|ref|YP_008797519.1|  68 IVDKRTGQVVALSGD-SVSVMDnQTLEIVE-VPLP---KDENLRAKIEPGVS--VEYWSIMNRYLLVNVK 130
                                       69*************.******99999999.****...5678888889**99..*********9999887 PP

>> DUF1609  Protein of unknown function (DUF1609)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   2.1e-06     0.013     100     141 ..      31      76 ..      17      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-06
                           DUF1609 100 gkymkgGserwkmvaigvleeggkkkvG....vvevGlfkdksges 141
                                       +k  k Gs + ++vaig+++e ++ +vG    +vev +   ++g+ 
  gi|557694465|ref|YP_008797519.1|  31 SKPGKHGSAKVRLVAIGIFDEVKRSMVGpadnKVEVPIVDKRTGQV 76 
                                       56679**********************9666668888776666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); 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:                         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 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1035.58
//
Query:       gi|557694466|ref|YP_008797520.1|  [L=225]
Description: ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-65  219.3   0.0    4.7e-65  219.2   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase
  ------ inclusion threshold ------
      0.026   14.0   0.0       0.08   12.4   0.0    1.8  2  QueC             Queuosine biosynthesis protein QueC
       0.25   11.3   2.5         22    5.1   0.1    3.6  4  RHH_1            Ribbon-helix-helix protein, copG family


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 !  219.2   0.0   7.8e-69   4.7e-65       1     218 [.       1     219 [.       1     220 [. 0.97

  Alignments for each domain:
  == domain 1  score: 219.2 bits;  conditional E-value: 7.8e-69
                   Diphthami_syn_2   1 mkvavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekeved 76 
                                       m+ a+l+sGGkDs++a+y a +  + ve L + +++  +sy fh +n+hl+ l+ae++G   i   +aG  e+e   
  gi|557694466|ref|YP_008797520.1|   1 MRLAALFSGGKDSTYAIYLAENMgHVVEVLLTFLPQSIDSYLFHYPNIHLTPLQAEAMGRHHIIYPVAGMDEEE--A 75 
                                       899*****************9987999*****************************************998886..6 PP

                   Diphthami_syn_2  77 Lkgtlkkld..veavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldesl 151
                                       Lk  l ++   v++vv Ga++s yq++r+ r  ++ G+  + PLW+++p ell +++ ++fe++vvav+a g+d+s+
  gi|557694466|ref|YP_008797520.1|  76 LKRALSEVAgrVDGVVAGALASSYQRERMKRAAEKHGFTVLTPLWGQNPGELLRQMLRNRFEIMVVAVAAAGMDRSW 152
                                       999***99778****************************************************************** PP

                   Diphthami_syn_2 152 LGrridkklidelkklsekygidkagegGeaetlvlDaPlfkkrlevkelekkwderrgyldierak 218
                                       LGr++d + + el+ lse++g+++agegGe+et+vlD Plf+kr++  e    w +++gyl iera+
  gi|557694466|ref|YP_008797520.1| 153 LGRILDEEAVKELEALSERHGVNPAGEGGEMETMVLDCPLFRKRIKPLEKSVVWRGVYGYLRIERAV 219
                                       ****************************************************************986 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.3e-05      0.08       4      29 ..       5      30 ..       2      39 .. 0.88
   2 ?   -2.6   0.0      0.52   3.1e+03     142     160 ..     103     121 ..      98     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.3e-05
                                      EE--SSHHHHHHHHHHHHH-SEEEEE CS
                              QueC  4 vllSGGlDSttvlalakkegkeveal 29
                                       l+SGG DSt +++la++ g+ ve+l
  gi|557694466|ref|YP_008797520.1|  5 ALFSGGKDSTYAIYLAENMGHVVEVL 30
                                      69*****************9999876 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.52
                                       HHHHHHHTS--EEE-TTTT CS
                              QueC 142 kalnlgedkkieieaPlid 160
                                       ++ +++e++ +++ +Pl  
  gi|557694466|ref|YP_008797520.1| 103 RMKRAAEKHGFTVLTPLWG 121
                                       5667889999999999975 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 ?   -2.5   0.1      0.97   5.8e+03      27      34 ..      74      81 ..      69      84 .. 0.64
   2 ?    3.0   0.0     0.017     1e+02      25      36 ..     124     135 ..     121     138 .. 0.81
   3 ?    0.3   0.0      0.13   7.6e+02      18      28 ..     143     153 ..     142     155 .. 0.87
   4 ?    5.1   0.1    0.0037        22       6      23 ..     157     174 ..     157     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.97
                                      HHHHHHHH CS
                             RHH_1 27 elIReAlr 34
                                      e++++Al 
  gi|557694466|ref|YP_008797520.1| 74 EALKRALS 81
                                      56666665 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHH CS
                             RHH_1  25 rSelIReAlrey 36 
                                        +el+R++lr++
  gi|557694466|ref|YP_008797520.1| 124 PGELLRQMLRNR 135
                                       589*******97 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.13
                                       HHHHTSSHHHH CS
                             RHH_1  18 arrrgrSrSel 28 
                                       +++ g+ rS+l
  gi|557694466|ref|YP_008797520.1| 143 VAAAGMDRSWL 153
                                       5789******7 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.0037
                                       EEHHHHHHHHHHHHHHTS CS
                             RHH_1   6 ldeellerLdelarrrgr 23 
                                       ldee +++L++l +r g+
  gi|557694466|ref|YP_008797520.1| 157 LDEEAVKELEALSERHGV 174
                                       8************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1720.17
//
Query:       gi|557694467|ref|YP_008797521.1|  [L=374]
Description: succinyl-CoA synthetase beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-62  210.5   2.4      3e-62  209.8   2.4    1.3  1  ATP-grasp_2   ATP-grasp domain
    1.4e-17   63.9   0.5    2.9e-17   62.9   0.5    1.5  1  Ligase_CoA    CoA-ligase
    1.3e-15   57.4   2.1    2.2e-15   56.7   2.1    1.3  1  ATP-grasp_5   ATP-grasp domain
    3.2e-09   36.8   0.8    6.7e-09   35.8   0.8    1.5  1  GARS_A        Phosphoribosylglycinamide synthetase, ATP-grasp
     0.0018   17.9   0.1     0.0033   17.0   0.1    1.4  1  ATP-grasp     ATP-grasp domain
     0.0068   16.2   1.7      0.013   15.3   0.1    2.1  2  Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain


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 !  209.8   2.4   9.9e-66     3e-62       1     202 []       3     196 ..       3     196 .. 0.99

  Alignments for each domain:
  == domain 1  score: 209.8 bits;  conditional E-value: 9.9e-66
                                       BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTT CS
                       ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellg 77 
                                       +l+E++++e++++yg++v++  v++saeea++aa+ lg+++ vvKaQvl+ GRGKagGvk+++++eea + a ++l 
  gi|557694467|ref|YP_008797521.1|   3 KLYEFEGRELFRRYGIPVNNYVVVRSAEEARRAAEALGGRT-VVKAQVLVAGRGKAGGVKVAENVEEAVMLAGKMLR 78 
                                       69**************************************9.*********************************** PP

                                       SEEE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB- CS
                       ATP-grasp_2  78 kelvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakgl 154
                                       +e++       G++ve ++v+e +++ kElYl+i++Dr ++ +vviaS+eGGv+iEe+a ++P ++ k++++p  gl
  gi|557694467|ref|YP_008797521.1|  79 SEIK-------GERVESLVVTEYTEVVKELYLGIIVDRFKRAPVVIASAEGGVEIEELARTSPGHVLKTEVNPLLGL 148
                                       ****.......****************************************************************** PP

                                       -HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEE CS
                       ATP-grasp_2 155 keeqareiakklglekelvkkaakiikklyklfveldatlvEiNPLvv 202
                                        ++q+r+i+  ++l+++l+++aa i+  ly+lfve d++l+EiNPLv+
  gi|557694467|ref|YP_008797521.1| 149 ADYQVRKIISFMKLDQKLAQQAAAILRGLYRLFVENDCELAEINPLVI 196
                                       **********************************************96 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   0.5   9.5e-21   2.9e-17       3     151 ..     254     370 ..     252     372 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 9.5e-21
                                       SSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEE CS
                        Ligase_CoA   3 nGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvill 79 
                                       nG++L++++md++k++              g+ +++++d+G++a           ++ + +a + l+  p+vkv+++
  gi|557694467|ref|YP_008797521.1| 254 NGAGLTMATMDMVKLK--------------GGSPANFLDVGGGAS----------EDVVEKAARLLLTHPRVKVVFV 306
                                       8***************..............***************..........899******************* PP

                                       EEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHH CS
                        Ligase_CoA  80 divlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraak 151
                                       +i +G+ +++++a +l++a+k++      + +v+r++Gt+++     e++++l e g+  ++s ++a++ a 
  gi|557694467|ref|YP_008797521.1| 307 NILGGITRCDEVARGLVSAYKSVG---AGKKIVVRMMGTNEE-----EGKRILIENGIYPLDSMEEAAAKAA 370
                                       ***********************8...88899**********.....***********99999999988765 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.7   2.1   7.4e-19   2.2e-15      10     222 .]       4     211 ..       2     211 .. 0.89

  Alignments for each domain:
  == domain 1  score: 56.7 bits;  conditional E-value: 7.4e-19
                       ATP-grasp_5  10 LteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeile 86 
                                       L+e+e +el++ ygipv +  +++saeea +aae++g   v+K ++  +  + ++gGv++    ae+v++a+    +
  gi|557694467|ref|YP_008797521.1|   4 LYEFEGRELFRRYGIPVNNYVVVRSAEEARRAAEALGGRTVVKAQVL-VAGRGKAGGVKV----AENVEEAVMLAGK 75 
                                       99*****************************************9975.999*********....8999999999999 PP

                       ATP-grasp_5  87 rvkekspeariegvlVqemakrggrElivgvteDpv.FGpv.ilfGlGGtavevlkdvavalpplnstlareliert 161
                                        ++++ +++r+e ++V e ++    El +g+  D +   pv i+  +GG+++e l+ ++ +++  ++ +    +   
  gi|557694467|ref|YP_008797521.1|  76 MLRSEIKGERVESLVVTEYTE-VVKELYLGIIVDRFkRAPVvIASAEGGVEIEELARTSPGHVLKTEVNPLLGLADY 151
                                       99999999***********99.8999999999998634665155678***************999999999999*** PP

                       ATP-grasp_5 162 kaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeeg.vvalDarirl 222
                                       ++ k+++ ++   ++  ++ + +l  l +L v+    +  +inPl++++++ +valD +i +
  gi|557694467|ref|YP_008797521.1| 152 QVRKIISFMKLD-QKLAQQAAAILRGLYRLFVE-NDCELAEINPLVITPDNrLVALDSKIIV 211
                                       ******999999.66667778899999999999.6788899********666******9976 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 !   35.8   0.8   2.3e-12   6.7e-09       7      90 ..      10      96 ..       6     119 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.3e-12
                                      HHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT....-EEEESSHHHHHHHHHHHCTS-TTCCCCS CS
                            GARS_A  7 kdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagK....gvivakseeealkavkeilekkkfGeage 81
                                      ++l++++gip  +y ++ ++eea+   e+++ ++ VvKa+ l ag+    gv+va+++eea+  + ++l+++  Ge  e
  gi|557694467|ref|YP_008797521.1| 10 RELFRRYGIPVNNYVVVRSAEEARRAAEALGGRT-VVKAQVLVAGRgkagGVKVAENVEEAVMLAGKMLRSEIKGERVE 87
                                      799******************************9.*********9844556**************************** PP

                                      SEEEEE--- CS
                            GARS_A 82 kvviEelle 90
                                      ++v+ e+ e
  gi|557694467|ref|YP_008797521.1| 88 SLVVTEYTE 96
                                      ***999876 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.1e-06    0.0033       3      62 ..      15      80 ..      13     122 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-06
                                      TTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEE.EECTCCGHHCHHHHC......G CS
                         ATP-grasp  3 klglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqs.vvrseedleqaleal......k 62
                                      + g+pv ++++v+s+ee+++aae+lg  +vvKa+ +   G+G+   v+ +e++e+a+  +      +
  gi|557694467|ref|YP_008797521.1| 15 RYGIPVNNYVVVRSAEEARRAAEALGGRTVVKAQ-VLVAGRGKAgGVKVAENVEEAVMLAgkmlrsE 80
                                      679*****************************55.55679998634777777777776664444550 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 ?   -0.4   0.2      0.32   9.4e+02      89     132 ..      28      70 ..      14      75 .. 0.64
   2 !   15.3   0.1   4.5e-06     0.013       2      98 ..     247     349 ..     246     370 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.32
                      Succ_CoA_lig  89 sGrseagaraaashtgalagsdavvdaafrqaGvl.rvdsleelf 132
                                       s   e+++raa +  g  + + +v+ a   +aG + +++++ee +
  gi|557694467|ref|YP_008797521.1|  28 S--AEEARRAAEALGGRTVVKAQVLVAGRGKAGGVkVAENVEEAV 70 
                                       3..356667777777777777777777666665541556777765 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 4.5e-06
                      Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGneadvdvad.lleylaedpetkvill.ylEsird....grkfl 72 
                                       G+i++i    +l +a +d+++ +g   ++++ +G  a  dv +   + l ++p++kv+++  l +i +    +r ++
  gi|557694467|ref|YP_008797521.1| 247 GDIGIIGNGAGLTMATMDMVKLKGGSPANFLDVGGGASEDVVEkAARLLLTHPRVKVVFVnILGGITRcdevARGLV 323
                                       99*********************************9999987626678999******9983457787777889**** PP

                      Succ_CoA_lig  73 saarraarkkpvvvlksGrseagara 98 
                                       sa +++ + k++vv  +G++e+  + 
  gi|557694467|ref|YP_008797521.1| 324 SAYKSVGAGKKIVVRMMGTNEEEGKR 349
                                       ******************98877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2670.89
//
Query:       gi|557694468|ref|YP_008797522.1|  [L=291]
Description: succinyl-CoA synthetase alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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   98.2   0.4    3.2e-28   98.2   0.4    2.1  3  CoA_binding    CoA binding domain
    1.9e-16   60.3   0.1    2.8e-16   59.7   0.1    1.2  1  Ligase_CoA     CoA-ligase
      4e-14   52.6   0.1    1.3e-13   50.9   0.0    1.8  2  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    1.5e-07   31.9   0.3    6.5e-07   29.8   0.0    2.1  3  CoA_binding_2  CoA binding domain
  ------ inclusion threshold ------
      0.025   15.4   0.2      0.072   13.9   0.1    1.9  2  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
      0.041   14.1   0.0      0.092   12.9   0.0    1.5  1  SH3_7          SH3 domain of SH3b2 type


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 !   98.2   0.4   1.1e-31   3.2e-28       2      96 .]       7     100 ..       6     100 .. 0.98
   2 ?   -1.7   0.0       1.7     5e+03      22      39 ..     165     182 ..     145     205 .. 0.54
   3 ?   -3.5   0.0       5.8   1.7e+04      76      88 ..     262     274 ..     252     284 .. 0.65

  Alignments for each domain:
  == domain 1  score: 98.2 bits;  conditional E-value: 1.1e-31
                                       TTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHC.TTTEEEEES-HHHHHH CS
                       CoA_binding   2 kdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleekt.evdvavitvPaesaqe 77 
                                        dt+v+v+G++g+  +g++h++ +lkyg+k+++gv+p+k g  v+g+pvy+sv+e++++  e+++++++vPa+ a +
  gi|557694468|ref|YP_008797522.1|   7 DDTRVLVQGITGR--QGAFHTRAMLKYGTKVLAGVTPGKSGHSVEGVPVYNSVEEAMANYpEINTSMVMVPAPYAGD 81 
                                       79***********..*********************************************77*************** PP

                                       HHHHHHHTT-SEEEEESST CS
                       CoA_binding  78 avdelveagikgiviiteg 96 
                                       av+e+++agik++v+ite+
  gi|557694468|ref|YP_008797522.1|  82 AVIEALDAGIKLVVVITEH 100
                                       *****************95 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                                       HHHHHHECEEEEEEC-TT CS
                       CoA_binding  22 fkeklkygikavfgvnpr 39 
                                        +  ++ g +  +g++++
  gi|557694468|ref|YP_008797522.1| 165 AITVKGLGQSTCIGIGGD 182
                                       444444444444444444 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.8
                                       HHHHHHHHHTT-S CS
                       CoA_binding  76 qeavdelveagik 88 
                                       +++v++l +ag+ 
  gi|557694468|ref|YP_008797522.1| 262 ASKVKALTQAGVH 274
                                       4556666666665 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.1   9.3e-20   2.8e-16       1     151 [.     152     272 ..     152     274 .. 0.95

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 9.3e-20
                                       EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEE CS
                        Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvi 77 
                                       ++++GtL+ye +++i+ +              g +q+++i++G+d            + ++i+ l+ + +d+e++++
  gi|557694468|ref|YP_008797522.1| 152 VSRSGTLTYEIAHAITVK--------------GLGQSTCIGIGGDPVV---------GLNFIDVLEMFRRDEETEAV 205
                                       689***************..............***************8.........9******************* PP

                                       EEEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHH CS
                        Ligase_CoA  78 lldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraak 151
                                       +l +++G g  e+ aa+++ +++  k      pvva++aG +a+p +++++a+a+ + g+   +sk +al  a+
  gi|557694468|ref|YP_008797522.1| 206 VLIGEIG-GDLEERAADYIVKTRYPK------PVVAYIAGRTAPPEKRMGHAGAIISLGAGDPASKVKALTQAG 272
                                       *******.**********99988887......****************************99999999988776 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 ?   -2.4   0.0       1.2   3.7e+03      52      76 ..      88     114 ..      84     115 .. 0.75
   2 !   50.9   0.0   4.4e-17   1.3e-13       2     133 ..     147     284 ..     146     289 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.2
                      Succ_CoA_lig  52 dpetkvillylEs..irdgrkflsaar 76 
                                       d  +k++++  E+  i+d+ kf+  ar
  gi|557694468|ref|YP_008797522.1|  88 DAGIKLVVVITEHvpIHDAMKFITYAR 114
                                       677888888888733578889988876 PP

  == domain 2  score: 50.9 bits;  conditional E-value: 4.4e-17
                      Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsird.grkflsaa 75 
                                       G ++++s SG+l  +++++ + +glg s+++ +G    + +++ d+le++ +d+et++++l  E  +d  ++ ++ +
  gi|557694468|ref|YP_008797522.1| 147 GVVGIVSRSGTLTYEIAHAITVKGLGQSTCIGIGGdpVVGLNFIDVLEMFRRDEETEAVVLIGEIGGDlEERAADYI 223
                                       889*******************************9344667788*********************999789999999 PP

                      Succ_CoA_lig  76 rraarkkpvvvlksGrseagaraaashtgal....agsdavvdaafrqaGvlrvdsleelfd 133
                                        +++  kpvv++ +Gr++  ++  + h ga+    ag+ a   +a+ qaGv ++++  e++d
  gi|557694468|ref|YP_008797522.1| 224 VKTRYPKPVVAYIAGRTAPPEKR-MGHAGAIislgAGDPASKVKALTQAGVHVASTPGEVAD 284
                                       999999**********8876665.67888875556899999**************9999876 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   2.2e-10   6.5e-07      14     115 ..      19     130 ..      10     131 .. 0.85
   2 ?   -2.4   0.0       2.1   6.4e+03       5      26 ..     148     169 ..     145     182 .. 0.54
   3 ?   -2.2   0.0       1.9   5.8e+03      56      72 ..     190     206 ..     185     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.2e-10
                                       SHHHHHHHHHHHHT--EEE.ESSS-..SEETTEES----T.......T--EEEE-S-HHHHGGGHHHHHHH--SEEE CS
                     CoA_binding_2  14 kfgykvlryllehglpvvp.Vnpke..eeilgekvyaslaed...pepvdlvdvftppeatpeivkealalgakavw 84 
                                       + g   +r +l+ g +v++ V+p +  ++++g++vy s++e+     ++ +  v++p+  + + v eal++g+k v+
  gi|557694468|ref|YP_008797522.1|  19 RQGAFHTRAMLKYGTKVLAgVTPGKsgHSVEGVPVYNSVEEAmanYPEINTSMVMVPAPYAGDAVIEALDAGIKLVV 95 
                                       5555556666666666654489988889************8447888899*************************** PP

                                       E-TT....---HHHHHHHHHTT-EEE.ES-HHHHH CS
                     CoA_binding_2  85 lqpg....sedeeaaelaeeagirvvgdrCilveg 115
                                       +  +        +++ +a+ +g ++vg++C++v++
  gi|557694468|ref|YP_008797522.1|  96 VITEhvpiHDAMKFITYARLRGSNIVGPNCPGVIT 130
                                       ****9998888899******************975 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.1
                                       EET--S-TTSHHHHHHHHHHHH CS
                     CoA_binding_2   5 VvGasdnpgkfgykvlrylleh 26 
                                       VvG  +++g   y +++ +  +
  gi|557694468|ref|YP_008797522.1| 148 VVGIVSRSGTLTYEIAHAITVK 169
                                       5555555555555555544333 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.9
                                       --EEEE-S-HHHHGGGH CS
                     CoA_binding_2  56 vdlvdvftppeatpeiv 72 
                                       +d++ +f++ e+t+++v
  gi|557694468|ref|YP_008797522.1| 190 IDVLEMFRRDEETEAVV 206
                                       799999****9999886 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   0.1   2.4e-05     0.072       2      93 ..      10     100 ..       9     121 .. 0.75
   2 ?   -3.4   0.0       5.5   1.6e+04      79      89 ..     265     275 ..     252     276 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.4e-05
                                       EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHH.HHHTCTTESEEEE-S-GGGHH CS
                      GFO_IDH_MocA   2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdle.elladpeidavivatpngthe 76 
                                       rv++ G+ G+ g  h r++ +   +++v a + p+++ +  v    gv++y+++e ++++ pei+  +v++p+    
  gi|557694468|ref|YP_008797522.1|  10 RVLVQGItGRQGAFHTRAMLKY--GTKVLAGVTPGKSGHS-V---EGVPVYNSVEeAMANYPEINTSMVMVPAPYAG 80 
                                       5667777677777777666666..5566666666665444.3...79******994555556*************** PP

                                       HHHHHHHHTT-...EEEEES CS
                      GFO_IDH_MocA  77 elakaaleagk...hvllEK 93 
                                       + +++al ag+    v+ E+
  gi|557694468|ref|YP_008797522.1|  81 DAVIEALDAGIklvVVITEH 100
                                       ***********776777776 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.5
                                       HHHHHHTT-EE CS
                      GFO_IDH_MocA  79 akaaleagkhv 89 
                                       +ka+++ag+hv
  gi|557694468|ref|YP_008797522.1| 265 VKALTQAGVHV 275
                                       68889999998 PP

>> SH3_7  SH3 domain of SH3b2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.1e-05     0.092      13      36 ..      92     114 ..      84     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                                       -EEEE-STTEEEE-TTS-EEEEE- CS
                             SH3_7  13 rfaviirdnvplyDatgqylftar 36 
                                       +++v+i ++vp++Da  ++ ++ar
  gi|557694468|ref|YP_008797522.1|  92 KLVVVITEHVPIHDAM-KFITYAR 114
                                       699*************.******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); 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):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 2225.79
//
Query:       gi|557694469|ref|YP_008797523.1|  [L=263]
Description: protein phosphatase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-22   80.5   0.1    2.9e-22   80.2   0.1    1.1  1  Metallophos    Calcineurin-like phosphoesterase
    1.2e-05   25.6   0.0    1.6e-05   25.1   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 !   80.2   0.1   3.3e-26   2.9e-22       3     203 ..      29     220 ..      28     221 .. 0.80

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 3.3e-26
                                       EEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHH.HHHHHHHTSEEEEEC-TTS... CS
                       Metallophos   3 ilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellel.laalvkypipvylllGNHe... 75 
                                       +lv+gD+H     g+ d+++k+l+ + ++  + ++l  GD+vdrg+++ e + l +++++++p+++ ll+GNHe   
  gi|557694469|ref|YP_008797523.1|  29 LLVVGDTH-----GDVDSTKKALEYADEKGAVAVFL--GDYVDRGPYQIENITLlFERKLAEPNRLLLLRGNHEtlt 98 
                                       59******.....**********9997777778888..*******66666666659******************544 PP

                                       .....CHHHHHHHHHHHHHHH.....HHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEE...THHHHHHHHHH CS
                       Metallophos  76 .....gfeeellnkygylgif.....sepwrsdaevfnnlplaslgsgs.lkvlllhGgspel...lvsldklgsln 138
                                            g       + +           ++++++ + f  lp a        +v+++hGg   +   l+ ++++++l+
  gi|557694469|ref|YP_008797523.1|  99 mntyyG-------FLDT---VtrrhgLKTYQQFLKAFAQLPYAL----RwRDVFFVHGG---IargLHMVEEVEKLE 158
                                       433333.......3222...244355778888899999999998....4468*******...44469********** PP

                                       HSCHHHHCC...HHHHHHHHHHTTCSEEEEEESSESS..........CSSSCSCCHHHHHHHHHHTTESEEEEESSS CS
                       Metallophos 139 leleapepg...dewlkdlekrekadwvivlgHsply..........rgsgylfgdealedllkkygvdlvisGHtH 202
                                       +  + pe+    +++++d                p++           g+  +fg++++  + +++g+ l i++H+ 
  gi|557694469|ref|YP_008797523.1| 159 RGEDDPEHPiafQLLWND----------------PHPgvkgfaeserGGGALYFGEDVFTSFMEQNGLRLLIRSHQP 219
                                       *999999999********................2223345556667799*************************97 PP

                                       S CS
                       Metallophos 203 v 203
                                        
  gi|557694469|ref|YP_008797523.1| 220 M 220
                                       5 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 !   25.1   0.0   1.8e-09   1.6e-05       3     105 ..      29     151 ..      28     170 .. 0.64

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.8e-09
                     Metallophos_2   3 laiiSDlHsnldaleavlealkevgvdaiihaGDl.....eeeepevleellela.....pvlaVrGNnD....... 62 
                                       l+++ D+H+ +d ++++le ++e      +++GD+     +  + e +  l+e++     ++l  rGN++       
  gi|557694469|ref|YP_008797523.1|  29 LLVVGDTHGDVDSTKKALEYADEK-GAVAVFLGDYvdrgpY--QIENITLLFERKlaepnRLLLLRGNHEtltmnty 102
                                       799*****************9999.4566899**8544222..22333333333356778**********9998766 PP

                     Metallophos_2  63 ....eevveedvlreaaelgtdlpeeaelelagekvlliHgdpl...gvk 105
                                           ++v +++ l+  +++ +++ ++    l+ ++v+++Hg      +  
  gi|557694469|ref|YP_008797523.1| 103 ygflDTVTRRHGLKTYQQFLKAF-AQLPYALRWRDVFFVHGGIArglHMV 151
                                       55555555555555555555555.44444445556*****9733555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1923.60
//
Query:       gi|557694470|ref|YP_008797524.1|  [L=292]
Description: metallo-beta-lactamase protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   55.2   3.1    1.3e-14   54.7   3.1    1.2  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.1e-05   25.1   1.0      2e-05   24.2   1.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.076   12.4   0.0       0.39   10.1   0.0    1.9  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 !   54.7   3.1   2.2e-18   1.3e-14       5     188 ..      20     206 ..      17     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.7 bits;  conditional E-value: 2.2e-18
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHC CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapa 81 
                                       +v +yl+  + ++ L+D+G+s+ a+      a+++ +  ++d++i TH HlDH G++  l+e+++ + ++ +  a +
  gi|557694470|ref|YP_008797524.1|  20 IVACYLV-MGRKTALVDAGYSSTADVVI--NALKEMGVTRLDYIIPTHVHLDHSGAVWRLAEHFKEAEVIAHQRAVK 93 
                                       6789**9.9******************8..599999******************************99999999999 PP

                                       CHCHHHHHHHHHCCHH.........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEEC CS
                       Lactamase_B  82 lfmeeaddaasrkgll.........lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftG 149
                                       ++ +  +  as  + +            +++ + ++   ++++ ++g+++l ++++pgh ++++ v   +g+v +t 
  gi|557694470|ref|YP_008797524.1|  94 HLVDPSKLVASVLEVYgpdilqvfgEVKPVEEHRVHSAADGETLVLGDVELTFIYTPGHAPHQFTVAVSDGSV-ITA 169
                                       99999988888888889********999**************************************9999986.789 PP

                                       TTTS..SHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHH CS
                       Lactamase_B 150 Dall..agetgridltlrgaevrdpsdaekyldsllklagl 188
                                       Da++   +  + i +    +++++  d  + +dsl kl +l
  gi|557694470|ref|YP_008797524.1| 170 DAVPikYPGKPFIIP----STPPPSFDLNQFIDSLAKLGKL 206
                                       998844444444444....6677777777777666666665 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 !   24.2   1.0   3.4e-09     2e-05       4     115 ..      33     154 ..      30     173 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.4e-09
                                       EES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   4 LiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                       L+Dag +  +     al    +   + ++d ++ th H DH   +  l+e + k+++++a+++  ++l + ++  a+
  gi|557694470|ref|YP_008797524.1|  33 LVDAGYSSTADvVINAL----KEMGVTRLDYIIPTHVHLDHSGAVWRLAE-HFKEAEVIAHQRAVKHLVDPSKLVAS 104
                                       78888884444333333....344689***************99999999.677799***********999999998 PP

                                       HTT................TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE-- CS
                     Lactamase_B_2  80 eee................pavnvheldwgesfelgdggleitatparhksg 115
                                         e                 + +vh  + ge++ lgd++l++  tp  + ++
  gi|557694470|ref|YP_008797524.1| 105 VLEvygpdilqvfgevkpvEEHRVHSAADGETLVLGDVELTFIYTP--GHAP 154
                                       8888999999999999887778888888999999997665555554..4444 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 ?   10.1   0.0   6.5e-05      0.39       8      61 ..      31      82 ..      25      93 .. 0.81
   2 ?   -0.4   0.0      0.11   6.5e+02      50      87 ..     252     288 ..     242     292 .] 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.5e-05
                     Lactamase_B_6  8 kiLlDvGwdeskvslesalkelekv.iptvdliLLshatlehlGayallyakfks 61
                                      + L+D G +++ +    +++ l+++ + ++d i+ +h  l+h Ga   l  +fk+
  gi|557694470|ref|YP_008797524.1| 31 TALVDAGYSSTADV---VINALKEMgVTRLDYIIPTHVHLDHSGAVWRLAEHFKE 82
                                      569******98543...5666666559******************9888887764 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.11
                     Lactamase_B_6  50 GayallyakfksklllnipvyatlpvvkLGrvslldly 87 
                                       G y+ l  k +++ + ++p+ya    vk+ ++ l+d++
  gi|557694470|ref|YP_008797524.1| 252 GIYMALERKLETEAGEKLPIYAQN-LVKISSMGLYDYF 288
                                       446677777888889999999864.4566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2166.12
//
Query:       gi|557694471|ref|YP_008797525.1|  [L=309]
Description: malate dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  133.4   0.6    9.1e-39  132.8   0.6    1.3  1  Ldh_1_N         lactate/malate dehydrogenase, NAD binding dom
    1.6e-23   83.5   0.0    2.8e-23   82.7   0.0    1.3  1  Ldh_1_C         lactate/malate dehydrogenase, alpha/beta C-te
     0.0037   16.9   0.0     0.0082   15.7   0.0    1.5  1  Glyco_hydro_4   Family 4 glycosyl hydrolase
  ------ inclusion threshold ------
       0.23   11.0   2.5       0.43   10.1   1.3    1.9  3  DAO             FAD dependent oxidoreductase
       0.44   10.1   4.0        1.5    8.3   2.3    2.5  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,


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 !  132.8   0.6   2.5e-42   9.1e-39       3     141 .]       4     141 ..       3     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 2.5e-42
                                       EEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEE.SSGGGGTTESEEEE--S CS
                           Ldh_1_N   3 vavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvse.keeealkdadvvvitag 78 
                                       ++vvG+ G +G s al++a ++l+d ++L+D+ +   +G+aldl+h+ ++l  +v v++ +++ +++++dvvv+tag
  gi|557694471|ref|YP_008797525.1|   4 ITVVGS-GRVGTSAALQIALRELGD-IVLVDVIQGLPQGEALDLNHACAILDLDVDVKGsNDYRDIQGSDVVVVTAG 78 
                                       89****.******************.*******************************999***************** PP

                                       -SS-TTTTHHHHHHHHHHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
                           Ldh_1_N  79 vprkpGetRddLlkvNakIvkeiveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                                        +rkp +tR+dLl +Na+I+ke+ ++i ++ap+ +v+vv+NP d++++v++ ++g++ +rv+g
  gi|557694471|ref|YP_008797525.1|  79 LTRKPDMTRLDLLLKNAEIIKEVSRHIRENAPKSKVIVVTNPLDVMAYVAYRVTGFESRRVMG 141
                                       *************************************************************98 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 !   82.7   0.0   7.8e-27   2.8e-23       3     162 ..     146     303 ..     145     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 7.8e-27
                                       HHHHHHHHHHHHHHTS-GGGEE--EEBSSST.......ETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHHHHHH CS
                           Ldh_1_C   3 LDivRaktflaekagvtprsvkvtViGgHsg.......vtiipllsqvkellklsekqleeliervqnggdevvkak 72 
                                       LD+ R ++++++k +v+ rs + +ViG+H++        t ++ ++    ++ l+ek  +e++e +++ g+e++  k
  gi|557694471|ref|YP_008797525.1| 146 LDVGRYRYLIRNKLNVSYRSIRGMVIGEHGDsmvllpsHTYVGTEAL---SKYLDEKTTAEIVEATRKMGAEIIRLK 219
                                       9******************************9877766555555333...456899********************* PP

                                       TTSSSS-HHHHHHHHHHHHHHHTTHTEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHH CS
                           Ldh_1_C  73 kGagsatlsmAvAgakfveallrdtkeilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfeeekl 149
                                           sa+ + ++ +a +vea+l+d k+i+++++ l+g++g kd   +y  +P+vlg++Gvekvle  +l+++e  k+
  gi|557694471|ref|YP_008797525.1| 220 G--WSAHHAPGAGVAVMVEAILKDQKSIIPTSTLLTGQYGEKD---VYAVLPCVLGAEGVEKVLE-PSLTPEELAKF 290
                                       6..9***************************************...9******************.89********* PP

                                       HHHHHHHHHHHHH CS
                           Ldh_1_C 150 eksvkeLkkeiek 162
                                       ++svk +++ +++
  gi|557694471|ref|YP_008797525.1| 291 RESVKIIRNAVNQ 303
                                       *******998875 PP

>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.3e-06    0.0082     119     160 ..      93     134 ..      89     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.3e-06
                                       HHHHHHHHHHHHHHHH-TTSEEEE-SSSHHHHHHHHHHHSTT CS
                     Glyco_hydro_4 119 rtipvlleIakdieelcPdawvlnytNPaavvteallrlvpn 160
                                       ++ +++ e+ ++i+e +P++ v+  tNP+ v++ + +r++++
  gi|557694471|ref|YP_008797525.1|  93 KNAEIIKEVSRHIRENAPKSKVIVVTNPLDVMAYVAYRVTGF 134
                                       5667899******************************99864 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.3   0.00012      0.43       2      27 ..       4      32 ..       4      40 .. 0.90
   2 ?   -2.3   0.0       0.7   2.5e+03     194     203 ..      71      80 ..      49     139 .. 0.63
   3 ?   -2.3   0.0      0.72   2.6e+03     263     289 ..     185     209 ..     151     235 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00012
                                      EEEECTSHHHHHHHHHHHHT..T.EEEEE CS
                               DAO  2 vviiGGGiiGlstAyeLarr..g.Vtlle 27
                                      + ++G+G +G s+A++ a r  g ++l++
  gi|557694471|ref|YP_008797525.1|  4 ITVVGSGRVGTSAALQIALRelGdIVLVD 32
                                      78****************98566999987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.7
                                       EEEEE--GGG CS
                               DAO 194 davVnaaGaw 203
                                       d vV++aG+ 
  gi|557694471|ref|YP_008797525.1|  71 DVVVVTAGLT 80 
                                       6677777754 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.72
                                       EEEEESSEEETTCSSTSCSHHHHHHHH CS
                               DAO 263 vlvGgtadeesgdddpevdeedidell 289
                                       ++vG++a   s++ d ++++e +++ +
  gi|557694471|ref|YP_008797525.1| 185 TYVGTEA--LSKYLDEKTTAEIVEATR 209
                                       5666655..444444344444444333 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 ?    8.3   2.3   0.00042       1.5       3     119 ..       4     117 ..       2     128 .. 0.72
   2 ?   -2.3   0.0      0.79   2.8e+03     104     126 ..     232     254 ..     230     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00042
                                       EEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-S CS
                    UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeig.hevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveead 78 
                                       i+v+G+G vG   a+ +a +   ++++vD+    ++ l +g+      +L++  +    +  +++++d++  ++ +d
  gi|557694471|ref|YP_008797525.1|   4 ITVVGSGRVGTSAALQIALRElGDIVLVDV----IQGLPQGEAL----DLNHACAILDLDVDVKGSNDYRD-IQGSD 71 
                                       99****************998789*****8....7778887764....44444444444556888888887.88888 PP

                                       EEEE-----B-TTTTCB-T.....HHHHHHHHHHHHHHHCEEEEEE CS
                    UDPG_MGDP_dh_N  79 vifiaVgTPskkkgkaaDl.....kyvesaarsiaealkkgkvvvv 119
                                       v++++ g   k +    Dl     + +++++r+i e + k kv+vv
  gi|557694471|ref|YP_008797525.1|  72 VVVVTAGLTRKPDMTRLDLllknaEIIKEVSRHIRENAPKSKVIVV 117
                                       8888888777765555565332224566666666666666777776 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.79
                                       HHHHHHHHHCEEEEEE-S---TT CS
                    UDPG_MGDP_dh_N 104 arsiaealkkgkvvvvkSTvpvg 126
                                       a +++ +lk++k ++  ST   g
  gi|557694471|ref|YP_008797525.1| 232 AVMVEAILKDQKSIIPTSTLLTG 254
                                       56788899999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2223.81
//
Query:       gi|557694472|ref|YP_008797526.1|  [L=44]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   27.2   0.3    4.3e-06   26.9   0.3    1.2  1  zf-C2H2        Zinc finger, C2H2 type
    2.9e-05   24.2   0.0    3.4e-05   24.0   0.0    1.1  1  zf-Di19        Drought induced 19 protein (Di19), zinc-bindin
    3.3e-05   24.4   0.3    4.2e-05   24.0   0.3    1.2  1  zf-C2H2_4      C2H2-type zinc finger
    0.00021   21.5   0.1     0.0003   21.0   0.1    1.3  1  zf-C2H2_jaz    Zinc-finger double-stranded RNA-binding
    0.00022   21.5   3.6     0.0058   17.0   1.8    2.1  2  zf-H2C2_2      Zinc-finger double domain
    0.00029   20.5   0.4    0.00052   19.7   0.4    1.5  1  zf-H2C2_5      C2H2-type zinc-finger domain
     0.0086   16.1   0.1     0.0099   15.9   0.1    1.2  1  zf-C2H2_6      C2H2-type zinc finger
  ------ inclusion threshold ------
       0.01   15.5   0.0       0.01   15.5   0.0    1.0  1  DUF2225        Uncharacterized protein conserved in bacteria 
      0.017   14.3   0.0      0.017   14.3   0.0    1.0  1  Actin_micro    Putative actin-like family
      0.022   14.7   0.3      0.028   14.3   0.3    1.2  1  PyrI_C         Aspartate carbamoyltransferase regulatory chai
      0.026   14.4   0.0      0.029   14.2   0.0    1.1  1  zf-C2H2_9      C2H2 type zinc-finger (1 copy)
       0.05   13.5   0.1      0.058   13.2   0.1    1.2  1  Rad50_zn_hook  Rad50 zinc hook motif
      0.055   13.9   0.0       0.07   13.6   0.0    1.1  1  zf-C2HE        C2HE / C2H2 / C2HC zinc-binding finger
       0.06   13.1   0.1      0.082   12.7   0.1    1.3  1  zinc_ribbon_5  zinc-ribbon domain
       0.06   13.7   0.1      0.069   13.5   0.1    1.1  1  zf-C2H2_2      C2H2 type zinc-finger (2 copies)


Domain annotation for each model (and alignments):
>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.3   3.6e-09   4.3e-06       1      23 []       8      31 ..       8      31 .. 0.97

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.6e-09
                                      EEETTTTEEESSHHHHHHHHHC.C CS
                           zf-C2H2  1 ykCpdCgksFkrksnLkrHirt.H 23
                                      ++Cp+C+ +Fk+  +L +Hi + H
  gi|557694472|ref|YP_008797526.1|  8 FRCPYCDSVFKTEAELSKHIDRiH 31
                                      8*******************9999 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 !   24.0   0.0   2.9e-08   3.4e-05       2      27 ..       7      33 ..       6      36 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.9e-08
                           zf-Di19  2 sftCPyCgk.eltvkeLveHvedeHrv 27
                                      +f CPyC     t++eL +H++  H  
  gi|557694472|ref|YP_008797526.1|  7 EFRCPYCDSvFKTEAELSKHIDRIHIG 33
                                      8********557999********9975 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 !   24.0   0.3   3.5e-08   4.2e-05       1      24 []       8      31 ..       8      31 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.5e-08
                         zf-C2H2_4  1 fkCpiCgksFsskkaLlrHlkthH 24
                                      f+Cp+C+ +F++  +L++H+ + H
  gi|557694472|ref|YP_008797526.1|  8 FRCPYCDSVFKTEAELSKHIDRIH 31
                                      89*****************99877 PP

>> zf-C2H2_jaz  Zinc-finger double-stranded RNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   2.5e-07    0.0003       2      21 ..       8      27 ..       7      28 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.5e-07
                                      CBBTTTTBBBSSHHHHHCCT CS
                       zf-C2H2_jaz  2 fYCvlCdKyFksenaldnHl 21
                                      f C++Cd  Fk+e  l +H+
  gi|557694472|ref|YP_008797526.1|  8 FRCPYCDSVFKTEAELSKHI 27
                                      99*****************8 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 !   17.0   1.8   4.8e-06    0.0058      12      26 .]       5      19 ..       2      19 .. 0.86
   2 ?    4.7   0.0     0.037        45       2      11 ..      23      33 ..      22      38 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.8e-06
                         zf-H2C2_2 12 ekpyeCplCdkaFkt 26
                                      +k++ Cp+Cd +Fkt
  gi|557694472|ref|YP_008797526.1|  5 KKEFRCPYCDSVFKT 19
                                      577**********97 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.037
                         zf-H2C2_2  2 LrrHi.rkHtg 11
                                      L++Hi r H g
  gi|557694472|ref|YP_008797526.1| 23 LSKHIdRIHIG 33
                                      99**9557987 PP

>> zf-H2C2_5  C2H2-type zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.4   4.4e-07   0.00052       1      24 [.       8      31 ..       8      33 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.4e-07
                         zf-H2C2_5  1 YKCsqCDYstawksnLkRHlrrkH 24
                                      ++C++CD + ++ ++L +H+ r+H
  gi|557694472|ref|YP_008797526.1|  8 FRCPYCDSVFKTEAELSKHIDRIH 31
                                      8*********************** PP

>> zf-C2H2_6  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   8.3e-06    0.0099       2      20 ..       8      26 ..       7      31 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.3e-06
                         zf-C2H2_6  2 heCsvCsksFpslqaLggH 20
                                      ++C++C+ +F++  +L +H
  gi|557694472|ref|YP_008797526.1|  8 FRCPYCDSVFKTEAELSKH 26
                                      89**********9999988 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   8.8e-06      0.01       3      25 ..       5      27 ..       3      40 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 8.8e-06
                           DUF2225  3 kkkieCPvCeekfkkkkvksssl 25
                                      kk+ +CP+C+++fk+++  s+++
  gi|557694472|ref|YP_008797526.1|  5 KKEFRCPYCDSVFKTEAELSKHI 27
                                      799************99888876 PP

>> Actin_micro  Putative actin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.4e-05     0.017     221     249 ..       3      32 ..       1      40 [. 0.91

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.4e-05
                       Actin_micro 221 kekkefsCkvCdvkfev.ekiseHllkkHi 249
                                        ekkef+C  Cd  f++  ++s+H+ + Hi
  gi|557694472|ref|YP_008797526.1|   3 SEKKEFRCPYCDSVFKTeAELSKHIDRIHI 32 
                                       5789************999********998 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 ?   14.3   0.3   2.3e-05     0.028      28      46 ..       2      20 ..       1      21 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.3e-05
                                      ETTTTEEEETTT--EEEHH CS
                            PyrI_C 28 dkekvklkCkYCekeisee 46
                                      ++ek +++C YC+ +++ e
  gi|557694472|ref|YP_008797526.1|  2 SSEKKEFRCPYCDSVFKTE 20
                                      57899*********99876 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 ?   14.2   0.0   2.5e-05     0.029       3      21 ..       9      27 ..       7      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                      B-TTT--B-SSHHHHHHHH CS
                         zf-C2H2_9  3 lCPvCevkfnswkdlseHi 21
                                      +CP C   f++ ++ls+Hi
  gi|557694472|ref|YP_008797526.1|  9 RCPYCDSVFKTEAELSKHI 27
                                      6*****************9 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 ?   13.2   0.1   4.9e-05     0.058      16      34 ..       3      23 ..       1      31 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.9e-05
                                      TT-SE.E-TTT--EE-HHH.H CS
                     Rad50_zn_hook 16 keakg.cCPlCgReldeeh.r 34
                                      +e+k+ +CP C++ + +e   
  gi|557694472|ref|YP_008797526.1|  3 SEKKEfRCPYCDSVFKTEAeL 23
                                      678889**********99755 PP

>> zf-C2HE  C2HE / C2H2 / C2HC zinc-binding finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.9e-05      0.07      34      59 ..       4      28 ..       2      30 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.9e-05
                           zf-C2HE 34 lktpLkCtrCganfgnkfpkLKeHLe 59
                                       k++++C +C+ + +++ ++L +H++
  gi|557694472|ref|YP_008797526.1|  4 EKKEFRCPYCD-SVFKTEAELSKHID 28
                                      5899*******.************86 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   6.9e-05     0.082       4      14 ..       9      19 ..       7      26 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
                     zinc_ribbon_5  4 rCpdCdtkFkl 14
                                      rCp Cd+ Fk 
  gi|557694472|ref|YP_008797526.1|  9 RCPYCDSVFKT 19
                                      8********96 PP

>> zf-C2H2_2  C2H2 type zinc-finger (2 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   5.7e-05     0.069      49      71 ..       6      28 ..       2      34 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                         zf-C2H2_2 49 ekleClyCekefkslealreHmk 71
                                      ++++C yC++ fk+ ++l +H+ 
  gi|557694472|ref|YP_008797526.1|  6 KEFRCPYCDSVFKTEAELSKHID 28
                                      569******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 331.03
//
Query:       gi|557694473|ref|YP_008797527.1|  [L=448]
Description: peptidase M20 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  115.4   0.0    3.6e-33  115.0   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    8.2e-17   61.1   0.0    1.4e-16   60.3   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.016   14.9   0.0    1.2  1  Peptidase_M28  Peptidase family M28
       0.13   12.9   0.0       0.41   11.4   0.0    1.8  1  dsrm           Double-stranded RNA binding motif


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 !  115.0   0.0   7.9e-37   3.6e-33       1     206 [.      82     439 ..      82     440 .. 0.90

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 7.9e-37
                                       EEEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTT CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   1 llgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrg 76 
                                       ++++H+Dv+p+e+ ++wtt pf++ +++GklyGrGa+d+kg ++a l+a+ al  + ++++ ++++l+++ EE+g+ 
  gi|557694473|ref|YP_008797527.1|  82 MFYNHYDVQPAEPLEKWTTpPFTPVVRNGKLYGRGAADNKGNIAARLAAVDALLSTLGELPVNLKFLIEGGEEVGSP 158
                                       79********88889**********************************************************9889 PP

                                       HHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                     Peptidase_M20  77 Gakallegleerekvdavfelhieepgileagklaigvv...................................... 115
                                       G ++++     + + + + +  i+e g+ ++ + ++ ++                                      
  gi|557694473|ref|YP_008797527.1| 159 GLEKFVR----ENRDKLFADGCIWEYGYVSRSG-SPVIYlgqkgmlyvemeiqgpasdlhsswgavvenrawrlvqa 230
                                       9999999....5566666666667677776555.4555588************************************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|557694473|ref|YP_008797527.1| 231 lstmrgpdgrvtvdgfyddvvyegeellekldisefspphkllksaeknplrqlfleptinlnglyagyigpgskti 307
                                       ***************************************************************************** PP

                                       ....................................EEEEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEE CS
                                       ....................................xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 116 ....................................kvevelleggapvtln.dsplvkalaeaaeelfgekveliv 155
                                                                           +++++ ++++++++++ d+ l k++a++a  ++g+    i+
  gi|557694473|ref|YP_008797527.1| 308 ipakasakldirlvprqtpekikqlllqhlekngltDIKLHIHQAYPAARTSpDNFLPKLVADTAATAYGKPSIIIP 384
                                       **********************************97699998899999999999999**********9996666667 PP

                                       ESSSBHTHHHH.TTT...EEE.EEEE.SSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxx.xxx...xxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 156 sgpggtdarff.agi...ptv.mifg.pgsglaHspnEyvdledlekgikvlarlle 206
                                       sg ++  +  +   i   p+v  ++g  g +  H+p+E+++l d+ + ik +a +++
  gi|557694473|ref|YP_008797527.1| 385 SGAASGPMY-ViTDIletPCVsTGCGyYG-SSPHGPDENIRLTDFTANIKHIALIML 439
                                       774444444.4555555599966688555.999**************9999887765 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   3.2e-20   1.4e-16       2     105 ..     194     341 ..     193     345 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 3.2e-20
                                       EB-EEEEEEEE..EE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.............................. CS
                         M20_dimer   2 ghkGlaggkit..vkgkagHsgapgagaNAieklarllaeledeegdia............................ 48 
                                       g+kG++ ++++      ++Hs+ +  ++N  + l+++l+ ++  +g+++                            
  gi|557694473|ref|YP_008797527.1| 194 GQKGMLYVEMEiqGPASDLHSSWGAVVENRAWRLVQALSTMRGPDGRVTvdgfyddvvyegeellekldisefspph 270
                                       8999999999933445689********************************************************** PP

                                       .............TCCTCCCCCEECCE-C....CCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTSCC CS
                         M20_dimer  49 ..........eerslprttlnvtgiegGs....aknvipdeaeakidiRllpgedpeevleeieeilekea 105
                                                 +++ + ++t+n++g+++G+    +k++ip++a+ak+diRl+p ++pe++++ + ++lek +
  gi|557694473|ref|YP_008797527.1| 271 kllksaeknpLRQLFLEPTINLNGLYAGYigpgSKTIIPAKASAKLDIRLVPRQTPEKIKQLLLQHLEKNG 341
                                       ********************************************************************976 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   3.5e-06     0.016       4      84 ..      71     166 ..      69     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.5e-06
                                       EEESTTCESEEEEEEEE--B-TTT...............TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEE CS
                     Peptidase_M28   4 atlegkatdevlllgAHyDsvgvg...............rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkrgvr 64 
                                       +t++ +a   +l++  HyD  + +               +g+    GA Dn   +aa L  + +l +   ++  +++
  gi|557694473|ref|YP_008797527.1|  71 GTINYEA-HATLMFYNHYDVQPAEplekwttppftpvvrNGKlYGRGAADNKGNIAARLAAVDALLSTLGELPVNLK 146
                                       5677777.789**********9999999*99999998885666778*******************9988899***** PP

                                       EEEESSCSGSSHHHHHHHHH CS
                     Peptidase_M28  65 flffdaEEagllGSkafaka 84 
                                       fl+ ++EE g  G ++f+++
  gi|557694473|ref|YP_008797527.1| 147 FLIEGGEEVGSPGLEKFVRE 166
                                       **********9999999952 PP

>> dsrm  Double-stranded RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.1e-05      0.41      37      64 ..     106     134 ..      80     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.1e-05
                                       EEETTEEEEEEEESSH.HHHHHHHHHHHH CS
                              dsrm  37 vkvngklygsGvgsnK.KeAeqsAAedal 64 
                                       v+ ngklyg+G + nK + A  +AA+dal
  gi|557694473|ref|YP_008797527.1| 106 VVRNGKLYGRGAADNKgNIAARLAAVDAL 134
                                       3448************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3114.32
//
Query:       gi|557694474|ref|YP_008797528.1|  [L=300]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   34.4  26.8    3.9e-06   26.9   4.8    2.5  3  VIT1          VIT family
    0.00033   21.1   8.8     0.0064   16.9   8.8    2.1  1  Rubrerythrin  Rubrerythrin
    0.00098   19.1   1.4     0.0016   18.4   0.4    1.7  2  Ferritin      Ferritin-like domain
      0.007   16.0   0.0      0.014   15.1   0.0    1.4  1  DUF4249       Domain of unknown function (DUF4249)
  ------ inclusion threshold ------
      0.048   13.4   1.2       0.16   11.7   1.2    1.9  1  COQ7          Ubiquinone biosynthesis protein COQ7
      0.061   13.7   6.6       0.12   12.8   6.6    1.5  1  MFS_MOT1      Molybdate transporter of MFS superfamily
      0.089   12.3   1.9        4.9    6.6   2.0    2.3  2  E1-E2_ATPase  E1-E2 ATPase
        0.1   13.0   1.2       0.63   10.4   1.2    2.3  1  ERGIC_N       Endoplasmic Reticulum-Golgi Intermediate Compar
       0.24   10.4   2.8       0.32   10.0   2.8    1.2  1  PalH          PalH/RIM21
       0.74    8.0  11.4        1.1    7.4  11.4    1.2  1  DUF2070       Predicted membrane protein (DUF2070)
        4.9    7.8   5.8         20    5.8   1.5    2.3  2  TMEM141       TMEM141 protein family
        8.1    6.3   8.1        1.4    8.8   0.3    3.4  3  LapA_dom      Lipopolysaccharide assembly protein A domain
        8.7    6.2   8.2        8.9    6.2   1.5    2.8  2  Adeno_E3_CR2  Adenovirus E3 region protein CR2


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 ?   -3.6   0.2       6.1   8.4e+03     102     124 ..     105     127 ..      93     138 .. 0.50
   2 !   20.3   8.1     3e-07   0.00041       6      62 ..     149     204 ..     146     208 .. 0.83
   3 !   26.9   4.8   2.8e-09   3.9e-06     132     214 ..     204     286 ..     200     287 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.1
                              VIT1 102 evaaellknpdallelmlreelg 124
                                       +v++++ ++++  +e  lr+e++
  gi|557694474|ref|YP_008797528.1| 105 KVINKVEEQHRGKVENFLRDEEE 127
                                       44444444444444433333322 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 3e-07
                              VIT1   6 lGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdl 62 
                                       lG++D ++ + ++ aG  +++ +s+ +  +aGl   +A +iSMg+ +Yl +kse  +
  gi|557694474|ref|YP_008797528.1| 149 LGLSDSIIEVSGVHAGFLGVT-SSTLIAGVAGLVVGFAASISMGVAAYLKAKSELRQ 204
                                       8*****************766.36666666777777899**************9765 PP

  == domain 3  score: 26.9 bits;  conditional E-value: 2.8e-09
                              VIT1 132 asplkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAaa 208
                                       +++++++l++++ +++  +i  lpy++++++ +a+ +s+a++++    f +  a++ ++s  +++l+++l+ +++aa
  gi|557694474|ref|YP_008797528.1| 204 QKSFTSGLITGIVYILSTIILALPYFLTHDMLEAFTASVALAIILASSFTYYVAVVNETSFKREVLENTLLIMGTAA 280
                                       56799************************************************************************ PP

                              VIT1 209 aaylig 214
                                       a++l+g
  gi|557694474|ref|YP_008797528.1| 281 ATFLFG 286
                                       ***988 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   8.8   4.6e-06    0.0064      10     135 ..      20     134 ..      18     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.6e-06
                                       HHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHH.HH CS
                      Rubrerythrin  10 EssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttak.nL 85 
                                       E+ ++ +Y+ela++ +  ++q +e++ +l+e+E+eH ++ + l  + +p            ++ +   +l+++   +
  gi|557694474|ref|YP_008797528.1|  20 EYFDHIVYRELARRER--NGQRREMLVKLSEMEKEHYEFWRTLAPDQRPVFS---------KLRFWFIMLLRRLlGI 85 
                                       6668889******999..99****************9999999988555555.........6666666666655489 PP

                                       HHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  86 eeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrk 135
                                       + +i+  +  e+e++  y ++ +k++++ ++  +++  ++E++He++l++
  gi|557694474|ref|YP_008797528.1|  86 TFVIKFLERHETEVINRYRKVINKVEEQ-HRGKVENFLRDEEEHEKTLQN 134
                                       9**********************88666.*****************9986 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.9     4e+03      82     129 ..      40      54 ..      24      62 .. 0.52
   2 !   18.4   0.4   1.2e-06    0.0016      85     137 ..      89     137 ..      83     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH CS
                          Ferritin  82 eevleaalehekkvteslrelielaeeegDpatadfledfleeqeehe 129
                                       +e+l ++ e+ek                                 eh 
  gi|557694474|ref|YP_008797528.1|  40 REMLVKLSEMEK---------------------------------EHY 54 
                                       344444444444.................................443 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  85 leaalehekkvteslrelielaeeegDpatadfledfleeqeehewelealle 137
                                       ++ +  he++v++++r++i+ +ee+     +   e+fl+++eehe++l+++++
  gi|557694474|ref|YP_008797528.1|  89 IKFLERHETEVINRYRKVINKVEEQ----HRGKVENFLRDEEEHEKTLQNQID 137
                                       566678*****************97....6777788899***********997 PP

>> DUF4249  Domain of unknown function (DUF4249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.9e-06     0.014     208     250 ..      15      61 ..       3      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.9e-06
                           DUF4249 208 fipfdDskfngkey....e.eekpektslrvrlysiseeaYrYlktlk 250
                                       f+  dD++f++  y    + e++ + +++ v+l+ + +e Y++++tl+
  gi|557694474|ref|YP_008797528.1|  15 FF-RDDEYFDHIVYrelaRrERNGQRREMLVKLSEMEKEHYEFWRTLA 61 
                                       44.67789999988****7799999*********************87 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.2   0.00012      0.16      28     139 ..      33     131 ..      20     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                              COQ7  28 akkdpelkpllkemleqEkeHlatfeellkerrvrpslllplwkvagfalGaltallGkeaamacteavEtvigeHY 104
                                       ++++ + +++l +  e EkeH++++++l  ++r   s l        +++ +l  llG   ++ + e  Et++ + Y
  gi|557694474|ref|YP_008797528.1|  33 RERNGQRREMLVKLSEMEKEHYEFWRTLAPDQRPVFSKL------RFWFIMLLRRLLGITFVIKFLERHETEVINRY 103
                                       35666778999999****************994333333......3344557899********************** PP

                              COQ7 105 neqlreleeleeeedkelleiikqfrddEleHldt 139
                                       ++ ++++ee       + +  +++f  dE eH++t
  gi|557694474|ref|YP_008797528.1| 104 RKVINKVEE-------QHRGKVENFLRDEEEHEKT 131
                                       ******995.......5567778888888888765 PP

>> MFS_MOT1  Molybdate transporter of MFS superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   6.6   8.9e-05      0.12      27     108 ..     166     251 ..     142     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.9e-05
                          MFS_MOT1  27 lsltalllsvGlmnlltglfggvPmchgAgglaaqyrfgartgaagillGlvllllgltg.....llerllrliPks 98 
                                       l +t+  l++G++ l++g++  + m  +A++l a+ +  +++ ++g+++G+v++l ++++     l +++l+++  s
  gi|557694474|ref|YP_008797528.1| 166 LGVTSSTLIAGVAGLVVGFAASISMG-VAAYLKAKSELRQKSFTSGLITGIVYILSTIILalpyfLTHDMLEAFTAS 241
                                       44788889999999999999999996.79999999677****************99999988888999999999999 PP

                          MFS_MOT1  99 vlgglllgaG 108
                                       v  +++l++ 
  gi|557694474|ref|YP_008797528.1| 242 VALAIILASS 251
                                       9999998865 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0      0.03        41      84     146 ..     105     171 ..     101     196 .. 0.71
   2 ?    6.6   2.0    0.0035       4.9     106     158 ..     197     248 ..     183     259 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.03
                                       EEEE-TTTSTTTTTSTTS--------HHHHHHHH.HHHHHHHHHHHHHHHHHHS-STTTSSTT...H CS
                      E1-E2_ATPase  84 vVtatgedtelgkiarlveeakskktplqkkldk.lgkvlvpvvlliallvflialllgksla...e 146
                                       +V++ +e+   gk+ + ++++++ ++ lq+++d+ + +++ +++l ++  ++ +  ++ ++l     
  gi|557694474|ref|YP_008797528.1| 105 KVINKVEEQHRGKVENFLRDEEEHEKTLQNQIDEpILRYIGFIALGLSDSIIEVSGVHAGFLGvtsS 171
                                       68888999999*********************98466777888777776666666555555434433 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0035
                                       ----HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHH CS
                      E1-E2_ATPase 106 skktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaa 158
                                       ++k++l +k    ++ ++ +v +++ +++++ ++l+++  ea++ ++al+++ 
  gi|557694474|ref|YP_008797528.1| 197 KAKSELRQKSFT-SGLITGIVYILSTIILALPYFLTHDMLEAFTASVALAIIL 248
                                       455555555443.334677777888888888899999999*******999986 PP

>> 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 ?   10.4   1.2   0.00045      0.63       6      37 ..     194     225 ..     191     275 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00045
                                       XXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXX CS
                           ERGIC_N   6 afpKvpedltqktlsGgiislvcillilfLll 37 
                                       a+ K +++l+qk+++ g+i+ ++++l +++l 
  gi|557694474|ref|YP_008797528.1| 194 AYLKAKSELRQKSFTSGLITGIVYILSTIILA 225
                                       899*****************999999887764 PP

>> PalH  PalH/RIM21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   2.8   0.00023      0.32     177     261 ..     204     284 ..     147     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                              PalH 177 kekriiilvGlaliildtilsalllfskkfldalpalsylfelalvtlyaalviyYliskrkyilspkrmketilll 253
                                       ++  +  l++ ++ il+ti+ al+ f   + d+l+a+   +  al++++a++ +yY+    + +++ +   +t+l++
  gi|557694474|ref|YP_008797528.1| 204 QKSFTSGLITGIVYILSTIILALPYF--LTHDMLEAFTASV--ALAIILASSFTYYVAVVNETSFKREVLENTLLIM 276
                                       5556677899999*************..789******9866..5667889****************98889999988 PP

                              PalH 254 ilnllvil 261
                                         + +++l
  gi|557694474|ref|YP_008797528.1| 277 GTAAATFL 284
                                       77777765 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  11.4   0.00082       1.1      28     133 ..     163     269 ..     142     295 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00082
                           DUF2070  28 igllaflssklfgillfglp...alvaflltlpvlrilggrltykrslflalltelivviisllaillsallqalvl 101
                                       +g+l +      ++l+ g+      +a+ +   v  +l+ + +++++ f + l++ iv i+s++ ++l ++l+  +l
  gi|557694474|ref|YP_008797528.1| 163 AGFLGV----TSSTLIAGVAglvVGFAASISMGVAAYLKAKSELRQKSFTSGLITGIVYILSTIILALPYFLTHDML 235
                                       334443....34455666662113344445666888888889*****999999999999999999999998844444 PP

                           DUF2070 102 lalvls..lalvfalrllvlvavsdesllkavlp 133
                                        a+  s  la+++a ++  +vav +e+ +k  ++
  gi|557694474|ref|YP_008797528.1| 236 EAFTASvaLAIILASSFTYYVAVVNETSFKREVL 269
                                       4444443378888888888888776655544333 PP

>> TMEM141  TMEM141 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.8     0.031        42      18      60 ..     165     207 ..     153     217 .. 0.74
   2 ?    5.8   1.5     0.015        20      23      77 ..     204     260 ..     191     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.031
                           TMEM141  18 YaeCqsrallkGlatfvlgtaaafflqklvkkklpyplkwnll 60 
                                       ++   s +l+ G+a+ v+g+aa   +  ++  k + +l++  +
  gi|557694474|ref|YP_008797528.1| 165 FLGVTSSTLIAGVAGLVVGFAASISMGVAAYLKAKSELRQKSF 207
                                       55667999*************9987776666666665555554 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.015
                           TMEM141  23 srallkGlatfvlgtaa..afflqklvkkklpyplkwnllvsvvagsvasykvtsve 77 
                                        +++  Gl+t ++   +  +++l  ++ + +  +++ ++ ++++ +s ++y v+ v+
  gi|557694474|ref|YP_008797528.1| 204 QKSFTSGLITGIVYILStiILALPYFLTHDMLEAFTASVALAIILASSFTYYVAVVN 260
                                       57899999987765544114567789999999********************99775 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 ?    8.8   0.3     0.001       1.4      25      52 ..     174     205 ..     165     208 .. 0.70
   2 ?   -2.2   0.1       2.8   3.9e+03      17      26 ..     240     249 ..     234     255 .. 0.46
   3 ?    0.5   0.1      0.38   5.3e+02      25      44 ..     281     300 .]     278     300 .] 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.001
                          LapA_dom  25 vafgiGallgwllsl....wsylrlrrelrrl 52 
                                       +a ++G+++g+ +s+     +yl+ ++elr++
  gi|557694474|ref|YP_008797528.1| 174 IAGVAGLVVGFAASIsmgvAAYLKAKSELRQK 205
                                       55556666666666633337888******987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.8
                          LapA_dom  17 lpLsllllva 26 
                                       ++++l +++a
  gi|557694474|ref|YP_008797528.1| 240 ASVALAIILA 249
                                       3333333332 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.38
                          LapA_dom  25 vafgiGallgwllslwsylr 44 
                                       ++f++G +lg l++++ y+r
  gi|557694474|ref|YP_008797528.1| 281 ATFLFGEFLGNLFGIPGYFR 300
                                       79*************98886 PP

>> Adeno_E3_CR2  Adenovirus E3 region protein CR2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.5    0.0065       8.9       2      17 ..     170     185 ..     169     188 .. 0.90
   2 ?    2.9   0.7     0.069        95       7      26 ..     210     229 ..     206     230 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0065
                      Adeno_E3_CR2   2 PsstiaIivaVvvGla 17 
                                       +s++ia++++ vvG+a
  gi|557694474|ref|YP_008797528.1| 170 SSTLIAGVAGLVVGFA 185
                                       689***********97 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.069
                      Adeno_E3_CR2   7 aIivaVvvGlaiIiicmlyY 26 
                                       + i+++v  l++Ii+ + y+
  gi|557694474|ref|YP_008797528.1| 210 GLITGIVYILSTIILALPYF 229
                                       6699**********998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1420  (0.0792013); expected 358.6 (0.02)
Passed bias filter:                      787  (0.0438954); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2013.22
//
Query:       gi|557694475|ref|YP_008797529.1|  [L=390]
Description: saccharopine dehydrogenase (NAD+, L-lysine forming) [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-27   97.5   0.0    1.8e-27   97.1   0.0    1.1  1  Sacchrp_dh_C     Saccharopine dehydrogenase C-terminal domain
    1.9e-13   50.8   0.1    4.8e-13   49.5   0.0    1.7  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    8.9e-05   22.0   0.0     0.0063   15.9   1.5    2.3  2  ThiF             ThiF family
    0.00012   22.1   0.1     0.0004   20.5   0.1    1.8  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0003   20.2   0.1    0.00055   19.3   0.1    1.3  1  AlaDh_PNT_C      Alanine dehydrogenase/PNT, C-terminal domain
     0.0015   18.6   0.1     0.0026   17.9   0.1    1.3  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.014   15.3   0.1      0.024   14.5   0.1    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.055   13.7   0.5       0.13   12.6   0.5    1.6  1  TrkA_N           TrkA-N domain
       0.14   11.7   0.2       0.27   10.8   0.2    1.5  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family


Domain annotation for each model (and alignments):
>> Sacchrp_dh_C  Saccharopine dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.0   8.9e-31   1.8e-27       1     265 []     126     375 ..     126     375 .. 0.80

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 8.9e-31
                                       BTTTBHHHHHHHHHHHCCCHTTBECCCCCCCCCCCCECCCCESTTCEEESS-HHHHHHHCCSEEEEEETTEEEECT. CS
                      Sacchrp_dh_C   1 GldPGidhllamkaidevkakggkiesflsycgglpapeasdnplgYkfsWspegvlreltnpakvlengqvkevp. 76 
                                       G dPG+++++a +a d+++     ++s+++++g +   ++ + pl     +spe++++e+++p  v+ ng+ +++p 
  gi|557694475|ref|YP_008797529.1| 126 GEDPGLSNIYARYAADKLDR----VNSIKIRDGEYS--KSRKYPL--IALFSPEIFFDEILSPSLVYVNGRFRKLPa 194
                                       77**************9966....89********99..4444466..678**************************4 PP

                                       CCCSGCC.TCEEEC.C.CCCEECTTECEEECTHCHHHHHHC.SCSEEEEEEEE....EH.HHHHHHHHHH...TTT- CS
                      Sacchrp_dh_C  77 gsellkgakkpiyi.l.pglslegypnrdslpyeelyglpeaktlfrgtlryp....gf.sellkslkel...Glls 143
                                       +s       + +++ + +g +l  y    s+ +ee+y+lp    ++ + +ry        +el+++ k l   Gll+
  gi|557694475|ref|YP_008797529.1| 195 LSGY-----EVYEFpEpVG-KLSVY----SVNHEEVYTLP---RFIGKGVRYVdfklALaDELINATKLLkriGLLR 258
                                       4442.....3344423222.55555....7**********...455566666655586668888777777777**** PP

                                       -SCECCCCCCHHSTT.C.EHHHHHHHHCCHHCCCCTTEEEEEEEEEEEEEETTSEEEEEEE...EEEEEEEHH.... CS
                      Sacchrp_dh_C 144 eepkeealkawlseg.e.spldvlaalLekklalepgerDlvvlqhefgiesdgkkkekkt...stlvgydee.... 211
                                       + +    +++   +  + sp+dv+ al++k+ + +++ +  ++l +e+++  +gk     t   +tl+   e+    
  gi|557694475|ref|YP_008797529.1| 259 SRR----MRV---KDaSvSPRDVFFALMPKPSEIAKHIEGYASLVVEVEGMYKGKA---VTysiYTLMSH-EQankl 324
                                       *99....555...333568*****************************88877775...33246888853.334579 PP

                                       .SSSHHHHHHHHHHHHHHHHHHTTSCTSSEEEEGGGS.CHHHHHHHHHHHHHCT- CS
                      Sacchrp_dh_C 212 .gssamaktvGvpaaiaaklildgkikkrGvvtpeelvdpeiyeplleeLekeGi 265
                                        ++ a+++ +G+  a++a +i++g+i++ Gv  pe+l dp+   p++e+L ++Gi
  gi|557694475|ref|YP_008797529.1| 325 fRANATSYLTGTVPAVVASMIARGEIEDVGVRVPEQL-DPT---PVVERLTRHGI 375
                                       9************************************.886...*********98 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 !   49.5   0.0   2.4e-16   4.8e-13       1     129 [.       8     121 ..       8     122 .. 0.89
   2 ?   -3.5   0.0       5.9   1.2e+04      92     101 ..     229     238 ..     227     250 .. 0.71

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 2.4e-16
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                       vl++G G+vG+++a+ la ++ v   + vad ++ +l++++  +l++r+e++ +  +  ++    +++++dlv+n +
  gi|557694475|ref|YP_008797529.1|   8 VLVLGVGAVGEVIAKHLAGEGGV--SLSVADIDELRLRRIKR-MLRSRVETRIVGGDGFDE----VVNDADLVINSA 77 
                                       89*********************..9**************85.69*********9999999....8999******** PP

                                       SGGGHHHHHHHHHHHT-EEEESS-BCGCCSCHCCSHHHHHTHHHHHHCTSEE CS
                   Sacchrp_dh_NADP  78 ppissldvlkaCietgvhyvdtsiskeertnyalreavlklkekakeagvta 129
                                        p+ +ld++k+C++ gv+y+d +            +++l++++ ++++ v a
  gi|557694475|ref|YP_008797529.1|  78 SPTINLDLMKTCLRYGVNYMDLAS--------DDIDKQLAMNRSWRRKEVLA 121
                                       *********************777........34567777777777776665 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.9
                                       HT-EEEESS- CS
                   Sacchrp_dh_NADP  92 tgvhyvdtsi 101
                                       +gv+yvd   
  gi|557694475|ref|YP_008797529.1| 229 KGVRYVDFKL 238
                                       7999999655 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   1.5   3.2e-06    0.0063      19      55 ..       6      42 ..       5      54 .. 0.90
   2 ?    2.3   0.0     0.044        88     180     201 ..     166     346 ..      49     353 .. 0.48

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.2e-06
                                      SEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--G CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 19 skvllvGaGglGsellknLalsGvgkltlvDnDkiel 55
                                      ++vl++G+G++G  ++k La+ G  +l ++D D+  l
  gi|557694475|ref|YP_008797529.1|  6 MRVLVLGVGAVGEVIAKHLAGEGGVSLSVADIDELRL 42
                                      69******************************98765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.044
                                       H............................................................................ CS
                                       x............................................................................ RF
                              ThiF 180 t............................................................................ 180
                                                                                                                    
  gi|557694475|ref|YP_008797529.1| 166 Alfspeiffdeilspslvyvngrfrklpalsgyevyefpepvgklsvysvnheevytlprfigkgvryvdfklalad 242
                                       14444444444444444444444444444445555555555555555555555555555555555555555555555 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              ThiF 181 ............................................................................. 180
                                                                                                                    
  gi|557694475|ref|YP_008797529.1| 243 elinatkllkrigllrsrrmrvkdasvsprdvffalmpkpseiakhiegyaslvvevegmykgkavtysiytlmshe 319
                                       55555555555555555555555555555555555555555555555555555555555555555555555555544 PP

                                       .....HHHCT.E-B-HHHHHHHHHHHH CS
                                       .....xxxxx.xxxxxxxxxxxxxxxx RF
                              ThiF 181 .....siagn.ipaiatttavvaglaa 201
                                            + a+  + +++t++avva+++a
  gi|557694475|ref|YP_008797529.1| 320 qanklFRANAtSYLTGTVPAVVASMIA 346
                                       333332223246678888888888887 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1     2e-07    0.0004      14      88 ..       7      79 ..       5     115 .. 0.84
   2 ?   -1.8   0.0       1.5   3.1e+03      31      55 ..      99     123 ..      92     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2e-07
                                      EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH.T.ET-EEEEGCGHHHHHHT-SEEEE-SSSSS- CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel.kgeeiealkleelkellaeadvvisataseep 88
                                      +vl++G G ++e +akhL+ +g  ++ va  +  r +++ + l + +e++++  +  +e++++ad+vi + +   p
  gi|557694475|ref|YP_008797529.1|  7 RVLVLGVGAVGEVIAKHLAGEGGVSLSVADIDELRLRRIKRMLrSRVETRIVGGDGFDEVVNDADLVINSAS---P 79
                                      89*******************9999**************99997788999999***************8865...3 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                                       HHCCT-CEEEEEESSHHHHHHHHHH CS
                      Shikimate_DH  31 LlakgvkkvvvaNRtlerakelaee 55 
                                       L++  ++k + +NR+ +r + la  
  gi|557694475|ref|YP_008797529.1|  99 LASDDIDKQLAMNRSWRRKEVLALI 123
                                       6677778888899999999988865 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 !   19.3   0.1   2.8e-07   0.00055      30      99 ..       7      77 ..       2      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 2.8e-07
                                      EEEEESTSHHHHH.HHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE-- CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlq.AiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtv 99
                                      +vlv+G+G +G   A + a + g +  v D+++ rl++++ + ++ ve++    + ++e v++ad+vi ++
  gi|557694475|ref|YP_008797529.1|  7 RVLVLGVGAVGEViAKHLAGEGGVSLSVADIDELRLRRIKRMLRSRVETRIVGGDGFDEVVNDADLVINSA 77
                                      8**********76155677788999****************66666**********************887 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.3e-06    0.0026       1      93 [.       6      95 ..       6      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS.--S-BEBSSHHHHHHH-SEEEE-S-HH CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellglg.klgvavtddleevlekadvliDFTtpe 78
                                      ++v+v+G+ G +G+ ++k +  + ++ l+ a d +e  l+ + + ++l ++ ++ +   d ++ev+++ad +i   +p+
  gi|557694475|ref|YP_008797529.1|  6 MRVLVLGV-GAVGEVIAKHLAGEGGVSLSVA-DIDE--LRLRRIKRMLRSRvETRIVGGDGFDEVVNDADLVINSASPT 80
                                      89*****9.*****************99877.4444..67778888888775777777799****************** PP

                                      HHHHHHHHHHHTT-E CS
                            DapB_N 79 avlenlklalekgvk 93
                                        l+++k++l++gv+
  gi|557694475|ref|YP_008797529.1| 81 INLDLMKTCLRYGVN 95
                                      *************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 ?   14.5   0.1   1.2e-05     0.024       2      50 ..       8      57 ..       7      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                      EEEE--SCCHHHHHHHHHHT.T-EEEEE-S-HHHHHHHHHHHHHHHHCCT CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasa.gleVvlvdiseealekalekieksleklv 50
                                      v v+G G +G+ ia+ +a + g++  + di+e +l++ ++++++++e  +
  gi|557694475|ref|YP_008797529.1|  8 VLVLGVGAVGEVIAKHLAGEgGVSLSVADIDELRLRRIKRMLRSRVETRI 57
                                      78****************9989********************99888765 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   0.5   6.3e-05      0.13       1      52 [.       8      65 ..       8      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT.....SEEEES-TTSH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg.....levvvgdatde 52
                                      ++++G+G vG+ +a+ L   gg + +v d de r++++++       +++v gd+ de
  gi|557694475|ref|YP_008797529.1|  8 VLVLGVGAVGEVIAKHLAGeGGVSLSVADIDELRLRRIKRMLrsrveTRIVGGDGFDE 65
                                      68*****************77766********88887765443333455787888776 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 ?   10.8   0.2   0.00014      0.27       1      41 [.       6      47 ..       6      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                                      SEEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCT CS
                    UDPG_MGDP_dh_N  1 mkisviGlGYvGlvtaavlaeig.hevigvDideekvdklns 41
                                      m++ v+G G vG v a  la  g + + + Dide + + +++
  gi|557694475|ref|YP_008797529.1|  6 MRVLVLGVGAVGEVIAKHLAGEGgVSLSVADIDELRLRRIKR 47
                                      89******************9887999999****99888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2840.29
//
Query:       gi|557694476|ref|YP_008797530.1|  [L=373]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  101.5   0.0    6.3e-29  101.2   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.7e-05   24.0   0.3       0.29   10.1   0.0    3.3  4  Peptidase_M42  M42 glutamyl aminopeptidase
    4.9e-05   23.2   0.0    9.9e-05   22.2   0.0    1.5  1  M20_dimer      Peptidase dimerisation domain
    0.00058   19.6   0.0     0.0018   18.0   0.0    1.7  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 !  101.2   0.0   1.4e-32   6.3e-29       2     206 ..      65     366 ..      64     367 .. 0.92

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 1.4e-32
                                       EEEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgGa 78 
                                       + +HlDvVpe +  +    f++++  +klyGrGa+dmkggv+++l +l++l++  ++p  ++ ++f++dEE  ++Ga
  gi|557694476|ref|YP_008797530.1|  65 FCGHLDVVPEYDMAD---AFRPRVVGDKLYGRGACDMKGGVVSLLLLLESLRQMEPEP--NVSFAFVVDEEMYGRGA 136
                                       779******444445...8******99***************************9666..***********877*** PP

                                       HHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE........................................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................ RF
                     Peptidase_M20  79 kallegleerekvdavfelhieepgileagklaigvv........................................ 115
                                       ++ll    ++ +++    ++i ep+  +     i v+                                        
  gi|557694476|ref|YP_008797530.1| 137 AELLR---RGMRAEM---CVITEPTSGV-----ICVGnascmefrltasgksghgasraggnavkslmgfyevferg 202
                                       *****...4445555...88999**999.....55669999************************************ PP

                                       ......................................................................EEEEEEE CS
                                       ......................................................................xxxxxxx RF
                     Peptidase_M20 116 ......................................................................kvevell 122
                                                                                                              ve++ l
  gi|557694476|ref|YP_008797530.1| 203 lmkeldvrgsdfpmspiinlgkfeggyggwvipskaycevlvhmhpsisyrdgldtvrrlveeiaeelgiVVELTML 279
                                       ********************************************************************988999999 PP

                                       EEESHEEEC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH...TTTEEEEEEESSG.GCTTSTTTEEEHHHH CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                     Peptidase_M20 123 eggapvtln.dsplvkalaeaaeelfgekvelivsgpggtdarff...agiptvmifgpgs.glaHspnEyvdledl 194
                                       +g   + l+  ++   +l++a++  +g k+++       td + +    gip++ ++gpg+   aHs  E+v+++d+
  gi|557694476|ref|YP_008797530.1| 280 HGCDGYILPqTNQHLHKLKQAYSMETGQKPKTGLIE-SETDGNALyhkGGIPCI-VYGPGDiTYAHSSQEHVSIKDV 354
                                       *********99999*********9999888888777.78888888887888988.6****88*************** PP

                                       HHHHHHHHHHHH CS
                                       xxxxxxxxxxxx RF
                     Peptidase_M20 195 ekgikvlarlle 206
                                        ++++vl r+++
  gi|557694476|ref|YP_008797530.1| 355 IECYRVLRRFIN 366
                                       *********985 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.12   5.2e+02      10      44 ..      22      58 ..      16      70 .. 0.73
   2 !   10.1   0.0   6.4e-05      0.29     125     176 ..      88     139 ..      78     155 .. 0.79
   3 ?   -1.6   0.0      0.23     1e+03     224     246 ..     258     280 ..     256     299 .. 0.80
   4 !    9.2   0.1   0.00012      0.56     247     290 ..     315     358 ..     283     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.12
                                      STTSSEEEEEEE--B-EEEEE..EEETTSEEEEEEES CS
                     Peptidase_M42 10 kekepkvmiaAHmDeiGfmVk..eIkedGflrfekvG 44
                                      +e++   ++a H+  +Gf+V+  e+ + G   ++k+G
  gi|557694476|ref|YP_008797530.1| 22 HEEKVCDLVAEHVESLGFVVErqEVYKTGYNVVTKLG 58
                                      5555566799999999999962256677766666666 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 6.4e-05
                                       TECEEETTHHHHHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTTTSHHHHHH CS
                     Peptidase_M42 125 ngkivskalDdragvavllellkelkeeeleatvylvatvqEEvGlrGakts 176
                                       ++ +   a D + gv+ ll ll++l++ e e +v +++ v EE   rGa+ +
  gi|557694476|ref|YP_008797530.1|  88 DKLYGRGACDMKGGVVSLLLLLESLRQMEPEPNVSFAFVVDEEMYGRGAAEL 139
                                       55344448899******************99************977777644 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHTT--EEEEEES CS
                     Peptidase_M42 224 klrkkllelAkknnipyqlevls 246
                                       ++r+ ++e+A++ +i ++l++l+
  gi|557694476|ref|YP_008797530.1| 258 TVRRLVEEIAEELGIVVELTMLH 280
                                       57888999999999999886654 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.00012
                                       SSSSTHHHHHTSTTTSEEEEEEEE.EBSTTSTTEEEEHHHHHHHH CS
                     Peptidase_M42 247 gggtDAgaihltgegvptalisip.tryiHspvevahlddleatv 290
                                       +  tD++a+ ++ +g+p+++ +++ + y Hs++e ++++d+ ++ 
  gi|557694476|ref|YP_008797530.1| 315 ESETDGNALYHK-GGIPCIVYGPGdITYAHSSQEHVSIKDVIECY 358
                                       567888777665.9********98689**************9986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   2.2e-08   9.9e-05       3     106 ..     163     268 ..     161     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2.2e-08
                                       B-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC........TCCTCCCCCEECCE-CCCCEESSEE CS
                         M20_dimer   3 hkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia...eerslprttlnvtgiegGsaknvipdea 76 
                                       +   +++++t+ gk+gH++   ag NA++ l+ + + +e    ++     + ++  + +n++ +egG+   vip++a
  gi|557694476|ref|YP_008797530.1| 163 NASCMEFRLTASGKSGHGA-SRAGGNAVKSLMGFYEVFERGLMKELdvrGSDFPMSPIINLGKFEGGYGGWVIPSKA 238
                                       556789************9.88899**********99998877766887788888999**********999****** PP

                                       EEEEEEEHHHHHHHHHHHHHHHHHHTSCCS CS
                         M20_dimer  77 eakidiRllpgedpeevleeieeilekeap 106
                                       ++++ ++  p  +  + l++++ ++e+ a+
  gi|557694476|ref|YP_008797530.1| 239 YCEVLVHMHPSISYRDGLDTVRRLVEEIAE 268
                                       *******99988888877777777777765 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0     4e-07    0.0018      14      82 ..      62     140 ..      52     156 .. 0.82
   2 ?   -1.6   0.0       0.4   1.8e+03     127     176 ..     298     346 ..     284     364 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4e-07
                                       EEEEEEE--B-TTT...........TCC..T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHH CS
                     Peptidase_M28  14 vlllgAHyDsvgvg...........rgp..ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllG 77 
                                        +l+++H+D v++              +     GA D   gv++lL l++ l +   +p+ +v f+f+  EE +  G
  gi|557694476|ref|YP_008797530.1|  62 DVLFCGHLDVVPEYdmadafrprvvG-DklYGRGACDMKGGVVSLLLLLESLRQ--MEPEPNVSFAFVVDEEMYGRG 135
                                       599*********98999998887751.345667********************9..57***************9999 PP

                                       HHHHH CS
                     Peptidase_M28  78 Skafa 82 
                                       +  + 
  gi|557694476|ref|YP_008797530.1| 136 AAELL 140
                                       99887 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.4
                                       HHHTT-TTSCCEEEEES.STT-STTHHHHTTT.--EEEECTSSS-TTT.TSTT CS
                     Peptidase_M28 127 akpvgraaaedpfders.grgrsDhspflkag.vpvldlaetgfpevy.Htpr 176
                                        ++++ +  ++p  +++ + +++D  ++ ++g +p++ +   + + +y H+++
  gi|557694476|ref|YP_008797530.1| 298 KQAYSMETGQKP--KTGlIESETDGNALYHKGgIPCIVY--GPGDITYaHSSQ 346
                                       333333222223..3334888899888776666999887..444444446555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2651.89
//
Query:       gi|557694477|ref|YP_008797531.1|  [L=462]
Description: glutamate-1-semialdehyde-2,1-aminomutase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-64  218.7   0.0    1.7e-64  218.0   0.0    1.3  1  Aminotran_3      Aminotransferase class-III
  ------ inclusion threshold ------
      0.024   13.8   0.0      0.043   13.0   0.0    1.5  1  Aminotran_1_2    Aminotransferase class I and II
       0.17   11.6   0.0       0.45   10.3   0.0    1.6  1  Methyltransf_31  Methyltransferase domain


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 !  218.0   0.0   2.8e-68   1.7e-64       9     357 ..      50     386 ..      45     446 .. 0.88

  Alignments for each domain:
  == domain 1  score: 218.0 bits;  conditional E-value: 2.8e-68
                                       SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT- CS
                       Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapk 85 
                                        +l +++++G++++dvdg++ylD+  ++ ++ +GhahP +v+ +++++++ ++     +++e ++k a+ l++ ++ 
  gi|557694477|ref|YP_008797531.1|  50 YPLYMSRGKGSRIWDVDGNMYLDFNMAFGALGVGHAHPILVEEMRKVIENGTIYG---FESEASVKTAKVLTERFGY 123
                                       457899*********************************************6555...9****************** PP

                                       ..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-T CS
                       Aminotran_3  86 gldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlky 162
                                         ++v +a++G eA++ A++lar+       t ++ki++f+g+fHG     +   ++ ++y+++ ++++  v+    
  gi|557694477|ref|YP_008797531.1| 124 --ERVRFATTGLEATMLAVRLARA------FTGRKKILKFEGCFHGSHEPLMVSVKP-NIYRAGHPKTPNSVPASMG 191
                                       ..**********************......****************99888877777.9*****9999888776555 PP

                                       TBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTT CS
                       Aminotran_3 163 pdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfG 239
                                         +e+++    +    l ++e++ +k+ ++va++i+Epi  ++Gvv+++ efl++lr l+++++ lli+DEv+t   
  gi|557694477|ref|YP_008797531.1| 192 MPQEFADLVTVAPYGDLDAVEKIMQKHGNDVAGIILEPIAMNMGVVIPPLEFLKGLRRLADEYNSLLIFDEVKT--- 265
                                       5556777888888999999***99*************************************************9... PP

                                       TTSSSS.GGGGC.TS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS..B--TTTT-HHHHHHHHHHHHHHHHTT CS
                       Aminotran_3 240 rTGklf.Aleha.gvspDlmtlaKaltgGlplsavlataevmqalapgs..hgsTfgGnplacavalavleiieeek 312
                                        +Gk++ +++++ gv+ D+m+ aK+++gG+p+savl  +ev + + p++  hg+Tf  npl   +a+ +l+ i + +
  gi|557694477|ref|YP_008797531.1| 266 -SGKFYrGVQEWcGVKGDIMVAAKSIAGGYPFSAVLSSKEVFDYVGPNKtaHGGTFNSNPLSVNAAHVTLTKILTVD 341
                                       .9****6566667********************************999899************************** PP

                                       HHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCE CS
                       Aminotran_3 313 llenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeae 357
                                        l++aq l+++l +g +++ ++ +  +++    + + i ++e+  
  gi|557694477|ref|YP_008797531.1| 342 NLRHAQTLSKELAKGYSDILEEAKITHNITHIATSGTIYFTEHPI 386
                                       ***************999999987777776665555554444444 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 ?   13.0   0.0   7.2e-06     0.043     131     301 ..     207     374 ..     197     442 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.2e-06
                                       -HHHHHHHHTTHHCTTETEEEEEEESS-.TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGG CS
                     Aminotran_1_2 131 dlealeealkeapegnkktkvilvesph.NPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatran 206
                                       dl+a+e+  +++  +++   +i++e +  N+  ++++le l+ l +la++yn ll++De+   + f   ++ + +++
  gi|557694477|ref|YP_008797531.1| 207 DLDAVEKIMQKH-GNDV--AGIILEPIAmNMGVVIPPLEFLKGLRRLADEYNSLLIFDEVKTSGKFY-RGV-QEWCG 278
                                       889999977774.4444..5666666651555567889*********************84433333.112.22666 PP

                                       STTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHH..HHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Aminotran_1_2 207 veeepnllivgslsKafGlaGeRvGyilgnaavvsql..rklsrpfls.ssllqaavaaalsdallkqseleemrqr 280
                                       v+ ++  + + s +  +         +l++++v +++  +k + ++++ s++l+  +a ++ ++ l+ ++l  ++  
  gi|557694477|ref|YP_008797531.1| 279 VKGDIM-VAAKSIAGGYPFSA-----VLSSKEVFDYVgpNKTAHGGTFnSNPLSVNAAHVTLTKILTVDNLRHAQTL 349
                                       666555.44455444444444.....555666666553345555555556666655555555555555555555555 PP

                                       HHHHHHHHHHHHHHS....TEEEEC CS
                     Aminotran_1_2 281 lqkrrkelrdeLael....glkvla 301
                                        ++++k   d L+e+    +++++a
  gi|557694477|ref|YP_008797531.1| 350 SKELAKGYSDILEEAkithNITHIA 374
                                       5555555555555555555555555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   7.6e-05      0.45      21      60 ..      89     130 ..      77     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.6e-05
                   Methyltransf_31  21 lae...elgpkaevvGiDiseeaielArenaqklgldnveFeq 60 
                                       l e   +++++++++G++ se +++ A+  +++ g+++v+F  
  gi|557694477|ref|YP_008797531.1|  89 LVEemrKVIENGTIYGFE-SEASVKTAKVLTERFGYERVRFAT 130
                                       4443448889*******8.899*******************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3209.54
//
Query:       gi|557694478|ref|YP_008797532.1|  [L=356]
Description: spermidine/putrescine ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  114.9   0.0    6.3e-33  114.2   0.0    1.3  1  ABC_tran     ABC transporter
    1.8e-09   37.6   0.0      5e-09   36.2   0.0    1.8  1  TOBE_2       TOBE domain
    0.00015   21.7   0.0     0.0016   18.3   0.0    2.0  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0032   17.0   0.1       0.49    9.8   0.0    2.2  2  PhoH         PhoH-like protein
     0.0051   16.7   0.0     0.0075   16.2   0.0    1.4  1  Rad17        Rad17 P-loop domain
     0.0066   16.9   0.0      0.011   16.1   0.0    1.5  1  AAA_16       AAA ATPase domain
     0.0072   16.2   0.0      0.014   15.3   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.073   13.5   0.0    2.0  2  AAA          ATPase family associated with various cellular a
      0.018   15.0   0.7        6.2    6.7   0.0    2.8  3  NTPase_1     NTPase
      0.023   14.7   0.1       0.17   11.9   0.0    2.3  2  ID           Intracellular delivery domain
      0.028   14.7   0.1      0.078   13.3   0.1    1.8  1  AAA_22       AAA domain
      0.037   13.9   0.0      0.063   13.2   0.0    1.3  1  ATPase_2     ATPase domain predominantly from Archaea
       0.04   13.7   0.0       0.15   11.8   0.0    1.9  2  IstB_IS21    IstB-like ATP binding protein
      0.046   14.6   0.0       0.21   12.5   0.0    2.1  1  OB_MalK      MalK OB fold domain
      0.051   13.3   0.0       0.09   12.5   0.0    1.3  1  AAA_30       AAA domain
      0.054   13.2   0.0       0.13   12.0   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
      0.055   14.0   0.5       0.11   13.0   0.2    1.6  2  AAA_23       AAA domain
      0.069   13.1   0.0       0.21   11.6   0.0    1.8  1  AAA_5        AAA domain (dynein-related subfamily)
      0.075   13.3   0.0       0.16   12.2   0.0    1.6  1  TOBE         TOBE domain
      0.081   12.8   0.0       0.16   11.9   0.0    1.4  1  NACHT        NACHT domain
      0.084   12.3   0.1        2.4    7.5   0.1    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
       0.11   12.7   0.1       0.22   11.8   0.1    1.7  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 !  114.2   0.0   7.7e-36   6.3e-33       1     136 [.      20     164 ..      20     165 .. 0.94

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 7.7e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ v+l ++++e   ++G++G+GK+tLl+++agl++++eGe+l+ gk++++   +  ++ +g ++q + +fp++tv+
  gi|557694478|ref|YP_008797532.1|  20 LRGVNLAIEKNEFFSLLGPSGCGKTTLLRIIAGLEQQDEGEVLIGGKNMDN--VPPHKRGVGLVFQGTAIFPHMTVY 94 
                                       6789*********************************************99..999********************* PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +n             e +e++ ++l+ ++++   ++ + ++ ++LSgG++qrv++ar+l+ +pk+lllDEp 
  gi|557694478|ref|YP_008797532.1|  95 DNiafglrmrkyprqEIRERVRNVLELMNMPF--EKYAWKKSHQLSGGERQRVEIARSLVIEPKVLLLDEPL 164
                                       **********9988888888999999999998..55555788*****************************6 PP

>> TOBE_2  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   6.2e-12     5e-09       1      74 [.     278     352 ..     278     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 6.2e-12
                            TOBE_2   1 laiRPEklrla.aagganglsGtVedveylGsstryvvelaggqlvvvrqpnadr.dsalapGdtVelswdpddav 74 
                                       l+iRPE + l  + +++n l+G+V+d +y+G +  + + + g+ l++v++   +  + ++++Gd V  +w++ d  
  gi|557694478|ref|YP_008797532.1| 278 LSIRPELIYLGnSIETENKLRGVVVDKTYMGPYATLKIGVSGEILLTVHVREPEFlQ-NIKVGDHVSFGWKASDSY 352
                                       79********75444468**********************************99866.9************99865 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 !   18.3   0.0     2e-06    0.0016       3      83 ..      34     110 ..      32     121 .. 0.70
   2 ?    0.7   0.0      0.44   3.6e+02     237     298 ..     137     196 ..     132     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2e-06
                            AAA_21   3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrle 79 
                                        l Gp g+GK++LL+++ +l    +  eg+  + +++ ++    ++  +  + + + f    ++ +++ +  ++r +
  gi|557694478|ref|YP_008797532.1|  34 SLLGPSGCGKTTLLRIIAGL---EQQDEGEVLIGGKNMDNVPPHKRGVGLVFQGTAIFPHM-TVYDNIAFGLRMRKY 106
                                       699****************9...66666666666666666666666666666666666666.777777777777777 PP

                            AAA_21  80 rsqv 83 
                                        +q 
  gi|557694478|ref|YP_008797532.1| 107 PRQE 110
                                       7777 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.44
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                       lS G ++   ++ +l   +   ++ll+DEp   L+ k+  +    lk+l++  g+ +i +TH+
  gi|557694478|ref|YP_008797532.1| 137 LSGGERQRVEIARSLVIEP---KVLLLDEPLGPLDLKIRQKMQLELKRLQKkVGTTFIYVTHD 196
                                       5555555555555666655...99******888888888888777766666677888888887 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0006      0.49      15      46 ..      26      58 ..      19      62 .. 0.78
   2 ?    4.9   0.1      0.02        16      48     109 ..     146     211 ..     136     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0006
                                      HHHH-SEEEEE--TTSSTT.HHHHHHHHHHHHT CS
                              PhoH 15 alkkndivfaiGpaGtGKt.ylavalavealkk 46
                                      a++kn++   +Gp+G+GKt +l + +++e+  +
  gi|557694478|ref|YP_008797532.1| 26 AIEKNEFFSLLGPSGCGKTtLLRIIAGLEQQDE 58
                                      789***************824566677766655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.02
                                       S-SEEEEEE-S--T.T----SS---------TTTHHHHHHHTTTS...-TTCHHHHHHTTSEEEEE CS
                              PhoH  48 kvkriiltrpavea.geelGflpgdleekvdpylrplydaLkdll...gaekvekllekgkievap 109
                                       ++ r +++ p+v   +e lG l+ ++++k++  l+ l  ++ +++    ++++e +  +++i v++
  gi|557694478|ref|YP_008797532.1| 146 EIARSLVIEPKVLLlDEPLGPLDLKIRQKMQLELKRLQKKVGTTFiyvTHDQTEAFAMSDRIAVME 211
                                       556667777888555***********************9998865455888888888888888875 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.1e-06    0.0075      33      68 ..      18      53 ..       4     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.1e-06
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLske 68
                                      e+l+   L  +k++   + GPsGCgk+t +++++  
  gi|557694478|ref|YP_008797532.1| 18 EALRGVNLAIEKNEFFSLLGPSGCGKTTLLRIIAGL 53
                                      5667777788888899999************99865 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   1.4e-05     0.011      25      63 ..      31      70 ..      17     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekd.ggif.lrgkcdql 63
                                      e   l G+sG+GK++l+r ++  le++ +g + + gk+ ++
  gi|557694478|ref|YP_008797532.1| 31 EFFSLLGPSGCGKTTLLRIIAG-LEQQdEGEVlIGGKNMDN 70
                                      567899************9995.555524555577777776 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.7e-05     0.014      98     130 ..      28      61 ..       3      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                                       TT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  98 kd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       ++ ++  l+G+SG GK+tL+  +++ +++  gev
  gi|557694478|ref|YP_008797532.1|  28 EKnEFFSLLGPSGCGKTTLLRIIAGLEQQDEGEV 61 
                                       4448899*****************9888887776 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 ?   13.5   0.0   8.9e-05     0.073       3      20 ..      35      52 ..      33      70 .. 0.92
   2 ?   -0.4   0.0       1.8   1.4e+03      47      66 ..     142     162 ..     108     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-05
                                      EESSTTSSHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavak 20
                                      l Gp G+GKT+l + +a 
  gi|557694478|ref|YP_008797532.1| 35 LLGPSGCGKTTLLRIIAG 52
                                      89*************996 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.8
                                       HHHHHHHHHTS.TSEEEEEET CS
                               AAA  47 relfkeakeka.kpsilfiDE 66 
                                       r+ ++ a++   +p++l++DE
  gi|557694478|ref|YP_008797532.1| 142 RQRVEIARSLViEPKVLLLDE 162
                                       445555555557899999998 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0076       6.2       4      25 ..      35      56 ..      33      82 .. 0.69
   2 ?    5.2   0.1     0.021        17      82     156 ..     141     219 ..     112     226 .. 0.84
   3 ?   -1.1   0.0       1.9   1.5e+03     127     146 ..     320     338 ..     314     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0076
                                      EE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellks 25
                                      + Gp+G GKtTl++ ++ l ++
  gi|557694478|ref|YP_008797532.1| 35 LLGPSGCGKTTLLRIIAGLEQQ 56
                                      569*********9888755443 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHH-EEEE--.-STTGGG-.HHHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE CS
                          NTPase_1  82 eelalealrkalseadviviDE.iGkmElks.kkfkeaveevLk.sekpvlavihrrk.dlalveeirerkdvkvfe 154
                                       e+  +e+ r  + e+ v+++DE  G++ lk+ +k++ +++++ k  ++ ++ v h ++   a+ ++i   +++ v++
  gi|557694478|ref|YP_008797532.1| 141 ERQRVEIARSLVIEPKVLLLDEpLGPLDLKIrQKMQLELKRLQKkVGTTFIYVTHDQTeAFAMSDRIAVMEKGLVVQ 217
                                       5566777777778999******99******835677788888888899*******9987888999999999888888 PP

                                       -- CS
                          NTPase_1 155 vt 156
                                       v 
  gi|557694478|ref|YP_008797532.1| 218 VG 219
                                       75 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.9
                                       EEEEE--SS--SHHHHHHHT CS
                          NTPase_1 127 pvlavihrrkdlalveeire 146
                                        +l ++h+r +++++++i+ 
  gi|557694478|ref|YP_008797532.1| 320 EILLTVHVR-EPEFLQNIKV 338
                                       5899*****.7899999986 PP

>> ID  Intracellular delivery domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0         2   1.6e+03       6      15 ..     303     312 ..     303     316 .. 0.84
   2 ?   11.9   0.0    0.0002      0.17      38      53 ..     329     344 ..     328     345 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2
                                ID   6 GktyeGifag 15 
                                       +kty+G +a+
  gi|557694478|ref|YP_008797532.1| 303 DKTYMGPYAT 312
                                       69****9986 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0002
                                ID  38 epeqLktLkkGDfvsF 53 
                                       epe+L++ k+GD+vsF
  gi|557694478|ref|YP_008797532.1| 329 EPEFLQNIKVGDHVSF 344
                                       69*************9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   9.5e-05     0.078       6      32 ..      31      57 ..      27     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.5e-05
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldee 32
                                       +  + G+sG+GKTtllr ++   +++
  gi|557694478|ref|YP_008797532.1| 31 EFFSLLGPSGCGKTTLLRIIAGLEQQD 57
                                      567799***********9888766543 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 ?   13.2   0.0   7.8e-05     0.063      18      45 ..      28      55 ..      17      63 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.8e-05
                          ATPase_2 18 epneiyfiYGpegsGKtaLlkeiienle 45
                                      e+ne+  + Gp g+GKt+Ll+ i+   +
  gi|557694478|ref|YP_008797532.1| 28 EKNEFFSLLGPSGCGKTTLLRIIAGLEQ 55
                                      558899999***********97765554 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 ?   11.8   0.0   0.00018      0.15      21      64 ..       3      47 ..       1      61 [. 0.83
   2 ?   -1.2   0.0       1.8   1.4e+03     106     149 ..     152     197 ..     138     207 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                         IstB_IS21 21 didfraarsldkrkvkeLatlsf.iekkenivllGpsGvGKshla 64
                                      +++ r+ +++ +  v++L++ +  iek+e + llGpsG GK+ l 
  gi|557694478|ref|YP_008797532.1|  3 EVEIRSVKKVYEGGVEALRGVNLaIEKNEFFSLLGPSGCGKTTLL 47
                                      566777888888889999998865999**************9875 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                         IstB_IS21 106 llkvdllilDd.lgllpldqaeaell.feviekryerrsiiitsnl 149
                                       ++++++l+lD+ lg l+l+  ++ +l ++ ++k+++++ i +t ++
  gi|557694478|ref|YP_008797532.1| 152 VIEPKVLLLDEpLGPLDLKIRQKMQLeLKRLQKKVGTTFIYVTHDQ 197
                                       5667788888756666666544444436666777777666666554 PP

>> OB_MalK  MalK OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00025      0.21       6      51 ..     241     283 ..     241     285 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00025
                           OB_MalK   6 NflpatveedgvlvegggvtlplpeeqklalklyagkevilGiRPE 51 
                                       N+++++v+++g+++++g   l++  e+    ++ ag++ +l iRPE
  gi|557694478|ref|YP_008797532.1| 241 NLIEGEVDAGGFFLAEGLPPLKIASEA---SEGLAGRKALLSIRPE 283
                                       9**********6666666667776666...999************* PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.09      15      50 ..      27      62 ..      20      69 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                            AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                       +++ +  l Gp G GKtt+l+ ++ + ++++g+v+
  gi|557694478|ref|YP_008797532.1| 27 IEKNEFFSLLGPSGCGKTTLLRIIAGLEQQDEGEVL 62
                                      4555688899***************99999977775 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 ?   12.0   0.0   0.00016      0.13      15      39 ..      23      47 ..      18      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                        + i+ ++++ l GpsG GK+Tll
  gi|557694478|ref|YP_008797532.1| 23 VNLAIEKNEFFSLLGPSGCGKTTLL 47
                                      567788788999************8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   0.00013      0.11      18      39 ..      29      50 ..      15      53 .. 0.81
   2 ?   -2.8   0.0       9.5   7.7e+03     118     146 ..     172     201 ..     136     214 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                            AAA_23 18 skgltlItGpNGaGKTTildAi 39
                                      ++ ++ + Gp G+GKTT+l+ i
  gi|557694478|ref|YP_008797532.1| 29 KNEFFSLLGPSGCGKTTLLRII 50
                                      4578999************987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.5
                            AAA_23 118 eqfisellgskkiil.nlilflgqerfeef 146
                                       +q+++ +l++ ++   + +++   +++e f
  gi|557694478|ref|YP_008797532.1| 172 RQKMQLELKRLQKKVgTTFIYVTHDQTEAF 201
                                       344444444333322255555555555555 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 ?   11.6   0.0   0.00025      0.21       4      24 ..      35      56 ..      33      70 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00025
                                      EE--SSSSHHHHHHHGGGGB.S CS
                             AAA_5  4 LvGppGtgKselaerlaaal.n 24
                                      L+Gp+G+gK++l + +a +  +
  gi|557694478|ref|YP_008797532.1| 35 LLGPSGCGKTTLLRIIAGLEqQ 56
                                      99************99987644 PP

>> TOBE  TOBE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0    0.0002      0.16       2      60 ..     292     349 ..     291     351 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                              TOBE   2 sarNqlpgtVvvveplgseveVrvdlgggatLtArvtrrsaeeLgLapGeeVfalikaa 60 
                                       +++N l+g Vv  +  g+ +++ + ++g+  Lt++v +  + +  +++G+ V +  ka+
  gi|557694478|ref|YP_008797532.1| 292 ETENKLRGVVVDKTYMGPYATLKIGVSGEILLTVHVREPEFLQ-NIKVGDHVSFGWKAS 349
                                       589*********************************9999999.999999999887776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.16       5      22 ..      35      52 ..      32      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                      EEC-TTTCHHHHHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlqklal 22
                                      l G++G+GKTtLl+ +a 
  gi|557694478|ref|YP_008797532.1| 35 LLGPSGCGKTTLLRIIAG 52
                                      78***********98875 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   0.1     0.003       2.4     135     205 ..     127     203 ..       9     215 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.003
                                       T........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHH CS
                                       x........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx RF
                             SMC_N 135 e........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreem 201
                                       e        +LSgGe++ v +a  + i   +p+ + llDe    LD k ++k+   lk+ +k+  + fi ++++++ 
  gi|557694478|ref|YP_008797532.1| 127 EkyawkkshQLSGGERQRVEIARSLVI---EPK-VLLLDEPLGPLDLKIRQKMQLELKRLQKKvgTTFIYVTHDQTE 199
                                       033333333788888888877766554...344.4578888888888888888888887777655677878877665 PP

                                       CCC- CS
                                       xxxx RF
                             SMC_N 202 leka 205
                                          +
  gi|557694478|ref|YP_008797532.1| 200 AFAM 203
                                       5444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00027      0.22       4      21 ..      35      55 ..      32     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00027
                            AAA_28  4 itGgestGKTtlleaLa...a 21
                                      ++G++++GKTtll+ +a   +
  gi|557694478|ref|YP_008797532.1| 35 LLGPSGCGKTTLLRIIAgleQ 55
                                      89***********99885532 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2603.21
//
Query:       gi|557694479|ref|YP_008797533.1|  [L=286]
Description: spermidine/putrescine ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   60.8  18.2    1.4e-16   60.8  18.2    1.8  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.59   10.5  17.0       0.29   11.5   0.9    3.6  4  DUF2484       Protein of unknown function (DUF2484)


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 ?   -0.9   0.5      0.13   1.1e+03      29      43 ..      14      34 ..       7      83 .. 0.55
   2 !   60.8  18.2   1.6e-20   1.4e-16       1     173 [.      88     277 ..      85     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.13
                      BPD_transp_1 29 slPsfv......laillvlvf 43
                                       lP+++      la++l++v 
  gi|557694479|ref|YP_008797533.1| 14 LLPPLLfyisffLAPFLTVVG 34
                                      444444222222333333222 PP

  == domain 2  score: 60.8 bits;  conditional E-value: 1.6e-20
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf................vilsilghlilpviilll 61 
                                       g+++++++a +++++ +++l  l+i++l++ +++ a  ++ ++                +   +l +  ++v++ +l
  gi|557694479|ref|YP_008797533.1|  88 GYPVAYFIA-FKGGRYKNFLILLVILPLWVTFVLRAYAVLSLLgpegvvnsfllnlgiiKQPLYLIYNEFAVMLGML 163
                                       678889999.9999*****99999999999999944444444455666666677777777888889999******** PP

                      BPD_transp_1  62 lsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.. 136
                                       ++++p+++l  +a l+ ++k  veaaralGa++++ f k++lP+++p +++g +l+f+ + g++v+++flg+ +   
  gi|557694479|ref|YP_008797533.1| 164 YGYLPFMILPLYASLEKISKTVVEAARALGAGPFTAFLKITLPLSKPGLVAGTLLTFIPAAGEFVIPSFLGGPSEvf 240
                                       ***********************************************************************7777*9 PP

                      BPD_transp_1 137 lgtlllea.ilgydyseisnggvlalviavlllnlvad 173
                                       +gt++ +a i++++ +++s +++l+++++vl+ +++++
  gi|557694479|ref|YP_008797533.1| 241 VGTMIYSAfISARNWNWGS-ALSLVYIALVLVGVALYM 277
                                       9998877636778888888.999999999999998876 PP

>> DUF2484  Protein of unknown function (DUF2484)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.9   3.2e-05      0.29      23      57 ..       1      35 [.       1      41 [. 0.88
   2 ?    1.3   2.0     0.048   4.3e+02      33      71 ..      84     122 ..      72     127 .. 0.78
   3 ?   -1.7   0.4      0.43   3.8e+03      42      46 ..     114     118 ..     101     153 .. 0.59
   4 ?    6.8   0.5    0.0009         8      19      42 ..     248     272 ..     239     278 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.2e-05
                           DUF2484 23 lRwhwsaaivLialgipllgyvtyehGPwwgllvl 57
                                      +R ++++++vL++l +pll y+ +   P+++++ +
  gi|557694479|ref|YP_008797533.1|  1 MRQRRKTGLVLLLLLPPLLFYISFFLAPFLTVVGV 35
                                      588999***********************999866 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.048
                           DUF2484  33 LialgipllgyvtyehGPwwgllvllaglSvlrwPliyl 71 
                                        ++lg p+ +++ ++ G +   l+ll +l + +  ++++
  gi|557694479|ref|YP_008797533.1|  84 CVLLGYPVAYFIAFKGGRYKNFLILLVILPLWVTFVLRA 122
                                       578899999999999999999999988887777666655 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.43
                           DUF2484  42 gyvty 46 
                                        +vt+
  gi|557694479|ref|YP_008797533.1| 114 LWVTF 118
                                       34443 PP

  == domain 4  score: 6.8 bits;  conditional E-value: 0.0009
                           DUF2484  19 allplR.whwsaaivLialgipllg 42 
                                       a++ +R w w+ a+ L+ ++ +l+g
  gi|557694479|ref|YP_008797533.1| 248 AFISARnWNWGSALSLVYIALVLVG 272
                                       7889999****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 2393.70
//
Query:       gi|557694480|ref|YP_008797534.1|  [L=251]
Description: spermidine/putrescine ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   52.0  15.7    6.7e-14   52.0  15.7    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 ?    0.2   3.8     0.029   5.3e+02     121     173 ..      21      77 ..       2      89 .. 0.35
   2 !   52.0  15.7   3.8e-18   6.7e-14       2     174 ..      70     243 ..      69     251 .] 0.77

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.029
                      BPD_transp_1 121 llggavlleflgswpG..lgtllleailgydyseis....nggvlalviavlllnlvad 173
                                       ++g + +   +  w G  +   +  +++++ +++ +    +  + ++ +a ++l l+a 
  gi|557694480|ref|YP_008797534.1|  21 VIGSFNAGRNIVEWVGftFDWYVRAFSNERILAAVYnsfwV--AGTVSLAAVVLALLAA 77 
                                       22222222222333333233333333333333333344331..2222222222223333 PP

  == domain 2  score: 52.0 bits;  conditional E-value: 3.8e-18
                      BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilpviillllsaapyvrlirra 74 
                                       ++l++laa    + + +++  + +++++   +P ++ a+ lvl+f    ++   l  +++il+ l ++p+v+++ ra
  gi|557694480|ref|YP_008797534.1|  70 VVLALLAAvavEKLSPRIQTGVNNIFYLSIVVPEIAEALTLVLFFL---WVNlPLGVGAVILGHLVWFPLVYVVLRA 143
                                       789999999999999*********************7776664432...3331344558999*************** PP

                      BPD_transp_1  75 alrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG...lgtllleailgy 148
                                        +  lpk ++ aar+lGas  ++f +v+lP+++p +itg++l f++++  ++ + f+  +pG   l   +++a  g+
  gi|557694480|ref|YP_008797534.1| 144 RMAGLPKVYEDAARVLGASGLKTFLNVTLPLLMPGVITGALLIFTWSWDSFIKTQFTR-GPGfetLPVYIWNAVGGR 219
                                       *********************************************************9.667566666666666666 PP

                      BPD_transp_1 149 dyseisnggvlalviavlllnlvadi 174
                                               + +++++++l+ +++a i
  gi|557694480|ref|YP_008797534.1| 220 GRGISP-EVNAVATVSLLVSVTLA-I 243
                                       555333.33333333333333333.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); 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):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1920.69
//
Query:       gi|557694481|ref|YP_008797535.1|  [L=386]
Description: spermidine/putrescine ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-18   67.7   0.3    1.9e-18   67.3   0.3    1.2  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    1.2e-11   44.5   0.6    1.4e-07   31.2   0.2    2.3  2  SBP_bac_6   Bacterial extracellular solute-binding protein
    1.4e-09   38.4   1.9    0.00022   21.3   0.2    2.3  2  SBP_bac_1   Bacterial extracellular solute-binding protein
     0.0001   22.1   0.0      0.099   12.4   0.0    2.3  2  SBP_bac_11  Bacterial extracellular solute-binding protein
  ------ inclusion threshold ------
      0.015   15.6   0.0        7.5    6.9   0.0    2.4  2  DUF641      Plant protein of unknown function (DUF641)
      0.062   13.7   0.1       0.12   12.9   0.1    1.3  1  ZapB        Cell division protein ZapB


Domain annotation for each model (and alignments):
>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.3   6.3e-22   1.9e-18       3     277 ..      68     349 ..      66     354 .. 0.78

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 6.3e-22
                                       HHHHHHH-TEEEEEEE-.-SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB-..-GGGSTTHHH...... CS
                         SBP_bac_8   3 akefekktgvkvnvvta.asndleqklkaalaagtapdidvvwanedalatlaeeglla..dlsdldnldd...... 70 
                                        k fe+ktgvkv + t+ +s+++ +kl +    g++p  dv++   + + +   e +l   dl+ ++n +       
  gi|557694481|ref|YP_008797535.1|  68 LKFFEEKTGVKVVFDTFeSSDEVYAKLFT----GQMPY-DVTSVTMGGMTRQEHERYLTklDLNRIPNFKRyaftgf 139
                                       6679*************888888888888....99995.77777766677777778888577779999999886666 PP

                                       -HHHHHTT.--TS.----EEEEEEE-EEEEEHHHHHHS.---BH.HHHHHH...HHHH......HHH-SEGG---GG CS
                         SBP_bac_8  71 ltdalaav.gydgklygvPyasetpyvliynkdllekaedpktw.dellaa...akkl......kgkfglpdpasgw 136
                                       ++d l++  + +   y+vP+  +t +++ y++d++ +++ p+++ d l+++   + k+      k ++++p   +  
  gi|557694481|ref|YP_008797535.1| 140 IKDILNPPfDPNR-DYSVPIELGT-TGVSYRTDKIAEEDWPTGFrDSLFDFegfLRKYspkdgvKRATMIPGGVETI 214
                                       5664433236644.6********9.8*********997455555555555433355774333334444555554432 PP

                                       GGGGTHHETTEE---H..HHH.HHHHHHHHHHHHTT-EE-S..--SSTTTTTSBSEEEE-TTHHHHHH-TTTSEEEE CS
                         SBP_bac_8 137 lqaallakdgksldddggkdglkealellkklkdngktydtgadavsefanGevaftingswdiaaaqkagkklgai 213
                                          +     gks +d  ++++++ea e+l + k++  ty   +++v  +a+ +++ + ++ w+     +   ++ ++
  gi|557694481|ref|YP_008797535.1| 215 PVVIKA-VMGKSINDI-TPENIAEAKEILIQQKPYLATYAGPSEFVPGLAEERFWVSETWVWQ-----DSANNVDYV 284
                                       233333.479999988.9*********************9999************98888775.....344599*** PP

                                       --S--EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTT..HHHHHH- CS
                         SBP_bac_8 214 vpkqgsfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnksaal..spevkkd 277
                                       +p +gs ++ ++l++pk+akn d aA +++++l++p+ q a +    ++++n  a++  +++ k+d
  gi|557694481|ref|YP_008797535.1| 285 APEEGSEIWEDSLVIPKSAKNVD-AAYALINYLLEPAVQVAHVLYNSLVTPNSLAYEmlPDDMKED 349
                                       ***********************.6******************************98778888887 PP

>> SBP_bac_6  Bacterial extracellular solute-binding 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      0.15      21      79 ..     117     183 ..     100     187 .. 0.70
   2 !   31.2   0.2   4.7e-11   1.4e-07     152     217 ..     267     334 ..     266     361 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.9e-05
                         SBP_bac_6  21 eglfqpldpanlpnvnkdfa........eeglkdp.dgkyypygvgplvlavnkdrlkgrpvPksWaD 79 
                                       e ++++ld +++pn+++ +a         +   dp + + +p++ g++++ + +d+++++++P+ + D
  gi|557694481|ref|YP_008797535.1| 117 ERYLTKLDLNRIPNFKR-YAftgfikdiLNPPFDPnRDYSVPIELGTTGVSYRTDKIAEEDWPTGFRD 183
                                       55555666555555553.22234444444566789555666***********************9987 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 4.7e-11
                         SBP_bac_6 152 ffadilpekkkgknlkvvwPedGalvspifmlvkkg.kkkelakafidfllspevqailakagg.vfP 217
                                       + + ++  +++ +n++ v Pe+G+ ++ ++++++k+ k+ + a+a+i++ll+p vq + +  ++ v P
  gi|557694481|ref|YP_008797535.1| 267 WVSETWVWQDSANNVDYVAPEEGSEIWEDSLVIPKSaKNVDAAYALINYLLEPAVQVAHVLYNSlVTP 334
                                       6677788889999*****************************************99887777764555 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 !   16.5   0.1   2.1e-06    0.0062      16     127 ..      65     175 ..      50     188 .. 0.77
   2 !   21.3   0.2   7.5e-08   0.00022     243     314 ..     272     322 ..     225     323 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                                       HH....HHHHHTTEEEEEEEE.CHHHHHHHHHHHHHTTSSSCSEEEECGGHHHHHHHTTSBECCHHHHHHTTECTTC CS
                         SBP_bac_1  16 ka....fekehpgikVeiesv.gsgslaqkltlaiaaGdgpaDviavdndwiarlakaglllpldpyvkaylapgvk 87 
                                       ++    fe+ ++g+kV++++  +s++++      + +G+ p+Dv  v   +++ + ++     l+++  +  ++ + 
  gi|557694481|ref|YP_008797535.1|  65 EQllkfFEE-KTGVKVVFDTFeSSDEVYA----KLFTGQMPYDVTSV---TMGGMTRQEHERYLTKLDLNRIPNFKR 133
                                       335553555.8*******99944555555....8888999*******...888999997777777777788888877 PP

                                       CTEEEEHHHHTHHHHCEEE.ES.EEEE.EEEEEEEETTTHHCT CS
                         SBP_bac_1  88 daadklsssvlpkildskv.ly.vPly.aargliYNkdlfeka 127
                                        a+  ++++ l   +d  +  y vP+  +++g+ Y++d+ +++
  gi|557694481|ref|YP_008797535.1| 134 YAFTGFIKDILNPPFD-PNrDYsVPIElGTTGVSYRTDKIAEE 175
                                       7777777777777777.447*******77**********9953 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 7.5e-08
                                       HHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEEEEEEEEEEBTTCSTHHHHHHHHHHHTSHHHH CS
                         SBP_bac_1 243 waalaamkvapkvafaadkekpkeelgvaplPagkggkpgilgayglaipkgsknpeaAkkFldfllspeaq 314
                                       w   ++ ++a++v+++a+ e+ ++                  + + l+ipk++kn +aA +++++ll+p+ q
  gi|557694481|ref|YP_008797535.1| 272 W---VWQDSANNVDYVAPEEGSEI------------------WEDSLVIPKSAKNVDAAYALINYLLEPAVQ 322
                                       3...45677899999999999988..................***************************998 PP

>> 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 !    7.3   0.0    0.0012       3.5      15      63 ..      66     116 ..      61     136 .. 0.82
   2 !   12.4   0.0   3.3e-05     0.099     168     221 ..     272     322 ..     246     325 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHH---EEEE.ESSHHHHHHHHHHH...-SEEEESSH.HHHHHH CS
                        SBP_bac_11  15 elaaaFeahtgvkvevs.aggsgklarqiadga.rpDvwipassawlella 63 
                                       +l + Fe++tgvkv++  + +s ++++++  g+ ++Dv + +  ++ ++ +
  gi|557694481|ref|YP_008797535.1|  66 QLLKFFEEKTGVKVVFDtFESSDEVYAKLFTGQmPYDVTSVTMGGMTRQEH 116
                                       566668********98659999*******99999****9887766665555 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 3.3e-05
                                       HHH..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHH CS
                        SBP_bac_11 168 eakaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaq 221
                                       +  +++ + ++++v++ eg  +   + +++++k+a++  aA a++++L+ p++q
  gi|557694481|ref|YP_008797535.1| 272 W-VWQDSANNVDYVAPEEGSEI--WEDSLVIPKSAKNVDAAYALINYLLEPAVQ 322
                                       3.4578899************8..778999**********************99 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 ?    6.1   0.1    0.0044        13      70      96 ..      27      53 ..      11      58 .. 0.64
   2 ?    6.9   0.0    0.0025       7.5       9      40 ..      76     107 ..      71     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0044
                            DUF641 70 eaeeseleaeiqeqrsllktyeitvkk 96
                                      +++ ++leaei+e++++l+ yei  k+
  gi|557694481|ref|YP_008797535.1| 27 NETIRALEAEINELKEKLAQYEIKDKE 53
                                      356666777777777777777776555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0025
                            DUF641   9 llaklFaavSalkaAYvqLQeAhsPydpekiq 40 
                                        ++ +F++  +  + Y++L + ++Pyd  +++
  gi|557694481|ref|YP_008797535.1|  76 GVKVVFDTFESSDEVYAKLFTGQMPYDVTSVT 107
                                       57889**********************98876 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.9e-05      0.12      18      46 ..      28      65 ..      23      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                              ZapB 18 dtitlLqmeieeLkeeneelkeenrele.........e 46
                                      +ti++L  ei eLke+ ++++ + +e++         e
  gi|557694481|ref|YP_008797535.1| 28 ETIRALEAEINELKEKLAQYEIKDKEVRfyfwsetipE 65
                                      8********************99999986666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      809  (0.0451224); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); 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 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2714.74
//
Query:       gi|557694482|ref|YP_008797536.1|  [L=387]
Description: saccharopine dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  110.4   0.0    2.9e-31  109.5   0.0    1.4  2  Sacchrp_dh_C     Saccharopine dehydrogenase C-terminal domain
    1.9e-20   73.4   0.3    2.8e-20   72.9   0.3    1.2  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
    9.5e-08   32.5   0.1    1.5e-07   31.9   0.1    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    2.8e-05   24.6   0.1    5.1e-05   23.8   0.1    1.4  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      5e-05   23.3   0.2      8e-05   22.6   0.2    1.3  1  NAD_binding_10   NAD(P)H-binding
    0.00015   20.9   0.0    0.00021   20.4   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    0.00044   19.9   0.5    0.00069   19.2   0.5    1.2  1  NmrA             NmrA-like family
      0.002   18.2   0.1     0.0035   17.4   0.1    1.5  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
     0.0031   17.0   0.0     0.0044   16.5   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.011   15.9   0.2      0.019   15.0   0.2    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.043   13.9   0.1      0.078   13.1   0.1    1.4  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do


Domain annotation for each model (and alignments):
>> Sacchrp_dh_C  Saccharopine dehydrogenase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.5     9e+03     103     143 ..      76     118 ..      62     121 .. 0.62
   2 !  109.5   0.0   1.8e-34   2.9e-31       1     265 []     129     378 ..     129     378 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.5
                                       EECTHCHHHHHHC.SCSEEEEEEEEEH.HHHHHHHHHH...TTT- CS
                      Sacchrp_dh_C 103 dslpyeelyglpeaktlfrgtlrypgf.sellkslkel...Glls 143
                                       +s++y  +y+l+ ++  +   ++y  +   +  +lk+l   Gl++
  gi|557694482|ref|YP_008797536.1|  76 NSVQY--YYNLEVMQAALKAGVHYVDHgGLYHVTLKQLeldGLFK 118
                                       56666..77777545556666666644444445555554456665 PP

  == domain 2  score: 109.5 bits;  conditional E-value: 1.8e-34
                                       BTTTBHHHHHHHHHHHCCCHTTBECCCCCCCCCCCCECCCCESTTCEEESS-HHHHHHHCCSEEEEEETTEEEECTC CS
                      Sacchrp_dh_C   1 GldPGidhllamkaidevkakggkiesflsycgglpapeasdnplgYkfsWspegvlreltnpakvlengqvkevpg 77 
                                       G++PG+++l+a++a+d++++    ++++++++g ++ +e+   pl   f+Wsp ++++e+t +a vl+ngq++++p 
  gi|557694482|ref|YP_008797536.1| 129 GAQPGLTNLVAKHAYDQLDE----MKAVYIRDGSVDLTENP--PL---FTWSPLTLFDEMTLDAVVLRNGQLVSIPP 196
                                       99***************977....89**********99988..77...****************************6 PP

                                       CCSGCC.TCEEEC.CCCCEECTTECEEECTHCHHHHHH.C.SCSEEEEEEEE..EH.HHHHHHHHHHTTT--SCECC CS
                      Sacchrp_dh_C  78 sellkgakkpiyi.lpglslegypnrdslpyeelyglp.eaktlfrgtlryp..gf.sellkslkelGllseepkee 149
                                        +l++     +++ +p   l +y     + ++el + p ++++     + +   ++   ++k+l ++G+ s+++   
  gi|557694482|ref|YP_008797536.1| 197 LSLME----RVEFpQPVGPLDTYV----TIHSELATFPrSFHDKGLSECDWMegSPgLIFVKKLADIGFASSDD--- 262
                                       66654....444433222555554....668899999965577799999999976666778************8... PP

                                       CCCCHHSTT.C.EHHHHHHHHCCHHC..CCCTTEE..EEEEEEEEEEEETTSEEEEEEEEEEEEE......EHH.SS CS
                      Sacchrp_dh_C 150 alkawlseg.e.spldvlaalLekkl..alepger..Dlvvlqhefgiesdgkkkekktstlvgy......dee.gs 213
                                        ++     g + sp+++l +lLe++    ++ +++  D  + +  + ++  gk+     ++lv y      ++e ++
  gi|557694482|ref|YP_008797536.1| 263 -IEI---GGcKiSPRRFLLKLLESRGlvGYRGDQTpnDWEITRLVIMGKRLGKN-----VKLV-YdilfppKPEwRM 329
                                       .555...667889*************7766654446666666666655544665.....5555.22222333338** PP

                                       SHHHHHHHHHHHHHHHHHHTTSCTSSEEEEGGGS.CHHHHHHHHHHHHHCT- CS
                      Sacchrp_dh_C 214 samaktvGvpaaiaaklildgkikkrGvvtpeelvdpeiyeplleeLekeGi 265
                                       s+ ++ vG+p++ aa++i++g++k+rGv++pe++++p+   ++l+++e +Gi
  gi|557694482|ref|YP_008797536.1| 330 SCAQTGVGIPSSTAAMMIAEGEVKQRGVIPPETCINPD---EFLKKVETHGI 378
                                       *************************************8...*********98 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 !   72.9   0.3   1.7e-23   2.8e-20       2     130 .]       4     125 ..       3     125 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 1.7e-23
                                       EEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
                   Sacchrp_dh_NADP   2 liiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77 
                                        ++G+ G +Gqa+++ l+++++v+ e+ v d +++ l++l +   +++++++++da  +e+ +aa l++ d+v+n +
  gi|557694482|ref|YP_008797536.1|   4 AVLGGaGLTGQAAVRNLLENKKVS-EVLVGDVNEKALQRLSNMFGSSKLTTAKIDARSIEE-TAAFLRGCDVVINSV 78 
                                       678777*****************5.****************999*****************.*************** PP

                                       SGGGHHHHHHHHHHHT-EEEESS-BCGCCSCHCCSHHHHHTHHHHHHCTSEEE CS
                   Sacchrp_dh_NADP  78 ppissldvlkaCietgvhyvdtsiskeertnyalreavlklkekakeagvtav 130
                                        ++++l+v++a++++gvhyvd         +y+++ ++l+l+  +k++  ta+
  gi|557694482|ref|YP_008797536.1|  79 QYYYNLEVMQAALKAGVHYVDHGG------LYHVTLKQLELDGLFKSKSLTAL 125
                                       *********************777......79****************99996 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 !   31.9   0.1     9e-11   1.5e-07       1     100 [.       2     104 ..       2     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 9e-11
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG....GGTTTECEBEEEGGGGGC.TT-SEEEE CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk....aleegkdlkvedvdeeel.kevdivfl 72 
                                       ++a++G+ G +Gq+ +r L e+++v++v +   +++a ++l+++++    +++++   ++e+ +++ + +++d+v+ 
  gi|557694482|ref|YP_008797536.1|   2 RIAVLGGAGLTGQAAVRNLLENKKVSEVLVGDVNEKALQRLSNMFGssklTTAKIDARSIEE-TAA-FlRGCDVVIN 76 
                                       69******************************9999********996443333333333444.333.36******** PP

                                       -SCHHHHHHHHHHHHHTTSEEEESSSTT CS
                    Semialdhyde_dh  73 alpagvskelapklaeagvkviDlssdf 100
                                       ++   +  e+++++++agv+ +D  + +
  gi|557694482|ref|YP_008797536.1|  77 SVQYYYNLEVMQAALKAGVHYVDHGGLY 104
                                       ***********************87765 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 !   23.8   0.1   3.1e-08   5.1e-05       1      81 [.       2      90 ..       2     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.1e-08
                                      EEEEE.TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC..........-EEECECHHHHHHH-SEEEE- CS
                     F420_oxidored  1 kigii.GaGnmgealasgllaagaqpheivvansrnpekaeelaeelg..........vkvtavdneeaaeeadvvvla 68
                                      +i+++ GaG  g+a +++ll++  + +e++v+ + n++ ++ l + +g          ++ ++ +++  ++ +dvv+ +
  gi|557694482|ref|YP_008797536.1|  2 RIAVLgGAGLTGQAAVRNLLENK-KVSEVLVG-DVNEKALQRLSNMFGssklttakidARSIE-ETAAFLRGCDVVINS 77
                                      79********************8.******88.*********************664433333.4555566******** PP

                                      S-HHHHHHHHHHC CS
                     F420_oxidored 69 vkpedveevlsel 81
                                      v++++  ev++++
  gi|557694482|ref|YP_008797536.1| 78 VQYYYNLEVMQAA 90
                                      *****99999887 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 !   22.6   0.2   4.9e-08     8e-05       1      70 [.       7      80 ..       7      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.9e-08
                                      TTTSHHHHHHHHHHHHC-T-EEEEEET.THHHCHHHH...CTTTCEEEE--TT-CCHHHHHHTT-SEEEES--- CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghevtalvR.npeklaele...aeeglevvegdvtdvedlaealkgadaVvsalgg 70
                                      G+ G +G+++v+ ll++++++ +++   n++ l++l+    +++l++ ++d+ + e+ a+ l+g+d+V+ ++  
  gi|557694482|ref|YP_008797536.1|  7 GGAGLTGQAAVRNLLENKKVSEVLVGDvNEKALQRLSnmfGSSKLTTAKIDARSIEETAAFLRGCDVVINSVQY 80
                                      999**************96655555431344444443333789**************************98864 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 !   20.4   0.0   1.3e-07   0.00021       1      72 [.       4      76 ..       4      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.3e-07
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlresp.elleelskvnvkkviegDvtdkdkleealegvdvvih 72
                                      +v+GgaG  G+a v++L++ +++ ev v D++e+  + l++++ +   ++ + D ++ ++  + l+g dvvi 
  gi|557694482|ref|YP_008797536.1|  4 AVLGGAGLTGQAAVRNLLENKKVSEVLVGDVNEKAlQRLSNMFGSSKLTTAKIDARSIEETAAFLRGCDVVIN 76
                                      59****************************998752334555555555599********************96 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.5   4.2e-07   0.00069       1      94 [.       3      95 ..       3     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.2e-07
                                      EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHS.TT...EEEES-TT-HHHHHHHHTT-SEEEE---GG CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslkea.Gv...elvkgdlddkeslvealkgvdvvfsvtgfy 75
                                      I+v+G++G  G++ vr ll+++    +lv d+++++++ l++  G    ++ k d+ + e  ++ l+g dvv+ ++++y
  gi|557694482|ref|YP_008797536.1|  3 IAVLGGAGLTGQAAVRNLLENKKVSEVLVGDVNEKALQRLSNMfGSsklTTAKIDARSIEETAAFLRGCDVVINSVQYY 81
                                      89*********************************9999997435411166688888888888899******9999866 PP

                                      S-HHHHHHHHHHHHHHHS- CS
                              NmrA 76 skeiedgkklvdAakeaGv 94
                                           +  ++ +Aa +aGv
  gi|557694482|ref|YP_008797536.1| 82 -----YNLEVMQAALKAGV 95
                                      .....44555666666666 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   2.2e-06    0.0035       1      95 [.       1      98 [.       1     126 [. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-06
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTT..TTBHH.HHSSSS--S-BEBSSHHHHHHH-SEEEE-S- CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkesele..gkdag.ellglgklgvavtddleevlekadvliDFTt 76
                                      +++av+G +G  G++ v+ + e++++  v + d +e++l+  ++ +g + l + k++    ++ +++l+ +dv+i   +
  gi|557694482|ref|YP_008797536.1|  1 MRIAVLGGAGLTGQAAVRNLLENKKVSEVLVGDVNEKALQrlSNMFGsSKLTTAKIDARSIEETAAFLRGCDVVINSVQ 79
                                      89**********************9987777777664333002333324455557777777888888889********9 PP

                                      HHHHHHHHHHHHHTT-EEE CS
                            DapB_N 77 peavlenlklalekgvklV 95
                                          le++++al++gv+ V
  gi|557694482|ref|YP_008797536.1| 80 YYYNLEVMQAALKAGVHYV 98
                                      99*************9988 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.7e-06    0.0044       1      71 [.       3      77 ..       3      92 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                                      EEEETTTSHHHHHHHHHHHHCT..SEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase  1 ilVtGatGfiGsalvkallekg..yevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihl 71
                                      i V+G++G+ G+a v++lle++   ev++ d +  +++ +rl +       +  ++d +  ++++++++  ++d+vi+ 
  gi|557694482|ref|YP_008797536.1|  3 IAVLGGAGLTGQAAVRNLLENKkvSEVLVGDVN--EKALQRLSNMfgssklTTAKIDARSIEETAAFLR--GCDVVINS 77
                                      68******************9986668888887..4444444444788988889999999999999999..9*****97 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.2   1.2e-05     0.019      16      84 ..       5      79 ..       1      94 [. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                                      EEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT......ET-EEEEGCGHHHHHHT-SEEEE-SS CS
                      Shikimate_DH 16 lliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelk.....geeiealkleelkellaeadvvisata 84
                                      +l GaG +++ ++++Ll++ +v +v+v   + +  ++l + ++     +++i a+++ee  + l+ +dvvi +++
  gi|557694482|ref|YP_008797536.1|  5 VLGGAGLTGQAAVRNLLENkKVSEVLVGDVNEKALQRLSNMFGsskltTAKIDARSIEETAAFLRGCDVVINSVQ 79
                                      4559**********99865499*****9999999999988775111114567889999*************9975 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 ?   13.1   0.1   4.8e-05     0.078       1      74 [.       1      75 [.       1      77 [. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.8e-05
                                      EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHH.HHCHCCSTS-EEEEESSGGGGTTESEEE CS
                           Ldh_1_N  1 vkvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldl.shistflsvkvkvsekeeealkdadvvv 74
                                      +++av+G aG  Gq+   +l+++k ++e+ + D+++++l+     + s   t++++++++ e++ + l+++dvv+
  gi|557694482|ref|YP_008797536.1|  1 MRIAVLGGAGLTGQAAVRNLLENKKVSEVLVGDVNEKALQRLSNMFgSSKLTTAKIDARSIEETAAFLRGCDVVI 75
                                      69*********************99999*******9977644333312333444566667778888899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); 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:                        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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2773.33
//
Query:       gi|557694483|ref|YP_008797537.1|  [L=763]
Description: molybdenum hydroxylase family protein large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-186  619.0   0.0   7.6e-186  618.8   0.0    1.0  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    5.3e-34  116.9   0.7    1.2e-33  115.7   0.3    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 !  618.8   0.0  8.5e-190  7.6e-186       1     550 []     149     696 ..     149     696 .. 0.97

  Alignments for each domain:
  == domain 1  score: 618.8 bits;  conditional E-value: 8.5e-190
                                       STTT-STTEEEEEEE..E-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHH CS
                     Ald_Xan_dh_C2   1 vheeapdnvlakiek..GdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlv 75 
                                       vhe+++dnv++++++  Gdve+ f+ead vve ++ ++r ++ ++E+++++a +d+ +  ltv+sstq ph +r+ +
  gi|557694483|ref|YP_008797537.1| 149 VHETLEDNVCYRWRRvyGDVEKLFKEADEVVETRLVIQRLAPSAMEPRGVVALYDGYNRMLTVWSSTQFPHRLRTWI 225
                                       69999******888666************************************************************ PP

                                       HHHHT--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS CS
                     Ald_Xan_dh_C2  76 aevlglpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdG 152
                                       +  l++pen++rvi+p+vGGGFG+K++++p+ev++ ++A+k+grpVk+ +dR+e++ at++++++++++++++++ G
  gi|557694483|ref|YP_008797537.1| 226 STSLNMPENRIRVIAPEVGGGFGSKLNHYPEEVIIPHLAMKLGRPVKWFEDRSENLSATTHGRDMIAHVSAAVKRTG 302
                                       ***************************************************************************** PP

                                       -EEEEEEEEEEEESST.HHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 153 kitaldvdlladaGay.adlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdel 228
                                        i+a++++llad Gay   +++  +  a+ +++g+Y ++ +++e+ +vytN++ ++a+RG+G+p+a +++Er++d++
  gi|557694483|ref|YP_008797537.1| 303 LILAIRLKLLADLGAYsYVYTQDNPIMAARMVQGCYMLQGLDLEVIGVYTNKMATDAYRGAGRPEASYIIERTVDAV 379
                                       ****************55889999999999999******************************************** PP

                                       HHHHT--HHHHHHHHBCECGCC.SEEET...EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEE CS
                     Ald_Xan_dh_C2 229 AeelgldplelRrrNlikpgeltpygqp...vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvve 302
                                       A++lg+dp+e+RrrN+i +++l py++    vydsgd++++ld+l++++dye++++ ++e +++++  Gigl++++e
  gi|557694483|ref|YP_008797537.1| 380 ARRLGMDPAEIRRRNFIPAEKL-PYKTLtgfVYDSGDYAKALDTLLAAADYEGLKKMRDELRKQGRYLGIGLSTFIE 455
                                       *****************99999.**9977899******************************88899********** PP

                                       EBS--S.EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT CS
                     Ald_Xan_dh_C2 303 giglgftakflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaS 379
                                        +++++       ++a+vrv+++G+ +v+t+++++GqG et++aqi+a++L+v+++dv+v++gdt  +p+g+gta+S
  gi|557694483|ref|YP_008797537.1| 456 VCNFSY-------QSASVRVEPSGKTLVFTSTSPHGQGEETAFAQIVADALDVSIDDVQVIHGDTLAIPYGWGTAGS 525
                                       **5444.......59************************************************************** PP

                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH.......TTSSEE CS
                     Ald_Xan_dh_C2 380 rstdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl.......ervsls 446
                                       ++ +++gnA+++A++++r+++ +iaa++le+sped+e edg+++vk   eksvs++e+aa ay         + +l+
  gi|557694483|ref|YP_008797537.1| 526 WTLTSGGNAILNACKQIRQKMVAIAAHHLECSPEDIEAEDGRFFVKdapEKSVSFEEVAAMAYDpeklpegVEMGLA 602
                                       *************************************************9**************9999988888*** PP

                                       EEEEE...EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT- CS
                     Ald_Xan_dh_C2 447 atgfyktldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmE 523
                                       at+fy          +p  +f+yga++a Vev +etg+v+v+++v v DvGk++Np++vegQi+GG+vq++G+al+E
  gi|557694483|ref|YP_008797537.1| 603 ATSFY----------NPDLTFPYGAYLALVEVFPETGKVEVKKAVLVNDVGKVVNPMLVEGQIHGGAVQALGQALYE 669
                                       *****..........7889********************************************************** PP

                                       --EEETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 524 elvydedGqlltasladYkiPtaadiP 550
                                       e+vyde+G llt+s+adY++P+a++iP
  gi|557694483|ref|YP_008797537.1| 670 EVVYDENGALLTSSFADYLLPSATEIP 696
                                       **************************9 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 !  115.7   0.3   1.4e-37   1.2e-33       2     110 .]      20     133 ..      19     133 .. 0.93
   2 ?   -2.9   0.0      0.95   8.5e+03      23      74 ..     282     331 ..     281     335 .. 0.59

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 1.4e-37
                                       T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT.TSSS-EE....EESS- CS
                      Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig.siledee....dalla 73 
                                       Ge vYvdD+ +pg+ly+ fvrS++ahA+i s+dv aa++l GVvav+t+kdl ++  +   ++++de+    ++ la
  gi|557694483|ref|YP_008797537.1|  20 GESVYVDDVRLPGMLYAVFVRSPHAHARIRSMDVAAARSLRGVVAVYTGKDLRGQVGSQVvETIMDEKrfvqRQPLA 96 
                                       9***************************************************9886555557777777688889*** PP

                                       SSEESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                      Ald_Xan_dh_C  74 edkvrsvgqavaavvAedeetArkAaklvkveYeelp 110
                                        d v++vg++va+vvAed +tAr+Aa+lv+veYe+lp
  gi|557694483|ref|YP_008797537.1|  97 VDVVKFVGEPVAVVVAEDLYTARDAAELVQVEYEPLP 133
                                       **********************************986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.95
                                       -SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-S CS
                      Ald_Xan_dh_C  23 StkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallae 74 
                                       S+  h++ +  +vsaa + +G +  i  k l++ +  +   ++d++  ++a 
  gi|557694483|ref|YP_008797537.1| 282 SATTHGRDMIAHVSAAVKRTGLILAIRLKLLADLGAYSYVYTQDNP--IMAA 331
                                       5566666666677777777777777777766666655543343333..5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (763 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 4995.42
//
Query:       gi|557694484|ref|YP_008797538.1|  [L=445]
Description: aminotransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-98  329.6   0.0    2.6e-98  329.4   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 !  329.4   0.0  1.4e-102   2.6e-98      11     406 .]      25     433 ..      17     433 .. 0.97

  Alignments for each domain:
  == domain 1  score: 329.4 bits;  conditional E-value: 1.4e-102
                                       EEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-.. CS
                       Aminotran_3  11 lvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgl 87 
                                       l i  aeG+y td+ gk+ylD+ s+   vnlGh++ +v++avk+ ++k+ +++ +a+t e  ++l++kl++++p gl
  gi|557694484|ref|YP_008797538.1|  25 LHIVDAEGCYFTDASGKKYLDFSSQLVCVNLGHRNRNVIEAVKNYLEKTPYLM-PAFTCEVRAELSRKLVEILPPGL 100
                                       67899************************************************.*********************** PP

                                       SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTB CS
                       Aminotran_3  88 dkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypd 164
                                        k+f+ +sG+eA+e+AlK+ar        t ++kiia   ++HG t ++l+vtg+     ++  + +p+ v+++ p+
  gi|557694484|ref|YP_008797538.1| 101 RKFFYSTSGTEANEAALKIARV------FTGRHKIIARYRSYHGATAASLAVTGDIRRWYAEAVDAVPGAVFAPDPY 171
                                       **********************......***************************99999999999*********** PP

                                       GGGTB-HHHHHHHHHHHHHHHH..CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTT CS
                       Aminotran_3 165 eevlkeneeeeaalleeleale..kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfG 239
                                       +++++ +    ++   ++  +      + +vaAvivEp+ g  Gv+v++pe++ klre++++h+vll++DEv++G G
  gi|557694484|ref|YP_008797538.1| 172 CYRCPLKLTYPDCGVACADYVDymLSYDGNVAAVIVEPVVGTNGVIVPPPEYMPKLREITRRHGVLLVADEVMSGWG 248
                                       ********999999999888887778999************************************************ PP

                                       TTSSSSGGGGCTS--SEEEE-GGGGTT.SS-EEEEEEHHHHTTS-TTS..B--TTTT-HHHHHHHHHHHHHHHHTTH CS
                       Aminotran_3 240 rTGklfAlehagvspDlmtlaKaltgG.lplsavlataevmqalapgs..hgsTfgGnplacavalavleiieeekl 313
                                       rTG++fA++h++v+pD++t+aK++t+  lpl  +++ +++ + + +    hg+T+ + pl  a+a+a+++   + +l
  gi|557694484|ref|YP_008797538.1| 249 RTGEWFAVNHWNVEPDILTTAKGITSAyLPLGLTATSEKISEYFDDHFfpHGHTYEAHPLTLAAAVAAIDEYRRLNL 325
                                       ********************************************666599*************************** PP

                                       HHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC................HHHHHHHHHCTEE- CS
                       Aminotran_3 314 lenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke................keilkkakekGvli 374
                                       +e+ +++g++l ++L+e+ +++  ++evRg+Gl+ a++l+++++++e                 ++++++ ++Gv +
  gi|557694484|ref|YP_008797538.1| 326 IERSRRMGEYLGKRLKEVGDRHPSVGEVRGLGLFWAVDLTKNQRTREpfnvpkdkysgaplmvDQVAAEMMKQGVFV 402
                                       *******************************************98889***************99************ PP

                                       EEETTTEEEE---TT--HHHHHHHHHHHHHHH CS
                       Aminotran_3 375 lsaGdnvirllppliitdeeidelleilkkal 406
                                       +s   n + ++ppli ++e+id+++e+l  al
  gi|557694484|ref|YP_008797538.1| 403 MSWI-NHLVIAPPLIAEKEDIDKGVEALDSAL 433
                                       **99.9999******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3333.73
//
Query:       gi|557694485|ref|YP_008797539.1|  [L=445]
Description: glutamate-1-semialdehyde-2,1-aminomutase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-70  235.6   0.0      1e-69  235.2   0.0    1.1  1  Aminotran_3    Aminotransferase class-III
     0.0019   17.5   0.0     0.0048   16.1   0.0    1.7  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
      0.071   12.7   0.0       0.33   10.5   0.0    1.9  2  DAO            FAD dependent oxidoreductase


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 !  235.2   0.0   1.7e-73     1e-69       9     375 ..      37     405 ..      29     429 .. 0.88

  Alignments for each domain:
  == domain 1  score: 235.2 bits;  conditional E-value: 1.7e-73
                                       SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT- CS
                       Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapk 85 
                                        ++++ ++ G++++dvdg++y+D + ++ +++ Gh+hP++v+avk qa++l  ++   +  e  +++a  + +++p+
  gi|557694485|ref|YP_008797539.1|  37 NPVFVVRGSGSRVWDVDGNEYIDYLLGFGSLINGHCHPRIVEAVKRQAEEL--LM-SGTPVELEMEVASRIQRVVPN 110
                                       4699***********************************************..44.5788999999*********** PP

                                       ..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB.-TSEEEE- CS
                       Aminotran_3  86 gldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpf.lpevvrlk 161
                                         ++v++a +G+eA++ A+++ar+       t ktkii+f+g++HG+  + l   +s ++   ++ pf +p  + ++
  gi|557694485|ref|YP_008797539.1| 111 -AEMVLFASTGTEATMEAIRIARA------VTGKTKIIKFEGSYHGHHDYVLWSVES-SNPGLEISPFrIPYYPGIP 179
                                       .9**********************......9******************99977777.4445555666566666666 PP

                                       TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT CS
                       Aminotran_3 162 ypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf 238
                                        +     k+   +    le+l+++ ++   ++aA+i Ep+ ++ Gv+ ++p+fl++l+el+++ d+lli+DEv tGf
  gi|557694485|ref|YP_008797539.1| 180 ESV---GKTVTIAPWNNLEALRKIVRRNRSNLAAIIAEPVMANNGVILPKPGFLKALKELAEESDALLIFDEVITGF 253
                                       665...3334445566688999999**************************************************** PP

                                       ..TTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS..B--TTTT-HHHHHHHHHHHHHHHH. CS
                       Aminotran_3 239 ..GrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs..hgsTfgGnplacavalavleiiee. 310
                                         +  G   A e++gv+pDl t++Kal+gG p++av++++++ + + pg+   g+T+ + pl  a ala l+i+   
  gi|557694485|ref|YP_008797539.1| 254 rlAPGG---AQEYFGVKPDLATFGKALGGGVPIAAVTGRRDILENIGPGKigFGGTYNAHPLSLAGALANLDILLGn 327
                                       867777...9***************************************9999********************9875 PP

                                       .TTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC............HHHHHHHHHCTEE- CS
                       Aminotran_3 311 .ekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke............keilkkakekGvli 374
                                         +  ++ + +g++l +gL+++ ++  v + v g+G ++ i +++  e  +            ++ + k+ ekGv+i
  gi|557694485|ref|YP_008797539.1| 328 gGEAYQRLHSTGEKLIKGLRQAIEDTGVEAIVQGLGPLFQIYFTNLPEISSyreklqtnsaayTAWALKMFEKGVYI 404
                                       67899******************99978888999*****99888777665577778888877766777778888887 PP

                                       E CS
                       Aminotran_3 375 l 375
                                       +
  gi|557694485|ref|YP_008797539.1| 405 Y 405
                                       6 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 !   16.1   0.0   8.1e-07    0.0048      49     300 ..      96     358 ..      73     429 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.1e-07
                                       HHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH.HTTT-EEEEEESS-THHHHHHHHT......TSE.. CS
                     Aminotran_1_2  49 leealakflgrseklklkreaavvvgsGagaliealifllk.lnpgdeilvpdptyasyknilrls......gge.. 116
                                       le ++a+ ++   ++  ++e  v++ s  +++   +i++++ +  +++i+ ++ +y  +++++ +s      g+e  
  gi|557694485|ref|YP_008797539.1|  96 LEMEVASRIQ---RVVPNAE-MVLFASTGTEATMEAIRIARaVTGKTKIIKFEGSYHGHHDYVLWSvessnpGLEis 168
                                       5555555555...4555555.44444444444444444444244455566666666666666655544444433311 PP

                                       EEEEEBEET...........TTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HH.HHHHHHHHHHHTT CS
                     Aminotran_1_2 117 vvryplyse...........edfhldlealeealkeapegnkktkvilvesphNPtGtvatle.eleklldlakkyn 181
                                        +r+p+y+            +   ++leal + ++++ ++      i+ e +  + G++++++  l++l +la++  
  gi|557694485|ref|YP_008797539.1| 169 PFRIPYYPGipesvgktvtiAP-WNNLEALRKIVRRNRSNL---AAIIAEPVMANNGVILPKPgFLKALKELAEESD 241
                                       4444555446666662222111.245666666666655444...5*************99987357888899***** PP

                                       EEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHH CS
                     Aminotran_1_2 182 lllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqa 258
                                       +ll++De+  gf + + +a++ +++v+++ +     +++Ka+G  G  +++++g  ++++ +   + +f  +  + +
  gi|557694485|ref|YP_008797539.1| 242 ALLIFDEVITGFRLAPGGAQE-YFGVKPDLA-----TFGKALGG-GVPIAAVTGRRDILENIGPGKIGFGGTYNAHP 311
                                       **************9879888.******988.....******84.66778888888888888877777777333333 PP

                                       HHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHS....TEEEE CS
                     Aminotran_1_2 259 avaaalsdallkqs.eleemrqrlqkrrkelrdeLael....glkvl 300
                                       + +a + + l++   +  e+ qrl++  ++l ++L+++    g++ +
  gi|557694485|ref|YP_008797539.1| 312 LSLAGALANLDILLgNGGEAYQRLHSTGEKLIKGLRQAiedtGVEAI 358
                                       33333333333333377777777777777777777766665555554 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.26   1.5e+03     145     176 ..     226     257 ..     197     277 .. 0.80
   2 ?   10.5   0.0   5.5e-05      0.33     131     294 ..     296     439 ..     277     442 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHHTT-EEEESECEEEEEEEE CS
                               DAO 145 pakltaalaraaealGveilegtevtgleeed 176
                                          +++al + ae+  + +++ + +tg++   
  gi|557694485|ref|YP_008797539.1| 226 KPGFLKALKELAEESDALLIFDEVITGFRLAP 257
                                       55699999999999999999999999996643 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 5.5e-05
                                       TS.EEEEETTEEEEEHHHHHHHHHHH..HHHTT-EEEESECEEEEEEEETCEEEEE...EECTEEEEEEEEEEE--G CS
                               DAO 131 ll.galfypdtgqvdpakltaalara..aealGveilegtevtgleeedgkvwgve...rttpgendaadavVnaaG 201
                                       +  g +++ +t +++p  l+ ala+   +  +G+e +++   tg +     ++g++   +      + ++a+V   G
  gi|557694485|ref|YP_008797539.1| 296 IGpGKIGFGGTYNAHPLSLAGALANLdiLLGNGGEAYQRLHSTGEKL----IKGLRqaiE----D-TGVEAIVQGLG 363
                                       4447789999999************9999**********99999644....777743212....2.24699****** PP

                                       GGHH.HHHTTCTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESSEEETTCSS CS
                               DAO 202 awsd.llgllkeldlpispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgtadeesgddd 277
                                       +  +  +    +l + is  r    + +        ++  ++     + ++gvy++++ + r+++ + +     d+d
  gi|557694485|ref|YP_008797539.1| 364 PLFQiYF---TNL-PEISSYREKLQTNSA-------AYTAWA---LKMFEKGVYIYADDGERIVLSTQH---T-DED 422
                                       *988644...445.455555555555522.......223333...78999*******976677777643...4.444 PP

                                       TSCSHHHHHHHHHHHHH CS
                               DAO 278 pevdeedidellealrk 294
                                       +e + ++++e  ++++k
  gi|557694485|ref|YP_008797539.1| 423 VELTVAAAEEAFREVKK 439
                                       47777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3310.85
//
Query:       gi|557694486|ref|YP_008797540.1|  [L=433]
Description: 4-aminobutyrate aminotransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-122  407.3   0.0   6.3e-122  407.1   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
  ------ inclusion threshold ------
        0.1   11.8   0.0        0.4    9.8   0.0    1.8  2  Aminotran_1_2  Aminotransferase class I and II
       0.22   11.3   0.0       0.36   10.6   0.0    1.3  1  REC114-like    Meiotic recombination protein REC114-like


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 !  407.1   0.0  1.1e-125  6.3e-122      10     406 .]      20     425 ..      11     425 .. 0.98

  Alignments for each domain:
  == domain 1  score: 407.1 bits;  conditional E-value: 1.1e-125
                                       CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-. CS
                       Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkg 86 
                                       ++ it++e++ l d +g++y+D++s+i v+nlGh + ++ +av++++++l+h++f + ++  +++++ekl++ +p++
  gi|557694486|ref|YP_008797540.1|  20 PITITRGENALLIDSEGNHYIDFTSGIGVINLGHGNTEIGEAVEKALKNLWHLCFMVANYPGYVEVVEKLVETVPGD 96 
                                       499************************************************************************** PP

                                       .S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-T CS
                       Aminotran_3  87 ld.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlky 162
                                       ++ + +l+nsG+eAve+A+K+ar+       t++++ ++f+++fHGrt++a+++tg+ ++yk +f+pf+p v ++++
  gi|557694486|ref|YP_008797540.1|  97 FEkRGVLFNSGAEAVENAVKIARH------VTKRPYAVSFENSFHGRTYLAMALTGKYEPYKVDFEPFPPAVEHAPF 167
                                       *9889*******************......9********************************************** PP

                                       TBGGGTB-HHHHHHHHHHHHHHHH......CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE- CS
                       Aminotran_3 163 pdeevlkeneeeeaalleeleale......kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDE 233
                                       p+++++++ ++   + le++  ++      ++   ++a +i+EpiqgegG+v+a+pe+l++lr++c++h++++i DE
  gi|557694486|ref|YP_008797540.1| 168 PYCYRCPFGQSYPGCGLECMDYIKkhffktRVPPHKIACFIIEPIQGEGGFVPAPPEYLRELRSVCDEHGIVFIDDE 244
                                       ***************99999999888898889999****************************************** PP

                                       TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHH CS
                       Aminotran_3 234 vqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiiee 310
                                       vqtGf rTG ++A+eh gv+pDl+t++Kal++Glplsav+++a +m+ + pgs gsTfgGnp+aca+a++v+ei+++
  gi|557694486|ref|YP_008797540.1| 245 VQTGFCRTGRFYAIEHSGVAPDLVTVGKALANGLPLSAVAGKASLMDKMPPGSLGSTFGGNPVACAAAVKVFEIMKR 321
                                       ***************************************************************************** PP

                                       TTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCTEE-EEETT.. CS
                       Aminotran_3 311 ekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekGvlilsaGd.. 379
                                       ++++ +a +lg+ +  +L e+ ++ e +++vRg+G+m a+el+++++ ke        +l+ a+  G+l+l+aG   
  gi|557694486|ref|YP_008797540.1| 322 DNMAARAMRLGELMARRLGEFFERFELVGDVRGLGVMRAFELVKDRRSKEpavketSMVLEHARRRGLLLLKAGLys 398
                                       ***********************************************9999**999889***************888 PP

                                       TEEEE---TT--HHHHHHHHHHHHHHH CS
                       Aminotran_3 380 nvirllppliitdeeidelleilkkal 406
                                       nv+rl ppl+i++e ++++l++++++l
  gi|557694486|ref|YP_008797540.1| 399 NVVRLHPPLTIQEELLEKGLDMVEECL 425
                                       **********************99886 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 ?   -0.7   0.0       0.1   6.3e+02       4      88 ..      49     119 ..      46     152 .. 0.66
   2 ?    9.8   0.0   6.7e-05       0.4     165     253 ..     221     305 ..     203     360 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.1
                                       EESSSSSTTSTTSSHHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHH CS
                     Aminotran_1_2   4 inLgsneylgdsgkptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGaga 79 
                                       inLg ++   +       e+++++ +   + + ++++y+ +    e+ e+l + +      ++++   v++ sGa a
  gi|557694486|ref|YP_008797540.1|  49 INLGHGNTEIG-------EAVEKALKnLWHLCFMVANYPGY---VEVVEKLVETVP----GDFEKR-GVLFNSGAEA 110
                                       55665555555.......44444444234444444444444...477777777776....467777.9999999999 PP

                                       HHHHHHHHH CS
                     Aminotran_1_2  80 liealifll 88 
                                       + +a++ + 
  gi|557694486|ref|YP_008797540.1| 111 VENAVKIAR 119
                                       988877665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 6.7e-05
                                       --HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH.HGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHH CS
                     Aminotran_1_2 165 atleeleklldlakkynlllfvDeaYagfvfgsldavat.ranveeepnllivgslsKafGlaGeRvGyilgnaavv 240
                                       a++e l++l +++++++++ + De+  gf+ +  +++a+ +++v+++       +++Ka++  G+ + +++g+a + 
  gi|557694486|ref|YP_008797540.1| 221 APPEYLRELRSVCDEHGIVFIDDEVQTGFCRT-GRFYAIeHSGVAPDLV-----TVGKALA-NGLPLSAVAGKASLM 290
                                       68899**************************9.6899988999998755.....7788873.455557777777777 PP

                                       HHHHHHHHHHTS..S CS
                     Aminotran_1_2 241 sqlrklsrpfls..s 253
                                       + +   s + ++   
  gi|557694486|ref|YP_008797540.1| 291 DKMPPGSLGSTFggN 305
                                       777777666665432 PP

>> REC114-like  Meiotic recombination protein REC114-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0     6e-05      0.36     209     233 ..      65      89 ..      59      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6e-05
                       REC114-like 209 dlepflrlCLlDqnFpaFVEeVEke 233
                                        l+++ +lC++  n+p++VE VEk 
  gi|557694486|ref|YP_008797540.1|  65 ALKNLWHLCFMVANYPGYVEVVEKL 89 
                                       688999*****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3071.61
//
Query:       gi|557694487|ref|YP_008797541.1|  [L=322]
Description: beta-lactamase domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   95.5   0.3    5.5e-27   95.1   0.3    1.2  1  Lactamase_B      Metallo-beta-lactamase superfamily
    1.2e-06   28.1   0.1    2.1e-06   27.4   0.1    1.5  1  Lactamase_B_2    Beta-lactamase superfamily domain
     0.0055   16.2   0.1     0.0088   15.5   0.1    1.3  1  Lactamase_B_6    Metallo-beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.023   14.6   0.0       0.04   13.8   0.0    1.4  1  Lactamase_B_3    Beta-lactamase superfamily domain
      0.042   14.1   0.0        6.2    7.2   0.0    2.4  2  Arg_decarb_HB    Arginine decarboxylase helical bundle domain
      0.052   13.4   0.0        6.8    6.6   0.0    2.4  2  Polysacc_deac_1  Polysaccharide deacetylase
      0.057   13.0   0.0      0.087   12.4   0.0    1.2  1  SRP54            SRP54-type protein, GTPase domain
       0.15   12.4   0.7       0.33   11.3   0.7    1.5  1  HTH_31           Helix-turn-helix 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 !   95.1   0.3   2.4e-30   5.5e-27       3     197 .]      21     211 ..      19     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 2.4e-30
                                       CCSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                       Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79 
                                       ++pv ++l+  d++ iL+DtG+++  ++++       l+ ++++ +ilTHlH+DH Gg+  +++a ++p++++++e+
  gi|557694487|ref|YP_008797541.1|  21 DLPVRCFLLKEDEKRILVDTGYGETVPQLL-----SILEKRNLSSIILTHLHIDHSGGALAVKKAKNIPIIYHKLEL 92 
                                       57899************************9.....6***************************************** PP

                                       HCCHCHHHHHHHHHCCHH.......TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEEC CS
                       Lactamase_B  80 palfmeeaddaasrkgll.......lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftG 149
                                       + l+     d + +            ++ ++ k+ ++++  +++++ +  +  +++pgh++gh+   + g++ ++tG
  gi|557694487|ref|YP_008797541.1|  93 ETLNQAVNLDKSIHRMFTdgsvdflQEALHVLKVLPPPDLFAEDGMAMSMWRLMHTPGHTPGHI--ILVGENHALTG 167
                                       ********9988888888*******666666666666666666666666666666666666555..5568899**** PP

                                       TTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 150 DallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       D++l+ et  +       + +  ++ ++yl+sl k+a l++e+lvp+H
  gi|557694487|ref|YP_008797541.1| 168 DLILVKETSNVAY----VPLPGYHPLRNYLESLVKVASLNVEMLVPSH 211
                                       *************....889999999*********************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 !   27.4   0.1   9.6e-10   2.1e-06       2      94 ..      35     112 ..      34     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 9.6e-10
                                       EEEES--TT.HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHH CS
                     Lactamase_B_2   2 riLiDagpd.lrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyl 77 
                                       riL+D+g + ++ q+l+ l      +  + +  ++lth H+DH  g+l +++   k++p++ +k  l++l++    +
  gi|557694487|ref|YP_008797541.1|  35 RILVDTGYGeTVPQLLSIL-----EK--RNLSSIILTHLHIDHSGGALAVKKA--KNIPIIYHKLELETLNQAVNLD 102
                                       9********5444444444.....33..59**********************4..56**999998888888875443 PP

                                       HCHTTTTEEEEEE-TTS CS
                     Lactamase_B_2  78 aleeepavnvheldwge 94 
                                        +       +h + +++
  gi|557694487|ref|YP_008797541.1| 103 KS-------IHRMFTDG 112
                                       33.......44444444 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 !   15.5   0.1   3.9e-06    0.0088       1      85 [.      28     102 ..      28     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.9e-06
                     Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnip.vyatlpvv 76 
                                       lL+ d+ +iL+D G  e+ v   + l+ lek   +++ i+L+h  ++h G+ al ++k      +nip +y  l   
  gi|557694487|ref|YP_008797541.1|  28 LLKEDEKRILVDTGYGET-V--PQLLSILEK--RNLSSIILTHLHIDHSGG-ALAVKK-----AKNIPiIYHKLELE 93 
                                       78999***********98.4..468888887..689**************9.334433.....24555246666666 PP

                     Lactamase_B_6  77 kLGrvslld 85 
                                        L + + ld
  gi|557694487|ref|YP_008797541.1|  94 TLNQAVNLD 102
                                       666665555 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 ?   13.8   0.0   1.8e-05      0.04       9      71 ..      26      92 ..      22     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.8e-05
                     Lactamase_B_3  9 sflletagarilvDPf...ka.nlgyeppaeeaDlvlisqaledHahletlkqlaenvkvleegesl 71
                                      +fll+ +++rilvD +   +  +l    ++++   +++++ + dH   +   + a+n++++ ++ +l
  gi|557694487|ref|YP_008797541.1| 26 CFLLKEDEKRILVDTGygeTVpQLLSILEKRNLSSIILTHLHIDHSGGALAVKKAKNIPIIYHKLEL 92
                                      9*************8855422578888889***************8654433336777777775444 PP

>> Arg_decarb_HB  Arginine decarboxylase helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0028       6.2      24      52 ..      92     120 ..      76     122 .. 0.89
   2 ?    4.6   0.0     0.017        38      22      52 ..     221     251 ..     191     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0028
                     Arg_decarb_HB  24 qEiyhDavhyldearelFrlGllsLeerA 52 
                                       +E+++ av + ++++ +F++G ++  + A
  gi|557694487|ref|YP_008797541.1|  92 LETLNQAVNLDKSIHRMFTDGSVDFLQEA 120
                                       799*******************9987776 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.017
                     Arg_decarb_HB  22 nlqEiyhDavhyldearelFrlGllsLeerA 52 
                                       +++Ei+    + l +a ++ ++G lsL+e A
  gi|557694487|ref|YP_008797541.1| 221 RVREIFSHHRERLRQAASALEKGRLSLREVA 251
                                       689999999*******************977 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.003       6.8      12      34 ..      37      59 ..      32      64 .. 0.89
   2 ?    4.1   0.0     0.018        41       6      29 ..     102     125 ..      98     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.003
                                      EEEESSCSCHHHHHHHHHHCT-- CS
                   Polysacc_deac_1 12 TfDdgprdntteilpvLkkykvk 34
                                       +D+g+ ++++++l++L+k ++ 
  gi|557694487|ref|YP_008797541.1| 37 LVDTGYGETVPQLLSILEKRNLS 59
                                      68*****************9875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.018
                                       STEEEEEEEESSCSCHHHHHHHHH CS
                   Polysacc_deac_1   6 kksvalTfDdgprdntteilpvLk 29 
                                       +ks++ +f dg+ d+ +e+l vLk
  gi|557694487|ref|YP_008797541.1| 102 DKSIHRMFTDGSVDFLQEALHVLK 125
                                       799999*****************8 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.9e-05     0.087     113     172 ..      30      87 ..      11     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                                       SSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHHHHHHTS-EEE CS
                             SRP54 113 kpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsiaaelklPikf 172
                                       k+de+ + +d+  g+++  q  +  e+ +++++ilt l  d +gG al+++++ ++Pi++
  gi|557694487|ref|YP_008797541.1|  30 KEDEKRILVDTGYGETV-PQLLSILEKRNLSSIILTHLHIDHSGG-ALAVKKAKNIPIIY 87 
                                       56666667777777654.45555566778**********999877.69**********98 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7   0.00015      0.33       8      32 ..     232     262 ..     226     264 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                            HTH_31   8 alRera......GLsqeevAerlgvsestls 32 
                                       +lR++a      +Ls++evAe +++s+   s
  gi|557694487|ref|YP_008797541.1| 232 RLRQAAsalekgRLSLREVAEEIRWSKGSFS 262
                                       688888999**99*************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2438.15
//
Query:       gi|557694488|ref|YP_008797542.1|  [L=270]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); 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:                         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: 00:00:00.42
# Mc/sec: 1947.98
//
Query:       gi|557694489|ref|YP_008797543.1|  [L=102]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   33.2   0.1    4.2e-08   32.8   0.1    1.3  1  DUF4325   STAS-like domain of unknown function (DUF4325)
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.52   10.6   0.0    1.8  2  DUF4382   Domain of unknown function (DUF4382)


Domain annotation for each model (and alignments):
>> 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 !   32.8   0.1   4.7e-12   4.2e-08       4      63 ..      21      71 ..      18      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 4.7e-12
                           DUF4325  4 rfrdkilkpllkegekvelDFdgvesigssFldeaFgglirefgeeeiskklkiknlnep 63
                                       ++d ++k+    +++v+lDF+gv+si+ sF+++ +  l r+ ++    k++k  n+ e+
  gi|557694489|ref|YP_008797543.1| 21 MLFDMVEKND---EKEVVLDFEGVRSISRSFAHQYV--LRRKSSP----KTIKEENVPEE 71
                                      5899999*65...********************998..8888888....77777777666 PP

>> DUF4382  Domain of unknown function (DUF4382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   5.8e-05      0.52     104     137 ..      23      55 ..       2      56 .. 0.85
   2 ?    0.3   0.0     0.086   7.7e+02      63      85 ..      59      81 ..      55      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.8e-05
                           DUF4382 104 ftvtvaageskdlvlDfDlrkslvkgnngkyiLk 137
                                       f+ +v+++++k++vlDf  ++s+  + +++y+L+
  gi|557694489|ref|YP_008797543.1|  23 FD-MVEKNDEKEVVLDFEGVRSISRSFAHQYVLR 55 
                                       34.799*******************999999996 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.086
                           DUF4382 63 katllaelelpaGeYsqirlvls 85
                                      + ++++e+++p+  +++ r+v +
  gi|557694489|ref|YP_008797543.1| 59 SPKTIKEENVPEEVLKMFRIVSE 81
                                      66789999****99999999866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 755.31
//
Query:       gi|557694490|ref|YP_008797544.1|  [L=151]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   50.7   2.5    2.4e-13   50.1   2.5    1.2  1  MS_channel       Mechanosensitive ion channel
  ------ inclusion threshold ------
      0.086   12.5   8.4       0.13   11.9   8.4    1.3  1  DUF4203          Domain of unknown function (DUF4203)
       0.33   11.3   1.8       0.53   10.7   0.1    2.1  2  UXS1_N           UDP-glucuronate decarboxylase N-terminal
       0.43   10.8   5.5        0.6   10.3   5.5    1.2  1  YbjM             Putative inner membrane protein of Enterobac
        1.5    8.2   6.1        1.8    7.9   6.1    1.2  1  GPI2             Phosphatidylinositol N-acetylglucosaminyltra


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 !   50.1   2.5   6.8e-17   2.4e-13       4     110 ..      38     143 ..      31     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 6.8e-17
                                       HHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE- CS
                        MS_channel   4 lkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVedig 80 
                                       +++  + vg + + + l   v  +la +Galgl  +lal  ++s+++a+i + ++  ++iG  +ei + +G+V++i+
  gi|557694490|ref|YP_008797544.1|  38 ILVAGVYVGYVGYVWRLLEFVVGVLATAGALGLLFALALVPYVSDVFASISIALDPYINIGADIEIDGKRGKVIEIS 114
                                       56667788888999999999********************************************************* PP

                                       SSEEEEEETTSEEEEEEHHHHHTS-EEESS CS
                        MS_channel  81 lrttkirtfdgrivtiPnsslvtsnieNls 110
                                       l+ t i   d  ++++Pn+ l +s ++ +s
  gi|557694490|ref|YP_008797544.1| 115 LTRTVIS-GDECLIVVPNKRLRDSVVVVYS 143
                                       ****996.5777*******99887776555 PP

>> DUF4203  Domain of unknown function (DUF4203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   8.4   3.6e-05      0.13      29      98 ..       8      76 ..       1      95 [. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.6e-05
                           DUF4203 29 gfllgsllvlvlilkvvvlp...sslvqgaslvaalvvGllgGllallfwelglfllga.lgGlllallilsll 98
                                        + +++++l ++l+        ++  + ++++++lv+G+ +G++  ++w+l +f++g+ ++  +l+ll+ ++l
  gi|557694490|ref|YP_008797544.1|  8 VVFGLVVVFLRFVLR----AkfrQEHRKVLYVALILVAGVYVGYV-GYVWRLLEFVVGVlATAGALGLLFALAL 76
                                      333333333333333....2233889999***************9.8888888888887555555555554444 PP

>> UXS1_N  UDP-glucuronate decarboxylase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3      0.42   1.5e+03      18      31 ..      39      52 ..      26      60 .. 0.58
   2 ?   10.7   0.1   0.00015      0.53      15      33 ..      68      86 ..      52     113 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.42
                            UXS1_N 18 LlalaliaYvasvw 31
                                      L+a  ++ Yv  vw
  gi|557694490|ref|YP_008797544.1| 39 LVAGVYVGYVGYVW 52
                                      22222444555555 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00015
                            UXS1_N 15 mklLlalaliaYvasvwGt 33
                                      + lL+alal+ Yv+ v+ +
  gi|557694490|ref|YP_008797544.1| 68 LGLLFALALVPYVSDVFAS 86
                                      779************9943 PP

>> YbjM  Putative inner membrane protein of Enterobacteriaceae
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   5.5   0.00017       0.6       7      84 ..       2      78 ..       1      87 [. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00017
                              YbjM  7 gvvlcfllftlvflsqklevsgasaaeglrgelgLLlfllPGivaallskekrllvpllGallaapvcllvlklvlas 84
                                      + ++++++f lv+++ +  +++++++e+ r  l + l l+ G+ + ++    rll+ ++G+l++a +  l++ l l++
  gi|557694490|ref|YP_008797544.1|  2 ATLVASVVFGLVVVFLRFVLRAKFRQEH-RKVLYVALILVAGVYVGYVGYVWRLLEFVVGVLATAGALGLLFALALVP 78
                                      6778999**************8888777.99999*********************************99999998776 PP

>> GPI2  Phosphatidylinositol N-acetylglucosaminyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   6.1    0.0005       1.8     198     259 ..       3      69 ..       1      90 [. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0005
                              GPI2 198 llfsievfglfPvfrrslrhrswrl..hvvltvllvllagagvgiilk...lllavvlllllalimg 259
                                       +l++  vfgl+ vf r + + ++r     vl v+l+l+ag+ vg +     ll +vv++l++a + g
  gi|557694490|ref|YP_008797544.1|   3 TLVASVVFGLVVVFLRFVLRAKFRQehRKVLYVALILVAGVYVGYVGYvwrLLEFVVGVLATAGALG 69 
                                       899999*********9988888877666788899999998888866554555555555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); 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):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1085.69
//
Query:       gi|557694491|ref|YP_008797545.1|  [L=424]
Description: threonine synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-57  195.8   2.7    1.2e-57  195.5   2.7    1.1  1  PALP           Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.029   14.7   0.0      0.077   13.3   0.0    1.7  1  Lambda_tail_I  Bacteriophage lambda tail assembly protein I
      0.078   13.2   1.0       0.27   11.4   0.0    2.2  2  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
      0.085   12.9   0.6        0.4   10.7   0.3    2.1  2  HypA           Hydrogenase/urease nickel incorporation, metal
       0.19   11.5   0.7         20    5.0   0.0    2.7  2  GP57           Phage Tail fiber assembly helper gene product 


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 !  195.5   2.7   3.4e-61   1.2e-57       3     294 .]      83     386 ..      81     386 .. 0.96

  Alignments for each domain:
  == domain 1  score: 195.5 bits;  conditional E-value: 3.4e-61
                                       GCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT CS
                              PALP   3 lgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallG 78 
                                        g+g+T lv+++ l + +gv+ l++K++ +np+ SfKdR a+ ++++++e  g + v +as+GN + a+ a a ++G
  gi|557694491|ref|YP_008797545.1|  83 IGAGGTALVHARELGRVIGVRnLYIKNDTTNPSFSFKDRPASVAVSKAREF-GLRIVGCASTGNLASATVAHAVAAG 158
                                       5789***********************************************.************************* PP

                                       -EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTT CS
                              PALP  79 lkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlg 155
                                       l   +++p+++   kv++   +G +v++v+g+yd+  ++a  l     ++ +v+    p  +eg +t+++E +e lg
  gi|557694491|ref|YP_008797545.1| 159 LTGFVLMPDTVELPKVRQASIYGGKVILVDGTYDDVNRLAYLLVDT-AEVGIVNVNLRPFYVEGSKTMMFETVEALG 234
                                       ***************************************9999999.99**************************** PP

                                       .TTEEEEEEE-SSSHHHHHHHHHHHH.......HSTT-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CCSTC CS
                              PALP 156 .gkpdavvvpvGgGgliaGiaaglke.......rrpdvrvigvepegsdalarslragrrvtvpvs..dtiadglav 222
                                        ++p ++vvp+ +G+l++++++gl+e       ++ d+ + gv+p g++++ +++++g ++ +pv   +t++++la+
  gi|557694491|ref|YP_008797545.1| 235 wRAPQHIVVPMASGALFGALYKGLHEfetfgaiSDADTVFHGVQPIGCSPISTAFEKGAEDVTPVRkpETLVKSLAI 311
                                       ****************************8887666669999**************9999888888788********* PP

                                       S..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 223 g..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                       g   ++ +a+ +++++++++  vsd+e++ea++lla+ +gi++ep +a+ +aa+ ++re g +++gd vv+ +tg
  gi|557694491|ref|YP_008797545.1| 312 GnpGDGIYALNVARKTGGTCQKVSDDETVEAVKLLAKYTGIFAEPGGAITVAAVkQMRENGVIDAGDEVVCCVTG 386
                                       *888889999999**********************************************************9998 PP

>> Lambda_tail_I  Bacteriophage lambda tail assembly protein I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.1e-05     0.077      37      82 ..     169     212 ..     131     213 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                     Lambda_tail_I  37 ldafkellqrskfavrvagvdVgesvpvdryaetlkdgkvvtivpv 82 
                                       ++ +k   q s ++++v++vd g++  v+r+a  l+d ++v iv v
  gi|557694491|ref|YP_008797545.1| 169 VELPKVR-QASIYGGKVILVD-GTYDDVNRLAYLLVDTAEVGIVNV 212
                                       4444434.689**********.********************9975 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 ?   -1.1   0.3      0.62   2.2e+03      43      58 ..     141     156 ..     137     161 .. 0.80
   2 ?   11.4   0.0   7.5e-05      0.27      53      83 ..     361     391 ..     351     397 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.62
                                       HHH-B-GGGHHHHHHH CS
                     ACP_syn_III_C  43 deyGntsaasiplaLd 58 
                                       + +Gn+++a++  a +
  gi|557694491|ref|YP_008797545.1| 141 ASTGNLASATVAHAVA 156
                                       6799*****9988765 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 7.5e-05
                                       HHHHHHHHHHTTSS-TT-EEEEEEEETTTEE CS
                     ACP_syn_III_C  53 iplaLdeaveegklkpgdlvllvgfGaGltw 83 
                                        + a +++ e+g +++gd v+ + +GaG+ +
  gi|557694491|ref|YP_008797545.1| 361 TVAAVKQMRENGVIDAGDEVVCCVTGAGFKV 391
                                       678999**********************976 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 ?   10.7   0.3   0.00011       0.4      64      94 ..      12      41 ..       5      51 .. 0.79
   2 ?   -0.7   0.0       0.4   1.4e+03      24      57 ..     389     422 ..     372     424 .] 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                                      EEEE--EEEETTTS-EEECHHHHHS-TTTSS CS
                              HypA 64 ieevpvkvrCreCgkefeleekalrCpkCgs 94
                                       +  ++k+ Cr+Cg+e+  e +   C kC +
  gi|557694491|ref|YP_008797545.1| 12 TRWSELKLVCRNCGSEYPNELR-NVCDKCLG 41
                                      56678999*********97755.57****66 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.4
                                       .EEEEEEEEEETTCT--HHHHHHHHHHHHCC.TT CS
                              HypA  24 rkvtkvkvevGelsgvepeaLefafellaegtvl 57 
                                        kv++v  +v   + v+p  L  ++e+l+ +++l
  gi|557694491|ref|YP_008797545.1| 389 FKVDEVVEQVSGPAYVVPARLDKILETLQTNQPL 422
                                       4788999999999999999999999999998876 PP

>> GP57  Phage Tail fiber assembly helper gene product 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0    0.0055        20      44      69 ..     322     347 ..     316     350 .. 0.88
   2 ?    3.9   0.1     0.013        46      50      65 ..     383     398 ..     364     401 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0055
                              GP57  44 eiaravGitGdtikveeiveavknlt 69 
                                       ++ar  G t + +  +e veavk l+
  gi|557694491|ref|YP_008797545.1| 322 NVARKTGGTCQKVSDDETVEAVKLLA 347
                                       689********************875 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.013
                              GP57  50 GitGdtikveeiveav 65 
                                        +tG   kv+e+ve v
  gi|557694491|ref|YP_008797545.1| 383 CVTGAGFKVDEVVEQV 398
                                       68************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3149.63
//
Query:       gi|557694492|ref|YP_008797546.1|  [L=330]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2580.84
//
Query:       gi|557694493|ref|YP_008797547.1|  [L=177]
Description: hypothetical protein CSUB_C1065 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.7   0.4      0.027   15.0   0.4    1.3  1  Sld5      GINS complex protein
      0.053   13.3   0.0      0.067   13.0   0.0    1.2  1  Med6      MED6 mediator sub complex component


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 ?   15.0   0.4     3e-06     0.027       4     108 ..      51     146 ..      48     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-06
                                       EHHHHHHHHHTTSCCCHHCHHHCHHHHHHCCCHHTTS.SSSTTTTTTHH.HHHHH.HHHHHT.HCHHHHHHHHHHHH CS
                              Sld5   4 PlWlaelLkrqrrveieppewlspesleailedetks.sdlpslpphfl.elavk.llelardldelkrllrdllev 77 
                                         W+ae L  +r +e +  +   +++l +i  +e+++  +l+ l+++f+ el    +l+     d   + lrd++  
  gi|557694493|ref|YP_008797547.1|  51 WRWVAEVLVARRCAEYVSKQS-PANQLLQIEWREKNNpGELQPLQKYFYvELLREgVLD-----DYAVKKLRDIITM 121
                                       579******999999999887.5999999*****9998555555555550444333333.....345799******* PP

                                       HHHHHHHTHCHHHHHHHTS-TCCHCCS-HHH CS
                              Sld5  78 RlakirkfaenledaagggggellsglseeE 108
                                       R+ ki ++a +  d +      + +++++eE
  gi|557694493|ref|YP_008797547.1| 122 RMMKIVSIAAKRLDGE------IVRRMTPEE 146
                                       *********9888888......666777766 PP

>> Med6  MED6 mediator sub complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.5e-06     0.067      54     117 ..      59     128 ..      10     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.5e-06
                              Med6  54 kkmkGleyvlahvqepdlfvirkqerksatevtvlaaYyiig...gni...Yqapslysvvqsrllsals 117
                                          +  eyv  ++  ++l  i+ +e++++ e ++l++Y+ ++   + +   Y   +l ++++ r+++++s
  gi|557694493|ref|YP_008797547.1|  59 VARRCAEYVSKQSPANQLLQIEWREKNNPGELQPLQKYFYVEllrEGVlddYAVKKLRDIITMRMMKIVS 128
                                       55566788888888889**********************99877744445599************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1276.07
//
Query:       gi|557694494|ref|YP_008797548.1|  [L=673]
Description: replicative DNA helicase Mcm [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-96  321.8   0.0    2.3e-96  321.2   0.0    1.2  1  MCM              MCM P-loop domain
    7.3e-36  122.8   0.4    1.3e-35  122.0   0.4    1.3  1  MCM_OB           MCM OB domain
    2.3e-25   88.8   4.0    5.1e-25   87.7   4.0    1.6  1  MCM_lid          MCM AAA-lid domain
    3.9e-10   40.2   0.2    1.2e-09   38.7   0.2    1.8  1  MCM_N            MCM N-terminal domain
    7.6e-08   32.0   0.1     0.0016   17.8   0.1    2.3  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    4.6e-07   29.9   0.0    1.3e-06   28.5   0.0    1.8  1  AAA_5            AAA domain (dynein-related subfamily)
    0.00076   19.9   1.0     0.0034   17.8   0.1    2.3  2  AAA_16           AAA ATPase domain
     0.0012   18.8   0.0     0.0039   17.1   0.0    1.8  1  AAA_3            ATPase family associated with various cellul
     0.0015   19.0   0.1     0.0055   17.1   0.0    2.0  2  AAA              ATPase family associated with various cellul
     0.0034   17.1   0.0        2.9    7.6   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
      0.027   14.4   0.1       0.43   10.5   0.0    2.5  2  NACHT            NACHT domain
      0.039   14.2   0.1        0.3   11.4   0.1    2.5  1  AAA_22           AAA domain
      0.055   13.4   0.7         13    5.7   0.0    2.6  2  NTPase_1         NTPase
       0.11   12.0   0.0       0.21   11.1   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
       0.14   12.7   0.5       0.51   10.9   0.0    2.2  2  AAA_18           AAA domain
       0.16   12.7   1.9       0.23   12.2   0.4    2.0  2  RsbRD_N          RsbT co-antagonist protein rsbRD N-terminal 
       0.61    9.8   3.8       0.37   10.5   0.9    2.1  2  AAA_30           AAA 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 !  321.2   0.0   2.2e-99   2.3e-96       2     224 .]     266     487 ..     265     487 .. 0.98

  Alignments for each domain:
  == domain 1  score: 321.2 bits;  conditional E-value: 2.2e-99
                                       HHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHH CS
                               MCM   2 veeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyve 78 
                                       ++ +k++a+++ ii+kl++s+apsiyg e++kk+ill+l+gg +k  +d+ ++rgdinvllvgdpgt+KsqlL+yv+
  gi|557694494|ref|YP_008797548.1| 266 ERLFKKMAEDPFIINKLTESVAPSIYGLEHIKKSILLLLIGGRTKVFPDGLRVRGDINVLLVGDPGTGKSQLLQYVA 342
                                       56799************************************************************************ PP

                                       HHSSSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESS CS
                               MCM  79 klapravytsgkgssaagLtaavvrdeetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKa 155
                                       +lapr++ytsg+gs+aagLtaav r++e g +vleaGa+vlad GvcciDe+dkm+eedr+a+hEam qqt+s+aK+
  gi|557694494|ref|YP_008797548.1| 343 SLAPRGIYTSGRGSTAAGLTAAVIREKE-GGMVLEAGAMVLADMGVCCIDEIDKMREEDRVAIHEAMAQQTVSVAKG 418
                                       ************************9985.66********************************************** PP

                                       SCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHHH CS
                               MCM 156 GivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivslh 224
                                       GivatLnart+vlaAanp  gryd+ k+++eninl+ ++LsrFDl+fvl+D+++ ++D+++++hi  lh
  gi|557694494|ref|YP_008797548.1| 419 GIVATLNARTAVLAAANPYLGRYDPYKNFIENINLPITILSRFDLMFVLRDEPNPDTDRKISSHISALH 487
                                       ****************************************************************98765 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.0   0.4   1.2e-38   1.3e-35       2     125 ..      98     228 ..      97     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 122.0 bits;  conditional E-value: 1.2e-38
                                       XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-..HHH.-EEE-GG CS
                            MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCe..skd.pfklete 70 
                                       +R++rseh+ klv+++G+v +as vkp l+  vf+c+ cg+ +ev     +l +P+ C +++C+  + + +f+l++e
  gi|557694494|ref|YP_008797548.1|  98 IREVRSEHLRKLVMIDGMVSKASAVKPLLRVGVFRCRYCGNLQEVeqvsqKLMTPEACLDRTCRgsK-RpSFELVPE 173
                                       8***************************************98887644544555*********9633.369****** PP

                                       GSEEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEEE CS
                            MCM_OB  71 kskfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyral 125
                                       +s+++d+q l +QE+pe++p+G+lPr +ev ++ddlvd v+PGdrv  +G+++++
  gi|557694494|ref|YP_008797548.1| 174 ESSYMDYQVLGVQEKPEDLPPGQLPRVIEVRVRDDLVDVVRPGDRVIAVGVVESV 228
                                       ***************************************************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 !   87.7   4.0   4.8e-28   5.1e-25       2      87 .]     502     584 ..     501     584 .. 0.96

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 4.8e-28
                                       HHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHH CS
                           MCM_lid   2 llrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedvee 78 
                                       +lrkYiaya+ +i+P +s++a ++l+++Y+++R + e  k+ +++it+Rq esliRL+eA+A+ rl++v++eed+  
  gi|557694494|ref|YP_008797548.1| 502 VLRKYIAYAK-RIEPSISPKALKQLEDFYLKMRAMYE--KTATVSITARQFESLIRLTEAHARARLRNVADEEDAAA 575
                                       79********.***********************995..489*********************************** PP

                                       HHHHHHHHH CS
                           MCM_lid  79 airllkesl 87 
                                       ai l+++sl
  gi|557694494|ref|YP_008797548.1| 576 AILLMRKSL 584
                                       *****9985 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.2   1.1e-12   1.2e-09      21      86 ..      16      81 ..       7     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.1e-12
                             MCM_N 21 ekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkeylplleealkevvkklepsykdd 86
                                      + kYr+ l+e a ++++++ +d++dL +fde++a++++++p+  l++l++a  + ++  +p+y+ +
  gi|557694494|ref|YP_008797548.1| 16 SEKYRELLREAAVKKRRSIPIDFNDLIKFDEKFARELVNKPYTLLKVLNRACFRQLQIEDPEYASA 81
                                      579************************************************999998888888776 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   0.00011      0.12      20      48 ..     319     347 ..     315     355 .. 0.90
   2 !   17.8   0.1   1.6e-06    0.0016      93     158 ..     371     436 ..     358     447 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                      Mg_chelatase  20 aGgHnlllvGppGsGKtmlakrlpsllpp 48 
                                        G  n+llvG pG+GK+ l + ++sl p+
  gi|557694494|ref|YP_008797548.1| 319 RGDINVLLVGDPGTGKSQLLQYVASLAPR 347
                                       5888*****************99999885 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1.6e-06
                      Mg_chelatase  93 ggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                       gg   + G++ la  Gv  +DE+ +++++   ++ e + +++v++++    ++  ar+ ++aa+Np
  gi|557694494|ref|YP_008797548.1| 371 GGMVLEAGAMVLADMGVCCIDEIDKMREEDRVAIHEAMAQQTVSVAKGGIVATLNARTAVLAAANP 436
                                       7888999**********************************************************9 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 !   28.5   0.0   1.2e-09   1.3e-06       1     122 [.     323     436 ..     323     445 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.2e-09
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--..........--------G-SEEEEESGGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik.ngttslvdsplvraaregeilvlDEver 76 
                                       +vlLvG+pGtgKs+l +++a++  r   ++   r+ t++ l+  +  + +g+ +l+ +++v       ++++DE+++
  gi|557694494|ref|YP_008797548.1| 323 NVLLVGDPGTGKSQLLQYVASLAPRG--IYTSGRGSTAAGLTAAVIREkEGGMVLEAGAMV--LADMGVCCIDEIDK 395
                                       69********************8665..56678999******9998767888999999998..77999********* PP

                                       --HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS CS
                             AAA_5  77 aesevlnsLlslleerrllleeggelvkaknddllerfrviatanp 122
                                       ++ e   + +  + ++++++++gg +   ++      + v+a+anp
  gi|557694494|ref|YP_008797548.1| 396 MREEDRVAIHEAMAQQTVSVAKGGIVATLNAR-----TAVLAAANP 436
                                       ***99999***********9999988888775.....788888887 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   3.2e-06    0.0034      26      63 ..     323     358 ..     316     438 .. 0.69
   2 ?   -0.5   0.1       1.4   1.4e+03      72     107 ..     545     583 ..     510     659 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.2e-06
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                                       +vll+G++G+GKs l++ ++ +l  + gi+++g+    
  gi|557694494|ref|YP_008797548.1| 323 NVLLVGDPGTGKSQLLQYVA-SLAPR-GIYTSGRGSTA 358
                                       79******************.78888.56666665555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.4
                            AAA_16  72 laqalareellrqlldeaesaeleawrekleeala......a 107
                                        a+++  e+l+r  +++a++++++ ++e  ++a+a      +
  gi|557694494|ref|YP_008797548.1| 545 TARQF--ESLIRLTEAHARARLRNVADE-EDAAAAillmrkS 583
                                       34444..245555544444433333322.2222223333331 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 !   17.1   0.0   3.7e-06    0.0039       2     112 ..     324     436 ..     323     442 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.7e-06
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvf.an..llladeinrap 75 
                                       vll g PG++k +l + +a+        i        +  l + v++eke  + +++G+++ a+  +   dei++  
  gi|557694494|ref|YP_008797548.1| 324 VLLVGDPGTGKSQLLQYVASLAPR---GIYTSGRGSTAAGLTAAVIREKEGGMVLEAGAMVlADmgVCCIDEIDKMR 397
                                       788899999999998888876543...3333333334444556789999999999999865255336789******* PP

                             AAA_3  76 pktqsalleameerqvtve..gethklpepflvlatqnP 112
                                          + a+ eam++++v+v+  g   +l+    vla+ nP
  gi|557694494|ref|YP_008797548.1| 398 EEDRVAIHEAMAQQTVSVAkgGIVATLNARTAVLAAANP 436
                                       **************999862256789************9 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 !   17.1   0.0   5.2e-06    0.0055       1      93 [.     324     412 ..     324     444 .. 0.54
   2 ?   -2.9   0.1       8.2   8.6e+03      60      79 ..     551     568 ..     531     587 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.2e-06
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHH.....HHHHH.HHHTS..TSEEEEEETGGG CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkir.....elfke.akeka..kpsilfiDEida 69 
                                       vll+G pGtGK+ l + va+ + + +++    +      g +++ ir     +++++ a      +  +  iDEid+
  gi|557694494|ref|YP_008797548.1| 324 VLLVGDPGTGKSQLLQYVASLAPRGIYTSGRGSTA---AGLTAAVIRekeggMVLEAgAM--VlaDMGVCCIDEIDK 395
                                       79******************985444333222222...2222222220000033333223..244569********* PP

                                       HHHHHTTCCCHHHHHHHHHHHHHH CS
                               AAA  70 laksrsgseseeeervvnqLltel 93 
                                       + +++       +  + +++ ++ 
  gi|557694494|ref|YP_008797548.1| 396 MREED-------RVAIHEAMAQQT 412
                                       *6655.......333333333333 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.2
                                       EEEEEETGGGHHHHHTTCCC CS
                               AAA  60 silfiDEidalaksrsgses 79 
                                       s + + E++a a+ r  +  
  gi|557694494|ref|YP_008797548.1| 551 SLIRLTEAHARARLR--NVA 568
                                       455555555555555..222 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0042       4.5      21      43 ..     320     342 ..     315     356 .. 0.84
   2 !    7.6   0.0    0.0027       2.9      85     145 ..     376     438 ..     369     457 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0042
                                       SSS-EEEECSTTSSHHHHHHHHH CS
                   Sigma54_activat  21 tdlsvlitGesGtGKellaraih 43 
                                        d++vl++G+ GtGK+ l + + 
  gi|557694494|ref|YP_008797548.1| 320 GDINVLLVGDPGTGKSQLLQYVA 342
                                       6799************9887765 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0027
                                       BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEE..SBTSSSEEE--EEEEEEESS-H CS
                   Sigma54_activat  85 kkGlfekadgGtlfLDeigelplelQekLlrvlqegeve..rvGsskeikvdvriiaatnedl 145
                                       ++G++  ad G+  +Dei ++  e  + + +++ +++v+  + G  ++ ++ + ++aa+n  l
  gi|557694494|ref|YP_008797548.1| 376 EAGAMVLADMGVCCIDEIDKMREEDRVAIHEAMAQQTVSvaKGGIVATLNARTAVLAAANPYL 438
                                       57999**************************99888764115566788888888888888665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00041      0.43       3      27 ..     324     348 ..     323     357 .. 0.86
   2 ?    1.0   0.0      0.34   3.6e+02      81     109 ..     606     639 ..     516     659 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00041
                                       EEEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaeg 27 
                                       v+l G++G GK+ Llq +a+++ +g
  gi|557694494|ref|YP_008797548.1| 324 VLLVGDPGTGKSQLLQYVASLAPRG 348
                                       799***************9987665 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.34
                                       CCEE.....EEEE-STT-SS-TCH.........H CS
                             NACHT  81 erlL.....lilDglDelvtdlgqkekqpvrtlL 109
                                        + +     l++D + +++++ g + +q++rt L
  gi|557694494|ref|YP_008797548.1| 606 PKSVrekmkLVIDTIKKFEEQSGYAAEQELRTAL 639
                                       3333566669999999999999886666666544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00028       0.3       8      37 ..     324     353 ..     319     417 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00028
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee 37 
                                       ++++G +GtGK+ ll+ +++ +++ ++   
  gi|557694494|ref|YP_008797548.1| 324 VLLVGDPGTGKSQLLQYVASLAPRGIYTSG 353
                                       689****************99988777665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.012        13       1      23 [.     323     345 ..     323     372 .. 0.79
   2 ?    5.1   0.3     0.018        19      93     135 ..     382     427 ..     365     436 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.012
                                       EEEEE--TTSSHHHHHHHHHHHH CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlell 23 
                                       +v++ G pG+GK+ l++ v++l 
  gi|557694494|ref|YP_008797548.1| 323 NVLLVGDPGTGKSQLLQYVASLA 345
                                       58999************998765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.018
                                       HHHH-EEEE---STT.GGG-HHHHHHH.HHHHT.TTSEEEEE--SS CS
                          NTPase_1  93 lseadviviDEiGkm.Elkskkfkeav.eevLk.sekpvlavihrr 135
                                       l + +v+ iDEi km E     ++ea+ +++++  +  ++a++  r
  gi|557694494|ref|YP_008797548.1| 382 LADMGVCCIDEIDKMrEEDRVAIHEAMaQQTVSvAKGGIVATLNAR 427
                                       46678**********6444555555552567776677777777766 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    0.0002      0.21      31      55 ..     319     343 ..     314     364 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                             AAA_7  31 knkkpvllvGptGtGKtviikdllk 55 
                                       + + +vllvG+ GtGK+ +++ + +
  gi|557694494|ref|YP_008797548.1| 319 RGDINVLLVGDPGTGKSQLLQYVAS 343
                                       56789*************9997665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00049      0.51       1      22 [.     324     345 ..     324     421 .. 0.71
   2 ?   -1.9   0.1       4.3   4.5e+03      85     119 ..     531     564 ..     522     577 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00049
                            AAA_18   1 IlltGtpGvGKttlakeLskrl 22 
                                       +ll G pG+GK++l ++++++ 
  gi|557694494|ref|YP_008797548.1| 324 VLLVGDPGTGKSQLLQYVASLA 345
                                       799**************98774 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.3
                            AAA_18  85 eleseaakdikk...vvLtaspeelleRlekRgyeeak 119
                                       +++ ++     k   v +ta+  e l Rl +   + + 
  gi|557694494|ref|YP_008797548.1| 531 KMRAMYE----KtatVSITARQFESLIRLTEAHARARL 564
                                       3333434....245599999999999999988766555 PP

>> RsbRD_N  RsbT co-antagonist protein rsbRD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.4   0.00022      0.23      39     102 ..     523     587 ..     503     588 .. 0.90
   2 ?   -2.2   0.1       6.2   6.6e+03      60      72 ..     628     640 ..     605     658 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
                           RsbRD_N  39 eqlrelldallaalaseql.dleseeeeelrealdelsrsRarqgftpsetasfvfaLKealfev 102
                                       +ql++++  + a+ +++   ++++ ++e+l ++ +++ r R r+  + +++a++++++++ l ev
  gi|557694494|ref|YP_008797548.1| 523 KQLEDFYLKMRAMYEKTATvSITARQFESLIRLTEAHARARLRNVADEEDAAAAILLMRKSLQEV 587
                                       68999999999999986667****************************************99875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.2
                           RsbRD_N  60 eseeeeelreald 72 
                                         ++e+elr+al 
  gi|557694494|ref|YP_008797548.1| 628 GYAAEQELRTALL 640
                                       4455555565554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.9   0.00035      0.37      20      96 ..     323     406 ..     315     432 .. 0.64
   2 ?   -2.9   0.1       4.3   4.6e+03     101     126 ..     545     571 ..     540     581 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                            AAA_30  20 vavltGpAGtGKttalkalreaweaa.ggrviglAptgkaAkvLaeelgi.eastiakllkrlk.....grarlepg 89 
                                        ++l+G +GtGK+ +l+ ++ ++ +    +  g +  g  A+v++e+ g    +  a +l  ++     +  +++++
  gi|557694494|ref|YP_008797548.1| 323 NVLLVGDPGTGKSQLLQYVASLAPRGiYTSGRGSTAAGLTAAVIREKEGGmVLEAGAMVLADMGvccidEIDKMREE 399
                                       5789***************9999987556667788888888888887774133333333322223333322333333 PP

                            AAA_30  90 tllivDE 96 
                                       + + + E
  gi|557694494|ref|YP_008797548.1| 400 DRVAIHE 406
                                       4444433 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.3
                            AAA_30 101 dtkqlaallkaaek.agakvilvGDer 126
                                        ++q+++l++  e+ a a+++ v De+
  gi|557694494|ref|YP_008797548.1| 545 TARQFESLIRLTEAhARARLRNVADEE 571
                                       456777777777763457777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (673 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      731  (0.0407719); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 4414.78
//
Query:       gi|557694495|ref|YP_008797549.1|  [L=711]
Description: helicase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-23   82.7   0.0    2.7e-22   79.4   0.0    2.2  2  DEAD             DEAD/DEAH box helicase
    5.8e-12   46.0   0.0    1.9e-11   44.4   0.0    1.9  1  HHH_5            Helix-hairpin-helix domain
    3.7e-10   40.1   0.0    2.3e-08   34.4   0.0    2.7  2  Helicase_C       Helicase conserved C-terminal domain
      2e-09   37.7   0.0    3.7e-09   36.8   0.0    1.4  1  ResIII           Type III restriction enzyme, res subunit
    5.9e-09   35.9   0.0    1.6e-08   34.5   0.0    1.7  1  HHH_2            Helix-hairpin-helix motif
    2.8e-07   30.2   0.0    6.9e-07   29.0   0.0    1.7  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
    3.6e-05   23.4   1.2       0.03   14.2   0.1    3.0  3  HHH              Helix-hairpin-helix motif
    0.00047   19.9   0.2      0.035   13.8   0.0    2.5  2  AAA_30           AAA domain
     0.0037   16.5   0.0     0.0061   15.8   0.0    1.3  1  Sec63            Sec63 Brl domain
  ------ inclusion threshold ------
      0.013   15.7   0.0       0.49   10.7   0.0    2.5  2  Cdd1             Pathogenicity locus
      0.035   14.4   0.1       0.11   12.8   0.0    1.8  2  HHH_3            Helix-hairpin-helix motif
       0.07   12.9   0.0       0.16   11.7   0.0    1.7  1  RNA_pol_A_CTD    Bacterial RNA polymerase, alpha chain C term
       0.15   12.3   0.6        2.9    8.1   0.2    2.7  2  LAL_C2           L-amino acid ligase C-terminal domain 2
       0.15   11.4   0.0       0.27   10.6   0.0    1.4  1  ATPase           KaiC


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 !   79.4   0.0   2.1e-25   2.7e-22       7     170 ..      33     184 ..      27     189 .. 0.83
   2 ?    0.6   0.0      0.32     4e+02      34      79 ..     234     274 ..     232     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 2.1e-25
                                       HHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEE CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   7 aiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvllii 82 
                                       a+   l +g+ ++va +T+sGKTl+++++++++v      +g k+l+++P+r+La + l++++ f+   + +++   
  gi|557694495|ref|YP_008797549.1|  33 ALSKGLlDGRPLMVATPTASGKTLIAMMAAYNHV-----ARGGKVLYLTPLRALAAEKLQEFTDFLGD-EFKAV--A 101
                                       5544444999***********************9.....5688************************5.33444..4 PP

                                       TTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  83 ggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklq 159
                                       +  ++++    l +++d++++t ++ d+ll+ g   +++v++lV DE+++l d +++++++  l++l++ +      
  gi|557694495|ref|YP_008797549.1| 102 STGDYDSADPWL-ANYDVIITTNEKADSLLRHGASWIDSVSLLVADEVHMLGDTDRGPTLEMTLTRLRNRNP----R 173
                                       444555566667.889**************999989*******************************54433....3 PP

                                       SEEEEEESSBS CS
                                       xxxxxxxxxxx RF
                              DEAD 160 rqvivlSATlp 170
                                        q+++lSAT+p
  gi|557694495|ref|YP_008797549.1| 174 AQLLALSATAP 184
                                       45*******99 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.32
                                       HHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  34 pvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvl 79 
                                       pv++ ++e   ++g ++++ + tr+ aeq ++++   ++    r+ 
  gi|557694495|ref|YP_008797549.1| 234 PVISLLLE-VVQDGGQVIVFANTRKRAEQYAEKAAAALS----RET 274
                                       56666666.5678889*************9999988877....333 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   1.5e-14   1.9e-11       4      53 ..     660     709 ..     657     711 .] 0.95

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.5e-14
                                       HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                                       L s++G+G+++A++l++aG++++edl +a++eeLa++p iG++ A +i+ 
  gi|557694495|ref|YP_008797549.1| 660 LVSLKGVGRVRARNLYNAGYRTIEDLRRASAEELAQVPSIGPRIAASIKS 709
                                       779********************************************986 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 ?   -3.4   0.0       9.9   1.3e+04      11      33 ..      64      87 ..      56     108 .. 0.58
   2 !   34.4   0.0   1.8e-11   2.3e-08       8     111 .]     237     389 ..     232     389 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9.9
                                      HHTTTTSEEEEEESSHH.HHHHHH CS
                        Helicase_C 11 kleeeggkilifvntid.rlekvk 33
                                      ++ ++ggk+l  ++ +   +ek++
  gi|557694495|ref|YP_008797549.1| 64 NHVARGGKVLYLTPLRAlAAEKLQ 87
                                      566888999998888885333322 PP

  == domain 2  score: 34.4 bits;  conditional E-value: 1.8e-11
                                       HHH.HHTTTTSEEEEEESSHHHH..............HHHHHH...................HHHT........... CS
                        Helicase_C   8 ell.kleeeggkilifvntidrl..............ekvkll...................lekk........... 39 
                                        ll +  ++gg++++f+nt++r+                   l                      +           
  gi|557694495|ref|YP_008797549.1| 237 SLLlEVVQDGGQVIVFANTRKRAeqyaekaaaalsreT----LvtdderdklngladelllsA--Eassftdrvaal 307
                                       443366799************88334444444444440....145544444444444444441..133445566677 PP

                                       .TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSS........SS..HHHHHHHHT CS
                        Helicase_C  40 .gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlp........rn..vtsyiqriG 105
                                           ++ +h+ l + +r+ + ++f++   +vL at  ++ G+++p +++Vi+ +l         rn  vt+y+q  G
  gi|557694495|ref|YP_008797549.1| 308 mRQGACFHHAGLGAVHRRFVEKAFRNRILKVLAATPTLAAGVNLP-ARVVIIPELRryevgeglRNisVTEYKQFCG 383
                                       67889999999***************999***************9.99999999997777777744447******** PP

                                       TSSSTT CS
                        Helicase_C 106 RtgRag 111
                                       R+gR g
  gi|557694495|ref|YP_008797549.1| 384 RAGRPG 389
                                       ****75 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 !   36.8   0.0   2.9e-12   3.7e-09      25     169 ..      42     183 ..      15     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.9e-12
                                       SEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--..... CS
                            ResIII  25 krglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekds 101
                                       + ++++ +T +GKTl+a+ ++++    g+  k+l l p ++l    l+ef++fl +++k++    + d+ ++     
  gi|557694495|ref|YP_008797549.1|  42 RPLMVATPTASGKTLIAMMAAYNHVARGG--KVLYLTPLRALAAEKLQEFTDFLGDEFKAVASTGDYDSADP---WL 113
                                       5788999**********888888888777..9*************************987666666666666...99 PP

                                       ..-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......TTHHHHHT---SEEEEEESS- CS
                            ResIII 102 tnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......swreilekfkeavllglTATp 169
                                        n ++++tt +++d+ +      +     d+  +++ DE+H lg+ +       + +++ + +++a ll+l+AT 
  gi|557694495|ref|YP_008797549.1| 114 ANYDVIITTNEKADSLL-----RHGASWIDSVSLLVADEVHMLGDTDrgptlemTLTRLRNRNPRAQLLALSATA 183
                                       9****************.....66777788888************84666777799999999999*********6 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   1.2e-11   1.6e-08       7      52 ..     662     708 ..     657     710 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.2e-11
                             HHH_2   7 GIrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsiv 52 
                                       +++ VG   A++L ++ +++++ L++as+eeL++v+ iG++iA+si+
  gi|557694495|ref|YP_008797549.1| 662 SLKGVGRVRARNLYNAgYRTIEDLRRASAEELAQVPSIGPRIAASIK 708
                                       6789*********9866****************************97 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 !   29.0   0.0   5.4e-10   6.9e-07       8      42 ..     665     700 ..     660     703 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5.4e-10
                   DNA_pol_lambd_f   8 GVGpktAkkwyakGirtledlra.krakLtreqqiG 42 
                                       GVG+++A+++y++G+rt+edlr+   ++L ++  iG
  gi|557694495|ref|YP_008797549.1| 665 GVGRVRARNLYNAGYRTIEDLRRaSAEELAQVPSIG 700
                                       9**********************7557777766666 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       6.3     8e+03       7      14 ..     400     407 ..     399     409 .. 0.80
   2 !    7.1   0.0    0.0041       5.3      13      26 ..     660     673 ..     660     677 .. 0.87
   3 !   14.2   0.1   2.3e-05      0.03       2      29 ..     682     709 ..     681     709 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.3
                                       TSSHHHHH CS
                               HHH   7 pasreeLl 14 
                                       ++s+eeL+
  gi|557694495|ref|YP_008797549.1| 400 ARSEEELE 407
                                       789****7 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0041
                                       HHTSTT-SHHHHHH CS
                               HHH  13 LlalPGVGpktAea 26 
                                       L++l+GVG+ +A+ 
  gi|557694495|ref|YP_008797549.1| 660 LVSLKGVGRVRARN 673
                                       899*********86 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 2.3e-05
                                       HHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   2 leglipasreeLlalPGVGpktAeaIls 29 
                                       +e l+ as eeL+++P +Gp  A +I s
  gi|557694495|ref|YP_008797549.1| 682 IEDLRRASAEELAQVPSIGPRIAASIKS 709
                                       7899****************99999975 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   2.7e-05     0.035       6     104 ..      30     155 ..      25     175 .. 0.74
   2 ?    3.5   0.1     0.039        51      44      77 ..     244     276 ..     235     314 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.7e-05
                            AAA_30   6 QaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgk.aAkvLaeelgieastiakllkrlk 81 
                                       Q+ a+ + l +g+ ++v+t  A +GKt +   ++  + a+gg+v+ l+p  + aA++L+e +++ ++  + + ++ +
  gi|557694495|ref|YP_008797549.1|  30 QSLALSKGLLDGRPLMVATPTA-SGKTLIAMMAAYNHVARGGKVLYLTPLRAlAAEKLQEFTDFLGDEFKAVASTGD 105
                                       7777778888888788888888.****988888888888899******976626667**966665555544443333 PP

                            AAA_30  82 ..........................grarlepg.tllivDEagmvdtkq 104
                                                                 + a++ ++ +ll+ DE+ m++ ++
  gi|557694495|ref|YP_008797549.1| 106 ydsadpwlanydviittnekadsllrHGASWIDSvSLLVADEVHMLGDTD 155
                                       44555666666699999999999999445666666**********97554 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.039
                            AAA_30  44 aaggrviglAptgkaAkvLaeelgieastiakll 77 
                                       ++gg+vi++A t k A++ ae++  +a + + l+
  gi|557694495|ref|YP_008797549.1| 244 QDGGQVIVFANTRKRAEQYAEKAA-AALSRETLV 276
                                       4688**************998854.333334444 PP

>> Sec63  Sec63 Brl domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.7e-06    0.0061       2      89 ..     494     595 ..     493     599 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.7e-06
                                       CHHHHHHHHHT--HHHHHHHHHHS-..TT.--HHHHHHHHHTSGGGGGS---TTHHHHHHHHHHT.......SSS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx..xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxx RF
                             Sec63   2 telGriaShYyisyetiklfneslk..pn.ttlkdlLeilssasEFeeipvReeEkkelkkLlek.......vpikv 68 
                                       t lG+ +++ yi   t   + +++   p+ +t+ +lL+++++ +E  ++p+R+ +   l++  e+       vp +v
  gi|557694495|ref|YP_008797549.1| 494 TRLGKRVAELYIDPLTALAIIQTCGnrPRlMTELSLLQVVCNTHEVPSVPMRRSDSARLERFVEEnreqffqVPDPV 570
                                       778888888899998888888877634332599******************************88799999988888 PP

                                       ....SSSTTSHHHHHHHHHHHHHTT CS
                                       ....xxxxxxxxxxxxxxxxxxxxx RF
                             Sec63  69 ....kediespeaKvniLlqayisr 89 
                                           + ++   ++K+ +L++a+i +
  gi|557694495|ref|YP_008797549.1| 571 espdDYEFFLDSVKTAVLMNAWIEE 595
                                       5443367778899********9975 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00038      0.49       8      42 ..     660     694 ..     654     696 .. 0.89
   2 ?    7.2   0.0    0.0047         6       2      22 ..     687     707 ..     686     709 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00038
                              Cdd1   8 lqdiPniGkalaedlvelGirsveelkgedpeely 42 
                                       l ++ ++G+  a++l++ G+r++e+l++ ++eel 
  gi|557694495|ref|YP_008797549.1| 660 LVSLKGVGRVRARNLYNAGYRTIEDLRRASAEELA 694
                                       678899*************************9986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0047
                              Cdd1   2 rkalkelqdiPniGkalaedl 22 
                                       r++++el ++P+iG+++a+ +
  gi|557694495|ref|YP_008797549.1| 687 RASAEELAQVPSIGPRIAASI 707
                                       57889************9875 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.3   1.1e+04      16      30 ..     660     674 ..     660     677 .. 0.82
   2 ?   12.8   0.0   8.7e-05      0.11       7      30 ..     684     707 ..     680     709 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.3
                             HHH_3  16 LqklpGlgpklAknI 30 
                                       L  l+G+g + A+n+
  gi|557694495|ref|YP_008797549.1| 660 LVSLKGVGRVRARNL 674
                                       567999999999997 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.7e-05
                             HHH_3   7 diNtAsaeeLqklpGlgpklAknI 30 
                                       d+  AsaeeL+++p +gp++A  I
  gi|557694495|ref|YP_008797549.1| 684 DLRRASAEELAQVPSIGPRIAASI 707
                                       7889*****************988 PP

>> RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.16      22      62 ..     669     708 ..     668     711 .] 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHTT--BHHHHHHS-HHHHTTSSS-SSHHHHHHH CS
                     RNA_pol_A_CTD  22 vRslNcLkragiktvgeLvklseeeLlkikNlGkKSleEIk 62 
                                       vR++N L +ag++t+++L + s eeL +++ +G +    Ik
  gi|557694495|ref|YP_008797549.1| 669 VRARN-LYNAGYRTIEDLRRASAEELAQVPSIGPRIAASIK 708
                                       68888.99*************************88766666 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 ?    8.1   0.2    0.0022       2.9      50      74 ..     247     271 ..     245     274 .. 0.93
   2 ?    1.0   0.0      0.37   4.7e+02       6      32 ..     480     506 ..     478     508 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0022
                            LAL_C2  50 Gyviatgdtaeeaeaaaeeaaaeir 74 
                                       G vi+ ++t++ ae+ ae+aaa++ 
  gi|557694495|ref|YP_008797549.1| 247 GQVIVFANTRKRAEQYAEKAAAALS 271
                                       89*******************9985 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.37
                            LAL_C2   6 prpGrlkaveGleearalpgvvevelt 32 
                                        r G ++a +Gle+ r  + v e+++ 
  gi|557694495|ref|YP_008797549.1| 480 ARHGFVEAADGLEATRLGKRVAELYID 506
                                       35899***********99999999985 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.27      13      81 ..      35     104 ..      23     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                            ATPase  13 kgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa..edlrenakslGwdlekleeeg 81 
                                       + G+ +gr   ++  + +GKt++a+  +++ +++ g ++++ t       e+l+e    lG +++++ ++g
  gi|557694495|ref|YP_008797549.1|  35 SKGLLDGRPLMVATPTASGKTLIAMMAAYNHVAR-GGKVLYLTPLRALaaEKLQEFTDFLGDEFKAVASTG 104
                                       689*******************************.******995433223777777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 5120.39
//
Query:       gi|557694496|ref|YP_008797550.1|  [L=163]
Description: dual specificity protein phosphatase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-21   74.8   0.0    6.4e-21   74.6   0.0    1.1  1  DSPc             Dual specificity phosphatase, catalytic doma
      3e-09   36.7   0.0    4.2e-09   36.2   0.0    1.1  1  Y_phosphatase2   Tyrosine phosphatase family
    2.3e-08   33.9   0.0    2.7e-08   33.7   0.0    1.1  1  Y_phosphatase    Protein-tyrosine phosphatase
    1.2e-07   31.9   0.0    1.5e-07   31.7   0.0    1.2  1  PTPlike_phytase  Inositol hexakisphosphate
    4.8e-06   26.3   0.0    6.6e-06   25.9   0.0    1.1  1  CDKN3            Cyclin-dependent kinase inhibitor 3 (CDKN3)
    0.00077   19.5   0.0     0.0012   18.9   0.0    1.4  1  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 !   74.6   0.0   2.1e-24   6.4e-21      11     132 ..      38     157 ..      31     158 .. 0.89

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 2.1e-24
                                       HHHHHHHTCSEEEEESSSSSECECCTTTTSEEEEECCESSTTSCCGGGHHHHHHHHHHHHHTT-EEEEEESSSSSHH CS
                              DSPc  11 lallsklgitlvinvtkevpnanalkkseieklripvedehetkiskyleeavefidkakqkgkkvlVHCqaGisRS 87 
                                        ++l  +git++i +t++   +++l++++i+++++p+ d++ ++ +k le + + ++++ ++g+kvlVHC aG+ R+
  gi|557694496|ref|YP_008797550.1|  38 IKFLRRQGITAIISLTEQPLPPQLLENENIKYFHYPLADHQAADPAKVLEIV-KHLQELVSSGEKVLVHCLAGLGRT 113
                                       478999**********665555999**************9*****9999865.679********************* PP

                                       HHHHHHHHHHHHTSCHHHHHHHHHHHSTT-SSTHHHHHHHHHHHH CS
                              DSPc  88 atliiaYlmktknlslneayeflkerrpaispnagfirqLleyek 132
                                       +++ +aY m +knl+ + a+e ++  rp  ++  ++   L+e+e+
  gi|557694496|ref|YP_008797550.1| 114 GMVLTAYTMLEKNLDWRTALETVRRIRPGSVEK-NQENCLREFER 157
                                       ***************************988887.88888888885 PP

>> Y_phosphatase2  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   1.4e-12   4.2e-09       4     112 ..      16     120 ..      15     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.4e-12
                                       -TT-EEEETTEEEESS--HH.HHHHHHHCT-SEEEE-SSS---HHHHHHHHHCT-EEEE-------GGG----HHHH CS
                    Y_phosphatase2   4 plnFsaveselyrssypras.nfsflksLkLktiislspeeesqdelqfleeekiklyhiaiesnkeelveiksdll 79 
                                       p nFs+  +++  s+ p+ +    fl++  +  iisl++++ + +    le+e+ik++h+ + + +    + k  ++
  gi|557694496|ref|YP_008797550.1|  16 PPNFSMLTENVAGSGLPSTRrHIKFLRRQGITAIISLTEQPLPPQ---LLENENIKYFHYPLADHQA-ADPAKVLEI 88 
                                       78***************9761579****************99975...5688***********9999.899999999 PP

                                       HHHHHHHH-GGG-SEEEE-SSSSSHHHHHHHHH CS
                    Y_phosphatase2  80 kkalklllnkenypvllhckrGkhrtglvigcl 112
                                       +k l+ l+   +  vl+hc  G  rtg+v  + 
  gi|557694496|ref|YP_008797550.1|  89 VKHLQELVSSGE-KVLVHCLAGLGRTGMVLTAY 120
                                       9*****999886.7***************9753 PP

>> Y_phosphatase  Protein-tyrosine phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.0     9e-12   2.7e-08     137     224 ..      69     148 ..      38     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 9e-12
                                       EEEESSS-SSSSGSCCHHHHHHHHHHHHHHSTTSS-EEEECSSSSHHHHHHHHHHHHHHHHHHHSEEEHHHHHHHHH CS
                     Y_phosphatase 137 qlqytnWpdhgvpesaksllklirkvekskeaksgpvvVhCsaGvgRtgtfvaldillqqleaeeevdvlqivkelr 213
                                        ++y    dh+  +++ ++l++++ +++   ++ + v+VhC aG gRtg+++++ ++l++     ++d   +++++r
  gi|557694496|ref|YP_008797550.1|  69 YFHYPL-ADHQ-AADPAKVLEIVKHLQELV-SSGEKVLVHCLAGLGRTGMVLTAYTMLEK-----NLDWRTALETVR 137
                                       444443.3444.357889999999999999.7889***************9999888764.....67799999**** PP

                                       TTSTTSS-SHH CS
                     Y_phosphatase 214 kqRpgmvqtle 224
                                       + Rpg+v++ +
  gi|557694496|ref|YP_008797550.1| 138 RIRPGSVEKNQ 148
                                       ******99865 PP

>> PTPlike_phytase  Inositol hexakisphosphate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   4.9e-11   1.5e-07      92     155 ..      59     123 ..      18     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4.9e-11
                                       HHHHHHTT-EEEEEEE-TTS---HHHHHHHHHHHHTS.-TT-EEEEE-SSSSHHHHHHHHHHHHH CS
                   PTPlike_phytase  92 relaeelslrYaRipitdekapeeedfdalvsilkea.pektalvfnCqmGrgRTTtamviatLl 155
                                        +l e+ +++Y+  p+ d++a ++ ++ ++v+ l+e+ ++ + ++++C +G gRT ++++++t+l
  gi|557694496|ref|YP_008797550.1|  59 PQLLENENIKYFHYPLADHQAADPAKVLEIVKHLQELvSSGEKVLVHCLAGLGRTGMVLTAYTML 123
                                       56778899*****************************999***********************97 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 !   25.9   0.0   2.2e-09   6.6e-06      97     152 ..      63     118 ..      50     128 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.2e-09
                                       HHTT-EEEE----TTS---HHHHHHHHHHHHHHHHTT--EEEE-SSSSSHHHHHHH CS
                             CDKN3  97 qqygivthhhpiadggtpdiascleimeelatclknyrktlihcygglgrsclvaa 152
                                       ++  i   h+p+ad  + d a +lei++ l   +    k l+hc  glgr+ +v +
  gi|557694496|ref|YP_008797550.1|  63 ENENIKYFHYPLADHQAADPAKVLEIVKHLQELVSSGEKVLVHCLAGLGRTGMVLT 118
                                       55667789******************************************988754 PP

>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0     4e-07    0.0012     109     139 ..      84     118 ..      33     128 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4e-07
                    Y_phosphatase3 109 ayrkvfealad.ee...pvlfHCtaGKDRTGvlaa 139
                                       ++ +++++l++  +    vl+HC aG  RTG++  
  gi|557694496|ref|YP_008797550.1|  84 KVLEIVKHLQElVSsgeKVLVHCLAGLGRTGMVLT 118
                                       44455555555422358**************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1226.10
//
Query:       gi|557694497|ref|YP_008797551.1|  [L=243]
Description: hypothetical protein CSUB_C1069 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-07   29.2   0.0    3.2e-06   27.3   0.0    1.9  2  ParBc     ParB-like nuclease 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 ?   -1.5   0.0      0.18   3.2e+03      52      64 ..      90     102 ..      88     107 .. 0.80
   2 !   27.3   0.0   1.8e-10   3.2e-06       2      85 ..     145     226 ..     144     231 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.18
                             ParBc  52 iaGerRlrAakrl 64 
                                       + GerR  Aa++ 
  gi|557694497|ref|YP_008797551.1|  90 VVGERRQIAAEME 102
                                       5799999999865 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 1.8e-10
                             ParBc   2 evplseir..pnplqprkdspekieelvasIkkkGllqPiivrktrqgryeiiaGerRlrAa.krlglkevpvivle 75 
                                       evp+ ++   p++ +p+  s+e++e l++  +   +l P++vr+ ++g +e++aG+r + ++ +rlg+++v+++vl+
  gi|557694497|ref|YP_008797551.1| 145 EVPVRRVIyqPSATAPM--SEEELETLAQYVE---ILGPVVVRPLDNGFFELVAGHRVFDVLvNRLGYESVKALVLD 216
                                       67788877445555555..99***********...999*********************98537889********** PP

                             ParBc  76 iddeeamals 85 
                                       +dd  a +++
  gi|557694497|ref|YP_008797551.1| 217 VDDASASSMR 226
                                       **99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1817.61
//
Query:       gi|557694498|ref|YP_008797552.1|  [L=71]
Description: hypothetical protein CSUB_C1070 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   11.8   0.0       0.12   11.8   0.0    1.0  1  LAP2alpha  Lamina-associated polypeptide 2 alpha


Domain annotation for each model (and alignments):
>> LAP2alpha  Lamina-associated polypeptide 2 alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   6.6e-06      0.12      12      52 ..      16      56 ..       7      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.6e-06
                                      SS--------------------BHHHHHHHHHHHHCCGSSS CS
                         LAP2alpha 12 lglevakpqsqhdkieaselsfplhesilkvveeewqqvdr 52
                                        ++v+  + + +++e  e+s+p+ e+il  v +e+  +  
  gi|557694498|ref|YP_008797552.1| 16 PTVDVSGMEKKLEQVEIPEPSLPVCEAILMPVSDEYTYIHH 56
                                      56899999999************************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.45
# Mc/sec: 479.21
//
Query:       gi|557694499|ref|YP_008797553.1|  [L=288]
Description: ribose-phosphate pyrophosphokinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-34  118.8   0.4    5.1e-30  103.8   0.0    2.2  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    1.2e-18   67.2   6.6      1e-17   64.1   0.5    3.5  4  Pribosyltran    Phosphoribosyl transferase domain
    7.3e-08   32.7   1.4    1.5e-07   31.6   0.2    2.1  3  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    1.8e-06   27.6   0.5    3.8e-06   26.5   0.3    1.7  2  UPRTase         Uracil phosphoribosyltransferase
    1.1e-05   25.1   0.2    2.1e-05   24.1   0.1    1.5  1  PRTase_2        Phosphoribosyl transferase
     0.0024   16.8   0.1     0.0037   16.2   0.1    1.2  1  Mfa_like_2      Fimbrillin-like


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 !  103.8   0.0   1.7e-33   5.1e-30       1     116 []       1     117 [.       1     117 [. 0.99
   2 !   13.4   0.1   1.9e-05     0.056       3      58 ..     163     222 ..     161     245 .. 0.81

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 1.7e-33
                    Pribosyltran_N   1 lkifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrra 77 
                                       +k+++g ss +Laek+a++l+ve +++  + f+dgE +v+++ +vrg+dv+++q +++p + n++ lll++da+ r 
  gi|557694499|ref|YP_008797553.1|   1 MKVVKGPSSAQLAEKVARYLNVEAVDVFARVFPDGESYVRLSGDVRGEDVVVVQGTHPPQDVNFVKLLLLVDAVTRM 77 
                                       89*************************************************************************** PP

                    Pribosyltran_N  78 sakritaViPylgysrqdrk.ksrepisaklvaklLeaaG 116
                                        ak++  ViPy++y+rqdr   + ep+s + ++k L+a+G
  gi|557694499|ref|YP_008797553.1|  78 GAKSVKTVIPYMAYARQDRVfLEGEPVSIQAMLKALKAVG 117
                                       *************************************998 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.9e-05
                    Pribosyltran_N   3 ifagssskeLaekiakrlgvelgkakvsrf.adgEikveieesvrgkdvfiiqsls...k 58 
                                       + +g++  e+a+++a+ +++    +k+ r  ++gE++v++ee   g++v+++ ++    +
  gi|557694499|ref|YP_008797553.1| 163 VSPGKKGSEMAAAVASVIETDYLAVKTMRSpETGEVEVKVEEIEEGRQVVVVDDIIstgT 222
                                       55788899************9999988776268*******************99874443 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1     0.024        71      41      93 ..      10      53 ..       7      54 .. 0.66
   2 ?   -1.4   0.0       0.5   1.5e+03     106     127 ..      70      94 ..      67     102 .. 0.69
   3 ?    1.4   0.0      0.07   2.1e+02     102     124 ..     105     127 ..     104     139 .. 0.81
   4 !   64.1   0.5   3.4e-21     1e-17      14     131 ..     143     255 ..     133     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.024
                                      HHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE CS
                      Pribosyltran 41 vpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliV 93
                                        +a ++a++L+v+ ++v ++ + ++ s  +        rl++d++g+ V++V
  gi|557694499|ref|YP_008797553.1| 10 AQLAEKVARYLNVEAVDVFARVFPDGESY-V--------RLSGDVRGEDVVVV 53
                                      56788888888888776655433333333.3........38899999999998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.5
                                       HHHHHHCC-BSEEEEEEEE...E-H CS
                      Pribosyltran 106 alelLkekgpeevriavlv...dkp 127
                                        ++++ + g+++v+++ ++   ++ 
  gi|557694499|ref|YP_008797553.1|  70 LVDAVTRMGAKSVKTVIPYmayARQ 94 
                                       5677888899999998888553444 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.07
                                       HHHHHHHHHHCC-BSEEEEEEEE CS
                      Pribosyltran 102 TllaalelLkekgpeevriavlv 124
                                       +++a+l++Lk++g+ e +++ ++
  gi|557694499|ref|YP_008797553.1| 105 SIQAMLKALKAVGADEAITVNIH 127
                                       6889999******9988887665 PP

  == domain 4  score: 64.1 bits;  conditional E-value: 3.4e-21
                                       EEEETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEE CS
                      Pribosyltran  14 avarlaaeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkV 90 
                                       ++  l+a+++++++ +++++v + ++G  +a ++a+ +e   +y+ ++  r++ ++e+  +       +e+ +g+ V
  gi|557694499|ref|YP_008797553.1| 143 DASGLLASYIMQAGVEKPLIVSPGKKGSEMAAAVASVIE--TDYLAVKTMRSPETGEVEVK------VEEIEEGRQV 211
                                       67889********************************99..88888888888877777643......799******* PP

                                       EEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE...E-HHHHH CS
                      Pribosyltran  91 liVDDildtGgTllaalelLkekgpeevriavlv...dkpatee 131
                                       ++VDDi++tG+T+ ++++ Lk+++p ++++a+++     +a e+
  gi|557694499|ref|YP_008797553.1| 212 VVVDDIISTGTTMAKTIQQLKNYRPSKIIVAAVHglfIGSAAEK 255
                                       ********************************986654444444 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.2   3.7e+03      58      89 ..      22      53 ..       6      67 .. 0.69
   2 ?   -2.0   0.0         1     3e+03     149     168 ..     131     150 ..     106     155 .. 0.58
   3 !   31.6   0.2     5e-11   1.5e-07      82     147 ..     207     272 ..     165     281 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                                      -------------------EES--TTSEEEEE CS
                    Pribosyl_synth 58 vekslelpellakekppltvvGdvgGriaiiv 89
                                      ve+++ + ++ +     + + Gdv G   ++v
  gi|557694499|ref|YP_008797553.1| 22 VEAVDVFARVFPDGESYVRLSGDVRGEDVVVV 53
                                      44555555556666666777788887766666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1
                                       HHHHT-TTEEEE--HHHHHH CS
                    Pribosyl_synth 149 iqklrcskiktvdislllae 168
                                          + + k+  +d s lla 
  gi|557694499|ref|YP_008797553.1| 131 TADQSAVKLTNIDASGLLAS 150
                                       33455667777777777765 PP

  == domain 3  score: 31.6 bits;  conditional E-value: 5e-11
                                       TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS-- CS
                    Pribosyl_synth  82 gGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntiph 147
                                       +Gr  ++vdd+i   +++ ++ + lk+    ki+v a hGl+  +a++++ ++  d +  t+t+p+
  gi|557694499|ref|YP_008797553.1| 207 EGRQVVVVDDIISTGTTMAKTIQQLKNYRPSKIIVAAVHGLFIGSAAEKISSAGADLIFTTDTVPN 272
                                       6999*************************************************************7 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.7   4.9e+03      22      41 ..       7      26 ..       4      31 .. 0.77
   2 !   26.5   0.3   1.3e-09   3.8e-06      78     159 ..     169     244 ..     105     267 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.7
                           UPRTase 22 kdfrelvdriarllaeeals 41
                                      ++  +l++++ar+l +ea+ 
  gi|557694499|ref|YP_008797553.1|  7 PSSAQLAEKVARYLNVEAVD 26
                                      55678899999999999976 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 1.3e-09
                           UPRTase  78 GegmeealrellpearvghlglqreeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekI 154
                                       G  m+ a+ +++ +   + ++  r++et e +  ++ +    + r+v+++D +i+TG ++a+ iq+Lk+   + +kI
  gi|557694499|ref|YP_008797553.1| 169 GSEMAAAVASVIET-DYLAVKTMRSPETGEVEVKVEEIE---EGRQVVVVDDIISTGTTMAKTIQQLKN--YRPSKI 239
                                       44888888887765.566778889999988665555444...679************************..999*** PP

                           UPRTase 155 lvlsv 159
                                       +v++v
  gi|557694499|ref|YP_008797553.1| 240 IVAAV 244
                                       *9987 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   6.9e-09   2.1e-05     115     158 ..     202     244 ..     186     270 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.9e-09
                          PRTase_2 115 eellaaakelvLvDDEistGktalnliralqeklprkryvvvsl 158
                                        e +++ +++v+vDD istG+t++++i++l++  p+k + v+++
  gi|557694499|ref|YP_008797553.1| 202 VEEIEEGRQVVVVDDIISTGTTMAKTIQQLKNYRPSKII-VAAV 244
                                       56778999***********************99987654.4444 PP

>> Mfa_like_2  Fimbrillin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.2e-06    0.0037      85     173 ..     141     233 ..     121     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-06
                                       .EE---..--EEE-SEEEEEEEEES-----T..TSS----SS---EE--TTBTTTS-EEEEE------EEEEE---E CS
                        Mfa_like_2  85 eidase..tPlyleaGtykfkiisPakavsk..dgkvtidnGeyllatddrytqtestavtiekndeGvqvvklnPi 157
                                       +idas   +   ++aG  k  i+sP k  s+       + +  yl     r  +t    v++e+++eG qvv ++ i
  gi|557694499|ref|YP_008797553.1| 141 NIDASGllASYIMQAGVEKPLIVSPGKKGSEmaAAVASVIETDYLAVKTMRSPETGEVEVKVEEIEEGRQVVVVDDI 217
                                       6677766678889************997665113455688899********************************** PP

                                       EESSEEEEEEEEE-TT CS
                        Mfa_like_2 158 isqtarlkftikkgeg 173
                                       is  + +  ti++ ++
  gi|557694499|ref|YP_008797553.1| 218 ISTGTTMAKTIQQLKN 233
                                       ********99998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2016.39
//
Query:       gi|557694500|ref|YP_008797554.1|  [L=338]
Description: methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   75.8   0.0    7.3e-20   71.5   0.0    2.2  1  UPF0020          Putative RNA methylase family UPF0020
    5.2e-07   29.5   0.0    8.2e-07   28.8   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    6.2e-07   29.6   0.3    9.8e-07   29.0   0.3    1.4  1  THUMP            THUMP domain
      5e-06   26.4   0.0    3.3e-05   23.7   0.0    2.1  2  N6_N4_Mtase      DNA methylase
  ------ inclusion threshold ------
      0.051   13.2   0.0      0.086   12.4   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
        0.2   10.9   0.0       0.67    9.2   0.0    1.8  1  N6_Mtase         N-6 DNA 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 !   71.5   0.0   2.5e-23   7.3e-20       2     195 ..     162     330 ..     161     332 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 2.5e-23
                                       SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH-- CS
                           UPF0020   2 gyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelk 78 
                                       g R+f  p++++++LA++lv+la   +g++ lDP+ GsG++ IEa+llg  +                         
  gi|557694500|ref|YP_008797554.1| 162 GNRPFRIPSAMQPKLARCLVNLAINSRGSKVLDPFAGSGALVIEAGLLGHVCL------------------------ 214
                                       579*************************************************9........................ PP

                                       EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHH.HHHHHHHHHHHHH CS
                           UPF0020  79 lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkal.ekLYseflrelkr 154
                                         g++ +  v +g  +N + +g+g   +++q da++L+  +  +d+++t+pPYG++ +  +   ++L ++f++ + +
  gi|557694500|ref|YP_008797554.1| 215 --GVEVKTWVCNGMWRNMQFYGIGLG-HAVQGDARHLP-FRRFFDAVATDPPYGRSATLGGIPfKTLLKAFAEDVVN 287
                                       ..*********************865.67788******.4457***************999877************* PP

                                       H-TT..-EEEEEES..SHHHHHCC---ESEEEEEEETTEEEEE CS
                           UPF0020 155 vlrgggrlvlltse..nkalekaleeralrkvkeknvklglll 195
                                       vl  ++rl++ +++  + +l +a+ + +l + +   v+ +l++
  gi|557694500|ref|YP_008797554.1| 288 VLTDDARLAVTVPHtaYHDLVEAFTDFRLLEHHDLYVHRSLTR 330
                                       *****99999887612568888888888888888888888776 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   2.7e-10   8.2e-07      40     128 ..     187     268 ..     177     321 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.7e-10
                                       HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEE CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdi 116
                                        +g++vLD faGsGal +EA   g + ++ ve + ++++ + +n++  ++       ++ ++++l+ +    + fd 
  gi|557694500|ref|YP_008797554.1| 187 SRGSKVLDPFAGSGALVIEAGLLG-HVCLGVEVKTWVCNGMWRNMQFYGIGL--GHAVQGDARHLPFR----RFFDA 256
                                       56889***************9988.89999*******************995..66667777777666....57*** PP

                                       EEE--SSSTTCH CS
                     Cons_hypoth95 117 vflDPPyakell 128
                                       v  DPPy ++++
  gi|557694500|ref|YP_008797554.1| 257 VATDPPYGRSAT 268
                                       *******99876 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.3   3.3e-10   9.8e-07      80     142 ..      84     146 ..      22     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 3.3e-10
                                       HHCT-EEEEEEEESSSTSSSHHHHHHHHHHHHHHCCTT.-EE-SSS-SEEEEEEEETTEEEEEE CS
                             THUMP  80 eeeketFaVrvkrrgkhfeftsreinrevGkaivektg.lkVdlenPdivvrveiikdkayisi 142
                                        e+  +F V v  +g   +++s+++++++++ai+  +   +V+l+ Pd ++ + i  ++++i++
  gi|557694500|ref|YP_008797554.1|  84 VEGRRSFDVSVYEVGGV-DVNSVDVEKKLAAAINAHIPgMRVNLTTPDARFVAVITLSNCFIGL 146
                                       33444***********9.********************************************97 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.1e-08   3.3e-05     173     222 ..     169     219 ..      63     225 .. 0.90
   2 ?    0.4   0.0      0.14   4.3e+02       2      14 ..     255     267 ..     254     316 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.1e-08
                                       SS---HHHHHHHHHHHS-T.T-EEEETT-TTTHHHHHHHHTT-EEEEEESS CS
                       N6_N4_Mtase 173 paqkPvallerlIklstkk.gdivlDpFaGSGtTavaakelgrkfiGieie 222
                                       p  +  +l++ l++l  +  g+ vlDpFaGSG  +++a  lg  ++G+e++
  gi|557694500|ref|YP_008797554.1| 169 PSAMQPKLARCLVNLAINSrGSKVLDPFAGSGALVIEAGLLGHVCLGVEVK 219
                                       5556678999999888887799***************************87 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.14
                                       EEEEE--SSSSSC CS
                       N6_N4_Mtase   2 dlivtdpPYntgk 14 
                                       d + tdpPY+ + 
  gi|557694500|ref|YP_008797554.1| 255 DAVATDPPYGRSA 267
                                       678999**99875 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 ?   12.4   0.0   2.9e-05     0.086       3      48 ..     191     236 ..     189     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.9e-05
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvs 48 
                                        +lD+f+G+G  vi+  l ++   ++e+++  ++ + +N ++Yg+ 
  gi|557694500|ref|YP_008797554.1| 191 KVLDPFAGSGALVIEAGLLGHVCLGVEVKTWVCNGMWRNMQFYGIG 236
                                       69*****************************************984 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00022      0.67      34     136 ..     176     264 ..     172     303 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00022
                          N6_Mtase  34 vsklivellepksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkir 110
                                       + + +v+l+ +++g++v+Dp +Gsg+l ++a                 G+e+++   +    N+   gi     ++ 
  gi|557694500|ref|YP_008797554.1| 176 LARCLVNLAINSRGSKVLDPFAGSGALVIEAGLL---------GHVCLGVEVKTWVCNGMWRNMQFYGIGLG--HAV 241
                                       6778999998889999************998652.........33455666665555555556666666655..455 PP

                          N6_Mtase 111 lgdtlekpkfekdkkfdvvvaNppfn 136
                                       +gd+ + p  +    fd+v++ pp++
  gi|557694500|ref|YP_008797554.1| 242 QGDARHLPFRR---FFDAVATDPPYG 264
                                       55555554443...566666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2408.20
//
Query:       gi|557694501|ref|YP_008797555.1|  [L=301]
Description: ribonuclease Z [Candidatus Caldiarchaeum subterraneum]
Scores for 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-24   87.2   0.0    8.6e-12   45.0   0.0    2.1  2  Lactamase_B_2  Beta-lactamase superfamily domain
    3.3e-08   33.8   0.5    1.8e-07   31.4   0.5    2.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
     0.0012   18.4   0.0     0.0024   17.5   0.0    1.4  1  Lactamase_B_4  tRNase Z endonuclease


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 !   40.3   0.0     4e-14   2.4e-10       4     132 ..      32     148 ..      30     156 .. 0.81
   2 !   45.0   0.0   1.4e-15   8.6e-12     132     201 .]     197     266 ..     173     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 4e-14
                                       EES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.....C--EEEEEEEEHHHHHHCCTTC CS
                     Lactamase_B_2   4 LiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre.....lrpkklplyapkgvlavleanf 74 
                                       L D+g ++  q   +          ++p   ++lth H DH+ g++ l       +r+k++++y+pk ++  ++a +
  gi|557694501|ref|YP_008797555.1|  32 LMDCGEGTQRQfIFSG-------LGVKPGFHIFLTHLHGDHVLGVPGLLFtlsmnGREKEVNIYGPKNTATLVKALT 101
                                       7788888655533333.......35778888***********999999888887777778***************98 PP

                                       GHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEEC CS
                     Lactamase_B_2  75 vylaleeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlrieg 132
                                        +     ++++n+hel + ++++++   +++ta+   h++           lG+++++
  gi|557694501|ref|YP_008797555.1| 102 LPYLGTLNFTINIHELSPTDTVHID--TVTVTAFKTDHTTNS---------LGYIVKE 148
                                       777777778***************8..578999999998887.........8888874 PP

  == domain 2  score: 45.0 bits;  conditional E-value: 1.4e-15
                                       CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 132 gggkrvyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeeaveaaadlgakrlvliHi 201
                                       ++g++++y+gDt  ++e ++   ++ad+l++d+t+ ++ + ++ + gH+t e+a++ aa+++akrl+l+Hi
  gi|557694501|ref|YP_008797555.1| 197 RPGRKIVYTGDTRPCEEVVK-AAQDADVLIHDATFDSSLREKAvEQGHSTAEDAAKTAAEASAKRLYLFHI 266
                                       689*************7766.99***********9999887779**************************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 !   31.4   0.5     3e-11   1.8e-07       8      71 ..      21      79 ..      16     265 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 3e-11
                                      EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCE CS
                       Lactamase_B  8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvp 71
                                      s+ i+  ++ +L D+G +t+++ ++      gl+ k+  +++lTHlH DH+ g++gl  +   +
  gi|557694501|ref|YP_008797555.1| 21 SVAIRMSKSILLMDCGEGTQRQFIF-----SGLGVKPGFHIFLTHLHGDHVLGVPGLLFTLSMN 79
                                      5678888999**************9.....6*************************98776655 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0     4e-07    0.0024      12      60 ..      18      65 ..      12      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4e-07
                     Lactamase_B_4 12 g.PlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkvswss 60
                                      g P++++++ +   l+ ++gEgtQR ++ +++ +    +iFLt+ +  ++
  gi|557694501|ref|YP_008797555.1| 18 GmPSVAIRMSKSILLM-DCGEGTQRQFIFSGLGVKPGFHIFLTHLH-GDH 65
                                      4489999999999999.***************************98.555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 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:                        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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2094.98
//
Query:       gi|557694502|ref|YP_008797556.1|  [L=126]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   52.5   0.0      2e-13   50.7   0.0    1.7  1  RNA_binding  RNA binding
  ------ inclusion threshold ------
      0.036   14.6   0.1      0.085   13.4   0.1    1.7  1  Pyr_redox    Pyridine nucleotide-disulphide oxidoreductase


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 !   50.7   0.0   2.2e-17     2e-13       3     118 ..       6     113 ..       4     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 2.2e-17
                                       EEEEEE-TTC-HHHHHHHHHTTSTTS....E---EEEEEE-CCC-EEEEEEEEESSHHHHHHHHHHHHHHCCCCH.. CS
                       RNA_binding   3 evrafvhaTEdeekVlealsnllpee....eveieeeeaeGhygnpitileaelekkkakkvlkkllellreeei.. 73 
                                       +v+a v+ TEdeekV++al n++p+     +            g+  +   a++e+    + ++kl+  +r+ +i  
  gi|557694502|ref|YP_008797556.1|   6 TVTAPVNFTEDEEKVAKALLNIFPKAvliqK------------GDGKV--VAHVEG---TAGFEKLRMIIRSRRIrn 65 
                                       78999*******************8865432............44444..455666...557888888888888843 PP

                                       ...HHHHHCCHCCB-TTSEEEEEEEHHHHHTT---BESSSS.....EEEEEEE CS
                       RNA_binding  74 ...keLlkeleervdekgklylrldKQaaylgklslvegdd.....vIkvkik 118
                                            L+k+l      ++++++ l+KQaa +gk+s+ e+++     +I+v+++
  gi|557694502|ref|YP_008797556.1|  66 tvrALLNKGLR-----DNTVTFYLNKQAASVGKVSFFEEGEvmalgPITVVVE 113
                                       33344444444.....6************************888888888876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   9.5e-06     0.085      26      68 ..      55      93 ..      42      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.5e-06
                                      EEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEE CS
                         Pyr_redox 26 tvversdkllrllDeeaskilqeklekngievllntkveeieg 68
                                       ++ rs +++    ++++++l + l++n ++++ln++++++ +
  gi|557694502|ref|YP_008797556.1| 55 RMIIRSRRIR----NTVRALLNKGLRDNTVTFYLNKQAASVGK 93
                                      5788888899....9************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 00:00:00.42
# Mc/sec: 893.10
//
Query:       gi|557694503|ref|YP_008797557.1|  [L=138]
Description: signal-transduction protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   92.7   2.9    4.5e-14   52.6   0.0    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 !   40.2   0.9   1.9e-14   3.3e-10       1      54 [.       7      59 ..       7      62 .. 0.89
   2 !   52.6   0.0   2.5e-18   4.5e-14       1      53 [.      71     122 ..      71     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.9e-14
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  1 Vgdimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllra 54
                                      V+d+m ++vv +++++t+++a+++m e++   +l VV  ++ ++G+vt+rD++r 
  gi|557694503|ref|YP_008797557.1|  7 VKDVMDKKVVEIDENATVADAVKKMLENEvW-SL-VVTRQKLPIGVVTERDIIRR 59
                                      89***********************9*9955.77.995555599*********96 PP

  == domain 2  score: 52.6 bits;  conditional E-value: 2.5e-18
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       Vg+im++++ t++pd++l+ea+ +++ek+++rl+V+ e+gk++G vt++ l++
  gi|557694503|ref|YP_008797557.1|  71 VGEIMSTPIETISPDASLGEAMAKLVEKNIRRLFVI-ENGKIIGRVTQTELFE 122
                                       89**********************************.9**********99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1013.81
//
Query:       gi|557694504|ref|YP_008797558.1|  [L=218]
Description: dTMP kinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-16   60.3   0.1    2.6e-15   56.6   0.1    2.0  1  Thymidylate_kin  Thymidylate kinase
    1.2e-06   28.7   0.2      0.044   13.9   0.1    2.2  2  AAA_33           AAA domain
    0.00085   19.9   0.8      0.011   16.3   0.8    2.2  1  AAA_18           AAA domain
     0.0019   18.1   0.0     0.0044   16.9   0.0    1.6  1  MobB             Molybdopterin guanine dinucleotide synthesis
      0.002   18.5   5.0        0.5   10.8   0.9    2.8  2  AAA_17           AAA domain
     0.0026   17.5   0.0     0.0039   16.9   0.0    1.4  1  AAA_30           AAA domain
     0.0044   17.0   0.1     0.0094   15.9   0.1    1.5  1  NACHT            NACHT domain
     0.0045   16.6   0.0       0.25   10.9   0.0    2.0  2  MCD              Malonyl-CoA decarboxylase C-terminal domain
  ------ inclusion threshold ------
      0.012   15.4   0.6       0.82    9.5   0.1    2.1  2  dNK              Deoxynucleoside kinase
      0.013   15.7   0.1      0.031   14.5   0.1    1.7  1  AAA_28           AAA domain
      0.017   14.3   0.1      0.029   13.6   0.1    1.4  1  NB-ARC           NB-ARC domain
      0.019   14.9   0.5      0.048   13.6   0.1    1.8  2  NTPase_1         NTPase
      0.024   13.6   0.3      0.067   12.2   0.1    1.8  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.032   14.2   0.5      0.055   13.4   0.5    1.9  1  ATPase_2         ATPase domain predominantly from Archaea
       0.04   14.2   0.0      0.087   13.1   0.0    1.6  1  AAA_22           AAA domain
      0.042   14.3   0.5       0.12   12.8   0.5    2.0  1  AAA              ATPase family associated with various cellul
      0.099   13.6   0.1          4    8.5   0.0    2.6  3  LytR_C           LytR cell envelope-related transcriptional a


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 !   56.6   0.1   2.5e-18   2.6e-15       2     162 ..       5     178 ..       4     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 2.5e-18
                                       EESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTH..HHHHHH CS
                   Thymidylate_kin   2 EGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehle..ekikpa 76 
                                       EG+DG+GKtt +++++++l e+g+ v + + p+++++G  + +  + + e +++t  llf+a+ ++  +  +ki+++
  gi|557694504|ref|YP_008797558.1|   5 EGVDGSGKTTLMKAVVNKLAEKGHGVETYKTPSSSPTGIFAVQHGN-RPETDPLTRMLLFLANTSDDSAviKKIIEE 80 
                                       9**********************99999**********99999988.99***************9988866666664 PP

                                       HHTT-EEEEES-HHHHHHH......HHTTTTTT.......CHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSS CS
                   Thymidylate_kin  77 lkqgktvivdRylfSslaY......qgakegvd.......ldlvlslnedvllkPdltflldvdpevalkRlakrde 140
                                        k+ +   +dRy + s++Y        +++gv+       +++v +l e+v+ kPdlt+ ++vd+e++ +R a++  
  gi|557694504|ref|YP_008797558.1|  81 -KKPDYMMIDRYSLCSVVYgfalwsRRFGRGVEdmlftrfIEIVETLGENVFAKPDLTVVVEVDEETRRRRTAQKTG 156
                                       .56688899**********4433332234444333333335566677777777******************998887 PP

                                       TTTSHHHHHHHHHHHHHHHHHH CS
                   Thymidylate_kin 141 ldeeeeeqldflrkvrerylel 162
                                         + + e  + l+k+  +y+++
  gi|557694504|ref|YP_008797558.1| 157 TSDRVLEVDEELQKLVSKYYDV 178
                                       4555555555555555555544 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   6.7e-05     0.071       2      25 ..       2      30 ..       1      88 [. 0.79
   2 !   13.9   0.1   4.2e-05     0.044      98     131 ..     134     167 ..     105     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.7e-05
                            AAA_33  2 vllvGlpGsGKstlaerllkklg.....a 25
                                      v   G+ GsGK+tl + +++kl+     +
  gi|557694504|ref|YP_008797558.1|  2 VAWEGVDGSGKTTLMKAVVNKLAekghgV 30
                                      6678**************99987554443 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.2e-05
                            AAA_33  98 pvrivvvetdeetlkeRlakRaangddrsevpee 131
                                       p++ vvve+deet ++R+a++  ++d+  ev+ee
  gi|557694504|ref|YP_008797558.1| 134 PDLTVVVEVDEETRRRRTAQKTGTSDRVLEVDEE 167
                                       5999*******************99988888876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.8     1e-05     0.011       4     120 ..       5     161 ..       2     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                            AAA_18   4 tGtpGvGKttlakeLskrl.gfgvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvi 79 
                                        G+ G+GKttl k++ ++l + g  +  + + + + ++ ++   +  +r ++d l + l  l + s+     ++ vi
  gi|557694504|ref|YP_008797558.1|   5 EGVDGSGKTTLMKAVVNKLaEKGHGVETYKTPSSSPTGIFAV--QHGNRPETDPLTRMLLFLANTSD-----DSAVI 74 
                                       599************888744477788888887788877777..88888888888888888888877.....66666 PP

                            AAA_18  80 dghlaeleseaakdikk..............................................vvLtaspeelleRl 110
                                         +++e  ++++ +  +                                              vv+++++e++++R 
  gi|557694504|ref|YP_008797558.1|  75 KKIIEEKKPDYMMIDRYslcsvvygfalwsrrfgrgvedmlftrfieivetlgenvfakpdltVVVEVDEETRRRRT 151
                                       666666665544444444666666666666677888888888888888889999999999999*************9 PP

                            AAA_18 111 ekRgyeeaki 120
                                       ++   ++++ 
  gi|557694504|ref|YP_008797558.1| 152 AQKTGTSDRV 161
                                       9988777765 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 !   16.9   0.0   4.1e-06    0.0044       5      34 ..       5      34 ..       1      40 [. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.1e-06
                              MobB  5 vgksgsGKTtLleklipelkarglrvgtiK 34
                                       g  gsGKTtL++ ++++l+++g  v t K
  gi|557694504|ref|YP_008797558.1|  5 EGVDGSGKTTLMKAVVNKLAEKGHGVETYK 34
                                      5889********************999988 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2    0.0022       2.3       2      19 ..       6      23 ..       5      35 .. 0.87
   2 !   10.8   0.9   0.00048       0.5     100     135 ..     132     168 ..      69     169 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0022
                                      E-TTSSHHHHHHHHHHHH CS
                            AAA_17  2 GgPGsGKgtqceklveky 19
                                      G+ GsGK+t+++ +v k+
  gi|557694504|ref|YP_008797558.1|  6 GVDGSGKTTLMKAVVNKL 23
                                      899***********9987 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00048
                                       H..SEEEEEE--HHHHHHHHHHH.TTST-TS-SHHHH CS
                            AAA_17 100 lkpdaiilleadpeeilerrlkd.rtrgrdddneesi 135
                                       +kpd+ +++e+d+e+ ++r +++  t++r  +  e++
  gi|557694504|ref|YP_008797558.1| 132 AKPDLTVVVEVDEETRRRRTAQKtGTSDRVLEVDEEL 168
                                       579************9999999845899988777766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.7e-06    0.0039      21      54 ..       2      40 ..       1      96 [. 0.77

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.7e-06
                            AAA_30 21 avltGpAGtGKttalkalreaweaag.....grviglAp 54
                                      ++++G+ G+GKtt++ka+++ ++++g     ++    +p
  gi|557694504|ref|YP_008797558.1|  2 VAWEGVDGSGKTTLMKAVVNKLAEKGhgvetYKTPSSSP 40
                                      5789**************999999984455544444455 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   8.9e-06    0.0094       3      28 ..       2      27 ..       1      42 [. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.9e-06
                                      EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegk 28
                                      v+ +G  GsGKTtL++ ++ ++ae+ 
  gi|557694504|ref|YP_008797558.1|  2 VAWEGVDGSGKTTLMKAVVNKLAEKG 27
                                      5678******************9976 PP

>> MCD  Malonyl-CoA decarboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.031        33     112     139 ..      14      41 ..       5      61 .. 0.83
   2 !   10.9   0.0   0.00024      0.25     112     206 ..      72     176 ..      64     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.031
                                       HHHHHHHHHHHHH-TT--EEEEEE--TT CS
                               MCD 112 fLiKrvveelkrelpklktfatLsPiPg 139
                                        L+K vv++l+++   ++t+ t s  P+
  gi|557694504|ref|YP_008797558.1|  14 TLMKAVVNKLAEKGHGVETYKTPSSSPT 41 
                                       69*******************9987775 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00024
                                       HHHHHHHHHHHHH-TT--EEEEEE--TTSHHHHHHHCCGCC-TT--HHHHCCHGGC..................... CS
                               MCD 112 fLiKrvveelkrelpklktfatLsPiPgfrkwlkrelkkesealleeeeaealael..............eaeaakl 174
                                        +iK+++ee k ++  +++++  s + gf+ w +r   +  e++l ++ +e +++l              e+++++ 
  gi|557694504|ref|YP_008797558.1|  72 AVIKKIIEEKKPDYMMIDRYSLCSVVYGFALWSRRFG-RGVEDMLFTRFIEIVETLgenvfakpdltvvvEVDEETR 147
                                       57******************************99764.666667766667777777777788777776543333332 PP

                                       .....TSSTCTSSCHHHHHHHHHHHHHHHHHH CS
                               MCD 175 lkklleeeewaedeelaeklkevllrlaarYl 206
                                        +++++++ +   ++   ++ e l++l+++Y+
  gi|557694504|ref|YP_008797558.1| 148 RRRTAQKTGT---SDRVLEVDEELQKLVSKYY 176
                                       2222222222...2223445555555555554 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.023        24       4      22 ..       5      23 ..       2      39 .. 0.80
   2 ?    9.5   0.1   0.00078      0.82     106     186 ..     116     198 ..      71     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.023
                                      EESTTSSHHHHHHHHHCCS CS
                               dNK  4 eGnIgaGKstlvklLskkl 22
                                      eG  g+GK+tl+k   +kl
  gi|557694504|ref|YP_008797558.1|  5 EGVDGSGKTTLMKAVVNKL 23
                                      8888********9766655 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00078
                                       HHHHHHHHHHHH.HHCCH-SEEEEEE--HHHHHHHHHHCTTCCCT..TS-HHHHHHHHHHHHHHHTSGGCS.-EEEE CS
                               dNK 106 lkiykelldnll.eelakpdlliYLkasletclerikkRgreeek..kieldYlekLhekyeewlkklnev.pvlvi 178
                                       ++ + e+ + l  + +akpdl + ++++ et  +r  ++  + +   +++++ l+kL +ky + + +     +v v+
  gi|557694504|ref|YP_008797558.1| 116 FTRFIEIVETLGeNVFAKPDLTVVVEVDEETRRRRTAQKTGTSDRvlEVDEE-LQKLVSKYYDVYLSWRPGeTVKVF 191
                                       555666666666566889*********************9999997777777.566666665555554444489999 PP

                                       ETSS.-TT CS
                               dNK 179 dveeldlv 186
                                       ++++ +l+
  gi|557694504|ref|YP_008797558.1| 192 NGDS-MLD 198
                                       9998.544 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   2.9e-05     0.031       5     146 ..       5     173 ..       1     183 [. 0.55

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-05
                            AAA_28   5 tGgestGKTtll....eaLaar..gypvv..pEaareileeklakgedalpwvedllafaervleeql..eeeaaaa 71 
                                        G  ++GKTtl+    ++La++  g++++  p +  + ++  +  ++ + +   ++l f +   +  +  ++  + +
  gi|557694504|ref|YP_008797558.1|   5 EGVDGSGKTTLMkavvNKLAEKghGVETYktPSSSPTGIFAVQHGNRPETDPLTRMLLFLANTSDDSAviKKIIEEK 81 
                                       57789*******44444555546677777444444443433333333333333466666665555444113334449 PP

                            AAA_28  72 ankvlfcDrglldtlaYaraygg............eaeaelea.........aarekrydlvfllppapei..dddg 125
                                       +++++++Dr +l++++Y  a+              +      +         +  + + dl +++++++e+  ++++
  gi|557694504|ref|YP_008797558.1|  82 KPDYMMIDRYSLCSVVYGFALWSrrfgrgvedmlfT------RfieivetlgENVFAKPDLTVVVEVDEETrrRRTA 152
                                       ****************97554332333333333331......33222212212224555777777777776655555 PP

                            AAA_28 126 eRredleereaiderlrealr 146
                                       + + + ++  ++de l++++ 
  gi|557694504|ref|YP_008797558.1| 153 QKTGTSDRVLEVDEELQKLVS 173
                                       556666666666666666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.8e-05     0.029      23      50 ..       2      29 ..       1      41 [. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.8e-05
                                      EEEEESTTSSHHHHHHHHCCSHCCCCCC CS
                            NB-ARC 23 valvGmgGvGKttlakqilnksdevegr 50
                                      va  G  G+GKttl+k ++nk++e  + 
  gi|557694504|ref|YP_008797558.1|  2 VAWEGVDGSGKTTLMKAVVNKLAEKGHG 29
                                      6678999**************9998775 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.6e-05     0.048       6      35 ..       6      35 ..       2      46 .. 0.85
   2 ?   -2.8   0.0       4.8   5.1e+03      94     157 ..     132     144 ..     114     154 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.6e-05
                                      --TTSSHHHHHHHHHHHH...GGGEEEEEE CS
                          NTPase_1  6 GppGvGKtTlvkkvlellkssgvkvgGfyt 35
                                      G  G+GKtTl+k v+++l+++g  v+   t
  gi|557694504|ref|YP_008797558.1|  6 GVDGSGKTTLMKAVVNKLAEKGHGVETYKT 35
                                      778******************988876555 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.8
                                       HHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE--T CS
                          NTPase_1  94 seadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfevte 157
                                        ++d+ v                                                   v+ev+e
  gi|557694504|ref|YP_008797558.1| 132 AKPDLTV---------------------------------------------------VVEVDE 144
                                       3444333...................................................334444 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   0.1   6.4e-05     0.067      35      70 ..       5      39 ..       1      46 [. 0.82
   2 ?   -1.6   0.0      0.98     1e+03     184     231 ..     163     210 ..     132     217 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.4e-05
                                      EE-TTSSHHHHHHHHHHHHHCTT--EEEEEE----- CS
                              MeaB 35 tGvPGaGkstlvealglelrrrGkrvavlavDPssp 70
                                       Gv G+Gk tl++a++ +l+++G+ v      Pss+
  gi|557694504|ref|YP_008797558.1|  5 EGVDGSGKTTLMKAVVNKLAEKGHGVETYKT-PSSS 39
                                      69**********************9987654.4444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.98
                                       HHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHHHHH CS
                              MeaB 184 kaarelraaleleeekekeWrpkvlktsavegeGidelvdaieehrev 231
                                       ++ +el++ +++ +  + +Wrp     +      +del++++ e   +
  gi|557694504|ref|YP_008797558.1| 163 EVDEELQKLVSKYYDVYLSWRPGETVKVFNGDSMLDELANTLAEKLVY 210
                                       334445555555555666777765555555556666666666665555 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 ?   13.4   0.5   5.2e-05     0.055      27      51 ..       6      30 ..       5     209 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                          ATPase_2 27 GpegsGKtaLlkeiienledkdkyv 51
                                      G  gsGKt+L+k ++++l +k+  v
  gi|557694504|ref|YP_008797558.1|  6 GVDGSGKTTLMKAVVNKLAEKGHGV 30
                                      7789**************9988754 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   8.2e-05     0.087      12      51 ..       6      39 ..       2      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.2e-05
                            AAA_22 12 GesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51
                                      G  G+GKTtl++ ++++l e       + +v +++ pss+
  gi|557694504|ref|YP_008797558.1|  6 GVDGSGKTTLMKAVVNKLAEK------GHGVETYKTPSSS 39
                                      778**************9653......4444444444444 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 ?   12.8   0.5   0.00012      0.12       5      23 ..       6      29 ..       2     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                                      SSTTSSHHHHHHHHHHHH.....T CS
                               AAA  5 GppGtGKTllakavakel.....g 23
                                      G  G GKT+l+kav+++l     g
  gi|557694504|ref|YP_008797558.1|  6 GVDGSGKTTLMKAVVNKLaekghG 29
                                      889**************8443332 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0038         4       8      47 ..       8      45 ..       7      78 .. 0.76
   2 ?   -2.1   0.0       7.6     8e+03       8       8 ..     144     144 ..     122     171 .. 0.57
   3 ?    2.2   0.0      0.35   3.7e+02       3      23 ..     187     208 ..     186     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0038
                            LytR_C  8 NgtgvsGlAarvadaLeerGftvgevgnagnadeettivy 47
                                      +g+g++ l ++v ++L+e+G  v + ++ +++  +t i++
  gi|557694504|ref|YP_008797558.1|  8 DGSGKTTLMKAVVNKLAEKGHGVETYKTPSSS--PTGIFA 45
                                      79******************988875544444..477775 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.6
                            LytR_C   8 N 8  
                                        
  gi|557694504|ref|YP_008797558.1| 144 E 144
                                       2 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.35
                            LytR_C   3 kVeVlNg.tgvsGlAarvadaL 23 
                                       +V+V+Ng +  + lA ++a++L
  gi|557694504|ref|YP_008797558.1| 187 TVKVFNGdSMLDELANTLAEKL 208
                                       799****777999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      601  (0.0335211); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 1588.90
//
Query:       gi|557694505|ref|YP_008797559.1|  [L=183]
Description: 2'-5' RNA ligase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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    5.3e-19   68.2   0.0    2.1  2  LigT_PEase       LigT like Phosphoesterase
    1.5e-14   54.1   0.0    1.9e-14   53.8   0.0    1.1  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    3.9e-13   49.8   0.0    4.9e-13   49.4   0.0    1.1  1  AKAP7_NLS        AKAP7 2'5' RNA ligase-like domain


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 !   68.2   0.0   8.8e-23   5.3e-19       4      87 .]      12      92 ..       8      92 .. 0.93
   2 !   29.2   0.0   1.3e-10   7.7e-07       2      87 .]      94     175 ..      93     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 8.8e-23
                                      CHHHHHHHHHHHHHHHHHHCCTTEEETSGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCS CS
                        LigT_PEase  4 peeiaeelarlaaeleralaklglkpvrpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlr 82
                                      +e++ ++l ++++el  ++a+ glkpv+p+n+HiTL flge d+++v+e+++al++i  +a+pfe+  +gvg+fp   r
  gi|557694505|ref|YP_008797559.1| 12 DEQTVKNLLAIQNELL-RAAGEGLKPVEPENLHITLLFLGELDDSQVSEAEKALQSI--EAKPFEIGMNGVGYFPGGGR 87
                                      788999**********.66689***********************************..777*************9889 PP

                                      CCEEE CS
                        LigT_PEase 83 prviy 87
                                       +vi+
  gi|557694505|ref|YP_008797559.1| 88 VNVIW 92
                                      99998 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 1.3e-10
                                       E-CHHHHHHHHHHHHHHHHHHCCTTEEET.SGGGSEEEEEEEEEES.HHHHHHHHHHHHHHHHTSBEEEEEEEEEEE CS
                        LigT_PEase   2 gppeeiaeelarlaaeleralaklglkpv.rpfnpHiTLaflgevd.eekvpellealaeiasgaepfelkvdgvgl 76 
                                       g ++e a++la ++++l+++   + ++++ ++f pH+T+ +++  + +  + e++++ ++  +g+      v++++l
  gi|557694505|ref|YP_008797559.1|  94 G-VKEGADNLADVHNQLRKR--LPRIRVEeQRFIPHLTICRVKYLRnRGPLLEAINRNSNTFFGR----QLVTRIVL 163
                                       6.68889***********55..5789*****************9997666778889999998997....77****** PP

                                       EEECC.SCCEEE CS
                        LigT_PEase  77 fpsrl.rprviy 87 
                                        +s l +++++y
  gi|557694505|ref|YP_008797559.1| 164 KKSVLtSSGPVY 175
                                       *********998 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 !   53.8   0.0   3.2e-18   1.9e-14      12     129 ..      27     145 ..      12     162 .. 0.80

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 3.2e-18
                   2_5_RNA_ligase2  12 lrrslydkayprwp..pHitLlypfvededl.adlaellsrlaketepfevrldgfgvFeh.kks.vvylsv.sdse 82 
                                       lr ++++++ p  p  +HitLl++++ d++  ++++++l+ +  e++pfe+  +g+g+F++     v+++ v ++ +
  gi|557694505|ref|YP_008797559.1|  27 LR-AAGEGLKPVEPenLHITLLFLGELDDSQvSEAEKALQSI--EAKPFEIGMNGVGYFPGgGRVnVIWVGVkEGAD 100
                                       45.5555554444444*************9766666666666..899**************84446*********** PP

                   2_5_RNA_ligase2  83 alqalraallealpeagdkedsgeftPHlTiaqsadstsaaellekl 129
                                        l +++++l++ lp  +  e  ++f PHlTi + +  +    lle++
  gi|557694505|ref|YP_008797559.1| 101 NLADVHNQLRKRLPRIRVEE--QRFIPHLTICRVKYLRNRGPLLEAI 145
                                       ****************9888..********98766655555555555 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 !   49.4   0.0   8.2e-17   4.9e-13       4     154 ..       5     138 ..       4     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 8.2e-17
                                       EEEEE---HHHHHHHHHHHHHHHHH-GGGGGGB.--TT--EEEEEEE---SHHHHHHHHHHHHHHHHHHHHHHTTS- CS
                         AKAP7_NLS   4 FlsiplnsnklrkklekfqesvlsklpgldeslfikpeklHlTllvlkLknkeeiaaakevLkevkeeikdaldnkp 80 
                                       F ++ + +++++k+l ++q+++l++  +  + +  +pe+lH+Tll l   +++++++a+++L++++     a   kp
  gi|557694505|ref|YP_008797559.1|   5 FYAVDIRDEQTVKNLLAIQNELLRAAGEGLKPV--EPENLHITLLFLGELDDSQVSEAEKALQSIE-----A---KP 71 
                                       77899999***************9766555555..8****************************95.....4...89 PP

                                       -EEEEEEEEEE.....TTTEEEEEE--SHHHHHHHHHHHHHHHHHHTTT--B--SS-.---EEEEEEGGG-THH CS
                         AKAP7_NLS  81 lslrlkGletfnddpakarVlYakveeesneekLqeladriikafeeaglvlekdkkkvklHaTlmnsrkrkkk 154
                                       +++ ++G+++f     +++V++++v+e    ++L +++++++k++       +++++ + +H+T+  +++ +++
  gi|557694505|ref|YP_008797559.1|  72 FEIGMNGVGYFP-GGGRVNVIWVGVKEG--ADNLADVHNQLRKRLPR---IRVEEQR-FIPHLTICRVKYLRNR 138
                                       ***********4.55679********65..7**************54...3445555.8*********998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1445.77
//
Query:       gi|557694506|ref|YP_008797560.1|  [L=453]
Description: tRNA nucleotidyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  124.4   0.0    4.4e-36  123.6   0.0    1.4  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
    2.2e-07   31.1   0.0    4.1e-07   30.2   0.0    1.4  1  NTP_transf_2     Nucleotidyltransferase domain
  ------ inclusion threshold ------
      0.072   13.3   0.0       0.17   12.0   0.0    1.7  1  SMODS            Second Messenger Oligonucleotide or Dinucleo


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 !  123.6   0.0   7.3e-40   4.4e-36       1     112 [.     153     259 ..     153     260 .. 0.94

  Alignments for each domain:
  == domain 1  score: 123.6 bits;  conditional E-value: 7.3e-40
                                       HHHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEET CS
                   tRNA_NucTransf2   1 devrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDP 77 
                                       d+vrllK+fl + ++YG+e+k++GfsGY++Ell++++gsf+++++aa++w+p+vvi  e+k     +  + l + DP
  gi|557694506|ref|YP_008797560.1| 153 DHVRLLKAFLMNDNLYGAEVKTRGFSGYVCELLITRFGSFTSLVQAASRWRPPVVIG-EDKP----APMTVLHLPDP 224
                                       78******************************************************5.3333....34789999*** PP

                                       TEEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGG CS
                   tRNA_NucTransf2  78 vDpkRNvaaalsleklaefilaareflkkpseeff 112
                                       vDp RN+aaa+sl++l++fil+++ fl+kps+++f
  gi|557694506|ref|YP_008797560.1| 225 VDPGRNTAAAVSLTTLSNFILKSKLFLTKPSIDYF 259
                                       **********************************9 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   6.8e-11   4.1e-07       3      82 ..      31     126 ..      29     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 6.8e-11
                                       HHHHHHHHHTTTSEEEEEHHHHCTTSCTT.SSEEEEEEESTTCHHH................HHHEHHHHHHHHCCC CS
                      NTP_transf_2   3 klleelkelepvakvvlfGSyarGtalkg.SDiDllvvlpeevsre................kkeegleklaeiikf 62 
                                       +l ++l++ +++ +v + GS+a+Gt+ +g  + D+++++   ++ +                   ++++++a ++++
  gi|557694506|ref|YP_008797560.1|  31 RLVQRLEDVFGKGRVSVEGSFAKGTMVRGrEESDIFIHFQPGFPVDeacrrvveegvkavveMGGVYRLRYASHPYV 107
                                       78889999999*******************************8877***************9778889********* PP

                                       EEECTTEEEEEECEEECCCC CS
                      NTP_transf_2  63 leellglevdlvtrekledp 82 
                                       +  + g++v +v+++  e  
  gi|557694506|ref|YP_008797560.1| 108 EGFVDGVRVNIVPCYDAE-Y 126
                                       ***************988.4 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 ?   12.0   0.0   2.9e-05      0.17       3     138 ..       4     129 ..       1     137 [. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.9e-05
                             SMODS   3 vssqFkeflsnielsqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllv 79 
                                       v++ ++  ++++++ ++t ++ ++ ++++ +rL+  f        +  + GS+a++T++++++++d+  ++   + v
  gi|557694506|ref|YP_008797560.1|   4 VEDVLRHVVEKLRPLPETLEKTEDVTARLVQRLEDVF-GK----GRVSVEGSFAKGTMVRGREESDIFIHFQPGFPV 75 
                                       5556677777788888889999999999999999999.32....345578***************888887776322 PP

                             SMODS  80 vvnevegdepsdlleklkkal.kktyksseirqdrqvvvvelneikidvvPavenkdgsy 138
                                             ++  ++++e+  ka+ +       +  +++ v   ++++++ +vP+   + g++
  gi|557694506|ref|YP_008797560.1|  76 ------DEACRRVVEEGVKAVvEMGGVYRLRYASHPYVEGFVDGVRVNIVPCYDAEYGKW 129
                                       ......234455665544444233333333444444444444888888888877776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3498.23
//
Query:       gi|557694507|ref|YP_008797561.1|  [L=234]
Description: serine/threonine protein kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   36.4   0.1    6.8e-09   35.6   0.1    1.4  1  RIO1            RIO1 family
    4.1e-06   26.4   0.0    6.3e-06   25.7   0.0    1.3  1  Pkinase         Protein kinase domain
    1.7e-05   24.3   0.3    2.5e-05   23.7   0.2    1.4  1  Pkinase_Tyr     Protein tyrosine kinase
     0.0064   16.1   0.1     0.0081   15.8   0.1    1.2  1  Choline_kinase  Choline/ethanolamine 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 !   35.6   0.1   1.5e-12   6.8e-09      54     162 ..      76     183 ..      62     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.5e-12
                                       HHHHHHHHHHHHHHTT--S--EEEEETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEES CS
                              RIO1  54 waekEfrnLkrleeagvpvPkpielkrhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHa 130
                                       + e+E + L+++++ +v  Pk  ++  h++vme+++  g  +++   ++++ e++e++e+vl++ + l+ + +l H+
  gi|557694507|ref|YP_008797561.1|  76 TMEQEATHLRKANTVNV-GPKLFNHSTHIIVMEYVE--GETLAEFITTKSRIEIAEIVEQVLDQ-AHLLDKIHLDHG 148
                                       56899999999988854.5*****************..99999999999899***********6.77788******* PP

                                       S-ST...TSEEEETTEEEE--GTTEEETTSTTHHH CS
                              RIO1 131 DLSe...yNvlvdedkvviIDvsQaveldhpnale 162
                                        LS+     ++  ++k+ iID s + ++++p+  +
  gi|557694507|ref|YP_008797561.1| 149 QLSNssdHVIISPRGKPCIIDYSHSSQQRKPRNVT 183
                                       **8522266777777********999999987655 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.4e-09   6.3e-06       7     148 ..      45     176 ..      43     196 .. 0.69

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.4e-09
                                       EEEESSEEEEEEEETTTTEEEEEEEEECHCHCHHHHHHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTE CS
                           Pkinase   7 lGeGsfGkVykaveketgkivAvKkikkekakkkkekkvlrEikilkklkhpnivrlyevfeekdelylvleyvegg 83 
                                       lG+G+ G V+ ++   ++  vAvK+ +++ a  ++e    +E + l+k +  n+      + ++++ ++v+eyveg+
  gi|557694507|ref|YP_008797561.1|  45 LGKGGRGMVFLGL--VDEACVAVKVARTDAAVPTME----QEATHLRKANTVNV---GPKLFNHSTHIIVMEYVEGE 112
                                       9************..79999************9887....78888777766665...444555677778******** PP

                                       BHHHHHHHHSS--HHHHHHHHHHHHHHHHHHHHTTEE-SS-S..GGGEEEETTTEEEE-SGTTSEES CS
                           Pkinase  84 eladllerkgslseeeakkiakqilegleylHskgiiHrDlK..peNiLidekgelKitDFGlakel 148
                                       +la+++++k+ +   e+ +i++q+l   + l + ++ H  l   ++ ++i+ +g+  i+D+ ++++ 
  gi|557694507|ref|YP_008797561.1| 113 TLAEFITTKSRI---EIAEIVEQVLDQAHLLDKIHLDHGQLSnsSDHVIISPRGKPCIIDYSHSSQQ 176
                                       ******975555...5555666665544444444444444431123455555555555555555555 PP

>> Pkinase_Tyr  Protein tyrosine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.2   5.7e-09   2.5e-05       7     113 ..      45     137 ..      43     190 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 5.7e-09
                                       EEEESSEEEEEEEEETTTTSSEEEEEEEEESTTSSHHHHHHHHHHHHHHHTS-BTTB--EEEEEESSSSEEEEEE-- CS
                       Pkinase_Tyr   7 lGeGafGkVvegtlkgekekkevkVavKtlkeeateeekeelleeakimkklkhpnivkllgvctkeepllivteyv 83 
                                       lG+G  G V+ g ++      e  VavK+ + +a       + +ea+ ++k    n v++     ++++++iv+eyv
  gi|557694507|ref|YP_008797561.1|  45 LGKGGRGMVFLGLVD------EACVAVKVARTDAAVP---TMEQEATHLRKA---NTVNVGPKLFNHSTHIIVMEYV 109
                                       9**************......999******7766665...888999877766...566666677788899******* PP

                                       TTEBHHHHHHHTCTTTSBHHHHHHHHHHHH CS
                       Pkinase_Tyr  84 kgGdLlkfLrkkekekltlkdllsfalqvA 113
                                       +g +L +f+++k  +++++ ++++ +l+ A
  gi|557694507|ref|YP_008797561.1| 110 EGETLAEFITTK--SRIEIAEIVEQVLDQA 137
                                       **********98..6777666666555544 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.8e-06    0.0081      15     125 ..      72     220 ..      62     234 .] 0.63

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.8e-06
                                       TTCCHHHHHHHHHHHHHHTTSSS-EEEEETTEEEEE--TCEE--TTGGGCHHHHHHHHHH....HHHHTTCHH.... CS
                    Choline_kinase  15 eelidretElvvfallserglgpklygifenGrieefiesrtlstedlrepeiskkiAkk....laelHslel.... 83 
                                        ++  +e+E+  ++  ++ ++gpkl++  +   + e++e++tl    + +++   +iA+     l + H l+     
  gi|557694507|ref|YP_008797561.1|  72 AAVPTMEQEATHLRKANTVNVGPKLFNHSTHIIVMEYVEGETLAE--FITTKSRIEIAEIveqvLDQAHLLDKihld 146
                                       5567899***********************************964..444444455555400014555655557888 PP

                                       ..........................TTSSSS-HHHHHHHHH.......HHCCS.TT..ECHHGGCCHCCCTHH CS
                    Choline_kinase  84 .........................eseskespslwktmqkw.......llnkeaqtkakkekkkkqlklinle 125
                                                                +s ++++p   + + ++        + ++ ++ +  +++k++ ++ +++
  gi|557694507|ref|YP_008797561.1| 147 hgqlsnssdhviisprgkpciidysHSSQQRKPRNVTAFTSYlirtilrERRNDPTLLTLLKQYKEKQDETSYA 220
                                       88888888888888888888888884455555555555555544444332222223333333333333444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); 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:                         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 0.23s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 1937.36
//
Query:       gi|557694508|ref|YP_008797562.1|  [L=464]
Description: glycolate oxidase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-60  203.5   0.1    5.9e-60  203.0   0.1    1.2  1  FAD-oxidase_C    FAD linked oxidases, C-terminal domain
    4.5e-43  146.3   0.4    1.5e-42  144.6   0.2    2.0  2  FAD_binding_4    FAD binding domain
  ------ inclusion threshold ------
       0.17   12.3   0.0       0.37   11.2   0.0    1.7  1  Terminase_4      Phage terminase, small subunit
       0.18   11.2   0.1        0.3   10.4   0.1    1.3  1  Guanylate_cyc_2  Guanylylate cyclase


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 !  203.0   0.1   1.3e-63   5.9e-60       7     249 ..     220     454 ..     217     455 .. 0.96

  Alignments for each domain:
  == domain 1  score: 203.0 bits;  conditional E-value: 1.3e-63
                                       EEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHHHHHHH CS
                     FAD-oxidase_C   7 valvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaeeeleal 83 
                                        + + f+++++a +a+ ei+ +++ p +le+ d++ l++++++ g+     +  ea+ll+ +e        +el  +
  gi|557694508|ref|YP_008797562.1| 220 RIYAVFDDWRDAGRAIIEIRTNRVVPRMLEFFDRIGLEAANKMHGT---SLPVGEAMLLIDVEEMT----GKELP-K 288
                                       56799*****************************************...7777889*******999....67777.9 PP

                                       HHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHHHHEEE CS
                     FAD-oxidase_C  84 veaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldkyglev 160
                                       v +ile++ a +v+va++e+eae+l+++R  ++     a +     v++eD++vP++r+ d+++++++l +k+gl++
  gi|557694508|ref|YP_008797562.1| 289 VLQILEKNHAREVRVAETEEEAEQLLQIRATMYL----AIRSVTKEVMVEDVCVPIDRIVDYLEKVQELSRKHGLTI 361
                                       999*******************************....99999********************************** PP

                                       EEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT---------------....--------THHHHHH CS
                     FAD-oxidase_C 161 vlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkka....ylerekgeeglalmr 233
                                       ++ gHagdgn+h++i +d+++++e++rae++v ++v+ a+e+gG+i+gEHGvG++k       le ++g e+l+lm+
  gi|557694508|ref|YP_008797562.1| 362 SMNGHAGDGNIHPLIFYDPDNPEEVKRAEQAVRDLVRFAIEVGGTITGEHGVGIQKMRelvqQLEAHNGIETLKLMQ 438
                                       ********************************************************98777799************* PP

                                       HHHHHH-TT--BSTT- CS
                     FAD-oxidase_C 234 riKaalDPkgiLNPgk 249
                                       +iK+a+DP++iLNPgk
  gi|557694508|ref|YP_008797562.1| 439 KIKKAFDPDNILNPGK 454
                                       ***************9 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.6   0.2   3.3e-46   1.5e-42       1     138 [.      40     176 ..      40     177 .. 0.98
   2 ?   -2.2   0.0      0.68     3e+03     109     109 ..     411     411 ..     379     435 .. 0.55

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 3.3e-46
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTCSCCEEEEEETTS--EEEEETTTTEEEEETTSBHHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqavatggvvldlsrlnrileideeegtatveaGvtlgdl 77 
                                       p++vvr++ +e+v+++lr+++++++p++v G+G+sl+g++v t+ ++ldls+++ril++d  + +a+veaGv+l++l
  gi|557694508|ref|YP_008797562.1|  40 PKLVVRASCVEDVSKLLRYCSRHKIPLTVWGAGTSLTGAVV-TDSLILDLSAMTRILKVDTVNYYAHVEAGVVLEQL 115
                                       789*************************************9.*********************************** PP

                                       HHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEE CS
                     FAD_binding_4  78 vealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrl 138
                                       ++ l+++g++++++p+s   +tvGGa+a+++gG ++ kyG+++d+vl ++vvla G vv +
  gi|557694508|ref|YP_008797562.1| 116 NNTLEEYGFFFPPDPASSFLCTVGGAVAEGSGGLRCVKYGTVKDWVLAVKVVLASGDVVVF 176
                                       **********************************************************976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.68
                                       E CS
                     FAD_binding_4 109 g 109
                                       +
  gi|557694508|ref|YP_008797562.1| 411 H 411
                                       2 PP

>> Terminase_4  Phage terminase, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.3e-05      0.37      19      96 ..     326     417 ..     311     420 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.3e-05
                       Terminase_4  19 seldseaLaayceayaryreaekkiek....eGvtittaegeg..........akkknpavtilnsaekelrklase 81 
                                       s +   +++  c  ++r+ +  +k+++    +G+ti  +   g             +  +v+ +++a ++l ++a e
  gi|557694508|ref|YP_008797562.1| 326 SVTKEVMVEDVCVPIDRIVDYLEKVQElsrkHGLTISMNGHAGdgnihplifyDPDNPEEVKRAEQAVRDLVRFAIE 402
                                       55667799999**9***99999999666666******8888779999999998788888899*************** PP

                       Terminase_4  82 lGLtpssRarlaakk 96 
                                        G t+++++ + ++k
  gi|557694508|ref|YP_008797562.1| 403 VGGTITGEHGVGIQK 417
                                       ******999988876 PP

>> Guanylate_cyc_2  Guanylylate cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   6.6e-05       0.3      87     192 ..     283     390 ..     278     403 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.6e-05
                   Guanylate_cyc_2  87 dkdekRvnklfkkakeagievekrsvsveelvehlasgkvaivLvnaalLkcdlcksnkllselrkllsrkseytGh 163
                                        k+  +v + ++k ++++++v +++ + e+l+++ a+  +ai  v ++++ +d+c     ++ + +++++ s+ +G 
  gi|557694508|ref|YP_008797562.1| 283 GKELPKVLQILEKNHAREVRVAETEEEAEQLLQIRATMYLAIRSVTKEVMVEDVCVPIDRIVDYLEKVQELSRKHGL 359
                                       567778999***********************************************98888889999999999**** PP

                   Guanylate_cyc_2 164 yvvlcGydak..ekkllyrnPassdkvcsis 192
                                        + + G   +   + l++ +P   ++v++++
  gi|557694508|ref|YP_008797562.1| 360 TISMNGHAGDgnIHPLIFYDPDNPEEVKRAE 390
                                       **99998654104558888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3256.73
//
Query:       gi|557694509|ref|YP_008797563.1|  [L=296]
Description: glucokinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-52  177.0   0.0    6.5e-52  176.8   0.0    1.0  1  ROK          ROK family
    0.00016   20.8   0.0     0.0034   16.4   0.0    2.6  1  Glucokinase  Glucokinase


Domain annotation for each model (and alignments):
>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.8   0.0   7.3e-56   6.5e-52       2     292 ..       4     293 ..       3     295 .. 0.86

  Alignments for each domain:
  == domain 1  score: 176.8 bits;  conditional E-value: 7.3e-56
                                       EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCH.TEEEEEEEEESSEEETTCCEBSS CS
                               ROK   2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerka.deliavgigspGlisdksgkivs 77 
                                       i++d G+t++++a+v ++g+i+ +    tp+  t ++++++ +   + + +    +   +gi+s G++s+k+g +++
  gi|557694509|ref|YP_008797563.1|   4 IAVDFGATYTRFAVVSSSGKIRRKIVTATPK--TIPAIRAMFKRGFSILRQTGvSAKTPLGIASIGPLSSKRGLVLN 78 
                                       89*******************9988885555..55566666665555544443034569****************** PP

                                       GGCGCCCCTTHHHHHHHHHTS-EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETTEEE--TTS-TT- CS
                               ROK  78 tpnitwenfdlvekleerlnvpvevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviingklitGrnGvage 154
                                       tpn+++  ++l+e +e+    p+ + nD naaa++E+vfg +   en++y+  gtG+G+G +++g+l+ G+ G+a e
  gi|557694509|ref|YP_008797563.1|  79 TPNLGGLSINLKEIVESFHRGPFALLNDCNAAAWGEKVFGVKTRLENLVYIAFGTGLGGGAVVDGNLLLGKDGNAVE 155
                                       ***************************************************************************** PP

                                       GGGSBS-TTS.-B-TTS-BSBHHHCCSHHHHHHCHTC...CGTTS-HHHHHHHHCTT-HHHHHHHHHHHHHHHHHHH CS
                               ROK 155 lGHiqldpeg.ekcgCGnqgClEtlasgralekraqq...kgekleakeiiklaekgdevaeevverlaeylakaia 227
                                       +GHi +d +  ++cgCG  g +E+++sg++l k a q   k    +  ei++   + d  a +vv ++aey a++ a
  gi|557694509|ref|YP_008797563.1| 156 IGHIVVDTNSrVRCGCGGIGHWEAFCSGTGLPKLAAQilgKRLWKTSWEIFESLPR-DGRARKVVAKMAEYNAAGYA 231
                                       *******665156*********************9997653333344577888877.99****************** PP

                                       HHHHHH--SEEEEEHCCCTSTTHHHHHHHHHHHCCTTTTCCCT-EEEE-S-STTHHHHHHHHHHC CS
                               ROK 228 dlinlfdpqaivlgGgvseadklleairklvkkylnkklevpvveivaaklgdkagllGaaaLak 292
                                        +in+fdp+  v+gGg+  ++    +++k   k+++kk +    +i  ++lg++a+llGaaa + 
  gi|557694509|ref|YP_008797563.1| 232 SVINTFDPEILVVGGGLALSHPRE-TLEK--PKHIMKKYQLLRTQIQLSSLGQDAALLGAAAYVL 293
                                       *****************9988754.5544..56677777766678****************9886 PP

>> Glucokinase  Glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.8e-07    0.0034       2     237 ..       5     237 ..       4     253 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.8e-07
                       Glucokinase   2 agDiGGTkarlalveaeeeelelleiekyasadyasleealqaflaea.eaevkrpksavlAvAgpvegdeveltNl 77 
                                       a D G T +r+a+v+ +++    ++i +   +  + + ++ ++ ++   ++ v++ +   +A  gp++ ++  + N 
  gi|557694509|ref|YP_008797563.1|   5 AVDFGATYTRFAVVSSSGKI--RRKIVTATPKTIPAIRAMFKRGFSILrQTGVSAKTPLGIASIGPLSSKRGLVLNT 79 
                                       679***************99..999999999999*******998886646666666668888889**9998776665 PP

                       Glucokinase  78 p....WviseeelakelgleaveliNDfeavayaiplleaedlvqlgggkkdaeapiavlGaGTGLGvallipeker 150
                                       p     +i+ +e+ +++    + l+ND +a a++ ++++ +           + ++++ ++ GTGLG + ++  +  
  gi|557694509|ref|YP_008797563.1|  80 PnlggLSINLKEIVESFHRGPFALLNDCNAAAWGEKVFGVKT----------RLENLVYIAFGTGLGGGAVVDGNL- 145
                                       5222358999************************87765443..........346788889999999988886543. PP

                       Glucokinase 151 rvvlasEGGhvdfapeseeevelleilrkklgrvsaErvlSGpGLvnlyealaaad.........kleeellepaei 218
                                          l   G  v+++         ++     +g+  +E ++SG+GL +l++ +  ++         +  ++  ++ ++
  gi|557694509|ref|YP_008797563.1| 146 --LLGKDGNAVEIGHIVVDTNSRVRCGCGGIGH--WEAFCSGTGLPKLAAQILGKRlwktsweifESLPRDGRARKV 218
                                       ..3444444444444333333333333444454..677888888877777776666544443333222233455555 PP

                       Glucokinase 219 teaalegedplarealelF 237
                                       ++  +e + +  ++++++F
  gi|557694509|ref|YP_008797563.1| 219 VAKMAEYNAAGYASVINTF 237
                                       5444455666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2171.95
//
Query:       gi|557694510|ref|YP_008797564.1|  [L=167]
Description: transcriptional regulator, AsnC family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   44.7   0.1    1.4e-07   31.3   0.0    2.2  2  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.047   13.6   0.1       0.15   12.0   0.0    1.8  2  GYD             GYD domain
       0.12   12.5   0.0       0.18   11.9   0.0    1.4  1  DUF4460         Domain of unknown function (DUF4460)


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 !   31.3   0.0   2.4e-11   1.4e-07      15      72 ..      17      72 ..       8      74 .. 0.88
   2 !   11.4   0.0   3.9e-05      0.23       3      70 ..      95     160 ..      93     167 .] 0.70

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.4e-11
                                      HHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEE CS
                    AsnC_trans_reg 15 efeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsiv 72
                                      e ++a++  ++V+e y + G+yd l kv v++l++l+ +l++  ++  gv +t+++iv
  gi|557694510|ref|YP_008797564.1| 17 ETIQAIRSDKNVEESYLIWGPYDVLSKVNVESLKHLNSVLDT--MRGYGVVDTNSLIV 72
                                      678999*********************************888..55668999999998 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.9e-05
                                       EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEE CS
                    AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartets 70 
                                       +++++ +  + +  e+ l  ++e++e + + G +d ++ v     e++ + + ++l  l +v  t+t+
  gi|557694510|ref|YP_008797564.1|  95 IKMRRPS--APKLWEKYLMSIDEILEGHELFGMWDVVVSVDEDAREDFFNRVFKRLWLLTEVNMTSTH 160
                                       5555555..667779999*********************98888887655555555555444444444 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.5e-05      0.15      34      78 ..      25      69 ..      11      73 .. 0.88
   2 ?   -2.1   0.1      0.62   3.7e+03      43      56 ..     122     135 ..     118     142 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                               GYD 34 GgkleslyatlGeyDvvvivEapDdetaaalslalaasGtvrtet 78
                                      + ++e++y++ G+yDv+  v+++  +    +  +++++G v+t  
  gi|557694510|ref|YP_008797564.1| 25 DKNVEESYLIWGPYDVLSKVNVESLKHLNSVLDTMRGYGVVDTNS 69
                                      6789***********************************999965 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.62
                               GYD  43 tlGeyDvvvivEap 56 
                                        +G  Dvvv v+ +
  gi|557694510|ref|YP_008797564.1| 122 LFGMWDVVVSVDED 135
                                       58889999999855 PP

>> DUF4460  Domain of unknown function (DUF4460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     3e-05      0.18      32      55 ..      41      64 ..      34      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3e-05
                           DUF4460 32 ekkvNeeSLklLnsyleelkkeek 55
                                        kvN eSLk Lns+l+++   + 
  gi|557694510|ref|YP_008797564.1| 41 LSKVNVESLKHLNSVLDTMRGYGV 64
                                      569**************9987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.48
# Mc/sec: 1050.19
//
Query:       gi|557694511|ref|YP_008797565.1|  [L=157]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  132.5   0.1    1.5e-38  132.3   0.1    1.0  1  Flavin_Reduct  Flavin reductase like domain
  ------ inclusion threshold ------
       0.06   13.1   0.0      0.073   12.8   0.0    1.1  1  DUF447         Protein of unknown function (DUF447)


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 !  132.3   0.1   1.7e-42   1.5e-38       1     152 [.       8     150 ..       8     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 132.3 bits;  conditional E-value: 1.7e-42
                                       HTTS-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS. CS
                     Flavin_Reduct   1 mrrvaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqk 77 
                                       mr+v+qpv+vvtt  ++++p+g+t+ssfts+sl+Pp+v+++l++  +t+ ++ ++g+f++nllse+q  + d f+  
  gi|557694511|ref|YP_008797565.1|   8 MRHVPQPVTVVTT-FHDGQPHGMTVSSFTSVSLEPPTVLIALEKTTKTCVNVLKSGRFCVNLLSEKQGWVSDVFAY- 82 
                                       9************.88************************************************************. PP

                                       ..SCCCCCCCCCCCEEECTCCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTTBEECCCCCEE CS
                     Flavin_Reduct  78 sgprtddksifagltweesptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddadeepLlywrrrya 152
                                            +++  f+ +++e + +g p+l+++l++l C+v g v++ +h +++g+V +v++ +++   pL+y+ rry 
  gi|557694511|ref|YP_008797565.1|  83 --SPHEER--FSRVKYELE-DGFPVLKDVLGVLFCEVSGHVDCSTHLIILGQVKRVRMFSEEL--PLIYHMRRYG 150
                                       ..456777..888888775.79**************************************966..9*******95 PP

>> DUF447  Protein of unknown function (DUF447)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.2e-06     0.073      23     103 ..      40     123 ..      16     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.2e-06
                                       SSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGG.EEEETTTC..TT.EETT-SEEEEEEEEE CS
                            DUF447  23 kgdkvvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesd.fdsetkpa..kiavlksaeawvevevee 96 
                                       +  +v+++l k ++T+ N+l++g++ +n+ +  +  +  ++   + ++ f++ + ++   ++vlk+   ++ +ev  
  gi|557694511|ref|YP_008797565.1|  40 EPPTVLIALEKTTKTCVNVLKSGRFCVNLLSEKQGWVSDVFAYSPHEErFSRVKYELedGFPVLKDVLGVLFCEVSG 116
                                       55668888999**********************99999888766544304444443335677999999999999987 PP

                                       ECTCECC CS
                            DUF447  97 vegdsea 103
                                         + s+ 
  gi|557694511|ref|YP_008797565.1| 117 HVDCSTH 123
                                       6555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1117.94
//
Query:       gi|557694512|ref|YP_008797566.1|  [L=440]
Description: aspartyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-87  293.3   0.6    2.3e-87  293.0   0.6    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    1.3e-09   37.9   1.5    2.3e-09   37.1   1.5    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0096   15.8   0.0      0.024   14.5   0.0    1.6  2  bacHORMA_2       Bacterial HORMA domain 2
  ------ inclusion threshold ------
       0.12   11.9   3.2       0.29   10.6   0.1    2.9  3  tRNA-synt_2d     tRNA synthetases class II core domain (F)


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 !  293.0   0.6   5.2e-91   2.3e-87       3     313 ..     127     434 ..     125     435 .. 0.96

  Alignments for each domain:
  == domain 1  score: 293.0 bits;  conditional E-value: 5.2e-91
                                       CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                       tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aL 75 
                                       + rl++r+ldlr+++v++v+ + s+v+ka+r++++ +gf+e+ tP L+ s+te+ga+lF v       ++f    +L
  gi|557694512|ref|YP_008797566.1| 127 DARLRHRILDLRRPEVRAVFLVGSEVLKAMRDFFHMKGFVEVRTPKLIGSATEGGAELFEV-------KYFdrvaYL 196
                                       679**********************************************************.......67777779* PP

                                       -S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  76 tqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakd 152
                                       +qspqly+e l    +++v +i++ FRaE s+t rh++EFt++++e sf+++ ++m+vleel+ ++ k+++e++ ++
  gi|557694512|ref|YP_008797566.1| 197 AQSPQLYKEQLTTV-FEKVCEIGPYFRAEASHTGRHISEFTSVDIEQSFADMYEVMDVLEELVVHVHKHLVENH-QH 271
                                       **************.*******************************************************9998.66 PP

                                       CCHTTTTTSEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 153 iefvirrnskdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeed 223
                                       + ++   n + +k++fkr+ty+ea+e+l+++      g+d  ++++r+l k +    +f+t+fP e kpFy +++e+
  gi|557694512|ref|YP_008797566.1| 272 LLQMLGVNLRVPKRHFKRFTYDEALEILRSEgvemrwGEDFGTPHLRLLGK-KYPTYYFITHFPTESKPFYIQETEK 347
                                       666666777788999**************99******9*************.88899******************** PP

                                       STTBBSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 224 dkkltesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllg 300
                                       d++++es+Dl+++ +El++G +R+ d+++le+kl++kgl+   ++ f++ l++++yG+p h+G+glG++R++m+l+ 
  gi|557694512|ref|YP_008797566.1| 348 DPRISESFDLMYQWLELASGGTRVSDHDVLERKLREKGLN---PAMFEDHLKVFSYGMPVHAGWGLGFERFLMVLTR 421
                                       ****************************************...********************************** PP

                                       -SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxx RF
                       tRNA-synt_2 301 sesIrdviaFPkl 313
                                        ++Ir++++FP+ 
  gi|557694512|ref|YP_008797566.1| 422 RTNIRETVLFPRD 434
                                       ***********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 !   37.1   1.5   5.1e-13   2.3e-09       1      74 [.      28     105 ..      28     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 5.1e-13
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEECTTS..SEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrrpgg..elelkve 71 
                                       V++ G+v+ i  r+ gk++fi lrD +g+ qvv+      +++++  + l++++ v v+G v + p+    +e++ +
  gi|557694512|ref|YP_008797566.1|  28 VNLFGWVHEI--RDLGKLVFILLRDVSGICQVVFRMeeveQSVRDAVKGLTNESAVFVEGVVVKQPRSklGVEVVGK 102
                                       7889******..************************9999999999999***************9665444776666 PP

                                       EEE CS
                   tRNA_anti-codon  72 eie 74 
                                       +++
  gi|557694512|ref|YP_008797566.1| 103 RLT 105
                                       665 PP

>> bacHORMA_2  Bacterial HORMA domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.2   9.9e+03      12      32 ..     144     164 ..     142     166 .. 0.83
   2 !   14.5   0.0   5.4e-06     0.024      79     146 ..     355     423 ..     349     429 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.2
                        bacHORMA_2  12 svtyvadnilkslkdiirlsG 32 
                                       +v  v  ++lk+++d  ++ G
  gi|557694512|ref|YP_008797566.1| 144 AVFLVGSEVLKAMRDFFHMKG 164
                                       67789999*****99988877 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 5.4e-06
                        bacHORMA_2  79 idivydy..sdsdGslwtdtdqlkyaikkaGlvpsqaeydlllknkpGrpdvaGwskgslrstdglvrqs 146
                                       +d++y++    s G+   d d+l+ +++  Gl p+  e +l + +  G p  aGw+ g  r    l+r++
  gi|557694512|ref|YP_008797566.1| 355 FDLMYQWleLASGGTRVSDHDVLERKLREKGLNPAMFEDHLKVFS-YGMPVHAGWGLGFERFLMVLTRRT 423
                                       7899***76679999***********************9999976.7*********99999888888876 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 ?   -1.2   0.0      0.26   1.2e+03      20      42 ..     150     172 ..     146     177 .. 0.86
   2 ?   -0.1   0.2      0.12   5.3e+02     103     145 ..     213     254 ..     204     291 .. 0.66
   3 ?   10.6   0.1   6.4e-05      0.29     212     234 ..     406     428 ..     329     435 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHCTTCEESSTTS CS
                      tRNA-synt_2d  20 tkvleeikeiflelgfeevegpe 42 
                                       ++vl+ ++++f+  gf ev+ p+
  gi|557694512|ref|YP_008797566.1| 150 SEVLKAMRDFFHMKGFVEVRTPK 172
                                       5789999*********9999775 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.12
                                       EEEEEEEEEBSST.-SSSB-SEEEEEEE..EEEETT--HHHHHHHH CS
                      tRNA-synt_2d 103 kiisigrvfRrda.vDathlaeFhqveg..lvvdenvsladlkgvl 145
                                       k+  ig  fR +a    +h  eF++v+    ++d    + +++ vl
  gi|557694512|ref|YP_008797566.1| 213 KVCEIGPYFRAEAsHTGRHISEFTSVDIeqSFAD----MYEVMDVL 254
                                       5666788889888556678888887653102223....23333333 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 6.4e-05
                                       EEEEEEHHHHHHHHHT-SSGHHH CS
                      tRNA-synt_2d 212 fafGlGveRlamlkygieDiRel 234
                                       +++GlG+eR+ m+ +  ++iRe 
  gi|557694512|ref|YP_008797566.1| 406 AGWGLGFERFLMVLTRRTNIRET 428
                                       46*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3449.99
//
Query:       gi|557694513|ref|YP_008797567.1|  [L=178]
Description: transcription elongation factor NusA [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.6   0.0      0.024   14.3   0.0    1.1  1  DUF2225   Uncharacterized protein conserved in bacteria (DUF2
       0.03   14.4   0.0      0.054   13.6   0.0    1.4  1  KH_5      NusA-like KH domain


Domain annotation for each model (and alignments):
>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.7e-06     0.024       6      85 ..      14      94 ..      10     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-06
                           DUF2225  6 ieCPvCeekfkkkkvkssslrlikrdsdlnakYeevnplfYevvvC.pkCgYaalkkdfeklskeekeklkekiskkwk 83
                                      + C  Ce+k+ + ++ s++l + +   dl  k+ ++++l Y  +   +  ++ ++++ f++l+++ ++ l++++s k  
  gi|557694513|ref|YP_008797567.1| 14 VLCSKCEQKIRRGELTSNDLEIMRFFLDLERKFPNISSLKYGRSLTaDGYLFVFFERGFSSLPADVQTALRNELSLKTG 92
                                      78***************************************87665056689********************9987765 PP

                           DUF2225 84 sr 85
                                       r
  gi|557694513|ref|YP_008797567.1| 93 MR 94
                                      55 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     6e-06     0.054      32      68 ..      82     121 ..      77     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-06
                              KH_5  32 avsseLk...gekidvvewseDlaefianalsPaevlsVk 68 
                                       a+ +eL+   g ++++++ s Dl +f +++ +Pa++l ++
  gi|557694513|ref|YP_008797567.1|  82 ALRNELSlktGMRVKLMDTSRDLNTFLQSLVAPARLLAIN 121
                                       566777777899************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1365.22
//
Query:       gi|557694514|ref|YP_008797568.1|  [L=94]
Description: archaea-specific DNA-binding protein AlbA [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-18   65.5   0.2    4.1e-18   65.0   0.2    1.3  1  Alba      Alba
     0.0017   18.3   0.6     0.0029   17.6   0.6    1.4  1  Rpp20     Rpp20 subunit of nuclear RNase MRP and P


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 !   65.0   0.2   4.6e-22   4.1e-18       2      65 ..       9      69 ..       8      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 4.6e-22
                                      EEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEEE CS
                              Alba  2 eiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvlts 65
                                      ++ V++ +p msyv+++l+ + +++ +e+v+ka+GraIs+Av+v++i+k+rf+ g + ++++ +
  gi|557694514|ref|YP_008797568.1|  9 TVLVGK-KPAMSYVLACLTGF-QSGSKEIVVKARGRAISRAVDVVQIVKNRFLQG-VNIKDIRI 69
                                      578999.**************.******************************976.88888876 PP

>> Rpp20  Rpp20 subunit of nuclear RNase MRP and P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.6   3.2e-07    0.0029      59     101 ..      30      75 ..      25      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.2e-07
                             Rpp20  59 lkkeeVfvkatGrAiekalsvgrwfqeke..eykv.rvetgsVevv 101
                                         ++e++vka GrAi +a+ v +  +++   ++++ +++ g+ ++ 
  gi|557694514|ref|YP_008797568.1|  30 SGSKEIVVKARGRAISRAVDVVQIVKNRFlqGVNIkDIRIGTEQIT 75 
                                       5689*****************9988655433444423555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 677.35
//
Query:       gi|557694515|ref|YP_008797569.1|  [L=53]
Description: large subunit ribosomal protein L40e [Candidatus Caldiarchaeum subterraneum]
Scores for 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   31.7   5.1    1.2e-07   31.5   5.1    1.1  1  Ribosomal_L40e  Ribosomal L40e family
     0.0015   18.2   2.4     0.0019   17.9   2.4    1.2  1  zinc_ribbon_2   zinc-ribbon domain
     0.0026   17.7   4.0     0.0059   16.6   4.0    1.6  1  zinc_ribbon_6   Zinc-ribbon
     0.0047   16.8   3.8      0.011   15.6   3.8    1.6  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0057   16.4   1.1     0.0084   15.8   1.1    1.2  1  Rubredoxin_2    Rubredoxin metal binding domain
     0.0082   16.2   0.3     0.0082   16.2   0.3    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0097   15.5   0.9     0.0097   15.5   0.9    1.0  1  CTV_P23         Citrus tristeza virus (CTV) P23 protein
  ------ inclusion threshold ------
      0.017   15.2   1.0      0.017   15.2   1.0    1.1  1  zf-RING_10      zinc RING finger of MSL2


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 !   31.5   5.1   5.4e-11   1.2e-07       2      48 ..       5      48 ..       4      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 5.4e-11
                    Ribosomal_L40e  2 epsLrqLAqKyncdKmiCrkCYArlpprAtnCrkkkCghsnnlrpKK 48
                                      +p+L qLAq  +   +iCr C Ar  + A++Cr  kC +s nlr K+
  gi|557694515|ref|YP_008797569.1|  5 DPALLQLAQSRRLLIKICRDCGARNAKTAVKCR--KC-RSYNLRWKR 48
                                      7********************************..89.788898886 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   2.4   8.4e-07    0.0019       2      21 ..      22      41 ..      21      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 8.4e-07
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                      C  CGa + ++a+ C +C++
  gi|557694515|ref|YP_008797569.1| 22 CRDCGARNAKTAVKCRKCRS 41
                                      ******************85 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   4.0   2.6e-06    0.0059      31      57 ..      21      43 ..       8      45 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.6e-06
                     zinc_ribbon_6 31 lCnDCekksevkfhvlglkCkeCgSYN 57
                                      +C+DC+++         +kC++C+SYN
  gi|557694515|ref|YP_008797569.1| 21 ICRDCGARNAK----TAVKCRKCRSYN 43
                                      6*****98775....479********* 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 !   15.6   3.8   4.9e-06     0.011       3      33 ..      11      41 ..       9      45 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.9e-06
                           DUF35_N  3 aaaegrLvgqrCpdCGtvqfPPravCphCgs 33
                                       a+  rL++  C+dCG+        C++C+s
  gi|557694515|ref|YP_008797569.1| 11 LAQSRRLLIKICRDCGARNAKTAVKCRKCRS 41
                                      68999**************7555******98 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.1   3.7e-06    0.0084       2      24 ..      21      43 ..      21      43 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.7e-06
                      Rubredoxin_2  2 vCsqCGfesakwfGrCpsCgsWn 24
                                      +C++CG++ ak   +C+ C+s+n
  gi|557694515|ref|YP_008797569.1| 21 ICRDCGARNAKTAVKCRKCRSYN 43
                                      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 !   16.2   0.3   3.6e-06    0.0082      69      99 ..      18      46 ..       5      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.6e-06
                                      -EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                              HypA 69 vkvrCreCgkefeleekalrCpkCgsadvei 99
                                      +   Cr+Cg++  ++  a++C kC s +++ 
  gi|557694515|ref|YP_008797569.1| 18 LIKICRDCGARNAKT--AVKCRKCRSYNLRW 46
                                      5568*****888866..579******99876 PP

>> CTV_P23  Citrus tristeza virus (CTV) P23 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.9   4.3e-06    0.0097      56      91 ..      10      45 ..       3      52 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.3e-06
                           CTV_P23 56 qgarfrariigvcvdcgrkhdkalkterkckvnntq 91
                                      q a+ r  +i +c dcg +  k++   rkc+  n +
  gi|557694515|ref|YP_008797569.1| 10 QLAQSRRLLIKICRDCGARNAKTAVKCRKCRSYNLR 45
                                      778889999*********************998865 PP

>> zf-RING_10  zinc RING finger of MSL2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.0   7.6e-06     0.017      24      47 ..      20      43 ..       6      52 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.6e-06
                        zf-RING_10 24 yvCrlCvgkkkklkpsCsqCkdye 47
                                       +Cr C  ++ k   +C++C++y+
  gi|557694515|ref|YP_008797569.1| 20 KICRDCGARNAKTAVKCRKCRSYN 43
                                      69*******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 402.66
//
Query:       gi|557694516|ref|YP_008797570.1|  [L=405]
Description: DNA primase small subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   45.8   0.0    3.9e-10   40.1   0.0    2.4  2  DNA_primase_S  DNA primase small subunit
  ------ inclusion threshold ------
        1.7    8.5   4.1        9.2    6.1   0.3    2.5  2  A2L_zn_ribbon  A2L zinc ribbon domain
        2.3    8.3   7.5        6.1    7.0   7.5    1.6  1  DZR            Double zinc ribbon


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 ?    3.3   0.1     0.013        78       1      21 [.      98     119 ..      98     132 .. 0.85
   2 !   40.1   0.0   6.5e-14   3.9e-10      16     174 ..     145     337 ..     136     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.013
                                       EEEEEETTT-..TT--HHHHHH CS
                     DNA_primase_S   1 FDiDmddydd.cseatvcekcw 21 
                                       FDiD+d++++ c+ a  +++c+
  gi|557694516|ref|YP_008797570.1|  98 FDIDADHLETsCKPAHDYYVCL 119
                                       9*********999887777775 PP

  == domain 2  score: 40.1 bits;  conditional E-value: 6.5e-14
                                       HHHHHHHHHHHHHHHHHHHH-----GGGEEEEE--SEEEEEEE--TTEEES-HHHHHHHHHH............... CS
                     DNA_primase_S  16 vcekcwkfvsvavkvldellredfgfkdilwvfsgrrGfHcwvsdkdarpltdeeraaivnylnly........... 81 
                                       vc  c++  ++   +l  +++ dfg   + + fsg+rG+H+ v  k++ +l++  r +iv+y++ +           
  gi|557694516|ref|YP_008797570.1| 145 VCDTCLEKTKQELLKLIDFMENDFGLGSFTVSFSGNRGYHLAVEAKEVLELGRDARQEIVDYVT-Gshigiefhglp 220
                                       77888877777777788899*****************************************533.346989999988 PP

                                       .....................................HCHHHHCT--------........................ CS
                     DNA_primase_S  82 .......rplhpflsrsmlkivkpvveeiileeqdpfeikkllrllpdkslre..........kkkw.......... 131
                                              ++ +p   ++    v +    i+le+    e ++l rll  ++  e          + +w          
  gi|557694516|ref|YP_008797570.1| 221 pssayapDYGDPGWRGR----VARGMRRIVLEAAAG-EDERLARLLGHRQVEElrsmsslwreRPRWellrqdrrsq 292
                                       88777664455555555....444444444444322.2333333333333333333644444433337777777776 PP

                                       ................-----------------....-------- CS
                     DNA_primase_S 132 ..eakedivlvllyprldeqvtkgikhllkapfcihgktgnvcvp 174
                                         e + +  ++     +d  vt+++++ll++   ++gktg ++  
  gi|557694516|ref|YP_008797570.1| 293 qfEKLVSLSVDEAASHIDTVVTTDVHRLLRLADTLNGKTGLRAMV 337
                                       6677777888888999************************77665 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 ?    6.1   0.3    0.0015       9.2      19      28 ..     113     122 ..     112     123 .. 0.91
   2 ?    3.0   0.3     0.015        89       6      13 ..     132     139 ..     128     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0015
                     A2L_zn_ribbon  19 qgylvCieCg 28 
                                       ++y+vC  Cg
  gi|557694516|ref|YP_008797570.1| 113 HDYYVCLSCG 122
                                       89*******9 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.015
                     A2L_zn_ribbon   6 CsvCggng 13 
                                       C vCgg++
  gi|557694516|ref|YP_008797570.1| 132 CGVCGGEM 139
                                       *******8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   7.5     0.001       6.1       1      36 [.     118     151 ..     109     157 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.001
                               DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCge 36 
                                       C +Cg+   ++ + C+ Cg ++   + + +C+ C e
  gi|557694516|ref|YP_008797570.1| 118 CLSCGQRGAEKTQRCGVCGGEMA--EVKMVCDTCLE 151
                                       66677777777777777776664..23466666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      545  (0.0303977); 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):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 2988.98
//
Query:       gi|557694517|ref|YP_008797571.1|  [L=152]
Description: signal-transduction protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   72.7   7.0      3e-13   50.0   0.3    2.5  3  CBS       CBS domain
     0.0052   15.6   0.0     0.0058   15.4   0.0    1.2  1  ArgJ      ArgJ family


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 !   26.3   0.9   8.7e-10   7.8e-06       1      55 [.       3      56 ..       3      58 .. 0.84
   2 !   50.0   0.3   3.4e-17     3e-13       1      56 [.      68     123 ..      68     124 .. 0.97
   3 ?   -2.6   0.0      0.92   8.2e+03      19      25 ..     130     136 ..     127     147 .. 0.46

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8.7e-10
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      Vg+im r   +v+   t++ea+ lm + + + l  V +++klvGi+t+rD +r +
  gi|557694517|ref|YP_008797571.1|  3 VGEIMLRVNNVVDAGITVREAAILMDRLDTGYL-LVKSEDKLVGIFTERDAVRRV 56
                                      78898884449**************76557666.8889999*********99976 PP

  == domain 2  score: 50.0 bits;  conditional E-value: 3.4e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+d+m+ +v+ v+pdt++e+a+ lm+ +g++rlPVV ++g+l G+vt +  +ral+
  gi|557694517|ref|YP_008797571.1|  68 VADVMSFPVIGVSPDTSVEDAVVLMAMHGFRRLPVVSKEGRLEGVVTITEAARALA 123
                                       89***********************999*************************996 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.92
                                       HHHHHHH CS
                               CBS  19 eealelm 25 
                                       ee+++ +
  gi|557694517|ref|YP_008797571.1| 130 EELFQHL 136
                                       4444443 PP

>> ArgJ  ArgJ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.5e-07    0.0058     193     250 ..      71     146 ..      31     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.5e-07
                                       HHTGGGB-SSS---SS-EEEEEE--TT..................TT.STTHHHHHHHHHHHHHHHHHHHHHTSTT CS
                              ArgJ 193 dksFnsisvDgdtSTnDtvlllAngaa..................eeeeedleefeealtevlqeLakqivrDGEG 250
                                         sF  i v  dtS  D+v+l+A                      +e+ ++l++++++++e++q+L + +  D E 
  gi|557694517|ref|YP_008797571.1|  71 VMSFPVIGVSPDTSVEDAVVLMAMHGFrrlpvvskegrlegvvtiTEAARALASMQKTVEELFQHLLRVVKTDEET 146
                                       369********************9874478999*********998666889999**************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); 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 0.28s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1115.07
//
Query:       gi|557694518|ref|YP_008797572.1|  [L=182]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); 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:                         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: 1307.13
//
Query:       gi|557694519|ref|YP_008797573.1|  [L=373]
Description: hypothetical protein CSUB_C1091 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  103.2   0.0    8.1e-29  100.8   0.0    1.9  2  CLP1_P      mRNA cleavage and polyadenylation factor CLP1 P-l
      0.002   18.3   0.0     0.0044   17.2   0.0    1.5  1  CLP1_N      N-terminal beta-sandwich domain of polyadenylatio
  ------ inclusion threshold ------
       0.07   13.3   0.1          3    8.1   0.0    2.5  2  PAC4        Proteasome assembly chaperone 4
      0.074   12.8   0.0       0.11   12.3   0.0    1.4  1  ATP_bind_1  Conserved hypothetical ATP binding protein


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 !  100.8   0.0   1.8e-32   8.1e-29       1     185 [.      94     264 ..      94     267 .. 0.86
   2 ?   -0.1   0.0      0.16     7e+02      65     105 ..     281     314 ..     277     318 .. 0.62

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 1.8e-32
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvGqseispPgtislalverpidveegfsldaplvyffGdtspsdnp 77 
                                       G++d+GK+++a++ +N+ ++k  ++v+v lD+Gq +++pP+++++al+++p++    + l+a l   +G+ s     
  gi|557694519|ref|YP_008797573.1|  94 GGVDTGKTSFATFAANMFAQKLGRCVVVGLDPGQTSFTPPCVVGCALMREPVHD--LTVLTAFLQRPVGSPS----A 164
                                       899*************************************************98..4445555555555555....4 PP

                            CLP1_P  78 slylalvkelareveekleenkkakasgliIntpGwvkglga.ellleliealepdvvvvldqeellnelkrdlpls 153
                                       +l+ a ++e  re+ + l+       ++ +++ +Gwv+g +a  ++++l++al++++vvv+++++ l+e  +++   
  gi|557694519|ref|YP_008797573.1| 165 ALCAAEIAEASREIAQALS------GEVYVVDVDGWVEGPAAtAHKVALVKALNCSHVVVMGENKPLAEALSQAG-- 233
                                       6777777777777774444......68************97638889***************9888888877777.. PP

                            CLP1_P 154 kvkvvklpkspgvvqrsreerrelreerireY 185
                                        v+v++ p s+ ++qr+ ++rr++re+ +r++
  gi|557694519|ref|YP_008797573.1| 234 -VEVFTAPLSRYIKQRETATRRKTREWLYRKH 264
                                       .**************************99986 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.16
                            CLP1_P  65 vyffGdtspsdnpslylalvkelareveekleenkkakasg 105
                                         f+G+t p   ++l++++ ++la++++e++e+    k+ g
  gi|557694519|ref|YP_008797573.1| 281 FTFCGQTPP---LELVKQVNEALAQTTQENSEN----KRRG 314
                                       567787777...556666667777777744444....4555 PP

>> CLP1_N  N-terminal beta-sandwich domain of polyadenylation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   9.8e-07    0.0044      17      67 ..      14      64 ..       8      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9.8e-07
                                      -EEEEEEEE--EETTEE--TT-EEEE-TT-EEEEEESS-EEEEEES-EEEE CS
                            CLP1_N 17 klkikllsGtaEifGtELaknkeytfskgtkfaiftwegcklevkgeaese 67
                                      + ++kl++G+  i G+ L  +k+y +++ +++ +++ e++k+e++  ae+e
  gi|557694519|ref|YP_008797573.1| 14 PASVKLVEGKGYIYGCPLKLRKNYVLRPWKRYPLYAEEDVKIELNLGAEAE 64
                                      578****************************************87655544 PP

>> PAC4  Proteasome assembly chaperone 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00066         3      55      79 ..     100     124 ..      84     124 .. 0.85
   2 ?    2.5   0.0     0.039   1.7e+02      34      67 ..     153     183 ..     135     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00066
                              PAC4  55 sdeaserlAqrLArRlgkqvfvScn 79 
                                        +++++  A+ +A++lg++v+v+++
  gi|557694519|ref|YP_008797573.1| 100 KTSFATFAANMFAQKLGRCVVVGLD 124
                                       46689999**************975 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.039
                              PAC4  34 AmpsrtnkktptisTtLlgdgsdeaserlAqrLA 67 
                                       A+ +r+  + + +s++L+  +  eas+ +Aq L+
  gi|557694519|ref|YP_008797573.1| 153 AFLQRPV-G-S-PSAALCAAEIAEASREIAQALS 183
                                       6666777.3.3.59999*99989********997 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 ?   12.3   0.0   2.5e-05      0.11       1     119 [.      92     212 ..      92     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavd...irelitledvmed...lglgpngalvva 71 
                                       v+G++  GKt+f    ++++ ++  ++ vv LDP+  +++ ++ v    +re ++   v        +g+  a   a
  gi|557694519|ref|YP_008797573.1|  92 VCGGVDTGKTSFATFAANMFAQKLGRCVVVGLDPGQTSFTPPCVVGcalMREPVHDLTVLTAflqRPVGSPSAALCA 168
                                       89************99999999999**************99998864446888877777776655677777888888 PP

                        ATP_bind_1  72 leflresldwldeelekeeddyllfDtPGQielfthseslakiveeLe 119
                                       +e+ + s  +++++l   + + +++D+ G +e     +  + +v++L+
  gi|557694519|ref|YP_008797573.1| 169 AEIAEASR-EIAQAL---SGEVYVVDVDGWVEGPAATAHKVALVKALN 212
                                       88776664.455555...667777887777777666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); 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: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2517.16
//
Query:       gi|557694520|ref|YP_008797574.1|  [L=218]
Description: hypothetical protein CSUB_C1092 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1524.35
//
Query:       gi|557694521|ref|YP_008797575.1|  [L=85]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   69.4   0.2    2.5e-19   69.1   0.2    1.0  1  Elf1             Transcription elongation factor Elf1 like
    2.1e-05   24.8   0.4    2.8e-05   24.4   0.4    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0083   16.8   0.3       0.41   11.3   0.1    2.4  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
  ------ inclusion threshold ------
      0.039   13.7   1.6      0.058   13.2   1.6    1.2  1  zinc_ribbon_5    zinc-ribbon domain
       0.17   12.0   3.1        1.5    9.0   0.1    2.1  2  Zn-ribbon_8      Zinc ribbon domain
       0.19   11.7   1.5       0.41   10.6   1.5    1.5  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.67   10.5   4.9        2.4    8.7   0.5    2.7  3  zf-H2C2_2        Zinc-finger double 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 !   69.1   0.2   9.6e-23   2.5e-19       3      76 ..       3      73 ..       2      75 .. 0.89

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 9.6e-23
                              Elf1  3 RkkkakkrkkkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesfetkvnalsepvDvYskwiDac 76
                                      Rk+++   +k++++++p++F+Cp C+++ +v+v  +kk+++a+v+C++C++s+e+ + + +++vDvY+kw D +
  gi|557694521|ref|YP_008797575.1|  3 RKRRK--IIKRTPRPFPKVFSCPLCGAT-AVRVVHEKKSETATVTCGNCNASAEIPWYPAYSEVDVYTKWYDIV 73
                                      33333..46788888*************.******************************************975 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 !   24.4   0.4   1.1e-08   2.8e-05       5      40 ..      21      56 ..      18      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.1e-08
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCga..stpw 40
                                       CP Cg  av + ++++++    +v+C +C+a    pw
  gi|557694521|ref|YP_008797575.1| 21 SCPLCGATAVRVVHEKKSET--ATVTCGNCNAsaEIPW 56
                                      6********99999888763..3*********442333 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 !   11.3   0.1   0.00016      0.41       3      20 ..      20      38 ..      18      40 .. 0.82
   2 ?    3.5   0.0     0.047   1.2e+02       2      12 ..      42      52 ..      41      80 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                           zf-ISL3  3 hrCPnCgsk.tvvkhgkke 20
                                        CP Cg++ ++v+h kk 
  gi|557694521|ref|YP_008797575.1| 20 FSCPLCGATaVRVVHEKKS 38
                                      68*******7779999875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.047
                           zf-ISL3  2 phrCPnCgskt 12
                                      + +C nC++  
  gi|557694521|ref|YP_008797575.1| 42 TVTCGNCNASA 52
                                      579****9874 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   1.6   2.3e-05     0.058       4      32 ..      21      49 ..      19      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.3e-05
                     zinc_ribbon_5  4 rCpdCd.tkFklvdsklKksgkkVrCakCa 32
                                      +Cp C+ t  ++v +k K     V C+ C 
  gi|557694521|ref|YP_008797575.1| 21 SCPLCGaTAVRVVHEK-KSETATVTCGNCN 49
                                      8****95679******.************6 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0006       1.5      28      40 .]      20      33 ..       6      33 .. 0.82
   2 ?    8.6   2.7   0.00079         2       6      35 ..      20      51 ..      19      54 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0006
                       Zn-ribbon_8 28 a.CPeCgsevrrvi 40
                                        CP Cg+++ rv+
  gi|557694521|ref|YP_008797575.1| 20 FsCPLCGATAVRVV 33
                                      44******999986 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00079
                       Zn-ribbon_8  6 YrCeeCghefe.vlqsis.dapltaCPeCgse 35
                                      + C  Cg +   v+++ + + + ++C +C++ 
  gi|557694521|ref|YP_008797575.1| 20 FSCPLCGATAVrVVHEKKsETATVTCGNCNAS 51
                                      67899997776544444435554449999875 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 ?    4.7   0.0     0.011        28      42      57 ..      15      30 ..       6      33 .. 0.74
   2 ?   10.6   1.5   0.00016      0.41      30      55 ..      21      51 ..      19      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.011
                    OrfB_Zn_ribbon 42 lsgrtfkCpnCgfead 57
                                      + +++f Cp Cg++a 
  gi|557694521|ref|YP_008797575.1| 15 PFPKVFSCPLCGATAV 30
                                      5567899999998875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00016
                    OrfB_Zn_ribbon 30 tCseCgsknke.....alsgrtfkCpnCgfe 55
                                      +C+ Cg++  +     + ++ t++C nC+++
  gi|557694521|ref|YP_008797575.1| 21 SCPLCGATAVRvvhekKSETATVTCGNCNAS 51
                                      6*******99999999999*********986 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 ?    8.7   0.5   0.00095       2.4      13      24 ..      16      29 ..       9      31 .. 0.74
   2 ?    3.6   0.1     0.041     1e+02       8      22 ..      33      50 ..      30      53 .. 0.72
   3 ?   -1.6   0.0       1.8   4.6e+03      10      16 ..      75      81 ..      73      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00095
                         zf-H2C2_2 13 kp..yeCplCdkaF 24
                                      +p  + CplC+ + 
  gi|557694521|ref|YP_008797575.1| 16 FPkvFSCPLCGATA 29
                                      45559*****9876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.041
                         zf-H2C2_2  8 kHtgekp...yeCplCdk 22
                                      +H ++++   ++C  C+ 
  gi|557694521|ref|YP_008797575.1| 33 VHEKKSEtatVTCGNCNA 50
                                      37777756679*****86 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.8
                         zf-H2C2_2 10 tgekpye 16
                                      +gekp+e
  gi|557694521|ref|YP_008797575.1| 75 RGEKPVE 81
                                      59**986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 621.23
//
Query:       gi|557694522|ref|YP_008797576.1|  [L=251]
Description: geranylgeranylglyceryl phosphate synthase-like protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-53  180.2   0.6    5.2e-53  179.8   0.6    1.0  1  PcrB            PcrB family
    6.2e-10   38.9   0.3    2.5e-09   36.9   0.1    1.8  2  His_biosynth    Histidine biosynthesis protein
    5.5e-07   29.0   0.8    3.9e-05   22.9   0.3    2.1  2  Dus             Dihydrouridine synthase (Dus)
    6.3e-07   28.9   3.4     0.0011   18.4   1.5    2.1  2  ThiG            Thiazole biosynthesis protein ThiG
    5.4e-06   25.8   2.0    6.9e-06   25.5   0.7    1.7  2  DHO_dh          Dihydroorotate dehydrogenase
    2.6e-05   23.5   0.6      0.034   13.3   0.2    2.2  2  NanE            Putative N-acetylmannosamine-6-phosphate epim
    4.3e-05   23.1   5.9     0.0013   18.2   3.8    2.5  3  NMO             Nitronate monooxygenase
      5e-05   22.3   1.5     0.0013   17.6   0.9    2.2  2  Trp_syntA       Tryptophan synthase alpha chain
    6.6e-05   22.1   2.3    0.00069   18.7   1.8    2.1  2  FMN_dh          FMN-dependent dehydrogenase
    0.00026   20.4   1.6    0.00057   19.3   0.5    2.0  3  G3P_antiterm    Glycerol-3-phosphate responsive antiterminato
    0.00046   19.3   4.4      0.017   14.1   1.4    2.1  2  IMPDH           IMP dehydrogenase / GMP reductase domain
     0.0021   17.4   2.9       0.01   15.2   0.4    2.3  2  TMP-TENI        Thiamine monophosphate synthase
     0.0086   15.2   1.0      0.015   14.5   0.2    1.7  2  Glu_synthase    Conserved region in glutamate synthase
  ------ inclusion threshold ------
      0.022   13.5   0.5      0.044   12.5   0.0    1.7  2  DHDPS           Dihydrodipicolinate synthetase family
      0.027   14.0   0.2       0.78    9.2   0.1    2.1  2  HMGL-like       HMGL-like
      0.027   13.9   0.7      0.064   12.6   0.4    1.7  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
      0.029   13.8   1.3        1.4    8.3   0.5    2.3  2  BtpA            BtpA family
      0.043   13.0   0.7       0.48    9.6   0.1    2.2  2  DUF561          Protein of unknown function (DUF561)


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 !  179.8   0.6   5.2e-56   5.2e-53       6     223 ..      18     242 ..      13     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 179.8 bits;  conditional E-value: 5.2e-56
                                       TS.EEEEE-TTSS-CHHHHHHH...HCTT-SEEEEECSTCHHHHHHHHHHHHH.CTSSS-EEEEESSGGG--TTSSE CS
                              PcrB   6 er.hltklDPeeenpdEiveiv...iesgtDavmigGsqsvtldntvrllkkv.sriklPivlepsnvegvvryaDa 77 
                                       e+ h+t++DP     d+++  +    e g+Da+m+gGs+  t+++  + +k + s+++lP++++p nv++++r aDa
  gi|557694522|ref|YP_008797576.1|  18 EKlHMTLIDPISISQDDAAALAasvEEMGSDAIMVGGSTVHTQEQLDNYIKTIkSKTRLPVIIFPNNVQSISRFADA 94 
                                       345*******998888887655343788***********666666666665552369******************** PP

                                       EEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHHHHHHHTT CS
                              PcrB  78 lFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayallaakllg 153
                                       +++msllns + ++ivgah +g+ +vk+++  +e+l++gY+v   +s+vaa++ +  +     +ia  + laa++lg
  gi|557694522|ref|YP_008797576.1|  95 IWFMSLLNSVDWYYIVGAHLQGALTVKHFN--LEALPMGYVVFGHESTVAAMGRVLpLSPHNVEIAVCYGLAAQYLG 169
                                       ******************************..***********************9966666778888889****** PP

                                       -SEEEEE-.TTSSS-H.HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHHHCHHHHHH CS
                              PcrB 154 lrliYlEa.sGaledv.eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekderkidail 223
                                       +r++YlEa sGa  ++  ++i+ +k+  ++ +ivGGGir + +A+ v+ a AD+iv+G++ e++ e+  + i 
  gi|557694522|ref|YP_008797576.1| 170 MRYLYLEAgSGAAAHIpPQTIKAVKHAVEIPVIVGGGIRTGKDAETVAAAgADIIVTGTAAEKNREKLAEIIN 242
                                       ****************99999*9***************************************99965544443 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.67   6.7e+02      30      72 ..      34      74 ..      18      81 .. 0.52
   2 !   36.9   0.1   2.5e-12   2.5e-09      63     120 ..     188     245 ..     160     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.67
                                      SHHHHHHHHHHHT-SEEEEEEHHHHC.TTHHHHHHHHHHHHHH- CS
                      His_biosynth 30 dpvelakryeeegadelhvvDldaak.egreanldlveeiaeev 72
                                      d ++la + ee g d ++v    ++  + +e+  +++++i +++
  gi|557694522|ref|YP_008797576.1| 34 DAAALAASVEEMGSDAIMVG---GSTvHTQEQLDNYIKTIKSKT 74
                                      44444444444444444432...222133333444455555554 PP

  == domain 2  score: 36.9 bits;  conditional E-value: 2.5e-12
                                       HHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHC CS
                      His_biosynth  63 dlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelikelaekfg 120
                                       + ++++ ++v+ipv vGGGIr+ +d+e++  agad ++ gtaa kn e + e+++++ 
  gi|557694522|ref|YP_008797576.1| 188 QTIKAVKHAVEIPVIVGGGIRTGKDAETVAAAGADIIVTGTAAEKNREKLAEIINAVK 245
                                       68999*********************************************99998775 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.015        15     136     188 ..      31      80 ..      21      95 .. 0.76
   2 !   22.9   0.3     4e-08   3.9e-05     173     230 ..     188     245 ..     178     249 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.015
                                       TTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEE CS
                               Dus 136 eeenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipvia 188
                                       ++++a  la  ve+ G +a++v g t  ++ e+ +++  Ik +k + ++pvi+
  gi|557694522|ref|YP_008797576.1|  31 SQDDAAALAASVEEMGSDAIMVGGSTVHTQ-EQLDNY--IKTIKSKTRLPVII 80 
                                       467788899999999999999988776654.555555..66667777777664 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 4e-08
                                       HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.HHHHH CS
                               Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.stavk 230
                                       ++Ik+vk av+ipvi+ G+I++ +da+ + +  Gad ++ g +a++n   +ae  +avk
  gi|557694522|ref|YP_008797576.1| 188 QTIKAVKHAVEIPVIVGGGIRTGKDAETVAAA-GADIIVTGTAAEKNREKLAEiINAVK 245
                                       79*************************99998.************99877777666666 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00029      0.29     128     180 ..      29      80 ..      10      95 .. 0.81
   2 !   18.4   1.5   1.1e-06    0.0011     163     213 ..     186     236 ..     175     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                                       EEE-S-H.HHHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEE CS
                              ThiG 128 pYvsdDl.vlarrleevGcaavmPlaapiGsglGllnkealkiiieeakvPviv 180
                                       +  +dD   la  +ee+G  a+m  ++ + + + l n   +k+i +++++Pvi+
  gi|557694522|ref|YP_008797576.1|  29 SISQDDAaALAASVEEMGSDAIMVGGSTVHTQEQLDN--YIKTIKSKTRLPVII 80 
                                       5556665268999******************998876..799**********97 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.1e-06
                                       -HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSH CS
                              ThiG 163 nkealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdp 213
                                        ++++k + + +++Pviv  Gi++ +da ++   Gad ++  ta  + ++ 
  gi|557694522|ref|YP_008797576.1| 186 PPQTIKAVKHAVEIPVIVGGGIRTGKDAETVAAAGADIIVTGTAAEKNREK 236
                                       4688999999****************************9999997766553 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.98   9.7e+02     157     188 ..      42      74 ..      26      92 .. 0.49
   2 !   25.5   0.7     7e-09   6.9e-06     231     287 ..     187     241 ..     173     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.98
                                       HHHHHSSEEEEEE-SSSSHHHHHHHHHHHH.HH CS
                            DHO_dh 157 vkevskvpvlvKlaPdltdeekkdiadvll.el 188
                                       v+e+ + +++v  +   t+e+ ++ ++ ++ ++
  gi|557694522|ref|YP_008797576.1|  42 VEEMGSDAIMVGGSTVHTQEQLDNYIKTIKsKT 74 
                                       333333333333333334444444444444444 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 7e-09
                                       HHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHH CS
                            DHO_dh 231 lkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakki 287
                                        ++i ++++ ++  ip+I  GGi +g+Da   + aGA ++  +ta  ++  k+a+ i
  gi|557694522|ref|YP_008797576.1| 187 PQTIKAVKHAVE--IPVIVGGGIRTGKDAETVAAAGADIIVTGTAAEKNREKLAEII 241
                                       578888988888..********************************88887776654 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 !    8.5   0.0     0.001         1     154     192 .]      34      72 ..      18      72 .. 0.87
   2 !   13.3   0.2   3.4e-05     0.034     137     191 ..     190     245 ..     166     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.001
                                       -SHHHHHHHHTT--SEEEE-HHHH-HHHHHHHHHHHT-X CS
                              NanE 154 ntPekakkaieiGvdavvvGsaitrleeiakkfveaiks 192
                                       ++ ++a+++ e+G da++vG++    +e  + ++++iks
  gi|557694522|ref|YP_008797576.1|  34 DAAALAASVEEMGSDAIMVGGSTVHTQEQLDNYIKTIKS 72 
                                       667899**********************9999*999985 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.4e-05
                                       HHHHHHT.T--EEEES---SHHHHHHHHTT--SEEEE-HHHH-HHHHHHHHHHHT- CS
                              NanE 137 vkalsea.glkviaeGrintPekakkaieiGvdavvvGsaitrleeiakkfveaik 191
                                       +ka+++a ++ vi+ G i t + a+++   G+d +v G+a  + +e     ++a+k
  gi|557694522|ref|YP_008797576.1| 190 IKAVKHAvEIPVIVGGGIRTGKDAETVAAAGADIIVTGTAAEKNREKLAEIINAVK 245
                                       56665543789*****************************9999888888888877 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.026        26      25      65 ..      36      78 ..      27     109 .. 0.84
   2 ?   -2.4   0.0       2.4   2.4e+03     207     228 ..     154     175 ..     152     186 .. 0.82
   3 !   18.2   3.8   1.3e-06    0.0013     185     224 ..     190     229 ..     184     239 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.026
                               NMO 25 arLaaavsnaGgLGvla..sgyltaDrlakeirkvkaltdkPf 65
                                      a+Laa v + G   ++   s ++t  +l + i+ +k+ t  P+
  gi|557694522|ref|YP_008797576.1| 36 AALAASVEEMGSDAIMVggSTVHTQEQLDNYIKTIKSKTRLPV 78
                                      68999999999877765458899***********999998885 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                               NMO 207 gvaaaLalGAsgvqigtrfLlt 228
                                       +v+ a ++G ++ ++g r+L  
  gi|557694522|ref|YP_008797576.1| 154 NVEIAVCYGLAAQYLGMRYLYL 175
                                       678899************9964 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 1.3e-06
                               NMO 185 vpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigtr 224
                                       ++ v+ av+iPvi  GGi ++++ +++ a+GA  +  gt+
  gi|557694522|ref|YP_008797576.1| 190 IKAVKHAVEIPVIVGGGIRTGKDAETVAAAGADIIVTGTA 229
                                       678999***************************9999997 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.036        35     175     203 ..      52      80 ..      32     100 .. 0.81
   2 !   17.6   0.9   1.3e-06    0.0013     188     232 ..     188     233 ..     176     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.036
                                       -SSTTSSB-TTHHHHHHHHHHCTSS-EEE CS
                         Trp_syntA 175 vTgaenavaaevdelverlkkltavPvav 203
                                       v g   ++++++d+ ++++k+ t +Pv +
  gi|557694522|ref|YP_008797576.1|  52 VGGSTVHTQEQLDNYIKTIKSKTRLPVII 80 
                                       55667788899999999999999999864 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.3e-06
                                       HHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHH CS
                         Trp_syntA 188 elverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkk 232
                                       ++++++k++ + Pv vG Gi+t +++++va ++ad ++ G a  k+
  gi|557694522|ref|YP_008797576.1| 188 QTIKAVKHAVEIPVIVGGGIRTGKDAETVAaAGADIIVTGTAAEKN 233
                                       7899*************************999********986555 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.11   1.1e+02     189     221 ..      46      80 ..       5      81 .. 0.56
   2 !   18.7   1.8   6.9e-07   0.00069     257     301 ..     182     228 ..     175     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                                       HHHH.HHCCCHB-TC--HH.HHHHHHHHHSSEEEE CS
                            FMN_dh 189 saaa.efvgkqldpsltwd.dikwlreqtklplvv 221
                                        + a  + g++++++ + d  ik+++++t+lp+++
  gi|557694522|ref|YP_008797576.1|  46 GSDAiMVGGSTVHTQEQLDnYIKTIKSKTRLPVII 80 
                                       22223444455555556664699999999999997 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 6.9e-07
                                       HHHCHHHHHHHH....SS-EEEESS--SHHHHHHHHHTT-SEEEESH CS
                            FMN_dh 257 tidvLpeiveavgg..rievlvDgGirrGsDvlkAlalGAdavllGR 301
                                       + ++ p+  +av++  +i+v+v gGir+G+D+    a GAd+++ G 
  gi|557694522|ref|YP_008797576.1| 182 AAHIPPQTIKAVKHavEIPVIVGGGIRTGKDAETVAAAGADIIVTGT 228
                                       55555666777776557*************************99986 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 ?   -1.5   0.0       1.5   1.5e+03      34     134 ..      65      70 ..      20      99 .. 0.66
   2 ?   -3.5   0.0         6     6e+03      48      66 ..     155     173 ..     154     177 .. 0.84
   3 !   19.3   0.5   5.7e-07   0.00057     127     169 ..     185     228 ..     182     230 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.5
                                       HHHHHHHHTT-EEEEEGGGEET--SSHHHHHHHHH.TT-SEEEES-HHHHHHHHHTT--EEEEEE--SHHHHHHHHH CS
                      G3P_antiterm  34 eiveklkkagkkvfvhiDlieGlskdeaaveflkkeikvdGiistksslikkakklglltiqrlfliDssalekalk 110
                                       ++                                                                           
  gi|557694522|ref|YP_008797576.1|  65 NY--------------------------------------------------------------------------- 66 
                                       22........................................................................... PP

                                       HHHHHT-SEEEEESGGGHHHHCTS CS
                      G3P_antiterm 111 qiekskpdavevlPglvpkvikei 134
                                                           ik i
  gi|557694522|ref|YP_008797576.1|  67 --------------------IKTI 70 
                                       ....................2222 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 6
                                       EEGGGEET--SSHHHHHHH CS
                      G3P_antiterm  48 vhiDlieGlskdeaavefl 66 
                                       v+i ++ Gl+++  ++++l
  gi|557694522|ref|YP_008797576.1| 155 VEIAVCYGLAAQYLGMRYL 173
                                       6777899999999999998 PP

  == domain 3  score: 19.3 bits;  conditional E-value: 5.7e-07
                                       G.HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE-- CS
                      G3P_antiterm 127 v.pkvikeikkelkipiiaGGLietkedveealkaGaiavstsn 169
                                       + p++ik++k++++ip+i GG i+t +d e++ +aGa+ + t++
  gi|557694522|ref|YP_008797576.1| 185 IpPQTIKAVKHAVEIPVIVGGGIRTGKDAETVAAAGADIIVTGT 228
                                       44899***********************************9976 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0044       4.3     103     149 ..      33      79 ..      11      95 .. 0.76
   2 !   14.1   1.4   1.7e-05     0.017     199     247 ..     190     238 ..     175     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0044
                                       TTHHHHHHHHHHTT-SEEEEE-STSSSHHHHH.HHHHHHHHTTTSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx RF
                             IMPDH 103 edalervkalveagvdvlvvdsahghsekvle.avkeikkkveevevi 149
                                       +da + ++ + e g d+++v  +  h++++l+  +k+ik+k++ + vi
  gi|557694522|ref|YP_008797576.1|  33 DDAAALAASVEEMGSDAIMVGGSTVHTQEQLDnYIKTIKSKTR-LPVI 79 
                                       3555667778899*************99998636999999984.5544 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.7e-05
                                       HHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 199 vaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspg 247
                                       + ++ +  ++pvi  GGi++ +d     aaGad+++ G      +E  +
  gi|557694522|ref|YP_008797576.1| 190 IKAVKHAVEIPVIVGGGIRTGKDAETVAAAGADIIVTGTAAEKNREKLA 238
                                       4455666788888888888888888888888888888877666666555 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.085        85      75     109 ..      26      63 ..       1      74 [. 0.59
   2 !   15.2   0.4     1e-05      0.01     135     176 ..     183     225 ..     150     230 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.085
                          TMP-TENI  75 dgvHlgqddlpv..aearellgpdliiGlSv.hsleea 109
                                       d + ++qdd+++  a+++e+  +  ++G S+ h++e++
  gi|557694522|ref|YP_008797576.1|  26 DPISISQDDAAAlaASVEEMGSDAIMVGGSTvHTQEQL 63 
                                       67778888875421455565555666776642666665 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1e-05
                          TMP-TENI 135 eplgleglkelaealeiPvvaiGGitl.envaevleagadgva 176
                                       + +  +++k++++a+eiPv++ GGi++ +++++v++agad + 
  gi|557694522|ref|YP_008797576.1| 183 AHIPPQTIKAVKHAVEIPVIVGGGIRTgKDAETVAAAGADIIV 225
                                       6778899******************87378999******9886 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 ?   -1.8   0.0       1.3   1.3e+03      78     110 ..      30      61 ..      28      78 .. 0.50
   2 !   14.5   0.2   1.5e-05     0.015     264     306 ..     188     230 ..     179     231 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.3
                                       S-HHHHHHHHHHHHHHT-B-EETTS---GGGGS CS
                      Glu_synthase  78 lseeahealakamnrlgtksntGEGGedeerlk 110
                                       +s++   ala +++++g+ +    GG   +  +
  gi|557694522|ref|YP_008797576.1|  30 ISQDDAAALAASVEEMGSDAIM-VGGSTVHTQE 61 
                                       5555555666666666543322.2333333333 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.5e-05
                                       HHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-SHHH CS
                      Glu_synthase 264 qtlkeeglrdrvsliadGglktgadvvkalalGAdavgigtaa 306
                                       qt+k+ ++  ++ +i+ Gg++tg+d    +a GAd + +gtaa
  gi|557694522|ref|YP_008797576.1| 188 QTIKAVKHAVEIPVIVGGGIRTGKDAETVAAAGADIIVTGTAA 230
                                       8899999999******************************986 PP

>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.4e-05     0.044      79     133 ..      29      81 ..      15      90 .. 0.87
   2 ?   -2.3   0.2       1.4   1.4e+03      70      93 ..     198     221 ..     187     242 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.4e-05
                                       -SSHHHHHHHHHCCCCCT-SEEEEE---SS---HHHHHHHHHHHHHCHSS-EEEE CS
                             DHDPS  79 snstseaiklakkaeeaGadgvlavtPYYnkpsqeglyqhfkaiieatdlpvilY 133
                                       s s ++a  la++ ee+G d++++        +qe+l+++ k+i ++t lpvi++
  gi|557694522|ref|YP_008797576.1|  29 SISQDDAAALAASVEEMGSDAIMVGG--STVHTQEQLDNYIKTIKSKTRLPVIIF 81 
                                       567899***************98644..355689*******************97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
                                       SSEEEEE---SSHHHHHHHHHCCC CS
                             DHDPS  70 ripviagvGsnstseaiklakkae 93 
                                       +ipvi g G    ++a ++a+  +
  gi|557694522|ref|YP_008797576.1| 198 EIPVIVGGGIRTGKDAETVAAAGA 221
                                       577888877777777766665544 PP

>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.064        64      20      62 ..      30      74 ..      13      97 .. 0.68
   2 ?    9.2   0.1   0.00079      0.78      27     101 ..     162     232 ..     151     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.064
                                      --HHHHHHHHHHHHHHT-SEE--.TSGGGT.THHHH.HHHS---T CS
                         HMGL-like 20 lsveeklaiakaLdeagvdeiEv.gfpaaseddfev.vraiakav 62
                                      +s ++  a+a+  +e+g d+i v g  ++++++++  +++i+++ 
  gi|557694522|ref|YP_008797576.1| 30 ISQDDAAALAASVEEMGSDAIMVgGSTVHTQEQLDNyIKTIKSKT 74
                                      566777888999999999999997778888877764245555444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00079
                                       HHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHHHHH....TT-SEEEEEEES-H CS
                         HMGL-like  27 aiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdikaavealkgagakrvhvfiatse 101
                                        +a++   +++ ++E+g +aa + + + ++a+++av+++ i++  + + kd +  ++    aga+++ + +a+ +
  gi|557694522|ref|YP_008797576.1| 162 GLAAQYLGMRYLYLEAGSGAAAHIPPQTIKAVKHAVEIPVIVGGGIRTGKDAETVAA----AGADIIVTGTAAEK 232
                                       5677777899999*****************************************999....*******9999876 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 ?   -1.9   0.0       1.8   1.8e+03      90     111 ..      59      80 ..      34     102 .. 0.58
   2 ?   12.6   0.4   6.5e-05     0.064     163     196 ..     195     229 ..     183     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.8
                                       T-TTHHHHHHHHHHTTSEEEEE CS
                    Ribul_P_3_epim  90 alehlkrtiqeikeaGakaglv 111
                                       + e+l++ i++ik++   + ++
  gi|557694522|ref|YP_008797576.1|  59 TQEQLDNYIKTIKSKTRLPVII 80 
                                       4455566666666655555444 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 6.5e-05
                                       HT---EEEEESS--T.TTCHHHHHHT--EEEESHH CS
                    Ribul_P_3_epim 163 keldlkievDGGvkl.dnieqiaeagadvlVagsa 196
                                       + +++ + v GG+++ + +e +a+agad++V+g+a
  gi|557694522|ref|YP_008797576.1| 195 HAVEIPVIVGGGIRTgKDAETVAAAGADIIVTGTA 229
                                       35678999*****8648899*************97 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.033        33     162     221 ..      36      92 ..      25     102 .. 0.73
   2 ?    8.3   0.5    0.0014       1.4     189     233 ..     187     233 ..     176     246 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.033
                              BtpA 162 savkdtvergladavilsGkatGgevdlee.lklaketvkvkvlvgsGvseenlekllsia 221
                                        a+  +ve    da+++ G +  ++ +l++ +k++k   +++v++      +n++ + ++a
  gi|557694522|ref|YP_008797576.1|  36 AALAASVEEMGSDAIMVGGSTVHTQEQLDNyIKTIKSKTRLPVIIF----PNNVQSISRFA 92 
                                       4566788999999999999999999888763677777777888763....45555555555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0014
                              BtpA 189 leelklaketvkvkvlvgsGvseenlekllsi..adGvivgtsikkd 233
                                        + +k++k++v+++v+vg G+ +   ++ + +  ad +++gt   k+
  gi|557694522|ref|YP_008797576.1| 187 PQTIKAVKHAVEIPVIVGGGIRTGKDAETVAAagADIIVTGTAAEKN 233
                                       4689*****************98777776665125667777766544 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.13   1.3e+02     126     171 ..      27      70 ..      17      86 .. 0.72
   2 ?    9.6   0.1   0.00048      0.48      50      88 ..     187     227 ..     180     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.13
                            DUF561 126 PyiLkleeqvkLakkLeslgvdliqteGkitsiskakkvndlieks 171
                                       P  +++++   La ++e++g d i   G++ +   ++++++ i+++
  gi|557694522|ref|YP_008797576.1|  27 PISISQDDAAALAASVEEMGSDAIMVGGSTVHT--QEQLDNYIKTI 70 
                                       555678888899999999999999998854433..34555555544 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00048
                            DUF561  50 pklvkkvksvsniPiCvs.aveakllleav.kaGadlveiG 88 
                                       p+ +k vk++++iP+ v  ++ + + +e+v +aGad++  G
  gi|557694522|ref|YP_008797576.1| 187 PQTIKAVKHAVEIPVIVGgGIRTGKDAETVaAAGADIIVTG 227
                                       799*************97369988877777257****9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1843.30
//
Query:       gi|557694523|ref|YP_008797577.1|  [L=76]
Description: DNA-directed RNA polymerase subunit H [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  112.7   0.4    5.8e-33  112.6   0.4    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 !  112.6   0.4   3.2e-37   5.8e-33       1      73 []       1      73 [.       1      73 [. 0.99

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 3.2e-37
                                      ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCCT--TTSEEEEEEEETTTEEEEEEEEE CS
                    RNA_pol_Rpb5_C  1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvarylglkkGdvvkItrksetageavtYRlV 73
                                      ++it+H+lvPkhevls+ee++ell+++++++++LP i+ sDp+++ l++k+Gd++kI+r+setageav+YR+V
  gi|557694523|ref|YP_008797577.1|  1 MDITEHVLVPKHEVLSPEEAEELLRRYGVSRDKLPYIHPSDPMVKRLKAKSGDIIKIIRRSETAGEAVYYRVV 73
                                      79*********************************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 573.11
//
Query:       gi|557694524|ref|YP_008797578.1|  [L=1117]
Description: DNA-directed RNA polymerase subunit B [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-117  393.0   0.0   2.4e-117  392.3   0.0    1.3  1  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6
      1e-43  149.2   0.0    1.5e-43  148.7   0.0    1.2  1  RNA_pol_Rpb2_1   RNA polymerase beta subunit
    4.4e-27   95.0   0.0    7.2e-27   94.3   0.0    1.4  1  RNA_pol_Rpb2_2   RNA polymerase Rpb2, domain 2
    4.4e-27   94.0   0.0      1e-26   92.9   0.0    1.7  1  RNA_pol_Rpb2_3   RNA polymerase Rpb2, domain 3
    1.2e-26   92.9   0.1    2.4e-26   91.9   0.1    1.5  1  RNA_pol_Rpb2_7   RNA polymerase Rpb2, domain 7
      8e-18   64.5   2.5    2.6e-17   62.8   2.5    2.0  1  RNA_pol_Rpb2_4   RNA polymerase Rpb2, domain 4
    1.8e-09   38.0   0.0    4.8e-09   36.6   0.0    1.7  1  RNA_pol_Rpb2_5   RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
      0.031   14.5   0.2       0.97    9.7   0.1    2.6  2  RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domai
      0.077   12.9   0.0       0.18   11.7   0.0    1.5  1  RRS1             Ribosome biogenesis regulatory protein (RRS1
        4.3    7.2   5.4        1.9    8.3   0.1    2.8  3  SAP              SAP domain


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 !  392.3   0.0  1.3e-120  2.4e-117       2     390 .]     648    1019 ..     647    1019 .. 0.95

  Alignments for each domain:
  == domain 1  score: 392.3 bits;  conditional E-value: 1.3e-120
                                        HHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS- CS
                    RNA_pol_Rpb2_6    2 aklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgela 76  
                                        a+l+p++eh+qspr++++aam+kqalg+ + n+  r++++++ll+++q+P+v+t+ ++++++         ++ +
  gi|557694524|ref|YP_008797578.1|  648 ASLIPYAEHNQSPRNVYEAAMAKQALGVFASNYALRTDSRSHLLVYPQRPIVTTR-TADLIG--------IDKRP 713 
                                        899****************************************************.9*****........9**** PP

                                        SEEEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS-.--.-S--..-....-SS-GGGS CS
                    RNA_pol_Rpb2_6   77 lGqnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklge.eeitrdipnv....seealkkL 146 
                                        lGqn+vVA+++ +GYn+EDa++ln+++v+r++  s+  + yevear+t++g+ +++    p+v    +e+ ++ L
  gi|557694524|ref|YP_008797578.1|  714 LGQNMVVAILTGKGYNMEDAVVLNRSSVERGLGLSLSWRIYEVEARQTPGGQrDKFGIPEPSVrgyrGEQFYRVL 788 
                                        ****************************************************6666666666699999******* PP

                                        -TTSB--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE.......E CS
                    RNA_pol_Rpb2_6  147 dedGivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgde 221 
                                        d+dG  ++++ v+ g ++vg +  ++ ++ +e + +     +++   +d+s +v+++e+g V+++ +       +
  gi|557694524|ref|YP_008797578.1|  789 DKDGFAHIESDVSGGTVIVGMM--SPPRFLEEYQRV----PTREMVWRDSSETVQPSETGNVENIFI-------T 850 
                                        *********************8..888888544433....33333489*******************.......9 PP

                                        E-TT--EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHH CS
                    RNA_pol_Rpb2_6  222 lkagvnklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEtl 296 
                                         +a++n lvk +v+++   ++GDKf+srhGqKGvv++++pqeDmP+++dGiv+D+++NP+++PSRmtigql+E+l
  gi|557694524|ref|YP_008797578.1|  851 INAEGNLLVKAKVRSTCFTEIGDKFSSRHGQKGVVGMLIPQEDMPYTKDGIVPDLLINPHAFPSRMTIGQLIESL 925 
                                        99************************************************************************* PP

                                        HHHCCCSSSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS--- CS
                    RNA_pol_Rpb2_6  297 lgkaaalegkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKiha 371 
                                        +gk ++++ + vd+t+F g++ ee++ +Le  g+++sG+e ly+G tG+ leae+f+Gv+Yy++L+hlv dKiha
  gi|557694524|ref|YP_008797578.1|  926 AGKLGSIKAEIVDGTPFLGKSLEELRAELEALGFKSSGRELLYNGATGKILEAEVFIGVVYYQRLHHLVRDKIHA 1000
                                        ******************9999***************************************************** PP

                                        -SS--B-TTT--B-SCGGG CS
                    RNA_pol_Rpb2_6  372 RstGpyslltqQPlgGkaq 390 
                                        R++G++++lt+QP++G+++
  gi|557694524|ref|YP_008797578.1| 1001 RARGQVQMLTRQPTEGRSR 1019
                                        *****************86 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 !  148.7   0.0   8.2e-47   1.5e-43       1     200 [.      22     393 ..      22     396 .. 0.96

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 8.2e-47
                                       CTTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCE.EES.HHHHHHCTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   1 gLvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdase.reiyPkearlrnlt 76 
                                       gLv+ +l SFn+fv++ l++ ++  ++ e++ +     +++ +kf+++ ++ P+ +e+da + + +yP earlrnlt
  gi|557694524|ref|YP_008797578.1|  22 GLVQHHLRSFNYFVKTGLQQLVNSMSDYEIKTK----HGTVVVKFGQVTIDIPTKREIDAPNpQPLYPWEARLRNLT 94 
                                       69********************99998888888....478*****************99765288************ PP

                                       XEEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1  77 YsaplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaq 153
                                       Y+ap+y+k+       d k    +e+v +G++P+M++s  c ls+++++el +++E+p+d+GGyFiinG+e+viv  
  gi|557694524|ref|YP_008797578.1|  95 YEAPIYIKMSIYF---DGKPIAPPENVWVGNIPVMVKSDICPLSKMTHDELLAHGEDPQDPGGYFIINGSERVIVGI 168
                                       *********9999...58888899***************************************************** PP

                                       EE........................................................................... CS
                                       xx........................................................................... RF
                    RNA_pol_Rpb2_1 154 ek........................................................................... 155
                                       e+                                                                           
  gi|557694524|ref|YP_008797578.1| 169 EDlapnriivtkkegdskpqysavilsaahgrqvrvevsyrkdspvkvyfsriykgvpaiimlralgltkdqeianl 245
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|557694524|ref|YP_008797578.1| 246 isplkevqellepsfreaegvetveqaldyigsriafgyaeeyrlekaeqivdtmfmlhlgttkaarmkkavhlcem 322
                                       ***************************************************************************** PP

                                       ..........................XHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHH CS
                                       ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1 156 ..........................laGeLlaslfrvllkklerdvkerlqksleklddlmlqllvnakp 200
                                                                 l   Ll++l+r++++kl rd++ +l++ + + + ++ +  v+   
  gi|557694524|ref|YP_008797578.1| 323 igrvletslglrepddrdhyankrlkLESALLTELYRMAFVKLLRDLRYQLERIIPTRQPISISTYVRHGI 393
                                       *****************************************************999999888887777655 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 !   94.3   0.0     4e-30   7.2e-27       3     190 .]     174     348 ..     172     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 4e-30
                                       SCEEEEE-SSSSSE..SSSCCEECCCE..EEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTS CS
                    RNA_pol_Rpb2_2   3 ngiyvekekdknki..satvtsslisq..rgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericy 75 
                                       n+i+v k++  +k   sa+  s  + +  r  v++ +++  +++++ri+k   +p++i+l+Algl++d+eI + i+ 
  gi|557694524|ref|YP_008797578.1| 174 NRIIVTKKEGDSKPqySAVILSAAHGRqvRVEVSYRKDSPVKVYFSRIYKG--VPAIIMLRALGLTKDQEIANLIS- 247
                                       777777777666662222222222222113334555677788899998887..********************999. PP

                                       SSTTHHHHHHHHHHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTSSSTC CS
                    RNA_pol_Rpb2_2  76 dsedsqlleelleeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlglsesle 152
                                           ++++e+l ++  e+e + t e+aldyig+++a++  ee rl++a++i +           +++ hlg+ +   
  gi|557694524|ref|YP_008797578.1| 248 --PLKEVQELLEPSFREAEGVETVEQALDYIGSRIAFGYAEEYRLEKAEQIVD----------TMFMLHLGTTKAAR 312
                                       ..58899******************************************9974..........56666*******55 PP

                                       HH..HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                    RNA_pol_Rpb2_2 153 nkrlkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                          +ka  + +mi r+l+ +lg re+DD+Dh++nkR++
  gi|557694524|ref|YP_008797578.1| 313 M--KKAVHLCEMIGRVLETSLGLREPDDRDHYANKRLK 348
                                       5..5********************************96 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 !   92.9   0.0   5.8e-30     1e-26       1      68 []     416     480 ..     416     480 .. 0.98

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 5.8e-30
                    RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                       q+l+r+n+l++lshlrrv+s+   ls+ + ++e+Rdlh +hwGr+Cp+eTPEG+n Glvk+Lal+a+v
  gi|557694524|ref|YP_008797578.1| 416 QLLNRTNYLATLSHLRRVQSP---LSRGQPHFEARDLHGTHWGRLCPCETPEGSNAGLVKNLALSAEV 480
                                       899******************...******************************************97 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 !   91.9   0.1   1.3e-29   2.4e-26       1      86 [.    1021    1112 ..    1021    1113 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 1.3e-29
                                        BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEE......EBTTTTCSSSEEEEEEEHHHH CS
                    RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaan......eCkivkseekiekveipeafk 69  
                                        GGl+fGEMErd+liayGa++lL +rl+++SD+++++ c++c++  +++       C++  ++ +++ v++++af 
  gi|557694524|ref|YP_008797578.1| 1021 GGLKFGEMERDCLIAYGASYLLLDRLLEQSDKYTAYFCEKCGMPCYYDlkqerfVCPVDGKDVRVKAVSMSYAFY 1095
                                        9*********************************************99*************************** PP

                                        HHHHHHHHTTBEEEEES CS
                    RNA_pol_Rpb2_7   70 lLlqeLqslgialklll 86  
                                        lLl+e++s++i++++ll
  gi|557694524|ref|YP_008797578.1| 1096 LLLNEMMSMCIHPRILL 1112
                                        *************9875 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 !   62.8   2.5   1.5e-20   2.6e-17       1      62 []     516     579 ..     516     579 .. 0.92

  Alignments for each domain:
  == domain 1  score: 62.8 bits;  conditional E-value: 1.5e-20
                                       EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TT..T--EEEE-SSEEB-EEEEE-S CS
                    RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnek..qkevkiatDgGRvcRPliiVe 62 
                                       Vfv+G+l G+++++  lv++lR+lRR+g is++++++l+     +ev i+tD+GR++RPli+V+
  gi|557694524|ref|YP_008797578.1| 516 VFVDGVLEGYHSNGVMLVNELRRLRREGIISQNINVALYTYghVQEVVINTDEGRIRRPLIVVQ 579
                                       9******************************9999866554339******************96 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 !   36.6   0.0   2.7e-12   4.8e-09       1      52 [.     600     634 ..     600     659 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 2.7e-12
                                       HHHHHHTTSEEEEEHHHHTT--EESSTTTCSST-SSTTTSS--TTSSSST-S CS
                    RNA_pol_Rpb2_5   1 wddLlregvvEylDaeEEetamIamtpedleksreekealeekenskshtyT 52 
                                       + dL++ g++EylDaeEEe+a++a++p++++++                 +T
  gi|557694524|ref|YP_008797578.1| 600 FRDLVSLGIIEYLDAEEEENAYVAISPDKVTNE-----------------HT 634
                                       88***************************9887.................23 PP

>> RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00054      0.97      12      35 ..     609     632 ..     599     639 .. 0.84
   2 ?    1.6   0.0      0.18   3.3e+02      37      56 ..     992    1011 ..     987    1014 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00054
                                       EEEEEHHHHTTSEEE-SSS-BETT CS
                   RNA_pol_Rpb2_45  12 vvYLtAdeEekyviAqAnapldee 35 
                                       ++YL A+eEe+ ++A +  ++ +e
  gi|557694524|ref|YP_008797578.1| 609 IEYLDAEEEENAYVAISPDKVTNE 632
                                       89*************887777655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.18
                                        CBSSSEEEEECSSCEEEEEG CS
                   RNA_pol_Rpb2_45   37 rfveerVlaRrkgevelvep 56  
                                        ++v+++++aR +g+v++ ++
  gi|557694524|ref|YP_008797578.1|  992 HLVRDKIHARARGQVQMLTR 1011
                                        789************99886 PP

>> RRS1  Ribosome biogenesis regulatory protein (RRS1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001      0.18      27      84 ..      29      88 ..      11      91 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                                      HHHHHHHHHHHHHHHHHHHHS-EEEE.TEEEEE-----S---..-SS-S---XXXXXXXX CS
                              RRS1 27 eelkelardnvqlLinqllslptesteegvlakLpepttkLP..RekplPkpkplTkWek 84
                                      ++ +   ++++q L+n++ + ++++++  v++k  + t+ +P  Re  +P+p+pl  We+
  gi|557694524|ref|YP_008797578.1| 29 RSFNYFVKTGLQQLVNSMSDYEIKTKHGTVVVKFGQVTIDIPtkREIDAPNPQPLYPWEA 88
                                      5666678899****************99*************97778888******99996 PP

>> SAP  SAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.5   4.6e+03       1       9 [.     134     142 ..     134     142 .. 0.92
   2 ?   -0.4   0.4      0.58     1e+03      23      31 ..     485     493 ..     485     493 .. 0.94
   3 ?    8.3   0.1    0.0011       1.9       7      23 ..     948     964 ..     945     965 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.5
                                       HTT--HHHH CS
                               SAP   1 lskltVaeL 9  
                                       lsk+t +eL
  gi|557694524|ref|YP_008797578.1| 134 LSKMTHDEL 142
                                       79*****98 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.58
                                       -HHHHHHHH CS
                               SAP  23 kKaeLieRL 31 
                                       +K+eL +RL
  gi|557694524|ref|YP_008797578.1| 485 NKKELLDRL 493
                                       7*******8 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHTT--TTS- CS
                               SAP   7 aeLKeeLkkrGLptsGk 23 
                                        eL++eL+++G ++sG+
  gi|557694524|ref|YP_008797578.1| 948 EELRAELEALGFKSSGR 964
                                       79**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                        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 0.29s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 7537.34
//
Query:       gi|557694525|ref|YP_008797579.1|  [L=1254]
Description: DNA-directed RNA polymerase subunit A' [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-91  307.1   0.0    2.2e-91  306.5   0.0    1.3  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
      1e-83  280.8   0.3    1.7e-83  280.1   0.3    1.3  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    5.9e-74  247.8   0.0    1.6e-73  246.4   0.0    1.8  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    3.1e-38  131.2   0.0    1.8e-37  128.7   0.0    2.2  2  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    2.9e-25   88.3   1.4    1.1e-24   86.5   0.0    2.6  3  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
     0.0016   18.3   5.1       0.95    9.4   0.1    3.5  3  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
        4.1    7.6   4.4         11    6.3   4.4    1.7  1  FYVE            FYVE zinc finger


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 !  306.5   0.0   8.6e-95   2.2e-91       3     312 .]       6     313 ..       4     313 .. 0.95

  Alignments for each domain:
  == domain 1  score: 306.5 bits;  conditional E-value: 8.6e-95
                                       ---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEECE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1   3 kikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLakP 79 
                                       ++  i+fgi+sp+ irk+Sv+e+ +++t++e+   P + +++D+rlgt +   +C+tCg+++  C+ghfG ieL  P
  gi|557694525|ref|YP_008797579.1|   6 SVAGIRFGILSPDLIRKMSVAEIISPDTYDEDG-LPIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVP 81 
                                       6889***************************95.9****************************************** PP

                                       EE-HHHHHHHHHHCTTCETTTTEBSS-TTSH....HHHHHHCSSSCC..CCHHHHHHHHCCS-BE-SSSSB-EEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1  80 vfhigffklilkilecvckecskllldeekkkllsklkkrekleelk..krlkaieelckkinlcekCgavqpklee 154
                                       v+h+gf k+i+++l+++c+ c+++ll e + k +  + +r + ++l   + + +i+++  + ++c +Cg +q kle 
  gi|557694525|ref|YP_008797579.1|  82 VIHVGFAKTIYELLKSTCRSCGRILLPEDDCKKYHAELERLRANNLPfkNLIYKIKQKAMNTQVCPHCGEKQLKLEL 158
                                       ***************************9977666666666555554344999*****************99999998 PP

                                       ETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 155 egeklkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrse 231
                                       e+ +  +++++s +   +kl++++v+  l+ri+d d+++l ++++ srPew++ltvlPVpP+ +RPs++l++g rse
  gi|557694525|ref|YP_008797579.1| 159 EKPTSFSEMSESGS---TKLNPSTVRARLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSE 232
                                       88888888888888...9*********************************************************** PP

                                       ECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 232 dDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrf 308
                                       dDlt+kl+di++  +rL++++++g p+ +iee  +lLQ+hv+t+f+ne  g+ pa+++s+r lk+l qrLkGKeGrf
  gi|557694525|ref|YP_008797579.1| 233 DDLTHKLVDILRVTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEAVGVVPAKHRSGRILKTLAQRLKGKEGRF 309
                                       ***************************************************************************** PP

                                       CCCT CS
                                       xxxx RF
                    RNA_pol_Rpb1_1 309 RgnL 312
                                       R nL
  gi|557694525|ref|YP_008797579.1| 310 RLNL 313
                                       ***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 !  280.1   0.3   6.6e-87   1.7e-83       1     265 [.     776    1198 ..     776    1200 .. 0.96

  Alignments for each domain:
  == domain 1  score: 280.1 bits;  conditional E-value: 6.6e-87
                                        B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETT.S-EEESSGGGTS........ CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx........ RF
                    RNA_pol_Rpb1_5    1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsg.geivqflygedg........ 66  
                                        GL++ efffh+ ggR GL+DtAv+T +sGY+qRrl++ale + ++yd+tvr ++ g+i+qf+ygedg        
  gi|557694525|ref|YP_008797579.1|  776 GLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRLINALEALYIDYDGTVRTADeGRIIQFAYGEDGvdpaksdh 850 
                                        9*************************************************9865389****************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                    RNA_pol_Rpb1_5   67 ........................................................................... 66  
                                                                                                                   
  gi|557694525|ref|YP_008797579.1|  851 gkavtvsnivnsvlasaysgkpasqeyieqklqqasdklnkkiieelraelrktnppaeavdkiveevvskynas 925 
                                        *************************************************************************** PP

                                        B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHC CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5   67 lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakeleka 141 
                                        l epG+avG++ aQSiGePgTQltl+TFHfaGv+++++ +G+prl ei+++ ++  ++ +++ l++e+a++l+ka
  gi|557694525|ref|YP_008797579.1|  926 LAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGLPRLIEIVDARRTPTTPIMYIPLTPEYASNLAKA 1000
                                        *************************************************************************** PP

                                        HHHHHHHSE.................................................................. CS
                                        xxxxxxxxx.................................................................. RF
                    RNA_pol_Rpb1_5  142 kkvkkaiek.................................................................. 150 
                                        +k++k+i++                                                                  
  gi|557694525|ref|YP_008797579.1| 1001 RKLAKQIQHttlgdlisevlvnykrgtlevqldaksleehgvtkrdiekalkgvgaeydeekrvisvkldeeglm 1075
                                        *************************************************************************** PP

                                        ............CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHH CS
                                        ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  151 ............gikkikrilvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaeileilgiea 213 
                                                    ++k+i+ri    a+  ke+ +e+v++teg nl+ev++v++ vd ++i +ndi ei+e++giea
  gi|557694525|ref|YP_008797579.1| 1076 diarvrerissiKVKGIRRIKK--ATVFKEK-DEYVIRTEGSNLREVMEVPG-VDWRRIKTNDIYEIAEVFGIEA 1146
                                        *******998776666666543..3444444.789*****************.********************** PP

                                        HHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  214 arkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrsGinkaels 265 
                                        ar+a+++e + v++ qg++v+ rHl l++d+mt  g++++++r+G+ k ++s
  gi|557694525|ref|YP_008797579.1| 1147 ARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVSGSVKQIGRHGVVKLKSS 1198
                                        **********************************************998876 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 !  246.4   0.0   6.2e-77   1.6e-73       1     166 []     315     482 ..     315     482 .. 0.98

  Alignments for each domain:
  == domain 1  score: 246.4 bits;  conditional E-value: 6.2e-77
                                       SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT CS
                    RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkak 77 
                                       Gkrvd+saR+vispdpn++++evgvP ++a++ltv+e+vt++n +k+r+lv+ng+++yPga+y++r dg++ +lk  
  gi|557694525|ref|YP_008797579.1| 315 GKRVDFSARTVISPDPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTLVRNGSDKYPGARYIIRPDGKRVRLKFV 391
                                       9**************************************************************************99 PP

                                       -S..CHHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--S CS
                    RNA_pol_Rpb1_2  78 kr..klakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpq 152
                                        +  +la++le g++verh++dgd+vl+NRqPsLh++simah+v+vl++ktlrln +v+t+yNaDFDGDemnlh+pq
  gi|557694525|ref|YP_008797579.1| 392 ANleELATALEPGYVVERHLQDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQ 468
                                       877569*********************************************************************** PP

                                       SHHHHHHHHHCSBT CS
                    RNA_pol_Rpb1_2 153 seearaEaeelllv 166
                                       seea++Ea+ell+v
  gi|557694525|ref|YP_008797579.1| 469 SEEAQTEARELLVV 482
                                       **********9875 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 !  128.7   0.0   7.1e-41   1.8e-37       1     157 []     485     638 ..     485     638 .. 0.96
   2 ?   -0.9   0.0      0.55   1.4e+03      64     137 ..    1005    1084 ..     958    1095 .. 0.69

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 7.1e-41
                                       CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSEBEEHHHHHHCCCHC CS
                    RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkpkelwtgkqtfsrilpn 77 
                                       ni+sp+ g P+ig ++D+l+++yllT++++ +++ e  +ll  +         ++pa++ p++ wtgkq+fs++lp+
  gi|557694525|ref|YP_008797579.1| 485 NIISPRYGAPIIGVIRDFLTSLYLLTRDETKLTKSELAMLLAAIKYR---GPIPPPAVKDPEPMWTGKQVFSLLLPK 558
                                       9*******************************************554...5699*********************** PP

                                       CCCEEEESSSSSTSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCEB-TG CS
                    RNA_pol_Rpb1_3  78 einyerkneekdgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyllqsgftigi 154
                                       ++n   k++ ++++v++kng+li+Gvidk  vg ++ +s++h la++yg++ +++fld++ rl+++++   gf++ +
  gi|557694525|ref|YP_008797579.1| 559 DFNHVTKSSFTNTEVVVKNGQLISGVIDKGSVGVEKANSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAV 635
                                       ******85555899*******************99****************************************** PP

                                       GGG CS
                    RNA_pol_Rpb1_3 155 gDt 157
                                       +D+
  gi|557694525|ref|YP_008797579.1| 636 DDL 638
                                       *95 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.55
                                        BEEHHHHHHCCCHC.CCCEEEE..SSSS..STSEEECSSEEEES--SHHHHS....SSSTTSHHHHHHHHCHHHH CS
                    RNA_pol_Rpb1_3   64 lwtgkqtfsrilpn.einyerk..neek..dgkvlikngelikGvidkkvvg....kksqgslihvlakeygike 129 
                                        +++  +t++ ++ +  +ny+r   +     d k l ++g++ k  i+k++ g     ++++ +i v  +e g+ +
  gi|557694525|ref|YP_008797579.1| 1005 KQIQHTTLGDLISEvLVNYKRGtlE--VqlDAKSLEEHGVT-KRDIEKALKGvgaeYDEEKRVISVKLDEEGLMD 1076
                                        4444555555555344466665332..25688888888888.888888888777765566777777777777777 PP

                                        HHHHHHHH CS
                    RNA_pol_Rpb1_3  130 tvrfldsl 137 
                                        ++r+  ++
  gi|557694525|ref|YP_008797579.1| 1077 IARVRERI 1084
                                        77665555 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 ?   -1.3   0.0      0.78     2e+03      23      59 ..     130     172 ..     113     174 .. 0.63
   2 !   86.5   0.0   4.2e-28   1.1e-24       5     108 .]     667     769 ..     663     769 .. 0.96
   3 ?   -2.3   0.1       1.6   4.1e+03      10      36 ..     878     904 ..     872     924 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.78
                                       HHHHHHHHHHHHHH......HHHHHHHCSTTTSHHHHHHHCTS CS
                    RNA_pol_Rpb1_4  23 eakinkilnkardk......agkiaskslaasNsiliMvksGa 59 
                                       +++i ki++ka ++       +k  + +l++  s+  M++sG+
  gi|557694525|ref|YP_008797579.1| 130 KNLIYKIKQKAMNTqvcphcGEKQLKLELEKPTSFSEMSESGS 172
                                       456666666666665544422223333333357999*****98 PP

  == domain 2  score: 86.5 bits;  conditional E-value: 4.2e-28
                                       CTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTB CS
                    RNA_pol_Rpb1_4   5 erygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegk 81 
                                       +  g++e  pg++ e+ fea + kil++ard+agk+++  ++ + s +iM+k+Ga+G ++n+ q+++++Gqq+v+ +
  gi|557694525|ref|YP_008797579.1| 667 QT-GEVEIPPGMTAEQAFEADVLKILSEARDSAGKLIRARVSQNSSAFIMAKTGARGTMLNLDQMIAVVGQQSVRRE 742
                                       44.889999*********************************879******************************** PP

                                       SS--SSTSCSSTTSSSSESSTTTSSEE CS
                    RNA_pol_Rpb1_4  82 ripkgfsgrtlphfkkidespesrGFv 108
                                       r+ +g+++r+l  fk++d sp++rGFv
  gi|557694525|ref|YP_008797579.1| 743 RVHRGYRKRVLSFFKQDDLSPRARGFV 769
                                       **************************8 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.6
                                       CHHHTTHCHHHHHHHHHHHHHHHHHHH CS
                    RNA_pol_Rpb1_4  10 ledlpgksleelfeakinkilnkardk 36 
                                       +e+++++++++l +++i+++  + r++
  gi|557694525|ref|YP_008797579.1| 878 IEQKLQQASDKLNKKIIEELRAELRKT 904
                                       334444444444444444444444433 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 !    5.2   0.3    0.0078        20      11      21 ..      56      66 ..      55      67 .. 0.86
   2 !    9.4   0.1   0.00037      0.95       4      26 ..      89     110 ..      88     116 .. 0.81
   3 ?    4.1   0.1     0.016        42      27      35 ..     145     153 ..     143     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0078
                           DUF35_N 11 gqrCpdCGtvq 21
                                      gqrC+ CG  +
  gi|557694525|ref|YP_008797579.1| 56 GQRCKTCGNTY 66
                                      8*******765 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00037
                           DUF35_N   4 aaegrLvgqrCpdCGtvqfPPra 26 
                                        ++++L+ + C++CG+    P+ 
  gi|557694525|ref|YP_008797579.1|  89 KTIYELLKSTCRSCGRILL-PED 110
                                       6789************976.444 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.016
                           DUF35_N  27 vCphCgsdd 35 
                                       vCphCg ++
  gi|557694525|ref|YP_008797579.1| 145 VCPHCGEKQ 153
                                       799999876 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.4    0.0041        11      24      65 ..      95     152 ..      54     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0041
                                       --EE-TTT--EE-..STTS-EEE.EE..............GGGTEEEEEEE-HHHHHH CS
                              FYVE  24 rrhhCrlCGkvvC..ekCssklvall..............ekeaeeksvrvCkeClae 65 
                                        +  Cr CG+++   ++C + +++l               + +++  +++vC +C ++
  gi|557694525|ref|YP_008797579.1|  95 LKSTCRSCGRILLpeDDCKKYHAELErlrannlpfknliyKIKQKAMNTQVCPHCGEK 152
                                       5788*******98778888777777677888888888887777888889******875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       957  (0.0533772); expected 358.6 (0.02)
Passed bias filter:                      831  (0.0463495); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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: 0.93u 0.30s 00:00:01.23 Elapsed: 00:00:00.46
# Mc/sec: 8185.79
//
Query:       gi|557694526|ref|YP_008797580.1|  [L=106]
Description: large subunit ribosomal protein L30e [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-09   37.6   0.0    1.5e-09   37.5   0.0    1.0  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
  ------ inclusion threshold ------
       0.17   11.9   0.0       0.25   11.4   0.0    1.2  1  Hpr_kinase_N    HPr Serine kinase N terminus


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 !   37.5   0.0   1.7e-13   1.5e-09       3      94 ..       3      94 ..       1      95 [. 0.92

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.7e-13
                                      HHHHHHHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEES.CHHHHHHHTTSSSEC CS
                    Ribosomal_L7Ae  3 ieevlkkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvk.skkeLGelvgkkrpv 80
                                      +++ l++ +++g l++G +e+++ +  ++a  v+ ++  +p+   k l +++k  +vp+v ++    eLG ++ k++ +
  gi|557694526|ref|YP_008797580.1|  3 LRQSLQVIARTGSLAVGFRETMRKVMERKAVAVVASAHSNPQLLAK-LRVVAKAFDVPVVVTElTPSELGLALRKPFST 80
                                      77889999**************************************.******99999876655779************ PP

                                      SEEEEEESTTTHHH CS
                    Ribosomal_L7Ae 81 salaikdegdskdl 94
                                      s +a++d+g s++l
  gi|557694526|ref|YP_008797580.1| 81 SFIAVVDAGSSDIL 94
                                      **********9986 PP

>> Hpr_kinase_N  HPr Serine kinase N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.8e-05      0.25      70     117 ..      21      70 ..      18      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.8e-05
                                       ..HHHHHHTT--S-EEEETTT--..-HHHHHHHHHH---EEEESS-HHHH CS
                      Hpr_kinase_N  70 kerleklfskkipciiltrglep..peellelaeeygvpllrtklstsef 117
                                       +e+++k+++ k  +++ +   +p    +l  +a++ +vp+++t+l+ se+
  gi|557694526|ref|YP_008797580.1|  21 RETMRKVMERKAVAVVASAHSNPqlLAKLRVVAKAFDVPVVVTELTPSEL 70 
                                       6899*************99777644899999*************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 790.11
//
Query:       gi|557694527|ref|YP_008797581.1|  [L=144]
Description: N utilization substance protein A [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   4.8    7.5e-10   38.8   0.2    2.7  2  KH_5      NusA-like KH domain
    6.7e-07   29.0   3.4     0.0016   18.2   0.3    2.3  2  KH_2      KH domain
    7.5e-05   22.5   0.0    0.00015   21.6   0.0    1.5  1  KH_4      KH domain
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.022   14.9   0.0    1.1  1  Ada3      Histone acetyltransferases subunit 3


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 !   38.8   0.2   1.7e-13   7.5e-10       3      66 ..      34      91 ..      32      95 .. 0.92
   2 ?    3.8   0.7     0.014        61       5      31 ..     105     126 ..     100     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 1.7e-13
                              KH_5  3 ertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevls 66
                                      + + ++V++++     + +++   G++ik++++ +  ++i+vve+s D + fi+n+l+Paev++
  gi|557694527|ref|YP_008797581.1| 34 DIITFVVRQGD-----LKKALMGHGAKIKELVRIF-RKRIKVVEYSTDASVFIKNLLYPAEVIE 91
                                      56778999999.....88899999***********.9*************************85 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.014
                              KH_5   5 tkvaVkshnpnvdpvGaivgkkGsrik 31 
                                       ++v V  ++      G ++gk G++i+
  gi|557694527|ref|YP_008797581.1| 105 MVVNVNPRD-----KGVAIGKDGKNIN 126
                                       677788888.....9999999999997 PP

>> KH_2  KH domain
   #    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       7      68 ..      18      80 ..       6      86 .. 0.76
   2 !   18.2   0.3   3.5e-07    0.0016      27      66 ..     105     143 ..      79     144 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.9e-05
                                      HHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTC...EEE CS
                              KH_2  7 aveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkk...Vkl 68
                                      ++ +++a v +++    ++ +++v+r +  + ++   G++ik++   +rk+i+++e++    V++
  gi|557694527|ref|YP_008797581.1| 18 FEAVTGAAVVDCVD--DEDIITFVVRQGDLKKALMGHGAKIKELVRIFRKRIKVVEYSTdasVFI 80
                                      55556666666644..458999999999966666556899****************997655554 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 3.5e-07
                                       EEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCE CS
                              KH_2  27 viiviresqpgivIGkgGsnikkigkelrkdieklegkkV 66 
                                        ++ +    +g++IGk G+ni+  +  +++ + ++e+  +
  gi|557694527|ref|YP_008797581.1| 105 MVVNVNPRDKGVAIGKDGKNINLARLLVKRHF-NIEHVTI 143
                                       456677889****************9999999.4877766 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   3.4e-08   0.00015      16      60 ..      91     134 ..      76     143 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.4e-08
                              KH_4  16 eevevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylvsa 60 
                                       e v+v e+  + ++ + +nv++ d+G+ IGk+G++++  + lv++
  gi|557694527|ref|YP_008797581.1|  91 EPVRVAEK-PDGKKIMVVNVNPRDKGVAIGKDGKNINLARLLVKR 134
                                       55777776.678999*********************988888776 PP

>> Ada3  Histone acetyltransferases subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   4.8e-06     0.022      12      77 ..      10      74 ..       6      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.8e-06
                              Ada3 12 qELreiGilepeedadkydgredDevaaeLrrlqaeLrevsliNgarkarLlelvkermayqeyqt 77
                                      +E+++i ++e+ + a  + +  dDe   +    q  L++     ga+ ++L+++ ++r++  ey+t
  gi|557694527|ref|YP_008797581.1| 10 KEIKYIQMFEAVTGAA-VVDCVDDEDIITFVVRQGDLKKALMGHGAKIKELVRIFRKRIKVVEYST 74
                                      899******9888886.7778888888889999*******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); 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):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1011.70
//
Query:       gi|557694528|ref|YP_008797582.1|  [L=123]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 927.42
//
Query:       gi|557694529|ref|YP_008797583.1|  [L=254]
Description: peptidylprolyl isomerase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   58.6   0.1    8.6e-16   57.8   0.1    1.4  1  FKBP26_C  FKBP26_C-terminal
    1.9e-08   34.5   0.0    6.2e-08   32.9   0.0    2.0  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase


Domain annotation for each model (and alignments):
>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8   0.1   9.6e-20   8.6e-16       3      71 ..     184     252 ..     182     253 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 9.6e-20
                                       HHHHHHHHHH-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEEEEEEEEE CS
                          FKBP26_C   3 ekikelIkryiPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevekVkFvdef 71 
                                       ek+k+lI+++ P +++ekf+++++   +++++peea+++ +iqlak+++Ak+  + +++ ekV F +e+
  gi|557694529|ref|YP_008797583.1| 184 EKVKNLIHMHFPDVSVEKFEVSLSPPLLRVKIPEEAFLAPGIQLAKRALAKEFKEAVKGLEKVVFEEEY 252
                                       9****************************************************************9988 PP

>> 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 !   32.9   0.0     7e-12   6.2e-08       6      82 ..      31     122 ..      27     176 .. 0.77
   2 ?   -3.7   0.0       1.7   1.5e+04      42      56 ..     230     244 ..     225     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 7e-12
                                       -TTCEEEEEEEEEET.TSSEEEEH.............CCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGG CS
                            FKBP_C   6 kegdtVtvhykgkle.dgkvfdss.............rsrakplefkvGsgqvikGfeealegmkvGekrtltippe 68 
                                       ++++ V v+y+ +++  g+++d++              + ++p  + vG+g ++k++e+ ++g+k  ek+ ++i pe
  gi|557694529|ref|YP_008797583.1|  31 EPSSYVLVDYTIRVKeTGELVDTTveeeavkagvrdaSKVYEPRLVIVGKGFLLKAIEDEMVGLKPSEKKSFEIAPE 107
                                       67889*********97899***9999999999987755599************************************ PP

                                       GTTTTTTBCTTT.B. CS
                            FKBP_C  69 laYgekglaggv.ip 82 
                                        a+g+++ a+ + ip
  gi|557694529|ref|YP_008797583.1| 108 KAFGQRDPANVKtIP 122
                                       *****8776544443 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.7
                                       SSSCHHHHHHHTTSB CS
                            FKBP_C  42 gqvikGfeealegmk 56 
                                       + + k f+ea++g++
  gi|557694529|ref|YP_008797583.1| 230 RALAKEFKEAVKGLE 244
                                       556788899998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1812.12
//
Query:       gi|557694530|ref|YP_008797584.1|  [L=220]
Description: proteasome beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-52  176.6   0.0    4.3e-52  176.4   0.0    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 !  176.4   0.0   2.4e-56   4.3e-52       3     190 .]      12     192 ..      10     192 .. 0.98

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 2.4e-56
                                       HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGT CS
                        Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpi 79 
                                       +Gtt+vG+  kd vv+a+d+r+t+g  ++ ++  +K+  + +h+++++aG +aDa+tl++ ++a+++ y++  g+ +
  gi|557694530|ref|YP_008797584.1|  12 TGTTTVGMVVKDAVVVATDTRVTSGFFVAHRR-GKKVLPLAPHVAITIAGRVADAQTLIDLIKANINYYQIMRGQVM 87 
                                       8***************************8888.7******************************************* PP

                                       CHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHST CS
                        Proteasome  80 pverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyke 156
                                       ++     +va+++++ +++s+  pf+++l++agvd+eg p+Ly++dp Gs++eek  +a+Gsgs +a+++le +y+e
  gi|557694530|ref|YP_008797584.1|  88 SLP----AVARLTSSLMFSSRYFPFYAQLILAGVDNEG-PHLYNLDPFGSVTEEK-LIATGSGSPVAYGVLEPNYRE 158
                                       ***....****************************888.***************8.********************* PP

                                       TBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 157 dltleeavelavkalkealerdklsgknievavi 190
                                       d++ ++avela +a+++a++rd+ sg+ ++va++
  gi|557694530|ref|YP_008797584.1| 159 DMDFNSAVELAFQAVSAAIRRDAGSGDSVDVAYV 192
                                       *******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1668.87
//
Query:       gi|557694531|ref|YP_008797585.1|  [L=635]
Description: beta-lactamase domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   81.0   0.0    6.1e-22   78.0   0.0    2.3  2  Beta-Casp      Beta-Casp domain
    8.6e-17   60.8   0.0    2.1e-16   59.6   0.0    1.7  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
      7e-16   58.2   0.0    5.4e-15   55.3   0.0    2.1  2  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    1.7e-15   57.6   0.1      5e-15   56.0   0.1    1.8  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.1e-13   50.0   0.8    6.3e-13   48.5   0.8    1.9  1  KH_7           KH domain
    1.1e-05   25.0   0.0    2.8e-05   23.7   0.0    1.7  1  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0025   17.7   0.0      0.007   16.3   0.0    1.7  2  Lactamase_B_3  Beta-lactamase superfamily 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 !   78.0   0.0   2.4e-25   6.1e-22       1     110 []     419     543 ..     419     543 .. 0.89
   2 ?   -0.0   0.0      0.41     1e+03      81     100 ..     584     603 ..     575     614 .. 0.79

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 2.4e-25
                                       HHHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG......................E-SHH....HHH CS
                         Beta-Casp   1 aqellylLeelwkekkledlklpiyldsplaskatevYkeyae......................veakslewmesk 55 
                                       aqe++++L++l +ekk   +++p++ld+ l+++at++++ +++                      +  k     es+
  gi|557694531|ref|YP_008797585.1| 419 AQEIMLVLNKLFTEKK--LVETPVFLDG-LVIEATAIHTGFPDyftaelqqrlregeniflseyfTPVKG----ESQ 488
                                       7*************66..5789******.************99999999999999999988888744334....445 PP

                                       H..HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  56 keelnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                       ++e+ + ++p+v++++sgmlegG++ ++lk++ +d++n++++v+yq+egTlgr+l
  gi|557694531|ref|YP_008797585.1| 489 RQEILEMREPMVVISTSGMLEGGPVLKYLKAFGGDENNLLLFVSYQVEGTLGRTL 543
                                       55677899*********************************************86 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.41
                                       HHHHHHHTTSTTSEEEESS- CS
                         Beta-Casp  81 rellkklledprntvilvgy 100
                                        +++k+++++prn ++  g 
  gi|557694531|ref|YP_008797585.1| 584 INYVKRVMPKPRNIILVHGE 603
                                       5899***********98875 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 !   59.6   0.0   8.3e-20   2.1e-16       3      62 .]     563     625 ..     561     625 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 8.3e-20
                             RMMBL   3 pvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidvfiP 62 
                                       +vk+++e++d fSgH+ +++l+++++++ p++  +ilvHGee+a ++la +l++ +  ++f+P
  gi|557694531|ref|YP_008797585.1| 563 NVKMQVEKVDgFSGHSSRQQLINYVKRVMPKPrnIILVHGEENAVESLATALTRITPASIFTP 625
                                       79**************************999999****************9976666777776 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 !   55.3   0.0   2.1e-18   5.4e-15       2     173 ..     197     363 ..     175     378 .. 0.85
   2 ?    0.1   0.0      0.18   4.7e+02      21      55 ..     579     613 ..     572     625 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 2.1e-18
                     Lactamase_B_6   2 LeldnvkiLlDvGwd...eskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpv 75 
                                       ++  + +++lD+G +    s++s+   ++ + + ++++d+++Lsha l+h+G    + + f  k++ + pvya  p+
  gi|557694531|ref|YP_008797585.1| 197 IQTSESTVMLDCGLSagaTSSLSFYPRFDAIPNLVEELDAVVLSHAHLDHVGL---VPYLF--KYGYRGPVYAVEPT 268
                                       6777899******993323355666678889999******************4...44444..5899********** PP

                     Lactamase_B_6  76 vkLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWki..s 150
                                         L  + ++d++  +g +g++       +di+ a ++  +lkY   ++++    ++ +  ynaGh lG +  ++   
  gi|557694531|ref|YP_008797585.1| 269 LPLMALEVTDYVSVAGKEGTFA--PYGESDIRLALQHSFPLKYGVVTNITP---DIRLIFYNAGHILGSSAVHLhiG 340
                                       ***********99999988775..56889***************9999985...799999*********99766226 PP

                     Lactamase_B_6 151 kesekivYavdwnhakeshLnga 173
                                       +++++ivY  d+  ++ + L+ +
  gi|557694531|ref|YP_008797585.1| 341 EGLHNIVYTGDFKYERSTALDPC 363
                                       8899*********9999999864 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.18
                     Lactamase_B_6  21 slesalkelekviptvdliLLshatlehlGayall 55 
                                       s ++ ++++++v+p+   i+L h + + + ++a  
  gi|557694531|ref|YP_008797585.1| 579 SRQQLINYVKRVMPKPRNIILVHGEENAVESLATA 613
                                       567899*****************999888777655 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.1     2e-18     5e-15       4     163 ..     190     378 ..     187     410 .. 0.83

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 2e-18
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHH...HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH.HCCEETCCE CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraal...elaalglkpkdvdavilTHlHlDHiGglgglvea.tdvpvgava 76 
                                       ++ +++li++ +++++ D+G+s+ a+  ++   +  a+    +++dav+l+H+HlDH+G +++l +  +  pv+av+
  gi|557694531|ref|YP_008797585.1| 190 VGRSCILIQTSESTVMLDCGLSAGATSSLSfypRFDAIPNLVEELDAVVLSHAHLDHVGLVPYLFKYgYRGPVYAVE 266
                                       6789************************99*99999**************************986652788888888 PP

                                       HHHHCCHCHHHHHHHHHCCHH.............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE CS
                       Lactamase_B  77 eeapalfmeeaddaasrkgll.............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey 140
                                        ++p +  e  d  +++++               l    + k +v++++++++++   ++ + ++ g++++h++++ 
  gi|557694531|ref|YP_008797585.1| 267 PTLPLMALEVTDYVSVAGKEGtfapygesdirlaLQHSFPLKYGVVTNITPDIRL--IFYNAGHILGSSAVHLHIGE 341
                                       888888888888888888888********88877777777777777777777654..5788889************* PP

                                       TTCCEEEECTTTSSHHCCCCCC............... CS
                       Lactamase_B 141 gggkvlftGDallagetgridl..............t 163
                                       g  ++++tGD+ ++++t+++++              t
  gi|557694531|ref|YP_008797585.1| 342 GLHNIVYTGDFKYERSTALDPCvskfprvetlimesT 378
                                       *********************9666666666655553 PP

>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.8   2.4e-16   6.3e-13      18      65 ..      22      69 ..       5      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 2.4e-16
                              KH_7 18 evkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDp 65
                                      e  ++++e+EGP +++Yt   + f e++++ r+l+  ++kR+viRpD 
  gi|557694531|ref|YP_008797585.1| 22 EQPVSRIEYEGPRIAVYTSSREVFRERDKIARELVTLIKKRVVIRPDV 69
                                      6679*******************************************5 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 !   23.7   0.0   1.1e-08   2.8e-05       3     145 ..     204     354 ..     202     396 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.1e-08
                                       EEES--TTHHHHHTCGG.S--S..SS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH....... CS
                     Lactamase_B_2   3 iLiDagpdlrqqalral.qPve..lrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla....... 68 
                                       + +D+g++  +  +++   P+     + ++++daV+l+haH DH+  ++ l + +   + p+ya + +l        
  gi|557694531|ref|YP_008797585.1| 204 VMLDCGLSAGAT-SSLSfYPRFdaIPNLVEELDAVVLSHAHLDHVGLVPYLFKyG--YRGPVYAVEPTLPlmalevt 277
                                       788999996666.333333443356777899**************6667777742..34688866555542222111 PP

                                       .HCCTTCGHHHCHTT..............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEE CS
                     Lactamase_B_2  69 .vleanfvylaleee..............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlri 130
                                        +++  +       +              +  +  +l+ g  + ++ +++++ +  a h  g         ++ l i
  gi|557694531|ref|YP_008797585.1| 278 dYVSVAG-------KegtfapygesdirlALQHSFPLKYGVVTNIT-PDIRLIFYNAGHILGS-------SAVHLHI 339
                                       1222111.......12334442333333333333444444444444.3444444444444443.......6777777 PP

                                       ECTTEEEEEESS-S- CS
                     Lactamase_B_2 131 egggkrvyyigDtgy 145
                                       ++g ++++y+gD +y
  gi|557694531|ref|YP_008797585.1| 340 GEGLHNIVYTGDFKY 354
                                       777777777777765 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 !   16.3   0.0   2.8e-06     0.007       5      50 ..     190     247 ..     188     252 .. 0.79
   2 ?   -3.7   0.0       3.9   9.9e+03     106     120 ..     344     358 ..     337     394 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.8e-06
                     Lactamase_B_3   5 lghnsflletagarilvDPf......kanlgyeppa.............eeaDlvlisqaledHa 50 
                                       +g +++l++t++ ++++D +      + +                    ee D+v++s+a+ dH 
  gi|557694531|ref|YP_008797585.1| 190 VGRSCILIQTSESTVMLDCGlsagatS-S------LsfyprfdaipnlvEELDAVVLSHAHLDHV 247
                                       589***************995544320.2......12344568888999***************7 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 3.9
                     Lactamase_B_3 106 ltiyhlGhlahelss 120
                                       ++i++ G+  +e+s 
  gi|557694531|ref|YP_008797585.1| 344 HNIVYTGDFKYERST 358
                                       578899998887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (635 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); 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:                         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: 00:00:00.44
# Mc/sec: 4325.54
//
Query:       gi|557694532|ref|YP_008797586.1|  [L=74]
Description: small nuclear ribonucleoprotein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   83.0   1.4    9.4e-24   82.9   1.4    1.0  1  LSM       LSM domain
    1.2e-07   31.8   0.1    1.5e-07   31.5   0.1    1.2  1  SM-ATX    Ataxin 2 SM domain
     0.0024   17.5   0.1     0.0028   17.3   0.1    1.2  1  Hfq       Hfq protein


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 !   82.9   1.4   1.6e-27   9.4e-24       2      67 .]       9      73 ..       8      73 .. 0.97

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 1.6e-27
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                       l+k+++++v+v+l+ng++lrG Lkg+Dq+mN+vLed+ e ++++ +++klg++++RG++iv+is+
  gi|557694532|ref|YP_008797586.1|  9 ILSKSVGSTVLVRLRNGKVLRGLLKGYDQHMNIVLEDTDELIDEN-TQNKLGTIVVRGDSIVMISP 73
                                      599*****************************************9.******************96 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.1   2.5e-11   1.5e-07       5      69 ..       7      62 ..       3      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.5e-11
                                      HHHHHTTTTSEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS...........-EEEEEE CS
                            SM-ATX  5 lflltslvGkevevtvknGevyeGifstvslekdfsvvLkmarkvkkanskssspssgeipdtli 69
                                      l +l ++vG++v v+++nG+v +G++++++    +++vL+ + ++ +   +++++       t++
  gi|557694532|ref|YP_008797586.1|  7 LKILSKSVGSTVLVRLRNGKVLRGLLKGYDQ--HMNIVLEDTDELID---ENTQN----KLGTIV 62
                                      567899*************************..*********99999...22222....222344 PP

>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   4.7e-07    0.0028       6      43 ..       7      46 ..       3      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.7e-07
                                      HHHHHHCT.-EEEEEETTS-EEEEEEEEE-SSE.EEEEET CS
                               Hfq  6 Lnqlrkek.ipvtifLvnGiklkGviksfDnft.vlLesd 43
                                      L+ l+k+  ++v + L nG  l+G +k++D+++ ++Le++
  gi|557694532|ref|YP_008797586.1|  7 LKILSKSVgSTVLVRLRNGKVLRGLLKGYDQHMnIVLEDT 46
                                      566666533789*******************984666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 576.49
//
Query:       gi|557694533|ref|YP_008797587.1|  [L=60]
Description: hypothetical protein CSUB_C1105 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.0   0.4      0.037   14.0   0.4    1.1  1  Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis 
       0.13   12.4   1.0       0.18   11.9   1.0    1.3  1  YojJ            Bacterial membrane-spanning protein N-terminu
       0.15   11.9   2.7       0.15   11.9   2.7    1.0  1  PCRF            PCRF domain
       0.53   10.7   4.8          2    8.9   4.8    1.8  1  Latarcin        Latarcin precursor


Domain annotation for each model (and alignments):
>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.4   8.4e-06     0.037      61     104 ..       2      45 ..       1      56 [. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 8.4e-06
                    Halogen_Hydrol  61 kelkyiretlkeakekikrlekalkrvrslevikqvreilriar 104
                                       +elk i e ++e k+ i+rle+a+   ++le+i++ +  ++  +
  gi|557694533|ref|YP_008797587.1|   2 SELKKIMEEISELKKRIERLEDAILTEDDLEAIEEAEMGYEEGK 45 
                                       58999****************************99887777655 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 ?   11.9   1.0   4.1e-05      0.18      17      47 ..       3      35 ..       1      43 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                              YojJ 17 eLeqiekeleevlkaldeedeClLce..lesir 47
                                      eL++i++e++e  k ++  ++ +L+e  le i 
  gi|557694533|ref|YP_008797587.1|  3 ELKKIMEEISELKKRIERLEDAILTEddLEAIE 35
                                      89***********************74466665 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   2.7   3.4e-05      0.15      32      89 ..       2      56 ..       1      60 [] 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.4e-05
                                      HHTHHHHHHHHHHHHHTTTHHH...HT....-S-..-GGGTHHHHHHHHHH..HHHHH CS
                              PCRF 32 aeleeivealeeleealedleeakelleedeelaelaeeeleelekeleeleeelkkl 89
                                      +el++i+e+++el+++ e le+  ++l ++++l++++e+e+   e +  +lee  k+l
  gi|557694533|ref|YP_008797587.1|  2 SELKKIMEEISELKKRIERLED--AIL-TEDDLEAIEEAEMGYEEGKTFSLEEARKRL 56
                                      7899999999999999999999..555.444666666666555555555554444444 PP

>> Latarcin  Latarcin precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.8   0.00044         2      24      60 ..       5      38 ..       2      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00044
                          Latarcin 24 rklmemvnnlRkvqgRLeemvenlrkvedledtEEAR 60
                                      +k+me + +l+k  +RLe+++      +dle +EEA 
  gi|557694533|ref|YP_008797587.1|  5 KKIMEEISELKKRIERLEDAILT---EDDLEAIEEAE 38
                                      89****************87743...45777778774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1643  (0.0916392); expected 358.6 (0.02)
Passed bias filter:                      969  (0.0540465); expected 358.6 (0.02)
Passed Vit filter:                       132  (0.00736237); 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 0.23s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 495.20
//
Query:       gi|557694534|ref|YP_008797588.1|  [L=66]
Description: plasmid stabilization system protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   27.5   0.7    4.2e-06   27.3   0.7    1.1  1  ParE_toxin  ParE toxin of type II toxin-antitoxin system, par
  ------ inclusion threshold ------
      0.015   15.4   0.0      0.018   15.2   0.0    1.1  1  Gp49        Phage derived protein Gp49-like (DUF891)
      0.032   14.6   0.0      0.042   14.2   0.0    1.4  1  SPOR        Sporulation related domain


Domain annotation for each model (and alignments):
>> ParE_toxin  ParE toxin of type II toxin-antitoxin system, parDE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.7     7e-10   4.2e-06       1      71 [.       5      65 ..       5      66 .] 0.71

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 7e-10
                                      EEEEHHHHHHHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHTTTSEECTSTC.CTTEEEEEECTEEEEEEE CS
                        ParE_toxin  1 vrltprAlkdlkkiadyiardgpaakrfldaleealellaenpalgrprrelg.lkglrririgdyriiYri 71
                                      v l++rA + l+ +++ +      +kr++++l    ++l +np + r +  ++  ++++rir+gdyr++Y i
  gi|557694534|ref|YP_008797588.1|  5 VVLSRRAYRTLETLDKTV------RKRIVEKL----DELGDNPYP-RGCIKIHeKNDIYRIRVGDYRVLYNI 65
                                      567888888888887665......66666665....666666665.4433444677**************98 PP

>> Gp49  Phage derived protein Gp49-like (DUF891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     3e-06     0.018       2      56 ..      14      63 ..      13      66 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 3e-06
                              Gp49  2 eldalpkkarakilaaldlleeggpdlgkplvkkle.dglwElrpksaggiiRvly 56
                                       l+ l+k +r++i++ ld l ++    ++  +k  e ++++ +r+    g +Rvly
  gi|557694534|ref|YP_008797588.1| 14 TLETLDKTVRKRIVEKLDELGDNP--YPRGCIKIHEkNDIYRIRV----GDYRVLY 63
                                      5899****************9996..566666666668*******....89****9 PP

>> SPOR  Sporulation related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     7e-06     0.042      19      51 ..      24      59 ..       3      61 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7e-06
                                      HHHHHHCCHHT--......EEECCSSSCEEEEESSB CS
                              SPOR 19 erlaakLrakgfaaav...avvsgggglyrVrvGpf 51
                                      +r ++kL   g +++    +++  +++ yr+rvG++
  gi|557694534|ref|YP_008797588.1| 24 KRIVEKLDELGDNPYPrgcIKIHEKNDIYRIRVGDY 59
                                      577899999999999999****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 487.07
//
Query:       gi|557694535|ref|YP_008797589.1|  [L=55]
Description: large subunit ribosomal protein L37e [Candidatus Caldiarchaeum subterraneum]
Scores for 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-23   80.7  10.0      7e-23   80.5  10.0    1.0  1  Ribosomal_L37e  Ribosomal protein L37e
    0.00024   20.7   9.3    0.00035   20.2   2.7    2.2  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.002   18.1   1.1     0.0024   17.9   1.1    1.2  1  DZR             Double zinc ribbon
     0.0045   16.3   2.6     0.0086   15.4   2.6    1.5  1  zf-ribbon_3     zinc-ribbon domain
     0.0065   16.5   0.8     0.0073   16.3   0.8    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
  ------ inclusion threshold ------
      0.013   15.2   5.9       0.43   10.3   0.3    2.3  2  Rubredoxin_2    Rubredoxin metal binding domain
      0.045   13.3   4.0        2.7    7.6   0.3    2.3  2  zn-ribbon_14    Zinc-ribbon
      0.059   13.2   3.7      0.076   12.9   3.7    1.2  1  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
       0.21   11.7   5.8        1.6    8.8   0.6    2.2  2  UPF0547         Uncharacterised protein family UPF0547
       0.24   11.0   1.3       0.35   10.5   1.3    1.3  1  MraY_sig1       Phospho-N-acetylmuramoyl-pentapeptide-transfe
       0.26   11.2   7.3       0.35   10.8   7.3    1.2  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
       0.29   11.1  13.3        1.8    8.6   2.5    2.4  2  PriA_CRR        PriA DNA helicase Cys-rich region (CRR) domai
       0.36   10.6   7.1        3.4    7.5   6.9    2.1  2  zinc_ribbon_2   zinc-ribbon domain


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 !   80.5  10.0   5.1e-26     7e-23       2      50 ..       3      50 ..       2      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 5.1e-26
                    Ribosomal_L37e  2 kGtssfGkrqkkktHilCrrCgkrsyhvqkktCascGypsaklrkynWs 50
                                      kGt+s+Gk  +k  Hi+CrrCg+rs+h  kk+Ca cGyps k+r+ynW 
  gi|557694535|ref|YP_008797589.1|  3 KGTPSMGKY-NKPQHIRCRRCGHRSFHKSKKRCAYCGYPSPKWRSYNWL 50
                                      9********.777***********************************6 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 !   20.2   2.7   2.6e-07   0.00035      16      30 ..      15      29 ..      10      31 .. 0.87
   2 ?    5.0   0.5     0.014        20      19      25 ..      33      39 ..      30      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.6e-07
                                      S----SSS-----B- CS
                    DNA_RNApol_7kD 16 dpiRCkeCGhRilYK 30
                                        iRC+ CGhR++ K
  gi|557694535|ref|YP_008797589.1| 15 QHIRCRRCGHRSFHK 29
                                      47***********99 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.014
                                      --SSS-- CS
                    DNA_RNApol_7kD 19 RCkeCGh 25
                                      RC +CG+
  gi|557694535|ref|YP_008797589.1| 33 RCAYCGY 39
                                      9****98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.1   1.7e-06    0.0024       7      38 ..      11      41 ..       5      47 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-06
                               DZR  7 elppdarfCseCgtklkavaaedrCpsCgekv 38
                                       ++p+ + C +Cg++    ++++rC  Cg++ 
  gi|557694535|ref|YP_008797589.1| 11 YNKPQHIRCRRCGHRSF-HKSKKRCAYCGYPS 41
                                      56777778888888753.44578888888775 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.6   6.3e-06    0.0086       1      25 [.      15      40 ..      15      40 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.3e-06
                       zf-ribbon_3  1 stvrCPnCGa.plssddnvCpyCGtk 25
                                      +++rC +CG+    ++ + C+yCG++
  gi|557694535|ref|YP_008797589.1| 15 QHIRCRRCGHrSFHKSKKRCAYCGYP 40
                                      689*********************96 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 !   16.3   0.8   5.3e-06    0.0073      67      95 ..      13      40 ..       7      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.3e-06
                                      E--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 67 vpvkvrCreCgkefeleekalrCpkCgsa 95
                                      +p ++rCr+Cg++  +++k  rC  Cg  
  gi|557694535|ref|YP_008797589.1| 13 KPQHIRCRRCGHRSFHKSK-KRCAYCGYP 40
                                      6889*******99886654.79****976 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.9    0.0025       3.4       2      10 ..      18      26 ..      18      28 .. 0.87
   2 ?   10.3   0.3   0.00031      0.43       2      13 ..      33      44 ..      33      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0025
                      Rubredoxin_2  2 vCsqCGfes 10
                                      +C++CG++s
  gi|557694535|ref|YP_008797589.1| 18 RCRRCGHRS 26
                                      7*****987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00031
                      Rubredoxin_2  2 vCsqCGfesakw 13
                                      +C  CG+ s+kw
  gi|557694535|ref|YP_008797589.1| 33 RCAYCGYPSPKW 44
                                      8*********** PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.3    0.0028       3.8       2      10 ..      18      26 ..      17      30 .. 0.84
   2 ?    7.6   0.3    0.0019       2.7       2      10 ..      33      41 ..      32      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0028
                      zn-ribbon_14  2 kCerCGylS 10
                                      +C+rCG+ S
  gi|557694535|ref|YP_008797589.1| 18 RCRRCGHRS 26
                                      7*****977 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0019
                      zn-ribbon_14  2 kCerCGylS 10
                                      +C  CGy S
  gi|557694535|ref|YP_008797589.1| 33 RCAYCGYPS 41
                                      8******99 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.7   5.5e-05     0.076      17      40 .]      13      37 ..       5      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                        zf-C3HC4_2 17 pCgHvfCqkCilrsLeekn.eCPlC 40
                                      + +H  C+ C +rs ++++ +C  C
  gi|557694535|ref|YP_008797589.1| 13 KPQHIRCRRCGHRSFHKSKkRCAYC 37
                                      558***********999999**988 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.5     0.012        17      16      23 ..      18      25 ..      16      26 .. 0.87
   2 ?    8.8   0.6    0.0012       1.6      15      22 ..      32      39 ..      30      40 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.012
                           UPF0547 16 fCphCGyv 23
                                      +C+ CG++
  gi|557694535|ref|YP_008797589.1| 18 RCRRCGHR 25
                                      7*9***95 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                           UPF0547 15 qfCphCGy 22
                                      ++C++CGy
  gi|557694535|ref|YP_008797589.1| 32 KRCAYCGY 39
                                      78*****9 PP

>> MraY_sig1  Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.3   0.00025      0.35       2       8 ..       3       9 ..       3       9 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00025
                         MraY_sig1 2 kGTPTMG 8
                                     kGTP+MG
  gi|557694535|ref|YP_008797589.1| 3 KGTPSMG 9
                                     8*****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 ?   10.8   7.3   0.00025      0.35      13      32 ..      18      38 ..      17      40 .. 0.97

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                           DUF35_N 13 rCpdCGtvqfPPr.avCphCg 32
                                      rC+ CG+  f +    C +Cg
  gi|557694535|ref|YP_008797589.1| 18 RCRRCGHRSFHKSkKRCAYCG 38
                                      9*******************8 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 ?    8.6   2.5    0.0013       1.8      11      25 ..      11      25 ..       7      26 .. 0.89
   2 ?    8.4   3.1    0.0015       2.1      10      27 .]      27      42 ..      26      42 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0013
                          PriA_CRR 11 HksrnrLrCHyCgyt 25
                                      ++++++ rC  Cg++
  gi|557694535|ref|YP_008797589.1| 11 YNKPQHIRCRRCGHR 25
                                      6899*********97 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0015
                          PriA_CRR 10 yHksrnrLrCHyCgyteP 27
                                      +Hks  + rC yCgy  P
  gi|557694535|ref|YP_008797589.1| 27 FHKS--KKRCAYCGYPSP 42
                                      5666..448******665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.4    0.0077        11      15      21 ..      18      24 ..       9      26 .. 0.64
   2 ?    7.5   6.9    0.0025       3.4       1      22 [.      18      40 ..      18      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0077
                     zinc_ribbon_2 15 FCpyCGt 21
                                       C +CG+
  gi|557694535|ref|YP_008797589.1| 18 RCRRCGH 24
                                      4666666 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0025
                     zinc_ribbon_2  1 fCpnCGael.qdnakFCpyCGtp 22
                                      +C +CG+    +  k C yCG+p
  gi|557694535|ref|YP_008797589.1| 18 RCRRCGHRSfHKSKKRCAYCGYP 40
                                      699*****98899999*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 405.99
//
Query:       gi|557694536|ref|YP_008797590.1|  [L=164]
Description: hypothetical protein CSUB_C1108 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1277.82
//
Query:       gi|557694537|ref|YP_008797591.1|  [L=642]
Description: glycosyl transferase family 2 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  106.1   0.0    3.8e-30  105.5   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.6e-23   83.3   0.0    2.8e-23   82.6   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    6.7e-23   81.6   1.7    6.7e-23   81.6   1.7    2.4  3  Glyco_trans_2_3  Glycosyl transferase family group 2
    6.7e-13   48.5   0.0    1.1e-12   47.8   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21
    4.7e-06   25.4   3.2    3.4e-05   22.6   0.7    2.1  2  Cellulose_synt   Cellulose synthase
    0.00029   21.3   0.0    0.00083   19.8   0.0    1.8  1  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.012   14.3   1.7      0.035   12.8   0.5    2.1  2  Tweety           Tweety


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 !  105.5   0.0   1.5e-33   3.8e-30       1     230 []      48     277 ..      48     277 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 1.5e-33
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvv.desdaetlevaeelaaalpdvrvrvvvnarnlgstgks 76 
                                       p+ ++v  p +ne  v++++++s+ + +ypr ++ ++v d sd++t e +  l++++++ + ++++ +r ++ + k+
  gi|557694537|ref|YP_008797591.1|  48 PN-VTVQLPIYNERYVVERLIHSVCSLDYPREKLQIIVaDDSDDDTSEICARLVEEYSRKGFNIIHLKRAGRQDFKA 123
                                       56.89999***********************8887777799*****************99***************** PP

                   Glyco_tranf_2_3  77 ralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaar 152
                                        al++al+  ++++++++D+D v   ++l+++l++f +p+vg v+++  +l+++ +l+++++al ++ ++  + + r
  gi|557694537|ref|YP_008797591.1| 124 GALQNALSKSTGEFIAIFDADFVPPRNFLRKTLPYFSDPSVGLVQVRWgHLNREYSLLTRAQALALDLHFSVEQRGR 200
                                       *********************************************888577778899**************999999 PP

                   Glyco_tranf_2_3 153 ralg.vltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwv 228
                                       +a g +l +nG+  ++rr++ ++ +g+ p  +l++D++l++r+  +g+r +y  +++   + p  + a+++q  Rw+
  gi|557694537|ref|YP_008797591.1| 201 DAAGlFLNFNGTAGVWRRSCIEDAGGWFP--SLAEDIDLSYRAQLRGWRLVYIDELEAPAEIPVQINAARRQQYRWA 275
                                       999977***********************..*********************************************9 PP

                   Glyco_tranf_2_3 229 yg 230
                                       +g
  gi|557694537|ref|YP_008797591.1| 276 FG 277
                                       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 !   82.6   0.0   1.1e-26   2.8e-23       3     132 ..      53     187 ..      51     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 1.1e-26
                                       EEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCH....C-TTEEEEEESSS-.HHHHHHHH CS
                   Glycos_transf_2   3 viptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelak....edprvrvirreenv.Gkagalna 73 
                                         p+yNe   ++++++s+++  +p+++++iiv+DD++ D+t ei+ +l++    ++ +++ ++r  ++  kagal +
  gi|557694537|ref|YP_008797591.1|  53 QLPIYNERYVVERLIHSVCSLdYPREKLQIIVADDSD-DDTSEICARLVEeysrKGFNIIHLKRAGRQdFKAGALQN 128
                                       579********************************99.99*9999999999988777777777777777******** PP

                                       HHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS CS
                   Glycos_transf_2  74 glraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv 132
                                       +l+++tg++i+++DaD +p++++l+k++ ++ ++ +++v + + + + e    +r++  
  gi|557694537|ref|YP_008797591.1| 129 ALSKSTGEFIAIFDADFVPPRNFLRKTLPYFSDPSVGLVQVRWGHLNREYSLLTRAQAL 187
                                       *****************************************999999988888888764 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 ?   -7.7   4.4         7   1.8e+04     167     186 ..       8      27 ..       2      33 .. 0.25
   2 !   81.6   1.7   2.6e-26   6.7e-23       2     194 ..     138     349 ..     137     357 .. 0.81
   3 ?   -2.6   1.1       1.6   4.2e+03     150     193 ..     421     463 ..     405     474 .. 0.56

  Alignments for each domain:
  == domain 1  score: -7.7 bits;  conditional E-value: 7
                   Glyco_trans_2_3 167 lplhlallllfsllalalvl 186
                                       l++ ++++  +  +++++++
  gi|557694537|ref|YP_008797591.1|   8 LLVFFIFVSAALPVYTLAYM 27 
                                       21111111111112222222 PP

  == domain 2  score: 81.6 bits;  conditional E-value: 2.6e-26
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgpvlvm.nvanwleelaalffaedhgkdilvrealgrvvpsvGsga 77 
                                       i++ DaD v+p+++lr+++  +++p v++vq   +   +  ++l++ +al  ++++   ++ r+a g ++ + G   
  gi|557694537|ref|YP_008797591.1| 138 IAIFDADFVPPRNFLRKTLPYFSDPSVGLVQVRWGHLnREYSLLTRAQALALDLHFSVEQRGRDAAGLFLNFNGTAG 214
                                       899******************************99863779************************************ PP

                   Glyco_trans_2_3  78 flrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc......elek 148
                                       ++rrs ++++ggw     s++ED d++ r+q +G+r+++++e     + p  + aa+rQ +Rwa+G+          
  gi|557694537|ref|YP_008797591.1| 215 VWRRSCIEDAGGWF---PSLAEDIDLSYRAQLRGWRLVYIDELEAPAEIPVQINAARRQQYRWAFGAiqttvrY--- 285
                                       *************7...9************************************************85444330... PP

                   Glyco_trans_2_3 149 lil...................lvrllgylgsll.wsalplhlallllfsllalalvlllllllaa 194
                                         l                   l+r+l++l + + ++ +pl ++  +l+   ++++++ l+ ++++
  gi|557694537|ref|YP_008797591.1| 286 --LkhvlqakipplarfhafihLTRHLAQLLLTVqVMMVPLVIRSGILQQSHSILVFMSLYPVTVT 349
                                       ..0333344555555555554455555543333314557788888888887777777655544433 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.6
                   Glyco_trans_2_3 150 illvrllgylgsllwsalplhlallllfsllalalvllllllla 193
                                       +++v ++++l++     + l  ++  l+ +++ a+++l+l+ l+
  gi|557694537|ref|YP_008797591.1| 421 LMYVPPFHWLALADIL-IGLYSLYGSLYAFYSRAYYFLPLTTLF 463
                                       4445455554432111.223334455555555666666665554 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 !   47.8   0.0   4.3e-16   1.1e-12      18     172 ..     122     275 ..     108     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 4.3e-16
                   Glyco_transf_21  18 KvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdak.glaaaleaaflntlagvlqa 93 
                                       K  +l +al++   +++ i D+d + ++++L++ l +++dp vglV+      +++ +l ++ +a+ l  +  v q+
  gi|557694537|ref|YP_008797591.1| 122 KAGALQNALSKSTGEFIAIFDADFVPPRNFLRKTLPYFSDPSVGLVQVRWGHLNREySLLTRAQALALDLHFSVEQR 198
                                       9999******************************************9977766655489998888889999888888 PP

                   Glyco_transf_21  94 ...klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaR 167
                                          +++ +   +G + ++rr+ +e++GG  +    LAeD  l+ + + +G+++v  ++  a  ++p    + a  ++
  gi|557694537|ref|YP_008797591.1| 199 grdAAGLFLNFNGTAGVWRRSCIEDAGGWFP---SLAEDIDLSYRAQLRGWRLVYIDELEAPAEIPV--QINAARRQ 270
                                       87556788999********************...***********************9755666664..68888999 PP

                   Glyco_transf_21 168 qlrWa 172
                                       q rWa
  gi|557694537|ref|YP_008797591.1| 271 QYRWA 275
                                       99**8 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.011        28      18      43 ..      63      88 ..      51      96 .. 0.86
   2 !   22.6   0.7   1.3e-08   3.4e-05     416     588 ..     226     393 ..     219     445 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.011
                    Cellulose_synt 18 tantvlsilavdypvekvscyvsddG 43
                                          + s+ ++dyp ek+ + v+dd 
  gi|557694537|ref|YP_008797591.1| 63 VERLIHSVCSLDYPREKLQIIVADDS 88
                                      556789*****************996 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.3e-08
                    Cellulose_synt 416 GwiyGsvtedvltGfkmharGwrsvycvtkrdafkGsapinlsdrlhqvlrwalGsveiffsrnnalfagykkklkl 492
                                       Gw + s++ed+   ++   rGwr vy     +      p+++    +q  rwa G+++  +     ++ +   k+  
  gi|557694537|ref|YP_008797591.1| 226 GW-FPSLAEDIDLSYRAQLRGWRLVYIDELEAP--AEIPVQINAARRQQYRWAFGAIQTTVRYLKHVLQA---KIPP 296
                                       44.789********************8665554..45677777777899*********998888888777...9999 PP

                    Cellulose_synt 493 lerlaylnviiypftsifllvycilpalsllsgkfi.vkelsnlasiyllllflslivlavlelkwsGvsleewwrn 568
                                       l r+  +      ++ + l v  ++ +l + sg +   +++ +++s+y ++++lsl++la + l+ +  ++ ++ ++
  gi|557694537|ref|YP_008797591.1| 297 LARFHAFIHLTRHLAQLLLTVQVMMVPLVIRSGILQqSHSILVFMSLYPVTVTLSLLLLAPVFLRKTFGGMSDFLKD 373
                                       9999777777888999999999999888888886651457888999**************999999999999**999 PP

                    Cellulose_synt 569 eqfwvigGvsahlfavlqGl 588
                                         + +i G+ + +   +  +
  gi|557694537|ref|YP_008797591.1| 374 VFMLIIWGTGTSVNNSIAVV 393
                                       99999988776654444333 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 !   19.8   0.0   3.2e-07   0.00083       2      81 ..      58     144 ..      57     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 3.2e-07
                   Glyco_tranf_2_4   2 neadiLpeflahhlalgfdr...ilvydndstDgtrailke......lpevkllhvdksyederrqvellkallary 69 
                                       ne  + ++ +   ++l++ r    +++ +ds+D+t++i+++       +  +++h + + + ++++  +l+++l + 
  gi|557694537|ref|YP_008797591.1|  58 NERYVVERLIHSVCSLDYPReklQIIVADDSDDDTSEICARlveeysRKGFNIIHLKRAGR-QDFKAGALQNALSK- 132
                                       888889999999999997433458999************9955443334466999988875.79999999999965. PP

                   Glyco_tranf_2_4  70 aeadwvlvvDaD 81 
                                       + +++++ +DaD
  gi|557694537|ref|YP_008797591.1| 133 STGEFIAIFDAD 144
                                       699********9 PP

>> Tweety  Tweety
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   1.4e-05     0.035     162     233 ..     284     355 ..     245     398 .. 0.73
   2 ?   -0.5   0.0      0.15   3.8e+02     147     206 ..     576     639 ..     535     641 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                            Tweety 162 pflkkk.dvsltelaeqvelvelyRWlaylllllldlviClvlllglarkskcllivvsvlgllalvlsWasl 233
                                       + lk++ + ++  la+  +++ l R la lll +  +++ lv+  g+ ++s+++l+++s+  + +++ls ++l
  gi|557694537|ref|YP_008797591.1| 284 RYLKHVlQAKIPPLARFHAFIHLTRHLAQLLLTVQVMMVPLVIRSGILQQSHSILVFMSLYPV-TVTLSLLLL 355
                                       34444347788899999*****************************************99876.555555544 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.15
                            Tweety 147 vqeqveevvqqlselp....flkkkdvsltelaeqvelvelyRWlaylllllldlviClvlllg 206
                                       +++ +e++++   +++    + +++   l ++a q  +   y Wl+ + l +++l + +++++ 
  gi|557694537|ref|YP_008797591.1| 576 IKNRLESAIKLEGDVElyhaTYEDSRRALLNIAGQLRYSMPYAWLGPVELAVILLTLYAITMVL 639
                                       4445555555555554222223334667888899999999999999999999888888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); 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:                         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 0.23s 00:00:00.82 Elapsed: 00:00:00.40
# Mc/sec: 4824.34
//
Query:       gi|557694538|ref|YP_008797592.1|  [L=256]
Description: hypothetical protein CSUB_C1110 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   12.4   0.0       0.19   11.5   0.0    1.5  1  SDH_C     Shikimate 5'-dehydrogenase C-terminal domain


Domain annotation for each model (and alignments):
>> 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 ?   11.5   0.0   1.1e-05      0.19      12      30 ..      80     100 ..      79     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.1e-05
                                       HHHHHHS---..-HHHHHHHH CS
                             SDH_C  12 qFelWTGrep..PvevMreal 30 
                                       + ++W+G+e+  P+++Mre+l
  gi|557694538|ref|YP_008797592.1|  80 SIKYWRGVEVerPYKIMRETL 100
                                       7899***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       278  (0.0155056); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1850.94
//
Query:       gi|557694539|ref|YP_008797593.1|  [L=459]
Description: anaerobic magnesium-protoporphyrin IX monomethyl ester cyclase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-25   90.3   0.6    1.2e-24   87.5   0.5    2.0  2  Radical_SAM  Radical SAM superfamily
    6.7e-16   58.4   0.0    1.7e-15   57.1   0.0    1.6  2  B12-binding  B12 binding domain
  ------ inclusion threshold ------
      0.039   14.5   0.1      0.072   13.6   0.1    1.4  1  Pox_H7       Late protein H7


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 ?    0.5   0.0      0.12     7e+02      30      68 ..      71     107 ..      45     136 .. 0.75
   2 !   87.5   0.5   2.1e-28   1.2e-24       2     166 ..     203     363 ..     202     364 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  30 sveeileevkelkaekgvkevilgggepllypdfvelle 68 
                                        v + ++++++++ + ++++++ gg  p++yp +  + +
  gi|557694539|ref|YP_008797593.1|  71 MVNNAIQIARRIR-D-RCEVLVAGGPMPSAYPAKFLDDF 107
                                       4556667777774.4.49999999999999987655544 PP

  == domain 2  score: 87.5 bits;  conditional E-value: 2.1e-28
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                       + +rgC++ CsfC+rp     ++++r++ +e+i++e++e++++ g + +++     +++++ v ++ +++  ++ ++
  gi|557694539|ref|YP_008797593.1| 203 IASRGCPFSCSFCWRPD---YGRVYRVRRPERIVDEMEEIRYRFGYERIWFADELFIANKKHVIKICEEIISRKLDV 276
                                       679*************9...7**************************************988888877777766777 PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGe 155
                                          + + + l+d+++++ ++++g+  + +glea+dd+ +lklmn++ t+++  +a+++  ++gik   ++i+g pGe
  gi|557694539|ref|YP_008797593.1| 277 LWECLARADLIDDDVAKYMRKAGCHKIIFGLEAGDDR-TLKLMNKQLTVKQSEKAVKTVVRHGIKAGGFFILGYPGE 352
                                       777777777788*************************.*************************************** PP

                                       SHHHHHHHHHH CS
                                       xxxxxxxxxxx RF
                       Radical_SAM 156 ndeeleellel 166
                                       + e++ +++++
  gi|557694539|ref|YP_008797593.1| 353 TTETMLKTIKF 363
                                       ********998 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.1   0.0   2.8e-19   1.7e-15      10     120 ..      19     122 ..      14     123 .. 0.89
   2 ?   -3.0   0.0       1.2   7.4e+03      20      45 ..     291     316 ..     290     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 2.8e-19
                       B12-binding  10 gdlhplGlavlaaalrdagfeVqllganven.edivaairaekpdvvglSalltsqleavkelvellkrirprvkvv 85 
                                       ++ +plG+ ++  +lr++g++V++++++++n +d v+  +a  ++vvg+ + + s ++++ +++++++ + +   +v
  gi|557694539|ref|YP_008797593.1|  19 FKFPPLGIGYISSYLREHGYSVKIVDCTFKNmDDAVR--QASGARVVGIYS-MLSMVNNAIQIARRIRDRCE--VLV 90 
                                       5789*************************77666666..44588*****99.**************999866..89* PP

                       B12-binding  86 vGGahpsldpeetleaklgiddvvvgegedaleal 120
                                       +GG+ ps++p+ +l     +d+vv gege ++ +l
  gi|557694539|ref|YP_008797593.1|  91 AGGPMPSAYPAKFLD---DFDIVVQGEGEITMLEL 122
                                       **************7...46*********999876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                       B12-binding  20 laaalrdagfeVqllganvenediva 45 
                                       +a ++r+ag + ++ g+++ ++++++
  gi|557694539|ref|YP_008797593.1| 291 VAKYMRKAGCHKIIFGLEAGDDRTLK 316
                                       67888888888888888877766665 PP

>> Pox_H7  Late protein H7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.2e-05     0.072      42     111 ..     234     307 ..     226     341 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                                       -TTS-EEEEEE-SS-BGGGGG....T---EE--HHHHHHTHHHHHHHHHHHHHHHH-HHHHHHH-HHHHHHHHH CS
                            Pox_H7  42 dkdgevvidfeYdgflaSdyl....naklkkltpdeyaahsaaiakeltaadiilediedyikeskklkrvikv 111
                                       d+ +e+   f Y+ ++  d l    ++++ k++ + +     ++ ++l+ ad+i++d+++y+++    k +  +
  gi|557694539|ref|YP_008797593.1| 234 DEMEEIRYRFGYERIWFADELfianKKHVIKICEEIISRKLDVLWECLARADLIDDDVAKYMRKAGCHKIIFGL 307
                                       566666677778877766654333235667888888888899999******************99877765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3264.05
//
Query:       gi|557694540|ref|YP_008797594.1|  [L=221]
Description: hypothetical protein CSUB_C1112 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   17.6   3.4     0.0043   17.6   3.4    3.1  3  DoxX      DoxX


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   1.8    0.0011        21      23      56 ..      17      54 ..       4      72 .. 0.76
   2 ?    2.1   0.1     0.017   3.1e+02      39      67 ..      81     109 ..      65     110 .. 0.84
   3 !   17.6   3.4   2.4e-07    0.0043       2      79 ..     108     190 ..     107     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0011
                              DoxX 23 g....fglegtaaslaalglpppellaylaalvElvgg 56
                                           + ++++a ++ +++lp+ +  a+laa+v +v+g
  gi|557694540|ref|YP_008797594.1| 17 LlwavALFAEPARFVHKIPLPQIAAVAHLAAAVLIVAG 54
                                      34444457888889999999999999999999988887 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.017
                              DoxX  39 pppellaylaalvElvgglllllGlltRl 67 
                                        +p+   +la+ v l++++l   +++tRl
  gi|557694540|ref|YP_008797594.1|  81 AEPQSVGILAISVALLVSMLHSENFFTRL 109
                                       45999999***********9999999998 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 2.4e-07
                              DoxX   2 llllRlllgvlfiahGlqkltgfglegtaaslaalglpp.......pellaylaalvElvgglllllGlltRlaAla 71 
                                       +lllR  l++ f+  Gl+ l+  ++  +aa+l+a  ++          +  ++ +++E+v+++  + G + ++a++ 
  gi|557694540|ref|YP_008797594.1| 108 RLLLRGGLAYPFFEWGLDALR--NPYHFAAYLTANTVTKplftylpLYPSIFALGAFEVVLSVWAVSGPGFKIACMT 182
                                       699******************..777777777744444434444446667778899******************999 PP

                              DoxX  72 lavtllva 79 
                                        a+tllv 
  gi|557694540|ref|YP_008797594.1| 183 SALTLLVF 190
                                       99999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); 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: 00:00:00.40
# Mc/sec: 1641.30
//
Query:       gi|557694541|ref|YP_008797595.1|  [L=401]
Description: hypothetical protein CSUB_C1113 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   8.0       0.16   12.2   1.4    1.9  2  Pox_A9    A9 protein conserved region


Domain annotation for each model (and alignments):
>> Pox_A9  A9 protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.4   8.7e-06      0.16      17      38 ..     192     214 ..     189     219 .. 0.89
   2 ?   -4.5   0.7         1   1.8e+04      29      37 ..     313     321 ..     312     321 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.7e-06
                            Pox_A9  17 lRp.NsfafVvlksiisMvmyLv 38 
                                       +Rp N++ fV++ s+++++m+L+
  gi|557694541|ref|YP_008797595.1| 192 FRPkNALTFVIVLSLVTLLMFLI 214
                                       77769*****************8 PP

  == domain 2  score: -4.5 bits;  conditional E-value: 1
                            Pox_A9  29 siisMvmyL 37 
                                       +i+++v++L
  gi|557694541|ref|YP_008797595.1| 313 IILTLVIFL 321
                                       578888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2921.75
//
Query:       gi|557694542|ref|YP_008797596.1|  [L=146]
Description: hypothetical protein CSUB_C1114 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1141.01
//
Query:       gi|557694543|ref|YP_008797597.1|  [L=192]
Description: imidazoleglycerol-phosphate dehydratase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-49  165.5   1.8    8.8e-49  165.5   1.8    1.3  2  IGPD      Imidazoleglycerol-phosphate dehydratase
  ------ inclusion threshold ------
      0.026   14.5   0.4       0.11   12.5   0.2    2.0  2  Fae       Formaldehyde-activating enzyme (Fae)


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 ?   -3.0   0.0      0.92   8.3e+03      59      84 ..       2      27 ..       1      29 [. 0.73
   2 !  165.5   1.8   9.8e-53   8.8e-49       1     144 []      32     172 ..      32     172 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.92
                                      --EEEEEEEETTEEEEEEEE--SS-E CS
                              IGPD 59 kRfgsallpmDealaevaldlsgrpy 84
                                      +R+g+a+    e+ +++ ++l g+ +
  gi|557694543|ref|YP_008797597.1|  2 TRTGKAFRETRETRISAEITLDGTGV 27
                                      57788888888888888888877665 PP

  == domain 2  score: 165.5 bits;  conditional E-value: 9.8e-53
                                       ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEE CS
                              IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaeval 77 
                                       Tg  fldhm+++lakh+ +d++++++gd++   Hh+ved++i+lGqa+++algd+ gikRfg a++pmDeala +a+
  gi|557694543|ref|YP_008797597.1|  32 TGYRFLDHMITTLAKHSLIDITLHAEGDMR---HHVVEDTAIVLGQAFDKALGDRVGIKRFGYAIVPMDEALALAAV 105
                                       9***************************98...******************************************** PP

                                       E--SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                              IGPD  78 dlsgrpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                       dl +rp  v++ +   +++ ++ ++ + +f+es++++ ++t+h++vl+g ++hh+vea+fKa+a+a+
  gi|557694543|ref|YP_008797597.1| 106 DLVKRPKPVIKLKTVLDTVEDIPVSEITHFLESFTTSLNATIHIRVLSGMDDHHKVEAAFKALAQAI 172
                                       ***********99999************************************************996 PP

>> Fae  Formaldehyde-activating enzyme (Fae)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.12   1.1e+03      92     127 ..      56      91 ..      51     108 .. 0.71
   2 ?   12.5   0.2   1.2e-05      0.11      86     146 ..     119     184 ..      95     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.12
                               Fae  92 eegiipkeeaddlviivsvfidpeakdkkkiyeyny 127
                                       +eg + ++ ++d+ i+ +   d +  d+  i ++ y
  gi|557694543|ref|YP_008797597.1|  56 AEGDMRHHVVEDTAIVLGQAFDKALGDRVGIKRFGY 91 
                                       567777777888888877777777666666665555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 1.2e-05
                               Fae  86 avadaveegiipk..eeaddlviivsvfidpea...kdkkkiyeynyeAtklAikrAlkeePside 146
                                        v+d+ve+  + +  +  + ++   +  i+ ++    d+++  e   +A  +Aik+A+++eP+++e
  gi|557694543|ref|YP_008797597.1| 119 TVLDTVEDIPVSEitHFLESFTTSLNATIHIRVlsgMDDHHKVEAAFKALAQAIKQAIEHEPRTNE 184
                                       56666665433321122345555566667777788855556668899***************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); 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: 0.43u 0.19s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1601.62
//
Query:       gi|557694544|ref|YP_008797598.1|  [L=336]
Description: ATP phosphoribosyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-41  141.6   0.0    3.4e-41  140.9   0.0    1.4  1  HisG      ATP phosphoribosyltransferase
    4.2e-16   58.9   0.0    1.5e-15   57.0   0.0    1.9  2  HisG_C    HisG, C-terminal domain


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 !  140.9   0.0   3.7e-45   3.4e-41       1     159 [.      50     236 ..      50     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 3.7e-45
                                       -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG.TT.....-.EEEEE CS
                              HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdlved.....kgkriaT 72 
                                       r+++ip++V+ ga+d+GitG D+v+E+++  +v +lldL++g +klv+a+p++s++k+l++++e+     k ++i T
  gi|557694544|ref|YP_008797598.1|  50 RPQEIPVFVAGGAYDIGITGVDWVRETGA--DVLQLLDLEYGYVKLVIAAPKNSPHKTLDQYIEEyarakKPLKIST 124
                                       89************************864..6****************************99444454557788*** PP

                                       S-HHHHHHHHHHT.......................T-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEE CS
                              HisG  73 sypnlakkyfeek.......................glkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLk 126
                                       +y n+a++y+++k                       +  v++  + G++Ea+p+ + aD+IvD   tG TL++n+L+
  gi|557694544|ref|YP_008797598.1| 125 EYLNTAASYIASKpvyrkiygdqqpmiitpwwrkgeNNMVRVYLSFGATEAKPPEE-ADIIVDASATGITLEQNNLT 200
                                       *************77777777777666666666664447****************6.******************** PP

                                       EEEEEEEEEEEEEEEHHHHHS...HHHHHHHHHHHH CS
                              HisG 127 aietilessavLiankkslkk...kekieellerlr 159
                                        ieti es+a+L+ank+s+++   +eki ++l+ l+
  gi|557694544|ref|YP_008797598.1| 201 PIETITESTAILVANKQSFNDpvkREKILDILTLLK 236
                                       *******************97566668888888776 PP

>> HisG_C  HisG, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.3   1.2e+04       7      21 ..       4      18 ..       3      24 .. 0.82
   2 !   57.0   0.0   1.7e-19   1.5e-15       4      68 ..     244     307 ..     242     309 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.3
                                      EEEEEEGGGHHHHHH CS
                            HisG_C  7 lmynvpkesleevlk 21
                                      +++ vpk sle +++
  gi|557694544|ref|YP_008797598.1|  4 IKFAVPKGSLETATQ 18
                                      678899999998875 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 1.7e-19
                                       EEEEEEEEEGGGHHHHHHH---SSS-EEEE-.SS-EEEEEEEEECCCHHHHHHHHHCTT-EEEEE CS
                            HisG_C   4 yvllmynvpkesleevlkilPGlrsPTvspladegwvaVsavveekevaevideLkaaGAsdIlv 68 
                                       +  + +nv++e+le++l+ lP+l+sPT+s+l+++gw+a+++v++++e+ ++++ L+++ A++++v
  gi|557694544|ref|YP_008797598.1| 244 KLHIFVNVHEENLEKLLTSLPALKSPTISQLSNKGWYAINTVIPKNEFLKILPTLRKL-AQGLVV 307
                                       667999***************************************************9.888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2543.67
//
Query:       gi|557694545|ref|YP_008797599.1|  [L=197]
Description: glutamine amidotransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.0    2.3e-19   69.9   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
    1.5e-05   24.7   0.0    2.2e-05   24.2   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
     0.0021   17.9   1.7      0.043   13.5   0.1    2.7  3  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 !   69.9   0.0   3.8e-23   2.3e-19      42     187 ..      35     192 ..       4     195 .. 0.76

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 3.8e-23
                                       STSEEEEEEESSCTT......TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT...........EEE...EEECE CS
                            GATase  42 npdgilvsgGpgspg......vegkieaikearenkiPiLGICLGmQllaiefgr...........kvv...kekek 98 
                                       +   ++v +G+gs +      +    e++  +re ++P LGICLGmQl ++e+ +            vv   +  ++
  gi|557694545|ref|YP_008797599.1|  35 KEIDCMVLPGVGSFSaaaeriAPMRDEIVDMVRE-GVPTLGICLGMQLFFEESEEgpgrglgvfggRVVmlpPSVKR 110
                                       33357999*******9855533333344455555.********************9999998888855578988889 PP

                                       EEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTT CS
                            GATase  99 ehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEsts 175
                                       +h+g++m   ++e+ ll + +    ++++H+y  +p    + +l+  a+ +++  + +++     ++g+QFHPE++s
  gi|557694545|ref|YP_008797599.1| 111 PHMGWSMLHVKRESPLLDNVGH-PWVYFNHSYHPKP---SNPQLVL-AEANHGIDFPAVVGFGT-VYGTQFHPEKSS 181
                                       ***********99999999955.589*********9...6666766.55558889999999998.*********877 PP

                                       STTHHHHHHHHH CS
                            GATase 176 tpegpellfnfl 187
                                          g+++l+nf+
  gi|557694545|ref|YP_008797599.1| 182 VA-GEKILRNFV 192
                                       55.599999985 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 !   24.2   0.0   3.7e-09   2.2e-05      34     116 ..      30     102 ..       9     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.7e-09
                          GATase_3  34 deslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageveglgl 110
                                        e+l +++d ++lpG  +  +  a++r   ++++i +++++g+p lgiC G+q++ ee e+  g         glg+
  gi|557694545|ref|YP_008797599.1|  30 SEKLVKEIDCMVLPGVGSFSA--AAERIAPMRDEIVDMVREGVPTLGICLGMQLFFEESEEGPGR--------GLGV 96 
                                       4566688********987655..5667777************************99887655443........6666 PP

                          GATase_3 111 Ldiete 116
                                       +  +++
  gi|557694545|ref|YP_008797599.1|  97 FGGRVV 102
                                       665555 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.1   7.3e-06     0.043      98     118 ..      62      82 ..      26      84 .. 0.79
   2 ?   -3.7   0.0       1.3     8e+03      36      46 ..      97     107 ..      95     113 .. 0.80
   3 ?    3.1   0.0     0.012        69     207     216 .]     169     178 ..     150     178 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.3e-06
                     Peptidase_C26  98 iraalergvPilgiCrGlqll 118
                                       i  ++++gvP lgiC+G+ql+
  gi|557694545|ref|YP_008797599.1|  62 IVDMVREGVPTLGICLGMQLF 82 
                                       4578899************96 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.3
                     Peptidase_C26  36 agglpvllpie 46 
                                       +gg++v+lp++
  gi|557694545|ref|YP_008797599.1|  97 FGGRVVMLPPS 107
                                       69999***987 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.012
                     Peptidase_C26 207 fvlgvQwHPE 216
                                       +v+g Q+HPE
  gi|557694545|ref|YP_008797599.1| 169 TVYGTQFHPE 178
                                       699******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1487.33
//
Query:       gi|557694546|ref|YP_008797600.1|  [L=106]
Description: phosphoribosyl-AMP cyclohydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-35  119.5   0.0    4.7e-35  119.3   0.0    1.1  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase
  ------ inclusion threshold ------
      0.038   14.3   0.0      0.038   14.3   0.0    1.2  1  DUF3239   Protein of unknown function (DUF3239)
      0.062   13.3   0.0      0.079   12.9   0.0    1.1  1  DUF98     p-hydroxybenzoic acid synthase


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 !  119.3   0.0   7.8e-39   4.7e-35       1      74 []      28     101 ..      28     101 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.3 bits;  conditional E-value: 7.8e-39
                                       EEEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS-- CS
                            PRA-CH   1 mlaymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCFy 74 
                                       m+ay+n+eal+ t+etg a+++Srsr++lWkKGe+Sgn+++v+e+r+DcD+D++l+ v+++g+aCHtg+++CFy
  gi|557694546|ref|YP_008797600.1|  28 MVAYANAEALRLTFETGFAHFWSRSRQRLWKKGEESGNIMHVVEVRVDCDGDTVLYIVKPTGPACHTGNKTCFY 101
                                       9************************************************************************7 PP

>> DUF3239  Protein of unknown function (DUF3239)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.4e-06     0.038       9      50 ..       7      49 ..       2     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.4e-06
                                      XXXXX-EEEEEEEEE-SS-EEEEEEEE-BSST.TS---EEEEE CS
                           DUF3239  9 lYdeyeLvPavvaevnprdvvllaLvdiakde.aaepeyalal 50
                                       +d++ LvP vv +v  r+v+++a+++++  + + e+ +a  +
  gi|557694546|ref|YP_008797600.1|  7 KFDAGGLVPVVVQDVDTREVLMVAYANAEALRlTFETGFAHFW 49
                                      5999***********************9864413344455554 PP

>> DUF98  p-hydroxybenzoic acid synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.3e-05     0.079      97     140 ..      24      69 ..      19      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.3e-05
                                       EEEEEEEEEE--HHHHHHT.SS-EEEEEE.EEEEETTEEEEEEEEE CS
                             DUF98  97 ReirglalgeadeLeeafg.ekgpfwsRh.YrlfhkgkpltvirEv 140
                                       Re+ ++a+ +a++L+ +f+     fwsR   rl++kg++  +i  v
  gi|557694546|ref|YP_008797600.1|  24 REVLMVAYANAEALRLTFEtGFAHFWSRSrQRLWKKGEESGNIMHV 69 
                                       9*****************945689****7368****9987777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); 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:                         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: 00:00:00.40
# Mc/sec: 794.96
//
Query:       gi|557694547|ref|YP_008797601.1|  [L=254]
Description: imidazoleglycerol-phosphate synthase cyclase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-87  292.7   1.0    1.9e-87  292.5   1.0    1.0  1  His_biosynth   Histidine biosynthesis protein
    1.5e-09   37.7   4.5    3.1e-07   30.1   4.5    2.2  1  NMO            Nitronate monooxygenase
    1.7e-08   34.1   3.8      0.001   18.4   0.4    2.2  2  ThiG           Thiazole biosynthesis protein ThiG
    1.7e-07   30.6   0.1     0.0019   17.3   0.1    2.2  2  Dus            Dihydrouridine synthase (Dus)
    7.2e-06   25.4   0.1     0.0014   17.9   0.0    2.1  2  DHO_dh         Dihydroorotate dehydrogenase
      1e-05   24.9   0.4       0.07   12.5   0.0    2.3  2  TMP-TENI       Thiamine monophosphate synthase
    0.00013   21.4   0.5      0.013   14.9   0.1    2.2  2  G3P_antiterm   Glycerol-3-phosphate responsive antiterminator
     0.0014   17.7   3.4       0.23   10.4   0.1    2.1  2  IMPDH          IMP dehydrogenase / GMP reductase domain
     0.0095   15.4   0.5      0.099   12.1   0.0    2.0  2  PcrB           PcrB family
  ------ inclusion threshold ------
      0.027   13.3   1.4      0.042   12.7   0.2    1.8  2  Trp_syntA      Tryptophan synthase alpha chain
      0.043   12.3   0.1       0.13   10.7   0.0    1.7  2  Met_asp_mut_E  Methylaspartate mutase E chain (MutE)
       0.32   10.0   5.3        3.9    6.4   0.8    2.4  2  FMN_dh         FMN-dependent 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 !  292.5   1.0   1.3e-90   1.9e-87       1     229 []       5     237 ..       5     237 .. 0.98

  Alignments for each domain:
  == domain 1  score: 292.5 bits;  conditional E-value: 1.3e-90
                                       EEEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEE CS
                      His_biosynth   1 riipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvq 77 
                                       riip+lD+++GkvV   kG+rf +lr+agdp++la +y+++gadel+++D++a++++r++  ++v+ +ae ++ip++
  gi|557694547|ref|YP_008797601.1|   5 RIIPCLDVDNGKVV---KGRRFVDLRVAGDPAQLAANYSDQGADELVFLDISASRQNRDILVNVVRSVAEVINIPFT 78 
                                       8*************...************************************************************ PP

                                       EESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE......CEEEEETTTTEEEEEE CS
                      His_biosynth  78 vGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr......gykvaikgwreetgld 148
                                       vGGGIr+++d++++l++gadkv+i+taavk+  l+k+l+e +g+q++vvaiDa+r      gy+v+i+g++  tgld
  gi|557694547|ref|YP_008797601.1|  79 VGGGIRTMSDADTVLQNGADKVSINTAAVKDNTLVKRLSETYGAQCVVVAIDAKRsdkmpsGYEVYIYGGTSPTGLD 155
                                       *******************************************************7665544*************** PP

                                       HHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHH.HTTCSEEEESHHHH CS
                      His_biosynth 149 avelakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelk.segvdavivgsaly 224
                                       av +a++++elgageillt+id dGt+sG+d+elt+++ eav++pviasGG+gs+e++++++ ++g+da++++s+++
  gi|557694547|ref|YP_008797601.1| 156 AVLWARRAAELGAGEILLTSIDMDGTESGYDIELTRKVVEAVDVPVIASGGAGSPEHIYRVFaEAGADAALAASIFH 232
                                       **************************************************************88888********** PP

                                       TTSS- CS
                      His_biosynth 225 egelt 229
                                       +g +t
  gi|557694547|ref|YP_008797601.1| 233 FGVYT 237
                                       *9875 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   4.5   2.1e-10   3.1e-07      25     224 ..      33     230 ..      33     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.1e-10
                               NMO  25 arLaaavsnaGg..LGvla..sgyltaDrlakeirkvkaltdkPfgvnlflpkkdaadraekykkeleeaalelnie 97 
                                       a+Laa+ s++G+  L +l   +  +  D l + +r v ++++ Pf v   +   + ad        l++ a ++ i+
  gi|557694547|ref|YP_008797601.1|  33 AQLAANYSDQGAdeLVFLDisASRQNRDILVNVVRSVAEVINIPFTVGGGIRTMSDADT------VLQNGADKVSIN 103
                                       589********9777776553777888************************99999999......677777777776 PP

                               NMO  98 e.gvrfyrkvevvlde.kvevvsfgfglpteevvarlkeagvvlipt...issvkearkvearGaDalivqGpeaGG 169
                                       + +v++ + v++++++ +++ v +++++++ + + +  e+ +    +     +v  ar ++++Ga  + ++  +  G
  gi|557694547|ref|YP_008797601.1| 104 TaAVKDNTLVKRLSETyGAQCVVVAIDAKRSDKMPSGYEVYIYGGTSptgLDAVLWARRAAELGAGEILLTSIDMDG 180
                                       61466899999999988*****************99999988765541015577789**************999877 PP

                               NMO 170 hqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLa.lGAsgvqigtr 224
                                        +    +     ++L  +v++avd+PviA GG    + +  ++a +GA ++  ++ 
  gi|557694547|ref|YP_008797601.1| 181 TES--GY----DIELTRKVVEAVDVPVIASGGAGSPEHIYRVFAeAGADAALAASI 230
                                       776..34....578***************************998579998876665 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.4     7e-07     0.001     166     214 ..      65     113 ..      57     140 .. 0.83
   2 !   16.7   0.2   2.3e-06    0.0035     133     205 ..     156     229 ..     137     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 7e-07
                                       HHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHH CS
                              ThiG 166 alkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpv 214
                                       +++ + e +++P  v  Gi++ sda ++++ Gad v +nta  + +  v
  gi|557694547|ref|YP_008797601.1|  65 VVRSVAEVINIPFTVGGGIRTMSDADTVLQNGADKVSINTAAVKDNTLV 113
                                       567888999*******************************987666555 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2.3e-06
                                       -HHHHHHHHHTT-SEBEEBSSST.TS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHH.HTT-SEEEESH CS
                              ThiG 133 DlvlarrleevGcaavmPlaapi.GsglGllnkealkiiieeakvPvivDAGigspsdaaqam.elGadavllnt 205
                                        ++ arr  e+G+  ++  +  + G+  G  + e  + ++e ++vPvi   G gsp+++  ++ e Gada l ++
  gi|557694547|ref|YP_008797601.1| 156 AVLWARRAAELGAGEILLTSIDMdGTESGY-DIELTRKVVEAVDVPVIASGGAGSPEHIYRVFaEAGADAALAAS 229
                                       456799999999988876665553777776.556778899*******************998659*****99875 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.1   1.3e-06    0.0019     171     226 ..      62     117 ..      19     133 .. 0.85
   2 !   11.5   0.0   7.9e-05      0.12     166     212 ..     181     227 ..     150     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.3e-06
                                       -CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHCCSTTHHHH.H CS
                               Dus 171 dweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgalgnPwlfae.s 226
                                         + +++v + ++ip+ + G+I++++da+ +l++ Gad v i  +a ++ +l+++ s
  gi|557694547|ref|YP_008797601.1|  62 LVNVVRSVAEVINIPFTVGGGIRTMSDADTVLQN-GADKVSINTAAVKDNTLVKRlS 117
                                       4567999*************************99.*******999999988887544 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 7.9e-05
                                       T-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEE CS
                               Dus 166 yegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmi 212
                                        e   d+e  ++v +av +pvia G+  ++e + ++ +e Gad+ ++
  gi|557694547|ref|YP_008797601.1| 181 TESGYDIELTRKVVEAVDVPVIASGGAGSPEHIYRVFAEAGADAALA 227
                                       555667788899*******************************9876 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   9.2e-07    0.0014     227     282 ..      59     112 ..      54     119 .. 0.90
   2 !    5.6   0.0    0.0054         8     232     291 ..     188     245 ..     184     248 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.2e-07
                                       HHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTC CS
                            DHO_dh 227 kdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpk 282
                                       +di ++v+r+++++++  ip    GGi +  Da   ++ GA  v + ta v+++  
  gi|557694547|ref|YP_008797601.1|  59 RDILVNVVRSVAEVIN--IPFTVGGGIRTMSDADTVLQNGADKVSINTAAVKDNTL 112
                                       78999***********..********************************877654 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0054
                                       HHHHHHHHHTTT.S-EEEESS--SHHHHHHH.HHHTECEEEESHHHHHHGTCHHHHHHHHH CS
                            DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDalek.ieaGAslvqvytalvfegpkiakkikkel 291
                                       ++ r++ + ++  +p+I++GG  s e  +   +eaGA +    + ++f g++ ++++k+ l
  gi|557694547|ref|YP_008797601.1| 188 ELTRKVVEAVD--VPVIASGGAGSPEHIYRVfAEAGADAALAASIFHF-GVYTVSDVKRFL 245
                                       66778888888..*************9998526899998877777755.677777777655 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   4.7e-05      0.07     139     178 ..      63     103 ..      31     106 .. 0.84
   2 !   10.7   0.1   0.00016      0.24     117     173 ..     163     223 ..     145     230 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                          TMP-TENI 139 leglkelaealeiPvvaiGGi.tlenvaevleagadgvavv 178
                                       ++ ++ +ae ++iP+ + GGi t++++++vl+ gad v++ 
  gi|557694547|ref|YP_008797601.1|  63 VNVVRSVAEVINIPFTVGGGIrTMSDADTVLQNGADKVSIN 103
                                       5678999999***********44689***********9975 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                          TMP-TENI 117 adYigvGpifpTdtKkda..eplgleglkelaealeiPvvaiGGi.tlenvaevl.eagad 173
                                       a  +g+G i  T+   d   +  ++e+ ++++ea+ +Pv+a GG  ++e++ +v+ eagad
  gi|557694547|ref|YP_008797601.1| 163 AAELGAGEILLTSIDMDGteSGYDIELTRKVVEAVDVPVIASGGAgSPEHIYRVFaEAGAD 223
                                       55578889988888888756778899******************83478888887566666 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 !   14.9   0.1     9e-06     0.013     127     169 ..      62     104 ..      60     107 .. 0.91
   2 ?    4.7   0.0     0.012        18     129     164 ..     188     224 ..     184     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9e-06
                                       GHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE-- CS
                      G3P_antiterm 127 vpkvikeikkelkipiiaGGLietkedveealkaGaiavstsn 169
                                       + +v++++ + ++ip+  GG i+t +d +++l++Ga+ vs  +
  gi|557694547|ref|YP_008797601.1|  62 LVNVVRSVAEVINIPFTVGGGIRTMSDADTVLQNGADKVSINT 104
                                       568999*********************************9865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.012
                                       HHHCTSTTS...EEEEESS--SHHHHHHHC.TT.SSE CS
                      G3P_antiterm 129 kvikeikkelkipiiaGGLietkedveeal.kaGaia 164
                                       ++++++ +++++p+ia+G   + e++ +++ +aGa+a
  gi|557694547|ref|YP_008797601.1| 188 ELTRKVVEAVDVPVIASGGAGSPEHIYRVFaEAGADA 224
                                       6789999***********9999999988762567776 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.5   0.00078       1.2     111     172 ..      38     102 ..      24     107 .. 0.72
   2 !   10.4   0.1   0.00016      0.23     195     239 ..     186     231 ..     165     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00078
                                       HHHHTT-SEEE.EE-STS..SSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE CS
                                       xxxxxxxxxxx.xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 111 alveagvdvlv.vdsahg..hsekvleavkeikkkveeveviaGnvataegakaLieagadavkv 172
                                       +  ++g+d lv +d++    + +  +++v+++ + ++    ++G + t + a +++++gad v +
  gi|557694547|ref|YP_008797601.1|  38 NYSDQGADELVfLDISASrqNRDILVNVVRSVAEVINIPFTVGGGIRTMSDADTVLQNGADKVSI 102
                                       55667777443267655511445677888899888855567899999999999999999999876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHCTCT-EEEEES---SHHHHHHHHH.TT-SEEEESCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                             IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAla.aGadavmlGsll 239
                                        +  + ++++  +vpvia GG  + ++i + +a aGada +  s++
  gi|557694547|ref|YP_008797601.1| 186 DIELTRKVVEAVDVPVIASGGAGSPEHIYRVFAeAGADAALAASIF 231
                                       56667789999********************9978***99887776 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   6.7e-05     0.099     157     212 ..      48     107 ..      32     120 .. 0.69
   2 ?    1.6   0.1      0.11   1.6e+02     166     205 ..     185     225 ..     164     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.7e-05
                                       EEEE-TTSSS-HHHHHHHH...HHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHH CS
                              PcrB 157 iYlEasGaledveevialk...kklekarlivGGGirsaEkAkevvea.ADvivvGnvve 212
                                       ++l+ s   ++ + +++++   + + ++ + vGGGir   +A  v++  AD + + ++  
  gi|557694547|ref|YP_008797601.1|  48 VFLDISASRQNRDILVNVVrsvAEVINIPFTVGGGIRTMSDADTVLQNgADKVSINTAAV 107
                                       5666666665554444444000444456678********************986655433 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.11
                                       S-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC..SSEE CS
                              PcrB 166 edveevialkkklekarlivGGGirsaEkAkevvea..ADvi 205
                                       +d+e++ +++  ++   +i  GG  s+E+ ++v     AD+ 
  gi|557694547|ref|YP_008797601.1| 185 YDIELTRKVVEAVD-VPVIASGGAGSPEHIYRVFAEagADAA 225
                                       67788888887775.557778888999998887544377765 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   2.8e-05     0.042     184     232 ..      60     109 ..      52     133 .. 0.84
   2 ?   -1.1   0.1      0.45   6.7e+02     190     227 ..     190     229 ..     185     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.8e-05
                                       TTHHHHHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHH CS
                         Trp_syntA 184 aevdelverlkkltavPvavGFGistkeqvkqva.kvadGvivGSalvkk 232
                                       + + ++v+ + ++ + P  vG Gi+t +++++v  ++ad v +  a vk+
  gi|557694547|ref|YP_008797601.1|  60 DILVNVVRSVAEVINIPFTVGGGIRTMSDADTVLqNGADKVSINTAAVKD 109
                                       4567899999***********************999*****999998876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.45
                                       HHHHHHCTSS-EEEESSS-SHHHHHHHH..TT-SEEEE-H CS
                         Trp_syntA 190 verlkkltavPvavGFGistkeqvkqva..kvadGvivGS 227
                                        +++ ++ +vPv    G  ++e++ +v   ++ad+++  S
  gi|557694547|ref|YP_008797601.1| 190 TRKVVEAVDVPVIASGGAGSPEHIYRVFaeAGADAALAAS 229
                                       5677788889999999999999999887567788776655 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 ?   -1.4   0.0       0.4     6e+02     284     324 ..      66     107 ..      50     131 .. 0.58
   2 ?   10.7   0.0   8.5e-05      0.13      89     141 ..     185     237 ..     183     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.4
                     Met_asp_mut_E 284 vKtphEalgvp.tkeanaaglratkqvlnlledqkleeteel 324
                                       v++++E++++p t    + ++  +++vl+  +d+   +t+++
  gi|557694547|ref|YP_008797601.1|  66 VRSVAEVINIPfTVGGGIRTMSDADTVLQNGADKVSINTAAV 107
                                       455555555553344555555555555555554444344443 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.5e-05
                     Met_asp_mut_E  89 hGvkacRkvveavdvpvqvrhgtpdarllaeitlagGftsfegggisynipya 141
                                       + ++ +Rkvveavdvpv    g+  +  +  +   +G+++  +++i ++  y+
  gi|557694547|ref|YP_008797601.1| 185 YDIELTRKVVEAVDVPVIASGGAGSPEHIYRVFAEAGADAALAASIFHFGVYT 237
                                       567899**********************************9999999888886 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2    0.0051       7.6     259     299 ..      60     102 ..      50     108 .. 0.85
   2 ?    6.4   0.8    0.0026       3.9     251     308 ..     178     236 ..     153     246 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0051
                                       HCHHHHHHHH....SS-EEEESS--SHHHHHHHHHTT-SEEEE CS
                            FMN_dh 259 dvLpeiveavgg..rievlvDgGirrGsDvlkAlalGAdavll 299
                                       d+L ++v+ v++  +i+  v gGir+ sD+   l  GAd v +
  gi|557694547|ref|YP_008797601.1|  60 DILVNVVRSVAEviNIPFTVGGGIRTMSDADTVLQNGADKVSI 102
                                       788899999998667888999********99999999999976 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0026
                                       STT---H..HHCHHHHHHHH..SS-EEEESS--SHHHHHHHHH.TT-SEEEESHHHHHHHH CS
                            FMN_dh 251 ldgapat..idvLpeiveavggrievlvDgGirrGsDvlkAla.lGAdavllGRpflygla 308
                                       +dg+ +   i+   ++veav+  ++v+++gG  + +++ +  a  GAda l +  f++g+ 
  gi|557694547|ref|YP_008797601.1| 178 MDGTESGydIELTRKVVEAVD--VPVIASGGAGSPEHIYRVFAeAGADAALAASIFHFGVY 236
                                       666666522555688999997..******************9967********99999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1773.11
//
Query:       gi|557694548|ref|YP_008797602.1|  [L=241]
Description: phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-52  177.5   0.4    3.1e-52  177.3   0.4    1.0  1  His_biosynth  Histidine biosynthesis protein


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 !  177.3   0.4   1.7e-56   3.1e-52       3     228 ..       5     229 ..       3     230 .. 0.98

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 1.7e-56
                                       EEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEE CS
                      His_biosynth   3 ipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvG 79 
                                       +  +Dl dG+v rlv+G+ +++  y g+p+e+a r+ +egad++hvvDldaa  +r+ n++l++++a   +  vq G
  gi|557694548|ref|YP_008797602.1|   5 YAGVDLLDGRVARLVRGRVEDAVFYHGSPAEFAGRWLDEGADWVHVVDLDAAL-ERGDNTALLRQVAAVAHGRVQAG 80 
                                       6679************************************************7.8999******************* PP

                                       SSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE.CEEEEETTTTEEEEEEHHHHHHH CS
                      His_biosynth  80 GGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr.gykvaikgwreetgldavelakk 155
                                       GG+r++ ++ +l++ag+++v+i++ ++++ e    l+   g++k++va+D+ + g  v+++gwre+t l + e +++
  gi|557694548|ref|YP_008797602.1|  81 GGVRNIAKALDLVDAGVSRVVISSLYFSRREDALTLLGSLGADKLCVALDFDEaG-MVVTRGWRERTRLRLKEAVEQ 156
                                       ****************************************************977.********************* PP

                                       HHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                      His_biosynth 156 leelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                       + + g++++l td+++dGtl+G + + + ++ e+++  ++++GG++s+ dl  l+++g+++++vg+alyeg+l
  gi|557694548|ref|YP_008797602.1| 157 VLSDGFRHVLATDVAADGTLAGANPTTLLTVDEELRQYMVVGGGISSVRDLLLLRDTGFAGAVVGKALYEGRL 229
                                       **********************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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: 00:00:00.41
# Mc/sec: 1754.82
//
Query:       gi|557694549|ref|YP_008797603.1|  [L=134]
Description: hypothetical protein CSUB_C1121 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 1043.22
//
Query:       gi|557694550|ref|YP_008797604.1|  [L=284]
Description: hypothetical protein CSUB_C1122 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.2   0.2      0.021   14.4   0.2    1.4  1  Ssu72     Ssu72-like protein
      0.088   12.8   0.5        4.1    7.5   0.1    2.5  2  NCD1      NAB conserved region 1 (NCD1)


Domain annotation for each model (and alignments):
>> Ssu72  Ssu72-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   2.4e-06     0.021      80     182 ..      71     176 ..      55     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-06
                                       HHHHHHH-SS--BGGG...---.--SEEEESSHHHHHHHHHH.HHHS--SS-EEEEEEEE---SSHHHHHHHHHHHH CS
                             Ssu72  80 ldrnrkiKkaPerwqe...aeekkfdvvitceervfdavved.llsreselnrpvhvinvdikDnheeAlvgakail 152
                                       l+r + iK + +r      ++++++ +++ +eer+f+av e  l +re+ ++       ++   n+ eA+    +  
  gi|557694550|ref|YP_008797604.1|  71 LRRLTLIKATRQRLGItskSAKTDIKILMMVEERCFKAVDETyLIMREKASTFRSLQRTLQQYKNRLEAAS-EDERE 146
                                       55666677777776552113345788999**********98636666665554444455555555555543.44567 PP

                                       HHHHHHHT-SS.HHHHHHHHHHHHHHHHT- CS
                             Ssu72 153 eLakaleeaedeleeevkeilaefeektkk 182
                                       +L ++++ +e++l+++ k+i++e e++++ 
  gi|557694550|ref|YP_008797604.1| 147 DLLDMVKITEKKLHRQAKRIVEEAERRYPV 176
                                       999999999999***********9998875 PP

>> NCD1  NAB conserved region 1 (NCD1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1   0.00045       4.1      33      74 ..      94     136 ..      88     139 .. 0.87
   2 ?    4.1   0.1    0.0053        48      36      61 ..     136     161 ..     134     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00045
                              NCD1  33 dveqlleaeeeefleime.lvGmaskPLhvrRlqkaLqewvan 74 
                                       d++ l+++ee+ f  + e  + m  k    r lq++Lq++++ 
  gi|557694550|ref|YP_008797604.1|  94 DIKILMMVEERCFKAVDEtYLIMREKASTFRSLQRTLQQYKNR 136
                                       8999999999999999763578******************975 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0053
                              NCD1  36 qlleaeeeefleimelvGmaskPLhv 61 
                                       +l +a+e+e  +++++v ++ k Lh 
  gi|557694550|ref|YP_008797604.1| 136 RLEAASEDEREDLLDMVKITEKKLHR 161
                                       678999*******************4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1366  (0.0761894); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2103.04
//
Query:       gi|557694551|ref|YP_008797605.1|  [L=313]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-63  213.7   0.2    4.7e-63  213.4   0.2    1.1  1  DUF4392   Domain of unknown function (DUF4392)


Domain annotation for each model (and alignments):
>> DUF4392  Domain of unknown function (DUF4392)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.4   0.2   2.6e-67   4.7e-63       2     287 ..      19     298 ..      18     306 .. 0.90

  Alignments for each domain:
  == domain 1  score: 213.4 bits;  conditional E-value: 2.6e-67
                           DUF4392   2 eeliardpggrgikkllkkgellkaaeslshak.......ksvlItTGFpvhpahsppeEtDGplGAialaraLqal 71 
                                       ++++++d  grg+ k l+++++  ++e+l+  +       + v+++TGFp+   +  ++E+DG+l+++++ar+L++ 
  gi|557694551|ref|YP_008797605.1|  19 DRVVTVDYVGRGVVKSLYAAARGLVDEPLCGRAaellsraRGVAVATGFPIIRFG-GAPESDGLLSSVLFARWLEER 94 
                                       678999999******99999988888888888888888888************99.7******************** PP

                           DUF4392  72 gkkvvivtdelnekiveaaveq.gvlktevpllelqdrsaeaaivfltkdgdkkeaeaeelleklkpdhliaiErpG 147
                                       g ++v+++d+  ekivea +++ g+ +++              ++ +++ +   e+  ++++e++  d+l+a+ErpG
  gi|557694551|ref|YP_008797605.1|  95 GGWSVLFVDKGFEKIVEAGLKAaGARSST--------------AETAPHGAG--EKTLTRIVEEAGADLLVAVERPG 155
                                       **********************5544443..............333333332..2357788888888********** PP

                           DUF4392 148 raadGnyynmrgeniselvaplddlfeaakeigiptigiGDgGNElGmGkvkeavkkhvpngek........iacav 216
                                       ++++G+y+n +geni++++apld++fe+++  g p+i++GDgGNE GmG +keav+khvp+g +        ia+a+
  gi|557694551|ref|YP_008797605.1| 156 ANKHGQYHNSVGENITAYIAPLDKVFEKLSGSGRPFIAVGDGGNEAGMGLIKEAVEKHVPYGGMcrcpcsggIASAT 232
                                       ***************************************************************************** PP

                           DUF4392 217 aadflivagvSNWggyalaaalallsskevsllpsvekeeevlealveagvvdGvtgeremsVDgleleeh 287
                                       aa++l+va++S+ g y+ +a++     +  ++++++    ++ +al+ ag+vd ++g +++ VDg++l+  
  gi|557694551|ref|YP_008797605.1| 233 AATHLVVASISDLGLYGAMALADNQAFQ--KVFKNIR---QAAKALFTAGCVDAFRGPHNPGVDGMGLDAV 298
                                       ********************99999888..8888776...699************************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2355.19
//
Query:       gi|557694552|ref|YP_008797606.1|  [L=272]
Description: circadian clock protein KaiC [Candidatus Caldiarchaeum subterraneum]
Scores for 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-56  190.4   0.0    3.8e-56  190.0   0.0    1.0  1  ATPase       KaiC
    5.6e-07   29.3   0.0    9.3e-07   28.6   0.0    1.2  1  AAA_25       AAA domain
    0.00015   21.0   0.1    0.00025   20.3   0.1    1.2  1  PAXNEB       PAXNEB protein
     0.0002   20.9   0.0    0.00054   19.5   0.0    1.6  2  RecA         recA bacterial DNA recombination protein
    0.00033   20.0   0.1    0.00079   18.8   0.1    1.6  1  Rad51        Rad51
    0.00048   19.8   0.0    0.00078   19.2   0.0    1.3  1  ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-bindi
      0.001   18.9   0.1     0.0039   17.0   0.0    1.8  2  MEDS         MEDS: MEthanogen/methylotroph, DcmR Sensory doma
     0.0014   17.3   0.5       0.99    8.0   0.1    2.1  2  GvpD         GvpD gas vesicle protein
     0.0017   18.6   0.0     0.0042   17.4   0.0    1.6  1  AAA_22       AAA domain
     0.0058   16.7   0.1      0.058   13.4   0.0    2.3  2  AAA_14       AAA domain
     0.0075   15.4   0.0      0.012   14.7   0.0    1.3  1  T2SSE        Type II/IV secretion system protein
  ------ inclusion threshold ------
      0.011   15.3   0.2      0.029   13.9   0.0    1.7  2  AAA_7        P-loop containing dynein motor region
      0.029   13.7   0.0      0.047   13.0   0.0    1.2  1  DnaB_C       DnaB-like helicase C terminal domain
      0.052   13.3   0.0       0.12   12.2   0.0    1.5  1  DEAD         DEAD/DEAH box helicase
      0.076   12.2   0.0       0.13   11.4   0.0    1.3  1  DAP3         Mitochondrial ribosomal death-associated protein
      0.083   13.3   0.2       0.17   12.2   0.2    1.7  1  AAA_16       AAA ATPase domain
      0.099   12.4   0.0       0.27   10.9   0.0    1.7  1  AAA_24       AAA domain
       0.14   11.9   0.0       0.29   10.9   0.0    1.5  1  IstB_IS21    IstB-like ATP binding protein


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 !  190.0   0.0   3.8e-59   3.8e-56       2     228 ..      24     250 ..      23     252 .. 0.96

  Alignments for each domain:
  == domain 1  score: 190.0 bits;  conditional E-value: 3.8e-59
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekle 78 
                                       +tg + lD++l gG+ +gr++l+tGe+G GKti++lq+l++g+ + +e +v+vt++e+ e + + a+slGw++ ++ 
  gi|557694552|ref|YP_008797606.1|  24 STGNPRLDKMLGGGLIRGRTYLVTGETGVGKTILSLQYLLNGLTQ-NETCVYVTIDERVEGVLRGAESLGWNFWAFM 99 
                                       7999**************************************999.******************************* PP

                            ATPase  79 eegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaReilrqlvrvl.kk 153
                                       e g+++ +++   a+e  ++k+ ++ +++++ + +a +  + +r+v+D++++l +  ++e  +Re+lr++++++ + 
  gi|557694552|ref|YP_008797606.1| 100 EAGRFIPLELRLYAAE--ARKYGKESRAFVDAIYNATRGRRFTRLVLDPVSALaQGAKDEFYVREYLREIITMIeER 174
                                       ***********99987..4589999****************************777788888************889 PP

                            ATPase 154 lgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte.egikvle 228
                                        gvT+++++++++++++++++ +eef+++gvivL +k+i ++lvRt+ ++kmR++++++ +++f+I++ +gi++ +
  gi|557694552|ref|YP_008797606.1| 175 FGVTTLMTTDIPTGSKKMSRFMLEEFLASGVIVLGVKQIGGSLVRTIYVRKMRWSSMDSTMYVFTIEPeKGIVIRQ 250
                                       9************************************************************************975 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   9.3e-10   9.3e-07      12     186 ..      20     182 ..      14     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 9.3e-10
                            AAA_25  12 vadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrr 88 
                                       +++l +  p++++ ++g l++g + l++G +g+GKt l l+  l  +t             +++yv  +++ +++ r
  gi|557694552|ref|YP_008797606.1|  20 DERLSTGNPRLDKMLGGGLIRGRTYLVTGETGVGKTILSLQYLLNGLTQN----------ETCVYVTIDERVEGVLR 86 
                                       56788889999999999999*************************99855..........489********999999 PP

                            AAA_25  89 Rlravgeal.rddarllvldlagveslpLfakd..rggtlltadvdaleaaieevegvrlvviDplsralgg..den 160
                                        ++ +g ++ ++ +  +++ l    +l+L+a++  + g+   a+vda+ +a +   +   +v+Dp+s++ +g  de 
  gi|557694552|ref|YP_008797606.1|  87 GAESLGWNFwAFMEAGRFIPL----ELRLYAAEarKYGKESRAFVDAIYNATRG-RRFTRLVLDPVSALAQGakDEF 158
                                       999999777655555555554....57788765213444489999999999999.67***********999978888 PP

                            AAA_25 161 snsdv.galvealeriarrtgaavllv 186
                                         ++  +++++++e+   r+g+++l++
  gi|557694552|ref|YP_008797606.1| 159 YVREYlREIITMIEE---RFGVTTLMT 182
                                       777766888888776...788887765 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   2.5e-07   0.00025      19      82 ..      23      85 ..      21      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.5e-07
                            PAXNEB 19 tStGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewl 82
                                       StG+p LDk+LgGGL  G   l+  + t   +++L   +l +G+ q+ + +++++d+  e +l
  gi|557694552|ref|YP_008797606.1| 23 LSTGNPRLDKMLGGGLIRGRTYLVTGE-TGVGKTILSLQYLLNGLTQNETCVYVTIDERVEGVL 85
                                      5***********************955.66667888899*************999988777665 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   5.5e-07   0.00054      32      93 ..      21      81 ..      16      96 .. 0.89
   2 ?   -2.4   0.0       2.6   2.6e+03       4      22 ..     165     183 ..     163     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 5.5e-07
                                      -EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS--- CS
                              RecA 32 etissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehal 93
                                      e +s+G+  ld  lG GGl +Gr   + G    Gkt l+l+ + +   ++ +++++  +  +
  gi|557694552|ref|YP_008797606.1| 21 ERLSTGNPRLDKMLG-GGLIRGRTYLVTGETGVGKTILSLQYLLNGLTQNETCVYVTIDERV 81
                                      5689***********.******************************9******999876655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHH-TTSS--T CS
                              RecA   4 eaalkqiekkfGkgsimkl 22 
                                       ++ ++ ie +fG  ++m  
  gi|557694552|ref|YP_008797606.1| 165 REIITMIEERFGVTTLMTT 183
                                       5678889999999998864 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1     8e-07   0.00079      18      57 ..      22      61 ..       8      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 8e-07
                                      EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHH CS
                             Rad51 18 qlttGskklDelLgGGietgsiteifGefrsGktqlchtl 57
                                      +l+tG+ +lD++LgGG+  g    + Ge + Gkt l+ + 
  gi|557694552|ref|YP_008797606.1| 22 RLSTGNPRLDKMLGGGLIRGRTYLVTGETGVGKTILSLQY 61
                                      599*******************************998774 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 !   19.2   0.0   7.8e-07   0.00078      11      55 ..      38      83 ..      26      93 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.8e-07
                                      EBTT-EEEEEESTTSSHHHHH.HHHHHHSSTSSEEEEEEESEEHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 11 ivqGqrtlipgafgvGktvis.qslskqsnsddaiiyvgiGergne 55
                                      +++G + l+ g+ gvGkt +s q l++  +++++++yv i er + 
  gi|557694552|ref|YP_008797606.1| 38 LIRGRTYLVTGETGVGKTILSlQYLLNGLTQNETCVYVTIDERVEG 83
                                      689******************99****998888*********9775 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 ?   -0.8   0.0       1.2   1.2e+03      34      75 ..      13      47 ..       9      58 .. 0.68
   2 !   17.0   0.0   3.9e-06    0.0039      18     121 ..      59     158 ..      54     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
                              MEDS 34 vasastldelrealrkagldvdaalesgqleildaeetylrg 75
                                      ++     +el e+l+ +++ +d++l  g    l   +tyl  
  gi|557694552|ref|YP_008797606.1| 13 MVY---MAELDERLSTGNPRLDKMLGGG----LIRGRTYLVT 47
                                      444...6889999999999999998888....2334455544 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 3.9e-06
                              MEDS  18 vpfikaglargekvlyvasastldelrealrkagldvdaalesgqleildaeetylrgggfdpermlealrralaka 94 
                                       ++++ +gl ++e ++yv+ +++++ +++  ++ g +  a++e+g  ++++ e  + +  +++ ++  +a+ +a+ +a
  gi|557694552|ref|YP_008797606.1|  59 LQYLLNGLTQNETCVYVTIDERVEGVLRGAESLGWNFWAFMEAG--RFIPLELRLYAAEARKYGKESRAFVDAIYNA 133
                                       689*****************************************..6666665444555555555555666666665 PP

                              MEDS  95 ladgyaglrvigemtwalrspaereel 121
                                       + +g +  r++ +++ al ++   +e+
  gi|557694552|ref|YP_008797606.1| 134 T-RGRRFTRLVLDPVSALAQG-AKDEF 158
                                       4.5688999999999998887.45554 PP

>> GvpD  GvpD gas vesicle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.1   0.00099      0.99      10      44 ..      41      76 ..      38      85 .. 0.85
   2 !    7.6   0.0    0.0012       1.2     163     205 ..     199     240 ..     177     250 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00099
                              GvpD 10 GktllikGaPGtGktlftlrgl.dvlrresdvlyvs 44
                                      G+t l+ G+ G Gkt++ l++l + l +++  +yv+
  gi|557694552|ref|YP_008797606.1| 41 GRTYLVTGETGVGKTILSLQYLlNGLTQNETCVYVT 76
                                      99*****************98538899999999986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0012
                              GvpD 163 eyivdGvvtlnvkeddrgrlrrdlrleklrGvrignrlqPftl 205
                                       e+++ Gv+ l vk+   g l+r + + k+r  ++++ ++ ft+
  gi|557694552|ref|YP_008797606.1| 199 EFLASGVIVLGVKQI-GGSLVRTIYVRKMRWSSMDSTMYVFTI 240
                                       899**********99.9************************97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.2e-06    0.0042       8     104 ..      44     151 ..      40     183 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.2e-06
                            AAA_22   8 lvvtGesGtGKTtl.lrrlleqldeeakaee...............erpevvfvtlpsstsskdllrellralglel 68 
                                        +vtGe+G+GKT l l+ ll+ l++     e               +++e +  +  + ++   +    lr +  e+
  gi|557694552|ref|YP_008797606.1|  44 YLVTGETGVGKTILsLQYLLNGLTQN----EtcvyvtidervegvlRGAESLGWNFWAFMEAGRFIPLELRLYAAEA 116
                                       79**********87155555555443....12344777776666666666667777777777777777777777777 PP

                            AAA_22  69 kaerlsseellealeqalraravielliiDEaqhlr 104
                                        +++++s+++++a+++a r r+    l++D +  l 
  gi|557694552|ref|YP_008797606.1| 117 RKYGKESRAFVDAIYNATRGRRF-TRLVLDPVSALA 151
                                       77777777777888888888888.888888776665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   5.8e-05     0.058       3      41 ..      42      80 ..      40     149 .. 0.88
   2 ?    0.8   0.0      0.46   4.5e+02       5      57 ..     205     257 ..     203     268 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.8e-05
                            AAA_14  3 kilvitGaRrvGKTtllkqlikellvkkesilyinldde 41
                                      + +++tG   vGKT l  q++ + l+++e ++y+++d+ 
  gi|557694552|ref|YP_008797606.1| 42 RTYLVTGETGVGKTILSLQYLLNGLTQNETCVYVTIDER 80
                                      6789****************999999*********9986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.46
                            AAA_14   5 lvitGaRrvGKTtllkqlikell.vkkesilyi.nldderdkkladpekllelil 57 
                                       +++ G++++G + +   ++++    + +s++y+ +++ e+   +++p  ++e+i+
  gi|557694552|ref|YP_008797606.1| 205 VIVLGVKQIGGSLVRTIYVRKMRwSSMDSTMYVfTIEPEKGIVIRQP--FDEYIK 257
                                       6899******9988655555555755555555513443443445555..555555 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 !   14.7   0.0   1.2e-05     0.012     118     175 ..      30      89 ..      15      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.2e-05
                             T2SSE 118 iaevlrkavrerglilvsGgTgsGKttl.lyallkeinksderi.vtvEDpvEiqlegan 175
                                       ++++l   + +  + lv+G Tg GKt+l l  ll+ + +++ ++ vt+   vE  l+ga+
  gi|557694552|ref|YP_008797606.1|  30 LDKMLGGGLIRGRTYLVTGETGVGKTILsLQYLLNGLTQNETCVyVTIDERVEGVLRGAE 89 
                                       566677777777889***********9736889999998877764789999998887765 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 ?   13.9   0.0   2.9e-05     0.029      32      62 ..      40      71 ..      27      81 .. 0.78
   2 ?   -2.1   0.0       2.4   2.4e+03     135     153 ..     221     238 ..     182     246 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-05
                             AAA_7 32 nkkpvllvGptGtGKtviikd.llkkldkeky 62
                                      +++  l++G+tG+GKt++  + ll+ l ++++
  gi|557694552|ref|YP_008797606.1| 40 RGRTYLVTGETGVGKTILSLQyLLNGLTQNET 71
                                      67889*************99989999985443 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                             AAA_7 135 wYdrkklefkeikdvqlva 153
                                       +Y rk + + ++  +++v 
  gi|557694552|ref|YP_008797606.1| 221 IYVRK-MRWSSMDSTMYVF 238
                                       23332.2444444444444 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 ?   13.0   0.0   4.7e-05     0.047       2      52 ..      23      74 ..      23      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-05
                                      BXSSTHHHHHHCT.SBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEE CS
                                      xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  2 lstgfkdLDklts.GlqkgdliiiAarpsmGktalalniaenaavkeklpva 52
                                      lstg  +LDk+++ Gl +g  +++ +  ++Gkt l l+   n  +++++ v 
  gi|557694552|ref|YP_008797606.1| 23 LSTGNPRLDKMLGgGLIRGRTYLVTGETGVGKTILSLQYLLNGLTQNETCVY 74
                                      5789999**999637***********************99987766555554 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.12      12      60 ..      39     151 ..      32     173 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                                       HTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
                              DEAD  12 lgggdvlvaaeTGsGKTlaflipvlqivyetkgktg......................................... 47 
                                       ++g+  lv +eTG GKT   l  +l+ ++++   ++                                         
  gi|557694552|ref|YP_008797606.1|  39 IRGRTYLVTGETGVGKTILSLQYLLNGLTQN---ETcvyvtidervegvlrgaeslgwnfwafmeagrfiplelrly 112
                                       468999*************999999988652...2223344444444455555555555555555555555555555 PP

                                       ..........................-EEEEEESSHHHH CS
                                       ..........................xxxxxxxxxxxxx RF
                              DEAD  48 ..........................pkalivePtreLa 60 
                                                                    l++ P  +La
  gi|557694552|ref|YP_008797606.1| 113 aaearkygkesrafvdaiynatrgrrFTRLVLDPVSALA 151
                                       555555555555555555555555555555555555555 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 ?   11.4   0.0   0.00013      0.13      26      55 ..      44      73 ..      40      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                      EEEE-SSSSSTTTTHHHHHHHGGGS--EEE CS
                              DAP3 26 lvltGekgsGKSvlLlqalayAlekgwvvl 55
                                      +++tGe+g+GK++l lq l  +l+++   +
  gi|557694552|ref|YP_008797606.1| 44 YLVTGETGVGKTILSLQYLLNGLTQNETCV 73
                                      789********************9964433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00017      0.17      24      52 ..      41      70 ..      28     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00017
                            AAA_16 24 pelvllsGesGvGKsslv.rellralekdg 52
                                      ++  l++Ge GvGK+ l  + ll+ l++++
  gi|557694552|ref|YP_008797606.1| 41 GRTYLVTGETGVGKTILSlQYLLNGLTQNE 70
                                      3789***********997677777777773 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00027      0.27       3      85 ..      42     158 ..      40     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00027
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie....swedfldevvel......... 59 
                                       + +l++G+ g+GKT l +++        ++ +++ +++ +  +        e    ++ +f+++  ++         
  gi|557694552|ref|YP_008797606.1|  42 RTYLVTGETGVGKTILSLQYllngltqNETCVYVTIDERVEGVLRGA----EslgwNFWAFMEAGRFIplelrlyaa 114
                                       6789****************999998888888887777443332222....12234555666666666666666666 PP

                            AAA_24  60 ..................aaeladyktlviDtideleelclaev 85 
                                                         a+  +++  lv+D ++ l + +++e+
  gi|557694552|ref|YP_008797606.1| 115 earkygkesrafvdaiynATRGRRFTRLVLDPVSALAQGAKDEF 158
                                       66677777777777777789999999999999999988887765 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 ?   10.9   0.0   0.00029      0.29      48      88 ..      42      82 ..      19      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                         IstB_IS21 48 enivllGpsGvGKshlaialgveavraglsvlfvrvedLve 88
                                         +++G +GvGK+ l+     ++ +++   ++v++++ ve
  gi|557694552|ref|YP_008797606.1| 42 RTYLVTGETGVGKTILSLQYLLNGLTQNETCVYVTIDERVE 82
                                      45789******************************988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1878.89
//
Query:       gi|557694553|ref|YP_008797607.1|  [L=1136]
Description: DNA polymerase II large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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 1029.2   0.0          0 1026.8   0.0    1.8  2  PolC_DP2        DNA polymerase II large subunit DP2
     0.0049   16.8  11.3      0.067   13.2   0.1    2.4  2  zinc-ribbons_6  zinc-ribbons
  ------ inclusion threshold ------
      0.035   14.0   0.0      0.035   14.0   0.0    3.3  3  HNH_5           HNH endonuclease
      0.061   13.1  16.5       0.16   11.7   1.3    3.3  3  Rubredoxin_2    Rubredoxin metal binding domain
      0.067   13.2  18.8       0.51   10.4   0.7    2.7  2  DZR             Double zinc ribbon
      0.069   12.8   0.1        1.7    8.4   0.0    2.5  2  AbrB_C          AbrB C-terminal domain
       0.34   10.9  16.1        0.5   10.4   0.3    3.4  3  HypA            Hydrogenase/urease nickel incorporation, meta
       0.58   10.3  19.1      0.093   12.9   1.5    3.5  3  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> 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 ! 1026.8   0.0         0         0       1     863 [.       7     878 ..       7     879 .. 0.96
   2 ?   -0.0   0.1     0.066   1.5e+02     617     673 ..    1044    1095 ..    1029    1128 .. 0.47

  Alignments for each domain:
  == domain 1  score: 1026.8 bits;  conditional E-value: 0
                          PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirelekelsreevalkiakeia 77 
                                       eY +++ +e++++y++a++ r+++ +p + vE  +A+ +++Rve l+g++gvae+ir+l+++ls  e a+k+++ei+
  gi|557694553|ref|YP_008797607.1|   7 EYRSNILREVDRVYAVASAYRERTREPLPFVETVFADRMEERVELLVGPHGVAEKIRRLRERLSGIELAFKLCEEIV 83 
                                       699************************************************************************** PP

                          PolC_DP2  78 egkvgeaeskeeavdkavrtalallteg.vvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaD 153
                                        +++g+ es+e+ +++av+tala+lt   ++aAP eGi++v+ik+nddgt+yl+vy+aGPiR+aGGt+ a  v++aD
  gi|557694553|ref|YP_008797607.1|  84 YSSLGA-ESEEKVIHQAVCTALAVLTPPcITAAPSEGISHVRIKENDDGTRYLAVYFAGPIRAAGGTELASVVVLAD 159
                                       ****87.89*****************86499********************************************** PP

                          PolC_DP2 154 yvrkklgldrykpreeeieRyveEielYer.vaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetn 229
                                       yvr+ lgldr+k+reee++R+veE+++Y r v ++qys+ d+ i ++ + +pvei+G at++  v ++rdler+etn
  gi|557694553|ref|YP_008797607.1| 160 YVRRLLGLDRFKAREEEVKRFVEELRTYIRhVGRFQYSVPDKLIAYAYRMTPVEISGVATDEIPVPSFRDLERIETN 236
                                       ****************************999********************************************** PP

                          PolC_DP2 230 rvRGGmllvlaeGialkakKikkkvkklklegWewleelikaekeekkeeeeekkevkpkekylrdliaGRpvlshp 306
                                        +RGG+l+v+++Gi+ +akK++++v+++k++gW+w+eel+ka+ +++++ ee +           ++i+GRpvls +
  gi|557694553|ref|YP_008797607.1| 237 YLRGGALRVVNDGIVGRAKKVLNTVRSMKMSGWDWVEELAKASIKKEENGEEGS----------LEVIGGRPVLSLA 303
                                       *****************************************9544444444444..........59*********** PP

                          PolC_DP2 307 srkGGfRLrYGRsrntglatagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGdvvriddve 383
                                        r GGfR+rYGR+++tg+a++gihP tm +l+ ++++Gtqlk++ PgK+ +v+pvd ie+P+vk ++Gdvv+++++e
  gi|557694553|ref|YP_008797607.1| 304 DRFGGFRIRYGRAFSTGMAAYGIHPLTMRVLKGYIVTGTQLKTDFPGKGGIVTPVDVIEPPVVKTRSGDVVKLTSEE 380
                                       ***************************************************************************** PP

                          PolC_DP2 384 ealeikkeveeildlGeiLvayGeflennhpLvpasyveewwiqelekaaakkeaee.................... 440
                                       + ++i+++++++l+lG+iLv+ G+++enn +L pa+y+eeww +++ +++a++  e+                    
  gi|557694553|ref|YP_008797607.1| 381 TFRKIADSIDRVLFLGDILVSVGDCVENNVELRPAGYCEEWWLKDYLNMVASHGLENvaektgiplkrlklfaanpf 457
                                       **********************************************999988877778999**************** PP

                          PolC_DP2 441 ..kpsaeealelseeldvpLhPkytylwhdisveelekLaeavaekkkleeeklvleleeevkeiLekllvehkvke 515
                                         kp+aeeal+ls ++++pLhP++ ++w++i+++++++L++++++  +++ ek+v++l++++k+iLe++l+eh++ +
  gi|557694553|ref|YP_008797607.1| 458 taKPTAEEALTLSIHTGIPLHPSHLHFWTNITTHQINQLRTWLKTGLMHHGEKHVYRLDPDIKQILEAILLEHRIID 534
                                       ***********************************************9999************************** PP

                          PolC_DP2 516 ekivi..eealallkslgldleeeklekeeekdalelvnelsglevrekaptrigaRmGRPeKskeRkmkpavhvLf 590
                                       +ki++  +++ +l + l+  +e e     +++ +l++++++sg+evr+k  ++++aRmGRPeK+ +Rk++pavh+Lf
  gi|557694553|ref|YP_008797607.1| 535 GKIILseQDQIVLSTLLRPGEEFEPF---TDEGPLQFIHRISGVEVRDKRGSSLTARMGRPEKAGPRKTSPAVHFLF 608
                                       *****755555566666666664444...6779******************************************** PP

                          PolC_DP2 591 pigeaggkrrsvkeaakkkgeieveiarrkCkkCgketlearCeeCgekteeklvCkkceeeve..eekcekcekea 665
                                       pig agg++r++ +a +  + ++ve+ +r C +Cgk +++ +C+eCg+ t+   vC++c+++ +   ekc+kc++++
  gi|557694553|ref|YP_008797607.1| 609 PIGLAGGATRDIVSAKT--SIVTVELVTRLCINCGKIGWRETCSECGSYTTLYGVCRNCKKQFTefVEKCDKCGEDV 683
                                       ***************77..788***************************************76646899******** PP

                          PolC_DP2 666 kavkkkkidlkellekaleklgereekleelkgvkgltskekipEpleKgilRakhdvsvfkdgtvRyDmtdlplth 742
                                         ++k+ +dl+++l++al+k+ge  +++ +l gvkglts+ k+pE++ Kg+lRa+ +++v+kdgtvR+D+t++plth
  gi|557694553|ref|YP_008797607.1| 684 VFSAKQVVDLRAELSAALQKIGE--SAPPRLSGVKGLTSRVKAPESFLKGLLRARYGLYVYKDGTVRFDATNAPLTH 758
                                       ***********************..78************************************************** PP

                          PolC_DP2 743 frpkeigvsveklrelGYteDieGkplesedqivelkvqDivlsedaaeyllkvakfvDdlLeklyglerfYnvekk 819
                                       f+p++igvsve+lr+lGY +D+ G+pl+s++q++elk+qDi+ls++aae+l+kv++++DdlL k+ gle+ Yn+++ 
  gi|557694553|ref|YP_008797607.1| 759 FTPRQIGVSVERLRSLGYLHDVFGNPLVSDEQVLELKPQDIILSRKAAEHLVKVSRYIDDLL-KHAGLEKLYNLRDI 834
                                       *************************************************************9.889*********** PP

                          PolC_DP2 820 edLiGklviglaPHtsagvlgRiiGftkasvgyahPyfHaakRR 863
                                        dL+G+lv+gl+PHt++gv++R+iG+ +a+  +ahP+fHaakRR
  gi|557694553|ref|YP_008797607.1| 835 GDLVGQLVVGLSPHTYVGVVARVIGMLDADLNFAHPVFHAAKRR 878
                                       *******************************************9 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.066
                          PolC_DP2  617 arrkCkkCgke....tlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkki 673 
                                        ++ +CkkC+k+     l+ +C++C++  + ++   ++e+ +e          ak++++k+i
  gi|557694553|ref|YP_008797607.1| 1044 QSFRCKKCNKKfrrlPLTGKCPSCQTDLSLTVFRGNVEKYIE---------LAKQMAEKNI 1095
                                        444555555441111233445555555444444444444322.........2222222222 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   7.1    0.0098        22      14      47 ..     647     681 ..     635     691 .. 0.62
   2 !   13.2   0.1     3e-05     0.067      15      42 ..    1044    1074 ..    1031    1090 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0098
                                       SSEEE-TTT--EEEEEEE-SSS-S-....--EEEETTE CS
                    zinc-ribbons_6  14 geqyhCeaCqedlkkealCpeCeqe....levlkaCga 47 
                                       +   +C++C +  +   +C +C+++    +e++ +Cg 
  gi|557694553|ref|YP_008797607.1| 647 E---TCSECGSYTTLYGVCRNCKKQftefVEKCDKCGE 681
                                       4...6888888888888888887663333455556654 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3e-05
                                        SEEE-TTT--EEEEEEE...-SSS-S---EE CS
                    zinc-ribbons_6   15 eqyhCeaCqedlkkeal...CpeCeqelevl 42  
                                        ++++C++C++++++ +l   Cp C+  l+  
  gi|557694553|ref|YP_008797607.1| 1044 QSFRCKKCNKKFRRLPLtgkCPSCQTDLSLT 1074
                                        6789999999887765333399999988765 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   5.4         1   2.3e+03      24      48 ..     652     674 ..     637     678 .. 0.78
   2 ?   -3.4   0.0       4.1   9.1e+03      19      29 ..     902     912 ..     902     916 .. 0.83
   3 ?   14.0   0.0   1.6e-05     0.035      16      44 ..    1028    1056 ..    1023    1059 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1
                             HNH_5  24 GGkltisnlvtlCkkCNqkkgqkvd 48 
                                       +G++t+     +C+ C ++++++v+
  gi|557694553|ref|YP_008797607.1| 652 CGSYTTLYG--VCRNCKKQFTEFVE 674
                                       677665555..89999999988876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.1
                             HNH_5  19 iPeslGGklti 29 
                                       iP+ +GGk ++
  gi|557694553|ref|YP_008797607.1| 902 IPDRIGGKMDT 912
                                       8999***9886 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 1.6e-05
                             HNH_5   16 eHIiPeslGGkltisnlvtlCkkCNqkkg 44  
                                         HI+P++lG+ + ++     CkkCN+k+ 
  gi|557694553|ref|YP_008797607.1| 1028 SHILPDILGNVKAFMVQSFRCKKCNKKFR 1056
                                        5**********99998889*******996 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   2.6   0.00027       0.6       3      21 ..     649     666 ..     648     667 .. 0.90
   2 ?   -1.2   0.3      0.76   1.7e+03       3       8 ..     676     681 ..     675     683 .. 0.73
   3 ?   11.7   1.3   7.2e-05      0.16       1      21 [.    1046    1068 ..    1046    1069 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                      Rubredoxin_2   3 CsqCGfesakwfGrCpsCg 21 
                                       Cs+CG+ + +++G C++C+
  gi|557694553|ref|YP_008797607.1| 649 CSECGS-YTTLYGVCRNCK 666
                                       *****5.889********8 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.76
                      Rubredoxin_2   3 CsqCGf 8  
                                       C++CG 
  gi|557694553|ref|YP_008797607.1| 676 CDKCGE 681
                                       888885 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 7.2e-05
                      Rubredoxin_2    1 YvCsqCGfesak..wfGrCpsCg 21  
                                        ++C++C+ ++++  + G+CpsC+
  gi|557694553|ref|YP_008797607.1| 1046 FRCKKCNKKFRRlpLTGKCPSCQ 1068
                                        8******999994459******8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  11.8    0.0053        12       1      49 []     637     680 ..     637     680 .. 0.83
   2 ?   10.4   0.7   0.00023      0.51      13      40 ..    1046    1073 ..    1041    1075 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0053
                               DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvdpearfCpeCG 49 
                                       C +Cg+      ++CseCg+         +C +C+++ ++  + C++CG
  gi|557694553|ref|YP_008797607.1| 637 CINCGKI--GWRETCSECGSYTTL---YGVCRNCKKQFTEFVEKCDKCG 680
                                       7777776..33459*****98653...69*******************9 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00023
                               DZR   13 rfCseCgtklkavaaedrCpsCgekvdp 40  
                                          C++C++k ++ +   +CpsC++++++
  gi|557694553|ref|YP_008797607.1| 1046 FRCKKCNKKFRRLPLTGKCPSCQTDLSL 1073
                                        56********99999********99876 PP

>> AbrB_C  AbrB C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0       0.1   2.2e+02      17      25 ..     534     542 ..     529     548 .. 0.87
   2 ?    8.4   0.0   0.00075       1.7      10      32 ..     789     811 ..     786     812 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.1
                            AbrB_C  17 nGkivLSke 25 
                                       +Gki+LS +
  gi|557694553|ref|YP_008797607.1| 534 DGKIILSEQ 542
                                       8******76 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00075
                            AbrB_C  10 eeNisLanGkivLSkeGAeiLik 32 
                                       e+ ++L + +i+LS+++Ae L+k
  gi|557694553|ref|YP_008797607.1| 789 EQVLELKPQDIILSRKAAEHLVK 811
                                       666889999************97 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 ?    3.2   0.6     0.039        86      63      96 ..     626     656 ..     604     660 .. 0.72
   2 ?    5.8   2.8    0.0062        14      71      95 ..     660     682 ..     654     691 .. 0.80
   3 ?   10.4   0.3   0.00022       0.5      70     102 ..    1045    1078 ..    1038    1085 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.039
                                       EEEEE--.EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  63 eieevpv.kvrCreCgkefeleekalrCpkCgsad 96 
                                       +i +v++ +  C +Cgk +  e    +C +Cgs  
  gi|557694553|ref|YP_008797607.1| 626 SIVTVELvTRLCINCGKIGWRE----TCSECGSYT 656
                                       45555540456*****777654....7*****975 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0062
                                       EEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  71 vrCreCgkefeleekalrCpkCgsa 95 
                                         Cr+C+k+f++    ++C kCg+ 
  gi|557694553|ref|YP_008797607.1| 660 GVCRNCKKQFTEFV--EKCDKCGED 682
                                       68********9663..58****985 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00022
                                        EEEETTTS-EEECHHHHHS-TTTSSS.-EEEEES CS
                              HypA   70 kvrCreCgkefeleekalrCpkCgsa.dveivsG 102 
                                        ++rC++C+k+f+    + +Cp+C++  ++++ +G
  gi|557694553|ref|YP_008797607.1| 1045 SFRCKKCNKKFRRLPLTGKCPSCQTDlSLTVFRG 1078
                                        79*********96544679****98656666665 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   0.8      0.51   1.1e+03      27      34 ..     647     654 ..     636     658 .. 0.76
   2 ?    6.7   2.8    0.0035       7.8       8      36 ..     662     683 ..     659     684 .. 0.87
   3 ?   12.9   1.5   4.2e-05     0.093       6      35 ..    1046    1070 ..    1045    1072 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.51
                       Zn-ribbon_8  27 taCPeCgs 34 
                                       ++C eCgs
  gi|557694553|ref|YP_008797607.1| 647 ETCSECGS 654
                                       46888988 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0035
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgsev 36 
                                       C++C+++f++++       ++C +Cg++v
  gi|557694553|ref|YP_008797607.1| 662 CRNCKKQFTEFV-------EKCDKCGEDV 683
                                       ***********8.......35****9976 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 4.2e-05
                       Zn-ribbon_8    6 YrCeeCghefevlqsisdaplta.CPeCgse 35  
                                        +rC++C+++f +l       lt  CP+C+ +
  gi|557694553|ref|YP_008797607.1| 1046 FRCKKCNKKFRRLP------LTGkCPSCQTD 1070
                                        9**********885......7778****876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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):               8  [number of targets reported over threshold]
# CPU time: 0.87u 0.33s 00:00:01.20 Elapsed: 00:00:00.52
# Mc/sec: 6575.79
//
Query:       gi|557694554|ref|YP_008797608.1|  [L=88]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-07   31.3   0.5    1.8e-07   30.9   0.5    1.2  1  HTH_5         Bacterial regulatory protein, arsR family
    6.5e-05   23.2   0.1    0.00023   21.5   0.0    1.8  2  FaeA          FaeA-like protein
      8e-05   22.6   0.3    0.00012   22.1   0.3    1.2  1  HTH_20        Helix-turn-helix domain
    9.8e-05   21.8   0.1    0.00014   21.4   0.1    1.3  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.002   18.4   0.1     0.0024   18.2   0.1    1.2  1  Rrf2          Transcriptional regulator
     0.0028   17.4   0.1      0.004   16.9   0.1    1.2  1  HTH_IclR      IclR helix-turn-helix domain
     0.0037   16.9   0.1     0.0038   16.9   0.1    1.2  1  RP-C          Replication protein C N-terminal domain
  ------ inclusion threshold ------
      0.011   15.5   0.0      0.014   15.3   0.0    1.1  1  TFIIE_alpha   TFIIE alpha subunit
      0.031   13.9   0.1      0.052   13.2   0.1    1.4  1  Sigma70_r4_2  Sigma-70, region 4
      0.047   13.6   0.1      0.069   13.0   0.1    1.2  1  MarR_2        MarR family
      0.066   13.1   0.0       0.11   12.4   0.0    1.3  1  TrmB          Sugar-specific transcriptional regulator TrmB
      0.078   13.1   0.0      0.087   12.9   0.0    1.0  1  Sld3_N        Sld3 N-terminal domain
      0.081   13.0   0.1       0.13   12.3   0.1    1.4  1  HTH_9         RNA polymerase III subunit RPC82 helix-turn-hel
      0.086   12.9   0.1       0.14   12.3   0.1    1.4  1  MerR_1        MerR HTH family regulatory 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 !   30.9   0.5   1.4e-10   1.8e-07       2      46 ..      19      63 ..      19      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.4e-10
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +tR+kI+  L+ege+++ e+++++gl+   v+hHLk+L    +Ve
  gi|557694554|ref|YP_008797608.1| 19 ETRSKIITVLEEGECSAIEISRKTGLPLHVVRHHLKRLTHDKIVE 63
                                      69************************************8777776 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.3   1.6e+03      49      56 ..      13      20 ..       5      21 .. 0.66
   2 !   21.5   0.0   1.8e-07   0.00023       4      60 ..      23      75 ..      20      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.3
                                      --SSSSS- CS
                              FaeA 49 pvrrGvst 56
                                      +vr+G +t
  gi|557694554|ref|YP_008797608.1| 13 NVRKGLET 20
                                      67777665 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 1.8e-07
                                      HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE--SSSSS-EEEE CS
                              FaeA  4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspvrrGvstlWel 60
                                      +I++ l +  + c   ei   +gl    +R+ L+ L + + +++   +rGv+  W+l
  gi|557694554|ref|YP_008797608.1| 23 KIITVLEE--GECSAIEISRKTGLPLHVVRHHLKRLTHDKIVEKRGRGRGVR--WRL 75
                                      78999988..99**************************************97..665 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.3     9e-08   0.00012      11      61 .]      20      69 ..      19      69 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 9e-08
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvregr 61
                                      +R +i   L ++++ +a e+ +  +l+   +++HL+ L    +ve ++ gr
  gi|557694554|ref|YP_008797608.1| 20 TRSKIITVL-EEGECSAIEISRKTGLPLHVVRHHLKRLTHDKIVEKRGRGR 69
                                      899******.*************************************9987 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   0.1   1.1e-07   0.00014       4      47 ..      20      62 ..      18      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-07
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      t+ kI+ +L++ + +s  e+++++gl++  v+ +lkrL+ + ++
  gi|557694554|ref|YP_008797608.1| 20 TRSKIITVLEE-GECSAIEISRKTGLPLHVVRHHLKRLTHDKIV 62
                                      67788888888.**************************876666 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.9e-06    0.0024      21      66 ..      29      74 ..      12      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.9e-06
                                      STCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE.TTT-TCEE CS
                              Rrf2 21 eeeepvsseeiaerqnispsylekilakLrkaglvksv.rGkgGGyr 66
                                      ee+  +s+ ei+++++++ +++++ l++L++ ++v+ + rG+g  +r
  gi|557694554|ref|YP_008797608.1| 29 EEG-ECSAIEISRKTGLPLHVVRHHLKRLTHDKIVEKRgRGRGVRWR 74
                                      444.49*****************************965455555555 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 !   16.9   0.1   3.2e-06     0.004      17      51 ..      31      65 ..      26      66 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.2e-06
                                      SS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR 17 qeltlselArrtglpkStvhRlLqtLvelGyveqd 51
                                      +e +  e++r+tglp   v+++L+ L++ ++ve+ 
  gi|557694554|ref|YP_008797608.1| 31 GECSAIEISRKTGLPLHVVRHHLKRLTHDKIVEKR 65
                                      567889**************************986 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 !   16.9   0.1     3e-06    0.0038      73     126 ..      34      88 .]       9      88 .] 0.95

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3e-06
                              RP-C  73 sNaqLsralglsestlrrhlaaLveaGliirrDspngkRyarrdre.GeieeAfG 126
                                       s+ ++sr++gl+   +r+hl++L +  ++  r    g R++  + +  +ieeA+G
  gi|557694554|ref|YP_008797608.1|  34 SAIEISRKTGLPLHVVRHHLKRLTHDKIVEKRGRGRGVRWRLTGAGqASIEEAVG 88 
                                       78899************************************9999889*****98 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.0   1.1e-05     0.014      15      60 ..      21      65 ..       9      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE CS
                       TFIIE_alpha 15 avlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkyk 60
                                        +++ vL  +ge +  ++++++++ l+++r+ L rL  +++v+ +
  gi|557694554|ref|YP_008797608.1| 21 RSKIITVLE-EGECSAIEISRKTGLPLHVVRHHLKRLTHDKIVEKR 65
                                      456777765.9*******************************9854 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 ?   13.2   0.1   4.1e-05     0.052      13      49 ..      19      55 ..      18      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.1e-05
                                      HHHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 13 erqreifllryleglsykEIAellgisegtVksrlsR 49
                                      e +++i++  ++ ++s  EI++++g++   V+++l+R
  gi|557694554|ref|YP_008797608.1| 19 ETRSKIITVLEEGECSAIEISRKTGLPLHVVRHHLKR 55
                                      6789999999*************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.4e-05     0.069      17      54 ..      30      65 ..      20      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.4e-05
                                      TTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 17 rpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +++  +++ e+ r++gl+ + v  +lkrL     ve+r
  gi|557694554|ref|YP_008797608.1| 30 EGE--CSAIEISRKTGLPLHVVRHHLKRLTHDKIVEKR 65
                                      333..89*****************************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 ?   12.4   0.0   8.3e-05      0.11      16      55 ..      26      65 ..      24      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.3e-05
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      ++l++g+ +a ei++++g+p   v   L++L    +Ve++
  gi|557694554|ref|YP_008797608.1| 26 TVLEEGECSAIEISRKTGLPLHVVRHHLKRLTHDKIVEKR 65
                                      789*****************************99999987 PP

>> Sld3_N  Sld3 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.8e-05     0.087       2      78 ..       7      83 ..       6      87 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.8e-05
                                      EEEEESS--TT--B-STT-EEEEGGGST.TTTS-STTTS-TT-EEEEE.-SS-EEEEEE-STTEEEEEEBSS--TTT- CS
                            Sld3_N  2 lvgsvkelpkslilsldspklleseelp.kevlselenspislKHllkdaddkyflLErYgkeywvlWevvsvdvtel 78
                                      +++svk+++k+l+ +++  ++le+ e +  e+ ++ +    +++H lk  + +  ++E+ g +  v+W+++    +++
  gi|557694554|ref|YP_008797608.1|  7 YLTSVKNVRKGLETRSKIITVLEEGECSaIEISRKTGLPLHVVRHHLKRLT-HDKIVEKRGRGRGVRWRLTGAGQASI 83
                                      799*********************999879*****************9744.44578***********9976655555 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 ?   12.3   0.1    0.0001      0.13      21      57 ..      26      62 ..      19      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
                                      HHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9 21 tLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                      t l++g  ++ e+++kt+L+l  V++ L  L++  +V
  gi|557694554|ref|YP_008797608.1| 26 TVLEEGECSAIEISRKTGLPLHVVRHHLKRLTHDKIV 62
                                      44699999********************999987777 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 ?   12.3   0.1   0.00011      0.14       5      34 ..      37      70 ..      33      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
                                      HHHHHHTS-HHHHHHHHHHTT...-S-EE.-TTS CS
                            MerR_1  5 evakilgvtthtlrywekegl...lkpkr.tegg 34
                                      e ++++g++ h++r++ k+     ++ kr +++g
  gi|557694554|ref|YP_008797608.1| 37 EISRKTGLPLHVVRHHLKRLThdkIVEKRgRGRG 70
                                      89*****************986667777755554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 637.57
//
Query:       gi|557694555|ref|YP_008797609.1|  [L=56]
Description: preprotein translocase subunit Sec61beta [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   58.4   0.2    5.7e-16   58.3   0.2    1.0  1  Sec61_beta     Sec61beta family
  ------ inclusion threshold ------
       0.15   11.3   0.0       0.17   11.2   0.0    1.0  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,


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 !   58.3   0.2   6.3e-20   5.7e-16       1      41 []      14      54 ..      14      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 6.3e-20
                                      XXXXXXXXXX----SS-B-THHHHHHHHHHHHHHHHHTSS- CS
                        Sec61_beta  1 SsaGLlryyeedapgikidPkvVlvlsvafiasVilLhila 41
                                      ++aGLlr++e++++g+k+ P++Vl++s+a+i++V++L++l+
  gi|557694555|ref|YP_008797609.1| 14 TAAGLLRFFEDESTGVKVRPEIVLGASAALIVAVLILRALF 54
                                      69***********************************9985 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 ?   11.2   0.0   1.9e-05      0.17      11      48 ..       6      43 ..       2      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.9e-05
                                      T--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTT CS
                     THF_DHG_CYH_C 11 geeallpctpkgvvellketgielegkkvvvvGrsniv 48
                                      ++ea +p+t++g +++ +++++ ++ +  +v+G+s  +
  gi|557694555|ref|YP_008797609.1|  6 RREAPMPATAAGLLRFFEDESTGVKVRPEIVLGASAAL 43
                                      57899*****************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 430.85
//
Query:       gi|557694556|ref|YP_008797610.1|  [L=318]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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    5.5e-05   23.0   0.0    1.7  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    3.3e-05   23.4   0.0    5.9e-05   22.6   0.0    1.4  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
     0.0087   15.6   0.6       0.14   11.7   0.7    2.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.078   13.0   2.6        2.7    7.9   2.5    2.4  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> 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 !   23.0   0.0   1.2e-08   5.5e-05      13      39 ..     272     298 ..     268     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.2e-08
                             RMMBL  13 fSgHadknellelirklkprnvilvHG 39 
                                       +S Had+++ll++++  +pr+v+ +HG
  gi|557694556|ref|YP_008797610.1| 272 LSSHADYRGLLNYVEENRPRKVYTIHG 298
                                       79************************9 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 !   22.6   0.0   1.3e-08   5.9e-05     112     164 ..      66     115 ..      19     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.3e-08
                     Lactamase_B_6 112 kiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskesekivYavdwnh 164
                                         k++ Y Q + l+   d +++ a+n+Gh+lG +++++  + e++vY  d+n 
  gi|557694556|ref|YP_008797610.1|  66 GYKPIPYRQDIGLS---DSVSVRALNSGHVLGSAMFRLDIGGESLVYTGDINT 115
                                       47899999999998...58********************************96 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 !   11.7   0.7     3e-05      0.14      35     171 ..      32     143 ..      30     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3e-05
                                       E-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE- CS
                     Lactamase_B_2  35 llthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeepavnvheldwgesfelgdggleitatpar 111
                                       +++haH DH+a      ++r    +++a++++++ +++  +            +++   + + l d  ++++a    
  gi|557694556|ref|YP_008797610.1|  32 FVSHAHSDHVA------AGR----NILATRETISLIRRVWQLSGG-------YKPIPYRQDIGLSD-SVSVRALNSG 90 
                                       6899*****93......332....377788888888888544333.......45688888888876.3455665555 PP

                                       EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT..-SEEEEE-S-SSTTH CS
                     Lactamase_B_2 112 hksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlgg..adllllditayedde 171
                                       h  g          + +r++ gg++++y+gD ++++    +  ++  ad+ +++ t+ ++d+
  gi|557694556|ref|YP_008797610.1|  91 HVLGS---------AMFRLDIGGESLVYTGDINTVQTLTTNPAEPvdADVFIIETTYGHPDY 143
                                       55555.........89999999*************977665555555999999999888876 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   2.5   0.00061       2.7      49     151 ..      32     113 ..      32     132 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00061
                                       E-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEH CS
                       Lactamase_B  49 ilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyv 125
                                       +++H+H+DH+++ + +  ++   + + + +  ++ +                        +   + g  +++     
  gi|557694556|ref|YP_008797610.1|  32 FVSHAHSDHVAAGRNILATRETISLIRRVWQLSGGYKPI---------------------PYRQDIGLSDSVSVRAL 87 
                                       589*******99999999998888888888887777776.....................55566666666666667 PP

                                       ECTTSTSCCEEEEEETTCCEEEECTT CS
                       Lactamase_B 126 tggpghghghgvveygggkvlftGDa 151
                                         g++ g+  +++++gg+++++tGD 
  gi|557694556|ref|YP_008797610.1|  88 NSGHVLGSAMFRLDIGGESLVYTGDI 113
                                       78888888888888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); 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:                         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 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2383.02
//
Query:       gi|557694557|ref|YP_008797611.1|  [L=585]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-111  373.1   0.9   2.2e-111  372.9   0.9    1.0  1  DUF2070    Predicted membrane protein (DUF2070)
  ------ inclusion threshold ------
      0.032   15.1   0.0      0.089   13.7   0.0    1.7  2  DHC        Dihaem cytochrome c
       0.26   11.6   3.2       0.66   10.3   0.5    2.9  3  ASFV_L11L  African swine fever virus (ASFV) L11L protein
          7    5.4  12.1       0.54    9.0   0.1    2.6  2  DUF4781    Domain of unknown function (DUF4781)


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 !  372.9   0.9    5e-115  2.2e-111       4     562 ..      12     575 ..       9     578 .. 0.86

  Alignments for each domain:
  == domain 1  score: 372.9 bits;  conditional E-value: 5e-115
                           DUF2070   4 lskyifr..lPswk.vsllliillalligllaflssklfgillfglpalvaflltlpvlrilggr....ltykrslf 73 
                                        +++i      +++  +ll+++ l+ +i +l++    +    +++  +l +++l+++v+ ++ g+    +t++r   
  gi|557694557|ref|YP_008797611.1|  12 RYRLIRGfyGGAVSlEALLVMASLSTVIIYLYSAD--VLVAAAVFAAFLGSTALLNRVVAFFLGIkcpsYTSRRLDS 86 
                                       56666663333334455666666666666655444..67888888999************999999**99******* PP

                           DUF2070  74 lalltelivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly.. 148
                                       l+++ + +v++ ++l++ll ++     l a v+ la+++a ++++ ++v ++     +  + i+plla+ll+++   
  gi|557694557|ref|YP_008797611.1|  87 LSVVETGVVFAGIMLSALLRWFS----LAAAVVVLAASAATSVFLSYSVRRA-----I-GYRIHPLLAALLSTPPml 153
                                       ***********999999999755....2222333333333333333333322.....2.444445555555555555 PP

                           DUF2070 149 ..........fspesfllllllslifalavylfivvvdrplkrnlgvsaldllsaFlahileg.skelEeffeeige 214
                                                  +++++l++ ++s++++++++ +++ +    k++ g+++++ll+aFla++l+g s+elEe++ ++g+
  gi|557694557|ref|YP_008797611.1| 154 lntltlqaflGNWAKALQISFTSFLVGVVSLEIVRHLIDLSKPIQGIRPFRLLQAFLASLLSGySRELEELMMRLGN 230
                                       555557777999***************************************************************** PP

                           DUF2070 215 eadvpvkvlsfrredgekallvvPniHPGPlgeiGGsnLpkilaerldel...vlvlHgtatHdfNlvserevekiv 288
                                       e++v ++++++rr ++ +++lvv++iHPGP++ +G+s++p ila++l e+    lvl+g ++H+ Nl++ + +ek++
  gi|557694557|ref|YP_008797611.1| 231 EDRVGCELFVLRRVGKPSVALVVSDIHPGPFRAVGSSMFPAILANKLAEKgfqPLVLKGLSSHEKNLANIELSEKVA 307
                                       **************************************************999************************ PP

                           DUF2070 289 eavkealeele....ysskaskpvrvesgdvkllgqrfgdslllvitrapegiDDiplsvglsimaeakaegfedvl 361
                                       e+++e++e+le    y s+a  p+r+  + v+ l++ + d+ ++v+t +p++++D+p +v          +++++ +
  gi|557694557|ref|YP_008797611.1| 308 EKIAEEAEWLEkngaYFSEARSPWRTIFNGVSSLSLNIADREVVVLTLNPQPMEDLPPEV-------LPPNHTGRKI 377
                                       ************************************************************.......333457899* PP

                           DUF2070 362 lVDaHNsfseeagevlpgsedaeeliraaekalekleaaeeselkvgvarsetpkltpeeglGdlgiqvlvlevdgq 438
                                       +VD+HNsfs++ ++    + ++e++++ + + +e  ++ + s+++vg+ar+ +++++p++g+G +g++++++ev+g 
  gi|557694557|ref|YP_008797611.1| 378 VVDSHNSFSDNLKNL--DNATIEKIRTFLTNSSE-HKPLPLSRMRVGYARTVPSDVGPSDGIGAGGVSCILFEVNGV 451
                                       ***********9994..59999999999999988.5***************************************** PP

                           DUF2070 439 ktayvliDgNNmepglreeirealke.vdlevevmTTDtHvvngvsl...gynpvGekvskdelielvlelvekAia 511
                                       k+ +v++D+NN  p++r  +++ ++e ++++ e++TTDtH+vn+vsl   gy+p+Ge++s+++l+ l++el ++A++
  gi|557694557|ref|YP_008797611.1| 452 KSSLVVADANNAMPWVRGVLQQVAREnGCVDTELCTTDTHMVNAVSLggrGYHPLGEAISTERLKTLFDELHKRAAS 528
                                       *************************99999*********************************************** PP

                           DUF2070 512 dlepvevgyaterve.vkvfgedrfeelvstvnsvvsvakilaaallllail 562
                                       dl++++++ +++++e vkvf +     ++++v+++vs++++ + ++ l+a l
  gi|557694557|ref|YP_008797611.1| 529 DLADADAAHKSVTLEnVKVFSD-----FLDVVSQAVSFGVRAYRVAALVAPL 575
                                       *******************655.....6777777777777666666665554 PP

>> DHC  Dihaem cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0         4   1.8e+04      39      54 ..     302     320 ..     284     338 .. 0.53
   2 ?   13.7   0.0     2e-05     0.089      12      59 ..     363     412 ..     362     433 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 4
                                       --HHHHHHHH...HHHHHT CS
                               DHC  39 ldeatkkeis...eyLean 54 
                                       l+e+ +++i    e+Le+n
  gi|557694557|ref|YP_008797611.1| 302 LSEKVAEKIAeeaEWLEKN 320
                                       3333333332111344444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2e-05
                                       --GGGS-.HHHHHHHHCGGGGBTTB---.--HHHHHHHHHHHHHTSTTTT CS
                               DHC  12 yppelLp.aasWkklladledHfGedas.ldeatkkeiseyLeanaaeks 59 
                                       +ppe+Lp +++ +k++ d+++ f ++++ ld+at ++i+++L++++ +k 
  gi|557694557|ref|YP_008797611.1| 363 LPPEVLPpNHTGRKIVVDSHNSFSDNLKnLDNATIEKIRTFLTNSSEHKP 412
                                       689999736789***************99**************9998775 PP

>> ASFV_L11L  African swine fever virus (ASFV) L11L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.5   0.00015      0.66       2      37 ..      26      59 ..      25      72 .. 0.72
   2 ?   -1.0   0.0      0.51   2.3e+03      49      70 ..     150     166 ..     142     173 .. 0.72
   3 ?   -1.4   0.0      0.69   3.1e+03      36      49 ..     234     247 ..     196     254 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                         ASFV_L11L  2 lepllvmapiplvliflysyfkiklhklitialflg 37
                                      le llvma +  v+i+lys     l      a flg
  gi|557694557|ref|YP_008797611.1| 26 LEALLVMASLSTVIIYLYSADV--LVAAAVFAAFLG 59
                                      89****************9643..333344455555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.51
                         ASFV_L11L  49 ppmlwtilqnitltlntilgnk 70 
                                       ppml +     tltl+++lgn 
  gi|557694557|ref|YP_008797611.1| 150 PPMLLN-----TLTLQAFLGNW 166
                                       666543.....67888999985 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.69
                         ASFV_L11L  36 lgclffilrdfcfp 49 
                                       +gc +f+lr    p
  gi|557694557|ref|YP_008797611.1| 234 VGCELFVLRRVGKP 247
                                       69999999987665 PP

>> DUF4781  Domain of unknown function (DUF4781)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   4.3     0.034   1.5e+02      88     138 ..      85     135 ..      74     140 .. 0.64
   2 ?    9.0   0.1   0.00012      0.54     135     174 ..     524     563 ..     523     579 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.034
                           DUF4781  88 nvlDvvstvvglvaavpvgaaalatP.vaapvllaalvvgvgsavYstgRsi 138
                                       + l vv t v + a++ ++a +  +   aa+v+laa +++ +  +Ys+ R+i
  gi|557694557|ref|YP_008797611.1|  85 DSLSVVETGV-VFAGIMLSALLRWFSlAAAVVVLAASAATSVFLSYSVRRAI 135
                                       5555555555.44566665555444424667778888888888889988887 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00012
                           DUF4781 135 gRsiqrLvDrstHeesisltdrearnswLgvaagvvglga 174
                                        R+++ L+D +  ++s+ l++ + ++++L v++ +v++g 
  gi|557694557|ref|YP_008797611.1| 524 KRAASDLADADAAHKSVTLENVKVFSDFLDVVSQAVSFGV 563
                                       69**********************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.39
# Mc/sec: 4482.42
//
Query:       gi|557694558|ref|YP_008797612.1|  [L=88]
Description: hypothetical protein CSUB_C1130 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-10   41.2   0.4      2e-10   40.8   0.4    1.2  1  PqqD            Coenzyme PQQ synthesis protein D (PqqD)
  ------ inclusion threshold ------
      0.083   13.1   0.0      0.092   12.9   0.0    1.1  1  VP4_haemagglut  Outer Capsid protein VP4 (Hemagglutinin) Conc
      0.085   13.1   0.1       0.14   12.4   0.1    1.5  1  PRODH           Proline utilization A proline dehydrogenase N


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 !   40.8   0.4   3.4e-14     2e-10       6      67 .]      27      87 ..      20      87 .. 0.92

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 3.4e-14
                                      -SS-..EEE--CHHHHHHHH-SSSS-HHHHHHHHHHHCT--HHHHHHHHHHHHHHHHCTT-- CS
                              PqqD  6 dpetgkyisLnetgafiWklldgersveeivaalaeeydvdeeeaeadvlafldqLrekgli 67
                                        e+g  ++ ne   ++W++ ++ ++v+++v ++ae+ + d++e++++++++ ++L+e+gli
  gi|557694558|ref|YP_008797612.1| 27 VNENGDAYKVNEAVVAVWNMFED-KTVSDVVGEVAEQVNRDPAELKEAIEQLAAKLVEAGLI 87
                                      44667888***************.**************9999*******************8 PP

>> VP4_haemagglut  Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain
   #    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      68 ..      13      61 ..       5      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                                      SEEEEEE..SSEEEEEECTECCEECCCEECCEEEEECCEEEE.SCCCCSS CS
                    VP4_haemagglut 19 drwllyqkplnavillkhnvdsenstlaifelwygkeqltvssvyyntin 68
                                      + wl  q p     l+++n d++  + a+  +w   e+ tvs v  +  +
  gi|557694558|ref|YP_008797612.1| 13 KGWL-SQTPEGDLLLVNENGDAYKVNEAVVAVWNMFEDKTVSDVVGEVAE 61
                                      5698.9************************************98766555 PP

>> PRODH  Proline utilization A proline dehydrogenase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.3e-05      0.14      29      46 ..      67      84 ..      53      84 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                             PRODH 29 peaeraairalArkLvea 46
                                      p+++++ai +lA+kLvea
  gi|557694558|ref|YP_008797612.1| 67 PAELKEAIEQLAAKLVEA 84
                                      8999************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      753  (0.041999); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 731.24
//
Query:       gi|557694559|ref|YP_008797613.1|  [L=94]
Description: archaea-specific DNA-binding protein AlbA [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   0.5    1.9e-08   34.0   0.1    1.4  2  Alba      Alba


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 !   34.0   0.1     1e-12   1.9e-08       5      58 ..      13      63 ..      10      70 .. 0.87
   2 ?   -2.1   0.1      0.19   3.4e+03       5      19 ..      77      91 ..      73      93 .. 0.66

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1e-12
                                      E-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.E CS
                              Alba  5 VsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkgly 58
                                      V++ +p+  yv + + l+ n + +eV l+a+G++I   v+++e l++ f ++  
  gi|557694559|ref|YP_008797613.1| 13 VGK-KPVFRYVTASIVLF-NRGSKEVELVARGKNIPLCVDTVELLRKSF-HQDL 63
                                      555.**************.****************************99.4335 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.19
                                      E-STS-HHHHHHHHH CS
                              Alba  5 Vsskspimsyvkral 19
                                      V  k++  sy+k ++
  gi|557694559|ref|YP_008797613.1| 77 VNGKTRRISYMKIVV 91
                                      666777777877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 732.72
//
Query:       gi|557694560|ref|YP_008797614.1|  [L=406]
Description: acyl-CoA dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  118.1   1.8    5.6e-34  117.5   1.8    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    7.2e-28   97.5   0.1    1.7e-27   96.3   0.1    1.7  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    6.1e-16   58.9   0.1    1.1e-15   58.1   0.1    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    1.2e-10   41.5   0.0      2e-10   40.7   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle 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 !  117.5   1.8   1.3e-37   5.6e-34       1     149 [.     242     399 ..     242     400 .. 0.97

  Alignments for each domain:
  == domain 1  score: 117.5 bits;  conditional E-value: 1.3e-37
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       + Gf++ame++n  R +++a ++g+a+  +e+a+e++r+rk fgkp++++q v++k+ae+a  leaa+ll y+aa+ 
  gi|557694560|ref|YP_008797614.1| 242 NGGFKIAMEGFNLARTMIGAVCVGCAEWLMERAVEWVRTRKVFGKPIAAYQGVSFKIAEFASALEAAKLLSYKAAWI 318
                                       78*************************************************************************** PP

                                       -------........HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSS.S-HHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpd........raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrige.Gtseiqrnii 145
                                       +d+   d         +  +maKl+++ la+++ ++ m+++Gga+y +e+p+ r++ +a ++ +g+ G+++i+++i+
  gi|557694560|ref|YP_008797614.1| 319 ADRYYRDgvgtlgdvAKLGAMAKLRCASLAVDIGEEVMKIYGGASYFKETPIFRAWLAAFSYVVGAeGAENILKLIV 395
                                       **999999999**9999**********************************9999999999999877********** PP

                                       HHHH CS
                     Acyl-CoA_dh_1 146 arrl 149
                                       ar +
  gi|557694560|ref|YP_008797614.1| 396 AREV 399
                                       *986 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 !   96.3   0.1   3.9e-31   1.7e-27       2     113 .]       7     119 ..       6     119 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 3.9e-31
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                        eq+ lrd+v ef+++ ++p+  e+d++ge++re+++k+ae Gl+g+t+  eygG+++++leaa++ae+la+++ +l
  gi|557694560|ref|YP_008797614.1|   7 SEQQLLRDKVSEFCKRVIEPKWIEVDDKGEIDREIIEKMAEVGLMGMTISSEYGGQDGSFLEAALAAEQLAYHGPAL 83 
                                       79*************************************************************************99 PP

                                       HH.HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  79 al.llgvhsslvapailrfGteeqkrryLpklasge 113
                                       ++ ++ + ++   ++i r+G+ee k++ Lp++a+g+
  gi|557694560|ref|YP_008797614.1|  84 SIaVMYLLQCSWPYIIQRYGSEEAKQEVLPRVAAGD 119
                                       995444433333389******************996 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 !   58.1   0.1   2.5e-19   1.1e-15       2     120 ..     258     374 ..     257     376 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 2.5e-19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       +i+av++G A+  ++ +ve++r+r+   +g+++a  + + +++ae a++l+AA++l ++aa+ a +  ++g     +
  gi|557694560|ref|YP_008797614.1| 258 MIGAVCVGCAEWLMERAVEWVRTRKV--FGKPIAAYQGVSFKIAEFASALEAAKLLSYKAAWIADRYYRDGVGTLGD 332
                                       799***********************..***********************************99999999887777 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHH CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlw 120
                                         + +++a+++ ++la+++ ++++++ Gg +++ke p+ R+w
  gi|557694560|ref|YP_008797614.1| 333 VAKLGAMAKLRCASLAVDIGEEVMKIYGGASYFKETPIFRAW 374
                                       77889***********************************99 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 !   40.7   0.0   4.5e-14     2e-10       1      97 []     123     230 ..     123     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 4.5e-14
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEE......EEEEETS---.----EEEEEEE..G CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatla......lvlartekpd.rarglslflvprda 70 
                                       ++a+TE  +Gsdv sv+ +a ++ +g++ ++GeK +++     + +      +++ar+++p  ++r+++ fl+  ++
  gi|557694560|ref|YP_008797614.1| 123 GIASTEAHGGSDVSSVQVRAERKGDGKWLISGEKSMVSLPSVIERMpwgggwFLIARSGDPGlKHRTITDFLLLMKR 199
                                       5899**************996666669**********998885555577777*****8888899*****99877544 PP

                                       G.....GEEE-----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  71 p.....gvsvrrieeklGlrglptgelvfedv 97 
                                       +     g+s +++ ++ ++rgl+t+ l+f++v
  gi|557694560|ref|YP_008797614.1| 200 NgvltkGISYKPW-TEFARRGLDTSVLTFQNV 230
                                       4457779999998.78*************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); 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:                         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 0.20s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 3293.47
//
Query:       gi|557694561|ref|YP_008797615.1|  [L=273]
Description: NAD+ synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-73  246.6   0.0    2.2e-73  246.4   0.0    1.0  1  NAD_synthase   NAD synthase
    8.8e-07   28.0   0.0    0.00016   20.6   0.0    2.3  2  tRNA_Me_trans  tRNA methyl transferase
    2.1e-05   24.3   0.0      3e-05   23.9   0.0    1.3  1  Asn_synthase   Asparagine synthase
  ------ inclusion threshold ------
      0.029   13.9   0.0      0.054   13.0   0.0    1.5  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 !  246.4   0.0   4.8e-77   2.2e-73       3     242 .]      19     262 ..      17     262 .. 0.97

  Alignments for each domain:
  == domain 1  score: 246.4 bits;  conditional E-value: 4.8e-77
                                       HHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE- CS
                      NAD_synthase   3 eelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievkti 79 
                                       +++++f+ e ++ +ga+g+vlGlSGGvDSs+vaal+ +a+  e++l+l++P+ +++ +dv da+alae+lgi + +i
  gi|557694561|ref|YP_008797615.1|  19 SAIQNFIAERLRLSGASGLVLGLSGGVDSSVVAALCARAVPGEKILGLIMPTGFTPAQDVADAQALAEKLGISTRHI 95 
                                       5789************************************************************************* PP

                                       --HHHHHHHHH....HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTT CS
                      NAD_synthase  80 dikpivrafeq....elkeakedlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapia 152
                                       +i+piv+ + +     ++e+   +a +Nl+aRiRm++ly +an +n+lv+gTg++sE+++Gy TkyGDg++d++pi+
  gi|557694561|ref|YP_008797615.1|  96 PIDPIVQRYAEqlgvGMDETGARMAYANLRARIRMTLLYFHANLQNMLVVGTGDRSEILLGYYTKYGDGGVDILPIG 172
                                       *********9956655667779******************************************************* PP

                                       TS-HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHT.HSSSS...HHHHHTTT--HHHHHHH CS
                      NAD_synthase 153 ellKtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLk.lvekkkspeeiikekelpaevveki 228
                                       +l+K++v++L  +l+ Pe++ +kp s +L pg    +eL+  Y++lD iL  l++kk sp+++++ k+++++vv ++
  gi|557694561|ref|YP_008797615.1| 173 GLYKSQVRRLGLALGLPEQLANKPSSPQLYPGHRAVDELPADYSILDPILYlLFDKKLSPQQVVD-KGFDKRVVDAV 248
                                       ***************************************************99*********999.*********** PP

                                       HHHHHHTGGGGSSS CS
                      NAD_synthase 229 eklvkksehKrklp 242
                                         ++  s hKr++p
  gi|557694561|ref|YP_008797615.1| 249 LARYVGSVHKREMP 262
                                       ************98 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.6e-08   0.00016       4      68 ..      38      95 ..      35     108 .. 0.81
   2 !    5.2   0.0    0.0018       7.9     165     194 ..     168     199 ..     166     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.6e-08
                     tRNA_Me_trans  4 vvalSgGVDSsvaaallkeq..gyevigvflklweeedeegkeccaeedlkdaervaeklgiplevv 68
                                      v +lSgGVDSsv+aal +++  g ++ g+++ +           +  +d++da++ aeklgi+++ +
  gi|557694561|ref|YP_008797615.1| 38 VLGLSGGVDSSVVAALCARAvpGEKILGLIMPTGF---------TPAQDVADAQALAEKLGISTRHI 95
                                      789*************9997335788888886543.........4568**************98876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0018
                     tRNA_Me_trans 165 lfPlgeltKeevrkiAkeagla..vaekkdSq 194
                                       ++P+g l K++vr++  + gl+  +a+k+ S 
  gi|557694561|ref|YP_008797615.1| 168 ILPIGGLYKSQVRRLGLALGLPeqLANKPSSP 199
                                       69******************988789999885 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   6.7e-09     3e-05      21      79 ..      38      97 ..      18     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.7e-09
                      Asn_synthase 21 GalLSGGlDSSliaalaarqsk.splk..tFsigfeekgsdeakyakevaehlgtehtelvl 79
                                       + LSGG+DSS++aal ar  + +++       gf     ++++ a+++ae+lg+  +++ +
  gi|557694561|ref|YP_008797615.1| 38 VLGLSGGVDSSVVAALCARAVPgEKILglIMPTGF--TPAQDVADAQALAEKLGISTRHIPI 97
                                      4559*****************98333311345688..999**************99777665 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.2e-05     0.054       3      62 ..      38      98 ..      36     131 .. 0.86
   2 ?   -3.7   0.0       1.5   6.8e+03     157     177 ..     170     190 ..     168     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.2e-05
                                      EEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-G CS
                              QueC  3 vvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildld 62
                                      v+ lSGG+DS++v+al  +++  +++  l +  g   ++++  a+++a++lg+ +++++ +d
  gi|557694561|ref|YP_008797615.1| 38 VLGLSGGVDSSVVAALCARAVpgEKILGLIMPTGFTPAQDVADAQALAEKLGI-STRHIPID 98
                                      6779*********999988754499****************************.55555555 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.5
                                       TTTT--HHHHHHHHHHTTHHH CS
                              QueC 157 PlidlsKaeivklgkelgvpl 177
                                       P+  l K+++ +lg  lg+p 
  gi|557694561|ref|YP_008797615.1| 170 PIGGLYKSQVRRLGLALGLPE 190
                                       888899999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2138.71
//
Query:       gi|557694562|ref|YP_008797616.1|  [L=373]
Description: hypothetical protein CSUB_C1134 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   26.0  30.5    8.7e-05   22.0  13.2    2.2  2  GAS              Growth-arrest specific micro-tubule binding
    3.1e-05   23.0  19.2     0.0093   14.9   2.8    2.1  2  Spc7             Spc7 kinetochore protein
    3.4e-05   24.3  13.7     0.0023   18.4   1.7    2.6  2  Spectrin         Spectrin repeat
    8.4e-05   20.9  18.0    0.00023   19.5  18.0    1.5  1  EzrA             Septation ring formation regulator, EzrA
    9.6e-05   22.1  23.0      0.038   13.7   3.0    4.6  4  DivIC            Septum formation initiator
     0.0001   22.4  21.9      0.023   14.7   9.3    2.5  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
    0.00011   22.0  12.7    0.00011   22.0  12.7    2.3  2  DUF4201          Domain of unknown function (DUF4201)
    0.00011   22.8  22.3      0.001   19.6  11.6    2.3  2  APG6_N           Apg6 coiled-coil region
    0.00011   22.4  18.3      0.012   15.9   3.3    3.5  3  BLOC1_2          Biogenesis of lysosome-related organelles co
    0.00012   21.2  11.8    0.00016   20.7  11.8    1.1  1  DUF812           Protein of unknown function (DUF812)
    0.00013   21.4  19.0      0.024   13.9  10.4    2.2  2  DUF3450          Protein of unknown function (DUF3450)
    0.00019   21.6  10.7    0.00019   21.6  10.7    1.9  2  Tropomyosin_1    Tropomyosin like
    0.00026   19.3  13.6     0.0004   18.8  12.9    1.6  1  FPP              Filament-like plant protein, long coiled-coi
     0.0005   20.0  15.0      0.071   13.0   6.2    2.9  2  Sec34            Sec34-like family
    0.00053   20.4  23.4       0.08   13.4   6.0    3.5  3  ZapB             Cell division protein ZapB
    0.00061   19.8  17.4       0.14   12.2   8.6    2.9  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    0.00067   19.8  21.2      0.021   14.9  10.3    2.4  2  ADIP             Afadin- and alpha -actinin-Binding
    0.00085   19.5  19.9      0.014   15.6   8.2    2.3  2  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
    0.00087   18.9  15.3      0.049   13.2   5.8    2.1  2  PspA_IM30        PspA/IM30 family
    0.00087   17.9   2.6     0.0011   17.5   2.6    1.2  1  S6OS1            Six6 opposite strand transcript 1 family
     0.0013   18.9  15.2      0.094   12.9   6.4    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
     0.0019   18.4  18.2     0.0075   16.5  12.3    2.3  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
     0.0021   17.9  12.3      0.018   14.8   8.2    2.1  2  TACC_C           Transforming acidic coiled-coil-containing p
     0.0028   16.0  12.3       0.32    9.1   6.7    2.5  2  COG6             Conserved oligomeric complex COG6
     0.0031   17.4  19.7       0.44   10.5   0.9    4.2  4  Prefoldin_2      Prefoldin subunit
     0.0035   16.4  18.6        0.1   11.6   3.0    2.2  2  IFT57            Intra-flagellar transport protein 57
     0.0043   16.2  13.9     0.0064   15.6  13.9    1.2  1  Atg14            Vacuolar sorting 38 and autophagy-related su
     0.0078   13.8  14.1       0.01   13.4  14.1    1.1  1  DUF3584          Protein of unknown function (DUF3584)
      0.009   16.3   2.6      0.009   16.3   2.6    3.3  2  DUF948           Bacterial protein of unknown function (DUF94
     0.0099   16.3  13.9      0.062   13.8  13.9    1.9  1  Fez1             Fez1
  ------ inclusion threshold ------
       0.01   14.5  12.6      0.036   12.7   4.5    2.1  2  FapA             Flagellar Assembly Protein A
      0.011   15.8  15.4        1.8    8.7   0.8    4.2  4  bZIP_1           bZIP transcription factor
      0.014   15.0  20.8       0.05   13.2   9.4    2.3  2  Filament         Intermediate filament protein
      0.014   16.1  13.1       0.43   11.3   5.6    3.2  3  Occludin_ELL     Occludin homology domain
      0.015   15.4  11.6        0.2   11.8  11.6    2.3  1  Spore_III_AB     Stage III sporulation protein AB (spore_III_
      0.016   14.9  20.6       0.13   11.9   7.1    2.2  2  SHE3             SWI5-dependent HO expression protein 3
      0.016   14.6  16.7      0.094   12.1   1.2    3.1  3  DUF4618          Domain of unknown function (DUF4618)
      0.018   14.9   6.0      0.035   13.9   1.4    2.4  2  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
      0.018   13.8   0.1      0.018   13.8   0.1    2.1  2  Rabaptin         Rabaptin
      0.019   15.2  23.1      0.072   13.3  15.9    2.4  1  ATG16            Autophagy protein 16 (ATG16)
      0.019   15.0  15.2       0.23   11.5   6.9    3.0  3  BRE1             BRE1 E3 ubiquitin ligase
      0.021   13.8   4.2      0.031   13.2   4.2    1.3  1  LMBR1            LMBR1-like membrane protein
      0.022   14.4  12.5       0.99    9.0   0.9    3.0  3  DUF4795          Domain of unknown function (DUF4795)
      0.032   14.3  21.6       0.23   11.5   6.4    2.7  2  Mod_r            Modifier of rudimentary (Mod(r)) protein
      0.038   14.3  15.8      0.047   14.0   7.6    2.3  2  OmpH             Outer membrane protein (OmpH-like)
       0.04   13.9  17.0       0.51   10.4   8.0    3.6  2  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
      0.045   13.5   6.6      0.074   12.8   6.6    1.3  1  Borrelia_lipo_1  Borrelia burgdorferi virulent strain associa
      0.045   13.1  13.7       0.37   10.1  12.6    2.6  1  DUF4407          Domain of unknown function (DUF4407)
      0.046   13.5  15.9       0.58   10.0   2.6    3.5  4  SKA2             Spindle and kinetochore-associated protein 2
      0.048   14.1   3.6        1.2    9.6   1.3    2.8  3  T3SSipB          Type III cell invasion protein SipB
       0.05   14.2   1.9       0.05   14.2   1.9    3.0  2  BST2             Bone marrow stromal antigen 2
       0.05   14.3  13.4       0.13   13.0   7.1    2.7  2  DUF4472          Domain of unknown function (DUF4472)
      0.053   13.1  19.7       0.24   10.9   4.4    2.1  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
      0.061   12.4   6.7        0.2   10.8   1.8    2.1  2  FH2              Formin Homology 2 Domain
      0.065   13.7   3.9       0.12   12.8   0.1    2.9  2  DUF4094          Domain of unknown function (DUF4094)
      0.065   12.9  23.0      0.097   12.3  14.0    2.2  2  Lebercilin       Ciliary protein causing Leber congenital ama
      0.066   13.4  16.2       0.72   10.1   7.8    3.0  3  JIP_LZII         JNK-interacting protein  leucine zipper II
      0.071   13.5  11.9        4.6    7.7   0.6    3.3  3  CC2-LZ           Leucine zipper of domain CC2 of NEMO, NF-kap
      0.073   12.6   4.4       0.17   11.4   4.4    1.7  1  Cir_Bir_Yir      Plasmodium variant antigen protein Cir/Yir/B
      0.081   12.6  17.1       0.13   11.9  17.1    1.2  1  Laminin_I        Laminin Domain I
      0.081   13.8  21.0       0.19   12.7  11.9    2.3  2  PRKG1_interact   cGMP-dependent protein kinase interacting do
      0.082   12.1  16.2        1.4    8.1   6.9    2.5  2  Taxilin          Myosin-like coiled-coil protein
      0.092   12.6  18.3       0.15   11.8  18.3    1.3  1  KASH_CCD         Coiled-coil region of CCDC155 or KASH
      0.093   12.8   6.6       0.12   12.4   2.4    2.5  2  LOH1CR12         Tumour suppressor protein
      0.098   12.8  20.4       0.52   10.4  10.8    2.5  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
        0.1   11.9  13.9       0.69    9.2   8.4    2.4  2  Tropomyosin      Tropomyosin
        0.1   12.7  29.0      0.085   12.9   6.9    3.4  3  TolA_bind_tri    TolA binding protein trimerisation
        0.1   11.6  12.1       0.14   11.2  12.1    1.1  1  Perilipin        Perilipin family
       0.11   12.6  22.5        1.1    9.3  11.3    2.9  3  DHR10            Designed helical repeat protein 10 domain
       0.11   11.1  11.7        0.1   11.2   5.0    1.8  2  AAA_13           AAA domain
       0.12   11.9  15.4        0.2   11.1   8.8    2.2  2  HMMR_N           Hyaluronan mediated motility receptor N-term
       0.13   12.1   9.1       0.81    9.5   2.8    2.0  2  DUF724           Protein of unknown function (DUF724)
       0.13   10.2  10.8        0.2    9.5  10.8    1.4  1  V_ATPase_I       V-type ATPase 116kDa subunit family
       0.13   11.4  20.6      0.081   12.1   9.6    2.2  2  HAP1_N           HAP1 N-terminal conserved region
       0.14   11.3  17.8        0.2   10.7  17.8    1.2  1  DUF4686          Domain of unknown function (DUF4686)
       0.14   12.6   3.4        3.6    8.1   0.4    3.5  3  LPP              Lipoprotein leucine-zipper
       0.14   11.4  10.5       0.72    9.0   2.8    2.2  2  TMPIT            TMPIT-like protein
       0.15   12.4  15.8        2.2    8.7   1.7    4.0  4  CLZ              C-terminal leucine zipper domain of cyclic n
       0.16   11.0  14.3       0.38    9.8   5.6    2.1  2  APG17            Autophagy protein Apg17
       0.17   12.5  13.4       0.87   10.2   6.2    3.2  2  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.17   12.5  16.9        2.4    8.9   4.8    3.3  3  YabA             Initiation control protein YabA
       0.18   12.2  12.6         11    6.5   0.3    4.4  4  FlaC_arch        Flagella accessory protein C (FlaC)
       0.21   11.5   2.8        4.4    7.2   0.1    3.2  2  DUF4041          Domain of unknown function (DUF4041)
       0.21   11.3  18.6        1.4    8.7  18.6    1.9  1  ERM              Ezrin/radixin/moesin family
       0.21   11.4  10.7       0.31   10.9   2.2    2.6  3  Sec8_exocyst     Sec8 exocyst complex component specific doma
       0.22   11.6  14.5       0.63   10.1   8.9    2.3  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
       0.22   11.2   7.0       0.36   10.5   7.0    1.3  1  LUC7             LUC7 N_terminus
       0.25   11.7  12.2       0.74   10.2   5.8    2.3  2  HrpB7            Bacterial type III secretion protein (HrpB7)
       0.27   11.9   8.3      0.041   14.5   3.4    2.0  2  Ead_Ea22         Ead/Ea22-like protein
       0.29   10.5  14.8      0.079   12.4   7.3    2.6  3  DUF4527          Protein of unknown function (DUF4527)
       0.31   10.6  11.8       0.11   12.0   1.7    2.4  2  Vps5             Vps5 C terminal like
       0.31   11.4  12.8        4.6    7.7  12.2    2.5  1  Syntaxin_2       Syntaxin-like protein
       0.32   11.5   9.0        1.2    9.7   3.8    2.8  2  DUF16            Protein of unknown function DUF16
       0.33   10.5  30.6       0.17   11.4  17.7    2.2  2  MscS_porin       Mechanosensitive ion channel porin domain
       0.35   10.5   4.1        3.8    7.1   0.2    2.5  2  DUF4988          Domain of unknown function
       0.35   10.5  15.7        0.7    9.5  15.7    1.5  1  YkyA             Putative cell-wall binding lipoprotein
       0.37   10.2   4.1       0.56    9.6   3.7    1.5  1  Mce4_CUP1        Cholesterol uptake porter CUP1 of Mce4, puta
       0.38   11.0  16.1       0.49   10.7   5.0    3.5  4  KxDL             Uncharacterized conserved protein
       0.38   10.4   9.0       0.61    9.8   8.1    1.8  2  CCDC106          Coiled-coil domain-containing protein 106
       0.39   10.8  11.8       0.23   11.5   3.2    3.2  2  DUF1664          Protein of unknown function (DUF1664)
       0.39   11.0  10.9        1.6    9.0   6.1    2.5  2  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.41    9.3  11.6        1.2    7.8  11.6    1.6  1  WEMBL            Weak chloroplast movement under blue light
       0.44   10.8  10.2         35    4.6  10.2    2.4  1  zf-C4H2          Zinc finger-containing protein
       0.44   10.2  14.3        1.8    8.2   0.7    3.4  4  GrpE             GrpE
       0.54   10.7  13.6        1.4    9.5   3.0    3.6  3  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
        0.8    9.8   6.8        3.6    7.7   4.0    2.3  2  Cob_adeno_trans  Cobalamin adenosyltransferase
       0.81   10.1  14.4        2.1    8.7   4.0    2.6  2  Uso1_p115_C      Uso1 / p115 like vesicle tethering protein, 
       0.83   10.0  15.5       0.37   11.2   1.3    3.8  3  Csm1_N           Csm1 N-terminal domain
       0.94    8.7  17.3       0.71    9.1   7.1    2.3  2  HemX             HemX, putative uroporphyrinogen-III C-methyl
       0.94    9.2  12.1        1.2    8.9   8.0    2.5  3  She9_MDM33       She9 / Mdm33 family
       0.98    9.7  17.4       0.63   10.3   3.0    3.5  4  ABC_tran_CTD     ABC transporter C-terminal domain
       0.99   10.3  16.5        2.2    9.1   1.1    3.5  3  Rho_Binding      Rho Binding
        1.1    9.4  24.7       0.85    9.7   8.6    3.2  3  Cep57_CLD_2      Centrosome localisation domain of PPC89
        1.1    8.8   9.2       0.39   10.2   3.8    2.4  2  Fzo_mitofusin    fzo-like conserved region
        1.1    7.6  13.0       0.95    7.9   2.5    1.9  2  FUSC             Fusaric acid resistance protein family
        1.2    9.9   9.2         64    4.3   9.2    2.6  1  DUF2203          Uncharacterized conserved protein (DUF2203)
        1.2    9.1  21.7        2.9    7.9  21.5    1.8  1  Rootletin        Ciliary rootlet component, centrosome cohesi
        1.2    9.4  20.4       0.53   10.5   2.2    5.0  4  HALZ             Homeobox associated leucine zipper
        1.2    9.1  11.2          3    7.9   1.4    2.8  3  Noelin-1         Neurogenesis glycoprotein
        1.3    8.9   5.5         30    4.5   0.0    4.0  3  DASH_Dam1        DASH complex subunit Dam1
        1.3    9.4  15.7        3.8    7.9   7.1    2.5  3  YlqD             YlqD protein
        1.4    9.4   5.3        8.3    7.0   2.0    3.2  2  NPV_P10          Nucleopolyhedrovirus P10 protein
        1.4    8.8  17.4        2.6    8.0   0.4    3.9  3  Prefoldin        Prefoldin subunit
        1.5    8.8  10.3        1.8    8.6   5.2    2.2  2  Laminin_II       Laminin Domain II
        1.6    7.2  16.8       0.52    8.8   3.2    2.1  2  Macoilin         Macoilin family
        1.7    8.9   7.8         15    5.9   0.4    2.7  2  XhlA             Haemolysin XhlA
        1.9    8.0  20.5         41    3.6  20.5    2.0  1  Exonuc_VII_L     Exonuclease VII, large subunit
        1.9    8.1  13.2        1.7    8.3   4.9    2.1  2  DUF745           Protein of unknown function (DUF745)
        2.2    8.2  17.3        1.4    8.8   5.5    3.6  3  EMP24_GP25L      emp24/gp25L/p24 family/GOLD
        2.3    7.8  18.2    4.3e+02    0.4  18.2    2.7  1  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
        2.4    7.3   8.8        7.5    5.7   8.4    2.1  1  Tho2             Transcription factor/nuclear export subunit 
        2.7    7.9  14.7       0.41   10.6   6.8    2.4  2  YscO             Type III secretion protein YscO
          3    7.8  15.6        9.9    6.2   0.5    3.6  3  DUF4298          Domain of unknown function (DUF4298)
        3.1    6.6  19.0        6.6    5.5   9.2    1.9  1  CALCOCO1         Calcium binding and coiled-coil domain (CALC
        3.4    7.2  15.1        7.6    6.0   1.6    2.2  2  HAUS6_N          HAUS augmin-like complex subunit 6 N-terminu
          4    8.0  12.5    1.8e+02    2.6   0.2    3.6  2  DUF4140          N-terminal domain of unknown function (DUF41
          4    7.2  19.3        5.8    6.6   6.7    2.7  2  DASH_Spc34       DASH complex subunit Spc34
        4.3    6.1  13.5    1.2e+02    1.3  13.4    2.1  1  Fmp27_WPPW       RNA pol II promoter Fmp27 protein domain
        4.3    7.8  17.2          3    8.3   1.5    2.6  3  CENP-H           Centromere protein H (CENP-H)
        4.6    6.9  12.6          1    9.0   2.3    2.8  3  LXG              LXG domain of WXG superfamily
        4.8    6.7   6.3        5.3    6.5   5.5    1.4  1  Paralemmin       Paralemmin
        5.1    7.3  12.7        7.5    6.7   2.2    3.8  2  Swi5             Swi5
        5.4    6.3  17.7        2.2    7.6  13.9    1.9  2  Cluap1           Clusterin-associated protein-1
        5.5    7.5  15.9         10    6.6   0.5    3.9  2  Fungal_TACC      Fungal Transforming acidic coiled-coil (TACC
        5.6    7.2  15.5        2.4    8.4   7.4    2.7  2  IFT20            Intraflagellar transport complex B, subunit 
        6.1    7.0   7.8         12    6.0   0.9    2.4  2  DUF1192          Protein of unknown function (DUF1192)
        6.3    7.3  18.6       0.19   12.2   8.4    2.6  2  Snapin_Pallidin  Snapin/Pallidin
        6.8    6.7  17.3        1.9    8.6   2.7    2.1  2  SYCE1            Synaptonemal complex central element protein


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 !   17.7   9.3   1.4e-05    0.0018      41     131 ..     151     245 ..     144     248 .. 0.80
   2 !   22.0  13.2   7.2e-07   8.7e-05      28     169 ..     180     317 ..     178     327 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.4e-05
                               GAS  41 keernekelseisqenkrlkepLkkaeeeveeLrkqlkn....yekdkqslknlkarlkelekelkdlkwehevleq 113
                                         +   ++l+ ++++ ++l+ +++ +e e++ Lr +l++         ++l+++++++k+le+ ++++++e+++l++
  gi|557694562|ref|YP_008797616.1| 151 TYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEalntAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLND 227
                                       55666788999999999999999999999998887665511005566778899999999999999999999999999 PP

                               GAS 114 rfekvekerdelykkfea 131
                                       r+ +   e ++l++++e+
  gi|557694562|ref|YP_008797616.1| 228 RYVSTVGELKALQASYEM 245
                                       999999999999998875 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 7.2e-07
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                       I++l+  +ee  + ++  + +l+   +e krl++ +++  ee  +L+    +y +   +lk+l+a +++l +e ++l
  gi|557694562|ref|YP_008797616.1| 180 INTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLND---RYVSTVGELKALQASYEMLSRENEAL 253
                                       99999999999999999999*************999999999999986...5778888******************* PP

                               GAS 105 kwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkkeaqleevl 169
                                       + ++++l + + ++ ke+  l+++f++ ++e+ +    ++   ++++  lq +l+++  +l ++ 
  gi|557694562|ref|YP_008797616.1| 254 STSYQQLLHDYRNLTKEYSMLQATFNQ-LHELYEGLVTRHESAKQQIGYLQSQLDENRRELGDLR 317
                                       **************************9.999***************************9998775 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   8.4   0.00014     0.017     174     248 ..     150     227 ..     142     232 .. 0.77
   2 !   14.9   2.8   7.7e-05    0.0093     147     226 ..     235     317 ..     229     337 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00014
                              Spc7 174 eekaeleeeleklqeaaeeles...idkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksele 247
                                       + +++l + l++ qe+ ++l +   i ++e+++lr +l+e+ ++ + + ++l++ +e++++le++i++++e++++l+
  gi|557694562|ref|YP_008797616.1| 150 RTYQDLLNDLNRAQEQINQLRTtiqILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLN 226
                                       34555555555555555555544336689999999999999999999999999999999999999999999999988 PP

                              Spc7 248 e 248
                                       +
  gi|557694562|ref|YP_008797616.1| 227 D 227
                                       6 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 7.7e-05
                              Spc7 147 nlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesid...keeLeelreelaelkaeieekkk 220
                                       +l++l++ +e+L++++e l++ +++l + + +l++e+ +lq+  ++l ++     ++ e++++++  l+++++e ++
  gi|557694562|ref|YP_008797616.1| 235 ELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYeglVTRHESAKQQIGYLQSQLDENRR 311
                                       57889999999999999999999999999999999999999977777664412234445666666666666666666 PP

                              Spc7 221 elaelq 226
                                       el +l+
  gi|557694562|ref|YP_008797616.1| 312 ELGDLR 317
                                       666655 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   5.1    0.0061      0.74      27      95 ..     153     228 ..     136     238 .. 0.72
   2 !   18.4   1.7   1.9e-05    0.0023      24      95 ..     246     316 ..     235     320 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0061
                                       SSCSSSHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTH...HHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  27 edlgkdleevqallk....khkaleaelaaqqervkalnelaeklldeghsas...eeieerleelnerWeeLkel 95 
                                       +dl +dl+ +q++++    + + le e+++ ++r+++   +a  l+++  s+    +++e+r++ + e +++L ++
  gi|557694562|ref|YP_008797616.1| 153 QDLLNDLNRAQEQINqlrtTIQILETEINTLRTRLEEALNTAAMLTARLNSSReeiKRLEQRIQTMSEEYRQLNDR 228
                                       45555555555555544449999****************9999997766555422377788888888888888776 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.9e-05
                                       HCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  24 lssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseeieerleelnerWeeLkel 95 
                                       l s++ +   ++ q+ll++++ l +e +  q  +++l el e l+++++sa+++i + +++l+e+ +eL +l
  gi|557694562|ref|YP_008797616.1| 246 L-SRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELGDL 316
                                       4.66666778999******************************************************99765 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5  18.0   1.9e-06   0.00023     265     420 ..     156     317 ..     143     326 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.9e-06
                                       HHHHTT-..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSS CS
                              EzrA 265 lerlkel..eledveeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqsYeLs 339
                                       l++l++   ++++ +  ++ +e+ei++L   le+  +     + +l++ +e++++le+ +++++ee+++l+++Y  +
  gi|557694562|ref|YP_008797616.1| 156 LNDLNRAqeQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVST 232
                                       44444332257777888999999999999999999999999999999999999999999999999999999999999 PP

                                       TTTSTTHHH....HHHHHHHHHHHHHHHHHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 340 eeeleklre....lekelkelekdyeeleekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrA 412
                                         el+ l+     l++e + l+++y++l ++ ++ +  YS+lq  +++l e  e + +++e+ +++++ l+++  + 
  gi|557694562|ref|YP_008797616.1| 233 VGELKALQAsyemLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDEN 309
                                       88887654411117777888999999999999999999999999999999999999999999999999999888888 PP

                                       HHHHHHHH CS
                              EzrA 413 reqldeik 420
                                       r++l +++
  gi|557694562|ref|YP_008797616.1| 310 RRELGDLR 317
                                       77776655 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   3.0   0.00032     0.038      16      52 ..     149     185 ..     138     195 .. 0.86
   2 ?    7.4   1.0      0.03       3.7      26      50 ..     201     225 ..     186     233 .. 0.57
   3 ?    8.9   0.4      0.01       1.2      16      56 ..     233     273 ..     228     277 .. 0.62
   4 ?    5.1   0.3      0.16        20      16      56 ..     289     328 ..     283     332 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00032
                                       XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX CS
                             DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLks 52 
                                       +++y++l +++++ q+++++l+ +++ Le e++ L+ 
  gi|557694562|ref|YP_008797616.1| 149 QRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRT 185
                                       789*******************************975 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.03
                                       HHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC  26 iaalqaelaklkaeneeLeaevkdL 50 
                                       ++   +e+++l ++++ + +e ++L
  gi|557694562|ref|YP_008797616.1| 201 LNSSREEIKRLEQRIQTMSEEYRQL 225
                                       3344455555555555555555555 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.01
                                       XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXX CS
                             DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedy 56 
                                       +  +k+l++ ++ l +e+++l+   ++L +  ++L++++++
  gi|557694562|ref|YP_008797616.1| 233 VGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSM 273
                                       44556666666666666666666666666666666666665 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.16
                                       XXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXXXXX CS
                             DivIC  16 llaykqlkqeiaalqaelaklkaeneeLeaevkdLksdedy 56 
                                       + +  + kq+i  lq +l++ + e  +L  + ++L sde+ 
  gi|557694562|ref|YP_008797616.1| 289 VTRHESAKQQIGYLQSQLDENRRELGDLRLRYSLL-SDENL 328
                                       55677899***************************.78875 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 !   14.7   9.3   0.00019     0.023      40     113 ..     147     223 ..     131     227 .. 0.51
   2 !   13.4  12.1   0.00049     0.059       3     122 ..     201     323 ..     199     326 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.00019
                        TPR_MLP1_2  40 eaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseeswe...eqkeelekelselekrie 113
                                         q+ Y+  l+  + + +++++lr+ ++ l++ei++l++++e+a ++ +  ++ ++   e+ ++le++++ + + + 
  gi|557694562|ref|YP_008797616.1| 147 VRQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNssrEEIKRLEQRIQTMSEEYR 223
                                       55556666666666666666666666666666666666666655444433333333000333333333333333333 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00049
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       l+s +eeik+l+++++   ++ ++l +   +   ++k+ q +Ye    ++++ +++ q+l  ++ +l++e++ l+a 
  gi|557694562|ref|YP_008797616.1| 201 LNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQAT 277
                                       78999*******************************************************************99998 PP

                        TPR_MLP1_2  80 aesaka...eleeseesweeqkeelekelselekriedlneqNklL 122
                                        +++++    l +  es ++q   l+++l+e ++ + dl    +lL
  gi|557694562|ref|YP_008797616.1| 278 FNQLHElyeGLVTRHESAKQQIGYLQSQLDENRRELGDLRLRYSLL 323
                                       8887761115667888888888889999999999999998777777 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0  12.7   8.8e-07   0.00011      41     172 ..     156     289 ..     155     294 .. 0.94
   2 ?    4.6   0.6       0.2        24      20      72 ..     269     320 ..     266     327 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 8.8e-07
                           DUF4201  41 lidFeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykv 117
                                       l+d + +q ++++l+++I+  + e++ l+ +    + + + l  +l+  ++e ++l+++++++ e+ ++l ++  ++
  gi|557694562|ref|YP_008797616.1| 156 LNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVST 232
                                       579999*********************************************************************** PP

                           DUF4201 118 klerdklrkqneklkqqggll..rvPaLlkDYdktkekveekrksvkkLrrkvkile 172
                                         e + l++ +e l+++++ l  ++ +Ll+DY +  +++  ++++ ++L + ++ l 
  gi|557694562|ref|YP_008797616.1| 233 VGELKALQASYEMLSRENEALstSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLV 289
                                       *******************9844599*******************999999887765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.2
                           DUF4201  20 hqlakiqeklekkeelgegLtlidFeqlqienqalnkkIeernkeLkrlkkkt 72 
                                       + ++ +q+  ++++el egL     e+++ ++  l+ +++e   eL  l++++
  gi|557694562|ref|YP_008797616.1| 269 KEYSMLQATFNQLHELYEGLV-TRHESAKQQIGYLQSQLDENRRELGDLRLRY 320
                                       456667777777778888874.4568888888888888888888888887776 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  11.6   8.4e-06     0.001      23     130 ..     147     247 ..     132     249 .. 0.90
   2 !   11.2   5.2    0.0033       0.4      48     117 ..     235     304 ..     226     326 .. 0.53

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 8.4e-06
                            APG6_N  23 kerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeee 99 
                                          ++Y++ l+ l++ +       e++++l+  ++ le e ++l + L+e+ ++ + l a l++ +ee ++le+  +
  gi|557694562|ref|YP_008797616.1| 147 VRQRTYQDLLNDLNRAQ-------EQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQ 216
                                       56789*********993.......47899************************************************ PP

                            APG6_N 100 rfwreynelqlelleleeeldsleaqyehaq 130
                                          +ey++l+    +   el++l+a+ye  +
  gi|557694562|ref|YP_008797616.1| 217 TMSEEYRQLNDRYVSTVGELKALQASYEMLS 247
                                       **************************99766 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0033
                            APG6_N  48 eleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlellelee 117
                                       el++l+ ++e l++e e+l +  ++l +  ++l +e + l+++ ++l+e  e  ++++ + + +   l+ 
  gi|557694562|ref|YP_008797616.1| 235 ELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQS 304
                                       3444445555555555555555555555555555555555555555555555444444444444444444 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   1.3     0.037       4.5      39      72 ..     152     185 ..     128     195 .. 0.55
   2 !   15.9   3.3    0.0001     0.012       6      62 ..     192     248 ..     188     253 .. 0.93
   3 !   13.4   3.9   0.00058      0.07      13      65 ..     234     286 ..     232     318 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.037
                           BLOC1_2  39 lkdvaaslekkleklnekyeelqpylqqidqiek 72 
                                       ++d +++l++  e++n++  ++q + ++i+ + +
  gi|557694562|ref|YP_008797616.1| 152 YQDLLNDLNRAQEQINQLRTTIQILETEINTLRT 185
                                       4444444444444444444444444444444444 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 0.0001
                           BLOC1_2   6 kvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqp 62 
                                       +++++l+a l++++e++k Le+  +++se+y +l+d+  s+  +l++l++ ye l+ 
  gi|557694562|ref|YP_008797616.1| 192 NTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSR 248
                                       57899***********************************************98876 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 0.00058
                           BLOC1_2  13 aeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylq 65 
                                       +el+a ++ y++L + Nea s+ y++l +   +l+k+ + l+++ ++l+++ +
  gi|557694562|ref|YP_008797616.1| 234 GELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYE 286
                                       69**********************************************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 !   20.7  11.8   1.3e-06   0.00016     336     486 ..     149     299 ..     138     300 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-06
                            DUF812 336 qeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalveasaqrl 412
                                       q+ +++l +++++ +e+i++l+++i+ +e e+++++   ++le+ ++++ ++ + l++  e i++L++ +++ +++ 
  gi|557694562|ref|YP_008797616.1| 149 QRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLR---TRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEY 222
                                       56799**************************99876...789999******************************** PP

                            DUF812 413 velakqWekhR...vplieeyrelkesksekekeaerkleeikklrekmkevaeelrqkeellkqLvaeleklpkdv 486
                                        +l +++ +     ++l + y+ l+ +++   +++++ l + ++l ++   +++   q  el++ Lv++ e++++++
  gi|557694562|ref|YP_008797616.1| 223 RQLNDRYVSTVgelKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQI 299
                                       *******986511167889******************************************************9986 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9  10.4    0.0002     0.024      29     100 ..     156     227 ..     144     242 .. 0.86
   2 !   12.4   2.0   0.00057     0.069      25      91 ..     236     302 ..     229     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.0002
                           DUF3450  29 vaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvp 100
                                        +   ++q++i++l    q l+ e+++l+++le++    + l++ ++s ++ei++le++i+ ++e  r+l  
  gi|557694562|ref|YP_008797616.1| 156 LNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLND 227
                                       5566789*******************************************************9998888765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00057
                           DUF3450  25 aekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                        ++ +a+ ++ +++ ++l+   q+ll +yr+l++e + l++  +ql +l + + ++ +s ++qi  +
  gi|557694562|ref|YP_008797616.1| 236 LKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYL 302
                                       56677777888899999**********************************************9765 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6  10.7   1.6e-06   0.00019      25     141 ..     154     274 ..     143     276 .. 0.87
   2 ?    0.7   0.1       4.3   5.2e+02      12      47 ..     288     323 ..     277     328 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-06
                     Tropomyosin_1  25 eleqenlekeqeiksLtkknqqleeevekleeklkeakekae.esekkktnne...altrkiqlLEeeleesdkkLk 97 
                                       +l ++  +  ++i++L + +q le e+++l ++l+ea ++a   +++++++ e    l+++iq + ee  + + +  
  gi|557694562|ref|YP_008797616.1| 154 DLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAmLTARLNSSREeikRLEQRIQTMSEEYRQLNDRYV 230
                                       555666778899***********************9876654156677777776879999***************** PP

                     Tropomyosin_1  98 ettekLretdvkaeelERkvkaLeqerdewekkyeeleekykea 141
                                       +t+  L+  ++  e l R+ +aL ++ ++  + y +l+++y+  
  gi|557694562|ref|YP_008797616.1| 231 STVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSML 274
                                       ******************************99999999999865 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 4.3
                     Tropomyosin_1  12 aqekaeeleekvKeleqenlekeqeiksLtkknqql 47 
                                        ++++e +++++  l+++  e+  e+ +L  + ++l
  gi|557694562|ref|YP_008797616.1| 288 LVTRHESAKQQIGYLQSQLDENRRELGDLRLRYSLL 323
                                       456677777777777777777777777776666665 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 !   18.8  12.9   3.3e-06    0.0004     686     808 ..     148     270 ..     113     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.3e-06
                               FPP 686 kkeenkllkeeleelksekenlevelksatenleslkaqlqesEqllaelkseLeslkeskslaetqlkcmkesyes 762
                                       ++ + + l ++l++ + + ++l + ++  + ++++l ++l+e  ++ a l++ L+s++e  + +e+ ++ m+e y++
  gi|557694562|ref|YP_008797616.1| 148 RQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQ 224
                                       35666778899999999999********************************************************* PP

                               FPP 763 letrateleaelnelkqkieaLeveLeeekksheeleakckelqeq 808
                                       l+ r      el+ l+   e L+ e e  ++s+++l+  +++l + 
  gi|557694562|ref|YP_008797616.1| 225 LNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKE 270
                                       ***************************************9999765 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   2.4    0.0053      0.64       8      58 ..     148     198 ..     145     210 .. 0.87
   2 !   13.0   6.2   0.00059     0.071       4      81 ..     214     288 ..     197     309 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0053
                             Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrle 58 
                                       +++++++ll+++++a+eq+++l++  +  +++ ++l+++ e+ l+    l+
  gi|557694562|ref|YP_008797616.1| 148 RQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLT 198
                                       6889************************************99998876665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00059
                             Sec34   4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLkyFeeldpitrk 80 
                                       ++++ +ee+++l ++  ++  +L+ l+ +++  s + ++l+++ +qll++ ++l++ +  +++    F++l ++ + 
  gi|557694562|ref|YP_008797616.1| 214 RIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQAT---FNQLHELYEG 287
                                       5677788888888888888888888888888888888888888888888888888888777754...5555555555 PP

                             Sec34  81 L 81 
                                       L
  gi|557694562|ref|YP_008797616.1| 288 L 288
                                       5 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  10.8     0.073       8.8       6      65 ..     159     218 ..     153     221 .. 0.91
   2 !   13.4   6.0   0.00066      0.08       6      60 ..     222     276 ..     206     281 .. 0.82
   3 !   11.1   2.2    0.0034      0.41       7      54 ..     251     298 ..     251     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.073
                              ZapB   6 LeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                       L++ +++i+++ +ti+ L  ei  L+ + ee  + ++ l++ ++  +ee + +++r++++
  gi|557694562|ref|YP_008797616.1| 159 LNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTM 218
                                       5566899*************************************************9975 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00066
                              ZapB   6 LeqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqe 60 
                                         qL  ++ +++ ++++Lq  +e L +ene+l+   ++l +   +l +e + +q+
  gi|557694562|ref|YP_008797616.1| 222 YRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQA 276
                                       4689999999999999999999999999999999999999888888888776665 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0034
                              ZapB   7 eqLEskiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkee 54 
                                       e L +++q+++  ++ L +e++ L++  ++l e  + l    e  k++
  gi|557694562|ref|YP_008797616.1| 251 EALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQ 298
                                       57899***************************9888777555555554 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 !   12.2   8.6    0.0011      0.14       7      73 ..     154     227 ..     148     240 .. 0.63
   2 ?    8.3   0.2     0.018       2.1      27      81 ..     272     326 ..     262     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0011
                    CENP-F_leu_zip   7 hvlekLKeserkadsLkdkvenLerelemseenqekvilea.......Etskaevetlkeeieelaeelrelel 73 
                                        +l+ L +++++ ++L+  ++ Le e++++   +e++   a        +s++e++ l++ i++++ee r+l+ 
  gi|557694562|ref|YP_008797616.1| 154 DLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAamltarlNSSREEIKRLEQRIQTMSEEYRQLND 227
                                       55667777777777777777777777777777766654333122222256777777777777777777777764 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.018
                    CENP-F_leu_zip  27 enLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrse 81 
                                         L++  +++ e  e +++  E++k+++  l+++++e ++el +l+l  + l+ e
  gi|557694562|ref|YP_008797616.1| 272 SMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELGDLRLRYSLLSDE 326
                                       56777778888889999***************************99988887776 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9  10.3   0.00018     0.021      56     122 ..     160     226 ..     149     234 .. 0.75
   2 !    9.9   3.7    0.0061      0.74      53     118 ..     248     313 ..     224     333 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 0.00018
                              ADIP  56 eslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlk 122
                                       +  +e+i++l+++i+ l+++i+ l t+le+  + +a ++a++++ + ++k+leq +++ +ee + l+
  gi|557694562|ref|YP_008797616.1| 160 NRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLN 226
                                       4456788888888888888888888888888888888888888888888888888888888776665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0061
                              ADIP  53 eqreslnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeel 118
                                       +++e+l++  ++l +++ +l+++++ l++   ql+   + +  ++ ++++++  l+++l + ++el
  gi|557694562|ref|YP_008797616.1| 248 RENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRREL 313
                                       678889999999999999999999999999999998888888888888888888888888888776 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 !   15.6   8.2   0.00011     0.014      11      83 ..     163     232 ..     153     234 .. 0.84
   2 !    9.9   3.7    0.0069      0.84      26     108 ..     234     320 ..     232     325 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 0.00011
                       TMF_TATA_bd  11 vqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetl 83 
                                       ++ +++l ++i+ lE+E+++l+++le   +  ++a+   ++l ++ ee k+l+++++++++e+++l++ry ++
  gi|557694562|ref|YP_008797616.1| 163 QEQINQLRTTIQILETEINTLRTRLE---EALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVST 232
                                       56789999999999999999998665...55566666677888999************************876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0069
                       TMF_TATA_bd  26 gElaslkeelerleaerdeareeivklmkeneelke....lkkeleelekeleelqeryetlLellGeksEeveELr 98 
                                       gEl++l+ ++e l++e ++++    +l+++  +l++    l+++ ++l + +e l +r+e++ + +G  + + +E r
  gi|557694562|ref|YP_008797616.1| 234 GELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKeysmLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENR 310
                                       57778888888888888888777777776655554411115666778888899999********************* PP

                       TMF_TATA_bd  99 aDvaDlKemy 108
                                        ++ Dl+  y
  gi|557694562|ref|YP_008797616.1| 311 RELGDLRLRY 320
                                       *****99665 PP

>> PspA_IM30  PspA/IM30 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   3.1    0.0028      0.34      94     145 ..     153     204 ..     144     209 .. 0.77
   2 !   13.2   5.8    0.0004     0.049      26     139 ..     209     317 ..     197     327 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0028
                         PspA_IM30  94 kslekqaealetqlaqqrsaveqlrkqlealetkieelkakkellkarekaa 145
                                       ++l +++++ ++q +q+r++++ l+++++ l t++ee+ +   +l ar+++ 
  gi|557694562|ref|YP_008797616.1| 153 QDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSS 204
                                       5666777888888888888888888888888888888888888888888775 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.0004
                         PspA_IM30  26 kileqairdmqselakarqalaqviarqkqlerkleeqkeqakklekkAkaALtkgeeeLArealaeikslekqaea 102
                                       k leq i+ m +e++++ +  ++++++ k+l+  +e  +++ ++l  + +++L   + +L +e       l+ + ++
  gi|557694562|ref|YP_008797616.1| 209 KRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHD-YRNLTKE----YSMLQATFNQ 280
                                       679**********************************************999976.5566665....3445555555 PP

                         PspA_IM30 103 letqlaqqrsaveqlrkqlealetkieelkakkellk 139
                                       l+++++ + +  e +++q+  l  +++e +++   l 
  gi|557694562|ref|YP_008797616.1| 281 LHELYEGLVTRHESAKQQIGYLQSQLDENRRELGDLR 317
                                       5555555555555555555555555555555544444 PP

>> S6OS1  Six6 opposite strand transcript 1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   2.6   9.3e-06    0.0011     152     239 ..     141     227 ..     124     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.3e-06
                             S6OS1 152 aLyivnlRlkt.ediLklAetltkkslelkkeadelEikinylkkqiarllesknlsevleekn.kelekrkelker 226
                                       + +i+ +R++t +d+L   + + ++  +l+  ++ lE++in l+    rl e+ n++ +l  +   + e  k l++r
  gi|557694562|ref|YP_008797616.1| 141 TWHIAAVRQRTyQDLLNDLNRAQEQINQLRTTIQILETEINTLR---TRLEEALNTAAMLTARLnSSREEIKRLEQR 214
                                       679*******989*******************************...7888888999999887537899******** PP

                             S6OS1 227 ifeedehslvlek 239
                                       i   +e+ + l+ 
  gi|557694562|ref|YP_008797616.1| 215 IQTMSEEYRQLND 227
                                       *999998555443 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 !   12.9   6.4   0.00078     0.094      59     129 ..     149     219 ..     138     224 .. 0.84
   2 !   10.4   2.7    0.0047      0.57      40     122 ..     232     317 ..     216     326 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00078
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  59 keikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidqke 129
                                       +++++ l ++ + ++++ n ++   + le+ei++l+ ++ +  ++   L+  l+s +++i++Leq i++  
  gi|557694562|ref|YP_008797616.1| 149 QRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMS 219
                                       555566666667777778888888999****************************************9865 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0047
                                       CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH...HHHHHHHHHHHH CS
                         Fib_alpha  40 leneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe...snirvLqnvles 113
                                          el+ ++ s++  ++  +++++s+++  + +++ ++ ++ ++ + ++ ++ ++  ++++e   ++i +Lq+ l++
  gi|557694562|ref|YP_008797616.1| 232 TVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHEsakQQIGYLQSQLDE 308
                                       4456778888888888888888888888888888778889999999999999999999999866789********** PP

                                       HHHHHHHHH CS
                         Fib_alpha 114 neqkiqkLe 122
                                       n++++ +L+
  gi|557694562|ref|YP_008797616.1| 309 NRRELGDLR 317
                                       *****9997 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 !   16.5  12.3   6.2e-05    0.0075      43     151 ..     157     268 ..     151     272 .. 0.85
   2 ?    7.0   4.5     0.052       6.4      67     136 ..     247     316 ..     235     337 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.2e-05
                     Jnk-SapK_ap_N  43 srneeeeaeleelreeleqLeteyerekelrkrae...eeleeiedqweeerkelqekveqleeenrelelkaknaa 116
                                       ++ ++ ++++++lr +++ Lete +  +   ++a      l    ++ +ee k l+++++ + ee r+l+ +  ++ 
  gi|557694562|ref|YP_008797616.1| 157 NDLNRAQEQINQLRTTIQILETEINTLRTRLEEALntaAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTV 233
                                       566788899999999999999998765544443333337777888999***************************** PP

                     Jnk-SapK_ap_N 117 dqlsrleekeaelkkeysklheretellkklkelv 151
                                        +l++l+ + + l++e+++l++++++ll+ ++ l+
  gi|557694562|ref|YP_008797616.1| 234 GELKALQASYEMLSRENEALSTSYQQLLHDYRNLT 268
                                       *****************************999876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.052
                     Jnk-SapK_ap_N  67 erekelrkraeeeleeiedqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeyskl 136
                                       +re+e+   + ++l+    ++ +e + lq+ ++ql+e  + l ++ ++a++q+  l+++ +e ++e   l
  gi|557694562|ref|YP_008797616.1| 247 SRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELGDL 316
                                       3344444444455555555555556666666666666666666666666666666666666666665555 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 ?    4.9   0.2      0.16        20      88     127 ..     149     188 ..     136     193 .. 0.78
   2 !   14.8   8.2   0.00015     0.018      16     126 ..     200     306 ..     187     321 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.16
                            TACC_C  88 eksfsdlfkryekqkevlegykkneeslkkcaeeylarvk 127
                                       +++++dl++ +++ +e ++++++  ++l ++++ + +r++
  gi|557694562|ref|YP_008797616.1| 149 QRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLE 188
                                       5778888888888888888888888888888887777766 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 0.00015
                            TACC_C  16 eveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqlladlnsveksfs 92 
                                         +   eei+ l+++++ + +e+++++   +++ +t+ +l +  q+  e+ ++e + +    +qll+d +++ k++s
  gi|557694562|ref|YP_008797616.1| 200 RLNSSREEIKRLEQRIQTMSEEYRQLN---DRYVSTVGELKAL-QASYEMLSRENEALSTSYQQLLHDYRNLTKEYS 272
                                       33445689999***************9...9****99998665.577778888999999****************** PP

                            TACC_C  93 dlfkryekqkevlegykkneeslkkcaeeylarv 126
                                        l   ++++ e  eg+ +  es k+++  + +++
  gi|557694562|ref|YP_008797616.1| 273 MLQATFNQLHELYEGLVTRHESAKQQIGYLQSQL 306
                                       *************************998555444 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   6.7    0.0027      0.32      33      99 ..     153     219 ..     149     246 .. 0.75
   2 !    9.1   0.2    0.0028      0.34      31      99 ..     256     324 ..     249     327 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0027
                              COG6  33 eefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkllk 99 
                                       ++ l+++++++eq+++++++++ l++ +++++++l++a ++ + l+   ++ +ee k+le++ +  +
  gi|557694562|ref|YP_008797616.1| 153 QDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMS 219
                                       67899*****************999999999999999988888888888777777777777766654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0028
                              COG6  31 ineefleefqpvaeqLkriesdveklnelcdemkkklssakeetsdlleeaeeLkeekkklelkqkllk 99 
                                       + ++ l++++++ ++ + +++++++l+el++ + ++ +sak++ + l ++ +e ++e+ +l+l+  ll+
  gi|557694562|ref|YP_008797616.1| 256 SYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELGDLRLRYSLLS 324
                                       45899*****************************************************99999999886 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   2.0    0.0045      0.54       2      37 ..     154     189 ..     153     195 .. 0.52
   2 !   10.5   0.9    0.0037      0.44      65      97 ..     195     227 ..     191     235 .. 0.89
   3 ?    4.3   0.6      0.31        37      65     100 ..     244     279 ..     231     284 .. 0.55
   4 ?    3.3   0.1      0.63        76      62      95 ..     283     316 ..     278     320 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0045
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   2 elinkfqqlqqqlqqlaqqikqletqlkelelvlee 37 
                                       +l+n +++ q+q+ ql + i+ let+++ l + lee
  gi|557694562|ref|YP_008797616.1| 154 DLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEE 189
                                       555555555555555555555555555554444433 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelke 97 
                                       ++L +r+++  +eik+le++++++ +e+++l +
  gi|557694562|ref|YP_008797616.1| 195 AMLTARLNSSREEIKRLEQRIQTMSEEYRQLND 227
                                       78999***********************99976 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  65 eeLeerketlekeiktlekqleklekeleelkeelq 100
                                       e+L  + e l++ +++l   +++l ke++ l+++ +
  gi|557694562|ref|YP_008797616.1| 244 EMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFN 279
                                       455555555555555555555555555555555444 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.63
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  62 evkeeLeerketlekeiktlekqleklekeleel 95 
                                       e+ e L +r+e+++++i  l++ql++ ++el +l
  gi|557694562|ref|YP_008797616.1| 283 ELYEGLVTRHESAKQQIGYLQSQLDENRRELGDL 316
                                       5666778888888888888888888888877665 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0  11.9    0.0098       1.2     245     322 ..     157     237 ..     140     260 .. 0.40
   2 !   11.6   3.0   0.00083       0.1     247     322 ..     239     314 ..     236     330 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0098
                             IFT57 245 sqlkklhedisktlekiesrEkylns...qleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvk 318
                                       + l++ +e+i++  + i+  E+ +n+   +lee l+    + ++l++ +e++k l+++++ +++e++++++++ ++ 
  gi|557694562|ref|YP_008797616.1| 157 NDLNRAQEQINQLRTTIQILETEINTlrtRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTV 233
                                       33333333333333333333333332111333333333333334444444444444444444444444443333333 PP

                             IFT57 319 qeme 322
                                        e++
  gi|557694562|ref|YP_008797616.1| 234 GELK 237
                                       3332 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00083
                             IFT57 247 lkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqeme 322
                                       l+  +e +s++ e +++  ++l   +++l++ey+ +q++++++ e y+ l ++ ++ +++   ++ +l++  +e+ 
  gi|557694562|ref|YP_008797616.1| 239 LQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELG 314
                                       6666777888889999999999999999999999999999999999999999999999999999999999888875 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 !   15.6  13.9   5.3e-05    0.0064      17     153 ..     159     309 ..     149     331 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.3e-05
                             Atg14  17 lrngperlyelrerlaklksekeslkkkiekalegke....eaeqledkiknkkakleelksliadlrer....... 82 
                                       l++ +e++++lr+ ++ l +e ++l++++e+al++      + ++++++ik++ ++++++  + ++l++r       
  gi|557694562|ref|YP_008797616.1| 159 LNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAmltaRLNSSREEIKRLEQRIQTMSEEYRQLNDRyvstvge 235
                                       566699******************************97777555566666666666666666666666665555555 PP

                             Atg14  83 lqelkdklsqlkkeieekkkklaklsdklk...kRrsdleslqneleerrkkqiaklqdaikrieqklsslssk 153
                                       l+ l+++ + l +e+e+ +   ++l ++     k +s l+++ n+l+e  + +++++ +a ++i + +s+l   
  gi|557694562|ref|YP_008797616.1| 236 LKALQASYEMLSRENEALSTSYQQLLHDYRnltKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDEN 309
                                       66666666666666666665555555544477799*************************99999998887665 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4  14.1   8.6e-05      0.01     603     760 ..     154     308 ..     143     333 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.6e-05
                           DUF3584 603 eLrerlqaleealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqnekesekdklekaiaerk 679
                                        L + l+ ++e++++ +  ++ +e e+++l+  leea + +a   + l+ +r++++rl++  ++ +++  +++++r 
  gi|557694562|ref|YP_008797616.1| 154 DLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEY-RQLNDRY 229
                                       566677888888888888888888888888888888888888888888888888888888888877776.5688888 PP

                           DUF3584 680 qqaeeqlqkldaqlkqleeqqkaaleelkedlseerlekkakwqevvgeldeqlaelkkaieaartqakarlkelee 756
                                        +   +l+ l+a  ++l ++++a++   ++ l++ r+ +k++   + +++ +ql+el + +  ++++ak+++  l+ 
  gi|557694562|ref|YP_008797616.1| 230 VSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEY--SMLQATFNQLHELYEGLVTRHESAKQQIGYLQS 304
                                       888888888999999998888888888888888888555555..457778888888888888888888888888887 PP

                           DUF3584 757 aykr 760
                                       + ++
  gi|557694562|ref|YP_008797616.1| 305 QLDE 308
                                       7655 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 !   16.3   2.6   7.4e-05     0.009      21      88 ..     159     226 ..     155     227 .. 0.95
   2 ?    1.2   0.0       3.6   4.4e+02      29      62 ..     237     270 ..     230     287 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.4e-05
                            DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88 
                                       l+++++ ++++++ti+ le +++ + + +e++l+++  l++ +n+  e++++l + +++++e  ++ln
  gi|557694562|ref|YP_008797616.1| 159 LNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLN 226
                                       56788999********************************************************9998 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 3.6
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelled 62 
                                       ++++a+ e l ++ +++++  ++ll+  ++l+++
  gi|557694562|ref|YP_008797616.1| 237 KALQASYEMLSRENEALSTSYQQLLHDYRNLTKE 270
                                       5566666667777777777777777776664443 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8  13.9   0.00051     0.062      19     149 ..     159     311 ..     137     324 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00051
                              Fez1  19 Lkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleee 95 
                                       L  +q +++q    i  l +++  lr++lee  +++  l ++l++  +e++++e+++q +++e   l+++  ++  e
  gi|557694562|ref|YP_008797616.1| 159 LNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGE 235
                                       34445555555555555555666666666666666666666666666666666666666666666666666666666 PP

                              Fez1  96 lkelreelselsleeeeaa...........lesdeakaqrqe.....................aeeleelkreverl 140
                                       lk l+ ++++ls+e+e  +           +                                 ++ e+ k+++  l
  gi|557694562|ref|YP_008797616.1| 236 LKALQASYEMLSRENEALStsyqqllhdyrN----------LtkeysmlqatfnqlhelyeglVTRHESAKQQIGYL 302
                                       6666665555554444433444443333330..........133333333334444455555545555555555556 PP

                              Fez1 141 raeLkeerq 149
                                       +++L e+r+
  gi|557694562|ref|YP_008797616.1| 303 QSQLDENRR 311
                                       656655555 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.5    0.0003     0.036     338     411 ..     151     225 ..     142     234 .. 0.64
   2 ?   12.1   5.6   0.00044     0.054     328     410 ..     197     287 ..     190     320 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0003
                              FapA 338 klkeleeeleeleeeleklkkkikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk 411
                                        +++l ++l++ +e++++l+ +i+ l+ + +      +e +++ ++l+  +++ +ee++ le+++++++ee ++ 
  gi|557694562|ref|YP_008797616.1| 151 TYQDLLNDLNRAQEQINQLRTTIQILETEINtLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQL 225
                                       448899999999999999999988888744433334445555555566666666666666666666666665555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00044
                              FapA 328 vgldepelkeklkeleeeleeleeeleklkkk.......ikklpklka.ekqlesekkeqlkklletkeklkeelee 396
                                       ++ + ++ +e++k+le++++ + ee ++l+++       +k l+++ +  ++ ++  + ++++ll+++ +l++e++ 
  gi|557694562|ref|YP_008797616.1| 197 LTARLNSSREEIKRLEQRIQTMSEEYRQLNDRyvstvgeLKALQASYEmLSRENEALSTSYQQLLHDYRNLTKEYSM 273
                                       4555568899***********************88866666666555545555555566666666666666666666 PP

                              FapA 397 leeelkelkeeles 410
                                       l++ +++l e  e 
  gi|557694562|ref|YP_008797616.1| 274 LQATFNQLHELYEG 287
                                       66666666654444 PP

>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.8     0.015       1.8      23      56 ..     161     194 ..     160     202 .. 0.87
   2 ?    6.6   0.7     0.068       8.3      25      48 ..     205     228 ..     204     239 .. 0.83
   3 ?    7.4   0.6     0.039       4.7      28      61 ..     236     269 ..     232     272 .. 0.73
   4 ?    2.0   0.1       1.8   2.2e+02      27      61 ..     270     304 ..     263     307 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  23 RKqaeieeLerrvkaLekeNksLkseleelkkev 56 
                                       R q++i++L +  + Le+e  +L+ +lee  ++ 
  gi|557694562|ref|YP_008797616.1| 161 RAQEQINQLRTTIQILETEINTLRTRLEEALNTA 194
                                       779************************9976655 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.068
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  25 qaeieeLerrvkaLekeNksLkse 48 
                                       ++ei++Le+r +++++e  +L ++
  gi|557694562|ref|YP_008797616.1| 205 REEIKRLEQRIQTMSEEYRQLNDR 228
                                       689************998888765 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.039
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  28 ieeLerrvkaLekeNksLkseleelkkevekLks 61 
                                        ++L+   + L+ eN++L+   ++l  ++ +L +
  gi|557694562|ref|YP_008797616.1| 236 LKALQASYEMLSRENEALSTSYQQLLHDYRNLTK 269
                                       5777777888888888888888887777777665 PP

  == domain 4  score: 2.0 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1  27 eieeLerrvkaLekeNksLkseleelkkevekLks 61 
                                       e + L+  + +L +  + L  + e+ k ++ +L+s
  gi|557694562|ref|YP_008797616.1| 270 EYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQS 304
                                       44556666666666666666666666666666655 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   9.4   0.00041      0.05     208     285 ..     156     229 ..     132     234 .. 0.81
   2 ?    7.8   3.1     0.018       2.2      48     139 ..     242     333 ..     230     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00041
                                       XXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 208 sealrsakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklseleeelaeireemarqlre 284
                                        ++l++a+e+i++lr +iq le+e++ l+   +   +    + ++l a l++ +e++++le+ ++++ ee  + ++ 
  gi|557694562|ref|YP_008797616.1| 156 LNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALN----TAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDR 228
                                       468999********************99876554444....556777788888999999999999999999888877 PP

                                       H CS
                          Filament 285 Y 285
                                       Y
  gi|557694562|ref|YP_008797616.1| 229 Y 229
                                       7 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Filament  48 lkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyekelnkreevEaelkalrkdldeatlarvdLek 124
                                        +e+  +e e l    ++l ++  +l  e++ l+++ ++l++ ye  +++ e++ +++  l+ +lde   +  dL  
  gi|557694562|ref|YP_008797616.1| 242 SYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELGDLRL 318
                                       45566666677777788888888888899999999999999999999999999999999999999999999999999 PP

                                       XXXXXXXXXXXXXXX CS
                          Filament 125 kvesLkeelaflkkv 139
                                       ++  L +e  + +++
  gi|557694562|ref|YP_008797616.1| 319 RYSLLSDENLLHRNI 333
                                       999999887777765 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.5       0.1        12      17      88 ..     152     221 ..     146     229 .. 0.62
   2 ?   11.3   5.6    0.0035      0.43       7      87 ..     205     283 ..     203     284 .. 0.89
   3 ?    6.9   0.4     0.086        10      10      50 ..     271     311 ..     268     321 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.1
                      Occludin_ELL  17 FnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrceyLkek 88 
                                       +++  +  ++ ++++++++ +++ Le+e+++l+++ +e  ++++ +  ++++    +e ++ ++r++ ++e+
  gi|557694562|ref|YP_008797616.1| 152 YQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSS--REEIKRLEQRIQTMSEE 221
                                       55555556666667777777777777777777777777777777766666666..45555555566555554 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0035
                      Occludin_ELL   7 aeqrerYkaeFnkeYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeykklkkdpeyqekkkrce 83 
                                        e+ +r ++  ++  +eY++l+++  ++  +++ L++  + l+++++  ++  +++l++y++l  ++ey   ++ ++
  gi|557694562|ref|YP_008797616.1| 205 REEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNL--TKEYSMLQATFN 279
                                       5666666777777789***********************************************..788999999999 PP

                      Occludin_ELL  84 yLke 87 
                                       +L+e
  gi|557694562|ref|YP_008797616.1| 280 QLHE 283
                                       9986 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.086
                      Occludin_ELL  10 rerYkaeFnkeYkeYkelhaeleevskkfseLerelkelke 50 
                                       ++  +a Fn+ ++ Y  l ++ e++++++  L+++l+e ++
  gi|557694562|ref|YP_008797616.1| 271 YSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRR 311
                                       5566799****************************998765 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 ?   11.8  11.6    0.0016       0.2      22      96 ..     158     236 ..     154     321 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0016
                                       XXXHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHH......HCS-TTHHHH...HHHHHHHHH.STSS-HHHHH CS
                      Spore_III_AB  22 rlkrrlkeleelkralellegeirygatpLpealekla......eksesplsef...feevaerleekegesfeeaw 89 
                                       +l+r  +++++l+  +++le+ei+  +t L+eal+  a      ++s+++++++   +++++e     e ++++++ 
  gi|557694562|ref|YP_008797616.1| 158 DLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAmltarlNSSREEIKRLeqrIQTMSE-----EYRQLNDRY 229
                                       688999********************************8886654444444444222222222.....344444443 PP

                                       HHHHHHH CS
                      Spore_III_AB  90 eeavekl 96 
                                        ++v +l
  gi|557694562|ref|YP_008797616.1| 230 VSTVGEL 236
                                       3333333 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.6      0.01       1.2      24     120 ..     133     225 ..     126     231 .. 0.85
   2 ?   11.9   7.1    0.0011      0.13      68     150 ..     236     314 ..     232     334 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.01
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC CS
                              SHE3  24 qqsqeLleklelaqkkeskflenlaslkhENdnLsslLkRKerrlkdlekelselkesveelklekkqlkkrlenss 100
                                       ++ q L++  ++a+ ++  + + l+ l    ++++ l  R +  ++ le+e++ l+++ ee+      l  rl++s 
  gi|557694562|ref|YP_008797616.1| 133 TTYQPLTHTWHIAAVRQRTYQDLLNDLNRAQEQINQL--RTT--IQILETEINTLRTRLEEALNTAAMLTARLNSSR 205
                                       5668888888999999999999999999999999887..555..566888999************************ PP

                                       CHHHHHHHHHHHHHHHHHHH CS
                              SHE3 101 aseteleeelerlkvqYdal 120
                                       ++ ++le++++ +  +Y  l
  gi|557694562|ref|YP_008797616.1| 206 EEIKRLEQRIQTMSEEYRQL 225
                                       *************9999766 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  68 lkdlekelselkesveelklekkqlkkrlenssaseteleeelerlkvqYdalvdsqkeYkehYqqeieeLkeslek 144
                                       lk l+  ++ l++++e l+++ +ql ++ +n++++ + l++ +++l+  Y+ lv  ++  k+    +i  L+ +l++
  gi|557694562|ref|YP_008797616.1| 236 LKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQ----QIGYLQSQLDE 308
                                       68889999999999999999999999999999999999999999999999999999988776....55555555555 PP

                                       HHHHHH CS
                              SHE3 145 lklene 150
                                        ++e  
  gi|557694562|ref|YP_008797616.1| 309 NRRELG 314
                                       555543 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.2   0.00077     0.094     184     226 ..     148     190 ..     132     195 .. 0.85
   2 ?    4.2   0.9       0.2        24     188     220 ..     193     226 ..     186     230 .. 0.71
   3 ?    7.9   1.9     0.015       1.8      39      97 ..     256     313 ..     234     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00077
                           DUF4618 184 ktlenqvlkkeiekfrefieeleeeipeLkaeveqLqaqaeep 226
                                       + +  q+l++ +++ +e+i++l+  i+ L+ e+++L+ + ee 
  gi|557694562|ref|YP_008797616.1| 148 RQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEA 190
                                       456678999999************************9998876 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.2
                           DUF4618 188 nqvlk.keiekfrefieeleeeipeLkaeveqLq 220
                                       +++++   ++  re+i++le++i+++ +e  qL+
  gi|557694562|ref|YP_008797616.1| 193 TAAMLtARLNSSREEIKRLEQRIQTMSEEYRQLN 226
                                       4444426778889999999999999988888886 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.015
                           DUF4618  39 kvrklLqqyeklktvisileksskkqleqakaeLqeweekeekklekLeqqleqlnakv 97 
                                       + ++lL+ y  l++  s+l+    +ql+++ + L + +e  ++++ +L+ ql++  +++
  gi|557694562|ref|YP_008797616.1| 256 SYQQLLHDYRNLTKEYSMLQATF-NQLHELYEGLVTRHESAKQQIGYLQSQLDENRREL 313
                                       55789*************99776.67**************************9987776 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.4   0.00029     0.035      94     173 ..     146     221 ..     123     224 .. 0.82
   2 ?    2.5   0.1      0.91   1.1e+02     104     130 ..     278     304 ..     254     316 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 0.00029
                      Bacillus_HBL  94 avdkkdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedl 170
                                       av + + ++ll++l++ qe+i+q   +++ l  e++ l+++l++  +    +++ lt+ l+++  +i+ l+++i+++
  gi|557694562|ref|YP_008797616.1| 146 AVRQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALN----TAAMLTARLNSSREEIKRLEQRIQTM 218
                                       45888889999999999999999999999999999999999987764....57889*******************99 PP

                      Bacillus_HBL 171 qgk 173
                                        ++
  gi|557694562|ref|YP_008797616.1| 219 SEE 221
                                       876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.91
                      Bacillus_HBL 104 lellekLqeeiqqnqkevkqlikeLkk 130
                                        ++l++L+e++++  +++kq+i+ L++
  gi|557694562|ref|YP_008797616.1| 278 FNQLHELYEGLVTRHESAKQQIGYLQS 304
                                       467899999999999999999998875 PP

>> Rabaptin  Rabaptin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   0.00015     0.018     159     201 ..     152     194 ..     143     203 .. 0.88
   2 ?    1.5   5.0      0.76        92      45     166 ..     204     333 ..     195     347 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00015
                          Rabaptin 159 eenledemkkaqedaeklrsvvmpmekeiaalkeklteaedki 201
                                        ++l +++ +aqe+ ++lr+ +  +e ei +l+ +l ea +  
  gi|557694562|ref|YP_008797616.1| 152 YQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTA 194
                                       57899********************************997765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.76
                          Rabaptin  45 keedlkrqnavlqaaqeeldalrvqlaearaelenikavatv.s.entk.qeaidevkkqwq...eevaslqaimke 115
                                         e++kr +  +q+  ee  +l+ + + +  el++++a   + s en     + +++ ++++   +e + lqa + +
  gi|557694562|ref|YP_008797616.1| 204 SREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMlSrENEAlSTSYQQLLHDYRnltKEYSMLQATFNQ 280
                                       46899999999999999999999999999999999998654313233221233444444443111688899999998 PP

                          Rabaptin 116 tvreye..vqfhrrleqeraqwaqyresaereiadlrrrlsegqeeenledem 166
                                           ye  v  h+  +q+    +   +   re  dlr r s   +e+ l  ++
  gi|557694562|ref|YP_008797616.1| 281 LHELYEglVTRHESAKQQIGYLQSQLDENRRELGDLRLRYSLLSDENLLHRNI 333
                                       88888833344555555555444455667799999999999888877776665 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  15.9   0.00059     0.072     100     177 ..     162     239 ..     143     261 .. 0.39

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00059
                             ATG16 100 laqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrk 176
                                        ++++++l +++q le+++++ ++rl+e+ ++ a l+ +l++ +ee++ +e+ +q++ +E+ +L+ ++ +   +l+ 
  gi|557694562|ref|YP_008797616.1| 162 AQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKA 238
                                       23333333344444444444444444444444444444444444444444444443333333333322222222222 PP

                             ATG16 177 l 177
                                       l
  gi|557694562|ref|YP_008797616.1| 239 L 239
                                       2 PP

>> BRE1  BRE1 E3 ubiquitin ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   7.3    0.0025       0.3      10      93 ..     157     240 ..     148     242 .. 0.90
   2 ?   11.5   6.9    0.0019      0.23       1      95 []     176     270 ..     176     273 .. 0.81
   3 ?    4.8   0.2      0.25        30       2      49 ..     268     315 ..     267     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0025
                              BRE1  10 kafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieqLkelekefv 86 
                                       +  + ++eq++++ + ++ile +++ l +  ++a +    +    ++ + e+k+L + ++  se   qL+++  ++v
  gi|557694562|ref|YP_008797616.1| 157 NDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTV 233
                                       66788999********************************************************9999999999999 PP

                              BRE1  87 rklkele 93 
                                        +lk+l+
  gi|557694562|ref|YP_008797616.1| 234 GELKALQ 240
                                       9988876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0019
                              BRE1   1 lqkELvklekafeelseqlskkvkeltileekklrleaekakadqkyfaamrskdalenelkkLnkllsKsselieq 77 
                                       l++E+  l +  ee+ +++ ++++ l +  e+++rle+ ++   ++y +++    +   elk+L+++++  s   e+
  gi|557694562|ref|YP_008797616.1| 176 LETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEA 252
                                       67899999999999999999999999999999999999999999999999999999999999999887776666666 PP

                              BRE1  78 Lkelekefvrklkeleke 95 
                                       L  +  ++ +   +l ke
  gi|557694562|ref|YP_008797616.1| 253 LSTSYQQLLHDYRNLTKE 270
                                       666666666665555554 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.25
                              BRE1   2 qkELvklekafeelseqlskkvkeltileekklrleaekakadqkyfa 49 
                                       +kE   l++ f++l+e+ + +v+ +++ ++++  l+++ ++ +++  +
  gi|557694562|ref|YP_008797616.1| 268 TKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELGD 315
                                       677788999**************************9999998887655 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   4.2   0.00026     0.031     195     323 ..     159     304 ..      97     354 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00026
                             LMBR1 195 ksdldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklks....... 264
                                         + +e++++l++ ++ l+te +    +le+ l+ ++ l+ ++++s +  k le+ ++++ ee+++ + +       
  gi|557694562|ref|YP_008797616.1| 159 LNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRyvstvge 235
                                       44555666666666666666666666777777777777777777777666777777777777777776667777776 PP

                             LMBR1 265 ..nenkteeslaklekqlika..............lqkrertekqwkrllekalelediiknksskekefksses 323
                                           ++++e l++++++l ++               +  + t +q+ +l       e ++   +s+++++  ++s
  gi|557694562|ref|YP_008797616.1| 236 lkALQASYEMLSRENEALSTSyqqllhdyrnltkeYSMLQATFNQLHELY------EGLVTRHESAKQQIGYLQS 304
                                       77555566666666655555522221111111000222222222222222......2345555555555555544 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.7       0.1        12      15      52 ..     151     188 ..     143     198 .. 0.57
   2 ?    9.0   0.9    0.0082      0.99       5      56 ..     204     255 ..     196     259 .. 0.88
   3 ?    6.9   0.7     0.034       4.1       9      54 ..     264     309 ..     248     333 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.1
                           DUF4795  15 aieklqeelekleekvkelekrledkekklealkkqie 52 
                                       ++++l ++l++ +e+ ++l ++++ +e ++++l+  +e
  gi|557694562|ref|YP_008797616.1| 151 TYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLE 188
                                       44555555555555555555555555555555554444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0082
                           DUF4795   5 saellkklqeaieklqeelekleekvkelekrledkekklealkkqieelek 56 
                                       s+e +k l++ i+ ++ee+ +l+++  ++ ++l++++ + e+l  + e+l +
  gi|557694562|ref|YP_008797616.1| 204 SREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEALST 255
                                       4566999**********************************99998888765 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.034
                           DUF4795   9 lkklqeaieklqeelekleekvkelekrledkekklealkkqieel 54 
                                       + +l ++++ lq+  ++l+e  + l +r+e  ++++  l++q++e 
  gi|557694562|ref|YP_008797616.1| 264 YRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDEN 309
                                       6788889999999999999999999999999999999999988875 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 ?    8.7   8.2     0.014       1.7       9      83 ..     153     228 ..     149     229 .. 0.66
   2 ?   11.5   6.4    0.0019      0.23      19      88 ..     227     299 ..     224     338 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.014
                             Mod_r   9 qelledeeklealvktl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqe 83 
                                       q+ll+d    ++ +++l  +++ l++e   l++  e+ ++    l  +l+  r+e++   + ++++++e+++++ +
  gi|557694562|ref|YP_008797616.1| 153 QDLLNDLNRAQEQINQLrTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDR 228
                                       6777777777777777756677777777777777777776666667777777777777777777777777766544 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0019
                             Mod_r  19 ealvktlpevkqlkeekeellaeneslaeknlsl.ep..eleelrselqekleelkelekefeekeqeldell 88 
                                       +++v+t+ e+k+l+++ e+l  ene+l  +  +l ++   l+++ s lq+++++l+el++ +   ++  ++ +
  gi|557694562|ref|YP_008797616.1| 227 DRYVSTVGELKALQASYEMLSRENEALSTSYQQLlHDyrNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQI 299
                                       7899999*********************766666333558888888888888888888887766666555555 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   7.6   0.00039     0.047       8      89 ..     153     231 ..     149     242 .. 0.64
   2 ?    4.9   1.8      0.26        31      15      58 ..     244     292 ..     231     326 .. 0.38

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00039
                                       HHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.....-HHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH   8 qkileespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkle....keekeqelqkkeqelqqkqqqka 80 
                                       q +l++ + +++  +ql ++++ l++e++++++ l+++ ++              +  ++e++++eq++q+ +++++
  gi|557694562|ref|YP_008797616.1| 153 QDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAA------MltarLNSSREEIKRLEQRIQT-MSEEY 222
                                       4555555666666666666666666666666666665555442......2445456666669999999999.99999 PP

                                       HHHHHHHHH CS
                              OmpH  81 qelqkkqqe 89 
                                       ++l+++   
  gi|557694562|ref|YP_008797616.1| 223 RQLNDRYVS 231
                                       999988755 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.26
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..........- CS
                              OmpH  15 pegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkl.e........k 58 
                                       +   + +e l + +++l  +++++ ke+  lq++++    +l e         
  gi|557694562|ref|YP_008797616.1| 244 EMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFN----QLhElyeglvtrH 292
                                       222222233333333333333333333333333332....1111223332221 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 ?   10.4   8.0    0.0042      0.51       7      69 ..     166     228 ..     154     232 .. 0.57
   2 ?    4.2   1.2      0.35        43      15      72 ..     237     294 ..     234     309 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0042
                        TMF_DNA_bd   7 lkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleer 69 
                                       +++   +I+ L +E   L+    +  nt  +L + ++ + +eik+l++++++ ++e  +l++r
  gi|557694562|ref|YP_008797616.1| 166 INQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDR 228
                                       333333444455555555555566666666666666666666666666666666666666665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.35
                        TMF_DNA_bd  15 aqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleeleerlke 72 
                                       ++L++  e Ls ++ +l+++  +L  + ++l+ke + l+   ++l +  e l  r+++
  gi|557694562|ref|YP_008797616.1| 237 KALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHES 294
                                       5677777777777778888888888888888887777777777777766666666555 PP

>> Borrelia_lipo_1  Borrelia burgdorferi virulent strain associated lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   6.6   0.00061     0.074      62     189 ..     162     284 ..     144     304 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00061
                   Borrelia_lipo_1  62 teeskkarkrlYasLnyneeeLkklseIlnnnekqkkkifntilelglnvQlklekvinhlyskkdtLdklei...e 135
                                       ++e+++  + +  +L   e e+++l + l+++++  + +   +++   +  ++le+ i+ + ++  +L+   +    
  gi|557694562|ref|YP_008797616.1| 162 AQEQINQLRTTIQIL---ETEINTLRTRLEEALNTAAMLTARLNSSREE-IKRLEQRIQTMSEEYRQLNDRYVstvG 234
                                       344444444455555...4566777777777888888888888888777.799***************987552237 PP

                   Borrelia_lipo_1 136 dLkklknslekllslreifskmikklLlDYqnntnsIktdnskLksyvnklykq 189
                                       +Lk+l  s e l    e  s++ ++lL DY+n    + ++ s L+  +n+l + 
  gi|557694562|ref|YP_008797616.1| 235 ELKALQASYEMLSRENEALSTSYQQLLHDYRN----LTKEYSMLQATFNQLHEL 284
                                       9*******************************....667888888888765443 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  12.6    0.0031      0.37     124     248 ..     148     293 ..     138     339 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0031
                           DUF4407 124 keqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk.............gtgttgvaGkgpaake 187
                                       ++++ ++l ++l+++++qi++l+++i+ +e+++++lr+ +++ l+ +              +  +++++   +++++
  gi|557694562|ref|YP_008797616.1| 148 RQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAmltarlnssreeiKRLEQRIQTMSEEYRQ 224
                                       44444555566666666666666666666666666666666555544455444544444443333445556666666 PP

                           DUF4407 188 kkaqldaaqaelaelkakld........atarlaalraelaeleaerakeraasqaaaaaddGllarle 248
                                        ++ +     el++l+a+ +         ++  ++l   +  l++e++  +a++++ ++   Gl +r e
  gi|557694562|ref|YP_008797616.1| 225 LNDRYVSTVGELKALQASYEmlsreneaLSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHE 293
                                       666666666777777766668888887866677777777777777777777777777777777777765 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   6.6      0.14        17      43     104 ..     155     217 ..     147     223 .. 0.84
   2 ?    2.3   8.7       1.1   1.4e+02       3      77 ..     165     231 ..     163     251 .. 0.57
   3 ?   10.0   2.6    0.0048      0.58      23      88 ..     209     276 ..     208     285 .. 0.84
   4 ?    2.4   0.0       1.1   1.3e+02       5      28 ..     286     309 ..     282     316 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.14
                              SKA2  43 LlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqqLqasa.elpplseeeqe 104
                                       Ll++l++ +e++++L++ ++ l +e   l ++++  l++  +l+ +L+ s  e++ l+++ q+
  gi|557694562|ref|YP_008797616.1| 155 LLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSReEIKRLEQRIQT 217
                                       899999999999999999999999999999999999999999999999888777776665555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 1.1
                              SKA2   3 avdklealFqkaesdLdyvqhrLekefqqsypdnaeNpvkLlerlkkvkeelqaLkeqceellaekkelidkirt 77 
                                       ++++l+++ q  e++++++  rLe+ ++++            +rl+  +ee++ L+++++ +++e ++l d+  +
  gi|557694562|ref|YP_008797616.1| 165 QINQLRTTIQILETEINTLRTRLEEALNTAAML--------TARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVS 231
                                       566777777777777777777777666555444........4455555555555555555555555555554444 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0048
                              SKA2  23 hrLekefqqsypdna...eNpvkLlerlkkvkeelqaLkeqceellaekkelidkirttlvanrellqq 88 
                                       +rLe+++q+  ++        v  + +lk++++ ++ L+++ e+l+++ ++l    r+ l + +++lq 
  gi|557694562|ref|YP_008797616.1| 209 KRLEQRIQTMSEEYRqlnDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRN-LTKEYSMLQA 276
                                       58888888877777676567888999***************************99986.5599999996 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 1.1
                              SKA2   5 dklealFqkaesdLdyvqhrLeke 28 
                                       ++l++  ++a++++ y+q++L++ 
  gi|557694562|ref|YP_008797616.1| 286 EGLVTRHESAKQQIGYLQSQLDEN 309
                                       788999999************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 ?    3.3   0.1      0.84     1e+02      56      92 ..     153     189 ..     146     195 .. 0.87
   2 ?    9.6   1.3    0.0097       1.2      25     106 ..     192     270 ..     187     298 .. 0.79
   3 ?    4.6   0.3      0.35        43      38      93 ..     247     302 ..     237     318 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.84
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                           T3SSipB  56 kgatddleaaiekadqaksaadaatkkvdeaqkrlke 92 
                                       +++ +dl+ a+e+++q+   ++ ++  ++   +rl+e
  gi|557694562|ref|YP_008797616.1| 153 QDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEE 189
                                       56778999999***********999999999999987 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0097
                                       HHHHHHHHHHHHTTTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--------- CS
                           T3SSipB  25 nrlaawkamskaqqeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeLaPdePeka 101
                                       n  a+  a  ++ +e+ ++l + +qt  +e +++ d +   + +++ +++ ++ + +  ++  ++ ++L     +++
  gi|557694562|ref|YP_008797616.1| 192 NTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLL---HDYR 265
                                       55677788889999999************************************99999999989888883...3333 PP

                                       CHHHH CS
                           T3SSipB 102 kleaa 106
                                       +l ++
  gi|557694562|ref|YP_008797616.1| 266 NLTKE 270
                                       33333 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.35
                                       TTTT----STHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                           T3SSipB  38 qeaasklSdelqtalseakgatddleaaiekadqaksaadaatkkvdeaqkrlkeL 93 
                                         ++++lS   q++l++ +++t+++   ++  +q++  ++ +  + + a++++  L
  gi|557694562|ref|YP_008797616.1| 247 SRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYL 302
                                       56788999999999999999999999999999999888877776666666655444 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.9   0.00041      0.05      40      87 ..     145     192 ..     132     196 .. 0.87
   2 ?    7.3   4.0      0.06       7.2      14      86 ..     189     261 ..     188     270 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 0.00041
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  40 aatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdaea 87 
                                       aa  ++t ++L ++L++ + q ++ ++ +q l+ ei++L  +L++a+ 
  gi|557694562|ref|YP_008797616.1| 145 AAVRQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALN 192
                                       667789**************************************9975 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  14 ecrnvtrlLerqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdae 86 
                                       e  n+  +L ++L+ ++e++++ e+ ++t ++   +L++     + + +  qa  + l +e++ L  + q+ +
  gi|557694562|ref|YP_008797616.1| 189 EALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLL 261
                                       56699999***************************************99999***********9998888766 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   7.1    0.0011      0.13      23     104 ..     173     254 ..     158     256 .. 0.85
   2 ?    8.4   1.3     0.029       3.5      47     102 ..     239     294 ..     231     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0011
                           DUF4472  23 reqheaekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkk 99 
                                        + +e+e+  l +++ ++ n+   l ++ +  +eei+ l++r +++ ee ++l+++yv++  +++al++ +e   ++
  gi|557694562|ref|YP_008797616.1| 173 IQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRE 249
                                       3456888888889998888999999999999*****************************************99999 PP

                           DUF4472 100 qqels 104
                                       ++ ls
  gi|557694562|ref|YP_008797616.1| 250 NEALS 254
                                       99987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.029
                           DUF4472  47 lelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqe 102
                                       l++  e + +e+++l++ +++l ++ ++l++ey++l+  + +l + +e  +++ + 
  gi|557694562|ref|YP_008797616.1| 239 LQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHES 294
                                       55556667889999999999999999999999999999999999988887777665 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 ?    8.0   7.7     0.016       1.9      64     135 ..     157     228 ..     143     239 .. 0.82
   2 ?   10.9   4.4     0.002      0.24      68     139 ..     238     309 ..     230     316 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.016
                      HAUS-augmin3  64 edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqee 135
                                       +d + +++++++++++++ Le+e+++L+   +  l+   +L++  +s  +e ++le++ ++++++ +++++ 
  gi|557694562|ref|YP_008797616.1| 157 NDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDR 228
                                       456677889999999999999999999999999999999999999999999999999999999999988775 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.002
                      HAUS-augmin3  68 llevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelrae 139
                                       +l+++ e +    eaL +  q+L +  + ++k++++Lq++ ++l++  + l +++++ak+++  +q++l ++
  gi|557694562|ref|YP_008797616.1| 238 ALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDEN 309
                                       5667778888899*************************************************9999998765 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.8    0.0016       0.2     278     348 ..     159     229 ..     152     245 .. 0.86
   2 ?    4.4   0.3      0.14        17     279     343 ..     251     315 ..     233     332 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                               FH2 278 leslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeakelvkelveYf 348
                                       l+  ++++++l++ ++ le+e+++ ++  e+  +  + l+  l++++e++k+le+  +++ e++ +l + +
  gi|557694562|ref|YP_008797616.1| 159 LNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRY 229
                                       566688999999999999999999999999999999**************************999987665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHHHHHHHHCCTTSSTT-THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                               FH2 279 eslekevkklekglkklekelessekkeepsdkflevlkeflkeaeeklkkleeelkeakelvke 343
                                       e+l+++ ++l ++ ++l ke +  +  +++ ++++e l +  ++a++++  l+++l+e ++++ +
  gi|557694562|ref|YP_008797616.1| 251 EALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELGD 315
                                       45555555555555566665555555666666688888888888888888888888877666655 PP

>> DUF4094  Domain of unknown function (DUF4094)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00099      0.12      50      87 ..     148     185 ..     122     186 .. 0.84
   2 ?    0.2   0.9       8.3     1e+03      65      81 ..     205     221 ..     192     311 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00099
                           DUF4094  50 aesrskdilgevskthkaiqtLdktissLemeLaaara 87 
                                        +++ +d+l++ +++++ i +L  ti  Le+e+ + r+
  gi|557694562|ref|YP_008797616.1| 148 RQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRT 185
                                       455578**************************998776 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 8.3
                           DUF4094  65 hkaiqtLdktissLeme 81 
                                       +++i++L+++i ++  e
  gi|557694562|ref|YP_008797616.1| 205 REEIKRLEQRIQTMSEE 221
                                       34444444444333322 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 ?   12.3  14.0    0.0008     0.097       6     108 ..     145     247 ..     141     254 .. 0.90
   2 ?    4.3   3.1      0.23        28      84     151 ..     258     324 ..     244     334 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0008
                        Lebercilin   6 lsarllkikeLqnelaelqskleelrkEnklLkrlqkrqekaLskyedteaeLpqllarhneEvrvlrerlRksqek 82 
                                          r++ +++L n l+ +q+++++lr+  ++L++       +L+   +t a L   l++ +eE++ l +r+  + e+
  gi|557694562|ref|YP_008797616.1| 145 AAVRQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEE 221
                                       567999999***********************988888888888888****************************** PP

                        Lebercilin  83 erelekklkekeaellrlkdklkklk 108
                                       +r+l+ +  ++  el+ l+ +++ l+
  gi|557694562|ref|YP_008797616.1| 222 YRQLNDRYVSTVGELKALQASYEMLS 247
                                       *******9999999999998877665 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.23
                        Lebercilin  84 relekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleakleekeekikeLerklelee 151
                                       ++l  + ++  +e   l+ + ++l++L  +     +e  ++++  l+++l+e+++++ +L+ +  l++
  gi|557694562|ref|YP_008797616.1| 258 QQLLHDYRNLTKEYSMLQATFNQLHELY-EGLVTRHESAKQQIGYLQSQLDENRRELGDLRLRYSLLS 324
                                       5555566777788888999999999999.4456688888999*************9999987666654 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 ?   10.1   7.8    0.0059      0.72      15      70 ..     167     222 ..     156     223 .. 0.94
   2 ?    3.0   0.2      0.99   1.2e+02      37      61 ..     238     262 ..     233     269 .. 0.71
   3 ?    4.7   0.1      0.28        34       9      51 ..     266     308 ..     262     326 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0059
                          JIP_LZII  15 teLletknaLnvvkddLIarvdeLtsereiLreEleslqkakerlesrikelEeel 70 
                                       ++L++t   L++  + L +r++e  +   +L+  l+s++++ +rle+ri+ + ee 
  gi|557694562|ref|YP_008797616.1| 167 NQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEY 222
                                       79**************************************************9985 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.99
                          JIP_LZII  37 eLtsereiLreEleslqkakerles 61 
                                        L+  +e+L+ E+e+l ++ ++l  
  gi|557694562|ref|YP_008797616.1| 238 ALQASYEMLSRENEALSTSYQQLLH 262
                                       5677778888888888888777755 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.28
                          JIP_LZII   9 nLikENteLletknaLnvvkddLIarvdeLtsereiLreEles 51 
                                       nL kE++ L++t n L    + L++r +  +++   L++ l++
  gi|557694562|ref|YP_008797616.1| 266 NLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDE 308
                                       7888888888888888777777777766666666566655555 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 ?    7.7   0.6     0.038       4.6      10      53 ..     146     189 ..     139     199 .. 0.86
   2 ?    6.4   3.9     0.097        12      17      93 ..     195     275 ..     188     281 .. 0.67
   3 ?    4.4   0.5      0.39        48      20      62 ..     264     307 ..     244     312 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.038
                            CC2-LZ  10 kvkkeeieeLkaqlqaaeealaakqeeidelkeeikkkeeelet 53 
                                        v+++ +++L + l+ a+e++++ +  i+ l++ei+  ++ le+
  gi|557694562|ref|YP_008797616.1| 146 AVRQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEE 189
                                       56688999***************************999998874 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.097
                            CC2-LZ  17 eeLkaqlqaaeealaakqeeidelkeeikkkee....eletisvlkaQaevYrsDFeaEReaReklheekerlaaql 89 
                                         L+a+l++  e +++ +++i+ + ee ++ ++     + +++ l+a  e+ ++  ea  ++ ++l ++  +l ++ 
  gi|557694562|ref|YP_008797616.1| 195 AMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDryvsTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEY 271
                                       67999************************999954444446666666666665555555555555555555555555 PP

                            CC2-LZ  90 eelq 93 
                                         lq
  gi|557694562|ref|YP_008797616.1| 272 SMLQ 275
                                       5555 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.39
                            CC2-LZ  20 kaqlqaaeealaakqeeidelkeeikkkeeele.tisvlkaQae 62 
                                       +++l++    l+a  ++++el+e +  ++e  + +i +l+ Q +
  gi|557694562|ref|YP_008797616.1| 264 YRNLTKEYSMLQATFNQLHELYEGLVTRHESAKqQIGYLQSQLD 307
                                       67888888899999999999999888777766669*****9987 PP

>> Cir_Bir_Yir  Plasmodium variant antigen protein Cir/Yir/Bir
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.4    0.0014      0.17     100     228 ..     142     322 ..      87     352 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0014
                       Cir_Bir_Yir 100 YnkyiennekYkkkindvteyknykdlIdkkkelmnidikdi.skfYdafklLCnmyteldekksnckkylekaneF 175
                                       +      ++ Y++  nd ++ ++  + + +  ++++++i+ +  ++ +a+++   +   l++++++ k++ +  +  
  gi|557694562|ref|YP_008797616.1| 142 WHIAAVRQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLrTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTM 218
                                       44445556778888888888888888888999999999999835799****************************** PP

                       Cir_Bir_Yir 176 vekYkelnndsnit................kdssynqvLstLsndYnnlkkkckkekkkipslpeikk......... 227
                                        e+Y++ln+ +  t                +++  +    +L  dY nl k+++  + ++++l e+ +         
  gi|557694562|ref|YP_008797616.1| 219 SEEYRQLNDRYVSTvgelkalqasyemlsrENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEglvtrhesa 295
                                       ********999888899999999998888777777777778999999999998766767888887776777676666 PP

                       Cir_Bir_Yir 228 ..........................t 228
                                                                  
  gi|557694562|ref|YP_008797616.1| 296 kqqigylqsqldenrrelgdlrlrysL 322
                                       666666666666666666666665552 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9  17.1    0.0011      0.13      28     193 ..     152     317 ..     138     322 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0011
                         Laminin_I  28 LqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilek 104
                                        q  l+  +  +++i+ l  +++ L+ e+++L ++++++l  a  + a+ +   +++k L++ i+ + ++   ++ +
  gi|557694562|ref|YP_008797616.1| 152 YQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDR 228
                                       466788888899999999999******************************************************98 PP

                         Laminin_I 105 .vatlne.neealpssklseela....eaqrlLeelrsRdftkqleeaeaelkaAqkLLsrvqtllqklqeenkaLk 175
                                        v+t++e ++ +++ + ls+e +      q+lL     R++tk+     a  ++  +L++   t+ ++ +++   L 
  gi|557694562|ref|YP_008797616.1| 229 yVSTVGElKALQASYEMLSRENEalstSYQQLLHDY--RNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYL- 302
                                       356677799999999999998762222468899998..9*************************999999999999. PP

                         Laminin_I 176 ealrdsLaeyeakLsDlr 193
                                          +++L+e   +L Dlr
  gi|557694562|ref|YP_008797616.1| 303 ---QSQLDENRRELGDLR 317
                                       ...677888888888887 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 ?   12.7  11.9    0.0015      0.19       8      93 ..     161     253 ..     151     255 .. 0.84
   2 ?    7.2   5.4     0.077       9.3       5      90 ..     242     327 ..     235     333 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0015
                    PRKG1_interact   8 eekeenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeel........... 73 
                                       +++e+ ++L+++++ le e+++l+++le++ +      +  ++ l+ +++e + le++i+ ++ee            
  gi|557694562|ref|YP_008797616.1| 161 RAQEQINQLRTTIQILETEINTLRTRLEEALN----TAAMLTARLNSSREEIKRLEQRIQTMSEEYrqlndryvstv 233
                                       566777899999*************9999873....46778888999999***********9888877788888777 PP

                    PRKG1_interact  74 keleeLraenqrLkdEngAL 93 
                                        el++L+a+ + L  En+AL
  gi|557694562|ref|YP_008797616.1| 234 GELKALQASYEMLSRENEAL 253
                                       888999999*********98 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.077
                    PRKG1_interact   5 LYeeekeenerLkreLeelekelselkseleklkqqrqesvskrssllelekrerrslerkiseleeelkeleeLra 81 
                                        Ye   +ene L +  ++l ++ ++l++e + l+ + ++  +  + l+   ++ ++++    s+l+e+ +el +Lr 
  gi|557694562|ref|YP_008797616.1| 242 SYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELGDLRL 318
                                       599999***********999999999999999986644444455566666777888888888899************ PP

                    PRKG1_interact  82 enqrLkdEn 90 
                                         + L dEn
  gi|557694562|ref|YP_008797616.1| 319 RYSLLSDEN 327
                                       ********9 PP

>> Taxilin  Myosin-like coiled-coil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   6.9     0.011       1.4     244     306 ..     164     226 ..     149     228 .. 0.91
   2 ?    7.1   8.0     0.022       2.7       4     104 ..     206     313 ..     204     316 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.011
                           Taxilin 244 kEmekmtkktkklEketnlwkskfektnkallemaeertekkkeieklkkkiqkLeklcraLq 306
                                       + + ++   ++ lE e n+++++ e++ ++ + +++  + + +ei++l+++iq++++ +r+L+
  gi|557694562|ref|YP_008797616.1| 164 EQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLN 226
                                       557788899999***************999999999999**********************98 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.022
                           Taxilin   4 eqlkeslsklespeekleaLvkkyaelleerkrlqkqlkklkkkl.......eqlqkekeqlqaelskaalaksKLe 73 
                                       e++k + +++++  e++ +L  +y   + e k lq ++  l++++       +ql  +  +l++e s   ++ + L 
  gi|557694562|ref|YP_008797616.1| 206 EEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENealstsyQQLLHDYRNLTKEYSMLQATFNQLH 282
                                       56777777888888899999999999999999998887777766611111114555666666667777777777799 PP

                           Taxilin  74 kLcRelqkqnkklkeeskqrareeeekrkel 104
                                       +L   l ++ +  k++   ++ + +e+r+el
  gi|557694562|ref|YP_008797616.1| 283 ELYEGLVTRHESAKQQIGYLQSQLDENRREL 313
                                       9999999999999999999999999999887 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 ?   11.8  18.3    0.0013      0.15      18     184 ..     153     323 ..     144     328 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0013
                          KASH_CCD  18 kkLaeenskLkkavetaeetnakLteeieeLkkklkstQqa.lqkak...lleeEleelkalvkeleEkrarlkaqn 90 
                                       + L ++ ++ ++++++   t + L  ei+ L+++l     + ++      +  eE+  l + ++++ E+ ++l+ + 
  gi|557694562|ref|YP_008797616.1| 153 QDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTaAMLTArlnSSREEIKRLEQRIQTMSEEYRQLNDRY 229
                                       77888888889999999999999999999999999754433033333011344555566666777778888888888 PP

                          KASH_CCD  91 kqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealleektkqieeLklti 167
                                            e + L+a  e L  en+ l +  ++l +  ++L+ke + L+    +l+el     +  e  ++qi +L++++
  gi|557694562|ref|YP_008797616.1| 230 VSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQL 306
                                       77888888888888888888888888888888888888888888888777777777666666677788999999999 PP

                          KASH_CCD 168 eEyssiieeLraeksrL 184
                                       +E+++    Lr+  s L
  gi|557694562|ref|YP_008797616.1| 307 DENRRELGDLRLRYSLL 323
                                       99999999988876655 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.4   0.00098      0.12      16     103 ..     165     253 ..     151     256 .. 0.80
   2 ?    2.8   0.3      0.89   1.1e+02      57     107 ..     249     299 ..     237     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00098
                          LOH1CR12  16 rtne..vleklssrhllrlctRlqeHlavcAkavAadqaklverikevdakiitllaelrekqkqyasyaealskvn 90 
                                       + n+  +  ++   ++  l tRl e l+++A   A   +   e+ik ++++i+t+ +e r+ +++y s + +l+ ++
  gi|557694562|ref|YP_008797616.1| 165 QINQlrTTIQILETEINTLRTRLEEALNTAAMLTA-RLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQ 240
                                       44443333344556778899********9887655.678889****************************9999999 PP

                          LOH1CR12  91 elsdqlsriqiil 103
                                          + lsr +  l
  gi|557694562|ref|YP_008797616.1| 241 ASYEMLSRENEAL 253
                                       9999999887766 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.89
                          LOH1CR12  57 rikevdakiitllaelrekqkqyasyaealskvnelsdqlsriqiilediv 107
                                       +   ++++ ++ll + r+  k+y+   +++++++el + l   +   ++++
  gi|557694562|ref|YP_008797616.1| 249 ENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQI 299
                                       555678888999999999999999999999999999988876555555555 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 ?    7.2   2.3     0.042       5.1     155     189 ..     149     183 ..     129     188 .. 0.90
   2 ?   10.4  10.8    0.0043      0.52      75     179 ..     199     306 ..     184     317 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.042
                           UPF0242 155 qetieeqrsvlekrqdqieqLeskVrDlnyEiktL 189
                                       q+t +++ + l++ q+qi+qL + ++ l  Ei tL
  gi|557694562|ref|YP_008797616.1| 149 QRTYQDLLNDLNRAQEQINQLRTTIQILETEINTL 183
                                       78889999999**********************99 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0043
                           UPF0242  75 aklteldeglktkeealeelqeeeeeLkee.......ldakeeelerlkeenqqLqekleaiaedfeelkleleeqL 144
                                       a l + +e++k  e+ ++ + ee ++L+++       l+a +   e l +en+ L+   ++  +d+ +l +e+   L
  gi|557694562|ref|YP_008797616.1| 199 ARLNSSREEIKRLEQRIQTMSEEYRQLNDRyvstvgeLKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYS-ML 274
                                       45666678888888888888888888888877777777777777788888888888888888888888888774.56 PP

                           UPF0242 145 aekqellqeyqetieeqrsvlekrqdqieqLeskV 179
                                       +   ++l+e+ e ++  +++    ++qi+ L+s+ 
  gi|557694562|ref|YP_008797616.1| 275 QATFNQLHELYEGLVTRHES---AKQQIGYLQSQL 306
                                       66666666666666666654...446677777765 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   8.4    0.0057      0.69       3      69 ..     173     239 ..     159     259 .. 0.72
   2 ?    4.3   0.2      0.18        22     180     225 ..     280     325 ..     264     332 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0057
                       Tropomyosin   3 lkqveeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleealekLeea 69 
                                       ++ +e+e+++ + rle+a +  +  +++ ++  +E   l++riq++ ee ++ ++r  ++  +L+ +
  gi|557694562|ref|YP_008797616.1| 173 IQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKAL 239
                                       5667777777777777777777777777777777777777777777777777777777777766654 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.18
                       Tropomyosin 180 tLeekLkeaeeRaeeAErsvqkLekevdrledeleaekekykaise 225
                                       +L+e     ++R e A +++  L++++d+   el   + +y  +s+
  gi|557694562|ref|YP_008797616.1| 280 QLHELYEGLVTRHESAKQQIGYLQSQLDENRRELGDLRLRYSLLSD 325
                                       4555555668999***************999999999999987776 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 ?   12.9   6.9    0.0007     0.085      12      71 ..     144     203 ..     138     207 .. 0.85
   2 ?    3.6   7.1      0.56        68       3      66 ..     205     268 ..     203     278 .. 0.88
   3 ?    6.8   1.0     0.058         7      15      38 ..     294     317 ..     280     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0007
                     TolA_bind_tri  12 ilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrklea 71 
                                       i++ r+++  +l++ l++ q+++++LR  i+ l+ ++++l++r  +  +    + ++l++
  gi|557694562|ref|YP_008797616.1| 144 IAAVRQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNS 203
                                       566788999**********************************98877766666666555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.56
                     TolA_bind_tri   3 edrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerl 66 
                                        + ++rLE+ ++  s+   +l  +  +   el+ L+ + E l+ ++e l +  ++l  d  ++ 
  gi|557694562|ref|YP_008797616.1| 205 REEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLT 268
                                       6789*******************************************99999888887766665 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.058
                     TolA_bind_tri  15 arsqlllelqqqlealqqelreLR 38 
                                       + +q +  lq+ql+++++el +LR
  gi|557694562|ref|YP_008797616.1| 294 SAKQQIGYLQSQLDENRRELGDLR 317
                                       4457777899*********99998 PP

>> Perilipin  Perilipin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2  12.1    0.0011      0.14     220     383 ..     146     308 ..     144     313 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HH--...----------------------------- CS
                         Perilipin 220 klrerAyqhsleklrqakqraqealaqlsstldLiel....akkglsaanqklseaqekllqswlewkkkqqeesee 292
                                        +r+r+yq  l+ l     raqe + ql +t++++e+    +++ l++a +       +l+ s  e k+ +   ++ 
  gi|557694562|ref|YP_008797616.1| 146 AVRQRTYQDLLNDLN----RAQEQINQLRTTIQILETeintLRTRLEEALNTAAMLTARLNSSREEIKRLE---QRI 215
                                       689999999999987....8899999999999999761111444444444444444444433333333222...233 PP

                                       ----..SHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHH...HHHHGGG--SGGG--HHH CS
                         Perilipin 293 eeeeeeeeqvEsrtLsllrsltqqLqttcqslvssiqglPssvqekvqqarrsaee...lqaslskasslqdlsssl 366
                                       ++ +ee  q+  r  s++++l + Lq++++ l  + + l +s q+ ++  r+ ++e   lqa++++ + l +   + 
  gi|557694562|ref|YP_008797616.1| 216 QTMSEEYRQLNDRYVSTVGEL-KALQASYEMLSRENEALSTSYQQLLHDYRNLTKEysmLQATFNQLHELYEGLVTR 291
                                       344444889999999999999.57****************8888888777666665222666666666666655666 PP

                                       HHHHHHHHHHHHHHHHH CS
                         Perilipin 367 lassreqlakvreslde 383
                                        +s+++q+  ++  lde
  gi|557694562|ref|YP_008797616.1| 292 HESAKQQIGYLQSQLDE 308
                                       67899999999999997 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 ?    9.3  11.3    0.0092       1.1      16      92 ..     150     227 ..     144     232 .. 0.59
   2 ?    4.5   2.2      0.28        34      41     106 ..     232     297 ..     226     298 .. 0.83
   3 ?    7.9   0.3     0.026       3.2      35      83 ..     274     323 ..     273     326 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0092
                             DHR10  16 rkarelqakidalqvvekdlrscikllee.ieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenae 91 
                                       r +++l + ++  q+  ++lr +i++le+ i++   +leea  +++ l ++l++ ++e + le++++ +     + +
  gi|557694562|ref|YP_008797616.1| 150 RTYQDLLNDLNRAQEQINQLRTTIQILETeINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLN 226
                                       55555666666666666666666666654466666666666666666666666666666666666666665555555 PP

                             DHR10  92 e 92 
                                       +
  gi|557694562|ref|YP_008797616.1| 227 D 227
                                       5 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.28
                             DHR10  41 lleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekre 106
                                        + e++a +a++e  +++ ++l+  ++++ ++ r l+++ ++lq   ++ +e +e l  ++e  ++
  gi|557694562|ref|YP_008797616.1| 232 TVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQ 297
                                       567888889999999999999999999999999999999999999999999999988877777665 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.026
                             DHR10  35 lrscikllee.ieaelakleeakkklkelrdaleekeielrelerkeerl 83 
                                       l++++++l+e  e  + ++e+ak+++  l+ +l+e+++el +l  + ++l
  gi|557694562|ref|YP_008797616.1| 274 LQATFNQLHElYEGLVTRHESAKQQIGYLQSQLDENRRELGDLRLRYSLL 323
                                       567788888845777899**********************9999887766 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   5.0   0.00083       0.1     365     452 ..     153     242 ..     134     248 .. 0.82
   2 ?    4.4   1.0     0.095        12     282     345 ..     240     314 ..     237     321 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00083
                            AAA_13 365 esikklvaeineliakhNekvanleeekeeakkklelhl..veeleseldeykkkykklekaieklekelkeeeael 439
                                       + + +++++++e+i++   +++ le+e +++++ le  l  ++ l++ l+   +++k+le+ i+ + +e ++ +++ 
  gi|557694562|ref|YP_008797616.1| 153 QDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALntAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRY 229
                                       55667788889999999999999999999999999987643577888888999999999999999999999999999 PP

                            AAA_13 440 kkleeeikeLekq 452
                                           +e k+L+++
  gi|557694562|ref|YP_008797616.1| 230 VSTVGELKALQAS 242
                                       9999999999986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.095
                            AAA_13 282 eekqerLekliekveskkselleklkavsdeasensafeed...........keelkaeaealeeqLkglqrale 345
                                       ++++e L++  e + ++ ++ll  + ++++e+s  +a++++           +e +k+++  l++qL++++r+l 
  gi|557694562|ref|YP_008797616.1| 240 QASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQlhelyeglvtrHESAKQQIGYLQSQLDENRRELG 314
                                       556666777777777777777777777777777777777665666555555577777777778888888887775 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 ?   11.1   8.8    0.0016       0.2     241     318 ..     157     237 ..     148     254 .. 0.80
   2 ?    4.5   1.7      0.16        20     255     310 ..     244     299 ..     231     338 .. 0.44

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0016
                            HMMR_N 241 eqlekykldiaqleellkekndeiesLkssLeek...eqelskqvkdlnekckllekekeelvreeeekeqtlsaEl 314
                                       + l++ +++i+ql+ +++  + ei++L++ Lee    + +l ++ ++  e++k le+  + + +e+++ ++++ + +
  gi|557694562|ref|YP_008797616.1| 157 NDLNRAQEQINQLRTTIQILETEINTLRTRLEEAlntAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTV 233
                                       567788999***********************96222568999*****************99999999999887755 PP

                            HMMR_N 315 eelk 318
                                       +elk
  gi|557694562|ref|YP_008797616.1| 234 GELK 237
                                       5554 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.16
                            HMMR_N 255 ellkekndeiesLkssLeekeqelskqvkdlnekckllekekeelvreeeekeqtl 310
                                       e+l+ +n+ +++  ++L     +l k+ + l++  ++l +  e lv+++e  +q++
  gi|557694562|ref|YP_008797616.1| 244 EMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQI 299
                                       34444444443333333333333444444444444444444443333333333321 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   2.8    0.0067      0.81     103     185 ..     151     233 ..     146     235 .. 0.79
   2 ?    7.3   0.3     0.032       3.9      93     180 ..     232     319 ..     228     324 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0067
                            DUF724 103 eqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaekleeeledveq 179
                                        ++ ll+ +++++++i + ++  + le+ei+ l  +  e  + +a+l ++ +++ +ei+rl++  ++++ee+++ ++
  gi|557694562|ref|YP_008797616.1| 151 TYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLND 227
                                       56677778888888888888888888888888888888888888888888889999999999999999999888888 PP

                            DUF724 180 eFeava 185
                                       ++ +++
  gi|557694562|ref|YP_008797616.1| 228 RYVSTV 233
                                       887775 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.032
                            DUF724  93 rlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlkseaek 169
                                        + +L +l+ +++ l +e ++l  + ++  ++ r+l +e + l+ +  +l++  + l +++e+a+++i  l+s+ ++
  gi|557694562|ref|YP_008797616.1| 232 TVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDE 308
                                       56688899******************************************************************999 PP

                            DUF724 170 leeeledveqe 180
                                        ++el d + +
  gi|557694562|ref|YP_008797616.1| 309 NRRELGDLRLR 319
                                       99999887765 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 ?    9.5  10.8    0.0017       0.2      22     133 ..     149     263 ..     143     360 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0017
                        V_ATPase_I  22 qrkfvkevrrcdemerklrfleeeieklekavikeeea...eesleapeekeldeleeelekleeelkelnenlekl 95 
                                       qr++ + +  ++  +++++ l+++i+ le+++ + ++    + +++a  +++l++  ee+++le+++++++e++++l
  gi|557694562|ref|YP_008797616.1| 149 QRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRleeALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQL 225
                                       7777766666666666666666666554444333333232255667777888999999999999********9**** PP

                        V_ATPase_I  96 kkelnelvelkavlekakefleeeeeeeeeeeseeeee 133
                                       ++++ + v + + l+   e+l++e+e  +++ ++  ++
  gi|557694562|ref|YP_008797616.1| 226 NDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHD 263
                                       99999999999999999999987644333322222222 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 ?   12.1   9.6   0.00066     0.081     217     305 ..     151     239 ..     143     242 .. 0.90
   2 ?    5.8   3.7     0.056       6.7     164     247 ..     235     307 ..     228     327 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00066
                            HAP1_N 217 qiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqekyaeveg 293
                                        +++l ++l+r +e++++ +  i+ L ++i +l+++l+e       l+++L++s+e  ++L++ +q + e y++ ++
  gi|557694562|ref|YP_008797616.1| 151 TYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLND 227
                                       5788999*********************************************************9999999999888 PP

                            HAP1_N 294 mLheaqeevkel 305
                                          ++  e+k l
  gi|557694562|ref|YP_008797616.1| 228 RYVSTVGELKAL 239
                                       777777777765 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.056
                            HAP1_N 164 qldlLqeklreLeeeNekLreeasqLktetdtlEekEqqLvldcveqlseanqqiaelseelarkleelerqqeeis 240
                                       +l +Lq   + L  eNe+L + ++qL ++  +l ++  +        l+ + +q++el e l+ + e+++   ++i 
  gi|557694562|ref|YP_008797616.1| 235 ELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSM--------LQATFNQLHELYEGLVTRHESAK---QQIG 300
                                       566777777777777777777777776666655443333........45566667777777777777664...3455 PP

                            HAP1_N 241 sLlaqiv 247
                                        L++q+ 
  gi|557694562|ref|YP_008797616.1| 301 YLQSQLD 307
                                       5555554 PP

>> DUF4686  Domain of unknown function (DUF4686)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  17.8    0.0017       0.2     158     306 ..     150     298 ..     143     327 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0017
                           DUF4686 158 ekikeaseneaklkqqlqeeqqkrklLdqnveeLqqqvrslrdkeaqlertnsqqqlriqqqeaqlkklenekrk.s 233
                                       +  +++ +++++ ++q++  + + ++L++++++L+++++   +  a l+    + +  i+  e++++ + +e r+ +
  gi|557694562|ref|YP_008797616.1| 150 RTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQlN 226
                                       566788999999999***********************9999999999988888889******************99 PP

                           DUF4686 234 dehl...ksnqeLsekLsslqqekealqeelqqvLkqldahvrkynekqehhkaklrrvkelllkeveqrderikq 306
                                       d+++      + L+     l +e eal + +qq+L+      r++ + +++ +a +++  el+   v+++++  +q
  gi|557694562|ref|YP_008797616.1| 227 DRYVstvGELKALQASYEMLSRENEALSTSYQQLLHD----YRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQ 298
                                       9999555455666777888999*********999976....56666666666666666666666666655554443 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.4      0.03       3.6       7      38 ..     164     195 ..     157     224 .. 0.67
   2 ?    2.5   0.1       1.6   1.9e+02       8      28 ..     207     227 ..     200     251 .. 0.77
   3 ?    0.7   0.1       5.9   7.1e+02      12      27 ..     253     268 ..     242     297 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.03
                               LPP   7 sqVsqLkskvdqlssdvnsakaaaqaakeEAa 38 
                                       +q++qL + ++ l+ ++n +++ +++a + Aa
  gi|557694562|ref|YP_008797616.1| 164 EQINQLRTTIQILETEINTLRTRLEEALNTAA 195
                                       57777777777777777777776666666554 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 1.6
                               LPP   8 qVsqLkskvdqlssdvnsaka 28 
                                       ++++L++ ++ +s++  ++++
  gi|557694562|ref|YP_008797616.1| 207 EIKRLEQRIQTMSEEYRQLND 227
                                       677777777777777766665 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 5.9
                               LPP  12 Lkskvdqlssdvnsak 27 
                                       L++  +ql  d  ++ 
  gi|557694562|ref|YP_008797616.1| 253 LSTSYQQLLHDYRNLT 268
                                       4444444443332222 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.8     0.006      0.72      20      97 ..     154     230 ..     140     234 .. 0.53
   2 ?    7.1   0.7     0.024       2.9      11      83 ..     236     314 ..     227     330 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.006
                             TMPIT  20 eykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkkvlkevesllpkkngly 96 
                                        + ++l++ ++++++++++i+  + +++ l+++l++  +++ +    ++++ +ee+k+ ++ ++ +++   + n +y
  gi|557694562|ref|YP_008797616.1| 154 DLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTA-AMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRY 229
                                       44444445555555555556666666666666665555543.34444455555555555555555555554445555 PP

                             TMPIT  97 l 97 
                                       +
  gi|557694562|ref|YP_008797616.1| 230 V 230
                                       5 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.024
                             TMPIT  11 fkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk......eeeeeeveelkeelkerkkv 81 
                                       +k+l+++ + + ++ e ls++ +++ ++ ++ +k+++ l++++++l++  +      e+ ++++  l+++l+e ++ 
  gi|557694562|ref|YP_008797616.1| 236 LKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEglvtrhESAKQQIGYLQSQLDENRRE 312
                                       55555555555555555555555555555555555555555555555553344444456666666666666666655 PP

                             TMPIT  82 lk 83 
                                       l 
  gi|557694562|ref|YP_008797616.1| 313 LG 314
                                       54 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 ?    8.7   1.7     0.018       2.2      20      61 ..     160     201 ..     152     204 .. 0.73
   2 ?    8.4   0.9     0.023       2.7      28      62 ..     203     237 ..     191     244 .. 0.63
   3 ?    1.7   0.3       2.7   3.3e+02      32      57 ..     242     267 ..     234     280 .. 0.68
   4 ?    2.9   1.1       1.2   1.4e+02      26      61 ..     264     299 ..     244     309 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.018
                               CLZ  20 akagaeqkeleekverLessLeaLqtrlarLlaeyessqrkL 61 
                                       + a+++ ++l + ++ Le+++++L trl+  l+      ++L
  gi|557694562|ref|YP_008797616.1| 160 NRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARL 201
                                       567788888999999999999999999988777665555555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.023
                               CLZ  28 eleekverLessLeaLqtrlarLlaeyessqrkLk 62 
                                       +  e ++rLe++++++   +++L + y s+  +Lk
  gi|557694562|ref|YP_008797616.1| 203 SSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELK 237
                                       44556666666666666666666666666655555 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 2.7
                               CLZ  32 kverLessLeaLqtrlarLlaeyess 57 
                                         e L  + eaL t +++Ll +y + 
  gi|557694562|ref|YP_008797616.1| 242 SYEMLSRENEALSTSYQQLLHDYRNL 267
                                       45556666677888888888777654 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 1.2
                               CLZ  26 qkeleekverLessLeaLqtrlarLlaeyessqrkL 61 
                                        ++l +  + L+++ ++L+  ++ L++ +es+++++
  gi|557694562|ref|YP_008797616.1| 264 YRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQI 299
                                       455666667788888888888888888888888776 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   5.6    0.0031      0.38     257     343 ..     155     238 ..     143     244 .. 0.61
   2 ?    6.9   2.4     0.024       2.9     245     327 ..     237     320 ..     236     322 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0031
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 257 akkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekieekleeleeLrefYegFlsa 333
                                         + l+  +e+i++l ++++ + +e+++++++l+e l+   +++ +++r ++ +e+i++  + ++ ++e Y++  + 
  gi|557694562|ref|YP_008797616.1| 155 LLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALN---TAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDR 228
                                       33344444455555555555555555555577777777...777777777777777777777777777777777777 PP

                                       HHHHHHHHHH CS
                             APG17 334 YdklllEveR 343
                                       Y + + E++ 
  gi|557694562|ref|YP_008797616.1| 229 YVSTVGELKA 238
                                       7777777654 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH....HHHHHHHHHHHH CS
                             APG17 245 kelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerw.eeekekieekleel 320
                                       k lq+++e +++++++ls+  +++ + +++l+k +++l++  ++l+e  + + + +e  +++    +++++e+ +el
  gi|557694562|ref|YP_008797616.1| 237 KALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQiGYLQSQLDENRREL 313
                                       67888888888888888888888888888888888888888777777777777777777776678888889999998 PP

                                       HHHHHHH CS
                             APG17 321 eeLrefY 327
                                        +Lr  Y
  gi|557694562|ref|YP_008797616.1| 314 GDLRLRY 320
                                       8888777 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 ?   10.2   6.2    0.0072      0.87      36      94 ..     145     221 ..     122     226 .. 0.68
   2 ?    0.8   7.1         6   7.2e+02      34      70 ..     213     249 ..     178     317 .. 0.48

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0072
                      Syntaxin-6_N  36 seeldetrteLrkalrsiewdledLeetvrivek..................npskfkidekelsrrrafveevree 94 
                                           ++t ++L + l+ +++++++L+ t++i+e                     ++ + + +e++r ++ ++ + ee
  gi|557694562|ref|YP_008797616.1| 145 AAVRQRTYQDLLNDLNRAQEQINQLRTTIQILETeintlrtrleealntaamLTARLNSSREEIKRLEQRIQTMSEE 221
                                       55667899999999999999999999999999887777777777666555443355666666666666666665555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 6
                      Syntaxin-6_N  34 stseeldetrteLrkalrsiewdledLeetvrivekn 70 
                                       ++ + ++e  ++L+  + s   +l+ L+ + ++++++
  gi|557694562|ref|YP_008797616.1| 213 QRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRE 249
                                       2233333333333333333333333333333333222 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   4.3      0.04       4.8      16      76 ..     151     211 ..     143     214 .. 0.85
   2 ?    8.9   4.8     0.019       2.4       8      77 ..     206     285 ..     202     288 .. 0.58
   3 ?    4.5   3.0      0.44        53       8      67 ..     241     300 ..     236     334 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA  16 qleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarl 76 
                                       + ++ll++l++ +e++++l    + Le+e ++lr+rlee+ ++++  +++l++++e+++rl
  gi|557694562|ref|YP_008797616.1| 151 TYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRL 211
                                       4578889999999999999999999999999999999999999999999999999988887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........XXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerl..........eeeekkekekkkelsegkenLa 74 
                                       +++++le+++++++ee ++l+++ ++++ e ++L++  e l ++            ++ ++ +++ + l+ + ++L+
  gi|557694562|ref|YP_008797616.1| 206 EEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENealstsyqqlLHDYRNLTKEYSMLQATFNQLH 282
                                       56788888888888888888888888888888888776555444422222223222222333334444445555555 PP

                                       XXX CS
                              YabA  75 rlY 77 
                                       +lY
  gi|557694562|ref|YP_008797616.1| 283 ELY 285
                                       555 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkels 67 
                                       ++ e l+++ e+l+++ ++l ++  +l++e + L++  ++l+e+ e   +++++ k++++
  gi|557694562|ref|YP_008797616.1| 241 ASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIG 300
                                       445556666666666666666666666666666666666666666444444444444444 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 ?    6.0   0.6      0.13        16      15      33 ..     165     183 ..     153     191 .. 0.43
   2 ?    6.5   0.3     0.089        11       2      33 ..     166     197 ..     165     201 .. 0.81
   3 ?    3.3   4.7      0.93   1.1e+02       9      38 ..     191     223 ..     180     279 .. 0.65
   4 ?    3.8   0.1      0.64        78      12      45 ..     253     286 ..     251     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.13
                         FlaC_arch  15 eletvkkeneelsksveel 33 
                                       +++ ++++++ l++++++l
  gi|557694562|ref|YP_008797616.1| 165 QINQLRTTIQILETEINTL 183
                                       3333333333333333333 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.089
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveel 33 
                                       i++l + ++ l+te++t+++ +ee  ++  +l
  gi|557694562|ref|YP_008797616.1| 166 INQLRTTIQILETEINTLRTRLEEALNTAAML 197
                                       78888899999999999999999977766665 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.93
                         FlaC_arch   9 lsklst...eletvkkeneelsksveelkenVk 38 
                                       l+   +   +l++ ++e++ l++ ++++ e+ +
  gi|557694562|ref|YP_008797616.1| 191 LNTAAMltaRLNSSREEIKRLEQRIQTMSEEYR 223
                                       444444444555555555555555555555443 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.64
                         FlaC_arch  12 lsteletvkkeneelsksveelkenVkdllsLYE 45 
                                       lst+ + +  +  +l k+  +l+ ++++l +LYE
  gi|557694562|ref|YP_008797616.1| 253 LSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYE 286
                                       6666677777788999*****************9 PP

>> DUF4041  Domain of unknown function (DUF4041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1     0.037       4.4      15      46 ..     144     175 ..     142     179 .. 0.93
   2 ?    2.5   0.5       1.1   1.4e+02      26      52 ..     197     222 ..     180     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.037
                           DUF4041  15 iskVkynnietlekRIeksfeainklgktmni 46 
                                       i+ V+ + ++ l + ++++ e+in+l +t++i
  gi|557694562|ref|YP_008797616.1| 144 IAAVRQRTYQDLLNDLNRAQEQINQLRTTIQI 175
                                       8899***********************99986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 1.1
                           DUF4041  26 lekRIeksfeainklgktmnirItpeY 52 
                                       l  R+++s+e i +l ++++  +++eY
  gi|557694562|ref|YP_008797616.1| 197 LTARLNSSREEIKRLEQRIQ-TMSEEY 222
                                       56788888888888887776.355555 PP

>> ERM  Ezrin/radixin/moesin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7  18.6     0.011       1.4      27     134 ..     158     265 ..     147     327 .. 0.45

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.011
                               ERM  27 aLreseetaelLaekarraeeeaelLeqkaaeaeeeiqrlkesaekeeeekeklerklreaeleaarleeeserkee 103
                                       +L++++e++++L    +++e+e + L  + +ea +  + l  + + + ee ++le++++ +++e ++l +       
  gi|557694562|ref|YP_008797616.1| 158 DLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVG 234
                                       45555555555555555555555555555555555555555555555555555555555555555555555555555 PP

                               ERM 104 eaerLkeeleeareaeeeakekllealstps 134
                                       e + L++  e+  +++e  ++  +++l   +
  gi|557694562|ref|YP_008797616.1| 235 ELKALQASYEMLSRENEALSTSYQQLLHDYR 265
                                       5555555555554444444333333333331 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 ?   10.9   2.2    0.0026      0.31      73     123 ..     151     201 ..     146     218 .. 0.82
   2 ?    0.6   0.1       3.9   4.8e+02      95     119 ..     201     225 ..     190     246 .. 0.49
   3 ?    4.6   1.3      0.24        29      35     111 ..     232     308 ..     224     324 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0026
                      Sec8_exocyst  73 sYskilssiqesqekvselKesleeakkklstkkkeLkelnarsakykevi 123
                                       +Y+ +l+ ++ +qe++++l+  ++  +++++t +  L+e  ++ a+++  +
  gi|557694562|ref|YP_008797616.1| 151 TYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARL 201
                                       8*************************************9888888776544 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 3.9
                      Sec8_exocyst  95 leeakkklstkkkeLkelnarsaky 119
                                       l+++++++++ ++ ++ ++++ +++
  gi|557694562|ref|YP_008797616.1| 201 LNSSREEIKRLEQRIQTMSEEYRQL 225
                                       3444444444443333333333332 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.24
                      Sec8_exocyst  35 svGlahrlkefkqlkkqieeaLqevvnehhqaFnssiasYskilssiqesqekvselKesleeakkklstkkkeLke 111
                                       +vG  + l+   ++ ++ +eaL +  ++  +++ +  + Ys+++ ++++ +e  ++l  + e+ak+++++ +++L+e
  gi|557694562|ref|YP_008797616.1| 232 TVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDE 308
                                       66666666666666666677777777777777888888899999999999999999999999999999888888876 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   8.9    0.0052      0.63      21      82 ..     155     217 ..     151     237 .. 0.71
   2 ?    4.6   0.2      0.26        31      35     100 ..     238     305 ..     229     316 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0052
                      Baculo_PEP_C  21 vLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalqdt 82 
                                       +Ln++   + qi +ql t+++ +et++n+l ++l+++l+  +    rl+++ +++++  +++q t
  gi|557694562|ref|YP_008797616.1| 155 LLNDLNRAQEQI-NQLRTTIQILETEINTLRTRLEEALNTAAMltaRLNSSREEIKRLEQRIQ-T 217
                                       799999999999.**********************9887433333355555444444444444.3 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.26
                      Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltnLlss 100
                                       +l++  + + ++ +als++ ++ll + + +l++  + L+++ n+l    + l ++ ++ ++++  L+s+
  gi|557694562|ref|YP_008797616.1| 238 ALQASYEMLSRENEALSTSYQQLLHDYR-NLTKEYSMLQATFNQLHelyEGLVTRHESAKQQIGYLQSQ 305
                                       5666666666666777777777777665.4666666666666666655544444444444444444444 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.0     0.003      0.36      82     179 ..     162     261 ..     139     311 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.003
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXX CS
                              LUC7  82 eeeflrfleklledvdrkiqkgkqrleltqeekeeeeeakakkqeqlkeleekiekllaeaeelgee..GkVdeaqk 156
                                        +e +++l+ +++ ++  i++ + rle+  ++    ++  +++ e++k+le++i+++ +e  +l  +    V e ++
  gi|557694562|ref|YP_008797616.1| 162 AQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRyvSTVGELKA 238
                                       5788999999*****************9988887777777799*********************9875579****** PP

                                       XXXXXXXXXXXXXXXXXXXXXX. CS
                              LUC7 157 lmkeveelkeekeeleqqyeaaa 179
                                       l +  e l +e e+l  +y++  
  gi|557694562|ref|YP_008797616.1| 239 LQASYEMLSRENEALSTSYQQLL 261
                                       ****************9998864 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   6.6     0.044       5.3      72     135 ..     164     227 ..     143     235 .. 0.68
   2 ?   10.2   5.8    0.0061      0.74       9     137 ..     186     320 ..     180     328 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.044
                             HrpB7  72 adylacrayrdvlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrr 135
                                       +++ ++r  +++le +++ +  +l+ a ++ +  +++++  +++i R++ +i+ + e  ++l++
  gi|557694562|ref|YP_008797616.1| 164 EQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLND 227
                                       3566667777777777777777777777777777777777777777777777777777777665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0061
                             HrpB7   9 lverrarreerlraeleaaraalaaaeaalaaaqaqveaardavraheerlddlttgsspfsiadylacrayrd... 82 
                                        +e      + l a l+ +r++ + +e+ ++  +++ ++  d+  +   +l++l +  + +s ++ + +  y +   
  gi|557694562|ref|YP_008797616.1| 186 RLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQllh 262
                                       444445556678899********************************************999876544444444000 PP

                             HrpB7  83 ...vlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraa 137
                                           l+ +   ++a   ++++ ++    + +  +++i+ +++q+d  r+ +  lr  +
  gi|557694562|ref|YP_008797616.1| 263 dyrNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELGDLRLRY 320
                                       11156779999*************************************9999888655 PP

>> Ead_Ea22  Ead/Ea22-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   3.4   0.00034     0.041      60     137 ..     143     217 ..      98     221 .. 0.86
   2 ?    2.9   0.9       1.4   1.7e+02      75     114 ..     207     268 ..     201     339 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 0.00034
                          Ead_Ea22  60 fiaaanpatvlaLLDelekkqqrikeleeeaenedialtvgklrveleaaekrlekenveqadaaeveitalrqria 136
                                       +iaa+   t + LL +l+++q++i +l++    + ++  +  lr  le+a + + ++++ + ++  +ei++l+qri+
  gi|557694562|ref|YP_008797616.1| 143 HIAAVRQRTYQDLLNDLNRAQEQINQLRTT--IQILETEINTLRTRLEEALNTA-AMLTARLNSSREEIKRLEQRIQ 216
                                       578889**********************66..99999************99977.9********************8 PP

                          Ead_Ea22 137 e 137
                                        
  gi|557694562|ref|YP_008797616.1| 217 T 217
                                       6 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 1.4
                          Ead_Ea22  75 elekkqqrikeleee..aenedialtvgklrv..........eleaaekrl..........e 114
                                       e+++ +qri+ + ee  + n ++ +tvg+l+           e+ea++++            
  gi|557694562|ref|YP_008797616.1| 207 EIKRLEQRIQTMSEEyrQLNDRYVSTVGELKAlqasyemlsrENEALSTSYqqllhdyrnlT 268
                                       55666677777776677777788888887777666666666666666665544444444440 PP

>> DUF4527  Protein of unknown function (DUF4527)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.76        92     128     158 ..     122     152 ..     120     160 .. 0.89
   2 ?   12.4   7.3   0.00065     0.079       8     108 ..     164     268 ..     158     281 .. 0.84
   3 ?    0.9   0.8       2.1   2.5e+02       8      64 ..     255     311 ..     249     315 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.76
                           DUF4527 128 aatFlapgvpetshhldvesektalvraqkc 158
                                       +atF+a  ++et++++  ++ ++a+vr+ ++
  gi|557694562|ref|YP_008797616.1| 122 TATFFANYTRETTYQPLTHTWHIAAVRQRTY 152
                                       79******************99999998877 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00065
                           DUF4527   8 aseedlrlrvkqLhHqvltLqcqLRdq....asahreLqasreeaerlreelqekleElqkkqhEanlAvtPLkAkl 80 
                                          ++lr  ++ L+  + tL+++L +     a +  +L +sree +rl +++q   eE ++ ++   + v  LkA  
  gi|557694562|ref|YP_008797616.1| 164 EQINQLRTTIQILETEINTLRTRLEEAlntaAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQ 240
                                       555789***************99877422215677899*************************************** PP

                           DUF4527  81 AsLvqkCreRnhlithLLqelhrhglen 108
                                       As     re + l t   q lh ++   
  gi|557694562|ref|YP_008797616.1| 241 ASYEMLSRENEALSTSYQQLLHDYRNLT 268
                                       **************99888787766544 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 2.1
                           DUF4527   8 aseedlrlrvkqLhHqvltLqcqLRdqasahreLqasreeaerlreelqekleElqk 64 
                                       +s ++l    ++L      Lq        ++  L + +e a++  + lq++l+E ++
  gi|557694562|ref|YP_008797616.1| 255 TSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRR 311
                                       555566666777888888889999999999999999999999999999999999776 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.7   0.00092      0.11     134     189 ..     170     225 ..     150     233 .. 0.89
   2 ?    3.5   2.9      0.38        46      39     122 ..     235     315 ..     228     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00092
                              Vps5 134 wqkwqsaeqelskkkeqleKlekaaksqqdklqqlkkeveelerkvqeaekeFeei 189
                                         ++q  e e++  +++le +  +a   + +l++ ++e++ le+++q++++e+ ++
  gi|557694562|ref|YP_008797616.1| 170 RTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQL 225
                                       56789999************99999999*************************987 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.38
                              Vps5  39 qLkkLykaiellvsqrkelasataelakslesLaslelskslsralsqlaeveerikellerqaeqdvltLgetide 115
                                       +Lk L+ + e+l+++ + l+++ ++l +   +L +  +   l + ++ql e+ e +   + ++a+q   +L+  +de
  gi|557694562|ref|YP_008797616.1| 235 ELKALQASYEMLSRENEALSTSYQQLLHDYRNLTK--EYSMLQATFNQLHELYEGLVTRH-ESAKQQIGYLQSQLDE 308
                                       6999*******************999999999975..55677888999999999887655.5799999999999999 PP

                              Vps5 116 ylrligs 122
                                       + r +g 
  gi|557694562|ref|YP_008797616.1| 309 NRRELGD 315
                                       9888775 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  12.2     0.038       4.6       3     100 ..     164     271 ..     147     298 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.038
                        Syntaxin_2   3 snlqkinsnvstleklvkqLgtk.....kdteelreklhelieeinelikktnellkklsqldnsssds.....qqk 69 
                                       +++ ++ + ++ le  +++L t+     +    l  +l++++eei++l ++++   ++  ql +   +      +  
  gi|557694562|ref|YP_008797616.1| 164 EQINQLRTTIQILETEINTLRTRleealNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTvgelkALQ 240
                                       45555555555555555555555332222244444777777777777777777777777776655533378776444 PP

                        Syntaxin_2  70 lqkekLkkdfkealqeFqkiqrqyaekekqi 100
                                        + e L+++ +++ +++q++  +y++ +k++
  gi|557694562|ref|YP_008797616.1| 241 ASYEMLSRENEALSTSYQQLLHDYRNLTKEY 271
                                       4667777777777777777777777776665 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.8    0.0098       1.2      40      89 ..     156     205 ..     105     229 .. 0.52
   2 ?    4.4   2.7      0.43        53      42      86 ..     200     244 ..     186     329 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0098
                                       HHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHH CS
                             DUF16  40 eakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlelil 89 
                                        + ++  +eqin+l  +++ ++ +i+ l+ + +   +    +   l++  
  gi|557694562|ref|YP_008797616.1| 156 LNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSR 205
                                       23334444444444444444444444444443333333333333333333 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.43
                                       HHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHH CS
                             DUF16  42 kvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetle 86 
                                       ++++  e+i++leq +++  e+ ++l+ +      el++++ + e
  gi|557694562|ref|YP_008797616.1| 200 RLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYE 244
                                       445555555555555555555555554443333333433333333 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 ?   11.4  17.7    0.0014      0.17     128     209 ..     148     224 ..     142     230 .. 0.88
   2 ?    4.5   4.8      0.19        23      73     142 ..     250     319 ..     233     336 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0014
                        MscS_porin 128 rlqeirnrLnstaaagealsqaqrtalqaelaaleaqieeleqellsnnnrqeLlklqrdllklriqqleqelqaLq 204
                                       r+ + ++ Ln++     + +q+q ++l++  + le++i+ l++ l+ + n  + l+++++  +++i++leq++q+  
  gi|557694562|ref|YP_008797616.1| 148 RQRTYQDLLNDL-----NRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMS 219
                                       555666667777.....899******************************************************998 PP

                        MscS_porin 205 ellne 209
                                       e   +
  gi|557694562|ref|YP_008797616.1| 220 EEYRQ 224
                                       86655 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.19
                        MscS_porin  73 eilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvelqtrperaqqqltearqrlqeirnrLnstaaa 142
                                       ++  ++s ++L   + +   + + lq++ +ql ++   l tr e a qq+   + +l+e r++L +++ +
  gi|557694562|ref|YP_008797616.1| 250 NEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELGDLRLR 319
                                       3333555667777777777777777777777777777888888888888888888888888777666444 PP

>> DUF4988  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.4      0.25        30       2      27 ..     163     188 ..     155     199 .. 0.75
   2 ?    7.1   0.2     0.032       3.8       2      28 ..     205     231 ..     204     268 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.25
                           DUF4988   2 eddvndlkdrvaaleeqvkelndnie 27 
                                       ++++n+l+  ++ le++++ l + +e
  gi|557694562|ref|YP_008797616.1| 163 QEQINQLRTTIQILETEINTLRTRLE 188
                                       46788888888888888888877664 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.032
                           DUF4988   2 eddvndlkdrvaaleeqvkelndniea 28 
                                       ++++  l++r++++ e++++lnd   +
  gi|557694562|ref|YP_008797616.1| 205 REEIKRLEQRIQTMSEEYRQLNDRYVS 231
                                       5799******************97543 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5  15.7    0.0058       0.7      18     170 ..     157     303 ..     150     317 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0058
                              YkyA  18 kefeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieei 94 
                                       ++++ +qe++++l    q l +ei++l +   ++  + ++ +++ ++  +e+++  ++ i+   ee+ ++++   ++
  gi|557694562|ref|YP_008797616.1| 157 NDLNRAQEQINQLRTTIQILETEINTLRTRL-EEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVST 232
                                       5678899999999999999999999988665.777777788888888888888888999999999999998876665 PP

                              YkyA  95 ..edeelkkeaeelieameeryeaydklykaYkealeldkeLYemLkkeeltleeleeqiekiNesyeevkeaneqF 169
                                         e ++l+   e l    e   ++y++l+ +Y +++++    Y+mL+    t+++l e  e + + +e +k+++  +
  gi|557694562|ref|YP_008797616.1| 233 vgELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKE----YSMLQA---TFNQLHELYEGLVTRHESAKQQIGYL 302
                                       58999999999999999999999999999999998876....888877...66666666666666666666665555 PP

                              YkyA 170 n 170
                                       +
  gi|557694562|ref|YP_008797616.1| 303 Q 303
                                       5 PP

>> Mce4_CUP1  Cholesterol uptake porter CUP1 of Mce4, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.7    0.0046      0.56      54     160 ..     138     247 ..     132     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0046
                         Mce4_CUP1  54 lredireladladvYadaapdllda...LdnavttsrTiveqqaeLdalllaavglsntgadllerngdnLirlaad 127
                                       l++ ++  a  + +Y+d  +dl +a   +++++tt + ++++ + L++ l +a +++  ++  l+++++++ rl + 
  gi|557694562|ref|YP_008797616.1| 138 LTHTWHIAAVRQRTYQDLLNDLNRAqeqINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQR 214
                                       5677777777789*********876333677788888888999999999**************************** PP

                         Mce4_CUP1 128 lrptlelLakYspeltCllrnladvepkvakal 160
                                        + ++e   + ++ +  ++ +l+ ++ +++  +
  gi|557694562|ref|YP_008797616.1| 215 IQTMSEEYRQLNDRYVSTVGELKALQASYEMLS 247
                                       ****99999999999999999999887766554 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.2      0.71        86      54      79 ..     149     174 ..     138     179 .. 0.84
   2 ?   10.7   5.0    0.0041      0.49      24      80 ..     161     217 ..     147     222 .. 0.84
   3 ?    3.9   1.4      0.56        68      22      59 ..     236     273 ..     234     284 .. 0.85
   4 ?    3.4   0.4      0.78        95      25      74 ..     267     316 ..     265     321 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.71
                              KxDL  54 tkllkevkkdLesifkkirslkakla 79 
                                       +++ +++ +dL+  +++i++l+++++
  gi|557694562|ref|YP_008797616.1| 149 QRTYQDLLNDLNRAQEQINQLRTTIQ 174
                                       57888999999999999999998875 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0041
                              KxDL  24 rlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkaklak 80 
                                       r +++ ++L + +++++++ + lr+r+++  +++  + + L+s+++ i++l++++++
  gi|557694562|ref|YP_008797616.1| 161 RAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQT 217
                                       34445557788899999************************************9987 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.56
                              KxDL  22 sgrlnkknreLlelnalsqerlaklrarfkqgtkllke 59 
                                       ++ l+++ ++L++ n+ +++ +++l +++++ tk  + 
  gi|557694562|ref|YP_008797616.1| 236 LKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSM 273
                                       5789999**********************999986655 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.78
                              KxDL  25 lnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirsl 74 
                                       l k+  +L++  +++ e ++ l +r ++ ++ +  ++++L+  ++ +  l
  gi|557694562|ref|YP_008797616.1| 267 LTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELGDL 316
                                       55667788888888888888888888888888888888888888877766 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 ?    9.8   8.1     0.005      0.61       8      73 ..     156     220 ..     151     272 .. 0.70
   2 ?    2.7   1.9      0.75        90       8      42 ..     198     228 ..     193     299 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.005
                           CCDC106   8 kkqLevkkEkiswlqkriedLeeeRdFLRcqlekfissksleaeaekeskskksekkaeksesess 73 
                                        + L+ ++E+i+ l+  i+ Le e + LR++le+++ ++++ + a+ +s  ++ ++ ++  ++ s+
  gi|557694562|ref|YP_008797616.1| 156 LNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLT-ARLNSSREEIKRLEQRIQTMSE 220
                                       568999******************************9999875.3333333333332222222222 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.75
                           CCDC106   8 kkqLevkkEkiswlqkriedLeeeRdFLRcqlekf 42 
                                        + L++++E i+ l++ri+ + ee      ql++ 
  gi|557694562|ref|YP_008797616.1| 198 TARLNSSREEIKRLEQRIQTMSEEYR----QLNDR 228
                                       6789*****************99954....33333 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.2    0.0019      0.23      39     115 ..     152     227 ..     142     235 .. 0.80
   2 ?    2.5   0.1       1.2   1.4e+02      47      79 ..     278     310 ..     265     317 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0019
                           DUF1664  39 lsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                        +d ++++ +  eq+ ++l++t + L+ +i+++ ++l+e  ++++ +++ +++ re+++++++ +++++e  ++l+ 
  gi|557694562|ref|YP_008797616.1| 152 YQDLLNDLNRAQEQI-NQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLND 227
                                       445555554444443.46777888999****************************************9999998876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 1.2
                           DUF1664  47 skqleqvseslaatkrhLssridrvdkkldeqk 79 
                                        +ql +++e l +  +  +++i  ++++lde+ 
  gi|557694562|ref|YP_008797616.1| 278 FNQLHELYEGLVTRHESAKQQIGYLQSQLDENR 310
                                       478999999999999999999999999999875 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 ?    9.0   6.1     0.013       1.6      19     100 ..     148     225 ..     144     233 .. 0.81
   2 ?    3.8   0.1      0.54        66      21      65 ..     248     291 ..     225     318 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.013
                                       CCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  19 kkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkelea 95 
                                       ++R  ++ ++ +l  ++e+  +l+++++ l +e N+l    ++a +    a+ l a+ ++  ee+k+le++ +++++
  gi|557694562|ref|YP_008797616.1| 148 RQR-TYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNT---AAMLTARLNSSREEIKRLEQRIQTMSE 220
                                       566.58899999*********************************86...666777777777777777777777777 PP

                                       HHHHH CS
                      Seryl_tRNA_N  96 elekl 100
                                       e  +l
  gi|557694562|ref|YP_008797616.1| 221 EYRQL 225
                                       66554 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.54
                                       CTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCT CS
                      Seryl_tRNA_N  21 RgedkadvdelleldekrrelqveleelqaerNelskeIgkakkk 65 
                                       R e +a+  ++ +l    r+l +e   lqa  N+l +  + +  +
  gi|557694562|ref|YP_008797616.1| 248 R-ENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTR 291
                                       3.3445555555555566666666666666666655544444444 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 ?    7.8  11.6    0.0098       1.2     246     393 ..     153     299 ..     146     317 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0098
                             WEMBL 246 kdlkskletasallldLkaeLaayvesklkeeaeeeeeekksetsikealasarkELeevkaniekakdevklLkva 322
                                       +dl + l+ a++ + +L++ ++  +e++++   ++ ee+ ++  ++++ l+s+r+E++ + + i+ + +e + L+  
  gi|557694562|ref|YP_008797616.1| 153 QDLLNDLNRAQEQINQLRTTIQ-ILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDR 228
                                       6788888888888888888775.556666666666666778888889999999999999999999999999999999 PP

                             WEMBL 323 aasLrseLekekaeLaslrqregmasiavssLeaelsrtkselelvqakekearekmvelpkeLqeAaqea 393
                                         s   eL+  +a+   l +++++ s++ ++L ++ ++ ++e +++qa+ ++ +e  + l    ++A+q++
  gi|557694562|ref|YP_008797616.1| 229 YVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQI 299
                                       99999999999999999999888889999999999999999999999988888777777777777776665 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  10.2      0.29        35      13     106 ..     195     289 ..     141     372 .. 0.59

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.29
                           zf-C4H2  13 eklknklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeey 89 
                                         l ++l +  e++++ e+ ++++++e  +L+    + v eL+ ++a  + l +  +   ++ ++ l+  ++l++ey
  gi|557694562|ref|YP_008797616.1| 195 AMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEY 271
                                       23344444444445555555555555555555555555555555555555555555555555555555555555555 PP

                           zf-C4H2  90 kklkeevnelrse.lgle 106
                                       + l+ + n+l +   gl 
  gi|557694562|ref|YP_008797616.1| 272 SMLQATFNQLHELyEGLV 289
                                       555555555444434444 PP

>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.1      0.25        30      11      54 ..     149     192 ..     143     200 .. 0.80
   2 ?    8.2   0.7     0.015       1.8       8      47 ..     202     241 ..     197     244 .. 0.84
   3 ?    7.5   0.3     0.024       2.9      13      49 ..     235     271 ..     230     283 .. 0.89
   4 ?   -0.8   0.1       8.5     1e+03      27      46 ..     291     310 ..     266     328 .. 0.49

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.25
                                       HHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHH CS
                              GrpE  11 edeeeeleeeleelekevkelkekllrllaefenlrkrtekeke 54 
                                       + + ++l ++l+++++++++l   ++ l+ e+  lr r+e+ ++
  gi|557694562|ref|YP_008797616.1| 149 QRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALN 192
                                       56678888889999999999999999999999999999888765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.015
                                       TTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHH CS
                              GrpE   8 eeeedeeeeleeeleelekevkelkekllrllaefenlrk 47 
                                       ++ ++e++ le++++++ +e+++l++++  +  e++ l+ 
  gi|557694562|ref|YP_008797616.1| 202 NSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQA 241
                                       567899999*******************999998887765 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.024
                                       HHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHH CS
                              GrpE  13 eeeeleeeleelekevkelkekllrllaefenlrkrt 49 
                                       e+++l++  e l +e ++l+ ++++ll ++ nl+k +
  gi|557694562|ref|YP_008797616.1| 235 ELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEY 271
                                       6789999**************************9987 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 8.5
                                       CTTSCCCCCCTTTTTTTTHH CS
                              GrpE  27 evkelkekllrllaefenlr 46 
                                       + +++k+++ +l+ ++++ r
  gi|557694562|ref|YP_008797616.1| 291 RHESAKQQIGYLQSQLDENR 310
                                       33333333333333333333 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.4       1.2   1.5e+02       5      42 ..     161     198 ..     157     210 .. 0.62
   2 ?    9.5   3.0     0.011       1.4       5      51 ..     203     249 ..     189     262 .. 0.72
   3 ?    4.1   2.2      0.53        64      10      43 ..     250     283 ..     244     310 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 1.2
                       Cep57_MT_bd   5 psqspkeaLaevlkeLedEfehlklelqelaaqynald 42 
                                        +q+  ++L + ++ Le E+  l+ +l+e   +   l+
  gi|557694562|ref|YP_008797616.1| 161 RAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLT 198
                                       45666666777777777777777777776655555555 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.011
                       Cep57_MT_bd   5 psqspkeaLaevlkeLedEfehlklelqelaaqynaldpslgkrkRk 51 
                                       +s +  + L+  ++++ +E ++l+ ++     +++al++s+++ +R+
  gi|557694562|ref|YP_008797616.1| 203 SSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRE 249
                                       55666667888888888888888888888888888888887654443 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.53
                       Cep57_MT_bd  10 keaLaevlkeLedEfehlklelqelaaqynaldp 43 
                                       +eaL++  ++L  + + l +e++ l+a++n+l  
  gi|557694562|ref|YP_008797616.1| 250 NEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHE 283
                                       4555555666666666666666666666666653 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   4.0     0.029       3.6      59     111 ..     161     231 ..     134     251 .. 0.50
   2 ?    4.0   0.1      0.42        51      23     105 ..     227     316 ..     223     336 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHT...................-BTCCG-S--HHHHHHHHHHHHHHHHHS--EESEEES CS
                   Cob_adeno_trans  59 eiqneLfdlgaelatp..................ekkkekkkiteeeveelekeideleaelpplksfilp 111
                                       + q+++ +l +++ +                   +  +++ + + ee+++le++i+++++e+ +l++  + 
  gi|557694562|ref|YP_008797616.1| 161 RAQEQINQLRTTIQILeteintlrtrleealntaAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVS 231
                                       33333333333322111112222222333333322222333334445777777777777777777654444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.42
                                       HHHHHHHHHHHHHHHHHHHHHHHCTTT.............THHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HH CS
                   Cob_adeno_trans  23 dprveayGtvDelnsaiglarallaee.............eeelkeaLeeiqneLfdlgaelatpekkkekkkitee 86 
                                       d  v+++G++  l++   ++    ++               ++  ++L+   n+L++l + l t      +++  ++
  gi|557694562|ref|YP_008797616.1| 227 DRYVSTVGELKALQASYEMLSRENEALstsyqqllhdyrnLTKEYSMLQATFNQLHELYEGLVT------RHESAKQ 297
                                       6678888888888888888774433334444444444333233333444444445555555543......3333445 PP

                                       HHHHHHHHHHHHHHHS--E CS
                   Cob_adeno_trans  87 eveelekeideleaelppl 105
                                       ++  l++++de + el  l
  gi|557694562|ref|YP_008797616.1| 298 QIGYLQSQLDENRRELGDL 316
                                       5777888888777777655 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 ?    8.7   4.0     0.017       2.1       5      70 ..     161     224 ..     149     236 .. 0.63
   2 ?    2.1   8.5         2   2.4e+02      18      75 ..     209     271 ..     199     326 .. 0.47

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.017
                       Uso1_p115_C   5 eleseaaslkdeneklkaelqslskalesleqkeakkaaesqakeleaenkklekeleklraelke 70 
                                        ++++ ++l++  + l++e++ l+++le++ ++   +  +++ ++ ++e+k+le++++++++e+++
  gi|557694562|ref|YP_008797616.1| 161 RAQEQINQLRTTIQILETEINTLRTRLEEALNT--AAMLTARLNSSREEIKRLEQRIQTMSEEYRQ 224
                                       456666666666666666666666666666666..4444555555555555555555555555554 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 2
                       Uso1_p115_C  18 eklkaelqslskalesleqk.....eakkaaesqakeleaenkklekeleklraelkeekeke 75 
                                       ++l++++q +s+++++l+        ++ka ++  ++l+ en++l+   ++l   +++  +++
  gi|557694562|ref|YP_008797616.1| 209 KRLEQRIQTMSEEYRQLNDRyvstvGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEY 271
                                       444444444444444444443333333444444444444444444443333333333333322 PP

>> Csm1_N  Csm1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.0      0.21        25      34      66 ..     157     189 ..     153     193 .. 0.82
   2 ?   11.2   1.3     0.003      0.37      30      64 ..     195     229 ..     188     235 .. 0.90
   3 ?    1.3   0.3       3.7   4.5e+02      34      53 ..     290     309 ..     265     324 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.21
                            Csm1_N  34 qkletkdqeiesLkeqlaeleekvkeleerrkk 66 
                                       ++l+  +++i++L+ +++ le++++ l +r ++
  gi|557694562|ref|YP_008797616.1| 157 NDLNRAQEQINQLRTTIQILETEINTLRTRLEE 189
                                       5677788999**********9999999888765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.003
                            Csm1_N  30 svLsqkletkdqeiesLkeqlaeleekvkeleerr 64 
                                        +L+ +l++  +ei++L+++++++ e+ ++l++r+
  gi|557694562|ref|YP_008797616.1| 195 AMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRY 229
                                       6899**************************99986 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 3.7
                            Csm1_N  34 qkletkdqeiesLkeqlael 53 
                                       ++ e+ +q+i  L+ ql+e 
  gi|557694562|ref|YP_008797616.1| 290 TRHESAKQQIGYLQSQLDEN 309
                                       34445555555555555554 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 ?    9.1   7.1    0.0059      0.71      32     103 ..     151     224 ..     138     232 .. 0.61
   2 ?    5.3   2.3     0.086        10      36      98 ..     242     308 ..     229     332 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0059
                              HemX  32 eltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsga..e 103
                                       +++   ++l+ + ++++q  ++++ ++++ ++l +rl+++ ++ + l+++l++  +++++l+q+++++s +  +
  gi|557694562|ref|YP_008797616.1| 151 TYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEyrQ 224
                                       23333344444444444444445557777777777777777777777888888888888888888887776444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.086
                              HemX  36 evaelqqqlaaleqqlaq....veaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlsk 98 
                                       + + l+ + +al+++++q     +++ ++ + l+++++ql+e  e l ++ e+ ++q+  lq+ql +
  gi|557694562|ref|YP_008797616.1| 242 SYEMLSRENEALSTSYQQllhdYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDE 308
                                       3333333333333333333333444555555555666666666666666666666666666666654 PP

>> She9_MDM33  She9 / Mdm33 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   8.0      0.01       1.2      23      87 ..     156     221 ..     144     265 .. 0.80
   2 ?    0.7   1.1       3.2   3.9e+02      17      75 ..     219     279 ..     211     284 .. 0.44
   3 ?    0.4   0.1       4.1     5e+02      33      61 ..     293     321 ..     266     329 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.01
                        She9_MDM33  23 lndvt.GYseieklkksieeleeeleeakeevreakeayeeaiekrsksqrevneLLqRkssWspe 87 
                                       lnd+    ++i++l+++i+ le+e+++ +++++ea ++ +  +++ ++s  e++ L qR ++ s+e
  gi|557694562|ref|YP_008797616.1| 156 LNDLNrAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEE 221
                                       5555413579*************************************************9988764 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 3.2
                        She9_MDM33  17 ltaskalnd..vtGYseieklkksieeleeeleeakeevreakeayeeaiekrsksqrevn 75 
                                       ++  ++lnd  v+   e+++l++s e+l +e e+  ++ +++ ++y++ +++ s  q   n
  gi|557694562|ref|YP_008797616.1| 219 SEEYRQLNDryVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFN 279
                                       2223333332223333444555555555555555555555555555555555555555544 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 4.1
                        She9_MDM33  33 eklkksieeleeeleeakeevreakeaye 61 
                                       e+ k++i  l+++l+e+++e+ +++ +y+
  gi|557694562|ref|YP_008797616.1| 293 ESAKQQIGYLQSQLDENRRELGDLRLRYS 321
                                       66788888899999999999988888886 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 ?    8.5   8.4      0.02       2.4       6      63 ..     162     214 ..     149     226 .. 0.73
   2 ?   10.3   3.0    0.0052      0.63      14      66 ..     205     259 ..     197     262 .. 0.73
   3 ?    0.1   2.2       8.4     1e+03      11      61 ..     237     285 ..     234     298 .. 0.52
   4 ?    0.4   0.2       6.8   8.2e+02      25      27 ..     286     288 ..     263     325 .. 0.46

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.02
                      ABC_tran_CTD   6 eqreleeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyer 63 
                                        q ++ +l  +I+ LE+ei +l ++l+++       + a l+a+l+  ++e+++l++r
  gi|557694562|ref|YP_008797616.1| 162 AQEQINQLRTTIQILETEINTLRTRLEEALN-----TAAMLTARLNSSREEIKRLEQR 214
                                       578899*********************9874.....4555555555555555555544 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0052
                      ABC_tran_CTD  14 eaeIeaLEeeiaelea...eladpelysdpeklaelsaeleeleaeLeelyerWee 66 
                                        +eI +LE++i+++ +   +l+d  + s+  +l++l+a +e l  e e+l   + +
  gi|557694562|ref|YP_008797616.1| 205 REEIKRLEQRIQTMSEeyrQLNDR-YVSTVGELKALQASYEMLSRENEALSTSYQQ 259
                                       456777777777777655455544.347779*************999998776665 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 8.4
                      ABC_tran_CTD  11 eeleaeIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeely 61 
                                       ++l a  e L  e ++l +  +  +l  d+  l++    l++  ++L ely
  gi|557694562|ref|YP_008797616.1| 237 KALQASYEMLSRENEALSTSYQ--QLLHDYRNLTKEYSMLQATFNQLHELY 285
                                       4444444445455555544444..233444444444444444444444444 PP

  == domain 4  score: 0.4 bits;  conditional E-value: 6.8
                      ABC_tran_CTD  25 ael 27 
                                       + l
  gi|557694562|ref|YP_008797616.1| 286 EGL 288
                                       222 PP

>> Rho_Binding  Rho Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   1.1     0.018       2.2      10      53 ..     150     197 ..     144     200 .. 0.87
   2 ?    8.1   1.4     0.038       4.6       1      45 [.     197     245 ..     197     253 .. 0.83
   3 ?    2.6   2.5         2   2.4e+02       4      45 ..     242     287 ..     239     330 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.018
                       Rho_Binding  10 kekeelnkklkkleeelekake....eeeeieklkasyekqLktErlL 53 
                                          ++l + l+ ++e+++++++     e ei++l++  e+ L+t  +L
  gi|557694562|ref|YP_008797616.1| 150 RTYQDLLNDLNRAQEQINQLRTtiqiLETEINTLRTRLEEALNTAAML 197
                                       567899***************658899***************997766 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.038
                       Rho_Binding   1 Ltkdvenlakekeelnkklkkleeelekake....eeeeieklkasyek 45 
                                       Lt +++  ++e + l++++++++ee++++++    +  e++ l+asye 
  gi|557694562|ref|YP_008797616.1| 197 LTARLNSSREEIKRLEQRIQTMSEEYRQLNDryvsTVGELKALQASYEM 245
                                       67788888999999**************996577788899999999984 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 2
                       Rho_Binding   4 dvenlakekeelnkklkkleeelekak.e...eeeeieklkasyek 45 
                                       + e l+ e+e l+   ++l +++++++ e    ++  ++l++ ye 
  gi|557694562|ref|YP_008797616.1| 242 SYEMLSRENEALSTSYQQLLHDYRNLTkEysmLQATFNQLHELYEG 287
                                       5667777888888877777777777762233344444555555544 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 ?    9.7   8.6    0.0071      0.85       6      65 ..     153     212 ..     149     217 .. 0.92
   2 ?    5.9   3.4      0.12        14       4      58 ..     221     275 ..     211     281 .. 0.86
   3 ?    3.8   1.3      0.51        62      15      62 ..     267     314 ..     266     327 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0071
                       Cep57_CLD_2   6 ktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkELkeqr 65 
                                       + L n+L+++++++    ++++ L +E ++  ++L +A+ ++  L+a++++ r+E k  +
  gi|557694562|ref|YP_008797616.1| 153 QDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLE 212
                                       6789***************************************************77655 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.12
                       Cep57_CLD_2   4 evktLqnrLdsltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealr 58 
                                       e  +L +r  s++ +l + +  +++L++E++   ++ ++ + + ++L+ e   l+
  gi|557694562|ref|YP_008797616.1| 221 EYRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQ 275
                                       55567777778888899999***************************99987765 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.51
                       Cep57_CLD_2  15 ltrklqvheeelkrLnkERdsalrqLgvAyeelneLkaevealrkELk 62 
                                       lt ++++ + + ++L  + ++ +++  +A + +  L+++++  r+EL 
  gi|557694562|ref|YP_008797616.1| 267 LTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRRELG 314
                                       677888888888889999999999999999999999999999999953 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   3.8    0.0032      0.39      93     160 ..     164     230 ..     144     231 .. 0.91
   2 ?    1.1   0.2         2   2.5e+02     117     141 ..     260     284 ..     234     324 .. 0.52

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0032
                     Fzo_mitofusin  93 hqvqqelsstfarlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekfeeqyl 160
                                       +q+ ++l +t++ l++++++ ++ lee +++     ++l++  ++ k l ++ +++++e ++ +++y+
  gi|557694562|ref|YP_008797616.1| 164 EQI-NQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYV 230
                                       344.469******************************************************9999997 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 2
                     Fzo_mitofusin 117 leeeikelekeiekleevqkkakll 141
                                       l ++ ++l+ke ++l+++ ++++ l
  gi|557694562|ref|YP_008797616.1| 260 LLHDYRNLTKEYSMLQATFNQLHEL 284
                                       3333333333333333333333322 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   4.4     0.062       7.5     252     322 ..     149     216 ..     129     221 .. 0.65
   2 ?    7.9   2.5    0.0079      0.95     213     351 ..     214     349 ..     212     354 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.062
                              FUSC 252 avpelaallaelaaleaaaaaealeaalaalrarlralrraleadadtaalllarlaellaelaqllaslr 322
                                       + ++ ++ll +l +  a+++ ++l++ ++ l+++++ lr++le++ +taa+l arl +  +e  +l + ++
  gi|557694562|ref|YP_008797616.1| 149 Q-RTYQDLLNDLNR--AQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQ 216
                                       2.237888888888..6667888888888888888888888886666666666666655555555544443 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0079
                              FUSC 213 rirararalrrllsrmlallallsslarllarlraeeaaavpelaallaelaaleaaaaaealeaalaalrarlral 289
                                       ri+  ++ +r+l+ r ++ +  l +l+   + l++e++a   + ++ll + ++l  ++  + l+a  ++l +  + l
  gi|557694562|ref|YP_008797616.1| 214 RIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNL--TKEYSMLQATFNQLHELYEGL 288
                                       78888999*******************************9999**********5..567888999999999999999 PP

                              FUSC 290 rraleadadtaalllarlaellaelaqllaslraleaaiaaarraerlarhrdhlaallngl 351
                                        +++e + ++ + l+++l+e  +el +l+  +  l+ +    +r  ++a  +  la++++++
  gi|557694562|ref|YP_008797616.1| 289 VTRHESAKQQIGYLQSQLDENRRELGDLRLRYSLLSDENLL-HRNIAYAEAFIILAVVVAAV 349
                                       99999999999999999999999999999888888888776.77777777666666666665 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   9.2      0.53        64      10      80 ..     154     226 ..     148     321 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.53
                           DUF2203  10 alLpllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGvevkdle 80 
                                       +lL  l++  e++++lr+ ++ le+e+++ +++ e+    aa l a+l++ ++ei++l ++i+ +  e+++l+
  gi|557694562|ref|YP_008797616.1| 154 DLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALntAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLN 226
                                       5666777777777777777777777666666665443345555555566666666666666655555555443 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  21.5     0.024       2.9      10     167 ..     148     316 ..     141     321 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.024
                         Rootletin  10 aqqrqaqLvskL...qaKvlqYkkrcseleqrllektselektkltlll.ssareleeeesadleealakLeeErq. 81 
                                       +q+ +++L++ L   q+++ q +  ++ le ++++  ++le+   t  + +   + ++ee++ le+ ++ + eE + 
  gi|557694562|ref|YP_008797616.1| 148 RQRTYQDLLNDLnraQEQINQLRTTIQILETEINTLRTRLEEALNTAAMlTARLNSSREEIKRLEQRIQTMSEEYRq 224
                                       688999998877555899****************9766666665554443344577888999999******999773 PP

                         Rootletin  82 ...rseklaqvnslLreqleearqaneaLtedlqkltkdwerlreeleqkekewreeeeafneylsse...hsrlls 152
                                          r  + + + + L+   e  +++neaL+++ q+l +d ++l++e  + ++++++  e ++  +++    ++++  
  gi|557694562|ref|YP_008797616.1| 225 lndRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHesaKQQIGY 301
                                       333444556667899****************************************9999998877654111345555 PP

                         Rootletin 153 LWrevvavrrqfsel 167
                                       L  ++ + rr++ +l
  gi|557694562|ref|YP_008797616.1| 302 LQSQLDENRRELGDL 316
                                       566666666666555 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       8.1   9.8e+02      29      42 ..     174     187 ..     163     188 .. 0.73
   2 ?   10.4   0.5     0.005      0.61      16      38 ..     238     260 ..     235     262 .. 0.63
   3 ?   10.5   2.2    0.0044      0.53       9      41 ..     252     284 ..     251     286 .. 0.88
   4 ?    8.1   1.8     0.026       3.2       5      38 ..     269     302 ..     259     308 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 8.1
                              HALZ  29 ekLkaelqeLkekl 42 
                                       + L++e+++L+ +l
  gi|557694562|ref|YP_008797616.1| 174 QILETEINTLRTRL 187
                                       66889999998876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.005
                              HALZ  16 aLksdydsLkkenekLkaelqeL 38 
                                       aL+++y+ L +ene+L +  q+L
  gi|557694562|ref|YP_008797616.1| 238 ALQASYEMLSRENEALSTSYQQL 260
                                       56666666667777776655554 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0044
                              HALZ   9 vLKasYdaLksdydsLkkenekLkaelqeLkek 41 
                                       +L  sY +L +dy +L ke   L+a  ++L e+
  gi|557694562|ref|YP_008797616.1| 252 ALSTSYQQLLHDYRNLTKEYSMLQATFNQLHEL 284
                                       78899**************99999999988875 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.026
                              HALZ   5 rDYdvLKasYdaLksdydsLkkenekLkaelqeL 38 
                                       ++Y +L+a +++L+  y+ L    e+ k+++  L
  gi|557694562|ref|YP_008797616.1| 269 KEYSMLQATFNQLHELYEGLVTRHESAKQQIGYL 302
                                       7788888888888877777777666666666555 PP

>> Noelin-1  Neurogenesis glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.3     0.076       9.2      53      96 ..     142     186 ..     130     192 .. 0.84
   2 ?    7.9   1.4     0.025         3      38      84 ..     205     254 ..     195     272 .. 0.70
   3 ?   -0.3   0.1         9   1.1e+03      42      79 ..     258     284 ..     249     315 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.076
                          Noelin-1  53 qsievldlRtsrdl.qyvrktetllktlesklkvveedrkelsak 96 
                                        +i  + +Rt++dl + ++++++++++l+++++ +e + ++l ++
  gi|557694562|ref|YP_008797616.1| 142 WHIAAVRQRTYQDLlNDLNRAQEQINQLRTTIQILETEINTLRTR 186
                                       57888999***99647899*************9999998888775 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.025
                          Noelin-1  38 srqlrqllekvqnlsqsievldlR...tsrdlqyvrktetllktlesklk 84 
                                        +++++l++++q +s++ ++l+ R   t  +l+ ++ + ++l+  ++ l+
  gi|557694562|ref|YP_008797616.1| 205 REEIKRLEQRIQTMSEEYRQLNDRyvsTVGELKALQASYEMLSRENEALS 254
                                       5689******************9944455556666665555554444333 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 9
                          Noelin-1  42 rqllekvqnlsqsievldlRtsrdlqyvrktetllktl 79 
                                       +qll   +nl+++  +l+            t ++l++l
  gi|557694562|ref|YP_008797616.1| 258 QQLLHDYRNLTKEYSMLQ-----------ATFNQLHEL 284
                                       455555555555444443...........333333333 PP

>> DASH_Dam1  DASH complex subunit Dam1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.3       3.5   4.3e+02      25      29 ..     169     173 ..     151     204 .. 0.56
   2 ?    3.0   0.2      0.72        87      15      24 ..     218     227 ..     197     260 .. 0.57
   3 ?    4.5   0.0      0.25        30       6      35 ..     265     294 ..     260     295 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 3.5
                         DASH_Dam1  25 ihesL 29 
                                       ++ ++
  gi|557694562|ref|YP_008797616.1| 169 LRTTI 173
                                       33332 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.72
                         DASH_Dam1  15 LdknledLqq 24 
                                       +++ +++L++
  gi|557694562|ref|YP_008797616.1| 218 MSEEYRQLND 227
                                       4444444432 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.25
                         DASH_Dam1   6 aeLaDsletLdknledLqqihesLsdfNeS 35 
                                       ++L+++ + L++ +++L+++ e L++  eS
  gi|557694562|ref|YP_008797616.1| 265 RNLTKEYSMLQATFNQLHELYEGLVTRHES 294
                                       6799999****************9998887 PP

>> YlqD  YlqD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   7.1     0.031       3.8      17      86 ..     147     218 ..     144     231 .. 0.66
   2 ?    7.8   6.1     0.033         4      23     109 ..     195     287 ..     187     299 .. 0.89
   3 ?    4.3   1.7      0.42        50      25      72 ..     239     306 ..     235     321 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.031
                              YlqD  17 lKeelqqqlqaqieqldkelqqLefqakrlikeikkqsaq..qieeiqeqvekekserlekkkqllqqleqv 86 
                                       ++++  q+l +++++++++++qL++  + l++ei++  ++  ++ +  + + ++ +  +e++k+l+q+++ +
  gi|557694562|ref|YP_008797616.1| 147 VRQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRleEALNTAAMLTARLNSSREEIKRLEQRIQTM 218
                                       678888999999999999999999999999999988666666333333444444445555555555555443 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.033
                              YlqD  23 qqlqaqieqldkelqqLefqakrlikeikkqsaq......qieeiqeqvekekserlekkkqllqqleqvqkLelgs 93 
                                       + l+a+++   +e+++Le+  + + +e ++ + +      + +++q+++e   +e ++   + +q l++ ++L+ + 
  gi|557694562|ref|YP_008797616.1| 195 AMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRyvstvgELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEY 271
                                       56889999999999999999999999999988889999999999*******9999999999**************** PP

                              YlqD  94 evkqgqveslvevkvG 109
                                        + q++ ++l e+ +G
  gi|557694562|ref|YP_008797616.1| 272 SMLQATFNQLHELYEG 287
                                       ****999999999888 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.42
                              YlqD  25 lqaqieqldkelqqLefqakrlikeikkqsaq....................qieeiqeqvekekser 72 
                                       lqa+ e l +e + L++  ++l+++ ++ +++                    ++e++++q+   +s++
  gi|557694562|ref|YP_008797616.1| 239 LQASYEMLSRENEALSTSYQQLLHDYRNLTKEysmlqatfnqlhelyeglvtRHESAKQQIGYLQSQL 306
                                       56666666666666666666666666554443333333344333333333333333333333333333 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   2.0     0.068       8.3      10      61 ..     163     218 ..     155     231 .. 0.78
   2 ?    2.8   0.3       1.3   1.6e+02      11      39 ..     206     235 ..     201     319 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.068
                           NPV_P10  10 radikavddkVdalqqqv....ddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                        + i+++ + ++ l++++    ++++e l++   l+++L++  ++++ le+ +++ 
  gi|557694562|ref|YP_008797616.1| 163 QEQINQLRTTIQILETEIntlrTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTM 218
                                       46778888888888888855555566777888889999999999999999988876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 1.3
                           NPV_P10  11 adikavddkVdalqqqvddvqenl.pdvte 39 
                                       ++ik ++++++ ++++  ++++    +v e
  gi|557694562|ref|YP_008797616.1| 206 EEIKRLEQRIQTMSEEYRQLNDRYvSTVGE 235
                                       555555555555555555554432022222 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.8       0.2        24      12     109 ..     159     182 ..     149     193 .. 0.45
   2 ?    4.6   1.0      0.24        29      82     110 ..     197     225 ..     187     235 .. 0.57
   3 ?    8.0   0.4     0.021       2.6      75     117 ..     239     281 ..     236     283 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHHHHHHHHHHHH CS
                         Prefoldin  12 laqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeAiellkkklee 88 
                                       l++ +e+i+ l++t+++l+                                                          
  gi|557694562|ref|YP_008797616.1| 159 LNRAQEQINQLRTTIQILE---------------------------------------------------------- 177
                                       3333333333333333333.......................................................... PP

                                       HHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  89 lekqlekleeeleklkdqitt 109
                                                       ++i+t
  gi|557694562|ref|YP_008797616.1| 178 ----------------TEINT 182
                                       ................33333 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  82 lkkkleelekqlekleeeleklkdqittl 110
                                       l  +l++ ++ ++ le+ ++  ++++ +l
  gi|557694562|ref|YP_008797616.1| 197 LTARLNSSREEIKRLEQRIQTMSEEYRQL 225
                                       44444444555555555555544444444 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  75 leeAiellkkkleelekqlekleeeleklkdqittleanlaql 117
                                       l+ + e l ++ e l+ + ++l ++ + l++++ +l+a+++ql
  gi|557694562|ref|YP_008797616.1| 239 LQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQL 281
                                       56778999*******************************9997 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.2     0.015       1.8      17      84 ..     150     217 ..     141     232 .. 0.67
   2 ?    3.1   0.3      0.72        87       9      85 ..     226     302 ..     220     317 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.015
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleea 84 
                                       +  ++l ++l++ +e++++++++++  + +++ + + +++A +    L+  ++   + +k+l+q+ + 
  gi|557694562|ref|YP_008797616.1| 150 RTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQT 217
                                       45567777777777777777777777777777777777777777777777777777776666666544 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.72
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH. CS
                        Laminin_II   9 netakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeas 85 
                                       n+  +++   l++l++  e ++ + + + +s ++  ++ ++++k     +    +L +l + L+ + ++ kq+    
  gi|557694562|ref|YP_008797616.1| 226 NDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYL 302
                                       55556666667777777777777777777777777777777777777777888888888888888777777765544 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   5.9      0.12        15     397     455 ..     172     230 ..     144     234 .. 0.65
   2 ?    8.8   3.2    0.0043      0.52     403     481 ..     234     312 ..     226     332 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.12
                          Macoilin 397 alvrLeadikkLkaeLqasrqteqelrskissltseerslkselqqlkkendllqtklh 455
                                        +  Le++i+ L++ L+++ +t   l  +++s  +e + l + +q++ +e+ +l  ++ 
  gi|557694562|ref|YP_008797616.1| 172 TIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYV 230
                                       23457777777777777777777777777777777777777777777777777777665 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0043
                          Macoilin 403 adikkLkaeLqasrqteqelrskissltseerslkselqqlkkendllqtklhelvsakqkdkqtlqqlekrLkeek 479
                                       +++k L+a  +   + ++ l   ++ l    r+l +e + l+  +++l + ++ lv  +   kq++  l+ +L+e++
  gi|557694562|ref|YP_008797616.1| 234 GELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENR 310
                                       679999**99999999999******************************************************9998 PP

                          Macoilin 480 ea 481
                                       ++
  gi|557694562|ref|YP_008797616.1| 311 RE 312
                                       75 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   6.0      0.51        62       5      46 ..     172     213 ..     154     216 .. 0.69
   2 ?    5.9   0.4      0.13        15      11      40 ..     199     228 ..     195     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.51
                              XhlA   5 rlerietkldnleervdkleekaaeaeekiknleedlkkles 46 
                                        ++ +et++++l +r+++  + aa   +++ +  e++k+le+
  gi|557694562|ref|YP_008797616.1| 172 TIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQ 213
                                       455567777777777777777777777777777777777775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.13
                              XhlA  11 tkldnleervdkleekaaeaeekiknleed 40 
                                       ++l++  e++++le++  ++ e+  +l+++
  gi|557694562|ref|YP_008797616.1| 199 ARLNSSREEIKRLEQRIQTMSEEYRQLNDR 228
                                       578888888888888888888888877765 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 ?    3.6  20.5      0.34        41     135     201 ..     194     262 ..     113     340 .. 0.38

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.34
                      Exonuc_VII_L 135 Aelvvpdkaeleeqleelerrlekaikrlleekkqrlekl..asrlkspeellerkrqrldeleerler 201
                                       A +++ + +  +e++++le+r+++  +++ + + + ++++   ++l+ + e+l+r++++l+   ++l +
  gi|557694562|ref|YP_008797616.1| 194 AAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVgeLKALQASYEMLSRENEALSTSYQQLLH 262
                                       111111111111111111111111111111111111111110111112222222222222222222222 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   4.9     0.014       1.7      64     134 ..     152     222 ..     144     229 .. 0.62
   2 ?    3.6   3.2      0.41        49      73     164 ..     224     315 ..     212     319 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.014
                            DUF745  64 veqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqel 134
                                        + l ++l+ a++++++  + +q  e+ +++ ++  ++a + +++l+a l++++e+++++eq  + +++e 
  gi|557694562|ref|YP_008797616.1| 152 YQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEY 222
                                       45566666666666666666666666666666666666666666666666666666666666555555544 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.41
                            DUF745  73 eaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektqlleaAkkRve 149
                                         ++   +   +l++ +a+ ++ ++ ++   +++++l + +++ +++++ ++++ ++  +  +   +  e+Ak+++ 
  gi|557694562|ref|YP_008797616.1| 224 QLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIG 300
                                       44444444445566666666677777777777777777777777777777777777777666666677789999999 PP

                            DUF745 150 eLkkqlkearkdlek 164
                                        L++ql+e r++l +
  gi|557694562|ref|YP_008797616.1| 301 YLQSQLDENRRELGD 315
                                       999999999998865 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 ?    8.8   5.5     0.012       1.4      74     155 ..     106     201 ..      52     233 .. 0.66
   2 ?    4.3   2.7      0.29        35     126     156 ..     200     230 ..     196     261 .. 0.61
   3 ?    0.8   0.2       3.3     4e+02     114     154 ..     293     333 ..     251     353 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.012
                       EMP24_GP25L  74 eykvCfdnsfstkss................kkvsfdievgseasdykdsakkekletleselkkleekldsikreq 134
                                       +y++C+ n + +  +                + ++  +++ + +++ +  +  ++l+  ++++++l + ++ +++e+
  gi|557694562|ref|YP_008797616.1| 106 TYSLCIPNVQRRD-PlvtatffanytrettyQPLTHTWHIAA-VRQRTYQDLLNDLNRAQEQINQLRTTIQILETEI 180
                                       6666666665543.2344444444444444455555555532.3333444456677777777777777777777777 PP

                       EMP24_GP25L 135 kylrereerlrdtnestnsrv 155
                                       + lr+r e+  +t+  ++ r+
  gi|557694562|ref|YP_008797616.1| 181 NTLRTRLEEALNTAAMLTARL 201
                                       777777777666665555544 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.29
                       EMP24_GP25L 126 kldsikreqkylrereerlrdtnestnsrvv 156
                                       +l+s+++e+k l++r +++ + + ++n+r+v
  gi|557694562|ref|YP_008797616.1| 200 RLNSSREEIKRLEQRIQTMSEEYRQLNDRYV 230
                                       5566666666666666666666666666654 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 3.3
                       EMP24_GP25L 114 etleselkkleekldsikreqkylrereerlrdtnestnsr 154
                                       e+ ++++  l+++ld+ +re+  lr r + l d n    ++
  gi|557694562|ref|YP_008797616.1| 293 ESAKQQIGYLQSQLDENRRELGDLRLRYSLLSDENLLHRNI 333
                                       45566777788888888888888888877777766543333 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 ?    0.4  18.2       3.5   4.3e+02      18     101 ..     151     282 ..     144     335 .. 0.55

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 3.5
                     PI3K_P85_iSH2  18 klrevskqlqekskeydqlkeeynkiseeiqlkrqaleaFneaikmFeeqiklqekfskeaq............... 79 
                                        ++++ ++l+  +++ +ql +  + ++ ei++ r+ le   ++  m+   ++   + +k  +               
  gi|557694562|ref|YP_008797616.1| 151 TYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEqriqtmseeyrqlnd 227
                                       57777777888888888888888888888888888888888888888777765544333332233334333334444 PP

                     PI3K_P85_iSH2  80 .................................ehEieklqenleqlksrlkelh 101
                                                                         h+ ++l++ ++ l++  ++lh
  gi|557694562|ref|YP_008797616.1| 228 ryvstvgelkalqasyemlsrenealstsyqqlLHDYRNLTKEYSMLQATFNQLH 282
                                       4444433333333333333222222222222223333333333333333333333 PP

>> Tho2  Transcription factor/nuclear export subunit protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   8.4     0.062       7.5      25      96 ..     174     245 ..     129     299 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.062
                              Tho2  25 eqYekeieklkseieelakdrsde.raaakkkkkekkrlkeliekLeeEkkeqiehvekvkkrLkeekkswfk 96 
                                       +  e+ei+ l++++ee   +  ++ +a+ +++++e+krl+++i++++eE  +   ++  +  +Lk  + s+  
  gi|557694562|ref|YP_008797616.1| 174 QILETEINTLRTRLEEA-LNTAAMlTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKALQASYEM 245
                                       44456677777766666.5566677999*************************99999999999987776543 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   6.8    0.0034      0.41      65     135 ..     156     226 ..     146     230 .. 0.92
   2 ?    1.7   0.5       1.9   2.3e+02      74     117 ..     270     313 ..     258     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  65 lkelekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqearraveKfaelarlvraeasrqq 135
                                       l++l ++++q+  Lr   + le+++  ++ +le+++++++ + + l   r + +++++  +++++e +++ 
  gi|557694562|ref|YP_008797616.1| 156 LNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLN 226
                                       6899*******************************************999999999999999999988876 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  74 qvalLrekeaelekqveeakqqleaerealrqarkelqearrav 117
                                       + ++L++  ++l +  e +  ++e + ++   ++ +l e rr++
  gi|557694562|ref|YP_008797616.1| 270 EYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRREL 313
                                       56778888888888888888888888888888888888888875 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.5      0.22        27      11      36 ..     152     177 ..     148     185 .. 0.75
   2 ?    6.2   0.5     0.082       9.9       4      40 ..     187     223 ..     185     247 .. 0.76
   3 ?    4.8   2.5      0.23        28       3      42 ..     249     288 ..     247     328 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHHHHHHHTHHHHHHHH CS
                           DUF4298  11 isallqqLeealeqwkklqkklakLd 36 
                                        ++ll++L++a+eq+++l ++++ L+
  gi|557694562|ref|YP_008797616.1| 152 YQDLLNDLNRAQEQINQLRTTIQILE 177
                                       57788888888888888888877665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.082
                                       HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHT CS
                           DUF4298   4 mekildeisallqqLeealeqwkklqkklakLdeYYq 40 
                                       +e+ l+ +  l++ L+ + e++k+l++ +++++e Y 
  gi|557694562|ref|YP_008797616.1| 187 LEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYR 223
                                       6788888888888888888888888888888877663 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHTSH CS
                           DUF4298   3 emekildeisallqqLeealeqwkklqkklakLdeYYqse 42 
                                       e e++  + ++ll +  ++ +++  lq+++++L+e Y+  
  gi|557694562|ref|YP_008797616.1| 249 ENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGL 288
                                       5678888899999999999999999999999999999764 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 ?    5.5   9.2     0.055       6.6     187     260 ..     152     222 ..     141     228 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.055
                          CALCOCO1 187 lrslskelqelrnslaerdtqvlqLqdtittltqkLttAqrkeaenEallkelrslqerlaaSerkvegLkeeL 260
                                        + l ++l++++++ ++  t ++ L+ +i+tl+++L++A    a    l++ l s++e ++  e++ +++ ee 
  gi|557694562|ref|YP_008797616.1| 152 YQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAA---MLTARLNSSREEIKRLEQRIQTMSEEY 222
                                       45666777777777777777777777777777777777665544...344556666666666666666666655 PP

>> HAUS6_N  HAUS augmin-like complex subunit 6 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   7.0     0.094        11     153     223 ..     149     224 ..     122     244 .. 0.64
   2 ?    6.0   1.6     0.063       7.6     138     204 ..     239     305 ..     230     320 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.094
                           HAUS6_N 153 rvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkae......keaakkekkeasedaeeekikk 223
                                       + +++ +l+++++a + +++++   q le ++  lr++lee  +    +      +++++++++e++++  +e++++
  gi|557694562|ref|YP_008797616.1| 149 QRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAA-MltarlnSSREEIKRLEQRIQTMSEEYRQ 224
                                       33455566666666666777777777777777777777777555433.13555555555555555555555555554 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.063
                           HAUS6_N 138 askkaqdlsklvaahrvslrrflrekaaadrarqkyqenaqllekkerelraeleelqaelkaekea 204
                                       ++ + ++ls+ ++a + s++++l+++++ ++   ++q   + l + ++ l ++ e  ++++   +++
  gi|557694562|ref|YP_008797616.1| 239 LQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQ 305
                                       4555668888888889999999999999888888888888888888888888888888877644333 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 ?    0.1   9.5       9.4   1.1e+03      73      95 ..     165     187 ..     128     260 .. 0.67
   2 ?    2.6   0.2       1.5   1.8e+02      65      97 ..     259     301 ..     230     323 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 9.4
                           DUF4140  73 eleeledelaaledelaaaearl 95 
                                       ++++l+++++ le e++++++rl
  gi|557694562|ref|YP_008797616.1| 165 QINQLRTTIQILETEINTLRTRL 187
                                       33333333333333333333333 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 1.5
                           DUF4140  65 e..........elkalraeleeledelaaledelaaaearlaf 97 
                                       +          e++ l+a+ ++l++  + l  + ++a++++ +
  gi|557694562|ref|YP_008797616.1| 259 QllhdyrnltkEYSMLQATFNQLHELYEGLVTRHESAKQQIGY 301
                                       0444444444445566666666666666666666666666554 PP

>> DASH_Spc34  DASH complex subunit Spc34
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   6.7     0.048       5.8     166     253 ..     137     216 ..     132     225 .. 0.84
   2 ?    4.0   5.9       0.3        36     154     207 ..     254     312 ..     219     330 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.048
                        DASH_Spc34 166 elltkyplleake.kieelreeYeelseeieeleaeiaeQkkqLeaqnknesessseddsesetskskdvdelirkE 241
                                        l++++ ++  ++ +++ l ++ +  +e+i++l+ +i+  + ++++ +++ +e  ++           + +  ++  
  gi|557694562|ref|YP_008797616.1| 137 PLTHTWHIAAVRQrTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNT---------AAMLTARLNSS 204
                                       578889988888878999**************************9999999887554.........67778888888 PP

                        DASH_Spc34 242 eeeIeeLerklk 253
                                       +eeI++Le++++
  gi|557694562|ref|YP_008797616.1| 205 REEIKRLEQRIQ 216
                                       888888888876 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.3
                        DASH_Spc34 154 dfdvelllkvleelltkyplleake.....kieelreeYeelseeieeleaeiaeQkkq 207
                                       +++ ++ll+  ++l+++y +l+a        +e l +++e+ +++i +l+++ +e +++
  gi|557694562|ref|YP_008797616.1| 254 STSYQQLLHDYRNLTKEYSMLQATFnqlheLYEGLVTRHESAKQQIGYLQSQLDENRRE 312
                                       66777888888888888888766433333344444455555555555555555554444 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 ?    1.3  13.4         1   1.2e+02     170     261 ..     163     254 ..     118     340 .. 0.61

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1
                        Fmp27_WPPW 170 rvqkelleeRleeleeqiekleekleelelksekedeelkeeieelekeikelkeklefletlledlkeseesse.. 244
                                       + q + l+  ++ le++i++l+++lee+ ++       l++++++ ++eik+l+++++++++ +++l+ +  s+   
  gi|557694562|ref|YP_008797616.1| 163 QEQINQLRTTIQILETEINTLRTRLEEALNTAAM----LTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVge 235
                                       2222223333344555555555555555444444....677777777777777777777777777777666533344 PP

                        Fmp27_WPPW 245 ........eeeskskelsaastses 261
                                               e       ls+++++ s
  gi|557694562|ref|YP_008797616.1| 236 lkalqasyE------MLSRENEALS 254
                                       443322220......2222222222 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 ?    3.4   8.8      0.79        96      16      85 ..     153     218 ..     140     239 .. 0.47
   2 ?    7.6   6.5     0.041       4.9       2      89 ..     188     278 ..     187     280 .. 0.81
   3 ?    8.3   1.5     0.024         3       5      76 ..     247     314 ..     236     325 .. 0.49

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.79
                            CENP-H  16 lklsqelrelqeeltevekenlrlkrknrelaael.lelakekesek..eklkeelekleaelkksrqrwrvv 85 
                                       ++l ++l+ +qe++++++  +  l+++ ++l ++l + l+ +++ +   +  +ee+++le+ +++       +
  gi|557694562|ref|YP_008797616.1| 153 QDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLeEALNTAAMLTArlNSSREEIKRLEQRIQT-------M 218
                                       33334444444444444444444444444444444223333333222443334444444443333.......2 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.041
                            CENP-H   2 lplieqrdelssellklsqelrelqeeltevekenlrlkrknrelaael.lelakekesek..eklkeelekleael 75 
                                        + ++   +l  +l    +e++ l+++++++ +e ++l+ + ++ + el + +a+ ++  +  e l+ + ++l  ++
  gi|557694562|ref|YP_008797616.1| 188 EEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELkALQASYEMLSRenEALSTSYQQLLHDY 264
                                       6778888889999999999******************************4433333333335767899999999999 PP

                            CENP-H  76 kksrqrwrvvknva 89 
                                       ++  ++  +++ ++
  gi|557694562|ref|YP_008797616.1| 265 RNLTKEYSMLQATF 278
                                       99999999999887 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.024
                            CENP-H   5 ieqrdelssellklsqelrelqeeltevekenlrlkrknrelaaellelakekesek...eklkeelekleaelk 76 
                                        +++++ls+++++l  ++r+l++e + +++   +l++  + l+++        es k     l+++l++ ++el 
  gi|557694562|ref|YP_008797616.1| 247 SRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRH-------ESAKqqiGYLQSQLDENRRELG 314
                                       3344455555555555555555555555555555544444444444.......3333122345555555555554 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.3    0.0083         1     131     192 ..     143     204 ..     127     209 .. 0.91
   2 ?    2.9   2.5      0.64        78     106     198 ..     209     297 ..     199     301 .. 0.68
   3 ?    2.0   0.9       1.2   1.4e+02      72     121 ..     256     305 ..     237     318 .. 0.55

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0083
                               LXG 131 divslpelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkalktyvseLeem 192
                                       +i ++ +++++++ ++l++a++++++  + ++ +++e +++ + le+ l++++ ++++L++ 
  gi|557694562|ref|YP_008797616.1| 143 HIAAVRQRTYQDLLNDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSS 204
                                       7888999**********************************************999999986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.64
                               LXG 106 nglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeqksalanlesdlkal 182
                                       ++l+++ ++++e   ++n+  + vs++ +l+ l+ s+  + l++ ++ +++  ++l +  ++++ +++ l++++++l
  gi|557694562|ref|YP_008797616.1| 209 KRLEQRIQTMSEEYRQLND--RYVSTVGELKALQASY--EMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQL 281
                                       5667777777777777777..7777777777777766..66677777777777777777777777888888888888 PP

                               LXG 183 ktyvseLeemtskgki 198
                                       + +++ L +  ++ k+
  gi|557694562|ref|YP_008797616.1| 282 HELYEGLVTRHESAKQ 297
                                       8887777776666665 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 1.2
                               LXG  72 qyeefLkkikealesvepssngfidedfLeqelenglkkakevteelkde 121
                                       +y++ L ++++ ++++ + + +f + + L + l  + + ak+++ +l+++
  gi|557694562|ref|YP_008797616.1| 256 SYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQ 305
                                       45555555555555555444444444555555555555555555555444 PP

>> Paralemmin  Paralemmin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   5.5     0.044       5.3       6      71 ..     161     226 ..     157     252 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.044
                        Paralemmin   6 edeakvrkLEesiqrLekeieeLeseesaisakeevlaeklketeksvedlqksllstdkekkvsl 71 
                                         ++++ +L  +iq Le+ei++L +   +  ++  +l+++l+++++++++l++  ++ ++e +  +
  gi|557694562|ref|YP_008797616.1| 161 RAQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLN 226
                                       56788999******************999999******************9999888777543332 PP

>> Swi5  Swi5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.2     0.062       7.5       2      43 ..     163     211 ..     162     214 .. 0.74
   2 ?    0.5   5.8       5.2   6.3e+02       2      46 ..     212     264 ..     197     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.062
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH........HHHHHHHHHHHH CS
                              Swi5   2 eaeikeleeqleelekelaelkeelkekk.......dpeetvkrhIklL 43 
                                       +++i++l+ +++ le+e+++l+ +l+e         +  +  ++ Ik+L
  gi|557694562|ref|YP_008797616.1| 163 QEQINQLRTTIQILETEINTLRTRLEEALntaamltARLNSSREEIKRL 211
                                       78999*******************9986655555555555555555555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 5.2
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.........HHHHHHHHHHHHHHH CS
                              Swi5   2 eaeikeleeqleelekelaelkeelkekk........dpeetvkrhIklLheY 46 
                                       e++i+++ e++++l++ + ++  elk+ +        + e+   ++ +lLh+Y
  gi|557694562|ref|YP_008797616.1| 212 EQRIQTMSEEYRQLNDRYVSTVGELKALQasyemlsrENEALSTSYQQLLHDY 264
                                       44555555555555555555555555444666666655555556666666666 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  13.9     0.018       2.2     145     250 ..     157     266 ..     129     277 .. 0.53
   2 ?    1.1   6.8       1.8   2.1e+02     171     263 ..     212     311 ..     211     316 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.018
                            Cluap1 145 kevelreartkalsrqleleeiekalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqslq. 220
                                       ++ ++              +e  ++l+++i+ +++e+++++++le+  ++ a L+a+++  ++e+ r ++r+q++  
  gi|557694562|ref|YP_008797616.1| 157 NDLNRA-------------QEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSe 220
                                       222222.............2233456666666666777777777776666666777777777777777777766662 PP

                            Cluap1 221 ..............svrPafmdeyekleee...LqelyeeYvekfrn 250
                                                     +++ a    ye+l +e   L++ y++ ++ +rn
  gi|557694562|ref|YP_008797616.1| 221 eyrqlndryvstvgELK-ALQASYEMLSREneaLSTSYQQLLHDYRN 266
                                       22222222222222333.45555555443322355555555555555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1.8
                            Cluap1 171 keaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqslqsvrPafmdeyekleeeLqelyeeY... 244
                                       +++i++++ee ++++++  ++  + ++L+a  e  ++e e  ++ +q+l +      +ey +l++  ++l+e Y   
  gi|557694562|ref|YP_008797616.1| 212 EQRIQTMSEEYRQLNDRYVSTVGELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYegl 288
                                       67899999999999999999999999999999999999999999999988877789999999997655555544222 PP

                            Cluap1 245 vekf....rnlsylekqlekknk 263
                                       v+++    +++ yl++ql+++++
  gi|557694562|ref|YP_008797616.1| 289 VTRHesakQQIGYLQSQLDENRR 311
                                       66652222345578888777655 PP

>> Fungal_TACC  Fungal Transforming acidic coiled-coil (TACC) proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.4      0.27        32      35      64 ..     161     190 ..     155     197 .. 0.88
   2 ?    6.6   0.5     0.086        10      26      67 ..     272     312 ..     268     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.27
                       Fungal_TACC  35 kyqkkldklelenkslkqeieqLkkqleae 64 
                                       + q+++++l++  + l++ei++L+ +le +
  gi|557694562|ref|YP_008797616.1| 161 RAQEQINQLRTTIQILETEINTLRTRLEEA 190
                                       67999********************99865 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.086
                       Fungal_TACC  26 kllkkgyeakyqkkldklelenkslkqeieqLkkqleaerkE 67 
                                       ++l++++ ++ ++  + l + ++s kq+i  L++ql+ +r+E
  gi|557694562|ref|YP_008797616.1| 272 SMLQATF-NQLHELYEGLVTRHESAKQQIGYLQSQLDENRRE 312
                                       5888899.8888999999*********************999 PP

>> IFT20  Intraflagellar transport complex B, subunit 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   7.4      0.02       2.4      31     109 ..     162     240 ..     146     248 .. 0.87
   2 ?    3.4   0.2      0.66        80      74     106 ..     292     324 ..     285     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.02
                             IFT20  31 FvkkinefqklvkelievleelakkvekeKlkAigarnllkseakqreaeqqqlqaliaekkaeleRlrvelesLqk 107
                                         ++in+++++++ l   +++l +++e++   A +   +l+s +++ ++ +q +q++ +e ++  +R+ +    L+ 
  gi|557694562|ref|YP_008797616.1| 162 AQEQINQLRTTIQILETEINTLRTRLEEALNTAAMLTARLNSSREEIKRLEQRIQTMSEEYRQLNDRYVSTVGELKA 238
                                       5678***************************************************************9987777666 PP

                             IFT20 108 ve 109
                                       ++
  gi|557694562|ref|YP_008797616.1| 239 LQ 240
                                       54 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.66
                             IFT20  74 akqreaeqqqlqaliaekkaeleRlrvelesLq 106
                                        ++ +++   lq+++ e + el  lr  +  L+
  gi|557694562|ref|YP_008797616.1| 292 HESAKQQIGYLQSQLDENRRELGDLRLRYSLLS 324
                                       5667777788****************9998886 PP

>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.9       0.1        12      22      46 ..     166     190 ..     165     196 .. 0.85
   2 ?    4.2   1.0      0.38        45      25      45 ..     197     217 ..     195     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.1
                           DUF1192  22 veELeerIalLeaEIaRleaaiakk 46 
                                       ++ L++ I+ Le EI  l++ ++++
  gi|557694562|ref|YP_008797616.1| 166 INQLRTTIQILETEINTLRTRLEEA 190
                                       5789************999999876 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.38
                           DUF1192  25 LeerIalLeaEIaRleaaiak 45 
                                       L++r    ++EI+Rle+ i++
  gi|557694562|ref|YP_008797616.1| 197 LTARLNSSREEIKRLEQRIQT 217
                                       6788888899*******9976 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   8.4    0.0016      0.19      13      85 ..     157     228 ..     150     232 .. 0.87
   2 ?    0.2   2.3       8.5     1e+03      15      58 ..     236     281 ..     229     317 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0016
                   Snapin_Pallidin  13 pkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkR 85 
                                        +l++ +e++++lr++ + L  ++++l+++L+e+ +++   + ++l++ ++ ++++++r+++++e  ++l++R
  gi|557694562|ref|YP_008797616.1| 157 NDLNRAQEQINQLRTTIQILETEINTLRTRLEEALNTAA-MLTARLNSSREEIKRLEQRIQTMSEEYRQLNDR 228
                                       6799999*************************9999998.667788888899999999999999998888888 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 8.5
                   Snapin_Pallidin  15 ldeldeklkelrqsQeeLleqldrlnekLkeleeaqe..aevlpdl 58 
                                       l++l+++ + l ++ e+L+ + ++l +++++l ++ +  ++++++l
  gi|557694562|ref|YP_008797616.1| 236 LKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSmlQATFNQL 281
                                       5555555555555555555555555555555544433233333333 PP

>> SYCE1  Synaptonemal complex central element protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   6.6      0.37        45      26     149 ..     157     225 ..     143     233 .. 0.46
   2 ?    8.6   2.7     0.015       1.9      27     111 ..     235     319 ..     228     332 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.37
                             SYCE1  26 eELgeaqalkealkrElDsLnaEkvhLeevlnkKqealriLqlhcqekeseaqrkqelseeckqrieeltskiqeek 102
                                       ++L++aq+  + l+  +  L++E                                                      
  gi|557694562|ref|YP_008797616.1| 157 NDLNRAQEQINQLRTTIQILETE------------------------------------------------------ 179
                                       45555555555555555555555...................................................... PP

                             SYCE1 103 lkrrklrlefeeqleelmeqhkdlwefhv.eqrlakeiralesskeqL 149
                                            lr ++ee l++ +    +l + +   +rl++ i+++++   qL
  gi|557694562|ref|YP_008797616.1| 180 --INTLRTRLEEALNTAAMLTARLNSSREeIKRLEQRIQTMSEEYRQL 225
                                       ..4444444444444443333333333333344444444444333333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.015
                             SYCE1  27 ELgeaqalkealkrElDsLnaEkvhLeevlnkKqealriLqlhcqekeseaqrkqelseeckqrieeltskiqeekl 103
                                       EL+  qa  e l rE ++L++   +L   +++    +++Lq   ++ ++  +   + +e  kq+i  l+s+++e+++
  gi|557694562|ref|YP_008797616.1| 235 ELKALQASYEMLSRENEALSTSYQQLLHDYRNLTKEYSMLQATFNQLHELYEGLVTRHESAKQQIGYLQSQLDENRR 311
                                       89999***************************************9999999998999999**************999 PP

                             SYCE1 104 krrklrle 111
                                       +   lrl+
  gi|557694562|ref|YP_008797616.1| 312 ELGDLRLR 319
                                       88777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1949  (0.108707); expected 358.6 (0.02)
Passed bias filter:                     1017  (0.0567237); expected 358.6 (0.02)
Passed Vit filter:                       257  (0.0143343); expected 17.9 (0.001)
Passed Fwd filter:                       175  (0.00976072); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):             148  [number of targets reported over threshold]
# CPU time: 1.72u 0.37s 00:00:02.09 Elapsed: 00:00:00.60
# Mc/sec: 1884.32
//
Query:       gi|557694563|ref|YP_008797617.1|  [L=386]
Description: molybdopterin biosynthesis protein MoeB [Candidatus Caldiarchaeum subterraneum]
Scores for 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-69  232.2   0.0      8e-69  231.7   0.0    1.1  1  ThiF             ThiF family
    5.5e-17   62.2   0.0      1e-16   61.4   0.0    1.5  1  Rhodanese        Rhodanese-like domain
     0.0036   17.4   0.5       0.15   12.1   0.1    2.8  3  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.054   13.6   0.9       0.12   12.4   0.9    1.7  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
       0.17   12.1   0.4       0.93    9.8   0.4    2.0  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


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 !  231.7   0.0   2.2e-72     8e-69       3     240 ..      23     254 ..      21     262 .. 0.94

  Alignments for each domain:
  == domain 1  score: 231.7 bits;  conditional E-value: 2.2e-72
                                       HHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHH CS
                                       xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   3 rqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaeva 77 
                                       r+l +  +g +gq+kL+++kvl+vGaGglGs++  +La++Gvgk+ lvD+D ++ sNl+Rq+l+++ d+++pK eva
  gi|557694563|ref|YP_008797617.1|  23 RHLIIpeVGMAGQKKLKAAKVLVVGAGGLGSPISLYLAAAGVGKIGLVDFDLVDESNLQRQVLYTTRDVKRPKLEVA 99 
                                       56555667789****************************************************************** PP

                                       HHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  78 aealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviip 154
                                       +e+l+++np++eve+++ r+t+e++  ++++++D+Vvd++Dn+++r+lvn+acv  g+p + ++  +f+gqv v++ 
  gi|557694563|ref|YP_008797617.1| 100 KERLTALNPHIEVETYETRLTSENA-LDIIKDYDIVVDGTDNFPTRYLVNDACVLLGKPNVYGSIFRFDGQVSVFDA 175
                                       **********************995.5************************************************88 PP

                                       CCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 155 gktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrfen 231
                                        + +cy+Cl+p   e p++  vp+c +  g   +++ +++v++ l+a e++kl+ g  +  + +l  +d+l+++f++
  gi|557694563|ref|YP_008797617.1| 176 RRGPCYRCLYP---EPPPPGLVPSC-AEGG---VLGVLPGVIGALQAMETIKLIIGIGEPLVGRLLLFDGLHMSFTE 245
                                       9**********...***********.9999...*********************6666666666669********** PP

                                       ECCEEEEEE CS
                                       xxxxxxxxx RF
                              ThiF 232 velerakks 240
                                       ++l++++++
  gi|557694563|ref|YP_008797617.1| 246 LKLRKDPNC 254
                                       ***998865 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0   2.9e-20     1e-16       1     106 [.     286     377 ..     286     378 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 2.9e-20
                         Rhodanese   1 sakelkellekgkva.llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgg 76 
                                       +++el+e l+kg+ + llDvR+p+eYe +h+++A+ +             pl +lpe + +l  +  +++v yc++g
  gi|557694563|ref|YP_008797617.1| 286 TPEELHEKLQKGEKVfLLDVREPVEYEICHLENALLI-------------PLSKLPEHVNKL--SLTDEIVAYCHTG 347
                                       699******7776557*********************.............***********9..************* PP

                         Rhodanese  77 graaaaaallkklGyknvsvldGGfkawke 106
                                        r++ a +ll+ lG+ +v++l GG++aw+e
  gi|557694563|ref|YP_008797617.1| 348 VRSSMAVKLLRDLGFRRVRNLAGGIDAWAE 377
                                       **9999********988***********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 !   12.1   0.1   4.1e-05      0.15       8      41 ..      36      69 ..      30      88 .. 0.88
   2 ?   -1.0   0.0      0.48   1.7e+03      58      83 ..     112     138 ..      99     150 .. 0.67
   3 ?    1.5   0.0      0.08   2.9e+02      87     131 ..     282     323 ..     273     329 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.1e-05
                                      S..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEE CS
                      Shikimate_DH  8 eslkekkvlliGaGemaelvakhLlakgvkkvvv 41
                                      ++lk +kvl++GaG +++ +  +L+a+gv k+  
  gi|557694563|ref|YP_008797617.1| 36 KKLKAAKVLVVGAGGLGSPISLYLAAAGVGKIGL 69
                                      4799************************998865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.48
                                       .ET-EEE.EGCGHHHHHHT-SEEEE-S CS
                      Shikimate_DH  58 geeieal.kleelkellaeadvvisat 83 
                                        e +e++ + e+  ++++++d+v+  t
  gi|557694563|ref|YP_008797617.1| 112 VETYETRlTSENALDIIKDYDIVVDGT 138
                                       44444330345677899*****99877 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.08
                                       S-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEE CS
                      Shikimate_DH  87 epilekeeveealkkrkkplllvDiavPRdvepevaeledvrlyt 131
                                       ++ ++ ee++e l+k  ++++l+D+  P  ve e+ +le++ l+ 
  gi|557694563|ref|YP_008797617.1| 282 SMHITPEELHEKLQK-GEKVFLLDVREP--VEYEICHLENALLIP 323
                                       455666666666644.3899********..999999999988775 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 ?   12.4   0.9   3.5e-05      0.12       2      35 ..      42      73 ..      41     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.5e-05
                                      EEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SS CS
                           Ldh_1_N  2 kvavvGaaGgiGqslalllankkladelaLlDia 35
                                      kv vvGa Gg G++++l la+ ++++ + L+D++
  gi|557694563|ref|YP_008797617.1| 42 KVLVVGA-GGLGSPISLYLAAAGVGK-IGLVDFD 73
                                      9******.*****************9.9999875 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 ?    9.8   0.4   0.00026      0.93       1      90 [.      43     152 ..      43     163 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00026
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......................TTTCEEEEE- CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......................lgvrfeaial 54 
                                       vl++GaG+ G+++  +la+ +    +i ++d+++    +l  ++                        ++++e+++ 
  gi|557694563|ref|YP_008797617.1|  43 VLVVGAGGLGSPISLYLAAAGVG--KIGLVDFDLVDESNLQRQVlyttrdvkrpklevakerltalnPHIEVETYET 117
                                       79999999999999999999866..8999999888877777766888888888888888888888666666666666 PP

                                       -TTTHHHHHHHHHTTSSEEEE-SSGG.GHHHHHHHHH CS
                   Sacchrp_dh_NADP  55 daenyeavLaallkegdlvvnlsppi.ssldvlkaCi 90 
                                           + a L+ ++k++d+vv+ + ++     v +aC+
  gi|557694563|ref|YP_008797617.1| 118 RLTSENA-LD-IIKDYDIVVDGTDNFpTRYLVNDACV 152
                                       6666666.55.48999999998888866666667776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.49
# Mc/sec: 2363.48
//
Query:       gi|557694564|ref|YP_008797618.1|  [L=228]
Description: ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-31  109.7   0.0      2e-31  109.3   0.0    1.2  1  ABC_tran     ABC transporter
    1.1e-07   31.5   0.1    0.00044   19.8   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    3.4e-06   27.1   0.4      0.047   13.5   0.5    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00022   21.5   0.2     0.0013   19.0   0.2    2.0  1  AAA_22       AAA domain
     0.0005   20.5   0.7     0.0011   19.4   0.7    1.6  1  AAA_16       AAA ATPase domain
    0.00078   19.1   0.0     0.0015   18.2   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
      0.001   18.9   0.1        1.4    8.6   0.0    2.7  3  IstB_IS21    IstB-like ATP binding protein
     0.0013   19.2   0.3     0.0051   17.3   0.3    2.0  1  AAA_23       AAA domain
     0.0028   17.6   0.4       0.83    9.5   0.0    2.2  2  NTPase_1     NTPase
     0.0043   16.8   0.2     0.0097   15.6   0.2    1.7  1  AAA_30       AAA domain
     0.0058   16.6   0.0      0.012   15.5   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.011   15.3   0.1      0.023   14.3   0.1    1.5  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.016   15.2   0.0      0.022   14.7   0.0    1.6  1  ATPase_2     ATPase domain predominantly from Archaea
      0.016   15.7   0.2       0.06   13.9   0.2    2.0  1  AAA_18       AAA domain
      0.017   15.4   0.0       0.39   11.0   0.0    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.018   14.5   0.0       0.04   13.4   0.0    1.6  2  PhoH         PhoH-like protein
      0.021   15.0   0.4      0.037   14.2   0.4    1.8  1  AAA_33       AAA domain
      0.021   14.0   0.0      0.081   12.1   0.0    1.8  2  NB-ARC       NB-ARC domain
      0.027   13.5   0.0      0.079   12.0   0.0    1.7  2  T2SSE        Type II/IV secretion system protein
      0.038   13.6   0.0       0.24   10.9   0.0    2.0  2  AAA_25       AAA domain
       0.04   13.6   0.0       0.81    9.3   0.0    2.1  2  AAA_15       AAA ATPase domain
      0.052   13.5   0.1       0.12   12.3   0.1    1.7  2  NACHT        NACHT domain
      0.055   13.6   0.8       0.44   10.6   0.1    2.3  2  MMR_HSR1     50S ribosome-binding GTPase
      0.073   12.5   0.0       0.92    8.9   0.0    2.2  2  SRPRB        Signal recognition particle receptor beta subuni
       0.08   12.7   0.1       0.13   11.9   0.0    1.5  2  AAA_24       AAA domain
       0.14   11.9   0.1       0.83    9.4   0.1    1.9  2  ATP_bind_1   Conserved hypothetical ATP binding protein
       0.15   12.1   0.0       0.26   11.3   0.0    1.4  1  AAA_14       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 !  109.3   0.0   3.1e-34     2e-31       1     136 [.      22     170 ..      22     171 .. 0.92

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 3.1e-34
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l+ v+l+l+++  va+vG++G+GK+tLl+l+  l kpt+G+i ldg + ++       +  r++ig+++q+ +l + 
  gi|557694564|ref|YP_008797618.1|  22 LRGVNLELERNDFVAVVGPSGSGKTTLLNLVGALDKPTQGDIILDGVSYSNldrkGFNKLRREKIGFIFQTYNLLSA 98 
                                       6789******************************************99999777666678899************** PP

                                       SBHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       lt+ en             ++++++ ++l+klg  ++++++     ++LSgG++qrva+aral+++p l+l+DEpt
  gi|557694564|ref|YP_008797618.1|  99 LTALENvemaaipnktdprTRRKKALDLLEKLGVADKANKKP----TELSGGEQQRVAIARALINDPALILADEPT 170
                                       *************99987777777888888888888666666....*****************************9 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 !   10.0   0.0   0.00063      0.42      24      42 ..      32      50 ..      21      55 .. 0.83
   2 !   19.8   0.0   6.6e-07   0.00044     135     209 ..     135     213 ..      73     221 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00063
                                      SSEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnlld 42
                                      + f a+vGp GSGK+ ll+
  gi|557694564|ref|YP_008797618.1| 32 NDFVAVVGPSGSGKTTLLN 50
                                      5699***********9875 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 6.6e-07
                                       T......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHCC CS
                                       x......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreemle 203
                                       +      +LSgGe++ va+a       ++  +l l De   +LD kn +kv ell+  ++s++  ++ ++++ e+ +
  gi|557694564|ref|YP_008797618.1| 135 KankkptELSGGEQQRVAIARA----LINDPALILADEPTGNLDSKNATKVGELLRevNESSEKAVLLVTHNLEVAR 207
                                       34444449*******9998754....46777899**********************443445578999999999999 PP

                                       C-SCEE CS
                                       xxxxxx RF
                             SMC_N 204 kadklv 209
                                        ad++ 
  gi|557694564|ref|YP_008797618.1| 208 YADRIA 213
                                       999876 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 !   13.5   0.5   7.1e-05     0.047       1      22 [.      34      55 ..      34      92 .. 0.67
   2 !   11.3   0.0   0.00033      0.22     235     301 ..     141     205 ..     123     207 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.1e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + +++Gp gsGK++LL +   l
  gi|557694564|ref|YP_008797618.1| 34 FVAVVGPSGSGKTTLLNLVGAL 55
                                      6789************988665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00033
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell...kelsr.ngaQviltTHSpll 301
                                       +elS G ++  a++ al+ ++   +l+l DEp  +L+ k  +++ ell   +   +     v+l+TH+ ++
  gi|557694564|ref|YP_008797618.1| 141 TELSGGEQQRVAIARALINDP---ALILADEPTGNLDSKNATKVGELLrevN---EsSEKAVLLVTHNLEV 205
                                       678999988889999999888...************************6443...435699******9875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.2   1.9e-06    0.0013       5      70 ..      32     136 ..      28     206 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.9e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee..........................................er 39 
                                         +++v+G+sG+GKTtll+ +   ++    +++                                          e+
  gi|557694564|ref|YP_008797618.1|  32 NDFVAVVGPSGSGKTTLLNLVGALDK----PTQgdiildgvsysnldrkgfnklrrekigfifqtynllsaltalEN 104
                                       6789***************9988873....22233556677777777777777666666666666666555544433 PP

                            AAA_22  40 pevvfvtlpsst...sskdllrellralglelka 70 
                                       +e +   +p++t   ++++ + +ll++lg+  ka
  gi|557694564|ref|YP_008797618.1| 105 VEMA--AIPNKTdprTRRKKALDLLEKLGVADKA 136
                                       3333..2233331124444444555555554444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.7   1.6e-06    0.0011      26     149 ..      34     208 ..      21     216 .. 0.53

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.6e-06
                            AAA_16  26 lvllsGesGvGKsslvrellralekd..........................ggiflrgkcdqlesaipysalaqal 76 
                                        v ++G+sG+GK++l++ +  al k                           ++ f+ +++  l         ++al
  gi|557694564|ref|YP_008797618.1|  34 FVAVVGPSGSGKTTLLNLVG-ALDKPtqgdiildgvsysnldrkgfnklrreKIGFIFQTYNLL-------SALTAL 102
                                       689*************9999.7777767666666555555555555555554344444444444.......233333 PP

                            AAA_16  77 areellrqlldeaesaeleawrekleeala.....................................avpelagaea 116
                                        ++  ++++ ++++ + ++  +  l+e l+                                     ++++l+    
  gi|557694564|ref|YP_008797618.1| 103 -ENVEMAAIPNKTDPRTRRKKALDLLEKLGvadkankkptelsggeqqrvaiaralindpaliladePTGNLD---- 174
                                       .224444444443333333333333333335555555444444665555555555554444443222222222.... PP

                            AAA_16 117 srllellkrll.allsrderplvlvlDdlqwade 149
                                       s  + ++ +ll +  ++ e+ ++lv  +l+ a+ 
  gi|557694564|ref|YP_008797618.1| 175 SKNATKVGELLrEVNESSEKAVLLVTHNLEVARY 208
                                       4444444444444444445556666666666655 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 !   18.2   0.0   2.2e-06    0.0015      14      39 ..      24      49 ..      19      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.2e-06
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTll 39
                                      g  +e+++++++ ++GpsGsGK+Tll
  gi|557694564|ref|YP_008797618.1| 24 GVNLELERNDFVAVVGPSGSGKTTLL 49
                                      5678899999***************9 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 !    8.6   0.0    0.0021       1.4      44      63 ..      29      48 ..      17      57 .. 0.86
   2 ?   -1.6   0.0         3     2e+03     112     129 ..      63      80 ..      49      83 .. 0.84
   3 !    7.3   0.0    0.0052       3.5     104     159 ..     155     213 ..     114     222 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0021
                         IstB_IS21 44 iekkenivllGpsGvGKshl 63
                                      +e+++ ++++GpsG GK+ l
  gi|557694564|ref|YP_008797618.1| 29 LERNDFVAVVGPSGSGKTTL 48
                                      578999************87 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3
                         IstB_IS21 112 lilDdlgllpldqaeael 129
                                       +ilD +++ +ld++  ++
  gi|557694564|ref|YP_008797618.1|  63 IILDGVSYSNLDRKGFNK 80 
                                       799*******99987666 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0052
                         IstB_IS21 104 krllkvdllilDdlgllpldqaeae...llfeviekryerrsiiitsnlpfaewdevlg 159
                                       ++l++   lil d  + +ld+++a+   +l++ +++  e++ +++t nl++a++ + ++
  gi|557694564|ref|YP_008797618.1| 155 RALINDPALILADEPTGNLDSKNATkvgELLREVNESSEKAVLLVTHNLEVARYADRIA 213
                                       344444445555555555655555511256777788999999***********998765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.3   7.7e-06    0.0051      11      38 ..      23      51 ..      17     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 7.7e-06
                            AAA_23 11 rdqeidF.skgltlItGpNGaGKTTildA 38
                                      r++++++  + +++++Gp G+GKTT+l+ 
  gi|557694564|ref|YP_008797618.1| 23 RGVNLELeRNDFVAVVGPSGSGKTTLLNL 51
                                      6778888556899**************85 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0013      0.83       2      34 ..      35      69 ..      34      89 .. 0.70
   2 ?    6.5   0.1     0.011         7      85     155 ..     150     223 ..     126     228 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0013
                                      EEEE--TTSSHHHHHHHH..HHHH...GGGEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkv..lellkssgvkvgGfy 34
                                      v++ Gp+G+GKtTl++ v  l++  + ++ ++G+ 
  gi|557694564|ref|YP_008797618.1| 35 VAVVGPSGSGKTTLLNLVgaLDKPTQGDIILDGVS 69
                                      6789**********998721333334455555555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHH-EEEE--.-STTGGG.-HHHHHHHHHHHT.TTSEEEEE--SS--SHHHHHHHT-TT-EEEE- CS
                          NTPase_1  85 alealrkalseadviviDE.iGkmElk.skkfkeaveevLk.sekpvlavihrrkdlalveeirerkdvkvfev 155
                                        +++ r  ++++ +i+ DE  G++  k + k+ e ++ev + sek vl v h+ +  +  ++i   +d+++ +v
  gi|557694564|ref|YP_008797618.1| 150 RVAIARALINDPALILADEpTGNLDSKnATKVGELLREVNEsSEKAVLLVTHNLEVARYADRIAYMRDGVIEKV 223
                                       455555556899999999978999987256899999***9999**********999999999999999877665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   1.5e-05    0.0097      18      50 ..      32      64 ..      25     202 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-05
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvi 50
                                      + +++++Gp G+GKtt+l+ + ++ +  +g++i
  gi|557694564|ref|YP_008797618.1| 32 NDFVAVVGPSGSGKTTLLNLVGALDKPTQGDII 64
                                      45899**************99998887766665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.8e-05     0.012      96     119 ..      28      52 ..       5      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-05
                                       HCTT.SEEEEECSTTSSHHHHHHHH CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinal 119
                                       +l+  +++++vG+SG GK+tL+n +
  gi|557694564|ref|YP_008797618.1|  28 ELERnDFVAVVGPSGSGKTTLLNLV 52 
                                       555548999**************76 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 ?   14.3   0.1   3.5e-05     0.023       3      43 ..      35      75 ..      33      92 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.5e-05
                                      EEEEESTTCCHHHHHHHHHCT--SS-EEEEESS-SSCHCCC CS
                              cobW  3 tvltGflGsGKTtLlnhllenraglklavivNefgevsiDa 43
                                      + ++G+ GsGKTtLln + +  +  +  +i+  ++  ++D+
  gi|557694564|ref|YP_008797618.1| 35 VAVVGPSGSGKTTLLNLVGALDKPTQGDIILDGVSYSNLDR 75
                                      5799***********98887777777777777766666665 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 ?   14.7   0.0   3.3e-05     0.022      15      40 ..      27      52 ..      21     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-05
                          ATPase_2 15 lerepneiyfiYGpegsGKtaLlkei 40
                                      le e+n+++ + Gp gsGKt+Ll+ +
  gi|557694564|ref|YP_008797618.1| 27 LELERNDFVAVVGPSGSGKTTLLNLV 52
                                      67899*****************9855 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2     9e-05      0.06       1      51 [.      35      86 ..      35     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgf..gvnlrdvakenglllevdpealdeskr 51
                                      +++ G++G+GKttl + +  + +   g+++ d ++ ++l    +++ l+++k+
  gi|557694564|ref|YP_008797618.1| 35 VAVVGPSGSGKTTLLNLVGALDKPtqGDIILDGVSYSNLDRKGFNK-LRREKI 86
                                      689************9997765223444444444444444444444.444444 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 ?   11.0   0.0   0.00059      0.39       5      89 ..     115     186 ..     112     187 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00059
                           SbcCD_C   5 dyRnylsfevevrdedgkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesi 81 
                                       d R++ +  ++  ++ g   + +++ ++lSGGe+q    +a+a   +al+++       ++l++ DE  ++lD++++
  gi|557694564|ref|YP_008797618.1| 115 DPRTRRKKALDLLEKLGVADKANKKPTELSGGEQQR---VAIA---RALIND-------PALILADEPTGNLDSKNA 178
                                       666666666666666777777888999999999954...4444...334444.......899999999999999999 PP

                           SbcCD_C  82 atllelle 89 
                                       +++ ell+
  gi|557694564|ref|YP_008797618.1| 179 TKVGELLR 186
                                       99999987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.1e-05      0.04      16      44 ..      29      58 ..      23     107 .. 0.84
   2 ?   -2.3   0.0       3.7   2.4e+03      62      86 ..     167     191 ..     144     222 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.1e-05
                                      HHH-SEEEEE--TTSSTT.HHHHHHHHHHH CS
                              PhoH 16 lkkndivfaiGpaGtGKt.ylavalaveal 44
                                      l++nd+v ++Gp+G+GKt +l ++ a++  
  gi|557694564|ref|YP_008797618.1| 29 LERNDFVAVVGPSGSGKTtLLNLVGALDKP 58
                                      779**************8245666666655 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.7
                                       T----SS---------TTTHHHHHH CS
                              PhoH  62 geelGflpgdleekvdpylrplyda 86 
                                       +e  G l+ + ++kv   lr + ++
  gi|557694564|ref|YP_008797618.1| 167 DEPTGNLDSKNATKVGELLREVNES 191
                                       5555666666666665555555444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   5.6e-05     0.037       2      19 ..      35      52 ..      34     214 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.6e-05
                            AAA_33  2 vllvGlpGsGKstlaerl 19
                                      v +vG++GsGK+tl+  +
  gi|557694564|ref|YP_008797618.1| 35 VAVVGPSGSGKTTLLNLV 52
                                      679***********8754 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012     0.081      21      38 ..      33      50 ..      25      61 .. 0.85
   2 ?   -0.8   0.0       1.1   7.2e+02     166     182 ..     125     141 ..     117     215 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                      EEEEEEESTTSSHHHHHH CS
                            NB-ARC 21 lvvalvGmgGvGKttlak 38
                                      ++va+vG  G+GKttl++
  gi|557694564|ref|YP_008797618.1| 33 DFVAVVGPSGSGKTTLLN 50
                                      69**************86 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                                       HHHHHCCTS-GGCHH.. CS
                            NB-ARC 166 ellenkvfekkleekes 182
                                       +lle+ +++ k+++k++
  gi|557694564|ref|YP_008797618.1| 125 DLLEKLGVADKANKKPT 141
                                       44444444444444433 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 ?   12.0   0.0   0.00012     0.079     127     149 ..      30      52 ..      15      66 .. 0.79
   2 ?   -1.4   0.0       1.5     1e+03      32      49 ..     182     198 ..     117     217 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                             T2SSE 127 rerglilvsGgTgsGKttllyal 149
                                       +++  + v G+ gsGKttll+ +
  gi|557694564|ref|YP_008797618.1|  30 ERNDFVAVVGPSGSGKTTLLNLV 52 
                                       556677899***********965 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                             T2SSE  32 dgielreveelekaaler 49 
                                       ++  lrev+e++++a+  
  gi|557694564|ref|YP_008797618.1| 182 GE-LLREVNESSEKAVLL 198
                                       22.333333333333333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00037      0.24      30      50 ..      29      49 ..       5      55 .. 0.85
   2 ?    0.1   0.0      0.78   5.2e+02     161     188 ..     174     201 ..     149     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      l ++++++++G++g+GKttl+
  gi|557694564|ref|YP_008797618.1| 29 LERNDFVAVVGPSGSGKTTLL 49
                                      47899**************97 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.78
                            AAA_25 161 snsdvgalvealeriarrtgaavllvhH 188
                                       +++ ++++ e l+++ +    avllv H
  gi|557694564|ref|YP_008797618.1| 174 DSKNATKVGELLREVNESSEKAVLLVTH 201
                                       4455688888888888889999999999 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0012      0.81      14      42 ..      22      51 ..      19      86 .. 0.84
   2 ?    2.0   0.0       0.2   1.4e+02     321     367 ..     158     204 ..     147     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0012
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilea 42
                                      l+ v ++l+ + +  ++G+ +sGK+++l++
  gi|557694564|ref|YP_008797618.1| 22 LRGVNLELERNdFVAVVGPSGSGKTTLLNL 51
                                      566777787777***************986 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.2
                            AAA_15 321 eeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                        ++++++l +EP  +L  ++ + + +ll+e+ +++++ v++ TH+  
  gi|557694564|ref|YP_008797618.1| 158 INDPALILADEPTGNLDSKNATKVGELLREVNESSEKAVLLVTHNLE 204
                                       57899***************************************976 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00018      0.12       2      18 ..      34      50 ..      33      67 .. 0.87
   2 ?   -2.6   0.0         7   4.7e+03      98     111 ..     174     187 ..     140     202 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                      CEEEEC-TTTCHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlq 18
                                       v++ G++GsGKTtLl 
  gi|557694564|ref|YP_008797618.1| 34 FVAVVGPSGSGKTTLLN 50
                                      589************96 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 7
                                       CH.........HHH CS
                             NACHT  98 gqkekqpvrtlLse 111
                                       + k++++v +lL+e
  gi|557694564|ref|YP_008797618.1| 174 DSKNATKVGELLRE 187
                                       33334444444433 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00066      0.44       2      18 ..      35      51 ..      34      63 .. 0.90
   2 ?    1.3   0.1      0.51   3.4e+02      44      82 ..     159     199 ..      94     224 .. 0.45

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00066
                                      EEEEESTTSSHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLina 18
                                      va+vG + +GK+tL+n 
  gi|557694564|ref|YP_008797618.1| 35 VAVVGPSGSGKTTLLNL 51
                                      89*************95 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.51
                                       TTEEEEEEECGG.CSSHHHHHHHHHHHHHHHHC.T.SEEEEE CS
                          MMR_HSR1  44 kgkeielvDtpG.liegaseekglgkaflalee.a.dlillv 82 
                                       +++ ++l+D p   ++ +++  ++g+ +++++e + +++llv
  gi|557694564|ref|YP_008797618.1| 159 NDPALILADEPTgNLD-SKNATKVGELLREVNEsSeKAVLLV 199
                                       2333555555541122.1111133333333333221333333 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 ?    8.9   0.0    0.0014      0.92       4      23 ..      33      52 ..      30      80 .. 0.82
   2 ?    1.2   0.0      0.32   2.1e+02      87     108 ..     173     194 ..     170     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0014
                                      -EEEEE-STTSSHHHHHHHH CS
                             SRPRB  4 pavllvGlsdsGKTslftrL 23
                                        v +vG+s sGKT+l++++
  gi|557694564|ref|YP_008797618.1| 33 DFVAVVGPSGSGKTTLLNLV 52
                                      56789************975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.32
                                       S-HHHHHHHHHHHHHHHHHHHH CS
                             SRPRB  87 idpkevkevAEllyeillitek 108
                                        d+k++++v Ell e+   +ek
  gi|557694564|ref|YP_008797618.1| 173 LDSKNATKVGELLREVNESSEK 194
                                       689***********99877764 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    0.0002      0.13       5      23 ..      35      57 ..      31     138 .. 0.75
   2 ?   -3.2   0.0       8.5   5.6e+03     108     130 ..     178     201 ..     175     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                            AAA_24  5 iliyGpsgiGKTtlakel....g 23
                                      ++++Gpsg+GKTtl++      +
  gi|557694564|ref|YP_008797618.1| 35 VAVVGPSGSGKTTLLNLVgaldK 57
                                      789***********988766441 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.5
                            AAA_24 108 aeefrrllkklqelrk.nvifiah 130
                                       a+++++ll+ ++e  +  v ++ h
  gi|557694564|ref|YP_008797618.1| 178 ATKVGELLREVNESSEkAVLLVTH 201
                                       678889999988888878888877 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 ?    9.4   0.1    0.0013      0.83       1      16 [.      37      52 ..      37      60 .. 0.88
   2 ?    0.2   0.0      0.81   5.4e+02     140     195 ..      87     144 ..      80     193 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                        ATP_bind_1  1 vvGpaGsGKttfvgal 16
                                      vvGp GsGKtt+ + +
  gi|557694564|ref|YP_008797618.1| 37 VVGPSGSGKTTLLNLV 52
                                      89*********98765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.81
                        ATP_bind_1 140 kfisgllsalsamlrle.lPhvvvlnkfDllkeklekeleffedvealslllekee..e 195
                                        fi ++   lsa+  le + +  + nk+D  +++++k+l+ +e +   +++++k +  +
  gi|557694564|ref|YP_008797618.1|  87 GFIFQTYNLLSALTALEnVEMAAIPNKTDP-RTRRKKALDLLEKLGVADKANKKPTelS 144
                                       566666555666555542455666799998.5578888888888887777777666452 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00039      0.26       3      49 ..      33      84 ..      31     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                            AAA_14  3 kilvitGaRrvGKTtllkqlikell.....vkkesilyinldderdkkladp 49
                                        ++++G+  +GKTtll+ +          +  + + y nld++ + kl+ +
  gi|557694564|ref|YP_008797618.1| 33 DFVAVVGPSGSGKTTLLNLVGALDKptqgdIILDGVSYSNLDRKGFNKLRRE 84
                                      6789************988865555767776667788888888888776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); 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: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 1551.79
//
Query:       gi|557694565|ref|YP_008797619.1|  [L=641]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   47.5   9.0      0.013   15.7   0.2    6.1  5  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
    1.2e-11   44.8  17.3     0.0014   18.9   0.3    5.5  6  CARDB            CARDB
    4.1e-06   26.2   4.2      0.035   13.2   0.1    3.7  4  PHTB1_C          PTHB1 C-terminus
    4.1e-06   26.3   6.0        0.1   12.0   0.2    4.4  4  TRAP_beta        Translocon-associated protein beta (TRAPB)
    2.5e-05   24.5   0.9       0.74   10.0   0.0    4.7  4  FixG_C           IG-like fold at C-terminal of FixG, putative
     0.0025   18.1   2.5     0.0025   18.1   2.5    5.0  5  DUF11            Domain of unknown function DUF11
  ------ inclusion threshold ------
      0.045   13.8   0.1        4.1    7.5   0.0    3.1  3  DUF2790          Protein of unknown function (DUF2790)
       0.11   13.1   0.6        1.6    9.4   0.0    2.8  2  Pur_ac_phosph_N  Purple acid Phosphatase, N-terminal domain


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 ?    1.6   0.0      0.15   3.3e+02      12      72 ..      54     117 ..      45     122 .. 0.69
   2 !   10.1   0.0   0.00033      0.73       3      75 ..     158     229 ..     156     232 .. 0.87
   3 !   10.0   0.7   0.00035      0.78       8      78 ..     274     344 ..     271     345 .. 0.82
   4 !    9.3   0.1   0.00057       1.3       4      67 ..     385     448 ..     383     458 .. 0.83
   5 !   15.7   0.2     6e-06     0.013       2      78 ..     495     572 ..     494     573 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.15
                       NPCBM_assoc  12 tvtndgtaaatnvslslslPeGWt...vvevspasaaslapGetveatvkVtppagaaaGdyev 72 
                                        + n  + a++  +l+lslPeG t    + +++  +++  pG   ea + + +  + ++G ++ 
  gi|557694565|ref|YP_008797619.1|  54 QILNRNNLAIRYAKLTLSLPEGITsttGSRSDVVYLSTMNPGTISEAVFYLNIDRNLKTGVHQA 117
                                       55677777888899********993222334444455888888877777777777776666655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00033
                       NPCBM_assoc   3 pGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtak 75 
                                       +G+++ l+l ++n+gt +a  v++ + + ++ +   + p++++++++Ge ve  v++ + ++ a +  ++t++
  gi|557694565|ref|YP_008797619.1| 158 AGRRNILNLILSNNGTGPAYMVRVVMATSQQVS-ILSYPTRFDKIDAGENVEIPVEIYVAPSLAGSPVTITVT 229
                                       8999**************************999.8999*******************9999888655555444 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00035
                       NPCBM_assoc   8 tltltvtndgtaaatnvslslsl..PeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                        ++l vtn g + +++v l+ls+  P    v +    +++++++Get+e  v + +++++a    +vt+++++
  gi|557694565|ref|YP_008797619.1| 274 DVRLKVTNAGLTVVRDVALTLSVnlPLVP-VGTDGKFNIPEIRAGETAEIPVSIYVSETTAS-SSPVTISLSY 344
                                       68999***********9999887555542.2334556999******************9996.5599999886 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.00057
                       NPCBM_assoc   4 Getvtltltvtndgtaaatnvslslsl..PeGWtvvevspasaaslapGetveatvkVtppagaaa 67 
                                       G  +++t++v+n g+++++++ ++ s+   + W   +    +++sl+pGe+ + ++ + +p++  +
  gi|557694565|ref|YP_008797619.1| 385 GTINNITVSVSNVGSTTIRDLTITPSAstQATWL--QENMVNIPSLEPGEEYKYQAGIFIPSDSPT 448
                                       667899**************99987772255576..89999********************99875 PP

  == domain 5  score: 15.7 bits;  conditional E-value: 6e-06
                       NPCBM_assoc   2 epGetvtltltvtndgtaaatnvslslsl.PeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                       +pG+t ++t++++n+gt  a++vsl+ s   +G +    s   +  ++++  +++t+  t+ +++ +G y++ ++++
  gi|557694565|ref|YP_008797619.1| 495 SPGQTFSVTIVLVNTGTVQASAVSLRPSEnIQGFRLFGQSRVFLGNVPTNTPTSVTFSFTAMNSTSPGRYQLPLVVS 571
                                       89*************************99789***9999999999**************************999998 PP

                       NPCBM_assoc  78 l 78 
                                       +
  gi|557694565|ref|YP_008797619.1| 572 Y 572
                                       7 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.31   6.9e+02      52      87 ..      87     124 ..      67     151 .. 0.53
   2 !    7.6   0.4     0.002       4.4       3      83 ..     146     229 ..     144     235 .. 0.80
   3 !   15.1   0.1   9.5e-06     0.021       9      79 ..     261     339 ..     255     355 .. 0.83
   4 !   18.9   0.3     6e-07    0.0014       9      84 ..     376     456 ..     370     461 .. 0.87
   5 !   11.0   0.1   0.00017      0.38       5      92 ..     488     578 ..     482     583 .. 0.85
   6 ?   -1.7   0.1       1.6   3.5e+03      12      38 ..     592     618 ..     581     623 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                                       EEESEE-CTEEEEEEEEEE-S..-S-CEEEEEEEESTT CS
                             CARDB  52 vtvpsLaagesttvsftwtte..ategevtltvvvDpd 87 
                                       v+++ +++g+ ++  f   ++  +++g ++ t++++  
  gi|557694565|ref|YP_008797619.1|  87 VYLSTMNPGTISEAVFYLNIDrnLKTGVHQATLYIEGI 124
                                       44455555555555444444443344444444443332 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.002
                                       -EEE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEESEE-CTEEEEEEEEEE-S..-S CS
                             CARDB   3 DLtvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtvpsLaagesttvsftwtte..at 74 
                                       DL v  +  ++++ +g+ n +++ ++N+Gt+ ++ ++v +  ++++      +   +++age++++ + + ++  ++
  gi|557694565|ref|YP_008797619.1| 146 DLHV--SNVEKTVIAGRRNILNLILSNNGTGPAYMVRVVMATSQQVSilsYPTRFDKIDAGENVEIPVEIYVApsLA 220
                                       7777..77889999************************999999986554444459999999999888776665566 PP

                                       -CEEEEEEE CS
                             CARDB  75 egevtltvv 83 
                                        + vt+tv+
  gi|557694565|ref|YP_008797619.1| 221 GSPVTITVT 229
                                       666777776 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 9.5e-06
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE.....EEEEESEE-CTEEEEEEEEEE-S...-S-CE CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv.....gtvtvpsLaagesttvsftwtte...atege 77 
                                       ++ p++++  + n ++++v+N G    +++ ++l ++  lv     g++++p++ age++++ +++ ++   a+++ 
  gi|557694565|ref|YP_008797619.1| 261 EIIPNQLTIYNLNDVRLKVTNAGLTVVRDVALTLSVNLPLVpvgtdGKFNIPEIRAGETAEIPVSIYVSettASSSP 337
                                       556788889999********************************999*****************9988853333344 PP

                                       EE CS
                             CARDB  78 vt 79 
                                       vt
  gi|557694565|ref|YP_008797619.1| 338 VT 339
                                       44 PP

  == domain 4  score: 18.9 bits;  conditional E-value: 6e-07
                                       EEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S.-S-CEEEE CS
                             CARDB   9 tlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtte.ategevtl 80 
                                        ++p+ ++ g+ n+itv+v+N G+ + ++ +++  ++ + +    + v++psL++ge+++ ++ ++++  ++ ++tl
  gi|557694565|ref|YP_008797619.1| 376 RITPNLLYSGTINNITVSVSNVGSTTIRDLTITPSASTQATwlqeNMVNIPSLEPGEEYKYQAGIFIPsDSPTSITL 452
                                       56788899********************************9999999999************999999666677777 PP

                                       EEEE CS
                             CARDB  81 tvvv 84 
                                        ++v
  gi|557694565|ref|YP_008797619.1| 453 AMTV 456
                                       6665 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.00017
                                       EE.EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE...EEEEE..SEE-CTEEEEEEEEEE-S..-S CS
                             CARDB   5 tvtntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv...gtvtv..psLaagesttvsftwtte..at 74 
                                       t    + p++ ++g+++++t+ + N+Gt ++ a++++   + +     g++ v   ++  ++ t+v+f++t++  ++
  gi|557694565|ref|YP_008797619.1| 488 T----ILPEAISPGQTFSVTIVLVNTGTVQASAVSLRPSENIQGFrlfGQSRVflGNVPTNTPTSVTFSFTAMnsTS 560
                                       4....489999********************9999999888777788955555559999999999999999998889 PP

                                       -CEEEEEEEESTT-SS-- CS
                             CARDB  75 egevtltvvvDpdnevaE 92 
                                       +g ++l +vv   + v E
  gi|557694565|ref|YP_008797619.1| 561 PGRYQLPLVVSYRDNVGE 578
                                       9*********99999988 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 1.6
                                       -SEEETTSEEEEEEEEEE-SSS-EEEE CS
                             CARDB  12 pseafvgeentitvtvkNqGtaasgat 38 
                                       p+      + + + tv+N+G  +  ++
  gi|557694565|ref|YP_008797619.1| 592 PAGFGRPGTARTQTTVANTGFLNTSNV 618
                                       444455556667788999997776665 PP

>> PHTB1_C  PTHB1 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00014      0.31      14      81 ..     178     245 ..     168     247 .. 0.94
   2 !   13.2   0.1   1.5e-05     0.035       3      79 ..     278     355 ..     276     363 .. 0.80
   3 ?   -0.5   0.0      0.23   5.1e+02       2      76 ..     392     466 ..     391     473 .. 0.78
   4 ?    1.1   0.1     0.076   1.7e+02      29      75 ..     533     579 ..     502     589 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00014
                           PHTB1_C  14 nvqlsvqvdkplaaskstfviesldesasteliisvflkgslipaslevevvasYtsktgiprvvqks 81 
                                       +v++++++++ + +    + ++++d++++ e+ ++++++ sl  + ++++v++ Y  + g pr+v++s
  gi|557694565|ref|YP_008797619.1| 178 MVRVVMATSQQVSILSYPTRFDKIDAGENVEIPVEIYVAPSLAGSPVTITVTMNYLDSYGNPRTVESS 245
                                       7999************************************************************9876 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.5e-05
                           PHTB1_C   3 kvtlkssttlenvqlsvqvdkpla..askstfviesldesasteliisvflkgslipaslevevvasYtsktgiprv 77 
                                       kvt    t +++v l+++v+ pl+   ++ +f i+++ ++++ e+ +s++++ +++ +s  v+++ sY  ++ + r+
  gi|557694565|ref|YP_008797619.1| 278 KVTNAGLTVVRDVALTLSVNLPLVpvGTDGKFNIPEIRAGETAEIPVSIYVS-ETTASSSPVTISLSYLDDSNQMRT 353
                                       777788899**************73368999******666666666666666.889999**********88888876 PP

                           PHTB1_C  78 vq 79 
                                        +
  gi|557694565|ref|YP_008797619.1| 354 ES 355
                                       55 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.23
                           PHTB1_C   2 vkvtlkssttlenvqlsvqvdkplaaskstfv.iesldesasteliisvflkgslipaslevevvasYtsktgipr 76 
                                       v+v+   stt+++++++ +++   +  ++++v i+sl+++++ +    +f+  s  p+s++   ++sY  ++ ++r
  gi|557694565|ref|YP_008797619.1| 392 VSVSNVGSTTIRDLTITPSASTQATWLQENMVnIPSLEPGEEYKYQAGIFIP-SDSPTSITLAMTVSYYGRDNMQR 466
                                       7777788888888888888877777666655449999999999999999995.45799**********97776665 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.076
                           PHTB1_C  29 kstfviesldesasteliisvflkgslipaslevevvasYtsktgip 75 
                                       +s++++ +++++++t++++s++  +s+ p   +   v+sY+ + g+ 
  gi|557694565|ref|YP_008797619.1| 533 QSRVFLGNVPTNTPTSVTFSFTAMNSTSPGRYQLPLVVSYRDNVGEV 579
                                       789999***99*****************************9877765 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.2   4.5e-05       0.1      27     122 ..     152     245 ..     147     259 .. 0.80
   2 ?   -0.1   0.1      0.24   5.3e+02      38      57 ..     274     293 ..     261     294 .. 0.88
   3 !    6.7   0.0     0.002       4.4      26      90 ..     377     438 ..     357     480 .. 0.69
   4 !    6.9   0.0    0.0017       3.7      26      57 ..     489     520 ..     483     584 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.5e-05
                         TRAP_beta  27 lnrllvegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvsh..sfvvepkksgsfn 101
                                       +++ + +g+++ +++ + N G+ +A+ V++v       + +v   s  + ++++++genv+    + v p   gs  
  gi|557694565|ref|YP_008797619.1| 152 VEKTVIAGRRNILNLILSNNGTGPAYMVRVVMA----TSQQVSILSYPTRFDKIDAGENVEIpvEIYVAPSLAGSPV 224
                                       6788999***********************954....33345555788899********996225678999999999 PP

                         TRAP_beta 102 gtaavvtYresekgaelqlal 122
                                          ++++Y +s+   + +++ 
  gi|557694565|ref|YP_008797619.1| 225 TITVTMNYLDSYGNPRTVESS 245
                                       999999998888766666554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.24
                         TRAP_beta  38 tveytiyNvGssaAldVslv 57 
                                        v+++++N+G + ++dV l+
  gi|557694565|ref|YP_008797619.1| 274 DVRLKVTNAGLTVVRDVALT 293
                                       68999************985 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.002
                         TRAP_beta  26 ilnrllvegedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsf 90 
                                       i  +ll  g  +++++++ NvGs++ +d++++     + ++     +  +++ +l+pge+ ++++
  gi|557694565|ref|YP_008797619.1| 377 ITPNLLYSGTINNITVSVSNVGSTTIRDLTITPSASTQATWL---QENMVNIPSLEPGEEYKYQA 438
                                       6667777788899*****************998777777762...33346667777777766665 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0017
                         TRAP_beta  26 ilnrllvegedltveytiyNvGssaAldVslv 57 
                                       il +  + g+  +v++ ++N G+ +A  Vsl+
  gi|557694565|ref|YP_008797619.1| 489 ILPEAISPGQTFSVTIVLVNTGTVQASAVSLR 520
                                       67777888999*******************98 PP

>> FixG_C  IG-like fold at C-terminal of FixG, putative oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.076   1.7e+02      24     102 ..      40     122 ..      26     139 .. 0.66
   2 ?    4.0   0.0     0.024        55      57     103 ..     187     232 ..     161     246 .. 0.66
   3 !   10.0   0.0   0.00033      0.74      34     114 ..     274     355 ..     270     361 .. 0.66
   4 ?    2.1   0.0     0.099   2.2e+02      36     106 ..     391     463 ..     378     474 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.076
                                       ------SEEEEEEEEEEE-SSS-EEE.EEEEES-SS-EE......E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSE CS
                            FixG_C  24 vevsdgsieNsYtlkilNktekprry.tlsveglpglel.....agraekeitvapgekrkvpvfvrvpaealkkks 94 
                                       vev  gs+     ++ilN+ + + ry +l+++  +g++      + +     t  pg+  + ++++ ++++  k + 
  gi|557694565|ref|YP_008797619.1|  40 VEVGPGSVNAPLSIQILNRNNLAIRYaKLTLSLPEGITSttgsrS-DVVYLSTMNPGTISEAVFYLNIDRNL-KTGV 114
                                       556666666667789999999999973466664457777322221.11234478899999999999999987.5566 PP

                                       EEEEEEEE CS
                            FixG_C  95 tpitfkvt 102
                                       ++ t+ ++
  gi|557694565|ref|YP_008797619.1| 115 HQATLYIE 122
                                       66666665 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.024
                                       SS-EE.E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE..E CS
                            FixG_C  57 pglelagraekeitvapgekrkvpvfvrvpaealkkkstpitfkvt..d 103
                                       +++++ +++++  ++++ge++++pv + v ++    +++p+t++vt  +
  gi|557694565|ref|YP_008797619.1| 187 QQVSILSYPTRFDKIDAGENVEIPVEIYVAPSL---AGSPVTITVTmnY 232
                                       455555566677789****************99...3456666665322 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00033
                                       EEEEEEEE-SSS-EE...EEEEEES-SS-EE..E.S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEEEGGG CS
                            FixG_C  34 sYtlkilNktekprr...ytlsveglpglel.agraekeitvapgekrkvpvfvrvpaealkkkstpitfkvtddde 106
                                         +lk++N   +  r   +tlsv+ lp + + ++++ +  ++ +ge+ ++pv++ v +    ++s+p+t+ +++ d+
  gi|557694565|ref|YP_008797619.1| 274 DVRLKVTNAGLTVVRdvaLTLSVN-LPLVPVgTDGKFNIPEIRAGETAEIPVSIYVSETT--ASSSPVTISLSYLDD 347
                                       556666666554433311444444.55444432355777799**************9987..7899******85555 PP

                                       TEEEEEEE CS
                            FixG_C 107 ketverks 114
                                       +++ +++s
  gi|557694565|ref|YP_008797619.1| 348 SNQMRTES 355
                                       56666555 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.099
                                       EEEEEE-SSS-EE.EEEEEES-SS-EE.E..S--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE.EG.GG CS
                            FixG_C  36 tlkilNktekprr.ytlsveglpglelag.raekeitvapgekrkvpvfvrvpaealkkkstpitfkvt.dd.de 106
                                       t+ + N  +++ r +t++ +   ++++ + +  +  +++pge+ k+ + + +p+++  ++s+++ ++v+ ++ d+
  gi|557694565|ref|YP_008797619.1| 391 TVSVSNVGSTTIRdLTITPSASTQATWLQeNMVNIPSLEPGEEYKYQAGIFIPSDS--PTSITLAMTVSyYGrDN 463
                                       555566655555546666665556666332233555789***************99..66677777775433132 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       2.2   4.9e+03      33      71 ..      66      99 ..      37     119 .. 0.62
   2 ?    1.7   0.2      0.15   3.3e+02      19      47 ..     165     193 ..     150     232 .. 0.71
   3 ?    0.6   0.4      0.32   7.1e+02      20      84 ..     277     334 ..     269     344 .. 0.75
   4 ?    1.6   0.1      0.15   3.4e+02      19      83 ..     391     416 ..     347     439 .. 0.66
   5 !   18.1   2.5   1.1e-06    0.0025       7      82 ..     491     594 ..     488     611 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.2
                             DUF11 33 vvvtDtlPaglayvsvsasqgtasaltsvgsLeagesat 71
                                      +++t  lP+g +  ++s s       ++  ++++g    
  gi|557694565|ref|YP_008797619.1| 66 AKLTLSLPEGITSTTGSRS-----DVVYLSTMNPGTISE 99
                                      5566667777775555555.....222224555555444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.15
                             DUF11  19 tltvtNtgpasangvvvtDtlPaglayvs 47 
                                       +l+++N+g+ +a+ v+v     +++++ s
  gi|557694565|ref|YP_008797619.1| 165 NLILSNNGTGPAYMVRVVMATSQQVSILS 193
                                       68899*******99988655555555555 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.32
                             DUF11  20 ltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaas 84 
                                       l vtN g +   +v +t  l  +l +v+v +       +++++++ age+a + +++ v+ t+as
  gi|557694565|ref|YP_008797619.1| 277 LKVTNAGLTVVRDVALT--LSVNLPLVPVGTD-----GKFNIPEIRAGETAEIPVSIYVSETTAS 334
                                       66777777777666664..6777777777777.....3556689999999999999999988887 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.15
                             DUF11  19 tltvtNtgpasangvvvtDtlPaglayvsvsasqgtasaltsvgsLeagesatlsftvrvtrtaa 83 
                                       t+ v                                        ++     + l++t++++++a+
  gi|557694565|ref|YP_008797619.1| 391 TVSV---------------------------------------SNVGSTTIRDLTITPSASTQAT 416
                                       3333.......................................5555555555555555555554 PP

  == domain 5  score: 18.1 bits;  conditional E-value: 1.1e-06
                             DUF11   7 ksevrpGdtvtytltvtNtgpasangvvvtDtl......................Paglayvsvsas....qgtasa 57 
                                       ++++ pG+t ++t+++ Ntg+++a+ v ++                         P+++++ s++a      g ++ 
  gi|557694565|ref|YP_008797619.1| 491 PEAISPGQTFSVTIVLVNTGTVQASAVSLRPSEniqgfrlfgqsrvflgnvptntPTSVTF-SFTAMnstsPGRYQL 566
                                       67899************************9776999**************97777666653.333334444688888 PP

                             DUF11  58 ltsv...gsLeagesatlsftvrvtrta 82 
                                          v    ++   ++ tls+ v+v++++
  gi|557694565|ref|YP_008797619.1| 567 PLVVsyrDNVGEVHTDTLSVNVNVRPAG 594
                                       888899999*************999987 PP

>> DUF2790  Protein of unknown function (DUF2790)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0018       4.1      51      69 ..     225     243 ..     204     248 .. 0.86
   2 ?    1.2   0.0      0.17   3.8e+02      40      66 ..     326     352 ..     317     354 .. 0.87
   3 ?    0.1   0.0      0.38   8.5e+02      53      67 ..     567     581 ..     558     584 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                                       EEEEEEEEE-TTS-EEEEE CS
                           DUF2790  51 vvparmtYeDsqGelhtve 69 
                                       +++++m Y Ds G+ +tve
  gi|557694565|ref|YP_008797619.1| 225 TITVTMNYLDSYGNPRTVE 243
                                       6789*************97 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.17
                                       EEE---TT--SEEEEEEEEE-TTS-EE CS
                           DUF2790  40 isvtdlsnkCgvvparmtYeDsqGelh 66 
                                       i+v++++++++ v++ + Y D + + +
  gi|557694565|ref|YP_008797619.1| 326 IYVSETTASSSPVTISLSYLDDSNQMR 352
                                       89999****************987765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.38
                                       EEEEEEE-TTS-EEE CS
                           DUF2790  53 parmtYeDsqGelht 67 
                                       p  + Y+D+ Ge+ht
  gi|557694565|ref|YP_008797619.1| 567 PLVVSYRDNVGEVHT 581
                                       67789********97 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 ?    9.4   0.0   0.00071       1.6      53      80 ..     404     439 ..     324     451 .. 0.75
   2 ?    0.8   0.1      0.34   7.6e+02      10      34 ..     543     573 ..     538     617 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00071
                   Pur_ac_phosph_N  53 t........tnyksgyshkatltgLepgttYyYrvg 80 
                                       +        t+ +    + +++ +Lepg +Y Y+ g
  gi|557694565|ref|YP_008797619.1| 404 DltitpsasTQATWLQENMVNIPSLEPGEEYKYQAG 439
                                       0333333336777788999***************87 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.34
                   Pur_ac_phosph_N  10 edtstsmtvsWitpektkks......vvryg 34 
                                       ++t+ts+t+s++  ++t+        vv y+
  gi|557694565|ref|YP_008797619.1| 543 TNTPTSVTFSFTAMNSTSPGryqlplVVSYR 573
                                       4599******998776333234444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); 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 0.27s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4310.68
//
Query:       gi|557694566|ref|YP_008797620.1|  [L=418]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   59.0   2.4    4.9e-16   59.0   2.4    3.1  3  FtsX      FtsX-like permease family
    3.7e-15   56.8   7.9    3.7e-15   56.8   7.9    2.6  3  MacB_PCD  MacB-like periplasmic core domain


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3     0.049   4.4e+02      30      49 ..      25      42 ..      18      81 .. 0.58
   2 ?   -2.2   2.2      0.65   5.8e+03      27      44 ..     259     276 ..     244     291 .. 0.48
   3 !   59.0   2.4   5.5e-20   4.9e-16       2      96 .]     295     411 ..     294     411 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.049
                              FtsX 30 lvalviGlglgllaaqllsd 49
                                      +va   ++g+++++a ++++
  gi|557694566|ref|YP_008797620.1| 25 VVAV--AIGVASVIALVSQT 42
                                      2222..22244444433333 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.65
                              FtsX  27 litlvalviGlglgllaa 44 
                                       +i+ ++ ++G ++g+ +a
  gi|557694566|ref|YP_008797620.1| 259 VIGQFGVLLGSVAGISLA 276
                                       333333333333332222 PP

  == domain 3  score: 59.0 bits;  conditional E-value: 5.5e-20
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllssvf.................s.... 57 
                                       +eig+++a+G++ +++l+++++e+l+i+l++ v+G++lg++ + +l  +++ ++                  +    
  gi|557694566|ref|YP_008797620.1| 295 KEIGVMKAVGYSEGDILQIFIMEALFIGLLGGVVGVVLGVASTLFLPMFFGGFLPfgggfrppaggpggpfgGqqal 371
                                       8**********************************999888888877777777444445566665555555414445 PP

                              FtsX  58 .selkisidlitvliiivlllllallagllsiskilkkep 96 
                                          +++ + ++++l+++ +++++ ++ag+++++++++++p
  gi|557694566|ref|YP_008797620.1| 372 qLTITPAFTPEIILTAFSIAVIISVAAGIYPAWRASRMDP 411
                                       588888899999999999999999999***********98 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 !   56.8   7.9   4.1e-19   3.7e-15       2     194 ..      22     238 ..      21     239 .. 0.77
   2 ?   -2.5   2.5      0.62   5.6e+03       5      36 ..     266     297 ..     263     318 .. 0.81
   3 ?   -2.9   1.9      0.84   7.5e+03       5      20 ..     327     342 ..     323     348 .. 0.78

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 4.1e-19
                          MacB_PCD   2 lltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvt.vtpgkgsgeslsdpdvealrrevp.veavapvv... 73 
                                       +l v+++aiGva+via+vs ++g+q++v +q++ lg +++ +tp    +++l+d+d+ al  ++p ++ v p++   
  gi|557694566|ref|YP_008797620.1|  22 ALLVVAVAIGVASVIALVSQTAGVQQAVVRQLQTLGPTAIvITP--IGRTQLTDADI-ALLSSIPnIQDVIPMLstr 95 
                                       7899*****************************99987741454..45677899999.55456899******98765 PP

                          MacB_PCD  74 ..tvrgggsgeeevtvvgvdp.dyfk..vfglklaeGrffteadlrggpnvvvigeela..............erlf 131
                                         ++r+g+    e t+vgvdp + ++  + +++l eG++ ++a++       v g+e+a              ++lf
  gi|557694566|ref|YP_008797620.1|  96 vyISRAGQ--DVELTLVGVDPlK-LEalLGDVRLIEGQLYPPAQVP----IGVAGYEVAypptlggvqeisvsQALF 165
                                       54335554..45589*****853.334467888899*999997665....557788888666666666666656677 PP

                          MacB_PCD 132 pvGdtirl....kpftVvGvledppgsgsalg.ddavylp...lttl....qrrsitvrlkdgadleaaaaelek 194
                                        v ++ +     +p+ ++G+l+ + g++++ + d ++++p   l+t+    +++ i+vr++  ++++ + ++l++
  gi|557694566|ref|YP_008797620.1| 166 -VEQRAQSftrrIPLMISGILDRY-GASAFVSiDGSIFMPidmLKTIlnrrDYNLILVRADTAENVQLVVDQLTT 238
                                       .7777777999**********667.766666689******777333355436888*****************987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.62
                          MacB_PCD   5 vLGiaiGvaaviaivslgeglqasvlsqisdl 36 
                                       +LG + G+   +a +++++ ++ +v ++ ++ 
  gi|557694566|ref|YP_008797620.1| 266 LLGSVAGISLAVAGLGIMNIMLVTVIERTKEI 297
                                       78999999999999999999999988877654 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.84
                          MacB_PCD   5 vLGiaiGvaaviaivs 20 
                                       v+G+++Gva+   + +
  gi|557694566|ref|YP_008797620.1| 327 VVGVVLGVASTLFLPM 342
                                       789******9876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2802.84
//
Query:       gi|557694567|ref|YP_008797621.1|  [L=419]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-31  108.1   0.0    5.5e-30  103.8   0.0    2.3  2  DUF1743          Domain of unknown function (DUF1743)
    1.1e-10   41.3   1.5    2.1e-10   40.4   1.5    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0015   17.9   1.7     0.0043   16.4   1.7    1.7  1  zf_Rg            Reverse gyrase zinc finger
     0.0022   17.9   0.5      0.005   16.8   0.5    1.6  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0028   17.8   0.0     0.0051   17.0   0.0    1.4  1  tRNA_anti_2      OB-fold nucleic acid binding domain
     0.0072   16.3   0.3      0.016   15.2   0.3    1.5  1  DZR              Double zinc ribbon
  ------ inclusion threshold ------
      0.016   14.7   1.0       0.68    9.6   0.1    2.4  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.052   13.3   6.0       0.65    9.8   0.1    2.6  2  zinc_ribbon_2    zinc-ribbon domain
      0.065   13.1   0.2       0.11   12.4   0.2    1.3  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.067   13.3   0.9         10    6.4   0.1    3.1  2  Zn-ribbon_8      Zinc ribbon domain
      0.083   12.8   1.8       0.18   11.8   1.8    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
       0.16   11.8   4.1        1.7    8.6   4.3    2.4  2  zf-FPG_IleRS     Zinc finger found in FPG and IleRS
       0.17   11.3   0.9         16    5.1   0.1    2.8  2  zf-ribbon_3      zinc-ribbon domain
        1.2    8.9   8.3        4.5    7.0   7.7    2.3  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
        6.5    6.4   7.2        3.7    7.1   2.7    2.8  3  TF_Zn_Ribbon     TFIIB zinc-binding


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 ?    1.9   0.0      0.18   2.2e+02      66     114 ..      44     106 ..      38     108 .. 0.77
   2 !  103.8   0.0   4.6e-33   5.5e-30       1     116 []     142     253 ..     142     253 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.18
                                       CCS-STTSS............EEEEEEES-HHHHHHHHHCSEE..S-EEC..EEEEEESTTS- CS
                           DUF1743  66 vlvPhtpdp............vlfGirgedpeallkaakeilskeeesee..mavfrtnqgtd 114
                                        l+P+ p +            v+ ++ ++ +e++l++++e  +k     +  ++v+r+ + +d
  gi|557694567|ref|YP_008797621.1|  44 RLNPNCPFKtrgnaalslhfkVFEAMVDKAVETVLQTVEEFYEKGFAETQpgVVVYRGEDVPD 106
                                       5667666667777777777779999***************99955444448899999988776 PP

  == domain 2  score: 103.8 bits;  conditional E-value: 4.6e-33
                                       TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT.---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEE CS
                           DUF1743   1 grgiiGAtaalganialedstyEllaYreperwg.erevdeesvieadektypetfdnvDlshklvvlvPhtpdpvl 76 
                                       grg+iGA+aa+++  +le+ tyE +aYr +++wg  r+vd++sv+e++++     fd++D +++++ ++Phtp+pvl
  gi|557694567|ref|YP_008797621.1| 142 GRGVIGALAAVAL--PLENPTYEAIAYRVRSNWGtMRQVDPSSVLELHRSG--LSFDSYDPETGEIRITPHTPCPVL 214
                                       89***********..56679***************************9985..69********************** PP

                                       EEEEES-HHHHHHHHHCSEE..S-EECEEEEEESTTS-TT CS
                           DUF1743  77 fGirgedpeallkaakeilskeeeseemavfrtnqgtdah 116
                                        G+r ++pe+ lk +++++  +ee+e ++vf tnq+td+h
  gi|557694567|ref|YP_008797621.1| 215 AGVRATSPENALKGLSMVRF-HEEVEYVTVFATNQATDMH 253
                                       ********************.9999**************9 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 !   40.4   1.5   1.7e-13   2.1e-10       1      75 [.     268     343 ..     268     344 .. 0.98

  Alignments for each domain:
  == domain 1  score: 40.4 bits;  conditional E-value: 1.7e-13
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrrpggelelkveeiel 75 
                                       V+v Grv+ +   ++g+++f+ + D+ g++ + + r  ++ +++ ++l eGdvv+v G vk+ p+g l+l+ve+ie+
  gi|557694567|ref|YP_008797621.1| 268 VVVTGRVVGRPFVKKGGHVFFRVGDDDGEVVCAAYRptGGLRRVVQQLIEGDVVKVMGAVKEKPEG-LTLNVEKIEV 343
                                       899********9999***************************************************.********97 PP

>> zf_Rg  Reverse gyrase zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.7   3.6e-06    0.0043      10      31 ..     357     378 ..     350     393 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.6e-06
                             zf_Rg  10 CPNCgGdisdeRlekGLpCkrC 31 
                                       CP CgG +++  ++kG  C+rC
  gi|557694567|ref|YP_008797621.1| 357 CPRCGGRMESLGVNKGFRCERC 378
                                       ********************** 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 !   16.8   0.5   4.2e-06     0.005      19      45 ..     355     380 ..     341     381 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 4.2e-06
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrk 45 
                                       + CP+Cg+r ++  +++   f+C++C++
  gi|557694567|ref|YP_008797621.1| 355 PFCPRCGGRmESLGVNK--GFRCERCGE 380
                                       67********9999997..9******86 PP

>> tRNA_anti_2  OB-fold nucleic acid binding 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    0.0051      17      94 ..     264     341 ..     252     342 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.3e-06
                       tRNA_anti_2  17 elkkavwvrGeisnlkr.kasghvYftLkDekakisavifr..sraaklkftledGmkVlvkgrlsvYeprGsyqli 90 
                                        + ++v+v+G +      k+ ghv+f   D++ ++ ++  r  +  +++  +l +G+ V v g ++  +p+G + l+
  gi|557694567|ref|YP_008797621.1| 264 PY-QNVVVTGRVVGRPFvKKGGHVFFRVGDDDGEVVCAAYRptGGLRRVVQQLIEGDVVKVMGAVKE-KPEG-LTLN 337
                                       45.459*******986335699******************966666888899************985.7778.8888 PP

                       tRNA_anti_2  91 vedi 94 
                                       ve+i
  gi|557694567|ref|YP_008797621.1| 338 VEKI 341
                                       8887 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   1.3e-05     0.016      12      43 ..     354     387 ..     348     389 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                               DZR  12 arfCseCgtklkavaa..edrCpsCgekvdpear 43 
                                         fC++Cg ++++       rC +Cgek++pear
  gi|557694567|ref|YP_008797621.1| 354 PPFCPRCGGRMESLGVnkGFRCERCGEKLPPEAR 387
                                       56********9755446699***********987 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.044        53       4      13 ..     356     365 ..     355     367 .. 0.83
   2 ?    9.6   0.1   0.00057      0.68       2      16 ..     372     386 ..     371     388 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.044
                            zf_UBZ   4 lCerCgkeip 13 
                                       +C+rCg +++
  gi|557694567|ref|YP_008797621.1| 356 FCPRCGGRME 365
                                       7****98775 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00057
                            zf_UBZ   2 tylCerCgkeipese 16 
                                        + CerCg+++p+++
  gi|557694567|ref|YP_008797621.1| 372 GFRCERCGEKLPPEA 386
                                       589*********976 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   2.1     0.024        28      15      20 ..     356     361 ..     355     363 .. 0.76
   2 ?    9.8   0.1   0.00054      0.65       1      14 [.     374     387 ..     374     388 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.024
                     zinc_ribbon_2  15 FCpyCG 20 
                                       FCp+CG
  gi|557694567|ref|YP_008797621.1| 356 FCPRCG 361
                                       788887 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00054
                     zinc_ribbon_2   1 fCpnCGaelqdnak 14 
                                       +C +CG++l+++a+
  gi|557694567|ref|YP_008797621.1| 374 RCERCGEKLPPEAR 387
                                       6*********9985 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 ?   12.4   0.2   9.4e-05      0.11       9      36 ..     352     380 ..     346     382 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.4e-05
                                       SS--B-TTT-SB--S.SSS-EEEETTT-- CS
                              C1_1   9 kqptfCkhCgeflwg.kekqglkCswCkl 36 
                                        +p fC  Cg  ++  +   g++C+ C++
  gi|557694567|ref|YP_008797621.1| 352 TRPPFCPRCGGRMESlGVNKGFRCERCGE 380
                                       6789*********999***********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 ?    6.4   0.1    0.0084        10      26      37 ..     353     365 ..     339     367 .. 0.71
   2 ?    4.0   0.1     0.046        55       6      14 ..     373     381 ..     372     389 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0084
                       Zn-ribbon_8  26 lta.CPeCgsevr 37 
                                        ++ CP+Cg++++
  gi|557694567|ref|YP_008797621.1| 353 RPPfCPRCGGRME 365
                                       5677*****9765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.046
                       Zn-ribbon_8   6 YrCeeCghe 14 
                                       +rCe+Cg++
  gi|557694567|ref|YP_008797621.1| 373 FRCERCGEK 381
                                       89*****75 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 ?   11.8   1.8   0.00015      0.18      31      55 ..     357     381 ..     356     383 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                    OrfB_Zn_ribbon  31 CseCgsknkealsgrtfkCpnCgfe 55 
                                       C++Cg +++    ++ f+C++Cg +
  gi|557694567|ref|YP_008797621.1| 357 CPRCGGRMESLGVNKGFRCERCGEK 381
                                       **********9999*********87 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 ?    8.6   4.3    0.0014       1.7       4      27 ..     357     378 ..     356     378 .. 0.95
   2 ?    2.8   1.1     0.095   1.1e+02       1      11 [.     372     382 ..     372     386 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0014
                                       -TTT--BBEEEECTTEEEEE-TTT CS
                      zf-FPG_IleRS   4 CpRCwryiervgqagrstyfCprC 27 
                                       CpRC++  e+ g+  +  + C+rC
  gi|557694567|ref|YP_008797621.1| 357 CPRCGGRMESLGV--NKGFRCERC 378
                                       *************..999999999 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.095
                                       TSB-TTT--BB CS
                      zf-FPG_IleRS   1 GepCpRCwryi 11 
                                       G +C+RC+  +
  gi|557694567|ref|YP_008797621.1| 372 GFRCERCGEKL 382
                                       568****9765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.013        16      18      25 ..     356     363 ..     350     364 .. 0.78
   2 ?    3.7   0.0     0.036        43       4      17 ..     374     387 ..     372     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.013
                       zf-ribbon_3  18 vCpyCGtk 25 
                                       +Cp CG++
  gi|557694567|ref|YP_008797621.1| 356 FCPRCGGR 363
                                       78888876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.036
                       zf-ribbon_3   4 rCPnCGaplssddn 17 
                                       rC +CG++l ++++
  gi|557694567|ref|YP_008797621.1| 374 RCERCGEKLPPEAR 387
                                       899****8788876 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 ?   -3.7   0.0       8.4     1e+04      17      22 ..     105     110 ..     104     110 .. 0.85
   2 ?    7.0   7.7    0.0037       4.5       4      15 ..     355     366 ..     353     381 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 8.4
                     zf-NADH-PPase  17 eggwar 22 
                                       +++w++
  gi|557694567|ref|YP_008797621.1| 105 PDEWKM 110
                                       79***8 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0037
                     zf-NADH-PPase   4 rFCgrCGaptep 15 
                                       +FC+rCG+++e 
  gi|557694567|ref|YP_008797621.1| 355 PFCPRCGGRMES 366
                                       6*********85 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.1   2.6e+03      12      20 ..     195     203 ..     192     204 .. 0.79
   2 ?   -1.2   0.0       1.2   1.5e+03      16      23 ..     293     300 ..     284     301 .. 0.75
   3 ?    7.1   2.7    0.0031       3.7       3      29 ..     357     382 ..     355     389 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.1
                                       HEETSTTCE CS
                      TF_Zn_Ribbon  12 veDpergel 20 
                                        +Dpe+ge+
  gi|557694567|ref|YP_008797621.1| 195 SYDPETGEI 203
                                       589****96 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                                       STTCEEES CS
                      TF_Zn_Ribbon  16 ergelvCt 23 
                                       + ge+vC 
  gi|557694567|ref|YP_008797621.1| 293 DDGEVVCA 300
                                       78*****6 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0031
                                       ETTTTCEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon   3 CPnCgstnlveDpergelvCtdCGlVl 29 
                                       CP Cg+++ +    +  ++C++CG+ l
  gi|557694567|ref|YP_008797621.1| 357 CPRCGGRM-ESLGVNKGFRCERCGEKL 382
                                       ******86.33334457*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3073.20
//
Query:       gi|557694568|ref|YP_008797622.1|  [L=268]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-08   33.7   0.0    4.5e-08   32.7   0.0    1.5  1  ACT       ACT domain
    1.7e-06   28.0   0.2    3.4e-06   27.0   0.2    1.4  1  V4R       V4R domain
    0.00058   20.4   0.5     0.0026   18.3   0.5    2.0  1  ACT_4     ACT domain
  ------ inclusion threshold ------
       0.11   11.4   0.1       0.16   10.9   0.1    1.1  1  FAM178    Family of unknown function, FAM178


Domain annotation for each model (and alignments):
>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0     1e-11   4.5e-08       2      38 ..      25      61 ..      24      77 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1e-11
                                      EEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEEST CS
                               ACT  2 vlrvgvpDrPGlLarvfgaladrgiNidsieqrssed 38
                                        +v++ DrPG La+v++++a +g+Ni++i ++ s +
  gi|557694568|ref|YP_008797622.1| 25 LFSVELVDRPGSLAEVLAVFATYGVNIVNIYTTQSIY 61
                                      567999*************************999965 PP

>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   7.5e-10   3.4e-06       6      59 ..     211     263 ..     207     265 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 7.5e-10
                                       EEES-S-TT---SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEE CS
                               V4R   6 eespelaglpgkeePvCyleaGllagalsellgkrveveEveCaaeGhdhCeFe 59 
                                       e+  e++   g ++P   +++G lag+l+e lg    v E++C a G+ +CeF+
  gi|557694568|ref|YP_008797622.1| 211 ESVYECEVGRGHGKPFSNIFRGSLAGILNEALGV-ETVVETKCIAAGDPYCEFV 263
                                       55556776667899**************999985.5788**************7 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.5   5.7e-07    0.0026      10      78 ..      27     102 ..      25     103 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.7e-07
                             ACT_4  10 eveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVk....dvehLsrviakLraipgVisV 78 
                                       +ve  dr+g La++++v++  ++niv++ +++      ++++e +i   +     ++e+L++ i+ L++++ V+ V
  gi|557694568|ref|YP_008797622.1|  27 SVELVDRPGSLAEVLAVFATYGVNIVNIYTTQSIYtdtSSTVEANIAADLTgknvSSEQLAKSINLLNSVKRVTVV 102
                                       6999************************988743233344444444444432222346777777777777777766 PP

>> FAM178  Family of unknown function, FAM178
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   3.5e-05      0.16     198     264 ..      36     100 ..      34     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.5e-05
                            FAM178 198 slqdvtevflnlGaslkaLfpleslqpsfneedllsevqlsekeqqkekeqetllevnlsyilkfLs 264
                                       sl++v +vf  +G+++ +++  +s+    ++++++ ++ ++ + ++ + +++ +  +nl + +k  +
  gi|557694568|ref|YP_008797622.1|  36 SLAEVLAVFATYGVNIVNIYTTQSIYT-DTSSTVEANIAADLTGKNVS-SEQLAKSINLLNSVKRVT 100
                                       8***********************999.45566677777776666666.788888899988887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); 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:                         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: 00:00:00.42
# Mc/sec: 1907.03
//
Query:       gi|557694569|ref|YP_008797623.1|  [L=330]
Description: phosphate uptake regulator [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-13   50.9   4.6    9.1e-08   32.5   0.9    2.5  2  PhoU            PhoU domain
    1.1e-05   25.2   0.1    3.6e-05   23.6   0.1    1.9  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
        0.1   12.9   0.8        2.7    8.3   0.2    2.5  2  DUF948          Bacterial protein of unknown function (DUF948
       0.21   11.7   0.0       0.41   10.8   0.0    1.5  1  Zf_RING         KIAA1045 RING finger


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 !   19.6   0.2   2.1e-07   0.00092       6      89 .]     143     230 ..     138     230 .. 0.81
   2 !   32.5   0.9     2e-11   9.1e-08       2      60 ..     245     304 ..     244     322 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHGG-SHHHHHHHH...HHHHHHHHHHH CS
                              PhoU   6 eiveemlddalealeekdtelarevierddeidrlekeierslleal.akrqplaedlrells...llriardlERi 78 
                                       + ++  ++d+ +al+ +d+ la + +er  e+ + ++++ r +++al ++   +a ++r+ +s    + ++r+l R+
  gi|557694569|ref|YP_008797623.1| 143 QFSRAVMRDSAKALRVGDKTLAHDAYERGFELTKHYRLLMRVCFQALhSTVVREAVKVRDTSSlvvRIVAVRELGRV 219
                                       66778899***************************************55544444456665442115669******* PP

                                       HHHHHHHHHHH CS
                              PhoU  79 gDhavniaerv 89 
                                       + ++ ++aerv
  gi|557694569|ref|YP_008797623.1| 220 AYYCMRMAERV 230
                                       *********86 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 2e-11
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HGG-SH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealak.rqplae 60 
                                       ++m  +v +ml+dal+al + d  la evi+r + +  l+ +  ++++++  k  + l+ 
  gi|557694569|ref|YP_008797623.1| 245 EEMVALVDKMLEDALTALLKHDLSLASEVIDRMENVRTLYTKAFKHIIRKPEKeANILGL 304
                                       79********************************************99998442555544 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 !   23.6   0.1     8e-09   3.6e-05       2      40 ..       9      47 ..       8      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8e-09
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCC CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiilrp 40
                                      + G +++v++Pk ++++lg+++   v ++v++d+i+l+p
  gi|557694569|ref|YP_008797623.1|  9 TTGGTYIVSLPKQMVKSLGLDKRQVVRVTVEDDRIVLTP 47
                                      89***********************************99 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 ?    2.4   0.0     0.041   1.8e+02      11      53 ..     121     163 ..     120     167 .. 0.81
   2 ?    8.3   0.2    0.0006       2.7      23      76 ..     232     286 ..     206     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.041
                            DUF948  11 vvLviflivvllklkktldeaaatieelekqvdpilkevedll 53 
                                       vvL  f+ ++ ++l k+l++++++ + ++++  + l+  +++l
  gi|557694569|ref|YP_008797623.1| 121 VVLQTFIDPTKFELDKLLEKFTQFSRAVMRDSAKALRVGDKTL 163
                                       6888899999999999999999999999998877776655555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0006
                            DUF948  23 klkktldeaaatieelekqvdpilkev.edllakvnelledvneklekvdpltea 76 
                                       +++++ de+aat+ee+   vd++l+++ ++ll++   l+++v +++e+v +l ++
  gi|557694569|ref|YP_008797623.1| 232 EIGRVEDELAATVEEMVALVDKMLEDAlTALLKHDLSLASEVIDRMENVRTLYTK 286
                                       4578889999999999999999887753677777778888999999998887655 PP

>> Zf_RING  KIAA1045 RING finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.1e-05      0.41      21      66 ..     181     226 ..     172     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.1e-05
                           Zf_RING  21 pCRvCtkvfHegClrklgylqdesalellkrAktetGWsCaeCdnl 66 
                                         RvC +  H + +r+  +++d s+l +   A  e G   ++C  +
  gi|557694569|ref|YP_008797623.1| 181 LMRVCFQALHSTVVREAVKVRDTSSLVVRIVAVRELGRVAYYCMRM 226
                                       56****************************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1011  (0.0563891); expected 358.6 (0.02)
Passed bias filter:                      704  (0.039266); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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: 00:00:00.42
# Mc/sec: 2366.03
//
Query:       gi|557694570|ref|YP_008797624.1|  [L=429]
Description: isocitrate lyase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-98  328.2   0.1    1.2e-51  175.8   0.0    2.0  2  ICL         Isocitrate lyase family
      3e-16   59.6   0.0    4.6e-16   59.0   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 !  175.8   0.0   1.4e-55   1.2e-51       4     254 ..      12     251 ..       9     254 .. 0.93
   2 !  152.2   0.1   1.9e-48   1.7e-44     352     521 ..     251     423 ..     249     428 .. 0.89

  Alignments for each domain:
  == domain 1  score: 175.8 bits;  conditional E-value: 1.4e-55
                                       XHHHHHTSGGGGG---SS-HHHHHHH--SS----THH.HHHHHHHHHHHHHHHHT--EEEEB--SHHHHHHHHHH.- CS
                               ICL   4 evkkwwsdsrwrktkrvysaedivskrGnlkieyass.eqakklfklleeheaektasktfGaldpvqvtqmaky.l 78 
                                       ++++ w+ +rw+   r+y+aed+ + rG+ k++y+ + + ++k++k+l+++    +  +t Gal   q  q+    +
  gi|557694570|ref|YP_008797624.1|  12 DLERVWRTPRWNGVSRKYTAEDVLKLRGSWKLDYTYArVTSEKFWKMLHTD----DYIFTAGALTGNQAIQLVEAgI 84 
                                       78899****************************986516789******865....568999****999999876439 PP

                                       S-EEE-HHHHHHH--TT----SS-S-S-TTHHHHHHHHHHHHHHHHHHHHHHHHHSS-HHHHTTS--------EEEE CS
                               ICL  79 dtiyvsGwqssstastsnepspdladypmdtvpnkvehlflaqlfhdrkqkeerlkvkkeereklanvdylrpiiad 155
                                        +iyvsGwq ++ +  s +  pdl  yp  + p+ v ++ +a +  d+ q+          +++ +++dy+ pi+ad
  gi|557694570|ref|YP_008797624.1|  85 KAIYVSGWQVAADNNQSGNMYPDLGLYPSSSGPDLVRKIVKALQRADQIQHL---------ENRPSKIDYMAPIVAD 152
                                       *****************************************98777766654.........356789********** PP

                                       -TT-SSSHHHHHHHHHHHHHTT-SEEEE-SB-TT---------EEE--HHHHHHHHHHHHHHHHHTT---EEEEE-- CS
                               ICL 156 adtGhGGltavvkltklfierGaaGihiedqasgtkkcGhmaGkvlvpiqehinrlvairaqadilgsdllvvartd 232
                                       +++G+GG      l k +ie GaaG+h edq+++ ++cGh+ Gkvlvp +     l a+r++ad+lg+  +++artd
  gi|557694570|ref|YP_008797624.1| 153 GEAGFGGPLHAYELMKAMIEAGAAGVHFEDQSPSERRCGHLGGKVLVPTKRFTSILSAARLAADVLGVPSVIIARTD 229
                                       ***************************************************************************** PP

                                       GGGEEEES-TT-GGGGGGEEEE CS
                               ICL 233 seaatlitstidtrdhafilGa 254
                                       +  a+++ts  d  d +f+ G+
  gi|557694570|ref|YP_008797624.1| 230 AIGAQFLTSDADPVDREFLTGS 251
                                       *******************997 PP

  == domain 2  score: 152.2 bits;  conditional E-value: 1.9e-48
                                       S--TT--EEE--SH..HHHHHHHHHHTTS-SEEE---SS--HHHHHHHHHHHHTT-TT-EEEEE--SSS-GGGTS-H CS
                               ICL 352 prvreGyyrykGgt..qcsvvravafapyadliwmesklpdyaqakefaeGvkakvpeqklaynlspsfnwkkamsa 426
                                       +r+ eGy+ +k gt  + +++r++++apyadl+w+e++ p +++ak fa+ ++ k+p + layn+spsfnw k +  
  gi|557694570|ref|YP_008797624.1| 251 SRTSEGYFELKPGTalDIAIQRGLSYAPYADLLWFETSKPSLEEAKRFADAIHRKYPGKLLAYNMSPSFNWLKVVDG 327
                                       69*********987446899********************************************************* PP

                                       HHHHSHHHHHHHTTEEEEEETTHHHHHHHHHHHHHHHHHHHHTHHHHHH.HTHHHHHHH.T-GGGSHHHHHTHHHHH CS
                               ICL 427 deqetyikrlaklGyvwqfitlaGlhtnalisdkfakdyakrGmkayge.evqeeeidn.GvdvvkhqkwsGaeyid 501
                                       d  +++ ++l+++Gy +qfitlaG+ht      ++ak+ a++Gm ay++ +  e e+++ G    khq++ G +y+d
  gi|557694570|ref|YP_008797624.1| 328 DTLREFNQKLGQMGYKFQFITLAGFHTLNASMFELAKKLAEEGMMAYANfQAHEVELEKmGYRAFKHQRFIGVHYYD 404
                                       ***************************999999**************97234455655449**************** PP

                                       HHHHHHH--XXXXXXXXXXX CS
                               ICL 502 ellklvtGGvsstaamGkGv 521
                                       e+l  ++G   + +a+ +  
  gi|557694570|ref|YP_008797624.1| 405 EVLMAIEGKE-AVSALAEST 423
                                       ***9998864.444555544 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   0.0   5.2e-20   4.6e-16      21     166 ..      75     277 ..      55     326 .. 0.81

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 5.2e-20
                        PEP_mutase  21 sakiveeagfkalatsSlavaasl...G..vpDgeelpleellaavraiaevvs..................lPliv 74 
                                        a  + eag+ka+ +s+++vaa     G  +pD    p ++  ++vr+i+++++                   P+ +
  gi|557694570|ref|YP_008797624.1|  75 QAIQLVEAGIKAIYVSGWQVAADNnqsGnmYPDLGLYPSSSGPDLVRKIVKALQradqiqhlenrpskidymAPIVA 151
                                       56667899*************97533345589*********************99********************** PP

                        PEP_mutase  75 DledGygespeevaetvrrliaaGvvgvniEDk.....kknd.aerqlldieefaekiaaaraaaeeag..fvinAR 143
                                       D e+G+g  p +  e  + +i+aG++gv++ED+     +++  +++ l++ + f++ ++aar aa+  g   vi+AR
  gi|557694570|ref|YP_008797624.1| 152 DGEAGFGG-PLHAYELMKAMIEAGAAGVHFEDQspserRCGHlGGKVLVPTKRFTSILSAARLAADVLGvpSVIIAR 227
                                       *******9.99**********************8764333356888888********************999***** PP

                        PEP_mutase 144 tdalll...........................sagagleeaieRaraYa 166
                                       tda+                             ++g +l+ ai+R+  Ya
  gi|557694570|ref|YP_008797624.1| 228 TDAIGAqfltsdadpvdrefltgsrtsegyfelKPGTALDIAIQRGLSYA 277
                                       ***76567777666666666666666666666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3115.26
//
Query:       gi|557694571|ref|YP_008797625.1|  [L=525]
Description: malate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-176  585.7   0.0   7.5e-176  585.5   0.0    1.0  1  Malate_synthase  Malate synthase
     0.0016   17.6   0.0       0.06   12.5   0.0    2.5  2  HpcH_HpaI        HpcH/HpaI aldolase/citrate lyase family


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 !  585.5   0.0  8.4e-180  7.5e-176       8     525 ..      12     524 ..       7     525 .] 0.98

  Alignments for each domain:
  == domain 1  score: 585.5 bits;  conditional E-value: 8.4e-180
                                       THHHHCHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHSHHHCCTCCCH-TSS---S-EECCCCE-TCC CS
                   Malate_synthase   8 vleaaeilteealefvaelvrdltprrrelLeeRdelqaeidkgelndflketkylreepewktatlhielqdrrve 84 
                                       ++++  +l+++a++fv +lv++  p+ r+lL++R+e+ +++ +g++ df  et+++r    wk++ ++++l  r+ve
  gi|557694571|ref|YP_008797625.1|  12 TKKYLTVLSKDAVDFVRHLVEKHGPELRRLLAKREETAEALRRGARLDFPAETAEIR-ASGWKVSDIPADLSVRHVE 87 
                                       5667789**************************************************.999**************** PP

                                       CCCCC-CCHCCCCCCCSSSEEEEESSTTS--HHHHHHCCHHCCCHCCTTT-EEEET-TSEEEEETTSESSSSEEEEE CS
                   Malate_synthase  85 iiGkadrkmiinalnesaittiaDfEDsvapnwenlvkGqlnledavrgrisfrkenkdksYklndglegrsllfvR 161
                                       i+G++drkm+inaln++a  ++aDfEDs +p w++  +Gq+nl davr++i +r+  ++k Y+l+   +++++l+vR
  gi|557694571|ref|YP_008797625.1|  88 ITGPVDRKMMINALNSGADAYMADFEDSFSPVWSQTLDGQINLMDAVRKTIEYRSP-DGKLYTLA---DKTATLLVR 160
                                       *******************************************************8.********...7******** PP

                                       ---TTTEEEEEECTTCEEEHHHHHHHHHHHHHHHHCSCCTTSSEEEEE-S-SSHHHHHHHHHHHHHHHHHCTSSTTS CS
                   Malate_synthase 162 nrGwhltekhilvdGeeisegilDfgliffhnakelklsrgggpyivlPKmegpqEaalwnevFsraedllglprgt 238
                                       +rG hl ek + ++G ++++ ++Dfgl+ fhna+el   rg+gpy++ PK+e++ Ea++w++vF  ae++l+lprgt
  gi|557694571|ref|YP_008797625.1| 161 PRGLHLVEKNMRINGSPVPAPLFDFGLYLFHNAAEL-RRRGTGPYFYIPKLEHYLEARWWANVFADAEKTLNLPRGT 236
                                       ************************************.9*************************************** PP

                                       CEEEEEE-SHHHHTTHHHHHHCTTTTEEEEEE-CHHHHHHHHHHTCCCCGCB...CGGGGCCSHHHHHHHHHHHHHH CS
                   Malate_synthase 239 ikatvliEtlraslnldeiiyelrdrvaglNcGrlDyifseiktlreagdmvLPdRkavtktapfikaYekllvktc 315
                                       ik +vliEt++a++++dei+yelrd v+ lN Gr+Dyifs+ik+l ++++ ++PdR++ t++++f+k+   l vktc
  gi|557694571|ref|YP_008797625.1| 237 IKCSVLIETVTAAFQMDEILYELRDYVTALNLGRWDYIFSFIKRLGHDPRYLMPDRSHLTMDKHFLKSAALLMVKTC 313
                                       ***************************************************************************** PP

                                       HHTT.CCCCCCCTCSEECCCEHHHCCCHHHHHHHCHHHHHCT-SEEEESSHHHHHHHHHHHHHCHCHCHHCCHHTTT CS
                   Malate_synthase 316 hkrgvhamgGlaakipikkdmeaneellekvredKlrevraGadgaWvahPtlatlaaevfeevdvapnQielakee 392
                                       h+rg+ a+gG+aa++pi+ ++ea e++++kvredKlre+ +G+dgaWvahP+l++l+++ f e  +apnQ ++++e+
  gi|557694571|ref|YP_008797625.1| 314 HRRGAYAIGGMAAQVPIRGNPEAQERAFAKVREDKLREISQGFDGAWVAHPDLVPLVKSLFAENLKAPNQLHVKHEN 390
                                       ***************************************************************************** PP

                                       HHHHHHHHCS.--BBHHHHHHHHHHHHHHHHHHHHHHCT-SSEEETTEEESHHHHHHHHHHHHHHHHTTSC-CCHSH CS
                   Malate_synthase 393 vritaddLltkipeaeeteeglrnnvqvglqYvvaWlrgvGcvpiihLmEDaATaeiSrqqlaqWirhgvvlkeqgv 469
                                         itaddLl+ +pe+e+t+eg+r+n++vgl+Y+++Wlrg Gcv+i+ LmEDaAT ei r+ ++qWirhg+ l + g+
  gi|557694571|ref|YP_008797625.1| 391 LVITADDLLK-VPEGERTAEGMRANMEVGLRYLESWLRGNGCVAINFLMEDAATFEIARALIWQWIRHGARLAD-GR 465
                                       *********6.***************************************************************.8* PP

                                       CHHHHHHHHHHHHHCCHHH.HHHH..CCTTHHHCHHHHHHHHHTTTCCC-CHHHHHCCH CS
                   Malate_synthase 470 kvslelmaklvdeenarle.elgk..edeayreaakllkkeataeefadfltlkaykel 525
                                       +v+++ +++ + +  ++l+ e+g+  +  ++++aa++l+k++ ++ef +f    ay++l
  gi|557694571|ref|YP_008797625.1| 466 TVTPQVFEEELGKVLQKLRgEMGPayQGTKFEQAAEILRKTVLSNEFIEFTPPIAYEHL 524
                                       *******************999999999**********************999999887 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 !    2.4   0.0    0.0083        74      11      33 ..      94     116 ..      90     135 .. 0.90
   2 !   12.5   0.0   6.7e-06      0.06      88     158 ..     205     277 ..     199     364 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0083
                                       HHHHHHHCTC--SEEEEESSTSS CS
                         HpcH_HpaI  11 aalaekaaiagaDsvliDlEdav 33 
                                        +++ +a  +gaD+ + D Ed+ 
  gi|557694571|ref|YP_008797625.1|  94 RKMMINALNSGADAYMADFEDSF 116
                                       6899999**************96 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.7e-06
                                       EEESS--SHHHHHHHHHHTSHTTTS---HCCC-EEEEEE-SHHHHHTHHHHH..TSTTEEEEEE-HHHHHHHT CS
                         HpcH_HpaI  88 vlvPkvetaeealevvsalrepekgirganketrllaqiEsaegvknaeeIa..avegldgvflGaeDlsadl 158
                                       + +Pk+e   ea+   ++++ +ek      ++++  + iE+ ++  +++eI+    + + ++ lG  D+  + 
  gi|557694571|ref|YP_008797625.1| 205 FYIPKLEHYLEARWWANVFADAEKTLNLPRGTIKCSVLIETVTAAFQMDEILyeLRDYVTALNLGRWDYIFSF 277
                                       679*************************************************9556789**********8764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); 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: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3651.03
//
Query:       gi|557694572|ref|YP_008797626.1|  [L=377]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-30  106.1   0.0    2.8e-30  105.5   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
    8.6e-20   71.3   0.2    1.6e-19   70.4   0.2    1.4  1  THUMP            THUMP domain
    1.8e-07   31.1   0.0    2.9e-06   27.2   0.0    2.2  2  Methyltransf_31  Methyltransferase domain
    0.00013   22.5   0.0    0.00038   21.1   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    0.00066   19.3   0.0     0.0011   18.6   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0056   16.3   0.0       0.02   14.5   0.0    1.8  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase


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 !  105.5   0.0   9.5e-34   2.8e-30       1     176 [.     161     349 ..     161     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 9.5e-34
                                       -SSS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SS............. CS
                           UPF0020   1 RgyRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvle............. 64 
                                       R yR  ++ a+L++t+A  lvrl+gw++  +llDP+ GsGti++E al g  i pg+ re+ ++             
  gi|557694572|ref|YP_008797626.1| 161 RFYRRGFHRAALSPTVANTLVRLSGWRRHMVLLDPFTGSGTIPLETALYGLAISPGARRENPSFekipvfksidsak 237
                                       679***********************************************************999*******99988 PP

                                       HHHHHHHHHH.HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.STTS---EEEE----------HH CS
                           UPF0020  65 lkaeaeeear.aelklygsDldrrvvqgareNaekagvgdliefsqadaakLr.lkegevdvivtnpPYGerlgskk 139
                                       +++e+ +++   +++ +g+D  ++ ++ a + +e  g +  + f+q d+  L    + evd +v+npP+G rl   +
  gi|557694572|ref|YP_008797626.1| 238 IREELLKREDpGTVEAIGIDVSPKSLNLALDSLETFGRETGVRFVQGDVFRLVeYVDREVDKVVCNPPFGVRLRL-R 313
                                       888888877766777*************************************9655669**************75.6 PP

                                       HHHHHHHHHHHHHHHH-TT..-EEEEEESSHHHHHCC CS
                           UPF0020 140 alekLYseflrelkrvlrgggrlvlltsenkalekal 176
                                       + ek+Y e  +++++ + + + +v+ +++   + kal
  gi|557694572|ref|YP_008797626.1| 314 EPEKFYTEAFTAIAQACPHASLTVI-VNKPVIVLKAL 349
                                       7799999999999998888555554.44444445555 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.2   5.5e-23   1.6e-19      25     144 .]      35     153 ..      18     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 5.5e-23
                                       EEECTEEEEEETHHHHHHHHHTSTTECEEEEE.EEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTSSSH CS
                             THUMP  25 vvelkgekpeedeellkealekargiqrvipv.cevceadledileaakeivkkkfeeeketFaVrvkrrgkhfeft 100
                                       ++  +        e+  + ++ a ++ r++   +++ +++l++i+++a +++  +f++ +++FaVr++r+g h  ft
  gi|557694572|ref|YP_008797626.1|  35 FFTAS-------LEECVKVNYAAQTVNRIFLLlLREHAETLDEIERLAASVDFGEFIDREQSFAVRAERVGLH-VFT 103
                                       44443.......4444555666678888888889***************************************.*** PP

                                       HHHHHHHHHHHHHCCTT......-EE-SSS-SEEEEEEEETTEEEEEEEC CS
                             THUMP 101 sreinrevGkaivektg......lkVdlenPdivvrveiikdkayisidr 144
                                       s +i+ +vGka+ +++       l+Vdl+nPdi v + +++ ++++++++
  gi|557694572|ref|YP_008797626.1| 104 SLDIAAAVGKAVIDSYRastgvrLRVDLNNPDIEVYAILRNTELLLGVNT 153
                                       ***********************************************985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.08   2.4e+02       3      22 ..     188     207 ..     187     217 .. 0.82
   2 !   27.2   0.0   9.6e-10   2.9e-06      26     100 ..     248     325 ..     235     355 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.08
                   Methyltransf_31   3 kglrvlDlGCGtGeltfela 22 
                                       +++++lD+ +G+G++ +e a
  gi|557694572|ref|YP_008797626.1| 188 RHMVLLDPFTGSGTIPLETA 207
                                       5799**********988877 PP

  == domain 2  score: 27.2 bits;  conditional E-value: 9.6e-10
                   Methyltransf_31  26 gpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDlilsnevl...naladpdkileei 97 
                                           e +GiD s+++++lA   ++  g +  v+F qgd++   e  + d+ +D +++n ++     l +p+k++ e+
  gi|557694572|ref|YP_008797626.1| 248 PGTVEAIGIDVSPKSLNLALDSLETFGREtGVRFVQGDVFRlVE--YVDREVDKVVCNPPFgvrLRLREPEKFYTEA 322
                                       446789**********************99***********666..99**********7777778888888888876 PP

                   Methyltransf_31  98 erv 100
                                       + +
  gi|557694572|ref|YP_008797626.1| 323 FTA 325
                                       554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         6   1.8e+04      24      32 ..     102     110 ..      84     129 .. 0.60
   2 !   21.1   0.0   1.3e-07   0.00038      16      91 ..     243     324 ..     235     329 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 6
                                       EEEEESSHH CS
                   Methyltransf_25  24 vtgvDisee 32 
                                       +t +Di+++
  gi|557694572|ref|YP_008797626.1| 102 FTSLDIAAA 110
                                       344444443 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 1.3e-07
                                       HCTS..TSSEEEEEESSHHHHHHHHHHHHH..TTTTEEEEESBCCGB.SSSTTTEEEEEEEST.GGG.SSHHHHHHH CS
                   Methyltransf_25  16 akrl..gkakvtgvDiseemleaareraee..eglnvefvqgdaedl.pfedgsfDlvvssga.lhh.lsdedleka 85 
                                       +kr   g  + +g+D+s++ l+ a   +e   ++  v+fvqgd+ +l ++ d+++D vv++   + + l  ++ ek+
  gi|557694572|ref|YP_008797626.1| 243 LKREdpGTVEAIGIDVSPKSLNLALDSLETfgRETGVRFVQGDVFRLvEYVDREVDKVVCN-PpFGVrLRLREPEKF 318
                                       44433457899*****************9855455*********775279**********5.547776777777888 PP

                                       HHHHHH CS
                   Methyltransf_25  86 lkeiar 91 
                                       + e++ 
  gi|557694572|ref|YP_008797626.1| 319 YTEAFT 324
                                       887766 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   3.5e-07    0.0011      58     112 ..     253     311 ..     241     352 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.5e-07
                                       EEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST..TS-EEEEEE---STTTCH CS
                               MTS  58 vtlvdvdarAlesakenleankle..vevvasdvleeve..ekkfdlivsNPPfhagka 112
                                          +dv+ ++l++a   le+ + e  v++v+ dv+  ve  ++++d +v+NPPf     
  gi|557694572|ref|YP_008797626.1| 253 AIGIDVSPKSLNLALDSLETFGREtgVRFVQGDVFRLVEyvDREVDKVVCNPPFGVRLR 311
                                       55689999***********9999999********98777779************87664 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 ?   -2.4   0.0       1.1   3.2e+03       3      12 ..     191     200 ..     190     210 .. 0.84
   2 !   14.5   0.0   6.7e-06      0.02      25      82 ..     253     307 ..     249     318 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                   Methyltransf_15   3 vilDlfsGaG 12 
                                       v+lD+f+G+G
  gi|557694572|ref|YP_008797626.1| 191 VLLDPFTGSG 200
                                       689*****99 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.7e-06
                   Methyltransf_15  25 viaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSpPwG 82 
                                        i+i+++++ l++a    e +g +  + +v+gdvf l++ +  e+   d v++ pP G
  gi|557694572|ref|YP_008797626.1| 253 AIGIDVSPKSLNLALDSLETFGRETGVRFVQGDVFRLVEYVDREV---DKVVCNPPFG 307
                                       589***********************************9976554...79******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 00:00:00.40
# Mc/sec: 2812.36
//
Query:       gi|557694573|ref|YP_008797627.1|  [L=182]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   11.5  12.2        0.3   10.0  12.3    1.8  1  MFS_1      Major Facilitator Superfamily
       0.18   12.1   0.3       0.18   12.1   0.3    2.4  2  DUF3382    Domain of unknown function (DUF3382)
       0.18   11.8   5.0        0.5   10.4   5.0    1.8  1  MARVEL     Membrane-associating 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 ?   10.0  12.3     5e-05       0.3     220     297 ..      78     160 ..       5     167 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 5e-05
                             MFS_1 220 ffgfsglltllplylqevlgls.......glllaglllallalvgailallagrlsdrlgrrrrlllallllllaal 289
                                       ff   ++ +l++ +   v g+        +   +++ ++l+ ++++ +++++ rl++r grrr++ l l++l+l+++
  gi|557694573|ref|YP_008797627.1|  78 FFLGKTVGMLVTPF-TIVVGFYgyetifhS-SNTVYDIGLFIAAVILGQFVSYRLIQRHGRRRFNALPLAVLILMTA 152
                                       33333333333332.222222222244431.2223233333333333477777888777777777777777777777 PP

                             MFS_1 290 glallavt 297
                                       +++l+ + 
  gi|557694573|ref|YP_008797627.1| 153 LFFLFTFQ 160
                                       77777765 PP

>> DUF3382  Domain of unknown function (DUF3382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.44   2.6e+03      13      34 ..      18      39 ..      12      57 .. 0.75
   2 ?   12.1   0.3     3e-05      0.18      18      68 ..      92     140 ..      83     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.44
                           DUF3382 13 alvlfvpilGlqleldgtrlvl 34
                                      ++vl++ +l ++ el+g+++ +
  gi|557694573|ref|YP_008797627.1| 18 FIVLAGSFLHFTYELSGGNMAV 39
                                      5677777887888887777655 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3e-05
                           DUF3382  18 vpilGlqleldgtrlvlep..rwglvaiavavvfvgqLlrplllqalkarkkl 68 
                                       + ++G+     g++++ ++  ++  +++++a+v +gq++   l+q+ ++r+  
  gi|557694573|ref|YP_008797627.1|  92 TIVVGF----YGYETIFHSsnTVYDIGLFIAAVILGQFVSYRLIQRHGRRRFN 140
                                       556666....7888888888899***********************9998765 PP

>> MARVEL  Membrane-associating domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.0   8.3e-05       0.5       8      91 ..       6     159 ..       3     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 8.3e-05
                            MARVEL   8 ilrilqlvfaiiilgliaslia....................................................... 29 
                                       +lr+l+lvf+i  + l++s+++                                                       
  gi|557694573|ref|YP_008797627.1|   6 VLRLLELVFGIPFIVLAGSFLHftyelsggnmavalisavnesvwehlklaffpalflavpafirlrrdypnfflgk 82 
                                       79*************************************************************************** PP

                            MARVEL  30 ................kldqllgspssalnfavfvavfsflyalfllvlylfk.....nsaftsilwplidli.vda 84 
                                                        + ++++s+++   + +f+a+       ++l   +++     +  +++++ pl++li ++a
  gi|557694573|ref|YP_008797627.1|  83 tvgmlvtpftivvgfyGYETIFHSSNTVYDIGLFIAA-------VILGQFVSYrliqrHGRRRFNALPLAVLIlMTA 152
                                       *********6666555444455555555555555554.......444444444444578888888888877662677 PP

                            MARVEL  85 laallwl 91 
                                       l++l+++
  gi|557694573|ref|YP_008797627.1| 153 LFFLFTF 159
                                       7777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); 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:                         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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1255.62
//
Query:       gi|557694574|ref|YP_008797628.1|  [L=191]
Description: hypothetical protein CSUB_C1146 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   25.0   0.1    0.00035   20.4   0.1    2.4  2  MarR          MarR family
    3.9e-05   23.4   0.1    0.00011   22.1   0.1    1.7  1  MarR_2        MarR family
    6.3e-05   22.9   0.7    0.00013   21.9   0.1    1.9  2  HTH_Crp_2     Crp-like helix-turn-helix domain
     0.0013   18.8   0.8     0.0026   17.8   0.1    1.9  2  HTH_20        Helix-turn-helix domain
     0.0025   17.6   0.0     0.0043   16.9   0.0    1.4  1  TrmB          Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.022   14.3   0.0    1.4  1  HTH_47        winged helix-turn-helix
      0.012   15.5   0.8       0.82    9.5   0.1    2.3  2  BAT           GAF and HTH_10 associated domain
      0.013   16.1   0.0      0.037   14.6   0.0    1.8  1  Reductase_C   Reductase C-terminal
      0.013   15.3   0.5      0.087   12.7   0.1    2.3  3  HTH_5         Bacterial regulatory protein, arsR family
      0.013   15.8   0.1       0.03   14.7   0.1    1.5  1  Rrf2          Transcriptional regulator
      0.019   14.8   0.2      0.052   13.4   0.2    1.8  2  HTH_IclR      IclR helix-turn-helix domain
      0.026   14.4   0.1      0.048   13.5   0.1    1.5  1  HxlR          HxlR-like helix-turn-helix
      0.036   14.6   0.1      0.073   13.6   0.1    1.5  1  HTH_27        Winged helix DNA-binding domain
      0.038   13.7   0.0      0.075   12.7   0.0    1.4  2  DUF4423       Domain of unknown function (DUF4423)
      0.039   14.1   0.1       0.21   11.8   0.0    2.0  2  HTH_34        Winged helix DNA-binding domain
      0.067   13.2   0.0       0.13   12.2   0.0    1.5  1  HTH_45        Winged helix-turn-helix
      0.095   12.8   0.0       0.22   11.6   0.0    1.6  1  z-alpha       Adenosine deaminase z-alpha domain
       0.17   12.0   1.0       0.33   11.0   0.1    1.8  2  Replic_Relax  Replication-relaxation


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 !   20.4   0.1   3.5e-07   0.00035      16      49 ..      26      59 ..      15      62 .. 0.85
   2 ?    2.2   0.0      0.18   1.8e+02       5      21 ..     121     137 ..     119     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.5e-07
                                      TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 16 gplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      g+ s + + ++lg+++  ++r+l+rLek+Gl++R
  gi|557694574|ref|YP_008797628.1| 26 GEVSFTGMRRALGMHQEKLSRILRRLEKHGLVDR 59
                                      5577778999**********************99 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHSTTEEHH CS
                              MarR   5 qfviLrilyeqgplsvs 21 
                                         ++Lr++++ g+l ++
  gi|557694574|ref|YP_008797628.1| 121 DAHVLRWISQDGELQIT 137
                                       679*******9998876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   1.1e-07   0.00011      10      54 ..      16      60 ..      12      65 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-07
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      vL  L  + +++++ +   r+lg+ +  +sril+rL+++GLv r 
  gi|557694574|ref|YP_008797628.1| 16 VLKTLSTASDGEVSFTGMRRALGMHQEKLSRILRRLEKHGLVDRG 60
                                      66677777777899999*************************986 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   0.1   1.3e-07   0.00013      30      55 ..      36      62 ..      33      85 .. 0.89
   2 ?   -2.3   0.0       4.5   4.5e+03      11      23 ..     129     141 ..     122     160 .. 0.57

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.3e-07
                                      HTTSSHHHHHHHHHHHHHTTSEEET.E CS
                         HTH_Crp_2 30 mlGltretvsrilseLkreglisrg.r 55
                                       lG+++e +sril++L+++gl++rg +
  gi|557694574|ref|YP_008797628.1| 36 ALGMHQEKLSRILRRLEKHGLVDRGdK 62
                                      69*********************8633 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.5
                                       HCTTTC.EEEEEHH CS
                         HTH_Crp_2  11 aeragg.eielplt 23 
                                       +++ g+ +i+l+l 
  gi|557694574|ref|YP_008797628.1| 129 SQD-GElQITLRLK 141
                                       333.3345666554 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.1   2.6e-06    0.0026      15      57 ..      16      60 ..      15      64 .. 0.90
   2 ?   -2.5   0.1       5.6   5.6e+03      12      24 ..     144     156 ..     143     167 .. 0.50

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.6e-06
                                      HHHHH..STCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 15 ilraL..araegltaselaerldlskntlsyHLrvLeeagLvevv 57
                                      +l+ L  a++++++++   ++l++++  ls+ Lr Le++gLv++ 
  gi|557694574|ref|YP_008797628.1| 16 VLKTLstASDGEVSFTGMRRALGMHQEKLSRILRRLEKHGLVDRG 60
                                      677788899*********************************975 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.6
                                       HHHHHHHHSTCTT CS
                            HTH_20  12 RrrilraLaraeg 24 
                                       R+ i++ L+++++
  gi|557694574|ref|YP_008797628.1| 144 RLTIMSNLNERRA 156
                                       5566666622222 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   4.4e-06    0.0043       4      58 ..       7      63 ..       5      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.4e-06
                                      CHHHHHCCCHCHHHH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  4 lGLseyEakvYlaLl..klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      ++++e E  v ++L   + g+ + +   ++lg  + k  ++Lr+Le+ GlV+r ++ 
  gi|557694574|ref|YP_008797628.1|  7 IDFREDEEAVLKTLStaSDGEVSFTGMRRALGMHQEKLSRILRRLEKHGLVDRGDKG 63
                                      689999999999998889999999***************************997665 PP

>> HTH_47  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   2.2e-05     0.022      31      77 ..      11      58 ..       3      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                                      --HHHHHHHHHH.-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 31 qaemallwvLnl.aDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                      ++e+a+l+ L+  +DG+ s  ++   +g+  +++  i+r+L+++gl+ 
  gi|557694574|ref|YP_008797628.1| 11 EDEEAVLKTLSTaSDGEVSFTGMRRALGMHQEKLSRILRRLEKHGLVD 58
                                      56788999998637********************************85 PP

>> BAT  GAF and HTH_10 associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.037        37      11      33 ..      11      33 ..       7      36 .. 0.90
   2 ?    9.5   0.1   0.00083      0.82      27     134 ..      50     169 ..      45     175 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.037
                               BAT 11 rdeddvlvalaaeldcrvelegl 33
                                      +de++vl +l+++ d++v++ g+
  gi|557694574|ref|YP_008797628.1| 11 EDEEAVLKTLSTASDGEVSFTGM 33
                                      68999***************997 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00083
                               BAT  27 rveleglvprsdgevlvfftvdgadpee............vrdaaedldavedvrvvseeddgtlleltv.sgpsla 90 
                                       r+e  glv+r+d ++++ + ++    ++            v+d+   l +v+ ++    ++ ++l    v  +  ++
  gi|557694574|ref|YP_008797628.1|  50 RLEKHGLVDRGDKGYRLSGKARKLVNARgqervfvivdtrVEDVGLVLAGVTALHGRWVDEMRWL-GYSVeNDAHVL 125
                                       67777888888866666666666443333333333333334444444444433333333333333.33330467788 PP

                               BAT  91 stlaehGgtvrsaeaedgrarlvvevPpgadvRsvvealeeryp 134
                                       +++++ G    +++  +gr ++   + ++++vR+ +  l+ +y+
  gi|557694574|ref|YP_008797628.1| 126 RWISQDGELQITLRLKEGRLTIMSNLNERRAVRAALAILRKAYE 169
                                       89999999999******************************995 PP

>> Reductase_C  Reductase C-terminal
   #    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      11      81 ..     111     179 ..     106     182 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.7e-05
                                       EEEEE--TT--EEEEEEETTTTEEEE.EEEETTEEEEEEEES-HHHHHHHHHHTTTT----HHHHH-TTS-H CS
                       Reductase_C  11 lQiaGlatgadevvvRgdpeerafsv.fylrdgrlvaveavnrprdlmaarrliaagasvdpaalaDpavdL 81 
                                       ++ +G++ ++d  v+R   ++ ++ + + l++grl+ ++ +n+ r+++aa  ++ ++ ++   al D+   L
  gi|557694574|ref|YP_008797628.1| 111 MRWLGYSVENDAHVLRWISQDGELQItLRLKEGRLTIMSNLNERRAVRAALAILRKAYEL---ALIDDTSTL 179
                                       6789*************9765655553788*******************99999888765...455555555 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   0.1   8.7e-05     0.087      13      46 ..      25      58 ..      15      59 .. 0.84
   2 ?    0.0   0.0       0.8     8e+02       2      14 ..     142     154 ..     141     162 .. 0.86
   3 ?   -2.8   0.0       5.9   5.9e+03      36      42 ..     161     167 ..     156     167 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.7e-05
                                      TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 13 egelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +ge +++   ++lg+ q ++S+ L++L++ GLV+
  gi|557694574|ref|YP_008797628.1| 25 DGEVSFTGMRRALGMHQEKLSRILRRLEKHGLVD 58
                                      48888888889**********************6 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.8
                                       HHHHHHHHHHTTS CS
                             HTH_5   2 ptRlkILklLaeg 14 
                                       ++Rl I++ L+e+
  gi|557694574|ref|YP_008797628.1| 142 EGRLTIMSNLNER 154
                                       78******99985 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.9
                                       HHHHHHT CS
                             HTH_5  36 LkkLrea 42 
                                       L++Lr+a
  gi|557694574|ref|YP_008797628.1| 161 LAILRKA 167
                                       8999997 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1     3e-05      0.03      15      72 ..      18      71 ..      15      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3e-05
                                      HHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCC CS
                              Rrf2 15 lyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppe 72
                                        L++ +++e vs + + +  +++++ l++il++L+k+glv   rG   GyrL+ +++
  gi|557694574|ref|YP_008797628.1| 18 KTLSTASDGE-VSFTGMRRALGMHQEKLSRILRRLEKHGLVD--RGD-KGYRLSGKAR 71
                                      5677777777.9999999**********************96..999.6899987766 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 ?   13.4   0.2   5.2e-05     0.052       8      50 ..      16      59 ..      15      61 .. 0.86
   2 ?   -2.9   0.0       6.3   6.3e+03       6      16 ..     122     132 ..     117     137 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.2e-05
                                      HHCT-CTTBSS.-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  8 iLdalaeapqe.ltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +L+ l++a  + ++++ + r++g++  + +R+L+ L+++G+v +
  gi|557694574|ref|YP_008797628.1| 16 VLKTLSTASDGeVSFTGMRRALGMHQEKLSRILRRLEKHGLVDR 59
                                      7777777766637*****************************86 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.3
                                       HHHHCT-CTTB CS
                          HTH_IclR   6 laiLdalaeap 16 
                                       +++L+ +++ +
  gi|557694574|ref|YP_008797628.1| 122 AHVLRWISQDG 132
                                       66777776654 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   4.8e-05     0.048      12      51 ..      21      59 ..      15      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.8e-05
                                      HHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEE CS
                              HxlR 12 vellkgkkRfselkralpkisqkmLaqrLreLeqdglier 51
                                       +  +g+  f+ ++ral ++ q+ L++ Lr+Le++gl++r
  gi|557694574|ref|YP_008797628.1| 21 STASDGEVSFTGMRRAL-GMHQEKLSRILRRLEKHGLVDR 59
                                      566789999********.788999***************9 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   7.4e-05     0.073      11      64 ..      19      66 ..      10      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.4e-05
                            HTH_27 11 lir.hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrl 64
                                      ++    +++++ +  +++l + +   s +l++L+++GLv       dr++k +rl
  gi|557694574|ref|YP_008797628.1| 19 TLStASDGEVSFTGMRRALGMHQEKLSRILRRLEKHGLV-------DRGDKGYRL 66
                                      555456777777888999*********************.......455555555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.5e-05     0.075      24      79 ..      15      67 ..       9      80 .. 0.87
   2 ?   -3.7   0.0       8.5   8.4e+03     116     132 ..     153     169 ..     148     171 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.5e-05
                           DUF4423 24 pvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqt 79
                                       v+ +l  + d++ +   + ++l+  + +e+ +++l++L+k gl+++  +  yr +
  gi|557694574|ref|YP_008797628.1| 15 AVLKTLSTASDGEVSFTGMRRALG--MHQEKLSRILRRLEKHGLVDRGDK-GYRLS 67
                                      67888999999999**********..*********************998.77765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8.5
                           DUF4423 116 eRdissltlaiskedye 132
                                       eR+     lai +++ye
  gi|557694574|ref|YP_008797628.1| 153 ERRAVRAALAILRKAYE 169
                                       55555555555555555 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 ?   11.8   0.0   0.00021      0.21       4      45 ..      15      58 ..      14      73 .. 0.89
   2 ?   -0.4   0.1       1.4   1.4e+03       2      15 ..     144     157 ..     143     171 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                            HTH_34  4 avlsyLas..vdeadfvelkealeatdgnLsvhlkkLekagYie 45
                                      avl +L++  + e++f+ ++ al++ + +Ls  l+ Lek g + 
  gi|557694574|ref|YP_008797628.1| 15 AVLKTLSTasDGEVSFTGMRRALGMHQEKLSRILRRLEKHGLVD 58
                                      578888877699****************************9875 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                            HTH_34   2 RlavlsyLasvdea 15 
                                       Rl ++s L++ + +
  gi|557694574|ref|YP_008797628.1| 144 RLTIMSNLNERRAV 157
                                       89999999985543 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.13       8      67 ..      16      75 ..      10      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            HTH_45  8 iadILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelle 67
                                      ++  L+  s+ge + T +  +  +  + l++ L  L + gl++  ++ Y+l  k ++l++
  gi|557694574|ref|YP_008797628.1| 16 VLKTLSTASDGEVSFTGMRRALGMHQEKLSRILRRLEKHGLVDRGDKGYRLSGKARKLVN 75
                                      66678888999999999999*********************************9999876 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 ?   11.6   0.0   0.00022      0.22       2      55 ..       9      61 ..       8      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00022
                                      HHHHHHHHHHHHHHC-TTCECCHHHHHHHHCC-HHHHHHHHHHHHHTTSEEEES CS
                           z-alpha  2 aqeqaekilelLeelgekkaatalalergLstpkreiNrvLydlerkgkvyred 55
                                       +e++e +l+ L   ++++ +      r L++      r+L +le+ g v r+d
  gi|557694574|ref|YP_008797628.1|  9 FREDEEAVLKTLSTASDGE-VSFTGMRRALGMHQEKLSRILRRLEKHGLVDRGD 61
                                      589************9766.444555566666678899***********99987 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00034      0.33      16      50 ..      34      67 ..      29      85 .. 0.79
   2 ?   -1.1   0.1       1.7   1.7e+03      19      37 ..     149     167 ..     142     178 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00034
                      Replic_Relax 16 arllfashratarrrLarLrelgllsrlrkrvgga 50
                                      +r+l +++++ ++r+L+rL+++gl++r +k ++  
  gi|557694574|ref|YP_008797628.1| 34 RRALGMHQEK-LSRILRRLEKHGLVDRGDKGYRLS 67
                                      6778888888.****************88874433 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                      Replic_Relax  19 lfashratarrrLarLrel 37 
                                        + ++r+ +r +La+Lr+ 
  gi|557694574|ref|YP_008797628.1| 149 SNLNERRAVRAALAILRKA 167
                                       4556666688888888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 00:00:00.39
# Mc/sec: 1476.88
//
Query:       gi|557694575|ref|YP_008797629.1|  [L=187]
Description: 20S proteasome beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-47  160.8   0.1    2.8e-47  160.6   0.1    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 !  160.6   0.1   1.6e-51   2.8e-47       5     188 ..       2     180 ..       1     182 [. 0.92

  Alignments for each domain:
  == domain 1  score: 160.6 bits;  conditional E-value: 1.6e-51
                                       -EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCH CS
                        Proteasome   5 ttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpipv 81 
                                       tt+vG+k+ dgvvla+d+ra++g  ++sk+  +Ki+k+dd +++a+aGl +Da +lv+ +rae +l  lr g+p++v
  gi|557694575|ref|YP_008797629.1|   2 TTIVGLKAVDGVVLASDRRASKGFFIASKT-TQKIMKVDDSLAIAVAGLLSDAVYLVNVVRAERKLIALRRGYPLSV 77 
                                       8**********************9996666.6********************************************* PP

                                       HHHHHHHHHHHHHHHHHCTTT...TTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHS CS
                        Proteasome  82 erlvarvaaklqaytqrsgrr...pfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyk 155
                                              ++kl +++++sg r   p++++l++agvd+eg p++++ d+sGs+++e+ +v+ Gsgs +a+++le++y+
  gi|557694575|ref|YP_008797629.1|  78 A-----ESSKLISNLFYSGLRnyiPYYAELIVAGVDDEG-PHVFSSDMSGSMVAEE-FVSSGSGSPVAYGVLESLYT 147
                                       *.....666666666666555122669*********888.***************6.******************** PP

                                       TTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEE CS
                        Proteasome 156 edltleeavelavkalkealerdklsgknieva 188
                                       + l+leea  +avka+++a++rd  sg++++v 
  gi|557694575|ref|YP_008797629.1| 148 PGLKLEEARAIAVKAVEAAMQRDPGSGNGVDVL 180
                                       ******************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1573.84
//
Query:       gi|557694576|ref|YP_008797630.1|  [L=229]
Description: 20S proteasome alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-37  129.0   0.0    1.8e-37  128.7   0.0    1.1  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 !  128.7   0.0   9.8e-42   1.8e-37       2     174 ..      29     194 ..      28     202 .. 0.95

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 9.8e-42
                                       HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                        Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                        +G  ++G+++  ++vla+  + t   kl+++s  +K+f +ddh+gv+ +G ++D   +v+++r eaq++rl ++  
  gi|557694576|ref|YP_008797630.1|  29 MRGAISIGLRFPRYAVLASMVKPT--RKLMKPS--DKVFIVDDHVGVTGSGYISDLYRIVDHMRIEAQRHRLLFDAA 101
                                       578999*************99999..***8888..7***************************************** PP

                                       TCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHS CS
                        Proteasome  79 ipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyk 155
                                       + v +lv +v+ + ++yt++  +rp gv+++i+gvd+ g  +Lyq+dpsG+ +  + a+a G +s+ a+ +le+ey+
  gi|557694576|ref|YP_008797630.1| 102 VDVGTLVDSVSGYFHGYTLYP-VRPQGVAVIIGGVDKLG-VQLYQVDPSGTAFNGD-AFALGVNSDKAIDILENEYR 175
                                       *********************.**************888.8**************6.*****99************* PP

                                       TTBSHHHHHHHHHHHHHHH CS
                        Proteasome 156 edltleeavelavkalkea 174
                                       +d++l+ea+ l+ ++++ +
  gi|557694576|ref|YP_008797630.1| 176 PDMSLDEALNLITSVVERT 194
                                       ************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       277  (0.0154498); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1930.87
//
Query:       gi|557694577|ref|YP_008797631.1|  [L=77]
Description: regulatory protein, AsnC/Lrp family [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-13   49.8   0.9    2.6e-13   49.7   0.9    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.024   14.6   0.0    1.2  1  GYD             GYD domain
      0.057   13.8   0.2      0.081   13.3   0.2    1.3  1  DUF641          Plant protein of unknown function (DUF641)


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 !   49.7   0.9   4.4e-17   2.6e-13       1      73 [.       6      75 ..       6      77 .] 0.97

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 4.4e-17
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                      vl+++e g+    ee+  +l+++ +++e+y+v G yd+++kv +  +e l ++++  +++l+ v++t t++v 
  gi|557694577|ref|YP_008797631.1|  6 VLINTEIGA---EEEVVNELKKISYIKEAYVVYGVYDIVAKVEADTMEKLKEVVSWSIRRLEKVRSTLTMLVV 75
                                      789999999...**********************************************************996 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     4e-06     0.024      37      78 ..      28      70 ..       7      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-06
                               GYD 37 leslyatlGeyDvvvivEapDdetaaal.slalaasGtvrtet 78
                                      +++ y++ G yD+v+ vEa+  e+   + s ++++  +vr+++
  gi|557694577|ref|YP_008797631.1| 28 IKEAYVVYGVYDIVAKVEADTMEKLKEVvSWSIRRLEKVRSTL 70
                                      6899****************99998764267777777777754 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 ?   13.3   0.2   1.4e-05     0.081      42      67 ..      14      39 ..      12      73 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                            DUF641 42 ADkavvseLkklselkrlyrkkqkkk 67
                                      A + vv+eLkk+s +k+ y+     +
  gi|557694577|ref|YP_008797631.1| 14 AEEEVVNELKKISYIKEAYVVYGVYD 39
                                      8899***************9876544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); 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:                         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 0.20s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 669.25
//
Query:       gi|557694578|ref|YP_008797632.1|  [L=218]
Description: beta-lactamase domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  101.2   0.8    8.4e-29  101.0   0.8    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
      3e-05   23.6   0.0      4e-05   23.2   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.083   11.4   0.0       0.12   10.9   0.0    1.2  1  Cytochrom_D1   Cytochrome D1 heme 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 !  101.0   0.8   1.4e-32   8.4e-29       2     197 .]      11     192 ..      10     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 1.4e-32
                                       CCCSSEEEEEE..ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCE CS
                       Lactamase_B   2 gpdpvnsylie..gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgava 76 
                                       gp+++nsy++      ++++iD+G ++   ++      l    ++v av  TH+H+DH+ ++++l++a ++p ++++
  gi|557694578|ref|YP_008797632.1|  11 GPLSSNSYIVYdeETREAVIIDAGDDAWLLLET-----LQERRLRVNAVYATHGHFDHVMAVDDLKQALKIPFYIHR 82 
                                       7999*******76669*********99999998.....7************************************** PP

                                       HHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS CS
                       Lactamase_B  77 eeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall 153
                                       ++++ l m  +++ +  +      +++++pd ++e+++++  g+++l+v+++pgh++g+++++  g++vlf+GD+l+
  gi|557694578|ref|YP_008797632.1|  83 LDLEILSMAREMTRRFLGI---DVGDPPSPDGFLEDGQTIQVGGKSLKVIHTPGHSPGSVCFY--GDGVLFSGDLLF 154
                                       *************999986...48888888888888888888888888888888877777766..899********* PP

                                       SHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
                       Lactamase_B 154 agetgridltlrgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                                        g+ gr+d        + +s ++ + + l+k+++l+++v v+ gH
  gi|557694578|ref|YP_008797632.1| 155 MGSVGRTDA-------PGGSAQQLTQSILEKVFKLPDDVKVYpGH 192
                                       *********.......44455555555566666999999776699 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 !   23.2   0.0   6.7e-09     4e-05       3     102 ..      29     125 ..      27     162 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.7e-09
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEE......HHHHHHCCTT CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyap......kgvlavlean 73 
                                       ++iDag d     l +l   + r+   +++aV  th+H+DH+  +++l++    k+p+y +      ++++++++++
  gi|557694578|ref|YP_008797632.1|  29 VIIDAGDDAWLL-LETL---QERRL--RVNAVYATHGHFDHVMAVDDLKQAL--KIPFYIHrldleiLSMAREMTRR 97 
                                       789999994434.3333...12333..89*********************43..49999884443333333333333 PP

                                       CGHHHCHTT...TTEEEEEE-TTSEEEECSTT CS
                     Lactamase_B_2  74 fvylaleee...pavnvheldwgesfelgdgg 102
                                       f  +    +   p+ +   l+ g+++++g+  
  gi|557694578|ref|YP_008797632.1|  98 FLGI----DvgdPPSPDGFLEDGQTIQVGGKS 125
                                       3322....223334555556666666666444 PP

>> Cytochrom_D1  Cytochrome D1 heme domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0     2e-05      0.12     122     156 ..      44      78 ..      13      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2e-05
                                       SSSS---EEEEEE-SSSSEEEEEETTTTEEEEEE- CS
                      Cytochrom_D1 122 vderesRVaaivasperpefvvnlkdtgeillvdy 156
                                        +er  RV a++a++++ ++v+++ d +++l +++
  gi|557694578|ref|YP_008797632.1|  44 LQERRLRVNAVYATHGHFDHVMAVDDLKQALKIPF 78 
                                       466899************************99988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       280  (0.0156172); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 00:00:00.43
# Mc/sec: 1528.29
//
Query:       gi|557694579|ref|YP_008797633.1|  [L=231]
Description: uracil-DNA glycosylase superfamily protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  110.7   0.0    7.7e-32  110.4   0.0    1.1  1  UDG       Uracil DNA glycosylase superfamily


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 !  110.4   0.0   4.3e-36   7.7e-32       1     147 [.      45     218 ..      45     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 110.4 bits;  conditional E-value: 4.3e-36
                                       HHC-CTT-SEEEEESSTCHH.HHHHSSSS.-.STT--HHHHHHHCCCCCCCHHG........CTEEEEESSS....S CS
                               UDG   1 pgegppdakvvivGeaPgae.edatglpFsg.ragnllrkllneaglkrdlese........qgvyitnvvkcrppg 67 
                                       pg+g+  a+v+++G aP a+ +++tg++F+g  +g++l ++l++ag++++  s         ++vyit vv+c+pp 
  gi|557694579|ref|YP_008797633.1|  45 PGFGDVGARVLVLGLAPAAHgGNRTGRMFTGdSSGDTLVRALHRAGFANMGRSIsindglvlKDVYITAVVRCAPPD 121
                                       79*****************************9999**************66555*********************** PP

                                       ECGCTTCCCCTCCHHHHHHHHHHHHSSE.EEEESHHHHHH...........HHHHS....CESCCCSCT........ CS
                               UDG  68 nrdtptsaeikacaplleeeiellkprl.ivllGktaakall.........geklg....klrgklleak....... 123
                                       n+  p ++e+++c p+l ee++ l++ + +v+lG+ a+++++             g    + +g++++ +       
  gi|557694579|ref|YP_008797633.1| 122 NK--PAKQEVENCLPYLIEELRMLENVVvVVALGRFAFETFFrlmrrmnayS---GriprFRHGAVYRLNgsfngkp 193
                                       99..*********************6666***********966666544431...0233345577777757788999 PP

                                       .SEEEEES-SSTTTTTTTTSHHHHH CS
                               UDG 124 .irvlplphPsplnrnffksnpelk 147
                                        ++v++++hPs +n+++++ +  + 
  gi|557694579|ref|YP_008797633.1| 194 lPTVIASYHPSRQNTSTGRLTQRMI 218
                                       ***************9877776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1711.01
//
Query:       gi|557694580|ref|YP_008797634.1|  [L=388]
Description: major facilitator superfamily MFS [Candidatus Caldiarchaeum subterraneum]
Scores for 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-35  121.4  53.5    1.1e-30  106.8  36.3    2.1  2  MFS_1       Major Facilitator Superfamily
    0.00029   19.4  26.7     0.0026   16.2  26.7    2.2  1  MFS_3       Transmembrane secretion effector
  ------ inclusion threshold ------
      0.014   14.3  25.4       0.12   11.2  15.9    2.1  2  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 !  106.8  36.3   1.9e-34   1.1e-30       1     317 [.       9     303 ..       9     304 .. 0.85
   2 !   22.0  15.5   1.1e-08   6.4e-05      91     166 ..     292     367 ..     288     387 .. 0.89

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 1.9e-34
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       l+ a+f s++++ +++p++ l+ a +lg++p ++g+++++ al+a+v+ +p++ ls r+G rr++++g++++++g++
  gi|557694580|ref|YP_008797634.1|   9 LWTAIFSSMFSAQMILPVIGLYAAVELGADPFTVGTIYGTSALTAFVSRIPAAMLSSRIGTRRIMVCGMAASSAGSI 85 
                                       68899**********************************************************************55 PP

                             MFS_1  78 lllfasslw.lllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllasslgWra 152
                                       l  fa+  +  ++v+ +l Glg++++fpa+++ + + +   e  ++ +g++ +g +lG++lgp++g++ +s+lg+r 
  gi|557694580|ref|YP_008797634.1|  86 LYGFAAE-PlHMIVGSFLRGLGSAFFFPAALTSLYEEAGNgEGDPKSLGYMLTGPALGMALGPVFGAASLSLLGYRP 161
                                       5558544.548*************************99999************************************ PP

                             MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltl 229
                                       +fy +a++sl++  l  + +  ++++ + + ++           ++ +k+ll +++  +ll++ +l+  ++ ++ ++
  gi|557694580|ref|YP_008797634.1| 162 TFYTAAAISLVG--L--ATI--SATKIQIPDERA----------TS-FKSLLEKRFT-SLLASRFLVNYVTGTIAAF 220
                                       ************..5..233..222222222222..........24.7778888855.588888888889999**** PP

                             MFS_1 230 lplylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll 305
                                       lpl+++  lg++     ++ll+ ++a+ +++++++ g+ +++l ++++  l+ + ++l+++++al   +     ++l
  gi|557694580|ref|YP_008797634.1| 221 LPLMAKLLLGYDeP--VVLLLFTAAAFTNLFSRVFMGAAAKKLDAQNYVALGSFTVSLSSIMFALGHDI----SVWL 291
                                       ************55..55555************************888888888888888888887777....5555 PP

                             MFS_1 306 vlvliGfglgfv 317
                                       +++++G+g+g++
  gi|557694580|ref|YP_008797634.1| 292 GVLVYGLGMGIF 303
                                       667778887775 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.1e-08
                             MFS_1  91 lrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafv 166
                                       + ++ Glg+g+++ ++++++  ++p+  r+++++l+++++ +G  +g  ++g+l+s +g+  vf ++a+v++ ++ 
  gi|557694580|ref|YP_008797634.1| 292 GVLVYGLGMGIFVLGSVYMTGLLVPPAMRTMGFALITLMIDMGNSVGNFVSGVLLSVGGFAEVFAVAAAVGAAGLF 367
                                       55689*******************************************************************9943 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2  26.7   4.4e-07    0.0026      15     400 ..       9     382 ..       6     387 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.4e-07
                             MFS_3  15 iWiaslvsnlGt.liqevaasWlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsv 90 
                                       +W+a   s + + +i  v   +   ++ a p +v  +  +++L  f+  i+a  l+  +  R++++ +++   ++s+
  gi|557694580|ref|YP_008797634.1|   9 LWTAIFSSMFSAqMILPVIGLYAAVELGADPFTVGTIYGTSALTAFVSRIPAAMLSSRIGTRRIMVCGMAASSAGSI 85 
                                       5666666655431445555556667889999**********************************999776666666 PP

                             MFS_3  91 lltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkr.rdvpaAvaLnsvginiaRsvGPAlgGvlvaav 166
                                       l          +p  +++ ++l g+G+a+  Pa   s+ e   + +  p+       g  +  + GP  g   ++++
  gi|557694580|ref|YP_008797634.1|  86 LYGFA-----AEPLHMIVGSFLRGLGSAFFFPAALTSLYEEAGNgEGDPKSLGYMLTGPALGMALGPVFGAASLSLL 157
                                       54333.....47999999**************999888776655166788899999999999*************** PP

                             MFS_3 167 GaalafavnalsylalivallrwkrevrksslprEkllealraglRftaasreikavlvRaalFglsasavlaLLPl 243
                                       G   +f  +a   l+ ++++ ++k +++ ++  +   +++l +  Rft         l+  +l    + ++ a LPl
  gi|557694580|ref|YP_008797634.1| 158 GYRPTFYTAAAISLVGLATISATKIQIPDERATS---FKSLLE-KRFTS-------LLASRFLVNYVTGTIAAFLPL 223
                                       ******9999999999*****9999988876654...333332.47764.......57777888889999******* PP

                             MFS_3 244 vardqldgdalvyGillgalGvGAilgalllsrLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaa 320
                                       +a+  l+ d  v  +l++a     +++ +++    ++l++++ v+l ++++ l  ++ al +++ v + vl+ g + 
  gi|557694580|ref|YP_008797634.1| 224 MAKLLLGYDEPVVLLLFTAAAFTNLFSRVFMGAAAKKLDAQNYVALGSFTVSLSSIMFALGHDISVWLGVLVYGLGM 300
                                       ************9******************************************************99***99999 PP

                             MFS_3 321 WitalstlnvavqlavPrWvvgRalavYltvlaGglaaGsllWGavaealsvtlaLlaaaaal...llaaaillllk 394
                                        i +l ++  +  l+vP  +++ ++a+   +++ g + G ++ G++ +  + +    +aaa     l + +i+ + +
  gi|557694580|ref|YP_008797634.1| 301 GIFVLGSVYMTG-LLVPPAMRTMGFALITLMIDMGNSVGNFVSGVLLSVGGFAEVFAVAAAVGaagLFVDLISRRWP 376
                                       9****9998875.7778889*************************99988877766666554300144555666677 PP

                             MFS_3 395 lpelea 400
                                       lp  ++
  gi|557694580|ref|YP_008797634.1| 377 LPYERQ 382
                                       776655 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 ?    8.7   1.9   0.00011      0.68      20     334 ..      25     114 ..       8     125 .. 0.63
   2 ?   11.2  15.9     2e-05      0.12     155     383 ..     131     355 ..     130     357 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00011
                        MFS_1_like  20 PYltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesk 96 
                                       P +++                                                                        
  gi|557694580|ref|YP_008797634.1|  25 PVIGL------------------------------------------------------------------------ 29 
                                       33333........................................................................ PP

                        MFS_1_like  97 levsvaqdvdaektfwilfllvvlasfflaailvlldaatlkelgedrkdyGrqrlfGsvGyaifafitGilidhys 173
                                                                                                                    
  gi|557694580|ref|YP_008797634.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                        MFS_1_like 174 vnllpysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienFlfl 250
                                                                                                                    
  gi|557694580|ref|YP_008797634.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                        MFS_1_like 251 YL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgis 326
                                       Y   elga  +++G++    ++   +  + a  l  ++G +++++ ++ a  +  +ly++  ++  +++  +L g+ 
  gi|557694580|ref|YP_008797634.1|  30 YAaVELGADPFTVGTIYGTSALTAFVSRIPAAMLSSRIGTRRIMVCGMAASSAGSILYGFAAEPLHMIVGSFLRGLG 106
                                       33335577777777777777777777777777777777777777777777777777777777777777777777777 PP

                        MFS_1_like 327 fgllwaaa 334
                                        + ++ aa
  gi|557694580|ref|YP_008797634.1| 107 SAFFFPAA 114
                                       66666665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 2e-05
                        MFS_1_like 155 svGyaifafitGi....lidhysvnllpysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpev 227
                                       s+Gy+++ +++G+    ++   s +ll+y+  +y++aa+ ++ l+ +        ++k+++   +   ++ l +++ 
  gi|557694580|ref|YP_008797634.1| 131 SLGYMLTGPALGMalgpVFGAASLSLLGYRPTFYTAAAISLVGLATI-------SATKIQIPDERATSFKSLLEKRF 200
                                       6788887766555111177888999999***********99999983.......3445555555556677888999* PP

                        MFS_1_like 228 iifllvalilgmswgiienFlflYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilr 303
                                         +l+  +++  + g i +Fl l     lg+ + ++  l +  ++ ++   +f+    +kl +++ + ++ +++ l 
  gi|557694580|ref|YP_008797634.1| 201 TSLLASRFLVNYVTGTIAAFLPLMAkLLLGYDEPVVLLLFTAAAFTNLFSRVFMGAAAKKLDAQNYVALGSFTVSLS 277
                                       ********************998885579********************************************9999 PP

                        MFS_1_like 304 fllyaii..enawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlks 378
                                        ++ a+   +++wl +   + +g+ +g++ +  v     ++p+ +++ g +l++ + + +G+ +G++++G+l    +
  gi|557694580|ref|YP_008797634.1| 278 SIMFALGhdISVWLGV---LVYGLGMGIFVLGSVYMTGLLVPPAMRTMGFALITLM-IDMGNSVGNFVSGVLLSVGG 350
                                       9999999655666655...46999***99777777777899***********9877.89************998777 PP

                        MFS_1_like 379 aiflF 383
                                        + +F
  gi|557694580|ref|YP_008797634.1| 351 FAEVF 355
                                       77666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2769.38
//
Query:       gi|557694581|ref|YP_008797635.1|  [L=358]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   24.3  27.3    2.3e-05   24.3  27.3    2.8  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 ?   -3.4   0.1      0.35   6.4e+03     136     145 ..      10      19 ..       5      27 .. 0.49
   2 !   24.3  27.3   1.3e-09   2.3e-05       1     174 [.      59     235 ..      58     274 .. 0.71
   3 ?   -7.2  10.5         1   1.8e+04       4      72 ..     277     344 ..     271     350 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.35
                              GT87 136 alvltalpll 145
                                       a++++++++l
  gi|557694581|ref|YP_008797635.1|  10 AVAAAVVSWL 19 
                                       2222222333 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 1.3e-09
                              GT87   1 FtYPPfaallfaplallp...yglalalwallnlaalllalrlllrrlgralasavalalllaalalepvlstlgfG 74 
                                       F YPP+a ll++   ll    ++  ++++ ll+l a++++   l r+        + l+    ++ l p +   g+ 
  gi|557694581|ref|YP_008797635.1|  59 FEYPPTACLLVYASRLLGgvsLTGYYVAFSLLSLPAFIAISICLSRL--------AGLPG--SFFILVPSMVVYGVY 125
                                       56**********99999955455555555666665555555555554........33444..489999**9****** PP

                              GT87  75 qinllllllvlldllllrrrrpllaGlliGlaaaiKltPalfllylll.rrrwralaaaaatalvltal...pllll 147
                                       +++ ++++ ++++ll+   +r ++a++l+Gl++ +Kl+ +l+l +l+l +++ r +a +++ +++ ++    p+ll+
  gi|557694581|ref|YP_008797635.1| 126 NFDHFFTAFLAAALLMQTMGRWRAAAVLLGLGFSVKLFTVLLLPLLMLeTGDKRKAAETGLLFAAGALPtwvPILLI 202
                                       ******************99999***************999999777779999999999766666666546688888 PP

                              GT87 148 ppssleyfle.tlfdtseri.......aedvgnqs 174
                                        p  l  f++                   d ++qs
  gi|557694581|ref|YP_008797635.1| 203 NPGWLFEFVSfHASWGL--EnswlvwlSNDPFSQS 235
                                       76666666652221111..1224445555555555 PP

  == domain 3  score: -7.2 bits;  conditional E-value: 1
                              GT87   4 PPfaallfaplallpyglalalwallnlaalllalrlllrrlgralasavalalllaalalepvlstlg 72 
                                        P ++l ++p+++    l ++l ++ ++ +++l+++ l+    +  ++   + +ll a+al++++ t+ 
  gi|557694581|ref|YP_008797635.1| 277 TPQMTLWLIPFTASFTRLWVWLPLFESANVAILFTWFLTDT-PTLPWTPPQTMALLRAIALSAMWATVY 344
                                       56666777777443333333333333333334444444333.333377777777788999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); 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: 00:00:00.42
# Mc/sec: 2553.62
//
Query:       gi|557694582|ref|YP_008797636.1|  [L=373]
Description: threonine synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  223.4   0.0    4.6e-66  223.2   0.0    1.0  1  PALP           Pyridoxal-phosphate dependent enzyme
     0.0028   18.0   0.0      0.022   15.2   0.0    2.1  2  NAD_binding_7  Putative NAD(P)-binding


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 !  223.2   0.0   5.1e-70   4.6e-66       1     294 []      65     360 ..      65     360 .. 0.94

  Alignments for each domain:
  == domain 1  score: 223.2 bits;  conditional E-value: 5.1e-70
                                       GGGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT.TTTSEEEEEBSSHHHHHHHHHHHH CS
                              PALP   1 ltlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg.tgaktvveassGNhgralAaaaal 76 
                                       +tlg+g TPlv++p  +      +++KlE+lnptgSfKdRg + ++++l++     ++v+e ssGN+g+++Aa++a 
  gi|557694582|ref|YP_008797636.1|  65 VTLGEGHTPLVHAPTPN------IYFKLEYLNPTGSFKDRGTAAMMTSLRNIlGNLRGVCEDSSGNAGASVAAYCAF 135
                                       5899***********76......*************************88887788********************* PP

                                       HT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHH CS
                              PALP  77 lGlkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileq 153
                                       +Gl+++i+   ++ +ekv++ r++Gae+++v+g+ +  ++ a ++a++ +g ++v ++ np+ ieg++t+++Ei+eq
  gi|557694582|ref|YP_008797636.1| 136 MGLPCVIFGGGSMVSEKVLQVRMYGAELRLVEGSRQKVEEEAVNYAER-NGLLYVGHTWNPYFIEGMKTVAYEIAEQ 211
                                       **********************************9999999*******.**************************** PP

                                       TT.TTEEEEEEE-SSSHHHHHHHHHHHH......HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCST CS
                              PALP 154 lg.gkpdavvvpvGgGgliaGiaaglke......rrpd..vrvigvepegsdalarslragrrvtvpvsdtiadgla 221
                                       +g + pd +++pv+ G l+ G+ +g+++         +  +r+++v+p+ +++l++++++ ++ +   + + ad+l 
  gi|557694582|ref|YP_008797636.1| 212 TGwNPPDIIYLPVSAGTLLLGLIKGFRDmveagvL--EkiPRIVAVQPQLNAPLYAAYKKLDPAPFLLGGSVADALT 286
                                       ****************************8865544..056******************88888888888******** PP

                                       CS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 222 vg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                              ++ +++l+++++++  vs+e++++a ++la  +g  +e ssa+a+aa++ r ++ ++ ++++++iltg
  gi|557694582|ref|YP_008797636.1| 287 QTnpPRLRQMVDVLEAFGGDVEVVSEEDIIKAHKQLA-WAGFYTEFSSATAYAAVRRRLDEIVSSQEKILIILTG 360
                                       *9777777899999***********************.*****************888888889999******98 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 !   15.2   0.0   2.5e-06     0.022       4      54 ..     134     184 ..     131     268 .. 0.81
   2 ?    0.6   0.0     0.088   7.9e+02      26      51 ..     300     325 ..     293     364 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-06
                     NAD_binding_7   4 dlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee 54 
                                        + g  ++++GgG++  +kv ++  +ga++ +v    ++  ee v++ae++
  gi|557694582|ref|YP_008797636.1| 134 AFMGLPCVIFGGGSMVSEKVLQVRMYGAELRLVEGSRQKVEEEAVNYAERN 184
                                       567889***************************999777777888887765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.088
                     NAD_binding_7  26 lleagakvtvvapevkeeleelvkla 51 
                                       l ++g +v vv++e   ++++++ +a
  gi|557694582|ref|YP_008797636.1| 300 LEAFGGDVEVVSEEDIIKAHKQLAWA 325
                                       5568899999*999533333444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2793.86
//
Query:       gi|557694583|ref|YP_008797637.1|  [L=366]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   67.8  59.0    5.4e-18   65.0  45.7    2.0  2  MFS_1     Major Facilitator Superfamily
     0.0028   16.6   0.2     0.0028   16.6   0.2    3.5  3  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
       0.14   11.9   1.4         26    4.7   1.6    2.7  2  B12D      NADH-ubiquinone reductase complex 1 MLRQ subunit
        2.2    6.5  12.0      0.045   12.0   1.7    2.5  2  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 !   65.0  45.7   1.2e-21   5.4e-18       2     326 ..       8     307 ..       7     326 .. 0.79
   2 !    6.3   9.2    0.0009         4     121     167 ..     316     362 ..     311     365 .. 0.92

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 1.2e-21
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltl.yalgaavaslplGrlsdrfGrrr.vlllglllfalgl 76 
                                       + + +l+++a +  + ++p + a +l++s +++g+l+++   + ++++s++++++  r+ r + +l  +++++ +++
  gi|557694583|ref|YP_008797637.1|   8 WTGSLLMGFALMSMMQNAP-IRAVELQASFTQVGFLMGFiRNFPYVLLSVFTMAVLLRM-RWSlLLPSSAIFMTVSS 82 
                                       6788899999999999999.78889**********77766999****************.55556666666666667 PP

                             MFS_1  77 llllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWra 152
                                       ll+++ +++  +++++ +++G+++ ++fp g +++a  fpk er ra++l+ +++s+G+++g l++g las lg + 
  gi|557694583|ref|YP_008797637.1|  83 LLMWL-ANSLdIVFFSQLVMGVAMFLFFPCGESIVANSFPKGERLRAFSLFLSAVSMGFLIGSLVSGTLASILGLQN 158
                                       77777.89999****************************************************************** PP

                             MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltl 229
                                        f+i a+vs  a+    +l  ++p++++   ++ +     p + ++        p    +++a+ +f ++++++++ 
  gi|557694583|ref|YP_008797637.1| 159 QFLISAAVSSAAAP---VLAKANPSNPEITISRNK----HPLKSFE--------P----IIYAAPYF-VVLASTYAV 215
                                       ************88...999999999999999999....6666666........4....55555555.69999**** PP

                             MFS_1 230 lplylqevlglsglllaglllallalvgailallagrlsdrlgr...rrrlllallllllaalglallavtssavll 303
                                       lp y     gl+  l +g  + ++ l+ga  ++l+++l+ rl++   +  l++  ++++++al+l++l+++  ++++
  gi|557694583|ref|YP_008797637.1| 216 LPGY-LVLEGLT-ELDVG--FLFFTLIGA--RVLTSYLLSRLKPssaKLLLTVLSIVTAVWALALVYLPAS--TAAY 284
                                       ****.*******.8****..999999995..88********988655555566666666666666666666..4444 PP

                             MFS_1 304 llvlvliGfglgfvfpsllalas 326
                                       + +++ +G +++++++  l+l+s
  gi|557694583|ref|YP_008797637.1| 285 IPLMIPAGATVSIAYVYTLYLVS 307
                                       43444455555555444443333 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0009
                             MFS_1 121 raigllsagfslGailgpllggllasslgWravfyilaivsllafvl 167
                                       + ig++ a ++  +++gp+++g+la+  g++av +++ + +l+++ l
  gi|557694583|ref|YP_008797637.1| 316 FLIGMFEALIGSCFLVGPVVAGFLADMCGFSAVLLFFSLSMLVGAFL 362
                                       679999999999******************************99775 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   1.5     0.015        66      76     116 ..      66     105 ..      53     110 .. 0.83
   2 !   16.6   0.2   6.3e-07    0.0028      48      97 ..     129     178 ..     115     188 .. 0.87
   3 !    3.5   4.9    0.0059        27      42      93 ..     312     363 ..     288     366 .] 0.76

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.015
                                       HHHHHH..HHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHH CS
                          Sugar_tr  76 kkslli..aavlfvigavlqaaakgknsvevlivgRvlvGigv 116
                                       ++sll   +a+++ ++++l+ +a+   s+ +++++++++G+++
  gi|557694583|ref|YP_008797637.1|  66 RWSLLLpsSAIFMTVSSLLMWLAN---SLDIVFFSQLVMGVAM 105
                                       677777656777789999999999...99***********976 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 6.3e-07
                                       HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TT CS
                          Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaak 97 
                                        +l++s+++ G +iGsl++g+l+ ++G ++ +li+a++++++a + a a+
  gi|557694583|ref|YP_008797637.1| 129 FSLFLSAVSMGFLIGSLVSGTLASILGLQNQFLISAAVSSAAAPVLAKAN 178
                                       589*********************************99999987766555 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.0059
                                       HH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  42 eessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlq 93 
                                       ++s  l+g++ ++     ++G ++ag+l+d+ G   +ll++++ +++ga+l 
  gi|557694583|ref|YP_008797637.1| 312 ASSVFLIGMFEALIGSCFLVGPVVAGFLADMCGFSAVLLFFSLSMLVGAFLA 363
                                       44555566666655555679*****************************985 PP

>> B12D  NADH-ubiquinone reductase complex 1 MLRQ subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0    0.0093        42      11      41 ..     161     192 ..     159     198 .. 0.75
   2 ?    4.7   1.6    0.0057        26       6      27 ..     285     306 ..     281     309 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0093
                              B12D  11 figagvggavf.ylvRllltnPDVrwnkknnp 41 
                                        i+a+v+ a+  +l++   +nP++++++++ p
  gi|557694583|ref|YP_008797637.1| 161 LISAAVSSAAApVLAKANPSNPEITISRNKHP 192
                                       56777766555277777789********9987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0057
                              B12D   6 iPLfvfigagvggavfylvRll 27 
                                       iPL+   ga v++a  y+++l+
  gi|557694583|ref|YP_008797637.1| 285 IPLMIPAGATVSIAYVYTLYLV 306
                                       9*******************97 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 ?   12.0   1.7     1e-05     0.045     132     194 ..      91     153 ..      67     160 .. 0.90
   2 ?    1.2   0.5     0.019        85     342     384 ..     234     277 ..     228     283 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1e-05
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 132 vllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllkl 194
                                       + ++f++ql++G++  ++++ G s + ++  k +    ++++ ++  +G  +G l+++ l+++
  gi|557694583|ref|YP_008797637.1|  91 LDIVFFSQLVMGVAMFLFFPCGESIVANSFPKGERLRAFSLFLSAVSMGFLIGSLVSGTLASI 153
                                       3399****************************************************9998875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.019
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 342 pgaalGi.llgGllvkklklsakklaklvlvvsllsllllllll 384
                                       ++  +G  +l  +l+++lk+s  kl+  vl + +   +l l++l
  gi|557694583|ref|YP_008797637.1| 234 FFTLIGArVLTSYLLSRLKPSSAKLLLTVLSIVTAVWALALVYL 277
                                       455555549999**********9999888877777777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); 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):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2534.09
//
Query:       gi|557694584|ref|YP_008797638.1|  [L=346]
Description: phosphate regulatory protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   41.8   7.1    4.9e-07   30.1   0.6    2.9  3  PhoU            PhoU domain
    9.7e-06   25.4   0.3      3e-05   23.8   0.1    1.9  2  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


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 ?   -3.1   0.0       1.2   1.1e+04      30      47 ..      37      54 ..      36      73 .. 0.71
   2 !   30.1   0.6   5.4e-11   4.9e-07       2      82 ..     142     225 ..     141     231 .. 0.87
   3 !   14.7   0.3   3.5e-06     0.031       3      88 ..     250     328 ..     248     329 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.2
                                      HHHHHHHHHHHHHHHHHH CS
                              PhoU 30 vierddeidrlekeiers 47
                                      +ie+ d + +le +ier+
  gi|557694584|ref|YP_008797638.1| 37 IIELSDAALKLETKIERA 54
                                      677777777888888776 PP

  == domain 2  score: 30.1 bits;  conditional E-value: 5.4e-11
                                       HHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...HGG-SHHHHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealak...rqplaedlrellsllriardl 75 
                                       +rm  +    +++++eal+e+ +e+++++ +++ ++d+l+++ +r++++ +++   +++ + ++ ++++ + ++r l
  gi|557694584|ref|YP_008797638.1| 142 KRMQVMLTMGINNLIEALKEGRKEALNDIAKMETKVDELYFLCIRQIFFNVKRevwGEEASDPYIAAIGDRLVVRAL 218
                                       6777777778899**************************************654655555558999999999***** PP

                                       HHHHHHH CS
                              PhoU  76 ERigDha 82 
                                       E ++D  
  gi|557694584|ref|YP_008797638.1| 219 EEVADSL 225
                                       *****75 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 3.5e-06
                                       HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHGG-SHHHHHHHHHHHHHHHHHHH CS
                              PhoU   3 rmaeiveemlddalealeekdtelarevierddeidrlekeierslleal.akrqplaedlrellsllriardlERi 78 
                                       ++ e ++  + ++++a+ + d +la+evi  +  + ++ +e+   +++ + +++  ++ dl +++sl++ +++   +
  gi|557694584|ref|YP_008797638.1| 250 KLLESIQVLFGKTMKAFLSLDINLANEVI--EVTAKQYGEEM---AFNDIfSHG--VS-DLATAVSLRNFVYNVISM 318
                                       56677788999*****************8..44444444444...355552332..32.6889************** PP

                                       HHHHHHHHHH CS
                              PhoU  79 gDhavniaer 88 
                                       ++ ++ iae 
  gi|557694584|ref|YP_008797638.1| 319 ARNCKIIAEV 328
                                       ********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 !   23.8   0.1   3.3e-09     3e-05       3      42 ..      11      51 ..       9      55 .. 0.89
   2 ?   -2.1   0.0      0.44   3.9e+03      24      33 ..     210     219 ..     200     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 3.3e-09
                                      ETTEEEEEE-CCCHHHCCEECTCEEEEEECTT.CCCCCCCH CS
                    MazE_antitoxin  3 vGnsgavriPkevrfelgireGdevelevdgd.kiilrplk 42
                                      ++ ++ v++P+ +++  g+++Gd v +++ +d  + l+ + 
  gi|557694584|ref|YP_008797638.1| 11 GSGTLTVSLPRKWVERSGLKPGDPVSIIELSDaALKLETKI 51
                                      677899**************************999888775 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.44
                                       TCEEEEEECT CS
                    MazE_antitoxin  24 Gdevelevdg 33 
                                       Gd+++++  +
  gi|557694584|ref|YP_008797638.1| 210 GDRLVVRALE 219
                                       8999888665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       617  (0.0344135); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2640.63
//
Query:       gi|557694585|ref|YP_008797639.1|  [L=509]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   73.8   0.0    3.3e-09   37.0   0.0    2.3  2  Nitroreductase  Nitroreductase 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 !   37.0   0.0   1.8e-13   3.3e-09      27     170 .]      92     243 ..      70     243 .. 0.87
   2 !   34.7   0.0   9.6e-13   1.7e-08       1     147 [.     325     470 ..     325     490 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.8e-13
                                       H...........HTS--GGG---EEEEEE..-CCCH....HHHHHHHHHHHHHHHTT-SS-GGGGGGHHHHHHHHHH CS
                    Nitroreductase  27 a...........rraPsagnlqpwrfvvv.qdkelr....yklaeaalelllkaeaqaelaqryrkeelklkaqkal 87 
                                                   r aP  g l+p++++vv  d + +    y + ++a+ l+  +  + +   +       ++ ++a+
  gi|557694585|ref|YP_008797639.1|  92 RvveygwetgyfRAAPATGALYPIELYVVaGDVDGLepgvYHFDPKAFCLTVLRLGDFRGFLS-------KYSNSAV 161
                                       04444466667788***************7788877**************9999999998888.......89***** PP

                                       HHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S...SEEE CS
                    Nitroreductase  88 agapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglp.deeeiv 163
                                       a++ + +v++    ++ +k+ er+yr  + d+g +a n+lL++++++l +  ++gf + +  v+ llg++   e  v
  gi|557694585|ref|YP_008797639.1| 162 AECSAAVVFTSIGWRNAWKYRERSYRHWFWDSGVMAANMLLTCNSFDLRCRLLTGFVDNE--VNMLLGVDgVREAAV 236
                                       *********999************************************************..********8558888 PP

                                       EEEEEE- CS
                    Nitroreductase 164 vliavGy 170
                                       ++ a+G+
  gi|557694585|ref|YP_008797639.1| 237 LVAALGH 243
                                       8888886 PP

  == domain 2  score: 34.7 bits;  conditional E-value: 9.6e-13
                                       HHH--B---B-S----HHHHHHHHHHH.HTS--GGG---EEEEEE..-CCCHHHHHHHHHHHHHHHHTT-SS-GGGG CS
                    Nitroreductase   1 irkRrSiRkFddepvpkeelekileaa.rraPsagnlqpwrfvvv.qdkelryklaeaalelllkaeaqaelaqryr 75 
                                       i++R S+RkF+ +p++ +++++i++ a + +P+  +   + ++v+ +d e  +  a  + + +l+  ++ +++++  
  gi|557694585|ref|YP_008797639.1| 325 ILRRGSTRKFSRTPITYDTFSTIVRKAfAEVPTDYHGPVVSLFVIvNDVEGVEPGAYMVCDGTLVTVKKGQFRRVSG 401
                                       789************************888***************99999996666665555555555555555544 PP

                                       GGHHHHHHHHHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGH CS
                    Nitroreductase  76 keelklkaqkalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaa 147
                                          +  ++q + ++a+++++  a l++   + ++r+yr+a l+ g+ a  ++LaA  lG+g+  ++++d++ 
  gi|557694585|ref|YP_008797639.1| 402 ---YLCLEQRLGEDAAAVFFPMAPLMNILGRMGNRGYRVAQLEGGIRAGLMYLAAYGLGIGATGLTFYDDDV 470
                                       ...6799*******************************************************9999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (509 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 3897.78
//
Query:       gi|557694586|ref|YP_008797640.1|  [L=398]
Description: thiamine biosynthesis protein ThiI [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-54  185.1   0.0    2.2e-54  184.0   0.0    1.5  2  ThiI            Thiamine biosynthesis protein (ThiI)
    1.8e-06   27.6   0.1      0.026   14.0   0.0    2.6  3  QueC            Queuosine biosynthesis protein QueC
    1.3e-05   25.4   0.4    4.8e-05   23.5   0.1    2.2  2  THUMP           THUMP domain
      6e-05   22.0   0.1    0.00025   20.0   0.0    2.0  2  tRNA_Me_trans   tRNA methyl transferase
  ------ inclusion threshold ------
      0.078   12.7   0.2        2.5    7.8   0.2    2.4  1  ATP_bind_3      PP-loop family
       0.12   12.0   0.0       0.18   11.3   0.0    1.2  1  Glyco_hydro_cc  Glycosyl hydrolase catalytic core


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 ?   -2.9   0.0       1.4   4.3e+03      40      93 ..      54     106 ..      45     109 .. 0.63
   2 !  184.0   0.0   7.5e-58   2.2e-54       2     192 ..     168     355 ..     167     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                              ThiI  40 gtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvkekltivllk 93 
                                         +eea ek++k+  + +  + +++v+ +v + ++ +++++ek    ++++ +k
  gi|557694586|ref|YP_008797640.1|  54 LVPEEAVEKLRKIFGIHSI-GIGVRVEPTVDEIENAVHHVVEKESLTSLCLEVK 106
                                       5667777777777766554.3346777777777777777777666666665555 PP

  == domain 2  score: 184.0 bits;  conditional E-value: 7.5e-58
                              ThiI   2 tqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlke 78 
                                       ++g+vl+L+SgG+DS Va+ ll+kRGcrv+++hl+++ +  e++ ek+ +l+e+l+ey+  l+ +l++ +f++  k+
  gi|557694586|ref|YP_008797640.1| 168 SSGRVLSLISGGVDSAVASLLLMKRGCRVDFLHLHSYRTSDEAVDEKIGELVEKLTEYN--LKSTLYTASFTPFYKH 242
                                       68*********************************************************..6*************** PP

                              ThiI  79 ilekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiikl 155
                                       i +k   +l ivl++r +lr+Ae++a   g++alv G+sL+qVaSqtl+N+ ++ +   ++i+rPLigldK eii+l
  gi|557694586|ref|YP_008797640.1| 243 IWDKR-TRLEIVLFRRYLLRVAEEIALSRGYRALVLGDSLAQVASQTLPNILAVGQ-PRIPIFRPLIGLDKSEIIEL 317
                                       *9985.6799*****************************************99976.58****************** PP

                              ThiI 156 Akeigtyeisieke.dkCsvlakhPttkakleevekae 192
                                       A++ g  e+  +++ d+Cs++a+h  tka   +ve++ 
  gi|557694586|ref|YP_008797640.1| 318 AQKYGVLETVSKPYkDCCSLIARHQATKADSRSVEREW 355
                                       *********999999****************9999875 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.96   2.9e+03      57      88 ..     112     140 ..      89     157 .. 0.57
   2 !   14.0   0.0   8.5e-06     0.026       2      42 ..     172     213 ..     171     240 .. 0.77
   3 !   10.8   0.0   8.5e-05      0.25     143     176 ..     292     324 ..     279     343 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.96
                                       EEEE-GGGGGGSCGGG-----------...-- CS
                              QueC  57 kildldllkelggsaLtdeeievpkeeleeee 88 
                                       + ++ + l+++  ++L+++  +++k +    +
  gi|557694586|ref|YP_008797640.1| 112 HPFTSQELRRMLATSLVQRGLQISKDS---GQ 140
                                       445556688888899999999888832...22 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 8.5e-06
                                       EEEE--SSHHHHHHHHHHHHH-SEEEEEEEE.SS-TTSHHHH CS
                              QueC   2 avvllSGGlDSttvlalakkegkevealtfd.Ygqrhkkele 42 
                                       ++ l+SGG+DS+++ +l +k+g +v  l+++ Y    ++  e
  gi|557694586|ref|YP_008797640.1| 172 VLSLISGGVDSAVASLLLMKRGCRVDFLHLHsYRTSDEAVDE 213
                                       6889************************98636555444444 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 8.5e-05
                                       HHHHHHTS--EEE-TTTT--HHHHHHHHHHTTHH CS
                              QueC 143 alnlgedkkieieaPlidlsKaeivklgkelgvp 176
                                       +l++g+  +i i  Pli l+K+ei++l++++gv 
  gi|557694586|ref|YP_008797640.1| 292 ILAVGQ-PRIPIFRPLIGLDKSEIIELAQKYGVL 324
                                       555555.7899*********************73 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.1   1.6e-08   4.8e-05      18     117 ..      42     132 ..      28     156 .. 0.74
   2 ?   -3.1   0.0       2.5   7.4e+03     104     117 ..     211     224 ..     204     229 .. 0.68

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.6e-08
                                       EEETTEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESS CS
                             THUMP  18 eagkgrivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrg 94 
                                       +++++ +++  + +      e++ e+l k++gi+++ ++   +e ++++i++a++ +v+k+      + + +vkr +
  gi|557694586|ref|YP_008797640.1|  42 RDENRLAIIADNLV-----PEEAVEKLRKIFGIHSIGIG-VRVEPTVDEIENAVHHVVEKESLT---SLCLEVKRSY 109
                                       44444444444433.....455557789999********.999999*************88755...********** PP

                                       STSSSHHHHHHHHHHHHHHCCTT CS
                             THUMP  95 khfeftsreinrevGkaivektg 117
                                       k + fts+e++r+++  +v+++ 
  gi|557694586|ref|YP_008797640.1| 110 KGHPFTSQELRRMLATSLVQRGL 132
                                       ***************99999987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHCCTT CS
                             THUMP 104 inrevGkaivektg 117
                                       +  ++G+++ ++t+
  gi|557694586|ref|YP_008797640.1| 211 VDEKIGELVEKLTE 224
                                       55677888877776 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   8.2e-08   0.00025       2      42 ..     171     211 ..     170     225 .. 0.88
   2 ?   -1.6   0.0      0.31   9.2e+02     167     199 ..     305     337 ..     301     352 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.2e-08
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeeg 42 
                                       +v+ ++SgGVDS+va +ll ++g  v  ++l+ + ++de+ 
  gi|557694586|ref|YP_008797640.1| 171 RVLSLISGGVDSAVASLLLMKRGCRVDFLHLHSYRTSDEAV 211
                                       79999*************************99999877764 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.31
                     tRNA_Me_trans 167 PlgeltKeevrkiAkeaglavaekkdSqgiCfi 199
                                       Pl  l K+e+ ++A+++g+     k  ++ C +
  gi|557694586|ref|YP_008797640.1| 305 PLIGLDKSEIIELAQKYGVLETVSKPYKDCCSL 337
                                       899999*********999875555556677744 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2   0.00084       2.5     122     160 ..     288     322 ..     171     325 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00084
                                       -CCHHH-S-SEEEETTCCEE-CCCT--HHHHHHHHHHTT CS
                        ATP_bind_3 122 glaglagikeaseiasirlvRPlLkvskeeleeylkekk 160
                                        l +++++ + +    i + RPl+ + k+e+ e++++ +
  gi|557694586|ref|YP_008797640.1| 288 TLPNILAVGQPR----IPIFRPLIGLDKSEIIELAQKYG 322
                                       333444444444....88999999999999999999876 PP

>> Glyco_hydro_cc  Glycosyl hydrolase catalytic core
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.1e-05      0.18     133     164 ..     191     222 ..     183     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.1e-05
                    Glyco_hydro_cc 133 skdckvdflavHwYkgdfeelkehieelheay 164
                                       +++c+vdfl +H Y ++ e + e+i+el e+ 
  gi|557694586|ref|YP_008797640.1| 191 KRGCRVDFLHLHSYRTSDEAVDEKIGELVEKL 222
                                       579***********888999999999987764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3074.45
//
Query:       gi|557694587|ref|YP_008797641.1|  [L=496]
Description: betaine-aldehyde dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-165  548.8   0.0   9.2e-165  548.6   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
      0.009   15.5   0.0       0.35   10.3   0.0    2.1  2  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 !  548.6   0.0    1e-168  9.2e-165       5     461 ..      15     476 ..      12     477 .. 0.97

  Alignments for each domain:
  == domain 1  score: 548.6 bits;  conditional E-value: 1e-168
                                       SS.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHH....HHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHH CS
                            Aldedh   5 es.etievinPatgeviakvpaataedvdaavaaAkeafk....awaklpaeeRaeiLrkaadlleerkeelaelet 76 
                                       +s + +e ++P +++++    a + edvdaav+aA++af+    +w + + + R ++L kaa+ll+++ + la++e+
  gi|557694587|ref|YP_008797641.1|  15 SSgKYLERHDPGDESNVIGLVADGFEDVDAAVDAARRAFDkdagGWVS-DYRLRMRVLLKAAELLRQNLDSLARMES 90 
                                       44255999****99999999999*****************76644654.8999************************ PP

                                       HHH---HHHHHH.HHHHHHHHHHHHHHHHHHHSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHH CS
                            Aldedh  77 letGkplaeara.eveeaidvlryyaelaeklegevlpssegklalvrrePlGvvgaItPWNfPlllaawklapala 152
                                       l +Gk+++ +r  ++++a++ l+yya+la+k+ g++   ++g l+ ++++P+Gvv+aI+PWNfPl+++++++apala
  gi|557694587|ref|YP_008797641.1|  91 LFAGKTIRTSRMsDIPRAAELLEYYAGLADKVLGTSQILRTGDLISIVKQPVGVVAAIVPWNFPLVILCRQVAPALA 167
                                       *******************************9997755688************************************ PP

                                       TT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTT CS
                            Aldedh 153 aGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknl 229
                                       +G+tvv KP++ tp++al la+++++ag Pkgv+nvvtg g++vg+ l+++++vd+v+ftGst+vgr+i+++a+++l
  gi|557694587|ref|YP_008797641.1| 168 VGCTVVAKPSSLTPATALELAKILDKAGAPKGVFNVVTGGGETVGDKLLKSEKVDLVNFTGSTSVGRNIMQKASSHL 244
                                       ***************************************************************************** PP

                                       SEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT- CS
                            Aldedh 230 krvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedt 306
                                       krv+lElGGknp+iv+edaDl++a++a+v ga+ n+G+ C a+srllv++ + ++fve +ve++k+++vg +lde +
  gi|557694587|ref|YP_008797641.1| 245 KRVVLELGGKNPNIVFEDADLERAANAVVYGAYANNGESCAAGSRLLVHSRVRKQFVEMVVERVKRIRVGYQLDERS 321
                                       ***************************************************************************** PP

                                       SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESS CS
                            Aldedh 307 dvGPliseaqlekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkd 382
                                       d+GPl+s+ qle+v +yv  a +eg k+ +Gge  +e  +++g++++Ptv+++++p++r++qeEiFGPVl+v++f+d
  gi|557694587|ref|YP_008797641.1| 322 DMGPLVSKGQLETVLEYVGAAASEGLKIACGGErMTEGFYSRGNYMQPTVIDDTPPESRLFQEEIFGPVLTVTEFRD 398
                                       *********************************8888999************************************* PP

                                       HHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEE CS
                            Aldedh 383 eeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytev 459
                                       e+ea+e+aN+t yGLaagv+++d+ ra+rva+r++aG v+iN++ t  +e+ p+gG+kqSg+Gr++   ++e+y+e 
  gi|557694587|ref|YP_008797641.1| 399 EDEAVEMANATIYGLAAGVWSSDPGRALRVASRVKAGAVWINTYYTLPVEM-PWGGFKQSGIGRNNTVLAIEHYLEP 474
                                       **************************************************9.************************9 PP

                                       EE CS
                            Aldedh 460 kt 461
                                       k 
  gi|557694587|ref|YP_008797641.1| 475 KG 476
                                       85 PP

>> DUF1487  Protein of unknown function (DUF1487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   3.9e-05      0.35       9      60 ..     258     311 ..     255     316 .. 0.84
   2 !    2.8   0.0    0.0078        70     115     169 ..     389     442 ..     367     451 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 3.9e-05
                           DUF1487   9 vifedgDlnsalealvesl..kePfaegavatvlveesirdefvervrsklkpl 60 
                                       ++fed+Dl+ a++a+v     ++  ++ a   +lv+  +r +fve v +++k++
  gi|557694587|ref|YP_008797641.1| 258 IVFEDADLERAANAVVYGAyaNNGESCAAGSRLLVHSRVRKQFVEMVVERVKRI 311
                                       89*************97651155566677779*****************99987 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0078
                           DUF1487 115 gvvTlhtFrnakEvvkllakeslkfasvsvwneklaavyelvarlnvdvftiNCa 169
                                        v+T+  Fr   E+v++++     + +  vw++  + +  ++ r++   + iN +
  gi|557694587|ref|YP_008797641.1| 389 PVLTVTEFRDEDEAVEMANATIYGL-AAGVWSSDPGRALRVASRVKAGAVWINTY 442
                                       489*************998765555.56899999999999999999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3481.35
//
Query:       gi|557694588|ref|YP_008797642.1|  [L=143]
Description: hypothetical protein CSUB_C1160 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-07   29.8   0.0    9.3e-07   29.4   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    1.8e-06   27.9   0.0    4.3e-06   26.7   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
    0.00015   22.5   0.0    0.00023   21.9   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    0.00016   22.3   0.0    0.00022   21.9   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    0.00024   21.3   0.0     0.0003   21.1   0.0    1.2  1  DRE2_N           Fe-S cluster assembly protein DRE2 N-terminu
    0.00029   20.8   0.0    0.00034   20.5   0.0    1.1  1  Methyltransf_8   Hypothetical methyltransferase
    0.00029   20.7   0.0    0.00041   20.2   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.021   14.2   0.0    1.5  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.015   14.9   0.0      0.022   14.3   0.0    1.3  1  MTS              Methyltransferase small domain


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 !   29.4   0.0   4.7e-10   9.3e-07      18      96 .]      18      97 ..       4      97 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 4.7e-10
                                      T.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCT.SS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11 18 g.arvvgvDlskemlklakekaseeglkvefvvadaekl.pfednsfDlvvssevlhhvedpekalkeiaRvLkpgGll 94
                                      g ++    D + + l+  ++ +s+ ++   +    +e+l  +++ +fD vv++ +l+   + ++++ e++R+Lk+gG+l
  gi|557694588|ref|YP_008797642.1| 18 GlSEAHVADDDSQSLQNLSTTSSTVKI-TPVYTRVIERLvELPSTTFDTVVAFYSLERALNKRAFMTEARRLLKQGGKL 95
                                      355555555555556555555555554.3345666777779*************************************9 PP

                                      EE CS
                   Methyltransf_11 95 vi 96
                                      ++
  gi|557694588|ref|YP_008797642.1| 96 IV 97
                                      96 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   2.1e-09   4.3e-06      78     130 ..      49     110 ..       8     129 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.1e-09
                   Methyltransf_23  78 e.........pqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrll 130
                                                 p+ +fd++v++++le+  +  + ++ +++llk gG l+++++ +   ++r l
  gi|557694588|ref|YP_008797642.1|  49 TrvierlvelPSTTFDTVVAFYSLERALNKRAFMTEARRLLKQGGKLIVLTHVRGFLRRRGL 110
                                       0333334444677**************************************97654344433 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.1e-07   0.00023      48      99 .]      44      95 ..       5      95 .. 0.65

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.1e-07
                   Methyltransf_12 48 nnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLkpgGrl 99
                                       + v  ++++ l + ++ +fD+vva+  l+   ++r+++ ++r+lLk+gG+l
  gi|557694588|ref|YP_008797642.1| 44 ITPVYTRVIERLVELPSTTFDTVVAFYSLERALNKRAFMTEARRLLKQGGKL 95
                                      344444444444445558********************************97 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   1.1e-07   0.00022       7      97 .]       5      93 ..       2      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.1e-07
                                      TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC.CG.BSSSTTTEEEEEEESTGGGSSHHHHH CS
                   Methyltransf_25  7 GtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda.ed.lpfedgsfDlvvssgalhhlsdedle 83
                                      G  +++++l k+lg ++ +  D +++ l++  +    + ++++ v   + e+ +++++ +fD vv++++l+     + +
  gi|557694588|ref|YP_008797642.1|  5 GGANIAADLVKQLGLSEAHVADDDSQSLQNLSTTS--STVKITPVYTRViERlVELPSTTFDTVVAFYSLERA--LNKR 79
                                      67788899999998899999999999999999888..5678888777765663468999*******9998873..3578 PP

                                      HHHHHHHHHEEEEE CS
                   Methyltransf_25 84 kalkeiarvLkpgG 97
                                      +++ e++r+Lk+gG
  gi|557694588|ref|YP_008797642.1| 80 AFMTEARRLLKQGG 93
                                      9************9 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 !   21.1   0.0   1.5e-07    0.0003      37     105 ..      49     120 ..      19     137 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.5e-07
                                       HHHHHT-----SSS--SEEEE---..SS-S----HHHHHHHHTT--TT--EE---H............HHHHHHHHH CS
                            DRE2_N  37 DRlaaglvsLpastYdlvllltdeeeeeeelliprkliqkivkaLkpgGklkgqdgkake........aqklealla 105
                                        R+ + lv+Lp+ t+d+v+ +     e  + l++r+ ++   ++Lk+gGkl + +    +        + +l+ lla
  gi|557694588|ref|YP_008797642.1|  49 TRVIERLVELPSTTFDTVVAFYSL--E--RALNKRAFMTEARRLLKQGGKLIVLTHV-RGflrrrglsKTELDKLLA 120
                                       6999******************88..4..55666*****************998874.3346677777777777766 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   1.7e-07   0.00034      75     181 ..      13     127 ..       8     141 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.7e-07
                                       -EEEES-TT-HHHHH--S-..EEEEESS-SSTT.EEES-T.TS-S--TT-EEEEEEES---.SS-HHHHHHHHHHHE CS
                    Methyltransf_8  75 vvadlGcGeakiaeavrekekvrsfdlvavner.vvacdl.akvPledesvdvavfclslm.gtnladflkeanrvl 148
                                        v  lG  ea++a   +++ +  s    +v+   v +  + + v l   + d +v   sl  + n + f+ ea+r+l
  gi|557694588|ref|YP_008797642.1|  13 LVKQLGLSEAHVADDDSQSLQNLSTTSSTVKITpVYTRVIeRLVELPSTTFDTVVAFYSLErALNKRAFMTEARRLL 89 
                                       577899999999977777765555444444432133333435577888999999999999626799*********** PP

                                       EEEEEEEE.EEEGGG-S....-HHHHHHHHHCTTEEEE CS
                    Methyltransf_8 149 kvGGllkv.aevksrfe....svklfaraltklGfevk 181
                                       k+GG l v + v+  +     s   + + l   Gf+ +
  gi|557694588|ref|YP_008797642.1|  90 KQGGKLIVlTHVRGFLRrrglSKTELDKLLATHGFKLV 127
                                       ****9987356666554223355555555566677654 PP

>> 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   2.1e-07   0.00041      72     114 ..      39     109 ..       8     136 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.1e-07
                   Methyltransf_31  72 d.....................ekfDlilsnevlnaladpdkileeiervlkpggilliedpr.......l 114
                                                              +fD ++++  l    ++ +++ e+ r+lk+gg l++ ++        +
  gi|557694588|ref|YP_008797642.1|  39 SstvkitpvytrvierlvelpsTTFDTVVAFYSLERALNKRAFMTEARRLLKQGGKLIVLTHVrgflrrrG 109
                                       345555555555555555555589***********************************999855554441 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     1e-05     0.021     110     154 ..      56     100 ..       2     109 .. 0.76
   2 ?   -2.2   0.0       1.1   2.2e+03     202     224 ..     113     135 ..     107     140 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1e-05
                                       -TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE CS
                   Ubie_methyltran 110 LpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlef 154
                                       ++    +fD+v   + l    +k   + ea+r lk GG+l+vl  
  gi|557694588|ref|YP_008797642.1|  56 VELPSTTFDTVVAFYSLERALNKRAFMTEARRLLKQGGKLIVLTH 100
                                       4556789***********************************965 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.1
                                       HHHHHHHHHTTEEEEEEEEEGGG CS
                   Ubie_methyltran 202 etlkeliedaGfksveyesltgG 224
                                        +l++l+   Gfk ve  + +g 
  gi|557694588|ref|YP_008797642.1| 113 TELDKLLATHGFKLVERIQKGGD 135
                                       56778888888888776555554 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.1e-05     0.022      45     139 ..       9      99 ..       4     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE---STTTCHCHHHHHHH CS
                               MTS  45 lgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsNPPfhagkatelavaee 120
                                       ++a l k+    e ++ d d ++l+   ++ ++ k+  v ++  + l e++   fd++v    + +  +      ++
  gi|557694588|ref|YP_008797642.1|   9 IAADLVKQLGLSEAHVADDDSQSLQNLSTTSSTVKITpVYTRVIERLVELPSTTFDTVVAFYSLERALN-----KRA 80 
                                       78888888889999****************9999999988888899999999*******9655555555.....789 PP

                                       HHHHHHHHEEEEEEEEEEE CS
                               MTS 121 liaeAkeaLkegGeLliVa 139
                                       +++eA++ Lk+gG+L++ +
  gi|557694588|ref|YP_008797642.1|  81 FMTEARRLLKQGGKLIVLT 99 
                                       ***************9875 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:                      458  (0.0255452); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1083.55
//
Query:       gi|557694589|ref|YP_008797643.1|  [L=198]
Description: multiple antibiotic resistance protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-37  128.6  15.7    3.2e-37  127.9  15.7    1.3  1  MarC      MarC family integral membrane protein


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 !  127.9  15.7   1.8e-41   3.2e-37       4     202 ..       9     194 ..       6     195 .. 0.92

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 1.8e-41
                              MarC   4 iikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgill 80 
                                       ++ka+v L++i++p+g +p ++sl+   s++er+r + + +++++++llvf + G+ +l ++gi ++++ +aGg+ll
  gi|557694589|ref|YP_008797643.1|   9 LLKAVVALFIIVDPVGVLPFVVSLTGGLSSHERRRLVDRSVVVGTVLLLVFSIGGQGVLWVLGIDLSSFTVAGGLLL 85 
                                       68999************************************************************************ PP

                              MarC  81 fliaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalit 157
                                       ++ a+++l    +     +       +  +  ++PLA+Pl+aGPgaittv+ +++           ++ +l+++ +t
  gi|557694589|ref|YP_008797643.1|  86 LILAVRILVQGGEG--WGT-------QGKSSGIFPLAFPLLAGPGAITTVIFSINALGIP----YSIIPVLIVMGLT 149
                                       ******98766663..222.......234679*********************9998874....667788999**** PP

                              MarC 158 llilllsslilrllgktginaleRlmGllLvalavqlivdGikei 202
                                       +lil++ + +l+ +g++g +a++R+m ++ +a++vq iv G++e+
  gi|557694589|ref|YP_008797643.1| 150 WLILRSIEPMLKIIGESGADAVARIMSVFVAAIGVQYIVSGLAEM 194
                                       ******************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1486.32
//
Query:       gi|557694590|ref|YP_008797644.1|  [L=168]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-11   45.0  12.7    1.9e-11   44.5  12.7    1.2  1  QueT           QueT transporter
  ------ inclusion threshold ------
      0.063   13.4   0.1      0.063   13.4   0.1    2.6  3  AA_permease_C  C-terminus of AA_permease
       0.24   11.1   0.6         35    4.2   0.0    2.7  2  NCE101         Non-classical export protein 1


Domain annotation for each model (and alignments):
>> QueT  QueT transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5  12.7   3.1e-15   1.9e-11       6     136 ..      14     145 ..      11     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 3.1e-15
                              QueT   6 viaAlYvvltlvlapisfgaiqvRiseaLtlLpv.ftpaailGltiGcliaNllsplgllDvifGslatliaallty 81 
                                       + aA+Y++ tl+l ++  g +qv+  e++t L++ f+ a +lGl+ G +iaN++splg+lD+i   + +l a+++  
  gi|557694590|ref|YP_008797644.1|  14 IFAAIYAAGTLALGNLPLGDLQVKTGEIMTPLVAlFGLASVLGLAFGQFIANMASPLGPLDLITPAI-SLGALIVLR 89 
                                       78*******************************99***************************98655.566666666 PP

                              QueT  82 llkkkr.........llaalppvlvnalivgavllelpflltvltvglgelivlyvlGlpllka 136
                                       +l+k+          ++++ + +l+++++ g    +      ++t ++ + i++ v+Gl ++++
  gi|557694590|ref|YP_008797644.1|  90 ALAKRSillgvaayyIISSTWLSLLTSVVTG---RS----DAFVTSFARQGIAM-VIGLAVYFV 145
                                       6655555544433221333333333333333...12....22333333344444.555555554 PP

>> AA_permease_C  C-terminus of AA_permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.49   2.9e+03      24      38 ..       4      18 ..       1      24 [. 0.51
   2 ?   -2.1   0.5      0.73   4.4e+03      36      45 ..      96     105 ..      79     111 .. 0.69
   3 ?   13.4   0.1   1.1e-05     0.063      27      49 ..     127     149 ..     125     151 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.49
                     AA_permease_C 24 Ldsltwirfgvwmli 38
                                      L+s+ +  f++  +i
  gi|557694590|ref|YP_008797644.1|  4 LTSTHFGIFVIFAAI 18
                                      555555445444443 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.73
                     AA_permease_C  36 mliglliYfl 45 
                                       +l+g+  Y++
  gi|557694590|ref|YP_008797644.1|  96 ILLGVAAYYI 105
                                       4567777764 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 1.1e-05
                     AA_permease_C  27 ltwirfgvwmliglliYflYgir 49 
                                       ++++r g+ m+igl +Yf+++ r
  gi|557694590|ref|YP_008797644.1| 127 TSFARQGIAMVIGLAVYFVVKSR 149
                                       689***************98765 PP

>> NCE101  Non-classical export protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.6    0.0069        41      13      22 ..      96     105 ..      95     108 .. 0.88
   2 ?    4.2   0.0    0.0059        35      11      31 ..     134     154 ..     133     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0069
                            NCE101  13 ifiGvaaYyl 22 
                                       i +GvaaYy+
  gi|557694590|ref|YP_008797644.1|  96 ILLGVAAYYI 105
                                       889******6 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0059
                            NCE101  11 LaifiGvaaYylyEkrterpe 31 
                                       +a++iG+a Y++  +r+ r e
  gi|557694590|ref|YP_008797644.1| 134 IAMVIGLAVYFVVKSRMPRQE 154
                                       699*********999987764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1311.40
//
Query:       gi|557694591|ref|YP_008797645.1|  [L=211]
Description: cytochrome c oxidase subunit III [Candidatus Caldiarchaeum subterraneum]
Scores for 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-23   81.9   9.8    8.2e-23   81.6   9.8    1.0  1  COX3      Cytochrome c oxidase subunit III


Domain annotation for each model (and alignments):
>> COX3  Cytochrome c oxidase subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   9.8   4.6e-27   8.2e-23      75     254 ..      23     201 ..      15     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 4.6e-27
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--GGGTSSSS-TT-----TTSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              COX3  75 GlklGlilfiisevllflalfwaffhsalsPtvelGatwpPvGikavnPlevPllntiillssGvtvtyahhslieg 151
                                       G+ +   +f+++ev lf+a f ++f   ls       +wpP G   ++ + +P l t +ll s  ++ ya +s+ + 
  gi|557694591|ref|YP_008797645.1|  23 GVGFPTAVFLFTEVALFAAGFSSYFVIRLSF-----PVWPPPGTPHLDDF-IPRLQTFMLLFSSLAIEYAVYSVKRD 93 
                                       66677789*****************999985.....47**********99.9*********************9887 PP

                                       BHHHHHHHHHHHHHHHHHHHHHHH.HHH....HH-SS-TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT- CS
                              COX3 152 nrkkalkgllltillavlftllqa.vey....leasftisdgvyGsvfylatGlhglhviigtillavallrllkyh 223
                                           +l g++ t l+++ f++l+  ve+     +  ft s g+y s+fy+  G hg hv+ g + l v  +r     
  gi|557694591|ref|YP_008797645.1|  94 RLGAVLGGVVATALFGLGFLVLKLgVEWphllFDVGFTPSTGIYASMFYILLGAHGAHVLGGVLALGVVAWRAKLRQ 170
                                       67777889999***9**9999875378733335789999************************************** PP

                                       -BSSB-HHHHHHHHHHHHHHHHHHHHHHHTT CS
                              COX3 224 ltknhhlGfeaailywhfvdvvwlflyvsvy 254
                                       ++++ +  +e+  +ywhfv +vwl+l+ ++y
  gi|557694591|ref|YP_008797645.1| 171 FSSTSYGLLESVSIYWHFVHLVWLLLFAFIY 201
                                       *****999**********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1679.38
//
Query:       gi|557694592|ref|YP_008797646.1|  [L=279]
Description: translation initiation factor eIF-2B [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  102.3   0.1    1.2e-28  100.1   0.1    1.8  1  IF-2B     Initiation factor 2 subunit 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 !  100.1   0.1   6.9e-33   1.2e-28      24     282 .]      30     262 ..      11     262 .. 0.85

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 6.9e-33
                                       C..CSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             IF-2B  24 k..tskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakksliekikelikeieeadekig 98 
                                       +  + ++++L+++l k ++l++ arP++  +    r++l+ is        +  +++++++++++ k  + + +  +
  gi|557694592|ref|YP_008797646.1|  30 RtlARESDNLSRDLPKYGELIETARPSMPLVKRFSREVLQRIS--------SPSSEEVLKAVEDVEKTYRSKLNHLV 98 
                                       222568899*******************999999999999544........4556677788888888888888999* PP

                                       HHHHTTC-TTEEEEEES--SHHHHHHHHHHHTTEEEEEEEEEXTTTTHHHTHHHHHHHTTXEEEEEEGGGHHHHHHC CS
                             IF-2B  99 diaaelikdgdtilTicnsktvlevlraaakekkkfkVivvEsrPrlqGrltakeLvqagipvtlitdsavayvmse 175
                                       ++a ++++    + T+++s+t++++l  ++      +V v+EsrP  +G l+a  L++    v + +d+avay  ++
  gi|557694592|ref|YP_008797646.1|  99 EHAVDKLSGIGSVTTMSHSGTIINILSRLEGLR---RVNVLESRPLREGVLMAAALRNSC-MVVVYVDAAVAYAVER 171
                                       ***************************999966...9*******************9865.567778********** PP

                                       TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGBESTSSSGGGSSXXBEXTHHHHEETTEESST CS
                             IF-2B 176 evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkfservqldedifieerdpeellnitgeriae 252
                                         d+v+vGAd++  +G+ ++k+G+  lA  Ak    p+ v++++ k+ e++      ++e++++       +++   
  gi|557694592|ref|YP_008797646.1| 172 -SDAVVVGADALYPDGSFSAKVGVKPLAATAKLLGKPFHVAVDTWKLAEEF------VNEMGPST------DVDE-- 233
                                       .**********************************************9993......44445554......4343.. PP

                                       TTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 253 eelkvvnpafDvtPpelItliITevGvlpp 282
                                        ++   np+f  +Pp+lI+ ++T++G+l+p
  gi|557694592|ref|YP_008797646.1| 234 -QMPAENPVFEKVPPDLIDFYLTDLGALTP 262
                                       .77899**********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2169.27
//
Query:       gi|557694593|ref|YP_008797647.1|  [L=340]
Description: alcohol dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  111.8   0.1    3.7e-32  111.1   0.1    1.4  1  ADH_zinc_N     Zinc-binding dehydrogenase
    2.5e-28   98.1   0.0    5.1e-28   97.1   0.0    1.5  1  ADH_N          Alcohol dehydrogenase GroES-like domain
    1.5e-21   77.8   0.0    2.6e-21   77.0   0.0    1.4  1  ADH_zinc_N_2   Zinc-binding dehydrogenase
    3.6e-05   23.2   0.6    5.6e-05   22.5   0.6    1.2  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
    3.7e-05   23.3   0.1    5.4e-05   22.8   0.1    1.2  1  Glu_dehyd_C    Glucose dehydrogenase C-terminus
  ------ inclusion threshold ------
       0.17   12.1   0.2       0.47   10.6   0.1    1.8  2  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.1   0.1   1.2e-35   3.7e-32       1     129 [.     176     303 ..     176     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 1.2e-35
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       gvG+ a+qlAk lG++vi++++ + k+e+a k+Gad+vin+++ +++e++ ++t+g gvd+v+e++G +a +e+a+k
  gi|557694593|ref|YP_008797647.1| 176 GVGISAIQLAKLLGCTVITTVGEDWKAEKAYKIGADYVINRRKQSVSEAVNKFTHGTGVDLVLEHAG-QAIWEEAVK 251
                                       9****************************************4449**********************.********* PP

                                       CEEEEEEEEECSC.TSSEEE.EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                        ADH_zinc_N  78 llkpgGrlvvvGg.gkgeee.fdlrnlllkeksilGsllgslreefkealdlla 129
                                       +l+pgG++v+ G+   ge+  +++r+  ++++s+lGs + + ++e++++l+l++
  gi|557694593|ref|YP_008797647.1| 252 SLAPGGKMVYLGAtT-GENAsINIRYTYRRQTSLLGSYGWN-KSEIPQVLQLFE 303
                                       *************54.44444********************.*********986 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 !   97.1   0.0   1.7e-31   5.1e-28       2     109 .]      28     133 ..      27     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 1.7e-31
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-G CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegee 78 
                                       +evl+k++aag+++ D+++ +g   ++ +lp i+G + +G+veevg++v+++++GdrV+++p+ +cg+C+ C++g +
  gi|557694593|ref|YP_008797647.1|  28 NEVLVKLEAAGMNRIDIWVRSG--VYKIPLPRIPGADGAGVVEEVGEDVTGFSKGDRVLINPALTCGTCRFCQRGWD 102
                                       89*******************9..7**************************************************** PP

                                       GG-TTBEETTTSS-SSSBSEEEECGGGEEEE CS
                             ADH_N  79 nlCeeakllgvsldGgfaeyvvvpekklvkl 109
                                       +lCe+++llg + dG++ae++++p+++l+k+
  gi|557694593|ref|YP_008797647.1| 103 SLCENHRLLGHGADGTYAEKITLPANNLHKI 133
                                       ***************************9986 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 !   77.0   0.0   8.8e-25   2.6e-21       1     133 []     208     338 ..     208     338 .. 0.86

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 8.8e-25
                                       TT-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EE CS
                      ADH_zinc_N_2   1 lGAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsv 73 
                                       +GAd vi+ r++++     + t g gvD+vl+ +g++ + e+++k l++gG++v +g+   +++ ++  + r + ++
  gi|557694593|ref|YP_008797647.1| 208 IGADYVINRRKQSVSeavnKFTHGTGVDLVLEHAGQAIW-EEAVKSLAPGGKMVYLGA---TTGENASINIRYTYRR 280
                                       59********99999899888888***********9999.9999999787****9996...2344444444777777 PP

                                       EE--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  74 kyeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                       ++++l s  ++ + + + ++++l+e+Gklrp +  +fpl+ea eAh+++es   +GKiVl
  gi|557694593|ref|YP_008797647.1| 281 QTSLLGSYGWN-KSE-IPQVLQLFEKGKLRPIIHTTFPLTEAEEAHKLMESDNFFGKIVL 338
                                       77777776666.888.*******************************************8 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 !   22.5   0.6   1.9e-08   5.6e-05      20     136 ..     159     271 ..     147     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.9e-08
                                       TCEETCB---EEEEESTSH.HHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEE CS
                       AlaDh_PNT_C  20 aGgvpgvepakvlviGgGv.aGlqAiatakglgakVtvlDvrparleqleslgakfvevlksqeellaeavkeadvv 95 
                                        Gg++    ++vlviGgG  +G++Ai+ ak lg +V  +  +  ++e+  ++ga    v+++ +++++eav++    
  gi|557694593|ref|YP_008797647.1| 159 RGGIT--PGSTVLVIGGGSgVGISAIQLAKLLGCTVITTVGEDWKAEKAYKIGAD--YVINRRKQSVSEAVNKFTHG 231
                                       56666..56789******769***************999999999999999****..8899999********99876 PP

                                       EE---BTTSS---SC-HHHHHTS-TTEEEEETTGGGT-SBT CS
                       AlaDh_PNT_C  96 igtvlipGkkaPkLvteemvksMkpgsVivDvAidqGGnve 136
                                        + v +  ++a + + ee vks+ pg  +v + + +G n  
  gi|557694593|ref|YP_008797647.1| 232 -TGVDLVLEHAGQAIWEEAVKSLAPGGKMVYLGATTGENAS 271
                                       .4566667889999999*********999999999997765 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 !   22.8   0.1   1.8e-08   5.4e-05      32     144 ..     166     276 ..     150     331 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.8e-08
                       Glu_dehyd_C  32 esalvlGaGs.lGLLalalleaeerglervyvlgrrdrpdptidlveelGatYv.dsretpvdeipea...seemdl 103
                                       +++lv+G Gs +G+ a ++l++   g + +++      +d +++   ++Ga Yv + r+++v+e  +     + +dl
  gi|557694593|ref|YP_008797647.1| 166 STVLVIGGGSgVGISA-IQLAK-LLGCTVITT----VGEDWKAEKAYKIGADYViNRRKQSVSEAVNKfthGTGVDL 236
                                       5789999998678777.45542.345554444....44688888889******7366788898876541114679** PP

                       Glu_dehyd_C 104 vvEaTGsakhafeaiealapnGvaaLlGvpedsevevdgge 144
                                       v+E  G+a    ea++ lap G ++ lG ++++++++++  
  gi|557694593|ref|YP_008797647.1| 237 VLEHAGQA-IWEEAVKSLAPGGKMVYLGATTGENASINIRY 276
                                       ******98.5679*****************99988887654 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 ?   10.6   0.1   0.00016      0.47      28      86 ..     120     182 ..     116     186 .. 0.69
   2 ?   -2.9   0.0       2.7     8e+03      17      31 ..     239     253 ..     236     270 .. 0.58

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                                       HHHHT--GGGB--THHHH-B-GGGHHH....HHHHHHHHTTSS-TT-EEEEEEEETTTEEEEE CS
                     ACP_syn_III_C  28 akklglpeekvvvnldeyGntsaasip....laLdeaveegklkpgdlvllvgfGaGltwgaa 86 
                                       a+k+ lp++   ++ +e+  t a  i+     a + +v +g + pg +vl++g G G+ + a+
  gi|557694593|ref|YP_008797647.1| 120 AEKITLPANNLHKIPEELSTTQAGCIMvtyaTAWHALVTRGGITPGSTVLVIGGGSGVGISAI 182
                                       556666666555555555555555444111167889999******************988876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.7
                                       -SSSHHHHHHHHHHH CS
                     ACP_syn_III_C  17 hqanlriidavakkl 31 
                                        +a + i+++++k l
  gi|557694593|ref|YP_008797647.1| 239 EHAGQAIWEEAVKSL 253
                                       556666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2498.04
//
Query:       gi|557694594|ref|YP_008797648.1|  [L=270]
Description: amidohydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-26   91.8   0.1    5.7e-26   91.4   0.1    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 !   91.4   0.1   3.2e-30   5.7e-26       1     212 [.       4     197 ..       4     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 3.2e-30
                                       EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHB...HSSSHHHHHHHHHHHHH CS
                      CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAe...aglgetlallaalarkn 74 
                                       rvAv+Q+++ + ++++nl+++++l++++  +  dL+ lPE++        + l+aA    + +  +l+ la+ a+++
  gi|557694594|ref|YP_008797648.1|   4 RVAVIQPKT-TNNFTKNLENIKTLLNKVSPHEPDLVTLPEAWQH-----SNTLAAANqlaEQENLVLDILAKQAQEM 74 
                                       79*******.79******************************97.....4455555567678899************ PP

                                       TEEEEEE..EEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SSS-EEEETTEEEE CS
                      CN_hydrolase  75 giavvig..liereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdgipvfdtpvgkiG 149
                                       + ++v+g  + +    ++ +   ++a ++ +dg+++g + K+hL         + e  lf++g++i+vf+ + +++G
  gi|557694594|ref|YP_008797648.1|  75 NAVIVGGglVVH---RGDGF--RMAAPVIAPDGSVMGWQEKIHL--------HKSEQLLFKRGESIQVFKHKDICFG 138
                                       *******54444...58888..99*******************8........589999******************* PP

                                       EEEGGGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBE CS
                      CN_hydrolase 150 aaiCyeigfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqv 212
                                       ++iC +i fpe++r++al+gae+++n    +++p +  +p++++ +rar len + ++ an +
  gi|557694594|ref|YP_008797648.1| 139 VQICLDIAFPEISRIMALRGAELIINP---SHMPSRAVEPWHDY-MRARCLENRVTAAGANVW 197
                                       ************************994...58999999999987.699999998877776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2095.91
//
Query:       gi|557694595|ref|YP_008797649.1|  [L=283]
Description: deoxyribonuclease IV [Candidatus Caldiarchaeum subterraneum]
Scores for 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-40  137.2   0.0    5.9e-40  136.9   0.0    1.1  1  AP_endonuc_2    Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
       0.04   13.9   0.0        1.1    9.2   0.0    2.3  2  VirD1           T-DNA border endonuclease VirD1
      0.069   12.8   0.1       0.38   10.3   0.0    2.0  2  Ala_racemase_N  Alanine racemase, N-terminal domain
       0.12   12.3   0.1       0.54   10.1   0.0    2.0  2  DUF2124         Uncharacterized protein conserved in archaea 


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 !  136.9   0.0   1.3e-43   5.9e-40       2     210 .]      21     239 ..      20     239 .. 0.95

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 1.3e-43
                                       HHHHHCT-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS...HHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederear...reesvdalk 73 
                                       ++a+++G +++++f+r+++ ++    +++e++e+ + ++++g+++a+ ++++ ++         +    e+sv+ l 
  gi|557694595|ref|YP_008797649.1|  21 DRASQLGCTTFQIFTRNPRGWTYTklKQSEVEEFIRKFRQAGYTVAMAHMPYLPNIASP-----KkliYEKSVKSLI 92 
                                       89*********************9********************999999998888544.....347888******* PP

                                       HHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHH CS
                      AP_endonuc_2  74 raielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarll 148
                                       +++e++ +LG+ llv+h+G   ++ + ++e  +e++a+++n ++++  +++vk++lE++ag+ +++g   e++a++l
  gi|557694595|ref|YP_008797649.1|  93 SEVERCGQLGINLLVVHIG---SHLGAGIEKGIENVAKAVNTALEKV-DNNVKILLENMAGQRNSCGSrfEDIAQIL 165
                                       *******************...************************7.7**************************** PP

                                       HHHTTTT.EEEEEEHHHHHHH......TTTHHHHHHHHHGG.....EEEEEE.EESSTTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 149 davdspn.vgvclDtgHllia......eedvddalraladr.....ikhvHikDakgdlgagrdrhvpigeGei 210
                                       ++++++  vgvclDt+Hl++a      ++ v+++l ++++      ++++H++D+kg lg+g drh+ ig+G i
  gi|557694595|ref|YP_008797649.1| 166 SKIKNKSrVGVCLDTCHLYAAgydiktRAAVEATLSKFDEIvglekLHAIHLNDSKGGLGSGLDRHEHIGKGYI 239
                                       ***********************999999999999999998******************************976 PP

>> VirD1  T-DNA border endonuclease VirD1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.035   1.6e+02      26      50 ..      44      68 ..      35      81 .. 0.91
   2 ?    9.2   0.0   0.00025       1.1      74     138 ..     117     183 ..      95     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.035
                             VirD1 26 trlrsaeyesfsrqarslglsdsma 50
                                      t+l+ +e e f r+ r+ g + +ma
  gi|557694595|ref|YP_008797649.1| 44 TKLKQSEVEEFIRKFRQAGYTVAMA 68
                                      89*****************999998 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00025
                             VirD1  74 ailksigtlssniaallsayaenpttdlealraeriafgkafadldgllrsilsvsrrr..idgcsl 138
                                       +i k i  +++ + + l+   +n +  le +  +r++ g  f d+  +l  i   sr    +d c l
  gi|557694595|ref|YP_008797649.1| 117 GIEKGIENVAKAVNTALEKVDNNVKILLENMAGQRNSCGSRFEDIAQILSKIKNKSRVGvcLDTCHL 183
                                       5667788888889999999999*******************************99996411577776 PP

>> Ala_racemase_N  Alanine racemase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.17   7.8e+02     151     192 ..      27      70 ..      13      71 .. 0.76
   2 ?   10.3   0.0   8.6e-05      0.38     100     178 ..     126     208 ..     120     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.17
                                       EEE-S-SSTTSTS..HHHHHHHHHHHHHHHHHHHTTGGGSEEEE CS
                    Ala_racemase_N 151 glmtHfasadepd..eeteaqlarfeealeelekaglrppvvsl 192
                                       g +t+  +  +p+  ++t+ +++ +ee++ ++++ag+   + ++
  gi|557694595|ref|YP_008797649.1|  27 GCTTFQIFTRNPRgwTYTKLKQSEVEEFIRKFRQAGYTVAMAHM 70 
                                       55566666666667788999999999999999999988888876 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.6e-05
                                       HHHHHHHHHHTTS-EEEEEEBESSSS.SSSBSCHHHHHHHHHHHHTTTEEEEEEE-S-SST..TSTS.HHHHHHHHH CS
                    Ala_racemase_N 100 lealaaaareagkplrvhlkidtgmg.RlGftpeeleellealaalpglrleglmtHfasa..depd.eeteaqlar 172
                                       ++a++ a+++ +++++++l+   g    +G + e+++++l+++++++++ ++  + H+  a  d ++ +++ea l++
  gi|557694595|ref|YP_008797649.1| 126 AKAVNTALEKVDNNVKILLENMAGQRnSCGSRFEDIAQILSKIKNKSRVGVCLDTCHLYAAgyDIKTrAAVEATLSK 202
                                       7899999999**********999976789*******************99999999999997766557788889999 PP

                                       HHHHHH CS
                    Ala_racemase_N 173 feeale 178
                                       f+e++ 
  gi|557694595|ref|YP_008797649.1| 203 FDEIVG 208
                                       999875 PP

>> DUF2124  Uncharacterized protein conserved in archaea (DUF2124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.31   1.4e+03      88     116 ..      76     104 ..      45     109 .. 0.80
   2 ?   10.1   0.0   0.00012      0.54      71     118 ..     130     179 ..     117     189 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.31
                                       GGSTTTS--HHHHHHHHHHHEEEEEEEEE CS
                           DUF2124  88 lampkikveaedvkeliekiekkkviGvc 116
                                       +a pk  +  + vk+li+++e+   +G+ 
  gi|557694595|ref|YP_008797649.1|  76 IASPKKLIYEKSVKSLISEVERCGQLGIN 104
                                       67788888888889999988888888875 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00012
                                       EEE-.-S-EEEEEEEGGGGST..TTS--HHHHHHHHHHHEEEEEEEEEET CS
                           DUF2124  71 eeeaeeekadvvvllGGlamp..kikveaedvkeliekiekkkviGvcfm 118
                                       + + e+ + +v +ll  +a +  +++ + ed++++++ki++k+ +Gvc+ 
  gi|557694595|ref|YP_008797649.1| 130 NTALEKVDNNVKILLENMAGQrnSCGSRFEDIAQILSKIKNKSRVGVCLD 179
                                       45556677778888888886511567789*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); 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:                         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: 00:00:00.37
# Mc/sec: 2298.88
//
Query:       gi|557694596|ref|YP_008797650.1|  [L=326]
Description: glyoxalase family protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   62.8   0.0    1.8e-07   31.4   0.0    2.2  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
      0.028   14.7   0.0         12    6.2   0.0    3.4  2  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge


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 !   31.4   0.0   2.1e-11   1.8e-07       2     127 ..      35     146 ..      34     147 .. 0.84
   2 !   29.5   0.0   7.7e-11   6.9e-07       1     128 []     200     319 ..     200     319 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 2.1e-11
                                       EEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBS.CTSEEE CS
                        Glyoxalase   2 idhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkie.etvhhv 77 
                                       +++v l v+ l +sldFY++vLGf+ +   +         +a++   +  + lv+ +   ga+++   ++  +  h+
  gi|557694596|ref|YP_008797650.1|  35 VGWVGLTVSSLGRSLDFYKGVLGFRQFGMLG---------GAAVLGADENVPLVILHEQRGAEPRP--PNrRGLYHF 100
                                       678999***********************99.........66677777778888888888888888..55449**** PP

                                       EEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEE CS
                        Glyoxalase  78 afialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGille 127
                                       a+++ +  d+++a+ r++ +  ++ +  ++ + +aly     Dpd + +e
  gi|557694596|ref|YP_008797650.1| 101 AVLYPSRRDLARAFTRVAHRW-SFEGFADHLVSEALY---LSDPDLHGIE 146
                                       ****************98665.999999999999998...8888866655 PP

  == domain 2  score: 29.5 bits;  conditional E-value: 7.7e-11
                                       EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBS.C.TSE CS
                        Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkie.e.tvh 75 
                                       +i+h+ l v+ lek+ +FY++ LG++++ ++        +++ f+ agg h+ +  n  ++  a++    e + +  
  gi|557694596|ref|YP_008797650.1| 200 RIGHIHLHVSSLEKAEQFYHGLLGLDVTLRSF-------PGALFLSAGGYHHHVGANIWAGLNAAPP--SEnHvQLK 267
                                       699***************************99.......8999999999999876665444444444..22124799 PP

                                       EEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEEEEEETTSEEEEE CS
                        Glyoxalase  76 hvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysfyfrDpdGillei 128
                                        + ++  +   ++  ++ l e+gv vv+++  h+f++ +++ + D dG+++e+
  gi|557694596|ref|YP_008797650.1| 268 SFSLVLPSRRSLELLVKWLLENGVDVVDGL-VHGFEGYEGVTVMDFDGNRVEL 319
                                       ******************************.99999999999*********96 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 ?    4.3   0.0    0.0052        47       3      75 ..      38     103 ..      37     122 .. 0.60
   2 ?    6.2   0.0    0.0014        12       2      26 ..     203     227 ..     202     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0052
                                       EEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT-THHHTS-EEEEEEEE CS
                      Glyoxalase_4   3 igivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegpeflaehgeglhhlayw 75 
                                       +g+ V +l + +++++++lG++++            a +l  +++v +   +  +g+e+   ++ gl+h+a+ 
  gi|557694596|ref|YP_008797650.1|  38 VGLTVSSLGRSLDFYKGVLGFRQFGMLG-------GAAVLGADENVPLVILHEQRGAEPRPPNRRGLYHFAVL 103
                                       6888899999999999999986654432.......22222233344555555555555555566666666665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0014
                                       EEEEE-S-HHHHHHHHHH.TT-EES CS
                      Glyoxalase_4   2 QigivVeDleaavarfsallGvgpw 26 
                                       +i + V +le+a +++ +llG++++
  gi|557694596|ref|YP_008797650.1| 203 HIHLHVSSLEKAEQFYHGLLGLDVT 227
                                       9999*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2473.54
//
Query:       gi|557694597|ref|YP_008797651.1|  [L=189]
Description: signal peptidase, type I [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-10   40.0   0.6    4.4e-10   39.4   0.6    1.3  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 !   39.4   0.6   2.5e-14   4.4e-10       2      55 ..      36     100 ..      35     117 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 2.5e-14
                                       XXSSTTCCTXXTTXEEEEECTS......---TTSEEEEEETTCE....-EEEEEEE.EETTEEEE CS
                     Peptidase_S24   2 vpGdSMeptlldGdlilVdkfs......epkrGdivvfrlpgee....eayiKrvi.glpgdrvl 55 
                                       v+++SM p ++ Gd+i+V + s      +p +Gd++vf  pge+     ++++r + +  g+ + 
  gi|557694597|ref|YP_008797651.1|  36 VKSGSMRPVIEVGDIIIVLPVSpddvraDPVNGDVIVFYRPGEKgvpgSIIVHRAVaRVSGGFIT 100
                                       9*******************99*************************999999988344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1496.94
//
Query:       gi|557694598|ref|YP_008797652.1|  [L=911]
Description: hypothetical protein CSUB_C1170 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-39  133.9  59.9    1.1e-07   32.0   4.2   10.3 10  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    5.7e-20   71.1  24.5    6.8e-05   22.8   0.2    9.0  9  CarbopepD_reg_2  CarboxypepD_reg-like domain
    1.7e-12   47.5  20.8     0.0022   18.3   0.0    9.2  9  SpaA             Prealbumin-like fold domain
    6.3e-12   45.3  31.2    0.00016   21.6   0.2    7.4  7  Big_1            Bacterial Ig-like domain (group 1)
    6.3e-11   42.3  10.2      0.024   14.8   0.0    7.0  7  MG4              Macroglobulin domain MG4
    2.3e-10   40.6   1.4       0.17   12.0   0.1    6.3  6  DUF2012          Protein of unknown function (DUF2012)
    1.2e-08   35.6   2.9     0.0073   16.7   0.0    4.8  5  DUF4198          Domain of unknown function (DUF4198)
    2.5e-06   27.4  12.5       0.18   11.8   0.1    7.5  8  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
    2.2e-05   24.6  30.0       0.77   10.0   0.1    8.2  9  SdrD_B           SdrD B-like domain
     0.0016   18.7   0.1         13    6.1   0.0    4.8  4  DUF5013          Domain of unknown function (DUF5013)
  ------ inclusion threshold ------
      0.017   15.0   5.9        0.4   10.6   0.0    4.9  5  DUF1416          Protein of unknown function (DUF1416)
      0.019   14.8  14.2       0.57   10.0   0.2    6.2  8  DUF824           Salmonella repeat of unknown function (DUF82
      0.069   12.6   0.8         19    4.6   0.0    3.8  5  Dioxygenase_C    Dioxygenase
      0.078   12.9   0.6        8.4    6.4   0.0    3.7  3  Y_Y_Y            Y_Y_Y domain
       0.51   10.2   0.0       0.51   10.2   0.0    5.5  7  Glyco_hydro2_C5  Glycoside hydrolase family 2 C-terminal doma


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 !   10.0   4.1   0.00066      0.79       3      64 ..      37      95 ..      35     124 .. 0.76
   2 !   32.0   4.2   9.6e-11   1.1e-07       9      81 ..     127     195 ..     117     196 .. 0.89
   3 !   29.9   1.6   4.3e-10   5.1e-07       2      75 ..     198     277 ..     197     285 .. 0.78
   4 !    7.4   0.8    0.0043       5.1      27      73 ..     314     357 ..     273     364 .. 0.64
   5 !    6.8   0.2    0.0069       8.2      32      74 ..     398     439 ..     379     447 .. 0.78
   6 ?    3.9   0.2     0.056        67       9      77 ..     457     524 ..     449     528 .. 0.80
   7 !   27.7   0.3   2.1e-09   2.5e-06       5      72 ..     535     600 ..     531     615 .. 0.85
   8 !   14.4   0.1   2.8e-05     0.034       5      67 ..     616     675 ..     612     689 .. 0.86
   9 !   13.4   0.1   5.7e-05     0.069       5      79 ..     695     764 ..     692     768 .. 0.81
  10 !   22.4   0.1   9.1e-08   0.00011       4      59 ..     773     826 ..     770     846 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00066
                   CarboxypepD_reg  3 sGrVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglpp.gtysvtvsapGyatatr 64
                                      +  V+ + +++p+ ga V+v       +++  t++ G+  + gl    + +v+v + G+  +  
  gi|557694598|ref|YP_008797652.1| 37 TINVRTSdTNQPVVGALVRVN-----GTSTNSTNSVGNAVFGGLNRkANATVEVLFRGFTVYYN 95
                                      5668776589***********.....6788899***********999*******9999987665 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 9.6e-11
                   CarboxypepD_reg   9 asgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttlditL 81 
                                       a g+p++++++t+t   ++ + +ttt++dG+ +++++p +ty++  ++ Gy+  t++  +   g   tld++L
  gi|557694598|ref|YP_008797652.1| 127 ALGNPVPNVRITLT--YGSYTNTTTTGSDGRASISFMPNTTYTISTTYRGYDVGTFT--RAYGGSGLTLDLNL 195
                                       579***********..8999********************************99986..56666677777766 PP

  == domain 3  score: 29.9 bits;  conditional E-value: 4.3e-10
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtv...tnadtgtv..astttdadGafrlrglppgtysvtvsapGyatat.reevtltag 72 
                                       i+  V d +g+p++ atV v    +++++t+   s+ttd++G   l+ lp+g+y + v++ G   +   +++ ++ g
  gi|557694598|ref|YP_008797652.1| 198 IRAIVEDLNGNPVPSATVKVwygVRQSGNTTgfESATTDSSGVAILDRLPAGNYPLDVEYRGENVYQtTSNIAVSSG 274
                                       78889**************7444224444444699***********************9888763331358999999 PP

                   CarboxypepD_reg  73 qtt 75 
                                       q +
  gi|557694598|ref|YP_008797652.1| 275 QVV 277
                                       875 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0043
                   CarboxypepD_reg  27 gtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagq 73 
                                       +     +t ++G+f +  ++  tys++v +   + ++  +  ++a +
  gi|557694598|ref|YP_008797652.1| 314 SPYGDPVTTSTGEFGFGLVKSRTYSLVVKMGDTEVFRG-D--VRAPD 357
                                       344556899********9999*******8876665554.2..44444 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.0069
                   CarboxypepD_reg  32 tttdadGafrlrglppgtysvtvsapGyatatreevtltagqt 74 
                                        +t  +Ga  ++++p+g+ys ++++  y   +  +v+++ +++
  gi|557694598|ref|YP_008797652.1| 398 ERTTVNGATGFQNIPAGRYSYEITRGTYVIGSG-TVEINQDEQ 439
                                       468888999999*************99998886.477776554 PP

  == domain 6  score: 3.9 bits;  conditional E-value: 0.056
                   CarboxypepD_reg   9 asgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttl 77 
                                         g++iaga V++++ d+ +    + d++Ga +++gl p  y+ +v ++G +     e+tl+a+q++ +
  gi|557694598|ref|YP_008797652.1| 457 DMGEGIAGA-VELKSYDDVSLGVFQADENGATTVSGLLPILYRGVVNYKGVKVNDGFEFTLDADQKEVV 524
                                       556777776.7777666666677789*************************988877899999998766 PP

  == domain 7  score: 27.7 bits;  conditional E-value: 2.1e-09
                   CarboxypepD_reg   5 rVtdasg.apiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltag 72 
                                       rV da+g ++++ a+Vtv+   ++ +a+ +td+dG+ ++++lp g+y++ v + +   ++  +v+++  
  gi|557694598|ref|YP_008797652.1| 535 RVFDADGeTALSSAQVTVS--LGEISAENVTDSDGRASVKNLPIGSYNIAVNYLNIGVHEE-TVRIDSS 600
                                       899*9862699********..68889**************************999998886.4666654 PP

  == domain 8  score: 14.4 bits;  conditional E-value: 2.8e-05
                   CarboxypepD_reg   5 rVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreev 67 
                                        V+d +gap++   V++     g+v+ +   ++G+  ++++p+ ty++ ++++G   + r++v
  gi|557694598|ref|YP_008797652.1| 616 EVVDDDGAPLESGDVEIV---LGVVKKAGEIENGRVIFKDIPASTYRLSARYKGVTVYDRQTV 675
                                       69***************9...7********************************988877544 PP

  == domain 9  score: 13.4 bits;  conditional E-value: 5.7e-05
                   CarboxypepD_reg   5 rVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttldi 79 
                                       +V+  ++++++ a V+v+ +++ +     td++G+  l+ lp g++ v+vs++     +++ ++l   qtt+l++
  gi|557694598|ref|YP_008797652.1| 695 TVKRMDDTVLPAAYVSVA-QGGRKIGDGFTDQSGRLELK-LPRGDFAVEVSYQDTVVLSQS-ISLV--QTTQLNL 764
                                       67888999**********.57778999***********7.***********9988777764.5555..5555554 PP

  == domain 10  score: 22.4 bits;  conditional E-value: 9.1e-08
                   CarboxypepD_reg   4 GrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGy 59 
                                        r+ d+sg+p+aga+V++   ++++  + +td++G+  l   + g+y+ t+    y
  gi|557694598|ref|YP_008797652.1| 773 VRIIDPSGEPVAGAEVSLN-RGDKVIERKVTDEEGKAVLY-AAEGDYTWTMKIGEY 826
                                       6899**************9.58888999999999999985.666999998844443 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 !    6.6   0.4    0.0064       7.7       5      55 ..      40      90 ..      39     100 .. 0.73
   2 !   13.4   0.4   4.9e-05     0.059      11      61 ..     129     181 ..     124     197 .. 0.80
   3 !   10.8   0.1   0.00031      0.37       5      67 ..     201     274 ..     200     285 .. 0.69
   4 ?    3.5   0.0     0.061        73      29      52 ..     320     343 ..     296     362 .. 0.92
   5 ?   -0.7   0.0       1.2   1.4e+03      34      64 ..     414     443 ..     396     457 .. 0.55
   6 !   22.8   0.2   5.7e-08   6.8e-05       4      71 ..     535     604 ..     535     619 .. 0.78
   7 ?    1.7   0.0      0.21   2.5e+02      32      62 ..     644     674 ..     616     687 .. 0.78
   8 !   12.8   0.0   7.4e-05     0.089      12      73 ..     702     765 ..     695     772 .. 0.75
   9 !    8.8   0.0    0.0014       1.6       5      55 ..     775     826 ..     774     851 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0064
                   CarbopepD_reg_2  5 VvdketkeplpgatVyvkgtkkgtvTdenGnFelknlpa.gkytLvvsyvGy 55
                                      V +++t++p+ ga V v+gt+++ +T++ Gn  +  l++  + t+ v + G+
  gi|557694598|ref|YP_008797652.1| 40 VRTSDTNQPVVGALVRVNGTSTN-STNSVGNAVFGGLNRkANATVEVLFRGF 90
                                      7778999************9986.5888887666655552345666666666 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.9e-05
                   CarbopepD_reg_2  11 keplpgatVyv..kgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekk 61 
                                       ++p+p + +++   + ++ t+T ++G+ +++ +p+ +yt+  +y Gy+  + +
  gi|557694598|ref|YP_008797652.1| 129 GNPVPNVRITLtyGSYTNTTTTGSDGRASISFMPNTTYTISTTYRGYDVGTFT 181
                                       689999988873244589999**************************976655 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00031
                   CarbopepD_reg_2   5 VvdketkeplpgatVyv......kgtk...kgtvTdenGnFelknlpagkytLvvsyvG...yktqekkvtvske 67 
                                       +v++ +++p+p atV v       g++     ++Td++G   l++lpag+y L v+y G   y+t + ++ vs++
  gi|557694598|ref|YP_008797652.1| 201 IVEDLNGNPVPSATVKVwygvrqSGNTtgfESATTDSSGVAILDRLPAGNYPLDVEYRGenvYQT-TSNIAVSSG 274
                                       6777888999999887643332222332335578***********************99444444.234445544 PP

  == domain 4  score: 3.5 bits;  conditional E-value: 0.061
                   CarbopepD_reg_2  29 vTdenGnFelknlpagkytLvvsy 52 
                                       vT + G+F +  +++ +y Lvv++
  gi|557694598|ref|YP_008797652.1| 320 VTTSTGEFGFGLVKSRTYSLVVKM 343
                                       7999******************87 PP

  == domain 5  score: -0.7 bits;  conditional E-value: 1.2
                   CarbopepD_reg_2  34 GnFelknlpagkytLvvsyvGyktqekkvtv 64 
                                       G+++ + +++g+y +    v  +++e+++t+
  gi|557694598|ref|YP_008797652.1| 414 GRYSYE-ITRGTYVIGSGTVEINQDEQRITL 443
                                       444443.445555555555555555555554 PP

  == domain 6  score: 22.8 bits;  conditional E-value: 5.7e-08
                   CarbopepD_reg_2   4 tVvdketkeplpga..tVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektld 71 
                                       +V+d++++++l  a  tV++ + ++  vTd++G+ ++knlp g y + v+y+     e++v +++  ++ 
  gi|557694598|ref|YP_008797652.1| 535 RVFDADGETALSSAqvTVSLGEISAENVTDSDGRASVKNLPIGSYNIAVNYLNIGVHEETVRIDSSREIV 604
                                       589999999998862266678889***************************8777777777776554443 PP

  == domain 7  score: 1.7 bits;  conditional E-value: 0.21
                   CarbopepD_reg_2  32 enGnFelknlpagkytLvvsyvGyktqekkv 62 
                                       enG+  +k++pa +y+L ++y G +   ++ 
  gi|557694598|ref|YP_008797652.1| 644 ENGRVIFKDIPASTYRLSARYKGVTVYDRQT 674
                                       7899999**************9988766554 PP

  == domain 8  score: 12.8 bits;  conditional E-value: 7.4e-05
                   CarbopepD_reg_2  12 eplpgatVyvkgtkkgtv...TdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvn 73 
                                       + lp a V+v + +++     Td++G+ elk lp+g++ + vsy      ++++++ + ++l+++
  gi|557694598|ref|YP_008797652.1| 702 TVLPAAYVSVAQGGRKIGdgfTDQSGRLELK-LPRGDFAVEVSYQDTVVLSQSISLVQTTQLNLQ 765
                                       456677666655443332225*********7.****************99999999887777655 PP

  == domain 9  score: 8.8 bits;  conditional E-value: 0.0014
                   CarbopepD_reg_2   5 VvdketkeplpgatVyvkgtk...kgtvTdenGnFelknlpagkytLvvsyvGy 55 
                                       ++d  ++ep++ga V+++         vTde+G+  l +  +g+yt +++   y
  gi|557694598|ref|YP_008797652.1| 775 IID-PSGEPVAGAEVSLNRGDkviERKVTDEEGKAVL-YAAEGDYTWTMKIGEY 826
                                       566.4689*********77642447889******999.5889999887776555 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.3     0.013        15      30      58 ..     140     168 ..      31     172 .. 0.73
   2 !   11.2   0.0    0.0003      0.36      11      57 ..     215     252 ..     196     272 .. 0.77
   3 ?    2.0   0.0      0.22   2.7e+02      22      59 ..     296     340 ..     275     340 .. 0.80
   4 ?    0.5   0.0      0.65   7.8e+02      39      56 ..     399     416 ..     357     427 .. 0.83
   5 ?    3.4   0.1     0.082        98      30      57 ..     471     498 ..     444     528 .. 0.68
   6 !   18.3   0.0   1.9e-06    0.0022       6      57 ..     529     580 ..     510     582 .. 0.78
   7 ?    1.6   0.0      0.29   3.5e+02      41      58 ..     643     660 ..     609     661 .. 0.85
   8 ?   -0.4   0.0       1.2   1.5e+03      29      58 ..     712     740 ..     682     760 .. 0.76
   9 !    7.2   0.2    0.0052       6.2       3      57 ..     780     818 ..     778     838 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.013
                                       TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA  30 ktgtevttlttdenGkatfegLplGtYll 58 
                                       ++g+ ++t tt+++G+a+++ +p  tY++
  gi|557694598|ref|YP_008797652.1| 140 TYGSYTNTTTTGSDGRASISFMPNTTYTI 168
                                       3444569999*****************98 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0003
                                       EEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEE CS
                              SpaA  11 FtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYl 57 
                                        +++             +  ++t  +++ttd+ G a  + Lp+G+Y 
  gi|557694598|ref|YP_008797652.1| 215 VKVWYGV---------RQSGNTTGFESATTDSSGVAILDRLPAGNYP 252
                                       4444333.........2244567789********************5 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.22
                                       CHCHHTT........TTCCEESEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA  22 gkdalea.......kktgtevttlttdenGkatfegLplGtYllv 59 
                                       g +++++       + +++ +++ +t ++G++ f+ ++ +tY lv
  gi|557694598|ref|YP_008797652.1| 296 GAEQITGitlqaqlYRDTSPYGDPVTTSTGEFGFGLVKSRTYSLV 340
                                       44555555566677778899999*******************886 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.65
                                       E-BTTSEEEEEEEESEEE CS
                              SpaA  39 ttdenGkatfegLplGtY 56 
                                        t  nG + f ++p+G Y
  gi|557694598|ref|YP_008797652.1| 399 RTTVNGATGFQNIPAGRY 416
                                       46669**********988 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.082
                                       TTCCEESEEE-BTTSEEEEEEEESEEEE CS
                              SpaA  30 ktgtevttlttdenGkatfegLplGtYl 57 
                                       +++   + +  denG +t++gL +  Y 
  gi|557694598|ref|YP_008797652.1| 471 YDDVSLGVFQADENGATTVSGLLPILYR 498
                                       44555688999**********9986664 PP

  == domain 6  score: 18.3 bits;  conditional E-value: 1.9e-06
                                       -TS-EEEEEETT.TSCCCHCHHTT.....TTCCEESEEE-BTTSEEEEEEEESEEEE CS
                              SpaA   6 LaGaeFtlykvd.tttdgkdalea....kktgtevttlttdenGkatfegLplGtYl 57 
                                       + +++F ++++d +t+ +     +       g+ +++ +td++G+a++++Lp G+Y 
  gi|557694598|ref|YP_008797652.1| 529 VFNVVFRVFDADgETALS-----SaqvtVSLGEISAENVTDSDGRASVKNLPIGSYN 580
                                       557888888888533333.....233344567888*********************6 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.29
                                       BTTSEEEEEEEESEEEEE CS
                              SpaA  41 denGkatfegLplGtYll 58 
                                        enG++ f+++p+ tY l
  gi|557694598|ref|YP_008797652.1| 643 IENGRVIFKDIPASTYRL 660
                                       58**************87 PP

  == domain 8  score: -0.4 bits;  conditional E-value: 1.2
                                       .TTCCEESEEE-BTTSEEEEEEEESEEEEE CS
                              SpaA  29 kktgtevttlttdenGkatfegLplGtYll 58 
                                       ++ g ++++  td+ G+++ + Lp G++ +
  gi|557694598|ref|YP_008797652.1| 712 AQGGRKIGDGFTDQSGRLELK-LPRGDFAV 740
                                       55678889999*******999.99998765 PP

  == domain 9  score: 7.2 bits;  conditional E-value: 0.0052
                                       CCB-TS-EEEEEETTTSCCCHCHHTT.TTCCEESEEE-BTTSEEEEEEEESEEEE CS
                              SpaA   3 gkpLaGaeFtlykvdtttdgkdaleakktgtevttlttdenGkatfegLplGtYl 57 
                                       g+p+aGae +l + d               +++++++tde+Gka     + G+Y+
  gi|557694598|ref|YP_008797652.1| 780 GEPVAGAEVSLNRGD---------------KVIERKVTDEEGKAVLY-AAEGDYT 818
                                       789999999999999...............799**********9988.4556655 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 ?    0.2   3.7      0.65   7.7e+02       7      43 ..      36      65 ..      30      81 .. 0.74
   2 !   15.5   2.9   1.1e-05     0.013       7      53 ..     118     161 ..     114     171 .. 0.83
   3 !   21.6   0.2   1.3e-07   0.00016       9      48 ..     198     241 ..     195     244 .. 0.80
   4 !    7.0   0.7    0.0049       5.9      12      51 ..     535     572 ..     527     573 .. 0.74
   5 ?   -0.3   0.2       0.9   1.1e+03       6      26 ..     610     630 ..     607     634 .. 0.81
   6 ?   -0.8   0.0       1.3   1.6e+03      11      51 ..     694     732 ..     691     733 .. 0.72
   7 !   12.7   0.0   7.9e-05     0.094       9      49 ..     771     809 ..     767     813 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.65
                             Big_1  7 ntltatvkDangnpvagatVtfsvsggalsassgtTd 43
                                      +t++++  D n +pv ga V ++ ++++ +      +
  gi|557694598|ref|YP_008797652.1| 36 VTINVRTSDTN-QPVVGALVRVNGTSTNST------N 65
                                      78888888865.999999999887774443......2 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.1e-05
                             Big_1   7 ntltatvkDangnpvagatVtfsvsggalsassgtTdanGkatvtlt 53 
                                       +t    ++ a gnpv+++ +t++  +    ++++tT+++G+a++++ 
  gi|557694598|ref|YP_008797652.1| 118 TTMVLFARTALGNPVPNVRITLTYGS---YTNTTTTGSDGRASISFM 161
                                       67778899***************888...46689*********9975 PP

  == domain 3  score: 21.6 bits;  conditional E-value: 1.3e-07
                             Big_1   9 ltatvkDangnpvagatVtfsvsg...gals.assgtTdanGka 48 
                                       ++a+v D ngnpv+ atV++       g+++   s+tTd++G+a
  gi|557694598|ref|YP_008797652.1| 198 IRAIVEDLNGNPVPSATVKVWYGVrqsGNTTgFESATTDSSGVA 241
                                       89****************86332223566666**********99 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0049
                             Big_1  12 tvkDang.npvagatVtfsvsggalsassgtTdanGkatvt 51 
                                       +v Da+g ++++ a+Vt+s     + +++ +Td++G+a+v+
  gi|557694598|ref|YP_008797652.1| 535 RVFDADGeTALSSAQVTVSLGE--I-SAENVTDSDGRASVK 572
                                       6666666457778888777554..4.889*********985 PP

  == domain 5  score: -0.3 bits;  conditional E-value: 0.9
                             Big_1   6 tntltatvkDangnpvagatV 26 
                                        + + + v+D +g p++   V
  gi|557694598|ref|YP_008797652.1| 610 VVDVIVEVVDDDGAPLESGDV 630
                                       5778999********987666 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 1.3
                             Big_1  11 atvkDangnpvagatVtfsvsggalsassgtTdanGkatvt 51 
                                        tvk  + ++++ a V++   g ++  + g Td++G+ + +
  gi|557694598|ref|YP_008797652.1| 694 LTVKRMDDTVLPAAYVSVAQGGRKI--GDGFTDQSGRLELK 732
                                       6777777777777777777666555..8999****997765 PP

  == domain 7  score: 12.7 bits;  conditional E-value: 7.9e-05
                             Big_1   9 ltatvkDangnpvagatVtfsvsggalsassgtTdanGkat 49 
                                       + +++ D +g pvaga+V+++  +   +    +Td++Gka+
  gi|557694598|ref|YP_008797652.1| 771 VDVRIIDPSGEPVAGAEVSLNRGD--KVIERKVTDEEGKAV 809
                                       789999************998555..44589********97 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.8   2.2e+03      18      46 ..      38      63 ..      35      81 .. 0.68
   2 !   13.1   0.0   6.9e-05     0.082      24      71 ..     126     168 ..     119     175 .. 0.83
   3 !   14.8   0.0     2e-05     0.024      16      60 ..     196     243 ..     195     267 .. 0.88
   4 ?    1.4   0.1       0.3   3.6e+02      16      60 ..     530     571 ..     527     584 .. 0.77
   5 ?    1.9   0.0      0.21   2.5e+02      18      60 ..     613     650 ..     610     665 .. 0.76
   6 ?    1.4   0.0       0.3   3.6e+02      16      60 ..     690     731 ..     686     752 .. 0.80
   7 !    8.3   0.0    0.0022       2.6      15      60 ..     768     810 ..     754     822 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.8
                               MG4 18 ikVlvkdpdgspaknvpVkiealksetee 46
                                      i V+ +d+ ++p+ + +V+++ ++  t++
  gi|557694598|ref|YP_008797652.1| 38 INVRTSDT-NQPVVGALVRVNGTS--TNS 63
                                      45555554.799999999999932..222 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.9e-05
                               MG4  24 dpdgspaknvpVkiealkseteekeslttdedGtakfsintpedaksl 71 
                                        ++g+p++nv +++++ +   ++ +++tt +dG+a++s+ +p+++ ++
  gi|557694598|ref|YP_008797652.1| 126 TALGNPVPNVRITLTY-G---SYTNTTTTGSDGRASISF-MPNTTYTI 168
                                       678*************.6...59999***********99.77776655 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2e-05
                               MG4  16 fsikVlvkdpdgspaknvpVkiea.lk..seteekeslttdedGtakf 60 
                                       fsi+  v+d +g+p++  +Vk+ + ++   +t+  es ttd++G+a +
  gi|557694598|ref|YP_008797652.1| 196 FSIRAIVEDLNGNPVPSATVKVWYgVRqsGNTTGFESATTDSSGVAIL 243
                                       89*********************974466678889999*******976 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.3
                               MG4  16 fsikVlvkdpdgspa.knvpVkiealkseteekeslttdedGtakf 60 
                                       f++  +v d+dg+ a +  +V++++ +   e   +  td+dG+a++
  gi|557694598|ref|YP_008797652.1| 530 FNVVFRVFDADGETAlSSAQVTVSL-G---EISAENVTDSDGRASV 571
                                       7888999999998653788999999.5...334455789***9986 PP

  == domain 5  score: 1.9 bits;  conditional E-value: 0.21
                               MG4  18 ikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakf 60 
                                       + V+v+d dg p++   V i + +      ++  + e+G++ f
  gi|557694598|ref|YP_008797652.1| 613 VIVEVVDDDGAPLESGDVEIVL-G----VVKKAGEIENGRVIF 650
                                       569************9999999.3....234445566666665 PP

  == domain 6  score: 1.4 bits;  conditional E-value: 0.3
                               MG4  16 fsikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakf 60 
                                       + +++ vk+ d++ ++   V++++ +    +     td++G+ ++
  gi|557694598|ref|YP_008797652.1| 690 YYLRLTVKRMDDTVLPAAYVSVAQ-G--GRKIGDGFTDQSGRLEL 731
                                       999*******************99.4..34444456677777665 PP

  == domain 7  score: 8.3 bits;  conditional E-value: 0.0022
                               MG4  15 PfsikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakf 60 
                                        + + V++ dp g+p+++  V+++  +  ++  e++ tde+G a +
  gi|557694598|ref|YP_008797652.1| 768 VYRVDVRIIDPSGEPVAGAEVSLNR-G--DKVIERKVTDEEGKAVL 810
                                       5999********************9.4..56677788999998765 PP

>> DUF2012  Protein of unknown function (DUF2012)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.027        32       5      51 ..     130     175 ..     126     180 .. 0.90
   2 ?    5.9   0.0     0.011        13      16      64 ..     225     274 ..     204     312 .. 0.66
   3 ?   -0.8   0.0       1.3   1.6e+03      25      48 ..     320     343 ..     296     349 .. 0.68
   4 ?    5.5   0.0     0.015        18      25      64 ..     399     438 ..     382     470 .. 0.80
   5 !   12.0   0.1   0.00014      0.17       9      65 ..     547     602 ..     541     641 .. 0.71
   6 ?    4.4   0.0     0.033        39      29      51 ..     645     667 ..     639     676 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.027
                           DUF2012   5 nllantrvlLdsgqqrkfkalvrrDGsFifrdlpegsYlLevespey 51 
                                       n ++n+r++L  g++ + ++ + +DG  +++ +p+ +Y++   +++y
  gi|557694598|ref|YP_008797652.1| 130 NPVPNVRITLTYGSY-TNTTTTGSDGRASISFMPNTTYTISTTYRGY 175
                                       6789******99999.89999*******************9999887 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                           DUF2012  16 sgqqrkfkalvrrDGsFifrdlpegsYlLevespeyv.Fep.yrVdvkdkg 64 
                                       ++++   +a + ++G  i+  lp+g Y L+ve+++ + +++   + v+ +g
  gi|557694598|ref|YP_008797652.1| 225 GNTTGFESATTDSSGVAILDRLPAGNYPLDVEYRGENvYQTtSNIAVS-SG 274
                                       44554457888899999***************9975414443445555.44 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.3
                           DUF2012  25 lvrrDGsFifrdlpegsYlLeves 48 
                                       ++++ G+F f  +++ +Y L v+ 
  gi|557694598|ref|YP_008797652.1| 320 VTTSTGEFGFGLVKSRTYSLVVKM 343
                                       45667**************98875 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.015
                           DUF2012  25 lvrrDGsFifrdlpegsYlLevespeyvFepyrVdvkdkg 64 
                                        ++++G   f+++p+g+Y  e+   +yv     V++++  
  gi|557694598|ref|YP_008797652.1| 399 RTTVNGATGFQNIPAGRYSYEITRGTYVIGSGTVEINQDE 438
                                       577888889*******************999999999332 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 0.00014
                           DUF2012   9 ntrvlLdsgqqrkfkalvrrDGsFifrdlpegsYlLevespeyvFepyrVdvkdkgk 65 
                                        ++v+++ g+  + + ++ +DG  ++++lp gsY++ v++ ++  ++  V++ ++ +
  gi|557694598|ref|YP_008797652.1| 547 SAQVTVSLGEI-SAENVTDSDGRASVKNLPIGSYNIAVNYLNIGVHEETVRIDSSRE 602
                                       45555555555.57899***********************99988886666663332 PP

  == domain 6  score: 4.4 bits;  conditional E-value: 0.033
                           DUF2012  29 DGsFifrdlpegsYlLevespey 51 
                                       +G  if+d+p+++Y L +++ ++
  gi|557694598|ref|YP_008797652.1| 645 NGRVIFKDIPASTYRLSARYKGV 667
                                       7889**************99876 PP

>> DUF4198  Domain of unknown function (DUF4198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0011       1.3     160     212 ..     128     173 ..     103     174 .. 0.77
   2 !   16.7   0.0   6.1e-06    0.0073     159     212 ..     205     258 ..     198     259 .. 0.86
   3 ?    0.4   0.0      0.61   7.3e+02     166     211 ..     547     585 ..     504     587 .. 0.68
   4 ?   -2.0   0.0       3.1   3.7e+03     160     212 ..     621     665 ..     604     681 .. 0.67
   5 ?    4.7   0.0     0.028        34     161     193 ..     780     815 ..     759     826 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                           DUF4198 160 dGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwlleaehe 212
                                        G P++++ ++++yg+  y + +     +t++dG++++ +    ++ ++++++
  gi|557694598|ref|YP_008797652.1| 128 LGNPVPNVRITLTYGS--YTNTT-----TTGSDGRASISFMPNTTYTISTTYR 173
                                       499***********75..33333.....79***********999999999886 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 6.1e-06
                           DUF4198 159 ldGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwlleaehe 212
                                       l+G P++ a+v+v+yg  ++ + ++   ++td+ Gv+ +    aG + l++e++
  gi|557694598|ref|YP_008797652.1| 205 LNGNPVPSATVKVWYGVRQSGNTTGFESATTDSSGVAILDRLPAGNYPLDVEYR 258
                                       79************987655555555555********************99986 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.61
                           DUF4198 166 gaeveveyggtryrdapdeikv..ktdadGvvtftlpkaGlwlleaeh 211
                                        a+v+v  g         ei +   td+dG+++++    G + +++++
  gi|557694598|ref|YP_008797652.1| 547 SAQVTVSLG---------EISAenVTDSDGRASVKNLPIGSYNIAVNY 585
                                       455555442.........22224489*******998888888887765 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3.1
                           DUF4198 160 dGkPlagaeveveyggtryrdapdeikvktdadGvvtftlpkaGlwlleaehe 212
                                       dG Pl+  +ve++    + +++++e      ++G+v f+   a ++ l+a+++
  gi|557694598|ref|YP_008797652.1| 621 DGAPLESGDVEIVL---GVVKKAGE-----IENGRVIFKDIPASTYRLSARYK 665
                                       56666666666665...34555555.....55666666665666666655554 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.028
                           DUF4198 161 GkPlagaeveveyggt...ryrdapdeikvktdadG 193
                                       G+P+agaev++ +g++   r++++++   v + a+G
  gi|557694598|ref|YP_008797652.1| 780 GEPVAGAEVSLNRGDKvieRKVTDEEGKAVLYAAEG 815
                                       9**********9988776666666655555666665 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 ?    2.5   0.2      0.12   1.4e+02      13      38 ..      34      59 ..      26      86 .. 0.77
   2 ?    1.8   0.0      0.21   2.5e+02      23      57 ..     127     159 ..     109     182 .. 0.76
   3 !    6.2   0.0    0.0089        11      18      59 ..     201     246 ..     188     273 .. 0.75
   4 ?   -0.9   0.0       1.4   1.7e+03      33      86 ..     466     538 ..     457     555 .. 0.65
   5 ?   -0.1   0.0      0.78   9.3e+02      32      58 ..     549     573 ..     540     582 .. 0.75
   6 ?    0.3   0.0      0.59     7e+02      24      46 ..     606     628 ..     587     666 .. 0.87
   7 ?    3.5   0.0     0.059        70      31      59 ..     707     734 ..     691     774 .. 0.72
   8 !   11.8   0.1   0.00015      0.18      24      58 ..     779     812 ..     760     823 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.12
                              bMG3 13 dkllvwvtsLdsgkPvagaeVrlldk 38
                                       ++++ v++ d+++Pv ga Vr+   
  gi|557694598|ref|YP_008797652.1| 34 TGVTINVRTSDTNQPVVGALVRVNGT 59
                                      578899999************99654 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.21
                              bMG3  23 dsgkPvagaeVrlldkkgevlaegtTDaqGvarfa 57 
                                       + g+Pv++++++l         ++tT ++G+a+++
  gi|557694598|ref|YP_008797652.1| 127 ALGNPVPNVRITLTYG--SYTNTTTTGSDGRASIS 159
                                       5699********9864..55567777777777765 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0089
                              bMG3  18 wvtsLdsgkPvagaeVrl...ldkkgev..laegtTDaqGvarfaal 59 
                                       +v+ L +g+Pv+ a+V++   + ++g++    ++tTD++Gva +++l
  gi|557694598|ref|YP_008797652.1| 201 IVEDL-NGNPVPSATVKVwygVRQSGNTtgFESATTDSSGVAILDRL 246
                                       55555.489999999999444345555423789*********99987 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.4
                              bMG3  33 VrlldkkgevlaegtTDaqGvarfaallar...................gkegaapylvsArkdedlaflkld 86 
                                       V+l + ++  l+  ++D++G  ++++ll+                    + ++++  +v+A+k   + f  +d
  gi|557694598|ref|YP_008797652.1| 466 VELKSYDDVSLGVFQADENGATTVSGLLPIlyrgvvnykgvkvndgfefTLDADQKEVVVATKVFNVVFRVFD 538
                                       7777888888888888888888888876666666666666666666666666666777777765555555544 PP

  == domain 5  score: -0.1 bits;  conditional E-value: 0.78
                              bMG3  32 eVrlldkkgevlaegtTDaqGvarfaa 58 
                                       +V+++   ge  ae  TD++G+a++++
  gi|557694598|ref|YP_008797652.1| 549 QVTVS--LGEISAENVTDSDGRASVKN 573
                                       55444..467778999*******9876 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 0.59
                              bMG3  24 sgkPvagaeVrlldkkgevlaeg 46 
                                       ++k v ++ V+++d++g+ l +g
  gi|557694598|ref|YP_008797652.1| 606 KAKNVVDVIVEVVDDDGAPLESG 628
                                       6889999**********999876 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.059
                              bMG3  31 aeVrlldkkgevlaegtTDaqGvarfaal 59 
                                       a V++ ++ g+ ++ g TD++G+++++ +
  gi|557694598|ref|YP_008797652.1| 707 AYVSV-AQGGRKIGDGFTDQSGRLELKLP 734
                                       44443.5789**************99987 PP

  == domain 8  score: 11.8 bits;  conditional E-value: 0.00015
                              bMG3  24 sgkPvagaeVrlldkkgevlaegtTDaqGvarfaa 58 
                                       sg+PvagaeV+l ++ ++v+ +  TD++G a + a
  gi|557694598|ref|YP_008797652.1| 779 SGEPVAGAEVSL-NRGDKVIERKVTDEEGKAVLYA 812
                                       89********97.78899***********998765 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       4.5   5.4e+03      39      57 ..      59      77 ..      35      94 .. 0.68
   2 !    6.6   2.6    0.0073       8.8      23      84 ..     131     192 ..     126     206 .. 0.81
   3 !   10.0   0.1   0.00065      0.77      18      76 ..     204     268 ..     199     278 .. 0.77
   4 ?    5.1   0.1     0.022        27      20      68 ..     296     345 ..     292     364 .. 0.77
   5 ?    3.0   0.1     0.094   1.1e+02      36      67 ..     393     423 ..     367     440 .. 0.70
   6 ?   -0.8   0.1       1.4   1.7e+03      22      98 ..     460     531 ..     453     541 .. 0.70
   7 !    8.3   0.0    0.0022       2.7      20      67 ..     541     587 ..     527     604 .. 0.79
   8 ?   -0.7   0.0       1.4   1.7e+03      35      74 ..     714     752 ..     700     761 .. 0.79
   9 ?    5.7   0.0     0.014        17      18      61 ..     777     818 ..     774     840 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.5
                            SdrD_B 39 vatttTdasGkYkFtnltp 57
                                      ++t  T++ G+  F +l+ 
  gi|557694598|ref|YP_008797652.1| 59 TSTNSTNSVGNAVFGGLNR 77
                                      3466778888888877765 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0073
                            SdrD_B  23 gisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVefta.pagy.tvtakkaGsddald 84 
                                        + +v +tL  + g+ ++tttT ++G+ + + + + +Y+++ t+   ++ t+t +  Gs  +ld
  gi|557694598|ref|YP_008797652.1| 131 PVPNVRITL--TYGSYTNTTTTGSDGRASISFMPNTTYTISTTYrGYDVgTFTRAYGGSGLTLD 192
                                       688889999..7788889**********************998865555678887777777666 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00065
                            SdrD_B  18 dagekgisgvtVtL...kdakgevv..atttTdasGkYkFtnltpGeYkVefta.pagytvtakk 76 
                                       d + + +   tV++    +++g+++  ++ tTd+sG    + l +G+Y + +++  +++ +t+++
  gi|557694598|ref|YP_008797652.1| 204 DLNGNPVPSATVKVwygVRQSGNTTgfESATTDSSGVAILDRLPAGNYPLDVEYrGENVYQTTSN 268
                                       6667788888898888867777777668********************99998864444444443 PP

  == domain 4  score: 5.1 bits;  conditional E-value: 0.022
                            SdrD_B  20 gekgisgvtVtLkdakgevv.atttTdasGkYkFtnltpGeYkVeftapa 68 
                                       g + i+g+t++ +  ++++     +T ++G++ F  +++ +Y++ ++  +
  gi|557694598|ref|YP_008797652.1| 296 GAEQITGITLQAQLYRDTSPyGDPVTTSTGEFGFGLVKSRTYSLVVKMGD 345
                                       5678999999985555555548999*****************99987744 PP

  == domain 5  score: 3.0 bits;  conditional E-value: 0.094
                            SdrD_B  36 gevvatttTdasGkYkFtnltpGeYkVeftap 67 
                                       g+  ++  T  +G+  F+n+ +G+Y+ e+t  
  gi|557694598|ref|YP_008797652.1| 393 GSF-SSERTTVNGATGFQNIPAGRYSYEITRG 423
                                       333.4556778899999999999999887664 PP

  == domain 6  score: -0.8 bits;  conditional E-value: 1.4
                            SdrD_B  22 kgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVeftapagytvtakkaGsddaldSdadpatgltktvt 98 
                                       +gi+g  V+Lk+ ++ ++     d++G+ + ++l p  Y+  +    +y+  + + G + +ld+d +++   tk+++
  gi|557694598|ref|YP_008797652.1| 460 EGIAG-AVELKSYDDVSLGVFQADENGATTVSGLLPILYRGVV----NYKGVKVNDGFEFTLDADQKEVVVATKVFN 531
                                       67777.4888888888888888888888888888888877554....444455667777777777777777776665 PP

  == domain 7  score: 8.3 bits;  conditional E-value: 0.0022
                            SdrD_B  20 gekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVefta.p 67 
                                       ge++ s  +Vt+  + ge+ a+ +Td++G+ + +nl  G+Y++++ +  
  gi|557694598|ref|YP_008797652.1| 541 GETALSSAQVTV--SLGEISAENVTDSDGRASVKNLPIGSYNIAVNYlN 587
                                       566666655555..5588889999*******************997644 PP

  == domain 8  score: -0.7 bits;  conditional E-value: 1.4
                            SdrD_B  35 kgevvatttTdasGkYkFtnltpGeYkVeftapagytvta 74 
                                        g ++    Td+sG+ + + l  G++ Ve+++ + +++++
  gi|557694598|ref|YP_008797652.1| 714 GGRKIGDGFTDQSGRLELK-LPRGDFAVEVSYQDTVVLSQ 752
                                       5666677889999999985.99*******99977766655 PP

  == domain 9  score: 5.7 bits;  conditional E-value: 0.014
                            SdrD_B  18 dagekgisgvtVtLkdakgevvatttTdasGkYkFtnltpGeYk 61 
                                       d   + ++g +V+L ++ ++v+++ +Td++Gk      ++G+Y+
  gi|557694598|ref|YP_008797652.1| 777 DPSGEPVAGAEVSL-NRGDKVIERKVTDEEGKAVLY-AAEGDYT 818
                                       677789********.77788889*****88874332.3445554 PP

>> DUF5013  Domain of unknown function (DUF5013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.011        13      71     101 ..     246     274 ..     242     284 .. 0.83
   2 ?   -1.0   0.0       1.6   1.9e+03      70      86 ..     572     589 ..     548     613 .. 0.80
   3 ?    4.5   0.0     0.032        39      56      91 ..     639     673 ..     607     683 .. 0.74
   4 ?    0.2   0.0       0.7   8.4e+02      69      97 ..     731     757 ..     724     764 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.011
                           DUF5013  71 LpaGkYelsvtvaeengqnsngtaylvvakg 101
                                       LpaG+Y l+v+++ en+ +    + ++v  g
  gi|557694598|ref|YP_008797652.1| 246 LPAGNYPLDVEYRGENVYQTT--SNIAVSSG 274
                                       9**************988876..66666655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                           DUF5013  70 t.LpaGkYelsvtvaeen 86 
                                       + Lp G+Y++ v++ +  
  gi|557694598|ref|YP_008797652.1| 572 KnLPIGSYNIAVNYLNIG 589
                                       459********9997765 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.032
                           DUF5013  56 dnaaieNgkiYQtvt.LpaGkYelsvtvaeengqnsn 91 
                                       ++ +ieNg++   ++ +pa +Y+ls+ ++  ++ + +
  gi|557694598|ref|YP_008797652.1| 639 KAGEIENGRVI--FKdIPASTYRLSARYKGVTVYDRQ 673
                                       344799**984..4449***********998877665 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.7
                           DUF5013  69 vtLpaGkYelsvtvaeengqnsngtaylv 97 
                                       ++Lp G + ++v+++++++ +++  + lv
  gi|557694598|ref|YP_008797652.1| 731 LKLPRGDFAVEVSYQDTVVLSQS--ISLV 757
                                       68***************999987..5555 PP

>> DUF1416  Protein of unknown function (DUF1416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.15   1.8e+02      18      51 ..      34      67 ..      26      84 .. 0.77
   2 ?   -1.7   0.0       2.3   2.7e+03      17      45 ..     267     296 ..     260     302 .. 0.77
   3 ?   -1.9   0.0       2.6   3.1e+03      14      37 ..     341     365 ..     333     374 .. 0.80
   4 ?   -0.3   0.1      0.81   9.7e+02      24      70 ..     499     545 ..     494     568 .. 0.68
   5 ?   10.6   0.0   0.00033       0.4      23      71 ..     772     822 ..     750     840 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.15
                           DUF1416 18 keaviqGkvtrdgepvggayvRLLdssgeFtaev 51
                                      + + i+ + +++++pv ga vR+  +s + t  v
  gi|557694598|ref|YP_008797652.1| 34 TGVTINVRTSDTNQPVVGALVRVNGTSTNSTNSV 67
                                      4556677777899*********988877777666 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.3
                           DUF1416  17 ekeaviqGkvtr.dgepvggayvRLLdssg 45 
                                       ++ av +G+v++ + + + +  vR+Ld +g
  gi|557694598|ref|YP_008797652.1| 267 SNIAVSSGQVVHrARTDLVNYRVRILDFDG 296
                                       456788899988677778887899999776 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.6
                           DUF1416  14 vdvekeaviqGkvtr.dgepvggay 37 
                                       v++ +  v  G v + d+++v+g +
  gi|557694598|ref|YP_008797652.1| 341 VKMGDTEVFRGDVRApDDTSVNGKF 365
                                       6677788999999999999999987 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.81
                           DUF1416  24 GkvtrdgepvggayvRLLdssgeFtaevvtsaeGefrFfaapGeWtv 70 
                                       G+v  +g  v+  +   Ld++   +   +   +  fr f a+Ge  +
  gi|557694598|ref|YP_008797652.1| 499 GVVNYKGVKVNDGFEFTLDADQKEVVVATKVFNVVFRVFDADGETAL 545
                                       66666777777777777777765443333444667999999987654 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.00033
                           DUF1416  23 qGkvtr.dgepvggayvRLLdssgeFtaevvtsaeGefrFfaapGe..WtvR 71 
                                         ++++ +gepv+ga v  L++ +      vt +eG+   +aa+G+  Wt++
  gi|557694598|ref|YP_008797652.1| 772 DVRIIDpSGEPVAGAEVS-LNRGDKVIERKVTDEEGKAVLYAAEGDytWTMK 822
                                       44566669*******998.588899999999**************6226665 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.3       1.8   2.2e+03      17      36 ..      36      56 ..      35      63 .. 0.84
   2 ?   -2.9   0.2       5.2   6.3e+03      21      34 ..      60      72 ..      43      72 .. 0.72
   3 ?   10.0   0.2   0.00048      0.57      22      39 ..     125     142 ..     112     146 .. 0.82
   4 ?    2.2   0.0      0.13   1.6e+02      21      36 ..     202     217 ..     201     221 .. 0.87
   5 ?   -1.9   0.0       2.5     3e+03      22      39 ..     537     555 ..     535     556 .. 0.87
   6 ?   -3.0   0.0       5.5   6.6e+03      21      33 ..     562     575 ..     561     576 .. 0.81
   7 ?   -0.0   0.0      0.67     8e+02      16      36 ..     612     632 ..     606     636 .. 0.78
   8 ?    6.2   0.0    0.0074       8.9      23      40 ..     777     794 ..     770     796 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.8
                            DUF824 17 ltitvkDasGn.Pvpnapftl 36
                                      +ti v+ +++n Pv  a +++
  gi|557694598|ref|YP_008797652.1| 36 VTINVRTSDTNqPVVGALVRV 56
                                      699999999999*98887765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.2
                            DUF824 21 vkDasGnPvpnapf 34
                                      +++ s+n+v+na f
  gi|557694598|ref|YP_008797652.1| 60 STN-STNSVGNAVF 72
                                      444.4677887765 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00048
                            DUF824  22 kDasGnPvpnapftltRg 39 
                                       + a+GnPvpn+ +tlt g
  gi|557694598|ref|YP_008797652.1| 125 RTALGNPVPNVRITLTYG 142
                                       679************977 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.13
                            DUF824  21 vkDasGnPvpnapftl 36 
                                       v D  GnPvp a++++
  gi|557694598|ref|YP_008797652.1| 202 VEDLNGNPVPSATVKV 217
                                       66889********987 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 2.5
                            DUF824  22 kDasGn.PvpnapftltRg 39 
                                        Da+G+ ++  a++t+++g
  gi|557694598|ref|YP_008797652.1| 537 FDADGEtALSSAQVTVSLG 555
                                       59999999999***99987 PP

  == domain 6  score: -3.0 bits;  conditional E-value: 5.5
                            DUF824  21 vkDasGn.Pvpnap 33 
                                       v+D++G  +v+n p
  gi|557694598|ref|YP_008797652.1| 562 VTDSDGRaSVKNLP 575
                                       89999998888866 PP

  == domain 7  score: -0.0 bits;  conditional E-value: 0.67
                            DUF824  16 pltitvkDasGnPvpnapftl 36 
                                        +++ v+D++G P+   ++ +
  gi|557694598|ref|YP_008797652.1| 612 DVIVEVVDDDGAPLESGDVEI 632
                                       6789*********86665555 PP

  == domain 8  score: 6.2 bits;  conditional E-value: 0.0074
                            DUF824  23 DasGnPvpnapftltRgd 40 
                                       D sG+Pv+ a ++l Rgd
  gi|557694598|ref|YP_008797652.1| 777 DPSGEPVAGAEVSLNRGD 794
                                       789**************9 PP

>> Dioxygenase_C  Dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.016        19      35      54 ..     201     220 ..     192     241 .. 0.79
   2 ?   -3.6   0.0       5.3   6.3e+03      33      62 ..     273     302 ..     260     339 .. 0.55
   3 ?   -3.5   0.0       4.8   5.8e+03      77      98 ..     560     581 ..     538     583 .. 0.79
   4 ?   -1.4   0.1       1.1   1.3e+03      35      51 ..     616     632 ..     598     634 .. 0.85
   5 ?    3.3   0.0     0.042        50      29      55 ..     768     794 ..     745     835 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.016
                                       EEE-TTSSB-TT-EEEEE-- CS
                     Dioxygenase_C  35 rvldeaGkplagalvelWha 54 
                                        v d +G+p++ a+v +W  
  gi|557694598|ref|YP_008797652.1| 201 IVEDLNGNPVPSATVKVWYG 220
                                       5889**************64 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.3
                                       EEEEE-TTSSB-TT-EEEEE---TTS--TT CS
                     Dioxygenase_C  33 sGrvldeaGkplagalvelWhanaeGrYsh 62 
                                       sG+v+ +a   l++ +v +   + + + + 
  gi|557694598|ref|YP_008797652.1| 273 SGQVVHRARTDLVNYRVRILDFDGAEQITG 302
                                       677777777777777776655554444443 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.8
                                       EEE--TTSEEEEEEE----EE- CS
                     Dioxygenase_C  77 riltdeeGryrirtikPapYpi 98 
                                         +td++Gr +++ +  ++Y+i
  gi|557694598|ref|YP_008797652.1| 560 ENVTDSDGRASVKNLPIGSYNI 581
                                       5689999999999988888876 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 1.1
                                       EEE-TTSSB-TT-EEEE CS
                     Dioxygenase_C  35 rvldeaGkplagalvel 51 
                                       +v+d +G pl+   ve+
  gi|557694598|ref|YP_008797652.1| 616 EVVDDDGAPLESGDVEI 632
                                       79**********99998 PP

  == domain 5  score: 3.3 bits;  conditional E-value: 0.042
                                       EEEEEEEEE-TTSSB-TT-EEEEE--- CS
                     Dioxygenase_C  29 rlvlsGrvldeaGkplagalvelWhan 55 
                                       +  +  r++d  G+p+aga v l + +
  gi|557694598|ref|YP_008797652.1| 768 VYRVDVRIIDPSGEPVAGAEVSLNRGD 794
                                       55577799*************987666 PP

>> Y_Y_Y  Y_Y_Y domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.17     2e+02      31      50 ..     241     260 ..     231     272 .. 0.75
   2 ?    6.4   0.0     0.007       8.4      25      49 ..     565     587 ..     555     597 .. 0.78
   3 ?   -3.4   0.0         8   9.6e+03      36      49 ..     733     746 ..     732     748 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.17
                                       EEEES--SEEEEEEEEEEET CS
                             Y_Y_Y  31 asytnlppGdYtlkVkakdn 50 
                                       a    lp+G+Y l V+++ +
  gi|557694598|ref|YP_008797652.1| 241 AILDRLPAGNYPLDVEYRGE 260
                                       555679*********99864 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.007
                                       SSTS.EEEEES--SEEEEEEEEEEE CS
                             Y_Y_Y  25 sdysqeasytnlppGdYtlkVkakd 49 
                                       sd +  as +nlp G+Y + V + +
  gi|557694598|ref|YP_008797652.1| 565 SD-G-RASVKNLPIGSYNIAVNYLN 587
                                       33.3.8*************998766 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 8
                                       --SEEEEEEEEEEE CS
                             Y_Y_Y  36 lppGdYtlkVkakd 49 
                                       lp Gd+ ++V++ d
  gi|557694598|ref|YP_008797652.1| 733 LPRGDFAVEVSYQD 746
                                       899******99877 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 ?   10.2   0.0   0.00043      0.51      18      59 ..     196     237 ..     192     241 .. 0.89
   2 ?   -2.6   0.0       4.1   4.9e+03       9      30 ..     276     297 ..     272     300 .. 0.83
   3 ?   -0.6   0.3      0.96   1.1e+03       5      41 ..     518     552 ..     515     566 .. 0.71
   4 ?    5.3   0.7     0.014        17      11      43 ..     604     636 ..     597     645 .. 0.81
   5 ?   -1.4   0.1       1.8   2.1e+03       5      24 ..     670     689 ..     668     690 .. 0.86
   6 ?    1.3   0.0      0.26   3.1e+02      16      37 ..     767     788 ..     756     792 .. 0.81
   7 ?   -3.0   0.0       5.5   6.5e+03      20      35 ..     797     812 ..     795     814 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00043
                   Glyco_hydro2_C5  18 afvtvevvDknGnlvpnadnevtfeveGpGelvgvdngdpts 59 
                                         +++ v D nGn+vp a+ +v   v+ +G+  g++++  +s
  gi|557694598|ref|YP_008797652.1| 196 FSIRAIVEDLNGNPVPSATVKVWYGVRQSGNTTGFESATTDS 237
                                       6688999****************************9987665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.1
                   Glyco_hydro2_C5   9 elkadgkDlafvtvevvDknGn 30 
                                       +++  ++Dl+  +v+++D +G 
  gi|557694598|ref|YP_008797652.1| 276 VVHRARTDLVNYRVRILDFDGA 297
                                       56677899**********9986 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.96
                   Glyco_hydro2_C5   5 adrtelkadgkDlafvtvevvDknGnlvpnadnevtf 41 
                                       ad++e+    + +  v ++v+D++G++    +++vt+
  gi|557694598|ref|YP_008797652.1| 518 ADQKEVVVA-TKVFNVVFRVFDADGETALS-SAQVTV 552
                                       555555544.46788999*******98655.444554 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.014
                   Glyco_hydro2_C5  11 kadgkDlafvtvevvDknGnlvpnadnevtfev 43 
                                         + k ++ v vevvD++G +++  d e+ + v
  gi|557694598|ref|YP_008797652.1| 604 VLKAKNVVDVIVEVVDDDGAPLESGDVEIVLGV 636
                                       55678899**************99999887765 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 1.8
                   Glyco_hydro2_C5   5 adrtelkadgkDlafvtvev 24 
                                        dr+++   ++Dl++v++ v
  gi|557694598|ref|YP_008797652.1| 670 YDRQTVFRADEDLVRVQAAV 689
                                       5899999999******9987 PP

  == domain 6  score: 1.3 bits;  conditional E-value: 0.26
                   Glyco_hydro2_C5  16 DlafvtvevvDknGnlvpnadn 37 
                                        + +v v+++D  G++v  a+ 
  gi|557694598|ref|YP_008797652.1| 767 KVYRVDVRIIDPSGEPVAGAEV 788
                                       5789*************99875 PP

  == domain 7  score: -3.0 bits;  conditional E-value: 5.5
                   Glyco_hydro2_C5  20 vtvevvDknGnlvpna 35 
                                       ++ +v+D++G+ v  a
  gi|557694598|ref|YP_008797652.1| 797 IERKVTDEEGKAVLYA 812
                                       677899****998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (911 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); 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:                        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: 0.73u 0.28s 00:00:01.01 Elapsed: 00:00:00.42
# Mc/sec: 6439.95
//
Query:       gi|557694599|ref|YP_008797653.1|  [L=182]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.6   0.4      0.066   13.2   0.1    1.8  2  Sdh5      Flavinator of succinate dehydrogenase
      0.044   13.6   0.7      0.068   13.0   0.7    1.4  1  DUF4515   Domain of unknown function (DUF4515)


Domain annotation for each model (and alignments):
>> Sdh5  Flavinator of succinate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.4e-06     0.066      20      69 ..      18      66 ..      16      70 .. 0.89
   2 ?   -2.4   0.0      0.55   4.9e+03      26      37 ..     114     125 ..     107     129 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.4e-06
                                      TTTHHHHHTTT--HHHHHHHHHHHTS--HHHHHHHHT-.---S-HHHHHH CS
                              Sdh5 20 LgrFaekhlatlseeeldaferLLdleDpdLldwltgrkeepedaelaal 69
                                      L++++e++l++l+ +e++a   LL+l D +L++  ++++++p++++ ++l
  gi|557694599|ref|YP_008797653.1| 18 LKTYLEQRLSDLE-KEAEAVRSLLELVDRELVAKSFKKAQPPPEPAEKEL 66
                                      78999****9995.67899*******************999999988776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.55
                                       HHTTT--HHHHH CS
                              Sdh5  26 khlatlseeeld 37 
                                       k l+++ e++l+
  gi|557694599|ref|YP_008797653.1| 114 KVLDSMREADLQ 125
                                       556777777776 PP

>> DUF4515  Domain of unknown function (DUF4515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.7   7.6e-06     0.068      72     117 ..      11      56 ..       3      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-06
                           DUF4515  72 alediaklkeqqerkiqtLeeekekvqaetaeklrelklqfLkeka 117
                                       +++ +a+lk   e+++ +Le+e e v++  +  +rel ++ +k+ +
  gi|557694599|ref|YP_008797653.1|  11 EVKRLAELKTYLEQRLSDLEKEAEAVRSLLELVDRELVAKSFKKAQ 56 
                                       688999*********************************9999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1298.75
//
Query:       gi|557694600|ref|YP_008797654.1|  [L=456]
Description: carbohydrate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-31  107.3   0.0    2.7e-29  102.5   0.0    2.6  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 
    4.1e-14   52.8   0.0    7.2e-14   52.0   0.0    1.5  1  FGGY_C       FGGY family of carbohydrate kinases, C-terminal 
     0.0059   16.1   0.3       0.14   11.7   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 !  102.5   0.0   4.5e-33   2.7e-29       2     245 .]       8     229 ..       7     229 .. 0.94

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 4.5e-33
                                       EEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE- CS
                            FGGY_N   2 ilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisgq 78 
                                       ++g+D+Gtt +ka+++de  +++a a+++l+++sp+ g   +d+ ei +++ e++r +++++  +   ++a+g+++q
  gi|557694600|ref|YP_008797654.1|   8 LIGVDVGTTAVKAVAVDECCQLLAEARLPLNIYSPSRGIFTHDAGEIRDKMFESLRLLMKKL--DGRRVEAMGVTAQ 82 
                                       58************************************************************..************* PP

                                       SS-EEEEETTTEESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHCEEEE CS
                            FGGY_N  79 reglvllDkndkpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekiekfll 155
                                        ++lvllD+ ++p+y++++  d+r+   +e+++   ++ ++  k          +  l Wl+++ep+v++ki k+l 
  gi|557694600|ref|YP_008797654.1|  83 SVSLVLLDRLGNPVYPVLSHLDKRADLAAEEMEG--SQGYIGRK---------LVGNLVWLRRHEPNVYAKISKVLD 148
                                       **************************99999876..44343333.........356799****************** PP

                                       HHHHHHHHHCT--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCCEEEEEECCCCCCTT.S-EEEE CS
                            FGGY_N 156 iddyLiwrLtgqfvtdvtnasesmlfnikklewdeellailgipeelLPklvesseiigelkpelaaklGlkegvpv 232
                                       +++y  + Ltg   +d        +f +++le    l+  +gi+++lL ++   + + g++ + +a+ ++lk+gvpv
  gi|557694600|ref|YP_008797654.1| 149 MKEYAGYLLTGRTSVDK------LWFMVEDLE---RLCLDAGINPSLLGEVQTYTDVLGYVDDDAAKRASLKPGVPV 216
                                       ************99995......899999985...888899************************************ PP

                                       EEEEEHHHHHHHH CS
                            FGGY_N 233 vggggDqqaaalG 245
                                       v ++gD  aa++G
  gi|557694600|ref|YP_008797654.1| 217 VVALGDSLAAMIG 229
                                       **********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 !   52.0   0.0   1.2e-17   7.2e-14     103     197 ..     319     410 ..     247     411 .. 0.83

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.2e-17
                            FGGY_C 103 wdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldrlavdGGgskndllmqllAdilgvpVer 179
                                       + +d+ g++++l+  +++ h+ar+ +eava+ lr ++e +e+    +++r++ +GGg++  ++ +l A ++g+p ++
  gi|557694600|ref|YP_008797654.1| 319 MTKDVWGSLVNLTYCHGWNHVARSFFEAVAYELRRVVEIFEQV--TKVRRIVSSGGGAT-GFVTKLKATVVGKPFQI 392
                                       467888999*******************************555..99**********97.799************** PP

                            FGGY_C 180 pktaeatalGaAilAava 197
                                       p+ +e++alGaA+ Aa a
  gi|557694600|ref|YP_008797654.1| 393 PEIRETAALGAALTAATA 410
                                       ***************987 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 !   11.7   0.0   2.3e-05      0.14       1      26 [.       9      34 ..       9      93 .. 0.68
   2 ?    2.4   0.1     0.015        92     204     267 .]     352     407 ..     337     407 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.3e-05
                                      EEEEE-SSEEEEEEEETTTEEEEEEE CS
                       BcrAD_BadFG  1 vGiDgGsTttkavlmdekgevlgrgi 26
                                      +G+D+G+T++kav +de  ++l+++ 
  gi|557694600|ref|YP_008797654.1|  9 IGVDVGTTAVKAVAVDECCQLLAEAR 34
                                      7****************999887764 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.015
                                       HHHHHHHHTT---SS.EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHHHHH CS
                       BcrAD_BadFG 204 lrvialisrsggvtdevtltGGvakneaavkelrklvkenygevkininpdsiytgalGAalfA 267
                                       +rv ++++++  v+  ++  GG a    +v +l    k  + ++   + p+   t+alGAal A
  gi|557694600|ref|YP_008797654.1| 352 RRVVEIFEQVTKVRR-IVSSGGGATG--FVTKL----KATVVGK-PFQIPEIRETAALGAALTA 407
                                       345555555555544.9999999988..55555....7777774.466788999*******987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); 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:                         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 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3324.56
//
Query:       gi|557694601|ref|YP_008797655.1|  [L=220]
Description: uracil phosphoribosyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   0.1    1.4e-48  165.1   0.1    1.0  1  UPRTase       Uracil phosphoribosyltransferase
    1.4e-08   34.4   0.1    2.2e-08   33.8   0.1    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.055   13.0   0.0      0.097   12.2   0.0    1.6  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 !  165.1   0.1   2.4e-52   1.4e-48       1     206 [.      10     220 .]      10     220 .] 0.97

  Alignments for each domain:
  == domain 1  score: 165.1 bits;  conditional E-value: 2.4e-52
                           UPRTase   1 vsshpllkakltilRdastsrkdfrelvdriarllaeealsallpveevtvttplgkeysg.elldeekialVpilR 76 
                                       v++hp ++  lt lRd+st + +fr+ + +++rl++ e+ ++ lpv+++ vttpl+ e +g e+ d +ki+l+ +lR
  gi|557694601|ref|YP_008797655.1|  10 VLDHPYAQMVLTRLRDKSTGQIEFRKGLVKLGRLIGFEIARH-LPVSKKLVTTPLEVEAEGvEIPDIDKIVLITVLR 85 
                                       689**************************************9.******************5566669********* PP

                           UPRTase  77 aGegmeealrellpearvghlglqreeet......lepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLker 147
                                       a  +++e+l++++p+ar g +   r eet       e ++ y ++P+   ++ v++ Dp++aTG+++  +++ + + 
  gi|557694601|ref|YP_008797655.1|  86 AAMPLAEGLLKIFPTARQGVVSARRVEETysggldFEIELTYLRIPRLNGSEIVIIADPMLATGSTMLRVVEEVYKV 162
                                       ***************************999999998899********99***************************8 PP

                           UPRTase 148 gvgeekIlvlsvlaseegvkrlaeefpkvkvvtaavDeeldekgyivpGlGDfGDRlFg 206
                                       g + ++ ++++v++  +g++r+++ +p+++++t+a+De+l+ekg+ivpGlGD+GDR Fg
  gi|557694601|ref|YP_008797655.1| 163 G-KPKRLMFATVISTMQGISRVHSVYPQTEIFTVAIDEKLNEKGFIVPGLGDAGDRAFG 220
                                       8.579*****************************************************7 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.1   3.6e-12   2.2e-08      30     133 ..      77     183 ..      71     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.6e-12
                                       GEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-T..TT--EE..........EE----TTSEEEEE-SEESSSH CS
                      Pribosyltran  30 pdvvvgiargGvpfakiladeL.evplayvrkvkyrp..dgseeaargssdes..rlledpagkkVliVDDildtGg 101
                                       + v+++++r ++p+a  l + + +++  +v+++++++  +g+ ++ + +   +  r +++   ++V+i D +l+tG+
  gi|557694601|ref|YP_008797655.1|  77 KIVLITVLRAAMPLAEGLLKIFpTARQGVVSARRVEEtySGGLDFEIEL---TylRIPRLNGSEIVIIADPMLATGS 150
                                       579*******************633433444444444004444444433...356888999999************* PP

                                       HHHHHHH.HHHCC-BSEEEEEEEEE-HHHHHHH CS
                      Pribosyltran 102 Tllaale.lLkekgpeevriavlvdkpateeev 133
                                       T+l+++e   k  +p+++ +a+++  +++  +v
  gi|557694601|ref|YP_008797655.1| 151 TMLRVVEeVYKVGKPKRLMFATVISTMQGISRV 183
                                       *******7777888**********888876665 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.6e-05     0.097      97     163 ..     110     178 ..      42     198 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                          PRTase_2  97 eFeEeHSHAtdhlly..aedeellaaakelvLvDDEistGktalnliralqeklprkryvvvslvdwrs 163
                                       + eE  S   d  +     +  +l++++ +++ D  ++tG+t+l++++++ +  + kr+++++++  ++
  gi|557694601|ref|YP_008797655.1| 110 RVEETYSGGLDFEIEltYLRIPRLNGSEIVIIADPMLATGSTMLRVVEEVYKVGKPKRLMFATVISTMQ 178
                                       5555555555555543244445667777777788899***************99999*99999987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); 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 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1601.34
//
Query:       gi|557694602|ref|YP_008797656.1|  [L=551]
Description: 3-oxosteroid 1-dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-97  327.7   0.0    1.3e-97  327.5   0.0    1.0  1  FAD_binding_2  FAD binding domain
    1.1e-08   34.9   0.6    1.5e-07   31.2   0.4    2.0  2  FAD_oxidored   FAD dependent oxidoreductase
    1.5e-07   31.4   0.6    0.00012   21.8   0.1    2.7  3  DAO            FAD dependent oxidoreductase
    1.9e-07   30.1   1.5      4e-07   29.1   0.9    1.8  2  HI0933_like    HI0933-like protein
    2.6e-06   27.6   2.9    2.4e-05   24.4   2.1    2.7  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    0.00015   21.1   0.8    0.00029   20.2   0.3    1.6  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    0.00025   20.4   0.2    0.00036   19.9   0.2    1.2  1  FAD_binding_3  FAD binding domain
     0.0087   15.3   3.1      0.014   14.7   1.7    2.0  2  Thi4           Thi4 family
  ------ inclusion threshold ------
      0.018   14.1   0.6      0.068   12.2   0.8    1.7  2  GIDA           Glucose inhibited division protein A
      0.031   13.5   0.4      0.053   12.8   0.4    1.3  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
        0.1   11.9   4.7       0.35   10.1   0.7    2.9  3  Amino_oxidase  Flavin containing amine oxidoreductase
        0.2   10.6   0.1       0.29   10.1   0.1    1.2  1  Lycopene_cycl  Lycopene cyclase protein
       0.27   11.8   1.7        1.8    9.2   1.3    2.2  2  Pyr_redox      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 !  327.5   0.0  9.5e-101   1.3e-97       1     417 []       8     532 ..       8     532 .. 0.95

  Alignments for each domain:
  == domain 1  score: 327.5 bits;  conditional E-value: 9.5e-101
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHT...T CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkal...d 74 
                                       Dv+V+GsG+AGL+ Al+ + aG +v+vvek++ +gg++a+s+Gg+++++++ +++ag++ds e+++t++ +++   +
  gi|557694602|ref|YP_008797656.1|   8 DVLVVGSGAAGLVGALTVRSAGYEVLVVEKTDLVGGSSAMSGGGLWIPNNHVSREAGVEDSFEAAWTYLSHVVpeaG 84 
                                       9**********************************************************************997745 PP

                                       T-S-HHHHHHHHHTHHHHHHHHHHTT----B..........CCTS..........SB-EEE-TT-SST......... CS
                     FAD_binding_2  75 eladqplveafveaapeavdeLeelgvpfsr..........tedg..........pvdvrelGglsat......... 122
                                       e   +++ +a+++++pe+v++L+++g+++ +          t++g          ++d+r+lG + ++         
  gi|557694602|ref|YP_008797656.1|  85 EATSPERLRAYLTHGPEMVKFLADMGFRWRPalgypdyypeTPGGsvkgrciegaVFDARKLGPWARKlrrypgapp 161
                                       5559***************************9999999998444455557777789999999999999********* PP

                                       ............................EEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECT CS
                     FAD_binding_2 123 ............................artlhdaadarretlvtghallarlvesarkagvdfqerteadeLived 171
                                                                   ++++h+ + +  ++l+ g  l+  l+  ++k gv+++ + ++++L+ve+
  gi|557694602|ref|YP_008797656.1| 162 ipihtneawkmylarsrigiaaflrlgaRLIGHSLLGR--KPLTMGGSLVGQLLYLCLKKGVRIWLESPLRSLVVEN 236
                                       ***************************88888877777..99*********************************** PP

                                       TEEEEEEEEETTTTCEEEEEES.EEEE-----GG.............GSSSBSSGTT-S-HHHHHHHCTTSSEES.. CS
                     FAD_binding_2 172 grvtGavvenpesgrevrirak.avvlatgGfgr..allkellgaa.aeaettnapavtGdglalalragaalnddr 244
                                       grvtGavv+  ++ r+v ++a+ +v+l++gGf++  ++ +++l+++ +++++++ p++tGd++++a+  gaa  +++
  gi|557694602|ref|YP_008797656.1| 237 GRVTGAVVN--HEDRDVVVAARgGVLLTSGGFEHnqSMREKYLPNPtKAEWAVGSPGNTGDAIQAAVKIGAA--TAL 309
                                       *********..************************98888888876256799*******************9..556 PP

                                       TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTHGGGS-HHHHHHHHH.HHHHTTTSCCBEEEE-TT.. CS
                     FAD_binding_2 245 meevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFmnelasrdvvsrailekeiaeggseanvyldash.. 319
                                       m++++ +P ++ p +++  iL   ++  + gi+vd +G+rFmne+as+ +  + i ++++  +   ++ +l++++  
  gi|557694602|ref|YP_008797656.1| 310 MDKAWGGPIAITPDGKPVFILA--ERSLPFGIIVDPNGERFMNESASYVDCWHNIYKHHKTTPCI-PA-WLIIDQrh 382
                                       ********************77..888899**********************************9.88.******** PP

                                       ......................................SSHHHHHHHSHHHHHHHHHCCT......S-TTTS..... CS
                     FAD_binding_2 320 .....................................gldaegleatleaineeaangldkdfgrgidpadr..... 354
                                                                            g+d++gl +t+e++ne a +g+d+df+rg +++dr     
  gi|557694602|ref|YP_008797656.1| 383 rsnylfgtlmpgrtpekatgpqyllrahsleelarkiGVDEKGLLRTVERFNEMAVKGVDEDFHRGESAYDRfysdp 459
                                       ***************************************************************************** PP

                                       ...EEE..............EEEEEEEES-EEEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHHH CS
                     FAD_binding_2 355 ...pip.......gpfyavkvvpaqhytmgGvetdengrvldadgqpipGLYAaGevaaggvhganrlgGnsl 417
                                          p+p        p+ya+ ++p+ ++t+gG+ tden+rv+  dg+pipGLYAaG+++a+ ++g+++++G++l
  gi|557694602|ref|YP_008797656.1| 460 rvkPNPnlgpltkPPYYATAIYPGELGTCGGLLTDENARVMHVDGHPIPGLYAAGNTTAAVFGGTYPGPGSTL 532
                                       **966677777777********************************************************987 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.4   1.1e-10   1.5e-07       1      65 [.       8      71 ..       8     109 .. 0.73
   2 ?    1.7   0.0     0.095   1.3e+02      98     136 ..     217     255 ..     205     259 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.1e-10
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiarefle 65
                                      Dv+VvG+g+aG++ A++   aG +vl+ve+++ +GG ++  +++ +i n++  +   g+ + f +
  gi|557694602|ref|YP_008797656.1|  8 DVLVVGSGAAGLVGALTVRSAGYEVLVVEKTDLVGGSSAMSGGGLWIPNNHV-SREAGVEDSFEA 71
                                      9************************************998888777776633.345555555444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.095
                      FAD_oxidored  98 aeagvtvllntrlvevekegkriesvtveske.grktirA 136
                                        ++gv+++l++ l++ ++e++r+++ +v+ +e  + +++A
  gi|557694602|ref|YP_008797656.1| 217 LKKGVRIWLESPLRSLVVENGRVTGAVVN-HEdRDVVVAA 255
                                       677***************999*******5.5525666666 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   8.7e-08   0.00012       1      46 [.       8      54 ..       8     162 .. 0.86
   2 !    7.5   0.0    0.0019       2.7     148     200 ..     208     255 ..     182     328 .. 0.81
   3 ?   -2.7   0.0       2.4   3.3e+03      74     106 ..     414     448 ..     395     510 .. 0.50

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 8.7e-08
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEES CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhs 46
                                      dv+++G+G +Gl  A+    +g  V+++ek d +g g+S  ++g l+ 
  gi|557694602|ref|YP_008797656.1|  8 DVLVVGSGAAGLVGALTVRSAGyeVLVVEKTDLVG-GSSAMSGGGLWI 54
                                      8*****************7779*************.999999998864 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEEEEE-- CS
                               DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgve.rttpgendaadavVnaa 200
                                       l+  l+  + ++Gv+i ++++ ++l  e+g+v+g   ++  +     + vV+aa
  gi|557694602|ref|YP_008797656.1| 208 LVGQLLYLCLKKGVRIWLESPLRSLVVENGRVTGAVvNH--ED----RDVVVAA 255
                                       666788899***************989999*99994321..22....3344444 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.4
                                       HHSSTTSEEEEEEEEEES..SHHHHHHHHHHHHHH CS
                               DAO  74 elgididyrrtGllslaa..deeelealdkllall 106
                                       el+ +i+++++Gll + +  +e    ++d+ ++++
  gi|557694602|ref|YP_008797656.1| 414 ELARKIGVDEKGLLRTVErfNEMAVKGVDEDFHRG 448
                                       34445666666666664333443344455555544 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.9   2.9e-10     4e-07       2      45 ..       8      51 ..       7      66 .. 0.94
   2 ?   -2.1   0.0      0.84   1.2e+03     353     382 ..     484     514 ..     477     518 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 2.9e-10
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCGGG CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisGgG 45
                                      dv+v+G GaAGl +A++++++g +Vl++ek++ +g   ++sGgG
  gi|557694602|ref|YP_008797656.1|  8 DVLVVGSGAAGLVGALTVRSAGYEVLVVEKTDLVGGSSAMSGGG 51
                                      89****************************************99 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.84
                                       -SEEEEEE-GGGB-TTT-BB..TTSTTEEE-G CS
                       HI0933_like 353 aevTaGGVdlkevssktmes..kkvpgLffaG 382
                                       +  T+GG  ++e +++ m++  + +pgL+ aG
  gi|557694602|ref|YP_008797656.1| 484 ELGTCGGLLTDE-NARVMHVdgHPIPGLYAAG 514
                                       56799**99998.7888876225789****99 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 !   24.4   2.1   1.8e-08   2.4e-05       1      36 [.      11      46 ..      11      55 .. 0.96
   2 ?    0.4   0.0      0.57   7.9e+02      11      40 ..     488     517 ..     487     544 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.8e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                      +vG+G++Glv A + + ag++vl++ek d +GG +a
  gi|557694602|ref|YP_008797656.1| 11 VVGSGAAGLVGALTVRSAGYEVLVVEKTDLVGGSSA 46
                                      8********************************875 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.57
                                       HHHHHHCCTEEEEEE-SSSSSSGGG-EECE CS
                     NAD_binding_8  11 aAylLakagfdvlllekrdrlGGraasyev 40 
                                       +  lL++++++v  ++ ++ +G  aa ++ 
  gi|557694602|ref|YP_008797656.1| 488 CGGLLTDENARVMHVDGHPIPGLYAAGNTT 517
                                       666899999*************88887654 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 !   20.2   0.3   2.1e-07   0.00029       2      39 ..       8      44 ..       7      70 .. 0.86
   2 ?   -2.4   0.0       1.5   2.1e+03     256     278 ..     489     517 ..     484     530 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.1e-07
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclngg 39
                                      dv+v+G+G+AGl  alt++ ag++v++v +++ +++g 
  gi|557694602|ref|YP_008797656.1|  8 DVLVVGSGAAGLVGALTVRSAGYEVLVV-EKTDLVGGS 44
                                      89**************************.666666555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                                       TEEE--TTSBE......SSTTEEE-GGGC CS
                                       xxxxxxxxxxx......xxxxxxxxxxxx RF
                       Pyr_redox_2 256 ggivvdeflrt......nvpgiyaiGDva 278
                                       gg+++de+ r+       +pg+ya+G  +
  gi|557694602|ref|YP_008797656.1| 489 GGLLTDENARVmhvdghPIPGLYAAGNTT 517
                                       666677777655555545999****9876 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   2.6e-07   0.00036       2      34 ..       7      39 ..       6      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.6e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                      +dVl+VG+G aGl+ al  ++aG +v++vek +
  gi|557694602|ref|YP_008797656.1|  7 VDVLVVGSGAAGLVGALTVRSAGYEVLVVEKTD 39
                                      79****************************975 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.7   9.9e-06     0.014      17      63 ..       6      53 ..       1      69 [. 0.79
   2 ?   -1.7   0.0         1   1.4e+03     208     233 ..     503     528 ..     493     529 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.9e-06
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT..TTTSTT CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGa..wlGGql 63
                                        Dv++vG+G++GL  a ++  + + +v+++e+   +GG +   +GG  
  gi|557694602|ref|YP_008797656.1|  6 SVDVLVVGSGAAGLVGALTVRSA-GYEVLVVEKTDLVGGSSamSGGGLW 53
                                      57*****************9998.*********9888886411445544 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                                       ECEEETTEEE-THHHHHHHT-EB--S CS
                              Thi4 208 trevvpnlyvaGmevaevdganRmGp 233
                                         + +p+ly+aG  +a+v g+   Gp
  gi|557694602|ref|YP_008797656.1| 503 DGHPIPGLYAAGNTTAAVFGGTYPGP 528
                                       556689***********999876665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.8   4.9e-05     0.068       1      37 [.       8      43 ..       8      68 .. 0.88
   2 ?   -1.6   0.0      0.81   1.1e+03     119     157 ..     230     272 ..     222     279 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.9e-05
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiae 37
                                      dv V+G G AG+  Al++  +G++vl + +k+d ++ 
  gi|557694602|ref|YP_008797656.1|  8 DVLVVGSGAAGLVGALTVRSAGYEVLVV-EKTDLVGG 43
                                      79***********************888.88887775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.81
                                       EEEEECTTEEEE.EEETTS-.EEEEC..EEEE--TT-BT-EEE CS
                              GIDA 119 eeliveekkvkg.vvtedge.tikak..avviatGtflkgkih 157
                                        +l+ve+++v+g vv ++++ ++ a    v +++G f + +++
  gi|557694602|ref|YP_008797656.1| 230 RSLVVENGRVTGaVVNHEDRdVVVAArgGVLLTSGGFEHNQSM 272
                                       6789999999996444443314444357899999999877765 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 ?   12.8   0.4   3.8e-05     0.053       1      33 [.      10      41 ..      10      46 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnig 33
                                      +++G G+aGl  a++++ ag  ++l++Ek  ++
  gi|557694602|ref|YP_008797656.1| 10 LVVGSGAAGLVGALTVRSAGY-EVLVVEKTDLV 41
                                      69*******************.7******9765 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.7   0.00025      0.35       2      28 ..      17      43 ..      16      55 .. 0.89
   2 ?    0.1   0.0      0.28   3.9e+02     220     266 ..     218     261 ..     206     289 .. 0.77
   3 ?    0.9   0.1      0.16   2.2e+02     414     438 ..     501     526 ..     469     527 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                                      HHHHHHHHHHHTTEEEEEEESSSSSBT CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGG 28
                                      aGL+ A +  saG++V+v+E +d vGG
  gi|557694602|ref|YP_008797656.1| 17 AGLVGALTVRSAGYEVLVVEKTDLVGG 43
                                      9************************** PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.28
                                       TTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHH CS
                     Amino_oxidase 220 lrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlk 266
                                       ++g++i l+++++++  e++ vt  +++ e+   + Vvv++  gvl 
  gi|557694602|ref|YP_008797656.1| 218 KKGVRIWLESPLRSLVVENGRVTGAVVNHED---RDVVVAARGGVLL 261
                                       5699999999999999999999888888887...8899999999997 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.16
                                       HCH.HCSTTEEE.SGGGCTTTTTSHH CS
                     Amino_oxidase 414 akp.egdprlffAGehtsreypgtve 438
                                       + + +++p+l+ AG+ t+  + gt +
  gi|557694602|ref|YP_008797656.1| 501 HVDgHPIPGLYAAGNTTAAVFGGTYP 526
                                       3336899***********99988865 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00021      0.29       1      35 [.       8      40 ..       8      96 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00021
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasps 35
                                      Dv+v+G+G+Agl  A  +    +g +v+++e  + 
  gi|557694602|ref|YP_008797656.1|  8 DVLVVGSGAAGLVGALTV--RSAGYEVLVVEKTDL 40
                                      9**************999..899999999997664 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.3    0.0013       1.8       2      35 ..       9      42 ..       8      48 .. 0.92
   2 ?    0.0   0.0      0.92   1.3e+03      52      78 ..     218     244 ..     208     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      v+vvG+G  gl  A + +  g +V vve  d + 
  gi|557694602|ref|YP_008797656.1|  9 VLVVGSGAAGLVGALTVRSAGYEVLVVEKTDLVG 42
                                      89**************************998765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.92
                                       HTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  52 kngievllntkveeiegsedgvesvkl 78 
                                       k+g++++l++ + +++ ++  v++ ++
  gi|557694602|ref|YP_008797656.1| 218 KKGVRIWLESPLRSLVVENGRVTGAVV 244
                                       89*************988766776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (551 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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):              13  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 4074.86
//
Query:       gi|557694603|ref|YP_008797657.1|  [L=72]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.5   3.4      0.048   13.3   3.4    1.0  1  DUF4131          Domain of unknown function (DUF4131)
      0.044   12.9   4.1      0.049   12.7   4.1    1.1  1  ABC2_membrane_3  ABC-2 family transporter protein
       0.11   12.9   7.2        1.2    9.5   7.2    1.9  1  DPM2             Dolichol phosphate-mannose biosynthesis regu
       0.17   11.7   0.2       0.17   11.7   0.2    1.7  2  MaAIMP_sms       Putative methionine and alanine importer, sm
       0.17   12.0   0.5       0.17   12.0   0.5    1.6  2  Internalin_N     Bacterial adhesion/invasion protein N termin
       0.65    9.3   3.3        0.7    9.2   3.3    1.0  1  TMEM43           Transmembrane protein 43
       0.89    8.8   9.6        1.1    8.4   9.6    1.0  1  ABC2_membrane_2  ABC-2 family transporter protein
          1    9.0   2.9        1.3    8.7   2.9    1.1  1  Tetraspanin      Tetraspanin family
        1.3    9.2   3.6         13    5.9   0.5    2.2  2  RAMP4            Ribosome associated membrane protein RAMP4
        3.2    6.4   4.8        3.6    6.3   4.8    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
        5.1    7.0   6.9         87    3.1   6.9    2.0  1  PIG-P            PIG-P
        5.2    7.1  10.3        4.4    7.4   0.4    2.3  2  FixQ             Cbb3-type cytochrome oxidase component FixQ


Domain annotation for each model (and alignments):
>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   3.4   3.2e-05     0.048       4      54 ..       8      64 ..       5      71 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                           DUF4131  4 plalvllalllllllllllllrr......rprrrvllllllllllallgfalrapqp 54
                                      ++ l +la+++++l +l+ll         +  ++++ll++l+l+l+ +++ + a+++
  gi|557694603|ref|YP_008797657.1|  8 GYLLMFLAVGGAILYVLWLLGAIpfldpdAAVKTTALLIMLFLFLVIGFIGYVAATT 64
                                      455556666666666666665559999996667777777777777777766655544 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 ?   12.7   4.1   3.3e-05     0.049     208     287 ..       4      60 ..       1      72 [] 0.45

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.3e-05
                   ABC2_membrane_3 208 skilgdflvyllqlllill.l.afglgipfgnlglll....llfllfglayialgyllsslfknsetaqilifivil 278
                                       +k+lg++l++l +   il+ l ++g +ipf +  +++    ll++lf++++i +                       
  gi|557694603|ref|YP_008797657.1|   4 GKLLGYLLMFLAVGGAILYvLwLLG-AIPFLDPDAAVkttaLLIMLFLFLVIGF----------------------- 56 
                                       5666666666666544443223444.4555544443333334444443333333....................... PP

                   ABC2_membrane_3 279 llsgffggl 287
                                            +g++
  gi|557694603|ref|YP_008797657.1|  57 -----IGYV 60 
                                       .....3333 PP

>> DPM2  Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   7.2    0.0008       1.2       3      73 ..       5      65 ..       3      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0008
                              DPM2  3 klvGlllllvalllfvYYtiwvi.llPfvdedhvlhkyflpreyairipvillvvlllfvgtFiglvliksk 73
                                      kl G ll+++a+   + Y +w++  +Pf+d d            a++  ++l++++l +v  Fig+v  ++k
  gi|557694603|ref|YP_008797657.1|  5 KLLGYLLMFLAVGGAILYVLWLLgAIPFLDPDA-----------AVKTTALLIMLFLFLVIGFIGYVAATTK 65
                                      7899999999999999*****99679******9...........8999999999999999999999987765 PP

>> MaAIMP_sms  Putative methionine and alanine importer, small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.8       1.4   2.2e+03      10      22 ..      10      21 ..       1      31 [. 0.50
   2 ?   11.7   0.2   0.00011      0.17       3      24 ..      42      63 ..      39      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                        MaAIMP_sms 10 vLFiviiWGGLvl 22
                                      +L   +  GG +l
  gi|557694603|ref|YP_008797657.1| 10 LLMF-LAVGGAIL 21
                                      3333.33344433 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00011
                        MaAIMP_sms  3 taAiimmvLFiviiWGGLvlal 24
                                      ta +im+ LF+vi + G v a+
  gi|557694603|ref|YP_008797657.1| 42 TALLIMLFLFLVIGFIGYVAAT 63
                                      55567888*****999999886 PP

>> Internalin_N  Bacterial adhesion/invasion protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.4   2.1e+03      21      22 ..      24      25 ..       6      41 .. 0.55
   2 ?   12.0   0.5   0.00011      0.17      11      44 ..      41      71 ..      36      72 .] 0.80

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                                      XX CS
                      Internalin_N 21 ll 22
                                      l+
  gi|557694603|ref|YP_008797657.1| 24 LW 25
                                      33 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00011
                                      XXXXXXXXXXXXXXXXXXXXXXGSXS-SSSEEHH CS
                      Internalin_N 11 ltvtlvLllsllvltsnGekvqAeasitpPaPIn 44
                                      +t+ l++l+++lv+ ++G    A+ + +pP+PI+
  gi|557694603|ref|YP_008797657.1| 41 TTALLIMLFLFLVIGFIG--YVAA-TTKPPKPIK 71
                                      577788888999999999..5555.6899****8 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.3   0.00047       0.7     190     241 ..       5      56 ..       2      66 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00047
                            TMEM43 190 RllGfllmflglllllsplsvlvslipllgelvglglalvalllslslsllv 241
                                       +llG+llmfl++  ++  + +l+  ip+l   +++ +  + ++l l l +  
  gi|557694603|ref|YP_008797657.1|   5 KLLGYLLMFLAVGGAILYVLWLLGAIPFLDPDAAVKTTALLIMLFLFLVIGF 56 
                                       689*************9***********955444443333333333333333 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 ?    8.4   9.6   0.00076       1.1     121     180 ..       3      62 ..       3      64 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00076
                   ABC2_membrane_2 121 lgKfigglaigla.iavallatvllalaiilalgivlaledllllvvasvlllllvvflal 180
                                       +gK++g+l+++la +  +l +  ll+ ++ l+   ++++ +ll+++++++++++++ ++a+
  gi|557694603|ref|YP_008797657.1|   3 TGKLLGYLLMFLAvGGAILYVLWLLGAIPFLDPDAAVKTTALLIMLFLFLVIGFIG-YVAA 62 
                                       59************999999999*******************************98.4444 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   2.9   0.00087       1.3      10      72 ..      11      63 ..       5      67 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00087
                                      XXXXXXXXXXXXXXXXXXXXXX.....................XXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin 10 llfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGcigal 72
                                      l+f+ +g ++l v +wl     + a   l    + d+a+ +++l+++ +l++++gf+G ++a 
  gi|557694603|ref|YP_008797657.1| 11 LMFLAVGGAILYV-LWL-----LGAIPFL----DPDAAVKTTALLIMLFLFLVIGFIGYVAAT 63
                                      4566666666666.577.....2233333....333333333455665788888888888875 PP

>> RAMP4  Ribosome associated membrane protein RAMP4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1      0.03        45      42      56 ..       9      23 ..       2      27 .. 0.81
   2 ?    5.9   0.5    0.0087        13      39      50 ..      44      55 ..      36      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.03
                             RAMP4 42 glfiFVViGSaifqi 56
                                       l++F  +G+ai+ +
  gi|557694603|ref|YP_008797657.1|  9 YLLMFLAVGGAILYV 23
                                      599*********865 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0087
                             RAMP4 39 wlLglfiFVViG 50
                                      +l+ lf+F ViG
  gi|557694603|ref|YP_008797657.1| 44 LLIMLFLFLVIG 55
                                      7899*******9 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.8    0.0024       3.6     382     430 ..      10      62 ..       2      70 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0024
                           DUF2207 382 klsalglgliilglilillallllvll..........lvfllilllillliaiivlllf 430
                                        l +l++g++il+++++l+a      +           + lli+l+++l+i++i ++ +
  gi|557694603|ref|YP_008797657.1|  10 LLMFLAVGGAILYVLWLLGA------IpfldpdaavkTTALLIMLFLFLVIGFIGYVAA 62 
                                       33344444444444444444......144555699975555555555556655555544 PP

>> PIG-P  PIG-P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   6.9     0.058        87       5      75 ..       7      67 ..       3      72 .] 0.71

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.058
                             PIG-P  5 ygFvlyllstlafllyllwallPeevlhalgityypnryWalavpayllmlvlyiyvalaslnlevltppl 75
                                       g+ l++l++   +ly+lw l   ++l+            a+   a+l+ml+l+ +++++ +   + t+p 
  gi|557694603|ref|YP_008797657.1|  7 LGYLLMFLAVGGAILYVLWLLGAIPFLDP---------DAAVKTTALLIMLFLFLVIGFIGYVA-ATTKPP 67
                                      57788888888888888887776666653.........34677778888888888888888888.777765 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 ?    3.8   4.0     0.039        58      12      31 ..       6      25 ..       3      26 .. 0.90
   2 ?    7.4   0.4    0.0029       4.4      15      27 ..      49      61 ..      40      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.039
                              FixQ 12 swgllflvllfygvviyafr 31
                                       +g l+++l   g+++y+++
  gi|557694603|ref|YP_008797657.1|  6 LLGYLLMFLAVGGAILYVLW 25
                                      67899**************9 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0029
                              FixQ 15 llflvllfygvvi 27
                                       lflv+ f+g+v+
  gi|557694603|ref|YP_008797657.1| 49 FLFLVIGFIGYVA 61
                                      5899999***996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 590.58
//
Query:       gi|557694604|ref|YP_008797658.1|  [L=141]
Description: regulatory protein, ArsR [Candidatus Caldiarchaeum subterraneum]
Scores for 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   22.2   0.0    0.00015   21.5   0.0    1.3  1  LexA_DNA_bind  LexA DNA binding domain
      0.005   16.6   0.0     0.0098   15.7   0.0    1.5  1  HTH_IclR       IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.6e-08   0.00015      19      61 ..      21      63 ..      17      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.6e-08
                                      HHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG CS
                     LexA_DNA_bind 19 ieetgypPsireiaralglkSpsaveehLkaLerKGyierdpg 61
                                      + + g p  +r++ r lgl+Sps + +hL++L+  G++e d++
  gi|557694604|ref|YP_008797658.1| 21 VLKAGRPVGVRDVQRGLGLSSPSVAFHHLEKLHGLGVLEKDEK 63
                                      667788999*****************************99864 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 !   15.7   0.0   1.1e-06    0.0098       5      51 ..      14      61 ..      12      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-06
                                      HHHHHCT-CTTBSS-BHHHHHHHHTS-HHHH.HHHHHHHHHTTSEE.. CS
                          HTH_IclR  5 alaiLdalaeapqeltlselArrtglpkStv.hRlLqtLvelGyveqd 51
                                      ++++  ++ +a+++++++++ r +gl+ ++v +++L  L+ lG +e+d
  gi|557694604|ref|YP_008797658.1| 14 TFDVYIYVLKAGRPVGVRDVQRGLGLSSPSVaFHHLEKLHGLGVLEKD 61
                                      5555566778999*************9777439*************99 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:                      305  (0.0170115); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1076.69
//
Query:       gi|557694605|ref|YP_008797659.1|  [L=573]
Description: Fe-S oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   52.3   0.0    7.1e-13   49.3   0.0    2.3  2  Radical_SAM  Radical SAM superfamily
    0.00086   19.3   0.0     0.0019   18.2   0.0    1.6  1  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 ?   -0.0   0.0      0.11     1e+03     123     155 ..     122     153 ..      74     166 .. 0.63
   2 !   49.3   0.0   7.9e-17   7.1e-13       2     166 ..     254     439 ..     253     440 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.11
                                       CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 123 rghtfeevlealeklreagikrvvdrivglpGe 155
                                        +++fe++l  ++ ++++ + r + ++vg+ Ge
  gi|557694605|ref|YP_008797659.1| 122 VTKEFEDLLHRIQVAKKNTGSRAK-VVVGGSGE 153
                                       456678888888888888777433.33333333 PP

  == domain 2  score: 49.3 bits;  conditional E-value: 7.9e-17
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE........SSTGGGSTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilg........ggepllypdfvellerl 70 
                                       +++rgC  +C fC ++     +++ r+ ++e+++eev  +  + g+++ +++          +p++ ++  e+++rl
  gi|557694605|ref|YP_008797659.1| 254 EIMRGCGIDCDFCEVT-----TRPLRYYPPEKVVEEVLVN-LRGGINNAWFVtdnqwaymVRDPMF-WPNKEAIFRL 323
                                       689*************.....69*****************.8999*******66666665555555.5566888888 PP

                                       HHTC......CCTEEEEEEECSSCHG..........HHHHHHHHHTT...-SEEEEEEBSSSHHHHHHHHTCTSHH. CS
                                       xxxx......xxxxxxxxxxxxxxxx..........xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       Radical_SAM  71 akla......vpgiritvetngtlpd..........eeklerllelg...vdrvslgleaaddekvlklmnrghtf. 127
                                        +         + ++          +             +++++ +g      v++gle+++d+ vlk+m  +  + 
  gi|557694605|ref|YP_008797659.1| 324 YRAVmqhvskANPMHA---------TlapvaadpeaAMGVAKIVGAGpdkHIGVQIGLETGSDKLVLKHMVNKAKPl 391
                                       8874455554444444.........4444444444777889999999999999***********9999997666668 PP

                                       .........HHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHHH CS
                                       .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 128 .........eevlealeklreagikrvvdrivglpGendeeleellel 166
                                                e v+ea + +++a + + +++i+g +Ge+de+ ++++ l
  gi|557694605|ref|YP_008797659.1| 392 kvgvdgtwaEIVVEAQKVYNAAYWIPAYTIILGQEGETDEDSWDTIGL 439
                                       999999999**************999***************9999866 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.1e-07    0.0019      61     117 ..     122     180 ..      76     184 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.1e-07
                       B12-binding  61 ltsqleavkelvel.lkrirprvkvvvGGah...psldpeetleaklgiddvvvgegedal 117
                                       +t+++e+  + ++  +k  ++r+kvvvGG +   ++  pe++ +  lgid+vv ge +d +
  gi|557694605|ref|YP_008797659.1| 122 VTKEFEDLLHRIQVaKKNTGSRAKVVVGGSGeweFEHRPEMIEQ--LGIDHVVQGEMDDII 180
                                       55666666555555899999*********854448999999665..**********98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (573 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); 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:                         2  (0.000111551); expected 0.2 (1e-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: 4193.81
//
Query:       gi|557694606|ref|YP_008797660.1|  [L=134]
Description: phage shock protein C, PspC [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.6    4.3e-15   55.2   0.6    2.3  2  PspC      PspC domain


Domain annotation for each model (and alignments):
>> PspC  PspC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.6   2.4e-19   4.3e-15       3      52 ..       6      61 ..       4      62 .. 0.94
   2 ?   -5.1   6.1         1   1.8e+04      20      20 ..      97      97 ..      72     128 .. 0.52

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 2.4e-19
                              PspC  3 LyRspdnkvlgGVcaGlAeyfgvdptlvRlifvlll......glllYiilwiilPe 52
                                      L Rs ++kvl+GV +Gl+ey++vdp+l+Rl+ v+ll      +++lY  +++++P+
  gi|557694606|ref|YP_008797660.1|  6 LERSDSKKVLAGVFGGLGEYLNVDPNLLRLVGVILLivspalMIVLYTFAALLIPR 61
                                      78*****************************988888999999999*********7 PP

  == domain 2  score: -5.1 bits;  conditional E-value: 1
                              PspC 20 A 20
                                      A
  gi|557694606|ref|YP_008797660.1| 97 A 97
                                      0 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); 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):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 916.18
//
Query:       gi|557694607|ref|YP_008797661.1|  [L=180]
Description: hypothetical protein CSUB_C1179 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.0   0.1      0.038   14.1   0.1    1.4  1  Sid-5         Sid-5 family
       0.16   12.0   0.0       0.24   11.4   0.0    1.2  1  RL10P_insert  Insertion domain in 60S ribosomal protein L10P


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 ?   14.1   0.1   4.3e-06     0.038      15      45 ..      85     115 ..      81     127 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.3e-06
                             Sid-5  15 ncvilLaisilllllNilqvvffnRakllkl 45 
                                       +  i L++++ll+ lN   ++++nR+ +  l
  gi|557694607|ref|YP_008797661.1|  85 EAFITLTVLTLLVSLNTAALIYLNRHGVCSL 115
                                       67899*********************99876 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 ?   11.4   0.0   2.7e-05      0.24      10      68 ..      71     129 ..      67     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                      RL10P_insert  10 dviipag.plelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLkl 68 
                                       ++ i  g  l+  P+ +  +L  l l ++l+   ++  +++ vc+ G+ l ++ a+lL  
  gi|557694607|ref|YP_008797661.1|  71 TIYISRGwALSINPEAF-ITLTVLTLLVSLNTAALIYLNRHGVCSLGKRLPASYAALLPS 129
                                       67788888899999999.89*************************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1293.12
//
Query:       gi|557694608|ref|YP_008797662.1|  [L=322]
Description: homoserine dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-50  169.6   0.1    9.5e-50  168.9   0.1    1.3  1  Homoserine_dh  Homoserine dehydrogenase
    2.1e-11   44.5   0.1    4.4e-11   43.5   0.1    1.5  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
     0.0009   19.0   0.1      0.002   17.9   0.1    1.6  1  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro


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 !  168.9   0.1   1.6e-53   9.5e-50       1     160 [.     155     315 ..     155     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 168.9 bits;  conditional E-value: 1.6e-53
                                       --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHH CS
                     Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarla 77 
                                       P++   +e+ ++dr+++ieGilngt+nyilt+meeeg +f ++l+eaq+lGyaeaDpt D++GlD+a K++ila+++
  gi|557694608|ref|YP_008797662.1| 155 PVLAFARECSKADRVEQIEGILNGTTNYILTRMEEEGLEFRQALAEAQRLGYAEADPTLDIKGLDTACKITILANEV 231
                                       899999*********************************************************************** PP

                                       CTTT--GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEE...CEEEEEEEEEETTSGGGHSSST-EEEEEEESSSEE CS
                     Homoserine_dh  78 fgleveledvevegiskltaedikeakeegkvlklvasa...vearVkpelvpkshplasvkgsenavlvetdrlge 151
                                       +g++ +++dv+v+gi++l+++++++a+  gk ++l++ a   v ++V+p+++++++pla vk ++nav ++t + g+
  gi|557694608|ref|YP_008797662.1| 232 LGMKATINDVKVTGIDTLSSQEVNRARMSGKAMRLIGYAgngV-LEVSPREIDAKDPLA-VKMAMNAVRFKTTYSGS 306
                                       **************************************98855.9**************.***************** PP

                                       EEEEES-SS CS
                     Homoserine_dh 152 lviqGpgaG 160
                                        vi+G+gaG
  gi|557694608|ref|YP_008797662.1| 307 HVISGKGAG 315
                                       ********9 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 !   43.5   0.1   7.3e-15   4.4e-11       1     109 [.       7     139 ..       7     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 7.3e-15
                                       --SHHHHHHHHHHHH---S......SEEEEEEEEESS.EEE-TT...............HHHHHT--CB---HHHHH CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqse......ielelvavadrd.sllskd...............rkallasealtldlddli 55 
                                       G+G++G+++l+++++++se      +++++v  adr+    + +                  ++a++++  +++d +
  gi|557694608|ref|YP_008797662.1|   7 GMGVVGQSLLRLIADNRSElvtrygLGVRVVYAADRSgAVHR-PtgfspeelleakkkgGVTQVADAKVFNNIFDAL 82 
                                       99*********************9989999999999933333.36********99987755679999999******* PP

                                       HHHS-EEEEE-S--HHHH.....TTHHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTT CS
                     NAD_binding_3  56 ahldpdvvVEcasseava.....elvlkaLkagkdvvtankgaladealyeeLreaaea 109
                                       +++++dv V++++ + v      +++ ka+ +g+dvvt++kga+a   +  +L e a++
  gi|557694608|ref|YP_008797662.1|  83 EDAEADVMVDATPTNIVDgepsySIIRKAILNGMDVVTVSKGAMA--LYMPALKEMASR 139
                                       *99***********99964444479********************..788888777765 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 !   17.9   0.1   3.3e-07     0.002      53     135 ..      31     108 ..       1     145 [. 0.73

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.3e-07
                                       HCT-EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HH CS
                     ELFV_dehydrog  53 elgakvvavsDssGviydpeGldieellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneidee 129
                                        lg +vv   D sG+++ p+G++ eelle k++ +  +  +   +k ++ i ++  l + ++d++v +   n +d+e
  gi|557694608|ref|YP_008797662.1|  31 GLGVRVVYAADRSGAVHRPTGFSPEELLEAKKKGGVTQVAD---AKVFNNIFDA--LEDAEADVMVDATPTNIVDGE 102
                                       36889999*********************998877644444...2234555553..566788888888877777777 PP

                                       HHTHTH CS
                     ELFV_dehydrog 130 nakali 135
                                          + i
  gi|557694608|ref|YP_008797662.1| 103 PSYSII 108
                                       665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2174.74
//
Query:       gi|557694609|ref|YP_008797663.1|  [L=467]
Description: aspartate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-56  191.2   0.1    3.7e-56  190.4   0.1    1.4  1  AA_kinase  Amino acid kinase family
    9.5e-23   79.8   0.9    1.6e-10   40.6   0.3    2.5  2  ACT_7      ACT domain
    2.2e-21   75.3   0.8    2.1e-11   43.4   0.0    3.1  3  ACT        ACT domain
  ------ inclusion threshold ------
      0.011   15.7   1.4       0.16   12.0   0.1    2.8  3  ACT_6      ACT domain
       0.07   14.1   0.0        4.2    8.4   0.0    2.8  2  LytR_C     LytR cell envelope-related transcriptional attenua


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 !  190.4   0.1     1e-59   3.7e-56       1     241 []       1     288 [.       1     288 [. 0.89

  Alignments for each domain:
  == domain 1  score: 190.4 bits;  conditional E-value: 1e-59
                                       TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHH....TCCCCCHHHC......... CS
                         AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllal....ksglssgelaa........ 64 
                                       +r+V+K+GGssl++++   ++++ + ++++ +++n++vvV+++ g +td ll+l    ++g s++ +++        
  gi|557694609|ref|YP_008797663.1|   1 MRIVMKFGGSSLATADL--IKHCSTLVKQH-TDKNEVVVVCSAsGDTTDDLLQLvetaRRGRSEEVEHRlseieehh 74 
                                       79***************..***********.***********************99985555555555456556665 PP

                                       ..............E..HHHHHHHHH.......................HHHHHHHHHHHHHHHHTTHGEEEE-GGG CS
                         AA_kinase  65 ...........glrstleeagevatr.......................dalaslgerlvaallaaglpavglsaaa 107
                                                        ee+ge +++                       d+++s+ge+ ++ ++a +l++ g++a++
  gi|557694609|ref|YP_008797663.1|  75 lglldavvderV----REETGETLKQwlrelrravlgilylreatprstDYVLSFGEKFSTLVMAGALNSLGVKAQY 147
                                       666776643332....33334444447778*********************************************** PP

                                       TCEECCCE......HHHTTTCEEE....CCHHHHHHHTT-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTS CS
                         AA_kinase 108 ldateagr....degsdgnvesvd....aeaieelleagvvpvltgfigldeege...lgrgssDtiaallAealgA 173
                                       ld  eag+    ++g+++++ +v+    ++ i ++l++g+ pv+tgfi+ +eeg    lgrg+sD++a++lA  l A
  gi|557694609|ref|YP_008797663.1| 148 LDGGEAGIvtdsNFGEAAPLIEVTrlniRRRIGRMLDEGITPVVTGFIATNEEGVtttLGRGGSDYTATILASSLPA 224
                                       ************777777777777666699999999*****************99********************** PP

                                       SEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 174 dkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvItn 241
                                       d++++++dVdG+++a+pk +p+a+++++is++ea e    +a +G+k +hp+al++++ ++ipv+I+n
  gi|557694609|ref|YP_008797663.1| 225 DEVWLWSDVDGLMTANPKLIPNAVVIKKISYNEAIE----MALFGAKGLHPRALEPVMAAQIPVRIKN 288
                                       ************************************....**************************98 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.3   4.6e-14   1.6e-10       5      64 ..     318     379 ..     315     380 .. 0.94
   2 !   37.3   0.0   4.8e-13   1.7e-09       3      65 .]     394     458 ..     392     458 .. 0.97

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 4.6e-14
                                       EEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHH CS
                             ACT_7   5 gwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLh 64 
                                       + ++l+v g+++ +  +G +ak+ + L  agI++ +iS   ++ +++++++ ++l+kAv a +
  gi|557694609|ref|YP_008797663.1| 318 DTAMLTVKGPSMVG-EPGTAAKILETLYHAGINVMMISqsiSESSISLIIKRKHLDKAVTAIE 379
                                       56899*****9988.********************************************9986 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 4.8e-13
                                       EEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE...-SS-EEEEEEGGGHHHHHHHHHH CS
                             ACT_7   3 edgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS...tyrtdyiLVpeedlekAveaLhe 65 
                                       e++++++ vvg+g+++ ++G+++k++++ a  gI+i +i+   ++  ++++V+e+d  +Av+a h+
  gi|557694609|ref|YP_008797663.1| 394 EEDVVVVAVVGEGMKG-TPGVASKVFGAVASRGINIRMIAqgsSELNISFVVKENDGPEAVKAIHD 458
                                       78999***********.***********************999********************996 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       2.6   9.4e+03      33      59 ..      27      49 ..      24      53 .. 0.61
   2 !   29.0   0.0   1.9e-10   6.7e-07       6      64 ..     328     380 ..     326     382 .. 0.87
   3 !   43.4   0.0   5.8e-15   2.1e-11       6      64 ..     406     458 ..     405     459 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.6
                                      EEEESTTECEEEEEEEEEEHHHHHHHH CS
                               ACT 33 qrssedkvagivfvvivvdeedleevl 59
                                      q++++    ++v+vv+ ++ + ++++l
  gi|557694609|ref|YP_008797663.1| 27 QHTDK----NEVVVVCSASGDTTDDLL 49
                                      55554....477777777666666666 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 1.9e-10
                                       EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT   6 gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                       ++ ++PG++a+++ +l  +giN+ +i+q+ s      ++ + +++  ++l++++ a++k
  gi|557694609|ref|YP_008797663.1| 328 SMVGEPGTAAKILETLYHAGINVMMISQSIS------ESSISLIIKRKHLDKAVTAIEK 380
                                       57889**************************......7788888888888888887776 PP

  == domain 3  score: 43.4 bits;  conditional E-value: 5.8e-15
                                       EEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT   6 gvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                       g+++ PG++++vfga+a rgiNi++i q+ss      + ++ +vv e+d +e+++a+++
  gi|557694609|ref|YP_008797663.1| 406 GMKGTPGVASKVFGAVASRGINIRMIAQGSS------ELNISFVVKENDGPEAVKAIHD 458
                                       68999**************************......7888889999999999888875 PP

>> ACT_6  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.6   5.7e+03       8      33 ..     195     220 ..     190     222 .. 0.79
   2 ?   12.0   0.1   4.4e-05      0.16      12      63 ..     332     383 ..     322     388 .. 0.94
   3 ?    1.4   0.0     0.092   3.3e+02      12      35 ..     410     433 ..     397     445 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                             ACT_6   8 tGpdrpGltasLtsvlaefgvnilDi 33 
                                       + ++  G+t  L +  +++ ++il +
  gi|557694609|ref|YP_008797663.1| 195 IATNEEGVTTTLGRGGSDYTATILAS 220
                                       56788899999999999999999866 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.4e-05
                             ACT_6  12 rpGltasLtsvlaefgvnilDieqavihgrlsLgllvsgpedalarlekaLl 63 
                                        pG  a+++++l   g+n++ i q++ +++ sL++  +  ++a++++ek Ll
  gi|557694609|ref|YP_008797663.1| 332 EPGTAAKILETLYHAGINVMMISQSISESSISLIIKRKHLDKAVTAIEKSLL 383
                                       59***********************************999********9997 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.092
                             ACT_6  12 rpGltasLtsvlaefgvnilDieq 35 
                                        pG+ +++++++a  g+ni  i q
  gi|557694609|ref|YP_008797663.1| 410 TPGVASKVFGAVASRGINIRMIAQ 433
                                       59*****************98887 PP

>> LytR_C  LytR cell envelope-related transcriptional attenuator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0012       4.2      11      81 ..     331     403 ..     329     406 .. 0.73
   2 ?    2.4   0.0     0.088   3.2e+02      11      61 ..     409     459 ..     407     466 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                            LytR_C  11 gvsGlAarvadaLeerGftvgevgnagnadee.ttivyreaaaaaakalaaalglgelqedsvkdas..vtvvl 81 
                                       g++G Aa++ + L  +G +v  ++++ + + + + i+ r+  ++a  a++++l +++++++ +++++  v+ v+
  gi|557694609|ref|YP_008797663.1| 331 GEPGTAAKILETLYHAGINVMMISQSISES-SiSLIIKRKHLDKAVTAIEKSLLGTRIVASVEPEEDvvVVAVV 403
                                       789*******************88654442.2477774343335888******888888888888885444445 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.088
                            LytR_C  11 gvsGlAarvadaLeerGftvgevgnagnadeettivyreaaaaaakalaaa 61 
                                       g++G+A++v  a ++rG ++  +++ ++  + + +v ++++ +a ka+ ++
  gi|557694609|ref|YP_008797663.1| 409 GTPGVASKVFGAVASRGINIRMIAQGSSELNISFVVKENDGPEAVKAIHDE 459
                                       89*****************99966544442225555333333566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3437.83
//
Query:       gi|557694610|ref|YP_008797664.1|  [L=180]
Description: hypothetical protein CSUB_C1182 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1309.66
//
Query:       gi|557694611|ref|YP_008797665.1|  [L=140]
Description: hypothetical protein CSUB_C1183 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       452  (0.0252106); 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:                         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 0.31s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 951.61
//
Query:       gi|557694612|ref|YP_008797666.1|  [L=76]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   49.2   0.8      6e-13   48.8   0.8    1.1  1  DUF2283   Protein of unknown function (DUF2283)


Domain annotation for each model (and alignments):
>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.8   3.3e-17     6e-13       3      49 .]       6      52 ..       5      52 .. 0.98

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 3.3e-17
                           DUF2283  3 tYDpeaDalYIylsegpveeseevdddiilDfDedGrlvGIEiLnAS 49
                                      +YD +aD+l I++ eg  ++++ +d+d++l fDe G++v +EiL+AS
  gi|557694612|ref|YP_008797666.1|  6 KYDAKADILVIRIGEGNLRDEKLLDNDVVLGFDERGNIVRVEILDAS 52
                                      8*********************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 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:                        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 0.30s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 548.61
//
Query:       gi|557694613|ref|YP_008797667.1|  [L=94]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.2   0.0      0.025   14.0   0.0    1.0  1  SBP_bac_3  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.4e-06     0.025     113     178 ..       5      74 ..       2      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.4e-06
                                       EEEETTSHHHHHHHHHHHC....TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHCCGCCEEEE CS
                                       xxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 113 vgvqagstaeellkeelkk....gaeivefdtleealqaLkngrvdavvadspvlaylvkknpdkkvvlv 178
                                         v +g++ ++ll+e +k     +   +++++ +e+l ++++gr  av +d  ++  + k+++++ vv v
  gi|557694613|ref|YP_008797667.1|   5 MIVLTGHARDKLLNELFKLgineDSVSITVNSPDELLYDVATGRFVAVKYDLNIAVIYEKTRDAQLVVTV 74 
                                       568899999999998655477753333579**********************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 653.47
//
Query:       gi|557694614|ref|YP_008797668.1|  [L=64]
Description: hypothetical protein CSUB_C1186 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      238  (0.0132746); 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: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 499.16
//
Query:       gi|557694615|ref|YP_008797669.1|  [L=204]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-20   71.5   4.8    6.8e-20   71.5   4.8    1.9  2  MS_channel  Mechanosensitive ion channel


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 ?   -2.4   1.5      0.16   2.8e+03       5      24 ..      23      42 ..      20      79 .. 0.61
   2 !   71.5   4.8   3.8e-24   6.8e-20      25     106 ..     117     198 ..      93     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.16
                                      HHHHHHHHHHHHHHTTT--S CS
                        MS_channel  5 kiliivvgilivlsllgvnv 24
                                       ++i+ v+  +vl+ll ++v
  gi|557694615|ref|YP_008797669.1| 23 MYVILYVAAAAVLQLLFFDV 42
                                      56677777777777666653 PP

  == domain 2  score: 71.5 bits;  conditional E-value: 3.8e-24
                                       CCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESSSEEEEEEEE-SSEEEEEETTSEEEEEEHHHH CS
                        MS_channel  25 sallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveigdieGtVediglrttkirtfdgrivtiPnssl 101
                                       ++ +a+ G++g+++g+a+++++ + +aG+++l+++pfkiGD+v++++ eG Ved+++++t + ++dg+ + iPn+++
  gi|557694615|ref|YP_008797669.1| 117 ASGVALGGFIGIVIGFASQQILGQALAGLFVLITRPFKIGDTVNLAGEEGLVEDVTTLFTIVAKPDGTRTLIPNNAI 193
                                       566899*********************************************************************** PP

                                       HTS-E CS
                        MS_channel 102 vtsni 106
                                       +  +i
  gi|557694615|ref|YP_008797669.1| 194 LGGKI 198
                                       98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1620.99
//
Query:       gi|557694616|ref|YP_008797670.1|  [L=371]
Description: metalloprotease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   68.7   7.5    1.9e-18   66.6   7.5    1.8  1  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
       0.11   12.4   0.3       0.25   11.2   0.3    1.5  1  PDZ_6          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 !   66.6   7.5   2.1e-22   1.9e-18       2     242 ..     110     347 ..     109     355 .. 0.76

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 2.1e-22
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeaka 78 
                                       ++l++ i+++ HE  H+++A+++g+ v++ +i++               i ++p GG+V+ ++e             
  gi|557694616|ref|YP_008797670.1| 110 LFLAFAIVLITHEGLHGIAARREGLPVKSAGIFM---------------IFVVP-GGFVEPDEEA------------ 158
                                       6899******************************...............*****.********99............ PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX............................-EEECE...CTTTSCEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................xxxxxx...xxxxxxxxxx RF
                     Peptidase_M50  79 flkkspwqrllivlAGplanfilailvfvv............................pkkske...seeekrgviG 124
                                       f+++sp +r+++++ G +an+ +++l++++                                         +rg++G
  gi|557694616|ref|YP_008797670.1| 159 FKSASPGARMRVAAVGSFANIAVGLLALMLmfgafvpqelglialqvepnsrikvndiI----VsvdDVPVNRGTLG 231
                                       *************************9999999999999999998888766555444431....03335556666666 PP

                                       EEEC-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 125 vspkpvkkegllealkegvektlkvvvltvkalgklitg.klslktlggpisiaqlaseaaeaglssflqllalisv 200
                                        s   ++   +    +e+v +t   v+     lg+++ g  +       p  i  l     + ++   l++l l+s+
  gi|557694616|ref|YP_008797670.1| 232 TSIIIKETIRIKTLTNEYVFDTNPDVRGREFTLGSVLRGlGVTQVDTFFPSRITWLD-PFSAYNFYRALYWLQLVSI 307
                                       666664444444445555555555555555577777777555444555565555554.45678999*********** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 201 nLgilNLlPipvLDGghllfalleairrkplserkeevanlv 242
                                        ++++N+lPi +LDG  +l+a+le++   +  + ++ ++n v
  gi|557694616|ref|YP_008797670.1| 308 GVAVFNMLPIYMLDGSLVLRAVLEKFV--KEGRHAKVIINTV 347
                                       **************************9..3333344444444 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   2.7e-05      0.25      16      35 ..     211     230 ..     211     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.7e-05
                             PDZ_6  16 lrvGDiilsvNGqpveglsl 35 
                                       ++v+Dii+sv+++pv++++l
  gi|557694616|ref|YP_008797670.1| 211 IKVNDIIVSVDDVPVNRGTL 230
                                       789************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2698.58
//
Query:       gi|557694617|ref|YP_008797671.1|  [L=308]
Description: ATPase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-18   66.0   0.0      8e-18   64.8   0.0    1.6  1  ATP_bind_3     PP-loop family
    0.00016   20.6   0.0    0.00021   20.2   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
  ------ inclusion threshold ------
      0.016   14.7   1.5      0.016   14.7   1.5    2.6  3  zn-ribbon_14   Zinc-ribbon
      0.018   15.1   0.0      0.039   14.0   0.0    1.6  2  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
       0.15   12.2   0.1       0.28   11.3   0.1    1.4  1  DUF2845        Protein of unknown function (DUF2845)
       0.38   10.4  10.9      0.099   12.2   1.1    3.8  4  RecR           RecR protein


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 !   64.8   0.0   2.7e-21     8e-18       1     181 [.      58     251 ..      58     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 2.7e-21
                                       EEEEE--SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H........ CS
                        ATP_bind_3   1 kvlvAvSgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklnikleiekvdv........ 68 
                                       k++vAvSgG DS+ Ll++l+k +k++    lva++vd g+    +e  e+v+e+ ++l+++l+ ++++         
  gi|557694617|ref|YP_008797671.1|  58 KIAVAVSGGKDSLSLLYVLKKIEKRFPRaGLVAVTVDEGIEGYRDEALEYVEEVTRMLEVPLYKTSFEEafgkslse 134
                                       579**********************99889**************************************999999999 PP

                                       ..HHCTTSTCCCHH....HHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCC CS
                        ATP_bind_3  69 ..akkkgknleeaA....RelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasir 139
                                         a+k+ ++   aA      lR ++++ a+k+ g++v+++Ah+ dD + t +l+ +rg+  ++ +g++ + ++  i 
  gi|557694617|ref|YP_008797671.1| 135 ivASKQFRSSGLAAcsvcGPLRRRAINIAAKRAGATVIATAHTLDDVVQTYFLKTFRGELGTSEIGLRLEGPF--IP 209
                                       984444343333441111568**************************************99999999987744..77 PP

                                       EE-CCCT--HHHHHHHHHHTT---B--CGGGCTTSHHHHHHH CS
                        ATP_bind_3 140 lvRPlLkvskeeleeylkekkikwveDesNadekyeRnriRk 181
                                        v P+  +   e+  y+  ++i++      +     Rn+iR+
  gi|557694617|ref|YP_008797671.1| 210 RVAPFRLTPEREVVFYAYLHNIPFQSQVCPNAATSMRNMIRR 251
                                       788999999999999999999999999888888888999986 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   7.1e-08   0.00021       2      85 ..      58     139 ..      57     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.1e-08
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeykekv 78 
                                       k++va+SgG DS   +++lk+  +   +  l  ++  de   e   +e l+++e+v + l++pl++ +fe+ + +++
  gi|557694617|ref|YP_008797671.1|  58 KIAVAVSGGKDSLSLLYVLKKIEKRFPRAGLVAVTV-DEGI-EGYRDEALEYVEEVTRMLEVPLYKTSFEEAFGKSL 132
                                       89******************9999998888877776.3333.67999**************************9987 PP

                     tRNA_Me_trans  79 feeflee 85 
                                        e + ++
  gi|557694617|ref|YP_008797671.1| 133 SEIVASK 139
                                       7665555 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.35   1.1e+03      10      19 ..      26      35 ..      24      36 .. 0.79
   2 ?   -1.0   0.1      0.44   1.3e+03       2       7 ..     148     153 ..     147     155 .. 0.83
   3 ?   14.7   1.5   5.5e-06     0.016       3      24 ..     285     306 ..     283     307 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.35
                      zn-ribbon_14 10 SSqkiCkACv 19
                                      S  ++C+ C 
  gi|557694617|ref|YP_008797671.1| 26 SGERLCRTCF 35
                                      66789*9995 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                      zn-ribbon_14   2 kCerCG 7  
                                        C+ CG
  gi|557694617|ref|YP_008797671.1| 148 ACSVCG 153
                                       5****9 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 5.5e-06
                      zn-ribbon_14   3 CerCGylSSqkiCkACvLLegL 24 
                                       C+ CG  SS ++C+ C L ++L
  gi|557694617|ref|YP_008797671.1| 285 CSYCGEPSSRELCRVCELTQTL 306
                                       ****************997776 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.3e-05     0.039       2      80 ..      59     143 ..      58     174 .. 0.79
   2 ?   -3.4   0.0       2.9   8.5e+03     135     155 ..     213     233 ..     209     235 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                                       EEEE--SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB..-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.....pvvfvdtghe..fpetiefvdeleeryglrlkvyepeeevaekinae 71 
                                       ++v+vsgGkdsl ll  + k+ k +       v vd g e   +e +e+v+e+++ +++ l  ++ ee + +++ + 
  gi|557694617|ref|YP_008797671.1|  59 IAVAVSGGKDSLSLLYVLKKIEKRFpraglVAVTVDEGIEgyRDEALEYVEEVTRMLEVPLYKTSFEEAFGKSLSEI 135
                                       799************999999998777887799999999844689***********999987777777776666665 PP

                                       H-S-THHHC CS
                       PAPS_reduct  72 khgsslyee 80 
                                          s+++++
  gi|557694617|ref|YP_008797671.1| 136 V-ASKQFRS 143
                                       5.4555555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.9
                                       CCCT--HHHHHHHHHHCT--B CS
                       PAPS_reduct 135 PllnWteedvwqyilrenipy 155
                                       P     e++v  y++ +nip 
  gi|557694617|ref|YP_008797671.1| 213 PFRLTPEREVVFYAYLHNIPF 233
                                       555556789999999999996 PP

>> DUF2845  Protein of unknown function (DUF2845)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   9.2e-05      0.28       9      30 ..     273     294 ..     266     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.2e-05
                           DUF2845   9 glvslGdskeeVlakCGePlsk 30 
                                       +  +lG++++ V + CGeP+s+
  gi|557694617|ref|YP_008797671.1| 273 KTTTLGKKMQRVCSYCGEPSSR 294
                                       56789****************9 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.14   4.3e+02      29      35 ..       9      15 ..       4      17 .. 0.67
   2 ?   -0.6   0.1      0.35     1e+03      17      23 ..      29      35 ..      23      38 .. 0.67
   3 ?    0.9   0.0      0.11   3.3e+02      17      24 ..     147     154 ..     143     159 .. 0.75
   4 ?   12.2   1.1   3.3e-05     0.099      17      35 ..     283     301 ..     279     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.14
                                      SS-CCCC CS
                              RecR 29 dlCaICs 35
                                       +C++C+
  gi|557694617|ref|YP_008797671.1|  9 AVCSVCR 15
                                      5677775 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.35
                                      EE-TTT- CS
                              RecR 17 rhCsrCg 23
                                      r C+ C+
  gi|557694617|ref|YP_008797671.1| 29 RLCRTCF 35
                                      5566665 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.11
                                       EE-TTT-- CS
                              RecR  17 rhCsrCgn 24 
                                         Cs+Cg 
  gi|557694617|ref|YP_008797671.1| 147 AACSVCGP 154
                                       56999985 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 3.3e-05
                                       EE-TTT--EESSSS-CCCC CS
                              RecR  17 rhCsrCgnlteedlCaICs 35 
                                       r Cs Cg  + ++lC++C 
  gi|557694617|ref|YP_008797671.1| 283 RVCSYCGEPSSRELCRVCE 301
                                       67****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); 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):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2355.98
//
Query:       gi|557694618|ref|YP_008797672.1|  [L=258]
Description: FdhD/NarQ family/nitrate assimilation protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-52  178.6   0.1    1.8e-52  178.4   0.1    1.0  1  FdhD-NarQ  FdhD/NarQ family


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 !  178.4   0.1     1e-56   1.8e-52       2     236 ..      15     248 ..      14     249 .. 0.89

  Alignments for each domain:
  == domain 1  score: 178.4 bits;  conditional E-value: 1e-56
                                       --EEEEEEETTEEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTTEEEE-S...........------- CS
                         FdhD-NarQ   2 eEepltivvngrelatlmatpadleelalGfllsegliesaediesievdedeasvavatra.kaedk.eerrtakr 76 
                                        E p++i+vn+++++t++atp++l+e+++G+ll+ g+++++e + ++e+d  +  v+v+ ++ + e++ e+ +t+ +
  gi|557694618|ref|YP_008797672.1|  15 LEFPINIYVNEKHFVTVFATPHELKEMVVGHLLGHGVVDDVEHVGDVEIDGLDVLVNVNIDNgELEKRlERYKTF-K 90 
                                       599***********************************************9998888888886555554444455.5 PP

                                       --------.---...--.H-----------EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE..TTEEEEEEEESS CS
                         FdhD-NarQ  77 vvtsgCglcgkesleel.letlelpesdlklsaeallrlmdalrekqelfketggvHaaalfd.adgellavreDvG 151
                                        + ++Cg   ++ l++   +t+++ +sd+++  ++l ++m+++ +++   k++ +vH a++++ ++g+l+ ++ Dv+
  gi|557694618|ref|YP_008797672.1|  91 HIMTSCGS-VEDYLRAFdNNTKPRINSDFRIGVDKLRNVMAEFGRYS---KRAVSVHTAGIYSdTEGQLVSLAMDVS 163
                                       66667777.455564555666666699****************9865...699********9758999********* PP

                                       HHHHHHHHHHHHHT.TSS-SSSEEEESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEEEEETTEEE CS
                         FdhD-NarQ 152 RHnAlDkviGaallegldlsdkilvvsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvgfvrgkrfn 228
                                       RH ++DkviG+a+l+++d+++++l+++gR +s+mv Kaar+gip+ vs  +p   +v  A +ag+t++ +vrgk ++
  gi|557694618|ref|YP_008797672.1| 164 RHVTVDKVIGKAALHRIDFTRCLLLTTGRQASDMVLKAARVGIPITVSLRGPIFSGVYAALKAGVTMASVVRGKGLT 240
                                       ***************************************************************************** PP

                                       EEE-GGGE CS
                         FdhD-NarQ 229 vYtgaeRi 236
                                       vY+ +eRi
  gi|557694618|ref|YP_008797672.1| 241 VYSYPERI 248
                                       *******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); 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 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1881.36
//
Query:       gi|557694619|ref|YP_008797673.1|  [L=420]
Description: molybdopterin biosynthesis protein MoeA [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-40  138.6   0.0    2.6e-40  137.8   0.0    1.4  1  MoeA_N         MoeA N-terminal region (domain I and II)
    2.1e-29  102.1   0.2    3.9e-29  101.2   0.2    1.5  1  MoCF_biosynth  Probable molybdopterin binding domain
      6e-17   61.6   0.6      2e-16   59.9   0.1    2.2  3  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 !  137.8   0.0   4.3e-44   2.6e-40       3     156 ..      15     181 ..      14     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 137.8 bits;  conditional E-value: 4.3e-44
                                       HHHHHHHHHHH-.HH.-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--............. CS
                            MoeA_N   3 veealaiilaal.el.eeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........ 68 
                                       ++eal+++ +++  + ++ e v+l +++lgr +aed+ +p+dvP f +Sa+DGYAv ae++ gas+++p        
  gi|557694619|ref|YP_008797673.1|  15 LSEALSLLFDKIsATpPDVEkVSL-EHSLGRYCAEDIFSPVDVPSFEKSAVDGYAVLAEDTFGASPNNPvylvvkgv 90 
                                       678889888888544766667***.889************************************************* PP

                                       ........-S---TT-.EEEE-TTSB--TT--EEEEGGGE...E....EETTE..S--STTTTEE-TTSSB-TTSEE CS
                            MoeA_N  69 ..saageeperllpgg.avrimTGaplPegadaVvpvEdte..eeeaketvev..kavkpgenvrraGedikaGevl 138
                                         +  ++ + +++++g av+i TGaplPega+aV++ E+++  +   ++ v +  ++v+p +nv r+Ged++ +e++
  gi|557694619|ref|YP_008797673.1|  91 shAGVRRMDVPKVSQGeAVEIYTGAPLPEGANAVLMAEYAKriG---EN-VLEvtRQVHPLQNVSRIGEDFRMNELV 163
                                       87555666667777777**********************96432...22.2224689******************** PP

                                       E-TTBB--CCCHHHHHHC CS
                            MoeA_N 139 lragtrltpaeigllasv 156
                                       +++gtr+++++ig+las+
  gi|557694619|ref|YP_008797673.1| 164 VASGTRIRSWHIGALASL 181
                                       ****************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 !  101.2   0.2   6.5e-33   3.9e-29       1     143 [.     195     333 ..     195     334 .. 0.96

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 6.5e-33
                                       EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSST CS
                     MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptp 70 
                                       +v+++G+el+       +g++ +++ p+l++ l+e+g+e  ++++v Dd + i++++ +a++  d++i+tGGt+++ 
  gi|557694619|ref|YP_008797673.1| 195 GVLSTGSELVepgtkpsEGQVINSSKPMLKASLEEHGAEPVDLGTVEDDSDLIAAKISEAVDVLDMLIITGGTSVGG 271
                                       69*******************************************************9998888************* PP

                                       T--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  71 dDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                       +Dv+pea++k+++      +++f++v+ +p kp+g a +   +   gk++++L G+p++++ ++ ++++p le
  gi|557694619|ref|YP_008797673.1| 272 KDVVPEAVKKAGDS-----DIIFHGVRIRPAKPTGAAVV---K---GKPVFMLSGYPVSAALGFMLFVKPLLE 333
                                       *************6.....9*************998888...4...458********************9997 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 ?   -2.5   0.0         1   6.3e+03      49      63 ..      65      79 ..      63      84 .. 0.79
   2 ?   -3.0   0.0       1.5   8.7e+03      59      70 ..     101     112 ..      96     113 .. 0.80
   3 !   59.9   0.1   3.3e-20     2e-16       2      72 .]     348     418 ..     347     418 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1
                                      -EEEEE-TT--EE-T CS
                            MoeA_C 49 nglivipegteglea 63
                                      +g++v+ e+t g+++
  gi|557694619|ref|YP_008797673.1| 65 DGYAVLAEDTFGASP 79
                                      89****999977665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.5
                                       -EE-TT-EEEEE CS
                            MoeA_C  59 egleaGeeVevi 70 
                                         ++ Ge Ve++
  gi|557694619|ref|YP_008797673.1| 101 PKVSQGEAVEIY 112
                                       56899****987 PP

  == domain 3  score: 59.9 bits;  conditional E-value: 3.3e-20
                                       EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       +rl+++++ ++  r+++Rv ++    ++ +ep+  +gSglLs+l +A+g++v+peg+eg+e+GeeVev++l
  gi|557694619|ref|YP_008797673.1| 348 GRLTRRVANPALTRTYVRVCVRRTPEGVLVEPLMLTGSGLLSTLTKADGILVVPEGVEGFEEGEEVEVEML 418
                                       79********************555668****************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3160.00
//
Query:       gi|557694620|ref|YP_008797674.1|  [L=652]
Description: molybdopterin biosynthesis protein MoeA [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-51  173.5   0.0    4.4e-51  172.8   0.0    1.3  1  PBP_like        PBP superfamily domain
    7.6e-45  152.5   0.8    1.6e-44  151.4   0.8    1.6  1  MoeA_N          MoeA N-terminal region (domain I and II)
    5.3e-22   78.0   0.1    1.2e-21   76.9   0.1    1.6  1  MoCF_biosynth   Probable molybdopterin binding domain
    2.1e-10   40.6   0.1    8.7e-10   38.6   0.0    2.1  2  MoeA_C          MoeA C-terminal region (domain IV)
    3.1e-05   23.7   0.0    5.5e-05   22.9   0.0    1.4  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
     0.0012   18.6   0.0     0.0029   17.4   0.0    1.6  1  SBP_bac_11      Bacterial extracellular solute-binding protei
     0.0055   16.2   0.0      0.011   15.1   0.0    1.5  1  SBP_bac_3       Bacterial extracellular solute-binding protei
  ------ inclusion threshold ------
      0.024   14.3   0.0      0.043   13.5   0.0    1.3  1  PBP_like_2      PBP superfamily domain


Domain annotation for each model (and alignments):
>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.8   0.0   1.9e-54   4.4e-51      10     192 ..     441     624 ..     436     625 .. 0.97

  Alignments for each domain:
  == domain 1  score: 172.8 bits;  conditional E-value: 1.9e-54
                                       TCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS--BG CS
                          PBP_like  10 gvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkkitnw 86 
                                       +++ +v+nvGs++G +a+++geadiag+hlld++t+eyn+  l ++  + ++vlv+++ r +g+v++k+np kit++
  gi|557694620|ref|YP_008797674.1| 441 ETETKVINVGSTAGWNAVKRGEADIAGTHLLDQKTREYNVFMLDRLGLRGKAVLVRGYARRIGFVTRKDNPIKITSF 517
                                       57789*****************************************88889************************** PP

                                       GGC-S-B-EEEEE-TTSHHHHHHHHHHC-CEECT..E-SSTTSEEESSHHHHHCCHCCETTCCECCCGG-HCCCCCC CS
                          PBP_like  87 kdladaplrlvnRetGSGtrdlfdellkkegisk..ssikgyaqearshlavaaaVaagradvgvgieavaeelkgl 161
                                       +dl+++++ +vnR +GSG r ++d +l++ g+    ++i+gy+ e+r+h  vaaaV+ gradvgv++e+va++ ++l
  gi|557694620|ref|YP_008797674.1| 518 RDLVEKNVSFVNRIKGSGVRTFIDIMLSEIGVTSpyKEIRGYDYEVRTHTGVAAAVKFGRADVGVTLESVAKQ-YDL 593
                                       *****************************9998899***********************************98.7** PP

                                       ECTTCE-EEEEEEEECTCCCSHHHHHHHHHH CS
                          PBP_like 162 dfvplaeerydlvvrkealddpevqaflefl 192
                                       df+pl ee +d++v+ + l+++ v++f++ l
  gi|557694620|ref|YP_008797674.1| 594 DFTPLGEEIFDFAVPVKSLEKKTVRKFIDKL 624
                                       ****************************865 PP

>> 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 !  151.4   0.8   7.3e-48   1.6e-44       2     157 .]      10     177 ..       9     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: 151.4 bits;  conditional E-value: 7.3e-48
                                       -HHHHHHHHHHH-.HH..-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--........... CS
                            MoeA_N   2 sveealaiilaal.el..eeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep...... 68 
                                       s++eal++i +al  l     e v+l  +algrvlaedv A++++Ppfd+S++DGYAv+a+++ +a+ee+p      
  gi|557694620|ref|YP_008797674.1|  10 SIDEALELIDKALnGLkpLGVErVSL-DRALGRVLAEDVLAKVSYPPFDRSTVDGYAVKASDTYTATEENPanlkiv 85 
                                       899****9999996668845555***.99************************************************ PP

                                       ........-S---TT-.EEEE-TTSB--TT--EEEEGGGE...E....EETTE...S--STTTTEE-TTSSB-TTSE CS
                            MoeA_N  69 ..saageeperllpgg.avrimTGaplPegadaVvpvEdte..eeeaketvev...kavkpgenvrraGedikaGev 137
                                         +  g++   ++++g +v+i+TGap+P+ga+aV +vE t+  +  +++   v   ++v+p+en+ +aG+di+ G++
  gi|557694620|ref|YP_008797674.1|  86 gyAGVGAPFIGEVKEGeCVEIATGAPVPRGANAVAMVEFTKrlD--TDR---VmvfRPVAPNENIAQAGSDISVGDT 157
                                       *9999999999999999***********************6321..333...23469******************** PP

                                       EE-TTBB--CCCHHHHHHCT CS
                            MoeA_N 138 llragtrltpaeigllasvG 157
                                       +lr+g  ++p+ei++lasvG
  gi|557694620|ref|YP_008797674.1| 158 VLRRGALISPREIAVLASVG 177
                                       *******************9 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.9   0.1   5.2e-25   1.2e-21       1     143 [.     190     329 ..     190     330 .. 0.92

  Alignments for each domain:
  == domain 1  score: 76.9 bits;  conditional E-value: 5.2e-25
                                       EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS.SEEEEESS-SSS CS
                     MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea.dviittGGtGpt 69 
                                       av ++G+e++        gki+D ngp+l ++l+elg+++  ++++pDd++ + +++++ ++   d++it+G t+++
  gi|557694620|ref|YP_008797674.1| 190 AVFSTGNEVTavgepleLGKIYDVNGPTLTAMLNELGARAVFRGIIPDDYDTMLREVREMIRLGyDMVITSGSTSAG 266
                                       68999999999999999****************************************66665556************ PP

                                       TT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTE.EEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  70 pdDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgkt.iigLPGspkavkealeeillpale 143
                                         D+ +++  ++ +      ++++++++ kpgkp++va +   +    k+ +igLPG+p ++++++ ++++p++e
  gi|557694620|ref|YP_008797674.1| 267 FGDMIYKVFGEISNG-----NVLVHGLKVKPGKPTVVAVA---G----KNlLIGLPGFPLSAMMVFLKLVKPVVE 329
                                       *********999996.....8***************9999...4....35599*************999999875 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 ?   -2.0   0.1       1.9   4.2e+03      60      70 ..      97     107 ..      93     108 .. 0.83
   2 !   38.6   0.0   3.9e-13   8.7e-10       1      72 []     343     413 ..     343     413 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.9
                                       EE-TT-EEEEE CS
                            MoeA_C  60 gleaGeeVevi 70 
                                       ++++Ge+Ve+ 
  gi|557694620|ref|YP_008797674.1|  97 EVKEGECVEIA 107
                                       599*****985 PP

  == domain 2  score: 38.6 bits;  conditional E-value: 3.9e-13
                                       EEEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE- CS
                            MoeA_C   1 karlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevill 72 
                                       ka++a ++ + +g+ e+++v++ + d e +a+p+  + Sg +  l+ A+g+++ pe++e++++GeeVe+ ll
  gi|557694620|ref|YP_008797674.1| 343 KAKMAYRIEAGKGKLELIPVQIVNSDAENIAYPL-IGQSGSTHLLSIADGILEAPENREFFQEGEEVEITLL 413
                                       689999*****************999999*****.*********************************9986 PP

>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   2.4e-08   5.5e-05      89     171 ..     504     591 ..     456     618 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.4e-08
                                       EEEETTSS..--SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT--HH..HHSSEE.EE--HHHHHHHHHTTSSSE CS
                    Phosphonate-bd  89 iivradsd..iqsledLkgktiafvspsStsGylvpaalLvkeagldpe..ddfsev.fsgshdaavlavlsgdada 160
                                       +++r+d++  i+s+ dL  k+++fv +   sG       +++e g+++   +  ++   + +h ++++av  g+ad+
  gi|557694620|ref|YP_008797674.1| 504 FVTRKDNPikITSFRDLVEKNVSFVNRIKGSGVRTFIDIMLSEIGVTSPykEIRGYDyEVRTHTGVAAAVKFGRADV 580
                                       79*****84456********************9876665559****988765556665799**************** PP

                                       EEEEHHHHHHH CS
                    Phosphonate-bd 161 aavsadaledl 171
                                       +++ +++++++
  gi|557694620|ref|YP_008797674.1| 581 GVTLESVAKQY 591
                                       **999988877 PP

>> 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 !   17.4   0.0   1.3e-06    0.0029      79     224 ..     500     633 ..     488     641 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                       EEEEEEESTT-TT---SHHHHHHSS--EEEE--T-TTTTHH.H..HHHGGG--HHHHHHHHHTEEEEESSHHHHHHH CS
                        SBP_bac_11  79 splviavpkgnpkkikgwadLlkpglklavadPttspsGlaal..alleaagaqellkalekkvvklgessrqllta 153
                                        ++ ++++k+np ki+++ dL  +++++  ++   ++sG +++   +l   g    +k+++ +   ++ + + +++a
  gi|557694620|ref|YP_008797674.1| 500 RRIGFVTRKDNPIKITSFRDLVEKNVSF--VNR-IKGSGVRTFidIMLSEIGVTSPYKEIR-GYDYEVRTHTGVAAA 572
                                       57899*****************998755..553.345555444347888888444445544.33345677799**** PP

                                       HHTTT-SEEEEEHHHHH..HSTTSSEEEE--TTT--...EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHH CS
                        SBP_bac_11 154 veageadagivyeseakaaengdkleavylpeglnldpldypaavlkkaakreaAraFlafLrspeaqail 224
                                       v+ g+ad+g++ es ak    + +l++ +l e++        +av+ k+ +++  r+F++ L  +  qa +
  gi|557694620|ref|YP_008797674.1| 573 VKFGRADVGVTLESVAK----QYDLDFTPLGEEIF------DFAVPVKSLEKKTVRKFIDKLSDKSFQAQI 633
                                       *****************....9***********98......478888888899999999999888777765 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0     5e-06     0.011      41     166 ..     445     591 ..     437     618 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5e-06
                                       EEEE-SGGGHHHHHHTTSSSEEESSEB--HHHHTTEEEESESEEEEEEEEEEETT.........SHGTCCHSSCGCG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxx RF
                         SBP_bac_3  41 efvpvswdelipalksgkvDiaiaaititpeReekvdFsqpyfsagqvllvrkkd.........askissiksladL 108
                                       ++++v  ++ ++a+k g++Dia + +  ++ Re +v + +     g ++lvr            ++++ +i+s+ dL
  gi|557694620|ref|YP_008797674.1| 445 KVINVGSTAGWNAVKRGEADIAGTHLLDQKTREYNVFMLDRLGLRGKAVLVRG-YarrigfvtrKDNPIKITSFRDL 520
                                       55556778999************************999999999999999994.4569999999788999******* PP

                                       TTSEEEEETTSH...HHHHHHHHHHC..TSEE...........EEESSHHHHHHHHHTTSSSEEEEEHHHHHHH CS
                                       xxxxxxxxxxxx...xxxxxxxxxxx..xxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 109 kgkkvgvqagst...aeellkeelkk..gaei...........vefdtleealqaLkngrvdavvadspvlayl 166
                                        +k v  ++        +++   + +  g  +            e+ t++ + +a+k gr+d+ v+ ++v++++
  gi|557694620|ref|YP_008797674.1| 521 VEKNVSFVNRIKgsgVRTFID-IMLSeiG--VtspykeirgydYEVRTHTGVAAAVKFGRADVGVTLESVAKQY 591
                                       **9988776544111333322.2333230..233444444444478999999999**********999999987 PP

>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.9e-05     0.043      39     157 ..     443     547 ..     416     615 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                        PBP_like_2  39 kvnyastGSgagikalrngdvdfagsdrplteseia.agwaang...aggliqvpvaigaialvvnkdnplnlsrea 111
                                       + ++  +GS+ag +a++ g++d+ag++  l +++ + +++  ++    g+++ v  +   i++v++kdnp +   + 
  gi|557694620|ref|YP_008797674.1| 443 ETKVINVGSTAGWNAVKRGEADIAGTH-LLDQKTREyNVFMLDRlglRGKAVLVRGYARRIGFVTRKDNPIK--ITS 516
                                       46799**********************.666666666788888899*9***********************9..334 PP

                        PBP_like_2 112 LakIfsgkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeq 157
                                       +++                +++++++v r +gsg ++++  +l+e 
  gi|557694620|ref|YP_008797674.1| 517 FRDL---------------VEKNVSFVNRIKGSGVRTFIDIMLSEI 547
                                       4444...............588999999999999888777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); 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 0.26s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 4640.38
//
Query:       gi|557694621|ref|YP_008797675.1|  [L=256]
Description: thiosulfate sulfurtransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-26   92.9   0.0    4.2e-12   46.5   0.0    2.1  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 !   46.5   0.0   2.4e-16   4.2e-12       2     105 ..      13     118 ..      12     120 .. 0.82
   2 !   44.5   0.0     1e-15   1.8e-11       5     104 ..     152     252 ..     148     254 .. 0.78

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.4e-16
                         Rhodanese   2 akelkellekgkvallDvRppeeYekghIpgAvnv...skdtlsrakkseapllelpeellelgidnkktvvvycdg 75 
                                       ++ l ++l++   +++DvR  +eY +ghIp A +    ++ +l +    +++ +++   l+  g+ +++++v+y++ 
  gi|557694621|ref|YP_008797675.1|  13 PDTLLNNLDNY--VVIDVRRLVEYRAGHIPRAYSCsfsHFIKLVGVALYPEDPDKISSLLAGTGVEKNTPIVIYDNF 87 
                                       67788888666..5*********************6665555555555555555555555555************** PP

                         Rhodanese  76 ggr.aaaaaallkklGyknvsvldGGfkawk 105
                                        gr ++++ ++l+ lG++n+s+l+  f+++ 
  gi|557694621|ref|YP_008797675.1|  88 YGRhSCRVSYTLELLGFENISILNMTFDEYT 118
                                       ***99999999999***99******999997 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 1e-15
                         Rhodanese   5 lkell.ekgkva..llDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr 78 
                                        +e+  +k++ +  l+D+R+ ++Y  +hIp A+n+++  l+++ k  +    + +++ + +id+ k++v+yc++g +
  gi|557694621|ref|YP_008797675.1| 152 IREIVaQKPR-DtlLIDTRDTQDYGVSHIPRAINIPWHVLYKPGKLFDIESIKKAAYGK-NIDDSKRLVFYCEEGTS 226
                                       5556633343.357*********************888888777766666666666666.6**************** PP

                         Rhodanese  79 aaaaaallkklGyknvsvldGGfkaw 104
                                       +a+a + ++++G+ n + +  ++ +w
  gi|557694621|ref|YP_008797675.1| 227 SAFAMYGFRAAGFLNTHTYLPSYPDW 252
                                       ****999999**97777666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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 0.26s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1951.82
//
Query:       gi|557694622|ref|YP_008797676.1|  [L=293]
Description: hypothetical protein CSUB_C1194 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   26.0   0.0      0.015   15.2   0.0    2.6  2  Big_1            Bacterial Ig-like domain (group 1)
     0.0076   16.5   0.0        0.6   10.4   0.0    2.5  2  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
  ------ inclusion threshold ------
      0.066   13.2   0.0        1.5    8.9   0.0    2.3  2  bMG3             Bacterial alpha-2-macroglobulin MG3 domain


Domain annotation for each model (and alignments):
>> 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 !   15.2   0.0   2.6e-06     0.015       9      58 ..      37      87 ..      34      92 .. 0.89
   2 !    7.9   0.0   0.00051       3.1      19      54 ..     214     243 ..     199     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-06
                             Big_1  9 ltatvkDangnpvagatVtfsvsggals.assgtTdanGkatvtltstkag 58
                                      + +++ D+ g+pv+g +V+ s   g++  +s   Td+nG a +t  s + g
  gi|557694622|ref|YP_008797676.1| 37 IVIVAMDETGHPVEGCKVNYSCELGVVDtNSYRETDKNGLALATYYSFRVG 87
                                      567899******************999989999**********99887766 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00051
                             Big_1  19 npvagatVtfsvsggalsassgtTdanGkatvtlts 54 
                                       npv++a+V +s        ++g+Td++G a+++++ 
  gi|557694622|ref|YP_008797676.1| 214 NPVPDAQVFLS------DGQTGITDKSGFARFKVKA 243
                                       78888888887......34789**********9975 PP

>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.013        80       7      64 ..      42     105 ..      36     121 .. 0.69
   2 !   10.4   0.0    0.0001       0.6       8      74 ..     208     271 ..     199     279 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.013
                   CarboxypepD_reg   7 tdasgapiagatVtvtnadt..gtvastttdadG.....afrlrglppgtysvtvsapGyatatr 64 
                                        d++g p++g +V  + + +  +t+++  td++G     ++++r +  +  ++  ++pG+ ++  
  gi|557694622|ref|YP_008797676.1|  42 MDETGHPVEGCKVNYSCELGvvDTNSYRETDKNGlalatYYSFR-VGKDVLKISLEKPGFLPTFA 105
                                       589999***99999874322114678888999996666667776.77788888888888887765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0001
                   CarboxypepD_reg   8 dasg..apiagatVtvtnadtgtvastttdadGafrlrglpp..gtysvtvsapGyatatreevtltagqt 74 
                                       d+sg  +p++ a+V ++       ++  td++G  r++ +++  g  ++++ +p   +  +e  +++ g++
  gi|557694622|ref|YP_008797676.1| 208 DHSGipNPVPDAQVFLS-----DGQTGITDKSGFARFK-VKAnsGLLKIKAKHPQLYECYQE-AEINIGNK 271
                                       4566557**********.....588899*********8.77768888888888877777653.66666655 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 ?    1.8   0.0     0.041   2.5e+02      23      54 ..      44      77 ..      33      89 .. 0.71
   2 ?    8.9   0.0   0.00025       1.5      26      69 ..     214     255 ..     203     279 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.041
                              bMG3 23 dsgkPvagaeVrlldkkgevlae...gtTDaqGva 54
                                      ++g Pv+g +V+  +++  v+ +    +TD++G+a
  gi|557694622|ref|YP_008797676.1| 44 ETGHPVEGCKVNY-SCELGVVDTnsyRETDKNGLA 77
                                      6899*****9995.555555555222478888877 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00025
                              bMG3  26 kPvagaeVrlldkkgevlaegtTDaqGvarfaallar...gkegaap 69 
                                       +Pv++a+V l+d +     +g TD++G arf+ ++++   + ++++p
  gi|557694622|ref|YP_008797676.1| 214 NPVPDAQVFLSDGQ-----TGITDKSGFARFKVKANSgllKIKAKHP 255
                                       68999999999875.....799**********997776654555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 2018.24
//
Query:       gi|557694623|ref|YP_008797677.1|  [L=255]
Description: hypothetical protein CSUB_C1195 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-11   42.3   0.0      9e-11   42.2   0.0    1.2  1  FdhE            Protein involved in formate dehydrogenase for
     0.0017   18.4  12.7     0.0092   16.0   2.7    2.3  2  DZR             Double zinc ribbon
     0.0099   16.6   4.5       0.04   14.7   2.5    2.5  2  zinc_ribbon_15  zinc-ribbon family
  ------ inclusion threshold ------
      0.037   13.5   0.9       0.15   11.5   1.3    1.6  2  NMD3            NMD3 family
        0.2   11.0   5.1       0.58    9.5   0.8    2.8  2  zf-TFIIB        Transcription factor zinc-finger
       0.25   10.9   8.6        2.2    7.9   0.8    3.4  3  TF_Zn_Ribbon    TFIIB zinc-binding
       0.43    9.3   2.7        0.7    8.6   2.7    1.3  1  NRDD            Anaerobic ribonucleoside-triphosphate reducta
       0.48   10.1   3.6        7.5    6.3   1.2    2.8  2  GATA            GATA zinc finger
       0.65   10.0   4.6       0.65   10.0   1.5    2.5  2  HypA            Hydrogenase/urease nickel incorporation, meta
        1.3    9.0   7.2       0.32   10.9   0.3    2.8  3  ADD_ATRX        Cysteine Rich ADD domain
        2.1    8.2  11.0       0.15   11.8   1.6    2.7  3  Rubredoxin_2    Rubredoxin metal binding domain
        3.6    7.5  14.1       0.47   10.4   0.3    3.8  4  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
          9    6.5   8.8      2e+02    2.2   6.1    3.4  2  Zn-ribbon_8     Zinc ribbon domain
        9.1    6.0  10.8        1.4    8.5   0.5    3.7  4  RecR            RecR protein


Domain annotation for each model (and alignments):
>> FdhE  Protein involved in formate dehydrogenase formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0     7e-14     9e-11     168     270 ..     146     246 ..       2     251 .. 0.69

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 7e-14
                                       -SS-TTT---EEEEEEE-------EEEEEETTT--EEE--TTS-TTT---..SS-EEE------C-EEEEEETTTTE CS
                              FdhE 168 kglCPvCgsaPvasvvriggeaeglRylhCslCeteWhvvRvkCsnCeet..kelaylsledekaavkAesCdeChs 242
                                        + C  Cg   + +v      + g Ry+ Cs C +  +v    C +C++t  + l+++++ de+   + e C  C +
  gi|557694623|ref|YP_008797677.1| 146 VRSCLTCGRNYILGVY-----RGGFRYMVCSACGHVARVDFFYCPTCGNTdpNLLSFKKMLDEPYF-QIEICRRCGA 216
                                       3678888888888887.....3478***********************996567899998888765.9********* PP

                                       EEEEEETTT..-TT--HHHHHHTTHHHHHH CS
                              FdhE 243 Ylkilyqek..dpevepvADDlAsLaLDll 270
                                       Y k+++++    ++ +p+  DlA++ LD +
  gi|557694623|ref|YP_008797677.1| 217 YYKMVNEDMvgTVSDDPLLLDLATIDLDNI 246
                                       ******9872256789************76 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   2.5   1.5e-05     0.019      13      49 .]     147     188 ..     134     188 .. 0.82
   2 !   16.0   2.7   7.2e-06    0.0092       1      36 [.     170     216 ..     170     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                               DZR  13 rfCseCgtk..lkavaa......edrCpsCgekvdpearfCpeCG 49 
                                       r C +Cg +  l             +C++Cg+ +  ++ +Cp CG
  gi|557694623|ref|YP_008797677.1| 147 RSCLTCGRNyiLG---VyrggfrYMVCSACGHVARVDFFYCPTCG 188
                                       6799999995432...1346888999******************9 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 7.2e-06
                               DZR   1 CpqCgeelppdarfCseCgtk....lkavaa...........edrCpsCge 36 
                                       C+ Cg+  + d  +C++Cg++    l    +            + C +Cg+
  gi|557694623|ref|YP_008797677.1| 170 CSACGHVARVDFFYCPTCGNTdpnlL----SfkkmldepyfqIEICRRCGA 216
                                       *******************9955542....345578888899999999997 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   2.5   3.1e-05      0.04      65      86 .]     167     188 ..     113     188 .. 0.79
   2 ?    1.0   0.0      0.56   7.2e+02      67      73 ..     210     216 ..     196     227 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.1e-05
                    zinc_ribbon_15  65 kkeCknCgkeveeefkyCpkCg 86 
                                       +++C+ Cg++   +f yCp Cg
  gi|557694623|ref|YP_008797677.1| 167 YMVCSACGHVARVDFFYCPTCG 188
                                       899******************9 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.56
                    zinc_ribbon_15  67 eCknCgk 73 
                                       +C++Cg+
  gi|557694623|ref|YP_008797677.1| 210 ICRRCGA 216
                                       4444443 PP

>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.7   2.2e+03      33      44 ..     144     155 ..     133     168 .. 0.70
   2 ?   11.5   1.3   0.00012      0.15       1      46 [.     170     219 ..     149     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.7
                              NMD3  33 ievevCkeCgry 44 
                                       + v+ C +Cgr 
  gi|557694623|ref|YP_008797677.1| 144 VPVRSCLTCGRN 155
                                       667778888775 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00012
                              NMD3   1 CcrCGkeieeling.lCedCllkevdite.....giekievevCkeCgrylp 46 
                                       C  CG+  +   +  +C+ C  ++ ++++      ++  ++e+C++Cg+y++
  gi|557694623|ref|YP_008797677.1| 170 CSACGHVAR-V-DFfYCPTCGNTDPNLLSfkkmlDEPYFQIEICRRCGAYYK 219
                                       778888884.4.4469****99998887744432444577*********984 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   0.3     0.084   1.1e+02       9      26 ..     157     174 ..     148     174 .. 0.75
   2 ?    9.5   0.8   0.00046      0.58       1      26 [.     183     215 ..     183     215 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.084
                          zf-TFIIB   9 leeserggveidyCpqCr 26 
                                          + rgg+   +C +C+
  gi|557694623|ref|YP_008797677.1| 157 ILGVYRGGFRYMVCSACG 174
                                       5567899**********7 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00046
                          zf-TFIIB   1 kCPkCqd.eleeser......ggveidyCpqCr 26 
                                       +CP+C++ +++ + +        ++i+ C +C+
  gi|557694623|ref|YP_008797677.1| 183 YCPTCGNtDPNLLSFkkmldePYFQIEICRRCG 215
                                       7****865788555555664355*********7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.8    0.0017       2.2       3      28 ..     149     176 ..     147     180 .. 0.76
   2 ?    4.4   0.2     0.021        27       1      10 [.     182     191 ..     182     199 .. 0.82
   3 ?    2.0   0.1      0.12   1.5e+02       2      16 ..     210     225 ..     209     230 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0017
                                       ETTTTCEEC..HEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon   3 CPnCgstnl..veDpergelvCtdCGlV 28 
                                       C  Cg  ++  v+      +vC++CG V
  gi|557694623|ref|YP_008797677.1| 149 CLTCGRNYIlgVYRGGFRYMVCSACGHV 176
                                       88888888646666555567******98 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.021
                                       EEETTTTCEE CS
                      TF_Zn_Ribbon   1 ykCPnCgstn 10 
                                       + CP Cg+t+
  gi|557694623|ref|YP_008797677.1| 182 FYCPTCGNTD 191
                                       5799999975 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.12
                                       EETTTTCEE.CHEETS CS
                      TF_Zn_Ribbon   2 kCPnCgstn.lveDpe 16 
                                       +C  Cg ++ +v++ +
  gi|557694623|ref|YP_008797677.1| 210 ICRRCGAYYkMVNEDM 225
                                       5888888776776655 PP

>> NRDD  Anaerobic ribonucleoside-triphosphate reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.7   0.00055       0.7     507     542 ..     167     219 ..     141     226 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00055
                                       EEEETT.--..EESSSB-TTT--B...........E.....EEEEEESSSSEE CS
                              NRDD 507 idvCnecgy..kgeiekCpkCgse...........ee....vevirRitGYlr 542
                                       + vC  cg+  +  ++ Cp+Cg++           +e    +e+ rR   Y++
  gi|557694623|ref|YP_008797677.1| 167 YMVCSACGHvaRVDFFYCPTCGNTdpnllsfkkmlDEpyfqIEICRRCGAYYK 219
                                       679******85555589*****9955555554444223444666666655655 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.065        84      21      27 ..     168     174 ..     165     178 .. 0.84
   2 ?    6.3   1.2    0.0058       7.5      18      32 ..     206     220 ..     184     223 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.065
                              GATA  21 sLCnaCG 27 
                                       ++C aCG
  gi|557694623|ref|YP_008797677.1| 168 MVCSACG 174
                                       79****9 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0058
                              GATA  18 gnksLCnaCGlyykk 32 
                                        +++ C  CG yyk+
  gi|557694623|ref|YP_008797677.1| 206 FQIEICRRCGAYYKM 220
                                       57889********97 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 ?   10.0   1.5   0.00051      0.65      71     101 ..     168     196 ..     113     203 .. 0.90
   2 ?   -0.6   0.1         1   1.3e+03      72      82 ..     210     220 ..     203     227 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00051
                                       EEETTTS-EEECHHHHHS-TTTSSS-EEEEE CS
                              HypA  71 vrCreCgkefeleekalrCpkCgsadveivs 101
                                       + C+ Cg+  +++   + Cp+Cg++d +++s
  gi|557694623|ref|YP_008797677.1| 168 MVCSACGHVARVD--FFYCPTCGNTDPNLLS 196
                                       6799***888877..468******9987766 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1
                                       EETTTS-EEEC CS
                              HypA  72 rCreCgkefel 82 
                                        Cr+Cg+ +++
  gi|557694623|ref|YP_008797677.1| 210 ICRRCGAYYKM 220
                                       48888877764 PP

>> ADD_ATRX  Cysteine Rich ADD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1       1.6     2e+03      13      19 ..     148     154 ..     144     157 .. 0.83
   2 ?    1.2   0.3      0.26   3.4e+02      12      19 ..     168     175 ..     164     182 .. 0.79
   3 ?   10.9   0.3   0.00025      0.32      11      48 ..     181     219 ..     174     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                          ADD_ATRX  13 sCtaCgq 19 
                                       sC +Cg+
  gi|557694623|ref|YP_008797677.1| 148 SCLTCGR 154
                                       7999998 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.26
                          ADD_ATRX  12 vsCtaCgq 19 
                                       + C+aCg+
  gi|557694623|ref|YP_008797677.1| 168 MVCSACGH 175
                                       67****96 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00025
                          ADD_ATRX  11 ivsCtaCgq.qvnhfqkdslykHPvLkVLiCksCfkyys 48 
                                        + C +Cg+   n+   + +   P  ++ iC+ C  yy+
  gi|557694623|ref|YP_008797677.1| 181 FFYCPTCGNtDPNLLSFKKMLDEPYFQIEICRRCGAYYK 219
                                       57799999734677777888999***************6 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       2.2   2.8e+03       3       9 ..     149     155 ..     148     157 .. 0.67
   2 ?   11.8   1.6   0.00011      0.15       2      21 ..     169     188 ..     169     190 .. 0.96
   3 ?    2.2   0.2      0.12   1.6e+02       3       8 ..     211     216 ..     210     219 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.2
                      Rubredoxin_2   3 CsqCGfe 9  
                                       C  CG  
  gi|557694623|ref|YP_008797677.1| 149 CLTCGRN 155
                                       7778865 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00011
                      Rubredoxin_2   2 vCsqCGfesakwfGrCpsCg 21 
                                       vCs+CG++++  f  Cp Cg
  gi|557694623|ref|YP_008797677.1| 169 VCSACGHVARVDFFYCPTCG 188
                                       7******************9 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.12
                      Rubredoxin_2   3 CsqCGf 8  
                                       C++CG+
  gi|557694623|ref|YP_008797677.1| 211 CRRCGA 216
                                       788876 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 ?   -1.5   0.5       1.9   2.5e+03      13      19 ..     148     154 ..     145     154 .. 0.67
   2 ?   10.4   0.3   0.00037      0.47       5      20 ..     161     176 ..     159     177 .. 0.91
   3 ?    2.3   0.4      0.13   1.6e+02      27      34 ..     183     190 ..     183     192 .. 0.65
   4 ?    2.6   0.0     0.099   1.3e+02      14      20 ..     211     217 ..     202     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.9
                           DUF35_N  13 rCpdCGt 19 
                                        C  CG+
  gi|557694623|ref|YP_008797677.1| 148 SCLTCGR 154
                                       5778876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00037
                           DUF35_N   5 aegrLvgqrCpdCGtv 20 
                                        +g ++++ C++CG+v
  gi|557694623|ref|YP_008797677.1| 161 YRGGFRYMVCSACGHV 176
                                       699***********98 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.13
                           DUF35_N  27 vCphCgsd 34 
                                       +Cp Cg +
  gi|557694623|ref|YP_008797677.1| 183 YCPTCGNT 190
                                       57777765 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.099
                           DUF35_N  14 CpdCGtv 20 
                                       C+ CG++
  gi|557694623|ref|YP_008797677.1| 211 CRRCGAY 217
                                       8888877 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.2   1.5e+03      29      34 ..     149     154 ..     136     156 .. 0.64
   2 ?    2.2   6.1      0.16     2e+02       8      34 ..     170     189 ..     161     221 .. 0.57

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
                       Zn-ribbon_8  29 CPeCgs 34 
                                       C +Cg 
  gi|557694623|ref|YP_008797677.1| 149 CLTCGR 154
                                       666664 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.16
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs 34 
                                       C +Cgh+  v           CP+Cg 
  gi|557694623|ref|YP_008797677.1| 170 CSACGHVARVD-------FFYCPTCGN 189
                                       66666444422.......123555554 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1         4   5.2e+03       2      16 ..      61      75 ..      61      75 .. 0.69
   2 ?   -1.2   0.2       1.2   1.6e+03      16      23 ..     146     153 ..     145     154 .. 0.89
   3 ?    8.5   0.5    0.0011       1.4      19      37 ..     170     190 ..     166     191 .. 0.85
   4 ?    2.4   0.0      0.09   1.2e+02      15      25 ..     207     217 ..     196     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 4
                                      HHHHHHHHHHHHHH- CS
                              RecR  2 aeeLaeaLqeakekv 16
                                      ae+L   L++++e+v
  gi|557694623|ref|YP_008797677.1| 61 AEALVMVLEALRERV 75
                                      567777788888776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.2
                                       -EE-TTT- CS
                              RecR  16 vrhCsrCg 23 
                                       vr C  Cg
  gi|557694623|ref|YP_008797677.1| 146 VRSCLTCG 153
                                       899****8 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0011
                                       -TTT--EESSS..S-CCCCST CS
                              RecR  19 CsrCgnlteed..lCaICsdp 37 
                                       Cs Cg+++  d   C+ C ++
  gi|557694623|ref|YP_008797677.1| 170 CSACGHVARVDffYCPTCGNT 190
                                       ***********656****875 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.09
                                       H-EE-TTT--E CS
                              RecR  15 kvrhCsrCgnl 25 
                                       ++  C+rCg +
  gi|557694623|ref|YP_008797677.1| 207 QIEICRRCGAY 217
                                       6788****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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):              14  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1756.43
//
Query:       gi|557694624|ref|YP_008797678.1|  [L=1021]
Description: formate dehydrogenase alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-46  157.1   3.4    1.3e-40  139.7   0.0    2.7  2  Molybdopterin    Molybdopterin oxidoreductase
    7.1e-14   51.8   0.0    1.6e-13   50.6   0.0    1.6  1  Molydop_binding  Molydopterin dinucleotide binding domain
    1.1e-12   47.7   0.5    2.6e-12   46.5   0.5    1.6  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
  ------ inclusion threshold ------
      0.035   13.9   0.2      0.062   13.2   0.2    1.4  1  TAT_signal       TAT (twin-arginine translocation) pathway si


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 !   15.9   1.6   1.1e-06    0.0047       1      40 [.     108     151 ..     108     158 .. 0.90
   2 !  139.7   0.0     3e-44   1.3e-40      48     411 ..     190     638 ..     180     649 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.1e-06
                                       B--S-EEEC....TTTTTSEEEE--HHHHHHHHHHHHHHHHHHC CS
                     Molybdopterin   1 RlkyPmvRk....qargeGkFvrvsWdeAleliaaslkytikky 40 
                                       Rl++P++R+    +++++  +++++W+eA+++i ++++++ k+ 
  gi|557694624|ref|YP_008797678.1| 108 RLRRPLMRTnpkkGENEDPMWREITWEEAFNIIIQKYEQIYKEW 151
                                       9********99988888899******************998875 PP

  == domain 2  score: 139.7 bits;  conditional E-value: 3e-44
                                       EEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECCGGGTTHHHHCHHCCCCCTTT...S-SS-CCGGGG-SEEEEESS- CS
                     Molybdopterin  48 fssgplmsmeslaslkkllsllggknlsfydwyadlppasaqqtigsdsrsny...essnpledlensdliilwGsN 121
                                        ++ +++s+e+ ++++kl+ l+g +n   +   ++  +       +++++++y   +++n+ +d++n+++ i +GsN
  gi|557694624|ref|YP_008797678.1| 190 RIATDYLSNEEAYLGRKLAMLMGTNNCDIEARRCHSTT-------VAGLADVYgfgAMTNSAVDFQNAKVTINIGSN 259
                                       577899******************88888888777743.......444445541115677888************** PP

                                       HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECH CS
                     Molybdopterin 122 vreerpilnarirkaalkkkakvivigpryaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygk 198
                                        +e +p +  ++  + ++k+ k+iv++pr+  ++++a+     +pgt aa++l+++++ +++ ++dk      t   
  gi|557694624|ref|YP_008797678.1| 260 HAEQHPEA-FKFTSKSIEKGGKLIVFDPRFGRTASKAHYFAWFRPGTEAAIVLGIMNYAIKNRLYDK------TFLQ 329
                                       ********.99999999999***********988888888888************************......6677 PP

                                       HHCCCCCCCEECCS..........................HHHHHHCCHHHHHHHHHHHHHHTSSE.EEEECHHHHT CS
                     Molybdopterin 199 eetdmpllvtleee..........................tgkkkevvariarelarnaaktagks.miivGaglnh 248
                                       e tdmpl  ++ e                           ++ +++v+a++ +++a+ + + a ++  +++  g+++
  gi|557694624|ref|YP_008797678.1| 330 ERTDMPLHFETREFledwetnpnsifskfkehvsrftpqeVERITGVPANKFIQMAQVYTDPANRPgQFVWCIGATQ 406
                                       889999999998889999*******************************************999984578899**** PP

                                       STTHHHHHHHHHHHHHHCTHCSSTTCEEEEESS............................................ CS
                     Molybdopterin 249 rqdgdaiyravinLallvgnvgqpgGgwahlnG............................................ 281
                                       ++ g++i+r   +L ll+gnvgqpgGg + l+G                                            
  gi|557694624|ref|YP_008797678.1| 407 HTCGTQIIRLFGQLQLLLGNVGQPGGGANVLRGitnvqgsndmnhlmhiwlgyrrvpgalgererlpggaeadirry 483
                                       *********************************77777777777777777777777777777766666666665555 PP

                                       ..CTTHHHCHHHHTCCTTCCCCCCCTT................................................HH CS
                     Molybdopterin 282 ..qlilagaaekvgalpvllsvkslke................................................ek 308
                                         +                       +                                                  
  gi|557694624|ref|YP_008797678.1| 484 qkY-----------------------KnlvkegktaqeiaqalniawvgdlrhyaswreaemnwgifigtypeddPD 537
                                       552.......................033333333444444444555666777777778888888888777756644 PP

                                       HHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHH.CSSEEEEEESCSSHHHHTSS CS
                     Molybdopterin 309 ikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekale.kldlvvvldgrltstalyaD 384
                                        ++++    +++  p+ + +e  + ++ + +k++ l g np+v+  ++++v++ l  +  +vvv+d +l++ta++aD
  gi|557694624|ref|YP_008797678.1| 538 NGVVI---SDVPVEPGLTTIEYFREMEAGRIKFMILQGMNPVVSVGNASQVIRGLSsPNAFVVVMDLFLSETAHFAD 611
                                       44444...47888999****************************************666788899************ PP

                                       EEEEBE-CCGSEEEEE-TTSEEEEEEE CS
                     Molybdopterin 385 iiLPaatwyEkedlytndegrfqhlkq 411
                                       i+LPaa+ yE ++ +tn+ + +q +++
  gi|557694624|ref|YP_008797678.1| 612 IVLPAASKYENSGSVTNTGHMIQWRHK 638
                                       ********************9997555 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   3.6e-17   1.6e-13       2     109 ..     891    1013 ..     890    1015 .. 0.86

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 3.6e-17
                                        EEEEE-BTTBSTTTT..TCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTE...EEEEEEEEESSB-T CS
                   Molydop_binding    2 rLitgrsldqlhsqt..rtrpvlrlakpepevveinpedAaalGikdGdlVevesrrG...svevrakvtervrp 71  
                                        +L++ r  ++ h+++  rt p+l++ +pe  +ve++p  A++lG+k+Gd+V++ s+r     v ++++vt+rvrp
  gi|557694624|ref|YP_008797678.1|  891 ILTSFRLTEHQHTGIltRTIPWLAEMMPE-LFVEMSPSLANQLGVKTGDRVKIVSKRNindPVIAKVMVTNRVRP 964 
                                        79****99999999844555555555555.5**************************99999************* PP

                                        TEE......EEESSHCC..........S-GHCTS--SCSTTT--CSTT- CS
                   Molydop_binding   72 Gvv......fmpfgwwe.....agekggnaNaltddatdplsgtpefks 109 
                                         v+      ++ ++w +      g+ ++ +N+l +da+d+ +g+pe k 
  gi|557694624|ref|YP_008797678.1|  965 LVIngklfeIIAMPWAYgfqkpLGRPNSITNKLFPDAMDEETGMPETKI 1013
                                        8886666666778888799**999**********************986 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.5   5.9e-16   2.6e-12       3      49 ..      51      97 ..      50     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 5.9e-16
                                      EEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTC CS
                    Molybdop_Fe4S4  3 vvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtl 49
                                      +++++CpyC vgC +  +v+dg++v + +d ++p +eg+lC KG++ 
  gi|557694624|ref|YP_008797678.1| 51 KIPSVCPYCAVGCTVVGTVVDGRVVDIAPDLEAPHTEGTLCSKGQAS 97
                                      689*****************************************976 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 ?   13.2   0.2   1.4e-05     0.062       2      20 ..       7      26 ..       6      32 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                        TAT_signal  2 lSRRdFLKgs.AAaaAAaal 20
                                      ++RRd+LK +  A++A+++l
  gi|557694624|ref|YP_008797678.1|  7 IKRRDLLKVAtTATTALTTL 26
                                      89******665555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1021 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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: 0.75u 0.29s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 6654.08
//
Query:       gi|557694625|ref|YP_008797679.1|  [L=339]
Description: formate dehydrogenase beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-20   72.1  12.1    1.4e-18   66.9   5.1    2.8  3  Fer4_11    4Fe-4S dicluster domain
    1.1e-18   67.6   0.0    5.9e-07   30.0   0.0    3.9  4  Fer4_7     4Fe-4S dicluster domain
    3.9e-10   39.1  33.8    8.6e-06   25.4   2.9    5.7  6  Fer4       4Fe-4S binding domain
    1.8e-08   34.4  23.9     0.0032   17.6   6.7    4.2  4  Fer4_10    4Fe-4S dicluster domain
      1e-07   32.0  24.9       0.02   15.1   5.6    4.1  3  Fer4_9     4Fe-4S dicluster domain
    1.9e-07   30.9  38.8    0.00014   21.8   3.8    5.3  5  Fer4_6     4Fe-4S binding domain
    6.8e-06   25.9  11.2     0.0002   21.2   1.2    5.0  5  Fer4_2     4Fe-4S binding domain
    6.5e-05   23.0  26.3    0.00054   20.0   8.1    3.5  4  Fer4_21    4Fe-4S dicluster domain
    0.00099   20.0  23.7        1.5    9.8   0.0    4.7  5  Fer4_16    4Fe-4S double cluster binding domain
     0.0011   19.8  35.8       0.39   11.8   2.9    4.8  4  Fer4_3     4Fe-4S binding domain
     0.0017   19.0  11.3      0.062   14.0   0.3    3.7  3  Fer4_15    4Fe-4S single cluster domain
     0.0047   17.3  33.9      0.043   14.3   1.8    4.8  5  Fer4_4     4Fe-4S binding domain
  ------ inclusion threshold ------
      0.029   14.5   0.0         11    6.2   0.0    2.5  2  Rv2175c_C  Rv2175c C-terminal domain of unknown function
      0.051   14.0  22.9        1.3    9.5  16.9    4.1  3  Fer4_8     4Fe-4S dicluster domain
      0.095   13.3  21.2       0.66   10.6   0.1    4.4  5  Fer4_17    4Fe-4S dicluster domain
          5    7.7  25.2        1.3    9.6   0.8    4.8  4  Fer4_13    4Fe-4S single cluster domain of Ferredoxin I
        5.9    7.8  18.5        2.2    9.2   0.4    3.5  3  Fer4_22    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 ?   -1.6   0.2       2.8   2.9e+03       8      54 ..      42      54 ..      35      68 .. 0.51
   2 !   66.9   5.1   1.3e-21   1.4e-18       2      90 ..     119     203 ..     118     213 .. 0.91
   3 !    8.8   0.0    0.0016       1.7      80      98 ..     224     242 ..     216     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.8
                           Fer4_11  8 eqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveac 54
                                      + C  C                                  r+++ ac
  gi|557694625|ref|YP_008797679.1| 42 DLCIGC----------------------------------RACQVAC 54
                                      444333..................................2222222 PP

  == domain 2  score: 66.9 bits;  conditional E-value: 1.3e-21
                           Fer4_11   2 ewlflpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneetgkvekCdmcldrv 78 
                                       +wlf+   C+hC+e+pCv  +p++a+ k + +G V +  + +  ++r+++e+cP++++r+n e g+vekC++c+dr+
  gi|557694625|ref|YP_008797679.1| 119 QWLFTRVSCMHCVEAPCVYGCPTTALWKHP-EGPVEVRTDLCI-GCRNCIETCPFDVPRTNPELGVVEKCTLCADRI 193
                                       799***************************.9**********7.********************************* PP

                           Fer4_11  79 eaGllpacvesc 90 
                                       +  ++p+ v + 
  gi|557694625|ref|YP_008797679.1| 194 T--QKPIVVGNF 203
                                       9..667666555 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0016
                           Fer4_11  80 aGllpacvescptgalnfg 98 
                                       + l+pacve+cpt al+ g
  gi|557694625|ref|YP_008797679.1| 224 NLLEPACVETCPTDALKWG 242
                                       5578**********99987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   5.6e-10   5.9e-07       2      52 .]      44     143 ..      43     143 .. 0.80
   2 !   17.3   2.2   5.2e-06    0.0055      31      52 .]     152     173 ..     144     173 .. 0.83
   3 !   14.1   6.4   5.2e-05     0.055       2      37 ..     159     185 ..     158     195 .. 0.78
   4 !   11.4   0.0   0.00035      0.37       7      28 ..     229     250 ..     227     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5.6e-10
                            Fer4_7   2 CigCgaCvaaC..............................................pvkaieldee.enekgtekv 31 
                                       CigC+aC++aC                                               + +++++ +   e +t ++
  gi|557694625|ref|YP_008797679.1|  44 CIGCRACQVACkrwnerkplyeevgdpvaqlgreiatgekgyagaeilsftnpqnleAHTWLTMKFDeFGEGETLQW 120
                                       ***********999999999999999999999999999999988888888887766645555554331344466888 PP

                            Fer4_7  32 eidpekClgCga..CvavCPtga 52 
                                        +   +C++C +  Cv  CPt a
  gi|557694625|ref|YP_008797679.1| 121 LFTRVSCMHCVEapCVYGCPTTA 143
                                       99999*****8889******986 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.2e-06
                            Fer4_7  31 veidpekClgCgaCvavCPtga 52 
                                       ve++ + C+gC++C+++CP+++
  gi|557694625|ref|YP_008797679.1| 152 VEVRTDLCIGCRNCIETCPFDV 173
                                       6788899***********9985 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 5.2e-05
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenekgtekveidpek 37 
                                       CigC++C ++Cp ++ ++++e          ++ ek
  gi|557694625|ref|YP_008797679.1| 159 CIGCRNCIETCPFDVPRTNPEL---------GVVEK 185
                                       ***************9999873.........34444 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 0.00035
                            Fer4_7   7 aCvaaCpvkaieldeeenekgt 28 
                                       aCv++Cp++a+++ ++++  ++
  gi|557694625|ref|YP_008797679.1| 229 ACVETCPTDALKWGPRNEIVRM 250
                                       8*************99776655 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   1.6   4.8e-07    0.0005       3      18 ..      39      54 ..      37      56 .. 0.93
   2 ?   -0.4   0.4       1.1   1.2e+03      10      17 ..     126     133 ..     125     133 .. 0.81
   3 ?    0.8   0.1      0.46   4.9e+02      14      23 ..     135     144 ..     135     145 .. 0.85
   4 !   25.4   2.9   8.1e-09   8.6e-06       2      22 ..     153     173 ..     152     175 .. 0.89
   5 ?    0.8   0.2      0.47   4.9e+02       6      11 ..     184     189 ..     182     190 .. 0.87
   6 !   12.0   0.4   0.00014      0.15      13      24 .]     229     240 ..     229     240 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.8e-07
                                      EETTTSSS-THHHHHS CS
                              Fer4  3 ideekCigCGaCvevC 18
                                      +d+++CigC aC  +C
  gi|557694625|ref|YP_008797679.1| 39 FDQDLCIGCRACQVAC 54
                                      79************** PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
                                       S-THHHHH CS
                              Fer4  10 gCGaCvev 17 
                                        C+ Cve+
  gi|557694625|ref|YP_008797679.1| 126 SCMHCVEA 133
                                       79999987 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.46
                                       HHHHSTTTEE CS
                              Fer4  14 CvevCPvgAI 23 
                                       Cv  CP+ A+
  gi|557694625|ref|YP_008797679.1| 135 CVYGCPTTAL 144
                                       9999**9776 PP

  == domain 4  score: 25.4 bits;  conditional E-value: 8.1e-09
                                       EEETTTSSS-THHHHHSTTTE CS
                              Fer4   2 videekCigCGaCvevCPvgA 22 
                                       ++ +++CigC +C+e CP+++
  gi|557694625|ref|YP_008797679.1| 153 EVRTDLCIGCRNCIETCPFDV 173
                                       6889***************97 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.47
                                       TTSSS- CS
                              Fer4   6 ekCigC 11 
                                       ekC+ C
  gi|557694625|ref|YP_008797679.1| 184 EKCTLC 189
                                       89**99 PP

  == domain 6  score: 12.0 bits;  conditional E-value: 0.00014
                                       HHHHHSTTTEEE CS
                              Fer4  13 aCvevCPvgAIt 24 
                                       aCve CP++A++
  gi|557694625|ref|YP_008797679.1| 229 ACVETCPTDALK 240
                                       7*********85 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   0.1   5.8e-06    0.0061       2      23 ..      37      56 ..      36      88 .. 0.76
   2 !   15.3  13.2   1.5e-05     0.016       6      56 .]     124     170 ..     119     170 .. 0.92
   3 !   17.6   6.7     3e-06    0.0032       4      49 ..     154     190 ..     151     196 .. 0.86
   4 ?    4.6   0.0     0.032        34      14      24 ..     229     246 ..     227     268 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.8e-06
                           Fer4_10  2 vvidddtCirCgkCvkaCPadl 23
                                      + +d+d Ci+C++C+ aC  + 
  gi|557694625|ref|YP_008797679.1| 37 MLFDQDLCIGCRACQVAC--KR 56
                                      6789**************..44 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.5e-05
                           Fer4_10   6 ddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       + +C++C    Cv  CP+      +   + +e++v++  + C+gc +C+e CP
  gi|557694625|ref|YP_008797679.1| 124 RVSCMHCVeaPCVYGCPT------TALWKHPEGPVEVRTDLCIGCRNCIETCP 170
                                       668****8779*******......99**************************9 PP

  == domain 3  score: 17.6 bits;  conditional E-value: 3e-06
                           Fer4_10   4 idddtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcg 49 
                                       + +d Ci+C++C + CP+            + +++ ++vekCt c 
  gi|557694625|ref|YP_008797679.1| 154 VRTDLCIGCRNCIETCPF---------DVPRTNPELGVVEKCTLCA 190
                                       56799*************.........7788888889999999995 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.032
                           Fer4_10  14 kCvkaCPadl.......t 24 
                                       +Cv+ CP+d+       +
  gi|557694625|ref|YP_008797679.1| 229 ACVETCPTDAlkwgprnE 246
                                       699999996655444331 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   9.9    0.0001      0.11       2      50 ..      44     143 ..      43     144 .. 0.74
   2 !   15.1   5.6   1.9e-05      0.02       2      40 ..     159     190 ..     158     192 .. 0.85
   3 !    6.6   0.0    0.0083       8.7       7      30 ..     229     252 ..     224     261 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                            Fer4_9   2 CtgCgaCveaC....................pagvvvedaaerkarlraase......................... 33 
                                       C+gC+aC+ aC                                                                  
  gi|557694625|ref|YP_008797679.1|  44 CIGCRACQVACkrwnerkplyeevgdpvaqlG-------------------Reiatgekgyagaeilsftnpqnlea 101
                                       ***********777766644433333322220...................13333446667777777788888888 PP

                            Fer4_9  34 .......................eaCigCga..CveaCpkga 50 
                                                               +C++C +  Cv  Cp++a
  gi|557694625|ref|YP_008797679.1| 102 htwltmkfdefgegetlqwlftrVSCMHCVEapCVYGCPTTA 143
                                       8888899999999999999****99**************986 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.9e-05
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCg 40 
                                       C+gC++C+e Cp++v +     + ++       +C+ C 
  gi|557694625|ref|YP_008797679.1| 159 CIGCRNCIETCPFDVPRTNPELGVVE-------KCTLCA 190
                                       ***************99888877777.......488775 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0083
                            Fer4_9   7 aCveaCpagvvvedaaerkarlra 30 
                                       aCve Cp+++ +    ++++r+ +
  gi|557694625|ref|YP_008797679.1| 229 ACVETCPTDALKWGPRNEIVRMAR 252
                                       588999988888888888877765 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   1.5   1.6e-07   0.00016       4      19 ..      39      54 ..      36      58 .. 0.93
   2 ?    0.4   5.9      0.77   8.1e+02      11      21 ..     126     141 ..     122     144 .. 0.58
   3 !   21.8   3.8   1.3e-07   0.00014       2      23 ..     152     173 ..     151     174 .. 0.91
   4 ?   -0.2   0.2       1.2   1.3e+03       7      13 ..     184     190 ..     183     191 .. 0.78
   5 !    6.5   0.6    0.0091       9.6      14      24 .]     229     239 ..     228     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-07
                            Fer4_6  4 idpdkCigCgdCvrvC 19
                                      +d+d+CigC++C ++C
  gi|557694625|ref|YP_008797679.1| 39 FDQDLCIGCRACQVAC 54
                                      9*************** PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.77
                            Fer4_6  11 gCgdCvrv.....CPe 21 
                                       +C+ Cv +     CP+
  gi|557694625|ref|YP_008797679.1| 126 SCMHCVEApcvygCPT 141
                                       5666666653333665 PP

  == domain 3  score: 21.8 bits;  conditional E-value: 1.3e-07
                            Fer4_6   2 veidpdkCigCgdCvrvCPega 23 
                                       ve+  d+CigC++C+  CP+++
  gi|557694625|ref|YP_008797679.1| 152 VEVRTDLCIGCRNCIETCPFDV 173
                                       78999**************976 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.2
                            Fer4_6   7 dkCigCg 13 
                                       +kC+ C 
  gi|557694625|ref|YP_008797679.1| 184 EKCTLCA 190
                                       6999995 PP

  == domain 5  score: 6.5 bits;  conditional E-value: 0.0091
                            Fer4_6  14 dCvrvCPegai 24 
                                       +Cv  CP++a+
  gi|557694625|ref|YP_008797679.1| 229 ACVETCPTDAL 239
                                       5*******997 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   1.2   1.9e-07    0.0002       3      20 ..      37      54 ..      35      56 .. 0.91
   2 ?    5.5   4.2     0.019        20       9      22 .]     126     141 ..     122     141 .. 0.90
   3 !   17.2   3.0   3.8e-06     0.004       2      21 ..     151     170 ..     150     171 .. 0.88
   4 ?   -0.4   0.1       1.4   1.5e+03       7      13 ..     183     189 ..     180     191 .. 0.83
   5 ?    0.4   2.9       0.8   8.4e+02      15      22 .]     229     236 ..     228     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.9e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaC 20
                                      + +d d CigC+aC+ aC
  gi|557694625|ref|YP_008797679.1| 37 MLFDQDLCIGCRACQVAC 54
                                      679*************** PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.019
                            Fer4_2   9 rCigC..gaCvsaCPa 22 
                                       +C++C   +Cv  CP+
  gi|557694625|ref|YP_008797679.1| 126 SCMHCveAPCVYGCPT 141
                                       5****977*******7 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 3.8e-06
                            Fer4_2   2 pvvvdtdrCigCgaCvsaCP 21 
                                       pv+v td CigC+ C+  CP
  gi|557694625|ref|YP_008797679.1| 151 PVEVRTDLCIGCRNCIETCP 170
                                       567789************** PP

  == domain 4  score: -0.4 bits;  conditional E-value: 1.4
                            Fer4_2   7 tdrCigC 13 
                                        ++C+ C
  gi|557694625|ref|YP_008797679.1| 183 VEKCTLC 189
                                       5899999 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.8
                            Fer4_2  15 aCvsaCPa 22 
                                       aCv  CP+
  gi|557694625|ref|YP_008797679.1| 229 ACVETCPT 236
                                       7******7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   1.5   5.7e-05      0.06       3      19 ..      39      55 ..      37      59 .. 0.90
   2 !   20.0   8.1   5.1e-07   0.00054       7      53 ..     126     171 ..     122     174 .. 0.88
   3 ?   -2.4   0.1       5.2   5.5e+03      44      47 ..     186     189 ..     182     195 .. 0.62
   4 ?    0.9   0.2      0.48     5e+02      47      56 ..     230     238 ..     228     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.7e-05
                           Fer4_21  3 idedkCigCgkCliaCe 19
                                      +d+d CigC  C +aC+
  gi|557694625|ref|YP_008797679.1| 39 FDQDLCIGCRACQVACK 55
                                      699*************8 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 5.1e-07
                           Fer4_21   7 kCigCgk..CliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPv 53 
                                       +C++C +  C+  C+   ++a+ ++++  ++v++d C+GC  C++ CP 
  gi|557694625|ref|YP_008797679.1| 126 SCMHCVEapCVYGCP---TTALWKHPEGPVEVRTDLCIGCRNCIETCPF 171
                                       799996444******...69999*************************6 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 5.2
                           Fer4_21  44 CnlC 47 
                                       C+lC
  gi|557694625|ref|YP_008797679.1| 186 CTLC 189
                                       4444 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.48
                           Fer4_21  47 CssvCPvedc 56 
                                       C++ CP+ d+
  gi|557694625|ref|YP_008797679.1| 230 CVETCPT-DA 238
                                       9999996.65 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 !    7.8   0.5     0.006       6.3      51      64 ..      41      54 ..      24      58 .. 0.73
   2 ?    4.5   1.0     0.066        70       2      25 ..     127     152 ..     126     158 .. 0.76
   3 !    8.3   5.3    0.0042       4.4       2      15 ..     159     172 ..     158     187 .. 0.79
   4 ?   -2.4   0.2       9.4   9.9e+03       4      10 ..     185     191 ..     182     192 .. 0.70
   5 !    9.8   0.0    0.0014       1.5       7      27 ..     229     249 ..     228     271 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.006
                           Fer4_16 51 qeaitgCdiCqdvC 64
                                      q  ++gC++Cq +C
  gi|557694625|ref|YP_008797679.1| 41 QDLCIGCRACQVAC 54
                                      45567777777777 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.066
                           Fer4_16   2 CgtCgk..CaevCPtnaikekkekei 25 
                                       C  C +  C+  CPt a+ +  e  +
  gi|557694625|ref|YP_008797679.1| 127 CMHCVEapCVYGCPTTALWKHPEGPV 152
                                       88887778*********987755555 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0042
                           Fer4_16   2 CgtCgkCaevCPtn 15 
                                       C++C++C+e+CP +
  gi|557694625|ref|YP_008797679.1| 159 CIGCRNCIETCPFD 172
                                       88899999999876 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 9.4
                           Fer4_16   4 tCgkCae 10 
                                       +C+ Ca+
  gi|557694625|ref|YP_008797679.1| 185 KCTLCAD 191
                                       6777775 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.0014
                           Fer4_16   7 kCaevCPtnaikekkekeiea 27 
                                       +C+e+CPt+a+k   ++ei  
  gi|557694625|ref|YP_008797679.1| 229 ACVETCPTDALKWGPRNEIVR 249
                                       6**********9665555433 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   3.6     0.002       2.1       1      11 [.      44      54 ..      44      58 .. 0.93
   2 ?    5.7   6.5     0.031        33       1      13 [.     127     141 ..     127     143 .. 0.81
   3 !   11.8   2.9   0.00037      0.39       1      14 [.     159     172 ..     159     173 .. 0.93
   4 !    9.2   0.7    0.0024       2.5       6      15 .]     229     238 ..     186     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.002
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+gC+aC ++C
  gi|557694625|ref|YP_008797679.1| 44 CIGCRACQVAC 54
                                      *********** PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.031
                            Fer4_3   1 CtgC..gaCvevCPv 13 
                                       C++C   +Cv  CP+
  gi|557694625|ref|YP_008797679.1| 127 CMHCveAPCVYGCPT 141
                                       ****6448******7 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00037
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       C+gC+ C e CP +
  gi|557694625|ref|YP_008797679.1| 159 CIGCRNCIETCPFD 172
                                       ************75 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0024
                            Fer4_3   6 aCvevCPvgA 15 
                                       aCve CP++A
  gi|557694625|ref|YP_008797679.1| 229 ACVETCPTDA 238
                                       8*******98 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 !   14.0   0.3   5.9e-05     0.062       3      20 ..      39      56 ..      37      83 .. 0.87
   2 !    8.6   1.5     0.003       3.2       1      19 [.     152     170 ..     152     177 .. 0.87
   3 ?    1.0   0.1      0.68   7.2e+02      56      66 .]     231     241 ..     229     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-05
                           Fer4_15  3 vDrdaCigcglCvaeape 20
                                      +D+d+Cigc +C  ++++
  gi|557694625|ref|YP_008797679.1| 39 FDQDLCIGCRACQVACKR 56
                                      8**************975 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.003
                           Fer4_15   1 VvvDrdaCigcglCvaeap 19 
                                       V+v  d+Cigc +C++ +p
  gi|557694625|ref|YP_008797679.1| 152 VEVRTDLCIGCRNCIETCP 170
                                       566689***********98 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.68
                           Fer4_15  56 araCPvdAIrv 66 
                                       +++CP+dA+ +
  gi|557694625|ref|YP_008797679.1| 231 VETCPTDALKW 241
                                       579****9876 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   1.8   4.1e-05     0.043       1      15 [.      41      55 ..      41      65 .. 0.92
   2 ?    4.5   3.2     0.057        60       3      16 ..     126     141 ..     122     142 .. 0.90
   3 !   13.4   2.4   8.2e-05     0.086       2      16 ..     157     171 ..     156     173 .. 0.91
   4 ?   -1.8   0.3       5.8   6.1e+03       2       7 ..     184     189 ..     184     190 .. 0.81
   5 ?    4.5   0.2     0.058        62       8      16 ..     228     236 ..     226     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-05
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      q+ CigC++C  aC+
  gi|557694625|ref|YP_008797679.1| 41 QDLCIGCRACQVACK 55
                                      799***********7 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.057
                            Fer4_4   3 rCigCgs..CvaaCPq 16 
                                       +C +C    Cv+ CP+
  gi|557694625|ref|YP_008797679.1| 126 SCMHCVEapCVYGCPT 141
                                       599999999******7 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 8.2e-05
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + CigC+ C+ +CP+
  gi|557694625|ref|YP_008797679.1| 157 DLCIGCRNCIETCPF 171
                                       78************7 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 5.8
                            Fer4_4   2 erCigC 7  
                                       e+C+ C
  gi|557694625|ref|YP_008797679.1| 184 EKCTLC 189
                                       689998 PP

  == domain 5  score: 4.5 bits;  conditional E-value: 0.058
                            Fer4_4   8 gsCvaaCPq 16 
                                       ++Cv +CP+
  gi|557694625|ref|YP_008797679.1| 228 PACVETCPT 236
                                       79******7 PP

>> Rv2175c_C  Rv2175c C-terminal domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0      0.01        11      15      43 ..     111     147 ..     103     156 .. 0.77
   2 ?    5.7   0.0     0.015        16      35      53 ..     234     252 ..     220     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.01
                         Rv2175c_C  15 GfddeeilrWLFteDesLp........grPidALreg 43 
                                        f + e l+WLFt    +         g P  AL ++
  gi|557694625|ref|YP_008797679.1| 111 EFGEGETLQWLFTRVSCMHcveapcvyGCPTTALWKH 147
                                       57889********877777777777777777777666 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.015
                         Rv2175c_C  35 rPidALregrkrEVkRrAq 53 
                                        P dAL+ g ++E++R A+
  gi|557694625|ref|YP_008797679.1| 234 CPTDALKWGPRNEIVRMAR 252
                                       69***************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 ?    9.5  16.9    0.0012       1.3       3      64 ..      42     172 ..      40     173 .. 0.68
   2 ?    4.2   7.7     0.055        58       5      17 ..     159     171 ..     155     193 .. 0.76
   3 ?    1.2   0.0      0.49   5.2e+02      56      63 ..     229     236 ..     225     265 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0012
                            Fer4_8   3 ekCieCgaCqsaC.......pvlrrtk.khlldargeaae..................dvqeeqvlee......... 44 
                                       + Ci+C aCq aC       p++++ +    +  r+ a++                  +        +         
  gi|557694625|ref|YP_008797679.1|  42 DLCIGCRACQVACkrwnerkPLYEEVGdPVAQLGREIATGekgyagaeilsftnpqnlE--------Ahtwltmkfd 110
                                       56***********6666666444444322222222222224444445666666665553........0333334456 PP

                            Fer4_8  45 ..........................................eealwsCttcgaCtevCpvg 64 
                                                                                 e   + C +c++C e Cp +
  gi|557694625|ref|YP_008797679.1| 111 efgegetlqwlftrvscmhcveapcvygcpttalwkhpegpvEVRTDLCIGCRNCIETCPFD 172
                                       67777777788888899999999999999999999999999999****************76 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.055
                            Fer4_8   5 CieCgaCqsaCpv 17 
                                       Ci+C  C ++Cp+
  gi|557694625|ref|YP_008797679.1| 159 CIGCRNCIETCPF 171
                                       6666666666663 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.49
                            Fer4_8  56 aCtevCpv 63 
                                       aC+e Cp+
  gi|557694625|ref|YP_008797679.1| 229 ACVETCPT 236
                                       57777775 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00063      0.66      45      56 ..      43      54 ..      23      89 .. 0.78
   2 ?    0.2   2.2       1.1   1.1e+03      45      57 ..     126     140 ..      92     144 .. 0.73
   3 ?    2.6  12.0      0.19     2e+02      43      60 ..     156     173 ..     126     174 .. 0.86
   4 ?   -2.1   0.1       5.7     6e+03      44      49 ..     184     189 ..     177     192 .. 0.68
   5 ?    0.2   0.0       1.1   1.2e+03      52      58 ..     230     236 ..     228     258 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00063
                           Fer4_17 45 lCieCgeCerkC 56
                                      lCi+C+ C+ +C
  gi|557694625|ref|YP_008797679.1| 43 LCIGCRACQVAC 54
                                      566666666666 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.1
                           Fer4_17  45 lCieCge..CerkCP 57 
                                       +C++C e  C++ CP
  gi|557694625|ref|YP_008797679.1| 126 SCMHCVEapCVYGCP 140
                                       566664433666666 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.19
                           Fer4_17  43 aslCieCgeCerkCPqgl 60 
                                        +lCi+C++C + CP ++
  gi|557694625|ref|YP_008797679.1| 156 TDLCIGCRNCIETCPFDV 173
                                       689************887 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 5.7
                           Fer4_17  44 slCieC 49 
                                       ++C+ C
  gi|557694625|ref|YP_008797679.1| 184 EKCTLC 189
                                       556655 PP

  == domain 5  score: 0.2 bits;  conditional E-value: 1.1
                           Fer4_17  52 CerkCPq 58 
                                       C++ CP 
  gi|557694625|ref|YP_008797679.1| 230 CVETCPT 236
                                       5555554 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 ?    9.6   0.8    0.0012       1.3       2      18 ..      40      56 ..      39      67 .. 0.85
   2 ?    9.4   3.4    0.0015       1.6       4      17 ..     157     170 ..     154     184 .. 0.89
   3 ?    2.5   0.0       0.2   2.1e+02      48      57 ..     231     240 ..     207     241 .. 0.79
   4 ?   -2.6   0.0       7.8   8.3e+03      17      32 ..     287     302 ..     286     305 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                           Fer4_13  2 DrdtCiacgaCvelaPd 18
                                      D+d Ci+c aC  ++  
  gi|557694625|ref|YP_008797679.1| 40 DQDLCIGCRACQVACKR 56
                                      899*********99965 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0015
                           Fer4_13   4 dtCiacgaCvelaP 17 
                                       d Ci+c +C e++P
  gi|557694625|ref|YP_008797679.1| 157 DLCIGCRNCIETCP 170
                                       78***********9 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.2
                           Fer4_13  48 adaCPvesIg 57 
                                       +++CP+++ +
  gi|557694625|ref|YP_008797679.1| 231 VETCPTDALK 240
                                       4678888876 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 7.8
                           Fer4_13  17 PdvFeeddeggasvva 32 
                                       P+v++e +     + +
  gi|557694625|ref|YP_008797679.1| 287 PKVYKERPSTRTERLV 302
                                       999*999987776655 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.4    0.0021       2.2      73      93 ..      35      55 ..      25      57 .. 0.85
   2 ?   -1.3   2.4       3.9   4.1e+03       2      15 ..     127     142 ..     126     149 .. 0.77
   3 ?    8.9   1.8    0.0025       2.7      77      94 ..     154     171 ..     145     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0021
                           Fer4_22 73 fkekfgesgCvGCgRCieacp 93
                                      f+  f++  C+GC  C+ ac+
  gi|557694625|ref|YP_008797679.1| 35 FAMLFDQDLCIGCRACQVACK 55
                                      56678999**********997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 3.9
                           Fer4_22   2 ClsCga..CtlvCptC 15 
                                       C++C +  C + Cpt 
  gi|557694625|ref|YP_008797679.1| 127 CMHCVEapCVYGCPTT 142
                                       999964449999**96 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0025
                           Fer4_22  77 fgesgCvGCgRCieacpv 94 
                                       + +  C+GC  Cie+cp 
  gi|557694625|ref|YP_008797679.1| 154 VRTDLCIGCRNCIETCPF 171
                                       56789***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); 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):              17  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2506.39
//
Query:       gi|557694626|ref|YP_008797680.1|  [L=290]
Description: formate-dependent nitrite reductase complex, transmembrane protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   62.4  30.8    1.3e-16   61.2  30.8    1.5  1  NrfD      Polysulphide reductase, NrfD


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 !   61.2  30.8     7e-21   1.3e-16       7     311 ..       4     290 .]       1     290 [] 0.82

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 7e-21
                              NrfD   7 nsvvWglliavylFligisAgalilaillklfkkkegkslkliirtgallaalavlagllilvldlgrperflklll 83 
                                        +++W+++i++  ++ g++Ag +il +ll l++ +++ sl + ++tg     l  ++g++ lv++lgrper  ++++
  gi|557694626|ref|YP_008797680.1|   4 GQFSWDWPIIIEEYVFGLAAGLAILGVLLSLRNYQRFASLIRPLITGST---LLAIIGMVTLVVELGRPERAANAII 77 
                                       689*******************************998774444555555...677889*************999888 PP

                              NrfD  84 yynf..sSimswgvlllslyivvlvlyllvifekdlaakglpalgilaklislaervakilaiialilavllgsytg 158
                                       +  +  +S+ms         ++vl+++++       aa +  a+ ++ k  sl+ rv + ++i++l+ a   g   g
  gi|557694626|ref|YP_008797680.1|  78 NLLVlgTSVMSR-------TVPVLMVFTA-------AAVI--ATIFWIKPTSLV-RVRRFFEIVLLLSAFPAGLQAG 137
                                       876555666664.......5555555542.......2222..344555556676.778999**************** PP

                              NrfD 159 fllsavlsrplwnspllpvlFlasaiasGlavlllasllaarfekesedagllkklellvilteagllvilfvglal 235
                                       +ll a  +r lw++p+lp l+l+ +i  +++vl l+++  +r  +e +d   +   +l      +++++ ++ + +l
  gi|557694626|ref|YP_008797680.1| 138 ILLMAASKRLLWQTPVLPYLYLFTGILAAIGVLGLMIIRNTRLYEEFTDLL-I---DLNTYTVILLVVSGFATIAHL 210
                                       ********************************99999999**999999983.3...455555567778889999999 PP

                              NrfD 236 eggekiealeaalsggfl...tvlFwlgvvllglaipllls.lavpr.lrenvavvviasilalvgvlllrflllia 307
                                         +e   a+ ++l+  ++   +  F +g +++gl +p   s +a    +  ++++++ + i+ +vg l+lr+ +l+a
  gi|557694626|ref|YP_008797680.1| 211 VLVESPAAVLNLLTN-PFplaAPTFYIGYLIVGLGLPATHSyIAFSAkTPLSRNILLRLFISLIVGALALRISILYA 286
                                       999999999997887.6657789**************9988456655688899999999****************** PP

                              NrfD 308 gqlt 311
                                       gql+
  gi|557694626|ref|YP_008797680.1| 287 GQLF 290
                                       **86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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: 00:00:00.40
# Mc/sec: 2170.03
//
Query:       gi|557694627|ref|YP_008797681.1|  [L=205]
Description: hypothetical protein CSUB_C1199 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.093   13.3   0.1       0.15   12.7   0.1    1.4  1  AF0941-like  AF0941-like


Domain annotation for each model (and alignments):
>> AF0941-like  AF0941-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   8.2e-06      0.15      16      58 ..      19      63 ..       5      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8.2e-06
                                      T.....TSS-GGGHHHHT-HHHHHHHHHHHHHHHHHHHHTTSS-H CS
                       AF0941-like 16 k..keviddiekvldelldkeeieelfrsdvedvleklkagdiee 58
                                      +  ke++d+ +k  +++l++e+i     +d+e v++++  gd ++
  gi|557694627|ref|YP_008797681.1| 19 TrlKEIVDERRKICKQVLSEENIDSAKAEDLELVFNNFLTGDFDK 63
                                      1447999**********************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.36
# Mc/sec: 1709.14
//
Query:       gi|557694628|ref|YP_008797682.1|  [L=126]
Description: hypothetical protein CSUB_C1201 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.4   0.3        4.5    8.3   0.0    2.1  2  Rotamase  PPIC-type PPIASE domain
      0.057   13.6   1.1        5.7    7.2   0.1    2.3  2  DUF2007   Putative prokaryotic signal transducing protein
        0.1   10.8   0.3       0.11   10.6   0.3    1.0  1  FTHFS     Formate--tetrahydrofolate ligase


Domain annotation for each model (and alignments):
>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00075       4.5      10      54 ..      16      59 ..       8      71 .. 0.82
   2 ?    4.2   0.5     0.014        84      11      42 ..      73     104 ..      63     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00075
                                      E----HHHHHHHHHHHHCCTCCCHHHHHHHHCCC-.-CHHHCCTT CS
                          Rotamase 10 asekeraeakakaeeileqlksgedtFeelArkySddknsakngG 54
                                      a + +ra a+a +e ++e+l+++   F+ + +++S d++ a+  G
  gi|557694628|ref|YP_008797682.1| 16 AWTGDRALAEALMELLMEELRKKDVVFKVVEKRWS-DTGLASIVG 59
                                      44789999****************99*********.887776555 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.014
                                       ----HHHHHHHHHHHHCCTCCCHHHHHHHHCC CS
                          Rotamase  11 sekeraeakakaeeileqlksgedtFeelArk 42 
                                       +++++++a++ +e+++ + k  +++  ++A++
  gi|557694628|ref|YP_008797682.1|  73 EDEDQEAAEKCLEAVYLDTKRLKEKVLNVAKE 104
                                       56899999***************999999997 PP

>> DUF2007  Putative prokaryotic signal transducing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.004        24       1      23 [.       9      34 ..       9      34 .. 0.87
   2 ?    7.2   0.1   0.00096       5.7      47      64 ..      68      85 ..      45      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.004
                           DUF2007  1 mkelyrt...ndpveaelikslLeea 23
                                      m+ ly+t   +d+ +ae +++lL e+
  gi|557694628|ref|YP_008797682.1|  9 MVILYSTawtGDRALAEALMELLMEE 34
                                      7888888888*************875 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00096
                           DUF2007 47 vrilVaeedleeAreile 64
                                       +i V +ed e+A++ le
  gi|557694628|ref|YP_008797682.1| 68 KEIEVEDEDQEAAEKCLE 85
                                      79************9887 PP

>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   1.9e-05      0.11     370     462 ..       6     114 ..       2     122 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 1.9e-05
                                       TT--EEEEEE--TT--...HHHHHHHHHHHHCTT.SEEEEE-HHHHGGGGGH...HHHHHHHHHCC....--..... CS
                             FTHFS 370 fgvpvvvainkfktDt...eaelelvkelaeaka.vevalsevwakGgeGal...elaeavveale....eke.... 431
                                       f+v v++   +++ D    ea +el+ e++++k+ v  ++ + w++ g  ++    l ++v++ +e    + +    
  gi|557694628|ref|YP_008797682.1|   6 FQVMVILYSTAWTGDRalaEALMELLMEELRKKDvVFKVVEKRWSDTGLASIvgdSLKNEVIKEIEvedeD-Qeaae 81 
                                       6666666666666664111455677777775554044566778999887653333899***9999986541.14555 PP

                                       ..---SS-TTS-HHHHHHHHHHHTT--SEEEE- CS
                             FTHFS 432 ..fkflYdlelsieekietiakeiYgadgvels 462
                                         ++ +Y +++ ++ek+ ++ake Y  d+ e++
  gi|557694628|ref|YP_008797682.1|  82 kcLEAVYLDTKRLKEKVLNVAKEKYIRDDDEFE 114
                                       66889********************88877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1280  (0.0713927); expected 358.6 (0.02)
Passed bias filter:                      706  (0.0393775); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 1064.70
//
Query:       gi|557694629|ref|YP_008797683.1|  [L=270]
Description: hypothetical protein CSUB_C1202 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.1   0.0       0.13   12.6   0.0    1.8  2  Big_3     Bacterial Ig-like domain (group 3)


Domain annotation for each model (and alignments):
>> Big_3  Bacterial Ig-like domain (group 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.48   8.6e+03       6      14 ..      94     102 ..      93     109 .. 0.82
   2 ?   12.6   0.0   7.2e-06      0.13       6      34 ..     130     163 ..     128     175 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.48
                             Big_3   6 ttyyvGDkl 14 
                                       t+y +GD +
  gi|557694629|ref|YP_008797683.1|  94 TDYVTGDRF 102
                                       789999987 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 7.2e-06
                             Big_3   6 ttyyvGDkldaedlfvsatykdGdae.....vpf 34 
                                       +++ vGD+++a+ + v  ++++G ++     +p+
  gi|557694629|ref|YP_008797683.1| 130 QSISVGDSWSAKSVAVVTVDTNGATRterleLPE 163
                                       5799********************9877744443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2028.84
//
Query:       gi|557694630|ref|YP_008797684.1|  [L=457]
Description: deoxyribodipyrimidine photo-lyase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   49.1   0.1    1.2e-12   48.2   0.1    1.5  1  DNA_photolyase  DNA photolyase


Domain annotation for each model (and alignments):
>> DNA_photolyase  DNA photolyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.1   6.6e-17   1.2e-12       2     162 ..      29     181 ..      28     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 6.6e-17
                                       EEEESS---STT-HHHHHH....HCTTSEEEEEEEE-HHHHTCGS-CHHHHHHHHHHHHHHHHHHHHTT--EEEEES CS
                    DNA_photolyase   2 lvWfrrDlRlhDNpALaaA....aasgepvipvfvldpekahklrvgaarvdfllesLadLdeeLrelgirLvvrrg 74 
                                       ++ +   lR   N+AL++A    ++ g+++++v+ ld++   + +++ ++ +f++  L++ de+L ++gi ++vr+ 
  gi|557694630|ref|YP_008797684.1|  29 VYVMDASLRAYGNHALEYAvfeaNRLGRSLVVVYNLDEK---QPFMNTRKLHFIHGALKKVDERLSRRGILFLVRKT 102
                                       5667889**********776665888999**********...23679***********************9999997 PP

                                       SHHHHHHHHHHHCTECEEEEE---SHHHHHHHHHHHHHHHHCTSEEEEE--SSSS-HHHHHTTTSSSHSSHHHHHHC CS
                    DNA_photolyase  75 dpadvlpelakelgasavvanreyepdererdeavkealrkagievesfddhtlvepgevktkkgkpykvFtpfrkr 151
                                       ++   l +l++  +a +vv+++ y+ +++  ++ ++++++    +v+ ++++++v+++++ t+ + ++++++p+  +
  gi|557694630|ref|YP_008797684.1| 103 ES---LLKLVN--EAVSVVVDAGYTGHQQTFRKTLAKYCD----SVKMVEGDVVVPVKTASTRAEPYARTIRPKLLN 170
                                       65...455554..5889**********************9....5888************9999999******9988 PP

                                       HHHHHCS-TTS CS
                    DNA_photolyase 152 wlkelkeplpa 162
                                        l++++e +p+
  gi|557694630|ref|YP_008797684.1| 171 KLDNFLETVPE 181
                                       88888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3533.67
//
Query:       gi|557694631|ref|YP_008797685.1|  [L=155]
Description: GCN5-related N-acetyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   57.4   0.0    1.9e-15   57.1   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.2e-12   47.2   0.1    3.1e-12   46.7   0.1    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.4e-11   44.4   0.0    1.9e-11   44.0   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    3.4e-09   37.0   0.0    4.1e-09   36.8   0.0    1.0  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    1.8e-06   28.0   0.0    3.5e-06   27.1   0.0    1.5  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      4e-05   23.5   0.0    6.2e-05   22.9   0.0    1.3  1  FR47             FR47-like protein
      0.002   18.8   0.0     0.0024   18.5   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.018   14.5   0.3      0.074   12.5   0.3    1.9  1  Acetyltransf_15  Putative acetyl-transferase
      0.098   11.2   0.0       0.24    9.9   0.0    1.6  2  AstA             Arginine N-succinyltransferase beta subunit


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 !   57.1   0.0   9.6e-19   1.9e-15      22     117 .]      41     144 ..      16     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 57.1 bits;  conditional E-value: 9.6e-19
                                       HH......HHHHHHSTTCEEEEEEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHH CS
                    Acetyltransf_1  22 ee......feesfsleaegllvaeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLlealeera 89 
                                        +      f+e    +++  +vae+ g+++Gf+ + ++     + + ++ i +++  peyr+k +G +Ll+++++++
  gi|557694631|ref|YP_008797685.1|  41 IAetskkyFAEAIKSPNSVVIVAEDSGRVVGFLKADIVERlfyQPKIEGKIVEFYLLPEYRRKKYGAELLDHAVQQL 117
                                       22333452333333455566779999*******999999999988999***************************** PP

                                       HHT.TESEEEEEEETT.EHHHHHHHHHTTE CS
                    Acetyltransf_1  90 ree.gikkivlaveed.ndaairlYeklGF 117
                                       +++ +i  i ++  ++ n+ a+++Y++lGF
  gi|557694631|ref|YP_008797685.1| 118 KDKvEI--ITAEF-PSlNEIAVEFYTRLGF 144
                                       ***666..55555.556************9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.1   1.6e-15   3.1e-12       2      75 ..      57     145 ..      56     146 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 1.6e-15
                                       TEEEEEEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHHH......TTSEEE..EE.EEEE CS
                    Acetyltransf_7   2 kgevfVaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLlea......aekgii..le.qlel 60 
                                       ++ v+Vaed g++vGf+ + +++         + i +++ +peyr+k +G +Ll++         +++  +     l
  gi|557694631|ref|YP_008797685.1|  57 NSVVIVAEDSGRVVGFLKADIVErlfyqpkieGKIVEFYLLPEYRRKKYGAELLDHavqqlkD--KVEiiTAeFPSL 131
                                       67799************99999999999776666666******************84433220..222212233444 PP

                                       THHHHHHHHHHTTEE CS
                    Acetyltransf_7  61 naekaikfYeklGFe 75 
                                       n+  a++fY +lGF+
  gi|557694631|ref|YP_008797685.1| 132 NE-IAVEFYTRLGFR 145
                                       44.9999*******7 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   9.5e-15   1.9e-11      19     109 ..      46     147 ..      34     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 9.5e-15
                   Acetyltransf_10  19 pealrerieegealllvaeeggkivGviel.rdgs.........hisllfVdpeyrgqGigkaLleaveeeaekdgi 85 
                                       ++ ++e i++++ +++vae++g++vG+++    ++         +i  ++  peyr++++g++Ll+++ +++ kd+ 
  gi|557694631|ref|YP_008797685.1|  46 KKYFAEAIKSPNSVVIVAEDSGRVVGFLKAdIVERlfyqpkiegKIVEFYLLPEYRRKKYGAELLDHAVQQL-KDKV 121
                                       355788899*******************5544444556666999****************************.8889 PP

                   Acetyltransf_10  86 kl.eltvnasp.yavpfYeklGFkav 109
                                       ++ + +  + +  av+fY +lGF+ +
  gi|557694631|ref|YP_008797685.1| 122 EIiTAEFPSLNeIAVEFYTRLGFRGI 147
                                       988999999999***********966 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   2.1e-12   4.1e-09       2     135 ..       7     145 ..       6     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.1e-12
                    Acetyltransf_4   2 raateeDakeilaiy.aeyvvntait..feyevssveefekfleal.dsekeyvflvaesdrivGyaylgqfkkr.a 73 
                                       r a+e+D+ ++ +++   +++n++++  f+   + +e  +k  ++  +s+++ v  +++s+r+vG +++  ++ r  
  gi|557694631|ref|YP_008797685.1|   7 RKAEEKDIPRLVELNiRLKRLNEEFDplFKTRDDIAETSKKYFAEAiKSPNSVVIVAEDSGRVVGFLKADIVE-RlF 82 
                                       7899***********5555999****886665666777777777775689999999999**********9555.557 PP

                    Acetyltransf_4  74 kdwkae...lsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFe 135
                                       ++ k e   +++yl     + + +g el+d+ +q lk   +e ++ae  s ne++++f+ +lGF+
  gi|557694631|ref|YP_008797685.1|  83 YQPKIEgkiVEFYLL-PEYRRKKYGAELLDHAVQQLKD-KVEIITAEFPSLNEIAVEFYTRLGFR 145
                                       77776433399***8.679****************975.69***********************8 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   1.8e-09   3.5e-06      28     126 ..      34     145 ..       6     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.8e-09
                                       ..........HHHHHHHHHHT..TSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE-CCGTTS-HHHHH CS
                    Acetyltransf_9  28 l........eeireyfrklle..esrvlgaedngelvgqlallplelnvpGktlkaagvtgVavapehrgrgvlskL 94 
                                       l        e+ ++yf + ++  +s v++aed g++vg l++  +e  ++  +++   ++     pe+r++++  +L
  gi|557694631|ref|YP_008797685.1|  34 LfktrddiaETSKKYFAEAIKspNSVVIVAEDSGRVVGFLKADIVERLFYQPKIEGK-IVEFYLLPEYRRKKYGAEL 109
                                       24443222232334444444444468999999******************9999965.6678899************ PP

                                       HHHHHHHHHHTT--EEEE--....SSHHHHHTTT-E CS
                    Acetyltransf_9  95 laraleemreegqplsllfP....ssipiYrrfGye 126
                                       l++a+++++++ + ++  fP    +++++Y r+G++
  gi|557694631|ref|YP_008797685.1| 110 LDHAVQQLKDKVEIITAEFPslneIAVEFYTRLGFR 145
                                       ********************9988889*******96 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   3.1e-08   6.2e-05      19      80 ..      85     147 ..      69     152 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.1e-08
                                       -TT.SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  19 kdg.gelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                       +++ g +   ++lpe rr+ +g  l     +++  + +++++     N+ + ++y++lGf+ i
  gi|557694631|ref|YP_008797685.1|  85 PKIeGKIVEFYLLPEYRRKKYGAELLDHAVQQLKDKVEIITAEFPSLNEIAVEFYTRLGFRGI 147
                                       4446999*****************************************************976 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.2e-06    0.0024       2     138 .]       4     145 ..       3     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                    Acetyltransf_3   2 LlLrplteeDlealfelrsdpe.vmr.ylpepltleeaeewlerawaeeseeegygwaivlkdtgv.iGsvglrdle 75 
                                       L++r+++e+D+++l+el+ + + +++ + p  +t+++  e  ++++ae  ++ +   +iv +d+g  +G+     +e
  gi|557694631|ref|YP_008797685.1|   4 LVFRKAEEKDIPRLVELNIRLKrLNEeFDPLFKTRDDIAETSKKYFAEAIKSPN-SVVIVAEDSGRvVGFLKADIVE 79 
                                       899***********9864433324432655555555555444444444333333.4566567776448888776555 PP

                    Acetyltransf_3  76 eedee.....aelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       +   +       ++++l p++++k y+ e +  +++ + +  ++e + a+    Ne  +  +++lGf+
  gi|557694631|ref|YP_008797685.1|  80 RLFYQpkiegKIVEFYLLPEYRRKKYGAELLDHAVQQL-K-DKVEIITAEFPSLNEIAVEFYTRLGFR 145
                                       55444666767788************************.3.3479999999999**999999999996 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   3.7e-05     0.074      35     104 ..      57     120 ..      24     152 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.7e-05
                   Acetyltransf_15  35 nkydivqykkkeeLva..svfivkkkyyslvssilieknvleiYtlyvsekyrgkGlakklLeeslkelkkn 104
                                       n  +iv  ++ ++ v+  ++ iv+  +y+    + ie +++e+Y     ++yr+k +  +lL +++++lk +
  gi|557694631|ref|YP_008797685.1|  57 NSVVIVA-EDSGRVVGflKADIVERLFYQ----PKIEGKIVEFYL---LPEYRRKKYGAELLDHAVQQLKDK 120
                                       4444443.566777763334455555554....567888888875...6*******************9754 PP

>> AstA  Arginine N-succinyltransferase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00012      0.24       2      74 ..       4      72 ..       3      81 .. 0.78
   2 ?   -1.6   0.0      0.37   7.4e+02     122     141 ..      90     109 ..      74     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00012
                              AstA  2 lviRparesDldallelaeesgvgltsLpadeeaLekkiarsersfakeveepgeesYlfvledtetgevvGt 74
                                      lv+R+a+e+D++ l+el  + ++   ++ +  ++  +  ++s++ fa+++++p+  s ++v ed  +g+vvG 
  gi|557694631|ref|YP_008797685.1|  4 LVFRKAEEKDIPRLVELNIRLKRLNEEFDPLFKTRDDIAETSKKYFAEAIKSPN--SVVIVAED--SGRVVGF 72
                                      689**************9886555555555555555566789999999876665..59999998..6****97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.37
                              AstA 122 elctlfldpeyrkgglgrll 141
                                       ++  ++l peyr++++g+ l
  gi|557694631|ref|YP_008797685.1|  90 KIVEFYLLPEYRRKKYGAEL 109
                                       588899******99988654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); 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: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1255.30
//
Query:       gi|557694632|ref|YP_008797686.1|  [L=440]
Description: malate dehydrogenase (oxaloacetate-decarboxylating) [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   96.9   0.5    1.5e-26   93.3   0.5    2.1  1  Malic_M        Malic enzyme, NAD binding domain
    1.3e-26   93.5   0.0      4e-24   85.4   0.0    2.7  1  malic          Malic enzyme, N-terminal domain
  ------ inclusion threshold ------
       0.22   11.9   1.2       0.56   10.6   0.1    2.2  3  Ribosomal_S11  Ribosomal protein S11


Domain annotation for each model (and alignments):
>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3   0.5   2.4e-30   1.5e-26       3     257 ..     164     394 ..     163     395 .. 0.83

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 2.4e-30
                                       HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S--- CS
                           Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekle 79 
                                       gTaa + a+l++alk+t+kkl++  iv++GaG+a i  a ++ +    +G+      +k+ lvD+kG+l ++re+++
  gi|557694632|ref|YP_008797686.1| 164 GTAAATTAALINALKLTNKKLNKVSIVLFGAGAANIATARLLEK----AGAD----ISKMMLVDTKGILYSEREDMD 232
                                       9**********************************988877654....4533....46899***************8 PP

                                       TTTGGGSBS--...SS--S....SHHHHHHHH--SEEEE-SSS.SS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS CS
                           Malic_M  80 eekkpfakkke...elkeakdkltLeevvkkvkptvliGlsgv.agafteeivremaksterPiilplSNPtskaEa 152
                                       e   ++  k e   ++++ak + +L ++++   ++vli +s+  +g  ++e ++ ma+   +P+++ l NP  +   
  gi|557694632|ref|YP_008797686.1| 233 ELMLKHPWKYElalKTNRAKLSGQLPDALEG--ADVLIAASTPgPGRVKKEWIQRMAQ---NPVVFLLANPVPE--M 302
                                       7655544333300122223345566666665..79*****996379**********97...6*********975..5 PP

                                       -HHHHHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHH CS
                           Malic_M 153 taedvlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseee 229
                                        + ++ +   g+a+va+G          +   ++Q NN+++fP++  g++ ++a++itd+m l aa+alae+vs+e+
  gi|557694632|ref|YP_008797686.1| 303 WPWEAKE--AGAAVVATG----------RSDFPNQVNNSLVFPAVFRGALDVKARTITDTMALRAAQALAEYVSDEK 367
                                       6666654..689999998..........556799******************************************* PP

                                       HHTT-SS--GGGHHHHHHHHHHHHHHHH CS
                           Malic_M 230 lkegsllPelseirevslkvavavakaa 257
                                       l+++++ P+++e  ev ++va++va++a
  gi|557694632|ref|YP_008797686.1| 368 LHRDHIIPTMDEW-EVYIHVAASVAEQA 394
                                       **********996.899********998 PP

>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.4   0.0   6.7e-28     4e-24       3     182 .]      19     150 ..      17     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 6.7e-28
                                       TECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSBT CS
                             malic   3 knetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeriL 79 
                                       k+e++++ ++k+   e+++++YtP+v+++ +++se+ +    +y+ + ++                ++vvt+g+r+L
  gi|557694632|ref|YP_008797686.1|  19 KLEIVPKIPVKSL--EDFSVWYTPGVAAVSKAISENKELSF-EYTWRWNT----------------IAVVTNGSRVL 76 
                                       6778888888888..9*********************9999.********................9********** PP

                                       TTBS-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHHH CS
                             malic  80 GlGdlG.vagvgimvGKlaLytalagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveavk 155
                                       GlGd+G  a++++m+GK  +++ l+g+d   ++p++l+v+                           + ++fve+vk
  gi|557694632|ref|YP_008797686.1|  77 GLGDIGpEAALPVMEGKSLIFKFLGGVD---AFPICLNVK---------------------------DPQKFVEVVK 123
                                       ****************************...*********...........................889******* PP

                                       HHHGCTSEEEE-S--CCHHHHHHHHHC CS
                             malic 156 elfppkaliqfEDfkaknafeileryr 182
                                       +l+p  ++i++ED++++++f+ile++r
  gi|557694632|ref|YP_008797686.1| 124 TLEPGLGGINLEDISSPECFYILENLR 150
                                       ***********************9986 PP

>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   9.4e-05      0.56      44      92 ..     167     215 ..     154     221 .. 0.89
   2 ?   -3.2   0.0       1.9   1.1e+04      63      75 ..     263     277 ..     256     280 .. 0.68
   3 ?   -2.4   0.0         1   6.2e+03      33      63 ..     341     370 ..     334     374 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 9.4e-05
                     Ribosomal_S11  44 aaqlaaekaaekvldkGikavevkvkgpGpGreaalralaraGlkigri 92 
                                       aa +aa   a k+++k +++v + + g+G+   a+ r l++aG  i+++
  gi|557694632|ref|YP_008797686.1| 167 AATTAALINALKLTNKKLNKVSIVLFGAGAANIATARLLEKAGADISKM 215
                                       78888888899999******************************99986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.9
                     Ribosomal_S11  63 avevkvkg..pGpGr 75 
                                        ++v + +  pGpGr
  gi|557694632|ref|YP_008797686.1| 263 GADVLIAAstPGPGR 277
                                       556666555599997 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1
                     Ribosomal_S11  33 gvkasrkssPyaaqlaaekaaekvldkGika 63 
                                        vka r  +   a +aa++ ae v d+ +++
  gi|557694632|ref|YP_008797686.1| 341 DVKA-RTITDTMALRAAQALAEYVSDEKLHR 370
                                       5554.44555567777777777777766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3478.30
//
Query:       gi|557694633|ref|YP_008797687.1|  [L=669]
Description: Fe-S oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-27   94.7   0.9    1.3e-15   57.4   0.0    2.8  2  CCG              Cysteine-rich domain
      8e-12   45.4   2.3      8e-12   45.4   2.3    2.0  1  Fer4_8           4Fe-4S dicluster domain
    6.4e-11   42.2   4.9    6.4e-11   42.2   4.9    2.1  2  Fer4_9           4Fe-4S dicluster domain
    3.2e-10   40.0   4.9    3.2e-10   40.0   4.9    2.6  3  Fer4_10          4Fe-4S dicluster domain
      1e-06   29.2   6.4      1e-06   29.2   6.4    2.3  1  Fer4_7           4Fe-4S dicluster domain
    2.4e-05   24.0   2.7    2.4e-05   24.0   2.7    1.7  1  Nitrate_red_gam  Nitrate reductase gamma subunit
    4.3e-05   24.4   9.9    0.00024   21.9  10.1    2.2  2  Fer4_16          4Fe-4S double cluster binding domain
    4.4e-05   23.9   6.6    4.4e-05   23.9   6.6    2.7  4  Fer4_17          4Fe-4S dicluster domain
    6.2e-05   22.6  17.6     0.0058   16.4   5.0    2.7  2  Fer4             4Fe-4S binding domain
     0.0003   21.1  14.9    0.00055   20.2   1.6    3.1  2  Fer4_4           4Fe-4S binding domain
    0.00051   20.0  19.0     0.0071   16.4   3.3    3.0  2  Fer4_2           4Fe-4S binding domain
    0.00076   19.5   5.7    0.00076   19.5   5.7    2.9  2  Fer4_6           4Fe-4S binding domain
     0.0018   19.1   7.4      0.047   14.5   0.2    3.5  3  Fer4_22          4Fe-4S dicluster domain
     0.0051   17.7  16.5       0.11   13.5   4.0    2.9  2  Fer4_3           4Fe-4S binding domain
  ------ inclusion threshold ------
       0.11   12.8   0.6        8.7    6.7   0.0    2.6  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
       0.33   11.4   4.8          9    6.8   0.0    3.8  4  E6               Early Protein (E6)
       0.36   11.0   6.5        1.5    9.1   0.2    2.9  2  Fer4_18          4Fe-4S dicluster domain
       0.49   10.6  15.2       0.39   10.9   0.9    3.1  2  Fer4_21          4Fe-4S dicluster domain
       0.53   11.1   5.9        6.5    7.6   0.3    2.6  2  Fer4_15          4Fe-4S single cluster domain
        1.7    8.3  12.1       0.12   12.0   0.7    3.3  3  DUF4131          Domain of unknown function (DUF4131)


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 !   57.4   0.0   1.4e-18   1.3e-15       1      85 []     431     517 ..     431     517 .. 0.98
   2 !   35.2   0.1   1.2e-11   1.1e-08       1      84 [.     555     643 ..     555     644 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 1.4e-18
                               CCG   1 vayfdgCh.llraaypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivt 75 
                                       ++y+ gC+ +++a+ +e  k+++k+l ++gv + +l  +e+C G++++r g+e ++++la +n+et++++ +++i++
  gi|557694633|ref|YP_008797687.1| 431 YVYWIGCAsIYDARGREIAKSVAKILLKAGVSFAVLgVEETCTGDPARRIGEEGRFQELALQNIETLKQKSVKKIIV 507
                                       68******999999*************************************************************** PP

                               CCG  76 acpgCllqlk 85 
                                       +cp+C+++lk
  gi|557694633|ref|YP_008797687.1| 508 NCPHCFNTLK 517
                                       *******996 PP

  == domain 2  score: 35.2 bits;  conditional E-value: 1.2e-11
                               CCG   1 vayfdgChllraa..ypevrkalkkl.lealgveleel.ekesCCGagggrsgkee.laealakrnvetaeetgada 72 
                                       ++++d+C+++r +   +e+r ++++   + + ve+ +  +k+ CCGagg   ++e  ++ +    ++++a+etga +
  gi|557694633|ref|YP_008797687.1| 555 ITLHDSCYIGRINdvFEEPRLVIQAAnKGGTYVEMSRSgRKSFCCGAGGSTYWYEVrRTDRESVIRLRQAMETGASV 631
                                       589**********99999999888882345779999*******************98888999999*********** PP

                               CCG  73 ivtacpgCllql 84 
                                       ++++cp C  ++
  gi|557694633|ref|YP_008797687.1| 632 LAVECPYCMQMF 643
                                       ********9887 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   2.3   8.9e-15     8e-12       2      63 ..     291     362 ..     290     364 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 8.9e-15
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaae...dvqeeqvlee.............eealwsCttcgaCtevCp 62 
                                       l++C+ Cg+C++aCp++ +    +l++r+ +++   + ++     +             ee +w+Cttc aC e+Cp
  gi|557694633|ref|YP_008797687.1| 291 LDACTDCGRCEAACPAYAAG--TPLSPRDIVQKlrrQLWRG----DgldedvfasglidEEEVWACTTCSACIEACP 361
                                       689************99986..6677777777743322222....23445777778888****************** PP

                            Fer4_8  63 v 63 
                                       v
  gi|557694633|ref|YP_008797687.1| 362 V 362
                                       8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   4.9   7.2e-14   6.4e-11       1      48 [.     293     362 ..     293     364 .. 0.97
   2 ?   -2.5   0.0       6.8   6.1e+03       4       9 ..     635     640 ..     612     642 .. 0.65

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 7.2e-14
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase......................eaCigCgaCveaCpk 48 
                                       +Ct+Cg+C++aCpa ++    ++r + ++ +++                      +aC++C aC+eaCp 
  gi|557694633|ref|YP_008797687.1| 293 ACTDCGRCEAACPAYAAGTPLSPRDIVQKLRRQlwrgdgldedvfasglideeevWACTTCSACIEACPV 362
                                       6***************************99999***********************************95 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.8
                            Fer4_9   4 gCgaCv 9  
                                       +C +C+
  gi|557694633|ref|YP_008797687.1| 635 ECPYCM 640
                                       344444 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   4.9   3.6e-13   3.2e-10       6      56 .]     291     361 ..     287     361 .. 0.81
   2 ?   -0.6   0.1       1.6   1.5e+03      34      50 ..     498     514 ..     490     518 .. 0.76
   3 ?   -2.9   0.1       8.6   7.7e+03      11      17 ..     635     641 ..     634     655 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 3.6e-13
                           Fer4_10   6 ddtCirCgkCvkaCPadl.....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        d C+ Cg+C +aCPa++                     ++ +   +as+   +++ v++Ct+c aC+eaCP
  gi|557694633|ref|YP_008797687.1| 291 LDACTDCGRCEAACPAYAagtplsprdivqklrrqlwrgDGLDEDVFASGL-IDEEEVWACTTCSACIEACP 361
                                       589*********************************844333333333333.34448**************9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.6
                           Fer4_10  34 eeeavrkkvekCtgcga 50 
                                       +++ v+k + +C++c++
  gi|557694633|ref|YP_008797687.1| 498 KQKSVKKIIVNCPHCFN 514
                                       56677788999999986 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 8.6
                           Fer4_10  11 rCgkCvk 17 
                                       +C  C++
  gi|557694633|ref|YP_008797687.1| 635 ECPYCMQ 641
                                       5777776 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   6.4   1.2e-09     1e-06       1      50 [.     293     362 ..     293     364 .. 0.65

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.2e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaield.....eeenek...gtekv.................eidpekClgCgaCvavCPt 50 
                                       +C+ Cg+C+aaCp++a  ++        ++k   +   +                 e + + C++C aC+++CP+
  gi|557694633|ref|YP_008797687.1| 293 ACTDCGRCEAACPAYAAGTPlsprdI--VQKlrrQ---LwrgdgldedvfasglidEEEVWACTTCSACIEACPV 362
                                       5************9999876333220..2223220...134444444456666555556678************7 PP

>> Nitrate_red_gam  Nitrate reductase gamma subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   2.7   2.7e-08   2.4e-05      93     206 ..     126     243 ..      84     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.7e-08
                   Nitrate_red_gam  93 iagvlalvGlllLllRRltnkrvraatsasDkvvlllLllqillGllttlvsal....dygseretispwlrslltl 165
                                       ++gv++l+Gl+lL++RR+ +++ r + +    + l+ Ll+  l G +   +  +       s  + + + + +++++
  gi|557694633|ref|YP_008797687.1| 126 VMGVAFLLGLALLIYRRFIRHEPRLRNRLEYSMALAGLLFIGLSGYVLEAIRLTveprP-WSGYSFVGKAMSTVFFV 201
                                       79******************999999999999999999888888888777766555431.23377888888888888 PP

                   Nitrate_red_gam 166 qpdaella.evplifklHvllglllfalfPFtrLvHvlsapl 206
                                       +  ae l+     i+  H++++++++a++P++ L H++s+ l
  gi|557694633|ref|YP_008797687.1| 202 NLPAEPLTlLYRGIWWSHAVVAFAMVAVLPYSPLGHMFSTLL 243
                                       87766555145778899*********************9755 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 !   21.9  10.1   2.7e-07   0.00024       2      66 ..     294     362 ..     293     363 .. 0.73
   2 !   10.3   4.3    0.0012       1.1       2      14 ..     350     362 ..     349     387 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.7e-07
                           Fer4_16   2 CgtCgkCaevCPtnaikek..kekeiearecisy..ntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       C++Cg+C  +CP+ a  ++   +  +++ + + +     +++ +a     +++ +a+t C +C ++CP+
  gi|557694633|ref|YP_008797687.1| 294 CTDCGRCEAACPAYAAGTPlsPRDIVQKLRRQLWrgDGLDEDVFASGLIDEEEVWACTTCSACIEACPV 362
                                       ***************999953222333333333355555566677777778888**************6 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0012
                           Fer4_16   2 CgtCgkCaevCPt 14 
                                       C+tC +C+e+CP+
  gi|557694633|ref|YP_008797687.1| 350 CTTCSACIEACPV 362
                                       ************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 !   12.5   2.6   0.00019      0.17      42      58 ..     290     306 ..     279     309 .. 0.82
   2 !   23.9   6.6   4.9e-08   4.4e-05       1      57 [.     293     361 ..     293     365 .. 0.75
   3 !   10.6   2.0   0.00071      0.64       1      31 [.     349     379 ..     349     393 .. 0.70
   4 ?   -2.3   0.1       7.4   6.6e+03       4      10 ..     635     641 ..     634     649 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                           Fer4_17  42 kaslCieCgeCerkCPq 58 
                                         + C+ Cg+Ce++CP+
  gi|557694633|ref|YP_008797687.1| 290 GLDACTDCGRCEAACPA 306
                                       5689***********96 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 4.9e-08
                           Fer4_17   1 rCiqCgyClpeCpsyea.ydnepkkllraakl..gllee.........aekeekaslCieCgeCerkCP 57 
                                       +C+ Cg C+++Cp y+a ++  p+ ++++++   ++ ++          ++ee++  C++C  C ++CP
  gi|557694633|ref|YP_008797687.1| 293 ACTDCGRCEAACPAYAAgTPLSPRDIVQKLRRqlWRGDGldedvfasgLIDEEEVWACTTCSACIEACP 361
                                       6**************9999999998888875544334442223333334555999************** PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00071
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraakl 31 
                                       +C+ C++C+++Cp +++  ++  +++ra++l
  gi|557694633|ref|YP_008797687.1| 349 ACTTCSACIEACPVLIRPMDYILEMRRALTL 379
                                       5************998866655556665555 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 7.4
                           Fer4_17   4 qCgyClp 10 
                                       +C yC++
  gi|557694633|ref|YP_008797687.1| 635 ECPYCMQ 641
                                       5777776 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   5.0   6.4e-06    0.0058       6      22 ..     292     308 ..     290     309 .. 0.91
   2 !   11.1   4.7    0.0003      0.27       8      20 ..     350     362 ..     349     364 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.4e-06
                                       TTSSS-THHHHHSTTTE CS
                              Fer4   6 ekCigCGaCvevCPvgA 22 
                                       + C+ CG+C+ +CP  A
  gi|557694633|ref|YP_008797687.1| 292 DACTDCGRCEAACPAYA 308
                                       89************866 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0003
                                       SSS-THHHHHSTT CS
                              Fer4   8 CigCGaCvevCPv 20 
                                       C+ C aC+e+CPv
  gi|557694633|ref|YP_008797687.1| 350 CTTCSACIEACPV 362
                                       ************8 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   1.6   6.1e-07   0.00055       2      16 ..     292     306 ..     291     316 .. 0.92
   2 !    9.4   1.0    0.0019       1.7       4      16 ..     350     362 ..     346     372 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.1e-07
                            Fer4_4   2 erCigCgsCvaaCPq 16 
                                       + C++Cg+C+aaCP 
  gi|557694633|ref|YP_008797687.1| 292 DACTDCGRCEAACPA 306
                                       89************4 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0019
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C+ C +C+ aCP+
  gi|557694633|ref|YP_008797687.1| 350 CTTCSACIEACPV 362
                                       ************4 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   3.3   7.9e-06    0.0071       7      22 .]     291     306 ..     287     306 .. 0.91
   2 !   13.8   2.0   5.3e-05     0.047       8      21 ..     345     361 ..     339     362 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.9e-06
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                        d+C+ Cg C  aCPa
  gi|557694633|ref|YP_008797687.1| 291 LDACTDCGRCEAACPA 306
                                       699************8 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.3e-05
                            Fer4_2   8 d...rCigCgaCvsaCP 21 
                                       +   +C+ C+aC+ aCP
  gi|557694633|ref|YP_008797687.1| 345 EevwACTTCSACIEACP 361
                                       44559************ PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   5.7   8.4e-07   0.00076       7      23 ..     292     308 ..     291     309 .. 0.93
   2 !    6.8   4.3    0.0087       7.8       8      21 ..     349     362 ..     349     365 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.4e-07
                            Fer4_6   7 dkCigCgdCvrvCPega 23 
                                       d+C++Cg+C+++CP++a
  gi|557694633|ref|YP_008797687.1| 292 DACTDCGRCEAACPAYA 308
                                       89************987 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0087
                            Fer4_6   8 kCigCgdCvrvCPe 21 
                                       +C+ C +C+ +CP 
  gi|557694633|ref|YP_008797687.1| 349 ACTTCSACIEACPV 362
                                       6************5 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   5.2e-05     0.047      73      94 ..     285     306 ..     272     308 .. 0.89
   2 ?    6.1   0.4     0.022        20      76      95 ..     344     363 ..     337     364 .. 0.76
   3 ?    0.1   0.1       1.6   1.4e+03      55      91 ..     479     515 ..     437     520 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-05
                           Fer4_22  73 fkekfgesgCvGCgRCieacpv 94 
                                       ++ek g  +C+ CgRC++acp+
  gi|557694633|ref|YP_008797687.1| 285 WMEKLGLDACTDCGRCEAACPA 306
                                       7899999*************97 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.022
                           Fer4_22  76 kfgesgCvGCgRCieacpvk 95 
                                       + +  +C+ C  Cieacpv 
  gi|557694633|ref|YP_008797687.1| 344 EEEVWACTTCSACIEACPVL 363
                                       55677899999999999875 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.6
                           Fer4_22  55 rkekkerlrqrllhklsefkekfgesgCvGCgRCiea 91 
                                       r  ++ r+++  l+ ++++k+k  ++  v C  C ++
  gi|557694633|ref|YP_008797687.1| 479 RIGEEGRFQELALQNIETLKQKSVKKIIVNCPHCFNT 515
                                       4456778899999999999999999999999999775 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   4.7    0.0039       3.5       1      13 [.     294     306 ..     294     308 .. 0.90
   2 !   13.5   4.0   0.00012      0.11       1      13 [.     350     362 ..     350     364 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0039
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       Ct Cg+C+ +CP 
  gi|557694633|ref|YP_008797687.1| 294 CTDCGRCEAACPA 306
                                       9***********5 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00012
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       Ct C+aC e+CPv
  gi|557694633|ref|YP_008797687.1| 350 CTTCSACIEACPV 362
                                       ************7 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 ?    3.5   0.1     0.097        87       4      14 ..     508     518 ..     505     535 .. 0.64
   2 ?    6.7   0.0    0.0097       8.7       3      16 ..     634     647 ..     633     655 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.097
                           zf-Di19   4 tCPyCgkeltv 14 
                                       +CP+C ++l++
  gi|557694633|ref|YP_008797687.1| 508 NCPHCFNTLKK 518
                                       79999886544 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0097
                           zf-Di19   3 ftCPyCgkeltvke 16 
                                       + CPyC +++++++
  gi|557694633|ref|YP_008797687.1| 634 VECPYCMQMFADAA 647
                                       68******998765 PP

>> E6  Early Protein (E6)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.7   1.5e+03      23      62 ..     283     321 ..     271     328 .. 0.71
   2 ?    2.0   0.1      0.32   2.9e+02      27      45 ..     346     364 ..     341     390 .. 0.76
   3 ?    6.8   0.0      0.01         9      52      87 ..     487     522 ..     456     541 .. 0.83
   4 ?    1.3   0.1      0.51   4.6e+02      33      63 ..     635     665 ..     598     669 .] 0.65

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.7
                                       XEEETTEEEBXXHHHHHHHHHHHHHHHEEEEEEHHHHHHH CS
                                E6  23 lvwreglpygvCkkClevlallelllhlerslkakeleel 62 
                                       l w e+l   +C++C ++ a+   ++   + l +++++++
  gi|557694633|ref|YP_008797687.1| 283 LGWMEKLGLDACTDCGRCEAACPAYAA-GTPLSPRDIVQK 321
                                       66888888999****999888776653.445555555555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.32
                                       TTEEEBXXHHHHHHHHHHH CS
                                E6  27 eglpygvCkkClevlalle 45 
                                       e +++ +C++C+e++ +l 
  gi|557694633|ref|YP_008797687.1| 346 EVWACTTCSACIEACPVLI 364
                                       5688999*****9997764 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.01
                                       EEEEHHHHHHHHTSTGGGSEEEETTT--B--HHHHH CS
                                E6  52 rslkakeleelvgkslsdleiRCvvClklLskeeKe 87 
                                       ++l+ +++e+l++ks++++ + C  C+++L+ke ++
  gi|557694633|ref|YP_008797687.1| 487 QELALQNIETLKQKSVKKIIVNCPHCFNTLKKEYRD 522
                                       56778999**********************988665 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.51
                                       XXHHHHHHHHHHHHHHHEEEEEEHHHHHHHH CS
                                E6  33 vCkkClevlallelllhlerslkakeleelv 63 
                                        C  C+++ a   +++ + ++l+ k+++e+v
  gi|557694633|ref|YP_008797687.1| 635 ECPYCMQMFADAARVTGVDQNLRIKDIAEIV 665
                                       2556666666666666665555555555555 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   0.1     0.041        37      57      73 ..     290     306 ..     278     309 .. 0.83
   2 ?    9.1   0.2    0.0017       1.5      55      75 ..     344     364 ..     330     371 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.041
                           Fer4_18  57 gagdcidcescvkvcPt 73 
                                       g   c+dc+ c + cP 
  gi|557694633|ref|YP_008797687.1| 290 GLDACTDCGRCEAACPA 306
                                       5678***********96 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                           Fer4_18  55 ekgagdcidcescvkvcPtgi 75 
                                       e+++  c++c++c++ cP+ i
  gi|557694633|ref|YP_008797687.1| 344 EEEVWACTTCSACIEACPVLI 364
                                       566778999999999999866 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.1    0.0018       1.6       6      19 ..     292     305 ..     286     311 .. 0.63
   2 ?   10.9   0.9   0.00043      0.39      40      53 ..     349     362 ..     338     369 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
                           Fer4_21   6 dkCigCgkCliaCe 19 
                                       d C +Cg+C  aC+
  gi|557694633|ref|YP_008797687.1| 292 DACTDCGRCEAACP 305
                                       45666666666665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00043
                           Fer4_21  40 eCvGCnlCssvCPv 53 
                                        C+ C  C++ CPv
  gi|557694633|ref|YP_008797687.1| 349 ACTTCSACIEACPV 362
                                       6************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 ?    5.2   1.1      0.04        36       6      21 ..     292     307 ..     288     312 .. 0.89
   2 ?    7.6   0.3    0.0073       6.5       6      23 ..     348     365 ..     342     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.04
                           Fer4_15   6 daCigcglCvaeapev 21 
                                       daC+ cg+C a++p +
  gi|557694633|ref|YP_008797687.1| 292 DACTDCGRCEAACPAY 307
                                       99************87 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0073
                           Fer4_15   6 daCigcglCvaeapevfe 23 
                                       +aC+ c +C++++p +++
  gi|557694633|ref|YP_008797687.1| 348 WACTTCSACIEACPVLIR 365
                                       69***********97765 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   2.9       1.9   1.7e+03       7      74 ..      21      87 ..      16      91 .. 0.54
   2 ?   12.0   0.7   0.00014      0.12      12      59 ..     129     183 ..     118     196 .. 0.75
   3 ?    1.6   0.0      0.21   1.9e+02     129     146 ..     388     405 ..     386     407 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.9
                           DUF4131  7 lvllalllllllllllllrrrprrrv.llllllllllallgfalrapqpnandlsqllesgqeviveGv 74
                                      +vl+ ++l++ +  +++l  r+   + ++ ll+  + +++++a + + + +   ++l+ + +  i++G 
  gi|557694633|ref|YP_008797687.1| 21 IVLVPFALVFVFGVVYRL--RRLGVRsFGELLYSVFRGVGYMARYGLLQRKVVSEHLAGLMHLLIYTGI 87
                                      556666666666666665..4445441444555555555555555555555555555555666666665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00014
                           DUF4131  12 lllllllllllllrr.......rprrrvllllllllllallgfalrapqpnandl 59 
                                       +++ll l+ll++ r+       r+r  + ++l+ ll+++l+g++l+a + ++++ 
  gi|557694633|ref|YP_008797687.1| 129 VAFLLGLALLIYRRFirheprlRNRLEYSMALAGLLFIGLSGYVLEAIRLTVEPR 183
                                       3333333333333335577999999999******************999988765 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.21
                           DUF4131 129 tgrlkrprpatNpggFDy 146
                                       t+ l   ++++Np+gFD 
  gi|557694633|ref|YP_008797687.1| 388 TAMLTNLSRYGNPYGFDQ 405
                                       567888999********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (669 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       914  (0.0509789); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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):              20  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.43
# Mc/sec: 4651.49
//
Query:       gi|557694634|ref|YP_008797688.1|  [L=271]
Description: electron transfer flavoprotein beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  155.4   1.3      2e-45  154.9   0.9    1.4  2  ETF       Electron transfer flavoprotein 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 ?   -3.9   0.0      0.62   1.1e+04      90     101 ..      12      23 ..       8      30 .. 0.75
   2 !  154.9   0.9   1.1e-49     2e-45      10     181 ..      42     219 ..      33     220 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 0.62
                                       -SEEEEESSCCH CS
                               ETF  90 pdlvlagataig 101
                                       pd+v++ +++++
  gi|557694634|ref|YP_008797688.1|  12 PDIVVCVKQTVD 23 
                                       899999998874 PP

  == domain 2  score: 154.9 bits;  conditional E-value: 1.1e-49
                                       CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHHHHH CS
                               ETF  10 dgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakalaalik 86 
                                       ++k +++dl+a+e+A+r+kek gg+v++v+vGp+ ++  +re+la mGad+++ ++dp+la++d  atakalaa+ik
  gi|557694634|ref|YP_008797688.1|  42 QWKNSDFDLNAVEEAVRIKEKSGGKVVVVSVGPEVKQLLVRECLA-MGADEAYILSDPSLAQADGGATAKALAAVIK 117
                                       678899***************99**********5555559*****.******************************* PP

                                       HC..--SEEEEESSCCH...HHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEEE-T CS
                               ETF  87 ke..dpdlvlagataig...kqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpavltvrp 158
                                           + d++l+g+ + +    q++prlA++++vp++++v +lev g  l++ R +e+  g+ evv+++lpav+tv  
  gi|557694634|ref|YP_008797688.1| 118 TAspKWDMILCGEASLDqnaYQTGPRLAEMFNVPHVSYVNKLEVGGRVLKAWRAVED--GV-EVVSCSLPAVVTVGL 191
                                       **8889**********55999***********************9777*********..**.*************** PP

                                       TSS--.....--S-TT---EEEE--HHH CS
                               ETF 159 gafep.....aaimaakkkeveevevad 181
                                       +++ p     + i+aa+kk+++e++++d
  gi|557694634|ref|YP_008797688.1| 192 EINTPrlpslLMIRAAQKKPLKELALSD 219
                                       *****9988877***********99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2034.29
//
Query:       gi|557694635|ref|YP_008797689.1|  [L=313]
Description: electron transfer flavoprotein alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  112.6   0.1      4e-32  110.1   0.0    2.3  3  ETF_alpha  Electron transfer flavoprotein FAD-binding domain
    7.1e-18   65.1   2.2    1.3e-17   64.3   2.2    1.4  1  ETF        Electron transfer flavoprotein domain


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 ?   -1.6   0.0      0.31   2.7e+03       5      24 ..      38      55 ..      35      82 .. 0.48
   2 ?   -1.8   0.0      0.36   3.2e+03      18      44 ..      88     114 ..      85     129 .. 0.71
   3 !  110.1   0.0   4.5e-36     4e-32       1      84 []     186     270 ..     186     270 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.31
                                      T-S-EEEE-GGGSSGGGHHH CS
                         ETF_alpha  5 eakvvvsgGrGlkskenlel 24
                                      e ++ + gG G+++   ++l
  gi|557694635|ref|YP_008797689.1| 38 ENELAMLGGAGVEK--LIHL 55
                                      55555666666643..1221 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.36
                                       SGGGHHHHHHHHHHHT-EEEE-HHHHT CS
                         ETF_alpha  18 skenlelleelaealgaavgasRavvd 44 
                                       sk+++e++ +la+ l+ a +    +++
  gi|557694635|ref|YP_008797689.1|  88 SKKGVEICGRLAQRLDVAYASEAFAIE 114
                                       678889999999999988776555555 PP

  == domain 3  score: 110.1 bits;  conditional E-value: 4.5e-36
                                       .-TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTT.TSS-CCCB-SSSS-----S-EEEES----HH CS
                         ETF_alpha   1 vdLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvda.gwipeerqvGqtGktvaPklyiavGisGaiq 76 
                                       vdLe+a+++vs+GrG+k+ke+l+l+eela+ +ga++g+sR++  + +w++eer +G +Gk v+P+lyia+GisG++q
  gi|557694635|ref|YP_008797689.1| 186 VDLEKASLIVSVGRGFKKKEDLSLAEELAKLIGAEIGCSRPISGDlKWLEEERHIGLSGKRVRPNLYIALGISGQVQ 262
                                       69****************************************9877******************************* PP

                                       HHGGGTT- CS
                         ETF_alpha  77 hlaGmkes 84 
                                       hl+Gm++s
  gi|557694635|ref|YP_008797689.1| 263 HLVGMRDS 270
                                       *****997 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   2.2   1.4e-21   1.3e-17      33     178 ..      26     165 ..       9     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 1.4e-21
                                       --EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHHHHHHC--SEEEEESSCCHHHHHHHHH CS
                               ETF  33 gevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakalaalikkedpdlvlagataigkqvaprlA 109
                                       ++++a  + p  +e+ l + l   G++k+i++    la + a a a+ala+l+kk+dp+lvl+ a+  g ++ +rlA
  gi|557694635|ref|YP_008797689.1|  26 AQIVAAAFKP-LTENEL-AMLGGAGVEKLIHLPEKYLA-AGAAASAAALAELVKKLDPNLVLIYASKKGVEICGRLA 99 
                                       5666666656.444553.456669********999998.6788********************************** PP

                                       HHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEEEEE-TTSS----S-TT---EEEE-- CS
                               ETF 110 alLgvplitdvteleveggkltvtRpieggnglaevveadlpavltvrpgafepaaimaakkkeveeve 178
                                       ++L+v +++++ ++e +g++ +++R + gg  +a+v  +++pa+++v+ +a e    ++  k +vee++
  gi|557694635|ref|YP_008797689.1| 100 QRLDVAYASEAFAIERDGNGFVAKRLVLGGGYVATVSLNSKPALASVKVSAPET---SKGPKPAVEEFD 165
                                       *****************999*************999999********9988777...444555666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2352.93
//
Query:       gi|557694636|ref|YP_008797690.1|  [L=202]
Description: hypothetical protein CSUB_C1209 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   33.7   0.0    5.9e-08   33.2   0.0    1.2  1  NTP_transf_3  MobA-like NTP transferase domain
  ------ inclusion threshold ------
      0.011   14.9   0.0      0.027   13.7   0.0    1.6  2  CofC          Guanylyl transferase CofC like
      0.074   12.8   0.1       0.16   11.7   0.0    1.6  2  PliI          Periplasmic lysozyme inhibitor of I-type lysozy


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 !   33.2   0.0   9.9e-12   5.9e-08      13     134 ..      14     136 ..       7     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 9.9e-12
                                       TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH...CHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SS CS
                      NTP_transf_3  13 ggdKallplggkpllervldalraagvdevvvvggd...eevlaalarlgvrvvededpgkgplaslaaalraaada 86 
                                       gg   l++++++p++e+vlda+ +   de+v+ +++   +e +  ++ +g++++   +++  +   l    r+  + 
  gi|557694636|ref|YP_008797690.1|  14 GGRRGLIKINKRPMIEYVLDAVPED-TDEIVIMTRQaslSEYRGIAENYGAELWDAGPEELDIRFHLEQLFREK-SC 88 
                                       78899******************98.8*******9944445566788999999999888888888888888886.9* PP

                                       SCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEE CS
                      NTP_transf_3  87 davlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfr 134
                                       +av+ l+cD+Pl+++e+v  l++  ++ +a +  p++++ +  p+ +r
  gi|557694636|ref|YP_008797690.1|  89 EAVVALSCDTPLINREVVMFLRDVVTRFSAGIPRPVFDKPEFTPASYR 136
                                       *********************999987777777777666555555444 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.5e-06     0.027      31     109 ..      25     109 ..       4     118 .. 0.81
   2 ?   -1.9   0.0      0.25   1.5e+03     194     210 ..     173     189 ..     140     194 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.5e-06
                              CofC  31 kamlldvidalkr.ld.vlvvsedeevleya..ldelgvevvkek..ekdlntavekafeeieekeviiipsdiPli 101
                                       + m+  v da+ +  d +++++++  + ey    ++ g+e+      e d+   +e+ f e   + v+ + +d Pli
  gi|557694636|ref|YP_008797690.1|  25 RPMIEYVLDAVPEdTDeIVIMTRQASLSEYRgiAENYGAELWDAGpeELDIRFHLEQLFREKSCEAVVALSCDTPLI 101
                                       46999999999877888************9733577899998765437899999*********************** PP

                              CofC 102 kkedvkdl 109
                                       ++e+v  l
  gi|557694636|ref|YP_008797690.1| 102 NREVVMFL 109
                                       **998755 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.25
                              CofC 194 ylrklgfsvepeessal 210
                                       +  kl+f v+ +  s++
  gi|557694636|ref|YP_008797690.1| 173 FDDKLRFLVKVQTQSDV 189
                                       33455555555555554 PP

>> PliI  Periplasmic lysozyme inhibitor of I-type lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.85   5.1e+03      70      83 ..      37      50 ..      29      57 .. 0.71
   2 ?   11.7   0.0   2.7e-05      0.16      72     116 ..     149     190 ..     140     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.85
                                      SSS-EEEEEEE-SS CS
                              PliI 70 dkkkelvvlkrsaG 83
                                      + + e+v+++r+a 
  gi|557694636|ref|YP_008797690.1| 37 EDTDEIVIMTRQAS 50
                                      45678999998876 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.7e-05
                                       S-EEEEEEE-SSTT--EEEEEEEEETTTEEEEEEEEEE-TTS-HH CS
                              PliI  72 kkelvvlkrsaGsGsylsvdAfkitkkslkllasveGlapdaDvv 116
                                       + ++v l++ +G   y+s + fki +++l++l++v+ +++  Dv 
  gi|557694636|ref|YP_008797690.1| 149 ELKMVDLVKHVGNVLYISLQSFKIFDDKLRFLVKVQ-TQS--DVR 190
                                       334566788999999*********************.333..333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1412.95
//
Query:       gi|557694637|ref|YP_008797691.1|  [L=326]
Description: hydrogenase expression/formation protein HypE [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   67.7   0.1    1.9e-18   67.1   0.1    1.2  1  AIRS_C    AIR synthase related protein, C-terminal domain
    1.7e-14   54.2   0.1    3.8e-14   53.1   0.1    1.6  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 !   67.1   0.1   2.1e-22   1.9e-18       1     148 [.     152     298 ..     152     305 .. 0.79

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 2.1e-22
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSE.HHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavq.lgdvlleptliyvkralaalkglvkaahDvTgGGLlgal 76 
                                       kpGd ++l++s Gl ga++++++  +        +++ ++  ll ++   v +al +++ +v+++hD T+GGLlg l
  gi|557694637|ref|YP_008797691.1| 152 KPGDEILLVKSPGLEGAAILSADFADILRRKGFTERElRVGSLLIKKTSVVEEALSLASTGVNCMHDPTEGGLLGGL 228
                                       79******************9998877777665566656666666555555555555589***************** PP

                                       HHHHHTTTEEEEEECG......THHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEE CS
                            AIRS_C  77 aemapasgvgaeidld......kvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevta 147
                                        e+a+a+gvg+e+d +       v+ ++e   ++++l+  +sG l +a +p  + +vla+++       ++IG++  
  gi|557694637|ref|YP_008797691.1| 229 YEVAEAAGVGFEVDRSrvpihpLVQRICEK-MDIDPLRLISSGAL-IATAPRFSSRVLAKVGG------RIIGKILS 297
                                       ****************66666655556665.68**********55.77777777799999985......46777766 PP

                                       S CS
                            AIRS_C 148 k 148
                                       +
  gi|557694637|ref|YP_008797691.1| 298 R 298
                                       5 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 !   53.1   0.1   4.2e-18   3.8e-14       1      92 [.      35     138 ..      35     140 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 4.2e-18
                                       SSSEEEEEEEEEE.EECCTCCCC....HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHH CS
                              AIRS   1 dDaavvvttdshnrpvlvepvhf....iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaae 67 
                                       +Da+ +v+  +    v ++p+++    +G++av++ ++D+a++G+rP +++ ++ lp      +l+++v++++ a++
  gi|557694637|ref|YP_008797691.1|  35 EDAG-AVKSSKDIYIVSMDPITGsksfVGWLAVHASANDVAVCGGRPQWFSSTILLPrgstaaDLKKIVDQIHLACR 110
                                       5888.6666656666777888889999************************************************** PP

                                       HTT-EEEEEEEEEESS...EEEEEEEEE CS
                              AIRS  68 elgvplvgGdtsfsne...ptisvtavG 92 
                                       +++v++v+G++++ +    p++   ++G
  gi|557694637|ref|YP_008797691.1| 111 RMDVAVVTGHSEVAPFvssPVVIGHMTG 138
                                       ************8764444655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2508.80
//
Query:       gi|557694638|ref|YP_008797692.1|  [L=169]
Description: nitroreductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   88.6   0.3    4.4e-15   56.1   0.1    2.1  2  Nitroreductase  Nitroreductase family
    1.4e-14   54.2   0.0    7.3e-06   25.7   0.0    2.8  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 !   56.1   0.1   4.9e-19   4.4e-15       1      70 [.       7      76 ..       7      82 .. 0.90
   2 !   32.9   0.0   6.8e-12   6.1e-08      85     170 .]      67     140 ..      64     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 4.9e-19
                                      HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS CS
                    Nitroreductase  1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqael 70
                                      i++R  i++F d+pvp+e++++ileaar +Ps+ n+q wrf+vv+  +++++lae + +  ++a a+++ 
  gi|557694638|ref|YP_008797692.1|  7 IKTRLEIKEFADKPVPREVVKEILEAARLSPSGRNTQHWRFIVVEGADELKQLAEMSTSGKWVANAALAV 76
                                      6778889*************************************9999999***9998888888777665 PP

  == domain 2  score: 32.9 bits;  conditional E-value: 6.8e-12
                                       HHHHHSSEEEEE---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHHHHHT-S..SE CS
                    Nitroreductase  85 kalagapvlivivatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevrkllglpdeee 161
                                       k++a+a++ +++            +  y++ l+dag +a  ++LaA+ + +gs + +g+de+a  +r+  g+p+e++
  gi|557694638|ref|YP_008797692.1|  67 KWVANAALAVIV----------LTSPKYPWHLFDAGRVAAHMQLAAWNRSVGSRVYTGYDEKA--MRTKYGIPQEYH 131
                                       567888888888..........89999************************************..************ PP

                                       EEEEEEEE- CS
                    Nitroreductase 162 ivvliavGy 170
                                       + ++i++Gy
  gi|557694638|ref|YP_008797692.1| 132 VACVIGFGY 140
                                       ********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   8.1e-10   7.3e-06     147     186 ..      12      52 ..       7      69 .. 0.75
   2 !   24.7   0.0   1.7e-09   1.5e-05      66     149 ..      73     158 ..      58     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8.1e-10
                                       HHBSS-GGGS-.HHHHHHHHHHHTS--GGG----EEE.E-S CS
                    TM1586_NiRdase 147 elcevkeeelp.ewfkeileaarlAPsAlNqqpwrfelkdd 186
                                       e+ e+ ++ +p e +keileaarl+Ps  N+q+wrf +++ 
  gi|557694638|ref|YP_008797692.1|  12 EIKEFADKPVPrEVVKEILEAARLSPSGRNTQHWRFIVVEG 52 
                                       4555666666625679********************98764 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.7e-09
                                       SSEEEE----SSHHHHHHHHHHHHHHHHHHHHTT-EE.EEES--SST...........T-S-EEEEE-BS----..- CS
                    TM1586_NiRdase  66 vpnyialvgekkedleekaGYygeqlvLkltalGlgt.cWvggtykkkkakvelkkgeklvivIalGyaktklv.ea 140
                                       +  +i+l ++k   ++  aG +  ++ L + ++ +g+  + g   k  ++k+ ++++ ++++vI +Gy+k+k++  +
  gi|557694638|ref|YP_008797692.1|  73 ALAVIVLTSPKYPWHLFDAGRVAAHMQLAAWNRSVGSrVYTGYDEKAMRTKYGIPQEYHVACVIGFGYPKQKIIgRK 149
                                       457899999999************************956999988889*************************9788 PP

                                       ----HHHHB CS
                    TM1586_NiRdase 141 krkpleelc 149
                                       +r+p+e l 
  gi|557694638|ref|YP_008797692.1| 150 NRQPIEALA 158
                                       888998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1330.79
//
Query:       gi|557694639|ref|YP_008797693.1|  [L=178]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-30  104.4   0.0    6.4e-30  104.0   0.0    1.2  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 !  104.0   0.0   3.6e-34   6.4e-30      14     168 ..      33     160 ..      15     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 3.6e-34
                                       EEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHHHHHHHTTB-ET CS
                    Oxidored_molyb  14 levdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlrdvLekagvkkp 90 
                                       l v g+v k++++sl++L++lpav++t +++C +              +w   +v ++eW+Gv+++++Le++gv  p
  gi|557694639|ref|YP_008797693.1|  33 LLVRGKVLKTVEFSLNELMRLPAVSLTFDFRCLE--------------GW---VVPDTEWQGVKVATILERVGVM-P 91 
                                       5689******************************..............8*...9********************7.* PP

                                       T..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBTTEEEEEEESS- CS
                    Oxidored_molyb  91 earhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvKwlkrievsdee 167
                                       +ar++vf++ +       y+++ p+++a   ++++Ay++ g+++p +hG PlRlv pg+  ++s+Kwl++ie+++e 
  gi|557694639|ref|YP_008797693.1|  92 DARYAVFKSGE-------YTECFPVSEAK--EMVVAYRYRGKEIPAEHGGPLRLVFPGQQCYQSIKWLEEIELTSEY 159
                                       *********75.......***********..9*****************************************9986 PP

                                       - CS
                    Oxidored_molyb 168 s 168
                                        
  gi|557694639|ref|YP_008797693.1| 160 V 160
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1509.29
//
Query:       gi|557694640|ref|YP_008797694.1|  [L=1062]
Description: isoleucyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-172  574.9   0.2   2.5e-172  574.3   0.2    1.3  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
    3.1e-34  118.1   1.0    6.9e-34  117.0   1.0    1.6  1  Anticodon_1      Anticodon-binding domain of tRNA
    1.3e-22   80.1   3.6    1.1e-09   37.5   0.1    3.9  3  tRNA-synt_1g     tRNA synthetases class I (M)
    1.1e-08   34.7   0.0     0.0044   16.4   0.0    2.3  2  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
     0.0016   17.5   0.0     0.0053   15.7   0.0    1.8  2  tRNA-synt_1f     tRNA synthetases class I (K)
  ------ inclusion threshold ------
      0.045   13.3   0.0        0.1   12.1   0.0    1.5  1  tRNA-synt_1_2    Leucyl-tRNA synthetase, Domain 2
       0.23   11.8   0.8         12    6.3   0.1    3.1  3  Lar_restr_allev  Restriction alleviation protein Lar
        0.4   10.3   1.9         22    4.8   0.1    2.5  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        3.6    7.8   7.7         55    4.0   0.1    3.9  3  zf-ACC           Acetyl-coA carboxylase zinc finger 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 !  574.3   0.2  1.3e-175  2.5e-172       3     599 ..      20     631 ..      18     634 .. 0.94

  Alignments for each domain:
  == domain 1  score: 574.3 bits;  conditional E-value: 1.3e-175
                       tRNA-synt_1   3 yekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieak 79 
                                        e W++ ++  k +e++ e + f++  gPP v+G +HiGh   ++ kdiv ryk+m+G++v ++ GwD+ Gl++e +
  gi|557694640|ref|YP_008797694.1|  20 SELWKNLNIVGKVFEANSEGPLFSFLEGPPTVNGYMHIGHTRGRVYKDIVLRYKTMRGYNVWRRGGWDCQGLPTEIE 96 
                                       578************************************************************************** PP

                       tRNA-synt_1  80 vekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgli 156
                                       vek+lg++ k++++k+g e+f+e+  + +++y +++r++ +rlG ++D+dr y T  +e++e v++ +++ ++ g +
  gi|557694640|ref|YP_008797694.1|  97 VEKRLGITSKRDVEKIGLERFVEEANKVVDHYLSHWRRASERLGLWLDYDRAYETRRDEYMEHVWHLLKKAHEMGDL 173
                                       ***************************************************************************** PP

                       tRNA-synt_1 157 yrgkklvnwstklktalselEv..eykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv...i 228
                                        ++ ++v+ +++++tals+ E+   y++++d++i+v+ pl+++    ++i+TTtP+Tl+g+ avav+p+  y    +
  gi|557694640|ref|YP_008797694.1| 174 VESLRVVPTCPHCETALSQHEMaqGYEEVSDPSIYVKMPLEEGGY--VIIWTTTPWTLPGNEAVAVKPDATYLelqV 248
                                       *********************9888***************99876..*************************99999 PP

                       tRNA-synt_1 229 tkeklilaeallkslvkke..sekkiledergkeLegkevelpl.......vnrkipiiaddyvdkeaGtGvVkiaP 296
                                        +e++ +ae+ll s+++ +  +++ki+ ++ g +L+gk++++pl       ++ +  ++a d+v  e+GtG V+iaP
  gi|557694640|ref|YP_008797694.1| 249 GEERWYVAENLLTSFTEITqtKNYKIVAKVDGISLVGKTYHHPLldkvphhADHRHILVASDHVSLEEGTGFVHIAP 325
                                       9999***********998853445*************************9989999999****************** PP

                       tRNA-synt_1 297 ahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpii 373
                                       +h+++Dye+g k++l++ +++++ g++t ea+ ++gl+v +a +k++++lkek+ll+k  +i hs+p+c+r +  +i
  gi|557694640|ref|YP_008797694.1| 326 GHGPEDYEIGVKNGLNIFCPVTSYGVFTAEAGAYSGLSVWEASEKIIQDLKEKNLLVKRAEIVHSYPHCWRCGSKLI 402
                                       ***************************************************************************** PP

                       tRNA-synt_1 374 yrateqWfvrvkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelk 449
                                       y a+ qWf rv+++++ +++++++v++ p++ + +r+ +wl n+qdWciSR+++WG+++ +++ ++ +e  v+ +  
  gi|557694640|ref|YP_008797694.1| 403 YLASVQWFLRVDRIKQRMVEENRSVKWWPEWaGSNRFGDWLLNAQDWCISRSKIWGTPLNVWRCESCGEKRVVGSRA 479
                                       *******************************99***********************************998888777 PP

                       tRNA-synt_1 450 elvagreeeeaekkalekeakdkl....kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlle 522
                                       el+++ e+ +++   l++  +d+     +k  g +++++ vlD+W +Sg  ++++++   ++te +kk fp d+++e
  gi|557694640|ref|YP_008797694.1| 480 ELEEAVEKPAVK--RLHRPWVDQYvfkcEKCGGLMRRVPFVLDTWIDSGVAFYASID-ALRNTELFKKLFPYDFITE 553
                                       777655444433..333333333333326667999**********************.7778*************** PP

                       tRNA-synt_1 523 GlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrd 598
                                        +D++rgW+++l+++s+ ltg++Pfk+vl +g v+de G+KmSKs gNvi  +d  ++yg+d lR +l+ +++  + 
  gi|557694640|ref|YP_008797694.1| 554 AIDQTRGWFYTLLFTSTLLTGKAPFKSVLNQGHVLDEFGKKMSKSRGNVIWAEDAFNTYGVDPLRIYLVsKAEPWST 630
                                       ********************************************************************966666655 PP

                       tRNA-synt_1 599 i 599
                                       i
  gi|557694640|ref|YP_008797694.1| 631 I 631
                                       5 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 !  117.0   1.0   3.4e-37   6.9e-34       1     149 [.     682     831 ..     682     834 .. 0.91

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 3.4e-37
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       d+wils++n+lv++vt+++ee+++++a++++++f+++dl+++yl++v++  ++e +++++  a++ l++vl++ l l
  gi|557694640|ref|YP_008797694.1| 682 DKWILSRVNDLVAKVTNYLEEMEIHRALREIMSFIVEDLSRTYLRSVRRLAWTEAETPEKMaAYACLHYVLRKTLLL 758
                                       9****************************************************99999977799************* PP

                       Anticodon_1  77 laPfmPfitEelwqreeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsse.lk 149
                                       laPf+P+++E l+q +++e  +kesi+l++wp+ + e   +++  e+++++ke+++ai ++r++ + k +s+ ++
  gi|557694640|ref|YP_008797694.1| 759 LAPFAPYTAEILYQLQKTE-TDKESIHLENWPQlDTELYSPKI-IEQMNIVKEVLTAILAARQKGGRKLRSPvAH 831
                                       *************873323.588*********97776668888.99******************99999998444 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 !   31.0   0.0   5.6e-11   1.1e-07      10     132 ..      51     192 ..      47     198 .. 0.66
   2 !    9.2   0.2   0.00022      0.44     167     237 ..     392     461 ..     378     471 .. 0.85
   3 !   37.5   0.1   5.7e-13   1.1e-09     248     374 ..     522     641 ..     517     652 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 5.6e-11
                                       -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HH.........HHHHHHHHHHHH CS
                      tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpe.........elvekvheeike 76 
                                       +ng +H+Gh +  +  Di+ Ryk +rg++v+  +g D  G p+e++ ek+ g+t +          +ve++++ +++
  gi|557694640|ref|YP_008797694.1|  51 VNGYMHIGHTRGRVYKDIVLRYKTMRGYNVWRRGGWDCQGLPTEIEVEKRlGITSKrdvekigleRFVEEANKVVDH 127
                                       8*******************************************999874455544111111111444444444444 PP

                                       HHHHTT.........---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-G CS
                      tRNA-synt_1g  77 lfkkln.........isfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpd 132
                                        ++++          + +d  ++t  +e  e v +++kk +e g + e+   +  cp++e+ l++
  gi|557694640|ref|YP_008797694.1| 128 YLSHWRraserlglwLDYDRAYETRRDEYMEHVWHLLKKAHEMGDLVESLRVVPTCPHCETALSQ 192
                                       43333211111112245666666666666666666777777778888888888888888887776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00022
                                       ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHH.HHHH.HHHHT----EE-ESS-SSS-EE CS
                      tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenv.kkivkewlkegLkdlaisrdldwGipv 237
                                       p++  +gsk ++  + ++f++++++++++ e   ++ k ++e + ++   +wl +  +d++isr   wG p+
  gi|557694640|ref|YP_008797694.1| 392 PHCWRCGSKLIYLASVQWFLRVDRIKQRMVEEN-RSVKWWPEWAgSNRFGDWLLN-AQDWCISRSKIWGTPL 461
                                       89***********************99987766.555557665526788999988.8************986 PP

  == domain 3  score: 37.5 bits;  conditional E-value: 5.7e-13
                                       HHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHHTT----S-EEEE--EEE- CS
                      tRNA-synt_1g 248 WldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillgaelklpkkvvaheyltve 324
                                       W+d  + + +++  l     + e +k+ +   +   +++ i +    F t++++++ll  +  + + +     l   
  gi|557694640|ref|YP_008797694.1| 522 WIDSGVAFYASIDALR----NTELFKKLF---PYDFITEAIDQTRGWFYTLLFTSTLLTGKAPFKSVLNQGHVLDEF 591
                                       6777766666666664....557777777...334566777777788************999988777777777788 PP

                                       -------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHH CS
                      tRNA-synt_1g 325 gkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfver 374
                                       gkK+SkSrg+v++a++a +++ +d lR yl+++a+  + ++f  +++ e+
  gi|557694640|ref|YP_008797694.1| 592 GKKMSKSRGNVIWAEDAFNTYGVDPLRIYLVSKAEPWSTINFVPSEVRET 641
                                       **********************************9999999998887665 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 !   16.4   0.0   2.2e-06    0.0044      17      48 ..      49      80 ..      34      82 .. 0.92
   2 !   15.9   0.0   3.1e-06    0.0062     232     294 ..     572     636 ..     566     643 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.2e-06
                                      EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EE CS
                      tRNA-synt_1e 17 ptvydashlGhaRslvafDilrrilqalgYdv 48
                                      ptv  ++h+Gh+R  v  Di+ r+  ++gY+v
  gi|557694640|ref|YP_008797694.1| 49 PTVNGYMHIGHTRGRVYKDIVLRYKTMRGYNV 80
                                      7*****************************98 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.1e-06
                                       HSSS--EEEEEEE--EEET.TBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-.TTS-EEE-HH CS
                      tRNA-synt_1e 232 afdkqlvkyflhnghlkie.gekmsksLknfitikdvlkkfdprqlRllllsah.yrsqldfkee 294
                                       +++k   k  l +gh+  e g+kmsks +n+i  +d+++++    lR++l+s+    s+++f  +
  gi|557694640|ref|YP_008797694.1| 572 LTGKAPFKSVLNQGHVLDEfGKKMSKSRGNVIWAEDAFNTYGVDPLRIYLVSKAePWSTINFVPS 636
                                       5666777788889998766589*************************999876314456666655 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 ?   -3.0   0.0       1.3   2.6e+03      32      54 ..      50      72 ..      45      80 .. 0.80
   2 !   15.7   0.0   2.7e-06    0.0053     273     340 ..     586     653 ..     568     673 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.3
                      tRNA-synt_1f 32 spSGliHiGnlrevltadlvara 54
                                      ++ G +HiG  r  +  d+v r 
  gi|557694640|ref|YP_008797694.1| 50 TVNGYMHIGHTRGRVYKDIVLRY 72
                                      5679********99999998775 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.7e-06
                      tRNA-synt_1f 273 lillkggekmssSkGnvltledwlevaepevlr.flilrrkPkkakkldldleilrlvdeYdklerkyf 340
                                        +l++ g+kms+S+Gnv+  ed+++ +  + lr +l+ +++P + +++ ++ e+ ++ ++ + l ++++
  gi|557694640|ref|YP_008797694.1| 586 HVLDEFGKKMSKSRGNVIWAEDAFNTYGVDPLRiYLVSKAEPWSTINFVPS-EVRETAEDLNILWNIFA 653
                                       689999*******************9999999867788999*******999.99999999877766665 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 ?   12.1   0.0   5.1e-05       0.1      14     137 ..     211     343 ..     206     375 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.1e-05
                     tRNA-synt_1_2  14 fkveeseeklevfttrpdtlfGvtfvalapehplvekl..aekkkelaafieevkkksesereletkekeGv.ftgl 87 
                                       +++ee    + ++tt p tl G + va+ p+    e    +e+    ++++++ ++ +++++ +  ++ +G+   g 
  gi|557694640|ref|YP_008797694.1| 211 MPLEEGG-YVIIWTTTPWTLPGNEAVAVKPDATYLELQvgEERWYVAENLLTSFTEITQTKNYKIVAKVDGIsLVGK 286
                                       5555554.7889******************988665444555556667889999999999999999999***88999 PP

                     tRNA-synt_1_2  88 kaihPitgek......ipiwva.nyvlmeygtgavmavPahdqrDfeFakkynlpik 137
                                       +  hP+ ++         i va ++v  e gtg v   P+h  +D+e   k +l+i 
  gi|557694640|ref|YP_008797694.1| 287 TYHHPLLDKVphhadhRHILVAsDHVSLEEGTGFVHIAPGHGPEDYEIGVKNGLNIF 343
                                       99***9876556666655665439***************************999985 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 ?    1.4   0.0      0.21   4.1e+02       4      23 ..     181     200 ..     178     219 .. 0.76
   2 ?   -0.4   0.0      0.77   1.5e+03      19      49 ..     386     418 ..     366     422 .. 0.72
   3 ?    6.3   0.1    0.0062        12       5      36 ..     465     510 ..     462     526 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.21
                   Lar_restr_allev   4 kpCPfCggravlersqrvva 23 
                                         CP+C  +   +++ ++++
  gi|557694640|ref|YP_008797694.1| 181 PTCPHCETALSQHEMAQGYE 200
                                       67****98776666666655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.77
                   Lar_restr_allev  19 qrvvaeigqcvyCadCga......stpwfkiaedeae 49 
                                       + v++    + +C  Cg       s +wf + ++ ++
  gi|557694640|ref|YP_008797694.1| 386 EIVHS----YPHCWRCGSkliylaSVQWFLRVDRIKQ 418
                                       22333....999999**98888888888887777665 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0062
                   Lar_restr_allev   5 pCPfCggravlersqrvvaeigq..............cvyCadCga 36 
                                        C  Cg++ v++ +    + +++              ++ C++Cg 
  gi|557694640|ref|YP_008797694.1| 465 RCESCGEKRVVGSRAELEEAVEKpavkrlhrpwvdqyVFKCEKCGG 510
                                       5999********999999888889************999*****97 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.011        22       4      14 ..     461     471 ..     459     475 .. 0.86
   2 ?    4.3   0.3     0.015        31       6      13 ..     502     509 ..     499     513 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.011
                                       T-EEE-TTT-- CS
                   Desulfoferrod_N   4 levYkCevCGn 14 
                                       l+v++Ce CG+
  gi|557694640|ref|YP_008797694.1| 461 LNVWRCESCGE 471
                                       689*******6 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.015
                                       EEE-TTT- CS
                   Desulfoferrod_N   6 vYkCevCG 13 
                                       v+kCe CG
  gi|557694640|ref|YP_008797694.1| 502 VFKCEKCG 509
                                       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 ?    4.0   0.1     0.028        55       4      17 ..     183     196 ..     182     200 .. 0.80
   2 ?    1.7   0.6      0.14   2.7e+02       2       9 ..     464     471 ..     464     471 .. 0.87
   3 ?    3.9   0.1     0.029        57       2      10 ..     503     511 ..     503     514 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.028
                            zf-ACC   4 CpsCgemlykkeLe 17 
                                       Cp+C++ l + e++
  gi|557694640|ref|YP_008797694.1| 183 CPHCETALSQHEMA 196
                                       *****999887776 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.14
                            zf-ACC   2 tKCpsCge 9  
                                       ++C+sCge
  gi|557694640|ref|YP_008797694.1| 464 WRCESCGE 471
                                       58****97 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.029
                            zf-ACC   2 tKCpsCgem 10 
                                       +KC++Cg +
  gi|557694640|ref|YP_008797694.1| 503 FKCEKCGGL 511
                                       5******76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1062 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      724  (0.0403815); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.78u 0.27s 00:00:01.05 Elapsed: 00:00:00.43
# Mc/sec: 7354.35
//
Query:       gi|557694641|ref|YP_008797695.1|  [L=220]
Description: hypothetical protein CSUB_C1214 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   33.0   5.9    3.3e-07   30.2   5.9    2.1  1  DZR             Double zinc ribbon
    6.5e-08   32.0   5.7    8.2e-05   22.2   1.0    2.4  2  zinc_ribbon_2   zinc-ribbon domain
     0.0062   16.2   5.9        6.5    6.5   0.1    3.5  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
  ------ inclusion threshold ------
      0.015   14.6   2.5      0.015   14.6   2.5    2.3  2  zf-RanBP        Zn-finger in Ran binding protein and others
      0.019   15.1  10.8      0.031   14.4   1.9    3.2  3  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.02   14.7   6.3      0.084   12.8   2.9    2.6  2  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
      0.022   14.8   3.2       0.79    9.8   3.3    2.2  1  zinc-ribbons_6  zinc-ribbons
      0.024   14.1  15.9       0.26   10.7   3.9    3.3  3  zf-ribbon_3     zinc-ribbon domain
      0.036   13.9   0.4         11    6.0   0.2    2.4  2  Ribosomal_L40e  Ribosomal L40e family
      0.058   13.3   0.9      0.058   13.3   0.9    3.3  4  DUF4428         Domain of unknown function (DUF4428)
      0.069   12.8   0.8      0.088   12.5   0.8    1.2  1  TackOD1         Thaumarchaeal output domain 1
      0.078   12.4   0.2       0.11   11.9   0.2    1.1  1  DUF373          Domain of unknown function (DUF373)
       0.14   12.1   5.4        1.6    8.7   0.1    3.2  3  YhfH            YhfH-like protein
       0.17   12.2   1.0       0.26   11.6   1.0    1.2  1  ABC_tran_CTD    ABC transporter C-terminal domain
       0.28   10.7  12.4        4.6    6.8   1.2    3.3  3  TF_Zn_Ribbon    TFIIB zinc-binding
       0.33   10.7   0.0       0.33   10.7   0.0    3.3  4  A2L_zn_ribbon   A2L zinc ribbon domain
       0.35   10.9   5.9        5.8    7.0   6.1    2.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.36   11.6   3.7        0.5   11.2   0.1    2.3  3  zinc_ribbon_15  zinc-ribbon family
       0.41   10.6  10.3          5    7.1   0.6    3.4  3  Nudix_N_2       Nudix N-terminal
       0.46   10.2  12.0        3.4    7.4   0.5    3.8  4  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
       0.52   10.3   7.0        6.4    6.8   2.0    3.1  3  Gin             Inhibitor of sigma-G Gin
       0.53   10.5   3.5        1.2    9.4   0.1    2.6  3  LIM             LIM domain
       0.73    9.7   3.2       0.46   10.4   0.3    2.0  2  Rad50_zn_hook   Rad50 zinc hook motif
       0.97    9.4   8.0       0.21   11.5   0.6    2.8  3  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        1.3    9.0  10.3        4.6    7.3   6.1    2.7  2  zf-C2HC5        Putative zinc finger motif, C2HC5-type
        1.5    9.2   6.3        3.5    8.0   2.0    2.3  2  zf-RING_2       Ring finger domain
          2    8.6  12.4         18    5.5   9.0    2.9  2  Zn-ribbon_8     Zinc ribbon domain
        3.1    8.0   4.7         18    5.5   2.4    2.3  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
        3.8    7.6   9.5        1.3    9.0   2.5    2.8  2  DUF1610         Domain of unknown function (DUF1610)
        5.6    7.0   5.9         21    5.1   5.9    2.1  1  DUF1451         Zinc-ribbon containing domain
        8.7    6.1  11.0         11    5.7   3.8    3.0  3  zf-tcix         Putative treble-clef, zinc-finger, Zn-binding
        9.2    6.3   7.4        5.9    6.9   0.5    3.0  3  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon


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 !   30.2   5.9     6e-10   3.3e-07       1      48 [.     158     211 ..     158     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 6e-10
                               DZR   1 CpqCgeelppdarfCseCgtklkavaa.edrCpsCgekvdpearf.....CpeC 48 
                                       C++Cg+ +p ++++Cs Cg++l ++   ++ Cp Cg+++d++ ++     C+ C
  gi|557694641|ref|YP_008797695.1| 158 CQSCGAVNPLGSKVCSSCGAQLFQPDPkAQPCPVCGAPLDETYKIgenivCKIC 211
                                       *********************8543335***********999887666667666 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   1.0   1.5e-07   8.2e-05       2      23 .]     158     179 ..     157     179 .. 0.95
   2 !   12.0   0.3   0.00024      0.13      11      23 .]     184     196 ..     182     196 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.5e-07
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtpl 23 
                                       C +CGa ++ ++k C+ CG+ l
  gi|557694641|ref|YP_008797695.1| 158 CQSCGAVNPLGSKVCSSCGAQL 179
                                       *******************986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00024
                     zinc_ribbon_2  11 dnakFCpyCGtpl 23 
                                       ++a+ Cp CG+pl
  gi|557694641|ref|YP_008797695.1| 184 PKAQPCPVCGAPL 196
                                       799********98 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 ?    6.5   0.1     0.012       6.5      13      29 ..     147     163 ..     145     164 .. 0.80
   2 ?    5.7   0.1     0.021        12      22      30 ..     170     178 ..     169     180 .. 0.72
   3 ?    5.3   0.2     0.028        16       6      13 ..     189     196 ..     187     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.012
                     zf-NADH-PPase  13 tepaeggwarvCpaCgl 29 
                                       ++++  g  +vC +Cg+
  gi|557694641|ref|YP_008797695.1| 147 MVVVTRGVDMVCQSCGA 163
                                       667777888*******7 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.021
                     zf-NADH-PPase  22 rvCpaCgle 30 
                                       +vC++Cg+ 
  gi|557694641|ref|YP_008797695.1| 170 KVCSSCGAQ 178
                                       788888875 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.028
                     zf-NADH-PPase   6 CgrCGapt 13 
                                       C+ CGap 
  gi|557694641|ref|YP_008797695.1| 189 CPVCGAPL 196
                                       9****995 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 ?   14.6   2.5   2.7e-05     0.015       7      26 ..     158     177 ..     157     178 .. 0.95
   2 ?    0.2   0.2      0.87   4.9e+02       7      26 ..     189     194 ..     184     195 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.7e-05
                                       -SSS--EEESSSSB-TTT-- CS
                          zf-RanBP   7 CskClvqNfawstkCvaCqa 26 
                                       C +C++ N++ s +C +C+a
  gi|557694641|ref|YP_008797695.1| 158 CQSCGAVNPLGSKVCSSCGA 177
                                       ******************98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.87
                                       -SSS--EEESSSSB-TTT-- CS
                          zf-RanBP   7 CskClvqNfawstkCvaCqa 26 
                                       C++C+              a
  gi|557694641|ref|YP_008797695.1| 189 CPVCG--------------A 194
                                       55554..............4 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 ?    1.3   0.3       0.7   3.9e+02      31      40 .]     153     162 ..     146     163 .. 0.73
   2 ?    4.1   0.1     0.095        53      15      27 ..     169     181 ..     167     187 .. 0.81
   3 ?   14.4   1.9   5.6e-05     0.031      15      39 ..     186     211 ..     185     211 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.7
                     Auto_anti-p27  31 ggkvyCvaCd 40 
                                       g++++C +C+
  gi|557694641|ref|YP_008797695.1| 153 GVDMVCQSCG 162
                                       5889999995 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.095
                     Auto_anti-p27  15 aetCpvCgvPLmr 27 
                                       +++C+ Cg+ L++
  gi|557694641|ref|YP_008797695.1| 169 SKVCSSCGAQLFQ 181
                                       589******9998 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 5.6e-05
                     Auto_anti-p27  15 aetCpvCgvPLmrdr.kggkvyCvaC 39 
                                       a+ CpvCg+PL ++   g++++C +C
  gi|557694641|ref|YP_008797695.1| 186 AQPCPVCGAPLDETYkIGENIVCKIC 211
                                       579**********98647999**999 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 ?   12.8   2.9   0.00015     0.084      23      49 ..     170     198 ..     150     199 .. 0.79
   2 ?    2.3   0.1      0.27   1.5e+02       4      11 ..     207     214 ..     201     219 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00015
                                       EEE-HHHHHHHHH...TT-B-TTT--B--E CS
                        zf-C3HC4_3  23 lvlCeeCaekllk...rkkkCpiCrrpiek 49 
                                         +C++C  +l +   + + Cp+C +p ++
  gi|557694641|ref|YP_008797695.1| 170 K-VCSSCGAQLFQpdpKAQPCPVCGAPLDE 198
                                       3.8**********************99876 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.27
                                       B-TTTSSS CS
                        zf-C3HC4_3   4 eCviCler 11 
                                        C+iC+++
  gi|557694641|ref|YP_008797695.1| 207 VCKICFSE 214
                                       46666654 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   3.3    0.0014      0.79       3      55 ..     158     211 ..     138     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0014
                                       -SSS-S--EE-SSEEE-TTT--EE....EEEEE-SSS-S---EEEETTEEEE--TTT CS
                    zinc-ribbons_6   3 CpeCqqelekrgeqyhCeaCqedl....kkealCpeCeqelevlkaCgavdyfCnkc 55 
                                       C++C +       +  C++C ++l     k + Cp C+ +l+   + g  +  C+ c
  gi|557694641|ref|YP_008797695.1| 158 CQSCGAVNP-L-GSKVCSSCGAQLfqpdPKAQPCPVCGAPLDETYKIGE-NIVCKIC 211
                                       666654322.2.3567999988542111356679999999999999988.8888887 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   3.9   0.00047      0.26       5      26 .]     158     179 ..     156     179 .. 0.93
   2 ?    7.3   0.3    0.0055       3.1       4      25 ..     171     178 ..     168     183 .. 0.60
   3 ?    7.1   4.2    0.0068       3.8       3      14 ..     187     198 ..     185     211 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00047
                       zf-ribbon_3   5 CPnCGa.plssddnvCpyCGtkl 26 
                                       C +CGa +   + +vC +CG++l
  gi|557694641|ref|YP_008797695.1| 158 CQSCGAvN-PLGSKVCSSCGAQL 179
                                       999***99.***********987 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0055
                       zf-ribbon_3   4 rCPnCGaplssddnvCpyCGtk 25 
                                        C++CGa              +
  gi|557694641|ref|YP_008797695.1| 171 VCSSCGA--------------Q 178
                                       4666666..............4 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0068
                       zf-ribbon_3   3 vrCPnCGaplss 14 
                                       + CP CGapl++
  gi|557694641|ref|YP_008797695.1| 187 QPCPVCGAPLDE 198
                                       57******9997 PP

>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.019        11      17      39 ..     156     176 ..     151     181 .. 0.91
   2 ?    5.8   0.0     0.022        13      16      30 ..     205     219 ..     196     220 .] 0.87

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.019
                    Ribosomal_L40e  17 miCrkCYArlpprAtnCrkkkCg 39 
                                       m+C+ C A  p+ ++ C    Cg
  gi|557694641|ref|YP_008797695.1| 156 MVCQSCGAVNPLGSKVCS--SCG 176
                                       9**************998..787 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.022
                    Ribosomal_L40e  16 KmiCrkCYArlpprA 30 
                                         +C+ C++ l+p+A
  gi|557694641|ref|YP_008797695.1| 205 NIVCKICFSELKPKA 219
                                       579**********98 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       6.9   3.9e+03      29      46 ..     105     122 ..     100     123 .. 0.79
   2 ?   -0.2   0.1       1.8     1e+03      21      26 ..     156     161 ..     143     163 .. 0.87
   3 ?    1.3   0.1      0.58   3.3e+02      21      30 ..     170     179 ..     168     186 .. 0.81
   4 ?   13.3   0.9    0.0001     0.058       1      31 [.     188     216 ..     188     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 6.9
                           DUF4428  29 Klseflsdvkikkiltle 46 
                                       ++s++l+++ + +i t++
  gi|557694641|ref|YP_008797695.1| 105 EISNLLDSQPAMEIRTVT 122
                                       678889999998888876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.8
                           DUF4428  21 yvCkdC 26 
                                        vC++C
  gi|557694641|ref|YP_008797695.1| 156 MVCQSC 161
                                       69**** PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.58
                           DUF4428  21 yvCkdClkKl 30 
                                       +vC +C  +l
  gi|557694641|ref|YP_008797695.1| 170 KVCSSCGAQL 179
                                       79****9987 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 0.0001
                           DUF4428   1 iCaiCgkKigllkrlkleDgyvCkdClkKls 31 
                                       +C++Cg  +      k+ +++vCk C+++l+
  gi|557694641|ref|YP_008797695.1| 188 PCPVCGAPLDE--TYKIGENIVCKICFSELK 216
                                       5*****98765..335************986 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.8   0.00016     0.088      74     134 ..     156     216 ..      95     218 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                           TackOD1  74 rlCpsCksghlnvrevCpkCkSidieeqe.lihhftCgnvgpeeeflkegkleCpkCktkLr 134
                                       ++C+sC   +    +vC++C++  ++ +     +  Cg+    e+++ +++++C  C ++L+
  gi|557694641|ref|YP_008797695.1| 156 MVCQSCGAVNPLGSKVCSSCGAQLFQPDPkAQPCPVCGAP-LDETYKIGENIVCKICFSELK 216
                                       68**********************99875155699***85.56789***********99996 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2    0.0002      0.11     156     214 ..       8      89 ..       4      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                            DUF373 156 tiLvplGlllliyallll.......................lglpelalaiillllGlylllrGfgldelleellek 209
                                       +iL+ +G++++++++l+l                       +g+   a+++ ++++Gl++++rG++   +   ++ +
  gi|557694641|ref|YP_008797695.1|   8 IILGAVGVVVVLLPILVLfitggydspiqrfydsplapglpMGVLVTAAGAAVTAVGLLIFIRGMRAGPTYPAAPPT 84 
                                       89***************************************99**********************998877777767 PP

                            DUF373 210 lkesl 214
                                       +++ l
  gi|557694641|ref|YP_008797695.1|  85 IRRPL 89 
                                       66655 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.6       1.5   8.3e+02      15      21 ..     157     163 ..     156     165 .. 0.84
   2 ?    8.7   0.1    0.0029       1.6      11      23 ..     167     179 ..     163     182 .. 0.86
   3 ?    3.8   0.0      0.11        59      16      25 ..     189     198 ..     184     201 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.5
                              YhfH  15 kCteCGk 21 
                                       +C++CG 
  gi|557694641|ref|YP_008797695.1| 157 VCQSCGA 163
                                       5999*95 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0029
                              YhfH  11 LPkKkCteCGkei 23 
                                       L++K+C++CG ++
  gi|557694641|ref|YP_008797695.1| 167 LGSKVCSSCGAQL 179
                                       899*******875 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.11
                              YhfH  16 CteCGkeieE 25 
                                       C+ CG  ++E
  gi|557694641|ref|YP_008797695.1| 189 CPVCGAPLDE 198
                                       ******9999 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 ?   11.6   1.0   0.00046      0.26       4      52 ..      93     142 ..      91     146 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00046
                      ABC_tran_CTD   4 ykeqreleeleaeIeaLEeeiaelea.eladpelysdpeklaelsaelee 52 
                                       ++e rele++e+eI  L   + ++e   + +p     p+k +++ ++ +e
  gi|557694641|ref|YP_008797695.1|  93 RQENRELEQIEQEISNLLDSQPAMEIrTVTQPPPKRAPAKQQAVAEQTAE 142
                                       689*************9888888887334444444444666666666655 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.4     0.012       6.6      19      28 ..     155     164 ..     151     166 .. 0.90
   2 ?    4.4   0.3     0.046        26      21      29 ..     171     179 ..     165     185 .. 0.84
   3 ?    6.8   1.2    0.0082       4.6       3      25 ..     189     211 ..     187     215 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.012
                                       CEEESSSSBE CS
                      TF_Zn_Ribbon  19 elvCtdCGlV 28 
                                       ++vC +CG+V
  gi|557694641|ref|YP_008797695.1| 155 DMVCQSCGAV 164
                                       89******98 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.046
                                       EESSSSBEE CS
                      TF_Zn_Ribbon  21 vCtdCGlVl 29 
                                       vC++CG+ l
  gi|557694641|ref|YP_008797695.1| 171 VCSSCGAQL 179
                                       9*****865 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0082
                                       ETTTTCEECHEETSTTCE.EESSS CS
                      TF_Zn_Ribbon   3 CPnCgstnlveDpergel.vCtdC 25 
                                       CP+Cg + l e ++ ge  vC+ C
  gi|557694641|ref|YP_008797695.1| 189 CPVCGAP-LDETYKIGENiVCKIC 211
                                       *****98.6788999999899988 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 ?   10.7   0.0   0.00059      0.33      21      32 ..     155     166 ..     144     167 .. 0.78
   2 ?    1.9   0.1      0.35     2e+02       4      11 ..     170     177 ..     169     180 .. 0.74
   3 ?   -1.5   0.2         4   2.2e+03      24      29 ..     189     194 ..     187     195 .. 0.77
   4 ?   -0.9   0.2       2.7   1.5e+03       3       9 ..     205     211 ..     204     215 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00059
                     A2L_zn_ribbon  21 ylvCieCgasfp 32 
                                       ++vC+ Cga+ p
  gi|557694641|ref|YP_008797695.1| 155 DMVCQSCGAVNP 166
                                       8********988 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.35
                     A2L_zn_ribbon   4 kvCsvCgg 11 
                                       kvCs Cg 
  gi|557694641|ref|YP_008797695.1| 170 KVCSSCGA 177
                                       68888875 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4
                     A2L_zn_ribbon  24 CieCga 29 
                                       C+ Cga
  gi|557694641|ref|YP_008797695.1| 189 CPVCGA 194
                                       777876 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 2.7
                     A2L_zn_ribbon   3 lkvCsvC 9  
                                       ++vC+ C
  gi|557694641|ref|YP_008797695.1| 205 NIVCKIC 211
                                       5789988 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 ?    7.0   6.1      0.01       5.8      50      96 ..     135     179 ..      98     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                                       HHHCC.TTTT-EEEEEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  50 llaegtvlegaeLeieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       ++ae+t+ ++  + + +  v + C++Cg+   l +k   C +Cg++ 
  gi|557694641|ref|YP_008797695.1| 135 AVAEQTAEKKGGMVVVTRGVDMVCQSCGAVNPLGSK--VCSSCGAQL 179
                                       556667777777888899999999999977777744..677777754 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00089       0.5      64      86 .]     140     176 ..     111     176 .. 0.76
   2 ?   -0.4   0.6       3.6     2e+03      67      77 ..     188     198 ..     180     211 .. 0.58
   3 ?    0.6   0.6       1.8   9.8e+02       3      25 ..     189     212 ..     187     218 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00089
                    zinc_ribbon_15  64 e..............kkeCknCgkeveeefkyCpkCg 86 
                                       +               ++C++Cg++    +k C++Cg
  gi|557694641|ref|YP_008797695.1| 140 TaekkggmvvvtrgvDMVCQSCGAVNPLGSKVCSSCG 176
                                       02235666788888899*******************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.6
                    zinc_ribbon_15  67 eCknCgkevee 77 
                                        C+ Cg+ ++e
  gi|557694641|ref|YP_008797695.1| 188 PCPVCGAPLDE 198
                                       44444444444 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.8
                    zinc_ribbon_15   3 CpkCgklskaelvk.kkkvlklff 25 
                                       Cp Cg   + +++  ++ v+k++f
  gi|557694641|ref|YP_008797695.1| 189 CPVCGAPLDETYKIgENIVCKICF 212
                                       777776555555431444566666 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.3     0.046        26      24      31 ..     157     164 ..     156     165 .. 0.86
   2 ?    3.7   0.2      0.11        60       3       8 ..     172     177 ..     170     182 .. 0.66
   3 ?    7.1   0.6    0.0089         5       3      21 ..     189     207 ..     189     213 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.046
                                       EETTTTEE CS
                         Nudix_N_2  24 vCpaCgti 31 
                                       vC++Cg++
  gi|557694641|ref|YP_008797695.1| 157 VCQSCGAV 164
                                       9*****98 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.11
                                       -TTT-- CS
                         Nudix_N_2   3 CsqCGt 8  
                                       Cs+CG+
  gi|557694641|ref|YP_008797695.1| 172 CSSCGA 177
                                       666666 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0089
                                       -TTT--B-EEE--TT-SS- CS
                         Nudix_N_2   3 CsqCGtpvelripdgDnre 21 
                                       C+ CG+p+      g+n  
  gi|557694641|ref|YP_008797695.1| 189 CPVCGAPLDETYKIGENIV 207
                                       ********98777788854 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 ?    3.7   0.1      0.09        51      23      30 ..     157     164 ..     156     164 .. 0.82
   2 ?    4.7   0.1     0.044        25      20      30 ..     168     178 ..     168     179 .. 0.86
   3 ?    7.4   0.5    0.0061       3.4       3      12 ..     185     194 ..     183     202 .. 0.79
   4 ?   -1.1   0.1       2.8   1.5e+03       4      10 ..     205     211 ..     203     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.09
                           zf-RRN7  23 yCrrChtq 30 
                                       +C++C+ +
  gi|557694641|ref|YP_008797695.1| 157 VCQSCGAV 164
                                       8****975 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.044
                           zf-RRN7  20 GfyyCrrChtq 30 
                                       G  +C +C+ q
  gi|557694641|ref|YP_008797695.1| 168 GSKVCSSCGAQ 178
                                       7789*****98 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0061
                           zf-RRN7   3 kgppCgvCgc 12 
                                       k  pC+vCg+
  gi|557694641|ref|YP_008797695.1| 185 KAQPCPVCGA 194
                                       668******8 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 2.8
                           zf-RRN7   4 gppCgvC 10 
                                       +++C +C
  gi|557694641|ref|YP_008797695.1| 205 NIVCKIC 211
                                       789*999 PP

>> Gin  Inhibitor of sigma-G Gin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.74   4.1e+02       7      23 ..     142     161 ..     139     165 .. 0.70
   2 ?    3.4   0.4      0.13        74      15      30 ..     167     182 ..     158     187 .. 0.78
   3 ?    6.8   2.0     0.011       6.4       1      27 [.     189     215 ..     189     216 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.74
                                       EESSEE-SSS-...-EEHHH CS
                               Gin   7 ekeeGiiilgk...fICeeC 23 
                                       ek++G++++++   ++C++C
  gi|557694641|ref|YP_008797695.1| 142 EKKGGMVVVTRgvdMVCQSC 161
                                       56778888876222679999 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.13
                                       SS--EEHHHHHHHHHH CS
                               Gin  15 lgkfICeeCekkivnt 30 
                                       lg+++C++C +++ + 
  gi|557694641|ref|YP_008797695.1| 167 LGSKVCSSCGAQLFQP 182
                                       7899*****9998765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.011
                                       -TTT--EESSEE-SSS--EEHHHHHHH CS
                               Gin   1 CiiCekekeeGiiilgkfICeeCekki 27 
                                       C +C+ + +e + i ++++C+ C +++
  gi|557694641|ref|YP_008797695.1| 189 CPVCGAPLDETYKIGENIVCKICFSEL 215
                                       99*********************7765 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         4   2.2e+03      28      32 ..     157     161 ..     143     164 .. 0.68
   2 ?    0.8   0.1       1.1   5.9e+02      28      37 ..     171     180 ..     170     187 .. 0.80
   3 ?    9.4   0.1    0.0021       1.2      29      56 ..     189     214 ..     184     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 4
                                       B-TTT CS
                               LIM  28 tCsdC 32 
                                       +C++C
  gi|557694641|ref|YP_008797695.1| 157 VCQSC 161
                                       45555 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.1
                                       B-TTT-SB-C CS
                               LIM  28 tCsdCqkeLk 37 
                                       +Cs+C+ +L 
  gi|557694641|ref|YP_008797695.1| 171 VCSSCGAQLF 180
                                       5999999885 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0021
                                       -TTT-SB-CTT.CEEETTEEEEHHHHHH CS
                               LIM  29 CsdCqkeLkegsfyekdgklyCkkdylk 56 
                                       C +C+ +L+e+  y + ++++Ck ++ +
  gi|557694641|ref|YP_008797695.1| 189 CPVCGAPLDET--YKIGENIVCKICFSE 214
                                       99*******99..789999******976 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 ?   -1.1   0.2       3.1   1.7e+03       3      16 ..      97     110 ..      95     113 .. 0.70
   2 ?   10.4   0.3   0.00082      0.46      22      31 ..     189     198 ..     184     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHT CS
                     Rad50_zn_hook   3 qeteelnkkieelk 16 
                                        e e++++ i++l 
  gi|557694641|ref|YP_008797695.1|  97 RELEQIEQEISNLL 110
                                       56777888887775 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00082
                                       -TTT--EE-H CS
                     Rad50_zn_hook  22 CPlCgRelde 31 
                                       CP+Cg +lde
  gi|557694641|ref|YP_008797695.1| 189 CPVCGAPLDE 198
                                       *********8 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 ?    1.4   0.2      0.56   3.1e+02      46      55 ..     155     164 ..     139     167 .. 0.78
   2 ?   11.5   0.6   0.00038      0.21      28      57 ..     169     197 ..     165     206 .. 0.92
   3 ?    6.2   0.3     0.017       9.5      29      53 ..     187     212 ..     185     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.56
                    OrfB_Zn_ribbon  46 tfkCpnCgfe 55 
                                        ++C++Cg++
  gi|557694641|ref|YP_008797695.1| 155 DMVCQSCGAV 164
                                       6788888875 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00038
                    OrfB_Zn_ribbon  28 SktCseCgsknkealsgrtfkCpnCgfead 57 
                                       Sk Cs Cg+++ + ++++   Cp Cg+ +d
  gi|557694641|ref|YP_008797695.1| 169 SKVCSSCGAQLFQ-PDPKAQPCPVCGAPLD 197
                                       9************.99**********8665 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.017
                    OrfB_Zn_ribbon  29 ktCseCgsknke.alsgrtfkCpnCg 53 
                                       + C++Cg+ ++e  + g++ +C+ C 
  gi|557694641|ref|YP_008797695.1| 187 QPCPVCGAPLDEtYKIGENIVCKICF 212
                                       67*********988999999999885 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 ?    7.3   6.1    0.0083       4.6      20      49 ..     158     184 ..     153     205 .. 0.55
   2 ?   -0.6   1.2       2.4   1.4e+03      37      44 ..     189     196 ..     189     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0083
                          zf-C2HC5  20 ClnCGkiiCakeglskpCsfCgspllssee 49 
                                       C +CG +        k Cs+Cg++l++++ 
  gi|557694641|ref|YP_008797695.1| 158 CQSCGAVNPLGS---KVCSSCGAQLFQPDP 184
                                       555555532222...345555555555432 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.4
                          zf-C2HC5  37 CsfCgspl 44 
                                       C+ Cg+pl
  gi|557694641|ref|YP_008797695.1| 189 CPVCGAPL 196
                                       66677665 PP

>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   2.0    0.0063       3.5      24      43 ..     170     192 ..     150     193 .. 0.79
   2 ?    3.0   0.1      0.24   1.3e+02       3      12 ..     208     217 ..     206     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0063
                         zf-RING_2  24 vfhreClerwlrssst...CPlC 43 
                                         + +C ++++++ ++   CP+C
  gi|557694641|ref|YP_008797695.1| 170 KVCSSCGAQLFQPDPKaqpCPVC 192
                                       48********************* PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.24
                         zf-RING_2   3 CpICleelss 12 
                                       C IC++el++
  gi|557694641|ref|YP_008797695.1| 208 CKICFSELKP 217
                                       *****99975 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   9.0     0.032        18       8      36 ..     172     196 ..     155     200 .. 0.76
   2 ?    3.9   1.6      0.11        60       8      34 ..     189     213 ..     189     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.032
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgsev 36 
                                       C +Cg     +q+  d++ ++CP Cg+++
  gi|557694641|ref|YP_008797695.1| 172 CSSCG--AQLFQP--DPKAQPCPVCGAPL 196
                                       88888..445565..777777*****976 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.11
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs 34 
                                       C  Cg   ++  +i +  +++C+ C s
  gi|557694641|ref|YP_008797695.1| 189 CPVCGAPLDETYKIGE--NIVCKICFS 213
                                       7778888888887775..677888865 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 ?    2.3   0.0      0.33   1.8e+02      13      24 ..     152     163 ..     128     166 .. 0.80
   2 ?    5.5   2.4     0.033        18       2      26 ..     172     196 ..     171     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.33
                          zf-Mss51  13 khvdfeCpdCGi 24 
                                       + vd+ C+ CG 
  gi|557694641|ref|YP_008797695.1| 152 RGVDMVCQSCGA 163
                                       6799*******6 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.033
                          zf-Mss51   2 CPvpkhkqtapkhvdfeCpdCGipt 26 
                                       C  + ++  +p + +  Cp CG p 
  gi|557694641|ref|YP_008797695.1| 172 CSSCGAQLFQPDPKAQPCPVCGAPL 196
                                       889999999999***********96 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.7      0.51   2.9e+02       1       7 [.     158     164 ..     158     164 .. 0.90
   2 ?    9.0   2.5    0.0024       1.3       1      23 [.     172     193 ..     172     194 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.51
                           DUF1610   1 CtSCGae 7  
                                       C SCGa+
  gi|557694641|ref|YP_008797695.1| 158 CQSCGAV 164
                                       99***97 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0024
                           DUF1610   1 CtSCGaelaprEravvFpCPNCG 23 
                                       C+SCGa l  +    + pCP CG
  gi|557694641|ref|YP_008797695.1| 172 CSSCGAQLFQPD-PKAQPCPVCG 193
                                       *********999.99999**999 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   5.9     0.037        21     105     140 ..     160     194 ..      91     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.037
                           DUF1451 105 qsGevvglGtlvCekCgkelalkkteeippCpkCga 140
                                         G v  lG  vC +Cg++l ++   + +pCp Cga
  gi|557694641|ref|YP_008797695.1| 160 SCGAVNPLGSKVCSSCGAQL-FQPDPKAQPCPVCGA 194
                                       45888889*********998.666667899****86 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 ?    5.7   3.8      0.02        11      13      28 ..     158     173 ..     150     176 .. 0.84
   2 ?    4.0   0.4      0.07        39       9      18 ..     168     177 ..     166     179 .. 0.85
   3 ?    2.5   0.8       0.2   1.1e+02      12      18 ..     188     194 ..     186     218 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.02
                           zf-tcix  13 CpkCGtyNGtRglsCk 28 
                                       C +CG+ N+  +++C+
  gi|557694641|ref|YP_008797695.1| 158 CQSCGAVNPLGSKVCS 173
                                       **********999996 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.07
                           zf-tcix   9 GvrkCpkCGt 18 
                                       G + C++CG+
  gi|557694641|ref|YP_008797695.1| 168 GSKVCSSCGA 177
                                       6699*****8 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.2
                           zf-tcix  12 kCpkCGt 18 
                                        Cp CG+
  gi|557694641|ref|YP_008797695.1| 188 PCPVCGA 194
                                       6*****8 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.95   5.3e+02      20      26 ..     156     162 ..     153     163 .. 0.89
   2 ?    1.1   0.1      0.68   3.8e+02      21      28 ..     171     178 ..     170     179 .. 0.88
   3 ?    6.9   0.5     0.011       5.9       4      28 ..     188     214 ..     184     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.95
                    PhnA_Zn_Ribbon  20 lvCpeCa 26 
                                       +vC  C+
  gi|557694641|ref|YP_008797695.1| 156 MVCQSCG 162
                                       99**997 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.68
                    PhnA_Zn_Ribbon  21 vCpeCahE 28 
                                       vC+ C+ +
  gi|557694641|ref|YP_008797695.1| 171 VCSSCGAQ 178
                                       8****977 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.011
                    PhnA_Zn_Ribbon   4 kCplCaS..eytYedgallvCpeCahE 28 
                                       +Cp C++  ++tY  g++ vC  C +E
  gi|557694641|ref|YP_008797695.1| 188 PCPVCGAplDETYKIGENIVCKICFSE 214
                                       69***99999************99888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       985  (0.0549389); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); 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):              32  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1579.75
//
Query:       gi|557694642|ref|YP_008797696.1|  [L=77]
Description: small nuclear ribonucleoprotein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   72.3   0.1    2.1e-20   72.2   0.1    1.0  1  LSM       LSM domain
  ------ inclusion threshold ------
      0.037   13.7   0.0      0.054   13.2   0.0    1.3  1  Hfq       Hfq protein
      0.056   13.6   0.0      0.074   13.2   0.0    1.2  1  SM-ATX    Ataxin 2 SM domain
       0.12   12.5   0.0       0.16   12.1   0.0    1.3  1  LSM14     Scd6-like 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 !   72.2   0.1   4.6e-24   2.1e-20       3      66 ..      11      73 ..       9      74 .. 0.97

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 4.6e-24
                                      HHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
                               LSM  3 lkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                                      l   ink v+v lkn+ +++Gt++++D +mN+ Le v+e++ d+ +++ + +vliRGnni++i+
  gi|557694642|ref|YP_008797696.1| 11 LMRQINKPVRVFLKNDARYEGTMVECDGYMNMLLEHVVEYMGDS-KTAGYPKVLIRGNNIMYII 73
                                      7889****************************************.*****************97 PP

>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05     0.054       9      40 ..      12      43 ..       7      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                      HHHCT-EEEEEETTS-EEEEEEEEE-SSEEEE CS
                               Hfq  9 lrkekipvtifLvnGiklkGviksfDnftvlL 40
                                      +r+ + pv +fL n  + +G++ + D ++ +L
  gi|557694642|ref|YP_008797696.1| 12 MRQINKPVRVFLKNDARYEGTMVECDGYMNML 43
                                      588899**********************9666 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.6e-05     0.074      14      78 ..      17      72 ..       8      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                                      SEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS...........-EEEEEEE-GGGEEEE CS
                            SM-ATX 14 kevevtvknGevyeGifstvslekdfsvvLkmarkvkkanskssspssgeipdtliikakdivdi 78
                                      k+v+v +kn+++yeG    ++    ++  L+++ +           s+++ +++++i++++i+ i
  gi|557694642|ref|YP_008797696.1| 17 KPVRVFLKNDARYEGTMVECDG--YMNMLLEHVVEYMG-------DSKTAGYPKVLIRGNNIMYI 72
                                      789*****************99..99999999999999.......66677777777777777766 PP

>> LSM14  Scd6-like Sm domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.5e-05      0.16       3      62 ..      15      74 ..      13      77 .] 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.5e-05
                             LSM14  3 IGskislisksdirYeGilceinledstiaLqnvrsfGtegrkdneq.ippskevyeyivF 62
                                      I + + +  k+d rYeG+++e +    ++ L++v  +  + ++ +   +  + +   yi+F
  gi|557694642|ref|YP_008797696.1| 15 INKPVRVFLKNDARYEGTMVECD-GYMNMLLEHVVEYMGDSKTAGYPkVLIRGNNIMYIIF 74
                                      788999****************9.5666778887776555544333335555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 548.71
//
Query:       gi|557694643|ref|YP_008797697.1|  [L=409]
Description: S-adenosylmethionine synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-157  524.2   1.5   2.1e-157  524.0   1.5    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
  ------ inclusion threshold ------
        0.1   12.6   0.0        0.2   11.7   0.0    1.5  1  GhoS             Endoribonuclease GhoS


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 !  524.0   1.5  2.3e-161  2.1e-157       3     394 ..       6     403 ..       4     405 .. 0.98

  Alignments for each domain:
  == domain 1  score: 524.0 bits;  conditional E-value: 2.3e-161
                                       EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEEEE CS
                   AdoMet_Synthase   3 ivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGGev 79 
                                       ++ve l+k+pve+qe+E+vErKG+GHPD+i D+++e++s +ls++yl+++g+ilhhn+Dk+llv+G++ ++fg G++
  gi|557694643|ref|YP_008797697.1|   6 VTVEPLDKTPVENQEIEMVERKGLGHPDYIIDSACEEASLHLSQYYLSNYGQILHHNLDKGLLVGGRAYNRFGYGRL 82 
                                       789************************************************************************** PP

                                       EE-EEEEEEEEEEEEE.....EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..- CS
                   AdoMet_Synthase  80 iepieillsgratkev....egekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevp 152
                                        epi+i+++gra ++v    ++ekip++ei++ea+++++k+n+r+ld+++++ ++++++++s dLk v+e  k+ +p
  gi|557694643|ref|YP_008797697.1|  83 EEPITIIIAGRASTSVktptGEEKIPYREIITEAVRSMVKRNFRFLDFDQHIELEIRVRESSPDLKAVVEMGKE-MP 158
                                       **************998888899************************************************766.9* PP

                                       BESSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHH CS
                   AdoMet_Synthase 153 laNDtSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlev 229
                                       laNDtS+gv+++p+++le+lvl+ter+lns ++k++++e+GeD+KvmglR+++ki+lTva  +v++l kd ++Y++v
  gi|557694643|ref|YP_008797697.1| 159 LANDTSYGVAFYPFTTLENLVLTTERHLNSPQFKSRVKESGEDVKVMGLRKGSKITLTVADGIVSTLTKDRDHYIAV 235
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHSTTSEEEEEE-TT-BGG....GTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S- CS
                   AdoMet_Synthase 230 keeikeeveelakkltkerevevevNtaDkke....eesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEA 302
                                       ke+ik+eve+la+kl+ +++vev+vNtaDk+     +e++ylt tGtsaE+gDdG++GRGNR+nGlitpnr+mslEA
  gi|557694643|ref|YP_008797697.1| 236 KEQIKKEVEDLAAKLAGNHDVEVYVNTADKYGtnigDEVFYLTFTGTSAEHGDDGNTGRGNRANGLITPNRQMSLEA 312
                                       *****************************997678899*************************************** PP

                                       -TTS-TTT-HHHHHHHHHHHHHHHHHHH-TTEEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHH CS
                   AdoMet_Synthase 303 aaGKNPvsHvGKiYnvlaneiakeiveevegvkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiid 379
                                       +aGKNP+sHvGKiYnv a  +a++i+ee+++vkevyvr+lsqiGkpi+ePl +svqvi+ +++++  v +++e i+ 
  gi|557694643|ref|YP_008797697.1| 313 TAGKNPISHVGKIYNVAAGLVARRIYEETKRVKEVYVRMLSQIGKPINEPLSVSVQVIPYDRMDVGLV-RDIEGIVY 388
                                       *****************************************************************987.89****** PP

                                       HHHT-HHHHHHHHTT CS
                   AdoMet_Synthase 380 eelekieeiteelie 394
                                       +e+++i+++te +i+
  gi|557694643|ref|YP_008797697.1| 389 DEVASIRRVTELIIS 403
                                       ***********9997 PP

>> GhoS  Endoribonuclease GhoS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.2e-05       0.2      31      91 ..     207     266 ..     189     269 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                                       HHTTEESEEE-SSS-EEE-TTS..EEEE---S-HHHHHHHHHHGGGTSS----EEEEEEHHHH CS
                              GhoS  31 tragFsltlaDeeGkpheLgtn..tfglisalseeeieelaaglaesalgkkpevevltveey 91 
                                        r+g + tl+ ++G++  L ++   +  +  + ++e+e+laa+la    ++++ev v t ++y
  gi|557694643|ref|YP_008797697.1| 207 LRKGSKITLTVADGIVSTLTKDrdHYIAVKEQIKKEVEDLAAKLAG---NHDVEVYVNTADKY 266
                                       57788999***********875226888888999999999988865...68999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       639  (0.0356406); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2811.51
//
Query:       gi|557694644|ref|YP_008797698.1|  [L=240]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-55  186.5   0.1    5.5e-55  186.2   0.1    1.0  1  NucS             Endonuclease NucS
  ------ inclusion threshold ------
      0.067   13.3   0.0       0.11   12.6   0.0    1.3  1  Cdc13_OB4_dimer  Cdc13 OB4 dimerization domain


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 !  186.2   0.1   6.1e-59   5.5e-55       4     218 ..      16     227 ..      13     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: 186.2 bits;  conditional E-value: 6.1e-59
                              NucS   4 vlvvlarCkvsyeGraksrLeegerlivikpdGaflvhkdrkvePvnWqppkssltaevedgslilksirrkpeeeL 80 
                                       v v+  rC++sy+Gra s+L egerl++ik dG++lvh+   +ePvnWqp++s++  ++ed+ ++l++ r  ++e L
  gi|557694644|ref|YP_008797698.1|  16 VAVIAGRCSISYVGRASSELGEGERLVIIKRDGSVLVHRPSGYEPVNWQPSGSKIELYMEDDAVVLRAAR--ADEVL 90 
                                       788999*************************************************************987..789** PP

                              NucS  81 kveieevehasayeledveelvldGseaelaeliiehpdLieeGfkpvareyav.aiGivdiLgkdeegklvivelk 156
                                       k+  ++  ++  y+l d+ e+v+  seae++  ++++p+LieeGf+ v+ e a   +G vd++g d++g + +velk
  gi|557694644|ref|YP_008797698.1|  91 KIRFHGEPQVNVYQLVDEAEMVMYASEAEMKRAVLMRPELIEEGFRAVEEERAAgRAGKVDVFGVDKNGVFTVVELK 167
                                       ***************************************************987258******************** PP

                              NucS 157 rrkaevdaveqLkryvellkedsvldkvrGvlvapsittdaekllkeeglefkeldppkdsk 218
                                       rr a  + v+qL ry+e l e+ + ++ rG+++aps t++a  l+k  +lef+ l  p+  +
  gi|557694644|ref|YP_008797698.1| 168 RRAATPEDVKQLGRYLESLAEEWG-KRPRGIIAAPSATKHALSLMKTMNLEFRCLT-PRTCM 227
                                       ************************.778***************************9.55554 PP

>> Cdc13_OB4_dimer  Cdc13 OB4 dimerization 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      0.11      25      68 ..      66     109 ..      61     127 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                                       ETTTEEEEEESS---T--B-GGG-EEEEEESHHHHHHHHSSS-- CS
                   Cdc13_OB4_dimer  25 dedkvelyvtndlilkkkvdpkeiLkveilGkenvnyFlgdeea 68 
                                       + +k+ely+ +d+ + +     e+Lk++  G+ +vn +   +ea
  gi|557694644|ref|YP_008797698.1|  66 SGSKIELYMEDDAVVLRAARADEVLKIRFHGEPQVNVYQLVDEA 109
                                       6799*******************************988764444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1724.73
//
Query:       gi|557694645|ref|YP_008797699.1|  [L=446]
Description: hypothetical protein CSUB_C1218 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-11   43.5  14.9    3.6e-11   43.5  14.9    2.7  2  PMT_2      Dolichyl-phosphate-mannose-protein mannosyltransfe
    4.9e-11   42.7  17.8    1.1e-08   35.0  17.2    4.0  4  PMT        Dolichyl-phosphate-mannose-protein mannosyltransfe
  ------ inclusion threshold ------
        0.2   11.5   0.5       0.47   10.3   0.3    1.7  1  Pox_LP_H2  Viral late protein H2


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 !   43.5  14.9     6e-15   3.6e-11       2     154 ..      81     236 ..      80     241 .. 0.84
   2 ?    0.3   7.4      0.12   7.1e+02      55     116 ..     337     405 ..     332     439 .. 0.64

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 6e-15
                             PMT_2   2 hPPliawllalftklfgfselairlvsalagvltilllyllarrlfg.kraallaalllavvplfvalsalftpdap 77 
                                       hPPl   l+a+++ +fg++ ++ rl++ l+++ +++l+ l+a rl+  + a ++++ll+a+  +f++++++  +d p
  gi|557694645|ref|YP_008797699.1|  81 HPPLSKLLIAASMLVFGDNPVGWRLMPSLLSSAAVALIPLIAYRLTRsRFATFFTTLLIAADVMFFNIGTIAMLDGP 157
                                       9*********************************************95667789*******9999999999999*** PP

                             PMT_2  78 lvllwalalylllraleknklkywllagvlfGlgflsKytaallliaall..yllis..arrilke.....kkpyl. 144
                                         +++ la+y++l+         +  ++++fGl++lsK  +++ + ++ll  +l i   +r+i+ +     +  ++ 
  gi|557694645|ref|YP_008797699.1| 158 AFFFLFLATYMFLQT-------RYTSTAIFFGLALLSKTSIVFNVAGLLLfsFLAIYsrHRKIMESlqdwsP--LFe 225
                                       ********9998864.......366789******************99988966665545556665665422..223 PP

                             PMT_2 145 .alllalllfs 154
                                        ++l++l++f+
  gi|557694645|ref|YP_008797699.1| 226 kTVLIGLAVFM 236
                                       47777777776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.12
                             PMT_2  55 aalllavvplfvalsalftpdaplvllwalalylllrale..knklkyw.....llagvlfGlgflsKy 116
                                       +al l +++++++ s+   + +++v+ w+++ yl + +l    +++ y       l +v++Gl+++ + 
  gi|557694645|ref|YP_008797699.1| 337 TALVLVYSLYMAVKSRGADTVNLFVFSWIAMSYLPYFLLAhlLQRWVYTfyflpTLPAVALGLSMMLRE 405
                                       556666666666667777788899999999999765555522666655543333344667777777765 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       0.6   3.6e+03     103     127 ..      11      35 ..       7      39 .. 0.72
   2 !   14.2   0.0   4.1e-06     0.025      21      65 ..      57     101 ..      52     103 .. 0.92
   3 !   35.0  17.2   1.8e-12   1.1e-08      80     202 ..      98     208 ..      94     250 .. 0.84
   4 ?   -5.9   7.7         3   1.8e+04     165     227 ..     333     391 ..     321     439 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.6
                               PMT 103 tllelgfskltallaallvllensl 127
                                       ++++lgf++  a+  ++++l   ++
  gi|557694645|ref|YP_008797699.1|  11 FVKKLGFDQKLAVAVFIILLGLRLM 35 
                                       7889999999998888887755555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.1e-06
                               PMT  21 vvfdevhfgkfasdYlehsffmdvhpplgkmllalggyLagkdgn 65 
                                        vfde+h+   + + l++++   +hppl+k+l+a ++ ++g ++ 
  gi|557694645|ref|YP_008797699.1|  57 LVFDEAHYVPAVRKLLRGESVNHEHPPLSKLLIAASMLVFGDNPV 101
                                       69***********************************99998775 PP

  == domain 3  score: 35.0 bits;  conditional E-value: 1.8e-12
                               PMT  80 vpyvslRlfsallgslivplvyltllelgfskltallaallvllenslitlsryilldspLlfftllsmyclvkfer 156
                                        + v+ Rl++ ll+s +v+l  l++++l++s++++ +++ll + +  ++ ++++++ld p  ff+ l+ y++++   
  gi|557694645|ref|YP_008797699.1|  98 DNPVGWRLMPSLLSSAAVALIPLIAYRLTRSRFATFFTTLLIAADVMFFNIGTIAMLDGPAFFFLFLATYMFLQTR- 173
                                       688999*********************************************************************5. PP

                               PMT 157 kapfsrswwlwllltgvalglavsvKwvglftvllvgllliwelwq 202
                                                  ++ t +  gla+++K  ++f v+ ++l  +  +  
  gi|557694645|ref|YP_008797699.1| 174 -----------YTSTAIFFGLALLSKTSIVFNVAGLLLFSFLAIYS 208
                                       ...........899****************9997777665555544 PP

  == domain 4  score: -5.9 bits;  conditional E-value: 3
                               PMT 165 wlwllltgvalglavsvKwvglftvllvgllliwelwqllgdkslllksivkhllaralaliv 227
                                       ++w +++ +  +l + vK+ g+ tv l+++ +i      ++ ++ ll+     ++ ++ +l  
  gi|557694645|ref|YP_008797699.1| 333 YWWTTALVLVYSLYMAVKSRGADTVNLFVFSWIAMSYLPYFLLAHLLQ----RWVYTFYFLPT 391
                                       677777777777777777777777766666666555555554444444....33333333333 PP

>> Pox_LP_H2  Viral late protein H2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   7.8e-05      0.47      25      78 ..     171     226 ..     149     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.8e-05
                         Pox_LP_H2  25 raakvstliffvlila..isvlllllqvsdnsvlselakyariknavksWkplves 78 
                                       ++  +st iff l l+   s+++ +  +  +s+l+  +++++i +++++W pl e+
  gi|557694645|ref|YP_008797699.1| 171 QTRYTSTAIFFGLALLskTSIVFNVAGLLLFSFLAIYSRHRKIMESLQDWSPLFEK 226
                                       667789999997766411344444445556666666677778999*******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3085.30
//
Query:       gi|557694646|ref|YP_008797700.1|  [L=499]
Description: elongator complex protein 3 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-24   84.8   0.1    6.7e-24   83.7   0.1    1.6  1  Radical_SAM_C    Radical_SAM C-terminal domain
    5.1e-23   82.3   0.0    1.3e-22   81.0   0.0    1.7  1  Radical_SAM      Radical SAM superfamily
    5.7e-07   29.8   0.2    1.2e-06   28.7   0.2    1.6  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    4.6e-06   26.6   0.1    1.1e-05   25.4   0.1    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0054   17.1   0.3      0.014   15.8   0.3    1.8  1  Acetyltransf_7   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 !   83.7   0.1   1.9e-27   6.7e-24       1      80 [.     271     350 ..     271     351 .. 0.99

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 1.9e-27
                     Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlrelie 77 
                                       pd++K+yp+lv+ gT+L+++++ g ykp+s +e+v ++ ++++++pp +r+ R++++ip + ++ g   +nlr+++e
  gi|557694646|ref|YP_008797700.1| 271 PDQLKIYPTLVLPGTGLETMWRHGLYKPYSDDELVYVLKEFMKRVPPYVRIARIQREIPLNIVLDGLHIPNLRQMVE 347
                                       89*************************************************************************** PP

                     Radical_SAM_C  78 krl 80 
                                       k+l
  gi|557694646|ref|YP_008797700.1| 348 KEL 350
                                       *97 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   3.5e-26   1.3e-22       5     158 ..      64     254 ..      60     260 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 3.5e-26
                                       SEESS-.-TTTSCCTT................HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTH CS
                                       xxxxxx.xxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlr.CsfCarpet................vrregrgrslsveeileevkelkaekg.vkevilgggepllypdf 63 
                                         C+++ C++C+ +                   ++ g+   ++ve  ++ ++ + ++ + v+ +i+gg      p+f
  gi|557694646|ref|YP_008797700.1|  64 YTCPHGkCIYCPGGAPlgtpqsytgeeaavktAAQLGYDPRKQVEAAVNRLRHMGHRVDkVELIIIGGTFTASPPEF 140
                                       5688877*******99****************999********************9999566666666666666889 PP

                                       HHHHHHHHHTC.................CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHHH CS
                                       xxxxxxxxxxx.................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  64 vellerlakla.................vpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlkl 120
                                       ++++ +++  a                 ++ i+++ +t +t+pd   +ek+  l+e+gv+rv++g++a+dd+ +l  
  gi|557694646|ref|YP_008797700.1| 141 QRWMIKECVDAlngvasssleealrintSSAIHVSGITVETKPDwakREKAVQLVEYGVTRVEIGVQALDDK-ILTT 216
                                       99999999999*************************************************************.**** PP

                                       HTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 121 mnrghtfeevlealeklreagikrvvdrivglpGende 158
                                       +nrgh++e+v+ea+  l++  +k+++++++ lpG + +
  gi|557694646|ref|YP_008797700.1| 217 LNRGHSVEDVVEATADLKDTAFKVCYHIMPNLPGSTPH 254
                                       **********************************9975 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.2   3.4e-10   1.2e-06      33     117 .]     386     488 ..     356     488 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 3.4e-10
                                       C.EEEE.EEET..TEEEEEEEEEEEET....TSTTEEEEEEEEE............SGGGTTSSHHHHHHHHHHHHH CS
                    Acetyltransf_1  33 e.gllv.aeed..geliGfisllkipd....ekggvayieslaV............speyrgkGlGsaLlealeera 89 
                                       + +++v +e++  + l+Gf+++++ p     e ++ + +++l+V              + +++G+G++L++++e ++
  gi|557694646|ref|YP_008797700.1| 386 GlEYFVsVEDEeaDALLGFVRVRIPPRtlrtELEDAGLVRELHVygsmkavgapadETTSQHRGIGKQLMQEAENIV 462
                                       346677544443366************99996678888889999999********77777***************** PP

                                       HHT.TESEE.EEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  90 ree.gikki.vlaveedndaairlYeklGF 117
                                        ee g+ ++ v+    +  + +++Y +lG+
  gi|557694646|ref|YP_008797700.1| 463 YEEhGLSRVaVI----SGAGVRGYYARLGY 488
                                       ***899997444....89999****99**8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.1     3e-09   1.1e-05      63     111 ..     445     493 ..     442     498 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 3e-09
                   Acetyltransf_10  63 yrgqGigkaLleaveee.aekdgikleltvnaspyavpfYeklGFkavge 111
                                        +++Gigk+L++++e+  +e++g++ ++ v +    +++Y +lG++  g+
  gi|557694646|ref|YP_008797700.1| 445 SQHRGIGKQLMQEAENIvYEEHGLS-RVAVISGAGVRGYYARLGYRLEGP 493
                                       59***************56666555.*******************98766 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.3     4e-06     0.014      35      75 ..     444     489 ..     388     490 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4e-06
                                       GGTTSSHHHHHHHHTT......SEEEEE.EEEETHH....HHHHHHHHTTEE CS
                    Acetyltransf_7  35 eyrgkGiGraLleaae......kgiile.qlelnae....kaikfYeklGFe 75 
                                         + +GiG++L++ ae      +g+  + ++           +++Y++lG++
  gi|557694646|ref|YP_008797700.1| 444 TSQHRGIGKQLMQEAEnivyeeHGL--SrVA----VisgaGVRGYYARLGYR 489
                                       5699********9522233333442..2112....122324466******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (499 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3553.45
//
Query:       gi|557694647|ref|YP_008797701.1|  [L=301]
Description: F420-dependent N5,N10-methenyltetrahydromethanopterin reductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-34  120.2   1.1    5.6e-34  118.0   1.1    1.8  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.0   1.1   3.1e-38   5.6e-34      28     314 .]      12     272 ..       5     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 118.0 bits;  conditional E-value: 3.1e-38
                    Bac_luciferase  28 laraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhlsgGRfglg 104
                                        a+++E++Gfd++wv+eh ++    +++f +l+ +a +T+ri lg av+++y++hPa +Aq+aatL +l++ R+++ 
  gi|557694647|ref|YP_008797701.1|  12 AAVLVEKHGFDGLWVSEHFFN----RNSFITLSTIARHTRRILLGPAVVNPYVYHPAQMAQAAATLWELAPHRVRMA 84 
                                       5899*****************....**************************************************** PP

                    Bac_luciferase 105 lgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiPvyvaaaspaglel 181
                                       +g+g + v  ++ G  ++++++    +ve +r  +++  +++     +     ++       i vyv+a +p++++ 
  gi|557694647|ref|YP_008797701.1|  85 IGAGDASVL-KQLGYTREKPVEKVMWAVEEMRNYLKR-LETY-----R-----VSD------IMVYVGAQGPRMVK- 142
                                       *****9999.999**********************32.2233.....2.....333......55***********9. PP

                    Bac_luciferase 182 aarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearaliagld...fyalds 255
                                       a + adg+l++ + +e + e i+ l    a+       ++ ++ l++++ d+ee+A++ a  + a l+      + +
  gi|557694647|ref|YP_008797701.1| 143 ASTKADGVLINWSNLEMLNESIRLLGDDVAK------GFTRAAYLMTSIHDDEEKAWKTAVPYAAYLMigsSLSYLN 213
                                       7889*********************984444......7889*******************77776677667777778 PP

                    Bac_luciferase 256 egagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvde 314
                                       +   +ea ++e  e   +++w++  ++ ++e v+ + ++G p+  +e +++++++g+de
  gi|557694647|ref|YP_008797701.1| 214 RIGVDEAHRKEVEELVISRNWDRLYQVARREWVDFFSVWGKPGRLREFVDEVVDMGFDE 272
                                       8888888888999999********9999****************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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 0.30s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1996.96
//
Query:       gi|557694648|ref|YP_008797702.1|  [L=274]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   98.0   0.1      3e-25   89.3   0.1    2.1  1  Abhydrolase_1    alpha/beta hydrolase fold
    9.8e-24   85.2   0.0    1.1e-23   85.0   0.0    1.0  1  Abhydrolase_6    Alpha/beta hydrolase family
    6.3e-16   58.4   0.0    1.3e-15   57.3   0.0    1.5  1  Hydrolase_4      Serine aminopeptidase, S33
    6.6e-07   29.3   0.0      0.023   14.6   0.0    2.2  2  Ser_hydrolase    Serine hydrolase
    4.1e-06   26.5   0.0      0.013   15.0   0.0    2.3  2  DLH              Dienelactone hydrolase family
    0.00013   20.8   0.0    0.00015   20.6   0.0    1.2  1  Ndr              Ndr family
    0.00025   20.8   0.0      0.005   16.5   0.0    2.5  2  FSH1             Serine hydrolase (FSH1)
     0.0013   18.7   0.0     0.0028   17.6   0.0    1.5  2  UPF0227          Uncharacterised protein family (UPF0227)
     0.0016   18.2   0.3       0.13   12.0   0.1    2.2  2  PGAP1            PGAP1-like protein
     0.0021   17.8   0.1     0.0052   16.4   0.1    1.6  2  Esterase         Putative esterase
     0.0039   17.1   0.0     0.0064   16.4   0.0    1.3  1  Abhydrolase_3    alpha/beta hydrolase fold
     0.0043   17.0   0.0      0.014   15.3   0.0    1.7  2  BAAT_C           BAAT / Acyl-CoA thioester hydrolase C termin
     0.0065   16.0   0.0       0.49    9.8   0.0    2.2  2  Peptidase_S9     Prolyl oligopeptidase family
     0.0079   16.3   0.0      0.015   15.4   0.0    1.5  1  Thioesterase     Thioesterase domain
     0.0088   16.1   0.0      0.014   15.5   0.0    1.3  1  Abhydrolase_4    TAP-like protein
     0.0097   15.7   0.0      0.031   14.0   0.0    1.7  2  Abhydrolase_5    Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.019   14.5   0.0    1.4  1  LIDHydrolase     Lipid-droplet associated hydrolase
      0.013   14.4   0.2      0.082   11.8   0.1    2.1  2  Chlorophyllase2  Chlorophyllase enzyme
      0.016   14.6   0.0       0.11   11.8   0.0    2.0  2  DUF915           Alpha/beta hydrolase of unknown function (DU
       0.13   12.2   0.1       0.22   11.4   0.1    1.3  1  Lipase_3         Lipase (class 3)
       0.16   11.0   0.0       0.69    8.9   0.0    1.7  2  DUF1057          Alpha/beta hydrolase of unknown function (DU
        0.2   10.7   0.0       0.28   10.2   0.0    1.3  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 !   89.3   0.1   3.7e-28     3e-25       2     256 ..      31     260 ..      30     261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 3.7e-28
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       ++v+lhG+++ss +w++    p +++ +f+ ++lDl+G+g S+++p+      ++ sv d+l + l +lg++k+ lv
  gi|557694648|ref|YP_008797702.1|  31 PVVFLHGWAASSFSWRK--TLPVISQ-HFRALALDLPGFGLSKRPPTG----ISLSSVTDILMKTLGRLGVEKFGLV 100
                                       8****************..*****99.*******************75....56888999999************** PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHH CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrh 155
                                       GhSmGG+i+++ a +ype+V +lvl+++    + l+ ++ +    +  + ++++ +     + +++  +  +++ + 
  gi|557694648|ref|YP_008797702.1| 101 GHSMGGAISAHIAVKYPEKVERLVLVNP----SLLGGDDGRRPLAMELARNRFFSVLITRLFVRKYFIKRVLSNIYV 173
                                       ****************************....666666666666677777777777777777666666666666665 PP

                                       HHHHHHHHHCHHHCCHHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHH CS
                     Abhydrolase_1 156 rlvdalkfpdkskrfpssgsdnasslatgalksieqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaled 232
                                       +          ++ + ++++   +    + +++ + w +  +++++       ++ +p l++ g  D++vp +   +
  gi|557694648|ref|YP_008797702.1| 174 DK------SALDDEAVEGYYESVKRAGPVLVEAGNIWREFRTDSVY-------DIRCPKLFVLGGMDNVVPFQKNLE 237
                                       53......44444444445555555555555566666666666666.......4578******************** PP

                                       HHHCHTSEEEEEEETCSSSHHHHS CS
                     Abhydrolase_1 233 laqllpkkrlvvisdagHlafleg 256
                                       laq++   + +v++dagH ++ e+
  gi|557694648|ref|YP_008797702.1| 238 LAQKIGA-EIHVEPDAGHSVHEEK 260
                                       *******.************9987 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.0   0.0   1.4e-26   1.1e-23       1     217 [.      32     264 ..      32     267 .. 0.71

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 1.4e-26
                                       EEEE--GC.....GC..HHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH..CHHH.HHHHCCTT..TTSEEEEEE CS
                     Abhydrolase_6   1 vlllHGagssassWl..vapLaallaagvhvlapDlpGhGrsdpppldled..ladl.aalldelaagggpvvlvGH 72 
                                       v++lHG  +s+ sW+   + +    +++++ la+DlpG+G s +pp++ +   + d+   +l +l  g  ++ lvGH
  gi|557694648|ref|YP_008797702.1|  32 VVFLHGWAASSFSWRktLPVI----SQHFRALALDLPGFGLSKRPPTGISLssVTDIlMKTLGRL--GVEKFGLVGH 102
                                       8*****999999995323344....888999*********8888887776633666665566666..58889***** PP

                                       TCHHHHHHH.HHHCC...EE.EEES-..----TTT...S----TTHHHHHH.TT-CCCCHCCH..........S-HS CS
                     Abhydrolase_6  73 SlGGalala.aapla.lvvg.vlldppptalpagl...laaalelllalla.llrllawlsre..........plpr 132
                                       S+GGa++++ a++++  v++ vl++p   +l  g+   ++ a+el++ +   +l++ ++++r+          ++++
  gi|557694648|ref|YP_008797702.1| 103 SMGGAISAHiAVKYPeKVERlVLVNP---SLLGGDdgrRPLAMELARNRFFsVLIT-RLFVRKyfikrvlsniYVDK 175
                                       *****9999777777766669*****...333333333555555555333333333.33322224444677765555 PP

                                       CCCCHHH...CCCCHCHCCCGHHHHCCHHCHTTCCHHTT-TTGCEEE.CTT-CHHHHCHHCCCH...STTEEETCE. CS
                     Abhydrolase_6 133 lfladed...adaawrarlarlaallaglgllpaaawadlpvpllvl.ggeDplvprllerlla...qagarlpvvl 202
                                       + l+de+   +++++ ++   l    + + +++ + + d+++p l + gg D +vp  +++ l    + ga++ +v 
  gi|557694648|ref|YP_008797702.1| 176 SALDDEAvegYYESVKRAGPVLVEAGNIWREFRTDSVYDIRCPKLFVlGGMDNVVP--FQKNLElaqKIGAEI-HVE 249
                                       777777754336666666666667777888999***********75559*******..888888878888999.*** PP

                                       ..SSS-HHHHSHHHH CS
                     Abhydrolase_6 203 pgaGHlphleepdev 217
                                       p+aGH++h+e+++ +
  gi|557694648|ref|YP_008797702.1| 250 PDAGHSVHEEKAESF 264
                                       *********988876 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   1.6e-18   1.3e-15       7     238 ..      32     260 ..      28     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 1.6e-18
                       Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrse.gkrghvpsfddyvdDlaafvekvkeehpelplfllG 82 
                                       vv++HG a +s    ++     +  f  +alD  G+G s+ +           +  +  ++ k   + + +++ l+G
  gi|557694648|ref|YP_008797702.1|  32 VVFLHGWAASSFSWRKTLPVISQ-HFRALALDLPGFGLSKrP-PT-----GISLSSVTDILMKTLGRLGVEKFGLVG 101
                                       88899999988888888887665.5999***********632.32.....233333333344444466677899*** PP

                       Hydrolase_4  83 hSmGGliallyllrypdkvaglilsaPalkikaklkappllkl.llkllgkllpklqvsnnlkadslsrdpevvaay 158
                                       hSmGG+i+++++ +yp+kv++l+l++P l    + + p +++l  +++++ l+ +l v ++   + + ++  v ++ 
  gi|557694648|ref|YP_008797702.1| 102 HSMGGAISAHIAVKYPEKVERLVLVNPSLLGGDDGRRPLAMELaRNRFFSVLITRLFV-RKYFIKRVLSNIYVDKSA 177
                                       ******************************9999875555555266777777777777.667777777777777777 PP

                       Hydrolase_4 159 eadplv.hgkitvr.lllelldamk....rleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypg 229
                                        +d+ v +   +v+  +  l++a++    + ++++ +i+ P l++ G+ D+vv+ ++  el++++g+   ++++ p 
  gi|557694648|ref|YP_008797702.1| 178 LDDEAVeGYYESVKrAGPVLVEAGNiwreFRTDSVYDIRCPKLFVLGGMDNVVPFQKNLELAQKIGA---EIHVEPD 251
                                       777777544444441333344444311113345677888***************************6...9****** PP

                       Hydrolase_4 230 lyHellnEp 238
                                       + H+++ E+
  gi|557694648|ref|YP_008797702.1| 252 AGHSVHEEK 260
                                       ******997 PP

>> Ser_hydrolase  Serine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.8e-05     0.023      56      90 ..      96     129 ..      85     147 .. 0.90
   2 !   12.7   0.0   0.00011     0.088     112     165 ..     214     267 ..     197     273 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.8e-05
                                       TEEEEEETCHHHHHHHHHHHTTSSSEEEEEEET-- CS
                     Ser_hydrolase  56 kvvlvAHSlgclavlhaaelqlakkvagalLVapa 90 
                                       k  lv HS+g ++++h+a ++ ++kv++ +LV p 
  gi|557694648|ref|YP_008797702.1|  96 KFGLVGHSMGGAISAHIA-VKYPEKVERLVLVNPS 129
                                       5569**************.*************996 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00011
                                       HHCCHCEEEEETTBTTC-HHHHHHHHHHCT-EEEEETT-TTSSGGGT-SS-HHH CS
                     Ser_hydrolase 112 klpfpslvvaSenDpyvsfeeaeelaeawgaelvdlgeaGHinadsgfgswpeg 165
                                         + p+l v    D++v+f++  ela+++gae+ + + aGH   ++  +s++++
  gi|557694648|ref|YP_008797702.1| 214 DIRCPKLFVLGGMDNVVPFQKNLELAQKIGAEIHVEPDAGHSVHEEKAESFNNV 267
                                       5667788888889****************************9988888888765 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00089      0.73      90     124 ..      87     122 ..      79     159 .. 0.87
   2 !   15.0   0.0   1.6e-05     0.013     139     199 ..     211     266 ..     203     268 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00089
                               DLH  90 ksvpevstkkvgvvGfCmGGalalllaaev.pevda 124
                                       k+ ++  ++k+g+vG  mGGa++  +a +  ++v++
  gi|557694648|ref|YP_008797702.1|  87 KTLGRLGVEKFGLVGHSMGGAISAHIAVKYpEKVER 122
                                       566677899******************998566665 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.6e-05
                               DLH 139 eaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsresyne 199
                                        + +i +p l+++g+ D+++p+++  +l++++      +e++v p+agH+ +++++es+n+
  gi|557694648|ref|YP_008797702.1| 211 SVYDIRCPKLFVLGGMDNVVPFQKNLELAQKI-----GAEIHVEPDAGHSVHEEKAESFNN 266
                                       567899*****************755555555.....89999**************99985 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.8e-07   0.00015      52     134 ..      52     130 ..      41     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.8e-07
                                       HHTTSEEEEEE-TT-STT-----TT-----HHHHHTTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEE CS
                               Ndr  52 ilekfvilhvdaPGqeegaaslpedyqfpslddladqllavldhfklksviglGvgaGAyilarfalkhperveglv 128
                                       i ++f  l +d PG     +  p++    sl +++d l++ l  + ++++  +G   G  i a+ a+k+pe+ve lv
  gi|557694648|ref|YP_008797702.1|  52 ISQHFRALALDLPGFGLS-KRPPTG---ISLSSVTDILMKTLGRLGVEKFGLVGHSMGGAISAHIAVKYPEKVERLV 124
                                       566666666666666543.333445...68999999***************************************** PP

                                       EES--- CS
                               Ndr 129 Linits 134
                                       L+n+  
  gi|557694648|ref|YP_008797702.1| 125 LVNPSL 130
                                       ***853 PP

>> FSH1  Serine hydrolase (FSH1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.9   1.6e+03       7      33 ..      32      58 ..      29      64 .. 0.80
   2 !   16.5   0.0   6.1e-06     0.005     104     202 ..      97     256 ..      69     263 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.9
                              FSH1  7 iLcLhGytqsgeiFraktsalrkllkk 33
                                      + +LhG++ s+  +r+ +  + ++++ 
  gi|557694648|ref|YP_008797702.1| 32 VVFLHGWAASSFSWRKTLPVISQHFRA 58
                                      789*****9999999888877777765 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6.1e-06
                              FSH1 104 dGiiGFSqGaalaallaslleellkea......................................shpslkfailvs 142
                                        G++G S G+a++a +a +  e+ ++                                                   
  gi|557694648|ref|YP_008797702.1|  97 FGLVGHSMGGAISAHIAVKYPEKVERLvlvnpsllggddgrrplamelarnrffsvlitrlfvrkY----------- 162
                                       688899999998888888888877766788888888888777776655444444444333333330........... PP

                              FSH1 143 Gfkleepk.............................................yeeyyeedkiqtptLhvlGelDtv 174
                                                                                             ++    ++i++p L+vlG  D+v
  gi|557694648|ref|YP_008797702.1| 163 -------FikrvlsniyvdksalddeavegyyesvkragpvlveagniwrefrTDSV---YDIRCPKLFVLGGMDNV 229
                                       .......24444455555555555555556655555555555555554333224444...489************** PP

                              FSH1 175 vdeerseaLaeafknsskvlkHpggHfv 202
                                       v+ ++  +La+++   +  ++ + gH+v
  gi|557694648|ref|YP_008797702.1| 230 VPFQKNLELAQKIGA-EIHVEPDAGHSV 256
                                       ************999.888899999988 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   3.4e-06    0.0028       2      91 ..      32     130 ..      31     135 .. 0.71
   2 ?   -3.4   0.0       9.7   7.9e+03     144     162 ..     226     244 ..     218     263 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.4e-06
                           UPF0227   2 llYlHGFdSSPlshkaql..lsqfiaedvlaielsvlklkedpqqalke....leklvaelgddnillvGssLGGyy 72 
                                       +++lHG++ S  s ++ l  +sq + +  l++    l  +      l      l k +  lg ++ +lvG s+GG  
  gi|557694648|ref|YP_008797702.1|  32 VVFLHGWAASSFSWRKTLpvISQHFRALALDLPGFGLSKRPPTGISLSSvtdiLMKTLGRLGVEKFGLVGHSMGGAI 108
                                       5899***9999999987533778777777766544444444433444440001456666677777************ PP

                           UPF0227  73 atrlgerfglrq...vllnPal 91 
                                       +++++ ++  +    vl+nP l
  gi|557694648|ref|YP_008797702.1| 109 SAHIAVKYPEKVerlVLVNPSL 130
                                       ********8766678*****86 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.7
                           UPF0227 144 qDevldyrravaefraaae 162
                                        D+v++ +++++  +++  
  gi|557694648|ref|YP_008797702.1| 226 MDNVVPFQKNLELAQKIGA 244
                                       5666666666555554433 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.034        28       4      23 ..      29      48 ..      26      68 .. 0.79
   2 !   12.0   0.1   0.00016      0.13      93     119 ..      97     120 ..      80     129 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.034
                             PGAP1  4 GipVlFvpGnagsykqvrsl 23
                                      G pV+F++G a s   +r  
  gi|557694648|ref|YP_008797702.1| 29 GQPVVFLHGWAASSFSWRKT 48
                                      99**********99999865 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00016
                             PGAP1  93 viliGHSmGGivara.altlknyikqsv 119
                                         l+GHSmGG ++   a+++++    +v
  gi|557694648|ref|YP_008797702.1|  97 FGLVGHSMGGAISAHiAVKYPE----KV 120
                                       569*******998430344443....44 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   6.4e-06    0.0052     108     143 ..      87     123 ..      79     133 .. 0.78
   2 ?   -3.0   0.0       5.5   4.5e+03     219     241 ..     178     208 ..     174     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.4e-06
                                       HHCSEECCC.EEEEEETHHHHHHHHHHHCSTTTCCEE CS
                          Esterase 108 anfrtapdg.ravaGqSmGGlgALilalkhpdrFgsv 143
                                       +++         ++G+SmGG ++ ++a+k+p++  + 
  gi|557694648|ref|YP_008797702.1|  87 KTLGRLGVEkFGLVGHSMGGAISAHIAVKYPEKVERL 123
                                       5555555555689*******************98765 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.5
                                       CCCCCCTT-SCCCC........--SSHHHHH CS
                          Esterase 219 laargvegedheyd........GghsweyWr 241
                                       l++++veg++++++        +g+ w+ +r
  gi|557694648|ref|YP_008797702.1| 178 LDDEAVEGYYESVKragpvlveAGNIWREFR 208
                                       6778899999999888777777888887777 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   7.8e-06    0.0064      71     172 ..      95     199 ..      80     203 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.8e-06
                                       CEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE....-SSTSSTTSHHHHHCHHT...TTSSSSCHHHHH.H CS
                     Abhydrolase_3  71 srivlaGdSaGGnlaaavalrardegepkvagqvliyP....vtdlertesesikkaeel...adgplltraald.l 139
                                       ++  l+G S GG ++a++a++  ++    v+ +vl+ P    + d +r+   +  +++ +    ++ ++ +  ++  
  gi|557694648|ref|YP_008797702.1|  95 EKFGLVGHSMGGAISAHIAVKYPEK----VERLVLVNPsllgGDDGRRPLAMELARNRFFsvlITRLFVRKYFIKrV 167
                                       6889*******************97....999******888644334554444433333311122222233333313 PP

                                       HHHHHSSGGGGGSTTTSGGGCS-SST---EEEE CS
                     Abhydrolase_3 140 fwrlylpeadrddplaspllaedlsglpptlvv 172
                                       + ++y++++ +dd +++  ++ +++++ p+lv 
  gi|557694648|ref|YP_008797702.1| 168 LSNIYVDKSALDDEAVEGYYE-SVKRAGPVLVE 199
                                       345677788888888885555.88888888885 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 !   15.3   0.0   1.7e-05     0.014      22      56 ..      95     130 ..      85     138 .. 0.91
   2 ?   -1.6   0.0       2.6   2.2e+03     113     136 ..     214     237 ..     211     257 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                                       SSEEEEEETHHHHHHHHHHHHSS.SEEEEEEES--S CS
                            BAAT_C  22 dkigllGiSkGgelalllasflk.kisavvlingsa 56 
                                       +k gl+G+S Gg +   +a++++ k++ +vl+n+s 
  gi|557694648|ref|YP_008797702.1|  95 EKFGLVGHSMGGAISAHIAVKYPeKVERLVLVNPSL 130
                                       689*******************************96 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.6
                                       G--SEEEEEEETT-SSS-HHHHHH CS
                            BAAT_C 113 kakgpillvvgedDknwpSkesae 136
                                       ++++p l+v g  D+++p ++  e
  gi|557694648|ref|YP_008797702.1| 214 DIRCPKLFVLGGMDNVVPFQKNLE 237
                                       678888999999998888665553 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.039        32      63      88 ..      94     119 ..      80     130 .. 0.79
   2 !    9.8   0.0    0.0006      0.49     142     193 ..     215     261 ..     200     273 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.039
                                       GGGEEEEEETHHHHHHHHHHHH-GGG CS
                      Peptidase_S9  63 serlaitGgSyGGyltgaalnqrpdl 88 
                                        e+ ++ G+S GG  ++ ++ + p++
  gi|557694648|ref|YP_008797702.1|  94 VEKFGLVGHSMGGAISAHIAVKYPEK 119
                                       578999***********999998886 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0006
                                       ---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHH CS
                      Peptidase_S9 142 aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkpra 193
                                       + +p L++ G +D+ vp+++ l+l+++       ++++++pd+gH+v +++a
  gi|557694648|ref|YP_008797702.1| 215 IRCPKLFVLGGMDNVVPFQKNLELAQKI-----GAEIHVEPDAGHSVHEEKA 261
                                       567889999999*****99999998765.....469*********9885554 PP

>> Thioesterase  Thioesterase domain
   #    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       3      89 ..      32     118 ..      30     126 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.9e-05
                                       EEEE--TTCCSGGGHHHHHHCTTCEEEEEEECSTTST..SHHHCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHH CS
                      Thioesterase   3 LflfppagGsasvfrslasklsdpvvevlavqlpgre..rdepplesieelaaeyaealrqiqpegPyalfGhSlGg 77 
                                       ++ +++  +s+ + r+    +s+   + la+ lpg++  +  p+  s+ ++ + ++++l +   e  + l+GhS+Gg
  gi|557694648|ref|YP_008797702.1|  32 VVFLHGWAASSFSWRKTLPVISQH-FRALALDLPGFGlsKRPPTGISLSSVTDILMKTLGRLGVE-KFGLVGHSMGG 106
                                       566666666666666666666665.788999999999755555667889***********99999.9********** PP

                                       HHHHHHHHHHHH CS
                      Thioesterase  78 llAfevArqLes 89 
                                       ++   +A ++ +
  gi|557694648|ref|YP_008797702.1| 107 AISAHIAVKYPE 118
                                       **9999988765 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.7e-05     0.014      35      92 ..     217     273 ..     204     274 .] 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.7e-05
                     Abhydrolase_4  35 apvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLl 92 
                                        p L++ +  D+++P++   +la+++g a+  ++ ++GH + +++ ++ ++ + ++L+
  gi|557694648|ref|YP_008797702.1| 217 CPKLFVLGGMDNVVPFQKNLELAQKIG-AEIHVEPDAGHSVHEEKAESFNNVILRFLR 273
                                       68899**********************.99999*********9*************97 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   3.8e-05     0.031      55      87 ..      93     126 ..      76     134 .. 0.87
   2 ?   -2.0   0.0       3.2   2.6e+03      95     127 ..     211     243 ..     208     249 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.8e-05
                     Abhydrolase_5  55 klekfvvgGhslGGvvasrfaaee.ekiegvvfl 87 
                                       ++ekf + Ghs+GG++++++a +  ek+e +v++
  gi|557694648|ref|YP_008797702.1|  93 GVEKFGLVGHSMGGAISAHIAVKYpEKVERLVLV 126
                                       5899****************99875799988875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.2
                     Abhydrolase_5  95 elselskkvlsivgteDgvlnvkslekakkflp 127
                                       ++ +   + l + g  D+v+++++  + ++++ 
  gi|557694648|ref|YP_008797702.1| 211 SVYDIRCPKLFVLGGMDNVVPFQKNLELAQKIG 243
                                       555666788889999999999998877777665 PP

>> LIDHydrolase  Lipid-droplet associated hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   2.3e-05     0.019      85     148 ..      95     155 ..      78     196 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                      LIDHydrolase  85 vklilvGHSvGaYialevlkrlsersikkvvlLfPtiediakSpngkkltkllaylpflalvvg 148
                                        k+ lvGHS G  i+ +++ +++e+ ++++vl+ P +    + ++   +     + +f+++++ 
  gi|557694648|ref|YP_008797702.1|  95 EKFGLVGHSMGGAISAHIAVKYPEK-VERLVLVNPSLLGGDDGRRPLAMELA--RNRFFSVLIT 155
                                       6889********************9.*********98776666655555533..4444443333 PP

>> Chlorophyllase2  Chlorophyllase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0001     0.082      21     126 ..      33     128 ..      26     139 .. 0.70
   2 ?   -3.7   0.0       5.5   4.5e+03     115     132 ..     239     256 ..     232     268 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                   Chlorophyllase2  21 lflhGylllnslYsqlLkhiashgfivvapqlyk..vaeadakeiksaakvlnWlakgLesvlpeevepdlsklals 95 
                                       +flhG+   +  +++ L  i+ h f ++a  l    ++++  + i s + v++ l k L        +  ++k++l+
  gi|557694648|ref|YP_008797702.1|  33 VFLHGWAASSFSWRKTLPVISQH-FRALALDLPGfgLSKRPPTGI-SLSSVTDILMKTLG-------RLGVEKFGLV 100
                                       56777777777777777666665.666666666632222222333.34455555555555.......345789**** PP

                   Chlorophyllase2  96 gHSrGgktafalalgkaktslkfsaligvdP 126
                                       gHS Gg +++++a+++ +   k++ l+ v+P
  gi|557694648|ref|YP_008797702.1| 101 GHSMGGAISAHIAVKYPE---KVERLVLVNP 128
                                       ***************999...8999999988 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.5
                   Chlorophyllase2 115 slkfsaligvdPvagask 132
                                       + k+ a i v+P ag s 
  gi|557694648|ref|YP_008797702.1| 239 AQKIGAEIHVEPDAGHSV 256
                                       347888888999888653 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 ?   -0.2   0.0      0.61     5e+02      12      29 ..      30      47 ..      26      55 .. 0.81
   2 ?   11.8   0.0   0.00013      0.11      92     124 ..      85     116 ..      74     123 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.61
                            DUF915 12 iPtifihGyggtaeslne 29
                                       P++f+hG+ ++  s  +
  gi|557694648|ref|YP_008797702.1| 30 QPVVFLHGWAASSFSWRK 47
                                      79*******999877665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
                            DUF915  92 vlseLkkkYnikkfnavGhSmGglaltsYleey 124
                                        ++ L  + +++kf +vGhSmGg   +  + +y
  gi|557694648|ref|YP_008797702.1|  85 LMKTLG-RLGVEKFGLVGHSMGGAISAHIAVKY 116
                                       455554.5689************9877666666 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00027      0.22      57      88 ..      87     118 ..      73     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                                       HHHHHTT-EEEEEEEETHHHHHHHHHHHHHHH CS
                          Lipase_3  57 rllekypeysivvtGHSLGgalAlLaaldlve 88 
                                       + l +    ++ ++GHS+Gga+++ +a+ + e
  gi|557694648|ref|YP_008797702.1|  87 KTLGRLGVEKFGLVGHSMGGAISAHIAVKYPE 118
                                       5555555568899*********9877776655 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 ?    8.9   0.0   0.00084      0.69      91     159 ..      80     153 ..      54     178 .. 0.79
   2 ?   -0.2   0.0      0.51   4.2e+02     214     255 ..     218     259 ..     204     267 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00084
                           DUF1057  91 syskalleelelk..gklillghsRGcenaLqlavtl..eahGlvlinptGlrvhkgirpls.rletielvykl 159
                                       s ++ l+++l     +k  l+ghs G+  +  +av++  ++  lvl+np  l    g rpl+  l +  +++ l
  gi|557694648|ref|YP_008797702.1|  80 SVTDILMKTLGRLgvEKFGLVGHSMGGAISAHIAVKYpeKVERLVLVNPSLLGGDDGRRPLAmELARNRFFSVL 153
                                       6678899998754489************99999*999667789******9998888888853134444455555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.51
                           DUF1057 214 kklivfggkDflveeeiveealkkfegldhfnidkeiseeek 255
                                        kl+v gg D +v  ++ +e+++k   + h + d+ +s +e 
  gi|557694648|ref|YP_008797702.1| 218 PKLFVLGGMDNVVPFQKNLELAQKIGAEIHVEPDAGHSVHEE 259
                                       479999*******************99999988777765543 PP

>> DUF2048  Abhydrolase domain containing 18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00034      0.28     165     204 ..      84     123 ..      42     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00034
                           DUF2048 165 vllhwlereGyGplgltGlSmGGhmaslaasnwpkplvlv 204
                                        l++ l r G  ++gl G SmGG  ++  a ++p  +  +
  gi|557694648|ref|YP_008797702.1|  84 ILMKTLGRLGVEKFGLVGHSMGGAISAHIAVKYPEKVERL 123
                                       588899999******************9999999887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1930.36
//
Query:       gi|557694649|ref|YP_008797703.1|  [L=235]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-23   79.1  23.6    1.4e-07   31.0   4.3    5.7  5  Hexapep    Bacterial transferase hexapeptide (six repeats)
    5.4e-12   45.2  23.3    1.9e-06   27.5   4.9    5.8  5  Hexapep_2  Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
       0.85    7.7   2.7        1.2    7.2   0.6    1.9  2  DUF4954    Domain of unknown function (DUF4954)


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 ?    0.4   0.0       0.1     6e+02       2      16 ..      25      39 ..      14      40 .. 0.62
   2 !   26.4   0.8   6.3e-10   3.8e-06       2      35 ..      69     102 ..      68     109 .. 0.79
   3 !   20.2   0.3   5.9e-08   0.00035       2      35 ..     105     138 ..     104     139 .. 0.93
   4 !   11.8   0.1   2.6e-05      0.16       2      17 ..     141     156 ..     140     158 .. 0.61
   5 !   31.0   4.3   2.3e-11   1.4e-07       3      36 .]     170     203 ..     168     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.1
                                      EEEETTEEE-TTEEE CS
                           Hexapep  2 tvIGsnvlIgpfavi 16
                                      t IG+ ++++  ++i
  gi|557694649|ref|YP_008797703.1| 25 TEIGEATFVDDMVTI 39
                                      456666666655555 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 6.3e-10
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       ++IG ++lI+ +++i++ V+I  +v +g++v i+
  gi|557694649|ref|YP_008797703.1|  69 SFIGPGCLIRRGCIIYDEVIIEGDVELGHNVLIR 102
                                       7999999999988888888888888888888775 PP

  == domain 3  score: 20.2 bits;  conditional E-value: 5.9e-08
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       t I  ++ Ig+++++ g V +G++v I ++v+i 
  gi|557694649|ref|YP_008797703.1| 105 TMIRAGSRIGSGSMLDGTVLVGRGVNIQSNVYIP 138
                                       679999**************************96 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 2.6e-05
                                       EEEETTEEE-TTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfavig 17 
                                       t+I +nv+Igp++v  
  gi|557694649|ref|YP_008797703.1| 141 TKIMDNVFIGPNVVMT 156
                                       5666666666666654 PP

  == domain 5  score: 31.0 bits;  conditional E-value: 2.3e-11
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                       +I  +++Ig++avi+++V++G+++++gag+v+++
  gi|557694649|ref|YP_008797703.1| 170 TIATGAIIGAGAVILPGVEVGEGAVVGAGSVVTR 203
                                       677799**************************85 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 ?   -2.0   0.0      0.54   3.2e+03      12      22 ..      17      29 ..      17      29 .. 0.79
   2 !    6.5   2.2    0.0011       6.8       4      32 ..      71     107 ..      68     109 .. 0.49
   3 !    9.3   0.9   0.00015      0.93       8      32 ..     111     137 ..     107     138 .. 0.91
   4 !    7.1   0.0   0.00075       4.5       6      15 ..     145     154 ..     141     163 .. 0.76
   5 !   27.5   4.9   3.2e-10   1.9e-06       8      34 .]     175     203 ..     173     203 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.54
                                      TT-EE.S.EEE-T CS
                         Hexapep_2 12 anagi.G.vslGd 22
                                      +na++ G +++G+
  gi|557694649|ref|YP_008797703.1| 17 PNAYVfGaTEIGE 29
                                      6999888788885 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0011
                                       E-TT-EE-TT-EE.......S.EEE-TT-EE-TT-EE CS
                         Hexapep_2   4 IGdnCliGanagi.......G.vslGdncvvgaGvvi 32 
                                       IG  Cli   ++i       G v+lG n+ + +G +i
  gi|557694649|ref|YP_008797703.1|  71 IGPGCLIRRGCIIydeviieGdVELGHNVLIRSGTMI 107
                                       3333344334443333334533666666666666666 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00015
                                       -EE-TT-EE.S.EEE-TT-EE-TT-EE CS
                         Hexapep_2   8 CliGanagi.G.vslGdncvvgaGvvi 32 
                                       + iG+ +   G v +G+++ ++++v+i
  gi|557694649|ref|YP_008797703.1| 111 SRIGSGSMLdGtVLVGRGVNIQSNVYI 137
                                       689*****988899************9 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.00075
                                       TT-EE-TT-E CS
                         Hexapep_2   6 dnCliGanag 15 
                                       dn++iG+n +
  gi|557694649|ref|YP_008797703.1| 145 DNVFIGPNVV 154
                                       8999999876 PP

  == domain 5  score: 27.5 bits;  conditional E-value: 3.2e-10
                                       -EE-TT-EE..SEEE-TT-EE-TT-EE-S CS
                         Hexapep_2   8 CliGanagi..GvslGdncvvgaGvvita 34 
                                        +iGa a+i  Gv++G+++vvgaG+v+t+
  gi|557694649|ref|YP_008797703.1| 175 AIIGAGAVIlpGVEVGEGAVVGAGSVVTR 203
                                       68*************************96 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.6    0.0002       1.2     217     257 ..      92     134 ..      69     146 .. 0.83
   2 ?   -0.5   0.1     0.043   2.6e+02     217     254 ..     146     183 ..     139     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0002
                           DUF4954 217 pveiGegViled.fiissGskikdgavis.rcfvGqavklkkq 257
                                        ve+G++V ++  ++i +Gs+i  g+++   ++vG++v+++ +
  gi|557694649|ref|YP_008797703.1|  92 DVELGHNVLIRSgTMIRAGSRIGSGSMLDgTVLVGRGVNIQSN 134
                                       6899****987626899***********83679******9876 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.043
                           DUF4954 217 pveiGegViledfiissGskikdgavisrcfvGqavkl 254
                                        v iG +V++++     Gs +k  ++++ +++G +  +
  gi|557694649|ref|YP_008797703.1| 146 NVFIGPNVVMTNDPYPVGSPLKGPTIATGAIIGAGAVI 183
                                       68899999999999999999999999999999988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); 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 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1780.46
//
Query:       gi|557694650|ref|YP_008797704.1|  [L=102]
Description: translation initiation factor SUI1 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-18   65.8   0.3    4.7e-18   65.5   0.3    1.1  1  SUI1      Translation initiation factor SUI1
  ------ inclusion threshold ------
      0.019   14.7   1.3      0.026   14.2   1.3    1.2  1  DTW       DTW domain
      0.048   14.0   0.2      0.073   13.4   0.2    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 !   65.5   0.3   7.8e-22   4.7e-18       2      75 ..      24      93 ..      23      95 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 7.8e-22
                              SUI1  2 kpkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekyg 75
                                      +++++i+le r+ +K  T+++gl   + dl+++a++lk+++ac+g v kdg  +i +QGd+r++v+++L++  g
  gi|557694650|ref|YP_008797704.1| 24 QQRVKIKLELRKWNKPTTVIEGLNGSKKDLQEIASKLKSTLACGGVV-KDG--VILLQGDHRERVRKALVDL-G 93
                                      899*******************************************8.999..9***************986.6 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.3   4.3e-06     0.026       2      29 ..       3      29 ..       2      42 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-06
                               DTW  2 elCerCllpaevclcsslppleklpikv 29
                                      e+C++C lp++ c+c+ + + e++++k+
  gi|557694650|ref|YP_008797704.1|  3 EICATCGLPKSICVCETISR-EQQRVKI 29
                                      68******************.7777776 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 ?   13.4   0.2   1.2e-05     0.073      22      79 ..      35      93 ..      22      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                              Img2 22 ggtkkltvirkieGDiaal...redLrkaleelvkvnevtgkieikGdrveevkkfLeskg 79
                                      + +k +tvi   +G+ ++l   +++L+++l+  +    + g i ++Gd++e+v+k L ++g
  gi|557694650|ref|YP_008797704.1| 35 KWNKPTTVIEGLNGSKKDLqeiASKLKSTLA--CGGVVKDGVILLQGDHRERVRKALVDLG 93
                                      468999********76655000556777777..66667899***************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 843.75
//
Query:       gi|557694651|ref|YP_008797705.1|  [L=307]
Description: transcription initiation factor TFIIB [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  100.9   5.2    7.7e-14   51.5   0.2    2.3  2  TFIIB            Transcription factor TFIIB repeat
    1.5e-13   50.0   1.9    2.7e-13   49.2   1.9    1.4  1  TF_Zn_Ribbon     TFIIB zinc-binding
    1.5e-06   28.0   1.7      0.001   18.8   0.3    2.1  2  Cyclin_N         Cyclin, N-terminal domain
    5.6e-06   26.2   0.1     0.0045   16.9   0.0    2.6  2  HTH_11           HTH domain
    6.8e-06   25.8   0.0       0.11   12.3   0.0    2.7  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    0.00032   20.4   1.9      0.049   13.4   0.0    3.1  2  HTH_23           Homeodomain-like domain
    0.00034   20.6   0.1     0.0079   16.2   0.0    2.6  2  HTH_3            Helix-turn-helix
    0.00043   20.1   0.4    0.00094   19.0   0.4    1.5  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    0.00058   19.8   0.1       0.35   10.9   0.0    2.6  2  HTH_36           Helix-turn-helix domain
     0.0023   17.5   0.0        2.2    7.9   0.0    2.6  2  HTH_24           Winged helix-turn-helix DNA-binding
     0.0036   16.7   0.1      0.055   12.9   0.0    2.6  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
     0.0051   16.4   0.1      0.052   13.2   0.0    2.4  2  Sigma70_r4_2     Sigma-70, region 4
     0.0067   16.4   0.0      0.054   13.5   0.0    2.3  2  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.009   15.8   0.2      0.071   12.9   0.0    2.5  2  TetR_N           Bacterial regulatory proteins, tetR family
     0.0093   15.7   1.3      0.022   14.5   1.3    1.6  1  Ribosomal_S27e   Ribosomal protein S27
     0.0095   16.0   0.9       0.83    9.8   0.0    3.4  4  HTH_28           Helix-turn-helix domain
  ------ inclusion threshold ------
       0.01   15.6   0.3       0.15   11.9   0.1    2.6  2  LacI             Bacterial regulatory proteins, lacI family
      0.012   15.6   0.0         11    6.2   0.0    2.7  3  HTH_Mga          M protein trans-acting positive regulator (M
      0.017   14.6   0.3      0.069   12.7   0.0    2.2  2  Sigma70_r4       Sigma-70, region 4
      0.018   14.7   0.0        1.5    8.5   0.0    2.6  2  GntR             Bacterial regulatory proteins, gntR family
      0.031   14.6   1.0       0.71   10.3   0.0    2.8  3  Rrf2             Transcriptional regulator
      0.046   13.7   0.0       0.19   11.7   0.0    2.0  1  Phage_terminase  Phage terminase small subunit
      0.051   13.2   0.5        2.6    7.7   0.0    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.054   13.6   0.3        1.5    8.9   0.0    2.6  2  Cyclin_C         Cyclin, C-terminal domain
      0.061   13.3   0.1       0.11   12.5   0.1    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.083   12.8   0.3       0.23   11.4   0.3    1.7  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.087   12.9   0.3       0.18   11.8   0.3    1.5  1  DZR              Double zinc ribbon
        0.1   13.1   0.2       0.26   11.9   0.0    1.8  1  RPA_interact_C   Replication protein A interacting C-terminal
       0.12   12.4   3.0          5    7.2   0.3    2.9  3  HypA             Hydrogenase/urease nickel incorporation, met
       0.15   11.5   2.1        4.2    6.9   2.0    2.3  2  zf-ribbon_3      zinc-ribbon domain
       0.17   11.7   0.4       0.42   10.4   0.4    1.7  1  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
       0.19   11.7   1.3         18    5.4   0.1    2.4  2  YhfH             YhfH-like protein
       0.21   11.8   0.3       0.43   10.8   0.3    1.5  1  IBR              IBR domain, a half RING-finger domain
       0.25   11.1   2.4        1.8    8.4   2.2    2.2  2  zinc_ribbon_2    zinc-ribbon domain
       0.29   11.1   1.7       0.31   11.0   0.3    1.7  1  zinc-ribbons_6   zinc-ribbons


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 !   51.5   0.2   1.5e-16   7.7e-14       5      61 ..     130     186 ..     126     197 .. 0.89
   2 !   51.3   1.1   1.7e-16   8.7e-14       1      71 []     221     291 ..     221     291 .. 0.98

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1.5e-16
                                       HHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHH CS
                             TFIIB   5 adaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeis 61 
                                       +d+l L+++Va++A  ++++al+ +++ Grs ++i+AA+ y Acr+ ++ r ++e+ 
  gi|557694651|ref|YP_008797705.1| 130 VDKLRLSQTVAERAMLIYRRALRAGLVRGRSIKSIMAAATYAACRMLGTPRDLREFE 186
                                       79*****************************************************96 PP

  == domain 2  score: 51.3 bits;  conditional E-value: 1.7e-16
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++++a++++L +   ++A  l+++a+++k + G+ p giaAA+ly+Ac+    + tqk+i++ + V+e+t+
  gi|557694651|ref|YP_008797705.1| 221 VNKIAAKVGLDQRTVQEAIRLLNEAVKRKATVGKDPVGIAAAALYMACQETTQNLTQKDIAKAAGVTEVTV 291
                                       6899********9999*****************************************************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 !   49.2   1.9   5.3e-16   2.7e-13       3      42 ..      12      51 ..      11      52 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 5.3e-16
                                      ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHH CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewre 42
                                      CP+Cg+++lv+D  +ge++C+ CG V+++ ++d gpewr 
  gi|557694651|ref|YP_008797705.1| 12 CPECGNEMLVTDQRTGEITCSVCGFVIQEKDVDMGPEWRN 51
                                      **************************************95 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.3     2e-06     0.001      10     123 ..      95     209 ..      89     212 .. 0.85
   2 !    8.4   0.1    0.0033       1.7      38      87 ..     221     270 ..     218     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2e-06
                                       HCHTS-STTCTTCTSSS-H.HHH..HHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHH CS
                          Cyclin_N  10 elkflpkpdyldqqpelnp.emR..ailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLll 83 
                                       +++++ + + ld  +++n+ e+R  +++++ l   + k++l++ ++  a+ ++ R l+   v+ + ++ ++a++ + 
  gi|557694651|ref|YP_008797705.1|  95 TREKMIRLKKLDATSQINSsETRnlQQAVNILQIYVDKLRLSQTVAERAMLIYRRALRAGLVRGRSIKSIMAAATYA 171
                                       4456666666777777777777733689999********************************************** PP

                                       HHHHHSSS---HHHHHHHTTTSS-HHHHHHHHHHHHHHTT CS
                          Cyclin_N  84 AaKveeisppkledlvyitdeafteeeilemErliLetLn 123
                                       A+++  + p +l+++      a+++++i +  rl+L+ L 
  gi|557694651|ref|YP_008797705.1| 172 ACRMLGT-PRDLREFERSYP-AVKRKTIAQGYRLLLKHLG 209
                                       ****999.9******99955.999************9996 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0033
                                       HHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHH CS
                          Cyclin_N  38 lvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKv 87 
                                       + ++a+k+ l+++t+  a+++l+  +++k +  ++   ++a++L++A++ 
  gi|557694651|ref|YP_008797705.1| 221 VNKIAAKVGLDQRTVQEAIRLLNEAVKRKATVGKDPVGIAAAALYMACQE 270
                                       66889999*******************9999999999***********85 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.014       7.1      16      42 ..     219     245 ..     215     255 .. 0.88
   2 !   16.9   0.0   8.8e-06    0.0045      11      43 ..     270     302 ..     262     307 .] 0.85

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.014
                            HTH_11  16 isgeeLAeeLnvSrrtvrrdIkaLeel 42 
                                       i  +++A + ++  rtv+  I+ L+e+
  gi|557694651|ref|YP_008797705.1| 219 IYVNKIAAKVGLDQRTVQEAIRLLNEA 245
                                       66789*******************996 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 8.8e-06
                            HTH_11  11 eargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43 
                                       e++++++ +++A+  +v++ tvr++ k L++ +
  gi|557694651|ref|YP_008797705.1| 270 ETTQNLTQKDIAKAAGVTEVTVRNRFKGLKDVL 302
                                       56667************************9876 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 !   10.6   0.0   0.00073      0.38      14      39 ..     215     240 ..     214     243 .. 0.89
   2 !   12.3   0.0   0.00022      0.11      19      41 ..     276     298 ..     272     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00073
                     HTH_AsnC-type  14 edaRisyaeLAervGlSestvlrRvr 39 
                                       +d++i + ++A++vGl++ tv++ +r
  gi|557694651|ref|YP_008797705.1| 215 ADPSIYVNKIAAKVGLDQRTVQEAIR 240
                                       68899999**************9887 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00022
                     HTH_AsnC-type  19 syaeLAervGlSestvlrRvrrL 41 
                                       + +++A++ G++e tv++R + L
  gi|557694651|ref|YP_008797705.1| 276 TQKDIAKAAGVTEVTVRNRFKGL 298
                                       789****************9866 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.038        20      22      42 ..     223     243 ..     219     248 .. 0.86
   2 !   13.4   0.0   9.5e-05     0.049       8      44 ..     261     296 ..     259     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.038
                            HTH_23  22 eIAreLgvsrrTvyrwlkryr 42 
                                       +IA++ g  +rTv+  ++  +
  gi|557694651|ref|YP_008797705.1| 223 KIAAKVGLDQRTVQEAIRLLN 243
                                       7*************9988765 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.5e-05
                            HTH_23   8 lrillllae....GlsvreIAreLgvsrrTvyrwlkryree 44 
                                       + +l+++ +     l++++IA++ gv++ Tv++    +  +
  gi|557694651|ref|YP_008797705.1| 261 AAALYMACQettqNLTQKDIAKAAGVTEVTVRNR---F--K 296
                                       5688888877888******************954...4..3 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.77   3.9e+02      15      27 ..     224     236 ..     221     241 .. 0.80
   2 !   16.2   0.0   1.5e-05    0.0079       8      32 ..     273     297 ..     269     304 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.77
                                       HHHHHTSSHHHHH CS
                             HTH_3  15 LAeklGvsrstis 27 
                                       +A+k+G+ ++t++
  gi|557694651|ref|YP_008797705.1| 224 IAAKVGLDQRTVQ 236
                                       7999999999987 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.5e-05
                                       TTHHHHHHHHHHTSSHHHHHHHHTT CS
                             HTH_3   8 lglsqeeLAeklGvsrstisriEnG 32 
                                       ++l+q+++A+++Gv+  t+++ ++G
  gi|557694651|ref|YP_008797705.1| 273 QNLTQKDIAKAAGVTEVTVRNRFKG 297
                                       79******************99999 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 !   19.0   0.4   1.8e-06   0.00094       4      29 ..      12      36 ..      10      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-06
                                      ESTTTSBEEEEECSCCCEEEESSSS- CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegknfeCrqCgY 29
                                      Cp+CgN +l+++ + g +  C+ Cg 
  gi|557694651|ref|YP_008797705.1| 12 CPECGNEMLVTDQRTGEI-TCSVCGF 36
                                      ****************85.*****95 PP

>> HTH_36  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   0.00068      0.35      29      51 ..     222     244 ..     215     245 .. 0.89
   2 ?    5.9   0.0     0.023        12      24      49 ..     273     298 ..     264     300 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00068
                            HTH_36  29 etlakrlglsknTvsraikeLeq 51 
                                         +a++ gl+ +Tv+ ai++L +
  gi|557694651|ref|YP_008797705.1| 222 NKIAAKVGLDQRTVQEAIRLLNE 244
                                       68*****************9965 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.023
                            HTH_36  24 cfpsqetlakrlglsknTvsraikeL 49 
                                        + +q+++ak+ g+ + Tv++  k L
  gi|557694651|ref|YP_008797705.1| 273 QNLTQKDIAKAAGVTEVTVRNRFKGL 298
                                       5789***************9988877 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 !    7.9   0.0    0.0043       2.2      15      41 ..     216     242 ..     214     245 .. 0.87
   2 !    6.9   0.0    0.0086       4.4      17      39 ..     274     296 ..     269     300 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0043
                            HTH_24  15 nprisqreLAerlglSpstvnrrlkrL 41 
                                       +p+i  + +A ++gl + tv + ++ L
  gi|557694651|ref|YP_008797705.1| 216 DPSIYVNKIAAKVGLDQRTVQEAIRLL 242
                                       77888899***************9977 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0086
                            HTH_24  17 risqreLAerlglSpstvnrrlk 39 
                                       +++q+++A++ g++  tv+ r k
  gi|557694651|ref|YP_008797705.1| 274 NLTQKDIAKAAGVTEVTVRNRFK 296
                                       79************999998876 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 ?    0.6   0.0      0.72   3.7e+02      32      48 ..     223     239 ..     221     242 .. 0.84
   2 !   12.9   0.0   0.00011     0.055      17      49 ..     264     296 ..     258     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.72
                      HTH_Tnp_ISL3  32 avArqlgvSwtTVwril 48 
                                        +A+ +g++ +TV+ ++
  gi|557694651|ref|YP_008797705.1| 223 KIAAKVGLDQRTVQEAI 239
                                       69***********9766 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00011
                      HTH_Tnp_ISL3  17 eayilelllesrsvkavArqlgvSwtTVwrild 49 
                                        +++ ++ +++ + k++A+  gv++ TV+++++
  gi|557694651|ref|YP_008797705.1| 264 LYMACQETTQNLTQKDIAKAAGVTEVTVRNRFK 296
                                       578888889999*******************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 ?   -0.3   0.0       1.7   8.6e+02      32      47 ..     224     239 ..     223     241 .. 0.86
   2 !   13.2   0.0    0.0001     0.052      25      46 ..     273     294 ..     271     296 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.7
                                       HHHHHT--HHHHHHHH CS
                      Sigma70_r4_2  32 IAellgisegtVksrl 47 
                                       IA++ g+  +tV+ ++
  gi|557694651|ref|YP_008797705.1| 224 IAAKVGLDQRTVQEAI 239
                                       99**********8665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.0001
                                       S---HHHHHHHHT--HHHHHHH CS
                      Sigma70_r4_2  25 eglsykEIAellgisegtVksr 46 
                                       ++l++k+IA+  g++e+tV++r
  gi|557694651|ref|YP_008797705.1| 273 QNLTQKDIAKAAGVTEVTVRNR 294
                                       789*****************98 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 ?   -0.4   0.0       2.3   1.2e+03      26      47 ..     223     244 ..     214     246 .. 0.86
   2 !   13.5   0.0    0.0001     0.054       7      47 ..     264     300 ..     259     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 2.3
                                       HHHHHTTSSHHHHHHHHHHHHH CS
                         HTH_Crp_2  26 elAsmlGltretvsrilseLkr 47 
                                        +A+ +Gl + tv  +++ L +
  gi|557694651|ref|YP_008797705.1| 223 KIAAKVGLDQRTVQEAIRLLNE 244
                                       689999*******999998865 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.0001
                                       HHHHHCTTTCEEEEEHHHHHHHHHTTSSHHHHHHHHHHHHH CS
                         HTH_Crp_2   7 LlrlaeraggeielpltqeelAsmlGltretvsrilseLkr 47 
                                       L+ +a++   e + +ltq+++A   G+t +tv   ++ Lk+
  gi|557694651|ref|YP_008797705.1| 264 LY-MACQ---ETTQNLTQKDIAKAAGVTEVTVRNRFKGLKD 300
                                       44.3443...24579*****************999988875 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 ?   -0.6   0.0       2.3   1.2e+03      19      33 ..     221     235 ..     217     235 .. 0.87
   2 !   12.9   0.0   0.00014     0.071      14      39 ..     272     297 ..     258     305 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.3
                                       HHHHHHHHTSSHHHH CS
                            TetR_N  19 vreIAkrAGvskgal 33 
                                       v++IA+++G+ ++++
  gi|557694651|ref|YP_008797705.1| 221 VNKIAAKVGLDQRTV 235
                                       689******999885 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00014
                                       TTT--HHHHHHHHTSSHHHHHHHTSS CS
                            TetR_N  14 ydattvreIAkrAGvskgalYryFps 39 
                                        +++t ++IAk+AGv++ ++  +F++
  gi|557694651|ref|YP_008797705.1| 272 TQNLTQKDIAKAAGVTEVTVRNRFKG 297
                                       578899**************999987 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.3   4.2e-05     0.022      10      36 ..      12      38 ..       8      41 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.2e-05
                                      -TTTS-EEEEESS-SS-EEESSSTCEE CS
                    Ribosomal_S27e 10 CpdCenetvvFshaatvvkCisCgkvL 36
                                      Cp+C+ne  v ++    ++C  Cg v+
  gi|557694651|ref|YP_008797705.1| 12 CPECGNEMLVTDQRTGEITCSVCGFVI 38
                                      ************************887 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       6.7   3.5e+03      14      30 ..     136     152 ..     128     157 .. 0.77
   2 ?   -1.1   0.1       4.3   2.2e+03       7      20 ..     152     166 ..     148     180 .. 0.69
   3 !    9.8   0.0    0.0016      0.83      16      38 ..     222     244 ..     212     245 .. 0.92
   4 ?    2.3   0.0      0.38   1.9e+02      12      30 ..     273     292 ..     260     296 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.7
                            HTH_28  14 svreaArelgisrrtvy 30 
                                       s++ a r++ i+rr ++
  gi|557694651|ref|YP_008797705.1| 136 SQTVAERAMLIYRRALR 152
                                       77888889999999886 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 4.3
                            HTH_28   7 kl.laaGhsvreaAr 20 
                                       ++ l +G+s++ +++
  gi|557694651|ref|YP_008797705.1| 152 RAgLVRGRSIKSIMA 166
                                       554668888888665 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.0016
                            HTH_28  16 reaArelgisrrtvyrWikryee 38 
                                       + +A+++g+++rtv+  i+ ++e
  gi|557694651|ref|YP_008797705.1| 222 NKIAAKVGLDQRTVQEAIRLLNE 244
                                       579****************9997 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.38
                            HTH_28  12 Gh.svreaArelgisrrtvy 30 
                                       ++ +++++A++ g+++ tv+
  gi|557694651|ref|YP_008797705.1| 273 QNlTQKDIAKAAGVTEVTVR 292
                                       3469999*******998887 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.99   5.1e+02      24      34 ..      89      99 ..      75     102 .. 0.75
   2 ?   11.9   0.1   0.00029      0.15       3      16 ..     278     291 ..     276     297 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.99
                                      SSSTHHHHHHH CS
                              LacI 24 erVseetrerV 34
                                      ++ s+etre+ 
  gi|557694651|ref|YP_008797705.1| 89 RKLSKETREKM 99
                                      789******96 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00029
                                       HHHHHHCTS-HHHH CS
                              LacI   3 kDVArlAGVSkaTV 16 
                                       kD+A++AGV+  TV
  gi|557694651|ref|YP_008797705.1| 278 KDIAKAAGVTEVTV 291
                                       9************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 ?   -2.3   0.1         9   4.6e+03      35      48 ..     117     130 ..      97     137 .. 0.66
   2 ?    6.2   0.0     0.021        11      19      50 ..     217     248 ..     215     254 .. 0.90
   3 ?    6.2   0.0     0.021        11      17      46 ..     271     300 ..     265     303 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 9
                           HTH_Mga  35 ltlqsdiseLnelF 48 
                                       + lq+ ++ L++ +
  gi|557694651|ref|YP_008797705.1| 117 RNLQQAVNILQIYV 130
                                       56788888888544 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.021
                           HTH_Mga  19 ksltldelakeLglseltlqsdiseLnelFpe 50 
                                       +s+++ ++a + gl  +t+q+ i+ Lne+++ 
  gi|557694651|ref|YP_008797705.1| 217 PSIYVNKIAAKVGLDQRTVQEAIRLLNEAVKR 248
                                       79999***********************9876 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.021
                           HTH_Mga  17 neksltldelakeLglseltlqsdiseLne 46 
                                        +  lt +++ak+ g +e+t++++   L++
  gi|557694651|ref|YP_008797705.1| 271 TTQNLTQKDIAKAAGVTEVTVRNRFKGLKD 300
                                       56789999**************98777765 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.2       7.2   3.7e+03      35      46 ..     141     152 ..     140     153 .. 0.82
   2 ?   12.7   0.0   0.00014     0.069      19      40 ..     273     294 ..     262     299 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.2
                                       HHHHHHHHHHHH CS
                        Sigma70_r4  35 erVrqiekrAlr 46 
                                       er+  i +rAlr
  gi|557694651|ref|YP_008797705.1| 141 ERAMLIYRRALR 152
                                       788889999998 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00014
                                       TT--HHHHHHHHTS-HHHHHHH CS
                        Sigma70_r4  19 eglTleEIgerlgiSrerVrqi 40 
                                       ++lT+++I++  g+++ +Vr +
  gi|557694651|ref|YP_008797705.1| 273 QNLTQKDIAKAAGVTEVTVRNR 294
                                       79******************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 ?    8.5   0.0    0.0029       1.5      27      50 ..     221     244 ..     216     249 .. 0.92
   2 ?    3.3   0.0      0.13        66      22      43 ..     273     293 ..     270     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0029
                                       HHHHHHHHTS-HHHHHHHHHHHHH CS
                              GntR  27 ereLaaefgVsrttvReALrrLea 50 
                                       ++++aa+ g +  tv+eA+r L +
  gi|557694651|ref|YP_008797705.1| 221 VNKIAAKVGLDQRTVQEAIRLLNE 244
                                       799*****************9975 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.13
                                       SB---HHHHHHHHTS-HHHHHH CS
                              GntR  22 dkLPsereLaaefgVsrttvRe 43 
                                       + L +++++a++ gV+  tvR 
  gi|557694651|ref|YP_008797705.1| 273 QNL-TQKDIAKAAGVTEVTVRN 293
                                       678.99**************95 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       8.2   4.2e+03      26      40 ..     100     114 ..      90     143 .. 0.54
   2 ?    1.7   0.0      0.63   3.2e+02      26      52 ..     219     245 ..     205     254 .. 0.87
   3 ?   10.3   0.0    0.0014      0.71      13      50 ..     262     299 ..     257     301 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 8.2
                                       B-HHHHHHHHTS-HH CS
                              Rrf2  26 vsseeiaerqnisps 40 
                                       ++++++ +  +i+ s
  gi|557694651|ref|YP_008797705.1| 100 IRLKKLDATSQINSS 114
                                       444444444444333 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.63
                                       B-HHHHHHHHTS-HHHHHHHHHHHHHT CS
                              Rrf2  26 vsseeiaerqnispsylekilakLrka 52 
                                       + +++ia+++++ ++ ++  ++ L++a
  gi|557694651|ref|YP_008797705.1| 219 IYVNKIAAKVGLDQRTVQEAIRLLNEA 245
                                       67899**************99999876 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.0014
                                       HHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHH CS
                              Rrf2  13 allyLakeeeeepvsseeiaerqnispsylekilakLr 50 
                                       a ly+a +e+ + ++ ++ia+  ++ ++ ++  ++ L+
  gi|557694651|ref|YP_008797705.1| 262 AALYMACQETTQNLTQKDIAKAAGVTEVTVRNRFKGLK 299
                                       56899*****99*******************9999887 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00038      0.19      17      41 ..     269     293 ..     256     298 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00038
                   Phage_terminase  17 kEsggtlklkdIAkvLdvsestvrk 41 
                                       +E  ++l  kdIAk  +v e tvr+
  gi|557694651|ref|YP_008797705.1| 269 QETTQNLTQKDIAKAAGVTEVTVRN 293
                                       69999******************98 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0     0.005       2.6       4      17 ..      11      24 ..       9      26 .. 0.86
   2 ?    3.5   0.1       0.1        54       3      17 ..      29      43 ..      27      44 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.005
                            zf_UBZ  4 lCerCgkeipesel 17
                                      lC++Cg e++++++
  gi|557694651|ref|YP_008797705.1| 11 LCPECGNEMLVTDQ 24
                                      6*********9964 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                            zf_UBZ  3 ylCerCgkeipesel 17
                                      ++C+ Cg  i+e ++
  gi|557694651|ref|YP_008797705.1| 29 ITCSVCGFVIQEKDV 43
                                      79********99775 PP

>> Cyclin_C  Cyclin, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0       0.4   2.1e+02      47      63 ..     165     180 ..     160     254 .. 0.52
   2 ?    8.9   0.0    0.0029       1.5      41      89 ..     253     301 ..     238     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.4
                                       HHHHHHHHCCHHHHS-- CS
                          Cyclin_C  47 iAaaalllarstlnspe 63 
                                       +Aa a ++a+++l++p 
  gi|557694651|ref|YP_008797705.1| 165 MAA-ATYAACRMLGTPR 180
                                       444.4555666663332 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0029
                                       CS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHH CS
                          Cyclin_C  41 syppSliAaaalllarstlnspewtetlehytgyskedlkpcvelilel 89 
                                       + +p  iAaaal++a+++  ++  ++ + +  g+++  +++  + ++++
  gi|557694651|ref|YP_008797705.1| 253 GKDPVGIAAAALYMACQETTQNLTQKDIAKAAGVTEVTVRNRFKGLKDV 301
                                       5566779***********9999999999999999998888777666665 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 ?   12.5   0.1   0.00021      0.11      14      44 ..       5      35 ..       1      37 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00021
                     Zn_Tnp_IS1595 14 rWpngfvCPhCgsrkayriktrglfqCkeCr 44
                                       W++   CP Cg++ + + ++ g   C+ C+
  gi|557694651|ref|YP_008797705.1|  5 TWKEVALCPECGNEMLVTDQRTGEITCSVCG 35
                                      6999999*******66666666******997 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 ?   11.4   0.3   0.00045      0.23      31      56 ..      12      38 ..       9      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00045
                    OrfB_Zn_ribbon 31 CseCgsknke.alsgrtfkCpnCgfea 56
                                      C+eCg ++   ++ + + +C+ Cgf++
  gi|557694651|ref|YP_008797705.1| 12 CPECGNEMLVtDQRTGEITCSVCGFVI 38
                                      *****99988789999*********95 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00036      0.18      13      40 ..      10      40 ..       3      43 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00036
                               DZR 13 rfCseCgtklkavaa...edrCpsCgekvdp 40
                                        C+eCg+++  + +   e++C+ Cg  +++
  gi|557694651|ref|YP_008797705.1| 10 ALCPECGNEMLVTDQrtgEITCSVCGFVIQE 40
                                      6899999996544446789999999987765 PP

>> RPA_interact_C  Replication protein A interacting C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00052      0.26       1      30 [.      11      43 ..      11      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00052
                    RPA_interact_C  1 lCPvCkkrklkets..evifCe.Cglrletsee 30
                                      lCP C ++ l  ++    i+C+ Cg+ ++ ++ 
  gi|557694651|ref|YP_008797705.1| 11 LCPECGNEMLVTDQrtGEITCSvCGFVIQEKDV 43
                                      6******99988663467**********99433 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 ?    7.2   0.3    0.0098         5      69      93 ..       8      35 ..       2      48 .. 0.77
   2 ?   -1.2   0.0       3.8   1.9e+03      74      74 ..     174     174 ..     107     213 .. 0.55
   3 ?    4.4   0.1     0.073        37      26      83 ..     221     278 ..     214     292 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0098
                                      -EEEETTTS-EEECHH.H..HHS-TTTS CS
                              HypA 69 vkvrCreCgkefelee.k..alrCpkCg 93
                                       ++ C eCg+e+ +++ +  +++C  Cg
  gi|557694651|ref|YP_008797705.1|  8 EVALCPECGNEMLVTDqRtgEITCSVCG 35
                                      5678999999999555335788999998 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.8
                                       T CS
                              HypA  74 r 74 
                                       r
  gi|557694651|ref|YP_008797705.1| 174 R 174
                                       2 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.073
                                       EEEEEEEEETTCT--HHHHHHHHHHHHCC.TTTT-EEEEEEE--EEEETTTS-EEECH CS
                              HypA  26 vtkvkvevGelsgvepeaLefafellaegtvlegaeLeieevpvkvrCreCgkefele 83 
                                       v+k+  +vG  +  ++ea++   e+++++ ++ +  + i    + + C+e  ++ +++
  gi|557694651|ref|YP_008797705.1| 221 VNKIAAKVGLDQRTVQEAIRLLNEAVKRKATVGKDPVGIAAAALYMACQETTQNLTQK 278
                                       899**************************9999999************9988877755 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   2.0    0.0083       4.2       5      25 ..      12      37 ..       8      38 .. 0.68
   2 ?    4.5   0.1     0.048        24       2      14 ..      28      40 ..      27      43 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0083
                       zf-ribbon_3  5 CPnCGa.p.l...ssddnvCpyCGtk 25
                                      CP+CG+   +   +++ ++C  CG +
  gi|557694651|ref|YP_008797705.1| 12 CPECGNeMlVtdqRTGEITCSVCGFV 37
                                      99999987343333456788888876 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.048
                       zf-ribbon_3  2 tvrCPnCGaplss 14
                                      +++C+ CG ++++
  gi|557694651|ref|YP_008797705.1| 28 EITCSVCGFVIQE 40
                                      6889999976565 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 ?   10.4   0.4   0.00082      0.42       3      20 ..      11      28 ..       9      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00082
                                      E-SSS--EEEEEE-SSSE CS
                    zf-C4_Topoisom  3 kCPkCggdLvlkrgkkGk 20
                                       CP+Cg+++++   + G+
  gi|557694651|ref|YP_008797705.1| 11 LCPECGNEMLVTDQRTGE 28
                                      7********988887775 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1     0.035        18      16      23 ..      12      19 ..      10      21 .. 0.93
   2 ?    4.8   0.1     0.053        27      15      26 ..      30      41 ..      24      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.035
                              YhfH 16 CteCGkei 23
                                      C+eCG+e+
  gi|557694651|ref|YP_008797705.1| 12 CPECGNEM 19
                                      ******98 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.053
                              YhfH 15 kCteCGkeieEq 26
                                      +C+ CG +i+E+
  gi|557694651|ref|YP_008797705.1| 30 TCSVCGFVIQEK 41
                                      8*********97 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 ?   10.8   0.3   0.00084      0.43      17      46 ..       8      36 ..       2      38 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00084
                               IBR 17 nlkwCprpdCeaiiekseg.cksvtCskCgf 46
                                      ++  Cp  +C++ +  +++ ++++tCs Cgf
  gi|557694651|ref|YP_008797705.1|  8 EVALCP--ECGNEMLVTDQrTGEITCSVCGF 36
                                      4677*9..9**888888887999******98 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.2    0.0036       1.8       2      21 ..      12      36 ..      11      38 .. 0.82
   2 ?    2.7   0.2      0.22   1.1e+02       2      12 ..      31      41 ..      30      43 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0036
                     zinc_ribbon_2  2 CpnCGael.qdnakF....CpyCGt 21
                                      Cp+CG+e    +++     C+ CG+
  gi|557694651|ref|YP_008797705.1| 12 CPECGNEMlVTDQRTgeitCSVCGF 36
                                      *******944777779999999996 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.22
                     zinc_ribbon_2  2 CpnCGaelqdn 12
                                      C+ CG  +q++
  gi|557694651|ref|YP_008797705.1| 31 CSVCGFVIQEK 41
                                      77788777776 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.3   0.00061      0.31       2      24 ..      11      36 ..       6      45 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00061
                                      --SSS-S--E...E-SSEEE-TTT-- CS
                    zinc-ribbons_6  2 kCpeCqqele...krgeqyhCeaCqe 24
                                       CpeC +e+    +r+ +++C+ C  
  gi|557694651|ref|YP_008797705.1| 11 LCPECGNEMLvtdQRTGEITCSVCGF 36
                                      699**999975334558999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1132  (0.0631379); expected 358.6 (0.02)
Passed bias filter:                      812  (0.0452898); expected 358.6 (0.02)
Passed Vit filter:                       144  (0.00803168); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 2438.76
//
Query:       gi|557694652|ref|YP_008797706.1|  [L=475]
Description: cysteinyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-112  374.7   0.0   5.4e-112  374.0   0.0    1.3  1  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    1.2e-16   61.0   0.1    3.2e-16   59.6   0.1    1.8  1  DALR_2        DALR domain
    7.7e-09   34.8   0.1    0.00055   18.8   0.0    2.2  2  tRNA-synt_1g  tRNA synthetases class I (M)
    1.8e-08   33.2   0.0    1.1e-05   23.9   0.0    2.3  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    2.7e-06   26.6   0.2    1.1e-05   24.5   0.0    1.9  2  tRNA-synt_1f  tRNA synthetases class I (K)
    0.00055   19.0   0.1     0.0059   15.6   0.1    2.2  2  tRNA-synt_1d  tRNA synthetases class I (R)
  ------ inclusion threshold ------
      0.092   12.7   0.6        4.7    7.2   0.1    2.4  2  EppA_BapA     Exported protein precursor (EppA/BapA)


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 !  374.0   0.0  2.1e-115  5.4e-112       4     300 ..      17     320 ..      14     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 374.0 bits;  conditional E-value: 2.1e-115
                                       -SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--.......SHHHHHHHHHTTS-HH CS
                      tRNA-synt_1e   4 pleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDi.......dDkiikrareeeksvk 73 
                                       p   ++vt+YvCGptvyd +hlGhaR++vafD + r+l+ +gY v++ +nvtD+       +D++i  a++  k+  
  gi|557694652|ref|YP_008797706.1|  17 PHLPGHVTMYVCGPTVYDVAHLGHARTYVAFDAVIRFLEFMGYRVKYARNVTDVghlretgEDRMIVGAERLRKHPM 93 
                                       566789************************************************77777778*************** PP

                                       HHHHHHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHH CS
                      tRNA-synt_1e  74 elaekfieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleel 150
                                       e+a+k++ ef++d++aL++++p+++pr+s +++eiie vekl++kgy Y+++ g vyfd sk+++Ygkls+ + eel
  gi|557694652|ref|YP_008797706.1|  94 EVADKYMMEFFRDMDALGIRRPDIQPRASMHIPEIIEAVEKLVDKGYGYVID-GSVYFDISKFPDYGKLSNIKPEEL 169
                                       ***************************************************9.************************ PP

                                       HHT----S--S-SSTT-EEEEEE--TTS.--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHH CS
                      tRNA-synt_1e 151 elgaegevseekkdkkDfaLWkaskege.pswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenel 226
                                        +++ +    +kk++ DfaLWk+s ++   sw++Pwg+G PGWhieCs+m++k+lg++idih+GG++L+fPhhene+
  gi|557694652|ref|YP_008797706.1| 170 LMHRIDPD-PRKKHPADFALWKESPPSYpFSWKTPWGRGFPGWHIECSIMSMKYLGEQIDIHGGGQELIFPHHENEI 245
                                       99999877.79**************998569********************************************** PP

                                       HHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHHH CS
                      tRNA-synt_1e 227 aqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelleeak 300
                                       aqsea+++ k++vky++h+g l++ g+ m ks +nfiti+d+lk++ + +lRl++lsahyr++ld++e+++e+a 
  gi|557694652|ref|YP_008797706.1| 246 AQSEALTGkKPFVKYWMHTGELTVGGRGMHKSYGNFITIQDALKTYPSDVLRLFILSAHYRTPLDYSEKAMEQAA 320
                                       ********899************************************************************9985 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.1   1.2e-19   3.2e-16       2      57 ..     360     415 ..     359     423 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 1.2e-19
                                       HHHHHTBT--HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHGGGT-S-S CS
                            DALR_2   2 FeeaMdDDFNTaeAiavlFelakeiNralkeedkaaasalkallrelaevLGllqe 57 
                                       F+eaM +DFNT++A+a +++  k++N++l++  +++a+ l++l+ e   vLGllq+
  gi|557694652|ref|YP_008797706.1| 360 FIEAMSEDFNTPNALAIVYDFMKKVNTRLDDIGHEQAAHLRQLFLETCRVLGLLQK 415
                                       9*****************************************************98 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 !   14.0   0.0   6.3e-06     0.016      12      87 ..      34     116 ..      25     154 .. 0.73
   2 !   18.8   0.0   2.1e-07   0.00055     313     371 ..     259     316 ..     235     333 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6.3e-06
                                       S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEE.E-.....--SH.HHHHHHHHTTS-HHHHHHHHHHHHHHHHHHT CS
                      tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcg.tD.....ehGt.pielkAekegvtpeelvekvheeikelfkkl 81 
                                       ++ HlGh++++++ D+++R+    g+ v +    tD     e G   + + Ae+   +p e+++k+  e+ ++++ l
  gi|557694652|ref|YP_008797706.1|  34 DVAHLGHARTYVAFDAVIRFLEFMGYRVKYARNvTDvghlrETGEdRMIVGAERLRKHPMEVADKYMMEFFRDMDAL 110
                                       679**********************9998865413422222556524567899999999999999999999999999 PP

                                       T---SE CS
                      tRNA-synt_1g  82 nisfdk 87 
                                       +i   +
  gi|557694652|ref|YP_008797706.1| 111 GIRRPD 116
                                       987655 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.1e-07
                                       S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHH CS
                      tRNA-synt_1g 313 kkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedf 371
                                       k  + ++ ltv g+ + kS g+++++++al+++++d+lR ++++++   + ld+s++ +
  gi|557694652|ref|YP_008797706.1| 259 KYWMHTGELTVGGRGMHKSYGNFITIQDALKTYPSDVLRLFILSAHY-RTPLDYSEKAM 316
                                       5556778899*****************************99988543.34455655544 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 !    7.1   0.0   0.00054       1.4      26      70 ..      24      68 ..       6     153 .. 0.73
   2 !   23.9   0.0   4.5e-09   1.1e-05     526     596 ..     236     306 ..     225     312 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00054
                       tRNA-synt_1 26 ilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwD 70
                                      ++++  P v    H+Gha + +  d vir+ ++ G++v+y   + 
  gi|557694652|ref|YP_008797706.1| 24 TMYVCGPTVYDVAHLGHARTYVAFDAVIRFLEFMGYRVKYARNVT 68
                                      5667778889999**************************976544 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 4.5e-09
                       tRNA-synt_1 526 iirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvg 596
                                        i+   ++ i +s altg++Pf +  +h   +   Gr m Ks gN i  +d +k+y  d+lRl+++++++ 
  gi|557694652|ref|YP_008797706.1| 236 LIFPHHENEIAQSEALTGKKPFVKYWMHTGELTVGGRGMHKSYGNFITIQDALKTYPSDVLRLFILSAHYR 306
                                       55555667789999***************999*********************************998875 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 ?   -0.8   0.1      0.21   5.4e+02      36      76 ..      35      75 ..      25      91 .. 0.87
   2 !   24.5   0.0   4.5e-09   1.1e-05     278     341 ..     270     334 ..     219     349 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.21
                      tRNA-synt_1f 36 liHiGnlrevltadlvaralrkrgeevrlilisDdmDglRk 76
                                        H+G +r  +  d+v r l+ +g +v+    + d+  lR 
  gi|557694652|ref|YP_008797706.1| 35 VAHLGHARTYVAFDAVIRFLEFMGYRVKYARNVTDVGHLRE 75
                                      57**********************99999988888888886 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 4.5e-09
                      tRNA-synt_1f 278 ggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf..a 341
                                       gg+ m++S Gn++t++d+l+ ++ +vlr++il+++ ++ ++ + +  + ++ +++dk+ + y   +
  gi|557694652|ref|YP_008797706.1| 270 GGRGMHKSYGNFITIQDALKTYPSDVLRLFILSAHYRTPLDYSEK-AMEQAAENFDKITNFYEnlS 334
                                       5569*************************************9999.************99997441 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 !   15.6   0.1   2.3e-06    0.0059      28      70 ..      29      71 ..      21      77 .. 0.89
   2 ?    0.4   0.0     0.095   2.4e+02     138     197 ..      94     155 ..      80     164 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.3e-06
                                      --BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SS CS
                      tRNA-synt_1d 28 sPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWG 70
                                       P +    h Gh r+ +  dav r lef+Gy v  +  v D G
  gi|557694652|ref|YP_008797706.1| 29 GPTVYDVAHLGHARTYVAFDAVIRFLEFMGYRVKYARNVTDVG 71
                                      68888889**************************999999988 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.095
                                       HHHHHHHHHHHHHHHHCT---EC..--CCCCCCCHHHHHHHHHCTT-EEECTTCEEEEECCC CS
                      tRNA-synt_1d 138 llvditrtelqklydrldvtlie..rGeslykeslneivkelkkkglvkesdGalvvfldef 197
                                        + d  + e+ +  d+l +   +     s++ + + e+v++l +kg+  ++dG    ++++f
  gi|557694652|ref|YP_008797706.1|  94 EVADKYMMEFFRDMDALGIRRPDiqPRASMHIPEIIEAVEKLVDKGYGYVIDGSVYFDISKF 155
                                       555555666666666666655333255689999999*****************999998887 PP

>> EppA_BapA  Exported protein precursor (EppA/BapA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0018       4.7      88     127 ..     284     325 ..     277     332 .. 0.79
   2 ?    3.4   0.0     0.027        68      19      67 ..     382     428 ..     366     455 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0018
                         EppA_BapA  88 iirliksypdsifdyliqlds..dkidyaekygekarenfkk 127
                                       i+  +k+yp  ++  +i        +dy+ek  e+a enf+k
  gi|557694652|ref|YP_008797706.1| 284 IQDALKTYPSDVLRLFILSAHyrTPLDYSEKAMEQAAENFDK 325
                                       56678999999999877654411569**************97 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.027
                         EppA_BapA  19 dllnkrldnydfkseyeksfvfadapeirgdlrkigikeksvlldalev 67 
                                       + +n rld+   ++  +   +f ++ ++ g l+ki  +  s   + +e 
  gi|557694652|ref|YP_008797706.1| 382 KKVNTRLDDIGHEQAAHLRQLFLETCRVLGLLQKIERR--SSAAEVMEF 428
                                       56899*****************************8644..433444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3385.36
//
Query:       gi|557694653|ref|YP_008797707.1|  [L=236]
Description: nucleotidyl transferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-38  131.6   0.0    4.4e-38  131.3   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    3.6e-10   40.4   0.0    5.4e-10   39.9   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
  ------ inclusion threshold ------
       0.01   15.6   0.0      0.017   14.9   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
      0.089   12.7   0.0       0.17   11.8   0.0    1.4  1  DUF4224          Domain of unknown function (DUF4224)


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 !  131.3   0.0   9.8e-42   4.4e-38       1     244 [.       2     223 ..       2     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: 131.3 bits;  conditional E-value: 9.8e-42
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kav+L+GG+G+RL PLt +l+k+l+ v+gk ++i  +++ l ++gi+e  +v+  + ++ + e l++g ++gv++ +
  gi|557694653|ref|YP_008797707.1|   2 KAVLLSGGYGKRLKPLTESLPKPLLEVAGK-PIIVWQIEWLKKHGIDE-FIVCVGYLREKIIETLGSGHRLGVKIGY 76 
                                       79****************************.*****************.**************************** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       ++e+e+ gt +A++ a+ ll+ +k   ++lvL+gD+l++ +  +++++  ++ a     + +  ++ ++ yG++e+d
  gi|557694653|ref|YP_008797707.1|  77 SVEDEPLGTGGALKNAEHLLKSDK---VFLVLNGDVLTTLNPLKLIDSLGSSIA-----C-MALTRLPSPYGIVEFD 144
                                       *********************999...5***********999999988776666.....4.45578999******** PP

                                       .TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE CS
                   NTP_transferase 155 .eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs 230
                                        e++ v+rf+EKP+ ++   ++++G+Y f+ +vl +l       +++ d  ++++p+++e++   +  l +d   W 
  gi|557694653|ref|YP_008797707.1| 145 rETRLVKRFEEKPRLPN---YINAGVYAFTADVLSYL-------PEQGDLEKQTFPRLVEKKALMAV-LYEDD-DWI 209
                                       77779*********977...****************9.......667888899*******9877755.55554.5** PP

                                       EXSSHHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleanek 244
                                        + ++++l ea++ 
  gi|557694653|ref|YP_008797707.1| 210 SIDSHKDLEEAKRV 223
                                       *******9999875 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 !   39.9   0.0   1.2e-13   5.4e-10       1      96 [.       3     109 ..       3     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.2e-13
                                       EEEEEESS-TTTT...T..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHH...TTCTS-E...EE CS
                      NTP_transf_3   1 aviLAGGrSsRmg...g..dKallplggkpllervldalraagvdevvvvggd..eevlaal...arlgvrv...ve 64 
                                       av+L GG ++R++   +  +K+ll+++gkp++ ++++ l+++g+de +v++g+  e++ + l    rlgv++   v 
  gi|557694653|ref|YP_008797707.1|   3 AVLLSGGYGKRLKpltEslPKPLLEVAGKPIIVWQIEWLKKHGIDEFIVCVGYlrEKIIETLgsgHRLGVKIgysV- 78 
                                       79**********8554269**********************************87666655433356688885333. PP

                                       -TTSS-SHHHHHHHHHHHH.SSSCEEEEETT- CS
                      NTP_transf_3  65 dedpgkgplaslaaalraaadadavlvlacDm 96 
                                        ed+  g++++l+ a + +++++ +lvl +D+
  gi|557694653|ref|YP_008797707.1|  79 -EDEPLGTGGALKNAEHLLKSDKVFLVLNGDV 109
                                       .44469**********9998999999999997 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 ?   14.9   0.0   3.7e-06     0.017       2      63 ..       2      65 ..       1      80 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.7e-06
                                      EEEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHH CS
                              IspD  2 vvvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqll 63
                                       +v+   G GkR+k   + lpK +le++g++++ + ++ l +++ +d+ +v v   + + +e+l 
  gi|557694653|ref|YP_008797707.1|  2 KAVLLSGGYGKRLKpltESLPKPLLEVAGKPIIVWQIEWLKKHG-IDEFIVCVGYLREKIIETLG 65
                                      6899999*****86444799******************999965.66666666555556666665 PP

>> DUF4224  Domain of unknown function (DUF4224)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.8e-05      0.17       8      29 ..      26      47 ..      23      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.8e-05
                           DUF4224  8 aeLTGykrrsaQakwLranGip 29
                                       e+ G+++  +Q++wL+++Gi+
  gi|557694653|ref|YP_008797707.1| 26 LEVAGKPIIVWQIEWLKKHGID 47
                                      57788888899*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1775.16
//
Query:       gi|557694654|ref|YP_008797708.1|  [L=170]
Description: ribosomal-protein-alanine N-acetyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-20   71.3   0.1    9.6e-20   71.0   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    3.8e-15   56.1   0.2    5.6e-15   55.5   0.2    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.4e-14   52.5   0.1    1.4e-13   50.9   0.1    1.7  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.6e-09   36.9   0.1    6.6e-09   35.6   0.1    1.7  1  FR47             FR47-like protein
    1.4e-07   31.6   0.0    2.3e-07   31.0   0.0    1.4  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
    9.9e-06   25.3   0.0    1.3e-05   24.9   0.0    1.3  1  Acetyltransf_8   Acetyltransferase (GNAT) domain
    3.7e-05   23.3   0.0    5.2e-05   22.8   0.0    1.3  1  Acetyltransf_15  Putative acetyl-transferase
     0.0013   18.9   0.2     0.0022   18.2   0.2    1.4  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.016   15.9   0.0      0.021   15.5   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
       0.11   12.7   0.0       0.23   11.6   0.0    1.7  1  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 !   71.0   0.1   5.3e-23   9.6e-20       3     117 .]      24     143 ..      22     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 5.3e-23
                                       HHHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEET.......TSTTEEEEEEEEESGGG CS
                    Acetyltransf_1   3 dlvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipd.......ekggvayieslaVspey 72 
                                       d++++ +++ ++++  ++++e ++     ++ ++vae +++l+G+i+++             ++ ++i s+aV p+y
  gi|557694654|ref|YP_008797708.1|  24 DVMNINRLCLPENYTYSFFDELAKD---YPKAFWVAEVGDKLVGYIMCRVERVfskidflKIRRAGHIVSVAVLPNY 97 
                                       5677777777666666666665555...888***************9999999999999977789************ PP

                                       TTSSHHHHHHHHHHHHHHHT.TESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  73 rgkGlGsaLlealeeraree.gikkivlaveedndaairlYeklGF 117
                                       r++G+G +L++ ++  + +  g+++ +l+v+++n+ ai+lY+k GF
  gi|557694654|ref|YP_008797708.1|  98 RNRGIGEQLIRRALYSLANDyGCEEAFLEVRVSNHVAIKLYRKIGF 143
                                       **************8777778**888***************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 !   55.5   0.2   3.1e-18   5.6e-15       4      75 ..      52     144 ..      49     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 3.1e-18
                                       EEEEEEETTEEEEEEEEEEES.............TCTEEEEE-GGGTTSSHHHHHHH.H....TT.SEEEEE...EE CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld.............aeitrlaVdpeyrgkGiGraLle.a....ae.kgiile...ql 58 
                                        ++Vae ++k vG+i + ++              ++i  +aV+p+yr++GiG +L++ a    a+  g++ e   ++
  gi|557694654|ref|YP_008797708.1|  52 AFWVAEVGDKLVGYIMCRVERvfskidflkirraGHIVSVAVLPNYRNRGIGEQLIRrAlyslANdYGCE-EaflEV 127
                                       69*************999998**9999988877666666*****************96455542267787.222334 PP

                                       EETHHHHHHHHHHTTEE CS
                    Acetyltransf_7  59 elnaekaikfYeklGFe 75 
                                       +++++ aik+Y+k GF+
  gi|557694654|ref|YP_008797708.1| 128 RVSNHVAIKLYRKIGFV 144
                                       555569**********8 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.9   0.1   7.7e-17   1.4e-13      29     123 ..      49     162 ..      34     166 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 7.7e-17
                   Acetyltransf_10  29 gealllvaeeggkivGvielrdgs..............hisllfVdpeyrgqGigkaLleaveee.aekdgikl.el 89 
                                         + ++vae+g+k+vG+i  r ++              hi  ++V p+yr +Gig++L+ +++   a++ g ++  l
  gi|557694654|ref|YP_008797708.1|  49 YPKAFWVAEVGDKLVGYIMCRVERvfskidflkirragHIVSVAVLPNYRNRGIGEQLIRRALYSlANDYGCEEaFL 125
                                       55789*************44555556688999999999*************************9955555556699* PP

                   Acetyltransf_10  90 tvnasp.yavpfYeklGFkav..geeqeenGirfvpM 123
                                       +v+ s+  a+++Y+k+GF++   ++  +++G   + M
  gi|557694654|ref|YP_008797708.1| 126 EVRVSNhVAIKLYRKIGFVVKevQRRYYADGEDAYVM 162
                                       ******99**********9885566677777666666 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.1   3.7e-12   6.6e-09      20      83 ..      84     149 ..      71     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 3.7e-12
                                       TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHH.S-.S-EEEEEETT-HHHHHHHHHHT-EEEEEE CS
                              FR47  20 dggelgalqvlpehrrrGlgsrlvkalakeiae.rg.ktvllvvvasNtpsirlyeklGfekieet 83 
                                         g + ++ vlp+ r+rG g +l++   + +a+  g ++++l v+ sN+ +i+ly k+Gf + e +
  gi|557694654|ref|YP_008797708.1|  84 RAGHIVSVAVLPNYRNRGIGEQLIRRALYSLANdYGcEEAFLEVRVSNHVAIKLYRKIGFVVKEVQ 149
                                       5699****************************9855489*********************987554 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   1.3e-10   2.3e-07       2     125 ..      14     143 ..      13     145 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.3e-10
                                       EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTT..SEEEEEEETTEEEEEEEE.EEEEEEETT..EEEEE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrkllee..srvlgaedngelvgqlal.lplelnvpG..ktlka 73 
                                       +r++t++dl +v+++ + +  ++ ++      +f++l ++  + +++ae +++lvg +++ + + ++  +  k+ +a
  gi|557694654|ref|YP_008797708.1|  14 FRNVTQTDLIDVMNINRLCLPENYTYS-----FFDELAKDypKAFWVAEVGDKLVGYIMCrVERVFSKIDflKIRRA 85 
                                       5999******************99995.....455666643368************8877234444445558***** PP

                                       EEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHT.T--EEEE--.....SSHHHHHTTT- CS
                    Acetyltransf_9  74 agvtgVavapehrgrgvlskLlaraleemree.gqplsllfP.....ssipiYrrfGy 125
                                       + +++Vav p++r+rg+ ++L++ral  ++ + g + ++l        +i++Yr+ G+
  gi|557694654|ref|YP_008797708.1|  86 GHIVSVAVLPNYRNRGIGEQLIRRALYSLANDyGCEEAFLEVrvsnhVAIKLYRKIGF 143
                                       *************************998887666666666665555555566666665 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   7.4e-09   1.3e-05      47     140 ..      54     146 ..      25     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 7.4e-09
                                       EEEEETTEEEEEEEEEEGGGCGGGGCS---TT-EEEEEE.ES.SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE-- CS
                    Acetyltransf_8  47 liglldgepvgyfeiYwakedelaeyydaepgdrGiHll.ig.eaeargkglttallralvhylfadprtrrvvvEP 121
                                       +++++ ++ vgy+ + ++++       d+ +  r  H++ ++  +++r++g++ +l+r+ +  l +d +++   +E 
  gi|557694654|ref|YP_008797708.1|  54 WVAEVGDKLVGYIMC-RVERV--FSKIDFLKIRRAGHIVsVAvLPNYRNRGIGEQLIRRALYSLANDYGCEEAFLEV 127
                                       555555555555544.44444..333355555555554314555899****************************** PP

                                       BTT-HHHHHHHHHTT-EEE CS
                    Acetyltransf_8 122 dvrNerairllekaGfeke 140
                                       +v+N+ ai+l++k+Gf+ +
  gi|557694654|ref|YP_008797708.1| 128 RVSNHVAIKLYRKIGFVVK 146
                                       ****************865 PP

>> Acetyltransf_15  Putative acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.9e-08   5.2e-05      45     137 ..      59     144 ..       5     158 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.9e-08
                   Acetyltransf_15  45 keeLvasvfivkkkyyslvssilieknvleiYtlyvsekyrgkGlakklLeeslkelkknYkvdnelllaLHlnpkD 121
                                        ++Lv+ ++ + +  +s+++ +l+ + +  i ++ v ++yr++G+  +l+ ++l +l + Y  + e+ l   ++   
  gi|557694654|ref|YP_008797708.1|  59 GDKLVGYIMCRVERVFSKID-FLKIRRAGHIVSVAVLPNYRNRGIGEQLIRRALYSLANDYGCE-EAFLEVRVSN-- 131
                                       789******99999999999.555555559********************************99.7777777765.. PP

                   Acetyltransf_15 122 ksMnisfalYyslgFr 137
                                          +++  lY++ gF+
  gi|557694654|ref|YP_008797708.1| 132 ---HVAIKLYRKIGFV 144
                                       ...6888888888886 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   1.2e-06    0.0022      51     154 ..      52     163 ..      34     164 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                    Acetyltransf_4  51 vflvae.sdrivGyaylg......qfkkr.akdwkaelsvylaerdnnkeglgreli.daleqvlkeqnienllaei 118
                                        f vae  d++vGy   +      ++++   ++   ++sv +     +++g+g +li  al   +  ++ e+ + e+
  gi|557694654|ref|YP_008797708.1|  52 AFWVAEvGDKLVGYIMCRvervfsKIDFLkIRRAGHIVSVAVL-PNYRNRGIGEQLIrRALYSLANDYGCEEAFLEV 127
                                       5888888899999876542121124666667888889999998.67999****997725777888************ PP

                    Acetyltransf_4 119 aspnensiqfhkalGFelvgifkkcikkngrwiDmi 154
                                        ++n  +i+++ ++GF +   +++++ ++   + m+
  gi|557694654|ref|YP_008797708.1| 128 RVSNHVAIKLYRKIGFVVKEVQRRYYADGEDAYVMV 163
                                       ************************999988888765 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   1.2e-05     0.021      37     137 ..      38     143 ..       6     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                    Acetyltransf_3  37 aeewlerawaeeseeegyg...waivlkdtgviGsvglrdleeedee.........aelgymlapsfwgkGyateav 101
                                       +++++++ +a++     y    w+  + +++ +G++++r     ++            ++  + p ++++G++    
  gi|557694654|ref|YP_008797708.1|  38 TYSFFDE-LAKD-----YPkafWVA-EVGDKLVGYIMCRVERVFSKIdflkirragHIVSVAVLPNYRNRGIGEQLI 107
                                       4444443.3322.....22221444.444437888888855555544777887875556677889************ PP

                    Acetyltransf_3 102 ralleyafeelglerlvavidkeNeaSirvleklGf 137
                                       r +l  + ++ g e+ + ++  +N+  i++++k+Gf
  gi|557694654|ref|YP_008797708.1| 108 RRALYSLANDYGCEEAFLEVRVSNHVAIKLYRKIGF 143
                                       **999999***************************9 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 ?   11.6   0.0   0.00013      0.23      27      51 ..      88     112 ..      67     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                   Acetyltransf_CG  27 fthTeVpeelrGkGiAkkLvkaald 51 
                                       +  + V + +r +Gi+++L+++al 
  gi|557694654|ref|YP_008797708.1|  88 IVSVAVLPNYRNRGIGEQLIRRALY 112
                                       6778899***************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1262.83
//
Query:       gi|557694655|ref|YP_008797709.1|  [L=235]
Description: metallophosphoesterase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   34.1   2.8    1.5e-07   32.2   2.7    1.7  1  Metallophos    Calcineurin-like phosphoesterase
    1.2e-05   25.6   0.0    1.7e-05   25.1   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 !   32.2   2.7   1.6e-11   1.5e-07       4     109 ..      41     139 ..      38     185 .. 0.64

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.6e-11
                                       EEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS..HHHHHHHHHHHHHHHHTSEEEEEC-TTS... CS
                       Metallophos   4 lvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrg..dlekellellaalvkypipvylllGNHe... 75 
                                       +++ DlH+++++ q ++ll +ld+    e+pd+v+l GD vd+   dl + + ++l++l      ++++lGNH+   
  gi|557694655|ref|YP_008797709.1|  41 VFLPDLHIHSENIQTSQLLSVLDR----EEPDAVVLGGDMVDELttDLGY-VRRFLSELPG--SEKFFVLGNHDyws 110
                                       678899977777777777777743....4**************8557777.7777999999..599********544 PP

                                       CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEE CS
                       Metallophos  76 gfeeellnkygylgifsepwrsdaevfnnlplas 109
                                       g    + +  + +++ ++++r   +v +  +l  
  gi|557694655|ref|YP_008797709.1| 111 G----YDEWLR-ENLRAMGYREVRSVAESRYLGK 139
                                       2....333322.2222455555544444444444 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 !   25.1   0.0   1.9e-09   1.7e-05       6     128 ..      43     183 ..      39     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.9e-09
                     Metallophos_2   6 iSDlH..snldaleavlealkevgvdaiihaGDl...eeeepevleellela...pvlaVrGNnDeevveedvlrea 74 
                                       + DlH  s+  ++ ++l+ l+++++da+++ GD+    ++++  ++++l+ +   +   V GN+D +   +++lre+
  gi|557694655|ref|YP_008797709.1|  43 LPDLHihSENIQTSQLLSVLDREEPDAVVLGGDMvdeLTTDLGYVRRFLSELpgsEKFFVLGNHDYWSGYDEWLREN 119
                                       5677766777778999*****************8543334444777777777999999*******333666777777 PP

                     Metallophos_2  75 aelgtdlpeeaelelagekvlliHgdpl............gvkdalaellkeaeegsdvvvcGHtH 128
                                        + +++  e + +  + + ++ iHg ++            g+  a ++ + ++ +g+ ++++GHtH
  gi|557694655|ref|YP_008797709.1| 120 LRAMGYR-EVRSVA-ESRYLGKIHGIDWrdnrsyepfkanGLVFAHDPHVADSVSGDCLIFAGHTH 183
                                       7776666.333333.5777999999988999999999988788888888888888888******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1665.89
//
Query:       gi|557694656|ref|YP_008797710.1|  [L=333]
Description: thioesterase superfamily protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-24   84.9   4.5    9.8e-12   45.1   0.2    2.3  2  4HBT             Thioesterase superfamily
  ------ inclusion threshold ------
      0.026   14.7   0.2       0.05   13.8   0.2    1.4  1  EIIBC-GUT_C      Sorbitol phosphotransferase enzyme II C-term
      0.028   14.0   0.1        1.9    8.1   0.0    2.3  2  MaoC_dehydratas  MaoC like domain


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   0.6   2.4e-14   1.4e-10       2      72 ..      25      94 ..      24     100 .. 0.95
   2 !   45.1   0.2   1.6e-15   9.8e-12       1      74 [.     187     259 ..     187     263 .. 0.96

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 2.4e-14
                                      SSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEE CS
                              4HBT  2 GvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrd 72
                                      G +hgGv+++++ +aa+++  +  ++  +v ++ + + f+ pv +gd ++v+a+v++ g +s++v v  ++
  gi|557694656|ref|YP_008797710.1| 25 GRLHGGVLMEWMVSAAALCGVRFSKG-EVVLAALDDLFFMNPVSVGDMVVVKAWVEYSGHSSMEVGVSAYA 94
                                      789**********************8.***************************************99886 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 1.6e-15
                                       TSSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETT CS
                              4HBT   1 gGvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrded 74 
                                       gG++ gG +l+llDe aga++ s++++  +v+++ +s  f+ p+r+g+ + ve  ++ +gr+sa+v  +v +e+
  gi|557694656|ref|YP_008797710.1| 187 GGIMSGGKLLHLLDEMAGAVAISYART-VAVTGAVDSTSFHYPIRQGSIVDVELVLTGVGRSSAEVAAKVITEN 259
                                       69*************************.*****************************************99887 PP

>> EIIBC-GUT_C  Sorbitol phosphotransferase enzyme II C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   8.3e-06      0.05      16      84 ..      40     107 ..      27     115 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.3e-06
                       EIIBC-GUT_C  16 gvliGteigkgaipvalalPalfainaqvgcdfvPvglslgeaepetvevGvpavllsrlltgpiavli 84 
                                       ++l G++++kg++    al  lf +n     d+v v   ++ +    +evGv+a  + r++  p+    
  gi|557694656|ref|YP_008797710.1|  40 AALCGVRFSKGEVVL-AALDDLFFMNPVSVGDMVVVKAWVEYSGHSSMEVGVSAYAYPRIVGEPMLTTT 107
                                       4699********965.69*****************************************9988876555 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00031       1.9      73     105 ..      50      82 ..      25      94 .. 0.71
   2 ?    3.5   0.0    0.0081        48      63     114 ..     203     252 ..     185     262 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00031
                                       TEGGGEEEEEEEE-S--BTTCEEEEEEEEEEEE CS
                   MaoC_dehydratas  73 nvvarvgeikvrFtkpVlpgdtlkvelevvgkr 105
                                       ++v     +++ F +pV +gd + v+++v+   
  gi|557694656|ref|YP_008797710.1|  50 GEVVLAALDDLFFMNPVSVGDMVVVKAWVEYSG 82 
                                       344667778899****************98655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0081
                                       HHHHHHHHSTTEGGGEEEEEEEE-S--BTTCEEEEEEEEEEEEEEEEEEEEE CS
                   MaoC_dehydratas  63 aklveeelgdnvvarvgeikvrFtkpVlpgdtlkvelevvgkrdvrktkkve 114
                                       a++v+  ++  v+     ++ +F  p + g+ ++vel+ +g+ +   +  v+
  gi|557694656|ref|YP_008797710.1| 203 AGAVAISYARTVAVTGAVDSTSFHYPIRQGSIVDVELVLTGVGRSSAE--VA 252
                                       555666666667677778999********************5554433..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2324.54
//
Query:       gi|557694657|ref|YP_008797711.1|  [L=331]
Description: FMN-dependent monooxygenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-57  193.3   0.4    8.1e-57  193.0   0.4    1.0  1  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.0   0.4   4.5e-61   8.1e-57      20     313 ..      18     306 ..       5     307 .. 0.90

  Alignments for each domain:
  == domain 1  score: 193.0 bits;  conditional E-value: 4.5e-61
                    Bac_luciferase  20 aslrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhl 96 
                                        ++++++e+a++aEelG+ ++w++e  +     + +  +laa+a +T+ri+lg+a++++++r+P+++A++aatL++l
  gi|557694657|ref|YP_008797711.1|  18 LTPQQFIEVAKRAEELGYSSLWMTEEMS-----RASPITLAAAALHTKRIKLGAAILNIFARTPMATAMEAATLQEL 89 
                                       478999**********************.....899999999999******************************** PP

                    Bac_luciferase  97 sgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgpiP..vyv 171
                                       s+ Rf+lglg ggp +  + +G+d + +++ + E++e++r+ ++ge+ +++G++++v+g++l+ ++   p+P  +y+
  gi|557694657|ref|YP_008797711.1|  90 SQNRFILGLGVGGPDISRKGHGADISNPVQKMSEYIEIVRKFLTGERLNYAGRHYRVDGVRLWIKQ---PRPteIYL 163
                                       *******************************************99999*********999999999...55666*** PP

                    Bac_luciferase 172 aaaspaglelaarhadglllageppeeaaelierlragaaeagrdpadirvgisltvivadtee..eAraearalia 246
                                       aa +p++l la+  adgl+l++++p +a+ + + +++g ++   +  +++    +  ++   +e   A+++  a+++
  gi|557694657|ref|YP_008797711.1| 164 AALNPQMLTLAGAKADGLILNLFDPRAAEYVHKAINKGLKNSHDQNRPFKKFSFVLAAASSEPEyfSALKRSVAFYL 240
                                       *************************************999977777777777777777666666224555559**** PP

                    Bac_luciferase 247 gldfyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvd 313
                                       ++++y+   ++ag++++ ++       +++++a + ++d++v++  ++ +  +v ++l++y++agv+
  gi|557694657|ref|YP_008797711.1| 241 SSPAYRRIMREAGHGEAVERFATVLETRGREAAVETIDDDVVESVSVICD-RDVSDQLERYRKAGVT 306
                                       ***************99998888888888888889999999999998876.57************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2421.70
//
Query:       gi|557694658|ref|YP_008797712.1|  [L=887]
Description: pyruvate phosphate dikinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-95  319.3   0.1    3.1e-95  318.7   0.1    1.3  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
      1e-53  182.8   0.0    1.6e-36  126.2   0.0    3.2  2  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
      5e-28   96.6   1.8    1.3e-27   95.4   1.8    1.7  1  PEP-utilizers    PEP-utilising enzyme, mobile domain
  ------ inclusion threshold ------
       0.15   12.6   0.0        2.5    8.7   0.0    2.8  3  DUF1801          Domain of unknown function (DU1801)


Domain annotation for each model (and alignments):
>> 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 !  318.7   0.1   6.9e-99   3.1e-95       5     293 ..     516     876 ..     512     877 .. 0.96

  Alignments for each domain:
  == domain 1  score: 318.7 bits;  conditional E-value: 6.9e-99
                                       TSCCCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHH.................. CS
                   PEP-utilizers_C   5 gklktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteee.................. 63 
                                       g+l++ll++++  +++ v aN+dtpe+a++a+++gaeGiGL+RtE++f+a e+lp+++e                  
  gi|557694658|ref|YP_008797712.1| 516 GELNKLLSLADRFRRLGVRANADTPEAAARARSFGAEGIGLCRTERMFNAPERLPIVREmimaetseerrralekll 592
                                       6778888999999**************************************************************** PP

                                       ..HHHHHHHHHHHTTTSEEEEEXXXSSCCGGSGGC.............................HHHH.XSXGGGSS CS
                   PEP-utilizers_C  64 ..qaeaykkvleamngrpvvvRtlDiggdkelpel.............................keepeevNPmlGf 109
                                         q+ ++ +++ am+g+pv+vR+lD + +++lp                               +  ++e NPmlG+
  gi|557694658|ref|YP_008797712.1| 593 pfQVGDFIGIFTAMKGLPVTVRLLDLPLHEFLPPAeeilkemfelvqkpgnekeiaarqellrkVLALKEHNPMLGH 669
                                       *********************************9999*************************998899********* PP

                                       XTHHHHCCSHHHHHHHHHHHHHHCCCC........EEEEEESSXXSHHHHHHHHHHHHHHHHHHHHCTCTXXTTXEE CS
                   PEP-utilizers_C 110 RgirlglsepelfetqlrAllrasaag........kleimlPmvasveeleeakkiieevkeelekegvkkkkkvkv 178
                                       Rg+rl++++pe++e+q+rA+l a++++        k++imlP+v++ +el   +kiiee++e+l ke ++++ ++kv
  gi|557694658|ref|YP_008797712.1| 670 RGCRLAIRYPEIYEMQVRAILTAAIEVrrrhgetaKIQIMLPLVSEKNELAYLRKIIEETAEKLFKE-LGERIDYKV 745
                                       *************************8888999999******************************99.********* PP

                                       EEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCCHCHHHH..........SXTTTCHHCCCHHHHHHHHH CS
                   PEP-utilizers_C 179 GiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdneevakl..........ydplepavlrlikevikaae 245
                                       G+MiE+p+aal+a ++a+ +dFfS+GtNDLtQ t + +Rd++e + +          ++p+e  + r++++++++a+
  gi|557694658|ref|YP_008797712.1| 746 GTMIETPRAALTAAEIAEVADFFSFGTNDLTQTTYGFSRDDAEAKFMadyleknivkHNPFESIDTRGVGRLVEMAT 822
                                       *******************************************665566678899********************** PP

                                       HCC......XEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
                   PEP-utilizers_C 246 ekg......lkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqve 293
                                       ++g      l+vgiCGe++gdp +v++++++Gld++S+s+++vp+ar a+aq++
  gi|557694658|ref|YP_008797712.1| 823 AEGkkanphLEVGICGEHGGDPDSVKFFHKAGLDYVSASPYRVPIARLAAAQAA 876
                                       ********9*****************************************9985 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 !  126.2   0.0   3.6e-40   1.6e-36       4     217 ..      21     289 ..      18     300 .. 0.96
   2 !   48.2   0.2     2e-16   9.2e-13     271     327 ..     301     355 ..     292     356 .. 0.94

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 3.6e-40
                            PPDK_N   4 vGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelPee 80 
                                       +GGKg++L ++ + +g+pvPpg +i ++a++ ++ e+    +i e l e                           e
  gi|557694658|ref|YP_008797712.1|  21 LGGKGYGLVQM-SAIGLPVPPGIIILTTACKMYYREG---GRIPEGLFE---------------------------E 66 
                                       8**********.66***********************...788888887...........................9 PP

                            PPDK_N  81 leeaikeayeelgkkfgde..elpvaVRSSataEDlpkasfaGqqdtyLnvggeeevle.................. 137
                                       l e+++ +++++gk++gd   +l+++VRS+      +  s++G++dt+Ln+g +++v e                  
  gi|557694658|ref|YP_008797712.1|  67 LMEKLRILEKKVGKRLGDPsnPLLLSVRSG------APYSMPGMMDTILNLGINDAVAEglakltgdrrfaydayrr 137
                                       ******************9999********......999************************************** PP

                            PPDK_N 138 ......................................................................aikavfa 144
                                                                                                             a++avf+
  gi|557694658|ref|YP_008797712.1| 138 fiqmfariamgvktdrfekileetkqrlgvrfdieipaeelrkiveefkrivkeetgrelpqdpseqlkmAVEAVFK 214
                                       ***************************************************************************** PP

                            PPDK_N 145 SlfnerAilYrkekgldheevalavvvqkmvnsdlg...asGVafsldpetG...fkdevlinasyGlGeaVVaGrv 215
                                       S++n+rAi+Yrk  +++ +++++av++q mv+++lg    +GV f++dp+tG     +e+l +a   +Ge+VVaG++
  gi|557694658|ref|YP_008797712.1| 215 SWNNPRAIEYRKFYKIP-DDLGTAVNIQMMVFGNLGensGTGVGFTRDPSTGekkLFGEYLPKA---QGEDVVAGIR 287
                                       *****************.********************99************655557888888...********** PP

                            PPDK_N 216 tp 217
                                       tp
  gi|557694658|ref|YP_008797712.1| 288 TP 289
                                       *9 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 2e-16
                            PPDK_N 271 eeLaeiakkiekhygtpmdiEfaideeegklyllQaRpetrtsekkekkaaetleee 327
                                       ++L e+a+k+ekh+++++d+Ef+++  +gklyllQ+R+++rt ++++k+a +++ee+
  gi|557694658|ref|YP_008797712.1| 301 RQLLEMAEKLEKHFRDMQDFEFTVE--NGKLYLLQTRNGKRTAQAAVKIAVDMFEEG 355
                                       799**********************..**************************9985 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 !   95.4   1.8   2.8e-31   1.3e-27       4      73 .]     418     500 ..     415     500 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 2.8e-31
                                       S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH..............HH--TEEEE CS
                     PEP-utilizers   4 egvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeati.............elkegdlit 67 
                                       e+vILv++et+p+di+g+ +a+G++t+rGGmtSHaA+vAr++g+PaVvg+++++i             +++ +d+it
  gi|557694658|ref|YP_008797712.1| 418 EKVILVRPETTPEDIKGIIAAQGVLTSRGGMTSHAAVVARGMGKPAVVGCESIKInmdeqlfvtadgvTVRHDDVIT 494
                                       45*****************************************************************888888**** PP

                                       EETTTT CS
                     PEP-utilizers  68 vDgstG 73 
                                       +DgstG
  gi|557694658|ref|YP_008797712.1| 495 IDGSTG 500
                                       *****9 PP

>> DUF1801  Domain of unknown function (DU1801)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.6   1.2e+04      63      82 ..      51      70 ..      48      71 .. 0.86
   2 ?   -0.0   0.0      0.28   1.3e+03      43      82 ..     148     184 ..     127     185 .. 0.67
   3 ?    8.7   0.0   0.00056       2.5       2      27 ..     716     745 ..     715     821 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.6
                                      EEEETTS---HHHHHHHHHH CS
                           DUF1801 63 irfkslddideelleelirk 82
                                      ++++++  i+e l+eel++k
  gi|557694658|ref|YP_008797712.1| 51 MYYREGGRIPEGLFEELMEK 70
                                      57889999*******99986 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.28
                                       ....HHTHHHHHH.-EEESSEEEEETTS---HHHHHHHHHH CS
                           DUF1801  43 Gak.edpkgllegkkgkgkrcirfkslddideelleelirk 82 
                                       G k +++++ le+  +k++  +rf  + +i++e+l++++++
  gi|557694658|ref|YP_008797712.1| 148 GVKtDRFEKILEE--TKQRLGVRF--DIEIPAEELRKIVEE 184
                                       3336667777765..455555555..589999999999986 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00056
                                       HHHHHHHHHHHHHHST....TSEEEEETTE CS
                           DUF1801   2 reelerLrklilealp....eveesikwgm 27 
                                       ++el +Lrk+i+e+++    e+ e+i +++
  gi|557694658|ref|YP_008797712.1| 716 KNELAYLRKIIEETAEklfkELGERIDYKV 745
                                       799***********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (887 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); 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: 0.74u 0.27s 00:00:01.01 Elapsed: 00:00:00.44
# Mc/sec: 6088.90
//
Query:       gi|557694659|ref|YP_008797713.1|  [L=138]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   20.3   0.0    0.00077   19.8   0.0    1.2  1  Penicillinase_R  Penicillinase repressor
     0.0031   17.6   0.2     0.0088   16.2   0.2    1.8  1  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
  ------ inclusion threshold ------
      0.013   15.3   0.0       0.03   14.1   0.0    1.6  1  HTH_IclR         IclR helix-turn-helix domain
      0.015   15.5   0.2      0.041   14.1   0.2    1.7  1  PaaX             PaaX-like protein
        0.1   12.5   0.0       0.14   12.0   0.0    1.3  1  SMC_Nse1         Nse1 non-SMC component of SMC5-6 complex
       0.11   12.5   0.0       0.32   10.9   0.0    1.7  2  MarR             MarR family


Domain annotation for each model (and alignments):
>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.6e-07   0.00077       8      70 ..      64     131 ..      58     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.6e-07
                                       HHHHHHHHS-...EEHHHHHHT--GG.G--.-HHHHHHHHHHHHHTTS-EEEEETTEEEEE----XXX CS
                   Penicillinase_R   8 vmeilwekge...atvkevveeleee.kel.aysTVktllrrLvkKgllsrekegrafiYsplvseee 70 
                                        m ++ ++ +    t++e+ e+ + e +e+   sT  t l rL ++g+l+r  +g+  +Y+ ++ e +
  gi|557694659|ref|YP_008797713.1|  64 LMSVIEKHFPysfFTSREIAEAYQYEfREPiPLSTASTYLARLAERGWLERTGSGNLARYRLVQGEAR 131
                                       566666665533468999999998887555599***************************99888766 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   2.9e-06    0.0088      14      44 ..      77     118 ..      73     118 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.9e-06
                           AbiEi_4  14 fttrel........ea.aGisp.sa.lrrLvrkGwLvrlrrG 44 
                                       ft+re+        ++   +s+ s+ l+rL ++GwL+r + G
  gi|557694659|ref|YP_008797713.1|  77 FTSREIaeayqyefREpIPLSTaSTyLARLAERGWLERTGSG 118
                                       56666555555555444445553336************9865 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     1e-05      0.03      30      51 ..      94     115 ..      93     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                                       S-HHHHHHHHHHHHHTTSEE.. CS
                          HTH_IclR  30 lpkStvhRlLqtLvelGyveqd 51 
                                       +p St++ +L+ L e+G++e+ 
  gi|557694659|ref|YP_008797713.1|  94 IPLSTASTYLARLAERGWLERT 115
                                       699*****************97 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   1.4e-05     0.041      42      66 ..     101     125 ..      95     128 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
                              PaaX  42 aalsRlakaGwlvrekegrrsfYrL 66 
                                       + l Rla++Gwl r+  g+ + YrL
  gi|557694659|ref|YP_008797713.1| 101 TYLARLAERGWLERTGSGNLARYRL 125
                                       5689********************9 PP

>> SMC_Nse1  Nse1 non-SMC component of SMC5-6 complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.7e-05      0.14     158     183 ..      94     119 ..      54     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.7e-05
                          SMC_Nse1 158 LtaseaeklLkrLveegWleksreGf 183
                                       +  s a + L+rL e gWle++ +G+
  gi|557694659|ref|YP_008797713.1|  94 IPLSTASTYLARLAERGWLERTGSGN 119
                                       56688999***************997 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.8   5.4e+03      20      31 ..      36      47 ..      34      49 .. 0.74
   2 ?   10.9   0.0   0.00011      0.32      32      50 ..      97     115 ..      93     119 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.8
                                      HHHHHHHHTS-H CS
                              MarR 20 vseLakklgvsk 31
                                      + +La++l++ +
  gi|557694659|ref|YP_008797713.1| 36 LYQLADFLELVS 47
                                      568999998765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHTTSEEEE CS
                              MarR  32 stvtrvldrLekkGlieRs 50 
                                       st+++ l rL ++G++eR+
  gi|557694659|ref|YP_008797713.1|  97 STASTYLARLAERGWLERT 115
                                       89****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1114.32
//
Query:       gi|557694660|ref|YP_008797714.1|  [L=256]
Description: proliferating cell nuclear antigen PCNA [Candidatus Caldiarchaeum subterraneum]
Scores for 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-18   65.2   0.1    3.1e-17   62.5   0.0    2.0  2  PCNA_N           Proliferating cell nuclear antigen, N-termin
    6.6e-09   36.0   0.3    7.7e-08   32.6   0.1    2.1  2  PCNA_C           Proliferating cell nuclear antigen, C-termin
      0.009   15.9   0.2      0.086   12.7   0.0    2.1  2  DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal 


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 !   62.5   0.0   5.1e-21   3.1e-17       5     114 ..      11     119 ..       7     125 .. 0.91
   2 ?    0.4   0.0     0.085   5.1e+02      59      82 ..     196     219 ..     172     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 5.1e-21
                                       EESSHHHHHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTT CS
                            PCNA_N   5 rleqasllkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkc 81 
                                        l  a  +  ++ ai  +v+e +f +d++ ++l  +D +hv+Lv++ ++ e+ e+y C++++ + vn++sl k lk 
  gi|557694660|ref|YP_008797714.1|  11 TLPSADYFASIVKAISAVVDEGSFTADSESLKLTGMDPAHVSLVNFVFNREAAEEYVCEKPVEIKVNISSLYKFLKR 87 
                                       5667778889******************************************************************* PP

                                       STTTSEEEEEEETTSSEEEEEEEECTSSEEEEE CS
                            PCNA_N  82 annedsvtlkaedeadtlalvfesekkdkiaey 114
                                       a+ne s+t++ ++++  l++vf ++ + k   +
  gi|557694660|ref|YP_008797714.1|  88 AGNE-SLTIEYDEDNKRLTIVFVNTAARKERRF 119
                                       *986.689999999********99998887754 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.085
                                       EEEESS-EEEEEEHHHHHHHHTTS CS
                            PCNA_N  59 kyrCDrnlalgvnlnslskilkca 82 
                                       +   D++++ + +l+ l ki+  +
  gi|557694660|ref|YP_008797714.1| 196 EISTDKEVSASFSLAYLEKIMSAS 219
                                       566799999999999999998655 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 ?    1.4   0.0     0.055   3.3e+02      11      42 ..      10      42 ..       2      96 .. 0.73
   2 !   32.6   0.1   1.3e-11   7.7e-08       2     127 ..     133     253 ..     132     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.055
                                      EEEEHHH.HHHHHHHHTTT-SEEEEEEETTEEE CS
                            PCNA_C 11 vklpsse.faricrdlsqlsdsvvisvtkegvk 42
                                      ++lps++ fa i++ +s + d+   ++  e++k
  gi|557694660|ref|YP_008797714.1| 10 LTLPSADyFASIVKAISAVVDEGSFTADSESLK 42
                                      567777657888888888777766666666655 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 1.3e-11
                                       ---SS-SEEEEEEHHHHHHHHHHHTTT-SEEEEEEETTEEEEEEEETTEEEEEEE--BEESSSGGGCBEEEESS-EE CS
                            PCNA_C   2 ipdseydavvklpssefaricrdlsqlsdsvvisvtkegvkfsasGdiGsasivlkqvkdvdkeeeavklelkepvt 78 
                                       ip + +da  ++ ++ f   + d + +sd   i +  + +  s++ d+ +  + l++  ++       +++ ++ v+
  gi|557694660|ref|YP_008797714.1| 133 IPKLTFDAKCRVDTAAFYEAVDDATIVSDYARIIIRPNELVISSKSDVQTHVTRLEKDGSL-----VHEISTDKEVS 204
                                       8999********************************************9985555444443.....4579******* PP

                                       EEEEHHHHHHHGGGG.GC-SEEEEEEETTSEEEEEEEETTCEEEEEEE-B CS
                            PCNA_C  79 ltfalkYlaeftkat.sLservtlslssevPlvveykikdvgllayllak 127
                                         f+l Yl +++ a+ +Ls++ +++ls + P+++ + +   g + +l+a+
  gi|557694660|ref|YP_008797714.1| 205 ASFSLAYLEKIMSASkTLSDETGIELSTNKPIKLSFPLTG-GKIEFLIAP 253
                                       ************99847*******************9975.566666665 PP

>> DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.057   3.4e+02      63     105 ..      63     106 ..      15     121 .. 0.71
   2 !   12.7   0.0   1.4e-05     0.086       8     105 ..     138     238 ..     132     253 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.057
                                       EEBEE.SS-EEEEEEHHHHHHHHHHH-SSEEEEEESSTTS-EEE CS
                   DNA_pol3_beta_3  63 dvnye.GeeleiafNvsYlldalkaleteevelqltdstkpvll 105
                                       + +y   +++ei  N+s l   lk   +e   +++ + +k + +
  gi|557694660|ref|YP_008797714.1|  63 AEEYVcEKPVEIKVNISSLYKFLKRAGNESLTIEYDEDNKRLTI 106
                                       33444478888888888888888888888888877777776655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 1.4e-05
                                       -SEEEEEEHHHHHHHHHHHHTTSSTSTGEEEEEEETTEEEEEEEETTSEEEEE...EEEEBEE.SS-EEEEEEHHHH CS
                   DNA_pol3_beta_3   8 fkkkvtvdlkelkealkRvalladeknrkvrLsleegqlklsaensevgeaeE...evdvnye.GeeleiafNvsYl 80 
                                       f++k  vd+++++ea++ + +++d  ++ + +  +e ++  +++ + + +  E    +  +++  +e++ +f+  Yl
  gi|557694660|ref|YP_008797714.1| 138 FDAKCRVDTAAFYEAVDDATIVSD--YARIIIRPNELVISSKSDVQTHVTRLEkdgSLVHEIStDKEVSASFSLAYL 212
                                       688999*****************8..66666666666666666655555555555555566667999*********9 PP

                                       HHHHHHH-S..SEEEEEESSTTS-EEE CS
                   DNA_pol3_beta_3  81 ldalkalet..eevelqltdstkpvll 105
                                          ++a +t  +e  ++l+++ kp++l
  gi|557694660|ref|YP_008797714.1| 213 EKIMSASKTlsDETGIELSTN-KPIKL 238
                                       777766554224555555443.46666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2114.30
//
Query:       gi|557694661|ref|YP_008797715.1|  [L=364]
Description: metalloprotease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   48.7  11.3    2.4e-08   33.6   0.5    2.9  2  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
       0.21   11.4   0.0       0.55   10.0   0.0    1.8  2  NETI           NETI protein


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 !   17.4   4.7   2.3e-07    0.0021       2     108 ..     129     208 ..     128     236 .. 0.81
   2 !   33.6   0.5   2.7e-12   2.4e-08     188     248 ..     256     316 ..     236     318 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.3e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallp.....LGGyVkmageepeeelse 73 
                                       f l+l+ ++++HE+GH + Ak  gv                   +++Y+i+ lp     LG+++  ++   +++   
  gi|557694661|ref|YP_008797715.1| 129 FSLALLGIIFIHEMGHKISAKIDGVAA-----------------SLPYFIPGLPgvlptLGAVIFQKEPLANRD--- 185
                                       889**********************99.................779999999988888888766555553333... PP

                                       X....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  74 eeakaflkkspwqrllivlAGplanfilailvfvv 108
                                                     +   ++Gp+a+f++a+lv ++
  gi|557694661|ref|YP_008797715.1| 186 ------------DMFDLGVSGPVAGFVVAVLVTFL 208
                                       ............78999999999999999999887 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 2.7e-12
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 188 lssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevanlvglalll 248
                                       + +++ ++a++++ ++ lNL+Pi++LDGg++++++l++ ++   s  + +++ l+g+ ++ 
  gi|557694661|ref|YP_008797715.1| 256 FFMTVGFAAWLGMVVTALNLMPIWQLDGGRIFRSFLSRRQHMIASYAALALLVLAGYYFMA 316
                                       457899*****************************99888777777777777777776665 PP

>> NETI  NETI protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   6.2e-05      0.55       2      33 ..      34      68 ..      33      72 .. 0.80
   2 ?   -3.6   0.0       1.1   9.6e+03      19      24 ..     250     255 ..     249     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.2e-05
                              NETI  2 feVeene...TIedcLeRmkkeGYmPvrRiEkPvF 33
                                      feV ++e     ++cL+ +kk G+++  R+E+ v 
  gi|557694661|ref|YP_008797715.1| 34 FEVLDGEiktAFKNCLAELKKIGFLASARREQSVI 68
                                      77777664435799*****************9775 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.1
                              NETI  19 keGYmP 24 
                                       ++GY+P
  gi|557694661|ref|YP_008797715.1| 250 RQGYVP 255
                                       79***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2704.55
//
Query:       gi|557694662|ref|YP_008797716.1|  [L=354]
Description: hypothetical protein CSUB_C1235 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); 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:                         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: 00:00:00.41
# Mc/sec: 2575.13
//
Query:       gi|557694663|ref|YP_008797717.1|  [L=213]
Description: nitroreductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-28   97.8   0.0    8.5e-28   97.5   0.0    1.1  1  Nitroreductase  Nitroreductase family
      0.004   16.7   0.0       0.13   11.8   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 !   97.5   0.0   9.5e-32   8.5e-28       1     169 [.      15     186 ..      15     187 .. 0.90

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 9.5e-32
                                       HHH--B---B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHH.HHHHHHHHTT-SS-GGGGG CS
                    Nitroreductase   1 irkRrSiRkFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaa.lelllkaeaqaelaqryrk 76 
                                       i++RrS + +    vp e++ k lea+ +a +a+n+qpwrfvvv+d +++++l e + +e+l  + a+ ++  + r 
  gi|557694663|ref|YP_008797717.1|  15 IKSRRSSKSLGVGEVPFEVVLKALEAGVWAANAHNAQPWRFVVVSDPDVKRRLIEEMgREWLSDLLADGVDEAKAR- 90 
                                       89******************************************99999966666651455556667777666666. PP

                                       GHHHHHHHHHHHHSSEEEEE....---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHH CS
                    Nitroreductase  77 eelklkaqkalagapvlivi....vatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaee 149
                                        +  ++ + +  +a  +iv+    ++   +++ k+++ +y   +++++aa+qn+lLa +alG+g+c+   +  a e 
  gi|557694663|ref|YP_008797717.1|  91 -QIVESSNGRSMRASYIIVAclcmRDMDVYWDSKRSRCEYVMGVQSVAAALQNILLAVHALGYGACWRCSPLFAPEA 166
                                       .6889******************999999999999999*************************************** PP

                                       HHHHHT-S..SEEEEEEEEE CS
                    Nitroreductase 150 vrkllglpdeeeivvliavG 169
                                       v+++lglp+ +e+++++ +G
  gi|557694663|ref|YP_008797717.1| 167 VKRVLGLPSSYEPMAFVEIG 186
                                       ********99*****99988 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   1.5e-05      0.13     158     191 ..      32      65 ..       2      79 .. 0.79
   2 !    3.0   0.0    0.0071        63      88     108 ..     140     160 ..     138     209 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHTS--GGG----EEE.E-SSEE.. CS
                    TM1586_NiRdase 158 ewfkeileaarlAPsAlNqqpwrfelkdddeiki 191
                                       e + ++lea   A  A N qpwrf +++d ++k 
  gi|557694663|ref|YP_008797717.1|  32 EVVLKALEAGVWAANAHNAQPWRFVVVSDPDVKR 65 
                                       556789*******************999888765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0071
                                       HHHHHHHHHHTT-EEEEES-- CS
                    TM1586_NiRdase  88 geqlvLkltalGlgtcWvggt 108
                                       +++++L + alG g cW  + 
  gi|557694663|ref|YP_008797717.1| 140 LQNILLAVHALGYGACWRCSP 160
                                       57899************7654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1569.20
//
Query:       gi|557694664|ref|YP_008797718.1|  [L=310]
Description: LPPG:Fo 2-phospho-L-lactate transferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-49  166.5   0.0    9.3e-49  166.2   0.0    1.0  1  UPF0052   Uncharacterised protein family UPF0052


Domain annotation for each model (and alignments):
>> UPF0052  Uncharacterised protein family UPF0052
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.2   0.0   5.2e-53   9.3e-49       2     274 ..       3     283 ..       2     299 .. 0.89

  Alignments for each domain:
  == domain 1  score: 166.2 bits;  conditional E-value: 5.2e-53
                                       EEEE-CHHHHHHHHHHCCSS..CEEEEEE-----SHHHHHHHHHHTS---HHHHHHHHHH..--S-C.......... CS
                           UPF0052   2 vvlgGGtGlskllrglkevt..aeltavvtvaDdggssGelrrelgllaigDirnvlval..idder.......... 64 
                                       ++l+GG+G+skll+gl++v   +   +vv++aDd    G       l + +Di+++++++  i d+           
  gi|557694664|ref|YP_008797718.1|   3 TALAGGVGGSKLLTGLRHVMypETGAVVVNTADDENFYG-------LHVSPDIDTIIYQMagIGDDAkgwgikddtf 72 
                                       689****************9977778899**********.......**************88555556888877778 PP

                                       .HHHHHCH-B-SS.....SSSSTT-BHHHHHHHHHHHHHS.-HHHHHHHHHHHTT-SSEEEES-SS--EEEEEETTS CS
                           UPF0052  65 .lleeLfqyRfkg.....dgdlaghslgnllLaalaeltg.sleeaiealskilkvrgrvlPatddpvelsaeledG 134
                                        +le L +  +++     d+d+a+h+++++ L++     g sl++++++l++ l+v+ r+lP+tddpv++ +e+e G
  gi|557694664|ref|YP_008797718.1|  73 nVLEMLGRMGLETwfkigDRDFATHIYRTIRLNE-----GaSLTQVTAELAEKLGVSWRILPMTDDPVKTIVETEIG 144
                                       877777777666688888****************.....99************************************ PP

                                       -EEESTTTGGGG-S....-EEE.EEEESTT----HHHHHHHHH-SEEEE-SS-IIIIIHHHHTSCCHHHHHHH-SSE CS
                           UPF0052 135 eeitgeskiseark.lkapikr.vflepegaeaapevleaikeAdlivlgpGslytSiiPiLlvpgiaealreskak 209
                                           + + +   ++  + +++   f + e+a++ +ev++a+++A+ i++ p+++++Si+PiL+++g+++ lr+s+a+
  gi|557694664|ref|YP_008797718.1| 145 PLPFQTYFV---KHrYSLKVHGiRFQGIEKAKPVKEVVTALSHAQHIIIPPSNPVVSIGPILALQGVRDLLRNSNAT 218
                                       *888*****...343699****9****************************************************** PP

                                       EEEE--SB--TTTSTT-BHHHHHHHHHHCH-.....SS....S...-SEEEEE-S---HHHHHHHHTTT--B- CS
                           UPF0052 210 kvlvsnimtqkGetdgfsvsdhvkaieravg.....kgvakay...vdavlvntsevpeellekyaaegkepv 274
                                       +++vs+i+       g +++++++++++++g      gva++y   +d ++ +t+  +eell++ ++ g +p+
  gi|557694664|ref|YP_008797718.1| 219 ILAVSPIVR------GQALRGPAAELMKSMGyepspVGVAEMYhdfLDILVFDTA--DEELLQDVKRLGVKPL 283
                                       ********8......****************999995666666676999999999..8888887666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2240.19
//
Query:       gi|557694665|ref|YP_008797719.1|  [L=196]
Description: hypothetical protein CSUB_C1238 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   70.4   0.0    1.6e-19   70.0   0.0    1.1  1  CofC          Guanylyl transferase CofC like
     0.0076   16.0   0.0      0.012   15.3   0.0    1.2  1  EcsC          EcsC protein family
  ------ inclusion threshold ------
      0.013   15.8   0.0      0.017   15.5   0.0    1.2  1  NTP_transf_3  MobA-like NTP transferase domain


Domain annotation for each model (and alignments):
>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0   2.6e-23   1.6e-19       3     184 ..       5     180 ..       3     191 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 2.6e-23
                              CofC   3 viiPvsainsaktrlseilseeerkellkamlldvidalkr..ldvlvvsedeevleyaldelgvevvkekekdlnt 77 
                                       +i+Pv++ ++ak+rls +l  + r +l+++++  v ++  +  l    v+ d+++   a  elg + + ++ ++ln 
  gi|557694665|ref|YP_008797719.1|   5 AILPVKNLAQAKSRLSTVLPMDSRLNLARKLFNHVWKTCLEagLRPYAVTSDKNL---AA-ELGKNAIPDTGHGLNR 77 
                                       799********************************99764424666777778765...33.7899************ PP

                              CofC  78 avekafeeieekeviiipsdiPlikkedvkdllelekradvviaParg.GGtnllllr.ksalevkyedfsflkhle 152
                                       a+++a+e  +     ii  d+P+++  d+k ++e     + v+ P ++  Gtn++++   ++ +  ++  sf+khl+
  gi|557694665|ref|YP_008797719.1|  78 AIKHALETLKPTSYFIILPDLPMLTATDLKTIYEIGC--EYVVCPDKKlRGTNIIYVNkWDGYQPCFGVNSFMKHLR 152
                                       **********************************998..77899988747*******9569***************6 PP

                              CofC 153 earkrglkvkiydsfylsvdinteedlgeill 184
                                             +  kiy  +  ++di++++dl  + l
  gi|557694665|ref|YP_008797719.1| 153 ----LHICPKIYYGLGTALDIDEPSDLSLLAL 180
                                       ....57999*****************987655 PP

>> EcsC  EcsC protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     2e-06     0.012     111     135 ..      92     116 ..      89     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-06
                              EcsC 111 llllaDiPlllglklkvlqeiAliY 135
                                       +++l+D+P+l++  lk+++ei+  Y
  gi|557694665|ref|YP_008797719.1|  92 FIILPDLPMLTATDLKTIYEIGCEY 116
                                       7899******************998 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 ?   15.5   0.0   2.8e-06     0.017      24     110 ..      33     112 ..      22     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-06
                                       CCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT-- CS
                      NTP_transf_3  24 kpllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacDmPllt 100
                                       + l+ +v ++  +ag+++ + v+ d++++   a+lg   ++d+  g g   ++++al+ + + + +++++ D+P+lt
  gi|557694665|ref|YP_008797719.1|  33 RKLFNHVWKTCLEAGLRP-YAVTSDKNLA---AELGKNAIPDT--GHGLNRAIKHALETL-KPTSYFIILPDLPMLT 102
                                       568889999999999866.6666666665...56888999997..89************9.999************* PP

                                       HHHHHHHHHC CS
                      NTP_transf_3 101 pelverllaa 110
                                       +  ++++ + 
  gi|557694665|ref|YP_008797719.1| 103 ATDLKTIYEI 112
                                       ***9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1462.50
//
Query:       gi|557694666|ref|YP_008797720.1|  [L=459]
Description: hypothetical protein CSUB_C1239 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   11.9   0.0       0.21   11.1   0.0    1.3  1  OLF       Olfactomedin-like domain


Domain annotation for each model (and alignments):
>> OLF  Olfactomedin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.2e-05      0.21     128     177 ..     124     167 ..     110     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.2e-05
                               OLF 128 idlavDEnGLWviYateenegnivvskldpetleveqtwntslkkesvgn 177
                                         la D++G++v+Y+   +     v kldp + +v  +wn+++++ s+++
  gi|557694666|ref|YP_008797720.1| 124 SSLAGDDTGVYVVYPRLGR-----VEKLDPVSRQVAASWNVRVSE-SIKA 167
                                       5799**************9.....*****************9864.4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3356.51
//
Query:       gi|557694667|ref|YP_008797721.1|  [L=417]
Description: beta-lactamase domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-12   47.6   0.0    2.6e-12   46.5   0.0    1.6  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    3.1e-12   46.4   0.1    7.1e-12   45.3   0.1    1.6  2  Lactamase_B_2  Beta-lactamase superfamily domain
    1.9e-11   44.3   0.0    3.7e-11   43.3   0.0    1.5  1  Beta-Casp      Beta-Casp domain
    3.4e-08   33.2   0.0    6.8e-08   32.2   0.0    1.5  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    1.9e-07   31.3   0.5    8.1e-07   29.2   0.5    2.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    0.00068   19.6   0.1      0.011   15.7   0.0    2.4  2  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> 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 !   46.5   0.0   8.5e-16   2.6e-12       3      62 .]     349     409 ..     347     409 .. 0.92

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 8.5e-16
                             RMMBL   3 pvkarieeidfSgHadknellelirklkprn.vilvHGeeeatsalarllkeeegidvfiP 62 
                                       p+++ i+++ fSgHa++++l +++rk++    ++ vHGe+e++++l  ++++e g ++ +P
  gi|557694667|ref|YP_008797721.1| 349 PANCIIKQFRFSGHAGRSQLHDYLRKIETNAkIFTVHGEPEMCKTLSTWAQQELGLEATAP 409
                                       67899**********************99889******************88889887665 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 !   45.3   0.1   2.4e-15   7.1e-12       1     171 [.      24     191 ..      24     217 .. 0.74
   2 ?   -3.1   0.0       1.6   4.7e+03      50      76 ..     372     400 ..     369     411 .. 0.62

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.4e-15
                                       SEEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH......... CS
                     Lactamase_B_2   1 rriLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla......... 68 
                                       +riL+D g  l  +  +   P + +++ ++++a++lthaH DH  g+++l   r+   +ly + ++++         
  gi|557694667|ref|YP_008797721.1|  24 TRILLDYGVMLNDH--PEF-PMP-VET-KKLNAIILTHAHLDHSGGIPMLYINRNP--KLYTTSMTRDtatllikdf 93 
                                       57777777776444..444.333.344.89**********************5554..4776666665444555554 PP

                                       .HCCTTCGHHHCHTT.........TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTE CS
                     Lactamase_B_2  69 .vleanfvylaleee.........pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggk 135
                                        +l+ +                     n++++   e+f++g  +lei+++ a h  g          + +++  g+k
  gi|557694667|ref|YP_008797721.1|  94 iKLSGQY-------LlfenqelekMLRNTRTFYYREPFTVG--DLEIELVDAGHIPGS---------AQVLVN-GDK 151
                                       4333332.......1343345778888999999*******9..699*****9999998.........555555.9** PP

                                       EEEEESS-S---....HHHHHHHCT-SEEEEE-S-SSTTH CS
                     Lactamase_B_2 136 rvyyigDtgyip....eeigerlggadllllditayedde 171
                                       +++y+gD  +++    + +++ +g++d ++++ t+ ++d 
  gi|557694667|ref|YP_008797721.1| 152 TLVYTGDFTTVKtrmlDGADTTIGDVDAVIIESTYAHEDH 191
                                       ***********96555556799999999999999988876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.6
                                       CCC..C--EE.EEEEEEHHHHHHCCTTCGH CS
                     Lactamase_B_2  50 lre..lrpkk.lplyapkgvlavleanfvy 76 
                                       lr+  + + k +++++ +++ ++l+++ ++
  gi|557694667|ref|YP_008797721.1| 372 LRKieTNA-KiFTVHGEPEMCKTLSTWAQQ 400
                                       45532222.247777778888888877543 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   1.3e-14   3.7e-11       2     108 ..     226     333 ..     225     335 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.3e-14
                                       HHHHHHH..HCTT..TTS-S-EEEEE-HHHHHHHHHGGGGGG.E-SHH.....HHH......H..HH....HS-SSE CS
                         Beta-Casp   2 qellylLeelwkekkledlklpiyldsplaskatevYkeyae.veaks.lewmesk......keeln....sskgpk 66 
                                       qe+l++L  +           pi ld+ +a+k++e Y + ++ v++ + le  ++k      +   +      ++p 
  gi|557694667|ref|YP_008797721.1| 226 QEILCILAAHNFP-------HPIWLDG-MAKKTLETYLSDKRfVDNVDiLEKASRKtrfvkgR---RgretALSEPG 291
                                       8999999888832.......39*****.*********99999966666666666664333322...044446789** PP

                                       EEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHH CS
                         Beta-Casp  67 vilassgmlegGrsrellkklledprntvilvgyqaegTlgr 108
                                       vi++  gml+gG++ ++  +++ed++++++l ++q +gT+g+
  gi|557694667|ref|YP_008797721.1| 292 VIVTPAGMLKGGPALYYAPEIVEDEKSAIFLSSFQIPGTPGE 333
                                       ****************************************97 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 !   32.2   0.0   2.3e-11   6.8e-08       1     176 [.      18     173 ..      18     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 2.3e-11
                     Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvk 77 
                                       l+++ n++iLlD G+  ++    +   ++    +++++i+L+ha l+h G+ ++ly++       n + y+t  +  
  gi|557694667|ref|YP_008797721.1|  18 LVSYKNTRILLDYGVMLNDH--PE--FPMPVETKKLNAIILTHAHLDHSGGIPMLYIN------RNPKLYTTSMTRD 84 
                                       5778899********98733..22..35666689**********************87......57899******** PP

                     Lactamase_B_6  78 LGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiskese 154
                                        + +++ d ++ +g         +e ++ +++  + +t  Y  ++++     +l i    aGh +G +   + ++ +
  gi|557694667|ref|YP_008797721.1|  85 TATLLIKDFIKLSGQYL-----LFENQELEKMLRNTRTFYYREPFTVG----DLEIELVDAGHIPGSAQ-VLVNGDK 151
                                       **999999988665543.....4667899***************9998....599**********9775.5677889 PP

                     Lactamase_B_6 155 kivYavdwnhakeshLngaall 176
                                       ++vY  d+   k ++L+ga++ 
  gi|557694667|ref|YP_008797721.1| 152 TLVYTGDFTTVKTRMLDGADTT 173
                                       ******************9864 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.5   2.7e-10   8.1e-07      13     160 ..      21     168 ..      12     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.7e-10
                                       ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHH CS
                       Lactamase_B  13 gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeadd 89 
                                        +++ iL D G+      ++       ++ k++ a+ilTH+HlDH Gg + l   ++ + +  + +    +   +d+
  gi|557694667|ref|YP_008797721.1|  21 YKNTRILLDYGVMLNDHPEFP----MPVETKKLNAIILTHAHLDHSGGIPMLYINRNPKLYTTSMTRDTATLLIKDF 93 
                                       566666666666666666664....7778899*******************************************99 PP

                                       HHHHCCHH....TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCC CS
                       Lactamase_B  90 aasrkgll....lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgri 160
                                           ++ l     + +    + ++   ++ ++ g+++ + +      ++  v+ +g++++++tGD++ +  + ++
  gi|557694667|ref|YP_008797721.1|  94 IKLSGQYLlfenQELEKMLRNTRTFYYREPFTVGDLEIELVDAGHIPGSAQVLVNGDKTLVYTGDFTTVKTRMLD 168
                                       999999889*99666666667777777777777777777777777777777777899999999999876665555 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 !   15.7   0.0   3.6e-06     0.011       6      88 ..      13     141 ..      11     184 .. 0.63
   2 ?    1.6   0.0     0.077   2.3e+02      35      57 ..     175     199 ..     140     222 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.6e-06
                     Lactamase_B_3   6 ghnsflletagarilvDPf.....kanlgyeppaeeaDlvlisqaledHahletlkql................... 58 
                                       g + +l++ +++ril+D++     +++  +  ++++ +++++++a+ dH    ++  +                   
  gi|557694667|ref|YP_008797721.1|  13 GRSGILVSYKNTRILLDYGvmlndHPEFPMPVETKKLNAIILTHAHLDHSGGIPMLYInrnpklyttsmtrdtatll 89 
                                       678889999**********776543366667777***************8766665554444445555555444444 PP

                     Lactamase_B_3  59 ......................aenvkvleegeslevggleiravatshdav 88 
                                                              +n+++    e ++vg+lei+ v + h ++
  gi|557694667|ref|YP_008797721.1|  90 ikdfiklsgqyllfenqelekmLRNTRTFYYREPFTVGDLEIELVDAGHIPG 141
                                       4444444444444444333333333333333677888888888887777433 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.077
                     Lactamase_B_3  35 eeaDlvlisq..aledHahletlkq 57 
                                        ++D+v+i +  a+edH+  ++l++
  gi|557694667|ref|YP_008797721.1| 175 GDVDAVIIEStyAHEDHNPRQELEK 199
                                       6788888865458999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2873.51
//
Query:       gi|557694668|ref|YP_008797722.1|  [L=80]
Description: hypothetical protein CSUB_C1241 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 624.20
//
Query:       gi|557694669|ref|YP_008797723.1|  [L=317]
Description: deoxyhypusine synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-81  273.8   0.0    1.7e-81  273.7   0.0    1.0  1  DS        Deoxyhypusine synthase


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 !  273.7   0.0   9.5e-86   1.7e-81       1     287 [.      30     311 ..      30     312 .. 0.97

  Alignments for each domain:
  == domain 1  score: 273.7 bits;  conditional E-value: 9.5e-86
                                DS   1 ellesyeki.gfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlik 76 
                                       ell+ ++++ gf++++l+ea+++l+++ +d++c  ++++t+nl+++Glr++++++ ++k++d++ tT+g +++D+++
  gi|557694669|ref|YP_008797723.1|  30 ELLRMMGRMgGFMGAHLAEAYQLLRDVLSDRECLRMVSFTGNLVATGLRGVLVEMLRRKWFDLVFTTCGAVDHDIAR 106
                                       6999************************************************************************* PP

                                DS  77 algkktylgdfelddeeLrekginRignllvpneny.ckfedwvreildkleeeqkvwspselikelGkeindeeSi 152
                                       + +  + +g+f++dd eL ek+i+R+gn+++++++y   +e+ v+e++ +l +   ++ + e+++++G+++ +e+S 
  gi|557694669|ref|YP_008797723.1| 107 TRSR-YRIGSFDADDWELAEKNIHRLGNVYIDQQSYgLVVEREVAELVGELGHG-AELPVYEVLWRVGEKLGSENSW 181
                                       *998.*******************************999************985.568******************* PP

                                DS 153 lywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanl 229
                                       lyw++++++pv +p++ Dg++G ql+l        k++l   kD + ln++++++++ + +i+GGG++Khh+l++ +
  gi|557694669|ref|YP_008797723.1| 182 LYWCHRHKVPVMVPGIFDGAFGYQLWLRG------KIRLSYEKDQNLLNEVMWSSRRKAGLIIGGGISKHHLLWWSQ 252
                                       ***********************999877......5999************************************** PP

                                DS 230 m.rngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlvaa 287
                                       + ++g++ avyi+ta+e+dGslsga+++Eav+w ki+++a++v v +DaT++lP+lv a
  gi|557694669|ref|YP_008797723.1| 253 FgGEGLEAAVYISTADEYDGSLSGARPREAVTWHKISSKARHVFVKTDATVALPILVLA 311
                                       *446****************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2355.39
//
Query:       gi|557694670|ref|YP_008797724.1|  [L=406]
Description: aspartate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-46  158.2   0.1    3.4e-46  157.8   0.1    1.2  1  AA_kinase  Amino acid kinase family
    2.2e-07   30.5   1.4    1.1e-06   28.3   0.2    2.5  2  ACT_7      ACT domain
  ------ inclusion threshold ------
      0.024   14.4   0.1        0.1   12.4   0.1    2.1  1  ACT        ACT domain
       0.14   12.1   0.0       0.61   10.0   0.0    2.1  2  YfdX       YfdX protein


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 !  157.8   0.1   7.6e-50   3.4e-46       3     233 ..       4     229 ..       2     236 .. 0.94

  Alignments for each domain:
  == domain 1  score: 157.8 bits;  conditional E-value: 7.6e-50
                                       EEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC.....E..HHHHHHH CS
                         AA_kinase   3 vVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllalksglssgelaa.glrstleeageva 77 
                                        VvKlGGs+l+d+    ++r+   i+ l e+gnk+vvV+++ +++td+ll+  + l+++   +              
  gi|557694670|ref|YP_008797724.1|   4 YVVKLGGSVLADEVS--IERASSWIKGLLEKGNKVVVVVSAlKGVTDELLRSSQRLHPDAPPEmL------------ 66 
                                       6************99..***********************************8888888877322............ PP

                                       HHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE............HHHTTTCEEECCHHHHHHHTT-EEEEE CS
                         AA_kinase  78 trdalaslgerlvaallaaglpavglsaaaldateagr..........degsdgnvesvdaeaieelleagvvpvlt 144
                                         d+++++ger +a+l++ +l+ +g+++  +d+ +  +           ++  +++++  +e +++l+e+g+vpv++
  gi|557694670|ref|YP_008797724.1|  67 --DEILAMGERTSARLFTLALRRQGVDSVLIDPASPHWpiitnnqhldATPLLETCRQKVSEGLAKLVEQGKVPVVC 141
                                       ..********************************9999******9999999999999999***************** PP

                                       SEEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTH CS
                         AA_kinase 145 gfigldeege...lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgG 218
                                       g++gl+ +g+    grg+sDt+a+ lA++l+Ad++i+++dV+GVy+ dp+k++ a++l+ ++++e+      l++gG
  gi|557694670|ref|YP_008797724.1| 142 GYVGLTIDGKittMGRGGSDTTAVVLANCLDADEVILVKDVSGVYSTDPRKDSEAEVLEVLTAEEVFR----LSKGG 214
                                       ********************************************************************....***** PP

                                       HHHCHHHHHHHHHCT CS
                         AA_kinase 219 mkvkhpaalaaarrg 233
                                       +kv+h +al +++  
  gi|557694670|ref|YP_008797724.1| 215 AKVIHSKALLFLHPR 229
                                       *********999764 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.18   8.2e+02       5      27 ..     263     284 ..     261     291 .. 0.76
   2 !   28.3   0.2   2.5e-10   1.1e-06       6      63 ..     337     394 ..     335     396 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.18
                                       EEEEEEE-S-.---SS--HHHHH CS
                             ACT_7   5 gwiklsvvgsglpfdvtGivakl 27 
                                       ++ +++++g+++ ++ ++i+a++
  gi|557694670|ref|YP_008797724.1| 263 NITMVTIIGESM-GEPSKIAAAV 284
                                       67899*****88.6566777665 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 2.5e-10
                                       EEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHHH CS
                             ACT_7   6 wiklsvvgsglpfdvtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAveaL 63 
                                        + +++ g+ l + v+G++ k ++pLa +g+++f +     ++ i+V  +d+ekAv+  
  gi|557694670|ref|YP_008797724.1| 337 LSLIKIYGAMLEL-VPGVIFKAVQPLATQGVNLFGVLtISSSIRIFVSTKDVEKAVNLI 394
                                       5679999**9999.********************8776999***************976 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   2.3e-05       0.1      10      60 ..     350     395 ..     350     397 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                                       STTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHH CS
                               ACT  10 rPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevle 60 
                                       +PG++++  + la  g+N+  + + ss     +i ++v + d e + ++++
  gi|557694670|ref|YP_008797724.1| 350 VPGVIFKAVQPLATQGVNLFGVLTISS-----SIRIFVSTKDVEKAVNLIK 395
                                       5**************************.....7888888888877776665 PP

>> YfdX  YfdX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.91   4.1e+03      12      34 ..     105     127 ..     104     137 .. 0.74
   2 ?   10.0   0.0   0.00014      0.61      16      89 ..     279     405 ..     276     406 .] 0.79

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.91
                                       HCTT-HHHHHHHHHHHHHHHTS- CS
                              YfdX  12 ldqgdtkeAkkllekAqgkleaa 34 
                                       + +++  +A++lle +++k ++ 
  gi|557694670|ref|YP_008797724.1| 105 ITNNQHLDATPLLETCRQKVSEG 127
                                       56677778999999999887665 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00014
                                       -HHHHHHHHHHHHHHHTS-HHHHHCCB-.................S--SSSS......................... CS
                              YfdX  16 dtkeAkkllekAqgkleaaladdpklvk.................kapasad......................... 50 
                                       ++++A+k +e+A gkl+aa+ ++ +l+                  ++++ ++                         
  gi|557694670|ref|YP_008797724.1| 279 KIAAAVKSVESAGGKLAAASVEEESLILylrgdgeiveklhdyfvQNRLGKAvshfpnlslikiygamlelvpgvif 355
                                       6789**********************889999988888887777744444446667788888888889999999999 PP

                                       ...........-EEEEEEEEEEE------HHHHHHHHHHHHHHHTT-HHH CS
                              YfdX  51 ...........alvPvdaevividdladtpekkaaikkanellkkgdtqa 89 
                                                  +l  v +    i  +++t+++++a++ ++++l +  tq+
  gi|557694670|ref|YP_008797724.1| 356 kavqplatqgvNLFGVLTISSSIRIFVSTKDVEKAVNLIKKNLSEYMTQE 405
                                       999999995554444444444455599****************9998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3040.32
//
Query:       gi|557694671|ref|YP_008797725.1|  [L=756]
Description: aldehyde oxidase and xanthine dehydrogenase, molybdopterin binding [Candidatus Caldiarchaeum subterraneum]
Scores for 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-157  523.6   0.1   6.5e-157  523.3   0.1    1.0  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    1.1e-27   96.6   0.0    2.8e-27   95.2   0.0    1.8  1  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a
  ------ inclusion threshold ------
       0.02   14.6   0.2       0.15   11.7   0.0    2.1  2  Peripla_BP_6   Periplasmic binding protein
      0.033   13.4   0.0      0.058   12.6   0.0    1.3  1  UvdE           UV-endonuclease UvdE


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 !  523.3   0.1  1.4e-160  6.5e-157       2     549 ..     144     688 ..     143     689 .. 0.96

  Alignments for each domain:
  == domain 1  score: 523.3 bits;  conditional E-value: 1.4e-160
                                       TTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHH CS
                     Ald_Xan_dh_C2   2 heeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlva 76 
                                       he  + n+ +  +i++G+ve++f++++ vve+e+rt  q h++lEt+a + ++ de+g +tv +  q p+  ++ + 
  gi|557694671|ref|YP_008797725.1| 144 HE--GGNISRstRITFGNVEEGFKASEAVVENEYRTAPQIHMFLETEAGFSYI-DEKGVITVVAGGQSPYRDHHEIV 217
                                       55..667766778999*************************************.89********************* PP

                                       HHHT--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS- CS
                     Ald_Xan_dh_C2  77 evlglpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGk 153
                                       ++l+lp++kvrv+ p vGG+FGgK ++v++++++al+++ktgr  ++v dR+e+ +a +krh+ ++++k+ga++dGk
  gi|557694671|ref|YP_008797725.1| 218 STLQLPPEKVRVVIPHVGGAFGGK-DDVSVQIYLALVTWKTGRAARFVWDRDESTIAGTKRHASIVRMKTGASADGK 293
                                       ************************.**************************************************** PP

                                       EEEEEEEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 154 italdvdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAe 230
                                       ++a dv+++ d+Gay+ l++avl+ a+ +++gpYkipn+++++++vytN++ ++afRGfG+pq+mfa+E+++d+lA+
  gi|557694671|ref|YP_008797725.1| 294 LLANDVEIIYDTGAYTALGHAVLDVAIENCNGPYKIPNIDIKAWLVYTNNMVASAFRGFGAPQVMFAMEQQVDQLAH 370
                                       ***************************************************************************** PP

                                       HHT--HHHHHHHHBCECGCC.SEEETEESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS-- CS
                     Ald_Xan_dh_C2 231 elgldplelRrrNlikpgeltpygqpvydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglg 307
                                       +lg+dp+e+R rN+++ g+++ +g+++  s +++++l++++++  +++++  + e +  w++rG+g+a++++g +lg
  gi|557694671|ref|YP_008797725.1| 371 KLGMDPIEFRLRNALRRGDVMVFGNKLETSVGIAQCLEAARNHPLWRQKETLKSENRLPWIRRGVGVAAAIKGYTLG 447
                                       ********************99****999*****************9888887777766***************777 PP

                                       S.EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHHH CS
                     Ald_Xan_dh_C2 308 ftakflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstdl 384
                                       +    ++++++ v++  dG  tv+ + te+GqG   ++aq+aa+ +++++e+v+vv +dt k+p++s t aSr+  l
  gi|557694671|ref|YP_008797725.1| 448 A---LPDKGSVAVELRRDGGLTVKGSFTEIGQGVVQAVAQLAADLFKIDIEKVEVVFADTGKTPDTSVTSASRQLFL 521
                                       5...578899******************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEETEEEECHHHHHHHHHHTTSSEEEEEEE......EEEE CS
                     Ald_Xan_dh_C2 385 ngnAvkkAaeklrerllkiaaellevspedleledgkvvvkeksvslaelaaaaylervslsatgfykt...ldeet 458
                                       +gnA kkAae+l   ++++  +l++ + ++ ++e+g+vv  + s+s++e+a+     + s +  g y++    +   
  gi|557694671|ref|YP_008797725.1| 522 AGNALKKAAENLLTHIQELLTNLYGQKGAEARFENGHVVGPGFSHSFEEIAHMLEKHGLSREVIGVYDVprlEPIPG 598
                                       *****************************************9999*******8866777777788898888644455 PP

                                       THCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEESS CS
                     Ald_Xan_dh_C2 459 gkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqllt 535
                                       + + p+  +++ga++a+Vev+++tg+v+v ++v + DvGk++Np++  gQ+eG+++qG+G+al+Ee ++d +G l+t
  gi|557694671|ref|YP_008797725.1| 599 SLEIPHLFYMFGATLAQVEVNILTGTVTVPKLVSIADVGKVVNPQTLTGQLEGAAAQGLGFALLEEPKID-KGILKT 674
                                       5667799**************************************************************5.****** PP

                                       -STTTS----GGGS CS
                     Ald_Xan_dh_C2 536 asladYkiPtaadi 549
                                       ++l++Y+iP+++di
  gi|557694671|ref|YP_008797725.1| 675 TNLSTYLIPSIKDI 688
                                       *************8 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 !   95.2   0.0   6.3e-31   2.8e-27       2     110 .]      23     127 ..      22     127 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 6.3e-31
                                       T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEES CS
                      Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkvr 78 
                                       G  +Y +D+ + ++l++a  rS+++hA i++idvs al++pGVvav+t+ d+p++++ +  + +d +  +l++d+vr
  gi|557694671|ref|YP_008797725.1|  23 GLTKYASDMFLDNMLWVAACRSKYPHAAIKRIDVSRALKSPGVVAVFTHRDVPNNRYGV--FVRDRP--VLCDDRVR 95 
                                       6679***************************************************9998..466665..******** PP

                                       STT-EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                      Ald_Xan_dh_C  79 svgqavaavvAedeetArkAaklvkveYeelp 110
                                       + g++va+v+Ae++e+A++ ++ + veYe+lp
  gi|557694671|ref|YP_008797725.1|  96 YIGDTVAIVAAESKEEAEQGVEEIVVEYEPLP 127
                                       *****************************986 PP

>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.13   5.7e+02      82     140 ..     187     250 ..     159     263 .. 0.82
   2 ?   11.7   0.0   3.3e-05      0.15      11      63 ..     468     517 ..     465     525 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.13
                                       HHHHHHHHHHHT-EEEESS-HHCCTTSTTEEESS--HHHHHHHHHHHHHHHTTSC.....EEEE CS
                      Peripla_BP_6  82 aaavaevlakdgvpvigpagltgekcspyvfslgpsysaqasalveylakelggk.....kval 140
                                       ++a  ++++++gv+ + ++g ++   +  ++s+++ +  +++ ++ ++   +ggk      ++l
  gi|557694671|ref|YP_008797725.1| 187 TEAGFSYIDEKGVITVVAGGQSPYRDHHEIVSTLQLPPEKVRVVIPHVGGAFGGKddvsvQIYL 250
                                       67778999**************************************999999988555555555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 3.3e-05
                                       SSTTHHHHHHHHHHHHHHHHHHHHTTEETTEEEEEEEEE-TTSHHHHHHHHHH CS
                      Peripla_BP_6  11 sGpyassgksllagaqaafeeiNaaGGinGrkielverDdaydpdraaeaarr 63 
                                        G + ++g+++++++   ++++    +i+  k+e+v +D++ +pd++++ a r
  gi|557694671|ref|YP_008797725.1| 468 KGSFTEIGQGVVQAVAQLAADL---FKIDIEKVEVVFADTGKTPDTSVTSASR 517
                                       6888889999888876666666...58999******************99875 PP

>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.3e-05     0.058     130     162 ..     212     244 ..     205     270 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.3e-05
                              UvdE 130 yHdklldalklaeqqdavliiHvGGkfgdkeaa 162
                                        H++++++l+l++++  v+i HvGG+fg+k++ 
  gi|557694671|ref|YP_008797725.1| 212 DHHEIVSTLQLPPEKVRVVIPHVGGAFGGKDDV 244
                                       59****************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (756 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); 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:                         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 0.26s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 5349.83
//
Query:       gi|557694672|ref|YP_008797726.1|  [L=290]
Description: molybdopterin dehydrogenase FAD-binding [Candidatus Caldiarchaeum subterraneum]
Scores for 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-46  157.1   0.1    4.9e-46  156.6   0.1    1.2  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
    4.5e-26   91.0   0.0    8.6e-26   90.1   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 !  156.6   0.1   5.5e-50   4.9e-46       4     170 ..       8     175 ..       4     176 .. 0.98

  Alignments for each domain:
  == domain 1  score: 156.6 bits;  conditional E-value: 5.5e-50
                                       EEEE-SSHHHHHHHHHH.CTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHHHH CS
                     FAD_binding_5   4 eylrpasleealallaa.epdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlselaa 79 
                                       ++++p++leeal+ll++ + +  ++aGgtdl++++++ +++ ++l++i  ++el++i++++g ++iGA++  + + +
  gi|557694672|ref|YP_008797726.1|   8 DVFTPKNLEEALELLDKhRGELAVLAGGTDLIIQLRKSQQKAPNLLNIYMLDELRYIKQDNGTIKIGALTDFATITE 84 
                                       5899*************7889******************************************************** PP

                                       HHHHHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETTEES CS
                     FAD_binding_5  80 ealvrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkgpgkta 156
                                       +++++++ p l+ea+ +i+s qi n+a+iGGN+++asp++D+ paL +l+A+++lrs++g+r+v++e+f+kg++k +
  gi|557694672|ref|YP_008797726.1|  85 SPIIQRHAPVLAEAAATIGSVQILNKASIGGNIVNASPAADSLPALYVLNATLSLRSKTGTRKVAIEQFYKGYKKLD 161
                                       ***************************************************************************** PP

                                       S-TT-EEEEEEEE- CS
                     FAD_binding_5 157 lepgelitaveiPa 170
                                       l++gel+t+v++Pa
  gi|557694672|ref|YP_008797726.1| 162 LQSGELLTEVSFPA 175
                                       *************7 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 !   90.1   0.0   9.6e-30   8.6e-26       3      99 ..     185     280 ..     183     284 .. 0.95

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 9.6e-30
                                       EEEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHHHT CS
                     CO_deh_flav_C   3 yklsrrrendiaivnaAfrveleedgkiedariafggvaptpvraekaeaaLiGkplseelleeaakaleeelspas 79 
                                       +k   r++++i++vn A+++e+ ++  ++daria+g+vapt+vra++ e++LiG++lse+++ +aa+a  + +sp++
  gi|557694672|ref|YP_008797726.1| 185 FKHGLRQGDAISVVNGAILLEVLNG-YVKDARIALGAVAPTVVRATESEKTLIGQRLSEDVILKAAQACLTSISPID 260
                                       59999*****************888.*************************************************** PP

                                       CTTC-HHHHHHHHHHHHHHH CS
                     CO_deh_flav_C  80 dprasaeYRrslavsllfrf 99 
                                       d+r+sa YR++++v++l+  
  gi|557694672|ref|YP_008797726.1| 261 DVRGSASYRKEMCVNYLYMT 280
                                       ****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2162.84
//
Query:       gi|557694673|ref|YP_008797727.1|  [L=156]
Description: carbon-monoxide dehydrogenase small subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   88.1   0.1    2.8e-25   88.1   0.1    1.5  2  Fer2_2     [2Fe-2S] binding domain
    1.2e-08   34.7   0.6    1.2e-08   34.7   0.6    2.2  2  Fer2       2Fe-2S iron-sulfur cluster binding domain
    1.8e-05   24.7   0.5    3.1e-05   23.9   0.1    1.6  1  Fer2_3     2Fe-2S iron-sulfur cluster binding domain
     0.0016   18.4   0.9      0.011   15.8   0.3    2.5  2  Fer2_4     2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.038   13.7   0.1       0.12   12.1   0.0    1.9  2  DUF5634_N  Family of unknown function (DUF5634)


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 ?   -4.5   1.5         5   1.8e+04      26      31 ..      51      56 ..      47      57 .. 0.79
   2 !   88.1   0.1   7.7e-29   2.8e-25       3      75 ..      83     148 ..      74     149 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 5
                            Fer2_2 26 qCGyCt 31
                                       CG Ct
  gi|557694673|ref|YP_008797727.1| 51 DCGACT 56
                                      599998 PP

  == domain 2  score: 88.1 bits;  conditional E-value: 7.7e-29
                            Fer2_2   3 eglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                       e +       ++v ea +++ga+qCGyCtpGfv+++a+ll++  ++p++ eire+l+gnlCRCtgY +i++Av
  gi|557694673|ref|YP_008797727.1|  83 EAVD------EKVAEAYARHGAVQCGYCTPGFVVATASLLSKI-TNPSDGEIREWLRGNLCRCTGYVKILKAV 148
                                       3333......589***************************999.88888***********************9 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 !   34.7   0.6   3.5e-12   1.2e-08       2      62 ..      14      77 ..      13      85 .. 0.82
   2 ?    1.0   1.1      0.12   4.1e+02       3      26 ..      74      97 ..      72     109 .. 0.66

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.5e-12
                                      ETTTEEEEEEEETTTHBHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCECTT...SSSSTHH CS
                              Fer2  2 tidgkevevevadgettlldaaee.nggidipysCggggCgtClvevlegevqsd...etelege 62
                                       ++g+ev+v +++g t ll+++++  + ++++ +C  g Cg+C+v ++   v+s+    + +eg+
  gi|557694673|ref|YP_008797727.1| 14 RLNGEEVRVRAPPGYT-LLEVLRHiLHLTGTKDGCSSGDCGACTVLLDGRAVHSCltlISQVEGR 77
                                      679*******988888.****************************87766668875555555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                                      TTTEEEEEEEETTTHBHHHHHHHT CS
                              Fer2  3 idgkevevevadgettlldaaeen 26
                                      ++g+ev++++a +e++   +a++ 
  gi|557694673|ref|YP_008797727.1| 74 VEGREVTTVEAVDEKVAEAYARHG 97
                                      678888888888888555555542 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 !   23.9   0.1   8.8e-09   3.1e-05      20      89 ..      19      83 ..       8      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 8.8e-09
                            Fer2_3 20 eyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlakqkseiele 89
                                      e +v+a ++ t+l++L +i + +      +  C++g CG+c+v ++G+    C + i++++ ++  +++e
  gi|557694673|ref|YP_008797727.1| 19 EVRVRAPPGYTLLEVLRHILHLT----GTKDGCSSGDCGACTVLLDGRAVHSCLTLISQVEGRE-VTTVE 83
                                      56677778888888888887765....34689***************************99876.45665 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 !   15.8   0.3     3e-06     0.011       2      72 ..       9      72 ..       8      84 .. 0.78
   2 ?    0.5   0.1      0.17   6.2e+02       8      30 ..      74      98 ..      72     136 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3e-06
                            Fer2_4  2 rpvtltfDGkevt..vpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracstpve 72
                                      ++ t++++G+ev+  +p+G t++++l     +++++  +    +  c+ g C  C V ++g+  v +c t + 
  gi|557694673|ref|YP_008797727.1|  9 KEFTFRLNGEEVRvrAPPGYTLLEVLR----HILHLTGT----KDGCSSGDCGACTVLLDGRA-VHSCLTLIS 72
                                      6789*****987511689***999985....67777777....667***************99.9***99764 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.17
                            Fer2_4  8 fDGkevtvpe..GdtvasAllangv 30
                                      ++G+evt  e  +++va+A +++g+
  gi|557694673|ref|YP_008797727.1| 74 VEGREVTTVEavDEKVAEAYARHGA 98
                                      6777776654346788888888874 PP

>> DUF5634_N  Family of unknown function (DUF5634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.1   4.1e+03      78      88 ..       8      18 ..       6      22 .. 0.77
   2 ?   12.1   0.0   3.5e-05      0.12      56      80 ..     126     150 ..     113     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
                                      SS-EEEEEEEE CS
                         DUF5634_N 78 eekltirLvge 88
                                      e+++t rL ge
  gi|557694673|ref|YP_008797727.1|  8 EKEFTFRLNGE 18
                                      67899999987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.5e-05
                                       EEEEEETTEEEEEEEE--SB-SSS- CS
                         DUF5634_N  56 svrvgtggalyRCkgvvetvedeek 80 
                                        +r + +g+l+RC g v+  +  e 
  gi|557694673|ref|YP_008797727.1| 126 EIREWLRGNLCRCTGYVKILKAVES 150
                                       6999************998876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); 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 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1107.49
//
Query:       gi|557694674|ref|YP_008797728.1|  [L=172]
Description: heat repeat-containing PBS lyase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   88.4   0.1    1.8e-14   53.9   0.0    2.2  2  HEAT_2     HEAT repeats
    1.4e-13   50.1   1.3    6.2e-05   23.3   0.0    3.7  4  HEAT_PBS   PBS lyase HEAT-like repeat
    1.3e-12   46.8   0.0       0.02   15.1   0.0    3.7  4  HEAT       HEAT repeat
    1.5e-07   31.7   0.0        1.4    9.6   0.0    3.8  4  HEAT_EZ    HEAT-like repeat
    4.9e-07   29.9   0.0      0.014   15.4   0.0    3.1  3  Cnd1       non-SMC mitotic condensation complex subunit 1
    0.00067   18.3   0.0     0.0094   14.5   0.0    2.0  3  Adaptin_N  Adaptin N terminal region
  ------ inclusion threshold ------
      0.026   14.8   0.0        1.3    9.4   0.0    2.4  2  RICTOR_V   Rapamycin-insensitive companion of mTOR, domain 5


Domain annotation for each model (and alignments):
>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   7.1e-18   1.8e-14       5      88 .]      32     115 ..      28     115 .. 0.93
   2 !   39.2   0.0   2.7e-13     7e-10       1      59 [.      91     149 ..      91     166 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 7.1e-18
                            HEAT_2   5 lqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddddvvR 80 
                                        ++l ++ d  +r++a   L++ig +++++ L e+l  d++p vR++aa +Lg++g  ea+p L e++++d++++vR
  gi|557694674|ref|YP_008797728.1|  32 RSLL-KSDDFVIRARATCILAEIGGRDYIQDLAEVLlHDDNPIVRHEAAYSLGQLGYREAIPYLVESVKRDPHPIVR 107
                                       5667.88999************************7779*************************************** PP

                            HEAT_2  81 eaAaeaLa 88 
                                        ++a+aL+
  gi|557694674|ref|YP_008797728.1| 108 HESAIALG 115
                                       *****996 PP

  == domain 2  score: 39.2 bits;  conditional E-value: 2.7e-13
                            HEAT_2   1 ldaLlqalendpdpevrraairaLgrignpealpaLvellededpavRraaaeaLgaig 59 
                                       +++L++ +++dp+p vr++ ++aLg ig ++ +p L+e+l+de p+v   a+ aL+ i 
  gi|557694674|ref|YP_008797728.1|  91 IPYLVESVKRDPHPIVRHESAIALGVIGRTDPVPDLLEALKDEAPEVVDSAIIALSNIE 149
                                       6899***************************************************9884 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.2   7.2e-05      0.18       1      26 [.      42      67 ..      42      68 .. 0.94
   2 !   23.3   0.0   2.4e-08   6.2e-05       1      23 [.      74      96 ..      74     100 .. 0.93
   3 !   11.1   0.0   0.00021      0.55       1      27 []     106     132 ..     106     132 .. 0.97
   4 ?   -2.4   0.0       4.7   1.2e+04       4      12 ..     140     148 ..     139     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.2e-05
                                      HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaipaLleaLq 26
                                      +R++A+  L+++g  ++i+ L e+L 
  gi|557694674|ref|YP_008797728.1| 42 IRARATCILAEIGGRDYIQDLAEVLL 67
                                      59*********************996 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 2.4e-08
                                      HHHHHHHHHHHCTSGGGHHHHHH CS
                          HEAT_PBS  1 vRraAakaLgqlgdeeaipaLle 23
                                      vR++Aa++Lgqlg  eaip L+e
  gi|557694674|ref|YP_008797728.1| 74 VRHEAAYSLGQLGYREAIPYLVE 96
                                      9********************98 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHCTSGGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLqd 27 
                                       vR++ a aLg +g ++ +p LleaL+d
  gi|557694674|ref|YP_008797728.1| 106 VRHESAIALGVIGRTDPVPDLLEALKD 132
                                       9************************98 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 4.7
                                       HHHHHHHHC CS
                          HEAT_PBS   4 aAakaLgql 12 
                                       +A+ aL ++
  gi|557694674|ref|YP_008797728.1| 140 SAIIALSNI 148
                                       588899877 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       2.7     7e+03       6      20 ..      32      46 ..      30      49 .. 0.72
   2 !   15.1   0.0   7.7e-06      0.02       7      27 ..      65      85 ..      59      87 .. 0.88
   3 !   12.3   0.0   6.2e-05      0.16       2      28 ..      91     118 ..      90     120 .. 0.92
   4 !   14.8   0.0   9.8e-06     0.025       3      27 ..     124     148 ..     123     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.7
                                      HHHHT-SSHHHHHHH CS
                              HEAT  6 lkllsDpspeVReaA 20
                                       +ll++++  +R+ A
  gi|557694674|ref|YP_008797728.1| 32 RSLLKSDDFVIRARA 46
                                      567888887788766 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 7.7e-06
                                      HHHT-SSHHHHHHHHHHHHHH CS
                              HEAT  7 kllsDpspeVReaAakaLgal 27
                                       ll+D++p VR  Aa++Lg+l
  gi|557694674|ref|YP_008797728.1| 65 VLLHDDNPIVRHEAAYSLGQL 85
                                      578*****************9 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 6.2e-05
                                       HHHHHHHH.T-SSHHHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkll.sDpspeVReaAakaLgala 28 
                                       +P l++   +Dp+p VR  +a aLg + 
  gi|557694674|ref|YP_008797728.1|  91 IPYLVESVkRDPHPIVRHESAIALGVIG 118
                                       799999988****************986 PP

  == domain 4  score: 14.8 bits;  conditional E-value: 9.8e-06
                                       HHHHHHHT-SSHHHHHHHHHHHHHH CS
                              HEAT   3 PlllkllsDpspeVReaAakaLgal 27 
                                       P ll++l+D++peV ++A+ aL ++
  gi|557694674|ref|YP_008797728.1| 124 PDLLEALKDEAPEVVDSAIIALSNI 148
                                       779*******************987 PP

>> HEAT_EZ  HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         1   2.7e+03      33      52 ..      31      50 ..      28      53 .. 0.60
   2 !    8.6   0.0    0.0011       2.7      31      55 .]      64      85 ..      42      85 .. 0.77
   3 !    9.6   0.0   0.00053       1.4      28      55 .]      89     117 ..      87     117 .. 0.92
   4 !    8.8   0.0    0.0009       2.3      32      55 .]     125     148 ..     122     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1
                           HEAT_EZ 33 LlalLnddsdeV.RaaAagaL 52
                                      + +lL++ +d V Ra A   L
  gi|557694674|ref|YP_008797728.1| 31 FRSLLKS-DDFViRARATCIL 50
                                      6677765.4455577766655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                           HEAT_EZ 31 paLlalLnddsdeVRaaAagaLgnl 55
                                        L   L dd++ VR  Aa+ Lg+l
  gi|557694674|ref|YP_008797728.1| 64 EVL---LHDDNPIVRHEAAYSLGQL 85
                                      444...47788899*********97 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.00053
                           HEAT_EZ  28 eilpaLlalL.nddsdeVRaaAagaLgnl 55 
                                       e++p+L+    +d+++ VR  +a+aLg +
  gi|557694674|ref|YP_008797728.1|  89 EAIPYLVESVkRDPHPIVRHESAIALGVI 117
                                       89********999999**********976 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0009
                           HEAT_EZ  32 aLlalLnddsdeVRaaAagaLgnl 55 
                                        Ll +L+d+ +eV   A++aL+n+
  gi|557694674|ref|YP_008797728.1| 125 DLLEALKDEAPEVVDSAIIALSNI 148
                                       58899999999***********98 PP

>> Cnd1  non-SMC mitotic condensation complex subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0       0.2   5.3e+02      63      88 ..      31      56 ..      19      65 .. 0.57
   2 !   10.6   0.0   0.00017      0.43      27      51 ..      64      88 ..      41      97 .. 0.76
   3 !   15.4   0.0   5.6e-06     0.014      31      87 ..     100     150 ..      90     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.2
                              Cnd1 63 laklleDenprVvanalaalteisek 88
                                      +++ll+ ++  ++a a ++l ei  +
  gi|557694674|ref|YP_008797728.1| 31 FRSLLKSDDFVIRARATCILAEIGGR 56
                                      44555555555555555555555443 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00017
                              Cnd1 27 rkrLkDedpyVRktaaivvakL.iln 51
                                      +  L+D++p VR  aa+ + +L + +
  gi|557694674|ref|YP_008797728.1| 64 EVLLHDDNPIVRHEAAYSLGQLgY-R 88
                                      34689************9999944.3 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 5.6e-06
                              Cnd1  31 kDedpyVRktaaivvakLilndmvkekgflselaklleDenprVvanalaalteise 87 
                                       +D++p VR   ai++       ++   + + +l+++l+De p+Vv++a++al++i  
  gi|557694674|ref|YP_008797728.1| 100 RDPHPIVRHESAIALG------VIGRTDPVPDLLEALKDEAPEVVDSAIIALSNIEF 150
                                       6999999999998885......5556667889*********************9975 PP

>> Adaptin_N  Adaptin N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.085   2.2e+02     493     517 ..      26      50 ..      12      56 .. 0.73
   2 !    6.4   0.0    0.0011       2.8      88     138 ..      35      82 ..      25      85 .. 0.87
   3 !   14.5   0.0   3.7e-06    0.0094      88     179 ..      67     148 ..      66     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.085
                                       HHHHHHHHHHHXXSHHHHHHHHHHH CS
                         Adaptin_N 493 kliqlvlslatssdlevrdRaveyl 517
                                       k  ++++sl++s+d+ +r Ra+++l
  gi|557694674|ref|YP_008797728.1|  26 KDAEYFRSLLKSDDFVIRARATCIL 50 
                                       4457888889988999999998876 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0011
                                       CCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHH CS
                         Adaptin_N  88 lkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalai 138
                                       lk+ + +ir+ A + L+ i+ ++  +dla+    ll+d++p vr +Aa+++
  gi|557694674|ref|YP_008797728.1|  35 LKSDDFVIRARATCILAEIGGRDYIQDLAE---VLLHDDNPIVRHEAAYSL 82 
                                       88999999*************999999996...579************987 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.7e-06
                                       CCSSSHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHT-SSHHHHHHHHHHHHHCCCCCHHCCCCCHHHHHHHCTT-S CS
                         Adaptin_N  88 lkdpnqlirglALrvLssirvpelaedlapaikkllkdrspyvrkkAalailklykkdpdllrkqlveeikellsdk 164
                                       l+d n+++r  A  +L++++ +e  ++l++ +k   +d++p vr ++a+a+  + + dp       v+++ e+l+d+
  gi|557694674|ref|YP_008797728.1|  67 LHDDNPIVRHEAAYSLGQLGYREAIPYLVESVK---RDPHPIVRHESAIALGVIGRTDP-------VPDLLEALKDE 133
                                       7899************************99999...5**************99999887.......45799****** PP

                                       SHHHHHHHHHHHHHH CS
                         Adaptin_N 165 dpgvvlaAvalleei 179
                                        p vv +A+ +l  i
  gi|557694674|ref|YP_008797728.1| 134 APEVVDSAIIALSNI 148
                                       ************999 PP

>> RICTOR_V  Rapamycin-insensitive companion of mTOR, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.044   1.1e+02      27      56 ..      57      86 ..      44      90 .. 0.85
   2 ?    9.4   0.0   0.00049       1.3      27      67 ..      89     129 ..      84     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.044
                          RICTOR_V 27 divedivelaeespvlslRGtafyvLglis 56
                                      d ++d++e+  + ++  +R  a y Lg ++
  gi|557694674|ref|YP_008797728.1| 57 DYIQDLAEVLLHDDNPIVRHEAAYSLGQLG 86
                                      7899**********************9775 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00049
                          RICTOR_V  27 divedivelaeespvlslRGtafyvLglissteegaeiLde 67 
                                       ++++ +ve +++ p+  +R     +Lg+i++t    ++L+ 
  gi|557694674|ref|YP_008797728.1|  89 EAIPYLVESVKRDPHPIVRHESAIALGVIGRTDPVPDLLEA 129
                                       67999***************************988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1307.38
//
Query:       gi|557694675|ref|YP_008797729.1|  [L=89]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-10   39.5   0.0    7.8e-10   39.3   0.0    1.1  1  ThiS      ThiS family
    5.3e-07   29.9   0.0    6.2e-07   29.7   0.0    1.2  1  Urm1      Urm1 (Ubiquitin related modifier)


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 !   39.3   0.0   8.7e-14   7.8e-10       1      77 []       4      89 .]       4      89 .] 0.94

  Alignments for each domain:
  == domain 1  score: 39.3 bits;  conditional E-value: 8.7e-14
                                      EEETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG......TTTTEEEEETTEEEGC.CTTTSB--TTCEEEE CS
                              ThiS  1 vllfaelrelag..eeelelaegstvaelleaLgerypela......lerrvavavNgeivpr.lwldtelkdgDevai 70
                                      v l + lr ++g     +el+e+ +++e+++  +e+  +          +++ ++vNg +v++  wldt++ + D+v +
  gi|557694675|ref|YP_008797729.1|  4 VELLGPLRAVVGkrFIDIELKEPIKLREVFMMFDEEVRRMImdeagrPQPGLLILVNGVDVRYlTWLDTVVDEDDVVTL 82
                                      678999999999977789******************98888******99**************77************** PP

                                      EESTTC- CS
                              ThiS 71 lppVaGG 77
                                      +p + GG
  gi|557694675|ref|YP_008797729.1| 83 IPSIHGG 89
                                      ******9 PP

>> Urm1  Urm1 (Ubiquitin related modifier)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   6.9e-11   6.2e-07      29      96 .]      25      89 .]       1      89 [] 0.73

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 6.9e-11
                                      SS-BHHHHHHHHCCCC-SSGHHHCBSTTSB-TTEEEEETTCEHHHCTCCCSB--TTEEEEEEETTT-- CS
                              Urm1 29 eevnleeliayikknlikerkevFlekdkvrPGilvLindaDwellgekdyelkdkDkivFistlhGG 96
                                      e+++l+e+  +  +++   r+ +  e ++ +PG+l+L+n +D+  l  +d+++ ++D+++ i ++hGG
  gi|557694675|ref|YP_008797729.1| 25 EPIKLREVFMMFDEEV---RRMIMDEAGRPQPGLLILVNGVDVRYLTWLDTVVDEDDVVTLIPSIHGG 89
                                      5666666655555443...334445588999************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 677.52
//
Query:       gi|557694676|ref|YP_008797730.1|  [L=177]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   47.6   0.1    2.3e-12   47.4   0.1    1.1  1  CGI-121     Kinase binding protein CGI-121
     0.0054   16.8   0.3     0.0054   16.8   0.3    1.6  2  Spidroin_N  Major ampullate spidroin 1, spider silk protein 1


Domain annotation for each model (and alignments):
>> CGI-121  Kinase binding protein CGI-121
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.1   2.5e-16   2.3e-12      22     160 ..      36     173 ..      18     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 2.5e-16
                                       T-EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEESSS- CS
                           CGI-121  22 dfafldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvsssea 98 
                                       d  + da+ il+     +A+++a+la ++++++ ++l++E+l++L  +++I ea+ + g+++ + + +   v+ss +
  gi|557694676|ref|YP_008797730.1|  36 DAQVFDADSILDWDVFDAALMNAVLAVKASRQRARSLSTEVLMRLAATTQIREAIAKVGLKPGSMRAVFLVVGSSRE 112
                                       45789**********************************************************87777777777778 PP

                                       -HHHHHHHHHHHS-SEEE--SHHHHHH--HHHHHHHTT--.....TT---SSHHHHHHHHHHHHH CS
                           CGI-121  99 deeevlkslkevvegelvpleeeleeltdwkkikkiYklne...leeekeeevkeledlvvsava 160
                                       + ee+ +++ ++  g +++l +      d  +++++Y ++e   ++ + + + + l+ ++++++a
  gi|557694676|ref|YP_008797730.1| 113 QVEEKGAKVLSLAGGGETDLPK----NPDQTRFEELYGVSEkvyKSVQAKTSIEALKLAIMQKIA 173
                                       9999999999999999997666....69************8775322333444447777887777 PP

>> Spidroin_N  Major ampullate spidroin 1, spider silk protein 1, N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.3     6e-07    0.0054       1      67 [.      16      82 ..      16      94 .. 0.87
   2 ?   -2.1   0.0       0.4   3.6e+03      57      99 ..     160     170 ..     146     176 .. 0.41

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6e-07
                                      TTSSHHHHHHHHHHHHHHHHTCSSS-HHHHHHHHHHHHHHHHHHHHHHHTTS--HHHHHHHHHHHHH CS
                        Spidroin_N  1 pwsspatAeafinsllqaisqsgvfsaqqmdDlesiadtilsavdkmarsgksskaklqAlnmafAs 67
                                      +w   +tA++f++++++ + +++vf a+ + D +    ++++av  +++s++ +++    + m +A+
  gi|557694676|ref|YP_008797730.1| 16 VWLRDETADDFVEKMRSVVDDAQVFDADSILDWDVFDAALMNAVLAVKASRQRARSLSTEVLMRLAA 82
                                      69999***************************************99998877777766666666665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHHHHHHHHHSSSSSHHHHHHHHHHHHHHHHHHH CS
                        Spidroin_N  57 klqAlnmafAssiAeiavaesggkslsakinaianalssaflq 99 
                                       ++                                +al+ a++q
  gi|557694676|ref|YP_008797730.1| 160 SI--------------------------------EALKLAIMQ 170
                                       22................................333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1307.28
//
Query:       gi|557694677|ref|YP_008797731.1|  [L=194]
Description: translation factor [Candidatus Caldiarchaeum subterraneum]
Scores for 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-52  176.2   0.2    4.9e-52  176.0   0.2    1.0  1  Sua5_yciO_yrdC  Telomere recombination


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 !  176.0   0.2   2.7e-56   4.9e-52       1     179 []       6     180 ..       6     180 .. 0.95

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 2.7e-56
                                       HHHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSS CS
                    Sua5_yciO_yrdC   1 ealrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGp 77 
                                       ea+++Gg++++pt+tvYg++cd+ + eaver++++K+r+ +kp +vlv+++++l+++a  ++eee+ + + r+wPG 
  gi|557694677|ref|YP_008797731.1|   6 EAVKRGGVIVYPTDTVYGIGCDPFKIEAVERVIHAKRRE-KKPAPVLVSDFDQLHEVAV-PTEEELEA-AIRLWPGA 79 
                                       5789***********************************.******************8.66666655.5567**** PP

                                       CEEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS CS
                    Sua5_yciO_yrdC  78 itlllkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildg 154
                                       +t+++ ++ e lp+ v++g ktvGvr+P++ + +l+++++++plv TSan+s+eps+t+ +++ + + e+vd+++d+
  gi|557694677|ref|YP_008797731.1|  80 VTIVMAKKPE-LPELVTAGEKTVGVRMPAHVVPLLIMQKAHRPLVGTSANISDEPSATTIDQIPSSVLEKVDVVVDA 155
                                       ******7555.****************************************************************** PP

                                       ---SSS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 155 geiavgvdstVvdltegkpkilRrG 179
                                       g++++  +stVv++ +g++ +lR+G
  gi|557694677|ref|YP_008797731.1| 156 GRTHHLLPSTVVKIQDGQVVVLREG 180
                                       ***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1422.83
//
Query:       gi|557694678|ref|YP_008797732.1|  [L=107]
Description: hypothetical protein CSUB_C1251 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0089   16.0   0.3     0.0089   16.0   0.3    3.1  4  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.7   1.6        1.4    9.0   0.1    2.5  2  ADK_lid        Adenylate kinase, active site lid
      0.063   13.3   1.0        1.2    9.2   1.0    2.2  1  HypA           Hydrogenase/urease nickel incorporation, metal
       0.12   12.3   1.5          3    7.8   0.1    2.8  3  Cys_rich_CPXG  Cysteine-rich CPXCG
       0.22   12.0   1.3       0.34   11.4   0.1    1.9  2  zf-C2HE        C2HE / C2H2 / C2HC zinc-binding finger


Domain annotation for each model (and alignments):
>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   1.5      0.36   1.3e+03      21      32 ..       3      14 ..       1      24 [. 0.53
   2 ?   -0.4   0.2      0.33   1.2e+03      17      23 ..      18      24 ..      15      31 .. 0.83
   3 !   16.0   0.3   2.5e-06    0.0089      15      34 ..      45      64 ..      41      72 .. 0.83
   4 ?   -2.2   0.0       1.2   4.2e+03      22      32 ..      91     101 ..      91     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.36
                     Zn_Tnp_IS1595 21 CPhCgsrkayri 32
                                      C  Cg + +y +
  gi|557694678|ref|YP_008797732.1|  3 CDVCGESVPYLL 14
                                      556666655544 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.33
                     Zn_Tnp_IS1595 17 ngfvCPh 23
                                      ++++CP+
  gi|557694678|ref|YP_008797732.1| 18 DKPRCPK 24
                                      5799997 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 2.5e-06
                     Zn_Tnp_IS1595 15 WpngfvCPhCgsrkayrikt 34
                                      W++g  CP+Cg +k+ ++++
  gi|557694678|ref|YP_008797732.1| 45 WKEGMKCPYCGDEKFQTMSR 64
                                      ***********999988887 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.2
                     Zn_Tnp_IS1595  22 PhCgsrkayri 32 
                                       P C+  ++ +i
  gi|557694678|ref|YP_008797732.1|  91 PPCHMNHLSKI 101
                                       77998898887 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 ?    9.0   0.1   0.00038       1.4      22      30 ..       1       9 [.       1      18 [. 0.87
   2 ?    5.8   0.2    0.0039        14      18      30 ..      45      57 ..      33      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00038
                                      TB-TTT--. CS
                           ADK_lid 22 glCDkCGep 30
                                      ++CD+CGe 
  gi|557694678|ref|YP_008797732.1|  1 MKCDVCGES 9 
                                      89*****95 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0039
                                      -SSTTB-TTT--. CS
                           ADK_lid 18 PkveglCDkCGep 30
                                       k+ ++C  CG +
  gi|557694678|ref|YP_008797732.1| 45 WKEGMKCPYCGDE 57
                                      699********76 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 ?    9.2   1.0   0.00033       1.2      72     100 ..       2      62 ..       1      73 [. 0.62

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00033
                                       EETTTS-EEECHH.HHH................................S-TTTSSS-EEEE CS
                              HypA  72 rCreCgkefelee.kal................................rCpkCgsadveiv 100
                                       +C++Cg+++     + l                                +Cp Cg ++++++
  gi|557694678|ref|YP_008797732.1|   2 KCDVCGESVPYLLlR-LdkprcpkghelgvwvacgnpeeshvylwkegmKCPYCGDEKFQTM 62 
                                       677777666633212.1335566666666666666666666677777779999999998864 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.034   1.2e+02       2      10 ..       2      10 ..       1      15 [. 0.80
   2 ?   -2.8   0.0       1.7   6.3e+03      30      34 ..      34      38 ..      25      44 .. 0.59
   3 ?    7.8   0.1   0.00083         3       2       9 ..      50      57 ..      49      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.034
                     Cys_rich_CPXG  2 qCPyCgeei 10
                                      +C  Cge++
  gi|557694678|ref|YP_008797732.1|  2 KCDVCGESV 10
                                      699999986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.7
                     Cys_rich_CPXG 30 CCrPi 34
                                      C +P 
  gi|557694678|ref|YP_008797732.1| 34 CGNPE 38
                                      44443 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00083
                     Cys_rich_CPXG  2 qCPyCgee 9 
                                      +CPyCg e
  gi|557694678|ref|YP_008797732.1| 50 KCPYCGDE 57
                                      7*****75 PP

>> zf-C2HE  C2HE / C2H2 / C2HC zinc-binding finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.62   2.2e+03      38      46 ..       1       9 [.       1      17 [. 0.81
   2 ?   11.4   0.1   9.4e-05      0.34      26      52 ..      37      63 ..      12      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.62
                           zf-C2HE 38 LkCtrCgan 46
                                      +kC  Cg++
  gi|557694678|ref|YP_008797732.1|  1 MKCDVCGES 9 
                                      79****965 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 9.4e-05
                           zf-C2HE 26 eeqskelilktpLkCtrCganfgnkfp 52
                                       e+s  ++ k+ +kC +Cg + ++++ 
  gi|557694678|ref|YP_008797732.1| 37 PEESHVYLWKEGMKCPYCGDEKFQTMS 63
                                      455666889************999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 765.01
//
Query:       gi|557694679|ref|YP_008797733.1|  [L=310]
Description: branched-chain amino acid aminotransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-49  167.2   0.0    5.7e-49  167.0   0.0    1.1  1  Aminotran_4  Amino-transferase class IV
  ------ inclusion threshold ------
      0.075   12.6   0.7       0.96    9.1   0.6    2.4  2  Plasmo_rep   Plasmodium repeat family


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.0   0.0   6.4e-53   5.7e-49       2     223 .]      39     267 ..      38     267 .. 0.94

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 6.4e-53
                       Aminotran_4   2 lfEtmrvy..ngei..ffldeHleRLrksaellglelpfdeeelrkileelleannsen.grlrllvsrgggglgaa 73 
                                       +fE++r y  n ei  f+l +Hl+RL +sa++++ ++p++ e+l+ ++ ++++an+++  +++r+++ +g++ ++  
  gi|557694679|ref|YP_008797733.1|  39 VFEGIRGYsqNEEIyvFRLRDHLKRLVESAKIVMFNNPYTVEQLQDAVIKTIRANGYRSnVYIRPIIYAGENIMSLN 115
                                       9*****887788889899****************************************9999*********999977 PP

                       Aminotran_4  74 tsepsvavyvsalppgpeseke.lplvtssdvrrdapsplpgaKtln.yldnvlarreakergadevllvdedgnvt 148
                                        +e  +  +++ +p++    k  l++++ss++r +  s  p+aK    yl+++la  eak  g+de+ll+d +g+v+
  gi|557694679|ref|YP_008797733.1| 116 ARELPIRASIIVFPLEKFFDKTgLRVCVSSWRRLPDTSMPPRAKAAAnYLNSILASTEAKMMGYDEALLLDHQGYVS 192
                                       777777777777777777777778********************9877***************************** PP

                       Aminotran_4 149 EgstsNvfivkggelitPplssgiLpGitrrallelakalgleveereitlkdleeadeafltntlrgvlpvrsi 223
                                       Eg+  N+f+vk+  l tPp+ss+iL+Gitr+++++ a ++g+ v er i+ ++l  ade+f+++t+++++p+ ++
  gi|557694679|ref|YP_008797733.1| 193 EGAGENLFLVKNEVLATPPISSSILEGITRDTVIKMASDQGFRVVERQISRTELYTADELFFSGTAAEITPIVEV 267
                                       ************************************************************************875 PP

>> Plasmo_rep  Plasmodium repeat family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.6   0.00011      0.96      12      20 ..      45      53 ..      44      54 .. 0.92
   2 ?    0.5   0.0     0.049   4.4e+02       6      16 ..     105     115 ..     105     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00011
                        Plasmo_rep 12 EieqNrEIY 20
                                       ++qN+EIY
  gi|557694679|ref|YP_008797733.1| 45 GYSQNEEIY 53
                                      69******* PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.049
                        Plasmo_rep   6 vYspkqEieqN 16 
                                       +Y+ ++++++N
  gi|557694679|ref|YP_008797733.1| 105 IYAGENIMSLN 115
                                       8999******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2365.86
//
Query:       gi|557694680|ref|YP_008797734.1|  [L=214]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   95.8   0.0    1.2e-20   73.3   0.1    2.1  2  Thioredoxin_3   Thioredoxin domain
    2.1e-12   47.0   0.4    8.8e-10   38.7   0.2    2.8  3  Glutaredoxin    Glutaredoxin
    2.1e-07   31.2   0.3     0.0091   16.2   0.0    3.0  3  Thioredoxin_4   Thioredoxin
    8.5e-07   28.9   0.0      0.047   13.7   0.1    2.1  2  Thioredoxin     Thioredoxin
    0.00028   21.3   1.1        0.4   11.1   0.2    3.6  2  Thioredoxin_2   Thioredoxin-like domain
    0.00037   20.3   0.0    0.00073   19.3   0.0    1.4  1  Thioredoxin_9   Thioredoxin
     0.0012   19.2   0.0       0.15   12.5   0.0    2.2  2  DUF836          Glutaredoxin-like domain (DUF836)
     0.0032   17.0   0.0        2.2    7.7   0.0    2.1  2  ABC_transp_aux  ABC-type uncharacterized transport system
  ------ inclusion threshold ------
      0.011   15.6   0.0       0.68    9.7   0.0    2.3  2  TraF            F plasmid transfer operon 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 !   20.6   0.0   1.7e-07   0.00033       4      75 ..      27     106 ..      24     107 .. 0.83
   2 !   73.3   0.1   6.1e-24   1.2e-20       1      75 [.     134     211 ..     134     212 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.7e-07
                                       EEESSS..STTCHHHHHHHHHHCHCC.T.CECEEECC.TTHHHHHHCT-SSSSEEECTT....CEEEESS---CCHH CS
                     Thioredoxin_3   4 kvlgpg..CakCpklekavkeaaaek.g.ikaevekv.tdfeeiekygVmsvPalvidg....kvvvsGkvpseeei 71 
                                       +v+++   C++C +l+++++e+++   g + +ev +   d ++ +  gV ++Pal++ g    kv++ G +p ++e+
  gi|557694680|ref|YP_008797734.1|  27 RVFTQEfeCQYCADLRSLAEELVEIGdGkLRLEVFDFeRDADKASAWGVDKIPALLLHGareyKVRYFG-LPAGYEF 102
                                       56544444****************99444667999998999999*************975555899***.9***999 PP

                                       HHHH CS
                     Thioredoxin_3  72 rkll 75 
                                       ++ll
  gi|557694680|ref|YP_008797734.1| 103 AALL 106
                                       9987 PP

  == domain 2  score: 73.3 bits;  conditional E-value: 6.1e-24
                                       EEEEE.ESSSSTTCH.HHHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEEECTTCEEEESS---CCHHHHH CS
                     Thioredoxin_3   1 meikv.lgpgCakCp.klekavkeaaaekgikaevekvtdfeei.ekygVmsvPalvidgkvvvsGkvpseeeirkl 74 
                                       ++i+v ++p+C++Cp ++++a++ a++++ i+a+++++ +f+ + +ky Vm+vP++vi++kv ++G++p+  +++++
  gi|557694680|ref|YP_008797734.1| 134 VHIQVfVTPTCPYCPrAVRTAHQMAIENELITADMVEAIEFPHLaNKYDVMAVPKVVINDKVSFEGALPDMHFLEHV 210
                                       68***99********99999999999999******************************************999987 PP

                                       H CS
                     Thioredoxin_3  75 l 75 
                                       l
  gi|557694680|ref|YP_008797734.1| 211 L 211
                                       6 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0091        18       4      22 ..      29      48 ..      25      85 .. 0.81
   2 ?   -2.2   0.0       2.6   5.1e+03      30      45 ..     111     131 ..     108     134 .. 0.58
   3 !   38.7   0.2   4.4e-13   8.8e-10       2      59 ..     137     195 ..     136     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0091
                                      EES.TSSHHHHHHHHHHHHT CS
                      Glutaredoxin  4 ftk.ptCpyCkkakrlLkel 22
                                      ft    C yC+  + l++el
  gi|557694680|ref|YP_008797734.1| 29 FTQeFECQYCADLRSLAEEL 48
                                      555689**********9987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                                       EGCCSH.....HHHHHHHHHH CS
                      Glutaredoxin  30 dvdkde.....eireelkels 45 
                                       dv+k +     ++r++++e+s
  gi|557694680|ref|YP_008797734.1| 111 DVSKGAsrlspSVRAKVREIS 131
                                       555544444447777777776 PP

  == domain 3  score: 38.7 bits;  conditional E-value: 4.4e-13
                                       EEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH.HHHHHHHHHHTSSSSSEEEETTEE CS
                      Glutaredoxin   2 vlftkptCpyCkkakrlLkelgvkfeeidvdkde.eireelkelsgvrtvPqvfidgkh 59 
                                        +f++ptCpyC++a+r+++++ ++ e i  d+ e  +   l ++ +v++vP v+i++k+
  gi|557694680|ref|YP_008797734.1| 137 QVFVTPTCPYCPRAVRTAHQMAIENELITADMVEaIEFPHLANKYDVMAVPKVVINDKV 195
                                       69******************************9876777777777***********996 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.5e-06    0.0091       7      66 ..      16      74 ..      10      93 .. 0.87
   2 !    8.2   0.2    0.0013       2.6      14      48 ..     133     169 ..     129     174 .. 0.75
   3 ?    4.3   0.0      0.02        39     131     154 ..     176     200 ..     154     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.5e-06
                                      EES-TT-SEEEEEEE.-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-..---STTTHH CS
                     Thioredoxin_4  7 viGnpdApvtvieye.dlrCphCakfeeeveklleeyidtGkvkfiirdfpldkekeslka 66
                                        Gn   pvt+ +++  ++C +Ca++    e+l+e    +Gk+++ + df  d +k s ++
  gi|557694680|ref|YP_008797734.1| 16 LEGNLVNPVTMRVFTqEFECQYCADLRSLAEELVEIG--DGKLRLEVFDFERDADKASAWG 74
                                      5688899*******746*****************987..***********99988877776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0013
                                       SEEEEEEE-TT-HHHHHHHHHHH..HHHHHHHHTTSE CS
                     Thioredoxin_4  14 pvtvieyedlrCphCakfeeeve..klleeyidtGkv 48 
                                       pv++ +++  +Cp+C +  ++    ++ +e i ++ v
  gi|557694680|ref|YP_008797734.1| 133 PVHIQVFVTPTCPYCPRAVRTAHqmAIENELITADMV 169
                                       89*************8876665535566666666555 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.02
                                       HHHHHHT--SS-EEEETTEE.E-TT CS
                     Thioredoxin_4 131 keakkagiestPtfiingek.veep 154
                                         a+k ++ ++P ++in+++ +e++
  gi|557694680|ref|YP_008797734.1| 176 HLANKYDVMAVPKVVINDKVsFEGA 200
                                       4679**************9966655 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   3.2e-05     0.064      30      89 ..      35      94 ..      25     108 .. 0.84
   2 !   13.7   0.1   2.3e-05     0.047      15      79 ..     128     192 ..     121     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                      SHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEE CS
                       Thioredoxin 30 CghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkye 89
                                      C  C  l +  e+l e   +k++l   d +  +d a+ ++v+ iP+l+l  + ++  +y 
  gi|557694680|ref|YP_008797734.1| 35 CQYCADLRSLAEELVEIGDGKLRLEVFDFERDADKASAWGVDKIPALLLHGAREYKVRYF 94
                                      888999999999999999999**************************9987776665555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.3e-05
                                       TTTSSEEEEE.EE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEE CS
                       Thioredoxin  15 akekklvlve.FyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklf 79 
                                       ++ +k+v ++ F  p C+ C +   + +++a e +  ++   v++ e ++la+ky+v ++P++++ 
  gi|557694680|ref|YP_008797734.1| 128 REISKPVHIQvFVTPTCPYCPRAVRTAHQMAIENE-LITADMVEAIEFPHLANKYDVMAVPKVVIN 192
                                       55444444433999******888777777777777.899999*******************99764 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.014        28       9      47 ..      26      68 ..      22     106 .. 0.64
   2 !   11.1   0.2    0.0002       0.4       9     106 ..     136     207 ..     128     210 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.014
                     Thioredoxin_2  9 lvvft.dpdCpyCkklkkelkel...ddvtvrvllfplkpsfe 47
                                      + vft   +C yC+ l+   +el    d + r+  f+++++++
  gi|557694680|ref|YP_008797734.1| 26 MRVFTqEFECQYCADLRSLAEELveiGDGKLRLEVFDFERDAD 68
                                      5577766689999887665555533355555544444554433 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0002
                     Thioredoxin_2   9 lvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv 85 
                                       + vf +p+CpyC +  ++  ++             ++  + a ++   + ++           la+ky+v ++P +v
  gi|557694680|ref|YP_008797734.1| 136 IQVFVTPTCPYCPRAVRTAHQM-----------AIENELITADMVEAIEFPH-----------LANKYDVMAVPKVV 190
                                       56899*********99999999...........3345456666777777776...........99999999999999 PP

                     Thioredoxin_2  86 fldgkeivarlpGyvpaeele 106
                                       + d+       +G++p   ++
  gi|557694680|ref|YP_008797734.1| 191 INDKV----SFEGALPDMHFL 207
                                       99999....889988877665 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.6e-07   0.00073      27     106 ..     118     194 ..     112     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.6e-07
                                       HHH---HHHHHT--S-EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEE CS
                     Thioredoxin_9  27 elseeteekiksiekklkilvltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtlii 103
                                       +ls+ +++k+++i+k+++i v+ ++ C+ + + v   +++a +n+ i+ +++   e + l ++y      a+P+++i
  gi|557694680|ref|YP_008797734.1| 118 RLSPSVRAKVREISKPVHIQVFVTPTCPYCPRAVRTAHQMAIENELITADMVEAIEFPHLANKYD---VMAVPKVVI 191
                                       6889999*******************************************************995...599999999 PP

                                       E-T CS
                     Thioredoxin_9 104 lde 106
                                        d+
  gi|557694680|ref|YP_008797734.1| 192 NDK 194
                                       886 PP

>> DUF836  Glutaredoxin-like domain (DUF836)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.019        37       9      62 ..      34      90 ..      28     125 .. 0.75
   2 !   12.5   0.0   7.6e-05      0.15       2      61 ..     136     197 ..     135     210 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.019
                                      T-HHHH...HHHHHHHHHCCCTTEEEEEEETTT-CCCHCCCC.TTTTEEEECTTCGGB CS
                            DUF836  9 gChlCe...qakekLkelkleegleleviDIakdeeleakYg.leipvlalegvkkts 62
                                      +C  C    ++ e L+e++ + +l+lev D ++d +  +++g ++ip l+l g ++++
  gi|557694680|ref|YP_008797734.1| 34 ECQYCAdlrSLAEELVEIG-DGKLRLEVFDFERDADKASAWGvDKIPALLLHGAREYK 90
                                      5999993334445555443.4449********99998888772468888888876665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.6e-05
                                       EEEEE-TT-HHHHHHHHHHHHHCCCTT.EEEEEEETTT-CCCHCCCCTT.TTEEEECTTCGG CS
                            DUF836   2 ltLyskpgChlCeqakekLkelkleeg.leleviDIakdeeleakYgle.ipvlalegvkkt 61 
                                       ++ +++p C+ C +a    +++++e++ ++ + +   + ++l +kY+++ +p+++++++ ++
  gi|557694680|ref|YP_008797734.1| 136 IQVFVTPTCPYCPRAVRTAHQMAIENElITADMVEAIEFPHLANKYDVMaVPKVVINDKVSF 197
                                       889*****************999999844444444446678******8549**999995544 PP

>> ABC_transp_aux  ABC-type uncharacterized transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0011       2.2      22      89 ..      19      77 ..      14     102 .. 0.77
   2 !    7.6   0.0    0.0012       2.3      12      52 ..     119     156 ..     111     207 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0011
                    ABC_transp_aux 22 nleepvtikvylsenlalppelkalekevkdlLeeyaaysggkisvefidpspneeeeeeaeaygitp 89
                                      nl +pvt++v+ +e +       ++  ++++l ee+ + ++gk+++e+ d + +    ++a+a g+ +
  gi|557694680|ref|YP_008797734.1| 19 NLVNPVTMRVFTQEFE------CQYCADLRSLAEELVEIGDGKLRLEVFDFERDA---DKASAWGVDK 77
                                      6778999999988884......26799************************9666...6665555555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0012
                    ABC_transp_aux  12 Lsdatkellknleepvtikvylsenla.lppelkalekevkd 52 
                                       Ls+  +  ++++++pv+i+v++++     p ++    + +++
  gi|557694680|ref|YP_008797734.1| 119 LSPSVRAKVREISKPVHIQVFVTPTCPyCPRAV----RTAHQ 156
                                       788888889***************954333333....33333 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.023        46     172     199 ..      57      84 ..      28      96 .. 0.84
   2 ?    9.7   0.0   0.00034      0.68     122     200 ..     125     193 ..     120     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.023
                              TraF 172 lpelpnarvdkgqaarlgvkrtPalvlv 199
                                         e+ ++++d ++a ++gv  +Pal+l 
  gi|557694680|ref|YP_008797734.1|  57 RLEVFDFERDADKASAWGVDKIPALLLH 84 
                                       44566788999**************985 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00034
                              TraF 122 aalkklakeygLlfFyrgkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvl 198
                                       a +++++k + + +F+ ++cpyc  ++ +  ++a + +     ++ d     e+p+       a+++ v  +P +v+
  gi|557694680|ref|YP_008797734.1| 125 AKVREISKPVHIQVFVTPTCPYCPRAVRTAHQMAIENE----LITADMVEAIEFPH------LANKYDVMAVPKVVI 191
                                       6788999999999**************99998876554....34444444444555......555777777777776 PP

                              TraF 199 vd 200
                                        d
  gi|557694680|ref|YP_008797734.1| 192 ND 193
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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: 00:00:00.46
# Mc/sec: 1383.88
//
Query:       gi|557694681|ref|YP_008797735.1|  [L=395]
Description: aminotransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-24   85.4   0.0    4.8e-24   85.0   0.0    1.1  1  Aminotran_5  Aminotransferase class-V


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 !   85.0   0.0   2.7e-28   4.8e-24      34     358 ..      33     351 ..      11     362 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 2.7e-28
                                       SSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHH CS
                       Aminotran_5  34 vhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelak 110
                                       + h+g e + ++ e+ +  a+++++++e  ++ t Gt  a+++ ++sl   ++pg+++v ++++  +++   +++a 
  gi|557694681|ref|YP_008797735.1|  33 MAHYGPEWAPIYSETLKLAAAIFKTKQEVFMMPTPGTV-ALETGVISL---VEPGEKVVAVVNGFFSER--LADIAS 103
                                       5678888899999999999******9866666666655.*********...******************..99**** PP

                                       HHTEEEEEEEBETTSCBEGGGHHHH-..-TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS-- CS
                       Aminotran_5 111 rtgakvkvipldeegeldldelekll..nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipi 185
                                        tga+  +++++ ++ +d++el++ l  n+ +k+v   +++++tG+++p++e +k+a++++al++vDa +++g  ++
  gi|557694681|ref|YP_008797735.1| 104 LTGAETLKVTAELGKVVDPNELDNVLskNKGVKAVLAVQNETSTGVLNPIPEYAKVARQHDALFVVDAISSYGGVEM 180
                                       **************************5457899******************************************** PP

                                       -HHHHTESEEEEETTTTTSS.TT-EEEEEEHHHHHTS....SS.STTSEEEEET.TEEE..EHCTTGGGS.SS--HH CS
                       Aminotran_5 186 dvkklgvDflafsghKllgP.tGiGvlyvrkellekl..eplllggemveevsl.eett..faeapskfeaGTpnva 256
                                       +++ +g+Df +  + K lg  +G+  + v+++++e++  + +++ +   +     ++    +++  + +   T    
  gi|557694681|ref|YP_008797735.1| 181 EFDSWGIDFCVGYANKCLGSiPGTVPVAVSDRAWEAFrrRRTQPRSFFTNLGVWrHY-IdeWSSIGHPYPT-TISPH 255
                                       ****************777549***************75445555554444333333.3357777787885.89999 PP

                                       HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHH...HHHH.HH CS
                       Aminotran_5 257 giiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaed...vatl.Ld 329
                                       ++  ++aa+e l + gle+  ++++  +++ +++++s++  +l  p++ ++++ ++++++++  ++d   v+++ L+
  gi|557694681|ref|YP_008797735.1| 256 AVLCFKAAAEALLQEGLENRYRRHRLVSAAFRKAVRSMGLETL--PEERDASPVVTAVALPSSLWKDggkVGQImLQ 330
                                       9999*************************************99..8999***********99888652225555255 PP

                                       HTTEEEEEE-TTTHHHHHHTT.S-EEEEE CS
                       Aminotran_5 330 eegIavrsGhhcaqplmkrlalegtvRaS 358
                                       ++ I++ +G + +         ++++R++
  gi|557694681|ref|YP_008797735.1| 331 KHRIMIGGGLAQL--------HNKIIRIG 351
                                       5599999998887........55666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 3071.29
//
Query:       gi|557694682|ref|YP_008797736.1|  [L=97]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.8   0.5       0.35   11.2   0.1    2.1  2  BON       BON domain


Domain annotation for each model (and alignments):
>> BON  BON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.018   3.2e+02       4      16 ..       6      18 ..       5      28 .. 0.81
   2 ?   11.2   0.1   1.9e-05      0.35      45      65 ..      62      82 ..      61      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.018
                                      CCHHHHHHHHHHH CS
                               BON  4 eiaakvkaalakd 16
                                      ++a++v++alak 
  gi|557694682|ref|YP_008797736.1|  6 DLAEEVRKALAKL 18
                                      79999***99985 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHHHCCTTEEEEEEEE CS
                               BON 45 kekAveiarnvaGVkkVvnel 65
                                      +e+A +ia +++GV+kV+ e+
  gi|557694682|ref|YP_008797736.1| 62 AEAAKRIASKTPGVAKVYVEV 82
                                      699**************9776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 720.10
//
Query:       gi|557694683|ref|YP_008797737.1|  [L=109]
Description: V-type H+-transporting ATPase subunit G [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.1   0.9      0.038   14.2   0.3    1.8  1  DUF1492          Protein of unknown function (DUF1492)
      0.029   12.6   0.4      0.031   12.5   0.4    1.2  1  COG6             Conserved oligomeric complex COG6
      0.029   14.9   3.6      0.037   14.5   3.6    1.3  1  FlgN             FlgN protein
       0.13   12.7  13.9       0.15   12.5  13.9    1.0  1  V-ATPase_G_2     Vacuolar (H+)-ATPase G subunit
       0.18   12.9   0.6       0.63   11.1   0.0    1.8  2  Methyltransf_24  Methyltransferase domain
        0.2   11.9   0.8          2    8.7   0.2    2.2  2  DUF948           Bacterial protein of unknown function (DUF94
       0.74   10.4   6.1        2.3    8.8   1.4    2.1  2  YtxH             YtxH-like protein
          1    9.6   8.7        2.6    8.3   8.7    1.7  1  THOC7            Tho complex subunit 7
        1.2    9.8   6.0       0.86   10.3   3.7    1.7  2  DUF2203          Uncharacterized conserved protein (DUF2203)
        1.5    9.5   9.7        3.9    8.2   1.3    2.3  2  DUF883           Bacterial protein of unknown function (DUF88
        1.9    9.0   6.5         30    5.2   1.8    3.0  2  HisKA_3          Histidine kinase
        9.5    6.5   7.1         32    4.7   7.2    1.6  1  zf-C4H2          Zinc finger-containing protein


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 ?   14.2   0.3   2.5e-05     0.038      44      89 ..      14      60 ..       3      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                           DUF1492 44 kklelqrlidklensdsrsvLrmvyidkltvwq.vidklnisrstyy 89
                                      +   +   i++l ns  r++L m y++  ++ q v++++   +s  y
  gi|557694683|ref|YP_008797737.1| 14 QVEKVVDEINELANSMRRALLDMAYVEAEKRKQaVLEEMRAWQSRLY 60
                                      445566789*****************988776537888887777666 PP

>> COG6  Conserved oligomeric complex COG6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   2.1e-05     0.031      35      83 ..       1      54 [.       1      77 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                              COG6 35 fleefqpvaeqLkriesdveklnelcdemkkkl.....ssakeetsdlleeaee 83
                                      +++e++++ ++L+++e+ v+++nel ++m+++l      +a+++ + +lee+ +
  gi|557694683|ref|YP_008797737.1|  1 MVDELRKIIDELQQVEKVVDEINELANSMRRALldmayVEAEKRKQAVLEEMRA 54
                                      5899**************************987322223455556666666655 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   3.6   2.5e-05     0.037      38     105 ..       6      76 ..       2     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SCHHHHHHHHCT...TCCHHHHHHHHHHHHHHHHHHH CS
                              FlgN  38 eaLeelleekqellekleqleqkrakllaelglsaeeatlsellak...eedeelkelwqelkelleelke 105
                                       +++ + l++ +++++++++l++ ++++l ++++++ e+  +++l++    +     e + + +e+++e+++
  gi|557694683|ref|YP_008797737.1|   6 RKIIDELQQVEKVVDEINELANSMRRALLDMAYVEAEKRKQAVLEEmraWQSRLYDEEVGKAEEAAREIQA 76 
                                       556666899*************************8888888888888844444457788888888888886 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 ?   12.5  13.9    0.0001      0.15       3      98 ..       5     100 ..       3     105 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                                       XXHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      V-ATPase_G_2   3 ssrllkeLaerEaeLdqrlEaArkeaereveaAeaeAarilreAeakakalqaeyeqelaeevarireeararaeae 79 
                                        +++++eL + E+  d+  E A    ++ ++ A  eA++  ++  ++++a q++  +e+  + ++ + e++a++  e
  gi|557694683|ref|YP_008797737.1|   5 LRKIIDELQQVEKVVDEINELANSMRRALLDMAYVEAEKRKQAVLEEMRAWQSRLYDEEVGKAEEAAREIQAKGVYE 81 
                                       5789**************************************************999999999************** PP

                                       HHHHHHHHHCSHHHHHHHH CS
                      V-ATPase_G_2  80 aqavrkraearlqqAveli 98 
                                       +++vr+rae+   qA el+
  gi|557694683|ref|YP_008797737.1|  82 VEKVRRRAEQVKPQAEELV 100
                                       *******998777776665 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00042      0.63      50      96 ..      14      60 ..       3      65 .. 0.86
   2 ?    0.5   0.1      0.84   1.3e+03      38      63 ..      71     101 ..      60     106 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00042
                   Methyltransf_24 50 rvrlikadseealaslaagsiDllfiDgghaaeavledleallprla 96
                                      +v+ ++++ +e++ s+++   D++++ ++  ++avle+++a++ rl 
  gi|557694683|ref|YP_008797737.1| 14 QVEKVVDEINELANSMRRALLDMAYVEAEKRKQAVLEEMRAWQSRLY 60
                                      577788888888889998999**********************9986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.84
                   Methyltransf_24  38 aaalare.........aglddrvrlikadseeala 63 
                                       a+    e         +++++r++++k ++ee+++
  gi|557694683|ref|YP_008797737.1|  71 AR----EiqakgvyevEKVRRRAEQVKPQAEELVR 101
                                       22....22223566667777788888777777654 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 ?    8.7   0.2    0.0013         2      28      63 ..       2      36 ..       1      57 [. 0.80
   2 ?    2.0   0.0      0.16   2.4e+02      35      55 ..      82     102 ..      60     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0013
                            DUF948 28 ldeaaatieelekqvdpilkevedllakvnelledv 63
                                      +de+++ i+el+ qv+++++e+++l + +++ l d+
  gi|557694683|ref|YP_008797737.1|  2 VDELRKIIDELQ-QVEKVVDEINELANSMRRALLDM 36
                                      788888888885.79999999999998888766665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.16
                            DUF948  35 ieelekqvdpilkevedllak 55 
                                       +e+++++++++  ++e+l++k
  gi|557694683|ref|YP_008797737.1|  82 VEKVRRRAEQVKPQAEELVRK 102
                                       455556666666666666655 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.035        53      26      53 ..       5      38 ..       2      56 .. 0.57
   2 ?    8.8   1.4    0.0016       2.3      31      73 ..      57     102 ..      50     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.035
                              YtxH 26 tRkdlkek..addlkekakelleeakeka....k 53
                                      +Rk + e   ++++ + ++el+++++        
  gi|557694683|ref|YP_008797737.1|  5 LRKIIDELqqVEKVVDEINELANSMRRALldmaY 38
                                      5555554333667777777777776655544441 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0016
                              YtxH  31 kekaddlkekakelleeakeka...kekaedlkekvkekadelkek 73 
                                       ++ +d+   ka+e++ e++ k+   +ek+   +e+vk +a+el+ k
  gi|557694683|ref|YP_008797737.1|  57 SRLYDEEVGKAEEAAREIQAKGvyeVEKVRRRAEQVKPQAEELVRK 102
                                       5566777789999*********99999999999********99765 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   8.7    0.0017       2.6      15      90 ..       4      77 ..       1     102 [. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0017
                             THOC7 15 plkrltkrllklltslaesteeeleqlkedllldfaafelsierlqllakanerereryeaekeeieseieavree 90
                                      +l++++ +l+++ ++   ++ +el++   ++lld+a  e + +++ +l+++ + + + y++e  + e+++ +++++
  gi|557694683|ref|YP_008797737.1|  4 ELRKIIDELQQVEKV--VDEINELANSMRRALLDMAYVEAEKRKQAVLEEMRAWQSRLYDEEVGKAEEAAREIQAK 77
                                      488888899986666..4668999************************************8777777555555444 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.7   0.00057      0.86      11      74 ..      11      79 ..       1      85 [. 0.75
   2 ?    0.4   0.2      0.69     1e+03      49      58 ..      83      92 ..      67     104 .. 0.38

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00057
                           DUF2203 11 lLpllkelleelralrkeleeleeeleeakaeaekse.....aaeleaeleeleaeieelveeieelGv 74
                                       L++++++++e+++l++ ++++  +++  +ae++k++     +a + + ++e   ++ee+ +ei++ Gv
  gi|557694683|ref|YP_008797737.1| 11 ELQQVEKVVDEINELANSMRRALLDMAYVEAEKRKQAvleemRAWQSRLYDEEVGKAEEAAREIQAKGV 79
                                      577888888888888888888888888777777666677765555556667888889999999999887 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.69
                           DUF2203 49 aeleaeleel 58
                                      ++ +++ e++
  gi|557694683|ref|YP_008797737.1| 83 EKVRRRAEQV 92
                                      1111111111 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 ?    8.0   4.3    0.0029       4.4       5      65 ..      13      74 ..       2      79 .. 0.81
   2 ?    8.2   1.3    0.0026       3.9      35      71 ..      66     102 ..      64     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                            DUF883  5 aeleslladleellkeaade.ageeaeelRerleerlerarerlrdaeeavaerakeaaeaa 65
                                      + +e+++++++el+++  +   +  + e+ +r ++ le++r+  ++++++ + +a+eaa++ 
  gi|557694683|ref|YP_008797737.1| 13 QQVEKVVDEINELANSMRRAlLDMAYVEAEKRKQAVLEEMRAWQSRLYDEEVGKAEEAAREI 74
                                      346778888888888766541567889999999***********************999875 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0026
                            DUF883  35 rleerlerarerlrdaeeavaerakeaaeaaddyVre 71 
                                       ++ee++++ +++     e+v++ra+++  +a++ Vr+
  gi|557694683|ref|YP_008797737.1|  66 KAEEAAREIQAKGVYEVEKVRRRAEQVKPQAEELVRK 102
                                       6788888888888888889999999999999998886 PP

>> HisKA_3  Histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2     0.022        33      40      63 ..      13      36 ..       1      41 [. 0.77
   2 ?    5.2   1.8      0.02        30      30      67 ..      59      96 ..      40      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.022
                                      HHHHHHHHHHHHHHHHHHHHHHHH CS
                           HisKA_3 40 eqlreieelarealqevRrllhnL 63
                                      +q++++ + ++e  + +Rr+l ++
  gi|557694683|ref|YP_008797737.1| 13 QQVEKVVDEINELANSMRRALLDM 36
                                      677788888888888888888765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.02
                                      HTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHH CS
                           HisKA_3 30 llekdpekaaeqlreieelarealqevRrllhnLrpaa 67
                                      l++++ +ka+e++rei++     ++ vRr  ++ +p+a
  gi|557694683|ref|YP_008797737.1| 59 LYDEEVGKAEEAAREIQAKGVYEVEKVRRRAEQVKPQA 96
                                      4577788**********************999999976 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   7.2     0.021        32      51     130 ..       2      81 ..       1     103 [. 0.55

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.021
                           zf-C4H2  51 veeLrlIhaDinalEsvikeaeeekek.slekakklyeeykklkeev.nelrselglekledleeeeeellkeeife 125
                                       v+eLr+I + ++++E+v+ e +e  +  + +   ++y e +k k+ v +e+r     ++l d e  + e   +ei +
  gi|557694683|ref|YP_008797737.1|   2 VDELRKIIDELQQVEKVVDEINELANSmRRALLDMAYVEAEKRKQAVlEEMRAW-Q-SRLYDEEVGKAEEAAREIQA 76 
                                       789999999999999999998775554144556777788888777762444443.2.22333333333333344433 PP

                           zf-C4H2 126 kqklk 130
                                       k   +
  gi|557694683|ref|YP_008797737.1|  77 KGVYE 81 
                                       33333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1822  (0.101623); expected 358.6 (0.02)
Passed bias filter:                      795  (0.0443416); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 792.03
//
Query:       gi|557694684|ref|YP_008797738.1|  [L=351]
Description: V-type H+-transporting ATPase subunit C [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-56  191.7   1.2    2.9e-56  191.4   1.2    1.0  1  vATP-synt_AC39   ATP synthase (C/AC39) subunit
  ------ inclusion threshold ------
      0.019   14.7   0.1      0.059   13.1   0.0    1.8  2  N_formyltrans_C  N-formyltransferase dimerization C-terminal 
      0.039   12.6   0.0      0.076   11.6   0.0    1.4  1  DHC_N1           Dynein heavy chain, N-terminal region 1
       0.13   11.9   0.1        0.3   10.7   0.1    1.6  1  2-oxogl_dehyd_N  2-oxoglutarate dehydrogenase N-terminus


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 !  191.4   1.2   6.4e-60   2.9e-56       2     329 ..      12     339 ..      11     344 .. 0.92

  Alignments for each domain:
  == domain 1  score: 191.4 bits;  conditional E-value: 6.4e-60
                                       HHHHHHHGGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--.....SSSHHHHHHHHHHHHHHHTTTGGGGS-H. CS
                    vATP-synt_AC39   2 eArvramrsglLteedyenLlqcesledvkryLketdYgnfladelseplsrsdiekalreklarefnklreqapgp 78 
                                       +++v a++s lL+++ +e L+ +++l+d++  L+ t Yg fla+ +  p++  ++ekal++ l++  +kl + a+ p
  gi|557694684|ref|YP_008797738.1|  12 VTKVYALKSMLLPAAGLEDLAYSKNLSDFVDRLRATTYGPFLAQLQK-PYTAVEVEKALTRGLVNIHHKLVQTANRP 87 
                                       79***************************************998876.9**************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH.T--GGGS-..--.S....SSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHH CS
                    vATP-synt_AC39  79 srefldyllyrydidNvklllrgklsgdldleeleeklhpl....gelsaldldklieaksveelyeallgtpyaky 151
                                         ++l++l+ ry + N+k++l++   g l+++e+++++         +  ++  ++++ak++ e+++ +l tpy  +
  gi|557694684|ref|YP_008797738.1|  88 --NLLKALFTRYVYFNIKTILKSRALG-LSQDEILKRIDLYpeelTGV-RDTALRALTAKDLGEFLKEFLATPYHGI 160
                                       ..9***********************5.77799999874446542233.3344699********************* PP

                                       HHHHHCC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T... CS
                    vATP-synt_AC39 152 leealdeleetgdleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkygelskedrkkl 228
                                       +++a++++++ +d++++++ +d+ y+e+l+k+ +++ ++++++l+++   eiD+r++ i++r + +g l ++  k++
  gi|557694684|ref|YP_008797738.1| 161 VQKAVEVWNNRRDFSAVDAVIDRDYIEQLYKAYRRSPRDERKLLQSAMVLEIDMRALAIAIRGRLWG-LVPSVLKEF 236
                                       **********************************9******************************99.777778888 PP

                                       --SS-.S--HHHHHHHHTT-G.....GG..GGSSTSSTTGGGTT-.-S.HHHHHHHHHHHHHHHHHT.TTSSSTSTH CS
                    vATP-synt_AC39 229 lipgg.slypeglealaeaedveellaal.kyteygelleealee.agslksledaldealvkllkk.afrqqfsvg 301
                                       l++   +++++ l+al+e++dv+++l+ l +++ ++++ +  +++ a+  +++e+ ++ ++vk +++ + +++f   
  gi|557694684|ref|YP_008797738.1| 237 LPEETvEVPRQLLDALVESDDVKRVLSQLpEKPVFSRIQA--EQDvAQVVSAIEETVKSYRVKWASQsFYKTPFKQL 311
                                       *****************************99999999844..4444444******************9999****** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHT-- CS
                    vATP-synt_AC39 302 vfyaYlklkeqEirnlrwIaegiaqglp 329
                                        ++a+++lke E+rnl +Ia+ i+ g++
  gi|557694684|ref|YP_008797738.1| 312 NLIAFIYLKEAEVRNLSTIAKYIEEGVS 339
                                       ************************9986 PP

>> N_formyltrans_C  N-formyltransferase dimerization C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.3e-05     0.059      14      31 ..      35      52 ..      30      54 .. 0.86
   2 ?   -2.8   0.0       1.2   5.2e+03      22      28 ..     136     142 ..     120     145 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                                      EEHHHHHHHHHHT--TT- CS
                   N_formyltrans_C 14 vtlrElidlLRAltfgpy 31
                                       +l +++d+LRA+t+gp+
  gi|557694684|ref|YP_008797738.1| 35 KNLSDFVDRLRATTYGPF 52
                                      57889***********97 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                       HHHHT-- CS
                   N_formyltrans_C  22 lLRAltf 28 
                                        LRAlt 
  gi|557694684|ref|YP_008797738.1| 136 ALRALTA 142
                                       5899985 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 ?   11.6   0.0   1.7e-05     0.076      79     144 ..     246     314 ..     232     318 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.7e-05
                            DHC_N1  79 telkkaleeAkdnvkyLktL.ek.pledLest.dleeikellpsllnairliwkiSryYntperivsLl 144
                                       ++l +al e+ d+ + L++L ek  + ++++  d+ ++ +++++ +++ r +w    +Y+tp + ++L+
  gi|557694684|ref|YP_008797738.1| 246 RQLLDALVESDDVKRVLSQLpEKpVFSRIQAEqDVAQVVSAIEETVKSYRVKWASQSFYKTPFKQLNLI 314
                                       67889***************5331455999955*****************************9988887 PP

>> 2-oxogl_dehyd_N  2-oxoglutarate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   6.7e-05       0.3      10      23 ..     184     197 ..     182     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.7e-05
                   2-oxogl_dehyd_N  10 aYiEelYeayleDP 23 
                                        YiE+lY+ay++ P
  gi|557694684|ref|YP_008797738.1| 184 DYIEQLYKAYRRSP 197
                                       5*********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2597.58
//
Query:       gi|557694685|ref|YP_008797739.1|  [L=103]
Description: SirA family protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   58.6   0.0      6e-16   58.0   0.0    1.3  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 !   58.0   0.0   3.4e-20     6e-16       2      70 .]      18      87 ..      17      87 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 3.4e-20
                                      EEEBTT-STTCCHHHHHHHHCCCGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-.GCC-EEEEEEE CS
                              TusA  2 elDlrGlvCPePllklkkalekleegevlevladdpaatediprfakklghelvevee.edgeyrivirk 70
                                      +lD+rG++CP+P l l +al+ +e +  le+l+d+p++te++pr+ ++++ e+++ e  + g+++i+ +k
  gi|557694685|ref|YP_008797739.1| 18 VLDVRGYSCPYPQLFLAQALKAVEKESLLEILTDNPPSTETLPRSIRNNKQEYISTEVvQPGVWKITAKK 87
                                      79******************************************************99777***998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); 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: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 810.22
//
Query:       gi|557694686|ref|YP_008797740.1|  [L=397]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  113.4  28.1    1.5e-18   67.4  12.9    2.3  2  Sulf_transp  Sulphur transport


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4  12.9   8.4e-23   1.5e-18     178     309 ..       7     156 ..       2     157 .. 0.75
   2 !   51.8   7.2   4.8e-18   8.6e-14       2     132 ..     223     360 ..     222     385 .. 0.76

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 8.4e-23
                       Sulf_transp 178 slvlgavllgllavlawllsak.tgrsfglgftvp....gakilqyl......vlgts......kflnwgvvlvlGi 237
                                       +++++a l+gl++v++ ++  + tgr + +g+t+     g+++ ++l      ++  +       f++ +  +v+ i
  gi|557694686|ref|YP_008797740.1|   7 KTYVSAFLIGLVSVAIAIAVYSvTGRGSLWGITGGeskiGGHLYKFLglpvelLTYYQqfklvpVFSDAAQTIVVAI 83 
                                       5799********9987776655489998888886512224444555432222211111111221345667789**** PP

                       Sulf_transp 238 ilGaflaallsgefkleapk.arellaallGGllMGfGarlAgGCniGaglsgiaslslsgwlalvflllGav 309
                                       +lG +l allsg+f l+  + +  ll+a+ GG+++G+G+rlA+GCniG++ls+     + ++ ++++ll+G++
  gi|557694686|ref|YP_008797740.1|  84 LLGGALPALLSGQFLLRHLPnRWMLLQAVSGGFMLGYGSRLALGCNIGNFLSAWTAAGINAVTFTAALLVGVY 156
                                       *****************7762667888999*****************************************97 PP

  == domain 2  score: 51.8 bits;  conditional E-value: 4.8e-18
                       Sulf_transp   2 srfcfagairdivvek..dgrllralllaiavaavgfqllaaaglidlpks...afpvvglivGGllFGvGMalaGg 73 
                                       s +cf +++rd+v ++  ++  ++a+ +++++ + g+ +++ +g+    ++   +++ +++++GGl+FGvG+alaG+
  gi|557694686|ref|YP_008797740.1| 223 SGICFGSCYRDLVKQEiaSWVNVKAIGIILLTFSTGIYVIQLLGIPVSFGGvvpNISQIQIALGGLIFGVGIALAGS 299
                                       679**********996447888899999999999999999999877654441114555889**************** PP

                       Sulf_transp  74 CasgtlyrvGeGslralitllffilgavalltgilsswleqlle..stvskeslyetlgls 132
                                       C  +t  r+G+Gs+ ++++ll  i+ ++ +l+ + ++w+  +    ++ s  +l  tl++ 
  gi|557694686|ref|YP_008797740.1| 300 CIYSTEWRAGSGSIYSMTVLLSTIFLGMPTLALHYDFWRAIIPPilPSFSLYTLSPTLAYL 360
                                       ****************************9*********96443300333334444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2842.07
//
Query:       gi|557694687|ref|YP_008797741.1|  [L=368]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-99  333.4   0.1    1.6e-99  333.2   0.1    1.0  1  DUF1464   Protein of unknown function (DUF1464)
  ------ inclusion threshold ------
       0.11   11.9   0.6       0.46    9.9   0.0    2.0  2  ROK       ROK family


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 !  333.2   0.1  1.7e-103   1.6e-99       1     327 []       5     353 ..       5     353 .. 0.94

  Alignments for each domain:
  == domain 1  score: 333.2 bits;  conditional E-value: 1.7e-103
                           DUF1464   1 GiDPGtksydvvvvdd.lgkvvlekeiptdevekdpsvlvkaieearadivalpSGyGlPlkriselaereillltl 76 
                                       GiDPGt+ +d++ ++d +++vvl++ i +++v++ p  +v+++  a +d+v++pSGyGl +k+ se++er++ l tl
  gi|557694687|ref|YP_008797741.1|   5 GIDPGTGNFDILCIEDdVDHVVLDETISSSTVAERPAEVVELVLSALPDVVVGPSGYGLSFKKLSEIDERDLALTTL 81 
                                       9*************9989*********************************************************** PP

                           DUF1464  77 aeeseegl...vGLrellkelaskelnaftiPgVieLptvPewRKvnkiDmGtADKlasavlavadeaeee..eyre 148
                                       ++ s+ g     G+r++l+ l++k++n++t+PgV++L++vP +RK+nkiDmGtADK ++++ av d+++ +   y e
  gi|557694687|ref|YP_008797741.1|  82 ERRSDYGApvlSGVRSMLRMLREKNVNGYTLPGVVQLKSVPMHRKYNKIDMGTADKTCVTAYAVWDQSRVHgaRYDE 158
                                       *****99888789**********************************************************999*** PP

                           DUF1464 149 lsFilvEvGsgfnaviaVknGkivDGlGgtilpG..flsaGalDgEvAyllgkvakiekslifsgGvasiagea..e 221
                                       +  i vE+G g+na++aV+nGkivDG+Ggti+pG  +ls+G +DgE+Ayll     ++k+++f+gG ++ia+ +  e
  gi|557694687|ref|YP_008797741.1| 159 TCLICVEMGLGYNAAMAVENGKIVDGVGGTIFPGpgYLSIGLMDGELAYLLD---GFSKKTLFEGGLSWIATGSkvE 232
                                       *******************************98777****************...9***************887678 PP

                           DUF1464 222 lekklsee......aferlke.vvksvaellssk.ykleeiivSGrlkrikelgkklesrleev.......kllela 283
                                       +ek ++        af   +e v k+va l + +  +++e+i+ Grl r++ +++ + s l+          l+  a
  gi|557694687|ref|YP_008797741.1| 233 VEKFAAGLttdyadAFRCFVEgVGKAVAMLAAVMdKRPREVILTGRLSRVESIREAVASWLQRKlgfkarrPLNVFA 309
                                       88877665778999*************9887765136789*****************99997667898886677789 PP

                           DUF1464 284 skaKeaaqGaAiianalaGgryrelvdhleiekssgtvldyvkl 327
                                       ++aK+ a+GaA+ian+l Gg+y+elv+ lei++++g+vldyv+l
  gi|557694687|ref|YP_008797741.1| 310 KRAKDVAMGAALIANGLGGGKYSELVENLEIRRARGSVLDYVRL 353
                                       99****************************************86 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1     0.066   5.9e+02     115     151 ..     151     188 ..     142     189 .. 0.82
   2 ?    9.9   0.0   5.1e-05      0.46     212     291 ..     245     323 ..     223     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.066
                                       HHCTTTTTS-EEEEEESSSEEEEE.EETTEEE--TTS- CS
                               ROK 115 vfgaskdvenviyvtvgtGvGaGv.iingklitGrnGv 151
                                       v ga+ d + +i+v +g G  a++ + ngk++ G +G+
  gi|557694687|ref|YP_008797741.1| 151 VHGARYDETCLICVEMGLGYNAAMaVENGKIVDGVGGT 188
                                       567888888899999999999987245999**999986 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 5.1e-05
                                       HHHHHHHHHHHHHHHHHHHHHH-..-SEEEEEHCCCTSTTHHHHHHHHHHHCCTTTTCCCT-EEEE-S-STTHHHHH CS
                               ROK 212 eevverlaeylakaiadlinlfd..pqaivlgGgvseadklleairklvkkylnkklevpvveivaaklgdkagllG 286
                                       +++ + ++e ++ka+a l++++d  p  ++l G +s ++ + ea+ + +++ l  k+++p  ++ a  ++    ++G
  gi|557694687|ref|YP_008797741.1| 245 ADAFRCFVEGVGKAVAMLAAVMDkrPREVILTGRLSRVESIREAVASWLQRKLGFKARRPL-NVFAKRAK--DVAMG 318
                                       56788899999******999997669***********998888888888877777777776.45554444..45789 PP

                                       HHHHH CS
                               ROK 287 aaaLa 291
                                       aa++a
  gi|557694687|ref|YP_008797741.1| 319 AALIA 323
                                       98887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); 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:                         2  (0.000111551); expected 0.2 (1e-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: 2632.44
//
Query:       gi|557694688|ref|YP_008797742.1|  [L=311]
Description: beta-ribofuranosylaminobenzene 5'-phosphate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-07   29.1   0.1    2.7e-06   27.6   0.1    1.8  1  GHMP_kinases_C  GHMP kinases C terminal
     0.0042   17.3   0.0      0.013   15.7   0.0    1.9  1  GHMP_kinases_N  GHMP kinases N terminal domain


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 !   27.6   0.1     3e-10   2.7e-06       2      82 ..     208     288 ..     207     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3e-10
                    GHMP_kinases_C   2 lealergdlellgellnlsqrs....elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeq 74 
                                       l+ l+++dl  +ge+l  +qr+         v     ++ e++++l+ +G  + ++ ++++Gp+v++lf d+ eae+
  gi|557694688|ref|YP_008797742.1| 208 LPTLLERDLTGFGECLSILQRLvgqyFA--SVQGGVFRMAEAVQLLRMAG--AKGVGQSSWGPAVYGLFGDRLEAEN 280
                                       56788999999**********7653322..33334445666666666666..************************* PP

                    GHMP_kinases_C  75 varalree 82 
                                       ++ ++r++
  gi|557694688|ref|YP_008797742.1| 281 AVFEVRKH 288
                                       **999887 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 !   15.7   0.0   1.5e-06     0.013       2      43 ..      77     118 ..      76     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-06
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHH CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklal 43 
                                       i+++s iPv++G+GS + l +al++A++++ +++++ +++a 
  gi|557694688|ref|YP_008797742.1|  77 IKVQSGIPVHRGFGSRTQLRLALATAICKAMDVEFQVHRIAE 118
                                       899****************************87765566654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 2188.90
//
Query:       gi|557694689|ref|YP_008797743.1|  [L=207]
Description: hypothetical protein CSUB_C1262 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  115.9   0.2    2.1e-33  115.6   0.2    1.0  1  DUF447          Protein of unknown function (DUF447)
  ------ inclusion threshold ------
      0.021   15.0   0.0      0.046   13.9   0.0    1.5  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
      0.095   13.4   0.0       0.16   12.7   0.0    1.4  1  HlyD_3          HlyD family secretion protein


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 !  115.6   0.2   3.5e-37   2.1e-33       1     165 [.      15     186 ..      15     191 .. 0.93

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 3.5e-37
                                       EEEEEEEE-TT.-EEEEEEEEEE.SSSEEEEEEETTSHHHHHHHHHSEEEEEE---HHHHHHHHHS---GGGEEEET CS
                            DUF447   1 yEvivtTksek.rpnaaPiGviv.kgdkvvlrlfkgsrTleNllengelvinvtdDpllfakaalgdleesdfdset 75 
                                       yEviv+T+ e+ +p++a++G    +++ ++++++  + T++Nll+++ +++nvt+ p+ f+ a++++    ++ ++ 
  gi|557694689|ref|YP_008797743.1|  15 YEVIVSTYLENgEPHFAAMGCGLiDDEHLIVKPYTNTETYRNLLSHRAAAVNVTNEPYHFYAAVFNKPLPHRRGEKV 91 
                                       8*******************99878999**************************************87777665555 PP

                                       TTCTT.EETT-SEEEEEEEEEE.CTCECCEEEEEEEEEEEEETTB---B-HHHHHHHHHHHHHHCCCC.......SH CS
                            DUF447  76 kpakiavlksaeawveveveev.egdsealelelepvkeeileervkpfnRgdaaviEaaVlatRldi.......ed 144
                                           ++ l++aeaw+e+ ve++  +++++ +++l+p+   + +++++p++R+ +a++E+++++tR ++       ++
  gi|557694689|ref|YP_008797743.1|  92 ---TAPLLDGAEAWIEAVVENIsADTPDRATVTLTPITITSAQPVTRPYSRASHAIVEMLIHYTRVKVfahssehSR 165
                                       ...457***************988999****************************************9999998888 PP

                                       HHHHHHHHHHHHHHHHHH--H CS
                            DUF447 145 keklleeieylssvikktgge 165
                                          l+e+i ++s +++++ ++
  gi|557694689|ref|YP_008797743.1| 166 AVSLAEKILDYSALVRRVTSN 186
                                       8899*************9876 PP

>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   7.7e-06     0.046      15      68 ..      17      69 ..      15      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 7.7e-06
                                      EEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEE CS
                    Putative_PNPOx 15 vvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallfld 68
                                      v ++T  e+G P+  +++    d++ ++++   + ++++rnl ++  +a+ + +
  gi|557694689|ref|YP_008797743.1| 17 VIVSTYLENGEPHFAAMGCGLIDDE-HLIVKPYTNTETYRNLLSHRAAAVNVTN 69
                                      5799999***********9999999.99999999999***********998766 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   2.7e-05      0.16      35      86 ..      71     121 ..      58     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.7e-05
                            HlyD_3  35 tllveakvpaadlgsikkkgqkvtlkldqgsdytlkgkierisp.tvdaktga 86 
                                        + ++a+v ++ l+  +  g kvt  l +g ++++++ +e+is+ t+d+ t +
  gi|557694689|ref|YP_008797743.1|  71 PYHFYAAVFNKPLPH-R-RGEKVTAPLLDGAEAWIEAVVENISAdTPDRATVT 121
                                       677889999999999.6.9***********************99555765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1590.95
//
Query:       gi|557694690|ref|YP_008797744.1|  [L=378]
Description: pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase) [Candidatus Caldiarchaeum subterraneum]
Scores for 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-82  275.5   0.6      4e-82  275.1   0.6    1.1  1  2-oxoacid_dh     2-oxoacid dehydrogenases acyltransferase (ca
    8.8e-20   70.3   3.4    8.8e-20   70.3   3.4    2.2  2  Biotin_lipoyl    Biotin-requiring enzyme
    2.4e-18   66.2   0.4    2.4e-18   66.2   0.4    2.5  3  E3_binding       e3 binding domain
    2.2e-08   33.8   4.9    8.6e-06   25.5   0.0    3.4  3  Biotin_lipoyl_2  Biotin-lipoyl like
    0.00035   21.2   1.3       0.04   14.6   0.0    2.9  3  HlyD_3           HlyD family secretion protein
     0.0019   17.4   0.1      0.059   12.6   0.0    2.6  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
     0.0085   16.0   1.1      0.058   13.3   0.0    2.4  2  RnfC_N           RnfC Barrel sandwich hybrid domain
     0.0096   15.7   0.5        3.6    7.4   0.1    2.6  2  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
  ------ inclusion threshold ------
      0.046   13.6   0.4       0.24   11.3   0.2    2.2  2  GCV_H            Glycine cleavage H-protein


Domain annotation for each model (and alignments):
>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.1   0.6     2e-85     4e-82       3     230 ..     148     374 ..     146     376 .. 0.98

  Alignments for each domain:
  == domain 1  score: 275.1 bits;  conditional E-value: 2e-85
                                       XXXXXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GG CS
                      2-oxoacid_dh   3 eeervplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPe 79 
                                       ee+r+p++g+r++ia+rl ++k+ ++ +t++++vd+++l++lr+el++ + ++  +k+t+l++++kav++A++++P+
  gi|557694690|ref|YP_008797744.1| 148 EETRIPIKGLRRIIADRLVQAKSRAALVTVFENVDAEELVKLRDELRSMQDEKG-VKMTYLPLIMKAVVAAVRDVPA 223
                                       799*********************************************886444.7********************* PP

                                       GG-EE.EESEEEE--SS--EEEE--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE-- CS
                      2-oxoacid_dh  80 lnasvdeeekeivvkkhvniGvAvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNl 156
                                       +n ++dee++eiv++k+vniG+Av+tp+GLlvP++kn+++k+++++a++++elaekar+gkl+ +d++ggt++is++
  gi|557694690|ref|YP_008797744.1| 224 MNGWIDEERNEIVLSKSVNIGIAVDTPDGLLVPIVKNVESKDVWTLARNIEELAEKARNGKLSLDDVRGGTISISSY 300
                                       ***************************************************************************** PP

                                       -------------TT-SEEEEE---.B--TTSTT-HT---EEEEEEEEETTT--HHHHHHHHHHHHHTT-HHXX CS
                      2-oxoacid_dh 157 GmlGvtsftPiinppqvaIlgvgrikerpvvkegelvvrkvmtlslsaDHRvidGaeaarFlntlkkllenpee 230
                                       G+lG+ s+tPiin+p+ aI+gvgr+++rpvvk++++vv++vm++ +++DHR++dG ++arF+n lk++len++ 
  gi|557694690|ref|YP_008797744.1| 301 GSLGSLSGTPIINYPEIAIVGVGRVEKRPVVKNDKVVVGQVMEIAVTMDHRAVDGGTMARFVNSLKHHLENIKA 374
                                       ***********************************************************************975 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   3.4   4.4e-23   8.8e-20       2      73 .]       3      75 ..       2      75 .. 0.97
   2 ?   -0.4   0.2      0.52     1e+03      20      33 ..     329     342 ..     312     358 .. 0.62

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 4.4e-23
                                      EEEESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl  2 eiksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73
                                       ik+P++Ge ++eg v+++lvk+Gd V++ q+l+ev + K+++ei++p++G+v+++l+keG+ ++vgd+ ++i
  gi|557694690|ref|YP_008797744.1|  3 VIKLPDVGEGIAEGeVLKFLVKEGDFVEKYQPLVEVMTVKVTVEIPSPVKGRVTKLLAKEGQVLKVGDPFIEI 75
                                      599******************************************************************9887 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.52
                                       SSSTTCEE-TTSEE CS
                     Biotin_lipoyl  20 lvkvGdkVkagqvl 33 
                                        v + dkV  gqv+
  gi|557694690|ref|YP_008797744.1| 329 PVVKNDKVVVGQVM 342
                                       44455555555543 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.9   5.7e+03      27      32 ..      52      57 ..      49      57 .. 0.90
   2 !   66.2   0.4   1.2e-21   2.4e-18       1      36 []     107     142 ..     107     142 .. 0.96
   3 ?   -3.0   0.0       5.1     1e+04      12      23 ..     281     292 ..     280     294 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.9
                                      TTBE-H CS
                        E3_binding 27 gGRItk 32
                                      +GR+tk
  gi|557694690|ref|YP_008797744.1| 52 KGRVTK 57
                                      7****8 PP

  == domain 2  score: 66.2 bits;  conditional E-value: 1.2e-21
                                       SBE-HHHHHHHHHCT--TTTS---CTTTBE-HHHHC CS
                        E3_binding   1 vlAsPaaRklAkelGidLsdvkGtGpgGRItkeDVl 36 
                                       v A+Pa++klAkelG+dLs+v+GtGpgGRIt+eDV+
  gi|557694690|ref|YP_008797744.1| 107 VQATPAVKKLAKELGVDLSTVVGTGPGGRITEEDVR 142
                                       569********************************6 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 5.1
                                       HHCT--TTTS-- CS
                        E3_binding  12 kelGidLsdvkG 23 
                                       +   ++L+dv G
  gi|557694690|ref|YP_008797744.1| 281 RNGKLSLDDVRG 292
                                       556677888874 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0     0.003         6      10      32 ..      15      37 ..       7      43 .. 0.85
   2 !   25.5   0.0   4.3e-09   8.6e-06       3      38 ..      45      80 ..      37      82 .. 0.93
   3 ?    1.2   1.2      0.17   3.3e+02      11      29 ..     323     341 ..     318     353 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.003
                   Biotin_lipoyl_2 10 sGrVaqlnVkdGqrVkaGdvLae 32
                                       G V + +Vk+G+ V++ + L+e
  gi|557694690|ref|YP_008797744.1| 15 EGEVLKFLVKEGDFVEKYQPLVE 37
                                      5889999*********9777765 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 4.3e-09
                   Biotin_lipoyl_2  3 vsIaapvsGrVaqlnVkdGqrVkaGdvLaelDsral 38
                                      v+I +pv GrV++l+ k+Gq+ k Gd  +e+++++l
  gi|557694690|ref|YP_008797744.1| 45 VEIPSPVKGRVTKLLAKEGQVLKVGDPFIEIETEEL 80
                                      999****************************99986 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.17
                   Biotin_lipoyl_2  11 GrVaqlnVkdGqrVkaGdv 29 
                                       GrV++  V  ++ V  G+v
  gi|557694690|ref|YP_008797744.1| 323 GRVEKRPVVKNDKVVVGQV 341
                                       8999999***********8 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1      0.01        21       8      43 ..      16      48 ..      14      49 .. 0.89
   2 !   14.6   0.0     2e-05      0.04       2      32 ..      47      77 ..      46      92 .. 0.87
   3 ?   -2.8   0.0       5.2     1e+04      66      80 ..     334     348 ..     324     366 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.01
                            HlyD_3  8 Gvvvelnveegevvqagdelleiippdtllveakvp 43
                                      G+v +  v+eg++v++ ++l+e++   t++v++++p
  gi|557694690|ref|YP_008797744.1| 16 GEVLKFLVKEGDFVEKYQPLVEVM---TVKVTVEIP 48
                                      8899999*****************...788888887 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2e-05
                            HlyD_3  2 lrApvdGvvvelnveegevvqagdelleiip 32
                                      + +pv G+v++l ++eg+v+  gd+  ei  
  gi|557694690|ref|YP_008797744.1| 47 IPSPVKGRVTKLLAKEGQVLKVGDPFIEIET 77
                                      569*************************984 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.2
                            HlyD_3  66 dytlkgkierisptv 80 
                                       d+++ g++ +i+ t 
  gi|557694690|ref|YP_008797744.1| 334 DKVVVGQVMEIAVTM 348
                                       455666666666554 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 ?    1.8   0.0     0.058   1.2e+02      27      53 ..      15      40 ..      12      45 .. 0.66
   2 !   12.6   0.0     3e-05     0.059      20      59 ..      45      83 ..      42     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.058
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 27 eGwveklyvnatgdkVkkGqpLaelys 53
                                      eG v k  v+ +gd V+k qpL+e+  
  gi|557694690|ref|YP_008797744.1| 15 EGEVLKFLVK-EGDFVEKYQPLVEVMT 40
                                      5666666666.7777777777777654 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 3e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 20 arvsarveGwveklyvnatgdkVkkGqpLaelyspelvaa 59
                                      +++ + v+G+v+kl ++ +g+  k G+p +e++ +elv++
  gi|557694690|ref|YP_008797744.1| 45 VEIPSPVKGRVTKLLAK-EGQVLKVGDPFIEIETEELVET 83
                                      45677788888888888.8888888888888888888876 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 !   13.3   0.0   2.9e-05     0.058      39      81 ..      16      59 ..      13      79 .. 0.83
   2 ?    0.5   0.2       0.3     6e+02      43      58 ..     327     342 ..     320     354 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                            RnfC_N 39 GapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaie 81
                                      G+  k lvk+gd V+k q + e  +  v++++ ++v G+V+++ 
  gi|557694690|ref|YP_008797744.1| 16 GEVLKFLVKEGDFVEKYQPLVEVMTvKVTVEIPSPVKGRVTKLL 59
                                      777899****************9886789***********9864 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.3
                            RnfC_N  43 kplvkvgdkVlkGqki 58 
                                       k  v ++dkV  Gq++
  gi|557694690|ref|YP_008797744.1| 327 KRPVVKNDKVVVGQVM 342
                                       444667899*9**986 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 !    7.4   0.1    0.0018       3.6      80     108 ..      15      43 ..       9      51 .. 0.87
   2 !    6.4   0.1    0.0036       7.2      80     110 ..      52      82 ..      40      88 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0018
                                       TTTTEEES----SEE-SEEEEEEE-HHHH CS
                        PTS_EIIA_1  80 kgegFellvkegdkVkagdklvevdleai 108
                                       +ge+ + lvkegd V++ ++lvev   ++
  gi|557694690|ref|YP_008797744.1|  15 EGEVLKFLVKEGDFVEKYQPLVEVMTVKV 43 
                                       79999******************977666 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0036
                                       TTTTEEES----SEE-SEEEEEEE-HHHHGG CS
                        PTS_EIIA_1  80 kgegFellvkegdkVkagdklvevdleaikk 110
                                       kg++ +ll+keg+  k gd+ +e++ e++ +
  gi|557694690|ref|YP_008797744.1|  52 KGRVTKLLAKEGQVLKVGDPFIEIETEELVE 82 
                                       899999******************9998866 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.54   1.1e+03      33      50 ..       1      18 [.       1      22 [. 0.87
   2 ?   11.3   0.2   0.00012      0.24      38      73 ..      22      57 ..      13      64 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.54
                                      EEEEE---TT-EE-TT-E CS
                             GCV_H 33 vvfvelpevgtkvkkges 50
                                      +v+++lp+vg+ +++ge 
  gi|557694690|ref|YP_008797744.1|  1 MVVIKLPDVGEGIAEGEV 18
                                      689**********99985 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00012
                                      ---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEE CS
                             GCV_H 38 lpevgtkvkkgeslaavEsvKaasevyapvsGevve 73
                                      l ++g+ v+k ++l  v +vK + e+++pv+G v++
  gi|557694690|ref|YP_008797744.1| 22 LVKEGDFVEKYQPLVEVMTVKVTVEIPSPVKGRVTK 57
                                      446899***************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 2898.88
//
Query:       gi|557694691|ref|YP_008797745.1|  [L=389]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-30  106.7  63.5    5.5e-21   74.9  36.6    2.3  2  MFS_1      Major Facilitator Superfamily
     0.0036   16.1   3.5     0.0036   16.1   3.5    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 !   74.9  36.6   6.1e-25   5.5e-21      10     294 ..      20     287 ..       5     289 .. 0.87
   2 !   45.5  19.0   5.2e-16   4.6e-12       3     167 ..     208     372 ..     202     385 .. 0.84

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 6.1e-25
                             MFS_1  10 larsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw 86 
                                        +r  ++++ p +l + + +s  e   + ++  lg+  +++++Gr+  + G r    +++l++a+++l++++  + +
  gi|557694691|ref|YP_008797745.1|  20 GTRVGISAITP-FLRQRYSLSTPETAAVPGILNLGFYSFAVLAGRIPAKTGYRNAAAAAALGSAAFMLAAALLDNRF 95 
                                       44445777778.******************************************88888888888845555338878 PP

                             MFS_1  87 lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsll 163
                                       +l+v+ +++G++ ++ +p+++ ++  +f++ ++g+ ig+  +++ +G  lgp++ ++l+s++g +++f +  ++ l+
  gi|557694691|ref|YP_008797745.1|  96 FLYVAVFMTGIFLSLHLPSAIPWLGTLFKGGRQGFIIGVHESAAPAGQTLGPIILAFLVSAAGVSYMFALWSLIPLF 172
                                       8**************************************************************************** PP

                             MFS_1 164 afv.lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlg 239
                                       a++ l  ll+++ +++ + k ++               +++l   +l  l ++ + + +g+ g+++ +pl l++++g
  gi|557694691|ref|YP_008797745.1| 173 AGLgL--LLFFRMDRQMPAKVQESG-------------GKILGAGFLA-LTLVTIANLVGNLGVVAIVPLHLVDTFG 233
                                       *9955..888888888888877777.............6788888774.88888888889999************** PP

                             MFS_1 240 lsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglall 294
                                       l     ++++++++ ++g+++++l+g+l+dr+g  r  l+  ++ l++ + ++l+
  gi|557694691|ref|YP_008797745.1| 234 LE-KTFVATVVGVSRFLGVFGQPLGGYLHDRYGFYRVALIVTVANLFSNIYMILA 287
                                       **.7899999***********************9888888877777777777665 PP

  == domain 2  score: 45.5 bits;  conditional E-value: 5.2e-16
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lll 78 
                                       l+++ +  +   + +++pl+l +++g+ ++++ +++++  ++ +++++++G+l dr+G  rv l+  ++ +++ +++
  gi|557694691|ref|YP_008797745.1| 208 LVTIANLVGNLGVVAIVPLHLVDTFGLEKTFVATVVGVSRFLGVFGQPLGGYLHDRYGFYRVALIVTVANLFSnIYM 284
                                       6677777777778999999******************************************************5555 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergrai.gllsagfslGailgpllggllasslgWrav 153
                                       +l  +++  +  v+  lq++ ++++fp++++ +++   + + ++++  ++ ++  +G+  +p+l+gl+a+ +g+ ++
  gi|557694691|ref|YP_008797745.1| 285 IL--APYNpVYPVAMTLQAFVTAMYFPLVYSHLVKTHGP-QASQYLgTMFFIAGLAGPTTAPILAGLIAERFGYAVA 358
                                       55..666669***************************99.666666155555777777999************8888 PP

                             MFS_1 154 fyilaivsllafvl 167
                                           a+++l + + 
  gi|557694691|ref|YP_008797745.1| 359 LGYPAALALAGSLT 372
                                       88888888877662 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   4.0       0.1   9.2e+02       8      94 ..       4      99 ..       1     198 [. 0.64
   2 !   16.1   3.5     4e-07    0.0036      28     119 ..     222     313 ..     208     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.1
                         LacY_symp  8 nfylfalffffyffimsayfplfpv..wlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkel....lwvi 80
                                      +f  + + +f +f+  ++   + ++  +l++   ls  et  v  +++l   +f +l G i  k G +       l + 
  gi|557694691|ref|YP_008797745.1|  4 KFAALLFTWFSWFWSHGTRVGISAItpFLRQRYSLSTPETAAVPGILNLGFYSFAVLAGRIPAKTGYRNAAaaaaLGSA 82
                                      4555666666666666766666665447999999999999999999999999999999999999999875411113333 PP

                         LacY_symp 81 slll...vlfapfliyv 94
                                      +++l   +l   f++yv
  gi|557694691|ref|YP_008797745.1| 83 AFMLaaaLLDNRFFLYV 99
                                      34432222334444444 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4e-07
                         LacY_symp  28 plfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkk.ellwvislllvlfapfliyv.fepllqln 102
                                       ++ p+ l +  gl kt + +v  v +++ +  qpl G + d+ G+ +  l+ +++   ++   ++i   ++p+  + 
  gi|557694691|ref|YP_008797745.1| 222 AIVPLHLVDTFGLEKTFVATVVGVSRFLGVFGQPLGGYLHDRYGFYRvALIVTVA--NLFSNIYMILApYNPVYPVA 296
                                       678999**************************************96614554444..445666776644******** PP

                         LacY_symp 103 ilvGalvGgvflGlvys 119
                                       +++ a+v ++++ lvys
  gi|557694691|ref|YP_008797745.1| 297 MTLQAFVTAMYFPLVYS 313
                                       ****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2865.49
//
Query:       gi|557694692|ref|YP_008797746.1|  [L=692]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-75  253.0   0.0    2.2e-75  252.1   0.0    1.5  1  Thioredox_DsbH   Protein of unknown function, DUF255
      4e-11   42.9   0.0    9.8e-11   41.7   0.0    1.7  1  Thioredoxin_7    Thioredoxin-like
    3.8e-07   29.9   0.4    2.9e-05   23.8   0.2    2.7  2  Glyco_hydro_76   Glycosyl hydrolase family 76
    1.1e-05   24.7   0.0     0.0025   17.0   0.0    2.5  2  Glyco_hydro_88   Glycosyl Hydrolase Family 88
    8.6e-05   21.6   0.0      0.026   13.4   0.0    3.0  3  Glyco_hydro_47   Glycosyl hydrolase family 47
    0.00059   19.2   0.1       0.15   11.3   0.0    3.0  3  GlcNAc_2-epim    N-acylglucosamine 2-epimerase (GlcNAc 2-epim
     0.0007   19.4   0.1     0.0016   18.2   0.1    1.6  1  HTH_10           HTH DNA binding domain
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.045   14.2   0.0    1.9  1  Thioredoxin_2    Thioredoxin-like domain
      0.029   13.9   0.5        0.3   10.5   0.0    2.7  4  C5-epim_C        D-glucuronyl C5-epimerase C-terminus
      0.035   12.6   1.0       0.48    8.8   0.2    2.4  2  Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
      0.039   13.3   0.0      0.076   12.3   0.0    1.4  1  Pec_lyase        Pectic acid lyase
       0.13   10.8   0.0        2.6    6.5   0.0    2.4  2  LANC_like        Lanthionine synthetase C-like protein


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 !  252.1   0.0   1.5e-78   2.2e-75       2     160 ..      16     174 ..      15     177 .. 0.98

  Alignments for each domain:
  == domain 1  score: 252.1 bits;  conditional E-value: 1.5e-78
                    Thioredox_DsbH   2 nrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkv 78 
                                       nrl++e+spYllqha npvdWypwgeea++ka+ e+kpi+lsiGys+chWChvmekesfede++a+lln+ fv+vkv
  gi|557694692|ref|YP_008797746.1|  16 NRLINERSPYLLQHAYNPVDWYPWGEEAIKKARGENKPIFLSIGYSSCHWCHVMEKESFEDEKIAELLNTFFVPVKV 92 
                                       9**************************************************************************** PP

                    Thioredox_DsbH  79 DreerPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleeea 155
                                       DreerPd+d++ym+av ++tg+ggWPl+vfltpdlkpffggtYfp+++r g  g+ e+l+ +aelw+++ +++ e+a
  gi|557694692|ref|YP_008797746.1|  93 DREERPDIDEVYMKAVIMMTGHGGWPLTVFLTPDLKPFFGGTYFPPRRRGGLRGLDEILRGVAELWRKDPKQVMEAA 169
                                       **************************************************************************999 PP

                    Thioredox_DsbH 156 eelle 160
                                       e+ ++
  gi|557694692|ref|YP_008797746.1| 170 EQNVS 174
                                       98765 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   6.5e-14   9.8e-11       1      83 []      35     125 ..      35     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 6.5e-14
                                       ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.........- CS
                     Thioredoxin_7   1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdani........le 69 
                                       +w+ + +ea  ka+ ++kp+++ +g s c+ C+++e++  +de+++++l+  fv ++vd +er + i        + 
  gi|557694692|ref|YP_008797746.1|  35 DWYPWGEEAIKKARGENKPIFLSIGYSSCHWCHVMEKESFEDEKIAELLNTFFVPVKVDREERPD-IdevymkavIM 110
                                       7*************************************99999****9************99987.54445555433 PP

                                       TT---.SSEEEEE-T CS
                     Thioredoxin_7  70 ldeqg.vPvvafldp 83 
                                       ++++g  P  +fl+p
  gi|557694692|ref|YP_008797746.1| 111 MTGHGgWPLTVFLTP 125
                                       333445999998887 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 ?   -0.7   0.0      0.54   8.1e+02     162     195 ..     290     321 ..     281     337 .. 0.75
   2 !   23.8   0.2   1.9e-08   2.9e-05      39     183 ..     432     582 ..     430     589 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.54
                                       HHHHHHHHH--CHHHHHHHHHHHHHHHHSCSBTT CS
                    Glyco_hydro_76 162 laarLarytgnetYlewAekvwdWvedvglidde 195
                                       + +  + +tg++ Y e   ++ dW+++ +++ + 
  gi|557694692|ref|YP_008797746.1| 290 VYMNHYLITGDSFYREIGASTLDWLVS-EMM-NP 321
                                       555558899999************999.676.44 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 1.9e-08
                                       HHHHHHHHHHHHHCTTCCCHHHHHH......HHHCCCTCEE-SSSTTCTCSSEHHHHHHHHHHHHHHHHH.....H- CS
                    Glyco_hydro_76  39 galfgalidywrltgdstyndlitq......allaqagenydympanqsrtegnDDqafwglaamtaaernfpeptd 109
                                       g +++al   +r+tg+++y d   +      + ++ ++  ++  ++  s + + DD a+++ a ++  e+     + 
  gi|557694692|ref|YP_008797746.1| 432 GFAVSALCTGYRATGEKRYLDAALKtidfiiSNMWLNNTLHRIYKNGASINGFLDDYAAVVNALLDVFEV-----SF 503
                                       667889999999999998877777744443333445555567777778889999***************9.....66 PP

                                       -HHHHHHHHHHHHHHHHC.B-SCSCCS-BBSEC..ESS--SEEEHH......HHHHHHHHHHHHHHHH--CHHHHHH CS
                    Glyco_hydro_76 110 epswLalAqavfntqasr.wdeetcgGGlrWqiftwnsgydyknsi......sngplfqlaarLarytgnetYlewA 179
                                       ep++La+A  v n +++  wd+   +GG ++ + ++   + +k++        n+ ++ + ++L + tg+ +Yl++ 
  gi|557694692|ref|YP_008797746.1| 504 EPRYLAVAVDVANRMVELfWDNV--DGGFYYTVEDVAGVTRIKDAYdgatpsGNTLAAAALLKLSELTGETKYLQYV 578
                                       788**************999985..8******987665555555432222227888888889************998 PP

                                       HHHH CS
                    Glyco_hydro_76 180 ekvw 183
                                       e++ 
  gi|557694692|ref|YP_008797746.1| 579 EETL 582
                                       8765 PP

>> Glyco_hydro_88  Glycosyl Hydrolase Family 88
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0    0.0063       9.4      69     116 ..     279     325 ..     223     341 .. 0.71
   2 !   17.0   0.0   1.7e-06    0.0025      31     164 ..     431     588 ..     411     601 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0063
                                       TTSGGGTGHHHHHHHHHHHH-THHHHHHHHHHHHHHHHCS-B.TTS.B CS
                    Glyco_hydro_88  69 elelDdidigllllllyeltkderykeaaeeladyvlakpprtseGgf 116
                                       ++  D++ ++ +++  y +t+d+ y+e      d++++++ +   Ggf
  gi|557694692|ref|YP_008797746.1| 279 KMLYDNALLARVYMNHYLITGDSFYREIGASTLDWLVSEMMN-PGGGF 325
                                       455566667777777777777777777777777777777766.34555 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.7e-06
                                       HHHHHHHHHHHHHHH--HHHHHHHHHHHHHCCCTTS-.............CTTSGGGTGH.HHHHHHHHHHH-THHH CS
                    Glyco_hydro_88  31 nGvflsglleayeatgdkeyldyakawadslideggk.............telelDdidi.gllllllyeltkdery 93 
                                       nG+++s+l   y atg+k+yld+a ++ d  i ++                +  lDd ++ +  ll+ +e   ++ry
  gi|557694692|ref|YP_008797746.1| 431 NGFAVSALCTGYRATGEKRYLDAALKTIDFIISNMWLnntlhriykngasINGFLDDYAAvVNALLDVFEVSFEPRY 507
                                       89**********************99666555555444456666667777777787766516677999********* PP

                                       HHHHHHHHHHHHHCS-B.TTS.B.S...........BTTSTTEEE.THHHHHHHHHHHHHHHHHCGTHHHHHHHHHH CS
                    Glyco_hydro_88  94 keaaeeladyvlakpprtseGgfwh...........kkkepeqlW.lDgLfMaipllaklskvtgepkyldeaikqf 158
                                        + a ++a+ +++   ++ +Ggf             k+ ++  +    +L  a+ +l+kls++tge+kyl+ + + +
  gi|557694692|ref|YP_008797746.1| 508 LAVAVDVANRMVELFWDNVDGGFYYtvedvagvtriKDAYDGATPsGNTL--AAAALLKLSELTGETKYLQYVEETL 582
                                       ***********************999977766666555555554434455..999************9998887777 PP

                                       HHHHHH CS
                    Glyco_hydro_88 159 lltarh 164
                                       + +a++
  gi|557694692|ref|YP_008797746.1| 583 KCFASR 588
                                       777666 PP

>> Glyco_hydro_47  Glycosyl hydrolase family 47
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.069     1e+02     373     397 ..     294     318 ..     290     338 .. 0.74
   2 ?    2.5   0.0     0.036        53     367     402 ..     435     470 ..     352     487 .. 0.77
   3 !   13.4   0.0   1.8e-05     0.026      86     194 ..     494     602 ..     488     613 .. 0.69

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.069
                                       HHHHH--THHHHHHHHHHHHHHHHC CS
                    Glyco_hydro_47 373 lYritgdekyrevgwemfealekat 397
                                        Y itgd+ yre+g + +  l + +
  gi|557694692|ref|YP_008797746.1| 294 HYLITGDSFYREIGASTLDWLVSEM 318
                                       699***********99988776655 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.036
                                       HHHHHHHHHHH--THHHHHHHHHHHHHHHHCEETTE CS
                    Glyco_hydro_47 367 iESlfylYritgdekyrevgwemfealekatktesg 402
                                       +  l   Yr+tg+++y++ + + +  + ++++ ++ 
  gi|557694692|ref|YP_008797746.1| 435 VSALCTGYRATGEKRYLDAALKTIDFIISNMWLNNT 470
                                       6667788*************9999988888877665 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHH.S-HHHHHHHHHHHHHHHHGGG.SSTTS.---SEEETTT--EE-.STCGCEEEHHHHCSSHHHHHHHH CS
                    Glyco_hydro_47  86 GLlsaydlsekkedvllekAveladrLlpAF.dtpsg.lpvarvnlkkrkaskkerassesvlAelgslslEftrLs 160
                                       +Ll  +++s   e+ +l+ Av++a+r+++ F d   g + ++  +++  ++ k+ ++    + +  +     + +Ls
  gi|557694692|ref|YP_008797746.1| 494 ALLDVFEVS--FEPRYLAVAVDVANRMVELFwDNVDGgFYYTVEDVAGVTRIKDAYDGA--TPSGNTLAAAALLKLS 566
                                       678888888..8999****************9555550555555554444444444332..22444444455689** PP

                                       HHHT-CHHHHHHHCCHHHHHCHC..C.HHHTTB-BS CS
                    Glyco_hydro_47 161 qlTgdkkYedlaervtkaleelq..ektklpglvpi 194
                                       +lTg++kY +++e++ k +++       +++gl++ 
  gi|557694692|ref|YP_008797746.1| 567 ELTGETKYLQYVEETLKCFASRLeaAPAEHTGLITV 602
                                       **************9998877443545556777765 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.23   3.4e+02      44     124 ..     242     326 ..     229     336 .. 0.72
   2 ?    3.3   0.0     0.026        39     281     310 ..     435     464 ..     395     473 .. 0.77
   3 !   11.3   0.0   9.8e-05      0.15     231     309 ..     504     587 ..     492     594 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.23
                                       HHHHHHHHTTT.TTB-TTTSSB-SEEETTEEEE--..EEHHHHH.HHHHHHHHHHTTT-TTHHHHHHHHHHHHHHHT CS
                     GlcNAc_2-epim  44 lvehGlkflek.vlrdaehggyfsalrdggvldas..kdaYdha.Fvllalasalaageeeakdlldetlavlekhl 116
                                       +v+  l+ +++  lrd+  gg+f+  +d+  l +   k +Yd a  +   + + l +g+  ++++ + tl+ l  ++
  gi|557694692|ref|YP_008797746.1| 242 MVSTTLENMARgGLRDHLGGGFFRYSTDRVWLVPHfeKMLYDNAlLARVYMNHYLITGDSFYREIGASTLDWLVSEM 318
                                       56666666654156899999999999999977665115678888344455667899999999999999999988888 PP

                                       EETTTTEE CS
                     GlcNAc_2-epim 117 weekaglv 124
                                        ++  g++
  gi|557694692|ref|YP_008797746.1| 319 MNPGGGFY 326
                                       88766665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHH--CHHHHHHHHHHHHHHHH CS
                     GlcNAc_2-epim 281 lkaaaalaeltgearylewyarvaeylerh 310
                                       + a+ ++++ tge+ryl+ + + ++++ ++
  gi|557694692|ref|YP_008797746.1| 435 VSALCTGYRATGEKRYLDAALKTIDFIISN 464
                                       566777777777777777777777666544 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 9.8e-05
                                       --THHHHHHHHHHHHHHHHBS-SSSSB-S-B-TTS-BSS.--EE..HHHHHHHHHHH..HHHHHHH--CHHHHHHHH CS
                     GlcNAc_2-epim 231 aakllekArkLfetalakgwdkdrgglvytldaagkpvd.dakl..lWpqtEalkaa..aalaeltgearylewyar 302
                                       ++ +l+ A ++ +++++  wd   gg++yt+++ + + + ++ +    p   +l+aa  ++l eltge +yl+  ++
  gi|557694692|ref|YP_008797746.1| 504 EPRYLAVAVDVANRMVELFWDNVDGGFYYTVEDVAGVTRiKDAYdgATPSGNTLAAAalLKLSELTGETKYLQYVEE 580
                                       6778999***********************98877777654444445688888887733567788********9998 PP

                                       HHHHHHH CS
                     GlcNAc_2-epim 303 vaeyler 309
                                        ++ +++
  gi|557694692|ref|YP_008797746.1| 581 TLKCFAS 587
                                       8777665 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.1e-06    0.0016      24      52 ..     383     411 ..     381     412 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.1e-06
                            HTH_10  24 vtlkeLAkelGIskstlsehLrkaeskli 52 
                                        +++eLA elG+ ++tl++ L++a++kl+
  gi|557694692|ref|YP_008797746.1| 383 KRTAELAAELGVDEPTLKQMLEEAKNKLL 411
                                       6789***********************98 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0     3e-05     0.045       1      50 [.      47     100 ..      47     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                     Thioredoxin_2   1 akgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfp....lkpsfepka 50 
                                       a+g++kp+++ +  ++C  C+ ++ke +e++++ + +  f     ++++  p +
  gi|557694692|ref|YP_008797746.1|  47 ARGENKPIFLSIGYSSCHWCHVMEKESFEDEKIAELLNTFFvpvkVDREERPDI 100
                                       6799**************************999998433333344444444444 PP

>> 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 ?   -3.0   0.0         3   4.5e+03      34      63 ..     287     316 ..     283     330 .. 0.73
   2 ?   10.5   0.0    0.0002       0.3      31      61 ..     431     461 ..     427     488 .. 0.92
   3 ?   -2.9   0.0       2.7     4e+03      35      61 ..     492     518 ..     487     537 .. 0.61
   4 ?   -0.6   0.0      0.55   8.2e+02      37      63 ..     561     587 ..     554     600 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3
                         C5-epim_C  34 aisvllrAYeltgdekYlkaakkalksfki 63 
                                       ++ v++  Y  tgd+ Y ++++  l+ +  
  gi|557694692|ref|YP_008797746.1| 287 LARVYMNHYLITGDSFYREIGASTLDWLVS 316
                                       567888899999999998888888776544 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0002
                         C5-epim_C  31 qgqaisvllrAYeltgdekYlkaakkalksf 61 
                                       +g a+s+l   Y++tg+++Yl+aa k ++++
  gi|557694692|ref|YP_008797746.1| 431 NGFAVSALCTGYRATGEKRYLDAALKTIDFI 461
                                       6899**********************99876 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.7
                         C5-epim_C  35 isvllrAYeltgdekYlkaakkalksf 61 
                                       + +ll  +e++ + +Yl +a  + + +
  gi|557694692|ref|YP_008797746.1| 492 VNALLDVFEVSFEPRYLAVAVDVANRM 518
                                       567788888999999987765544433 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 0.55
                         C5-epim_C  37 vllrAYeltgdekYlkaakkalksfki 63 
                                       +ll+  eltg+ kYl++ ++ lk f+ 
  gi|557694692|ref|YP_008797746.1| 561 ALLKLSELTGETKYLQYVEETLKCFAS 587
                                       555566889999999999999998865 PP

>> Glyco_hydro_127  Beta-L-arabinofuranosidase, GH127
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.4   3.6e+03     182     199 ..     289     306 ..     276     319 .. 0.71
   2 ?    8.8   0.2   0.00032      0.48     131     201 ..     435     512 ..     423     591 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHT-CHHHHH CS
                   Glyco_hydro_127 182 ealvklyelTgdkrYldl 199
                                        ++++ y +Tgd+ Y ++
  gi|557694692|ref|YP_008797746.1| 289 RVYMNHYLITGDSFYREI 306
                                       456677888888888765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHH--HHHHHHHHHHHHHHHHHHCCS-CCHHHHHTTT..........HHCTHHHHHHHHHHHHT-CHHH CS
                   Glyco_hydro_127 131 iegavayyqatgkeklldvatrladyleevleklgdeqlqkalvp..........ehggieealvklyelTgdkrYl 197
                                       +++++  y+atg+++ ld+a++  d++   ++++  ++  +++++          +   +  al++++e+  ++rYl
  gi|557694692|ref|YP_008797746.1| 435 VSALCTGYRATGEKRYLDAALKTIDFI---ISNMWLNNTLHRIYKngasingfldDYAAVVNALLDVFEVSFEPRYL 508
                                       567888888888888888888888877...22222222222222212222222223334446666777777777777 PP

                                       HHHH CS
                   Glyco_hydro_127 198 dlAk 201
                                        +A 
  gi|557694692|ref|YP_008797746.1| 509 AVAV 512
                                       7775 PP

>> Pec_lyase  Pectic acid lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.1e-05     0.076      45      86 ..     435     476 ..     398     504 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.1e-05
                         Pec_lyase  45 llflaevykatkdekykdavrkglefllkaqYsnGgwpqfyP 86 
                                       +  l + y+at++++y da++k+++f+++  + n  +  +y 
  gi|557694692|ref|YP_008797746.1| 435 VSALCTGYRATGEKRYLDAALKTIDFIISNMWLNNTLHRIYK 476
                                       6789999*********************99998888888775 PP

>> LANC_like  Lanthionine synthetase C-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.063        94     174     202 ..     437     465 ..     396     517 .. 0.85
   2 ?    6.5   0.0    0.0018       2.6      15      62 ..     559     606 ..     549     637 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.063
                                       HHHCCCHT.-HHHHHHHHHHHHHHHHHTS CS
                         LANC_like 174 allalykgtksekllelikkllkylkslk 202
                                       al   y++t+++++l+++ k+++++ s+ 
  gi|557694692|ref|YP_008797746.1| 437 ALCTGYRATGEKRYLDAALKTIDFIISNM 465
                                       44455778888888888888888887776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHCCH.-S--STTTSHHHH CS
                         LANC_like  15 allllelykvtknekylklahkylekikkelselglesisffsGaagi 62 
                                       a +ll+l++ t++ kyl+++++ l++ +++l++ + e++++ +  ag+
  gi|557694692|ref|YP_008797746.1| 559 AAALLKLSELTGETKYLQYVEETLKCFASRLEAAPAEHTGLITVLAGF 606
                                       789******************************999999988755555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (692 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); 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: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 4481.77
//
Query:       gi|557694693|ref|YP_008797747.1|  [L=363]
Description: tyrosyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  152.6   0.0    1.5e-29  103.2   0.0    2.0  2  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 !  103.2   0.0   8.5e-34   1.5e-29       5     196 ..      33     217 ..      29     222 .. 0.95
   2 !   47.5   0.0   7.9e-17   1.4e-12     198     292 ..     236     336 ..     229     337 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 8.5e-34
                                       --EEEEEEETSSS-BGG.GHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTC CS
                      tRNA-synt_1b   5 plrvysGidPTgklHlG.ylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgl 80 
                                         ++y G++P+g  H+   l+   kl+++++ag++  +l+aD+hA i++++  +++k+rk  e+++++   + a+g+
  gi|557694693|ref|YP_008797747.1|  33 SPIAYDGFEPSGLAHIPfALLRAIKLRDMLEAGCRFKLLLADWHAAINRKMGGDLEKIRKVGEYFVEV---WKASGI 106
                                       5689***********************************************99***************...****** PP

                                       HTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEE CS
                      tRNA-synt_1b  81 dpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgG 157
                                       d +++e+v+ s+  +  +++ l+ ++ + ++l+r+l++  ++ r e  e   +++++Yp +q aDi+ l+a+++  G
  gi|557694693|ref|YP_008797747.1| 107 DTSRVEIVWASDLAADRDYWRLVIEVLQNTTLRRVLRCLPIMGRKEG-ELQEAAQLLYPGMQVADIFKLEAKICQLG 182
                                       ***********************999999***********9999998.3459************************* PP

                                       GGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTS CS
                      tRNA-synt_1b 158 sDQkqnielgrdlarrfnkkevfkkpegltvplltgldG 196
                                        DQ+   +l+r++ ++++      kp+++ +++l gl+G
  gi|557694693|ref|YP_008797747.1| 183 LDQRRANILAREIGPKLGFW----KPVAVHHHMLMGLEG 217
                                       ****************9666....**********99998 PP

  == domain 2  score: 47.5 bits;  conditional E-value: 7.9e-17
                                       SBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHHHHTHHH....CHHHHHHHHCCSEEESSHHHHHH CS
                      tRNA-synt_1b 198 kKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllklktelsn....elierleavsgkkpkreaeella 268
                                       +KmSKS ++s If  d+ e++k ki++a++ +++  ++  l++ ++ +++     ++er  +++g+ +++ +  l++
  gi|557694693|ref|YP_008797747.1| 236 SKMSKSIPESSIFVHDDAETIKRKINNAYCPPRQatGNPVLEYCRYIIFPlkqtIVVERPAKYGGEITYTNYPSLEK 312
                                       6***********************************9************99998999******************** PP

                                       HHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 269 eevtklvhggdlkkalaealnell 292
                                       ++ ++++h+ dlk+ +a+ l ell
  gi|557694693|ref|YP_008797747.1| 313 DYLEGKLHPLDLKNTVARYLDELL 336
                                       ******************999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2725.41
//
Query:       gi|557694694|ref|YP_008797748.1|  [L=1028]
Description: ribonucleoside-diphosphate reductase alpha chain [Candidatus Caldiarchaeum subterraneum]
Scores for 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-134  447.5   0.0   1.2e-111  373.8   0.0    2.3  2  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    2.3e-40  136.7   0.0      6e-40  135.4   0.0    1.7  1  Ribonuc_red_2_N  Class II vitamin B12-dependent ribonucleotid
     0.0048   16.8   0.1      0.021   14.7   0.0    2.0  2  UBA_6            UBA-like domain
  ------ inclusion threshold ------
      0.044   14.2   0.1       0.85   10.1   0.0    3.0  3  RuvA_C           RuvA, C-terminal domain
       0.11   12.8   0.0       0.27   11.6   0.0    1.7  1  MqsR_toxin       Motility quorum-sensing regulator, toxin of 
       0.18   11.8   1.7       0.54   10.2   1.7    1.8  1  OrfB_Zn_ribbon   Putative transposase DNA-binding 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 !  373.8   0.0  4.1e-115  1.2e-111       2     449 ..     181     650 ..     180     671 .. 0.91
   2 !   71.4   0.0   1.9e-23   5.6e-20     432     524 .]     722     827 ..     687     827 .. 0.86

  Alignments for each domain:
  == domain 1  score: 373.8 bits;  conditional E-value: 4.1e-115
                                       EE.....BSS-...EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
                                       xxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                   Ribonuc_red_lgC   2 sCfvlsvedsl...esIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgG. 74 
                                       +Cf+ls++d+l    +I++t  ++a++ k+g+G G n s+lRakg++++g +g +sG++sf+k+ dava  +k+gG 
  gi|557694694|ref|YP_008797748.1| 181 ACFILSIKDDLvnpGGIMDTWVKQARIYKYGSGEGCNYSTLRAKGEPLSG-GGVSSGVMSFLKVGDAVAGSIKSGGt 256
                                       8**********88889********************************99.************************** PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......................XXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  75 kRrGAamvylevwHpDiekfidaKekntgee.....................enrlsnlnisvgvpdlFmeavkedk 130
                                       +Rr+A+mv+l+++Hp+ie+fid+K+k+   e                     +++ +n n+sv+v+++Fm+av ed+
  gi|557694694|ref|YP_008797748.1| 257 TRRAAKMVVLNIDHPEIEDFIDWKMKE---EqkvaalvaagyspdfegeayqTVSGQNSNNSVRVTNEFMRAVLEDR 330
                                       ************************994...3456888888888888888888************************* PP

                                       XXXXXXXXXXXX.........................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 131 dwtLfsPrtvvkleklygeefeeeyeeleekakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakg 207
                                       dw L+   +        g                  k vka+ L+e+ia++aw++++Pg++f  tiN++n++   ++
  gi|557694694|ref|YP_008797748.1| 331 DWALTRRTD--------G---------------KPVKFVKARYLWEKIAKAAWACADPGLQFDTTINEWNTC--PET 382
                                       *****9662........2...............23458**********************************..778 PP

                                       XXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 208 gkIratNlCgEiplleyesvavCnLasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekn 284
                                       g+I+atN+C+E  +l++++   CnLas+nL kf+   +e+k  fd++ ++++++l + +L+  + + +yp pei++ 
  gi|557694694|ref|YP_008797748.1| 383 GRINATNPCSEFNFLDNTA---CNLASLNLVKFY---DEEKGVFDVEAFRHAVRLWTIVLEITVGMAQYPSPEIAEM 453
                                       9******************...************...578************************************* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 285 tkktRriGlGvmgladalaklgipydseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdef 361
                                       + ktR++GlG+++l+ +l+++g+pyds+e++++a+ it l+t + y +S+e+A   gpf++fek++++     +++ 
  gi|557694694|ref|YP_008797748.1| 454 SYKTRSLGLGYANLGGLLMRMGLPYDSDEGRAVAAVITALMTGEVYATSAEIASIAGPFEEFEKNRVHVLR-VLNNH 529
                                       **************************************************************998776553.22222 PP

                                       X........................................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXX CS
                                       xxxx..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxx RF
                   Ribonuc_red_lgC 362 eeke..................................kedweeLreeikkyGlrnamvtalaPTgsiSlia.gtss 403
                                          +                                  + +w+++++  +kyG+rna+ t +aPTg+i+l++ + + 
  gi|557694694|ref|YP_008797748.1| 530 ---RraiyqakpheyegleikphlpplelapkylldeaRASWDRAVAMAEKYGVRNAQATLIAPTGTIGLLMdCDTL 603
                                       ...112233344557788888899999999999***99*********************************978899 PP

                                       XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 404 giePifalvykksvtv.geflevnpvfeeeLkklglwseellkkile 449
                                       g+eP f+lv+ k+ +  g f  vn+++e +L+klg++++++++ i+ 
  gi|557694694|ref|YP_008797748.1| 604 GVEPDFSLVKLKKLVGgGYFKLVNRSLEPALRKLGYSEKQIRDVIEY 650
                                       ***********99998788**********************999843 PP

  == domain 2  score: 71.4 bits;  conditional E-value: 1.9e-23
                                       XXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXXXXXXX........XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 432 eLkklglwseellkki.....lesvqgleeipeeikrvfktal........didqedhikaqaaiqkwidqsiSkti 495
                                        Lk lg ++ee++          +v+g+++i+ e+ +vf++a+         ++ ++hi ++aaiq++++ +iSkt+
  gi|557694694|ref|YP_008797748.1| 722 LLKYLGFSDEEIRVSEdvicgSLTVEGAPHIKPEHIPVFDCAVpagrkgkrFVHYRAHILMMAAIQPFLSGAISKTV 798
                                       477888888887766545654445**************************99************************* PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC 496 nlpneatvedvkelyllAwklGlKgvtyY 524
                                       n+pneatvedv+++y+ Aw+lGlK +++Y
  gi|557694694|ref|YP_008797748.1| 799 NMPNEATVEDVAQVYMDAWRLGLKCIAIY 827
                                       **************************998 PP

>> Ribonuc_red_2_N  Class II vitamin B12-dependent ribonucleotide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.4   0.0     2e-43     6e-40       2      99 .]      31     130 ..      30     130 .. 0.96

  Alignments for each domain:
  == domain 1  score: 135.4 bits;  conditional E-value: 2e-43
                   Ribonuc_red_2_N   2 GsvvfemedvevPeewsqvatdilaqKYFrkagvpkedeealael..eeeerlgsEtsakqvvdRlagtwtewgkke 76 
                                       G+v+fem+dvevP+ wsqvatdilaqKYFrk+gvp+ de+++  l  + +++lg E+s+kqvv+Rlag+w++wg++ 
  gi|557694694|ref|YP_008797748.1|  31 GNVIFEMKDVEVPSFWSQVATDILAQKYFRKTGVPQYDENGHPILdkDGKPVLGPERSLKQVVRRLAGCWRYWGERF 107
                                       99***************************************99995556789************************* PP

                   Ribonuc_red_2_N  77 gyfdteedakafydElvymllkQ 99 
                                       +yf+++eda+af+dE+ yml++Q
  gi|557694694|ref|YP_008797748.1| 108 NYFASQEDAQAFQDEIEYMLISQ 130
                                       *********************98 PP

>> UBA_6  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   7.2e-06     0.021       9      29 ..     635     656 ..     630     661 .. 0.84
   2 ?   -1.8   0.0         1   3.1e+03      11      19 ..     726     734 ..     723     735 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.2e-06
                             UBA_6   9 lKLGYseeqvqavLekL.Gpea 29 
                                       +KLGYse+q++ v+e + G+++
  gi|557694694|ref|YP_008797748.1| 635 RKLGYSEKQIRDVIEYViGTNT 656
                                       7*************96437777 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1
                             UBA_6  11 LGYseeqvq 19 
                                       LG+s e+++
  gi|557694694|ref|YP_008797748.1| 726 LGFSDEEIR 734
                                       9*****997 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.55   1.6e+03       5      18 ..     285     298 ..     282     327 .. 0.70
   2 ?   10.1   0.0   0.00028      0.85       9      27 ..     633     651 ..     628     657 .. 0.87
   3 ?   -2.5   0.0       2.5   7.3e+03      11      21 ..     724     734 ..     723     734 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.55
                                       HHHHHHHHCTS-HH CS
                            RuvA_C   5 daveALlaLGYkek 18 
                                       + v+AL+a GY++ 
  gi|557694694|ref|YP_008797748.1| 285 QKVAALVAAGYSPD 298
                                       5689*******986 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00028
                                       HHHHCTS-HHHHHHHHHHH CS
                            RuvA_C   9 ALlaLGYkekeaekAvakv 27 
                                       AL  LGY+ek+++ +++ v
  gi|557694694|ref|YP_008797748.1| 633 ALRKLGYSEKQIRDVIEYV 651
                                       999************9866 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.5
                                       HHCTS-HHHHH CS
                            RuvA_C  11 laLGYkekeae 21 
                                       + LG++ +e++
  gi|557694694|ref|YP_008797748.1| 724 KYLGFSDEEIR 734
                                       56******995 PP

>> MqsR_toxin  Motility quorum-sensing regulator, toxin of MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.2e-05      0.27       2      45 ..     607     650 ..     606     661 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.2e-05
                                       -SS-HHHHHHHHHTT-EEEE.HHHHHHHHHTT--HHHHHHHHHC CS
                        MqsR_toxin   2 PhyaLskvkalvkegkvraitrkalkgaaalGldeedvvdvias 45 
                                       P ++L k+k+lv  g ++ ++r+ + ++++lG++e+++ dvi+ 
  gi|557694694|ref|YP_008797748.1| 607 PDFSLVKLKKLVGGGYFKLVNRSLEPALRKLGYSEKQIRDVIEY 650
                                       8999*************************************975 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 ?   10.2   1.7   0.00018      0.54      30      55 ..    1001    1024 ..     988    1026 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00018
                    OrfB_Zn_ribbon   30 tCseCgsknkealsgrtfkCpnCgfe 55  
                                         C eCgs++ +  sg  ++C+nCg++
  gi|557694694|ref|YP_008797748.1| 1001 ACRECGSIMAR--SGSCYVCTNCGAT 1024
                                        6**********..***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1028 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); 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: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 6374.74
//
Query:       gi|557694695|ref|YP_008797749.1|  [L=486]
Description: multicomponent Na+:H+ antiporter subunit D [Candidatus Caldiarchaeum subterraneum]
Scores for 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  28.2    3.5e-74  249.6  28.2    1.7  2  Proton_antipo_M  Proton-conducting membrane transporter
      5e-05   23.3   0.3     0.0003   20.8   0.3    2.4  1  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 ?   -2.0   0.4      0.19   1.7e+03     208     230 ..      78      93 ..      42     122 .. 0.55
   2 !  249.6  28.2   3.9e-78   3.5e-74       1     287 [.     125     413 ..     125     421 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.19
                   Proton_antipo_M 208 halfkallFllagsviyerektr 230
                                        ++f al+Fl++g +        
  gi|557694695|ref|YP_008797749.1|  78 LSIFLALIFLVVGLL-------S 93 
                                       344444444444333.......2 PP

  == domain 2  score: 249.6 bits;  conditional E-value: 3.9e-78
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal..elg 75 
                                       ++dL+++++++El+++++ylL++++++  +++eAslk+++++++g  ++L+g++l+y+l+gtle+  l +al  +++
  gi|557694695|ref|YP_008797749.1| 125 SGDLFTFFIFWELMSISSYLLVAFRYRTWEAVEASLKYLIMSAAGAAAILFGMSLMYGLAGTLELSRLGEALasQAV 201
                                       78*********************************************************************999999 PP

                   Proton_antipo_M  76 lnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlll 151
                                       ++++ + l++ ll+ g+ v +a++p+h Wlpda+ +aP p+sa+l++++ kagv+++ir+l+ ++  s   ++  l+
  gi|557694695|ref|YP_008797749.1| 202 AAEPWAYLAIALLITGFGVNAAMAPFHSWLPDAHPAAPSPISAMLSGVVIKAGVYAMIRVLMGVFpPSLFGWQLGLA 278
                                       9999999****************************************************9887777999******** PP

                   Proton_antipo_M 152 ilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerek 228
                                       i ai++m lg+l+al q diKrllA+Ssi+h+Gy++ ++++at+ g+++ i+h+l hal+kallFl ag++i++  +
  gi|557694695|ref|YP_008797749.1| 279 IFAILTMSLGNLLALLQEDIKRLLAFSSIAHIGYIVFGISIATVTGLTGGIFHVLNHALMKALLFLSAGAFIHAA-Q 354
                                       ***********************************************************************9998.9 PP

                   Proton_antipo_M 229 trdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlav 287
                                       tr +++++g+ kk P+ a+++ ++++slaG+P++  F+s+f+i +aa++++ i  +la 
  gi|557694695|ref|YP_008797749.1| 355 TRRLDDLAGIGKKLPLAATCFGIGAFSLAGIPGLNVFWSEFTIVTAALQAGGIYSILAA 413
                                       **************************************************999888873 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 !   20.8   0.3   3.4e-08    0.0003      15      55 ..      72     110 ..      69     123 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.4e-08
                   Proton_antipo_N  15 gfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfa 55 
                                       ++++D+ls+  +l+  +v+ll  ++++gY ++  +++ F+ 
  gi|557694695|ref|YP_008797749.1|  72 QIYVDGLSIFLALIFLVVGLLSTVFAFGYIEE--RKPEFYP 110
                                       589***************************94..5777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (486 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3380.74
//
Query:       gi|557694696|ref|YP_008797750.1|  [L=365]
Description: DNA topoisomerase VI subunit A [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   48.2   0.0    1.5e-12   47.3   0.0    1.5  1  TP6A_N    Type IIB DNA topoisomerase
     0.0001   22.3   0.0    0.00019   21.3   0.0    1.4  1  DUF2399   Protein of unknown function C-terminus (DUF2399)
  ------ inclusion threshold ------
       0.14   12.4   0.0       0.37   11.0   0.0    1.9  2  Toprim    Toprim domain


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 !   47.3   0.0   2.6e-16   1.5e-12       2      62 .]      78     141 ..      77     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.6e-16
                                       HHHHHHHHHHHHHHHHHTT--EEHHHHHHH...GGGS-SSHHHHHHHHHHHHHHHTS-GGGGTE CS
                            TP6A_N   2 kfaqllkvlelihelleegkvvTkRdiYYr...dvelFksQaesdrliddievllgvsReeLnv 62 
                                        +aql +++ +  +l++++k++T+Rd +Y+       F++Q+esd+++  +e+++g  Re++n+
  gi|557694696|ref|YP_008797750.1|  78 PLAQLSWMAMFASQLIRSRKTSTLRDAFYNalgYDVDFEDQQESDEAVTELETIIGTVREDFNI 141
                                       589***************************8773678**************************8 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 !   21.3   0.0   3.2e-08   0.00019      13      87 ..     186     263 ..     181     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 3.2e-08
                           DUF2399  13 aaraeegravyVvENpavlaaaadr.lga.kaaplvctsGqpsaaalelldkl.aaagarlrYhGDfDwpGlaiank 86 
                                       ++   ++++v+VvE  a+ +  +++ +    +a +v t+Gq  +a+ +++++l ++ g  ++   D D+ G++ia  
  gi|557694696|ref|YP_008797750.1| 186 KFVKSSAKQVFVVEKGAIYQRFLEEnVPSkYKAIVVHTAGQAPRATRKFIRRLnTELGLPVYIFTDADPWGMHIASV 262
                                       456677888***************9543324556678****************7888******************87 PP

                           DUF2399  87 l 87 
                                       +
  gi|557694696|ref|YP_008797750.1| 263 I 263
                                       7 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.2e-05      0.37      37      84 ..     207     264 ..     120     280 .. 0.68
   2 ?   -3.3   0.0       1.8   1.1e+04      46      63 ..     320     337 ..     291     340 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.2e-05
                                       S...TTEEEEE..ECTTTHHHHHHHHHHHHHHS.....EEEEECSSSHHHHHHHHHHH CS
                            Toprim  37 t...efkpvye..eiedkkkvlkalkelakrad.....eiilatDpDreGeaiawell 84 
                                       +   +++ +y+  +++++ ++  a ++  +r +      +++ tD+D  G +ia  ++
  gi|557694696|ref|YP_008797750.1| 207 FleeNVPSKYKaiVVHTAGQAPRATRKFIRRLNtelglPVYIFTDADPWGMHIASVIV 264
                                       234444444445555555555555444444444445579***************8877 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.8
                                       CTTTHHHHHHHHHHHHHH CS
                            Toprim  46 iedkkkvlkalkelakra 63 
                                        ++ k  ++ +k+l k+a
  gi|557694696|ref|YP_008797750.1| 320 SDPWKREISNFKKLQKKA 337
                                       444455555566666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); 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: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2635.63
//
Query:       gi|557694697|ref|YP_008797751.1|  [L=261]
Description: metallophosphoesterase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-07   32.3   0.2    1.5e-07   31.8   0.2    1.2  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    9.5e-06   26.2   0.7    5.4e-05   23.8   0.0    2.0  2  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 !   31.8   0.2   1.6e-11   1.5e-07       2     128 ..      17     156 ..      16     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.6e-11
                     Metallophos_2   2 klaiiSDlH................snldaleavlealkevgvdaiihaGD..........l.eeeepevleellel 51 
                                       k ++++DlH                +++++++++++ ++++g+ +++++GD          l +e+ p +++ +++l
  gi|557694697|ref|YP_008797751.1|  17 KTLAVADLHlgfeeelrskgvrvplQSIKIVDELMAVIESTGAKRLVVVGDlkhniqgpssLeYEVLPRFVKPVKSL 93 
                                       6789***********************************************77777777665667777888888888 PP

                     Metallophos_2  52 a.pvlaVrGNnDeevveedvlreaaelgtdlpeeaelelagekvlliHgdplgvkdalaellkeaeegsdvvvcGHt 127
                                         ++++ +GN+D      ++ +  a+++t    ++ + +++e+++++Hg+   vk +++ +  +      v+v GH 
  gi|557694697|ref|YP_008797751.1|  94 VdELIILPGNHD-----GKIEKVLAGHATLC-RADGFVVEEESIGFTHGH---VKPSIHVASMD------VIVTGHL 155
                                       8***********.....33333344444444.44444459999******9...66666666656......9999999 PP

                     Metallophos_2 128 H 128
                                       H
  gi|557694697|ref|YP_008797751.1| 156 H 156
                                       9 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0     6e-09   5.4e-05       2      76 ..      17     111 ..      16     142 .. 0.61
   2 ?    0.5   0.8     0.082   7.4e+02     190     203 ..     144     157 ..     127     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 6e-09
                                       EEEEEESBTB...........TTCCTHHHHHHHHHHHH...HHHTTESEEEEESTSSSSS....HHHHHHHHH.HHH CS
                       Metallophos   2 rilvigDlHl...........algggqlddllkllddl...lreekpdlvllaGDlvdrg....dlekellel.laa 59 
                                       + l ++DlHl                   + +k++d+l   +++ ++  ++++GDl +      +le+e+l   +++
  gi|557694697|ref|YP_008797751.1|  17 KTLAVADLHLgfeeelrskgvR----VPLQSIKIVDELmavIESTGAKRLVVVGDLKHNIqgpsSLEYEVLPRfVKP 89 
                                       7899*****9999999966641....333333333333333344355555556**9999866665555555553333 PP

                                       HHHHTSEEEEEC-TTS.....C CS
                       Metallophos  60 lvkypipvylllGNHe.....g 76 
                                       + ++ + +++l+GNH+      
  gi|557694697|ref|YP_008797751.1|  90 VKSLVDELIILPGNHDgkiekV 111
                                       33336678********444440 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.082
                                       HTTESEEEEESSSS CS
                       Metallophos 190 kygvdlvisGHtHv 203
                                           d+++ GH H+
  gi|557694697|ref|YP_008797751.1| 144 VASMDVIVTGHLHP 157
                                       55689********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       341  (0.0190195); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1883.48
//
Query:       gi|557694698|ref|YP_008797752.1|  [L=114]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   26.0   0.1    9.2e-06   25.2   0.1    1.3  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 !   25.2   0.1   5.1e-10   9.2e-06       3      38 ..      42      85 ..      36      86 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.1e-10
                              SWIM  3 Vtldder...vrlnkatCsCpefqk.....ngipCkHalAvlla 38
                                      V +++ r   v  +  +CsC +f +      +++C H+lAv++a
  gi|557694698|ref|YP_008797752.1| 42 VVVGKTRdylVLPEAGYCSCEDFFFrvmshEKPLCYHLLAVKIA 85
                                      677777788888899********99****************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 876.68
//
Query:       gi|557694699|ref|YP_008797753.1|  [L=122]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   46.8   0.0    2.3e-12   46.4   0.0    1.2  1  Cupin_2          Cupin domain
    3.2e-07   30.1   0.0    3.9e-07   29.8   0.0    1.1  1  Cupin_1          Cupin
    0.00022   21.2   0.0    0.00028   20.8   0.0    1.1  1  AraC_binding     AraC-like ligand binding domain
     0.0045   16.9   0.0     0.0054   16.6   0.0    1.1  1  MannoseP_isomer  Mannose-6-phosphate isomerase
  ------ inclusion threshold ------
      0.013   15.2   0.1      0.022   14.4   0.0    1.4  1  Cupin_3          Protein of unknown function (DUF861)
      0.043   13.6   0.0      0.067   12.9   0.0    1.4  1  EutQ             Ethanolamine utilisation protein EutQ
      0.073   13.2   0.0      0.084   13.0   0.0    1.2  1  TetR_C_23        Tetracyclin repressor-like, C-terminal domai
      0.089   12.2   0.0      0.099   12.1   0.0    1.2  1  Cupin_4          Cupin superfamily protein
       0.09   13.0   0.0        0.1   12.8   0.0    1.2  1  ARD              ARD/ARD' family
      0.097   12.7   0.0       0.11   12.5   0.0    1.1  1  Pirin            Pirin
       0.11   12.2   0.1       0.17   11.5   0.1    1.5  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
       0.13   12.2   0.0       0.16   11.9   0.0    1.2  1  Cupin_7          ChrR Cupin-like domain


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 !   46.4   0.0   1.5e-15   2.3e-12       4      63 ..      37      96 ..      34     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.5e-15
                                      EEETTEEEEEECSSSEEEEEEEEESEEEEEECTE.EEEEETTEEEEE-TT-EEEEEE-SSS CS
                           Cupin_2  4 elppGesapshrHpgedeffyVleGegeltvdge.eveleaGdsvyfpagtpHrfrNtgde 63
                                       l++G+  ++hrH +e ++ +VleG ++++ d++ e + ++Gd+v++p+++ H+ +  +d+
  gi|557694699|ref|YP_008797753.1| 37 LLKKGARVQMHRHVNE-QLTVVLEGSIKFWFDDNtELVAKTGDVVVIPSNVGHAAEALEDT 96
                                      578999**********.*************77666******************99887754 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   2.6e-10   3.9e-07      27     114 ..      25     105 ..      18     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.6e-10
                                       TTHSSTEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEES CS
                           Cupin_1  27 glntlgisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsg 103
                                       + +++++ +a++ l++g+ +++h h   +++++vl+G+    f + +n     + + + Gdv+v+P+++ h++ + +
  gi|557694699|ref|YP_008797753.1|  25 MVSGERVMVAKLLLKKGARVQMHRH-VNEQLTVVLEGSIK--FWFDDN----TELVAKTGDVVVIPSNVGHAAEALE 94 
                                       67889999999999***********.889***********..888887....677899******************7 PP

                                       SSSEEEEEEEE CS
                           Cupin_1 104 depavaivvfd 114
                                       d+ ++ i++  
  gi|557694699|ref|YP_008797753.1|  95 DTVTFDIFCTA 105
                                       66666666554 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 !   20.8   0.0   1.9e-07   0.00028      15      63 ..      43      92 ..      39     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.9e-07
                                      SEEEETT-SEEEEEEEEE-EEEEETTEE.EEE-TT-EEEE-TTS-EEEEE CS
                      AraC_binding 15 sfpphvhdeyvihyvteGtgrlrlngrt.ydlgpGdlfLlppgepHdyes 63
                                      +++ h+h + ++ +v+eG+ +++++++t   +++Gd++ +p ++ H  e+
  gi|557694699|ref|YP_008797753.1| 43 RVQMHRHVNEQLTVVLEGSIKFWFDDNTeLVAKTGDVVVIPSNVGHAAEA 92
                                      6788******************9999888***************998877 PP

>> MannoseP_isomer  Mannose-6-phosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.6e-06    0.0054      56     123 ..      24      91 ..      17     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.6e-06
                   MannoseP_isomer  56 vldegeryqvkritvkPgeklslqkhhhraehW.vvvkGtakvtvddevlllk.enestyiplgaihrle 123
                                        + +ger  v ++ +k g++  +q+h+h  e   vv++G  k   dd++ l+    + + ip ++ h+ e
  gi|557694699|ref|YP_008797753.1|  24 KMVSGERVMVAKLLLKKGAR--VQMHRHVNEQLtVVLEGSIKFWFDDNTELVAkTGDVVVIPSNVGHAAE 91 
                                       56789999999999999987..6999999998637889******99998776515678899999999876 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 ?   14.4   0.0   1.5e-05     0.022      21      64 ..      46      90 ..      27     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                      ECESS.EEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEEECC CS
                           Cupin_3 21 ltyee.dEfcyileGevkvtpeggetvelraGDlvvlpkglsgtw 64
                                      ++    +++  +leG +k+  ++  +   + GD+vv+p +   + 
  gi|557694699|ref|YP_008797753.1| 46 MHRHVnEQLTVVLEGSIKFWFDDNTELVAKTGDVVVIPSNVGHAA 90
                                      55555255669***************************9874444 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.5e-05     0.067      97     128 ..      53      85 ..      23      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.5e-05
                              EutQ  97 eidyvieGrldvlidGr.kvvaeaGdviliPkg 128
                                       ++ +v+eG ++  +d + ++va++Gdv++iP +
  gi|557694699|ref|YP_008797753.1|  53 QLTVVLEGSIKFWFDDNtELVAKTGDVVVIPSN 85 
                                       5789*******998765169***********87 PP

>> TetR_C_23  Tetracyclin repressor-like, C-terminal 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     0.084      66     101 ..      45      80 ..      14     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.6e-05
                         TetR_C_23  66 flekklsellwlqllfvlkFWvkDtSegfekTdvli 101
                                       ++ + ++e l + l + +kFW +D+ e  +kT  ++
  gi|557694699|ref|YP_008797753.1|  45 QMHRHVNEQLTVVLEGSIKFWFDDNTELVAKTGDVV 80 
                                       456889999**********************96543 PP

>> Cupin_4  Cupin superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.6e-05     0.099     174     207 ..      68     101 ..      32     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.6e-05
                                       -SEEEEE-TT-EEEE-TT-EEEEEBBT-CCEEEE CS
                           Cupin_4 174 pvedfvLepGDlLYlPrgviHqgvaedesltlSv 207
                                          ++v ++GD+  +P+ v H ++a+++++t+ +
  gi|557694699|ref|YP_008797753.1|  68 DNTELVAKTGDVVVIPSNVGHAAEALEDTVTFDI 101
                                       55689999********************999865 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.9e-05       0.1      86     134 ..      45      89 ..       9     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.9e-05
                               ARD  86 eEhlhedeeirliveGtgyFdvrskdeawirvlvekGDLivlPagiyhr 134
                                       + h h +e++ +++eG+  F   ++ e       + GD +v+P ++ h 
  gi|557694699|ref|YP_008797753.1|  45 QMHRHVNEQLTVVLEGSIKFWFDDNTEL----VAKTGDVVVIPSNVGHA 89 
                                       6699****************99888764....46************995 PP

>> Pirin  Pirin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.4e-05      0.11      33      86 ..      33      86 ..       2      99 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.4e-05
                                      ETTEEEE...T-EEEEEEEBSEEEEEEEECSEEEEEETTS-EEEEETT-EEEEE-TT CS
                             Pirin 33 vgeedvi...gagfpphphrgletvtylleGevehrDslGnkgvirpGdvqwmtAgs 86
                                      v++   +   ga +++h h + e +t +leG++++     ++ v ++Gdv ++ +  
  gi|557694699|ref|YP_008797753.1| 33 VAK--LLlkkGARVQMHRHVN-EQLTVVLEGSIKFWFDDNTELVAKTGDVVVIPSNV 86
                                      333..2244466677777766.88**********999999999******98876655 PP

>> 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 ?   11.5   0.1   0.00012      0.17      86     131 ..      60     105 ..       9     112 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                       TSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS CS
                   dTDP_sugar_isom  86 gSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvte 131
                                       gS +f    ++eL a++   + ip +++h+  +l+d++++   +t+
  gi|557694699|ref|YP_008797753.1|  60 GSIKFWFDDNTELVAKTGDVVVIPSNVGHAAEALEDTVTFDIFCTA 105
                                       666777778899**************************99988875 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.16      25      86 ..      32      98 ..      13     100 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      EEEEEEE-TTEE---EE-TT-EEEEEEEEE....EEETTEEE.ETTEEEEE-TT-EE--EESS-EEE CS
                           Cupin_7 25 atslvryapgsafsahkHpggeeilVLeGv....fsdeegdy.paGsylrnppgsshapvseeGcti 86
                                      +++ + +++g++ + h+H +   ++VLeG     f d+++   + G+ +  p +  ha  + e++++
  gi|557694699|ref|YP_008797753.1| 32 MVAKLLLKKGARVQMHRHVNEQLTVVLEGSikfwFDDNTELVaKTGDVVVIPSNVGHAAEALEDTVT 98
                                      444455799********************75553455554445778888888888888777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); 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:                        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 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1009.41
//
Query:       gi|557694700|ref|YP_008797754.1|  [L=378]
Description: hypothetical protein CSUB_C1273 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   30.0   0.0      0.011   15.8   0.0    2.9  2  HAD_2        Haloacid dehalogenase-like hydrolase
    1.5e-06   28.6   0.0    5.8e-06   26.8   0.0    1.9  1  Hydrolase    haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.041   14.0   0.0       0.18   11.9   0.0    2.1  2  Hydrolase_6  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 !   10.8   0.1   6.3e-05      0.38       1      28 [.      34     105 ..      34     176 .. 0.56
   2 !   15.8   0.0   1.9e-06     0.011      85     170 ..     236     329 ..     231     332 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.3e-05
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleey............................................g 28 
                                       +iFD Dg+l+d+++ + ++++e+                                                 
  gi|557694700|ref|YP_008797754.1|  34 VIFDCDGVLIDEKTSYDKVIQEVTVYLthmltgytvdasaikqetiydiraigsfnndsntiqllvewlvdR 105
                                       7*************9999999998666666776666555444444444444444444444443333333332 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.9e-06
                             HAD_2  85 kelLeeLkeagyklgivTsksreaveekleqlg...ie...syFdvivtsedvekk...KPdpeviekaleklklkk 152
                                       +e+Le+L++ g+++gi T + + ++++ l ++    ++    +++  +t + v+ +   KP+p ++++al+ l+ ++
  gi|557694700|ref|YP_008797754.1| 236 RETLEKLSQYGIRMGICTGRGSWETWRTLGEFSryfVKeacMFISDYITIDPVKYSyleKPSPIPLLEALKGLGGDE 312
                                       79******************999999999877522233122456777899999987888**************9875 PP

                             HAD_2 153 eeviyvGDsptDieaakk 170
                                          +yvG s  D +  ++
  gi|557694700|ref|YP_008797754.1| 313 -PKLYVGNSAEDHIMFQR 329
                                       .5589**99999887666 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   9.6e-10   5.8e-06       4     209 ..      34     330 ..      31     330 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 9.6e-10
                                       EEEESBTTTBCHHHHHHHHHHHH................CHHHHHHHHHHHHCHHHHHHHHHHHHH.HHHHHHHHHE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                         Hydrolase   4 vvfDkdGTLttgepsvedvivsa................alalaaaletgsehpigkalvaaakar.sgaltgfatf 63 
                                       v+fD+dG+L++ + s  +vi+++                a                       k++   ++  ++ f
  gi|557694700|ref|YP_008797754.1|  34 VIFDCDGVLIDEKTSYDKVIQEVtvylthmltgytvdasA----------------------IKQEtIYDIRAIGSF 88 
                                       89***********888888888833334444444333221......................222221111222222 PP

                                       TTTEHHHHTHHHHHHHH...HCHHHHHHHHHHHHHHCHHHHHH.................................. CS
                                       xxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx.................................. RF
                         Hydrolase  64 igrgayaigkpewltal...dippdlgaaigsaqsqgrtvall.................................. 103
                                       +         +ewl +    +  +++ ++++++ s+  t++                                    
  gi|557694700|ref|YP_008797754.1|  89 NNDSNTIQLLVEWLVDRisaELDNKVTERMTELRSKNFTEMQGvlqsrgkvssssvenwlrdlsgkvapfsgsaaal 165
                                       22222222222232222222233333333333333333333334444444444445556666666666666666666 PP

                                       ..................................................TTHHHHHHHHH.HTHHBHTTHH.HHHH CS
                                       ..................................................xxxxxxxxxxx.xxxxxxxxxx.xxxx RF
                         Hydrolase 104 ..................................................qaralavftia.dplkvkpeaa.eava 128
                                                                                         +a     ft + d+   k  +  e+++
  gi|557694700|ref|YP_008797754.1| 166 taleeeigidmqltkmvkdvlkpggrygesllttvfdeafygsenvqkvrNAGPFFSFTGKlDE--EKLIVSrETLE 240
                                       6777777777778899999999999999999999999**********99999999999999666..6666666**** PP

                                       HHHHTTEEEEEEESSEHHHHHHHHHHTT......GGGE.SEEEEHHCES...STTTSHHHHHHHHHHHTST.GGGEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxx.xxxxxxxxxx...xxxxxxxxxxxxxxxxxxx.xxxxx RF
                         Hydrolase 129 sLkaagievvlltgdnpetaeraanqlG......ddyf.daviasdiet...vakpspegkvaaireLqgk.peeva 194
                                       +L + gi+++++tg  +   +r++ ++       +  f +  i++d ++     kpsp  +++a++ L+g+ p   +
  gi|557694700|ref|YP_008797754.1| 241 KLSQYGIRMGICTGRGSWETWRTLGEFSryfvkeACMFiSDYITIDPVKysyLEKPSPIPLLEALKGLGGDeP--KL 315
                                       *****************88888888866576665555555555555555*******************96646..89 PP

                                       EEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxx RF
                         Hydrolase 195 mVGDgvnDaaalaaA 209
                                        VG ++ D  ++++A
  gi|557694700|ref|YP_008797754.1| 316 YVGNSAEDHIMFQRA 330
                                       ******998888765 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     3e-05      0.18       1      21 [.      34      54 ..      34      69 .. 0.86
   2 ?   -2.8   0.0       1.2   7.2e+03      20      37 ..     236     253 ..     229     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3e-05
                                      EEEESTTTSEETTEE-TTHHH CS
                       Hydrolase_6  1 flfDidGvLwrgdkaipgaae 21
                                      ++fD+dGvL+++++ ++++ +
  gi|557694700|ref|YP_008797754.1| 34 VIFDCDGVLIDEKTSYDKVIQ 54
                                      69*********9999998865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                       HHHHHHHHHTT-EEEEEE CS
                       Hydrolase_6  20 aealnalraagkpvvllT 37 
                                        e+l+ l + g+++ ++T
  gi|557694700|ref|YP_008797754.1| 236 RETLEKLSQYGIRMGICT 253
                                       567777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2700.07
//
Query:       gi|557694701|ref|YP_008797755.1|  [L=304]
Description: homoserine kinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   35.2   0.9    1.1e-08   35.2   0.9    2.2  2  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 !   35.2   0.9     6e-13   1.1e-08       2      66 .]      85     147 ..      84     147 .. 0.89
   2 ?   -1.8   0.2      0.21   3.8e+03      20      31 ..     204     215 ..     203     247 .. 0.56

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 6e-13
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDvaasvyGg 66 
                                       ++i+  iP+ +GLG S+A a+a+v+ l+ ll+l l  ee ++la +ae        + ++vaas++Gg
  gi|557694701|ref|YP_008797755.1|  85 LTIDASIPPRKGLGASGAEAAAAVYGLNTLLELGLtrEEmVELASTAEP-----GQHADNVAASLLGG 147
                                       799****************************988776336999999994.....569**********8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHH CS
                    GHMP_kinases_N  20 lavalvaAllal 31 
                                       + +al+aA+ a 
  gi|557694701|ref|YP_008797755.1| 204 AETALAAAAIAR 215
                                       556666665443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2359.83
//
Query:       gi|557694702|ref|YP_008797756.1|  [L=339]
Description: 3-isopropylmalate dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-87  292.3   0.0    5.8e-87  292.1   0.0    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


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 !  292.1   0.0   3.2e-91   5.8e-87       2     348 .]       4     330 ..       3     330 .. 0.94

  Alignments for each domain:
  == domain 1  score: 292.1 bits;  conditional E-value: 3.2e-91
                                       EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSSSS CS
                            Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpkeke 78 
                                       +++++gdgiGp +ve++ ++++ + ++ g +lef ++ +G a+ ++tg++lp e+le i ++d+ l+g+vg      
  gi|557694702|ref|YP_008797756.1|   4 VSVIKGDGIGPHIVEETCRLVDWLCQRLGVKLEFVDAPAGDAVKEATGSALPPESLETIMKSDACLKGPVGETA--- 77 
                                       89********************************************************************9888... PP

                                       SSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEE CS
                            Iso_dh  79 vrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtk 155
                                             ++ Lr+ ldl+an+rp k +   +vks+       +vd+v+vRe+t+++Y   e +  +      +av + 
  gi|557694702|ref|YP_008797756.1|  78 ---RDVIVFLRQRLDLYANIRPFKNL--PGVKSKWS-----GVDFVVVRENTEDVYKSVEDVGVD------YAVALL 138
                                       ...445799*****************..57777766.....69*************999988777......79**** PP

                                       EEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHHHHHHHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGG CS
                            Iso_dh 156 lyseeeieriaraafelAlkrgkkkvtlvdKanvlksselwrkiveevaeeeypdielehqlvDsaamqlvkspkqf 232
                                       ++s+++ eriar+afe+A++r + kvt+v+K+nv +++ ++r+++ +va+ +y d+ +++++vD+aa+q+v +p+qf
  gi|557694702|ref|YP_008797756.1| 139 VVSRRAAERIARVAFEMAETR-RRKVTVVHKSNVVRAYGFFRDVCFQVAK-NYRDVVVDEMYVDNAAYQMVLNPQQF 213
                                       *********************.****************************.************************** PP

                                       SEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHHHHHHHHHTTT-HH CS
                            Iso_dh 233 dVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilSaalmLryslglee 309
                                       d+++t+N+fGDilSD+aa +vG +G++ Sa++g +++++fE+vHGsap +   ++aNp++++l+a +mL   lg  +
  gi|557694702|ref|YP_008797756.1| 214 DIVLTPNMFGDILSDLAAGVVGTIGIAGSANVG-DRFGLFEPVHGSAPTLN-PEQANPTGQLLAAKMMLDW-LGRFK 287
                                       *********************************.79*************98.899**************99.77665 PP

                                       HH.......HHHHHHHHHHHHH.TSCCHHHCTTSTCCCHHHHHHHHH CS
                            Iso_dh 310 aA.......dkiekAvekvlea.givTkDlageaakevstsefgdav 348
                                       +        + +ekAv +vl +  ++T Dl+g+a    ++s+f+++v
  gi|557694702|ref|YP_008797756.1| 288 QDkrftdagEVLEKAVYNVLSEgLVLTMDLGGSA----TCSQFVEEV 330
                                       55555666699***********5578********....******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2561.47
//
Query:       gi|557694703|ref|YP_008797757.1|  [L=422]
Description: pyruvate formate lyase activating enzyme [Candidatus Caldiarchaeum subterraneum]
Scores for 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-10   40.3   0.0    1.3e-08   35.4   0.1    2.4  2  Radical_SAM  Radical SAM superfamily
    3.3e-07   30.7   0.0    6.4e-07   29.7   0.0    1.5  1  Fer4_12      4Fe-4S single cluster domain
    1.7e-05   24.9   0.0      6e-05   23.2   0.0    1.9  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 !   35.4   0.1   2.1e-12   1.3e-08       2     157 ..     157     337 ..     156     347 .. 0.84
   2 ?    2.2   0.0     0.034     2e+02     117     143 ..     379     404 ..     360     410 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 2.1e-12
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla.... 74 
                                       +++  Cn+rC+fC++   +++ + g + ++++++  + +l+   g++++ l+ggep+ + + ++++ ++ +      
  gi|557694703|ref|YP_008797757.1| 157 IFFTSCNMRCVFCQNADISHDKDNGIVFTPQMLAWAMWQLR-MEGCHNINLVGGEPTIHLHTIVEAINMLRFFkety 232
                                       67889***********************************6.777**************777666666666556888 PP

                                       .........................CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSH CS
                                       .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 .........................vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrght 126
                                                                + +  i   +n ++   e ++ l el  d    + + +++++   l + ++ 
  gi|557694703|ref|YP_008797757.1| 233 aeavdakadiyypysldtrnayyegEFNTPILWNSNMYMS-GETMKILHELV-DIWLPDFKFGNNKCATWLSRTPWY 307
                                       8878888888899999988888877777777777777776.*********99.*************555555588** PP

                                       HHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 127 feevlealeklreagikrvvdrivglpGend 157
                                       fe v ++ + + e g +++v+r++++pG  +
  gi|557694703|ref|YP_008797757.1| 308 FETVSQNHKQIYEWG-EDIVIRHLVMPGHVE 337
                                       **************5.55*********9866 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.034
                                       HHHHHTCTSHHHHHHHHHHHHHHTTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 117 vlklmnrghtfeevlealeklreagik 143
                                       + ++  r +t ee++e+ +++r++gi+
  gi|557694703|ref|YP_008797757.1| 379 YSDMA-RYPTEEEIMESYRYARSLGIN 404
                                       55555.778999999999999999987 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 !   29.7   0.0   1.1e-10   6.4e-07       3      80 ..     150     232 ..     148     280 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 1.1e-10
                           Fer4_12   3 GeGvrlslfvsgCnlsCkgCfnketw.sfksgkeftkelleeiiedlkkesiegltllGGEPllpena....ealle 74 
                                       G+++  ++f++ Cn++C +C n ++  + ++g  ft ++l+ ++ +l  e    + l+GGEP  + ++      +l+
  gi|557694703|ref|YP_008797757.1| 150 GTKGSGTIFFTSCNMRCVFCQNADIShDKDNGIVFTPQMLAWAMWQLRMEGCHNINLVGGEPTIHLHTiveaINMLR 226
                                       66666799**************9986367789999***************************996554422123344 PP

                           Fer4_12  75 lvkevk 80 
                                       ++ke +
  gi|557694703|ref|YP_008797757.1| 227 FFKETY 232
                                       444444 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 !   23.2   0.0     1e-08     6e-05       2      75 ..     158     226 ..     157     267 .. 0.78
   2 ?   -2.8   0.0       1.1   6.6e+03      15      38 ..     366     392 ..     341     402 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 1e-08
                           Fer4_14   2 fvrlsgCnlsCkgCdnke.twkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlk 75 
                                       f+   +Cn+ C++C n + + +++ g ++t ++l   + +l  + +  +++ l+GGeP ++   +++++ +++l+
  gi|557694703|ref|YP_008797757.1| 158 FF--TSCNMRCVFCQNADiSHDKDNGIVFTPQMLAWAMWQLRMEGC--HNINLVGGEPTIH--LHTIVEAINMLR 226
                                       44..99*********887256679999*******999977777777..88********988..555555555544 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                           Fer4_14  15 Cd...nketwkselgkpqteelleqil 38 
                                       C+       +++++     + ++e+i+
  gi|557694703|ref|YP_008797757.1| 366 CYcnpSDPRFDKRYSDMARYPTEEEIM 392
                                       333333334555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); 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:                         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 0.21s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3328.72
//
Query:       gi|557694704|ref|YP_008797758.1|  [L=193]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
        0.3   10.9   1.7        2.1    8.2   0.2    2.4  2  IL28A     Interleukin-28A


Domain annotation for each model (and alignments):
>> IL28A  Interleukin-28A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.2   0.00012       2.1      59      94 ..      10      45 ..       2      49 .. 0.89
   2 ?    1.9   0.1      0.01   1.8e+02      38      90 ..      77     133 ..      48     171 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00012
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             IL28A 59 valeaelaltlkvLeavtdsalaevleqpLetLrhi 94
                                      +a+ ae+a +l+ L++ ++ +l ++ +q+L+t+ ++
  gi|557694704|ref|YP_008797758.1| 10 LAVDAEIADSLSKLAEAKHMTLYSLTNQILQTFVEM 45
                                      799*****************************9876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.01
                                       BSS-SSSTTS-GGGS-CCCHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHH..HHHH CS
                             IL28A  38 cssrlfprkwdlrqlqvseRlvaleaelaltlkvLeavtds..alaevleq..pLet 90 
                                       +   l+     +++ ++ eR + l +++   lkv +a  ++  +la+++ q  pL+ 
  gi|557694704|ref|YP_008797758.1|  77 FMDMLIADLYAVNKEKLLERFRQLGRDVGKVLKVYAASVEElfELAKTVGQffPLKR 133
                                       444555666666666777777777777777777776655543445555554334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      687  (0.0383178); 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 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1365.75
//
Query:       gi|557694705|ref|YP_008797759.1|  [L=178]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   70.8   0.1    1.6e-19   70.8   0.1    1.6  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 !   70.8   0.1   8.8e-24   1.6e-19       5     130 ..       7     138 ..       3     139 .. 0.86
   2 ?   -2.0   0.6      0.29   5.3e+03      77      87 ..     165     175 ..     155     178 .] 0.56

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 8.8e-24
                                       HHHHHHHHHHHHHHHH.HHHHHHHHHHCCC...HCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH...CCC.HHHHHH CS
                       Hemerythrin   5 aldeeHralrallerl.raladaaaevhga...lrklaelldelvdeleaHhaaEEellfPlle..drpggravldv 75 
                                        l+++H+ +++ ++rl +++++   +++ +   l+k+ e+++ + d    Hh +EE++lfP +e  ++p+  +++ v
  gi|557694705|ref|YP_008797759.1|   7 SLLRDHEVILRAVARLeSRVSEWRRSRRIErgsLEKFIEFAKLFTDR--CHHGKEERCLFPCMEkrGVPREGGPIGV 81 
                                       6899************65666664444444799*************8..**************************** PP

                                       HHHHHHHHHHHHHHHHHHCHTCGGSTCHHHHH...HHHHHHHHHHHHHHHHHHTHHHH CS
                       Hemerythrin  76 lereHdeirelleelrellkgleepsaaafae...lleeladllreHiakEesilfpl 130
                                       +  eH+  r+l+++l+++++++   +++ ++e     e+++ l+r+HiakE++ilfp+
  gi|557694705|ref|YP_008797759.1|  82 MLYEHQLGRQLISRLEKAAETYF-NEGRGLEEvltVCEDYIGLIRQHIAKENDILFPM 138
                                       ****************8888887.33333344466999999****************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHH CS
                       Hemerythrin  77 ereHdeirell 87 
                                       e+eH+++++ +
  gi|557694705|ref|YP_008797759.1| 165 EEEHHRLERAA 175
                                       44455444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1263.76
//
Query:       gi|557694706|ref|YP_008797760.1|  [L=402]
Description: hypothetical protein CSUB_C1279 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2956.25
//
Query:       gi|557694707|ref|YP_008797761.1|  [L=909]
Description: peptide/nickel ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   99.7   2.6    4.5e-24   85.1   0.1    2.5  2  SBP_bac_5     Bacterial extracellular solute-binding proteins
     0.0057   16.0   0.2      0.058   12.7   0.1    2.1  2  SF-assemblin  SF-assemblin/beta giardin
  ------ inclusion threshold ------
      0.074   13.1   2.9       0.14   12.2   2.9    1.3  1  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C


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 !   85.1   0.1   7.5e-28   4.5e-24     148     365 ..      38     277 ..      31     287 .. 0.83
   2 !   13.8   0.5   3.6e-06     0.021      31     144 ..     506     708 ..     504     737 .. 0.64

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 7.5e-28
                                       SCSSSSEEEEEE-.SHHHHHHHHHTTSSSEE.ESTTCCTHCHHHHHTTEEEEEEEEEEEEEEEEETTT......... CS
                         SBP_bac_5 148 gkpkldriefkvipdsdaraaalqsGeiddv.aepppsdieqlkeakglkvlyespgggvtylafNtk......... 214
                                       + p +d++ f v +d++ ++++l++Ge +++  ++  +++ +   ++   + y   +g ++ l+fN           
  gi|557694707|ref|YP_008797761.1|  38 RGPWVDEVSFFVEQDQAKAIDMLEKGEMHVFfRDLRDPELFRRVRESPNLW-YIYSYGLFYELTFNPVgpefpatgk 113
                                       56789*****99999999**********98865555555555555555555.78888888888999999***99999 PP

                                       STGGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH.......SHHHHHHHHHHHTT- CS
                         SBP_bac_5 215 kppfddkrvRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka.......ydpekAkklLkeaGy 284
                                        +pf+ +r+R+A++y iDr  i++++++g+++p +++l p +p +  + ++   +       y+ ekA+++++e   
  gi|557694707|ref|YP_008797761.1| 114 LNPFSVPRIREAMNYLIDRGYIANEIMGGLGVPRYTALTPAFPDYARYADTL--KqiekeyaYNFEKARQIINEEMT 188
                                       77******************************************99998875..25799999************999 PP

                                       BCSSTSCEETC.....EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHH....HHHHHHHHCTTESEEE CS
                         SBP_bac_5 285 kdgdggglrek.....klkltlllasgspaekaiaeliqqqlkkiGikvevktvdwa....atylervkdgdfdmil 352
                                       k g + +++ k     +++++++l      +++i +++++ql+k+G++v+ ++  +      +      dg++ ++ 
  gi|557694707|ref|YP_008797761.1| 189 KLGAE-LREGKwfykgEPVTLIFLIRVEDQRRQIGDYVASQLEKLGFTVDRQYKTSReaspIWLRGNPADGNWHLYT 264
                                       99964.55555899967777777777777777*******************999666688844444588******** PP

                                       EEEECTTSTTHHH CS
                         SBP_bac_5 353 lgwgadypdpdnf 365
                                       +gw a+ +d ++ 
  gi|557694707|ref|YP_008797761.1| 265 GGWIATVIDRNEA 277
                                       ******9998765 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.6e-06
                                       TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC............................................ CS
                         SBP_bac_5  31 sDGtpltAeDvvfsferlldpdtasgyasllee............................................ 63 
                                       +DG+ +  +D+v+s+  + d  ++ ++ ++ ++                                            
  gi|557694707|ref|YP_008797761.1| 506 HDGSTFSLADIVYSYILTFDRADPKSPLYDESYvpvfeefravfkglriisedplvievysdrtyldaewianeaas 582
                                       9********************999999999999*********65555555555555555555555555555555555 PP

                                       .............TCTEEEEEEEETTEEEEEESSETTTTTTHCHHHHHHHGC......................... CS
                         SBP_bac_5  64 .............dqdikkveavddytvrftlkkpnalfltllaavpasiak......................... 102
                                                    +                                                               
  gi|557694707|ref|YP_008797761.1| 583 wfftdylygpapwH-------------------------------------Vvavgalaeeagelafsadkadaqki 622
                                       55555555555541.....................................03334555555555555555555555 PP

                                       ............................................CHTCTCTTT.TTGTTTSE-BSSSEEEEEEETTT CS
                         SBP_bac_5 103 ............................................kaaekeddk.dkdtnekpvgtGPYklkefkpgq 134
                                                                                   +   ++ ++    +   +vg+GP+ +++++p  
  gi|557694707|ref|YP_008797761.1| 623 ewmnllagpslpilaaqldkaiaqqyipyenvlgkyvtkeeavnR--YQNLKRwYQSKGHFLVGNGPFYIEKVDPTA 697
                                       555555555555555666666666*****************9643..34444304555556799***********88 PP

                                       EEE.EEE-TTS CS
                         SBP_bac_5 135 kiv.lernpdY 144
                                       k+v ++++ ++
  gi|557694707|ref|YP_008797761.1| 698 KAVvIKAFREF 708
                                       66625554444 PP

>> SF-assemblin  SF-assemblin/beta giardin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.039   2.3e+02      79     111 ..     165     197 ..     159     202 .. 0.81
   2 !   12.7   0.1   9.6e-06     0.058      69     140 ..     829     900 ..     824     909 .] 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.039
                      SF-assemblin  79 ikeevddlalelkkaveelnekinnveanvene 111
                                        k+  ++ a++++ka + +ne+++ + a +++ 
  gi|557694707|ref|YP_008797761.1| 165 LKQIEKEYAYNFEKARQIINEEMTKLGAELREG 197
                                       4555567899***************99999875 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 9.6e-06
                      SF-assemblin  69 kkeikklqekikeevddlalelkkaveelnekinnveanvenekakrrdaieklakelvkelneleaaideE 140
                                       k +++    k + + d + + l++++++ln+++nnv++ ++  + +   a +  a  +v +l+ l  a+ + 
  gi|557694707|ref|YP_008797761.1| 829 KDSVLSEIAKARADADSKIAGLRSSIDNLNNQLNNVNTSIQGVQGSITLATALAAVAIVLSLASLGLAFTRG 900
                                       5556556667778889999**********************9988888888888888888888887777655 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   2.9   2.3e-05      0.14      75     125 ..     822     877 ..     804     890 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.3e-05
                      Baculo_PEP_C  75 alnalq..dtlrneLtn....lnsiltnLlssvtNinstLnnllqalnnldlgalsq 125
                                       ++n l+  d++ +e+       +s+++ L ss+ N+n+ Lnn+ +++++++ g+++ 
  gi|557694707|ref|YP_008797761.1| 822 SINVLSfkDSVLSEIAKaradADSKIAGLRSSIDNLNNQLNNVNTSIQGVQ-GSITL 877
                                       555555555555555431111588999999999999999999999999984.44443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (909 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); 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: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.45
# Mc/sec: 6012.95
//
Query:       gi|557694708|ref|YP_008797762.1|  [L=354]
Description: peptide/nickel ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   88.8  13.6    3.5e-25   88.8  13.6    2.2  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 ?   -2.6   0.2      0.21   3.8e+03      62      72 ..      21      31 ..      10      43 .. 0.51
   2 !    3.2   0.2    0.0036        65      91     125 ..     116     151 ..     112     154 .. 0.80
   3 !   88.8  13.6   1.9e-29   3.5e-25       1     184 [.     146     350 ..     143     351 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.21
                      BPD_transp_1 62 lsaapyvrlir 72
                                      + aa yv++++
  gi|557694708|ref|YP_008797762.1| 21 VVAAVYVTILI 31
                                      22222222222 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0036
                      BPD_transp_1  91 GasrwqifrkvvlPnalppi.itglilafggllgga 125
                                       G +  +i+   +lPn++  +  t+lil f+gl+gg 
  gi|557694708|ref|YP_008797762.1| 116 GSRNVRIILMERLPNTVLLFtTTQLILFFIGLFGGL 151
                                       67778999999***9876651678999999999996 PP

  == domain 3  score: 88.8 bits;  conditional E-value: 1.9e-29
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.......................vilsilghlil 54 
                                       g+++G+++ +++++++dk+++ l   l++lP    +++l+ vf                       + ls+  h+il
  gi|557694708|ref|YP_008797762.1| 146 GLFGGLYLSRKYGSRTDKIVSLLAP-LSALPGWFYGLFLIIVFasvlrilpyggmvdippptdrfeYALSVMRHMIL 221
                                       788999999************9999.99******9999999999********************************* PP

                      BPD_transp_1  55 pviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllefl 131
                                       p++  l+ ++++ ++  r  +l    +d+ve+a+a+G+++  + r+++l+ +lppi+t l l+++++++gav++e++
  gi|557694708|ref|YP_008797762.1| 222 PIMSWLVAYSFFNIYTRRTFFLIFSKEDFVEVAKAKGLPEDLVRRRYILRPTLPPIVTDLSLTLIASWTGAVITETV 298
                                       *988887777666666666666666789************************************************* PP

                      BPD_transp_1 132 gswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       ++wpG+g+l+ ea   +d++ i  g+v++++ ++++ ++v+ +++++ldpr+r
  gi|557694708|ref|YP_008797762.1| 299 FNWPGVGRLFYEAAALFDTPVIV-GLVVIYAYLLAITVFVLELVYAILDPRIR 350
                                       ***********************.***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2504.44
//
Query:       gi|557694709|ref|YP_008797763.1|  [L=468]
Description: peptide/nickel ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   66.7  12.3    2.1e-18   66.7  12.3    2.0  2  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
      0.014   15.4   1.0       0.21   11.6   0.1    2.9  2  OppC_N        N-terminal TM domain of oligopeptide transport 
       0.23   11.3   2.3       0.74    9.7   2.3    1.8  1  CoatB         Bacteriophage coat protein B


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 ?   -1.1   0.5      0.22   1.3e+03      54      70 ..      20      37 ..       9      40 .. 0.65
   2 !   66.7  12.3   3.6e-22   2.1e-18       2     184 ..     281     466 ..     280     467 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.22
                      BPD_transp_1 54 lp.viillllsaapyvrl 70
                                      ++ +iil+l+++  y+++
  gi|557694709|ref|YP_008797763.1| 20 IGaAIILMLVGISVYTVV 37
                                      333677777777777765 PP

  == domain 2  score: 66.7 bits;  conditional E-value: 3.6e-22
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrs 78 
                                       + +G+++a  +++++d++++++++v+  lP++  +i++      l ++  + + +++++lls++p v   r+ +l+ 
  gi|557694709|ref|YP_008797763.1| 281 MAIGAISA-WFGGVVDNFIQRVTEVFIVLPFLPTLIMVS----TLYKIDIWTILLVVIILLSFGPGVKNYRAVFLQL 352
                                       579*****.************************888888....2344444444456666777777778888889999 PP

                      BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis. 154
                                        +++++eaa+a Ga+  +i+  +++P ++p++i+ ++++++ ++   ++l +lg    +g+++ ++++g+ +     
  gi|557694709|ref|YP_008797763.1| 353 KESQYIEAAKAFGAGAPRIILLHLVPRVIPTMIPAIVYSVADFVFLEAALAILG----IGDPR-TPTWGKVIEDSFy 424
                                       9******************************************99999999999....88665.5788888887778 PP

                      BPD_transp_1 155 ............nggvlalviavlllnlvadilqrlldprvr 184
                                                     +++ l+i  l + lv   l ++++pr+r
  gi|557694709|ref|YP_008797763.1| 425 ggalfkglyywtLQPAFLLLITSLSFALVGLTLDKIFNPRLR 466
                                       8899************************************98 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 ?   11.6   0.1   3.5e-05      0.21      14      41 ..      16      43 ..      10      64 .. 0.80
   2 ?    0.7   0.1     0.086   5.2e+02      21      36 ..     328     342 ..     325     360 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.5e-05
                            OppC_N 14 klAvvglvilllllliaifaPliaPydp 41
                                      k A++g +i+l l+ i+++  + +Pyd 
  gi|557694709|ref|YP_008797763.1| 16 KSALIGAAIILMLVGISVYTVVAIPYDE 43
                                      78*****************866679985 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.086
                            OppC_N  21 villlllliaifaPli 36 
                                       ++l++++l++ f+P +
  gi|557694709|ref|YP_008797763.1| 328 ILLVVIILLS-FGPGV 342
                                       5666777776.66766 PP

>> CoatB  Bacteriophage coat protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.3   0.00012      0.74      21      39 ..      16      34 ..      11      37 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00012
                             CoatB 21 diaaiGaaVLvvlVgvavf 39
                                        a+iGaa++  lVg+ v+
  gi|557694709|ref|YP_008797763.1| 16 KSALIGAAIILMLVGISVY 34
                                      5699**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); 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:                         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: 00:00:00.47
# Mc/sec: 2976.06
//
Query:       gi|557694710|ref|YP_008797764.1|  [L=327]
Description: peptide/nickel ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   92.3   0.0    4.7e-26   91.9   0.0    1.2  1  ABC_tran      ABC transporter
    5.4e-17   62.1   0.5    8.9e-17   61.4   0.5    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    2.3e-10   40.8   0.0    2.9e-08   33.9   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    5.9e-07   29.1   0.2    1.8e-06   27.5   0.2    1.6  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0011   18.4   0.1      0.012   15.0   0.1    2.1  2  TniB          Bacterial TniB protein
     0.0022   18.3   0.2      0.032   14.5   0.2    2.1  1  AAA_22        AAA domain
     0.0028   17.4   0.1       0.27   10.9   0.0    2.1  2  IstB_IS21     IstB-like ATP binding protein
     0.0042   16.8   0.0     0.0081   15.9   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
  ------ inclusion threshold ------
       0.01   16.2   0.0      0.054   13.9   0.0    2.1  3  AAA_16        AAA ATPase domain
      0.023   13.5   0.0      0.045   12.5   0.0    1.4  1  ABC_ATPase    Predicted ATPase of the ABC class
      0.035   14.1   0.0       0.09   12.8   0.0    1.7  2  AAA_5         AAA domain (dynein-related subfamily)
      0.038   13.9   1.1       0.33   10.9   0.2    2.5  3  RsgA_GTPase   RsgA GTPase
       0.13   11.7   0.1       0.24   10.9   0.1    1.4  1  Hpr_kinase_C  HPr Serine kinase C-terminal domain
       0.16   11.5   0.0       0.34   10.4   0.0    1.5  1  AAA_7         P-loop containing dynein motor region
       0.17   12.3   0.1       0.53   10.7   0.1    1.9  1  AAA           ATPase family associated with various cellular 
       0.19   11.0   0.0        0.3   10.4   0.0    1.2  1  AIG1          AIG1 family
       0.21   11.7   0.1       0.37   10.8   0.1    1.4  1  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 !   91.9   0.0   4.5e-29   4.7e-26       2     137 .]      31     188 ..      30     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 4.5e-29
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGGB-HHHCCHC.....EEEE-SS.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxx.. RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlkeqeleslrke.....igvlpqe.. 67 
                                       + vs+++++ge++a+vGe+G+GKS+ + ++++ll        G+i +++++l + + e++rk+     i++++q   
  gi|557694710|ref|YP_008797764.1|  31 DGVSFSVRHGETLALVGESGSGKSSTALAIIRLLPRnvaaYRGSIIFEKTELMNLDDEEFRKRvrvggISMVFQGam 107
                                       78**********************98888887776666669***********9955555555511111667777766 PP

                                       --S-TTSBHHHH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  68 pqlfpeltvren...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       ++++p l+v+ +            ++e  +ka + l+l++l+ + +++ p +LSgG+kqr  +a+al+++pkll+lD
  gi|557694710|ref|YP_008797764.1| 108 NSFNPVLRVGFQvaeplvvnmgmPREEAYKKAEDALELVGLERSMAQRYPFELSGGMKQRALIAMALITNPKLLILD 184
                                       5555555555558999*****9955555666666666666667888888**************************** PP

                                       STTT CS
                                       xxxx RF
                          ABC_tran 134 Epta 137
                                       Ept+
  gi|557694710|ref|YP_008797764.1| 185 EPTS 188
                                       **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 !   61.4   0.5   8.4e-20   8.9e-17       2      63 ..     240     300 ..     239     303 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 8.4e-20
                         oligo_HPY   2 ErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfale 63 
                                       E gps++l  +p+HPYT++L++svp l++ k+  + ikg++p++ + ++GC+F+pRCp+  +
  gi|557694710|ref|YP_008797764.1| 240 ELGPSDELYPQPRHPYTELLINSVPFLRQDKE-PTFIKGSPPDPVEPPTGCRFHPRCPYFIK 300
                                       99*************************99999.999**********************9765 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 ?    5.1   0.0     0.016        17       3      22 ..      44      63 ..      43     119 .. 0.77
   2 !   33.9   0.0   2.8e-11   2.9e-08     232     301 ..     155     222 ..     128     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.016
                            AAA_21  3 vliGpNgsGKSnLLdaldll 22
                                      +l+G  gsGKS+   a+  l
  gi|557694710|ref|YP_008797764.1| 44 ALVGESGSGKSSTALAIIRL 63
                                      79********9876666444 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 2.8e-11
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                       + ++elS G+k+  al+++ l +++  +ll++DEp + L+   ++ ++ llk+l++  g   i+ TH+  l
  gi|557694710|ref|YP_008797764.1| 155 RYPFELSGGMKQR-ALIAMALITNP--KLLILDEPTSALDVMTQANVMNLLKKLKKeLGLTYIFITHDLAL 222
                                       5789*********.99999999999..7***********************777777***********887 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   0.2   1.7e-09   1.8e-06      26     204 ..      42     225 ..      32     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.7e-09
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCC...CCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrsekl...sdlihk..skekasvkkaeveitfdnedkklkiekeev 97 
                                         a+vG+ GSGKs+   Ai  +L   +  + r + +   ++l++   ++ +++v  + ++++f+   ++    ++ +
  gi|557694710|ref|YP_008797764.1|  42 TLALVGESGSGKSSTALAIIRLLPR-NVAAYRGSIIfekTELMNLddEEFRKRVRVGGISMVFQGAMNS---FNPVL 114
                                       5689***************999984.5547776643222445554556778999999999999888777...67777 PP

                                       EEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HH..HHHHHHHHHHHHHHCCS--SEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkgeseykingkevtkkevsellesagiske.......lLSgG..ektLvalaLlfAiqkvkpaplyllD 165
                                        +  +v +    ++ + ++e+  k+ ++ le +g++++       +LSgG  +++L+a+aL+      +p  l +lD
  gi|557694710|ref|YP_008797764.1| 115 RVGFQVAEPLVVNMGMPREEAY-KKAEDALELVGLERSmaqrypfELSGGmkQRALIAMALI-----TNP-KLLILD 184
                                       7777777777777777776664.45678888888888888888889****666789999999.....444.5889** PP

                                       TTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                             SMC_N 166 eidaaLDeknvkkvaellkekskn..aQfivislreemlek 204
                                       e  +aLD +  ++v +llk+ +k+    +i i+++  + ++
  gi|557694710|ref|YP_008797764.1| 185 EPTSALDVMTQANVMNLLKKLKKElgLTYIFITHDLALASE 225
                                       ********************999955667888887666554 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      0.22   2.3e+02      37      52 ..      42      57 ..      35      72 .. 0.83
   2 !   15.0   0.1   1.2e-05     0.012     108     160 ..     166     216 ..     126     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.22
                              TniB 37 nlllvGdsnnGKtmiv 52
                                       l lvG+s  GK++ +
  gi|557694710|ref|YP_008797764.1| 42 TLALVGESGSGKSSTA 57
                                      689*********9865 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.2e-05
                              TniB 108 eqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       +++ +++   +++++Li+DE  ++l   + +q +++n+lk+L+ el ++ + +
  gi|557694710|ref|YP_008797764.1| 166 QRALIAMALITNPKLLILDEPTSAL--DVMTQANVMNLLKKLKKELGLTYIFI 216
                                       4444555556789***********9..8999***************9998876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   3.1e-05     0.032       5     117 ..      40     207 ..      37     222 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.1e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee............................................ 37 
                                          l+++GesG+GK+ ++  + + l++  +a +                                            
  gi|557694710|ref|YP_008797764.1|  40 GETLALVGESGSGKSSTALAIIRLLPRNVAAYRgsiifektelmnlddeefrkrvrvggismvfqgamnsfnpvlrv 116
                                       56789****************99997654444467777766666666666666666666666666666666666665 PP

                            AAA_22  38 ....erpevvfvtlpsstsskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEaqh.lr. 104
                                           ++p vv + +p ++   + +++ l+ +gle++ +     el   + ++al a a    ++lli+DE    l+ 
  gi|557694710|ref|YP_008797764.1| 117 gfqvAEPLVVNMGMPREE-AYKKAEDALELVGLERSMAQRYPFELSgGMKQRALIAMALitnPKLLILDEPTSaLDv 192
                                       555555555555555555.3333455555555555553333444443444444444444666667777766666655 PP

                            AAA_22 105 ..seealeeLrslln 117
                                         ++++++ L++l +
  gi|557694710|ref|YP_008797764.1| 193 mtQANVMNLLKKLKK 207
                                       544666666666655 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 !   10.9   0.0   0.00026      0.27      34      67 ..      26      60 ..      15      85 .. 0.84
   2 ?    4.3   0.0     0.027        29     102     152 ..     171     223 ..     161     228 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                         IstB_IS21 34 kvkeLatlsf.iekkenivllGpsGvGKshlaial 67
                                       v+++ + sf +++ e ++l+G sG GKs  a a+
  gi|557694710|ref|YP_008797764.1| 26 MVRAVDGVSFsVRHGETLALVGESGSGKSSTALAI 60
                                      5677777888577889*************999997 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.027
                         IstB_IS21 102 alkrllkvdllilDd..lgllpldqaeaellfeviekryerrsiiitsnlpfa 152
                                       a++ +++++llilD+   +l  + qa+  +l++ ++k  + + i it +l +a
  gi|557694710|ref|YP_008797764.1| 171 AMALITNPKLLILDEptSALDVMTQANVMNLLKKLKKELGLTYIFITHDLALA 223
                                       45667889******944467788999999999999999999999999988765 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 !   15.9   0.0   7.7e-06    0.0081      13      46 ..      31      64 ..      28      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.7e-06
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      dg +++++  ++  l+G+sGsGKS+   Ai+ lL
  gi|557694710|ref|YP_008797764.1| 31 DGVSFSVRHGETLALVGESGSGKSSTALAIIRLL 64
                                      66778887555999*********98666887776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.1e-05     0.054      20      51 ..      38      67 ..      27      94 .. 0.79
   2 ?   -1.9   0.0       3.6   3.8e+03     101     137 ..     237     273 ..     186     275 .. 0.64
   3 ?   -2.1   0.0       4.3   4.5e+03      53      63 ..     296     306 ..     290     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.1e-05
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekd 51
                                      r g  e + l+GesG+GKss + ++ r l ++
  gi|557694710|ref|YP_008797764.1| 38 RHG--ETLALVGESGSGKSSTALAIIRLLPRN 67
                                      444..7899*************9999877776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 3.6
                            AAA_16 101 leealaavpelagaeasrllellkrllallsrderpl 137
                                       l+++l++++el ++ ++   ell + + +l++d++p+
  gi|557694710|ref|YP_008797764.1| 237 LLAELGPSDELYPQPRHPYTELLINSVPFLRQDKEPT 273
                                       3334447777777777888888888888887777775 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 4.3
                            AAA_16  53 giflrgkcdql 63 
                                        +f++gkcd +
  gi|557694710|ref|YP_008797764.1| 296 PYFIKGKCDVS 306
                                       79*******98 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 ?   12.5   0.0   4.3e-05     0.045     324     371 ..     161     208 ..     157     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.3e-05
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG- CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskeke 371
                                       SG + q a i+ al  + kll++DE tsA   m + + m+ l + +ke
  gi|557694710|ref|YP_008797764.1| 161 SGGMKQRALIAMALITNPKLLILDEPTSALDVMTQANVMNLLKKLKKE 208
                                       9*********************************99999988765555 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 ?   12.8   0.0   8.6e-05      0.09       3      34 ..      44      75 ..      42      97 .. 0.86
   2 ?   -2.4   0.0       4.1   4.4e+03      58      88 ..     170     201 ..     150     206 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.6e-05
                                      EEE--SSSSHHHHHHHGGGGBS--EEEEE--T CS
                             AAA_5  3 lLvGppGtgKselaerlaaalnreveyvqltr 34
                                       LvG++G+gKs+ a  + ++l r+v  + ++ 
  gi|557694710|ref|YP_008797764.1| 44 ALVGESGSGKSSTALAIIRLLPRNVAAYRGSI 75
                                      69*******************99998887665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.1
                                       -------G-SEEEEESGGG--.HHHHHHHHHH CS
                             AAA_5  58 plvraaregeilvlDEverae.sevlnsLlsl 88 
                                       +++  ++++++l+lDE + a    +++ +++l
  gi|557694710|ref|YP_008797764.1| 170 IAMALITNPKLLILDEPTSALdVMTQANVMNL 201
                                       34444458888888887766634445555555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00031      0.33      86     116 ..      26      57 ..       2      75 .. 0.75
   2 ?   -0.9   0.0       1.3   1.3e+03      50      83 ..      74     105 ..      56     129 .. 0.80
   3 ?    0.4   0.0       0.5   5.3e+02      56     106 ..     190     235 ..     164     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00031
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHH CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLi 116
                                         ++++ ++  +++ +t +lvG+SG GKS+  
  gi|557694710|ref|YP_008797764.1|  26 MVRAVDGVSFSVRHgETLALVGESGSGKSSTA 57 
                                       4566677777777769*************965 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                                       EEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE-- CS
                       RsgA_GTPase  50 vivlnKiDlleeeeeleelkeelealgyevllvs 83 
                                        i++ K++l++ ++  ee++++++  g+++++  
  gi|557694710|ref|YP_008797764.1|  74 SIIFEKTELMNLDD--EEFRKRVRVGGISMVFQG 105
                                       69999999999999..888888888888777765 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.5
                                       GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEEC CS
                       RsgA_GTPase  56 iDlleeeeeleelkeelealgyevllvsaktkegleelkellkdktsvlvG 106
                                       +D++++++ ++ lk+  ++lg++ +++  +      +l+++l+d+++v+ G
  gi|557694710|ref|YP_008797764.1| 190 LDVMTQANVMNLLKKLKKELGLTYIFITHD-----LALASELADRVAVMYG 235
                                       688888887888888888999999999666.....7899999999999887 PP

>> Hpr_kinase_C  HPr Serine kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00023      0.24      10      41 ..      31      63 ..      25     102 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                                      ESEEEEE.TTEEEEEEESTCHHHHHHHHHHHTT CS
                      Hpr_kinase_C 10 hGvlvdv.ygvGvLitGesgvGKselaleLikr 41
                                       Gv  +v +g  + ++Gesg GKs +al +i+ 
  gi|557694710|ref|YP_008797764.1| 31 DGVSFSVrHGETLALVGESGSGKSSTALAIIRL 63
                                      566666645777889**************9975 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 ?   10.4   0.0   0.00032      0.34      28      60 ..      35      67 ..      24      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                             AAA_7 28 lllknkkpvllvGptGtGKtviikdllkkldke 60
                                        ++++  + lvG++G+GK++++  +++ l+++
  gi|557694710|ref|YP_008797764.1| 35 FSVRHGETLALVGESGSGKSSTALAIIRLLPRN 67
                                      56899999**************99999888844 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 ?   10.7   0.1    0.0005      0.53       2      38 ..      44      91 ..      43     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0005
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS...........S CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgsellsk...........y 38
                                       l+G  G GK+++a a+++ l +++    gs +++k            
  gi|557694710|ref|YP_008797764.1| 44 ALVGESGSGKSSTALAIIRLLPRNVAAYRGSIIFEKtelmnlddeefR 91
                                      599*****************9777666666666655444333333331 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00029       0.3       2      22 ..      42      62 ..      41      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                                      EEEEESSTTSSHHHHHHHHHT CS
                              AIG1  2 tivlvGktgnGkSaTgNsilg 22
                                      t+ lvG +g+GkS+T+ +i++
  gi|557694710|ref|YP_008797764.1| 42 TLALVGESGSGKSSTALAIIR 62
                                      788************999985 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   0.1   0.00035      0.37      26      48 ..      43      65 ..      33      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00035
                             DUF87 26 lAilgsTGsGKSntvavLleell 48
                                      lA +g++GsGKS t+  +++ l 
  gi|557694710|ref|YP_008797764.1| 43 LALVGESGSGKSSTALAIIRLLP 65
                                      799***************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2365.45
//
Query:       gi|557694711|ref|YP_008797765.1|  [L=331]
Description: peptide/nickel ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  112.9   0.0      2e-32  112.6   0.0    1.1  1  ABC_tran      ABC transporter
    2.5e-19   69.6   0.1    3.9e-19   68.9   0.1    1.3  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
     0.0012   19.2   0.0     0.0021   18.4   0.0    1.5  1  AAA_16        AAA ATPase domain
     0.0029   17.1   0.0      0.013   15.0   0.0    1.8  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0049   16.7   0.9       0.14   12.0   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
  ------ inclusion threshold ------
      0.012   15.9   1.1       0.04   14.2   1.1    1.9  1  AAA_22        AAA domain
      0.012   15.3   0.1      0.025   14.3   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.017   15.0   0.1      0.032   14.1   0.1    1.4  1  RsgA_GTPase   RsgA GTPase
      0.052   13.6   0.0      0.094   12.8   0.0    1.4  1  MMR_HSR1      50S ribosome-binding GTPase
      0.055   13.2   0.1       0.11   12.2   0.1    1.5  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.069   13.6   0.3       0.11   13.0   0.3    1.6  1  AAA           ATPase family associated with various cellular 
      0.071   13.0   0.7       0.13   12.2   0.6    1.6  1  NACHT         NACHT domain
      0.076   12.7   0.1       0.16   11.7   0.1    1.5  1  IstB_IS21     IstB-like ATP binding protein
      0.084   12.2   0.0       0.14   11.5   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.12   11.9   0.1       0.19   11.2   0.1    1.3  1  AAA_7         P-loop containing dynein motor region
       0.13   12.3   0.3        0.3   11.1   0.3    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
       0.17   11.9   0.2        0.3   11.1   0.2    1.4  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
       0.23   10.0   0.5          1    8.0   0.0    1.8  2  AAA_13        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 !  112.6   0.0     2e-35     2e-32       2     136 ..      32     184 ..      31     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 2e-35
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfpe 73 
                                       + v+l++ + e+va+vGe+G+GK+tL ++l+gl+kp++G+il+dg dl++   +el+ +r+++gv++q+  ++l+p 
  gi|557694711|ref|YP_008797765.1|  32 DGVNLSIGRKETVALVGESGCGKTTLGRALLGLVKPKSGKILFDGIDLTTlgeRELKLMRRRMGVVFQDpyASLNPS 108
                                       789*************************************************9****************999***** PP

                                       SBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        tv++               e++e + kal++++l+  ++  +++ p+ LSgGq+qrva+ara+++kp++++ DEp 
  gi|557694711|ref|YP_008797765.1| 109 FTVYRIveeplvvnkigtgeERREMVLKALEEVKLNP-AEFFASKYPHMLSGGQRQRVAIARAIITKPEFVVTDEPV 184
                                       **9999999********88666666999999999988.777888889*****************************7 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 !   68.9   0.1   3.9e-22   3.9e-19       1      65 []     236     303 ..     236     303 .. 0.91

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 3.9e-22
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd..klekikgeapslerldeGCpFapRCpfalee.C 65 
                                       vE+gp++++++ep+HPYT+aL++++p++d+ ++    +   g++psl + ++GC+F+pRCpf ++  C
  gi|557694711|ref|YP_008797765.1| 236 VETGPTKAVLSEPRHPYTQALVDAIPDPDPANRfvMRKVPVGQPPSLVNPPKGCRFHPRCPFFMPGkC 303
                                       8********************************955555668888*****************998756 PP

>> AAA_16  AAA ATPase 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    0.0021      20      50 ..      37      67 ..      28     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.1e-06
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralek 50
                                      + gr e v l+GesG+GK++l r+ll  ++ 
  gi|557694711|ref|YP_008797765.1| 37 SIGRKETVALVGESGCGKTTLGRALLGLVKP 67
                                      67899******************99955544 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   0.0   1.3e-05     0.013      24     205 ..      41     223 ..      25     236 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                       SSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  24 ksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsis 100
                                       k+  a+vG+ G+GK+ l  A+l +   +s  k+  + + dl +  +++ ++++ ++ ++f+++ ++    ++++++ 
  gi|557694711|ref|YP_008797765.1|  41 KETVALVGESGCGKTTLGRALLGLVKPKSG-KILFDGI-DLTTLGERELKLMRRRMGVVFQDPYAS---LNPSFTVY 112
                                       567899***************333333333.3333333.4444468899999999*****999998...67777777 PP

                                       EEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 101 rrvkrkgeseykingkevtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDeid 168
                                       r v++      ki   e +++ v + le++++++          +LSgG+++ va+a    i  + +  +++ De  
  gi|557694711|ref|YP_008797765.1| 113 RIVEEPLV-VNKIGTGEERREMVLKALEEVKLNPAeffaskyphMLSGGQRQRVAIARA--I--ITKPEFVVTDEPV 184
                                       76665554.66788888889999999999999999999999999********9998754..3..3445699****** PP

                                       TTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                             SMC_N 169 aaLDeknvkkvaellkekskn..aQfivislreemleka 205
                                       + LD++ + ++  l++e +k+  + f+ i+++  + +  
  gi|557694711|ref|YP_008797765.1| 185 SMLDASIRVEILLLFREIQKKhsVSFLYITHDLATAKYF 223
                                       ******999999999976655448899999987776655 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 !   12.0   0.1   0.00014      0.14       3      23 ..      45      65 ..      44     140 .. 0.72
   2 ?    3.2   0.1     0.063        63     237     299 ..     157     217 ..     152     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                            AAA_21  3 vliGpNgsGKSnLLdaldlla 23
                                      +l+G  g+GK++L +al +l 
  gi|557694711|ref|YP_008797765.1| 45 ALVGESGCGKTTLGRALLGLV 65
                                      79***************9982 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.063
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                       lS G+++  a++ a++  +    +++ DEp + L+ ++  ++l l++e ++ + + ++  TH+ 
  gi|557694711|ref|YP_008797765.1| 157 LSGGQRQRVAIARAIITKP---EFVVTDEPVSMLDASIRVEILLLFREIQKkHSVSFLYITHDL 217
                                       5677776656666666555...99999****************99966666688********96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.1     4e-05      0.04       7      29 ..      43      65 ..      38     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                       ++++GesG+GKTtl r ll   
  gi|557694711|ref|YP_008797765.1| 43 TVALVGESGCGKTTLGRALLGLV 65
                                      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 ?   14.3   0.1   2.5e-05     0.025      13      50 ..      32      69 ..      28      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.5e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      dg  ++i +k+++ l+G+sG GK+Tl  A+  l  p++
  gi|557694711|ref|YP_008797765.1| 32 DGVNLSIGRKETVALVGESGCGKTTLGRALLGLVKPKS 69
                                      677889999999**************888887777766 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   3.2e-05     0.032      98     126 ..      40      68 ..      15      75 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                                       TTSEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelk 126
                                       +++t++lvG+SG GK+tL  all+  + k
  gi|557694711|ref|YP_008797765.1|  40 RKETVALVGESGCGKTTLGRALLGLVKPK 68 
                                       45899*************99998866555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   9.5e-05     0.094       2      31 ..      44      74 ..      43      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.5e-05
                                      EEEEESTTSSHHHHHHHHHTS.TEEESSSTT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsdkpg 31
                                      va+vG +  GK+tL +al+g  k + +++ +
  gi|557694711|ref|YP_008797765.1| 44 VALVGESGCGKTTLGRALLGLvKPKSGKILF 74
                                      9******************975666666655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00011      0.11       3      23 ..      43      63 ..      41      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
                         PduV-EutP  3 killiGkvgsGKttLtqalkg 23
                                       + l+G++g+GKttL +al g
  gi|557694711|ref|YP_008797765.1| 43 TVALVGESGCGKTTLGRALLG 63
                                      5889************99865 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 ?   13.0   0.3   0.00011      0.11       2      23 ..      45      66 ..      44     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00011
                                      EEESSTTSSHHHHHHHHHHHHT CS
                               AAA  2 llyGppGtGKTllakavakelg 23
                                       l+G  G+GKT+l +a+   ++
  gi|557694711|ref|YP_008797765.1| 45 ALVGESGCGKTTLGRALLGLVK 66
                                      699*************998775 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.6   0.00013      0.13       2      21 ..      43      62 ..      42      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      +v+l Ge+G+GKTtL + l 
  gi|557694711|ref|YP_008797765.1| 43 TVALVGESGCGKTTLGRALL 62
                                      89*************87775 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 ?   11.7   0.1   0.00016      0.16      44      67 ..      38      61 ..      27      81 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                         IstB_IS21 44 iekkenivllGpsGvGKshlaial 67
                                      i +ke ++l+G sG GK+ l  al
  gi|557694711|ref|YP_008797765.1| 38 IGRKETVALVGESGCGKTTLGRAL 61
                                      789*****************9997 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.14       6      52 ..      25      71 ..      21     108 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                      Mg_chelatase  6 kGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplsee 52
                                      +G+ +a   +++++  +  + lvG +G+GKt l ++l +l+ p s +
  gi|557694711|ref|YP_008797765.1| 25 VGEVKAVDGVNLSIGRKETVALVGESGCGKTTLGRALLGLVKPKSGK 71
                                      57777788888888888999*******************99887765 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   0.1   0.00019      0.19      25      58 ..      33      66 ..      19      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                             AAA_7 25 llelllknkkpvllvGptGtGKtviikdllkkld 58
                                       ++l + +k  v lvG++G+GKt++ + ll  ++
  gi|557694711|ref|YP_008797765.1| 33 GVNLSIGRKETVALVGESGCGKTTLGRALLGLVK 66
                                      5678889999**************9888776555 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 ?   11.1   0.3   0.00031       0.3       2      23 ..      44      65 ..      43      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                                      EEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                      v LvG++G+gK++l + l+ ++
  gi|557694711|ref|YP_008797765.1| 44 VALVGESGCGKTTLGRALLGLV 65
                                      679************9998876 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   0.00031       0.3      19      40 ..      41      62 ..      20      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                                      TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                      +++++L G+ G+GKTtl r+l+
  gi|557694711|ref|YP_008797765.1| 41 KETVALVGESGCGKTTLGRALL 62
                                      678***************9987 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      0.27   2.7e+02      23      39 ..      48      64 ..      45      88 .. 0.84
   2 ?    8.0   0.0     0.001         1     524     581 ..     172     227 ..     164     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.27
                            AAA_13 23 GwNGaGKTtLSrllrsl 39
                                      G  G GKTtL r+l  l
  gi|557694711|ref|YP_008797765.1| 48 GESGCGKTTLGRALLGL 64
                                      7789********99776 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.001
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkknt 581
                                       i+k + vv D PvS LD+ +   +  l ++    kk+   ++  TH l   k++++++
  gi|557694711|ref|YP_008797765.1| 172 ITKPEFVVTDEPVSMLDASIRVEILLLFREIQ--KKHSVSFLYITHDLATAKYFSDKI 227
                                       68999********************9999986..6666666667****9999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 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:                        88  (0.00490825); 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: 00:00:00.42
# Mc/sec: 2358.27
//
Query:       gi|557694712|ref|YP_008797766.1|  [L=240]
Description: hypothetical protein CSUB_C1285 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00072   18.6   0.6    0.00087   18.3   0.6    1.1  1  MFS_1      Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.028   14.2   2.0      0.029   14.2   0.1    2.1  2  TnpW       Transposon-encoded protein TnpW
        0.2   11.6   1.6        0.3   11.0   1.6    1.2  1  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


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 !   18.3   0.6   1.5e-07   0.00087     124     184 ..     155     216 ..     137     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-07
                             MFS_1 124 gllsagfslGailgpllgglla.sslgWravfyilaivsllafvlfllllpeepperkrksp 184
                                       +++++++ l ++l  +++++l+ s++  r+++++ +iv++   v ++ l+++e+ ++  +++
  gi|557694712|ref|YP_008797766.1| 155 AVVALFIILTPALWIAISSFLTeSLFYPRWAMILSGIVGIGITVYVVRLYFRENFPELFEKT 216
                                       7899999***************99999*****************777777777776665555 PP

>> TnpW  Transposon-encoded protein TnpW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3       0.9   5.4e+03       5      10 ..     117     122 ..     116     124 .. 0.87
   2 ?   14.2   0.1   4.8e-06     0.029       5      20 ..     194     209 ..     191     215 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.9
                              TnpW   5 IGgTTY 10 
                                       IG+T Y
  gi|557694712|ref|YP_008797766.1| 117 IGKTFY 122
                                       9***88 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.8e-06
                              TnpW   5 IGgTTYvVrvhFseta 20 
                                       IG T+YvVr++F+e+ 
  gi|557694712|ref|YP_008797766.1| 194 IGITVYVVRLYFRENF 209
                                       888***********97 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.6     5e-05       0.3      67     115 ..     158     205 ..     144     214 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5e-05
                         RseC_MucC  67 allvYllPllllilgallgsallgssellaalgallglvlgflivrlls 115
                                       al++ l+P l + ++ +l ++l +   ++ +l +++g+ +++++vrl+ 
  gi|557694712|ref|YP_008797766.1| 158 ALFIILTPALWIAISSFLTESL-FYPRWAMILSGIVGIGITVYVVRLYF 205
                                       3444578***************.8**********************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1839.12
//
Query:       gi|557694713|ref|YP_008797767.1|  [L=495]
Description: multicomponent Na+:H+ antiporter subunit D [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  273.3  27.1    2.3e-81  273.3  27.1    1.8  2  Proton_antipo_M  Proton-conducting membrane transporter
    2.7e-11   43.4   0.4    1.3e-10   41.2   0.4    2.3  1  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 ?   -3.5   0.3      0.52   4.7e+03      43      51 ..      40      48 ..      11      72 .. 0.55
   2 !  273.3  27.1   2.5e-85   2.3e-81       2     293 .]     137     430 ..     136     430 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.52
                   Proton_antipo_M 43 llgsliLLl 51
                                      l++s++LL+
  gi|557694713|ref|YP_008797767.1| 40 LFSSVVLLV 48
                                      233333333 PP

  == domain 2  score: 273.3 bits;  conditional E-value: 2.5e-85
                   Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal..elgl 76 
                                       ++L+l+y+++El+l+p+y Li++w++  +    ++k+f+ t +g l+LL+gi++l ++ g+l++  ls+ +      
  gi|557694713|ref|YP_008797767.1| 137 SNLFLFYIFWELMLIPSYALIAYWGTG-NPRLIGFKYFIFTHAGALSLLIGIAWLAAVFGDLNIFSLSEKAmlASET 212
                                       59**********************999.55567***********************************997665566 PP

                   Proton_antipo_M  77 nslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqllli 152
                                         + l+ +++l+++g++vK+a++p+h+Wlpda+ eaPtp+s+ll++++ k gv++++rl+l ++ +   +++  ++i
  gi|557694713|ref|YP_008797767.1| 213 LRPVLTSIAVLIFIGAAVKMAVFPFHTWLPDAHAEAPTPISVLLSGVMIKTGVYAVARLVLGIMpFTMMDLRLPIAI 289
                                       667889999**************************************************9999989*********** PP

                   Proton_antipo_M 153 laiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerekt 229
                                       la+ism+ g+++al+q+d+KrllAySsis++Gy++ +la+a+  gv++a++h+l h++ k+llF++ag +i+e  ++
  gi|557694713|ref|YP_008797767.1| 290 LALISMVWGGVMALVQSDVKRLLAYSSISQIGYIVFGLAAANLAGVQGALFHVLNHGFAKSLLFMAAGVLIHEV-HE 365
                                       *******************************************************************7777665.9* PP

                   Proton_antipo_M 230 rdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvlt 293
                                       rdir++ggL+ kmP++ +++lv+ ls+aG+Pp+ gF+s+++i+++ v++++ ++v++ v+a+++t
  gi|557694713|ref|YP_008797767.1| 366 RDIRKLGGLSSKMPLTTIAMLVGGLSIAGTPPLGGFMSEWMIFAGGVEAGWSIFVAVaVFATAIT 430
                                       ***************************************************9999998***9997 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 !   41.2   0.4   1.4e-14   1.3e-10       2      57 ..      70     123 ..      69     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.4e-14
                   Proton_antipo_N   2 ftWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57 
                                       ++W+++    +++g+ lD+ls  ++l++t+v++l  +YS +YM+++ g + +f++l
  gi|557694713|ref|YP_008797767.1|  70 YEWVPFL--GLSVGLVLDSLSYPFVLLITLVGFLATVYSGKYMEKEHGLTSYFTLL 123
                                       6888855..489*****************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (495 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); 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:                         7  (0.000390429); expected 0.2 (1e-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 0.23s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3640.61
//
Query:       gi|557694714|ref|YP_008797768.1|  [L=468]
Description: hypothetical protein CSUB_C1287 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   35.1   3.0    3.2e-07   30.2   2.4    2.5  2  V4R       V4R domain


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.8   0.0    0.0066   1.2e+02       4      38 ..     304     338 ..     301     340 .. 0.91
   2 !   30.2   2.4   1.8e-11   3.2e-07       2      61 ..     404     465 ..     403     466 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.0066
                                       EEEEES-S-TT---SS---HHHHHHHHHHHHHHHS CS
                               V4R   4 sieespelaglpgkeePvCyleaGllagalsellg 38 
                                        +e s++++  ++ ++++   +++ +++++++ +g
  gi|557694714|ref|YP_008797768.1| 304 PVERSFLAEKVGNYGQKLAVVFTAGFEELAETVTG 338
                                       589**************************999876 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 1.8e-11
                                       -EEEEEES-S-TT---SS---..HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEEEE CS
                               V4R   2 elsieespelaglpgkeePvC..yleaGllagalsellgkrveveEveCaaeGhdhCeFeve 61 
                                       +++++++p++ +l  +e+P++  +++   l+ga+   l+  vev E eC ++G+++C+F+v+
  gi|557694714|ref|YP_008797768.1| 404 VVEVKSCPVCGELDTIEDPQHcqEAFSPMLSGAARAVLKTGVEVSELECSGKGGKKCVFVVK 465
                                       7899****************944467799*******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3208.20
//
Query:       gi|557694715|ref|YP_008797769.1|  [L=637]
Description: NADH dehydrogenase I subunit L [Candidatus Caldiarchaeum subterraneum]
Scores for 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-84  283.3  19.8      2e-84  283.3  19.8    2.6  3  Proton_antipo_M  Proton-conducting membrane transporter
    3.2e-19   68.8   0.4    2.4e-17   62.7   0.1    3.3  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
    5.9e-06   26.1   2.6      0.037   13.6   0.0    2.5  2  Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I
      0.002   17.7   0.0      0.002   17.7   0.0    3.1  3  NADH5_C          NADH dehydrogenase subunit 5 C-terminus


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 !    3.2   0.9    0.0092        41     115     159 ..      83     130 ..      41     133 .. 0.75
   2 !  283.3  19.8   4.4e-88     2e-84       1     292 [.     133     436 ..     133     437 .. 0.92
   3 ?   -3.0   0.0      0.75   3.3e+03     145     162 ..     467     484 ..     461     495 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.0092
                   Proton_antipo_M 115 pvsallAatlvkagvlllirlllllavssneis...qlllilaiisml 159
                                       p s+l+A+++  +g l+++  +  +a+ ++  +   ++l++++ +++l
  gi|557694715|ref|YP_008797769.1|  83 PLSVLMASIATGIGSLIVLYSVGYMAHEEGLPRyyfYMLFFIGGMTLL 130
                                       679****************99999985555544001555566666665 PP

  == domain 2  score: 283.3 bits;  conditional E-value: 4.4e-88
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal....e 73 
                                       +++Ll+ly+g+E+v+l++y Li ++ kkp++++A++k+f++t++g+ ++L+gil+l++l gt +  elsk +     
  gi|557694715|ref|YP_008797769.1| 133 SENLLMLYIGWEIVGLCSYGLISFYNKKPEANHAGIKAFVTTRIGDASMLVGILILFALFGTFSYSELSKSIaeglR 209
                                       78*********************************************************************999995 PP

                   Proton_antipo_M  74 lglnslellll.lllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirllllla.......v 141
                                       +g+ s ++l++ llll+ g++ Ksaq+plh+Wlpda +e+Ptpvsal+ Aat+vkagv+l++r++  ++        
  gi|557694715|ref|YP_008797769.1| 210 TGVVSAGFLVIpLLLLFGGAVGKSAQFPLHVWLPDA-MEGPTPVSALIhAATMVKAGVYLVARMIYTVIpfeefppA 285
                                       6666666555516778889*****************.***************************9877654444444 PP

                   Proton_antipo_M 142 ssneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFll 218
                                          +++ ++++la  +++++++++l+ +diKr++AyS+is+lG+ml al++++++g+ +  +hll+h++fkallFl+
  gi|557694715|ref|YP_008797769.1| 286 LFADWYLIVATLAGFTAFFAATMGLVSNDIKRVIAYSTISQLGLMLAALGMGSEIGLFGGTFHLLSHSIFKALLFLA 362
                                       5678************************************************************************* PP

                   Proton_antipo_M 219 agsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasvl 292
                                       ag+vi++  +t++++++ggL+k+mPi++++ +v++lsl+G+P+++gF+sk+l++e+++++  i + l+ + as+l
  gi|557694715|ref|YP_008797769.1| 363 AGAVIHAV-HTNNLDEMGGLRKSMPITFWTSAVGVLSLSGVPLFSGFWSKDLVIESSLQALNIPVYLFiTGASIL 436
                                       ****9987.9************************************************99888777774666666 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.75
                   Proton_antipo_M 145 eisqlllilaiismllgs 162
                                        +++ l+ila++s+++g 
  gi|557694715|ref|YP_008797769.1| 467 VMTIPLIILAALSVFIGV 484
                                       567788899999999885 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 !   62.7   0.1   5.5e-21   2.4e-17       3      57 ..      65     120 ..      64     121 .. 0.94
   2 ?    2.1   0.0     0.046   2.1e+02      18      44 ..     419     445 ..     410     459 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 5.5e-21
                   Proton_antipo_N   3 tWlsvgg.lsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayl 57 
                                        W++ gg   ie ++l+D+ls+lm+ + t++++l+ lYS+gYMa++eg +R+++y+
  gi|557694715|ref|YP_008797769.1|  65 PWIPLGGdRFIEASLLVDPLSVLMASIATGIGSLIVLYSVGYMAHEEGLPRYYFYM 120
                                       6999665499*********************************************8 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.046
                   Proton_antipo_N  18 lDklsalmllvvtfvsllvhlYSigYM 44 
                                       l  l + + l++t+ s l   YS+  +
  gi|557694715|ref|YP_008797769.1| 419 LQALNIPVYLFITGASILTVAYSLRWL 445
                                       5668888999*************8765 PP

>> Proton_antipo_C  NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   8.3e-06     0.037      93     124 ..     461     492 ..     445     498 .. 0.87
   2 !   11.6   0.7   3.6e-05      0.16     215     242 ..     552     579 ..     545     580 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.3e-06
                   Proton_antipo_C  93 PhEsdntmlfpllvLvlftlfvGliGipfnqe 124
                                        hE+++ m++pl++L+ +++f+G+ G  f++e
  gi|557694715|ref|YP_008797769.1| 461 VHEAPKVMTIPLIILAALSVFIGVAGPFFEEE 492
                                       59***********************9877765 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.6e-05
                   Proton_antipo_C 215 ynrgYiDvfYekvlvkgiRrLaeltsff 242
                                        nr YiD+fY kv+v+g+ rL  +++ f
  gi|557694715|ref|YP_008797769.1| 552 ENRYYIDAFYYKVFVNGLDRLGSIIYRF 579
                                       599******************9999877 PP

>> NADH5_C  NADH dehydrogenase subunit 5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   1.0      0.48   2.1e+03     141     179 ..      92     130 ..      83     141 .. 0.65
   2 ?   -3.4   0.1       1.4   6.1e+03     156     176 ..     417     437 ..     410     438 .. 0.82
   3 !   17.7   0.0   4.5e-07     0.002       1      45 [.     440     484 ..     440     486 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.48
                           NADH5_C 141 pkglaklllklskliqnlqkglikiyLlsflltllllll 179
                                       + g+ +l++ +s  + + ++gl + y+ +++++  ++ll
  gi|557694715|ref|YP_008797769.1|  92 ATGIGSLIVLYSVGYMAHEEGLPRYYFYMLFFIGGMTLL 130
                                       456666666677777777777766666655555444444 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.4
                           NADH5_C 156 qnlqkglikiyLlsflltlll 176
                                       ++lq  +i +yL+++  ++l+
  gi|557694715|ref|YP_008797769.1| 417 SSLQALNIPVYLFITGASILT 437
                                       678889999999999988875 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 4.5e-07
                           NADH5_C   1 YSlRliyyvllgsprfsslspineenptllnpilrLalgsiiaGs 45 
                                       YSlR++y v+l  p+    ++++e  + ++ p+++La +s++ G+
  gi|557694715|ref|YP_008797769.1| 440 YSLRWLYKVFLAPPSNGHHNHVHEAPKVMTIPLIILAALSVFIGV 484
                                       ******************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 4613.77
//
Query:       gi|557694716|ref|YP_008797770.1|  [L=110]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-24   83.4   0.1    8.5e-24   83.3   0.1    1.0  1  CutA1     CutA1 divalent ion tolerance protein
  ------ inclusion threshold ------
       0.17   11.6   0.1       0.25   11.1   0.1    1.3  1  L27       L27 domain


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 !   83.3   0.1   9.5e-28   8.5e-24       3      98 ..       5      99 ..       3     100 .. 0.95

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 9.5e-28
                                      EEEEESSHHHHHHHHHHHHHTTS-SEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEGGGHHHHHHHHHHHSSSSS-EEE CS
                             CutA1  3 vlvtapseeeakklaralveeklaACvnilpkieSvYrWkgkieedkEvllliktreekveelekrvkelhpyevpeii 81
                                      +lv +p + +  + +r+lv+++laA++n  + + S++ W+++++e +Evll+ikt+++k++el k++++ hpy vp+ii
  gi|557694716|ref|YP_008797770.1|  5 FLVPYPRDRDYASWCRSLVSRRLAASINAAN-VVSFFLWENRLNEVEEVLLFIKTSSAKADELRKVLESEHPYRVPAII 82
                                      567778888889999*************988.*********************************************** PP

                                      EEEESEEEHHHHHHHHH CS
                             CutA1 82 alpieagseaYlkWiee 98
                                      +++ e+++++Yl+W+ e
  gi|557694716|ref|YP_008797770.1| 83 EISPEKVNTKYLEWVVE 99
                                      **************986 PP

>> L27  L27 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   2.8e-05      0.25      16      32 ..      58      74 ..      44      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.8e-05
                               L27 16 dvnedlaeLqkvLqsph 32
                                       ++ ++ eL+kvL+s+h
  gi|557694716|ref|YP_008797770.1| 58 TSSAKADELRKVLESEH 74
                                      45689**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 863.50
//
Query:       gi|557694717|ref|YP_008797771.1|  [L=179]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-21   74.1   0.1    8.1e-21   73.5   0.1    1.4  1  DUF309           Domain of unknown function (DUF309)
     0.0081   15.0   0.0     0.0081   15.0   0.0    1.1  1  Pneumo_ncap      Pneumovirus nucleocapsid protein
  ------ inclusion threshold ------
      0.025   14.2   0.0      0.031   13.9   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
       0.11   12.8   0.1       0.23   11.7   0.1    1.5  1  UPF0102          Uncharacterised protein family UPF0102


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 !   73.5   0.1   1.8e-24   8.1e-21       2      58 ..      78     134 ..      77     135 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 1.8e-24
                            DUF309   2 eeaielfnegeffeaHEvlEelWkeageperkllqglIqlAvAlyhlrrgnvrgakr 58 
                                       ++a+ lfn ++f+eaHE+lE lW++a++pe+++l+glI  A+A++hl+++ v+g ++
  gi|557694717|ref|YP_008797771.1|  78 KKAVTLFNSERFWEAHETLEPLWRQAKPPEKEILHGLILTAAAFVHLQKNDVKGFRS 134
                                       6899*******************999999*************************875 PP

>> Pneumo_ncap  Pneumovirus nucleocapsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.8e-06    0.0081     151     216 ..     101     168 ..      20     176 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-06
                       Pneumo_ncap 151 rhdapdtgiil..lcvaalvitklaatievGleavvrranrvlkdelkrykrldipkiarsfyelfek 216
                                       r+  p    il  l ++a  +  l   +  G+ +++rra + l+++ k y+++ i  + +   +++e+
  gi|557694717|ref|YP_008797771.1| 101 RQAKPPEKEILhgLILTAAAFVHLQKNDVKGFRSILRRALKALSNAPKTYQGISIDSLRKEIEHVMEN 168
                                       55444444443346778889999********************************9988888877775 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.8e-06     0.031     158     202 ..      61     104 ..      42     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.8e-06
                                       BEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSC CS
                   NTP_transferase 158 rverfvEKPkeakaselassGiYvfnsevllflakdleelkrged 202
                                       ++ +++EKP+ a+ se++++ + +fnse + ++ + le+l+r+++
  gi|557694717|ref|YP_008797771.1|  61 AILEITEKPASAP-SETIKKAVTLFNSERFWEAHETLEPLWRQAK 104
                                       8999*********.*******************77*****98764 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1     5e-05      0.23      10      67 ..      26      92 ..      20      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5e-05
                                      HHTT-EEEEEEEEETTEEEEEEE........TTEEEEEEEEE-.......-------HHHHHHHHHH CS
                           UPF0102 10 ekkgyeilernwrcragEiDiia........tevlvfvEVKtR.ssekfgspaeavtprKqrrlrra 67
                                      ++kg+++++ ++ +++ E+Di          +ev+++ E+  + +s+ +++ ++avt    +r ++a
  gi|557694717|ref|YP_008797771.1| 26 RTKGLKVVDVRVATNHVEVDILHerapelsgEEVIAILEITEKpASAPSETIKKAVTLFNSERFWEA 92
                                      789***************************9899******999555556788888887777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1414.84
//
Query:       gi|557694718|ref|YP_008797772.1|  [L=243]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   96.7  20.5    1.7e-20   73.7  14.5    2.1  2  ECF-ribofla_trS  ECF-type riboflavin transporter, S component
    6.2e-06   26.4  17.2    6.2e-06   26.4  17.2    2.1  2  ECF_trnsprt      ECF transporter, substrate-specific componen
    0.00033   20.2  26.0    0.00073   19.1  10.6    2.6  2  5TM-5TMR_LYT     5TMR of 5TMR-LYT


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 !   73.7  14.5   2.8e-24   1.7e-20       5     137 ..       4     135 ..       1     153 [. 0.81
   2 !   26.9   0.4   6.7e-10     4e-06      94     171 ..     161     233 ..     146     234 .. 0.82

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 2.8e-24
                                       THHHHHHHHHHHHHHHHHH---B-S.SS-B--TTHHHHHHHHHHSS--STHHHHHHHHHHHHHHHSS-GGGHHHHHH CS
                   ECF-ribofla_trS   5 kkvvatailaAlvvvltlfisIplpantegsinlgdavlalaallfGpvvGflvGaiGsalaDllsgYgiwapftli 81 
                                        +v+++ +++Alv+++t+++s+  p  t g++nlg+++++laal+ GpvvG+++G++GsalaD+l gY+++ap tl+
  gi|557694718|ref|YP_008797772.1|   4 SEVALLVVFTALVAAATMILSVYFP-LTRGYFNLGETMVYLAALVGGPVVGAFAGGVGSALADVLLGYTAFAPGTLL 79 
                                       57889999***************99.999************************************************ PP

                                       HHHHHHHHHHHH--S-S-SSH...HHHHHHHHHHHHHH...HHHHHHHHHH........ CS
                   ECF-ribofla_trS  82 ikgliGlivGliakklkknkengvfkilalvlfaivmv...igyviaegllpildiiiy 137
                                       ik+ +G +++++ ++l++    + + + a+v++  +++   +g +++ g++   +i++y
  gi|557694718|ref|YP_008797772.1|  80 IKAAEGATAAILYRRLRNVSVPNALLLSAIVVGLYFGIlvsVGVFLMSGIV---EITLY 135
                                       ****************77777666666666665555551114555555555...44444 PP

  == domain 2  score: 26.9 bits;  conditional E-value: 6.7e-10
                                       --S-S-SSH...HHHHHHHHHHHHHHHHHHHHHHHH..........S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                   ECF-ribofla_trS  94 akklkknkengvfkilalvlfaivmvigyviaegllpildiiiysepaekvalqsipaniiqavvgaiialpLlkal 170
                                       a++  ++ke + + + +l+l+++vmv+gy++ e l+     +        + l+++p ni q+vvg  +a+p++ka+
  gi|557694718|ref|YP_008797772.1| 161 AYYGFRRKEYEAWLVGSLLLAGLVMVAGYFLYESLA-----VFLGVLPDILPLAEVPLNIGQVVVGSAVAIPIYKAV 232
                                       34444556666788888*******************.....666778899*************************98 PP

                                       H CS
                   ECF-ribofla_trS 171 a 171
                                       +
  gi|557694718|ref|YP_008797772.1| 233 R 233
                                       6 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4  17.2     1e-09   6.2e-06       3     126 ..      10     125 ..       5     132 .. 0.86
   2 ?    2.4  10.8     0.024   1.5e+02      36     121 ..     108     198 ..     102     232 .. 0.63

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1e-09
                                       HHHHHHHHHHHHHHHHHHEEE.STSEEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHHHHHHHH CS
                       ECF_trnsprt   3 lvitglliAisivlsllgyiplpnikitiihipvllggllfGpikGailgiitsvlkailtggtgalssfvpiafls 79 
                                       +v+t+l +A  ++ls   y+pl +  + +    v+l++l+ Gp++Ga++g+++s l+ +l  g +a++   p+  l+
  gi|557694718|ref|YP_008797772.1|  10 VVFTALVAAATMILS--VYFPLTRGYFNLGETMVYLAALVGGPVVGAFAGGVGSALADVL-LGYTAFA---PGTLLI 80 
                                       577888888888888..****************************************999.6777777...****** PP

                                       HHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHCCCCCHHHHHHHCCCH CS
                       ECF_trnsprt  80 riligliagllykkgkkknlkeivvsfilagvlgtivatllvlliil 126
                                        ++ g  a++ly+  ++++  +  + +++a+v+g  ++ l++++++l
  gi|557694718|ref|YP_008797772.1|  81 KAAEGATAAILYRRLRNVSVPN--ALLLSAIVVGLYFGILVSVGVFL 125
                                       ************8888888765..77888888888888887777765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.024
                                       HHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHH.HHHHHHHHCHHHHHHHHHHCCCHTTHHHHHHHHHHHHC CS
                       ECF_trnsprt  36 vllggllfGpikGailgiitsvlkailtggtgalssfv.piaflsriligliagllykkgkkknlkeivvsfilagv 111
                                       ++++gl+fG ++ + + +++ ++  +l  g + l + v p+  +  +l+g ++   y +++k    + v s++lag+
  gi|557694718|ref|YP_008797772.1| 108 AIVVGLYFGILVSVGVFLMSGIVEITLYTGES-LQLAVnPGTWVLLALLGSAVPAYYGFRRKEYEAWLVGSLLLAGL 183
                                       44456666666666666666666666654443.33333677766666666655566777777777777888888888 PP

                                       CCCCHHHHH.....H CS
                       ECF_trnsprt 112 lgtivatll.....v 121
                                       ++    +l+     +
  gi|557694718|ref|YP_008797772.1| 184 VMVAGYFLYeslavF 198
                                       888777777443321 PP

>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1  10.6   1.2e-07   0.00073      19     121 ..       7     109 ..       2     111 .. 0.79
   2 !    7.0   9.1   0.00065       3.9      49     124 ..     106     187 ..      99     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.2e-07
                      5TM-5TMR_LYT  19 lllglifglfsilgtytgieie..gaiantRaigvvvaGllgGplvGliagliaglhRyllgGftalacgisti..l 91 
                                       +ll++++ l++   ++ ++ +     ++n+   +v +a+l+gGp+vG++ag ++ ++  +l G ta+a g   i  +
  gi|557694718|ref|YP_008797772.1|   7 ALLVVFTALVAAATMILSVYFPltRGYFNLGETMVYLAALVGGPVVGAFAGGVGSALADVLLGYTAFAPGTLLIkaA 83 
                                       566667777777777777777654589**************************999999999999999876665337 PP

                      5TM-5TMR_LYT  92 agllaGlihrklkrrrkkltvlvalligll 121
                                       +g+ a++++r+l++    ++v  all++++
  gi|557694718|ref|YP_008797772.1|  84 EGATAAILYRRLRN----VSVPNALLLSAI 109
                                       88999999888885....777777777665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00065
                      5TM-5TMR_LYT  49 igvvvaGllgGplvGliagliaglhRyllgGftalacgi...stilagllaGlihrklkrrr...kkltvlvallig 119
                                       + ++v Gl++G lv++++ l++g++ ++l   ++l  ++   + +l +ll++ + +++  rr   +++ v+ +ll g
  gi|557694718|ref|YP_008797772.1| 106 LSAIVVGLYFGILVSVGVFLMSGIVEITLYTGESLQLAVnpgTWVLLALLGSAVPAYYGFRRkeyEAWLVGSLLLAG 182
                                       568999*********************97665555544433234455555555444433333347888888888888 PP

                      5TM-5TMR_LYT 120 llvei 124
                                       l++ +
  gi|557694718|ref|YP_008797772.1| 183 LVMVA 187
                                       88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1844.56
//
Query:       gi|557694719|ref|YP_008797773.1|  [L=257]
Description: Fe-S cluster assembly ATP-binding protein SufC [Candidatus Caldiarchaeum subterraneum]
Scores for 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-21   75.4   0.0    7.8e-21   75.0   0.0    1.1  1  ABC_tran         ABC transporter
    1.8e-07   30.8   0.5     0.0043   16.5   0.0    2.4  3  SMC_N            RecF/RecN/SMC N terminal domain
    0.00069   19.3   0.1     0.0014   18.3   0.1    1.5  1  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.013   15.4   0.1      0.024   14.5   0.1    1.4  1  RsgA_GTPase      RsgA GTPase
      0.015   14.9   0.0      0.044   13.4   0.0    1.7  2  AAA_25           AAA domain
      0.043   14.0   0.0      0.061   13.5   0.0    1.3  1  AAA_33           AAA domain
      0.066   12.1   0.0       0.11   11.4   0.0    1.3  1  AAA_PrkA         PrkA AAA domain
      0.068   13.0   0.0       0.12   12.1   0.0    1.5  1  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      0.083   13.4   0.1       0.19   12.2   0.1    1.6  2  AAA_23           AAA domain
      0.087   12.9   0.0       0.15   12.1   0.0    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like
       0.11   12.5   0.0        6.9    6.7   0.0    2.7  3  AAA_5            AAA domain (dynein-related subfamily)
       0.12   12.1   0.0       0.19   11.5   0.0    1.3  1  AAA_30           AAA domain
       0.17   11.8   0.0        8.4    6.3   0.0    2.3  2  APS_kinase       Adenylylsulphate kinase


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 !   75.0   0.0   5.6e-24   7.8e-21       1     135 [.      18     175 ..      18     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 5.6e-24
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpel 74 
                                       lk v+l+++ege++ ++G+nG+GKStL+++++g+ k   +eG+illdg+++ +  + +++rk +   +q p   +++
  gi|557694719|ref|YP_008797773.1|  18 LKGVNLTVREGEIHTLMGPNGSGKSTLAAVIMGHPKYtvDEGDILLDGESIVDlSPDQRARKGLFLAFQYPVEISGV 94 
                                       799******************************9777669*************99********************** PP

                                       BHHHH..................HHHTC...HHHHH.HHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSS CS
                                       xxxxx..................xxxxx...xxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren..................esdee...iekal.sklglkelkdtvvkssp.ssLSgGqkqrvalarallkkpk 128
                                       t+++                           ++k+l +k+++ +l+ +++++   + +SgG+k+r ++ ++ +  p+
  gi|557694719|ref|YP_008797773.1|  95 TLANFlrrayinmkyggdadkskI---SvpeFQKLLkEKIEMLKLDPSIARRYLnEGFSGGEKKRCEVLQMAILSPR 168
                                       9888899****9999998664441...14454443314555555666666555569********************* PP

                                       EEEEEST CS
                                       xxxxxxx RF
                          ABC_tran 129 llllDEp 135
                                       + +lDE 
  gi|557694719|ref|YP_008797773.1| 169 IAILDET 175
                                       ******6 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   0.1   6.1e-05     0.085      25      44 ..      29      48 ..      15      55 .. 0.83
   2 ?   -2.3   0.0       1.7   2.4e+03     159     176 ..      51      68 ..      46      72 .. 0.83
   3 !   16.5   0.0   3.1e-06    0.0043     135     204 ..     135     214 ..      90     229 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.1e-05
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      ++  ++GpNGSGKs l   i
  gi|557694719|ref|YP_008797773.1| 29 EIHTLMGPNGSGKSTLAAVI 48
                                      57789*********998766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.7
                                       -SEEEECTTTTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N 159 aplyllDeidaaLDeknv 176
                                       +p y +De d  LD + +
  gi|557694719|ref|YP_008797773.1|  51 HPKYTVDEGDILLDGESI 68 
                                       7889*********98765 PP

  == domain 3  score: 16.5 bits;  conditional E-value: 3.1e-06
                                       T............CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-S CS
                                       x............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                             SMC_N 135 e............lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivisl 197
                                       +             +SgGek+ + + L +Ai + +   + +lDe d+ LD   vk+va+ +k+ s    +  +vi++
  gi|557694719|ref|YP_008797773.1| 135 KldpsiarrylneGFSGGEKKRCEV-LQMAILSPR---IAILDETDSGLDIDGVKIVADGVKTISAAtgMGALVITH 207
                                       044555555555579*****99886.788888765...679*********************6554433899***** PP

                                       SHHHCCC CS
                                       xxxxxxx RF
                             SMC_N 198 reemlek 204
                                        +++l+ 
  gi|557694719|ref|YP_008797773.1| 208 YQRILNY 214
                                       9998875 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 !   18.3   0.1     1e-06    0.0014      15      39 ..      21      45 ..      15      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                        +++++ +++ l+Gp+GsGKSTl 
  gi|557694719|ref|YP_008797773.1| 21 VNLTVREGEIHTLMGPNGSGKSTLA 45
                                      56667755599************95 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.8e-05     0.024      83     127 ..      11      56 ..       2      61 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                       -TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  83 saktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                       s++ k+ l+ ++  +++ ++ +l+G+ G GKStL  +++++ +  +
  gi|557694719|ref|YP_008797773.1|  11 SVEGKQILKGVNLTVREgEIHTLMGPNGSGKSTLAAVIMGHPKYTV 56 
                                       5566666667777777669******************999877666 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.2e-05     0.044      30      53 ..      25      48 ..      13      60 .. 0.87
   2 ?   -1.9   0.0       1.5   2.1e+03     165     188 ..     184     207 ..     168     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                            AAA_25 30 lpagelallaGapgtGKttlaldl 53
                                      +++ge++ l+G+ g+GK+tla  +
  gi|557694719|ref|YP_008797773.1| 25 VREGEIHTLMGPNGSGKSTLAAVI 48
                                      689*****************9865 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.5
                            AAA_25 165 vgalvealeriarrtgaavllvhH 188
                                       v+ + + ++ i+++tg   l++ H
  gi|557694719|ref|YP_008797773.1| 184 VKIVADGVKTISAATGMGALVITH 207
                                       677888889999999988888888 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   4.4e-05     0.061       4      32 ..      33      61 ..      30     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.4e-05
                            AAA_33  4 lvGlpGsGKstlaerllkklgavllssdt 32
                                      l G++GsGKstla  ++ + ++++ + d+
  gi|557694719|ref|YP_008797773.1| 33 LMGPNGSGKSTLAAVIMGHPKYTVDEGDI 61
                                      78************999888877655555 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.8e-05      0.11      89     182 ..      29     126 ..      20     142 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.8e-05
                          AAA_PrkA  89 qilyllGPvggGksslverlkklleaapiyalegsPvf...eePlhlipeelrkk...leeeygirlegllsPlatk 159
                                       +i  l+GP g+Gks+l+      +  +p y++++  +    e+ + l p++ ++k   l  +y ++++g       +
  gi|557694719|ref|YP_008797773.1|  29 EIHTLMGPNGSGKSTLAAV----IMGHPKYTVDEGDILldgESIVDLSPDQRARKglfLAFQYPVEISGVTLANFLR 101
                                       5778***********9975....557899999777764333667777787766544446778999999875544444 PP

                          AAA_PrkA 160 r..leeefgGdiekfkvekilfsil 182
                                       r  ++ ++gGd +k k++   f +l
  gi|557694719|ref|YP_008797773.1| 102 RayINMKYGGDADKSKISVPEFQKL 126
                                       4226789999988776665554443 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   0.0   8.9e-05      0.12       3      19 ..      32      48 ..      30      85 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.9e-05
                            AAA_21  3 vliGpNgsGKSnLLdal 19
                                       l GpNgsGKS+L   +
  gi|557694719|ref|YP_008797773.1| 32 TLMGPNGSGKSTLAAVI 48
                                      688*********97766 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.19      23      38 ..      32      47 ..      11      49 .. 0.81
   2 ?   -2.4   0.0       4.2   5.8e+03     113     167 ..     119     132 ..      85     147 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                            AAA_23 23 lItGpNGaGKTTildA 38
                                       + GpNG+GK+T+   
  gi|557694719|ref|YP_008797773.1| 32 TLMGPNGSGKSTLAAV 47
                                      578*********9765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                            AAA_23 113 eideleqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleeled 167
                                       ++                                          e++k l+e+ +
  gi|557694719|ref|YP_008797773.1| 119 SV-----------------------------------------PEFQKLLKEKIE 132
                                       33.........................................334444444433 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 ?   12.1   0.0   0.00011      0.15      57      83 ..     199     225 ..     161     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00011
                   Glyco_trans_4_2  57 pleylkafklkklikkikPDvvhahya 83 
                                        ++ l + ++ ++++ +kPDvvh++y 
  gi|557694719|ref|YP_008797773.1| 199 GMGALVITHYQRILNYLKPDVVHVMYG 225
                                       56666678****************995 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 ?   -3.2   0.0       5.4   7.5e+03      28      47 ..       4      23 ..       2      29 .. 0.79
   2 ?    6.7   0.0     0.005       6.9       4      18 ..      33      47 ..      31      54 .. 0.89
   3 ?    2.7   0.0     0.084   1.2e+02      18      75 ..     122     176 ..     115     180 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.4
                                      EEEE--TT--HHHHH--B-- CS
                             AAA_5 28 eyvqltrdtteedlkgrrei 47
                                       +v+l+++ + ++++ ++++
  gi|557694719|ref|YP_008797773.1|  4 KIVNLHASVEGKQILKGVNL 23
                                      68999999999999999887 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.005
                                      EE--SSSSHHHHHHH CS
                             AAA_5  4 LvGppGtgKselaer 18
                                      L Gp G+gKs+la  
  gi|557694719|ref|YP_008797773.1| 33 LMGPNGSGKSTLAAV 47
                                      89**********976 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.084
                                       HGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGG CS
                             AAA_5  18 rlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEve 75 
                                       ++ ++l+ ++e+  l  ++ ++ l  + +   g+++ +  +l  a+ +++i++lDE +
  gi|557694719|ref|YP_008797773.1| 122 EFQKLLKEKIEMLKLDPSIARRYLNEGFS---GGEKKRCEVLQMAILSPRIAILDETD 176
                                       56778888888888888888888888888...7888888999999**********976 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00014      0.19      14      79 ..      24     102 ..      12     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                            AAA_30  14 ltsgdrvavltGpAGtGKttalkalreaweaa.g........grviglAptgkaAkvLaeelg....ieastiakll 77 
                                       +  +  +++l Gp G+GK+t+ +++  + +            ++++ l+p ++a k L  +++    i + t+a++l
  gi|557694719|ref|YP_008797773.1|  24 TVREGEIHTLMGPNGSGKSTLAAVIMGHPKYTvDegdilldgESIVDLSPDQRARKGLFLAFQypveISGVTLANFL 100
                                       44555699************999996554433224589999899999999999999876433322226777888887 PP

                            AAA_30  78 kr 79 
                                       +r
  gi|557694719|ref|YP_008797773.1| 101 RR 102
                                       65 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0061       8.4       6      41 ..      32      68 ..      27      76 .. 0.71
   2 ?    3.2   0.0     0.052        72      13      59 ..     113     159 ..     109     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0061
                                      EEESSTTSSHHHHHHHHHHHHHHTT.--EEEEEHHHH CS
                        APS_kinase  6 wltGlsgsGKstianalekkLvekg.isvylLdGdnv 41
                                       l G  gsGKst+a  +  + + +     +lLdG+++
  gi|557694719|ref|YP_008797773.1| 32 TLMGPNGSGKSTLAAVIMGHPKYTVdEGDILLDGESI 68
                                      5789*********988765443333255667777766 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.052
                                       SSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT--SSHHHHHHH CS
                        APS_kinase  13 sGKstianalekkLvekgisvylLdGdnvRhgLnkdLgfseedRken 59 
                                       + Ks i++   +kL +++i++  Ld    R+ Ln++ +  e++R e 
  gi|557694719|ref|YP_008797773.1| 113 ADKSKISVPEFQKLLKEKIEMLKLDPSIARRYLNEGFSGGEKKRCEV 159
                                       5689999988899**********************998888888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1817.12
//
Query:       gi|557694720|ref|YP_008797774.1|  [L=467]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-11   42.2   3.5    1.7e-09   37.5   0.3    2.5  2  Lactamase_B_2  Beta-lactamase superfamily domain
    2.4e-08   33.8   0.0    9.8e-08   31.8   0.0    2.1  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
     0.0028   17.6   0.2       0.17   11.8   0.0    2.4  2  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0031   17.6   6.4      0.012   15.7   6.4    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily


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 !   37.5   0.3   3.8e-13   1.7e-09      29     170 ..      87     228 ..      71     255 .. 0.72
   2 !    5.2   0.1     0.003        13     173     200 ..     408     435 ..     383     436 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 3.8e-13
                                       .SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT......TTEEEEEE-TTSEEEEC CS
                     Lactamase_B_2  29 ppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee......pavnvheldwgesfelg 99 
                                       p  +aV++th+H DH+  +  lr+    ++ply  + ++  ++a+    ++ +e       + +v+ + +g ++ ++
  gi|557694720|ref|YP_008797774.1|  87 PFAEAVVITHGHLDHYGHASLLRP----DIPLYMGETTRLLIQARENTKQKSPEnlfnknEEHPVEVFRTGSKLVFE 159
                                       5678************55555555....4778866666666666655555555555555566788888899999998 PP

                                       STTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---......HHHHHHHCT..-SEEEEE-S-SS CS
                     Lactamase_B_2 100 dggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip......eeigerlgg..adllllditaye 168
                                       d+   i ++ + h+ +         ++Gl+ie+g+  ++y+gD+          ++  e+  +  ++ l++++t+++
  gi|557694720|ref|YP_008797774.1| 160 DAI--IYPVHVDHSIPA--------AYGLVIETGEGVLAYTGDLRMHGpksemtHDFVEKCVKmnVETLVIEGTRVD 226
                                       754..************........*******************955533311133333333245777777777777 PP

                                       TT CS
                     Lactamase_B_2 169 dd 170
                                       + 
  gi|557694720|ref|YP_008797774.1| 227 ET 228
                                       65 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.003
                                       HHHHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 173 irhmgHltpeeaveaaadlgakrlvliH 200
                                       i++ gH+++++ +++++++++++ +++H
  gi|557694720|ref|YP_008797774.1| 408 IHSSGHAPQKDLIKIVEEINPRKIIPVH 435
                                       3389************************ 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 !   31.8   0.0   2.2e-11   9.8e-08       7      45 ..     404     442 ..     401     455 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.2e-11
                             RMMBL   7 rieeidfSgHadknellelirklkprnvilvHGeeeats 45 
                                       r e+i+ SgHa + +l+++++ ++pr++i+vH  + ++ 
  gi|557694720|ref|YP_008797774.1| 404 RYEHIHSSGHAPQKDLIKIVEEINPRKIIPVHTLKPMLM 442
                                       67899***************************9887765 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 !   11.8   0.0   3.7e-05      0.17      34     114 ..      86     193 ..      54     223 .. 0.71
   2 ?    3.5   0.0     0.013        58     144     163 .]     416     435 ..     407     435 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.7e-05
                     Lactamase_B_3  34 aeeaDlvlisqaledHahletlkql.................................aenvkvleegeslevggle 77 
                                       ++ a++v+i++++ dH+ ++ l +                                  ++ v+v ++g++l ++++ 
  gi|557694720|ref|YP_008797774.1|  86 TPFAEAVVITHGHLDHYGHASLLRPdiplymgettrlliqarentkqkspenlfnkneEHPVEVFRTGSKLVFEDAI 162
                                       47899************888776645677777777777777777777777777766666666666667777777777 PP

                     Lactamase_B_3  78 iravatshdavggsergenngflleqdgltiyhlGhl 114
                                       i  v+ +h           +g ++e ++  +++ G+l
  gi|557694720|ref|YP_008797774.1| 163 IYPVHVDHS------IPAAYGLVIETGEGVLAYTGDL 193
                                       777777772......2234566666666666666666 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.013
                     Lactamase_B_3 144 qeealelakrLkpklvlPmh 163
                                       q++ ++++++++p+ ++P+h
  gi|557694720|ref|YP_008797774.1| 416 QKDLIKIVEEINPRKIIPVH 435
                                       8999***************9 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   6.4   2.6e-06     0.012      46     159 ..      90     201 ..      89     252 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-06
                                       EEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEE CS
                       Lactamase_B  46 davilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrra 122
                                       +av++TH+HlDH+G +  l+   +   g+    +   +++ ++++++  +   + + ++  ++ +    ++++ +  
  gi|557694720|ref|YP_008797774.1|  90 EAVVITHGHLDHYGHASLLRPDIPLYMGETTRLLIQARENTKQKSPENLF--NKNEEHPVEVFRTGSKLVFEDAIIY 164
                                       59**************9997555544444444444444444444444433..4555555555555555555555555 PP

                                       EEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCC CS
                       Lactamase_B 123 lyvtggpghghghgvveygggkvlftGDallagetgr 159
                                        +++ +  + + ++v+e g+g +++tGD+   g+  +
  gi|557694720|ref|YP_008797774.1| 165 PVHVDHSIPAAYGLVIETGEGVLAYTGDLRMHGPKSE 201
                                       5555566677778899999999999999977666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3261.21
//
Query:       gi|557694721|ref|YP_008797775.1|  [L=231]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-52  177.7   0.0    2.7e-52  177.5   0.0    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 !  177.5   0.0   1.5e-56   2.7e-52       1     200 [.       3     208 ..       3     209 .. 0.97

  Alignments for each domain:
  == domain 1  score: 177.5 bits;  conditional E-value: 1.5e-56
                                       EEEESS.SS-EEEEEE-TT-EEEE-CCGEEEEETTEEEEE.....--------.------EEEEEEES.SS-EEEEE CS
                             AIM24   1 fevlge.pssllsvtLspgeelyaerGalvamsgkvemet.....gllkalkr.lltgeslfllkftakissgtvll 70 
                                       +e+ ++ +++ll+v+L pge++ ae+Ga+++m+++++++t     ++ kal+  ll+g+s+f++++ta ++sg + l
  gi|557694721|ref|YP_008797775.1|   3 YEIKHRpSYALLEVELMPGEAIEAEAGAMTYMTPSIRVQTriresSFVKALGLkLLGGQSFFVNEYTAVEKSGRLGL 79 
                                       79999999*************************************999999877***************9******* PP

                                       --SSSEEEEEEEGGTT.EEEEEGGGEEEEETT-EEEEEEEE--.SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEE CS
                             AIM24  71 apklpgtivtlelgggdwlivqkdafLAatgnveldikfqkgl.kglfggeglflqkltGrGlvalsgyGaiyeiel 146
                                        +  +g+i++l++++++ +i+q++a++A++ +v+ldik+q g+ +g+f g+glf+ + +G+G+++++ +Ga+ + +l
  gi|557694721|ref|YP_008797775.1|  80 VSAPLGDIAQLRVSPENGYIIQRSAYVASSPTVDLDIKWQ-GFtRGIF-GQGLFMIRCSGSGDLFINTFGALEKFTL 154
                                       *************9999***********************.5769999.78************************** PP

                                       E.EEEEEEEGGGEEEEETTEEEEEEEETT---STTTTS-EEEEEEEEEEEEEES CS
                             AIM24 147 kageelvvdpghlvafsgslkfdiervgglkrrligGeglflkltGpgtvllqs 200
                                        +geelvvd+ hl afs ++++d+ +  +lk++l+gGegl+++++Gpg +++q+
  gi|557694721|ref|YP_008797775.1| 155 SPGEELVVDNFHLAAFSTTCQYDVMKFDNLKSTLLGGEGLVVRVRGPGELYVQT 208
                                       *****************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       214  (0.011936); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1813.06
//
Query:       gi|557694722|ref|YP_008797776.1|  [L=624]
Description: arginyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   87.2   0.2    2.6e-24   85.7   0.0    2.0  2  DALR_1           DALR anticodon binding domain
    1.9e-22   79.7   0.0    6.6e-20   71.3   0.0    2.2  2  tRNA-synt_1d     tRNA synthetases class I (R)
    5.1e-15   55.8   0.0    1.9e-14   54.0   0.0    2.0  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
     0.0035   16.7   0.0     0.0069   15.8   0.0    1.4  1  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
  ------ inclusion threshold ------
      0.021   13.6   0.1      0.076   11.7   0.1    1.9  2  tRNA-synt_1g     tRNA synthetases class I (M)
      0.051   11.8   0.0       0.14   10.4   0.0    1.7  1  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)


Domain annotation for each model (and alignments):
>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.5   7.5e+03      56      68 ..     395     407 ..     377     421 .. 0.47
   2 !   85.7   0.0   8.7e-28   2.6e-24       1     119 []     510     624 .]     510     624 .] 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.5
                                       T-THHHHHHHHHH CS
                            DALR_1  56 lephklaeylyeL 68 
                                        +p+++  y+ye+
  gi|557694722|ref|YP_008797776.1| 395 ADPSRYIHYAYEV 407
                                       2344444444443 PP

  == domain 2  score: 85.7 bits;  conditional E-value: 8.7e-28
                                       HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHH CS
                            DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYn 77 
                                       +qya+aR+  il+ka+++ + +++ +  l  +++e+ L+k++  +p v eea+++l+++++a+yl eLa +f++fY+
  gi|557694722|ref|YP_008797776.1| 510 IQYAYARATRILEKADTQPNPQNPPT-TL--DPKEIMLIKQIGMLPLVYEEAVRNLSVKRIATYLRELAFAFNDFYE 583
                                       7***************9886654444.44..89******************************************** PP

                                       HCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                            DALR_1  78 kervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                       +++vl ++e+++   RLaLv+a r+ ++++ d  Gi+ +e+m
  gi|557694722|ref|YP_008797776.1| 584 NCPVLSADEKVK-VFRLALVEAFRSAVSSAADAAGIPLVEEM 624
                                       **********99.****************************9 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 !   71.3   0.0   2.2e-23   6.6e-20      16     223 ..     108     328 ..      93     343 .. 0.80
   2 !    6.4   0.0    0.0013       3.8     279     335 ..     428     482 ..     345     495 .. 0.81

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 2.2e-23
                                       -SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHT..TTTTTS CS
                      tRNA-synt_1d  16 srekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkq..dekllq 90 
                                       ++  + v+v+++s n  k +h+Gh r   +Gd+++rll   Gy+v  +n++ D G q+  L+  +++ +   e + +
  gi|557694722|ref|YP_008797776.1| 108 LGGGQYVLVEHTSVNPNKALHIGHARNVCLGDSLARLLKKNGYHVAVANYIDDSGVQMAELLLAFKHLGysMEPTKG 184
                                       566789*****************************************************999999986511566665 PP

                                       -----SCCCHHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHH.HHHHHHH...HHHHHCT---EC--C CS
                      tRNA-synt_1d  91 eqelqdLeafykeakkdydeeeifaerarnyvvkLqsgdedirklwkllvd.itrtelq...klydrldvtlierGe 163
                                       e+  +    +y e+ k+ + +  ++   r+   +L++ d ++ +l +l+v+ + +++l+   +l +r+dv   +  +
  gi|557694722|ref|YP_008797776.1| 185 EKFDEYCGRVYTEVSKRIEADPRLETLRRQLAAQLEDHDSETSQLNRLVVErVLMEQLRtcwRLGARYDVLN-KESD 260
                                       555566789*************************************99665266666652224557888877.4555 PP

                                       CCCCCCHHHHHHHHHCTT-EEE.CT....TCEEEEECCC...TSSCCEECC-TTS-B-HHHHHHHHHH CS
                      tRNA-synt_1d 164 slykeslneivkelkkkglvke.sd....Galvvfldef...gkrlgvvvqksDGgylytttDiaaak 223
                                        l+ +   e+ k l++ g+  + ++    G  + +l+ +   +k+   vv+ksDG+++y ++D + a 
  gi|557694722|ref|YP_008797776.1| 261 ILFFDLWSEVFKRLREMGVLYVaEEgpkkGCWLFDLSGHpklSKEGDEVVVKSDGSTTYVARDFGYAA 328
                                       69***************9754413322225567777665776888888***************98775 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0013
                                       SBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS-CCCCHCHHHHHHHHHHHHCC CS
                      tRNA-synt_1d 279 kkfktrkGetvkLadlLdealeralqlikeknkdkvlqadelekvaeavgvgaikya 335
                                        +++ r G  v+++ lLd   ++a +  +++ +d   +     +vae ++v+ai+y 
  gi|557694722|ref|YP_008797776.1| 428 VHMSGRGGIYVNVDPLLDYVKQKAAEGARQRHPD--WSESRVSEVAEKIAVAAIRYF 482
                                       37999*********************99999999..999999************995 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0   6.2e-18   1.9e-14      16      84 ..      12      82 ..       2      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 6.2e-18
                                      SS-HHHHGGG-E-.SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT..EEEEEEETT.EEEEE CS
                   Arg_tRNA_synt_N 16 gadleeeeiviekpknpkfGDyatnvamqlakklkknPreiAeeiaekleksei..iekvevagpGFiNff 84
                                       ad  + ++++  +k+  fGD+++  a+ lakk +k+P e A+e++e+++ s +  +e++evag+G+iNf+
  gi|557694722|ref|YP_008797776.1| 12 LADVGVGQPRVSLAKDARFGDVSSSDAFDLAKKTGKKPVEMAKELVERMDLSRTvyVERAEVAGAGYINFY 82
                                      34556778899988*************************************98889*************96 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 !   15.8   0.0   2.3e-06    0.0069      22      55 ..     126     159 ..     119     232 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.3e-06
                                       --BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB CS
                      tRNA-synt_1e  22 ashlGhaRslvafDilrrilqalgYdvqfvqnvt 55 
                                       a h+GhaR++   D l+r+l++ gY+v+  + + 
  gi|557694722|ref|YP_008797776.1| 126 ALHIGHARNVCLGDSLARLLKKNGYHVAVANYID 159
                                       78************************98554433 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 ?   11.7   0.1   2.6e-05     0.076      10      52 ..     123     165 ..     114     174 .. 0.88
   2 ?   -1.8   0.0      0.34     1e+03     339     360 ..     468     489 ..     465     497 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.6e-05
                                       -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHH CS
                      tRNA-synt_1g  10 angklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpi 52 
                                       +n +lH+Gh+++v  +D +aR  +++g++v      D  G+++
  gi|557694722|ref|YP_008797776.1| 123 PNKALHIGHARNVCLGDSLARLLKKNGYHVAVANYIDDSGVQM 165
                                       7999**************************9999999888876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.34
                                       HHHHHHH-HHHHHHHHHHHS-T CS
                      tRNA-synt_1g 339 kealerldadllRYylaaeape 360
                                       +e++e++ + ++RY+l+++ p 
  gi|557694722|ref|YP_008797776.1| 468 SEVAEKIAVAAIRYFLIRADPD 489
                                       67889999*********98876 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 ?   10.4   0.0   4.7e-05      0.14      35      76 ..     124     165 ..     112     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4.7e-05
                       tRNA-synt_1  35 tGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlai 76 
                                       + +lHiGha +  l d + r  + +G++v     +D  G+ +
  gi|557694722|ref|YP_008797776.1| 124 NKALHIGHARNVCLGDSLARLLKKNGYHVAVANYIDDSGVQM 165
                                       5689*****************************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); 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):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.24s 00:00:00.86 Elapsed: 00:00:00.40
# Mc/sec: 4647.39
//
Query:       gi|557694723|ref|YP_008797777.1|  [L=179]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   5.0    1.7e-33  115.7   5.0    1.6  2  DUF420    Protein of unknown function (DUF420)
    8.2e-07   29.3   6.3    6.1e-05   23.3   2.1    2.4  2  DUF2306   Predicted membrane protein (DUF2306)


Domain annotation for each model (and alignments):
>> DUF420  Protein of unknown function (DUF420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.7      0.46   4.1e+03     116     132 .]       9      25 ..       2      25 .. 0.59
   2 !  115.7   5.0   1.9e-37   1.7e-33       1     132 []      41     176 ..      41     176 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.46
                            DUF420 116 piwlyvavtGvvvYllL 132
                                       ++ l  a+ Gv+ YllL
  gi|557694723|ref|YP_008797777.1|   9 TLVLTLAAYGVLGYLLL 25 
                                       33444567788888876 PP

  == domain 2  score: 115.7 bits;  conditional E-value: 1.9e-37
                            DUF420   1 lpalnavlnalaavllllglvaikkgkieaHrklmllafvlsalFlvlYllkhalagetkfggpeeegvirpvYlai 77 
                                       lp+++a++n++a+v+ll g++aik+++i++H+ lml++f+l++ Fl +Yl + +l+g ++f+gp    +  +vYl+ 
  gi|557694723|ref|YP_008797777.1|  41 LPHAIAAVNSAAVVTLLSGYRAIKRRDIRLHKLLMLASFILITSFLTMYLGRLFLGGVKHFTGPVL--IRDFVYLPS 115
                                       79************************************************************9996..999****** PP

                            DUF420  78 LitHivLavvvvplvlvtlvlalkg......kfekHrkiaritvpiwlyvavtGvvvYllL 132
                                       L++H+ L++v vplvl++++++l        + ++Hr+++r+ v +w +++v+Gv+vY+lL
  gi|557694723|ref|YP_008797777.1| 116 LAIHLGLSIVSVPLVLYNILTGLFTpvpeigRKTRHRAVGRWGVRLWSLSLVLGVFVYFLL 176
                                       ************************99*********************************98 PP

>> DUF2306  Predicted membrane protein (DUF2306)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   2.1   6.8e-09   6.1e-05      60     123 ..      37      99 ..       5     122 .. 0.72
   2 !    8.4   0.3   0.00027       2.4       3      53 ..     118     173 ..     116     178 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.8e-09
                           DUF2306  60 lvlllgfll..lallwlvftvlalvairrrdfaaHrawmirsYalalaavtlrlvllvlillvged 123
                                       lv +l+ ++  ++++ +v+++ +++ai+rrd++ H+  m+ s++l  +   l+++l  l+l  g++
  gi|557694723|ref|YP_008797777.1|  37 LVETLPHAIaaVNSAAVVTLLSGYRAIKRRDIRLHKLLMLASFILITSF--LTMYLGRLFL-GGVK 99 
                                       55555555411556889999************************77765..5556666666.3333 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00027
                           DUF2306   3 lHialalvalllGalqlvkrlr.......akrpklHrlaGrvyvlavllaalsglfls 53 
                                       +H  l++v ++l + +++++l        +k    Hr++Gr  v +  l+ + g+f+ 
  gi|557694723|ref|YP_008797777.1| 118 IHLGLSIVSVPLVLYNILTGLFtpvpeigRK--TRHRAVGRWGVRLWSLSLVLGVFVY 173
                                       6666666666655555555555555432155..56******99999888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1414.10
//
Query:       gi|557694724|ref|YP_008797778.1|  [L=385]
Description: GTP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-19   69.6   0.2      8e-19   67.4   0.5    2.0  2  TGS           TGS domain
    1.7e-10   41.0   0.1    3.9e-10   39.8   0.0    1.8  2  MMR_HSR1      50S ribosome-binding GTPase
    1.5e-07   31.4   0.0    3.7e-07   30.1   0.0    1.7  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    9.6e-06   25.2   0.0    5.1e-05   22.8   0.0    2.0  2  FeoB_N        Ferrous iron transport protein B
     0.0011   19.3   1.4       0.37   11.1   0.0    3.0  3  AAA_22        AAA domain
  ------ inclusion threshold ------
      0.046   12.9   0.0      0.051   12.7   0.0    1.3  1  G-alpha       G-protein alpha subunit
      0.064   13.8   1.6        1.4    9.4   0.1    2.5  2  ABC_tran      ABC transporter
      0.089   11.9   0.0       0.18   10.9   0.0    1.4  1  DUF815        Protein of unknown function (DUF815)
      0.091   13.0   0.5       0.44   10.8   0.1    2.4  2  DnaB_bind     DnaB-helicase binding domain of primase
       0.12   11.7   0.5       0.82    8.9   0.0    2.2  2  TcdA_TcdB     TcdA/TcdB catalytic glycosyltransferase domain
       0.15   11.6   0.5        6.5    6.2   0.0    2.9  3  GTP_EFTU      Elongation factor Tu GTP binding domain
       0.16   12.0   0.4       0.99    9.5   0.2    2.3  2  Ubiquitin_4   Ubiquitin-like domain


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 ?   -1.7   0.0       2.1   3.2e+03      15      29 ..     296     310 ..     294     312 .. 0.80
   2 !   67.4   0.5   5.4e-22     8e-19       1      59 [.     314     384 ..     314     385 .] 0.95

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.1
                                       TTB-HHHHHHHHSTT CS
                               TGS  15 rgatveDfAykIhrs 29 
                                       + +t +D+A kI + 
  gi|557694724|ref|YP_008797778.1| 296 KPETFRDLAEKIFQN 310
                                       568999*****9665 PP

  == domain 2  score: 67.4 bits;  conditional E-value: 5.4e-22
                                       EEEEE.TTSSEEE....EETTB-HHHHHHHHSTTHHHHEEEEEECS.......EEEETTSBB-SSEEEEEE CS
                               TGS   1 irvyt.PdGkvpd....lprgatveDfAykIhrslakkfiyAlVnG.......qrvgldhvLedgdvveIv 59 
                                       +r+yt +dG v      +++g+tv+++A+ Ihr++a++++yA+V+G       q+vg +hvL+dgd+ve+v
  gi|557694724|ref|YP_008797778.1| 314 VRIYTqKDGVVNRkpvvVKKGTTVKELAQIIHREIAEELKYARVWGrsvkiqgQQVGPSHVLMDGDIVELV 384
                                       79***8888776699******************************************************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 ?   -3.2   0.1         6   8.9e+03      91      97 ..      43      49 ..      12      68 .. 0.45
   2 !   39.8   0.0   2.6e-13   3.9e-10       2      98 ..      84     180 ..      83     237 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6
                                      HHHHHHH CS
                          MMR_HSR1 91 kpldeel 97
                                      ++++ +l
  gi|557694724|ref|YP_008797778.1| 43 EKMRAQL 49
                                      2222222 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 2.6e-13
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHH..HHHHHHHHHHCT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseek..glgkaflaleea 76 
                                       va++G  N+GKSt+i+ +t++ka+vs +  tT+ ++ + + +++  i+lv +p ++ + + e     +++++a + a
  gi|557694724|ref|YP_008797778.1|  84 VALLGVANSGKSTIIRFMTNAKAEVSMYELTTTRPIPAMMLYEDVYIQLVELPAVLTS-RLETtpFTSRSIAAARGA 159
                                       99************************************9999999*********8763.33333467777777777* PP

                                       SEEEEEEETTTTCSHHHHHHHH CS
                          MMR_HSR1  77 dlillvvdaseeklkpldeele 98 
                                       dlill +d   ++l+++  +l 
  gi|557694724|ref|YP_008797778.1| 160 DLILLTLDGM-RDLEEQYLRLV 180
                                       ********44.33444434444 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 !   30.1   0.0   2.5e-10   3.7e-07      15     106 .]     217     313 ..     204     313 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.5e-10
                      MMR_HSR1_Xtn  15 ldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldelare..pnsvv...iS 86 
                                        + e+ k+ l++ ++ na v+i ++++vD + + + + +vY+++++++ + D +s e +++l+r   ++ ++   + 
  gi|557694724|ref|YP_008797778.1| 217 GSLEELKRELQQIGLRNAVVKIYGEADVDSVLEQVLHPTVYKKAMVAVGRSDYASAEGVERLRRLtsQHGLPflqLT 293
                                       455778888999****************************************************6454555533377 PP

                      MMR_HSR1_Xtn  87 aekelnldeLkekiweeLnL 106
                                         k   + +L eki+++L+L
  gi|557694724|ref|YP_008797778.1| 294 ETKPETFRDLAEKIFQNLEL 313
                                       7788899**********997 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 !   22.8   0.0   3.4e-08   5.1e-05       2      59 ..      83     140 ..      82     190 .. 0.79
   2 ?   -0.3   0.0      0.45   6.7e+02     106     156 .]     258     307 ..     234     307 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.4e-08
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYs 59 
                                       tval+G  n+Gk+t++  +t+ak +v+ +  +t     + + +++  +++v lP + +
  gi|557694724|ref|YP_008797778.1|  83 TVALLGVANSGKSTIIRFMTNAKAEVSMYELTTTRPIPAMMLYEDVYIQLVELPAVLT 140
                                       79****************************************************8743 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.45
                                       SSEEEEEETHHHHHHTTEEE-HHHHHHHHTS-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N 106 vpvvlalnmideaekkgieidlkkLsekLgvpvvktsakkkegieellkai 156
                                       ++ ++a+  +d a+++g+e  l++L+++ g+p ++++ +k e +++l ++i
  gi|557694724|ref|YP_008797778.1| 258 KKAMVAVGRSDYASAEGVE-RLRRLTSQHGLPFLQLTETKPETFRDLAEKI 307
                                       6788999999999999998.6889999999999999999999999988775 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       6.6   9.9e+03      75      88 ..      42      55 ..      15      67 .. 0.53
   2 !   11.1   0.0   0.00025      0.37       4     129 ..      80     213 ..      77     239 .. 0.77
   3 !    6.4   0.0     0.007        11      23      71 ..     279     333 ..     267     359 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.6
                            AAA_22 75 seellealeqalra 88
                                      +e ++++l   l +
  gi|557694724|ref|YP_008797778.1| 42 TEKMRAQLKTTLAK 55
                                      33333333333333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00025
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka...erlssee 77 
                                       +a  +++ G + +GK+t +r +++ +         +++ ++ t + +     l++++  +l + l a   +rl++  
  gi|557694724|ref|YP_008797778.1|  80 GAATVALLGVANSGKSTIIRFMTNAKA--------EVSMYELTTTRPIPAMMLYEDVYIQLVE-LPAvltSRLETTP 147
                                       566678999***************963........5666666666666999999999999985.4445888999999 PP

                            AAA_22  78 llealeqalraravielliiDEaqhlrseealeeLrsllnl.................srkgvqliLvG 129
                                       + ++   a+r ++   ll +D +  l  ee++  L++ll++                 ++ g++++L+G
  gi|557694724|ref|YP_008797778.1| 148 FTSRSIAAARGADL-ILLTLDGMRDL--EEQYLRLVELLEDsgitlgaksfevevekkDSGGIRIVLFG 213
                                       99999999999999.***********..66666666665543444444444445555556666666666 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.007
                            AAA_22  23 rrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka...............e 71 
                                       rrl++q+         + +++  t +++++ +dl+++++++l+l + +               +
  gi|557694724|ref|YP_008797778.1| 279 RRLTSQH---------GLPFLQLTETKPETFRDLAEKIFQNLELVRIYtqkdgvvnrkpvvvkK 333
                                       4555555.........8899999999*****************988775555555554444444 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.4e-05     0.051      17      61 ..      75     118 ..      47     321 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                                       XXXE..EEEEEEEESTTSSHHHHHHHHHHHCS----HHHHHCCHH CS
                           G-alpha  17 arkkkrevkllllGqseSGKsTilkqlkllykkgfseeelatwra 61 
                                       a++k+   ++ llG + SGKsTi++ +   +  ++s  el t r+
  gi|557694724|ref|YP_008797778.1|  75 AFRKEGAATVALLGVANSGKSTIIRFMTNAK-AEVSMYELTTTRP 118
                                       445556669***************9988544.3355555555555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.2      0.11   1.6e+02      50     105 ..      15      69 ..       7      75 .. 0.79
   2 ?    9.4   0.1   0.00093       1.4      12      33 ..      82     103 ..      74     111 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.11
                                       GGB-HHHCCHCEEEE-SS--S-TTSBHHHHHHHTCHHHHHHHSTTGGTTCBGESTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  50 keqeleslrkeigvlpqepqlfpeltvrenesdeeiekalsklglkelkdtvvkss 105
                                       k+qe + ++++i+ l++   l p++  +++++++++++ l+kl+ +  +++ +k s
  gi|557694724|ref|YP_008797778.1|  15 KYQEARTVEEKIRALEEALPLIPDH-KGTEKMRAQLKTTLAKLRKEAERKKSAKVS 69 
                                       5588899999999999999999999.566689999999999999988888777655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00093
                                       SEEEEEESTTSSHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllag 33 
                                        +va++G   +GKSt+++ +++
  gi|557694724|ref|YP_008797778.1|  82 ATVALLGVANSGKSTIIRFMTN 103
                                       689***************9986 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.18      22      79 ..      48     107 ..      36     121 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                            DUF815  22 vdevklddLv.gidkqkealventeqfl.eglpannvLLwGarGtGKSslvkallneyae 79 
                                         +++l++L+ + +++k+a v+ t  f+ +++ a  v L G   +GKS+++++++n+ ae
  gi|557694724|ref|YP_008797778.1|  48 QLKTTLAKLRkEAERKKSAKVSRTDLFAfRKEGAATVALLGVANSGKSTIIRFMTNAKAE 107
                                       555666677426788888889999988636778999******************998765 PP

>> DnaB_bind  DnaB-helicase binding domain of primase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00029      0.44      15      31 ..      20      36 ..      13      37 .. 0.92
   2 ?   -2.8   0.0         5   7.4e+03      27      40 ..      49      62 ..      47      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
                                      TSHHHHHHHHHHHHHHH CS
                         DnaB_bind 15 stpegkaravrealpll 31
                                      +t+e+k+ra++ealpl+
  gi|557694724|ref|YP_008797778.1| 20 RTVEEKIRALEEALPLI 36
                                      799************98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5
                                      HHHHHTTSSSHHHH CS
                         DnaB_bind 27 alpllaripdpieR 40
                                      ++ +la+++ ++eR
  gi|557694724|ref|YP_008797778.1| 49 LKTTLAKLRKEAER 62
                                      67789999999999 PP

>> TcdA_TcdB  TcdA/TcdB catalytic glycosyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.18   2.6e+02     136     167 ..      12      42 ..       5      63 .. 0.81
   2 ?    8.9   0.0   0.00055      0.82     264     335 ..     261     338 ..     219     354 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.18
                                       HHHHH.............HHHHHHHHHTTTEE CS
                         TcdA_TcdB 136 elesykklkeinkeklaalekslneildedgv 167
                                        l +y + +++  ek++ale+ l+ i d++g 
  gi|557694724|ref|YP_008797778.1|  12 KLAKY-QEARTVEEKIRALEEALPLIPDHKGT 42 
                                       67888.788999***********999888775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00055
                                       .........---CCCCTS-CCHHHHHHHHHHC--SGG.GTB------EE-TT-E.EEEEETTEEEEEE.EEE-TT-H CS
                         TcdA_TcdB 264 v......evassedverldeelktklkallkskeeksielFkslddlkvrplelykelaalksglNqa.lvskkgsl 333
                                       +      + as e verl     ++   +l+  e k  e F+ l++++ ++lel+++ +  ++++N+  +v kkg +
  gi|557694724|ref|YP_008797778.1| 261 MvavgrsDYASAEGVERLRRLTSQHGLPFLQLTETKP-ETFRDLAEKIFQNLELVRIYTQKDGVVNRKpVVVKKGTT 336
                                       3333444667777777777666555555666555555.****************************97366777766 PP

                                       HH CS
                         TcdA_TcdB 334 vv 335
                                       v 
  gi|557694724|ref|YP_008797778.1| 337 VK 338
                                       64 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 ?    0.8   0.2       0.2     3e+02      34      64 ..      44      74 ..      34      83 .. 0.75
   2 ?    0.6   0.0      0.24   3.6e+02       5      31 ..      83     109 ..      79     117 .. 0.79
   3 ?    6.2   0.0    0.0044       6.5      82     154 ..     147     241 ..     145     349 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.2
                                      HHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE CS
                          GTP_EFTU 34 gekaeeervlDtlkeErergiTiksaaisle 64
                                      +++a+ +++l +l +E er  + k++ + l+
  gi|557694724|ref|YP_008797778.1| 44 KMRAQLKTTLAKLRKEAERKKSAKVSRTDLF 74
                                      34445578899*************9999877 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.24
                                       EEEEEESTTSSHHHHHHHHHHHTTSSC CS
                          GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgais 31 
                                       +++++g  ++GK+T++  ++ ++ ++s
  gi|557694724|ref|YP_008797778.1|  83 TVALLGVANSGKSTIIRFMTNAKAEVS 109
                                       67889999*******988877766655 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0044
                                       GGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTE.....EEEEEESCGST......HHHHHHHHHHHH CS
                          GTP_EFTU  82 dFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvp.....iivfiNKmDrl......kaelkeiveevk 147
                                        F++  i+++r +D+ +l +d +++ e+q  ++++l+ + g+      + v + K D          ++  + ee+k
  gi|557694724|ref|YP_008797778.1| 147 PFTSRSIAAARGADLILLTLDGMRDLEEQYLRLVELLEDSGITlgaksFEVEVEKKDSGgirivlFGRFHGSLEELK 223
                                       59999*******************************99999876555666677777766666666555555555555 PP

                                       HHHHHH...........H CS
                          GTP_EFTU 148 qklsrk...........e 154
                                       ++l++            e
  gi|557694724|ref|YP_008797778.1| 224 RELQQIglrnavvkiygE 241
                                       555444444455555550 PP

>> Ubiquitin_4  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.1   1.6e+03      21      76 ..     217     230 ..     195     237 .. 0.51
   2 ?    9.5   0.2   0.00066      0.99      14      39 ..     328     353 ..     314     369 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.1
                       Ubiquitin_4  21 atvkdLkkaierkvelklkrekekkkisWkyvWktycLsfegekLkddkaklkeyg 76 
                                        ++++Lk                                           +l+++g
  gi|557694724|ref|YP_008797778.1| 217 GSLEELK------------------------------------------RELQQIG 230
                                       4444444..........................................4444444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00066
                       Ubiquitin_4  14 evvvkqnatvkdLkkaierkvelklk 39 
                                       +vvvk+++tvk+L + i+r++++ lk
  gi|557694724|ref|YP_008797778.1| 328 PVVVKKGTTVKELAQIIHREIAEELK 353
                                       79******************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1051  (0.0586201); expected 358.6 (0.02)
Passed bias filter:                      743  (0.0414412); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 2884.59
//
Query:       gi|557694725|ref|YP_008797779.1|  [L=98]
Description: V-type H+-transporting ATPase subunit F [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   51.5   0.0    9.3e-14   51.5   0.0    1.0  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit
  ------ inclusion threshold ------
      0.022   14.5   0.0      0.023   14.4   0.0    1.1  1  LUD_dom     LUD 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 !   51.5   0.0     1e-17   9.3e-14       1      74 [.       3      78 ..       3      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 1e-17
                                      EEEEESHHHHHHHHHTTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCS.SSSEEEEE.S CS
                        ATP-synt_F  1 iavIGdedtvtgfrlaGvgevevtdeeeieealkelleredigiilitekiaeeirelideykee.alPaileI.P 74
                                      ++++G   +v gf laG ++v v+++ee+ +++kel+ r+d+g+i+++e++ e++r+++++++ + ++P++ e+ P
  gi|557694725|ref|YP_008797779.1|  3 VYAVGGATFVNGFILAGAEGVAVNTPEEAFKTIKELMGRPDVGLIIVSEDLSEKFRDELNDLRARkPTPLVYELsP 78
                                      578999***********************************************************9*****99844 PP

>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.6e-06     0.023      11      48 ..      18      55 ..       9      74 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-06
                           LUD_dom 11 ngaevyyaktaeealelilellkeksvvseggstdlge 48
                                       gae + ++t eea ++i+el+ + +v++  +s+dl e
  gi|557694725|ref|YP_008797779.1| 18 AGAEGVAVNTPEEAFKTIKELMGRPDVGLIIVSEDLSE 55
                                      68999*******************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 718.36
//
Query:       gi|557694726|ref|YP_008797780.1|  [L=199]
Description: V-type H+-transporting ATPase subunit E [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-12   47.2  11.1      2e-12   46.9  11.1    1.1  1  vATP-synt_E    ATP synthase (E/31 kDa) subunit
  ------ inclusion threshold ------
      0.032   14.4   0.8      0.054   13.6   0.8    1.4  1  RasGAP_C       RasGAP C-terminus
       0.23   12.3   0.9         11    6.9   0.9    2.5  1  CTD_bind       RNA polymerase II-binding domain.
       0.24   11.1   2.5        1.9    8.1   0.3    2.2  2  NUC173         NUC173 domain
        0.3   11.2   4.1        6.6    6.9   0.2    3.5  3  ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein


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 !   46.9  11.1   5.7e-16     2e-12       2     198 ..      12     195 ..      11     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 5.7e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       vATP-synt_E   2 IrqeAeekAeeIkakaeeefeiekaklveeeeekieeayekkeKqaelqkkiaiSnalnkarlkvLkareevleevf 78 
                                       + q+A + A ++ + ae+e+ + ++++++e  +++++  e+ +   +++ ++++S+a  +++     a ee ++++f
  gi|557694726|ref|YP_008797780.1|  12 VLQDALANALRVLEAAENEALEVVNRVEREVLQELAQMEESGKASRQAAVQRILSTAEIQSKNMAIAAVEEEVNKIF 88 
                                       689***************************77777777776666666677789************************ PP

                                       HHHHHHHHHHTTSHHCCCCHHHHHHCCCCCCC-SSCEEEEECCCCHHCCCCTHCCCCCCHHCCSSSS--SEEEEESS CS
                       vATP-synt_E  79 eeaekkLaeveedkdeYkellkkLivqalvkleepevivrarkeDaelveealdkaaeeykaktkkktvevagdeed 155
                                       e + +k+a+ +    e+k++l+kL+++  v++++ +++v  +++  +l++e+   a ++y  k     v v+++   
  gi|557694726|ref|YP_008797780.1|  89 ESVLEKIAKESGAP-EFKKVLTKLLDET-VQVMGRDIVVETNEAALPLLREV--VADKKYGVK-----VVVSDK--- 153
                                       *********99999.**********996.7899999***************7..456666664.....223344... PP

                                       EBTTSSSEEEECCSSSCEEECCCHHHCHHHHHHHHHHCCCCCH CS
                       vATP-synt_E 156 fledvlGGvvleaadgkikvnnTlearLelvleqllpeirkaL 198
                                        ++ ++ G    + dg ++ +n+ earLe+++  l+ ei+k L
  gi|557694726|ref|YP_008797780.1| 154 -PAPIMAGLRATSLDGSMRYDNSVEARLERLKPILRTEIAKML 195
                                       .488***********************************9987 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.8   1.5e-05     0.054       3      65 ..      37      98 ..      35     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.5e-05
                          RasGAP_C  3 elkkkalenlkeLeelgvisrennyqellneIakdirnkgrlrekrkeElesl.eetlktLsek 65
                                      ++ +++l+ l ++ee+g+ sr+   q +l+  +++i++k+ ++  ++eE++++ e++l+++ + 
  gi|557694726|ref|YP_008797780.1| 37 RVEREVLQELAQMEESGKASRQAAVQRILS--TAEIQSKNMAIAAVEEEVNKIfESVLEKIAKE 98
                                      67799*************************..69***************976538899999875 PP

>> CTD_bind  RNA polymerase II-binding domain.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.9     0.003        11      20      55 ..      77     113 ..       8     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.003
                          CTD_bind  20 kdefapaFapvlpeafadayk.kapekikkklkrlln 55 
                                          + ++  +++++++++++k + +++ kk l++ll+
  gi|557694726|ref|YP_008797780.1|  77 IAAVEEEVNKIFESVLEKIAKeSGAPEFKKVLTKLLD 113
                                       4445556666667777777777667778888888886 PP

>> NUC173  NUC173 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.3     0.012        43      14      69 ..      13      68 ..       4      72 .. 0.82
   2 ?    8.1   0.3   0.00053       1.9      28      80 ..      76     126 ..      56     143 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.012
                            NUC173 14 yqaawkevlevlsalfeklgkrsspllkkilktlgelreseefelkkeadevigaa 69
                                       q a  + l+vl+a+ ++  + ++ + +++l++l++++es +++ + ++++++++a
  gi|557694726|ref|YP_008797780.1| 13 LQDALANALRVLEAAENEALEVVNRVEREVLQELAQMEESGKASRQAAVQRILSTA 68
                                      4678888888998888888888888899***********99988888998888776 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00053
                            NUC173  28 lfeklgkrsspllkkilktlgelreseefelkkeadevigaairamGpevvLe 80 
                                       ++ +++++++++++++l+++++   ++  e+kk +++ +   +++mG + v e
  gi|557694726|ref|YP_008797780.1|  76 AIAAVEEEVNKIFESVLEKIAKESGAP--EFKKVLTKLLDETVQVMGRDIVVE 126
                                       334444555666777777776666665..579***************999975 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 ?    3.3   0.1     0.024        87      51      77 ..       4      30 ..       4      34 .. 0.79
   2 ?   -0.6   0.1      0.39   1.4e+03      56      75 ..      38      57 ..      35      66 .. 0.75
   3 ?    6.9   0.2    0.0018       6.6       5      48 ..     103     145 ..      80     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.024
                                      CHHHHHHHHTHHHHHHHHHTTSSSTTS CS
                     ClpB_D2-small 51 pLrriiqreiedplaeeilsgelkegd 77
                                      pL ++i++ ++d+la+++   e +e++
  gi|557694726|ref|YP_008797780.1|  4 PLSKVINEVLQDALANALRVLEAAENE 30
                                      8999***********998766666655 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.39
                                      HHHHTHHHHHHHHHTTSSST CS
                     ClpB_D2-small 56 iqreiedplaeeilsgelke 75
                                      ++re++++la++  sg+ + 
  gi|557694726|ref|YP_008797780.1| 38 VEREVLQELAQMEESGKASR 57
                                      68899999998877776554 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0018
                                       HHHHHHHHHHHHHHHHSCTTTEEEEEHHHHHHHHHHHTSBTTTB CS
                     ClpB_D2-small   5 elkkIvdlalkklekrlkergvelevtdealdalaekgydpeyG 48 
                                       e kk++++ l++  + +  r++ +e  ++al  l e   d++yG
  gi|557694726|ref|YP_008797780.1| 103 EFKKVLTKLLDETVQVMG-RDIVVETNEAALPLLREVVADKKYG 145
                                       567899999999888776.9***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1939  (0.108149); expected 358.6 (0.02)
Passed bias filter:                      820  (0.045736); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 1523.15
//
Query:       gi|557694727|ref|YP_008797781.1|  [L=267]
Description: 5'-nucleotidase SurE [Candidatus Caldiarchaeum subterraneum]
Scores for 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-52  176.7   0.0    5.4e-52  176.4   0.0    1.1  1  SurE      Survival protein SurE


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.4   0.0     3e-56   5.4e-52       1     194 [.       4     198 ..       4     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 3e-56
                                       EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHH CS
                              SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvkla 77 
                                       iL+tNDDG+   g+ al + l++ g ev+vvaP+s rS++g+++tl++plr+++ +  +++ +y++sGtP+dcv +a
  gi|557694727|ref|YP_008797781.1|   4 ILVTNDDGVLKTGLWALHDVLKDLG-EVTVVAPESMRSAVGMSITLHKPLRLRKIRV-GGKIAYSCSGTPSDCVIMA 78 
                                       8*********************888.*************************995554.8****************** PP

                                       HHTTTTTS.SSEEEEEEEES---GGGG.GG-HHHHHHHHHHHTTSEEEEEEEESSS....SS-SSS---HHHHHHHH CS
                              SurE  78 leellkekkpdlVvSGiNhGaNlgtdv.lySGTvgAaleaalegipaiAvSlaskk....eeekkeedtfeaaakva 149
                                       ++++++ k pdlVvSGiN+G+N++ +  + SGT+gAa++a+l+g+pa A+Sl+  +    + ++  ++ +++aa+ a
  gi|557694727|ref|YP_008797781.1|  79 VRQVYRGKGPDLVVSGINEGNNVSLQSvYGSGTIGAAIRACLMGYPAAAFSLSLPEdrvpS-AEWMKTMMTKAAAKA 154
                                       *****999****************988688**********************998888843.334455588889999 PP

                                       HHHHTTETTS-...SS-EEEEEEESS.GCG-SEEEE-B--CCSCE CS
                              SurE 150 aklveklieklllekvellnvNvPeleeeeikgvkvtrlgrrrys 194
                                       + +++ ++e+ l + v++ln+N+P+   ++ +++ +tr +r+ry+
  gi|557694727|ref|YP_008797781.1| 155 KPIISYMLEHGLPPGVDYLNINFPHE-LTDSTRYVITRAARNRYK 198
                                       999999999999************65.44445599********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 00:00:00.39
# Mc/sec: 2066.18
//
Query:       gi|557694728|ref|YP_008797782.1|  [L=157]
Description: hypothetical protein CSUB_C1301 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1155.00
//
Query:       gi|557694729|ref|YP_008797783.1|  [L=143]
Description: transcriptional regulator, AsnC family [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-16   59.6   0.4    3.3e-16   58.8   0.4    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    5.8e-16   58.2   0.1    1.1e-15   57.3   0.1    1.5  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    1.5e-15   56.5   0.1    3.6e-15   55.2   0.3    1.6  2  HTH_24           Winged helix-turn-helix DNA-binding
    7.8e-07   28.5   0.1    1.4e-06   27.8   0.1    1.4  1  Sigma70_r4       Sigma-70, region 4
    0.00044   19.6   0.0    0.00069   19.0   0.0    1.3  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
    0.00096   19.0   1.8      0.045   13.6   0.0    2.8  3  TrmB             Sugar-specific transcriptional regulator Trm
     0.0019   18.0   0.0      0.004   17.0   0.0    1.5  1  HTH_5            Bacterial regulatory protein, arsR family
     0.0041   17.0   0.0     0.0073   16.2   0.0    1.4  1  MarR_2           MarR family
     0.0055   16.6   0.0      0.012   15.5   0.0    1.7  1  HTH_11           HTH domain
     0.0065   16.2   0.0      0.011   15.5   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
      0.009   16.1   0.0      0.017   15.1   0.0    1.4  1  HTH_20           Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.8   3.0       0.02   15.1   0.0    2.5  2  DUF4777          Domain of unknown function (DUF4777)
      0.027   15.0   0.2        0.1   13.2   0.2    2.0  2  ACT_4            ACT domain
      0.038   13.7   0.1       0.12   12.0   0.1    1.9  1  Sigma70_r4_2     Sigma-70, region 4
      0.041   13.7   0.0      0.084   12.7   0.0    1.5  1  HTH_23           Homeodomain-like domain
      0.051   13.2   0.2       0.19   11.4   0.2    2.0  1  HTH_50           Helix-turn-helix domain
      0.051   13.3   0.0        0.1   12.4   0.0    1.4  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.082   12.5   0.0       0.18   11.3   0.0    1.5  2  Chlor_dismutase  Chlorite dismutase
        0.1   12.6   0.1       0.36   10.8   0.0    1.9  2  MarR             MarR family
        0.1   13.0   0.0          3    8.3   0.0    2.3  2  FaeA             FaeA-like protein
        0.1   12.6   0.0       0.38   10.8   0.0    1.9  2  HTH_Mga          M protein trans-acting positive regulator (M
       0.11   12.4   0.0       0.26   11.3   0.0    1.5  1  HTH_1            Bacterial regulatory helix-turn-helix protei
       0.19   12.2   0.5       0.61   10.5   0.1    1.8  2  DUF2805          Protein of unknown function (DUF2805)


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 !   58.8   0.4   4.3e-19   3.3e-16       1      41 [.       5      45 ..       5      46 .. 0.97

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 4.3e-19
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      +DeiDrkI+e L+edaR+ ++e+++++GlSe +v+rRv+ L
  gi|557694729|ref|YP_008797783.1|  5 IDEIDRKIIEMLREDARRNFTEVGKALGLSEGAVRRRVKNL 45
                                      6**************************************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 !   57.3   0.1   1.5e-18   1.1e-15       3      75 .]      70     139 ..      68     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 1.5e-18
                                       EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEEE CS
                    AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivlet 75 
                                       +s+ p+   ++ e++++l +l+ V+e+y +tG  d +++++v+++ al+++++e ++++ gv +t+tsi+l++
  gi|557694729|ref|YP_008797783.1|  70 ISVHPSV--PTPEVADKLIKLEGVEEVYEITGTRDVMAIITVPSMSALNKVIEE-IRNISGVNETNTSIILRQ 139
                                       5666555..889******************************************.****************86 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 !   55.2   0.3   4.7e-18   3.6e-15       2      48 .]       6      52 ..       5      52 .. 0.98
   2 ?   -3.4   0.0       9.7   7.5e+03      15      27 ..      73      85 ..      70      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 4.7e-18
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      de+drkI+e L++++r + +e+ ++lglS ++v+rr+k+L+++G+Ik
  gi|557694729|ref|YP_008797783.1|  6 DEIDRKIIEMLREDARRNFTEVGKALGLSEGAVRRRVKNLMDKGVIK 52
                                      9*********************************************8 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.7
                            HTH_24 15 nprisqreLAerl 27
                                      +p+ +  e+A++l
  gi|557694729|ref|YP_008797783.1| 73 HPSVPTPEVADKL 85
                                      6777888999986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   1.7e-09   1.4e-06       6      47 ..       6      48 ..       3      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.7e-09
                                      -HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHHHHHH CS
                        Sigma70_r4  6 pererevlelrf.geglTleEIgerlgiSrerVrqiekrAlrk 47
                                      +e +r+++e+ + +  +++ E+g+ lg+S+++Vr++ k+ ++k
  gi|557694729|ref|YP_008797783.1|  6 DEIDRKIIEMLReDARRNFTEVGKALGLSEGAVRRRVKNLMDK 48
                                      7889******999************************998887 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 !   19.0   0.0   8.9e-07   0.00069      17      50 ..       9      44 ..       6      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.9e-07
                      HTH_Tnp_ISL3 17 eayilellles..rsvkavArqlgvSwtTVwrildr 50
                                      +++i+e+l+e+  r++++v + lg+S+  V+r+++ 
  gi|557694729|ref|YP_008797783.1|  9 DRKIIEMLREDarRNFTEVGKALGLSEGAVRRRVKN 44
                                      799******************************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 !   13.6   0.0   5.8e-05     0.045      17      53 ..      16      52 ..       3      57 .. 0.85
   2 ?    4.2   0.0     0.053        41      17      64 ..      57     106 ..      51     110 .. 0.82
   3 ?   -0.4   0.1       1.4   1.1e+03      25      45 ..     119     139 ..     113     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.8e-05
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEE CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVe 53
                                      L +  + + +e+ ++lg+++  v + +++L+dkG+++
  gi|557694729|ref|YP_008797783.1| 16 LREDARRNFTEVGKALGLSEGAVRRRVKNLMDKGVIK 52
                                      4467788999************************986 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.053
                                       HH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                              TrmB  17 Ll..klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64 
                                       +l   +g + ++ i+ +  vp + v + L +Le    V+ + g++ ++  
  gi|557694729|ref|YP_008797783.1|  57 VLskDYGVKAVTFISVHPSVPTPEVADKLIKLEGVEEVYEITGTRDVMAI 106
                                       5555578888888999999*******************999999877765 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.4
                                       HCHHCCCTTSSCHCHHHHHHH CS
                              TrmB  25 adeiaeelgvprskvYevLrs 45 
                                       ++ei +++gv +++   +Lr+
  gi|557694729|ref|YP_008797783.1| 119 IEEIRNISGVNETNTSIILRQ 139
                                       689999999999988877775 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   5.2e-06     0.004       5      45 ..      10      51 ..       6      52 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.2e-06
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +kI+ +L+e   + ++e  ++lgls+++v++  k L++ G++
  gi|557694729|ref|YP_008797783.1| 10 RKIIEMLREdARRNFTEVGKALGLSEGAVRRRVKNLMDKGVI 51
                                      79*******888****************************98 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   9.3e-06    0.0073      14      51 ..      15      51 ..       9      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.3e-06
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSE CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLv 51
                                        r++ r+ + +e+ ++lgls +av r++k L ++G +
  gi|557694729|ref|YP_008797783.1| 15 MLREDARR-NFTEVGKALGLSEGAVRRRVKNLMDKGVI 51
                                      45666665.9**************************98 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.6e-05     0.012       3      44 ..      10      54 ..       9      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.6e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....v 44
                                      ++i+e+L+e +   +  e  + L++S+ +vrr++k L ++g    +
  gi|557694729|ref|YP_008797783.1| 10 RKIIEMLRE-DARRNFTEVGKALGLSEGAVRRRVKNLMDKGvikgF 54
                                      699****55.555899*********************999954444 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 !   15.5   0.0   1.4e-05     0.011       8      48 ..      12      51 ..      11      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      i+++l+e +++ +++e+ +++gl+  +v+R ++ L+  G +
  gi|557694729|ref|YP_008797783.1| 12 IIEMLREDARR-NFTEVGKALGLSEGAVRRRVKNLMDKGVI 51
                                      899*******9.************************99976 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   2.2e-05     0.017      12      55 ..       9      52 ..       4      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                                      HHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 12 RrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                       r+i  +L++++ + ++e+ ++l+ls   ++++++ L + g ++
  gi|557694729|ref|YP_008797783.1|  9 DRKIIEMLREDARRNFTEVGKALGLSEGAVRRRVKNLMDKGVIK 52
                                      599**********************************9998886 PP

>> DUF4777  Domain of unknown function (DUF4777)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   2.6e-05      0.02      28      56 ..      26      54 ..      24      62 .. 0.92
   2 ?    0.3   0.1       1.1   8.4e+02      22      38 ..     115     131 ..     103     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.6e-05
                           DUF4777 28 rvaerydlseeelkkvVkntLeaAvrhGF 56
                                       v++ ++lse  +++ Vkn+++++v++GF
  gi|557694729|ref|YP_008797783.1| 26 EVGKALGLSEGAVRRRVKNLMDKGVIKGF 54
                                      588999**********************9 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.1
                           DUF4777  22 ldEivervaerydlsee 38 
                                       l  ++e ++++ +++e 
  gi|557694729|ref|YP_008797783.1| 115 LNKVIEEIRNISGVNET 131
                                       67899999999998875 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       2.1   1.6e+03      65      79 ..      81      95 ..      70      98 .. 0.82
   2 ?   13.2   0.2   0.00013       0.1      47      77 ..     100     130 ..      78     132 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.1
                             ACT_4 65 viakLraipgVisVe 79
                                      v +kL +++gV++V+
  gi|557694729|ref|YP_008797783.1| 81 VADKLIKLEGVEEVY 95
                                      678888888888885 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00013
                             ACT_4  47 laeikitveVkdvehLsrviakLraipgVis 77 
                                       + ++   + V +++ L++vi+ +r+i+gV++
  gi|557694729|ref|YP_008797783.1| 100 TRDVMAIITVPSMSALNKVIEEIRNISGVNE 130
                                       556777899********************86 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 ?   12.0   0.1   0.00016      0.12      13      48 ..       7      43 ..       3      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHHTS---.HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 13 erqreifllrylegls.ykEIAellgisegtVksrls 48
                                      e++r+i+++ +++      E+ + lg+seg+V++r++
  gi|557694729|ref|YP_008797783.1|  7 EIDRKIIEMLREDARRnFTEVGKALGLSEGAVRRRVK 43
                                      8899999999999765279***************986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00011     0.084       9      45 ..      11      49 ..      10      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                            HTH_23  9 rillllae..GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      +i+ +l+e  + + +e+ ++Lg s+  v+r +k    +G
  gi|557694729|ref|YP_008797783.1| 11 KIIEMLREdaRRNFTEVGKALGLSEGAVRRRVKNLMDKG 49
                                      59999**999********************999887776 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00024      0.19       9      45 ..       6      43 ..       3      45 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                            HTH_50  9 eefErelikkayek.YpStRklAkrLGvShtaianklr 45
                                      +e++r++i+ + e     +  ++k+LG+S  a+ ++++
  gi|557694729|ref|YP_008797783.1|  6 DEIDRKIIEMLREDaRRNFTEVGKALGLSEGAVRRRVK 43
                                      6777777776665413455679**************98 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   0.0   0.00013       0.1       4      45 ..      11      52 ..       9      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                      +i+e+l+++   + +e+   lg Se  +RR  ++L  +g+++
  gi|557694729|ref|YP_008797783.1| 11 KIIEMLREDARRNFTEVGKALGLSEGAVRRRVKNLMDKGVIK 52
                                      8*************************************9975 PP

>> Chlor_dismutase  Chlorite dismutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.1   3.2e+03     168     184 ..      11      26 ..       2      31 .. 0.52
   2 ?   11.3   0.0   0.00024      0.18      17      57 ..      89     125 ..      78     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.1
                                       HHHHHHCTSHHHHHHEE CS
                   Chlor_dismutase 168 dlvyelRfdeasakvae 184
                                       ++++ lR+d a++ ++e
  gi|557694729|ref|YP_008797783.1|  11 KIIEMLRED-ARRNFTE 26 
                                       455555554.5555544 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00024
                                       SCEEEEEEEETSTTTT-SEEEEEEESSHHHHHHHHHHHHHS CS
                   Chlor_dismutase  17 egvlralysvlGlradaDlmlwllretleelqeaerelrrt 57 
                                       eg + ++y+++G+r   D+m +++ +++++l+++ +e+r+ 
  gi|557694729|ref|YP_008797783.1|  89 EG-VEEVYEITGTR---DVMAIITVPSMSALNKVIEEIRNI 125
                                       45.789********...********************9983 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00046      0.36       8      47 ..      12      51 ..      10      52 .. 0.88
   2 ?   -2.0   0.0       4.7   3.7e+03      21      39 ..     120     138 ..     116     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      i+++l+e    + +e +k+lg+s ++v r ++ L +kG i
  gi|557694729|ref|YP_008797783.1| 12 IIEMLREDARRNFTEVGKALGLSEGAVRRRVKNLMDKGVI 51
                                      5667777777789999**********************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.7
                                       HHHHHHHTS-HHHHHHHHH CS
                              MarR  21 seLakklgvskstvtrvld 39 
                                        e+ + +gv+ ++++ +l+
  gi|557694729|ref|YP_008797783.1| 120 EEIRNISGVNETNTSIILR 138
                                       5788888888888887776 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0038         3       4      46 ..      11      52 ..       8      57 .. 0.90
   2 ?    2.3   0.0      0.29   2.3e+02       7      24 ..      68      84 ..      65      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0038
                                      HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEE CS
                              FaeA  4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkik 46
                                      +I+e l +  a    +e+ +algls   +R   ++L  +g ik
  gi|557694729|ref|YP_008797783.1| 11 KIIEMLRE-DARRNFTEVGKALGLSEGAVRRRVKNLMDKGVIK 52
                                      68999999.999999*********************9999997 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.29
                                      HHHHH.S----HHHHHHH CS
                              FaeA  7 eylnsikapckTreiAda 24
                                      +++ s++ ++ T e+Ad 
  gi|557694729|ref|YP_008797783.1| 68 TFI-SVHPSVPTPEVADK 84
                                      555.56**********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 ?   10.8   0.0   0.00049      0.38       9      58 ..      11      60 ..       5      62 .. 0.88
   2 ?   -1.5   0.0       3.3   2.6e+03      33      45 ..     111     123 ..     108     126 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00049
                           HTH_Mga  9 kLlelLteneksltldelakeLglseltlqsdiseLnel.Fpeelsivikk 58
                                      k++e L e + + + +e+ k+Lglse +++ ++ +L +  +++ +++v++k
  gi|557694729|ref|YP_008797783.1| 11 KIIEMLRE-DARRNFTEVGKALGLSEGAVRRRVKNLMDKgVIKGFTVVLSK 60
                                      79999999.99999**********************988788888887777 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.3
                           HTH_Mga  33 seltlqsdiseLn 45 
                                       s+++l++ i+e++
  gi|557694729|ref|YP_008797783.1| 111 SMSALNKVIEEIR 123
                                       7899999999986 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   0.00033      0.26      14      37 ..      22      45 ..      19      48 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                                      SSHHHHHHHHTS-HHHHHHHHHHH CS
                             HTH_1 14 gsftrAAeeLglsqpavsrqikrL 37
                                      ++ft+  ++Lgls  av r++k+L
  gi|557694729|ref|YP_008797783.1| 22 RNFTEVGKALGLSEGAVRRRVKNL 45
                                      79********************98 PP

>> DUF2805  Protein of unknown function (DUF2805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00078      0.61       2      37 ..      11      47 ..      10      52 .. 0.88
   2 ?   -1.0   0.0         3   2.3e+03      15      34 ..     120     139 ..     117     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00078
                           DUF2805  2 riiemAweD.RtpFeaIeeqfglsekeviklMrkelk 37
                                      +iiem  eD R  F  + +  glse  v +  ++ + 
  gi|557694729|ref|YP_008797783.1| 11 KIIEMLREDaRRNFTEVGKALGLSEGAVRRRVKNLMD 47
                                      8*******9999*************999887777665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3
                           DUF2805  15 eaIeeqfglsekeviklMrk 34 
                                       e I++  g++e ++  ++r+
  gi|557694729|ref|YP_008797783.1| 120 EEIRNISGVNETNTSIILRQ 139
                                       78999999999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); 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: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1030.50
//
Query:       gi|557694730|ref|YP_008797784.1|  [L=355]
Description: N-acetyl-gamma-glutamyl-phosphate reductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  116.0   0.0    2.1e-33  115.3   0.0    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    3.4e-12   46.8   0.0      6e-12   46.0   0.0    1.4  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
  ------ inclusion threshold ------
      0.025   15.4   0.0       0.05   14.4   0.0    1.4  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


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 !  115.3   0.0   3.5e-37   2.1e-33       1     121 []       7     147 ..       7     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 3.5e-37
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTT.TECEBEEEGGGGGC.TT-SEEEE-SC CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkalee.gkdlkvedvdeeel.kevdivflalp 75 
                                       +v++vG++Gy+G ellr+L+ hp+ve+++++s++  aGk++++ +++l++ +k lk+++vd e++ ++++ vf  +p
  gi|557694730|ref|YP_008797784.1|   7 RVGVVGGSGYTGGELLRILAVHPNVEVTYVTSREY-AGKPFTAIHPHLRGfYKGLKFSNVDVEAIvEKCETVFVNTP 82 
                                       79*********************************.**********77763789*****8888888*********** PP

                                       HHHHHHHHHHHHHTTSEEEESSSTTTTST...................TSEBE-HHHHGGGGGGH CS
                    Semialdhyde_dh  76 agvskelapklaeagvkviDlssdfRlkd...................davyvlpevnreaikka 121
                                       +gvs+ l+p+++e+g++v Dls+dfRl++                   +avy+lpe++re+ik+a
  gi|557694730|ref|YP_008797784.1|  83 HGVSSTLTPQFLERGLRVLDLSADFRLRNptdyekwyetkhprpelldKAVYGLPEIYRETIKNA 147
                                       **************************************************************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 !   46.0   0.0     1e-15     6e-12       2     184 .]     165     325 ..     164     325 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1e-15
                                       HHHHHC.TT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHH CS
                   Semialdhyde_dhC   2 kPLlda.lgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetree 77 
                                        P +++ +++le+++v+ + + S aG k                 ++ g+++ + a  + py  +  +++  e+++e
  gi|557694730|ref|YP_008797784.1| 165 VPAVENgIIDLEKIVVDIKVGSSEAGIK-----------------PSLGTHHPERANVMRPYEAE-GHRHVAEVEQE 223
                                       57788889999****************8.................99***************998.9********** PP

                                       HHHHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCS..TTEEEEESS..HCHHSSHHH CS
                   Semialdhyde_dhC  78 lkavaetkkileftekvsatcvrVPvlrGhseavtiklklkdveveeveellaaa..pevkvvvne..eedrPtpaa 150
                                       l+ +a + ++++  +      + V+++rG ++++++ ++++d++ + v++ +a+   +e+++++ +    ++P p+ 
  gi|557694730|ref|YP_008797784.1| 224 LSLLAGKPVRVALVP------HAVGAVRGALATAHVWFSNQDADENMVWKVYASRyaKEPFIRIVHgtPFRYPDPKY 294
                                       ***************......89****************5555555555555444555999999998788******* PP

                                       HTTCSSSEEEEEEEEETTCTTEEEEEEEEETTTT CS
                   Semialdhyde_dhC 151 vaggtnsvsVGRirkdemgdeglklvvvgDNllk 184
                                       v+g +n+++VG + + ++  +  +l++++DNl+k
  gi|557694730|ref|YP_008797784.1| 295 VVG-SNFADVG-FAVEKRIGR-AALFAAIDNLMK 325
                                       **9.9******.*****9998.**********97 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 ?   14.4   0.0   8.3e-06      0.05       1      90 [.       6     101 ..       6     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.3e-06
                                       EEEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE......EESS..HHHHHTCTTESEEEE CS
                      GFO_IDH_MocA   1 lrvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgve......aysd..leelladpeidaviv 68 
                                       +rv+++G+ G+ g + l  + + +++ ev+ + +++ +     a + ++        +s+  +e++++  +++ v+v
  gi|557694730|ref|YP_008797784.1|   6 VRVGVVGGsGYTGGELL-RILAVHPNVEVTYVTSREYAGKPFTAIHPHLRgfykglKFSNvdVEAIVE--KCETVFV 79 
                                       589***99777788888.555555**************999999999999844444444455666666..******* PP

                                       -S-GGGHHHHHHHHHHTT-EEE CS
                      GFO_IDH_MocA  69 atpngtheelakaaleagkhvl 90 
                                        tp g    l+ ++le+g  vl
  gi|557694730|ref|YP_008797784.1|  80 NTPHGVSSTLTPQFLERGLRVL 101
                                       ******************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2615.61
//
Query:       gi|557694731|ref|YP_008797785.1|  [L=264]
Description: acetylglutamate/acetylaminoadipate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-36  124.8   6.3    4.6e-36  124.6   6.3    1.0  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 !  124.6   6.3   2.6e-40   4.6e-36       2     241 .]       1     244 [.       1     244 [. 0.93

  Alignments for each domain:
  == domain 1  score: 124.6 bits;  conditional E-value: 2.6e-40
                                       EEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC........E..HHHH CS
                         AA_kinase   2 rvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa....glrstleeag 74 
                                       ++VvK GG +l+++ +    +++e +a+++++g  +v VhGgg ++ +  ++  g++++   +    + r+t+ ++ 
  gi|557694731|ref|YP_008797785.1|   1 MIVVKAGGRALESNRQ----KILESVARHSSDG--VVFVHGGGDVVSEFERR-LGVEPKIVVSpsgvRSRLTDSAEI 70 
                                       59**********6655....7999999996666..*****************.999999999999999********* PP

                                       HHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..................HHHTTTCEEECCHHHHHH CS
                         AA_kinase  75 evatrdalaslgerlvaallaaglpavglsaaaldateagr................degsdgnvesvdaeaieell 135
                                       ev t++++++lg+++ a l + g++av+ls+ +  +++a+r                d g++g+++ vdae i++ll
  gi|557694731|ref|YP_008797785.1|  71 EVYTMVMAGKLGKEIAATLNRLGVKAVNLSGVDASIIKAQRkkkivivdergrkrvvDGGYTGTITDVDAELIKHLL 147
                                       ***************************************************************************** PP

                                       HTT-EEEEESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSS CS
                         AA_kinase 136 eagvvpvltgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesas 212
                                         g v v+++++ + +egel+++++D +aa++A  ++Ad+l +ltdV+G++  d+  v   + l+   + e+++   
  gi|557694731|ref|YP_008797785.1| 148 GLGLVLVVSPLA-IGDEGELLNVDGDSAAAAIASSMRADRLYLLTDVEGLLL-DGQLV---KSLTAAQALEMLD--- 216
                                       **********97.999***9******************************84.45566...6666666666666... PP

                                       S.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 213 elatgGmkvkhpaalaaarrggipvvItn 241
                                         +  Gm+ k+  a++a+++g+ +++I++
  gi|557694731|ref|YP_008797785.1| 217 -KIGPGMNRKVMMAARAVQSGVKRAHICS 244
                                       .8999**********************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1833.28
//
Query:       gi|557694732|ref|YP_008797786.1|  [L=58]
Description: lysine biosynthesis protein LysW [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-06   27.8   0.2    2.9e-06   27.5   0.2    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0012   18.4   2.6     0.0021   17.6   2.6    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0037   17.2   0.2     0.0058   16.5   0.1    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0058   16.7   1.3        2.3    8.4   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
     0.0074   16.2   0.3        1.9    8.4   0.1    2.1  2  Cys_rich_CPXG    Cysteine-rich CPXCG
  ------ inclusion threshold ------
      0.011   15.7   2.1      0.067   13.2   0.6    2.2  2  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
      0.016   15.2   0.1      0.031   14.2   0.1    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.024   14.5   0.8        6.7    6.7   0.0    2.2  2  Nudix_N_2        Nudix N-terminal
      0.032   14.5   0.9       0.63   10.4   0.7    2.1  2  Prim_Zn_Ribbon   Zinc-binding domain of primase-helicase
      0.052   13.3   0.5        4.6    7.1   0.1    2.2  2  zf-HYPF          HypF finger
      0.062   13.2   0.7      0.092   12.6   0.7    1.3  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.069   13.5   0.0      0.081   13.2   0.0    1.1  1  DUF5497          Family of unknown function (DUF5497)
      0.098   12.4   3.1        5.7    6.7   0.2    2.2  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.28   11.6   2.5        7.9    7.0   0.1    2.3  2  zf-IS66          zinc-finger binding domain of transposase IS


Domain annotation for each model (and alignments):
>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.2   2.3e-09   2.9e-06       4      50 ..       4      45 ..       2      58 .] 0.73

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.3e-09
                   Lar_restr_allev  4 kpCPfCggravlersqrvvaeigqcvyCadCgastpwfkiaedeaea 50
                                      + CP Cgg  ++ ++ ++ +     ++C dCga + ++ i+e+   +
  gi|557694732|ref|YP_008797786.1|  4 LNCPVCGGSVEVPNDALPGE----LFECGDCGA-QLEYFIDEKNNSS 45
                                      58*****************9....9********.4555555444333 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.6   1.6e-06    0.0021       3      33 ..       6      38 ..       4      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                                      ETTTTCEE.CHEETSTTCE.EESSSSBEEEECC CS
                      TF_Zn_Ribbon  3 CPnCgstn.lveDpergel.vCtdCGlVledns 33
                                      CP+Cg++  + +D+  gel  C+dCG+ le+++
  gi|557694732|ref|YP_008797786.1|  6 CPVCGGSVeVPNDALPGELfECGDCGAQLEYFI 38
                                      ******5448888999***89*********984 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 !   16.5   0.1   4.5e-06    0.0058      30      55 ..       5      33 ..       4      39 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.5e-06
                    OrfB_Zn_ribbon 30 tCseCgsknke...alsgrtfkCpnCgfe 55
                                      +C++Cg  ++    al g++f+C +Cg++
  gi|557694732|ref|YP_008797786.1|  5 NCPVCGGSVEVpndALPGELFECGDCGAQ 33
                                      6******9999999*************87 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0029       3.7      27      37 ..       4      14 ..       1      15 [. 0.77
   2 !    8.4   0.1    0.0018       2.3       6      18 ..      25      37 ..      24      48 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8 27 taCPeCgsevr 37
                                        CP Cg+ v+
  gi|557694732|ref|YP_008797786.1|  4 LNCPVCGGSVE 14
                                      45*****9775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0018
                       Zn-ribbon_8  6 YrCeeCghefevl 18
                                      ++C +Cg + e +
  gi|557694732|ref|YP_008797786.1| 25 FECGDCGAQLEYF 37
                                      89******99955 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1    0.0015       1.9       2      17 ..       5      20 ..       4      23 .. 0.84
   2 !    6.3   0.0    0.0067       8.6       2      18 ..      26      42 ..      25      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0015
                     Cys_rich_CPXG  2 qCPyCgeeievlvDls 17
                                      +CP Cg ++ev  D+ 
  gi|557694732|ref|YP_008797786.1|  5 NCPVCGGSVEVPNDAL 20
                                      6*********998876 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0067
                     Cys_rich_CPXG  2 qCPyCgeeievlvDlsa 18
                                      +C  Cg+++e ++D  +
  gi|557694732|ref|YP_008797786.1| 26 ECGDCGAQLEYFIDEKN 42
                                      6999**********766 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 ?   13.2   0.6   5.2e-05     0.067       1      10 [.       5      14 ..       5      20 .. 0.84
   2 ?    2.2   0.0      0.14   1.8e+02       2      11 ..      27      36 ..      26      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-05
                    DNA_ligase_ZBD  1 hCPvCGsavv 10
                                      +CPvCG  v+
  gi|557694732|ref|YP_008797786.1|  5 NCPVCGGSVE 14
                                      6******998 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                    DNA_ligase_ZBD  2 CPvCGsavvR 11
                                      C  CG+ ++ 
  gi|557694732|ref|YP_008797786.1| 27 CGDCGAQLEY 36
                                      5579999985 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 ?   14.2   0.1   2.5e-05     0.031      20      46 .]       5      33 ..       2      33 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                     Zn_Tnp_IS1595 20 vCPhCgsr..kayriktrglfqCkeCrkq 46
                                       CP Cg++   +      +lf+C +C++q
  gi|557694732|ref|YP_008797786.1|  5 NCPVCGGSveVPNDALPGELFECGDCGAQ 33
                                      6*****9986666666589*******998 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0053       6.8       3      11 ..       6      14 ..       5      22 .. 0.89
   2 ?    6.7   0.0    0.0052       6.7       3      17 ..      27      41 ..      27      45 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0053
                                      -TTT--B-E CS
                         Nudix_N_2  3 CsqCGtpve 11
                                      C+ CG+ ve
  gi|557694732|ref|YP_008797786.1|  6 CPVCGGSVE 14
                                      ******997 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0052
                                      -TTT--B-EEE--TT CS
                         Nudix_N_2  3 CsqCGtpvelripdg 17
                                      C  CG+++e+ i + 
  gi|557694732|ref|YP_008797786.1| 27 CGDCGAQLEYFIDEK 41
                                      999******999665 PP

>> Prim_Zn_Ribbon  Zinc-binding domain of primase-helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7   0.00049      0.63       5      12 ..       5      12 ..       3      13 .. 0.86
   2 ?    2.4   0.0      0.16     2e+02       5      23 ..      26      44 ..      23      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00049
                                      --TTTT-T CS
                    Prim_Zn_Ribbon  5 pCPvCGGr 12
                                       CPvCGG+
  gi|557694732|ref|YP_008797786.1|  5 NCPVCGGS 12
                                      6*****96 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.16
                                      --TTTT-TTTEEETT.... CS
                    Prim_Zn_Ribbon  5 pCPvCGGrDrFrfddkdgr 23
                                      +C  CG++  + +d+k+++
  gi|557694732|ref|YP_008797786.1| 26 ECGDCGAQLEYFIDEKNNS 44
                                      7888999888888887775 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0036       4.6      20      29 ..       2      11 ..       1      15 [. 0.80
   2 ?    4.9   0.0     0.018        22      24      32 ..      27      35 ..      23      37 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0036
                                      TT---TTTS- CS
                           zf-HYPF 20 qfisCtnCGP 29
                                      +  +C+ CG 
  gi|557694732|ref|YP_008797786.1|  2 PALNCPVCGG 11
                                      678******6 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.018
                                      -TTTS--EE CS
                           zf-HYPF 24 CtnCGPrls 32
                                      C +CG +l 
  gi|557694732|ref|YP_008797786.1| 27 CGDCGAQLE 35
                                      99***9985 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 ?   12.6   0.7   7.2e-05     0.092       4      30 ..       6      33 ..       6      43 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.2e-05
                                      ESTTTSBEEEEECSCCCE.EEESSSS-E CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedkegkn.feCrqCgYe 30
                                      Cp Cg   ++++d +    feC  Cg+ 
  gi|557694732|ref|YP_008797786.1|  6 CPVCGGSVEVPNDALPGElFECGDCGAQ 33
                                      ***************9889******987 PP

>> DUF5497  Family of unknown function (DUF5497)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.4e-05     0.081      16      45 ..      23      52 ..      17      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-05
                           DUF5497 16 elfkigevaqrlnyylqeyanlemqieeei 45
                                      elf  g+   +l+y+++e  n  +++ ee+
  gi|557694732|ref|YP_008797786.1| 23 ELFECGDCGAQLEYFIDEKNNSSLKVAEEV 52
                                      9***************************98 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 ?    6.5   0.3    0.0053       6.7       6      12 ..       5      11 ..       2      18 .. 0.80
   2 ?    6.7   0.2    0.0045       5.7       6      18 ..      26      39 ..      23      40 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0053
                           zf-RRN7  6 pCgvCgc 12
                                       C+vCg+
  gi|557694732|ref|YP_008797786.1|  5 NCPVCGG 11
                                      5*****8 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0045
                           zf-RRN7  6 pCgvCgc.rsftld 18
                                       Cg Cg+  ++++d
  gi|557694732|ref|YP_008797786.1| 26 ECGDCGAqLEYFID 39
                                      7******6588876 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 ?    7.0   0.1    0.0062       7.9       3      14 ..       5      15 ..       4      20 .. 0.74
   2 ?    4.9   0.4     0.027        34       4      12 ..      27      35 ..      26      54 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0062
                           zf-IS66  3 tCpcCGgllkpi 14
                                      +Cp CGg  +++
  gi|557694732|ref|YP_008797786.1|  5 NCPVCGGS-VEV 15
                                      6******6.354 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.027
                           zf-IS66  4 CpcCGgllk 12
                                      C +CG++l 
  gi|557694732|ref|YP_008797786.1| 27 CGDCGAQLE 35
                                      *****9654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 418.35
//
Query:       gi|557694733|ref|YP_008797787.1|  [L=281]
Description: lysine biosynthesis protein LysX [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-27   96.2   0.0    2.4e-27   95.8   0.0    1.2  1  RimK         RimK-like ATP-grasp domain
    2.8e-07   30.1   0.0      4e-07   29.6   0.0    1.2  1  GSH-S_ATP    Prokaryotic glutathione synthetase, ATP-grasp do
      6e-05   22.6   0.0    0.00026   20.6   0.0    1.9  2  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
    0.00013   21.3   0.0      0.016   14.5   0.0    2.1  2  ATPgrasp_ST  Sugar-transfer associated ATP-grasp
    0.00023   20.8   0.0    0.00051   19.6   0.0    1.5  1  ATP-grasp    ATP-grasp domain
    0.00098   19.2   0.1      0.013   15.6   0.1    2.5  1  ATP-grasp_3  ATP-grasp domain
     0.0011   18.5   0.0     0.0015   18.0   0.0    1.3  1  ATP-grasp_5  ATP-grasp domain


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 !   95.8   0.0   9.4e-31   2.4e-27       2     186 ..      86     273 ..      85     275 .. 0.90

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 9.4e-31
                                       H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--.. CS
                              RimK   2 rdKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlealkeai.. 76 
                                        dKl++  lLa++++++p+ta+a + e a +  +ki  +fPvvvK v gs G ++  a +eq+l ++le  +e++  
  gi|557694733|ref|YP_008797787.1|  86 ADKLLTSCLLARKNVPTPVTAIAFNRETALNAAKKI--GFPVVVKPVSGSWGRNIARAFDEQSLLDILEL-RENMpn 159
                                       69*********************************9..6****************************996.333334 PP

                                       ......EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEE CS
                              RimK  77 ......lvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvva 147
                                              +qe++++  ++diR + v +ev  a+ rvsk+  +++n  +Gg+a++  +++e+ +l ika +a++  v+
  gi|557694733|ref|YP_008797787.1| 160 pqmkihYIQEHVDK-PERDIRAFYVWGEVPVAIYRVSKN--WKTNTALGGKAQPCPVTDELADLVIKAGDAVGGGVL 233
                                       44244556666654.349********************9..************************************ PP

                                       EEEEEEE.TTEEEEEEEESS--SHHHHHHHT--HHHHHHH CS
                              RimK 148 GvDllra.krgllvlEvnsspglekiektlgidiakklie 186
                                       GvD+l++ ++g+lv Evn  ++ ++    +g d+ +k++e
  gi|557694733|ref|YP_008797787.1| 234 GVDVLESrEKGMLVSEVNGVVEFRNTVLVTGYDLPTKIVE 273
                                       ***88763799*************999999*999999987 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 !   29.6   0.0   1.6e-10     4e-07      12     154 ..     102     240 ..      88     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.6e-10
                                       S--EEEES-HHHHHHHHHHHSS.EEEEESS--TTTT-EEE-TT-TTHHHHH...HHHTTTTTS-EEEEE--GGGGG- CS
                         GSH-S_ATP  12 ipktlvskdkeeirafleeqgd.vilKPldgkgGegvfrvkksdpnlksil...ellteegkepviaqrylpeikeG 84 
                                       +p t ++ ++e+  + +++ g  v++KP++g+ G+++ r  +++ +l  il   e + + + +   +q+++++ ++ 
  gi|557694733|ref|YP_008797787.1| 102 TPVTAIAFNRETALNAAKKIGFpVVVKPVSGSWGRNIARAFDEQ-SLLDILelrENMPNPQMKIHYIQEHVDKPER- 176
                                       68899998888777777777766****************98754.4444550005555556666666777666555. PP

                                       EEEEEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETT CS
                         GSH-S_ATP  85 DkRillvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigd 154
                                       D R + v Ge    a+ Rv++  + ++n a gg+a+  ++t++   +  + +    + G  + G+Dv+++
  gi|557694733|ref|YP_008797787.1| 177 DIRAFYVWGEVP-VAIYRVSK--NWKTNTALGGKAQPCPVTDELADLVIKAG---DAVGGGVLGVDVLES 240
                                       *********965.59****86..6889*************997665555544...455666778888765 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     1e-07   0.00026       1      70 [.      87     154 ..      87     178 .. 0.78
   2 ?   -0.7   0.0      0.32   8.3e+02     163     195 ..     237     267 ..     216     274 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1e-07
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkka 70 
                                       Dk   + +l++ nvp+   ++a   + e+al++ak+ig+Pv++k+  g  G+    a +e+ l ++++  
  gi|557694733|ref|YP_008797787.1|  87 DKLLTSCLLARKNVPTPVTAIA--FNRETALNAAKKIGFPVVVKPVSGSWGRNIARAFDEQSLLDILELR 154
                                       5666666778888888777777..899*******************999999888888888888887655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.32
                                       EEETTTTEEEEEEEESS--CCHHHHHHHHS--H CS
                       CPSase_L_D2 163 lldpkskeyyviEvNtRlsvesalaekaTGldl 195
                                       +l++++k + v EvN  ++   ++   +TG+dl
  gi|557694733|ref|YP_008797787.1| 237 VLESREKGMLVSEVNGVVEFRNTV--LVTGYDL 267
                                       345567777778888877666655..6888887 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 !   14.5   0.0   6.1e-06     0.016      10      80 ..      76     142 ..      73     161 .. 0.87
   2 !    4.7   0.0    0.0058        15     223     264 ..     212     252 ..     199     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.1e-06
                       ATPgrasp_ST  10 yNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvit 80 
                                       +N+ + + + +dKl+++ l+ r+ +++p + + ++ +  +++++++  ++ + vv+Kp+ gs+G+ i  ++
  gi|557694733|ref|YP_008797787.1|  76 VNNTQVLRNSADKLLTSCLLARKNVPTPVTAIAFNRETALNAAKKI--GF-P-VVVKPVSGSWGRNIARAF 142
                                       57777888889******************99999999999988876..56.5.7***********997664 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0058
                       ATPgrasp_ST 223 PnweevlelaakaaeklpglgylGwDivldeekgplllElNa 264
                                       P  +e+ +l+ ka +  +g g+lG+D+   +ekg l+ E+N 
  gi|557694733|ref|YP_008797787.1| 212 PVTDELADLVIKAGD-AVGGGVLGVDVLESREKGMLVSEVNG 252
                                       67789999******9.99**********************96 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0     2e-07   0.00051       3     156 ..      97     250 ..      95     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2e-07
                                       TTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC.......GTTCEEEEE-- CS
                         ATP-grasp   3 klglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal.......keekvivEefv 72 
                                       + ++p+p  +++ ++e + +aa+++g+pvvvK ++ g+ G+      +e++l ++le          + + i E++ 
  gi|557694733|ref|YP_008797787.1|  97 RKNVPTPVTAIAFNRETALNAAKKIGFPVVVK-PVSGSWGRNIARAFDEQSLLDILELRenmpnpqMKIHYIQEHVD 172
                                       67899999999999999999************.*****************999999988888887444444555555 PP

                                       --SEEEEEEEEEETTC-EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTC CS
                         ATP-grasp  73 pfekElsvlvvrsaeGetafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledg 149
                                       + e+ + +  v  +   +a+y v ++ + +  l    +p++v+     + ++++ k+ +++gg Gv++v + + +++
  gi|557694733|ref|YP_008797787.1| 173 KPERDIRAFYVWGEVP-VAIYRVSKNWKTNTALGGKAQPCPVT----DELADLVIKAGDAVGG-GVLGVDVLESREK 243
                                       6799999999998877.9**********************977....5667788888888886.9********9888 PP

                                       TEEEEEE CS
                         ATP-grasp 150 ellvnEl 156
                                        +lv+E+
  gi|557694733|ref|YP_008797787.1| 244 GMLVSEV 250
                                       8***998 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   4.9e-06     0.013       2     155 ..      86     251 ..      85     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.9e-06
                                       TSHHHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE.............. CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve....... 64 
                                       +dKl t   L +++v++P        ++  + +++   ++vvKp++G+ g  +  + +++++  ++e  e       
  gi|557694733|ref|YP_008797787.1|  86 ADKLLTSCLLARKNVPTPvtaiafnRETALNAAKKIGFPVVVKPVSGSWGRNIARAFDEQSLLDILELREnmpnpqm 162
                                       7*****************99988877777777788899**********99999888777777766665556677888 PP

                                       ...EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEE CS
                       ATP-grasp_3  65 ...lvqefieGkplSvsllsdgekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyv 138
                                           +qe ++  +  + +       +++a+ r   ++ +++ +  G+  p +   ++e+ +l+ ++  ++    G++
  gi|557694733|ref|YP_008797787.1| 163 kihYIQEHVDKPERDIRAFY-VWGEVPVAIYRVSKNW-KTNTALGGKAQPCP--VTDELADLVIKAGDAV--GGGVL 233
                                       87778888887777777666.4456677777666655.34477777777777..5667777777777777..46788 PP

                                       EEEEEESS..SEEEEEEE CS
                       ATP-grasp_3 139 GvDlvlkd.eepyviEvN 155
                                       GvD++ +  ++  v EvN
  gi|557694733|ref|YP_008797787.1| 234 GVDVLESReKGMLVSEVN 251
                                       888885443677777777 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     6e-07    0.0015      17      55 ..      93     131 ..      80     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6e-07
                       ATP-grasp_5  17 elleaygipvvetrlassaeeaveaaeeigypvvlKivs 55 
                                        ll+  ++p++ t +a + e a++aa++ig+pvv+K vs
  gi|557694733|ref|YP_008797787.1|  93 CLLARKNVPTPVTAIAFNRETALNAAKKIGFPVVVKPVS 131
                                       5899999*****************************888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1996.23
//
Query:       gi|557694734|ref|YP_008797788.1|  [L=393]
Description: acetylornithine aminotransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-110  368.9   0.0   3.3e-110  368.5   0.0    1.0  1  Aminotran_3     Aminotransferase class-III
    0.00052   19.3   0.0    0.00066   19.0   0.0    1.3  1  Aminotran_1_2   Aminotransferase class I and II
     0.0015   17.6   0.0     0.0026   16.8   0.0    1.3  1  Aminotran_5     Aminotransferase class-V
  ------ inclusion threshold ------
       0.11   12.8   0.0       0.21   11.8   0.0    1.5  1  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
       0.11   12.8   0.0       0.49   10.7   0.0    2.0  2  LIG3_BRCT       DNA ligase 3 BRCT domain


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 !  368.5   0.0  9.1e-114  3.3e-110      12     405 ..      15     380 ..       9     381 .. 0.98

  Alignments for each domain:
  == domain 1  score: 368.5 bits;  conditional E-value: 9.1e-114
                                       EEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..S CS
                       Aminotran_3  12 vitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgld 88 
                                        + +aeG y++d +g+rylD++ ++ ++ lGh+hP+vvka++eq+   + +  +a+ ++ + ++ + l k++p +l 
  gi|557694734|ref|YP_008797788.1|  15 RVARAEGQYVWDTEGRRYLDFYMGYGAAFLGHRHPRVVKALEEQLSRYMTIT-PAFDTDVLDACLDALGKILPPHLT 90 
                                       689*********************************************8888.************************ PP

                                       EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBG CS
                       Aminotran_3  89 kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypde 165
                                       +vf+ nsGseAve AlKl+rk       t + k++af+++fHGrt++als+t++ +ky+++f+pf+ evv+++++d 
  gi|557694734|ref|YP_008797788.1|  91 RVFFLNSGSEAVELALKLSRK------LTGRRKVLAFNNGFHGRTMAALSTTWN-PKYREGFEPFPFEVVFAPFND- 159
                                       *********************......9**************************.********************9. PP

                                       GGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTS CS
                       Aminotran_3 166 evlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTG 242
                                                       + a+e+k ++e aAvi+Ep+qgegG+++a+pef++++ + +++ +v ++vDEvq+GfGrTG
  gi|557694734|ref|YP_008797788.1| 160 ----------------IGAVEEKLSEEFAAVIFEPVQGEGGIIPAKPEFMKAVEKRAREMGVYVVVDEVQSGFGRTG 220
                                       ................99*********************************************************** PP

                                       SSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHHHHHHH CS
                       Aminotran_3 243 klfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekllenaqe 319
                                        ++A+e  g++pD++t aKa++gG+p+s +++t++v++ +++ +hgsT+gGnpla a++ a+ +++ ee+  e+a+ 
  gi|557694734|ref|YP_008797788.1| 221 VVWAHERGGIKPDMLTAAKAVAGGFPASLIAVTEDVASKVKDTDHGSTYGGNPLALAAITAATHVLREENIPEQAEV 297
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHCTT-.TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE---TT--HHHH CS
                       Aminotran_3 320 lgaalkegLeelqkky.evikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllppliitdeei 395
                                       +ga+l e+L +l +++  v++ +R++Glmi+i++    +    +++k ++e+G++  +aG +v+r+lpp+ it ++i
  gi|557694734|ref|YP_008797788.1| 298 KGAMLAEELAPLLQEHgRVFRGLRQAGLMIGIDMRTTPT----QFIKMLQENGLIGFKAGLTVLRFLPPYLITRDDI 370
                                       *************9999******************9999....9********************************* PP

                                       HHHHHHHHHH CS
                       Aminotran_3 396 delleilkka 405
                                         ++e++ k+
  gi|557694734|ref|YP_008797788.1| 371 LYAVETIRKT 380
                                       ****999875 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 !   19.0   0.0   1.8e-07   0.00066      91     273 ..     125     301 ..      51     348 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.8e-07
                                       TTT-EEEEEESS-.THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B-- CS
                     Aminotran_1_2  91 npgdeilvpdpty.asyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvat 166
                                       ++g+   + + t+ + y ++++   +evv  p        +d+ a+ee+l+e      +   +++e ++   G ++ 
  gi|557694734|ref|YP_008797788.1| 125 FHGRTMAALSTTWnPKYREGFEPFPFEVVFAP-------FNDIGAVEEKLSE------EFAAVIFEPVQGEGGIIPA 188
                                       566666666777746799999999********.......99***********......6789**************9 PP

                                       HHHHHHHHH.HHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTT.EEEEEESSSTT..SSGGG-EEEEEEEHHH CS
                     Aminotran_1_2 167 leeleklld.lakkynlllfvDeaYagfvfgsldavatranveeepn.llivgslsKaf..GlaGeRvGyilgnaav 239
                                       ++e  k ++  a++ +++++vDe+ +gf  +      ++a    +++ ++   + +Ka   G +      i+++++v
  gi|557694734|ref|YP_008797788.1| 189 KPEFMKAVEkRAREMGVYVVVDEVQSGFGRTGV----VWAHERGGIKpDM--LTAAKAVagGFPA---SLIAVTEDV 256
                                       999888776156677***************943....3555555555334..4666666448888...9999999** PP

                                       HHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHH..........H CS
                     Aminotran_1_2 240 vsqlrklsrpfls.ssllqaavaaalsdallkqs..........e 273
                                       +s +++   + ++  ++l+ a+ +a+ ++l++++           
  gi|557694734|ref|YP_008797788.1| 257 ASKVKDTDHGSTYgGNPLALAAITAATHVLREENipeqaevkgaM 301
                                       *****9999999998888888888888887665544444444443 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.1e-07    0.0026      63     179 ..      91     214 ..      83     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.1e-07
                                       GEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHH....HHHHTEEEEEEEBETTSCBEGGGHHHH CS
                       Aminotran_5  63 eiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqel....akrtgakvkvipldeegeldldelekl 135
                                       ++ f+ +++ea++l+++   r+l  +++++  +++ h+ ++++       + r+g++   +++      d+ ++e++
  gi|557694734|ref|YP_008797788.1|  91 RVFFLNSGSEAVELALKLS-RKLTGRRKVLAFNNGFHGRTMAALSTtwnpKYREGFEPFPFEVVFAPFNDIGAVEEK 166
                                       688999*******987655.78***************999988766233256889999999999999999******* PP

                                       --TTEEEEEEESBETTTTEB....--HHHHHHHHHHTT-EEEEE-TTT CS
                       Aminotran_5 136 lnektklvaithvsnvtGti....qpveeigklakkkgalvlvDaaqa 179
                                       l+e+ ++v++  v+ + G+i    + ++++ k+a++ g++v+vD +q+
  gi|557694734|ref|YP_008797788.1| 167 LSEEFAAVIFEPVQGEGGIIpakpEFMKAVEKRAREMGVYVVVDEVQS 214
                                       *******************922223456666778888**********8 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 ?   11.8   0.0     6e-05      0.21       7      94 ..      65     241 ..      62     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6e-05
                                       --TT--HHHHHHHH............................................................... CS
                    Asparaginase_C   7 lhpgmdtkvlkall............................................................... 20 
                                       ++p +dt+vl+a+l                                                               
  gi|557694734|ref|YP_008797788.1|  65 ITPAFDTDVLDACLdalgkilpphltrvfflnsgseavelalklsrkltgrrkvlafnngfhgrtmaalsttwnpky 141
                                       67888999999999999999999999999999999999999999999999999999999999999999999999999 PP

                                       ..........................HTT--EEEEE.EBTTTB--H...HHHHHHHHHHTTT-EEEEEESSSBS--- CS
                    Asparaginase_C  21 ..........................kkgakGvvle.gtGvGnlps...allealkeakargivvvatsqcpsgsvs 67 
                                                                 +++  +v++e   G G++ +   ++++a+++  ++  v v++  + sg   
  gi|557694734|ref|YP_008797788.1| 142 regfepfpfevvfapfndigaveeklSEEFAAVIFEpVQGEGGIIPakpEFMKAVEKRAREMGVYVVVDEVQSGFGR 218
                                       9999999999999999999999988888999****945699999876889999998875554444444444444444 PP

                                       --H.....HHHHHTEEE-TT--HHHHH CS
                    Asparaginase_C  68 nseyeagkelerlgvisaddmtpeaar 94 
                                        ++      +++ g+i++d +t+++a+
  gi|557694734|ref|YP_008797788.1| 219 TGV----VWAHERGGIKPDMLTAAKAV 241
                                       442....499***************97 PP

>> LIG3_BRCT  DNA ligase 3 BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.79   2.8e+03      21      36 ..      57      75 ..      49      80 .. 0.76
   2 ?   10.7   0.0   0.00014      0.49      13      59 ..     252     298 ..     245     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.79
                         LIG3_BRCT 21 kklrRYfi...AydGdlvk 36
                                      ++l RY++   A+d d+++
  gi|557694734|ref|YP_008797788.1| 57 EQLSRYMTitpAFDTDVLD 75
                                      4788998666799999986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                         LIG3_BRCT  13 ipksvedykklrRYfiAydGdlvkeekekeaTHvvvskkeeskkeke 59 
                                       + ++v    k + +   y+G+++  +  ++aTHv+ +++  +++e++
  gi|557694734|ref|YP_008797788.1| 252 VTEDVASKVKDTDHGSTYGGNPLALAAITAATHVLREENIPEQAEVK 298
                                       55666555555577889*******************97754555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); 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:                         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 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2867.48
//
Query:       gi|557694735|ref|YP_008797789.1|  [L=403]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   0.3    1.1e-06   28.4   0.3    2.0  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
     0.0038   16.9   0.0     0.0081   15.9   0.0    1.5  1  Thymidylate_kin  Thymidylate kinase
     0.0039   17.2   0.2     0.0094   16.0   0.2    1.6  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
  ------ inclusion threshold ------
      0.012   15.0   2.3      0.088   12.2   0.9    2.2  2  ParA             NUBPL iron-transfer P-loop NTPase
      0.019   14.8   0.0      0.034   14.0   0.0    1.4  1  AAA_26           AAA domain
      0.042   13.7   0.5       0.11   12.4   0.5    1.7  1  AAA_31           AAA domain
      0.077   12.8   0.0       0.16   11.7   0.0    1.5  1  CLP1_P           mRNA cleavage and polyadenylation factor CLP
      0.081   13.3   0.0       0.15   12.5   0.0    1.5  1  Lipase_GDSL_2    GDSL-like Lipase/Acylhydrolase family
      0.089   12.5   0.0       0.25   11.0   0.0    1.7  2  PRK              Phosphoribulokinase / Uridine kinase family
       0.09   11.9   1.1       0.44    9.6   0.3    2.2  2  LpxK             Tetraacyldisaccharide-1-P 4'-kinase
       0.13   12.2   0.1         14    5.6   0.0    2.3  2  RsgA_GTPase      RsgA GTPase
        0.2   11.3   1.6       0.43   10.3   0.2    2.1  2  AAA_30           AAA domain
       0.33    9.9   5.9       0.17   10.9   0.5    2.3  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 


Domain annotation for each model (and alignments):
>> 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   0.3   7.7e-10   1.1e-06     113     176 ..     205     265 ..      91     266 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.7e-10
                                       CEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHHHHTTS-EE CS
                              cobW 113 davvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerlrqlnpeakvl 176
                                       d  ++vvDa++   e  +++  +e  + +ad+++l K+D ++ee+l ++ +e++r++np+a+v+
  gi|557694735|ref|YP_008797789.1| 205 DLHITVVDATR--PELITNSYPGETNIHMADVIILHKADKVSEEQL-DRAAEMVRKVNPGAEVV 265
                                       789******55..456667777899*******************76.**************997 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.9e-06    0.0081       6      34 ..     100     129 ..      99     146 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.9e-06
                                       TSSHHHHHHHHHHHHHHTTE..EEEESSST CS
                   Thymidylate_kin   6 GaGKttqaellkerlkeegik.vvltrepg 34 
                                       GaGK+t++++l++ l+e+g++ vv++++  
  gi|557694735|ref|YP_008797789.1| 100 GAGKSTVSRMLVKLLREKGHRpVVVRHPMP 129
                                       9**********************9999965 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 !   16.0   0.2   6.8e-06    0.0094       1      32 [.      92     123 ..      92     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.8e-06
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVll 32 
                                       +a+++ k G+GK+t++  L ++l ++g+r ++
  gi|557694735|ref|YP_008797789.1|  92 VAVTAVKTGAGKSTVSRMLVKLLREKGHRPVV 123
                                       6899***********************99655 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 ?   12.2   0.9   6.4e-05     0.088       3      34 ..      89     120 ..      87     126 .. 0.91
   2 ?    1.9   0.0     0.092   1.3e+02     133     164 ..     228     259 ..     198     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.4e-05
                              ParA   3 kkviavlSgKGGVGKStvavnlAlaLakkglk 34 
                                       kkv+av++ K G GKStv+  l   L++kg++
  gi|557694735|ref|YP_008797789.1|  89 KKVVAVTAVKTGAGKSTVSRMLVKLLREKGHR 120
                                       799***********************999986 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.092
                              ParA 133 klplagaviVttpqevaladvkkaiemfkkvk 164
                                       ++++a+++i     +v+ ++  +a+em++kv+
  gi|557694735|ref|YP_008797789.1| 228 NIHMADVIILHKADKVSEEQLDRAAEMVRKVN 259
                                       4577899**********************997 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.5e-05     0.034       3     103 ..      92     191 ..      90     197 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                            AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvk.vgyfKPiqtgieededselikellgldqtyelpeplalsaplspela 78 
                                       + vt++ tg+GK++vs +Lv+ l++kg + v +  P+  g     + ++++++++ld+   +++++   ++++p+l 
  gi|557694735|ref|YP_008797789.1|  92 VAVTAVKTGAGKSTVSRMLVKLLREKGHRpVVVRHPMPYGVL---EKQVVQRFASLDDLDRYRCSIEEREEFEPHLR 165
                                       679********************9999984555556666665...45666666666666666666666666666665 PP

                            AAA_26  79 arqe.gedidlekivkelekdadivv 103
                                               +d e + ke ek+ d++v
  gi|557694735|ref|YP_008797789.1| 166 EGTIvYAGVDYEMVLKEAEKEGDVIV 191
                                       54441344445555566666666666 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   7.8e-05      0.11       2      36 ..      90     124 ..      89     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.8e-05
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlv 36 
                                       kv+a++  K G GK+T s +l + l ++g++  +v
  gi|557694735|ref|YP_008797789.1|  90 KVVAVTAVKTGAGKSTVSRMLVKLLREKGHRPVVV 124
                                       9****************************997665 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 ?   11.7   0.0   0.00012      0.16       3      28 ..      99     124 ..      98     125 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                            CLP1_P   3 kdsGKSTlarlLlNyalrkgrkpvyv 28 
                                       + +GKST++r+L+  + +kg++pv+v
  gi|557694735|ref|YP_008797789.1|  99 TGAGKSTVSRMLVKLLREKGHRPVVV 124
                                       689********************987 PP

>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00011      0.15      19     108 ..     106     282 ..      94     362 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                       HCCCCCCCHHHTT-EEEEE.....EEHCCH-H......HHHHHHHH....CTGGG-T.................... CS
                     Lipase_GDSL_2  19 ypaylarllaarlgldvvnn....lgvsGatt....allrllerlr....dllrlkp.................... 63 
                                        ++ l +ll+++++++vv+     +gv    +    a+l+ l+r+r    + ++++p                    
  gi|557694735|ref|YP_008797789.1| 106 VSRMLVKLLREKGHRPVVVRhpmpYGVLEKQVvqrfASLDDLDRYRcsieEREEFEPhlregtivyagvdyemvlke 182
                                       55666778888888888877777777777766666655666666666666777788888888888888888888888 PP

                                       .....SEEEEE--CCCCCTT--HHHHHHH....................................HHHHHHHHCCC. CS
                     Lipase_GDSL_2  64 .....dlvtiliGtNDlgrgvpaaaaaand..................................nleelidalraaa 101
                                            d+++   G NDl + +p+ +++  d                                  +l++  +++r+ +
  gi|557694735|ref|YP_008797789.1| 183 aekegDVIVWDGGNNDLPFYWPDLHITVVDatrpelitnsypgetnihmadviilhkadkvseeQLDRAAEMVRKVN 259
                                       88888999999999**888888888777778889999999999999999**************************** PP

                                       ..GEEE................C CS
                     Lipase_GDSL_2 102 pgaril................v 108
                                       pga ++                 
  gi|557694735|ref|YP_008797789.1| 260 PGAEVVataskirvedvplrgrR 282
                                       ******76666665555554440 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.25       2      34 ..      92     125 ..      91     163 .. 0.78
   2 ?   -2.3   0.0       2.2     3e+03      59      84 ..     329     354 ..     324     358 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                               PRK   2 Igvag.sSGaGkttvarklekifgrekvkaaeie 34 
                                       ++v++ + GaGk+tv+r l+k++++++ +++++ 
  gi|557694735|ref|YP_008797789.1|  92 VAVTAvKTGAGKSTVSRMLVKLLREKGHRPVVVR 125
                                       66766479****************9999988883 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                               PRK  59 kevsflspeandfdllyevlkelkeg 84 
                                       +e+++l+p    ++  +e+l+ l+e+
  gi|557694735|ref|YP_008797789.1| 329 REYQHLGPVVPALGYTEEQLRDLGET 354
                                       7899999999999*********9998 PP

>> LpxK  Tetraacyldisaccharide-1-P 4'-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3   0.00032      0.44      34      71 ..      88     124 ..      81     139 .. 0.88
   2 ?    0.5   0.0      0.19   2.6e+02     130     197 ..     188     250 ..     176     391 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00032
                                       SS-EEEEEESBSS-HSHHHHHHHHHHHTTTS..-EEEE CS
                              LpxK  34 pvpVivVGNitvGGtGKTPlvialvkllqarglkvgvl 71 
                                       + +V+ V  +++ G+GK  +  +lvkll+++g +++v+
  gi|557694735|ref|YP_008797789.1|  88 GKKVVAVTAVKT-GAGKSTVSRMLVKLLREKGHRPVVV 124
                                       567888888877.69********************998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.19
                                       SEEEEET-SS-TTB-.-SEEEEEE..EHHHHC--BTTTSSBSS-GGGGGG-SEEEE..........-TT CS
                              LpxK 130 dviilDDGlQhyaLa.rdleivvvdaergfgngrllPaGpLREplsrlkradlvilngakaeeeeaeka 197
                                       dvi+ D G  ++     dl i vvda+r+       P        ++++ ad++il++a++ +ee+ + 
  gi|557694735|ref|YP_008797789.1| 188 DVIVWDGGNNDLPFYwPDLHITVVDATRPELITNSYPG------ETNIHMADVIILHKADKVSEEQLDR 250
                                       56666666555554335666666666666555555442......2345666666665544443333332 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.026        36      71     121 ..      67     112 ..      37     123 .. 0.66
   2 ?    5.6   0.0      0.01        14      48      87 ..     232     270 ..     217     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.026
                                       HHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  71 elealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallp 121
                                       ++ alg++++l+  +     +++ +  k+ ++v + ++G+GKSt+  +l+ 
  gi|557694735|ref|YP_008797789.1|  67 KVLALGCDFMLLGPR-----STMLKSGKKVVAVTAVKTGAGKSTVSRMLVK 112
                                       445566666666444.....44555566677888889*******9888765 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.01
                                       EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTH CS
                       RsgA_GTPase  48 epvivlnKiDlleeeeeleelkeelealgyevllvsaktk 87 
                                         vi+l K+D ++ee+ l++ +e +++++    +v + +k
  gi|557694735|ref|YP_008797789.1| 232 ADVIILHKADKVSEEQ-LDRAAEMVRKVNPGAEVVATASK 270
                                       568*************.99888888888765555544444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2   0.00031      0.43      13      50 ..      84     123 ..      81     128 .. 0.80
   2 ?   -1.1   0.1      0.93   1.3e+03      82     120 ..     225     265 ..     208     270 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00031
                            AAA_30  13 lltsgdrvavltGp.AGtGKttalkalreaweaag.grvi 50 
                                       +l+sg++v+++t++  G+GK+t+ + l+++++++g ++v+
  gi|557694735|ref|YP_008797789.1|  84 MLKSGKKVVAVTAVkTGAGKSTVSRMLVKLLREKGhRPVV 123
                                       6788888888888538*****************9725554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.93
                            AAA_30  82 grarlepgtllivDEagmvdtkqlaallkaaeka..gakvi 120
                                       g+++++ ++++i   a  v+ +ql++ ++ ++k   ga+v+
  gi|557694735|ref|YP_008797789.1| 225 GETNIHMADVIILHKADKVSEEQLDRAAEMVRKVnpGAEVV 265
                                       55778888999999999998888888888887752356665 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   0.5   0.00012      0.17      25      63 ..      86     124 ..      78     126 .. 0.82
   2 ?    1.1   0.3      0.11   1.6e+02     166     191 ..     229     254 ..     226     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                                       G-S-SEEEEEEE-.TTSSHHHHHHHHHHHHHCTT--EEEE CS
                              MeaB  25 kaGraqvvGltGv.PGaGkstlvealglelrrrGkrvavl 63 
                                       k+G+ +vv +t v  GaGkst+   l+  lr++G+r  v+
  gi|557694735|ref|YP_008797789.1|  86 KSGK-KVVAVTAVkTGAGKSTVSRMLVKLLREKGHRPVVV 124
                                       5555.5788888746********************97665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                                       HHH-SEEEEE---HHHHHHHHHHHHH CS
                              MeaB 166 leiaDiivvnkaDkkeaekaarelra 191
                                       + +aD+i++ kaDk   e+  r  ++
  gi|557694735|ref|YP_008797789.1| 229 IHMADVIILHKADKVSEEQLDRAAEM 254
                                       568**********6665555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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 0.30s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 2788.73
//
Query:       gi|557694736|ref|YP_008797790.1|  [L=354]
Description: acetyl-lysine deacetylase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   97.0   0.1    1.5e-27   96.7   0.1    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    2.1e-12   46.9   0.0    3.9e-12   46.1   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain
    0.00061   19.5   0.1    0.00086   19.1   0.1    1.2  1  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 !   96.7   0.1   2.4e-31   1.5e-27       1     206 [.      64     348 ..      64     349 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 2.4e-31
                                       EEEEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   1 llgsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgG 77 
                                       +l sH D+Vp +e        + ++ +Gk+yGrGa+d kg + a+l a  a + +  k +  + ++  +dEEg++ G
  gi|557694736|ref|YP_008797790.1|  64 MLVSHVDTVP-GE-------LRVRVSEGKVYGRGAVDAKGPLSAMLLAGSAAASHL-K-NIRLIVAGLVDEEGNGYG 130
                                       678*******.44.......4677889**********************9977775.2.56***********999** PP

                                       HHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE....................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................... RF
                     Peptidase_M20  78 akallegleerekvdavfelhieepgileagklaigvv....................................... 115
                                       ak+l+e   e+ ++da   ++i+ep++      +i ++                                       
  gi|557694736|ref|YP_008797790.1| 131 AKKLVE---EGLEADA---IIIGEPTGTT----GIALSyrgslsikiraqargghasapyiaesalekilrlwklve 197
                                       ******...6888999...66*******9....3444477899999******************************* PP

                                       ...........................................................EEEEEEEEEESHEEEC.C CS
                                       ...........................................................xxxxxxxxxxxxxxxx.x RF
                     Peptidase_M20 116 ...........................................................kvevelleggapvtln.d 132
                                                                                                  ++++e +   +pv++  +
  gi|557694736|ref|YP_008797790.1| 198 ehyggkryeevtsalttlhagdwvsripdraegsinirfphpysskeilsrleefakiaDCQMEVIDITEPVVTHvN 274
                                       **********************************************************87999988999999999** PP

                                       HHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHHTTT.EEEEEEESSG.GCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 133 splvkalaeaaeelfgekvelivsgpggtdarffagi.ptvmifgpgs.glaHspnEyvdledlekgikvlarlle 206
                                       +  ++ l++a+ +l g+k++ + +  g++d++ + ++ p+++ +gpg+  laH+  E v+++d+ +++++++++++
  gi|557694736|ref|YP_008797790.1| 275 NYAARGLQRAMLRL-GLKPRIVKKT-GTSDMNTLVAVtPNIVACGPGDsTLAHTSAEAVEIKDIITAAQIYVEFVK 348
                                       *************9.*999999888.********8888***99****77************************997 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   6.5e-16   3.9e-12       4     102 ..     160     254 ..     157     257 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 6.5e-16
                                       -EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEE CS
                         M20_dimer   4 kGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeaki 80 
                                       +G+++ ki+++ ++gH++ap  +++A+ek  rl    e+++g +       + t ++t++++G++   ipd+ae +i
  gi|557694736|ref|YP_008797790.1| 160 RGSLSIKIRAQARGGHASAPYIAESALEKILRLWKLVEEHYGGKR----YEEVTSALTTLHAGDWVSRIPDRAEGSI 232
                                       9****************************************9855....**************************** PP

                                       EEEHHHHHHHHHHHHHHHHHHT CS
                         M20_dimer  81 diRllpgedpeevleeieeile 102
                                       +iR++   + +e+l ++ee+++
  gi|557694736|ref|YP_008797790.1| 233 NIRFPHPYSSKEILSRLEEFAK 254
                                       ******************9876 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.4e-07   0.00086      12      84 ..      60     137 ..      51     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.4e-07
                                       SEEEEEEEE--B-TTT......TCC.T---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSGSSHHHHHH CS
                     Peptidase_M28  12 devlllgAHyDsvgvg......rgp.ifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEagllGSkaf 81 
                                       +++++l +H+D+v+ +      +g+    GA D   + +a+L    + a+  +  + +++++ +  EE   +G+k++
  gi|557694736|ref|YP_008797790.1|  60 ERTVMLVSHVDTVPGElrvrvsEGKvYGRGAVDAKGPLSAMLLAGSAAAS--HLKNIRLIVAGLVDEEGNGYGAKKL 134
                                       689***********999999885555678*****9999999988888886..35599******************** PP

                                       HHH CS
                     Peptidase_M28  82 aka 84 
                                       +++
  gi|557694736|ref|YP_008797790.1| 135 VEE 137
                                       *53 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2573.49
//
Query:       gi|557694737|ref|YP_008797791.1|  [L=477]
Description: argininosuccinate lyase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-43  149.5   1.2    3.8e-43  148.1   0.3    2.0  2  Lyase_1        Lyase
    7.1e-06   26.7   0.1    2.7e-05   24.9   0.1    2.1  1  ASL_C2         Argininosuccinate lyase C-terminal
  ------ inclusion threshold ------
      0.028   14.8   0.1         10    6.6   0.0    2.4  2  Ribosomal_S13  Ribosomal protein S13/S18


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 !  148.1   0.3   6.3e-47   3.8e-43       8     312 .]      14     297 ..       9     297 .. 0.94
   2 ?   -0.3   0.0     0.095   5.7e+02      72      83 ..     342     353 ..     301     439 .. 0.56

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 6.3e-47
                                       CHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHH CS
                           Lyase_1   8 dklmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavn 84 
                                       d+  + +t ++++++++ e+++ + aa  k ++k +++ k+ a+++++al+++l+  ++       + +e+++  ++
  gi|557694737|ref|YP_008797791.1|  14 DEEAARYTSSASFDAEIYEATVCVNAAHIKMLEKQGLISKTSAEKAVSALKQLLQ-TRQT----PPPTTEDIHIYLE 85 
                                       55567899***********************************************.3333....3688899998888 PP

                                       HHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTE CS
                           Lyase_1  85 mnlnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlq 161
                                            +++   ++  e+++ +  g+S+nD+v  a+++ +++++++ + ++l   ++al+ k++e++ +v++ +Thlq
  gi|557694737|ref|YP_008797791.1|  86 Q----LLA---QKAPEAAEMLALGKSRNDAVVAAVKIEARRRVYK-VAEELLGAVEALVMKSREHAATVFPVYTHLQ 154
                                       7....777...5667****************************66.999**************************** PP

                                       EEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCSTEESSSHHHH CS
                           Lyase_1 162 dAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglpvkapnsfea 238
                                       +A P t+g  l++ya  l r  + l + l+  + ++lg+++ +gt + +d+e   ++a+ l+ ++    ++ n ++a
  gi|557694737|ref|YP_008797791.1| 155 RAAPATFGFLLQSYAIRLLRCCNTLLNNLEACEESPLGSAAVAGTSAPVDRE---YIAQLLG-FKR---ISWNALDA 224
                                       *****************************9**********************...9999999.888...9******* PP

                                       HHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHHHH CS
                           Lyase_1 239 vsdrDavvellgalkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvagrvvG 312
                                       +++r +++ ll+ l  +a+ +s fae++ l+ss e+gl+++        SSiMP+K+NPv +E ++ + + v+G
  gi|557694737|ref|YP_008797791.1| 225 TASREFLLLLLSPLHAIALVISSFAEEMVLYSSEEFGLIQIPEELAA-TSSIMPQKRNPVVAEIMRTKTAEVLG 297
                                       *****************************************988777.8**********************998 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.095
                                       HBSSSSSHHHHH CS
                           Lyase_1  72 lkviqegsgtav 83 
                                       ++ i+ +   a+
  gi|557694737|ref|YP_008797791.1| 342 VEMIEVNKERAM 353
                                       222222222222 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   4.5e-09   2.7e-05       3      68 ..     361     429 ..     360     430 .. 0.74

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 4.5e-09
                                       THHHHHHHHHHC.TS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-...TT--.GGGGGGSSHHHHT CS
                            ASL_C2   3 tATdlADyLvrk.GlpFReAHeivgravrlaeekgkeleeltleelkeis...plle.edveeaLdpeasV 68 
                                        A +lA +L+ k  + FR+AH+i++++ r   ek  +l +  l+++ + +   p+ +  +v +++dp a V
  gi|557694737|ref|YP_008797791.1| 361 AAVELANHLTLKhRIGFRKAHQIAAKISRSIAEK--TLTQTRLDTIFQEHglkPIYTvGEVLNIMDPVATV 429
                                       699********99***************995443..34455555444322333667778899999998888 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0017        10      20      64 ..      98     142 ..      89     155 .. 0.87
   2 ?    5.7   0.0     0.003        18      16     103 ..     368     453 ..     352     457 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0017
                     Ribosomal_S13  20 ikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqy 64 
                                       +  +G+ +  +++++++++ + r+ +++ee +  +e +v + +++
  gi|557694737|ref|YP_008797791.1|  98 MLALGKSRNDAVVAAVKIEARRRVYKVAEELLGAVEALVMKSREH 142
                                       56789********************************99996654 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.003
                     Ribosomal_S13  16 altaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwinrqkdikdGkdshvvendlrrk 92 
                                        lt  + iG rka++i++  ++++++  + lt+  +++i ++   k  y + +++n  + + + + +    +   + 
  gi|557694737|ref|YP_008797791.1| 368 HLTLKHRIGFRKAHQIAA--KISRSIAEKTLTQTRLDTIFQEHGLKPIYTVGEVLNIMDPVATVERYTAKGSANPSM 442
                                       4777888*********75..589999999**********99988888888888888887777777777777777777 PP

                     Ribosomal_S13  93 lredieRlkki 103
                                       ++e+++Rl ki
  gi|557694737|ref|YP_008797791.1| 443 VSENVDRLLKI 453
                                       77777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3505.49
//
Query:       gi|557694738|ref|YP_008797792.1|  [L=394]
Description: argininosuccinate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-154  513.9   0.0   3.8e-154  513.7   0.0    1.0  1  Arginosuc_synth  Arginosuccinate synthase
    0.00062   19.3   0.1     0.0011   18.5   0.1    1.4  1  QueC             Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.028   13.9   0.2         19    4.7   0.0    3.0  3  Diphthami_syn_2  Diphthamide synthase
      0.047   13.7   0.0       0.12   12.4   0.0    1.7  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 !  513.7   0.0  8.5e-158  3.8e-154       2     386 ..       5     387 ..       4     389 .. 0.99

  Alignments for each domain:
  == domain 1  score: 513.7 bits;  conditional E-value: 8.5e-158
                   Arginosuc_synth   2 LaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanalY 78 
                                       LaysGGlDt+v+ik++++++++ev++v+vdvGq+ ed+ e++eka k gavk++ +Dak+ f+++++ +aikana+Y
  gi|557694738|ref|YP_008797792.1|   5 LAYSGGLDTTVMIKWISQRYNAEVVTVTVDVGQD-EDFAEIEEKAYKSGAVKHYSIDAKKKFADEFLSRAIKANAMY 80 
                                       9*********************************.****************************************** PP

                   Arginosuc_synth  79 edrYllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieyak 155
                                       e  Y+l++al+RPlia++  +va keg++avahGctGkGnDq+Rf++++++ aP lk+iaPvRe++++R+eeieya 
  gi|557694738|ref|YP_008797792.1|  81 ERSYPLSSALSRPLIAEETAKVALKEGCDAVAHGCTGKGNDQLRFDATFAAVAPGLKIIAPVREWNMSRDEEIEYAL 157
                                       ***************************************************************************** PP

                   Arginosuc_synth 156 ekgipvevtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeelsv 232
                                       e+++pv+   k+ +siDenl+grsiea  Ledp+++pp ++++l+k++ ++pd+pee +i+f++GvP  ++ge+ + 
  gi|557694738|ref|YP_008797792.1| 158 EHNLPVNPV-KSRFSIDENLWGRSIEAAELEDPWTEPPTEAFKLVKPLDQTPDKPEEFTIGFRNGVPEYINGERKDL 233
                                       ******987.566**************************************************************** PP

                   Arginosuc_synth 233 lelieklneiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvYkG 309
                                       ++l++ ln ++g hG G +D+vedR+vglksRe+Ye paal+Li+ah dlek+ l r+ + fk++v++ +a+lvY+G
  gi|557694738|ref|YP_008797792.1| 234 VSLVRMLNVLGGMHGYGLVDHVEDRVVGLKSREVYEVPAALILINAHMDLEKMFLGRRFQAFKQQVDSLWADLVYSG 310
                                       ***************************************************************************** PP

                   Arginosuc_synth 310 lwfsPlkealdafiektqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikihglqakl 386
                                       lw++Pl++aldafi+++q+  +G+vr++l+kGs++++gR+ e+ lY+ +  +y +e+ fdq++ eGf k+++l+++l
  gi|557694738|ref|YP_008797792.1| 311 LWMDPLRKALDAFIDESQKGLDGEVRLRLYKGSLRIVGRRGEKPLYSPKYITYARESVFDQRAGEGFSKLWSLETRL 387
                                       *************************************************************************9986 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.5e-07    0.0011       5      64 ..       6      70 ..       2     104 .. 0.66

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.5e-07
                                      E--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTS.HHHH...HHHHHHHHT--.-EEEEE-GGG CS
                              QueC  5 llSGGlDSttvlalakkeg.kevealtfdYgqrhk.kele...aakkiakelgveehkildldll 64
                                        SGGlD t+++ + ++++ +ev ++t+d gq ++ +e+e   + +  +k++ + ++k +  ++l
  gi|557694738|ref|YP_008797792.1|  6 AYSGGLDTTVMIKWISQRYnAEVVTVTVDVGQDEDfAEIEekaYKSGAVKHYSIDAKKKFADEFL 70
                                      57**************999679**********954134330002223344444544444444444 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0043        19       1      29 [.       1      29 [.       1      46 [. 0.76
   2 ?    4.3   0.0    0.0055        25      86     160 ..     108     185 ..      95     190 .. 0.72
   3 ?    1.0   0.0     0.058   2.6e+02     133     164 ..     269     302 ..     259     306 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0043
                   Diphthami_syn_2  1 mkvavlysGGkDsilaLykalkesevesL 29
                                      mkva  ysGG D ++ + ++ ++++ e +
  gi|557694738|ref|YP_008797792.1|  1 MKVALAYSGGLDTTVMIKWISQRYNAEVV 29
                                      899***********999999998765543 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0055
                   Diphthami_syn_2  86 veavviGaieseyqksriervCrel..GlksvaPL..WkkdpeelleeiveekfevivvavkaegldeslLGrridk 158
                                        +av  G     +++ r++     +  Glk +aP+  W+ + +e +e+ +e++  v  v  ++   de+l Gr i+ 
  gi|557694738|ref|YP_008797792.1| 108 CDAVAHGCTGKGNDQLRFDATFAAVapGLKIIAPVreWNMSRDEEIEYALEHNLPVNPVK-SRFSIDENLWGRSIEA 183
                                       5666666666666677777665544349******88899999999999999888776654.3456799999*99986 PP

                   Diphthami_syn_2 159 kl 160
                                         
  gi|557694738|ref|YP_008797792.1| 184 AE 185
                                       55 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.058
                   Diphthami_syn_2 133 ekfevivvavkaegldeslLGrrid..kklidel 164
                                       e   ++++  + + l++ +LGrr++  k+ +d l
  gi|557694738|ref|YP_008797792.1| 269 EVPAALILINAHMDLEKMFLGRRFQafKQQVDSL 302
                                       55566777788899*********97446666665 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.7e-05      0.12       2     157 ..       3     165 ..       2     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.7e-05
                                       EEEE--SSCTCHHHHHHHHHHCTT.HEEEEEE-S..TB-HHHHH..HHHHHHHHTT-EEEEEE-SCHHHHHHHHHH- CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkp.vpvvfvdtg..hefpetie..fvdeleeryglrlkvyepeeevaekinaekh 73 
                                       +++++sgG d +V+++ +++  +  v +v vd g  + f e+ e  +    +++y ++ k    +e  +++i+a+  
  gi|557694738|ref|YP_008797792.1|   3 VALAYSGGLDTTVMIKWISQRYNAeVVTVTVDVGqdEDFAEIEEkaYKSGAVKHYSIDAKKKFADEFLSRAIKANAM 79 
                                       6899************9998666536677777662267999876337788999*****9999999999999999986 PP

                                       S-THHHC..HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-.CCCT--..HHHHH CS
                       PAPS_reduct  74 gsslyee..aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfekslrvf.PllnWt..eedvw 145
                                        ++ y    a++r   +e+  k   k + da+  G      k   +l++  + ++  ++l++  P+ +W+    +  
  gi|557694738|ref|YP_008797792.1|  80 YERSYPLssALSRPLIAEETAKVALKEGCDAVAHGC---TGKGNDQLRFDATFAAVAPGLKIIaPVREWNmsRDEEI 153
                                       555555488676666666555544455558888886...56677777877777888889998889998862245678 PP

                                       HHHHHCT--B-C CS
                       PAPS_reduct 146 qyilrenipynp 157
                                       +y+l++n+p+np
  gi|557694738|ref|YP_008797792.1| 154 EYALEHNLPVNP 165
                                       999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2833.57
//
Query:       gi|557694739|ref|YP_008797793.1|  [L=136]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      217  (0.0121033); 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: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 959.76
//
Query:       gi|557694740|ref|YP_008797794.1|  [L=116]
Description: DNA-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   86.7  10.7    1.7e-24   86.2  10.7    1.2  1  dsDNA_bind      Double-stranded DNA-binding domain
  ------ inclusion threshold ------
      0.026   14.1   4.0      0.027   14.0   4.0    1.2  1  Ebp2            Eukaryotic rRNA processing protein EBP2
      0.032   14.2   0.4       0.07   13.2   0.0    1.7  2  SASP            Small, acid-soluble spore proteins, alpha/bet
        8.3    6.0  14.3         25    4.5  13.7    1.8  2  Casc1_N         Cancer susceptibility candidate 1 N-terminus


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 !   86.2  10.7   3.9e-28   1.7e-24       1     110 [.      14     111 ..      14     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 3.9e-28
                                       XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                        dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaq 77 
                                       ir++++aelqa+a ++          +++++  +e ++ a++++iL+peAr+RL++++l kpe ae+ve +Liq+ q
  gi|557694740|ref|YP_008797794.1|  14 IRQQKMAELQARAAEE----------QARRQ--RELERAAVMRTILTPEARQRLNNLKLIKPEIAEKVETYLIQVSQ 78 
                                       89********977632..........22233..68899*************************************** PP

                                       --SS-----HHHHHHHHHHHS---XXXXX..XX CS
                        dsDNA_bind  78 sGqlrskvteeqLkeLLeqvaekkketkivisr 110
                                       +G++r  v++e+Lk +L+++  kk+et+i+++ 
  gi|557694740|ref|YP_008797794.1|  79 TGNIRLPVDDETLKLILDKIMPKKRETRIEFRS 111
                                       *****************************9976 PP

>> Ebp2  Eukaryotic rRNA processing protein EBP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   4.0     6e-06     0.027     108     158 ..       4      54 ..       3     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 6e-06
                              Ebp2 108 MvKsDehMekvkekLleeqaakkaseearkqRelkkfgKqvqveklqeRqk 158
                                       M  +De  e+++++ ++e +a  a e+ar+qRel + +    + + + Rq+
  gi|557694740|ref|YP_008797794.1|   4 MSAEDEELERIRQQKMAELQARAAEEQARRQRELERAAVMRTILTPEARQR 54 
                                       6779******************************99876665555555554 PP

>> SASP  Small, acid-soluble spore proteins, alpha/beta type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.2      0.94   4.2e+03      18      24 ..      17      23 ..       6      35 .. 0.53
   2 ?   13.2   0.0   1.6e-05      0.07       1      34 [.      44      80 ..      44      88 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.94
                                      HHHHHHT CS
                              SASP 18 EvAaElG 24
                                         aEl 
  gi|557694740|ref|YP_008797794.1| 17 QKMAELQ 23
                                      3223332 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.6e-05
                                      ---SSGGGHHHHHHH...HHHHHHHHT---ST..... CS
                              SASP  1 nkllvpeakeaLdql...KyEvAaElGvslgkdgyng 34
                                      +++l pea++ L++l   K E+A+ +   l + ++ g
  gi|557694740|ref|YP_008797794.1| 44 RTILTPEARQRLNNLkliKPEIAEKVETYLIQVSQTG 80
                                      5789***********88888***99984444434444 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 ?    4.5  13.7    0.0057        25      10      49 ..       3      41 ..       1      59 [. 0.80
   2 ?    0.3   0.0      0.11   4.7e+02      81     102 ..      60      81 ..      54     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0057
                           Casc1_N 10 Rlraeeeererleeerrekeereqlaaeqarrkeeleelk 49
                                      R+ ae ee er+++++ ++  + ++a+eqarr+ ele ++
  gi|557694740|ref|YP_008797794.1|  3 RMSAEDEELERIRQQKMAE-LQARAAEEQARRQRELERAA 41
                                      999**********999775.455569**********9875 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.11
                           Casc1_N  81 lPdptdekeiNtflslwseeee 102
                                       l +p+  + + t+l ++s++ +
  gi|557694740|ref|YP_008797794.1|  60 LIKPEIAEKVETYLIQVSQTGN 81 
                                       6678888999999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1598  (0.0891293); expected 358.6 (0.02)
Passed bias filter:                      674  (0.0375927); 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):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 837.36
//
Query:       gi|557694741|ref|YP_008797795.1|  [L=233]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-31  107.4   0.1    1.2e-30  107.1   0.1    1.0  1  PAC2      PAC2 family
  ------ inclusion threshold ------
      0.064   13.0   0.2        8.3    6.1   0.0    2.2  2  TadZ_N    Pilus assembly protein TadZ N-terminal


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 !  107.1   0.1   1.3e-34   1.2e-30       1     199 [.      22     220 ..      22     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 1.3e-34
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT.EEE-SEEEEEE.TTT.SEEEEEEE. CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg.relepprlyak.dsgsrdllvlqg. 74 
                                       L++G+pgiG+V+++av +L+ +++ +kv +++s++ +p      + +++eg    ++  +y+  +  + +ll+l g 
  gi|557694741|ref|YP_008797795.1|  22 LVEGLPGIGLVAKVAVAYLLKNMKVRKVVRFYSPF-FP-----AIGYISEGkIIFSFADIYVAeH--DPPLLILYGn 90 
                                       89*********************************.**.....9999999988888889988875..58*******7 PP

                                       ...E-HSCHHH...HHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHH.H..CT..-C CS
                              PAC2  75 ...repilqye...efakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleel.e..es..ey 140
                                               +++   +++++++++a++lg+++v+++gg++ +   +v+  ++  v+  +tde+llee  +  +     
  gi|557694741|ref|YP_008797795.1|  91 aqpS----TSYgqyDLCTKIIQVAKDLGCSTVLTIGGYGKE---TVS--EKRTVYCSSTDEKLLEEWiKvvDGvrYS 158
                                       5533....3333557************************43...333..33369**********9886566336677 PP

                                       EEEEHHHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---H...CHHHH CS
                              PAC2 141 ggivgitglLlsaakergipavgllaevphylpdPkaaaalleflskllglevd...tedLe 199
                                       g ivg++glL  +a+e+g++  ++l+e+ +  pd  aa++++e+++kll+l ++   +e+L+
  gi|557694741|ref|YP_008797795.1| 159 GQIVGAAGLLTVLASEAGLKNFSMLVETAEMAPDFFAAKRAVEAVAKLLNLPLKipsAEELS 220
                                       889***********************************************765422333665 PP

>> TadZ_N  Pilus assembly protein TadZ N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0   0.00093       8.3      50      94 ..       6      49 ..       2      64 .. 0.79
   2 ?    4.8   0.0    0.0023        20      69     125 ..     160     215 ..     147     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.00093
                                      EEEEEE-TTTHHHHHHHHHHHHHH-TT-EEEEEE-TT-HHHHHHH CS
                            TadZ_N 50 vlfislgksnlvsqgalveglvsarpmlsvvaigdgldnqlvlaa 94
                                      v f+  g+   vs+g lvegl     +++ va+   l n  v   
  gi|557694741|ref|YP_008797795.1|  6 VSFVDGGREVKVSDGILVEGLPGI-GLVAKVAVAYLLKNMKVRKV 49
                                      789999**************9764.57777888877777766655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0023
                                       HHHHH-TT-EEEEEE-TT-HHHHHHHHHHT-SEEEETT-BHHHHHHHHHHHHTTS-S CS
                            TadZ_N  69 glvsarpmlsvvaigdgldnqlvlaamragardfitygaraseltglirrlggrlps 125
                                        +v a  +l+v+a   gl n  +l      a df +   ra e    +  l  ++ps
  gi|557694741|ref|YP_008797795.1| 160 QIVGAAGLLTVLASEAGLKNFSMLVETAEMAPDFFA-AKRAVEAVAKLLNLPLKIPS 215
                                       4789999*****************99999999*987.46788877777677777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1693.64
//
Query:       gi|557694742|ref|YP_008797796.1|  [L=519]
Description: queuine tRNA-ribosyltransferas [Candidatus Caldiarchaeum subterraneum]
Scores for 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-71  240.2   0.0    4.8e-71  239.7   0.0    1.1  1  TGT              Queuine tRNA-ribosyltransferase
     0.0027   17.6   0.1     0.0052   16.7   0.1    1.5  1  DUF5591          Domain of unknown function (DUF5591)
  ------ inclusion threshold ------
      0.076   12.6   0.0       0.16   11.5   0.0    1.4  1  NTP_transferase  Nucleotidyl transferase
       0.19   11.2   0.0       0.45   10.0   0.0    1.6  1  Creatininase     Creatinine amidohydrolase


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 !  239.7   0.0   1.1e-74   4.8e-71       3     349 ..      15     338 ..      12     339 .. 0.95

  Alignments for each domain:
  == domain 1  score: 239.7 bits;  conditional E-value: 1.1e-74
                                       EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EE CS
                               TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpil 79 
                                       +R+G+l++ ++++etPaf+pv  ++  + + p+e+++ +g+ i+++n+y+l +r  ++ v+  +g+h+++g+d+ ++
  gi|557694742|ref|YP_008797796.1|  15 GRVGSLQVGGKKVETPAFVPV-INPVSQVVPPEEIRRRFGCGIVITNAYILFKRFRSRAVE--EGVHRLIGFDGLVM 88 
                                       7********************.8999999*******99**************999999985..5************* PP

                                       EE-SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHH CS
                               TGT  80 tdsggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwld 156
                                       tdsgg+qv+               + G+ v+ tp+++  +qe++gsDi+++ld  ++    + ++ek ve+Tl+ ++
  gi|557694742|ref|YP_008797796.1|  89 TDSGGYQVLV--------------Y-GD-VEATPDDIAFFQESIGSDIAVPLDR-PTGLVGRREAEKTVEETLANVR 148
                                       *******874..............4.**.************************9.5556899*************** PP

                                       HHHHHH....SE.EEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EE CS
                               TGT 157 rcleah....qa.lfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkpry 225
                                       r +e         ++g+vqGgly+dl +++++e ++++f+ y++g+  +++   +++el++++++++  l + kp +
  gi|557694742|ref|YP_008797796.1| 149 RTVELVghggRCvWVGPVQGGLYRDLVQKCVDEYKRLGFSLYCLGSpTPLMTayRYRELVSMITTTRHVLGTVKPLH 225
                                       ***98899*9666*********************************8888887899********************* PP

                                       ETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHH CS
                               TGT 226 lmGvgtPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhll 302
                                       l+G+g+P++++ avalGvDmfd++ +++ a+++r++ +eg+++l++ ++     p    CsC +C++++ ++l++l 
  gi|557694742|ref|YP_008797796.1| 226 LFGAGHPMMFALAVALGVDMFDSASYALFAKEDRYILPEGTVRLEQLSHL----P----CSCEVCTRFSAKELRELE 294
                                       ********************************************977776....9....******99*********9 PP

                                       HTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                               TGT 303 ktkemlgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                       ++++    + l++HNl++ ++++++i++aI eg++ e+ e+ ar+++
  gi|557694742|ref|YP_008797796.1| 295 REER---FRNLALHNLFVCFQEVEAIKQAIWEGRMYELLERKARSHP 338
                                       9999...99********************************999986 PP

>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   1.2e-06    0.0052      11     135 ..     391     516 ..     382     519 .] 0.67

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.2e-06
                                       H---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT----------------H CS
                           DUF5591  11 rYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqYdiavtgewse 87 
                                       r++p++  +  vL+   a    +  k ++ +a+ +++   + ++ +   P+G+vP +l +v+P++q   + t   ++
  gi|557694742|ref|YP_008797796.1| 391 RWSPSC-VDAAVLVSHRAVVNRRLEKLFELLAKVVGDS--CFEVFVHDTPYGLVPLSLYHVFPISQTTYPET-LVKQ 463
                                       566665.6667777777777777777788888888887..78999999******************999999.4555 PP

                                       HHHHHHHHHHHHHHHHHT-SE.EEE---TH.HH....HHHHHHHTT-SSEEEE- CS
                           DUF5591  88 eeiefvaellakylektkyek.viahleee.yr....eiveevaeelgleiiyt 135
                                        e ++ +e+ a++l+k+ ++k +i+   +e y     +++++ + +l++e++yt
  gi|557694742|ref|YP_008797796.1| 464 LEDKIFREA-AETLAKHGFKKiIIIETRREtYPgysrKLAHSLQTSLSKEVVYT 516
                                       566666655.66788899988445555544454222244444444444666655 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   3.7e-05      0.16      13      57 ..     448     492 ..     447     516 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                                       GTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTT CS
                   NTP_transferase  13 LwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqeh 57 
                                       ++P+++t+++  + +  +++++   +++la++g+++ii++ t+++
  gi|557694742|ref|YP_008797796.1| 448 VFPISQTTYPETLVKQLEDKIFREAAETLAKHGFKKIIIIETRRE 492
                                       58*********99999999*****************999977654 PP

>> Creatininase  Creatinine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   9.9e-05      0.45      73     107 ..     449     488 ..     414     515 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 9.9e-05
                      Creatininase  73 fpGTislspetlia.....vlrdileslarhGfrrivlvn 107
                                       fp + +  petl +     + r+ +e la+hGf++i+++ 
  gi|557694742|ref|YP_008797796.1| 449 FPISQTTYPETLVKqledkIFREAAETLAKHGFKKIIIIE 488
                                       777777777777651111155778999***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3810.43
//
Query:       gi|557694743|ref|YP_008797797.1|  [L=288]
Description: acylphosphatase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   92.8   0.3    2.9e-26   91.7   0.3    1.7  1  Acylphosphatase  Acylphosphatase
  ------ inclusion threshold ------
       0.35   11.6  14.8      0.087   13.5   4.3    3.5  2  PMC2NT           PMC2NT (NUC016) domain
        3.5    7.5  10.4         12    5.8   1.3    3.4  4  Glutaredoxin2_C  Glutaredoxin 2, C terminal domain
        5.2    7.6  22.2       0.89   10.1   9.6    3.0  3  DUF16            Protein of unknown function DUF16
        6.3    6.2  28.5        4.9    6.5   9.4    3.1  3  DUF3552          Domain of unknown function (DUF3552)
        8.9    5.9  11.3        4.9    6.7   1.1    3.3  4  DUF4843          Domain of unknown function (DUF4843)


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 !   91.7   0.3   9.7e-30   2.9e-26       2      85 .]      12      95 ..      11      95 .. 0.98

  Alignments for each domain:
  == domain 1  score: 91.7 bits;  conditional E-value: 9.7e-30
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      +++v+G VQgvgFR+fvrr+A++lg+kG+v+Nl+ g V+ivae ++e vek++e++ks pp++ vde++v+ ++ ++ef
  gi|557694743|ref|YP_008797797.1| 12 EIVVEGDVQGVGFRYFVRRAARRLGVKGFVENLESGAVKIVAEASKERVEKLVEKIKSAPPPIAVDEITVTYSKPTGEF 90
                                      689**************************************************************************** PP

                   Acylphosphatase 81 kdFei 85
                                      k+F+i
  gi|557694743|ref|YP_008797797.1| 91 KTFKI 95
                                      ***98 PP

>> PMC2NT  PMC2NT (NUC016) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   3.3      0.19   5.6e+02      62      86 ..     164     188 ..     113     196 .. 0.60
   2 ?   13.5   4.3   2.9e-05     0.087      42      92 .]     208     257 ..     188     257 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.19
                            PMC2NT  62 eddveekfksvvdvvDsllEkadtc 86 
                                       +d + ek +++    D++lEk+d  
  gi|557694743|ref|YP_008797797.1| 164 QDLMLEKQDQMLHKQDQMLEKMDVT 188
                                       2222333333444444444444444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2.9e-05
                            PMC2NT  42 sllklaaskseisassklededdveekfksvvdvvDsllEkadtcLDeltg 92 
                                       ++l  ++   e+++ s+l+++d++ +k++ +v+  D++lE+ d++ De++g
  gi|557694743|ref|YP_008797797.1| 208 QMLGKMDIMLEKQD-STLQKQDQMLSKMDLMVEKHDEMLERQDMLVDEVKG 257
                                       33333333333333.58899999999**********************997 PP

>> Glutaredoxin2_C  Glutaredoxin 2, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.74   2.2e+03      36      89 ..      25      79 ..      23      82 .. 0.64
   2 ?   -0.2   0.1      0.28   8.3e+02      40      61 ..     120     141 ..     100     159 .. 0.46
   3 ?    4.0   1.9     0.014        42      40      75 ..     162     197 ..     147     204 .. 0.60
   4 ?    5.8   1.3    0.0039        12      41      80 ..     205     244 ..     198     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.74
                   Glutaredoxin2_C 36 eyftkkkeksig..dfeellaktp.eliaelnalLeelepliksseavngelSvdDi 89
                                      +yf+++  + +g   f e+l+  + +++ae ++  e++e+l+++ ++    + vd+i
  gi|557694743|ref|YP_008797797.1| 25 RYFVRRAARRLGvkGFVENLESGAvKIVAEASK--ERVEKLVEKIKSAPPPIAVDEI 79
                                      577777777777667888888777666666555..5666666666665556666665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.28
                   Glutaredoxin2_C  40 kkkeksigdfeellaktpelia 61 
                                       +k+ k++ +++ l+++++ ++ 
  gi|557694743|ref|YP_008797797.1| 120 EKQDKALVKLDTLIERQDLMLV 141
                                       2222222233333333322222 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.014
                   Glutaredoxin2_C  40 kkkeksigdfeellaktpeliaelnalLeeleplik 75 
                                       +k+  ++++ +++l+k+++++++++  Le+  +++ 
  gi|557694743|ref|YP_008797797.1| 162 EKQDLMLEKQDQMLHKQDQMLEKMDVTLEKQGQMLL 197
                                       344455556666666666666666666666666555 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0039
                   Glutaredoxin2_C  41 kkeksigdfeellaktpeliaelnalLeelepliksseav 80 
                                       k+ +++g+++ +l+k+++ +++ +++L +++ ++++++++
  gi|557694743|ref|YP_008797797.1| 205 KQDQMLGKMDIMLEKQDSTLQKQDQMLSKMDLMVEKHDEM 244
                                       67889999999********************999877665 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.57   1.7e+03      47      59 ..      57      69 ..      41     104 .. 0.62
   2 ?   10.1   9.6    0.0003      0.89       6      86 ..     119     204 ..     114     214 .. 0.84
   3 ?    2.9   5.1     0.052   1.6e+02      32      79 ..     206     253 ..     198     284 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.57
                                      .HHHHHHHHHHHH CS
                             DUF16 47 geqinkleqkvek 59
                                      +e+++kl +k++ 
  gi|557694743|ref|YP_008797797.1| 57 KERVEKLVEKIKS 69
                                      3334444444333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0003
                                       XXXXXXX.X.XTTB-BHHHHHHB-.......BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH. CS
                             DUF16   6 fneivKkiPvkteYVTrkqlnefkds.....nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgee 77 
                                       f+++ K + + +  + r++l   k++      +q L k++  ++k++  ++k+ q  +kq++ ++++ v+ ++qg+ 
  gi|557694743|ref|YP_008797797.1| 119 FEKQDKALVKLDTLIERQDLMLVKQDlmlqkQDQMLGKMDLMLEKQDLMLEKQDQMLHKQDQMLEKMDVTLEKQGQM 195
                                       777778777778888888888888888888899*******************************************8 PP

                                       ......HHH CS
                             DUF16  78 lnkvdetle 86 
                                       l ++d+ l 
  gi|557694743|ref|YP_008797797.1| 196 LLTQDQMLL 204
                                       887777664 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.052
                                       BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH... CS
                             DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln 79 
                                        +q L k++  ++k++  ++k+ q  +k +  +++  +  + q+  ++
  gi|557694743|ref|YP_008797797.1| 206 QDQMLGKMDIMLEKQDSTLQKQDQMLSKMDLMVEKHDEMLERQDMLVD 253
                                       345555555555555555555555555555555555554444444333 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.084   2.5e+02      28      55 ..      40      67 ..      19      71 .. 0.71
   2 ?    4.8  10.3    0.0055        16      80     130 ..     140     190 ..     118     196 .. 0.57
   3 ?    6.5   9.4    0.0016       4.9      80     149 ..     189     261 ..     186     281 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.084
                           DUF3552 28 kiaeAeeeAkkiieeAkkeAeakkkeal 55
                                       +++ e+ A ki++eA ke  +k  e++
  gi|557694743|ref|YP_008797797.1| 40 FVENLESGAVKIVAEASKERVEKLVEKI 67
                                      5677788999******999776665555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0055
                           DUF3552  80 lqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleekeeele 130
                                       l +++  l++++++L + +  lek++  le++++ l+++ q le+++ +le
  gi|557694743|ref|YP_008797797.1| 140 LVKQDLMLQKQDQMLGKMDLMLEKQDLMLEKQDQMLHKQDQMLEKMDVTLE 190
                                       344444555555555555555555555555555555555555555555444 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0016
                           DUF3552  80 lqrlekRllqkeetLdrkeeslekkeesleekekelkqkeqsleeke...eeleelveeqrqeLerisgLtke 149
                                       l+++ + ll ++++L ++++ l k +  le++++ l+++ q l++++   e+ +e++e+q+  + ++ gL ++
  gi|557694743|ref|YP_008797797.1| 189 LEKQGQMLLTQDQMLLKQDQMLGKMDIMLEKQDSTLQKQDQMLSKMDlmvEKHDEMLERQDMLVDEVKGLRRD 261
                                       5677778888888888888888888888888888888888877766522266677788888888888887776 PP

>> DUF4843  Domain of unknown function (DUF4843)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2     0.045   1.4e+02      82     109 ..     121     148 ..      91     150 .. 0.87
   2 ?    1.7   2.5     0.058   1.7e+02      76     123 ..     142     190 ..     128     198 .. 0.68
   3 ?    6.7   1.1    0.0017       4.9      76     108 ..     199     231 ..     188     244 .. 0.85
   4 ?    2.2   0.1      0.04   1.2e+02      82     107 ..     226     251 ..     222     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.045
                           DUF4843  82 padsvlvslpvivyntdteLeketlvle 109
                                       + d+ lv+l+ ++ ++d +L k+ l+l+
  gi|557694743|ref|YP_008797797.1| 121 KQDKALVKLDTLIERQDLMLVKQDLMLQ 148
                                       579999******************9997 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.058
                           DUF4843  76 keeytl.padsvlvslpvivyntdteLeketlvlelklkasedlklglk 123
                                       k+ ++l + d++l+++++++ ++d +Lek+  +l+ + +  e+++++l+
  gi|557694743|ref|YP_008797797.1| 142 KQDLMLqKQDQMLGKMDLMLEKQDLMLEKQDQMLHKQDQMLEKMDVTLE 190
                                       5555551458889999999999999999988877666555555555555 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0017
                           DUF4843  76 keeytlpadsvlvslpvivyntdteLeketlvl 108
                                       ++++ l+ d++l+++++++ ++d+ L+k+  +l
  gi|557694743|ref|YP_008797797.1| 199 QDQMLLKQDQMLGKMDIMLEKQDSTLQKQDQML 231
                                       78999**********************997665 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.04
                           DUF4843  82 padsvlvslpvivyntdteLeketlv 107
                                       + d++l++++++v ++d++Le++ + 
  gi|557694743|ref|YP_008797797.1| 226 KQDQMLSKMDLMVEKHDEMLERQDML 251
                                       67999***************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1275  (0.0711138); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2041.41
//
Query:       gi|557694744|ref|YP_008797798.1|  [L=374]
Description: hypothetical protein CSUB_C1317 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2783.24
//
Query:       gi|557694745|ref|YP_008797799.1|  [L=145]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   25.5   4.7    3.1e-05   24.8   3.6    1.8  2  Pilin_N      Archaeal Type IV pilin, N-terminal
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.016   15.2   0.0    1.3  1  Urease_beta  Urease beta subunit


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 !   24.8   3.6   3.5e-09   3.1e-05       1      63 [.       7      71 ..       7      85 .. 0.83
   2 ?   -0.7   0.0      0.32   2.9e+03      37      64 ..     105     131 ..      96     142 .. 0.57

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.5e-09
                           Pilin_N  1 eAVSpViGviLmvaitvIlaAviaafvlglasneekapqasievk..idssastgknavslehkg 63
                                      ++ Sp + viL++aitv +a v++++ ++la+ + + p a i+    + + a++g+ av++++ g
  gi|557694745|ref|YP_008797799.1|  7 RGLSPLVAVILLIAITVAAAVVVSGVFFNLAGIAGRRPTAVIDQVrlVATPAGAGTWAVVVKNTG 71
                                      589***************************99999999999965557677777666667776655 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.32
                           Pilin_N  37 apqasievkidssastgkna.vslehkgG 64 
                                       ++ a++ + ++ ++++     ++++ ++G
  gi|557694745|ref|YP_008797799.1| 105 SATANVATGCTLGTTYR--IvLTITFQDG 131
                                       33344444444444432..2477777777 PP

>> Urease_beta  Urease beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.8e-06     0.016      10      64 ..      53     113 ..      44     142 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                                       EEETTTT---EEEEEEE-SSS-EE.EETTS-GGGS-TTEES.....-HHHHTTEEE-SSTT CS
                       Urease_beta  10 eielnagretiklkvantgdrpiq.vgshyhflevnkaLef.....dRekalGlrldipag 64 
                                        ++  ag  t  + v+ntgd pi  +++ y ++ +n+aL+f     +  ++     ++++g
  gi|557694745|ref|YP_008797799.1|  53 LVATPAGAGTWAVVVKNTGDVPITaITASYPVASCNPALTFtplplNPGATASATANVATG 113
                                       566677888999***********6499**************55555333444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); 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):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1010.87
//
Query:       gi|557694746|ref|YP_008797800.1|  [L=461]
Description: hypothetical protein CSUB_C1319 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.1     0.0014   18.5   0.1    3.8  3  T2SSF     Type II secretion system (T2SS), protein F
  ------ inclusion threshold ------
       0.12   10.8   0.0       0.17   10.3   0.0    1.1  1  Nic96     Nup93/Nic96


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 !   18.5   0.1   1.6e-07    0.0014       2     123 ..      54     177 ..      53     179 .. 0.88
   2 ?   -3.5   1.2       1.1   9.8e+03     103     122 ..     222     241 ..     218     242 .. 0.70
   3 !    5.4   2.4    0.0019        17      35     118 ..     280     383 ..     263     393 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.6e-07
                                       HHHHHHHHHTT--HHHHHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC..T-TT.TS-HHHHHHHHHHHHHT- CS
                             T2SSF   2 lrqlatllsaGvplveaLellaeeaengplaeelkriarrlraGgslseale..rtpssefpelvvqlirageeggn 76 
                                       l  l++ +++G ++++a++ +a+ +++++    +++ + r ++ ++l+e l+   +ps ef+ l+ +l +  e+g  
  gi|557694746|ref|YP_008797800.1|  54 LVILYIFMKSGKTVLTAFREAAARKKYIKHLSDVSSYLVRESEQKTLAEGLKtyVHPSREFTLLLGSLGEDLESGFG 130
                                       5678999************999999955555555555555555568******8878889****************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXXX CS
                             T2SSF  77 LaevLerlaeyleeerelrrkllaallepllllvvallvllillail 123
                                       + e  e+l e+   +++ r+++   + e+l ++vv +++l++l+ ++
  gi|557694746|ref|YP_008797800.1| 131 VVEKVEKLIEQAISREADRWRRYVDSVETLGEVVVSVILLIPLIYVV 177
                                       *******************************************9876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.1
                                       HTTXXXXXXXXXXXXXXXXX CS
                             T2SSF 103 lepllllvvallvllillai 122
                                       +++++++v++++++  ll++
  gi|557694746|ref|YP_008797800.1| 222 ASTAMIFVFGGVLATSLLGF 241
                                       56778888888887777766 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHTTSSHHHHHC...................T-TT.TS-HHHHHHHHHHHHHT-HHHHHHHHHHHHHHHH CS
                             T2SSF  35 lkriarrlraGgslseale...................rtpssefpelvvqlirageeggnLaevLerlaeyleeer 92 
                                       l+ +a+rlraG++l ++le                    tp + f  l++  + +++ gg  ae+L+ la+     +
  gi|557694746|ref|YP_008797800.1| 280 LDGVAARLRAGYPLGRSLEavvdprykryahsiahgleITPLNRFMALAMETVKVARLGGLGAEALSLLARLALSIY 356
                                       66788899999988888887777777776666666666666688888888888888888888888888888888777 PP

                                       HHH.HHHHHHHHTTXXXXXXXXXXXXX CS
                             T2SSF  93 elr.rkllaallepllllvvallvlli 118
                                        +    ++ ++l+++l ++ +++++++
  gi|557694746|ref|YP_008797800.1| 357 LSFtGARARMKLYTALAIASGAAIVAV 383
                                       776334444445555555555555444 PP

>> Nic96  Nup93/Nic96
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   1.9e-05      0.17     346     407 ..      79     141 ..      55     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 1.9e-05
                                       HHHHGGGGS-S....CCHHHHHHHHHHHHHHHH--HHHHHEEE-TTS-EEE-HHHHTGGGGT- CS
                             Nic96 346 eYlylirllkdleg.keqrelchealrelvletrefalLLGdirsdGtripGlieerlklikl 407
                                       +Y+  +++++++   +++++ + e l+  v  +ref+lLLG++ +d +   G++e+  kli+ 
  gi|557694746|ref|YP_008797800.1|  79 KYIKHLSDVSSYLVrESEQKTLAEGLKTYVHPSREFTLLLGSLGEDLESGFGVVEKVEKLIEQ 141
                                       5666666666553356667999************************99999****99888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); 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:                         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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3084.83
//
Query:       gi|557694747|ref|YP_008797801.1|  [L=292]
Description: hypothetical protein CSUB_C1320 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   72.2   4.0    5.4e-20   71.8   4.0    1.1  1  TackOD1          Thaumarchaeal output domain 1
    1.1e-05   25.4  13.7      0.015   15.3   5.0    3.1  2  DZR              Double zinc ribbon
    0.00018   21.5  10.0       0.21   11.6   0.2    3.2  3  HypA             Hydrogenase/urease nickel incorporation, met
     0.0011   18.8   0.4     0.0011   18.8   0.4    3.9  4  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0015   18.0   2.1     0.0015   18.0   2.1    3.8  4  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0021   18.0   7.2      0.012   15.6   0.2    3.5  3  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0034   17.5  16.3        1.7    8.8   3.9    4.4  4  Zn-ribbon_8      Zinc ribbon domain
     0.0066   16.6   0.0      0.012   15.7   0.0    1.4  1  Y1_Tnp           Transposase IS200 like
  ------ inclusion threshold ------
      0.018   15.0   0.8      0.018   15.0   0.8    3.9  4  Nudix_N_2        Nudix N-terminal
      0.027   14.1   7.9         14    5.4   0.0    4.3  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.033   14.1   0.3      0.033   14.1   0.3    3.6  4  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.075   13.1   1.0      0.075   13.1   1.0    3.3  3  DUF1451          Zinc-ribbon containing domain
      0.091   12.1   1.9        0.4   10.0   0.8    2.6  2  zf-TFIIB         Transcription factor zinc-finger
       0.12   12.4  10.9       0.22   11.5   2.8    2.4  3  zinc-ribbons_6   zinc-ribbons
       0.21   11.0  20.6        5.1    6.6   0.8    5.5  6  zf-ribbon_3      zinc-ribbon domain
        0.3   11.9  10.1        5.1    7.9   0.1    3.1  2  zinc_ribbon_15   zinc-ribbon family
       0.31   11.2  11.8       0.04   14.0   3.3    2.4  2  DUF2318          Predicted membrane protein (DUF2318)
       0.53    9.9   3.9       0.22   11.1   0.7    1.9  2  DpnI             Dam-replacing family
       0.55   10.4  13.1      0.086   12.9   2.0    4.3  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.66   10.1  10.7      0.026   14.6   2.6    2.0  2  DUF2054          Uncharacterized conserved protein (DUF2054)
       0.67    9.9  11.5        4.3    7.3   0.8    2.6  3  zf-C3HC4_3       Zinc finger, C3HC4 type (RING finger)
       0.79   10.0  10.1       0.21   11.8   0.7    3.3  3  LIM              LIM domain
          1    9.6  14.5        1.1    9.4   2.0    3.1  3  Ribosomal_L37e   Ribosomal protein L37e
          1    9.2  25.7        2.8    7.8   1.6    5.8  4  zinc_ribbon_2    zinc-ribbon domain
        1.3    9.0  12.8        1.5    8.8   1.2    2.8  3  C1_1             Phorbol esters/diacylglycerol binding domain
        3.4    8.1   8.6        2.1    8.7   0.1    2.7  2  C1_2             C1 domain
        5.9    7.2  12.4    7.3e+02    0.5  12.4    2.7  1  IBR              IBR domain, a half RING-finger domain
        5.9    7.0  17.3        3.9    7.5   1.4    3.5  3  zf-C2HC5         Putative zinc finger motif, C2HC5-type


Domain annotation for each model (and alignments):
>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   4.0   8.5e-23   5.4e-20      48     187 .]      38     172 ..       5     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 8.5e-23
                           TackOD1  48 ekeeseelleelvkrglleeelvdrirlCpsCksghlnvrevCpkCkSidieeqelihhftCgnvgpeeeflkegkl 124
                                       e +e  ++le+l++r l++  + ++i lC++C  g ++ +  C +C+S +i++  +    +Cg+  pe+     +  
  gi|557694747|ref|YP_008797801.1|  38 ELTELLKVLERLESRALVKSFFEKKIALCSRCGKGIFQTHLNCVSCGSENIDKVMVYV-HNCGASIPETLLASVK-- 111
                                       4458899********************************************9876555.59***99999877666.. PP

                           TackOD1 125 eCpkCktkLrhiGvDYdrplevykCnsCkslfsepevkarClsCekesesddlkvreiysykl 187
                                       +CpkC + L++  +D+      ++Cn+C+++f  pev a+C+sC+ +s++ + ++ ++++yk+
  gi|557694747|ref|YP_008797801.1| 112 TCPKCGDALEK--KDFVASHGRFVCNNCGEVFEHPEVFAECVSCGYSSKVTENVYLTMRRYKV 172
                                       9********98..8***********************************************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   2.6    0.0012      0.74      13      49 .]      64      99 ..      59      99 .. 0.73
   2 !   15.3   5.0   2.3e-05     0.015       1      43 [.     113     162 ..     113     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                               DZR 13 rfCseCgtklkavaaedrCpsCgek.vdpearfCpeCG 49
                                        Cs+Cg+ +   +++ +C+sCg++ +d+   + ++CG
  gi|557694747|ref|YP_008797801.1| 64 ALCSRCGKGIF--QTHLNCVSCGSEnIDKVMVYVHNCG 99
                                      57999999985..6789999999985555555666666 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.3e-05
                               DZR   1 CpqCgee.......lppdarfCseCgtklkavaaedrCpsCgekvdpear 43 
                                       Cp+Cg +        +++  +C++Cg+  + ++    C+sCg++ + +++
  gi|557694747|ref|YP_008797801.1| 113 CPKCGDAlekkdfvASHGRFVCNNCGEVFEHPEVFAECVSCGYSSKVTEN 162
                                       9****9977777755566669********988889*******99887766 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 !   11.6   0.2   0.00032      0.21      25      98 ..      16      89 ..       4      94 .. 0.69
   2 ?    4.8   0.1     0.044        28      70      95 ..      92     119 ..      88     126 .. 0.74
   3 !   10.7   1.0   0.00065      0.42      67      95 ..     128     156 ..     120     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00032
                                      EEEEEEEEEETTCT--HHHHHHHHHHHHCC.T.TTT-EEE.EEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 25 kvtkvkvevGelsgvepeaLefafellaegtv.legaeLe.ieevpvkvrCreCgkefeleekalrCpkCgsadve 98
                                      k   + v+ G+++ v +  ++  ++ l +    le+  L     ++  + C++Cgk + ++  +l+C +Cgs++++
  gi|557694747|ref|YP_008797801.1| 16 KLFDIDVKTGDMKLVAEPPMKLELTELLKVLErLESRALVkSFFEKKIALCSRCGKGIFQT--HLNCVSCGSENID 89
                                      55678888888888888777766654444333366555541446677889*****888766..589******9986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.044
                                       EEEETTTS-EEECHH.H.HHS-TTTSSS CS
                              HypA  70 kvrCreCgkefelee.k.alrCpkCgsa 95 
                                        v+ ++Cg+++ ++  +   +CpkCg a
  gi|557694747|ref|YP_008797801.1|  92 MVYVHNCGASIPETLlAsVKTCPKCGDA 119
                                       566678999998665434569****975 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00065
                                       E--EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA  67 vpvkvrCreCgkefeleekalrCpkCgsa 95 
                                        + ++ C++Cg+ fe+ e  ++C +Cg +
  gi|557694747|ref|YP_008797801.1| 128 SHGRFVCNNCGEVFEHPEVFAECVSCGYS 156
                                       56799**********8865568****975 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 ?   -1.1   3.6       2.8   1.8e+03      31      55 ..      66      86 ..      64     103 .. 0.58
   2 !   18.8   0.4   1.7e-06    0.0011      29      56 ..     111     141 ..     105     146 .. 0.91
   3 ?   -0.4   0.1       1.7   1.1e+03      30      40 ..     149     159 ..     148     176 .. 0.74
   4 ?   -1.8   0.1       4.7     3e+03      11      22 ..     278     289 ..     277     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.8
                    OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfe 55
                                      Cs+Cg+   +      ++C +Cg e
  gi|557694747|ref|YP_008797801.1| 66 CSRCGKGIFQ----THLNCVSCGSE 86
                                      6666655444....45555555543 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 1.7e-06
                    OrfB_Zn_ribbon  29 ktCseCgsknke...alsgrtfkCpnCgfea 56 
                                       ktC++Cg  +++     s+ +f+C+nCg ++
  gi|557694747|ref|YP_008797801.1| 111 KTCPKCGDALEKkdfVASHGRFVCNNCGEVF 141
                                       9***********999999**********985 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.7
                    OrfB_Zn_ribbon  30 tCseCgsknke 40 
                                       +C  Cg+ +k 
  gi|557694747|ref|YP_008797801.1| 149 ECVSCGYSSKV 159
                                       68888887775 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 4.7
                    OrfB_Zn_ribbon  11 kakeyGikveev 22 
                                        a+ +G++ve+v
  gi|557694747|ref|YP_008797801.1| 278 TAETFGVEVEVV 289
                                       5899*****998 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1         1   6.7e+02      21      26 ..      65      70 ..      61      71 .. 0.88
   2 ?    0.7   0.1      0.59   3.8e+02       3      10 ..      80      87 ..      78      94 .. 0.77
   3 !   18.0   2.1   2.3e-06    0.0015       2      30 ..     112     142 ..     112     149 .. 0.86
   4 ?   -1.8   0.1       3.7   2.3e+03      22      27 ..     150     155 ..     147     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1
                                      EESSSS CS
                      TF_Zn_Ribbon 21 vCtdCG 26
                                      +C++CG
  gi|557694747|ref|YP_008797801.1| 65 LCSRCG 70
                                      7****9 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.59
                                      ETTTTCEE CS
                      TF_Zn_Ribbon  3 CPnCgstn 10
                                      C  Cgs+n
  gi|557694747|ref|YP_008797801.1| 80 CVSCGSEN 87
                                      78888877 PP

  == domain 3  score: 18.0 bits;  conditional E-value: 2.3e-06
                                       EETTTTCEECHEE..TSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveD..pergelvCtdCGlVle 30 
                                       +CP+Cg      D  +++g +vC +CG+V e
  gi|557694747|ref|YP_008797801.1| 112 TCPKCGDALEKKDfvASHGRFVCNNCGEVFE 142
                                       6*****9754666889*************98 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 3.7
                                       ESSSSB CS
                      TF_Zn_Ribbon  22 CtdCGl 27 
                                       C +CG+
  gi|557694747|ref|YP_008797801.1| 150 CVSCGY 155
                                       777875 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 ?    3.9   0.6     0.082        53       8      44 ..      52      84 ..      50      91 .. 0.73
   2 !   15.6   0.2   1.8e-05     0.012      20      44 ..     112     138 ..     103     140 .. 0.88
   3 ?   -0.4   0.0       1.8   1.2e+03      21      27 ..     150     156 ..     142     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.082
                     Zn_Tnp_IS1595  8 alLealrWpngfv.CPhCgsrkayriktrglfqCkeCr 44
                                      ++L + ++  +   C +Cg  k ++ ++   + C +C+
  gi|557694747|ref|YP_008797801.1| 52 RALVKSFFEKKIAlCSRCG--KGIFQTH---LNCVSCG 84
                                      5677778888855599999..6666665...7777776 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.8e-05
                     Zn_Tnp_IS1595  20 vCPhCgsr..kayriktrglfqCkeCr 44 
                                       +CP+Cg +  k  ++++ g+f C+ C+
  gi|557694747|ref|YP_008797801.1| 112 TCPKCGDAleKKDFVASHGRFVCNNCG 138
                                       7******9*988888889********8 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 1.8
                     Zn_Tnp_IS1595  21 CPhCgsr 27 
                                       C  Cg++
  gi|557694747|ref|YP_008797801.1| 150 CVSCGYS 156
                                       6666665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.12        77      17      34 ..      53      71 ..      47      75 .. 0.72
   2 ?    3.9   0.9     0.094        60       8      40 .]      66      92 ..      65      92 .. 0.66
   3 !    8.3   0.3    0.0039       2.5      26      38 ..     110     122 ..      96     123 .. 0.72
   4 !    8.8   3.9    0.0026       1.7       6      33 ..     132     154 ..     131     161 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                       Zn-ribbon_8 17 vlqsisdaplta.CPeCgs 34
                                      +l++++ ++++a C +Cg+
  gi|557694747|ref|YP_008797801.1| 53 ALVKSFFEKKIAlCSRCGK 71
                                      5677774556677****96 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.094
                       Zn-ribbon_8  8 CeeCghefevlqsisdapltaCPeCgs.evrrvi 40
                                      C +Cg+    +q+        C +Cgs +  +v+
  gi|557694747|ref|YP_008797801.1| 66 CSRCGKGI--FQT-----HLNCVSCGSeNIDKVM 92
                                      66676433..332.....3459*****9999886 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0039
                       Zn-ribbon_8  26 ltaCPeCgsevrr 38 
                                        ++CP+Cg ++++
  gi|557694747|ref|YP_008797801.1| 110 VKTCPKCGDALEK 122
                                       567*****99988 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0026
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCg 33 
                                       + C++Cg++fe+          +C +Cg
  gi|557694747|ref|YP_008797801.1| 132 FVCNNCGEVFEHPEV-----FAECVSCG 154
                                       89*********4332.....23488887 PP

>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.8e-05     0.012      37     120 ..      12      97 ..       5      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
                            Y1_Tnp  37 kkevkilelelmpDHvHllvelppklsiskivkalkgassrlinkefpelkkkklkk..eslWqrgYfvstvgeasl 111
                                       + +vk+  ++++   + l+ e+p kl++++++k l +  sr + k f e k +   +  + ++q+   ++++g++++
  gi|557694747|ref|YP_008797801.1|  12 EEGVKLFDIDVKTGDMKLVAEPPMKLELTELLKVLERLESRALVKSFFEKKIALCSRcgKGIFQTHLNCVSCGSENI 88 
                                       6789999999999999***********************************9999999999**************** PP

                            Y1_Tnp 112 etvkrYIen 120
                                       ++v  Y++n
  gi|557694747|ref|YP_008797801.1|  89 DKVMVYVHN 97 
                                       *******98 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.2      0.68   4.3e+02       3       8 ..      66      71 ..      64      75 .. 0.77
   2 ?   -1.1   0.1       2.9   1.8e+03       3       8 ..      80      85 ..      79      90 .. 0.75
   3 ?   15.0   0.8   2.7e-05     0.018       3      31 ..     113     140 ..     111     141 .. 0.87
   4 ?   -1.9   0.4       5.4   3.4e+03      25      30 ..     150     155 ..     149     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.68
                                      -TTT-- CS
                         Nudix_N_2  3 CsqCGt 8 
                                      Cs CG+
  gi|557694747|ref|YP_008797801.1| 66 CSRCGK 71
                                      788876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.9
                                      -TTT-- CS
                         Nudix_N_2  3 CsqCGt 8 
                                      C +CG+
  gi|557694747|ref|YP_008797801.1| 80 CVSCGS 85
                                      777776 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 2.7e-05
                                       -TTT--B-EEE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2   3 CsqCGtpvelripdgDnreRlvCpaCgti 31 
                                       C++CG ++e +     ++ R+vC++Cg +
  gi|557694747|ref|YP_008797801.1| 113 CPKCGDALEKKDF-VASHGRFVCNNCGEV 140
                                       *********7753.589**********98 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 5.4
                                       ETTTTE CS
                         Nudix_N_2  25 CpaCgt 30 
                                       C +Cg+
  gi|557694747|ref|YP_008797801.1| 150 CVSCGY 155
                                       777775 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   1.1     0.046        30       4      12 ..      65      73 ..      64      84 .. 0.88
   2 ?    1.4   0.0      0.39   2.5e+02       8      17 ..      98     107 ..      96     109 .. 0.83
   3 ?    3.7   0.1     0.072        46       4      13 ..     112     121 ..     110     127 .. 0.80
   4 ?    5.4   0.0     0.022        14       2      16 ..     131     145 ..     130     146 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.046
                            zf_UBZ  4 lCerCgkei 12
                                      lC+rCgk i
  gi|557694747|ref|YP_008797801.1| 65 LCSRCGKGI 73
                                      6*****977 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.39
                            zf_UBZ   8 Cgkeipesel 17 
                                       Cg++ipe+ l
  gi|557694747|ref|YP_008797801.1|  98 CGASIPETLL 107
                                       ******9865 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.072
                            zf_UBZ   4 lCerCgkeip 13 
                                       +C++Cg  ++
  gi|557694747|ref|YP_008797801.1| 112 TCPKCGDALE 121
                                       8****98765 PP

  == domain 4  score: 5.4 bits;  conditional E-value: 0.022
                            zf_UBZ   2 tylCerCgkeipese 16 
                                        ++C  Cg+ ++++e
  gi|557694747|ref|YP_008797801.1| 131 RFVCNNCGEVFEHPE 145
                                       59*********9887 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 ?   -2.6   0.2       8.3   5.3e+03       4       8 ..      66      70 ..      62      71 .. 0.70
   2 ?    0.7   0.1      0.79   5.1e+02      22      30 ..      78      86 ..      74      87 .. 0.78
   3 ?   14.1   0.3   5.1e-05     0.033       4      32 ..     113     142 ..     110     145 .. 0.89
   4 ?    2.4   0.5      0.23   1.5e+02      23      30 ..     149     156 ..     144     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.3
                                      ESTTT CS
                    RNA_POL_M_15KD  4 CpkCg 8 
                                      C+ Cg
  gi|557694747|ref|YP_008797801.1| 66 CSRCG 70
                                      66665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.79
                                      EEESSSS-E CS
                    RNA_POL_M_15KD 22 feCrqCgYe 30
                                      + C +Cg+e
  gi|557694747|ref|YP_008797801.1| 78 LNCVSCGSE 86
                                      569999987 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 5.1e-05
                                       ESTTTSBEEEEECSCCCE.EEESSSS-EEE CS
                    RNA_POL_M_15KD   4 CpkCgNlLlpkedkegkn.feCrqCgYeep 32 
                                       CpkCg+ L+ k+ +     f C +Cg +++
  gi|557694747|ref|YP_008797801.1| 113 CPKCGDALEKKDFVASHGrFVCNNCGEVFE 142
                                       ***********98877778*******9988 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.23
                                       EESSSS-E CS
                    RNA_POL_M_15KD  23 eCrqCgYe 30 
                                       eC +CgY 
  gi|557694747|ref|YP_008797801.1| 149 ECVSCGYS 156
                                       8******6 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.95   6.1e+02     130     144 ..      61      75 ..      54      77 .. 0.84
   2 ?    2.9   0.3      0.16   1.1e+02     118     140 ..      96     118 ..      86     120 .. 0.86
   3 ?   13.1   1.0   0.00012     0.075     109     140 ..     126     155 ..     120     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.95
                           DUF1451 130 eeippCpkCgateFr 144
                                       ++i  C++Cg+  F+
  gi|557694747|ref|YP_008797801.1|  61 KKIALCSRCGKGIFQ 75 
                                       78999****998886 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.16
                           DUF1451 118 ekCgkelalkkteeippCpkCga 140
                                       ++Cg+++  +    +++CpkCg 
  gi|557694747|ref|YP_008797801.1|  96 HNCGASIPETLLASVKTCPKCGD 118
                                       68999999999999*******96 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00012
                           DUF1451 109 vvglGtlvCekCgkelalkkteeippCpkCga 140
                                       v++ G++vC++Cg+   ++++e+  +C +Cg 
  gi|557694747|ref|YP_008797801.1| 126 VASHGRFVCNNCGE--VFEHPEVFAECVSCGY 155
                                       6889*********8..599***********96 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.9   1.2e+03      20      26 ..      64      70 ..      53      74 .. 0.77
   2 ?   10.0   0.8   0.00063       0.4       2      26 ..     113     138 ..     112     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.9
                          zf-TFIIB 20 dyCpqCr 26
                                        C +C+
  gi|557694747|ref|YP_008797801.1| 64 ALCSRCG 70
                                      5688886 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00063
                          zf-TFIIB   2 CPkCqdeleeser.ggveidyCpqCr 26 
                                       CPkC+d+le+ ++      ++C++C+
  gi|557694747|ref|YP_008797801.1| 113 CPKCGDALEKKDFvASHGRFVCNNCG 138
                                       *********99987444456777775 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.3     0.037        24      17      38 ..      64      86 ..      52     102 .. 0.66
   2 ?    8.5   6.5    0.0029       1.9      18      58 ..      79     140 ..      64     147 .. 0.64
   3 ?   11.5   2.8   0.00035      0.22       2      36 ..     112     154 ..     111     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.037
                                      EE-TTT--.EEEEEEE-SSS-S- CS
                    zinc-ribbons_6 17 yhCeaCqe.dlkkealCpeCeqe 38
                                      + C+ C +  ++ +  C  C++e
  gi|557694747|ref|YP_008797801.1| 64 ALCSRCGKgIFQTHLNCVSCGSE 86
                                      56888877667777888888764 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0029
                                       E-TTT--....................EEEEEEE-SSS-S---EEEETTEE.EE--TTTT-- CS
                    zinc-ribbons_6  18 hCeaCqe....................dlkkealCpeCeqelevlkaCgav.dyfCnkcneL 58 
                                       +C +C +                     l  +++Cp+C++ le+    ++   + Cn+c e+
  gi|557694747|ref|YP_008797801.1|  79 NCVSCGSenidkvmvyvhncgasipetLLASVKTCPKCGDALEKKDFVASHgRFVCNNCGEV 140
                                       4444444444444444444444666656788999********99887666525999999875 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00035
                                       --SSS-S--EE-S.....SEEE-TTT--...EEEEEEE-SSS- CS
                    zinc-ribbons_6   2 kCpeCqqelekrg.....eqyhCeaCqe...dlkkealCpeCe 36 
                                       +Cp+C  +lek++      ++ C++C e   + ++ a C  C+
  gi|557694747|ref|YP_008797801.1| 112 TCPKCGDALEKKDfvashGRFVCNNCGEvfeHPEVFAECVSCG 154
                                       7*******99888899989999****99554455667777776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   2.5     0.035        22       5      24 ..      66      85 ..      65      87 .. 0.86
   2 ?    5.5   0.2     0.019        12       4      13 ..      79      89 ..      76      92 .. 0.84
   3 ?    5.5   2.5     0.019        12      15      23 ..     109     117 ..      97     120 .. 0.64
   4 ?    6.6   0.8     0.008       5.1       3       9 ..     111     117 ..     109     124 .. 0.68
   5 ?    4.8   0.1      0.03        19       5      10 ..     134     139 ..     132     142 .. 0.68
   6 ?    1.5   0.1      0.33   2.1e+02       4       9 ..     149     154 ..     147     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.035
                       zf-ribbon_3  5 CPnCGa.plssddnvCpyCGt 24
                                      C++CG+ +      +C +CG+
  gi|557694747|ref|YP_008797801.1| 66 CSRCGKgI-FQTHLNCVSCGS 85
                                      99999977.999999999997 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.019
                       zf-ribbon_3  4 rCPnCGa.pls 13
                                      +C +CG+ +++
  gi|557694747|ref|YP_008797801.1| 79 NCVSCGSeNID 89
                                      7*****99987 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.019
                       zf-ribbon_3  15 ddnvCpyCG 23 
                                       ++++Cp+CG
  gi|557694747|ref|YP_008797801.1| 109 SVKTCPKCG 117
                                       566777776 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.008
                       zf-ribbon_3   3 vrCPnCG 9  
                                       ++CP+CG
  gi|557694747|ref|YP_008797801.1| 111 KTCPKCG 117
                                       5677777 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.03
                       zf-ribbon_3   5 CPnCGa 10 
                                       C+nCG+
  gi|557694747|ref|YP_008797801.1| 134 CNNCGE 139
                                       777776 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.33
                       zf-ribbon_3   4 rCPnCG 9  
                                       +C +CG
  gi|557694747|ref|YP_008797801.1| 149 ECVSCG 154
                                       799999 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1     0.008       5.1      64      86 .]      56      84 ..      34      84 .. 0.77
   2 ?    3.2   6.3      0.24   1.5e+02      39      86 .]     112     154 ..      86     154 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.008
                    zinc_ribbon_15 64 e......kkeCknCgkeveeefkyCpkCg 86
                                      +         C++Cgk + +    C +Cg
  gi|557694747|ref|YP_008797801.1| 56 KsffekkIALCSRCGKGIFQTHLNCVSCG 84
                                      1444444789******************9 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.24
                    zinc_ribbon_15  39 acskCkslleaskelgkeiekkesse.......kkeCknCgkeveee..fkyCpkCg 86 
                                       +c kC+  le+              +         +C+nCg++ e+   f+ C +Cg
  gi|557694747|ref|YP_008797801.1| 112 TCPKCGDALEK--------------KdfvashgRFVCNNCGEVFEHPevFAECVSCG 154
                                       34444444444..............14455555889999999987653478899998 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   2.1      0.77   4.9e+02      35      59 ..      64      85 ..      55     104 .. 0.66
   2 ?   14.0   3.3   6.3e-05      0.04      29      68 ..     105     148 ..      98     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.77
                           DUF2318 35 daCevCekkgYvqegeelvCknCgv 59
                                        C+ C+k  ++    +l C +Cg+
  gi|557694747|ref|YP_008797801.1| 64 ALCSRCGKGIFQ---THLNCVSCGS 85
                                      456667666554...3566666665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.3e-05
                           DUF2318  29 klrvaldaCevC....ekkgYvqegeelvCknCgvrfaldsige 68 
                                       +l + + +C  C    ekk +v +  + vC+nCg++f+ +++ +
  gi|557694747|ref|YP_008797801.1| 105 TLLASVKTCPKCgdalEKKDFVASHGRFVCNNCGEVFEHPEVFA 148
                                       5567899*****99999********************9988864 PP

>> DpnI  Dam-replacing family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       1.7   1.1e+03      30      40 ..      76      86 ..      50      98 .. 0.64
   2 ?   11.1   0.7   0.00035      0.22      25      85 ..     104     168 ..      97     194 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.7
                                      HH---TTT--S CS
                              DpnI 30 knlyCpkCgsk 40
                                      + l C +Cgs+
  gi|557694747|ref|YP_008797801.1| 76 THLNCVSCGSE 86
                                      34455555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00035
                                       HHHHHHH---TTT--SS-EE--------EEE-TTT--EEEEEEEES.....S--SEEEEEEHHHHH CS
                              DpnI  25 EkWvaknlyCpkCgskklsefennkpvaDfyCesckeefeLkskks.....klskkivdgaystmi 85 
                                       E+ +a+   CpkCg+  l++ +       f C++c e fe     +       s+k+++  y tm 
  gi|557694747|ref|YP_008797801.1| 104 ETLLASVKTCPKCGDA-LEKKDFVASHGRFVCNNCGEVFEHPEVFAecvscGYSSKVTENVYLTMR 168
                                       666777789******9.999888889999**********965443334455778888888888874 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 ?    1.4   0.0      0.54   3.5e+02       4      13 ..      66      75 ..      66      79 .. 0.85
   2 ?    0.1   0.4       1.4   8.9e+02       3       9 ..      79      85 ..      78      87 .. 0.86
   3 ?   12.9   2.0   0.00013     0.086       4      26 .]     113     137 ..     111     137 .. 0.89
   4 ?   -1.3   0.1       3.8   2.4e+03       3       8 ..     149     154 ..     147     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.54
                            zf-ACC  4 CpsCgemlyk 13
                                      C +Cg  +++
  gi|557694747|ref|YP_008797801.1| 66 CSRCGKGIFQ 75
                                      99***99987 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.4
                            zf-ACC  3 KCpsCge 9 
                                      +C sCg+
  gi|557694747|ref|YP_008797801.1| 79 NCVSCGS 85
                                      6****96 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 0.00013
                            zf-ACC   4 CpsCgemlykkeLernl..yVCPkC 26 
                                       Cp+Cg  l kk++ +++  +VC +C
  gi|557694747|ref|YP_008797801.1| 113 CPKCGDALEKKDFVASHgrFVCNNC 137
                                       **************986559**999 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 3.8
                            zf-ACC   3 KCpsCg 8  
                                        C sCg
  gi|557694747|ref|YP_008797801.1| 149 ECVSCG 154
                                       599**8 PP

>> DUF2054  Uncharacterized conserved protein (DUF2054)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.9       1.8   1.1e+03      50      74 ..      65      87 ..      50     101 .. 0.77
   2 ?   14.6   2.6     4e-05     0.026      34      86 ..     116     169 ..      85     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.8
                           DUF2054 50 sCktCdkkseCCeeyeyCvsCClep 74
                                       C++C   +   +++  CvsC  e 
  gi|557694747|ref|YP_008797801.1| 65 LCSRC--GKGIFQTHLNCVSCGSEN 87
                                      68888..6788889999****7654 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 4e-05
                           DUF2054  34 CCeveee.keeekskrfsCktCdkkseCCeeyeyCvsCClepdkkelleevlek 86 
                                       C ++ e+    +++ rf C++C +  e  e++  CvsC  +++ +e +  ++++
  gi|557694747|ref|YP_008797801.1| 116 CGDALEKkDFVASHGRFVCNNCGEVFEHPEVFAECVSCGYSSKVTENVYLTMRR 169
                                       222222113344559***********************9998877765555544 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 ?    7.3   0.8    0.0068       4.3      24      46 ..      64      86 ..      61      91 .. 0.88
   2 ?    3.2   0.2      0.13        80      35      47 ..     104     120 ..      96     123 .. 0.66
   3 ?    7.1   3.5    0.0074       4.8       3      44 ..     111     154 ..     109     158 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0068
                                      EE-HHHHHHHHHTT-B-TTT--B CS
                        zf-C3HC4_3 24 vlCeeCaekllkrkkkCpiCrrp 46
                                      +lC++C + + + + +C  C ++
  gi|557694747|ref|YP_008797801.1| 64 ALCSRCGKGIFQTHLNCVSCGSE 86
                                      69******************875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.13
                                       H....TT-B-TTT--B- CS
                        zf-C3HC4_3  35 k....rkkkCpiCrrpi 47 
                                       +    + k+Cp C    
  gi|557694747|ref|YP_008797801.1| 104 EtllaSVKTCPKCGDAL 120
                                       344448899****8765 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0074
                                       SB-TTTSSS..BS-EEETTEEEEEE-HHHHHHHHH..TT-B-TTT- CS
                        zf-C3HC4_3   3 eeCviCler..prnvvllpCgHlvlCeeCaekllk..rkkkCpiCr 44 
                                       ++C+ C ++  ++++v  + + +  C++C e ++     ++C  C 
  gi|557694747|ref|YP_008797801.1| 111 KTCPKCGDAleKKDFVASHGRFV--CNNCGEVFEHpeVFAECVSCG 154
                                       68******544999999999988..********8899999999995 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.9      0.29   1.8e+02       1      13 [.      66      78 ..      66      98 .. 0.70
   2 ?   11.8   0.7   0.00033      0.21      28      53 ..     112     137 ..     111     142 .. 0.95
   3 ?   -2.3   0.0       8.3   5.3e+03      24      33 ..     144     154 ..     143     166 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.29
                                      -TTT--BE-TTTE CS
                               LIM  1 CagCnkkiadrel 13
                                      C++C+k+i +++l
  gi|557694747|ref|YP_008797801.1| 66 CSRCGKGIFQTHL 78
                                      7777777766554 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00033
                                       B-TTT-SB-CTT.CEEETTEEEEHHH CS
                               LIM  28 tCsdCqkeLkegsfyekdgklyCkkd 53 
                                       tC +C++ L++++f+   g+++C+++
  gi|557694747|ref|YP_008797801.1| 112 TCPKCGDALEKKDFVASHGRFVCNNC 137
                                       7***********************98 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.3
                                       TTTS.B-TTT- CS
                               LIM  24 eeCF.tCsdCq 33 
                                       +e F  C +C+
  gi|557694747|ref|YP_008797801.1| 144 PEVFaECVSCG 154
                                       55552377776 PP

>> Ribosomal_L37e  Ribosomal protein L37e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.0    0.0018       1.1      16      38 ..      63      84 ..      56      99 .. 0.84
   2 ?   -0.9   0.1       2.9   1.9e+03      32      38 ..     111     117 ..     108     125 .. 0.70
   3 ?    7.4   1.2    0.0076       4.9      17      42 ..     132     158 ..     122     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0018
                    Ribosomal_L37e 16 HilCrrCgkrsyhvqkktCascG 38
                                        lC rCgk  + ++  +C scG
  gi|557694747|ref|YP_008797801.1| 63 IALCSRCGKGIFQTH-LNCVSCG 84
                                      579*********975.6899999 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.9
                    Ribosomal_L37e  32 ktCascG 38 
                                       ktC +cG
  gi|557694747|ref|YP_008797801.1| 111 KTCPKCG 117
                                       5677776 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0076
                    Ribosomal_L37e  17 ilCrrCgkrsyhvqk.ktCascGypsa 42 
                                        +C+ Cg+   h +   +C scGy s+
  gi|557694747|ref|YP_008797801.1| 132 FVCNNCGEVFEHPEVfAECVSCGYSSK 158
                                       5799***98888775489******887 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   0.2     0.083        53       2       7 ..      66      71 ..      64      73 .. 0.58
   2 ?    4.8   0.2     0.037        24       2      12 ..      80      90 ..      79      92 .. 0.85
   3 ?    7.8   1.6    0.0044       2.8      12      20 ..     109     117 ..      96     120 .. 0.63
   4 ?   -0.1   6.0       1.3   8.1e+02       2      21 ..     134     155 ..     133     157 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.083
                     zinc_ribbon_2  2 CpnCGa 7 
                                      C++CG+
  gi|557694747|ref|YP_008797801.1| 66 CSRCGK 71
                                      555555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.037
                     zinc_ribbon_2  2 CpnCGaelqdn 12
                                      C +CG e+ d+
  gi|557694747|ref|YP_008797801.1| 80 CVSCGSENIDK 90
                                      99*****9876 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0044
                     zinc_ribbon_2  12 nakFCpyCG 20 
                                        +k Cp+CG
  gi|557694747|ref|YP_008797801.1| 109 SVKTCPKCG 117
                                       488899999 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 1.3
                     zinc_ribbon_2   2 CpnCGaelqdnakF..CpyCGt 21 
                                       C nCG+  +  ++F  C  CG+
  gi|557694747|ref|YP_008797801.1| 134 CNNCGEVFEHPEVFaeCVSCGY 155
                                       9999987777777777888886 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 ?    8.8   1.2    0.0023       1.5       9      35 ..      61      84 ..      54      87 .. 0.82
   2 ?    7.1   0.8    0.0079       5.1      10      38 ..     109     141 ..     103     144 .. 0.83
   3 ?    4.5   1.3      0.05        32      13      36 ..     133     155 ..     124     157 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0023
                                      SS--B-TTT-SB--SSSS-EEEETTT- CS
                              C1_1  9 kqptfCkhCgeflwgkekqglkCswCk 35
                                      k+ + C+ Cg+ +   + ++l C  C+
  gi|557694747|ref|YP_008797801.1| 61 KKIALCSRCGKGI---FQTHLNCVSCG 84
                                      67899********...88888998886 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0079
                                       S--B-TTT-SB-...-S.SSS-EEEETTT--EE CS
                              C1_1  10 qptfCkhCgefl...wg.kekqglkCswCkllv 38 
                                       + ++C +Cg+ l    +  ++  + C++C++++
  gi|557694747|ref|YP_008797801.1| 109 SVKTCPKCGDALekkDFvASHGRFVCNNCGEVF 141
                                       6689********998555889999*****9987 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.05
                                       B-TTT-SB--SSSS-EEEETTT-- CS
                              C1_1  13 fCkhCgeflwgkekqglkCswCkl 36 
                                        C+ Cge + ++  +   C  C++
  gi|557694747|ref|YP_008797801.1| 133 VCNNCGEVF-EHPEVFAECVSCGY 155
                                       5*******9.76777889999987 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0033       2.1      13      38 ..      58      83 ..      35      91 .. 0.82
   2 ?    0.5   4.6       1.2   7.6e+02      14      40 ..     127     155 ..     109     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0033
                              C1_2 13 edssesfnCsaCgrkidgffYsCseC 38
                                        +++   Cs Cg+ i++++ +C  C
  gi|557694747|ref|YP_008797801.1| 58 FFEKKIALCSRCGKGIFQTHLNCVSC 83
                                      56777889********9999***989 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                              C1_2  14 dssesfnCsaCgrk..idgffYsCseCdf 40 
                                        s+++f C+ Cg+     + f +C  C +
  gi|557694747|ref|YP_008797801.1| 127 ASHGRFVCNNCGEVfeHPEVFAECVSCGY 155
                                       5789999**99998432222256766765 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 ?    0.5  12.4       1.1   7.3e+02      17      48 ..     109     141 ..      45     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 1.1
                               IBR  17 nlkwCprpdCeaiiekseg...cksvtCskCgfef 48 
                                       ++k Cp  +C+ ++ek++     ++  C++Cg+ f
  gi|557694747|ref|YP_008797801.1| 109 SVKTCP--KCGDALEKKDFvasHGRFVCNNCGEVF 141
                                       5789*9..9****9999997443336677777665 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 ?    4.5   2.9     0.053        34      18      43 ..      64      86 ..      59      91 .. 0.71
   2 ?   -2.4   8.7       7.5   4.8e+03      14      42 ..      74      85 ..      66     128 .. 0.64
   3 ?    7.5   1.4    0.0061       3.9      19      42 ..     133     155 ..     128     164 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.053
                          zf-C2HC5 18 pnClnCGkiiCakeglskpCsfCgsp 43
                                       +C  CGk i + +    +C +Cgs+
  gi|557694747|ref|YP_008797801.1| 64 ALCSRCGKGIFQTHL---NCVSCGSE 86
                                      578888887766554...48888876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.5
                          zf-C2HC5 14 leaapnClnCGkiiCakeglskpCsfCgs 42
                                      +++  nC++CG                 s
  gi|557694747|ref|YP_008797801.1| 74 FQTHLNCVSCG-----------------S 85
                                      33444444444.................3 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0061
                          zf-C2HC5  19 nClnCGkiiCakeglskpCsfCgs 42 
                                        C nCG +    e + ++C +Cg 
  gi|557694747|ref|YP_008797801.1| 133 VCNNCGEVFEHPEVF-AECVSCGY 155
                                       6********999999.******94 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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):              28  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 1761.52
//
Query:       gi|557694748|ref|YP_008797802.1|  [L=525]
Description: type II secretion system protein E [Candidatus Caldiarchaeum subterraneum]
Scores for 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-38  130.5   0.2    1.3e-37  129.4   0.0    1.5  2  T2SSE            Type II/IV secretion system protein
    0.00012   22.6   0.0    0.00063   20.3   0.0    2.2  2  AAA_18           AAA domain
    0.00039   20.7   0.0     0.0012   19.1   0.0    1.8  1  AAA_22           AAA domain
    0.00039   20.9   0.0     0.0018   18.8   0.0    2.0  1  ABC_tran         ABC transporter
     0.0004   20.1   0.5    0.00083   19.1   0.1    1.7  1  AAA_29           P-loop containing region of AAA domain
    0.00047   19.7   0.1    0.00088   18.8   0.1    1.3  1  AAA_7            P-loop containing dynein motor region
     0.0012   19.0   0.1     0.0035   17.5   0.0    1.9  1  AAA_33           AAA domain
     0.0021   18.5   0.0      0.004   17.5   0.0    1.5  1  AAA_16           AAA ATPase domain
     0.0021   18.6   1.0     0.0071   16.9   0.0    2.2  2  AAA_23           AAA domain
     0.0046   16.8   0.0     0.0093   15.8   0.0    1.5  1  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0082   15.7   0.2      0.024   14.2   0.2    1.8  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.022   14.1   0.0    1.4  1  Zeta_toxin       Zeta toxin
      0.018   14.8   0.0      0.045   13.5   0.0    1.6  1  AAA_30           AAA domain
       0.02   14.3   0.0      0.033   13.6   0.0    1.3  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.021   14.6   0.0       0.04   13.7   0.0    1.4  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.024   14.6   0.0       0.05   13.6   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
      0.025   14.6   0.2       0.15   12.1   0.0    2.2  2  AAA_14           AAA domain
      0.031   13.6   0.1      0.063   12.6   0.1    1.4  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.031   14.2   0.0      0.067   13.1   0.0    1.5  1  NACHT            NACHT domain
      0.031   14.2   0.0      0.079   12.9   0.0    1.6  1  ATPase_2         ATPase domain predominantly from Archaea
      0.034   14.5   0.1       0.15   12.4   0.2    1.9  1  AAA_19           AAA domain
      0.034   13.9   0.0      0.063   13.1   0.0    1.3  1  AAA_11           AAA domain
      0.035   13.5   0.0        0.1   12.0   0.0    1.7  1  SMC_N            RecF/RecN/SMC N terminal domain
      0.036   13.5   0.0      0.081   12.4   0.0    1.5  1  PhoH             PhoH-like protein
      0.042   13.4   0.0       0.19   11.3   0.0    2.0  2  AAA_27           AAA domain
      0.042   13.6   0.1      0.071   12.9   0.1    1.6  1  DEAD             DEAD/DEAH box helicase
      0.046   13.3   0.1       0.13   11.8   0.1    1.8  1  AAA_25           AAA domain
       0.05   13.5   0.1       0.12   12.2   0.1    1.6  1  RsgA_GTPase      RsgA GTPase
      0.082   11.6   0.0       0.14   10.9   0.0    1.2  1  RNA12            RNA12 protein
      0.095   12.1   0.0       0.27   10.6   0.0    1.7  1  Pox_A32          Poxvirus A32 protein
      0.098   13.1   0.0       0.27   11.7   0.0    1.8  1  AAA              ATPase family associated with various cellul
      0.099   12.3   0.1       0.18   11.4   0.1    1.4  1  SRP54            SRP54-type protein, GTPase domain
        0.1   12.3   0.0       0.17   11.6   0.0    1.3  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.11   12.4   0.0       0.31   10.9   0.0    1.8  1  NTPase_1         NTPase
       0.12   12.4   0.1       0.32   11.0   0.1    1.7  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.13   12.1   0.0       0.36   10.7   0.0    1.7  1  MobB             Molybdopterin guanine dinucleotide synthesis
       0.15   12.1   0.0       0.29   11.1   0.0    1.4  1  ResIII           Type III restriction enzyme, res subunit
       0.15   11.5   0.0       0.36   10.3   0.0    1.6  1  SRPRB            Signal recognition particle receptor beta su
       0.16   12.1   0.0       0.32   11.0   0.0    1.6  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai


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 !  129.4   0.0   2.8e-40   1.3e-37       5     255 ..     162     419 ..     159     433 .. 0.87
   2 ?   -2.7   0.0       5.1   2.4e+03      93     125 ..     481     516 ..     468     524 .. 0.67

  Alignments for each domain:
  == domain 1  score: 129.4 bits;  conditional E-value: 2.8e-40
                             T2SSE   5 leallddekvsdihvekper.vkvrervdg.ielreveelekaalerlisriaalakldiseerplqdarlp.ekgv 78 
                                       le+l++de+  di + kp+  ++++ r  +   +++  +l++++l   ++ +a   ++++s  +p   a+++ ++g 
  gi|557694748|ref|YP_008797802.1| 162 LEPLMRDEGLEDITITKPGPvYVIHRRHPDlGWIETNITLTAEELDKQARMLAERNGAELSIAKPA--AEIMtGEGD 236
                                       678999**************8888777766456777788999999999999999999999999986..566656777 PP

                             T2SSE  79 rlrvvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkei 153
                                       r+ +  +  +     +++iRk   + +t+ dl+ +++l+   a+ l +a+++++ ++v+G+TgsGKttll all+ +
  gi|557694748|ref|YP_008797802.1| 237 RIALTYAGELTPgtSTITIRKFPRSPYTIIDLIRRGTLTVVTAAYLWTALENKKFVMVAGPTGSGKTTLLSALLQLL 313
                                       7777766654433588************************************************************* PP

                             T2SSE 154 nksderivtvED.pvEiql.eganqvqlnak....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGH 224
                                       +++  +++t+ED   Ei+l  ++n  + +++    ++   +ad lr +LR+rPD  +vGE+R+ e+  + +A+ TGH
  gi|557694748|ref|YP_008797802.1| 314 PSN-AKLLTLEDyHPEINLsWHKNWHRFVTRrtlgETAYSLADILRLSLRHRPDYTIVGEVRGVEARVMFSAAATGH 389
                                       **9.********447****558999999999999999**************************************** PP

                             T2SSE 225 lgslsTlHansaagalerLeqlgaeveaael 255
                                           sT+Ha+s  ++ +rL   ++ v ++el
  gi|557694748|ref|YP_008797802.1| 390 GM-ASTIHAESLEDVYQRLTGASMGVLKEEL 419
                                       99.****************876654555544 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.1
                             T2SSE  93 lviRkksakeltlddlgaeealk...ekiaevlrka 125
                                        ++R+  +++l++ ++ ++   +   e++aev++k 
  gi|557694748|ref|YP_008797802.1| 481 PALRRDYENKLNILEYLMSSGEElkaEQLAEVVEKL 516
                                       578999999999999988754443336666666655 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       8.7     4e+03      97     113 ..     107     123 ..      68     138 .. 0.69
   2 !   20.3   0.0   1.4e-06   0.00063       1      64 [.     292     360 ..     292     407 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 8.7
                            AAA_18  97 vvLtaspeelleRlekR 113
                                         Lt ++ee  +R+e++
  gi|557694748|ref|YP_008797802.1| 107 PSLTEDEEEIVRRVEQQ 123
                                       56777888888888765 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.4e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf..gvnlrdvakenglllevdpe..aldeskrldedkldklldal 64 
                                       ++++G+ G+GKttl  +L ++l  +     l d+++e +l++  +++   +++++ +    l+ +l++ 
  gi|557694748|ref|YP_008797802.1| 292 VMVAGPTGSGKTTLLSALLQLLpSNakLLTLEDYHPEINLSWHKNWHrfVTRRTLGETAYSLADILRLS 360
                                       79****************88875557889************9999996666666655555555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.6e-06    0.0012       4      35 ..     288     319 ..     285     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.6e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeaka 35 
                                       ++++++v G++G+GKTtll  ll+ l+  ak 
  gi|557694748|ref|YP_008797802.1| 288 NKKFVMVAGPTGSGKTTLLSALLQLLPSNAKL 319
                                       789*********************99876554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.8e-06    0.0018       8      40 ..     286     318 ..     282     353 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.8e-06
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteG 40 
                                       l++ + v + G++G+GK+tLl++l++ll  ++ 
  gi|557694748|ref|YP_008797802.1| 286 LENKKFVMVAGPTGSGKTTLLSALLQLLPSNAK 318
                                       67888999*****************99865544 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 !   19.1   0.1   1.8e-06   0.00083      22      49 ..     289     316 ..     281     320 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.8e-06
                            AAA_29  22 kgatlltGpsGsGKSTllDAiqalLvpa 49 
                                       k +++++Gp+GsGK+Tll A+  lL ++
  gi|557694748|ref|YP_008797802.1| 289 KKFVMVAGPTGSGKTTLLSALLQLLPSN 316
                                       44799****************9999766 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 !   18.8   0.1   1.9e-06   0.00088      19      60 ..     275     316 ..     271     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.9e-06
                             AAA_7  19 tvrysyllelllknkkpvllvGptGtGKtviikdllkkldke 60 
                                       tv +   l + l+nkk v++ GptG+GKt++++ ll+ l+++
  gi|557694748|ref|YP_008797802.1| 275 TVVTAAYLWTALENKKFVMVAGPTGSGKTTLLSALLQLLPSN 316
                                       555666777889************************999843 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   7.6e-06    0.0035       2      38 ..     292     330 ..     291     441 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 7.6e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlf 38 
                                       v++ G+ GsGK+tl+  ll+ l+  a ll+  +++  + 
  gi|557694748|ref|YP_008797802.1| 292 VMVAGPTGSGKTTLLSALLQLLPsnAKLLTLEDYHPEIN 330
                                       899*****************9999999999888666554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   8.8e-06     0.004      23      51 ..     289     316 ..     269     408 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 8.8e-06
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekd 51 
                                           v++ G+ G+GK++l+ +ll+ l  +
  gi|557694748|ref|YP_008797802.1| 289 K-KFVMVAGPTGSGKTTLLSALLQLLPSN 316
                                       3.789******************655554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.6e-05    0.0071      18      42 ..     288     312 ..     257     324 .. 0.89
   2 ?   -1.1   0.0         5   2.3e+03     156     191 ..     485     519 ..     423     523 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-05
                            AAA_23  18 skgltlItGpNGaGKTTildAikla 42 
                                       +k+++ + Gp+G+GKTT+l A+   
  gi|557694748|ref|YP_008797802.1| 288 NKKFVMVAGPTGSGKTTLLSALLQL 312
                                       67889999*************9765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5
                            AAA_23 156 eelekeleeledekkllekleqekekekeleeleee 191
                                       +++e++l+ le   +  e+l ++++  +  e+l++e
  gi|557694748|ref|YP_008797802.1| 485 RDYENKLNILEYLMSSGEEL-KAEQLAEVVEKLRKE 519
                                       44555555555544444432.333444444555544 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 !   15.8   0.0     2e-05    0.0093       2      37 ..     292     328 ..     291     369 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2e-05
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarl.drdvegltdels 37 
                                        ++ Gp gsGK++LL al  l    ++ ++ + + + 
  gi|557694748|ref|YP_008797802.1| 292 VMVAGPTGSGKTTLLSALLQLLPSnAKLLTLEDYHPE 328
                                       6789**************9986545444444444444 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 !   14.2   0.2   5.2e-05     0.024       3      22 ..     292     311 ..     290     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.2e-05
                                       EEEEESTTCCHHHHHHHHHC CS
                              cobW   3 tvltGflGsGKTtLlnhlle 22 
                                       ++++G+ GsGKTtLl++ll+
  gi|557694748|ref|YP_008797802.1| 292 VMVAGPTGSGKTTLLSALLQ 311
                                       6899*************995 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.7e-05     0.022      14      47 ..     287     320 ..     277     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-05
                        Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvv 47 
                                       e++k ++++G +G+GK++l+++l + l ++ + +
  gi|557694748|ref|YP_008797802.1| 287 ENKKFVMVAGPTGSGKTTLLSALLQLLPSNAKLL 320
                                       78999*****************999886655555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.7e-05     0.045      14      43 ..     286     314 ..     279     327 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.7e-05
                            AAA_30  14 ltsgdrvavltGpAGtGKttalkalreawe 43 
                                       l+ +++++++ Gp G+GKtt+l+al +++ 
  gi|557694748|ref|YP_008797802.1| 286 LE-NKKFVMVAGPTGSGKTTLLSALLQLLP 314
                                       44.45699****************988765 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   7.3e-05     0.033      24      55 ..     291     322 ..     278     350 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.3e-05
                      Mg_chelatase  24 nlllvGppGsGKtmlakrlpsllpplseeeal 55 
                                        ++++Gp GsGKt l ++l +llp+  +  +l
  gi|557694748|ref|YP_008797802.1| 291 FVMVAGPTGSGKTTLLSALLQLLPSNAKLLTL 322
                                       57889*******************87765555 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 ?   13.7   0.0   8.6e-05      0.04       1      23 [.     294     316 ..     294     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.6e-05
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelr 23 
                                       v+Gp GsGKtt+ +al ++l+++
  gi|557694748|ref|YP_008797802.1| 294 VAGPTGSGKTTLLSALLQLLPSN 316
                                       89****************99987 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 ?   13.6   0.0   0.00011      0.05       2      44 ..     292     334 ..     291     379 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00011
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH-- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgr 44 
                                       v++ Gp+G+gK++l   l+++l ++     l ++ +e +l ++
  gi|557694748|ref|YP_008797802.1| 292 VMVAGPTGSGKTTLLSALLQLLPSNAKLLTLEDYHPEINLSWH 334
                                       6889******************888888777777776666655 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2       2.9   1.3e+03      41      87 ..     107     152 ..      79     158 .. 0.66
   2 ?   12.1   0.0   0.00033      0.15       2      42 ..     289     326 ..     288     359 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.9
                            AAA_14  41 erdkkladpekllelilek.lkeekktylflDEiqevpewekalkslv 87 
                                       +++++  d+e++ + + ++ +k+ ++ + +l E + +++ ek+lk+++
  gi|557694748|ref|YP_008797802.1| 107 PSLTE--DEEEIVRRVEQQyVKKGGDPFKLLEEYKVSEDREKVLKYFL 152
                                       33332..23346666777654556889999999999999999999987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00033
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldder 42 
                                       +k +++ G+  +GKTtll  l++ l    ++   ++l+d +
  gi|557694748|ref|YP_008797802.1| 289 KKFVMVAGPTGSGKTTLLSALLQLLP---SNAKLLTLEDYH 326
                                       7899****************995444...777777777754 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   0.1   0.00014     0.063      41      61 ..     291     311 ..     275     317 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00014
                                       SEEEE--TTSSHHHHHHHHHH CS
                      FtsK_SpoIIIE  41 hllvaGatgsGKStalntLil 61 
                                        ++vaG tgsGK+t l +L++
  gi|557694748|ref|YP_008797802.1| 291 FVMVAGPTGSGKTTLLSALLQ 311
                                       58****************986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00015     0.067       3      25 ..     292     314 ..     290     326 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                                       EEEEC-TTTCHHHHHHHHHHHHC CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                                       v++ G+ GsGKTtLl  l +++ 
  gi|557694748|ref|YP_008797802.1| 292 VMVAGPTGSGKTTLLSALLQLLP 314
                                       899**************999875 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   0.00017     0.079      14      45 ..     283     314 ..     281     337 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00017
                          ATPase_2  14 ilerepneiyfiYGpegsGKtaLlkeiienle 45 
                                       +   e+++++++ Gp gsGKt+Ll  +++ l 
  gi|557694748|ref|YP_008797802.1| 283 WTALENKKFVMVAGPTGSGKTTLLSALLQLLP 314
                                       56678999****************99988774 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00032      0.15       9      39 ..     288     318 ..     282     432 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00032
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelgg 39 
                                       ++k ++v ++ G+GKT++l + ++ll ++ +
  gi|557694748|ref|YP_008797802.1| 288 NKKFVMVAGPTGSGKTTLLSALLQLLPSNAK 318
                                       56777888888**********9999877765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00014     0.063      12      42 ..     284     314 ..     278     339 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                            AAA_11  12 salseseitliqGPPGtgKTktivellsqll 42 
                                       +al++++++++ GP G+gKT+ + +ll+ l 
  gi|557694748|ref|YP_008797802.1| 284 TALENKKFVMVAGPTGSGKTTLLSALLQLLP 314
                                       6899*******************99999883 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 ?   12.0   0.0   0.00022       0.1      23      50 ..     288     315 ..     283     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00022
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGe 50 
                                       +k+f ++ Gp GSGK+ ll A+l +L  
  gi|557694748|ref|YP_008797802.1| 288 NKKFVMVAGPTGSGKTTLLSALLQLLPS 315
                                       5789******************988873 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00018     0.081      13      36 ..     283     306 ..     276     316 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                                       HHHHHH-SEEEEE--TTSSTTHHH CS
                              PhoH  13 lealkkndivfaiGpaGtGKtyla 36 
                                        +al+++++v+++Gp+G+GKt l 
  gi|557694748|ref|YP_008797802.1| 283 WTALENKKFVMVAGPTGSGKTTLL 306
                                       57899****************874 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       4.5   2.1e+03      77     111 ..      50      84 ..      41     121 .. 0.56
   2 ?   11.3   0.0   0.00042      0.19      24      50 ..     287     313 ..     267     331 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.5
                            AAA_27  77 adgeelefaRrkgrkktlldaddqalpeevlaall 111
                                       a+   l+ +Rr + ++ l+ +++++ ++ev+++++
  gi|557694748|ref|YP_008797802.1|  50 AAVVILKTRRRSSAEEPLVLEAEETSAPEVIDQYV 84 
                                       44456788899999999988888765555444432 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00042
                            AAA_27  24 eeadlhliyGpNEAGKstalrAisdll 50 
                                       e++++ ++ Gp  +GK+t+l+A+ +ll
  gi|557694748|ref|YP_008797802.1| 287 ENKKFVMVAGPTGSGKTTLLSALLQLL 313
                                       5789*********************98 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00015     0.071      10      34 ..     285     308 ..     276     523 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                                       HHHTTCEEEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  10 lilgggdvlvaaeTGsGKTlaflip 34 
                                       ++ +++ v+va++TGsGKT+  + +
  gi|557694748|ref|YP_008797802.1| 285 ALENKKFVMVAGPTGSGKTTLLS-A 308
                                       444667899**********9854.3 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00028      0.13      31      53 ..     287     309 ..     257     313 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00028
                            AAA_25  31 pagelallaGapgtGKttlaldl 53 
                                         ++++++aG++g+GKttl++ l
  gi|557694748|ref|YP_008797802.1| 287 ENKKFVMVAGPTGSGKTTLLSAL 309
                                       67899**************9987 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00027      0.12      93     121 ..     282     311 ..     269     322 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00027
                                       HHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  93 lkellkd.ktsvlvGqSGvGKStLinallp 121
                                       l ++l++ k+++++G++G GK+tL+ all+
  gi|557694748|ref|YP_008797802.1| 282 LWTALENkKFVMVAGPTGSGKTTLLSALLQ 311
                                       5667777699999************99975 PP

>> RNA12  RNA12 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0003      0.14      11      34 ..     283     306 ..     277     323 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0003
                             RNA12  11 wleEnvntFivvkGPrGSGkkeLv 34 
                                       w + +++ F++v GP GSGk+ L+
  gi|557694748|ref|YP_008797802.1| 283 WTALENKKFVMVAGPTGSGKTTLL 306
                                       66667889*************997 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0006      0.27       8      38 ..     285     314 ..     279     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0006
                           Pox_A32   8 sLlkkpFrlalvGgsGsGktvyLlsLlrtlv 38 
                                        L +k+F ++  G +GsGkt+ L +Ll+ l 
  gi|557694748|ref|YP_008797802.1| 285 ALENKKFVMV-AGPTGSGKTTLLSALLQLLP 314
                                       6889999886.7**************98775 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   0.0   0.00059      0.27       1      25 [.     292     316 ..     292     367 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00059
                                       EEEESSTTSSHHHHHHHHHHHHTHE CS
                               AAA   1 vllyGppGtGKTllakavakelgve 25 
                                       v++ Gp G GKT+l +a+ + l ++
  gi|557694748|ref|YP_008797802.1| 292 VMVAGPTGSGKTTLLSALLQLLPSN 316
                                       6899**************9987433 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00039      0.18       2      29 ..     290     317 ..     289     323 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00039
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTT CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkeg 29 
                                       + ++++G++G+GKTt l+ L +ll +++
  gi|557694748|ref|YP_008797802.1| 290 KFVMVAGPTGSGKTTLLSALLQLLPSNA 317
                                       579***************9998887665 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   0.00037      0.17       2      56 ..     293     340 ..     292     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00037
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrtsliltvnrptaelltegkpklpnlsvrtvdsflma 56 
                                       +v+G  G+GK+tl+  ll+        +++a+llt   ++ p  + ++ + ++  
  gi|557694748|ref|YP_008797802.1| 293 MVAGPTGSGKTTLLSALLQL------LPSNAKLLTLE-DYHPEINLSWHKNWHRF 340
                                       799***************99......88888888887.47777777777777665 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   0.00068      0.31       2      25 ..     292     315 ..     291     320 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00068
                                       EEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellks 25 
                                       v++ Gp G+GKtTl++ +l+ll s
  gi|557694748|ref|YP_008797802.1| 292 VMVAGPTGSGKTTLLSALLQLLPS 315
                                       789***************999955 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1    0.0007      0.32      16      43 ..     284     313 ..     273     323 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0007
                                       HCH..TEEEEEEESTTSSHHHHHHHHHHHT CS
                              TsaE  16 kal..gdvilLeGdLGaGKTtlvrglakal 43 
                                       +al  +++++  G+ G+GKTtl  +l++ l
  gi|557694748|ref|YP_008797802.1| 284 TALenKKFVMVAGPTGSGKTTLLSALLQLL 313
                                       33344778*****************99876 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 ?   10.7   0.0   0.00078      0.36       2      25 ..     292     315 ..     291     330 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00078
                              MobB   2 lgivgksgsGKTtLleklipelka 25 
                                       + ++g  gsGKTtLl+ l++ l +
  gi|557694748|ref|YP_008797802.1| 292 VMVAGPTGSGKTTLLSALLQLLPS 315
                                       678999*************99865 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 ?   11.1   0.0   0.00063      0.29      22      51 ..     287     316 ..     254     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00063
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S. CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierllkk 51 
                                       +++k ++++ +TG+GKT ++ +l + l ++
  gi|557694748|ref|YP_008797802.1| 287 ENKKFVMVAGPTGSGKTTLLSALLQLLPSN 316
                                       6788899**********9998888777654 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 ?   10.3   0.0   0.00077      0.36       2      25 ..     288     311 ..     287     335 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00077
                                       ---EEEEE-STTSSHHHHHHHHHH CS
                             SRPRB   2 skpavllvGlsdsGKTslftrLtt 25 
                                       +k+ v+++G++ sGKT+l+  L++
  gi|557694748|ref|YP_008797802.1| 288 NKKFVMVAGPTGSGKTTLLSALLQ 311
                                       67889**************99986 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 ?   11.0   0.0    0.0007      0.32       3      67 ..     293     517 ..     291     523 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0007
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................... RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep......................... 54 
                                       ++++  G+GKTtl+ +L+++l  + +   l D  p+ n++ +  + +   ++                         
  gi|557694748|ref|YP_008797802.1| 293 MVAGPTGSGKTTLLSALLQLLPSNAKLLTLEDYHPEINLSWHKNWHRFVTRRtlgetaysladilrlslrhrpdyti 369
                                       5677889**************99777777778888888887633322222224444666666666666666666666 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|557694748|ref|YP_008797802.1| 370 vgevrgvearvmfsaaatghgmastihaesledvyqrltgasmgvlkeelsflnvvalvrntsrgrrvvgvweiert 446
                                       66666666666666666666666666666666666666666666666666666666666666666666655555555 PP

                                       ..........................................................CCHCCCHHHHHHC CS
                                       ..........................................................xxxxxxxxxxxxx RF
                              CbiA  55 ..........................................................dlkrllellealg 67 
                                                                                                  +++l e++e+l+
  gi|557694748|ref|YP_008797802.1| 447 gnehliswydeesgkffpetgkqlvvsspmlvhnpalrrdyenklnileylmssgeelKAEQLAEVVEKLR 517
                                       55555555555555555555555555555555555555555555555555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      807  (0.0450109); expected 358.6 (0.02)
Passed Vit filter:                       133  (0.00741815); 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: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 3479.25
//
Query:       gi|557694749|ref|YP_008797803.1|  [L=112]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0072   15.8   0.0     0.0088   15.5   0.0    1.1  1  Glu_dehyd_C  Glucose dehydrogenase C-terminus


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 !   15.5   0.0   4.9e-07    0.0088     158     210 ..      56     109 ..      41     111 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.9e-07
                       Glu_dehyd_C 158 GsvNanrrhfeaavdtLaalpeslldelvtkvvdldeleeAfe..dddetiKtvv 210
                                         v ++   f+ a+++La+     +++l+ +v  lde+eeAf+   ++et+K+ +
  gi|557694749|ref|YP_008797803.1|  56 SVVGSRCGPFKPAIKALATGM-VQVEKLIDRVFSLDEYEEAFAlaAEKETLKVLL 109
                                       345678999********9765.4589****************6447788999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 839.08
//
Query:       gi|557694750|ref|YP_008797804.1|  [L=146]
Description: UspA domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-31  109.0   1.9    3.2e-31  108.7   1.9    1.1  1  Usp           Universal stress protein family
     0.0049   16.3   0.0     0.0092   15.4   0.0    1.5  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
      0.051   13.9   0.0      0.066   13.5   0.0    1.3  1  GAF_2         GAF domain
       0.13   11.9   0.0       0.16   11.6   0.0    1.1  1  CDPS          Cyclodipeptide synthase


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 !  108.7   1.9   7.2e-35   3.2e-31       1     141 []       1     146 []       1     146 [] 0.89

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 7.2e-35
                                       S-SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHH....HHH CS
                               Usp   1 mykrIlVavDgseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleada....aka 73 
                                       m++++lVavDgse skkA++ A++l k+ gae+  +hv+  +++  ++ + ++a+ ++  + + ++ +       ++
  gi|557694750|ref|YP_008797804.1|   1 MFRKVLVAVDGSEFSKKAVDVAVRLCKQLGAEISFVHVVQQPPYLFAASGVPPAALKQFIDDAVREGRRYveeaVET 77 
                                       9******************************************9999999988888888877777766667888777 PP

                                       HHHCTTCEEEEEEEES.SHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  74 aaeaggvkvevvveeg.dpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       aa+ g+++v  v+e+  ++ e+i+ +ae +++dliV+G+rg+sg+++++lGSv++ v+ ha+c+VlvV+
  gi|557694750|ref|YP_008797804.1|  78 AARMGVKAVGEVLEMRpSVVEAITGFAETHGVDLIVTGTRGLSGFKKVVLGSVASGVVSHAHCSVLVVK 146
                                       777777777777766526899***********************************************8 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 !   15.4   0.0   2.1e-06    0.0092      65     131 ..      12      89 ..       3     107 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-06
                                       HHHHHHHHHHHHHHHHHHTBSEEEEEBCC...........GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE CS
                      AP_endonuc_2  65 reesvdalkraielaaaLGapllvlhpGt...........agagpkgseeeawerlaeslneladyaekegvklalE 130
                                       +e+s++a+  a++l+++LGa++  +h+ +            +a  k+ +++a++  ++ ++e+++ a++ gvk + E
  gi|557694750|ref|YP_008797804.1|  12 SEFSKKAVDVAVRLCKQLGAEISFVHVVQqppylfaasgvPPAALKQFIDDAVREGRRYVEEAVETAARMGVKAVGE 88 
                                       45566666777777777777777777666666666666665555666666777777777777777777777776655 PP

                                       - CS
                      AP_endonuc_2 131 t 131
                                        
  gi|557694750|ref|YP_008797804.1|  89 V 89 
                                       5 PP

>> GAF_2  GAF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.5e-05     0.066       7      66 ..      18      78 ..      12     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHHHHSS..EEEEEEE-TTS-EEEE.EEEES-TTSTT-S-B---TT.H.HHHHHHHT CS
                             GAF_2  7 lldlvldelvelgaalgyillvdddgglrla.awgeaeeefgaaldrplgeg.l.vgealrtg 66
                                       +d +++ + +lga+++++++v++ ++  l  a+g +++ + + +d++++eg   v+ea++t 
  gi|557694750|ref|YP_008797804.1| 18 AVDVAVRLCKQLGAEISFVHVVQQPPY--LFaASGVPPAALKQFIDDAVREGrRyVEEAVETA 78
                                      4566777777789**********9998..6647777777778888888888877788888874 PP

>> CDPS  Cyclodipeptide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.6e-05      0.16      26      97 ..       9      80 ..       3      95 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.6e-05
                                      TTBTTS-HHHHHHHHHHHHHHSSEEEEEE--TTHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              CDPS 26 pgnsyfsedrlaalirwaareFaqvdvvvadtevaellealGyspeeArrkaarelravrarieraleeagp 97
                                      +  s fs++ +   +r+ ++  a++++v+  ++   l++a+G +p+  ++    ++r+ r+++e+a+e+a  
  gi|557694750|ref|YP_008797804.1|  9 VDGSEFSKKAVDVAVRLCKQLGAEISFVHVVQQPPYLFAASGVPPAALKQFIDDAVREGRRYVEEAVETAAR 80
                                      45699*****************************************9999999***************9974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); 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:                         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 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1113.69
//
Query:       gi|557694751|ref|YP_008797805.1|  [L=150]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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: 00:00:00.40
# Mc/sec: 1116.19
//
Query:       gi|557694752|ref|YP_008797806.1|  [L=267]
Description: zinc ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-43  148.7  33.9    2.4e-43  148.5  33.9    1.0  1  ABC-3     ABC 3 transport family
    0.00034   19.7  34.6     0.0005   19.2  34.6    1.3  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.5  33.9   2.7e-47   2.4e-43       2     256 ..       7     259 ..       6     261 .. 0.97

  Alignments for each domain:
  == domain 1  score: 148.5 bits;  conditional E-value: 2.7e-47
                             ABC-3   2 yeflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrkt 78 
                                        +f+qra+ a+i+ +l  +l+g ++v +r sl+gda sHaa++ +al  llg+  ++ + ++ ++a  ++  l+r+ 
  gi|557694752|ref|YP_008797806.1|   7 QPFMQRAFGAAIVTGLLLPLIGNYLVPKRLSLVGDASSHAAFAVIALSSLLGFGATFLTYIAPVAAIYTILQLMRRF 83 
                                       579***************************************************9999999999999999******* PP

                             ABC-3  79 klkedtaigivlsvflalglvlvslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfde 155
                                       +++ d a++ +l+v+ a + +++sl    +v+l+++LfG+i+ ++ ed+i+ a ++a+v l +   + + l++t++e
  gi|557694752|ref|YP_008797806.1|  84 HVSGDQALATLLAVGGATASLAISLGA--RVNLNAILFGSIILVQVEDIIVGASVAAFVTLFVAGNFGKTLVYTVSE 158
                                       ************************998..9*********************************************** PP

                             ABC-3 156 elAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllS 232
                                       elAkv+g++v+++ l++++  +l++v+ ++++Gv+Lv+all iP  +A ++++s+++ +++++l+g  s+++G+l+S
  gi|557694752|ref|YP_008797806.1| 159 ELAKVRGVQVETYTLVFAVAAGLSIVTGIKIAGVLLVTALLAIPTTAASLISNSFKKSIMLSMLFGGTSTTLGVLMS 235
                                       ***************************************************************************** PP

                             ABC-3 233 yyldlatGavivlvatllfllall 256
                                       y+ld+a+Ga  v+v+++++++ l+
  gi|557694752|ref|YP_008797806.1| 236 YFLDIAPGAASVMVLMIFLVFCLV 259
                                       *********999999977777654 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2  34.6   5.6e-08    0.0005      85     310 ..      45     260 ..      10     262 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.6e-08
                             FecCD  85 lgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllneeale 161
                                        +a+++++l  +sl  f+ +++  +  ++a+  +l l  +r + s  + + + +av+  +++l+  l +        
  gi|557694752|ref|YP_008797806.1|  45 HAAFAVIAL--SSLLGFGATFLTYIAPVAAIYTILQLM-RRFHVSGDQALATLLAVGGATASLAISLGAR------V 112
                                       223333333..566667777777777777777788887.7777777777777778888888888777766......5 PP

                             FecCD 162 silfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltavaval 238
                                       +++ +l+Gs+  ++ +++++ + ++++++l+++ +  k  ++++++e+Ak  Gv+ve+++l++++++ l + + + +
  gi|557694752|ref|YP_008797806.1| 113 NLNAILFGSIILVQVEDIIVGASVAAFVTLFVAGNFGKTLVYTVSEELAKVRGVQVETYTLVFAVAAGLSIVTGIKI 189
                                       69999************************************************************************ PP

                             FecCD 239 vGpigFvGLi.vPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiyll 310
                                       +G++   +L+ +P +a  l++++++k ++ls+l+G++  +l  l++ +l  ++   +  v+ l++ ++f+++l
  gi|557694752|ref|YP_008797806.1| 190 AGVLLVTALLaIPTTAASLISNSFKKSIMLSMLFGGTSTTLGVLMSYFL--DIAPGAASVMVLMIFLVFCLVL 260
                                       ****99997626**************************99998888777..3443445555566666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); 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:                         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 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1935.20
//
Query:       gi|557694753|ref|YP_008797807.1|  [L=251]
Description: zinc ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   0.0    1.5e-27   96.8   0.0    1.2  1  ABC_tran   ABC transporter
    4.5e-11   43.1   0.1    0.00016   21.6   0.0    2.2  2  AAA_21     AAA domain, putative AbiEii toxin, Type IV TA syst
    1.1e-05   25.0   0.1      0.053   13.0   0.0    2.2  2  SMC_N      RecF/RecN/SMC N terminal domain
    0.00028   21.3   0.0      0.017   15.6   0.0    2.3  1  AAA        ATPase family associated with various cellular act
    0.00092   18.9   0.1     0.0017   18.0   0.1    1.4  1  AAA_29     P-loop containing region of AAA domain
     0.0065   15.7   0.1      0.038   13.2   0.0    1.9  2  PIF1       PIF1-like helicase
     0.0068   16.1   0.2       0.06   13.1   0.2    2.1  1  AAA_30     AAA domain
  ------ inclusion threshold ------
      0.026   14.2   0.2        4.4    7.0   0.1    2.3  2  IstB_IS21  IstB-like ATP binding protein
      0.027   14.4   0.0      0.065   13.2   0.0    1.8  2  NTPase_1   NTPase
      0.039   13.9   0.0      0.095   12.6   0.0    1.5  2  ATPase_2   ATPase domain predominantly from Archaea
      0.039   13.7   0.0      0.067   12.9   0.0    1.4  1  AAA_24     AAA domain
      0.046   14.2   0.2      0.071   13.6   0.2    1.2  1  AAA_23     AAA domain
      0.082   13.2   0.9        0.4   10.9   0.9    2.2  1  AAA_22     AAA domain
      0.092   12.7   0.8       0.17   11.8   0.8    1.7  1  NACHT      NACHT domain
       0.11   12.9   0.0       0.15   12.5   0.0    1.4  1  AAA_16     AAA ATPase domain
       0.22   11.9   0.5       0.44   10.9   0.4    1.8  1  AAA_19     AAA domain
        3.1    7.3   4.7        2.4    7.7   0.9    2.7  2  AAA_25     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 !   96.8   0.0   1.4e-30   1.5e-27       1     136 [.      25     166 ..      25     167 .. 0.86

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 1.4e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSB. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx. RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpelt. 75 
                                       l+nvslk+  ge++ i+G+nG GK+tLlk++ g l+p+ G+++l g ++++    + r ++g++pq+ + lf+++  
  gi|557694753|ref|YP_008797807.1|  25 LDNVSLKVLMGERLFIIGPNGGGKTTLLKTMVGVLRPDRGTVKLFGVPIQR---FRERWRLGYVPQNaAALFERTPl 98 
                                       79************************************************9...7778889******8888888864 PP

                                       .HHHH......HHHTC......HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       .xxxx......xxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 .vren......esdee......iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        v  +      +   +      + +al+ +g +e +d++++ + s LSgG  q+ +la al++kp+ll+lDEpt
  gi|557694753|ref|YP_008797807.1|  99 sV--EellrsgA---QtgraldPVEALALVGVDE-PDKILHIRVSDLSGGNLQKTMLALALINKPQLLILDEPT 166
                                       24..24696663...3333445667777777666.999999999*****************************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 !   19.3   0.1   7.5e-07   0.00079       3      24 ..      39      60 ..      38      94 .. 0.76
   2 !   21.6   0.0   1.5e-07   0.00016     232     299 ..     134     199 ..     105     203 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 7.5e-07
                            AAA_21  3 vliGpNgsGKSnLLdaldllar 24
                                      ++iGpNg GK++LL+++ ++ r
  gi|557694753|ref|YP_008797807.1| 39 FIIGPNGGGKTTLLKTMVGVLR 60
                                      69**************998865 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 1.5e-07
                            AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSp 299
                                       + +++lS G ++   +l++ l   +   ll++DEp    +   ++ l+ ++++ +r +g  vi++TH+ 
  gi|557694753|ref|YP_008797807.1| 134 IRVSDLSGGNLQK-TMLALALINKP--QLLILDEPTVYVDQTGVAALMNVVNRVNRdWGMTVIIATHDV 199
                                       5567899999999.88888887666..9***********************888888**********95 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 !   10.2   0.0   0.00034      0.36      28      45 ..      39      56 ..      26      65 .. 0.85
   2 !   13.0   0.0     5e-05     0.053     131     202 ..     133     202 ..      93     219 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00034
                                      EEEESTTSSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 28 aivGpNGSGKsnlldAil 45
                                      +i+GpNG GK+ ll  + 
  gi|557694753|ref|YP_008797807.1| 39 FIIGPNGGGKTTLLKTMV 56
                                      8************99886 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 5e-05
                                       T-STTCS-HH..HHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHC CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                             SMC_N 131 giskelLSgG..ektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn..aQfivislreeml 202
                                       +i  + LSgG  +kt++alaL+      ++  l +lDe     D++ v+++ +++++ + +  + +i+ +++   +
  gi|557694753|ref|YP_008797807.1| 133 HIRVSDLSGGnlQKTMLALALI------NKPQLLILDEPTVYVDQTGVAALMNVVNRVNRDwgMTVIIATHDVAAI 202
                                       577778****666888888888......4555899********************987777446777777765554 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 !   15.6   0.0   1.6e-05     0.017       2      92 ..      39     151 ..      38     216 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                                       EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSS............STTHHHHHHHHHHHH.HHHTS... CS
                               AAA   2 llyGppGtGKTllakavakel.....gvefleisgsellsk............yvgesekkirelfke.akeka... 57 
                                        ++Gp G GKT+l k ++  l      v+++ +   ++++             +++ ++ +++el+++ a++ +   
  gi|557694753|ref|YP_008797807.1|  39 FIIGPNGGGKTTLLKTMVGVLrpdrgTVKLFGVPIQRFRERwrlgyvpqnaaaLFERTPLSVEELLRSgAQTGRald 115
                                       579*****************955544377777777777755666666666666444444444444444222222455 PP

                                       ...TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
                               AAA  58 ...kpsilfiDEidalaksrsgseseeeervvnqLlte 92 
                                          +   + +DE d++   r   ++ ++ ++++++l+ 
  gi|557694753|ref|YP_008797807.1| 116 pveALALVGVDEPDKILHIR--VSDLSGGNLQKTMLAL 151
                                       77444778888888888888..5555555555555543 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 !   18.0   0.1   1.6e-06    0.0017      16      50 ..      29      63 ..      21      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++++ + +  +++Gp+G GK+Tll  +  +L p++
  gi|557694753|ref|YP_008797807.1| 29 SLKVLMGERLFIIGPNGGGKTTLLKTMVGVLRPDR 63
                                      55665555899*******************99987 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   3.6e-05     0.038      13      52 ..      28      65 ..      20      69 .. 0.82
   2 ?    0.1   0.0      0.33   3.5e+02      81     114 ..     135     168 ..     130     200 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                                      H......HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCC CS
                              PIF1 13 iieavlnekgklfFvtGsgGtgKtflwkallkklrsegki 52
                                      +  +++   g+ +F+ G  G gKt l+k+++ +lr+ + +
  gi|557694753|ref|YP_008797807.1| 28 V--SLKVLMGERLFIIGPNGGGKTTLLKTMVGVLRPDRGT 65
                                      4..455578999***********************97655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.33
                                       SSS-HHHHHHHTSCCCHHHHHC-SEEEEECGGGS CS
                              PIF1  81 ekdeestckikrgsklaellkktsliiwDEapmv 114
                                       ++++ s  ++++      l++k +l+i+DE  + 
  gi|557694753|ref|YP_008797807.1| 135 RVSDLSGGNLQKTMLALALINKPQLLILDEPTVY 168
                                       5556666677777777788888888888886553 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.2   5.7e-05      0.06      21     114 ..      38     183 ..      28     198 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-05
                            AAA_30  21 avltGpAGtGKttalkalreaweaa.g..............grviglAptgkaAkvLaeelgieastiakllkrlk. 81 
                                        ++ Gp G GKtt+lk+++ +++ + g              +               +  lg   ++ a l +r+  
  gi|557694753|ref|YP_008797807.1|  38 LFIIGPNGGGKTTLLKTMVGVLRPDrGtvklfgvpiqrfreR--------------WR--LGYVPQNAAALFERTPl 98 
                                       6799******************99944544444444444331..............22..22222222222222222 PP

                            AAA_30  82 ...................................................grarlepgtllivDEagmv.dtkqla 106
                                                                                          + a +++ +lli DE  +  d++ +a
  gi|557694753|ref|YP_008797807.1|  99 sveellrsgaqtgraldpvealalvgvdepdkilhirvsdlsggnlqktmlALALINKPQLLILDEPTVYvDQTGVA 175
                                       22222222333334444444555566666666666666777788887777755556666888888865533777777 PP

                            AAA_30 107 allkaaek 114
                                       al++ +++
  gi|557694753|ref|YP_008797807.1| 176 ALMNVVNR 183
                                       77776665 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 ?    5.2   0.0     0.015        16      48      64 ..      36      52 ..      14      64 .. 0.87
   2 ?    7.0   0.1    0.0042       4.4      98     137 ..     146     184 ..     117     206 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.015
                         IstB_IS21 48 enivllGpsGvGKshla 64
                                      e + ++Gp G GK+ l 
  gi|557694753|ref|YP_008797807.1| 36 ERLFIIGPNGGGKTTLL 52
                                      7799**********885 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0042
                         IstB_IS21  98 klaralkrllkvdllilDdlgllpldqaeaellfeviekr 137
                                       k   al+ + k++llilD+   + +dq   + l++v+++ 
  gi|557694753|ref|YP_008797807.1| 146 KTMLALALINKPQLLILDEPT-VYVDQTGVAALMNVVNRV 184
                                       44556788999********75.579999999999999754 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   6.1e-05     0.065       1      40 [.      37      78 ..      37     130 .. 0.77
   2 ?   -3.7   0.0       9.5     1e+04      45      55 ..     235     245 ..     222     247 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-05
                                      EEEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEEEE-- CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkss..gvkvgGfyteevre 40
                                      ++fi Gp G GKtTl+k ++ +l+ +   vk+ G+  ++ re
  gi|557694753|ref|YP_008797807.1| 37 RLFIIGPNGGGKTTLLKTMVGVLRPDrgTVKLFGVPIQRFRE 78
                                      589********************9772234555555555554 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.5
                                       -EEEEEET.T- CS
                          NTPase_1  45 igFkivdlasg 55 
                                        gF++ +++ g
  gi|557694753|ref|YP_008797807.1| 235 YGFHVYTIQHG 245
                                       46777776665 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 ?   12.6   0.0     9e-05     0.095      23      53 ..      38      69 ..      31      81 .. 0.79
   2 ?   -2.1   0.0       2.8   2.9e+03     106     114 ..     177     185 ..     126     217 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9e-05
                          ATPase_2 23 yfiYGpegsGKtaLlkeiienl.edkdkyviy 53
                                      +fi Gp g GKt+Llk ++  l  d +  +++
  gi|557694753|ref|YP_008797807.1| 38 LFIIGPNGGGKTTLLKTMVGVLrPDRGTVKLF 69
                                      79****************98884455555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.8
                          ATPase_2 106 ielllekik 114
                                       + ++ + ++
  gi|557694753|ref|YP_008797807.1| 177 LMNVVNRVN 185
                                       222222222 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   6.3e-05     0.067       2      26 ..      35      56 ..      34      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.3e-05
                            AAA_24  2 klkiliyGpsgiGKTtlakelgpkp 26
                                      + +++i+Gp+g GKTtl+k++   +
  gi|557694753|ref|YP_008797807.1| 35 GERLFIIGPNGGGKTTLLKTM---V 56
                                      56899***************9...3 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   6.8e-05     0.071      23      37 ..      39      53 ..      36      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.8e-05
                            AAA_23 23 lItGpNGaGKTTild 37
                                       I+GpNG GKTT+l 
  gi|557694753|ref|YP_008797807.1| 39 FIIGPNGGGKTTLLK 53
                                      599**********96 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.9   0.00038       0.4       8      26 ..      38      56 ..      36     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                            AAA_22  8 lvvtGesGtGKTtllrrll 26
                                      l+++G+ G GKTtll++++
  gi|557694753|ref|YP_008797807.1| 38 LFIIGPNGGGKTTLLKTMV 56
                                      689*************987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8   0.00016      0.17       3      26 ..      38      61 ..      36     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                                      EEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawae 26
                                      +++ G++G GKTtLl+ ++  ++ 
  gi|557694753|ref|YP_008797807.1| 38 LFIIGPNGGGKTTLLKTMVGVLRP 61
                                      799*************99876665 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   0.00014      0.15      20      85 ..      33      88 ..      22     193 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrql 85
                                       +g  e ++++G+ G GK++l+++    l+ d+g + l g   q         + +   r +++ q 
  gi|557694753|ref|YP_008797807.1| 33 LMG--ERLFIIGPNGGGKTTLLKTMVGVLRPDRGTVkLFGVPIQR--------FRERW-RLGYVPQN 88
                                      555..6799*************99998888886666666665555........33333.22333333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.4   0.00042      0.44      10      36 ..      35      61 ..      28     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00042
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallve 36
                                       + l+++++ G GKT++lk++v +l  
  gi|557694753|ref|YP_008797807.1| 35 GERLFIIGPNGGGKTTLLKTMVGVLRP 61
                                      56789****************998864 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9    0.0022       2.4      30      97 ..      32     114 ..       5     198 .. 0.55
   2 ?   -1.7   0.2       1.7   1.8e+03     173     188 ..     229     244 ..     223     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0022
                            AAA_25  30 lpagelallaGapgtGKttlaldlalava...tGkpwlg............pvapeqgkVlyvsaEdsedelrrRlr 91 
                                       + +ge   ++G+ g GKttl+  ++  +       +++g             ++p++++ l+  +  s +el r  +
  gi|557694753|ref|YP_008797807.1|  32 VLMGERLFIIGPNGGGKTTLLKTMVGVLRpdrGTVKLFGvpiqrfrerwrlGYVPQNAAALFERTPLSVEELLRSGA 108
                                       44799999***********9755543333554223344455554555444444445555555555555555555555 PP

                            AAA_25  92 avgeal 97 
                                       ++g+al
  gi|557694753|ref|YP_008797807.1| 109 QTGRAL 114
                                       555555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.7
                            AAA_25 173 eriarrtgaavllvhH 188
                                       e+++r +g +v  + H
  gi|557694753|ref|YP_008797807.1| 229 EELCRIYGFHVYTIQH 244
                                       799***********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 1815.19
//
Query:       gi|557694754|ref|YP_008797808.1|  [L=306]
Description: hypothetical protein CSUB_C1327 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   0.0    3.2e-58  197.2   0.0    1.0  1  ZnuA      Zinc-uptake complex component A periplasmic


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.2   0.0   1.8e-62   3.2e-58       1     256 []      39     303 ..      39     303 .. 0.91

  Alignments for each domain:
  == domain 1  score: 197.2 bits;  conditional E-value: 1.8e-62
                                       EEESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA   1 VvattsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrvev 77 
                                       V +t   lg++v ++    vev+ ++ppga++H++eptp  v+k+ ++ +l+++  +++ w +kl++s+    rv+ 
  gi|557694754|ref|YP_008797808.1|  39 VAVTWGLLGEVVHRLTDGTVEVHQILPPGAEIHDWEPTPDVVEKVRSSRMLFWTVEGFDDWGEKLASSA----RVKA 111
                                       789999***********************************************************6444....4556 PP

                                       EETTTTC......CSEBCSS.......ESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxx......xxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  78 idlsegv......eeeeeee.......DpHiWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldae 141
                                        ++s+gv      +e++  +       DpH+Wl+p++ +++v+n+a+ L++  p++ +t+++n +ayi+++ +l+++
  gi|557694754|ref|YP_008797808.1| 112 FKVSTGVelmpyeDEHN--HdhvhgayDPHFWLDPSRFATIVQNMAQILSQEFPQKRETIQRNSEAYIQEILQLNQQ 186
                                       66666665556542333..235789**************************************************** PP

                                       HHHHHTTSSGTEGEEEESSSTTHHHHHHTT-EEEEEESSSSS..HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 142 ireelaeipeekrklvtthdafgylarayglevagiagiste..aaqiaalieeikeagvkaifveplaspklaetl 216
                                       ++e+l+  +++ ++++t+h+af+yla+a+glev+++ g ++e  aa++a++ e i++++++++f+e    + ++etl
  gi|557694754|ref|YP_008797808.1| 187 YKETLS--KHQGKIFITQHNAFRYLAQAFGLEVVAVLGGEEEpsAAHLAEIYELIEKEKIRVVFAEDGNISPILETL 261
                                       ******..888999***********************999889************************9999****** PP

                                       HHHHT-EEEEE-STSSSTSTT.S.TTSHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxx RF
                              ZnuA 217 aeeagvkvatlysldslgdeg.s.aetYidmmranleslkea 256
                                       a++ gv++ tly+++ l  ++   ++ Yi  mr+nl +l++a
  gi|557694754|ref|YP_008797808.1| 262 AHDLGVEIKTLYTMEPLLSDDyRrGQGYIVRMRQNLAALVDA 303
                                       ****************8666656799************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1199  (0.0668749); expected 358.6 (0.02)
Passed bias filter:                      882  (0.049194); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2154.19
//
Query:       gi|557694755|ref|YP_008797809.1|  [L=142]
Description: metal dependent repressor, DtxR family [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   0.2    3.3e-20   72.0   0.2    1.4  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    1.1e-07   31.9   0.1    1.9e-07   31.2   0.1    1.3  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      5e-05   23.1   0.0    8.6e-05   22.3   0.0    1.3  1  MarR_2          MarR family
     0.0034   17.0   0.0     0.0058   16.3   0.0    1.3  1  GntR            Bacterial regulatory proteins, gntR family
     0.0086   16.0   0.1      0.019   14.9   0.0    1.7  2  MarR            MarR family
  ------ inclusion threshold ------
      0.013   15.3   0.0      0.026   14.3   0.0    1.5  1  LexA_DNA_bind   LexA DNA binding domain
      0.042   13.8   0.0      0.084   12.9   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.049   12.4   0.0      0.051   12.3   0.0    1.1  1  Lipoprotein_8   Hypothetical lipoprotein (MG045 family)
      0.095   12.4   0.0       0.12   12.1   0.0    1.1  1  DUF4423         Domain of unknown function (DUF4423)
       0.12   12.8   0.0       0.18   12.2   0.0    1.4  1  Rrf2            Transcriptional regulator


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 !   72.0   0.2   1.8e-23   3.3e-20       1      67 [.      67     133 ..      67     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 1.8e-23
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdp 67 
                                       T++G+ +A+r++++hr+le+f+++ lg++ ++a+ eA+r+++a+ +e++ rl++ l++p++c hg++
  gi|557694755|ref|YP_008797809.1|  67 TPRGHAVALRVIHNHRILETFFHKELGLETDKACIEASRIDYAIGDEVVIRLCQRLNNPSTCIHGKE 133
                                       99***************************************************************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 !   31.2   0.1   1.1e-10   1.9e-07       8      52 ..      12      56 ..       6      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.1e-10
                                      HHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress  8 dYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                       YL  +Y++ e++  ++t +la++ +v+p+s+   l++L+++ +v
  gi|557694755|ref|YP_008797809.1| 12 SYLLELYRAHENQHTPTTGELAKAFAVKPASAVDVLNRLSEKKLV 56
                                      69***************************************9888 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   4.8e-08   8.6e-05       7      53 ..      10      58 ..       6      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4.8e-08
                                      HHHHHHHHHCTTTS..EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  7 qarvLaaLgrrpgr..dltvgelarrlglsksavsrilkrLvaaGLver 53
                                      +   L++L+r+ ++    t gela+++ ++++++  +l+rL+++ Lv++
  gi|557694755|ref|YP_008797809.1| 10 ESSYLLELYRAHENqhTPTTGELAKAFAVKPASAVDVLNRLSEKKLVTK 58
                                      667899999999998755*****************************86 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.2e-06    0.0058      25      55 ..      27      57 ..      17      60 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.2e-06
                                      --HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 25 PsereLaaefgVsrttvReALrrLeaeglve 55
                                      P+  eLa++f+V+  +   +L+rL++++lv+
  gi|557694755|ref|YP_008797809.1| 27 PTTGELAKAFAVKPASAVDVLNRLSEKKLVT 57
                                      9999*************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05     0.019      14      49 ..      23      58 ..       6      59 .. 0.77
   2 ?   -2.7   0.0       3.4   6.1e+03       6      15 ..      72      81 ..      69      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                                      HSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 14 eqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      +q  ++  eLak++ v+++++  vl rL +k l+++
  gi|557694755|ref|YP_008797809.1| 23 NQHTPTTGELAKAFAVKPASAVDVLNRLSEKKLVTK 58
                                      23334555**********************999986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.4
                                      HHHHHHHHHS CS
                              MarR  6 fviLrilyeq 15
                                       v+Lr ++++
  gi|557694755|ref|YP_008797809.1| 72 AVALRVIHNH 81
                                      5789999998 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 ?   14.3   0.0   1.5e-05     0.026      20      56 ..      21      56 ..      13      60 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.5e-05
                                      HHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSE CS
                     LexA_DNA_bind 20 eetgypPsireiaralglkSpsaveehLkaLerKGyi 56
                                      +e+++ P+  e+a+a+ +k p+++   L++L+ K ++
  gi|557694755|ref|YP_008797809.1| 21 HENQHTPTTGELAKAFAVK-PASAVDVLNRLSEKKLV 56
                                      589****************.8899999****999665 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 ?   12.9   0.0   4.7e-05     0.084       5      54 ..      12      60 ..      11      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.7e-05
                                      HHHHHHHCTTTCEEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.ET CS
                         HTH_Crp_2  5 rfLlrlaeraggeielpltqeelAsmlGltretvsrilseLkreglis.rg 54
                                      ++Ll+l++  ++  +   t  elA    + + +   +l++L++++l++  g
  gi|557694755|ref|YP_008797809.1| 12 SYLLELYRAHEN--QHTPTTGELAKAFAVKPASAVDVLNRLSEKKLVTkIG 60
                                      799999776443..56789***************************99435 PP

>> Lipoprotein_8  Hypothetical lipoprotein (MG045 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.9e-05     0.051      55     122 ..      20      90 ..       2     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                     Lipoprotein_8  55 tydnneklislikakisdvavasayev.aelakngllkkidWakfnlkkennqsik..vnsiedlkklftk 122
                                        ++n    +++  ak + v+ asa +v  +l ++ l++ki W kf l           +++   l  +f k
  gi|557694755|ref|YP_008797809.1|  20 AHENQHTPTTGELAKAFAVKPASAVDVlNRLSEKKLVTKIGWGKFSLTPRGHAVALrvIHNHRILETFFHK 90 
                                       45555555667779999********99468****************9865544332235565555555555 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.6e-05      0.12      26      80 ..      14      68 ..       5      80 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.6e-05
                           DUF4423 26 irellplkdf..kadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqte 80
                                      ++el +++++  ++++ elak++   ++ + + + l++L + +l++k + gk+  t 
  gi|557694755|ref|YP_008797809.1| 14 LLELYRAHENqhTPTTGELAKAFA--VKPASAVDVLNRLSEKKLVTKIGWGKFSLTP 68
                                      67787777774467789*******..*********************9999988775 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   9.9e-05      0.18      14      57 ..      14      58 ..       8      80 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.9e-05
                                      HHHHHH.SSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 14 llyLak.eeeeepvsseeiaerqnispsylekilakLrkaglvks 57
                                      ll+L + +e++++ ++ e+a+ + ++p  +  +l++L++++lv+ 
  gi|557694755|ref|YP_008797809.1| 14 LLELYRaHENQHTPTTGELAKAFAVKPASAVDVLNRLSEKKLVTK 58
                                      5666541555556999**************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1105.74
//
Query:       gi|557694756|ref|YP_008797810.1|  [L=147]
Description: ADP-ribose pyrophosphatase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   56.4   0.1    3.4e-15   56.3   0.1    1.1  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 !   56.3   0.1   1.9e-19   3.4e-15       3     117 ..      11     123 ..       9     137 .. 0.73

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 1.9e-19
                                       EEEEEEE.EEETTSEEEEEEESSSSTTT...EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   3 rravgvv.llnekgevLlvrrskkpfpg...WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapyd 75 
                                       + av+vv llne  e++lv+++ +   g    e+P+G++e +E+pee+A+REleEEtG++a  l+ +g      +y 
  gi|557694756|ref|YP_008797810.1|  11 PGAVAVVpLLNES-ELVLVEQF-RAAVGevlVEVPAGTLE-NESPEECAARELEEETGYSAGSLKKIG-----EFYL 79 
                                       5689999899999.6*******.5555556558*******.********************8888888.....2333 PP

                                       EEEEEEEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHH..HH CS
                             NUDIX  76 gpygdeheilyvfl.eevegelepndenevsevrwvpleel..lk 117
                                       +p    +e+++v+l +++  +   n ++e  +v  + lee+  + 
  gi|557694756|ref|YP_008797810.1|  80 APGY-STELMHVYLaKNLRKTEGRNMPDEKISVITCGLEEAfeMV 123
                                       3333.8899999996444444444467777777689999885444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1078.38
//
Query:       gi|557694757|ref|YP_008797811.1|  [L=319]
Description: thiamine monophosphate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   69.3   0.0    6.5e-19   68.4   0.0    1.5  1  AIRS      AIR synthase related protein, N-terminal domain
      2e-07   31.3   0.0      3e-07   30.7   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 !   68.4   0.0   7.2e-23   6.5e-19       1      92 [.      32     139 ..      32     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 7.2e-23
                                       SSSE.......EEEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHH CS
                              AIRS   1 dDaa.......vvvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......wle 56 
                                       dDaa       +v+++d     +lv +++         +G+kav++++sDlaa GArP ++llslal+      ++ 
  gi|557694757|ref|YP_008797811.1|  32 DDAAafwftgqLVASVD-----TLVWETDVpprmtfrqVGWKAVTAAVSDLAAKGARPKYILLSLALKpstefsEFL 103
                                       79997777666688999.....4443333344445799*********************************999999 PP

                                       HHHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEE CS
                              AIRS  57 evvrglaeaaeelgvplvgGdtsfsneptisvtavG 92 
                                       ++v+g +ea +++g+++vgGd+++s++ +isvta+G
  gi|557694757|ref|YP_008797811.1| 104 DLVNGAQEASKKYGAAIVGGDINESSSHSISVTALG 139
                                       9************************99********9 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 !   30.7   0.0   3.3e-11     3e-07      41     153 ..     186     302 ..     151     305 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 3.3e-11
                                       HHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHH........HHHHHHHC CS
                            AIRS_C  41 vlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdele........splemlls 109
                                       v+    ++++  ala   g+v+a+ D ++ GL+++l+++ +a++vg+ +d+   p+ + ++        +p e+ + 
  gi|557694757|ref|YP_008797811.1| 186 VYSPVARVDEGVALATC-GGVSACIDSSD-GLAESLHQLSEANDVGFIVDSL--PLDSSAQrycvdnnlDPVEAVFY 258
                                       44445678888899998.***********.8*********************..77777777889978855555554 PP

                                       .STTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEEE CS
                            AIRS_C 110 .ensGrllvavppeeadavlaileeeglpeaavIGevtakeelsv 153
                                         ++  l+++v+p   d v ++l++ g  e+ +IG v  ++++++
  gi|557694757|ref|YP_008797811.1| 259 gGEEYELVFTVKPGWGDVVEKALARLGK-EVVWIGSVNQGRGVYF 302
                                       4777888888888888***********8.8********9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2381.97
//
Query:       gi|557694758|ref|YP_008797812.1|  [L=240]
Description: dolichol-phosphate mannosyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   96.1   0.0    3.4e-27   95.3   0.0    1.4  2  Glycos_transf_2  Glycosyl transferase family 2
    1.3e-09   38.3   0.0      3e-09   37.1   0.0    1.6  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00029   20.4   0.0    0.00039   20.0   0.0    1.2  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0054   17.2   0.0      0.029   14.9   0.0    2.0  2  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 !   95.3   0.0   7.5e-31   3.4e-27       1     168 [.       8     173 ..       8     175 .. 0.97
   2 ?   -3.0   0.0       1.3   5.7e+03      15      31 ..     188     203 ..     187     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 7.5e-31
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       +vviptyNe+ ++ + l  + +  p p++  +vvDDgS+D+t+++++++++ +pr+++  r  ++G+++a+ +g++ 
  gi|557694758|ref|YP_008797812.1|   8 CVVIPTYNEAMNIGKILQQIMQL-PFPRLWAVVVDDGSPDGTADVVKKISETNPRIILHNRGAKKGLGSAYYEGFKI 83 
                                       79********************9.***************************************************** PP

                                       --SS...EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCS CS
                   Glycos_transf_2  78 atgd...yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnl 151
                                       a +    +il +DaD  ++ + +++lv+a e+ gad+++++r+ ++g++     +      +r+ +   +  ++ +l
  gi|557694758|ref|YP_008797812.1|  84 ALTLnprVILSMDADGSHPVELVPELVKAVED-GADAAVASRYIRGGKWSSDFSRML---VSRGANLLARLATGAKL 156
                                       *999999*************************.*********************997...7**************** PP

                                       TTCSTCCCEEEEHHHHH CS
                   Glycos_transf_2 152 sfeigsaallrrealee 168
                                        ++++++++++++a+++
  gi|557694758|ref|YP_008797812.1| 157 RDMTSGYRAYSQRAVQH 173
                                       ***********999876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
                                       HHHHHHHHHGGCCEEEE CS
                   Glycos_transf_2  15 etlesllaqdpypdfei 31 
                                       e+l++ll+q  y+ +ei
  gi|557694758|ref|YP_008797812.1| 188 ELLHRLLSQ-GYKVVEI 203
                                       789999999.8888887 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 !   37.1   0.0   6.8e-13     3e-09       3      98 ..       6      99 ..       4     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 6.8e-13
                   Glyco_tranf_2_3  3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81
                                      d+ v++pt+ne+  +g++l ++   + pr+  vvv+d+s ++t++v++ + ++ p++   +++n  ++ ++g   a++e
  gi|557694758|ref|YP_008797812.1|  6 DICVVIPTYNEAMNIGKILQQIMQLPFPRLWAVVVDDGSPDGTADVVKKISETNPRI---ILHN--RGAKKGLGSAYYE 79
                                      588***********************************************9999998...6655..4678899999*** PP

                   Glyco_tranf_2_3 82 alravk...sdlvllvDdDt 98
                                      +++++    ++++l +D+D 
  gi|557694758|ref|YP_008797812.1| 80 GFKIALtlnPRVILSMDADG 99
                                      ***7444559********95 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 !   20.0   0.0   8.8e-08   0.00039       2      91 ..       9      98 ..       8     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 8.8e-08
                   Glyco_tranf_2_2  2 vviplraseerhyieervlqkakyy.deeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGask 79
                                      vvip +++  +  i  ++lq+  +   + +  +vvddgS++ ++++v++i + n ++ l++      +l+ a   G++ 
  gi|557694758|ref|YP_008797812.1|  9 VVIPTYNEAMN--I-GKILQQIMQLpFPRLWAVVVDDGSPDGTADVVKKISETNPRIILHNR-GAKKGLGSAYYEGFKI 83
                                      89****99999..5.56666666654788888*************************98888.4556888888889888 PP

                   Glyco_tranf_2_2 80 aes...dlvlFlDaD 91
                                      a +    ++l +DaD
  gi|557694758|ref|YP_008797812.1| 84 ALTlnpRVILSMDAD 98
                                      866433577777777 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 !   14.9   0.0   6.5e-06     0.029       1      51 [.      14      69 ..      14      99 .. 0.73
   2 ?   -0.2   0.0      0.33   1.5e+03      45      76 ..     156     185 ..     132     201 .. 0.53

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.5e-06
                   Glyco_tranf_2_4  1 rneadiLpeflahhlalgfdr..ilvydndstDgtrailkelpevk...llhvdks 51
                                      +nea  +++ l+ + +l f r   +v+d++s Dgt++++k+  e +   +lh++++
  gi|557694758|ref|YP_008797812.1| 14 YNEAMNIGKILQQIMQLPFPRlwAVVVDDGSPDGTADVVKKISETNpriILHNRGA 69
                                      69*****************9955669**************9655444445555554 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.33
                   Glyco_tranf_2_4  45 llhvdksyederrqvellkallaryaeadwvl 76 
                                       l + ++ y+  ++  ++ ++l ++  e+ +v+
  gi|557694758|ref|YP_008797812.1| 156 LRDMTSGYR--AYSQRAVQHLVEKPFEKGYVF 185
                                       444444443..233333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1841.88
//
Query:       gi|557694759|ref|YP_008797813.1|  [L=224]
Description: hypothetical protein CSUB_C1332 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   39.7   0.2    2.4e-09   37.2   0.0    2.2  2  DnaJ         DnaJ domain
  ------ inclusion threshold ------
      0.036   14.2   0.2         13    6.0   0.0    2.6  2  KIP1         KIP1-like protein
      0.075   13.0   0.5       0.16   11.9   0.2    1.7  2  PaREP1       Archaeal PaREP1/PaREP8 family
       0.15   12.4   0.2       0.62   10.4   0.0    2.1  3  SO_alpha_A3  Sarcosine oxidase A3 domain


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   5.4e-13   2.4e-09       3      52 ..      41      96 ..      40     103 .. 0.80
   2 ?   -1.0   0.0      0.45     2e+03       5      21 ..     121     137 ..     120     148 .. 0.71

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 5.4e-13
                                      HHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHH......HHHHHHHHHHHHHHH CS
                              DnaJ  3 YeiLgvskdasedeIkkaYrklalkyHPDknpkdp......eaeekFkeineAyev 52
                                      +++Lgv++d   deIkk Yr l+++yHPD  p+d         ee+  ++n+Ay++
  gi|557694759|ref|YP_008797813.1| 41 FSVLGVNPDDPLDEIKKTYRSLVKRYHPDTLPQDAspqvrrLYEERLIKLNTAYKT 96
                                      78***************************664444333334567799999999986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.45
                                       HHTSSTTG-HHHHHHHH CS
                              DnaJ   5 iLgvskdasedeIkkaY 21 
                                       +L ++k+a e++ +ka 
  gi|557694759|ref|YP_008797813.1| 121 MLRLAKNAAENDARKAL 137
                                       67888888877766664 PP

>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0041        19      59      73 ..      52      66 ..      50      67 .. 0.91
   2 ?    6.0   0.0    0.0029        13      21      61 ..     112     153 ..     108     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0041
                              KIP1 59 veefyrsyrsLaery 73
                                      ++e++++yrsL +ry
  gi|557694759|ref|YP_008797813.1| 52 LDEIKKTYRSLVKRY 66
                                      6899**********9 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0029
                              KIP1  21 seldekvkemlklieedadsfakra.emyykkrpeLielvee 61 
                                       +e+   v+eml+l ++ a++ a++a e+ y   + L++ +++
  gi|557694759|ref|YP_008797813.1| 112 EEMLAPVEEMLRLAKNAAENDARKAlENAYTAAETLVKTLHN 153
                                       5777889*******9999988877647889999999988765 PP

>> PaREP1  Archaeal PaREP1/PaREP8 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   3.6e-05      0.16       5      41 ..     117     152 ..     113     167 .. 0.89
   2 ?   -2.9   0.0       1.4   6.1e+03      10      23 ..     185     198 ..     177     216 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.6e-05
                            PaREP1   5 eaekeleeAeellekGdlrqAaeKaykAvkalvkala 41 
                                         e++l++A+   e+ d+r A e ay A++ lvk l 
  gi|557694759|ref|YP_008797813.1| 117 PVEEMLRLAKNAAEN-DARKALENAYTAAETLVKTLH 152
                                       56899******9998.******************985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                            PaREP1  10 leeAeellekGdlr 23 
                                       l eA+++ + G+ r
  gi|557694759|ref|YP_008797813.1| 185 LAEARRYTSMGNGR 198
                                       45555555555444 PP

>> SO_alpha_A3  Sarcosine oxidase A3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.1   9.4e+03      30      39 ..      62      71 ..      55      76 .. 0.68
   2 ?   -2.4   0.0       1.4   6.2e+03      11      29 ..     127     145 ..     120     156 .. 0.64
   3 ?   10.4   0.0   0.00014      0.62       3      45 ..     162     202 ..     160     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.1
                       SO_alpha_A3 30 hvKRYttlgm 39
                                      +vKRY   ++
  gi|557694759|ref|YP_008797813.1| 62 LVKRYHPDTL 71
                                      5899976655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                       SO_alpha_A3  11 Dvtvkdielavregfesie 29 
                                          ++d ++a+++ +   e
  gi|557694759|ref|YP_008797813.1| 127 NAAENDARKALENAYTAAE 145
                                       4555666666666666655 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00014
                       SO_alpha_A3   3 rqFvdlqnDvtvkdielavregfesiehvKRYttlgmgtdQgk 45 
                                       +++ dl +D+ ++d+   + e fe +   +RYt++g g + + 
  gi|557694759|ref|YP_008797813.1| 162 SHYYDLLTDLMINDVI--TVEEFEVLAEARRYTSMGNGREHAT 202
                                       5688999999999985..5799***************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1801.90
//
Query:       gi|557694760|ref|YP_008797814.1|  [L=141]
Description: thioesterase superfamily protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-06   28.1   0.0    2.7e-06   27.9   0.0    1.0  1  4HBT_2       Thioesterase-like superfamily
    3.2e-06   26.6   0.0    3.8e-06   26.4   0.0    1.3  1  Acyl-ACP_TE  Acyl-ACP thioesterase
     0.0011   19.3   0.0     0.0015   18.8   0.0    1.3  1  4HBT         Thioesterase superfamily


Domain annotation for each model (and alignments):
>> 4HBT_2  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   4.5e-10   2.7e-06       1     121 [.       6     131 ..       6     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 4.5e-10
                            4HBT_2   1 vrpndvDlnghlnnarylryleearvkflertgl....ksrsiarr...giglilssahvryrrplkfpdrltvefr 70 
                                       v+++d+D  g ++ ++y+r++++a ++ l   g+    + r+++ +      l++++ h+r  +p  + d+++ve  
  gi|557694760|ref|YP_008797814.1|   6 VGFQDTDSTGRVYFPSYVRWFDIAFIERLRSRGIvfdpQGRLKTGNtllNSTLVIGEYHCRIEKPSGYDDEVEVEIA 82 
                                       7889*******************9999999555544443444443333366************************** PP

                            4HBT_2  71 vididaktliiehrflsnadgkkaarveerivvmdygkrskkapvPpellk 121
                                        ++   k+l++++ ++++  g + a +  ++v++d +++ + +p+++ llk
  gi|557694760|ref|YP_008797814.1|  83 SSEPGNKSLKVFFNLRDP-WGSLLAHGYITYVMVDLETG-RAVPLDEKLLK 131
                                       *****************6.4889***************9.99**9998876 PP

>> Acyl-ACP_TE  Acyl-ACP thioesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   6.3e-10   3.8e-06      54     132 ..      56     134 ..       1     141 [] 0.79

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 6.3e-10
                       Acyl-ACP_TE  54 lvWvvakyeieierlpefgdkveietwaesenklfcyrdfkvrdekgekiieaksvfvlmdqetrrlsrvtdeilae 130
                                          v+ +y+  ie++  + d+ve+e   +  ++   +  f++rd  g  +++  +++v++d et r++ + + +l+ 
  gi|557694760|ref|YP_008797814.1|  56 STLVIGEYHCRIEKPSGYDDEVEVEIASSEPGNKSLKVFFNLRDPWGSLLAHGYITYVMVDLETGRAVPLDEKLLKT 132
                                       45699**********************9999**************************************99999998 PP

                       Acyl-ACP_TE 131 ye 132
                                       + 
  gi|557694760|ref|YP_008797814.1| 133 IL 134
                                       83 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.6e-07    0.0015       2      72 ..      15      99 ..      14     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.6e-07
                                      SSB-HHHHHHHHHHHHHHHHHHTTST..............TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEE CS
                              4HBT  2 GvvhgGvylallDeaagaalrslggr..............gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavv 66
                                      G v+ + y++++D a  + lrs+g                ++ +v+ e +++  +p  ++de++ve   ++ g++s++v
  gi|557694760|ref|YP_008797814.1| 15 GRVYFPSYVRWFDIAFIERLRSRGIVfdpqgrlktgntllNSTLVIGEYHCRIEKPSGYDDEVEVEIASSEPGNKSLKV 93
                                      789***************************************************************************9 PP

                                      EEEEEE CS
                              4HBT 67 evevrd 72
                                         +rd
  gi|557694760|ref|YP_008797814.1| 94 FFNLRD 99
                                      988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       231  (0.0128842); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1083.55
//
Query:       gi|557694761|ref|YP_008797815.1|  [L=137]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   68.2   1.1      5e-19   68.1   0.4    1.4  2  OB_aCoA_assoc   DUF35 OB-fold domain, acyl-CoA-associated
    1.4e-15   56.8   2.3    2.4e-15   56.1   2.3    1.4  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.023   14.5   0.0      0.025   14.4   0.0    1.1  1  Sterol-sensing  Sterol-sensing domain of SREBP cleavage-activ
      0.025   15.0   0.0      0.052   13.9   0.0    1.5  1  Qn_am_d_aIII    Quinohemoprotein amine dehydrogenase, alpha s
      0.037   13.7   0.1      0.046   13.4   0.1    1.1  1  TackOD1         Thaumarchaeal output domain 1
       0.31   10.7   3.0       0.43   10.3   0.2    2.2  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit


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 !   68.1   0.4   1.7e-22     5e-19       1      64 [.      56     121 ..      56     122 .. 0.95
   2 ?   -3.5   0.0       3.7   1.1e+04       9      14 ..     129     134 ..     126     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 1.7e-22
                                       EEEE-GG-EEEEEEEEEE-T...TS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE- CS
                     OB_aCoA_assoc   1 wvelsgrGtvysftvvhrap...pgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravf 64 
                                       w+ +sg+Gt+ sftv++r     p f  + P+vv+ V+Ldegvri ar+  + p++vr+G+rV+a+f
  gi|557694761|ref|YP_008797815.1|  56 WIKSSGKGTIHSFTVIRRVVansPDFQRDIPFVVAEVDLDEGVRIYARVEAA-PEQVRVGQRVEARF 121
                                       899**********************************************965.678*********99 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.7
                                       EEEEEE CS
                     OB_aCoA_assoc   9 tvysft 14 
                                       t+ysf+
  gi|557694761|ref|YP_008797815.1| 129 TLYSFS 134
                                       899997 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 !   56.1   2.3   7.9e-19   2.4e-15       1      36 [.      19      54 ..      19      55 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 7.9e-19
                           DUF35_N  1 wdaaaegrLvgqrCpdCGtvqfPPravCphCgsddl 36
                                      w+aa+ g+L++q+C++CG+ q++Pr++C+ Cgs dl
  gi|557694761|ref|YP_008797815.1| 19 WKAAKNGELMIQQCRKCGHRQWYPRPSCTACGSLDL 54
                                      9********************************887 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 ?   14.4   0.0   8.4e-06     0.025      42      91 ..      85     134 ..      52     137 .] 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.4e-06
                                       HHHHHHHHCHHCCHHCHHHHHHHHTTTCHHHHHHHHHHHHCCCCHHCCCH CS
                    Sterol-sensing  42 lPflvlavgvdnifvlvkavqrtsrsldeseriaealgevgpsilltslt 91 
                                       +Pf+v  v++d+  ++   v++ +++ ++ +r+   + e+ p i+l+s++
  gi|557694761|ref|YP_008797815.1|  85 IPFVVAEVDLDEGVRIYARVEAAPEQVRVGQRVEARFMEATPEITLYSFS 134
                                       8********************************************99876 PP

>> Qn_am_d_aIII  Quinohemoprotein amine dehydrogenase, alpha subunit domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.7e-05     0.052      28      60 ..      89     121 ..      86     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-05
                      Qn_am_d_aIII  28 aadvdlgkgvevvkvveaspnevvlrvkvaada 60 
                                       +a+vdl +gv++   vea+p++v++  +v+a  
  gi|557694761|ref|YP_008797815.1|  89 VAEVDLDEGVRIYARVEAAPEQVRVGQRVEARF 121
                                       699**********************99998865 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.6e-05     0.046      73      99 ..      29      55 ..      11      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                           TackOD1 73 irlCpsCksghlnvrevCpkCkSidie 99
                                      i++C++C + +   r +C  C+S d+ 
  gi|557694761|ref|YP_008797815.1| 29 IQQCRKCGHRQWYPRPSCTACGSLDLG 55
                                      799********************9985 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 ?   10.3   0.2   0.00014      0.43      19      27 ..      31      39 ..      25      42 .. 0.87
   2 ?    0.1   0.2      0.22   6.5e+02      20      25 ..      46      51 ..      45      52 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00014
                                      --SSS---- CS
                    DNA_RNApol_7kD 19 RCkeCGhRi 27
                                      +C++CGhR 
  gi|557694761|ref|YP_008797815.1| 31 QCRKCGHRQ 39
                                      6*******5 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.22
                                      -SSS-- CS
                    DNA_RNApol_7kD 20 CkeCGh 25
                                      C+ CG+
  gi|557694761|ref|YP_008797815.1| 46 CTACGS 51
                                      888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1066.38
//
Query:       gi|557694762|ref|YP_008797816.1|  [L=393]
Description: thiolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.4   0.0       0.47   10.1   0.0    2.3  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 ?    1.5   0.0     0.012   2.1e+02      25      42 ..      33      50 ..      14      56 .. 0.78
   2 ?   10.1   0.0   2.6e-05      0.47      21      98 ..     259     351 ..     245     372 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.012
                                      HHHHHHHHHHHT--GGGE CS
                        Thiolase_C 25 ayaikkvlkkagltvedi 42
                                      a a ++vl+++gl+++d+
  gi|557694762|ref|YP_008797816.1| 33 AWALSMVLQQTGLSLNDL 50
                                      457899**********98 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 2.6e-05
                                       GGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH- CS
                        Thiolase_C  21 glgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialG 79 
                                       ++g  +a+k++l+  g + +di lf + + ++ ++++ +++ ++ +                    +N  GG ++ G
  gi|557694762|ref|YP_008797816.1| 259 TTGVKNAVKQALEMSGTKQRDIGLFNAYDDYTPVVIMQLEDAGFCEkgkagkfleetditykghLPLNTGGGLLSYG 335
                                       567789**********************************9999888888888888888888776788888888888 PP

                                       B-TTTHHHHHHHHHHHHHH CS
                        Thiolase_C  80 HPlGasGaRivvtllselk 98 
                                          G++G   + +l+++++
  gi|557694762|ref|YP_008797816.1| 336 QA-GMAGG--MHHLVEAVR 351
                                       65.54443..334444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 3134.67
//
Query:       gi|557694763|ref|YP_008797817.1|  [L=797]
Description: carbon-monoxide dehydrogenase large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-165  551.3   1.3   2.5e-165  551.1   1.3    1.0  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    1.1e-30  106.2   0.0    2.8e-29  101.7   0.0    2.9  2  Ald_Xan_dh_C   Aldehyde oxidase and xanthine dehydrogenase, a
  ------ inclusion threshold ------
      0.058   13.3   0.6       0.19   11.7   0.6    1.9  1  RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain


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 !  551.1   1.3  4.3e-169  2.5e-165       1     550 []     154     732 ..     154     732 .. 0.97

  Alignments for each domain:
  == domain 1  score: 551.1 bits;  conditional E-value: 4.3e-169
                                       STTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHH CS
                     Ald_Xan_dh_C2   1 vheeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlv 75 
                                       +heea++n++a  ++++Gd+++a a+ad++++ ++ ++r + ++lE++a+la + de++ +t+y+++q+p+++   +
  gi|557694763|ref|YP_008797817.1| 154 IHEEAGTNIAAmvDYNYGDYDSAAAQADRIIRTSLVFHRFSSTPLEPNAVLASY-DEKDGYTIYCNNQMPMFLSPSI 229
                                       699999**99999999**************************************.89999***************** PP

                                       HHHHT--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS CS
                     Ald_Xan_dh_C2  76 aevlglpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdG 152
                                        ++l+ +  +vr+i++++GGGFG+K+  +++ vl+a+++k +grpVk++++R+e+m+a++++ + ++++++++++dG
  gi|557694763|ref|YP_008797817.1| 230 LRALDTDITHVRIITQDIGGGFGVKITNYTYMVLVAALSKLVGRPVKWIETRSEHMMASSHGADRHFNVEAAVKNDG 306
                                       ***************************************************************************** PP

                                       -EEEEEEEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 153 kitaldvdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelA 229
                                       ++++l v +++d Gaya ++pa l+  ++ + g+ k++++r ++++v+tN++p+++ RGf +  + f++Er++d++A
  gi|557694763|ref|YP_008797817.1| 307 TLLGLNVVTVDDIGAYARHEPAGLTVWAQVASGCCKFKHLRQRMYAVFTNKCPAGPNRGFSRAPHQFMIERVLDKIA 383
                                       ***************************************************************************** PP

                                       HHHT--HHHHHHHHBCECGCC.SEEET...EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEE CS
                     Ald_Xan_dh_C2 230 eelgldplelRrrNlikpgeltpygqp...vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvveg 303
                                       +elg dp+e+Rr+N+++ + ++py++    vyd gd+  +l+k++e++dy ++r++q++ + +++ +G+g+ +++ +
  gi|557694763|ref|YP_008797817.1| 384 RELGKDPVEVRRINYVTRD-MQPYRTLngcVYDGGDYIGALEKAAEMVDYWGWRRRQKQLRTEGRYIGVGVGVTIDS 459
                                       ****************876.55**9977899******************************76688*********** PP

                                       BS--S..EETTEE........EEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-S.BTTSS CS
                     Ald_Xan_dh_C2 304 iglgf.takflnq........egalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvveg.dtdkv 370
                                        +++f + ++ln+        e+a+v++++dG+++v++g+ ++Gq +et   qi+a++Lg+++ed++v +g d+ + 
  gi|557694763|ref|YP_008797817.1| 460 GAANFgQVRMLNPslpnvgtsEAATVQMTPDGKILVKLGTIPQGQSHETIASQIVADVLGIDYEDITVATGfDSGSH 536
                                       *9999744556668889999899****************************************************** PP

                                       S-..---S-TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH.. CS
                     Ald_Xan_dh_C2 371 pn..gsgtaaSrstdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl.. 440
                                       p+  +sgt+aSr + +++ A++ Aa++l++ +++iaa++le+++ed+ ++ g ++v+   e++vs++++a++ay   
  gi|557694763|ref|YP_008797817.1| 537 PYtlHSGTYASRFAGTGMVAIYMAAQRLKDMVAAIAAKILEARKEDIVVQGGVAYVRdapERKVSFKRIARTAYAnp 613
                                       **55569****************************************************99**************** PP

                                       ......TTSSEEEEEEE......EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHH CS
                     Ald_Xan_dh_C2 441 ......ervslsatgfykt...ldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQ 508
                                             ++++l+a++ +++    ++e++ g+ + +++y a++++VevD+etg+vk+l++ iv+D+G++iNpaiv+gQ
  gi|557694763|ref|YP_008797817.1| 614 felpegMEPGLTAHAVFSPpfqPPDENKVGNLTLTYSYQAHAVVVEVDPETGRVKILDYAIVDDCGRVINPAIVDGQ 690
                                       *****************99*998899999************************************************ PP

                                       HHHHHHHHHHHHHT---EEETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 509 ieGGfvqGiGlalmEelvydedGqlltasladYkiPtaadiP 550
                                       ++G++ +GiG++l+E++ y+edG llt++++dY+ Pta +iP
  gi|557694763|ref|YP_008797817.1| 691 VHGAAYHGIGAVLYENFEYNEDGVLLTSNFSDYLAPTAVEIP 732
                                       ****************************************99 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 !  101.7   0.0   4.6e-33   2.8e-29       2     109 ..      26     137 ..      25     138 .. 0.92
   2 ?    0.8   0.0      0.11   6.3e+02      18      36 ..     645     663 ..     637     673 .. 0.84

  Alignments for each domain:
  == domain 1  score: 101.7 bits;  conditional E-value: 4.6e-33
                                       T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT..TSSS-EE..EESS-S CS
                      Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig..siledee..dallae 74 
                                       G++++vdD+ +p ++y+ f+rS+++hA i+s+dvs a +++GV+ v+t++d+++  k     +++  ++  d+ +a 
  gi|557694763|ref|YP_008797817.1|  26 GRGRFVDDVVLPRMAYVSFLRSPYPHALIKSLDVSRAAKAEGVLGVFTGADIASVTKPFPqlTVPPASKvvDYSMAV 102
                                       99****************************************************9998876533333335699**** PP

                                       SEESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                      Ald_Xan_dh_C  75 dkvrsvgqavaavvAedeetArkAaklvkveYeel 109
                                       +kvr+vg++vaavvAe++++Ar+A++l++veYe+l
  gi|557694763|ref|YP_008797817.1| 103 KKVRFVGEPVAAVVAENAYQARDAVELIDVEYEPL 137
                                       *********************************98 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                                       EEEEE-SSSSEEEEEEE-H CS
                      Ald_Xan_dh_C  18 lafvrStkahAkivsidvs 36 
                                       l++ +S +ahA +v++d +
  gi|557694763|ref|YP_008797817.1| 645 LTLTYSYQAHAVVVEVDPE 663
                                       67899***********976 PP

>> RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   3.1e-05      0.19       4      29 ..     654     679 ..     652     686 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                     RNase_II_C_S1   4 dAvVvdvddrggtVqladPaVeArve 29 
                                        AvVv+vd++ g+V + d+a++  ++
  gi|557694763|ref|YP_008797817.1| 654 HAVVVEVDPETGRVKILDYAIVDDCG 679
                                       59*******************99983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (797 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.42
# Mc/sec: 5753.14
//
Query:       gi|557694764|ref|YP_008797818.1|  [L=389]
Description: acyl-CoA dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-38  131.6   0.0    3.5e-38  131.1   0.0    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    8.8e-21   73.9   0.0    1.4e-20   73.3   0.0    1.3  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    4.5e-20   72.4   0.3    4.5e-20   72.4   0.3    1.7  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.6e-19   70.5   0.9    2.5e-19   69.9   0.9    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 !  131.1   0.0   7.9e-42   3.5e-38       1     149 [.     234     382 ..     234     383 .. 0.97

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 7.9e-42
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       +kG+++ +  ln eR+++a  ++g+a+  l+++++ya +r+ fg+p++++q++++ lae++aele+arl++ +aa++
  gi|557694764|ref|YP_008797818.1| 234 DKGWEALTPLLNAERVCTASISIGVAEYLLNRSVDYASNRRVFGRPIGSNQAIQFPLAEVKAELEVARLMTQKAAWL 310
                                       58*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       +d+gk+   ea++a + a+++a ++ad+a+q +Gg+G++e++ +er++rdar++  +  ++e+ +n i+ r+
  gi|557694764|ref|YP_008797818.1| 311 FDNGKECAFEANVAAFTAARVAFKAADRAVQTFGGNGFAEDNDIERFFRDARLFKTAPVPEEMVLNYIGTRI 382
                                       *****************************************************9999888888888888776 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 !   73.3   0.0   3.1e-24   1.4e-20       1      96 [.     124     221 ..     124     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 3.1e-24
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE...TS---...----EEEEEEE..GG CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar...tekpd...rarglslflvprdap 71 
                                       +f+ TEp+aG ++ +++t+a  r+g++y+lnG+Kiwit a+ a++++++ar   +e  +   +++gl+lflv++++p
  gi|557694764|ref|YP_008797818.1| 124 SFGHTEPNAGVNTFDIQTSA-VREGDGYRLNGQKIWITLAHLADIIVTVARttpKE--KarkKSEGLTLFLVDAKQP 197
                                       699***************55.555556************************85433..35589************** PP

                                       GEEE-----BSS-TTS-EEEEEEE. CS
                     Acyl-CoA_dh_M  72 gvsvrrieeklGlrglptgelvfed 96 
                                       gv+ ++i+  ++lr l +  ++fed
  gi|557694764|ref|YP_008797818.1| 198 GVKTSKIP-GMALRPLTSNVVYFED 221
                                       *******5.7******999999998 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 !   72.4   0.3     1e-23   4.5e-20       2     113 .]       7     120 ..       6     120 .. 0.90
   2 ?   -2.7   0.0       2.1   9.4e+03       6      25 ..     318     337 ..     315     348 .. 0.75

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 1e-23
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-..HHHHHHHHHHHHHH-H CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagld..yleaaivaeelarada 76 
                                       ee   +r++v+ef+++   ++ +++d e++fp+e wk++ae+G+lgi++ e+ygG+gl+  ++++ai+    a +++
  gi|557694764|ref|YP_008797818.1|   7 EEVLFIRRSVAEFMKRFPLEYWRKADVERRFPEEYWKAVAEQGFLGICIGEQYGGLGLGlqAVSEAIIGVAAAGGGL 83 
                                       666779**********9999******9999*************************9854449********9999999 PP

                                       HHHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  77 glalllgvhsslvapailrfGteeqkrryLpklasge 113
                                       + + ll+  +  ++ +i r G ee +++yLp+l++ge
  gi|557694764|ref|YP_008797818.1|  84 PAGDLLMRTNVFAGMTIERLGREEVRQQYLPRLVRGE 120
                                       977777666667779*********************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.1
                                       HHHHHHHHHHHHHTHHHHHH CS
                     Acyl-CoA_dh_N   6 alrdtvrefaeeelaphaae 25 
                                       a+ + v++f + ++a +aa+
  gi|557694764|ref|YP_008797818.1| 318 AFEANVAAFTAARVAFKAAD 337
                                       67888999999988766655 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 !   69.9   0.9   5.6e-23   2.5e-19       2     125 ..     250     363 ..     249     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 5.6e-23
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       + a + +G+A+  l+  v++a +r    +g+++  ++a+q+ lae++a+l+ Ar+++++aa+      ++gke+   
  gi|557694764|ref|YP_008797818.1| 250 CTASISIGVAEYLLNRSVDYASNRRV--FGRPIGSNQAIQFPLAEVKAELEVARLMTQKAAWL----FDNGKEC--- 317
                                       678999*****************999..***********************************....*******... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHH CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDaha 125
                                          ea +aa +a++ a +a+d++++++Gg++ ++++ ++R++RDa+ 
  gi|557694764|ref|YP_008797818.1| 318 -AFEANVAAFTAARVAFKAADRAVQTFGGNGFAEDNDIERFFRDARL 363
                                       .899*****************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2874.20
//
Query:       gi|557694765|ref|YP_008797819.1|  [L=466]
Description: tryptophan synthase beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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  124.5   0.0    6.5e-36  124.2   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 !  124.2   0.0   3.6e-40   6.5e-36       5     294 .]      76     415 ..      72     415 .. 0.82

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 3.6e-40
                                       SSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHH.HHTTTTTSEEEEEBSSHHHHHHHHHHHHHT CS
                              PALP   5 igpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllar.lkegtgaktvveassGNhgralAaaaallG 78 
                                        +pTPl r+ +l+k l++p  +++K E+  p gS+K ++a+   ++  keg   +  +e+++G++g al++a +++G
  gi|557694765|ref|YP_008797819.1|  76 WRPTPLYRAYNLEKMLKTParIYYKHEGVSPPGSHKPNTAVAQAYYnMKEG-VERLTTETGAGQWGSALSFATRMFG 151
                                       69***************************************9888878888.8999999999*************** PP

                                       -EEEEEEETTS-...HHHHHHHHHTT-EEEEECCH............HHHHHHHHHHHHHH........STTCEE-- CS
                              PALP  79 lkvtivvpadas...pekvallrllGaevvevggd............ydeavaaaaelaae........gegaylvs 132
                                       lk+t+++ + +    p+++ l+ ++Gaev  +++d            +++  ++  ++ +         ++++ l s
  gi|557694765|ref|YP_008797819.1| 152 LKCTVYMVRASYqqkPARKMLMHSWGAEVYPSPSDktnfgrsllakdPNHPGSLGIAISEAledcvtheNTKYSLGS 228
                                       ******8777665668****************444444444444444444444422222222124432123333333 PP

                                       TTTSHHHHHHHHTHHHHHHHHTT...TTEEEEEEE-SSSHHHHHHHHHHHH.....HSTT.-EEEEEEECTTCGGTT CS
                              PALP 133 qfdnptviegygtiglEileqlg...gkpdavvvpvGgGgliaGiaaglke.....rrpd.vrvigvepegsdalar 200
                                            +v   ++  glE +eql+   + pd v  +vGgG+ ++G+  ++ +     + p+ v++++ ep+ ++++++
  gi|557694765|ref|YP_008797819.1| 229 V--LNHVLMHQTVQGLEAIEQLKqvdDYPDIVAGCVGGGSSFSGLTWPFYYeviskKAPKqVQFVATEPTACPTMTK 303
                                       3..3445555888888888777777799999********************9998877779**************** PP

                                       CC...S..S.SS..B.................SSS.CCSTCS.CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHH CS
                              PALP 201 sl...ragrrvtvpvs................dtiadglavg.spselafelldrlvdeivtvsdeealeamrllar 257
                                       ++   + g+  +   +                +  a gl+ +  + +l++ l+++ ++  ++ ++  +++a++++ar
  gi|557694765|ref|YP_008797819.1| 304 GIytyDFGDTAK---MtpllpmytlgsdfvppPIHAGGLRYHgDAPTLCLLLHEGWIK-PYAYDQVSVFDAAVTFAR 376
                                       **5553333333...2555888********************9999999999999999.9***************** PP

                                       HHSB-B-H.HHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 258 regivvep.ssaaalaal.klreagelkegdrvvviltg 294
                                       +eg +++p  s++   ++ +++++++ +e++++++ l+g
  gi|557694765|ref|YP_008797819.1| 377 AEGFLPGPePSHTIRYVIdEALRCKQTGEEKVILFNLCG 415
                                       ********8888888888*******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 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:                        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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3257.81
//
Query:       gi|557694766|ref|YP_008797820.1|  [L=229]
Description: ERCC4 domain-containing protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-10   41.5   0.0    2.3e-10   40.9   0.0    1.3  1  ERCC4     ERCC4 domain


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 !   40.9   0.0   1.3e-14   2.3e-10       1     150 [.       9     127 ..       9     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.3e-14
                                       EEGGGCTSHHHH..HHTTT..SEEEEE--SSSSE.EE...CTT...............EEEEEEEHHHHHHHHCCSH CS
                             ERCC4   1 iDsrelksgieeylleelg..vevvietlpigdyilwrrkvkaeynleldieepceekvlverksaddlvasikdgr 75 
                                       +Ds+e   +   +l e+l   ve+++++l+ gdy+++    ++e++             lverk++ d+ +s+k  r
  gi|557694766|ref|YP_008797820.1|   9 VDSNE--ASENSRLVESLAkvVETAVKPLQAGDYLII----GREKH------------ALVERKTVMDFLNSLKG-R 66 
                                       57777..222222356666646************555....44333............8**************66.* PP

                                       HHHHHHHHHH.H-SEEEEEEES.-GGGTT................THHH.HHHHHHHHHHHHS-EEEEESSHHHHH CS
                             ERCC4  76 leeqvsrlkrngykkpillveg.ldqykrknknsrnkqykakvrqinrktiesaLvqlqldfgvsilttesaneta 150
                                       l+eq+s +k  + +k +l++eg l  y+++               + + +i + +  +  d+g++i+ t +   t 
  gi|557694766|ref|YP_008797820.1|  67 LWEQLSAMKMFEGEK-VLILEGyLGLYRKRG--------------WKEVSILALMDKIVHDWGIPIIPTPDIRGTL 127
                                       ********9944444.666899777777776..............88889999999999999*****998876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1737.14
//
Query:       gi|557694767|ref|YP_008797821.1|  [L=442]
Description: branched-chain amino acid ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  134.0   2.1    1.1e-38  133.7   2.1    1.1  1  Peripla_BP_6    Periplasmic binding protein
    1.1e-12   47.7   0.0    1.4e-11   44.1   0.0    2.1  1  ANF_receptor    Receptor family ligand binding region
    4.1e-09   35.9   0.0    9.7e-06   24.8   0.0    2.8  2  Peripla_BP_5    Periplasmic binding protein domain
  ------ inclusion threshold ------
       0.19   12.4   0.1       0.35   11.5   0.1    1.5  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.7   2.1   2.5e-42   1.1e-38       2     341 ..      44     422 ..      43     423 .. 0.81

  Alignments for each domain:
  == domain 1  score: 133.7 bits;  conditional E-value: 2.5e-42
                                       EEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEET..TE..EEEEEEEE-TT.SH....HHHHHHHHHHHHCT- CS
                      Peripla_BP_6   2 ikiGlltplsGpyassgksllagaqaafeeiNaaGGin..Gr..kielverDday.dp....draaeaarrlvdqdg 69 
                                       i iGl  pl+ p+   g+ + ++a++a+eeiN aGG+   G+  ++ lv +D+   dp    d++++a++rl++  g
  gi|557694767|ref|YP_008797821.1|  44 IIIGLSLPLTNPV---GIHAKYAAEMAVEEINSAGGVVlnGTryELVLVAEDTNEmDPlipvDQGVTAFKRLIEVHG 117
                                       7899999999887...899999**************96678834566668886554555555*************** PP

                                       -SEEEE-BSHHHHHHHHHHHHHHT-EEEE......SS-HH...CCTTSTTEEESS-........-HHHHHHHHHHHH CS
                      Peripla_BP_6  70 vdalvgplssavaaavaevlakdgvpvig......paglt...gekcspyvfslgp........sysaqasalveyl 129
                                       + ++vg++ ++v+ a +++l + +++++       +++++   + +++ y+f++ +         y a   ++++ +
  gi|557694767|ref|YP_008797821.1| 118 AHVIVGGVRTDVVVAQSQLLSQYKIVYLDvesnqrIVEDRvqsDYENYKYYFHFFAggrnssagPYIATIPSALRNA 194
                                       *****************************553333222224437799999999998555554433334444444445 PP

                                       HHHTT....SCEEEEEEES..SHHHHHHHH....HHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEE CS
                      Peripla_BP_6 130 akelg....gkkvalvyad..yafgregia....alkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavll 196
                                       ak+      ++++alv+ +  +  g +g++    ++ + +k++G+++v  e +p++++dfs+++++ika+ga  ++l
  gi|557694767|ref|YP_008797821.1| 195 AKNNPdfpnVTRIALVAENalWTVGLAGRPagnsTFFQRLKQQGFDLVFAELYPTTQSDFSSYLARIKASGAGLIIL 271
                                       55433788899*****988566666666655555889*********999**************************** PP

                                       ESSHHHHHHHHHHHHHTT-SS..SCEEEE.CCC-CHHH.HHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHH CS
                      Peripla_BP_6 197 agtgadlaallkaaaeaGlda..krillv.swsgseed.lkalggeaaegvlavtpyfpdldnpavrafvaayeaay 269
                                        + g++ +a+ k+ a+ ++++  k+i+++ ++ g+ ++   +++g aa+g+++  + +  + +p +  f ++++++y
  gi|557694767|ref|YP_008797821.1| 272 LFSGPPGVAFTKQWAAYDWSPgkKPIIFGpGLLGGFSWfWTQTEG-AAQGTIWWPATVKVPVTPKTVPFIEKFTQRY 347
                                       *******************97545566665333444551555555.9******9999998889************** PP

                                       TTGGC--HHHHHHHHHHHHHHHHHHCCTHCCHHHHHHHHHHS-BECCCTCCBEECTTSBE.....E--EEEEEE-TS CS
                      Peripla_BP_6 270 ggapppsqfaaggyiaadlllealkaagsltreavraaleslgfdgllgplkftaedhqa.....srpvyvvqvdgg 341
                                       +++  p+++a  +y+a+ +l++al++a +  ++ +++ale+ +++g++g+++f ++ h +     +  +y+ q+++g
  gi|557694767|ref|YP_008797821.1| 348 KET--PNTAAFDTYDAIYVLKQALERANTWKADRLVTALEQTDYEGVIGRIQFNRKLHGLnlalpNLYWYFGQWQNG 422
                                       **9..***************************************************98873333357799****987 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 !   44.1   0.0   3.1e-15   1.4e-11       4     340 ..      62     403 ..      59     409 .. 0.76

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 3.1e-15
                                       HHHHHHHHHHHT-TTSSTTE.EEEEEE..EE-T.....T-HHHHHHHHHHHCCCC.EEEEEE-SSHHHHHHHHHHHC CS
                      ANF_receptor   4 eAmklAveeinsdpnllpgi.klgyei..idtc.....cdfslaleaaldflkgk.vvaviGpssssvsdavaslan 71 
                                        A+++Aveeins +++  +  + ++    +dt+       + +++ a+  +++ + + +++G +  +v+ a ++l++
  gi|557694767|ref|YP_008797821.1|  62 YAAEMAVEEINSAGGVVLNGtRYELVLvaEDTNemdplIPVDQGVTAFKRLIEVHgAHVIVGGVRTDVVVAQSQLLS 138
                                       699**********99865543777766668988766664445555555555553258******************** PP

                                       CTT-EEEESS-.....--GG.GG-TTTTTTE...............EESS--CHHHHHHHHHHHHHTT--EEEEEEE CS
                      ANF_receptor  72 lfkiPvisygs.....tspe.lsdknryptf...............lrtvpsdtsqaqAivdilkhfgWkkvaliys 127
                                       ++ki  + + s       +   sd + y++                + t+ps   +  A  +   + + +++al+++
  gi|557694767|ref|YP_008797821.1| 139 QYKIVYLDVESnqrivE-DRvQSDYENYKYYfhffaggrnssagpyIATIPS--ALRNAAKNNPDFPNVTRIALVAE 212
                                       *******9999666632.22255555555558889*****************..59999999999************ PP

                                       SS..HHHHHHH....HHHHHHHHHTT-EEEEEEEESTCHHHCHHHHHHHHHHTT.T--EEEEEE-HHHHHHHHHHHH CS
                      ANF_receptor 128 dd..dygesgl....qaleeeleergicvalkekipessnddevvrkllkeiks.karvivlfcssedarellkaar 197
                                       +   + g+ g      ++ ++l++ g+ +++ e +p   + +++++++l +ik   a  i+l +s++    + k+  
  gi|557694767|ref|YP_008797821.1| 213 NAlwTVGLAGRpagnSTFFQRLKQQGFDLVFAELYP---TTQSDFSSYLARIKAsGAGLIILLFSGPPGVAFTKQWA 286
                                       **887777665111146777****************...556666666666666699******************66 PP

                                       HTTS-STTEEEEETCHCCCECTTS-CC............HHHHHTT-EE..EEE--B-HHHHHHHHHST--CCCSSS CS
                      ANF_receptor 198 rlgltgeeyvwiasdawtsslvldkpe..........ltgleaaegvlg..frlkdpnspkfsefldkreklsdekq 262
                                           + ++   i    ++        +          ++++ aa+g++    + k p  pk+  f+         ++
  gi|557694767|ref|YP_008797821.1| 287 AYDWSPGKKPII----FG--------PgllggfswfwTQTEGAAQGTIWwpATVKVPVTPKTVPFI---------EK 342
                                       666666555555....12........1223333446666888888887522556889999999999.........33 PP

                                       TCCGSTTCCHHHHH...HHHHHHHHHHHHHHHCHHSSSHCCB-HHHHCCHHHHHHHHHHHT-EEEETTSCEEB-TTS CS
                      ANF_receptor 263 nyenegkeqisyqaalmYdaVyllaeAlnkllrkkkpgralscntlkpweggqkllrylrnvnfeGltGdvkfdeng 339
                                         ++  ke ++++a  +Yda+y+l +Al++++               +w+  ++++ +l+++ +eG+ G+++f+++ 
  gi|557694767|ref|YP_008797821.1| 343 -FTQRYKETPNTAAFDTYDAIYVLKQALERAN---------------TWKADRLVT-ALEQTDYEGVIGRIQFNRKL 402
                                       .4555566668888899***************...............799888888.****************9986 PP

                                       B CS
                      ANF_receptor 340 d 340
                                       +
  gi|557694767|ref|YP_008797821.1| 403 H 403
                                       6 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0   0.00038       1.7      20      50 ..      60      92 ..      53     151 .. 0.73
   2 !   24.8   0.0   2.2e-09   9.7e-06     151     327 ..     227     404 ..     223     433 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00038
                      Peripla_BP_5 20 lkdaallaieeinaagGvl..grkieavvvdpa 50
                                      +k aa +a+eein+agGv   g++ e v+v  +
  gi|557694767|ref|YP_008797821.1| 60 AKYAAEMAVEEINSAGGVVlnGTRYELVLVAED 92
                                      567899***********9645877776665333 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 2.2e-09
                      Peripla_BP_5 151 nrilkallkakggevvgeeYlplgssdvqkivakikkakpdvvlstinGdsnvafykelkeagikaekipvvsls.. 225
                                       n  + + lk++g + v  e  p  +sd+++ +a+ik+ ++ +++    G   vaf k+ ++ + ++ k p++     
  gi|557694767|ref|YP_008797821.1| 227 NSTFFQRLKQQGFDLVFAELYPTTQSDFSSYLARIKASGAGLIILLFSGPPGVAFTKQWAAYDWSPGKKPIIFGPgl 303
                                       5566678999******99999*************************************************9954411 PP

                      Peripla_BP_5 226 .vaeeelaaidaealvGhlaawnYfqsvdtpenkafvakfkarvgedrvtndpmeaayiqvklwaqAvekagstdve 301
                                         + + + +  + a++G +      +   tp+   f++kf++r++e+   n+ +  +y ++++++qA+e+a++ +++
  gi|557694767|ref|YP_008797821.1| 304 lGGFSWFWTQTEGAAQGTIWWPATVKVPVTPKTVPFIEKFTQRYKETP--NTAAFDTYDAIYVLKQALERANTWKAD 378
                                       03444455555556666665555555556899999*********9865..6677899******************** PP

                      Peripla_BP_5 302 kvreallgqelkapeGevkidpenhh 327
                                       ++ +al ++ ++   G+++++++ h 
  gi|557694767|ref|YP_008797821.1| 379 RLVTALEQTDYEGVIGRIQFNRKLHG 404
                                       ******************99986654 PP

>> 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 ?   11.5   0.1   7.9e-05      0.35      99     126 ..      51      78 ..      10      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.9e-05
                                       ---.--EEEESEE-HHHHHHHHHTT-EE CS
                    Ribosomal_L27A  99 eltkklkvkaskfSkkAkekIeaaGGkv 126
                                        lt+++ ++a+++ + A+e+I++aGG v
  gi|557694767|ref|YP_008797821.1|  51 PLTNPVGIHAKYAAEMAVEEINSAGGVV 78 
                                       6899**********************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3073.60
//
Query:       gi|557694768|ref|YP_008797822.1|  [L=288]
Description: branched-chain amino acid ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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  114.2  41.0    6.9e-33  114.0  41.0    1.1  1  BPD_transp_2   Branched-chain amino acid transport system / p
  ------ inclusion threshold ------
        1.2    8.8  23.1       0.25   11.0   2.6    3.3  3  DUF4131        Domain of unknown function (DUF4131)
        4.7    6.9  32.4        4.7    6.9   8.1    2.9  2  Cation_efflux  Cation efflux family


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 !  114.0  41.0   1.1e-36   6.9e-33       2     262 ..      11     269 ..      10     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 114.0 bits;  conditional E-value: 1.1e-36
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvl 78 
                                       ++ +  +++++a++A G++l+fg+a++i+ + g  ++ +ay+a+ l++ +  + l+++ + +++ +a+g++++++vl
  gi|557694768|ref|YP_008797822.1|  11 LVYGFITSLVYALFAEGFSLIFGVARMIDAAYGMWYTAAAYMAFALVTVYNIPSLVTFFATVAALFAAGFIYYWAVL 87 
                                       5678899********************************************96666666666666666777777666 PP

                      BPD_transp_2  79 rlkvdeliitllllsvlvgltl..llltgitsgvkgqssvkellgfagallsflsavivllalllvlavllllrrtr 153
                                       r +++e i  ++++++++++++  ++l      + +++ +++ + ++g++++  + + ++ a +l+++++ll++rt+
  gi|557694768|ref|YP_008797822.1|  88 R-RIKEHIEMIMTTFLIALVIQnlIVLLFTNFPWSTPAVFPGSTPVFGVSVFNQQLAAAVAASALLILLWLLIYRTK 163
                                       6.555555555554444444440033445555667777777777777777777777777****************** PP

                      BPD_transp_2 154 fGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGgagsllg 230
                                       +G+a+r v+++ +aa ++Gi+++r+ +l+  +s alAgla +l++ ++++ p   g+++   a+a+vvlGg+g  +g
  gi|557694768|ref|YP_008797822.1| 164 VGLAIRSVAQDVDAAVCVGIRPERTMALVLGLSTALAGLASLLVTPQSTITP-VLGWPMLTLAFAIVVLGGLGDYRG 239
                                       ***********************************************99988.************************ PP

                      BPD_transp_2 231 tviGaliigvvksllltllgiptelarvllga 262
                                       t+++a++ig+v++   +l+ + + ++ + + +
  gi|557694768|ref|YP_008797822.1| 240 TLLAAFVIGYVEITVQNLV-S-PLYSGAASLI 269
                                       *************666655.3.4444444333 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   3.4   0.00012      0.69       8      64 ..      45      99 ..      39     124 .. 0.79
   2 ?   11.0   2.6   4.1e-05      0.25       6      56 ..     143     213 ..     138     219 .. 0.79
   3 ?   -0.9   2.4      0.19   1.1e+03      18      46 ..     232     276 ..     214     280 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
                           DUF4131  8 vllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqlle 64
                                      +  a++ ++++l  +++   p+  ++++  ++l++a++ +++ ++++ +++++ +++
  gi|557694768|ref|YP_008797822.1| 45 WYTAAAYMAFALVTVYN--IPSLVTFFATVAALFAAGFIYYWAVLRRIKEHIEMIMT 99
                                      44444444444444444..9********************************99986 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.1e-05
                           DUF4131   6 alvllalllllllllllllrr.....................rprrrvllllllllllallgfalrapqpna 56 
                                       a+ + a++ll+ll+ll++                        rp r+++l+l+l  +la+l  +l +pq + 
  gi|557694768|ref|YP_008797822.1| 143 AAAVAASALLILLWLLIYR-TkvglairsvaqdvdaavcvgiRPERTMALVLGLSTALAGLASLLVTPQSTI 213
                                       4444444444444444443.258****************************************999999765 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.19
                           DUF4131  18 lllllllrr..................rprrrvllllllllllallg 46 
                                         l+ +  r                    ++ + ++++l+++l++l+
  gi|557694768|ref|YP_008797822.1| 232 GGLGDY--RgtllaafvigyveitvqnLVSPLYSGAASLIAVLLTLW 276
                                       333333..123444444444455554455556666666666666665 PP

>> Cation_efflux  Cation efflux family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  16.3    0.0056        33      16     122 ..      11     113 ..       2     118 .. 0.84
   2 ?    6.9   8.1   0.00079       4.7     100     185 ..     137     272 ..     129     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0056
                     Cation_efflux  16 livgllt.nSlalladafhslsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllglavfllleaiq 91 
                                       l++g++t    al+a++f  ++ ++  + +  +++++     + +  + +++ +l++++  +  l++a f+ + a+ 
  gi|557694768|ref|YP_008797822.1|  11 LVYGFITsLVYALFAEGFSLIFGVARMIDAAYGMWYTAAAYMAFALVTVYNIPSLVTFFATVAALFAAGFIYYWAVL 87 
                                       33444442679****************************************************************** PP

                     Cation_efflux  92 klikegereihaglalvvalvslvvnlalll 122
                                       + i      +h+++++   l++lv++ +++l
  gi|557694768|ref|YP_008797822.1|  88 RRI-----KEHIEMIMTTFLIALVIQNLIVL 113
                                       ***.....78888888888888888654444 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00079
                     Cation_efflux 100 eihaglalvvalvslvvnlalllilrragrkl............................................. 131
                                       + +  la++va+ +l++ l+ll++  ++g ++                                             
  gi|557694768|ref|YP_008797822.1| 137 VFNQQLAAAVAASALLILLWLLIYRTKVGLAIrsvaqdvdaavcvgirpertmalvlglstalaglasllvtpqsti 213
                                       668899**************************99***************************************9999 PP

                     Cation_efflux 132 .....rsaalkaaalhvlgDaltslgvlvsalvillfnlksgplaDpvaslligliily 185
                                              ++  a a+ vlg +    g+l++a+vi +++ + ++l+ p+ s + +li + 
  gi|557694768|ref|YP_008797822.1| 214 tpvlgWPMLTLAFAIVVLGGLGDYRGTLLAAFVIGYVEITVQNLVSPLYSGAASLIAVL 272
                                       99996666666777888888889999999999999999999966666666666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); 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):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2072.66
//
Query:       gi|557694769|ref|YP_008797823.1|  [L=311]
Description: branched-chain amino acid ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  109.5  35.2    1.6e-31  109.5  35.2    1.5  2  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
       0.26   11.4   1.3       0.47   10.5   0.0    2.2  2  NB            NB glycoprotein


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 ?   -3.4   0.7      0.47   4.3e+03      57      63 ..      12      18 ..       4      27 .. 0.42
   2 !  109.5  35.2   1.8e-35   1.6e-31       2     243 ..      31     267 ..      30     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.47
                      BPD_transp_2 57 lallval 63
                                      l++++a+
  gi|557694769|ref|YP_008797823.1| 12 LLIVLAI 18
                                      1111111 PP

  == domain 2  score: 109.5 bits;  conditional E-value: 1.8e-35
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvl 78 
                                       i+++ltl+ i+a++A++++l+ g++G+++lgh+ f+a G+y+aa+l+ +++ ++ +a+ ++ lv  a+g l+gl++l
  gi|557694769|ref|YP_008797823.1|  31 IIFILTLTNIFAMLAVSWNLLSGYMGLLSLGHSFFFAGGGYAAAILSISYGVPPVAAVFLGALVITALGSLIGLPSL 107
                                       789************************************************************************** PP

                      BPD_transp_2  79 rlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsavivllalllvlavllllrrtrfG 155
                                       +l+ + ++ ++l++ v+++ +  +   + +g  g+ +++ l+++a a+   +     l al+  ++v +l+ r+r+G
  gi|557694769|ref|YP_008797823.1| 108 KLRGHFFALVTLIIPVIAYQVT-NAIPQLGGHDGIFGIPSLFQSAEAFYLAS-----LAALAGSVLVSYLVMRSRLG 178
                                       *************999999988.66666777777777777777777776666.....89****************** PP

                      BPD_transp_2 156 ralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGgagsllgt 231
                                       ++   + ++e aa+a+Gi+v r+kll  +is ++Ag+aGa++a l g+i+p    ++    ++++ +lGg  ++lg+
  gi|557694769|ref|YP_008797823.1| 179 LIFTCIKDDEIAAKAAGIDVPRYKLLGLAISIFIAGVAGAFYAYLNGVISPaTYELEKASLPLLMTLLGGRATILGP 255
                                       ***************************************************************************** PP

                      BPD_transp_2 232 viGaliigvvks 243
                                       v+Ga+ii ++ +
  gi|557694769|ref|YP_008797823.1| 256 VVGAFIIETLIE 267
                                       *******76544 PP

>> NB  NB glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.8       1.1     1e+04      29      41 ..       9      21 ..       6      35 .. 0.61
   2 ?   10.5   0.0   5.2e-05      0.47      69      95 ..     183     209 ..     165     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.1
                                NB 29 livilivfgciak 41
                                      + v+liv++++a 
  gi|557694769|ref|YP_008797823.1|  9 IAVLLIVLAILAA 21
                                      3455555555544 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 5.2e-05
                                NB  69 cnkrddistpragvdipsfilpglnls 95 
                                       c k d+i++  ag+d+p + l gl +s
  gi|557694769|ref|YP_008797823.1| 183 CIKDDEIAAKAAGIDVPRYKLLGLAIS 209
                                       99**********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       871  (0.0485805); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.97
# Mc/sec: 966.03
//
Query:       gi|557694770|ref|YP_008797824.1|  [L=238]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   96.4   0.0    4.1e-27   95.4   0.0    1.5  2  ABC_tran      ABC transporter
    6.9e-06   25.9   0.0    1.5e-05   24.8   0.0    1.6  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
    0.00082   19.3   1.9     0.0027   17.6   0.6    2.3  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0037   17.2   0.0      0.013   15.4   0.0    1.8  2  Rad17         Rad17 P-loop domain
     0.0046   17.5   0.2     0.0083   16.6   0.2    1.4  1  AAA_23        AAA domain
  ------ inclusion threshold ------
       0.01   16.1   0.3       0.33   11.2   0.2    2.4  2  AAA_22        AAA domain
      0.011   15.1   0.0       0.67    9.2   0.0    2.1  2  Zeta_toxin    Zeta toxin
      0.017   15.1   0.0      0.088   12.8   0.0    2.0  2  AAA_14        AAA domain
      0.028   14.2   0.1      0.054   13.2   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.042   13.4   0.0      0.065   12.8   0.0    1.3  1  AAA_27        AAA domain
      0.061   13.7   0.0       0.11   12.9   0.0    1.6  1  AAA_16        AAA ATPase domain
      0.083   11.5   0.0        0.1   11.2   0.0    1.1  1  AAA_13        AAA domain
       0.14   11.3   0.1       0.67    9.1   0.1    1.9  2  NB-ARC        NB-ARC 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 !   95.4   0.0     3e-30   4.1e-27       2     136 ..      20     162 ..      19     163 .. 0.95
   2 ?   -2.4   0.0       4.6   6.3e+03      27      49 ..     197     219 ..     196     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 3e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       ++vs+++k+ e+++++G+nGaGK+tL++l++g +kp++G++ l+g+d+++ ++ +++ k +   +q  + f+ ltv+
  gi|557694770|ref|YP_008797824.1|  20 DDVSFTVKQHEILGVIGPNGAGKTTLFSLISGTEKPDAGKVYLNGEDITNtKPYHRAIKGLVRTFQIVRPFKSLTVE 96 
                                       89***********************************************989999999999999************* PP

                                       HH...........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       +n             +ee+ ++l++lgl  +++t+     + L +G+ +++++ar l+ kp++l+lDEp+
  gi|557694770|ref|YP_008797824.1|  97 QNlrapltvrgnkFNEEEAMALLRQLGLAAKRNTPT----TLLTHGELKKLEVARGLIAKPRVLMLDEPF 162
                                       *********998666667999*********999999....*****************************6 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.6
                                       HHHHHTTSS--SEEEEEETTCEG CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  27 LlkllagllkpteGeilldgkdl 49 
                                       L+kl+ + l  ++G++ ++g++ 
  gi|557694770|ref|YP_008797824.1| 197 LMKLIQRALVMDQGKLIFEGAPA 219
                                       78999999999999999988765 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   1.1e-08   1.5e-05       1      23 []     211     233 ..     211     233 .. 0.97

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.1e-08
                      BCA_ABC_TP_C   1 rvIAeGtPaEvrndPrVieAYLG 23 
                                       ++I eG Pa+v +   Vi+AYLG
  gi|557694770|ref|YP_008797824.1| 211 KLIFEGAPADVARSDVVIKAYLG 233
                                       68********************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 !   17.6   0.6   1.9e-06    0.0027       3      21 ..      33      51 ..      31      67 .. 0.88
   2 ?    0.2   0.0      0.38   5.2e+02     257     282 ..     152     177 ..      64     191 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                            AAA_21  3 vliGpNgsGKSnLLdaldl 21
                                      ++iGpNg+GK++L+ ++++
  gi|557694770|ref|YP_008797824.1| 33 GVIGPNGAGKTTLFSLISG 51
                                      79*************9964 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.38
                            AAA_21 257 kgsllliDEpEngLHPkllrrllell 282
                                       k+++l +DEp  gL  + ++++ ++l
  gi|557694770|ref|YP_008797824.1| 152 KPRVLMLDEPFGGLTVAEIEEVTQVL 177
                                       23677777776666555555555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.6e-06     0.013      41     141 ..      25     122 ..      17     159 .. 0.82
   2 ?   -0.9   0.0      0.95   1.3e+03     149     169 ..     170     190 ..     150     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.6e-06
                             Rad17  41 esrkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdnqksdfkgltekesrflsqiesfkeleLkd 116
                                         ++++iL + GP G gk+t    +s    ++  + +ln+  + +++  +  +kgl+ +++     +  fk l + +
  gi|557694770|ref|YP_008797824.1|  25 TVKQHEILGVIGPNGAGKTTLFSLISGTEKPDAgKVYLNGEDITNTKPYHRAIKGLVRTFQ----IVRPFKSLTVEQ 97 
                                       557799*******************9887776626799********9999*******9999....777788888777 PP

                             Rad17 117 akylklqklGddlrtdkklilvedl 141
                                            l  +G++ + +  + l+ +l
  gi|557694770|ref|YP_008797824.1|  98 NLRAPLTVRGNKFNEEEAMALLRQL 122
                                       7777888888888888888887776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.95
                             Rad17 149 sdalrevirkylrssealpli 169
                                        + + +v+r+y+  +++l +i
  gi|557694770|ref|YP_008797824.1| 170 IEEVTQVLREYVAEGGTLVII 190
                                       577889999999999996554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.2   6.1e-06    0.0083      17      39 ..      26      49 ..      10      52 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.1e-06
                            AAA_23 17 F.skgltlItGpNGaGKTTildAi 39
                                         + +  ++GpNGaGKTT++  i
  gi|557694770|ref|YP_008797824.1| 26 VkQHEILGVIGPNGAGKTTLFSLI 49
                                      3566788899**********9776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00024      0.33       4      29 ..      28      53 ..      25     160 .. 0.74
   2 ?    2.8   0.0     0.094   1.3e+02      37      90 ..     147     209 ..     128     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00024
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      ++ il v+G+ G+GKTtl   +  + 
  gi|557694770|ref|YP_008797824.1| 28 QHEILGVIGPNGAGKTTLFSLISGTE 53
                                      567888***********998776665 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.094
                            AAA_22  37 e...erpevvfvtlpsst.sskdl..lrellralglelka...erlsseellealeqalrara 90 
                                       +   ++p+v+  + p ++ + +++   +++lr++  e+ +    +++++el++++++al   +
  gi|557694770|ref|YP_008797824.1| 147 RgliAKPRVLMLDEPFGGlTVAEIeeVTQVLREYVAEGGTlviIEHRLRELMKLIQRALVMDQ 209
                                       145578888888888888888888778889999998888899999999999999999997655 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00049      0.67      22      64 ..      35      77 ..      20     115 .. 0.83
   2 ?    3.9   0.0      0.02        28      73     107 ..     163     197 ..     157     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00049
                        Zeta_toxin 22 gGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyeei 64
                                       G  GAGK++l +l+    +++ + v l++ d+ +  P  ++i
  gi|557694770|ref|YP_008797824.1| 35 IGPNGAGKTTLFSLISGTEKPDAGKVYLNGEDITNTKPYHRAI 77
                                      4889*************9999********99987666655553 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.02
                        Zeta_toxin  73 seltqkdaselvekllqeaiengyniivegtlrsp 107
                                         lt +++ e+++ l+++++e g  +i+e  lr+ 
  gi|557694770|ref|YP_008797824.1| 163 GGLTVAEIEEVTQVLREYVAEGGTLVIIEHRLREL 197
                                       56888999*********************999876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.4e-05     0.088       2      45 ..      29      71 ..      28      98 .. 0.81
   2 ?   -0.0   0.0      0.62   8.5e+02      65      90 ..     153     184 ..     118     219 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.4e-05
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk 45
                                      ++il + G+  +GKTtl   +  ++  ++   +y+n +d +++k
  gi|557694770|ref|YP_008797824.1| 29 HEILGVIGPNGAGKTTLFSLISGTEK-PDAGKVYLNGEDITNTK 71
                                      68999************777766666.99999*****9998865 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.62
                            AAA_14  65 ktylflDE......iqevpewekalkslvdeg 90 
                                        ++l+lDE      + e++e+ ++l+++v eg
  gi|557694770|ref|YP_008797824.1| 153 PRVLMLDEpfggltVAEIEEVTQVLREYVAEG 184
                                       55666666554444566777777777777776 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 ?   13.2   0.1   3.9e-05     0.054      13      39 ..      20      46 ..      17      52 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.9e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTll 39
                                      d+ +++++++++  ++Gp+G+GK+Tl+
  gi|557694770|ref|YP_008797824.1| 20 DDVSFTVKQHEILGVIGPNGAGKTTLF 46
                                      55667778778888***********97 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.7e-05     0.065       8      44 ..      10      47 ..       1      51 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.7e-05
                            AAA_27  8 LeryGkf.tdrsldfsaeeadlhliyGpNEAGKstalr 44
                                      ++r+G + +   ++f  +++++  ++GpN AGK+t+++
  gi|557694770|ref|YP_008797824.1| 10 VKRFGGIvAVDDVSFTVKQHEILGVIGPNGAGKTTLFS 47
                                      478876514468999999*****************987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.9e-05      0.11      25      85 ..      30      90 ..      18     199 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.9e-05
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrql 85
                                      e++ ++G+ G GK++l   +    + d +  ++ + ++ +   py   +  +  + +++r  
  gi|557694770|ref|YP_008797824.1| 30 EILGVIGPNGAGKTTLFSLISGTEKPD-AGKVYLNGEDITNTKPYHRaIKGLVRTFQIVRPF 90
                                      7889*************9999665655.4445555555545788844222222222444443 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.4e-05       0.1      23      51 ..      36      64 ..      30     116 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.4e-05
                            AAA_13 23 GwNGaGKTtLSrllrslelgetepkfang 51
                                      G NGaGKTtL +l++  e+  + + + ng
  gi|557694770|ref|YP_008797824.1| 36 GPNGAGKTTLFSLISGTEKPDAGKVYLNG 64
                                      99**************9887776666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00048      0.67      20      40 ..      29      49 ..      21      58 .. 0.86
   2 ?   -0.2   0.0      0.33   4.5e+02     159     183 ..     110     134 ..      85     203 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00048
                                      SEEEEEEESTTSSHHHHHHHH CS
                            NB-ARC 20 slvvalvGmgGvGKttlakqi 40
                                        ++++ G  G GKttl++ i
  gi|557694770|ref|YP_008797824.1| 29 HEILGVIGPNGAGKTTLFSLI 49
                                      459**************9876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.33
                                       --HHHHHHHHHHCCTS-GGCHH..C CS
                            NB-ARC 159 Lekdeawellenkvfekkleekesl 183
                                       ++++ea  ll + + ++k ++ ++l
  gi|557694770|ref|YP_008797824.1| 110 FNEEEAMALLRQLGLAAKRNTPTTL 134
                                       4444555555544444444444332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); 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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 1769.71
//
Query:       gi|557694771|ref|YP_008797825.1|  [L=238]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-30  104.6   0.0    9.4e-30  103.9   0.0    1.3  1  ABC_tran     ABC transporter
    4.2e-11   43.2   0.6    1.3e-05   25.2   0.2    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.2e-05   24.0   0.0      0.018   14.5   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    4.7e-05   23.7   0.2     0.0002   21.6   0.2    1.9  1  AAA_22       AAA domain
    0.00011   21.9   0.2    0.00041   20.0   0.2    1.9  1  AAA_25       AAA domain
     0.0003   21.2   0.0    0.00042   20.7   0.0    1.3  1  AAA_16       AAA ATPase domain
    0.00038   21.0   0.0    0.00053   20.5   0.0    1.3  1  AAA_23       AAA domain
    0.00058   19.5   0.1     0.0012   18.6   0.1    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0017   18.1   0.1      0.017   14.9   0.0    2.2  2  IstB_IS21    IstB-like ATP binding protein
     0.0017   18.1   0.0     0.0022   17.7   0.0    1.3  1  AAA_15       AAA ATPase domain
     0.0018   18.0   0.0     0.0034   17.0   0.0    1.4  1  SRP54        SRP54-type protein, GTPase domain
     0.0026   17.9   0.0     0.0089   16.2   0.0    1.9  1  AAA_33       AAA domain
     0.0027   17.8   0.0      0.006   16.7   0.0    1.5  1  Dynamin_N    Dynamin family
     0.0086   15.8   0.5      0.013   15.2   0.3    1.7  1  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.011   14.4   0.0       0.42    9.2   0.0    2.0  2  AAA_13       AAA domain
      0.013   15.0   0.1      0.029   13.8   0.1    1.5  1  PhoH         PhoH-like protein
      0.021   15.3   0.3      0.076   13.4   0.3    2.0  1  AAA          ATPase family associated with various cellular a
      0.024   14.2   0.0      0.054   13.1   0.0    1.5  1  AAA_27       AAA domain
      0.024   14.5   0.1      0.045   13.6   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
       0.04   14.0   0.2      0.064   13.3   0.2    1.7  1  MMR_HSR1     50S ribosome-binding GTPase
      0.041   13.9   0.1       0.21   11.6   0.0    2.2  2  AAA_14       AAA domain
      0.052   12.6   1.1      0.071   12.1   0.1    1.7  2  T2SSE        Type II/IV secretion system protein
      0.057   13.3   0.7       0.26   11.2   0.4    2.0  2  NACHT        NACHT domain
      0.061   12.1   0.1        9.3    4.9   0.0    2.8  3  ABC_ATPase   Predicted ATPase of the ABC class
      0.066   13.5   1.6      0.077   13.2   0.2    1.9  2  AAA_28       AAA domain
       0.12   12.3   0.0       0.22   11.4   0.0    1.4  1  Rad17        Rad17 P-loop domain
       0.12   11.2   0.1       0.19   10.5   0.1    1.2  1  DLIC         Dynein light intermediate chain (DLIC)
       0.13   12.2   0.0       0.23   11.3   0.0    1.7  1  ATPase_2     ATPase domain predominantly from Archaea
       0.16   11.1   0.1       0.35   10.0   0.1    1.5  1  NB-ARC       NB-ARC domain
       0.17   11.6   0.0       0.28   10.9   0.0    1.3  1  AAA_24       AAA domain
        0.2    9.1   0.0       0.28    8.6   0.0    1.1  1  DUF3584      Protein of unknown function (DUF3584)
       0.21   11.8   0.5       0.77   10.0   0.1    2.1  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.23   11.0   0.6        0.7    9.4   0.2    1.9  2  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 !  103.9   0.0   1.7e-32   9.4e-30       2     136 ..      21     165 ..      20     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 103.9 bits;  conditional E-value: 1.7e-32
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       +++s++++e e+va++G+nGaGK+tL+ +lagl + ++G+ ll+++d+++  + e++ k +    +  +lfp++tv+
  gi|557694771|ref|YP_008797825.1|  21 EDISVEVREREIVAVIGPNGAGKTTLMLALAGLATVKSGKTLLNNEDITRlPPYERVVKGLVLSLERRRLFPDMTVY 97 
                                       789***********************************************99999999999999999********** PP

                                       HH.....HHHTCHHHHHHHSTTGG.....TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.....xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.....esdeeiekalsklglke.....lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en     +++++ e++++ ++++      + +++ k+ + +LSgG++q+valaral+ +p++lllDEp+
  gi|557694771|ref|YP_008797825.1|  98 ENvmtgaYRRRDRENIRKDYEMVAelfpiI-EKRRKQLAGTLSGGEQQMVALARALMARPRVLLLDEPS 165
                                       ******945555555555555555444422.22224457*****************************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 !   25.2   0.2   2.4e-08   1.3e-05       1      29 [.      32      60 ..      32      88 .. 0.73
   2 !   16.4   0.0   1.1e-05    0.0061     229     278 ..     130     174 ..      99     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.4e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdv 29
                                      + ++iGpNg+GK++L+ al +la + +  
  gi|557694771|ref|YP_008797825.1| 32 IVAVIGPNGAGKTTLMLALAGLATVKSGK 60
                                      5789******************9862222 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.1e-05
                            AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrl 278
                                       +++  a  lS G +++ al+ al +++   ++ll+DEp  gL P  ++rl
  gi|557694771|ref|YP_008797825.1| 130 RRKQLAGTLSGGEQQMVALARALMARP---RVLLLDEPSVGLAP--IARL 174
                                       455667889***************999...**************..3333 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 !   14.5   0.0   3.4e-05     0.018      23      46 ..      29      52 ..      19      71 .. 0.78
   2 !    8.3   0.0    0.0026       1.4     135     187 ..      93     184 ..      53     214 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.4e-05
                                      TSSEEEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnlldAilF 46
                                      ++++ a++GpNG+GK+ l+ A+  
  gi|557694771|ref|YP_008797825.1| 29 EREIVAVIGPNGAGKTTLMLALAG 52
                                      56799**************99864 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0026
                                       T...........................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTT CS
                                       x...........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e...........................................lLSgGektLvalaLlfAiqkvkpaplyllDeid 168
                                       +                                           +LSgGe+++vala      +++p+   llDe  
  gi|557694771|ref|YP_008797825.1|  93 DmtvyenvmtgayrrrdrenirkdyemvaelfpiiekrrkqlagTLSGGEQQMVALARA---LMARPRV-LLLDEPS 165
                                       055555555555555666666666666666666666666677779**********9965...3455554.3667766 PP

                                       TTS-HHHHHHHHHHHHHHC CS
                                       xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 169 aaLDeknvkkvaellkeks 187
                                         L    + +v e ++e +
  gi|557694771|ref|YP_008797825.1| 166 VGLAPIARLAVFEKVREIR 184
                                       6666666666666666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.2   3.7e-07    0.0002       4     128 ..      29     194 ..      25     201 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.7e-07
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...................................erpevvfv 45 
                                       ++ i++v+G+ G+GKTtl+  l+  ++  +  +                                    e++ +  +
  gi|557694771|ref|YP_008797825.1|  29 EREIVAVIGPNGAGKTTLMLALAGLATVKSGKTLlnneditrlppyervvkglvlslerrrlfpdmtvyENVMTGAY 105
                                       7889********************996555544499999999*9999999999999966666533333222222255 PP

                            AAA_22  46 tlpsstsskdllrellralglelkaerlsseellealeqalrarav.....ielliiDEaqh.lr...seealeeLr 113
                                            ++ ++ ++++++ +    k+ r+++   l+  eq++ a a+     +++l++DE    l    + +++e++r
  gi|557694771|ref|YP_008797825.1| 106 RRRDRENIRKDYEMVAELFPIIEKR-RKQLAGTLSGGEQQMVALARalmarPRVLLLDEPSVgLApiaRLAVFEKVR 181
                                       5555557777777777777766666.778888888888888888888888999******988887665589999999 PP

                            AAA_22 114 sllnlsrkgvqliLv 128
                                       ++ +  r+++++++v
  gi|557694771|ref|YP_008797825.1| 182 EIRE--RQNIAILVV 194
                                       8888..888888776 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   7.6e-07   0.00041      31     149 ..      28     162 ..      21     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.6e-07
                            AAA_25  31 pagelallaGapgtGKttlaldlalava..tGkpwlg........pvapeqgkVlyvsaEdsedelr..rRlravg. 94 
                                       ++ e+++++G+ g+GKttl l la   +  +Gk +l         p   + +k l++s+E ++  ++    ++ v+ 
  gi|557694771|ref|YP_008797825.1|  28 REREIVAVIGPNGAGKTTLMLALAGLATvkSGKTLLNneditrlpP-YERVVKGLVLSLERRR-LFPdmTVYENVMt 102
                                       578999*****************9666668****999****96633.35999********999.4443223333443 PP

                            AAA_25  95 ealrddarllvldlagv..eslpLfakdrggtl..l...tadvdaleaaieevegvrlvviD 149
                                        a+r+++r+ + +  ++  e  p+++k+r++ +  l   ++++ al++a+ +  ++r++ +D
  gi|557694771|ref|YP_008797825.1| 103 GAYRRRDRENIRKDYEMvaELFPIIEKRRKQLAgtLsggEQQMVALARALMA--RPRVLLLD 162
                                       4445555555544333333344444443333335433335555555555555..25666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   7.8e-07   0.00042      24     143 ..      30     163 ..      18     192 .. 0.65

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 7.8e-07
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesa....ipy...sa.laqalareellrqllde.... 88 
                                        e+v ++G+ G GK++l+ +l+  ++ +     +gk+  + ++     py   +  l+  l+r++l+ +   +    
  gi|557694771|ref|YP_008797825.1|  30 REIVAVIGPNGAGKTTLMLALAGLATVK-----SGKTLLNNEDitrlPPYervVKgLVLSLERRRLFPD---Mtvye 98 
                                       389***************9999766655.....666666655522225555552225555555555555...15556 PP

                            AAA_16  89 ..aesaeleawrekleeala...........avpelagaea...srllellkrllallsrderplvlvlDd 143
                                          + a ++++re +++ ++             ++lag ++   +    ++ +l++ l   +rp vl+lD+
  gi|557694771|ref|YP_008797825.1|  99 nvMTGAYRRRDRENIRKDYEmvaelfpiiekRRKQLAGTLSggeQ----QMVALARALM--ARPRVLLLDE 163
                                       664555677777777777776666666544444444444445533....4444442223..5689999996 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   9.8e-07   0.00053      18      46 ..      29      57 ..      17     154 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 9.8e-07
                            AAA_23 18 skgltlItGpNGaGKTTildAiklaLyge 46
                                      ++ +++++GpNGaGKTT++ A+    + +
  gi|557694771|ref|YP_008797825.1| 29 EREIVAVIGPNGAGKTTLMLALAGLATVK 57
                                      6678999************9998655544 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 !   18.6   0.1   2.1e-06    0.0012      16      48 ..      24      56 ..      18      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.1e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                      ++e+++++++ ++Gp+G+GK+Tl+ A++ l + 
  gi|557694771|ref|YP_008797825.1| 24 SVEVREREIVAVIGPNGAGKTTLMLALAGLATV 56
                                      567777779***************998877665 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 !   14.9   0.0   3.1e-05     0.017      44      76 ..      27      60 ..      19      68 .. 0.83
   2 ?    0.8   0.0      0.67   3.6e+02     103     144 ..     150     190 ..     117     208 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
                         IstB_IS21 44 iekkenivllGpsGvGKshlaialg.veavragl 76
                                      ++++e ++++Gp G+GK+ l  al+  ++v++g+
  gi|557694771|ref|YP_008797825.1| 27 VREREIVAVIGPNGAGKTTLMLALAgLATVKSGK 60
                                      678999*****************96155566665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.67
                         IstB_IS21 103 lkrllkvdllilDd..lgllpldqaeaellfeviekryerrsii 144
                                        + ++++++l+lD+  +gl p+   ++  +fe + +  er+ i+
  gi|557694771|ref|YP_008797825.1| 150 RALMARPRVLLLDEpsVGLAPI---ARLAVFEKVREIRERQNIA 190
                                       3345678999999833445444...4555666666666666555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.1e-06    0.0022      14      64 ..      20      67 ..      19     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.1e-06
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikieked 64
                                      ++d+++++ e  +  +iG+N++GK++++ al  + + k    + ++ +++ed
  gi|557694771|ref|YP_008797825.1| 20 IEDISVEVREReIVAVIGPNGAGKTTLMLALAGLATVK----SGKTLLNNED 67
                                      57888888888899*****************9999988....3344444444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   6.3e-06    0.0034       3      42 ..      32      71 ..      30      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.3e-06
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSST CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRa 42
                                      +++++G++GaGKTt +  La l + +  k+ll   D+ R 
  gi|557694771|ref|YP_008797825.1| 32 IVAVIGPNGAGKTTLMLALAGLATVKSGKTLLNNEDITRL 71
                                      7899********************************9997 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.6e-05    0.0089       2     108 ..      33     198 ..      32     209 .. 0.61

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg....avllssdt.......................................... 32 
                                       v ++G++G+GK+tl   l+   +     +ll+  +                                          
  gi|557694771|ref|YP_008797825.1|  33 VAVIGPNGAGKTTLMLALAGLATvksgKTLLNNEDitrlppyervvkglvlslerrrlfpdmtvyenvmtgayrrrd 109
                                       789************99964444555555665555799999999999999999444444444444443333322222 PP

                            AAA_33  33 .lrrrlfgtdqqskt....................dytrvldrlyqilnelarkalsagrnvildat......nlsr 82 
                                        +            +                    +++  l+   q++ +lar  +++ r ++ld +       ++ 
  gi|557694771|ref|YP_008797825.1| 110 rE------------NirkdyemvaelfpiiekrrkQLAGTLSGGEQQMVALARALMARPRVLLLDEPsvglapIARL 174
                                       20............144555566666666555332333333445556668888888888888888885554444445 PP

                            AAA_33  83 rerarflklarrlgvpvrivvvetde 108
                                       + +++++++ +r++  ++i+vve d 
  gi|557694771|ref|YP_008797825.1| 175 AVFEKVREIRERQN--IAILVVEQDA 198
                                       66677777777777..4444444444 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-05     0.006       1     143 [.      33     201 ..      33     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-05
                                       EEEEEBTTTTHHHHHHHHHTS--S---SS.S---S-EEEEE......................CCT---CCS...SS CS
                         Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpn.ptTrrplelql......................geeeeaseravkee 54 
                                       +av+G   +GK++++ aL g +   +g++ +    ++ l                            +++ ++  ++
  gi|557694771|ref|YP_008797825.1|  33 VAVIGPNGAGKTTLMLALAGLATVKSGKTlLNNEDITRLPPyervvkglvlslerrrlfpdmtV---YENVMTGAYR 106
                                       89********************999999834456788888899999999999999888885542...3333333333 PP

                                       EEEE...T-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTS...HHHHHH CS
                         Dynamin_N  55 lkek...ekkledfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdq...elvkey 125
                                        +++   +k++e + e+   iek+++++ag+++g  ++++ l      ++++ l+D P +   +  +    e v+e+
  gi|557694771|ref|YP_008797825.1| 107 RRDReniRKDYEMVAELFPIIEKRRKQLAGTLSGGEQQMVALARALMARPRVLLLDEPSVGLAPIARLavfEKVREI 183
                                       3333445999************************************************7766666666456777777 PP

                                       HSTTEEEEEEEETTS-CC CS
                         Dynamin_N 126 ikkadiilavtsanhdls 143
                                        ++++i ++v++ + +l+
  gi|557694771|ref|YP_008797825.1| 184 RERQNIAILVVEQDAALA 201
                                       755555555554444443 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   2.5e-05     0.013      17      46 ..      29      59 ..      24     182 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaa.g 46
                                      ++ ++++ Gp G+GKtt++ al+ +++ + g
  gi|557694771|ref|YP_008797825.1| 29 EREIVAVIGPNGAGKTTLMLALAGLATVKsG 59
                                      566999****************999988755 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00078      0.42      22      46 ..      36      60 ..      26     100 .. 0.73
   2 ?    3.3   0.0     0.047        25     484     510 ..     122     148 ..     110     150 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00078
                            AAA_13 22 YGwNGaGKTtLSrllrslelgetep 46
                                       G NGaGKTtL  +l+ l + +  +
  gi|557694771|ref|YP_008797825.1| 36 IGPNGAGKTTLMLALAGLATVKSGK 60
                                      59***********999997654443 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.047
                            AAA_13 484 kgYrivrkggsqaaetLSeGEktaIaf 510
                                       + + i+ k+ +q a+tLS GE+ ++a+
  gi|557694771|ref|YP_008797825.1| 122 ELFPIIEKRRKQLAGTLSGGEQQMVAL 148
                                       6678999999***************98 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   5.3e-05     0.029      16      44 ..      27      56 ..      19      63 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.3e-05
                                      HHH-SEEEEE--TTSSTTHHHHHHH.HHHH CS
                              PhoH 16 lkkndivfaiGpaGtGKtylavala.veal 44
                                      +++ +iv +iGp G+GKt l +ala ++ +
  gi|557694771|ref|YP_008797825.1| 27 VREREIVAVIGPNGAGKTTLMLALAgLATV 56
                                      66899**************99987614444 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 ?   13.4   0.3   0.00014     0.076       2      26 ..      34      82 ..      33     165 .. 0.56

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00014
                                      EEESSTTSSHHHHHHHHHHHHTHE........................E CS
                               AAA  2 llyGppGtGKTllakavakelgve........................f 26
                                       ++Gp G GKT+l+ a+a  + v+                        +
  gi|557694771|ref|YP_008797825.1| 34 AVIGPNGAGKTTLMLALAGLATVKsgktllnneditrlppyervvkglV 82
                                      689***************9986543334444444444444444444443 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   9.9e-05     0.054      17      49 ..      23      53 ..      12      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.9e-05
                            AAA_27 17 rsldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                       s+  +  e+++  ++GpN AGK+t++ A+  l
  gi|557694771|ref|YP_008797825.1| 23 ISV--EVREREIVAVIGPNGAGKTTLMLALAGL 53
                                      344..445889999*************999765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   8.3e-05     0.045      90     127 ..      20      58 ..       7      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.3e-05
                                       HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                       +e+++ ++++ ++++++G+ G+GK+tL+ al++ +++k 
  gi|557694771|ref|YP_008797825.1|  20 IEDISVEVRErEIVAVIGPNGAGKTTLMLALAGLATVKS 58 
                                       6777778888799***************99998766665 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   0.00012     0.064       2      30 ..      33      62 ..      32     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                                      EEEEESTTSSHHHHHHHHHTS.TEEESSST CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaivsdkp 30
                                      va++G   +GK+tL+ al g  +++ +++ 
  gi|557694771|ref|YP_008797825.1| 33 VAVIGPNGAGKTTLMLALAGLaTVKSGKTL 62
                                      89****************994344444333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00039      0.21       2      26 ..      30      54 ..      29      81 .. 0.80
   2 ?   -0.7   0.0       2.5   1.3e+03      81     106 ..     204     227 ..     142     237 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00039
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikel 26
                                      r+i+++ G+  +GKTtl+  l+   
  gi|557694771|ref|YP_008797825.1| 30 REIVAVIGPNGAGKTTLMLALAGLA 54
                                      689***************9998544 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.5
                            AAA_14  81 kalkslvdegknldvivtGSnsklls 106
                                       +a + +v eg  +++ + GS   lls
  gi|557694771|ref|YP_008797825.1| 204 TADRAYVMEG--GRITLEGSGTNLLS 227
                                       3333334444..56666666666665 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 ?   12.1   0.1   0.00013     0.071     122     165 ..      23      67 ..      16      79 .. 0.77
   2 ?   -2.8   0.1       4.7   2.6e+03     160     190 ..     174     204 ..     170     212 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                             T2SSE 122 lrkavrerglilvsGgTgsGKttllyal..lkeinksderivtvED 165
                                       ++  vrer ++ v G+ g GKttl+ al  l+++++  + ++  ED
  gi|557694771|ref|YP_008797825.1|  23 ISVEVREREIVAVIGPNGAGKTTLMLALagLATVKSG-KTLLNNED 67 
                                       566799*****************99665115555555.66666666 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.7
                             T2SSE 160 ivtvEDpvEiqleganqvqlnakkakvtfad 190
                                       + + E  +Ei+ +++ ++ +++++a + +++
  gi|557694771|ref|YP_008797825.1| 174 LAVFEKVREIRERQNIAILVVEQDAALALQT 204
                                       5556666677666666666666655555554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00048      0.26       2      22 ..      32      52 ..      31      63 .. 0.85
   2 ?   -0.3   0.0       1.6   8.7e+02     105     159 ..      78     135 ..      67     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00048
                                      CEEEEC-TTTCHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklal 22
                                      +v++ G++G GKTtL+  la 
  gi|557694771|ref|YP_008797825.1| 32 IVAVIGPNGAGKTTLMLALAG 52
                                      689*************98875 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.6
                                       ....HHHHHCTTTTT--EEEEEEECCCHHH.HCTTSSCE....EEEE--TCCHHHHHH CS
                             NACHT 105 vrtlLselirkkllpeasllltvrpralrd.leeqleea..ivlevegfsesrrkqlv 159
                                       v+ l  +l r+ l+p  ++   v ++a r+  +e +++    v+e+ +++e+rrkql+
  gi|557694771|ref|YP_008797825.1|  78 VKGLVLSLERRRLFPDMTVYENVMTGAYRRrDRENIRKDyeMVAELFPIIEKRRKQLA 135
                                       5566677778888888888888877777665666666667677899999999999986 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 ?    4.9   0.0     0.017       9.3     244     265 ..      30      51 ..      25      53 .. 0.88
   2 ?    2.1   0.0      0.12        67     310     348 ..     125     163 ..     109     166 .. 0.83
   3 ?    1.1   0.0      0.25   1.3e+02     377     412 ..     177     212 ..     169     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.017
                                       SSEEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 244 kGvtlIvGggfhGKsTLLeAle 265
                                       + +++++G++  GK+TL+ Al+
  gi|557694771|ref|YP_008797825.1|  30 REIVAVIGPNGAGKTTLMLALA 51 
                                       45999*************9996 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.12
                                       CCC--STTEEESS--HHHHHHHHHHHHHHTT-SEEEEEG CS
                        ABC_ATPase 310 PegkdttkfstedASGStsqAanimealeagakllLiDE 348
                                       P  ++ +k    + SG   q +++++al a+ ++lL+DE
  gi|557694771|ref|YP_008797825.1| 125 PIIEKRRKQLAGTLSGGEQQMVALARALMARPRVLLLDE 163
                                       555555666677789***********************9 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.25
                                       HHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEE CS
                        ABC_ATPase 377 vdrvrelykklgvstilvvggsgdyldvAdtvilme 412
                                        ++vre++++ ++ +++v   +   l+ Ad+  +me
  gi|557694771|ref|YP_008797825.1| 177 FEKVREIRERQNIAILVVEQDAALALQTADRAYVME 212
                                       689***********99999************99997 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   0.00014     0.077       2      20 ..      33      51 ..      32      70 .. 0.86
   2 ?   -1.4   0.1       4.5   2.4e+03      79      79 ..     162     162 ..      98     208 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
                            AAA_28  2 ivitGgestGKTtlleaLa 20
                                      ++++G+ ++GKTtl+ aLa
  gi|557694771|ref|YP_008797825.1| 33 VAVIGPNGAGKTTLMLALA 51
                                      799***************9 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.5
                            AAA_28  79 D 79 
                                       D
  gi|557694771|ref|YP_008797825.1| 162 D 162
                                       3 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0004      0.22      38     112 ..      23     100 ..      16     123 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                             Rad17  38 dvLesrkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdnqksdfkglte..kesrflsqiesfke 111
                                        ++e r+++i+ + GP G gk+t +  L+   ++k  +  ln   +   +  +  +kgl+      r+ + + ++++
  gi|557694771|ref|YP_008797825.1|  23 ISVEVREREIVAVIGPNGAGKTTLMLALAGLATVKSgKTLLNNEDITRLPPYERVVKGLVLslERRRLFPDMTVYEN 99 
                                       567888899***************99999876655414455655554433333444444430034445677777766 PP

                             Rad17 112 l 112
                                       +
  gi|557694771|ref|YP_008797825.1| 100 V 100
                                       5 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00035      0.19      28      57 ..      33      62 ..      22      66 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00035
                              DLIC 28 vlvlGedgsGkttliaklqGveeekkGrGl 57
                                      v v+G +g+Gkttl+  l G+   k G+ l
  gi|557694771|ref|YP_008797825.1| 33 VAVIGPNGAGKTTLMLALAGLATVKSGKTL 62
                                      789*********************999876 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 ?   11.3   0.0   0.00043      0.23      16      41 ..      26      51 ..      18     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlkeii 41
                                      e  ++ei+ + Gp g GKt+L+  ++
  gi|557694771|ref|YP_008797825.1| 26 EVREREIVAVIGPNGAGKTTLMLALA 51
                                      455789****************8765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00065      0.35      16      37 ..      28      47 ..      16      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00065
                                      TTSCSEEEEEEESTTSSHHHHH CS
                            NB-ARC 16 delqslvvalvGmgGvGKttla 37
                                       e    +va+ G  G GKttl+
  gi|557694771|ref|YP_008797825.1| 28 RER--EIVAVIGPNGAGKTTLM 47
                                      344..5***************8 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00051      0.28       5      22 ..      33      50 ..      30      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00051
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      ++++Gp+g+GKTtl++ l
  gi|557694771|ref|YP_008797825.1| 33 VAVIGPNGAGKTTLMLAL 50
                                      789***********9987 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00052      0.28      11      34 ..      25      47 ..      23      50 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00052
                           DUF3584 11 vaeldldghtnieGtNaaGKTtLl 34
                                      v e++ ++ + + G N+aGKTtL+
  gi|557694771|ref|YP_008797825.1| 25 V-EVREREIVAVIGPNGAGKTTLM 47
                                      5.8899999**************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 ?   10.0   0.1    0.0014      0.77      24      47 ..     129     149 ..     108     170 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                           SbcCD_C  24 kelsrssgtlSGGekqflaylala 47 
                                       k+ ++ +gtlSGGe+q++a    a
  gi|557694771|ref|YP_008797825.1| 129 KRRKQLAGTLSGGEQQMVAL---A 149
                                       3467889********65443...3 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 ?    9.4   0.2    0.0013       0.7       3      21 ..      33      51 ..      31      68 .. 0.77
   2 ?   -1.2   0.0       2.4   1.3e+03      71      90 ..     178     196 ..     143     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
                                      EEEEESTTCCHHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhll 21
                                      + + G+ G+GKTtL+ +l 
  gi|557694771|ref|YP_008797825.1| 33 VAVIGPNGAGKTTLMLALA 51
                                      6789**********99887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHTT-SEEEEEE CS
                              cobW  71 kelealeereerldviliEt 90 
                                       ++++++ er+ ++ ++++E+
  gi|557694771|ref|YP_008797825.1| 178 EKVREIRERQ-NIAILVVEQ 196
                                       4455555555.566666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 1681.00
//
Query:       gi|557694772|ref|YP_008797826.1|  [L=447]
Description: amidohydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  151.9   0.0    3.1e-44  151.7   0.0    1.0  1  Amidohydro_1  Amidohydrolase family
    1.7e-16   60.8   0.1    5.8e-15   55.7   0.0    2.8  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 !  151.7   0.0   3.5e-48   3.1e-44       1     344 []      56     412 ..      56     412 .. 0.90

  Alignments for each domain:
  == domain 1  score: 151.7 bits;  conditional E-value: 3.5e-48
                                       EEEE-EEEEEEECETTECSSS...GHHHHH............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga...tledwl............vppetaaealesgiktalksGtttvadmgattstg 62 
                                       ivlPGl++ H H + +l++      l +              ++pe+ + a++ ++ ++  +G+tt+ad g     +
  gi|557694772|ref|YP_008797826.1|  56 IVLPGLVNCHYHSREQLSQTMfpdGLGETTwfnnfclpyhaaLTPEEEKTAFRLALYAMALNGVTTFADGGLL---Y 129
                                       79***********98876555777333333668999************************************8...9 PP

                                       HHHHHHHHHTSSSEEEEEEESSEGGS.....GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHH CS
                      Amidohydro_1  63 iealleaaeelplglrilggkvsldr.....gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeel 134
                                        +  le ++e+   lr+l++  + dr     ++ae   ++  +l++++    +g  +g+++v  +p + +++s+ +l
  gi|557694772|ref|YP_008797826.1| 130 PSTTLETLDEI--PLRCLASTWCWDRadiipKTAEEAFEELTHLHREF----RGGFGGRLDVCATPISVTTCSQKLL 200
                                       **********8..99****************999999*******9999....88889******************** PP

                                       HHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHH CS
                      Amidohydro_1 135 kealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlk 211
                                       +++++ a++ +++  iH+++ ++eve a+  fg      t++ ++ + gll    + + h +hl++++++++     
  gi|557694772|ref|YP_008797826.1| 201 RQVVEWARENNVKTFIHVSSFREEVEKALSTFG-----VTPVQYLFERGLLSR-DVNILHSIHLSMDDVARIVSS-- 269
                                       *********************************.....678888877888888.89999****************.. PP

                                       HHCEEHHHHHHHHSEHHHH...HHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTT.TTHCHCHHHH CS
                      Amidohydro_1 212 eagvahcpfsnsilrsgre...alrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllye.deegglslke 284
                                       +agv++cp s+++ ++g+     + ++l eGv+vglg Dga s   +++l++l l +    gl ++ + ++ l+l++
  gi|557694772|ref|YP_008797826.1| 270 GAGVVSCPYSSLKKGKGISvrgVFPEMLAEGVRVGLGGDGAPSAQHVDMLRTLSLFT----GLCRDiRMNASLPLAK 342
                                       *************888865222699************************99999999....6777787788888776 PP

                                       .HHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC...CT......CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 285 .alrmaTingAkalglddkvGsievGkdADlvvvdl...di......laafvglkkdgnvkkvivkGklv 344
                                        a+r++T  +A+ lgl ++vGs+e+Gk+AD+v++d    d       l ++v+++    v++viv+G++v
  gi|557694772|ref|YP_008797826.1| 343 dAIRFVTSTAADLLGLGHRVGSLEKGKKADIVLLDMrfpDFipvldmLQSVVFSATGAAVDTVIVDGRVV 412
                                       6***********************************88722555666********************998 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.018   1.6e+02       8      20 ..      55      67 ..      55      79 .. 0.84
   2 !   55.7   0.0   6.5e-19   5.8e-15     133     473 .]      76     413 ..      68     413 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.018
                      Amidohydro_3  8 rlvlPGFvDsHtH 20
                                      ++vlPG+v  H H
  gi|557694772|ref|YP_008797826.1| 55 KIVLPGLVNCHYH 67
                                      68*********** PP

  == domain 2  score: 55.7 bits;  conditional E-value: 6.5e-19
                      Amidohydro_3 133 egatgllreg.afhlvldla..plareaeaaavaaalaalasyGitsveagggnvsslddleplfeltaeeklplrv 206
                                        ++ gl +++ +++  +  +  +l++e+e++a++ al a+a +G+t+  a+gg+   + +le+l      ++ plr+
  gi|557694772|ref|YP_008797826.1|  76 MFPDGLGETTwFNNF-CLPYhaALTPEEEKTAFRLALYAMALNGVTTF-ADGGLLYPSTTLETL------DEIPLRC 144
                                       566777776633333.33336455************************.555554333333333......3456777 PP

                      Amidohydro_3 207 i............ikelldaaerlglplspgseeltigavklfadgvlgsrtalltepyftgwpdfedealaelvaa 271
                                                    +k   +a+e+l++ +              f +g +g+  +++t     ++++++++ l+++v++
  gi|557694772|ref|YP_008797826.1| 145 LastwcwdradiiPKTAEEAFEELTHLHR------------EFRGGFGGRLDVCATP---ISVTTCSQKLLRQVVEW 206
                                       66677799988888888888888888888............4455555666667776...6788999888******* PP

                      Amidohydro_3 272 adergldvaihaigdaavd.dvldafeaa.....aekngnqdrr.rlehaegvtesqiervaalqvaagvqpvfnfe 341
                                       a+e+ +   ih+         +l +f  +      e+  +      + h+  ++ ++++r+ + ++    +p +   
  gi|557694772|ref|YP_008797826.1| 207 ARENNVKTFIHVSSFREEVeKALSTFGVTpvqylFERGLLSR-DvNILHSIHLSMDDVARIVSSGAGVVSCPYSSL- 281
                                       ***********9886666657777776655444233333332.246666666699**********99999977766. PP

                      Amidohydro_3 342 delldsrlgperargs...tpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrgg....evlrpdeelsle 411
                                                 ++++g+     + e+l+ gv+v lg D        +p+ ++ +m++t +      +  r++  l+l 
  gi|557694772|ref|YP_008797826.1| 282 ----------KKGKGIsvrGVFPEMLAEGVRVGLGGD-------GAPSAQHVDMLRTLSLFtglcRDIRMNASLPLA 341
                                       ..........3334443466789**************.......55555555555554332555699999999*996 PP

                      Amidohydro_3 412 .ealalyTrgpAkalgledrkGtLevGadADlvvld......adpldvdppelaear...vrltvvdGrvvy 473
                                        +a++ +T+++A +lgl +r G+Le+G++AD+v+ld      +  ld+ ++ +++a+   v  ++vdGrvv+
  gi|557694772|ref|YP_008797826.1| 342 kDAIRFVTSTAADLLGLGHRVGSLEKGKKADIVLLDmrfpdfIPVLDMLQSVVFSATgaaVDTVIVDGRVVV 413
                                       37***********************************998887778888888888779*9**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 3181.96
//
Query:       gi|557694773|ref|YP_008797827.1|  [L=212]
Description: homing endonuclease I-ApeI [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   45.0   0.0    1.2e-08   35.1   0.0    2.2  2  LAGLIDADG_3     LAGLIDADG-like domain
     0.0014   18.7   0.0        1.9    8.6   0.0    2.2  2  LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
  ------ inclusion threshold ------
      0.074   12.6   2.7        1.1    8.8   0.0    2.8  3  LEM             LEM domain


Domain annotation for each model (and alignments):
>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00064       3.8      12      79 ..      40     104 ..      35     106 .. 0.84
   2 !   35.1   0.0   2.1e-12   1.2e-08       3      83 .]     120     193 ..     118     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00064
                                       HHCCECCECSTTTTS.EEEEES-HH.HHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGG CS
                       LAGLIDADG_3  12 daDGsvskskkkgvs.isltssske.lledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlkrFl 79 
                                       ++D +   ++ kg + +++++++++ l ++v   L+rlG   + +       rg y+++++ ++ l  +l
  gi|557694773|ref|YP_008797827.1|  40 SCDAYMGCRRSKGEYvVEFYQKNLSwLCKEVVSRLQRLGFRPRCRVF-----RGRYYRVVVYSKKLYQLL 104
                                       5888999999999999*******77367999999***********99.....888888888887777665 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 2.1e-12
                                       HHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGG CS
                       LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisgenlkrFl 79 
                                       ++ f rG+ da+Gsv +s ++   i++++++ +lle v+r+L++ G++    ++     r+vy l i+++  +  F 
  gi|557694773|ref|YP_008797827.1| 120 MLWFVRGMVDAEGSVITSLHR---ITIWQNDVKLLEAVRRVLENHGLKCGKITR----SRNVYALPIYGRGRMAQFM 189
                                       578*****************9...**********************98555555....599999************* PP

                                       TTTX CS
                       LAGLIDADG_3  80 ekig 83 
                                       ++ig
  gi|557694773|ref|YP_008797827.1| 190 KHIG 193
                                       **98 PP

>> LAGLIDADG_WhiA  WhiA LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00052       3.1      19      71 ..      51     104 ..      46     109 .. 0.79
   2 !    8.6   0.0   0.00032       1.9       4      75 ..     123     193 ..     121     205 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00052
                    LAGLIDADG_WhiA  19 ekkyhLEivspdee.laeqlqkllnefeleakilerrkkyvvylKkaeqIvdlL 71 
                                       + +y  E++ ++ + l++++ + l+++++  + +  r++y  ++  +++  +lL
  gi|557694773|ref|YP_008797827.1|  51 KGEYVVEFYQKNLSwLCKEVVSRLQRLGFRPRCRVFRGRYYRVVVYSKKLYQLL 104
                                       455******999873689***************999988866665666666665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00032
                    LAGLIDADG_WhiA   4 flrGaflasGsindpekkyhLEivspdeelaeqlqkllnefele.akilerrkkyvvylKkaeqIvdlLkiig 75 
                                       f+rG+  a+Gs+    + + + i  +d +l+e++  +l++ +l+  ki++ r+ y + +    + ++++k ig
  gi|557694773|ref|YP_008797827.1| 123 FVRGMVDAEGSVIT--SLHRITIWQNDVKLLEAVRRVLENHGLKcGKITRSRNVYALPIYGRGRMAQFMKHIG 193
                                       99**********98..4489*********************99845999999999998888888888888887 PP

>> LEM  LEM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.28   1.7e+03       9      21 ..      69      81 ..      68      81 .. 0.77
   2 ?    2.1   0.9     0.024   1.4e+02      31      40 .]      95     104 ..      94     104 .. 0.91
   3 ?    8.8   0.0   0.00019       1.1      10      32 ..     154     175 ..     152     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.28
                               LEM  9 eLreeLkkyGvsp 21
                                      e  ++L+++G+ p
  gi|557694773|ref|YP_008797827.1| 69 EVVSRLQRLGFRP 81
                                      6778999999865 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.024
                               LEM  31 lYekKLkkLl 40 
                                       +Y kKL++Ll
  gi|557694773|ref|YP_008797827.1|  95 VYSKKLYQLL 104
                                       8******996 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00019
                               LEM  10 LreeLkkyGvspGPItasTRklY 32 
                                        r+ L  +G+++G It+s R++Y
  gi|557694773|ref|YP_008797827.1| 154 VRRVLENHGLKCGKITRS-RNVY 175
                                       5899**************.***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); 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:                         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: 00:00:00.42
# Mc/sec: 1516.45
//
Query:       gi|557694774|ref|YP_008797828.1|  [L=362]
Description: homing endonuclease I-ApeII [Candidatus Caldiarchaeum subterraneum]
Scores for 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-18   65.2   0.0    2.5e-11   44.5   0.0    2.5  2  LAGLIDADG_1  LAGLIDADG endonuclease
  ------ inclusion threshold ------
       0.14   12.1   0.0       0.26   11.2   0.0    1.4  1  DUF1308      Protein of unknown function (DUF1308)
       0.15   12.4   0.1          2    8.8   0.0    2.7  2  LAGLIDADG_3  LAGLIDADG-like domain
        0.3   11.2   1.2       0.72   10.0   0.2    2.2  2  HECW1_helix  Helical box domain of E3 ubiquitin-protein ligas


Domain annotation for each model (and alignments):
>> LAGLIDADG_1  LAGLIDADG endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   5.5e-15   2.5e-11       1     100 [.      57     156 ..      57     158 .. 0.87
   2 !   18.3   0.0   7.5e-07    0.0034       2     101 ..     226     311 ..     225     312 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 5.5e-15
                                       HHHHHHHHEEEEEEEEETTTTTTSEEEEEEEEEEEE..GGGHHHHHHHHHHHTECEEEEETTTEEEEEEE-SHHHHH CS
                       LAGLIDADG_1   1 laGFiDgdGsfsitvtkskskktslkvqlefqielk..kkdesllekikeylglgsikkrkkdkyvsyiisnssksl 75 
                                       ++GF+DgdGsf i  + +  kk+++ +q++f++el+  ++ e +l+ i++ + +  +    ++ yv++i++n    l
  gi|557694774|ref|YP_008797828.1|  57 ITGFVDGDGSFPIILSPDAGKKFGWLIQPRFEVELRrnEDSEVMLKVICRAMLIRPRIFAGEN-YVKLIVTNRRILL 132
                                       68*****************9****************966666677777888778888888887.********9**** PP

                                       HTHHHHHHHST-SSTHHHHHHHHHH CS
                       LAGLIDADG_1  76 kilipyfdkypllssKyldyldfkk 100
                                       ++++p+f+ky     K ld++ + +
  gi|557694774|ref|YP_008797828.1| 133 EKVVPFFEKY-RPAVKWLDFKIMSE 156
                                       **********.67788888886655 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 7.5e-07
                                       HHHHHHHEEEEEEEEETTTTTTSEEEEEEEEEEEEGGGHHHHHHHHHHHTECEEEEETTTEEEEEEE-SHHHHHHTH CS
                       LAGLIDADG_1   2 aGFiDgdGsfsitvtkskskktslkvqlefqielkkkdesllekikeylglgsikkrkkdkyvsyiisnsskslkil 78 
                                       aGFiD++Gs    v+++++     ++++ ++i+ +  + ++l+ki  +lg+g i+    +   +y + n   +++ +
  gi|557694774|ref|YP_008797828.1| 226 AGFIDAEGSLGFAVNRETR-----SITPYLTITSS--ETDVLRKIRWLLGCGEISGGRLQ---IYGVDN---IVNRV 289
                                       8********7777777771.....26666666666..9****************977665...566666...9**** PP

                                       HHHHHHST-SSTHHHHHHHHHHH CS
                       LAGLIDADG_1  79 ipyfdkypllssKyldyldfkkv 101
                                        p++d+ +l+  K   y+ fk +
  gi|557694774|ref|YP_008797828.1| 290 APFLDRQKLIA-KRTTYKMFKHI 311
                                       ******99986.56788888876 PP

>> DUF1308  Protein of unknown function (DUF1308)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.7e-05      0.26      44      94 ..     288     338 ..     282     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.7e-05
                           DUF1308  44 vleellkgkkLivcetAvedfqeilstvgGpkEkeraeeLlkrievvpDka 94 
                                        +  +l+ +kLi+ +t ++ f++il+tv     k+ ++e ++ +++++ +a
  gi|557694774|ref|YP_008797828.1| 288 RVAPFLDRQKLIAKRTTYKMFKHILETVVRGDHKRNFQETVELVNMLNKTA 338
                                       56778999********************99999999999999999987655 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.21   9.2e+02       7      17 ..      57      67 ..      52      70 .. 0.85
   2 ?    8.8   0.0   0.00045         2       5      44 ..     223     267 ..     220     328 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.21
                                      HHHHHHHCCEC CS
                       LAGLIDADG_3  7 LrGlfdaDGsv 17
                                      + G+ d+DGs+
  gi|557694774|ref|YP_008797828.1| 57 ITGFVDGDGSF 67
                                      679******97 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00045
                                       HHHHHHHHHCCECCECSTTTTS.....EEEEES-HHHHHHHHHHH CS
                       LAGLIDADG_3   5 afLrGlfdaDGsvskskkkgvs.....isltssskelledvqrlL 44 
                                        + +G++da+Gs     ++ ++     +++tss+ ++l++++ lL
  gi|557694774|ref|YP_008797828.1| 223 HYVAGFIDAEGSLGFAVNRETRsitpyLTITSSETDVLRKIRWLL 267
                                       6899*******96433333333346789************99888 PP

>> HECW1_helix  Helical box domain of E3 ubiquitin-protein ligase HECW1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.5   6.7e+03      37      49 ..     173     185 ..     170     193 .. 0.76
   2 ?   10.0   0.2   0.00016      0.72      34      65 ..     306     336 ..     296     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.5
                       HECW1_helix  37 khmvskirrdpek 49 
                                       k +v ki + p+ 
  gi|557694774|ref|YP_008797828.1| 173 KEIVRKIYSIPRD 185
                                       8999999887765 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00016
                       HECW1_helix  34 silkhmvskirrdpekferYqhnrdlVallNl 65 
                                       ++ kh+++ + r  +   ++q  ++lV++lN+
  gi|557694774|ref|YP_008797828.1| 306 KMFKHILETVVRGDH-KRNFQETVELVNMLNK 336
                                       689******999655.578************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2804.20
//
Query:       gi|557694775|ref|YP_008797829.1|  [L=241]
Description: homing endonuclease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   28.9   0.0     0.0022   18.3   0.0    2.3  2  LAGLIDADG_3  LAGLIDADG-like domain
  ------ inclusion threshold ------
       0.07   14.1   0.1        4.7    8.2   0.0    2.5  2  LAGLIDADG_1  LAGLIDADG endonuclease


Domain annotation for each model (and alignments):
>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00033         3      14      83 .]      31     101 ..      22     101 .. 0.89
   2 !   18.3   0.0   2.4e-07    0.0022       5      80 ..     127     205 ..     125     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00033
                                       CCECCECSTTTTS....EEEEES-HHHHHHHHHHHH.HCT.HSCEEEEEEE-SCCCCECCCHCHCTTCGGGTTTX CS
                       LAGLIDADG_3  14 DGsvskskkkgvs....isltssskelledvqrlLl.rlGIestiyekkkakgrgvyrlliisgenlkrFlekig 83 
                                       DG+v k  +++++    i++++++   l ++++  +   G++ ++  +     + +++l+ +s+  ++ F+ek g
  gi|557694775|ref|YP_008797829.1|  31 DGYVGKYTDNHGKihyvITVYNKDVYWLHQLAEFFEtIYGVKPKLNIT----PNRTPYLRLYSRTLVQYFAEKFG 101
                                       999999999999989999999999999999999999889999999999....666666************99976 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 2.4e-07
                                       HHHHHHHHHCCECCECSTTTTSEEEEES-....HHHHHHHHHHHHHCT.HSCEEEE..EEE-SCCCCECCCHCHCTT CS
                       LAGLIDADG_3   5 afLrGlfdaDGsvskskkkgvsisltsss....kelledvqrlLlrlGIestiyek..kkakgrgvyrlliisgenl 75 
                                        +++G+fda+G ++ +++    i++ +s        l d++  L+r+  + t      +++kg+    +l+i + + 
  gi|557694775|ref|YP_008797829.1| 127 SYIAGYFDAEGGIDINRRQ---IKFHTSWdgdtCPPLMDIKIALARFFEIRTGEVCmyRNDKGNIPRFVLRILKADN 200
                                       689**************99...9999887677788899999999998666666666765555555557777777777 PP

                                       CGGGT CS
                       LAGLIDADG_3  76 krFle 80 
                                       +rF++
  gi|557694775|ref|YP_008797829.1| 201 ERFFK 205
                                       77765 PP

>> LAGLIDADG_1  LAGLIDADG endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.013   1.1e+02      28      56 ..      43      72 ..      24     102 .. 0.75
   2 ?    8.2   0.0   0.00052       4.7       1      25 [.     129     152 ..     129     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.013
                                      EEEEEEEEEGGGHHHHHHHHHHHT.ECEEE CS
                       LAGLIDADG_1 28 qlefqielkkkdesllekikeylg.lgsik 56
                                      ++++ i++ +kd++ l +++e+++ ++ +k
  gi|557694775|ref|YP_008797829.1| 43 KIHYVITVYNKDVYWLHQLAEFFEtIYGVK 72
                                      56677888899***********99755444 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00052
                                       HHHHHHHHEEEEEEEEETTTTTTSE CS
                       LAGLIDADG_1   1 laGFiDgdGsfsitvtkskskktsl 25 
                                       +aG++D++G + i+  + k   ts+
  gi|557694775|ref|YP_008797829.1| 129 IAGYFDAEGGIDINRRQIK-FHTSW 152
                                       79************99888.45555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1796.49
//
Query:       gi|557694776|ref|YP_008797830.1|  [L=460]
Description: dehydrogenase (flavoprotein)-like protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-08   34.5   0.8    2.6e-08   33.6   0.8    1.4  1  FAD_oxidored   FAD dependent oxidoreductase
    2.7e-08   33.8   0.5     0.0016   18.1   0.0    2.4  2  DAO            FAD dependent oxidoreductase
    4.1e-07   29.6   0.9    0.00036   19.9   0.2    2.2  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    6.9e-07   28.3   4.9    0.00066   18.5   0.0    2.8  3  HI0933_like    HI0933-like protein
    4.3e-06   26.0   0.6    0.00032   19.9   0.1    2.1  2  Lycopene_cycl  Lycopene cyclase protein
    6.8e-06   25.6   9.1    2.2e-05   23.9   3.0    2.9  2  FAD_binding_3  FAD binding domain
    1.7e-05   24.3   2.4      0.031   13.5   0.1    2.8  3  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.2e-05   23.8   0.1    6.8e-05   22.2   0.1    1.8  1  Thi4           Thi4 family
      0.001   18.2   0.3     0.0098   15.0   0.2    2.2  2  FAD_binding_2  FAD binding domain
     0.0021   17.4   3.1       0.13   11.5   0.0    3.0  3  Amino_oxidase  Flavin containing amine oxidoreductase
  ------ inclusion threshold ------
      0.016   15.4   0.0      0.052   13.8   0.0    1.9  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
       0.02   15.4   0.7        3.4    8.3   0.1    2.6  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.029   13.5   3.0       0.12   11.4   0.0    2.3  2  GIDA           Glucose inhibited division protein A
        1.6    8.4   4.9       0.29   10.9   0.2    2.1  3  TfuA           TfuA-like protein


Domain annotation for each model (and alignments):
>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.8   2.1e-11   2.6e-08       1     136 [.      86     228 ..      86     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.1e-11
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee.qvvtgiareflerlrq..rggar 74 
                                       DvvVvGG + G++AA  +a++G ++++ ee++v+G     +++ +++g ++ +  v++   + +++        g+r
  gi|557694776|ref|YP_008797830.1|  86 DVVVVGGSSTGLIAARESAKRGLRTVVFEEDKVIGRPEKCAGLYSIEGVRSLNiPVQGPYLQNIVRGAVFvsPSGKR 162
                                       9**********************************999999999999988666666666777777766554322222 PP

                      FAD_oxidored  75 lk..krskwn....tfepevakavleemlaeagvtvllntrlvevekegkriesvtveske.g.rktirA 136
                                        +  +    +    +++ e +   l +  aeag ++  +tr++ev+ +g++   v++ s++   r++i+A
  gi|557694776|ref|YP_008797830.1| 163 FEvdAS---RdvavVYNRERLDLFLAQQAAEAGAEIHVDTRVTEVKSSGQN-LIVKTSSQTiStRHVISA 228
                                       222122...133459********************************9843.333333222222555544 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   2.8e-05     0.036       1      33 [.      86     120 ..      86     128 .. 0.93
   2 !   18.1   0.0   1.3e-06    0.0016     141     258 ..     172     284 ..     166     316 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.8e-05
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33 
                                       dvv++GG  +Gl +A+e a+rg  ++++e ++ +g
  gi|557694776|ref|YP_008797830.1|  86 DVVVVGGSSTGLIAARESAKRGlrTVVFEEDKVIG 120
                                       9****************************997776 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.3e-06
                                       EEE.EHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTTCTTT CS
                               DAO 141 gqv.dpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gllkeld 214
                                       ++v + ++l  +la++a+++G+ei+  t+vt+++  +g+   v  +t+  ++++ ++v+ a G  ++ + ++l++ +
  gi|557694776|ref|YP_008797830.1| 172 AVVyNRERLDLFLAQQAAEAGAEIHVDTRVTEVKS-SGQNLIV--KTSsQTIST-RHVISAEGRTATVArQMLPRYR 244
                                       55668889999**********************65.4454444..665344444.99****9977777767776554 PP

                                       .SEEEEEEEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEE CS
                               DAO 215 .lpispvrgqvlvlkplseklvspaailpvpetdddgrgvyvtpr 258
                                         +  p+  ++++         sp+ ++ ++++  +++  y++p 
  gi|557694776|ref|YP_008797830.1| 245 tGKWLPIIQYMIANHGN-----SPDMVYLYFKKYLPEFFGYLVPV 284
                                       36778888888887332.....33444444554455555566664 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 !    8.2   0.0     0.001       1.3     157     201 ..      77     121 ..      56     132 .. 0.81
   2 !   19.9   0.2   2.8e-07   0.00036      83     134 ..     180     231 ..     154     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.001
                       Pyr_redox_3 157 kefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiek 201
                                       k+++   + +vvV+Gg+ ++  aA e +++g +  v+ +++ i +
  gi|557694776|ref|YP_008797830.1|  77 KKLMAEMDYDVVVVGGSSTGLIAARESAKRGLRTVVFEEDKVIGR 121
                                       4455556889***********************999999988776 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 2.8e-07
                       Pyr_redox_3  83 aleYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                       +  +l++ a++   +i+ +++V++vk+++++ +v+ts++t+++++vi A G+
  gi|557694776|ref|YP_008797830.1| 180 LDLFLAQQAAEAGAEIHVDTRVTEVKSSGQNLIVKTSSQTISTRHVISAEGR 231
                                       555677788889999**********************************996 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   5.1e-07   0.00066       1      38 [.      85     122 ..      85     132 .. 0.91
   2 !   10.9   0.2    0.0001      0.13     114     164 ..     183     231 ..     174     236 .. 0.88
   3 ?   -1.3   0.2      0.54   6.9e+02     374     393 ..     334     354 ..     329     362 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.1e-07
                                       -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like   1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38 
                                       +dv+v+Gg   Gl aA + akrg r++++e+ k +gr 
  gi|557694776|ref|YP_008797830.1|  85 YDVVVVGGSSTGLIAARESAKRGLRTVVFEEDKVIGRP 122
                                       59********************************9985 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       +l +++ eag +++++t+v++v++ +++++ vkt s++++++++++ A G 
  gi|557694776|ref|YP_008797830.1| 183 FLAQQAAEAGAEIHVDTRVTEVKS-SGQNLIVKT-SSQTISTRHVISAEGR 231
                                       588999****************66.6666*****.9**********99885 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.54
                                       TSTTEEE-GGGB.SEEE-TTT CS
                       HI0933_like 374 kvpgLffaGEvl.DvegvtGG 393
                                       +v + f+aGEv   v++ tGG
  gi|557694776|ref|YP_008797830.1| 334 RVGNFFLAGEVAgQVKATTGG 354
                                       67899******8579999999 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   2.5e-07   0.00032       1     145 [.      86     234 ..      86     251 .. 0.80
   2 ?    4.6   0.0     0.011        14     241     308 ..     322     388 ..     295     458 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.5e-07
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlgaleecvehsWsgtivyl.....ddg 72 
                                       Dvvv+G+   gl  A ++  ak gl+ v+ e  + + +p +    +  e++ +l+  v+  + + iv+      + g
  gi|557694776|ref|YP_008797830.1|  86 DVVVVGGSSTGLIAARES--AKRGLRTVVFEEDKVIGRPEKCAGLYSIEGVRSLNIPVQGPYLQNIVRGavfvsPSG 160
                                       9************99999..**********99999999999999999999999777777777766666511111566 PP

                     Lycopene_cycl  73 kkillg..raYgrv.sskrlkeellerlvengvk.lleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                       k+ +++  r  + v +++rl   l+++ +e+g++  ++ +v++v+ + +   l+v    ++i  r v+ a g   ++
  gi|557694776|ref|YP_008797830.1| 161 KRFEVDasRDVAVVyNRERLDLFLAQQAAEAGAEiHVDTRVTEVKSSGQ--NLIVKTSSQTISTRHVISAEGR-TAT 234
                                       77777766555555579************88876157899999987765..9999999**************4.333 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.011
                     Lycopene_cycl 241 gviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalresslsarawatlw 308
                                       + i v  gg+l+ +     + +G  ag v+ +TG  v+   ++a+  a+ ia  +  ++l+++  ++l 
  gi|557694776|ref|YP_008797830.1| 322 SAIYV--GGPLEPMRVGnFFLAGEVAGQVKATTGGGVVTGGKAAEAAAQHIAGQGTYEQLYRETLHELK 388
                                       55556..777666554426789******************************99998888777666554 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   3.0   1.7e-08   2.2e-05       2     172 ..      85     239 ..      84     249 .. 0.79
   2 ?    0.6   0.4      0.21   2.7e+02     279     307 ..     331     359 ..     326     373 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 1.7e-08
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyn 78 
                                       +dV++VG++ +Gl++a++ +++G r+v+ e  +   +  +  gl   ++e  r+l +     +  + +++++ a+  
  gi|557694776|ref|YP_008797830.1|  85 YDVVVVGGSSTGLIAARESAKRGLRTVVFEEDKVIGRPEKCAGLY--SIEGVRSLNIP---VQGPYLQNIVRGAVFV 156
                                       79****************************998887777877774..45555555544...3444444555555555 PP

                                       ECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEE CS
                     FAD_binding_3  79 elsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvra 155
                                       +      +  + e+++s     vy+ ++l+  L+++a+e+g++++ +t+v+ ++  +++    v+   t   +t++ 
  gi|557694776|ref|YP_008797830.1| 157 S-----PSGKRFEVDASRDVAVVYNRERLDLFLAQQAAEAGAEIHVDTRVTEVKSSGQNL--IVK---TSS-QTIST 222
                                       5.....57778888899**********************************777766662..333...333.49*** PP

                                       EEEEE--GTT-HHHHHH CS
                     FAD_binding_3 156 kYlvGaDGgrStvrktl 172
                                       + ++ a+G   tv++++
  gi|557694776|ref|YP_008797830.1| 223 RHVISAEGRTATVARQM 239
                                       **********9998875 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.21
                                       SSSEETTEEE-GGGTEEE-STTSHHHHHH CS
                     FAD_binding_3 279 ekyrkgrvflaGDAaHihpPtgGqGlNta 307
                                       e++r g+ flaG  a  +  t+G G+ t+
  gi|557694776|ref|YP_008797830.1| 331 EPMRVGNFFLAGEVAGQVKATTGGGVVTG 359
                                       789********************998777 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 !   13.5   0.1   2.5e-05     0.031       1      33 [.      85     117 ..      85     154 .. 0.87
   2 !    9.6   0.2   0.00038      0.48     183     240 ..     178     234 ..     152     246 .. 0.84
   3 ?   -2.8   0.0       2.3   2.9e+03     243     270 ..     287     313 ..     282     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlveleg 33 
                                       +dvvv+Gg   Gl aa++ a+ g++++++e+++
  gi|557694776|ref|YP_008797830.1|  85 YDVVVVGGSSTGLIAARESAKRGLRTVVFEEDK 117
                                       69***************************6444 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00038
                                       HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 183 kelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrps 240
                                       ++l  +l+++  + G e+++ t+v+e+++ g++l  v ++ ++i ++ v+ a G+++ 
  gi|557694776|ref|YP_008797830.1| 178 ERLDLFLAQQAAEAGAEIHVDTRVTEVKSSGQNL-IVKTSSQTISTRHVISAEGRTAT 234
                                       55667888999999*****************944.67777788***********9986 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.3
                                       HCSHCCT-EEEETTEEE--TTSBESSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 243 lleeklglelderggivvdeflrtnvpg 270
                                        +  klg++  ++ +++vd+ lr n p+
  gi|557694776|ref|YP_008797830.1| 287 EF-GKLGVAASKGTQLLVDKLLRENFPH 313
                                       34.7899999999999999999988876 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   5.3e-08   6.8e-05      10      54 ..      77     120 ..      70     129 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.3e-08
                                       HHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS-- CS
                              Thi4  10 edllkyaesDvvivGaGssGLtaayylakkpdlkvailersvspG 54 
                                       ++l+  ++ Dvv+vG+ s+GL aa+  ak+ +l+++++e+   +G
  gi|557694776|ref|YP_008797830.1|  77 KKLMAEMDYDVVVVGGSSTGLIAARESAKR-GLRTVVFEEDKVIG 120
                                       567778899*********************.********976666 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   7.6e-06    0.0098       1      33 [.      86     118 ..      86     128 .. 0.92
   2 ?    0.8   0.0      0.15     2e+02      51     103 ..     158     211 ..     151     320 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.6e-06
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                       Dv+V+G+   GL AA e a++Gl+++v e  ++
  gi|557694776|ref|YP_008797830.1|  86 DVVVVGGSSTGLIAARESAKRGLRTVVFEEDKV 118
                                       9***************************98876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.15
                                       .SSGGSTC.CHHHHHHHHHHHHTTT-S-HHHHHHHHH.THHHHHHHHHHTT--- CS
                     FAD_binding_2  51 peqkkagikdspelhrtdtlkaldeladqplveafve.aapeavdeLeelgvpf 103
                                       p  k+ +++ s++ ++ + ++ ld   +q+++ea++e ++   v+e ++ g  +
  gi|557694776|ref|YP_008797830.1| 158 PSGKRFEVDASRDVAVVYNRERLDLFLAQQAAEAGAEiHVDTRVTEVKSSGQNL 211
                                       556677777788888888888888777888888888888888777777765444 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.02        26       2      27 ..      95     120 ..      94     120 .. 0.95
   2 !   11.5   0.0    0.0001      0.13     218     259 ..     186     228 ..     173     272 .. 0.85
   3 ?    1.0   0.4      0.16     2e+02     418     450 ..     334     365 ..     312     367 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHTTEEEEEEESSSSSB CS
                     Amino_oxidase   2 aGLaaArqLlsaGfdVtvlEardrvG 27 
                                       +GL+aAr+ + +G++++v+E +  +G
  gi|557694776|ref|YP_008797830.1|  95 TGLIAARESAKRGLRTVVFEEDKVIG 120
                                       7*******************999998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0001
                                       H..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE- CS
                     Amino_oxidase 218 e..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvT 259
                                       +   + g +i+++trV+e+k +g    v++ ++++++ ++V+++
  gi|557694776|ref|YP_008797830.1| 186 QqaAEAGAEIHVDTRVTEVKSSGQNLIVKT-SSQTISTRHVISA 228
                                       334479**************9777777765.56667******98 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.16
                                       CSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHH CS
                     Amino_oxidase 418 gdprlffAGehtsreypgtvegAilSGlraAar 450
                                        ++++f+AGe  + ++ +t+ g + +G +aA++
  gi|557694776|ref|YP_008797830.1| 334 RVGNFFLAGEV-AGQVKATTGGGVVTGGKAAEA 365
                                       579*******9.56999**************87 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 ?   13.8   0.0   4.1e-05     0.052       1      32 [.      89     120 ..      89     125 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.1e-05
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32 
                                       +vG+  +Gl aA++ ak+g++ +++e    +G
  gi|557694776|ref|YP_008797830.1|  89 VVGGSSTGLIAARESAKRGLRTVVFEEDKVIG 120
                                       8*************************998887 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0026       3.4       2      35 ..      87     120 ..      86     141 .. 0.85
   2 ?    4.8   0.0     0.032        42      45      72 ..     183     210 ..     166     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0026
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35 
                                       vvvvGg+ +gl +A + a+ g ++ v+e  + + 
  gi|557694776|ref|YP_008797830.1|  87 VVVVGGSSTGLIAARESAKRGLRTVVFEEDKVIG 120
                                       8********************9999998776665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.032
                                       HHHHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  45 ilqeklekngievllntkveeiegsedg 72 
                                        l+++  + g e++ +t+v+e++ s+++
  gi|557694776|ref|YP_008797830.1| 183 FLAQQAAEAGAEIHVDTRVTEVKSSGQN 210
                                       567788999**************99887 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   0.0   9.6e-05      0.12       1      30 [.      86     115 ..      86     138 .. 0.86
   2 ?    1.5   0.9     0.096   1.2e+02     350     389 ..     330     367 ..     319     370 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.6e-05
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLith 30 
                                       dv+V+Gg   G+ AA ++a++G++++ + +
  gi|557694776|ref|YP_008797830.1|  86 DVVVVGGSSTGLIAARESAKRGLRTVVFEE 115
                                       79************************9933 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.096
                                       SBBSSSBTEEE-CGGGTB-SHHHHHHHHHHHHHHHHHHHC CS
                              GIDA 350 LetkkvkgLflAGqinGteGYeEaaaqGllAGinaarkak 389
                                       Le  +v + flAG++ G     + ++ G+++G  aa  a+
  gi|557694776|ref|YP_008797830.1| 330 LEPMRVGNFFLAGEVAGQV--KATTGGGVVTGGKAAEAAA 367
                                       6677899*********998..7889999**9999998765 PP

>> TfuA  TfuA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00022      0.29       8      47 ..      72     111 ..      67     115 .. 0.88
   2 ?   -2.3   0.0       2.7   3.5e+03      58      76 ..     164     182 ..     152     228 .. 0.57
   3 ?   -3.0   0.2       4.4   5.6e+03      35      57 ..     361     383 ..     350     389 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                              TfuA   8 pavahkEilaalkegvavvGaasmGALRAaElaafGmigv 47 
                                       +a   k ++a ++ +v vvG++s G + A E a+ G++ v
  gi|557694776|ref|YP_008797830.1|  72 KAYIAKKLMAEMDYDVVVVGGSSTGLIAARESAKRGLRTV 111
                                       5667789999************************999865 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.7
                              TfuA  58 eledDdeVavlhapaelgy 76 
                                       e+++  +Vav+++ + l++
  gi|557694776|ref|YP_008797830.1| 164 EVDASRDVAVVYNRERLDL 182
                                       4555567777776665432 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 4.4
                              TfuA  35 RAaElaafGmigvGeiyeayrsg 57 
                                       +AaE aa  + g G+  + yr++
  gi|557694776|ref|YP_008797830.1| 361 KAAEAAAQHIAGQGTYEQLYRET 383
                                       78999999999999877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3457.21
//
Query:       gi|557694777|ref|YP_008797831.1|  [L=347]
Description: pyruvate dehydrogenase E1 component subunit alpha [Candidatus Caldiarchaeum subterraneum]
Scores for 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-85  285.3   0.0    4.8e-85  285.1   0.0    1.0  1  E1_dh           Dehydrogenase E1 component
      7e-06   25.9   1.3      9e-05   22.3   0.3    2.5  2  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
    1.3e-05   24.5   0.0    2.2e-05   23.8   0.0    1.3  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
  ------ inclusion threshold ------
      0.029   15.4   0.0      0.054   14.5   0.0    1.4  1  RNase_J_C       Ribonuclease J C-terminal domain


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  285.1   0.0   1.1e-88   4.8e-85       2     298 ..      25     320 ..      24     322 .. 0.96

  Alignments for each domain:
  == domain 1  score: 285.1 bits;  conditional E-value: 1.1e-88
                                       HHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-TT CS
                             E1_dh   2 klvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkvk 78 
                                       + ++ +rv+d+  + ++r ++ig+ ++s gqea++vg a al  +D+i++ YRe +v++ar +++  i+     +  
  gi|557694777|ref|YP_008797831.1|  25 RDMVCARVLDRWLMRLQRMGKIGIHAPSEGQEAAGVGTAYALGTNDWIFPLYRELPVFVARRVPIADIVNRNLANSA 101
                                       67999************************************************************************ PP

                                       TSSGTT-.-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EE CS
                             E1_dh  79 gkggsrhelmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvi 155
                                       + +++r    y+  + ri+++ ++v+   p + G al  k+++  ev+i ++GDgA+++Gd++ealn+a ++k+p++
  gi|557694777|ref|YP_008797831.1| 102 DPLKGRDFAVYGDIKHRIVPAPIPVAVHIPSAVGFALSLKYKKLSEVVINYFGDGATSKGDFHEALNFAGVFKAPIV 178
                                       *******566688888************************************************************* PP

                                       EEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SST CS
                             E1_dh 156 fvveNNkygisTeaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyggHse 232
                                       fv++NN+y+is+++++++a+++l+ +a+++g  g+ VdgnD++a+y A+k A+e ar+g+gp+lie+vtYR+g+H++
  gi|557694777|ref|YP_008797831.1| 179 FVCVNNQYAISVPVSRQTAVEHLSLKAAAYGFEGVSVDGNDVVACYLAAKKAVEKARRGEGPTLIEAVTYRIGPHTT 255
                                       ***************************************************************************** PP

                                       TSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS---- CS
                             E1_dh 233 sDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskkele 298
                                        Ddps+yr  +eve +r   dpi+rl+ +L  +g++s ee++++ +  ++ ++ ++++ e++  l+
  gi|557694777|ref|YP_008797831.1| 256 ADDPSRYRDDKEVEMWRRR-DPITRLRSHLLRRGLWSMEEDEKLWRTTEQTIQKTIEECEKNRPLP 320
                                       ********88888777766.**************************************99987665 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 ?   -2.5   0.0      0.88     4e+03       8      40 ..      36      68 ..      33      70 .. 0.70
   2 !   22.3   0.3     2e-08     9e-05      33     152 ..     129     244 ..     124     245 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.88
                                      HHHHHHTTSSSSEEECETTTS-TTTHHHHHHHH CS
                      TPP_enzyme_C  8 waarllkvkrprsyltsgglgtmGyglpaAiGa 40
                                      w+ rl ++ + +    s g  + G+g ++A+G 
  gi|557694777|ref|YP_008797831.1| 36 WLMRLQRMGKIGIHAPSEGQEAAGVGTAYALGT 68
                                      666665555554444588999999999999995 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 2e-08
                                       HHHHHHHHHH....HSTTSEEEEEEEHHHHHHT.GGGHHH.HHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTTTS CS
                      TPP_enzyme_C  33 glpaAiGakl....akpdrevvaivGDGgflmi.lqelat.avrrnlpitvvvlnNegygmtggqqepfggkrksgp 103
                                        +p A+G +l    +k ++ v+ + GDG++    ++e  + a   ++pi++v++nN++   +    + + +      
  gi|557694777|ref|YP_008797831.1| 129 HIPSAVGFALslkyKKLSEVVINYFGDGATSKGdFHEALNfAGVFKAPIVFVCVNNQYAISVPVSRQTAVE------ 199
                                       68999999996532233689*********998886665551566788**********98666555333332...... PP

                                       BB.BS----HHHHHHHTTSEEEEESSH.HHHH....HHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C 104 agkdlkpvdfaklaealGakgarvekadveel....eealkealekkgpalie 152
                                               ++   a+a+G +g++v+ +dv       ++a+++a++ +gp+lie
  gi|557694777|ref|YP_008797831.1| 200 --------HLSLKAAAYGFEGVSVDGNDVVACylaaKKAVEKARRGEGPTLIE 244
                                       ........223336677777665554444433333388899999999***998 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 !   23.8   0.0     5e-09   2.2e-05     117     181 ..     130     194 ..     126     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 5e-09
                    DXP_synthase_N 117 isaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisknvGa 181
                                       i  a+G+a + ++k+ ++ v+   GDga + G  +ealn +g  k+ ++ +  +N+ +is +v  
  gi|557694777|ref|YP_008797831.1| 130 IPSAVGFALSLKYKKLSEVVINYFGDGATSKGDFHEALNFAGVFKAPIVFVCVNNQYAISVPVSR 194
                                       67899*******************************************************99864 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.054       5      40 ..     285     320 ..     283     331 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                         RNase_J_C   5 vsRGfvyvkeseeLieeakkvvretieealeekesd 40 
                                       + RG   ++e+e+L + +++++++tiee+++++   
  gi|557694777|ref|YP_008797831.1| 285 LRRGLWSMEEDEKLWRTTEQTIQKTIEECEKNRPLP 320
                                       67****************************997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 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:                        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: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2852.32
//
Query:       gi|557694778|ref|YP_008797832.1|  [L=135]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-05   24.5   0.3    2.7e-05   24.0   0.3    1.2  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.094   12.7   0.4       0.14   12.2   0.4    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated


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 !   24.0   0.3     3e-09   2.7e-05       3      32 ..      21      50 ..      19      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3e-09
                           DUF35_N  3 aaaegrLvgqrCpdCGtvqfPPravCphCg 32
                                      ++  g+++++rC +C + ++PPra+C  C+
  gi|557694778|ref|YP_008797832.1| 21 GLHNGKIIASRCGKCSSKHVPPRAYCLDCF 50
                                      556799***********************8 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 ?   12.2   0.4   1.5e-05      0.14       2      65 .]      57     118 ..      56     118 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.5e-05
                                       EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                     OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                       +e+ + ++v ++t  ++ ++g+ + +  v++ V++ +    + ++ ++     r Gm+V+ vfr
  gi|557694778|ref|YP_008797832.1|  57 IEVDPAAVVQTYTRSRMLADGE-AGEEIVWVFVRFVDTLGGLLHMLDPSKT-PRTGMKVKPVFR 118
                                       688999*******999999555.556689********88888888877765.58********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1141.51
//
Query:       gi|557694779|ref|YP_008797833.1|  [L=211]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   3.6    2.2e-08   33.8   3.6    1.4  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
    1.6e-08   34.5   0.3    2.5e-08   33.8   0.3    1.3  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
  ------ inclusion threshold ------
      0.045   13.8   0.1      0.075   13.1   0.1    1.3  1  DZR            Double 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 !   33.8   3.6   3.7e-12   2.2e-08       2      29 ..      77     104 ..      76     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.7e-12
                           DUF35_N   2 daaaegrLvgqrCpdCGtvqfPPravCp 29 
                                       ++++egrL g+rC+ CG+v  PPr +C 
  gi|557694779|ref|YP_008797833.1|  77 QGLREGRLFGTRCSGCGRVLIPPRLFCE 104
                                       79*************************6 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 !   33.8   0.3   4.2e-12   2.5e-08       1      65 []     113     191 ..     113     191 .. 0.99

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 4.2e-12
                                       EEEE-GG-EEEEEEEEEE-T.TS-EEEEEEEEEEEE-TT................-EE-EEEEEEES..TT-B-EEE CS
                     OB_aCoA_assoc   1 wvelsgrGtvysftvvhrap.pgfaeeaPyvvgvVeLdegvr.............imarlvgvdpdevriGmrVrav 63 
                                       wve  g+++v +++  +    pg +  +P +v+v  + + vr             +m+ + ++ p++vriGmrV+ v
  gi|557694779|ref|YP_008797833.1| 113 WVEHNGEAVVSTYSLAYIGTdPGVRLAEPNIVAVLWFKDTVRetpssktvfhaagLMHIIRECGPGDVRIGMRVKPV 189
                                       9**************************************************************************** PP

                                       -S CS
                     OB_aCoA_assoc  64 fr 65 
                                       ++
  gi|557694779|ref|YP_008797833.1| 190 WK 191
                                       96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.3e-05     0.075      27      48 ..      74     106 ..      53     107 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
                               DZR  27 a...........edrCpsCgekvdpearfCpeC 48 
                                       +            +rC+ Cg+ + p   fC  C
  gi|557694779|ref|YP_008797833.1|  74 KflqglregrlfGTRCSGCGRVLIPPRLFCEWC 106
                                       244455566666799*****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.35
# Mc/sec: 1809.83
//
Query:       gi|557694780|ref|YP_008797834.1|  [L=384]
Description: acetyl-CoA C-acetyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-10   39.9   0.0    6.1e-09   35.6   0.0    2.5  1  Thiolase_N     Thiolase, N-terminal domain
    1.1e-05   25.1   0.0      0.016   14.9   0.0    3.3  3  Thiolase_C     Thiolase, C-terminal domain
  ------ inclusion threshold ------
      0.019   15.1   0.0       0.36   11.0   0.0    2.6  3  DXP_redisom_C  1-deoxy-D-xylulose 5-phosphate reductoisomeras
       0.11   12.1   0.5       0.23   11.1   0.1    1.6  2  ThiJ_like      ThiJ/PfpI family-like
       0.24   11.3   0.2       0.54   10.1   0.0    1.5  2  DUF2797        Protein of unknown function (DUF2797)


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 !   35.6   0.0   1.7e-12   6.1e-09       1     259 [.       5     222 ..       5     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.7e-12
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSE CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevp 77 
                                       v+iv+a +t + +    +  +++ee+  ea++++l++ag+d+ +vd v+ G    a++g   +  +a++   +   p
  gi|557694780|ref|YP_008797834.1|   5 VAIVGAGMTYFRS----MLPMTSEEMVFEAVRKCLDDAGLDAGDVDAVVGGSAPDAFDGYHHKGLVAVEPSGAFAKP 77 
                                       79**********9....7889999*************************************9999999988889999 PP

                                       EEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSE CS
                        Thiolase_N  78 avtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneeh 154
                                       +++v    + g+   + ++  +a+g +d v+++  E+ms+ +  ++  +rs  +    ++++ l p+ +        
  gi|557694780|ref|YP_008797834.1|  78 FSRVFVGGGTGVGVAISGWWHVASGLFDKVLVVAWEKMSHPYPHAQPLFRSIFEP---ILEQPLGPNLI------WI 145
                                       99999999999999999***********************877666566554443...33334444411......24 PP

                                       HHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-B CS
                        Thiolase_N 155 mGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkp 231
                                        +l  +++ +k+++ +e  +++Avk++++a + + ++ +  +i              + d+ ++s+v + ++++l  
  gi|557694780|ref|YP_008797834.1| 146 FALEMRRYMEKHALEKELIARVAVKNKANALDHPYSQ-LGAKI--------------TVDDVLKSPVLVWPVHRL-- 205
                                       7999***************************999999.77767..............677777777877777777.. PP

                                       SSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 232 aFkkeGtvtAgnasqisDGaaavllmse 259
                                                  + s+ sDGa a+l++se
  gi|557694780|ref|YP_008797834.1| 206 -----------DISPTSDGAVALLFASE 222
                                       ...........77888888877777776 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.4   0.0    0.0075        27      26      45 ..      29      48 ..      17      60 .. 0.89
   2 ?    1.5   0.0     0.059   2.1e+02      67      92 ..     165     190 ..     146     195 .. 0.79
   3 !   14.9   0.0   4.5e-06     0.016      26     117 ..     260     370 ..     252     376 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0075
                                      HHHHHHHHHHT--GGGESEE CS
                        Thiolase_C 26 yaikkvlkkagltvedidlf 45
                                       a++k+l++agl+  d+d++
  gi|557694780|ref|YP_008797834.1| 29 EAVRKCLDDAGLDAGDVDAV 48
                                      699***************86 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.059
                                       GGBSTT--HHHH-B-TTTHHHHHHHH CS
                        Thiolase_C  67 ekvNvnGGaialGHPlGasGaRivvt 92 
                                        +v v+  a al HP    Ga+i+v 
  gi|557694780|ref|YP_008797834.1| 165 ARVAVKNKANALDHPYSQLGAKITVD 190
                                       6788889999************9985 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 4.5e-06
                                       HHHHHHHHHHT--..GGGESEEEE--SBHHHHHHHHHHHT--G.................GGBSTT--HHHH-B-TT CS
                        Thiolase_C  26 yaikkvlkkaglt..vedidlfEinEAFaaqaLavakaldldl.................ekvNvnGGaialGHPlG 83 
                                        a++++ k ag+t  +++id+fE  + F+ + L  + al  ++                 + +   GG + +G P+ 
  gi|557694780|ref|YP_008797834.1| 260 LAAQQAYKMAGITnpLKEIDVFEPYDPFTYKELHHLDALLGKPglaprlleegqlerdgdHPTSPSGGLLGVGNPIA 336
                                       5889999*****9889******************9999988888999************9999************** PP

                                       THHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEE CS
                        Thiolase_C  84 asGaRivvtllselkkeggklgvaalCigggqgv 117
                                       a+G   v+ l  +l  + gk  v  +  g +q+ 
  gi|557694780|ref|YP_008797834.1| 337 AAGLMKVAELYWQLSGRAGKRQVPNAYVGVAQAW 370
                                       ***************9999999988888877775 PP

>> DXP_redisom_C  1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.64   2.3e+03       2      55 ..      19      77 ..      18      80 .. 0.69
   2 ?   11.0   0.0    0.0001      0.36      44      66 ..     168     190 ..     157     193 .. 0.80
   3 ?   -0.1   0.0      0.29     1e+03      47      75 ..     224     252 ..     215     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.64
                                      EE-SHH...HHHHHHHS..GCCCCTTEEEEEEEE--GTTTTS-HHHHCT-SHHHHHS-S CS
                     DXP_redisom_C  2 lpvDsE...hsaifqll..keekkkevekiiltasGGpfrklkleeleevtveealkhP 55
                                      lp+ sE   ++a+ ++l  +  ++ +v+ ++  ++  +f  ++++ l +v+++ a++ P
  gi|557694780|ref|YP_008797834.1| 19 LPMTSEemvFEAVRKCLddAGLDAGDVDAVVGGSAPDAFDGYHHKGLVAVEPSGAFAKP 77
                                      56666622235788888443335577888888888888999999999988888888877 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0001
                                       CT-SHHHHHS-SS----HHHHHH CS
                     DXP_redisom_C  44 eevtveealkhPnWsmGkkitvd 66 
                                       +  ++++al+hP  ++G+kitvd
  gi|557694780|ref|YP_008797834.1| 168 AVKNKANALDHPYSQLGAKITVD 190
                                       4456788***************9 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.29
                                       SHHHHHS-SS----HHHHHHHHHSHHHHH CS
                     DXP_redisom_C  47 tveealkhPnWsmGkkitvdsatlmNkgl 75 
                                       ++++ ++ P W  G    +ds    N+ l
  gi|557694780|ref|YP_008797834.1| 224 EAKKITDTPVWVDGVGACLDSQYWTNRDL 252
                                       56788899******999999999888765 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.2   4.3e+03      83      98 ..      76      91 ..      73      92 .. 0.85
   2 ?   11.1   0.1   6.5e-05      0.23     130     179 ..     209     261 ..     202     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                         ThiJ_like 83 eeydlvllpGGsdkav 98
                                      ++++ v++ GG++ +v
  gi|557694780|ref|YP_008797834.1| 76 KPFSRVFVGGGTGVGV 91
                                      57999******99776 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.5e-05
                         ThiJ_like 130 aicqgvlalafakpeldlktttlPlwmertsillgstaek...lgyyYktyli 179
                                        ++ g++al fa+++   k t +P+w++ +   l s+ ++   l y+Y  yl+
  gi|557694780|ref|YP_008797834.1| 209 PTSDGAVALLFASEHEAKKITDTPVWVDGVGACLDSQYWTnrdLCYPYYVYLA 261
                                       5789**********8888999*********99999998862225677777776 PP

>> DUF2797  Protein of unknown function (DUF2797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3   4.5e+03     158     197 ..     155     194 ..     147     198 .. 0.58
   2 ?   10.1   0.0   0.00015      0.54      55      88 ..     239     273 ..     234     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                           DUF2797 158 aeeselgaeaiesleae.eeveikypveeypekikslnlek 197
                                       ++ + l++e+i ++  + +  ++++p++++ +ki++ ++ k
  gi|557694780|ref|YP_008797834.1| 155 EK-HALEKELIARVAVKnKANALDHPYSQLGAKITVDDVLK 194
                                       33.44555666666555566777777777777777666555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00015
                           DUF2797  55 gtclrdpeweekaclqphvVYLanssevKV.GiTr 88 
                                       g cl  + w +++ + p++VYLa++++ K  GiT 
  gi|557694780|ref|YP_008797834.1| 239 GACLDSQYWTNRDLCYPYYVYLAAQQAYKMaGITN 273
                                       778777889999999********999999658985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3142.44
//
Query:       gi|557694781|ref|YP_008797835.1|  [L=366]
Description: acetyl-CoA C-acetyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-06   27.1   0.1    7.6e-06   25.6   0.0    1.8  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 ?   -3.1   0.0      0.33     6e+03      26      45 ..      28      47 ..      24      49 .. 0.86
   2 !   25.6   0.0   4.3e-10   7.6e-06      41      99 ..     264     339 ..     249     362 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.33
                                      HHHHHHHHHHT--GGGESEE CS
                        Thiolase_C 26 yaikkvlkkagltvedidlf 45
                                       a k++l++ + +v++id++
  gi|557694781|ref|YP_008797835.1| 28 KAFKNCLEDSESEVSEIDAV 47
                                      57899999999999999975 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 4.3e-10
                                       GESEEEE--SBHHHHHHHHHHHT--G.................GGBSTT--HHHH-B-TTTHHHHHHHHHHHHHHH CS
                        Thiolase_C  41 didlfEinEAFaaqaLavakaldldl.................ekvNvnGGaialGHPlGasGaRivvtllselkk 99 
                                        ++++E+ E Fa+  L+v+ +l++                     vN  GG i +G Pl a+G   vv++++ l+ 
  gi|557694781|ref|YP_008797835.1| 264 VVEFVEVSESFASTELMVLDELGVYDgdvlkgvrggdfmfdgaLPVNPSGGCIGMGYPLNAAGLQRVVQAVKLLRM 339
                                       5899********************9999*************9999*******************999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2735.31
//
Query:       gi|557694782|ref|YP_008797836.1|  [L=380]
Description: acyl-CoA dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-31  109.9   0.3    1.9e-31  109.3   0.3    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    4.3e-17   62.1   0.0      7e-17   61.4   0.0    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      2e-11   44.3   2.0    3.5e-11   43.5   2.0    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    1.2e-05   25.9   0.3    3.3e-05   24.5   0.0    1.8  2  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
  ------ inclusion threshold ------
      0.022   14.4   0.0      0.033   13.9   0.0    1.2  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 !  109.3   0.3   5.3e-35   1.9e-31       2     128 ..     226     358 ..     225     364 .. 0.92

  Alignments for each domain:
  == domain 1  score: 109.3 bits;  conditional E-value: 5.3e-35
                                       BHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH-- CS
                     Acyl-CoA_dh_1   2 kGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaeal 78 
                                       +G++v   +ln+eR+++aa ++gl   +l++a+ey r+r  fg p++++q +++++a+ +a+leaar l+y+aa+++
  gi|557694782|ref|YP_008797836.1| 226 RGVDVLFDGLNVERMLIAACSIGLGDHVLRRAAEYGRQRVVFGHPVGSYQGLQFRMARAKARLEAARVLNYEAASLF 302
                                       899************************************************************************** PP

                                       ------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTT......SGGGHHHHHHHHT CS
                     Acyl-CoA_dh_1  79 dagkpdraeasmaKlfaselaqevadlamqllGgaGy......leeypverlyrda 128
                                       dagkp +aea+maKl+ase+  e+ + amq +Gg +y       + ypv rl+  a
  gi|557694782|ref|YP_008797836.1| 303 DAGKPCGAEANMAKLVASEAGLEAFEAAMQTFGGSAYdlgtdiITFYPVIRLFLTA 358
                                       *************************************6666644666666666655 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 !   61.4   0.0     2e-20     7e-17       1      79 [.     115     196 ..     115     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 2e-20
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE...TS---....----EEEEEEE..G CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar...tekpd....rarglslflvprda 70 
                                       +falTE +aGs++ ++kt  aer +g++vlnG+K++it+a+++++++v+ar       +    +++g+s+f++++++
  gi|557694782|ref|YP_008797836.1| 115 SFALTEAEAGSETWRIKT-FAERRNGGFVLNGQKTFITGARESDYLVVVARtkpL---QkvsdKRDGISVFALETRT 187
                                       69****************.66777779************************7653...234478************* PP

                                       GGEEE---- CS
                     Acyl-CoA_dh_M  71 pgvsvrrie 79 
                                       +gv ++++ 
  gi|557694782|ref|YP_008797836.1| 188 SGVMFEPLN 196
                                       ***998875 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 !   43.5   2.0   9.6e-15   3.5e-11       2     111 ..     241     340 ..     240     345 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 9.6e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       +iaa  +G+   +l  ++e+ r+rv   +g ++   + +q++ a+a+arl+AAr l ++aa+      +agk++   
  gi|557694782|ref|YP_008797836.1| 241 LIAACSIGLGDHVLRRAAEYGRQRVV--FGHPVGSYQGLQFRMARAKARLEAARVLNYEAASL----FDAGKPC--- 308
                                       689***********************..***********************************....*******... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGB CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalr 111
                                         aea +a+++a+e   +a +a+++++Ggsa++
  gi|557694782|ref|YP_008797836.1| 309 -GAEANMAKLVASEAGLEAFEAAMQTFGGSAYD 340
                                       .******************************97 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 !   24.5   0.0   9.2e-09   3.3e-05       2     110 ..       7     108 ..       6     110 .. 0.76
   2 ?   -1.7   0.0       1.3   4.6e+03       6      58 ..     281     338 ..     278     358 .. 0.57

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 9.2e-09
                                       HHHHHHHHHHHHHHHHHTHHHHHHHH..HHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-H CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewd..eegefprelwkklaelGllgitvpeeygGagldyleaaivaeelarada 76 
                                       +eq  + +t+ ++ e+  + +   +   +++ +p  lw++l + Gl+g  v   + G+g  +l+a++v e lara++
  gi|557694782|ref|YP_008797836.1|   7 DEQVLVLQTAEKVGERFGRRNWLAYGreRREPVP--LWEELQKSGLTGAGV---VEGSG--TLDAILVQEGLARAGI 76 
                                       6777777777777777664444344311333455..9**************...67787..69************** PP

                                       HHHHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_N  77 glalllgvhsslvapailrfGteeqkrryLpkla 110
                                       +l  +l +h s v  +i+r+Gt  q +r++ + +
  gi|557694782|ref|YP_008797836.1|  77 PLLHFLTTHFSRV--MIARHGTRMQFERFVDPTV 108
                                       *866888888777..8*************98876 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHTHHHHHHHHHHTSGH..HHH.HHHH..HHTTCTSTTS-.GGGTS-- CS
                     Acyl-CoA_dh_N   6 alrdtvrefaeeelaphaaewdeegefp..rel.wkkl..aelGllgitvp.eeygGag 58 
                                       + r+++r  a++ l+  aa   ++g+ p   e+ + kl   e+Gl +     + +gG+ 
  gi|557694782|ref|YP_008797836.1| 281 MARAKARLEAARVLNYEAASLFDAGK-PcgAEAnMAKLvaSEAGLEAFEAAmQTFGGSA 338
                                       66677777777777666666666664.22233335555323566655444435555554 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 ?   13.9   0.0   9.1e-06     0.033     172     228 ..     134     192 ..     103     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.1e-06
                                       EEE-SSEEEEEEEEEEEE-.--SSEEEE---SS-..TT..SGGG-EEEEEETT-TTEEE CS
                            HpaB_N 172 veetddGivVrGakvlaTgaaladeilvlptramlkee..dkdyavafavpvdapGlkl 228
                                        e+++ G v +G k ++Tga  +d+++v+   ++l++   ++d   +fa+++ + G+ +
  gi|557694782|ref|YP_008797836.1| 134 AERRNGGFVLNGQKTFITGARESDYLVVVARTKPLQKVsdKRDGISVFALETRTSGVMF 192
                                       488999********************999885555543337788999********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2749.65
//
Query:       gi|557694783|ref|YP_008797837.1|  [L=210]
Description: hypothetical protein CSUB_C1356 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   18.6   9.3       0.33   11.5   1.2    2.5  2  DUF4405   Domain of unknown function (DUF4405)
  ------ inclusion threshold ------
        5.1    7.2   8.8       0.34   11.0   0.6    2.8  4  DUF1634   Protein of unknown function (DUF1634)


Domain annotation for each model (and alignments):
>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   1.2   3.7e-05      0.33      11      64 ..      66     121 ..      62     122 .. 0.70
   2 !   11.0   1.5   5.3e-05      0.47      39      65 ..     171     197 ..     145     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                           DUF4405  11 lvlaiSGillsfavlpsgrgaywa...flgl..skhqwrdiHeilgllflilvvlHlgl 64 
                                       l+l  +G++  + +++   ++ +a   +++   + + w  iHeil ++  il+++H gl
  gi|557694783|ref|YP_008797837.1|  66 LALSGTGLMVVAQFYS---VVKRAgrlWMKRlgGPRAWLIIHEILDVVGPILILVHAGL 121
                                       4555666666655433...33333345555569999********************987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.3e-05
                           DUF4405  39 skhqwrdiHeilgllflilvvlHlglh 65 
                                       + + wr +H+ l  +f ++ + H++++
  gi|557694783|ref|YP_008797837.1| 171 QFRHWRTVHIALTAIFYVAGLTHVLVN 197
                                       3366********************987 PP

>> DUF1634  Protein of unknown function (DUF1634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.6   3.8e-05      0.34      48      80 ..       9      41 ..       5      46 .. 0.82
   2 ?   -2.5   0.0      0.61   5.5e+03       8      26 ..      59      77 ..      55      85 .. 0.68
   3 ?   -0.1   0.0      0.11     1e+03      15      45 ..     107     134 ..      98     157 .. 0.59
   4 ?   -1.4   0.2      0.28   2.5e+03       9      27 ..     180     198 ..     176     206 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.8e-05
                           DUF1634 48 lelkglaiiqlGllvLiatPvlrVvlsliaFlk 80
                                      + + g++i+ lG+l+L+++Pv  ++++l + ++
  gi|557694783|ref|YP_008797837.1|  9 MLMPGKKIVVLGILILLIIPVSLLAVNLPQIFT 41
                                      5567899**************999998866555 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.61
                           DUF1634  8 GvllsaavvllGlilllvk 26
                                      G   ++++ l G+ l++v 
  gi|557694783|ref|YP_008797837.1| 59 GNPYALSLALSGTGLMVVA 77
                                      5556777777777777665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.11
                           DUF1634  15 vvllGlilllvkhgssesenseltslseile 45 
                                       + ++G il+lv+ g s   + ++++ls + +
  gi|557694783|ref|YP_008797837.1| 107 LDVVGPILILVHAGLS---KPNFINLSWLAK 134
                                       5578999999999843...334444443333 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.28
                           DUF1634   9 vllsaavvllGlilllvkh 27 
                                       ++l a++ ++Gl+ +lv++
  gi|557694783|ref|YP_008797837.1| 180 IALTAIFYVAGLTHVLVNT 198
                                       5667778888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 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:                        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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1630.75
//
Query:       gi|557694784|ref|YP_008797838.1|  [L=666]
Description: acetoacetyl-CoA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  147.5   0.0      5e-43  147.3   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    6.9e-09   35.5   0.8    6.9e-09   35.5   0.8    2.8  3  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
  ------ inclusion threshold ------
      0.046   14.7   0.0       0.16   12.9   0.0    2.0  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 !  147.3   0.0   8.4e-47     5e-43      10     421 ..     111     539 ..     101     541 .. 0.79

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 8.4e-47
                                       TSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-H CS
                       AMP-binding  10 dkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlta 83 
                                          al+    +ge + + + e++++v ++A+gL + Gv  gdrVa +lpn pe v+a+l++ ++Ga  + + ++l+ 
  gi|557694784|ref|YP_008797838.1| 111 HEAALIGvreDGETNAMRFLEFYNEVAAVARGLSESGVAAGDRVAGYLPNIPETVIAMLGATSLGASWSSVGTELGV 187
                                       5566766888899999******************88***************************************** PP

                                       HHHHHHHHHHTESEEE.........ETCTCCC.HHHHHHHHSCC-EECEEEEESC.CS-HCCHCCCHCCCCSCTTS. CS
                       AMP-binding  84 eelayiledseakvli.........atvdsel.leklleaaakleavklvivlda.dellkeeelkeeeeseekae. 148
                                       +++   + + e+kvl+         ++    + le++ ++ +++++ ++v+v+    e+++ + l e+   ++  + 
  gi|557694784|ref|YP_008797838.1| 188 DAVVDRIGQIEPKVLFtvdgylyrgKA---FDvLERVSQVVERVKSIQKVVVIPYlSESPRIDGLAEAVLYPDF-Ka 260
                                       ****************99888764413...33344444445444444444444430333333334444433333.14 PP

                                       ...-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHH CS
                       AMP-binding 149 ...kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletrfklkeddvvlsilplahifglilel 221
                                             + +++ +d+++yi+++SGTTGkPK  +    + lv++++++    + +lk+++v+  i   ++++    +l
  gi|557694784|ref|YP_008797838.1| 261 regGAIDFAQVPSDTPLYIMFSSGTTGKPKCMVQPAaGVLVNQLKDVV-I-HSDLKRGEVITYITTPSWMMW--NWL 333
                                       567344677899*******************99999666788888863.3.445678899977777777776..68* PP

                                       HHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHH..HHCCCHHCHHHHCCGTT-SEEEEESS-E CS
                       AMP-binding 222 llallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleal..lesgalkaakkakdlsslrlvllggepl 295
                                         +l++G+tv l+++d+  +d +++++li++++++++ +  + ++ l  +   a    +++  l slr +   g+pl
  gi|557694784|ref|YP_008797838.1| 334 VSSLAAGGTVLLYDGDPNyPDWRRMWRLIDEYGISIFGCSASYINLLrgMG--ASP--RSEFGLESLREISQTGSPL 406
                                       ******************88888899*********************5533..333..1233899****988***** PP

                                       BHHHHHHHHHHHTC..EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEE CS
                       AMP-binding 296 spellrffralfge..evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvr 370
                                       s+e  +++++ +++  ++  + G T   g +++   +   +++g +  p  g++++  De  gepv  + eGel+  
  gi|557694784|ref|YP_008797838.1| 407 SAEGFKWIYDEVKRdlHFNSISGGTDINGTFAN-GSPILPVYAGQIQSPSLGMKIMCYDER-GEPV-FDREGELVCE 480
                                       ************9999899999*********95.445555678999999999999999*98.9999.899******* PP

                                       ETT.S-SEBTT-.H..HHHHHHEEE...TCCEEEEEEEEEEETT.SEEEEEEECCCEEE CS
                       AMP-binding 371 gpg.vmkgYlkk.p..eataeafds...egrwlrTGDlgrlded.GyleivgRkkdlik 421
                                        p   m+ Y+ + p  e+  +a++    ++r  r GD + ++ d G + ++gR++ ++k
  gi|557694784|ref|YP_008797838.1| 481 APApPMPLYFLNdPgdEKYLDAYFRyytHKRVWRHGDYVIFHSDtGGITFLGRSDAVLK 539
                                       **658898986524336666666548854789999******9877**********9987 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 ?   -2.2   0.1      0.66   3.9e+03      28      43 ..      15      31 ..       7      34 .. 0.66
   2 !   35.5   0.8   1.2e-12   6.9e-09       1      54 [.      48     104 ..      48     105 .. 0.92
   3 ?   -0.0   0.0      0.14   8.6e+02       6      21 ..     644     661 ..     642     664 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.66
                                      --S-SECSTTTC.T-EE CS
                            ACAS_N 28 pfdkvldgskgp.fikW 43
                                      p + v+ +s+++ fik+
  gi|557694784|ref|YP_008797838.1| 15 PSTDVVAKSNMNsFIKF 31
                                      44578889999878886 PP

  == domain 2  score: 35.5 bits;  conditional E-value: 1.2e-12
                                       HHHHHHHHHH-HHHHHHHHHCC..S--SB--S-SEC.STTTCT-EESTT-EE-HHHH CS
                            ACAS_N   1 ykelykeSiedpeaFWaeqake..ldWekpfdkvld.gskgpfikWFeGGklNicyN 54 
                                       y +ly++S+++  +FW ++++   ++ +k f++v+d  sk p ++W++G++lN ++N
  gi|557694784|ref|YP_008797838.1|  48 YFKLYRWSVTNIPRFWMHVWDFfgIKCSKRFETVVDdLSKFPGARWYVGARLNFAEN 104
                                       779******************667***********7258889*************99 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.14
                                       HHHHH-HH..HHHHHHHC CS
                            ACAS_N   6 keSiedpe..aFWaeqak 21 
                                       +eSi++pe   F++++a+
  gi|557694784|ref|YP_008797838.1| 644 RESIRNPEslDFFEKAAE 661
                                       79*****96679999997 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 ?   12.9   0.0   2.7e-05      0.16       4      65 ..     552     612 ..     549     626 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.7e-05
                                       HHHHSSTTEEEEEEE-----TTS.---EEEEEE---.---HHHHHHHHHHHHT-TTTS-SEEE.E CS
                     AMP-binding_C   4 salvshpaVaeaaVvGvpdevkG.ealvafVvlkdg.sealeeeLkahvrkelgpyavpkkvv.f 65 
                                       s++ s  +Va+  +vG      G ++++ fV  ++g +  l eeLk +++++l + a p++v  +
  gi|557694784|ref|YP_008797838.1| 552 SIVESFREVADSLAVGQEWR--GdQRIILFVKMAEGyV--LTEELKNRIKQALRERASPRHVPaI 612
                                       77888889999999997776..779********88952..4466666666666666666655422 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (666 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); 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:                         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: 4433.22
//
Query:       gi|557694785|ref|YP_008797839.1|  [L=203]
Description: hypothetical protein CSUB_C1358 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-05   22.9  16.6    3.4e-05   22.9  16.6    1.8  1  COX1      Cytochrome C and Quinol oxidase polypeptide I
  ------ inclusion threshold ------
      0.092   12.6  16.5       0.17   11.7  16.5    1.4  1  DUF4386   Domain of unknown function (DUF4386)


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 !   22.9  16.6   3.8e-09   3.4e-05     314     403 ..      49     144 ..      13     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 3.8e-09
                                       HHHHHHHHHHHT..SHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHSB--...HHHHHHHHHHHHHH CS
                              COX1 314 fiigGltGvlla..lpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyllpkltgrml...serlaklhfwllfi 385
                                       f++ G  G++    ++ + + + +t ++v++  + ++g++++++ a++y++++++ g+ +    + la+lh +l+++
  gi|557694785|ref|YP_008797839.1|  49 FWVIGQLGFMKPefSRVIAFGSAGTWFTVGYLSYLIVGVIGVAVTALFYHYIENVLGKPYkglANGLAWLHLILMNV 125
                                       36667777776422567788889*********************************99887778999********** PP

                                       HHHHHHHHHHHHHHT.THB CS
                              COX1 386 GlvlmflpmhilGll.gmp 403
                                       G++  +  m+++G+l g +
  gi|557694785|ref|YP_008797839.1| 126 GVIGATWLMMVSGYLaGAA 144
                                       **************98765 PP

>> DUF4386  Domain of unknown function (DUF4386)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7  16.5   1.9e-05      0.17       4     172 ..      35     195 ..      33     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                           DUF4386   4 llylliivlgiiaelllrsplivpgdaaatlaniaanesllrlgllaellmalllvvlavlLyp....llrrvnpgl 76 
                                       ++y+ ++++++   +++ ++l   +++ + +  +++ ++ + +g+l +l+++++ v++++l+y+    +l +  +gl
  gi|557694785|ref|YP_008797839.1|  35 AAYVQGALAVGNTLFWVIGQLGFMKPEFSRVIAFGSAGTWFTVGYLSYLIVGVIGVAVTALFYHyienVLGKPYKGL 111
                                       5899999**************9999**************************************83333455557789 PP

                           DUF4386  77 allaaafrlveaaviavgllrllallpllaeaaalaapalraalallllalhdygyllgliff.glwllllgllllr 152
                                       a + a++ l+   v ++g   l+++  +la+a            a+l  ++   g++ g++ + ++ +++lg+  + 
  gi|557694785|ref|YP_008797839.1| 112 ANGLAWLHLILMNVGVIGATWLMMVSGYLAGA------------AMLPPEVGGRGWNAGQVHTnIFYGIPLGYPTWI 176
                                       99999999999999999999999999998888............455555555666666666666666666665555 PP

                           DUF4386 153 srllPrwlgllgllagllyl 172
                                       + ++   l++  + +gl+y+
  gi|557694785|ref|YP_008797839.1| 177 ALFIF-LLAIGVACGGLGYI 195
                                       54444.55555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); 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:                         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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1487.48
//
Query:       gi|557694786|ref|YP_008797840.1|  [L=238]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   26.1   0.4    6.2e-06   25.9   0.4    1.1  1  Snf7            Snf7
  ------ inclusion threshold ------
      0.019   15.2   0.0      0.059   13.6   0.0    1.8  1  DUF948          Bacterial protein of unknown function (DUF948
      0.021   14.9   0.3       0.06   13.4   0.3    1.7  2  LOH1CR12        Tumour suppressor protein
      0.031   12.6   0.0      0.034   12.5   0.0    1.1  1  SpecificRecomb  Site-specific recombinase


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 !   25.9   0.4   1.4e-09   6.2e-06       5     166 ..      71     229 ..      67     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.4e-09
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Snf7   5 sLrkaerkldkkqeslekkikkleaelkklakkgnkdralllLKqkkryekqldqldnqlanleqvslaienlksnk 81 
                                       +L + ++++d k + ++ +  +l +++ + + +++++ra ++++++ +++k++  +  ++a+le v+l +e   + +
  gi|557694786|ref|YP_008797840.1|  71 RLMTIQNRMDYKARAMQMRGRELFNQIVRAKMEKDEERAAVYANELAQLRKMMHATVRSQASLEGVVLRLEAVRDYN 147
                                       677778999******************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHCTC..CHHHHHHHHHHHHHHHHHTCHHHHHHHHHTT-GGTTHHHHHHHHHHHHHHHHHC CS
                              Snf7  82 evlnamkqgakamkamnkkvd..idkidklmdeiedqmekaeeisEalsrslddadeedEeeleaeLdaLeqelgde 156
                                       ev +  + +a++  a++k v   +++i   ++ ++d +e  +    ++s+++ ++++  + e ea+L + ++e++++
  gi|557694786|ref|YP_008797840.1| 148 EVRKVIGPVAAVVMAVQKDVGgvMPEISSGLRGVQDLLEDLSVSVGTVSDTY-IGASTADPEAEAILRE-ASEVAAQ 222
                                       *****************99954478888888888888888888888888888.3466666666666554.2333333 PP

                                       SH.HHHHHHH CS
                              Snf7 157 elldesvklp 166
                                            ++++p
  gi|557694786|ref|YP_008797840.1| 223 R---LKKDMP 229
                                       3...244444 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 ?   13.6   0.0   1.3e-05     0.059      19      71 ..     144     196 ..     135     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.3e-05
                            DUF948  19 vvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvd 71 
                                       +  ++++k++  +aa +  ++k+v++++ e+   l+ v++lled++  + +v 
  gi|557694786|ref|YP_008797840.1| 144 RDYNEVRKVIGPVAAVVMAVQKDVGGVMPEISSGLRGVQDLLEDLSVSVGTVS 196
                                       5567899**************************************99998886 PP

>> LOH1CR12  Tumour suppressor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   1.3e-05      0.06      52     115 ..      77     145 ..      62     158 .. 0.74
   2 ?   -2.5   0.0       1.1   4.9e+03      91     110 ..     173     192 ..     169     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                          LOH1CR12  52 aklverikevdakiitllae.....lrekqkqyasyaealskvnelsdqlsriqiiledivpllEtlne 115
                                       +++  + + ++ +  +l+++     + + +++ a ya++l++++++ +   r q  le +v  lE++ +
  gi|557694786|ref|YP_008797840.1|  77 NRMDYKARAMQMRGRELFNQivrakMEKDEERAAVYANELAQLRKMMHATVRSQASLEGVVLRLEAVRD 145
                                       55555555555555555554100005566788899***************************9999865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                          LOH1CR12  91 elsdqlsriqiiledivpll 110
                                       e+s+ l+ +q++led   ++
  gi|557694786|ref|YP_008797840.1| 173 EISSGLRGVQDLLEDLSVSV 192
                                       68889999999999875555 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.6e-06     0.034      70     176 ..      39     146 ..      10     195 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.6e-06
                    SpecificRecomb  70 srsgffselaerleekllPeapdeedlsdllsllfpkeeDaewlealddetlarLlell.eeeeeeeeeaaeklree 145
                                       sr++  se+++ +++k  P++p +++ls+++++l++ ++  ++ +   + + ++L++ + +++ e++ee a+ + +e
  gi|557694786|ref|YP_008797840.1|  39 SRDSSSSEMFRLFRKKEPPKPPFDQRLSEIVTRLMTIQNRMDYKARAMQMRGRELFNQIvRAKMEKDEERAAVYANE 115
                                       6778899*******************************999999999999999999998678888888899999999 PP

                    SpecificRecomb 146 llealevlsvqiaalglepelrrrlpeleee 176
                                       l +  +++ +++++    + ++ rl+ ++++
  gi|557694786|ref|YP_008797840.1| 116 LAQLRKMMHATVRSQASLEGVVLRLEAVRDY 146
                                       9999999999999988777777777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1807.83
//
Query:       gi|557694787|ref|YP_008797841.1|  [L=978]
Description: leucyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-57  195.2   0.0    2.4e-48  164.8   0.0    2.4  2  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.4e-20   73.4   0.1    1.2e-09   37.4   0.0    4.0  4  tRNA-synt_1g   tRNA synthetases class I (M)
    4.1e-16   59.3   0.0    1.1e-15   57.9   0.0    1.7  1  Anticodon_1    Anticodon-binding domain of tRNA
    8.1e-13   48.4   0.1    4.6e-08   32.7   0.0    3.2  3  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
      4e-08   33.0   0.0    9.6e-08   31.8   0.0    1.6  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
  ------ inclusion threshold ------
      0.026   13.5   0.0       0.14   11.1   0.0    2.0  2  tRNA-synt_1f   tRNA synthetases class I (K)


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 !  164.8   0.0   7.9e-52   2.4e-48       1     432 [.      30     525 ..      30     542 .. 0.84
   2 !   27.7   0.0   2.7e-10   8.2e-07     507     597 ..     593     684 ..     582     689 .. 0.86

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 7.9e-52
                       tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                       k++++W  + vf+++   e+ +++f + ++  y +G lH+Gh ++ t  d v ry rm+G++vl+   w   G a+ 
  gi|557694787|ref|YP_008797841.1|  30 KWMSRWRVDRVFEAQ--PEHGRRKFFICVPYSYQNGPLHLGHGFTFTRGDAVARYMRMRGYNVLFPWAWHWTGEAVA 104
                                       58899********99..677799*****************************************************9 PP

                       tRNA-synt_1  78 akvekklgakekkerkklgreefrekvre.......wkaeyaeeirkqvkrlGvsvDfdreylT..ldkeleeavke 145
                                        + e+    +e   r+ l  +   e   +       + a+y++e rk v  +G svD++re  T  l++ ++  +++
  gi|557694787|ref|YP_008797841.1| 105 GTSERLKKGDESVRRMLLEIDGVPESLLSnfthpefICAYYTAENRKVVDAMGWSVDWSREFHTtdLHPYYSRFIEW 181
                                       9988865555555555555554444332211112236789999******************999455678999**** PP

                       tRNA-synt_1 146 vfvrladkgliyrgkklvnwstklktalselEveykdkk..dalihvafpladkeevklviaTTtPeTllgdtavav 220
                                        +  l  +gl+ +g ++v w++k+++a  + +    +    +  ++v f+l++   vkl +aT +PeT++g t v +
  gi|557694787|ref|YP_008797841.1| 182 QYHVLRRNGLLVQGRHPVVWCPKCQSATGDHDRLRGEGIypEEYTMVFFELDG---VKLAAATLRPETIFGVTNVWI 255
                                       ******************************99855543322566677777765...578****************** PP

                       tRNA-synt_1 221 npeldyvitkeklilaeallkslvkkesek...kiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVki 294
                                       +p+  y + +++ i++    ++++k  ++    k++++++g+eL gk+v+ p+++r++pi+  ++vd   GtGvV  
  gi|557694787|ref|YP_008797841.1| 256 HPDGVYQVVERNGIMLLMSREAVAKLGEQLglgKVVKEMHGRELLGKYVKSPFTGRAVPILPAEFVDVSLGTGVVYS 332
                                       ******988888887777777777776433356******************************************** PP

                       tRNA-synt_1 295 aPahdedDyevgkkynlevinildedgtlteea............................................ 327
                                        Pah + Dy + k+ +   +  + e+g   + +                                            
  gi|557694787|ref|YP_008797841.1| 333 VPAHAPYDYIAVKELKN-NPAKMREKGLDPKLVetiqpikvietpglgehpavdaveraritsqlderleeltrdiy 408
                                       *********99987654.3344444443333224446666666667777777************************* PP

                       tRNA-synt_1 328 ...........aefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaa 391
                                                   ef+ ++v  ar+kv+e l+++g      + + +v +c  +++ i+  + +qWf + ++   ++ +
  gi|557694787|ref|YP_008797841.1| 409 skefysgkmvvDEFRDVSVSVAREKVIERLRQNGDGDVFYDLSGKV-ICRSGDECIVKIVDDQWFLNFSNpeWKARV 484
                                       **********************************999988888887.688888889999999*****9987677888 PP

                       tRNA-synt_1 392 lkavekvqfvpkskekryaswleniqdWciSRqrwWGhrip 432
                                        + +++++ +p+ +++   + +   +dW+  R+   G+r+p
  gi|557694787|ref|YP_008797841.1| 485 KSLISSMNVYPEAARTWLLNVVDWLHDWACTRKTGLGTRLP 525
                                       88888**********************************98 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 2.7e-10
                       tRNA-synt_1 507 dteelkkffpadmlleGlDiirgWvarlillslaltgsePf.kevlvhglvrdeeGrKmSKslgNvidpldvikkyg 582
                                        ++e+   +  d+ ++G D +   ++  ++  + +++++ + + v v+g+++  eG KmSKs gN +  ++ + ++g
  gi|557694787|ref|YP_008797841.1| 593 MRREFLYWYGVDLRVSGKDLVANHLTFYLFHHTGIFEERHWpRGVAVNGMIT-IEGNKMSKSRGNFVTLKQALARHG 668
                                       5788888999************************9999977478*****997.58********************** PP

                       tRNA-synt_1 583 adalRltli.lsdvgr 597
                                        da Rl+l+ +++ + 
  gi|557694787|ref|YP_008797841.1| 669 SDATRLALLlSAEDLD 684
                                       ********95555555 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 !   27.4   0.0   4.5e-10   1.3e-06       2      44 ..      53      95 ..      52     120 .. 0.86
   2 ?    0.4   0.0     0.069   2.1e+02      62     132 ..     137     211 ..     132     219 .. 0.75
   3 ?    2.0   0.0     0.023        69     182     240 ..     469     527 ..     449     540 .. 0.79
   4 !   37.4   0.0   4.2e-13   1.2e-09     286     369 ..     606     691 ..     588     700 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.5e-10
                                      EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEE CS
                      tRNA-synt_1g  2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcg 44
                                      ++ ++  Y ng+lHlGh  +   +D++aRy r+rg++vlf  +
  gi|557694787|ref|YP_008797841.1| 53 FICVPYSYQNGPLHLGHGFTFTRGDAVARYMRMRGYNVLFPWA 95
                                      788999*********************************9655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.069
                                       -HHHHHHHHHHHHHHHHHHTT---S...EEEETTSH.HHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-G CS
                      tRNA-synt_1g  62 tpeelvekvheeikelfkklnisfd...kygrttse.ehkelvqeifkklkekgliyekeieqlycpkderflpd 132
                                       +pe +++ +++e++++ + ++ s d   ++++t+ +   +++ +  ++ l ++gl+ +++  +++cpk+++   d
  gi|557694787|ref|YP_008797841.1| 137 HPEFICAYYTAENRKVVDAMGWSVDwsrEFHTTDLHpYYSRFIEWQYHVLRRNGLLVQGRHPVVWCPKCQSATGD 211
                                       577788888899999988888777744446666543145567777799999999999999999999999886655 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.023
                                       EEEEE-GG..GGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EETTE CS
                      tRNA-synt_1g 182 ehlffkls..kfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvPga 240
                                       +++f++ s  +++ ++k+ i ++ +  +e +++ ++++++  L+d+a +r++  G ++P +
  gi|557694787|ref|YP_008797841.1| 469 DQWFLNFSnpEWKARVKSLI-SSMNVYPEAARTWLLNVVDW-LHDWACTRKTGLGTRLPWD 527
                                       56776665226888999999.55558999999999999999.**********999999954 PP

  == domain 4  score: 37.4 bits;  conditional E-value: 4.2e-13
                                       EEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-T CS
                      tRNA-synt_1g 286 hfigkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeape 360
                                        + gkd +  H  f+    +g  +e + p+ v++++++t+eg+K+SkSrg++v+ k+al r  +d+ R  l+ +a+ 
  gi|557694787|ref|YP_008797841.1| 606 RVSGKDLVANHLTFYLFHHTGifEERHWPRGVAVNGMITIEGNKMSKSRGNFVTLKQALARHGSDATRLALLLSAED 682
                                       567************999999999999*********************************************99999 PP

                                       TS-EEE-HH CS
                      tRNA-synt_1g 361 kkDldfswe 369
                                        +D d++ +
  gi|557694787|ref|YP_008797841.1| 683 LDDPDWRDK 691
                                       999888765 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 !   57.9   0.0   3.6e-19   1.1e-15       1     114 [.     722     819 ..     722     854 .. 0.82

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 3.6e-19
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrll 77 
                                       d w+l+ +++  + v e++e+++ + a+s++ + ++n+  +wy++ +++r+            ++ + ++e+++ +l
  gi|557694787|ref|YP_008797841.1| 722 DEWLLAATDRSCEIVAENLEKLKTRSACSEAVYGMLNNW-RWYIRRNRDRIT-----------RAAKVFAEKWILIL 786
                                       89*************************************.***********5...........5677899******* PP

                       Anticodon_1  78 aPfmPfitEelwqreeeelgkkesimlaewpekaeel 114
                                       +Pf+Pf +Ee+w    e+lg k   +l+ewp+ ++  
  gi|557694787|ref|YP_008797841.1| 787 SPFAPFAAEEAW----EKLGMKGYASLQEWPKPSTGS 819
                                       ************....9**************744322 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 !   10.9   0.0     7e-05      0.21       7      50 ..      47      92 ..      41      94 .. 0.87
   2 !   32.7   0.0   1.6e-11   4.6e-08     199     282 ..     593     678 ..     583     692 .. 0.89
   3 ?    0.2   0.0      0.12   3.7e+02      49      77 ..     698     726 ..     691     933 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7e-05
                                      TTEEEEEEEEEBTTS-..-BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1e  7 ekkvtlYvCGptvyda..shlGhaRslvafDilrrilqalgYdvqf 50
                                      +++ ++++C p  y++   hlGh+ ++   D ++r+++++gY+v f
  gi|557694787|ref|YP_008797841.1| 47 HGRRKFFICVPYSYQNgpLHLGHGFTFTRGDAVARYMRMRGYNVLF 92
                                      5566899999999986448*************************87 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 1.6e-11
                                       HHHHHH-.SSEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-H CS
                      tRNA-synt_1e 199 maskllg.seidihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdp 273
                                       m +++l    +d+ + G+DL+  h    l  ++  f+ +++ +    ng+++ieg+kmsks +nf+t+k++l ++ +
  gi|557694787|ref|YP_008797841.1| 593 MRREFLYwYGVDLRVSGKDLVANHLTFYLFHHTGIFEeRHWPRGVAVNGMITIEGNKMSKSRGNFVTLKQALARHGS 669
                                       66666653679*************************9899************************************* PP

                                       HHHHHHHHS CS
                      tRNA-synt_1e 274 rqlRlllls 282
                                        + Rl+ll 
  gi|557694787|ref|YP_008797841.1| 670 DATRLALLL 678
                                       ****99875 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.12
                                       EEEEEBB--SHHHHHHHHHTTS-HHHHHH CS
                      tRNA-synt_1e  49 qfvqnvtDidDkiikrareeeksvkelae 77 
                                       +fv+n+  i +ki k+a ++   ++e+  
  gi|557694787|ref|YP_008797841.1| 698 AFVKNFLSIVEKIAKEASDDVGPCDEWLL 726
                                       58999999999999999988877554432 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 !   31.8   0.0   3.2e-11   9.6e-08      14     126 ..     230     341 ..     223     353 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 3.2e-11
                     tRNA-synt_1_2  14 fkveeseeklevfttrpdtlfGvtfvalapehplveklaekkkelaafieevkkkse.sereletkekeGv.ftglk 88 
                                       f++++   kl   t rp+t+fGvt v + p+  + + ++++   l    e v+k  e     +  ke +G    g +
  gi|557694787|ref|YP_008797841.1| 230 FELDG--VKLAAATLRPETIFGVTNVWIHPDG-VYQVVERNGIMLLMSREAVAKLGEqLGLGKVVKEMHGReLLGKY 303
                                       55554..35888899*************9986.333344444444433444433333033334455667876889** PP

                     tRNA-synt_1_2  89 aihPitgekipiwvanyvlmeygtgavmavPahdqrDf 126
                                       +  P+tg+ +pi  a++v ++ gtg+v +vPah   D+
  gi|557694787|ref|YP_008797841.1| 304 VKSPFTGRAVPILPAEFVDVSLGTGVVYSVPAHAPYDY 341
                                       *********************************98887 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 ?   -1.1   0.0      0.23   6.9e+02      34      64 ..      62      92 ..      38      97 .. 0.88
   2 ?   11.1   0.0   4.5e-05      0.14     234     301 ..     602     669 ..     598     681 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.23
                      tRNA-synt_1f 34 SGliHiGnlrevltadlvaralrkrgeevrl 64
                                       G++H+G      ++d+var +r rg +v +
  gi|557694787|ref|YP_008797841.1| 62 NGPLHLGHGFTFTRGDAVARYMRMRGYNVLF 92
                                      599********************99988755 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.5e-05
                      tRNA-synt_1f 234 gVdfEpaGkDhaaaGgSvdvsskiaeilggea.PekvvYe.lillkggekmssSkGnvltledwlevaep 301
                                       gVd+  +GkD++a+   + + ++ + i++ ++ P +v  + +i+++g+ kms+S+Gn++tl+++l     
  gi|557694787|ref|YP_008797841.1| 602 GVDLRVSGKDLVANHLTFYLFHH-TGIFEERHwPRGVAVNgMITIEGN-KMSKSRGNFVTLKQALARHGS 669
                                       77888888888884444444333.266665544888876526666666.**************9976555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (978 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); 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: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 6315.21
//
Query:       gi|557694788|ref|YP_008797842.1|  [L=118]
Description: hypothetical protein CSUB_C1361 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   33.5   0.0    4.9e-08   33.4   0.0    1.0  1  DrsE         DsrE/DsrF-like family
  ------ inclusion threshold ------
      0.038   14.5   0.0      0.077   13.5   0.0    1.5  1  GMC_oxred_C  GMC oxidoreductase


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 !   33.4   0.0   5.4e-12   4.9e-08       3     117 .]       6     118 .]       4     118 .] 0.84

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 5.4e-12
                                       EEEEE-S-TTTBSHHHHHHHHHHHHHTTT..-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEE CS
                              DrsE   3 vfilvtggpygseaarealelalaaaalg..hevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvC 77 
                                       +++++ +gp + e+ar++l++a+  a+ +   ev++ f g+G++ll        + +  ++    +l ++g++  vC
  gi|557694788|ref|YP_008797842.1|   6 ILFVILSGPNDFEKARQGLRIARNIAKEKiaTEVKLLFVGPGTTLLDP----DNQHYDIVKHYATELNQAGARCTVC 78 
                                       7899999***************988777778*****************....23334456777788999******** PP

                                       HHHHHHTT--GGG..E-T--EEEE-HHHHHHHHHH-SEEEE- CS
                              DrsE  78 gqaakargldede..dlgvgvevsglgelaelqnegdrvitf 117
                                       +  +  ++l+e+   +  + ++  + + +ae++++g+ ++tf
  gi|557694788|ref|YP_008797842.1|  79 AGNLRVYKLEEKIdkN--LFIADDSTAVVAEAALNGFTILTF 118
                                       **********653433..348888888999999999999998 PP

>> GMC_oxred_C  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.6e-06     0.077      20     124 ..       6     102 ..       2     117 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.6e-06
                                       EE--TT-SHHHHHHHHHHHHHHHHHCTSGGGTTEECCEECCCTT.TTS.HCHHCHHCHHCHHHHH-EE-S--B-TT- CS
                       GMC_oxred_C  20 idpnylsdprdlaalvealkaarkilaaaaldvleeeltpgaae.etsdaavesdealekfvkeavltsaHplGtcr 95 
                                       i +  ls p+d ++++++l+ ar+i++++     e++l ++  +    d +++      ++vk+ + t   + G  +
  gi|557694788|ref|YP_008797842.1|   6 ILFVILSGPNDFEKARQGLRIARNIAKEK--IATEVKLLFVGPGtTLLDPDNQHY----DIVKH-YATELNQAGARC 75 
                                       56678999*********************..233333333332303333333333....34444.444444444444 PP

                                       B-STCGCBSB-TTSBBTT-.....CSEEE-SGGG CS
                       GMC_oxred_C  96 MGadpkdsVVDsdlrvhgv.....dnLrVvDaSv 124
                                              +V+  +lrv+ +     +nL+++D S+
  gi|557694788|ref|YP_008797842.1|  76 -------TVCAGNLRVYKLeekidKNLFIADDST 102
                                       .......677778888777333334777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 856.42
//
Query:       gi|557694789|ref|YP_008797843.1|  [L=142]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-07   31.4   0.1    2.6e-07   30.8   0.1    1.4  1  NTP_transf_2  Nucleotidyltransferase domain
      1e-06   28.8   0.0    1.8e-06   27.9   0.0    1.6  1  Polbeta       Polymerase beta, Nucleotidyltransferase
     0.0042   16.9   0.0     0.0068   16.2   0.0    1.4  1  DUF294        Putative nucleotidyltransferase DUF294


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 !   30.8   0.1   4.4e-11   2.6e-07      14      74 ..      31      95 ..      17     131 .. 0.68

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 4.4e-11
                                      TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHH....HHHEHHHHHHHHCCCEEECTTEEEEEE CS
                      NTP_transf_2 14 vakvvlfGSyarGtalkgSDiDllvvlpeevsre....kkeegleklaeiikfleellglevdlv 74
                                      +  v+lfGS+arG+ ++ SD Dllv+ ++  +r     + +  ++   e  ++l++l+ l  d v
  gi|557694789|ref|YP_008797843.1| 31 SLLVILFGSRARGEETPLSDYDLLVIKKRRGDRVvlkwPAQIFNYTVDEVFEELSRLNTLVLDAV 95
                                      6889**********************999976658888444445555555555555555555555 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0     3e-10   1.8e-06      14      50 ..      32      67 ..      21     107 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3e-10
                                      HSTTEEEEEE-S------EEEEEEEESS---HHHHHH CS
                           Polbeta 14 elaylFGSrakgkareeSDiDlavllkekldleeele 50
                                       l++lFGSra+g+ ++ SD+Dl v+ k++      l+
  gi|557694789|ref|YP_008797843.1| 32 LLVILFGSRARGEETPLSDYDLLVIKKRR-GDRVVLK 67
                                      589*********************99988.2222333 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-06    0.0068      33      86 ..      10      68 ..       2      89 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-06
                            DUF294 33 rrlielaeeelgk.....ppvpfallvmGSeGReEqtlktDqDnalvledeeeeaarey 86
                                      r+l +l e+e++         +  ++ +GS +R+E t  +D D   + +++ ++ + ++
  gi|557694789|ref|YP_008797843.1| 10 RKLSTLKEKEFEAikdelCGDSLLVILFGSRARGEETPLSDYDLLVIKKRRGDRVVLKW 68
                                      566666666666655432345666889****************8777666444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1101.75
//
Query:       gi|557694790|ref|YP_008797844.1|  [L=109]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-14   53.3   0.0    3.4e-14   53.0   0.0    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 !   53.0   0.0   1.9e-18   3.4e-14      28      93 ..      34     101 ..      31     106 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.9e-18
                                       HHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT.....-HHHHHHHHHHHCCCHHCCCTSS- CS
                              HEPN  28 cfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke..seelreeleeLekayiesrYpdak 93 
                                       +f aqq++e +lK+ll+k +g  p+th+++e+l+ l+   ++  +++l  ++++Le++y  +rYpd+ 
  gi|557694790|ref|YP_008797844.1|  34 LFFAQQSVEMLLKGLLVKRTGARPYTHSITEMLNTLSIIFQKevPQDLLICASKLERHYAAARYPDTG 101
                                       79********************************8888887778*********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 790.08
//
Query:       gi|557694791|ref|YP_008797845.1|  [L=353]
Description: sulfonate/nitrate/taurine ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  152.6   0.1    1.8e-44  152.3   0.1    1.1  1  NMT1       NMT1/THI5 like
    8.9e-09   35.4   0.3    9.3e-08   32.1   0.3    2.2  1  NMT1_2     NMT1-like family
     0.0095   15.4   0.0      0.052   13.0   0.0    2.5  1  SBP_bac_3  Bacterial extracellular solute-binding proteins, f
  ------ inclusion threshold ------
      0.048   12.6   0.0       0.08   11.9   0.0    1.3  1  Bmp        ABC transporter substrate-binding protein PnrA-lik
      0.067   12.8   0.3       0.92    9.0   0.3    2.4  1  OpuAC      Substrate binding domain of ABC-type glycine betai


Domain annotation for each model (and alignments):
>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.3   0.1     5e-48   1.8e-44       4     216 .]      56     271 ..      53     271 .. 0.93

  Alignments for each domain:
  == domain 1  score: 152.3 bits;  conditional E-value: 5e-48
                                       GHHHHHHHHTTHHHHTTEEEEEE--SSTTHHHHHHHCTS-SEEEE-HHHHH..HHHHTT--EEEEEEEE-S--EEEE CS
                              NMT1   4 haglyvAkekGYFkeeGldVeivepadpsdatelvasgkadfgvsyqesll..aarakglpvvsvaallqeplsgli 78 
                                        a+++vA ekGYF++eGl V +  + +++da++ vasg+ ++g  + + ++    +  g ++ +v+ +l++p++++i
  gi|557694791|ref|YP_008797845.1|  56 QAPFVVALEKGYFAQEGLAVIVDRGYGSADAVTKVASGAYQMGYGSLDAMIefNVKNPGKELIAVYIVLNNPPYSVI 132
                                       589***********************************************97567779******************* PP

                                       EECCC--SSGGGGTTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHH CS
                              NMT1  79 vlkdsgikspkDLkGkrigyvgspfekallkallakdggdpsdvtlvnvggtslakalltgkvDaaiggyenwegve 155
                                       +lk++gi+spkDL+Gk+ig ++++  + l+  + ++ g+dp++v+ v+++     ++l++g+vDa++g+y +  ++ 
  gi|557694791|ref|YP_008797845.1| 133 TLKGKGINSPKDLEGKKIGAPEGDAPRRLFPVFAKATGIDPNKVEWVSMSPPLREPSLVKGEVDAITGFYFTGYLNL 209
                                       *************************************************9999889***********9887754444 PP

                                       HH..HTT--EEEE-GGGTT-----SEEEEEEHHHHHH-HHHHHHHHHHHHHHHHHHHHSHHHH CS
                              NMT1 156 le..segkelrifaladlgvpdyyslvlitnekllkenpelvkkFlrAlkkGyeyalahPeea 216
                                       l+      ++ +f+++d+gv ++y + +++ ++++++ p++v+kF+rA++++++ ++a+Pe a
  gi|557694791|ref|YP_008797845.1| 210 LAlnVNPNDIIAFKYTDYGV-ELYGNAIMVRKDFMQQYPDAVAKFVRAVNRAFKEVIANPEMA 271
                                       441155559***********.***************************************976 PP

>> NMT1_2  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.3   2.6e-11   9.3e-08      18     249 ..      56     275 ..      49     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2.6e-11
                            NMT1_2  18 aaplvvakekglfakeGltvelekqaswaelrdkllagelDaahvltpapllidlGiggakadmkvlaslnlnGqai 94 
                                        ap vva ekg+fa+eGl v + +  + a +++k+++g + +++ +  a++ ++      k+ ++v + ln  + ++
  gi|557694791|ref|YP_008797845.1|  56 QAPFVVALEKGYFAQEGLAVIVDRGYGSADAVTKVASGAYQMGYGSLDAMIEFNVKN-PGKELIAVYIVLNNPPYSV 131
                                       699******************************************555555554433.3478888999999999999 PP

                            NMT1_2  95 tlsnklkdkkvsdakalkdlvakkkaskplkiavtfpgsthdlllrywLaaaGldpeadvklvvvpppqmvanlkag 171
                                       +  ++      +  ++ kdl       ++ ki++  +g +++ l+  + +a G+dp + v+ v + pp   + l +g
  gi|557694791|ref|YP_008797845.1| 132 ITLKG------KGINSPKDL-------EGKKIGA-PEGDAPRRLFPVFAKATGIDP-NKVEWVSMSPPLREPSLVKG 193
                                       88776......788888888.......6789999.99*******************.99****************99 PP

                            NMT1_2 172 tidgfcv...gePwnaqavaegiGvtal...tsqelwkdhPekvlgvredfveknpntaralvkalleAtkwldakk 242
                                       ++d+ ++   +   n  a++ +   +++   t++ +  +  + +++vr+df++++p+++ ++v+a+ +A k + a++
  gi|557694791|ref|YP_008797845.1| 194 EVDAITGfyfTGYLNLLALNVNPNDIIAfkyTDYGV--ELYGNAIMVRKDFMQQYPDAVAKFVRAVNRAFKEVIANP 268
                                       998766544377777777766665455546666666..556779*************************99998898 PP

                            NMT1_2 243 enraeaa 249
                                       e +a+ +
  gi|557694791|ref|YP_008797845.1| 269 EMAADFV 275
                                       8888776 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   1.4e-05     0.052      87     214 ..     129     269 ..      61     276 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                                       EEEEEEETTSHGTCCHSSCGCGTTSEEEEETTSHHHHHHHHHHHC...TSEEEEESSHHHHHHH..HHTTSSSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxxxxxxxx RF
                         SBP_bac_3  87 qvllvrkkdaskissiksladLkgkkvgvqagstaeellkeelkk...gaeivefdtleealqa..Lkngrvdavva 158
                                        ++++ k+     ++i+s++dL+gkk+g+  g +   l+   +k+   + + ve+ +++  l++  L +g+vda+ +
  gi|557694791|ref|YP_008797845.1| 129 YSVITLKG-----KGINSPKDLEGKKIGAPEGDAPRRLFPVFAKAtgiDPNKVEWVSMSPPLREpsLVKGEVDAITG 200
                                       56677755.....4799999*************988886653333555666678877777777666********987 PP

                                       EHHHHH.HHHHHCCGCCEEEE....ECGGCECEEEEEEETT........THHHHHHHHHHHHHHHHTTH CS
                                       xxxxxx.xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 159 dspvla.ylvkknpdkkvvlv....eeplsseeyaiavrkg........dseLrkainkalaelkadgt 214
                                          + + +l++ n +++ +++    +  ++ ++ ai+vrk+          +++ a+n+a++e++a+ +
  gi|557694791|ref|YP_008797845.1| 201 FYFTGYlNLLALNVNPNDIIAfkytDYGVELYGNAIMVRKDfmqqypdaVAKFVRAVNRAFKEVIANPE 269
                                       776654133344444444444557877777788888888862222221124556666666666666655 PP

>> Bmp  ABC transporter substrate-binding protein PnrA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.2e-05      0.08      56     100 ..      68     112 ..      62     121 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.2e-05
                                       HHCTT-SEEEEESCCHHHHHHHHHHH-TTS-EEEESS--TT-STT CS
                               Bmp  56 lkeegsdlivatgfalqdalqevssdfpkvkFliiDavvekeykn 100
                                       +++eg+ +iv  g+  +da+ +v+s   +++++ +Da++e ++kn
  gi|557694791|ref|YP_008797845.1|  68 FAQEGLAVIVDRGYGSADAVTKVASGAYQMGYGSLDAMIEFNVKN 112
                                       899***********************************9977644 PP

>> OpuAC  Substrate binding domain of ABC-type glycine betaine transport system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.3   0.00026      0.92     202     228 ..     232     261 ..      55     281 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00026
                                       EEEEEEEEHHHHHHSCT.HHHHHHHHC..- CS
                             OpuAC 202 ynvvpvvrkefaekaPe.vaafLekls..l 228
                                       y  +++vrk+f +++P+ va+f+++++  +
  gi|557694791|ref|YP_008797845.1| 232 YGNAIMVRKDFMQQYPDaVAKFVRAVNraF 261
                                       77899************99***99988553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2597.59
//
Query:       gi|557694792|ref|YP_008797846.1|  [L=261]
Description: sulfonate/nitrate/taurine ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  106.1   0.0    2.8e-30  105.6   0.0    1.2  1  ABC_tran      ABC transporter
    2.3e-09   37.5   0.3      0.001   19.0   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0005   20.4   0.2     0.0032   17.8   0.2    2.1  1  AAA_22        AAA domain
     0.0011   18.9   0.0     0.0021   18.0   0.0    1.5  1  Rad17         Rad17 P-loop domain
     0.0016   18.9   0.1     0.0025   18.4   0.1    1.2  1  AAA_23        AAA domain
     0.0023   17.5   0.1      0.081   12.5   0.0    2.3  2  AAA_25        AAA domain
     0.0027   18.1   0.0     0.0039   17.6   0.0    1.5  1  AAA_16        AAA ATPase domain
     0.0032   17.2   0.0     0.0066   16.2   0.0    1.5  2  AAA_15        AAA ATPase domain
     0.0039   16.9   0.0     0.0071   16.1   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.007   15.8   0.0       0.13   11.6   0.1    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0086   15.8   0.0      0.015   15.0   0.0    1.4  1  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.025   14.5   0.1      0.045   13.6   0.1    1.4  1  RsgA_GTPase   RsgA GTPase
      0.027   14.9   0.3       0.05   14.0   0.3    1.8  1  AAA           ATPase family associated with various cellular 
      0.032   14.2   0.1      0.077   12.9   0.1    1.6  2  ATPase_2      ATPase domain predominantly from Archaea
      0.058   13.4   0.0       0.15   12.0   0.0    1.7  1  AAA_5         AAA domain (dynein-related subfamily)
      0.063   12.4   1.6       0.23   10.6   1.6    1.9  1  NB-ARC        NB-ARC domain
       0.11   11.9   0.0          1    8.8   0.0    2.1  2  TniB          Bacterial TniB protein
       0.13   12.0   0.0       0.19   11.5   0.0    1.2  1  AAA_11        AAA domain
       0.15   12.5   0.1       0.36   11.2   0.0    1.6  1  RNA_helicase  RNA helicase
        0.2   10.4   0.0        7.5    5.2   0.0    2.1  2  ABC_ATPase    Predicted ATPase of the ABC class


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 !  105.6   0.0   3.1e-33   2.8e-30       1     136 [.      26     172 ..      26     173 .. 0.89

  Alignments for each domain:
  == domain 1  score: 105.6 bits;  conditional E-value: 3.1e-33
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+nv+l +++g+ + ivG++G+GK+t+lk+++gl +p eGe+ ++ k++++         +g+ +q+p l p  +v 
  gi|557694792|ref|YP_008797846.1|  26 LRNVNLVVEKGSFTSIVGPSGCGKTTILKIVSGLIQPSEGEVYINRKKVEK-----PLPIVGMAFQNPVLLPWRSVL 97 
                                       78****************************************888666555.....8899***************** PP

                                       HH.................HHHTC..HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xx.................xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.................esdee..iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       +n                 +  +   ++kal+ l+l++  +  ++++p +LSgG++qrv+l+ral+ +p++lllDEp
  gi|557694792|ref|YP_008797846.1|  98 QNillplevvephrsqlqkN--RSiyVDKALQLLRLVG-LEGFADKKPWELSGGMQQRVSLCRALIHDPEILLLDEP 171
                                       ***********998876432..3366888888888888.455557888***************************** PP

                                       T CS
                                       x RF
                          ABC_tran 136 t 136
                                       +
  gi|557694792|ref|YP_008797846.1| 172 F 172
                                       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 !   19.0   0.0   1.1e-06     0.001       1      37 [.      38      71 ..      38      88 .. 0.79
   2 !   16.4   0.1   6.7e-06     0.006     234     298 ..     142     204 ..     127     207 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdels 37
                                      ++ ++Gp g+GK+++L++ ++l   ++ +eg+ ++++
  gi|557694792|ref|YP_008797846.1| 38 FTSIVGPSGCGKTTILKIVSGL---IQPSEGEVYINR 71
                                      789*******************...555555555544 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 6.7e-06
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                       ++elS G+++   l  al+ ++    +ll+DEp   L+    ++l+ +l +l   ++  v+++TH+
  gi|557694792|ref|YP_008797846.1| 142 PWELSGGMQQRVSLCRALIHDP---EILLLDEPFGALDLFTREELWNVLQNLWLqTRCTVLMVTHD 204
                                       589999*999989999999888...9***********************9999999*********8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   3.5e-06    0.0032       4      99 ..      35     170 ..      32     209 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.5e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...........erpevvfvtlpsst..sskdllrellralgle 67 
                                       + +++ ++G+sG+GKTt l+ +    +      e           ++ ++v +  +++    ++++l+++l  l++ 
  gi|557694792|ref|YP_008797846.1|  35 KGSFTSIVGPSGCGKTTILKIVSGLIQPS----EgevyinrkkveKPLPIVGMAFQNPVllPWRSVLQNILLPLEVV 107
                                       67899**************9988876422....12356777777655555544444444448888888888777776 PP

                            AAA_22  68 lka...........................erlsseellealeqalrarav....ielliiDE 99 
                                         +                           + ++  el   ++q ++ +++    +e+l++DE
  gi|557694792|ref|YP_008797846.1| 108 EPHrsqlqknrsiyvdkalqllrlvglegfADKKPWELSGGMQQRVSLCRAlihdPEILLLDE 170
                                       666666555555555555555555555555444455555555555555544555555555555 PP

>> Rad17  Rad17 P-loop 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    0.0021      44      70 ..      35      61 ..      17      77 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.4e-06
                             Rad17 44 kkriLLisGPsGCgkstvvkvLskelg 70
                                      k     i GPsGCgk+t++k++s    
  gi|557694792|ref|YP_008797846.1| 35 KGSFTSIVGPSGCGKTTILKIVSGLIQ 61
                                      45566799*************997655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   2.8e-06    0.0025       6      37 ..      16      54 ..      12      58 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2.8e-06
                            AAA_23  6 nfrsf......rdqeidF...skgltlItGpNGaGKTTild 37
                                      +fr +      r+++  +   +  +t I+Gp G+GKTTil 
  gi|557694792|ref|YP_008797846.1| 16 GFRTLnelealRNVN--LvveKGSFTSIVGPSGCGKTTILK 54
                                      566663333224444..444444699*************96 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0     9e-05     0.081      26      50 ..      29      53 ..       6      57 .. 0.85
   2 ?    2.6   0.0     0.096        86     170     188 ..     185     203 ..     179     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9e-05
                            AAA_25 26 vkgllpagelallaGapgtGKttla 50
                                      v  ++ +g+++ ++G++g+GKtt++
  gi|557694792|ref|YP_008797846.1| 29 VNLVVEKGSFTSIVGPSGCGKTTIL 53
                                      667899*****************86 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.096
                            AAA_25 170 ealeriarrtgaavllvhH 188
                                       + l+++  +t+++vl+v H
  gi|557694792|ref|YP_008797846.1| 185 NVLQNLWLQTRCTVLMVTH 203
                                       567778889*********9 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.4e-06    0.0039       8      59 ..      22      73 ..      20     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.4e-06
                            AAA_16  8 eleqLlsalervrsgrpelvllsGesGvGKsslvrellralekd..ggiflrgk 59
                                      ele+L+++   v +g  + + ++G+sG+GK+++++ +   ++ +  +++  r k
  gi|557694792|ref|YP_008797846.1| 22 ELEALRNVNLVVEKG--SFTSIVGPSGCGKTTILKIVSGLIQPSegEVYINRKK 73
                                      778887776677777..67999************98887777663223334444 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   7.4e-06    0.0066      14      64 ..      26      73 ..      17     119 .. 0.85
   2 ?   -2.2   0.0       2.9   2.6e+03     340     365 ..     179     204 ..     160     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.4e-06
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikieked 64
                                      l++v + +++  +t ++G+ ++GK++il++   +++ +    + +++i+ ++
  gi|557694792|ref|YP_008797846.1| 26 LRNVNLVVEKGsFTSIVGPSGCGKTTILKIVSGLIQPS----EGEVYINRKK 73
                                      566666666667******************99999988....4555555544 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.9
                            AAA_15 340 aqkvlikllkelandnktQviitTHS 365
                                         ++l++ l++l  ++++ v++ TH 
  gi|557694792|ref|YP_008797846.1| 179 TREELWNVLQNLWLQTRCTVLMVTHD 204
                                       56789999999999999999999995 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 !   16.1   0.0   7.9e-06    0.0071      19      50 ..      33      64 ..      20      71 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.9e-06
                            AAA_29 19 idlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                      ++ kg +t ++GpsG GK+T+l  ++ l+ p++
  gi|557694792|ref|YP_008797846.1| 33 VE-KGsFTSIVGPSGCGKTTILKIVSGLIQPSE 64
                                      44.5669**************988887777776 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 !   11.6   0.1   0.00015      0.13      23      42 ..      35      54 ..      12      61 .. 0.82
   2 ?    2.2   0.0      0.12   1.1e+02     159     199 ..     163     205 ..      60     225 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                      TSSEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnlld 42
                                      + sft+ivGp G+GK+ +l 
  gi|557694792|ref|YP_008797846.1| 35 KGSFTSIVGPSGCGKTTILK 54
                                      357*************9986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                                       -SEEEECTTTTTS-HHHHHHHHHHHHHH..CTTSEEEEE-SSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                             SMC_N 159 aplyllDeidaaLDeknvkkvaellkek..sknaQfivislre 199
                                         + llDe   aLD   ++++ ++l++   ++++ +++++++ 
  gi|557694792|ref|YP_008797846.1| 163 PEILLLDEPFGALDLFTREELWNVLQNLwlQTRCTVLMVTHDL 205
                                       33679999999****9999999999976114445566666653 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.7e-05     0.015      13      49 ..      32      67 ..      24      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                            AAA_30 13 lltsgdrvavltGpAGtGKttalkalreaweaaggrv 49
                                      ++++g  ++ ++Gp G GKtt+lk +  +++ ++g+v
  gi|557694792|ref|YP_008797846.1| 32 VVEKG-SFTSIVGPSGCGKTTILKIVSGLIQPSEGEV 67
                                      44444.5999****************99999886555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   5.1e-05     0.045      88     126 ..      24      63 ..       6      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.1e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelk 126
                                       e+l++++ ++++ +++ +vG+SG GK+t+++ + +  + +
  gi|557694792|ref|YP_008797846.1|  24 EALRNVNLVVEKgSFTSIVGPSGCGKTTILKIVSGLIQPS 63 
                                       555666666766699***************9887765555 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 ?   14.0   0.3   5.6e-05      0.05       3      22 ..      41      60 ..      39     207 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.6e-05
                                      EESSTTSSHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel 22
                                      ++Gp G+GKT++ k v   +
  gi|557694792|ref|YP_008797846.1| 41 IVGPSGCGKTTILKIVSGLI 60
                                      68************998765 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   0.1   8.5e-05     0.077       7      54 ..      25      69 ..      20      77 .. 0.72
   2 ?   -2.4   0.0       4.1   3.7e+03     125     148 ..     169     190 ..     163     210 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.5e-05
                          ATPase_2  7 elkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyy 54
                                      +l++++ ++e+   ++  i Gp g+GKt++lk i++ l + ++  +y+
  gi|557694792|ref|YP_008797846.1| 25 ALRNVNLVVEK--GSFTSIVGPSGCGKTTILK-IVSGLIQPSEGEVYI 69
                                      56666666666..6788899*********987.555555556666666 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.1
                          ATPase_2 125 DelqklidlglngaellvkeLlnl 148
                                       De + + dl  +  e+l + L+nl
  gi|557694792|ref|YP_008797846.1| 169 DEPFGALDLFTR--EELWNVLQNL 190
                                       555555544433..4444444444 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 ?   12.0   0.0   0.00017      0.15       4      33 ..      41      71 ..      39      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                      EE--SSSSHHHHHHHGGGGB.S--EEEEE-- CS
                             AAA_5  4 LvGppGtgKselaerlaaal.nreveyvqlt 33
                                      +vGp+G+gK+++ + ++ ++  +e e++ ++
  gi|557694792|ref|YP_008797846.1| 41 IVGPSGCGKTTILKIVSGLIqPSEGEVYINR 71
                                      69*****************965555555554 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   1.6   0.00026      0.23      22      41 ..      38      57 ..      23     216 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00026
                                      EEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 22 vvalvGmgGvGKttlakqil 41
                                      + ++vG  G+GKtt++k + 
  gi|557694792|ref|YP_008797846.1| 38 FTSIVGPSGCGKTTILKIVS 57
                                      679************98665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0011         1      19      55 ..      19      56 ..       9     132 .. 0.75
   2 ?    1.1   0.0      0.25   2.2e+02     119     160 ..     162     201 ..     139     213 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                              TniB 19 ilerLeeLleypk.rkrmpnlllvGdsnnGKtmivekF 55
                                       l++Le+L ++    ++ +   +vG+s +GKt+i++  
  gi|557694792|ref|YP_008797846.1| 19 TLNELEALRNVNLvVEKGSFTSIVGPSGCGKTTILKIV 56
                                      5677777777754255557788************9865 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.25
                              TniB 119 kvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                       ++++L++DE   +l     +++e+ n+l++L  + ++++ +v
  gi|557694792|ref|YP_008797846.1| 162 DPEILLLDEPFGAL--DLFTREELWNVLQNLWLQTRCTVLMV 201
                                       67899999988877..7888999******9999999887766 PP

>> AAA_11  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      0.19       8      43 ..      27      61 ..      20      95 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                            AAA_11  8 eaiksalseseitliqGPPGtgKTktivellsqlls 43
                                      ++++ ++++ ++t i GP G+gKT ti++++s l++
  gi|557694792|ref|YP_008797846.1| 27 RNVNLVVEKGSFTSIVGPSGCGKT-TILKIVSGLIQ 61
                                      56688899999************9.46667666653 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0004      0.36       3      39 ..      41      72 ..      39      77 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkklklkkkdsvysrnp 39
                                      ++Gpsg+GK+t+ k  ++ l     ++++++vy++ +
  gi|557694792|ref|YP_008797846.1| 41 IVGPSGCGKTTILKI-VSGLI----QPSEGEVYINRK 72
                                      79***********99.33333....577788888544 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 ?    3.0   0.1      0.04        36     241     263 ..      32      55 ..      20      61 .. 0.87
   2 ?    5.2   0.0    0.0084       7.5     324     372 ..     146     194 ..     141     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.04
                                       EE-SS.EEEEEE-TTSSHHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLeA 263
                                        + kG  t IvG+   GK+T+L+ 
  gi|557694792|ref|YP_008797846.1|  32 VVEKGsFTSIVGPSGCGKTTILKI 55 
                                       5778889**************985 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0084
                                       -HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG-- CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekep 372
                                       SG + q +++ +al  + ++lL+DE   A  l  r e+ + l + + ++
  gi|557694792|ref|YP_008797846.1| 146 SGGMQQRVSLCRALIHDPEILLLDEPFGALDLFTREELWNVLQNLWLQT 194
                                       9**********************************99877766555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 1987.98
//
Query:       gi|557694793|ref|YP_008797847.1|  [L=259]
Description: sulfonate/nitrate/taurine ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   80.1  19.4    1.7e-22   80.1  19.4    1.9  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 ?    0.2   0.4      0.03   5.4e+02      29     122 ..      18      35 ..       6      79 .. 0.58
   2 !   80.1  19.4   9.2e-27   1.7e-22       2     183 ..      81     253 ..      80     255 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.03
                      BPD_transp_1  29 slPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPn 105
                                       +lP+ v+a +++l                                                                
  gi|557694793|ref|YP_008797847.1|  18 ALPTAVFAGFFLL---------------------------------------------------------------- 30 
                                       3333333333332................................................................ PP

                      BPD_transp_1 106 alppiitglilafggll 122
                                                   + ++ 
  gi|557694793|ref|YP_008797847.1|  31 ------------WEAVT 35 
                                       ............22222 PP

  == domain 2  score: 80.1 bits;  conditional E-value: 9.2e-27
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraal 76 
                                       i++G+l++  + +++++ ++++pl  ++ ++P ++++++lv       ++g +  p++++++l ++++++++++ al
  gi|557694793|ref|YP_008797847.1|  81 IVFGLLLGlaVGYSSIIYRAVYPLLVAFNTIPKVAIVPILV------IWFGIGKVPAVLTAFLISFFPIVVNVAVAL 151
                                       778888888888*****************************......9***************************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                        +++ + + + r lGas+ q+f+k+ +P ++p+++ +l +a+++++ gav+ e ++s+ G g+l++ a++ +d++  
  gi|557694793|ref|YP_008797847.1| 152 ATIEPEIRDVLRSLGASKTQLFVKIGVPRSMPYFFGSLKVASTLAFVGAVISESVASNEGTGYLMIAASSRFDVP-- 226
                                       ***************************************************************************.. PP

                      BPD_transp_1 154 snggvlalviavlllnlvadilqrlldprv 183
                                          +v+a+++++  + ++++++ +ll++r+
  gi|557694793|ref|YP_008797847.1| 227 ---LVFAGLLVISFIGISLFLVFALLEKRL 253
                                       ...566666666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1871.78
//
Query:       gi|557694794|ref|YP_008797848.1|  [L=135]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  111.3   0.0    3.6e-32  111.1   0.0    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 !  111.1   0.0     2e-36   3.6e-32       1     123 [.       5     130 ..       5     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.1 bits;  conditional E-value: 2e-36
                                       -S---SHHHHHGGGSBSS-EEHHHHHHT--EEEB.TTS-EEE--HHHHHHHHTTS-GGGGGT-EESEEEEE-SSSSE CS
                             DUF61   1 drilakeiksinkhlPaerktLkelLeeekptivtkdgsehrfdkeeleklkeilpeelwdklkLPIllemdpelge 77 
                                       d++la++++++n+ lP++ ++L+ lLe+ekp+++t  g  h+fdk+ele+l ++lp+e+ ++l+LPI+++++pelge
  gi|557694794|ref|YP_008797848.1|   5 DDWLAETMRHVNDALPRRAEKLSTLLEMEKPSVETVGGGLHYFDKKELEELLRKLPREVSENLYLPIVFAKNPELGE 81 
                                       579************************************************************************** PP

                                       ..EEEES-HH.HHHHHHHHT--.....-SSEEEHH.HHHHHHHH-ST.. CS
                             DUF61  78 svylvrgkae.vkvvskilgke..reeedelviykpevrelrrklptat 123
                                       s+y+v+ +   +++ ++++g++   +  ++ + ykp v+e+++++pt+ 
  gi|557694794|ref|YP_008797848.1|  82 STYIVKARGSeAEAFRILMGLRtlPRVGNQPYTYKPLVTEFINRYPTLA 130
                                       ********999***********99889********************86 PP



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:                      365  (0.0203581); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 999.87
//
Query:       gi|557694795|ref|YP_008797849.1|  [L=102]
Description: hypothetical protein CSUB_C1368 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.089   12.8   0.1      0.089   12.8   0.1    2.0  2  Phage_holin_2_1  Bacteriophage P21 holin S
        0.4   10.7   4.1         12    6.0   0.2    2.3  2  DUF543           Domain of unknown function (DUF543)
       0.83   10.1   3.9        1.1    9.7   3.7    1.4  1  DUF4231          Protein of unknown function (DUF4231)
          6    7.3   9.8        6.5    7.2   2.9    2.3  2  FUN14            FUN14 family


Domain annotation for each model (and alignments):
>> Phage_holin_2_1  Bacteriophage P21 holin S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.3      0.43   1.9e+03      34      42 ..      17      25 ..       9      47 .. 0.68
   2 ?   12.8   0.1     2e-05     0.089      19      49 ..      68      98 ..      62     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.43
                   Phage_holin_2_1 34 aigvlgglv 42
                                      +ig  +gl+
  gi|557694795|ref|YP_008797849.1| 17 FIGFGAGLA 25
                                      444444443 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2e-05
                   Phage_holin_2_1 19 wlkqlldklspeeWsaigvlgglvigllTyl 49
                                      +++ l   l +++ sa+g + g+++gllTy+
  gi|557694795|ref|YP_008797849.1| 68 GVNLLASLLASNNYSALGFIVGVILGLLTYA 98
                                      566666778999*****************97 PP

>> DUF543  Domain of unknown function (DUF543)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.5    0.0028        13      52      65 ..      12      25 ..       9      28 .. 0.90
   2 ?    6.0   0.2    0.0027        12      31      45 ..      81      95 ..      72     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0028
                            DUF543 52 apvalGaGvGiGaA 65
                                      a++++ +G+G+G A
  gi|557694795|ref|YP_008797849.1| 12 AVIWFFIGFGAGLA 25
                                      789*********87 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0027
                            DUF543 31 kvglgllvGvvasvl 45
                                      +++lg++vGv++++l
  gi|557694795|ref|YP_008797849.1| 81 YSALGFIVGVILGLL 95
                                      689**********98 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.7   0.00025       1.1      13      62 ..      25      78 ..      21      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00025
                           DUF4231 13 akrrfrllrlitivlgallpilvs....sklgagvsvlkiltallsalvailaa 62
                                      a  rf+ + ++ +vl++llp+++s    s   ++ +v++++  ++++l+++la+
  gi|557694795|ref|YP_008797849.1| 25 ALLRFWKVLILVVVLAVLLPFIISlagvSSPLTPEQVIAAFFNGVNLLASLLAS 78
                                      56699999****************999955666666777777777777776665 PP

>> FUN14  FUN14 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   2.9    0.0014       6.5       5      37 ..      16      48 ..      13      54 .. 0.86
   2 ?    4.1   0.6     0.013        60      72      91 .]      75      94 ..      59      94 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0014
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             FUN14  5 aviGlvtGfalkkvgKlaaiavGggllllqila 37
                                      ++iG+ +G+al ++ K+++++v +++ll  i++
  gi|557694795|ref|YP_008797849.1| 16 FFIGFGAGLALLRFWKVLILVVVLAVLLPFIIS 48
                                      789*******************99999876666 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.013
                                      xxxxxxxxxxxxxxxxxxxx RF
                             FUN14 72 lltenlpfsagFlaGfllGl 91
                                      ll +n   + gF+ G++lGl
  gi|557694795|ref|YP_008797849.1| 75 LLASNNYSALGFIVGVILGL 94
                                      55667778899999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); 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:                         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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 728.45
//
Query:       gi|557694796|ref|YP_008797850.1|  [L=128]
Description: translation initiation inhibitor [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  132.8   0.1    6.8e-39  132.6   0.1    1.0  1  Ribonuc_L-PSP  Endoribonuclease L-PSP
  ------ inclusion threshold ------
      0.057   13.2   0.0      0.068   13.0   0.0    1.1  1  Capsid_NCLDV   Large eukaryotic DNA virus major capsid protei


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 !  132.6   0.1   7.6e-43   6.8e-39       2     120 ..       9     125 ..       8     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: 132.6 bits;  conditional E-value: 7.6e-43
                                       TTSTTTSSS-BSEEEETTEEEEEEE-SB-TTTSCB.-SSHHHHHHHHHHHHHHHHHHTT--GGGEEEEEEEESSGGG CS
                     Ribonuc_L-PSP   2 eaapaaaapYsqavkagnlvyvsGqlpldpetgelvegdveeqtrqalenlkavLaaagaslsdvVkvtvFladied 78 
                                       e+ap++++pYsqav++g+++++sG ++++p+tg++ e+d++ qtr+++en+ka+L+aag+s+++vVk+tv+la+ +d
  gi|557694796|ref|YP_008797850.1|   9 EKAPKPIGPYSQAVRVGDFLFLSGMVAINPATGKVEETDIRSQTRRVMENAKAILEAAGLSFEHVVKATVYLANPDD 85 
                                       79*************************************************************************** PP

                                       HHHHHHHHHHHSSSSTS--EEEEEE-SBSGGG-SEEEEEEEE CS
                     Ribonuc_L-PSP  79 faevnevyaeafdelkeaParsaveVaaLpkgakvEIeaiav 120
                                       fa++nevy ++f+++   Par++v+V    k+++vEI+ ia+
  gi|557694796|ref|YP_008797850.1|  86 FAAMNEVYSQYFPQNP--PARTTVAVHFPRKEFLVEIDFIAY 125
                                       ***************5..*********999**********97 PP

>> Capsid_NCLDV  Large eukaryotic DNA virus major capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.6e-06     0.068      17      70 ..      48     101 ..      35     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.6e-06
                                       EEEEEEEE--SSS--EEEEEE---SEEEEEEEEEE-TTSTT--S---T-BTTS- CS
                      Capsid_NCLDV  17 vqftgeevvsatssnsakekLnFnhpvkalyfvvrntalqdaksmtsqYtvtdp 70 
                                       ++ ++++v++++++  +   L+F h+vka ++  + +++   +++ sqY   +p
  gi|557694796|ref|YP_008797850.1|  48 IRSQTRRVMENAKAILEAAGLSFEHVVKATVYLANPDDFAAMNEVYSQYFPQNP 101
                                       66788888899999999999********************99997777755555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 948.13
//
Query:       gi|557694797|ref|YP_008797851.1|  [L=708]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  152.4   0.3    2.2e-44  151.4   0.3    1.5  1  LUD_dom   LUD domain
    5.3e-09   36.4  11.5    5.7e-08   33.1   5.7    2.7  2  Fer4_8    4Fe-4S dicluster domain
    1.1e-08   35.0   2.2    0.00092   19.3   0.2    2.4  2  Fer4_10   4Fe-4S dicluster domain
    7.2e-07   29.7   2.3    2.4e-06   28.0   2.3    2.0  1  Fer4_17   4Fe-4S dicluster domain
    1.2e-06   28.0  16.2     0.0013   18.4   3.7    2.4  2  Fer4      4Fe-4S binding domain
    1.7e-06   28.1   0.2    1.3e-05   25.4   0.9    2.2  2  CCG       Cysteine-rich domain
    2.4e-06   27.4  11.5     0.0054   16.8   2.1    2.4  2  Fer4_6    4Fe-4S binding domain
      1e-05   25.7   9.3     0.0063   16.9   2.2    2.6  2  Fer4_4    4Fe-4S binding domain
    6.8e-05   23.0   8.4     0.0031   17.7   9.9    2.4  2  Fer4_9    4Fe-4S dicluster domain
    0.00011   21.9   0.9      0.026   14.3   0.1    2.5  2  Fer4_20   Dihydroprymidine dehydrogenase domain II, 4Fe-4S cl
    0.00013   22.5   9.1     0.0014   19.2   9.5    2.3  2  Fer4_7    4Fe-4S dicluster domain
    0.00015   21.9   5.7      0.085   13.0   0.9    2.6  2  Fer4_21   4Fe-4S dicluster domain
    0.00018   21.7   2.4       0.26   11.5   0.3    2.7  2  Fer4_18   4Fe-4S dicluster domain
    0.00034   21.5   6.3       0.41   11.6   1.6    2.6  2  Fer4_16   4Fe-4S double cluster binding domain
    0.00049   20.0  12.6      0.021   14.9   2.6    2.6  2  Fer4_2    4Fe-4S binding domain
     0.0034   17.9  10.6      0.077   13.6   0.3    3.1  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.071   12.8   0.0    1.7  2  DUF460    Protein of unknown function (DUF460)
      0.025   15.5  14.9       0.19   12.7   3.6    2.7  2  Fer4_3    4Fe-4S binding domain
      0.039   14.8   8.1        1.8    9.5   0.2    2.7  2  Fer4_22   4Fe-4S dicluster domain
      0.051   14.3   2.6        3.3    8.5   0.1    2.8  2  Fer4_15   4Fe-4S single cluster 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 !  151.4   0.3   2.5e-47   2.2e-44       1     188 [.      72     295 ..      72     296 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.4 bits;  conditional E-value: 2.5e-47
                           LUD_dom   1 leefienleangaevyyaktaeealelilellkeksv.......................vseggstdlgeigl... 51 
                                       l++fi+n+e++g++vy+ak+ae+a++++++++++k++                       ++ +++tdlge+++   
  gi|557694797|ref|YP_008797851.1|  72 LQQFIQNCEKRGTRVYVAKDAEDACRIVYRIAEQKNArlitksksmtteeiglnqflekhGLRVVDTDLGELIVqla 148
                                       689************************************************************************** PP

                           LUD_dom  52 ........apalhsgreevldlfeekl...........treareelrekfltadvgitganfaiAetGtlvlvdneg 109
                                                pa+h++r++v++lf+++            +++are lre+flta+ +itg+n+aiAetGt+++ +neg
  gi|557694797|ref|YP_008797851.1| 149 gerpfhlvYPAVHKTRQDVAELFSREAgrklsddiselMNFAREYLRERFLTAELAITGVNIAIAETGTVIVETNEG 225
                                       ***************************************************************************** PP

                           LUD_dom 110 nrraltflpkvhivvvginkivpdledavkrlktaprnatrlqkktpyvsfisgpsrtadielvlvygvhgpkrihv 186
                                       n r+ +   k++i+v+g++k+v+++eda+k++   p + t+ q +t+yvsf sg    a +           +++h+
  gi|557694797|ref|YP_008797851.1| 226 NDRLGNIPAKTYIAVMGMEKLVEKIEDALKLIVAHPVSSTG-QWLTNYVSFLSGRTPLAGHA--------EEREMHI 293
                                       *****************************************.**********9976555544........5666666 PP

                           LUD_dom 187 il 188
                                       ++
  gi|557694797|ref|YP_008797851.1| 294 VI 295
                                       66 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   5.7   6.3e-11   5.7e-08       2      63 ..     312     377 ..     311     379 .. 0.81
   2 !   15.4   0.3   2.2e-05      0.02       5      32 ..     365     392 ..     360     414 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 6.3e-11
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtk.khlldargeaae.....dvqeeqvlee....eealwsCttcgaCtevCpv 63 
                                       + +Ci+CgaC++ Cp++++ + +   + + + ++            +++    +e +  C +cg C+e Cp+
  gi|557694797|ref|YP_008797851.1| 312 ALYCIRCGACMNICPTYSSLGgHVFGHIYTGPIGipwtaF------VHGlekaAEFAPLCISCGLCKEICPT 377
                                       679******************8888899999999666431......2223344899***************7 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 2.2e-05
                            Fer4_8   5 CieCgaCqsaCpvlrrtkkhlldargea 32 
                                       Ci Cg+C++ Cp++ ++  ++ + +++ 
  gi|557694797|ref|YP_008797851.1| 365 CISCGLCKEICPTIIDMPYMIAEVKHRY 392
                                       ***********98777665555544443 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2     1e-06   0.00092       6      22 ..     312     328 ..     307     349 .. 0.83
   2 !   15.0   0.1   2.3e-05     0.021       8      24 ..     364     390 ..     358     411 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1e-06
                           Fer4_10   6 ddtCirCgkCvkaCPad 22 
                                       +  CirCg+C++ CP++
  gi|557694797|ref|YP_008797851.1| 312 ALYCIRCGACMNICPTY 328
                                       567************94 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.3e-05
                           Fer4_10   8 tCirCgkCvkaCPadl..........t 24 
                                        Ci Cg C++ CP+ +          +
  gi|557694797|ref|YP_008797851.1| 364 LCISCGLCKEICPTIIdmpymiaevkH 390
                                       5*************6666666654442 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   2.3   2.7e-09   2.4e-06       2      60 ..     315     379 ..     314     380 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.7e-09
                           Fer4_17   2 CiqCgyClpeCpsyeaydnepkkllraakl.....glleea.ekeekaslCieCgeCerkCPqgl 60 
                                       Ci+Cg+C++ Cp+y   + +    ++   +     + +++  ++ e a lCi+Cg+C++ CP  +
  gi|557694797|ref|YP_008797851.1| 315 CIRCGACMNICPTYSSLGGHVFGHIYTGPIgipwtAFVHGLeKAAEFAPLCISCGLCKEICPTII 379
                                       **************997775333333333333545333334034689***************865 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   3.7   1.5e-06    0.0013       8      20 ..     315     327 ..     312     328 .. 0.93
   2 !   14.8   4.7   2.1e-05     0.019       7      20 ..     364     377 ..     363     377 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
                                       SSS-THHHHHSTT CS
                              Fer4   8 CigCGaCvevCPv 20 
                                       Ci+CGaC+++CP+
  gi|557694797|ref|YP_008797851.1| 315 CIRCGACMNICPT 327
                                       ************8 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 2.1e-05
                                       TSSS-THHHHHSTT CS
                              Fer4   7 kCigCGaCvevCPv 20 
                                       +Ci CG+C e+CP+
  gi|557694797|ref|YP_008797851.1| 364 LCISCGLCKEICPT 377
                                       6************7 PP

>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.4   4.8e+03      52      79 ..     519     548 ..     509     554 .. 0.70
   2 !   25.4   0.9   1.4e-08   1.3e-05       2      84 ..     601     685 ..     600     686 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.4
                               CCG  52 elaealakrnvetaeet..gadaivtacpg 79 
                                       ++a++la+ nv ++ ++  +  +iv++ p+
  gi|557694797|ref|YP_008797851.1| 519 DKARKLAEYNVGNLSKAlgDGAVIVSIEPT 548
                                       588999999999999965456777777776 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.4e-08
                               CCG   2 ayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkee.....laealakrnvetaeetgadai 73 
                                       a++ +Ch    ++ +  + + +ll+ +g++  + e  +CCG +g++ +k+      l++ ++++ ++ ++  g  ++
  gi|557694797|ref|YP_008797851.1| 601 AVHIPCH---ERAFNSCREVVALLNTAGIDATVVETGTCCGMAGTFGMKHGvlgyeLSNVVGEELFSRMKASGCSYV 674
                                       79999*4...55555666688899*************************8777777999****************** PP

                               CCG  74 vtacpgCllql 84 
                                       v++++ C++++
  gi|557694797|ref|YP_008797851.1| 675 VSTSSVCKIHI 685
                                       ********998 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   2.1     6e-06    0.0054       9      22 ..     315     328 ..     311     331 .. 0.93
   2 !   15.1   2.2     2e-05     0.018       7      21 ..     363     377 ..     359     382 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6e-06
                            Fer4_6   9 CigCgdCvrvCPeg 22 
                                       Ci Cg+C+++CP++
  gi|557694797|ref|YP_008797851.1| 315 CIRCGACMNICPTY 328
                                       ************85 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2e-05
                            Fer4_6   7 dkCigCgdCvrvCPe 21 
                                        +Ci+Cg C  +CP+
  gi|557694797|ref|YP_008797851.1| 363 PLCISCGLCKEICPT 377
                                       69************8 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.2     7e-06    0.0063       4      16 ..     315     327 ..     311     330 .. 0.93
   2 !   12.1   0.8   0.00025      0.22       4      16 ..     365     377 ..     358     387 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 7e-06
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       Ci+Cg+C+++CP+
  gi|557694797|ref|YP_008797851.1| 315 CIRCGACMNICPT 327
                                       ************6 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00025
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       Ci Cg C  +CP+
  gi|557694797|ref|YP_008797851.1| 365 CISCGLCKEICPT 377
                                       ************5 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   1.8   6.9e-05     0.062      34      48 ..     313     327 ..     290     330 .. 0.69
   2 !   17.7   9.9   3.4e-06    0.0031       1      48 [.     314     377 ..     314     381 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.9e-05
                            Fer4_9  34 eaCigCgaCveaCpk 48 
                                         Ci CgaC+++Cp+
  gi|557694797|ref|YP_008797851.1| 313 LYCIRCGACMNICPT 327
                                       458888888888886 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3.4e-06
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase................eaCigCgaCveaCpk 48 
                                       +C++CgaC++ Cp+    + ++ + +     +                   Ci+Cg C e+Cp+
  gi|557694797|ref|YP_008797851.1| 314 YCIRCGACMNICPTYSSLGGHVFGHIYTGPIGIpwtafvhglekaaefaPLCISCGLCKEICPT 377
                                       6***********666655555555555444444566667777777777778************7 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 ?    5.5   0.1     0.015        14      13      41 ..     304     330 ..     296     337 .. 0.81
   2 !   14.3   0.1   2.9e-05     0.026      15      59 ..     356     398 ..     350     406 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.015
                                       -HHHHHHHHTT----TT-HHHHCSTT--- CS
                           Fer4_20  13 teeealeeAsRClqCkkapcvkgCPveid 41 
                                       +++ + +eA  C++C    c++ CP+  +
  gi|557694797|ref|YP_008797851.1| 304 RDDPVFREALYCIRC--GACMNICPTYSS 330
                                       5566789********..78******9765 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHTT----TT-HHHHCSTT---HHHHHHHHHTT-HHHHHH CS
                           Fer4_20  15 eealeeAsRClqCkkapcvkgCPveidipefikkiaegnleeaak 59 
                                       e+a+e A  C++C    c++ CP+ id+p +i +++++ +++  +
  gi|557694797|ref|YP_008797851.1| 356 EKAAEFAPLCISC--GLCKEICPTIIDMPYMIAEVKHRYVQKGGQ 398
                                       678888999****..89*******************999887765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   9.5   1.5e-06    0.0014       2      50 ..     315     377 ..     314     379 .. 0.69
   2 !   10.1   1.8     0.001      0.92       2      14 ..     365     377 ..     364     398 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.5e-06
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenek..............gtekveidpekClgCgaCvavCPt 50 
                                       Ci CgaC++ Cp++      +  +               g ek++  +  C++Cg C + CPt
  gi|557694797|ref|YP_008797851.1| 315 CIRCGACMNICPTYSSLGGHVFGHIytgpigipwtafvhGLEKAAEFAPLCISCGLCKEICPT 377
                                       ************66666554433333444444343333355777777788************8 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.001
                            Fer4_7   2 CigCgaCvaaCpv 14 
                                       Ci Cg C + Cp+
  gi|557694797|ref|YP_008797851.1| 365 CISCGLCKEICPT 377
                                       7888888888874 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.3   0.00063      0.57       8      20 ..     315     327 ..     299     333 .. 0.71
   2 !   13.0   0.9   9.5e-05     0.085      39      58 ..     363     380 ..     349     381 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00063
                           Fer4_21   8 CigCgkCliaCed 20 
                                       Ci Cg C+  C++
  gi|557694797|ref|YP_008797851.1| 315 CIRCGACMNICPT 327
                                       6666666666654 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 9.5e-05
                           Fer4_21  39 deCvGCnlCssvCPvedcie 58 
                                         C+ C lC ++CP+   i+
  gi|557694797|ref|YP_008797851.1| 363 PLCISCGLCKEICPT--IID 380
                                       57************6..555 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.1    0.0016       1.4      58      73 ..     312     327 ..     287     332 .. 0.84
   2 !   11.5   0.3   0.00029      0.26      59      77 ..     363     381 ..     351     385 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0016
                           Fer4_18  58 agdcidcescvkvcPt 73 
                                       a  ci c++c+++cPt
  gi|557694797|ref|YP_008797851.1| 312 ALYCIRCGACMNICPT 327
                                       556************9 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00029
                           Fer4_18  59 gdcidcescvkvcPtgidi 77 
                                         ci+c+ c ++cPt id+
  gi|557694797|ref|YP_008797851.1| 363 PLCISCGLCKEICPTIIDM 381
                                       56***************96 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 !   11.6   1.6   0.00046      0.41       2      14 ..     315     327 ..     314     334 .. 0.90
   2 !   11.5   0.2   0.00051      0.46       2      14 ..     365     377 ..     364     408 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00046
                           Fer4_16   2 CgtCgkCaevCPt 14 
                                       C++Cg+C+++CPt
  gi|557694797|ref|YP_008797851.1| 315 CIRCGACMNICPT 327
                                       ************9 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00051
                           Fer4_16   2 CgtCgkCaevCPt 14 
                                       C++Cg C e+CPt
  gi|557694797|ref|YP_008797851.1| 365 CISCGLCKEICPT 377
                                       9***********8 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   2.6   2.3e-05     0.021       7      22 .]     312     327 ..     306     327 .. 0.82
   2 !    9.9   2.6   0.00089       0.8       9      22 .]     364     377 ..     358     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.3e-05
                            Fer4_2   7 tdrCigCgaCvsaCPa 22 
                                       +  Ci+CgaC + CP+
  gi|557694797|ref|YP_008797851.1| 312 ALYCIRCGACMNICPT 327
                                       556************7 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00089
                            Fer4_2   9 rCigCgaCvsaCPa 22 
                                        Ci+Cg C   CP+
  gi|557694797|ref|YP_008797851.1| 364 LCISCGLCKEICPT 377
                                       5************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 !    7.8   2.9    0.0054       4.9       6      18 ..     315     327 ..     313     328 .. 0.93
   2 !   13.6   0.3   8.5e-05     0.077       6      22 ..     365     381 ..     363     398 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0054
                           Fer4_13   6 CiacgaCvelaPd 18 
                                       Ci cgaC +++P 
  gi|557694797|ref|YP_008797851.1| 315 CIRCGACMNICPT 327
                                       ************6 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 8.5e-05
                           Fer4_13   6 CiacgaCvelaPdvFee 22 
                                       Ci+cg+C e++P + ++
  gi|557694797|ref|YP_008797851.1| 365 CISCGLCKEICPTIIDM 381
                                       ************98665 PP

>> DUF460  Protein of unknown function (DUF460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     8e-05     0.071      65     113 ..      73     121 ..      59     134 .. 0.92
   2 ?   -3.5   0.0       8.5   7.6e+03      87     106 ..     243     262 ..     240     265 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8e-05
                            DUF460  65 eevieliselGkpvivAtDvspppetvkklarslkavlyvPeedlsvee 113
                                       ++ i+   + G+ v vA D +++ ++v ++a++ +a+l + ++++++ee
  gi|557694797|ref|YP_008797851.1|  73 QQFIQNCEKRGTRVYVAKDAEDACRIVYRIAEQKNARLITKSKSMTTEE 121
                                       57899999*************************************9987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.5
                            DUF460  87 ppetvkklarslkavlyvPe 106
                                       + ++v+k++ +lk ++ +P 
  gi|557694797|ref|YP_008797851.1| 243 MEKLVEKIEDALKLIVAHPV 262
                                       67899999999998888885 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.6   0.00021      0.19       1      13 [.     315     327 ..     315     329 .. 0.94
   2 ?    7.8   3.5    0.0082       7.4       1      13 [.     365     377 ..     365     377 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+ CgaC++ CP+
  gi|557694797|ref|YP_008797851.1| 315 CIRCGACMNICPT 327
                                       ************6 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0082
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+ Cg+C e CP+
  gi|557694797|ref|YP_008797851.1| 365 CISCGLCKEICPT 377
                                       ************6 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   2.9     0.011       9.7       2      15 ..     315     328 ..     314     332 .. 0.89
   2 ?    9.5   0.2     0.002       1.8       2      15 ..     365     378 ..     364     410 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.011
                           Fer4_22   2 ClsCgaCtlvCptC 15 
                                       C++CgaC  +Cpt 
  gi|557694797|ref|YP_008797851.1| 315 CIRCGACMNICPTY 328
                                       ************95 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.002
                           Fer4_22   2 ClsCgaCtlvCptC 15 
                                       C+sCg C+ +Cpt 
  gi|557694797|ref|YP_008797851.1| 365 CISCGLCKEICPTI 378
                                       999********996 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 ?    4.9   0.3      0.05        45       8      22 ..     315     329 ..     310     342 .. 0.88
   2 ?    8.5   0.1    0.0037       3.3       7      24 ..     364     381 ..     362     403 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.05
                           Fer4_15   8 CigcglCvaeapevf 22 
                                       Ci cg+C+  +p++ 
  gi|557694797|ref|YP_008797851.1| 315 CIRCGACMNICPTYS 329
                                       ************985 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0037
                           Fer4_15   7 aCigcglCvaeapevfel 24 
                                       +Ci+cglC + +p+++ +
  gi|557694797|ref|YP_008797851.1| 364 LCISCGLCKEICPTIIDM 381
                                       7************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (708 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); 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: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 4761.67
//
Query:       gi|557694798|ref|YP_008797852.1|  [L=194]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-20   72.9   0.0    1.4e-18   67.3   0.0    2.0  1  LUD_dom       LUD domain
  ------ inclusion threshold ------
      0.034   13.7   0.0       0.15   11.6   0.1    1.7  2  Peripla_BP_4  Periplasmic binding protein domain
      0.086   12.5   0.0       0.15   11.8   0.0    1.4  1  OB_RNB        Ribonuclease B OB 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 !   67.3   0.0   2.3e-22   1.4e-18       4     187 ..      17     189 ..      14     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 2.3e-22
                           LUD_dom   4 fienleangaevyyaktaeealelilellkeksvvseggstdlgeiglapalhsgreevldlfeekl.treareelr 79 
                                       f+e+++  g+ + +a++ e a+  +++ l+++      gs +++ + l   l +  e++l+ +  +  t ++ e+  
  gi|557694798|ref|YP_008797852.1|  17 FMERFRILGGYAALADNPESAATVAADFLRQH------GSRTVFVYKLPTGLTQPVEKKLKEMGIQAyTYDSSEDPV 87 
                                       88888899999999999999999999999999......557777777755555555544444444444455577777 PP

                           LUD_dom  80 ekfltadvgitganfaiAetGtlvlvdnegnrraltflpkvhivvvginkivpdledavkrlktaprnatrlqkktp 156
                                       +    +d+gi+ a +a+AetGtlv v      r++++lpk++++ v  + +v++++   ++l+  ++     ++   
  gi|557694798|ref|YP_008797852.1|  88 NVVKIVDAGISTAAAAVAETGTLVEVAFDDVERLVSSLPKTYVCFVNGSSVVKSVYMTSDLLRS-AM-----ERDRV 158
                                       777889**********************************************************.23.....34558 PP

                           LUD_dom 157 yvsfisgpsrtadielvlvygvhgpkrihvi 187
                                        v+fisgpsr++die+ lv g hgp  +  +
  gi|557694798|ref|YP_008797852.1| 159 AVTFISGPSRSGDIEQRLVLGIHGPHHVLAV 189
                                       9************************877655 PP

>> Peripla_BP_4  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   2.5e-05      0.15     154     221 ..      20      85 ..       4     124 .. 0.69
   2 ?    8.9   0.1   0.00017         1      67     133 ..      60     137 ..      53     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.5e-05
                                       TCEECCEEESTTTCHHHHHHHHHHHHHTT.T.ECEEEESSCCHHHCHHHHHHHTTTTSTEEEEEES-HHH CS
                      Peripla_BP_4 154 gikivaevaganwdaekaqqalealltan.p.ldgilaandgmaegalealeaaglagkvvvtgqDatpe 221
                                        + i++ +a+  +++e a + ++++l+++ +  ++++   +g ++++ ++l++ g++     +++D+++ 
  gi|557694798|ref|YP_008797852.1|  20 RFRILGGYAALADNPESAATVAADFLRQHgSrTVFVYKLPTGLTQPVEKKLKEMGIQ----AYTYDSSED 85 
                                       678888999999***************884599********************9986....344444333 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00017
                                       HHHH.HHHHHHHHTT-EEEEESTTGCTTT-CEEEEEC-HHHHHHHHH.............HHHHHHCTTH.EEEEEE CS
                      Peripla_BP_4  67 tala.palkkakaaGIpVvafdsddapsgerlayvgfdneaaGelqa.............eylaeklggkkgkvvil 129
                                       t+l+ p+ kk+k+ GI   ++ds   +  +++  v +   +a+++ a             e l++ l++    v+ +
  gi|557694798|ref|YP_008797852.1|  60 TGLTqPVEKKLKEMGIQAYTYDSS-EDPVNVVKIVDAGISTAAAAVAetgtlvevafddvERLVSSLPK--TYVCFV 133
                                       5666477778**************.99999999999999999999998888888888888888888884..577777 PP

                                       TSCC CS
                      Peripla_BP_4 130 aGsp 133
                                       +Gs 
  gi|557694798|ref|YP_008797852.1| 134 NGSS 137
                                       7765 PP

>> OB_RNB  Ribonuclease B OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.4e-05      0.15      11      56 ..     131     177 ..     122     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.4e-05
                                       EEEEECT.TEEEEE-HHHHTTS-TT-EEEEEEEE.SSSEEEEEEEEE CS
                            OB_RNB  11 GFlipdegkeDifippeqmkkamhGDrVlvritk.gdrrgrregrvv 56 
                                       +F+   +  ++++  ++ +++am  DrV v+  +  +r g+ e+r+v
  gi|557694798|ref|YP_008797852.1| 131 CFVNGSSVVKSVYMTSDLLRSAMERDRVAVTFISgPSRSGDIEQRLV 177
                                       677777777999*******************9998899888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 00:00:00.39
# Mc/sec: 1488.63
//
Query:       gi|557694799|ref|YP_008797853.1|  [L=122]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   44.2   0.4      4e-11   43.3   0.4    1.5  1  Trm112p       Trm112p-like protein
  ------ inclusion threshold ------
      0.035   14.2   0.2        0.1   12.7   0.2    1.8  2  zf-Dof        Dof domain, zinc finger
       0.11   12.7   0.0       0.14   12.4   0.0    1.1  1  Pox_vIL-18BP  Orthopoxvirus interleukin 18 binding protein


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 !   43.3   0.4   6.8e-15     4e-11       1      68 []       2      84 ..       2      84 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 6.8e-15
                                      BTGGCCC-B-TTTHH.C--HHHHHHHHHTT---.S-SS----S................CHHTTEECCCCEEEETTTTE CS
                           Trm112p  1 kllllniLaCpackg.pLdwealvevaalglne.lpkekpedy................ellleldieegeLvCpncgr 61
                                      k++l++iLaCp+ck+ pL++ ++ e+    +++ +   ++e y                e ++ l+i +g   C  cgr
  gi|557694799|ref|YP_008797853.1|  2 KYRLMDILACPMCKSfPLKLVVFEERI---IEKpPFIRQCELYcalhggyvrdfsktdcERCYGLEIASGYVECGGCGR 77
                                      79**************99544444444...344344455666699**************99****************** PP

                                      EEEEETT CS
                           Trm112p 62 aYpIkdG 68
                                      +Yp+ d+
  gi|557694799|ref|YP_008797853.1| 78 WYPVVDE 84
                                      ****995 PP

>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.7e-05       0.1       3      48 ..       8      53 ..       6      61 .. 0.86
   2 ?   -0.6   0.2      0.26   1.6e+03       4      13 ..      55      64 ..      52      76 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                            zf-Dof  3 alkCprCestntkFcYyNNyslsqPRyfCkaCrryWt.kgGklRnvp 48
                                      +l Cp C+s   k   +    +++P ++ ++C  y   +gG +R+  
  gi|557694799|ref|YP_008797853.1|  8 ILACPMCKSFPLKLVVFEERIIEKPPFI-RQCELYCAlHGGYVRDFS 53
                                      579**********************986.99**99865999999975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.26
                            zf-Dof  4 lkCprCestn 13
                                      + C rC   +
  gi|557694799|ref|YP_008797853.1| 55 TDCERCYGLE 64
                                      6799997655 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 ?   12.4   0.0   2.3e-05      0.14       8      75 ..      43     110 ..      36     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                      Pox_vIL-18BP   8 afmygcvhsyvnaveikcpnldivtssgefrcsgcvkfmpkfsym.ywlakdmksde.dakfiehlgegi 75 
                                       a+  g v  + +++  +c  l+i  +sg + c gc ++ p +  +   l  +m+  + d  f+e  ge +
  gi|557694799|ref|YP_008797853.1|  43 ALHGGYVRDFSKTDCERCYGLEI--ASGYVECGGCGRWYPVVDEIpRMLPDEMRDRKlDKSFVERWGEKL 110
                                       55667888999999999999998..6999***********999872456777887652566999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 918.44
//
Query:       gi|557694800|ref|YP_008797854.1|  [L=485]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-38  129.8   0.0    1.3e-37  129.3   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    2.5e-35  122.4   0.0    3.6e-35  121.9   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
      4e-27   95.4   0.4      4e-27   95.4   0.4    2.2  2  Glyco_trans_2_3  Glycosyl transferase family group 2
      6e-15   55.1   0.1      9e-15   54.6   0.1    1.2  1  Glyco_transf_21  Glycosyl transferase family 21
      6e-11   42.3   0.0    1.8e-10   40.8   0.0    1.7  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    3.1e-10   39.3   0.1    2.3e-08   33.1   0.0    3.0  3  Chitin_synth_2   Chitin synthase
    1.6e-06   28.5   0.0    4.6e-06   27.1   0.0    1.7  2  Glyco_tranf_2_4  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.041   13.6   0.0    1.8  3  Glyco_tranf_2_5  Glycosyltransferase like family
      0.073   12.7   0.2       0.15   11.8   0.2    1.4  1  DNA_pol3_theta   DNA polymerase III, theta subunit


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 !  129.3   0.0   6.4e-41   1.3e-37       1     166 [.     133     293 ..     133     297 .. 0.95

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 6.4e-41
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       sv++p+yNeek +  ++e+ll++ +yp +eiivvDDgStD+t ei+ +++  + +v+v+r++ n Gka+aln g+  
  gi|557694800|ref|YP_008797854.1| 133 SVIVPAYNEEKWIGHCIEALLEN-DYPSKEIIVVDDGSTDKTYEIASRYV--RRGVTVLRKP-NGGKASALNYGMLF 205
                                       8**********************.*************************9..5*********.55************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                       atg++i+++DaD++ ++d+l+++v ++ ++ + +v+g++++ + e++  + +   ++ + l++ +r  s  g ++++
  gi|557694800|ref|YP_008797854.1| 206 ATGEIIVTVDADSILTRDTLRRIVMPFRDEKVVGVAGNVMVVNRENWLTKNQAL-EYVTQLNIARRATSFLGVVQVM 281
                                       ****************************************99999988887655.79******************** PP

                                       STCCCEEEEHHH CS
                   Glycos_transf_2 155 igsaallrreal 166
                                        g+ a++rr+++
  gi|557694800|ref|YP_008797854.1| 282 PGPLAAFRRSMA 293
                                       *********987 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 !  121.9   0.0   1.8e-38   3.6e-35       1     230 []     130     350 ..     130     350 .. 0.92

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 1.8e-38
                   Glyco_tranf_2_3   1 prdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                       p+ ++v+Vp++nee+ +g ++e+ll ++yp+ e++vv+d+s+++t e a     ++ + +v+v+++++    +gk+ 
  gi|557694800|ref|YP_008797854.1| 130 PP-VSVIVPAYNEEKWIGHCIEALLENDYPSKEIIVVDDGSTDKTYEIAS----RYVRRGVTVLRKPN----GGKAS 197
                                       88.*****************************************999665....788889***98888....59*** PP

                   Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaar.r 153
                                       aln ++  +++++++ vD+D+++  dtl+r++  f+++kv  v ++v++ nr+++++  +ale+  ++l++ +++  
  gi|557694800|ref|YP_008797854.1| 198 ALNYGMLFATGEIIVTVDADSILTRDTLRRIVMPFRDEKVVGVAGNVMVVNRENWLTKNQALEY-VTQLNIARRAtS 273
                                       **************************************************************95.555555555514 PP

                   Glyco_tranf_2_3 154 algv.ltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvy 229
                                        lgv   + G + ++rr++ + l+g d+   lt+D++l++ l ++g+ ++  pga+  ++ p+ l +++kqr Rw++
  gi|557694800|ref|YP_008797854.1| 274 FLGVvQVMPGPLAAFRRSMAATLGGYDR-ITLTEDFDLTVKLLKTGGVIQAPPGAFAFTEAPARLRDLYKQRLRWYR 349
                                       5576255569******************.***********************************************8 PP

                   Glyco_tranf_2_3 230 g 230
                                       g
  gi|557694800|ref|YP_008797854.1| 350 G 350
                                       6 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 ?   -4.1   3.1       6.4   1.3e+04     173     192 ..      15      39 ..       2      50 .. 0.36
   2 !   95.4   0.4     2e-30     4e-27       1     190 [.     210     402 ..     210     426 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 6.4
                   Glyco_trans_2_3 173 llllfslla.....lalvlllllll 192
                                        lll +++      ++++++ ++++
  gi|557694800|ref|YP_008797854.1|  15 TLLLIPFVVgspsvFWAFVISVIFA 39 
                                       2222222222232222222222222 PP

  == domain 2  score: 95.4 bits;  conditional E-value: 2e-30
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsga 77 
                                       ii+ +DaD+ l++d lr+i+  +++ +v  v g+v+v+n+ nwl++ +al++  + + +++ ++ lg v  ++G  a
  gi|557694800|ref|YP_008797854.1| 210 IIVTVDADSILTRDTLRRIVMPFRDEKVVGVAGNVMVVNRENWLTKNQALEYVTQLNIARRATSFLGVVQVMPGPLA 286
                                       79*******************99999**************************999999******************* PP

                   Glyco_trans_2_3  78 flrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc...el.ekli 150
                                       ++rrs++  +gg+d    +++EDfd+ ++l++ G ++   p+++ +++ p +lr+ ++Qr Rw++G+   ++ +   
  gi|557694800|ref|YP_008797854.1| 287 AFRRSMAATLGGYD--RITLTEDFDLTVKLLKTGGVIQAPPGAFAFTEAPARLRDLYKQRLRWYRGNtqvLIrHSDA 361
                                       **************..99************************************************86431142223 PP

                   Glyco_trans_2_3 151 llvrllgylgsllwsalplhlallllfslla.lalvlllll 190
                                       +++r++g l +l++  ++l  ++ ++ +++a  a++l++l+
  gi|557694800|ref|YP_008797854.1| 362 FRIRRYGRLSQLVFPLMVLQQIVIPVLGVAAiPAAILIILT 402
                                       35566666666666666666667766666653233333332 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 !   54.6   0.1   4.5e-18     9e-15      17     173 .]     194     349 ..     179     349 .. 0.90

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 4.5e-18
                   Glyco_transf_21  17 pKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaafl...ntlagv 90 
                                        K ++l++++  a  +++v+ D+d ++++d+L++++ +++d+kv  V + +++++++++ ++ +a+        a++
  gi|557694800|ref|YP_008797854.1| 194 GKASALNYGMLFATGEIIVTVDADSILTRDTLRRIVMPFRDEKVVGVAGNVMVVNRENWLTKNQALEYvtqLNIARR 270
                                       389999999999**********************************************9999877775443355777 PP

                   Glyco_transf_21  91 lqaklsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslrallaR 167
                                       ++++l+ ++ + G   a+rr+  + +GG+     +L eD+ l+  l + G  +   p ++a t++p    lr+l+++
  gi|557694800|ref|YP_008797854.1| 271 ATSFLGVVQVMPGPLAAFRRSMAATLGGYDR--ITLTEDFDLTVKLLKTGGVIQAPPGAFAFTEAPA--RLRDLYKQ 343
                                       777678889999*******************..58*****************************996..79****** PP

                   Glyco_transf_21 168 qlrWar 173
                                        lrW r
  gi|557694800|ref|YP_008797854.1| 344 RLRWYR 349
                                       ****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 !   40.8   0.0   8.9e-14   1.8e-10       1     223 [.     133     338 ..     133     355 .. 0.78

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 8.9e-14
                   Glyco_tranf_2_2   1 svviplraseerhyieerv..lqkakyydeeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarN 74 
                                       sv++p +++e+  +i   +  l+++ y  +  e+ivvddgS++k+ e  s  +     v   ++      ++a a N
  gi|557694800|ref|YP_008797854.1| 133 SVIVPAYNEEK--WIGHCIeaLLENDY--PSKEIIVVDDGSTDKTYEIASRYVRRGVTVlRKPN-----GGKASALN 200
                                       78999988664..79999988888999..9**************98888888877777733333.....49****** PP

                   Glyco_tranf_2_2  75 rGaskaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledll 151
                                        G+  a +++++ +DaD   + D + +i+       +r+     v+  v+  n+e+     +  + +++ ++ + + 
  gi|557694800|ref|YP_008797854.1| 201 YGMLFATGEIIVTVDADSILTRDTLRRIVM-----PFRDEKVVGVAGNVMVVNRENWLTKNQALEYVTQLNIARRAT 272
                                       ****************************99.....677777777777777777776555555545555666666665 PP

                   Glyco_tranf_2_2 152 aakstlvkffapssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykaraksls 223
                                        +    v  ++  +  +  +r +   +GGyD       +EDfdl ++l+k    ++ +p    + +    l+
  gi|557694800|ref|YP_008797854.1| 273 SFLG--VVQVM-PGPLAAFRRSMAATLGGYDRIT---LTEDFDLTVKLLKTGGVIQAPPGAFAFTEAPARLR 338
                                       5332..33444.4678889************754...79***********9999998888887776666555 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.25     5e+02      29      66 ..     134     168 ..     117     173 .. 0.83
   2 !   33.1   0.0   1.2e-11   2.3e-08     202     288 ..     208     292 ..     200     307 .. 0.88
   3 ?    2.6   0.1     0.021        41     322     417 ..     301     401 ..     290     430 .. 0.62

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.25
                    Chitin_synth_2  29 clvtaysegeeglrttldslastdyddkrklllvvcdG 66 
                                       ++v+ay e+ + + +++++l + dy++k+  ++vv dG
  gi|557694800|ref|YP_008797854.1| 134 VIVPAYNEE-KWIGHCIEALLENDYPSKE--IIVVDDG 168
                                       679999885.6799***********9865..6777777 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 1.2e-11
                    Chitin_synth_2 202 yeivlmvdadtkvapdsltrlvaalvkdpeilglcGetkiankkeswvtaiqvfeyyishhlskafesvfGsvtclP 278
                                        ei+++vdad+ ++ d+l+r+v  + +d++++g+ G+  + n+ e w+t  q  ey    + ++   s +G v  +P
  gi|557694800|ref|YP_008797854.1| 208 GEIIVTVDADSILTRDTLRRIVMPF-RDEKVVGVAGNVMVVNR-ENWLTKNQALEYVTQLNIARRATSFLGVVQVMP 282
                                       599*****************99876.7899**********996.67******************************* PP

                    Chitin_synth_2 279 Gcfslyrika 288
                                       G ++++r   
  gi|557694800|ref|YP_008797854.1| 283 GPLAAFRRSM 292
                                       ****999654 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.021
                    Chitin_synth_2 322 llllGedrylttlllktfpkrktvfvpqakcktvaPdtfkvllsqrrrwinstvhnll...elvlvrdlc..Gtfcf 393
                                        + l ed  lt  llkt    +    p a + t aP + + l  qr rw       l+   +  ++r       ++f
  gi|557694800|ref|YP_008797854.1| 301 RITLTEDFDLTVKLLKTGGVIQA--PPGAFAFTEAPARLRDLYKQRLRWYRGNTQVLIrhsDAFRIRRYGrlSQLVF 375
                                       56777888888888888776654..48999*******************9776666652112344443321122333 PP

                    Chitin_synth_2 394 smrfv..vfieligtvvlPvaiaftl 417
                                        +  +  + i ++g   +P+ai+ +l
  gi|557694800|ref|YP_008797854.1| 376 PLMVLqqIVIPVLGVAAIPAAILIIL 401
                                       32222123455566666666665554 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 !   27.1   0.0   2.3e-09   4.6e-06       1      88 [.     139     224 ..     139     229 .. 0.80
   2 ?   -3.1   0.0       5.9   1.2e+04      59      85 ..     338     364 ..     302     373 .. 0.61

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.3e-09
                   Glyco_tranf_2_4   1 rneadiLpeflahhlalgf..drilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwv 75 
                                       +ne++ ++++++++l++++  ++i+v+d++stD+t++i +++ +  +   +k+  +++ + ++   l+   a ++ +
  gi|557694800|ref|YP_008797854.1| 139 YNEEKWIGHCIEALLENDYpsKEIIVVDDGSTDKTYEIASRYVRRGVTVLRKPNGGKASALNYGM-LF---ATGEII 211
                                       69****************86689******************988777777777665444443333.33...45799* PP

                   Glyco_tranf_2_4  76 lvvDaDEflvvpd 88 
                                       ++vDaD +l+ ++
  gi|557694800|ref|YP_008797854.1| 212 VTVDADSILTRDT 224
                                       ******9999987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.9
                   Glyco_tranf_2_4  59 vellkallaryaeadwvlvvDaDEflv 85 
                                       ++l+k+ l++y+ ++ vl   +D f +
  gi|557694800|ref|YP_008797854.1| 338 RDLYKQRLRWYRGNTQVLIRHSDAFRI 364
                                       456666666666655555555555555 PP

>> Glyco_tranf_2_5  Glycosyltransferase like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       4.3   8.5e+03      40      62 ..      60      82 ..      59      88 .. 0.85
   2 ?   -2.8   0.0       2.1   4.1e+03     177     194 ..     134     151 ..     131     166 .. 0.55
   3 ?   13.6   0.0   2.1e-05     0.041      42     120 ..     196     270 ..     185     281 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.3
                   Glyco_tranf_2_5 40 siaeaynkalsasdakykvYlhq 62
                                      s+  +y   +  s a  +v++++
  gi|557694800|ref|YP_008797854.1| 60 SMVLGYSTVVVPSLATLLVFVEE 82
                                      89999999999999999999986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.1
                   Glyco_tranf_2_5 177 vvVpnqekp.Wvihdsgfk 194
                                       v+Vp  +++ W+ h+ +  
  gi|557694800|ref|YP_008797854.1| 134 VIVPAYNEEkWIGHCIE-A 151
                                       56665554448766443.3 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 2.1e-05
                   Glyco_tranf_2_5  42 aeaynkalsasdakykvYlhqDvliinkdfikdlleiFkkdkkiGmiGvvGakslpesgvwweskkkvgkvietske 118
                                       a+a n ++  +  ++ v ++ D  i+++d +++++  F  d+k  ++Gv+G+  + ++ +w+ +++    v++ +  
  gi|557694800|ref|YP_008797854.1| 196 ASALNYGMLFATGEIIVTVDADS-ILTRDTLRRIVMPF-RDEK--VVGVAGNVMVVNRENWLTKNQALEYVTQLNIA 268
                                       8999******************6.77899999******.6666..69***************888877777777665 PP

                   Glyco_tranf_2_5 119 ea 120
                                       ++
  gi|557694800|ref|YP_008797854.1| 269 RR 270
                                       54 PP

>> DNA_pol3_theta  DNA polymerase III, theta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   7.5e-05      0.15      42      67 ..     332     357 ..     328     359 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.5e-05
                    DNA_pol3_theta  42 eqPeaLreYFreRlayyReeskklsr 67 
                                       e P+ Lr+ +++Rl+ yR +++ l r
  gi|557694800|ref|YP_008797854.1| 332 EAPARLRDLYKQRLRWYRGNTQVLIR 357
                                       88*****************9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); 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: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3448.14
//
Query:       gi|557694801|ref|YP_008797855.1|  [L=248]
Description: dimethyladenosine rRNA methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   62.5   0.0    5.3e-17   61.8   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
    4.3e-06   27.3   0.0    7.8e-06   26.5   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
      5e-06   26.3   0.0    6.4e-05   22.7   0.0    2.1  2  Cons_hypoth95    Conserved hypothetical protein 95
    1.8e-05   24.3   0.0    3.8e-05   23.3   0.0    1.5  1  MTS              Methyltransferase small domain
    2.4e-05   24.2   0.2    0.00014   21.7   0.1    2.0  2  Met_10           Met-10+ like-protein
     0.0004   19.9   0.0    0.00058   19.3   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0005   20.7   0.0    0.00098   19.7   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
      0.001   18.9   0.0     0.0014   18.5   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.049   13.5   0.0      0.065   13.1   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
      0.056   13.1   0.0        1.6    8.3   0.0    2.7  3  UPF0020          Putative RNA methylase family UPF0020
      0.061   13.3   0.0       0.11   12.5   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
      0.062   12.7   0.0       0.11   11.9   0.0    1.4  1  SAM_MT           Putative SAM-dependent methyltransferase
       0.12   11.4   0.0       0.19   10.8   0.0    1.2  1  DREV             DREV methyltransferase
       0.17   11.6   0.1       0.41   10.4   0.0    1.6  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl


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 !   61.8   0.0   4.1e-20   5.3e-17       9     147 ..       8     132 ..       3     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 4.1e-20
                                       G--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-C CS
                            RrnaAD   9 gqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkklskdeklkvvhqDf 85 
                                        q+fl+++ v+   +++++l  ++ vl++g+G+G+l  e ak a++v ++E d+ L+k l++k +++++++ v  ++
  gi|557694801|ref|YP_008797855.1|   8 DQHFLVDRAVVMHLVVAAELGSEDVVLDVGAGTGVLAFEAAKFARKVYAVERDPILYKTLSEKAKEYGNVEPVRGNI 84 
                                       69*************************************************************************** PP

                                       CGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH- CS
                            RrnaAD  86 lkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrlla 147
                                       l   +p  +          ++van P  + ++l+ + l    +  v+m l+++k fa  +l 
  gi|557694801|ref|YP_008797855.1|  85 LRLRLPA-Y---------TKIVANPPFSLLEPLIIRHLR--NP--VTMSLLTPKHFADSILT 132
                                       *******.3.........49******************6..44..88*********998775 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   6.1e-09   7.8e-06       1      66 [.      33      93 ..      33     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 6.1e-09
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEE CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfD 66
                                      vLd+G+GtG l++++ak     kv++v+ ++ + ++  e+a+e g nve v+g++ +l +++  + 
  gi|557694801|ref|YP_008797855.1| 33 VLDVGAGTGVLAFEAAKFA--RKVYAVERDPILYKTLSEKAKEYG-NVEPVRGNILRLRLPA--YT 93
                                      9***************885..9*******************8776.*********9998775..44 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0     5e-08   6.4e-05      40      95 ..      28      79 ..      18     126 .. 0.77
   2 ?    1.5   0.0      0.16     2e+02     104     155 ..     143     193 ..     133     218 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 5e-08
                                      HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEE CS
                     Cons_hypoth95 40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetae 95
                                      + +  vLD+ aG+G+l++EA+   a+k+++ve+d+  +k+l+e+ +e ++ e    
  gi|557694801|ref|YP_008797855.1| 28 GSEDVVLDVGAGTGVLAFEAA-KFARKVYAVERDPILYKTLSEKAKEYGNVE---P 79
                                      567789**************7.789*********************999554...2 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.16
                                       HCTS--SS-EEEEEEE--SSSTTCH.HHHHHHHHHTT-EEEEEEEEE.EEECC CS
                     Cons_hypoth95 104 llklakkkeefdivflDPPyakellieevlelleekkllkenalvvv.eteke 155
                                       l+  +++k+++d    +PPy  +l  + +l+ ++ + +l++  ++++ ++ ++
  gi|557694801|ref|YP_008797855.1| 143 LSYAVSEKAVYDGSVCEPPYIGKLS-HVLLKPVQ-RTALQDAMVMFLlQRGSK 193
                                       55666778888888899***99975.66666666.566665544443033333 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   2.9e-08   3.8e-05      31     107 ..      29     101 ..      13     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.9e-08
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                        ++ vlD+G+G+Gvl+ ++ak+  +  v +v+ d    +   e +++ + +ve v  ++l       +  iv NPPf
  gi|557694801|ref|YP_008797855.1|  29 SEDVVLDVGAGTGVLAFEAAKFARK--VYAVERDPILYKTLSEKAKEYG-NVEPVRGNILRLRL-PAYTKIVANPPF 101
                                       45679****************9988..9999999887777777776665.599999**999888.89*********9 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   1.1e-07   0.00014      94     145 ..      23      72 ..      12      83 .. 0.86
   2 ?    0.2   0.0      0.43   5.4e+02      69      99 ..     189     219 ..     172     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.1e-07
                                       HHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHH CS
                            Met_10  94 laklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkenik 145
                                       +a+     +vV+dv AG G +a  +ak   a++v+a++ +P  +k l e  k
  gi|557694801|ref|YP_008797855.1|  23 VAAELGSEDVVLDVGAGTGVLAFEAAK--FARKVYAVERDPILYKTLSEKAK 72 
                                       455567889******************..67789***********9998765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.43
                                       ETTEEEEEETTTS---GGGHHHHHHHHTT-- CS
                            Met_10  69 EngcrfklDvskvyfsskleaErerlaklve 99 
                                         g++ +  + +v++ ++ + E ++l++l +
  gi|557694801|ref|YP_008797855.1| 189 QRGSKVRNSLRNVLWKTRTKREATKLVELSS 219
                                       5677777778899*********999999876 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.6e-07   0.00058     162     198 ..      30      65 ..      19      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.6e-07
                              PrmA 162 geevlDvGtGSGiLaiaaakLgakkvvavDiDevAvk 198
                                       ++ vlDvG+G+G+La  aak+ a+kv+av  D++  k
  gi|557694801|ref|YP_008797855.1|  30 EDVVLDVGAGTGVLAFEAAKF-ARKVYAVERDPILYK 65 
                                       5689****************9.689*******98655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   7.7e-07   0.00098       1      58 [.      34      90 ..      34      95 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 7.7e-07
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS- CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfe 58
                                      LdvG+GtG la + ak +++v++v+ ++ + k+ +eka+e g+ ve v++++ +l ++
  gi|557694801|ref|YP_008797855.1| 34 LDVGAGTGVLAFEAAKFARKVYAVERDPILYKTLSEKAKEYGN-VEPVRGNILRLRLP 90
                                      8*************************************99995.88999999888776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.1e-06    0.0014       3      66 ..      29      87 ..      27     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                   Methyltransf_31  3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieel 66
                                      ++ +vlD+G+GtG l+fe+a +     +v+ +++++   +   e+a+  ++ nve  +g+i  l
  gi|557694801|ref|YP_008797855.1| 29 SEDVVLDVGAGTGVLAFEAA-KF--ARKVYAVERDPILYKTLSEKAK--EYGNVEPVRGNILRL 87
                                      6789****************.43..4579999999987777777544..777787777777665 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.1e-05     0.065      20      59 ..      27      66 ..      10     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.1e-05
                   Methyltransf_23 20 lraggrvLdiGcGtGillevlrengfsvtgvDlspeavei 59
                                      l +   vLd+G+GtG l+ +++++  +v++v+ +p++ + 
  gi|557694801|ref|YP_008797855.1| 27 LGSEDVVLDVGAGTGVLAFEAAKFARKVYAVERDPILYKT 66
                                      567779*********99999999999******99986555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0013       1.6      20      65 ..      21      66 ..      15      82 .. 0.76
   2 ?    1.2   0.0      0.19   2.5e+02     101     131 ..      73     101 ..      65     103 .. 0.74
   3 ?    0.1   0.0      0.44   5.6e+02     116     134 ..     148     165 ..     131     218 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0013
                                      HHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSH CS
                           UPF0020 20 lvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlel 65
                                      lv  a++  +++ lD   G+G ++ Eaa  ++++++    +  ++ 
  gi|557694801|ref|YP_008797855.1| 21 LVVAAELGSEDVVLDVGAGTGVLAFEAAKFARKVYAVERDPILYKT 66
                                      6778999999999**9******************965444444553 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.19
                                       -GGGEEEEE--GGG--STTS---EEEE---- CS
                           UPF0020 101 vgdliefsqadaakLrlkegevdvivtnpPY 131
                                         + +e +  ++  Lrl+   +  iv+npP+
  gi|557694801|ref|YP_008797855.1|  73 EYGNVEPVRGNILRLRLPA--YTKIVANPPF 101
                                       5566777778888888444..899******9 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.44
                                       -STTS---EEEE------- CS
                           UPF0020 116 rlkegevdvivtnpPYGer 134
                                         +++ +d  v++pPY  +
  gi|557694801|ref|YP_008797855.1| 148 S-EKAVYDGSVCEPPYIGK 165
                                       4.45568888999999544 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.4e-05      0.11      24      75 ..      28      75 ..      13      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.4e-05
                   Methyltransf_32 24 sgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75
                                       ++  v+DvGaG g L+f  a     +  kv++++    l ++ ++ a+++g
  gi|557694801|ref|YP_008797855.1| 28 GSEDVVLDVGAGTGVLAFEAAK----FARKVYAVERDPILYKTLSEKAKEYG 75
                                      4567789************999....7999******9999999999999887 PP

>> SAM_MT  Putative SAM-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   8.4e-05      0.11      65     111 ..      23      69 ..       8      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.4e-05
                            SAM_MT  65 vglkkgvlptvlDaTaGlGrDafvlaslGckvtliErhpvvaaLLed 111
                                       v ++ g +  vlD  aG G  af  a +  kv  +Er+p+++  L++
  gi|557694801|ref|YP_008797855.1|  23 VAAELGSEDVVLDVGAGTGVLAFEAAKFARKVYAVERDPILYKTLSE 69 
                                       4455566789******************************9988775 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.19      95     135 ..      30      70 ..      11      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                              DREV  95 dkklldlGaGdGeitkrvaptfeevyatelsetmrdrlkkk 135
                                       +  +ld+GaG G ++   a++  +vya e    + + l+ k
  gi|557694801|ref|YP_008797855.1|  30 EDVVLDVGAGTGVLAFEAAKFARKVYAVERDPILYKTLSEK 70 
                                       4569*************************988888877665 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 ?   10.4   0.0   0.00032      0.41      65     114 ..      18      67 ..      11      82 .. 0.74
   2 ?   -2.3   0.0       2.4     3e+03     169     208 ..     170     209 ..     169     211 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                                       HHHHTT...--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHH CS
                              PCMT  65 alelle...lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveea 114
                                       ++ l+    l   + vL+vG+G+G l+   a++ +++    ++er + l+++ 
  gi|557694801|ref|YP_008797855.1|  18 VMHLVVaaeLGSEDVVLDVGAGTGVLAFEAAKFARKVY---AVERDPILYKTL 67 
                                       455544445888999**********9988888877766...788877777654 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                                       EEEEESBSSSEEEEEEEEETTTEEEEEEEEEE---B-BCC CS
                              PCMT 169 lvvPvgeeeeQvlklvdkkadgkvvikkleevrfvpltdk 208
                                       l+ Pv+++  Q+++++   + g+ v ++l +v++ + t++
  gi|557694801|ref|YP_008797855.1| 170 LLKPVQRTALQDAMVMFLLQRGSKVRNSLRNVLWKTRTKR 209
                                       5679999888888888777778888888888888777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1868.14
//
Query:       gi|557694802|ref|YP_008797856.1|  [L=105]
Description: hypothetical protein CSUB_C1375 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       230  (0.0128284); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 797.69
//
Query:       gi|557694803|ref|YP_008797857.1|  [L=180]
Description: Appr-1-p processing enzyme family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-38  128.8   0.0    1.2e-37  128.5   0.0    1.1  1  Macro     Macro domain
  ------ inclusion threshold ------
       0.16   11.3   0.0       0.62    9.3   0.0    1.7  2  Macro_2   Macro-like 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 !  128.5   0.0   1.4e-41   1.2e-37       1     118 []      25     135 ..      25     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 128.5 bits;  conditional E-value: 1.4e-41
                                       EEEEETTSS-CSHHHHHHHHHHHHHHHHHHHHHHHHHHS--TTSEEEEE-TTSSSSEEEEEESE-TTTSTSTTHHHH CS
                             Macro   1 VnAaNsrllggggvagaihraagkalkeeckelekkqggcllGeavvtpaynlpakyvihtvgplftsskskeeeel 77 
                                       VnAaN+ l++gggvagai r++g++++eec+++    g c++G av+t a++l a+yvih+vgp++   ++ +ee +
  gi|557694803|ref|YP_008797857.1|  25 VNAANQWLKMGGGVAGAILRKGGPSIQEECDRI----GYCPVGGAVITGAGKLRARYVIHAVGPRM---GEGDEERK 94 
                                       9********************************....99***************************...6999**** PP

                                       HHHHHHHHHHHHHHTT-SEEEEE-TTSSTTSBTHHHHHHHH CS
                             Macro  78 lakayknalelaeekgiksvafPaistGifgvpweeaarva 118
                                       l++a+ n+l+la+  +++s+a+PaistG fg+p+eeaa+v+
  gi|557694803|ref|YP_008797857.1|  95 LRDAVINSLKLADTYNLTSIAMPAISTGAFGYPLEEAAKVI 135
                                       **************************************985 PP

>> Macro_2  Macro-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0     0.073   6.5e+02      67      91 ..      19      43 ..       3      68 .. 0.81
   2 ?    9.3   0.0   6.9e-05      0.62     169     239 ..      97     166 ..      89     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.073
                           Macro_2 67 gekyaivspGnsfGylGGGfdlalf 91
                                       e  aiv   n +  +GGG   a++
  gi|557694803|ref|YP_008797857.1| 19 VEADAIVNAANQWLKMGGGVAGAIL 43
                                      5667899999999999999988776 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 6.9e-05
                           Macro_2 169 namwnslmsap.kdvdgliisGlctGyaGvpaeiscksmafalslymlqdkiskelknvlimyylgypfedf 239
                                       +a+ nsl+ a   ++ ++ ++ + tG  G p e + k +  a++ y l ++    lk vl + y ++ f+ f
  gi|557694803|ref|YP_008797857.1|  97 DAVINSLKLADtYNLTSIAMPAISTGAFGYPLEEAAKVIITAVTDYLLREN--SGLKKVLFVLYDEHAFRVF 166
                                       5778888766515788999*****************************996..6799999999999999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1302.15
//
Query:       gi|557694804|ref|YP_008797858.1|  [L=174]
Description: hypothetical protein CSUB_C1377 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-05   22.7   0.2       0.19   11.7   0.1    2.2  2  zinc_ribbon_4   zinc-ribbon domain
    0.00013   21.8   1.6       0.26   11.2   0.0    2.3  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
     0.0013   18.4   4.7     0.0017   18.1   4.7    1.1  1  Peptidase_M50B  Peptidase M50B-like
     0.0015   18.6   1.8     0.0029   17.7   1.8    1.5  1  Zn-ribbon_8     Zinc ribbon domain
     0.0018   17.8   1.2       0.77    9.3   0.1    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0024   17.8   0.6       0.11   12.5   0.6    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
     0.0032   17.1   2.7      0.096   12.4   0.1    2.5  2  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
     0.0053   16.8   0.3     0.0074   16.3   0.3    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0081   16.2   0.7      0.012   15.6   0.7    1.2  1  DZR             Double zinc ribbon
     0.0083   15.8   5.6      0.087   12.6   5.6    2.1  1  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.5   2.5        1.9    8.3   0.1    2.2  2  zf-HYPF         HypF finger
      0.014   15.1   3.2      0.031   14.0   3.2    1.5  1  Rubredoxin_2    Rubredoxin metal binding domain
      0.023   14.8   1.0      0.042   13.9   1.0    1.4  1  DUF1272         Protein of unknown function (DUF1272)
      0.025   15.2   0.5       0.11   13.2   0.5    1.9  1  FYDLN_acid      Protein of unknown function (FYDLN_acid)
      0.031   14.2   0.3        4.4    7.4   0.0    2.3  2  ADK_lid         Adenylate kinase, active site lid
      0.074   12.8   3.7       0.45   10.3   3.7    1.9  1  A2L_zn_ribbon   A2L zinc ribbon domain
        0.2   11.3   0.8        3.2    7.4   0.1    2.2  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.21   11.1   6.5       0.76    9.3   0.8    2.1  2  zf-ribbon_3     zinc-ribbon domain
       0.25   11.3   2.0        8.7    6.3   0.1    2.2  2  zf-trcl         Probable zinc-ribbon domain
       0.28   10.5   0.3       0.36   10.1   0.3    1.1  1  Sarcoglycan_1   Sarcoglycan complex subunit protein
       0.36   10.9   1.8        1.9    8.5   0.1    2.1  2  CpXC            CpXC protein
       0.42   10.3   2.9         11    5.8   0.2    2.2  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
       0.81    9.7   3.2         11    6.1   0.1    2.1  1  Prok-RING_1     Prokaryotic RING finger family 1
        2.3    8.3   4.3        6.6    6.8   0.3    2.5  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        2.6    8.1   4.7         26    4.8   0.3    2.3  3  Nudix_N_2       Nudix N-terminal
        6.4    6.8   7.9        3.3    7.7   1.0    2.4  2  DUF1610         Domain of unknown function (DUF1610)


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0011      0.77       4      18 ..       7      21 ..       6      23 .. 0.90
   2 !   11.7   0.1   0.00028      0.19       3      16 ..      22      35 ..      21      40 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0011
                     zinc_ribbon_4  4 tCpsCkakyeiddek 18
                                      +C +C+a+y ++++k
  gi|557694804|ref|YP_008797858.1|  7 VCTNCGAEYMLQAWK 21
                                      7**********9987 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00028
                     zinc_ribbon_4  3 itCpsCkakyeidd 16
                                       +Cp+C+a++++++
  gi|557694804|ref|YP_008797858.1| 22 AVCPNCGAEFTLEA 35
                                      68*********986 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 !    9.8   0.4    0.0011      0.73       1      15 [.       2      16 ..       2      19 .. 0.89
   2 !   11.2   0.0   0.00038      0.26       3      15 ..      20      32 ..      18      39 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
                    Zn_ribbon_SprT  1 kkyvYrCtgCgreyt 15
                                      k+y  +Ct+Cg ey+
  gi|557694804|ref|YP_008797858.1|  2 KRYPFVCTNCGAEYM 16
                                      69999******9996 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00038
                    Zn_ribbon_SprT  3 yvYrCtgCgreyt 15
                                      ++++C++Cg e+t
  gi|557694804|ref|YP_008797858.1| 20 WKAVCPNCGAEFT 32
                                      9********8775 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   4.7   2.4e-06    0.0017      69     178 ..      53     162 ..      42     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.4e-06
                    Peptidase_M50B  69 tllaGYlgpallGlllillsasgkarlllvllvllllvllllvrnlfglvlllllgallllvlllaedelleflllf 145
                                        +l GY+ +++++ +++ ++ +g   ++++ ++ll l++l     ++g++lll l +l++ +l+l  + l   +l +
  gi|557694804|ref|YP_008797858.1|  53 AALLGYVVSSFFFPGVLSVIGQGLGPVAMGAMALLALLMLTGSYIFIGTALLLSLTILVYHLLWLSAEGLPGLVLAA 129
                                       4678*************************999999999999999999999999999999999998866665555555 PP

                    Peptidase_M50B 146 lgvflllgsvrdiddli.rrkapesDasqlaklt 178
                                        +  +  g+ ++  +l  rrka+e+Da  + ++ 
  gi|557694804|ref|YP_008797858.1| 130 AT-AIGSGMALSRIRLHgRRKAKETDARTMPEYS 162
                                       55.5555555554555439999*****9987765 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   1.8   4.2e-06    0.0029       1      35 [.       1      30 [.       1      35 [. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.2e-06
                       Zn-ribbon_8  1 MPiYeYrCeeCghefevlqsisdapltaCPeCgse 35
                                      M  Y + C++Cg e+  lq+     + +CP+Cg+e
  gi|557694804|ref|YP_008797858.1|  1 MKRYPFVCTNCGAEYM-LQAW----KAVCPNCGAE 30
                                      55799*******8888.7743....467*****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 !    7.3   0.1    0.0049       3.4      19      27 ..       5      13 ..       2      16 .. 0.79
   2 !    9.3   0.1    0.0011      0.77       2      12 ..      23      33 ..      22      38 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0049
                                      CEEESSSSB CS
                      TF_Zn_Ribbon 19 elvCtdCGl 27
                                       +vCt+CG+
  gi|557694804|ref|YP_008797858.1|  5 PFVCTNCGA 13
                                      589999996 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                                      EETTTTCEECH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlv 12
                                      +CPnCg ++++
  gi|557694804|ref|YP_008797858.1| 23 VCPNCGAEFTL 33
                                      7*****99844 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.6   0.00016      0.11       5      29 ..       8      31 ..       5      32 .. 0.85
   2 !   11.1   0.0   0.00042      0.29       5      15 ..      24      34 ..      22      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                    PhnA_Zn_Ribbon  5 CplCaSeytYedgallvCpeCahEw 29
                                      C +C++ey ++     vCp+C+ E+
  gi|557694804|ref|YP_008797858.1|  8 CTNCGAEYMLQAWKA-VCPNCGAEF 31
                                      999*******76654.9*****998 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00042
                    PhnA_Zn_Ribbon  5 CplCaSeytYe 15
                                      Cp+C++e+t+e
  gi|557694804|ref|YP_008797858.1| 24 CPNCGAEFTLE 34
                                      99999999996 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 ?    4.7   0.1     0.036        25      23      31 ..       7      15 ..       6      15 .. 0.91
   2 !   12.4   0.1   0.00014     0.096      20      31 ..      20      31 ..      17      31 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.036
                     zf-NADH-PPase 23 vCpaCgleh 31
                                      vC +Cg+e+
  gi|557694804|ref|YP_008797858.1|  7 VCTNCGAEY 15
                                      8*****997 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00014
                     zf-NADH-PPase 20 warvCpaCgleh 31
                                      w+ vCp+Cg+e+
  gi|557694804|ref|YP_008797858.1| 20 WKAVCPNCGAEF 31
                                      9********985 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 !   16.3   0.3   1.1e-05    0.0074      70      95 ..       5      30 ..       1      42 [. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-05
                                      EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 70 kvrCreCgkefeleekalrCpkCgsa 95
                                       + C++Cg+e+ l++ ++ Cp+Cg++
  gi|557694804|ref|YP_008797858.1|  5 PFVCTNCGAEYMLQAWKAVCPNCGAE 30
                                      579*********9986788*****96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.7   1.8e-05     0.012      14      42 ..       7      35 ..       2      37 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                               DZR 14 fCseCgtklkavaaedrCpsCgekvdpea 42
                                      +C +Cg++   +a + +Cp+Cg++ ++ea
  gi|557694804|ref|YP_008797858.1|  7 VCTNCGAEYMLQAWKAVCPNCGAEFTLEA 35
                                      69999999765555999999999877765 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   5.6   0.00013     0.087       2      22 ..       8      30 ..       7      31 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                     zinc_ribbon_2  2 CpnCGael.qdnakF.CpyCGtp 22
                                      C+nCGae      k  Cp+CG++
  gi|557694804|ref|YP_008797858.1|  8 CTNCGAEYmLQAWKAvCPNCGAE 30
                                      ********5589999******98 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0048       3.3      22      32 ..       6      16 ..       2      18 .. 0.75
   2 ?    8.3   0.1    0.0028       1.9      23      33 ..      23      33 ..      17      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0048
                                      ---TTTS--EE CS
                           zf-HYPF 22 isCtnCGPrls 32
                                        CtnCG  + 
  gi|557694804|ref|YP_008797858.1|  6 FVCTNCGAEYM 16
                                      359****9886 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0028
                                      --TTTS--EEE CS
                           zf-HYPF 23 sCtnCGPrlsl 33
                                       C+nCG  ++l
  gi|557694804|ref|YP_008797858.1| 23 VCPNCGAEFTL 33
                                      6******9998 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   3.2   4.5e-05     0.031       1      22 [.       6      29 ..       6      30 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-05
                      Rubredoxin_2  1 YvCsqCGfesakwfGr..CpsCgs 22
                                      +vC +CG+e+    ++  Cp+Cg+
  gi|557694804|ref|YP_008797858.1|  6 FVCTNCGAEYMLQAWKavCPNCGA 29
                                      8*********99999777****96 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.0   6.1e-05     0.042      27      52 ..       6      32 ..       3      39 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.1e-05
                           DUF1272 27 yEctFC.aeCaeevlenvCPncgGelv 52
                                      + ct C ae + +  + vCPncg e++
  gi|557694804|ref|YP_008797858.1|  6 FVCTNCgAEYMLQAWKAVCPNCGAEFT 32
                                      55666632344455589*******985 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.5   0.00016      0.11      11      41 ..       7      36 ..       1      52 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00016
                        FYDLN_acid 11 iCpscgakFYDLnkdPivcpkcgeefepeev 41
                                      +C +cga  Y L+   +vcp+cg+ef++e+ 
  gi|557694804|ref|YP_008797858.1|  7 VCTNCGAE-YMLQAWKAVCPNCGAEFTLEAK 36
                                      7*****99.56****************9987 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 ?    4.8   0.0     0.041        28       3      11 ..       7      15 ..       6      19 .. 0.87
   2 ?    7.4   0.0    0.0064       4.4       3      15 ..      23      35 ..      22      45 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.041
                                      E-TTT--EE CS
                           ADK_lid  3 vCpkCGrsY 11
                                      vC +CG+ Y
  gi|557694804|ref|YP_008797858.1|  7 VCTNCGAEY 15
                                      9*****988 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0064
                                      E-TTT--EEETTT CS
                           ADK_lid  3 vCpkCGrsYhvvf 15
                                      vCp+CG+ + ++ 
  gi|557694804|ref|YP_008797858.1| 23 VCPNCGAEFTLEA 35
                                      9*****9987553 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 ?   10.3   3.7   0.00066      0.45       5      32 ..       7      32 ..       5      33 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00066
                     A2L_zn_ribbon  5 vCsvCggngilnseqgylvCieCgasfp 32
                                      vC++Cg +  l++     vC++Cga+f+
  gi|557694804|ref|YP_008797858.1|  7 VCTNCGAEYMLQAW--KAVCPNCGAEFT 32
                                      8*******999544..56*******997 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.1      0.18   1.2e+02       3      11 ..       6      14 ..       5      18 .. 0.88
   2 ?    7.4   0.1    0.0046       3.2       4      19 ..      23      38 ..      21      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.18
                            zf_UBZ  3 ylCerCgke 11
                                      ++C  Cg+e
  gi|557694804|ref|YP_008797858.1|  6 FVCTNCGAE 14
                                      89*****86 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0046
                            zf_UBZ  4 lCerCgkeipeselqE 19
                                      +C+ Cg+e+  ++++E
  gi|557694804|ref|YP_008797858.1| 23 VCPNCGAEFTLEAKPE 38
                                      7********9999998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.7     0.043        29      18      24 ..       7      13 ..       7      15 .. 0.84
   2 ?    9.3   0.8    0.0011      0.76       4      10 ..      23      29 ..      21      34 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.043
                       zf-ribbon_3 18 vCpyCGt 24
                                      vC++CG+
  gi|557694804|ref|YP_008797858.1|  7 VCTNCGA 13
                                      699**97 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0011
                       zf-ribbon_3  4 rCPnCGa 10
                                       CPnCGa
  gi|557694804|ref|YP_008797858.1| 23 VCPNCGA 29
                                      3555555 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2      0.04        28       4      14 ..       5      15 ..       4      21 .. 0.84
   2 ?    6.3   0.1     0.013       8.7       5      18 ..      22      35 ..      18      39 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.04
                           zf-trcl  4 tltCkdCgaef 14
                                      +++C++Cgae 
  gi|557694804|ref|YP_008797858.1|  5 PFVCTNCGAEY 15
                                      589******96 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
                           zf-trcl  5 ltCkdCgaefvFta 18
                                       +C +Cgaef+  a
  gi|557694804|ref|YP_008797858.1| 22 AVCPNCGAEFTLEA 35
                                      68********9665 PP

>> Sarcoglycan_1  Sarcoglycan complex subunit protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.3   0.00052      0.36      19      54 ..      97     141 ..      83     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00052
                     Sarcoglycan_1  19 LlllaivnLaltiwilkvLrissnGmgsleiipdv.........g 54 
                                       +++ + + L lti++++ L++s +G+++l++              
  gi|557694804|ref|YP_008797858.1|  97 IFIGTALLLSLTILVYHLLWLSAEGLPGLVLAAATaigsgmalsR 141
                                       67778888999*******************998875544444444 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.38   2.6e+02      38      50 ..       6      18 ..       4      20 .. 0.76
   2 ?    8.5   0.1    0.0028       1.9      37      52 ..      21      36 ..      18      38 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.38
                              CpXC 38 atCpkCgatakle 50
                                      ++C +Cga+ +l+
  gi|557694804|ref|YP_008797858.1|  6 FVCTNCGAEYMLQ 18
                                      6799999887776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0028
                              CpXC 37 eatCpkCgatakleap 52
                                      +a+Cp+Cga+++lea+
  gi|557694804|ref|YP_008797858.1| 21 KAVCPNCGAEFTLEAK 36
                                      6789999999999875 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 ?    4.8   0.2     0.033        23       5      12 ..       6      13 ..       3      16 .. 0.65
   2 ?    5.8   0.2     0.016        11       6      18 ..      23      34 ..      22      35 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.033
                           zf-RRN7  5 ppCgvCgc 12
                                      ++C  Cg+
  gi|557694804|ref|YP_008797858.1|  6 FVCTNCGA 13
                                      56666665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.016
                           zf-RRN7  6 pCgvCgcrsftld 18
                                      +C+ Cg+ +ftl+
  gi|557694804|ref|YP_008797858.1| 23 VCPNCGA-EFTLE 34
                                      7*****9.77775 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 ?    6.1   0.1     0.015        11      22      36 ..       7      21 ..       6      23 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.015
                       Prok-RING_1 22 vCpeCgtpyHraCye 36
                                      vC++Cg+ y  + ++
  gi|557694804|ref|YP_008797858.1|  7 VCTNCGAEYMLQAWK 21
                                      9********988887 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 ?    3.2   0.2      0.13        91      19      27 ..       6      14 ..       2      22 .. 0.75
   2 ?    6.8   0.3    0.0096       6.6      19      27 ..      22      30 ..      13      36 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.13
                     Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                      fvC +Cg +
  gi|557694804|ref|YP_008797858.1|  6 FVCTNCGAE 14
                                      99****976 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0096
                     Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                       vCP+Cg +
  gi|557694804|ref|YP_008797858.1| 22 AVCPNCGAE 30
                                      79*****65 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.6     0.091        63      24      29 ..       7      12 ..       3      15 .. 0.79
   2 ?    3.0   4.8      0.14        98       3      29 ..       8      28 ..       6      31 .. 0.76
   3 ?    4.8   0.3     0.038        26       3      11 ..      24      32 ..      23      38 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.091
                                      EETTTT CS
                         Nudix_N_2 24 vCpaCg 29
                                      vC++Cg
  gi|557694804|ref|YP_008797858.1|  7 VCTNCG 12
                                      888887 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.14
                                      -TTT--B-EEE--TT-SS-EEEETTTT CS
                         Nudix_N_2  3 CsqCGtpvelripdgDnreRlvCpaCg 29
                                      C++CG++  l+       + +vCp+Cg
  gi|557694804|ref|YP_008797858.1|  8 CTNCGAEYMLQA------WKAVCPNCG 28
                                      777877766666......678999998 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.038
                                      -TTT--B-E CS
                         Nudix_N_2  3 CsqCGtpve 11
                                      C++CG++ +
  gi|557694804|ref|YP_008797858.1| 24 CPNCGAEFT 32
                                      778887755 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.0      0.21   1.4e+02      17      23 ..       6      12 ..       5      14 .. 0.66
   2 ?    7.7   1.0    0.0048       3.3      19      23 ..      24      28 ..      22      29 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.21
                           DUF1610 17 FpCPNCG 23
                                      F C NCG
  gi|557694804|ref|YP_008797858.1|  6 FVCTNCG 12
                                      6666776 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0048
                           DUF1610 19 CPNCG 23
                                      CPNCG
  gi|557694804|ref|YP_008797858.1| 24 CPNCG 28
                                      ****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       833  (0.046461); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1184.98
//
Query:       gi|557694805|ref|YP_008797859.1|  [L=103]
Description: Rieske (2Fe-2S) type ferredoxin [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   56.6   0.0    2.2e-15   56.4   0.0    1.1  1  Rieske    Rieske [2Fe-2S] domain
    3.5e-07   30.1   0.0      4e-07   29.9   0.0    1.0  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 !   56.4   0.0   2.4e-19   2.2e-15       3      89 .]       5      90 ..       3      90 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2.4e-19
                                      EEEEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE-T CS
                            Rieske  3 vavakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikgP 80
                                      v+va++s++p+g+++t+++ g+ +++ +  dg +yA++ +C+H+++ lseg + e+++++C  Hg+++d ++Gk+   +
  gi|557694805|ref|YP_008797859.1|  5 VKVAAVSELPTGSMKTFDIEGKLILLANV-DGVFYAMDAICSHEEWDLSEGML-EGTHVTCAGHGAVWDlTTGKAEFDE 81
                                      799*******************9999997.***********************.788*******************999 PP

                                      THHHEEEET CS
                            Rieske 81 aprplatyp 89
                                        +pl+ty+
  gi|557694805|ref|YP_008797859.1| 82 ELQPLKTYK 90
                                      999999995 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 !   29.9   0.0   4.5e-11     4e-07       3     103 ..       5     100 ..       3     101 .. 0.92

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4.5e-11
                                       EEEEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT- CS
                          Rieske_2   3 vpvckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktG 79 
                                       v+v+++++l+ ++ ++  ++gk ++l+ + ++  yA+d+++   e+  ls+G+++ +     v++  ++ ++dL+tG
  gi|557694805|ref|YP_008797859.1|   5 VKVAAVSELPTGSMKTFDIEGKLILLANV-DGVFYAMDAICSH-EEWDLSEGMLEGT----HVTCAGHGAVWDLTTG 75 
                                       6899***********************99.9***********9.6999*****9877....89************** PP

                                       BBSS-TT.SB-BEE-EEESTSEEEE CS
                          Rieske_2  80 ecledee.vslkvypvrvedgkvev 103
                                       +   dee ++lk+y++ ++dg+v +
  gi|557694805|ref|YP_008797859.1|  76 KAEFDEElQPLKTYKTLLKDGEVFI 100
                                       *965555499*************88 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 762.93
//
Query:       gi|557694806|ref|YP_008797860.1|  [L=328]
Description: thioredoxin reductase (NADPH) [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  172.5   5.1    1.3e-50  172.3   5.1    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.8e-23   81.2   4.3      7e-20   71.5   0.1    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    3.2e-19   69.3   7.6    2.4e-17   63.3   1.1    3.2  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    3.3e-07   30.0   5.0    4.5e-07   29.6   0.6    2.3  2  FAD_oxidored    FAD dependent oxidoreductase
    6.3e-07   29.3  11.5      0.041   13.5   0.0    4.0  4  DAO             FAD dependent oxidoreductase
    6.8e-07   28.7   8.3    0.00011   21.4   0.9    3.3  3  FAD_binding_2   FAD binding domain
     0.0001   21.6  14.9    0.00023   20.4   1.9    4.5  5  GIDA            Glucose inhibited division protein A
    0.00031   20.1   4.4    0.00068   18.9   0.4    3.0  4  Thi4            Thi4 family
    0.00044   19.6   2.5      0.097   11.9   0.1    3.0  3  FAD_binding_3   FAD binding domain
     0.0021   18.5   2.8       0.41   11.1   0.6    2.7  2  NAD_binding_7   Putative NAD(P)-binding
     0.0023   16.7   5.7     0.0028   16.4   0.5    3.2  5  HI0933_like     HI0933-like protein
     0.0033   16.5   0.8      0.088   11.8   0.3    2.5  2  Lycopene_cycl   Lycopene cyclase protein
     0.0053   16.0   1.7        2.1    7.4   0.1    3.3  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
  ------ inclusion threshold ------
      0.011   16.0   1.7       0.16   12.2   0.3    2.3  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.016   15.2   1.8       0.48   10.5   0.1    2.9  3  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.023   13.5   2.4      0.043   12.7   0.9    2.0  2  Trp_halogenase  Tryptophan halogenase


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 !  172.3   5.1   1.2e-53   1.3e-50       1     291 [.       9     294 ..       9     297 .. 0.92

  Alignments for each domain:
  == domain 1  score: 172.3 bits;  conditional E-value: 1.2e-53
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.........HHHHCHHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.........evvkklnqgie 68 
                                       +dvvviGgGpAG++aa++  +a++k++++   g   +g+ +l+ ++++++++a+ +          +  +  nqg e
  gi|557694806|ref|YP_008797860.1|   9 YDVVVIGGGPAGYTAAIYTCRANLKTLVI--AGIEAGGQLMLTREVENYPGFANGVIgpelmenmrQ--QAENQGAE 81 
                                       69***********************9999..88899*****************99989999987642..45577788 PP

                                       CCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  69 lllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkri 145
                                        +++ +++++d+ k+ +++   + g  e +    +++AtG+sp+ lg++G+     k+v++++++++   k +   +
  gi|557694806|ref|YP_008797860.1|  82 IVYD-NATGVDFSKHPFEVY--V-G-DEVYRGRVVIVATGASPKWLGVEGERRLLAKGVSSCATCDGPLFKGTS-TT 152
                                       8888.89****999999992..3.4.469999**************************************9998.9* PP

                                       EEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT.TEEEEESCEEEEEEETTE....EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx....xxx RF
                       Pyr_redox_2 146 vvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealeke.Gvevklgtsvkeidgnge....kle 217
                                       vvvGgG +++E+A +l++l ++v++v++rd+l       +s+ l+e+ +++  +e++++++v+ei+g+++    +++
  gi|557694806|ref|YP_008797860.1| 153 VVVGGGDTAMEYALYLSNLVEKVVVVHRRDTLR------ASKVLAERARNNpRIEFVWNSVVTEIIGDNKveavRVK 223
                                       ********************************7......8999999999999******************9977666 PP

                                       .EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 218 .vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAv 291
                                        +++++++ i ++ v+va+G +p+te++  + +le+de g+i+    + t+v+g++a+GDv   ++++++a +A 
  gi|557694806|ref|YP_008797860.1| 224 nLKTGEEQIIRTESVFVAIGHKPNTEIF--AGQLEMDEEGYIKLFNGMMTSVKGVFAAGDVH--DKKYRQAITAA 294
                                       899999999*****************95..9*******************************..88888888876 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 !   11.5   0.8   0.00011      0.13       1      26 [.      12      37 ..      12      57 .. 0.82
   2 !   71.5   0.1   6.2e-23     7e-20      88     305 .]      72     280 ..      47     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledyli 26
                                      ++iG+GPaG +aai   +a+l++++i
  gi|557694806|ref|YP_008797860.1| 12 VVIGGGPAGYTAAIYTCRANLKTLVI 37
                                      79*******************76555 PP

  == domain 2  score: 71.5 bits;  conditional E-value: 6.2e-23
                       Pyr_redox_3  88 revaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek.lvkhyskvk..efhk 161
                                       r+ a+++  +i +  + + v+ +++ fev    e+y+ + vi+AtG    P++l+++Ge + l+k  s     +   
  gi|557694806|ref|YP_008797860.1|  72 RQQAENQGAEIVY-DNATGVDFSKHPFEVYVGDEVYRGRVVIVATGA--SPKWLGVEGERRlLAKGVSSCAtcDGPL 145
                                       5555555555554.456899999***********************9..**********975455444444124445 PP

                       Pyr_redox_3 162 ya.gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevke 237
                                       ++ +   vV+Gg+++a+++Al l +   +V vv+r++++++++       ++++++r+e ++++   +++ +++v++
  gi|557694806|ref|YP_008797860.1| 146 FKgTSTTVVVGGGDTAMEYALYLSNLVEKVVVVHRRDTLRASK---VLAERARNNPRIEFVWNSVVTEIIGDNKVEA 219
                                       664567899****************************998875...5566999*****9999998789********* PP

                       Pyr_redox_3 238 ikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       ++ k    ++kt + +++  ++ v++a+G kp++++++  ++e de+g+++l +  + t v+g+f aG
  gi|557694806|ref|YP_008797860.1| 220 VRVK----NLKTGE-EQIIRTESVFVAIGHKPNTEIFA-GQLEMDEEGYIKLFNG-MMTSVKGVFAAG 280
                                       **87....466777.67777899999***********9.99999******99876.5577******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 !    6.8   0.7    0.0089       9.9       2      28 ..      11      37 ..      10      94 .. 0.85
   2 !   63.3   1.1   2.1e-20   2.4e-17       2      79 ..     152     223 ..     151     230 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0089
                                      EEEECSSHHHHHHHHHHHHTTSEEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvv 28
                                      vvv+GgG  g  +A +  + + k+ v+
  gi|557694806|ref|YP_008797860.1| 11 VVVIGGGPAGYTAAIYTCRANLKTLVI 37
                                      8*************9998877766655 PP

  == domain 2  score: 63.3 bits;  conditional E-value: 2.1e-20
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvk 77 
                                        vvvGgG++++E+A +l++l  kV vv+r+d+l+      ask+l+e+ ++n  ie+++n++v+ei g+++ ve+v+
  gi|557694806|ref|YP_008797860.1| 152 TVVVGGGDTAMEYALYLSNLVEKVVVVHRRDTLR------ASKVLAERARNNpRIEFVWNSVVTEIIGDNK-VEAVR 221
                                       69********************************......******************************9.9***9 PP

                                       EE CS
                         Pyr_redox  78 lk 79 
                                       +k
  gi|557694806|ref|YP_008797860.1| 222 VK 223
                                       97 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.6     4e-10   4.5e-07       1      93 [.      10     106 ..      10     124 .. 0.71
   2 ?    2.3   0.1     0.078        87      88     134 ..     185     233 ..     160     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4e-10
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrgga.... 73 
                                       DvvV+GGgpaG++AAi  +ra  k+l++      GG+l    ++  ++n+ ++++++ i  e++e++rq+ +     
  gi|557694806|ref|YP_008797860.1|  10 DVVVIGGGPAGYTAAIYTCRANLKTLVIA-GIEAGGQLM---LTREVENY-PGFANGVIGPELMENMRQQAENqgae 81 
                                       9************************8885.677888763...33334445.77889999999999999933332222 PP

                      FAD_oxidored  74 ...rlkkrskwn.....tfepevakavl 93 
                                          +   +++ +     +fe+ v  +v+
  gi|557694806|ref|YP_008797860.1|  82 ivyD---NATGVdfskhPFEVYVGDEVY 106
                                       3221...222213444578887777776 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.078
                      FAD_oxidored  88 vakavleeml.aeagvtvllntrlvevekegkriesvtveske.g.rkti 134
                                        a +vl e   ++++++ + n++++e++ ++ ++e+v+v++ + g ++ i
  gi|557694806|ref|YP_008797860.1| 185 RASKVLAERArNNPRIEFVWNSVVTEIIGDN-KVEAVRVKNLKtGeEQII 233
                                       45566666664789**************996.9*******9998855555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   2.0   0.00049      0.55       1      28 [.      10      42 ..      10      47 .. 0.78
   2 !   13.5   0.0   3.7e-05     0.041     147     205 ..      66     120 ..      55     141 .. 0.75
   3 ?    3.4   0.1     0.043        48       2      31 ..     152     183 ..     151     189 .. 0.83
   4 !    8.1   0.0    0.0016       1.8     147     227 ..     185     273 ..     179     303 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00049
                                      EEEEECTSHHHHHHHHHHHHTT.....EEEEES CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg.....Vtllek 28
                                      dvv+iGGG +G ++A +  r++     ++ +e+
  gi|557694806|ref|YP_008797860.1| 10 DVVVIGGGPAGYTAAIYTCRANlktlvIAGIEA 42
                                      9****************9888776454444444 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.7e-05
                                       HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHH CS
                               DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsd 205
                                       +l+  ++++ae++G+ei++  ++tg++   +   +v++   g +  + + v++a+Ga  +
  gi|557694806|ref|YP_008797860.1|  66 ELMENMRQQAENQGAEIVYD-NATGVDFS-KHPFEVYV---GDEvYRGRVVIVATGASPK 120
                                       58999***************.****9442.34455542...444334589******9865 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.043
                                       EEEECTSHHHHHHHHHHHHT.T.EEEEESSSS CS
                               DAO   2 vviiGGGiiGlstAyeLarr.g.Vtllekgdi 31 
                                        v++GGG + +  A++L+     V+++ ++d 
  gi|557694806|ref|YP_008797860.1| 152 TVVVGGGDTAMEYALYLSNLvEkVVVVHRRDT 183
                                       69***************876437***999965 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHTT.-EEEESECEEEEEEEETCEEEEE..EECTEEEEEEEE..EEE--GGGHH.HH..HTT.CTTT CS
                               DAO 147 kltaalaraaealG.veilegtevtgleeedgkvwgve..rttpgendaada..vVnaaGawsd.ll..gll.keld 214
                                       ++ + la++a+++  +e++ ++ vt++   d+kv  v+  + + ge++++++  v +a G+  + ++  g+l  + +
  gi|557694806|ref|YP_008797860.1| 185 RASKVLAERARNNPrIEFVWNSVVTEI-IGDNKVEAVRvkNLKTGEEQIIRTesVFVAIGHKPNtEIfaGQLeMDEE 260
                                       5667799999999669**********9.45678899988754446665567777******98777443444432223 PP

                                       SEEEEEEEEEEEE CS
                               DAO 215 lpispvrgqvlvl 227
                                         i+ + g +  +
  gi|557694806|ref|YP_008797860.1| 261 GYIKLFNGMMTSV 273
                                       4455555555554 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.9     1e-07   0.00011       1      37 [.      10      45 ..      10      50 .. 0.91
   2 ?   -0.5   0.1      0.44   4.9e+02       3      33 ..     153     183 ..     151     191 .. 0.85
   3 !   10.0   0.2    0.0003      0.33     145     204 ..     188     247 ..     185     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                      Dv+ViG+G AG++AA+   +a+lk++v+   ++ gg+
  gi|557694806|ref|YP_008797860.1| 10 DVVVIGGGPAGYTAAIYTCRANLKTLVIAGIEA-GGQ 45
                                      9***************************98886.555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.44
                                       EEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                                       +V+G+G   +  Al +++   kv+vv   + 
  gi|557694806|ref|YP_008797860.1| 153 VVVGGGDTAMEYALYLSNLVEKVVVVHRRDT 183
                                       9****************99999999987665 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.0003
                                       HHHHHHHHTCT.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 145 arlvesarkag.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                       ++l+e+ar+++ ++f  +  ++e+i  d++v  + v+n+++g+e+ ir   v +a g  ++
  gi|557694806|ref|YP_008797860.1| 188 KVLAERARNNPrIEFVWNSVVTEIIG-DNKVEAVRVKNLKTGEEQIIRTESVFVAIGHKPN 247
                                       57999**9999*************77.*******************999999999886665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   1.9   2.1e-07   0.00023       1      29 [.      10      40 ..      10      89 .. 0.77
   2 ?    0.8   0.0      0.18     2e+02     133     150 ..     100     117 ..      66     129 .. 0.66
   3 ?    0.8   0.0      0.18   2.1e+02       3      34 ..     153     183 ..     151     187 .. 0.85
   4 ?    3.4   0.1     0.029        32      98     163 ..     187     257 ..     178     264 .. 0.74
   5 ?    2.4   0.1      0.06        67     347     389 ..     266     309 ..     262     312 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.1e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE..E CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi..t 29
                                      dv+ViGgG AG+ AA+ + r+++k+l i   
  gi|557694806|ref|YP_008797860.1| 10 DVVVIGGGPAGYTAAIYTCRANLKTLVIagI 40
                                      79************************99663 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.18
                                       ETTS-EEEECEEEE--TT CS
                              GIDA 133 tedgetikakavviatGt 150
                                          +e+++ ++v++atG+
  gi|557694806|ref|YP_008797860.1| 100 YVGDEVYRGRVVIVATGA 117
                                       34578999*********8 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.18
                                       EEE-SSHHHHHHHHHHHHTT--EEEEES-GGG CS
                              GIDA   3 iViGgGhAGceAAlaaarlGakvlLithkldt 34 
                                       +V+GgG   +e Al +++l  kv+ + h+ dt
  gi|557694806|ref|YP_008797860.1| 153 VVVGGGDTAMEYALYLSNLVEKVVVV-HRRDT 183
                                       8*****************99999988.66555 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.029
                                       HHHHHHHHHTSTTEE.EEES-EEEEEECT....TEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEE CS
                              GIDA  98 skevteklenepnle.iieeeveelivee....kkvkgvvtedgetikakavviatGtflkgkihigekel 163
                                       sk + e+ +n+p +e +++  v+e+i ++     +vk ++t ++++i++++v +a G   + +i  g+ e+
  gi|557694806|ref|YP_008797860.1| 187 SKVLAERARNNPRIEfVWNSVVTEIIGDNkveaVRVKNLKTGEEQIIRTESVFVAIGHKPNTEIFAGQLEM 257
                                       56677778888999845567778886654555556666777888999999*******97788888887766 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.06
                                       -TTSBBSSSBTEEE-CGGGTB-SHHH...HHHHHHHHHHHHHHHHC CS
                              GIDA 347 lntLetkkvkgLflAGqinGteGYeE...aaaqGllAGinaarkak 389
                                        n + t+ vkg+f+AG++   + Y     aa+ G++A++ a r ++
  gi|557694806|ref|YP_008797860.1| 266 FNGMMTS-VKGVFAAGDVHDKK-YRQaitAAGFGCMAAMEAIRFIE 309
                                       5566665.9**********998.76511156699****99988765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4   6.1e-07   0.00068      18      48 ..       9      38 ..       2      50 .. 0.85
   2 ?   -1.3   0.0      0.91     1e+03     135     169 ..      83     118 ..      68     135 .. 0.75
   3 ?    0.6   0.1      0.25   2.8e+02      19      49 ..     151     180 ..     147     188 .. 0.83
   4 ?   -2.1   0.0       1.7   1.9e+03     171     207 ..     198     235 ..     181     243 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.1e-07
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvaile 48
                                       Dvv++G+G++G taa y  ++ +lk++++ 
  gi|557694806|ref|YP_008797860.1|  9 YDVVVIGGGPAGYTAAIYTCRA-NLKTLVIA 38
                                      6********************9.****9995 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.91
                                       EEEEEHHHHTC.TTTSS.-B-EEEEEEEEEE--GSS CS
                              Thi4 135 vvinwtlvela.hdtqscvDPlvirakvvvdatGhd 169
                                       v  n t v+ + h  +  v   v r +vv+ atG  
  gi|557694806|ref|YP_008797860.1|  83 VYDNATGVDFSkHPFEVYVGDEVYRGRVVIVATGAS 118
                                       445677777777888888888999999999999975 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.25
                                       EEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4  19 DvvivGaGssGLtaayylakkpdlkvailer 49 
                                         v+vG+G + +  a yl++    kv+++ r
  gi|557694806|ref|YP_008797860.1| 151 TTVVVGGGDTAMEYALYLSNL-VEKVVVVHR 180
                                       5699**************998.557777766 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 1.7
                                       TTTTHHHHHH.HHCTTTS-----ECB-HHHHHHHHHHH CS
                              Thi4 171 eivavvvkki.kleakiekvkgeksldaekaedaivkk 207
                                       + +++v   + +++  ++kv+  +    +++e++i+++
  gi|557694806|ref|YP_008797860.1| 198 PRIEFVWNSVvTEIIGDNKVEAVRVKNLKTGEEQIIRT 235
                                       55555544442344456788888888888888888864 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   8.7e-05     0.097       2      30 ..       9      37 ..       8      89 .. 0.67
   2 ?    3.9   0.1     0.023        25       3      40 ..     151     187 ..     149     189 .. 0.83
   3 ?    3.4   0.0     0.033        37     107     155 ..     186     235 ..     183     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.7e-05
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEE CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlv 30
                                      +dV+++G+GpaG ++a   ++a  +++++
  gi|557694806|ref|YP_008797860.1|  9 YDVVVIGGGPAGYTAAIYTCRANLKTLVI 37
                                      59**************8655554443332 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.023
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp 40 
                                       ++++VG+G + +  al Ls+  v+ v+v  r++t + +
  gi|557694806|ref|YP_008797860.1| 151 TTVVVGGGDTAMEYALYLSNL-VEKVVVVHRRDTLRAS 187
                                       578******************.9988777777777665 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHHT.EEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEE CS
                     FAD_binding_3 107 leriLvehaeerg.lqvrfktevesleqdeegvtaevrdketgeeetvra 155
                                         ++L+e+a++ + +++ ++  v+ +  d++ ++ +v++ +tgee+ +r 
  gi|557694806|ref|YP_008797860.1| 186 ASKVLAERARNNPrIEFVWNSVVTEIIGDNKVEAVRVKNLKTGEEQIIRT 235
                                       6799*****************************************98876 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 !    7.0   0.1    0.0069       7.7       9      39 ..      10      40 ..       6     117 .. 0.80
   2 !   11.1   0.6   0.00037      0.41       9      69 ..     151     242 ..     147     294 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0069
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvape 39
                                       v+v+GgG+ +++ +   ++a+ k  v+a  
  gi|557694806|ref|YP_008797860.1| 10 DVVVIGGGPAGYTAAIYTCRANLKTLVIAGI 40
                                      59***********************999976 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00037
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapevkeele..............................elvklaeeel 55 
                                       + +vvGgG+ A++ +  l +   kv+vv  + +  ++                              e v++++ + 
  gi|557694806|ref|YP_008797860.1| 151 TTVVVGGGDTAMEYALYLSNLVEKVVVVHRRDTLRASkvlaerarnnpriefvwnsvvteiigdnkvEAVRVKNLKT 227
                                       789*************************9995333332333333333333344443333333333222222222222 PP

                     NAD_binding_7  56 .ekdlegadlviaat 69 
                                        e+++ +++ v++a+
  gi|557694806|ref|YP_008797860.1| 228 gEEQIIRTESVFVAI 242
                                       344455555555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.5   2.5e-06    0.0028       1      31 [.       9      39 ..       9      49 .. 0.87
   2 ?    0.1   0.0      0.22   2.5e+02     112     166 ..      68     118 ..      64     135 .. 0.73
   3 ?   -0.4   0.0      0.33   3.7e+02       2      34 ..     151     183 ..     150     192 .. 0.84
   4 ?   -2.0   0.0      0.96   1.1e+03     123     164 ..     199     244 ..     188     248 .. 0.64
   5 ?   -4.1   0.0       4.2   4.8e+03     372     386 ..     270     284 ..     268     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.5e-06
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllek 31
                                      +dv+viGgG+AG  aAi   +++ ++l++  
  gi|557694806|ref|YP_008797860.1|  9 YDVVVIGGGPAGYTAAIYTCRANLKTLVIAG 39
                                      59***********************999865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.22
                                       HHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS CS
                       HI0933_like 112 vdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlS 166
                                       ++ + ++++++g ++ ++++ ++v+ +++  f+v + ++e ++ + +++AtG  S
  gi|557694806|ref|YP_008797860.1|  68 MENMRQQAENQGAEIVYDNA-TGVDFSKHP-FEVYV-GDEVYRGRVVIVATGA-S 118
                                       56677788888888877654.567665555.99999.9999999999999874.3 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.33
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34 
                                       +++v+GgG   +  A+ +++  ++V+++ + ++
  gi|557694806|ref|YP_008797860.1| 151 TTVVVGGGDTAMEYALYLSNLVEKVVVVHRRDT 183
                                       579***************999999999987665 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.96
                                       T-EEE-S--EEEE....ECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 123 gvklrletevksv....ekeedgkfrvktkseeeleadklvlAtGG 164
                                       ++++  ++ v+++    + e+ ++ ++kt +e+ ++++++ +A+G 
  gi|557694806|ref|YP_008797860.1| 199 RIEFVWNSVVTEIigdnKVEAVRVKNLKTGEEQIIRTESVFVAIGH 244
                                       5666666666666333233334445566668889999999999995 PP

  == domain 5  score: -4.1 bits;  conditional E-value: 4.2
                                       BTTSTTEEE-GGGBS CS
                       HI0933_like 372 skkvpgLffaGEvlD 386
                                       + +v+g+f aG v D
  gi|557694806|ref|YP_008797860.1| 270 MTSVKGVFAAGDVHD 284
                                       46899******9965 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.3   7.9e-05     0.088       1      39 [.      10      49 ..      10      55 .. 0.79
   2 ?    2.1   0.0      0.07        79      89     145 ..      67     120 ..      60     136 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.9e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakp.glkvvlieaspsllfp 39
                                      DvvviG+GpAg   A    +a+   l +  iea+ +l+ +
  gi|557694806|ref|YP_008797860.1| 10 DVVVIGGGPAGYTAAIYTCRANLkTLVIAGIEAGGQLMLT 49
                                      9**************9996665415666678999888876 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.07
                     Lycopene_cycl  89 lkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglaslk 145
                                       l e++ ++  ++g++ +   ++ v  ++      v  g++  r+r+v++a+g as+k
  gi|557694806|ref|YP_008797860.1|  67 LMENMRQQAENQGAEIVYDNATGVDFSKH--PFEVYVGDEVYRGRVVIVATG-ASPK 120
                                       55666666666665555544444444444..22344589999**********.6655 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      0.22   2.5e+02       2      23 ..       8      29 ..       7      42 .. 0.75
   2 ?    4.5   0.0     0.014        16     146     228 ..     105     184 ..      80     191 .. 0.63
   3 !    7.4   0.1    0.0019       2.1     115     161 ..     204     247 ..     190     260 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.22
                       K_oxygenase  2 ilDligiGiGpsnLsLaillee 23
                                      ++D++ iG Gp+  + ai +  
  gi|557694806|ref|YP_008797860.1|  8 VYDVVVIGGGPAGYTAAIYTCR 29
                                      7999999999998877776654 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.014
                       K_oxygenase 146 elearnlvlgvGtepkiPevleklegkervvH...sseylerkeellakkriaVvGsGqSaaeifedllrrqkkvel 219
                                        ++ r +++++G +pk   +l  +eg+ r++    ss ++ + +  +   + +VvG+G +a e +  l +  +  ++
  gi|557694806|ref|YP_008797860.1| 105 VYRGRVVIVATGASPK---WLG-VEGERRLLAkgvSSCATCDGPLFKGTSTTVVVGGGDTAMEYALYLSNLVE--KV 175
                                       5666677777776643...443.2222333321112222222233566677899*********9999888776..56 PP

                       K_oxygenase 220 klvtrseal 228
                                        +v r++ l
  gi|557694806|ref|YP_008797860.1| 176 VVVHRRDTL 184
                                       666666665 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0019
                       K_oxygenase 115 fgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepk 161
                                       +++ v+e+  d++   e+++v++  ++gee+ ++++++ +++G +p+
  gi|557694806|ref|YP_008797860.1| 204 WNSVVTEIIGDNKV--EAVRVKN-LKTGEEQIIRTESVFVAIGHKPN 247
                                       67778888877754..4666665.48999999999999999999997 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 ?   12.2   0.3   0.00014      0.16       1      35 [.      13      46 ..      13      63 .. 0.84
   2 ?    2.7   0.0      0.14   1.5e+02       1      29 [.     154     182 ..     154     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      ++G+G +G +aA +  +a+++ l++ ++   GG++
  gi|557694806|ref|YP_008797860.1| 13 VIGGGPAGYTAAIYTCRANLKTLVI-AGIEAGGQL 46
                                      8********************9999.777777764 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.14
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                                       +vG+G +++ +A +L++   +v+++ +rd
  gi|557694806|ref|YP_008797860.1| 154 VVGGGDTAMEYALYLSNLVEKVVVVHRRD 182
                                       8***************9877888877776 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1      0.11   1.2e+02      13      43 ..       9      39 ..       2      55 .. 0.87
   2 ?   10.5   0.1   0.00043      0.48      13      56 ..     150     193 ..     145     212 .. 0.81
   3 ?   -1.5   0.0       2.2   2.4e+03      57      86 ..     216     245 ..     199     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                                      -EEEEES-SHHHHHHHHHHHCCT-CEEEEEE CS
                      Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvvaN 43
                                        v++iG G  +  +a + +++++k +v+a+
  gi|557694806|ref|YP_008797860.1|  9 YDVVVIGGGPAGYTAAIYTCRANLKTLVIAG 39
                                      579************************9986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00043
                                       -EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH CS
                      Shikimate_DH  13 kkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel 56 
                                       ++ +++G G +a + a +L++   k vvv  R+  ra+++  e 
  gi|557694806|ref|YP_008797860.1| 150 STTVVVGGGDTAMEYALYLSNLVEKVVVVHRRDTLRASKVLAER 193
                                       6789****************988888888888888988765443 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 2.2
                                       T.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH  57 kgeeiealkleelkellaeadvvisatase 86 
                                       k e +++++l+  +e + + + v++a++++
  gi|557694806|ref|YP_008797860.1| 216 KVEAVRVKNLKTGEEQIIRTESVFVAIGHK 245
                                       334455666666677888888888888765 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.9   3.8e-05     0.043       1      32 [.      10      41 ..      10      44 .. 0.81
   2 ?   -0.3   0.0      0.34   3.8e+02       3      31 ..     153     178 ..     151     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                                      ++v++GGG+aG++aA++  +a  ++l +  +e
  gi|557694806|ref|YP_008797860.1| 10 DVVVIGGGPAGYTAAIYTCRANLKTLVIAGIE 41
                                      69**************9988876666666555 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.34
                                       EEE--SHHHHHHHHHHHHHTTTSSEEEEE CS
                    Trp_halogenase   3 vivGGGtaGwlaAaalakalkgklevtlv 31 
                                       v+vGGG  +   A +l++ +++   v +v
  gi|557694806|ref|YP_008797860.1| 153 VVVGGGDTAMEYALYLSNLVEK---VVVV 178
                                       89**************999944...5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); 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 0.29s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 2337.11
//
Query:       gi|557694807|ref|YP_008797861.1|  [L=120]
Description: ferredoxin [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   75.4   0.0    3.1e-21   75.1   0.0    1.1  1  Rieske       Rieske [2Fe-2S] domain
      2e-16   59.8   0.0    2.4e-16   59.6   0.0    1.1  1  Rieske_2     Rieske-like [2Fe-2S] domain
  ------ inclusion threshold ------
      0.058   12.8   0.0      0.068   12.6   0.0    1.2  1  Urocanase_C  Urocanase C-terminal domain
       0.17   11.9   0.0       0.26   11.3   0.0    1.3  1  TT_ORF2a     pORF2a truncated protein


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 !   75.1   0.0   6.9e-25   3.1e-21       3      89 .]      23     108 ..      21     108 .. 0.96

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 6.9e-25
                                       EEEEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE CS
                            Rieske   3 vavakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvik 78 
                                       v+v++e+++ egd++ v+ gge+++vlr+ +g+++A+s++CtH+ a l +g ++ +g+++Cp+H ++++ ++G+v++
  gi|557694807|ref|YP_008797861.1|  23 VKVCREDELGEGDMRVVEAGGEQVLVLRH-KGKLFAVSNICTHEYAELVNGLVV-DGTITCPVHLSRFRlETGEVLN 97 
                                       79**************************6.***********************5.66******************** PP

                                       -TTHHHEEEET CS
                            Rieske  79 gPaprplatyp 89 
                                        Pa+++l+ty+
  gi|557694807|ref|YP_008797861.1|  98 PPATKNLKTYK 108
                                       *********96 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 !   59.6   0.0   5.3e-20   2.4e-16       3     103 ..      23     118 ..      21     119 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 5.3e-20
                                       EEEEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT- CS
                          Rieske_2   3 vpvckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktG 79 
                                       v+vc+ ++l ++   ++  +g+qv+++r  k++++A++n+++ +  + l +Glv d     ++++P++ ++f+L+tG
  gi|557694807|ref|YP_008797861.1|  23 VKVCREDELGEGDMRVVEAGGEQVLVLRH-KGKLFAVSNICTHE-YAELVNGLVVDG----TITCPVHLSRFRLETG 93 
                                       68**************************9.9************6.667899***998....**************** PP

                                       BBSS-TT.SB-BEE-EEESTSEEEE CS
                          Rieske_2  80 ecledee.vslkvypvrvedgkvev 103
                                       e+l+ ++ ++lk+y++ v +g++ v
  gi|557694807|ref|YP_008797861.1|  94 EVLNPPAtKNLKTYKIHVLEGEIFV 118
                                       ****765489************998 PP

>> Urocanase_C  Urocanase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.5e-05     0.068      68     103 ..      64      99 ..      25     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.5e-05
                                       HHHHHHHHHHHHHSSSSS-EEEEE-S-STTSEE-TT CS
                       Urocanase_C  68 ekialafnelvregeikapvvlgRDhlDvgsvasPf 103
                                       ++ a  +n lv +g+i+ pv l+R  l++g v +P 
  gi|557694807|ref|YP_008797861.1|  64 HEYAELVNGLVVDGTITCPVHLSRFRLETGEVLNPP 99 
                                       678999*************************99985 PP

>> TT_ORF2a  pORF2a truncated protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.8e-05      0.26       9      36 ..      27      54 ..      22      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.8e-05
                          TT_ORF2a  9 rsGeateGdLrvPraGaeGefthrsqGa 36
                                      r  e  eGd+rv  aG e  +  r +G 
  gi|557694807|ref|YP_008797861.1| 27 REDELGEGDMRVVEAGGEQVLVLRHKGK 54
                                      778999************9888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 857.36
//
Query:       gi|557694808|ref|YP_008797862.1|  [L=182]
Description: methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   52.3   0.0    6.6e-14   52.0   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    5.9e-13   49.3   0.0    8.6e-13   48.8   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    2.7e-12   46.5   0.0    3.5e-12   46.2   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    6.6e-11   42.8   0.0    9.6e-11   42.3   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    1.3e-10   41.8   0.1    2.9e-10   40.7   0.0    1.6  2  Methyltransf_11  Methyltransferase domain
      4e-07   30.0   0.0    5.9e-07   29.5   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    9.4e-07   28.8   0.0    1.6e-06   28.1   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    7.1e-06   26.1   0.0    8.7e-06   25.8   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
    0.00021   20.7   0.0    0.00026   20.4   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00035   20.3   0.0    0.00049   19.8   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    0.00038   20.1   0.0    0.00052   19.6   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0038   16.4   0.0      0.095   11.8   0.0    2.1  2  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.023   14.2   0.0    1.3  1  Methyltransf_4   Putative methyltransferase
      0.022   14.2   0.0      0.028   13.8   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.032   14.2   0.0      0.059   13.3   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
      0.093   12.3   0.0       0.11   12.0   0.0    1.1  1  FmrO             Ribosomal RNA methyltransferase (FmrO)
      0.097   12.2   0.0       0.12   11.9   0.0    1.2  1  DOT1             Histone methylation protein DOT1
        0.1   11.7   0.0       0.55    9.3   0.0    1.8  2  DREV             DREV methyltransferase
       0.12   12.4   0.0       0.15   12.2   0.0    1.2  1  FtsJ             FtsJ-like methyltransferase
       0.13   11.9   0.0       0.17   11.5   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.18   11.1   0.0       0.24   10.7   0.0    1.2  1  GidB             rRNA small subunit methyltransferase G
       0.19   10.9   0.0       0.23   10.6   0.0    1.2  1  Methyltransf_3   O-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 !   52.0   0.0   8.2e-17   6.6e-14       6     113 ..      34     140 ..      30     167 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 8.2e-17
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       r+lD+GCG+G+ltf +a+ +g+k+ v+ +D see +e  +++a+ lgl nv++ +   e+le        + +++++
  gi|557694808|ref|YP_008797862.1|  34 RFLDVGCGKGFLTFPAASVVGEKGMVYAVDVSEEYLEIVKSRAAALGLGNVKVLKTAGEDLEG-----VPNHVIDRA 105
                                       68*****************************************************88888773.....335566655 PP

                   Methyltransf_31  83 vl....naladpdkileeiervlkpggilliedpr 113
                                       +     +++ d  k le + + l ++g + i dp 
  gi|557694808|ref|YP_008797862.1| 106 AYlfslHHIGDIRKSLETLRSKLVDDGLVYILDPI 140
                                       555666***********************999875 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   1.1e-15   8.6e-13       2      97 .]      36     132 ..      35     132 .. 0.93

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 1.1e-15
                                       EEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBS.SSTTTEEEEEEESTGG CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaedlp.fedgsfDlvvssgalh 75 
                                       Ld+GcG+G lt+ +a  +g k+ v++vD+see+le++++ra++ gl nv++++   edl+  +++ +D     ++lh
  gi|557694808|ref|YP_008797862.1|  36 LDVGCGKGFLTFPAASVVGeKGMVYAVDVSEEYLEIVKSRAAALGLgNVKVLKTAGEDLEgVPNHVIDRAAYLFSLH 112
                                       9****************9779**************************************9679999***999999** PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       h+   d++k l+ +++ L ++G
  gi|557694808|ref|YP_008797862.1| 113 HIG--DIRKSLETLRSKLVDDG 132
                                       *98..89999999998887766 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   0.0   4.3e-15   3.5e-12      40     153 ..      24     138 ..       7     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 4.3e-15
                                       HHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TT.S-T CS
                   Ubie_methyltran  40 eklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpf.edd 115
                                          v+ ++ +++lDv +G g l+f  ++ vgekg v  +D++e+ L++ + ++   g  n++ l++ +e+L+   + 
  gi|557694808|ref|YP_008797862.1|  24 LAEVGLRPMHRFLDVGCGKGFLTFPAASVVGEKGMVYAVDVSEEYLEIVKSRAAALGLGNVKVLKTAGEDLEGvPNH 100
                                       45556677789************************************************************961568 PP

                                       -EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEE CS
                   Ubie_methyltran 116 sfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvle 153
                                         D  +  f l  + D+ k+L++++  l   G +++l+
  gi|557694808|ref|YP_008797862.1| 101 VIDRAAYLFSLHHIGDIRKSLETLRSKLVDDGLVYILD 138
                                       99***********************9999999999986 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   1.2e-13   9.6e-11       1      98 [.      36     133 ..      36     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 1.2e-13
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L++GcG G l+++ +    +   +++vD+s++ +e  k + a+ +  n+++++   +dl +  +++  D    ++ l
  gi|557694808|ref|YP_008797862.1|  36 LDVGCGKGFLTFPAASVVgEKGMVYAVDVSEEYLEIVKSRAAALGLGNVKVLKTAGEDL-EGVPNHVIDRAAYLFSL 111
                                       8**************9997888888***********************99999999996.566678*********** PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGr 98 
                                       hh+ dir++l+ +r+ L+++G 
  gi|557694808|ref|YP_008797862.1| 112 HHIGDIRKSLETLRSKLVDDGL 133
                                       *******************996 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   3.6e-13   2.9e-10       1      96 []      36     136 ..      36     136 .. 0.95
   2 ?   -2.1   0.0       7.6   6.2e+03       4      24 ..     148     168 ..     145     170 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 3.6e-13
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCT.SS-TT-EEEEEEES-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl.kvefvvadaekl.pfednsfDlvvssevlh 72 
                                       LdvGcG+G l+ + a+ +   + v++vD+s+e l+++k++a   gl +v++++   e+l  ++++ +D     ++lh
  gi|557694808|ref|YP_008797862.1|  36 LDVGCGKGFLTFPAASVVgekGMVYAVDVSEEYLEIVKSRAAALGLgNVKVLKTAGEDLeGVPNHVIDRAAYLFSLH 112
                                       8**************6666778*************************************88**************** PP

                                       C-CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  73 hvedpekalkeiaRvLkpgGllvi 96 
                                       h+ d +k l+ ++  L  +Gl++i
  gi|557694808|ref|YP_008797862.1| 113 HIGDIRKSLETLRSKLVDDGLVYI 136
                                       ****************99999875 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.6
                                       T-TTSHHHHHHHHTTSEEEEE CS
                   Methyltransf_11   4 GcGtGrlaealakrgarvvgv 24 
                                       G+    ++  l+++g++v+g+
  gi|557694808|ref|YP_008797862.1| 148 GTSPSHVLSILEETGYKVTGF 168
                                       555677888889999999986 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 !   29.5   0.0   7.2e-10   5.9e-07      69     134 ..      27      92 ..      20     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 7.2e-10
                                       TT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GG CS
                              PCMT  69 lelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGr 134
                                       + l++  r L+vG+G G+lt   a +vgekg v +++ ++e  e  k +  +l+l nv+v  + G+
  gi|557694808|ref|YP_008797862.1|  27 VGLRPMHRFLDVGCGKGFLTFPAASVVGEKGMVYAVDVSEEYLEIVKSRAAALGLGNVKVLKTAGE 92 
                                       56999***************************************************9999877664 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.9e-09   1.6e-06      15     121 ..      26     140 ..       6     177 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.9e-09
                   Methyltransf_23  15 rllpklraggrvLdiGcGtG.illevlrengf..svtgvDlspeaveiae.........kakkaqkdqfdeqeaaep 79 
                                       +++  lr+  r Ld+GcG+G  + + ++  g    v++vD s+e  ei++         + k  +   +  + + +p
  gi|557694808|ref|YP_008797862.1|  26 EVG--LRPMHRFLDVGCGKGfLTFPAASVVGEkgMVYAVDVSEEYLEIVKsraaalglgNVKVLKTAGE--DLEGVP 98 
                                       222..67777**********77777777777766799***********999999999885555555555..66788* PP

                   Methyltransf_23  80 qgkfdlIvlrevlehvpdppellrqiatllkpgGylllsepl 121
                                       +  +d +   ++l+h+ d  + l ++++ l ++G++++++p 
  gi|557694808|ref|YP_008797862.1|  99 NHVIDRAAYLFSLHHIGDIRKSLETLRSKLVDDGLVYILDPI 140
                                       ***************************************973 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.1e-08   8.7e-06      27      78 ..      33      81 ..      21     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.1e-08
                   Methyltransf_32 27 ltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkf 78
                                       + +DvG+Gkg+L+f  a+  +  k  v+++d++ee  e  + ra++lg  +
  gi|557694808|ref|YP_008797862.1| 33 HRFLDVGCGKGFLTFPAAS-VVGEKGMVYAVDVSEEYLEIVKSRAAALG--L 81
                                      5789**************9.56689*********************999..3 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.2e-07   0.00026      54     160 ..      23     132 ..      18     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.2e-07
                                       HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--E..EEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG---.. CS
                              CMAS  54 ileklelkpGmtlLdiGcGWGslvrraverydvk..vvglTlSkeqaklakkrvdeldlerkvevklldyedlde.. 126
                                       il  ++l+p ++ Ld+GcG G l+  a++  + k  v ++ +S+e  + +k r ++l+l + v+v+ +  edl++  
  gi|557694808|ref|YP_008797862.1|  23 ILAEVGLRPMHRFLDVGCGKGFLTFPAASVVGEKgmVYAVDVSEEYLEIVKSRAAALGLGN-VKVLKTAGEDLEGvp 98 
                                       6778899*****************999998876544999*******************876.556666667777755 PP

                                       ..--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT- CS
                              CMAS 127 ..kvdrvvsvgafehvgkenydtffkklkkllkedG 160
                                          +dr   +  + h+g  +  +  ++l ++l +dG
  gi|557694808|ref|YP_008797862.1|  99 nhVIDRAAYLFSLHHIGDIR--KSLETLRSKLVDDG 132
                                       45567777777777777544..33455555555555 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 !   19.8   0.0     6e-07   0.00049       9      82 ..      32     104 ..      26     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6e-07
                                       T-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEE CS
                   Methyltr_RsmB-F   9 eetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDr 82 
                                         ++lD+ ++ G  T   a ++ +kg v+Avd+++e l+ v++    Lg+ n++vl++ +   + v   +++Dr
  gi|557694808|ref|YP_008797862.1|  32 MHRFLDVGCGKGFLTFPAASVVGEKGMVYAVDVSEEYLEIVKSRAAALGLGNVKVLKTAGEDLEGVPN-HVIDR 104
                                       5689*****************************************************99988877776.47777 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   6.4e-07   0.00052      32      84 ..      32      86 ..      21     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 6.4e-07
                                      CSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC.EEE CS
                               MTS 32 sgkvlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle.vev 84
                                       ++ lD+GcG G+l+  +a+   e   v +vdv+ + le+ k  ++a +l  v+v
  gi|557694808|ref|YP_008797862.1| 32 MHRFLDVGCGKGFLTFPAASVVGEKGmVYAVDVSEEYLEIVKSRAAALGLGnVKV 86
                                      5679****************99988779*************99999887765555 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00012     0.095      63     107 ..      24      68 ..      15      78 .. 0.87
   2 ?    2.5   0.0     0.081        66      81      97 ..     147     163 ..     126     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                       -S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHH CS
                       Fibrillarin  63 lkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprv 107
                                       l+e+ +++ ++ L +G + G      + +vge+g+vyav++s+  
  gi|557694808|ref|YP_008797862.1|  24 LAEVGLRPMHRFLDVGCGKGFLTFPAASVVGEKGMVYAVDVSEEY 68 
                                       678889999999********999999**************99865 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.081
                                       TSHHHHHHHHHHTTTSE CS
                       Fibrillarin  81 sGttvsHvsDivgeegv 97 
                                        Gt++sHv  i++e+g 
  gi|557694808|ref|YP_008797862.1| 147 HGTSPSHVLSILEETGY 163
                                       79**********99984 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.8e-05     0.023       5      60 ..      35      91 ..      31     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.8e-05
                                      EEEET-TTSHHHHHHHHHSTTSEEE.EEES-HHHHHHHHHHHHHCTTSSEEEEES-C CS
                    Methyltransf_4  5 vleiGcGkGeflvalAkknPdknfl.GiEirvkvvakvlkkiealelkNlrilrgda 60
                                      +l++GcGkG ++   A    +k ++ +++++++ ++ v ++++al+l N+++l++  
  gi|557694808|ref|YP_008797862.1| 35 FLDVGCGKGFLTFPAASVVGEKGMVyAVDVSEEYLEIVKSRAAALGLGNVKVLKTAG 91
                                      89***************999997655**************************98755 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.5e-05     0.028     159     201 ..      29      73 ..      20      95 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-05
                              PrmA 159 vkegeevlDvGtGSGiLai.aaakLgak.kvvavDiDevAvkvak 201
                                       +++ +++lDvG+G G L+  aa+ +g k  v+avD+ e  +++ k
  gi|557694808|ref|YP_008797862.1|  29 LRPMHRFLDVGCGKGFLTFpAASVVGEKgMVYAVDVSEEYLEIVK 73 
                                       6778899***********95556667653699***9987666655 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.2e-05     0.059      15      69 ..      32      86 ..      16     106 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.2e-05
                   Methyltransf_18 15 gsrvaDiGtDHgylpiylvk.egkakkviasDinegplekakeniekagledkiev 69
                                       +r++D+G+  g+l++ +++  g    v+a+D++e+ le  k+ ++  gl + ++v
  gi|557694808|ref|YP_008797862.1| 32 MHRFLDVGCGKGFLTFPAASvVGEKGMVYAVDVSEEYLEIVKSRAAALGLGN-VKV 86
                                      56899*********99877525777899*************99999998853.444 PP

>> FmrO  Ribosomal RNA methyltransferase (FmrO)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.11     106     190 ..      31     119 ..      20     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                              FmrO 106 apasvlDvaCgLnpLavpwllla.adatylasDidsdlvefldrflalvevegrvevr....DlvadvpapraDlaL 177
                                       +++  lDv+Cg   L++p  +    + + +a D+  +++e+++   a +++  +v+v     +   +vp   +D a 
  gi|557694808|ref|YP_008797862.1|  31 PMHRFLDVGCGKGFLTFPAASVVgEKGMVYAVDVSEEYLEIVKSRAAALGLG-NVKVLktagEDLEGVPNHVIDRAA 106
                                       567789************987651567889***********98766666653.333320011334456667777777 PP

                              FmrO 178 vLktlpvLeqrrr 190
                                        L  l+ + ++r+
  gi|557694808|ref|YP_008797862.1| 107 YLFSLHHIGDIRK 119
                                       7777666666664 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00015      0.12      33      95 ..      22      78 ..       7     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                                      HHHHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHH CS
                              DOT1 33 evldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlkl 95
                                      ++l +v l++ + F+D G G G +++ aa  vg k       m  a +++e+  e++k+r++ 
  gi|557694808|ref|YP_008797862.1| 22 KILAEVGLRPMHRFLDVGCGKGFLTFPAASVVGEK------GMVYAVDVSEEYLEIVKSRAAA 78
                                      6899**********************999988877......3444444455555555555555 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00067      0.55      95     136 ..      32      76 ..      13     135 .. 0.73
   2 ?    0.2   0.0      0.39   3.2e+02     222     240 ..     152     170 ..     136     172 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00067
                              DREV  95 dkklldlGaGdGeitkrvaptfee...vyatelsetmrdrlkkkk 136
                                        ++ ld+G G+G +t   a+ + e   vya ++se+  + +k + 
  gi|557694808|ref|YP_008797862.1|  32 MHRFLDVGCGKGFLTFPAASVVGEkgmVYAVDVSEEYLEIVKSRA 76 
                                       589*******************99999*******99877766554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.39
                              DREV 222 arlievlkkagfeveaftr 240
                                       ++++ +l+++g++v  ft+
  gi|557694808|ref|YP_008797862.1| 152 SHVLSILEETGYKVTGFTK 170
                                       578899***********98 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   0.00018      0.15      12      57 ..      23      67 ..      17     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                      HHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS CS
                              FtsJ 12 idekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm 57
                                      i+++++ ++p ++++D+g++ G  +  ++  +g+kg+v+avD+ + 
  gi|557694808|ref|YP_008797862.1| 23 ILAEVG-LRPMHRFLDVGCGKGFLTFPAASVVGEKGMVYAVDVSEE 67
                                      566677.7899**********************9*********765 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   0.00021      0.17      33      98 ..      21      89 ..      14     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00021
                                      HHHHCCC..HCC-EEEETT-TTSHHHHHHHHTT-SE..EEEEES-HHHHHHHHHHHCCCT--TTTEEEEE CS
                     Cons_hypoth95 33 Fnilaae..iegarvLDlfaGsGalglEAlSRgakk..avlvekdkeavkilkenleelkleeetaelke 98
                                      F ila+       r+LD+ +G G l + A+S   +k  +++v+ ++e ++i+k   ++l+l + +++lk 
  gi|557694808|ref|YP_008797862.1| 21 FKILAEVglRPMHRFLDVGCGKGFLTFPAASVVGEKgmVYAVDVSEEYLEIVKSRAAALGLGN-VKVLKT 89
                                      77777776445679*****************7655422789*******************997.444443 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00029      0.24      51     109 ..      34      93 ..      10     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                                       .EEEETSTTTTTHHHHHHH-TTSE.EEEEES-HHHHHHHHHHHHHCT-SSEEEEES-CCC CS
                              GidB  51 kviDvGsGaGlPGipLaiarpelk.ltLleslekkiaFLeevkeelklenveivearaee 109
                                       +++DvG G G+   p a +  e+  ++ ++ +e   +  +   ++l+l nv+++++  e+
  gi|557694808|ref|YP_008797862.1|  34 RFLDVGCGKGFLTFPAASVVGEKGmVYAVDVSEEYLEIVKSRAAALGLGNVKVLKTAGED 93 
                                       69*************9977777665999*****999999999999*********998777 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00029      0.23      48      92 ..      32      76 ..      21     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00029
                                      --EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHH CS
                    Methyltransf_3 48 akrvleiGvftGyslLatalalPeDGkilaididreayeialkfi 92
                                        r l++G  +G+  +  a  + e G + a+d+ +e+ ei ++  
  gi|557694808|ref|YP_008797862.1| 32 MHRFLDVGCGKGFLTFPAASVVGEKGMVYAVDVSEEYLEIVKSRA 76
                                      57899***********************************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1267.90
//
Query:       gi|557694809|ref|YP_008797863.1|  [L=492]
Description: DNA polymerase II small subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   56.6   0.0    3.5e-15   55.9   0.0    1.3  1  DNA_pol_E_B      DNA polymerase alpha/epsilon subunit B
    1.4e-07   32.2   0.0    2.1e-07   31.6   0.0    1.3  1  Metallophos      Calcineurin-like phosphoesterase
    2.6e-05   24.5   0.0    9.8e-05   22.6   0.0    1.8  1  Metallophos_2    Calcineurin-like phosphoesterase superfamily
  ------ inclusion threshold ------
       0.03   14.3   0.0      0.061   13.3   0.0    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.099   12.6   0.0         19    5.2   0.0    2.5  2  FIST_C           FIST C domain
       0.12   12.0   0.1       0.27   10.9   0.1    1.7  1  CHASE2           CHASE2 domain


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   1.2e-18   3.5e-15       2     200 ..     233     432 ..     232     438 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 1.2e-18
                                       EEEES--S-TT---...-HHHHHHHHHHH..HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHH CS
                       DNA_pol_E_B   2 vivsglnldndnrs...leaLrkiLqgya.peesppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsil 74 
                                        ++s++++ ++++    +e + ++L+       ++ + l++ G +v+      +++k  +  +++ ++ l++  + l
  gi|557694809|ref|YP_008797863.1| 233 CLISDIHVGSKHFRrdyFESFLDWLNRGRdGVVKRLTHLVIGGDLVEGVGIYPGQEK--DLMYRNVEEQLREAGKLL 307
                                       567777777777764444444444444335666777888888888885555554443..468999999999****** PP

                                       TTS-TTSEEEEE--TTBTT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEES CS
                       DNA_pol_E_B  75 esllekttvvlvPgpnDpanstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkreslk 151
                                        ++ +++++v++Pg   p+ + +lPq+Pl++ + + ++++ + ++ ++NP ++ +++ +v ++ ++ ++d+ ++   
  gi|557694809|ref|YP_008797863.1| 308 AEIPPNIEIVFIPGNHEPVRK-ALPQPPLQDRYRKLLDEYRR-MIHLSNPAELVFDGRRVTVYHGQGLDDIIQSLPT 382
                                       *********************.**********9999999855.*********************9999999988877 PP

                                       HHHHH.S-HHHHHHHHHHHHTBS---SS--B-GGGGGGGB-GGG---SEE CS
                       DNA_pol_E_B 152 esntd.verlrklvktildqrhlaPlaptlrpvswdkddalvleplPdvl 200
                                        s ++  e+++++v ++l+ rhlaP++   +     k d lv+ + P++l
  gi|557694809|ref|YP_008797863.1| 383 TSYSTlPENAAEVVTALLRYRHLAPIYGGSVQLLPSKEDRLVIVEQPNLL 432
                                       77654147899*****************9999999999999999999987 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   7.2e-11   2.1e-07       3     123 ..     232     371 ..     230     440 .. 0.53

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 7.2e-11
                                       EEEEESBTB...TTCCTHHHHHHHHHHHHHHH.....TTESEEEEESTSSSSS.........HHHHHHHHH.HHHHH CS
                       Metallophos   3 ilvigDlHl...algggqlddllkllddllre.....ekpdlvllaGDlvdrg.........dlekellel.laalv 61 
                                       i +i+D+H+   +    + d+++ +ld+l+r      ++   +++ GDlv++                ++  +++ +
  gi|557694809|ref|YP_008797863.1| 232 ICLISDIHVgskH---FRRDYFESFLDWLNRGrdgvvKRLTHLVIGGDLVEGVgiypgqekdL-----MYRnVEEQL 300
                                       789******5554...555555555555533322255455888889******77999555551.....444444444 PP

                                       HH..........TSEEEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEE.EETTEEEEEEEESE CS
                       Metallophos  62 ky..........pipvylllGNHegfeeellnkygylgifsepwrsdaevfnnlplas.lgsgslkvlllhGg 123
                                       ++          +i +++++GNHe    + l++ + + ++ ++   +       + a+   +g  +v ++hG 
  gi|557694809|ref|YP_008797863.1| 301 REagkllaeippNIEIVFIPGNHE-PVRKALPQPPLQDRYRKLLDEYRRMIHLSNPAElVFDG-RRVTVYHGQ 371
                                       444445666788999*********.55567777777776644444443333222222212222.244444444 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 !   22.6   0.0   3.3e-08   9.8e-05       3     145 ..     232     455 ..     231     468 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.3e-08
                     Metallophos_2   3 laiiSDlH........snldaleavlealkevg...vdaiihaGD.......leeeep............evleell 49 
                                       +++iSD+H        + ++    +l++ ++     + +++  GD       +    p            e l+e+ 
  gi|557694809|ref|YP_008797863.1| 232 ICLISDIHvgskhfrrDYFESFLDWLNRGRDGVvkrLTHLVIGGDlvegvgiY----PgqekdlmyrnveEQLREAG 304
                                       689*****99988777444444444444444430005666666**55555540....14445555555544555555 PP

                     Metallophos_2  50 ela.......pvlaVrGNnD.........eevveedvlreaaelgtdl......peeaelelagekvlliHgdpl.. 102
                                       +l+       +++ ++GN++         +  ++++  +   e    +       + ael ++g++v ++Hg+ l  
  gi|557694809|ref|YP_008797863.1| 305 KLLaeippniEIVFIPGNHEpvrkalpqpP--LQDRYRKLLDE----YrrmihlSNPAELVFDGRRVTVYHGQGLdd 375
                                       5556777888**********8877775331..22222222222....2222333688888889*********988** PP

                     Metallophos_2 103 .......................................gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlv 140
                                                                               ++ + ++l+    e+ +++  GH+Hv   +  +gv +
  gi|557694809|ref|YP_008797863.1| 376 iiqslpttsystlpenaaevvtallryrhlapiyggsvqLLPSKEDRLVIV--EQPNLLQTGHIHVLVNTSYRGVKL 450
                                       ***************999999999999999999988887666777777766..7778******************** PP

                     Metallophos_2 141 vnPGs 145
                                       vn+ +
  gi|557694809|ref|YP_008797863.1| 451 VNAAA 455
                                       **865 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 ?   13.3   0.0     2e-05     0.061       3      52 ..     146     195 ..     144     198 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                                       EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEE CS
                   tRNA_anti-codon   3 vaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvv 52 
                                       va ++ s+  ++g + i i+ +D +g+++vv+ +  ++ +k+a +l  ++vv
  gi|557694809|ref|YP_008797863.1| 146 VAVMILSK--KEGPGNIKITCDDPSGQLEVVASKrnQQLYKQALELLTDTVV 195
                                       78899999..************************887777777777777777 PP

>> FIST_C  FIST C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0093        28       6      78 ..     119     191 ..     115     224 .. 0.76
   2 ?    5.2   0.0    0.0065        19      34      81 ..     264     310 ..     230     330 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0093
                            FIST_C   6 lellgeedeelaqsalfplgleelggdflvrhllgvdpedgslaladdveeGq.rlqlmlrdaealiedlerll 78 
                                       +++l++++ e++  +    +++++g++++   +l   ++ g + + +d ++Gq +++  +r+++  +++le l 
  gi|557694809|ref|YP_008797863.1| 119 KRILSKRRLEFTPVSE-VPAIRDGGETVVAVMILSKKEGPGNIKITCDDPSGQlEVVASKRNQQLYKQALELLT 191
                                       5666666666666544.5566766767777777778999*************9888899999999999888774 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0065
                            FIST_C  34 lvrhllg.vdpedgslaladdveeGqrlqlmlrdaealiedlerlleea 81 
                                       +v +l + v    g l+ +  + +Gq+  lm+r++e+++ ++ +ll+e+
  gi|557694809|ref|YP_008797863.1| 264 VVKRLTHlVI--GGDLVEGVGIYPGQEKDLMYRNVEEQLREAGKLLAEI 310
                                       5555555333..456666667999*********************9988 PP

>> CHASE2  CHASE2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   8.9e-05      0.27      41     127 ..      25     283 ..      22     426 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.9e-05
                            CHASE2  41 eeslae.grwpwsravlarllerLeaagakaiglDi.lfsepeey..............................de 85 
                                       e++l++  +++ + ++l  ++erL++ ++ a+++D+  +++                                  d 
  gi|557694809|ref|YP_008797863.1|  25 ERALRRlEEYSNPFQALTSAIERLKKNRPEAVVIDVeDLQQ---PvekpaesspppasekpihvprletisvidnD- 97 
                                       5566545556667789999*****************11111...01222333344444434433333333333330. PP

                            CHASE2  86 alaealakgpnvv................................................................ 98 
                                                   +                                                                
  gi|557694809|ref|YP_008797863.1|  98 ------------Yriegdiaefrsyflsryhlikrilskrrleftpvsevpairdggetvvavmilskkegpgniki 162
                                       ............03333333333333333344444444444444555555555555555556666666666666666 PP

                            CHASE2  99 .............................paa......aglGfvnvvpDa........................... 113
                                                                             ++lG +n+ ++                            
  gi|557694809|ref|YP_008797863.1| 163 tcddpsgqlevvaskrnqqlykqalelltD-TvvamriKRLGGINILTEIihpdideqqfrrtpqteeayiclisdi 238
                                       666666655555555554444433333330.0333344666666664211222334455555555555666666666 PP

                            CHASE2 114 .......................DgvvRr..pllvese......l 127
                                                              Dgvv+r  +l++  +      +
  gi|557694809|ref|YP_008797863.1| 239 hvgskhfrrdyfesfldwlnrgrDGVVKRltHLVIGGDlvegvgI 283
                                       666666666667777777777777777776555544445555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3188.44
//
Query:       gi|557694810|ref|YP_008797864.1|  [L=438]
Description: hypothetical protein CSUB_C1383 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   39.1   0.2    6.7e-08   32.4   0.2    2.6  2  PQQ_2          PQQ-like domain
  ------ inclusion threshold ------
       0.06   13.3   0.2       0.17   11.8   0.0    1.8  2  Mu-transpos_C  Mu transposase, C-terminal


Domain annotation for each model (and alignments):
>> PQQ_2  PQQ-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.5   0.0    0.0052        47      25      68 ..      28      73 ..      16      90 .. 0.76
   2 !   32.4   0.2   7.5e-12   6.7e-08      37     153 ..      96     223 ..      86     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0052
                             PQQ_2 25 lgggvsravlsggtlfva...tgggrlvaldaatGkvlWettlegpv 68
                                      + + v++++  g++++v     +++    + ++ ++++We +++g  
  gi|557694810|ref|YP_008797864.1| 28 FAEYVDDPL-TGDRVVVMadpHTRRSAFIYHPEKKQIIWEHRVTGSQ 73
                                      677888999.666666665775788888899*********9997754 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 7.5e-12
                             PQQ_2  37 gtlfvatgggrlvaldaatGkvlWettl.egpvvga..plvaegrvvvvasdg.qlialdaedGkrlWstqqrse.e 108
                                       g +++a+  +r + +d++t++v+W+t + +++  ++  p+ + ++v+  + ++  l+++d  +Gk +Ws+++  +  
  gi|557694810|ref|YP_008797864.1|  96 GDIVCADLDNRYIVVDRKTKSVKWSTGFsDAKWAHDimPTKDHEHVLTTDYGNgMLRRID-GSGKIVWSRELGKGlA 171
                                       55788899********************866666667889999999888877769999**.********99999766 PP

                             PQQ_2 109 pae.lrssaspava.....gdtvvvges.sgklvaldpkdGkvlWerelaap 153
                                       +++ +++ + ++v+     gd ++++ +   +++ l+ +dG+v+W+ +   p
  gi|557694810|ref|YP_008797864.1| 172 KLSrVAGETPSTVHsnsfgGDLLAAVNQdIRGVYELREEDGEVVWSCPPLNP 223
                                       66678888888888999999999999994456899**********9765555 PP

>> Mu-transpos_C  Mu transposase, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.9e-05      0.17      23      59 ..      30      63 ..      16      65 .. 0.83
   2 ?   -3.5   0.0       1.2   1.1e+04      47      59 ..      96     108 ..      94     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.9e-05
                                      EEE-SHHHHSS-SEEEEEE-GGGTTEEEEEETTS-EE CS
                     Mu-transpos_C 23 rYwspeLaglvgkkVvvryDPrdlsrvyVydldgrfi 59
                                       Y+++ L+   g++Vvv  DP+   + ++y+++++ i
  gi|557694810|ref|YP_008797864.1| 30 EYVDDPLT---GDRVVVMADPHTRRSAFIYHPEKKQI 63
                                      47788877...8*******************888755 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
                                       TEEEEEETTS-EE CS
                     Mu-transpos_C  47 srvyVydldgrfi 59 
                                       +++ + dld+r+i
  gi|557694810|ref|YP_008797864.1|  96 GDIVCADLDNRYI 108
                                       5677889999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 3038.85
//
Query:       gi|557694811|ref|YP_008797865.1|  [L=83]
Description: hypothetical protein CSUB_C1384 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); 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:                         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: 644.49
//
Query:       gi|557694812|ref|YP_008797866.1|  [L=248]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-29  103.5   0.0    2.1e-29  102.8   0.0    1.3  1  ABC_tran     ABC transporter
    3.4e-12   46.8   5.9    9.7e-06   25.6   0.1    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.2e-05   25.9   0.1    2.2e-05   25.1   0.1    1.4  1  AAA_23       AAA domain
    8.4e-05   22.2   0.0    0.00019   21.1   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
      9e-05   22.3   0.0    0.00035   20.4   0.0    1.8  2  AAA_15       AAA ATPase domain
    0.00013   21.8   0.0    0.00043   20.1   0.0    1.8  1  AAA_30       AAA domain
    0.00027   20.4   0.2       0.11   11.9   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0013   19.1   0.4     0.0088   16.3   0.4    2.1  1  AAA_22       AAA domain
     0.0014   18.2   0.2      0.011   15.3   0.2    2.2  1  AAA_25       AAA domain
     0.0031   17.3   0.0     0.0051   16.7   0.0    1.3  1  MukB         MukB N-terminal
      0.008   16.1   0.0      0.015   15.3   0.0    1.4  1  RsgA_GTPase  RsgA GTPase
  ------ inclusion threshold ------
      0.022   14.4   0.0      0.036   13.6   0.0    1.3  1  AAA_27       AAA domain
      0.028   14.5   0.3       0.11   12.6   0.3    2.0  1  MMR_HSR1     50S ribosome-binding GTPase
      0.035   13.7   0.4      0.091   12.4   0.2    1.8  2  SRP54        SRP54-type protein, GTPase domain
      0.044   14.1   0.2       0.12   12.6   0.2    1.8  1  AAA_19       AAA domain
      0.059   13.8   0.0        0.1   13.0   0.0    1.4  1  AAA_16       AAA ATPase domain
      0.086   13.1   0.1       0.16   12.2   0.1    1.5  1  AAA_28       AAA domain
       0.14   12.7   0.0       0.33   11.5   0.0    1.6  1  HTH_27       Winged helix DNA-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 !  102.8   0.0   2.1e-32   2.1e-29       3     136 ..      33     176 ..      31     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 102.8 bits;  conditional E-value: 2.1e-32
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvre 78 
                                       n+++k++e +++a++G nGaGK+tL+k+l+gllkp +G++ ++g d++    ++  +  ++ +p+  +lfp+ltv +
  gi|557694812|ref|YP_008797866.1|  33 NIDFKVEEKSVTALIGANGAGKTTLIKVLTGLLKPYSGHVFFKGVDVTGyPAHRMRQMGLSLVPEGRRLFPNLTVMD 109
                                       99**********************************************95566666779****************** PP

                                       H............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n            e +e++e +l+ +   +   ++ ++ ++ LSgG+ q++a+aral++ ++ll++DEp+
  gi|557694812|ref|YP_008797866.1| 110 NllmgaymlrrqdEFEERLEIVLELFPVLK---ERRNQPARLLSGGEAQMLAIARALITPSDLLIVDEPS 176
                                       ******888777777777777777777554...3333445*****************************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 !   23.5   1.0   4.1e-08   4.1e-05       1      24 [.      43      66 ..      43      83 .. 0.84
   2 !   25.6   0.1   9.7e-09   9.7e-06     229     294 ..     141     203 ..     135     204 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.1e-08
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                                      +++liG+Ng+GK++L++ l +l  
  gi|557694812|ref|YP_008797866.1| 43 VTALIGANGAGKTTLIKVLTGLLK 66
                                      69*****************99964 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 9.7e-09
                            AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                       +++ par lS G  ++la++ al+      +ll++DEp +gL Pkl+  +++ l+el+++g  +++
  gi|557694812|ref|YP_008797866.1| 141 RRNQPARLLSGGEAQMLAIARALITPS---DLLIVDEPSSGLAPKLVDLIFKKLEELRETGLTILV 203
                                       6789************66666666655...9********************999999998888776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.1   2.2e-08   2.2e-05      13      41 ..      32      63 ..      23      69 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 2.2e-08
                            AAA_23 13 qeidF...skgltlItGpNGaGKTTildAikl 41
                                      ++idF   +k +t+++G NGaGKTT++  ++ 
  gi|557694812|ref|YP_008797866.1| 32 WNIDFkveEKSVTALIGANGAGKTTLIKVLTG 63
                                      89*************************98875 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 !   21.1   0.0   1.9e-07   0.00019      17      50 ..      36      69 ..      32      75 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.9e-07
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +++++k++t l+G++G+GK+Tl+  ++ lL p +
  gi|557694812|ref|YP_008797866.1| 36 FKVEEKSVTALIGANGAGKTTLIKVLTGLLKPYS 69
                                      5566666****************99999999877 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.5e-07   0.00035      20      48 ..      35      66 ..      25     106 .. 0.84
   2 ?   -0.6   0.0      0.87   8.6e+02     322     354 ..     165     197 ..     153     207 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.5e-07
                            AAA_15 20 dlsee...ltvliGkNnsGKSsilealdlFln 48
                                      d++ e   +t liG+N++GK++++++l  +l+
  gi|557694812|ref|YP_008797866.1| 35 DFKVEeksVTALIGANGAGKTTLIKVLTGLLK 66
                                      44444445*******************98887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.87
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkeland 354
                                       +++++l+++EP   L p++   ++k+l el ++
  gi|557694812|ref|YP_008797866.1| 165 TPSDLLIVDEPSSGLAPKLVDLIFKKLEELRET 197
                                       67899**************99999999998766 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.3e-07   0.00043      17      99 ..      40     177 ..      35     206 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.3e-07
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrvi..glAptgkaAkvLaeelgi....eastiakllkrlk...... 81 
                                       ++ v++l G+ G+GKtt++k+l+ +++   g+v+  g+  tg  A+++++ +g+    e++++   l+ ++      
  gi|557694812|ref|YP_008797866.1|  40 EKSVTALIGANGAGKTTLIKVLTGLLKPYSGHVFfkGVDVTGYPAHRMRQ-MGLslvpEGRRLFPNLTVMDnllmga 115
                                       56799************************767765699999999999994.34333333333333332222334444 PP

                            AAA_30  82 ............................................grarlepgtllivDEagm 99 
                                                                                   +ra ++p++llivDE + 
  gi|557694812|ref|YP_008797866.1| 116 ymlrrqdefeerleivlelfpvlkerrnqparllsggeaqmlaiARALITPSDLLIVDEPSS 177
                                       66666777777888888888899999999999999999999999889999999999999775 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   0.0   0.00011      0.11      23      43 ..      40      60 ..      33      67 .. 0.86
   2 !    6.9   0.0    0.0038       3.8     136     190 ..     148     198 ..      86     226 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      TSSEEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 23 sksftaivGpNGSGKsnlldA 43
                                      +ks+ta++G+NG+GK+ l+  
  gi|557694812|ref|YP_008797866.1| 40 EKSVTALIGANGAGKTTLIKV 60
                                      5789************99875 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0038
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskna 190
                                       lLSgGe +++a+a       + p+ l ++De  + L  k v  + + l+e +++ 
  gi|557694812|ref|YP_008797866.1| 148 LLSGGEAQMLAIARA----LITPSDLLIVDEPSSGLAPKLVDLIFKKLEELRETG 198
                                       79******9998654....579999******999999999999999999998763 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   8.8e-06    0.0088       4     103 ..      40     179 ..      37     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.8e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..................................erpevv.fv 45 
                                       ++++++++G  G+GKTtl++ l+  l+ ++ +                                    ++  ++  +
  gi|557694812|ref|YP_008797866.1|  40 EKSVTALIGANGAGKTTLIKVLTGLLKPYSGHVFfkgvdvtgypahrmrqmglslvpegrrlfpnltvMDNLLMgAY 116
                                       7899******************9999766555447777777777766666666666655555533333333333555 PP

                            AAA_22  46 tlpsstsskdllrellralglelkaerlsseellealeqalrarav.....ielliiDEaqh.l 103
                                        l  + + ++ l+ +l+ + + +++ r++  +ll+  e ++ a a+       lli+DE    l
  gi|557694812|ref|YP_008797866.1| 117 MLRRQDEFEERLEIVLELFPVLKER-RNQPARLLSGGEAQMLAIARalitpSDLLIVDEPSSgL 179
                                       5555555555555555555555555.77777777777777777777777777788888865555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.1e-05     0.011      24      54 ..      32      62 ..       9     212 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                            AAA_25 24 wlvkgllpagelallaGapgtGKttlaldla 54
                                      w ++  + ++++++l+Ga g+GKttl   l 
  gi|557694812|ref|YP_008797866.1| 32 WNIDFKVEEKSVTALIGANGAGKTTLIKVLT 62
                                      88887789*****************975443 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.1e-06    0.0051      25      66 ..      40      81 ..      29      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.1e-06
                                      HHHHHHHHS--SHHHHHHHHHHHHHHS--TTT---------- CS
                              MukB 25 delvttlsGgnGaGksttmaafvtaliPdlsllhfrntteaG 66
                                      ++ vt+l G+nGaGk+t +  +   l P    + f+ +  +G
  gi|557694812|ref|YP_008797866.1| 40 EKSVTALIGANGAGKTTLIKVLTGLLKPYSGHVFFKGVDVTG 81
                                      367************998887777777877777777666655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.5e-05     0.015      94     121 ..      35      63 ..      13      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                                       HHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  94 kellkd.ktsvlvGqSGvGKStLinallp 121
                                         ++++ ++++l+G  G+GK+tLi++l++
  gi|557694812|ref|YP_008797866.1|  35 DFKVEEkSVTALIGANGAGKTTLIKVLTG 63 
                                       556666589*****************987 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.6e-05     0.036      18      50 ..      33      65 ..      18      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.6e-05
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdll 50
                                      ++df+ ee++++ ++G+N AGK+t+++ ++ ll
  gi|557694812|ref|YP_008797866.1| 33 NIDFKVEEKSVTALIGANGAGKTTLIKVLTGLL 65
                                      79************************9998886 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   0.00011      0.11       3      29 ..      45      72 ..      43     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                      EEEESTTSSHHHHHHHHHTS.TEEESSS CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltge.kaivsdk 29
                                      a++G   +GK+tLi+ ltg  k   ++ 
  gi|557694812|ref|YP_008797866.1| 45 ALIGANGAGKTTLIKVLTGLlKPYSGHV 72
                                      89****************9644444554 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   9.1e-05     0.091       2      38 ..      42      78 ..      41      90 .. 0.82
   2 ?   -1.7   0.0       1.9   1.8e+03     145     163 ..     186     204 ..     155     215 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.1e-05
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      +v++l+G +GaGKTt +  L  llk    +v +  +D
  gi|557694812|ref|YP_008797866.1| 42 SVTALIGANGAGKTTLIKVLTGLLKPYSGHVFFKGVD 78
                                      6899*************99998888776666666665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.9
                                       EEEESTTSSSSTTHHHHHH CS
                             SRP54 145 viltklDgdakgGaalsia 163
                                       +i+ kl++  + G ++ ++
  gi|557694812|ref|YP_008797866.1| 186 LIFKKLEELRETGLTILVV 204
                                       3444444444433333333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2   0.00013      0.12       9      69 ..      40     104 ..      34     206 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                            AAA_19   9 kekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae......a 69 
                                       +++v ++++  G GKT+++k    ll+   g     +  v +tg  a+++r+   +l  e       
  gi|557694812|ref|YP_008797866.1|  40 EKSVTALIGANGAGKTTLIKVLTGLLKPYSGH--VFFKGVDVTGYPAHRMRQMGLSLVPEgrrlfpN 104
                                       578999***************99999998876..566677778888888887654444444444441 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0    0.0001       0.1      25     107 ..      42     145 ..      35     208 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                            AAA_16  25 elvllsGesGvGKsslvrellralekdg.gif......lrgkcdql..esaipysa.laqalareellrqlldeaes 91 
                                       +++ l+G+ G GK++l++ l   l k + g++      ++g   +   ++++++++   +++ + +++  ll     
  gi|557694812|ref|YP_008797866.1|  42 SVTALIGANGAGKTTLIKVLT-GLLKPYsGHVffkgvdVTGYPAHRmrQMGLSLVPeGRRLFPNLTVMDNLLMG--- 114
                                       67889************7777.5555532444224433444444445555666666566666555555555544... PP

                            AAA_16  92 aeleawrekleeala...............a 107
                                       a   + ++++ee+l+               +
  gi|557694812|ref|YP_008797866.1| 115 AYMLRRQDEFEERLEivlelfpvlkerrnqP 145
                                       2334444444444443334554555444441 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00016      0.16       3      20 ..      45      62 ..      43      96 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                            AAA_28  3 vitGgestGKTtlleaLa 20
                                      +++G+ ++GKTtl++ L+
  gi|557694812|ref|YP_008797866.1| 45 ALIGANGAGKTTLIKVLT 62
                                      79************9886 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 ?   11.5   0.0   0.00033      0.33       7      45 ..      29      67 ..      25      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                            HTH_27  7 lvLhlirhrrrrkkladlcgrlnvedshisyslkkLtek 45
                                      ++L++i   +++k+ ++l+g+   ++++ +++l  L ++
  gi|557694812|ref|YP_008797866.1| 29 QILWNIDFKVEEKSVTALIGANGAGKTTLIKVLTGLLKP 67
                                      89********************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 1886.39
//
Query:       gi|557694813|ref|YP_008797867.1|  [L=244]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   89.4   0.0    3.7e-25   89.0   0.0    1.1  1  ABC_tran        ABC transporter
      2e-09   37.1   0.5    5.4e-09   35.8   0.0    2.0  2  BCA_ABC_TP_C    Branched-chain amino acid ATP-binding cassett
      3e-05   23.8   0.1    5.6e-05   23.0   0.1    1.4  1  AAA_30          AAA domain
      5e-05   23.2   0.2     0.0011   18.9   0.0    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
     0.0005   19.7   0.8       0.17   11.4   0.3    2.4  2  AAA_25          AAA domain
     0.0025   18.3   0.2     0.0046   17.5   0.1    1.4  1  AAA_23          AAA domain
     0.0059   17.0   0.3      0.098   13.1   0.3    2.3  1  AAA             ATPase family associated with various cellula
     0.0064   16.9   0.0       0.01   16.2   0.0    1.4  1  AAA_16          AAA ATPase domain
     0.0087   15.8   0.0      0.022   14.5   0.0    1.7  1  AAA_29          P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.012   15.9   0.8       0.15   12.4   0.8    2.1  1  AAA_22          AAA domain
      0.019   14.4   1.0        1.6    8.1   0.2    2.2  2  SMC_N           RecF/RecN/SMC N terminal domain
      0.029   13.2   0.3      0.029   13.2   0.3    1.9  2  ABC_ATPase      Predicted ATPase of the ABC class
      0.036   13.5   0.5       0.53    9.7   0.2    2.1  2  TniB            Bacterial TniB protein
      0.057   13.1   0.0      0.063   13.0   0.0    1.1  1  AAA_15          AAA ATPase domain
      0.059   12.4   0.2      0.093   11.7   0.2    1.3  1  Asparaginase_2  Asparaginase
      0.061   13.4   0.2       0.11   12.5   0.2    1.7  1  MMR_HSR1        50S ribosome-binding GTPase
       0.11   12.4   0.1       0.22   11.4   0.1    1.5  1  RsgA_GTPase     RsgA GTPase
       0.14   12.1   0.4         14    5.7   0.1    2.4  2  AAA_14          AAA domain
       0.16   11.9   0.0        0.5   10.4   0.0    1.8  1  TsaE            Threonylcarbamoyl adenosine biosynthesis 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 !   89.0   0.0   3.9e-28   3.7e-25       1     135 [.      22     166 ..      22     168 .. 0.96

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 3.9e-28
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l nv++ ++ ge+v+++G+nGaGK+tL+++++g  kp+ G+++l g+d++  q+++++ + ++  +q  + f ++tv
  gi|557694813|ref|YP_008797867.1|  22 LTNVNMRVQVGEVVGLIGPNGAGKTTLFNIVTGFIKPDRGRVKLFGEDVTGlQPHQIAARGVARTFQIVKPFLGMTV 98 
                                       689************************************************************************** PP

                                       HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEp 135
                                       +e+              +++++e+a++  g  +l+d+ +    ++L   q + v+lar+l+++pkll+lDE 
  gi|557694813|ref|YP_008797867.1|  99 YETvlvgaylrernedSARQRAEEAMKLTGVYHLRDRYA----RELNTPQLKLVELARSLATQPKLLMLDEI 166
                                       ***********9997766777*****************9....****************************6 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2       3.3   3.2e+03       7      11 ..     171     175 ..     171     175 .. 0.94
   2 !   35.8   0.0   5.7e-12   5.4e-09       1      23 []     217     239 ..     217     239 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.3
                      BCA_ABC_TP_C   7 tPaEv 11 
                                       tPaEv
  gi|557694813|ref|YP_008797867.1| 171 TPAEV 175
                                       9***9 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 5.7e-12
                      BCA_ABC_TP_C   1 rvIAeGtPaEvrndPrVieAYLG 23 
                                       +vIAeG+P Ev ++ +VieAYLG
  gi|557694813|ref|YP_008797867.1| 217 EVIAEGSPSEVSSNLKVIEAYLG 239
                                       69********************9 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   5.9e-08   5.6e-05      19     122 ..      33     196 ..      21     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.9e-08
                            AAA_30  19 rvavltGpAGtGKttalkalreaweaa.g......grviglAptgkaAkvLaeelgi..........eastiakllk 78 
                                        v+ l Gp G+GKtt+ + ++  ++ + g      ++v gl p + aA+ +a+ ++i          e+  +     
  gi|557694813|ref|YP_008797867.1|  33 EVVGLIGPNGAGKTTLFNIVTGFIKPDrGrvklfgEDVTGLQPHQIAARGVARTFQIvkpflgmtvyETVLVG---- 105
                                       48889********************99779****9*****************755543333222222222222.... PP

                            AAA_30  79 rlk............................................grarlepg.tllivDE..agmv..dtkqla 106
                                         +                                            +  +l+++ +ll+ DE  ag++    ++++
  gi|557694813|ref|YP_008797867.1| 106 --AylrernedsarqraeeamkltgvyhlrdryarelntpqlklvelA-RSLATQpKLLMLDEivAGLTpaEVDSMT 179
                                       ..13333345666666666666666777889**************975.4555556*******44344466999*** PP

                            AAA_30 107 allkaaeka.gakvilv 122
                                       al+k+++++ g++v+lv
  gi|557694813|ref|YP_008797867.1| 180 ALVKRIRDEmGVTVLLV 196
                                       *******9537888887 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 !   18.9   0.0   1.1e-06    0.0011       2      22 ..      35      55 ..      34      81 .. 0.82
   2 ?    2.4   0.0      0.12   1.1e+02     253     284 ..     153     187 ..     142     196 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       +liGpNg+GK++L+ +  ++
  gi|557694813|ref|YP_008797867.1| 35 VGLIGPNGAGKTTLFNIVTGF 55
                                      68*************999766 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                            AAA_21 253 ralkkgsllliDEpEngLHP...kllrrllellke 284
                                       +++  ++ll +DE+ +gL P     ++ l++ +++
  gi|557694813|ref|YP_008797867.1| 153 SLATQPKLLMLDEIVAGLTPaevDSMTALVKRIRD 187
                                       3444459*************777555555555544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.3   0.0    0.0066       6.2      32      49 ..      31      48 ..      23      50 .. 0.87
   2 !   11.4   0.3   0.00018      0.17     129     189 ..     146     199 ..      90     201 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0066
                            AAA_25 32 agelallaGapgtGKttl 49
                                       ge++ l+G+ g+GKttl
  gi|557694813|ref|YP_008797867.1| 31 VGEVVGLIGPNGAGKTTL 48
                                      589999***********8 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00018
                            AAA_25 129 dvdaleaaieevegvrlvviDplsralggdensnsdvgalvealeriarrtgaavllvhHv 189
                                       ++ +l++ +    +++l+ +D + + l       ++v+++ + ++ri+++ g++vllv Hv
  gi|557694813|ref|YP_008797867.1| 146 KLVELARSLAT--QPKLLMLDEIVAGLTP-----AEVDSMTALVKRIRDEMGVTVLLVEHV 199
                                       44456666666..4788888877775554.....345677777788999***********8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   4.8e-06    0.0046      20      39 ..      33      52 ..      13      64 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.8e-06
                            AAA_23 20 gltlItGpNGaGKTTildAi 39
                                       ++ ++GpNGaGKTT+++ +
  gi|557694813|ref|YP_008797867.1| 33 EVVGLIGPNGAGKTTLFNIV 52
                                      577899***********976 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 !   13.1   0.3    0.0001     0.098       3      74 ..      37     173 ..      35     204 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.0001
                                       EESSTTSSHHHHHHHHHHHHT.....HE..........EEEEETTTCSSS........................... CS
                               AAA   3 lyGppGtGKTllakavakelg.....ve..........fleisgsellsk........................... 37 
                                       l+Gp G GKT+l + v   ++     v+                     +                           
  gi|557694813|ref|YP_008797867.1|  37 LIGPNGAGKTTLFNIVTGFIKpdrgrVKlfgedvtglqP----------Hqiaargvartfqivkpflgmtvyetvl 103
                                       89**************99986332223333333333331..........1344444444455555555555555555 PP

                                       ................................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHH CS
                               AAA  38 ................................yvgesekkirelfkeakeka.kpsilfiDEidalaksr 74 
                                                                       y  e +    +l++ a++ a +p+ l++DEi a  +  
  gi|557694813|ref|YP_008797867.1| 104 vgaylrernedsarqraeeamkltgvyhlrdrYARELNTPQLKLVELARSLAtQPKLLMLDEIVAGLTPA 173
                                       5666666666666666777777777777777799999998999999999988888999999987655554 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-05      0.01      20     144 ..      30     166 ..      17     199 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                            AAA_16  20 rsgrpelvllsGesGvGKsslvrellralekd................ggiflrgkcdqlesaipysalaqalaree 80 
                                         g  e+v l+G+ G GK++l + +   ++ d                + i++rg ++ ++   p++  + +  +  
  gi|557694813|ref|YP_008797867.1|  30 QVG--EVVGLIGPNGAGKTTLFNIVTGFIKPDrgrvklfgedvtglqpHQIAARGVARTFQIVKPFLGMTVYE-T-V 102
                                       333..7899**********************944444444444444443333444444444445553333333.2.4 PP

                            AAA_16  81 llrqlldeaesaeleawrekleeala..........avpelagaea...srllellkrllallsrderplvlvlDdl 144
                                       l+ + l+e   ++ + +r++ eea++                   a   +    +l +l++ l++ + p +l lD++
  gi|557694813|ref|YP_008797867.1| 103 LVGAYLRE---RNEDSARQRAEEAMKltgvyhlrdrY--------ArelNTPQLKLVELARSLAT-Q-PKLLMLDEI 166
                                       44444444...33444444444444444444333330........33335555555555544444.2.345555554 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 !   14.5   0.0   2.3e-05     0.022      15      40 ..      25      50 ..      16      64 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllD 40
                                        +++++ +++ l+Gp+G+GK+Tl+ 
  gi|557694813|ref|YP_008797867.1| 25 VNMRVQVGEVVGLIGPNGAGKTTLFN 50
                                      567777777999************85 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.8   0.00015      0.15      10     128 ..      37     196 ..      30     198 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee....................................erpevvfvtlpss 50 
                                       ++G+ G+GKTtl + ++   +     ++                                                 
  gi|557694813|ref|YP_008797867.1|  37 LIGPNGAGKTTLFNIVTGFIKP----DRgrvklfgedvtglqphqiaargvartfqivkpflgmT------------ 97 
                                       89************99999743....233344666666666666665555554444444444442............ PP

                            AAA_22  51 tsskdllrellralglelka.......................................erlsseell.ealeqalr 87 
                                                                                                  ++l++ +l    l++ l 
  gi|557694813|ref|YP_008797867.1|  98 -------------------VyetvlvgaylrernedsarqraeeamkltgvyhlrdryaRELNTPQLKlVELARSLA 155
                                       ...................0334444444444444444444444444444445558888777777777788888888 PP

                            AAA_22  88 aravielliiDEaqh.lr..seealeeL.rsllnlsrkgvqliLv 128
                                       ++ +  ll++DE+   l+  + + ++ L +++ +  + gv+++Lv
  gi|557694813|ref|YP_008797867.1| 156 TQPK--LLMLDEIVAgLTpaEVDSMTALvKRIRD--EMGVTVLLV 196
                                       8877..******9999965445555555488899..999999987 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   0.2    0.0017       1.6      26      42 ..      34      50 ..      13      56 .. 0.81
   2 ?    5.0   0.0     0.015        14     159     202 ..     158     201 ..     118     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0017
                                      EEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlld 42
                                      +  ++GpNG+GK+ l++
  gi|557694813|ref|YP_008797867.1| 34 VVGLIGPNGAGKTTLFN 50
                                      6679*********9986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.015
                                       -SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 159 aplyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                         l +lDei a L  ++v  +  l+k+ ++++ + v  +++ m 
  gi|557694813|ref|YP_008797867.1| 158 PKLLMLDEIVAGLTPAEVDSMTALVKRIRDEMGVTVLLVEHVMR 201
                                       34889*********************999998887776666654 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 ?   -0.5   0.2      0.42     4e+02     241     262 ..      28      50 ..      25      56 .. 0.81
   2 ?   13.2   0.3     3e-05     0.029     355     412 ..     160     214 ..     155     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.42
                                       EE-SS.EEEEEE-TTSSHHHHHH CS
                        ABC_ATPase 241 gipkG.vtlIvGggfhGKsTLLe 262
                                        ++ G v+ ++G++  GK+TL +
  gi|557694813|ref|YP_008797867.1|  28 RVQVGeVVGLIGPNGAGKTTLFN 50 
                                       56667788899**********87 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3e-05
                                       HH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEEEE CS
                        ABC_ATPase 355 lmirDermqelvskekepitplvdrvrelykklgvstilvvggsgdyldvAdtvilme 412
                                       l++ De ++ l++ e + +t+lv+r+r+   ++gv+++lv   +   ++++d+v++++
  gi|557694813|ref|YP_008797867.1| 160 LLMLDEIVAGLTPAEVDSMTALVKRIRD---EMGVTVLLVEHVMRFVMNISDRVVVLN 214
                                       5667999999*99998888888887765...6***********************997 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.14   1.4e+02      23      53 ..      19      50 ..      10      60 .. 0.76
   2 ?    9.7   0.2   0.00056      0.53     116     160 ..     154     196 ..     129     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.14
                              TniB 23 LeeLleypkrkrm.pnlllvGdsnnGKtmive 53
                                      L++L ++  r ++ + + l+G+   GKt++++
  gi|557694813|ref|YP_008797867.1| 19 LAALTNVNMRVQVgEVVGLIGPNGAGKTTLFN 50
                                      6666666666666456679*********9875 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00056
                              TniB 116 relkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                        ++++++L++DEi   l  +  +   +++++k++ +e+ +++ lv
  gi|557694813|ref|YP_008797867.1| 154 LATQPKLLMLDEIVAGL--TPAEVDSMTALVKRIRDEMGVTVLLV 196
                                       46799********9999..899999***************99887 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.7e-05     0.063       9      50 ..      14      59 ..      12     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.7e-05
                            AAA_15  9 kNFRslkd.veidlsee...ltvliGkNnsGKSsilealdlFlnnk 50
                                      kNF++l   + +++  +   +  liG+N++GK+++ ++   F++ +
  gi|557694813|ref|YP_008797867.1| 14 KNFGALAAlTNVNMRVQvgeVVGLIGPNGAGKTTLFNIVTGFIKPD 59
                                      7888888877777776677799*************99988887755 PP

>> Asparaginase_2  Asparaginase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   9.8e-05     0.093      74     107 ..       2      35 ..       1      36 [. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.8e-05
                                       --EEEEEEETTTTEEEEEEEESSBS-HHHHHHHH CS
                    Asparaginase_2  74 veldAsimdgktlraGaVagvkrvknpislArlv 107
                                       + +dA++++g ++++Ga a++++v+  +++ ++v
  gi|557694813|ref|YP_008797867.1|   2 NSMDALVLEGISKNFGALAALTNVNMRVQVGEVV 35 
                                       68**********************9999987765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00012      0.11       2      21 ..      35      54 ..      34     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                      v+++G   +GK+tL+n  tg
  gi|557694813|ref|YP_008797867.1| 35 VGLIGPNGAGKTTLFNIVTG 54
                                      89**************9998 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00024      0.22      97     121 ..      29      54 ..       8      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                                       CTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  97 lkd.ktsvlvGqSGvGKStLinallp 121
                                       ++  +++ l+G+ G+GK+tL n +++
  gi|557694813|ref|YP_008797867.1|  29 VQVgEVVGLIGPNGAGKTTLFNIVTG 54 
                                       44448899**************9876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.015        14       3      20 ..      33      50 ..      31      63 .. 0.84
   2 ?    4.3   0.0      0.04        37      40      77 ..     134     197 ..     113     242 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.015
                            AAA_14  3 kilvitGaRrvGKTtllk 20
                                      +++ + G+  +GKTtl +
  gi|557694813|ref|YP_008797867.1| 33 EVVGLIGPNGAGKTTLFN 50
                                      68999**********964 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.04
                            AAA_14  40 derdkkladpe.kllelileklkeekktylflDEiqev...........................p 77 
                                       d   ++l++p+ kl el +++  + + ++l+lDEi                              +
  gi|557694813|ref|YP_008797867.1| 134 DRYARELNTPQlKLVELARSL-AT-QPKLLMLDEIVAGltpaevdsmtalvkrirdemgvtvllvE 197
                                       444455555544555555554.34.7899*****97655555554444444444444444444444 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   0.0   0.00053       0.5      18      38 ..      29      51 ..      13      63 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00053
                                      H..TEEEEEEESTTSSHHHHHHH CS
                              TsaE 18 l..gdvilLeGdLGaGKTtlvrg 38
                                      +  g+v+ L G+ GaGKTtl   
  gi|557694813|ref|YP_008797867.1| 29 VqvGEVVGLIGPNGAGKTTLFNI 51
                                      134889*************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 1865.49
//
Query:       gi|557694814|ref|YP_008797868.1|  [L=321]
Description: branched-chain amino acid ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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  127.5  33.6      7e-37  127.0  33.6    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 !  127.0  33.6   3.9e-41     7e-37       3     267 ..      27     296 ..      25     297 .. 0.91

  Alignments for each domain:
  == domain 1  score: 127.0 bits;  conditional E-value: 3.9e-41
                      BPD_transp_2   3 lnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlr 79 
                                       l+l+tl+++++ ++++++l+ g++G+++lg+g+  +lGa++++ l+++++ + +++llv+ +++a v++l+g+++ r
  gi|557694814|ref|YP_008797868.1|  27 LFLVTLILLYTTIVVAWQLIGGYGGQLDLGAGAYHGLGAVITGFLMVNYGVSGWVGLLVSGAAAAGVAFLIGYPSFR 103
                                       68999*********************************88888777777777************************* PP

                      BPD_transp_2  80 lkvdel...iitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv.....llalllvlavlll 148
                                       l+++e+   +++l+l+++l+ ++l     ++ +v+g+ +   + + ++ l+++++  i+     + +l+++++++ +
  gi|557694814|ref|YP_008797868.1| 104 LGLKEVwyaLSSLALVLILQKIFL-----LWTDVAGPLERYIPYAEFDPLFMRAGTKIFyyyitAALLAATFLIVSR 175
                                       ******777777888888888888.....7778888887777777777777888888888999999999999***** PP

                      BPD_transp_2 149 lrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvglgfnaiaavvlGg 224
                                       +rr+++G+ l  ++eneeaa++lG++v+r+kl++ +i +++A++ G ++a + g+  p  ++  +++++ + +++Gg
  gi|557694814|ref|YP_008797868.1| 176 IRRSKTGLYLISIRENEEAAEMLGVDVRRYKLQALMIYSFIAAVTGGIYASMVGFYHPtLFDSWISIQTATLAIVGG 252
                                       ***************************************************************************** PP

                      BPD_transp_2 225 agsllgtviGaliigvvksllltllgi.ptelarvllgallilv 267
                                       +g+llg+ i+++i+ +v++ l+  lg+    l++v++g++l+++
  gi|557694814|ref|YP_008797868.1| 253 LGHLLGPPIVSIILLTVQEYLRITLGAvIIGLHQVIFGIILVII 296
                                       *******************777777764599**********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       857  (0.0477997); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2375.07
//
Query:       gi|557694815|ref|YP_008797869.1|  [L=292]
Description: branched-chain amino acid ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-34  118.5  36.7    3.3e-34  118.3  36.7    1.0  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 !  118.3  36.7   1.9e-38   3.3e-34       2     268 .]      14     281 ..      13     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 118.3 bits;  conditional E-value: 1.9e-38
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl....lllallvallvgaavgl.ll 73 
                                       il++++l++++a+aA+Glal+fg+a+++n++hg+ ++l++y+a++ ++   +     +l+ +++ +++g++ +l ++
  gi|557694815|ref|YP_008797869.1|  14 ILFGVMLGGVYALAAMGLALLFGVANLVNFAHGEYIMLAMYMAFVFSVTIFQDpvltPLFNIPLFFAIGVITYLgIF 90 
                                       6789999*************************************999887766678888888888888888877467 PP

                      BPD_transp_2  74 gllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv.llalllvlavllll 149
                                        +l+    + ++++t+++l++l++l+l    ++    + + +v +++++ g  +  l + ++ l+ l+ +l++ l+l
  gi|557694815|ref|YP_008797869.1|  91 KRLIKAPPLSQIAATVGILVLLRNLAL--AIWAAEPKAPPYTVFATSFNIGPVIVPLDKLLAmLVSLVTLLVLNLFL 165
                                       788888889999***************..88888888888888888888777776666666669999999999**** PP

                      BPD_transp_2 150 rrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGgag 226
                                        rtr+G+a+ra +++ ea+ ++G++++r+ llt  is al gl+G l+ +++++ p   g+ +g+ ++a+v l+g+g
  gi|557694815|ref|YP_008797869.1| 166 ERTRLGVAMRASADDVEAVSLMGVDTNRLFLLTAGISLALVGLSGSLIMTYQAVTP-TSGLLFGLLTWAIVALAGLG 241
                                       ***************************************************99999.******************** PP

                      BPD_transp_2 227 sllgtviGaliigvvksllltllgiptelarvllgallilvl 268
                                       ++ g++i+++i+g+++sl++ l   ++  + ++l+ l+il+l
  gi|557694815|ref|YP_008797869.1| 242 TVKGILIASIIFGLADSLASGLW--DPRGREIVLYGLFILIL 281
                                       *****************888887..78999999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      218  (0.0121591); 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):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2101.67
//
Query:       gi|557694816|ref|YP_008797870.1|  [L=429]
Description: branched-chain amino acid ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  186.2   1.2    1.5e-54  186.0   1.2    1.0  1  Peripla_BP_6     Periplasmic binding protein
    8.7e-21   74.3   0.0    2.2e-20   72.9   0.0    1.6  1  Peripla_BP_5     Periplasmic binding protein domain
  ------ inclusion threshold ------
      0.082   12.9   0.0       0.18   11.9   0.0    1.5  1  Glyco_trans_4_2  Glycosyl transferase 4-like


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.0   1.2   2.4e-58   1.5e-54       1     341 [.      47     409 ..      47     410 .. 0.89

  Alignments for each domain:
  == domain 1  score: 186.0 bits;  conditional E-value: 2.4e-58
                                       EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEET...TEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEE CS
                      Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaGGin...GrkielverDdaydpdraaeaarrlvdqdgvdalv 74 
                                       +i++Gl+ plsG ya +g +++ +a++ +eeiN +GGi    G k++l ++D ++++d+a  aa++lv+ d+v +++
  gi|557694816|ref|YP_008797870.1|  47 EIRVGLVEPLSGNYAVFGNEARMAAELVIEEINSKGGIAslgGAKLKLFVEDSKSTADGARLAAEKLVNVDKVHVII 123
                                       69***************************************9*********************************** PP

                                       E-BSHHHHHHHHHHHHHHT-EEEESS..-HHCCTTSTTEEESS--HHHHHHHHHHHHHHHTT.....SCEEEEEEES CS
                      Peripla_BP_6  75 gplssavaaavaevlakdgvpvigpa..gltgekcspyvfslgpsysaqasalveylakelg.....gkkvalvyad 144
                                       g++ s+ ++ +++v++ ++v+v+  a  ++ +  ++ y+++l p +sa ++++v++++  +      + + ++v  d
  gi|557694816|ref|YP_008797870.1| 124 GAFISSHTLTMLDVTEPKKVVVMADAlvDYLTARGFKYIVRLPPKASAHGATAVDFAIGVFQqngmkIQRPVIVHFD 200
                                       ************************553366689***********************9864433335588******** PP

                                       SHHHHHHHHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHHHHHHTT-SSSCEE CS
                      Peripla_BP_6 145 yafgregiaalkaaakaaGgevvgeepvplgttdfsaqvlqikaagadavllagtgadlaallkaaaeaGldakril 221
                                         fg  +++++   ++ +G+  v+ +++p++ td+s+++ +i++a++d+v+++ + ad + ++ka+a+ Gl+ + i 
  gi|557694816|ref|YP_008797870.1| 201 GLFGEVTADGVYTRLRDLGIRPVDRIKYPTDITDMSPIIERIRQANPDVVFVVPYYADSVLFAKAVASLGLKVPLIV 277
                                       *********************99*************************************************98676 PP

                                       EE.CCC-CHHHHHHHHHHHHTTEEEEESCSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHHHHHHHCCT CS
                      Peripla_BP_6 222 lv.swsgseedlkalggeaaegvlavtpyfpdldnpavrafvaayeaayggapppsqfaaggyiaadlllealkaag 297
                                       ++ +++++++d  ++ geaae+++ +++y p l++  ++++v+a++++yg+   p+++a   + +++ l+eal+ +g
  gi|557694816|ref|YP_008797870.1| 278 GAgGTGFADPDSIKASGEAAEYMINTYSYDPFLPTNYNKQLVQAFQNRYGKL--PTEAAGIIFYTLWTLKEALEVSG 352
                                       666666889998888888*************9*******************8..**********************6 PP

                                       .....H.CCHHHHHHHHHHS-.BEC......CCTCCBEECTTSBEE--EEEEEE-TS CS
                      Peripla_BP_6 298 .....s.ltreavraaleslg.fdg......llgplkftaedhqasrpvyvvqvdgg 341
                                            + l+++ +++a+ sl+ + g      + g +   ++   +  ++  +qv+gg
  gi|557694816|ref|YP_008797870.1| 353 knypnDpLSGDNLMKAFMSLDlTSGpaaetyPSGHIRLAPNGDNLYAQAVALQVQGG 409
                                       666664499999********9665633333344554444444446777777777766 PP

>> Peripla_BP_5  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   3.8e-24   2.2e-20       1     295 [.      48     351 ..      48     360 .. 0.84

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 3.8e-24
                      Peripla_BP_5   1 ikvGvLhSlsGtmaisekslkdaallaieeinaagGvl...grkieavvvdpasdwelfaekaeklieedkvevvfG 74 
                                       i+vG++  lsG +a+  +++  aa l+ieein++gG++   g k++  v+d++s+++  +  aekl++ dkv+v++G
  gi|557694816|ref|YP_008797870.1|  48 IRVGLVEPLSGNYAVFGNEARMAAELVIEEINSKGGIAslgGAKLKLFVEDSKSTADGARLAAEKLVNVDKVHVIIG 124
                                       89**********************************987778*********************************** PP

                      Peripla_BP_5  75 cwtSasRkavlpvveelnalLfYp..vqYEGeEssknviYtGaapnqqaipavdyl...lselg..akrvflvGsdy 144
                                       +++S+   ++l+v e ++ ++     v Y      k ++     +  +   avd++   ++++g  ++r ++v  d 
  gi|557694816|ref|YP_008797870.1| 125 AFISSHTLTMLDVTEPKKVVVMADalVDYLTARGFKYIVRLPPKASAHGATAVDFAigvFQQNGmkIQRPVIVHFDG 201
                                       ***************99887775423677777777777777777777777788886111567778899********* PP

                      Peripla_BP_5 145 vypretnrilkallkakggevvgeeYlplgssdvqkivakikkakpdvvlstinGdsnvafykelkeagikae.kip 220
                                        +   t+  +   l++ g++ v+    p + +d++ i+++i++a+pdvv+        v f k++++ g+k    + 
  gi|557694816|ref|YP_008797870.1| 202 LFGEVTADGVYTRLRDLGIRPVDRIKYPTDITDMSPIIERIRQANPDVVFVVPYYADSVLFAKAVASLGLKVPlIVG 278
                                       **************************************************99999999************9651344 PP

                      Peripla_BP_5 221 vvslsvaeeelaaidaealvGhlaawnYfqsvdtpenkafvakfkarvgedrvtndpmeaayiqvklwaqAveka 295
                                          +  a+ +  +   ea++  + + +Y   + t+ nk+ v++f++r+g+    ++ +   ++++  +++A+e  
  gi|557694816|ref|YP_008797870.1| 279 AGGTGFADPDSIKASGEAAEYMINTYSYDPFLPTNYNKQLVQAFQNRYGKL--PTEAAGIIFYTLWTLKEALEVS 351
                                       4455566666666666677777889999999*****************983..3344444444555555666555 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 ?   11.9   0.0     3e-05      0.18      54     113 ..     226     286 ..     207     307 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3e-05
                   Glyco_trans_4_2  54 rkgpleylkafklkklikkikPDvvhah..yakpygllgslaarlsgvipvvlsvwGldvlk 113
                                       +k+p     +  +++ i++ +PDvv ++  ya   +l+++++a l+ ++p+++ + G+++ +
  gi|557694816|ref|YP_008797870.1| 226 IKYPTDITDMSPIIERIRQANPDVVFVVpyYAD-SVLFAKAVASLGLKVPLIVGAGGTGFAD 286
                                       6777777779999999*********99642555.57999999999999********998743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       621  (0.0346366); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3131.46
//
Query:       gi|557694817|ref|YP_008797871.1|  [L=443]
Description: hypothetical protein CSUB_C1390 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-40  137.5   0.3    5.7e-40  137.0   0.3    1.2  1  YjeF_N    YjeF-related protein N-terminus


Domain annotation for each model (and alignments):
>> YjeF_N  YjeF-related protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.0   0.3   3.2e-44   5.7e-40       3     170 ..      27     197 ..      25     198 .. 0.88

  Alignments for each domain:
  == domain 1  score: 137.0 bits;  conditional E-value: 3.2e-44
                            YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeee.kldedaeralell 78 
                                       +Lmenag+ava+ l ++l ++ a+kkvlvl+G+gnnGgdglaaArhLa  ga+Vtv+ll+e+e  ++ +a+ ++e++
  gi|557694817|ref|YP_008797871.1|  27 MLMENAGAAVARQLVSHL-GQAAGKKVLVLCGPGNNGGDGLAAARHLACIGADVTVFLLAEPEkIRTVEARVNFEAV 102
                                       8***********777777.59***********************************7666666488899******** PP

                            YjeF_N  79 kkaggkvveekpeedleekls.....apvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtG 150
                                       ++++ ++   + +   e+ l+     ++vd v+DA+lG+g +  l++ ++++i+  n+ + + lavD+P Gld+dtG
  gi|557694817|ref|YP_008797871.1| 103 QNMRASIRLFTVDT-VEKLLElanvfEEVDAVVDAVLGTGAKPGLPDLYKTAIKLSNAVNCTRLAVDLPTGLDTDTG 178
                                       *9987776444433.2333444569**************************************************** PP

                            YjeF_N 151 avsgtavkadvtvtfgapkr 170
                                       + + t++++d++v++++ k+
  gi|557694817|ref|YP_008797871.1| 179 EGE-TYFEPDIIVALHMKKP 197
                                       ***.9**********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3630.39
//
Query:       gi|557694818|ref|YP_008797872.1|  [L=427]
Description: seryl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  121.8   0.0    4.5e-35  121.2   0.0    1.2  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
    1.4e-24   86.4   3.0    2.1e-24   85.8   3.0    1.3  1  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
     0.0025   17.9   1.2     0.0075   16.3   1.2    1.7  1  TRPM_tetra    Tetramerisation domain of TRPM
     0.0033   15.7   1.3     0.0046   15.2   1.3    1.1  1  HOOK          HOOK protein
  ------ inclusion threshold ------
      0.044   12.7   0.8      0.067   12.1   0.8    1.2  1  DUF677        Protein of unknown function (DUF677)
       0.12   12.6   7.0       0.24   11.6   7.0    1.4  1  TMF_TATA_bd   TATA element modulatory factor 1 TATA binding
       0.16   12.4   0.1       0.71   10.3   0.0    2.0  3  MtrB          Tetrahydromethanopterin S-methyltransferase sub
       0.17   11.9   0.1       0.33   11.0   0.1    1.4  1  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C
       0.35   11.3   2.8       0.59   10.5   2.8    1.3  1  DUF1690       Protein of Unknown function (DUF1690)
       0.43    9.4   4.1       0.71    8.7   4.1    1.2  1  Spc7          Spc7 kinetochore protein
       0.53    8.8   2.2       0.77    8.3   2.2    1.1  1  FapA          Flagellar Assembly Protein A


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 !  121.2   0.0   2.8e-38   4.5e-35       7     179 .]     220     399 ..     215     399 .. 0.94

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 2.8e-38
                                       TSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeasldds 79 
                                       ++++++L+ t+e++++ l+  e+l  ++LPl+++ i++++R+E+     d++G++Rv++F++ ++++f ++++++ +
  gi|557694818|ref|YP_008797872.1| 220 EGEDLYLIGTAEHPLAGLHAGEILDGRKLPLRYAGISPCFRKEAGahgkDTKGIFRVHQFEKVEQFSFTKPSQSWAE 296
                                       4679******************888888****************77899**************************** PP

                                       HHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTS.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                      tRNA-synt_2b  80 lrdlikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldenn.. 154
                                        + li  +++++++lgl++r++  + ++  + +++k+++e++++ ++k++e+++++++ ++++  lg+++ +     
  gi|557694818|ref|YP_008797872.1| 297 HEFLISNAEELYRSLGLPYRVVNICVGELGPVAAKKYDLEVWMPAQNKYREVVSCSNCTDYQAVGLGIRYREAPHie 373
                                       ********************99999**9****************************************997766543 PP

                                       SEEEEEEEEEE.EEHHHHHHHHHHHH CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxx RF
                      tRNA-synt_2b 155 reksvimicaa.igveRllsaileqn 179
                                       +   v++++ + i++eR++ aile++
  gi|557694818|ref|YP_008797872.1| 374 ETDYVHTLNSTlIATERTIVAILENY 399
                                       6778********************96 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 !   85.8   3.0   1.3e-27   2.1e-24       1     108 []       1     108 [.       1     108 [. 0.99

  Alignments for each domain:
  == domain 1  score: 85.8 bits;  conditional E-value: 1.3e-27
                                       ---HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCH CS
                      Seryl_tRNA_N   1 MLDiklirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevk 77 
                                       ML+ik +r+np  +++ ++kR++ ++ vde+l lde++r+++++l+el+++rN ++++I+ akk++e++++++ e++
  gi|557694818|ref|YP_008797872.1|   1 MLNIKAVRTNPGFYRAGMEKRRRPPEIVDEILGLDEEKRSIMKTLQELRHRRNLAAEKIAAAKKRGEKTDHILLEMQ 77 
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCTS---- CS
                      Seryl_tRNA_N  78 elkeelkaleaelkeleaeleklllaiPNip 108
                                       e+++++++le +l+e++++le+ll + PN p
  gi|557694818|ref|YP_008797872.1|  78 EVNQKIEELESRLTEVDNRLETLLKTAPNPP 108
                                       *****************************76 PP

>> TRPM_tetra  Tetramerisation domain of TRPM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.2   4.6e-06    0.0075       9      42 ..      67     100 ..      61     101 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.6e-06
                        TRPM_tetra   9 ERvEnmsmkveevneKenlikaSLqsldfrLgkL 42 
                                       E+++++ + ++evn+K    ++ L+++d rL+ L
  gi|557694818|ref|YP_008797872.1|  67 EKTDHILLEMQEVNQKIEELESRLTEVDNRLETL 100
                                       9******************************876 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   1.3   2.8e-06    0.0046     124     199 ..      27     101 ..      22     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.8e-06
                              HOOK 124 yIqqimtleEsvqhvvmtaiQellskeglaslseeslgeldsqlrklleelkeaqeekdelaQrcheldkqlsllq 199
                                        + +i++l+E+ ++ +m+ +Qel +++ la+ +  ++++  ++  ++l e++e++++ +el+ r+ e+d++l +l 
  gi|557694818|ref|YP_008797872.1|  27 IVDEILGLDEE-KRSIMKTLQELRHRRNLAAEKIAAAKKRGEKTDHILLEMQEVNQKIEELESRLTEVDNRLETLL 101
                                       6789*****99.789***********97777777777777777788899*********************999875 PP

>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   4.1e-05     0.067     258     321 ..      37     100 ..      24     106 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.1e-05
                            DUF677 258 dvenisilverleseiksilktvefAvekeeneaavklaleeikkkvekltekieevgeeaakc 321
                                       +  +i + +++l+ + +   +++  A +++e+  ++ l ++e+++k+e+l + ++ev+++ +  
  gi|557694818|ref|YP_008797872.1|  37 EKRSIMKTLQELRHRRNLAAEKIAAAKKRGEKTDHILLEMQEVNQKIEELESRLTEVDNRLETL 100
                                       5568999999999999999999999*9**99999************************998765 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 ?   11.6   7.0   0.00015      0.24      22      82 ..      32      92 ..      26     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                       TMF_TATA_bd 22 rrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryet 82
                                        l+ E++s++++l++l + r+ a+e i++  k+ e++++   e++e+++++eel++r+ +
  gi|557694818|ref|YP_008797872.1| 32 LGLDEEKRSIMKTLQELRHRRNLAAEKIAAAKKRGEKTDHILLEMQEVNQKIEELESRLTE 92
                                      56899*******************************9888777777777777777776543 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00044      0.71      22      53 ..      67      98 ..      53     114 .. 0.85
   2 ?   -3.1   0.0       6.7   1.1e+04       4      26 ..     192     215 ..     191     218 .. 0.76
   3 ?   -2.9   0.0       5.7   9.3e+03      57      71 ..     394     408 ..     373     419 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00044
                              MtrB 22 aredvvllsldpvleeidkLekiaddlvnsLd 53
                                      ++ d +ll++++v+++i++Le+   ++ n L+
  gi|557694818|ref|YP_008797872.1| 67 EKTDHILLEMQEVNQKIEELESRLTEVDNRLE 98
                                      46799****************99888888875 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.7
                              MtrB   4 vlpelnlvldpetgvvaea.redv 26 
                                       v p + l+  ++ gvv+ +  ed+
  gi|557694818|ref|YP_008797872.1| 192 VQPPYMLTRKIMEGVVSFQdFEDM 215
                                       678888999999999987656665 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 5.7
                              MtrB  57 allesypgRektlvi 71 
                                       a+le y+ R++++ i
  gi|557694818|ref|YP_008797872.1| 394 AILENYQTRDGAVEI 408
                                       456677777777666 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 ?   11.0   0.1    0.0002      0.33      47     117 ..      34     106 ..      26     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                      Baculo_PEP_C  47 LnalsedlksllaeldtrldtlltnLtdalnalq..dtlrneLtnlnsiltnLlssvtNinstLnnllqalnn 117
                                       L++ + ++ + l+el++r + +++++ +a ++ +  d +  e++ +n+++ +L s +t + + L+ ll++  n
  gi|557694818|ref|YP_008797872.1|  34 LDEEKRSIMKTLQELRHRRNLAAEKIAAAKKRGEktDHILLEMQEVNQKIEELESRLTEVDNRLETLLKTAPN 106
                                       55666677777777777777777777777776667799*****************************998655 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.8   0.00036      0.59      39     100 ..      41      98 ..      35     114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00036
                           DUF1690  39 VaeeLkkLraeeeetlkkfeeklekellkdeadakdelsskalnekieeLrkkleefkkkee 100
                                       + + L++Lr++ + + +k+ ++ ++ +++d    +  l  +++n+kieeL+++l+e++++ e
  gi|557694818|ref|YP_008797872.1|  41 IMKTLQELRHRRNLAAEKIAAAKKRGEKTD----HILLEMQEVNQKIEELESRLTEVDNRLE 98 
                                       567788886666666666665555555444....5899******************988876 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   4.1   0.00043      0.71     171     239 ..      33     100 ..      23     105 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00043
                              Spc7 171 eleeekaeleeeleklqeaaeelesidkeeLeelreelaelka...eieekkkelaelqeqleeleekieel 239
                                        l+eek +++++l++l+ ++    ++  e++++++++ ++ +    e++e +++++el+++l+e+++++e+l
  gi|557694818|ref|YP_008797872.1|  33 GLDEEKRSIMKTLQELRHRR----NLAAEKIAAAKKRGEKTDHillEMQEVNQKIEELESRLTEVDNRLETL 100
                                       58899999999999999955....467788888888777666411266666666666666666666666654 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   2.2   0.00047      0.77     341     402 ..      33      98 ..      17     110 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00047
                              FapA 341 eleeeleeleeeleklkkk....ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelk 402
                                        l+ee +++ + l++l+ +     +k+ + k++++ + +++ +++++ ++ e+l+++l+e++++l+
  gi|557694818|ref|YP_008797872.1|  33 GLDEEKRSIMKTLQELRHRrnlaAEKIAAAKKRGEKTDHILLEMQEVNQKIEELESRLTEVDNRLE 98 
                                       344444444444444444444444444444444444444444444444444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1396  (0.0778627); expected 358.6 (0.02)
Passed bias filter:                     1077  (0.0600703); expected 358.6 (0.02)
Passed Vit filter:                       145  (0.00808746); 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: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 2947.70
//
Query:       gi|557694819|ref|YP_008797873.1|  [L=413]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-14   53.8   0.7    2.1e-14   53.8   0.7    2.9  3  FtsX          FtsX-like permease family
    2.2e-14   54.3   1.7    2.2e-14   54.3   1.7    2.4  4  MacB_PCD      MacB-like periplasmic core domain
  ------ inclusion threshold ------
       0.11   12.7   4.9      0.063   13.5   2.5    1.7  2  EI24          Etoposide-induced protein 2.4 (EI24)


Domain annotation for each model (and alignments):
>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.42   2.5e+03      29      45 ..      24      39 ..      21      72 .. 0.57
   2 ?   -0.2   1.0      0.24   1.4e+03      35      54 ..     263     282 ..     237     294 .. 0.47
   3 !   53.8   0.7   3.5e-18   2.1e-14       2      96 .]     298     406 ..     297     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.42
                              FtsX 29 tlvalviGlglgllaaq 45
                                      t++++v+G +l +++ +
  gi|557694819|ref|YP_008797873.1| 24 TVLGIVVGPALITAL-N 39
                                      555555552222222.2 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.24
                              FtsX  35 iGlglgllaaqllsdvllss 54 
                                       iG+++ ++ + +++++l ++
  gi|557694819|ref|YP_008797873.1| 263 IGTLNVFFSTVASMSLLVAF 282
                                       22222222222222222222 PP

  == domain 3  score: 53.8 bits;  conditional E-value: 3.5e-18
                              FtsX   2 reigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllss.........vfs.....selkisi 64 
                                       reig+++alG+++++vll +l+e+++i++++ v+G+++g++aa +ls  ++           v +     +++++ i
  gi|557694819|ref|YP_008797873.1| 298 REIGLIKALGFRTRDVLLSFLSEAVIIGILGGVFGTAVGVVAAFALSGIFSGPpadtrpgsfVTGpagegPRITPLI 374
                                       8*************************************99999886666555544444443321144456******* PP

                              FtsX  65 dlitvliiivlllllallagllsiskilkkep 96 
                                       +++ +l ++++++ + +lag+l+++++++ ep
  gi|557694819|ref|YP_008797873.1| 375 SPELILMGVAVAVGVSVLAGMLPAYRASRFEP 406
                                       ****************************9887 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 !   54.3   1.7   3.7e-18   2.2e-14       1     194 [.      21     241 ..      21     242 .. 0.72
   2 ?   -1.2   0.2      0.36   2.2e+03      12      37 ..     276     301 ..     269     327 .. 0.80
   3 ?   -2.9   0.2       1.3   7.5e+03       5      23 ..     330     348 ..     327     350 .. 0.82
   4 ?   -3.5   0.6       1.9   1.1e+04       5      18 ..     382     395 ..     378     404 .. 0.53

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 3.7e-18
                          MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgk.gsgeslsdpdvealrrevpveavapvv... 73 
                                       + ltvLGi++G a ++a+ + ++gl++s+ s+++  g+ + v +++ g+ + ++d+ v  ++  ++v++  p++   
  gi|557694819|ref|YP_008797873.1|  21 TTLTVLGIVVGPALITALNATTAGLTQSIVSNLEVFGTDL-VLVQRvGDFN-FDDNVVNYISSLQGVKETYPYYlia 95 
                                       78********************************887544.3344333333.45655544443345******98755 PP

                          MacB_PCD  74 ...tvrgggsg.....eeevtvvgvd.pdyfkvf.glklaeGrffteadlrggpnvvvigeelaerlf......pvG 134
                                          +++ g+ +     +++ tv +v+  d++k+f ++k+ +G      ++ ++p ++v+g+++++ +        vG
  gi|557694819|ref|YP_008797873.1|  96 sgeIKTRGK-TfpmdpTKSYTVLAVElRDLPKLFpNIKVDSG------AIVDNPSAAVVGYNAWNPRDpdlppiDVG 165
                                       443222222.23344434456666664355553314443444......45569***********99889997666** PP

                          MacB_PCD 135 dtirl.........kpftVvGvledppgsgsalg.ddavylp......lttl.qrrsitvrlkdgadleaaaaelek 194
                                       +  ++         ++ftV++ l ++ g++ +l+ d++++++      +t+  +++ ++v+l+d+   +++  ++e+
  gi|557694819|ref|YP_008797873.1| 166 SIFTVtplsgtgttRSFTVTARLGKY-GQSLFLNpDNQIFVSpeagrlITNRrSYSGVFVKLTDPGYSDQVVLAIEQ 241
                                       ************9999******9666.88877778******8797776444324777****9998888999888876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.36
                          MacB_PCD  12 vaaviaivslgeglqasvlsqisdlg 37 
                                       +  ++a++++++++  sv++++++ g
  gi|557694819|ref|YP_008797873.1| 276 MSLLVAFLGIMTTMFTSVTERVREIG 301
                                       56788888999999988888877555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.3
                          MacB_PCD   5 vLGiaiGvaaviaivslge 23 
                                       v+G a+Gv a  a+ ++ +
  gi|557694819|ref|YP_008797873.1| 330 VFGTAVGVVAAFALSGIFS 348
                                       6788999999999988766 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 1.9
                          MacB_PCD   5 vLGiaiGvaaviai 18 
                                        +++a+Gv ++ ++
  gi|557694819|ref|YP_008797873.1| 382 GVAVAVGVSVLAGM 395
                                       23444444444444 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 ?   -2.2   0.0      0.69   4.1e+03     111     128 ..      24      41 ..      17      53 .. 0.67
   2 ?   13.5   2.5     1e-05     0.063      40     126 ..     258     348 ..     208     350 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.69
                                       TTHHH....HHHHHHHHH CS
                              EI24 111 Pvvglilsplllswltay 128
                                       +v+g+++ p+l   l+a 
  gi|557694819|ref|YP_008797873.1|  24 TVLGIVVGPALITALNAT 41 
                                       566666666666666654 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1e-05
                                       TTHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHH.HHCCTTSHHHHHHHHHHHHHHHHHHHHH...HH. CS
                              EI24  40 vllasllvllllllplwlfp..lvalllaapfygllaekvekrhlglvkslaeslkslllllllllvllpl...li. 110
                                       ++++++ +l +++  +  ++  +  l ++ +++  + e+v++   gl+k+l++  + +ll +l+ +v++ +   ++ 
  gi|557694819|ref|YP_008797873.1| 258 TVQQIIGTLNVFFSTVASMSllVAFLGIMTTMFTSVTERVRE--IGLIKALGFRTRDVLLSFLSEAVIIGIlggVFg 332
                                       334444455555555444444344445556667777788875..389*****9999999999999999998887557 PP

                                       TTHHH....HHHHHHH CS
                              EI24 111 Pvvglilsplllswlt 126
                                       + vg++++++l+++++
  gi|557694819|ref|YP_008797873.1| 333 TAVGVVAAFALSGIFS 348
                                       8899999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2901.39
//
Query:       gi|557694820|ref|YP_008797874.1|  [L=489]
Description: hypothetical protein CSUB_C1393 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   32.1   3.3     0.0061   16.8   0.2    4.7  4  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
    2.3e-07   31.0   2.1      0.021   15.1   0.0    3.4  4  CARDB            CARDB
     0.0018   17.7   2.7       0.96    8.8   0.2    3.5  3  TRAP_beta        Translocon-associated protein beta (TRAPB)
  ------ inclusion threshold ------
      0.013   15.8   2.0       0.02   15.2   0.2    2.3  2  Alpha_adaptinC2  Adaptin C-terminal domain
      0.053   12.6   0.3        6.4    5.8   0.1    2.2  2  PHTB1_C          PTHB1 C-terminus
       0.16   11.1   0.2        2.6    7.2   0.1    2.1  2  TRAP_alpha       Translocon-associated protein (TRAP), alpha 
        7.2    7.0   5.9    1.4e+02    2.9   0.7    3.9  3  DUF11            Domain of unknown function DUF11


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 ?   -3.0   0.0       3.6   9.2e+03      21      69 ..      29      77 ..      17      85 .. 0.55
   2 !    9.5   0.1   0.00043       1.1      11      78 ..     129     196 ..     120     197 .. 0.80
   3 ?    2.3   0.0     0.082   2.1e+02       5      58 ..     235     290 ..     231     310 .. 0.65
   4 !   16.8   0.2   2.4e-06    0.0061       1      77 [.     346     422 ..     346     424 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.6
                       NPCBM_assoc 21 atnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGd 69
                                      + nv+  l+lP++     v  + ++++++   ++  + + +p++ + G+
  gi|557694820|ref|YP_008797874.1| 29 VANVEGWLTLPDEFGGGVVYANYLQQIPASGVFRLMFPIIVPDTVEVGE 77
                                      5555555555554442233334445566666666666666666666665 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00043
                       NPCBM_assoc  11 ltvtndgtaaatnvslslsl..PeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                         +tn+gta+a nv+l+++   P   + v   + ++ +++pG+t+++ v + + ++++++ y +  ++++
  gi|557694820|ref|YP_008797874.1| 129 YLITNNGTAPAYNVELNIRSeiPTI-R-VLQPVYTIGTIEPGRTTQVPVPIFIDKTTQPSLYGLSSTISY 196
                                       5689**********98876544853.3.3444557779***********999999999999999998887 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.082
                       NPCBM_assoc   5 etvtltltvtndgtaaatnvslslslPeGWtvvevspas...aaslapGetveatvk 58 
                                        t+ + + +tn+   +a++v+++++  ++   v +++++   ++ ++pG+t +++++
  gi|557694820|ref|YP_008797874.1| 235 HTTPVSIIFTNKNPFPARDVKIAIRSSSQQV-VIIEGDTdlfIPVIQPGQTISTQLR 290
                                       5677888889999999999998887655533.3333322222447777777777665 PP

  == domain 4  score: 16.8 bits;  conditional E-value: 2.4e-06
                       NPCBM_assoc   1 vepGetvtltltvtndgtaaatnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakar 77 
                                       v+pGetv +   v+n+gt  a++v++++++ +  +v     + + ++ p + + +t++  + ++a++G+yev +k+ 
  gi|557694820|ref|YP_008797874.1| 346 VQPGETVDIAGDVVNEGTGIARAVYVEIDGQPPFKVLGEPSTFIGQINPSQVAAFTLNFIVDSQAKPGTYEVNVKVV 422
                                       689***************************777996666666667****************************9986 PP

>> CARDB  CARDB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.2   5.9e-05      0.15      15      76 ..     119     184 ..     110     198 .. 0.80
   2 ?   -2.3   0.0       2.2   5.6e+03      30      69 ..     200     243 ..     200     272 .. 0.67
   3 ?    0.5   0.0      0.28   7.2e+02      44      78 ..     260     300 ..     244     321 .. 0.70
   4 !   15.1   0.0   8.1e-06     0.021       2      88 ..     330     425 ..     329     430 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                                       EETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEEE-S-S-C CS
                             CARDB  15 afvgeentitvtvkNqGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftwtteateg 76 
                                        ++++ + +++ ++N+Gta ++++++++  +  +        t+  +++g +t+v + ++++ t++
  gi|557694820|ref|YP_008797874.1| 119 FTANSVSILNYLITNNGTAPAYNVELNIRSEIPTIrvlqPVYTIGTIEPGRTTQVPVPIFIDKTTQ 184
                                       567778889***************99999887666656677788************9999994333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                                       -SSS-EEEEEEEEEETTEEE....EEEEESEE-CTEEEEEEEEE CS
                             CARDB  30 qGtaasgatkvalyldgelv....gtvtvpsLaagesttvsftw 69 
                                       qG++ s+++++ ++++++ +    + ++ p + a  +t vs+ +
  gi|557694820|ref|YP_008797874.1| 200 QGNIRSKQFSMPFVVEENAKpgftARTSQPFITAAHTTPVSIIF 243
                                       68888888888888887776443333333555555555555555 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.28
                                       ETTEEE......EEEEESEE-CTEEEEEEEEEE-S-S-CEE CS
                             CARDB  44 ldgelv......gtvtvpsLaagesttvsftwtteategev 78 
                                        + ++v      ++  +p +++g++++ ++   ++ ++g++
  gi|557694820|ref|YP_008797874.1| 260 SSSQQVviiegdTDLFIPVIQPGQTISTQLRLLAIPQAGDT 300
                                       44444445553336677********9999888777555555 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 8.1e-06
                                       --EEE....EEEC-SEEETTSEEEEEEEEEE-SSS-EEEEEEEEEETTEEE......EEEEESEE-CTEEEEEEEEE CS
                             CARDB   2 pDLtv...tntlnpseafvgeentitvtvkNqGtaasgatkvalyldgelv......gtvtvpsLaagesttvsftw 69 
                                       +D  +   + +l+p+ + +ge++ i   v N+Gt+ ++a+ v+  +dg+         ++ + ++++++ +  ++++
  gi|557694820|ref|YP_008797874.1| 330 ADISIrlrSLALSPQRVQPGETVDIAGDVVNEGTGIARAVYVE--IDGQPPfkvlgePSTFIGQINPSQVAAFTLNF 404
                                       5777777778999************************997766..56665444888777888*************** PP

                                       E-S..-S-CEEEEEEEESTT- CS
                             CARDB  70 tte..ategevtltvvvDpdn 88 
                                        ++  a++g+++++v+v  +n
  gi|557694820|ref|YP_008797874.1| 405 IVDsqAKPGTYEVNVKVVYKN 425
                                       ***99999*******998887 PP

>> TRAP_beta  Translocon-associated protein beta (TRAPB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.2   0.00037      0.96      39      57 ..     127     145 ..     114     212 .. 0.71
   2 !    5.2   0.0     0.005        13      37      92 ..     237     291 ..     225     301 .. 0.84
   3 ?    1.5   0.1     0.067   1.7e+02      33     109 ..     348     423 ..     339     461 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00037
                         TRAP_beta  39 veytiyNvGssaAldVslv 57 
                                       ++y i+N G+++A++V+l+
  gi|557694820|ref|YP_008797874.1| 127 LNYLITNNGTAPAYNVELN 145
                                       6899*************96 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.005
                         TRAP_beta  37 ltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapgenvshsfvv 92 
                                         v++  +N    +A+dV++   s +++   +++g +++ + +++pg+++s+++ +
  gi|557694820|ref|YP_008797874.1| 237 TPVSIIFTNKNPFPARDVKIAIRSSSQQV-VIIEGDTDLFIPVIQPGQTISTQLRL 291
                                       56788888889999999999998866655.79*******************99876 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.067
                         TRAP_beta  33 egedltveytiyNvGssaAldVslvDdsfpeeaFevvsgslsakwerlapge..nvshsfvvepkksgsfngtaavv 107
                                        ge + ++ +++N G+  A+ V +  d+ p+  F+v++ + s+ + +++p +   ++ +f+v ++++   +   + v
  gi|557694820|ref|YP_008797874.1| 348 PGETVDIAGDVVNEGTGIARAVYVEIDGQPP--FKVLG-EPSTFIGQINPSQvaAFTLNFIVDSQAKPGTYEVNVKV 421
                                       5788899999************998888664..77764.45555667777651134455666665554444445555 PP

                         TRAP_beta 108 tY 109
                                        Y
  gi|557694820|ref|YP_008797874.1| 422 VY 423
                                       55 PP

>> Alpha_adaptinC2  Adaptin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.2     8e-06      0.02      23      97 ..     234     313 ..     223     326 .. 0.80
   2 ?   -2.5   0.1       2.4   6.3e+03      45      45 ..     431     431 ..     401     466 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8e-06
                                       TTEEEEEEEEEE-SSS-EEEEEEEEEEBTTCEEEEEEES-S-B-.TTCEEEEEEEEEEES...CTTS-EEEEEEEEE CS
                   Alpha_adaptinC2  23 pgqiritlsftNkssqpisnfsfqaavpkslklqlqppsstvlp.pnpggqitqvllien...pskkplrmrlrisy 95 
                                        +++ + + ftNk + p  ++++ +   + + + ++  +   +p  +pg++i+ +l++ +   +++  ++ ++ + y
  gi|557694820|ref|YP_008797874.1| 234 AHTTPVSIIFTNKNPFPARDVKIAIRSSSQQVVIIEGDTDLFIPvIQPGQTISTQLRLLAipqAGDTVIPIKTSLEY 310
                                       5778899************************999******9999888***********8885555555556666666 PP

                                       E.C CS
                   Alpha_adaptinC2  96 k.v 97 
                                       k +
  gi|557694820|ref|YP_008797874.1| 311 KdD 313
                                       632 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.4
                                       E CS
                   Alpha_adaptinC2  45 f 45 
                                       f
  gi|557694820|ref|YP_008797874.1| 431 F 431
                                       3 PP

>> PHTB1_C  PTHB1 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0025       6.4      14     106 ..     141     259 ..     130     311 .. 0.67
   2 ?    4.9   0.0    0.0047        12      15      78 ..     369     442 ..     360     452 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0025
                           PHTB1_C  14 nvqlsvqvd.kplaaskstfviesldesasteliisvflkgslipaslevevvasYt.................... 69 
                                       nv+l ++ + + +++ +  ++i +++++ +t++ + +f+ + + p+    + ++sY+                    
  gi|557694820|ref|YP_008797874.1| 141 NVELNIRSEiPTIRVLQPVYTIGTIEPGRTTQVPVPIFIDKTTQPSLYGLSSTISYRdlqgnirskqfsmpfvveen 217
                                       6666666652458999999**************************************66666665555555555555 PP

                           PHTB1_C  70 .....sktgiprvvqksvkLPlkLvlkpaqPvKeakhkltld 106
                                            + +  +  +++  + P++++    +P  + ++k+ + 
  gi|557694820|ref|YP_008797874.1| 218 akpgfTARTSQPFITAAHTTPVSIIFTNKNPFPARDVKIAIR 259
                                       555555555555555555555555555555555555555555 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0047
                           PHTB1_C  15 vqlsvqvdkplaas.kstfviesldesasteliisvflkgslipaslevevvasYt.........sktgiprvv 78 
                                       v + +  ++p+++  + +++i ++++s+   +++++++  ++ p   ev+v ++Y+         s+t +++vv
  gi|557694820|ref|YP_008797874.1| 369 VYVEIDGQPPFKVLgEPSTFIGQINPSQVAAFTLNFIVDSQAKPGTYEVNVKVVYKngfgdefqaSRTLVYQVV 442
                                       5666777888887624578899*********************************9666666655555555555 PP

>> TRAP_alpha  Translocon-associated protein (TRAP), alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.055   1.4e+02     157     182 ..     179     204 ..     159     213 .. 0.74
   2 ?    7.2   0.1     0.001       2.6     142     184 ..     391     433 ..     387     445 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.055
                        TRAP_alpha 157 paeafagRPfGlvinlaYkdaeGnqf 182
                                       + ++ +   +Gl+ +++Y+d +Gn  
  gi|557694820|ref|YP_008797874.1| 179 IDKTTQPSLYGLSSTISYRDLQGNIR 204
                                       5555555669*************975 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.001
                        TRAP_alpha 142 vvkPkkqatleYsFipaeafagRPfGlvinlaYkdaeGnqfqe 184
                                       +++P++ a+++ +Fi+  +     + +++++ Yk+  G +fq 
  gi|557694820|ref|YP_008797874.1| 391 QINPSQVAAFTLNFIVDSQAKPGTYEVNVKVVYKNGFGDEFQA 433
                                       699*************************************996 PP

>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.7     0.054   1.4e+02      22      35 ..     131     144 ..     116     175 .. 0.88
   2 ?    0.8   0.0      0.24   6.1e+02      10      35 ..     231     256 ..     218     257 .. 0.82
   3 ?    2.8   0.2     0.056   1.4e+02       6      36 ..     342     372 ..     337     443 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.054
                             DUF11  22 vtNtgpasangvvv 35 
                                        tN+g+a+a++v +
  gi|557694820|ref|YP_008797874.1| 131 ITNNGTAPAYNVEL 144
                                       58*******99987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.24
                             DUF11  10 vrpGdtvtytltvtNtgpasangvvv 35 
                                       +++  t+ + +++tN  p +a +v++
  gi|557694820|ref|YP_008797874.1| 231 ITAAHTTPVSIIFTNKNPFPARDVKI 256
                                       556678999***********999986 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.056
                             DUF11   6 dksevrpGdtvtytltvtNtgpasangvvvt 36 
                                       ++++v+pG+tv+    v N g+  a  v v+
  gi|557694820|ref|YP_008797874.1| 342 SPQRVQPGETVDIAGDVVNEGTGIARAVYVE 372
                                       56799*******9999999999999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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 0.27s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3547.01
//
Query:       gi|557694821|ref|YP_008797875.1|  [L=174]
Description: hypothetical protein CSUB_C1394 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.0   0.1        1.4    9.2   0.0    2.3  2  NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosi


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 ?    3.4   0.0     0.005        90      62      77 ..      41      56 ..      39      68 .. 0.84
   2 ?    9.2   0.0   7.7e-05       1.4      34      78 ..      85     130 ..      79     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.005
                       NPCBM_assoc 62 pagaaaGdyevtakar 77
                                      p++a++Gd+++ ++++
  gi|557694821|ref|YP_008797875.1| 41 PEKAIPGDQKIDLTIT 56
                                      8889999999988876 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 7.7e-05
                       NPCBM_assoc  34 Wtvvevspasaa.slapGetveatvkVtppagaaaGdyevtakarl 78 
                                       W  + v  as+a  ++pG  ++ t kV + ++  +G y+ ++++++
  gi|557694821|ref|YP_008797875.1|  85 WDSRPVLSASVAsPIQPGVLASLTYKVNVRPDVSPGVYTAELRLSY 130
                                       66666667777779**************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       270  (0.0150594); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1271.91
//
Query:       gi|557694822|ref|YP_008797876.1|  [L=236]
Description: lipoprotein-releasing system ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-36  124.2   0.0    7.2e-36  123.7   0.0    1.2  1  ABC_tran        ABC transporter
    7.6e-10   38.6   0.6    4.1e-06   26.4   0.1    2.1  2  SMC_N           RecF/RecN/SMC N terminal domain
      2e-08   34.4   0.3     0.0013   18.6   0.0    2.2  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    6.2e-07   30.0   0.1    1.4e-06   28.8   0.1    1.5  1  AAA_16          AAA ATPase domain
    1.8e-05   24.4   0.0    3.3e-05   23.5   0.0    1.4  1  AAA_29          P-loop containing region of AAA domain
    3.7e-05   22.6   0.0    0.00027   19.7   0.0    1.9  2  AAA_13          AAA domain
    0.00011   22.5   0.1    0.00087   19.6   0.1    2.1  1  AAA_22          AAA domain
    0.00011   22.2   0.2    0.00026   20.9   0.0    1.7  2  RsgA_GTPase     RsgA GTPase
    0.00042   20.1   0.1      0.044   13.5   0.0    2.2  2  IstB_IS21       IstB-like ATP binding protein
    0.00064   19.5   0.0       0.52   10.0   0.0    2.2  2  AAA_15          AAA ATPase domain
     0.0013   19.2   0.0     0.0026   18.3   0.0    1.5  1  AAA_23          AAA domain
     0.0016   18.2   0.1      0.027   14.2   0.0    2.2  2  AAA_30          AAA domain
     0.0042   16.8   0.1      0.044   13.5   0.0    2.1  2  AAA_24          AAA domain
     0.0058   16.7   2.3      0.016   15.3   0.2    2.4  2  MMR_HSR1        50S ribosome-binding GTPase
     0.0076   15.5   0.2       0.55    9.4   0.0    2.1  2  NB-ARC          NB-ARC domain
      0.008   16.1   0.6        3.4    7.6   0.0    2.3  2  NTPase_1        NTPase
     0.0081   16.4   0.0      0.042   14.1   0.0    2.2  2  AAA_28          AAA domain
     0.0088   15.6   0.0       0.13   11.9   0.0    2.2  2  AAA_25          AAA domain
  ------ inclusion threshold ------
       0.01   14.9   1.3      0.031   13.3   0.0    2.1  2  T2SSE           Type II/IV secretion system protein
      0.011   15.7   0.6       0.24   11.3   0.1    2.4  2  NACHT           NACHT domain
      0.012   14.7   0.0      0.013   14.7   0.0    1.1  1  G-alpha         G-protein alpha subunit
      0.013   15.7   0.4      0.036   14.2   0.4    2.0  1  AAA_33          AAA domain
      0.014   15.0   0.3      0.023   14.3   0.3    1.7  1  cobW            CobW/HypB/UreG, nucleotide-binding domain
      0.017   14.5   0.4      0.041   13.3   0.2    1.7  2  HK              Hydroxyethylthiazole kinase family
      0.018   15.6   0.4       0.28   11.7   0.1    2.4  2  AAA_18          AAA domain
      0.028   14.7   0.0       0.42   10.9   0.0    2.2  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
      0.045   13.8   0.1       0.11   12.4   0.0    1.6  2  Glyco_transf_4  Glycosyltransferase Family 4
      0.058   13.5   0.2        0.2   11.7   0.0    1.9  2  Dynamin_N       Dynamin family
      0.069   13.0   0.1        2.9    7.8   0.0    2.4  2  MobB            Molybdopterin guanine dinucleotide synthesis 


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 !  123.7   0.0   1.2e-38   7.2e-36       1     136 [.      26     174 ..      26     175 .. 0.86

  Alignments for each domain:
  == domain 1  score: 123.7 bits;  conditional E-value: 1.2e-38
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpe 73 
                                       l+ v++k+++ge+vaivG++G+GKStLl++l  l +pteG++ +dg d+++    ++  + +k ig+++q  +l ++
  gi|557694822|ref|YP_008797876.1|  26 LNGVDFKVRRGEMVAIVGPSGSGKSTLLNMLGALDRPTEGRVIIDGVDISHadddKRALIRNKLIGFVFQSYNLINR 102
                                       789************************************************99865666677889************ PP

                                       SBHHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  74 ltvren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       lt+ +n           ++e+ + al+ l+ ++l+  +++++p++LSgG++qrva+aral++kp+++l+DEpt
  gi|557694822|ref|YP_008797876.1| 103 LTAIKNvemplaiqnvPEQERRKLALEMLKEVGLES-KAYKKPTQLSGGEQQRVAIARALVTKPSIILADEPT 174
                                       **88888*******9955555555555555555333.444667*****************************9 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 !   10.9   0.1   0.00037      0.23      25      42 ..      37      54 ..      24      60 .. 0.86
   2 !   26.4   0.1   6.6e-09   4.1e-06     125     212 ..     129     219 ..      69     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                                      SEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlld 42
                                      ++ aivGp GSGKs ll+
  gi|557694822|ref|YP_008797876.1| 37 EMVAIVGPSGSGKSTLLN 54
                                      5789**********9886 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 6.6e-09
                                       HHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEE CS
                                       xxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                             SMC_N 125 ellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfiv 194
                                       e+l+++g++++      +LSgGe++ va+a  +    v + ++ l De   +LD k  ++v++llk+  ++   +iv
  gi|557694822|ref|YP_008797876.1| 129 EMLKEVGLESKaykkptQLSGGEQQRVAIARAL----VTKPSIILADEPTGNLDSKSGAIVVQLLKNLAQKgHTVIV 201
                                       556666666556666779*******99987654....556679999********************98777699*** PP

                                       E-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N 195 islreemlekadklvgvt 212
                                       ++++ e+ ++ad+++ ++
  gi|557694822|ref|YP_008797876.1| 202 VTHNMEVAREADRIIYIR 219
                                       *************99876 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   2.5e-05     0.015       2      37 ..      39      71 ..      38     106 .. 0.64
   2 !   18.6   0.0   2.2e-06    0.0013     233     301 ..     143     208 ..      58     210 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.5e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdels 37
                                       +++Gp gsGKS+LL  l  l   dr  eg+ ++++
  gi|557694822|ref|YP_008797876.1| 39 VAIVGPSGSGKSTLLNMLGAL---DRPTEGRVIIDG 71
                                      68*************999877...444444444433 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.2e-06
                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpll 301
                                        +++lS G ++  a++ al   +   s++l DEp  +L+ k  + +++llk+l+++g  vi++TH+ ++
  gi|557694822|ref|YP_008797876.1| 143 KPTQLSGGEQQRVAIARALVTKP---SIILADEPTGNLDSKSGAIVVQLLKNLAQKGHTVIVVTHNMEV 208
                                       45677888888867777777655...***************************************9765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1   2.3e-09   1.4e-06      18     152 ..      32     214 ..      15     219 .. 0.58

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.3e-09
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd.ggif.lrgkcdqlesaipysa.laqalareellrqllde... 88 
                                       +vr+g  e+v ++G+sG+GKs+l+++l  al +  +g + + g   ++ +         +al r++l+  + +    
  gi|557694822|ref|YP_008797876.1|  32 KVRRG--EMVAIVGPSGSGKSTLLNMLG-ALDRPtEGRViIDGVDISH-A-----DdDKRALIRNKLIGFVFQSynl 99 
                                       56666..89*******************.7777743555333333333.1.....1123333344444444444333 PP

                            AAA_16  89 ..............aesaeleawrekleeala............................................. 106
                                                     a     +  +e+ ++ la                                             
  gi|557694822|ref|YP_008797876.1| 100 inrltaiknvemplA----IQNVPEQERRKLAlemlkevgleskaykkptqlsggeqqrvaiaralvtkpsiilade 172
                                       333333344443332....2222222222222445577778999999888888888888887777777777665444 PP

                            AAA_16 107 avpelagaeasrllellkrllallsrderplvlvlDdlqwadeasl 152
                                       ++++l++++   + +llk+l+   ++ ++++++v  +++ a+ea++
  gi|557694822|ref|YP_008797876.1| 173 PTGNLDSKSGAIVVQLLKNLA---QK-GHTVIVVTHNMEVAREADR 214
                                       444444444444444444444...55.8889999999999999886 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   5.4e-08   3.3e-05      13      40 ..      27      54 ..      23      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 5.4e-08
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllD 40
                                      +g ++++++ +++ ++GpsGsGKSTll 
  gi|557694822|ref|YP_008797876.1| 27 NGVDFKVRRGEMVAIVGPSGSGKSTLLN 54
                                      56788898667***************95 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.25   1.6e+02      21      41 ..      41      61 ..      34      94 .. 0.83
   2 !   19.7   0.0   4.4e-07   0.00027     523     580 ..     161     215 ..     137     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.25
                            AAA_13 21 iYGwNGaGKTtLSrllrslel 41
                                      i G  G+GK+tL ++l  l +
  gi|557694822|ref|YP_008797876.1| 41 IVGPSGSGKSTLLNMLGALDR 61
                                      67899*******999988754 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 4.4e-07
                            AAA_13 523 eigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkn 580
                                        ++k  i+  D P   LDs+s  iv+ l+k+ +   +k   +++ THn+e  +e+++ 
  gi|557694822|ref|YP_008797876.1| 161 LVTKPSIILADEPTGNLDSKSGAIVVQLLKNLA---QKGHTVIVVTHNMEVAREADRI 215
                                       46799***************************9...99999***********999875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1   1.4e-06   0.00087       4      30 ..      35      61 ..      33     210 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.4e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                                      +  +++++G+sG+GK+tll++l   + 
  gi|557694822|ref|YP_008797876.1| 35 RGEMVAIVGPSGSGKSTLLNMLGALDR 61
                                      56799****************998863 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   4.3e-07   0.00026      94     120 ..      30      57 ..       7      69 .. 0.72
   2 ?   -2.9   0.0       8.7   5.4e+03      41      61 ..     191     211 ..     178     232 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.3e-07
                                       HHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  94 kellkd.ktsvlvGqSGvGKStLinall 120
                                         +++  +++++vG+SG GKStL+n+l 
  gi|557694822|ref|YP_008797876.1|  30 DFKVRRgEMVAIVGPSGSGKSTLLNMLG 57 
                                       44444449*****************985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.7
                                       HHHHTT-EEEEEEE-GGG--H CS
                       RsgA_GTPase  41 laeekgiepvivlnKiDllee 61 
                                        + +kg ++++v   ++++ e
  gi|557694822|ref|YP_008797876.1| 191 NLAQKGHTVIVVTHNMEVARE 211
                                       344444444444444444444 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 !   13.5   0.0   7.1e-05     0.044      36      68 ..      24      57 ..      12      69 .. 0.85
   2 ?    4.5   0.0     0.042        26     103     153 ..     158     210 ..     145     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.1e-05
                         IstB_IS21 36 keLatlsf.iekkenivllGpsGvGKshlaialg 68
                                       +L + +f +++ e ++++GpsG GKs l   lg
  gi|557694822|ref|YP_008797876.1| 24 VALNGVDFkVRRGEMVAIVGPSGSGKSTLLNMLG 57
                                      4778888878999**************9988777 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.042
                         IstB_IS21 103 lkrllkvdllilDdlgllpldqaeaellfeviekrye..rrsiiitsnlpfae 153
                                       +++l+    +il d  + +ld+++ + + +++++  +  ++ i++t n+++a+
  gi|557694822|ref|YP_008797876.1| 158 ARALVTKPSIILADEPTGNLDSKSGAIVVQLLKNLAQkgHTVIVVTHNMEVAR 210
                                       3444555556777778899*************987651167788899998875 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   0.0   0.00084      0.52      23      46 ..      37      59 ..      29      90 .. 0.76
   2 !    7.3   0.0    0.0054       3.3     323     367 ..     164     207 ..     150     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00084
                            AAA_15 23 eeltvliGkNnsGKSsilealdlF 46
                                      e +  ++G+ +sGKS++l++l  +
  gi|557694822|ref|YP_008797876.1| 37 E-MVAIVGPSGSGKSTLLNMLGAL 59
                                      4.789***************9766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0054
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                       k+ i+l +EP  +L  +   ++++llk+la++++  vi+ TH+  
  gi|557694822|ref|YP_008797876.1| 164 KPSIILADEPTGNLDSKSGAIVVQLLKNLAQKGH-TVIVVTHNME 207
                                       77899999999999999999*************8.9******965 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.2e-06    0.0026      16      39 ..      30      56 ..       7      59 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.2e-06
                            AAA_23 16 dF...skgltlItGpNGaGKTTildAi 39
                                      dF      +++I+Gp G+GK+T+l+ +
  gi|557694822|ref|YP_008797876.1| 30 DFkvrRGEMVAIVGPSGSGKSTLLNML 56
                                      5566555799**************976 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   4.3e-05     0.027      19      50 ..      37      68 ..      30      79 .. 0.85
   2 ?    1.7   0.1      0.29   1.8e+02      38      60 ..     188     210 ..     123     235 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.3e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrvi 50
                                       +++++Gp G+GK+t+l+ l ++ +  +grvi
  gi|557694822|ref|YP_008797876.1| 37 EMVAIVGPSGSGKSTLLNMLGALDRPTEGRVI 68
                                      5899***************9999988877777 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.29
                            AAA_30  38 lreaweaaggrviglAptgkaAk 60 
                                       l + ++++g++vi+++++ ++A+
  gi|557694822|ref|YP_008797876.1| 188 LLKNLAQKGHTVIVVTHNMEVAR 210
                                       22333344555555555555555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   7.2e-05     0.044       3      23 ..      37      59 ..      35      88 .. 0.83
   2 ?    1.1   0.1      0.44   2.7e+02     111     136 ..     185     210 ..     179     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.2e-05
                            AAA_24  3 lkiliyGpsgiGKTtlakel..g 23
                                       +++i+Gpsg+GK+tl+++l   
  gi|557694822|ref|YP_008797876.1| 37 EMVAIVGPSGSGKSTLLNMLgaL 59
                                      5799*************999652 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.44
                            AAA_24 111 frrllkklqelrknvifiahektrkd 136
                                       +++llk+l + +++vi++ h  +   
  gi|557694822|ref|YP_008797876.1| 185 VVQLLKNLAQKGHTVIVVTHNMEVAR 210
                                       5789999999999*****99887655 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   2.6e-05     0.016       2      19 ..      39      56 ..      38      73 .. 0.88
   2 ?    1.1   0.1      0.64   3.9e+02      65      84 ..     201     220 ..      98     235 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-05
                                      EEEEESTTSSHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                      vaivG + +GKStL+n l
  gi|557694822|ref|YP_008797876.1| 39 VAIVGPSGSGKSTLLNML 56
                                      8***************98 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHCTSEEEEEEE CS
                          MMR_HSR1  65 glgkaflaleeadlillvvd 84 
                                        ++++++  +ead i+++ d
  gi|557694822|ref|YP_008797876.1| 201 VVTHNMEVAREADRIIYIRD 220
                                       34444444556777777777 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0   0.00089      0.55      22      38 ..      38      54 ..      29      65 .. 0.89
   2 ?    4.3   0.0     0.031        19      64     147 ..     122     212 ..      97     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00089
                                      EEEEEESTTSSHHHHHH CS
                            NB-ARC 22 vvalvGmgGvGKttlak 38
                                      +va+vG  G+GK+tl++
  gi|557694822|ref|YP_008797876.1| 38 MVAIVGPSGSGKSTLLN 54
                                      89*************86 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.031
                                       HHHHHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCCCTTEEEEEEEE-SHHH...H.....HHHH.CHTTSE CS
                            NB-ARC  64 kseeiletilkeLslseddleekeeves...lkrklvrlLltkrfllvlDDVweeed...wdkigvvlpa.renrlr 133
                                       + +++  ++lke++l+++  ++ ++          + r+L tk ++++ D    + d      + + l++  +++  
  gi|557694822|ref|YP_008797876.1| 122 ERRKLALEMLKEVGLESKAYKKPTQLSGgeqQRVAIARALVTKPSIILADEPTGNLDsksGAIVVQLLKNlAQKGHT 198
                                       56788889999999998888877776557668889************999865554433222233334431456678 PP

                                       EEEEESBCCCCCCS CS
                            NB-ARC 134 vllTTRdeevanav 147
                                       v++ T ++eva ++
  gi|557694822|ref|YP_008797876.1| 199 VIVVTHNMEVAREA 212
                                       88888888888766 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0055       3.4       2      19 ..      39      56 ..      38      85 .. 0.79
   2 !    6.8   0.4    0.0096       5.9      80     149 ..     149     220 ..     104     235 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0055
                                      EEEE--TTSSHHHHHHHH CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkv 19
                                      v+i Gp+G+GK+Tl++ +
  gi|557694822|ref|YP_008797876.1| 39 VAIVGPSGSGKSTLLNML 56
                                      7899**********9754 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0096
                                       HHHHHHHHHHHHHHHHH-EEEE--.-STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS--SHHHHHHHT-TT CS
                          NTPase_1  80 sfeelalealrkalseadviviDE.iGkmElkskkfkeaveevLk.sekpvlavihrrkdlalveeirerkd 149
                                         e+  +++ r  ++++ +i+ DE  G++  ks  +  ++ + L+ ++  v++v h+ +  +  ++i   +d
  gi|557694822|ref|YP_008797876.1| 149 GGEQQRVAIARALVTKPSIILADEpTGNLDSKSGAIVVQLLKNLAqKGHTVIVVTHNMEVAREADRIIYIRD 220
                                       456666666666679999******88*******999888888777688889999998875455555544444 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   6.8e-05     0.042       2      25 ..      39      62 ..      38      82 .. 0.85
   2 ?   -1.4   0.0         4   2.5e+03      15      33 ..     188     211 ..     187     224 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.8e-05
                            AAA_28  2 ivitGgestGKTtlleaLaargyp 25
                                      ++i+G++++GK+tll+ L a + p
  gi|557694822|ref|YP_008797876.1| 39 VAIVGPSGSGKSTLLNMLGALDRP 62
                                      89****************976444 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4
                            AAA_28  15 lleaLaargypvv.....pEaare 33 
                                       ll++La++g++v+      E+are
  gi|557694822|ref|YP_008797876.1| 188 LLKNLAQKGHTVIvvthnMEVARE 211
                                       678888876653322334555554 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    0.0002      0.13      31      51 ..      34      54 ..      29     124 .. 0.92
   2 ?    1.6   0.0      0.29   1.8e+02     162     188 ..     179     204 ..     169     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                            AAA_25 31 pagelallaGapgtGKttlal 51
                                      ++ge ++++G++g+GK+tl+ 
  gi|557694822|ref|YP_008797876.1| 34 RRGEMVAIVGPSGSGKSTLLN 54
                                      689***************985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.29
                            AAA_25 162 nsdvgalvealeriarrtgaavllvhH 188
                                       ++  + +v+ l+++ +++g +v++v H
  gi|557694822|ref|YP_008797876.1| 179 SKSGAIVVQLLKNL-AQKGHTVIVVTH 204
                                       44457788888888.6999******99 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     5e-05     0.031     125     160 ..      32      67 ..      10      96 .. 0.76
   2 ?    0.6   0.3      0.37   2.3e+02     153     180 ..     192     219 ..      93     236 .] 0.56

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5e-05
                             T2SSE 125 avrerglilvsGgTgsGKttllyallkeinksderi 160
                                        vr+  ++ + G+ gsGK+tll++l +    ++ r+
  gi|557694822|ref|YP_008797876.1|  32 KVRRGEMVAIVGPSGSGKSTLLNMLGALDRPTEGRV 67 
                                       577888999**************8654433334444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.37
                             T2SSE 153 inksderivtvEDpvEiqleganqvqln 180
                                       ++++ + +++v   +E+  e++  + ++
  gi|557694822|ref|YP_008797876.1| 192 LAQKGHTVIVVTHNMEVAREADRIIYIR 219
                                       4444444444444444444444444333 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00038      0.24       2      19 ..      38      55 ..      37      59 .. 0.89
   2 ?    2.7   0.1      0.18   1.1e+02      79     111 ..      61      87 ..      55     133 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00038
                                      CEEEEC-TTTCHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqk 19
                                      +v++ G++GsGK+tLl  
  gi|557694822|ref|YP_008797876.1| 38 MVAIVGPSGSGKSTLLNM 55
                                      689************976 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.18
                                       SCCCEEEEEE-STT-SS-TCH.........HHH CS
                             NACHT  79 lperlLlilDglDelvtdlgqkekqpvrtlLse 111
                                       +p+    i+Dg+D  ++d+++      r l+++
  gi|557694822|ref|YP_008797876.1|  61 RPTEGRVIIDGVDISHADDDK------RALIRN 87 
                                       6666668********999999......444433 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.1e-05     0.013      26     107 ..      39     137 ..      17     227 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.1e-05
                                       EEEEESTTSSHHHHHHHHHHHCS--............--HHHHHC.CHHHHHHHHHHHHHHHHHHHHHTT....... CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkg............fseeelat.wraviqlnivrsiktilealesleselsesf 89 
                                       + ++G s+SGKsT+l+ l  l +++            + ++++++ +r+ ++  + +s ++i +     + e+   +
  gi|557694822|ref|YP_008797876.1|  39 VAIVGPSGSGKSTLLNMLGALDRPTegrviidgvdisHADDDKRAlIRNKLIGFVFQSYNLINRLTAIKNVEMPLAI 115
                                       7799******************99999******99875555555557777777777777766554444333332222 PP

                                       ....HHHC-SS-SCCCS-HCHH CS
                           G-alpha  90 ....elqelkerldplkkveas 107
                                           e++ +k +l+ lk+v  +
  gi|557694822|ref|YP_008797876.1| 116 qnvpEQERRKLALEMLKEVGLE 137
                                       4444455555555555544333 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   5.8e-05     0.036       1      19 [.      38      56 ..      38     220 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-05
                            AAA_33  1 lvllvGlpGsGKstlaerl 19
                                      +v +vG++GsGKstl+  l
  gi|557694822|ref|YP_008797876.1| 38 MVAIVGPSGSGKSTLLNML 56
                                      6889***********9765 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 ?   14.3   0.3   3.7e-05     0.023       3      44 ..      39      82 ..      37     233 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.7e-05
                                      EEEEESTTCCHHHHHHHHHCT--SS-EEEEES..S-SSCHCCCC CS
                              cobW  3 tvltGflGsGKTtLlnhllenraglklavivN..efgevsiDae 44
                                      + ++G+ GsGK+tLln l +  +  +  vi+   ++++ + D++
  gi|557694822|ref|YP_008797876.1| 39 VAIVGPSGSGKSTLLNMLGALDRPTEGRVIIDgvDISHADDDKR 82
                                      679*************9985555555555554235555555555 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.2   2.6e+03     126     168 ..      24      66 ..      11      70 .. 0.70
   2 ?   13.3   0.2   6.6e-05     0.041     131     177 ..     177     222 ..     166     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.2
                                       CCSCSSSSSS-SHHHHHHHHHHHHHHTSEEEEESSSEEEEESS CS
                                HK 126 lkvkGvDskeaataavaavqkvAqklrvvvvvtGevDvvsdgk 168
                                       +   GvD k  + ++va+v       +++  + G++D  ++g+
  gi|557694822|ref|YP_008797876.1|  24 VALNGVDFKVRRGEMVAIVGPSGSGKSTLLNMLGALDRPTEGR 66 
                                       5667888888777777777777777777777777777666665 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 6.6e-05
                                       SSSSS-SHHHHHHHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S- CS
                                HK 131 vDskeaataavaavqkvAqklrvvvvvtGevDvvsdgkkvyklknGt 177
                                       +Dsk++a  +v+  +++Aqk ++v+vvt +++v  ++ +++ +++G+
  gi|557694822|ref|YP_008797876.1| 177 LDSKSGAI-VVQLLKNLAQKGHTVIVVTHNMEVAREADRIIYIRDGK 222
                                       79999999.6*********************************9996 PP

>> AAA_18  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      0.28       1      20 [.      39      58 ..      39      81 .. 0.83
   2 ?    1.6   0.0      0.62   3.9e+02      53      93 ..     178     215 ..     115     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00045
                            AAA_18  1 IlltGtpGvGKttlakeLsk 20
                                      +++ G++G+GK+tl + L  
  gi|557694822|ref|YP_008797876.1| 39 VAIVGPSGSGKSTLLNMLGA 58
                                      689***********998855 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.62
                            AAA_18  53 dedkldklldaleenssaleegknlvidghlaeleseaakd 93 
                                       d +  + ++++l++ +   ++g+++++  h  e   ea+++
  gi|557694822|ref|YP_008797876.1| 178 DSKSGAIVVQLLKNLA---QKGHTVIVVTHNMEVAREADRI 215
                                       5555556666677765...4777777777776666666555 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 ?   10.9   0.0   0.00068      0.42      10      81 ..     124     182 ..     120     191 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00068
                           SbcCD_C  10 lsfevevrdedgkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesi 81 
                                        ++ +e+ +e g e++ +++ ++lSGGe+q +   a+a al+          +++++++ DE  ++lD++s 
  gi|557694822|ref|YP_008797876.1| 124 RKLALEMLKEVGLESKAYKKPTQLSGGEQQRV---AIARALV----------TKPSIILADEPTGNLDSKSG 182
                                       45667777779999999************653...3443322..........22455555555555555555 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       7.7   4.8e+03       3      31 ..      20      48 ..      18      74 .. 0.65
   2 ?   12.4   0.0   0.00018      0.11       8      36 ..     185     213 ..     182     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 7.7
                    Glyco_transf_4  3 GverhvleLaraLarrGheVtvvtpgddg 31
                                      G+e+++l+ +    rrG  V +v p+++g
  gi|557694822|ref|YP_008797876.1| 20 GIETVALNGVDFKVRRGEMVAIVGPSGSG 48
                                      66666666555555666555555555544 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00018
                    Glyco_transf_4   8 vleLaraLarrGheVtvvtpgddgpleee 36 
                                       v++L ++La++Gh V vvt++ + + e  
  gi|557694822|ref|YP_008797876.1| 185 VVQLLKNLAQKGHTVIVVTHNMEVAREAD 213
                                       889****************9987766665 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00032       0.2       1      18 [.      39      56 ..      39      66 .. 0.92
   2 ?   -0.9   0.1       2.4   1.5e+03     155     155 ..     193     193 ..     116     233 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00032
                                      EEEEEBTTTTHHHHHHHH CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaL 18
                                      +a+vG   sGKS++ln L
  gi|557694822|ref|YP_008797876.1| 39 VAIVGPSGSGKSTLLNML 56
                                      79**************98 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.4
                                       S CS
                         Dynamin_N 155 d 155
                                        
  gi|557694822|ref|YP_008797876.1| 193 A 193
                                       2 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 ?    7.8   0.0    0.0048       2.9       2      19 ..      39      56 ..      38      67 .. 0.89
   2 ?    2.8   0.0      0.16        99      14      38 ..     183     207 ..     175     214 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0048
                              MobB  2 lgivgksgsGKTtLlekl 19
                                      ++ivg sgsGK tLl+ l
  gi|557694822|ref|YP_008797876.1| 39 VAIVGPSGSGKSTLLNML 56
                                      89************9876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.16
                              MobB  14 tLleklipelkarglrvgtiKhahh 38 
                                       +++ +l++ l+++g +v ++ h+ +
  gi|557694822|ref|YP_008797876.1| 183 AIVVQLLKNLAQKGHTVIVVTHNME 207
                                       57899***************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1556.29
//
Query:       gi|557694823|ref|YP_008797877.1|  [L=448]
Description: glycine hydroxymethyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-81  273.6   0.0      3e-81  273.0   0.0    1.2  1  SHMT             Serine hydroxymethyltransferase
      2e-08   33.8   0.0    5.2e-08   32.4   0.0    1.6  1  Aminotran_1_2    Aminotransferase class I and II
    1.5e-07   31.0   0.0    3.1e-07   30.0   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
      3e-05   23.2   0.0    4.9e-05   22.5   0.0    1.3  1  SelA             L-seryl-tRNA selenium transferase
     0.0003   19.8   0.2     0.0012   17.9   0.2    1.9  1  Aminotran_5      Aminotransferase class-V
     0.0093   15.3   0.0      0.013   14.8   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.026   14.8   0.0      0.069   13.5   0.0    1.7  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


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 !  273.0   0.0   1.2e-84     3e-81       6     399 .]      18     404 ..      14     404 .. 0.91

  Alignments for each domain:
  == domain 1  score: 273.0 bits;  conditional E-value: 1.2e-84
                                       HHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-S CS
                              SHMT   6 pevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkld 82 
                                       ++v ++++k ++  ++++ liasen++s+av eal s +  +yaeG+PG+r y Gc ++deve la++  k +++++
  gi|557694823|ref|YP_008797877.1|  18 QKVLDLLEKHHSMMRRSLPLIASENVVSPAVREALVSDFMHRYAEGWPGERLYAGCRYIDEVELLAIELGKAVYRAE 94 
                                       679999*********************************************************************** PP

                                       TTTEEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HH CS
                              SHMT  83 pakwgvnvqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidyd 159
                                           +v+v+p sG  anl  y+a+ +pgd +++l +++GGh++hG +      + +    ++ +y+ d+e+  id d
  gi|557694823|ref|YP_008797877.1|  95 ----FVDVRPISGVVANLVAYSAFARPGDMMVALTIPHGGHISHGKEKWG-GTAGVVRGLDVERYEFDEENFEIDVD 166
                                       ....*****************************************98777.56677788999**************9 PP

                                       HHHHHHHH......H--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCC.TSSEEEEE CS
                              SHMT 160 elekkake......fkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfe.yadvvttt 229
                                       +  ++ ++       kP+l + G+s +      + +r +ad+ gay++ d ah+aGl+a+g++ +P++  ad +t  
  gi|557694823|ref|YP_008797877.1| 167 ATARRLRKieaetgKKPRLFMLGASVFLFPHPVKEIRSLADQYGAYVVYDAAHVAGLIAGGMFQDPLReGADCMTMS 243
                                       8654332211112369**************************************************96269****** PP

                                       SSSTT-S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHH CS
                              SHMT 230 thktlrGprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvl 306
                                       thktl+Gp+ g++++               +++ +++++  fPgl    + h++a++a+al eal   +++y++q++
  gi|557694823|ref|YP_008797877.1| 244 THKTLAGPQHGMVVSW--------------NKYGERLKQIAFPGLLSNHHLHAVAGLAIALAEALA-FYREYASQII 305
                                       *************998..............45667899999***********************96.6********* PP

                                       HHHHHHHHHHHHTT-EEG...GGS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS...S.TTTT-SEEE CS
                              SHMT 307 knakalaealkekgyklv...sgGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd...k.salvtsGlr 376
                                       +nak lae l e g++ +    g t++h ++ d+ +k +dG++ae+ le++ i +n+n +P+d   k     +sG+r
  gi|557694823|ref|YP_008797877.1| 306 RNAKILAESLYELGIDALypnKGFTESHTIVADV-SKYMDGRTAEERLEQAGIIVNRNLIPKDyrlKtDYRRPSGIR 381
                                       ***************9763434669*****9997.688*************************7432123579**** PP

                                       EESHHHHHTT--HHHHHHHHHHH CS
                              SHMT 377 lGtpaltsrgfkeedlekvakfi 399
                                       lG+  +t+ g+ke++++++a+fi
  gi|557694823|ref|YP_008797877.1| 382 LGSQEVTRLGMKESEMKQIAEFI 404
                                       ********************997 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 !   32.4   0.0     2e-11   5.2e-08     103     307 ..     139     330 ..      97     375 .. 0.77

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 2e-11
                                       -THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTE..TEEEEEEESS-TTT--B--HHHHHHHHHHH CS
                     Aminotran_1_2 103 yasyknilrlsggevvryplyseedfhldlealeealkeapegnk..ktkvilvesphNPtGtvatleeleklldla 177
                                       ++    ++r  ++e +++    ee+f++d++a  + l++  ++    ++ ++l +s++     +++   ++++ +la
  gi|557694823|ref|YP_008797877.1| 139 WGGTAGVVRGLDVERYEFD---EENFEIDVDATARRLRKIEAETGkkPRLFMLGASVF-----LFP-HPVKEIRSLA 206
                                       4444444444444455554...9***************95443325589999999998.....444.447777777* PP

                                       HHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSH CS
                     Aminotran_1_2 178 kkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsss 254
                                       ++y+++++ D a+ ++      +      + e+ +   + ++s+   laG   G++++  ++ + l++++ p+l s+
  gi|557694823|ref|YP_008797877.1| 207 DQYGAYVVYDAAHVAGLIAGGMF---QDPLREGAD---CMTMSTHKTLAGPQHGMVVSWNKYGERLKQIAFPGLLSN 277
                                       *************9999986655...567777777...99***********************************99 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSE CS
                     Aminotran_1_2 255 llqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmf 307
                                       +  +ava  + +  +   +  e ++++++++k l ++L elg++ l ++ g+ 
  gi|557694823|ref|YP_008797877.1| 278 HHLHAVAGLAIALAEALAFYREYASQIIRNAKILAESLYELGIDALYPNKGFT 330
                                       999999999999888888***************************99999985 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   1.2e-10   3.1e-07      55     274 ..     102     408 ..      89     425 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.2e-10
                                       -HHHHHHHHHHHH--TTEEEEE.ETT.....-HHHHSSTTHHHHCC--EEEEE-EBTT.TBE-HHHHHHHS--S-T. CS
                   Beta_elim_lyase  55 qGtaAnsillkillqrgeeviv.tep.....ahihfdetgaiaelagvklrdlknkea.Gkmdlekleaaikevga. 123
                                       +G  An +++++++++g+ +++ t+p     +h+  +  g + ++ g  +   + +e+  ++d+++ ++ +++ +a 
  gi|557694823|ref|YP_008797877.1| 102 SGVVANLVAYSAFARPGDMMVAlTIPhgghiSHGKEKWGGTAGVVRGLDVERYEFDEEnFEIDVDATARRLRKIEAe 178
                                       899***********999987752555897778888888888889999999999988765455666666655555554 PP

                                       TS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT CS
                   Beta_elim_lyase 124 heekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdl 200
                                         +k++l +l   +       + +  ++e++ +a++yg  +++D+A +a    + g     + +++D +tms  K l
  gi|557694823|ref|YP_008797877.1| 179 TGKKPRLFMLGASVF------LFPHPVKEIRSLADQYGAYVVYDAAHVAGLI-AGGMFQDPLREGADCMTMSTHKTL 248
                                       556999999988877......57788999999***************99765.78888888889************* PP

                                       --SS-EEEEE-HH.......................................HHHHHHHHHHHHT---SSTHHHHH. CS
                   Beta_elim_lyase 201 lanvGgvlafrddel...................................edylaerveqrkylggglrqagvlaa. 241
                                         +  g+++  ++ +                                    +y ++ ++ +k l++ l++ g+ a  
  gi|557694823|ref|YP_008797877.1| 249 AGPQHGMVVSWNK-YgerlkqiafpgllsnhhlhavaglaialaealafyREYASQIIRNAKILAESLYELGIDALy 324
                                       ******9999888.668********************************999*9*******************9999 PP

                                       .....................................................HHHHHHHHSSTTHHHHHHHHHHHH CS
                   Beta_elim_lyase 242 ...................................................leagiraleeglaslerdhktaeqla 267
                                                                                          +  gir   +++ +l+ +    +q a
  gi|557694823|ref|YP_008797877.1| 325 pnkgfteshtivadvskymdgrtaeerleqagiivnrnlipkdyrlktdyrRPSGIRLGSQEVTRLGMKESEMKQIA 401
                                       99999999999999999999999999998888888888888888888888777888888888888888888888888 PP

                                       HHHHHCT CS
                   Beta_elim_lyase 268 eklelvr 274
                                       e +++v 
  gi|557694823|ref|YP_008797877.1| 402 EFIADVI 408
                                       8777764 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0   1.9e-08   4.9e-05     188     298 ..     221     334 ..     195     378 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1.9e-08
                                       GT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HHHHHHHHHSTHHHHTB--HHH.HH....HHHHHHHHH CS
                              SelA 188 yglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkkelieklkknplkraLrvDklt.la....aleatlrly 259
                                        gl    ++q+ l+eG+d ++ s  k l gpq G++v   ++ e+lk+  +   L    l  +a    al+++l +y
  gi|557694823|ref|YP_008797877.1| 221 AGLIAGGMFQDPLREGADCMTMSTHKTLAGPQHGMVVSWNKYGERLKQIAFPGLLSNHHLHaVAglaiALAEALAFY 297
                                       5778888999**************************************99998888877753341112456677777 PP

                                       H..TT-GGGSHHHHHHH--HHHHHHHHHHHHHHHTTSTT CS
                              SelA 260 ldpeklaeklptlrlltqkleelrakaerlqkelkealg 298
                                       +  e +++ +   ++l+++l el   a   +k ++e+ +
  gi|557694823|ref|YP_008797877.1| 298 R--EYASQIIRNAKILAESLYELGIDALYPNKGFTESHT 334
                                       7..888888899999999998888888777766666665 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   4.7e-07    0.0012     156     228 ..     197     273 ..     188     361 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.7e-07
                                       --HHHHHHHHHHTT-EEEEE-TTTT....TTS---HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.S CS
                       Aminotran_5 156 qpveeigklakkkgalvlvDaaqav....ghipidvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllg 227
                                       +pv+ei +la ++ga+v+ Daa  +    g +  d  + g+D +++s+hK l gP+  G+++  +++ e+l+++ ++
  gi|557694823|ref|YP_008797877.1| 197 HPVKEIRSLADQYGAYVVYDAAHVAgliaGGMFQDPLREGADCMTMSTHKtLAGPQ-HGMVVSWNKYGERLKQIAFP 272
                                       69********************9861122567789999************666665.56666666677777777776 PP

                                       T CS
                       Aminotran_5 228 g 228
                                       g
  gi|557694823|ref|YP_008797877.1| 273 G 273
                                       6 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 !   14.8   0.0   5.1e-06     0.013     123     188 ..     195     261 ..     138     296 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.1e-06
                                       B---HHHHHHHHHHCT-EEEEE-TT-TT-EETT...EECCCSSSEEEEE-BTTSSS-SSS-EEEEESTH CS
                   DegT_DnrJ_EryC1 123 qvadmdalkaiaakhglkvieDaAhAlGatykg...kkvGalgdaavfSFyptKnlttGeGGavvtnde 188
                                        +  +++++ +a+++g +v+ DaAh  G    g    ++ + +d+ ++S +  K+l+    G+vv+ ++
  gi|557694823|ref|YP_008797877.1| 195 FPHPVKEIRSLADQYGAYVVYDAAHVAGLIAGGmfqDPLREGADCMTMSTH--KTLAGPQHGMVVSWNK 261
                                       5667899**********************9999887777777777777765..8999999999998764 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 ?   13.5   0.0   2.7e-05     0.069      36      73 ..     193     231 ..     178     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.7e-05
                                       --BS--HHHHHHHSTT-SEEEEEE-S--TT-G.-HHHHH CS
                           PFOR_II  36 tlrPFPeeelkellkkvkkvvvldrnisfgse.Gqlvee 73 
                                       +l+P P +e+++l++++ ++vv+d ++  g   G ++++
  gi|557694823|ref|YP_008797877.1| 193 FLFPHPVKEIRSLADQYGAYVVYDAAHVAGLIaGGMFQD 231
                                       79*************************999878888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3078.67
//
Query:       gi|557694824|ref|YP_008797878.1|  [L=425]
Description: glutamate-1-semialdehyde-2,1-aminomutase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-61  208.0   0.0    2.3e-61  207.7   0.0    1.1  1  Aminotran_3    Aminotransferase class-III
  ------ inclusion threshold ------
      0.027   13.7   0.0       0.24   10.5   0.0    2.0  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 !  207.7   0.0   2.5e-65   2.3e-61       6     387 ..      24     391 ..      19     414 .. 0.85

  Alignments for each domain:
  == domain 1  score: 207.7 bits;  conditional E-value: 2.5e-65
                                       B--SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHH CS
                       Aminotran_3   6 ednlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllkl 82 
                                       +d++++ +++aeG+y++d  g+r+lD   +  ++++Gh    v++a+ +q+ak  h     + +   +k+a+++ ++
  gi|557694824|ref|YP_008797878.1|  24 VDPVPVYVERAEGAYVYDISGRRFLDCWMGHGALLMGHGYRPVIEAAMDQLAKGAHFG---YPHIWEVKWAKQVCSM 97 
                                       5677899***********************************************9988...7777889********* PP

                                       CT-..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHH.HHHSS--TTT.TTTCTTB.-TS CS
                       Aminotran_3  83 apkgldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlga.lsvtgskkky.ktlfgpf.lpe 156
                                       +p  + +v   nsG+eA++ A+++ar       +t ++ + +++g++HG   g  ++vt + +k  + +++p  +++
  gi|557694824|ref|YP_008797878.1|  98 VPS-VKMVRPTNSGTEANMYAVRTARG------YTGRKLVGKIEGGWHGGYDGLqIGVTYPIDKPsSLGIPPEtTAN 167
                                       **9.9**********************......9***************9987438999886554044566555788 PP

                                       EEEE-TTBGGGTB-HHHHHHHHHHHHHHHH.CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE CS
                       Aminotran_3 157 vvrlkypdeevlkeneeeeaalleeleale.kkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivD 232
                                       ++ l+y+d                 le +e + k +e+aA++vEp+ g+gG+++a+ e+l+++re+c+++++lli+D
  gi|557694824|ref|YP_008797878.1| 168 TILLPYND-----------------LEGVEkRIKGKELAAIVVEPVLGAGGFIPADIEYLKGVREICDREGILLIFD 227
                                       88888887.................7777768899****************************************** PP

                                       -TTTTT..TTTSSSSGGGGCTS--SEEEE-GGGGTT.SS-EEEEEEHHHHTTS-TTS.........B--TTTT-HHH CS
                       Aminotran_3 233 EvqtGf..GrTGklfAlehagvspDlmtlaKaltgG.lplsavlataevmqalapgs.........hgsTfgGnpla 297
                                       Ev tGf  +  G   A + +gv pD+++l+K+++gG +p+ a+ ++++vm++l + +         hg+T++Gnpl 
  gi|557694824|ref|YP_008797878.1| 228 EVITGFrlAPGG---AQQRFGVLPDITVLGKVIGGGpFPAGAFGGREDVMEVLDQRKrvnfyervfHGGTYSGNPLT 301
                                       ******867777...99************************************9988******************** PP

                                       HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE- CS
                       Aminotran_3 298 cavalavleiieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvli 374
                                       +++    l+ +e+ ++ e+ ++lg++ + gL+++ +     + + g G ++ i ++ e+ ++  + +++ k+  + i
  gi|557694824|ref|YP_008797878.1| 302 MRAGYVLLKELEKGEVYERLEKLGERARRGLRDALEP--LGAYITGIGSLVCIHFTREEPRD-IHTANRTKDLKLTI 375
                                       *********************************9966..588899********999999844.44444444444444 PP

                                       EEETT...TEEEE--- CS
                       Aminotran_3 375 lsaGd...nvirllpp 387
                                         + +   + i ++pp
  gi|557694824|ref|YP_008797878.1| 376 EFSKHlyrRGILFVPP 391
                                       3322233334444444 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 ?   10.5   0.0   2.7e-05      0.24     165     362 ..     205     413 ..     171     413 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 2.7e-05
                                       --HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHH CS
                     Aminotran_1_2 165 atleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvs 241
                                       a+ e l+ + +++++ ++ll++De+  gf + + +a++ r++v +++       l+K  G   +  G++ g ++v +
  gi|557694824|ref|YP_008797878.1| 205 ADIEYLKGVREICDREGILLIFDEVITGFRLAPGGAQQ-RFGVLPDIT-----VLGKVIGGGPFPAGAFGGREDVME 275
                                       46777888889999999999999999999999777766.999998766.....478888877777788889885554 PP

                                       HHHHHHHHHTS..........SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHSTEEEECCSCSSE CS
                     Aminotran_1_2 242 qlrklsrpfls..........ssllqaavaaalsdallkqseleemrqrlqkr.rkelrdeLaelglkvlasqsgmf 307
                                        l + +r   +           ++l   +  +l ++l+k  e+ e+ ++l +r r+ lrd+L+ lg  +++  + ++
  gi|557694824|ref|YP_008797878.1| 276 VLDQRKRVNFYervfhggtysGNPLTMRAGYVLLKELEKG-EVYERLEKLGERaRRGLRDALEPLGAYITGI-GSLV 350
                                       4444444433344444441114444444445566666655.777777777665267899***7778777775.8899 PP

                                       EEEEETHH..............CHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHHHHHHHH CS
                     Aminotran_1_2 308 lltdlsae..............takelskkLleevgvyvtpgtsftvpgrlRitvAglteeeleelvea 362
                                       +++ +++e                 e+sk L  + g++ +p   ++    l i+  ++++e++++l+ea
  gi|557694824|ref|YP_008797878.1| 351 CIHFTREEprdihtanrtkdlkLTIEFSKHLYRR-GILFVPPYNPH----LFISA-AHSQEDIDNLIEA 413
                                       9999999999***999998888788888889999.99999944444....66777.9*******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2997.07
//
Query:       gi|557694825|ref|YP_008797879.1|  [L=177]
Description: NUDIX hydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-18   65.0   0.1    8.5e-18   64.7   0.1    1.1  1  NUDIX     NUDIX domain
      0.009   16.0   0.0      0.012   15.6   0.0    1.3  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 !   64.7   0.1   9.5e-22   8.5e-18       4     116 ..      22     134 ..      19     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 9.5e-22
                                       EEEEEEEEETTSEEEEEEES...SSSTTT.EESSEEECBTTS.HHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   4 ravgvvllnekgevLlvrrs...kkpfpg.WelPgGkvepgE.tpeeAArREleEEtGleaellellgrlhylapyd 75 
                                       +av++vl+++  evLlv+r    ++p++g  ++PgG+ +p + +++++A+REl EE+ l+ae + ++g l+ + p +
  gi|557694825|ref|YP_008797879.1|  22 AAVAIVLRDGP-EVLLVKRVerdDDPWSGqVAFPGGRWRPEDaDFAATALRELHEEASLPAEAVGFIGFLEAVSPRN 97 
                                       56777777777.7*******666666666446************************************888877777 PP

                                       EEEEEEEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHH CS
                             NUDIX  76 gpygdeheilyvfleevegelepndenevsevrwvpleell 116
                                        p      +  v+++ ++++ +++  +evs+v w+pl+ l+
  gi|557694825|ref|YP_008797879.1|  98 MPTL---KVKPVVFRLLHETSPHP-GAEVSKVFWLPLNNLQ 134
                                       7666...46655555555555555.7************992 PP

>> NUDIX_4  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.3e-06     0.012       2      48 ..      24      74 ..      23     137 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-06
                                      EEEEEEC.TEEEEEE--TTS..SSTT-EE-SEEE-TTS-HH.HHHHHHHHS CS
                           NUDIX_4  2 vllirdd.grvllekRpekg..llggLwefPggeeegeele.ealareelg 48
                                      v+++++d  +vll kR e++   + g   fPgg++  e+++ +a a +el+
  gi|557694825|ref|YP_008797879.1| 24 VAIVLRDgPEVLLVKRVERDddPWSGQVAFPGGRWRPEDADfAATALRELH 74
                                      6667777589******987545************88777332222223444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       234  (0.0130515); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1312.66
//
Query:       gi|557694826|ref|YP_008797880.1|  [L=471]
Description: Fe-S cluster assembly protein SufB [Candidatus Caldiarchaeum subterraneum]
Scores for 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-57  192.2   1.2    1.2e-56  191.9   1.2    1.1  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 !  191.9   1.2   6.5e-61   1.2e-56       3     218 .]     193     417 ..     191     417 .. 0.95

  Alignments for each domain:
  == domain 1  score: 191.9 bits;  conditional E-value: 6.5e-61
                           UPF0051   3 fertlivveegaevtiieey.......agc...gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelt 69 
                                       f +++ v e+ga ++iiee+       +     +++ ++  ++++lk++++qn s++ + +s++ a++gr ++  ++
  gi|557694826|ref|YP_008797880.1| 193 FSKVVAVTEPGAVASIIEEVhglpgadE-SvfgHHTHLYSLDDSSLKHSTLQNLSHGQTYVSNRVADVGRGSSAMVV 268
                                       6788899**********99977776551.05559999999999*************999999999************ PP

                           UPF0051  70 tvslggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrk 146
                                        + +gg+++  ++++ + g+g++++  ++++++++q++d++ +++h g +t++r+l+kgv+kd+a+++f+g i+++k
  gi|557694826|ref|YP_008797880.1| 269 GAVIGGQVSKVRVDSSMHGDGSSVNDLEIVFGDAEQRIDVTANLHHIGFGTQGRVLAKGVVKDKAKSIFKGVITIEK 345
                                       ***************************************************************************** PP

                           UPF0051 147 gaqktdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       +a++t+a+  ++++++s++ara++iP lei +d+vka+H A+v++id eql+YLm+RG++e+eAr+++  gf
  gi|557694826|ref|YP_008797880.1| 346 QAKNTSAYLAEHAMIMSPEARAYAIPSLEIMTDEVKATHSASVSQIDPEQLYYLMARGIPEQEARKMLALGF 417
                                       ********************************************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3241.16
//
Query:       gi|557694827|ref|YP_008797881.1|  [L=138]
Description: hypothetical protein CSUB_C1400 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00062   19.7   4.1       0.26   11.3   2.8    2.3  2  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.046   13.8   2.3        1.4    9.0   0.3    2.2  2  ArfGap          Putative GTPase activating protein for Arf
      0.051   13.3   5.4          5    6.9   0.2    3.5  3  Rubredoxin_2    Rubredoxin metal binding domain
       0.29   11.4   3.6       0.95    9.7   0.2    2.3  2  LIM             LIM domain
       0.44   10.9   3.9         16    5.9   4.7    2.6  2  C1_2            C1 domain
       0.83    9.2  12.4        1.3    8.6   0.0    3.9  3  TF_Zn_Ribbon    TFIIB zinc-binding
        1.1    9.2   5.0        1.7    8.6   0.0    3.1  3  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
        4.7    7.4  13.3        5.7    7.1   5.1    3.3  3  Zn-ribbon_8     Zinc ribbon domain
        6.1    6.9  15.2         12    5.9   3.9    3.8  3  zf-dskA_traR    Prokaryotic dksA/traR C4-type zinc finger


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 !   11.3   2.8   0.00013      0.26      11      39 ..      11      56 ..       7      59 .. 0.79
   2 !   10.0   2.9   0.00036      0.71      12      36 ..      45      74 ..      38      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                               DZR 11 darfCseCgtklkavaa.................edrCpsCgekvd 39
                                      ++++C  Cg+  +++ +                 + +C+ Cg+kv 
  gi|557694827|ref|YP_008797881.1| 11 ENIVCRVCGAVAEKPDShhyvtgfgyvcrrcglqPVVCDGCGAKVR 56
                                      6778999999887666688999998888888888899999999875 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00036
                               DZR 12 arfCseCgtklkavaa.....edrCpsCge 36
                                        +C+ Cg+k+++++       + C +C +
  gi|557694827|ref|YP_008797881.1| 45 PVVCDGCGAKVRRMTVtvlrgRTLCLNCYR 74
                                      557999999998777789999999999966 PP

>> ArfGap  Putative GTPase activating protein for Arf
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.016        32       4      39 ..       3      41 ..       1      45 [. 0.67
   2 ?    9.0   0.3   0.00069       1.4      15      49 ..      47      82 ..      44     103 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.016
                                      HHHHCCSCCCCB-TTT....-SBS--EEETTTTEEE-HHH CS
                            ArfGap  4 lkellkepenkvCaDC....gakeptWaslnlgvflCieC 39
                                      l +l k+ en vC  C    +++++++ ++ +  ++C +C
  gi|557694827|ref|YP_008797881.1|  3 LGHLGKRAENIVCRVCgavaEKPDSHHYVTGF-GYVCRRC 41
                                      567788999*******6633333444444444.4799999 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00069
                                      B-TTT-SBS--EEET.TTTEEE-HHHHHHHCCS.TT CS
                            ArfGap 15 vCaDCgakeptWasl.nlgvflCieCsgvHrslgvh 49
                                      vC  Cgak  + +++   g +lC++C  v r+ g +
  gi|557694827|ref|YP_008797881.1| 47 VCDGCGAKVRRMTVTvLRGRTLCLNCYRVEREKGEK 82
                                      79999999988776636799***********98754 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.017        33       2      11 ..      14      23 ..      14      25 .. 0.82
   2 ?    6.9   0.2    0.0025         5       1       8 [.      36      43 ..      36      45 .. 0.89
   3 ?    3.0   0.1     0.044        87       2      12 ..      47      57 ..      47      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.017
                      Rubredoxin_2  2 vCsqCGfesa 11
                                      vC+ CG+++ 
  gi|557694827|ref|YP_008797881.1| 14 VCRVCGAVAE 23
                                      7*****9875 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0025
                      Rubredoxin_2  1 YvCsqCGf 8 
                                      YvC++CG 
  gi|557694827|ref|YP_008797881.1| 36 YVCRRCGL 43
                                      9******6 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.044
                      Rubredoxin_2  2 vCsqCGfesak 12
                                      vC+ CG++ ++
  gi|557694827|ref|YP_008797881.1| 47 VCDGCGAKVRR 57
                                      79999988765 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4     0.075   1.5e+02      27      53 ..      13      41 ..      10      46 .. 0.79
   2 ?    9.7   0.2   0.00047      0.95      28      54 ..      47      73 ..      43      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.075
                                      SB-TTT-SB-CTT..CEEETT.EEEEHHH CS
                               LIM 27 FtCsdCqkeLkegs.fyekdg.klyCkkd 53
                                       +C +C+   ++ + ++ + g   +C+++
  gi|557694827|ref|YP_008797881.1| 13 IVCRVCGAVAEKPDsHHYVTGfGYVCRRC 41
                                      58999999998888866666668999988 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00047
                                      B-TTT-SB-CTT.CEEETTEEEEHHHH CS
                               LIM 28 tCsdCqkeLkegsfyekdgklyCkkdy 54
                                      +C  C+ + +++++++  g+ +C ++y
  gi|557694827|ref|YP_008797881.1| 47 VCDGCGAKVRRMTVTVLRGRTLCLNCY 73
                                      7*************************9 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   4.7    0.0078        16      16      40 ..      10      43 ..       5      51 .. 0.82
   2 ?    1.4   0.2       0.2     4e+02      20      28 ..      47      55 ..      44      59 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0078
                              C1_2 16 sesfnCsaCgrk.........idgffYsCseCdf 40
                                       e+  C++Cg           ++gf Y C +C  
  gi|557694827|ref|YP_008797881.1| 10 AENIVCRVCGAVaekpdshhyVTGFGYVCRRCGL 43
                                      57789****98888889888888999***99*64 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.2
                              C1_2 20 nCsaCgrki 28
                                       C++Cg k+
  gi|557694827|ref|YP_008797881.1| 47 VCDGCGAKV 55
                                      6****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 ?    8.6   0.0   0.00064       1.3      18      31 ..      11      24 ..       8      29 .. 0.82
   2 ?    4.2   0.2     0.015        30      20      27 ..      36      43 ..      34      44 .. 0.88
   3 ?    2.3   0.7     0.059   1.2e+02      21      29 ..      47      55 ..      46      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00064
                                      TCEEESSSSBEEEE CS
                      TF_Zn_Ribbon 18 gelvCtdCGlVled 31
                                       ++vC  CG+V e 
  gi|557694827|ref|YP_008797881.1| 11 ENIVCRVCGAVAEK 24
                                      467********886 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.015
                                      EEESSSSB CS
                      TF_Zn_Ribbon 20 lvCtdCGl 27
                                      +vC +CGl
  gi|557694827|ref|YP_008797881.1| 36 YVCRRCGL 43
                                      89****98 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.059
                                      EESSSSBEE CS
                      TF_Zn_Ribbon 21 vCtdCGlVl 29
                                      vC  CG+ +
  gi|557694827|ref|YP_008797881.1| 47 VCDGCGAKV 55
                                      9*****976 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 ?    8.6   0.0   0.00083       1.7      11      33 ..       2      24 ..       1      27 [. 0.73
   2 ?    0.6   0.7      0.26   5.2e+02      23      28 ..      37      42 ..      30      45 .. 0.80
   3 ?   -0.5   0.1       0.6   1.2e+03      24      30 ..      48      54 ..      43      55 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00083
                                      EEEEECSCCCEEEESSSS-EEES CS
                    RNA_POL_M_15KD 11 LlpkedkegknfeCrqCgYeepa 33
                                      +l   +k   n  Cr Cg++ ++
  gi|557694827|ref|YP_008797881.1|  2 MLGHLGKRAENIVCRVCGAVAEK 24
                                      5555566666677******9986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.26
                                      EESSSS CS
                    RNA_POL_M_15KD 23 eCrqCg 28
                                       Cr Cg
  gi|557694827|ref|YP_008797881.1| 37 VCRRCG 42
                                      599997 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.6
                                      ESSSS-E CS
                    RNA_POL_M_15KD 24 CrqCgYe 30
                                      C+ Cg++
  gi|557694827|ref|YP_008797881.1| 48 CDGCGAK 54
                                      9999975 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1     0.028        56      24      37 ..      10      23 ..       5      25 .. 0.71
   2 ?    7.1   5.1    0.0029       5.7       6      39 ..      36      58 ..      34      59 .. 0.85
   3 ?   -2.7   0.1       3.5     7e+03       8      12 ..      69      73 ..      66      78 .. 0.62

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.028
                       Zn-ribbon_8 24 apltaCPeCgsevr 37
                                      a++++C  Cg+ ++
  gi|557694827|ref|YP_008797881.1| 10 AENIVCRVCGAVAE 23
                                      55677999998655 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgsevrrv 39
                                      Y C++Cg     lq      +++C  Cg++vrr+
  gi|557694827|ref|YP_008797881.1| 36 YVCRRCG-----LQ------PVVCDGCGAKVRRM 58
                                      9999999.....77......566**********7 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.5
                       Zn-ribbon_8  8 CeeCg 12
                                      C +C 
  gi|557694827|ref|YP_008797881.1| 69 CLNCY 73
                                      66664 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 ?    1.9   0.1      0.11   2.1e+02       6      10 ..      15      19 ..       9      24 .. 0.63
   2 ?    4.6   0.5     0.015        31       2      10 ..      33      42 ..      32      44 .. 0.90
   3 ?    5.9   3.9     0.006        12       6      32 ..      48      74 ..      45      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
                      zf-dskA_traR  6 CeeCG 10
                                      C +CG
  gi|557694827|ref|YP_008797881.1| 15 CRVCG 19
                                      66666 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.015
                      zf-dskA_traR  2 iygs.CeeCG 10
                                      ++g+ C +CG
  gi|557694827|ref|YP_008797881.1| 33 GFGYvCRRCG 42
                                      5999*****9 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.006
                      zf-dskA_traR  6 CeeCGEpIpeaRlralPgarlCveCqe 32
                                      C++CG ++    + +l g++lC++C +
  gi|557694827|ref|YP_008797881.1| 48 CDGCGAKVRRMTVTVLRGRTLCLNCYR 74
                                      99999999888877778********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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):               9  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 989.59
//
Query:       gi|557694828|ref|YP_008797882.1|  [L=258]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   22.1   0.0     0.0029   17.5   0.0    2.4  2  HTH_Crp_2        Crp-like helix-turn-helix domain
    0.00031   20.6   1.0     0.0011   18.7   0.1    2.3  2  TrmB             Sugar-specific transcriptional regulator Trm
     0.0033   17.3   0.0      0.022   14.6   0.0    2.2  2  MarR_2           MarR family
     0.0051   16.4   0.0      0.026   14.2   0.0    2.0  2  Crp              Bacterial regulatory proteins, crp family
     0.0072   16.3   0.0      0.034   14.1   0.0    2.0  1  HTH_36           Helix-turn-helix domain
     0.0096   15.8   0.0       0.03   14.2   0.0    1.8  1  MarR             MarR family
  ------ inclusion threshold ------
      0.014   15.7   0.2       0.69   10.3   0.0    2.4  2  Penicillinase_R  Penicillinase repressor
      0.018   14.9   0.3       0.49   10.3   0.0    2.9  3  HTH_5            Bacterial regulatory protein, arsR family
      0.023   14.3   0.1       0.25   10.9   0.0    2.4  2  HTH_24           Winged helix-turn-helix DNA-binding
      0.023   14.6   2.6       0.54   10.2   0.2    2.2  2  DUF3600          Domain of unknown function (DUF3600)
      0.038   13.9   3.7      0.039   13.8   0.8    2.1  3  Apolipoprotein   Apolipoprotein A1/A4/E domain
      0.043   13.6   0.2      0.083   12.7   0.2    1.4  1  Phage_GP20       Phage minor structural protein GP20
      0.081   13.3   0.2       0.19   12.1   0.1    1.6  1  PfUIS3           Plasmodium falciparum UIS3 membrane protein
      0.095   11.3   0.3       0.14   10.8   0.3    1.2  1  SWI-SNF_Ssr4     Fungal domain of unknown function (DUF1750)
       0.14   11.9   0.1       0.38   10.6   0.1    1.7  1  rve_3            Integrase core domain


Domain annotation for each model (and alignments):
>> 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 ?    1.8   0.0      0.19   2.3e+02      29      48 ..      52      71 ..      52      77 .. 0.90
   2 !   17.5   0.0   2.5e-06    0.0029      25      52 ..     224     251 ..     201     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.19
                                      HHTTSSHHHHHHHHHHHHHT CS
                         HTH_Crp_2 29 smlGltretvsrilseLkre 48
                                      +ml  +re ++r+  +L+ +
  gi|557694828|ref|YP_008797882.1| 52 DMLARSREYFNRTVEALQAK 71
                                      68999*********999975 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.5e-06
                                       HHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2  25 eelAsmlGltretvsrilseLkreglis 52 
                                       e  A+ l l +etvs il+ L ++gli+
  gi|557694828|ref|YP_008797882.1| 224 ETCANALSLDPETVSNILKNLHEKGLIQ 251
                                       66799**********************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 ?   -1.0   0.1       1.4   1.7e+03      25      47 ..     127     149 ..     117     151 .. 0.76
   2 !   18.7   0.1   9.6e-07    0.0011       6      54 ..     202     252 ..     201     257 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
                                       HCHHCCCTTSSCHCHHHHHHHHH CS
                              TrmB  25 adeiaeelgvprskvYevLrsLe 47 
                                        + +aee+    + + e LrsL+
  gi|557694828|ref|YP_008797882.1| 127 LENVAEEISYVTPEASEHLRSLM 149
                                       56789999989999999999997 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 9.6e-07
                                       HHHHCCCHCHHHH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB   6 LseyEakvYlaLl..klgpatadeiaeelgvprskvYevLrsLedkGlVer 54 
                                       L++ E  vY ++l  + ++++ ++ a++l ++  +v ++L++L +kGl++ 
  gi|557694828|ref|YP_008797882.1| 202 LTDVEKAVYEYVLgaNIEELDLETCANALSLDPETVSNILKNLHEKGLIQL 252
                                       7999**********999*******************************985 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.4   1.6e+03      31      48 ..      54      71 ..      51      72 .. 0.83
   2 !   14.6   0.0   1.9e-05     0.022      29      54 ..     228     253 ..     226     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.4
                                      HTSSHHHHHHHHHHHHHT CS
                            MarR_2 31 lglsksavsrilkrLvaa 48
                                      l  s+ + +r+++ L+a+
  gi|557694828|ref|YP_008797882.1| 54 LARSREYFNRTVEALQAK 71
                                      667899999******997 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.9e-05
                                       HHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  29 rrlglsksavsrilkrLvaaGLverr 54 
                                        +l l++ +vs+ilk L ++GL++ +
  gi|557694828|ref|YP_008797882.1| 228 NALSLDPETVSNILKNLHEKGLIQLE 253
                                       5799*******************865 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.2   1.5e+03      12      29 ..      54      71 ..      52      71 .. 0.81
   2 !   14.2   0.0   2.2e-05     0.026       9      32 .]     227     250 ..     226     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.2
                                      HTS-HHHHHHHHHHHHHT CS
                               Crp 12 lGlTrETVSRlLtrLrek 29
                                      l+ +rE  +R++  L++k
  gi|557694828|ref|YP_008797882.1| 54 LARSREYFNRTVEALQAK 71
                                      677899999*99999976 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.2e-05
                                       HHHHTS-HHHHHHHHHHHHHTTSE CS
                               Crp   9 AdylGlTrETVSRlLtrLrekGLI 32 
                                       A++l l +ETVS  L+ L ekGLI
  gi|557694828|ref|YP_008797882.1| 227 ANALSLDPETVSNILKNLHEKGLI 250
                                       8999999****************9 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.8e-05     0.034      29      55 .]     224     250 ..     200     250 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                            HTH_36  29 etlakrlglsknTvsraikeLeqlGyi 55 
                                       et a++l l+ +Tvs+++k+L ++G+i
  gi|557694828|ref|YP_008797882.1| 224 ETCANALSLDPETVSNILKNLHEKGLI 250
                                       6779999******************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.5e-05      0.03      24      48 ..     227     251 ..     216     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                       HHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  24 akklgvskstvtrvldrLekkGlie 48 
                                       a++l++++ tv+++l+ L +kGli+
  gi|557694828|ref|YP_008797882.1| 227 ANALSLDPETVSNILKNLHEKGLIQ 251
                                       89*********************96 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.088   1.1e+02      21      80 ..      22      83 ..      11     115 .. 0.77
   2 ?   10.3   0.0   0.00058      0.69      25      52 ..     224     251 ..     202     257 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.088
                                      HHHHHT--GGG---HHHHHHHHHHHHHT..TS-EEEEETTEEEEE----XXXXXXXXXXXXX CS
                   Penicillinase_R 21 kevveeleeekelaysTVktllrrLvkK..gllsrekegrafiYsplvseeeavasavkqll 80
                                       e+ ee+ ++ e a ++    ++rL +K  ++l+r +e       +l+ +++a+a+   + +
  gi|557694828|ref|YP_008797882.1| 22 FEITEEFRARVEKAVTSLNAHIERLNNKyrDMLARSREYFNRTVEALQAKDDAKAKLYASEI 83
                                      58999999999999999999999999885568888887555555777777777777666555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00058
                                       HT--GGG---HHHHHHHHHHHHHTTS-E CS
                   Penicillinase_R  25 eeleeekelaysTVktllrrLvkKglls 52 
                                       e +++  +l ++TV  +l++L++Kgl++
  gi|557694828|ref|YP_008797882.1| 224 ETCANALSLDPETVSNILKNLHEKGLIQ 251
                                       4466668999***************997 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 ?   -1.1   0.0       1.4   1.7e+03      13      24 ..      75      86 ..      74      90 .. 0.79
   2 ?    0.8   0.0      0.38   4.6e+02      30      40 ..     139     149 ..     130     151 .. 0.77
   3 ?   10.3   0.0   0.00041      0.49      19      45 ..     224     250 ..     216     251 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.4
                                      TSSEEHHHHHHH CS
                             HTH_5 13 egelcvcelaee 24
                                      + +l+++e+ae+
  gi|557694828|ref|YP_008797882.1| 75 KAKLYASEIAEI 86
                                      678999****98 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.38
                                       HHHHHHHHHHH CS
                             HTH_5  30 stvShHLkkLr 40 
                                       +  S+HL+ L+
  gi|557694828|ref|YP_008797882.1| 139 PEASEHLRSLM 149
                                       6679****996 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00041
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  19 celaeelglsqstvShHLkkLreaGLV 45 
                                         +a++l l + tvS  Lk L+e GL+
  gi|557694828|ref|YP_008797882.1| 224 ETCANALSLDPETVSNILKNLHEKGLI 250
                                       5689**********************9 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      0.38   4.5e+02      26      42 ..      31      47 ..      30      49 .. 0.80
   2 ?   10.9   0.0   0.00021      0.25      24      48 .]     227     251 ..     227     251 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.38
                            HTH_24 26 rlglSpstvnrrlkrLe 42
                                      r+   ++ +n++++rL 
  gi|557694828|ref|YP_008797882.1| 31 RVEKAVTSLNAHIERLN 47
                                      566778999******95 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00021
                            HTH_24  24 AerlglSpstvnrrlkrLeeeGlIk 48 
                                       A +l l p tv+  lk+L e+GlI+
  gi|557694828|ref|YP_008797882.1| 227 ANALSLDPETVSNILKNLHEKGLIQ 251
                                       77899******************95 PP

>> DUF3600  Domain of unknown function (DUF3600)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00045      0.54      74     139 ..      24      89 ..      22      97 .. 0.86
   2 ?    4.6   0.2     0.024        28      76     146 ..     107     177 ..     101     194 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00045
                           DUF3600  74 iskekreeikkalyelqPyfdklndqpsskevltaeeydqyieallteetvrvklgvssaikveev 139
                                       i++e r  + ka++ l+ + ++ln++       + e +++ +eal  ++  ++kl  s   +++++
  gi|557694828|ref|YP_008797882.1|  24 ITEEFRARVEKAVTSLNAHIERLNNKYRDMLARSREYFNRTVEALQAKDDAKAKLYASEIAEIKKL 89 
                                       77888999*****************9755545567889****************999988888765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.024
                           DUF3600  76 kekreeikkalyelqPyfdklndqpsskevltaeeydqyieallteetvrvklgvssaikveevPeelkee 146
                                        e  +e+ +al+ l+P    l++       +t e  ++    ++  +  ++ +gv+  ++ e++Pe  +e 
  gi|557694828|ref|YP_008797882.1| 107 LESILELGEALTLLKPLATLLENVAEEISYVTPEASEHLRSLMVMIDDFMATAGVYVEPSSEKMPEFSEEA 177
                                       566778888888888888888877777777777666655444556799*****************976653 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.8   3.2e-05     0.039     115     168 ..      24      77 ..      23      91 .. 0.86
   2 ?   -0.3   0.1      0.72   8.6e+02       4      25 ..     154     175 ..     115     208 .. 0.54
   3 ?   -0.7   0.0       0.9   1.1e+03       3      45 ..     153     195 ..     151     225 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                                       HHHHHCHHHHHHHHHHHHHHHHHHH-----..-----SSSHHHHHHHTS-TTSH CS
                    Apolipoprotein 115 lkarlapyveelrqklaerleelkeslaphaeeveerlssrveelrekleeqae 168
                                       + + + + ve+++++l +++e l+++ ++ +++++e ++++ve+l++k +++a+
  gi|557694828|ref|YP_008797882.1|  24 ITEEFRARVEKAVTSLNAHIERLNNKYRDMLARSREYFNRTVEALQAKDDAKAK 77 
                                       678899999999999999999999999999999999999999999999777665 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.72
                                       HCCCCHHHHHCCHHHCHHCHHH CS
                    Apolipoprotein   4 esldelkayaeeleeqlaplaq 25 
                                       + ++++  y+e  +e++ ++++
  gi|557694828|ref|YP_008797882.1| 154 DFMATAGVYVEPSSEKMPEFSE 175
                                       3333333333333333333333 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.9
                                       HHCCCCHHHHHCCHHHCHHCHHHHHHHHHHHHHHHHHHHHHHH CS
                    Apolipoprotein   3 eesldelkayaeeleeqlaplaqelrdrlskeleelrarlrae 45 
                                       ++ ++++  y+e  +e++ ++++e+   l+++ + + +++r+ 
  gi|557694828|ref|YP_008797882.1| 153 DDFMATAGVYVEPSSEKMPEFSEEASFILEEARKIAAEKVRET 195
                                       5666666666666666666666666655555555555555444 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 ?   12.7   0.2   6.9e-05     0.083      15      82 ..      24      89 ..      12      97 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
                        Phage_GP20 15 itkakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkld 82
                                      it++  ++ve+++++l+  ++  +++  d+ +     e  ++++e lqak +++ + y+++ia++k+ 
  gi|557694828|ref|YP_008797882.1| 24 ITEEFRARVEKAVTSLNAHIERLNNKYRDMLAR--SREYFNRTVEALQAKDDAKAKLYASEIAEIKKL 89
                                      667777889999999999999999999998666..99***************************9975 PP

>> PfUIS3  Plasmodium falciparum UIS3 membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00016      0.19      25      80 ..      29      84 ..      24      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHHHHHHHHS-HHHHHHHTT-HHHHHHHHHHHHHHTT----HHHHHHH CS
                            PfUIS3 25 nifvdivklaiqkhfedlsndqkdslvndyeylrkivqtldesrdvslskaqedka 80
                                         v+++  +++ h+e l n+ +d l    ey+++ v++l+ + d +   +  ++a
  gi|557694828|ref|YP_008797882.1| 29 RARVEKAVTSLNAHIERLNNKYRDMLARSREYFNRTVEALQAKDDAKAKLYASEIA 84
                                      556778888999*****************************998887766666665 PP

>> SWI-SNF_Ssr4  Fungal domain of unknown function (DUF1750)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.3   0.00012      0.14     350     383 ..      24      57 ..      18      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                      SWI-SNF_Ssr4 350 kaeeFrkrvaekveetkaeieklkaeHakrlakl 383
                                         eeFr rv++ v + +a ie+l+++   +la+ 
  gi|557694828|ref|YP_008797882.1|  24 ITEEFRARVEKAVTSLNAHIERLNNKYRDMLARS 57 
                                       579***********************99999864 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00032      0.38      15      42 ..      39      67 ..      31      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                             rve_3 15 qNglvEsfngtlrdellneel.frslaea 42
                                       N+++E++n+++rd l  ++  f +  ea
  gi|557694828|ref|YP_008797882.1| 39 LNAHIERLNNKYRDMLARSREyFNRTVEA 67
                                      59**************9999974444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1404  (0.0783089); expected 358.6 (0.02)
Passed bias filter:                      960  (0.0535445); expected 358.6 (0.02)
Passed Vit filter:                       123  (0.00686039); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 1951.01
//
Query:       gi|557694829|ref|YP_008797883.1|  [L=380]
Description: AAA family ATPase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  134.2   0.0    4.8e-37  127.3   0.0    2.5  2  AAA            ATPase family associated with various cellular
    4.8e-11   42.6   1.7    1.6e-10   40.9   1.7    1.9  1  MIT            MIT (microtubule interacting and transport) do
    1.5e-09   37.5   0.0    3.5e-09   36.3   0.0    1.7  1  AAA_lid_3      AAA+ lid domain
    2.4e-07   31.0   0.0    6.5e-07   29.6   0.0    1.7  1  AAA_2          AAA domain (Cdc48 subfamily)
    5.5e-07   29.9   0.1    9.7e-05   22.7   0.0    2.9  2  AAA_22         AAA domain
    7.2e-07   29.3   0.0    2.4e-06   27.6   0.0    1.9  1  AAA_5          AAA domain (dynein-related subfamily)
    3.1e-06   27.1   0.4    0.00011   22.1   0.0    2.5  2  Vps4_C         Vps4 C terminal oligomerisation domain
    6.3e-06   26.7   0.0     0.0023   18.3   0.0    2.7  2  AAA_16         AAA ATPase domain
    3.5e-05   23.6   0.0    9.3e-05   22.2   0.0    1.7  1  RuvB_N         Holliday junction DNA helicase RuvB P-loop dom
    8.7e-05   22.6   0.0    0.00032   20.7   0.0    1.9  2  AAA_14         AAA domain
    0.00093   18.5   0.6      0.005   16.1   0.0    2.3  3  TIP49          TIP49 P-loop domain
     0.0021   18.4   0.0      0.018   15.4   0.0    2.6  2  RNA_helicase   RNA helicase
     0.0025   18.0   0.0     0.0056   16.8   0.0    1.7  1  AAA_33         AAA domain
     0.0027   17.3   0.0     0.0099   15.4   0.0    1.8  1  AAA_7          P-loop containing dynein motor region
     0.0035   16.9   0.1      0.011   15.3   0.0    1.8  1  AAA_25         AAA domain
     0.0052   17.3   0.0       0.17   12.4   0.0    2.3  2  ABC_tran       ABC transporter
     0.0069   15.8   0.0      0.018   14.4   0.0    1.7  1  Mg_chelatase   Magnesium chelatase, subunit ChlI
     0.0073   16.3   0.0        1.2    9.0   0.0    2.9  3  ATPase_2       ATPase domain predominantly from Archaea
     0.0086   15.4   0.0        2.1    7.6   0.0    2.5  2  ATPase         KaiC
     0.0087   15.8   0.0      0.017   14.8   0.0    1.5  1  IstB_IS21      IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.011   16.0   0.0      0.036   14.3   0.0    2.0  1  AAA_28         AAA domain
      0.015   15.8   0.0      0.055   14.0   0.0    2.0  2  AAA_18         AAA domain
      0.033   13.9   0.0       0.06   13.1   0.0    1.4  1  AAA_24         AAA domain
      0.058   13.8   0.0       0.19   12.2   0.0    2.0  1  AAA_17         AAA domain
      0.064   12.9   0.0       0.11   12.1   0.0    1.3  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
      0.066   12.4   0.0       0.21   10.8   0.0    1.6  2  KAP_NTPase     KAP family P-loop domain
       0.07   12.6   0.0       0.15   11.5   0.0    1.5  1  PhoH           PhoH-like protein
      0.071   13.4   0.5        1.4    9.3   0.0    3.0  2  TPR_8          Tetratricopeptide repeat
      0.081   12.9   0.0       0.29   11.1   0.0    1.8  2  ResIII         Type III restriction enzyme, res subunit
      0.092   12.7   0.0       0.21   11.5   0.0    1.6  1  NACHT          NACHT domain
       0.11   11.8   0.0        0.3   10.3   0.0    1.7  1  Zeta_toxin     Zeta toxin
       0.11   12.6   0.0       0.31   11.1   0.0    1.7  1  Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
       0.12   12.6   0.5       0.71   10.1   0.1    2.3  2  TPR_2          Tetratricopeptide repeat


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 !  127.3   0.0   8.8e-40   4.8e-37       1     132 []     144     278 ..     144     278 .. 0.95
   2 ?    4.4   0.0     0.088        48      39      98 ..     323     377 ..     302     380 .] 0.78

  Alignments for each domain:
  == domain 1  score: 127.3 bits;  conditional E-value: 8.8e-40
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakeka...kpsilfiDEidalaksr 74 
                                       +ll+GppG+GKTlla ava el+++f+ +++++++sk++gese++++++f++++++a   kp+i+fiDEid+l+ +r
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAELDASFYVLDAASIMSKWLGESERNVSKIFNQCRQEArngKPCIIFIDEIDSLTAER 220
                                       69******************************************************9**999************999 PP

                                       TTCCCHHHHHHHHHHHHHHHHTTTS..SSTEEEEEEESSGGGSTHHHHSTTSSEEEETTS CS
                               AAA  75 sgseseeeervvnqLlteldgvkkk..eskvivigatnrpdkldpallrgRfdrkieiel 132
                                          e + e rv nqL++e+dg  +k  ++ + v++atn+p++ld++++ +Rf+++i+++l
  gi|557694829|ref|YP_008797883.1| 221 -FMEVGGEARVRNQLIKEMDGILDKgrRDFLYVLAATNKPWHLDEPFI-RRFQKRIFVPL 278
                                       .6688899*************988866566899***************.7******9985 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.088
                                       TTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTT CS
                               AAA  39 vgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkk 98 
                                       ++++ k ++e+f++   ++ +p  + +D++ +++k+r      +++ v++ L + ld+ +k
  gi|557694829|ref|YP_008797883.1| 323 MEAQLKVVSEFFASNTGEKgEPRPITMDDFMEIIKKR------KQSVVLENLKKLLDWNSK 377
                                       555566677777764444468999*************......899999999999999887 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 !   40.9   1.7     3e-13   1.6e-10       4      65 .]      15      77 ..      14      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 3e-13
                               MIT  4 AlelvkkAveeDnagnyeeAlelYkealelLlqalk.ekneerrellrekieeYleRaeeLke 65
                                      A + +++Av++D++g+  +A++ Y+ea+++L ++ +   + + +  + eki+eY++R+eeL++
  gi|557694829|ref|YP_008797883.1| 15 AASRAREAVQYDRSGQRHKAIKSYREAIDVLWKLYRlSPDGTVKRIYAEKIKEYQARIEELQN 77
                                      566789******************************66888********************86 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   6.5e-12   3.5e-09       2      45 .]     301     354 ..     300     354 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 6.5e-12
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAallAlrr.........gike.itmedfee 45 
                                       v l++LA+ T+GyS AD+  +c eA l  +++         g++  itm+df+e
  gi|557694829|ref|YP_008797883.1| 301 VELSQLAKITDGYSAADIHDICMEAQLKVVSEffasntgekGEPRpITMDDFME 354
                                       889*************************999988877766566667*****986 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.2e-09   6.5e-07       6     100 ..     144     235 ..     142     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.2e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                       ill gp g+Gkt+la a+a  l++    ++ ++da +++     e+e+ vs+   +     +  +  i+++DEid  
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAELDA----SFYVLDAASIMSkwLGESERNVSKIFNQCRQEARNGKPCIIFIDEIDSL 216
                                       7899*******************6....************776789999999999999999999999********99 PP

                                       ------------H.HHHHHHH CS
                             AAA_2  81 hpkessgadvSre.gVqrdLL 100
                                       ++  +   +v +e  V + L 
  gi|557694829|ref|YP_008797883.1| 217 TA--ERFMEVGGEaRVRNQLI 235
                                       98..45555555423555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       7.9   4.3e+03      40      70 ..      42      74 ..      23     102 .. 0.67
   2 !   22.7   0.0   1.8e-07   9.7e-05       8     109 ..     144     221 ..     141     241 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 7.9
                            AAA_22 40 pevv..fvtlpsstsskdllrellralglelka 70
                                       +v+  ++ l+ +++ k ++ e  ++++ + ++
  gi|557694829|ref|YP_008797883.1| 42 IDVLwkLYRLSPDGTVKRIYAEKIKEYQARIEE 74
                                      444466777788888888887777777766555 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 1.8e-07
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeq 84 
                                       ++++G++G+GKT+l++ ++ +l         +++++  +++s       +++ l + ++       + + ++++++q
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAEL---------DASFYVLDAASI------MSKWLGESER-------NVSKIFNQCRQ 198
                                       799*******************.........788777766554......4666666664.......777899***** PP

                            AAA_22  85 alraravielliiDEaqhlrseeal 109
                                        +r+ +   ++ iDE++ l ++e +
  gi|557694829|ref|YP_008797883.1| 199 EARNGKP-CIIFIDEIDSL-TAERF 221
                                       ******9.**********9.65544 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 !   27.6   0.0   4.4e-09   2.4e-06       2     138 .]     144     270 ..     143     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.4e-09
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------......G-SEEEEE CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar......egeilvlD 72 
                                       +lL GppG+gK+ la  +aa l +++ +    + +++     +r++         s++ +++r      +++i+++D
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAELDASFYVLDAASIMSKWLGESERNV---------SKIFNQCRqearngKPCIIFID 211
                                       89**********************9988877776666655666666.........6666666666668999****** PP

                                       SGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  73 EveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                       E++ +  e ++++      r  l+ e+++  ++ + d    ++v+a++n++      l++++++Rf
  gi|557694829|ref|YP_008797883.1| 212 EIDSLTAERFMEVGGEARVRNQLIKEMDGILDKGRRD---FLYVLAATNKPW----HLDEPFIRRF 270
                                       ***9999999999999999999999998888887754...278999999999....8999999998 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 ?    2.5   0.1      0.27   1.5e+02      38      55 ..     100     117 ..      97     120 .. 0.88
   2 !   22.1   0.0   2.1e-07   0.00011      23      61 .]     340     379 ..     323     379 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.27
                            Vps4_C  38 lkkarptVskeDLekhee 55 
                                       l++ +p Vs +D+ ++ee
  gi|557694829|ref|YP_008797883.1| 100 LQSEKPNVSWDDIVNIEE 117
                                       8999*********99886 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 2.1e-07
                            Vps4_C  23 klleP.pvtlkDflkalkkarptVskeDLekheeFTkefG 61 
                                       +  eP p+t++Df++++kk + +V  e L+k+ ++ ++ G
  gi|557694829|ref|YP_008797883.1| 340 EKGEPrPITMDDFMEIIKKRKQSVVLENLKKLLDWNSKHG 379
                                       556777*****************************87765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.2e-06    0.0023      24      56 ..     141     172 ..     136     181 .. 0.88
   2 ?    5.5   0.0     0.038        21     120     149 ..     190     218 ..     173     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.2e-06
                            AAA_16  24 pelvllsGesGvGKsslvrellralekdggifl 56 
                                       p+ +ll G++G+GK+ l+ +++ +l ++ +++l
  gi|557694829|ref|YP_008797883.1| 141 PRGILLFGPPGCGKTLLAAAVAAELDAS-FYVL 172
                                       689*******************999998.7775 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.038
                            AAA_16 120 lellkrllallsrderplvlvlDdlqwade 149
                                          ++++ + +++ ++p ++++D+++ + +
  gi|557694829|ref|YP_008797883.1| 190 SKIFNQCRQEARN-GKPCIIFIDEIDSLTA 218
                                       5556666677777.999*********7665 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 !   22.2   0.0   1.7e-07   9.3e-05      36      97 ..     144     217 ..     139     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.7e-07
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleekd......vlfideihrls 97 
                                       +ll+GpPG Gkt la+ +a+el++++ +  +  +      e +++++ ++++ +++       ++fidei  l+
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAELDASFYVLDAASImskwlgESERNVSKIFNQCRQEArngkpcIIFIDEIDSLT 217
                                       89**********************99876655542222234567888888887654333445588999998775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       5.7   3.1e+03      63      85 ..     102     124 ..      63     129 .. 0.76
   2 !   20.7   0.0   5.8e-07   0.00032       5      90 ..     144     245 ..     141     273 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.7
                            AAA_14  63 ekktylflDEiqevpewekalks 85 
                                       ++k  +  D i +++e++ka+++
  gi|557694829|ref|YP_008797883.1| 102 SEKPNVSWDDIVNIEEAKKAIRE 124
                                       35666888999999999999886 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 5.8e-07
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe....kllelileklkeekktylflDEiqev. 76 
                                       +++ G+  +GKT l+  ++ el     s+  ++  +   k l ++e    k+ + +++++++ k  ++f+DEi  + 
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAELD---ASFYVLDAASIMSKWLGESErnvsKIFNQCRQEARNGKPCIIFIDEIDSLt 217
                                       6899***************9988...888888888888866655552112344444444434566669*****9987 PP

                            AAA_14  77 ..............pewekalkslvdeg 90 
                                                     +++ k + +++d+g
  gi|557694829|ref|YP_008797883.1| 218 aerfmevggearvrNQLIKEMDGILDKG 245
                                       7777777766666666666666666666 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.8   1.5e+03     163     181 ..      97     117 ..      35     125 .. 0.54
   2 !   16.1   0.0   9.2e-06     0.005      51      93 ..     142     182 ..     139     194 .. 0.86
   3 ?    0.6   0.0      0.48   2.6e+02     254     295 ..     177     221 ..     172     224 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.8
                                       HHHHH..HHT--TT-EEEEET CS
                             TIP49 163 aeell..kekvkegDviviek 181
                                        ++l+  k +v+ +D++ ie+
  gi|557694829|ref|YP_008797883.1|  97 RQQLQseKPNVSWDDIVNIEE 117
                                       233330033455566666665 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 9.2e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslev 93 
                                       r++Ll Gp+g Gkt la a++ el     f +l ++ + s  +
  gi|557694829|ref|YP_008797883.1| 142 RGILLFGPPGCGKTLLAAAVAAELD--ASFYVLDAASIMSKWL 182
                                       89**********************8..6789999998888655 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.48
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXX CS
                             TIP49 254 iteklreeinkkvakyveegkaeivpG...vlfiDevhmlDiecf 295
                                       i +k   e ++ v+k  ++ + e   G   ++fiDe+  l  e f
  gi|557694829|ref|YP_008797883.1| 177 IMSKWLGESERNVSKIFNQCRQEARNGkpcIIFIDEIDSLTAERF 221
                                       5556666677777777777666654433339*******9999988 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   3.3e-05     0.018       1      27 [.     144     175 ..     144     258 .. 0.77
   2 ?   -0.5   0.0       2.9   1.6e+03      53      85 ..     347     364 ..     300     378 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.3e-05
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl.....k 27 
                                       i+l+Gp+g+GK++la  +a++l  ++      
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAELDASFyvldaA 175
                                       689**************999998777433331 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.9
                      RNA_helicase  53 vvidDfgqvkdeenpsdlaelirlvsstpypln 85 
                                       +                + +++++++  +  + 
  gi|557694829|ref|YP_008797883.1| 347 I---------------TMDDFMEIIKKRKQSVV 364
                                       2...............34444444444444444 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     1e-05    0.0056       2      40 ..     144     184 ..     144     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1e-05
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgt 40 
                                       +ll G+pG+GK+ la  ++++l+  +++l+  +++++  g+
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAELDasFYVLDAASIMSKWLGE 184
                                       6899*******************887777777766655553 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 !   15.4   0.0   1.8e-05    0.0099      36     117 ..     144     221 ..     141     236 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                             AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrkgvygPpggkklvvFvDDlnmp 112
                                       +ll Gp G+GKt+++  +  +ld + y+    ++ ++   ++  + + + +++ r     + +gk +++F+D+++  
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAELDASFYVLDAASIMSKWLGES-ERNVSKIFNQCR---QEARNGKPCIIFIDEIDSL 216
                                       89*********************7777766666665544333.333333343333...357899*********9988 PP

                             AAA_7 113 akeky 117
                                       + e++
  gi|557694829|ref|YP_008797883.1| 217 TAERF 221
                                       88876 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     2e-05     0.011      12      56 ..     122     164 ..     113     168 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-05
                            AAA_25  12 vadlaapppprrwlvk.gllpagelallaGapgtGKttlaldlala 56 
                                       ++++ + p++r +l++ g+ p+g  +ll+G+pg+GKt la  +a++
  gi|557694829|ref|YP_008797883.1| 122 IRESIVFPTRRPDLFPlGW-PRG--ILLFGPPGCGKTLLAAAVAAE 164
                                       5667778899999999677.877..78*************999986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.34   1.9e+02      40      98 ..      21      85 ..      11     108 .. 0.81
   2 !   12.4   0.0   0.00032      0.17      15      67 ..     145     195 ..     142     266 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.34
                                      EEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH......HHHTCHHHHHHHSTTGGTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 40 Geilldgkdlkeqeleslrkeigvlpqepqlfpeltvren......esdeeiekalsklglkelk 98
                                      + +++d    +++ ++s+r+ i vl +  +l p+ tv++       e++++ie++ + ++ + ++
  gi|557694829|ref|YP_008797883.1| 21 EAVQYDRSGQRHKAIKSYREAIDVLWKLYRLSPDGTVKRIyaekikEYQARIEELQNGVEGPSVR 85
                                      567777777777899********************999999999998888899998888877654 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00032
                                       EEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  15 aivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe 67 
                                        ++G+ G+GK+ L++++a +l+  +  + ld +++ ++ l +++++++ ++ +
  gi|557694829|ref|YP_008797883.1| 145 LLFGPPGCGKTLLAAAVAAELDA-SFYV-LDAASIMSKWLGESERNVSKIFNQ 195
                                       689*****************984.4444.788888888888888888888877 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.3e-05     0.018      25      44 ..     144     163 ..     141     191 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.3e-05
                      Mg_chelatase  25 lllvGppGsGKtmlakrlps 44 
                                       +ll+GppG+GKt+la+++++
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAA 163
                                       89*************99875 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 !    9.0   0.0    0.0021       1.2      23      50 ..     144     170 ..     140     177 .. 0.80
   2 ?    3.3   0.0      0.12        67     103     131 ..     186     217 ..     172     256 .. 0.64
   3 ?   -1.9   0.0       4.7   2.5e+03     122     149 ..     347     372 ..     318     378 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0021
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdky 50 
                                       ++++Gp g+GKt L   ++ +l d ++y
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAEL-DASFY 170
                                       679*********9999888888.44444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                          ATPase_2 103 fkaielllekikkkgkk...iiiiiDelqkli 131
                                       ++++++++++ +++++     ii+iDe+  l 
  gi|557694829|ref|YP_008797883.1| 186 ERNVSKIFNQCRQEARNgkpCIIFIDEIDSLT 217
                                       44455555555555444444778888876654 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.7
                          ATPase_2 122 iiiDelqklidlglngaellvkeLlnli 149
                                       i +D++ ++i  + +++  ++++L +l+
  gi|557694829|ref|YP_008797883.1| 347 ITMDDFMEII--KKRKQSVVLENLKKLL 372
                                       4456666666..5555555555555554 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0039       2.1      21      37 ..     143     159 ..     134     164 .. 0.85
   2 ?    5.4   0.0     0.019        10      82     142 ..     168     226 ..     160     241 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0039
                            ATPase  21 vvlitGepGtGKtifal 37 
                                        +l+ G pG+GKt++a+
  gi|557694829|ref|YP_008797883.1| 143 GILLFGPPGCGKTLLAA 159
                                       489************97 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.019
                            ATPase  82 klaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaRe 142
                                       +++++da++ +++    +++ +++++ ++ ++  ++ k   + iD i++l + e+ +++  
  gi|557694829|ref|YP_008797883.1| 168 SFYVLDAASIMSKWLG-ESERNVSKIFNQCRQEARNGKPCIIFIDEIDSL-TAERFMEVGG 226
                                       5889999998877444.8999*****************************.5555555444 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 !   14.8   0.0   3.2e-05     0.017      49      70 ..     143     164 ..     138     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.2e-05
                         IstB_IS21  49 nivllGpsGvGKshlaialgve 70 
                                       +i+l+Gp+G GK+ la+a++ e
  gi|557694829|ref|YP_008797883.1| 143 GILLFGPPGCGKTLLAAAVAAE 164
                                       699***************9876 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.6e-05     0.036       2      72 ..     144     204 ..     143     269 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.6e-05
                            AAA_28   2 ivitGgestGKTtlleaLaar..gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaaaa 72 
                                       i ++G++++GKT l++a aa+     +v +aa  + + +++++++ ++              +q ++ea++ +
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAEldASFYVLDAASIMSKWLGESERNVSKIF------------NQCRQEARNGK 204
                                       789****************9874444678888888888888777644332............23344444444 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    0.0001     0.055       1      25 [.     144     183 ..     144     265 .. 0.72
   2 ?   -2.0   0.0         9   4.9e+03      72      84 ..     342     354 ..     300     377 .. 0.55

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.0001
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf..............g 25 
                                       Ill G+pG+GKt la +++ +l ++              g
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAELdASfyvldaasimskwlG 183
                                       99****************9998433455544433333330 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 9
                            AAA_18  72 eegknlvidghla 84 
                                       +e+ ++ +d++++
  gi|557694829|ref|YP_008797883.1| 342 GEPRPITMDDFME 354
                                       4444444444333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011      0.06       5      78 ..     144     217 ..     141     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                            AAA_24   5 iliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie......swedfldevvelaaeladyktlviDtid 75 
                                       il++Gp+g GKT la+          +++++  lda+ + +        ++ ++ +++ + a++ +++ +++iD id
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAV-----AAELDASFYVLDAASIMSKWlgeserNVSKIFNQCRQEARNGKPC-IIFIDEID 214
                                       89*************999.....444455555555555442224443448888888888888888887.89999999 PP

                            AAA_24  76 ele 78 
                                        l 
  gi|557694829|ref|YP_008797883.1| 215 SLT 217
                                       885 PP

>> AAA_17  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      0.19       1      35 [.     147     183 ..     147     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00034
                                       EE-TTSSHHHHHHHHHHHH..TEEEEEHHHHHHHHHH CS
                            AAA_17   1 lGgPGsGKgtqceklveky..gfthlsaGdllreeak 35 
                                       +G+PG+GK+ +++ ++ ++   f +l a +++ +   
  gi|557694829|ref|YP_008797883.1| 147 FGPPGCGKTLLAAAVAAELdaSFYVLDAASIMSKWLG 183
                                       6****************99556777888888876654 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 ?   12.1   0.0    0.0002      0.11       8      87 ..     135     221 ..     134     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                       HS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS.....S.EEEEEEESEEHHHHHHHHHHCHHSS.GGGGEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                       ATP-synt_ab   8 lfpivqGqrtlipgafgvGktvisqslskqsnsd.....d.aiiyvgiGergnevaevleefpegt.imkrtvlvan 77 
                                       lfp++    +l++g  g+Gkt ++++++ + +++        i     Ge +++v++++++ +++    k +++++ 
  gi|557694829|ref|YP_008797883.1| 135 LFPLGWPRGILLFGPPGCGKTLLAAAVAAELDASfyvldAaSIMSKWLGESERNVSKIFNQCRQEArNGKPCIIFID 211
                                       68888888899*****************99755566663223344559*************9996647778888888 PP

                                       ETTS-HHHHH CS
                                       xxxxxxxxxx RF
                       ATP-synt_ab  78 tsnepvaare 87 
                                       + ++ +a+r+
  gi|557694829|ref|YP_008797883.1| 212 EIDSLTAERF 221
                                       8888887776 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 ?   -2.3   0.0       3.8   2.1e+03      25      46 ..     146     167 ..     141     182 .. 0.80
   2 ?   10.8   0.0   0.00039      0.21     160     193 ..     188     224 ..     177     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.8
                        KAP_NTPase  25 LygkWGsGKssllnkledelke 46 
                                       L g+ G+GK+ l + +  el+ 
  gi|557694829|ref|YP_008797883.1| 146 LFGPPGCGKTLLAAAVAAELDA 167
                                       667779****999988888765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00039
                        KAP_NTPase 160 lladmektLda...lqkrlVvviDdLDrceteevlql 193
                                       + +++++  ++   + k+ +++iD++D+++ e+ +++
  gi|557694829|ref|YP_008797883.1| 188 NVSKIFNQCRQearNGKPCIIFIDEIDSLTAERFMEV 224
                                       5566666666567889*****************9987 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00028      0.15      23      43 ..     145     165 ..     142     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00028
                                       EEE--TTSSTTHHHHHHHHHH CS
                              PhoH  23 faiGpaGtGKtylavalavea 43 
                                         +Gp G+GKt+la a+a+e+
  gi|557694829|ref|YP_008797883.1| 145 LLFGPPGCGKTLLAAAVAAEL 165
                                       579**************9875 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0026       1.4      11      29 ..      25      43 ..      21      44 .. 0.93
   2 ?    0.5   0.1       1.8   9.5e+02      16      28 ..     114     126 ..     114     126 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0026
                                      HHHTT-HHHHHHHHHHHHH CS
                             TPR_8 11 ylklgdyeeAkeyyekale 29
                                      y+  g+ ++A+++y++a++
  gi|557694829|ref|YP_008797883.1| 25 YDRSGQRHKAIKSYREAID 43
                                      8899*************96 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.8
                                       -HHHHHHHHHHHH CS
                             TPR_8  16 dyeeAkeyyekal 28 
                                       ++eeAk+++++ +
  gi|557694829|ref|YP_008797883.1| 114 NIEEAKKAIRESI 126
                                       689*****99875 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 ?   11.1   0.0   0.00054      0.29      27      84 ..     144     195 ..     115     221 .. 0.78
   2 ?    0.3   0.0       1.2   6.3e+02     122     147 ..     194     219 ..     175     256 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00054
                                       EEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.... CS
                            ResIII  27 glikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke 84 
                                       +l+  + G+GKTl+aa+++++l  ++       + +  s+++++l e ++  s+ +++
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAELDASF------YVLDAASIMSKWLGESERNVSKIFNQ 195
                                       5677789****************984......48899999999997766666655443 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.2
                                       .....HHHTTT-SEEEEETGGGTTS. CS
                            ResIII 122 eeeseellrdrfdviiiDEaHrlgak 147
                                       ++ ++e+++++  +i+iDE   l+a+
  gi|557694829|ref|YP_008797883.1| 194 NQCRQEARNGKPCIIFIDEIDSLTAE 219
                                       66677888888889999998777774 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00038      0.21       3      26 ..     144     167 ..     142     178 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00038
                                       EEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawae 26 
                                       ++l G++G+GKT L++ +a ++ +
  gi|557694829|ref|YP_008797883.1| 144 ILLFGPPGCGKTLLAAAVAAELDA 167
                                       7899**************998865 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   0.00055       0.3      16      44 ..     141     167 ..     136     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00055
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqg 44 
                                       P  ill G pG+GK+ la+++++el+   
  gi|557694829|ref|YP_008797883.1| 141 PRGILLFGPPGCGKTLLAAAVAAELD--A 167
                                       67799*******************94..4 PP

>> Lipase_GDSL_3  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00058      0.31      53     145 ..     160     256 ..     152     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00058
                     Lipase_GDSL_3  53 dvlaevdasvfvldllpNasa..eeirerleyfvktlrka.hPktp.illvedlsttkglvdeklekeveaknkale 125
                                       +v ae+das++vld  + +s+   e ++ + ++ ++ r++ +  +p i+++++++  +++   +++ e +  n+ ++
  gi|557694829|ref|YP_008797883.1| 160 AVAAELDASFYVLDAASIMSKwlGESERNVSKIFNQCRQEaRNGKPcIIFIDEIDSLTAERFMEVGGEARVRNQLIK 236
                                       5679***********999665223455556666666654313344439999999988877777799999999***** PP

                     Lipase_GDSL_3 126 elvkklkkekekklylissk 145
                                       e+   l k ++  ly++++ 
  gi|557694829|ref|YP_008797883.1| 237 EMDGILDKGRRDFLYVLAAT 256
                                       *9999988888888988765 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1    0.0013      0.71       6      29 ..      20      43 ..      15      44 .. 0.89
   2 ?   -0.6   0.0       3.5   1.9e+03      16      28 ..     114     126 ..     114     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0013
                             TPR_2  6 nlGlayyklgdyeeAleafekAle 29
                                      + +  y ++g+  +A++ +++A+ 
  gi|557694829|ref|YP_008797883.1| 20 REAVQYDRSGQRHKAIKSYREAID 43
                                      67889*****************95 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 3.5
                             TPR_2  16 dyeeAleafekAl 28 
                                       + eeA++a ++++
  gi|557694829|ref|YP_008797883.1| 114 NIEEAKKAIRESI 126
                                       6799***999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); 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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.38
# Mc/sec: 2961.76
//
Query:       gi|557694830|ref|YP_008797884.1|  [L=584]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  126.0   0.0    1.7e-36  125.7   0.0    1.1  1  SMC_N          RecF/RecN/SMC N terminal domain
    5.2e-18   66.3   0.1    5.2e-18   66.3   0.1    2.2  2  AAA_23         AAA domain
    2.1e-12   47.4   0.1    5.3e-11   42.8   0.1    2.6  1  AAA_15         AAA ATPase domain
    3.6e-11   43.4   2.6    8.1e-06   25.9   0.0    2.8  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    0.00035   20.2   0.0     0.0017   18.0   0.0    2.0  2  AAA_29         P-loop containing region of AAA domain
     0.0012   19.4   2.5      0.014   16.0   2.5    3.0  1  ABC_tran       ABC transporter
     0.0036   16.9   0.0     0.0036   16.9   0.0    3.2  4  AAA_27         AAA domain
  ------ inclusion threshold ------
      0.022   15.0  23.7      0.022   15.0   3.4    2.4  2  Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
      0.089   12.5   2.2        1.2    8.8   0.3    2.7  2  Med4           Vitamin-D-receptor interacting Mediator subuni
        0.1   12.9   0.1        5.6    7.3   0.0    3.4  3  DUF948         Bacterial protein of unknown function (DUF948)
       0.13   12.2   0.0       0.89    9.4   0.0    2.3  2  RsgA_GTPase    RsgA GTPase
       0.28   10.9   1.8        2.2    7.9   0.2    2.4  2  MctB           Copper transport outer membrane protein, MctB
       0.34   10.9   2.6       0.85    9.6   0.2    2.4  2  ApoO           Apolipoprotein O
       0.43   11.1   3.1       0.45   11.1   0.2    2.4  2  Di19_C         Stress-induced protein Di19, C-terminal
       0.69   10.0   4.6        1.2    9.2   2.0    2.4  2  DUF87          Helicase HerA, central domain
       0.83   10.0   5.2        0.4   11.0   1.9    2.2  1  Flu_NS2        Influenza non-structural protein (NS2)
          5    7.5   8.2        4.8    7.5   0.7    2.9  2  Rx_N           Rx N-terminal domain
        5.6    5.5  13.9        6.1    5.4   0.0    2.8  3  AAA_13         AAA domain
        7.9    5.3  20.0        3.7    6.4   9.5    2.7  3  Spc7           Spc7 kinetochore protein
        8.7    6.8   7.1        4.9    7.6   1.0    3.2  3  FlaC_arch      Flagella accessory protein C (FlaC)


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 !  125.7   0.0   1.9e-39   1.7e-36       1     212 [.      12     559 ..      12     566 .. 0.96

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 1.9e-39
                                       EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkka 77 
                                       +++++++enF s   +   +p+ +++++ivGpNG+GKs++l Ai+  LG+ ++ + r ++l dli +       ++a
  gi|557694830|ref|YP_008797884.1|  12 YIREVILENFMSH--EYSRIPLRRGLNVIVGPNGAGKSSILLAISVALGQ-TY-TERGQRLADLIRR-----GYESA 79 
                                       6999*********..799*******************************4.55.78**********8.....899** PP

                                       EEEEEEEETTEE.....SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.............. CS
                                       xxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                             SMC_N  78 eveitfdnedkk.....lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.............. 135
                                       +v+++fdn   +      +i+++ v+i+r +k++ge  +++n++  tk+ev +ll++ gi+++              
  gi|557694830|ref|YP_008797884.1|  80 RVAVVFDNRPVDgvrpiPSINSDTVTITRFLKKTGEYWHYVNNRFKTKAEVGNLLSRIGINPDnvliimhqnmieqf 156
                                       ******9998887788788999******************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|557694830|ref|YP_008797884.1| 157 vsrdsreklalieeavgaaglrerirdteaklsallaeeavlrktldearsavefwreeyekltilrrleerrklle 233
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|557694830|ref|YP_008797884.1| 234 leylwslvreaeksrerleekiesirretesleakitearntvstyyqslvkglregwservlmetvdgivaaaesl 310
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|557694830|ref|YP_008797884.1| 311 grflerreiredelrqlryevtaldkeiirrrgeaeakgprtdtgrkpaevseeikavglqiaalgtpnpqaeemyl 387
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|557694830|ref|YP_008797884.1| 388 iaeskyreaelkaqqlsenakktmaeveyrkqkwaefvrelvnsvepeyqhilslvggagkielrnlhdidkasiei 464
                                       ***************************************************************************** PP

                                       ...............CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT...SEEEE CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                             SMC_N 136 ...............lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn...aQfiv 194
                                                      + SgGe+ ++ +a+l+A+qk  ++p+  +De+d +LD  n++++ ++l ++ kn   +Q+iv
  gi|557694830|ref|YP_008797884.1| 465 yvgfrgveptlldthTQSGGERIVATMAFLLAVQKHIKSPFRAVDEFDVHLDPLNRERIIHILTSSAKNdpnTQYIV 541
                                       ***************9************************************************888765669**** PP

                                       E-SSHHHCCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N 195 islreemlekadklvgvt 212
                                       i+  +  +++  +++ v+
  gi|557694830|ref|YP_008797884.1| 542 ITPGRVPFTEEMNVIIVQ 559
                                       **8766665555555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.1   5.8e-21   5.2e-18       2     198 ..      16     268 ..      15     277 .. 0.59
   2 ?   -2.0   2.3       4.9   4.3e+03      93     123 ..     395     427 ..     306     459 .. 0.60

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 5.8e-21
                            AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrks....grgfeksdveiese...... 68 
                                       + +enf+s++   i + +gl++I+GpNGaGK++il Ai  aL+   ++ + +     +rg+e++ v++ ++      
  gi|557694830|ref|YP_008797884.1|  16 VILENFMSHEYSRIPLRRGLNVIVGPNGAGKSSILLAISVALGQTYTERGQRLadliRRGYESARVAVVFDnrpvdg 92 
                                       689****************************************9875444433788877777777776666569988 PP

                            AAA_23  69 .......gkvkayveltfenkdgry..........................trsiererelskkkgkttkkaklell 112
                                              +++   +++ + +k+g+y                          ++ i   ++ +++  ++ + +kl l+
  gi|557694830|ref|YP_008797884.1|  93 vrpipsiNSDTVTITRFL-KKTGEYwhyvnnrfktkaevgnllsriginpdNVLIIMHQNMIEQFVSRDSREKLALI 168
                                       888877433333355544.5556554555555555555555555555555544444444444444444444455555 PP

                            AAA_23 113 eideleqfisellgskkiilnlilflgqerfeefelkdkke........rleeleke..leeledekkllekl.... 175
                                       e++     ++e +  +++  +l+++l++e   ++ l    +          ee+ek   l+ le+++klle +    
  gi|557694830|ref|YP_008797884.1| 169 EEAVGAAGLRERIRDTEA--KLSALLAEEAVLRKTL----DearsavefWREEYEKLtiLRRLEERRKLLELEylws 239
                                       554444444444443333..4555555555322222....1233344445555555544555666666666667776 PP

                            AAA_23 176 ......eqekekekeleeleeeleeilke 198
                                             + ++  e+++e +++e e+++ +
  gi|557694830|ref|YP_008797884.1| 240 lvreaeKSRERLEEKIESIRRETESLEAK 268
                                       66544434444444555555555555554 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.9
                            AAA_23  93 erelskkkgkttkkaklellei..deleqfise 123
                                       e el+ ++ ++  k++  ++e   ++  +f++e
  gi|557694830|ref|YP_008797884.1| 395 EAELKAQQLSENAKKTMAEVEYrkQKWAEFVRE 427
                                       222222222222222222222222333444444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.1   5.9e-14   5.3e-11       2     363 ..      12     543 ..      12     543 .. 0.67

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 5.9e-14
                            AAA_15   2 kIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn........................ 54 
                                       +I++++++NF s+++  i+l   l+v++G+N++GKSsil a+ + l +++                           
  gi|557694830|ref|YP_008797884.1|  12 YIREVILENFMSHEYSRIPLRRGLNVIVGPNGAGKSSILLAISVALGQTYTERgqrladlirrgyesarvavvfdnr 88 
                                       699****************************************9999884444789999999999999999999999 PP

                            AAA_15  55 ......................................................kkvikiekedleifeniseskdi 77 
                                                                                             +                      
  gi|557694830|ref|YP_008797884.1|  89 pvdgvrpipsinsdtvtitrflkktgeywhyvnnrfktkaevgnllsriginpdN---------------------- 143
                                       9988888888888887776666666655555544444444444444444444443...................... PP

                            AAA_15  78 kIdvef...............................................aekekakeyektlkskekkkadll 107
                                                                                                ++ +  ktl++ ++  +   
  gi|557694830|ref|YP_008797884.1| 144 -----VliimhqnmieqfvsrdsreklalieeavgaaglrerirdteaklsalL--AEEAVLRKTLDEARSAVEFWR 213
                                       .....0444444555555555555555555555888888877777755433330..444444444444444444433 PP

                            AAA_15 108 lkkkesdlkktikdkklklkknelsdekisvekkks.........kkelpkekeeklekekeelkidkedlkklikk 175
                                        + ++  +  +++++   l+ ++l++   ++ek  +         ++e ++++ +  e +++   ++          
  gi|557694830|ref|YP_008797884.1| 214 EEYEKLTILRRLEERRKLLELEYLWSLVREAEKSRErleekiesiRRETESLEAKITEARNTVSTYY---------- 280
                                       3333334445555555555555555555555555553333222223333333333333333333333.......... PP

                            AAA_15 176 leeslkkee................elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl.. 234
                                               +                e    + +a++ l  + ++R++ +++  + +   ++l+++i++  ++ ++  
  gi|557694830|ref|YP_008797884.1| 281 --------QslvkglregwservlmETVDGIVAAAESLGRFLERREIREDELRQLRYEVTALDKEIIRRRGEAEAkg 349
                                       ........133333345555555666688889999999999999999999999999999999999999988888899 PP

                            AAA_15 235 ........................................eeelteklkeiqeklkeidkklaeelkkilkkkidki 271
                                                                               e + +e+  + q   ++++k++ae +    k+k+ ++
  gi|557694830|ref|YP_008797884.1| 350 prtdtgrkpaevseeikavglqiaalgtpnpqaeemyliaESKYREAELKAQQLSENAKKTMAEVEY--RKQKWAEF 424
                                       9999999999999999999999999999988877777777555555555555555555555543333..35666666 PP

                            AAA_15 272 kkfnykgkkneeieik...............................ddeelplnknGsGvqrllllillileaekk 317
                                       + + +++++ e+  i                                + + l+ + ++ G +    +++l++  +  
  gi|557694830|ref|YP_008797884.1| 425 VRELVNSVEPEYQHILslvggagkielrnlhdidkasieiyvgfrgvEPTLLDTHTQSGGERIVATMAFLLAVQKHI 501
                                       66666666666655556777777777777778889999999999998888999999998888888888888888777 PP

                            AAA_15 318 dekeeknvilliEEPEahLHpqaqkvlikllkelandnkt.QviitT 363
                                            k+ +++++E ++hL p + + +i+ l + a+++ + Q i+ T
  gi|557694830|ref|YP_008797884.1| 502 -----KSPFRAVDEFDVHLDPLNRERIIHILTSSAKNDPNtQYIVIT 543
                                       .....9999************99999999999999998888988866 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 !   25.9   0.0     9e-09   8.1e-06       1      57 [.      35      80 ..      35     129 .. 0.68
   2 !   16.2   1.3   8.1e-06    0.0073     237     296 ..     481     543 ..     195     544 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 9e-09
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeip 57
                                      lnv++GpNg+GKS++L a++++ +           ++ +   +  + l+++++++ +
  gi|557694830|ref|YP_008797884.1| 35 LNVIVGPNGAGKSSILLAISVALG-----------QTYTERGQRLADLIRRGYESAR 80
                                      7******************99964...........3333344455555555555555 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 8.1e-06
                            AAA_21 237 lSdGtkrll..alltallralkkgsllliDEpEngLHPkllrrllellkelsr..ngaQviltT 296
                                        S G + ++  a+l+a+     k+++ ++DE++ +L+P   +r++ +l + ++   ++Q i+ T
  gi|557694830|ref|YP_008797884.1| 481 QSGGERIVAtmAFLLAVQKHI-KSPFRAVDEFDVHLDPLNRERIIHILTSSAKndPNTQYIVIT 543
                                       399999998544444444433.33************************4444446899*99988 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 !   18.0   0.0   1.9e-06    0.0017      15      46 ..      27      57 ..      14      63 .. 0.80
   2 ?   -1.6   0.0       2.6   2.4e+03      24      39 ..     553     568 ..     546     581 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                       +i+++ +g  +++Gp+G+GKS++l Ai++ L
  gi|557694830|ref|YP_008797884.1| 27 SRIPLR-RGLNVIVGPNGAGKSSILLAISVAL 57
                                      556676.6789**************9999876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.6
                            AAA_29  24 atlltGpsGsGKSTll 39 
                                       + +++ +s  GKS++l
  gi|557694830|ref|YP_008797884.1| 553 MNVIIVQSVKGKSAVL 568
                                       4566667778888754 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   2.5   1.5e-05     0.014      15      37 ..      37      59 ..      32     501 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                                      EEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 15 aivGenGaGKStLlkllagllkp 37
                                      +ivG+nGaGKS++l +++  l +
  gi|557694830|ref|YP_008797884.1| 37 VIVGPNGAGKSSILLAISVALGQ 59
                                      79************999865533 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   4.1e-06    0.0036      25      47 ..      32      54 ..      13      60 .. 0.83
   2 ?   -0.6   0.4      0.94   8.4e+02     147     200 ..     166     219 ..     154     224 .. 0.83
   3 ?   -1.5   0.2       1.8   1.6e+03     158     192 ..     244     278 ..     239     286 .. 0.74
   4 ?   -2.2   0.6       2.9   2.6e+03     168     207 .]     381     421 ..     325     421 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.1e-06
                            AAA_27 25 eadlhliyGpNEAGKstalrAis 47
                                      +++l +i+GpN AGKs++l Ais
  gi|557694830|ref|YP_008797884.1| 32 RRGLNVIVGPNGAGKSSILLAIS 54
                                      479******************97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.94
                            AAA_27 147 lLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelrea 200
                                       +L+e + G a+lre + + ea+ ++l ++++  ++++ ea++++e  ++e+++ 
  gi|557694830|ref|YP_008797884.1| 166 ALIEEAVGAAGLRERIRDTEAKLSALLAEEAVLRKTLDEARSAVEFWREEYEKL 219
                                       688888999999999999999999999999999999999999888888777765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.8
                            AAA_27 158 lrevleaLeaeadelfkprkskkrainealeelee 192
                                        ++ +e+Le++ +++ ++++s +++i+ea++++++
  gi|557694830|ref|YP_008797884.1| 244 AEKSRERLEEKIESIRRETESLEAKITEARNTVST 278
                                       56778888888888888888888888888877765 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 2.9
                            AAA_27 168 eadelfkprkskkraine.aleeleeakkelreaqvraeew 207
                                       +a+e++   +sk r++   a++  e+akk++ e + r+++w
  gi|557694830|ref|YP_008797884.1| 381 QAEEMYLIAESKYREAELkAQQLSENAKKTMAEVEYRKQKW 421
                                       45555555555554443303333445666666666666666 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 ?    5.1  12.9     0.027        24      38     122 ..     188     279 ..     186     294 .. 0.79
   2 ?   15.0   3.4   2.4e-05     0.022      23     151 ..     295     432 ..     280     435 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.027
                     Jnk-SapK_ap_N  38 LeslasrneeeeaeleelreeleqLeteyerekelrkrae.eeleeiedqw......eeerkelqekveqleeenre 107
                                       L +l+++++    +l+e r ++e  ++eye+ + lr+ +e ++l+e+e  w      e+ r+ l+ek+e+ + e++ 
  gi|557694830|ref|YP_008797884.1| 188 LSALLAEEAVLRKTLDEARSAVEFWREEYEKLTILRRLEErRKLLELEYLWslvreaEKSRERLEEKIESIRRETES 264
                                       556777777888899999999999999999999999998875566666544333222889999************** PP

                     Jnk-SapK_ap_N 108 lelkaknaadqlsrl 122
                                       le+k+ +a + +s+ 
  gi|557694830|ref|YP_008797884.1| 265 LEAKITEARNTVSTY 279
                                       **9999999888765 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.4e-05
                     Jnk-SapK_ap_N  23 vvkgLmPkvVkvLElLeslasrneeeeaeleelreeleqLeteyerekelrkrae..eeleeiedqweeerkelqek 97 
                                       v+ + +  +V+  E+L  +++r+e +e el++lr e++ L +e  r++ + +++    +  ++  ++ ee k++  +
  gi|557694830|ref|YP_008797884.1| 295 VLMETVDGIVAAAESLGRFLERREIREDELRQLRYEVTALDKEIIRRRGEAEAKGprTDTGRKPAEVSEEIKAVGLQ 371
                                       555667779999**********************************9977776655588899999************ PP

                     Jnk-SapK_ap_N  98 veqleeenrele.......lkaknaadqlsrleekeaelkkeysklheretellkklkelv 151
                                       ++ l + n + e        k ++a+ ++++l+e+ ++ + e +  +++  e +++l+  v
  gi|557694830|ref|YP_008797884.1| 372 IAALGTPNPQAEemyliaeSKYREAELKAQQLSENAKKTMAEVEYRKQKWAEFVRELVNSV 432
                                       *****99999996665555666666667777777776666666666667777777776655 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 ?    8.8   0.3    0.0013       1.2      27      61 ..     251     285 ..     235     294 .. 0.86
   2 ?    2.2   0.1      0.14   1.2e+02      22      45 ..     315     338 ..     303     341 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0013
                              Med4  27 nearilqLraeveslDekikeivksLkeyekeLka 61 
                                        e++i+++r e+esl+ ki e  +++ +y+++L +
  gi|557694830|ref|YP_008797884.1| 251 LEEKIESIRRETESLEAKITEARNTVSTYYQSLVK 285
                                       4789**************************99865 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.14
                              Med4  22 eehqknearilqLraeveslDeki 45 
                                       e+ + +e++++qLr ev +lD++i
  gi|557694830|ref|YP_008797884.1| 315 ERREIREDELRQLRYEVTALDKEI 338
                                       55666899*************986 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 ?   -0.8   0.0       2.1   1.8e+03      24      39 ..     198     213 ..     176     220 .. 0.75
   2 ?    7.3   0.0    0.0063       5.6      27      82 ..     240     312 ..     231     316 .. 0.66
   3 ?    0.5   0.0      0.84   7.5e+02      34      53 ..     399     418 ..     387     450 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.1
                            DUF948  24 lkktldeaaatieele 39 
                                       l+ktldea++++e  +
  gi|557694830|ref|YP_008797884.1| 198 LRKTLDEARSAVEFWR 213
                                       6888888888887555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0063
                            DUF948  27 tldeaaatieelekqvdpilkevedllakvne...........lledvne......klekvdplteavadlge 82 
                                       +++ea+++ e le+++++i +e+e l ak+ e           l+++++e       +e+vd +++a++ lg+
  gi|557694830|ref|YP_008797884.1| 240 LVREAEKSRERLEEKIESIRRETESLEAKITEarntvstyyqsLVKGLREgwservLMETVDGIVAAAESLGR 312
                                       5677777777788888888888777777777733333334444333333377777778888888888888775 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.84
                            DUF948  34 tieelekqvdpilkevedll 53 
                                         ++l +++++++ eve   
  gi|557694830|ref|YP_008797884.1| 399 KAQQLSENAKKTMAEVEYRK 418
                                       44444444444444444333 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00099      0.89      97     121 ..      31      55 ..      19      80 .. 0.84
   2 ?   -1.5   0.0       2.3   2.1e+03      64     113 ..     399     449 ..     383     459 .. 0.57

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00099
                                       CTTSEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallp 121
                                       l+  + v+vG+ G+GKS+++ a+  
  gi|557694830|ref|YP_008797884.1|  31 LRRGLNVIVGPNGAGKSSILLAISV 55 
                                       667789*************988765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHH CS
                       RsgA_GTPase  64 eleelkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKS 113
                                       ++++l+e+ +++  ev + ++k  e ++el + ++     +l    G+GK 
  gi|557694830|ref|YP_008797884.1| 399 KAQQLSENAKKTMAEVEYRKQKWAEFVRELVNSVEPeYQHILSLVGGAGKI 449
                                       455555556666566666666666666666666665323333334466665 PP

>> MctB  Copper transport outer membrane protein, MctB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.23   2.1e+02     117     175 ..     150     205 ..     145     227 .. 0.76
   2 ?    7.9   0.2    0.0025       2.2      33      80 ..     240     287 ..     234     302 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.23
                              MctB 117 vtltdkfvdpdeadklrslaaqvlpgaqlspeaadpgekagallgaalltaeeeassee 175
                                        ++ ++fv+ d+++kl+ + +  + +a l+++  d+++k++all++  +++  ++ +e 
  gi|557694830|ref|YP_008797884.1| 150 QNMIEQFVSRDSREKLALIEEA-VGAAGLRERIRDTEAKLSALLAEEAVLR--KTLDEA 205
                                       5677899999999999877777.3489999999999********9987773..233333 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0025
                              MctB  33 lldtlegqveelreekeelraeadaleaqleaaddfaaavaprlvagr 80 
                                       l+ + e+ +e+l+e+ e+ r+e+++lea++++a + +++++++lv+g 
  gi|557694830|ref|YP_008797884.1| 240 LVREAEKSRERLEEKIESIRRETESLEAKITEARNTVSTYYQSLVKGL 287
                                       567789999************************************995 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00095      0.85      10      50 ..     245     285 ..     229     293 .. 0.78
   2 ?    0.3   0.2      0.68   6.1e+02      29      63 ..     384     418 ..     377     440 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00095
                              ApoO  10 eeptdrLeegvrslRkslepytsavqdelnkvkskvetaeq 50 
                                       e+ ++rLee+++s+R+++e+  ++++++ n+v+++++++++
  gi|557694830|ref|YP_008797884.1| 245 EKSRERLEEKIESIRRETESLEAKITEARNTVSTYYQSLVK 285
                                       56778888888888888888888888888888888887776 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.68
                              ApoO  29 pytsavqdelnkvkskvetaeqsvtdtiasLkepp 63 
                                       + +  +++++++++ k++++ ++ ++t+a++   +
  gi|557694830|ref|YP_008797884.1| 384 EMYLIAESKYREAELKAQQLSENAKKTMAEVEYRK 418
                                       55666666666666666666666666666655443 PP

>> Di19_C  Stress-induced protein Di19, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.3       2.7   2.4e+03      63      98 ..     247     284 ..     235     286 .. 0.60
   2 ?   11.1   0.2    0.0005      0.45      53     100 ..     385     431 ..     374     432 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.7
                            Di19_C  63 kksseekvlersvd..sslseeereekarrseFVqgLl 98 
                                       +++  e+++e+     +sl ++  e +   s++ q L+
  gi|557694830|ref|YP_008797884.1| 247 SRERLEEKIESIRRetESLEAKITEARNTVSTYYQSLV 284
                                       22222333333222248888888888888888888886 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.0005
                            Di19_C  53 pessveessvkksseekvlersvdsslseeereekarrseFVqgLllS 100
                                       +  ++e+++++ + ++++l+++++++++e e  +k++ +eFV++L+ S
  gi|557694830|ref|YP_008797884.1| 385 MYLIAESKYREAELKAQQLSENAKKTMAEVEY-RKQKWAEFVRELVNS 431
                                       55678889999999999999999666655555.999*********988 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.0    0.0013       1.2     117     185 ..     194     268 ..     181     290 .. 0.78
   2 ?   -0.0   0.0      0.87   7.8e+02     144     216 ..     392     462 ..     353     468 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0013
                             DUF87 117 qrsvleealdqaka.....keekeklssdepveklleelkkeke.elrklknqaiarlldkledllrkggsfsns 185
                                       +++vl+++ld+a++     +ee+ekl++ + +e+ ++ l+ e + +l ++++++++rl++k+e++ r+++s  ++
  gi|557694830|ref|YP_008797884.1| 194 EEAVLRKTLDEARSavefwREEYEKLTILRRLEERRKLLELEYLwSLVREAEKSRERLEEKIESIRRETESLEAK 268
                                       67899999999999999999********************66666788888888888888888888877777222 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.87
                             DUF87 144 eklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaq 216
                                       ++ + elk  +++l++++++++a+++ ++++  +  ++  ns +  ++++l + +  gki   +l+ +d+   
  gi|557694830|ref|YP_008797884.1| 392 KYREAELK--AQQLSENAKKTMAEVEYRKQKWAEFVRELVNSVEPEYQHILSLVGGAGKIELRNLHDIDKASI 462
                                       34444444..556666666666666666666666666665555555555556666666666666665555555 PP

>> Flu_NS2  Influenza non-structural protein (NS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.9   0.00044       0.4      26      67 ..     235     276 ..     213     289 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00044
                                       XXXXXXXXXX-CHHHHHHHHHHHHHHHHHHHHHC----TTSH CS
                           Flu_NS2  26 tdlhslqnrnekwreqlgqkreeirllieelrhklkiaessi 67 
                                         l sl    ek re+l  k e ir  +e l  k+  a +++
  gi|557694830|ref|YP_008797884.1| 235 EYLWSLVREAEKSRERLEEKIESIRRETESLEAKITEARNTV 276
                                       567899999**********************99988777765 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   0.4     0.081        73       8      37 ..     187     219 ..     184     233 .. 0.81
   2 ?    7.5   0.7    0.0053       4.8       7      45 ..     235     273 ..     231     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.081
                              Rx_N   8 kLadllaeea...kllkgvkeeleklkdeLesi 37 
                                       kL++llaeea   k l + ++ +e++++e e++
  gi|557694830|ref|YP_008797884.1| 187 KLSALLAEEAvlrKTLDEARSAVEFWREEYEKL 219
                                       9*********888888888889******99876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0053
                              Rx_N   7 qkLadllaeeakllkgvkeeleklkdeLesiqavLedae 45 
                                       + L +l+ e  k+++ ++e++e++++e es++a + +a 
  gi|557694830|ref|YP_008797884.1| 235 EYLWSLVREAEKSRERLEEKIESIRRETESLEAKITEAR 273
                                       67889999999*********************9998886 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0068       6.1      18      33 ..      35      50 ..      21      68 .. 0.83
   2 ?    0.6   9.6      0.19   1.7e+02     305     455 ..     167     340 ..     149     405 .. 0.56
   3 ?   -0.1   0.7      0.31   2.8e+02     414     455 ..     389     430 ..     354     500 .. 0.67

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0068
                            AAA_13 18 iNliYGwNGaGKTtLS 33
                                       N+i G NGaGK+++ 
  gi|557694830|ref|YP_008797884.1| 35 LNVIVGPNGAGKSSIL 50
                                      7************975 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.19
                            AAA_13 305 klkavsdeasensafeed...keelkaeaealeeqLkglqraleaKrkepfksvelesvkakie............s 366
                                        +++++ +a ++++ ++     + l ae  +l+++L+++++a+e  r+e  k   l +++++ +            +
  gi|557694830|ref|YP_008797884.1| 167 LIEEAVGAAGLRERIRDTeakLSALLAEEAVLRKTLDEARSAVEFWREEYEKLTILRRLEERRKlleleylwslvrE 243
                                       44444444333333333300133333455666666666666666666655554444444444434445555666659 PP

                            AAA_13 367 ikklvaeineliakhNekvanleeekeeakkklelhlv......................eeleseldeykkkykkl 421
                                       ++k+ ++++e i++  + +++le++ +ea++ +  ++                         + + l ++ +  +  
  gi|557694830|ref|YP_008797884.1| 244 AEKSRERLEEKIESIRRETESLEAKITEARNTVSTYYQslvkglregwservlmetvdgiVAAAESLGRFLERREIR 320
                                       99999999999999999999999999999999998876555555544444444444433322333333333333344 PP

                            AAA_13 422 ekaieklekelkeeeaelkkleeeikeLekqlrd 455
                                       e              +el++l+ e+ +L k++  
  gi|557694830|ref|YP_008797884.1| 321 E--------------DELRQLRYEVTALDKEIIR 340
                                       4..............4444455555555555443 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.31
                            AAA_13 414 ykkkykklekaieklekelkeeeaelkkleeeikeLekqlrd 455
                                        ++ky+++e ++++l +++k+  ae++ ++++ +e  ++l +
  gi|557694830|ref|YP_008797884.1| 389 AESKYREAELKAQQLSENAKKTMAEVEYRKQKWAEFVRELVN 430
                                       345666666666666666666666666666665554444332 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   9.5    0.0041       3.7     145     244 ..     185     277 ..     173     289 .. 0.45
   2 ?    5.5   0.1    0.0076       6.8     194     252 ..     317     374 ..     292     377 .. 0.79
   3 ?   -1.5   1.1         1     9e+02     235     265 ..     392     422 ..     359     439 .. 0.48

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0041
                              Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkke 221
                                       e +l++l +++++L k  +e+ ++++  +ee+++l+  l++l+e        +  eLe l + ++e+++  e+++++
  gi|557694830|ref|YP_008797884.1| 185 EAKLSALLAEEAVLRKTLDEARSAVEFWREEYEKLTI-LRRLEE------RRKLLELEYLWSLVREAEKSRERLEEK 254
                                       2333334444444444444444444444444443332.222222......223445555555555555555555555 PP

                              Spc7 222 laelqeqleeleekieelkeqks 244
                                       +++ +++ e+le+ki+e+++  s
  gi|557694830|ref|YP_008797884.1| 255 IESIRRETESLEAKITEARNTVS 277
                                       55555555555555555554444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0076
                              Spc7 194 esidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeiae 252
                                        +i ++eL++lr e+++l++ei  +++  ae +  +++   k +e++e+++ +  +ia+
  gi|557694830|ref|YP_008797884.1| 317 REIREDELRQLRYEVTALDKEII-RRRGEAEAKGPRTDTGRKPAEVSEEIKAVGLQIAA 374
                                       56889*****************9.66677888888888888999999999988888875 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1
                              Spc7 235 kieelkeqkseleeeiaeaervleeckgwse 265
                                       k  e++ + ++l e+ ++    +e +k+  +
  gi|557694830|ref|YP_008797884.1| 392 KYREAELKAQQLSENAKKTMAEVEYRKQKWA 422
                                       3333333333333333333333333333222 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 ?    0.4   0.1         1   8.9e+02       1      31 [.     180     210 ..     180     219 .. 0.85
   2 ?    7.6   1.0    0.0055       4.9       4      37 ..     243     276 ..     241     285 .. 0.77
   3 ?   -1.4   0.1       3.7   3.3e+03      20      37 ..     321     338 ..     318     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksve 31 
                                       ri + E kls l  e + ++k+++e ++ ve
  gi|557694830|ref|YP_008797884.1| 180 RIRDTEAKLSALLAEEAVLRKTLDEARSAVE 210
                                       7888899999999999999999999999887 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0055
                         FlaC_arch   4 elEnklsklsteletvkkeneelsksveelkenV 37 
                                       e E+  ++l+ ++e++++e e+l+ +++e   +V
  gi|557694830|ref|YP_008797884.1| 243 EAEKSRERLEEKIESIRRETESLEAKITEARNTV 276
                                       6677778899999999999999999998888777 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.7
                         FlaC_arch  20 kkeneelsksveelkenV 37 
                                       ++e+ +l+ +v+ l++++
  gi|557694830|ref|YP_008797884.1| 321 EDELRQLRYEVTALDKEI 338
                                       678889999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1430  (0.079759); expected 358.6 (0.02)
Passed bias filter:                      810  (0.0451782); expected 358.6 (0.02)
Passed Vit filter:                       129  (0.00719505); 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):              20  [number of targets reported over threshold]
# CPU time: 0.79u 0.30s 00:00:01.09 Elapsed: 00:00:00.40
# Mc/sec: 4370.72
//
Query:       gi|557694831|ref|YP_008797885.1|  [L=254]
Description: hypothetical protein CSUB_C1404 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.8   1.8       0.98    9.3   0.2    2.0  2  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 ?    9.3   0.2   5.5e-05      0.98      26      84 ..       5      83 ..       2     160 .. 0.69
   2 ?    4.4   0.1    0.0017        31      49      73 ..     159     183 ..     149     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 5.5e-05
                                      HHHHHHHHHHHHHHHHTTTSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHH.....................H CS
                              CHAD 26 HqmRvalRRlRsalrlfapvldkeeaaalekelrwlaraLGeaRDldVllerllsrle....................e 84
                                        +R  l Rl ++++ +a+  +++   ++++ l +l ++L + R+++Vl+ + ++ ++                     
  gi|557694831|ref|YP_008797885.1|  5 KVAREELERLIALCEAVAKSGTDPYNLDVKAMLSKLRGILEKSRNAEVLVLDAETLYRiavvvalqhkwlkdranslfL 83
                                      557778889999999998888778888999*******************999999987666655555555544444440 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              CHAD  49 eeaaalekelrwlaraLGeaRDldV 73 
                                        ++++le+ +r++ ++L eaRD d 
  gi|557694831|ref|YP_008797885.1| 159 SQYERLEEDVRRIHGELLEARDVDG 183
                                       5799******************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); 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 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2127.52
//
Query:       gi|557694832|ref|YP_008797886.1|  [L=191]
Description: hypothetical protein CSUB_C1405 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.6   0.0       0.47   10.3   0.0    2.1  2  SMC_Nse1  Nse1 non-SMC component of SMC5-6 complex


Domain annotation for each model (and alignments):
>> SMC_Nse1  Nse1 non-SMC component of SMC5-6 complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0    0.0064   1.1e+02      39     121 ..      41     132 ..       9     137 .. 0.67
   2 ?   10.3   0.0   2.6e-05      0.47     158     193 ..     137     172 ..     133     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.0064
                          SMC_Nse1  39 tqedleeyiakinealspldyeirsvrhqlgk........ervyyalVNttsdeetklATtfsaeeiafiKrlldam 107
                                         +++ ++i+++n +l+p+ + ++   + + +        + +y+       + +  +A   +++e+a + ++l  +
  gi|557694832|ref|YP_008797886.1|  41 LGKNYLKVIEALNHRLEPMGLRVKILFETVVEqpgeedydRARYFITLAEPLTLSEVVAAGWRVDELAVLAAALALL 117
                                       55677889999999999999998876666652333344446665655555555666677777888888888888888 PP

                          SMC_Nse1 108 fet.sntrrlevmai 121
                                       f +  + +r +vm +
  gi|557694832|ref|YP_008797886.1| 118 FSRgGKAPRKDVMEL 132
                                       877777777777765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 2.6e-05
                          SMC_Nse1 158 LtaseaeklLkrLveegWleksreGfysLdlRallE 193
                                       + +  +e+ L+++++ g+l  s +G +s++ Ra++E
  gi|557694832|ref|YP_008797886.1| 137 MPKWRVESALEKFMRRGYLVDSGDGVLSVGWRAVAE 172
                                       566789***************************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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 0.20s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1521.86
//
Query:       gi|557694833|ref|YP_008797887.1|  [L=951]
Description: ATP-dependent helicase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-30  103.8   0.0    2.5e-29  102.3   0.0    1.8  1  DEAD           DEAD/DEAH box helicase
    3.3e-26   92.2   0.5    3.3e-26   92.2   0.5    3.6  5  DEAD_assoc     DEAD/H associated
    1.2e-15   57.8   0.1    1.1e-13   51.5   0.0    3.0  3  Helicase_C     Helicase conserved C-terminal domain
    5.8e-10   39.4   0.0    3.4e-09   36.9   0.0    2.0  2  ResIII         Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.036   14.4   0.0       0.14   12.5   0.0    2.1  1  AAA_19         AAA domain
      0.038   14.3   2.0       0.69   10.2   0.5    3.3  3  AAA_22         AAA domain
      0.075   12.9   0.0       0.18   11.6   0.0    1.6  1  MciZ           Mother cell inhibitor of FtsZ
      0.078   12.8   0.0       0.34   10.7   0.0    2.0  2  AAA_11         AAA domain
       0.14   11.7   0.0       0.35   10.4   0.0    1.6  1  UvrD-helicase  UvrD/REP helicase N-terminal 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 !  102.3   0.0   1.3e-32   2.5e-29       4     170 ..      33     198 ..      30     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.3 bits;  conditional E-value: 1.3e-32
                                       HHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvll 80 
                                       Q +aip++l+g+++l+ a+TG+GKT+a+lip++++++ + + +g k+l+++P+r+L ++ l++++ + +  d++v +
  gi|557694833|ref|YP_008797887.1|  33 QIQAIPHVLNGENILLMAPTGTGKTEAALIPLINNLLLSSSFEGVKILYITPLRALNRDLLDRIEWWASRFDMTVGV 109
                                       99*********************************99989********************************99998 PP

                                       EETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  81 iiggvaardqlskldngvdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                         g++ +r+ +++  + + i+++tp+ l+ ll+ + l+  l++v+ +V+DE+++l  ++++ +++  l++l +it +
  gi|557694833|ref|YP_008797887.1| 110 RHGDTGQRERRAQALSPPTILITTPETLQILLTARILRqyLKRVEAVVVDEVHELAGDKRGSQLSLALERLVEITGR 186
                                       89988887777777577*************9966666667*******************************888876 PP

                                       STTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxx RF
                              DEAD 156 gklqrqvivlSATlp 170
                                            q i lSAT+ 
  gi|557694833|ref|YP_008797887.1| 187 D---FQRIGLSATVG 198
                                       4...569******96 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.07   1.4e+02      33      72 ..     135     175 ..     132     201 .. 0.78
   2 ?   -3.2   0.1       3.1   6.1e+03     135     153 ..     586     605 ..     561     608 .. 0.41
   3 !   92.2   0.5   1.7e-29   3.3e-26       1     190 [.     617     790 ..     617     791 .. 0.95
   4 ?   -2.3   0.0       1.7   3.3e+03      19      39 ..     811     831 ..     806     835 .. 0.84
   5 ?   -2.3   0.0       1.7   3.3e+03     151     181 ..     906     936 ..     901     940 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.07
                        DEAD_assoc  33 ealalllaarlsrrfgidvqvaanDdgivlll.pleerlpl 72 
                                       e+l  ll+ar+ r++   v++++ D+  +l   +  ++l l
  gi|557694833|ref|YP_008797887.1| 135 ETLQILLTARILRQYLKRVEAVVVDEVHELAGdKRGSQLSL 175
                                       7999**********************999965633344433 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.1
                        DEAD_assoc 135 Lldvareyp.dfpllleavr 153
                                       L   a++y  ++ ll++ +r
  gi|557694833|ref|YP_008797887.1| 586 LEMLAQQYRtSTTLLKKSLR 605
                                       22223344444444444444 PP

  == domain 3  score: 92.2 bits;  conditional E-value: 1.7e-29
                        DEAD_assoc   1 lPtdrtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlll.pleerlplllde 76 
                                       +P+dr ++ E++ +     ++v+h + G +vn++la+ +a+++s+++g+ v+v+ + ++iv  + + ++   + l++
  gi|557694833|ref|YP_008797887.1| 617 VPSDRLVMLEETPE-----YVVLHVCGGLKVNRTLARTIAYQVSSELGTAVTVQQDAYRIVYKSrEITAD--AVLNA 686
                                       8***********87.....8******************************************88633333..45678 PP

                        DEAD_assoc  77 llellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavr 153
                                       + +l +++   e  ++a+++s+lf+rr+ +vA++++++ ++            + +a+L dv++   d++ ++ea++
  gi|557694833|ref|YP_008797887.1| 687 VKNLADERSWWESFRKAVESSSLFRRRLVHVARKMGMIAKDASL-------LDIDTAKLADVLK---DTVTYEEALQ 753
                                       99**************************************9988.......*************...********** PP

                        DEAD_assoc 154 evledqlDlerlaellrriaageirvvevetprpSpf 190
                                        ++  +++ e++++ll++i +ge++++ v++ +pSp+
  gi|557694833|ref|YP_008797887.1| 754 HCFLADFEPEKAHNLLKSIYSGELELTVVRLLEPSPL 790
                                       ************************************8 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.7
                        DEAD_assoc  19 wrlvvhspfGrrvnealalll 39 
                                       +rlvv+++ Gr  ne+  l+ 
  gi|557694833|ref|YP_008797887.1| 811 QRLVVNAVRGRLNNEPVTLVC 831
                                       599************998876 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 1.7
                        DEAD_assoc 151 avrevledqlDlerlaellrriaageirvve 181
                                       av     ++lD+e++a++l++ ++  +r+ve
  gi|557694833|ref|YP_008797887.1| 906 AVFTLASKYLDIEEAAAILEKESSVGVRLVE 936
                                       556677899**********998888888877 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 ?    2.6   0.0     0.083   1.7e+02      11      58 ..      71     122 ..      61     212 .. 0.72
   2 !   51.5   0.0   5.3e-17   1.1e-13      11     108 ..     260     359 ..     250     361 .. 0.89
   3 ?   -2.8   0.0       3.9   7.7e+03      11      40 ..     897     931 ..     890     947 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.083
                                       HHTTTTSEEEEEESSHH....HHHHHHHHHHHTTSTEEEESTTSTHHHHHHH CS
                        Helicase_C  11 kleeeggkilifvntid....rlekvklllekkgikvavlhgelpqnereei 58 
                                       +++ eg kil +++ +      l+++++  ++++++v v hg++ q+er++ 
  gi|557694833|ref|YP_008797887.1|  71 SSSFEGVKILYITPLRAlnrdLLDRIEWWASRFDMTVGVRHGDTGQRERRAQ 122
                                       555566677777777775554444478888999****************954 PP

  == domain 2  score: 51.5 bits;  conditional E-value: 5.3e-17
                                       HHTTTTSEEEEEESSHHHHHHHHHHHHHT.....TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTS CS
                        Helicase_C  11 kleeeggkilifvntidrlekvklllekk.....gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidi 82 
                                        l e+++ +l+f+nt+      ++l++++     +  + ++hg+l ++ r+ + ++ ++g    +i+t+ +e+Gid+
  gi|557694833|ref|YP_008797887.1| 260 RLVEQHESTLVFTNTRPLS---EILTNRFrawdeAAPIGIHHGSLAKSTRIGAEQALKAGGLSGVICTSSLEMGIDV 333
                                       456999***********88...6666666667779****************************************** PP

                                       TTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  83 pkvnlVinfdlprnvtsyiqriGRtg 108
                                        +++l+i+++ pr+vt+++qr+GR g
  gi|557694833|ref|YP_008797887.1| 334 GRIELCIQYNSPREVTRLVQRVGRSG 359
                                       ************************87 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.9
                                       HHTTTTSEEEEEESSHHHHHH..HHHHHHHT...T CS
                        Helicase_C  11 kleeeggkilifvntidrlek..vklllekk...g 40 
                                       kl e+ gk+ +f+   + l+   +  +lek+   g
  gi|557694833|ref|YP_008797887.1| 897 KLVEKYGKAAVFTLASKYLDIeeAAAILEKEssvG 931
                                       66788999999999999555444444445443343 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 !   36.9   0.0   1.7e-12   3.4e-09       8     169 ..      33     197 ..      15     199 .. 0.80
   2 ?   -0.7   0.0       0.6   1.2e+03      42      78 ..     255     289 ..     252     308 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 1.7e-12
                                       HHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG. CS
                            ResIII   8 QeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkee..kflflvprkslleqtleefkkflsea 81 
                                       Q++ai  +l      + +++l+ ++TGtGKT  a + li +ll + + e  k+l + p ++l   +l++++ ++s  
  gi|557694833|ref|YP_008797887.1|  33 QIQAIPHVL------NGENILLMAPTGTGKTEAAlIPLINNLLLSSSFEgvKILYITPLRALNRDLLDRIEWWASRF 103
                                       555555555......557899*************99*******99998899********************999987 PP

                                       ...GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.......T CS
                            ResIII  82 ykeigkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.......s 149
                                       ++ + ++ +gd+ ++  ++++ +   il+tt ++l+  +   +    ++  +r + +++DE+H l+++k       +
  gi|557694833|ref|YP_008797887.1| 104 DM-TVGVRHGDTGQRerRAQALSPPTILITTPETLQILL---TARILRQYLKRVEAVVVDEVHELAGDKrgsqlslA 176
                                       66.55666666666644567788899************9...5555566667777999*********9655555566 PP

                                       THHHHHT-.--SEEEEEESS- CS
                            ResIII 150 wreilekf.keavllglTATp 169
                                        ++++e   +++ ++gl+AT 
  gi|557694833|ref|YP_008797887.1| 177 LERLVEITgRDFQRIGLSATV 197
                                       6665555446699*******6 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.6
                                       HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII  42 aklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       ++li+rl ++++   +l++ +++ l e + ++f+ + 
  gi|557694833|ref|YP_008797887.1| 255 LSLIRRLVEQHE--STLVFTNTRPLSEILTNRFRAWD 289
                                       578999999755..99********9999999998765 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.2e-05      0.14       1     114 [.      33     164 ..      33     181 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.2e-05
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrv.lkhivallvelggvkpeeillvaftgrAakelrerlaalgae....... 68 
                                       q +a+   l+ +++l++a+ GtGKT+  l   ++ l+   + +  +il +++ +   + l +r++    +       
  gi|557694833|ref|YP_008797887.1|  33 QIQAIPhVLNGENILLMAPTGTGKTEAaLIPLINNLLLSSSFEGVKILYITPLRALNRDLLDRIEWWASRfdmtvgv 109
                                       66788658999**************752566777777777778899*****99988889999995555555444444 PP

                            AAA_19  69 ...........atTiHrlal.......ldfddlltealelle..........eaeeekklqeeellivDEfqdv 114
                                                  a               l                         +  ++ l++ e+++vDE+ ++
  gi|557694833|ref|YP_008797887.1| 110 rhgdtgqrerrA-------QalspptiLI------------TtpetlqilltARILRQYLKRVEAVVVDEVHEL 164
                                       444444444441.......0333333221............022222222224444566766668899988776 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.5   0.00035      0.69       8     115 ..      46     183 ..      41     207 .. 0.60
   2 ?   -3.5   0.0       5.6   1.1e+04      75     107 ..     345     380 ..     330     401 .. 0.64
   3 ?   -3.5   0.0       5.7   1.1e+04      38      65 ..     581     608 ..     569     627 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00035
                            AAA_22   8 lvvtGesGtGKTtllrr.lleqldeeakaee..erpevvfvtlpsst..sskdllrellralglelka......... 70 
                                       +++++++GtGKT  +   l ++l    +     e+++++++t+      ++ d  ++ ++ ++    +         
  gi|557694833|ref|YP_008797887.1|  46 ILLMAPTGTGKTEAALIpLINNLLL--S--SsfEGVKILYITPLRALnrDLLDRIEWWASRFDM---Tvgvrhgdtg 115
                                       6788888888887554312222211..1..1234555555544333324444444555555443...0334777788 PP

                            AAA_22  71 .................erlsseell.ealeqalraravielliiDEaqhlr...s....eealeeLrsl 115
                                                         + +++ ll +++ ++  +r    ++++DE++ l    +      ale L+++
  gi|557694833|ref|YP_008797887.1| 116 qrerraqalspptilitTPETLQILLtARILRQYLKRVE--AVVVDEVHELAgdkRgsqlSLALERLVEI 183
                                       888888888888888888899999999999999999866..**********8765243455555555443 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5.6
                            AAA_22  75 seellealeqalrarav.....ielliiDEaqh.lrsee 107
                                        +e+ +++++  r+ ++     ++++i+ + +  l   e
  gi|557694833|ref|YP_008797887.1| 345 PREVTRLVQRVGRSGHTvsgtaKGVIIVTDSDDaL---E 380
                                       45555555555555555556777888887777644...3 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 5.7
                            AAA_22  38 erpevvfvtlpsstsskdllrellralg 65 
                                       e+ + +++ +++  +s++ll++ lr+++
  gi|557694833|ref|YP_008797887.1| 581 EEEKALEMLAQQYRTSTTLLKKSLREVK 608
                                       4555556666666666666666666665 PP

>> MciZ  Mother cell inhibitor of FtsZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.3e-05      0.18       9      19 ..     518     528 ..     515     531 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.3e-05
                                       EEEEESEHHHH CS
                              MciZ   9 giiLvGKAWEI 19 
                                       ++iL GKAWEI
  gi|557694833|ref|YP_008797887.1| 518 RFILMGKAWEI 528
                                       79********9 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00017      0.34       5      43 ..      32      89 ..      28     136 .. 0.65
   2 ?   -1.1   0.0      0.66   1.3e+03     191     225 ..     122     160 ..      97     161 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                            AAA_11  5 sqreaiksalseseitliqGPPGtgKT.ktivellsqll...................s 43
                                       q +ai ++l+ ++  l+  P GtgKT  +++ l+++ll                   +
  gi|557694833|ref|YP_008797887.1| 32 PQIQAIPHVLNGEN-ILLMAPTGTGKTeAALIPLINNLLlsssfegvkilyitplralN 89
                                      699***********.6999999*****88899999999755555555555555444440 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.66
                            AAA_11 191 evldeaeivltTlsga....gsklleklakkfdvviIDE 225
                                       + l+   i +tT  +     +++ l+++ k++++v++DE
  gi|557694833|ref|YP_008797887.1| 122 QALSPPTILITTPETLqillTARILRQYLKRVEAVVVDE 160
                                       555555555555433311136788999999********9 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00017      0.35       8      67 ..      36      98 ..      30     168 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                                      HHHS..-SSEEEEEE-TTSSHHH.HHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHH CS
                     UvrD-helicase  8 aias..lggpilveAsAGsGKTf.vlaerilrlikeeeiepdrilvvTFTnkAaeElkeRiee 67
                                      ai +   g++il++A  G+GKT   l+ +i +l+   + e  +il +T  ++  + l  Rie 
  gi|557694833|ref|YP_008797887.1| 36 AIPHvlNGENILLMAPTGTGKTEaALIPLINNLLLSSSFEGVKILYITPLRALNRDLLDRIEW 98
                                      333334899*************637999*********9***9***999877777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (951 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); 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 0.28s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 6296.85
//
Query:       gi|557694834|ref|YP_008797888.1|  [L=190]
Description: hypothetical protein CSUB_C1407 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-05   23.2   0.3    0.00012   22.8   0.3    1.2  1  zinc_ribbon_15   zinc-ribbon family
     0.0002   21.3   0.5    0.00033   20.6   0.5    1.3  1  DZR              Double zinc ribbon
     0.0019   17.8   0.9     0.0032   17.1   0.9    1.4  1  zinc_ribbon_2    zinc-ribbon domain
     0.0085   16.4   0.2       0.01   16.2   0.2    1.1  1  zf-C4H2          Zinc finger-containing protein
  ------ inclusion threshold ------
      0.021   14.2   0.7      0.039   13.4   0.7    1.5  1  zf-ribbon_3      zinc-ribbon domain
      0.024   14.8   0.5      0.038   14.1   0.5    1.2  1  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
      0.073   13.2   3.1       0.12   12.4   3.1    1.3  1  UPF0547          Uncharacterised protein family UPF0547
       0.13   12.0   0.1       0.32   10.7   0.1    1.6  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.13   12.3   0.2       0.25   11.4   0.2    1.5  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
       0.22   11.1   5.8      0.034   13.7   2.0    1.5  2  Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
       0.24   11.4   0.1       0.24   11.4   0.1    1.8  2  Nudix_N_2        Nudix N-terminal
        2.9    8.3  11.3       0.89    9.9   6.9    2.0  2  DUF3995          Protein of unknown function (DUF3995)


Domain annotation for each model (and alignments):
>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.3   7.9e-08   0.00012      49      86 .]     136     172 ..     113     172 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.9e-08
                    zinc_ribbon_15  49 askelgkeiekkesse...........kkeCknCgkeveeefkyCpkCg 86 
                                        s                         +k+Ck C++++  e+++Cp Cg
  gi|557694834|ref|YP_008797888.1| 136 PSP------------AtsppqenvqqvMKICKFCSSVIPGESRFCPMCG 172
                                       332............0223333444559********************9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.5   2.2e-07   0.00033       1      24 [.     154     177 ..     154     185 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.2e-07
                               DZR   1 CpqCgeelppdarfCseCgtklka 24 
                                       C+ C + +p ++rfC+ Cg+kl +
  gi|557694834|ref|YP_008797888.1| 154 CKFCSSVIPGESRFCPMCGAKLVE 177
                                       9********************975 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.9   2.1e-06    0.0032       2      23 .]     154     175 ..     153     175 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.1e-06
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtpl 23 
                                       C+ C   ++ +++FCp CG++l
  gi|557694834|ref|YP_008797888.1| 154 CKFCSSVIPGESRFCPMCGAKL 175
                                       999*****************97 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   6.9e-06      0.01     159     201 ..     126     174 ..      80     175 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.9e-06
                           zf-C4H2 159 qapsapstatasfrqqpPP......MKsClsChqqIHRNAPiCPlCKaK 201
                                       q++sa+++ ++s    pP       MK C+ C   I      CP+C aK
  gi|557694834|ref|YP_008797888.1| 126 QQSSATQKIEPSPATSPPQenvqqvMKICKFCSSVIPGESRFCPMCGAK 174
                                       1122222333333333333666666*********************998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   2.6e-05     0.039       2      26 .]     151     175 ..     150     179 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                       zf-ribbon_3   2 tvrCPnCGaplssddnvCpyCGtkl 26 
                                       ++ C  C +++  + ++Cp CG+kl
  gi|557694834|ref|YP_008797888.1| 151 MKICKFCSSVIPGESRFCPMCGAKL 175
                                       789999*9*99***********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 ?   14.1   0.5   2.6e-05     0.038       3      32 ..     146     174 ..     145     179 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.6e-05
                      NOB1_Zn_bind   3 rvkswvlrChaCfkvtkdmtkkFCpkCGnk 32 
                                       +v++ +  C  C +v++  + +FCp CG k
  gi|557694834|ref|YP_008797888.1| 146 NVQQVMKICKFCSSVIPGES-RFCPMCGAK 174
                                       6889999*********9866.6******87 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.1   8.3e-05      0.12       1      21 [.     152     172 ..     152     172 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.3e-05
                           UPF0547   1 KvCPeCeakvPvaaqfCphCG 21 
                                       K C+ C++ +P   +fCp CG
  gi|557694834|ref|YP_008797888.1| 152 KICKFCSSVIPGESRFCPMCG 172
                                       67******************9 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 ?   10.7   0.1   0.00021      0.32       3      13 ..     165     175 ..     164     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
                     zf-NADH-PPase   3 hrFCgrCGapt 13 
                                       +rFC+ CGa+ 
  gi|557694834|ref|YP_008797888.1| 165 SRFCPMCGAKL 175
                                       6********96 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 ?   11.4   0.2   0.00017      0.25       2      15 ..     168     181 ..     167     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00017
                    DNA_ligase_ZBD   2 CPvCGsavvReege 15 
                                       CP CG+++v + +e
  gi|557694834|ref|YP_008797888.1| 168 CPMCGAKLVETGEE 181
                                       *********99877 PP

>> Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       2.4   3.6e+03     171     184 ..      10      23 ..       7      31 .. 0.57
   2 ?   13.7   2.0   2.3e-05     0.034      15      78 ..      54     115 ..      39     118 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.4
                   Gpr1_Fun34_YaaH 171 ggvfgiiaaflawY 184
                                       + v+ ++ afl  Y
  gi|557694834|ref|YP_008797888.1|  10 ATVLSFVIAFLLIY 23 
                                       44555555555554 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.3e-05
                   Gpr1_Fun34_YaaH  15 rkfaNPaPl.gllafalttfvlslvnlgargitepnvvvglalfyGGlvqllaGiwefavgntFg 78 
                                        k a +a++ g++afal+ f l++      ++++ ++vv+ +l +GG+  +laG++ +++gn F 
  gi|557694834|ref|YP_008797888.1|  54 AKSALAAAVgGVAAFALSRF-LNFSLWSPSQLET-DLVVSRLLLIGGA-TFLAGLMGYVAGNVFV 115
                                       45555555526999****99.5666677777766.7999999999996.6*************96 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.5       1.9   2.8e+03       1       4 [.     155     158 ..     152     160 .. 0.61
   2 ?   11.4   0.1   0.00016      0.24       1      12 [.     166     177 ..     166     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.9
                                       -B-T CS
                         Nudix_N_2   1 kFCs 4  
                                       kFCs
  gi|557694834|ref|YP_008797888.1| 155 KFCS 158
                                       5665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00016
                                       -B-TTT--B-EE CS
                         Nudix_N_2   1 kFCsqCGtpvel 12 
                                       +FC++CG+++  
  gi|557694834|ref|YP_008797888.1| 166 RFCPMCGAKLVE 177
                                       8*******9653 PP

>> DUF3995  Protein of unknown function (DUF3995)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.9    0.0006      0.89      40     117 ..       6      82 ..       2      89 .. 0.88
   2 ?    3.0   2.3     0.081   1.2e+02      41      93 ..      58     111 ..      54     129 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0006
                           DUF3995  40 atlavallllaaAllvlalarllgaplssrllrlaawvvaavlllRgilgdfkyvgvfkrvkdtaafarldtllysP 116
                                        ++a ++l +++A l++ l +++ +pl +++l++++++ aa l++R+  +    +  + +v+  a  + l+  l+sP
  gi|557694834|ref|YP_008797888.1|   6 RLAAATVLSFVIAFLLIYLENIYLNPLQPAILSMLLTASAAGLVARAS-AKSALAAAVGGVAAFALSRFLNFSLWSP 81 
                                       578889999999***********************************8.6666888888888888789999999999 PP

                           DUF3995 117 l 117
                                        
  gi|557694834|ref|YP_008797888.1|  82 S 82 
                                       5 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.081
                           DUF3995  41 tlavallllaaAllvlalarll.gaplssrllrlaawvvaavlllRgilgdfky 93 
                                       ++a ++ ++a+Al  +++  l+ +++l + l+   ++++++  +l g++g++  
  gi|557694834|ref|YP_008797888.1|  58 LAAAVGGVAAFALSRFLNFSLWsPSQLETDLVVSRLLLIGGATFLAGLMGYVAG 111
                                       344444445555555555555522233333433333333333344455565543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1029  (0.0573931); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1380.22
//
Query:       gi|557694835|ref|YP_008797889.1|  [L=401]
Description: acyl-CoA dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-44  149.8   3.8    8.2e-44  149.4   3.8    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.3e-32  112.8   0.0    2.8e-32  111.7   0.0    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    3.5e-27   94.4   0.0    7.2e-27   93.4   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      1e-18   67.9   1.5    1.5e-18   67.4   1.5    1.2  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 !  149.4   3.8   1.8e-47   8.2e-44       1     149 [.     242     391 ..     242     392 .. 0.99

  Alignments for each domain:
  == domain 1  score: 149.4 bits;  conditional E-value: 1.8e-47
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       g+Gf++am t +h+R++vaa+a+g+a+++le +l+y+ +r+ f +pli +q+v++++ em + le+arl++y a+ +
  gi|557694835|ref|YP_008797889.1| 242 GQGFKIAMDTYDHGRIGVAAQAVGVAQACLEKTLQYSLQRRVFERPLIYFQAVQFHVSEMLTMLEGARLMLYWATTL 318
                                       79*************************************************************************** PP

                                       -------.HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpd.raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       +++++p+  ++asmaKl+a+e+a+++a +a+ ++Gg G+++++ ver++rd++v+ i+eG+++iq+++i r++
  gi|557694835|ref|YP_008797889.1| 319 ANKNRPEaVMAASMAKLYATEVAEKAALKAITVHGGVGVATDGLVERFLRDSQVFKIYEGANDIQKLVILRQM 391
                                       *******99*************************************************************998 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 !  111.7   0.0   6.3e-36   2.8e-32       2     113 .]      17     127 ..      16     127 .. 0.96

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 6.3e-36
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                       ee e +r++vr+fae+e++p ++e+++++++p++l+kk+ae+G+lg+ +pe y G+g d++++ +++ee++r + ++
  gi|557694835|ref|YP_008797889.1|  17 EEYEIFRKSVRAFAEKEIEPLVKEIERTNTIPKALLKKAAEQGYLGLGIPETYDGQGTDMMYSTLFVEEVSRICPAF 93 
                                       8999**********************999************************************************ PP

                                       HHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  79 alllgvhsslvapailrfGteeqkrryLpklasge 113
                                        ++  v+  l +++++ +Gteeqkr+yLp++a+ge
  gi|557694835|ref|YP_008797889.1|  94 TVATLVGV-LFTYPVMVYGTEEQKRKYLPPIARGE 127
                                       99887865.6669*********************8 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 !   93.4   0.0   1.6e-30   7.2e-27       2      97 .]     132     230 ..     131     230 .. 0.91

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 1.6e-30
                                       EE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEE.TS---...----EEEEEEE..GGGEE CS
                     Acyl-CoA_dh_M   2 falTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlar.tekpd...rarglslflvprdapgvs 74 
                                        a TEp+aG+dva+++t +a+r++g++ +nG+K +i++a +a++++vlar +  p+   r++gls+f+v+r++pg++
  gi|557694835|ref|YP_008797889.1| 132 HATTEPGAGTDVAGIET-TAKRKNGGWEINGRKYFISGADKADYFIVLARtSPPPSrkeRHKGLSFFIVERGTPGFR 207
                                       589**************.77777779************************7444446678***************** PP

                                       E-----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  75 vrrieeklGlrglptgelvfedv 97 
                                       v+++ e +G+rg + +e+ +++v
  gi|557694835|ref|YP_008797889.1| 208 VGEKIEVIGIRGSHPCEVILDNV 230
                                       *9999***************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 !   67.4   1.5   3.3e-22   1.5e-18       1     133 [.     257     380 ..     257     381 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 3.3e-22
                                       .HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----H CS
                     Acyl-CoA_dh_2   1 lgiaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtv 77 
                                       +g+aa+a+G+A+a+l++++++  +r    ++++l  ++a+q+ + e+ + l+ Ar++l+ a++        ++++ +
  gi|557694835|ref|YP_008797889.1| 257 IGVAAQAVGVAQACLEKTLQYSLQRRV--FERPLIYFQAVQFHVSEMLTMLEGARLMLYWATTL-------ANKNRP 324
                                       589********************9999..9******************************9999.......333356 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  78 edraearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                       e +  a++a+++a+e a +a+ +++ ++Gg +++++  ++R++RD ++ ++++++n
  gi|557694835|ref|YP_008797889.1| 325 EAVMAASMAKLYATEVAEKAALKAITVHGGVGVATDGLVERFLRDSQVFKIYEGAN 380
                                       889*************************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); 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:                         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: 2697.77
//
Query:       gi|557694836|ref|YP_008797890.1|  [L=122]
Description: hypothetical protein CSUB_C1409 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
       0.22   10.9   2.3        0.3   10.5   2.3    1.2  1  Clc-like  Clc-like
        3.2    8.3  11.6       0.78   10.3   1.6    2.3  2  DUF4405   Domain of unknown function (DUF4405)


Domain annotation for each model (and alignments):
>> Clc-like  Clc-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.3   3.4e-05       0.3     116     198 ..      30     113 ..      22     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.4e-05
                          Clc-like 116 llaalsllsgicasvssseailftillvlaallalvadiiFfvaaervdsrfl.kgi..vgtYEkriGyafylalag 189
                                       + aa+ +l ++++    ++  +  ++++l+a+++lv+++   va  +   r++  gi      E ++G+a+ l ++g
  gi|557694836|ref|YP_008797890.1|  30 VHAAIGILGIFVVGAYLATGRVSRVVTALTAVVLLVTLTQ--VAMGMGLMRWVdLGIgqGALEESHRGTAYILLVLG 104
                                       5567777777777777777778888999999998888765..555677778887566314567899*********** PP

                          Clc-like 190 alislvall 198
                                        ++slva +
  gi|557694836|ref|YP_008797890.1| 105 LVVSLVAAI 113
                                       ******976 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   2.8     0.014   1.3e+02      14      59 ..       7      43 ..       1      47 [. 0.78
   2 ?   10.3   1.6   8.7e-05      0.78      11      59 ..      54     105 ..      51     106 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.014
                           DUF4405 14 aiSGillsfavlpsgrgaywaflglskhqwrdiHeilgllflilvv 59
                                      +  G+l  +a+ +sg++a+          ++ +H  +g+l +++v+
  gi|557694836|ref|YP_008797890.1|  7 IGVGVLVQIAIGESGFAAGS---------LQLVHAAIGILGIFVVG 43
                                      55688888887776666555.........89***********9986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.7e-05
                           DUF4405  11 lvlaiSGillsfavlpsgrgaywa....flglskhqwrdiHeilgllflilvv 59 
                                       +v+a++ ++l  + l ++  + +      lg++++ +++ H+ +++++l+l +
  gi|557694836|ref|YP_008797890.1|  54 VVTALTAVVLLVT-LTQVAMGMGLmrwvDLGIGQGALEESHRGTAYILLVLGL 105
                                       5666666666655.333333333356457888******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 868.44
//
Query:       gi|557694837|ref|YP_008797891.1|  [L=542]
Description: thermosome beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-173  577.3  16.0   2.8e-173  577.1  16.0    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 !  577.1  16.0  1.5e-177  2.8e-173       1     490 [.      35     525 ..      35     526 .. 0.98

  Alignments for each domain:
  == domain 1  score: 577.1 bits;  conditional E-value: 1.5e-177
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a+iv+ttlGPkGmdK+lv+++g+v+vTnDGatil+++++ehPaak+++e+a+sqd+ vGDGTtt+viLageLl++a
  gi|557694837|ref|YP_008797891.1|  35 IAEIVRTTLGPKGMDKLLVDNIGDVIVTNDGATILEKIDVEHPAAKMIIEVAKSQDHVVGDGTTTAVILAGELLRKA 111
                                       79*************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHH.HCH CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAv.kli 153
                                       e+li++++h +tii+gy+kal+kale ++e+  +i+++ kdr +L+kv++tsl+sk      ++l +++vd+v +++
  gi|557694837|ref|YP_008797891.1| 112 EELIEQKIHASTIISGYKKALDKALEVINEN--AIKIDLKDRATLRKVITTSLGSKSLGFALDKLVDIAVDSVlSVV 186
                                       *******************************..6666677*********************************9999 PP

                                       CCCS..EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                        Cpn60_TCP1 154 eene..keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                       +e +  ++ d + i++vk+ g+sl ++el++G+v+dk+v+++ mpk++ena+++l+d ++eiekte +++++++d+ 
  gi|557694837|ref|YP_008797891.1| 187 KEVNgkQRADKDDIQIVKKIGRSLGETELIRGVVVDKEVVHAAMPKRVENARIALIDSPFEIEKTEFSAEIRIRDPL 263
                                       8888888889999**************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGG CS
                        Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledlt 305
                                       ++++++++e+++l+ +++k+++ g+nvv+cqkgidd a+ flak+gila+rrvkk+d+e+lakatG+++v+++edl+
  gi|557694837|ref|YP_008797891.1| 264 KIKEFLDEETNILKGMVDKVKAVGANVVFCQKGIDDAAQFFLAKEGILAVRRVKKSDMEKLAKATGGRVVTNFEDLS 340
                                       ***************************************************************************** PP

                                       CGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHH CS
                        Cpn60_TCP1 306 peelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatele 382
                                       p++lG a+ vee+kig+++++++e+++++k++ +llr+  +  lde+era++dA+  +  +++d+++vpGGGa+e e
  gi|557694837|ref|YP_008797891.1| 341 PKDLGRAGLVEERKIGEDRMVFVEKCENPKAVAVLLRAGLERQLDEAERALNDAIMNMIDLVDDPRIVPGGGAIEEE 417
                                       ***************************************************************************** PP

                                       HHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTX CS
                        Cpn60_TCP1 383 lakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagv 459
                                       +a++l++ a ++sg+eqla+ afa+A e+ip+tLaeNaGl+p e++a++r+ah++g+  +g+++  g +id++++gv
  gi|557694837|ref|YP_008797891.1| 418 IARQLRQTAGKLSGKEQLAYLAFAEAVEAIPRTLAENAGLEPVEIMAQIRHAHENGQRAVGVNIFGGGVIDMLANGV 494
                                       ***************************************************************************** PP

                                       EEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 460 vDplkvkrqalksAteaastiLrideiikak 490
                                       ++p+kvk  al s++eaas+iLrid+++ a 
  gi|557694837|ref|YP_008797891.1| 495 IEPAKVKLHALRSSFEAASMILRIDDVVAAS 525
                                       ****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3684.23
//
Query:       gi|557694838|ref|YP_008797892.1|  [L=79]
Description: archaeal histone [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   55.8   0.9    4.9e-15   55.6   0.9    1.1  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
      1e-07   32.4   0.2    1.1e-07   32.2   0.2    1.1  1  Histone        Core histone H2A/H2B/H3/H4
    0.00046   20.0   0.9     0.0032   17.3   0.1    2.0  2  AAA_lid_2      AAA lid domain
    0.00067   19.7   0.1    0.00077   19.6   0.1    1.1  1  CENP-T_C       Centromere kinetochore component CENP-T histon
  ------ inclusion threshold ------
      0.019   15.0   0.0      0.022   14.8   0.0    1.0  1  TFIID-31kDa    Transcription initiation factor IID, 31kD subu
      0.064   13.6   1.5       0.32   11.4   0.2    2.3  2  Ribosomal_L12  Ribosomal protein L7/L12 C-terminal domain
      0.067   13.4   0.6      0.082   13.1   0.6    1.2  1  TAF            TATA box binding protein associated factor (TA


Domain annotation for each model (and alignments):
>> CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) and archaeal histone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.9   1.9e-18   4.9e-15       2      64 ..       7      68 ..       6      69 .. 0.96

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 1.9e-18
                                      XXXHHHHHHHHHCCTTXS-B-HHHHHHHHHHHHHHHHHHHHHHHHHHCCTTSSCE-HHHHHHH CS
                     CBFD_NFYB_HMF  2 eLPiarvkkImksdpdarkiakdAkeliaecveefieelaseAaeickkekrKtikaehiklA 64
                                       +P a++ +Imk++ +a+++++dA + + +++e     +a+eA e+++ ++r+t+k+e+++ A
  gi|557694838|ref|YP_008797892.1|  7 DIPSAPIHRIMKKA-GAARVSEDAADELRKILENVGAMIAKEAFELAQYAGRRTVKKEDVERA 68
                                      58************.********************************************9876 PP

>> Histone  Core histone H2A/H2B/H3/H4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.2   4.5e-11   1.1e-07      56     129 ..       2      70 ..       1      72 [. 0.92

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 4.5e-11
                                       HXXSXXSXHHHHHHHHHHHH.TTSSSXEEXHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTXSEEXHHHHHHHHH CS
                           Histone  56 kstdlliqklpfaRvvreivksekedlrisaeavlalqealEallvelfeeAnllakhaKRvTitpkDiqlArr 129
                                       ++++ +i+++p+ R++++         r+s +a + l ++lE+  + +++eA  la +a R+T+ ++D++ A++
  gi|557694838|ref|YP_008797892.1|   2 SEKEADIPSAPIHRIMKKAGA-----ARVSEDAADELRKILENVGAMIAKEAFELAQYAGRRTVKKEDVERAAK 70 
                                       578899********7777665.....********************************************9987 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1       0.1   2.6e+02      53      72 ..      14      35 ..       8      36 .. 0.66
   2 !   17.3   0.1   1.3e-06    0.0032      29      52 ..      51      74 ..      42      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.1
                         AAA_lid_2 53 HRlrrepeaeg..etteeivee 72
                                      HR+ +++ a +  e++ +++++
  gi|557694838|ref|YP_008797892.1| 14 HRIMKKAGAARvsEDAADELRK 35
                                      9999666666634666666665 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 1.3e-06
                         AAA_lid_2 29 lAalegrdyVtpeDvkeaaplVLa 52
                                      lA ++gr +V +eDv++aa+ VL+
  gi|557694838|ref|YP_008797892.1| 51 LAQYAGRRTVKKEDVERAAKTVLR 74
                                      899*******************97 PP

>> CENP-T_C  Centromere kinetochore component CENP-T histone fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.1     3e-07   0.00077       9      71 ..       9      66 ..       2      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3e-07
                          CENP-T_C  9 PaavvkklakrfakasgskaklekealkalekasdkffeqvgeDLeayakHagRKtidesDvi 71
                                      P+a ++++ k++       a+++++a + l k++++    ++++    a+ agR+t++++Dv+
  gi|557694838|ref|YP_008797892.1|  9 PSAPIHRIMKKA-----GAARVSEDAADELRKILENVGAMIAKEAFELAQYAGRRTVKKEDVE 66
                                      666666665555.....677*****************************************97 PP

>> TFIID-31kDa  Transcription initiation factor IID, 31kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   8.6e-06     0.022      11      70 ..      13      72 ..       4      77 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.6e-06
                       TFIID-31kDa 11 ihliLaslgvteyeerVvlqLldfayrytssvLedAkvlaehakkkevslddvrlAiqsr 70
                                      ih i+++ g   ++e+  + L  +  +  + + ++A  la++a++++v+ +dv+ A ++ 
  gi|557694838|ref|YP_008797892.1| 13 IHRIMKKAGAARVSEDAADELRKILENVGAMIAKEAFELAQYAGRRTVKKEDVERAAKTV 72
                                      9****************************************************9997765 PP

>> Ribosomal_L12  Ribosomal protein L7/L12 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00012      0.32      44      64 ..      24      44 ..      10      47 .. 0.90
   2 ?    1.7   0.1      0.13   3.3e+02      31      56 ..      46      71 ..      43      76 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      EE-HHHHHHHHHHHHCTT-EE CS
                     Ribosomal_L12 44 gvskeeAeeikkkLeeaGAev 64
                                       vs++ A+e+ k Le++GA +
  gi|557694838|ref|YP_008797892.1| 24 RVSEDAADELRKILENVGAMI 44
                                      699****************76 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.13
                                      HHHHTTTTSTEEEEE-HHHHHHHHHH CS
                     Ribosomal_L12 31 KdlVeaapkvvkegvskeeAeeikkk 56
                                      K+  e a  + +  v+ke+ e ++k+
  gi|557694838|ref|YP_008797892.1| 46 KEAFELAQYAGRRTVKKEDVERAAKT 71
                                      55555555556667888888877665 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   3.2e-05     0.082       5      64 ..       9      68 ..       6      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.2e-05
                                      -HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHH CS
                               TAF  5 pkesvkviAeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLtvaDvdsA 64
                                      p+  ++ i    G + +s++aa +L + +e     i++ea    + + R++   +Dv++A
  gi|557694838|ref|YP_008797892.1|  9 PSAPIHRIMKKAGAARVSEDAADELRKILENVGAMIAKEAFELAQYAGRRTVKKEDVERA 68
                                      666677788888999***************999*************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      673  (0.037537); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 595.94
//
Query:       gi|557694839|ref|YP_008797893.1|  [L=279]
Description: hypothetical protein CSUB_C1412 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   31.3  19.1    2.1e-06   27.6   1.7    3.3  4  CdvA            CdvA-like coiled-coil domain
     0.0022   17.9   4.2     0.0022   17.9   4.2    2.6  2  FTA4            Kinetochore complex Fta4 of Sim4 subunit, or 
     0.0034   17.0   1.6     0.0034   17.0   1.6    2.7  2  PI3K_P85_iSH2   Phosphatidylinositol 3-kinase regulatory subu
      0.009   16.0   3.1        1.6    8.7   0.4    2.6  2  Phasin          Poly(hydroxyalcanoate) granule associated pro
  ------ inclusion threshold ------
      0.018   15.1   0.5      0.031   14.3   0.5    1.3  1  DZR             Double zinc ribbon
      0.025   14.0   1.6      0.044   13.3   1.5    1.5  1  Phi-29_GP3      Phi-29 DNA terminal protein GP3
      0.026   14.5   0.1        3.8    7.5   0.1    2.2  2  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,
      0.077   13.1  17.1       0.15   12.1  11.4    2.7  2  DHR10           Designed helical repeat protein 10 domain
       0.08   13.3   0.9       0.13   12.6   0.9    1.4  1  zf-C6H2         zf-MYND-like zinc finger, mRNA-binding
      0.081   13.0   3.9       0.49   10.4   1.1    2.4  2  DUF1664         Protein of unknown function (DUF1664)
        0.1   12.5   4.8       0.58   10.0   2.7    2.3  2  Sec34           Sec34-like family
       0.11   12.8   0.6       0.21   11.8   0.6    1.5  1  Ribosomal_L32p  Ribosomal L32p protein family
       0.12   12.5   0.3        0.2   11.8   0.3    1.3  1  zf-Dof          Dof domain, zinc finger
       0.13   13.4   2.0       0.36   12.0   2.0    1.8  1  DUF3484         Membrane-attachment and polymerisation-promot
       0.14   11.2   0.2        2.5    7.1   0.0    2.0  2  DUF3131         Protein of unknown function (DUF3131)
       0.67    8.5  11.3        1.8    7.1   0.4    2.1  2  FapA            Flagellar Assembly Protein A
       0.73    9.9   7.3        8.7    6.4   2.6    3.0  2  GvpG            Gas vesicle protein G
       0.89    9.7  10.8        2.8    8.1   1.2    2.9  2  DUF5595         Domain of unknown function (DUF5595)
        1.3    8.9  10.1        2.4    8.0   4.8    3.5  3  SHOCT           Short C-terminal domain
        1.3    9.1   6.0       0.36   10.9   0.9    2.2  2  DUF1003         Protein of unknown function (DUF1003)
        2.8    7.9  10.2         18    5.3   0.3    3.6  3  Prefoldin       Prefoldin subunit
          3    7.7   7.6         32    4.4   7.6    2.2  1  zinc_ribbon_2   zinc-ribbon domain
        4.9    7.7  14.4        5.1    7.6   2.7    3.4  3  Spectrin        Spectrin repeat
        5.9    5.7  14.1        1.9    7.3   3.3    2.5  3  IFT57           Intra-flagellar transport protein 57
        7.8    5.6   8.5        3.6    6.7   0.1    2.2  2  TMPIT           TMPIT-like protein
        8.1    6.9  10.2         15    6.1   0.5    3.9  5  FlaC_arch       Flagella accessory protein C (FlaC)


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 ?   -2.5   0.1       6.1   4.2e+03      97     115 ..      38      56 ..      32      64 .. 0.57
   2 !   27.6   1.7     3e-09   2.1e-06      29      94 ..     107     172 ..      91     185 .. 0.84
   3 ?   -0.8   0.0       1.9   1.3e+03      20      39 ..     190     209 ..     175     215 .. 0.69
   4 !   12.8   3.9   0.00011     0.076      48      92 ..     231     275 ..     218     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.1
                              CdvA  97 ekeeikklleklsklelee 115
                                       e ee+++++e+l +  +e+
  gi|557694839|ref|YP_008797893.1|  38 EVEEAEEVVEQLPESPAES 56 
                                       5666677777764433333 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 3e-09
                              CdvA  29 ealkklkekakelkeklkkrlkeledqikslekalanlkisyasGEidEeaYksaieairellesa 94 
                                       e + + + + k+l e+ +++++++e+ i++l+++l +lk++++ GEi++++Y +++ +i++++ ++
  gi|557694839|ref|YP_008797893.1| 107 ELFHEYRSRLKTLDERRQAEIAKVEERINTLNSSLEKLKVKHEVGEIPDRQYITQKLEIEREMGRL 172
                                       4455667788888888899999999999999999*********************99999887665 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.9
                              CdvA  20 yeeikekleealkklkekak 39 
                                          +k +lee l+k+k +  
  gi|557694839|ref|YP_008797893.1| 190 LPTFKTQLEERLQKVKTNGR 209
                                       55677777777777776655 PP

  == domain 4  score: 12.8 bits;  conditional E-value: 0.00011
                              CdvA  48 rlkeledqikslekalanlkisyasGEidEeaYksaieairelle 92 
                                        l+ l +q ++++k l +l+++y++GE++ ++Y s +++++++le
  gi|557694839|ref|YP_008797893.1| 231 ALEVLMEQHQKIKKELNKLELRYKIGELKQSEYLSLKQKLERQLE 275
                                       4677899*****************************999999987 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   4.2   3.2e-06    0.0022     100     192 ..      43     173 ..      23     179 .. 0.78
   2 ?    1.5   2.7      0.35   2.4e+02     115     162 ..     225     272 ..     184     278 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.2e-06
                              FTA4 100 eelIkeLPeswe.........................................veekeaeeepleallerYaelrar 135
                                       ee++++LPes                                                 +e++ e   e ++e r+r
  gi|557694839|ref|YP_008797893.1|  43 EEVVEQLPESPAesaeqqavqppagedvaveekrlvdqmstvylwyfrlidlfL----DREADPEVFGELFHEYRSR 115
                                       567777777777777777777777777777777777777777777777765432....233334666789******* PP

                              FTA4 136 Lielserrqqlqarla.rlrklkallepflgsedpqesvqenlvtrdgeleaElermR 192
                                       L+ l+errq+  a+++ r ++l++ le+++   +  e  +++ +t++ e+e+E+ r+R
  gi|557694839|ref|YP_008797893.1| 116 LKTLDERRQAEIAKVEeRINTLNSSLEKLKVKHEVGEIPDRQYITQKLEIEREMGRLR 173
                                       **************96489**********665666666678899************99 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.35
                              FTA4 115 keaeeepleallerYaelrarLielserrqqlqarlarlrklkallep 162
                                        ++  + le l e+ ++++++L +l+ r++  + + +++ +lk++le+
  gi|557694839|ref|YP_008797893.1| 225 VQSALKALEVLMEQHQKIKKELNKLELRYKIGELKQSEYLSLKQKLER 272
                                       344445567788888888888888888888888888888888888876 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 !   17.0   1.6   4.9e-06    0.0034      69     137 ..     117     181 ..      74     196 .. 0.84
   2 ?   -1.0   8.0       1.7   1.2e+03      58     114 ..     215     273 ..     187     277 .. 0.53

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.9e-06
                     PI3K_P85_iSH2  69 klqekfskeaqehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqk 137
                                       k+      e  ++Ei k++e ++ l+s l++l+ + e  e   +q +++++e+eRe+ +l+p l+ L++
  gi|557694839|ref|YP_008797893.1| 117 KT----LDERRQAEIAKVEERINTLNSSLEKLKVKHEVGEIPDRQYITQKLEIEREMGRLRPKLMYLRN 181
                                       33....3356799********************99998888889999*******************997 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                     PI3K_P85_iSH2  58 neaikmFeeqiklqekfskea.qehEieklqenleqlksrlkelhsske.kLeedlkqq 114
                                       +e i+mFe+ ++   k  +   ++h + k + n  +l+ ++ el++s   +L+++l+ q
  gi|557694839|ref|YP_008797893.1| 215 EEFINMFEQDVQSALKALEVLmEQHQKIKKELNKLELRYKIGELKQSEYlSLKQKLERQ 273
                                       56666666666555554433312333334455555556666666655432455555544 PP

>> Phasin  Poly(hydroxyalcanoate) granule associated protein (phasin)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0076       5.2      94     125 ..     114     145 ..     103     146 .. 0.88
   2 !    8.7   0.4    0.0024       1.6      63     117 ..     194     249 ..     186     261 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0076
                            Phasin  94 kaLsrlgvpsredveaLsarvdeLtkelekla 125
                                       + L++l+  ++ +++++++r+++L+++lekl+
  gi|557694839|ref|YP_008797893.1| 114 SRLKTLDERRQAEIAKVEERINTLNSSLEKLK 145
                                       679999999*******************9985 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0024
                            Phasin  63 resvkskveevkekae..eqwdklekafdervakaLsrlgvpsredveaLsarvdeL 117
                                       ++++++++++vk++    +  ++  ++f++ v++aL+ l+v  ++  +++++++++L
  gi|557694839|ref|YP_008797893.1| 194 KTQLEERLQKVKTNGRdlGMQEEFINMFEQDVQSALKALEVLMEQH-QKIKKELNKL 249
                                       56677777777765441156678889**************987553.5555555555 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5   4.5e-05     0.031      31      49 .]       8      25 ..       2      43 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.5e-05
                               DZR 31 CpsCgekvdpearfCpeCG 49
                                      Cp+C++ + ++ +fC +CG
  gi|557694839|ref|YP_008797893.1|  8 CPNCHRLTIKG-KFCIYCG 25
                                      55555544333.5555555 PP

>> Phi-29_GP3  Phi-29 DNA terminal protein GP3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.5   6.4e-05     0.044     159     233 ..     190     266 ..     121     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.4e-05
                                       HHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHH-BSHHHHHH.HHHHHTS-HH.HHHHHHHHHTTT-------- CS
                        Phi-29_GP3 159 ledkeesmeeradgdyyekkdiqlklnfiksveqsfnsfddadel.ikklkkippd.dfveltlvideidfeeydsk 233
                                       l + +  +eer +    + +d+ ++++fi++ eq  +s  +a e+ +++ +ki  + + +el  +i e++  ey s 
  gi|557694839|ref|YP_008797893.1| 190 LPTFKTQLEERLQKVKTNGRDLGMQEEFINMFEQDVQSALKALEVlMEQHQKIKKElNKLELRYKIGELKQSEYLSL 266
                                       4456677999999999999*******************888888625778899876467889999999999999775 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   0.0     0.038        26      70     101 ..     110     141 ..      97     147 .. 0.63
   2 ?    7.5   0.1    0.0056       3.8      32      91 ..     187     250 ..     171     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.038
                      Baculo_PEP_C  70 tnLtdalnalqdtlrneLtnlnsiltnLlssv 101
                                       ++  + l++l +  + e+  ++  +++L+ss+
  gi|557694839|ref|YP_008797893.1| 110 HEYRSRLKTLDERRQAEIAKVEERINTLNSSL 141
                                       44455566666666666666666666666665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0056
                      Baculo_PEP_C  32 ilaqlatlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq......dtlrneLtnln 91 
                                       + a+l t ++++e++L++++++ ++ l  +++ ++ + + +++al+al+      +++++eL+ l+
  gi|557694839|ref|YP_008797893.1| 187 L-ADLPTFKTQLEERLQKVKTNGRD-LGMQEEFINMFEQDVQSALKALEvlmeqhQKIKKELNKLE 250
                                       4.89999999999999999998888.4556777788888888888888877788889999999876 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 ?    3.5   0.3       0.1        70      40      66 ..     117     144 ..     100     176 .. 0.61
   2 ?   12.1  11.4   0.00022      0.15      11      88 ..     201     275 ..     194     277 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.1
                             DHR10  40 kllee.ieaelakleeakkklkelrdal 66 
                                       k l+e  +ae+ak+ee   +l++  ++l
  gi|557694839|ref|YP_008797893.1| 117 KTLDErRQAEIAKVEERINTLNSSLEKL 144
                                       4444434444444444444443333333 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00022
                             DHR10  11 laelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrql 87 
                                       l++   + r+l ++ + ++ +e+d++s++k+le + ++ +k +++     +l+ +++  e +++e+ + ++ l+rql
  gi|557694839|ref|YP_008797893.1| 201 LQKVKTNGRDLGMQEEFINMFEQDVQSALKALEVLMEQHQKIKKELN---KLELRYKIGELKQSEYLSLKQKLERQL 274
                                       555566779***********************999988888876655...555556666666699999999999999 PP

                             DHR10  88 e 88 
                                       e
  gi|557694839|ref|YP_008797893.1| 275 E 275
                                       8 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 ?   12.6   0.9   0.00019      0.13      10      29 ..       3      24 ..       1      27 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00019
                           zf-C6H2 10 assLqCptClklgike..sfFC 29
                                      +++++Cp C++l ik+   ++C
  gi|557694839|ref|YP_008797893.1|  3 TTRIECPNCHRLTIKGkfCIYC 24
                                      4469***********6444455 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1      0.19   1.3e+02     100     122 ..     124     146 ..     108     153 .. 0.72
   2 ?   10.4   1.1   0.00071      0.49      57     119 ..     190     255 ..     183     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.19
                           DUF1664 100 gedvesvkeavegleskleriee 122
                                       + ++ +v+e +++l+s+le+++ 
  gi|557694839|ref|YP_008797893.1| 124 QAEIAKVEERINTLNSSLEKLKV 146
                                       55677777777777777777664 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00071
                           DUF1664  57 laatkrhLssridrvdkk...ldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       l + k +L++r+++v ++   l  q+e ++  +++v+++ + l+ + e+ +++k+  ++le + + 
  gi|557694839|ref|YP_008797893.1| 190 LPTFKTQLEERLQKVKTNgrdLGMQEEFINMFEQDVQSALKALEVLMEQHQKIKKELNKLELRYKI 255
                                       6678999****99997543238899*********************************99975444 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.25   1.7e+02      23      53 ..     116     147 ..     100     176 .. 0.67
   2 ?   10.0   2.7   0.00084      0.58       5      69 ..     211     275 ..     208     276 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.25
                             Sec34  23 leqLeel.eekfksvsektsslheaceqllee 53 
                                       l++L+e  + +  +v+e+ ++l+++ e+l  +
  gi|557694839|ref|YP_008797893.1| 116 LKTLDERrQAEIAKVEERINTLNSSLEKLKVK 147
                                       55554431345666666666666666665433 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00084
                             Sec34   5 LeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                       L ++ee ++ + +++++al+ Le l e++++++++ ++l+ + +    +q+++ +l++++e +L+
  gi|557694839|ref|YP_008797893.1| 211 LGMQEEFINMFEQDVQSALKALEVLMEQHQKIKKELNKLELRYKIGELKQSEYLSLKQKLERQLE 275
                                       6677888899999*****************************99999999999999999999986 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.6   0.00031      0.21      25      48 ..       4      27 ..       1      33 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00031
                                      -EEEETTTCCEECTTC-BTTTTBS CS
                    Ribosomal_L32p 25 nlvecpncgelklpHrvcpscGyY 48
                                      +  ecpnc+ l++    c +cGy 
  gi|557694839|ref|YP_008797893.1|  4 TRIECPNCHRLTIKGKFCIYCGYT 27
                                      5679*****************985 PP

>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00029       0.2       4      27 ..       6      31 ..       3      33 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
                            zf-Dof  4 lkCprCe..stntkFcYyNNyslsqP 27
                                      ++Cp C+  + + kFc y  y l+qP
  gi|557694839|ref|YP_008797893.1|  6 IECPNCHrlTIKGKFCIYCGYTLEQP 31
                                      79****93345679***********9 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 ?   12.0   2.0   0.00053      0.36      17      52 ..      29      68 ..      16      81 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00053
                           DUF3484 17 rqPvdp.q..vqenpqvqeqaqeqPvpskeqeekep.kke 52
                                      +qPv+p +  v+e+++v+eq +e P++s eq++ +p  +e
  gi|557694839|ref|YP_008797893.1| 29 EQPVEPpKpeVEEAEEVVEQLPESPAESAEQQAVQPpAGE 68
                                      79***4453467**************97777776665444 PP

>> DUF3131  Protein of unknown function (DUF3131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.12        84      54      89 ..     128     165 ..     124     171 .. 0.86
   2 ?    7.1   0.0    0.0036       2.5      67     147 ..     187     264 ..     183     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.12
                           DUF3131  54 kefderirklLktLaklplf..kgelPnkvyntrtlem 89 
                                       ++++eri++l ++L+kl+     ge+P + y t++le+
  gi|557694839|ref|YP_008797893.1| 128 AKVEERINTLNSSLEKLKVKheVGEIPDRQYITQKLEI 165
                                       57899**********999884468*********99987 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0036
                           DUF3131  67 LaklplfkgelPnkvyntrtlemvdygnnpkeegigwsAlDigRllaaLkvlktrypeyadaveaivarWslsrlvk 143
                                       La lp+fk++l +++ +++t    d+g +++   i++   D+   l aL+vl +++ + +++++++ +r+++ +l +
  gi|557694839|ref|YP_008797893.1| 187 LADLPTFKTQLEERLQKVKTNGR-DLGMQEE--FINMFEQDVQSALKALEVLMEQHQKIKKELNKLELRYKIGELKQ 260
                                       77888888888888888887766.7777666..678888999999***************************99988 PP

                           DUF3131 144 dgql 147
                                        + l
  gi|557694839|ref|YP_008797893.1| 261 SEYL 264
                                       7665 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.4    0.0026       1.8     367     436 ..      99     170 ..      68     178 .. 0.71
   2 ?    5.3   5.1    0.0088       6.1     335     408 ..     183     253 ..     175     276 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0026
                              FapA 367 kaekqlesekk.eqlkklletkeklkeeleeleeelkelkeeleskkeea.kikvnkeiypgvkikigkkkl 436
                                       +a++++  e + e   +l++  e+ + e++++ee++++l+++le+ k +    ++ ++ y   k++i +++ 
  gi|557694839|ref|YP_008797893.1|  99 EADPEVFGELFhEYRSRLKTLDERRQAEIAKVEERINTLNSSLEKLKVKHeVGEIPDRQYITQKLEIEREMG 170
                                       555555555440444555555589999999999999999999999965555778888888888887776655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0088
                              FapA 335 lkeklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeel 408
                                       ++ +l++l +   +lee+l+k+k + + l +   ++++   ++++++++l+++e l+e+ +++++el++l+ + 
  gi|557694839|ref|YP_008797893.1| 183 FNIRLADLPTFKTQLEERLQKVKTNGRDLGM---QEEFINMFEQDVQSALKALEVLMEQHQKIKKELNKLELRY 253
                                       5667788888889999999999999666666...6667778888888888888888888888888888766444 PP

>> GvpG  Gas vesicle protein G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.1     0.041        28      31      58 ..     135     162 ..     119     175 .. 0.83
   2 ?    6.4   2.6     0.013       8.7      26      56 ..     235     265 ..     223     277 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.041
                              GvpG  31 enlrkeLaaLqqeLdaGeIdeeeFdrrE 58 
                                       ++l+  L +L+ + + GeI + ++  + 
  gi|557694839|ref|YP_008797893.1| 135 NTLNSSLEKLKVKHEVGEIPDRQYITQK 162
                                       579999*************999997765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                              GvpG  26 qlddqenlrkeLaaLqqeLdaGeIdeeeFdr 56 
                                        +++ ++++keL +L+++ + Ge ++ e+  
  gi|557694839|ref|YP_008797893.1| 235 LMEQHQKIKKELNKLELRYKIGELKQSEYLS 265
                                       5677899********************9965 PP

>> DUF5595  Domain of unknown function (DUF5595)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.2    0.0041       2.8       7      69 ..      71     129 ..      66     147 .. 0.60
   2 ?    5.5   2.7     0.027        18      35      71 ..     214     250 ..     212     252 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0041
                           DUF5595   7 ievnkLFldYtvkcYekFmqgeDtFeeedaeleskLkelynvdeaqlesleeeekrLeeEier 69 
                                       ++++k ++d +++ Y  + +  D F + +a  e  + el++ ++++l++l+e ++      ++
  gi|557694839|ref|YP_008797893.1|  71 AVEEKRLVDQMSTVYLWYFRLIDLFLDREADPE-VFGELFHEYRSRLKTLDERRQAEI---AK 129
                                       556666666666777777777777766666654.366677777777776666554322...22 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.027
                           DUF5595  35 daeleskLkelynvdeaqlesleeeekrLeeEierle 71 
                                        +e+ + +++ ++   + le l e++++ ++E+++le
  gi|557694839|ref|YP_008797893.1| 214 QEEFINMFEQDVQSALKALEVLMEQHQKIKKELNKLE 250
                                       6899999999999999*******************98 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.47   3.3e+02       2      12 ..     115     125 ..     114     127 .. 0.85
   2 ?   -0.5   0.0       1.7   1.1e+03       3      15 ..     141     153 ..     139     153 .. 0.84
   3 ?    8.0   4.8    0.0035       2.4       2      27 ..     245     270 ..     244     271 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.47
                             SHOCT   2 aLekLkeLyar 12 
                                       +L++L+e++++
  gi|557694839|ref|YP_008797893.1| 115 RLKTLDERRQA 125
                                       89******976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                             SHOCT   3 LekLkeLyarGeI 15 
                                       LekLk  ++ GeI
  gi|557694839|ref|YP_008797893.1| 141 LEKLKVKHEVGEI 153
                                       9****98888887 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0035
                             SHOCT   2 aLekLkeLyarGeIteEEFeakKakL 27 
                                       +L kL  +y  Ge+ + E+   K+kL
  gi|557694839|ref|YP_008797893.1| 245 ELNKLELRYKIGELKQSEYLSLKQKL 270
                                       799**********************9 PP

>> DUF1003  Protein of unknown function (DUF1003)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.4       1.1   7.7e+02      76     100 ..     120     144 ..     111     149 .. 0.71
   2 ?   10.9   0.9   0.00053      0.36      44      93 ..     224     273 ..     216     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1.1
                           DUF1003  76 nlkaeaeiekLtrevaalrealgev 100
                                       +++ +aei+k+ +++++l+++l++ 
  gi|557694839|ref|YP_008797893.1| 120 DERRQAEIAKVEERINTLNSSLEKL 144
                                       5677777888888887777776654 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00053
                           DUF1003  44 slqaalaaplIllsqnRqadrdrvraeedrqvnlkaeaeiekLtrevaal 93 
                                       ++q+al a  +l++q  + +++  + e+ +++ + ++ e   L ++++ +
  gi|557694839|ref|YP_008797893.1| 224 DVQSALKALEVLMEQHQKIKKELNKLELRYKIGELKQSEYLSLKQKLERQ 273
                                       799******************************************99876 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.84   5.8e+02      20      51 ..      37      72 ..      25      87 .. 0.68
   2 ?    5.3   0.3     0.026        18       8      30 ..     123     145 ..     115     153 .. 0.79
   3 ?    4.9   2.0     0.033        23      79     111 ..     218     250 ..     214     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.84
                                      HHHHHHHHHHHHHTT.....-TT-EEEEEEETTEEE CS
                         Prefoldin 20 eelektletlktlkk....edegkevlvplgaglyv 51
                                      +e+e+++e ++ l +    + e + v+ p g+++ v
  gi|557694839|ref|YP_008797893.1| 37 PEVEEAEEVVEQLPEspaeSAEQQAVQPPAGEDVAV 72
                                      677888888888877766666666666666666655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin   8 lqaelaqlkeaieelektletlk 30 
                                        qae+a+++e+i++l+++le lk
  gi|557694839|ref|YP_008797893.1| 123 RQAEIAKVEERINTLNSSLEKLK 145
                                       58888888888888888888876 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  79 iellkkkleelekqlekleeeleklkdqittle 111
                                       i  +++ ++++ k+le+l e+++k+k+++++le
  gi|557694839|ref|YP_008797893.1| 218 INMFEQDVQSALKALEVLMEQHQKIKKELNKLE 250
                                       567889999*******************99886 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   7.6     0.047        32       2      22 ..       8      27 ..       7      28 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.047
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGtp 22
                                      CpnC++ l  + kFC yCG+ 
  gi|557694839|ref|YP_008797893.1|  8 CPNCHR-LTIKGKFCIYCGYT 27
                                      888888.677779******95 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2       2.2   1.5e+03      46      75 ..      28      57 ..      27      63 .. 0.68
   2 ?    6.6   0.2     0.015        11      44      83 ..     121     164 ..      98     176 .. 0.76
   3 ?    7.6   2.7    0.0074       5.1      26      58 ..     222     254 ..     211     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.2
                                      HHHHHHHHHHHHHHHHHHHHHHHHTTHTTH CS
                          Spectrin 46 leaelaaqqervkalnelaeklldeghsas 75
                                      le+ ++  +++v++ +e+ e+l ++  +++
  gi|557694839|ref|YP_008797893.1| 28 LEQPVEPPKPEVEEAEEVVEQLPESPAESA 57
                                      677777888999999999999955543333 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHHHHHH.HHTT...HTTHHHHHHHHH CS
                          Spectrin  44 kaleaelaaqqervkalnelaekl.ldeg...hsaseeieerle 83 
                                       ++ +ae+a  +er+++ln   ekl ++++    ++ ++i+++le
  gi|557694839|ref|YP_008797893.1| 121 ERRQAEIAKVEERINTLNSSLEKLkVKHEvgeIPDRQYITQKLE 164
                                       46689*************99999977776666666677777774 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0074
                                       CSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  26 sedlgkdleevqallkkhkaleaelaaqqervk 58 
                                       ++d+ + l +++ l+++h+ +++el+  + r k
  gi|557694839|ref|YP_008797893.1| 222 EQDVQSALKALEVLMEQHQKIKKELNKLELRYK 254
                                       7888999******************99876655 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.4       3.4   2.3e+03     124     155 ..      30      62 ..      24      82 .. 0.53
   2 ?    6.4   0.1    0.0054       3.7     238     278 ..     107     147 ..     102     153 .. 0.86
   3 ?    7.3   3.3    0.0028       1.9     269     323 ..     194     248 ..     156     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.4
                             IFT57 124 kpkypkeeeeeeeeev.eddaelelekveeeel 155
                                       +p  p++ e ee+eev e+  e  +e+ e++++
  gi|557694839|ref|YP_008797893.1|  30 QPVEPPKPEVEEAEEVvEQLPESPAESAEQQAV 62 
                                       555555555444444435545555555555444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0054
                             IFT57 238 eslpetksqlkklhedisktlekiesrEkylnsqleellqe 278
                                       e ++e++s lk l e  + ++ k+e+r + lns+le+l  +
  gi|557694839|ref|YP_008797893.1| 107 ELFHEYRSRLKTLDERRQAEIAKVEERINTLNSSLEKLKVK 147
                                       56789999999999999**********99999999998665 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0028
                             IFT57 269 nsqleellqeyreaqeelsevkekykqlsegvseltrelaeiseelekvkqemee 323
                                        +qlee lq+ +++ + l  ++e +++ ++ v++  + l+ + e+ +k+k+e+++
  gi|557694839|ref|YP_008797893.1| 194 KTQLEERLQKVKTNGRDLGMQEEFINMFEQDVQSALKALEVLMEQHQKIKKELNK 248
                                       5788999999999999999999999999999999999999999999999998876 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0052       3.6      22      76 ..     110     164 ..     101     179 .. 0.75
   2 ?    0.1   5.1      0.56   3.9e+02       6      77 ..     196     272 ..     192     277 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0052
                             TMPIT  22 kqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelk 76 
                                       ++   +l++l ++ + ei+k ++r++ l+ssl+klk + +  e    + ++++l+
  gi|557694839|ref|YP_008797893.1| 110 HEYRSRLKTLDERRQAEIAKVEERINTLNSSLEKLKVKHEVGEIPDRQYITQKLE 164
                                       55667788999999**********************9977444333344433333 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.56
                             TMPIT   6 elekefkeleetakeykqkleelsklqskcskeikkqk...krlkelksslkklkksvk..eeeeeeveelkeelke 77 
                                       +le+++++++++ + +  + e ++ +++++++++k  +   ++ +++k++l+kl+ + k  e +++e+ +lk++l++
  gi|557694839|ref|YP_008797893.1| 196 QLEERLQKVKTNGRDLGMQEEFINMFEQDVQSALKALEvlmEQHQKIKKELNKLELRYKigELKQSEYLSLKQKLER 272
                                       56677777777777666666666555555555554443111444555556665555533444455555555555544 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 ?   -2.2   0.0       8.4   5.8e+03      22      33 ..      38      49 ..      27      52 .. 0.50
   2 ?    4.8   0.2     0.055        38       8      27 ..     126     145 ..     115     154 .. 0.59
   3 ?   -1.3   0.0       4.3   2.9e+03       4      20 ..     164     180 ..     163     184 .. 0.77
   4 ?   -1.3   0.0       4.3     3e+03       4      14 ..     196     206 ..     190     216 .. 0.70
   5 ?    6.1   0.5     0.022        15       2      34 ..     218     250 ..     217     255 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 8.4
                         FlaC_arch 22 eneelsksveel 33
                                      e ee ++ ve+l
  gi|557694839|ref|YP_008797893.1| 38 EVEEAEEVVEQL 49
                                      444444444444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.055
                         FlaC_arch   8 klsklsteletvkkeneels 27 
                                       ++ k++ +++t+ +++e+l+
  gi|557694839|ref|YP_008797893.1| 126 EIAKVEERINTLNSSLEKLK 145
                                       34444444444444444443 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.3
                         FlaC_arch   4 elEnklsklsteletvk 20 
                                       e+E ++++l  +l  ++
  gi|557694839|ref|YP_008797893.1| 164 EIEREMGRLRPKLMYLR 180
                                       79999999987776555 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 4.3
                         FlaC_arch   4 elEnklsklst 14 
                                       +lE++l+k++t
  gi|557694839|ref|YP_008797893.1| 196 QLEERLQKVKT 206
                                       46666666665 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.022
                         FlaC_arch   2 idelEnklsklsteletvkkeneelsksveelk 34 
                                       i+ +E+++++    le + ++ ++++k++++l+
  gi|557694839|ref|YP_008797893.1| 218 INMFEQDVQSALKALEVLMEQHQKIKKELNKLE 250
                                       6789**************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1783  (0.0994478); expected 358.6 (0.02)
Passed bias filter:                      816  (0.0455129); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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):              26  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 1928.29
//
Query:       gi|557694840|ref|YP_008797894.1|  [L=198]
Description: adenylate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  116.4   0.0    1.8e-33  115.8   0.0    1.3  1  AAA_17           AAA domain
    1.2e-08   35.5   0.0    2.4e-08   34.6   0.0    1.5  1  AAA_18           AAA domain
    3.9e-05   23.9   0.0    0.00011   22.4   0.0    1.8  1  AAA_33           AAA domain
    0.00053   19.5   0.0    0.00059   19.4   0.0    1.1  1  KTI12            Chromatin associated protein KTI12
     0.0013   18.7   0.2     0.0027   17.7   0.2    1.5  1  NTPase_1         NTPase
     0.0057   17.1   0.5      0.021   15.2   0.5    2.0  1  AAA              ATPase family associated with various cellul
      0.006   16.9   0.3      0.013   15.8   0.1    1.7  2  AAA_19           AAA domain
     0.0068   16.1   0.1        1.3    8.6   0.0    2.3  2  Thymidylate_kin  Thymidylate kinase
      0.009   16.3   0.0      0.015   15.6   0.0    1.5  1  AAA_28           AAA domain
      0.009   16.6   0.2      0.071   13.7   0.0    2.3  2  DUF134           Protein of unknown function  DUF134
  ------ inclusion threshold ------
      0.016   15.3   0.1       0.71   10.0   0.0    2.3  2  ADK              Adenylate kinase
      0.018   15.3   0.2      0.044   14.1   0.2    1.9  1  AAA_22           AAA domain
      0.028   14.1   0.0      0.046   13.4   0.0    1.3  1  AAA_24           AAA domain
      0.029   14.1   0.0      0.041   13.6   0.0    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.036   13.3   0.1      0.076   12.2   0.0    1.6  2  NB-ARC           NB-ARC domain
      0.067   12.5   0.2       0.21   10.8   0.0    2.0  2  Zeta_toxin       Zeta toxin
       0.11   12.0   0.0       0.23   11.0   0.0    1.6  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.18   11.6   0.5          1    9.2   0.5    2.1  1  dNK              Deoxynucleoside kinase
       0.45   10.2   4.0       0.16   11.7   0.7    2.1  2  AAA_30           AAA domain


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 !  115.8   0.0   1.9e-36   1.8e-33       3     135 ..       8     143 ..       6     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 1.9e-36
                                       -TTSSHHHHHHHHHHHH.TEEEEEHHHHHHHHHHTTTSHSSHHHHC.TSHHHHHHHHHHHHHHHHHHHHHSSEEEEE CS
                            AAA_17   3 gPGsGKgtqceklveky.gfthlsaGdllreeakrgglakardemr.klpleekkelqkeaaekiaeeakkkgvlvd 77 
                                       +PGsGK+t ++k+vek+  + ++++Gdl++eea++   +++rd+mr kl l++ ++lqk aae+ia +   ++v+vd
  gi|557694840|ref|YP_008797894.1|   8 LPGSGKTTTVKKVVEKMpSLVVINYGDLMFEEASKLYGISHRDDMRkKLGLRDYQRLQKSAAERIAAM---DNVVVD 81 
                                       8****************88*****************999*******779*****************86...89**** PP

                                       E-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH..TT..ST-TS-SHHHH CS
                            AAA_17  78 ghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd..rt..rgrdddneesi 135
                                       +h +ik++ g+++glp+e ++ ++p++i++l++ pe+il+rrlkd  ++  r+r+ ++ e i
  gi|557694840|ref|YP_008797894.1|  82 THSVIKTPFGYYPGLPSEAVRIMNPHLIVFLDCRPEDILSRRLKDvaEGvdRKRETESVEAI 143
                                       *********************************************75334588888888887 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   2.5e-11   2.4e-08       1     129 [.       3     143 ..       3     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.5e-11
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.gvnlrdvakenglllevdpe..aldeskrldedkldklldaleenssalee 73 
                                       +++t  pG+GKtt  k + +++  + ++n++d+ +e+ + l+   +  + ++++ l++ ++ + + a +      + 
  gi|557694840|ref|YP_008797894.1|   3 VIVTALPGSGKTTTVKKVVEKMpSLvVINYGDLMFEEASKLYGISHrdDMRKKLGLRDYQRLQKSAAERI-----AA 74 
                                       79*******************9555*99999999999999999999555555555555554444443333.....45 PP

                            AAA_18  74 gknlvidghlaeleseaakdikk............vvLtasp.eelleRlekRgyeeakikeneeaeil 129
                                        +n+v+d h +   +  +  +              v+L+++p ++l +Rl++  +  ++++e e++e++
  gi|557694840|ref|YP_008797894.1|  75 MDNVVVDTHSVIKTPFGYYPGLPseavrimnphliVFLDCRPeDILSRRLKDVAEGVDRKRETESVEAI 143
                                       79********999988887766699999**************777777788777777777788887765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.2e-07   0.00011       7     118 ..       8     126 ..       3     149 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.2e-07
                            AAA_33   7 lpGsGKstlaerllkklg.avllssdtlrr.rlfg....tdqqsktdytrvldrlyqilnelarkalsagrnvilda 77 
                                       lpGsGK+t ++++++k +  v+++  +l++    +    +++++ +  +++  r yq+l++ a+++ +a  nv++d 
  gi|557694840|ref|YP_008797894.1|   8 LPGSGKTTTVKKVVEKMPsLVVINYGDLMFeEASKlygiSHRDDMR--KKLGLRDYQRLQKSAAERIAAMDNVVVDT 82 
                                       8*****************9999998885553333333365555444..345666799******************98 PP

                            AAA_33  78 tnlsrrer.......arflklarrlgvpvrivvvetdeetlkeRlakR 118
                                         + +  +       ++ +++ +    p++iv++++ +e + +R  k 
  gi|557694840|ref|YP_008797894.1|  83 HSVIKTPFgyypglpSEAVRIMN----PHLIVFLDCRPEDILSRRLKD 126
                                       76655555444444466666665....888888888777777765554 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   6.2e-07   0.00059       4     117 ..       3     132 ..       1     191 [. 0.69

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.2e-07
                                       EEEE--TTSSHHHHHHHHHHHHHH...TT--EEEE-THHHH...TTSS.S--GGGHHHHHHHHHHHHHHHHTT.SEE CS
                             KTI12   4 vvltGlPssGKstrakeLakalee...ekrsvvviddeslg..iekds.ykdsakekalRsslrsavkrdLskekvV 74 
                                       v++t lP sGK+t +k++ +++ +    ++   + +++s    i++ +  +++   ++ + +l++++++++   + V
  gi|557694840|ref|YP_008797894.1|   3 VIVTALPGSGKTTTVKKVVEKMPSlvvINYGDLMFEEASKLygISHRDdMRKKLGLRDYQ-RLQKSAAERIAAMDNV 78 
                                       89***************9999987666444444444444332344444244444444444.4556666778888999 PP

                                       EE-S---SH...HHHHHHHHHHHHTT-EEEEEEEE--HHHHHHHH........H CS
                             KTI12  75 IvDslnyik...gfRYeLyciakaakttlcvvyvvapldvlvkwn........e 117
                                       +vD    ik   g+   L  +a  ++ ++ +v++ + ++ +++++        +
  gi|557694840|ref|YP_008797894.1|  79 VVDTHSVIKtpfGYYPGLPSEAVRIMNPHLIVFLDCRPEDILSRRlkdvaegvD 132
                                       9********7666777899****************9999999988655543331 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   2.8e-06    0.0027       1      25 [.       2      26 ..       2      38 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.8e-06
                                      EEEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellks 25
                                      kv++T+ pG+GKtT vkkv+e++ s
  gi|557694840|ref|YP_008797894.1|  2 KVIVTALPGSGKTTTVKKVVEKMPS 26
                                      699******************9855 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 !   15.2   0.5   2.2e-05     0.021       2      36 ..       4      38 ..       3     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-05
                                      EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS.S CS
                               AAA  2 llyGppGtGKTllakavakelgvefleisgsell.s 36
                                      +++  pG GKT+++k v++++ + ++ i+  +l+ +
  gi|557694840|ref|YP_008797894.1|  4 IVTALPGSGKTTTVKKVVEKMPS-LVVINYGDLMfE 38
                                      67788***************854.777777777733 PP

>> AAA_19  AAA 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     0.013      13      34 ..       3      24 ..       1      37 [. 0.88
   2 ?   -2.9   0.0       8.2   7.8e+03      94     110 ..      66      82 ..      46      90 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.4e-05
                            AAA_19 13 llvtaGpGtGKTrvlkhivall 34
                                      ++vta pG+GKT+++k++v+ +
  gi|557694840|ref|YP_008797894.1|  3 VIVTALPGSGKTTTVKKVVEKM 24
                                      79****************9987 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 8.2
                            AAA_19  94 aeeekklqeeellivDE 110
                                       ++  + + + + ++vD 
  gi|557694840|ref|YP_008797894.1|  66 KSAAERIAAMDNVVVDT 82 
                                       23334443444555554 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0014       1.3       6      68 ..      10      74 ..       8      87 .. 0.69
   2 ?    5.6   0.0     0.012        12     116     149 ..     102     143 ..      92     175 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0014
                                      TSSHHHHHHHHHHHHHHTTE...EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHT CS
                   Thymidylate_kin  6 GaGKttqaellkerlkeegik..vvltrepggteiGekirelllkeeeleeqteallfaadrieh 68
                                      G+GKtt +++++e++++        l +e+ +  +G + r+ + k+  l +++ +   aa+ri +
  gi|557694840|ref|YP_008797894.1| 10 GSGKTTTVKKVVEKMPSLVVInyGDLMFEEASKLYGISHRDDMRKKLGLRDYQRLQKSAAERIAA 74
                                      9*************998653224456677777777766666666666666666666666666555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.012
                                       S..E-SEEEEEESSHHHHHTS.CCTTSS.....TTTSHHHHH CS
                   Thymidylate_kin 116 l..kPdltflldvdpevalkR.lakrde.....ldeeeeeql 149
                                       +   P+l+++ld+ pe  l R l++ +e     ++ e  e +
  gi|557694840|ref|YP_008797894.1| 102 RimNPHLIVFLDCRPEDILSRrLKDVAEgvdrkRETESVEAI 143
                                       33489999***9999887765155555555433333344444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.6e-05     0.015       6     119 ..       7     116 ..       2     192 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.6e-05
                            AAA_28   6 GgestGKTtlleaLaargyp.vvpEaareileeklakgedalpwv.edllafaervleeqleeeaaa...aankvlf 77 
                                         +++GKTt++++  ++  + vv  ++  ++ee ++  +   ++  +++l ++    + q+ +  aa   aa + ++
  gi|557694840|ref|YP_008797894.1|   7 ALPGSGKTTTVKKVVEKMPSlVVINYGDLMFEEASKLYGISHRDDmRKKLGLR----DYQRLQKSAAeriAAMDNVV 79 
                                       559************9965526799*999999998776653333324444443....33322222221234555555 PP

                            AAA_28  78 cDrglldtlaYarayggeaeaeleaaarekrydlvfllppap 119
                                       +D+ ++  + +  + g +      +a+r ++ +l+++l+  p
  gi|557694840|ref|YP_008797894.1|  80 VDTHSVIKTPFGYYPGLP-----SEAVRIMNPHLIVFLDCRP 116
                                       566555444444444443.....4455555556655555444 PP

>> DUF134  Protein of unknown function  DUF134
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   7.5e-05     0.071      24      65 ..       9      49 ..       2      57 .. 0.81
   2 ?   -0.0   0.0       1.4   1.3e+03      43      61 ..      56      74 ..      50      87 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.5e-05
                            DUF134 24 PeaveetgkvaisldeleairlvdyedlkqeeaaklmGiska 65
                                      P +  +t  v+  ++ + ++ +++y dl +eea+kl Gis++
  gi|557694840|ref|YP_008797894.1|  9 PGS-GKTTTVKKVVEKMPSLVVINYGDLMFEEASKLYGISHR 49
                                      443.344448899999************************87 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.4
                            DUF134 43 irlvdyedlkqeeaaklmG 61
                                      + l+dy+ l++  a ++  
  gi|557694840|ref|YP_008797894.1| 56 LGLRDYQRLQKSAAERIAA 74
                                      6799999887665555444 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00075      0.71       4      36 ..       8      41 ..       5      55 .. 0.85
   2 ?    3.1   0.1     0.095        90     100     131 ..     103     134 ..      98     148 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00075
                                      STTSSHHHHHHHHHHHH.TSEEEEHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                               ADK  4 aPgaGKGtqaeklvkky.glahlstGdllRaevk 36
                                       Pg+GK t  +k+v+k+ +l+ +  Gdl+ +e +
  gi|557694840|ref|YP_008797894.1|  8 LPGSGKTTTVKKVVEKMpSLVVINYGDLMFEEAS 41
                                      7*************9984688999****988765 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.095
                                       TSEESEEEEEE--HHHHHHHHHTGSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK 100 kvkldlvleldvpeevlveRltgDneetvkkR 131
                                       +++ +l++ ld++ e +++R ++D +e v ++
  gi|557694840|ref|YP_008797894.1| 103 IMNPHLIVFLDCRPEDILSRRLKDVAEGVDRK 134
                                       5778899*****99999888889999988654 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   4.7e-05     0.044       9      29 ..       4      24 ..       2     162 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-05
                            AAA_22  9 vvtGesGtGKTtllrrlleql 29
                                      +vt+ +G+GKTt++++++e+ 
  gi|557694840|ref|YP_008797894.1|  4 IVTALPGSGKTTTVKKVVEKM 24
                                      89***************9985 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.9e-05     0.046       4      75 ..       2      84 ..       1      91 [. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.9e-05
                            AAA_24  4 kiliyGpsgiGKTtlakel...gpkplfi.....dtekGlksldadkfpdie...swedfldevvel.........aae 62
                                      k+++++ +g+GKTt++k+     p+ ++i      +e+ +k     + +d++   ++                   a+ 
  gi|557694840|ref|YP_008797894.1|  2 KVIVTALPGSGKTTTVKKVvekMPSLVVInygdlMFEEASKLYGISHRDDMRkklGL---------RdyqrlqksaAER 71
                                      89999**************98888888886666556665544444444444444444.........3444444555888 PP

                            AAA_24 63 ladyktlviDtid 75
                                       a  + +v+Dt +
  gi|557694840|ref|YP_008797894.1| 72 IAAMDNVVVDTHS 84
                                      8889999999866 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 ?   13.6   0.0   4.3e-05     0.041       2      22 ..       4      24 ..       3      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-05
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrts 22
                                      +v + pG+GK+t ++k++++ 
  gi|557694840|ref|YP_008797894.1|  4 IVTALPGSGKTTTVKKVVEKM 24
                                      899***************983 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     8e-05     0.076      26      93 ..       6      72 ..       1      86 [. 0.83
   2 ?   -2.4   0.0       2.3   2.2e+03     137     163 ..     121     147 ..     118     164 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8e-05
                                      EESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTSHH CS
                            NB-ARC 26 vGmgGvGKttlakqilnksdeveg.rFdsvawvvvsktdkseeiletilkeLslseddleekeeveslk 93
                                         +G+GKtt +k++++k+ ++   ++  +++   sk + +++  +++ k+L+l++ ++ +k+  e   
  gi|557694840|ref|YP_008797894.1|  6 TALPGSGKTTTVKKVVEKMPSLVViNYGDLMFEEASKLYGISH-RDDMRKKLGLRDYQRLQKSAAER-I 72
                                      5579***************998888***************999.5669*******999999988774.3 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
                                       EESBCCCCCCS-S-EEEEEESS--HHH CS
                            NB-ARC 137 TTRdeevanavsatsekievelLekde 163
                                         R ++va+ v  + e+  ve +e d+
  gi|557694840|ref|YP_008797894.1| 121 SRRLKDVAEGVDRKRETESVEAIEADQ 147
                                       568888888888888888888877775 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00022      0.21      19      50 ..       3      31 ..       1      82 [. 0.82
   2 ?   -0.5   0.1      0.68   6.4e+02     168     191 ..     138     161 ..     117     195 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvrld 50
                                      +++ + pG+GK+++ +++ +++    + v+++
  gi|557694840|ref|YP_008797894.1|  3 VIVTALPGSGKTTTVKKVVEKM---PSLVVIN 31
                                      678888***************9...3555555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.68
                        Zeta_toxin 168 esvealeeekqldrvkikdrdgkt 191
                                       esvea+e ++q+ +  ++  ++++
  gi|557694840|ref|YP_008797894.1| 138 ESVEAIEADQQMGKFFVAAAANTA 161
                                       344444444444444444444333 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 ?   11.0   0.0   0.00025      0.23       3      24 ..       3      24 ..       1      41 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                                      EEEEESTTCCHHHHHHHHHCT- CS
                              cobW  3 tvltGflGsGKTtLlnhllenr 24
                                      +++t  +GsGKTt +++++e+ 
  gi|557694840|ref|YP_008797894.1|  3 VIVTALPGSGKTTTVKKVVEKM 24
                                      689***************9774 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.5    0.0011         1     114     144 ..      98     128 ..       5     196 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0011
                                       HHHHHHCCH-SEEEEEE--HHHHHH.HHHHCT CS
                               dNK 114 dnlleelakpdlliYLkasletcle.rikkRg 144
                                       + ++  + +p+l+++L++ +e +l  r+k  +
  gi|557694840|ref|YP_008797894.1|  98 SEAV-RIMNPHLIVFLDCRPEDILSrRLKDVA 128
                                       5555.3455************99861566533 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.7   0.00017      0.16      21      42 ..       3      24 ..       1      88 [. 0.90
   2 ?   -1.6   0.1         2   1.9e+03      46      63 ..     149     166 ..     137     194 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00017
                            AAA_30 21 avltGpAGtGKttalkalreaw 42
                                      +++t+ +G+GKtt++k+++e +
  gi|557694840|ref|YP_008797894.1|  3 VIVTALPGSGKTTTVKKVVEKM 24
                                      589**************99865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2
                            AAA_30  46 ggrviglAptgkaAkvLa 63 
                                        g+ +++A  ++aA  L+
  gi|557694840|ref|YP_008797894.1| 149 MGKFFVAAAANTAACYLK 166
                                       256666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); 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: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1406.81
//
Query:       gi|557694841|ref|YP_008797895.1|  [L=236]
Description: tRNA (adenine-N1-)-methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-36  123.9   0.0    8.7e-35  120.6   0.0    1.9  2  GCD14            tRNA methyltransferase complex GCD14 subunit
      7e-09   35.7   0.0    9.6e-09   35.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.1e-06   27.4   0.0    4.6e-06   26.4   0.0    1.6  1  GCD14_N          tRNA methyltransferase complex GCD14 subunit
    2.8e-05   24.7   0.0    4.9e-05   23.9   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    4.5e-05   23.3   0.0    6.3e-05   22.8   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    0.00043   21.3   0.0    0.00088   20.3   0.0    1.5  1  Methyltransf_24  Methyltransferase domain
    0.00063   19.7   0.0     0.0009   19.2   0.0    1.2  1  Methyltransf_18  Methyltransferase domain
    0.00096   19.8   0.0     0.0022   18.6   0.0    1.6  1  Methyltransf_11  Methyltransferase domain
     0.0016   18.0   0.0     0.0024   17.5   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0031   17.5   0.0      0.004   17.2   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
  ------ inclusion threshold ------
      0.037   13.3   0.0      0.058   12.7   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family


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 !  120.6   0.0   5.3e-38   8.7e-35       3     181 ..      39     212 ..      37     217 .. 0.94
   2 ?    1.8   0.0     0.097   1.6e+02     228     246 ..     214     232 ..     212     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 120.6 bits;  conditional E-value: 5.3e-38
                             GCD14   3 vyvlaptPeLWtlaLphrtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqrae 79 
                                       ++v++pt     + Lp  tqi+y +D+  i     + pG +vve+GtG+g l+  ++  v PtG++++++   + +e
  gi|557694841|ref|YP_008797895.1|  39 MHVFKPTFLDLLMFLPRTTQIVYPKDLGYIAAVSGVGPGYRVVEAGTGTGVLAAFLTYLVRPTGRVYSYDVRLENIE 115
                                       57777777666788*************************************************************** PP

                             GCD14  80 kareefrehelsqlvtvthrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtc 156
                                       +a   +r+ +l +++ +++ Dvc++  ++e+    Da  +D+P+Pw a+++  +al k +g+  s+sP +eqv +t 
  gi|557694841|ref|YP_008797895.1| 116 TATVRMRQLGLLDYIELKQGDVCEKIVEKEL----DAAVIDIPEPWRAVQSCYDAL-KPSGVWVSLSPTVEQVVQTY 187
                                       ***********************98776665....*********************.88999*************** PP

                             GCD14 157 eaLrelgfteietlevllrtyevrk 181
                                       eaL++ gf +++ +e+llr+  v++
  gi|557694841|ref|YP_008797895.1| 188 EALEAGGFSDLSCVELLLRNMRVKR 212
                                       ********************99986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.097
                             GCD14 228 llkPvselkghtgyLtfat 246
                                       +++P   ++ght+yL+ a+
  gi|557694841|ref|YP_008797895.1| 214 MTRPEFLMRGHTTYLVTAR 232
                                       67888889*******9997 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.2   0.0   5.9e-12   9.6e-09       4     117 ..      77     182 ..      75     213 .. 0.86

  Alignments for each domain:
  == domain 1  score: 35.2 bits;  conditional E-value: 5.9e-12
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlil 79 
                                       g+rv+++G+GtG l+  l  +++p ++v++ D   e ie A+ + ++lgl   +e++qgd+ e+   +e +  D  +
  gi|557694841|ref|YP_008797895.1|  77 GYRVVEAGTGTGVLAAFLTYLVRPTGRVYSYDVRLENIETATVRMRQLGLLdYIELKQGDVCEKI--VE-KELDAAV 150
                                       789**********************************************8659********9954..45.6788855 PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedprllae 117
                                             ++++p  + ++  ++lkp g+ ++ +p   ++
  gi|557694841|ref|YP_008797895.1| 151 I-----DIPEPWRAVQSCYDALKPSGVWVSLSPT-VEQ 182
                                       5.....7**********************99998.333 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 !   26.4   0.0   2.8e-09   4.6e-06      22      50 ..       2      30 ..       1      31 [. 0.96

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.8e-09
                           GCD14_N 22 itLepGgefhthrGaieHDdlIGrpeGsV 50
                                      ++L+ G++fht  G+i+  +lIG+p G+V
  gi|557694841|ref|YP_008797895.1|  2 VQLRSGKKFHTSEGFIDLSNLIGQPSGCV 30
                                      79*************************99 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0     3e-08   4.9e-05       1      97 []      80     171 ..      80     171 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 3e-08
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgal 74 
                                       v+++G+GtG l++ l   + + ++v+  D+  e +e+a  r+++ gl   +e+ qgd+ +   e ++ D+ v+    
  gi|557694841|ref|YP_008797895.1|  80 VVEAGTGTGVLAAFLTYLVrPTGRVYSYDVRLENIETATVRMRQLGLldYIELKQGDVCEKIVE-KELDAAVID--- 152
                                       899*************999669**********************999***********765444.479999993... PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                         +  ++  +a++ ++++Lkp G
  gi|557694841|ref|YP_008797895.1| 153 --I--PEPWRAVQSCYDALKPSG 171
                                       ..3..456689**********98 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 !   22.8   0.0   3.9e-08   6.3e-05      70     132 ..      73     136 ..      45     159 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.9e-08
                                       T--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES- CS
                              PCMT  70 elkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgD 132
                                        + +g rv+e G+G+G l+a l+ lv+++grv s +   e +e+a+ ++++l+l   + ++ gD
  gi|557694841|ref|YP_008797895.1|  73 GVGPGYRVVEAGTGTGVLAAFLTYLVRPTGRVYSYDVRLENIETATVRMRQLGLLdYIELKQGD 136
                                       47899********************************99999*******999975367777777 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   5.4e-07   0.00088       1      93 [.      81     169 ..      81     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.4e-07
                   Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpg.aeeaaalareaglddrvrlikadseealaslaagsiDllfiD 76 
                                       vE G+  Gv +++l +++r +g+  +++ d   +  e+a+  +r++gl d+++l ++d  e +  ++ ++ D ++iD
  gi|557694841|ref|YP_008797895.1|  81 VEAGTGTGVLAAFLTYLVRPTGR--VYSYDVRLEnIETATVRMRQLGLLDYIELKQGDVCEKI--VE-KELDAAVID 152
                                       89*******************96..88888866435567777889************998885..44.78******* PP

                   Methyltransf_24  77 gghaaeavledleallp 93 
                                        +   +av+  ++al p
  gi|557694841|ref|YP_008797895.1| 153 IPEPWRAVQSCYDALKP 169
                                       **888888886666654 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.5e-07    0.0009      10      88 ..      72     151 ..      67     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.5e-07
                   Methyltransf_18  10 slvekgsrvaDiGtDHgylpiylv.kegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdt 85 
                                       s v +g+rv+  Gt  g+l+++l+   + + +v+  D++ + +e+a   +++ gl d ie+  +d  ek+ e+e+d+
  gi|557694841|ref|YP_008797895.1|  72 SGVGPGYRVVEAGTGTGVLAAFLTyLVRPTGRVYSYDVRLENIETATVRMRQLGLLDYIELKQGDVCEKIVEKELDA 148
                                       56778999***********999873567899*********************************************9 PP

                   Methyltransf_18  86 vvi 88 
                                       +vi
  gi|557694841|ref|YP_008797895.1| 149 AVI 151
                                       998 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.4e-06    0.0022       2      94 ..      82     173 ..      81     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-06
                                       EET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhh 73 
                                       ++G+GtG la+ l+  +   +rv+  D+  e +++a  + ++ gl   +e+ ++d+ + ++ ++  D+ v+      
  gi|557694841|ref|YP_008797895.1|  82 EAGTGTGVLAAFLTYLVrptGRVYSYDVRLENIETATVRMRQLGLldYIELKQGDVCE-KIVEKELDAAVID----- 152
                                       78************4445669***************9999999999888999****98.7888899999876..... PP

                                       -CCHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  74 vedpekalkeiaRvLkpgGll 94 
                                       +++p +a++ ++  Lkp G+ 
  gi|557694841|ref|YP_008797895.1| 153 IPEPWRAVQSCYDALKPSGVW 173
                                       79****************975 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.5e-06    0.0024      34     103 ..      79     151 ..      70     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.5e-06
                                       EEEEET-TTSHHHHHHHHH.TTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE CS
                               MTS  34 kvlDlGcGaGvlgaalake.speaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivs 103
                                       +v+  G+G+Gvl+a l     p+ +v  +dv  + +e a+  +++ +l   +e+ + dv e++ ek++d+ v 
  gi|557694841|ref|YP_008797895.1|  79 RVVEAGTGTGVLAAFLTYLvRPTGRVYSYDVRLENIETATVRMRQLGLLdyIELKQGDVCEKIVEKELDAAVI 151
                                       68999**********9986267888****************999999878******************98765 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.4e-06     0.004      27      96 ..      78     144 ..      67     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.4e-06
                   Methyltransf_32  27 ltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsieeatssk 96 
                                        +vv++G G g L+  l +  ++   +v++ d++ e++e+a  r ++lg  + + ++ +++++ e++ +k
  gi|557694841|ref|YP_008797895.1|  78 YRVVEAGTGTGVLAAFLTY-LVRPTGRVYSYDVRLENIETATVRMRQLG--LLDYIELKQGDVCEKIVEK 144
                                       68*****************.556799***********************..7688888888777766644 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   3.6e-05     0.058      39     151 ..      68     175 ..      61     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.6e-05
                                       HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS- CS
                   Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfed 114
                                       +  +++v +g +v++  +Gtg la+ l+  v+ +g+v   D+  + ++++  ++++ g    ie+ q++  e   e+
  gi|557694841|ref|YP_008797895.1|  68 IAAVSGVGPGYRVVEAGTGTGVLAAFLTYLVRPTGRVYSYDVRLENIETATVRMRQLGLLdYIELKQGDVCEKIVEK 144
                                       66778889999***********************************************9967898888766544443 PP

                                       T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEE CS
                   Ubie_methyltran 115 dsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvv 151
                                          D   +     ++++  +a+++ y  lkp G  v 
  gi|557694841|ref|YP_008797895.1| 145 -ELDAAVI-----DIPEPWRAVQSCYDALKPSGVWVS 175
                                       .3444444.....456666666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 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:                        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):              11  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1753.46
//
Query:       gi|557694842|ref|YP_008797896.1|  [L=866]
Description: hypothetical protein CSUB_C1415 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-07   29.0   0.0    4.6e-06   26.6   0.0    2.1  2  Peptidase_M10   Matrixin
    0.00057   19.6   0.0      0.001   18.7   0.0    1.4  1  Reprolysin_4    Metallo-peptidase family M12B Reprolysin-like
     0.0084   16.0   0.0      0.015   15.2   0.0    1.3  1  Reprolysin_2    Metallo-peptidase family M12B Reprolysin-like
  ------ inclusion threshold ------
      0.014   15.0   0.0      0.023   14.3   0.0    1.3  1  Peptidase_M57   Dual-action HEIGH metallo-peptidase
      0.021   14.3   0.1      0.037   13.4   0.1    1.3  1  Zn_peptidase_2  Putative neutral zinc metallopeptidase
      0.037   14.5   0.0      0.073   13.6   0.0    1.5  1  Reprolysin_3    Metallo-peptidase family M12B Reprolysin-like
      0.046   13.9   0.0      0.078   13.1   0.0    1.3  1  Reprolysin_5    Metallo-peptidase family M12


Domain annotation for each model (and alignments):
>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.54   1.4e+03      39      58 ..     104     122 ..      60     132 .. 0.72
   2 !   26.6   0.0   1.8e-09   4.6e-06     109     138 ..     162     191 ..     144     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.54
                                       SSEEEEE.SSSCESEEEEEES CS
                                       xxxxxxx.xxxxxxxxxxxxx RF
                     Peptidase_M10  39 plkFtev.kkgeadikieFgr 58 
                                       +++F  v ++++adi+i++ +
  gi|557694842|ref|YP_008797896.1| 104 SMTF--VtRDEDADITIRYVS 122
                                       3444..448899*****9986 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 1.8e-09
                                       HHHHHHHHHHHHTTBESXSSTTSTTSSSCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 109 lflVaaHEiGHalGLeHssdkdalmyplyk 138
                                       ++ V+aHE+GHalG+ Hss++ +lmy  ++
  gi|557694842|ref|YP_008797896.1| 162 AYKVVAHEYGHALGIGHSSNPVDLMYERVN 191
                                       4689**********************8765 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 !   18.7   0.0   4.1e-07     0.001      89     154 ..     109     181 ..      93     209 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.1e-07
                      Reprolysin_4  89 skdyDlaallrdtrasqqn.vgv......awvgalclsarqnkkasgvaasrdeydifAHEiGHtfGaaHdls 154
                                       ++d+D    +r   + ++n +gv      ++++ + + + q  +a + + +   y+++AHE GH +G+ H+ +
  gi|557694842|ref|YP_008797896.1| 109 TRDEDADITIRYVSTLGGNiCGVttirygGFLYEIVSATIQISRACVGSDAELAYKVVAHEYGHALGIGHSSN 181
                                       555555555555555666668882222223445555556666666666665679****************865 PP

>> Reprolysin_2  Metallo-peptidase family M12B Reprolysin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   5.8e-06     0.015      71     146 ..      98     183 ..      38     207 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.8e-06
                      Reprolysin_2  71 dydlahlvllgtf.sggvlGLayvg....qicqkeassrk......tntglsttansgsavee...tkeidvvaHEv 133
                                       +y l  +++  t  +++ + + yv+    +ic    + r+          +s+t++   a +    + + +vvaHE+
  gi|557694842|ref|YP_008797896.1|  98 NYLLSLSMTFVTRdEDADITIRYVStlggNICG-VTTIRYggflyeI---VSATIQISRACVGsdaELAYKVVAHEY 170
                                       777777777777777888888888766667773.3333335553331...4444444444433333567889***** PP

                      Reprolysin_2 134 GHaFGatHdndgs 146
                                       GHa G  H  + +
  gi|557694842|ref|YP_008797896.1| 171 GHALGIGHSSNPV 183
                                       ********98755 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 ?   14.3   0.0   9.1e-06     0.023      76     150 ..     102     179 ..      58     189 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.1e-06
                     Peptidase_M57  76 tfrltrgtntqasdmvvaditaktasgaggsaGfPsgGlPyk....viqigtglesysvdvnehvithelGhtvGlR 148
                                       ++++t+ t+ +  d +++  + +  ++  g++ +  gG  y+    +iqi+ +  ++  ++   v+ he Gh++G+ 
  gi|557694842|ref|YP_008797896.1| 102 SLSMTFVTRDEDAD-ITIRYVSTLGGNICGVTTIRYGGFLYEivsaTIQISRACVGSDAELAYKVVAHEYGHALGIG 177
                                       44444555544333.33444444444455555566666666522226899999999********************* PP

                     Peptidase_M57 149 hs 150
                                       hs
  gi|557694842|ref|YP_008797896.1| 178 HS 179
                                       *9 PP

>> Zn_peptidase_2  Putative neutral zinc metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.4e-05     0.037      62     132 ..     140     207 ..     126     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                    Zn_peptidase_2  62 ltDhYdprkkvvrLseevyngrsvaavavAAHevGhaiqhaegyaplklrsalvpvvnigsklslilllig 132
                                       l   Y+  + ++++s++   ++   a  v AHe Gha+   ++ +p+ l  + v+ + + s+l +++l + 
  gi|557694842|ref|YP_008797896.1| 140 L---YEIVSATIQISRACVGSDAELAYKVVAHEYGHALGIGHSSNPVDLMYERVNTATYPSTLNVYALAVA 207
                                       5...999999***************************************9999999999999988877665 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 ?   13.6   0.0   2.9e-05     0.073     104     124 .]     159     179 ..      89     179 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.9e-05
                      Reprolysin_3 104 gkvgadtvaHEiGHnfganHt 124
                                        ++ +++vaHE GH +g  H+
  gi|557694842|ref|YP_008797896.1| 159 AELAYKVVAHEYGHALGIGHS 179
                                       23556*************995 PP

>> Reprolysin_5  Metallo-peptidase family M12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     3e-05     0.078     137     160 ..     157     180 ..     107     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3e-05
                      Reprolysin_5 137 vstatevqvvaHElGHnfGavHDc 160
                                       +++  +++vvaHE+GH++G  H  
  gi|557694842|ref|YP_008797896.1| 157 SDAELAYKVVAHEYGHALGIGHSS 180
                                       34455699************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (866 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); 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:                         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: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 5661.10
//
Query:       gi|557694843|ref|YP_008797897.1|  [L=360]
Description: chorismate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-140  465.6   0.0   6.9e-140  465.4   0.0    1.0  1  Chorismate_synt  Chorismate synthase
  ------ inclusion threshold ------
       0.08   13.5   0.5       0.28   11.8   0.1    2.1  3  Plug             TonB-dependent Receptor Plug Domain
       0.19   11.8   0.0       0.39   10.8   0.0    1.5  1  Nfu_N            Scaffold protein Nfu/NifU N terminal


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 !  465.4   0.0  1.2e-143  6.9e-140       2     327 .]      11     354 ..      10     354 .. 0.96

  Alignments for each domain:
  == domain 1  score: 465.4 bits;  conditional E-value: 1.2e-143
                                       EEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE- CS
                   Chorismate_synt   2 rvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallieN 78 
                                        v +fGeShg+ +g+++dg+p+g+el+e+d+q eLdrRrpgqs +tt+r E+D+veilsGvf+gkt+G+pi +l++N
  gi|557694843|ref|YP_008797897.1|  11 VVASFGESHGRCVGVLVDGCPPGIELTEADVQVELDRRRPGQSLVTTTRAEEDRVEILSGVFQGKTTGAPILMLVWN 87 
                                       6889************************************************************************* PP

                                       TTS-..SSSSSTSBE-TTSTCHHHHHHC.-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE. CS
                   Chorismate_synt  79 kdqrskdyeeikevpRpgHADltyalkY.girdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei. 153
                                       kd++s+ ye ++++pRpgHAD+ + +kY g++d+rgggr+S+R Ta+ v+aGavakklL++lg+e+ ay  +ig++ 
  gi|557694843|ref|YP_008797897.1|  88 KDVDSRPYEMLRNTPRPGHADYPAYIKYrGFNDYRGGGRFSGRITAGYVMAGAVAKKLLSKLGVEVLAYSLEIGGVk 164
                                       **************************************************************************777 PP

                                       ..........CHHHHHTT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHTS CS
                   Chorismate_synt 154 ..........ekeaenpvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalmsi 220
                                                 +++ +n+vrcpd eaae+m++++ ea+k+gds+Gg+ve+++ ++p+GlGepvfd+ld++Lakal+si
  gi|557694843|ref|YP_008797897.1| 165 arqlsvdeirRNRYANEVRCPDFEAAERMKQVVLEARKQGDSVGGIVECIALNLPIGLGEPVFDNLDSDLAKALFSI 241
                                       7777877765334788************************************************************* PP

                                       TTEEEEEETTGGGGGGSBHHHHS--EE......EESS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS- CS
                   Chorismate_synt 221 pAvkgveiGsGfeaaelkGseanDeiv......lrktnnaGGieGGisnGepivvrvavKpipsiakeqktvdletk 291
                                       pAvkgve+G+Gfeaa+l+Gse+nD+++       +++nn+GGi+GG+s+Ge++v rva+Kp +sia++qktvd+ +k
  gi|557694843|ref|YP_008797897.1| 242 PAVKGVEFGRGFEAARLRGSENNDPFIlvdgkiRTASNNSGGILGGLSTGEQLVTRVAFKPASSIARPQKTVDIVEK 318
                                       ***************************77766433****************************************** PP

                                       E-EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHHH CS
                   Chorismate_synt 292 eevelevkgrhDpcvvpravvvveamvalvladall 327
                                       +e+e+ v grhDp+vvprav+vvea+va+vlad++l
  gi|557694843|ref|YP_008797897.1| 319 KETEIVVPGRHDPTVVPRAVPVVEAVVAFVLADHVL 354
                                       **********************************97 PP

>> Plug  TonB-dependent Receptor Plug Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.83   4.9e+03      59      67 ..      23      31 ..       8      72 .. 0.60
   2 ?   -3.8   0.0         3   1.8e+04      45      57 ..     109     121 ..      98     129 .. 0.74
   3 ?   11.8   0.1   4.7e-05      0.28      22      75 ..     231     282 ..     227     305 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.83
                                      SEEEETTEE CS
                              Plug 59 vlvlvDGvp 67
                                      v+vlvDG p
  gi|557694843|ref|YP_008797897.1| 23 VGVLVDGCP 31
                                      667788776 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3
                                       TSEEEEETTB-GG CS
                              Plug  45 gassisiRGlgsn 57 
                                       + + i  RG+++ 
  gi|557694843|ref|YP_008797897.1| 109 YPAYIKYRGFNDY 121
                                       5567888998764 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 4.7e-05
                                       TSSHHHHHTTSTTEEEECCCCSTTSEEEEETTB-GGCSEEEETTEEESCCCCSC CS
                              Plug  22 atsladalqgvpgvnvsssgggggassisiRGlgsnrvlvlvDGvpianggsga 75 
                                       +++la+al ++p v       g g++   +RG + n++ +lvDG   + +++++
  gi|557694843|ref|YP_008797897.1| 231 DSDLAKALFSIPAVK--GVEFGRGFEAARLRGSENNDPFILVDGKIRTASNNSG 282
                                       5799***********..9**************************8655544444 PP

>> Nfu_N  Scaffold protein Nfu/NifU N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.6e-05      0.39      36      58 ..     231     253 ..     223     255 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.6e-05
                             Nfu_N  36 asplakkLfkiegVksVfigsdF 58 
                                       +s lak+Lf+i+ Vk+V +g  F
  gi|557694843|ref|YP_008797897.1| 231 DSDLAKALFSIPAVKGVEFGRGF 253
                                       699**************999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 2593.44
//
Query:       gi|557694844|ref|YP_008797898.1|  [L=92]
Description: 4a-hydroxytetrahydrobiopterin dehydratase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   99.3   0.0    1.2e-28   99.1   0.0    1.0  1  Pterin_4a  Pterin 4 alpha carbinolamine dehydratase


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 !   99.1   0.0   6.5e-33   1.2e-28       3      91 .]       2      89 ..       1      89 [. 0.96

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 6.5e-33
                         Pterin_4a  3 lseeeiqkllaelpgWrleeaeelerefkfkdfeeaiafvnrvaalaeeenHhpdilvsynkvtvrltThdaggltenD 81
                                      l+eee++k+l++ +gW l ++ +l r+ +f+df e+i+f+ +va  ae+++Hhp+++++yn+++++l Thd+gg++  D
  gi|557694844|ref|YP_008797898.1|  2 LKEEELAKALKTIEGWGL-KDGKLYRKLEFRDFVECIGFMVKVAIEAEKMQHHPEWFNVYNQLEIWLVTHDLGGISTFD 79
                                      789*******888****9.666********************************************************* PP

                         Pterin_4a 82 fklAakidel 91
                                      +klA++i+el
  gi|557694844|ref|YP_008797898.1| 80 VKLAQRINEL 89
                                      ********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 657.22
//
Query:       gi|557694845|ref|YP_008797899.1|  [L=336]
Description: phosphate uptake regulator [Candidatus Caldiarchaeum subterraneum]
Scores for 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-24   85.2   9.4    1.4e-20   73.5   1.9    2.3  2  PhoU            PhoU domain
    0.00019   21.3   0.1    0.00039   20.3   0.1    1.5  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0036   17.8   0.4       0.01   16.3   0.4    1.7  1  DUF2682         Protein of unknown function (DUF2682)
  ------ inclusion threshold ------
      0.036   14.4   0.1        8.6    6.7   0.0    2.4  2  IGPD            Imidazoleglycerol-phosphate dehydratase
       0.05   13.9   0.8       0.34   11.3   0.0    2.4  2  BLOC1_2         Biogenesis of lysosome-related organelles com
      0.082   12.7   0.0       0.16   11.7   0.0    1.5  1  DUF2080         Putative transposon-encoded protein (DUF2080)
       0.53   10.2   3.8         72    3.3   0.0    4.4  4  DUF86           Protein of unknown function DUF86


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 !   73.5   1.9   5.5e-24   1.4e-20       1      89 []     140     232 ..     140     232 .. 0.93
   2 !   16.2   1.0   4.3e-06     0.011       7      88 ..     251     324 ..     245     325 .. 0.75

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 5.5e-24
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SH....HHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplae....dlrellsllriar 73 
                                       l+rm+ei+  ml++a  a++++d+ la++v++rdde+dr+++ i r+l  a+  +  l++    d  e ++++ +a+
  gi|557694845|ref|YP_008797899.1| 140 LERMGEITTHMLEEAFAAFYRNDKALAEDVVRRDDEVDRFYHFIVRQLNIAVRDYATLRNlnlsDPSECINYVLVAK 216
                                       68*********************************************7666677888888888889999******** PP

                                       HHHHHHHHHHHHHHHH CS
                              PhoU  74 dlERigDhavniaerv 89 
                                       ++ER +Dhav i++r+
  gi|557694845|ref|YP_008797899.1| 217 SIERAADHAVTISNRT 232
                                       ************9875 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 4.3e-06
                                       HHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   7 iveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERigDhav 83 
                                        v e ++ +l+++  + t+la++ +   ++i +l  e+  + l   +++++l  dl++ l+ l ++++l R++ +a+
  gi|557694845|ref|YP_008797899.1| 251 KVVELFKTSLTSFIYPSTDLANRTL---NQIADLASEMNAY-LS--SQKKNL--DLEQRLTELVVINSLRRVAEYAA 319
                                       6889999**************7773...6666666666555.22..223444..6777777799************* PP

                                       HHHHH CS
                              PhoU  84 niaer 88 
                                       +i+e 
  gi|557694845|ref|YP_008797899.1| 320 DISEA 324
                                       **996 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 !   20.3   0.1   1.5e-07   0.00039       2      38 ..      12      48 ..      11      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.5e-07
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCC CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiil 38
                                      ++ ++ ++++Pke+++++g+++ d+v +++ + ++++
  gi|557694845|ref|YP_008797899.1| 12 TGRSTFIISLPKEWVEKAGLKKLDTVKIVTLPSGLLV 48
                                      677999****************999999998866665 PP

>> DUF2682  Protein of unknown function (DUF2682)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   3.9e-06      0.01       6      39 ..     276     307 ..     272     312 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.9e-06
                           DUF2682   6 envLdlasevdafLnsktpdafkeleerLtklli 39 
                                       +++ dlase++a+L+s++++   +le+rLt+l++
  gi|557694845|ref|YP_008797899.1| 276 NQIADLASEMNAYLSSQKKN--LDLEQRLTELVV 307
                                       67889***************..9********986 PP

>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0068        17      89     116 ..     136     163 ..     103     183 .. 0.77
   2 ?    6.7   0.0    0.0034       8.6      70     112 ..     219     261 ..     164     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0068
                                       ..-SB--TT.--HHHHHHHHHHHHHHHT CS
                              IGPD  89 aelkrekigeldtelveeffeslaeaag 116
                                        +++ e++ge++t+++ee f+++ ++ +
  gi|557694845|ref|YP_008797899.1| 136 LKMSLERMGEITTHMLEEAFAAFYRNDK 163
                                       3466788899999999999999887765 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0034
                                       TEEEEEEEE--SS-EEE--..-SB--TT.--HHHHHHHHHHHH CS
                              IGPD  70 ealaevaldlsgrpylvleaelkrekigeldtelveeffesla 112
                                       e  a  a+++s+r   + + + ++++i ++++++ve f  sl+
  gi|557694845|ref|YP_008797899.1| 219 ERAADHAVTISNRTLTTTNISKPDQRIAKINAKVVELFKTSLT 261
                                       5567889*****************************9999987 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 ?   11.3   0.0   0.00013      0.34       6      58 ..     178     230 ..     173     259 .. 0.71
   2 ?    0.4   0.1      0.31     8e+02      75      93 ..     276     294 ..     267     327 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                           BLOC1_2   6 kvskyleaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekye 58 
                                       ++ +++  +l+++v dy +L +lN +  +++ ++  va+s+e+ +++    ++
  gi|557694845|ref|YP_008797899.1| 178 RFYHFIVRQLNIAVRDYATLRNLNLSDPSECINYVLVAKSIERAADHAVTISN 230
                                       56678999***************************999999998877655433 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.31
                           BLOC1_2  75 teLeeavseLDeyskeLEa 93 
                                       +++ +++se+++y +++++
  gi|557694845|ref|YP_008797899.1| 276 NQIADLASEMNAYLSSQKK 294
                                       3444444444444444332 PP

>> DUF2080  Putative transposon-encoded protein (DUF2080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.4e-05      0.16      14      38 ..       1      26 [.       1      30 [. 0.92

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.4e-05
                           DUF2080 14 ilpffegkVkpfGnSAkv.siPkeyl 38
                                      + p++ ++V + G S  + s+Pke++
  gi|557694845|ref|YP_008797899.1|  1 MQPAYTRRVQKTGRSTFIiSLPKEWV 26
                                      5699*************9******98 PP

>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.53   1.4e+03      41      61 ..      18      39 ..      16      44 .. 0.83
   2 ?    1.9   0.1     0.073   1.9e+02      31      47 ..     137     153 ..      90     204 .. 0.64
   3 ?    3.3   0.0     0.028        72      25      63 ..     209     247 ..     201     255 .. 0.87
   4 ?    1.8   0.2     0.081   2.1e+02       5      49 ..     282     326 ..     276     335 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.53
                                      HHHHHHHHHHHTT----SSC.H CS
                             DUF86 41 aidiakhlakklgikkpgdy.i 61
                                      +i ++k++++k g+kk ++  i
  gi|557694845|ref|YP_008797899.1| 18 IISLPKEWVEKAGLKKLDTVkI 39
                                      5789***********9887654 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.073
                                       HHHHHHHHHHHHHHHHH CS
                             DUF86  31 ernlqvigEaaidiakh 47 
                                       ++ l+ +gE ++++ ++
  gi|557694845|ref|YP_008797899.1| 137 KMSLERMGEITTHMLEE 153
                                       44444555555555444 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.028
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSCHHH CS
                             DUF86  25 leydavernlqvigEaaidiakhlakklgikkpgdyife 63 
                                       ++y  v + ++ + + a  i+++++   +i kp++ i +
  gi|557694845|ref|YP_008797899.1| 209 INYVLVAKSIERAADHAVTISNRTLTTTNISKPDQRIAK 247
                                       7888999**************************998554 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.081
                                       HHHHCCHH...TSTSCC.GSHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DUF86   5 leklkefteeldeeefl.sdeleydavernlqvigEaaidiakhla 49 
                                       ++++ +++ + ++++++ +++l+   v+  l  + E a di++ ++
  gi|557694845|ref|YP_008797899.1| 282 ASEMNAYL-SSQKKNLDlEQRLTELVVINSLRRVAEYAADISEAAI 326
                                       55677777.44444554489999999999************99855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2579.45
//
Query:       gi|557694846|ref|YP_008797900.1|  [L=347]
Description: phosphate ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  100.1   0.0    3.3e-28   99.2   0.0    1.5  1  PBP_like_2    PBP superfamily domain
      3e-25   88.5   0.1    3.8e-24   84.9   0.0    2.2  2  PBP_like      PBP superfamily domain
     0.0021   17.6   2.6     0.0033   16.9   2.6    1.2  1  Peptidase_A4  Peptidase A4 family


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   0.0   5.6e-32   3.3e-28       8     279 ..      48     298 ..      31     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 5.6e-32
                        PBP_like_2   8 svgeifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngdvdfagsdrplteseiaagwaangagg 84 
                                        +g i + Gs+t++p+ +++a++f++ ++g+++ +  +G+g+g k++  g++d+  ++rp+  +e  +++a+ng  +
  gi|557694846|ref|YP_008797900.1|  48 LAGDIEVDGSSTVYPLTEAAAEQFMNIHKGVTISVGISGTGGGFKRFVIGETDINDASRPILRAEA-ETAAKNG-VE 122
                                       34559***********************************************************99.7889999.** PP

                        PBP_like_2  85 liqvpvaigaialvvnkdnpln..lsreaLakIfs..gkItnWndvlglpadgpIkvvhrsdgsgttflfstalaeq 157
                                        i+vpvai+a+++vv+++n+    ++  +L++I +   +++ W+d+ +  +++pIk++ ++++sgt+++f++ +  +
  gi|557694846|ref|YP_008797900.1| 123 WIEVPVAIDALVVVVHPSNNWVdcITISELRAIWRpdSTVKLWSDIRPEWPNQPIKLYGPGPDSGTFDYFTERVVGK 199
                                       ****************8877667***********986679*****999999***********************988 PP

                        PBP_like_2 158 gpwtasgigasgsegvasavsnngaigyvsvaywlavkgysladvtngagkfvlptaataasalkvakias.nplaw 233
                                              ++as ++ vas    n    ++ v+      + +l+      g+f+ ++ a++++ +kv+k++    + +
  gi|557694846|ref|YP_008797900.1| 200 -------SKASRTDYVASE-DDNVL--VAGVE------SDRLSL-----GYFGFSYFAENKDRIKVLKVKDdLAGGE 255
                                       .......443334544444.33333..33333......334555.....9*******************99944555 PP

                        PBP_like_2 234 slqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyll 279
                                        ++p+ e++   +yPl r+++i+v+++ +++  + +++++F+ y +
  gi|557694846|ref|YP_008797900.1| 256 CVEPSDETARTFTYPLARPLFIYVNKK-SWD--TKPHLREFVIYYV 298
                                       69******99****************7.455..6999999998865 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.4     0.043   2.6e+02      12      33 ..      17      38 ..      13      56 .. 0.82
   2 !   84.9   0.0   6.3e-28   3.8e-24       1     189 [.      68     294 ..      68     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.043
                                      EEEEEES-HHHHHHHHHTTS-S CS
                          PBP_like 12 rvavanvGsggGlkalragead 33
                                      +v+v++ G+ggG++ + +  + 
  gi|557694846|ref|YP_008797900.1| 17 TVTVTVGGTGGGVQTVTRTVTV 38
                                      58999********999987765 PP

  == domain 2  score: 84.9 bits;  conditional E-value: 6.3e-28
                                       HHHHHHH-TTCEEEEEES-HHHHHHHHHTTS-SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHC CS
                          PBP_like   1 aeelaeknpgvrvavanvGsggGlkalrageadiagshlldketeeynapalrkaldgievvlvnlarreqglvvak 77 
                                       ae++++ ++gv+++v+ +G+ggG+k++  ge+di  +++++ + e+  a+      +g e+++v++a+++  +vv +
  gi|557694846|ref|YP_008797900.1|  68 AEQFMNIHKGVTISVGISGTGGGFKRFVIGETDINDASRPILRAEAETAA-----KNGVEWIEVPVAIDALVVVVHP 139
                                       6899999**********************************855433333.....36889***************** PP

                                       CHHHS.................--BGGGC....-S-B-EEEEE-TTSHHHHHHHHHHC-CEECTE-SSTTSEEESSH CS
                          PBP_like  78 gnpkk.................itnwkdl....adaplrlvnRetGSGtrdlfdellkkegiskssikgyaqearsh 133
                                        n++                  ++ w+d+    +++p+ l++++ +SGt+d+f+e + ++  sk+s+++y + ++++
  gi|557694846|ref|YP_008797900.1| 140 SNNWVdcitiselraiwrpdstVKLWSDIrpewPNQPIKLYGPGPDSGTFDYFTERVVGK--SKASRTDYVASEDDN 214
                                       ****667777777788888888********99999**********************665..********9999999 PP

                                       HHHHCCHCCETTCCEC.CCGG-HCCCCCCECTTCE-.......................EEEEEEEECTCCCS.HHH CS
                          PBP_like 134 lavaaaVaagradvgv.gieavaeelkgldfvplae.......................erydlvvrkealdd.pev 185
                                       + va  V+++r   g+ g++  ae+ + ++ +++++                       ++++++v+k+ +d  p +
  gi|557694846|ref|YP_008797900.1| 215 VLVAG-VESDRLSLGYfGFSYFAENKDRIKVLKVKDdlaggecvepsdetartftyplaRPLFIYVNKKSWDTkPHL 290
                                       88854.7777777776666666666666666666666666666666666666666666679*****99999864778 PP

                                       HHHH CS
                          PBP_like 186 qafl 189
                                       ++f+
  gi|557694846|ref|YP_008797900.1| 291 REFV 294
                                       8887 PP

>> Peptidase_A4  Peptidase A4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   2.6   5.5e-07    0.0033      41     144 ..      18     124 ..       5     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.5e-07
                      Peptidase_A4  41 asawVGiDGaa.dtcss.allqaGvdftvdsnGeqsydawyewyP.ayavdfsg.lavsaGDsvtvtvtatsatsgt 113
                                       +++ VG  G   +t++   ++ +G++++v+  G+ ++d+   +yP       ++ +++ +G +++v ++ t+     
  gi|557694846|ref|YP_008797900.1|  18 VTVTVGGTGGGvQTVTRtVTVTTGTQTSVQLAGDIEVDGSSTVYPlT-EAAAEQfMNIHKGVTISVGISGTGGGFKR 93 
                                       66777774434455554499*************************63.444555589*****************999 PP

                      Peptidase_A4 114 vtieNlstgqsvtktlsapssklcgqsAeWi 144
                                       ++i  ++ +   +  l a++++ +++ +eWi
  gi|557694846|ref|YP_008797900.1|  94 FVIGETDINDASRPILRAEAETAAKNGVEWI 124
                                       9998888888888888888888999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2398.45
//
Query:       gi|557694847|ref|YP_008797901.1|  [L=308]
Description: phosphate ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   70.5  19.2    1.5e-19   70.5  19.2    2.2  2  BPD_transp_1   Binding-protein-dependent transport system inn
  ------ inclusion threshold ------
        1.1    9.2   4.3        2.8    7.9   0.3    3.3  2  Deltameth_res  Deltamethrin resistance


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 ?    2.2   5.9     0.014   1.3e+02     106     168 ..      39      96 ..      38     109 .. 0.58
   2 !   70.5  19.2   1.6e-23   1.5e-19       2     176 ..      99     301 ..      98     306 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.014
                      BPD_transp_1 106 alppiitglilafggllggavlleflgswpGlgtllleailgydyseisnggvlalviavlll 168
                                       a+ +i+ +lil + +++g+ +l+efl+     gt ++   + + +      ++ al+ a++l+
  gi|557694847|ref|YP_008797901.1|  39 AIVVILGSLILESSIFFGQVSLVEFLT-----GTEWTVLFSDKKFGVLPLLTATALTSAIALV 96 
                                       7889***********************.....3333333333333322212222222222222 PP

  == domain 2  score: 70.5 bits;  conditional E-value: 1.6e-23
                      BPD_transp_1   2 illGilaa....lnrnkkldkllrpliivllslPsfvlaillvlvf......vilsilg.hlilpviillllsaapy 67 
                                       i++G+ +a     + +  ++ ++ ++i+vl ++P++v + + ++++       +  + g +++l+v +++ + ++p+
  gi|557694847|ref|YP_008797901.1|  99 IPAGLATAiylsEYARPGIRGVIKNIIEVLAGIPTVVYGYFALYFIspnllmRFVPGTGvFSALAVGLMIGVLIIPI 175
                                       56666666666688888899*****************777777766777777444455558899999********** PP

                      BPD_transp_1  68 vrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtlllea 144
                                       v  + ++al+s+p+d++ aa+ lGa+++ ++++v++P+al+ i++ +ilaf++++g+++++ + g+  ++ ++  + 
  gi|557694847|ref|YP_008797901.1| 176 VASLSEDALYSVPEDFRLAAYSLGARKIDVVFRVIVPAALSGILAAIILAFTRAMGETMIAAIAGGFRPFYSFDPRE 252
                                       *****************************************************************999999999999 PP

                      BPD_transp_1 145 ilgydyseis.................nggvlalviavlllnlvadilq 176
                                        ++ ++s+i+                 +++ + l i+++++nlva +++
  gi|557694847|ref|YP_008797901.1| 253 AMQTMTSFIAqvatgdaphgtieyqsiFAVGILLFIITMVFNLVALAVV 301
                                       9999999999*************66666666666666666666665554 PP

>> Deltameth_res  Deltamethrin resistance
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.4     0.062   5.6e+02      15      39 ..      16      43 ..       7      65 .. 0.57
   2 ?    7.9   0.3   0.00032       2.8      21      40 ..     276     295 ..     274     305 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.062
                     Deltameth_res 15 sakqrkYNav....LaaGiviligTiala 39
                                      +++qr  N v    Laa+ v++ ++i+++
  gi|557694847|ref|YP_008797901.1| 16 RRRQRATNLVnsllLAAASVSF-IAIVVI 43
                                      5666666666665333333333.333333 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00032
                     Deltameth_res  21 YNavLaaGiviligTialak 40 
                                       Y  ++a+Gi+ +i+T+++  
  gi|557694847|ref|YP_008797901.1| 276 YQSIFAVGILLFIITMVFNL 295
                                       7889************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); 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):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2182.07
//
Query:       gi|557694848|ref|YP_008797902.1|  [L=224]
Description: phosphate ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   73.1  15.3    3.1e-20   72.7  15.3    1.1  1  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 !   72.7  15.3   1.7e-24   3.1e-20       2     183 ..      20     222 ..      19     223 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 1.7e-24
                      BPD_transp_1   2 illGilaa.....lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirr 73 
                                       i+lGi +a      +++++l+++l + +  l ++Ps++++++ + ++    +lg +i++++++l ++++p+v++  +
  gi|557694848|ref|YP_008797902.1|  20 IPLGIASAlylteWSSHRRLRRFLEFNMANLAGVPSIIFGLVGLSILTYGLGLGRSIIAGAFTLGIMTLPLVTVSAA 96 
                                       899999999988999999999999999999************999998888************************** PP

                      BPD_transp_1  74 aalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydy 150
                                       +a++s+p+ l+  a+alGa++ q+ r+++lP +lp+++tg+ila+ +++g+a+ ++ +    Gl   ++++++ +d 
  gi|557694848|ref|YP_008797902.1|  97 EAIKSVPEALKHGAYALGATKLQVTRHIILPRSLPMMMTGAILAISRAIGEAAPILVIS---GLLFIRTDPTSVFDR 170
                                       ***********************************************************...888888888888888 PP

                      BPD_transp_1 151 seis...................nggvlalviavlllnlvadilqrlldprv 183
                                          +                    +++++l+++++ +n++a ++    ++rv
  gi|557694848|ref|YP_008797902.1| 171 FTVMplqifnwvsrpqpafqelsSAAIIVLLALLMMFNAAAIAIRYRYQRRV 222
                                       87779**************998888888888888888888888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1744.33
//
Query:       gi|557694849|ref|YP_008797903.1|  [L=263]
Description: phosphate ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  111.1   0.0    8.4e-32  110.6   0.0    1.2  1  ABC_tran        ABC transporter
    8.9e-15   55.3   0.0    1.9e-07   31.2   0.0    2.1  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
      1e-10   41.4   0.7    8.2e-05   22.1   0.2    2.7  3  SMC_N           RecF/RecN/SMC N terminal domain
    3.3e-06   27.4   0.0    8.5e-06   26.1   0.0    1.8  1  AAA_22          AAA domain
    4.2e-06   26.7   0.2    0.00057   19.7   0.0    2.1  2  AAA_15          AAA ATPase domain
      5e-06   27.2   0.1    1.2e-05   26.0   0.0    1.6  2  AAA_23          AAA domain
    1.2e-05   25.8   0.1      4e-05   24.1   0.1    2.0  1  AAA_16          AAA ATPase domain
    0.00011   22.2   0.0    0.00034   20.6   0.0    1.8  2  RsgA_GTPase     RsgA GTPase
    0.00018   21.2   0.0    0.00043   20.0   0.0    1.6  1  AAA_29          P-loop containing region of AAA domain
    0.00041   20.3   0.3    0.00091   19.2   0.1    1.8  2  ATPase_2        ATPase domain predominantly from Archaea
     0.0014   18.6   0.1     0.0049   16.8   0.0    1.7  2  Rad17           Rad17 P-loop domain
      0.004   16.9   0.1       0.36   10.5   0.0    2.1  2  AAA_30          AAA domain
  ------ inclusion threshold ------
       0.01   15.6   0.1          4    7.1   0.1    2.3  2  IstB_IS21       IstB-like ATP binding protein
      0.012   14.4   0.1      0.085   11.6   0.0    2.1  2  Adeno_IVa2      Adenovirus IVa2 protein
      0.047   12.9   0.1      0.066   12.4   0.1    1.5  1  NB-ARC          NB-ARC domain
       0.06   12.8   0.1          4    6.8   0.0    2.2  2  TniB            Bacterial TniB protein
      0.066   13.5   0.1        0.1   12.9   0.1    1.3  1  CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/C
      0.071   13.5   0.1       0.48   10.9   0.1    2.2  1  AAA             ATPase family associated with various cellula
      0.076   12.9   0.0       0.19   11.6   0.0    1.6  2  NACHT           NACHT domain
      0.076   12.8   0.4        2.5    7.8   0.1    2.7  2  PduV-EutP       Ethanolamine utilisation - propanediol utilis
      0.095   13.2   0.0       0.25   11.9   0.0    1.7  1  AAA_18          AAA domain
        0.1   12.1   0.0        0.2   11.2   0.0    1.4  1  AAA_27          AAA domain
       0.13   12.7   0.0       0.32   11.4   0.0    1.7  1  RNA_helicase    RNA helicase
       0.13   12.3   0.0       0.35   10.9   0.0    1.7  2  AAA_14          AAA domain
       0.13   12.3   0.0       0.54   10.4   0.0    1.9  2  MMR_HSR1        50S ribosome-binding GTPase
       0.14   12.4   0.0       0.37   11.0   0.0    1.7  1  AAA_28          AAA domain
       0.21   11.2   0.0       0.38   10.3   0.0    1.3  1  Relaxase        Relaxase/Mobilisation nuclease 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 !  110.6   0.0   1.3e-34   8.4e-32       2     136 ..      27     182 ..      26     183 .. 0.94

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 1.3e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepqlf 71 
                                       k+++lk+++++++ai+G++G+GKStLl+++ ++ +       +G++ ++g d+ +   +   +r  ig+++q p+ f
  gi|557694849|ref|YP_008797903.1|  27 KDINLKFERSRITAIIGPSGCGKSTLLRCINRMNDLipdakVQGKVYYRGLDIYSkdVDPVAVRTAIGMVFQRPNPF 103
                                       89******************************9988788889*******99998855677899************** PP

                                       TTSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  72 peltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       p + + +n               ++ e++++al+k  l +  +++++ ++ sLSgGq+qr+++aral+ +p+++llD
  gi|557694849|ref|YP_008797903.1| 104 PMS-IFDNvafglrvngvkltkqQMYEKVKDALEKAALWDEVKDRLDAQAFSLSGGQQQRLCIARALAVDPDVILLD 179
                                       ***.99999*********9998888888************************************************* PP

                                       STT CS
                                       xxx RF
                          ABC_tran 134 Ept 136
                                       Ept
  gi|557694849|ref|YP_008797903.1| 180 EPT 182
                                       **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 !   22.1   0.0   1.7e-07   0.00011       1      26 [.      38      65 ..      38     107 .. 0.82
   2 !   31.2   0.0   2.8e-10   1.9e-07     220     298 ..     138     212 ..     116     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.7e-07
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarl..d 26
                                      ++++iGp g+GKS+LL+++  + +l  d
  gi|557694849|ref|YP_008797903.1| 38 ITAIIGPSGCGKSTLLRCINRMNDLipD 65
                                      79*****************999776441 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 2.8e-10
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                          + e +d+ + +a++lS G+++ l+++ al+ ++   +++l+DEp  +L+P  ++++ +ll++ s+ +  +i++T
  gi|557694849|ref|YP_008797903.1| 138 AALWDEVKDRLDAQAFSLSGGQQQRLCIARALAVDP---DVILLDEPTVSLDPISTAKIEQLLRNISQ-DYTIIIVT 210
                                       44466788999999***********99999999999...9****************************.******** PP

                            AAA_21 297 HS 298
                                       H+
  gi|557694849|ref|YP_008797903.1| 211 HN 212
                                       *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 !   15.8   0.0   1.1e-05    0.0072      11      44 ..      22      56 ..      15      61 .. 0.85
   2 ?    0.7   0.0      0.43   2.9e+02     151     186 ..      95     130 ..      86     135 .. 0.74
   3 !   22.1   0.2   1.2e-07   8.2e-05     126     216 ..     134     230 ..     113     233 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                                      TTEECEEEEEETTS.SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 11 ksyagktvilpfsk.sftaivGpNGSGKsnlldAi 44
                                      + ya k + l+f++ ++tai+Gp G+GKs ll  i
  gi|557694849|ref|YP_008797903.1| 22 RKYAIKDINLKFERsRITAIIGPSGCGKSTLLRCI 56
                                      66888999999986269*************99877 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.43
                                       HHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 151 fAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                                       +  q+ +p p+ ++D+++  L  + vk   + + ek
  gi|557694849|ref|YP_008797903.1|  95 MVFQRPNPFPMSIFDNVAFGLRVNGVKLTKQQMYEK 130
                                       44688999*********9988887777776666665 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 1.2e-07
                                       HHHCTT-STT..........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEE CS
                                       xxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 126 llesagiske..........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQf 192
                                        le+a +  e          +LSgG+++ + +a  +A+   +p  + llDe    LD   ++k+ +ll++ s++  +
  gi|557694849|ref|YP_008797903.1| 134 ALEKAALWDEvkdrldaqafSLSGGQQQRLCIARALAV---DPD-VILLDEPTVSLDPISTAKIEQLLRNISQDYTI 206
                                       444444444455555555557******99999988886...455.679***************************** PP

                                       EEE-SSHHHCCC-SCEEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 193 ivislreemlekadklvgvtkven 216
                                       i+++++ ++ ++++    v++ ++
  gi|557694849|ref|YP_008797903.1| 207 IIVTHNMQQAARVSDYTAVMMPDE 230
                                       *********999999999988555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   1.3e-08   8.5e-06       4      91 ..      35     140 ..      31     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.3e-08
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...................erpevv..fvtlpsstsskdllre 59 
                                       + +i++++G+sG+GK+tllr + + +d  ++a+                    + ++ +   ++ p++  + +++ +
  gi|557694849|ref|YP_008797903.1|  35 RSRITAIIGPSGCGKSTLLRCINRMNDLIPDAKVqgkvyyrgldiyskdvdpvAVRTAIgmVFQRPNPF-PMSIFDN 110
                                       5689**********************9777766699***********9988876666664455666666.9****** PP

                            AAA_22  60 llralglelkaerlsseellealeqalrarav 91 
                                       ++  l +++ +  l++++++e++ +al+++a 
  gi|557694849|ref|YP_008797903.1| 111 VAFGLRVNGVK--LTKQQMYEKVKDALEKAAL 140
                                       *******9999..99*****999999998875 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   8.6e-07   0.00057      14      50 ..      26      63 ..      24     146 .. 0.80
   2 ?    5.2   0.2     0.022        15     323     365 ..     172     212 ..     159     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.6e-07
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk 50
                                      +kd+ ++++ + +t +iG+ ++GKS++l+ ++ + +  
  gi|557694849|ref|YP_008797903.1| 26 IKDINLKFERSrITAIIGPSGCGKSTLLRCINRMNDLI 63
                                      899999999989*******************9998855 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.022
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       +++++l++EP ++L p     + +ll+++++d    +ii TH+
  gi|557694849|ref|YP_008797903.1| 172 DPDVILLDEPTVSLDPISTAKIEQLLRNISQDYT--IIIVTHN 212
                                       7899*****************************6..******8 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.8e-08   1.2e-05       9      40 ..      23      57 ..      21      59 .. 0.84
   2 ?   -2.2   0.0       7.5     5e+03     123     123 ..     146     146 ..     119     210 .. 0.56

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.8e-08
                            AAA_23  9 sf..rdqeidF.skgltlItGpNGaGKTTildAik 40
                                      ++  +d ++ F  + +t+I+Gp G+GK+T+l++i 
  gi|557694849|ref|YP_008797903.1| 23 KYaiKDINLKFeRSRITAIIGPSGCGKSTLLRCIN 57
                                      55557778888666*******************96 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 7.5
                            AAA_23 123 e 123
                                       +
  gi|557694849|ref|YP_008797903.1| 146 D 146
                                       1 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   6.1e-08     4e-05       2      46 ..      19      58 ..      18     224 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.1e-08
                            AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellr 46
                                      ++GR+  ++ ++  +er      +++ ++G+sG+GKs+l+r++ r
  gi|557694849|ref|YP_008797903.1| 19 VYGRKYAIKDINLKFERS-----RITAIIGPSGCGKSTLLRCINR 58
                                      699999999999999966.....899****************986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   5.1e-07   0.00034      78     121 ..      17      58 ..       4      72 .. 0.77
   2 ?   -2.8   0.0       7.5     5e+03      77      89 ..     128     140 ..     113     162 .. 0.48

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5.1e-07
                                       EEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  78 evllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       +v++    +k ++++++ +++  ++++++G+SG GKStL+  ++ 
  gi|557694849|ref|YP_008797903.1|  17 TVVYG---RKYAIKDINLKFERsRITAIIGPSGCGKSTLLRCINR 58 
                                       44444...456888999888888****************998876 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.5
                                       SEEEE--TTTHTT CS
                       RsgA_GTPase  77 yevllvsaktkeg 89 
                                       ye ++   ++ + 
  gi|557694849|ref|YP_008797903.1| 128 YEKVKDALEKAAL 140
                                       2333333333333 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 !   20.0   0.0   6.4e-07   0.00043      16      39 ..      30      53 ..      23      67 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.4e-07
                            AAA_29 16 tieidlkgatlltGpsGsGKSTll 39
                                       ++++++ +t ++GpsG GKSTll
  gi|557694849|ref|YP_008797903.1| 30 NLKFERSRITAIIGPSGCGKSTLL 53
                                      57888888***************8 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 !   19.2   0.1   1.4e-06   0.00091       4      44 ..      22      59 ..      19     150 .. 0.78
   2 ?   -0.9   0.1       1.9   1.2e+03     103     130 ..     190     216 ..     109     225 .. 0.64

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.4e-06
                          ATPase_2  4 RekelkeleeilerepneiyfiYGpegsGKtaLlkeiienl 44
                                      R+ ++k+++   er  ++i  i Gp g+GK++Ll+ i  + 
  gi|557694849|ref|YP_008797903.1| 22 RKYAIKDINLKFER--SRITAIIGPSGCGKSTLLRCIN-RM 59
                                      88999999988888..99****************9653.33 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.9
                          ATPase_2 103 fkaielllekikkkgkkiiiiiDelqkl 130
                                       +++ie+ll++i+++ + iii+   +q++
  gi|557694849|ref|YP_008797903.1| 190 TAKIEQLLRNISQDYT-IIIVTHNMQQA 216
                                       4566666777766644.66666666665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.4e-06    0.0049      39      67 ..      30      58 ..      21      67 .. 0.82
   2 ?   -1.1   0.0       2.2   1.5e+03     112     170 ..     153     208 ..     116     220 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.4e-06
                             Rad17 39 vLesrkkriLLisGPsGCgkstvvkvLsk 67
                                       L+ ++ ri  i GPsGCgkst ++ + +
  gi|557694849|ref|YP_008797903.1| 30 NLKFERSRITAIIGPSGCGKSTLLRCINR 58
                                      56667789***************998765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.2
                             Rad17 112 leLkdakylklqklGddlrtdkklilvedlP.nkfyrdsdalrevirkylrssealplil 170
                                       + L + + ++l      l  d  +il+++   +   +++ ++++++r+    s+ +++i+
  gi|557694849|ref|YP_008797903.1| 153 FSLSGGQQQRLC-IARALAVDPDVILLDEPTvSLDPISTAKIEQLLRNI---SQDYTIII 208
                                       445555554444.445556666677777644344446666777776653...33334444 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   0.00055      0.36      17      41 ..      35      59 ..      29      70 .. 0.86
   2 ?    4.3   0.2     0.045        30      87     130 ..     171     217 ..     122     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00055
                            AAA_30 17 gdrvavltGpAGtGKttalkalrea 41
                                      + r++++ Gp G GK+t+l+ ++++
  gi|557694849|ref|YP_008797903.1| 35 RSRITAIIGPSGCGKSTLLRCINRM 59
                                      45799***************99775 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.045
                            AAA_30  87 epgtllivDEagmv....dtkqlaallkaaekagakvilvGDerQlas 130
                                        + ++++ DE  +     +t+++++ll+ +++ + ++i+v  + Q a+
  gi|557694849|ref|YP_008797903.1| 171 VDPDVILLDEPTVSldpiSTAKIEQLLRNISQ-DYTIIIVTHNMQQAA 217
                                       344899999988866777************99.888888887777654 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 ?    6.1   0.0     0.012       8.1      47      64 ..      36      53 ..      26      67 .. 0.84
   2 ?    7.1   0.1     0.006         4     102     151 ..     166     215 ..     140     237 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.012
                         IstB_IS21 47 kenivllGpsGvGKshla 64
                                      +   +++GpsG GKs l 
  gi|557694849|ref|YP_008797903.1| 36 SRITAIIGPSGCGKSTLL 53
                                      556789*********885 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.006
                         IstB_IS21 102 alkrllkvdllilDd..lgllpldqaeaellfeviekryerrsiiitsnlpf 151
                                       a +  + +d+++lD+  ++l p++ a+ e+l++ i++ y    ii+t n++ 
  gi|557694849|ref|YP_008797903.1| 166 ARALAVDPDVILLDEptVSLDPISTAKIEQLLRNISQDYT--IIIVTHNMQQ 215
                                       444456789*****9667899****************995..6899998764 PP

>> Adeno_IVa2  Adenovirus IVa2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013     0.085      88     108 ..      37      57 ..      21      68 .. 0.75
   2 ?   -0.2   0.0      0.51   3.4e+02     234     249 ..     202     217 ..     189     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                        Adeno_IVa2  88 viGviyGPtGsGksqllrnli 108
                                        i  i GP G+Gks llr + 
  gi|557694849|ref|YP_008797903.1|  37 RITAIIGPSGCGKSTLLRCIN 57 
                                       578899************874 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.51
                        Adeno_IVa2 234 tgfsvlvvlhnlnPrs 249
                                         +++++v hn++  +
  gi|557694849|ref|YP_008797903.1| 202 QDYTIIIVTHNMQQAA 217
                                       4699********8665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   9.9e-05     0.066      21      45 ..      37      61 ..      25     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.9e-05
                                      EEEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC 21 lvvalvGmgGvGKttlakqilnksd 45
                                       + a+ G  G+GK+tl++ i++  d
  gi|557694849|ref|YP_008797903.1| 37 RITAIIGPSGCGKSTLLRCINRMND 61
                                      4789**************9998755 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.006         4      33      61 ..      34      62 ..      29      74 .. 0.79
   2 ?    3.9   0.1     0.046        31      92     168 ..     146     219 ..     122     235 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.006
                              TniB 33 krmpnlllvGdsnnGKtmivekFarlhpp 61
                                      +r +   ++G+s +GK+++++   r++  
  gi|557694849|ref|YP_008797903.1| 34 ERSRITAIIGPSGCGKSTLLRCINRMNDL 62
                                      5777889************9988877755 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.046
                              TniB  92 ealgaplkararvskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteealra 168
                                       ++l a++  + +  ++++ +++   ++++ v+++DE    l     +  ++ ++l+++++++ i iv+   ++a r+
  gi|557694849|ref|YP_008797903.1| 146 DRLDAQA-FSLSGGQQQRLCIARALAVDPDVILLDEPTVSL--DPISTAKIEQLLRNISQDYTIIIVTHNMQQAARV 219
                                       5555553.444555666666666778899999999988888..67777888899*************9999888876 PP

>> CobA_CobO_BtuR  ATP:corrinoid adenosyltransferase BtuR/CobO/CobP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00015       0.1      67     149 ..     123     222 ..     105     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00015
                    CobA_CobO_BtuR  67 vkmeeeekeedaaaakealekakealase....................eydlvvlDEinyalklglldeeevlell 123
                                       +k++  ek +da + ++ ++++k++l ++                    + d+++lDE +  ++l+ ++++++ +ll
  gi|557694849|ref|YP_008797903.1| 123 TKQQMYEKVKDALEKAALWDEVKDRLDAQafslsggqqqrlciaralavDPDVILLDEPT--VSLDPISTAKIEQLL 197
                                       4445556677777788889999999988856666666666666666655666******76..56789********** PP

                    CobA_CobO_BtuR 124 kkkpeklelvlTGrnapeelleaADl 149
                                       ++ +++  +++  +n++++   + D+
  gi|557694849|ref|YP_008797903.1| 198 RNISQDYTIIIVTHNMQQA-ARVSDY 222
                                       **********999998875.445555 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 ?   10.9   0.1   0.00072      0.48       3      38 ..      41     153 ..      39     218 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00072
                                       EESSTTSSHHHHHHHHHHH......HTHE...........................................E.EEE CS
                               AAA   3 lyGppGtGKTllakavake......lgve...........................................f.lei 29 
                                       ++Gp G+GK++l + + +       ++v+                                           f l++
  gi|557694849|ref|YP_008797903.1|  41 IIGPSGCGKSTLLRCINRMndlipdAKVQgkvyyrgldiyskdvdpvavrtaigmvfqrpnpfpmsifdnvaFgLRV 117
                                       68***********9997774433331222333333444444444444444444444444444444444444433555 PP

                                       ETTTCSSS...........................S CS
                               AAA  30 sgsellsk...........................y 38 
                                       +g +l+++                           +
  gi|557694849|ref|YP_008797903.1| 118 NGVKLTKQqmyekvkdalekaalwdevkdrldaqaF 153
                                       555555324555555555555555555555555544 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00028      0.19       1      20 [.      37      56 ..      37      60 .. 0.88
   2 ?   -2.5   0.0       6.4   4.3e+03     138     163 ..     177     201 ..     163     204 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                                      SCEEEEC-TTTCHHHHHHHH CS
                             NACHT  1 rlvilqGeaGsGKTtLlqkl 20
                                      r+ ++ G++G+GK+tLl+ +
  gi|557694849|ref|YP_008797903.1| 37 RITAIIGPSGCGKSTLLRCI 56
                                      56799************976 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.4
                                       TSSCE..EEEE--TCCHHHHHHHHCT CS
                             NACHT 138 qleeaivlevegfsesrrkqlvrkyf 163
                                       +l e+  + + ++s  +++ql+r   
  gi|557694849|ref|YP_008797903.1| 177 LLDEP-TVSLDPISTAKIEQLLRNIS 201
                                       45555.78888999999999988765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.1    0.0037       2.5       5      23 ..      40      58 ..      36     142 .. 0.89
   2 ?   -1.5   0.0       2.9   1.9e+03      55      87 ..     195     226 ..     186     236 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0037
                         PduV-EutP  5 lliGkvgsGKttLtqalkg 23
                                       +iG++g+GK tL + ++ 
  gi|557694849|ref|YP_008797903.1| 40 AIIGPSGCGKSTLLRCINR 58
                                      589*********9988875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.9
                         PduV-EutP  55 salivtsaeadvialvqdateeesvfppgfasv 87 
                                       + l+ +s +  +i + +++++     ++  a +
  gi|557694849|ref|YP_008797903.1| 195 QLLRNISQDYTIIIVTHNMQQAA-RVSDYTAVM 226
                                       55677777777776666655544.444444444 PP

>> AAA_18  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      0.25       3      25 ..      41      65 ..      40      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00037
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf..g 25
                                      + G++G+GK+tl + +++++ +   
  gi|557694849|ref|YP_008797903.1| 41 IIGPSGCGKSTLLRCINRMNDLipD 65
                                      89************99999644452 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    0.0003       0.2      14      48 ..      26      58 ..      17      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                            AAA_27 14 ftdrsldfsaeeadlhliyGpNEAGKstalrAisd 48
                                      ++d +l+f+  +++++ i+Gp   GKst+lr i++
  gi|557694849|ref|YP_008797903.1| 26 IKDINLKFE--RSRITAIIGPSGCGKSTLLRCINR 58
                                      567778887..99******************9976 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   0.00048      0.32       3      37 ..      41      75 ..      39      80 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00048
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkkl.klkkkdsvysr 37
                                      + Gpsg+GKStl +  ++++ + + + k +++vy+r
  gi|557694849|ref|YP_008797903.1| 41 IIGPSGCGKSTLLRC-INRMNDLIpDAKVQGKVYYR 75
                                      78**********998.66666655445556666665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00053      0.35       2      24 ..      36      58 ..      35      86 .. 0.82
   2 ?   -1.8   0.0       4.4   2.9e+03      66      72 ..     174     180 ..     123     213 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00053
                            AAA_14  2 rkilvitGaRrvGKTtllkqlik 24
                                      ++i +i G+  +GK+tll+ + +
  gi|557694849|ref|YP_008797903.1| 36 SRITAIIGPSGCGKSTLLRCINR 58
                                      5899*************976644 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.4
                            AAA_14  66 tylflDE 72 
                                        +++lDE
  gi|557694849|ref|YP_008797903.1| 174 DVILLDE 180
                                       4555555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00081      0.54       3      21 ..      40      58 ..      38      84 .. 0.84
   2 ?   -0.8   0.0       2.3   1.5e+03      48      83 ..     175     209 ..     118     233 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00081
                                      EEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltg 21
                                      ai+G +  GKStL++ + +
  gi|557694849|ref|YP_008797903.1| 40 AIIGPSGCGKSTLLRCINR 58
                                      8*************98754 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.3
                                       EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEE CS
                          MMR_HSR1  48 ielvDtpGliegaseekglgkaflaleeadlillvv 83 
                                       ++l+D p  ++ +  +    +++l++++ d  +++v
  gi|557694849|ref|YP_008797903.1| 175 VILLDEPT-VSLDPISTAKIEQLLRNISQDYTIIIV 209
                                       55555555.221111122233333333334444444 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   0.00056      0.37       3      20 ..      40      57 ..      38      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00056
                            AAA_28  3 vitGgestGKTtlleaLa 20
                                      +i+G++++GK+tll+ ++
  gi|557694849|ref|YP_008797903.1| 40 AIIGPSGCGKSTLLRCIN 57
                                      79***********98665 PP

>> Relaxase  Relaxase/Mobilisation nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00058      0.38     168     206 ..     122     160 ..     112     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00058
                          Relaxase 168 sykeeirqalkkalenasdfedlkealkekglelrrktg 206
                                       ++k+++++++k+ale+a  + ++k++l+++ ++l+  ++
  gi|557694849|ref|YP_008797903.1| 122 LTKQQMYEKVKDALEKAALWDEVKDRLDAQAFSLSGGQQ 160
                                       789******************************994333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      841  (0.0469072); expected 358.6 (0.02)
Passed Vit filter:                       136  (0.00758548); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.39
# Mc/sec: 2040.83
//
Query:       gi|557694850|ref|YP_008797904.1|  [L=210]
Description: phosphate uptake regulator [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   89.0   0.6    1.5e-13   51.0   0.5    2.1  2  PhoU      PhoU domain
  ------ inclusion threshold ------
      0.015   14.8   0.1      0.025   14.1   0.1    1.5  1  Pil1      Eisosome component PIL1
      0.034   14.2   0.7       0.12   12.4   0.3    1.9  2  Mod_r     Modifier of rudimentary (Mod(r)) protein


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 !   36.4   0.0   8.9e-13   5.3e-09       1      88 [.      16     102 ..      16     103 .. 0.96
   2 !   51.0   0.5   2.5e-17   1.5e-13       3      88 ..     119     197 ..     117     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 8.9e-13
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlER 77 
                                       l++ma +++++++ a+e + ++     +ev ++ +++  l++e+ + ++e++a++qp+a+dlr+l s++++a+   R
  gi|557694850|ref|YP_008797904.1|  16 LNDMATLSRTAVEAAVEGFIKGT-PNEDEVFQLSEKLRWLQDEVADLAVELIARYQPVATDLRFLRSCMEVAYGFSR 91 
                                       799******************97.677************************************************** PP

                                       HHHHHHHHHHH CS
                              PhoU  78 igDhavniaer 88 
                                        g++a +i++ 
  gi|557694850|ref|YP_008797904.1|  92 FGRYAYDISQV 102
                                       ********986 PP

  == domain 2  score: 51.0 bits;  conditional E-value: 2.5e-17
                                       HHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   3 rmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlERig 79 
                                       + ae+v+ m+++++++++ek+ ela e+ ++d  +d+ +k+   + l++ + +++  +      + + i r+lERi+
  gi|557694850|ref|YP_008797904.1| 119 ETAEVVKAMIEKSVKSFVEKNLELAAELEKLDSVVDKAYKNHLQRSLNKPGSKKCD-M------ATMLILRYLERIA 188
                                       66899***********************************9988888888544443.3......2789********* PP

                                       HHHHHHHHH CS
                              PhoU  80 Dhavniaer 88 
                                       Dha+ i e 
  gi|557694850|ref|YP_008797904.1| 189 DHATYIGEA 197
                                       ******986 PP

>> Pil1  Eisosome component PIL1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   4.1e-06     0.025      68     135 ..      14      81 ..       8     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-06
                              Pil1  68 nlvraheaaarerksiakqlseWGedtdddvsDvsDklgvllselgeledayadrldqsRatlKsirn 135
                                       n+++++ + +r + ++a + +  G+ ++d+v  +s kl  l  e+++l+ ++++r++   + l+ +r 
  gi|557694850|ref|YP_008797904.1|  14 NMLNDMATLSRTAVEAAVEGFIKGTPNEDEVFQLSEKLRWLQDEVADLAVELIARYQPVATDLRFLRS 81 
                                       6788999*************************************************999999988886 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 ?   -0.1   0.0      0.15   9.2e+02      26      53 ..      42      70 ..       9      86 .. 0.59
   2 ?   12.4   0.3   2.1e-05      0.12      27      71 ..     117     162 ..     100     184 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.15
                             Mod_r 26 pevkqlkeekeellaeneslaeknlsl.e 53
                                      +ev ql e++  l +e  +la + +++ +
  gi|557694850|ref|YP_008797904.1| 42 DEVFQLSEKLRWLQDEVADLAVELIARyQ 70
                                      33445555555555555555554444444 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.1e-05
                             Mod_r  27 evkqlkeekeellaeneslaeknlslepeleelrselqekle.elk 71 
                                        +++ +  k +++++ +s+ eknl+l  ele+l s + ++++ +l+
  gi|557694850|ref|YP_008797904.1| 117 VLETAEVVKAMIEKSVKSFVEKNLELAAELEKLDSVVDKAYKnHLQ 162
                                       4677788999******************************996665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1276  (0.0711696); expected 358.6 (0.02)
Passed bias filter:                      858  (0.0478554); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
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: 00:00:00.41
# Mc/sec: 1547.95
//
Query:       gi|557694851|ref|YP_008797905.1|  [L=142]
Description: metal-dependent protease, PAD1/JA B1 superfamily [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   34.0   0.1    3.9e-08   33.1   0.1    1.4  1  Prok-JAB  Prokaryotic homologs of the JAB domain
  ------ inclusion threshold ------
      0.016   15.2   0.1      0.034   14.1   0.1    1.5  1  RadC      RadC-like JAB domain


Domain annotation for each model (and alignments):
>> 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 !   33.1   0.1   4.3e-12   3.9e-08       4     107 ..      27     119 ..      24     131 .. 0.75

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 4.3e-12
                          Prok-JAB   4 vlsalvaharrahpeEtcGlllgkeseseevivvplvnewsnrfeipdpedslarlkfearerglevvgiwHSHpgg 80 
                                       v + l++  r+ hp+E   ll g++ e+ ++ v +   ++   ++i   ++s+++ +      + + +g++HSHp g
  gi|557694851|ref|YP_008797905.1|  27 VAALLLEISRNIHPNEMIVLLHGRR-EKTSYFVEEISFPP---QSI--YGESFSSFNPYQLPIDHSFLGVAHSHPSG 97 
                                       566777888888************9.78888888877643...344..3444444443899999************* PP

                          Prok-JAB  81 sarPSetDrrdaaalarvkalliivgd 107
                                       ++ PS +D++++ +    + l++iv +
  gi|557694851|ref|YP_008797905.1|  98 APHPSVEDLNNMMG----E-LMVIVTA 119
                                       ************87....3.4454443 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   3.7e-06     0.034      69      86 ..      90     107 ..      85     115 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.7e-06
                                       EEEE-TTS--S--HHHHH CS
                              RadC  69 laHnhPsgdlepSeeDie 86 
                                       +aH hPsg ++pS eD++
  gi|557694851|ref|YP_008797905.1|  90 VAHSHPSGAPHPSVEDLN 107
                                       79**************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1079.19
//
Query:       gi|557694852|ref|YP_008797906.1|  [L=226]
Description: triosephosphate isomerase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   51.3   0.0    1.1e-12   47.8   0.0    1.9  2  TIM           Triosephosphate isomerase
    5.7e-08   32.4   1.5    5.7e-08   32.4   1.5    1.6  2  ThiG          Thiazole biosynthesis protein ThiG
    2.6e-06   27.1   0.6    4.5e-06   26.3   0.6    1.3  1  NMO           Nitronate monooxygenase
    0.00033   20.2   0.4    0.00087   18.8   0.0    1.9  3  His_biosynth  Histidine biosynthesis protein
    0.00043   19.4   0.2    0.00078   18.6   0.2    1.4  1  FMN_dh        FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.015   14.2   0.3      0.091   11.6   0.1    2.2  3  DUF711        Uncharacterised ACR (DUF711)
      0.023   13.9   0.0      0.035   13.3   0.0    1.4  1  IGPS          Indole-3-glycerol phosphate synthase
      0.056   13.5   0.5       0.13   12.3   0.1    2.0  2  B12-binding   B12 binding domain
      0.074   12.0   0.5       0.15   11.1   0.5    1.4  1  IMPDH         IMP dehydrogenase / GMP reductase domain
       0.14   12.1   0.9       0.49   10.4   0.0    2.3  3  FlpD          Methyl-viologen-reducing hydrogenase, delta sub


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 !   47.8   0.0   6.2e-16   1.1e-12       2     129 ..       7     129 ..       6     136 .. 0.84
   2 ?    1.8   0.0     0.073   1.3e+02     159     235 ..     139     209 ..     129     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 6.2e-16
                                       EEEEE-TBTS-H..HHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BH CS
                               TIM   2 liagNwKmnktl..eeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsa 76 
                                       li+ N+K+  +   ++a el+k ++ + +e+ v+v+++p+++ l +v++ +   ++++ aq ++    Ga+TG+v a
  gi|557694852|ref|YP_008797906.1|   7 LIVLNFKTFRESigKKALELAKIAERAAEETGVSVAVCPSLVDLATVAANV---SVHVFAQHCDPYMPGAYTGSVVA 80 
                                       6778999887542255666666666666779**************998887...5********************** PP

                                       HHHHHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE---HHH CS
                               TIM  77 emlkdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGEtlee 129
                                       e lk+ g+   ++ HsE++  +++ +e v+    ++ ++gl  i+C  +++++
  gi|557694852|ref|YP_008797906.1|  81 EALKESGAAGSLLNHSEKKLKLSDLSEAVN----RLRANGLVSIVCADDHYAA 129
                                       *******************99998877665....68899999****9998776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.073
                                       EEEE--GGGSSSS----HHHHHHHHHHHHHHHHHHSTHHHHTTSEEEEESS--TTTHHHHHTSTT--EEEESGGGCS CS
                               TIM 159 viAYePvWAiGtgktatpeqaqevhaairkelaekvskevaekirilYGGsvnkenakellkqkdidGlLvGgaslk 235
                                       ++A eP   iGtg +++  + + v +++ ++      k +a ++r+l G  v++++  +   +   dG+L  +a +k
  gi|557694852|ref|YP_008797906.1| 139 MLAVEPPELIGTGISVSRAKPEVVTETVSRV------KAIAPSVRVLCGAGVSTAEDVSKALELGTDGVLLASAFVK 209
                                       5788888889999988887777666666554......5678888888888887654444444455677777766665 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.79   1.4e+03     127     145 ..      70      88 ..      20     100 .. 0.54
   2 !   32.4   1.5   3.2e-11   5.7e-08     112     220 ..     105     220 ..      94     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.79
                                       EEEE-S-HHHHHHHHHTT- CS
                              ThiG 127 lpYvsdDlvlarrleevGc 145
                                       +p      v+a++l+e G+
  gi|557694852|ref|YP_008797906.1|  70 MPGAYTGSVVAEALKESGA 88 
                                       3444444555555555555 PP

  == domain 2  score: 32.4 bits;  conditional E-value: 3.2e-11
                                       HHHHHHHHHHTT-EEEEEE-S-HHHHHHHHHTT-S..EBEEBSSSTTS----S-..HHHH....HHHHHH-.SS-BE CS
                              ThiG 112 tlkaaeiLvkeGFevlpYvsdDlvlarrleevGca..avmPlaapiGsglGlln..keal....kiiieea.kvPvi 179
                                       + +a + L ++G + ++ + dD ++a +   +G    av P    iG+g  ++   +e++    + + + a +v v+
  gi|557694852|ref|YP_008797906.1| 105 LSEAVNRLRANGLVSIV-CADDHYAATAAAALGPDmlAVEP-PELIGTGISVSRakPEVVtetvSRVKAIApSVRVL 179
                                       66788888888876664.78899999998888866114444.456888877653113444000034444446799** PP

                                       EES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHH CS
                              ThiG 180 vDAGigspsdaaqamelGadavllntavaeakdpvamAraf 220
                                         AG+ +++d+ +a+elG+d+vll++a  +a+dp a+   +
  gi|557694852|ref|YP_008797906.1| 180 CGAGVSTAEDVSKALELGTDGVLLASAFVKASDPFALLLKM 220
                                       **********************************9876555 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.6   2.5e-09   4.5e-06     127     230 ..     107     212 ..     101     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.5e-09
                               NMO 127 evvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgd.kglfaLvpqvldavd..iPviAaG 200
                                       e+v+rl + g+v i+ +   ++a +++a+G+D+l v+ pe  G   +++ ++ +  ++ v +v+  ++  + v+   
  gi|557694852|ref|YP_008797906.1| 107 EAVNRLRANGLVSIVCADDHYAATAAAALGPDMLAVEPPELIGTGISVSRAKpEVVTETVSRVKA-IApsVRVLCGA 182
                                       7899************************************8775443444443344444444433.224599***** PP

                               NMO 201 GiidrrgvaaaLalGAsgvqigtrfLltke 230
                                       G+ ++++v  aL lG  gv ++++f+ +++
  gi|557694852|ref|YP_008797906.1| 183 GVSTAEDVSKALELGTDGVLLASAFVKASD 212
                                       *************************99987 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.2   2.1e+03      99     124 ..      17      41 ..       9      63 .. 0.73
   2 ?   -2.9   0.0       2.1   3.8e+03     146     166 ..     102     122 ..      78     124 .. 0.59
   3 !   18.8   0.0   4.9e-07   0.00087      63     111 ..     167     213 ..     148     224 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.2
                                       EEESHHHHH-THHHHHHHHHHCGGGE CS
                      His_biosynth  99 viigtaavknpelikelaekfgsqki 124
                                        +ig +a++  ++ +++ae+ g  ++
  gi|557694852|ref|YP_008797906.1|  17 ESIGKKALELAKIAERAAEETGV-SV 41 
                                       56777777777777777777776.33 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                                       EEEHHHHHHHHHHTT-SEEEE CS
                      His_biosynth 146 gldavelakkleelgageill 166
                                         d++e +++l   g+ +i++
  gi|557694852|ref|YP_008797906.1| 102 LSDLSEAVNRLRANGLVSIVC 122
                                       334555555555555555555 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 4.9e-07
                                       HHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THH CS
                      His_biosynth  63 dlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpel 111
                                       + v++ia +  + v  G G+++ edv ++le+g d v +++a vk ++ 
  gi|557694852|ref|YP_008797906.1| 167 SRVKAIAPS--VRVLCGAGVSTAEDVSKALELGTDGVLLASAFVKASDP 213
                                       223333333..88899999999999999999999999999998887765 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.2   4.3e-07   0.00078     265     304 ..     169     208 ..     150     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.3e-07
                                       HHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHH CS
                            FMN_dh 265 veavggrievlvDgGirrGsDvlkAlalGAdavllGRpfl 304
                                       v+a++ ++ vl+  G+++ +Dv kAl lG d+vll+ +f+
  gi|557694852|ref|YP_008797906.1| 169 VKAIAPSVRVLCGAGVSTAEDVSKALELGTDGVLLASAFV 208
                                       5556669****************************99887 PP

>> DUF711  Uncharacterised ACR (DUF711)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.097   1.7e+02     226     255 ..      13      42 ..       8      53 .. 0.53
   2 ?   11.6   0.1   5.1e-05     0.091     168     235 ..      41     112 ..      19     144 .. 0.74
   3 ?   -1.0   0.0      0.34   6.1e+02     201     222 ..     151     172 ..     114     200 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.097
                            DUF711 226 eelaeaikktafkitrlgelvarevakrlg 255
                                       +++ e i k+a+++ +++e++a+e+  + +
  gi|557694852|ref|YP_008797906.1|  13 KTFRESIGKKALELAKIAERAAEETGVSVA 42 
                                       455555555555555555555555443333 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.1e-05
                            DUF711 168 d.........glgnaklvvfanvpednPFfpgAfhgvgeaeavinvGvsgpgvvkkaleeakkeasleelaeaikkt 235
                                                 ++ +a++ v + +++  P++pgA++g     +v++ ++ ++g + ++l++ +k+ +l++l+ea+++ 
  gi|557694852|ref|YP_008797906.1|  41 VavcpslvdlATVAANVSVHVFAQHCDPYMPGAYTG-----SVVAEALKESGAAGSLLNHSEKKLKLSDLSEAVNRL 112
                                       244444444455567888888889999********9.....59999***************9999999999988764 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.34
                            DUF711 201 vinvGvsgpgvvkkaleeakke 222
                                        i+v   +p+vv++ ++++k+ 
  gi|557694852|ref|YP_008797906.1| 151 GISVSRAKPEVVTETVSRVKAI 172
                                       3444444678888888877553 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     2e-05     0.035     194     247 ..     161     213 ..      98     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                                       E-CHHHHHHCHCC-TTSEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTH CS
                              IGPS 194 vdlntteeLaklvpkdvllvaeSGiktredveklkeegvnafLvGeslmrqedv 247
                                       v  +t++++++ +  +v + +  G++t+edv+k  e g +++L  +++++++d 
  gi|557694852|ref|YP_008797906.1| 161 VVTETVSRVKAIA-PSVRVLCGAGVSTAEDVSKALELGTDGVLLASAFVKASDP 213
                                       5556666666644.58999999***************************99885 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       2.3   4.1e+03      21      45 ..      31      55 ..      23      60 .. 0.62
   2 ?   12.3   0.1   7.2e-05      0.13      40     104 ..     125     197 ..      77     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.3
                       B12-binding 21 aaalrdagfeVqllganvenediva 45
                                       +a ++ g++V +    v+ ++++a
  gi|557694852|ref|YP_008797906.1| 31 ERAAEETGVSVAVCPSLVDLATVAA 55
                                      4556666777777666666666555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.2e-05
                       B12-binding  40 nedivaairaekpdvvgl..........SalltsqleavkelvellkrirprvkvvvGGahpsldpeetleak.lg 104
                                       ++  + a++a+ pd++++          S+ + ++ e v+e+v ++k+i p v+v++G  + s++ e++ +a  lg
  gi|557694852|ref|YP_008797906.1| 125 DHYAATAAAALGPDMLAVeppeligtgiSV-SRAKPEVVTETVSRVKAIAPSVRVLCGAGV-STA-EDVSKALeLG 197
                                       455566888889999888888888878788.999999*******************99644.443.3333332466 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.5   8.1e-05      0.15      47     170 ..      76     201 ..      40     205 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.1e-05
                                       SHHHHHHHHHTTSEEEE-SS....S-HHHHHHHHHHHHTS...TTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  47 esemAialareGgigvihkn....lsieeqaeevkkvkrs...pnaakdekgrllvgaavgvkedalervkalveag 116
                                       +s +A al ++G+ g + ++    l+ ++  e v++++ +   +  + d++   + +aa+g       +  +l+ +g
  gi|557694852|ref|YP_008797906.1|  76 GSVVAEALKESGAAGSLLNHsekkLKLSDLSEAVNRLRANglvSIVCADDHYAATAAAALGPDM-LAVEPPELIGTG 151
                                       5556666666666666543300113344444555555544555555667777777777777664.444455666666 PP

                                       -SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEE.E-SHHHHHHHHHTT-SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                             IMPDH 117 vdvlvvdsahghsekvleavkeikkkveeveviaGn.vataegakaLieagadav 170
                                       +      ++ ++ e v+e+v+++k+ +++v+v+ G  v tae +++ +e g d+v
  gi|557694852|ref|YP_008797906.1| 152 I-----SVSRAKPEVVTETVSRVKAIAPSVRVLCGAgVSTAEDVSKALELGTDGV 201
                                       4.....5588888999999999999999999987744999999999999999987 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 ?   -1.9   0.0       1.8   3.2e+03       9      34 ..      29      54 ..      24      61 .. 0.67
   2 ?   -1.8   0.0       1.7     3e+03       2      18 ..     118     134 ..     117     144 .. 0.81
   3 ?   10.4   0.0   0.00027      0.49      30      58 ..     175     204 ..     153     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.8
                              FlpD  9 cayaaadlagvsrlqyppnvriirvp 34
                                      +a+ aa++ gvs   +p+ v +  v 
  gi|557694852|ref|YP_008797906.1| 29 IAERAAEETGVSVAVCPSLVDLATVA 54
                                      56677777777777777776666665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.7
                              FlpD   2 laFlCnwcayaaadlag 18 
                                       + ++C  + yaa  +a+
  gi|557694852|ref|YP_008797906.1| 118 VSIVCADDHYAATAAAA 134
                                       56899999999988776 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00027
                              FlpD  30 iirvpCsgrvdp.efilkalekGadgVlvl 58 
                                        +rv C + v++ e + kale G dgVl++
  gi|557694852|ref|YP_008797906.1| 175 SVRVLCGAGVSTaEDVSKALELGTDGVLLA 204
                                       699****99985278*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1674.85
//
Query:       gi|557694853|ref|YP_008797907.1|  [L=456]
Description: glycine dehydrogenase subunit 1 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-107  357.5   0.0   1.1e-106  357.3   0.0    1.0  1  GDC-P            Glycine cleavage system P-protein
    2.7e-08   33.2   0.0    5.4e-08   32.2   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
    8.3e-06   24.6   0.0    1.5e-05   23.7   0.0    1.4  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
       0.16   11.7   0.1          1    9.0   0.0    2.1  2  DNA_pol_A_exo1   3'-5' exonuclease
       0.17   11.7   0.0        0.3   10.9   0.0    1.4  1  ATP-synt_D       ATP synthase subunit D


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 !  357.3   0.0    3e-110  1.1e-106       3     427 ..       7     449 ..       6     452 .. 0.90

  Alignments for each domain:
  == domain 1  score: 357.3 bits;  conditional E-value: 3e-110
                                       H-SS.-HHHHHHHHHHHT-SSHHHHHHHHS-GGGB--S---------HHHHHHHHHHHHTTB--.-EE--BTTB--- CS
                             GDC-P   3 higp.sekdqkemLetlGlkslddliekavPkeiklkkelkleapksEeellaelekiasknkv.vksfiGaGyydt 77 
                                       +ig+ +++d ++mL+++G+k++ +l  +++P++  l+ + ++e p +E el+++++ i +kn+  ++ f+G G++ +
  gi|557694853|ref|YP_008797907.1|   7 YIGHhTDEDLRQMLQAIGVKDIMELY-SDIPSKYILSSPPSIEGPLTEPELIKRVKDILAKNRQgLRLFLGGGVWPH 82 
                                       6776257889****************.99****99***************************999************ PP

                                       ---HHHHHHTTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS- CS
                             GDC-P  78 ilPaviqrnilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkka 154
                                       ++Pa+++  i++++e++t+YtPYq+EisqG L al++fq+lvadl  +d  n+s++D +tA++EA  +a+r + ++ 
  gi|557694853|ref|YP_008797907.1|  83 HVPAAVKE-IVSRSEFVTSYTPYQPEISQGVLTALFEFQSLVADLYEIDAVNSSMYDWATAVGEAFRMAYRYNGRN- 157
                                       ******99.**************************************************************99888. PP

                                       -EEEEETTS-HHHHHHHHHHHGGGT-EEEEE-GGG--S-..........S-EEEEEEEES-TTSB-.---HHHHHHH CS
                             GDC-P 155 kkvvvdkkvhpqtlevlktrakglgieivevdlteekvtd.......kekevagvlvqypnteGri.edlkelveka 223
                                        k+v + ++ p  ++v +t+ k+lg+ +v++   +++  d       + +e+++v v  p   G++ e+++++ e a
  gi|557694853|ref|YP_008797907.1| 158 -KIVYAGHCGPGRIRVAETYVKPLGLRLVKASFDDRGNVDeeslktlVDRETSAVYVENPCYLGAVvENVEAVGEIA 233
                                       .******************************999988888899999999***************9725699****** PP

                                       HHTT-EEEEEE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GG..GGGG--S-EEEEEEBTTS- CS
                             GDC-P 224 kkkkslvvvaadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkek..lkRkiPGRlvGvskDaegk 298
                                       +++++l++v a++ +L+ll pPg lgaDivvG++q +G+P+ +GGP  g + ++e+  l  ++PGR+vG+++  e+k
  gi|557694853|ref|YP_008797907.1| 234 HDRNALFIVGAEPTSLGLLCPPGALGADIVVGEGQPLGLPMNFGGPLLGILGCREDrkLIHSMPGRMVGMAETLEDK 310
                                       *****************************************************9866699***********997765 PP

                                       .EEEEEE-CCGSHHCCHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT....T-EE- CS
                             GDC-P 299 .ralrlalqtREqHirRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkk...leeelk 371
                                        ra++++l +REq i+R+kAtsniCt+qaL A+ aa y  ++Gk+gl+++ar+i++kt ++ ++l+k        lk
  gi|557694853|ref|YP_008797907.1| 311 rRAFTMVLRAREQDIKREKATSNICTNQALCAITAAAYLALLGKHGLQSLARHIFEKTCYFIEALQKVdgvKAPLLK 387
                                       27***************************************************************998652234588 PP

                                       -SSBSSEEEEE--TTTHHHHHHHHHHTT......EE-EEESTT.EEEEE--TT--HHHHHHHH CS
                             GDC-P 372 kkkffdtllieveekaaekvlkkaekeg......lnlrkvelk.tvgialdEtvtkedieall 427
                                         ++ ++  ++ + +++ek+l+k ++ g      ++    +l+  v+  ++E    edi++ +
  gi|557694853|ref|YP_008797907.1| 388 APHYMEFTYRKEG-HSSEKLLSKLLNVGivggirIGEDFPQLGdGVLTCVTEVHSVEDIQEYV 449
                                       8999999988666.7777888887776643222222222333336777788888888887765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   1.5e-11   5.4e-08     100     332 ..     168     412 ..     142     424 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.5e-11
                                       GGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B--HHHHHHHHHHTT-EEEEE CS
                       Aminotran_5 100 anlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt.iqpveeigklakkkgalvlvD 175
                                       + +  ++   k  g++++++++d++g++d + l++l++ +t++v++  +   +G  ++ ve++g++a++++al++v 
  gi|557694853|ref|YP_008797907.1| 168 GRIRVAETYVKPLGLRLVKASFDDRGNVDEESLKTLVDRETSAVYVE-NPCYLGAvVENVEAVGEIAHDRNALFIVG 243
                                       5566677777889*******************************886.66778877********************* PP

                                       -TTTTTTS---HHHHTESEEEEETTTT.....TSSTT-EEEEEEHH..HHHTS..SS.STTSEEEEET.TEEE.... CS
                       Aminotran_5 176 aaqavghipidvkklgvDflafsghKl.....lgPtGiGvlyvrke..llekleplllggemveevsl.eett.... 240
                                       a  + +       +lg+D+++  g+ l     +g + +G+l +r++  l+++++     g mv   +  e++     
  gi|557694853|ref|YP_008797907.1| 244 AEPTSLGLLCPPGALGADIVVGEGQPLglpmnFGGPLLGILGCREDrkLIHSMP-----GRMVGMAETlEDKRraft 315
                                       ************************97522222555669******8422566664.....344433333333333456 PP

                                       ....EHCTTGGGS.SS--HHHHHHH.....HHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTC CS
                       Aminotran_5 241 ....faeapskfeaGTpnvagiigl.....gaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerr 308
                                            +e++ k e  T n+    +l     +a l +l + gl++ ++h  e++ y  e+l++++gv+   p    + 
  gi|557694853|ref|YP_008797907.1| 316 mvlrAREQDIKREKATSNICTNQALcaitaAAYLALLGKHGLQSLARHIFEKTCYFIEALQKVDGVKA--P--LLKA 388
                                       677799************9865444111114456777999**************************99..3..5899 PP

                                       BSEEEEEE..TTCSHHHHHHHHHHTT CS
                       Aminotran_5 309 asivsfnf..kgvhaedvatlLdeeg 332
                                       ++ + f++  +g+++e++ + L   +
  gi|557694853|ref|YP_008797907.1| 389 PHYMEFTYrkEGHSSEKLLSKLL--N 412
                                       99999999423333344443333..3 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 !   23.7   0.0   4.3e-09   1.5e-05     119     193 ..     187     264 ..     129     267 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.3e-09
                                       EEEEST..TSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTH.TTTS-GGGGT-SEE CS
                   Cys_Met_Meta_PP 119 vkfvdt..sdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfas.pllqrplklgaDiv 192
                                       ++f d    d+e+l++ ++ +t++vy+E p      v  +e++ ++a+++++l +v +  +s +ll+ p +lgaDiv
  gi|557694853|ref|YP_008797907.1| 187 ASFDDRgnVDEESLKTLVDRETSAVYVENPCYLGAVVENVEAVGEIAHDRNALFIVGAEPTSlGLLCPPGALGADIV 263
                                       444444225678899************************************9999988766637************* PP

                                       E CS
                   Cys_Met_Meta_PP 193 v 193
                                       v
  gi|557694853|ref|YP_008797907.1| 264 V 264
                                       8 PP

>> DNA_pol_A_exo1  3'-5' exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.27   9.6e+02      78      98 ..       5      25 ..       2      40 .. 0.83
   2 ?    9.0   0.0   0.00029         1      77     132 ..     313     367 ..     294     389 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.27
                                      SEEEESSHHHHHHHHHHHHTS CS
                    DNA_pol_A_exo1 78 itkvghnakfDlevlardfgi 98
                                      ++ +gh  ++Dl+ + + +g+
  gi|557694853|ref|YP_008797907.1|  5 FPYIGHHTDEDLRQMLQAIGV 25
                                      5679***********997654 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00029
                                       TSEEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTTHSTTSSHHHHHHHHHSB- CS
                    DNA_pol_A_exo1  77 nitkvghnakfDlevlardfgielenlfdtmlaayvldyershsLdsLaekylgdl 132
                                        +t+v+ + ++D++  + +  i++    +   aa+ l++  +h+L+sLa++ ++  
  gi|557694853|ref|YP_008797907.1| 313 AFTMVLRAREQDIKREKATSNICTNQALCAITAAAYLALLGKHGLQSLARHIFE-K 367
                                       5789999999999999999***********888888888888*********998.3 PP

>> ATP-synt_D  ATP synthase subunit D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   8.5e-05       0.3      16     100 ..     304     388 ..     300     455 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTST..TSTSHHHHHHHSSS.SS-..TSS-SEEEEEEB CS
                        ATP-synt_D  16 hslLkkKrdaLilefreilkelkelreeleeelkeayfslaea..faaggeediesavlesvklakvvkvelktenv 90 
                                        ++L++Kr a ++ +r+  +++k+ +   +   ++a  +++ a   a+ g++ ++s++ +  +  k        ++v
  gi|557694853|ref|YP_008797907.1| 304 AETLEDKRRAFTMVLRAREQDIKREKATSNICTNQALCAITAAayLALLGKHGLQSLARHIFE--KTCYFIEALQKV 378
                                       589***********************************9997766678999999999998877..445666667789 PP

                                       TTSEEEEEEE CS
                        ATP-synt_D  91 aGVkvpvfel 100
                                        GVk p ++ 
  gi|557694853|ref|YP_008797907.1| 379 DGVKAPLLKA 388
                                       9999999855 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3365.99
//
Query:       gi|557694854|ref|YP_008797908.1|  [L=508]
Description: glycine dehydrogenase subunit 2 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.0    8.5e-15   54.5   0.0    1.3  1  GDC-P            Glycine cleavage system P-protein
    3.7e-06   26.1   0.0    5.1e-06   25.7   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
    0.00016   21.1   0.0    0.00021   20.7   0.0    1.3  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 !   54.5   0.0   1.4e-18   8.5e-15      31     286 ..      43     305 ..      27     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1.4e-18
                                       S-GGGB--S---------HHHHHHHHHHHHTTB--.-EE--BTTB------HHHHHHTTT-HHHHS--S-SSG.GG- CS
                             GDC-P  31 vPkeiklkkelkleapksEeellaelekiasknkv.vksfiGaGyydtilPaviqrnilenpewytaYtPYqa.Eis 105
                                       +Pk++ l+ +l+l++  sE  ++++++++++ n    + f   G   ++  +v+++ + e+   ++   P q+ E  
  gi|557694854|ref|YP_008797908.1|  43 IPKKL-LRDNLNLPE-LSELTVVRHFTRLSQMNYSiSTGFYPLGSCTMKYNPVVNNQLAEQ---VADIHPLQPaETV 114
                                       66666.344444443.89*************99886889***********9***9966555...56667777449** PP

                                       HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHH.HHHHHH-SSS.....--EEEEETTS-HHHHHHHHHHHG CS
                             GDC-P 106 qGrLeallnfqtlvadltGldianasllDegtAaaEAv.llaaraskkk.....akkvvvdkkvhpqtlevlktrak 176
                                       qG Le l n  + +  ltG+d    s++  + A +E v  l+ ra +++     + k++v  + h  +       a 
  gi|557694854|ref|YP_008797908.1| 115 QGCLEILYNLEQALKTLTGMDA--FSMVPAAGAHGELVgCLIIRAYHSEkegkpRPKIIVPDSAHGTNP----ASAA 185
                                       ********************95..69**********874354554433301112457777777766554....3456 PP

                                       GGT-EEEEE-GGG--S-..........S-EEEEEEEES-TTSB--.--HHHHHHHHHTT-EEEE.EE-TTGGGTB-- CS
                             GDC-P 177 glgieivevdlteekvtd.......kekevagvlvqypnteGrie.dlkelvekakkkkslvvv.aadllaLtllkp 244
                                         g+e+ +v ++e++  d       +  ++ag+++  pnt G  e d++++v  +++++sl+    a+l a++ ++ 
  gi|557694854|ref|YP_008797908.1| 186 MAGFEVSVVRTREDGCVDlemlekmVDGDIAGIMLTNPNTVGLFEkDIEDIVRIMHQNDSLLYYdGANLNAIVGVAR 262
                                       6667777777777777777787788899**************98636************99876368999******* PP

                                       HHHHT-SEE.EEE-TTTT---GGG----EEEEE-GGGGGG--S CS
                             GDC-P 245 PgelgaDiv.vGsaqrfGvPlgyGGPhagffAvkeklkRkiPG 286
                                       Pg++g Div +   + f  P g GGP ag + v +kl++ +P 
  gi|557694854|ref|YP_008797908.1| 263 PGDMGFDIVhLNLHKTFSTPHGGGGPGAGPVGVVAKLAKYLPP 305
                                       ********94566789*********************999973 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   8.5e-10   5.1e-06      85     207 ..     164     284 ..     151     397 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8.5e-10
                                       -TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B--HHH CS
                       Aminotran_5  85 lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt.iqpvee 160
                                        kp+ +i+v ++ h  n   + +++   g++v v++  e+g +dl+ lek ++ +++ +++t  ++v G   +++e+
  gi|557694854|ref|YP_008797908.1| 164 GKPRPKIIVPDSAHGTNP--ASAAM--AGFEVSVVRTREDGCVDLEMLEKMVDGDIAGIMLTNPNTV-GLfEKDIED 235
                                       677788888888888777..44443..69******************************99977665.6659***** PP

                                       HHHHHHHTT-EEEEE-TT.TTTTS---HHHHTESEEEEETTT.TTSSTT CS
                       Aminotran_5 161 igklakkkgalvlvDaaq.avghipidvkklgvDflafsghK.llgPtG 207
                                       i++++++++ l+  D+a  ++        ++g D++ +  hK +  P G
  gi|557694854|ref|YP_008797908.1| 236 IVRIMHQNDSLLYYDGANlNAIVGVARPGDMGFDIVHLNLHKtFSTPHG 284
                                       *****************844556667788999****9999997777776 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.5e-08   0.00021      34     173 ..     121     255 ..     112     420 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.5e-08
                                       HHHHHHHHHHHTT-SEEEEES-.HHHHHHHHH........HHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE CS
                   Beta_elim_lyase  34 vnrLedavaelfgkeaalfvpq.GtaAnsill........killqrgeevivtepahihfdetgaiaelagvklrdl 101
                                        ++Le+a++ l+g++a   vp  G  ++ + +        +   ++ +++iv + ah+   ++ a a++ag ++  +
  gi|557694854|ref|YP_008797908.1| 121 LYNLEQALKTLTGMDAFSMVPAaGAHGELVGCliirayhsEKEGKPRPKIIVPDSAHG---TNPASAAMAGFEVSVV 194
                                       689*************9999955*******9977875543333467778899999998...55677778999999** PP

                                       -EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHH CS
                   Beta_elim_lyase 102 knkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfan 173
                                       +++e+G +dle le++++   +    i+ i+lt+ n +  G  +  + ++ +  i ++++  l +DgA + n
  gi|557694854|ref|YP_008797908.1| 195 RTREDGCVDLEMLEKMVDG--D----IAGIMLTNPNTV--G--LFEKDIEDIVRIMHQNDSLLYYDGANL-N 255
                                       ******************9..4....89********98..5..7799********************943.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); 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:                         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: 00:00:00.40
# Mc/sec: 3777.45
//
Query:       gi|557694855|ref|YP_008797909.1|  [L=360]
Description: glycine cleavage system aminomethyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  254.5   0.0    1.2e-75  254.2   0.0    1.1  1  GCV_T     Aminomethyltransferase folate-binding domain
    9.8e-15   54.3   0.1    1.9e-14   53.3   0.1    1.5  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 !  254.2   0.0   1.4e-79   1.2e-75       2     257 .]       7     254 ..       6     254 .. 0.97

  Alignments for each domain:
  == domain 1  score: 254.2 bits;  conditional E-value: 1.4e-79
                             GCV_T   2 ydrhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgka 78 
                                        d+h++  ++++efagw   + +  +s ++eh+avr++ag+fD+Shm++ ++sGp+a+++Lq++lt d++klkpg++
  gi|557694855|ref|YP_008797909.1|   7 LDFHEKTAKELGEFAGWRTVITF--SSLREEHEAVRKDAGIFDISHMTRTKISGPHATKFLQEVLTIDVEKLKPGRM 81 
                                       689********************..**************************************************** PP

                             GCV_T  79 tytlllnedGgvidDlivarldedefllvvnaankekdlawlekaaekkdldvevedvteelallalqGPkarevls 155
                                       +y l+ln dGg+idD++v+++ +d++l+v+na ++ ++l wl++  +  d +v ved+te+ a +a+qGP + + +s
  gi|557694855|ref|YP_008797909.1|  82 KYGLILNMDGGIIDDVTVYKVTDDSYLMVSNALTRVRVLGWLRE-KM--DGEVLVEDITESSAFFAVQGPHSSSYVS 155
                                       ********************************************.66..8*************************** PP

                             GCV_T 156 kllgadlselkffsfaevelaggkkvlvsRtgytGedGfeiyipaeeaeelweaLleagkeegvkpaGlgArdtlRl 232
                                        l+   +s +k+f+    +++ ++++lv+R+gytG dG+e+++     e+l+e++++  +e+gv+p+Gl++rd+ R+
  gi|557694855|ref|YP_008797909.1| 156 SLV-GAVSGFKWFEGGFRTVD-DCRLLVTRSGYTGGDGYELMTLCG-EEQLYEKVWSFFTEKGVRPCGLACRDVCRI 229
                                       ***.589*********99999.*******************98776.578*************************** PP

                             GCV_T 233 EaglrlyghdldeettPleaglgwa 257
                                       Eag++lyg+d+de+ +Pleagl wa
  gi|557694855|ref|YP_008797909.1| 230 EAGFPLYGQDFDEKNDPLEAGLFWA 254
                                       **********************996 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 !   53.3   0.1   2.1e-18   1.9e-14       1      78 [.     278     354 ..     278     355 .. 0.93

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 2.1e-18
                           GCV_T_C   1 RrlvglelddgapllrggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvkkp 77 
                                       ++l  +e+ d+  ++r g++++ ++ + G vTSg+ sp +++ ++lAy+++ l+  g ev+v+vrg+r +a v  kp
  gi|557694855|ref|YP_008797909.1| 278 KKLSLIEMVDQ-GVPRPGYKVYVGDVEAGVVTSGCLSPMINRGVCLAYLPPSLQVDGYEVYVDVRGRRRKAVVRTKP 353
                                       67888888755.589**********************************************************9888 PP

                           GCV_T_C  78 f 78 
                                       +
  gi|557694855|ref|YP_008797909.1| 354 L 354
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2723.44
//
Query:       gi|557694856|ref|YP_008797910.1|  [L=270]
Description: hypothetical protein CSUB_C1429 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2031.32
//
Query:       gi|557694857|ref|YP_008797911.1|  [L=511]
Description: hypothetical protein CSUB_C1430 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-06   27.5   2.2    3.7e-06   26.8   1.6    1.7  2  tRNA_anti-codon  OB-fold nucleic acid binding 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 !   26.8   1.6     2e-10   3.7e-06       2      69 ..     145     212 ..     144     219 .. 0.93
   2 ?   -3.0   0.0      0.41   7.3e+03      38      74 ..     465     502 ..     446     504 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2e-10
                                       EEEEEEEEEE...EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEE CS
                   tRNA_anti-codon   2 tvaGrvtsis...drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelk 69 
                                       +++Grv+ ++    ++g+ +i ++l Dgtg+++v  +     +++ ++++Gdv+ +  ++v r +++ +++ 
  gi|557694857|ref|YP_008797911.1| 145 NIVGRVVGKRtgvSQDGRAYIVLKLSDGTGSVEVLGDV---ADVLREIRVGDVLAAHgCTVVRKNNK-ITIR 212
                                       699*********************************99...****************9999999988.8875 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.41
                                       HHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEEEEE CS
                   tRNA_anti-codon  38 eatklaenlkeGdvvrvt.Grvkrrpggelelkveeie 74 
                                         ++  ++lkeG  +      +k+ + ge e++ ++++
  gi|557694857|ref|YP_008797911.1| 465 PISEKVNELKEGEPLTLVfPLIKKNQFGESEVHFDRFT 502
                                       55566677777776666667777888888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3794.24
//
Query:       gi|557694858|ref|YP_008797912.1|  [L=410]
Description: electron transfer flavoprotein beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   55.4   0.0    2.3e-09   37.4   0.0    2.6  2  ETF       Electron transfer flavoprotein 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 !   37.4   0.0   1.3e-13   2.3e-09       3      88 ..      23     121 ..      21     129 .. 0.89
   2 !   15.2   0.0   8.1e-07     0.015      92     160 ..     201     277 ..     182     296 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.3e-13
                                       EEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES.................S-.CHHHHHHCT-SEEEEEE CS
                               ETF   3 vlaehgvdgklnpvdlealeaArrlkekaggevtavvvGp.............peaeea.lrealaamGadkvilvd 65 
                                       vl +++ + +lnp+d  a+eaA  +k++ gg+++a+++Gp             p++e+  + +     G d+ i ++
  gi|557694858|ref|YP_008797912.1|  23 VLRREEMELVLNPHDVKAVEAAYYVKKTVGGKIVAMTMGPepklvpimadlmePREESKyVPRISF-EGFDERIILS 98 
                                       677888899*******************99*******************99987777775666666.********** PP

                                       -GGGSS--CCHHHHHHHHHHHHC CS
                               ETF  66 dpalagydaeatakalaalikke 88 
                                       d+++ag+d++at+++la  ik +
  gi|557694858|ref|YP_008797912.1|  99 DRRMAGADTWATSYTLACGIKRY 121
                                       ********************986 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 8.1e-07
                                       EEEEESSCC.H..HHHHHHHHHHCT-EEEEEESEEEEETCC.........EEEEEECCCCTEEEEEE-TSSSEEEEE CS
                               ETF  92 lvlagatai.g..kqvaprlAalLgvplitdvteleveggk.........ltvtRpieggnglaevveadlpavltv 156
                                       ++l+g ++  g  ++v+p++A+ L   l   + ++     +         + ++R i    +++++++  lp++lt+
  gi|557694858|ref|YP_008797912.1| 201 IILTGMKTSdGetGNVGPQTAEALSQMLGVTIPSIAFT-RDfeispeldhVMAERRIGR--VIQRMRT-VLPCLLTI 273
                                       89*******88************986666666655554.23355556899*******99..**55555.5******* PP

                                       -TTS CS
                               ETF 157 rpga 160
                                       +   
  gi|557694858|ref|YP_008797912.1| 274 DHHY 277
                                       9843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); 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 0.22s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3171.88
//
Query:       gi|557694859|ref|YP_008797913.1|  [L=364]
Description: electron transfer flavoprotein alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  102.6   0.0    3.4e-29  102.0   0.0    1.2  1  ETF        Electron transfer flavoprotein domain
      6e-25   87.1   1.5    6.9e-25   86.9   0.4    1.7  2  ETF_alpha  Electron transfer flavoprotein FAD-binding 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 !  102.0   0.0   3.8e-33   3.4e-29       4     173 ..      12     189 ..       9     197 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 3.8e-33
                                       EE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHH CS
                               ETF   4 laehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeataka 80 
                                       +   + +g+l + +le ++aAr++++k  ++v av++G++   +a++ea+a +Gad v+++d p l  y+ ++++++
  gi|557694859|ref|YP_008797913.1|  12 YCALD-NGRLTRPSLEIIAAARKVADKIEQRVGAVIIGHDLD-NAVEEAIA-RGADVVYYADEPWLRSYQCLPYTRI 85 
                                       55555.999******************779*********655.556*****.************************* PP

                                       HHHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCC............EEEEEECCCCTEEEEE CS
                               ETF  81 laalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggk............ltvtRpieggnglaev 145
                                       + ++++k++p   l+ a   g+++ pr+A +L+++l+td ++l ve ++            l ++Rp ++   +a++
  gi|557694859|ref|YP_008797913.1|  86 VCEMVEKYKPYALLFVADELGRDLSPRVAYRLNTGLATDNINLAVE-DYyfgplnttfknvLAQIRPDFA-TRVAKI 160
                                       **********************************************.667********************.555599 PP

                                       E-T.SSSEEEEE-TTSS----S-TT---E CS
                               ETF 146 vea.dlpavltvrpgafepaaimaakkke 173
                                        ++ ++p+++++rpg f+p+++++++ +e
  gi|557694859|ref|YP_008797913.1| 161 YTPrHRPQIASIRPGNFDPLPEDRSRIGE 189
                                       9999***************9999988766 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 ?   -2.9   0.0      0.78     7e+03      22      38 ..      28      44 ..      24      45 .. 0.76
   2 !   86.9   0.4   7.7e-29   6.9e-25       1      84 []     217     321 ..     217     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.78
                                      HHHHHHHHHHHT-EEEE CS
                         ETF_alpha 22 lelleelaealgaavga 38
                                      ++ ++++a++++  vga
  gi|557694859|ref|YP_008797913.1| 28 IAAARKVADKIEQRVGA 44
                                      56678889999888886 PP

  == domain 2  score: 86.9 bits;  conditional E-value: 7.7e-29
                                       .-TTT-S-EEEE-GGG.........SSGGGHH....HHHHHHHHHT..-EEEE-HHHHTT......TSS-CCCB-SS CS
                         ETF_alpha   1 vdLeeakvvvsgGrGl.........kskenle....lleelaealg..aavgasRavvda......gwipeerqvGq 56 
                                       v+Leeakvvvs+G G+         + +e++e    l+e ++++lg  a++ga+Ra+++a      g+i++erqvGq
  gi|557694859|ref|YP_008797913.1| 217 VELEEAKVVVSIGLGIlkdgsgnprNPREGYElakkLVEVIKTHLGvkAELGATRALIHAelkeleGLITSERQVGQ 293
                                       689*************9999888762255555111255555666767799**********8877777********** PP

                                       SS-----S-EEEES----HHHHGGGTT- CS
                         ETF_alpha  57 tGktvaPklyiavGisGaiqhlaGmkes 84 
                                       tGktv+P++y+a+GisG++qh +Gm +s
  gi|557694859|ref|YP_008797913.1| 294 TGKTVSPDIYVALGISGSVQHRVGMIKS 321
                                       *************************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2912.63
//
Query:       gi|557694860|ref|YP_008797914.1|  [L=562]
Description: electron transfer flavoprotein-quinone oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   52.8   1.5    1.8e-12   47.5   1.5    2.2  1  DAO             FAD dependent oxidoreductase
    5.3e-12   45.3   0.1    1.9e-06   27.0   0.0    2.2  2  Trp_halogenase  Tryptophan halogenase
    9.2e-11   41.7   0.4    1.8e-10   40.8   0.4    1.4  1  FAD_oxidored    FAD dependent oxidoreductase
    1.9e-09   37.2   2.4      3e-08   33.2   0.7    2.7  3  FAD_binding_2   FAD binding domain
    4.2e-08   32.8   1.1    1.5e-06   27.7   0.3    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.5e-08   31.9   1.3    1.3e-06   27.8   0.4    2.3  2  Thi4            Thi4 family
    8.1e-08   31.9   0.3    4.7e-07   29.4   0.3    1.9  1  FAD_binding_3   FAD binding domain
    1.4e-07   31.6   0.3    4.2e-07   30.1   0.3    1.8  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    2.7e-07   29.7   0.4    2.5e-06   26.5   0.2    2.0  2  HI0933_like     HI0933-like protein
    7.8e-07   28.5   0.4    2.9e-05   23.3   0.5    2.2  2  GIDA            Glucose inhibited division protein A
    6.7e-05   22.3   0.3    0.00015   21.1   0.2    1.6  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0011   18.1   0.4     0.0087   15.1   0.2    2.0  2  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
      0.056   12.7   0.1        2.3    7.4   0.0    2.2  2  Amino_oxidase   Flavin containing amine oxidoreductase
       0.18   11.7   0.9       0.28   11.0   0.1    1.7  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
       0.25   11.3   0.5       0.51   10.3   0.1    1.7  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 !   47.5   1.5   1.5e-15   1.8e-12       1     269 [.       6     245 ..       6     279 .. 0.68

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.5e-15
                                       EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeel 75 
                                       dvv++G+G +G+++A  Lar+g  V++lek+ ++  g+   ++g+l +g++   ++       l ++++l e+ee+ 
  gi|557694860|ref|YP_008797914.1|   6 DVVVVGAGPAGSAAAIKLAREGfdVLVLEKA-QLP-GQRNVSGGVLFGGFE---NG-------LGLVDLLPEFEEQ- 69 
                                       9******************************.888.9***********985...33.......3457888888887. PP

                                       SSTTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTTST.TTSEEEEETTEEEEEHHHHHHH CS
                               DAO  76 gididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepalp.gllgalfypdtgqvdpakltaa 151
                                       ++ ++ +  G+  +         l +  +l +ea +++  ld++    l+  l    l a  + ++  v   ++ ++
  gi|557694860|ref|YP_008797914.1|  70 AP-VERKIVGHELYM--------LSEPRKLNGEASYRYIKLDKS---SLFTKLGlTMLDA-TTGHDYSVLRTRFDRW 133
                                       54.444433333332........222222223344443347775...4443211123333.4444466666779999 PP

                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHH.HTT...CTT.TSEEEEEEE CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdll.gll...kel.dlpispvrg 222
                                       +a  a + G+ + ++ +v++l  +dg+v+gv  +t  +e+  ad v+ + G+ s ll +++   ++l + +++    
  gi|557694860|ref|YP_008797914.1| 134 FAGVATEEGAMLTTRKTVEDLIWKDGRVVGV--KTVdEEV-YADLVIDCGGVTS-LLpEKAgirPKLtPDQVYHGVK 206
                                       ********************9899*******..5554554.4699******997.6665554454444456677888 PP

                                       EEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEEESS CS
                               DAO 223 qvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvGgta 269
                                       +v+ ++p   ++ ++        t d+ ++vy++ +  ++v+ Gg  
  gi|557694860|ref|YP_008797914.1| 207 HVFKVNPERIEEFFA--------TGDGYKSVYLIGPFMHGVVGGGFV 245
                                       888886644433333........999999999998865656655544 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.3e-06     0.004       1      37 [.       6      39 ..       6      44 .. 0.94
   2 !   27.0   0.0   1.6e-09   1.9e-06     136     217 ..     112     190 ..      65     196 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeig 37
                                      ++v+vG+G+aG+ aA+ la+ +   ++v+++e+++++
  gi|557694860|ref|YP_008797914.1|  6 DVVVVGAGPAGSAAAIKLAREG---FDVLVLEKAQLP 39
                                      69*******************9...9********998 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 1.6e-09
                                       SB-TTS-B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-I CS
                    Trp_halogenase 136 prekdglsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrledgreveadlfiDcsGfrgl 212
                                        ++ d  +++ + y++ + +++++   va+++G   +  k ve  + +dgrv ++++ d++ v adl+iDc G  +l
  gi|557694860|ref|YP_008797914.1| 112 LTMLD--ATTGHDYSVLRTRFDRWFAGVATEEGAMLTTRKTVEDLIWKDGRVVGVKTVDEE-VYADLVIDCGGVTSL 185
                                       44444..789999********************************************8887.99************* PP

                                       IIIII CS
                    Trp_halogenase 213 lieqa 217
                                       l e+a
  gi|557694860|ref|YP_008797914.1| 186 LPEKA 190
                                       *9987 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.4   1.5e-13   1.8e-10       1     149 [.       6     186 ..       6     196 .. 0.71

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.5e-13
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdig...........nkaee..qvvtgiarefl 64 
                                       DvvVvG+gpaG aAAi  ar+G  vl++e+ +  G    sg+v  + g           ++ ee   v ++i+++ l
  gi|557694860|ref|YP_008797914.1|   6 DVVVVGAGPAGSAAAIKLAREGFDVLVLEKAQLPGQRNVSGGV-LFGGfenglglvdllPEFEEqaPVERKIVGHEL 81 
                                       9****************************76655544444432.222211122223333333335688888887766 PP

                      FAD_oxidored  65 erlrq....rgga....rlkkrskwn...................tfepevakavleeml....aeagvtvllntrl 110
                                         l +    +g+a            +                    ++ +v+++ ++ +     +e+g  + + +++
  gi|557694860|ref|YP_008797914.1|  82 YMLSEprklNGEAsyryI-------KldksslftklgltmldattGHDYSVLRTRFDRWFagvaTEEGAMLTTRKTV 151
                                       666553323222233220.......122334556788899999877*************99999999********** PP

                      FAD_oxidored 111 vevekegkriesvtveskegrktirAkvfiDATgdGdla 149
                                       ++ + +++r+ +v++     ++++ A+++iD+ g   l+
  gi|557694860|ref|YP_008797914.1| 152 EDLIWKDGRVVGVKTV----DEEVYADLVIDCGGVTSLL 186
                                       *****999*******8....699*********9877766 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.7   2.5e-11     3e-08       1      46 [.       6      50 ..       6      55 .. 0.93
   2 ?    2.2   0.0     0.063        75     153     180 ..     140     167 ..     113     192 .. 0.81
   3 ?   -1.5   0.0      0.85     1e+03      59     109 ..     428     484 ..     416     521 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.5e-11
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgid 46
                                      Dv+V+G+G AG aAA+++a++G +v+v+ek+q   g+   s+G ++
  gi|557694860|ref|YP_008797914.1|  6 DVVVVGAGPAGSAAAIKLAREGFDVLVLEKAQL-PGQRNVSGGVLF 50
                                      9******************************96.889999999876 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.063
                                       TCTEEEEESEEEEEEEECTTEEEEEEEE CS
                     FAD_binding_2 153 kagvdfqerteadeLivedgrvtGavve 180
                                       + g  + +r  +++Li +dgrv+G+   
  gi|557694860|ref|YP_008797914.1| 140 EEGAMLTTRKTVEDLIWKDGRVVGVKTV 167
                                       44578899****************9766 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.85
                                       .CHHHHHHHHHHHHTTT-S-HHHHHHHHHTHHHHHHHHHHT..T----B....CCTS CS
                     FAD_binding_2  59 kdspelhrtdtlkaldeladqplveafveaapeavdeLeel..gvpfsr....tedg 109
                                       +++ ++ ++++++ l +++d+ ++++ v++ ++ +d ++++   +p+s     te+g
  gi|557694860|ref|YP_008797914.1| 428 QRDSVQKIQQYIGKLEYHEDKVRSHITVDEEAASRDPFKAWipLCPVSCytlvTEKG 484
                                       345788999999999999999999999999999999999998866666644443333 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 !   27.7   0.3   1.3e-09   1.5e-06       1      39 [.       5      42 ..       5      56 .. 0.86
   2 ?    3.6   0.0     0.027        33     179     239 ..     124     184 ..      98     231 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.3e-09
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclngg 39
                                      +dvvv+G+GpAG aaa++la+ g++v+++ ++ ++++++
  gi|557694860|ref|YP_008797914.1|  5 FDVVVVGAGPAGSAAAIKLAREGFDVLVL-EKAQLPGQR 42
                                      69***************************.555565554 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.027
                                       TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 179 raldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrp 239
                                       + l  ++ ++ + + ++eG  + ++++v++++ ++ ++  v +  ee+ adlv+ + Gv+ 
  gi|557694860|ref|YP_008797914.1| 124 SVLRTRFDRWFAGVATEEGAMLTTRKTVEDLIWKDGRVVGVKTVDEEVYADLVIDCGGVTS 184
                                       566788999999999**************99999986664444555579*****9999874 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.4   1.1e-09   1.3e-06      18      64 ..       5      50 ..       2      54 .. 0.95
   2 ?    2.5   0.0     0.061        73     111     137 ..     141     166 ..     115     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.1e-09
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTB CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlf 64
                                       Dvv+vGaG++G +aa  la++ ++ v++le+   pG     GG lf
  gi|557694860|ref|YP_008797914.1|  5 FDVVVVGAGPAGSAAAIKLARE-GFDVLVLEKAQLPGQRNVSGGVLF 50
                                      6*********************.*********************999 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.061
                                       TTEEEEESEEEEEEEEETBTEEEEEEE CS
                              Thi4 111 anvkllnavaveDlivregegvaGvvi 137
                                        ++ l +  +veDli ++  +v Gv +
  gi|557694860|ref|YP_008797914.1| 141 EGAMLTTRKTVEDLIWKD-GRVVGVKT 166
                                       5667778889********.78888865 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.3   3.9e-10   4.7e-07       2     197 ..       5     214 ..       4     273 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 3.9e-10
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyn 78 
                                        dV++VGaGpaG  +a  L++ G +v+++ek +   +   ++g+    +e  + lGl d + +   +  + +++++ 
  gi|557694860|ref|YP_008797914.1|   5 FDVVVVGAGPAGSAAAIKLAREGFDVLVLEKAQLPGQRNVSGGVLFGGFE--NGLGLVDLLPEFEEQAPVERKIVGH 79 
                                       69******************************999999988888888888..5677777666666666666666666 PP

                                       E....................CCCC.CEEEEEHH...CHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECC CS
                     FAD_binding_3  79 e....................lsdt.pkaradle...lesspervtvypqteleriLvehaeerglqvrfktevesl 131
                                       e                    l    +   ++l    l+++  + + +  t+++r  +  a+e+g+ +   + ve l
  gi|557694860|ref|YP_008797914.1|  80 ElymlseprklngeasyryikL--DkSSLFTKLGltmLDATTGHDYSVLRTRFDRWFAGVATEEGAMLTTRKTVEDL 154
                                       6666677777666655554432..14333333334344555556666667889999999999999888888888855 PP

                                       EECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGG.EEEEEEEEEEEEEEEEEEC-SC CS
                     FAD_binding_3 132 eqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgie.fegeetvyeagvldvlfdadls 197
                                          +      v + +t  +e+v a+ ++ + G+ S   +++gi+   ++++v   + ++ +f+++ +
  gi|557694860|ref|YP_008797914.1| 155 IWKDGR----VVGVKT-VDEEVYADLVIDCGGVTSLLPEKAGIRpKLTPDQV--YHGVKHVFKVNPE 214
                                       544444....444432.23479999999999999999999999844444545..4445555555554 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 !   30.1   0.3   3.5e-10   4.2e-07       1      32 [.       9      40 ..       9      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.5e-10
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      +vGaG +G++aA  La++gfdvl+lek++ +G
  gi|557694860|ref|YP_008797914.1|  9 VVGAGPAGSAAAIKLAREGFDVLVLEKAQLPG 40
                                      8**************************98877 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.2   2.1e-09   2.5e-06       1      38 [.       5      42 ..       5      50 .. 0.91
   2 ?    0.9   0.0      0.12   1.4e+02     119     165 ..     138     182 ..      88     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.1e-09
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                      +dv+v+G+G+AG  aAi++a++g +Vl+leka+ +g++
  gi|557694860|ref|YP_008797914.1|  5 FDVVVVGAGPAGSAAAIKLAREGFDVLVLEKAQLPGQR 42
                                      59******************************999986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                                       HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 119 lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                       ++e+g  l ++++v+++  ++++++ vkt  +ee+ ad lv+ +GG 
  gi|557694860|ref|YP_008797914.1| 138 ATEEGAMLTTRKTVEDLIWKDGRVVGVKT-VDEEVYAD-LVIDCGGV 182
                                       578899999********************.78888876.67777875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.5   2.4e-08   2.9e-05       1      28 [.       6      33 ..       6      47 .. 0.90
   2 ?    2.6   0.0     0.048        57      91     140 ..     124     173 ..     102     182 .. 0.78

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.4e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dv+V+G+G AG++AA+++ar G++vl +
  gi|557694860|ref|YP_008797914.1|  6 DVVVVGAGPAGSAAAIKLAREGFDVLVL 33
                                      79***********************987 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.048
                                       EE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEE CS
                              GIDA  91 qvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetik 140
                                       +v r ++ +++  +  +e  +   +++ve+li ++++v gv+t d+e++ 
  gi|557694860|ref|YP_008797914.1| 124 SVLRTRFDRWFAGVATEEGAMLTTRKTVEDLIWKDGRVVGVKTVDEEVYA 173
                                       55566666666666666667777899******************999886 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 !   21.1   0.2   1.2e-07   0.00015       1      32 [.       8      38 ..       8      41 .. 0.94
   2 ?   -3.0   0.0       2.9   3.4e+03      87     143 ..     134     192 ..     124     214 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgni 32
                                      +++GaGPaG aaai+l + g+ d+l+lEk+++
  gi|557694860|ref|YP_008797914.1|  8 VVVGAGPAGSAAAIKLAREGF-DVLVLEKAQL 38
                                      79*******************.8******975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.9
                       Pyr_redox_3  87 lrevaksfelpiklfeeVes.vkkedegfevetsketyeAkkviiAtGefd.kPnklni 143
                                       ++ va+++     + ++Ve+ + k+++   v+t  e++ A+ vi   G  +  P+k +i
  gi|557694860|ref|YP_008797914.1| 134 FAGVATEEGAMLTTRKTVEDlIWKDGRVVGVKTVDEEVYADLVIDCGGVTSlLPEKAGI 192
                                       56677777777777788876244566778899999999999999877765423555555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   7.3e-06    0.0087       1      34 [.       6      37 ..       6      45 .. 0.89
   2 ?    0.6   0.0      0.19   2.2e+02      84     157 ..     125     204 ..     116     213 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.3e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasp 34
                                      Dvvv+GaGpAg + A +l  a+ g  v+++e ++
  gi|557694860|ref|YP_008797914.1|  6 DVVVVGAGPAGSAAAIKL--AREGFDVLVLEKAQ 37
                                      9*****************..9********98765 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.19
                     Lycopene_cycl  84 vsskrlkeellerlvengvkl.leakvesveeeeageslvvleggrkirarlvvdarglaslk......karrlglQ 153
                                       v ++r+ +  +    e+g+ l ++ +ve    ++  +++ v   +++++a lv+d  g+ sl       +++ +  Q
  gi|557694860|ref|YP_008797914.1| 125 VLRTRFDRWFAGVATEEGAMLtTRKTVEDLIWKDG-RVVGVKTVDEEVYADLVIDCGGVTSLLpekagiRPKLTPDQ 200
                                       55666777777766755555514556666666555.7777888899************8887655555544444445 PP

                     Lycopene_cycl 154 tfyG 157
                                       +++G
  gi|557694860|ref|YP_008797914.1| 201 VYHG 204
                                       5555 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0019       2.3       2      27 ..      15      40 ..      14      45 .. 0.86
   2 ?    3.1   0.0     0.038        46     218     278 ..     139     201 ..      85     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0019
                                      HHHHHHHHHHHTTEEEEEEESSSSSB CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvG 27
                                      aG aaA +L++ GfdV+vlE  + +G
  gi|557694860|ref|YP_008797914.1| 15 AGSAAAIKLAREGFDVLVLEKAQLPG 40
                                      5669****************877666 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.038
                                       HTTTTEEEETSEEEEEEEE.ETTCEEEEETTSTEEEESEEEE-S-HHHHH..SSEEESCC.SHHH CS
                     Amino_oxidase 218 eelrgldirlntrVkeikr.egdgvtvtledgevveaDaVvvTvplgvlk..ailfsPpl.pdek 278
                                         + g  + +++ V ++ + +g  v+v+++d ev  aD V+ +  +  l   +   +P+l pd++
  gi|557694860|ref|YP_008797914.1| 139 T-EEGAMLTTRKTVEDLIWkDGRVVGVKTVDEEV-YADLVIDCGGVTSLLpeKAGIRPKLtPDQV 201
                                       3.77889999*********88999******9999.89***9888888888776666777766655 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 ?   11.0   0.1   0.00024      0.28       2      31 ..       7      36 ..       6      44 .. 0.92
   2 ?   -2.7   0.1       3.7   4.5e+03      23      50 ..     420     448 ..     416     462 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdis 31
                                      v v+GaG  G+  a  +a++g++V +++ +
  gi|557694860|ref|YP_008797914.1|  7 VVVVGAGPAGSAAAIKLAREGFDVLVLEKA 36
                                      89***********************99876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.7
                                       -EEEEE-S-HHHHHHHHHHHHH.HHHCCT CS
                           3HCDH_N  23 leVvlvdiseealekalekiek.sleklv 50 
                                         +++ d+++++++k ++ i k ++++ +
  gi|557694860|ref|YP_008797914.1| 420 RVINMRDVQRDSVQKIQQYIGKlEYHEDK 448
                                       55788899999999988888874333333 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 ?   10.3   0.1   0.00043      0.51       1      38 [.       8      41 ..       8      46 .. 0.83
   2 ?   -3.3   0.0       6.7     8e+03     104     149 ..     130     176 ..     125     181 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00043
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.ga 38
                                      ++vGaGp+G a++ +L+++      +++ + +++++ g+
  gi|557694860|ref|YP_008797914.1|  8 VVVGAGPAGSAAAIKLARE-----GFDVLVLEKAQLpGQ 41
                                      69***************99.....599999999655475 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.7
                     NAD_binding_9 104 feellarl.pegvtvevhraevvdleeradgqavlladgaslaadaV 149
                                       f+++ a +  e+  +   r++v+dl  +++++  +++ ++++ ad V
  gi|557694860|ref|YP_008797914.1| 130 FDRWFAGVaTEEGAMLTTRKTVEDLIWKDGRVVGVKTVDEEVYADLV 176
                                       44444444333333444555666665555555544555555556655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (562 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); 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: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 4002.74
//
Query:       gi|557694861|ref|YP_008797915.1|  [L=283]
Description: thiosulfate sulfurtransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-42  143.0   0.0    1.5e-20   73.7   0.0    2.1  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 !   67.6   0.0   6.4e-23   1.2e-18       2     105 ..      12     120 ..      11     122 .. 0.84
   2 !   73.7   0.0   8.5e-25   1.5e-20       4     105 ..     154     272 ..     151     274 .. 0.88

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 6.4e-23
                         Rhodanese   2 akelkellekgkvallDvR..ppeeYekghIpgAvnvskdtlsrakkseapllelpeellel....gidnkktvvvy 72 
                                       +++lk++l+k ++a++ v   p+ +Ye+ghIpgA+ +  d++++ +k+++++   pee+++l    g++n+++v++y
  gi|557694861|ref|YP_008797915.1|  12 VEWLKANLGKSGIAVIEVDydPKLAYEQGHIPGALLI--DWRRDMNKPNERDIIGPEEFEKLmsrlGVSNDTHVILY 86 
                                       79**********9976666558888************..66666666666666666666666666************ PP

                         Rhodanese  73 cdgggr.aaaaaallkklGyknvsvldGGfkawk 105
                                       +d ++  a++a + ++ +G+k+v++l+GG k+w 
  gi|557694861|ref|YP_008797915.1|  87 GDYNNWfATFAFWVFEIYGHKKVQILNGGRKKWI 120
                                       ******99999888888**777***********6 PP

  == domain 2  score: 73.7 bits;  conditional E-value: 8.5e-25
                         Rhodanese   4 elkellekgkvallDvRppeeY...............ek.ghIpgAvnvskdtlsrakkseapllelpeellelgid 64 
                                        l+e  +k + +l+DvR+p+e+               ++ ghIpgA+n+++  + r++ + ++  el + + ++g++
  gi|557694861|ref|YP_008797915.1| 154 LLREKVGKADLVLVDVRSPAEFtgeitappeypnehaQRgGHIPGAINIPWGQAIREDGTFKSAEELKQLYTSKGVT 230
                                       566777888888*********99999999999****9555*********9999999999999999999999999*** PP

                         Rhodanese  65 nkktvvvycdgggraaaaaallkk.lGyknvsvldGGfkawk 105
                                       ++k vv+yc+ g+ra+ ++  lk  lGy++v+v+dG++++w 
  gi|557694861|ref|YP_008797915.1| 231 PDKDVVTYCRIGERASVTWFVLKHlLGYPRVRVYDGSWTEWG 272
                                       **************66667777767****************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2069.34
//
Query:       gi|557694862|ref|YP_008797916.1|  [L=218]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   45.7   0.0    7.9e-12   45.1   0.0    1.3  1  GCV_H     Glycine cleavage H-protein
    1.2e-06   28.3   0.0      3e-06   26.9   0.0    1.6  1  TusA      Sulfurtransferase TusA


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 !   45.1   0.0   8.9e-16   7.9e-12       2     103 ..      15     114 ..      13     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 8.9e-16
                                       EE-TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGG CS
                             GCV_H   2 yytkehewvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNekl 78 
                                       y ++++ wv++  d++++vG+ +     +g+   v+++++g   kk+  la+    +a + + apv+  ++e N++l
  gi|557694862|ref|YP_008797916.1|  15 YLVEQDLWVQTLSDNIYRVGVVKPFLFFVGKPHKVTVRQAGSLAKKNTMLAVFSNPRADAALLAPVDCYILETNRDL 91 
                                       5667777********************************************************************** PP

                                       TT-TTHHHH-TTTTT--EEEEES-G CS
                             GCV_H  79 eeepeliNkdpyeegWliklklsnl 103
                                       +  pel+ ++py+egWl+k++++++
  gi|557694862|ref|YP_008797916.1|  92 T--PELLVQKPYDEGWLAKIRVEEP 114
                                       6..******************9875 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   3.4e-10     3e-06      24      64 ..     170     210 ..     164     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 3.4e-10
                                       CGCT-EEEEEESSCHHHHHHHHHHHHHTEEEEEEE-GCC-E CS
                              TusA  24 leegevlevladdpaatediprfakklghelveveeedgey 64 
                                       l+ ge l v+++dpa++ d  ++a+++gh+l+e+++ ++  
  gi|557694862|ref|YP_008797916.1| 170 LKVGESLHVITTDPATEVDMIAYADRTGHKLLEIKKIGKLL 210
                                       699*******************************9966554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1659.61
//
Query:       gi|557694863|ref|YP_008797917.1|  [L=178]
Description: tRNA-intron endonuclease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-25   88.5   0.0      5e-25   87.4   0.0    1.5  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
    8.1e-19   67.1   0.3    1.9e-18   65.9   0.1    1.7  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 ?   -3.0   0.0      0.88   7.9e+03      56      72 ..      48      64 ..      40      70 .. 0.72
   2 !   87.4   0.0   5.5e-29     5e-25       1      85 []      87     170 ..      87     170 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.88
                                      HHHHHHHHHHHHTTSEE CS
                     tRNA_int_endo 56 pdlsaavrlahsvkKkl 72
                                       dl++a+ la++ k + 
  gi|557694863|ref|YP_008797917.1| 48 LDLVEALYLARQRKLRI 64
                                      67788888888877665 PP

  == domain 2  score: 87.4 bits;  conditional E-value: 5.5e-29
                                       HHHHHHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEE CS
                     tRNA_int_endo   1 falkyavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaiv 77 
                                       f +ky+vy dLr++G+vv +G+kFG+dF+vY+++p+ +h+ +++++ + de+l+  ++++a+rla+svkK + + + 
  gi|557694863|ref|YP_008797917.1|  87 FPTKYRVYSDLRDRGFVVLPGIKFGSDFAVYRHGPGIDHAPFIIQIKKGDEKLSALEIIRAGRLATSVKKHFTISVP 163
                                       678*********************************************************************99997 PP

                                       TTTSCEEE CS
                     tRNA_int_endo  78 daegdvty 85 
                                        ae++v y
  gi|557694863|ref|YP_008797917.1| 164 -AEEKVVY 170
                                       .5555655 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 !   65.9   0.1   2.1e-22   1.9e-18       2      66 ..       3      76 ..       2      77 .. 0.98
   2 ?   -1.5   0.0      0.23     2e+03      52      66 ..     130     144 ..     129     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 2.1e-22
                                      EEEEETTEEEESSHHHHHHHHHTTT-SEE.........CCTSSEEEEHHHHHHHHHTTSEEEETTSEEE-HHHH CS
                   tRNA_int_endo_N  2 egeLsgdrvlvedeeaakrlyekgfYGkp.........lidepLqLslvEAlYLlekGklevvkggeplsfeel 66
                                      eg L+gd+v+v+d e+a++ly+ gfYGkp         + d+pL+L+lvEAlYL+++ kl++ +gg ++s++e+
  gi|557694863|ref|YP_008797917.1|  3 EGLLLGDSVVVWDVEQARQLYRLGFYGKPlgipkpkdmNFDAPLVLDLVEALYLARQRKLRILRGGVEVSPKEF 76
                                      689********************************************************************997 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.23
                                       EEEETTSEEE-HHHH CS
                   tRNA_int_endo_N  52 levvkggeplsfeel 66 
                                       ++++kg+e+ls  e+
  gi|557694863|ref|YP_008797917.1| 130 IQIKKGDEKLSALEI 144
                                       899999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      229  (0.0127726); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1446.42
//
Query:       gi|557694864|ref|YP_008797918.1|  [L=221]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   60.7  12.6    1.7e-16   60.2  12.6    1.2  1  PhoU_div  Protein of unknown function DUF47
    2.3e-05   24.7  13.1     0.0021   18.5   1.8    2.6  2  PhoU      PhoU domain


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 !   60.2  12.6     2e-20   1.7e-16      34     211 ..      41     216 ..      12     218 .. 0.83

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 2e-20
                          PhoU_div  34 llegdyekveellkeiselEreADeikreirlklek.glflPvdRedllelveslDeildvlediamlvt.l..rkv 106
                                       ++e d +k+ee   e+ ++ + A + +r+++ ++ + g++l   Red+++lv+s+D+i+d +e +a++v  l   k+
  gi|557694864|ref|YP_008797918.1|  41 TREPDIKKIEEAYSEVLQIDEAAKNCRRQVEKEVSEiGAIL-TNREDFIRLVNSIDKIADIAEGVAFRVVsLvkSKM 116
                                       456799****************************9857777.88**********************98752322578 PP

                          PhoU_div 107 efpeelkdeflallkktveaiealaevieeleklletalskkdiveeieslEdeiDqlqrklikklfsredasnple 183
                                       ++++e+  ++l+l + +++++  l e+i ++  l  + +   ++++e e++E ++D+l+r++    +  e    + +
  gi|557694864|ref|YP_008797918.1| 117 KLDKEITSKVLELGELVLQTVTRLREAILAVT-LNSETFY--QKLKETEEFERKVDELYRNIDLTILMSEM--KIGQ 188
                                       99****************************99.5666666..49*****************9766666455..5667 PP

                          PhoU_div 184 vlllveiieklenvsdraedvadrisii 211
                                        lll ei+  le ++d+ae+ +++++++
  gi|557694864|ref|YP_008797918.1| 189 LLLLREIVSMLEDIADKAEESGETLRVL 216
                                       89*********************99987 PP

>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   3.9   4.4e-05       0.4       6      86 ..      28     105 ..      13     108 .. 0.54
   2 !   18.5   1.8   2.4e-07    0.0021       2      85 ..     127     209 ..     126     213 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HGG-SHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU   6 eiveemlddalealeekdtelarevierddeidrlekeiersllealak.rqplaedlrellsllriardlERigDh 81 
                                       ++ ++ + ++  + +e+d + ++e +++  +id+  k+ +r++ +++++ +  l++  +   +++r+++++  i+D 
  gi|557694864|ref|YP_008797918.1|  28 DLLRKTVVMVEMVTREPDIKKIEEAYSEVLQIDEAAKNCRRQVEKEVSEiGAILTN-RE---DFIRLVNSIDKIADI 100
                                       33333333333344555654444444444444444444444444444222333332.22...49************* PP

                                       HHHHH CS
                              PhoU  82 avnia 86 
                                       a+ +a
  gi|557694864|ref|YP_008797918.1| 101 AEGVA 105
                                       *9887 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2.4e-07
                                       HHHHHHHHHHHHHHHHHH..HCT-HHHH.HHHHHH...HHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHH CS
                              PhoU   2 rrmaeiveemlddaleal..eekdtela.revier...ddeidrlekeiersllealakrqplaedlrellsllria 72 
                                        +++e+v++ + ++ ea+  ++ + e+  +++ e    ++++d+l+++i+  +l   +k       + +ll l++i+
  gi|557694864|ref|YP_008797918.1| 127 LELGELVLQTVTRLREAIlaVTLNSETFyQKLKETeefERKVDELYRNIDLTILMSEMK-------IGQLLLLREIV 196
                                       5788999999999988865555566655455544444599*********6654443333.......3334447779* PP

                                       HHHHHHHHHHHHH CS
                              PhoU  73 rdlERigDhavni 85 
                                       + lE i+D a++ 
  gi|557694864|ref|YP_008797918.1| 197 SMLEDIADKAEES 209
                                       ********99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1136  (0.063361); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1617.65
//
Query:       gi|557694865|ref|YP_008797919.1|  [L=198]
Description: molybdopterin-guanine dinucleotide biosynthesis protein A [Candidatus Caldiarchaeum subterraneum]
Scores for 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-27   95.4   0.3    5.7e-27   95.0   0.3    1.1  1  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 !   95.0   0.3   3.2e-31   5.7e-27       1     157 [.       6     160 ..       6     164 .. 0.94

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 3.2e-31
                                       EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHH CS
                      NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplasla 77 
                                       a++LA G ++R+g dK+   lggkpl+ ++l+  + +  d    v+++e++ ++  +  v+v++++ ++kg++++l+
  gi|557694865|ref|YP_008797919.1|   6 AAVLASGFAKRFGADKLSTMLGGKPLYTWALEGTALC--DYRAFVVRPEQLGKYSVPEHVSVLVNRRADKGMSEALK 80 
                                       68******************************99965..7777888889999999999******************* PP

                                       HHHHHH..SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHHCTHTTHHHC CS
                      NTP_transf_3  78 aalraaa.dadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsalaallgdqgarrl 153
                                        a+++ + +a+++l++++DmP+++p +v++ll+ ++++ga++v++  +g++  p++f++r++++l+ l+gd gar +
  gi|557694865|ref|YP_008797919.1|  81 LAVSWTPyQASGLLIVLGDMPFIKP-VVQKLLKIFHETGAEAVAAGLDGKPLTPAVFSRRVFQRLLNLRGDVGARGV 156
                                       *****777**************986.9************************************************** PP

                                       HHHH CS
                      NTP_transf_3 154 lrrl 157
                                       l + 
  gi|557694865|ref|YP_008797919.1| 157 LSEI 160
                                       9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1569.57
//
Query:       gi|557694866|ref|YP_008797920.1|  [L=309]
Description: hypothetical protein CSUB_C1439 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   32.4   0.0    1.4e-07   31.8   0.0    1.2  1  S_layer_C  S-layer like family, C-terminal region
      4e-05   23.4   0.0    0.00012   21.9   0.0    1.7  1  MarR_2     MarR family
     0.0022   17.5   0.0      0.021   14.4   0.0    2.2  2  HTH_24     Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.024   14.7   0.0    1.6  1  HTH_20     Helix-turn-helix domain
      0.052   13.6   0.1       0.15   12.1   0.1    1.8  1  HTH_29     Winged helix-turn helix
       0.12   11.9   1.2       0.25   10.9   1.2    1.5  1  EF-hand_5  EF hand


Domain annotation for each model (and alignments):
>> S_layer_C  S-layer like family, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   4.6e-11   1.4e-07     137     218 ..     174     269 ..     171     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 4.6e-11
                         S_layer_C 137 vLDtEvelds.vdknLiLvGGPvvNkvtkeLedklkvaityee............dnksaatiavienaan.gndvl 199
                                        LD +v+ ++   +nL L+GGP  N +t++++++  ++   ++            + + ++ +a+  n+ n    v+
  gi|557694866|ref|YP_008797920.1| 174 RLDVDVKSEKlYTENLFLIGGPGTNLLTAAVNKEMPINFLENNywgglvspktvyTSEFTGLVAKTVNPFNeSRRVI 250
                                       68888866652578************************977669**********99999************8899** PP

                         S_layer_C 200 vvAGsDRegTkaAalalie 218
                                       v+AG   +gTkaA+ al +
  gi|557694866|ref|YP_008797920.1| 251 VLAGLRAAGTKAAVIALTN 269
                                       ***************9976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   3.9e-08   0.00012       4      54 ..      28      74 ..      25      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.9e-08
                                      -HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  4 tpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      tp+ + vL a  ++      ++  a+ +glsk+ vs +++r+v+aGL+ ++
  gi|557694866|ref|YP_008797920.1| 28 TPTAWKVLRAFVDGN----YISRAAAQTGLSKQLVSLHVERMVKAGLLKEV 74
                                      789999999998888....899**************************877 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 ?    0.4   0.0      0.16   4.8e+02      29      47 ..      26      44 ..      26      45 .. 0.92
   2 !   14.4   0.0   7.1e-06     0.021      24      48 .]      48      72 ..      46      72 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.16
                            HTH_24 29 lSpstvnrrlkrLeeeGlI 47
                                      lS +t ++ l+ +++  +I
  gi|557694866|ref|YP_008797920.1| 26 LSTPTAWKVLRAFVDGNYI 44
                                      799**********999998 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 7.1e-06
                            HTH_24 24 AerlglSpstvnrrlkrLeeeGlIk 48
                                      A ++glS++ v+ +++r++++Gl+k
  gi|557694866|ref|YP_008797920.1| 48 AAQTGLSKQLVSLHVERMVKAGLLK 72
                                      789*******************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 ?   14.7   0.0   7.9e-06     0.024       7      59 ..      26      76 ..      11      77 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.9e-06
                                      HS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECT CS
                            HTH_20  7 LahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvre 59
                                      L+ P+  ++lra+   +g   s  a++ +lsk+ +s H++ +++agL++ v+e
  gi|557694866|ref|YP_008797920.1| 26 LSTPTAWKVLRAF--VDGNYISRAAAQTGLSKQLVSLHVERMVKAGLLKEVGE 76
                                      6679999999999..88888888899999*******************99986 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   4.9e-05      0.15       2      44 ..      32      71 ..      32      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.9e-05
                            HTH_29  2 aqallllaeGvstvsqiAkllglsrrtvyrwlkrfeegGlaal 44
                                      +++l++  +G + +s++A+++gls++ v  +++r+++ Gl  l
  gi|557694866|ref|YP_008797920.1| 32 WKVLRAFVDGNY-ISRAAAQTGLSKQLVSLHVERMVKAGL--L 71
                                      68999999***9.************************996..3 PP

>> EF-hand_5  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.2   8.4e-05      0.25       8      17 ..     291     300 ..     291     301 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.4e-05
                                       H-SS-SSCE- CS
                         EF-hand_5   8 iDlNgDGkIs 17 
                                       +DlNgDGkI+
  gi|557694866|ref|YP_008797920.1| 291 LDLNGDGKID 300
                                       6********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 2543.68
//
Query:       gi|557694867|ref|YP_008797921.1|  [L=605]
Description: glucosamine--fructose-6-phosphate aminotransferase (isomerizing) [Candidatus Caldiarchaeum subterraneum]
Scores for 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-43  145.5   0.1    3.8e-21   75.3   0.2    2.7  3  SIS         SIS domain
    4.3e-18   65.8   0.0    7.7e-18   65.0   0.0    1.4  1  GATase_6    Glutamine amidotransferase domain
    1.4e-14   54.0   0.0    2.3e-14   53.4   0.0    1.3  1  GATase_7    Glutamine amidotransferase domain
     0.0014   17.6   0.1     0.0052   15.7   0.1    1.8  2  GATase_4    Glutamine amidotransferases class-II
     0.0089   16.0   1.0          4    7.4   0.1    3.1  3  SIS_2       SIS domain
     0.0094   16.0   0.1        1.3    9.0   0.0    3.1  3  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
  ------ inclusion threshold ------
        0.1   13.2   0.2       0.29   11.8   0.2    1.8  1  SnoaL_2     SnoaL-like 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 ?   -2.5   0.0       1.7   4.3e+03      10      36 ..     181     208 ..     175     216 .. 0.80
   2 !   75.3   0.2   1.5e-24   3.8e-21       5     130 ..     287     412 ..     282     413 .. 0.95
   3 !   67.2   0.0   4.7e-22   1.2e-18       5     130 ..     461     587 ..     457     588 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.7
                                       EEESHHHHH.HHHHHHHHHHHHHTSEEE CS
                               SIS  10 vlGaGtsya.iakelalkleeiggivve 36 
                                       ++G G  ++ +a+++ + +e ++++v+ 
  gi|557694867|ref|YP_008797921.1| 181 IIGVGDGFNmVASDMTALIEMTNQMVFL 208
                                       7888888888999999999998888876 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 1.5e-24
                                       SSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTS CS
                               SIS   5 akriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakerga 81 
                                        + +++lGaGtsy++++ +++ +  ++ +++  + ase++ ++ + +  d++++++s+sget+d+++a+  a+ r  
  gi|557694867|ref|YP_008797921.1| 287 GRVVFLLGAGTSYNACLAGSYLFSAVARMPSYPVIASEFVANYGGAVGADTVILAVSQSGETADVLNALDFARMRAC 363
                                       456899*********************************************************************** PP

                                       EEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                               SIS  82 kiiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                       +i+++T+  gs+l r ++  +  n++pe++va+tk++t+q ++l ++a+
  gi|557694867|ref|YP_008797921.1| 364 TILGLTNTVGSTLTRVSRAYVLQNSGPEIGVAATKTFTSQVLVLAQIAL 412
                                       *******************************************999876 PP

  == domain 3  score: 67.2 bits;  conditional E-value: 4.7e-22
                                       SSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHH.HHHHTT CS
                               SIS   5 akriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaae.lakerg 80 
                                       +  +++lG+G s ++a e++lk++e+++i++ +++++e khg++++i+e+ +vi++++ +e ++ +     ++k+rg
  gi|557694867|ref|YP_008797921.1| 461 SPFLFILGRGVSVSTAYEGRLKVMELSYIPCIAYPSGESKHGPISVIEEKIPVIFVAPPDEFRKQNIGSImEMKARG 537
                                       55689****************************************************88887665555555****** PP

                                       SEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHHHHH CS
                               SIS  81 akiiaITdskgsplareadlalyinaepetlvastksltaqlaaldalav 130
                                       akii++ d ++  l   ad+ + +++    l +++++++ ql+a++++++
  gi|557694867|ref|YP_008797921.1| 538 AKIIIFGDREDEELRSLADHYIGLPKTHPLLSPIIYTVPFQLLAYYLAVL 587
                                       *********************999999988****************9986 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.0     3e-21   7.7e-18      11     133 ..      64     193 ..      44     194 .. 0.85

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 3e-21
                          GATase_6  11 edevalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall.....e 82 
                                        +++++aH+R+a++g + +  a+P +  +g++++vhNG  +n+ +lr+el +  ++++ sr+Dtev+ +l+     +
  gi|557694867|ref|YP_008797921.1|  64 PGNIGIAHTRWATHGAPSKVNAHPHTDCTGTVAVVHNGVLENFLQLRKELTD-LNHNIVSRTDTEVVPHLVedfmkR 139
                                       4569*************77777******************************.******************888775 PP

                          GATase_6  83 elG.....eevlerlrGmfafaiwdkrentlila.rdrlgvkplyyavdesglafas 133
                                        +G       +++rl+G +a a++  re  li++ r    ++pl+++v ++  ++as
  gi|557694867|ref|YP_008797921.1| 140 GMGfeeafVNAVRRLEGSYALAAICLREPDLIMVaRK---EAPLIIGVGDGFNMVAS 193
                                       5558766677788********9999966666555144...48999999888888888 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.0   8.9e-18   2.3e-14      12     122 ..      84     199 ..      71     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 8.9e-18
                          GATase_7  12 gaQPmvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.........ewgeealerlnGmfA 79 
                                       +a P + + +g++++v+nG + N+ +lr+eL++ +h++ +++Dtev+ +l+e+         e   +a++rl+G++A
  gi|557694867|ref|YP_008797921.1|  84 NAHPHT-DCTGTVAVVHNGVLENFLQLRKELTDLNHNIVSRTDTEVVPHLVEDfmkrgmgfeEAFVNAVRRLEGSYA 159
                                       566777.5799**************************************************999************* PP

                          GATase_7  80 faiwdeeek.rlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       +a +  +e   +++aR    + PL++g  +g   ++aS + al 
  gi|557694867|ref|YP_008797921.1| 160 LAAICLREPdLIMVARK---EAPLIIGVGDG-FNMVASDMTALI 199
                                       *9888666615566777...89*******85.999*****9985 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1     2e-06    0.0052      71     133 ..      65     129 ..      39     157 .. 0.77
   2 ?   -1.8   0.0      0.45   1.1e+03     139     184 ..     257     301 ..     254     319 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-06
                          GATase_4  71 sknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlke...ykpkl.egrfePvGsTDsEla 133
                                        ++ +aH R at+G+ ++ n+hp +   +       HnG l++   ++++l + +++ v +TD+E++
  gi|557694867|ref|YP_008797921.1|  65 GNIGIAHTRWATHGAPSKVNAHPHTDCTGT--VAVVHNGVLENflqLRKELtDLNHNIVSRTDTEVV 129
                                       5678*******************9976554..4556*****99333344445567788999***975 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.45
                          GATase_4 139 eelasrfekaepsaeeleralaelakeiaelGvfnlllsdgralfa 184
                                       +e+ ++  ++ ++a   +r   +l++e+ ++G + +ll  g    a
  gi|557694867|ref|YP_008797921.1| 257 KEIFEQP-NSLRDALRTQREYVDLLAELLDKGRVVFLLGAGTSYNA 301
                                       5554444.345666667777889999999*********99987655 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0032       8.2      25      47 ..     277     299 ..     264     328 .. 0.75
   2 !    7.4   0.1    0.0016         4      90     137 ..     320     369 ..     303     370 .. 0.81
   3 ?   -3.2   0.1       3.1     8e+03     121     134 ..     528     541 ..     525     544 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0032
                                       HHHHHHHHHTT--EEEEESGGGH CS
                             SIS_2  25 aeliadslenggkvlvfGsGhSa 47 
                                       ++l+a+ l +g++v+++G+G S 
  gi|557694867|ref|YP_008797921.1| 277 VDLLAELLDKGRVVFLLGAGTSY 299
                                       7899****************994 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
                                       THHHHHHHHTT-..-TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE CS
                             SIS_2  90 gyakqilrlvrl..kpgDvLlviSnsGnnavvveaaeaakergmkviAlt 137
                                       ++a+++ +++ +   +  v+l +S+sG+ a v++a+  a+ r +++ +lt
  gi|557694867|ref|YP_008797921.1| 320 VIASEFVANYGGavGADTVILAVSQSGETADVLNALDFARMRACTILGLT 369
                                       5666777776663345668999**************************99 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3.1
                                       HHHHHHHHHT-EEE CS
                             SIS_2 121 eaaeaakergmkvi 134
                                         +++ k+rg+k+i
  gi|557694867|ref|YP_008797921.1| 528 GSIMEMKARGAKII 541
                                       56788888888887 PP

>> 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 ?   -3.0   0.0       2.6   6.6e+03      70     102 ..     220     252 ..     192     258 .. 0.63
   2 ?   -3.8   0.0       4.6   1.2e+04      14      52 ..     286     324 ..     279     328 .. 0.64
   3 !    9.0   0.0   0.00052       1.3       6     141 ..     452     594 ..     448     600 .. 0.52

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.6
                                       TEEEEEESSHH........HHHHHHHHTTTSSE CS
                        bact-PGI_C  70 rlrlvllrdeeehprvkkraeivkelaeergvr 102
                                        +r++ + d++  +r  k + +++e+ae++g +
  gi|557694867|ref|YP_008797921.1| 220 GYRVFRVADGQIVERPVKTVALTVEMAEKQGHP 252
                                       444444555555567777788888888888765 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.6
                                       T.SEEEEE-..TT-THHHHHHHHHHHHTT----B---.SS CS
                        bact-PGI_C  14 g.klpviygssellevaArRfknqlnenAKipafagvlpe 52 
                                       + +++ ++g +++ + a       +++ A++p++  +  e
  gi|557694867|ref|YP_008797921.1| 286 KgRVVFLLG-AGTSYNACLAGSYLFSAVARMPSYPVIASE 324
                                       447777777.666666666677778888888887666555 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00052
                                       HHHHHHHTT.SEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTT.................... CS
                        bact-PGI_C   6 kqlAlelag.klpviygssellevaArRfknqlnenAKipafagvlpeanhneivgl.................... 61 
                                       k+lA+ l++     i+g  ++  + A+  + +  e + ip++a    e++h  i ++                    
  gi|557694867|ref|YP_008797921.1| 452 KELAETLVNsPFLFILG-RGVSVSTAYEGRLKVMELSYIPCIAYPSGESKHGPISVIeekipvifvappdefrkqni 527
                                       67777777755666666.77777777777777777777777777777777777777733333333222222222222 PP

                                       ...SS-GGGGTTEEEEEESSHH........HHHHHHHHTTTSSEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHC CS
                        bact-PGI_C  62 ...eaeeelkkrlrlvllrdeeehprvkkraeivkelaeergvrvtevkaegesplerlaslillgDfvSvylAllr 135
                                             e + +  ++++++d+e+ ++ + +a+             + + + + +pl   +  ++ + + ++ylA+l+
  gi|557694867|ref|YP_008797921.1| 528 gsiM--EMKARGAKIIIFGDRED-EELRSLAD-------------HYIGLPKTHPLLSPIIYTVPFQLLAYYLAVLK 588
                                       2110..12222222222222221.11111111.............12233345555555555666788999999999 PP

                                       T---S- CS
                        bact-PGI_C 136 gvDPtp 141
                                       g+DP +
  gi|557694867|ref|YP_008797921.1| 589 GYDPDK 594
                                       999975 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   0.00011      0.29      60     101 ..     190     233 ..     184     234 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                       EEEETTEEEEEEEEEEE..EETTSSEEEEEEEEEEEEETTEEEE CS
                           SnoaL_2  60 vvadgdrvavewtvtgt..ipatgrgvtvrgvdvfrvrdGkive 101
                                       +va++ ++++e+t ++   +  + ++v+  g+ vfrv+dG+ive
  gi|557694867|ref|YP_008797921.1| 190 MVASDMTALIEMTNQMVflHDGDAAAVRANGYRVFRVADGQIVE 233
                                       67888888889888888666666666777**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); 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: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 4703.05
//
Query:       gi|557694868|ref|YP_008797922.1|  [L=153]
Description: hypothetical protein CSUB_C1441 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0031   17.5   0.0     0.0036   17.3   0.0    1.1  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 !   17.3   0.0     2e-07    0.0036      19     144 ..      27     147 ..       3     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-07
                                       HHHCEEE-EE-GHHHHHHHCC--TT-EEEEEETSSSS-EEEEEEEEECEEEE-GGGG-TTSTT--TTTBTTS-.-EE CS
                               EVE  19 rkkeegWdgvrnyqarnllramkkGDlvlfYhsgeklqaivgiaeVvseaypdetqfdpkskyydpkskkekp.wlr 94 
                                       r k++ W  v       ++++ ++G  ++f+ +g + + ++g +  ++ + p + ++      ++ k  ++++ ++ 
  gi|557694868|ref|YP_008797922.1|  27 RVKHGFWL-VSS--RIAAMKELAEGGSAIFFSTGSEGRLFIGEGVFSQPPMPITDEM-----RFHIKGYPSEKlTHF 95 
                                       55566663.333..35678899*********99999899***998887777755444.....455666767776889 PP

                                       EEEEEEEEEEEEEEHHHHTTHG.TCTTSHHHHCC.T-SEEEE-HHHHHHHHH CS
                               EVE  95 vdvkpvkklkrplslkelkaep.elegmkllrkg.rlsvrpvteedwelile 144
                                       +++ + + ++ p++l+e+ ++  +++++  +    r svr+++e+d++++++
  gi|557694868|ref|YP_008797922.1|  96 IKLDMARLWTTPIKLEEVLENLsFIKNKLRWYGYfRGSVRKIPEQDYQYLVS 147
                                       ******************99763556666666669************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1158.86
//
Query:       gi|557694869|ref|YP_008797923.1|  [L=453]
Description: ferredoxin-dependent glutamate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-19   70.8   0.0    3.1e-19   69.4   0.0    1.7  1  Glu_synthase  Conserved region in glutamate synthase
    4.9e-18   65.3   1.7      1e-12   47.8   0.5    2.1  2  FMN_dh        FMN-dependent dehydrogenase
    1.8e-05   24.3   0.3    2.7e-05   23.7   0.3    1.2  1  NMO           Nitronate monooxygenase


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 !   69.4   0.0   5.2e-23   3.1e-19     137     308 ..     221     394 ..     210     401 .. 0.80

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 5.2e-23
                                       EEEEE---TTSTTS--EE-.GGG--HHH.......HHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-TTSE CS
                      Glu_synthase 137 aleikiaQGakpgeGgqlp.geKvseei.......akiRkikpgvdliSPaphhdiysiedlaqliedLkevnkeak 205
                                        +eik++QGakpg Gg+    + +  ++       a+ R+++  ++l+        y +e l ++i+ +++  ++a+
  gi|557694869|ref|YP_008797923.1| 221 GFEIKLGQGAKPGLGGETLiERELAIKLadkyvfdADPRNVQ--KKLYERHSAPGTYTEEILRSMIRIMRNNYPRAR 295
                                       58**************85413444444400001223334443..44555555557899999**************** PP

                                       EEEEEE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS CS
                      Glu_synthase 206 vsvKlvaeagvetiaagvakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGg 282
                                       + vK++  + +e++a   ++ ++d+  +dG eGGTG sp +  k  GlPl++ l ++ +  +      +++  a+G+
  gi|557694869|ref|YP_008797923.1| 296 IWVKMGPYRDIEDVARLCSQEKVDAFWVDGKEGGTGLSPVTALKDLGLPLLALLGKIMKLSR----ETNMDYVASGR 368
                                       **************************************************998887765544....4567789**** PP

                                       --SHHHHHHHHHHT-SEEE-SHHHHH CS
                      Glu_synthase 283 lktgadvvkalalGAdavgigtaali 308
                                       l  gadvvk l +GA a g+g+  ++
  gi|557694869|ref|YP_008797923.1| 369 LVDGADVVKVLCFGARAAGLGRPFVV 394
                                       ********************997666 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.9e-07    0.0029      44      96 ..     100     151 ..      93     175 .. 0.91
   2 !   47.8   0.5   1.7e-16     1e-12     262     347 ..     350     436 ..     307     437 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.9e-07
                                       SS-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEETT CS
                            FMN_dh  44 skvdlsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvlstv 96 
                                       ++vd+s+++ G  +slPv +a++g + +++ +  l +a+a a+agip++++++
  gi|557694869|ref|YP_008797923.1| 100 TDVDTSCRVGGFMSSLPVAVASMGSTPVYN-KVSLDVAKASAEAGIPMGVGEN 151
                                       679**********************99998.899**************99876 PP

  == domain 2  score: 47.8 bits;  conditional E-value: 1.7e-16
                                       HHHHHHH...SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SB CS
                            FMN_dh 262 peiveavgg.rievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvks 337
                                        +i++  ++ +++ +++g    G+Dv+k l+ GA+a +lGRpf++ + a+G eGv+++le+++ e++     +G  s
  gi|557694869|ref|YP_008797923.1| 350 GKIMKLSREtNMDYVASGRLVDGADVVKVLCFGARAAGLGRPFVVTAYAAGVEGVKKYLETIKMEVQLLTSAVGKYS 426
                                       455555554358888899999******************************************************** PP

                                       HHHHHCGGEE CS
                            FMN_dh 338 vaeldrslls 347
                                       va+l+++ ++
  gi|557694869|ref|YP_008797923.1| 427 VASLGPEDIR 436
                                       ****998775 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.3   4.6e-09   2.7e-05     149     258 ..     310     425 ..     301     443 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 4.6e-09
                               NMO 149 arkvearGaDalivqGpeaG.GhqGtpevgd..kglfaLvpqvldavd...iPviAaGGiidrrgvaaaLalGAsgv 219
                                       ar   +   Da+ v+G+e+G G  +  + +d    l+aL+ ++++      +  +A G ++d+ +v  +L+ GA ++
  gi|557694869|ref|YP_008797923.1| 310 ARLCSQEKVDAFWVDGKEGGtGLSPVTALKDlgLPLLALLGKIMKLSRetnMDYVASGRLVDGADVVKVLCFGARAA 386
                                       566777789*********997788866666655667778888877766889************************** PP

                               NMO 220 qigtrfLltkesdakdahkkklleaklddteltsavsGr 258
                                        +g  f++t  +   + +kk l   k++  +ltsav+ +
  gi|557694869|ref|YP_008797923.1| 387 GLGRPFVVTAYAAGVEGVKKYLETIKMEVQLLTSAVGKY 425
                                       **********99999999999999999999999999844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3431.68
//
Query:       gi|557694870|ref|YP_008797924.1|  [L=347]
Description: asparaginyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-62  211.0   0.0    2.5e-62  210.7   0.0    1.0  1  tRNA-synt_2  tRNA synthetases class II (D, K and N)


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 !  210.7   0.0   1.4e-66   2.5e-62       5     313 ..      29     341 ..      26     342 .. 0.89

  Alignments for each domain:
  == domain 1  score: 210.7 bits;  conditional E-value: 1.4e-66
                                       HHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS-..-SSSS--EEEEETTT.TEEE-E-S-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2   5 rlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksd..teegarlFkvksrekekeffaLtqsp 79 
                                       +l++ y  +rt++++ +lr+++++ +avr++l+++gf+e  +Pi+   +  +  ga++ ++      +e+     s 
  gi|557694870|ref|YP_008797924.1|  29 QLEKYYKTVRTPRMRLILRVQAEANRAVRSWLDSHGFLELLPPIIGPVTdpGIRGAKQVTI--DYYGREY-KVMSSA 102
                                       677778888************************************9985334557777777..2222244.599*** PP

                                       HHHHHHHHHCTHSEEEEEEEEE--S--B...TTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  80 qlylellivagidrvfqiaraFRaEdsr...tdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdi 153
                                        ly+++l+ a +d+++ ++++ R E ++   t rhl EF+qi++e + +++   m+++e+l+ ++v++v e+ ++++
  gi|557694870|ref|YP_008797924.1| 103 ILYKQMLATA-FDKIYFFSPNIRLEPLEsatTGRHLVEFVQIDIEEADVDYRAAMSTAENLLAYVVNTVAETARQEL 178
                                       **********.************9877655589************************************99999999 PP

                                       CHTTTTTSEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 154 efvirrnskdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeedd 224
                                       e+  r+    +k+pf+++t++eaie+l+ +      + ++  ++e  l  k +nep+f+td+P+  + Fy +++ ++
  gi|557694870|ref|YP_008797924.1| 179 EQLGRKLP-RFKTPFRKITHAEAIEILRAHgeqvqpNAEIPWPQEEKLS-KIINEPFFITDYPKGARGFYDKEDPQR 253
                                       98888866.9********************4444444444445555544.59************************* PP

                                       TTBBSEEEEEET.TE.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHC CS
                                       xxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 225 kkltesyDllin.gv.ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlll 299
                                       + + + +Dl+++ g+ E ++G+ R+ ++ +  e+lk+ g +   ++k++wyl++l+ G+ p++G+g+G++Rl+ +l+
  gi|557694870|ref|YP_008797924.1| 254 PGILKDFDLMYPeGYgEAASGAEREYEYSKVLERLKQSGEN---PAKYGWYLDMLREGIRPTSGFGIGVERLTRYLC 327
                                       ***********9889**************************...********************************* PP

                                       T-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxx RF
                       tRNA-synt_2 300 gsesIrdviaFPkl 313
                                       g++ + ++ ++Pk+
  gi|557694870|ref|YP_008797924.1| 328 GLQAVWEARPYPKV 341
                                       ************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2779.16
//
Query:       gi|557694871|ref|YP_008797925.1|  [L=164]
Description: hypothetical protein CSUB_C1444 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   19.7   0.0    0.00057   19.6   0.0    1.0  1  MecA        Negative regulator of genetic competence (MecA)
  ------ inclusion threshold ------
      0.015   14.3   0.6      0.018   14.0   0.6    1.1  1  Miga        Mitoguardin
       0.05   13.2   0.9       0.19   11.3   0.2    1.9  2  DUF2067     Uncharacterized protein conserved in archaea (DUF
      0.071   11.0   3.9      0.094   10.6   3.9    1.1  1  V_ATPase_I  V-type ATPase 116kDa subunit family


Domain annotation for each model (and alignments):
>> MecA  Negative regulator of genetic competence (MecA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.3e-07   0.00057      84     169 ..      74     156 ..      17     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.3e-07
                                       ............XXXXXXXX...................XXXXXXXXXXXXX--SEEEEEESSHHHHHHHHT.E... CS
                              MecA  84 eeldtrfskftkledlleklleelekeeeekkdkakeakekekekeeeeekeqsltrifsfdsledvirlakalkki 160
                                       e+  +r++k+ +  ++le+ ++++    ++ + ++++  ++e++ e+e  +++++  i s +sled+irla++lk+ 
  gi|557694871|ref|YP_008797925.1|  74 EDYLKRLEKLDETLKMLEEKIKNQP--AKNPEPAKTTTPNDENTREQEPVQPVEEDEIQSPESLEDIIRLARELKEE 148
                                       2333366666666666666666543..444444555555555666666777888899*****************977 PP

                                       .EEEEEEE. CS
                              MecA 161 yessLYkde 169
                                         ++L k +
  gi|557694871|ref|YP_008797925.1| 149 -LNTLMKTN 156
                                       .78888875 PP

>> Miga  Mitoguardin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.6   4.1e-06     0.018     140     229 ..      70     159 ..      61     164 .] 0.74

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.1e-06
                              Miga 140 ltpenlylmGmelleealrrweqaLtvrsrqaedeascssvklgagdaiaeeevedvksae..fiekleslLerayr 214
                                         p++ yl  +e l+e+l+  e+ ++ + +++ + a++++   ++ ++ ++e v+ v+++e    e le +++ a +
  gi|557694871|ref|YP_008797925.1|  70 QPPQEDYLKRLEKLDETLKMLEEKIKNQPAKNPEPAKTTTP--NDENTREQEPVQPVEEDEiqSPESLEDIIRLARE 144
                                       568999*****************988887777555555554..455555555555555555115689********** PP

                              Miga 215 lqeefellllaepss 229
                                       l+ee+++l+ ++ ++
  gi|557694871|ref|YP_008797925.1| 145 LKEELNTLMKTNRQN 159
                                       *******99774444 PP

>> DUF2067  Uncharacterized protein conserved in archaea (DUF2067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.09     4e+02     119     142 ..      78     101 ..      68     107 .. 0.62
   2 ?   11.3   0.2   4.3e-05      0.19     103     142 ..     125     163 ..     120     164 .] 0.93

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.09
                           DUF2067 119 elaerlseiykelrfknlskaakr 142
                                       + +e+l+e +k l++k + ++ak+
  gi|557694871|ref|YP_008797925.1|  78 KRLEKLDETLKMLEEKIKNQPAKN 101
                                       555666666666666666655554 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.3e-05
                           DUF2067 103 reenvlktnapleevvelaerlseiykelrfknlskaakr 142
                                       + e+ +++  +le++ +la++l+e +++l ++n+ +a+k+
  gi|557694871|ref|YP_008797925.1| 125 E-EDEIQSPESLEDIIRLARELKEELNTLMKTNRQNAVKN 163
                                       5.899*****************************999998 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 ?   10.6   3.9   2.1e-05     0.094      26     105 ..      74     155 ..      63     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.1e-05
                        V_ATPase_I  26 vkevrrcdemerklrfleeeieklekavikeeea..eesleapeekeldeleeelekleeelkelnenleklkkeln 100
                                        ++++r+++++++l++lee+i+++  ++ +  ++   ++++++e++ ++ +ee+  +  e+l+++ + +++lk+eln
  gi|557694871|ref|YP_008797925.1|  74 EDYLKRLEKLDETLKMLEEKIKNQPAKNPEPAKTttPNDENTREQEPVQPVEEDEIQSPESLEDIIRLARELKEELN 150
                                       568999999999*********99655555444433445555666666777777777778888888888888888888 PP

                        V_ATPase_I 101 elvel 105
                                       +l+++
  gi|557694871|ref|YP_008797925.1| 151 TLMKT 155
                                       87765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1865  (0.104021); expected 358.6 (0.02)
Passed bias filter:                      915  (0.0510346); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 00:00:00.44
# Mc/sec: 1112.09
//
Query:       gi|557694872|ref|YP_008797926.1|  [L=496]
Description: hypothetical protein CSUB_C1445 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   27.5   2.6      0.016   15.2   0.1    2.9  2  T2SSF     Type II secretion system (T2SS), protein F


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 !   11.5   0.3   1.2e-05      0.22      13     122 ..      29     144 ..      18     147 .. 0.84
   2 !   15.2   0.1   8.7e-07     0.016      18      93 ..     287     365 ..     271     402 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 1.2e-05
                                       --HHHHHH..HHHHHHSSHHHHHHHHHHHHHHHTTS.SHHHHHC....T-TT.TS-HHHHHHHHHHHHHT-HHHHHH CS
                             T2SSF  13 vplveaLe..llaeeaengplaeelkriarrlraGg.slseale....rtpssefpelvvqlirageeggnLaevLe 82 
                                       +++ + ++  +l+e+  +  +++++++ ++ ++ +   +se le      ++s+++ lv++l +++++g +++++ +
  gi|557694872|ref|YP_008797926.1|  29 LSVRQMIKqlSLSEVV-PEHIGKIFRKSRNLMERWNyGVSETLEylesALKHSKLKGLVIRLQHSIKAGVSIEDFAR 104
                                       5555555532445555.8999999999999999999766888888877555579*********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHTTXXXXXXXXXXXXXXXXX CS
                             T2SSF  83 rlaeyleeerelrrkllaallepllllvvallvllillai 122
                                            +++e++++ ++ +++l  l++++++l+ ++ ll++
  gi|557694872|ref|YP_008797926.1| 105 IEYVKHRAEQDNELEKGLEKLRRLVEAYTTLISVVSLLSV 144
                                       ********************************99999876 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 8.7e-07
                                       HHHHHHHHHSSHHHHHHHHHHHHHHHTTSSHHHHHC...T-TT.TS.-HHHHHHHHHHHHHT-HHHHHHHHHHHHHH CS
                             T2SSF  18 aLellaeeaengplaeelkriarrlraGgslseale...rtpssef.pelvvqlirageeggnLaevLerlaeylee 90 
                                       + ++l  ++  gpl + +k+  +rlr G+s +ea++   r +   + +++++ l +++e+g + a ++  l+ey+ +
  gi|557694872|ref|YP_008797926.1| 287 SAHMLTLSD-LGPLNRLVKAFEQRLRLGISQKEAIAmvgRETVGRLgDNVFTILGEVIEAGARPATACGILSEYVSN 362
                                       444444455.9*************************99955555888**************************9977 PP

                                       HHH CS
                             T2SSF  91 ere 93 
                                        + 
  gi|557694872|ref|YP_008797926.1| 363 VLF 365
                                       554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3555.21
//
Query:       gi|557694873|ref|YP_008797927.1|  [L=553]
Description: archaeal flagellar protein FlaI [Candidatus Caldiarchaeum subterraneum]
Scores for 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-48  162.6   0.0    1.5e-47  162.0   0.0    1.2  1  T2SSE     Type II/IV secretion system protein
     0.0046   16.7   0.1       0.19   11.5   0.1    2.8  3  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.053   13.3   0.0        0.1   12.3   0.0    1.4  1  PCMT      Protein-L-isoaspartate(D-aspartate) O-methyltransfe
       0.14   12.4   0.5        1.9    8.8   0.1    2.4  2  Rx_N      Rx N-terminal domain
       0.15   11.6   0.1       0.25   10.9   0.1    1.3  1  DUF927    Domain of unknown function (DUF927)


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 !  162.0   0.0   4.1e-51   1.5e-47       4     245 ..     164     409 ..     161     435 .. 0.93

  Alignments for each domain:
  == domain 1  score: 162.0 bits;  conditional E-value: 4.1e-51
                             T2SSE   4 lleallddekvsdihvekpervkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrl 80 
                                       +lea+++d+ + di  +  + ++v+ ++ g    +++++++++l +++ ++a   ++ ++ ++p++da+lp +g r+
  gi|557694873|ref|YP_008797927.1| 164 TLEAFIRDQYIEDISCNGVGPIFVEHKIFGSCETNISFSDQEELDAFVVKLAERIGRPVNFRKPIVDASLP-DGSRI 239
                                       689999******************9999998999*************************************.***** PP

                             T2SSE  81 rvvllPvvag..ealviRkksakeltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                       ++v+   v     +++iRk s+k ++++dl+  ++++   a+ l   +++ ++i + G T sGKtt l a+  +in 
  gi|557694873|ref|YP_008797927.1| 240 NIVFGSDVSRhgSNFTIRKFSEKPVSIADLISWGTMSSLEAAYLWIMLEHGMSIWFCGETASGKTTALRAASVFINP 316
                                       ***98766655799*********************************999999************************ PP

                             T2SSE 156 sderivtvEDpvEiqleganqvqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgs 227
                                       s  +iv +ED+ Ei + ++n v+ +++     ++++t+ dll+aaLR+rP  i+vGEiR++e+  + +A++TGH++ 
  gi|557694873|ref|YP_008797927.1| 317 S-AKIVSIEDTPEIVVPHENWVREVTRqgeqgEGDITLFDLLKAALRQRPNYIIVGEIRGAEASVAFQAMQTGHPV- 391
                                       *.********************999999**999*******************************************. PP

                             T2SSE 228 lsTlHansaagalerLeq 245
                                       l+T Ha+s+ + ++rL  
  gi|557694873|ref|YP_008797927.1| 392 LATFHAGSVEKLIQRLTG 409
                                       ***************975 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 !   11.5   0.1   5.3e-05      0.19       5      51 ..     268     319 ..     265     322 .. 0.77
   2 ?   -2.5   0.0       1.2   4.4e+03      29      46 ..     344     361 ..     342     365 .. 0.85
   3 ?    1.6   0.0     0.064   2.3e+02       3      23 ..     461     480 ..     459     486 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.3e-05
                            AAA_29   5 qlvNWgtfdg.ht...ieidlkg.atlltGpsGsGKSTllDAiqalLvpakk 51 
                                       +l+ Wgt++  +    + + ++g ++ + G++ sGK+T l A ++ + p+ k
  gi|557694873|ref|YP_008797927.1| 268 DLISWGTMSSlEAaylWIMLEHGmSIWFCGETASGKTTALRAASVFINPSAK 319
                                       578899998765422234445778999*************999999888765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.2
                            AAA_29  29 GpsGsGKSTllDAiqalL 46 
                                       G++G G  Tl+D ++a L
  gi|557694873|ref|YP_008797927.1| 344 GEQGEGDITLFDLLKAAL 361
                                       89999999***9887766 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.064
                            AAA_29   3 rlqlvNWgtfdg.htieidlkg 23 
                                       +++l+NW +  + h+++ +  g
  gi|557694873|ref|YP_008797927.1| 461 YIELFNWESSADkHEFRGE--G 480
                                       699****998876766654..4 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 ?   12.3   0.0   2.9e-05       0.1      49     120 ..     263     339 ..     250     351 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.9e-05
                                       EEETTEEE--HHHHHHHHHHTT..--TT-EEEEES.-TTSHHHHHHH..HHHCTTCEEEEEESBHHHHHHHHHHHHH CS
                              PCMT  49 sigynatiSaphmvalalelle..lkkgarvLevG.sGsGyltavla..rlvgekgrvvsierikelveeakrnlkk 120
                                       +++    iS   m +l   +l   l++g+++   G + sG  ta+ a   ++++++++vsie ++e+v   ++ +++
  gi|557694873|ref|YP_008797927.1| 263 PVSIADLISWGTMSSLEAAYLWimLEHGMSIWFCGeTASGKTTALRAasVFINPSAKIVSIEDTPEIVVPHENWVRE 339
                                       345566788888888777777666**********96789*****865115779999************988887776 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.15   5.5e+02      15      40 ..      20      45 ..      14      47 .. 0.87
   2 ?    8.8   0.1   0.00052       1.9      47      79 ..      99     131 ..      90     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.15
                              Rx_N 15 eeakllkgvkeeleklkdeLesiqav 40
                                      ee +l+ +  + +e+l +e++s++++
  gi|557694873|ref|YP_008797927.1| 20 EELRLQGKTASYVEQLSREMRSLRSF 45
                                      677899999999**********9987 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00052
                              Rx_N  47 rqikdeavkeWlkelrdlaydaeDvlDefetea 79 
                                         ++ e+ ++ l+el d+  +++D l++f ++ 
  gi|557694873|ref|YP_008797927.1|  99 DYTTREEHEKLLNELLDMFLEIDDTLEDFDYKP 131
                                       5567888999*******************9985 PP

>> DUF927  Domain of unknown function (DUF927)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1     7e-05      0.25     179     221 ..     275     316 ..     248     326 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7e-05
                            DUF927 179 saAlaapLLkllgaeggglhlygeSstGKttalklAaSvwGnp 221
                                       +++l a+ L ++ + g+ + + ge+ +GKttal++ aSv+ np
  gi|557694873|ref|YP_008797927.1| 275 MSSLEAAYLWIMLEHGMSIWFCGETASGKTTALRA-ASVFINP 316
                                       67888889999999999****************95.5776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); 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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3608.58
//
Query:       gi|557694874|ref|YP_008797928.1|  [L=233]
Description: archaeal flagellar protein FlaH [Candidatus Caldiarchaeum subterraneum]
Scores for 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-18   65.9   0.0    3.9e-18   65.6   0.0    1.0  1  ATPase    KaiC
    3.6e-07   30.0   0.1    5.2e-07   29.5   0.1    1.2  1  DUF835    Protein of unknown function (DUF835)
    0.00025   21.1   0.1       0.21   11.6   0.0    2.1  2  MutS_V    MutS domain V
      0.007   15.5   0.2      0.008   15.3   0.2    1.1  1  PAXNEB    PAXNEB protein
  ------ inclusion threshold ------
      0.022   14.8   0.1        1.1    9.3   0.1    2.3  1  AAA_14    AAA domain
      0.038   14.3   0.0      0.074   13.3   0.0    1.5  1  AAA_22    AAA domain
      0.063   13.0   0.1       0.85    9.4   0.0    2.3  2  AAA_29    P-loop containing region of AAA domain
       0.13   11.9   0.0       0.24   10.9   0.0    1.7  1  AAA_25    AAA 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 !   65.6   0.0   1.8e-21   3.9e-18       7     228 ..      12     227 ..       6     230 .. 0.89

  Alignments for each domain:
  == domain 1  score: 65.6 bits;  conditional E-value: 1.8e-21
                            ATPase   7 glDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegkl 83 
                                       +lD+ + g i   +  li G  ++GK+++ lq+ +  + + g ++ + ++e +++++re+++sl w+   +  +g+l
  gi|557694874|ref|YP_008797928.1|  12 ELDRKI-GHIKTPALCLIEGPNDSGKSVLTLQYCYGALLS-GFNCYLLSTEGSMRAVRESMASLSWNPSYFIITGRL 86 
                                       578887.88999999********************99999.************************************ PP

                            ATPase  84 aiidasesaeesaeekdkedleelieelaeaikeika.krvviDsitglayeekeavaReilrqlvrvlkklgvTai 159
                                        i ++   +       ++++  +l++ ++  i++    +   iDs t l +++++  + + +  l +++ + g T i
  gi|557694874|ref|YP_008797928.1|  87 KIGEMHVRNFS----WSSQQYTKLLRLVTAFIQSRSKeNVFFIDSMTYLLTNASTTDILNFFTVLRNIVDEEGKT-I 158
                                       ***99988776....447788888888888887765526779*******77777788888899999999998887.6 PP

                            ATPase 160 lvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte.egikvle 228
                                       + s  s+  ++  + ++   i+d  +vL +ke+ e++vR+l+++k+ g++ s  ++ fe+++  gi+vl+
  gi|557694874|ref|YP_008797928.1| 159 FLSIHSHALDTDLFLRLRS-ISDVHFVLSVKEMGERIVRVLQVMKLKGAEKSGLTIAFEVDQvFGIRVLP 227
                                       666667888999999****.***********************************************987 PP

>> DUF835  Protein of unknown function (DUF835)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.1   2.3e-10   5.2e-07      57     126 ..      99     169 ..      64     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2.3e-10
                            DUF835  57 sPtnlekltetivkflkeaekg.vvliDgleyLvlengFesvlkflltlkDavllkngtlilvidkealee 126
                                       s ++ +kl++ +  f+++++k+ v +iD++ yL+++ +  ++l f++ l+ +v ++++t+ l+i  +al++
  gi|557694874|ref|YP_008797928.1|  99 SSQQYTKLLRLVTAFIQSRSKEnVFFIDSMTYLLTNASTTDILNFFTVLRNIVDEEGKTIFLSIHSHALDT 169
                                       5678899**********99988799********************************************97 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   9.4e-05      0.21       2      43 ..      27      68 ..      26      78 .. 0.89
   2 !    7.7   0.1    0.0015       3.3     100     167 ..     144     214 ..     105     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.4e-05
                                      EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SE CS
                            MutS_V  2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdk 43
                                      li Gpn +Gks++  q +  +ll+   +++ +++ +++ v +
  gi|557694874|ref|YP_008797928.1| 27 LIEGPNDSGKSVLTLQYCYGALLSGFNCYLLSTEGSMRAVRE 68
                                      899***************************999999887765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHTT--EEEEEES-GGG.GGHHHHSTTEEEEEE..EEEEETTEEEEEEEEEES--SS--HHHHH CS
                            MutS_V 100 lavaeyllekikaktlfatHyhel.tklaekleevknlhl..avkeeeedivflykvkegaaeksyGikva 167
                                        +v++ ++++   + +++ H h l t+l  +l++++ +h+  +vke  e+iv + +v + +  +  G+++a
  gi|557694874|ref|YP_008797928.1| 144 FTVLRNIVDEEGKTIFLSIHSHALdTDLFLRLRSISDVHFvlSVKEMGERIVRVLQVMKLKGAEKSGLTIA 214
                                       46899999999999999*******7789999****9888522677889*********99999999999987 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   3.6e-06     0.008     181     281 ..     100     185 ..      55     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.6e-06
                            PAXNEB 181 spryssllnqiqqllkkesfsaptkknvlRivipsLlspllydyppeeskpedllkFLhsLrallrssnlvalitlp 257
                                       s++y++ll+ +++++++    ++++  v    i s+   l       +++ +d+l+F++ Lr ++ ++  +++ ++ 
  gi|557694874|ref|YP_008797928.1| 100 SQQYTKLLRLVTAFIQS---RSKEN--V--FFIDSMTYLLT------NASTTDILNFFTVLRNIVDEEGKTIFLSIH 163
                                       44466666666666666...22222..3..35566655555......7899************************** PP

                            PAXNEB 258 lsliarssslvrkieqlvDtvieL 281
                                       ++ +  ++ l  ++++++D  + L
  gi|557694874|ref|YP_008797928.1| 164 SHAL--DTDLFLRLRSISDVHFVL 185
                                       ****..*************97766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00049       1.1       5      92 ..      26     156 ..      22     173 .. 0.54

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00049
                            AAA_14   5 lvitGaRrvGKTtllkqlikell................vkkesilyinldderd...................... 43 
                                       ++i+G+  +GK++l  q+ +  l                + +es+                                
  gi|557694874|ref|YP_008797928.1|  26 CLIEGPNDSGKSVLTLQYCYGALlsgfncyllstegsmrAVRESMA--------Slswnpsyfiitgrlkigemhvr 94 
                                       5788888888888888887777644444444333333332222222........02333333355555555544332 PP

                            AAA_14  44 ....kkladpekllelileklke.ekktylflDEiqev.........pewekalkslvdegkn 92 
                                           + +++++kll+l+ + +++ +k++++f+D + ++          +++++l+++vde+ +
  gi|557694874|ref|YP_008797928.1|  95 nfswS-SQQYTKLLRLVTAFIQSrSKENVFFIDSMTYLltnasttdiLNFFTVLRNIVDEEGK 156
                                       22211.111223344444332224677788888888888888887777888888888887634 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.3e-05     0.074       4     129 ..      22     162 ..      18     169 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.3e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.......... 70 
                                       t  ++++ G+  +GK++l  ++ + +          +++  + l+ ++s + +++ +++   ++             
  gi|557694874|ref|YP_008797928.1|  22 TPALCLIEGPNDSGKSVLTLQYCYGAL--------LSGFNCYLLSTEGSMRAVRESMASLSWNPSYFiitgrlkige 90 
                                       56678999***************9996........788889999999999999999999999988889999999999 PP

                            AAA_22  71 ........erlsseellealeqalraravielliiDEaqhlr...s.eealeeLrsllnl.srkgvqliLvG 129
                                               + ++   ll++++  +++r++  ++ iD + +l    s  ++l+++  l n+ ++ g +++L +
  gi|557694874|ref|YP_008797928.1|  91 mhvrnfswSSQQYTKLLRLVTAFIQSRSKENVFFIDSMTYLLtnaStTDILNFFTVLRNIvDEEGKTIFLSI 162
                                       99**************************************66577366666666444444426666666655 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 ?    9.4   0.0   0.00038      0.85      22      38 ..      23      39 ..      11      42 .. 0.80
   2 ?    0.9   0.0      0.18     4e+02      38      50 ..     124     136 ..     123     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00038
                            AAA_29 22 kgatlltGpsGsGKSTl 38
                                         +l+ Gp+ sGKS l
  gi|557694874|ref|YP_008797928.1| 23 PALCLIEGPNDSGKSVL 39
                                      4468***********87 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.18
                            AAA_29  38 llDAiqalLvpak 50 
                                       ++D++++lL+ a+
  gi|557694874|ref|YP_008797928.1| 124 FIDSMTYLLTNAS 136
                                       69*******9987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.24      28      58 ..      18      48 ..      15     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
                            AAA_25 28 gllpagelallaGapgtGKttlaldlalava 58
                                      g++   +l+l+ G+ ++GK++l+l+ ++  +
  gi|557694874|ref|YP_008797928.1| 18 GHIKTPALCLIEGPNDSGKSVLTLQYCYGAL 48
                                      6788889******************998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1760.20
//
Query:       gi|557694875|ref|YP_008797929.1|  [L=165]
Description: hypothetical protein CSUB_C1448 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); 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 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1205.53
//
Query:       gi|557694876|ref|YP_008797930.1|  [L=162]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   28.2   0.0    2.3e-06   27.9   0.0    1.1  1  Arch_flagellin  Archaebacterial flagellin
  ------ inclusion threshold ------
      0.053   13.6   0.0       0.26   11.3   0.0    2.1  2  Wzt_C           Wzt C-terminal domain


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 !   27.9   0.0   2.5e-10   2.3e-06       5     152 ..       7     148 ..       3     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.5e-10
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS-- CS
                    Arch_flagellin   5 igtlIvfIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGssp 81 
                                       ++++I  I++++ A++ a+++   ++ l q+ q++++++  ++ +++e +  ++ ++++     +++++k n G ++
  gi|557694876|ref|YP_008797930.1|   7 VAEAIFVISLIITASAYASTMFSFVDELKQANQAKVSRMKREALTSVEPLMGYVSDNRSV----VYLWLK-NVGTER 78 
                                       679**********************************************99988444443....9*****.****** PP

                                       EE...GGG-EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--TTT---TT-EEEEEE CS
                    Arch_flagellin  82 id...lnkttisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvneddgitagdevsvev 152
                                       i    ++ ++i++++ ++  l++  +  + +  +   ++ n+ + ++ ge++++++++   + + + +e++v++
  gi|557694876|ref|YP_008797930.1|  79 ISyaeIEASDIFLVGRDTFFLMKHGHGPYRWRYSILKETLND-NGWSWGETLAITMQL---ETPLNPGEYTVKI 148
                                       972224556677777773333444477777777777777776.**************9...4555556666766 PP

>> Wzt_C  Wzt C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.19   1.7e+03      49      86 ..      55      90 ..      36     107 .. 0.68
   2 ?   11.3   0.0   2.9e-05      0.26      83     106 ..     126     149 ..     107     157 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.19
                             Wzt_C 49 pvfgfaikdrngqevfgtntelekksfeleelkagerv 86
                                      p +g+   +r  ++++ +n  +e++s  + e++a++++
  gi|557694876|ref|YP_008797930.1| 55 PLMGYVSDNRSVVYLWLKNVGTERIS--YAEIEASDIF 90
                                      55555556666666666677666666..6666666665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.9e-05
                             Wzt_C  83 gervevefefklpLapGeYlltva 106
                                       ge++ ++++++ pL+pGeY++ +a
  gi|557694876|ref|YP_008797930.1| 126 GETLAITMQLETPLNPGEYTVKIA 149
                                       89999*****77*********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1168.46
//
Query:       gi|557694877|ref|YP_008797931.1|  [L=206]
Description: hypothetical protein CSUB_C1450 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.2   1.8       0.19   11.8   1.0    2.2  2  DUF1192   Protein of unknown function (DUF1192)


Domain annotation for each model (and alignments):
>> DUF1192  Protein of unknown function (DUF1192)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.0   1.1e-05      0.19      26      45 ..       8      27 ..       8      43 .. 0.85
   2 ?   -1.1   0.0      0.11     2e+03      20      33 ..      88     101 ..      63     102 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
                           DUF1192 26 eerIalLeaEIaRleaaiak 45
                                      ++rI++Le+EI R+++ ++k
  gi|557694877|ref|YP_008797931.1|  8 DKRIKKLEEEIRRIREPLEK 27
                                      58*************98887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.11
                           DUF1192  20 LSveELeerIalLe 33 
                                        + +EL+  I++L 
  gi|557694877|ref|YP_008797931.1|  88 QGFNELDSFITTLA 101
                                       56789999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      804  (0.0448435); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 1509.96
//
Query:       gi|557694878|ref|YP_008797932.1|  [L=169]
Description: archaeal flagellin FlaB [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   89.6   6.2    2.7e-25   89.5   6.2    1.0  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 !   89.5   6.2   1.5e-29   2.7e-25      11     163 ..       1     155 [.       1     156 [. 0.89

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 1.5e-29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--EEEEEEEEEE-SSSSSEEEEEEE--TTS--EEGGG- CS
                    Arch_flagellin  11 fIAmVlVAAvaagvlintagflqqkaqstgeesteqvssgleitgdvgdsatngtineitiyvklnaGsspidlnkt 87 
                                       +IA+V+VA++++ +++n + f++qk  ++++ + e+  s++e+ g+v+++++ng+i+ei iy+k + G+ ++d+ + 
  gi|557694878|ref|YP_008797932.1|   1 MIAFVIVASAFSFAVLNLGLFTTQKTGEVMQAGLEETLSSIETAGAVVAKSSNGSITEIVIYIKSSVGKGEVDVRSG 77 
                                       6**************************************************************************** PP

                                       EEEEEESS--EE--E..................T-EE-TT-EEEEEEE--..TTT---TT-EEEEEEE-SSS--EEE CS
                    Arch_flagellin  88 tisvtddgqetlltadefgivvisdtdgsltngdevlekgekvelevnvn..eddgitagdevsvevvpenGastti 162
                                       ++ +t+ +++    +  ++ ++i++  + + +gd vle+ge+++++++v+     ++ ++d +sve++p++G+ + +
  gi|557694878|ref|YP_008797932.1|  78 KLVITYRDKAIFRENIYTNNSTITTVYQVTGDGDTVLEYGEVFAVKIDVTaiSGASLAPNDVFSVEIKPPQGSLLKV 154
                                       ********4444444344555555555555555*****************999999****************98777 PP

                                       E CS
                    Arch_flagellin 163 e 163
                                       e
  gi|557694878|ref|YP_008797932.1| 155 E 155
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1313.41
//
Query:       gi|557694879|ref|YP_008797933.1|  [L=222]
Description: hypothetical protein CSUB_C1452 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-23   81.5   0.0    6.8e-23   81.1   0.0    1.1  1  DUF3786   Domain of unknown function (DUF3786)


Domain annotation for each model (and alignments):
>> DUF3786  Domain of unknown function (DUF3786)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.0   3.8e-27   6.8e-23      18     173 ..      51     209 ..      33     211 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 3.8e-27
                           DUF3786  18 k..ltlpflgreyrisypggeisdgedeeeddlnekilllnylleakgapptgkwvsfrelpggavyyrafekraek 92 
                                          +++++l+++++++ ++g++ d  +++ +  ++  ++l yll  + a+ +++w ++  l +++ y + ++k++++
  gi|557694879|ref|YP_008797933.1|  51 PsrYIVNVLNKTFTVELDEGKVVDLMTGKDAGEKLSYVILEYLLGEG-AAGQDSWQPLDTLLKTSAYLSYYQKTVLN 126
                                       14499***********************99999***********977.99*************************** PP

                           DUF3786  93 plaktfggdpeklkkaaeklggkpldkgDaayvfealpkipvlllfwegD..eeFpasaniLFDksaeeyldaEdla 167
                                       pl ktfg+++ +++++ + lggk+++ g  ay f +lpk+ +l+++w gD  e    s+n  ++ sa ++l++  l 
  gi|557694879|ref|YP_008797933.1| 127 PLLKTFGNQALLFEESSRMLGGKREKLGGTAYSFTFLPKVRLLIQVWFGDetEMRKTSINASYNMSAAKFLKPTPLL 203
                                       **************************************************777889999999**9*99999998888 PP

                           DUF3786 168 vlgell 173
                                       ++ e+l
  gi|557694879|ref|YP_008797933.1| 204 IAFEIL 209
                                       877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1658.80
//
Query:       gi|557694880|ref|YP_008797934.1|  [L=170]
Description: ATP--cobalamin adenosyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-40  137.5   0.0    5.3e-40  137.2   0.0    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase


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 !  137.2   0.0     3e-44   5.3e-40      10     164 .]       8     158 ..       5     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 3e-44
                                       XXXXXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HH CS
                   Cob_adeno_trans  10 tTslvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekkkekkkitee 86 
                                       +T l g  +v+K++p +ea+GtvDel++++g+ar+l+   +eel++ L++iq+ Lf++g+ la+p++  +  ++++ 
  gi|557694880|ref|YP_008797934.1|   8 ETFLPGRGKVKKNHPLLEALGTVDELSAFVGVARSLT--VDEELRQSLKKIQEALFHIGSYLAVPNHPLD--RVRAC 80 
                                       68998999**************************776..4689********************9954444..44444 PP

                                       HHHHHHHHHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS..HHHHHHHHHHHHHHHHHHHH CS
                   Cob_adeno_trans  87 eveelekeideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee.veeevlkylNRLSDlLfvlar 162
                                        ++el    +e+e++lp l++fi pgg +aaa lhv+R+v+RraER +v+l +++ v++ + ++lN LS ++f++ar
  gi|557694880|ref|YP_008797934.1|  81 -LDELRLFEKEMENRLPLLRRFIYPGGAEAAAYLHVCRAVARRAERTLVRLGDTSeVDPLAFSFLNFLSKFFFTAAR 156
                                       .7777777788999*************************************9977899******************* PP

                                       HH CS
                   Cob_adeno_trans 163 vv 164
                                       +v
  gi|557694880|ref|YP_008797934.1| 157 YV 158
                                       85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1244.26
//
Query:       gi|557694881|ref|YP_008797935.1|  [L=375]
Description: branched-chain amino acid ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-44  149.8  28.1    1.1e-43  149.4  28.1    1.2  1  BPD_transp_2  Branched-chain amino acid transport system / pe
  ------ inclusion threshold ------
       0.02   14.7   0.1       0.05   13.4   0.1    1.6  1  Coa1          Cytochrome oxidase complex assembly protein 1


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 !  149.4  28.1   1.2e-47   1.1e-43       2     268 .]      10     347 ..       9     347 .. 0.95

  Alignments for each domain:
  == domain 1  score: 149.4 bits;  conditional E-value: 1.2e-47
                      BPD_transp_2   2 ilnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl........................ 54 
                                       +ln+l ++ai++++ ++l++ +g++G++n+g   ++a Ga+v++ +  + l++                        
  gi|557694881|ref|YP_008797935.1|  10 LLNVLGYVAIYLMVNVSLNFEYGFTGIPNFGKVLAVAGGAFVVGAVPGRILASqlnlfagyravqdnpvlaeclstl 86 
                                       6899*****************************************999999989999******************** PP

                      BPD_transp_2  55 ......................................lllallvallvgaavglllgllvlrlkvdeliitlllls 93 
                                                                             l +++ +a +vga +g++  ++++rl++d+l++tll++ 
  gi|557694881|ref|YP_008797935.1|  87 vqvkpklmdsidyiednavvidcvrrvlvndpvlsialLVAMVGLAAIVGAGLGFIASYPSIRLREDYLAMTLLAMG 163
                                       *********************************999999999999999***************************** PP

                      BPD_transp_2  94 vlvgltlllltgitsgvkgqssvkellgfagallsflsavivllalllvlavllllrrtrfGralravgeneeaara 170
                                       ++++ + +l +++ +g+ g++  +++ g+ g l++++   + l++++l ++ +  +++++ Gr lrav+++e aa++
  gi|557694881|ref|YP_008797935.1| 164 EFLRQIGYLDRTLVGGTLGVAV-PDPYGWLGGLRPYAATLVMLTVAVLFFLYVRSVTYSPAGRVLRAVRDSEMAAEV 239
                                       *******888888888888775.66789999999999999999999999999999********************** PP

                      BPD_transp_2 171 lGinvkrvklltfvisgalAglaGallalllgsipp..nigvglgfnaiaavvlGgagsllgtviGaliigvvksll 245
                                       lGi+v rvk +  v+s+++A++aGal a+ ++++ +  + +++++f ++++v++Ggag+++g+++G+l+++++ + +
  gi|557694881|ref|YP_008797935.1| 240 LGIDVVRVKQKILVVSSMMAAVAGALWAFNSVAVIAnnYDRFTWTFWPWVMVIIGGAGNNRGVLLGTLVFVILRQAI 316
                                       *******************************999999999************************************* PP

                      BPD_transp_2 246 ltllgi.....p...telarvllgallilvl 268
                                       lt+ +      p    +l r+l+g+ li+vl
  gi|557694881|ref|YP_008797935.1| 317 LTYNYLlepfiPfsiVWLDRLLFGIALIIVL 347
                                       ***999987662667**************97 PP

>> Coa1  Cytochrome oxidase complex assembly protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.5e-06      0.05       7      68 ..     201     263 ..     196     266 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-06
                              Coa1   7 fvvgvvvalayifnyektsssivrsvlyqlrrspevrelLG.eeipfkssipwisGelntvkG 68 
                                        +v+++va+++++  + +  s+   vl+++r s+ + e+LG + +++k++i+ +s  +  v+G
  gi|557694881|ref|YP_008797935.1| 201 TLVMLTVAVLFFLYVRSVTYSPAGRVLRAVRDSEMAAEVLGiDVVRVKQKILVVSSMMAAVAG 263
                                       4455555555555566666667789****************9999*****9988887777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2890.35
//
Query:       gi|557694882|ref|YP_008797936.1|  [L=312]
Description: branched-chain amino acid ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  132.2  33.1    2.3e-38  131.9  33.1    1.1  1  BPD_transp_2     Branched-chain amino acid transport system /
  ------ inclusion threshold ------
       0.49    9.8   5.5        1.1    8.7   5.5    1.5  1  DUF2417          Region of unknown function (DUF2417)


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 !  131.9  33.1   2.5e-42   2.3e-38       5     254 ..      11     273 ..       7     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 131.9 bits;  conditional E-value: 2.5e-42
                      BPD_transp_2   5 lltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrlk 81 
                                        +  a+ l ++ lGl+l +  + v+n++hg+f+ +G+++++++  ++ ++ +l+ll a+l+g++++l+l+llvlr  
  gi|557694882|ref|YP_008797936.1|  11 AVIFASMLSLLTLGLTLNYLTTKVPNFSHGSFASIGMMTMLTMTSAFNQPAYLSLLPAFLLGGLAALALYLLVLRPL 87 
                                       567899******************************************99*************************99 PP

                      BPD_transp_2  82 vdel.......iitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv...llalllvlavlll 148
                                       + +        i+t+++ ++l+++++ ++  ++ +++ ++s   l++++++ ++   +v+    +la+  v++++ll
  gi|557694882|ref|YP_008797936.1|  88 ISRDaslvsqmIATIAFELILIAVLN-IYADYFTQTFKVQSRGFLIRKFDVRIFGEPGVFIiapALAVSTVFLLYLL 163
                                       97765555553444444444444444.3333444444444444444444444444444444699************* PP

                      BPD_transp_2 149 lrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsippnigvglgfnaiaavvlGga 225
                                       l++trfG  lra+ en+++a  lGinvkr  +++++++g+l+g+aG llal ++++p n g +l ++++aa+++Gg+
  gi|557694882|ref|YP_008797936.1| 164 LNKTRFGIGLRAAIENPSLAGTLGINVKRAYTFSWFLAGGLGGVAGSLLALWFQGSP-NYGSELLISIFAAAIVGGL 239
                                       *******************************************************99.******************* PP

                      BPD_transp_2 226 gsllgtviGaliigvvksllltllgip.....te 254
                                        +++g+v+G++++g+v+ l++ +lg +     t 
  gi|557694882|ref|YP_008797936.1| 240 QNIYGAVAGGYLLGFVEVLGTRQLGLSfgpwiTV 273
                                       *********************9998833334333 PP

>> DUF2417  Region of unknown function (DUF2417)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   5.5   0.00012       1.1      69     165 ..      27     126 ..      11     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00012
                           DUF2417  69 lpglnnrgsgFndlalillslianllnllffglpSkldrvlnivlavLllvnllllllvkytReregfvgiasvlWa 145
                                       l  l+++   F + +++++ ++++l     f  p++l     + l +L ++ l ll+l + +++  ++v  ++   a
  gi|557694882|ref|YP_008797936.1|  27 LNYLTTKVPNFSHGSFASIGMMTMLTMTSAFNQPAYLSLLPAFLLGGLAALALYLLVLRPLISRDASLVSQMIATIA 103
                                       556778888999999*******99999999***************************************98877776 PP

                           DUF2417 146 a...ltfllgilldryvekgkke 165
                                       +   l+++l+i++d+ ++++k +
  gi|557694882|ref|YP_008797936.1| 104 FeliLIAVLNIYADYFTQTFKVQ 126
                                       43237888999999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); 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:                         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 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2209.37
//
Query:       gi|557694883|ref|YP_008797937.1|  [L=443]
Description: branched-chain amino acid ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-32  113.4   1.2    2.4e-32  112.9   1.2    1.2  1  Peripla_BP_6  Periplasmic binding protein
    3.6e-20   72.4   0.0    5.4e-20   71.8   0.0    1.3  1  ANF_receptor  Receptor family ligand binding region
  ------ inclusion threshold ------
      0.039   13.5   0.0       0.34   10.5   0.0    2.3  2  PrpR_N        Propionate catabolism activator


Domain annotation for each model (and alignments):
>> Peripla_BP_6  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.9   1.2   4.1e-36   2.4e-32       1     311 [.      64     388 ..      64     403 .. 0.84

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 4.1e-36
                                       EEEEEEEE-SSSTTHHHHHHHHHHHHHHHHHHHHTTEET..TEEEEEEEEE-TTSHHHHHHHHHHHHHCT--SEEEE CS
                      Peripla_BP_6   1 pikiGlltplsGpyassgksllagaqaafeeiNaaGGin..GrkielverDdaydpdraaeaarrlvdqdgvdalvg 75 
                                       +++iG l +ls  ++s+ ++ + ++++a++e+N+       G +i+ + +D+a +p++a e+ r l   +gv+++vg
  gi|557694883|ref|YP_008797937.1|  64 EVTIGSLLCLSAVLSSYAENERVAMDLAAREVNDFLQRAgaGFRIRMIHEDTACNPATAEEKIRSLNA-RGVKLVVG 139
                                       599******************************9543332477***********************77.******** PP

                                       -BSHHHHHHHHHHHHHHT-EEEESS-HHCCTTSTTEEESS--HHHHHH.HHHHHHHHHTTSCEEEEEEESSHHHHHH CS
                      Peripla_BP_6  76 plssavaaavaevlakdgvpvigpagltgekcspyvfslgpsysaqas.alveylakelggkkvalvyadyafgreg 151
                                       p++sa + ++ ++++++++++i+ ++++++   p+ f+++++++++    ++  lak lg++ +  v   +a+g+ +
  gi|557694883|ref|YP_008797937.1| 140 PMTSAEVRQIKSYVDANKILIISQSSTAPDLKIPNDFVFRFTTADDIQgPIGPRLAKLLGITHFLYVWRGDAWGDGL 216
                                       ****************************99888887777777776655379999*********************** PP

                                       HHHHHHHHHCCTEEEEEEEEE-TTHHHHHHHHHHHHTTT-S..........EEEEESSHHHHHHHHHHHHHTT.-SS CS
                      Peripla_BP_6 152 iaalkaaakaaGgevvgeepvplgttdfsaqvlqikaagad..........avllagtgadlaallkaaaeaG.lda 217
                                       +   +  ak++G+++v e ++ ++ t+fsa v q+ a+  +          + + + +++ ++a+l aa e   l+ 
  gi|557694883|ref|YP_008797937.1| 217 HTVSTGEAKKLGLNLVFELRYAPDKTEFSAEVSQLNAKVTEllnqgvspdkIMVEIVGFDEVVAFLSAANEYPnLK- 292
                                       **************999********************9555555555566658889999***********996244. PP

                                       SCEEEE...CCC-CHHHHHHHHH.HHHTTEEEEES.CSTCCCSHHHHHHHHHHHHHHTTGGC--HHHHHHHHHHHHH CS
                      Peripla_BP_6 218 krillv...swsgseedlkalgg.eaaegvlavtp.yfpdldnpavrafvaayeaayggapppsqfaaggyiaadll 289
                                        ri+ +   +++++++  + +++ + ae v ++ p +f + ++p  +a v+a + ++ g  pp+++++++y+a++++
  gi|557694883|ref|YP_008797937.1| 293 -RIKWFgsdGTAVTAAIFQDPAAtGFAEQVKWINPlFF-A-TTPDRKARVDAEVLRVLGRSPPDAYSYAAYSAVWAY 366
                                       .4666611255555555555555455777777777444.3.467777778888888877779*************** PP

                                       HHHHHCCTHCCHHHHHHHHHHS CS
                      Peripla_BP_6 290 lealkaagsltreavraalesl 311
                                       + al a+ + ++eavra l ++
  gi|557694883|ref|YP_008797937.1| 367 ALALMATQKYDAEAVRAVLPTI 388
                                       ****************998765 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 !   71.8   0.0     9e-24   5.4e-20       4     296 ..      86     376 ..      83     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 9e-24
                                       HHHHHHHHHHHT-TTSST.TEEEEEEEEE-TT-HHHHHHHHHHHCCCCEEEEEE-SSHHHHHHHHHHHCCTT-EEEE CS
                      ANF_receptor   4 eAmklAveeinsdpnllp.giklgyeiidtccdfslaleaaldflkgkvvaviGpssssvsdavaslanlfkiPvis 79 
                                        Am+lA +e+n+     + g++++++++dt+c++++a e+  ++ +  v+ v+Gp +s+++++++s+ +++ki +is
  gi|557694883|ref|YP_008797937.1|  86 VAMDLAAREVNDFLQRAGaGFRIRMIHEDTACNPATAEEKIRSLNARGVKLVVGPMTSAEVRQIKSYVDANKILIIS 162
                                       69*********7665544155999999******************966***************************** PP

                                       SS---GGGG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHH.HHHHTT-EEEEEEE CS
                      ANF_receptor  80 ygstspelsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqalee.eleergicvalkek 155
                                        +st+p l+  n +   +r +  d  q+    ++ k +g +++ +++  d  +  gl+++++ e+++ g++++++ +
  gi|557694883|ref|YP_008797937.1| 163 QSSTAPDLKIPNDFV--FRFTTADDIQGPIGPRLAKLLGITHFLYVWRGD-AWGDGLHTVSTgEAKKLGLNLVFELR 236
                                       *************88..88888899*************************.777888888888************** PP

                                       EST.....CHHHCHHHHHHHHHHTT...T--EEEEEE-HHHHHHHHHHHHHTTS-STTEEEEETCHCCCECTTS-CC CS
                      ANF_receptor 156 ipe.....ssnddevvrkllkeiks...karvivlfcssedarellkaarrlgltgeeyvwiasdawtsslvldkpe 224
                                       +++     s + +++ +k+ + +++     ++ v  +  +++  +l aa +     +   w++sd+ +    + +++
  gi|557694883|ref|YP_008797937.1| 237 YAPdktefSAEVSQLNAKVTELLNQgvsPDKIMVEIVGFDEVVAFLSAANEYPNLKR-IKWFGSDGTAVTAAIFQDP 312
                                       **9977773344444444455555555344899999999*********999877764.****888865555555554 PP

                                       ..HHHHHTT-EEEEE--B-HHHHHHHHH..........ST--CCCSSSTCCGSTTCCHHHHH...HHHHHHHHHHHH CS
                      ANF_receptor 225 ltgleaaegvlgfrlkdpnspkfsefld..........kreklsdekqnyenegkeqisyqaalmYdaVyllaeAln 291
                                                           ++f e ++           ++k++   +  + +g++++++ +++ Y aV+++a Al 
  gi|557694883|ref|YP_008797937.1| 313 ------------------AATGFAEQVKwinplffattPDRKARVDAEVLRVLGRSPPDAYSYAAYSAVWAYALALM 371
                                       ..................44444444444444444444223333334556678888888888888***********9 PP

                                       HHHCH CS
                      ANF_receptor 292 kllrk 296
                                        +++ 
  gi|557694883|ref|YP_008797937.1| 372 ATQKY 376
                                       99854 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.7e-05      0.34     104     133 ..     118     147 ..      77     167 .. 0.80
   2 ?    0.0   0.0     0.094   5.6e+02      39      80 ..     256     300 ..     253     311 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.7e-05
                            PrpR_N 104 seeeaeaavkelkaegvevvvGdgvvadlA 133
                                       ++ +ae++++ l+a+gv++vvG++++a++ 
  gi|557694883|ref|YP_008797937.1| 118 NPATAEEKIRSLNARGVKLVVGPMTSAEVR 147
                                       66789*******************998764 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.094
                            PrpR_N  39 aellrkhvsvPVveikvsgyDilralkqakklge...kialvgfe 80 
                                       +ell + vs   +++++ g+D + a+ +a ++     +i  +g +
  gi|557694883|ref|YP_008797937.1| 256 TELLNQGVSPDKIMVEIVGFDEVVAFLSAANEYPnlkRIKWFGSD 300
                                       578888899999999999999777777766655324466666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3191.06
//
Query:       gi|557694884|ref|YP_008797938.1|  [L=253]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   90.6   0.0    1.5e-25   90.3   0.0    1.1  1  ABC_tran      ABC transporter
      1e-06   28.8   1.8     0.0009   19.1   0.6    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    9.4e-06   25.4   0.0      2e-05   24.4   0.0    1.6  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
    1.8e-05   24.4   0.1    3.6e-05   23.4   0.1    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00027   20.6   1.2       0.13   11.8   0.2    2.2  2  AAA_25        AAA domain
     0.0011   19.5   0.9     0.0017   18.9   0.4    1.5  2  AAA_23        AAA domain
     0.0024   17.6   0.1     0.0054   16.5   0.0    1.5  2  AAA_30        AAA domain
     0.0027   18.0   0.5      0.016   15.5   0.5    2.0  1  AAA_22        AAA domain
     0.0039   16.6   0.6      0.035   13.5   0.2    2.1  2  SMC_N         RecF/RecN/SMC N terminal domain
      0.004   16.9   0.1      0.027   14.2   0.2    1.9  2  AAA_15        AAA ATPase domain
      0.008   16.6   0.2      0.018   15.4   0.1    1.6  2  AAA_16        AAA ATPase domain
     0.0087   16.0   0.1      0.015   15.2   0.1    1.3  1  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.029   13.9   0.1      0.044   13.4   0.1    1.3  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
      0.043   13.5   0.0      0.074   12.7   0.0    1.3  1  SRP54         SRP54-type protein, GTPase domain
      0.047   12.5   0.4       0.17   10.7   0.1    1.8  2  DLIC          Dynein light intermediate chain (DLIC)
      0.051   12.6   0.2      0.079   12.0   0.2    1.2  1  T2SSE         Type II/IV secretion system protein
      0.053   13.7   0.1      0.074   13.2   0.1    1.6  1  AAA_33        AAA domain
       0.06   13.4   0.1       0.15   12.2   0.1    1.6  1  MMR_HSR1      50S ribosome-binding GTPase
      0.066   12.7   0.1       0.13   11.8   0.1    1.4  1  AAA_7         P-loop containing dynein motor region
       0.07   13.5   0.1       0.17   12.2   0.1    1.5  1  AAA_19        AAA domain
      0.073   12.4   0.0      0.098   12.0   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.075   12.2   0.0      0.075   12.2   0.0    1.2  1  G-alpha       G-protein alpha subunit
      0.078   13.4   0.1       0.19   12.2   0.1    1.7  1  AAA           ATPase family associated with various cellular 
       0.13   12.1   0.4       0.34   10.8   0.1    1.7  2  NACHT         NACHT domain
       0.14   11.8   0.0       0.21   11.3   0.0    1.2  1  AAA_24        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 !   90.3   0.0   2.1e-28   1.5e-25       1     136 [.      21     180 ..      21     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 2.1e-28
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltv 76 
                                       l+  sl +k+g++  ++G+nG+GK+tL+++++g +kp++G+i +++++++  +++ +++  +    q pq f+ +tv
  gi|557694884|ref|YP_008797938.1|  21 LNGASLRVKKGSLSLLIGPNGSGKTTLINTVTGVYKPEAGKIIFEDRNITGlKPHVIYKLGLVRTWQIPQPFYSMTV 97 
                                       6789***********************************************99999999999999999********* PP

                                       HHH...........................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHT CS
                                       xxx...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren...........................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkk 126
                                        en                           e ++++ ++l+ l+l++l d+++    s+LSgGq + ++  ral++ 
  gi|557694884|ref|YP_008797938.1|  98 LENllvsdknkkgdgllsallrsrwidremELTQKAFEILKLLKLDHLWDHRA----SELSGGQMKLLETGRALMSG 170
                                       ************************88887777777999999999999999998....******************** PP

                                       SSEEEEESTT CS
                                       xxxxxxxxxx RF
                          ABC_tran 127 pkllllDEpt 136
                                       +k++l+DEp 
  gi|557694884|ref|YP_008797938.1| 171 AKMILMDEPA 180
                                       *********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 !   19.1   0.6   1.3e-06    0.0009       2      22 ..      34      54 ..      33      89 .. 0.81
   2 !    8.6   0.0     0.002       1.4     234     293 ..     150     207 ..     127     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.3e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       +liGpNgsGK++L+ +  ++
  gi|557694884|ref|YP_008797938.1| 34 SLLIGPNGSGKTTLINTVTGV 54
                                      68*************887665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.002
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQvi 293
                                       a+elS G+ +ll    al + +   + +l DEp +gL+P l +++++ l + +++ ga ++
  gi|557694884|ref|YP_008797938.1| 150 ASELSGGQMKLLETGRALMSGA---KMILMDEPAAGLNPVLAHEVFTHLrNVCKKLGATLL 207
                                       5678888888877777777766...99**************99999777666666666665 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   2.8e-08     2e-05       1      23 []     230     252 ..     230     252 .. 0.98

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.8e-08
                      BCA_ABC_TP_C   1 rvIAeGtPaEvrndPrVieAYLG 23 
                                       +vIAeG P+Ev  +  V+e YLG
  gi|557694884|ref|YP_008797938.1| 230 KVIAEGEPQEVLTNSLVVESYLG 252
                                       79********************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 !   23.4   0.1     5e-08   3.6e-05      13      50 ..      22      59 ..      19      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5e-08
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      +g +++++  +  ll+Gp+GsGK+Tl+  ++ +  p+ 
  gi|557694884|ref|YP_008797938.1| 22 NGASLRVKKGSLSLLIGPNGSGKTTLINTVTGVYKPEA 59
                                      667788885559***************99998877766 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.2   0.00018      0.13      31      50 ..      29      48 ..      25      52 .. 0.90
   2 !    7.4   0.1     0.004       2.9     166     188 ..     189     211 ..     174     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                            AAA_25 31 pagelallaGapgtGKttla 50
                                       +g+l+ll+G+ g+GKttl 
  gi|557694884|ref|YP_008797938.1| 29 KKGSLSLLIGPNGSGKTTLI 48
                                      689***************95 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.004
                            AAA_25 166 galvealeriarrtgaavllvhH 188
                                        +++++l+++++++ga++llv H
  gi|557694884|ref|YP_008797938.1| 189 HEVFTHLRNVCKKLGATLLLVEH 211
                                       578899****************9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.4   2.4e-06    0.0017      20      39 ..      32      51 ..      13      60 .. 0.85
   2 ?   -2.4   0.0       8.1   5.8e+03     119     137 ..     121     139 ..      93     159 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.4e-06
                            AAA_23 20 gltlItGpNGaGKTTildAi 39
                                       l l++GpNG+GKTT+++ +
  gi|557694884|ref|YP_008797938.1| 32 SLSLLIGPNGSGKTTLINTV 51
                                      4889*************966 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 8.1
                            AAA_23 119 qfisellgskkiilnlilf 137
                                       + i+++++ +++ ++++ +
  gi|557694884|ref|YP_008797938.1| 121 RWIDREMELTQKAFEILKL 139
                                       3333333333333333333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   7.5e-06    0.0054      17      50 ..      30      63 ..      24      75 .. 0.84
   2 ?   -2.5   0.0       4.9   3.5e+03      82      96 ..     164     178 ..     130     209 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.5e-06
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                      +  +++l Gp G+GKtt++++++ +++ + g++i
  gi|557694884|ref|YP_008797938.1| 30 KGSLSLLIGPNGSGKTTLINTVTGVYKPEAGKII 63
                                      55699*********************99966665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.9
                            AAA_30  82 grarlepgtllivDE 96 
                                       gra ++ +++++ DE
  gi|557694884|ref|YP_008797938.1| 164 GRALMSGAKMILMDE 178
                                       333344446666666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.5   2.2e-05     0.016       4      30 ..      30      56 ..      26     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.2e-05
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                                      + ++ +++G+ G+GKTtl+++++  ++
  gi|557694884|ref|YP_008797938.1| 30 KGSLSLLIGPNGSGKTTLINTVTGVYK 56
                                      677889**************9987664 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 !   13.5   0.2   4.9e-05     0.035      25      44 ..      32      51 ..      12      60 .. 0.84
   2 ?    1.5   0.0      0.24   1.7e+02     135     171 ..     126     183 ..      89     212 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.9e-05
                                      SEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldAi 44
                                      s++ ++GpNGSGK+ l++ +
  gi|557694884|ref|YP_008797938.1| 32 SLSLLIGPNGSGKTTLINTV 51
                                      57899***********9876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.24
                                       T.........................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS CS
                                       x.........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e.........................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaL 171
                                       e                         +LSgG+ +L+          ++ a + l+De +a L
  gi|557694884|ref|YP_008797938.1| 126 EmeltqkafeilkllkldhlwdhrasELSGGQMKLLETGRA----LMSGAKMILMDEPAAGL 183
                                       44444445555555555555555555899999999764322....23445555666655555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   3.7e-05     0.027      23      41 ..      30      49 ..      20      59 .. 0.84
   2 ?    0.0   0.0      0.77   5.5e+02     326     353 ..     173     200 ..     168     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                            AAA_15 23 ee.ltvliGkNnsGKSsile 41
                                      +  l++liG+N+sGK+++++
  gi|557694884|ref|YP_008797938.1| 30 KGsLSLLIGPNGSGKTTLIN 49
                                      4459*************986 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.77
                            AAA_15 326 illiEEPEahLHpqaqkvlikllkelan 353
                                        +l++EP a L p +  +++  l+++ +
  gi|557694884|ref|YP_008797938.1| 173 MILMDEPAAGLNPVLAHEVFTHLRNVCK 200
                                       689**************99999998876 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   0.1   2.5e-05     0.018      18      45 ..      27      52 ..      18      88 .. 0.82
   2 ?   -1.4   0.0       3.8   2.8e+03      80     123 ..     135     195 ..      96     214 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                            AAA_16 18 rvrsgrpelvllsGesGvGKsslvrell 45
                                      rv++g  +l ll+G+ G+GK++l++++ 
  gi|557694884|ref|YP_008797938.1| 27 RVKKG--SLSLLIGPNGSGKTTLINTVT 52
                                      56666..6889*************9986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.8
                            AAA_16  80 ellrqllde....aesaeleawrekleeala.............avpelagaeasrllell 123
                                       e+l+ l+ +    ++++el+  + kl+e+ +             +++ l + +a+ ++ +l
  gi|557694884|ref|YP_008797938.1| 135 EILKLLKLDhlwdHRASELSGGQMKLLETGRalmsgakmilmdePAAGLNPVLAHEVFTHL 195
                                       4444444443333334444444444444333555555554444444444444444444444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   2.1e-05     0.015      98     128 ..      30      60 ..      23      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                                       TTSEEEEECSTTSSHHHHHHHHCTT-----S CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelelktg 128
                                       k+++s+l+G+ G GK+tLin++++  + + g
  gi|557694884|ref|YP_008797938.1|  30 KGSLSLLIGPNGSGKTTLINTVTGVYKPEAG 60 
                                       56899****************9987665555 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 ?   13.4   0.1   6.2e-05     0.044       4      25 ..      35      56 ..      32      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.2e-05
                                      EEEESTTCCHHHHHHHHHCT-- CS
                              cobW  4 vltGflGsGKTtLlnhllenra 25
                                      +l G+ GsGKTtL+n+++   +
  gi|557694884|ref|YP_008797938.1| 35 LLIGPNGSGKTTLINTVTGVYK 56
                                      789*************984333 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0    0.0001     0.074       4      32 ..      34      62 ..      32      65 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-E CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkv 32
                                       ll+G++G+GKTt +  +  ++k e+ k+
  gi|557694884|ref|YP_008797938.1| 34 SLLIGPNGSGKTTLINTVTGVYKPEAGKI 62
                                      699*************9999999886665 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00023      0.17      28      55 ..      34      61 ..      23      65 .. 0.85
   2 ?   -0.9   0.0      0.76   5.4e+02     227     243 ..     193     209 ..     190     230 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00023
                              DLIC 28 vlvlGedgsGkttliaklqGveeekkGr 55
                                       l++G +gsGkttli  + Gv ++  G+
  gi|557694884|ref|YP_008797938.1| 34 SLLIGPNGSGKTTLINTVTGVYKPEAGK 61
                                      5899*****************9988876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.76
                              DLIC 227 shirrfclqyGaallyt 243
                                       +h+r+ c + Ga+ll  
  gi|557694884|ref|YP_008797938.1| 193 THLRNVCKKLGATLLLV 209
                                       79***********9975 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 ?   12.0   0.2   0.00011     0.079     130     161 ..      32      63 ..      22      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                             T2SSE 130 glilvsGgTgsGKttllyallkeinksderiv 161
                                        l l+ G+ gsGKttl++++    + +  +i+
  gi|557694884|ref|YP_008797938.1|  32 SLSLLIGPNGSGKTTLINTVTGVYKPEAGKII 63 
                                       455888*************9998888766665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1    0.0001     0.074       3      19 ..      35      51 ..      33     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                            AAA_33  3 llvGlpGsGKstlaerl 19
                                      ll+G++GsGK+tl+  +
  gi|557694884|ref|YP_008797938.1| 35 LLIGPNGSGKTTLINTV 51
                                      89***********9876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1    0.0002      0.15       4      34 ..      36      67 ..      34      86 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                                      EEESTTSSHHHHHHHHHTS.TEEESSSTTSSS CS
                          MMR_HSR1  4 ivGrpNvGKStLinaltge.kaivsdkpgtTr 34
                                      ++G   +GK+tLin+ tg  k +++++ +  r
  gi|557694884|ref|YP_008797938.1| 36 LIGPNGSGKTTLINTVTGVyKPEAGKIIFEDR 67
                                      89***************955555555544444 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 ?   11.8   0.1   0.00018      0.13      30      58 ..      28      56 ..      24      65 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                             AAA_7 30 lknkkpvllvGptGtGKtviikdllkkld 58
                                      +k++   ll+Gp G+GKt++i++++  ++
  gi|557694884|ref|YP_008797938.1| 28 VKKGSLSLLIGPNGSGKTTLINTVTGVYK 56
                                      7788889***************9876655 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00023      0.17       9      37 ..      30      58 ..      24      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00023
                            AAA_19  9 kekvllvtaGpGtGKTrvlkhivallvel 37
                                      k ++ l++++ G+GKT++++++  +++ +
  gi|557694884|ref|YP_008797938.1| 30 KGSLSLLIGPNGSGKTTLINTVTGVYKPE 58
                                      567899**************998887755 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   0.0   0.00014     0.098      26      65 ..      35      74 ..      26     138 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                      Mg_chelatase 26 llvGppGsGKtmlakrlpsllpplseeealevakiasvag 65
                                      ll+Gp GsGKt l++ ++++  p   + ++e ++i+ ++ 
  gi|557694884|ref|YP_008797938.1| 35 LLIGPNGSGKTTLINTVTGVYKPEAGKIIFEDRNITGLKP 74
                                      79******************99999888888888887765 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    0.0001     0.075      27      65 ..      35      79 ..      22     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                      EEEESTTSSHHHHHHHHHHHCS--.....--HHHHHC.CHHHHHH CS
                           G-alpha 27 lllGqseSGKsTilkqlkllykkg.....fseeelat.wraviql 65
                                      ll+G ++SGK+T+++ +  +yk++     f+++++      vi++
  gi|557694884|ref|YP_008797938.1| 35 LLIGPNGSGKTTLINTVTGVYKPEagkiiFEDRNITGlKPHVIYK 79
                                      89*******************999889988888777734446665 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 ?   12.2   0.1   0.00026      0.19       2      20 ..      35      53 ..      34      81 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00026
                                      EEESSTTSSHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllakavak 20
                                      ll+Gp G GKT+l++ v  
  gi|557694884|ref|YP_008797938.1| 35 LLIGPNGSGKTTLINTVTG 53
                                      89************99865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00048      0.34       2      20 ..      33      51 ..      32      56 .. 0.88
   2 ?   -1.7   0.0       3.4   2.4e+03      53      71 ..     113     131 ..      82     150 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00048
                                      CEEEEC-TTTCHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkl 20
                                      l++l G++GsGKTtL+  +
  gi|557694884|ref|YP_008797938.1| 33 LSLLIGPNGSGKTTLINTV 51
                                      6799***********9765 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 3.4
                                       -HCHHHCCCCTS--SSS-C CS
                             NACHT  53 sladllfsqlpepaapvse 71 
                                        l  ll+s + + +++ ++
  gi|557694884|ref|YP_008797938.1| 113 LLSALLRSRWIDREMELTQ 131
                                       4555666666666665555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0003      0.21       6      23 ..      35      56 ..      32      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                            AAA_24  6 liyGpsgiGKTtlakel....g 23
                                      l++Gp+g+GKTtl+++     +
  gi|557694884|ref|YP_008797938.1| 35 LLIGPNGSGKTTLINTVtgvyK 56
                                      799***********99866552 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1835.00
//
Query:       gi|557694885|ref|YP_008797939.1|  [L=233]
Description: branched-chain amino acid ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  112.5   0.0    3.8e-32  111.7   0.0    1.4  1  ABC_tran      ABC transporter
    2.5e-17   63.6   0.1    9.1e-08   32.3   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    6.4e-09   35.6   0.5    7.1e-05   22.3   0.0    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
    5.2e-06   26.4   0.1    0.00012   22.0   0.0    2.1  2  AAA_15        AAA ATPase domain
    4.1e-05   24.2   0.1    8.7e-05   23.1   0.0    1.5  2  AAA_23        AAA domain
     0.0004   20.1   0.0    0.00097   18.8   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
    0.00093   19.5   0.0     0.0017   18.6   0.0    1.5  1  AAA_22        AAA domain
     0.0023   17.5   0.0     0.0042   16.7   0.0    1.3  1  AAA_27        AAA domain
     0.0057   16.4   0.1      0.014   15.1   0.1    1.8  2  AAA_30        AAA domain
     0.0087   15.7   0.4       0.29   10.7   0.3    2.2  2  cobW          CobW/HypB/UreG, nucleotide-binding domain
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.017   15.5   0.0    1.5  1  AAA_16        AAA ATPase domain
      0.013   14.6   0.2      0.027   13.5   0.1    1.6  2  T2SSE         Type II/IV secretion system protein
       0.02   15.1   0.2      0.052   13.7   0.2    1.7  2  AAA_33        AAA domain
      0.029   14.4   0.8       0.33   11.0   0.1    2.5  2  AAA_14        AAA domain
       0.03   14.2   0.1      0.054   13.4   0.1    1.4  1  RsgA_GTPase   RsgA GTPase
       0.04   13.8   0.3       0.08   12.9   0.2    1.6  1  NACHT         NACHT domain
      0.057   12.8   0.1        0.1   11.9   0.1    1.3  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
      0.058   12.7   0.0       0.12   11.7   0.0    1.5  1  Septin        Septin
      0.069   12.7   0.0       0.22   11.1   0.0    1.7  2  AAA_25        AAA domain
       0.08   13.0   0.1       0.13   12.3   0.1    1.6  1  Dynamin_N     Dynamin family
      0.087   11.6   0.2       0.85    8.3   0.1    2.2  2  ABC_ATPase    Predicted ATPase of the ABC class
      0.091   12.7   0.1       0.23   11.4   0.0    1.8  2  Rad17         Rad17 P-loop domain
       0.11   12.2   0.2       0.22   11.2   0.2    1.5  1  AAA_24        AAA domain
       0.13   12.0   0.1       0.29   10.9   0.1    1.6  1  CUE           CUE domain
       0.13   12.2   0.6       0.67    9.8   0.2    2.0  2  ATPase_2      ATPase domain predominantly from Archaea


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 !  111.7   0.0   5.3e-35   3.8e-32       3     136 ..      19     159 ..      17     160 .. 0.93

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 5.3e-35
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvre 78 
                                       +vs+++ e +++++vG+nG+GKSt+lk++ gl+k  +G+i ldg d++  q++e++ + i+++pq +++f++ltv+e
  gi|557694885|ref|YP_008797939.1|  19 DVSVTVPEKQLTVVVGPNGSGKSTFLKTIFGLTKIYSGKIMLDGVDITGlQPHEIAYHGISYVPQVDNIFSNLTVYE 95 
                                       89*************************************************************************** PP

                                       H.........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n          +++ i+++++ +   +   t  +++++ +SgG++q++a+a++ll+kpk++l+DEpt
  gi|557694885|ref|YP_008797939.1|  96 NlliathgldIDESAIDDVMEMFPHLK---TYRNKKAALMSGGERQMLAIAMSLLRKPKIMLFDEPT 159
                                       *******99888888999999998555...3333455*****************************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 !   32.3   0.1   1.3e-10   9.1e-08       1      83 [.      29      98 ..      29     127 .. 0.88
   2 !   29.6   0.0   8.3e-10     6e-07     234     293 ..     129     185 ..     120     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 1.3e-10
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrle 79
                                      l+v++GpNgsGKS++L+++ +l            ++  +g+i  +   +++ +p + + ++i+  + q  ++  +l+++
  gi|557694885|ref|YP_008797939.1| 29 LTVVVGPNGSGKSTFLKTIFGL------------TKIYSGKIMLDGVDITGLQPHEIAYHGIS-YVPQVDNIFSNLTVY 94
                                      79*****************999............78999999999999999999999999999.999999988888888 PP

                            AAA_21 80 rsqv 83
                                      ++ +
  gi|557694885|ref|YP_008797939.1| 95 ENLL 98
                                      8776 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 8.3e-10
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvi 293
                                       a+ +S G +++la++ +llr +   ++ l+DEp  +L Pk+  +++ ++k+l++n ++ i
  gi|557694885|ref|YP_008797939.1| 129 AALMSGGERQMLAIAMSLLRKP---KIMLFDEPTGNLSPKMAITIFNIIKDLRENYGKTI 185
                                       5689****************99...9*************************999666655 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 !   22.3   0.0   9.9e-08   7.1e-05      22      49 ..      25      51 ..      12      59 .. 0.84
   2 !   11.8   0.1   0.00017      0.12     121     189 ..     112     180 ..      78     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 9.9e-08
                                      TTSSEEEEEESTTSSHHHHHHHHHHHCT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 22 fsksftaivGpNGSGKsnlldAilFvLG 49
                                       +k++t++vGpNGSGKs +l  i F L 
  gi|557694885|ref|YP_008797939.1| 25 PEKQLTVVVGPNGSGKSTFLKTI-FGLT 51
                                      4788******************9.7665 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00017
                                       HHHHHHHHCTT-STT....CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT CS
                                       xxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 121 kevsellesagiske....lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn 189
                                        +v+e++++ + +++    l+SgGe++++a+a+ +     ++  ++l+De   +L  k    + +++k  ++n
  gi|557694885|ref|YP_008797939.1| 112 DDVMEMFPHLKTYRNkkaaLMSGGERQMLAIAMSL----LRKPKIMLFDEPTGNLSPKMAITIFNIIKDLREN 180
                                       44555555444444355558********9999873....5555688999999999999999999999998887 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   1.6e-07   0.00012      23      43 ..      26      47 ..      10     103 .. 0.79
   2 ?    2.5   0.0      0.13        93     323     356 ..     149     182 ..     128     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.6e-07
                            AAA_15 23 ee.ltvliGkNnsGKSsileal 43
                                      e+ ltv++G+N+sGKS++l+ +
  gi|557694885|ref|YP_008797939.1| 26 EKqLTVVVGPNGSGKSTFLKTI 47
                                      225*****************98 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.13
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnk 356
                                       k++i l++EP  +L p++   +++ +k+l ++  
  gi|557694885|ref|YP_008797939.1| 149 KPKIMLFDEPTGNLSPKMAITIFNIIKDLRENYG 182
                                       5789***********************9988765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0   1.2e-07   8.7e-05      12      39 ..      13      47 ..       9      52 .. 0.78
   2 ?   -2.7   0.0       9.9   7.1e+03     169     169 ..     178     178 ..     118     200 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1.2e-07
                            AAA_23 12 dqeidF.......skgltlItGpNGaGKTTildAi 39
                                      + ++ F       +k lt+++GpNG+GK+T+l  i
  gi|557694885|ref|YP_008797939.1| 13 KLQVLFdvsvtvpEKQLTVVVGPNGSGKSTFLKTI 47
                                      555445556666799****************9877 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 9.9
                            AAA_23 169 k 169
                                       +
  gi|557694885|ref|YP_008797939.1| 178 R 178
                                       1 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 !   18.8   0.0   1.4e-06   0.00097      17      39 ..      22      44 ..      16      50 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.4e-06
                            AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                      +++ +k+ t+++Gp+GsGKST+l
  gi|557694885|ref|YP_008797939.1| 22 VTVPEKQLTVVVGPNGSGKSTFL 44
                                      55555679*************98 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   2.3e-06    0.0017       5     116 ..      27     178 ..      25     196 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.3e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee...........erpevv....fvtlpsst..sskdllrellral 64 
                                       ++++vv+G+ G+GK+t l++++   ++++   +           +  e++    ++ +++++  s  +++++ll a+
  gi|557694885|ref|YP_008797939.1|  27 KQLTVVVGPNGSGKSTFLKTIFGLTKIYSGKIMldgvditglqpH--EIAyhgiSYVPQVDNifSNLTVYENLLIAT 101
                                       7899******************99987776666999999998542..222356577777777788888888888888 PP

                            AAA_22  65 glelka................erlsseellealeqalrarav.....ielliiDEaqh.lrs....eealeeLrsl 115
                                       +    +                +r+++ +l++  e+++ a a+     +++++ DE    l s     ++++ +++l
  gi|557694885|ref|YP_008797939.1| 102 HGLDIDesaiddvmemfphlktYRNKKAALMSGGERQMLAIAMsllrkPKIMLFDEPTGnL-SpkmaITIFNIIKDL 177
                                       7655557888888888888888888888888888888888888888888888888865556.423445555555555 PP

                            AAA_22 116 l 116
                                        
  gi|557694885|ref|YP_008797939.1| 178 R 178
                                       4 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.8e-06    0.0042      20      47 ..      23      48 ..      16      53 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.8e-06
                            AAA_27 20 dfsaeeadlhliyGpNEAGKstalrAis 47
                                      +    e++l++++GpN +GKst l+ i 
  gi|557694885|ref|YP_008797939.1| 23 TV--PEKQLTVVVGPNGSGKSTFLKTIF 48
                                      33..489*****************9885 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.9e-05     0.014      16      45 ..      25      54 ..      12     149 .. 0.67
   2 ?   -2.9   0.0       6.3   4.5e+03      46      60 ..     182     196 ..     169     212 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.9e-05
                            AAA_30 16 sgdrvavltGpAGtGKttalkalreaweaa 45
                                       +++++v++Gp G+GK+t lk++  + +  
  gi|557694885|ref|YP_008797939.1| 25 PEKQLTVVVGPNGSGKSTFLKTIFGLTKIY 54
                                      56789****************997776666 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.3
                            AAA_30  46 ggrviglAptgkaAk 60 
                                       g++++++  ++k A 
  gi|557694885|ref|YP_008797939.1| 182 GKTILLAEQNAKKAL 196
                                       433333333333333 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 !   10.7   0.3    0.0004      0.29       2      21 ..      29      48 ..      28      61 .. 0.86
   2 ?    3.0   0.0     0.092        66      84     109 ..     152     180 ..     116     211 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                                      EEEEEESTTCCHHHHHHHHH CS
                              cobW  2 vtvltGflGsGKTtLlnhll 21
                                       tv++G+ GsGK+t+l+++ 
  gi|557694885|ref|YP_008797939.1| 29 LTVVVGPNGSGKSTFLKTIF 48
                                      589**************986 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.092
                                       SEEEEEECTTTTHHHH..HTT.SHHHHHC CS
                              cobW  84 dviliEttGlaePapv..aft.eeelksd 109
                                        +++ E tG+++P++   +f+  ++l+++
  gi|557694885|ref|YP_008797939.1| 152 IMLFDEPTGNLSPKMAitIFNiIKDLREN 180
                                       47888*********995333343444433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.0   2.4e-05     0.017      10      45 ..      12      48 ..       5     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-05
                            AAA_16 10 eqLlsale.rvrsgrpelvllsGesGvGKsslvrell 45
                                      ++L+ +++ +v  ++ +l++++G+ G+GKs+ +++++
  gi|557694885|ref|YP_008797939.1| 12 KKLQVLFDvSVTVPEKQLTVVVGPNGSGKSTFLKTIF 48
                                      67777888666667779****************9998 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 ?   13.5   0.1   3.7e-05     0.027     125     161 ..      23      59 ..       9      80 .. 0.84
   2 ?   -2.6   0.0         3   2.2e+03     119     138 ..     193     210 ..     165     211 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                             T2SSE 125 avrerglilvsGgTgsGKttllyallkeinksderiv 161
                                        v e++l +v G+ gsGK+t+l ++    + ++ +i+
  gi|557694885|ref|YP_008797939.1|  23 TVPEKQLTVVVGPNGSGKSTFLKTIFGLTKIYSGKIM 59 
                                       466889999***************9988777776766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3
                             T2SSE 119 aevlrkavrerglilvsGgT 138
                                       +++l+     + ++lvsG T
  gi|557694885|ref|YP_008797939.1| 193 KKALEIG--DKAILLVSGKT 210
                                       4444433..67788888877 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   7.3e-05     0.052       1      19 [.      29      47 ..      29      55 .. 0.87
   2 ?   -1.8   0.0       4.5   3.2e+03      63      78 ..     143     158 ..      93     202 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.3e-05
                            AAA_33  1 lvllvGlpGsGKstlaerl 19
                                      l+++vG++GsGKst+++ +
  gi|557694885|ref|YP_008797939.1| 29 LTVVVGPNGSGKSTFLKTI 47
                                      6799***********9875 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.5
                            AAA_33  63 arkalsagrnvildat 78 
                                       a + l++ + +++d +
  gi|557694885|ref|YP_008797939.1| 143 AMSLLRKPKIMLFDEP 158
                                       4444444444444433 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00046      0.33       3      25 ..      28      50 ..      26     149 .. 0.75
   2 ?    1.5   0.0       0.4   2.8e+02      13      39 ..     181     209 ..     165     229 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                            AAA_14  3 kilvitGaRrvGKTtllkqlike 25
                                      ++ v++G+  +GK+t+lk+++  
  gi|557694885|ref|YP_008797939.1| 28 QLTVVVGPNGSGKSTFLKTIFGL 50
                                      6789**************99854 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.4
                            AAA_14  13 vGKTtllkql.ikell.vkkesilyinld 39 
                                        GKT ll +  +k+ l + ++ il ++ +
  gi|557694885|ref|YP_008797939.1| 181 YGKTILLAEQnAKKALeIGDKAILLVSGK 209
                                       699*9986551666668888888877755 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   7.5e-05     0.054      98     125 ..      26      53 ..      11      61 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.5e-05
                                       TTSEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  98 kdktsvlvGqSGvGKStLinallpelel 125
                                       +++++v+vG+ G GKSt+++++ + +++
  gi|557694885|ref|YP_008797939.1|  26 EKQLTVVVGPNGSGKSTFLKTIFGLTKI 53 
                                       5699****************99886665 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00011      0.08       2      21 ..      29      48 ..      28      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      l ++ G++GsGK+t+l+ + 
  gi|557694885|ref|YP_008797939.1| 29 LTVVVGPNGSGKSTFLKTIF 48
                                      6799*************985 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00014       0.1      42      59 ..      30      47 ..      13      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                                      EEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE 42 llvaGatgsGKStalntL 59
                                      ++v+G  gsGKSt+l+t+
  gi|557694885|ref|YP_008797939.1| 30 TVVVGPNGSGKSTFLKTI 47
                                      69*************996 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00016      0.12       8      29 ..      31      52 ..      26      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00016
                                      EEEEBTTSSCCCCCCTTSSSS- CS
                            Septin  8 mvvGesglGkttlintlfetdl 29
                                      +vvG +g Gk+t+++t+f  + 
  gi|557694885|ref|YP_008797939.1| 31 VVVGPNGSGKSTFLKTIFGLTK 52
                                      689**************97544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00031      0.22      30      50 ..      24      44 ..      18      47 .. 0.92
   2 ?   -1.9   0.0       2.9   2.1e+03     170     191 ..     172     193 ..     164     195 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                            AAA_25 30 lpagelallaGapgtGKttla 50
                                      +p++ l++++G+ g+GK+t++
  gi|557694885|ref|YP_008797939.1| 24 VPEKQLTVVVGPNGSGKSTFL 44
                                      799****************96 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                            AAA_25 170 ealeriarrtgaavllvhHvgK 191
                                       + ++++++++g ++ll  + +K
  gi|557694885|ref|YP_008797939.1| 172 NIIKDLRENYGKTILLAEQNAK 193
                                       5677888999999998877666 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00018      0.13       2      28 ..      31      57 ..      30     177 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                      EEEEBTTTTHHHHHHHHHTS--S---S CS
                         Dynamin_N  2 avvGsqSsGKSSvlnaLlgedilprgp 28
                                      +vvG   sGKS++l  + g     +g+
  gi|557694885|ref|YP_008797939.1| 31 VVVGPNGSGKSTFLKTIFGLTKIYSGK 57
                                      7****************9976555555 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 ?    8.3   0.1    0.0012      0.85     242     264 ..      24      47 ..      20      54 .. 0.88
   2 ?    1.0   0.0      0.21   1.5e+02     356     410 ..     153     204 ..      96     214 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0012
                                       E-SS.EEEEEE-TTSSHHHHHHHH CS
                        ABC_ATPase 242 ipkG.vtlIvGggfhGKsTLLeAl 264
                                       +p++ +t++vG++  GKsT L+ +
  gi|557694885|ref|YP_008797939.1|  24 VPEKqLTVVVGPNGSGKSTFLKTI 47 
                                       66666****************987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.21
                                       H---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GCCTTT-SEEEE CS
                        ABC_ATPase 356 mirDermqelvskekepitplvdrvrelykklgvstilvvggsgdyldvAdtvil 410
                                       m+ De   +l +k +  it + + +++l++++g +++l    +++ l+++d+ il
  gi|557694885|ref|YP_008797939.1| 153 MLFDEPTGNLSPKMA--IT-IFNIIKDLRENYGKTILLAEQNAKKALEIGDKAIL 204
                                       444444444443333..33.34566666666666666666666666666666665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00032      0.23      44      81 ..      26      64 ..      12     114 .. 0.62
   2 ?   -3.0   0.0       7.9   5.6e+03      38      52 ..     194     208 ..     183     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                             Rad17 44 kkriLLisGPsGCgkstvvkv...Lskelgiklrewlnpvs 81
                                      +k++ ++ GP G gkst +k    L+k+++ k+   l++v 
  gi|557694885|ref|YP_008797939.1| 26 EKQLTVVVGPNGSGKSTFLKTifgLTKIYSGKI--MLDGVD 64
                                      57899************9997333455554443..444444 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.9
                             Rad17  38 dvLesrkkriLLisG 52 
                                       + Le   k iLL+sG
  gi|557694885|ref|YP_008797939.1| 194 KALEIGDKAILLVSG 208
                                       457777788999998 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2    0.0003      0.22       5      22 ..      30      47 ..      26      67 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0003
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                       +++Gp+g+GK+t++k++
  gi|557694885|ref|YP_008797939.1| 30 TVVVGPNGSGKSTFLKTI 47
                                      689*************97 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    0.0004      0.29       2      15 ..     108     121 ..     107     123 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0004
                                       HHHHHHHHHHSTTS CS
                               CUE   2 eqmletLkemFPdl 15 
                                       e+++++++emFP+l
  gi|557694885|ref|YP_008797939.1| 108 ESAIDDVMEMFPHL 121
                                       799**********8 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 ?    9.8   0.2   0.00093      0.67      21      41 ..      28      48 ..      22      58 .. 0.86
   2 ?    0.1   0.0      0.86   6.1e+02      29      63 ..     179     214 ..     163     227 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00093
                          ATPase_2 21 eiyfiYGpegsGKtaLlkeii 41
                                      +  ++ Gp gsGK+++lk i 
  gi|557694885|ref|YP_008797939.1| 28 QLTVVVGPNGSGKSTFLKTIF 48
                                      67899*************986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.86
                          ATPase_2  29 egsGKtaLlkeiienl.edkdkyviyyialreesis 63 
                                       e+ GKt Ll e   ++ ++ +++ i + + +++++ 
  gi|557694885|ref|YP_008797939.1| 179 ENYGKTILLAEQNAKKaLEIGDKAILLVSGKTVYQG 214
                                       899999999776555447777777766666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1492.50
//
Query:       gi|557694886|ref|YP_008797940.1|  [L=206]
Description: HAD-superfamily hydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   46.1   0.0      9e-12   45.4   0.0    1.3  1  HAD_2           Haloacid dehalogenase-like hydrolase
    9.2e-08   32.6   0.0    1.1e-05   25.8   0.0    2.1  1  Hydrolase       haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.02   15.0   0.0       0.04   14.0   0.0    1.5  1  Hydrolase_like  HAD-hyrolase-like
       0.15   11.8   0.0       0.39   10.5   0.0    1.6  1  UPF0175         Uncharacterised protein family (UPF0175)


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 !   45.4   0.0     2e-15     9e-12       3     176 ..       6     182 ..       4     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2e-15
                             HAD_2   3 FDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeee...........kieellrk 68 
                                        D+DgTl+ ++++  + +++++            +++++g +  e+++kl ++++ ++           ++ ++++ 
  gi|557694886|ref|YP_008797940.1|   6 LDIDGTLYRSSDYEQHLLTSAV----------TVIAECLGVDKAEAFKKLYQTKKIHKtvsksvevlgiDRRKFYSL 72 
                                       5999999999988877777776..........335566666666666666665555555666666666666677788 PP

                             HAD_2  69 yneekkk.kevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgies.yFdvivtsedvekkKPdpeviek 143
                                         e+ +  +++ p   +k +  e++++++ +g+ T++ ++ + + l  lg+++  +d  vts+d+e +KP+ e ++ 
  gi|557694886|ref|YP_008797940.1|  73 LAEKVQPcRFLAPDASLKRFFAEVRDRKLFVGLHTNSGKKLALKVLGCLGVDDgCYDALVTSDDAE-PKPSLEGFRL 148
                                       888888889******************************************962778888888865.66******** PP

                             HAD_2 144 aleklklkkeeviyvGDsp.tDieaakkagikvi 176
                                       +l   ++++ee++yvGD     +e ak++g++++
  gi|557694886|ref|YP_008797940.1| 149 LLSMADASPEEALYVGDRCeVELEPAKRLGMRTA 182
                                       ******************99***********997 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.6e-09   1.1e-05       1     203 [.       1     171 [.       1     178 [. 0.73

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.6e-09
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewl 77 
                                       +k++++D+dGTL++++     ++ sa                   ++a++ ++  + + f +      y+  k   +
  gi|557694886|ref|YP_008797940.1|   1 MKAIFLDIDGTLYRSSDYEQHLLTSA-----------------VTVIAECLGV-DKAEAFKK-----LYQTKKIHKT 54 
                                       799**********7774444444444.................2223444443.33345555.....5555555544 PP

                                       HHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  78 taldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq 154
                                        +          ++ +  + r  + l a+ ++   +  p      ++ ++a+ +++++ v+l t++ ++ a +++  
  gi|557694886|ref|YP_008797940.1|  55 VSK--------SVEVLGIDRRKFYSLLAEKVQPCRFLAP---DASLKRFFAEVRDRKLFVGLHTNSGKKLALKVLGC 120
                                       444........6666666666666665566666666655...77778****************************** PP

                                       TT..GGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HH CS
                                       xx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                         Hydrolase 155 lG..ddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvn.Da 203
                                       lG  d ++da ++sd+ +  kps eg++ ++    ++pee + VGD+    +
  gi|557694886|ref|YP_008797940.1| 121 LGvdDGCYDALVTSDDAE-PKPSLEGFRLLLSMADASPEEALYVGDRCEvEL 171
                                       ***888889999998887.9**************************876555 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0     9e-06      0.04       4      47 ..     140     183 ..     138     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9e-06
                                       TTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEE CS
                    Hydrolase_like   4 KPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvL 47 
                                       KP+ e ++  l   ++ pee l++GDr +  ++ A++ G++++ 
  gi|557694886|ref|YP_008797940.1| 140 KPSLEGFRLLLSMADASPEEALYVGDRCEVELEPAKRLGMRTAE 183
                                       8888888899999999*************************975 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   8.7e-05      0.39      27      57 ..      44      76 ..      37      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.7e-05
                           UPF0175 27 klYeegrl..SlgkAaelaglsrveflelLarr 57
                                      klY+ +++  + +k  e++g++r  f+ lLa++
  gi|557694886|ref|YP_008797940.1| 44 KLYQTKKIhkTVSKSVEVLGIDRRKFYSLLAEK 76
                                      89****9977789*****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1559.37
//
Query:       gi|557694887|ref|YP_008797941.1|  [L=336]
Description: glyceraldehyde-3-phosphate dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-20   72.9   0.0      4e-20   72.0   0.0    1.4  1  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
      6e-11   42.5   0.6    1.4e-10   41.4   0.4    1.7  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
    2.4e-07   31.0   2.7    1.1e-06   28.9   0.3    2.9  3  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
    1.6e-05   25.7   0.1    4.1e-05   24.4   0.0    1.7  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
    0.00059   20.5   0.1     0.0018   18.9   0.1    1.9  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
     0.0007   19.9   0.0     0.0016   18.7   0.0    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.015   14.6   2.7      0.075   12.4   0.4    2.7  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
      0.062   13.6   0.0       0.26   11.6   0.0    2.0  2  TrkA_N           TrkA-N domain
      0.068   13.6   0.0       0.17   12.3   0.0    1.7  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma


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 !   72.0   0.0     2e-23     4e-20       1     154 [.     145     295 ..     145     298 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 2e-23
                                       HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT..CSSEEEE-THHHHHHHHSGGGTTTEEEE CS
                           Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa..eniiptstgaakavglVlpelkgkldgl 75 
                                       L++++++++++fg++++++++ ++++++         ++  ++ + a   +++ +++++a++v++Vlp+  +++ ++
  gi|557694887|ref|YP_008797941.1| 145 LCRVLNAFDSAFGLERARVVIARRAVDP---------EETSKGVIDAvvLDPVEIPSHHAEDVNTVLPH--IDIVTM 210
                                       89**************************.........6677777766679******************5..99**** PP

                                       EEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH....TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCEE CS
                           Gp_dh_C  76 AvrVPtpnvsvvdlvvelekevtveevnaalkeaae....galkgilsyteeelvssDlvgdph..ssifdaketiv 146
                                       A++VPt+ +++++l++ l+++ t+e+v ++l e+++     + +g+ ++++  ++ ++l + +   ++  +   + +
  gi|557694887|ref|YP_008797941.1| 211 ALKVPTTHMHLHSLILSLRQKPTRENVLKTLAETTRvklfWKSEGFKGTANLYEYGRELGRPRGdiYEACVIGDSVT 287
                                       ************************************9999899****************998877899999999999 PP

                                       ETTTEEEE CS
                           Gp_dh_C 147 veenlvkv 154
                                       v++n+v++
  gi|557694887|ref|YP_008797941.1| 288 VKDNEVFL 295
                                       99999987 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.4   6.8e-14   1.4e-10       1      96 [.       2     107 ..       2     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 6.8e-14
                                       EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH............HHSSSS--S-BEBSSHHHHH CS
                            DapB_N   1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag............ellglgklgvavtddleevl 65 
                                       i+v+++G+ G++G++v++av +++d++lv++v++++ +++++ a              + ++++ g+ v+  l+++l
  gi|557694887|ref|YP_008797941.1|   2 IRVGINGY-GTIGRRVADAVMKQNDMKLVGVVKNTP-DYKARLAVekniplycvdesGVSKFRRAGFDVSGVLDDLL 76 
                                       79******.**************************9.666666667888899999866677779************* PP

                                       HH-SEEEE-S-HHHHHHHHHHHHHTT-EEEE CS
                            DapB_N  66 ekadvliDFTtpeavlenlklalekgvklVi 96 
                                       +++dv++D T  ++ + + + ++ +gv++V+
  gi|557694887|ref|YP_008797941.1|  77 KEVDVIVDCTPGDVGKTYREKYFGAGVRAVF 107
                                       **********999999999999999**9998 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 !   28.9   0.3   5.5e-10   1.1e-06       1      36 [.       2      36 ..       2      48 .. 0.84
   2 ?    0.2   0.1      0.48   9.5e+02      87      96 ..      78      87 ..      75      90 .. 0.88
   3 ?   -2.2   0.0       2.7   5.3e+03      21      34 ..     131     144 ..     123     174 .. 0.57

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 5.5e-10
                                      CEEEEESTSHHHHHHHHHHHHHTTCEEEEEE-TS-H CS
                           Gp_dh_N  1 vkvainGfGRIGrlvlralleekelevvaindltdl 36
                                      ++v+inG+G IGr v+ a+++++++++v + +  ++
  gi|557694887|ref|YP_008797941.1|  2 IRVGINGYGTIGRRVADAVMKQNDMKLVGVVKN-TP 36
                                      69****************************983.33 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.48
                                      TSSEEEE-SS CS
                           Gp_dh_N 87 gvdlVvestG 96
                                      +vd++v++t 
  gi|557694887|ref|YP_008797941.1| 78 EVDVIVDCTP 87
                                      79******95 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.7
                                       HHTTCEEEEEE-TS CS
                           Gp_dh_N  21 eekelevvaindlt 34 
                                        +++++vv  n+++
  gi|557694887|ref|YP_008797941.1| 131 GRNSVRVVSCNTTG 144
                                       45555555555533 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 !   24.4   0.0   2.1e-08   4.1e-05       1      91 [.       2     108 ..       2     109 .. 0.92
   2 ?   -2.7   0.1       4.9   9.9e+03      52      78 ..     196     221 ..     175     228 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 2.1e-08
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS..................HHHHHT CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd..................leella 59 
                                       +rv+i G+G ig++ + +++++ ++ ++v+++++ +    ++a + +++ y                    l++ll+
  gi|557694887|ref|YP_008797941.1|   2 IRVGINGYGTIGRRVADAVMKQ-NDMKLVGVVKNTPDYKARLAVEKNIPLYCVdesgvskfrragfdvsgvLDDLLK 77 
                                       69**************888777.*******************99999995555569999********9999999999 PP

                                       CTTESEEEE-S-GGGHHHHHHHHHHTT-.EEEE CS
                      GFO_IDH_MocA  60 dpeidavivatpngtheelakaaleagk.hvll 91 
                                         e+d+++ +tp + ++ + ++ + ag+ +v++
  gi|557694887|ref|YP_008797941.1|  78 --EVDVIVDCTPGDVGKTYREKYFGAGVrAVFQ 108
                                       ..9********************9999988885 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.9
                                       SSHHHHHTCTTESEEEE-S-G.GGHHHH CS
                      GFO_IDH_MocA  52 sdleelladpeidavivatpn.gtheel 78 
                                       +d++ +l   +id+v+ a    +th+ l
  gi|557694887|ref|YP_008797941.1| 196 EDVNTVLP--HIDIVTMALKVpTTHMHL 221
                                       44555555..778887777654556554 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 !   18.9   0.1   9.3e-07    0.0018       1      70 [.       8      89 ..       8     107 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.3e-07
                                      --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TT.................HHHHHT--CB---HHHHHHHHS-EE CS
                     NAD_binding_3  1 GlGaiGsavleqlkrqqseielelvavadrdsllskd.................rkallasealtldlddliahldpdv 62
                                      G+G+iG++v++++++q++   ++lv+v+++ +  +++                  k  +a  ++   lddl++  ++dv
  gi|557694887|ref|YP_008797941.1|  8 GYGTIGRRVADAVMKQND---MKLVGVVKNTPDYKARlavekniplycvdesgvSKFRRAGFDVSGVLDDLLK--EVDV 81
                                      99**************96...8999999999444444699999999999999987777888899999******..**** PP

                                      EEE-S--H CS
                     NAD_binding_3 63 vVEcasse 70
                                      +V+c++ +
  gi|557694887|ref|YP_008797941.1| 82 IVDCTPGD 89
                                      ****9865 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 !   18.7   0.0   8.1e-07    0.0016       2      78 ..       5      87 ..       4      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8.1e-07
                                      EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH.......TTTCEEEEE--TTTHHHHHHHHHTTSSEE CS
                   Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka.......lgvrfeaialdaenyeavLaallkegdlv 73
                                       i G+G +G+ va+ + +++d++  + v+  + +  ++la ++        ++ +++      +++ vL+ llke d++
  gi|557694887|ref|YP_008797941.1|  5 GINGYGTIGRRVADAVMKQNDMK-LVGVVKNTPDYKARLAVEKniplycvDESGVSKFRRAGFDVSGVLDDLLKEVDVI 82
                                      567*******************6.888999999988888777789*****99999999999999999************ PP

                                      EE-SS CS
                   Sacchrp_dh_NADP 74 vnlsp 78
                                      v+++p
  gi|557694887|ref|YP_008797941.1| 83 VDCTP 87
                                      ***98 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 ?   12.4   0.4   3.8e-05     0.075      38      69 ..       3      35 ..       2      93 .. 0.86
   2 ?   -0.7   0.1      0.38   7.6e+02      81     102 ..     194     215 ..     181     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.8e-05
                                      EEEEES-SHHHHHHHHHHH.HTT-EEEEESSSH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlk.afgmkviaydrsk 69
                                      +vGi G+G IG++va+ +  + +mk++++ ++ 
  gi|557694887|ref|YP_008797941.1|  3 RVGINGYGTIGRRVADAVMkQNDMKLVGVVKNT 35
                                      69*************875439999999876654 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.38
                                       EECSHHHHHHH-SEEEE-S--S CS
                      2-Hacid_dh_C  81 elvsleellaesDivslhlplt 102
                                       + ++++++l + Div+++l + 
  gi|557694887|ref|YP_008797941.1| 194 HAEDVNTVLPHIDIVTMALKVP 215
                                       4568999********9988754 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   0.00013      0.26       3      59 ..       6      65 ..       4      70 .. 0.68
   2 ?   -2.3   0.0       2.6   5.3e+03      58      71 ..     156     169 ..     154     178 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                      EES-SHHHHHHHHHHHHTT.EEEEEEESSH.HH.HHHHHHTTSEEEES-TTSHHHHHHTT CS
                            TrkA_N  3 iiGlGrvGrslaeeLsegg.kdvvvidkde.er.veelreeglevvvgdatdeevLeeag 59
                                      i G+G++Gr++a+ +++++ ++ v++ k+  +  ++ + e++++ ++ d +  +  ++ag
  gi|557694887|ref|YP_008797941.1|  6 INGYGTIGRRVADAVMKQNdMKLVGVVKNTpDYkARLAVEKNIPLYCVDESGVSKFRRAG 65
                                      77***************5555566555554244255555777888877766666555555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.6
                                       TTGGGESEEEE-SS CS
                            TrkA_N  58 agiekadaviaatg 71 
                                        g+e+a++via   
  gi|557694887|ref|YP_008797941.1| 156 FGLERARVVIARRA 169
                                       68999999998655 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 ?   12.3   0.0   8.4e-05      0.17       2      93 ..       4     105 ..       3     109 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.4e-05
                                       EEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTT..TTTSBHHHHSG.........GGTTTECEBEEEGGGGGCTT- CS
                    Semialdhyde_dh   2 vaivGatGyvGqellrlLeehpevelvvllsssr..saGkklaeavk.........aleegkdlkvedvdeeelkev 67 
                                       v+i G  G +G++++  + ++ +++lv ++ ++   +a  +++++ +         +   ++ + v+ v ++ lkev
  gi|557694887|ref|YP_008797941.1|   4 VGING-YGTIGRRVADAVMKQNDMKLVGVVKNTPdyKARLAVEKNIPlycvdesgvSKFRRAGFDVSGVLDDLLKEV 79 
                                       55555.56667777777777777777776666664444444444444666666633222333344444666788*** PP

                                       SEEEE-SCHHHHHHHHHHHHHTTSEE CS
                    Semialdhyde_dh  68 divflalpagvskelapklaeagvkv 93 
                                       d+++ ++p++v k + +k+  agv+ 
  gi|557694887|ref|YP_008797941.1|  80 DVIVDCTPGDVGKTYREKYFGAGVRA 105
                                       *******************9999864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2580.80
//
Query:       gi|557694888|ref|YP_008797942.1|  [L=406]
Description: phosphoglycerate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-102  342.1   0.0   4.2e-102  341.9   0.0    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 !  341.9   0.0  2.4e-106  4.2e-102       1     377 [.       9     385 ..       9     386 .. 0.93

  Alignments for each domain:
  == domain 1  score: 341.9 bits;  conditional E-value: 2.4e-106
                                       GGGS--TT-EEEEEE-----EECT.TEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHH CS
                               PGK   1 vkdldlkgkrvlvRvDfNvplkke.gkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLs 76 
                                       ++d+d++gk+v+vR+D+N p++ e g++ + +rir++  T+++l  +gak+vl sH+gr+ g+ + +sl+ +ae Ls
  gi|557694888|ref|YP_008797942.1|   9 IDDFDVSGKTVFVRADLNTPIDPEtGRLLELHRIRESSFTVRHL--NGAKIVLGSHQGRV-GRYDYVSLSIHAEALS 82 
                                       68*******************9988*******************..9************9.899************* PP

                                       HHHTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTTTTT-H.......HHHHHHHHT-SEEEE--GGGTTS CS
                               PGK  77 ellgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeEeknde.......elakklasladvyVnDAFgtahr 146
                                       e+lgk+Vkfvedv+ge+ ++ai++lk+gevllLeN+rf +eE+ + +       +++k+la l+d++V DAF tahr
  gi|557694888|ref|YP_008797942.1|  83 EVLGKRVKFVEDVFGEASRAAIKSLKPGEVLLLENLRFAAEENYEYSpeeaaktHIVKRLAPLFDICVLDAFPTAHR 159
                                       *****************************************97432223333347********************** PP

                                       --TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHHHHH CS
                               PGK 147 ahaStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgmantFl 221
                                       ah S+vg+a+vl+++aG+l+++El+ l++v+ + + p++a+lGG+kvsd+++ i++L+++   d+++++G++  +Fl
  gi|557694888|ref|YP_008797942.1| 160 AHPSIVGFAEVLPTCAGYLVARELKSLNRVMMTSKAPYTAVLGGSKVSDRLEAITALIQNGraDNVLLTGLIGLVFL 236
                                       ************99********************************************98777************** PP

                                       HHTT-B-TTSS-..-GGGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEE.ECCG--TT-EEEEE-HHHHH CS
                               PGK 222 kaqgleigkslv..eedklelakellekakkkgvkillpvDvvvakeeaekeakvv.eveaipedemalDigpktie 295
                                       +a+g    k l+   e+ +  a+++l++++    k+ lp Dv+++k+     ++v  ++++i++  ++lDig++ti+
  gi|557694888|ref|YP_008797942.1| 237 RAAGAL-KKPLTgdLEKYVPKAQSILHEYR---GKFSLPDDVAIEKDG----ERVEiPISSIEDPGKVLDIGEQTIR 305
                                       **9986.4666643334699******9998...89**********832....23334899***************** PP

                                       HHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSEEESSSHHHH CS
                               PGK 296 lfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvshvStGGgAsL 372
                                       +++++ik++ t+++ Gp G+fe + f++GT +++ a+a +    +siv+Gg+  aa+e+lg++d v+hvSt+GgA++
  gi|557694888|ref|YP_008797942.1| 306 KYSKIIKSSGTIFISGPPGMFEKKGFERGTDELLLAAAGSLG--TSIVSGGHLSAALERLGVKDWVDHVSTAGGALV 380
                                       *************************************99855..********************************* PP

                                       HHHCT CS
                               PGK 373 elLeg 377
                                        +L g
  gi|557694888|ref|YP_008797942.1| 381 MFLAG 385
                                       ***98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 2965.69
//
Query:       gi|557694889|ref|YP_008797943.1|  [L=373]
Description: glucose sorbosone dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-75  252.1   0.0    1.1e-74  251.7   0.0    1.1  1  GSDH         Glucose / Sorbosone dehydrogenase
  ------ inclusion threshold ------
       0.13   12.5   0.0       0.23   11.7   0.0    1.4  1  Laminin_G_1  Laminin G domain


Domain annotation for each model (and alignments):
>> GSDH  Glucose / Sorbosone dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.7   0.0   1.3e-78   1.1e-74       2     329 ..      49     358 ..      48     367 .. 0.90

  Alignments for each domain:
  == domain 1  score: 251.7 bits;  conditional E-value: 1.3e-78
                                       S-EEEEEE-TTS-EEEEETTTEEEEEE..TTEE.EEEEE-.----STT-SEEEEEE-TTTTTS-EEEEEEEE-...T CS
                              GSDH   2 ehPwslaflpdgrlLvtersGrlrlvk.adgklkepiagvpevvakgqgGlldvalhpdfaenrlvYltyaeaeeek 77 
                                       + Pws++f+  +++L+ter+G ++l++ ++g++ e++  + ev+a g+gGll++ +      + + Yl+++   +e+
  gi|557694889|ref|YP_008797943.1|  49 SVPWSISFISGDEALFTERNGAVKLLTlSTGRV-EEVGRF-EVAAVGEGGLLGIETLRA-GGKTIAYLYHSY--REG 120
                                       68********99**************9667777.888887.9************98776.555566777773..477 PP

                                       TSSEEEEEEEEE-SS..-EEEEEEEEEEE---TT-------EEE-TTS-EEEE---TT-GGGGG-TT-SSSEEEEE- CS
                              GSDH  78 ggagtavararlsedeaaledlevifrqepkvesgahfGsrlafgpdgtLfvtvGdrskreeaqdlsselGkilrln 154
                                       g+  ++v+r   s+    l+d  +i + +p   ++ h+G+rl +gpd+ L++t+G+ + ++ +qd++s  Gkilrl 
  gi|557694889|ref|YP_008797943.1| 121 GKIFNKVVRTIYSGR---LQDHVEIISGIPG--GTVHNGGRLKIGPDNLLYITTGEGGVPDLSQDTDSLGGKILRLM 192
                                       888899999999665...*************..999***************************************** PP

                                       TTSSB-TT-TTTT-TTS-TTEEEE--SCE---EE-TTT--EEEEEE--SSS......EEEEEE-TT-B--TTT-S.. CS
                              GSDH 155 kdGsvpadnpfvgkagakpeiwsyGhRnpqGlaldpdtgeLwesEhGprgg......DelnlieaGknYGWplvsyg 225
                                       +dG vp+dnpf      k  ++++G RnpqGla++p+tg+L+ ++hGp+g+      De+nli++G+nYGWp+v   
  gi|557694889|ref|YP_008797943.1| 193 PDGGVPQDNPF------KTPVYALGLRNPQGLAWHPETGRLYCTDHGPSGEglriahDEVNLIKPGANYGWPIVI-- 261
                                       ***********......579******************************99**********************9.. PP

                                       ....S-.....-S-TTS---SE.EETT---EEEEEEE........TTEEEEEETTTTEEEEEEE.EEEEEEEEEEEE CS
                              GSDH 226 eeYsgkkigesetreglekpvl.vwtpsiapsglafytgdafpewkgdllvggLksqsllrlel.degekvveeerl 300
                                           g+       +e++ kpv+ +  +++apsg+ fytg    e++ ++++++L+ ++l+rl + +eg +vv  e+l
  gi|557694889|ref|YP_008797943.1| 262 ----GD-----AGDEKYVKPVIhSGLETWAPSGCCFYTGRGNQEFRSSFFFAALRGRHLHRLVFdEEGYRVVLSEKL 329
                                       ....33.....34566777776478899************************************5456789*****9 PP

                                       E.ESS-.-EEEEEE-TTS-EEEEE-TTTTT CS
                              GSDH 301 l.eelgeriRdVeqgpdGalyvltdeedgk 329
                                       +  ++g r+RdV +gpdG+ly+lt+++dg+
  gi|557694889|ref|YP_008797943.1| 330 FdGQFG-RLRDVVEGPDGNLYILTSNRDGR 358
                                       945555.*********************96 PP

>> Laminin_G_1  Laminin G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.6e-05      0.23       2      33 ..     279     313 ..     278     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.6e-05
                                       EESSSSEEEEEEEESSTT...EEEEEEEETTEEEE CS
                       Laminin_G_1   2 rTtepsGlllylgtkaek...dflaleLvdGrlev 33 
                                        T++psG  +y+g+ +++   +f+ ++L++ +l+ 
  gi|557694889|ref|YP_008797943.1| 279 ETWAPSGCCFYTGRGNQEfrsSFFFAALRGRHLHR 313
                                       69**********99999999*********999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2729.68
//
Query:       gi|557694890|ref|YP_008797944.1|  [L=85]
Description: hypothetical protein CSUB_C1463 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   2.2     0.0073   16.4   2.2    1.3  1  bZIP_1     bZIP transcription factor
  ------ inclusion threshold ------
      0.017   14.8   0.5      0.021   14.5   0.5    1.1  1  VPS28      VPS28 protein
      0.029   14.8   2.1      0.056   13.9   2.1    1.4  1  FlaC_arch  Flagella accessory protein C (FlaC)
       0.14   12.5   1.3       0.29   11.6   1.0    1.6  2  LPP        Lipoprotein leucine-zipper


Domain annotation for each model (and alignments):
>> bZIP_1  bZIP transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   2.2   1.6e-06    0.0073      32      62 ..      23      53 ..      19      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.6e-06
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            bZIP_1 32 errvkaLekeNksLkseleelkkevekLksk 62
                                       ++v+ L++e+++L+s l+  ++evekL ++
  gi|557694890|ref|YP_008797944.1| 23 DSEVSSLSSEMEKLRSSLKLSEDEVEKLADE 53
                                      679*************************887 PP

>> VPS28  VPS28 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.5   4.6e-06     0.021     130     183 ..       7      59 ..       2      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-06
                             VPS28 130 LveslnkleklekdfegksklvkWliklnkmkasdeLseeearqllfdlesaYk 183
                                       L++ +n++ +  +d++  s++ +   +++k++ s +Lse+e+++l+ +l++ Y 
  gi|557694890|ref|YP_008797944.1|   7 LYSLVNRM-RFFRDLKMDSEVSSLSSEMEKLRSSLKLSEDEVEKLADELDEYYI 59 
                                       55556666.557899999*********************************995 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 ?   13.9   2.1   1.2e-05     0.056       5      37 ..      22      54 ..      20      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                         FlaC_arch  5 lEnklsklsteletvkkeneelsksveelkenV 37
                                      +++++s+ls+e+e ++++++  +++ve+l ++ 
  gi|557694890|ref|YP_008797944.1| 22 MDSEVSSLSSEMEKLRSSLKLSEDEVEKLADEL 54
                                      78999**********************998865 PP

>> LPP  Lipoprotein leucine-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.6   7.3e+03      15      26 ..       3      14 ..       2      15 .. 0.62
   2 ?   11.6   1.0   6.4e-05      0.29       5      36 ..      22      53 ..      20      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.6
                               LPP 15 kvdqlssdvnsa 26
                                      kv+ l s vn +
  gi|557694890|ref|YP_008797944.1|  3 KVERLYSLVNRM 14
                                      677777666665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 6.4e-05
                               LPP  5 LssqVsqLkskvdqlssdvnsakaaaqaakeE 36
                                      + s+Vs+L+s++++l s ++ +++++++  +E
  gi|557694890|ref|YP_008797944.1| 22 MDSEVSSLSSEMEKLRSSLKLSEDEVEKLADE 53
                                      5689*********************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1171  (0.0653132); expected 358.6 (0.02)
Passed bias filter:                      825  (0.0460148); expected 358.6 (0.02)
Passed Vit filter:                       131  (0.0073066); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 636.39
//
Query:       gi|557694891|ref|YP_008797945.1|  [L=83]
Description: hypothetical protein CSUB_C1464 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 598.68
//
Query:       gi|557694892|ref|YP_008797946.1|  [L=822]
Description: aminopeptidase N [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-52  178.1   0.5    4.2e-52  176.9   0.3    1.7  2  Peptidase_M1    Peptidase family M1 domain
    1.2e-29  102.5   4.6    8.5e-11   42.1   0.3    3.6  3  HEAT_2          HEAT repeats
    2.6e-16   60.3   0.0    6.9e-16   59.0   0.0    1.7  1  Peptidase_M1_N  Peptidase M1 N-terminal domain
    2.2e-12   46.4   2.9    0.00055   20.4   0.3    4.6  5  HEAT_PBS        PBS lyase HEAT-like repeat
    1.2e-06   28.2   0.7        2.3    8.7   0.0    5.0  4  HEAT            HEAT repeat
     0.0072   14.8   1.0       0.83    8.0   0.1    2.1  2  Vitellogenin_N  Lipoprotein amino terminal region
  ------ inclusion threshold ------
       0.01   15.7   0.9      0.093   12.5   0.9    2.1  1  DUF445          Protein of unknown function (DUF445)


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 !  176.9   0.3   1.6e-55   4.2e-52       2     216 ..     227     434 ..     226     436 .. 0.93
   2 ?   -2.4   0.0       1.1   2.9e+03     157     174 ..     619     636 ..     589     641 .. 0.79

  Alignments for each domain:
  == domain 1  score: 176.9 bits;  conditional E-value: 1.6e-55
                                       HHHHHHHHHHHHHHHHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHHH CS
                      Peptidase_M1   2 alevtkkllefleeyfkvpYplpkldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaHq 78 
                                       ++++t+ +++f+++y+++pYp++ + +v++p+f  g+MEn+ ++t+++ +l  d    +++   s   ++aHE aHq
  gi|557694892|ref|YP_008797946.1| 227 SFNKTADIIRFFSNYLNYPYPFKSYRQVCVPEFVVGGMENTTATTLTDLTLHDD----HAHMDFSSDPLVAHEAAHQ 299
                                       57999*******************************************999988....4445567789********* PP

                                       HBTTTEEESSGGGGHHHHHHHHHHHHHHHHHHSCCCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTSS CS
                      Peptidase_M1  79 WfGnlVtmkwWddlwLnEGfatyleylildklepewevseqllleeveealsedaldeshpitqevekpseidevFd 155
                                       WfG+lVt++ W+++wLnE+fatyle l l + +++ e+  +l  +++++ l e   + s+p+  +v k   ++e+Fd
  gi|557694892|ref|YP_008797946.1| 300 WFGDLVTCRDWSHIWLNESFATYLENLYLRHDKGNDEFLYEL-YNDLQSYLDEYKRRYSRPVVYRVYKY--PEELFD 373
                                       *******************************99999977777.799999999999999****9888866..99**** PP

                                       HHHHHHHHHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCCSCHHTHHH CS
                      Peptidase_M1 156 siaYeKGasllrmlekllgeevFqkglksYlkefkyknaetedlwdaleealnkdisevmd 216
                                       ++aY KG  +l+ +++++gee F+k+l+ +l++++y+na+tedl +alee+++  +++v++
  gi|557694892|ref|YP_008797946.1| 374 RHAYPKGGLVLHTIKNIVGEESFRKALNLFLTRHQYSNADTEDLRKALEESSGMMLEKVFE 434
                                       ***************************************************9999998876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHCT CS
                      Peptidase_M1 157 iaYeKGasllrmlekllg 174
                                        ++eK  +++rml+k++ 
  gi|557694892|ref|YP_008797946.1| 619 GSFEKDTEVMRMLAKVVE 636
                                       4789999******99985 PP

>> HEAT_2  HEAT repeats
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   3.9e-12     1e-08       3      86 ..     533     617 ..     531     619 .. 0.92
   2 !   42.1   0.3   3.3e-14   8.5e-11       3      79 ..     597     676 ..     596     686 .. 0.88
   3 !   35.0   0.8   5.6e-12   1.4e-08       5      85 ..     698     779 ..     694     781 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.9e-12
                            HEAT_2   3 aLlqalendpdpevrraairaLgrignpealpaLvell.ededpavRraaaeaLgaigdpealpaLkellddddddv 78 
                                         l+ +e++ +   r++ i++L++ g +++++ L +++  d+ + v + aa+aLg+i+++ea +aL++ l+  +++ 
  gi|557694892|ref|YP_008797946.1| 533 EALSMVEKCGSVVCRIEMIDSLAKHGGRRVVEVLERVIsGDPFWGVSYRAAKALGEIKTEEAKAALLRVLQKVKHPK 609
                                       56777888899999************************889*******************************99**9 PP

                            HEAT_2  79 vReaAaea 86 
                                       +R+ ++ea
  gi|557694892|ref|YP_008797946.1| 610 IRRGIVEA 617
                                       99999887 PP

  == domain 2  score: 42.1 bits;  conditional E-value: 3.3e-14
                            HEAT_2   3 aLlqalendpdpevrraairaLgri.gnpealpaLvelled..edpavRraaaeaLgaigdpealpaLkellddddd 76 
                                       aLl +l++ ++p++rr +++a g++ +++e++++L +++ed  e+ +vR+aaa +Lg+++++ea+p+L ++ld +++
  gi|557694892|ref|YP_008797946.1| 597 ALLRVLQKVKHPKIRRGIVEARGSFeKDTEVMRMLAKVVEDtvESYYVRQAAAISLGRLKLDEAVPVLVKALDYPSH 673
                                       7999*******************997789**********9978899****************************998 PP

                            HEAT_2  77 dvv 79 
                                       + v
  gi|557694892|ref|YP_008797946.1| 674 AHV 676
                                       543 PP

  == domain 3  score: 35.0 bits;  conditional E-value: 5.6e-12
                            HEAT_2   5 lqalendpdpevrraairaLgrignp.ealpaLvellededpavRraaaeaLgaigdpealpaLkellddddddvvR 80 
                                        +++e++  + vr  a  aL+++ ++ e+  +L +l ed++++vR+a++ a+ ++ dp+ lp L +++  d +++vR
  gi|557694892|ref|YP_008797946.1| 698 SKRVEKSYPTPVRVSATVALAKFPEKhETYTLLERLSEDSNERVRHAVVAAARELMDPRLLPMLDKMAEKDLNERVR 774
                                       57788888899************88747888888888**************************************** PP

                            HEAT_2  81 eaAae 85 
                                       + A e
  gi|557694892|ref|YP_008797946.1| 775 RGARE 779
                                       99876 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 !   59.0   0.0   2.7e-19   6.9e-16       3     186 .]      31     192 ..      29     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 2.7e-19
                                       EEEEEEEEEETTTTEEEEEEEEEEEESS-ECEEEEEESSEEEECEEEEECTTCTCEEEEEEEECTTTTCEEEEECCE CS
                    Peptidase_M1_N   3 ehYdldlkidlkektfkGsvtitlqlkeatseivldakdlkiksvslsaevksesvkidfkieqkdeelltiklkes 79 
                                       +hY+l+lk+d++++ ++G ++i+l+ +   s   lda d++i  +++             k+ ++d++llt+ ++  
  gi|557694892|ref|YP_008797946.1|  31 NHYRLELKVDIEDRRVDGYAEIRLTSN--GSMAELDAVDFQI--LEVT----------GVKERDYDGKLLTLFFDG- 92 
                                       7************************99..677789*******..2222..........2346799***********. PP

                                       EETTCEEEEEEEEEEE-BSSSSEEEEEEEEETSCEEEEEEEE-TTTTGGGTS-B--STTSEBEEEEEEEEETTSEEE CS
                    Peptidase_M1_N  80 lqqtskytLeieyegelndklaGlykstYtdkgekkvvvvTqfeatdARsafPCfDePsvKAtftisikapkeetal 156
                                           ++  + i y++    +++G+   + ++kg   ++v+++ e+++ R+++P +D+P++K t ++ +++p++  ++
  gi|557694892|ref|YP_008797946.1|  93 ---AGEKVVGIRYRA---WPRTGVHFVE-KEKGYGFPFVWSHGEPEYHRNWMPIYDYPNMKFTTELLVTVPQPLEVV 162
                                       ...78899*******...7888887555.569********************************************* PP

                                       ESSECCCEEEETTCEEEEEEEEEESBEGGG CS
                    Peptidase_M1_N 157 SnmpeeeseklengqkiteFeqtpkmstYL 186
                                       Sn++  ++ ++++g ++++++   ++++YL
  gi|557694892|ref|YP_008797946.1| 163 SNGELLDRRNNADGTSTFHWQMDKPHPAYL 192
                                       *****************************8 PP

>> HEAT_PBS  PBS lyase HEAT-like repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.4   3.6e+03       4      24 ..     549     569 ..     547     571 .. 0.82
   2 !   19.1   0.3   5.4e-07    0.0014       3      26 ..     580     603 ..     578     604 .. 0.95
   3 !   20.4   0.3   2.2e-07   0.00055       1      26 [.     644     669 ..     644     670 .. 0.96
   4 ?   -3.3   0.0         7   1.8e+04       5      18 ..     681     694 ..     680     696 .. 0.78
   5 ?    2.9   0.0     0.089   2.3e+02       1      27 []     709     736 ..     709     736 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.4
                                       HHHHHHHHCTSGGGHHHHHHH CS
                          HEAT_PBS   4 aAakaLgqlgdeeaipaLlea 24 
                                       + + +L++ g  +++++L ++
  gi|557694892|ref|YP_008797946.1| 549 EMIDSLAKHGGRRVVEVLERV 569
                                       55678999*********9886 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 5.4e-07
                                       HHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   3 raAakaLgqlgdeeaipaLleaLq 26 
                                       ++AakaLg++++eea +aLl++Lq
  gi|557694892|ref|YP_008797946.1| 580 YRAAKALGEIKTEEAKAALLRVLQ 603
                                       89********************98 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHHCTSGGGHHHHHHHCT CS
                          HEAT_PBS   1 vRraAakaLgqlgdeeaipaLleaLq 26 
                                       vR aAa +Lg+l+ +ea+p+L++aL+
  gi|557694892|ref|YP_008797946.1| 644 VRQAAAISLGRLKLDEAVPVLVKALD 669
                                       8************************8 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 7
                                       HHHHHHHCTSGGGH CS
                          HEAT_PBS   5 AakaLgqlgdeeai 18 
                                       A+ +L++ g e ++
  gi|557694892|ref|YP_008797946.1| 681 AVQGLAETGLEKVY 694
                                       89999999987666 PP

  == domain 5  score: 2.9 bits;  conditional E-value: 0.089
                                       HHHHHHHHHHHCTS.GGGHHHHHHHCTC CS
                          HEAT_PBS   1 vRraAakaLgqlgd.eeaipaLleaLqd 27 
                                       vR +A+ aL+++    e + +L ++ +d
  gi|557694892|ref|YP_008797946.1| 709 VRVSATVALAKFPEkHETYTLLERLSED 736
                                       8***********9988888888877765 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.022        55      10      27 ..     572     589 ..     562     590 .. 0.83
   2 !    8.7   0.0   0.00088       2.3       2      27 ..     628     655 ..     627     656 .. 0.86
   3 !    7.2   0.1    0.0026       6.8       5      23 ..     729     748 ..     727     754 .. 0.77
   4 ?    1.6   0.0      0.17   4.5e+02       1      18 [.     757     775 ..     757     777 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.022
                                       T-SSHHHHHHHHHHHHHH CS
                              HEAT  10 sDpspeVReaAakaLgal 27 
                                        Dp + V + AakaLg++
  gi|557694892|ref|YP_008797946.1| 572 GDPFWGVSYRAAKALGEI 589
                                       89**************98 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00088
                                       HHHHHHHHT-..SSHHHHHHHHHHHHHH CS
                              HEAT   2 lPlllkllsD..pspeVReaAakaLgal 27 
                                       + +l k  +D  +s  VR+aAa +Lg+l
  gi|557694892|ref|YP_008797946.1| 628 MRMLAKVVEDtvESYYVRQAAAISLGRL 655
                                       66777878888899************97 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0026
                                       HHHHH.T-SSHHHHHHHHHH CS
                              HEAT   5 llkll.sDpspeVReaAaka 23 
                                       ll+ l +D++ +VR a++ a
  gi|557694892|ref|YP_008797946.1| 729 LLERLsEDSNERVRHAVVAA 748
                                       445555***********987 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.17
                                       HHHHHHHHH.T-SSHHHHH CS
                              HEAT   1 llPlllkll.sDpspeVRe 18 
                                       llP+l k+  +D + +VR+
  gi|557694892|ref|YP_008797946.1| 757 LLPMLDKMAeKDLNERVRR 775
                                       89******99*******97 PP

>> Vitellogenin_N  Lipoprotein amino terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.1    0.0014       3.6     516     592 ..     584     656 ..     580     677 .. 0.84
   2 !    8.0   0.1   0.00032      0.83     574     618 ..     703     746 ..     651     749 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0014
                                       HHHHHHT-GGGHHHHHTTSS----S-HHHHHHHHHTTTTGGGT-HHHHHHHHHHHHH-TTS-HHHHHHHHHHHHHT- CS
                    Vitellogenin_N 516 kaLgNlGhpeilkvlepylegkeevstfvRlaavlaLrnlakkaprkvrsvllriyentaekpevRvaAvlalmetk 592
                                       kaLg +++ e  + l + l +k ++  ++R  +v+a       ++ +v  +l +++e+t e + vR aA++ l + k
  gi|557694892|ref|YP_008797946.1| 584 KALGEIKTEEAKAALLRVL-QKVKH-PKIRRGIVEARG--SFEKDTEVMRMLAKVVEDTVESYYVRQAAAISLGRLK 656
                                       8999999999999999999.44444.468889999999..56678899**********************9997665 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00032
                                       TTS-HHHHHHHHHHHHHT---HHHHHHHHHHHTT-S-HHHHHHHH CS
                    Vitellogenin_N 574 taekpevRvaAvlalmetkPsaallqriaestnkdpskqVaafvk 618
                                       +  ++ vRv A +al ++ P+ +   ++ e +++d+++ V+ +v 
  gi|557694892|ref|YP_008797946.1| 703 KSYPTPVRVSATVALAKF-PEKHETYTLLERLSEDSNERVRHAVV 746
                                       567888************.**********************9996 PP

>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.9   3.6e-05     0.093      71     291 ..     540     797 ..     520     816 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
                            DUF445  71 klaewlknptnkeslaaiveellkeiledlddesikellkknlkkkleevipepllgkllellleeerhkkllddll 147
                                       k ++++ +++  +sla++  + + e+le++++ +    ++ ++ k l e+  e+ ++ l  ++l++ +h+k+   ++
  gi|557694892|ref|YP_008797946.1| 540 KCGSVVCRIEMIDSLAKHGGRRVVEVLERVISGDPFWGVSYRAAKALGEIKTEEAKAAL-LRVLQKVKHPKIRRGIV 615
                                       44555556666677777777777777777777777777777778999999999999998.56788999999999999 PP

                            DUF445 148 driknllkdeevkekikelidelieeesgklv...............................lesivsmflrelts 193
                                       +    + kd ev++ +++++++++e+++ + +                               ++ +     ++l++
  gi|557694892|ref|YP_008797946.1| 616 EARGSFEKDTEVMRMLAKVVEDTVESYYVRQAaaislgrlkldeavpvlvkaldypshahvipSGAVQGLAETGLEK 692
                                       99999999999999999999999999987777899999999888888888888888888777644444444444555 PP

                            DUF445 194 ilekvksdpdhllreeedkkvreliadllndpelaakveklkkkklsdlevqeyeea...lwealkdlllkdlneee 267
                                       ++e v + ++++     +   +  +a++ ++ e+ + +e+l ++  ++++ ++ + a   +  +l  +l k +++ +
  gi|557694892|ref|YP_008797946.1| 693 VYEHVSKRVEKSYPTPVRVSATVALAKFPEKHETYTLLERLSEDSNERVRHAVVAAArelMDPRLLPMLDKMAEK-D 768
                                       555555555555555555555555666666666666666666665555555555555554333333333333333.2 PP

                            DUF445 268 ..sllrerisklleklgeklaed...pkl 291
                                           +r+ + ++ +k+ ++l++    + l
  gi|557694892|ref|YP_008797946.1| 769 lnERVRRGAREVSKKIRDHLEKGveyKSL 797
                                       12233333333333333333333332333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (822 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      789  (0.0440069); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.79u 0.30s 00:00:01.09 Elapsed: 00:00:00.47
# Mc/sec: 5207.96
//
Query:       gi|557694893|ref|YP_008797947.1|  [L=132]
Description: signal-transduction protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-31  109.1   7.1    1.5e-16   60.5   1.5    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 !   52.0   0.4     4e-18   7.2e-14       1      55 [.      11      64 ..      11      66 .. 0.95
   2 !   60.5   1.5   8.6e-21   1.5e-16       1      53 [.      74     126 ..      74     129 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 4e-18
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      V++im+r+vvt++ d+ l++++e+m++++vs++ VV +dgk+ Givt++D +++ 
  gi|557694893|ref|YP_008797947.1| 11 VSEIMSRRVVTAKGDEKLSDIAEKMIQSKVSSVVVV-SDGKVAGIVTEKDFVKFF 64
                                      89*******************************778.9*************9986 PP

  == domain 2  score: 60.5 bits;  conditional E-value: 8.6e-21
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       ++d+mtr+v++v++d++l ea ++m+++++++lPVVd +++lvG++t rD+++
  gi|557694893|ref|YP_008797947.1|  74 ISDYMTREVIVVREDASLNEAKNIMVSNNIRHLPVVDRNNNLVGMITVRDIVE 126
                                       589************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 958.68
//
Query:       gi|557694894|ref|YP_008797948.1|  [L=264]
Description: 4-nitrophenyl phosphatase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-26   91.2   0.0    1.1e-25   89.6   0.0    1.8  2  Hydrolase_6      Haloacid dehalogenase-like hydrolase
    3.6e-18   65.4   0.1    1.6e-17   63.3   0.0    2.1  2  Hydrolase_like   HAD-hyrolase-like
    4.9e-13   49.8   2.0    1.8e-11   44.8   2.0    3.0  1  Hydrolase        haloacid dehalogenase-like hydrolase
    3.6e-12   46.7   0.2    1.2e-07   32.0   0.0    2.6  3  HAD_2            Haloacid dehalogenase-like hydrolase
    4.7e-05   23.1   0.0    0.00067   19.3   0.0    2.3  2  PGP_phosphatase  Mitochondrial PGP phosphatase
  ------ inclusion threshold ------
      0.033   13.1   0.0      0.049   12.6   0.0    1.2  1  Myotub-related   Myotubularin-like phosphatase domain


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 !   89.6   0.0   3.8e-29   1.1e-25       1     100 [.      11     109 ..      11     110 .. 0.97
   2 ?   -1.8   0.0       1.1   3.3e+03      15      30 ..     164     179 ..     160     212 .. 0.68

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 3.8e-29
                                       EEEESTTTSEETTEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT----GGGEEEHHHHHHHHHHHH CS
                       Hydrolase_6   1 flfDidGvLwrgdkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgvditeeqvvtsataaaeylkkr 77 
                                       +++D+dG+++ g+k++pga+ea+n+lr++  ++v++TNns+ ++ +y++kl+++g+++  ++++ts++ aa+y++++
  gi|557694894|ref|YP_008797948.1|  11 LVLDMDGTIYIGSKPLPGAPEAVNRLRKK-LKLVFMTNNSTLTRTQYLEKLNRMGIHAYVSEILTSGYLAARYVATE 86 
                                       589************************98.89********************************************* PP

                                       SXXXEEEEESXHHHHHHHHHTTX CS
                       Hydrolase_6  78 kadkkvlvigeeglreelkeagf 100
                                       +++  vlv+geeg+ +e+ + g+
  gi|557694894|ref|YP_008797948.1|  87 HPGAHVLVVGEEGISREALQLGL 109
                                       ***************99998886 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
                                       E-TTHHHHHHHHHHTT CS
                       Hydrolase_6  15 aipgaaealnalraag 30 
                                        +pga  ++ +l aa 
  gi|557694894|ref|YP_008797948.1| 164 FMPGAGSIIAMLSAAT 179
                                       6788888888887763 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.84   2.5e+03      10      28 ..      77      96 ..      74      98 .. 0.69
   2 !   63.3   0.0   5.5e-21   1.6e-17       2      74 ..     186     256 ..     185     257 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.84
                                      HHHHHHHH---.GGGEEEEE CS
                    Hydrolase_like 10 ydfalevlgsd.peevlmiG 28
                                      y +a+ v +++  ++vl++G
  gi|557694894|ref|YP_008797948.1| 77 YLAARYVATEHpGAHVLVVG 96
                                      67778887666255688888 PP

  == domain 2  score: 63.3 bits;  conditional E-value: 5.5e-21
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHHHHHT---SEEES CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepehkptyvaddlae 74 
                                       +gKP+p++  +ale lg++ +ev+++GDr++tD+a+A+++G++++LV+tG+++  +  ++  +++ v+d+l e
  gi|557694894|ref|YP_008797948.1| 186 VGKPSPISSQMALETLGLQASEVVFVGDRVDTDVAAARAVGARCILVKTGAFELFR--DKISEADMVVDSLVE 256
                                       49**************************************************9966..55689******9987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   2.0     6e-15   1.8e-11       1     210 []       8     226 ..       8     226 .. 0.68

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 6e-15
                                       SSEEEEESBTTTBCHH...HHHHHHHHHHCHHHHHHHHHH.........HHCHHHHHHHHHHHHH.......HHHH. CS
                                       xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxx.......xxxx. RF
                         Hydrolase   1 iktvvfDkdGTLttge...psvedvivsaalalaaaletg.........sehpigkalvaaakar.......sgal. 57 
                                       +k +v+D+dGT++ g+   p   ++++++ ++l+ ++ t           e+     +              sg l 
  gi|557694894|ref|YP_008797948.1|   8 VKGLVLDMDGTIYIGSkplPGAPEAVNRLRKKLKLVFMTNnstltrtqyLEKLNRMGIH-----AyvseiltSGYLa 79 
                                       6889************9999999999999777777777766666333332333333333.....2344335533333 PP

                                       HHHHHETTTE..HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHH CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  58 tgfatfigrg..ayaigkpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLka 132
                                       +++ + +  g  ++ +g++   ++           +   +    + ++   a  v++  d  + +++aa a ++++ 
  gi|557694894|ref|YP_008797948.1|  80 ARYVATEHPGahVLVVGEEGISREA---------LQLGLRIIDHSQWK--LAEYVVAGLDRGFTYQKAANASQAIR- 144
                                       4444423333635555555555555.........44444444444444..688888999***************99. PP

                                       TTEEEEEEESSEHHHHHHHHHH.TT.GGGE.SEEEEHHCES..STTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HH CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xx.xxxx.xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                         Hydrolase 133 agievvlltgdnpetaeraanq.lG.ddyf.daviasdiet..vakpspegkvaaireLqgkpeevamVGDgvn.Da 203
                                       +g + +    dn  + e+     +G   ++ +a  ++      v+kpsp   + a++ L+ + +ev++VGD+v  D+
  gi|557694894|ref|YP_008797948.1| 145 NGAKFIATNLDNIYPTEEGFMPgAGsIIAMlSAATGVK--PfsVGKPSPISSQMALETLGLQASEVVFVGDRVDtDV 219
                                       99966666679999999666666**4222224444444..266********************************** PP

                                       HHHHHTT CS
                                       xxxxxxx RF
                         Hydrolase 204 aalaaAg 210
                                       aa++a+g
  gi|557694894|ref|YP_008797948.1| 220 AAARAVG 226
                                       ****987 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.67     2e+03       2      10 ..      12      20 ..      11      21 .. 0.85
   2 !   11.6   0.0   7.4e-05      0.22      79     128 ..      24      75 ..      20      80 .. 0.88
   3 !   32.0   0.0     4e-11   1.2e-07     123     178 .]     176     232 ..     169     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.67
                             HAD_2  2 iFDlDgTll 10
                                      + D+DgT++
  gi|557694894|ref|YP_008797948.1| 12 VLDMDGTIY 20
                                      67*****96 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 7.4e-05
                             HAD_2  79 kpydgvkelLeeLkeagyklgivTsk...sreaveekleqlgiesyFdvivts 128
                                       kp++g+ e+++ L ++++kl  +T++   +r +  ekl+++gi+ y + i+ts
  gi|557694894|ref|YP_008797948.1|  24 KPLPGAPEAVNRL-RKKLKLVFMTNNstlTRTQYLEKLNRMGIHAYVSEILTS 75 
                                       89***********.99**********6555777788999999****9999987 PP

  == domain 3  score: 32.0 bits;  conditional E-value: 4e-11
                             HAD_2 123 dvivtsedvekkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                       +   + + ++  KP+p + + ale l+l+++ev++vGD   tD+ aa+++g ++i v
  gi|557694894|ref|YP_008797948.1| 176 SAATGVKPFSVGKPSPISSQMALETLGLQASEVVFVGDRVdTDVAAARAVGARCILV 232
                                       556677778889******************************************986 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.071   2.1e+02      39      54 ..       6      21 ..       2      65 .. 0.80
   2 !   19.3   0.0   2.2e-07   0.00067     135     166 ..     204     235 ..     171     237 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.071
                   PGP_phosphatase 39 ktikavvlDKDnclaa 54
                                      +++k++vlD D ++  
  gi|557694894|ref|YP_008797948.1|  6 EKVKGLVLDMDGTIYI 21
                                      689********99865 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.2e-07
                   PGP_phosphatase 135 eadeiavvgDRllTdvllanmmGslgvwlrdg 166
                                       +a+e+++vgDR+ Tdv +a+ +G+  ++++ g
  gi|557694894|ref|YP_008797948.1| 204 QASEVVFVGDRVDTDVAAARAVGARCILVKTG 235
                                       69**********************99999877 PP

>> Myotub-related  Myotubularin-like phosphatase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.6e-05     0.049     184     247 ..      39     104 ..      29     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                                       HHHHHH...TSS--HHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHCS-..--EEEE-SSSSSHHH CS
                    Myotub-related 184 klvealkdsekeasekkwlsaLekskWlkhiksiLeaaaliaksvelek..ssvLvhcsdGwDrts 247
                                       kl  ++ +++++ +++++l++L++++    +++iL++  l a+ v++e+  ++vLv +++G+ r +
  gi|557694894|ref|YP_008797948.1|  39 KLKLVFMTNNSTLTRTQYLEKLNRMGIHAYVSEILTSGYLAARYVATEHpgAHVLVVGEEGISREA 104
                                       444444444567899******************************9886337*********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 1874.56
//
Query:       gi|557694895|ref|YP_008797949.1|  [L=149]
Description: transcriptional regulator, lrp family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   67.5   0.0    1.6e-18   66.4   0.0    1.6  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    4.6e-14   51.7   0.8    2.5e-13   49.4   0.3    2.0  2  HTH_24           Winged helix-turn-helix DNA-binding
    5.5e-13   48.5   0.6    1.4e-12   47.2   0.4    1.8  2  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    1.4e-07   31.3   0.0    2.3e-07   30.6   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
    1.1e-06   28.3   0.0      2e-06   27.6   0.0    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
    6.8e-06   25.9   0.0    1.1e-05   25.3   0.0    1.5  1  HTH_43           Winged helix-turn helix
      5e-05   23.1   0.0    8.2e-05   22.4   0.0    1.3  1  MarR_2           MarR family
    0.00015   22.2   0.1    0.00031   21.2   0.1    1.4  1  Mga              Mga helix-turn-helix domain
    0.00018   21.5   0.0    0.00039   20.4   0.0    1.4  1  HTH_20           Helix-turn-helix domain
     0.0011   18.8   0.3     0.0096   15.8   0.1    2.2  2  MarR             MarR family
     0.0014   18.5   1.6     0.0015   18.5   0.3    1.8  2  HTH_11           HTH domain
     0.0017   18.1   0.0     0.0027   17.5   0.0    1.3  1  HTH_IclR         IclR helix-turn-helix domain
     0.0026   17.8   0.0     0.0047   17.0   0.0    1.4  1  HTH_28           Helix-turn-helix domain
     0.0051   16.9   0.2     0.0092   16.1   0.2    1.3  1  DUF2250          Uncharacterized protein conserved in archaea
     0.0068   16.8   0.7     0.0087   16.5   0.7    1.2  1  DUF1690          Protein of Unknown function (DUF1690)
  ------ inclusion threshold ------
      0.017   14.9   0.0       0.03   14.1   0.0    1.4  1  HTH_23           Homeodomain-like domain
      0.021   14.8   0.5      0.056   13.4   0.5    1.8  1  RHH_1            Ribbon-helix-helix protein, copG family
      0.026   14.2   0.2      0.037   13.7   0.2    1.4  1  DUF4423          Domain of unknown function (DUF4423)
      0.035   13.9   0.0      0.057   13.2   0.0    1.3  1  HTH_30           PucR C-terminal helix-turn-helix domain
      0.037   14.4   0.4      0.092   13.1   0.1    1.7  2  Rrf2             Transcriptional regulator
      0.048   13.6   0.1       0.14   12.1   0.0    1.8  2  HTH_36           Helix-turn-helix domain
      0.049   13.7   0.0      0.092   12.8   0.0    1.5  1  Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_Yhc
      0.079   12.5   0.2       0.16   11.5   0.2    1.5  1  Sigma70_r4       Sigma-70, region 4
       0.08   12.6   0.2      0.095   12.4   0.2    1.2  1  Stk19            Serine-threonine protein kinase 19
      0.095   12.4   0.1       0.22   11.2   0.1    1.6  1  GntR             Bacterial regulatory proteins, gntR family
        0.1   12.7   0.1       0.26   11.4   0.1    1.6  1  HTH_9            RNA polymerase III subunit RPC82 helix-turn-
       0.14   12.2   0.0       0.26   11.3   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
       0.15   11.9   0.2       0.36   10.7   0.1    1.6  2  RuvB_C           RuvB C-terminal winged helix domain


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 !   66.4   0.0   2.5e-21   1.6e-18       2      73 ..      72     142 ..      71     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 2.5e-21
                                       EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73 
                                       lvs ++g   + ++++e +a+lpeVve++++tG++d+++kv++++++++  ++++k++++pgv++t t + l
  gi|557694895|ref|YP_008797949.1|  72 LVSFQQGT-TSQKKLAEDIAKLPEVVEAHVITGEWDIIVKVRSESMQSIGSLVVDKIRNMPGVGKTITCVSL 142
                                       56666555.7899*****************************************************999987 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 !   49.4   0.3   3.9e-16   2.5e-13       1      48 []       5      52 ..       5      52 .. 0.99
   2 ?    0.4   0.0      0.75   4.8e+02      15      26 ..      77      88 ..      75      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 3.9e-16
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      ld++d+kILe+L +++  + + +A ++ ++++tv +r+krL++ G+Ik
  gi|557694895|ref|YP_008797949.1|  5 LDDKDLKILEELVEDAEQTVSAIAAKVKMPRTTVQERIKRLKQLGVIK 52
                                      79*********************************************8 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.75
                            HTH_24 15 nprisqreLAer 26
                                      ++ +sq+ LAe 
  gi|557694895|ref|YP_008797949.1| 77 QGTTSQKKLAED 88
                                      6789******95 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 !   47.2   0.4   2.2e-15   1.4e-12       1      42 []       5      46 ..       5      46 .. 0.98
   2 ?   -2.0   0.0         5   3.2e+03      15      26 ..      77      88 ..      76      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 2.2e-15
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      LD+ D+kILe+L eda  +++++A++v + ++tv++R++rL+
  gi|557694895|ref|YP_008797949.1|  5 LDDKDLKILEELVEDAEQTVSAIAAKVKMPRTTVQERIKRLK 46
                                      8***************************************96 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5
                     HTH_AsnC-type 15 daRisyaeLAer 26
                                      ++ +s ++LAe 
  gi|557694895|ref|YP_008797949.1| 77 QGTTSQKKLAED 88
                                      578999999985 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   3.6e-10   2.3e-07       6      55 ..       5      54 ..       2      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 3.6e-10
                                      HHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB  6 LseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      L + + k+   L++  + t++ ia +++ pr++v+e +++L++ G++++ 
  gi|557694895|ref|YP_008797949.1|  5 LDDKDLKILEELVEDAEQTVSAIAAKVKMPRTTVQERIKRLKQLGVIKKF 54
                                      78899*****************************************9986 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 !   27.6   0.0   3.1e-09     2e-06       5      47 .]      10      53 ..       6      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.1e-09
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      lkIL  L e  e++v+ +a+++++++ tv +  k+L+++G+++k
  gi|557694895|ref|YP_008797949.1| 10 LKILEELVEdAEQTVSAIAAKVKMPRTTVQERIKRLKQLGVIKK 53
                                      89*******9*******************************986 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.7e-08   1.1e-05      14      60 ..      15      61 ..      10      94 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.7e-08
                                      HHHHHS-B-HHHHHHHH---HHHHHHHHHGGGGGT-EEEEE--TTS- CS
                            HTH_43 14 ylideeeanvpklieltgmPRRtlqDtlkalaeldielefvqegern 60
                                       l++++e++v ++ ++++mPR t+q+ +k l++l++  +f+ +  ++
  gi|557694895|ref|YP_008797949.1| 15 ELVEDAEQTVSAIAAKVKMPRTTVQERIKRLKQLGVIKKFTVQLDHS 61
                                      589999******************************99998665554 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   1.3e-07   8.2e-05       9      53 ..      11      53 ..       5      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.3e-07
                                      HHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2  9 rvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                       +L +L    +   tv+++a++ ++++ +v+ ++krL + G + +
  gi|557694895|ref|YP_008797949.1| 11 KILEELVEDAE--QTVSAIAAKVKMPRTTVQERIKRLKQLGVIKK 53
                                      58899999998..8***************************9986 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   4.9e-07   0.00031      17      68 ..       8      61 ..       4      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 4.9e-07
                                      HHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHHH..CHCCT-EEETT CS
                               Mga 17 lkyqllkflfeeeevsieelaqelyiSestlkrkikelnkl..Lkefdleltkk 68
                                       ++++l+ l+e++e+++  +a+++ + ++t++  ik+l++l  +k+f  +l ++
  gi|557694895|ref|YP_008797949.1|  8 KDLKILEELVEDAEQTVSAIAAKVKMPRTTVQERIKRLKQLgvIKKFTVQLDHS 61
                                      6899***********************************955599999999554 PP

>> HTH_20  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     6e-07   0.00039      13      55 ..      10      52 ..       6      55 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6e-07
                                      HHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 13 rrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      ++il +L +++++t+s++a+ + ++++t+  +++ L + g ++
  gi|557694895|ref|YP_008797949.1| 10 LKILEELVEDAEQTVSAIAAKVKMPRTTVQERIKRLKQLGVIK 52
                                      68**********************************9999886 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   1.5e-05    0.0096       6      49 ..      10      53 ..       5      56 .. 0.93
   2 ?    0.5   0.0      0.89   5.7e+02      14      25 ..      76      87 ..      74      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      ++iL+ l e  +++vs +a k+++ ++tv + ++rL + G i++
  gi|557694895|ref|YP_008797949.1| 10 LKILEELVEDAEQTVSAIAAKVKMPRTTVQERIKRLKQLGVIKK 53
                                      789999**********************************9986 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.89
                                      HSTTEEHHHHHH CS
                              MarR 14 eqgplsvseLak 25
                                      +qg  s+++La+
  gi|557694895|ref|YP_008797949.1| 76 QQGTTSQKKLAE 87
                                      8999*******8 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   2.3e-06    0.0015       3      44 ..      10      50 ..       8      64 .. 0.87
   2 ?   -2.2   0.1       6.7   4.3e+03      13      24 ..      77      88 ..      76      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.3e-06
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      l+ile L e  ++ + + +A + ++ r+tv+ +Ik+L+ lgv
  gi|557694895|ref|YP_008797949.1| 10 LKILEELVEDAEQ-TVSAIAAKVKMPRTTVQERIKRLKQLGV 50
                                      699****999985.9**************************3 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 6.7
                            HTH_11 13 rgpisgeeLAee 24
                                      +g+ s ++LAe 
  gi|557694895|ref|YP_008797949.1| 77 QGTTSQKKLAED 88
                                      567899999996 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   0.0   4.3e-06    0.0027       6      49 ..      10      52 ..       7      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.3e-06
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      l iL+ l e ++  t+s +A++  +p++tv   ++ L +lG ++
  gi|557694895|ref|YP_008797949.1| 10 LKILEELVEDAEQ-TVSAIAAKVKMPRTTVQERIKRLKQLGVIK 52
                                      6677777777776.9**************************987 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   7.4e-06    0.0047       3      41 ..      10      50 ..      10      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 7.4e-06
                            HTH_28  3 leiikllaaGh..svreaArelgisrrtvyrWikryeegGi 41
                                      l+i+++l +    +v+++A+++ + r+tv+  ikr+ + G+
  gi|557694895|ref|YP_008797949.1| 10 LKILEELVEDAeqTVSAIAAKVKMPRTTVQERIKRLKQLGV 50
                                      6899999965336************************9995 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 !   16.1   0.2   1.4e-05    0.0092       5      56 ..       4      55 ..       2      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                           DUF2250  5 eedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                      e d+++lk+l+ l +        ia ++++p++ v+e +k+L++lG +++ +
  gi|557694895|ref|YP_008797949.1|  4 ELDDKDLKILEELVEDAEQTVSAIAAKVKMPRTTVQERIKRLKQLGVIKKFT 55
                                      56788999999999999999999*************************9976 PP

>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.7   1.4e-05    0.0087      13      94 ..      12      98 ..       7     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.4e-05
                           DUF1690 13 lvsqLessketdasraqalekliqerVaeeLkkLraeeeetlkkfeeklekellkde.......adakdelsskalnek 84
                                      ++++L + +e+++s   a  k+ +  V+e++k+L  ++  ++kkf  +l++++l +        + ++ ++s+k+l+e+
  gi|557694895|ref|YP_008797949.1| 12 ILEELVEDAEQTVSAIAAKVKMPRTTVQERIKRL--KQLGVIKKFTVQLDHSKLGKPatafvlvSFQQGTTSQKKLAED 88
                                      6788888888888888888888889999999999..8889**************99999****977899********** PP

                           DUF1690 85 ieeLrkklee 94
                                      i++L + +e+
  gi|557694895|ref|YP_008797949.1| 89 IAKLPEVVEA 98
                                      ****998876 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.7e-05      0.03      10      43 ..      12      47 ..      10      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-05
                            HTH_23 10 illllae..GlsvreIAreLgvsrrTvyrwlkryre 43
                                      il  l e   ++v++IA++  ++r Tv+  +kr ++
  gi|557694895|ref|YP_008797949.1| 12 ILEELVEdaEQTVSAIAAKVKMPRTTVQERIKRLKQ 47
                                      55555656789*****************88888655 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   0.5   8.8e-05     0.056       6      28 ..       5      27 ..       2      29 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.8e-05
                                      EEHHHHHHHHHHHHHHTSSHHHH CS
                             RHH_1  6 ldeellerLdelarrrgrSrSel 28
                                      ld+++l+ L+el+++ ++++S++
  gi|557694895|ref|YP_008797949.1|  5 LDDKDLKILEELVEDAEQTVSAI 27
                                      9********************98 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   5.8e-05     0.037      33      70 ..      18      53 ..      11      92 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.8e-05
                           DUF4423 33 kdfkadpeelakrlrpkisaeevekalefLlklgllkk 70
                                      +d++++++++a +++  ++   v++ +++L++lg++kk
  gi|557694895|ref|YP_008797949.1| 18 EDAEQTVSAIAAKVK--MPRTTVQERIKRLKQLGVIKK 53
                                      57789**********..*******************98 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 ?   13.2   0.0   8.9e-05     0.057      10      39 ..      19      48 ..      10      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-05
                                      HTTT-HHHHHHHHTS-HHHHHHHHHHHHHH CS
                            HTH_30 10 enggnisatAkaLhvHrnTlryRLrrieel 39
                                      ++ + +sa A++  + r T++ R++r+++l
  gi|557694895|ref|YP_008797949.1| 19 DAEQTVSAIAAKVKMPRTTVQERIKRLKQL 48
                                      566889*********************997 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   0.00014     0.092      22      56 ..      18      52 ..       8      55 .. 0.83
   2 ?   -2.0   0.0       7.3   4.7e+03      26      37 ..      80      91 ..      69     101 .. 0.52

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00014
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      e+   ++++ia++++++++ ++  +++L++ g++k
  gi|557694895|ref|YP_008797949.1| 18 EDAEQTVSAIAAKVKMPRTTVQERIKRLKQLGVIK 52
                                      444579***************************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7.3
                                      B-HHHHHHHHTS CS
                              Rrf2 26 vsseeiaerqni 37
                                       s +++ae    
  gi|557694895|ref|YP_008797949.1| 80 TSQKKLAEDIAK 91
                                      455555554433 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00022      0.14      27      55 .]      23      51 ..      11      51 .. 0.92
   2 ?   -1.9   0.0       5.4   3.5e+03      16      34 ..      74      88 ..      71      91 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00022
                            HTH_36 27 sqetlakrlglsknTvsraikeLeqlGyi 55
                                      +++ +a++ ++ + Tv+  ik L qlG i
  gi|557694895|ref|YP_008797949.1| 23 TVSAIAAKVKMPRTTVQERIKRLKQLGVI 51
                                      5788***********************76 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.4
                            HTH_36 16 sfanknggcfpsqetlakr 34
                                      sf  +++    sq+ la++
  gi|557694895|ref|YP_008797949.1| 74 SFQ-QGTT---SQKKLAED 88
                                      555.5555...78888876 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 ?   12.8   0.0   0.00014     0.092      61      95 ..      81     115 ..      59     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00014
                   Spore_YhcN_YlaJ  61 taqniaqrverlegVedarvlvtgndvlVavqtde 95 
                                         +++a+ +++l++V +a+v++ + d++V v+ ++
  gi|557694895|ref|YP_008797949.1|  81 SQKKLAEDIAKLPEVVEAHVITGEWDIIVKVRSES 115
                                       34579************************998764 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   0.00026      0.16       4      43 ..       4      44 ..       3      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00026
                                      HS-HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  4 sLpererevlelrf.geglTleEIgerlgiSrerVrqiekr 43
                                      +L++++ ++le    + ++T + I+++  ++r +V  ++kr
  gi|557694895|ref|YP_008797949.1|  4 ELDDKDLKILEELVeDAEQTVSAIAAKVKMPRTTVQERIKR 44
                                      699999999999888********************999998 PP

>> Stk19  Serine-threonine protein kinase 19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00015     0.095      35      89 ..      24      77 ..      20     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                             Stk19 35 vahlhsllaqsptkvereleelirkgklrklvingrgkdisklgevlvltedyek 89
                                      v+ + + ++  +t+v+ ++++l++ g+++k++++  ++++ k   + vl++  ++
  gi|557694895|ref|YP_008797949.1| 24 VSAIAAKVKMPRTTVQERIKRLKQLGVIKKFTVQLDHSKLGKPATAFVLVSF-QQ 77
                                      566677777889**********************999887765555555543.33 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00034      0.22      26      54 ..      23      51 ..      12      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00034
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 26 sereLaaefgVsrttvReALrrLeaeglv 54
                                      +++++aa+ +  rttv+e ++rL++ g++
  gi|557694895|ref|YP_008797949.1| 23 TVSAIAAKVKMPRTTVQERIKRLKQLGVI 51
                                      5799*********************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 ?   11.4   0.1    0.0004      0.26      17      53 ..      11      47 ..      10      54 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0004
                                      HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHH CS
                             HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksLvvLiq 53
                                      k+ e L++ + +t++ ++ k+k++++ V      L q
  gi|557694895|ref|YP_008797949.1| 11 KILEELVEDAEQTVSAIAAKVKMPRTTVQERIKRLKQ 47
                                      78999**********************9876655555 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 ?   11.3   0.0   0.00041      0.26      25      53 ..      25      53 ..       9      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00041
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisr 53
                                        +A+ + + r tv   +++Lk+ g+i++
  gi|557694895|ref|YP_008797949.1| 25 SAIAAKVKMPRTTVQERIKRLKQLGVIKK 53
                                      679999*********************94 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 ?   10.7   0.1   0.00056      0.36       4      44 ..       5      42 ..       3      54 .. 0.80
   2 ?   -2.5   0.0       7.4   4.7e+03      18      34 ..      74      90 ..      70     100 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00056
                                      --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTT CS
                            RuvB_C  4 LdeldikyLkllkekfkggpvglktlaailgeeketiedvi 44
                                      Ld++d k+L+ l    ++ +  ++++aa ++++++t+++ i
  gi|557694895|ref|YP_008797949.1|  5 LDDKDLKILEELV---EDAEQTVSAIAAKVKMPRTTVQERI 42
                                      5566666666665...899******************9987 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 7.4
                                      T.TT--B-HHHHHHHTT CS
                            RuvB_C 18 kfkggpvglktlaailg 34
                                      +f++g+++ k la+ + 
  gi|557694895|ref|YP_008797949.1| 74 SFQQGTTSQKKLAEDIA 90
                                      57888887777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1144  (0.0638072); expected 358.6 (0.02)
Passed bias filter:                      757  (0.0422221); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1080.98
//
Query:       gi|557694896|ref|YP_008797950.1|  [L=350]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   52.8   0.0    7.9e-14   51.6   0.0    1.7  1  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    1.4e-06   27.9   0.5    2.1e-06   27.3   0.5    1.3  1  Thiolase_N      Thiolase, N-terminal domain
    1.1e-05   25.2   1.7     0.0066   16.1   0.0    2.5  3  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
    0.00053   19.8   0.5     0.0014   18.4   0.5    1.7  1  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
      0.002   17.7   0.1       0.03   14.0   0.0    2.3  2  Thiolase_C      Thiolase, C-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 !   51.6   0.0   2.2e-17   7.9e-14       1      88 [.     223     310 ..     223     312 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 2.2e-17
                                       HHHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEE CS
                     ACP_syn_III_C   1 Lekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllv 75 
                                       Le++g+t +did++v+hq n ++  av k l +p ekv   +  d +Gnt aa +++ L++ ++    kpg++++++
  gi|557694896|ref|YP_008797950.1| 223 LEENGFTINDIDYFVFHQPNVKFPLAVSKILSIPVEKVKPGIvaDVVGNTYAACSMIGLAKVLD--IAKPGQRIVMT 297
                                       799*********************************8865444699******************..99********* PP

                                       EEETTTEEEEEEE CS
                     ACP_syn_III_C  76 gfGaGltwgaall 88 
                                       + G G    + +l
  gi|557694896|ref|YP_008797950.1| 298 SYGSGAGSDSFVL 310
                                       *****88777776 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.5   5.9e-10   2.1e-06      23     113 ..      53     143 ..      39     161 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 5.9e-10
                                       HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHH CS
                        Thiolase_N  23 aeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsi 99 
                                       +  ++aea++ +l++agv+p++v+ v+vG+  +  + +     +a  +g++++v++   + +c  g +a+ +++  +
  gi|557694896|ref|YP_008797950.1|  53 TITMAAEAARIALARAGVEPSKVQAVHVGTESKPYAVKPSGTLVAEILGVSRHVTTADFEFACKAGTEAMQMVTALV 129
                                       557899*****************************99999999********************************** PP

                                       HTTSHSEEEEEEEE CS
                        Thiolase_N 100 aageadvvvagGvE 113
                                        +g+++  +a+G+ 
  gi|557694896|ref|YP_008797950.1| 130 ETGRIEFGLAIGAD 143
                                       ************86 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 ?   -3.0   0.1       1.2   4.5e+03     260     278 ..     178     196 ..     171     197 .. 0.79
   2 !    8.1   0.1   0.00052       1.8      61      82 ..     224     245 ..     209     254 .. 0.80
   3 !   16.1   0.0   1.8e-06    0.0066     142     208 ..     258     319 ..     250     348 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                                       -TT-EEEEEE-TTS-EEEE CS
                    HMG_CoA_synt_C 260 aegtyyLeevDdkfRRsYa 278
                                          t y+++  d +RRsY+
  gi|557694896|ref|YP_008797950.1| 178 EYSTSYVSDTPDFWRRSYE 196
                                       5678899999999999997 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00052
                                       ------GGG-SEEEE--SSHHH CS
                    HMG_CoA_synt_C  61 adkeftlddfdyvifhsPfckl 82 
                                       +++ ft++d+dy +fh P  k+
  gi|557694896|ref|YP_008797950.1| 224 EENGFTINDIDYFVFHQPNVKF 245
                                       47889*************9985 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 1.8e-06
                                       HHTGGGGHHHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STT CS
                    HMG_CoA_synt_C 142 kkvkpsllvptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvsed 208
                                       +kvkp + v+  vGn Y a     la +l  ++     g+ri++ sYGsG  +  f l+v +  +e+
  gi|557694896|ref|YP_008797950.1| 258 EKVKPGI-VADVVGNTYAACSMIGLAKVLDIAK----PGQRIVMTSYGSGAGSDSFVLTVCDGIEEK 319
                                       5777765.56789*******999******4443....59******************9999877764 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 !   18.4   0.5   3.9e-07    0.0014       2      66 ..     110     171 ..     109     182 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.9e-07
                                       EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEESS CS
                       ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGDGAgAvvleasee 66 
                                       D++ aC++ + a+++++al+e+g+++  L iga+t      +   +  ++ + GA+A ++++++ 
  gi|557694896|ref|YP_008797950.1| 110 DFEFACKAGTEAMQMVTALVETGRIEFGLAIGADTAQG---RPGDALEYTAASGAAAYLIGRNGS 171
                                       8899*******************************777...555777888899999999998743 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1     0.084     3e+02       8      45 ..      42      78 ..      37      83 .. 0.82
   2 !   14.0   0.0   8.5e-06      0.03      26      70 ..     217     261 ..     201     310 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.084
                                      EEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEE CS
                        Thiolase_C  8 rsyaevgvdpeilglgPayaikkvlkkagltvedidlf 45
                                      ++ a++g d+++++++ a a++ +l +ag++ ++++++
  gi|557694896|ref|YP_008797950.1| 42 KEKAVAGLDEDTITMA-AEAARIALARAGVEPSKVQAV 78
                                      5667889999999887.6788999******99999876 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 8.5e-06
                                       HHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBS CS
                        Thiolase_C  26 yaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvN 70 
                                        a k +l+++g+t++did+f ++       Lav k l +  ekv 
  gi|557694896|ref|YP_008797950.1| 217 SALKTLLEENGFTINDIDYFVFHQPNVKFPLAVSKILSIPVEKVK 261
                                       68999*************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); 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 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2683.18
//
Query:       gi|557694897|ref|YP_008797951.1|  [L=384]
Description: acetyl-CoA C-acetyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   53.8   4.2    3.8e-14   52.7   4.2    1.6  1  Thiolase_N     Thiolase, N-terminal domain
    2.2e-07   30.6   0.9    6.2e-06   25.9   0.0    2.6  3  Thiolase_C     Thiolase, C-terminal domain
    0.00012   21.9   7.6    0.00038   20.3   0.3    2.9  3  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas
  ------ inclusion threshold ------
       0.03   13.9   4.2      0.035   13.7   2.9    1.8  2  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 !   52.7   4.2   8.4e-18   3.8e-14       2     259 ..       4     220 ..       3     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 8.4e-18
                                       EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT.TSTSC.HHHHHHHHTTS-TTS CS
                        Thiolase_N   2 vivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa.gegqn.iarqaalkagipeev 76 
                                       v+v+a  t++ +    + d   +eL aea  ++l++agv+  +vd v+v+n   +  ++q  i   +a ++gi + v
  gi|557694897|ref|YP_008797951.1|   4 VLVGAGLTKVEE----HWDKGLTELMAEASLQALDSAGVS--TVDAVYVSNAFGQvLQEQSnIGAYLAEELGI-RGV 73 
                                       678888888888....889999****************96..69999999988776555544***********.*** PP

                                       EEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT.TGGSSSSEEEEEHHHHHHTEETTTT CS
                        Thiolase_N  77 pavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr.sglklgdekakdllipdgladafne 152
                                        a++ +   +Sgl+av++a+ ++ +g ++ v+++G+E+ms+a+  + +++  ++ + ++  a +++           
  gi|557694897|ref|YP_008797951.1|  74 SASRFEAGGASGLAAVIAAVAAVSSGLYKSVLVVGGEKMSEATSEDFVSLLtTEESAESVAALGVTQ---------L 141
                                       ******************************************9988755431233333333333333.........3 PP

                                       SEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS CS
                        Thiolase_N 153 ehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLakl 229
                                         ++l  ++++k+  +  e+ + f v  h++++ a++a+ ++  i              + d+ ++s+v+a+++++l
  gi|557694897|ref|YP_008797951.1| 142 AEAALLYKEYLKRNRLEHEDVAYFSVLGHEHSQTAPHAQ-YQFRI--------------TLDNVVNSPVVADPIRRL 203
                                       4789***********************************.88888..............899*************** PP

                                       -BSSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 230 kpaFkkeGtvtAgnasqisDGaaavllmse 259
                                                +tA      +DGaaavl++s+
  gi|557694897|ref|YP_008797951.1| 204 --------ETTA-----PADGAAAVLIASR 220
                                       ........3444.....479*****99987 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1     0.025   1.1e+02      26      90 ..      27      89 ..      16     106 .. 0.72
   2 ?   -3.0   0.0       1.2   5.5e+03      27      46 ..     147     166 ..     132     168 .. 0.78
   3 !   25.9   0.0   1.4e-09   6.2e-06      25     120 ..     258     378 ..     248     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.025
                                      HHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT-.-GGGBSTT--HHHH-B-TTTHHHHHH CS
                        Thiolase_C 26 yaikkvlkkagltvedidlfEinEAFaaqaLavakaldl.dlekvNvnGGaialGHPlGasGaRiv 90
                                       a+ ++l+ ag++   +d++ +  AF  q+L+ + +++   +e + ++G + +     GasG   v
  gi|557694897|ref|YP_008797951.1| 27 EASLQALDSAGVS--TVDAVYVSNAFG-QVLQEQSNIGAyLAEELGIRGVSASRFEAGGASGLAAV 89
                                      5777899999965..6999999****6.66766666665145777777777666666666665555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                                       HHHHHHHHHT--GGGESEEE CS
                        Thiolase_C  27 aikkvlkkagltvedidlfE 46 
                                         k+ lk++ l+ ed+ +f 
  gi|557694897|ref|YP_008797951.1| 147 LYKEYLKRNRLEHEDVAYFS 166
                                       45788999999999998875 PP

  == domain 3  score: 25.9 bits;  conditional E-value: 1.4e-09
                                       HHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-TT CS
                        Thiolase_C  25 ayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPlG 83 
                                         a++++l+ ag +v+++d++E+++ ++  a  +++a++ ++                    vN  GG    G P+G
  gi|557694897|ref|YP_008797951.1| 258 SLASQRALELAGRKVSELDFLEVHDSYSLLAPLSLEAIGAAEagepchlarkgwwtlsgeMPVNTFGGLKGRGNPVG 334
                                       5799***********************************9999****************889*************** PP

                                       THHHHHHHHHHHHHHHC.......TTSEEEEEEEETTTEEEEEE CS
                        Thiolase_C  84 asGaRivvtllselkke.......ggklgvaalCigggqgvalv 120
                                       asG   +v    +l+ +       g+k+g+++  +g g  +a+v
  gi|557694897|ref|YP_008797951.1| 335 ASGLYALVESYLQLTGRagknqvdGAKVGMVSSMAGLGSLAAAV 378
                                       ****9999999988765111111145677777666666544443 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   0.3   8.4e-08   0.00038       6      41 ..      81     116 ..      78     126 .. 0.88
   2 !    5.4   0.1    0.0037        17      42      65 ..     198     221 ..     190     237 .. 0.77
   3 ?   -2.7   0.4       1.2   5.4e+03      52      63 ..     371     382 ..     360     382 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8.4e-08
                                       GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS CS
                       ACP_syn_III   6 aCsgfvyalsvAdaliesgaakrvLvigaetlskil 41 
                                       + ++ ++a+  A a+++sg +k vLv+g+e++s+ +
  gi|557694897|ref|YP_008797951.1|  81 GGASGLAAVIAAVAAVSSGLYKSVLVVGGEKMSEAT 116
                                       5678899**************************865 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0037
                                       -TTTHHHHTTB-EEEEEEEEEEES CS
                       ACP_syn_III  42 DwkdrstavlfGDGAgAvvlease 65 
                                       D+ +r   +  +DGA+Av++   e
  gi|557694897|ref|YP_008797951.1| 198 DPIRRLETTAPADGAAAVLIASRE 221
                                       555666667789*******98864 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.2
                                       B-EEEEEEEEEE CS
                       ACP_syn_III  52 fGDGAgAvvlea 63 
                                       +G  A+Avv+ea
  gi|557694897|ref|YP_008797951.1| 371 LGSLAAAVVVEA 382
                                       566699999986 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 ?   13.7   2.9   7.8e-06     0.035     127     208 ..      28     115 ..       3     135 .. 0.73
   2 ?   -2.5   0.0      0.67     3e+03     238     253 .]     208     223 ..     205     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.8e-06
                                       HHHHHHHHHTT....GGGSCTTHHHH..HSTTHHHHHHHHHHT--SSEEE.EESGGGHHHHHHHHHHHHHHTTS-SE CS
                     ketoacyl-synt 127 aalaaldedgs....evkaspkavga..vlanviagrisyalglrGpsvt.vdtACsSslvavhaavqslrsgeadv 196
                                       a l+ald++g+     v +s  a g     ++ i + ++ +lg+rG+s +  ++  +S+l+av aav ++ sg  + 
  gi|557694897|ref|YP_008797951.1|  28 ASLQALDSAGVstvdAVYVSN-AFGQvlQEQSNIGAYLAEELGIRGVSASrFEAGGASGLAAVIAAVAAVSSGLYKS 103
                                       556666666665433222222.33333446788999***********987589************************ PP

                                       EEEEEEE---SH CS
                     ketoacyl-synt 197 alaGGvellltp 208
                                       +l+ G e + ++
  gi|557694897|ref|YP_008797951.1| 104 VLVVGGEKMSEA 115
                                       ****99977654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.67
                                       BB-EEEEEEEEECHHH CS
                     ketoacyl-synt 238 lGEGvGavvLkrleda 253
                                       +++G++av++ ++e+a
  gi|557694897|ref|YP_008797951.1| 208 PADGAAAVLIASRETA 223
                                       79*******9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3112.08
//
Query:       gi|557694898|ref|YP_008797952.1|  [L=140]
Description: nucleic-acid-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   61.9   0.5    6.4e-17   61.3   0.5    1.2  1  OB_aCoA_assoc   DUF35 OB-fold domain, acyl-CoA-associated
    5.9e-05   22.8   2.8    0.00012   21.9   2.8    1.5  1  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
     0.0018   18.3   0.2     0.0029   17.6   0.2    1.3  1  DZR             Double zinc ribbon
     0.0026   17.8   1.7     0.0063   16.6   1.7    1.6  1  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.027   14.2   0.1      0.037   13.7   0.1    1.2  1  TackOD1         Thaumarchaeal output domain 1
      0.069   12.7   0.3        1.7    8.2   0.0    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.18   11.9   2.1       0.35   11.0   2.1    1.4  1  UPF0547         Uncharacterised protein family UPF0547
       0.28   11.2   1.3       0.47   10.5   0.6    1.6  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.35   10.3   3.4       0.81    9.2   3.4    1.6  1  zf-ribbon_3     zinc-ribbon domain
        0.8    9.5   4.4        1.8    8.4   4.4    1.6  1  zinc_ribbon_2   zinc-ribbon domain
        2.2    8.3   7.1        5.8    6.9   1.0    2.5  2  Nudix_N_2       Nudix N-terminal
        3.3    7.5   9.2         12    5.7   0.7    2.0  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
        3.6    7.7   5.6        5.9    7.0   0.3    2.3  2  YhfH            YhfH-like protein


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 !   61.3   0.5   4.6e-20   6.4e-17       3      64 ..      57     118 ..      56     119 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 4.6e-20
                                       EE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE- CS
                     OB_aCoA_assoc   3 elsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravf 64 
                                       +l+grG++  ftvv+++ +gf++++Pyvv+ Ve+ +g +i++++++++p e+ +Gm V+ v+
  gi|557694898|ref|YP_008797952.1|  57 RLAGRGKLRHFTVVYQPQTGFEKTVPYVVAWVEMSDGTQIIGQVTDCEPSELSVGMDVETVV 118
                                       589********************************************************886 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 !   21.9   2.8   8.5e-08   0.00012       7      37 .]      24      54 ..      19      54 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 8.5e-08
                           DUF35_N  7 grLvgqrCpdCGtvqfPPravCphCgsddle 37
                                      +rL g rC+ CG++   +r +C++Cgs+ le
  gi|557694898|ref|YP_008797952.1| 24 YRLEGNRCTQCGHFNPLARKICRKCGSRRLE 54
                                      8**************9999********9987 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.2   2.1e-06    0.0029       1      21 [.      31      51 ..      16      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.1e-06
                               DZR  1 CpqCgeelppdarfCseCgtk 21
                                      C qCg+ +p   + C +Cg++
  gi|557694898|ref|YP_008797952.1| 31 CTQCGHFNPLARKICRKCGSR 51
                                      888888888888888888875 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.7   4.5e-06    0.0063       7      38 ..      30      55 ..      22      56 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.5e-06
                       Zn-ribbon_8  7 rCeeCghefevlqsisdapltaCPeCgs.evrr 38
                                      rC++Cg  f++l+       + C +Cgs +++r
  gi|557694898|ref|YP_008797952.1| 30 RCTQCG-HFNPLA------RKICRKCGSrRLER 55
                                      4*****.*****9......456******99998 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   2.7e-05     0.037      75     102 ..      30      57 ..      24      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-05
                           TackOD1  75 lCpsCksghlnvrevCpkCkSidieeqe 102
                                        C++C + +   r++C+kC+S ++e++ 
  gi|557694898|ref|YP_008797952.1|  30 RCTQCGHFNPLARKICRKCGSRRLERDR 57 
                                       7**********************99876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.11   1.5e+02      21      26 ..      30      35 ..      24      37 .. 0.82
   2 ?    8.2   0.0    0.0012       1.7       2      17 ..      44      61 ..      44      65 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                                      EESSSS CS
                      TF_Zn_Ribbon 21 vCtdCG 26
                                      +Ct CG
  gi|557694898|ref|YP_008797952.1| 30 RCTQCG 35
                                      7****9 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
                                      EETTTTCEECHEE..TST CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveD..per 17
                                      +C +Cgs++l++D  + r
  gi|557694898|ref|YP_008797952.1| 44 ICRKCGSRRLERDrlAGR 61
                                      5***********955555 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.1   0.00025      0.35       2      21 ..      30      49 ..      30      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                           UPF0547  2 vCPeCeakvPvaaqfCphCG 21
                                      +C +C ++ P+a ++C+ CG
  gi|557694898|ref|YP_008797952.1| 30 RCTQCGHFNPLARKICRKCG 49
                                      599****************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 ?   10.5   0.6   0.00034      0.47      72      98 ..      30      54 ..      26      62 .. 0.83
   2 ?   -2.1   0.0       2.7   3.7e+03      33      47 ..      97     111 ..      89     126 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00034
                                      EETTTS-EEECHHHHHS-TTTSSS-EE CS
                              HypA 72 rCreCgkefeleekalrCpkCgsadve 98
                                      rC++Cg+   l++k   C kCgs+++e
  gi|557694898|ref|YP_008797952.1| 30 RCTQCGHFNPLARK--ICRKCGSRRLE 54
                                      8*****77778855..7******9876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.7
                                       EETTCT--HHHHHHH CS
                              HypA  33 vGelsgvepeaLefa 47 
                                       +G+++  ep+ L+  
  gi|557694898|ref|YP_008797952.1|  97 IGQVTDCEPSELSVG 111
                                       455555555555443 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   3.4   0.00059      0.81       3      24 ..      29      50 ..      27      51 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00059
                       zf-ribbon_3  3 vrCPnCGa.plssddnvCpyCGt 24
                                      +rC +CG+ +     ++C +CG+
  gi|557694898|ref|YP_008797952.1| 29 NRCTQCGHfN-PLARKICRKCGS 50
                                      69******77.666689*****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 ?    8.4   4.4    0.0013       1.8       1      21 [.      30      50 ..      30      51 .. 0.95

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0013
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGt 21
                                      +C++CG+ ++   k C +CG+
  gi|557694898|ref|YP_008797952.1| 30 RCTQCGHFNPLARKICRKCGS 50
                                      6*******************6 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   4.2      0.13   1.8e+02       3       8 ..      31      36 ..      29      50 .. 0.47
   2 ?    6.9   1.0    0.0042       5.8       3      23 ..      45      66 ..      43      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.13
                                      -TTT-- CS
                         Nudix_N_2  3 CsqCGt 8 
                                      C+qCG+
  gi|557694898|ref|YP_008797952.1| 31 CTQCGH 36
                                      555555 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0042
                                      -TTT--B.-EEE--TT-SS-EE CS
                         Nudix_N_2  3 CsqCGtp.velripdgDnreRl 23
                                      C++CG++ +e+   +g  + R+
  gi|557694898|ref|YP_008797952.1| 45 CRKCGSRrLERDRLAGRGKLRH 66
                                      ******9999999999888887 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 ?    5.7   0.7    0.0086        12      19      25 ..      30      36 ..      25      37 .. 0.92
   2 ?    5.5   9.2    0.0099        14       3      27 ..      31      52 ..      29      57 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0086
                                      --SSS-- CS
                    DNA_RNApol_7kD 19 RCkeCGh 25
                                      RC++CGh
  gi|557694898|ref|YP_008797952.1| 30 RCTQCGH 36
                                      9*****9 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0099
                                      -SSS--B----SSS----SSS---- CS
                    DNA_RNApol_7kD  3 CgeCgaevslkkgdpiRCkeCGhRi 27
                                      C +Cg+ + l ++    C++CG+R 
  gi|557694898|ref|YP_008797952.1| 31 CTQCGHFNPLARK---ICRKCGSRR 52
                                      *************...9******95 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.9     0.071        98      13      20 ..      28      35 ..      23      37 .. 0.76
   2 ?    7.0   0.3    0.0043       5.9       8      21 ..      37      50 ..      36      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.071
                              YhfH 13 kKkCteCG 20
                                         Ct+CG
  gi|557694898|ref|YP_008797952.1| 28 GNRCTQCG 35
                                      55799999 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0043
                              YhfH  8 frnLPkKkCteCGk 21
                                      f+ L  K C +CG+
  gi|557694898|ref|YP_008797952.1| 37 FNPLARKICRKCGS 50
                                      677999*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1173.06
//
Query:       gi|557694899|ref|YP_008797953.1|  [L=264]
Description: hypothetical protein CSUB_C1472 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   7.2     0.0084   16.0   6.1    2.2  2  ATP-synt_D     ATP synthase subunit D
  ------ inclusion threshold ------
      0.014   15.9   0.5       0.11   13.0   0.1    2.4  2  NPV_P10        Nucleopolyhedrovirus P10 protein
      0.016   14.0   1.5      0.021   13.7   1.2    1.4  1  Fmp27_WPPW     RNA pol II promoter Fmp27 protein domain
       0.02   15.1   1.4       0.15   12.3   0.1    2.3  2  Fib_alpha      Fibrinogen alpha/beta chain family
      0.029   14.4   1.4       0.29   11.2   0.5    2.8  2  DUF1664        Protein of unknown function (DUF1664)
      0.054   13.6   4.5      0.085   13.0   0.8    2.8  3  Med9           RNA polymerase II transcription mediator compl
      0.087   13.1   7.6        0.1   12.9   4.8    2.4  2  THOC7          Tho complex subunit 7
       0.12   12.2   3.2        3.4    7.5   0.3    2.4  2  STAT_alpha     STAT protein, all-alpha domain
       0.15   12.6   2.1       0.89   10.2   1.9    2.5  1  Syntaxin-6_N   Syntaxin 6, N-terminal
       0.21   11.4   6.0       0.07   12.9   1.9    2.0  2  T6SS_VipA      Type VI secretion system, VipA, VC_A0107 or Hc
       0.31   10.6   6.7       0.48   10.0   5.8    1.8  1  HAUS-augmin3   HAUS augmin-like complex subunit 3
       0.35   11.0   8.3        3.9    7.6   0.4    3.5  3  Cep57_CLD_2    Centrosome localisation domain of PPC89
       0.42   11.1  11.9      0.095   13.2   6.6    2.2  3  FlgN           FlgN protein
       0.75    9.6  11.0         37    4.1  11.0    2.8  1  FTA4           Kinetochore complex Fta4 of Sim4 subunit, or C
       0.99    7.9  11.4       0.67    8.5   3.0    2.1  2  FapA           Flagellar Assembly Protein A
          1    9.5  10.7       0.27   11.4   3.8    2.3  2  CENP-Q         CENP-Q, a CENPA-CAD centromere complex subunit
        1.3    9.8   4.7        2.8    8.7   0.6    3.0  2  Occludin_ELL   Occludin homology domain
        1.7    8.9  13.9      0.036   14.3   2.7    2.8  3  Cortex-I_coil  Cortexillin I, coiled coil
          2    8.8   6.1         19    5.7   0.1    3.2  3  kleA_kleC      Uncharacterized KorC regulated protein A
        3.4    6.7   6.4        4.8    6.2   6.4    1.2  1  Atg14          Vacuolar sorting 38 and autophagy-related subu
        3.4    8.1   9.2       0.23   11.9   0.7    3.2  3  FlaC_arch      Flagella accessory protein C (FlaC)


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 ?    1.8   0.0      0.22   1.9e+02     117     145 ..      54      82 ..      24      84 .. 0.81
   2 !   16.0   6.1   9.9e-06    0.0084      10     153 ..      94     221 ..      86     223 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.22
                                       TCHHHHHHHHCHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 117 gaqldeavealrellellvelasletsle 145
                                       g +ldea + + el++++ +l  l ++++
  gi|557694899|ref|YP_008797953.1|  54 GDELDEALKMYDELMREIERLRGLDRNFM 82 
                                       6699***********99999998888876 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 9.9e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-..TSS-SEEE CS
                        ATP-synt_D  10 klaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvklakvvkvelk 86 
                                       +l+++++s L +Kr+aL+ +  e+l++lk ++e l+ e+ ++++ l      +++ +++          + +++e  
  gi|557694899|ref|YP_008797953.1|  94 QLVRNILSRLAEKRNALLEKSGEVLERLKAAKEALGSEFAQVEEELI-----WSSIELN----------T-MQLEKD 154
                                       67899999**************************************9.....4222333..........3.666666 PP

                                       EEEBTTSEEEEEEE-...S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  87 tenvaGVkvpvfeleee.ksdstelygllrtgaqldeavealrellellvelasletslelLdeeikk 153
                                       +++  GV + + ele +  + +++l++l +  ++++e+v++l++l ++++++   ++   +L eeikk
  gi|557694899|ref|YP_008797953.1| 155 SDSGRGVGIRE-ELEAKiPELRKKLASLRNRLKMVEEMVKQLSDLPRNIADITTNKEEPAKLFEEIKK 221
                                       66666666666.4444444445689*****************************************98 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.4   1.2e+03      13      46 ..      41      73 ..      35      79 .. 0.66
   2 ?   13.0   0.1   0.00013      0.11      15      57 ..     166     208 ..     163     249 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.4
                           NPV_P10 13 ikavddkVdalqqqv.ddvqenlpdvtelnekLda 46
                                      +k v++ V   qq v d+++e l+  +el  ++++
  gi|557694899|ref|YP_008797953.1| 41 VKPVEEAV--TQQPVgDELDEALKMYDELMREIER 73
                                      55555555..4666667777777777777776665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00013
                           NPV_P10  15 avddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletk 57 
                                       +++ k+  l ++++++++ l+ v+e+ ++L +++ ++a++ t+
  gi|557694899|ref|YP_008797953.1| 166 ELEAKIPELRKKLASLRNRLKMVEEMVKQLSDLPRNIADITTN 208
                                       6889**********************************99983 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 ?   13.7   1.2   2.5e-05     0.021     186     247 ..     138     206 ..      94     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.5e-05
                        Fmp27_WPPW 186 qiekleekleelelkseke.......deelkeeieelekeikelkeklefletlledlkeseesseeee 247
                                       ++   + +l++++l++ ++       +eel+++i el+k++++l+++l+++e+++++l+   ++ ++ +
  gi|557694899|ref|YP_008797953.1| 138 ELIWSSIELNTMQLEKDSDsgrgvgiREELEAKIPELRKKLASLRNRLKMVEEMVKQLSDLPRNIADIT 206
                                       444444555555555555556677999*******************************99887444222 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 ?    1.4   0.1      0.38   3.2e+02      72     122 ..      42      92 ..      31     102 .. 0.66
   2 ?   12.3   0.1   0.00017      0.15      21      77 ..     162     218 ..     159     249 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.38
                                       HHHHHHHHHH.HHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  72 kkdndnvikk.sskeleeeilrlketidaqesnirvLqnvlesneqkiqkLe 122
                                       k+ ++ v+++ + +el+ e l++ +++ ++++++r L  ++     k+++L+
  gi|557694899|ref|YP_008797953.1|  42 KPVEEAVTQQpVGDELD-EALKMYDELMREIERLRGLDRNFMLYCIKMEELR 92 
                                       33334444443678888.7777778888888888888888877777777776 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00017
                                       HHHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  21 glqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndn 77 
                                       g+++ l+ + ++++k+l++l+n+l+ ++++ k+ ++l ++i d++++k++ +k  ++
  gi|557694899|ref|YP_008797953.1| 162 GIREELEAKIPELRKKLASLRNRLKMVEEMVKQLSDLPRNIADITTNKEEPAKLFEE 218
                                       566777777778888888888888888888888888888888888888777664344 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.5   1.3e+03      71      93 ..      53      75 ..      37     105 .. 0.75
   2 ?   11.2   0.5   0.00035      0.29      40     114 ..     122     196 ..     101     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.5
                           DUF1664 71 vdkkldeqkeiskeikeevtevr 93
                                      v+++lde  ++  e+ +e++++r
  gi|557694899|ref|YP_008797953.1| 53 VGDELDEALKMYDELMREIERLR 75
                                      66667777777777766666665 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00035
                           DUF1664  40 sdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       + a e ++++  qv e+l     +L+    + d+       i +e+++++ e+r++l+++++ ++ v+e+v++l 
  gi|557694899|ref|YP_008797953.1| 122 KAAKEALGSEFAQVEEELIWSSIELNTMQLEKDSDSGRGVGIREELEAKIPELRKKLASLRNRLKMVEEMVKQLS 196
                                       566666677777777777777777766555556666677789999***************************996 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 ?   -0.8   0.1       1.9   1.6e+03      42      67 ..      71      96 ..      61     113 .. 0.68
   2 ?    0.7   0.1      0.69   5.9e+02      22      42 ..     108     128 ..      82     136 .. 0.74
   3 ?   13.0   0.8    0.0001     0.085      22      71 ..     165     214 ..     147     223 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.9
                              Med9 42 irelpgidrsveeqeaeieeleeqla 67
                                      i+ l g+dr+ +    ++eel+ ql 
  gi|557694899|ref|YP_008797953.1| 71 IERLRGLDRNFMLYCIKMEELRPQLV 96
                                      55666666666666666666666654 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.69
                              Med9  22 kdletktgelrhkLkkareli 42 
                                       + l  k ge+  +Lk a+e++
  gi|557694899|ref|YP_008797953.1| 108 NALLEKSGEVLERLKAAKEAL 128
                                       566677778888888888876 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 0.0001
                              Med9  22 kdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKre 71 
                                       ++le+k+ elr+kL + r+ ++ ++++ +   +  + i++   + +   +
  gi|557694899|ref|YP_008797953.1| 165 EELEAKIPELRKKLASLRNRLKMVEEMVKQLSDLPRNIADITTNKEEPAK 214
                                       46677777777777777777777777766666666666665555554444 PP

>> THOC7  Tho complex subunit 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.8   1.5e+03     109     122 ..      62      75 ..      56      82 .. 0.79
   2 ?   12.9   4.8   0.00012       0.1      17     122 ..     101     209 ..      94     222 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.8
                             THOC7 109 keydelaekItsnp 122
                                       k ydel+++I++ +
  gi|557694899|ref|YP_008797953.1|  62 KMYDELMREIERLR 75 
                                       56999999998876 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 0.00012
                             THOC7  17 krltkrllklltslaesteeeleqlkedllldfaafelsierlqllakanerere....ryeaekeeieseieavre 89 
                                       +rl+++ ++ll+ +  +  e+l+++ke+l  +fa+ e ++  +   +++++ e++    r    +ee+e++i+++r+
  gi|557694899|ref|YP_008797953.1| 101 SRLAEKRNALLEKS-GEVLERLKAAKEALGSEFAQVEEELIWSSIELNTMQLEKDsdsgRGVGIREELEAKIPELRK 176
                                       55666666655554.77799*********************887777777777762222455689************ PP

                             THOC7  90 eieelkaqLeearatranrkeydelaekItsnp 122
                                       + ++l+++L+   ++ ++     +    It+n+
  gi|557694899|ref|YP_008797953.1| 177 KLASLRNRLKMVEEMVKQLSDLPRNIADITTNK 209
                                       **********99999888666666666666665 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 ?    7.5   0.3     0.004       3.4      59      93 ..      94     128 ..      50     134 .. 0.87
   2 ?    5.2   0.2     0.021        18       3      28 ..     173     198 ..     166     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.004
                        STAT_alpha  59 ellqqmlnaLdqkRkelvdklkellnlleslqekl 93 
                                       +l+++ l++L +kR++l++k  e+l++l+   e l
  gi|557694899|ref|YP_008797953.1|  94 QLVRNILSRLAEKRNALLEKSGEVLERLKAAKEAL 128
                                       677889999******************99877765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.021
                        STAT_alpha   3 eieqrleelrskvqeteqdirkLede 28 
                                       e++++l+ lr++ +++e+ +++L d+
  gi|557694899|ref|YP_008797953.1| 173 ELRKKLASLRNRLKMVEEMVKQLSDL 198
                                       67888888888888888888888765 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 ?   10.2   1.9     0.001      0.89      34      73 ..     153     201 ..      47     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.001
                      Syntaxin-6_N  34 s.........tseeldetrteLrkalrsiewdledLeetvriveknpsk 73 
                                       +          +eel+    eLrk+l s+++ l+  ee v+ ++  p++
  gi|557694899|ref|YP_008797953.1| 153 KdsdsgrgvgIREELEAKIPELRKKLASLRNRLKMVEEMVKQLSDLPRN 201
                                       02334456678999**************************888775554 PP

>> T6SS_VipA  Type VI secretion system, VipA, VC_A0107 or Hcp2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.91   7.7e+02      94     125 ..      87     115 ..      42     134 .. 0.71
   2 ?   12.9   1.9   8.2e-05      0.07     103     154 ..     167     219 ..     165     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.91
                                       SGGGGSHHHHHCC-HHHHHHHHHHHHHHHHHT CS
                         T6SS_VipA  94 slkDFsPeavaeqvpeLkkLlelReaLadLks 125
                                       ++++++P+  ++++  L++L e R+aL +  +
  gi|557694899|ref|YP_008797953.1|  87 KMEELRPQL-VRNI--LSRLAEKRNALLEKSG 115
                                       566666643.3433..6677777777765544 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 8.2e-05
                                       HHCC-HHHH.HHHHHHHHHHHHHTTTTTXTTHHHHHHHHHHXXHHHHHHHXXX CS
                         T6SS_VipA 103 vaeqvpeLk.kLlelReaLadLkskldnkekleklleevlkdeellekLakel 154
                                       +  ++peL+ kL +lR++L+  ++ +++ ++l ++++++ +++e+ +kL +e+
  gi|557694899|ref|YP_008797953.1| 167 LEAKIPELRkKLASLRNRLKMVEEMVKQLSDLPRNIADITTNKEEPAKLFEEI 219
                                       56799***736999***********************************9987 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 ?   10.0   5.8   0.00056      0.48      30     162 ..      61     207 ..      57     236 .. 0.47

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00056
                      HAUS-augmin3  30 lqayeeLkksGkpiLegeaLeeaLktie.........psdlkq..........edvellevileeeeesleaLeqel 87 
                                       l+ y+eL+++ +  L g ++++ L  i+              +             e++ + le +++++eaL +e+
  gi|557694899|ref|YP_008797953.1|  61 LKMYDELMREIE-RLRGLDRNFMLYCIKmeelrpqlvR----NilsrlaekrnALLEKSGEVLERLKAAKEALGSEF 132
                                       556666666666.6666666666666665333322221....12221111111222333334444444444444444 PP

                      HAUS-augmin3  88 qeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelraenaetnavLqqlteeakqlaeyfe 162
                                        + ++e      +ln +q+   s + +     ee +++  +l++  ++lr + +++++  +ql++  +++a   +
  gi|557694899|ref|YP_008797953.1| 133 AQVEEELIWSSIELNTMQLEKDSDSGRGVGIREELEAKIPELRKKLASLRNRLKMVEEMVKQLSDLPRNIADITT 207
                                       444444444444444444444444444444444444444444444444444444444444444444444444444 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 ?    4.5   0.1     0.042        36      40      59 ..      57      76 ..      55      80 .. 0.90
   2 ?    1.9   0.2      0.29   2.5e+02       1      37 [.     121     157 ..     118     159 .. 0.84
   3 ?    7.6   0.4    0.0046       3.9       1      30 [.     167     196 ..     167     202 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.042
                       Cep57_CLD_2 40 LgvAyeelneLkaevealrk 59
                                      L +A+   +eL++e e+lr+
  gi|557694899|ref|YP_008797953.1| 57 LDEALKMYDELMREIERLRG 76
                                      78999999**********95 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.29
                       Cep57_CLD_2   1 LeaevktLqnrLdsltrklqvheeelkrLnkERdsal 37 
                                       L+a++++L  +  +++++l    +el+++  E ds+ 
  gi|557694899|ref|YP_008797953.1| 121 LKAAKEALGSEFAQVEEELIWSSIELNTMQLEKDSDS 157
                                       6788888888888888888888999999999999975 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0046
                       Cep57_CLD_2   1 LeaevktLqnrLdsltrklqvheeelkrLn 30 
                                       Lea + +L+ +L sl+ +l + ee  k+L+
  gi|557694899|ref|YP_008797953.1| 167 LEAKIPELRKKLASLRNRLKMVEEMVKQLS 196
                                       8999********************999998 PP

>> FlgN  FlgN protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1       1.8   1.5e+03      38      57 ..      55      74 ..      34      80 .. 0.67
   2 ?   13.2   6.6   0.00011     0.095      16     113 ..      94     195 ..      90     207 .. 0.73
   3 ?   -1.4   0.1       3.7   3.1e+03      70      70 ..     221     221 ..     188     259 .. 0.49

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.8
                                      HHHHHHHHHHHHHHHHHHHH CS
                              FlgN 38 eaLeelleekqellekleql 57
                                      ++L+e l+   el++++e+l
  gi|557694899|ref|YP_008797953.1| 55 DELDEALKMYDELMREIERL 74
                                      56666666666666666655 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--........SCHHHHHHHHCTT CS
                              FlgN  16 elleeLlelleeEteaLkagdieaLeelleekqellekleqleqkrakllaelgls........aeeatlsellake 84 
                                       +l++++l+ l+e++ aL ++  e Le+l   k++l  + +q e+++  +  el++             +++e    e
  gi|557694899|ref|YP_008797953.1|  94 QLVRNILSRLAEKRNALLEKSGEVLERLKAAKEALGSEFAQVEEELIWSSIELNTMqlekdsdsGRGVGIRE----E 166
                                       6788999****************************************9999999988876443322233333....4 PP

                                       CCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FlgN  85 edeelkelwqelkelleelkelnelNgrl 113
                                        ++++ el+++l +l ++lk + e+ ++l
  gi|557694899|ref|YP_008797953.1| 167 LEAKIPELRKKLASLRNRLKMVEEMVKQL 195
                                       55555555555555555555444444433 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.7
                                       - CS
                              FlgN  70 l 70 
                                       +
  gi|557694899|ref|YP_008797953.1| 221 K 221
                                       1 PP

>> FTA4  Kinetochore complex Fta4 of Sim4 subunit, or CENP-50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  11.0     0.043        37     122     168 ..     160     210 ..      17     243 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.043
                              FTA4 122 l....eallerYaelrarLielserrqqlqarlarlrklkallepflgsed 168
                                            e+l ++  elr++L++l++r++++++ +++l++l ++++++++ ++
  gi|557694899|ref|YP_008797953.1| 160 GvgirEELEAKIPELRKKLASLRNRLKMVEEMVKQLSDLPRNIADITTNKE 210
                                       144558999999********************************9966533 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.1     0.013        11     340     411 ..      55     131 ..      34     148 .. 0.53
   2 ?    8.5   3.0   0.00079      0.67     323     387 ..     162     230 ..     157     252 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.013
                              FapA 340 keleeeleeleeeleklkkk.......ikklpklka.ekqlesekkeqlkklletkeklkeeleeleeelkelkeel 408
                                       +el+e l+ + e ++++++        +  + k+++ ++ql    ++ l +l e++++l e+  e+ e+lk+ ke l
  gi|557694899|ref|YP_008797953.1|  55 DELDEALKMYDELMREIERLrgldrnfMLYCIKMEElRPQL---VRNILSRLAEKRNALLEKSGEVLERLKAAKEAL 128
                                       44555555555555555555555555755555544434544...444444444444444444444444444444443 PP

                              FapA 409 esk 411
                                        s 
  gi|557694899|ref|YP_008797953.1| 129 GSE 131
                                       333 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00079
                              FapA 323 kteievgldepelkeklkeleeeleeleeeleklkkk...ikklpklka.ekqlesekkeqlkklletk 387
                                        ++ e++ + pel++kl+ l+++l+ +ee +++l +    i+ +   k+ + +l +e+k+++   + ++
  gi|557694899|ref|YP_008797953.1| 162 GIREELEAKIPELRKKLASLRNRLKMVEEMVKQLSDLprnIADITTNKEePAKLFEEIKKKYILSHGQR 230
                                       466777788888999998888888888666666666644444444433324444444444444333333 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 ?    1.8   0.6      0.29   2.5e+02      10      58 ..      27      74 ..      23      77 .. 0.78
   2 ?   11.4   3.8   0.00032      0.27      52     161 ..     101     196 ..      93     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.29
                            CENP-Q 10 pfPpatqsdggkekeldfeklldekaaleaqLspelhslelLeaeieke 58
                                      p Pp+++++ + e+++ +e+++ + + + ++L+ +l+  ++L +eie++
  gi|557694899|ref|YP_008797953.1| 27 PTPPQEEQTVKEESVKPVEEAVTQ-QPVGDELDEALKMYDELMREIERL 74
                                      556655778888888888888875.556799999999999999999986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00032
                            CENP-Q  52 eaeiekeeralerdyeaLreLeknakaearerkeklkkehvllqesdseelslleassdevlgeasgtvfsdlepel 128
                                        +  ek  ++le+  e L++L++  +a+ +e  + +++   l  +s + +  +le+ sd           s      
  gi|557694899|ref|YP_008797953.1| 101 SRLAEKRNALLEKSGEVLERLKAAKEALGSEFAQVEEE---LIWSSIELNTMQLEKDSD-----------SGRGVGI 163
                                       5566889999******************9999997666...555443444444444444...........3333445 PP

                            CENP-Q 129 deellpllqqLgshLesmrgnlaqlegllpale 161
                                        eel++ +++L+++L s+r+ l+ +e+++ +l 
  gi|557694899|ref|YP_008797953.1| 164 REELEAKIPELRKKLASLRNRLKMVEEMVKQLS 196
                                       677888888888888888888888888777765 PP

>> Occludin_ELL  Occludin homology domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.82     7e+02      41      86 ..      44      92 ..      31     105 .. 0.63
   2 ?    8.7   0.6    0.0033       2.8      20      67 ..     177     224 ..     164     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.82
                      Occludin_ELL 41 Lerelkelkegsk..eykkieeeilqeykklkk.dpeyqekkkrceyLk 86
                                      +e+ + +++ g++  e  k+ +e+++e ++l+  d++++    ++e+L+
  gi|557694899|ref|YP_008797953.1| 44 VEEAVTQQPVGDEldEALKMYDELMREIERLRGlDRNFMLYCIKMEELR 92
                                      5555555666665556666666666666666666666666666655555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0033
                      Occludin_ELL  20 eYkeYkelhaeleevskkfseLerelkelkegskeykkieeeilqeyk 67 
                                       + ++ ++  +++ee+ k++s+L r++ + +++++e +k+ eei ++y 
  gi|557694899|ref|YP_008797953.1| 177 KLASLRNRLKMVEEMVKQLSDLPRNIADITTNKEEPAKLFEEIKKKYI 224
                                       445555566677777777888888888888888888888888888775 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 ?   -1.0   1.7       2.4     2e+03      69      80 ..      90     101 ..      34     128 .. 0.50
   2 ?    0.7   0.4      0.72   6.2e+02       5      25 ..     119     139 ..     112     157 .. 0.73
   3 ?   14.3   2.7   4.2e-05     0.036       4      85 ..     164     240 ..     162     254 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.4
                                       HHHHHHHHHHHH CS
                     Cortex-I_coil  69 ealknlelekla 80 
                                       e   +l  + l+
  gi|557694899|ref|YP_008797953.1|  90 ELRPQLVRNILS 101
                                       222222222222 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.72
                                       XXXXXXXXXHHHHHHHHHHHH CS
                     Cortex-I_coil   5 erleasknelanklaglensl 25 
                                       erl+a+k+ l + +a +e+ l
  gi|557694899|ref|YP_008797953.1| 119 ERLKAAKEALGSEFAQVEEEL 139
                                       788889999998888888776 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 4.2e-05
                                       XXXXXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Cortex-I_coil   4 kerleasknelanklaglenslesekvsreelikqkdelesllasleseaaerekrlreleakldealknlelekla 80 
                                       +e lea   el +kla+l+n l+      ee++kq  +l   +a + ++++e  k + e++ k     ++   e +a
  gi|557694899|ref|YP_008797953.1| 164 REELEAKIPELRKKLASLRNRLKM----VEEMVKQLSDLPRNIADITTNKEEPAKLFEEIKKKYI-LSHGQRAEAVA 235
                                       799******************964....689*****************************99852.22445556666 PP

                                       HHHHH CS
                     Cortex-I_coil  81 rlele 85 
                                       r e+e
  gi|557694899|ref|YP_008797953.1| 236 RAEIE 240
                                       66665 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.022        19      24      45 ..      55      76 ..      33      83 .. 0.89
   2 ?   -1.7   0.1       4.4   3.7e+03      20      32 ..     104     116 ..      87     137 .. 0.60
   3 ?    5.0   0.3     0.036        30      14      72 ..     176     233 ..     164     237 .. 0.65

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.022
                         kleA_kleC 24 dkiAaklaeAeeLvrqaeeLRa 45
                                      d++ + l+  +eL+r++e+LR+
  gi|557694899|ref|YP_008797953.1| 55 DELDEALKMYDELMREIERLRG 76
                                      7788899999***********6 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.4
                         kleA_kleC  20 varRdkiAaklae 32 
                                         +R+++ +k  e
  gi|557694899|ref|YP_008797953.1| 104 AEKRNALLEKSGE 116
                                       4444444444333 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.036
                         kleA_kleC  14 evatdlvarRdkiAaklaeAeeLvrqaeeLRakvyeesaaLedrakkrWtleeveqAka 72 
                                       +    l++r   + +++++  +L r+++++ ++ +ee a L +++kk++ l   ++A a
  gi|557694899|ref|YP_008797953.1| 176 KKLASLRNRLKMVEEMVKQLSDLPRNIADITTN-KEEPAKLFEEIKKKYILSHGQRAEA 233
                                       333445555555667777777777777777554.6788999999999988877777765 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   6.4    0.0057       4.8      24     137 ..     111     243 ..      85     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0057
                             Atg14  24 lyelrerlaklksekeslkkkiekalegke......................eaeqledkiknkkakleelksliad 78 
                                       l++  e l +lk++ke+l++++ + +e+                          e+le+ki  +++kl +l+++   
  gi|557694899|ref|YP_008797953.1| 111 LEKSGEVLERLKAAKEALGSEFAQVEEELIwssielntmqlekdsdsgrgvgIREELEAKIPELRKKLASLRNRLKM 187
                                       55666778999999999999999888877767788888888888877777777777777777777777777777777 PP

                             Atg14  79 lrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdleslqneleerrkkqiaklq 137
                                        +e +++l+d  ++  + i   k++ akl +++kk++    s+ ++ e+  +++i+k+ 
  gi|557694899|ref|YP_008797953.1| 188 VEEMVKQLSDLPRN-IADITTNKEEPAKLFEEIKKKYIL--SHGQRAEAVARAEIEKIA 243
                                       77777777764444.456777788888888888777776..888888888888888875 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 ?   -1.4   0.1       3.7   3.2e+03      38      44 ..      58      64 ..      32      75 .. 0.53
   2 ?    0.1   0.2       1.3   1.1e+03       4      22 ..     134     152 ..     111     155 .. 0.79
   3 ?   11.9   0.7   0.00027      0.23       3      35 ..     165     197 ..     164     210 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.7
                         FlaC_arch 38 kdllsLY 44
                                       + l++Y
  gi|557694899|ref|YP_008797953.1| 58 DEALKMY 64
                                      3333344 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                         FlaC_arch   4 elEnklsklsteletvkke 22 
                                       ++E++l   s+el+t++ e
  gi|557694899|ref|YP_008797953.1| 134 QVEEELIWSSIELNTMQLE 152
                                       4677777788888888755 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 0.00027
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelke 35 
                                       +elE k+++l  +l+++++ ++ +++ v++l +
  gi|557694899|ref|YP_008797953.1| 165 EELEAKIPELRKKLASLRNRLKMVEEMVKQLSD 197
                                       689999999999999999988888888777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1741  (0.0971052); expected 358.6 (0.02)
Passed bias filter:                      927  (0.0517039); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); 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):              21  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.40
# Mc/sec: 1989.46
//
Query:       gi|557694900|ref|YP_008797954.1|  [L=202]
Description: 26S proteasome regulatory subunit N11-like protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   79.5   0.0    2.6e-22   79.0   0.0    1.3  1  JAB       JAB1/Mov34/MPN/PAD-1 ubiquitin protease
    4.8e-10   39.2   0.0      7e-10   38.7   0.0    1.2  1  Prok-JAB  Prokaryotic homologs of the JAB domain
    4.8e-07   30.0   0.1    8.8e-07   29.2   0.1    1.3  1  UPF0172   Uncharacterised protein family (UPF0172)


Domain annotation for each model (and alignments):
>> JAB  JAB1/Mov34/MPN/PAD-1 ubiquitin protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.0   4.3e-26   2.6e-22       6     115 ..       3     106 ..       1     109 [. 0.94

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 4.3e-26
                                       EEEEHHHHHHHHHHHHHHHHHTS--EEEEEEEESSSEEEEEEEEEEESEEEESSECEEEEEHHHHHHHHHHHHHHHC CS
                               JAB   6 vhleslvllkildhalrtekeeeevmGlliGelnddttveitnvfalpfeetekdvdavsldqeylekksellkklr 82 
                                       v++ +l+l k+++ha +  ++  ev+Gll+G+  ++ ++ei + +  ++ +t      v+ld++ + k  e+l k +
  gi|557694900|ref|YP_008797954.1|   3 VRIYPLALAKVVKHAASSLQR--EVAGLLVGKSAGK-VLEIWDAVTGEQYGTPAY---VQLDEMVMAKVAEELSKSD 73 
                                       8999*****************..*************.******************...6777777779999999999 PP

                                       TTSEEEEEEEESSSS-SS--HHHHHHHHHHHHH CS
                               JAB  83 grervvGWYhshpditvwlsevdvrtqalyqrm 115
                                       +++++vGWYhshp+++v+ls+ d++tq+ yq+m
  gi|557694900|ref|YP_008797954.1|  74 KNLYIVGWYHSHPGLDVFLSPTDIDTQKRYQAM 106
                                       99*****************************99 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 !   38.7   0.0   1.2e-13     7e-10       5      95 ..      10     103 ..       7     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.2e-13
                          Prok-JAB   5 lsalvaharrahpeEtcGlllgkeseseevivvplvnewsn....rfeipdpedslarlkf.......earerglev 70 
                                       l++ v+ha ++ ++E +Gll+gk+    + ++++ v+  ++    + +++  e       +       + ++++l +
  gi|557694900|ref|YP_008797954.1|  10 LAKVVKHAASSLQREVAGLLVGKS-AGKVLEIWDAVT--GEqygtPAYVQLDEMV-----MakvaeelSKSDKNLYI 78 
                                       7889*******************9.888888888775..3323543333222222.....1444668999******* PP

                          Prok-JAB  71 vgiwHSHpggsarPSetDrrdaaal 95 
                                       vg +HSHpg   + S tD+ + ++ 
  gi|557694900|ref|YP_008797954.1|  79 VGWYHSHPGLDVFLSPTDIDTQKRY 103
                                       ******************9988764 PP

>> UPF0172  Uncharacterised protein family (UPF0172)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.1   1.5e-10   8.8e-07       2     121 ..       3     122 ..       2     145 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.5e-10
                           UPF0172   2 vevssqAYvKlllHaaKyptqaVnGvLlgkkssskskvevtDavPLfH.ssltlspmlevAlaqvesyake..kglv 75 
                                       v++ + A +K++ Haa   +++V G+L+gk+  +   +e+ Dav      + +   + e+ +a v + +++  k+l 
  gi|557694900|ref|YP_008797954.1|   3 VRIYPLALAKVVKHAASSLQREVAGLLVGKSAGKV--LEIWDAVTGEQyGTPAYVQLDEMVMAKVAEELSKsdKNLY 77 
                                       567889************************98888..9******876535555566668888888777555458*** PP

                           UPF0172  76 ivGyYqanerlsdtelsslaekiadkiaenfsdavllvvdnkkles 121
                                       ivG+Y+++  l d  ls++     ++ ++ fs+av+lvvd   +++
  gi|557694900|ref|YP_008797954.1|  78 IVGWYHSHPGL-DVFLSPTDIDTQKRYQAMFSKAVALVVDPVDYAK 122
                                       ******99877.567899999999**************99865543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1558.99
//
Query:       gi|557694901|ref|YP_008797955.1|  [L=87]
Description: ubiquitin-like protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   49.1   0.0      4e-13   48.9   0.0    1.0  1  ubiquitin    Ubiquitin family
    1.8e-07   30.9   0.0      2e-07   30.8   0.0    1.1  1  Rad60-SLD    Ubiquitin-2 like Rad60 SUMO-like
     0.0042   17.7   0.1     0.0061   17.2   0.1    1.4  1  YukD         WXG100 protein secretion system (Wss), protein Y
     0.0071   16.5   0.0     0.0094   16.2   0.0    1.2  1  TUG-UBL1     TUG ubiquitin-like domain
  ------ inclusion threshold ------
       0.13   12.4   0.0       0.33   11.1   0.0    1.7  1  Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
       0.14   12.8   0.0       0.16   12.5   0.0    1.1  1  DUF2407      DUF2407 ubiquitin-like domain


Domain annotation for each model (and alignments):
>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   1.3e-16     4e-13       9      70 ..      13      74 ..       6      76 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.3e-16
                                      EEEEEEEETTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE-TTSBHGGHTTSTTEEEEEEES CS
                         ubiquitin  9 kkitleveesdtveelKekiaekegipaeqqrLiysGkvLedertleeygiqdgstlhlvlr 70
                                      + ++lev+++ tv  +  k+++ +++p++  rL y+G+ L+d +tle++g++dg++ +l  r
  gi|557694901|ref|YP_008797955.1| 13 SPLELEVAPNATVGAVRTKVCAMKKLPPDTTRLTYKGRALKDTETLESLGVADGDKFVLITR 74
                                      5679****************************************************999887 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 !   30.8   0.0   6.6e-11     2e-07       9      67 ..      11      68 ..       1      72 [. 0.91

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 6.6e-11
                                      SS--EEEEEETTSBHHHHHHHHHHHHT----TT-EEEETTEE--TTSBGGGSS--TTEE CS
                         Rad60-SLD  9 dgkevkikVkptttvskLieayrkkkgipeeqkvrLiFDGeeLdpnstvedldiedgdt 67
                                      +g +++++V+p+ tv  + ++ + +k++p+ ++ rL+++G+ L++++t+e+l++ dgd 
  gi|557694901|ref|YP_008797955.1| 11 GGSPLELEVAPNATVGAVRTKVCAMKKLPP-DTTRLTYKGRALKDTETLESLGVADGDK 68
                                      56799*************************.**************************96 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 !   17.2   0.1     2e-06    0.0061      52      76 .]      47      71 ..       2      71 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2e-06
                                      GGGEEEETTSBCGGGT--TT-EEEE CS
                              YukD 52 vggapLsgdrtLaeagVrDGdlLvL 76
                                       +g++L++++tL+++gV+DGd  vL
  gi|557694901|ref|YP_008797955.1| 47 YKGRALKDTETLESLGVADGDKFVL 71
                                      45799****************8776 PP

>> TUG-UBL1  TUG ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.2e-06    0.0094       8      62 ..      15      68 ..      11      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.2e-06
                          TUG-UBL1  8 fkvkvtpnttlndvLeeackkfklddsasytLkhnnkpldlslpfRlsnLpngak 62
                                       +  v+pn t+  v  ++c+  kl ++++  L++++++l  + ++  ++ + g k
  gi|557694901|ref|YP_008797955.1| 15 LELEVAPNATVGAVRTKVCAMKKL-PPDTTRLTYKGRALKDTETLESLGVADGDK 68
                                      5678********************.889**********98887777777666655 PP

>> Rad60-SLD_2  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00011      0.33      23      76 ..      22      68 ..       1      76 [. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                                      T-BHHHHHHHHHHHS-TT-SSS--SCCCEEEEETTEEE-TTSBCCCCS-TTTTT CS
                       Rad60-SLD_2 23 aatvaelkekviaqWPkdkeekpksvndlklilaGkiLennktlkelrlplgev 76
                                      +atv +++ kv+a      ++    ++  +l ++G+ L+++ tl++l++  g+ 
  gi|557694901|ref|YP_008797955.1| 22 NATVGAVRTKVCAM-----KK--LPPDTTRLTYKGRALKDTETLESLGVADGDK 68
                                      55555555555542.....11..2245569****************99887775 PP

>> DUF2407  DUF2407 ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.5e-05      0.16      33      63 ..      28      60 ..      13      70 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.5e-05
                           DUF2407 33 iRerl..paelasrrLrLIyaGrlLedttslas 63
                                      +R+++   ++l     rL y+Gr+L+dt++l+s
  gi|557694901|ref|YP_008797955.1| 28 VRTKVcaMKKLPPDTTRLTYKGRALKDTETLES 60
                                      33333223345555669*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       186  (0.0103743); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 647.52
//
Query:       gi|557694902|ref|YP_008797956.1|  [L=168]
Description: ubiquitin-conjugating enzyme E2-like protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  100.2   0.0      9e-29   99.9   0.0    1.1  1  UQ_con     Ubiquitin-conjugating enzyme
  ------ inclusion threshold ------
      0.091   12.5   0.0       0.25   11.0   0.0    1.7  1  Prok-E2_B  Prokaryotic E2 family B


Domain annotation for each model (and alignments):
>> UQ_con  Ubiquitin-conjugating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.9   0.0     1e-32     9e-29       2     139 ..      17     149 ..      16     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 99.9 bits;  conditional E-value: 1e-32
                                       HHHHHHHHHHSTTTTEEEEEEETTEECEEEEEEEB.TTSTTTTEEEEEEEE--TTTTTS--EEEESST-SCTTBE.. CS
                            UQ_con   2 lqkelkelakkkpsgisaklvddenlfewkvlikgpedtpYeggvFklelefpedYPlkpPkvkfvtkifHPnvd.. 76 
                                       l+ e++ +++++p+    ++v++ +l++++++i+g   + Yegg+F++e+ +p++YP+ pP v   t+i+HPn +  
  gi|557694902|ref|YP_008797956.1|  17 LALEYALIQENEPTF---TPVEN-DLTHYEGVIVG--SGEYEGGFFRVEIIIPRSYPYFPPDVIWHTRIWHPNFSds 87 
                                       666777666666654...45554.9**********..999**********************************965 PP

                                       TTSBB-CGGGSTTT--TTSHHHHHHHHHHHHHHS--TTS-SSHHHHHHHHHTHHHHHHHHHHH CS
                            UQ_con  77 ksGevcldiLkeekWspaltlesvllsiqsLlaepnpesplnkeaakllkkdreeykkkvkey 139
                                          +vc +i+k ++Wsp+l++  v+ s+ +Ll++pnpe+pln  aa ++k+ ++ + ++v+++
  gi|557694902|ref|YP_008797956.1|  88 VPARVCESIFK-DHWSPSLRIVAVIESLRNLLTNPNPEDPLNPVAAFEYKNRPDLFYSRVRQF 149
                                       669********.55*********************************************9876 PP

>> Prok-E2_B  Prokaryotic E2 family B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.8e-05      0.25      20     111 ..      39     125 ..      20     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.8e-05
                         Prok-E2_B  20 kdgkkaierssvktsggtvdlrlvypdsfpllppavflqdpeqlkllpHintfg...gaLClleeeldldewdpngs 93 
                                         ++++i +s  + +gg +++++++p s+p+ pp v+   +       H n+ +     +C        d w p   
  gi|557694902|ref|YP_008797956.1|  39 THYEGVIVGSG-EYEGGFFRVEIIIPRSYPYFPPDVIWHTRI-----WHPNFSDsvpARVCE---SIFKDHWSPSLR 106
                                       44555555533.448********************9977666.....355554434556776...677888888888 PP

                         Prok-E2_B  94 vadvleqlqqvLn.egisg 111
                                       + +v+e+l+++L+  ++++
  gi|557694902|ref|YP_008797956.1| 107 IVAVIESLRNLLTnPNPED 125
                                       8888888888887666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1323.80
//
Query:       gi|557694903|ref|YP_008797957.1|  [L=394]
Description: ubiquitin-activating enzyme E1-like protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-57  193.0   0.0    7.1e-57  192.6   0.0    1.1  1  ThiF          ThiF family
  ------ inclusion threshold ------
      0.018   14.8   0.0       0.12   12.2   0.0    2.1  2  ubiquitin     Ubiquitin family
      0.054   13.6   0.2        4.7    7.3   0.0    2.7  3  Ubiquitin_4   Ubiquitin-like domain
        0.1   11.9   0.0       0.49    9.7   0.0    2.0  2  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 
       0.17   11.6   0.0       0.28   10.8   0.0    1.3  1  USP7_C2       Ubiquitin-specific protease C-terminal


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 !  192.6   0.0     2e-60   7.1e-57       1     240 [.      11     309 ..      11     316 .. 0.88

  Alignments for each domain:
  == domain 1  score: 192.6 bits;  conditional E-value: 2e-60
                                       THHHHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   1 ysrqlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaeva 77 
                                       y+rql+ l   +q+kL + +v + G+G+lG+e++knLal+Gvg+l l+DnD +elsNl+Rq+l++++diG+pKa +a
  gi|557694903|ref|YP_008797957.1|  11 YDRQLR-LEGWDQNKLLSGRVIVAGVGALGCEVAKNLALMGVGELLLIDNDYVELSNLSRQMLYTDQDIGRPKASTA 86 
                                       677764.55589***************************************************************** PP

                                       HHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  78 aealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviip 154
                                       +++++ +np v+ + ++ ++ + +  ee + ++D++v a+Dn+++rr++n+++v+ g+pl++ +t g++g+v+++ip
  gi|557694903|ref|YP_008797957.1|  87 EKKISLMNPLVKAKGLHTDVRKIP--EETFAEADVIVSAVDNWPTRRWMNSMAVHVGTPLVDVATDGYYGNVQTVIP 161
                                       ********************9953..79************************************************* PP

                                       CCS-ECTSS-TGGS.EECCCCEEHHH................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                              ThiF 155 gktgcyeCldpsstedptekkvplct................................................... 180
                                       g t+c+eC+       p++ +++ c                                                    
  gi|557694903|ref|YP_008797957.1| 162 GVTSCLECHAE--ALIPSDIQASECSlrrrtpndlvkdlsergisinlsdaetlfqhniktvydikfapqtvldqmd 236
                                       *********84..444555555555555555999999999**********************************999 PP

                                       ...........HHHCT....E-B-HHHHHHHHHHHHHHHHHHH...TTBCGGGCCEEEECCTTTTEEEEECCEEEEE CS
                                       ...........xxxxx....xxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 181 ...........siagn....ipaiatttavvaglaalellkll...sgkeklenslltqvdllesrfenvelerakk 239
                                                  s        +pa+ ++ a v+gla  e+++ll   s  + + n ++  +d+l+ r+++++ler+ +
  gi|557694903|ref|YP_008797957.1| 237 kslreqviqlrS---LlnpkMPALQSISATVSGLASFEVVRLLhkgSLGR-SLNGMM-VFDGLRGRLSRIKLERNVN 308
                                       999997665542...04469***********************8643333.444444.7999999**9999998775 PP

                                       E CS
                                       x RF
                              ThiF 240 s 240
                                       +
  gi|557694903|ref|YP_008797957.1| 309 C 309
                                       4 PP

>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.34   1.2e+03      48      60 ..     207     219 ..     205     225 .. 0.88
   2 ?   12.2   0.0   3.3e-05      0.12      11      70 ..     320     377 ..     315     379 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.34
                                       E-TTSBHGGHTTS CS
                         ubiquitin  48 Ledertleeygiq 60 
                                       L+d +tl +++i+
  gi|557694903|ref|YP_008797957.1| 207 LSDAETLFQHNIK 219
                                       89*********98 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.3e-05
                                       EEEEEETTSBHHHHHHHHHHHHTSSGGGEEEEETTEEE-TTSBHGGHTTSTTEEEEEEES CS
                         ubiquitin  11 itleveesdtveelKekiaekegipaeqqrLiysGkvLedertleeygiqdgstlhlvlr 70 
                                       + + v++++t+++l e+i+    +p    rL +  k+L+d   +++ gi dg++l  + +
  gi|557694903|ref|YP_008797957.1| 320 VQINVAPNETIADLRERISNLLMFPD--TRLQHGAKLLDDTADITSAGICDGDILYIHSS 377
                                       6789***************9887775..5899**********************998765 PP

>> Ubiquitin_4  Ubiquitin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.5   1.3e+04      22      40 ..     220     238 ..     212     243 .. 0.66
   2 ?    3.4   0.0     0.022        78       9      32 ..     316     339 ..     311     349 .. 0.86
   3 ?    7.3   0.0    0.0013       4.7      61      84 ..     350     373 ..     346     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.5
                       Ubiquitin_4  22 tvkdLkkaierkvelklkr 40 
                                       tv d+k a +  +++++k 
  gi|557694903|ref|YP_008797957.1| 220 TVYDIKFAPQTVLDQMDKS 238
                                       7777877777666666555 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.022
                       Ubiquitin_4   9 dgeslevvvkqnatvkdLkkaier 32 
                                       +++ +++ v+ n t++dL++ i +
  gi|557694903|ref|YP_008797957.1| 316 EDKPVQINVAPNETIADLRERISN 339
                                       567899**************9987 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0013
                       Ubiquitin_4  61 egekLkddkaklkeygirnksels 84 
                                       +g+kL+dd+a +++ gi++++ l+
  gi|557694903|ref|YP_008797957.1| 350 HGAKLLDDTADITSAGICDGDILY 373
                                       799*****************9885 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 ?    9.7   0.0   0.00014      0.49       8      66 ..       5      58 ..       1      76 [. 0.78
   2 ?   -0.8   0.0      0.23   8.2e+02      84     103 ..     109     128 ..      82     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00014
                                      HTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEES CS
                      2-Hacid_dh_C  8 lrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgm.kviayd 66
                                      +  l+++d+++r + w       +++l   +v + G+G++G +vak l+ +g+ +++ +d
  gi|557694903|ref|YP_008797957.1|  5 VDALSRYDRQLRLEGW------DQNKLLSGRVIVAGVGALGCEVAKNLALMGVgELLLID 58
                                      5567889999999999......34455556899*****************9996666666 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.23
                                       SHHHHHHH-SEEEE-S--ST CS
                      2-Hacid_dh_C  84 sleellaesDivslhlpltp 103
                                         ee +ae+D+++ ++   p
  gi|557694903|ref|YP_008797957.1| 109 IPEETFAEADVIVSAVDNWP 128
                                       468999******99887554 PP

>> USP7_C2  Ubiquitin-specific protease C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   7.9e-05      0.28     129     159 ..     318     348 ..     291     373 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7.9e-05
                           USP7_C2 129 iPFlfklkegEtfsetkeRlqkrlgvkdkeF 159
                                        P ++++ ++Et+++++eR+++ l ++d  +
  gi|557694903|ref|YP_008797957.1| 318 KPVQINVAPNETIADLRERISNLLMFPDTRL 348
                                       4888899999999999999998888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); 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:                         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 0.22s 00:00:00.70 Elapsed: 00:00:00.36
# Mc/sec: 3240.64
//
Query:       gi|557694904|ref|YP_008797958.1|  [L=75]
Description: hypothetical protein CSUB_C1477 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   35.3   6.8    1.4e-08   34.9   6.8    1.2  1  zf-RING_2       Ring finger domain
    6.1e-07   29.7   1.2    2.3e-06   27.8   0.2    1.9  2  C1_2            C1 domain
    1.9e-06   27.4   5.5    2.6e-06   27.0   5.5    1.2  1  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
    2.1e-05   24.3   5.8    3.1e-05   23.7   5.8    1.3  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
    3.4e-05   23.7   6.2    0.00068   19.5   3.0    2.1  2  Prok-RING_1     Prokaryotic RING finger family 1
    7.7e-05   22.5   4.6    0.00016   21.5   4.6    1.5  1  Prok-RING_4     Prokaryotic RING finger family 4
    0.00017   21.8   8.4    0.00038   20.7   8.4    1.7  1  zf-rbx1         RING-H2 zinc finger domain
     0.0017   18.1   7.8     0.0047   16.7   7.8    1.7  1  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
     0.0092   15.8   3.1     0.0092   15.8   3.1    2.3  2  zf-HIT          HIT zinc finger
  ------ inclusion threshold ------
      0.012   15.6   3.5      0.015   15.3   3.5    1.1  1  zf-RING_9       Putative zinc-RING and/or ribbon
      0.021   14.7   7.3      0.043   13.7   7.3    1.5  1  PHD             PHD-finger
      0.026   14.6   4.7       0.29   11.2   4.7    2.0  1  zf-ANAPC11      Anaphase-promoting complex subunit 11 RING-H2
      0.033   14.3   4.2      0.051   13.7   4.1    1.4  1  Zf_RING         KIAA1045 RING finger
      0.038   13.8   5.8       0.91    9.4   0.2    2.1  2  zf-RING_4       RING/Ubox like zinc-binding domain
      0.054   13.5   7.0        2.2    8.4   7.0    2.2  1  DZR             Double zinc ribbon
      0.062   13.6   3.6      0.062   13.6   3.6    1.6  2  zf-RING-like    RING-like domain
      0.063   13.0   6.8       0.19   11.5   3.1    2.3  2  zinc_ribbon_2   zinc-ribbon domain
      0.082   12.8   5.3       0.17   11.8   0.5    2.3  2  Rad50_zn_hook   Rad50 zinc hook motif
       0.11   11.9  10.9       0.19   11.2   1.6    3.0  3  zf-ribbon_3     zinc-ribbon domain
       0.15   12.2   7.3        1.7    8.8   7.3    2.1  1  FANCL_C         FANCL C-terminal domain
       0.19   11.6   6.6       0.32   10.9   5.2    1.8  2  C1_1            Phorbol esters/diacylglycerol binding domain 
       0.23   11.7   6.6         13    6.2   0.0    3.0  2  zinc_ribbon_9   zinc-ribbon
       0.25   11.3   7.8       0.65    9.9   0.2    2.9  3  zf-FPG_IleRS    Zinc finger found in FPG and IleRS
       0.25   11.3   3.3       0.22   11.5   0.7    1.9  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
       0.31   11.1   8.1       0.79    9.7   8.0    2.0  1  zf-RING_5       zinc-RING finger domain
       0.35   11.2   7.4        5.1    7.4   0.2    2.5  3  zf-LITAF-like   LITAF-like zinc ribbon domain
       0.45   10.6   5.0       0.28   11.2   1.6    1.9  2  HypA            Hydrogenase/urease nickel incorporation, meta
       0.56   10.4   6.4        6.9    6.9   0.2    3.0  3  DUF2256         Uncharacterized protein conserved in bacteria
       0.57   10.1   8.1        6.3    6.8   0.2    2.2  2  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)
       0.92   10.0   4.1         30    5.1   0.0    2.8  3  DUF983          Protein of unknown function (DUF983)
        1.3   10.1   6.2         15    6.8   0.3    3.2  3  zf-C2H2_4       C2H2-type zinc finger
        2.1    8.9   6.2        4.4    7.9   0.1    2.5  2  zf-H2C2_2       Zinc-finger double domain
        2.4    8.3   8.8        3.4    7.8   0.3    2.8  3  UPF0547         Uncharacterised protein family UPF0547
        5.1    7.3   9.3          3    8.0   5.2    2.5  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
        5.3    7.4   8.8        4.3    7.7   1.2    2.8  3  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
        8.6    6.4   9.8        2.3    8.2   1.7    2.9  3  Zn_ribbon_SprT  SprT-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   6.8   2.8e-11   1.4e-08       2      44 .]      27      69 ..      26      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.8e-11
                         zf-RING_2  2 eCpICleelssadsvlllpCgHvfhreClerwlrssstCPlCr 44
                                      +C+IC  e+ +++++ + +Cg v h +C+++wl  ++tCPlCr
  gi|557694904|ref|YP_008797958.1| 27 NCVICGLEMGNEKTYSCPHCGAVGHMSCFDDWLVVKQTCPLCR 69
                                      7****88998866666668***********************9 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.2   4.6e-09   2.3e-06      11      46 ..      18      54 ..       2      55 .. 0.85
   2 ?    1.1   0.0         1   5.1e+02      19      27 ..      63      71 ..      61      75 .] 0.79

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 4.6e-09
                              C1_2 11 kgedssesfnCsaCgrkidgff.YsCseCdfslhvrC 46
                                      +++++ ++ nC +Cg ++ +++ YsC+ C  + h++C
  gi|557694904|ref|YP_008797958.1| 18 EPKPRPKQENCVICGLEMGNEKtYSCPHCGAVGHMSC 54
                                      578899999********644446************** PP

  == domain 2  score: 1.1 bits;  conditional E-value: 1
                              C1_2 19 fnCsaCgrk 27
                                       +C +C+r+
  gi|557694904|ref|YP_008797958.1| 63 QTCPLCRRP 71
                                      68999*998 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 !   27.0   5.5   5.2e-09   2.6e-06       4      46 ..      25      66 ..      22      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 5.2e-09
                      Zn_ribbon_17  4 lksCayCelav.kgrvvlcgvCeHvlHasCarewfenddlaeCp 46
                                      +++C++C l++ + +++ c+ C+ v H sC ++w+  ++   Cp
  gi|557694904|ref|YP_008797958.1| 25 QENCVICGLEMgNEKTYSCPHCGAVGHMSCFDDWLVVKQ--TCP 66
                                      789*******94467889****************98877..676 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 !   23.7   5.8   6.2e-08   3.1e-05       2      47 ..      25      72 ..      24      75 .] 0.77

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.2e-08
                                      GSB-TTTSS...SBS-EEETTE...EEEEE-HHHHHHHHHTT-B-TTT--B- CS
                        zf-C3HC4_3  2 deeCviCle...rprnvvllpC...gHlvlCeeCaekllkrkkkCpiCrrpi 47
                                      +e CviC     ++++  + +C   gH+    +C++++l  k++Cp+Crrp 
  gi|557694904|ref|YP_008797958.1| 25 QENCVICGLemgNEKTYSCPHCgavGHM----SCFDDWLVVKQTCPLCRRPL 72
                                      689****984445888999999555588....777777777*********97 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 !   19.5   3.0   1.4e-06   0.00068       4      36 ..      25      56 ..      22      58 .. 0.90
   2 ?    5.6   0.1     0.031        16       4      14 ..      62      72 ..      60      75 .] 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.4e-06
                       Prok-RING_1  4 gkkCpvCgkelkeedDiVvCpeCgtpyHraCye 36
                                      +++C +Cg e+ +e     Cp+Cg++ H +C++
  gi|557694904|ref|YP_008797958.1| 25 QENCVICGLEMGNE-KTYSCPHCGAVGHMSCFD 56
                                      789********999.6889************97 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.031
                       Prok-RING_1  4 gkkCpvCgkel 14
                                      ++ Cp+C+++l
  gi|557694904|ref|YP_008797958.1| 62 KQTCPLCRRPL 72
                                      899*****987 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 !   21.5   4.6   3.2e-07   0.00016       1      39 [.      28      71 ..      28      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 3.2e-07
                       Prok-RING_4  1 CvlCgeqekkailepCgHl..vCk.eCfdsk..dlssCPlCqrr 39
                                      Cv+Cg +  +    +C H   v + +Cfd++    ++CPlC+r 
  gi|557694904|ref|YP_008797958.1| 28 CVICGLEMGNEKTYSCPHCgaVGHmSCFDDWlvVKQTCPLCRRP 71
                                      *******9999999999977665438*****65555******96 PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   8.4   7.7e-07   0.00038      11      55 .]      25      69 ..      21      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 7.7e-07
                           zf-rbx1 11 eeacieckapgdeecpvvlGeCgHaFHlhCiskWlktrkvCPlcr 55
                                      +e+c+ c  +  +e +  + +Cg + H+ C ++Wl  +++CPlcr
  gi|557694904|ref|YP_008797958.1| 25 QENCVICGLEMGNEKTYSCPHCGAVGHMSCFDDWLVVKQTCPLCR 69
                                      678999988887778888889999********************8 PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   7.8   9.4e-06    0.0047       2      40 .]      28      68 ..      27      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.4e-06
                        zf-C3HC4_2  2 CpiCldmlkdpsvvt..pCgHvfCqkCilrsLeekneCPlC 40
                                      C iC  ++ +  +     Cg v + +C++ +L  k+ CPlC
  gi|557694904|ref|YP_008797958.1| 28 CVICGLEMGNEKTYScpHCGAVGHMSCFDDWLVVKQTCPLC 68
                                      9***8777765333335777899****************** PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   3.1   1.9e-05    0.0092       3      21 ..      26      48 ..      24      54 .. 0.89
   2 ?    1.7   0.7      0.48   2.4e+02      15      22 ..      64      71 ..      62      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                                      -B-TTT-S....B-SEE-TTT-- CS
                            zf-HIT  3 klCgvCgf....pakYkCpkCnt 21
                                      + C++Cg     ++ Y+Cp C++
  gi|557694904|ref|YP_008797958.1| 26 ENCVICGLemgnEKTYSCPHCGA 48
                                      67****999999*********96 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.48
                                      E-TTT--E CS
                            zf-HIT 15 kCpkCntr 22
                                      +Cp C+ +
  gi|557694904|ref|YP_008797958.1| 64 TCPLCRRP 71
                                      89999877 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 ?   15.3   3.5     3e-05     0.015     172     203 ..      37      70 ..      22      72 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-05
                         zf-RING_9 172 lktverCekCkavfHkeClkk..kekkecpkcer 203
                                       ++++  C++C+av H++C+ +    k++cp c+r
  gi|557694904|ref|YP_008797958.1|  37 NEKTYSCPHCGAVGHMSCFDDwlVVKQTCPLCRR 70 
                                       566778*************762233459****98 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   7.3   8.7e-05     0.043       2      50 ..      28      69 ..      27      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.7e-05
                                      BTTTTSTTSTTSCEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTTH CS
                               PHD  2 CavCkkksdeeeelvqCdgCkrwfHqkClkppleseekpegewlCekCk 50
                                      C +C+  +  +e++ +C +C+   H++C +  l    +++   +C+ C+
  gi|557694904|ref|YP_008797958.1| 28 CVICGL-EMGNEKTYSCPHCGAVGHMSCFDDWLV---VKQ---TCPLCR 69
                                      ******.999******************998776...222...477775 PP

>> zf-ANAPC11  Anaphase-promoting complex subunit 11 RING-H2 finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.7   0.00059      0.29      42      80 ..      36      71 ..       1      74 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00059
                                      TTTS-EEEBTTS-EEEHHHHHHHHHHHSTSSB-TTTSSB CS
                        zf-ANAPC11 42 GddcplvlGkckhnfhlhcilkwletetskglcpmcrqt 80
                                      G++ +    +c  + h+ c   wl    +k+ cp+cr+ 
  gi|557694904|ref|YP_008797958.1| 36 GNEKTYSCPHCGAVGHMSCFDDWLV---VKQTCPLCRRP 71
                                      455555556788899********96...7899****975 PP

>> Zf_RING  KIAA1045 RING finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   4.1    0.0001     0.051       4      36 ..      24      57 ..      22      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.0001
                           Zf_RING  4 edelCeiCevyta.eelypCRvCtkvfHegClrk 36
                                      ++e C iC  + + e++y C  C  v H +C+  
  gi|557694904|ref|YP_008797958.1| 24 KQENCVICGLEMGnEKTYSCPHCGAVGHMSCFDD 57
                                      5789****998761568**************976 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 ?    7.1   1.2    0.0095       4.7      25      43 ..      28      46 ..      24      49 .. 0.92
   2 ?    9.4   0.2    0.0018      0.91      27      46 ..      53      71 ..      50      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0095
                         zf-RING_4 25 ClfCyhrileeeegrCPaC 43
                                      C+ C  ++ +e++  CP C
  gi|557694904|ref|YP_008797958.1| 28 CVICGLEMGNEKTYSCPHC 46
                                      9****************** PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0018
                         zf-RING_4 27 fCyhrileeeegrCPaCree 46
                                       C+++ l   ++ CP Cr++
  gi|557694904|ref|YP_008797958.1| 53 SCFDDWLV-VKQTCPLCRRP 71
                                      58888884.6899*****97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   7.0    0.0045       2.2       1      21 [.      28      49 ..      17      75 .] 0.48

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0045
                               DZR  1 CpqCgeelppdar.fCseCgtk 21
                                      C  Cg e+ +++   C++Cg+ 
  gi|557694904|ref|YP_008797958.1| 28 CVICGLEMGNEKTySCPHCGAV 49
                                      3334433333333134444444 PP

>> zf-RING-like  RING-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       9.3   4.6e+03      39      43 .]      27      31 ..      23      33 .. 0.57
   2 ?   13.6   3.6   0.00012     0.062      12      43 .]      41      68 ..      37      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9.3
                      zf-RING-like 39 kCpkC 43
                                      +C  C
  gi|557694904|ref|YP_008797958.1| 27 NCVIC 31
                                      44444 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00012
                      zf-RING-like 12 vrCsnesCnvrlHvdCfqhyirthsskkCpkC 43
                                      + C+  +C +  H  Cf+  +   ++++Cp C
  gi|557694904|ref|YP_008797958.1| 41 YSCP--HCGAVGHMSCFDDWL--VVKQTCPLC 68
                                      5799..*************99..78889***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 ?   11.5   3.1   0.00039      0.19       2      21 ..      28      48 ..      27      50 .. 0.89
   2 ?    3.0   0.1      0.17        87      15      23 .]      64      72 ..      62      73 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00039
                     zinc_ribbon_2  2 CpnCGaelqdnakF.CpyCGt 21
                                      C  CG e  ++ ++ Cp+CG+
  gi|557694904|ref|YP_008797958.1| 28 CVICGLEMGNEKTYsCPHCGA 48
                                      888*****9999999*****8 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.17
                     zinc_ribbon_2 15 FCpyCGtpl 23
                                       Cp C+ pl
  gi|557694904|ref|YP_008797958.1| 64 TCPLCRRPL 72
                                      588888876 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 ?    3.4   0.4      0.14        71      17      26 ..      37      47 ..      30      49 .. 0.75
   2 ?   11.8   0.5   0.00034      0.17      19      29 ..      62      72 ..      60      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.14
                                      T-SE.E-TTT- CS
                     Rad50_zn_hook 17 eakg.cCPlCg 26
                                      ++k  +CP Cg
  gi|557694904|ref|YP_008797958.1| 37 NEKTySCPHCG 47
                                      455569****8 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00034
                                      SEE-TTT--EE CS
                     Rad50_zn_hook 19 kgcCPlCgRel 29
                                      k+ CPlC R+l
  gi|557694904|ref|YP_008797958.1| 62 KQTCPLCRRPL 72
                                      679*******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 ?    5.5   0.1     0.024        12      13      25 ..      22      34 ..      18      35 .. 0.80
   2 ?   11.2   1.6   0.00037      0.19       2      11 ..      40      49 ..      39      54 .. 0.84
   3 ?    0.5   0.3       0.9   4.5e+02       3       8 ..      63      68 ..      61      71 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.024
                       zf-ribbon_3 13 ssddnvCpyCGtk 25
                                      ++ + +C  CG +
  gi|557694904|ref|YP_008797958.1| 22 RPKQENCVICGLE 34
                                      7889999999976 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00037
                       zf-ribbon_3  2 tvrCPnCGap 11
                                      t++CP+CGa+
  gi|557694904|ref|YP_008797958.1| 40 TYSCPHCGAV 49
                                      7899999985 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.9
                       zf-ribbon_3  3 vrCPnC 8 
                                      ++CP C
  gi|557694904|ref|YP_008797958.1| 63 QTCPLC 68
                                      567766 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   7.3    0.0035       1.7       2      44 ..      25      62 ..      24      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0035
                                      --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHH CS
                           FANCL_C  2 eveCgiCyayrldsgevpdisCdnekCnkkfHsaCLkeWlrsl 44
                                      + +C iC  +    g+  ++sC  ++C+   H +C  +Wl   
  gi|557694904|ref|YP_008797958.1| 25 QENCVICGLE---MGNEKTYSC--PHCGAVGHMSCFDDWLVVK 62
                                      5678888654...567778999..89*************9755 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 ?   10.9   5.2   0.00063      0.32      10      44 ..      24      56 ..      18      66 .. 0.89
   2 ?    0.3   0.0       1.3   6.5e+02      11      21 ..      62      72 ..      56      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00063
                                      S--B-TTT-SB--SSSS-EEEETTT--EE-CCCCT CS
                              C1_1 10 qptfCkhCgeflwgkekqglkCswCkllvHkkChe 44
                                      ++  C  Cg  +  ++   ++C  C+ + H +C+ 
  gi|557694904|ref|YP_008797958.1| 24 KQENCVICGLEM--GNEKTYSCPHCGAVGHMSCFD 56
                                      5678********..9999***************97 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 1.3
                                      --B-TTT-SB- CS
                              C1_1 11 ptfCkhCgefl 21
                                      +++C  C+ +l
  gi|557694904|ref|YP_008797958.1| 62 KQTCPLCRRPL 72
                                      57899998776 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   4.5      0.12        60      22      28 ..      40      47 ..      16      50 .. 0.81
   2 ?    6.2   0.0     0.026        13      23      33 ..      64      74 ..      55      75 .] 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.12
                     zinc_ribbon_9 22 v.lCPhCg 28
                                      + +CPhCg
  gi|557694904|ref|YP_008797958.1| 40 TySCPHCG 47
                                      236****8 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.026
                     zinc_ribbon_9 23 lCPhCgggFVE 33
                                      +CP C+   VE
  gi|557694904|ref|YP_008797958.1| 64 TCPLCRRPLVE 74
                                      7*****98887 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 ?   -2.1   0.2       7.3   3.6e+03       4       8 ..      28      32 ..      26      32 .. 0.80
   2 ?    9.9   0.2    0.0013      0.65      16      27 ..      35      46 ..      33      47 .. 0.90
   3 ?    5.4   0.3     0.035        17       2      13 ..      63      74 ..      62      75 .] 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 7.3
                                      -TTT- CS
                      zf-FPG_IleRS  4 CpRCw 8 
                                      C  C+
  gi|557694904|ref|YP_008797958.1| 28 CVICG 32
                                      88887 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0013
                                      CTTEEEEE-TTT CS
                      zf-FPG_IleRS 16 qagrstyfCprC 27
                                      ++++ ty Cp+C
  gi|557694904|ref|YP_008797958.1| 35 MGNEKTYSCPHC 46
                                      7899******** PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.035
                                      SB-TTT--BBEE CS
                      zf-FPG_IleRS  2 epCpRCwryier 13
                                      + Cp C+r++++
  gi|557694904|ref|YP_008797958.1| 63 QTCPLCRRPLVE 74
                                      67******9875 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 ?   11.5   0.7   0.00043      0.22      30      57 ..      27      51 ..      14      52 .. 0.87
   2 ?    0.1   0.1       1.6     8e+02      29      36 ..      63      70 ..      62      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00043
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfead 57
                                      +C  Cg ++ +   ++t+ Cp+Cg++ +
  gi|557694904|ref|YP_008797958.1| 27 NCVICGLEMGN---EKTYSCPHCGAVGH 51
                                      7999**99999...9*********9865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.6
                    OrfB_Zn_ribbon 29 ktCseCgs 36
                                      +tC+ C +
  gi|557694904|ref|YP_008797958.1| 63 QTCPLCRR 70
                                      79999976 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 ?    9.7   8.0    0.0016      0.79       1      44 []      27      70 ..      27      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0016
                         zf-RING_5  1 hCnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCrk 44
                                      +C +C  ++ +e+ +    Cg + + +C++  l  +++Cp+Cr+
  gi|557694904|ref|YP_008797958.1| 27 NCVICGLEMGNEKTYSCPHCGAVGHMSCFDDWLVVKQTCPLCRR 70
                                      6********99999999***9999999999999999******95 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 ?    0.8   0.1       1.2   6.2e+02       2      12 ..      22      32 ..      21      40 .. 0.79
   2 ?    6.7   2.1     0.017       8.7      43      65 ..      28      49 ..      27      53 .. 0.79
   3 ?    7.4   0.2      0.01       5.1      48      66 ..      54      72 ..      49      75 .] 0.86

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 1.2
                     zf-LITAF-like  2 eptqvdCpaCq 12
                                      +p q +C +C+
  gi|557694904|ref|YP_008797958.1| 22 RPKQENCVICG 32
                                      58888899997 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.017
                     zf-LITAF-like 43 cliPfcvdslkdvehyCpnCgal 65
                                      c + + +++ ++++++Cp+Cga+
  gi|557694904|ref|YP_008797958.1| 28 C-VICGLEMGNEKTYSCPHCGAV 49
                                      4.3477788889999*****985 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.01
                     zf-LITAF-like 48 cvdslkdvehyCpnCgall 66
                                      c+d+   v+++Cp C++ l
  gi|557694904|ref|YP_008797958.1| 54 CFDDWLVVKQTCPLCRRPL 72
                                      8999999********9876 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 ?   11.2   1.6   0.00056      0.28      68      96 ..      23      50 ..      18      63 .. 0.81
   2 ?    1.4   0.1      0.63   3.2e+02      76      97 ..      54      73 ..      51      75 .] 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00056
                                      --EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA 68 pvkvrCreCgkefeleekalrCpkCgsad 96
                                      p +  C  Cg e+  e+ +++Cp+Cg+ +
  gi|557694904|ref|YP_008797958.1| 23 PKQENCVICGLEMGNEK-TYSCPHCGAVG 50
                                      66778*****9999774.589*****865 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.63
                                      TS-EEECHHHHHS-TTTSSS-E CS
                              HypA 76 CgkefeleekalrCpkCgsadv 97
                                      C  ++ + +   +Cp C +  v
  gi|557694904|ref|YP_008797958.1| 54 CFDDWLVVK--QTCPLCRRPLV 73
                                      555555443..48****98766 PP

>> DUF2256  Uncharacterized protein conserved in bacteria (DUF2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.035        17       6      21 ..      24      39 ..      19      42 .. 0.75
   2 ?    0.8   0.2       1.1   5.3e+02       9      14 ..      42      47 ..      36      49 .. 0.79
   3 ?    6.9   0.2     0.014       6.9       7      17 ..      62      72 ..      59      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.035
                           DUF2256  6 psKiCavCgrpftwRk 21
                                      ++  C++Cg ++   k
  gi|557694904|ref|YP_008797958.1| 24 KQENCVICGLEMGNEK 39
                                      6779*****9997665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 1.1
                           DUF2256  9 iCavCg 14
                                       C++Cg
  gi|557694904|ref|YP_008797958.1| 42 SCPHCG 47
                                      7****8 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.014
                           DUF2256  7 sKiCavCgrpf 17
                                      + +C+ C rp+
  gi|557694904|ref|YP_008797958.1| 62 KQTCPLCRRPL 72
                                      679******97 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.9     0.017       8.6      22      41 .]      28      46 ..      24      46 .. 0.89
   2 ?    6.8   0.2     0.013       6.3      24      41 .]      53      68 ..      50      68 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.017
                                      -CHHHHHHHHCTSSB--TTT CS
                          zf-C3HC4 22 CskCirkilksrkkvkCPlC 41
                                      C  C +++ + +k+++CP C
  gi|557694904|ref|YP_008797958.1| 28 CVICGLEMGN-EKTYSCPHC 46
                                      8889999999.99999**99 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.013
                                      HHHHHHHHCTSSB--TTT CS
                          zf-C3HC4 24 kCirkilksrkkvkCPlC 41
                                      +C + +l    k++CPlC
  gi|557694904|ref|YP_008797958.1| 53 SCFDDWLV--VKQTCPLC 68
                                      68889998..7889**** PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   2.1      0.33   1.7e+02       8      27 ..      25      44 ..      23      46 .. 0.83
   2 ?    1.6   0.4      0.74   3.7e+02      10      16 ..      42      48 ..      39      53 .. 0.85
   3 ?    5.1   0.0     0.061        30       1      17 [.      55      71 ..      55      74 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.33
                            DUF983  8 adaCeaCgldlsharaddgP 27
                                      +++C  Cgl+++ +++   P
  gi|557694904|ref|YP_008797958.1| 25 QENCVICGLEMGNEKTYSCP 44
                                      589********999876666 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.74
                            DUF983 10 aCeaCgl 16
                                      +C++Cg+
  gi|557694904|ref|YP_008797958.1| 42 SCPHCGA 48
                                      7****96 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.061
                            DUF983  1 FkgfLkvadaCeaCgld 17
                                      F+ +L v+++C+ C   
  gi|557694904|ref|YP_008797958.1| 55 FDDWLVVKQTCPLCRRP 71
                                      899***********876 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 ?    0.7   0.1       2.7   1.3e+03       3       8 ..      28      33 ..      27      40 .. 0.78
   2 ?    6.8   0.3     0.029        15       1       8 [.      41      48 ..      41      49 .. 0.85
   3 ?    4.2   0.1      0.19        97       2       9 ..      64      71 ..      63      74 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 2.7
                         zf-C2H2_4  3 CpiCgk 8 
                                      C iCg 
  gi|557694904|ref|YP_008797958.1| 28 CVICGL 33
                                      99**75 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.029
                         zf-C2H2_4  1 fkCpiCgk 8 
                                      + Cp+Cg+
  gi|557694904|ref|YP_008797958.1| 41 YSCPHCGA 48
                                      89****86 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.19
                         zf-C2H2_4  2 kCpiCgks 9 
                                      +Cp+C+++
  gi|557694904|ref|YP_008797958.1| 64 TCPLCRRP 71
                                      6****886 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 ?    7.9   0.1    0.0087       4.4      11      21 ..      37      47 ..      34      50 .. 0.87
   2 ?    4.4   0.1      0.11        56      16      21 ..      64      69 ..      59      70 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0087
                         zf-H2C2_2 11 gekpyeCplCd 21
                                      +ek y Cp C+
  gi|557694904|ref|YP_008797958.1| 37 NEKTYSCPHCG 47
                                      6899******8 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.11
                         zf-H2C2_2 16 eCplCd 21
                                      +CplC+
  gi|557694904|ref|YP_008797958.1| 64 TCPLCR 69
                                      8****8 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       3.5   1.7e+03      13      17 ..      27      31 ..      26      34 .. 0.68
   2 ?    7.8   0.3    0.0068       3.4      16      21 ..      42      47 ..      38      49 .. 0.88
   3 ?    5.1   0.4      0.05        25       1       9 [.      63      71 ..      63      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.5
                           UPF0547 13 aaqfC 17
                                      ++++C
  gi|557694904|ref|YP_008797958.1| 27 NCVIC 31
                                      67777 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0068
                           UPF0547 16 fCphCG 21
                                      +CphCG
  gi|557694904|ref|YP_008797958.1| 42 SCPHCG 47
                                      7****9 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.05
                           UPF0547  1 KvCPeCeak 9 
                                      ++CP C+++
  gi|557694904|ref|YP_008797958.1| 63 QTCPLCRRP 71
                                      589999986 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 ?    8.0   5.2     0.006         3       2      29 ..      28      53 ..      14      58 .. 0.81
   2 ?   -0.2   0.1       2.2   1.1e+03      16      23 ..      62      69 ..      60      73 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.006
                          zf-Mss51  2 CPvpkhkqtapkhvdfeCpdCGiptycs 29
                                      C ++  ++   ++ ++ Cp+CG + ++s
  gi|557694904|ref|YP_008797958.1| 28 CVICGLEM--GNEKTYSCPHCGAVGHMS 53
                                      44554444..78999********99988 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.2
                          zf-Mss51 16 dfeCpdCG 23
                                      + +Cp C 
  gi|557694904|ref|YP_008797958.1| 62 KQTCPLCR 69
                                      55777774 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 ?   -0.6   0.1       3.5   1.7e+03      31      38 ..      25      32 ..      21      38 .. 0.64
   2 ?    7.7   1.2    0.0087       4.3       2      12 ..      40      51 ..      39      55 .. 0.80
   3 ?    3.9   0.1      0.13        65       4       9 ..      64      69 ..      61      75 .] 0.62

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.5
                           zf-Di19 31 evvCPvCa 38
                                      +  C +C 
  gi|557694904|ref|YP_008797958.1| 25 QENCVICG 32
                                      45577775 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0087
                           zf-Di19  2 sftCPyCgk.el 12
                                      ++ CP+Cg  ++
  gi|557694904|ref|YP_008797958.1| 40 TYSCPHCGAvGH 51
                                      799****98554 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.13
                           zf-Di19  4 tCPyCg 9 
                                      tCP C+
  gi|557694904|ref|YP_008797958.1| 64 TCPLCR 69
                                      555555 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 ?    0.7   0.0         1   5.1e+02      19      31 ..      22      32 ..      18      39 .. 0.68
   2 ?    8.2   1.7    0.0046       2.3       4      11 ..      40      47 ..      40      54 .. 0.87
   3 ?    1.3   0.4      0.67   3.3e+02       7      11 ..      65      69 ..      63      73 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1
                    Zn_ribbon_SprT 19 sirrhnYrCrrCk 31
                                      + + +n  C +C+
  gi|557694904|ref|YP_008797958.1| 22 RPKQEN--CVICG 32
                                      667777..77776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0046
                    Zn_ribbon_SprT  4 vYrCtgCg 11
                                      +Y+C++Cg
  gi|557694904|ref|YP_008797958.1| 40 TYSCPHCG 47
                                      7******9 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.67
                    Zn_ribbon_SprT  7 CtgCg 11
                                      C+ C+
  gi|557694904|ref|YP_008797958.1| 65 CPLCR 69
                                      77776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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):              36  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 594.63
//
Query:       gi|557694905|ref|YP_008797959.1|  [L=103]
Description: hypothetical protein CSUB_C1478 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00056   19.8   0.1    0.00069   19.5   0.1    1.1  1  MCPsignal      Methyl-accepting chemotaxis protein (MCP) sign
     0.0029   17.7   0.4     0.0043   17.1   0.4    1.2  1  Baculo_PEP_C   Baculovirus polyhedron envelope protein, PEP, 
     0.0052   17.1   1.1      0.007   16.6   1.1    1.2  1  BLOC1_2        Biogenesis of lysosome-related organelles comp
     0.0054   17.1   4.6       0.18   12.3   0.3    2.2  2  Cep57_MT_bd    Centrosome microtubule-binding domain of Cep57
     0.0073   16.2   2.6        1.1    9.2   0.1    2.1  2  Prefoldin      Prefoldin subunit
  ------ inclusion threshold ------
      0.011   15.8   1.1      0.014   15.4   1.1    1.2  1  DUF1664        Protein of unknown function (DUF1664)
      0.011   16.3   5.7       0.53   10.9   0.7    2.2  2  SlyX           SlyX
      0.011   15.6   0.3      0.012   15.5   0.3    1.2  1  Cauli_AT       Aphid transmission protein
      0.012   15.2   0.5      0.016   14.8   0.5    1.2  1  Vps5           Vps5 C terminal like
      0.015   14.8   0.5      0.025   14.0   0.5    1.4  1  HBM            Helical bimodular sensor domain
      0.017   14.5   1.7      0.022   14.1   1.7    1.2  1  GAS            Growth-arrest specific micro-tubule binding
      0.017   13.8   0.7      0.018   13.7   0.7    1.0  1  FapA           Flagellar Assembly Protein A
      0.017   15.6   1.5      0.052   14.0   1.5    1.8  1  NPV_P10        Nucleopolyhedrovirus P10 protein
      0.017   15.4   0.7      0.066   13.5   0.7    1.8  1  DUF948         Bacterial protein of unknown function (DUF948)
      0.021   15.0   0.6       0.11   12.7   0.6    2.0  1  T3SchapCesA    Type III secretion system filament chaperone C
      0.023   14.4   0.2      0.024   14.3   0.2    1.0  1  LUC7           LUC7 N_terminus
      0.024   14.4   0.9      0.071   12.9   0.2    1.9  2  DASH_Duo1      DASH complex subunit Duo1
      0.029   13.0   0.6      0.031   12.9   0.6    1.0  1  AAA_13         AAA domain
       0.03   14.5   4.0      0.031   14.4   4.0    1.2  1  Tropomyosin_1  Tropomyosin like
      0.033   15.0   0.4       0.13   13.1   0.2    1.9  2  Csm2_III-A     Csm2 Type III-A
      0.039   14.1   0.5      0.048   13.8   0.5    1.3  1  DUF3461        Protein of unknown function (DUF3461)
      0.042   13.8   1.2      0.059   13.4   1.2    1.3  1  FlxA           FlxA-like protein
      0.062   13.9   1.9        2.1    9.0   0.7    2.1  2  YabA           Initiation control protein YabA
      0.062   14.0   0.8      0.072   13.8   0.8    1.1  1  DUF2203        Uncharacterized conserved protein (DUF2203)
       0.07   12.9   1.8        2.6    7.9   0.2    2.1  2  SKA2           Spindle and kinetochore-associated protein 2
      0.073   13.6   4.9      0.038   14.5   3.1    1.4  1  APG6_N         Apg6 coiled-coil region
      0.084   13.0   2.4       0.38   10.9   1.6    2.1  2  Med9           RNA polymerase II transcription mediator compl
       0.11   13.0   1.7       0.17   12.4   1.7    1.3  1  Syntaxin-6_N   Syntaxin 6, N-terminal
       0.29   10.4   3.9       0.76    9.0   0.8    1.9  2  CorA           CorA-like Mg2+ transporter protein
       0.32   11.1   5.6        2.1    8.4   2.8    2.1  2  DHR10          Designed helical repeat protein 10 domain
       0.37   11.3   3.1        2.3    8.8   0.4    2.6  2  MobC           Bacterial mobilisation protein (MobC)
       0.52   10.6   3.5        4.2    7.6   2.1    2.1  2  XhlA           Haemolysin XhlA


Domain annotation for each model (and alignments):
>> 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 !   19.5   0.1   1.2e-06   0.00069      93     165 ..      30     101 ..      18     103 .] 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-06
                                       HHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  93 aliieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqav 165
                                       +l  e+ +e+ + ++ ++e  q  +e+s++ e+ ++ lk i ++   ++d v+ei  a  e+sa++ ++ +a+
  gi|557694905|ref|YP_008797959.1|  30 QLA-EVLAEVIEEIDKMKERLQTLSESSQTPENLERRLKYIEDQLIVLSDDVREILNALGELSATVAQIKKAL 101
                                       333.56666666777888899999999999999************************************9986 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 !   17.1   0.4   7.8e-06    0.0043      35     108 ..      30     101 ..      23     102 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.8e-06
                      Baculo_PEP_C  35 qlatlldaietqLnalsedlksllaeldt..rldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstL 108
                                       qla+ l+++ +++++++e+l+ l+++ +t  +l+  l+ ++d+l  l+d++r+ L++    l +L + v+ i+++L
  gi|557694905|ref|YP_008797959.1|  30 QLAEVLAEVIEEIDKMKERLQTLSESSQTpeNLERRLKYIEDQLIVLSDDVREILNA----LGELSATVAQIKKAL 101
                                       666666666666777777777766666666688888888888888888888877765....455666666666655 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 !   16.6   1.1   1.2e-05     0.007      23      94 ..      29     100 ..      20     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                           BLOC1_2  23 klLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEak 94 
                                       + L ++  +++e+++k+k++++ l+++++  ++++  l+   +q+  + ++v+e+ +a  eL + + ++++ 
  gi|557694905|ref|YP_008797959.1|  29 RQLAEVLAEVIEEIDKMKERLQTLSESSQTPENLERRLKYIEDQLIVLSDDVREILNALGELSATVAQIKKA 100
                                       56777778999**************************************************99999988765 PP

>> Cep57_MT_bd  Centrosome microtubule-binding domain of Cep57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.3   0.00094      0.53      11      37 ..      29      55 ..      25      58 .. 0.91
   2 !   12.3   0.3   0.00031      0.18       1      43 [.      50      92 ..      50     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00094
                       Cep57_MT_bd 11 eaLaevlkeLedEfehlklelqelaaq 37
                                      ++Laevl e  +E++++k +lq+l++ 
  gi|557694905|ref|YP_008797959.1| 29 RQLAEVLAEVIEEIDKMKERLQTLSES 55
                                      68**********************985 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00031
                       Cep57_MT_bd  1 atlrpsqspkeaLaevlkeLedEfehlklelqelaaqynaldp 43
                                      +tl++s++  e+L++ lk +ed++  l+ +  e    + +l +
  gi|557694905|ref|YP_008797959.1| 50 QTLSESSQTPENLERRLKYIEDQLIVLSDDVREILNALGELSA 92
                                      589**************************99998888777764 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.4    0.0044       2.5      13      37 ..      33      57 ..      24      62 .. 0.73
   2 !    9.2   0.1    0.0019       1.1      80     118 ..      60      98 ..      56     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0044
                                      HHHHHHHHHHHHHHHHHHHHTT.-T CS
                         Prefoldin 13 aqlkeaieelektletlktlkkede 37
                                      + l e iee++k +e+l+tl+++ +
  gi|557694905|ref|YP_008797959.1| 33 EVLAEVIEEIDKMKERLQTLSESSQ 57
                                      5577889999999999999998444 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  80 ellkkkleelekqlekleeeleklkdqittleanlaqly 118
                                       e l+++l+++e+ql +l ++++++ +++ +l a++aq+ 
  gi|557694905|ref|YP_008797959.1|  60 ENLERRLKYIEDQLIVLSDDVREILNALGELSATVAQIK 98 
                                       5699******************************99975 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.1   2.5e-05     0.014      44     116 ..      29     100 ..      24     103 .] 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-05
                           DUF1664  44 esvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesk 116
                                        ++++ l +v e++ + k++L+  + +  ++ ++ ++  k i++++  +++d++ei + + +++++v ++++ 
  gi|557694905|ref|YP_008797959.1|  29 RQLAEVLAEVIEEIDKMKERLQ-TLSESSQTPENLERRLKYIEDQLIVLSDDVREILNALGELSATVAQIKKA 100
                                       5566666666666666666664.45555666666666677777777777777777777777777777777665 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.7   0.00095      0.53      19      48 ..      28      57 ..      26      61 .. 0.85
   2 ?    8.4   0.6     0.006       3.3       6      47 ..      60     101 ..      56     103 .] 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00095
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHT-X CS
                              SlyX 19 ieeLndvvaeqqqqidrlqrqlrllaerlk 48
                                      + +L +v+ae  ++id+++++l+ l e  +
  gi|557694905|ref|YP_008797959.1| 28 VRQLAEVLAEVIEEIDKMKERLQTLSESSQ 57
                                      679999999999********9999998755 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT- CS
                              SlyX   6 eeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerl 47 
                                       e+LE +l + ed++  L+d v e    + +l + ++++++ l
  gi|557694905|ref|YP_008797959.1|  60 ENLERRLKYIEDQLIVLSDDVREILNALGELSATVAQIKKAL 101
                                       68999*************999999999999999999988876 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.3   2.2e-05     0.012     108     162 ..      30      84 ..      13     102 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.2e-05
                          Cauli_AT 108 klletLkeaqnrikkleeetkklaekivtekllkeevkdlderlseirdslkaii 162
                                       +l e+L e+ + i+k++e+ + l+e  +t + l+  +k ++++l  + d++++i+
  gi|557694905|ref|YP_008797959.1|  30 QLAEVLAEVIEEIDKMKERLQTLSESSQTPENLERRLKYIEDQLIVLSDDVREIL 84 
                                       5677888888888888888888888888888888888888888888888888875 PP

>> Vps5  Vps5 C terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5   2.9e-05     0.016      11      70 ..      37      96 ..      28     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.9e-05
                              Vps5 11 sisksstkfeEqDewFedkkqeldslesqLkkLykaiellvsqrkelasataelaksles 70
                                       + + + k++E  + +++  q+ ++le +Lk +++ +  l++  +e+ +a++el++++++
  gi|557694905|ref|YP_008797959.1| 37 EVIEEIDKMKERLQTLSESSQTPENLERRLKYIEDQLIVLSDDVREILNALGELSATVAQ 96
                                      3444489*************************************************9986 PP

>> HBM  Helical bimodular sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   4.4e-05     0.025      44      93 ..      36      86 ..      24     102 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.4e-05
                                      HHHHHHHHHHHHHHHHHHHH--SHHHH.HHHHHHHHHHHHHHHHHHHHHHH CS
                               HBM 44 aavqkkldelkaqlqklkakfkspenv.rlLqeqlalvqeyrksfnelraa 93
                                      a+v +++d++k+ lq+l +++++pen+ r+L+ + +++  + + + e+ +a
  gi|557694905|ref|YP_008797959.1| 36 AEVIEEIDKMKERLQTLSESSQTPENLeRRLKYIEDQLIVLSDDVREILNA 86
                                      679***********************8445665555544444444444433 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 ?   14.1   1.7     4e-05     0.022      57     124 ..      29      96 ..      24     102 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-05
                               GAS  57 krlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerde 124
                                       ++l e L ++ ee+++++++l++ ++  q  +nl++rlk  e++l  l+ + +     + ++++   +
  gi|557694905|ref|YP_008797959.1|  29 RQLAEVLAEVIEEIDKMKERLQTLSESSQTPENLERRLKYIEDQLIVLSDDVREILNALGELSATVAQ 96 
                                       7999****************************************998888877777777666665555 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.7   3.2e-05     0.018     337     411 ..      26      97 ..      12     103 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.2e-05
                              FapA 337 eklkeleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeelesk 411
                                       e +++l e l e+ ee++k k++++ l++   ++q +++ +  lk ++ +++ l+++++e+ + l el++ +++ 
  gi|557694905|ref|YP_008797959.1|  26 EGVRQLAEVLAEVIEEIDKMKERLQTLSE---SSQTPENLERRLKYIEDQLIVLSDDVREILNALGELSATVAQI 97 
                                       566899999999999********999999...6677788888888899999999999999999999999988876 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.5   9.2e-05     0.052      14      66 ..      36      88 ..      27     102 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.2e-05
                           NPV_P10 14 kavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66
                                      ++v + +d ++++++ ++e +++ ++l+ +L  + +qL  l++ v +I + L 
  gi|557694905|ref|YP_008797959.1| 36 AEVIEEIDKMKERLQTLSESSQTPENLERRLKYIEDQLIVLSDDVREILNALG 88
                                      6788899999************************************9999886 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 ?   13.5   0.7   0.00012     0.066      23      87 ..      30      97 ..      23     102 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00012
                            DUF948 23 klkktldeaaatieelekqvdpilkevedllakvnelledvne....klekvdplteavadlgesvsel 87
                                      +l+++l e+ + i++++++++ +  e+ ++ ++ ++ l+ +++     +++v ++ +a+++l+++v+++
  gi|557694905|ref|YP_008797959.1| 30 QLAEVLAEVIEEIDKMKERLQTL-SESSQTPENLERRLKYIEDqlivLSDDVREILNALGELSATVAQI 97
                                      67777888888888888777654.466777777777666666622223577777777777777777765 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 ?   12.7   0.6   0.00019      0.11      17      60 ..      28      70 ..      23      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00019
                       T3SchapCesA 17 irseieaikkiiaefdvvkesvnilsekaktdpqaaeklnklie 60
                                      +r   e +  +i e+d +ke ++ lse ++t p+  e+  k ie
  gi|557694905|ref|YP_008797959.1| 28 VRQLAEVLAEVIEEIDKMKERLQTLSESSQT-PENLERRLKYIE 70
                                      577789999******************9988.667777777777 PP

>> LUC7  LUC7 N_terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   4.2e-05     0.024      85     147 ..      27      92 ..      12     103 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......XXXXXXXXXXXXXXXXXXXXXXX CS
                              LUC7  85 flrfleklledvdrkiqkgkqrleltqeekeeeeeaka...kkqeqlkeleekiekllaeaeelge 147
                                        +r+l ++l++v + i+k k+rl+  +e++++ e+ ++     ++ql  l++ +++ l+   el+ 
  gi|557694905|ref|YP_008797959.1|  27 GVRQLAEVLAEVIEEIDKMKERLQTLSESSQTPENLERrlkYIEDQLIVLSDDVREILNALGELSA 92 
                                       579999******************888877777666556777788999999999988887766643 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.2   0.00013     0.071       7      40 ..      26      59 ..      23      72 .. 0.90
   2 ?    0.0   0.0       1.3   7.4e+02       9      27 ..      80      98 ..      62     102 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                         DASH_Duo1  7 eqLrkinevienviesLkkaksniervketvest 40
                                      e +r++ ev+  vie+++k+k+ +++++e+ ++ 
  gi|557694905|ref|YP_008797959.1| 26 EGVRQLAEVLAEVIEEIDKMKERLQTLSESSQTP 59
                                      789*************************998765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.3
                         DASH_Duo1  9 LrkinevienviesLkkak 27
                                      +r+i +++  + ++  ++k
  gi|557694905|ref|YP_008797959.1| 80 VREILNALGELSATVAQIK 98
                                      4444444444444443333 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6   5.6e-05     0.031     403     468 ..      34     102 ..      17     103 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                            AAA_13 403 lveeleseldeyk...kkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeLk 468
                                       +++e+ +e+d++k   +++++ +++ e+le++lk +e++l  l ++++e+ + l +   ++++i k Lk
  gi|557694905|ref|YP_008797959.1|  34 VLAEVIEEIDKMKerlQTLSESSQTPENLERRLKYIEDQLIVLSDDVREILNALGELSATVAQIKKALK 102
                                       345566666666633356667778888999999999999999999999999999999999999999886 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   4.0   5.5e-05     0.031      45     116 ..      29     100 ..       4     103 .] 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.5e-05
                     Tropomyosin_1  45 qqleeevekleeklkeakekaeesekkktnnealtrkiqlLEeeleesdkkLkettekLretdvkaeelERk 116
                                       +ql e + ++ e++ ++ke ++  ++ +++ e+l+r+++ +E++l   + +++e ++ L e +++  ++ ++
  gi|557694905|ref|YP_008797959.1|  29 RQLAEVLAEVIEEIDKMKERLQTLSESSQTPENLERRLKYIEDQLIVLSDDVREILNALGELSATVAQIKKA 100
                                       4566666677778888888888888899999**************************999999888777665 PP

>> Csm2_III-A  Csm2 Type III-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2   0.00023      0.13      67      99 ..      21      53 ..       3      70 .. 0.89
   2 ?    0.7   0.0       1.6   8.9e+02      53      87 ..      62      96 ..      51     102 .. 0.41

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00023
                                      HHHHHHHHHHHHHHHHHHHHH--SH.HHHHHHH CS
                        Csm2_III-A 67 aagreeavkelsevlkkaidkvkkskekfkrfv 99
                                      a+ r e v++l+evl ++i++++k ke++++++
  gi|557694905|ref|YP_008797959.1| 21 AVARFEGVRQLAEVLAEVIEEIDKMKERLQTLS 53
                                      67899*********************9998875 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.6
                                      THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        Csm2_III-A 53 ilrklkllkpklaYaagreeavkelsevlkkaidk 87
                                      ++r+lk++  +l+  +   +++ +   +l++ +++
  gi|557694905|ref|YP_008797959.1| 62 LERRLKYIEDQLIVLSDDVREILNALGELSATVAQ 96
                                      44444444444443333322222222233333333 PP

>> DUF3461  Protein of unknown function (DUF3461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.5   8.6e-05     0.048      64     122 ..      23      87 ..      11      98 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.6e-05
                           DUF3461  64 eeykevseisavlrkvleeLdklte...kkkeekdikekllkdlkhlek...vvnskikeierkl 122
                                        +++ v++ ++vl +v+ee+dk+ e   + +e++++ e+l + lk++e    v+++ + ei + l
  gi|557694905|ref|YP_008797959.1|  23 ARFEGVRQLAEVLAEVIEEIDKMKErlqTLSESSQTPENLERRLKYIEDqliVLSDDVREILNAL 87 
                                       68999******************884445567888999999999999965557888888887666 PP

>> FlxA  FlxA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   1.2   0.00011     0.059      17      66 ..      33      81 ..      27     100 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00011
                              FlxA 17 sqiasLqkQiknlqkqLkelsesdeltkeekkkqqqliqaQIqqlqaQIa 66
                                      + +a+  ++i+++++ L+ lses ++t+e+ + + + i+ Q+ +l   ++
  gi|557694905|ref|YP_008797959.1| 33 EVLAEVIEEIDKMKERLQTLSES-SQTPENLERRLKYIEDQLIVLSDDVR 81
                                      556777789**************.*****************999887766 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.7    0.0038       2.1       7      39 ..      25      57 ..      21      67 .. 0.86
   2 ?    4.6   0.1     0.093        52      13      50 ..      62      99 ..      57     102 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0038
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  7 fdkleeleeqleelleeleelkeelaelleena 39
                                      f+ +++l e l+e+ ee++++ke+l++l e  +
  gi|557694905|ref|YP_008797959.1| 25 FEGVRQLAEVLAEVIEEIDKMKERLQTLSESSQ 57
                                      788999********************9999766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.093
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA 13 leeqleelleeleelkeelaelleenaeLeleneklre 50
                                      le++l+ + ++l  l +++ e+l+   eL++   ++++
  gi|557694905|ref|YP_008797959.1| 62 LERRLKYIEDQLIVLSDDVREILNALGELSATVAQIKK 99
                                      55555555555555555555555555555554444444 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.8   0.00013     0.072      13      81 ..      29      99 ..      17     102 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00013
                           DUF2203 13 pllkelleelralrkeleeleeeleeakaeaekse..aaeleaeleeleaeieelveeieelGvevkdlea 81
                                       +l e+l+e+++  ++++e+ + l+e++++ e+ e   ++ e +l  l++ ++e+++ + el + v ++++
  gi|557694905|ref|YP_008797959.1| 29 RQLAEVLAEVIEEIDKMKERLQTLSESSQTPENLErrLKYIEDQLIVLSDDVREILNALGELSATVAQIKK 99
                                      34444444444444444444444555444444433668899999999999999999999999888877765 PP

>> SKA2  Spindle and kinetochore-associated protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0046       2.6      40      61 ..      35      56 ..      17      61 .. 0.64
   2 ?    5.6   0.1     0.023        13      40      73 ..      59      92 ..      53     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0046
                              SKA2 40 pvkLlerlkkvkeelqaLkeqc 61
                                      +++++e++ k+ke+lq+L+e  
  gi|557694905|ref|YP_008797959.1| 35 LAEVIEEIDKMKERLQTLSESS 56
                                      3455666666666666666554 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.023
                              SKA2 40 pvkLlerlkkvkeelqaLkeqceellaekkelid 73
                                      p  L +rlk + ++l  L+++++e+l++  el  
  gi|557694905|ref|YP_008797959.1| 59 PENLERRLKYIEDQLIVLSDDVREILNALGELSA 92
                                      6678889999999999999999999887666554 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   3.1   6.8e-05     0.038      13      85 ..      30     102 ..      28     103 .] 0.92

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.8e-05
                            APG6_N  13 eldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaela 85 
                                       +l + l+++ +e+d+++e l++l ++++++e+ +  l+ +e++l  l+++ +e l+ L el ++ ++++++l+
  gi|557694905|ref|YP_008797959.1|  30 QLAEVLAEVIEEIDKMKERLQTLSESSQTPENLERRLKYIEDQLIVLSDDVREILNALGELSATVAQIKKALK 102
                                       6778899**********************99999999999999999*********************999886 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 ?   10.9   1.6   0.00067      0.38      35      68 ..      42      75 ..      27      83 .. 0.88
   2 ?    0.9   0.0      0.88   4.9e+02      38      59 ..      80     101 ..      77     103 .] 0.68

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00067
                              Med9 35 Lkkarelirelpgidrsveeqeaeieeleeqlak 68
                                      ++k++e +++l++ + ++e+ e++++  e+ql  
  gi|557694905|ref|YP_008797959.1| 42 IDKMKERLQTLSESSQTPENLERRLKYIEDQLIV 75
                                      89****************************9965 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.88
                              Med9  38 arelirelpgidrsveeqeaei 59 
                                       +re ++ l +++ +v++ ++ +
  gi|557694905|ref|YP_008797959.1|  80 VREILNALGELSATVAQIKKAL 101
                                       6777777777777777766665 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   1.7   0.00031      0.17       5      69 ..      33      99 ..      29     102 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00031
                      Syntaxin-6_N  5 evkeeVqkslnkaeslyrrwerlledtss..stseeldetrteLrkalrsiewdledLeetvrivek 69
                                      ev +eV ++++k+++ +++ ++  +++++  ++ + ++++   L   +r+i + l +L  tv+ ++k
  gi|557694905|ref|YP_008797959.1| 33 EVLAEVIEEIDKMKERLQTLSESSQTPENleRRLKYIEDQLIVLSDDVREILNALGELSATVAQIKK 99
                                      6789999999***999999988666655554466666666667788888888899999999877765 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2     0.084        47     123     220 ..      31      54 ..      22      61 .. 0.43
   2 ?    9.0   0.8    0.0014      0.76     127     168 ..      59     102 ..      50     103 .] 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.084
                              CorA 123 lfellekleeeldeledeledstkkeilrelaqlrrrlvklrralapnrevlkrllakaddkllddedkeylrdlld 199
                                       l+e+l ++ ee+d+  ++l                                                          
  gi|557694905|ref|YP_008797959.1|  31 LAEVLAEVIEEIDKMKERL---------------------------------------------------------- 49 
                                       2333333333333333333.......................................................... PP

                              CorA 200 elerllemlealrerleslqd 220
                                                       + l++
  gi|557694905|ref|YP_008797959.1|  50 ----------------QTLSE 54 
                                       ................22222 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                              CorA 127 lekleeeldeledel..edstkkeilrelaqlrrrlvklrrala 168
                                        e+le++l+ +ed+l   ++  +eil+ l +l  +++++++al+
  gi|557694905|ref|YP_008797959.1|  59 PENLERRLKYIEDQLivLSDDVREILNALGELSATVAQIKKALK 102
                                       589************************************99985 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 ?    8.4   2.8    0.0038       2.1      35      92 ..      28      71 ..      25      76 .. 0.55
   2 ?    5.5   0.5     0.031        17      19      56 ..      64     101 ..      60     103 .] 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0038
                             DHR10 35 lrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaee 92
                                      +r++ ++l e+ +e+ k++e  ++l+e +++ e++e++l+                e+
  gi|557694905|ref|YP_008797959.1| 28 VRQLAEVLAEVIEEIDKMKERLQTLSESSQTPENLERRLK--------------YIED 71
                                      4555555555555555555555555555555555555554..............4444 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.031
                             DHR10  19 relqakidalqvvekdlrsciklleeieaelakleeak 56 
                                       r l+   d l v+  d+r+++++l e++a +a+ ++a 
  gi|557694905|ref|YP_008797959.1|  64 RRLKYIEDQLIVLSDDVREILNALGELSATVAQIKKAL 101
                                       555556678889999**************999999886 PP

>> MobC  Bacterial mobilisation protein (MobC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.4    0.0041       2.3      24      45 .]      31      52 ..      29      52 .. 0.90
   2 ?    2.4   0.1      0.38   2.1e+02      28      39 ..      87      98 ..      67     102 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0041
                              MobC 24 sqavlaelkeelaeinkeLdql 45
                                       ++vlae++ee+++++++L+ l
  gi|557694905|ref|YP_008797959.1| 31 LAEVLAEVIEEIDKMKERLQTL 52
                                      5789***************976 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.38
                              MobC 28 laelkeelaein 39
                                      l el++++a+i+
  gi|557694905|ref|YP_008797959.1| 87 LGELSATVAQIK 98
                                      345555555555 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   2.1    0.0076       4.2       8      47 ..      37      72 ..      30      83 .. 0.48
   2 ?    6.6   0.2     0.016         9       8      49 ..      61     102 ..      57     102 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0076
                              XhlA  8 rietkldnleervdkleekaaeaeekiknleedlkklesn 47
                                      ++ +++d+++er+    +  +e  +  +nle +lk +e++
  gi|557694905|ref|YP_008797959.1| 37 EVIEEIDKMKERL----QTLSESSQTPENLERRLKYIEDQ 72
                                      5555555555553....33333344444555555554443 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.016
                              XhlA   8 rietkldnleervdkleekaaeaeekiknleedlkklesnqk 49 
                                        +e++l+ +e+++  l ++ +e ++ + +l  +++++++ +k
  gi|557694905|ref|YP_008797959.1|  61 NLERRLKYIEDQLIVLSDDVREILNALGELSATVAQIKKALK 102
                                       5899******************99999999999999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1957  (0.109153); expected 358.6 (0.02)
Passed bias filter:                     1219  (0.0679904); expected 358.6 (0.02)
Passed Vit filter:                       192  (0.0107089); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.38
# Mc/sec: 807.53
//
Query:       gi|557694906|ref|YP_008797960.1|  [L=284]
Description: hypothetical protein CSUB_C1479 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-05   23.7  26.9       0.01   15.9   6.7    3.7  4  DUF1664          Protein of unknown function (DUF1664)
    0.00015   20.8  23.8    0.00015   20.8  23.8    2.1  2  DUF812           Protein of unknown function (DUF812)
    0.00018   21.3  42.2    0.00084   19.1  15.5    3.3  3  DUF4201          Domain of unknown function (DUF4201)
    0.00058   18.2  23.3    0.00058   18.2  23.3    2.9  3  EzrA             Septation ring formation regulator, EzrA
    0.00065   18.7  49.1      0.006   15.5  18.8    3.1  3  Spc7             Spc7 kinetochore protein
     0.0014   18.7  16.1         14    5.7  10.3    3.7  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
     0.0015   18.8  50.1       0.17   12.1   5.5    4.5  5  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
     0.0029   17.7   9.8     0.0029   17.7   9.8    4.1  3  COG2             COG (conserved oligomeric Golgi) complex com
     0.0035   16.1  38.8     0.0037   16.1   0.1    4.0  4  Tektin           Tektin family
      0.005   17.0  39.4        0.2   11.9  16.7    3.3  3  FliJ             Flagellar FliJ protein
     0.0075   16.3  14.2     0.0075   16.3  14.2    4.1  4  DHR10            Designed helical repeat protein 10 domain
  ------ inclusion threshold ------
      0.014   16.0   2.5      0.014   16.0   2.5    3.7  2  BST2             Bone marrow stromal antigen 2
       0.02   15.3  52.5      0.052   14.0   1.4    5.4  4  ZapB             Cell division protein ZapB
      0.021   14.8   3.3      0.021   14.8   3.3    4.0  2  YscO             Type III secretion protein YscO
      0.024   13.9  37.3       0.11   11.8   6.8    3.8  4  DUF3450          Protein of unknown function (DUF3450)
      0.026   14.7  39.2      0.045   14.0   9.0    4.1  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
      0.027   14.7  15.0      0.099   12.9   0.4    4.3  4  DUF948           Bacterial protein of unknown function (DUF94
      0.027   14.5   1.7      0.027   14.5   1.7    4.8  5  TMF_DNA_bd       TATA element modulatory factor 1 DNA binding
       0.04   13.6  10.6       0.14   11.9   0.7    4.0  4  DUF2937          Protein of unknown function (DUF2937)
      0.058   12.7  46.2       0.15   11.4  18.2    3.0  3  GAS              Growth-arrest specific micro-tubule binding
      0.059   13.3  11.3       0.78    9.7   0.0    4.7  4  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
      0.067   12.7  34.5      0.015   14.8  16.2    2.2  2  Leu_zip          Leucine zipper
      0.068   12.5  23.0          1    8.7  16.4    2.8  2  DUF4407          Domain of unknown function (DUF4407)
      0.072   13.4   4.3       0.77   10.1   0.1    3.5  4  PRANC            PRANC domain
       0.08   13.3   0.7       0.08   13.3   0.7    4.0  4  HrpB7            Bacterial type III secretion protein (HrpB7)
        0.1   12.1  45.2       0.98    8.8  21.4    3.1  3  HMMR_N           Hyaluronan mediated motility receptor N-term
       0.11   13.0  28.2       0.18   12.3   1.6    3.6  3  DUF16            Protein of unknown function DUF16
       0.11   12.6   0.2       0.53   10.4   0.0    2.3  2  MHC_II_beta      Class II histocompatibility antigen, beta do
       0.12   12.1   8.8        3.1    7.6   0.3    3.7  2  Sigma70_r4_2     Sigma-70, region 4
       0.12   12.4  50.7       0.63   10.1  18.9    4.1  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.13   12.7  11.7      0.097   13.2   1.3    4.2  4  NPV_P10          Nucleopolyhedrovirus P10 protein
       0.15   10.0  19.8       0.03   12.3   9.8    2.0  2  Prominin         Prominin
       0.15   12.3   2.0        1.5    9.1   0.6    2.7  2  NFRKB_winged     NFRKB Winged Helix-like
        0.2   11.4  50.1       0.21   11.4  29.8    3.1  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
       0.24   11.6  28.2        2.5    8.3   9.3    3.5  3  Fib_alpha        Fibrinogen alpha/beta chain family
        0.4   10.7  29.0       0.34   10.9   5.5    3.6  4  Laminin_II       Laminin Domain II
       0.41   10.8  25.2       0.27   11.4   1.9    3.8  3  COG5             Golgi transport complex subunit 5
       0.55   10.0  15.5        2.7    7.8   0.5    3.2  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.56    8.5  47.5        1.4    7.2  47.5    1.5  1  MAD              Mitotic checkpoint protein
       0.57    9.3  45.7      0.034   13.3   9.0    3.1  3  HAP1_N           HAP1 N-terminal conserved region
       0.73    9.8  34.5       0.17   11.8   0.7    5.7  6  Prefoldin        Prefoldin subunit
        1.2    9.6  56.5         12    6.4   3.0    3.7  3  APG6_N           Apg6 coiled-coil region
        1.3    7.5  33.1        1.6    7.3   0.9    2.1  2  AAA_13           AAA domain
        1.8    7.8  28.5       0.88    8.8   2.8    3.1  3  HemX             HemX, putative uroporphyrinogen-III C-methyl
        2.5    7.6  32.4    1.1e+04   -4.3  32.4    2.6  0  Exonuc_VII_L     Exonuclease VII, large subunit
        3.1    7.4  33.2        9.7    5.8   0.5    4.1  3  SHE3             SWI5-dependent HO expression protein 3
        3.7    7.6  44.0        2.3    8.3  16.7    2.8  3  UPF0242          Uncharacterised protein family (UPF0242) N-t
        3.9    7.6   6.2        2.5    8.2   0.3    3.5  4  DUF4248          Domain of unknown function (DUF4248)
        4.1    7.3  21.0       0.73    9.7   4.0    3.3  3  Cauli_AT         Aphid transmission protein
        5.1    7.4  38.8          2    8.7  13.1    3.6  3  OmpH             Outer membrane protein (OmpH-like)
        5.4    7.2  50.2        8.3    6.6  28.8    3.5  2  ATG16            Autophagy protein 16 (ATG16)
        6.1    7.5  37.4        2.4    8.9   6.3    4.3  3  YabA             Initiation control protein YabA
        6.5    6.9  34.1        1.1    9.4   3.4    4.4  3  TolA_bind_tri    TolA binding protein trimerisation
        7.9    6.4  40.8         26    4.7  19.6    3.0  2  Rootletin        Ciliary rootlet component, centrosome cohesi
        9.1    5.6  37.4         20    4.5  20.8    3.1  2  DUF4618          Domain of unknown function (DUF4618)
        9.1    5.9  44.4         16    5.1   7.3    3.4  3  YkyA             Putative cell-wall binding lipoprotein


Domain annotation for each model (and alignments):
>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   1.5    0.0029      0.94      66     111 ..      31      76 ..      10      87 .. 0.63
   2 !   15.9   6.7   3.1e-05      0.01      37     118 ..      89     173 ..      81     179 .. 0.74
   3 ?    5.7   2.4     0.043        14      48     109 ..     142     203 ..     133     215 .. 0.85
   4 !    8.8   3.6    0.0048       1.5      56     117 ..     210     274 ..     186     281 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0029
                           DUF1664  66 sridrvdkkldeqkeiskeikeevtevredlseigedvesvkeave 111
                                       + i+++++++   +e+ +++ke+v +v e++s+ ++ ++s++++ve
  gi|557694906|ref|YP_008797960.1|  31 QVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVE 76 
                                       4466666666666666667777777777777777777777776666 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.1e-05
                           DUF1664  37 rslsdavesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeav... 110
                                       r+l++ v+s+s++l +  + l++++ +L ++++r+ ++ ++ +++ +e+ +  +e++++ ++i e  e++k+++   
  gi|557694906|ref|YP_008797960.1|  89 RGLTEEVKSLSESLHETADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLItkk 165
                                       899*******************************9998888887777766555555555555555555555555111 PP

                           DUF1664 111 egleskle 118
                                       e le++++
  gi|557694906|ref|YP_008797960.1| 166 EALETEIN 173
                                       34555555 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.043
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkea 109
                                       ++le+  +++a++++ L++ i + ++   e + +s+      +e++++l+++g++++++ ++
  gi|557694906|ref|YP_008797960.1| 142 EELESKEKQIAEAQETLKQLITKKEALETEINILSERYLTSFEEAQKKLENFGREMDKLFKL 203
                                       689999999*********99999888888888889999999**************9998775 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0048
                           DUF1664  56 slaatkrhLssridrvdkk...ldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                        + +  r+L++r++ ++k+    +  +e+s++++eev++++   +++ +++ ++++  ++l++ +
  gi|557694906|ref|YP_008797960.1| 210 RMIRRERELEERLAALEKSkaeAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELI 274
                                       34444455555555554431113334455555555555555555555555555555555555554 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8  23.8   4.7e-07   0.00015     330     487 ..      23     173 ..      12     176 .. 0.88
   2 ?   -1.6  13.4         3   9.5e+02     338     407 ..     207     276 ..     176     283 .. 0.45

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.7e-07
                            DUF812 330 eeleelqeq.ieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalv 405
                                       +e+++++ q ie+le++i+ lee ++kl+++++qv e++   +++ + l++ v+++     ll++a  + + L ++v
  gi|557694906|ref|YP_008797960.1|  23 KEVAAIRVQvIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKA----YLLDQALDSYRGLTEEV 95 
                                       56777775538999*********************999999999999998877654....699************** PP

                            DUF812 406 easaqrlvelakqWekhRvplieeyrelkesksekekeaerkleeikklrekmkevaeelrqkeellkqLvaelekl 482
                                       ++ +++l e a+   ++R+ l++e ++l ++     ++ +r  ee+ k+re+++  ++++++ +e lkqL ++ e+l
  gi|557694906|ref|YP_008797960.1|  96 KSLSESLHETADLLSNQRAELVKEVQRLMQER----ESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEAL 168
                                       **************************997764....56789999*******************************99 PP

                            DUF812 483 pkdvs 487
                                       + +++
  gi|557694906|ref|YP_008797960.1| 169 ETEIN 173
                                       98875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3
                            DUF812 338 qieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlellpdaeeniekLqalvea 407
                                       ++e++ ++  elee +++le+s  ++e  +e+ ++ +ee +k  + k+ ++  +++ e    +L++l+ +
  gi|557694906|ref|YP_008797960.1| 207 RMERMIRRERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELITE 276
                                       3334444444444444444444444444444444444444444444444444444444444444444433 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.8     0.016         5      65     123 ..      18      77 ..      11      87 .. 0.79
   2 !   19.1  15.5   2.6e-06   0.00084      43     134 ..      87     178 ..      81     208 .. 0.95
   3 ?    4.2  13.6       0.1        32      55     117 ..     215     277 ..     182     280 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.016
                           DUF4201  65 Lkrlkkkttk.tvhalthlkeklhmleselselkkelkekeerlaklrkelykvklerdk 123
                                       +  l+k ++   v++++ l e+ + le+ l++lk++ ++  e+  + ++ l++++   +k
  gi|557694906|ref|YP_008797960.1|  18 IADLRKEVAAiRVQVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEK 77 
                                       555655554426999999999999999999999999999999999999999998876666 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 2.6e-06
                           DUF4201  43 dFeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvkl 119
                                        +  l  e+++l++ + e  + L++ +    k+v++l +++e l+ l++e+ + ++el++ke+++a+ ++ l ++ +
  gi|557694906|ref|YP_008797960.1|  87 SYRGLTEEVKSLSESLHETADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLIT 163
                                       5777999********************************************************************** PP

                           DUF4201 120 erdklrkqneklkqq 134
                                       +++ l+++ + l+++
  gi|557694906|ref|YP_008797960.1| 164 KKEALETEINILSER 178
                                       *********999875 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.1
                           DUF4201  55 nkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelykv 117
                                       + ++eer + L++ k  + + + + + l+e  + le+  ++l  e+ e+e+r+++l + +++ 
  gi|557694906|ref|YP_008797960.1| 215 ERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELITEM 277
                                       678999***************************999999999999999999999999988876 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.7     0.017       5.5     445     495 ..      10      61 ..       3      68 .. 0.67
   2 !   18.2  23.3   1.8e-06   0.00058     306     485 ..      49     226 ..      44     232 .. 0.85
   3 ?   -0.1   7.1      0.62     2e+02     102     153 ..     224     275 ..     202     283 .. 0.43

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.017
                                       HSTTTSTTTHHHHHHHT-TT--.HHHHHHHHHTTTTTSGGGTHHHHHHHHHH CS
                              EzrA 445 elkeasdeieelakeLekkpin.ikevnkrldeardlveklyektneliktA 495
                                        l   sd+i +l+ke+   +++ i+++++r++  ++++ kl+e + ++++++
  gi|557694906|ref|YP_008797960.1|  10 LLPRKSDSIADLRKEVAAIRVQvIEKLEERISLLEEALAKLKEDVRQVLEQV 61 
                                       5556677777777777777775357777777777777777777777777765 PP

  == domain 2  score: 18.2 bits;  conditional E-value: 1.8e-06
                                       TTSSSSSHHHHT--HHHHTTGGG-TTTS-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS---STTGGGTH CS
                              EzrA 306 knlkelkeklehlekqnkelkeeldrlkqsYeLseeeleklrelekelkelekdyeeleekleekkvaYSelqeele 382
                                       k  + +++ le++ +  ++l++  + +++ Y L ++ l+++r+l++e+k+l+++++e  + l+++ +   +  ++l 
  gi|557694906|ref|YP_008797960.1|  49 KLKEDVRQVLEQVSSPQRTLSSLQSVVEKAYLL-DQALDSYRGLTEEVKSLSESLHETADLLSNQRAELVKEVQRLM 124
                                       5566778888899999999999999999*****.9********************************9999999999 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-SS-S-TTTHHHHSTTTSTTTHHHHHH CS
                              EzrA 383 eleekleeieekqeeileslkslrkdEkrAreqldeikkelkeikrkieksnLPgiPesyleelkeasdeieelake 459
                                       +  e+l+++ e++ + +e+l+s +k+ ++A+e+l+++ ++ + ++ +i      +++e+yl+ ++ea++++e+  +e
  gi|557694906|ref|YP_008797960.1| 125 QERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEI-----NILSERYLTSFEEAQKKLENFGRE 196
                                       99999****************999999999999999987776666655.....59*****************99999 PP

                                       HT-....TT--HHHHHHHHHTTTTTSGGGT CS
                              EzrA 460 Lek....kpinikevnkrldeardlvekly 485
                                       ++k    + i +++  +r +e ++ +  l+
  gi|557694906|ref|YP_008797960.1| 197 MDKlfklREIRMERMIRRERELEERLAALE 226
                                       988444456777777776666666666665 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.62
                                       HHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTHHHHHHHHHHHHHHHHT-- CS
                              EzrA 102 klaeleeeldeveekikkileelkelteseeknreeieklkekYrelrkkll 153
                                       +l++ ++e +++ e+++k++ee+k+l   +e    ei +++ +  el++ ++
  gi|557694906|ref|YP_008797960.1| 224 ALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELIT 275
                                       2222223333333333344444444444444444444444444333333333 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   3.5    0.0035       1.1     198     259 ..      15      77 ..      12      84 .. 0.83
   2 !   15.5  18.8   1.9e-05     0.006     145     256 ..      85     193 ..      78     208 .. 0.70
   3 ?    5.5  14.8     0.021       6.6     170     253 ..     195     277 ..     180     282 .. 0.42

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0035
                              Spc7 198 keeLeelreelaelkae.ieekkkelaelqeqleeleekieelkeqkseleeeiaeaervlee 259
                                       +++++ lr+e+a++ ++ ie+++++++ l+e l++l+e++ ++ eq s+ +  +++ ++v+e+
  gi|557694906|ref|YP_008797960.1|  15 SDSIADLRKEVAAIRVQvIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEK 77 
                                       577889999999998873577788899999999999999999999999999999999999987 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.9e-05
                              Spc7 145 eenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkke 221
                                        + + gl+e+ + L    e l+e  + l++++ael +e+++l +++e+l+ + +ee+ + reel++ +++i+e ++ 
  gi|557694906|ref|YP_008797960.1|  85 LDSYRGLTEEVKSL---SESLHETADLLSNQRAELVKEVQRLMQERESLSRL-REEVLKWREELESKEKQIAEAQET 157
                                       44455555555555...45677777778899999999999999988776665.566778999999999999999999 PP

                              Spc7 222 laelqeqleeleekieelkeqk.seleeeiaeaerv 256
                                       l++l +++e+le++i+ l+e++ +++ee+ ++ e++
  gi|557694906|ref|YP_008797960.1| 158 LKQLITKKEALETEINILSERYlTSFEEAQKKLENF 193
                                       999999999999999988877524555555555554 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.021
                              Spc7 170 peleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqksel 246
                                        e+++ ++  e ++e++ ++++ele+   + Le+ + e ++l ++ +++++e+++l++ +e+l+ +i+e++ +++el
  gi|557694906|ref|YP_008797960.1| 195 REMDKLFKLREIRMERMIRRERELEE-RLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTEL 270
                                       33333333333333333333333333.34444444444444444444444444444444444444444444444444 PP

                              Spc7 247 eeeiaea 253
                                       +e i e 
  gi|557694906|ref|YP_008797960.1| 271 NELITEM 277
                                       4444443 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 ?    5.7  10.3     0.044        14      16     101 ..      19     102 ..      14     201 .. 0.72
   2 ?    3.0   4.4      0.31        99      51     103 ..     222     276 ..     149     282 .. 0.57

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.044
                      Baculo_PEP_C  16 ldLtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt...rldtlltnLtdalnalq..dtlrneL 87 
                                        dL + ++ai    vq++ +l++ +  +e+ L +l+ed++++l+++++        l+ L++ + +    d+     
  gi|557694906|ref|YP_008797960.1|  19 ADLRKEVAAI---RVQVIEKLEERISLLEEALAKLKEDVRQVLEQVSSpqrT----LSSLQSVVEKAYllDQALDSY 88 
                                       5666666666...566777777777777777777777777777777663331....333333333322224444444 PP

                      Baculo_PEP_C  88 tnlnsiltnLlssv 101
                                        +l+ ++ +L  s+
  gi|557694906|ref|YP_008797960.1|  89 RGLTEEVKSLSESL 102
                                       44444444444444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.31
                      Baculo_PEP_C  51 sedlksllaeldt......rldtlltnLtdalnalq...dtlrneLtnlnsiltnLlssvtN 103
                                        ++l+       +       l +++++L + +++l+   +tl  e+  ++   t+L+  +t 
  gi|557694906|ref|YP_008797960.1| 222 LAALE-------KskaeaeTLIETSNKLREEVKKLEaykETLAREIAEMERRRTELNELITE 276
                                       22222.......11112225555666666666666666666666666666665555555555 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 ?   -0.9   0.0       5.7   1.8e+03      83     102 ..       7      26 ..       4      29 .. 0.77
   2 !   12.1   5.5   0.00053      0.17       8      83 ..      27     105 ..      21     109 .. 0.79
   3 !   10.2   8.6    0.0021      0.68      30      79 ..     101     150 ..      89     154 .. 0.86
   4 ?    3.7  12.1      0.22        69      20      87 ..     143     212 ..     141     224 .. 0.78
   5 ?    6.7  12.4     0.026       8.2      30      89 ..     217     276 ..     206     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 5.7
                       TMF_TATA_bd  83 lLellGeksEeveELraDva 102
                                       ++ ll  ks+ + +Lr++va
  gi|557694906|ref|YP_008797960.1|   7 AMGLLPRKSDSIADLRKEVA 26 
                                       56678889999999999987 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00053
                       TMF_TATA_bd   8 gpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkel...eelekeleelqerye 81 
                                          vq++e+l+ +i  lE  la+lke++ ++ ++ ++ ++ + +l + +e+   l++ l   + l++e+++l+e + 
  gi|557694906|ref|YP_008797960.1|  27 AIRVQVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKAYLLDQALdsyRGLTEEVKSLSESLH 103
                                       5679***********************************99999999999876655555000556667777766655 PP

                       TMF_TATA_bd  82 tl 83 
                                       ++
  gi|557694906|ref|YP_008797960.1| 104 ET 105
                                       55 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0021
                       TMF_TATA_bd  30 slkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqer 79 
                                       sl+e+   l+++r e+ +e+ +lm+e e+l++l +e+ + ++ele+ +++
  gi|557694906|ref|YP_008797960.1| 101 SLHETADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWREELESKEKQ 150
                                       5677777899**********************************999886 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.22
                       TMF_TATA_bd  20 eirrlEgElaslkeelerleaerdeareeivklmke.neelkelkkeleelekeleelqe.ryetlLell 87 
                                       e+ ++E ++a+++e+l++l +++++++ ei  l+++   + +e++k+le+  +e+++l + r+  +  ++
  gi|557694906|ref|YP_008797960.1| 143 ELESKEKQIAEAQETLKQLITKKEALETEINILSERyLTSFEEAQKKLENFGREMDKLFKlREIRMERMI 212
                                       6889***************************999772567899999999999999988542444454455 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.026
                       TMF_TATA_bd  30 slkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryetlLellGe 89 
                                       +l+e+l+ le+++ ea+  i +  k  ee+k+l++  e+l +e++e+++r  +l el+ e
  gi|557694906|ref|YP_008797960.1| 217 ELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELITE 276
                                       467899999999999999999999999999999999999999999999999999888876 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 ?    7.1   2.9     0.016       5.3      61     123 ..      15      78 ..      14      88 .. 0.77
   2 !   17.7   9.8     9e-06    0.0029      47     130 ..     106     191 ..      85     194 .. 0.78
   3 ?    0.6   6.0       1.8   5.7e+02      29     100 ..     191     257 ..     176     282 .. 0.40

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.016
                              COG2  61 SghLvglqeeleevespl.aaarkkvesvreklsereeeveskleeakeleekrellklllkld 123
                                       S++  +l++e+  +++++ +++ ++++ ++e+l++ +e+v++ le+ ++ +++  +l+++++ +
  gi|557694906|ref|YP_008797960.1|  15 SDSIADLRKEVAAIRVQViEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKA 78 
                                       5667788889999998864678889999999999999999999999888888888887777655 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 9e-06
                              COG2  47 lelvnedyadFvslSghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrell..klllk 121
                                       ++l  +  a+ v+  ++L+  +e+l++++ ++++ r+++es +++++e++e++++ + ++++le + ++l  + l +
  gi|557694906|ref|YP_008797960.1| 106 ADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINILseRYLTS 182
                                       445555566666667899*************************************************7663367788 PP

                              COG2 122 ldevvekle 130
                                       ++e  +kle
  gi|557694906|ref|YP_008797960.1| 183 FEEAQKKLE 191
                                       888888887 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 1.8
                              COG2  29 eslrrdLeaylkllekellelvnedyadFvslSghLvglqeeleevesplaaarkkvesvreklsereeeve 100
                                       e+  r++++  kl e ++ ++++++     +l ++L  l+++  e e+ l ++ +k+++ ++kl++ +e++ 
  gi|557694906|ref|YP_008797960.1| 191 ENFGREMDKLFKLREIRMERMIRRER----ELEERLAALEKSKAEAET-LIETSNKLREEVKKLEAYKETLA 257
                                       44444444444444444444444332....122333333222222221.22223333333333333333333 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.2e-05    0.0037     228     288 ..      15      75 ..       3      79 .. 0.90
   2 ?    1.3   0.9      0.37   1.2e+02     321     355 ..      90     128 ..      81     132 .. 0.46
   3 !    9.9   6.6   0.00086      0.27     320     363 ..     131     174 ..     126     179 .. 0.93
   4 ?    2.4  13.1      0.16        52       9      94 ..     180     267 ..     176     280 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.2e-05
                            Tektin 228 dsilkqtandlraqaeavnealrkrieetedaknkleeqlkkvleeiaeleknieeLekai 288
                                       +++++++++++ a + +v e l++ri+ +e+a  kl+e+ ++vle++++ ++++++L++ +
  gi|557694906|ref|YP_008797960.1|  15 SDSIADLRKEVAAIRVQVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVV 75 
                                       5688999***********************************************9999755 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.37
                            Tektin 321 rLveEvkeleetiea....LkeklaeaeaslkaLertrl 355
                                       +L+eEvk l+e++ +    L ++ ae  +++++L+++r 
  gi|557694906|ref|YP_008797960.1|  90 GLTEEVKSLSESLHEtadlLSNQRAELVKEVQRLMQERE 128
                                       555555554443322111144444444444444444444 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00086
                            Tektin 320 yrLveEvkeleetieaLkeklaeaeaslkaLertrleleediav 363
                                        rL eEv + +e++e+ ++++aea+++lk+L  ++ +le +i++
  gi|557694906|ref|YP_008797960.1| 131 SRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINI 174
                                       5899**************************************98 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.16
                            Tektin   9 lkeaeaerneaerlrnesrrlideteektkktqadsnkrLeeRiediefwkeeLekele...elkeeieaLeeekrr 82 
                                       l++ e+ +++ e+   e+++l +  e++ +++ +  +++LeeR+  +e+ k e e+ +e   +l+ee+++Le++k+ 
  gi|557694906|ref|YP_008797960.1| 180 LTSFEEAQKKLENFGREMDKLFKLREIRMERMIR-RERELEERLAALEKSKAEAETLIEtsnKLREEVKKLEAYKET 255
                                       5566777777788888888888887777777554.578999999999999999888776222677799999999999 PP

                            Tektin  83 lekalealeepl 94 
                                       l ++++++e+  
  gi|557694906|ref|YP_008797960.1| 256 LAREIAEMERRR 267
                                       999999998754 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   1.4   0.00066      0.21      43     100 ..      29      79 ..      13      89 .. 0.60
   2 !   11.9  16.7   0.00063       0.2      19     112 ..      93     192 ..      81     204 .. 0.79
   3 ?    4.5   6.8      0.12        38       5      80 ..     206     279 ..     202     283 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00066
                              FliJ  43 saaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkklekLkerek 100
                                        +       + i++l+e+i+ ++++la+++++v +  e+  + ++ + +l+ + e+++
  gi|557694906|ref|YP_008797960.1|  29 RV-------QVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKAY 79 
                                       34.......4555666666666666666666666666666666666666655555543 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00063
                              FliJ  19 ekleeleqyrqeyqkqlsgea.q.glsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkkle 93 
                                       e++ +l + ++e +  ls++  +   ++++l++ ++ +s+l+e++ + ++el+ +ekq+ +a+e +++   ++++le
  gi|557694906|ref|YP_008797960.1|  93 EEVKSLSESLHETADLLSNQRaElVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALE 169
                                       3344444444444444444444448899**********************************************999 PP

                              FliJ  94 k....LkerekkeeqkeenrrEq 112
                                       +    L er+ + + +++++ E+
  gi|557694906|ref|YP_008797960.1| 170 TeiniLSERYLTSFEEAQKKLEN 192
                                       66666**************9996 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.12
                              FliJ   5 reLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekare 80 
                                        +++++ r+ ++ ee+l++le+  +e +  ++ +      +e ++++a++++l ++ia+ ++  + +++ + + r+
  gi|557694906|ref|YP_008797960.1| 206 IRMERMIRRERELEERLAALEKSKAEAETLIETSN--KLREEVKKLEAYKETLAREIAEMERRRTELNELITEMRR 279
                                       67888889999999999999999988844333333..447999999999999999999988877777777766665 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 ?    3.0   2.7      0.31        98      24      61 ..      14      52 ..      10      60 .. 0.70
   2 ?    6.3  19.4      0.03       9.6       2     112 ..      52     162 ..      51     167 .. 0.93
   3 ?    2.6  15.6      0.43   1.4e+02      34     113 ..     119     198 ..     114     202 .. 0.49
   4 !   16.3  14.2   2.4e-05    0.0075      14      82 ..     211     279 ..     207     280 .. 0.94

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.31
                             DHR10 24 kidalqvvekdlrsc.iklleeieaelakleeakkklke 61
                                      k d+++++ k+++++ ++++e++e+ +  leea +klke
  gi|557694906|ref|YP_008797960.1| 14 KSDSIADLRKEVAAIrVQVIEKLEERISLLEEALAKLKE 52
                                      667777777777776467777788888888888887776 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.03
                             DHR10   2 eslaeekeelaelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielreler 78 
                                       e++ +  e++++ +r    lq  ++    +++ l s   l ee+++  ++l e+ + l+++r++l +  ++l +   
  gi|557694906|ref|YP_008797960.1|  52 EDVRQVLEQVSSPQRTLSSLQSVVEKAYLLDQALDSYRGLTEEVKSLSESLHETADLLSNQRAELVKEVQRLMQERE 128
                                       56777789999999*************************************************************** PP

                             DHR10  79 keerlqrqlenaeeklerlreqaeekreaakarl 112
                                         +rl+  + +++e+le  ++q +e +e  k+ +
  gi|557694906|ref|YP_008797960.1| 129 SLSRLREEVLKWREELESKEKQIAEAQETLKQLI 162
                                       *************************999998855 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.43
                             DHR10  34 dlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreqaeekreaaka 110
                                       +++++++  e +++  +++ + +++l++ +++++e +++l++l +k+e l+  ++   e++    e+a++k e+  +
  gi|557694906|ref|YP_008797960.1| 119 EVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINILSERYLTSFEEAQKKLENFGR 195
                                       33333333333333333334444455555555555555555555555555555555555555555555555555555 PP

                             DHR10 111 rle 113
                                       +++
  gi|557694906|ref|YP_008797960.1| 196 EMD 198
                                       555 PP

  == domain 4  score: 16.3 bits;  conditional E-value: 2.4e-05
                             DHR10  14 lErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeer 82 
                                       + r+ rel+++++al++ +++ + +i+  +++ +e++kle  k++l++  +++e +++el+el ++ +r
  gi|557694906|ref|YP_008797960.1| 211 MIRRERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELITEMRR 279
                                       5699***********************************************************988766 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   2.5   4.4e-05     0.014      12      86 ..      33     106 ..      25     111 .. 0.89
   2 ?    9.3   6.2    0.0051       1.6      23      85 ..     215     277 ..     205     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  12 eqecrnvtrlLerqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqdae 86 
                                        +++++   lLe+ L++ +e +r+   q+++ ++t+ +L++  ek      +++   + l +e+k+L ++L+++ 
  gi|557694906|ref|YP_008797960.1|  33 IEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKAYLL-DQALDSYRGLTEEVKSLSESLHETA 106
                                       578889999*******************************999988877.5566899**************9875 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  23 erqLtqaqeslreaeaqaatcnqtvvtLkasLekekaqsqkqqakvqelqgeikkLnqkLqda 85 
                                       er+L +    l++ +a+a t  +t+ +L++  +k +a ++   +++ e+++  ++Ln+ + + 
  gi|557694906|ref|YP_008797960.1| 215 ERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELITEM 277
                                       677778888999*********************************************988775 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   1.4   0.00016     0.052      31      62 ..      29      61 ..      16      79 .. 0.48
   2 ?   -1.2  19.2         9   2.9e+03      18      68 ..     104     164 ..      80     178 .. 0.66
   3 ?    0.1   1.8       3.6   1.1e+03      11      36 ..     206     231 ..     196     234 .. 0.58
   4 ?    7.7  10.5     0.015       4.7      13      52 ..     232     271 ..     219     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 0.00016
                              ZapB 31 keen.eelkeenreleeeneqlkeereawqerl 62
                                      + ++ e+l+e++  lee + +lke+  ++ e +
  gi|557694906|ref|YP_008797960.1| 29 RVQViEKLEERISLLEEALAKLKEDVRQVLEQV 61
                                      444444444444444444444444444333332 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 9
                              ZapB  18 dtitlLqmeieeLkeeneelkeenrele..........eeneqlkeereawqerlkkLLgk 68 
                                       +t +lL+++ +eL +e++ l +e + l+          ee+e  +++ ++ qe lk+L+ k
  gi|557694906|ref|YP_008797960.1| 104 ETADLLSNQRAELVKEVQRLMQERESLSrlreevlkwrEELESKEKQIAEAQETLKQLITK 164
                                       4555555555555555555555555555555555577777777777777777777777765 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 3.6
                              ZapB  11 skiqkaidtitlLqmeieeLkeenee 36 
                                        + + +i + ++L +++++L++ ++e
  gi|557694906|ref|YP_008797960.1| 206 IRMERMIRRERELEERLAALEKSKAE 231
                                       45555555556666666666655554 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.015
                              ZapB  13 iqkaidtitlLqmeieeLkeeneelkeenreleeeneqlk 52 
                                        +++i+t  +L++e+++L++ +e+l++e++e+e+   +l 
  gi|557694906|ref|YP_008797960.1| 232 AETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELN 271
                                       5689****************************95555544 PP

>> YscO  Type III secretion protein YscO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   3.3   6.7e-05     0.021      61     113 ..      26      78 ..      13      80 .. 0.93
   2 ?   -0.4  13.6       3.1   9.9e+02      81     141 ..     214     273 ..     207     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.7e-05
                                       TT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  61 klvllkelekvkqqvalLrekeaelekqveeakqqleaerealrqarkelqea 113
                                       ++++++ +ek+ ++++lL+e+ a+l+++v ++ +q+    ++l +++  +++a
  gi|557694906|ref|YP_008797960.1|  26 AAIRVQVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKA 78 
                                       5789999*************************************999998887 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YscO  81 keaelekqveeakqqleaerealrqarkelqearraveKfaelarlvraeasrqqerkEeq 141
                                       +e+ele++++ + ++ +ae+e+l + +++l+e  +++e ++e  +++ ae++r +  + e+
  gi|557694906|ref|YP_008797960.1| 214 RERELEERLAAL-EKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNEL 273
                                       789999999855.567888889999999999999999999999999999999998887776 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.4     0.025       8.1      33      75 ..      34      76 ..       6      79 .. 0.55
   2 ?    7.5   6.5    0.0072       2.3      15      96 ..      51     135 ..      46     138 .. 0.69
   3 ?    4.0  16.6     0.082        26      15      97 ..      82     160 ..      74     226 .. 0.73
   4 ?   11.8   6.8   0.00033      0.11      39      92 ..     225     278 ..     208     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.025
                           DUF3450 33 aqsqkkidklddekqellaeyralkeeleslevyneqlerlva 75
                                      ++ +++i+ l++  ++l++++r++ e+++s +   + l+++v+
  gi|557694906|ref|YP_008797960.1| 34 EKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVE 76
                                      4445555555555555555555555555555555555555444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0072
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqei....asleeq 87 
                                       +++++q+l++ ++ +++ ++ q+ ++k     q  l+ yr l+ee++sl+    + ++l+++q++e+    ++l ++
  gi|557694906|ref|YP_008797960.1|  51 KEDVRQVLEQVSSPQRTLSSLQSVVEKAYLLDQA-LDSYRGLTEEVKSLSESLHETADLLSNQRAELvkevQRLMQE 126
                                       6778888888888888888888888888877654.578999999999999999888888888887652111445555 PP

                           DUF3450  88 ieeieeier 96 
                                        e+++++++
  gi|557694906|ref|YP_008797960.1| 127 RESLSRLRE 135
                                       555555554 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.082
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                       +++ld+ +  +e+  + +++ ++  d l+++++el++e+++l +e esl+  +e++ ++     +e++s e+qi+e+
  gi|557694906|ref|YP_008797960.1|  82 DQALDSYRGLTEEVKSLSESLHETADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWR----EELESKEKQIAEA 154
                                       677888888888888888888888888888888888888888888888887666655544....4444444444444 PP

                           DUF3450  92 eeiere 97 
                                       +e+ ++
  gi|557694906|ref|YP_008797960.1| 155 QETLKQ 160
                                       444333 PP

  == domain 4  score: 11.8 bits;  conditional E-value: 0.00033
                           DUF3450  39 idklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeie 92 
                                        +k++ e+++l +  ++l+ee+++le+y+e l+r +a++e+++++l+e i+e++
  gi|557694906|ref|YP_008797960.1| 225 LEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELITEMR 278
                                       46778889999999999******************************9999886 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 ?    5.8   1.8     0.051        16      59     104 ..      18      61 ..      12      68 .. 0.77
   2 ?   14.0   9.0   0.00014     0.045      40     102 ..     101     163 ..      72     165 .. 0.87
   3 ?    5.4  12.7     0.064        20      27      99 ..     196     262 ..     171     280 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.051
                                       CCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                      Seryl_tRNA_N  59 Igkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                       I+ + k  e a+  ++ +++l e+++ le++l++l++++ ++l ++
  gi|557694906|ref|YP_008797960.1|  18 IADLRK--EVAAIRVQVIEKLEERISLLEEALAKLKEDVRQVLEQV 61 
                                       555554..45666677789999999999999999999999998776 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Seryl_tRNA_N  40 elqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklll 102
                                       +l  +++ l ++r el ke+++++++ e  ++l++ev +  eel+ +e++ +e+++ l++l++
  gi|557694906|ref|YP_008797960.1| 101 SLHETADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLIT 163
                                       45667788999************************************************9875 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.064
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  27 dvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelek 99 
                                       ++d+l++l       ++++e + ++  el +  + + k+k++ae li+ +++l ee+k+lea  ++l  e+ +
  gi|557694906|ref|YP_008797960.1| 196 EMDKLFKLR------EIRMERMIRRERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAE 262
                                       444444443......4455555566667777788888888888888888888888888888877777666654 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 ?   12.9   0.4   0.00031     0.099      18      88 ..      30      99 ..      23     104 .. 0.77
   2 ?    5.0   0.1     0.093        30      31      60 ..      95     124 ..      81     140 .. 0.46
   3 ?    4.1   0.6      0.18        56      25      68 ..     148     191 ..     128     205 .. 0.53
   4 ?    4.0   0.3      0.18        58      42      80 ..     225     263 ..     197     272 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00031
                            DUF948 18 ivvllklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvseln 88
                                      + v+ kl++ ++ +++++++l+++v+++l++v    ++    l+ v ek   +d+  ++ + l+e v++l+
  gi|557694906|ref|YP_008797960.1| 30 VQVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSS-LQSVVEKAYLLDQALDSYRGLTEEVKSLS 99
                                      56777788888888888888888888888888777777666.88888888888888888888888888875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.093
                            DUF948  31 aaatieelekqvdpilkevedllakvnell 60 
                                       +++  e+l + +d ++++ ++l+++v++l+
  gi|557694906|ref|YP_008797960.1|  95 VKSLSESLHETADLLSNQRAELVKEVQRLM 124
                                       333333333333333333333333333333 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.18
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvnekle 68 
                                       +k + ea++t+++l  + +++ +e++ l +   +  e+ ++kle
  gi|557694906|ref|YP_008797960.1| 148 EKQIAEAQETLKQLITKKEALETEINILSERYLTSFEEAQKKLE 191
                                       33344444444444444444444444444444445555555544 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.18
                            DUF948  42 vdpilkevedllakvnelledvneklekvdplteavadl 80 
                                       +++   e+e+l++++n+l e+v++  +  ++l  ++a++
  gi|557694906|ref|YP_008797960.1| 225 LEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEM 263
                                       455678999999999998888876544445555555555 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 ?   14.5   1.7   8.5e-05     0.027       2      73 ..       6      78 ..       5      79 .. 0.90
   2 ?    0.3   4.7       2.2     7e+02      23      58 ..      97     129 ..      89     139 .. 0.40
   3 ?   -1.1  16.1       6.2     2e+03      14      68 ..     120     170 ..     103     179 .. 0.52
   4 ?    2.4  12.6      0.49   1.6e+02      17      66 ..     140     193 ..     134     203 .. 0.79
   5 ?    8.0  12.1    0.0085       2.7       7      67 ..     218     278 ..     215     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.5e-05
                        TMF_DNA_bd  2 slekklkeKDeqIaqLmeEGekLskke.lklnntikkLrkknkelekeikelkkkleklekeleeleerlkea 73
                                      s+  +l  K + Ia L++E  + + +   kl++ i+ L + +++l +++++  +++++ ++ l++l+++ ++a
  gi|557694906|ref|YP_008797960.1|  6 SAMGLLPRKSDSIADLRKEVAAIRVQViEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKA 78
                                      566778899****************963799************************************988765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.2
                        TMF_DNA_bd  23 kLskkelklnntikkLrkknkelekeikelkkklek 58 
                                        Ls +   l +t + L  + +el ke+++l ++ e+
  gi|557694906|ref|YP_008797960.1|  97 SLSES---LHETADLLSNQRAELVKEVQRLMQERES 129
                                       33222...2223333333333333344333333333 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 6.2
                        TMF_DNA_bd  14 IaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleelee 68 
                                       ++ Lm+E e Ls    +l++ + k r++++  ek+i+e ++ l++l  + e le 
  gi|557694906|ref|YP_008797960.1| 120 VQRLMQERESLS----RLREEVLKWREELESKEKQIAEAQETLKQLITKKEALET 170
                                       344444444444....445555555555555555555555444444444444433 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.49
                        TMF_DNA_bd  17 LmeEGekLskkelklnntikkLrkknkelekeikelk....kkleklekeleel 66 
                                        +eE+e  +k+  +  +t+k+L  k + le+ei+ l+       e+ +k+le+ 
  gi|557694906|ref|YP_008797960.1| 140 WREELESKEKQIAEAQETLKQLITKKEALETEINILSerylTSFEEAQKKLENF 193
                                       589999999999******************999999855555566666666665 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.0085
                        TMF_DNA_bd   7 lkeKDeqIaqLmeEGekLskkelklnntikkLrkknkelekeikelkkkleklekeleele 67 
                                       l+e+ + +++ ++E e L  + +kl++ +kkL +  + l  ei+e++++  +l++ ++e++
  gi|557694906|ref|YP_008797960.1| 218 LEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELITEMR 278
                                       5555566677789******************************************999986 PP

>> DUF2937  Protein of unknown function (DUF2937)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.87   2.8e+02      75      98 ..      29      52 ..      22      70 .. 0.77
   2 ?    3.2   0.1       0.2        62      70     120 ..      72     120 ..      65     125 .. 0.83
   3 ?    2.0   0.1      0.47   1.5e+02      66      98 ..     145     177 ..     140     184 .. 0.87
   4 ?   11.9   0.7   0.00044      0.14      46     100 ..     176     229 ..     158     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.87
                           DUF2937 75 daesiqalverlerLeqelqalqq 98
                                      + + i++l er + Le++l++l++
  gi|557694906|ref|YP_008797960.1| 29 RVQVIEKLEERISLLEEALAKLKE 52
                                      568899999***********9998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.2
                           DUF2937  70 pvvradaesiqalverlerLeqelqalqqasllerlvvllraadaeileet 120
                                       ++v ++a  ++++++ ++ L++e+++l++   l+ ++ ll++ +ae+++e+
  gi|557694906|ref|YP_008797960.1|  72 QSVVEKAYLLDQALDSYRGLTEEVKSLSE--SLHETADLLSNQRAELVKEV 120
                                       57788899999999*************99..77888888888888888876 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.47
                           DUF2937  66 qsedpvvradaesiqalverlerLeqelqalqq 98 
                                       +s+++ +++  e++++l+++ e+Le+e + l++
  gi|557694906|ref|YP_008797960.1| 145 ESKEKQIAEAQETLKQLITKKEALETEINILSE 177
                                       688999999999***************999987 PP

  == domain 4  score: 11.9 bits;  conditional E-value: 0.00044
                           DUF2937  46 qatAkrffkgdlealiahyrqsedpvvradaesiqalverlerLeqelqalqqas 100
                                       ++    +f+ + ++ ++ + +  d+ ++ +  +++++++r ++Le+ l+al++++
  gi|557694906|ref|YP_008797960.1| 176 SERYLTSFE-EAQKKLENFGREMDKLFKLREIRMERMIRRERELEERLAALEKSK 229
                                       555556777.899999************************************964 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 ?   11.4  18.2   0.00047      0.15      35     169 ..      18     155 ..      10     157 .. 0.90
   2 ?    6.5  19.8     0.015       4.9      42     150 ..      99     211 ..      92     214 .. 0.64
   3 ?    7.5  11.0    0.0073       2.3      70     127 ..     215     272 ..     207     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00047
                               GAS  35 ieelkkkeerne.kelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehev 110
                                       i++l+k+ ++ + + +++++++ + l+e L k++e+v +  +q+   ++  +sl+++ ++   l++ l + +   e 
  gi|557694906|ref|YP_008797960.1|  18 IADLRKEVAAIRvQVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKAYLLDQALDSYRGLTEE 94 
                                       56666665555415678999999****************************************************** PP

                               GAS 111 leqrfekvekerdelykkfeaaiqevqqktglknll..LekklkalqeelEkkeaqleevl 169
                                       ++   e++++  d l+++  + ++evq  ++ ++ l  L   + + +eelE+ke+q++e+ 
  gi|557694906|ref|YP_008797960.1|  95 VKSLSESLHETADLLSNQRAELVKEVQRLMQERESLsrLREEVLKWREELESKEKQIAEAQ 155
                                       **********************************9955677788889**********9975 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.015
                               GAS  42 eernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekv 118
                                        e+     + +s++  +l+++++++ +e+e L +  ++  k +++l++ ++++ e+++ lk+l  ++e le +++ +
  gi|557694906|ref|YP_008797960.1|  99 SESLHETADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINIL 175
                                       44445555556667777777777777777777777777777777777777777777777777777777777777777 PP

                               GAS 119 ek....erdelykkfeaaiqevqqktglknllLekk 150
                                       ++    +++e +kk e+  +e+ +  +l+++ +e++
  gi|557694906|ref|YP_008797960.1| 176 SEryltSFEEAQKKLENFGREMDKLFKLREIRMERM 211
                                       665555666777777777777776666666666666 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0073
                               GAS  70 veeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelyk 127
                                         eL+++l+  ek k++ + l +  ++l +e+k+l+  +e l  +++++e+ r el++
  gi|557694906|ref|YP_008797960.1| 215 ERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNE 272
                                       4688999999999999999999999999999999999999999999999999998876 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 ?    1.5   0.1      0.86   2.7e+02      16      34 ..      44      62 ..      36      68 .. 0.83
   2 ?   -1.2   0.0       5.9   1.9e+03      22      36 ..      91     105 ..      87     108 .. 0.84
   3 ?    6.0   0.5     0.035        11      15      38 ..     126     149 ..     120     154 .. 0.87
   4 ?    9.7   0.0    0.0024      0.78       5      31 ..     173     199 ..     172     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.86
                   HU-CCDC81_bac_2 16 eeAlqkiekeveelkqeLe 34
                                      eeAl k++++v+++ ++  
  gi|557694906|ref|YP_008797960.1| 44 EEALAKLKEDVRQVLEQVS 62
                                      89**********9998876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.9
                   HU-CCDC81_bac_2  22 iekeveelkqeLeee 36 
                                       + +ev++l + L+e+
  gi|557694906|ref|YP_008797960.1|  91 LTEEVKSLSESLHET 105
                                       6789********986 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.035
                   HU-CCDC81_bac_2  15 yeeAlqkiekeveelkqeLeeegr 38 
                                        +e l+++++ev ++++eLe++++
  gi|557694906|ref|YP_008797960.1| 126 ERESLSRLREEVLKWREELESKEK 149
                                       5678999************99876 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.0024
                   HU-CCDC81_bac_2   5 nsiaeaegisyeeAlqkiekeveelkq 31 
                                       n ++e + +s+eeA++k+e++ +e+ +
  gi|557694906|ref|YP_008797960.1| 173 NILSERYLTSFEEAQKKLENFGREMDK 199
                                       778999***************999865 PP

>> Leu_zip  Leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8  16.2   4.6e-05     0.015     133     264 ..      31     166 ..      22     172 .. 0.89
   2 ?    3.4  10.1      0.15        47     137     230 ..     189     282 ..     177     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.6e-05
                           Leu_zip 133 keierLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdekenskeiskleeklaelkldlektle 209
                                       + ie+L+e  + L+e l +l + + ++le+ s  +++l++lq+ ++++    +   +   l e++++l   l++t +
  gi|557694906|ref|YP_008797960.1|  31 QVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKAYLLDQALDSYRGLTEEVKSLSESLHETAD 107
                                       5699*****************************************999999999999******************99 PP

                           Leu_zip 210 ektasaksleed...lastkhelLkvqeqLelaekeLekkfqqta.ayknlkemltkkn 264
                                         +++ ++l ++   l++ ++ l +++e++   ++eLe k +q a a + lk+++tkk 
  gi|557694906|ref|YP_008797960.1| 108 LLSNQRAELVKEvqrLMQERESLSRLREEVLKWREELESKEKQIAeAQETLKQLITKKE 166
                                       9999999998763336788999*******************998725678*******96 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.15
                           Leu_zip 137 rLkeenekLkerlkelEkqatsaleeksklekalkelqkelgekkdekenskeiskleeklaelkldlektleekta 213
                                       +L++  + + + +k  E +++++++ +++le+ l++l+k+  e+++  e+s+++ +  +kl++ k  l ++  e ++
  gi|557694906|ref|YP_008797960.1| 189 KLENFGREMDKLFKLREIRMERMIRRERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMER 265
                                       55555566666677788899999999999999999999999998888888999999999999999999999999999 PP

                           Leu_zip 214 saksleedlastkhelL 230
                                       +  +l+e ++++++ +L
  gi|557694906|ref|YP_008797960.1| 266 RRTELNELITEMRRAFL 282
                                       99999999998888776 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.8    0.0078       2.5     133     227 ..      23     128 ..      12     136 .. 0.44
   2 ?    8.7  16.4    0.0032         1     116     253 ..     113     252 ..     108     280 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0078
                           DUF4407 133 aelaele.aqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld. 207
                                       +e+a+++ + i++l++ i+ +e++l++l++++++ l++ ++ +  ++    ++  ek   ld+a      l+++++ 
  gi|557694906|ref|YP_008797960.1|  23 KEVAAIRvQVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQ--RTLSSLQSVVEKAYLLDQALDSYRGLTEEVKs 97 
                                       3333332122335555555555555555555555555543333..22333344444444444444444444444333 PP

                           DUF4407 208 ...........atarlaalraelaeleaera 227
                                                   + ++a+l +e ++l +er+
  gi|557694906|ref|YP_008797960.1|  98 lseslhetadlLSNQRAELVKEVQRLMQERE 128
                                       3333334333355555555555555555554 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0032
                           DUF4407 116 qqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk..gtgttg.vaGkgpaakekk 189
                                       ++e +ke+++ ++   ++ l++l++++ ++++e++++e++++++++++++ ++ +    t+++   +++ ++++e++
  gi|557694906|ref|YP_008797960.1| 113 RAELVKEVQRLMQ--ERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEalETEINIlSERYLTSFEEAQ 187
                                       4455555555555..78889999999999999999999999999999999999877884444431467888888888 PP

                           DUF4407 190 aqldaaqaelaelkakld.atarlaalraelaeleaerakeraasqaaaaaddGllarlealdrl 253
                                       ++l+   +e+++l + ++ + +r+ ++++el+e  a+++k++a+ ++ ++ ++ l ++ + l++ 
  gi|557694906|ref|YP_008797960.1| 188 KKLENFGREMDKLFKLREiRMERMIRRERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAY 252
                                       88888888888888877785555555555555555555555555555555555554444444443 PP

>> PRANC  PRANC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       1.3   4.2e+02      43      66 ..      31      54 ..      27      62 .. 0.86
   2 ?    0.3   0.1       2.7   8.6e+02      41      69 ..     137     169 ..     106     178 .. 0.67
   3 ?    0.3   0.1       2.8   8.9e+02       8      46 ..     160     202 ..     150     220 .. 0.61
   4 ?   10.1   0.1    0.0024      0.77      23      63 ..     239     278 ..     221     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 1.3
                             PRANC 43 kiiksakkrykliekaievlnnic 66
                                      ++i+++++r +l+e+a+ +l++ +
  gi|557694906|ref|YP_008797960.1| 31 QVIEKLEERISLLEEALAKLKEDV 54
                                      6899*************9998765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 2.7
                             PRANC  41 ikkiiksakkrykliekaievlnnicsk....k 69 
                                       + k  +++++++k+i +a e+l+++++k    +
  gi|557694906|ref|YP_008797960.1| 137 VLKWREELESKEKQIAEAQETLKQLITKkealE 169
                                       555566777888888888888888887744444 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2.8
                             PRANC   8 dllfnknninllvrlinkkklkklk....slkiYgklikkiik 46 
                                       +l+++k+  +  ++++++  l++++    +l ++g+ + k+ k
  gi|557694906|ref|YP_008797960.1| 160 QLITKKEALETEINILSERYLTSFEeaqkKLENFGREMDKLFK 202
                                       4555555555555555555555553333466666666666555 PP

  == domain 4  score: 10.1 bits;  conditional E-value: 0.0024
                             PRANC  23 inkkklkklkslkiYgklikkiiksakkrykliekaievln 63 
                                         +k + ++k+l  Y++++ + i ++++r++ ++++i+ + 
  gi|557694906|ref|YP_008797960.1| 239 S-NKLREEVKKLEAYKETLAREIAEMERRRTELNELITEMR 278
                                       4.55566999**************************99886 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.7   0.00025      0.08      80     126 ..      32      78 ..      23      95 .. 0.88
   2 ?    6.3   2.1     0.035        11      80     144 ..      80     144 ..      77     148 .. 0.87
   3 ?    4.5   7.5      0.13        43      23      90 ..     122     189 ..     105     205 .. 0.68
   4 ?    2.2   9.3      0.64   2.1e+02      24      91 ..     212     277 ..     199     282 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00025
                             HrpB7  80 yrdvlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidac 126
                                       +++ le+r+  +e++la++++ +++  ++v+  +r+++++++ +++ 
  gi|557694906|ref|YP_008797960.1|  32 VIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKA 78 
                                       56789************************************999975 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.035
                             HrpB7  80 yrdvlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidacrerierlrraaerareda 144
                                       ++d++ +  r + +e++ + + l + +d ++ +++++++   ++ + re + rlr++  + re+ 
  gi|557694906|ref|YP_008797960.1|  80 LLDQALDSYRGLTEEVKSLSESLHETADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWREEL 144
                                       57999999999999999999999999999999999999999999999999999999888777775 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.13
                             HrpB7  23 eleaaraalaaaeaalaaaqaqveaardavraheerlddlttgsspfsiadylacrayrdvlegrvra 90 
                                        l + r+ l  + +++ +  +++e ++++ ++ +e l++l+t ++++  +  + +++y++  e+  ++
  gi|557694906|ref|YP_008797960.1| 122 RLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINILSERYLTSFEEAQKK 189
                                       45566666666666777777777777777777777777777777777777777777777766666555 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.64
                             HrpB7  24 leaaraalaaaeaalaaaqaqveaardavraheerlddlttgsspfsiadylacrayrdvlegrvraa 91 
                                       ++   ++l+++ aal++ +a++e   + +++ +e++++l + ++  ++ +++ +++ r++l++ ++++
  gi|557694906|ref|YP_008797960.1| 212 IRRE-RELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKE-TLAREIAEMERRRTELNELITEM 277
                                       3333.356666666666666666666666666666666666665.44556666666666666655555 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 ?    6.5   4.3     0.016       5.1     217     280 ..      23      83 ..      11     102 .. 0.61
   2 ?    8.8  21.4    0.0031      0.98     202     314 ..      92     197 ..      65     210 .. 0.55
   3 ?    4.6  10.3      0.06        19     203     271 ..     213     277 ..     195     281 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.016
                            HMMR_N 217 kekieekset.eklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelsk 280
                                       ke +  + ++ ekl+e   ++s + e l k k+d++q+ e +++ ++ ++sL+s +e+    l++
  gi|557694906|ref|YP_008797960.1|  23 KEVAAIRVQViEKLEE---RISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKAYL-LDQ 83 
                                       4444444444355555...455555555555999999999999999999999877654433.444 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0031
                            HMMR_N 202 kakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLee...ke 275
                                        ++v  L e l ++ ++  +++    +l++++++l +++e+l + ++++ + +e l++k+++i + +++L++   k+
  gi|557694906|ref|YP_008797960.1|  92 TEEVKSLSESLHETADLLSNQR---AELVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQlitKK 165
                                       3566666666666666654444...4577777777777777777777777777777777777777777666522234 PP

                            HMMR_N 276 qelskqvkdlnekckllekekeelvreeeekeqtlsaEl 314
                                       ++l+++++ l+e++           +e+++k ++   E+
  gi|557694906|ref|YP_008797960.1| 166 EALETEINILSERY-------LTSFEEAQKKLENFGREM 197
                                       44555555544443.......223333333333333333 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.06
                            HMMR_N 203 akvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssL 271
                                        + ++L+e+l +lek     k+e e l+e  ++l+++ ++le yk+ +a     ++ +  e+++L +++
  gi|557694906|ref|YP_008797960.1| 213 RRERELEERLAALEKS----KAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELITEM 277
                                       5557899999999998....8888888888888888888888888887777777777777777665554 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.6   0.00055      0.18      38     100 ..      23      86 ..      13      90 .. 0.64
   2 ?    3.0   9.4      0.44   1.4e+02      34      93 ..     128     191 ..      81     202 .. 0.59
   3 ?    7.0   4.5     0.025       7.9      32      95 ..     214     277 ..     176     281 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00055
                                       HHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..........HHHHHHHHHHHHHHHHH CS
                             DUF16  38 kieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln...kvdetleliletLqkinkRlD 100
                                       k  a ++   + i+kle+ ++ ++e + +lk+++ +  e++    +  ++l++++e    +++ lD
  gi|557694906|ref|YP_008797960.1|  23 KEVAAIR--VQVIEKLEERISLLEEALAKLKEDVRQVLEQVSspqRTLSSLQSVVEKAYLLDQALD 86 
                                       4333333..445788889999999999899888888888888444555556666666555555555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH...........HHHHHHHHHH CS
                             DUF16  34 qrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeeln....kvdetleliletLq 93 
                                       + L ++ ++v k  e+++  e+++ + +e +k+l  + +a + e+n    +   ++e   + L+
  gi|557694906|ref|YP_008797960.1| 128 ESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINilseRYLTSFEEAQKKLE 191
                                       3444455555555555555555555555555555555566666555544444444444444455 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.025
                                       BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHH CS
                             DUF16  32 nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqki 95 
                                        + +L++  a ++k + + + l ++ +k+ e++k+l++  ++  +e+ ++++    + e ++++
  gi|557694906|ref|YP_008797960.1| 214 RERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELITEM 277
                                       3444444444555777788888899999999999999999999888887776666665555555 PP

>> MHC_II_beta  Class II histocompatibility antigen, beta domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0017      0.53      29      63 ..      82     116 ..      76     132 .. 0.90
   2 ?   -1.7   0.0        10   3.2e+03      52      53 ..     242     243 ..     218     273 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0017
                                       ETTTSSEEESSGGGHHHHHHHHTSHHHHHHHHTHH CS
                       MHC_II_beta  29 DsdvgefvavtelgrplaeywNkqkdllerlraev 63 
                                       D  +++++++te ++ l+e++ +  dll ++rae+
  gi|557694906|ref|YP_008797960.1|  82 DQALDSYRGLTEEVKSLSESLHETADLLSNQRAEL 116
                                       5567899**************************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 10
                                       SH CS
                       MHC_II_beta  52 qk 53 
                                         
  gi|557694906|ref|YP_008797960.1| 242 LR 243
                                       33 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 ?    7.6   0.3    0.0096       3.1       3      20 ..      42      59 ..      40      61 .. 0.91
   2 ?    7.0   1.6     0.014       4.6       9      34 ..     128     153 ..     121     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0096
                                      HHHHHHTTS-HHHHHHHH CS
                      Sigma70_r4_2  3 alrealaeLperqreifl 20
                                       l+eala+L e+ r++++
  gi|557694906|ref|YP_008797960.1| 42 LLEEALAKLKEDVRQVLE 59
                                      589*************97 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.014
                                       TTS-HHHHHHHHHHHTS---HHHHHH CS
                      Sigma70_r4_2   9 aeLperqreifllryleglsykEIAe 34 
                                       ++L+  + e++  r++ +++ k+IAe
  gi|557694906|ref|YP_008797960.1| 128 ESLSRLREEVLKWREELESKEKQIAE 153
                                       89***********************9 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  12.0     0.023       7.3      10     115 ..      33     130 ..      17     132 .. 0.56
   2 ?   10.1  18.9     0.002      0.63      24     112 ..      88     179 ..      67     181 .. 0.79
   3 ?    7.2  24.9     0.016         5       1     117 [.     149     272 ..     149     273 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.023
                        TPR_MLP1_2  10 ikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreel...nelkaeiaelkaeaesa 83 
                                       i++l+e+++ +e++l+kl+ed+++  e+++  q+           ++ +lq++ e++   +++ + ++ l++e++s+
  gi|557694906|ref|YP_008797960.1|  33 IEKLEERISLLEEALAKLKEDVRQVLEQVSSPQR-----------TLSSLQSVVEKAyllDQALDSYRGLTEEVKSL 98 
                                       4555666666666666666666666666666665...........44444444444433344445555566666666 PP

                        TPR_MLP1_2  84 kaeleeseesweeqkeelekelselekriedl 115
                                       +++l e    +++q+ el ke++ l + +e l
  gi|557694906|ref|YP_008797960.1|  99 SESLHETADLLSNQRAELVKEVQRLMQERESL 130
                                       66666666666666666666666666655555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.002
                        TPR_MLP1_2  24 lqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakaeleeseeswee...q 97 
                                        + l e++++ +e++ e  +  +++  +  ++v+ l + re l++l++e+ ++++e+es +++++e++e +++   +
  gi|557694906|ref|YP_008797960.1|  88 YRGLTEEVKSLSESLHETADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQlitK 164
                                       45577888888888888888888888888888999999999999999999999999999999999999888754449 PP

                        TPR_MLP1_2  98 keelekelselekri 112
                                       ke+le+e++ l +r+
  gi|557694906|ref|YP_008797960.1| 165 KEALETEINILSERY 179
                                       ********9999986 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.016
                        TPR_MLP1_2   1 kelksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvk....haedvkelqalreelnelkaei 73 
                                       k++++++e++k+l ++ke++e++++ l e   +  e+a++  +++ re+ k     +  ++ + +   el+e  a +
  gi|557694906|ref|YP_008797960.1| 149 KQIAEAQETLKQLITKKEALETEINILSERYLTSFEEAQKKLENFGREMDKlfklREIRMERMIRRERELEERLAAL 225
                                       5899*********************************************8733112223333333334445555555 PP

                        TPR_MLP1_2  74 aelkaeaesa...kaeleeseesweeqkeelekelselekriedlne 117
                                       ++ kaeae++   +++l e+ +++e  ke+l +e++e+e+r+++lne
  gi|557694906|ref|YP_008797960.1| 226 EKSKAEAETLietSNKLREEVKKLEAYKETLAREIAEMERRRTELNE 272
                                       55666666541115678899999**********************97 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   1.0     0.019       6.1      11      59 ..      31      76 ..      11      78 .. 0.73
   2 ?   13.2   1.3    0.0003     0.097       6      67 ..      47     111 ..      40     121 .. 0.89
   3 ?    2.6   0.6       0.6   1.9e+02      13      24 ..     158     169 ..     114     206 .. 0.55
   4 ?    0.9   0.0         2   6.5e+02      32      52 ..     237     257 ..     211     277 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.019
                           NPV_P10 11 adikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59
                                      + i++++++++ l++++++++e++++   + e++ + + +L +l++ ve
  gi|557694906|ref|YP_008797960.1| 31 QVIEKLEERISLLEEALAKLKEDVRQ---VLEQVSSPQRTLSSLQSVVE 76
                                      44677888888888888888886666...45677777777777777665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.0003
                           NPV_P10   6 LlvIradikavddkVdalqqqvddvqenlpdvtelnekLd...aqsaqLaeletkvenIqdiLnp 67 
                                       L   ++d+++v ++V++ q  + ++q+ +++   l + Ld   ++++++++l++++++  d+L++
  gi|557694906|ref|YP_008797960.1|  47 LAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKAYLLDQALDsyrGLTEEVKSLSESLHETADLLSN 111
                                       77889**************************999*****9444589****************994 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.6
                           NPV_P10  13 ikavddkVdalq 24 
                                        k++ +k +al+
  gi|557694906|ref|YP_008797960.1| 158 LKQLITKKEALE 169
                                       222223333333 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 2
                           NPV_P10  32 enlpdvtelnekLdaqsaqLa 52 
                                       e ++++ e  +kL+a  ++La
  gi|557694906|ref|YP_008797960.1| 237 ETSNKLREEVKKLEAYKETLA 257
                                       333333333444444444443 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   9.8   9.4e-05      0.03     261     412 ..      32     191 ..      15     198 .. 0.71
   2 ?    2.6   5.2     0.082        26     625     719 ..     189     264 ..     164     283 .. 0.43

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.4e-05
                          Prominin 261 lekeLrksgsqLrdglrgvkrdlnqalsnlCqseeCskilssleiekldtskcldqlpnvdevlealeevletnlss 337
                                       + ++L +  s L+++l + k+d++q+l+++ + +++ + l+s+  + + +++ ld+   ++e++++l e l++  + 
  gi|557694906|ref|YP_008797960.1|  32 VIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKAYLLDQALDSYRGLTEEVKSLSESLHETADL 108
                                       5678999999*******************66656666666666666888999999999******************* PP

                          Prominin 338 ivkeglarlneipekvknq..taevvpdlkk...alakgreqikklakkip..realdavisdle.nterssktfdd 406
                                       + ++  + ++e+++++++   ++++ +++ k   +l+++++qi + ++ ++   ++ +a+  +++  +er++ +f++
  gi|557694906|ref|YP_008797960.1| 109 LSNQRAELVKEVQRLMQEResLSRLREEVLKwreELESKEKQIAEAQETLKqlITKKEALETEINiLSERYLTSFEE 185
                                       **999999****99998742244555544432226777777777766666421122233445555555666666665 PP

                          Prominin 407 vvekye 412
                                         +k+e
  gi|557694906|ref|YP_008797960.1| 186 AQKKLE 191
                                       555554 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.082
                          Prominin 625 nletlaekleelanelsngkknlkqslkneaqdlraiqqelvlplessvkklkksvkklde...ensdlqesikkll 698
                                        le++                       +e+ +l ++ + +++++ +  ++l++++ +l++   e+++l e+ +kl 
  gi|557694906|ref|YP_008797960.1| 189 KLENF----------------------GREMDKLFKLREIRMERMIRRERELEERLAALEKskaEAETLIETSNKLR 243
                                       23333......................33333344444444444444444444444444444444444444444444 PP

                          Prominin 699 aaveraenflkkngseiinne 719
                                       ++v+++e + ++ + ei + e
  gi|557694906|ref|YP_008797960.1| 244 EEVKKLEAYKETLAREIAEME 264
                                       444444444444333333222 PP

>> NFRKB_winged  NFRKB Winged Helix-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0         1   3.3e+02      18      44 ..      46      72 ..      16     108 .. 0.67
   2 ?    9.1   0.6    0.0046       1.5       4      51 ..     116     162 ..     114     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1
                      NFRKB_winged 18 tlseleekvkewqespasalnewlsla 44
                                       l++l+e v++  e+ +s++ +  sl+
  gi|557694906|ref|YP_008797960.1| 46 ALAKLKEDVRQVLEQVSSPQRTLSSLQ 72
                                      345667777766666666655554443 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0046
                      NFRKB_winged   4 LlrdilvstaekrltlseleekvkewqespasalnewlslapdWselv 51 
                                       L++++  + +++r +ls+l+e+v +w+e+ +s+ ++ ++ ++  ++l+
  gi|557694906|ref|YP_008797960.1| 116 LVKEVQ-RLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLI 162
                                       566665.8899*****************99998888877776665555 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 ?   11.4  29.8   0.00064      0.21       9     163 ..      17     179 ..      15     201 .. 0.51
   2 ?   -1.4  21.4       5.3   1.7e+03      56     172 ..     159     279 ..     154     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00064
                          KASH_CCD   9 tvadLqlnNkkLaeen.skLkkavetaeetnakLteeieeLkkklkstQqal.......qkaklleeEl.......e 70 
                                       ++adL+     +  ++ +kL + +   ee+ akL e++ +  +++ s Q++l       +ka ll++ l       e
  gi|557694906|ref|YP_008797960.1|  17 SIADLRKEVAAIRVQViEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLsslqsvvEKAYLLDQALdsyrgltE 93 
                                       57777777777777654678888888888888888888777777766666650000000555555655522222224 PP

                          KASH_CCD  71 elkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleella 147
                                       e+k l ++l E +  l++q+ +l ke q L+++ esL    + +l  ++el++k k++++ +++Lk+ +       +
  gi|557694906|ref|YP_008797960.1|  94 EVKSLSESLHETADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLI-------T 163
                                       555555555566666666666666666666555555444444444444444444444444444444444.......4 PP

                          KASH_CCD 148 ekealleektkqieeL 163
                                       +keal +e +   e  
  gi|557694906|ref|YP_008797960.1| 164 KKEALETEINILSERY 179
                                       4444444444333333 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 5.3
                          KASH_CCD  56 QqalqkaklleeEleelk.alvkeleEkrarlkaqnkqlekenqsLiakiesL...qeenikllaekdelkkklkeL 128
                                        q++ k+++le E++ l  + +++ eE +++l++  ++++k  +  ++++e +   + e++  la  +++k   + L
  gi|557694906|ref|YP_008797960.1| 159 KQLITKKEALETEINILSeRYLTSFEEAQKKLENFGREMDKLFKLREIRMERMirrERELEERLAALEKSKAEAETL 235
                                       67888999999999988625788999999999999999998777666666665333677788888889999999999 PP

                          KASH_CCD 129 lkekaeLkkqlheleellaekealleektkqieeLkltieEyss 172
                                       +++ ++L++++++le+ + +  +++ e +++  eL+  i E+++
  gi|557694906|ref|YP_008797960.1| 236 IETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELITEMRR 279
                                       99999999999999999999999999999999999999999886 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 ?    7.2   1.2     0.017       5.3      89     132 ..      17      61 ..      13      72 .. 0.77
   2 ?    8.3   9.3    0.0078       2.5      40     130 ..      81     177 ..      65     182 .. 0.68
   3 ?    6.7   2.9     0.024       7.8      38      99 ..     216     276 ..     205     281 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.017
                                       CCCHHHHHHHCCH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                         Fib_alpha  89 eilrlketidaqe.snirvLqnvlesneqkiqkLeqdidqkerkC 132
                                        i++l++++ a   + i++L + ++ +e+ ++kL++d+ q  ++ 
  gi|557694906|ref|YP_008797960.1|  17 SIADLRKEVAAIRvQVIEKLEERISLLEEALAKLKEDVRQVLEQV 61 
                                       567777778776668889999999999999999999888876664 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0078
                                       CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHH..HHHHHHHHCCCHHHHHHHCCHHHHHHHHHH CS
                         Fib_alpha  40 leneleeisnstkeaeelvkeikdslrekqkskkdn....dnvik..ksskeleeeilrlketidaqesnirvLqnv 110
                                       l + l++++  t+e+++l+++++++     ++ ++     +++++  +s ++l+ee+l+ +e++ ++e++i + q++
  gi|557694906|ref|YP_008797960.1|  81 LDQALDSYRGLTEEVKSLSESLHETADLLSNQRAELvkevQRLMQerESLSRLREEVLKWREELESKEKQIAEAQET 157
                                       5566666666666666665555554332222222211122444441156789999********************** PP

                                       HHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 111 lesneqkiqkLeqdidqker 130
                                       l+++  k + Le++i+++ +
  gi|557694906|ref|YP_008797960.1| 158 LKQLITKKEALETEINILSE 177
                                       ***************99876 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.024
                                       CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHC CS
                         Fib_alpha  38 ekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketida 99 
                                       ++le++l+ +++s+ eae+l+++ +++lre+ k+ +  ++++ +   e+e++ ++l+e i++
  gi|557694906|ref|YP_008797960.1| 216 RELEERLAALEKSKAEAETLIET-SNKLREEVKKLEAYKETLAREIAEMERRRTELNELITE 276
                                       68999999999999999999875.55566666666656666666666677799999998876 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.5     0.001      0.34       5      95 ..      33     123 ..      30     125 .. 0.89
   2 ?    9.2   5.6    0.0036       1.1      24      81 ..     121     178 ..     114     192 .. 0.87
   3 ?   -0.3   0.2       3.1   9.9e+02      43      82 ..     172     210 ..     164     220 .. 0.73
   4 ?    2.4   4.0      0.45   1.4e+02      33      92 ..     219     274 ..     202     280 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.001
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II   5 aaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       +++ +e ++  +e la+l++++ ++ e++s+ +r++   + +v++    +++A +s + L++++  L + l+e   l
  gi|557694906|ref|YP_008797960.1|  33 IEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEK-AYLLDQALDSYRGLTEEVKSLSESLHETADL 108
                                       66677788888999*********************9999888865.5789**************************9 PP

                                       HHH....HHHHHHHH CS
                        Laminin_II  82 eeasss.lsdnisei 95 
                                        +++ + l ++++++
  gi|557694906|ref|YP_008797960.1| 109 LSNQRAeLVKEVQRL 123
                                       999888999999986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0036
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHH CS
                        Laminin_II  24 qnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkql 81 
                                       q+l +++e+ls+++++v +  e+++++ k+i++A++  k+L  + + L+  ++ l ++
  gi|557694906|ref|YP_008797960.1| 121 QRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINILSER 178
                                       578899***********************************99999999888777665 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 3.1
                                       XXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II  43 tnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       +n + + + +  ++A+++  +  +++++L+ kl+e+++ +
  gi|557694906|ref|YP_008797960.1| 172 INILSERYLTSFEEAQKKLENFGREMDKLF-KLREIRMER 210
                                       555556677777888888888888888888.577777665 PP

  == domain 4  score: 2.4 bits;  conditional E-value: 0.45
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHHHH CS
                        Laminin_II  33 lseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsdni 92 
                                        ++++  +e+ +++++ + ++ +  r++vkkLe   + L   + e++ ++ + +   + i
  gi|557694906|ref|YP_008797960.1| 219 EERLA-ALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELN---ELI 274
                                       33333.347778888888888888999999999999999999999999998844...434 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.9   0.00086      0.27      73     117 ..      32      76 ..      14      86 .. 0.86
   2 ?    6.2   8.4     0.033        11      27     108 ..     112     192 ..      94     212 .. 0.80
   3 ?    2.1   1.0      0.64     2e+02      58      96 ..     233     261 ..     202     280 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00086
                                       XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHHHHHHHHHHHH CS
                              COG5  73 vlselksslesLsasyerlkskvlepyeeaeklqsalkrlhqtld 117
                                       v ++l+++++ L++++ +lk++v +  e++++ q++l++l++ ++
  gi|557694906|ref|YP_008797960.1|  32 VIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVE 76 
                                       7899999****************************9999998776 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.033
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTHHHHHHHH CS
                              COG5  27 teldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslssvlselksslesLsasyerlkskvlepyeeae 103
                                       + + l  +++rl +  + l +rlr+++ +  +eL ++ +++++++++l++l ++ e+L+  ++ l++  l+ +eea+
  gi|557694906|ref|YP_008797960.1| 112 QRAELVKEVQRLMQERESL-SRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINILSERYLTSFEEAQ 187
                                       4555666666666664444.789999999999999999999999999999999999999999999999999999999 PP

                                       HHHHH CS
                              COG5 104 klqsa 108
                                       k+ + 
  gi|557694906|ref|YP_008797960.1| 188 KKLEN 192
                                       98665 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.64
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-TTH CS
                              COG5  58 leLlehlskskslssvlselksslesLsasyerlkskvl 96 
                                       ++L+e          + ++l++++++L+a  e l +++ 
  gi|557694906|ref|YP_008797960.1| 233 ETLIE----------TSNKLREEVKKLEAYKETLAREIA 261
                                       22222..........233344444444444444444433 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 ?    6.5   0.8      0.02       6.6      94     163 ..      32     107 ..      15     114 .. 0.62
   2 ?    4.6   3.4     0.078        25      80     147 ..     109     175 ..      89     200 .. 0.60
   3 ?    7.8   0.5    0.0083       2.7      94     164 ..     211     280 ..     202     283 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.02
                                       HH.................HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  94 liieiqke...indsvesleetrqrveegselveetgealkeiveavaevadlv...qeiaaaseeqsasieevnq 163
                                       +i+++++     +++++ l+e +++v e ++  ++t ++l+++ve++  +++ +   + ++  ++ +s+s++e+++
  gi|557694906|ref|YP_008797960.1|  32 VIEKLEERislLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKAYLLDQALdsyRGLTEEVKSLSESLHETAD 107
                                       3333333311146677777777777777888888888899999988765555541114566667777777777765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.078
                                       HHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  80 LAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqei 147
                                       L ++ a+  ke+++l+ +  +   +  e + + r++ e+  ++++e++e+lk++ ++ + ++++++ +
  gi|557694906|ref|YP_008797960.1| 109 LSNQRAELVKEVQRLM-QERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINIL 175
                                       2223333333333333.222233334445556678888888899999999999888888777777644 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0083
                                       HH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  94 liieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasieevnqa 164
                                       +i + ++e ++ +++le+++ ++e+  e+ ++ +e++k++ +  + +a ++ e+ +  +e+ + i+e+ +a
  gi|557694906|ref|YP_008797960.1| 211 MI-RRERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELITEMRRA 280
                                       44.567889999999*****************************************999999999998776 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  47.5    0.0045       1.4      46     263 ..      29     272 ..       7     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0045
                               MAD  46 esdrnqelqkrikllekreeekeealreqiElarlkkknlealnkkekekesklaearevisalknelaelkrqiek 122
                                        ++  ++l++ri+lle+  ++ +e +r+ +E++ + +++l +l++ + ek   l +a +  + l++e++ l +++++
  gi|557694906|ref|YP_008797960.1|  29 RVQVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQS-VVEKAYLLDQALDSYRGLTEEVKSLSESLHE 104
                                       45556789**************************99999998865.569999************************* PP

                               MAD 123 qelelsekeseleelqerldllkkklseleqli....qqlekkqkelaeaeqrikeLefeiqs.............. 181
                                       +   ls+++ el +  +rl  +++ ls l + +    ++le+k+k+ aea++++k+L+ + +               
  gi|557694906|ref|YP_008797960.1| 105 TADLLSNQRAELVKEVQRLMQERESLSRLREEVlkwrEELESKEKQIAEAQETLKQLITKKEAleteinilserylt 181
                                       *999999997765555555555555555544444444*********************9999888999999999999 PP

                               MAD 182 .........qeddslivknskselaripelekelerlreenkklnelkenkelLkEevedlkkkLereEkareelvk 249
                                                 +   ++ k  k +  r+ ++ +  ++l+e+ + l+++k + e L E  + l++  ++ E ++e+l+ 
  gi|557694906|ref|YP_008797960.1| 182 sfeeaqkklENFGREMDKLFKLREIRMERMIRRERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAR 258
                                       97766332222222333334445566667777777778888888999999999999999999999999999999999 PP

                               MAD 250 LelekekleqeLks 263
                                          e e+  +eL++
  gi|557694906|ref|YP_008797960.1| 259 EIAEMERRRTELNE 272
                                       88888888888886 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 ?   13.3   9.0   0.00011     0.034     204     303 ..      18     117 ..      13     123 .. 0.87
   2 ?    3.7  11.2     0.092        30     216     270 ..     121     175 ..     114     192 .. 0.67
   3 ?    2.0  13.7      0.31        98     209     299 ..     188     278 ..     183     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                            HAP1_N 204 vldcveqlseanqq.iaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLta 279
                                       ++d+ ++++  + q i++l+e ++  +e l++ +e++ ++l q+ + q+ l +l++  e+    L  + +  r Lt+
  gi|557694906|ref|YP_008797960.1|  18 IADLRKEVAAIRVQvIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKA-YLLDQALDSYRGLTE 93 
                                       567777777777662689********************************99998887775.5789999999***** PP

                            HAP1_N 280 ELqdlqekyaevegmLheaqeevk 303
                                       E++ l e  +e+ ++L +++ e+ 
  gi|557694906|ref|YP_008797960.1|  94 EVKSLSESLHETADLLSNQRAELV 117
                                       ******************999864 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.092
                            HAP1_N 216 qqiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaas 270
                                       q + +  e l+r +ee+ + +ee +s   qi + q+ lk+l + +e l++++++ 
  gi|557694906|ref|YP_008797960.1| 121 QRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINIL 175
                                       3344446778888888888888888888888888888888888888877766554 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.31
                            HAP1_N 209 eqlseanqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlq 285
                                       ++l++  +++++l +  + ++e + r  +e ++ la + + +   ++l + +++l+++ +     ++ L+ E+ +++
  gi|557694906|ref|YP_008797960.1| 188 KKLENFGREMDKLFKLREIRMERMIRRERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEME 264
                                       5677777889999999999****************************************999999************ PP

                            HAP1_N 286 ekyaevegmLheaq 299
                                        + +e +++++e++
  gi|557694906|ref|YP_008797960.1| 265 RRRTELNELITEMR 278
                                       ***********997 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   0.00053      0.17      79     118 ..      33      72 ..      15      73 .. 0.93
   2 ?    3.6   0.4      0.19        59      75     119 ..      81     125 ..      78     126 .. 0.79
   3 ?   -0.2   5.1       2.9   9.2e+02      74     104 ..     101     131 ..      93     156 .. 0.59
   4 ?    2.5   4.7      0.41   1.3e+02      13      45 ..     142     174 ..     133     191 .. 0.57
   5 ?    3.9   2.4      0.15        47       6      37 ..     216     247 ..     211     252 .. 0.70
   6 ?    5.9   0.6     0.037        12      75     106 ..     249     280 ..     246     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00053
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  79 iellkkkleelekqlekleeeleklkdqittleanlaqly 118
                                       ie l+++++ le++l kl+e++++  +q+ + +++l+ l+
  gi|557694906|ref|YP_008797960.1|  33 IEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQ 72 
                                       78899***************************99999876 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  75 leeAiellkkkleelekqlekleeeleklkdqittleanlaqlyq 119
                                       l++A + +    ee+++ +e+l e ++ l++q  +l +++++l q
  gi|557694906|ref|YP_008797960.1|  81 LDQALDSYRGLTEEVKSLSESLHETADLLSNQRAELVKEVQRLMQ 125
                                       566777777777888999999999999999999999999998876 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 2.9
                                       EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  74 sleeAiellkkkleelekqlekleeeleklk 104
                                       sl+e  +ll ++ +el k ++ l +e e l+
  gi|557694906|ref|YP_008797960.1| 101 SLHETADLLSNQRAELVKEVQRLMQERESLS 131
                                       5555556666666666665555555555444 PP

  == domain 4  score: 2.5 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEE CS
                         Prefoldin  13 aqlkeaieelektletlktlkkedegkevlvpl 45 
                                       ++l+++ + + ++ etlk l++++e  e+ +++
  gi|557694906|ref|YP_008797960.1| 142 EELESKEKQIAEAQETLKQLITKKEALETEINI 174
                                       444445555555555555555544444444444 PP

  == domain 5  score: 3.9 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-T CS
                         Prefoldin   6 eslqaelaqlkeaieelektletlktlkkede 37 
                                        +l+++la+l++++ e e+++et ++l++e +
  gi|557694906|ref|YP_008797960.1| 216 RELEERLAALEKSKAEAETLIETSNKLREEVK 247
                                       56777777888888888888887777777444 PP

  == domain 6  score: 5.9 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  75 leeAiellkkkleelekqlekleeeleklkdq 106
                                       le  +e+l ++++e+e+ +++l+e +++ +++
  gi|557694906|ref|YP_008797960.1| 249 LEAYKETLAREIAEMERRRTELNELITEMRRA 280
                                       55558999999999999999999999998875 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   3.0     0.038        12      78     116 ..      34      72 ..      11      83 .. 0.64
   2 ?    5.3  23.8     0.085        27      10     124 ..      80     192 ..      77     208 .. 0.56
   3 ?    4.9  19.6      0.11        35      18      96 ..     208     272 ..     183     281 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.038
                            APG6_N  78 eeleaelaaleeelealeeeeerfwreynelqlellele 116
                                       e+le+ ++ lee l++l+e+ ++ +++ ++ q++l++l+
  gi|557694906|ref|YP_008797960.1|  34 EKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQ 72 
                                       456666666666666666666666666666666666665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.085
                            APG6_N  10 LleeldkqleqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereel...eae 83 
                                       Ll++    ++ +++e ++++e l++  +  ++      +++el +e+++l +e+e+l +  +e+ k reel   e++
  gi|557694906|ref|YP_008797960.1|  80 LLDQALDSYRGLTEEVKSLSESLHETADLLSN------QRAELVKEVQRLMQERESLSRLREEVLKWREELeskEKQ 150
                                       56666666666666666666666666655333......455566666666665555444444444433333111456 PP

                            APG6_N  84 laaleeelealeeeeerfwreyne.lqlelleleeeldslea 124
                                       +a+++e+l++l  ++e+  +e n   ++ l+++ee +++le+
  gi|557694906|ref|YP_008797960.1| 151 IAEAQETLKQLITKKEALETEINIlSERYLTSFEEAQKKLEN 192
                                       666666666666666666666666445555666666555554 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.11
                            APG6_N  18 leqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeeleal 94 
                                       +e++ +  +++ee                  le+++ e e+l ++ ++l ee k+le+ +e l++e+a+ e+   +l
  gi|557694906|ref|YP_008797960.1| 208 MERMIRRERELEER--------------LAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTEL 270
                                       22223333333333..............4445555555555666666666666666666666666666666655555 PP

                            APG6_N  95 ee 96 
                                       +e
  gi|557694906|ref|YP_008797960.1| 271 NE 272
                                       54 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.9     0.005       1.6     412     467 ..      19      75 ..      11      79 .. 0.78
   2 ?    5.0  25.3     0.025       8.1     277     463 ..      91     277 ..      80     282 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.005
                            AAA_13 412 deykkkykkl.ekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeeinkeL 467
                                         + k+++++  + iekle++++  e++l+kl+e++++  +q+++++++ + + + +
  gi|557694906|ref|YP_008797960.1|  19 ADLRKEVAAIrVQVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVV 75 
                                       455555555514668999999999999999999999999999999999988877655 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.025
                            AAA_13 277 FddefeekqerLekliekveskkselleklkavsdeasensafeedkeelkaeaealeeqLkglqralea...Krke 350
                                        ++e++   e+L ++++ + ++++el+++++ +++e +  s+ +e++ + ++e+e  e+q+ ++q+ l++   K++ 
  gi|557694906|ref|YP_008797960.1|  91 LTEEVKSLSESLHETADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQlitKKEA 167
                                       5789999999*************************999999999999999999999999999988888763325555 PP

                            AAA_13 351 pfksvelesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlveeleseldeykkkykkle...ka 424
                                       + +++++ s     e+   + +e+++  +++ + +++l + +e   + + + +  ele+ l +++k ++++e   ++
  gi|557694906|ref|YP_008797960.1| 168 LETEINILS-----ERYLTSFEEAQKKLENFGREMDKLFKLREIRMERMIRRE-RELEERLAALEKSKAEAEtliET 238
                                       555555433.....222234444444445555555555554444443333322.23455555555444444411134 PP

                            AAA_13 425 ieklekelkeeeaelkkleeeikeLekqlrdekpaaeei 463
                                        +kl +e+k+ ea +++l+ ei+e+e++ ++ ++ ++e+
  gi|557694906|ref|YP_008797960.1| 239 SNKLREEVKKLEAYKETLAREIAEMERRRTELNELITEM 277
                                       445556666666666666666666666666655555555 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 ?    6.5   1.6     0.013       4.3      38     109 ..      19      81 ..       9      87 .. 0.53
   2 ?    3.9   9.1     0.086        28      34      96 ..     110     172 ..      91     192 .. 0.51
   3 ?    8.8   2.8    0.0028      0.88      33      98 ..     211     276 ..     197     282 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.013
                              HemX  38 aelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlskvsgaerkdWlL 109
                                       a+l++++aa+  q+          ++leer+  l+e+l++l++ + q  +q+++ q+ ls +++  +k +lL
  gi|557694906|ref|YP_008797960.1|  19 ADLRKEVAAIRVQV---------IEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKAYLL 81 
                                       34444444444443.........4455555555555555555555555555555555555555555555555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.086
                              HemX  34 taevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqql 96 
                                       + + ael ++++ l q+ ++++ ++e+  ++ e+l+ +++++++++++l+ql  + e+l++++
  gi|557694906|ref|YP_008797960.1| 110 SNQRAELVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEI 172
                                       222234444444444444444444444444444444444444444444444444444444444 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0028
                              HemX  33 ltaevaelqqqlaaleqqlaqveaekeqkqeleerlqqlaeklealekeleqlqkqleelqqqlsk 98 
                                       +  +  el+++laale+++a++e++ e+ ++l e++++l+   e+l++e+++ +++  el++ +++
  gi|557694906|ref|YP_008797960.1| 211 MIRRERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELNELITE 276
                                       444558899999999999999787777777777777777777777777777777766666665555 PP

>> Exonuc_VII_L  Exonuclease VII, large subunit
   [No individual domains that satisfy reporting thresholds (although complete target did)]

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.5      0.03       9.7       3      42 ..      31      70 ..      29      79 .. 0.86
   2 ?    5.2  11.6     0.047        15       6     109 ..     100     192 ..      97     200 .. 0.83
   3 ?    1.7  20.9      0.57   1.8e+02      76     221 ..     124     276 ..     118     280 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.03
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  3 kVIesLHeqiDaLtktnlqLtqqsqeLleklelaqkkesk 42
                                      +VIe L e+i  L + +++L++  ++ le+ ++ q++ s+
  gi|557694906|ref|YP_008797960.1| 31 QVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSS 70
                                      69***********************999999988776554 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.047
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3   6 esLHeqiDaLtktnlqLtqqsqeLleklelaqkkeskflenlaslkhENdnLsslLkRKerrlkdlekelselkesv 82 
                                       esLHe+ D L+++ ++L ++ q L++  e           +l+ l++E  +    L+ Ke+++ + ++ l++l ++ 
  gi|557694906|ref|YP_008797960.1| 100 ESLHETADLLSNQRAELVKEVQRLMQERE-----------SLSRLREEVLKWREELESKEKQIAEAQETLKQLITKK 165
                                       89999999999999999999999886554...........567777777777777999******************* PP

                                       HHHHHHHHHHHHHHHHCCCHHHHHHHH CS
                              SHE3  83 eelklekkqlkkrlenssaseteleee 109
                                       e l++e + l++r  +s+++ ++  e+
  gi|557694906|ref|YP_008797960.1| 166 EALETEINILSERYLTSFEEAQKKLEN 192
                                       ********9999999998887776555 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS CS
                              SHE3  76 selkesveelklekkqlkkrlenssaseteleeelerlkvqYdalvdsqkeYkehYqqeieeLkesleklklenekq 152
                                        + +es   l++e  + +++le+++++ +e +e l++l  + +al    +   e+Y +  ee +++le++ +e +k 
  gi|557694906|ref|YP_008797960.1| 124 MQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINILSERYLTSFEEAQKKLENFGREMDKL 200
                                       334444445555555556677777777788888899999999****9**************************9998 PP

                                       S...XXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....XXXXXXXXXXXXXXXXX CS
                              SHE3 153 l...eelqerissndkdidtkldsynnkkknlesieeeknkkllkkleslaseld.....leswlelykelkelile 221
                                       +   e  +er+ + +++++++l  ++++k++ e + e+  +kl +++++l +  +     ++++ ++  el+eli e
  gi|557694906|ref|YP_008797960.1| 201 FklrEIRMERMIRRERELEERLAALEKSKAEAETLIETS-NKLREEVKKLEAYKEtlareIAEMERRRTELNELITE 276
                                       7222346788999999*********99999988876554.4555555544433223335577777777777777766 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 ?    6.3  17.2     0.028       9.1      78     174 ..      34     153 ..       8     156 .. 0.67
   2 ?    8.3  16.7    0.0072       2.3      66     155 ..     105     194 ..      88     200 .. 0.85
   3 ?    4.1  20.1      0.14        44      65     176 ..     163     274 ..     155     279 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.028
                           UPF0242  78 teldeglktkeealeelqeeeeeLkee....................ldakeeelerlkeenqqLqekleaiae... 131
                                        +l+e ++  eeal +l+e+ ++  e+                    ld+     + l+ee ++L+e l+++a    
  gi|557694906|ref|YP_008797960.1|  34 EKLEERISLLEEALAKLKEDVRQVLEQvsspqrtlsslqsvvekaylLDQALDSYRGLTEEVKSLSESLHETADlls 110
                                       33333333444444443333333333334444444444666888887888888888888888888888888888554 PP

                           UPF0242 132 .dfeelkleleeqLaekqellqeyqetieeqrsvlekrqdqieq 174
                                        + +el +e+ ++L +++e l+ ++e++ + r++le++++qi++
  gi|557694906|ref|YP_008797960.1| 111 nQRAELVKEV-QRLMQERESLSRLREEVLKWREELESKEKQIAE 153
                                       3555555555.5788999999*********************86 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0072
                           UPF0242  66 ekskleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelklelee 142
                                        +  l+++ a l+++ + l++++e+l  l+ee  + +eel++ke+++++ +e  +qL  k+ea   +++ l+  +  
  gi|557694906|ref|YP_008797960.1| 105 TADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINILSERYLT 181
                                       45667777777777778***************************************************999999999 PP

                           UPF0242 143 qLaekqellqeyq 155
                                         +e q++l+++ 
  gi|557694906|ref|YP_008797960.1| 182 SFEEAQKKLENFG 194
                                       9999999988765 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.14
                           UPF0242  65 lekskleekeaklteld.eglktkeealeelqeeeeeLkeeldakeeelerlkee.nqqLqekleaiaedfeelkle 139
                                       ++k+ le++++ l+e    ++++ +++le+   e ++L +  + + e + r+++e ++ L   le++++  +e + e
  gi|557694906|ref|YP_008797960.1| 163 TKKEALETEINILSERYlTSFEEAQKKLENFGREMDKLFKLREIRMERMIRRERElEERLA-ALEKSKA-EAETLIE 237
                                       3788899999999998877888888899999888888866655444443333333033444.5555444.4567788 PP

                           UPF0242 140 leeqLaekqellqeyqetieeqrsvlekrqdqieqLe 176
                                         ++L+e+ ++l+ y+et+    +++e+r  + ++L 
  gi|557694906|ref|YP_008797960.1| 238 TSNKLREEVKKLEAYKETLAREIAEMERRRTELNELI 274
                                       999***************************9999985 PP

>> DUF4248  Domain of unknown function (DUF4248)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       9.7   3.1e+03      20      44 ..      64      88 ..      60     105 .. 0.64
   2 ?   -0.5   0.1       4.1   1.3e+03      22      41 ..     153     172 ..     148     189 .. 0.83
   3 ?    8.2   0.3    0.0079       2.5      26      48 ..     207     229 ..     206     237 .. 0.88
   4 ?   -1.7   0.0       9.6   3.1e+03      31      46 ..     236     251 ..     230     264 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 9.7
                           DUF4248 20 pksAvrrLrrwIkrnpeLkeeLtat 44
                                      p+  +  L++ +++   L ++L + 
  gi|557694906|ref|YP_008797960.1| 64 PQRTLSSLQSVVEKAYLLDQALDSY 88
                                      5566677777777777777777654 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 4.1
                           DUF4248  22 sAvrrLrrwIkrnpeLkeeL 41 
                                        A ++L++ I ++++L+ e+
  gi|557694906|ref|YP_008797960.1| 153 EAQETLKQLITKKEALETEI 172
                                       57889999999999999886 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0079
                           DUF4248  26 rLrrwIkrnpeLkeeLtatgykk 48 
                                       r+ r I+r++eL+e+L+a+  +k
  gi|557694906|ref|YP_008797960.1| 207 RMERMIRRERELEERLAALEKSK 229
                                       799**************998665 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 9.6
                           DUF4248  31 IkrnpeLkeeLtatgy 46 
                                       I+ +++L+ee +++  
  gi|557694906|ref|YP_008797960.1| 236 IETSNKLREEVKKLEA 251
                                       6666666666666553 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.7      0.39   1.2e+02     117     161 ..      15      57 ..       4      63 .. 0.64
   2 ?    9.7   4.0    0.0023      0.73      47     150 ..      68     178 ..      59     190 .. 0.58
   3 ?    4.4   4.3     0.098        31      94     160 ..     181     248 ..     172     277 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.39
                          Cauli_AT 117 qnrikkleeetkklaekivtekllkeevkdlderlseirdslkai 161
                                       ++ i +l +e+  +  ++   ++l+e +  l+e l +++++++++
  gi|557694906|ref|YP_008797960.1|  15 SDSIADLRKEVAAIRVQV--IEKLEERISLLEEALAKLKEDVRQV 57 
                                       445555555555554443..3456777777777777777777766 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0023
                          Cauli_AT  47 cnnlneivarslLklskllsylGLekDesealsksksPfgsvfkklk.kifkeggedkek.......ktklletLke 115
                                       +  l ++v +++L    l sy GL  +   +ls+s    ++++++ + +  ke++   ++       + + l+  +e
  gi|557694906|ref|YP_008797960.1|  68 LSSLQSVVEKAYLLDQALDSYRGLTEEV-KSLSESLHETADLLSNQRaELVKEVQRLMQEreslsrlREEVLKWREE 143
                                       567899******************8543.335655555555554443133444444333300000003333344444 PP

                          Cauli_AT 116 aqnrikkleeetkklaekivtekllkeevkdlder 150
                                        +++ k++ e+++ l++ i  ++ l++e+  l er
  gi|557694906|ref|YP_008797960.1| 144 LESKEKQIAEAQETLKQLITKKEALETEINILSER 178
                                       44466666666666666666666666666666554 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.098
                          Cauli_AT  94 kifkeggedkekktklletLkeaqn.rikkleeetkklaekivtekllkeevkdlderlseirdslka 160
                                       ++f+e++++ e+  ++++ L + ++ r++++ ++ ++l+e++ + ++ k+e   l e+ +++r+++k+
  gi|557694906|ref|YP_008797960.1| 181 TSFEEAQKKLENFGREMDKLFKLREiRMERMIRRERELEERLAALEKSKAEAETLIETSNKLREEVKK 248
                                       56777777777777777777777777777777777777777777777777777777777777777775 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   4.8      0.26        84      12      99 ..      38     125 ..      14     127 .. 0.70
   2 ?    8.7  13.1    0.0063         2      17      90 ..     130     197 ..     119     209 .. 0.76
   3 ?    3.4  10.0      0.27        87      33      96 ..     209     275 ..     195     283 .. 0.54

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.26
                                       HHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.....-HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  12 eespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkle....keekeqelqkkeqelqqkqqqkaqelq 84 
                                       e     ++a ++l+++ ++  +++ + ++ l +lq   +k+           + ++ l ++++ l +++ ++a  l 
  gi|557694906|ref|YP_008797960.1|  38 ERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKA----YlldqALDSYRGLTEEVKSLSESLHETADLLS 110
                                       44445566667777777777777777777777777777532....12223555666699999999999999999999 PP

                                       HHHHHHHHHHHHHHH CS
                              OmpH  85 kkqqellkpildkin 99 
                                       ++++el+k+++  ++
  gi|557694906|ref|YP_008797960.1| 111 NQRAELVKEVQRLMQ 125
                                       999999999887665 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0063
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  17 gkaaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkqqel 90 
                                             +l ++  k+++ele+kek++ ++qe+l++     +ke+ e e++ + +++ +++++++++l++  +e+
  gi|557694906|ref|YP_008797960.1| 130 LS----RLREEVLKWREELESKEKQIAEAQETLKQLIT--KKEALETEINILSERYLTSFEEAQKKLENFGREM 197
                                       33....45555699*******************73333..39999999*****999999999999988877664 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHHHHHHHHTTTS.....-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  33 aeleakekelqklqeelqkkakkl.e...keekeqelqkkeqelqqkqqqkaqelqkkqqellkpild 96 
                                       + + ++e+el++  ++l+k+++++ +   + +k +e  kk +++++ ++++  e+++++ el + ++ 
  gi|557694906|ref|YP_008797960.1| 209 ERMIRRERELEERLAALEKSKAEAeTlieTSNKLREEVKKLEAYKETLAREIAEMERRRTELNE-LIT 275
                                       4445566666666666665555543355533333333333344444466666888888877766.333 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  28.8     0.026       8.3      20     181 ..      29     186 ..      18     200 .. 0.77
   2 ?    0.4  16.5         2   6.5e+02      82     157 ..     199     278 ..     184     283 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.026
                             ATG16  20 liqaynrLldrtsaleaenaklekaaasakssksskksakekeasasqsnskqsakiqsleqklaqlreelaelyks 96 
                                        +q   +L +r+s+le+  akl++   ++ ++ ss    +++++s ++   +++  + +  +    l ee++ l  s
  gi|557694906|ref|YP_008797960.1|  29 RVQVIEKLEERISLLEEALAKLKEDVRQVLEQVSS---PQRTLSSLQS-VVEKAYLLDQALDSYRGLTEEVKSLSES 101
                                       567788999*************8887777762222...2333333333.3334444555556677788999999999 PP

                             ATG16  97 rgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEek 173
                                         e+a+ l +  +el k  ++l++++e+l +l++e+ + +++l+++e++++e ++++++l    +aL+ + n + e+
  gi|557694906|ref|YP_008797960.1| 102 LHETADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINILSER 178
                                       999**************************************************999999999999999999988887 PP

                             ATG16 174 lrklekEN 181
                                       + +  +E+
  gi|557694906|ref|YP_008797960.1| 179 YLTSFEEA 186
                                       66555554 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 2
                             ATG16  82 klaqlre.elaelyksrgelaqrllelneelqklee...klkedeerlaeleaeraaletklkdreeelrekeklvq 154
                                       kl++lre  ++ + ++  el++rl +l+++ ++ e+   ++++ +e++++lea +++l +++++ e +  e+++l+ 
  gi|557694906|ref|YP_008797960.1| 199 KLFKLREiRMERMIRRERELEERLAALEKSKAEAETlieTSNKLREEVKKLEAYKETLAREIAEMERRRTELNELIT 275
                                       55555553455666777777777777665444444311155555667777777777777777777777777777766 PP

                             ATG16 155 dlq 157
                                       +++
  gi|557694906|ref|YP_008797960.1| 276 EMR 278
                                       655 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   8.3       1.4   4.5e+02       9      53 ..      32      82 ..      26     133 .. 0.69
   2 ?    8.9   6.3    0.0075       2.4       6      76 ..     133     203 ..     130     206 .. 0.88
   3 ?    3.6   7.3      0.32     1e+02       8      62 ..     209     266 ..     204     282 .. 0.65

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......X CS
                              YabA  9 kleeleeqleelleeleelkeelaelleenaeLeleneklrerl......e 53
                                       +e+lee+++ l e l++lke++ ++le+ ++ +   ++l++ +      +
  gi|557694906|ref|YP_008797960.1| 32 VIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVekayllD 82
                                      578999999999999999999999999998877777777766664444440 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0075
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   6 lfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarl 76 
                                       l +++ +  e+le+  ++++e +e+l++l+ + ++Le+e + l er  ++ +++++k ++ ++  ++L +l
  gi|557694906|ref|YP_008797960.1| 133 LREEVLKWREELESKEKQIAEAQETLKQLITKKEALETEINILSERYLTSFEEAQKKLENFGREMDKLFKL 203
                                       56778888999***********************************9888888888888888888888776 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...XXXXXXXXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerl...eeeekkekek 62 
                                       +++ + e++lee l+ le+ k+e ++l+e  ++L+ e +kl       ++e ++ +++
  gi|557694906|ref|YP_008797960.1| 209 ERMIRRERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKetlAREIAEMERR 266
                                       5666778888888899999999999999999999999888865441112222222222 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 ?    9.4   3.4    0.0035       1.1       2      70 ..      36     103 ..      35     108 .. 0.89
   2 ?    3.3   7.4      0.28        89      18      61 ..     121     164 ..      97     178 .. 0.82
   3 ?    6.1   6.2     0.038        12       2      58 ..     218     270 ..     207     281 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0035
                     TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkle 70 
                                       le+r++ LE++l++ ++   ++++q+++ q+ l++L+  +E+ +y l+q++   r l +++ +++++l 
  gi|557694906|ref|YP_008797960.1|  36 LEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEK-AYLLDQALDSYRGLTEEVKSLSESLH 103
                                       8************************************99997.79999999999988888888877765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.28
                     TolA_bind_tri  18 qlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYld 61 
                                       q l++  + l++l++e+ + R ++E  + q+ +++e  ++l ++
  gi|557694906|ref|YP_008797960.1| 121 QRLMQERESLSRLREEVLKWREELESKEKQIAEAQETLKQLITK 164
                                       778888889******************************99876 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.038
                     TolA_bind_tri   2 ledrvarLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdl 58 
                                       le+r+a LE+  +   ++l+e     ++l++e+++L    E l+ ++ ++e+r  +l
  gi|557694906|ref|YP_008797960.1| 218 LEERLAALEKSKAE-AETLIETS---NKLREEVKKLEAYKETLAREIAEMERRRTEL 270
                                       89999999986655.46666665...57899*********************98776 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7  19.6     0.082        26      17     146 ..      32     165 ..      13     168 .. 0.63
   2 ?    3.8  24.1      0.16        51      19     122 ..     131     271 ..     131     281 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.082
                         Rootletin  17 LvskLqaKvlqYkkrcseleqrlle...ktselektkltlllssareleeeesadleealakLeeE.rqrseklaqv 89 
                                       +++kL +++    +  ++l + + +   + s +++t  +l+  s  e +    + l++  + L eE +  se+l ++
  gi|557694906|ref|YP_008797960.1|  32 VIEKLEERISLLEEALAKLKEDVRQvleQVSSPQRTLSSLQ--SVVEKAYLLDQALDSY-RGLTEEvKSLSESLHET 105
                                       44444444444444444444333332112222222221111..1111112222333444.45666626689****** PP

                         Rootletin  90 nslLreqleearqaneaL...tedlqkltkdwerlreeleqkekewreeeeafneylsse 146
                                        +lL +q  e  ++ ++L   +e+l +l++++ + reele+kek+  e +e++++ +++ 
  gi|557694906|ref|YP_008797960.1| 106 ADLLSNQRAELVKEVQRLmqeRESLSRLREEVLKWREELESKEKQIAEAQETLKQLITKK 165
                                       **********999999993333568999*************************9998765 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.16
                         Rootletin  19 skLqaKvlqYkkrcseleqrllektselektkltlll......................................ss 57 
                                       s+L++ vl+ ++  ++ e++++e + +l k+ +t++                                       + 
  gi|557694906|ref|YP_008797960.1| 131 SRLREEVLKWREELESKEKQIAEAQETL-KQLITKKEaleteinilseryltsfeeaqkklenfgremdklfklrEI 206
                                       699*******************933333.333333334555566666666666666665555555555555554422 PP

                         Rootletin  58 areleeeesadleealakLeeErqrseklaqvnslLreqleearqaneaLtedlqkltkdwerlr 122
                                         e+   ++++lee la Le  +  +e+l ++ + Lre++++ ++  e+L +++  +++  ++l+
  gi|557694906|ref|YP_008797960.1| 207 RMERMIRRERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLAREIAEMERRRTELN 271
                                       255555678899***************************************99987654433333 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5  20.8     0.061        20      67     213 ..      31     176 ..      13     179 .. 0.79
   2 ?   -2.7  28.2        10   3.2e+03      65     224 ..      95     254 ..      93     277 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.061
                           DUF4618  67 qakaeLqeweekeekklekLeqqleqlnakvqklqeelnvLstYkDkeYpv.kav.qIanlvrqlqqlkdsqqdeld 141
                                       q+ ++L+e  + +e+ l+kL+++++q+ ++v + q  l+ L++  +k Y + +a+     l+++++ l++s ++  d
  gi|557694906|ref|YP_008797960.1|  31 QVIEKLEERISLLEEALAKLKEDVRQVLEQVSSPQRTLSSLQSVVEKAYLLdQALdSYRGLTEEVKSLSESLHETAD 107
                                       56789********************************************9835563457899999999998877777 PP

                           DUF4618 142 eleelikevleklskkiqkkkekllkslaektlkatqeaLlqktlenqvlkkeiekfrefieeleeeipeLk 213
                                        l++ + e  ++ ++ +q  +++ l+ l e++lk  +e L+ k  + ++ ++ +++   + e le ei+ L 
  gi|557694906|ref|YP_008797960.1| 108 LLSNQRAELVKEVQRLMQ--ERESLSRLREEVLKW-REELESKEKQIAEAQETLKQLITKKEALETEINILS 176
                                       777777777776655554..456678888887776.677888888888888888888888888888888876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 10
                           DUF4618  65 leqakaeLqeweekeekklekLeqqleqlnakvqklqeelnvLstYkDkeYpvkavqIanlvrqlqqlkdsqqdeld 141
                                       ++++ + L e+++ ++++ ++L +++++l ++ ++l+   + +  ++ +e   k  qIa+ ++ l+ql ++++    
  gi|557694906|ref|YP_008797960.1|  95 VKSLSESLHETADLLSNQRAELVKEVQRLMQERESLSRLREEVLKWR-EELESKEKQIAEAQETLKQLITKKEALET 170
                                       45555556666666666666666666655544333333222222222.47889999**************9999999 PP

                           DUF4618 142 eleelikevleklskkiqkkkekllkslaektlkatqeaLlqktlenqvlk...keiekfrefieeleeeipeLkae 215
                                       e++ l ++ l+++++ +qkk e+  +++  k +k  +  ++++++ +++l+     +ek + + e+l e  ++L++e
  gi|557694906|ref|YP_008797960.1| 171 EINILSERYLTSFEE-AQKKLENFGREM-DKLFKLREIRMERMIRRERELEerlAALEKSKAEAETLIETSNKLREE 245
                                       ************987.566777777776.556665555555555555555411167889999999999999999999 PP

                           DUF4618 216 veqLqaqae 224
                                       v++L+a  e
  gi|557694906|ref|YP_008797960.1| 246 VKKLEAYKE 254
                                       999998766 PP

>> YkyA  Putative cell-wall binding lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   7.3     0.049        16      61     157 ..      24     122 ..       5     132 .. 0.67
   2 ?    1.8  13.6      0.53   1.7e+02      49     108 ..     117     173 ..      91     181 .. 0.38
   3 ?    4.6  15.5     0.073        23      19     111 ..     182     278 ..     176     281 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.049
                              YkyA  61 enveeReellekekesieeakeefekikeeieei..edeelkkeaeelieameeryeaydklykaYkealeldkeLY 135
                                       e +  R + +ek +e i+  +e++ k+ke++ ++  + ++ +  +++l++++e+ y   d+ +++Y  ++e+ k+L 
  gi|557694906|ref|YP_008797960.1|  24 EVAAIRVQVIEKLEERISLLEEALAKLKEDVRQVleQVSSPQRTLSSLQSVVEKAY-LLDQALDSYRGLTEEVKSLS 99 
                                       33444777777777777777888888888777775434456778888887777777.67999999999999999999 PP

                              YkyA 136 emLkk.eeltleeleeqiekiNe 157
                                       e L +  +l  ++  e ++++ +
  gi|557694906|ref|YP_008797960.1| 100 ESLHEtADLLSNQRAELVKEVQR 122
                                       99988344444444444444444 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.53
                              YkyA  49 fdkikklsdealenveeReellekekesieeakeefekikeeieeiedeelkkeaeelie 108
                                        ++++ l +e  ++   Ree l+  +e +e+ ++++ +++e+++++   ++k+ +e+ i+
  gi|557694906|ref|YP_008797960.1| 117 VKEVQRLMQERESLSRLREEVLKW-REELESKEKQIAEAQETLKQLI--TKKEALETEIN 173
                                       333333333333333333333333.3334444444444444444442..11333333333 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.073
                              YkyA  19 efeeqqekLtelekkeqelyeeiielgmdefdkikklsdealenveeReellekekesieeakeefekikeeieei. 94 
                                       +fee+q+kL++  ++  +l++   e  m+++ + + + +e l+ +e+ + + e+  e  ++ +ee++k++++ e + 
  gi|557694906|ref|YP_008797960.1| 182 SFEEAQKKLENFGREMDKLFKLR-EIRMERMIRRERELEERLAALEKSKAEAETLIETSNKLREEVKKLEAYKETLa 257
                                       7999**************99755.88999999999999999999999999999999999999999999999999888 PP

                              YkyA  95 ....edeelkkeaeelieame 111
                                           e e  ++e++eli+ m 
  gi|557694906|ref|YP_008797960.1| 258 reiaEMERRRTELNELITEMR 278
                                       888888899999999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2851  (0.159016); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); expected 358.6 (0.02)
Passed Vit filter:                       209  (0.0116571); expected 17.9 (0.001)
Passed Fwd filter:                       154  (0.00858944); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              56  [number of targets reported over threshold]
# CPU time: 1.95u 0.39s 00:00:02.34 Elapsed: 00:00:00.59
# Mc/sec: 1454.26
//
Query:       gi|557694907|ref|YP_008797961.1|  [L=250]
Description: hypothetical protein CSUB_C1480 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   36.3   4.9      8e-09   35.7   4.9    1.2  1  zf-RING_2       Ring finger domain
    0.00022   21.0   4.5    0.00034   20.4   4.5    1.3  1  zf-C3HC4_2      Zinc finger, C3HC4 type (RING finger)
    0.00043   20.5   1.8    0.00076   19.7   1.8    1.4  1  zf-rbx1         RING-H2 zinc finger domain
    0.00084   19.6   6.4     0.0018   18.6   6.5    1.6  1  zf-RING-like    RING-like domain
    0.00084   19.4   2.4     0.0012   18.9   2.4    1.1  1  zf-RING_9       Putative zinc-RING and/or ribbon
     0.0014   18.5   4.8     0.0022   17.9   4.8    1.3  1  PHD             PHD-finger
     0.0018   17.9   3.0     0.0032   17.2   3.0    1.4  1  zf-RING_11      RING-like zinc finger
     0.0028   17.3   4.4       0.22   11.3   0.6    2.3  2  zinc_ribbon_2   zinc-ribbon domain
     0.0032   17.3   1.9     0.0032   17.3   1.9    1.6  1  C1_1            Phorbol esters/diacylglycerol binding domain 
     0.0038   17.3   4.7     0.0062   16.6   4.7    1.4  1  Zf_RING         KIAA1045 RING finger
     0.0067   16.4   5.3     0.0098   15.8   5.3    1.3  1  zf-RING_5       zinc-RING finger domain
     0.0097   15.8   5.8      0.014   15.3   5.8    1.2  1  zf-C3HC4        Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
       0.05   13.2   5.6      0.084   12.5   5.6    1.2  1  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
      0.053   13.4   4.3      0.087   12.7   4.3    1.4  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.06   13.2   5.8       0.52   10.2   6.2    2.0  2  Prok-RING_4     Prokaryotic RING finger family 4
       0.07   13.1   9.8      0.049   13.6   6.3    2.1  2  Prok-RING_1     Prokaryotic RING finger family 1
       0.12   12.4   7.3       0.93    9.6   7.3    2.0  1  DZR             Double zinc ribbon
       0.15   12.1   3.4       0.25   11.4   3.4    1.3  1  zf-RING_UBOX    RING-type zinc-finger
       0.28   10.7   8.6          1    8.9   2.5    2.4  2  TF_Zn_Ribbon    TFIIB zinc-binding
        0.4   10.8   5.1        1.4    9.1   2.0    2.4  2  Zn-ribbon_8     Zinc ribbon domain
       0.41   10.8   8.7       0.35   11.0   2.9    2.3  2  UPF0547         Uncharacterised protein family UPF0547
       0.48   10.6   7.5         15    5.9   7.5    2.3  1  FANCL_C         FANCL C-terminal domain
       0.92    9.3   6.8        5.2    7.0   6.9    1.9  1  zf-RING_4       RING/Ubox like zinc-binding domain
          1    9.4   8.0        7.8    6.6   1.6    2.9  2  DUF1610         Domain of unknown function (DUF1610)
        1.1    9.2   5.1        6.7    6.7   0.6    2.4  2  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
        1.7    8.5   4.3         26    4.7   0.2    2.5  2  Rubredoxin_2    Rubredoxin metal binding domain
          2    8.6   5.4        3.6    7.7   5.4    1.4  1  DUF1272         Protein of unknown function (DUF1272)
        2.6    7.8  14.2        8.1    6.2  14.2    1.7  1  Trp_oprn_chp    Tryptophan-associated transmembrane protein (
        2.8    7.5  12.1        4.6    6.8  11.5    1.7  1  DUF5336         Family of unknown function (DUF5336)
        5.7    7.1   7.6        2.7    8.2   2.0    2.1  2  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
        7.3    6.4   6.2        2.8    7.7   1.4    2.2  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
        7.6    6.5   7.9        2.2    8.3   2.1    2.2  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        8.2    6.5   7.5         41    4.3   0.2    2.7  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        9.6    6.5  10.1         10    6.4   2.1    3.2  3  zf-RING_7       C4-type zinc ribbon domain
        9.8    5.7  12.1        5.7    6.5   0.4    3.1  2  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> zf-RING_2  Ring finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   4.9   1.6e-11     8e-09       3      43 ..     205     245 ..     204     246 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.6e-11
                         zf-RING_2   3 CpICleelssadsvlllpCgHvfhreClerwlrssstCPlC 43 
                                       CpIC+ +++ ++ v++  Cg vfh  Cl+ +++ + tCP+C
  gi|557694907|ref|YP_008797961.1| 205 CPICYTSVEAENAVRCSSCGVVFHSGCLDAYVNINGTCPNC 245
                                       ********9999999889*********************** PP

>> zf-C3HC4_2  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   4.5   6.7e-07   0.00034       2      40 .]     205     245 ..     204     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 6.7e-07
                        zf-C3HC4_2   2 CpiCldml..kdpsvvtpCgHvfCqkCilrsLeekneCPlC 40 
                                       CpiC+ +   +++++   Cg vf++ C++ + + +  CP C
  gi|557694907|ref|YP_008797961.1| 205 CPICYTSVeaENAVRCSSCGVVFHSGCLDAYVNINGTCPNC 245
                                       *****987225889999************************ PP

>> zf-rbx1  RING-H2 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   1.8   1.5e-06   0.00076      13      54 ..     204     245 ..     198     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-06
                           zf-rbx1  13 acieckapgdeecpvvlGeCgHaFHlhCiskWlktrkvCPlc 54 
                                        c+ c ++ ++e  v +++Cg +FH  C++ +++ + +CP c
  gi|557694907|ref|YP_008797961.1| 204 VCPICYTSVEAENAVRCSSCGVVFHSGCLDAYVNINGTCPNC 245
                                       69999999999899999***********************99 PP

>> zf-RING-like  RING-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   6.5   3.4e-06    0.0018      10      43 .]     216     245 ..     205     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.4e-06
                      zf-RING-like  10 qGvrCsnesCnvrlHvdCfqhyirthsskkCpkC 43 
                                        +vrCs  sC v +H  C+++y+  + + +Cp+C
  gi|557694907|ref|YP_008797961.1| 216 NAVRCS--SCGVVFHSGCLDAYV--NINGTCPNC 245
                                       589***..***************..56778**** 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 !   18.9   2.4   2.3e-06    0.0012     154     203 ..     201     247 ..     199     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.3e-06
                         zf-RING_9 154 kgfiCelCkseellfpfqlktverCekCkavfHkeClkkkekk..ecpkcer 203
                                       +g++C +C ++      ++++++rC++C+ vfH+ Cl +  +   +cp+c r
  gi|557694907|ref|YP_008797961.1| 201 EGVVCPICYTS-----VEAENAVRCSSCGVVFHSGCLDAYVNIngTCPNCGR 247
                                       68899999876.....47899999*************776655789****88 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   4.8   4.2e-06    0.0022       1      49 [.     204     245 ..     204     248 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 4.2e-06
                                       SBTTTTSTTSTTSCEEEETTTSCEEETTTSSSTHSHHSHHSSTBSSTTT CS
                               PHD   1 rCavCkkksdeeeelvqCdgCkrwfHqkClkppleseekpegewlCekC 49 
                                       +C +C   s e e+ v C +C+  fH  Cl+  ++   +     +C++C
  gi|557694907|ref|YP_008797961.1| 204 VCPICYT-SVEAENAVRCSSCGVVFHSGCLDAYVN---ING---TCPNC 245
                                       5******.99********************99877...333...46666 PP

>> zf-RING_11  RING-like zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.0   6.2e-06    0.0032       2      29 .]     205     232 ..     205     232 .. 0.98

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.2e-06
                        zf-RING_11   2 CsICLeefkpgqalfilpCsHtFHfkCI 29 
                                       C IC  +++ ++a+++ +C+ +FH+ C+
  gi|557694907|ref|YP_008797961.1| 205 CPICYTSVEAENAVRCSSCGVVFHSGCL 232
                                       ***************************5 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.6   0.00043      0.22       2      20 ..     205     224 ..     204     225 .. 0.93
   2 !    7.5   0.2    0.0069       3.5       2       7 ..     242     247 ..     241     250 .] 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00043
                     zinc_ribbon_2   2 CpnCGaelq.dnakFCpyCG 20 
                                       Cp C + ++ +na+ C+ CG
  gi|557694907|ref|YP_008797961.1| 205 CPICYTSVEaENAVRCSSCG 224
                                       ********868********9 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0069
                     zinc_ribbon_2   2 CpnCGa 7  
                                       CpnCG+
  gi|557694907|ref|YP_008797961.1| 242 CPNCGR 247
                                       888886 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 !   17.3   1.9   6.3e-06    0.0032      10      45 ..     201     234 ..     195     242 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 6.3e-06
                                       S--B-TTT-SB--SSSS-EEEETTT--EE-CCCCTT CS
                              C1_1  10 qptfCkhCgeflwgkekqglkCswCkllvHkkChek 45 
                                       +   C  C  ++  ++  +++Cs C++++H  C+  
  gi|557694907|ref|YP_008797961.1| 201 EGVVCPICYTSV--EAENAVRCSSCGVVFHSGCLDA 234
                                       6678999*****..*******************976 PP

>> Zf_RING  KIAA1045 RING finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   4.7   1.2e-05    0.0062       2      36 ..     199     234 ..     198     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.2e-05
                           Zf_RING   2 veedelCeiC.evytaeelypCRvCtkvfHegClrk 36 
                                       vee  +C iC    +ae+ + C  C  vfH gCl  
  gi|557694907|ref|YP_008797961.1| 199 VEEGVVCPICyTSVEAENAVRCSSCGVVFHSGCLDA 234
                                       67889*****87899*******************87 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 !   15.8   5.3   1.9e-05    0.0098       2      43 ..     205     246 ..     204     247 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                         zf-RING_5   2 CnkCfeklskeekfyltsCgHifCekClkkllekeavCpiCr 43 
                                       C++C+++++ e ++   sCg +f++ Cl+ + + + +Cp C+
  gi|557694907|ref|YP_008797961.1| 205 CPICYTSVEAENAVRCSSCGVVFHSGCLDAYVNINGTCPNCG 246
                                       ********99999****************************7 PP

>> zf-C3HC4  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   5.8   2.7e-05     0.014       1      41 []     205     245 ..     205     245 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-05
                                       -TTT-S--SS-E...E-TTS--B-CHHHHHHHHCTSSB--TTT CS
                          zf-C3HC4   1 CpiCleeakepn..elleCkHsfCskCirkilksrkkvkCPlC 41 
                                       CpiC + ++ +n  + + C+  f+s C++ +++   + +CP+C
  gi|557694907|ref|YP_008797961.1| 205 CPICYTSVEAENavRCSSCGVVFHSGCLDAYVN--INGTCPNC 245
                                       ******999999889******************..9999**** 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 ?   12.5   5.6   0.00016     0.084       6      49 ..     204     245 ..     200     249 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                      Zn_ribbon_17   6 sCayCelavk.grvvlcgvCeHvlHasCarewfenddlaeCpsGC 49 
                                        C +C ++v+  + v c +C+ v H+ C+++  + +    Cp  C
  gi|557694907|ref|YP_008797961.1| 204 VCPICYTSVEaENAVRCSSCGVVFHSGCLDAYVNING--TCPN-C 245
                                       599******8356889***************998888..8885.4 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 ?   12.7   4.3   0.00017     0.087       3      47 ..     203     249 ..     201     250 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00017
                                       SB-TTTSSS...BS-EEETTEEEEEE-HHHHHHHHHTT-B-TTT--B- CS
                        zf-C3HC4_3   3 eeCviCler...prnvvllpCgHlvlCeeCaekllkrkkkCpiCrrpi 47 
                                         C+iC+++   +  v +  Cg + + + C++ + + + +Cp C r +
  gi|557694907|ref|YP_008797961.1| 203 VVCPICYTSveaENAVRCSSCGVV-FHSGCLDAYVNINGTCPNCGRAV 249
                                       57*****96443556778889987.889999999999*******9865 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 ?    4.8   0.1     0.049        25      32      44 ..     204     216 ..     198     218 .. 0.80
   2 ?   10.2   6.2     0.001      0.52       1      39 [.     205     248 ..     205     250 .] 0.84

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.049
                       Prok-RING_4  32 sCPlCqrrisksd 44 
                                        CP+C + +++++
  gi|557694907|ref|YP_008797961.1| 204 VCPICYTSVEAEN 216
                                       5****99988776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.001
                       Prok-RING_4   1 CvlCgeq...ekkailepCgHlvCkeCfdsk.dls.sCPlCqrr 39 
                                       C +C ++   e+ ++ ++Cg ++   C+d+  + + +CP C r 
  gi|557694907|ref|YP_008797961.1| 205 CPICYTSveaENAVRCSSCGVVFHSGCLDAYvNINgTCPNCGRA 248
                                       6666655555999****************9878889*****987 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   6.3   9.6e-05     0.049       3      37 ..     201     234 ..     199     244 .. 0.85
   2 ?    0.2   0.4       1.4   7.3e+02      22      27 ..     241     246 ..     239     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9.6e-05
                       Prok-RING_1   3 tgkkCpvCgkelkeedDiVvCpeCgtpyHraCyek 37 
                                       +g  Cp+C   ++ e  +V C  Cg ++H  C + 
  gi|557694907|ref|YP_008797961.1| 201 EGVVCPICYTSVEAE-NAVRCSSCGVVFHSGCLDA 234
                                       5789********998.9***************764 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.4
                       Prok-RING_1  22 vCpeCg 27 
                                       +Cp+Cg
  gi|557694907|ref|YP_008797961.1| 241 TCPNCG 246
                                       488887 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   7.3    0.0018      0.93      14      49 .]     204     246 ..     198     250 .] 0.65

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0018
                               DZR  14 fCseCgtklkavaaedrCpsCgekvdpearf........CpeCG 49 
                                       +C+ C t+++ ++++ rC+sCg   ++++          Cp+CG
  gi|557694907|ref|YP_008797961.1| 204 VCPICYTSVE-AENAVRCSSCGVVFHSGCLDayvningtCPNCG 246
                                       6888888886.455667777776666665444455566666665 PP

>> zf-RING_UBOX  RING-type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   3.4   0.00049      0.25       1      39 []     205     243 ..     205     243 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00049
                      zf-RING_UBOX   1 CpIClelft..dPlv.lpCGHtFCreClwelskslegafkCP 39 
                                       CpIC+ + +  + +   +CG +F++ Cl   +   + + +CP
  gi|557694907|ref|YP_008797961.1| 205 CPICYTSVEaeNAVRcSSCGVVFHSGCL---DAYVNINGTCP 243
                                       *****9998554444458**********...66666666776 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   2.5     0.002         1       2      28 ..     204     226 ..     203     229 .. 0.80
   2 ?    5.0   0.4     0.033        17       2       8 ..     241     247 ..     240     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                                       EETTTTCEECHEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlV 28 
                                       +CP+C ++   + ++++ ++C++CG+V
  gi|557694907|ref|YP_008797961.1| 204 VCPICYTS---V-EAENAVRCSSCGVV 226
                                       8*****86...2.455679******99 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.033
                                       EETTTTC CS
                      TF_Zn_Ribbon   2 kCPnCgs 8  
                                       +CPnCg 
  gi|557694907|ref|YP_008797961.1| 241 TCPNCGR 247
                                       7999996 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.39     2e+02      15      36 ..     193     212 ..     190     215 .. 0.62
   2 ?    9.1   2.0    0.0026       1.4       7      36 ..     219     249 ..     217     250 .] 0.70

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.39
                       Zn-ribbon_8  15 fevlqsisdapltaCPeCgsev 36 
                                       fev  ++   + ++CP C   v
  gi|557694907|ref|YP_008797961.1| 193 FEVAGEVE--EGVVCPICYTSV 212
                                       55554433..2456****7655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0026
                       Zn-ribbon_8   7 rCeeCghefe.....vlqsisdapltaCPeCgsev 36 
                                       rC +Cg +f      + +      + +CP+Cg +v
  gi|557694907|ref|YP_008797961.1| 219 RCSSCGVVFHsgcldAYVN----INGTCPNCGRAV 249
                                       9*****9999654433332....2556*****865 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.9   0.00068      0.35       2      25 ..     204     228 ..     204     229 .. 0.92
   2 ?    2.8   0.3      0.24   1.3e+02       2       8 ..     241     247 ..     241     249 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00068
                           UPF0547   2 vCPeCeakv.PvaaqfCphCGyvFq 25 
                                       vCP C + v +++a++C+ CG vF 
  gi|557694907|ref|YP_008797961.1| 204 VCPICYTSVeAENAVRCSSCGVVFH 228
                                       7********899*********9995 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.24
                           UPF0547   2 vCPeCea 8  
                                       +CP C +
  gi|557694907|ref|YP_008797961.1| 241 TCPNCGR 247
                                       5888876 PP

>> FANCL_C  FANCL C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   7.5     0.029        15       3      42 ..     203     237 ..     201     250 .] 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.029
                                       -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHH CS
                           FANCL_C   3 veCgiCyayrldsgevpdisCdnekCnkkfHsaCLkeWlr 42 
                                       v C+iCy+    ++    + C   +C+  fHs CL  +++
  gi|557694907|ref|YP_008797961.1| 203 VVCPICYTSVEAEN---AVRC--SSCGVVFHSGCLDAYVN 237
                                       56*****9988444...4556..479*********87654 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 ?    7.0   6.9      0.01       5.2       1      43 [.     205     245 ..     205     248 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                         zf-RING_4   1 cplCdeeldetdkdlkpCeCgyqiClfCyhrileeeegrCPaC 43 
                                       cp+C + ++  +++++  +Cg  +   C++  + + +g CP+C
  gi|557694907|ref|YP_008797961.1| 205 CPICYTSVE-AENAVRCSSCGVVFHSGCLDAYV-NINGTCPNC 245
                                       99**99995.455565559**999999988777.689****** PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.6      0.03        15       1       8 [.     220     227 ..     220     230 .. 0.86
   2 ?    6.6   1.6     0.015       7.8      19      23 ..     242     246 ..     241     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.03
                           DUF1610   1 CtSCGael 8  
                                       C+SCG++ 
  gi|557694907|ref|YP_008797961.1| 220 CSSCGVVF 227
                                       *****986 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.015
                           DUF1610  19 CPNCG 23 
                                       CPNCG
  gi|557694907|ref|YP_008797961.1| 242 CPNCG 246
                                       ****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 ?    6.7   0.6     0.013       6.7      13      22 ..     219     228 ..     217     229 .. 0.90
   2 ?    4.3   0.4     0.076        39      13      20 ..     241     248 ..     240     250 .] 0.63

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                           DUF35_N  13 rCpdCGtvqf 22 
                                       rC++CG v++
  gi|557694907|ref|YP_008797961.1| 219 RCSSCGVVFH 228
                                       9*******97 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.076
                           DUF35_N  13 rCpdCGtv 20 
                                        Cp+CG+ 
  gi|557694907|ref|YP_008797961.1| 241 TCPNCGRA 248
                                       47777765 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.7     0.052        27       2      11 ..     219     228 ..     219     230 .. 0.85
   2 ?    4.7   0.2      0.05        26      15      21 ..     240     246 ..     235     247 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.052
                      Rubredoxin_2   2 vCsqCGfesa 11 
                                       +Cs+CG +++
  gi|557694907|ref|YP_008797961.1| 219 RCSSCGVVFH 228
                                       7*****9887 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.05
                      Rubredoxin_2  15 GrCpsCg 21 
                                       G Cp+Cg
  gi|557694907|ref|YP_008797961.1| 240 GTCPNCG 246
                                       89****8 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.4     0.007       3.6       8      48 ..     205     246 ..     202     250 .] 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.007
                           DUF1272   8 CecCdkdlppdseearicsyEctFCaeCaeevl..envCPncg 48 
                                       C  C +++++++ + r  s    F + C ++ +  +++CPncg
  gi|557694907|ref|YP_008797961.1| 205 CPICYTSVEAEN-AVRCSSCGVVFHSGCLDAYVniNGTCPNCG 246
                                       899999999887.5555567889*****999764489*****9 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  14.2     0.016       8.1       4     140 ..      39     164 ..      37     172 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.016
                      Trp_oprn_chp   4 lalgAallllasrltWvtvtvsdalggprtvalsGadwapaltalAlvllAaavAvlavrglg.rrvvgvllalaga 79 
                                       lal++ + +l+  l+W tv++++  ++  +  l  +++a  ++   l++l  +v  +  r+++ r+v+ vl +l g+
  gi|557694907|ref|YP_008797961.1|  39 LALAGSIHVLTLLLPWYTVRADSVSTSVLSGYLLPETLALSVAGGVLAGLSLLVTSFSQRPMAvRTVLVVLSLLGGV 115
                                       7888999999999*************9999999999************************9863778888899999* PP

                      Trp_oprn_chp  80 gaavaalslltdpadaaraaaaaatgvasaaaaveltawpvlala.ggvllllagvllllra 140
                                       +a+v++l l + +  a   a +   g+           +  +al  + v+l+l+gv+l+ r+
  gi|557694907|ref|YP_008797961.1| 116 LAMVSPLYLGLVRVPALSVAGEP--GI-----------GFFIALFsAIVILALGGVALMTRP 164
                                       ******99988877777766644..22...........333333303444555555555555 PP

>> DUF5336  Family of unknown function (DUF5336)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  11.5     0.009       4.6      43     123 ..      40     117 ..      23     155 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.009
                           DUF5336  43 aaLGliayllgFgplltvsassadleeasatsgglglavvllLlagLlAgvslLPkqksktavaAvlsvlgfLlvla 119
                                       a  G i  l   +p  tv a+s  ++++ ++   l  +++l++++g+lAg+slL    s+++ +Av  vl +L +l 
  gi|557694907|ref|YP_008797961.1|  40 ALAGSIHVLTLLLPWYTVRADS--VSTSVLSGYLLPETLALSVAGGVLAGLSLLVTSFSQRP-MAVRTVLVVLSLLG 113
                                       3447888888889999999998..666666666666779***************98875544.34444444444444 PP

                           DUF5336 120 evin 123
                                        v++
  gi|557694907|ref|YP_008797961.1| 114 GVLA 117
                                       4333 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 ?    8.2   2.0    0.0053       2.7       2      27 ..     205     228 ..     204     232 .. 0.88
   2 ?    2.2   0.3      0.38     2e+02      15      25 ..     238     248 ..     232     250 .] 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0053
                          zf-Mss51   2 CPvpkhkqtapkhvdfeCpdCGipty 27 
                                       CP++ +    +++ ++ C  CG++ +
  gi|557694907|ref|YP_008797961.1| 205 CPICYTSV--EAENAVRCSSCGVVFH 228
                                       ****7666..999**********998 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.38
                          zf-Mss51  15 vdfeCpdCGip 25 
                                       ++ +Cp+CG  
  gi|557694907|ref|YP_008797961.1| 238 INGTCPNCGRA 248
                                       5668*****65 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 ?    7.7   1.4    0.0055       2.8       8      24 ..     210     224 ..     204     226 .. 0.72
   2 ?    0.6   0.2       0.9   4.6e+02      20      25 ..     242     247 ..     239     250 .] 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0055
                                       -B----SSS----SSS- CS
                    DNA_RNApol_7kD   8 aevslkkgdpiRCkeCG 24 
                                       ++  ++++ ++RC  CG
  gi|557694907|ref|YP_008797961.1| 210 TS--VEAENAVRCSSCG 224
                                       44..566777******* PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.9
                                       -SSS-- CS
                    DNA_RNApol_7kD  20 CkeCGh 25 
                                       C +CG 
  gi|557694907|ref|YP_008797961.1| 242 CPNCGR 247
                                       888885 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 ?    8.3   2.1    0.0042       2.2      29      58 ..     203     229 ..     190     240 .. 0.80
   2 ?    1.4   0.4       0.6   3.1e+02      30      36 ..     241     247 ..     239     250 .] 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0042
                    OrfB_Zn_ribbon  29 ktCseCgsknkealsgrtfkCpnCgfeadr 58 
                                         C+ C   ++    ++ ++C++Cg++++ 
  gi|557694907|ref|YP_008797961.1| 203 VVCPICYTSVEA---ENAVRCSSCGVVFHS 229
                                       67****988888...999*********996 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.6
                    OrfB_Zn_ribbon  30 tCseCgs 36 
                                       tC++Cg+
  gi|557694907|ref|YP_008797961.1| 241 TCPNCGR 247
                                       7888886 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 ?    3.9   2.6       0.1        51      17      44 ..     201     224 ..     200     226 .. 0.80
   2 ?    2.2   0.1      0.36   1.8e+02      17      26 ..     216     225 ..     212     230 .. 0.77
   3 ?    4.3   0.2      0.08        41      20      26 ..     241     247 ..     237     250 .] 0.81

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.1
                     Zn_Tnp_IS1595  17 ngfvCPhCgsrkayriktrglfqCkeCr 44 
                                       +g+vCP C     +++++    +C++C+
  gi|557694907|ref|YP_008797961.1| 201 EGVVCPICY----TSVEAENAVRCSSCG 224
                                       5899****8....667777788999996 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.36
                     Zn_Tnp_IS1595  17 ngfvCPhCgs 26 
                                       n ++C  Cg+
  gi|557694907|ref|YP_008797961.1| 216 NAVRCSSCGV 225
                                       5578999997 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.08
                     Zn_Tnp_IS1595  20 vCPhCgs 26 
                                       +CP+Cg 
  gi|557694907|ref|YP_008797961.1| 241 TCPNCGR 247
                                       7****95 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 ?   -0.9   0.1       3.8   1.9e+03      18      29 ..     200     208 ..     192     209 .. 0.65
   2 ?    3.6   0.1      0.15        78      24      31 ..     218     225 ..     211     226 .. 0.80
   3 ?    6.4   2.1      0.02        10      25      31 ..     241     247 ..     240     247 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 3.8
                                       CCSTB-EE-TTT CS
                         zf-RING_7  18 ragdevvtCpeC 29 
                                         g   v Cp C
  gi|557694907|ref|YP_008797961.1| 200 EEG---VVCPIC 208
                                       333...89**99 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.15
                                       EE-TTT-- CS
                         zf-RING_7  24 vtCpeCGR 31 
                                       v+C +CG+
  gi|557694907|ref|YP_008797961.1| 218 VRCSSCGV 225
                                       99****96 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.02
                                       E-TTT-- CS
                         zf-RING_7  25 tCpeCGR 31 
                                       tCp+CGR
  gi|557694907|ref|YP_008797961.1| 241 TCPNCGR 247
                                       8*****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 ?    4.8   0.5     0.037        19       3       9 ..     218     224 ..     216     227 .. 0.85
   2 ?    6.5   0.4     0.011       5.7       5       9 ..     242     246 ..     240     250 .] 0.70

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.037
                       zf-ribbon_3   3 vrCPnCG 9  
                                       vrC++CG
  gi|557694907|ref|YP_008797961.1| 218 VRCSSCG 224
                                       8999999 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.011
                       zf-ribbon_3   5 CPnCG 9  
                                       CPnCG
  gi|557694907|ref|YP_008797961.1| 242 CPNCG 246
                                       77777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       947  (0.0528195); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); expected 358.6 (0.02)
Passed Vit filter:                       120  (0.00669307); expected 17.9 (0.001)
Passed Fwd filter:                        41  (0.0022868); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1739.12
//
Query:       gi|557694908|ref|YP_008797962.1|  [L=482]
Description: glycyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-22   78.8   0.1    4.4e-22   78.1   0.1    1.4  1  HGTP_anticodon  Anticodon binding domain
    4.2e-12   46.4   0.0    2.4e-11   44.0   0.0    2.1  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
      0.092   12.7   0.1      0.092   12.7   0.1    3.3  5  zinc_ribbon_4   zinc-ribbon domain
       0.13   12.4   0.1        7.9    6.7   0.0    2.5  2  Zn-ribbon_8     Zinc ribbon domain


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 !   78.1   0.1   9.7e-26   4.4e-22       2      93 ..     390     478 ..     389     479 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.1 bits;  conditional E-value: 9.7e-26
                                       EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCE CS
                    HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtre 78 
                                       ++v pl + + el+++a++l+++L+ + +++ + d+++sig+++r+ d++g+pf+++v++++le++tvtvrdrdt++
  gi|557694908|ref|YP_008797962.1| 390 IAVFPLLD-RPELTQVAQQLYNKLQLD-FDTFY-DEKGSIGRRYRRQDEIGTPFCITVDYQTLEDNTVTVRDRDTMK 463
                                       67899998.899*************65.76666.59***************************************** PP

                                       EEEEETTHHHHHHHH CS
                    HGTP_anticodon  79 qervsldelveklke 93 
                                       qerv ++ l++++++
  gi|557694908|ref|YP_008797962.1| 464 QERVNIEVLKSYISD 478
                                       **********99976 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 !   44.0   0.0   5.2e-15   2.4e-11       8     178 ..     154     368 ..     150     369 .. 0.77
   2 ?   -2.7   0.0       1.1     5e+03     124     155 ..     446     477 ..     400     482 .] 0.51

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 5.2e-15
                                       SEEEEE-SSSHHHHHHHHHH.HEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   8 dreyiLkPtneetfvelird.evlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdl 83 
                                       ++e +L+P+ ++ +   +     +  ++LPl l+q++  +R+E s  + L+R+reF+q + +vf  +    +++++ 
  gi|557694908|ref|YP_008797962.1| 154 GDEGYLRPETCQNIFIDFPRvYKISRRKLPLALAQVGKSFRNEISPRQSLIRLREFTQAEIEVFFNPR-TANEFAKA 229
                                       57889***99998765554303343355****************9556******************98.56667777 PP

                                       HHHHHHHHHHT.T.SCEEEEEEGTTSC........................................BTTSEEEEEE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxx........................................xxxxxxxxxx RF
                      tRNA-synt_2b  84 ikaisriferl.glefraiielmsaks........................................adykdkkefe 119
                                        +++++ ++   g  + +i      +s                                        + +++  ++e
  gi|557694908|ref|YP_008797962.1| 230 KTVADKELNMWvGERVEKITCERAVESglvsswlvayylwlvqdfyfrlgigsdrlrfrrlgddekaFYAAEAWDLE 306
                                       77777666665243444444333333367889999***************************999966667788999 PP

                                       EEETTTSEEEEEEEEEEEET.HH.....HHHTTEEEECTTSSEEEEEEEEEEEEHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx.xx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 120 avsesltkgieigtiqklgt.rl.....serlgatvldennreksvimicaaigveRllsaileq 178
                                       +++   t  +e++ ++++ +  l     ++  +++v  e++++  +++   ++gv R l+a+le+
  gi|557694908|ref|YP_008797962.1| 307 VLTS--TGWVELVACNNRTDyDLgghqrVSGVDLRV-TEDGESFLPHVFELSMGVDRSLLALLEH 368
                                       9998..88889****999543222211144455566.9999*********************996 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                                       TTSEEEEEEEEEEEETHHHHHTTEEEECTTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 124 sltkgieigtiqklgtrlserlgatvldennr 155
                                        +t + +++t+  ++t   er +++vl++  +
  gi|557694908|ref|YP_008797962.1| 446 YQTLEDNTVTVRDRDTMKQERVNIEVLKSYIS 477
                                       24455566777777677777777777666555 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   0.1     2e-05     0.092       2      16 ..      85      99 ..      85     109 .. 0.79
   2 ?    1.3   0.1     0.073   3.3e+02      27      32 ..     128     133 ..     126     134 .. 0.61
   3 ?   -2.4   0.1       1.1   4.8e+03      30      35 ..     163     168 ..     162     169 .. 0.82
   4 ?   -3.3   0.0       2.1   9.4e+03      11      20 ..     174     183 ..     174     185 .. 0.88
   5 ?   -3.7   0.1       2.7   1.2e+04       2       7 ..     247     252 ..     247     252 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                     zinc_ribbon_4  2 kitCpsCkakyeidd 16
                                      +++C+sCk++y+id 
  gi|557694908|ref|YP_008797962.1| 85 ITRCKSCKSVYRIDR 99
                                      579**********97 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.073
                     zinc_ribbon_4  27 rCskCg 32 
                                       rC++Cg
  gi|557694908|ref|YP_008797962.1| 128 RCPACG 133
                                       566664 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.1
                     zinc_ribbon_4  30 kCghvF 35 
                                        C+++F
  gi|557694908|ref|YP_008797962.1| 163 TCQNIF 168
                                       699999 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 2.1
                     zinc_ribbon_4  11 kyeiddeklp 20 
                                       +y+i+ +klp
  gi|557694908|ref|YP_008797962.1| 174 VYKISRRKLP 183
                                       699****998 PP

  == domain 5  score: -3.7 bits;  conditional E-value: 2.7
                     zinc_ribbon_4   2 kitCps 7  
                                       kitC++
  gi|557694908|ref|YP_008797962.1| 247 KITCER 252
                                       689975 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.025   1.1e+02      24      34 ..      83      93 ..      77     101 .. 0.66
   2 ?    6.7   0.0    0.0018       7.9      28      39 ..     128     139 ..     116     142 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.025
                       Zn-ribbon_8 24 apltaCPeCgs 34
                                      +p t C++C+s
  gi|557694908|ref|YP_008797962.1| 83 DPITRCKSCKS 93
                                      45666999987 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0018
                       Zn-ribbon_8  28 aCPeCgsevrrv 39 
                                        CP+Cg+e+ +v
  gi|557694908|ref|YP_008797962.1| 128 RCPACGGELDKV 139
                                       378887777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); 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 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3287.82
//
Query:       gi|557694909|ref|YP_008797963.1|  [L=124]
Description: NADH dehydrogenase I subunit A [Candidatus Caldiarchaeum subterraneum]
Scores for 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   44.8   0.1    1.7e-11   44.2   0.1    1.3  1  Oxidored_q4      NADH-ubiquinone/plastoquinone oxidoreductase
    0.00036   19.8   3.3    0.00043   19.5   3.3    1.0  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
          1    9.5   4.4         13    6.0   0.3    2.5  3  MPS-4            MinK-related peptide, potassium channel acce
        2.6    8.2   8.5       0.24   11.6   4.0    1.7  2  DUF3325          Protein of unknown function (DUF3325)


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 !   44.2   0.1   3.7e-15   1.7e-11       3      92 ..      26     114 ..      24     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 3.7e-15
                                       HHHHHHCHSS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHHHHHHHH CS
                       Oxidored_q4   3 lllllsallgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkelglfgliemll 79 
                                       ll++ s+ll+pkkp ++k+ ++E+G  p+g ++++f+v+++ +a++++ + v ++ +f  +v++ + +  + +++++
  gi|557694909|ref|YP_008797963.1|  26 LLIIGSKLLSPKKPARRKRLSFESGQVPFGWTESSFPVEYFPYAIIYIAYAVIALAVFLSVVAVID-NPGAALNVVV 101
                                       678899**********************************************98877776665543.3456789999 PP

                                       HHHHHHHHHHHHH CS
                       Oxidored_q4  80 FllillvglvYew 92 
                                       +l++l +  +Y+ 
  gi|557694909|ref|YP_008797963.1| 102 LLAVLSASSIYAA 114
                                       ********99986 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 !   19.5   3.3   9.5e-08   0.00043     214     295 ..      13     122 ..      10     124 .] 0.74

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 9.5e-08
                   ABC2_membrane_3 214 flvyllqlllill.lafgl..........................gipfg.nlglllllfllfglayialgyllssl 262
                                       +++y+++++l+ + l++g+                          + +f  +++   + ++ ++ +++a+++ + ++
  gi|557694909|ref|YP_008797963.1|  13 LIIYIVVSALLPVlLIIGSkllspkkparrkrlsfesgqvpfgwtESSFPvEYFPYAIIYIAYAVIALAVFLSVVAV 89 
                                       455555555554414666677777999999********888877744444477888899999*************** PP

                   ABC2_membrane_3 263 fknsetaqilifivilllsgffggl.fpledlps 295
                                       ++n+++a  +++++ + ls+ +++   +l++lp 
  gi|557694909|ref|YP_008797963.1|  90 IDNPGAALNVVVLLAV-LSASSIYAaATLKNLPQ 122
                                       *******999999988.66655555255777775 PP

>> MPS-4  MinK-related peptide, potassium channel accessory sub-unit protein 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0063        28      42      78 .]       8      44 ..       3      44 .. 0.68
   2 ?    6.0   0.3    0.0029        13      36      62 ..      60      86 ..      55      93 .. 0.80
   3 ?   -2.2   0.1       1.1   4.8e+03      46      59 ..      99     112 ..      96     115 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0063
                             MPS-4 42 fdfllvviisvvslglvylllwievllnsvrpdskkr 78
                                       d l ++i  vvs  l  ll+    ll   +p  +kr
  gi|557694909|ref|YP_008797963.1|  8 ADTLSLIIYIVVSALLPVLLIIGSKLLSPKKPARRKR 44
                                      5667666666666656566666677889999999987 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0029
                             MPS-4 36 systkyfdfllvviisvvslglvylll 62
                                      s++ +yf + ++ i   v   +v+l +
  gi|557694909|ref|YP_008797963.1| 60 SFPVEYFPYAIIYIAYAVIALAVFLSV 86
                                      9********999887777777888855 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                             MPS-4  46 lvviisvvslglvy 59 
                                       +vv+++v+s + +y
  gi|557694909|ref|YP_008797963.1|  99 VVVLLAVLSASSIY 112
                                       46777777777776 PP

>> DUF3325  Protein of unknown function (DUF3325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       2.3     1e+04      68      79 ..      15      26 ..       9      28 .. 0.58
   2 ?   11.6   4.0   5.3e-05      0.24      43      87 ..      79     123 ..      69     124 .] 0.91

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.3
                           DUF3325 68 gllslaAlllvl 79
                                      + + ++All vl
  gi|557694909|ref|YP_008797963.1| 15 IYIVVSALLPVL 26
                                      445566666665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 5.3e-05
                           DUF3325  43 wlllllslalavaawgwavGlvlwlgllslaAlllvllLayrprl 87 
                                       +l++ ls+++ +  +g+a+ +v++l++ls++ + ++++L   p++
  gi|557694909|ref|YP_008797963.1|  79 ALAVFLSVVAVIDNPGAALNVVVLLAVLSASSIYAAATLKNLPQR 123
                                       578999********************************9887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       957  (0.0533772); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 912.68
//
Query:       gi|557694910|ref|YP_008797964.1|  [L=343]
Description: NADH dehydrogenase I subunit H [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-84  284.0  24.5    1.7e-84  283.7  24.5    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 !  283.7  24.5   9.4e-89   1.7e-84       9     298 ..      32     332 ..      23     333 .. 0.97

  Alignments for each domain:
  == domain 1  score: 283.7 bits;  conditional E-value: 9.4e-89
                                       HHHHHHHHHHHHHHHHHHHHTTS--S-SSTTT.TTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTT CS
                            NADHdh   9 vlllvvalltlleRkvlAriqdRlGPnrvGpl.GllqplaDalKlllKediipkkadkllfllapvlalilallafa 84 
                                       +++++ +l +++eRk+lAri  R GP +vG++ G+lq++aDa+K+l Ke iip++a+k lf+++p+ al+l+ l+fa
  gi|557694910|ref|YP_008797964.1|  32 FVAVLGILSVWYERKLLARIMLRPGPLHVGKYgGWLQVIADAVKFLSKEFIIPARAKKKLFVTMPLTALFLSALLFA 108
                                       455566699*********************8779******************************************* PP

                                       TS-SSS..SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-H CS
                            NADHdh  85 viPfge..vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagslsl 159
                                       ++Pf+e  v++  ++g+ll+++l++l+++ +++aGwa++skY+++G lR a q+ +yEv+l+++l +v+l+a+++++
  gi|557694910|ref|YP_008797964.1| 109 FLPFSEywVIYRSEIGVLLVFVLIALTPIPLIIAGWAAGSKYSFVGMLRFAFQIFAYEVPLFIALAGVILAAKTFDI 185
                                       *****87899999**************************************************************** PP

                                       HHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHHHHH CS
                            NADHdh 160 seiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsalav 236
                                        eiv+aq +  fi++q+++f++f+ia++ e++r+PFDlp ae+ELv+G+++EY+g+ f  + la y+++ ++ +l+v
  gi|557694910|ref|YP_008797964.1| 186 VEIVNAQYALPFIVTQFIGFLVFFIAAVSEAERIPFDLPTAEQELVEGWMVEYGGVGFLGIQLAMYTKLDALLFLTV 262
                                       *******99999***************************************************************** PP

                                       HHCT.SS-HCCS........HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHHH CS
                            NADHdh 237 llFlgGwllpfs........gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlllt 298
                                        l+lgGw++p +        + +w+++K+l+ll +++++r ++ R+ + ++++lgw +l+pl ++nl+l+
  gi|557694910|ref|YP_008797964.1| 263 NLYLGGWHGPAIpgvpetilHPFWVFVKFLILLTIVFMFRGVYTRITIRKILDLGWRYLIPLGFINLFLV 332
                                       **********999*******99*********************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); 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):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2466.41
//
Query:       gi|557694911|ref|YP_008797965.1|  [L=118]
Description: hypothetical protein CSUB_C1484 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.0       0.24   11.6   0.0    1.2  1  E1_4HB    Ubiquitin-activating enzyme E1 four-helix bundle


Domain annotation for each model (and alignments):
>> E1_4HB  Ubiquitin-activating enzyme E1 four-helix bundle
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.3e-05      0.24      17      64 ..      28      76 ..       7      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.3e-05
                                      .-BE-S.-GGGTTCHHHHHHHHHHHHHHHHCTT----TT-HHHHHHHHH CS
                            E1_4HB 17 eeflis.DfakfdrpeqlHlafqALhaFeeehgrlPrplneedaekvva 64
                                      ++fl + Df+ f ++  +H  ++++  +++  g+l   +n+e  +k+++
  gi|557694911|ref|YP_008797965.1| 28 RSFLDTeDFTYFTESVKIHQEIRGIPIYQHLSGHLDLDNNMEQLQKIYE 76
                                      6888888***********************************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 919.36
//
Query:       gi|557694912|ref|YP_008797966.1|  [L=302]
Description: hypothetical protein CSUB_C1485 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   40.2  10.7    1.7e-07   30.7   2.7    2.3  2  Fer4      4Fe-4S binding domain
    3.6e-09   37.1   2.3    4.8e-05   23.9   0.2    2.3  2  Fer4_7    4Fe-4S dicluster domain
    3.4e-07   30.3   1.2     0.0043   17.1   0.1    2.3  2  Fer4_10   4Fe-4S dicluster domain
    5.1e-07   29.7   0.7      0.007   16.5   0.1    2.3  2  Fer4_9    4Fe-4S dicluster domain
    5.5e-07   29.9   0.5      0.015   15.7   0.1    2.3  2  Fer4_8    4Fe-4S dicluster domain
    1.4e-06   28.3   3.0       0.02   15.0   0.4    2.3  2  Fer4_21   4Fe-4S dicluster domain
    1.6e-05   25.7   1.5     0.0067   17.3   0.1    2.5  2  Fer4_16   4Fe-4S double cluster binding domain
      5e-05   23.8   2.5       0.11   13.1   0.2    2.3  2  Fer4_17   4Fe-4S dicluster domain
    0.00011   22.0  11.4     0.0083   16.2   2.7    2.4  2  Fer4_2    4Fe-4S binding domain
    0.00024   21.0   2.3    0.00024   21.0   2.3    2.3  2  Fer4_6    4Fe-4S binding domain
     0.0004   21.2   1.2      0.082   13.8   0.0    2.2  2  Fer4_22   4Fe-4S dicluster domain
     0.0081   16.6  10.9      0.023   15.2   1.5    2.2  2  Fer4_4    4Fe-4S binding domain
     0.0089   16.2   1.9       0.49   10.6   0.0    2.3  2  Fer4_18   4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.23   12.2   6.9        1.4    9.7   0.8    2.4  2  Fer4_15   4Fe-4S single cluster domain
        1.5    9.9  16.3       0.57   11.2   3.9    2.3  2  Fer4_3    4Fe-4S binding domain
        2.9    8.5   9.3        2.5    8.7   0.5    2.6  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


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 !   14.2   1.1   2.6e-05     0.029       5      21 ..      63      79 ..      59      80 .. 0.86
   2 !   30.7   2.7   1.6e-10   1.7e-07       2      24 .]     234     256 ..     233     256 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                                      TTTSSS-THHHHHSTTT CS
                              Fer4  5 eekCigCGaCvevCPvg 21
                                       +kC+gC +C  +C + 
  gi|557694912|ref|YP_008797966.1| 63 LDKCTGCSLCDIACQNV 79
                                      69************875 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 1.6e-10
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        +d+ +C++CG Cv++CP+ A++
  gi|557694912|ref|YP_008797966.1| 234 AVDYGRCVFCGFCVDACPFYALE 256
                                       69*****************9985 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   0.00012      0.13       1      21 [.      65      87 ..      65     120 .. 0.76
   2 !   23.9   0.2   4.2e-08   4.8e-05       1      22 [.     239     260 ..     239     279 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                            Fer4_7  1 rCigCgaCvaaCp..vkaielde 21
                                      +C+gC  C  aC   ++ai++ +
  gi|557694912|ref|YP_008797966.1| 65 KCTGCSLCDIACQnvAEAIMMVY 87
                                      7***********96677777665 PP

  == domain 2  score: 23.9 bits;  conditional E-value: 4.2e-08
                            Fer4_7   1 rCigCgaCvaaCpvkaieldee 22 
                                       rC+ Cg+Cv+aCp +a+e+++e
  gi|557694912|ref|YP_008797966.1| 239 RCVFCGFCVDACPFYALEMTPE 260
                                       8******************986 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.1   0.00017      0.19       6      21 ..      63      77 ..      59     120 .. 0.77
   2 !   17.1   0.1   3.8e-06    0.0043       4      23 ..     235     254 ..     232     280 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                           Fer4_10  6 ddtCirCgkCvkaCPa 21
                                       d+C++C  C  aC +
  gi|557694912|ref|YP_008797966.1| 63 LDKCTGCSLCDIAC-Q 77
                                      589***********.3 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.8e-06
                           Fer4_10   4 idddtCirCgkCvkaCPadl 23 
                                       +d  +C+ Cg Cv+aCP+++
  gi|557694912|ref|YP_008797966.1| 235 VDYGRCVFCGFCVDACPFYA 254
                                       56778999999999999954 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.1   0.00021      0.24      33      48 ..      55      78 ..      25      83 .. 0.70
   2 !   16.5   0.1   6.2e-06     0.007      33      48 ..     231     252 ..     190     255 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                            Fer4_9 33 e........eaCigCgaCveaCpk 48
                                               ++C+gC  C  aC++
  gi|557694912|ref|YP_008797966.1| 55 FkgrhilylDKCTGCSLCDIACQN 78
                                      044555666789999999999986 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6.2e-06
                            Fer4_9  33 e......eaCigCgaCveaCpk 48 
                                       +       +C++Cg Cv+aCp 
  gi|557694912|ref|YP_008797966.1| 231 YfpavdyGRCVFCGFCVDACPF 252
                                       155555678***********95 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00015      0.17       2      31 ..      63     106 ..      62     143 .. 0.67
   2 !   15.7   0.1   1.4e-05     0.015       4      21 ..     239     256 ..     236     284 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                            Fer4_8   2 lekCieCgaCqsaCp..............vlrrtkkhlldarge 31 
                                       l+kC++C++C  aC               +l+  kk+  d r++
  gi|557694912|ref|YP_008797966.1|  63 LDKCTGCSLCDIACQnvaeaimmvygfnaSLKLGKKFVEDYRKG 106
                                       67999999999999643444333333333444444555555544 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.4e-05
                            Fer4_8   4 kCieCgaCqsaCpvlrrt 21 
                                       +C+ Cg+C +aCp++  +
  gi|557694912|ref|YP_008797966.1| 239 RCVFCGFCVDACPFYALE 256
                                       8************88654 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.4   1.8e-05      0.02      38      58 ..      63      84 ..      49      87 .. 0.72
   2 !   13.4   0.1   5.7e-05     0.064      29      56 ..     227     254 ..     210     257 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                           Fer4_21 38 edeCvGCnlCssvCP.vedcie 58
                                       d+C+GC lC + C  v ++i 
  gi|557694912|ref|YP_008797966.1| 63 LDKCTGCSLCDIACQnVAEAIM 84
                                      5788888888888842566665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.7e-05
                           Fer4_21  29 daktvlkvv.edeCvGCnlCssvCPvedc 56 
                                       ++k++++ v   +Cv C  C++ CP   +
  gi|557694912|ref|YP_008797966.1| 227 NKKSYFPAVdYGRCVFCGFCVDACPF-YA 254
                                       44556655525799999999999996.45 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 !    7.1   0.1    0.0097        11      51      64 ..      63      76 ..      23      79 .. 0.63
   2 !   17.3   0.1     6e-06    0.0067       1      28 [.     239     264 ..     239     282 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0097
                           Fer4_16 51 qeaitgCdiCqdvC 64
                                        ++tgC  C  +C
  gi|557694912|ref|YP_008797966.1| 63 LDKCTGCSLCDIAC 76
                                      37899999999999 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 6e-06
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiear 28 
                                       rC+ Cg C+++CP  a++++  +eie  
  gi|557694912|ref|YP_008797966.1| 239 RCVFCGFCVDACPFYALEMT--PEIELS 264
                                       6*****************99..555443 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   0.1   0.00062      0.69      42      57 ..      62      77 ..      30      80 .. 0.76
   2 !   13.1   0.2   9.8e-05      0.11       1      17 [.     239     255 ..     239     280 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00062
                           Fer4_17 42 kaslCieCgeCerkCP 57
                                      + ++C++C +C+ +C 
  gi|557694912|ref|YP_008797966.1| 62 YLDKCTGCSLCDIACQ 77
                                      6799********9996 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 9.8e-05
                           Fer4_17   1 rCiqCgyClpeCpsyea 17 
                                       rC  Cg+C+++Cp+y+ 
  gi|557694912|ref|YP_008797966.1| 239 RCVFCGFCVDACPFYAL 255
                                       6999*********9987 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.5   0.00042      0.47       7      20 ..      63      76 ..      58      78 .. 0.85
   2 !   16.2   2.7   7.4e-06    0.0083       3      21 ..     233     251 ..     231     252 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00042
                            Fer4_2  7 tdrCigCgaCvsaC 20
                                       d+C+gC+ C  aC
  gi|557694912|ref|YP_008797966.1| 63 LDKCTGCSLCDIAC 76
                                      59********8889 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 7.4e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaCP 21 
                                       ++vd  rC+ Cg Cv+aCP
  gi|557694912|ref|YP_008797966.1| 233 PAVDYGRCVFCGFCVDACP 251
                                       789**************** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   3.0      0.03        34       7      19 ..      64      76 ..      63      83 .. 0.87
   2 !   21.0   2.3   2.1e-07   0.00024       1      24 []     232     255 ..     232     255 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.03
                            Fer4_6  7 dkCigCgdCvrvC 19
                                      dkC+gC  C ++C
  gi|557694912|ref|YP_008797966.1| 64 DKCTGCSLCDIAC 76
                                      8********7777 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.1e-07
                            Fer4_6   1 vveidpdkCigCgdCvrvCPegai 24 
                                       ++++d+ +C+ Cg Cv++CP++a+
  gi|557694912|ref|YP_008797966.1| 232 FPAVDYGRCVFCGFCVDACPFYAL 255
                                       689******************996 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2     0.016        18      80      93 ..      64      77 ..      36      80 .. 0.85
   2 !   13.8   0.0   7.3e-05     0.082      44      93 ..     202     251 ..     189     254 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
                           Fer4_22 80 sgCvGCgRCieacp 93
                                       +C+GC  C+ ac+
  gi|557694912|ref|YP_008797966.1| 64 DKCTGCSLCDIACQ 77
                                      57999999999997 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 7.3e-05
                           Fer4_22  44 eftkvaggenvrkekkerlrqrllhklsefkekfgesgCvGCgRCieacp 93 
                                       e++++++g+     + +++ ++l h  +++   ++   Cv Cg C++acp
  gi|557694912|ref|YP_008797966.1| 202 EYHRLSNGTYEAVLAITKIDEKLAHNKKSYFPAVDYGRCVFCGFCVDACP 251
                                       56666666566666778899999**************************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 ?    6.2   2.3     0.015        17       2      14 ..      64      76 ..      63      82 .. 0.91
   2 !   15.2   1.5     2e-05     0.023       3      16 ..     239     252 ..     237     258 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.015
                            Fer4_4  2 erCigCgsCvaaC 14
                                      ++C+gC  C +aC
  gi|557694912|ref|YP_008797966.1| 64 DKCTGCSLCDIAC 76
                                      99*******9999 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 2e-05
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       rC+ Cg Cv+aCP+
  gi|557694912|ref|YP_008797966.1| 239 RCVFCGFCVDACPF 252
                                       9************6 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.4     0.028        32      84     103 ..      65      84 ..      54      91 .. 0.85
   2 !   10.6   0.0   0.00044      0.49      47      73 ..     226     252 ..     193     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.028
                           Fer4_18  84 eciscllcidacdkvmeklg 103
                                       +c  c+lc  ac++v e++ 
  gi|557694912|ref|YP_008797966.1|  65 KCTGCSLCDIACQNVAEAIM 84 
                                       699***********999876 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00044
                           Fer4_18  47 lkekeerkekgagdcidcescvkvcPt 73 
                                       +++k    + + g c+ c++cv+ cP 
  gi|557694912|ref|YP_008797966.1| 226 HNKKSYFPAVDYGRCVFCGFCVDACPF 252
                                       445555556778899999999999995 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 ?    5.5   0.7     0.026        29       6      22 ..      64      80 ..      62      90 .. 0.88
   2 ?    9.7   0.8    0.0013       1.4       3      20 ..     235     252 ..     234     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.026
                           Fer4_15  6 daCigcglCvaeapevf 22
                                      d+C+gc lC  ++++v 
  gi|557694912|ref|YP_008797966.1| 64 DKCTGCSLCDIACQNVA 80
                                      89*******98888775 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0013
                           Fer4_15   3 vDrdaCigcglCvaeape 20 
                                       vD  +C  cg Cv+++p 
  gi|557694912|ref|YP_008797966.1| 235 VDYGRCVFCGFCVDACPF 252
                                       8999************84 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   4.5     0.077        86       1      11 [.      66      76 ..      66      79 .. 0.87
   2 ?   11.2   3.9   0.00051      0.57       1      15 []     240     254 ..     240     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.077
                            Fer4_3  1 CtgCgaCvevC 11
                                      CtgC++C  +C
  gi|557694912|ref|YP_008797966.1| 66 CTGCSLCDIAC 76
                                      *****998888 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00051
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ Cg Cv++CP  A
  gi|557694912|ref|YP_008797966.1| 240 CVFCGFCVDACPFYA 254
                                       ************765 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 ?    3.1   2.7      0.12   1.4e+02       4      19 ..      64      79 ..      63      81 .. 0.88
   2 ?    8.7   0.5    0.0022       2.5       1      17 [.     235     251 ..     235     264 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
                           Fer4_13  4 dtCiacgaCvelaPdv 19
                                      d+C++c +C  ++ +v
  gi|557694912|ref|YP_008797966.1| 64 DKCTGCSLCDIACQNV 79
                                      79*******9999776 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0022
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       VD  +C+ cg Cv+++P
  gi|557694912|ref|YP_008797966.1| 235 VDYGRCVFCGFCVDACP 251
                                       78899************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2196.30
//
Query:       gi|557694913|ref|YP_008797967.1|  [L=524]
Description: cytochrome c oxidase subunit I [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-148  495.0  66.4   2.1e-148  494.8  66.4    1.0  1  COX1      Cytochrome C and Quinol oxidase polypeptide I
  ------ inclusion threshold ------
       0.97    9.6   6.9       0.13   12.4   0.8    2.8  2  COX2_TM   Cytochrome C oxidase subunit II, transmembrane doma


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 !  494.8  66.4  2.4e-152  2.1e-148       2     432 .]      30     466 ..      29     466 .. 0.99

  Alignments for each domain:
  == domain 1  score: 494.8 bits;  conditional E-value: 2.4e-152
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT.....-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCTSS- CS
                              COX1   2 igllylilalvlllvggllgllirlqlafp.....dletynqlrtlHgnlmiflfatpfilgfgnylvplllgardl 73 
                                       ig+ly++++ v+l++ggll+ll+r++la+p     d++ty+ l+t+Hg+lm+f++a+p+++g+gnyl+p+++ga+d+
  gi|557694913|ref|YP_008797967.1|  30 IGMLYIAASYVFLVIGGLLALLMRFELATPqgnlvDSNTYSSLFTIHGTLMVFFWAMPVFAGLGNYLIPKMIGAPDM 106
                                       89**************************998888888**************************************** PP

                                       S-HHHHHHHHHHHHHHHHHHHHHHHCSS-STTTTTTTC.......SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              COX1  74 afprlnalsfwlvvlgvvllllsllgaattgwteYapls......evdlwllglllvvvssllgainfivtilkrra 144
                                       + p+lnalsfwl+++++vll++s+   a+ gwt Ya ls      +vdlw+l+l+++++ss++ga+nfivt ++ r+
  gi|557694913|ref|YP_008797967.1| 107 YYPKLNALSFWLFLAAGVLLMSSW---ANIGWTGYATLSviepsvGVDLWILSLHVAGTSSMVGALNFIVTTWRLRR 180
                                       ************************...9************************************************* PP

                                       HTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT.-SSSC...E-HHHHHHHHHHHHTHHHHHHHHHH CS
                              COX1 145 pgmtvaklplfvwavlatailillalpvlalalllllldrslg.kffsp...gdplldqhlfWffgHpeVyililpa 217
                                         m +++lplfvw++++ta++i++a+p la++l++llldr+lg  f+ p   gdp+l+qhlfWffgHpeVyil++pa
  gi|557694913|ref|YP_008797967.1| 181 ADMGWWRLPLFVWSWVVTAFIIIFAVPPLAFGLTMLLLDRNLGtGFYLPaqgGDPILWQHLFWFFGHPEVYILVIPA 257
                                       ***********************************************77899************************* PP

                                       HHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHHHHHHCCCHHHHCCT CS
                              COX1 218 lgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliavPsglkvfnwlatlw 294
                                       +gi+++ilp+++++p+++y++++l+ +li++lsf vwaHH+fttgl++ + a ++++++l+a+Psg+kv+nw atlw
  gi|557694913|ref|YP_008797967.1| 258 MGIISEILPRLVKKPIVGYRMIALSSVLIAVLSFGVWAHHMFTTGLSPLTLAPFMIMTMLVAIPSGVKVVNWEATLW 334
                                       ***************************************************************************** PP

                                       TS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHSB-- CS
                              COX1 295 rgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyllpkltgrml 371
                                       +g+ir++tp++f+l f+ +fi+gG+tGv++ + +v+++vh+tywvv+H+H++l+ga+  ++faa+yy++p lt+rm+
  gi|557694913|ref|YP_008797967.1| 335 GGKIRYNTPTIFTLSFIATFIVGGITGVFHPAIPVDWHVHDTYWVVGHMHFILFGAISQAAFAATYYYFPYLTKRMY 411
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHHH CS
                              COX1 372 serlaklhfwllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrtiggvl 432
                                       se l+k+h +++++G +l+f++m+ilGl+gmprr+++y      vpe+qp++v++++g++l
  gi|557694913|ref|YP_008797967.1| 412 SESLGKIHAITANVGQYLVFMSMMILGLMGMPRRYYSY------VPEYQPWHVVASVGAFL 466
                                       ************************************99......89************986 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 ?   12.4   0.8   1.5e-05      0.13      22      87 ..      27      89 ..      20      90 .. 0.89
   2 ?   -2.7   0.7      0.76   6.8e+03      72      86 ..     307     322 ..     306     324 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                           COX2_TM 22 elhdyilliltlililVlyilvlilvefrrrknkitakylvhgqeiEiiWTiiPalililialpSl 87
                                      + h  +l+i++  ++lV++ l+ +l++f   + ++++ +lv++++   + Ti  +l++++ a+p +
  gi|557694913|ref|YP_008797967.1| 27 HAHIGMLYIAASYVFLVIGGLLALLMRF---ELATPQGNLVDSNTYSSLFTIHGTLMVFFWAMPVF 89
                                      556679999******************9...55788999************************987 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 0.76
                           COX2_TM  72 TiiPalil.ilialpS 86 
                                       T+ P +i+ +l+a+pS
  gi|557694913|ref|YP_008797967.1| 307 TLAPFMIMtMLVAIPS 322
                                       6778777646788887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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 0.26s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3971.99
//
Query:       gi|557694914|ref|YP_008797968.1|  [L=138]
Description: cytochrome c oxidase subunit II [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   56.8   0.0      9e-14   51.4   0.0    2.1  2  COX2          Cytochrome C oxidase subunit II, periplasmic do
    9.3e-10   38.6   0.0    1.5e-09   37.9   0.0    1.4  1  Cupredoxin_1  Cupredoxin-like domain
  ------ inclusion threshold ------
       0.15   11.6   0.0        7.7    6.0   0.0    2.2  2  SoxE          Sulfocyanin (SoxE) domain


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 !    3.6   0.0    0.0098        59       1      18 [.      41      58 ..      41      63 .. 0.91
   2 !   51.4   0.0   1.5e-17     9e-14      50     114 ..      67     131 ..      60     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0098
                              COX2  1 ltikaiGhqwywsyeytd 18
                                      lt+k + +q+ w++ y+d
  gi|557694914|ref|YP_008797968.1| 41 LTVKVVARQFAWQFVYPD 58
                                      79**************99 PP

  == domain 2  score: 51.4 bits;  conditional E-value: 1.5e-17
                              COX2  50 lpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhssmp 114
                                       +   +++rl + +edv+hsf +  +g+k d+vpGr n + ++   +G++  qc+e+cG  h sm 
  gi|557694914|ref|YP_008797968.1|  67 VKAGQTVRLELNSEDVIHSFYLRDFGLKKDVVPGRTNVLYVTPLEPGTYLIQCAEFCGQGHYSMR 131
                                       566789*******************************************************9995 PP

>> Cupredoxin_1  Cupredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   2.5e-13   1.5e-09       6      95 ..      21     123 ..      15     136 .. 0.69

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.5e-13
                      Cupredoxin_1   6 avllllsskaa...aaaektveitvkdg..........gfePskievkagekvklkiknkdktpeefesedlgeekv 69 
                                       ++ +++ +  +   a++ +  +++v             g    ++ vkag+ v+l+++ +d   ++f+ +d+g +k+
  gi|557694914|ref|YP_008797968.1|  21 VIGFWSWNVLNdleANKPADLTVKVVARqfawqfvypdGTVSGELRVKAGQTVRLELNSED-VIHSFYLRDFGLKKD 96 
                                       33333333222222333333555555445577777777677789*******9999997666.57************* PP

                      Cupredoxin_1  70 lapgktttitiaplkpGeYeftcd.mh 95 
                                       + pg t+++ ++pl+pG+Y + c  ++
  gi|557694914|ref|YP_008797968.1|  97 VVPGRTNVLYVTPLEPGTYLIQCAeFC 123
                                       *********************996544 PP

>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0    0.0067        40      18      61 ..      44      84 ..      26      90 .. 0.66
   2 ?    6.0   0.0    0.0013       7.7     100     138 ..      97     136 ..      90     138 .] 0.82

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0067
                              SoxE 18 ylvvsssasnlfnf.nGtsnGqlkiyiPagwsvlvklvneeslph 61
                                       +v+   a  +f + +Gt +G+l+  + ag +v ++l   e + h
  gi|557694914|ref|YP_008797968.1| 44 KVVARQFAW-QFVYpDGTVSGELR--VKAGQTVRLELNS-EDVIH 84
                                      334444444.444448******98..5799**9999855.44555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0013
                              SoxE 100 issGqsasGlledlsaGtywlacg.ilGhaesGmWvdliv 138
                                       +  G++++  + +l +Gty++ c+   G  +  m ++++v
  gi|557694914|ref|YP_008797968.1|  97 VVPGRTNVLYVTPLEPGTYLIQCAeFCGQGHYSMRANMVV 136
                                       5667778888899**********74789999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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: 00:00:00.40
# Mc/sec: 1022.92
//
Query:       gi|557694915|ref|YP_008797969.1|  [L=77]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   1.7          2    8.9   0.0    2.1  2  FeoB_associated  FeoB-associated Cys-rich membrane protein
       0.26   10.0   1.0       0.28    9.9   1.0    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
       0.66    9.7   5.5        1.3    8.8   5.4    1.5  1  DUF5381          Family of unknown function (DUF5381)


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 ?    1.9   1.1     0.051   3.1e+02       4      14 ..      10      20 ..       7      26 .. 0.57
   2 ?    8.9   0.0   0.00033         2       5      24 ..      57      76 ..      55      77 .] 0.91

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.051
                   FeoB_associated  4 IVgliiaaava 14
                                      +V+++i+ a++
  gi|557694915|ref|YP_008797969.1| 10 LVLALIIFAIF 20
                                      45555554443 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00033
                   FeoB_associated  5 Vgliiaaavafvirrlikkk 24
                                      Vg i ++a++f++++++ k+
  gi|557694915|ref|YP_008797969.1| 57 VGSIFIGALFFMMYKFREKG 76
                                      899*************9875 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.0   4.8e-05      0.28     385     439 ..       9      74 ..       2      77 .] 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 4.8e-05
                           DUF2207 385 alglgliilglilillallllvll..............lvfllilllillliaiivlllfsrllgrrte 439
                                       +l l+lii++++ +ll+l+ ++ l                f +i + +++ i+i++l+++   ++++ e
  gi|557694915|ref|YP_008797969.1|   9 YLVLALIIFAIFSTLLILGNFGQLfrplspqtieinrlYQFVYIAGSAVGSIFIGALFFM---MYKFRE 74 
                                       444455555555555555444444789**********99999999999999999999887...455444 PP

>> DUF5381  Family of unknown function (DUF5381)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   5.4   0.00021       1.3      31      64 ..      38      71 ..       8      77 .] 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00021
                           DUF5381 31 feglkfeskysllyiiigiigtifgliillmvlp 64
                                       ++++++  y+++yi+++ +g if+  ++ m+++
  gi|557694915|ref|YP_008797969.1| 38 PQTIEINRLYQFVYIAGSAVGSIFIGALFFMMYK 71
                                      47899999*********************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 565.50
//
Query:       gi|557694916|ref|YP_008797970.1|  [L=152]
Description: cytochrome AA3 controlling protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-10   39.0  16.7    9.1e-06   25.0  10.2    2.0  2  COX15-CtaA    Cytochrome oxidase assembly protein
  ------ inclusion threshold ------
        6.5    6.5   9.4         22    4.8   9.4    1.8  1  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr


Domain annotation for each model (and alignments):
>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   9.2e-08   0.00083       4      36 ..      10      42 ..       7      49 .. 0.90
   2 !   25.0  10.2     1e-09   9.1e-06     247     322 ..      52     124 ..      44     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 9.2e-08
                        COX15-CtaA  4 lllvlllvllvvvlGgltRltdsGlsitdWppc 36
                                      +l+++ll++l   lG ++   ++G+ ++dWp c
  gi|557694916|ref|YP_008797970.1| 10 ALGTSLLAILTMSLGSYVSKVGAGMACPDWPLC 42
                                      5789999999*********************99 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1e-09
                        COX15-CtaA 247 vqfaHRllAilvllvllllailllrkarspklarlavllaallllQv.alGistvllavplslavaHqlgaalllla 322
                                       + f HR++A++++l  ++ ++l +r    ++l+ lav ++a+lllQv ++G + +++a+p  + +aHq++aa++l++
  gi|557694916|ref|YP_008797970.1|  52 LEFGHRIVAFITFLSGVYTFYLGWR----TTLRPLAVYAFAALLLQVfVVGAVVIFTAIPPIVIAAHQAVAATVLAL 124
                                       5799***************444444....699*******99999997368************************986 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   9.4    0.0025        22      65     135 ..      54     129 ..      49     148 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0025
                      Trp_oprn_chp  65 lgrrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaavelta......wpvlalaggvllllagvl 135
                                       +g r+v+ ++ l+g+ + + +++  + p ++ + aa   +++  +a  + +ta      ++  a+a++vl+l  +++
  gi|557694916|ref|YP_008797970.1|  54 FGHRIVAFITFLSGVYTFYLGWRTTLRPLAVYAFAALLLQVFVVGAVVI-FTAippiviAAHQAVAATVLALHSSLA 129
                                       6777888888888888888888877777777777763333332222222.222112333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1105.45
//
Query:       gi|557694917|ref|YP_008797971.1|  [L=295]
Description: luciferase family protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-53  180.9   0.0    4.2e-51  174.3   0.0    2.0  2  Bac_luciferase  Luciferase-like monooxygenase


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  174.3   0.0   2.3e-55   4.2e-51       2     207 ..       4     211 ..       1     224 [. 0.93
   2 !    4.8   0.0   0.00086        15     286     314 .]     238     266 ..     227     266 .. 0.84

  Alignments for each domain:
  == domain 1  score: 174.3 bits;  conditional E-value: 2.3e-55
                    Bac_luciferase   2 efgvflptrqggalgaasaslrylvelaraaEelGfdavwvaehhggpgga.......ldaftllaalaaaTerirl 71 
                                       efgv+lp+ +      +  s++ +  +a +aEelG+++vw+++h++ p ++       l+a+t++a++a++Te +++
  gi|557694917|ref|YP_008797971.1|   4 EFGVCLPNFG------KHLSPKSIDVIASEAEELGYESVWITDHLLLPPTQrypygniLEAITTMAHVASVTEEVKV 74 
                                       6777777777......22367788889*******************999999************************* PP

                    Bac_luciferase  72 gtavtplytrhPavlAqqaatLdhlsgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeG 148
                                       g++v++l+ r+P+ +A++ a +d lsgGR++ g g+g+ ++e+ + G++++ r +r++E+++++++lw+g+ev+f+G
  gi|557694917|ref|YP_008797971.1|  75 GSSVLILPMREPVQVAKALAAIDVLSGGRVVAGFGAGWCEEEFQNLGMNFRNRGRRFDEALQLIKQLWQGGEVSFKG 151
                                       ***************************************************************************** PP

                    Bac_luciferase 149 effsvkgalllprpgqgp.iPvyvaaaspaglelaarhadglllageppeeaaelierlr 207
                                       ++++v+ +   p p+q++ +P+++++ s+ +l+ a +h+++++++g +++ + e++ ++ 
  gi|557694917|ref|YP_008797971.1| 152 RYYKVEAGIFEPAPAQNGgPPIWIGGNSEHALRRAMKHGQAWHFTGITLDTLSERVSNIS 211
                                       **************9999788*************************99999999988776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.00086
                    Bac_luciferase 286 elvaatalvGtpeqvaerlaayaeagvde 314
                                       ++ ++++l G+p+ +++ +++y ++ v++
  gi|557694917|ref|YP_008797971.1| 238 AGENRAILTGSPNKIIDTIEQYINLNVTH 266
                                       56678889****************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1971.91
//
Query:       gi|557694918|ref|YP_008797972.1|  [L=453]
Description: phosphomethylpyrimidine kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-98  326.9   3.0    9.4e-98  326.5   3.0    1.2  1  Phos_pyr_kin    Phosphomethylpyrimidine kinase
    1.3e-63  213.6   0.2    2.8e-63  212.4   0.2    1.6  1  ThiP_synth      Thiamine-phosphate synthase
    1.4e-12   47.5   0.6    2.4e-12   46.8   0.6    1.3  1  PfkB            pfkB family carbohydrate kinase
    0.00022   20.8   4.0    0.00033   20.2   4.0    1.3  1  Carb_kinase     Carbohydrate kinase
  ------ inclusion threshold ------
       0.14   12.6   0.0       0.85   10.1   0.0    2.3  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,


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 !  326.5   3.0  2.6e-101   9.4e-98       1     246 []      14     257 ..      14     257 .. 0.99

  Alignments for each domain:
  == domain 1  score: 326.5 bits;  conditional E-value: 2.6e-101
                                       ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHH CS
                      Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiiev 77 
                                       Ds+GGAGiqADlktf+algv+gms+it++taqnt+ v+++h++pae++++q++ v+ d++vdavK+Gml+s+eiie 
  gi|557694918|ref|YP_008797972.1|  14 DSGGGAGIQADLKTFAALGVHGMSAITCITAQNTETVTAIHQVPAEIIREQIRVVTVDIGVDAVKTGMLFSEEIIES 90 
                                       9**************************************************************************** PP

                                       HHHHHHHTTSSEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHT CS
                      Phos_pyr_kin  78 vaeklkkykvpvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllkl 154
                                       va++l++ kvp+V+DPV vaksg++ll+++av+al ++Llplatv+tPN+ Ea+ L+g +i+++e+m +aa++++++
  gi|557694918|ref|YP_008797972.1|  91 VADELSEIKVPLVVDPVAVAKSGAPLLKPNAVDALVKKLLPLATVVTPNINEAKLLTGIEISSAEEMVDAAHRIAEM 167
                                       ***************************************************************************** PP

                                       T-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHH CS
                      Phos_pyr_kin 155 gakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvtea 231
                                       g +aV++kGghl+ge++   d+l+  ++++++ ae+i+t+nthGtGC+++sa aa+lakg ++++Av+ A+++v+ea
  gi|557694918|ref|YP_008797972.1| 168 GPEAVVVKGGHLPGETTM--DILLYAGNIYKFAAEKIHTRNTHGTGCVFASATAAYLAKGWKIPQAVQAAQRFVNEA 242
                                       ************887777..********************************************************* PP

                                       HHCG-BSTSSS-B-- CS
                      Phos_pyr_kin 232 ikealelgkgagpvn 246
                                       ik++l++g+g+gpv+
  gi|557694918|ref|YP_008797972.1| 243 IKRGLDIGRGYGPVH 257
                                       *************97 PP

>> ThiP_synth  Thiamine-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.4   0.2   7.9e-67   2.8e-63       2     164 ..     275     442 ..     274     443 .. 0.99

  Alignments for each domain:
  == domain 1  score: 212.4 bits;  conditional E-value: 7.9e-67
                                       HHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC- CS
                        ThiP_synth   2 leralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfd 78 
                                       l++al+++e+ee+f++liPe gsNi++a+++A+s+eDv++vpGRIv++ ++ + + ep fgas+hva+++l+amk+d
  gi|557694918|ref|YP_008797972.1| 275 LKEALKMIEREESFQRLIPESGSNIVVATEYASSPEDVVGVPGRIVKTPDGFTSALEPWFGASRHVANAVLTAMKHD 351
                                       89*************************************************************************** PP

                                       TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCC....T-HHHHHHHHHHHCC.S-ECEEEE--BCTB--EEE CS
                        ThiP_synth  79 pevraainirydekilealeelglkvvefdreeepeev....gstmewgvaeaieel.evpdviydeGgvGkEpmiy 150
                                       p+v++a+nir+d++il+ le+lgl+v+++dr +epeev    g+t++wg++eai+++ +v dv+y++G+vGkEpm++
  gi|557694918|ref|YP_008797972.1| 352 PSVKSAANIRFDDEILSTLEALGLSVSSYDRGAEPEEVkkeeGRTIPWGIEEAIRKAgGVVDVVYHRGDVGKEPMAV 428
                                       *********************************************************99****************** PP

                                       EEESSHHHHHHHHH CS
                        ThiP_synth 151 vlgkdaeevvekvl 164
                                       v+g da +vv+k+l
  gi|557694918|ref|YP_008797972.1| 429 VFGVDAYDVVRKLL 442
                                       ***********986 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.6   6.7e-16   2.4e-12     138     285 ..      82     238 ..      69     249 .. 0.84

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 6.7e-16
                                       EECTTSHHHHHHHHHHHHHHTTEEEEEECESSSHH......HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHH CS
                              PfkB 138 llsselpeavleelaeaaknggtfdpnlldplgaq......fkeallellaladllkpneeElealtgekledieea 208
                                       l+s+e+ e+v  el+e++     +dp+ ++++ga       +   +++ll+la++++pn +E++ ltg ++ + ee 
  gi|557694918|ref|YP_008797972.1|  82 LFSEEIIESVADELSEIKVPLV-VDPVAVAKSGAPllkpnaVDALVKKLLPLATVVTPNINEAKLLTGIEISSAEEM 157
                                       6666666666667777766666.688888888888888887777789999*************************** PP

                                       HHHHHHHHHTTSSEEEEEEGGGEEEEEE.....TTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHH CS
                              PfkB 209 laalhklkakgaktvvvtlGkeGalvve.....kdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealr 280
                                       ++a+h + + g++ vvv+ G  +           ++ +k+ a  k+   +t G+G  f+++ +a l++g+++ +a++
  gi|557694918|ref|YP_008797972.1| 158 VDAAHRIAEMGPEAVVVKGGHLPGETTMdillyAGNIYKFAA-EKIHTRNTHGTGCVFASATAAYLAKGWKIPQAVQ 233
                                       ******************997653222224446999999999.99******************************** PP

                                       HHHHH CS
                              PfkB 281 fanav 285
                                       +a+++
  gi|557694918|ref|YP_008797972.1| 234 AAQRF 238
                                       **986 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   4.0   9.3e-08   0.00033       2     217 ..       8     238 ..       7     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 9.3e-08
                                       EEEE-BTTCHHHHHHHHHHHHCT.T.-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE-TT CS
                       Carb_kinase   2 lvigGsedytGAallaalaalrl.g.aglvsvateseaiavlksylpevivhplledeqakileklerldavviGpG 76 
                                       l ++Gs+   GA++ a l + ++ g  g+  + +   + ++  +++ +v ++ ++e + + ++     +dav  G+ 
  gi|557694918|ref|YP_008797972.1|   8 LTVAGSDSGGGAGIQADLKTFAAlGvHGMSAITCITAQNTETVTAIHQVPAEIIRE-QIR-VVTVDIGVDAVKTGM- 81 
                                       6799********99888776543244799999998888888888888888888884.333.45555569******9. PP

                                       -SSSHCHHHHCHHHCCCCS-EEEEGGGGGSGGGG............TTTTSSEEEE--HHHHHHHCTTTCHHCCSHH CS
                       Carb_kinase  77 LgrdekikklleevlekdeplviDAdgLnllaqkne.........lserkaeviLTPhkkEfkrLlkaivkkeddrl 144
                                       L ++e i+ + +e  e ++plv+D  + ++               ++    +++ TP++ E k L++  + + ++ +
  gi|557694918|ref|YP_008797972.1|  82 LFSEEIIESVADELSEIKVPLVVDPVAVAKSGAPLLkpnavdalvKKLLPLATVVTPNINEAKLLTGIEISSAEEMV 158
                                       9999999*****************8777654433223334567677778889******************9****** PP

                                       HHHHHHHHHHTTEEEEESTT.......SEEEECTTEEEEE----GGG-.STTHHHHHHHHHHHHHHCTSSHHHHHHH CS
                       Carb_kinase 145 elarelaqklnavvllkgek.......dvivspegevlinstgssala.kGGsGDvLaGligalLaqneasyeaaia 213
                                       ++a+++a++ +  v++kg +       d++ + +g++++  +++   + + G+G v a + +a La   +  +a+ a
  gi|557694918|ref|YP_008797972.1| 159 DAAHRIAEMGPEAVVVKGGHlpgettmDILLY-AGNIYKFAAEKIHTRnTHGTGCVFASATAAYLAKGWKIPQAVQA 234
                                       *****************976444332244444.88888887777654416799999888888888887777777666 PP

                                       HHHH CS
                       Carb_kinase 214 aawl 217
                                       a+  
  gi|557694918|ref|YP_008797972.1| 235 AQRF 238
                                       6655 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 ?   -2.1   0.1       1.5   5.2e+03      24      66 ..      58      97 ..      51     111 .. 0.62
   2 ?   10.1   0.0   0.00024      0.85      22      76 ..     366     417 ..     363     420 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                                      HHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT CS
                    UDPG_MGDP_dh_C 24 eeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkg 66
                                      +e+ +e+++v+++D  v++ +  +     + e+++s++++l++
  gi|557694918|ref|YP_008797972.1| 58 AEIIREQIRVVTVDIGVDAVKTGMLF---SEEIIESVADELSE 97
                                      66677778888888877777776643...34444444444444 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00024
                                       HHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S-- CS
                    UDPG_MGDP_dh_C  22 iieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaivilteh 76 
                                       i+ +L++ g  v+ yD  +++e+v++   e+g ++   +eea+++a  +v ++ h
  gi|557694918|ref|YP_008797972.1| 366 ILSTLEALGLSVSSYDRGAEPEEVKK---EEGRTIPWGIEEAIRKAGGVVDVVYH 417
                                       788999*******************9...7899****************988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3126.71
//
Query:       gi|557694919|ref|YP_008797973.1|  [L=421]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   92.3   0.0    5.3e-26   91.8   0.0    1.2  1  NTP_transf_4  Sugar nucleotidyl transferase
      1e-05   25.0   5.9       0.34   10.7   0.0    3.8  3  Hexapep       Bacterial transferase hexapeptide (six repeats)


Domain annotation for each model (and alignments):
>> NTP_transf_4  Sugar nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   0.0   5.9e-30   5.3e-26       1     151 [.       3     167 ..       3     172 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 5.9e-30
                      NTP_transf_4   1 iilFddeaveqLlPltftRPvadlrvGiltlreKwekllga.atvsfltreyLaevyqekyPl...nvleeee.nll 72 
                                       i++++d+   ++ Plt t+Pv+d+ +G+ t  eK+++++   a++ + tr++L +v+ ekyP+   n  ++e+  ll
  gi|557694919|ref|YP_008797973.1|   3 ICVYEDPGLLRFWPLTTTKPVYDIFIGTGTNVEKIKHHFTDvAQIHLYTRQHLSQVLGEKYPEaivNMPPTEGeTLL 79 
                                       89***********************************77776********************8899777777779** PP

                      NTP_transf_4  73 ingrvlpdealveaikelkageallkgdellaarvteaeaakleksllsd.........ekveleeeelkllrrpwD 140
                                       ingr++ ++ ++e++++ ++g  +++g+e++a+++ e+++ ++  + l+          ++++ +e e +l++++wD
  gi|557694919|ref|YP_008797973.1|  80 INGRLVVNKVVAETLRKAEPGCVFYVGGEVAAVKLAEPDLPENFWQSLTTpgkrveipvHHLTKRELEANLVNNLWD 156
                                       *************************************99998888888889********555555588********* PP

                      NTP_transf_4 141 ifskngealer 151
                                       i++   + + +
  gi|557694919|ref|YP_008797973.1| 157 IVELSPKLILD 167
                                       **988877755 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.0   3.8e-05      0.34       3      35 ..     204     236 ..     202     237 .. 0.89
   2 !    9.2   0.2   0.00011         1      17      35 ..     267     285 ..     265     286 .. 0.87
   3 !    6.1   0.3    0.0011       9.6       6      23 ..     316     333 ..     311     333 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 3.8e-05
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       v+ ++v++ +f++i g++ +G+ ++I ++++i+
  gi|557694919|ref|YP_008797973.1| 204 VLDEGVVVESFTKIVGPCYVGKSSRIFPNSYIA 236
                                       56689*********************9999886 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00011
                                       ETTEEE-TTEEEETTEEEE CS
                           Hexapep  17 ggnVkIGdnvkIgagvvig 35 
                                       +g+ ++G+ v I+ag+++ 
  gi|557694919|ref|YP_008797973.1| 267 LGHSVVGEWVNIAAGTTVS 285
                                       57888************97 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0011
                                       TTEEE-TTEEEETTEEE- CS
                           Hexapep   6 snvlIgpfaviggnVkIG 23 
                                       ++v+ g ++++ g+VkIG
  gi|557694919|ref|YP_008797973.1| 316 DHVKTGIGTMVSGGVKIG 333
                                       899**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2983.67
//
Query:       gi|557694920|ref|YP_008797974.1|  [L=184]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00057   20.3   0.1     0.0007   20.0   0.1    1.6  1  AAA_16         AAA ATPase domain
     0.0019   18.2   0.1     0.0037   17.2   0.1    1.5  1  NACHT          NACHT domain
     0.0032   17.8   0.1      0.011   16.1   0.1    2.1  1  AAA_22         AAA domain
      0.004   17.3   0.0     0.0077   16.3   0.0    1.5  1  DUF87          Helicase HerA, central domain
     0.0054   16.3   0.1     0.0093   15.5   0.1    1.4  1  UvrD-helicase  UvrD/REP helicase N-terminal domain
     0.0055   16.4   0.0     0.0096   15.7   0.0    1.4  1  AAA_30         AAA domain
     0.0088   15.4   0.0      0.015   14.7   0.0    1.3  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
     0.0097   16.4   0.4      0.011   16.2   0.4    1.5  1  ABC_tran       ABC transporter
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.018   14.9   0.0    1.6  1  ATPase_2       ATPase domain predominantly from Archaea
       0.01   15.6   0.1      0.018   14.8   0.1    1.3  1  AAA_29         P-loop containing region of AAA domain
      0.015   14.8   0.1      0.035   13.6   0.1    1.6  1  AAA_7          P-loop containing dynein motor region
      0.022   14.5   0.0      0.051   13.3   0.0    1.6  2  AAA_24         AAA domain
      0.039   14.2   0.0      0.075   13.3   0.0    1.5  1  Roc            Ras of Complex, Roc, domain of DAPkinase
      0.048   13.3   0.0      0.079   12.6   0.0    1.5  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
      0.053   13.9   0.0       0.12   12.8   0.0    1.7  1  AAA            ATPase family associated with various cellular
      0.062   13.6   0.1       0.16   12.3   0.0    1.7  2  AAA_19         AAA domain
      0.065   13.0   0.0        0.1   12.3   0.0    1.4  1  PduV-EutP      Ethanolamine utilisation - propanediol utilisa
       0.08   12.5   0.2       0.13   11.8   0.2    1.4  1  cobW           CobW/HypB/UreG, nucleotide-binding domain
       0.11   11.7   0.1       0.21   10.7   0.1    1.4  1  DAP3           Mitochondrial ribosomal death-associated prote
       0.11   12.4   0.1        0.2   11.5   0.1    1.4  1  RsgA_GTPase    RsgA GTPase
       0.13   11.6   0.1       0.22   10.9   0.1    1.2  1  Mg_chelatase   Magnesium chelatase, subunit ChlI
       0.15   12.6   0.5       0.31   11.5   0.1    1.6  2  AAA_23         AAA domain
       0.16   11.4   0.4       0.35   10.3   0.1    1.6  2  SRPRB          Signal recognition particle receptor beta subu
       0.18   10.7   0.0       0.29   10.0   0.0    1.3  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-


Domain annotation for each model (and alignments):
>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   9.3e-07    0.0007      27      51 ..      11      35 ..       4     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.3e-07
                            AAA_16 27 vllsGesGvGKsslvrellralekd 51
                                      +l++Ge+G+GK+sl+ ++l+ l ++
  gi|557694920|ref|YP_008797974.1| 11 TLIIGEAGSGKTSLLAQVLQNLLTK 35
                                      79*****************999877 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   4.9e-06    0.0037       3      24 ..      11      32 ..       9      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.9e-06
                                      EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                       ++ GeaGsGKT Ll+++ + +
  gi|557694920|ref|YP_008797974.1| 11 TLIIGEAGSGKTSLLAQVLQNL 32
                                      6899*************99877 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.4e-05     0.011       8      30 ..      11      33 ..       8     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.4e-05
                            AAA_22  8 lvvtGesGtGKTtllrrlleqld 30
                                      ++++Ge+G+GKT ll+++l++l 
  gi|557694920|ref|YP_008797974.1| 11 TLIIGEAGSGKTSLLAQVLQNLL 33
                                      68****************99884 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0     1e-05    0.0077      18      59 ..       3      45 ..       1      47 [. 0.84

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-05
                             DUF87 18 lnklvtrHlAilgsTGsGKSntvavLleellekkga.tililD 59
                                       ++l+ ++++i+g++GsGK+ + a  l++ll k g  +i ++D
  gi|557694920|ref|YP_008797974.1|  3 PEELLGKRTLIIGEAGSGKTSLLAQVLQNLLTKLGPcSITVID 45
                                      68999************************99654436777777 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.3e-05    0.0093      10      41 ..       5      36 ..       1      44 [. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                                      HS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTS CS
                     UvrD-helicase 10 aslggpilveAsAGsGKTfvlaerilrlikee 41
                                      + lg+ +l++  AGsGKT  la++  +l+++ 
  gi|557694920|ref|YP_008797974.1|  5 ELLGKRTLIIGEAGSGKTSLLAQVLQNLLTKL 36
                                      568999******************99999875 PP

>> AAA_30  AAA 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    0.0096      21      54 ..      11      48 ..       4      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.3e-05
                            AAA_30 21 avltGpAGtGKttalkal.reaweaag...grviglAp 54
                                      +++ G AG+GKt +l+++ ++++++ g    +vi lAp
  gi|557694920|ref|YP_008797974.1| 11 TLIIGEAGSGKTSLLAQVlQNLLTKLGpcsITVIDLAP 48
                                      6899************9978888888989889999998 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     2e-05     0.015      42      77 ..      11      46 ..       3      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                                      EEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE CS
                      FtsK_SpoIIIE 42 llvaGatgsGKStalntLilSlatthtPeeVqlili 77
                                      +l++G  gsGK+  l   +++l+t+  P  ++ i +
  gi|557694920|ref|YP_008797974.1| 11 TLIIGEAGSGKTSLLAQVLQNLLTKLGPCSITVIDL 46
                                      79***********************99988887755 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4   1.5e-05     0.011      11      35 ..       8      32 ..       6     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-05
                                      TSEEEEEESTTSSHHHHHHHHTTSS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 11 gekvaivGenGaGKStLlkllagll 35
                                      g+++ i+Ge G+GK++Ll+ ++++l
  gi|557694920|ref|YP_008797974.1|  8 GKRTLIIGEAGSGKTSLLAQVLQNL 32
                                      899**************98777665 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 ?   14.9   0.0   2.5e-05     0.018      24     128 ..      12     120 ..       7     182 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-05
                          ATPase_2  24 fiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskldefieeeeekkklekalgiavpkaeleeilk.ek 98 
                                       +i G  gsGKt+Ll ++++nl  +++   i +i+l   +i  +   + e+  ++ l  +   ++   +l ++   e 
  gi|557694920|ref|YP_008797974.1|  12 LIIGEAGSGKTSLLAQVLQNLlTKLGPCSITVIDLAPPRIMDVGGPLTEHMRVDGLHYKRPPNIYAPRLMACNAeEL 88 
                                       799*****************967777788889998888888888888888888888887766666666655544577 PP

                          ATPase_2  99 sklvfkaielllekikkkgkk..iiiiiDelq 128
                                       +k+v +++e +++  ++  +   +++ + ++ 
  gi|557694920|ref|YP_008797974.1|  89 KKYVHSNLETAKRLFNEFIQNptPVLAVNDVT 120
                                       77777777777777777666666777777775 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 ?   14.8   0.1   2.4e-05     0.018      24      39 ..      10      25 ..       4      35 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.4e-05
                            AAA_29 24 atlltGpsGsGKSTll 39
                                       tl++G+ GsGK++ll
  gi|557694920|ref|YP_008797974.1| 10 RTLIIGEAGSGKTSLL 25
                                      69*************9 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 ?   13.6   0.1   4.7e-05     0.035      33      61 ..       8      35 ..       6      45 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.7e-05
                             AAA_7 33 kkpvllvGptGtGKtviikdllkkldkek 61
                                      +k +l++G++G+GKt+++ ++l++l  +k
  gi|557694920|ref|YP_008797974.1|  8 GKRTLIIGEAGSGKTSLLAQVLQNLL-TK 35
                                      5789****************999987.44 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.8e-05     0.051       2      25 ..       8      31 ..       7      50 .. 0.87
   2 ?   -2.4   0.0       4.4   3.3e+03     132     169 ..     148     179 ..     128     183 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.8e-05
                            AAA_24  2 klkiliyGpsgiGKTtlakelgpk 25
                                      +++ li+G++g+GKT+l+++  ++
  gi|557694920|ref|YP_008797974.1|  8 GKRTLIIGEAGSGKTSLLAQVLQN 31
                                      5799**************998555 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.4
                            AAA_24 132 ktrkdedpegeakytrlepklgkktanelkeevDlvlr 169
                                        tr  ed  ++       ++ +k+  +el ++v +v+ 
  gi|557694920|ref|YP_008797974.1| 148 GTRLAEDFGTG------LTESEKRRVEELSKHVNIVIN 179
                                       44444444333......333334445555555555555 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 ?   13.3   0.0    0.0001     0.075       2      23 ..      11      32 ..      10      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.0001
                                      EEEESSTTSSHHHHHHCHCT-C CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedk 23
                                       +++G++g+GKtsll +++++ 
  gi|557694920|ref|YP_008797974.1| 11 TLIIGEAGSGKTSLLAQVLQNL 32
                                      589*************999875 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 ?   12.6   0.0   0.00011     0.079      14      47 ..       8      43 ..       5     160 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                                      T-EEEEEESTTSSHHHHHHHHHHHSSTS.S.EEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxx RF
                       ATP-synt_ab 14 GqrtlipgafgvGktvisqslskqsnsd.d.aiiyv 47
                                      G+rtli+g++g Gkt ++++++++  ++   ++i v
  gi|557694920|ref|YP_008797974.1|  8 GKRTLIIGEAGSGKTSLLAQVLQNLLTKlGpCSITV 43
                                      99****************888777544432344544 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 ?   12.8   0.0   0.00017      0.12       2      35 ..      12      52 ..      11     131 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                                      EEESSTTSSHHHHHHHHHHHH.......THEEEEEETTTCS CS
                               AAA  2 llyGppGtGKTllakavakel.......gvefleisgsell 35
                                      l++G  G GKT+l  +v ++l       +++++ +  ++++
  gi|557694920|ref|YP_008797974.1| 12 LIIGEAGSGKTSLLAQVLQNLltklgpcSITVIDLAPPRIM 52
                                      899*****************755443334555555544444 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00022      0.16      10      38 ..       8      36 ..       3      50 .. 0.81
   2 ?   -1.5   0.0       3.8   2.9e+03      67      71 ..     136     140 ..      89     177 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelg 38
                                       k  l+++ +G+GKT +l ++++ l+   
  gi|557694920|ref|YP_008797974.1|  8 GKRTLIIGEAGSGKTSLLAQVLQNLLTKL 36
                                      56789***************999887665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.8
                            AAA_19  67 aeatT 71 
                                       ++a+T
  gi|557694920|ref|YP_008797974.1| 136 EKAST 140
                                       33333 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00014       0.1       2      23 ..       9      31 ..       8      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                         PduV-EutP  2 kkilliGkvgsGKttL.tqalkg 23
                                      k+ l+iG+ gsGKt+L +q l++
  gi|557694920|ref|YP_008797974.1|  9 KRTLIIGEAGSGKTSLlAQVLQN 31
                                      899************72566666 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 ?   11.8   0.2   0.00018      0.13       3      23 ..      11      31 ..       9      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                      EEEEESTTCCHHHHHHHHHCT CS
                              cobW  3 tvltGflGsGKTtLlnhllen 23
                                      t++ G  GsGKT+Ll ++l+n
  gi|557694920|ref|YP_008797974.1| 11 TLIIGEAGSGKTSLLAQVLQN 31
                                      78999*************976 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 ?   10.7   0.1   0.00028      0.21      24      45 ..       9      30 ..       5      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                                      -EEEEE-SSSSSTTTTHHHHHH CS
                              DAP3 24 krlvltGekgsGKSvlLlqala 45
                                      kr ++ Ge gsGK+ lL+q+l 
  gi|557694920|ref|YP_008797974.1|  9 KRTLIIGEAGSGKTSLLAQVLQ 30
                                      7999***************986 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00027       0.2      96     128 ..       5      37 ..       3      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00027
                                       HCTTSEEEEECSTTSSHHHHHHHHCTT-----S CS
                       RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallpelelktg 128
                                       +l +k ++++G+ G GK++L+ ++l++l +k g
  gi|557694920|ref|YP_008797974.1|   5 ELLGKRTLIIGEAGSGKTSLLAQVLQNLLTKLG 37 
                                       56688999**************99998766665 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   0.00029      0.22      25      50 ..      11      37 ..       7      46 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00029
                      Mg_chelatase 25 lllvGppGsGKt.mlakrlpsllppls 50
                                       l++G +GsGKt +la+ l++ll++l 
  gi|557694920|ref|YP_008797974.1| 11 TLIIGEAGSGKTsLLAQVLQNLLTKLG 37
                                      5899*******7489********9875 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00042      0.31      22      37 ..      11      26 ..       7      38 .. 0.91
   2 ?   -1.5   0.0       4.1   3.1e+03     146     146 ..     132     132 ..      82     181 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00042
                            AAA_23 22 tlItGpNGaGKTTild 37
                                      tlI+G+ G+GKT++l 
  gi|557694920|ref|YP_008797974.1| 11 TLIIGEAGSGKTSLLA 26
                                      8*************95 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.1
                            AAA_23 146 f 146
                                       +
  gi|557694920|ref|YP_008797974.1| 132 L 132
                                       0 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 ?   10.3   0.1   0.00046      0.35       5      29 ..      10      34 ..       8      47 .. 0.83
   2 ?   -3.4   0.0       7.6   5.7e+03     116     124 ..      80      88 ..      77      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00046
                                      EEEEE-STTSSHHHHHHHHHHSS-- CS
                             SRPRB  5 avllvGlsdsGKTslftrLttdsvk 29
                                      + l++G   sGKTsl+ +++++  +
  gi|557694920|ref|YP_008797974.1| 10 RTLIIGEAGSGKTSLLAQVLQNLLT 34
                                      579***************9998544 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.6
                                       EEEEE-TTS CS
                             SRPRB 116 liACnKqel 124
                                       l+ACn +el
  gi|557694920|ref|YP_008797974.1|  80 LMACNAEEL 88 
                                       899*99886 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 ?   10.0   0.0   0.00039      0.29      16      40 ..       9      33 ..       3      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00039
                     TrwB_AAD_bind 16 qhilivGttGsGKtqalekllrair 40
                                      + +li+G +GsGKt  l + l+++ 
  gi|557694920|ref|YP_008797974.1|  9 KRTLIIGEAGSGKTSLLAQVLQNLL 33
                                      579**************99998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1276.10
//
Query:       gi|557694921|ref|YP_008797975.1|  [L=193]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-31  109.9  19.0      1e-30  106.9  19.0    1.9  1  ThiW          Thiamine-precursor transporter protein (ThiW)
    7.9e-06   26.1  20.4    3.1e-05   24.2  20.1    1.8  1  ECF_trnsprt   ECF transporter, substrate-specific component
     0.0012   18.4  12.6     0.0012   18.4  12.6    2.3  2  5TM-5TMR_LYT  5TMR of 5TMR-LYT


Domain annotation for each model (and alignments):
>> ThiW  Thiamine-precursor transporter protein (ThiW)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.9  19.0   1.7e-34     1e-30       2     148 ..       8     176 ..       7     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 106.9 bits;  conditional E-value: 1.7e-34
                              ThiW   2 allavlialgvvlssllsipvgvakvaPvqhvvNvvaavllGPwyalavalvisliRnllgtgtllalpGsiiGall 78 
                                       al++ l alg+v+s++ +++   ++++P qh++Nv+++vllGP+++ +va++i+++R++lgtgt++a pG+i+Ga+l
  gi|557694921|ref|YP_008797975.1|   8 ALASALSALGIVISPM-MFEWLGSRAFPGQHFINVLSGVLLGPLWGAIVAIIIGTVRIALGTGTVFAYPGGIPGAVL 83 
                                       678899**********.99999******************************************************* PP

                              ThiW  79 agllyrltrkl......llaalgEvlGtgiiGallaypv.aklllg....keaal.............lvlvisFil 131
                                       +gl+y l ++l      +laa++E++Gt++iG+++a+ v a+ +      +++ +             l+l+  +++
  gi|557694921|ref|YP_008797975.1|  84 VGLFYILLKRLrnprlrYLAAFAEPIGTVLIGGTIALAVvAPGIGPavgpAAV-MlrnletlgfwpalLLLWGGWAV 159
                                       ***998887766667779***************97765425444321111222.13566666778887888999*** PP

                              ThiW 132 stliGsviallvlkale 148
                                       s++iG+v+++l+l a e
  gi|557694921|ref|YP_008797975.1| 160 SSIIGTVAGFLFLLAAE 176
                                       ***********998876 PP

>> ECF_trnsprt  ECF transporter, substrate-specific component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2  20.1   5.1e-09   3.1e-05       1     119 [.       5     170 ..       5     175 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.1e-09
                                       HHHHHHHHHHHHHHHHHHHHEEE.STS.EEESHHHHHHHHHHCTTCHHHHHHHHHHHHHHHHCHT-SSTTHHHHHHH CS
                       ECF_trnsprt   1 kklvitglliAisivlsllgyiplpni.kitiihipvllggllfGpikGailgiitsvlkailtggtgalssfvpia 76 
                                       kk+++++ l+A+ iv+s + +++ +    +   h++ +l+g+l+Gp++Gai++ii+ +++  l g++++++   p+ 
  gi|557694921|ref|YP_008797975.1|   5 KKVALASALSALGIVIS-PMMFEWLGSrAFPGQHFINVLSGVLLGPLWGAIVAIIIGTVRIAL-GTGTVFAY--PGG 77 
                                       78999************.63333333337**********************************.66666666..888 PP

                                       HHHHHCHHHHHHHHHHCCCHTTHHHH................................................... CS
                       ECF_trnsprt  77 flsriligliagllykkgkkknlkei................................................... 102
                                       ++ ++l+gl + ll +  ++ +l +                                                    
  gi|557694921|ref|YP_008797975.1|  78 IPGAVLVGLFYILLKR-LRNPRLRYLaafaepigtvliggtialavvapgigpavgpaavmlrnletlgfwpallll 153
                                       8888888888775555.555555444688888888888888777777777777777777777777777777777777 PP

                                       HHHHHHHHCCCCCHHHH CS
                       ECF_trnsprt 103 vvsfilagvlgtivatl 119
                                       + + ++++++gt++++l
  gi|557694921|ref|YP_008797975.1| 154 WGGWAVSSIIGTVAGFL 170
                                       33344444444333333 PP

>> 5TM-5TMR_LYT  5TMR of 5TMR-LYT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4  12.6   1.9e-07    0.0012      51     120 ..      40     107 ..       2     129 .. 0.72
   2 ?   -2.1   3.7      0.38   2.3e+03      56      72 ..     153     169 ..     108     189 .. 0.62

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-07
                      5TM-5TMR_LYT  51 vvvaGllgGplvGliagliaglhRyllgGftalacgistilagllaGlihrklkrrrkkltvlvalligl 120
                                        v++G+l Gpl+G+i+++i+g +R++lg  + +++    i  ++l+Gl++  lkr  ++++++++++++ 
  gi|557694921|ref|YP_008797975.1|  40 NVLSGVLLGPLWGAIVAIIIGTVRIALGT-GTVFAYPGGIPGAVLVGLFYILLKRL-RNPRLRYLAAFAE 107
                                       589**********************9988.88999999999999999999999963.5555555554433 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.38
                      5TM-5TMR_LYT  56 llgGplvGliagliagl 72 
                                       l gG+ v+ i g +ag+
  gi|557694921|ref|YP_008797975.1| 153 LWGGWAVSSIIGTVAGF 169
                                       45666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); 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:                         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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1440.91
//
Query:       gi|557694922|ref|YP_008797976.1|  [L=88]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-14   53.1   0.7      4e-14   52.8   0.7    1.1  1  GtrA       GtrA-like protein
  ------ inclusion threshold ------
       0.04   13.4   1.6          3    7.2   0.2    2.0  2  SbmA_BacA  SbmA/BacA-like family


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 !   52.8   0.7   4.5e-18     4e-14       1      57 [.      15      73 ..      15      81 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 4.5e-18
                              GtrA  1 rFlivGvlgtlvdlallllllel..lglsyllAnaiafivailfnFilnrrwtFkdrek 57
                                      +F +vG++g +v++++l+ll+++   +  yl+A +i+ +++il+nF+ln++wtF+dr  
  gi|557694922|ref|YP_008797976.1| 15 KFSVVGGVGLVVNTVALFLLTNYvfGERLYLIAAVISLEISILNNFFLNEYWTFRDRAG 73
                                      79*******************887667779**************************975 PP

>> SbmA_BacA  SbmA/BacA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.2   0.00033         3      59      88 ..      13      42 ..       8      47 .. 0.90
   2 ?    6.3   0.1   0.00063       5.7      62      89 ..      44      72 ..      41      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00033
                         SbmA_BacA 59 lldfllialvavviavlnaffvshyifrWr 88
                                      l++f+++  v++v+++++ f+ + y+f  r
  gi|557694922|ref|YP_008797976.1| 13 LIKFSVVGGVGLVVNTVALFLLTNYVFGER 42
                                      789************************766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00063
                         SbmA_BacA 62 fllialvavviavlnaffvs.hyifrWrt 89
                                      +l+ a++ + i++ln+ff + ++ fr r+
  gi|557694922|ref|YP_008797976.1| 44 YLIAAVISLEISILNNFFLNeYWTFRDRA 72
                                      45678999*********986256899875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); 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):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 722.44
//
Query:       gi|557694923|ref|YP_008797977.1|  [L=363]
Description: DNA polymerase IV [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-42  145.0   0.3    2.7e-42  144.3   0.1    1.5  2  IMS       impB/mucB/samB family
    5.5e-08   33.5   0.7    1.2e-07   32.5   0.7    1.6  1  IMS_C     impB/mucB/samB family C-terminal domain
    9.2e-07   28.8   0.0    2.7e-06   27.4   0.0    1.9  1  IMS_HHH   IMS family HHH motif
    1.9e-05   25.2   0.1     0.0001   22.8   0.0    2.3  2  HHH_5     Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.062   13.4   0.1       0.53   10.4   0.0    2.3  2  TfoX_C    TfoX C-terminal domain
      0.097   13.0   0.1        1.4    9.2   0.0    2.5  2  mCpol     minimal CRISPR polymerase 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 !  144.3   0.1   9.2e-46   2.7e-42       1     149 [.       8     159 ..       8     160 .. 0.94
   2 ?   -3.6   0.0       3.2   9.7e+03      63      86 ..     253     276 ..     248     283 .. 0.59

  Alignments for each domain:
  == domain 1  score: 144.3 bits;  conditional E-value: 9.2e-46
                                       EEETTHHHHHHHHHT.T-TTS-EEEEET.......TEEEEE-HHHHTTT--TTSBHHHHHTTHTT.-EEEEEE-HHH CS
                               IMS   1 iDmdaFyasverardpeLkgkPvvvaqgsek...rgiviavsyeArayGvkrgmrikeakklcpd.livvkvdleky 73 
                                       +D+d F+a++e++++peL+gkP++v+  s +   +g+v +++y Ar++Gvk+gm+ik akkl p+ +++++v+le y
  gi|557694923|ref|YP_008797977.1|   8 LDLDYFFAQIEEVENPELRGKPLCVCVFSGRtsdSGVVSSANYVARRFGVKAGMPIKAAKKLLPEeAVILPVRLEHY 84 
                                       7***********************99877777779*****************************77*********** PP

                                       HHHHHHHHHHHHHH-S..EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHHHHH CS
                               IMS  74 rraskkileilkrfispkvekasiDEayldltgleelaesegaalakelrkaikeelgltvsiGiasnkllAKlas 149
                                        ++s++i++ lk+f +  ++  s+DEa++d+t+ +    +e++++ake+++ i +++glt+s+Gi++n+++AK+a+
  gi|557694923|ref|YP_008797977.1|  85 ANISRQIMDNLKKF-NTPLRVESVDEAVMDVTQAVGSDYAEAEEFAKEVKEMIRANFGLTCSVGIGPNRVVAKMAA 159
                                       **************.5589999***********777777778********************************97 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.2
                                       -EEEEEE-HHHHHHHHHHHHHHHH CS
                               IMS  63 livvkvdlekyrraskkileilkr 86 
                                       ++++k + ++++++ + +++ +++
  gi|557694923|ref|YP_008797977.1| 253 IVTLKRNTREVEEVMETLAAAASQ 276
                                       555666666666666666555555 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 !   32.5   0.7   3.9e-11   1.2e-07       2     114 ..     241     355 ..     240     358 .. 0.82

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.9e-11
                             IMS_C   2 vearpepksissektfpepydesk.lkkelreLaeelarrLrdkglvartitlklrysdfh.asrsatLprptsdtr 76 
                                       +e+rp+pk++s+  t+++ + e + + + l   a++++ rL +++++a++i l   +   + ++r+a +     + +
  gi|557694923|ref|YP_008797977.1| 241 IEERPPPKQLSKIVTLKRNTREVEeVMETLAAAASQAYTRLASAKFFASKIGLIAITTRLEtITRQADIR-FGASLD 316
                                       689**************933322235555559999****************99995443446*****885.458999 PP

                             IMS_C  77 eileaalkLlrrlide.pglpirligvsasnlvekaesq 114
                                       e+l++++ Ll +l  + +++ +r++gv++++l + ++++
  gi|557694923|ref|YP_008797977.1| 317 EVLRTLRILLTKLLETdEKMMLRRVGVRFTGLKPVSGQT 355
                                       999**********999****************9666654 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0     9e-10   2.7e-06       1      32 []     172     203 ..     172     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 9e-10
                           IMS_HHH   1 pddvkefLwplpitkipGiGgklgekLeklGi 32 
                                       p++++efL++lp++ +pGiG k++  L+ + i
  gi|557694923|ref|YP_008797977.1| 172 PENLEEFLSDLPVKNLPGIGAKTESILAEHQI 203
                                       799*********************99988765 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.5   7.5e+03       9      17 ..     147     155 ..     147     170 .. 0.76
   2 !   22.8   0.0   3.5e-08    0.0001       6      54 ..     186     232 ..     180     234 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.5
                                       T--HHHHHH CS
                             HHH_5   9 GiGpktAla 17 
                                       GiGp +++a
  gi|557694923|ref|YP_008797977.1| 147 GIGPNRVVA 155
                                       899998877 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 3.5e-08
                                       TSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHH CS
                             HHH_5   6 svsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriile 54 
                                        ++GiG+kt   l+++ i++v dl +++ e+L ++  +G+k+A+ + l+
  gi|557694923|ref|YP_008797977.1| 186 NLPGIGAKTESILAEHQIKTVGDLSRQSLEKLEEL--FGPKKAQYLYLA 232
                                       68*********************************..*******88876 PP

>> TfoX_C  TfoX C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00018      0.53       5      32 ..     184     211 ..     181     216 .. 0.92
   2 ?   -0.5   0.0      0.47   1.4e+03      30      58 ..     269     297 ..     260     307 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                            TfoX_C   5 LkdLpNlglklerlLkkaGIktveeLre 32 
                                       +k+Lp +g k+e++L++  Iktv +L +
  gi|557694923|ref|YP_008797977.1| 184 VKNLPGIGAKTESILAEHQIKTVGDLSR 211
                                       699*********************9975 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.47
                            TfoX_C  30 LrelGaveaylkiketgtsvslelLyaLe 58 
                                         +  a +ay ++ ++++ +s+  L a++
  gi|557694923|ref|YP_008797977.1| 269 TLAAAASQAYTRLASAKFFASKIGLIAIT 297
                                       45667899*****9999988887776665 PP

>> mCpol  minimal CRISPR polymerase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00048       1.4      67     105 ..     126     164 ..      73     170 .. 0.62
   2 ?    0.9   0.0      0.19   5.6e+02       9      56 ..     190     233 ..     189     286 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00048
                             mCpol  67 edllvelsrvyqkitgltvSiGvGktlrealiaLkkAks 105
                                       e+ + e++++ +++ glt+S+G+G +   a +a  ++k 
  gi|557694923|ref|YP_008797977.1| 126 EEFAKEVKEMIRANFGLTCSVGIGPNRVVAKMAADYSKP 164
                                       244556666666666*********999888888777775 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.19
                             mCpol   9 iGkklealllsndeeeleklskevkeaikklkkllkdelgasvifaaG 56 
                                       iG k e++l +++++ +  ls +   +++kl++l+  + +a+ ++ a 
  gi|557694923|ref|YP_008797977.1| 190 IGAKTESILAEHQIKTVGDLSRQ---SLEKLEELFGPK-KAQYLYLAS 233
                                       88999999999999999888865...666666666666.666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 2846.11
//
Query:       gi|557694924|ref|YP_008797978.1|  [L=317]
Description: acetoin utilization protein AcuC [Candidatus Caldiarchaeum subterraneum]
Scores for 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-72  243.7   0.0    3.9e-72  243.3   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 !  243.3   0.0   2.2e-76   3.9e-72       1     306 [.      22     312 ..      22     313 .. 0.95

  Alignments for each domain:
  == domain 1  score: 243.3 bits;  conditional E-value: 2.2e-76
                                       SCCGTHHHHHHHHHHHHT.THHHHCCE.EE-----HHHHTTTS-HHHHHHHHCHHHHCHHT.TTHCCHHHCCTSTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl   1 hpenpkRlsaileslaesvglldelelliqpseatkeellkvHskeYlelleslsnelkkkeeakekeleeiaskll 77 
                                       hp n+ Rl+a +++l +  + l +  l+++p++a k+++  +H+++Y+e++e+ +   k                l 
  gi|557694924|ref|YP_008797978.1|  22 HPLNRVRLEAFYQKLDSEGKNL-QGLLFVEPEKAGKDDVMLFHTPAYVEFVEERCRVGKGY--------------LD 83 
                                       78999**********9985555.67779************************988554443..............34 PP

                                       SSSTHCTTTCCHHHHHHHHHHHHHHHHHHTTSSSEEEETTSS--TT-BTTB-BTTBSS-HHHHHHHHHHHCC-SS-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl  78 dddtpvspktlkaallavgavleavdavlsgsvkaafvlvrPpgHHakaseasGFClvNnvaiaikylqakhelkrv 154
                                        +dtp++p+ ++aa+++vg +l++++ ++sg+++a+f  + ++ HHa++++a+GFC++N++ +ai+yl ++ +++ v
  gi|557694924|ref|YP_008797978.1|  84 YGDTPAFPGCFEAASYVVGTTLKLLRMIISGEISAGFNPM-GGLHHARRDRAGGFCIFNDAGVAIEYLLRRENMRNV 159
                                       799****************************999999766.*****************************999**** PP

                                       EEEE-SSS--HHHHHHCTT-TTEEEEEEEE-CCTSTTSS--TT---SGGGTTSEEEEEE-TT-BHHHHHHHHHHCHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 155 ailDvDvHhGnGteeafysdpdvltlSiHryegifyPgtgaledlgegkgkgfnlnvpleegtgdeeylkvfeeilr 231
                                       a++D+D+HhG+G+   fys+++v++++iH+ ++++yPgtg  +++geg+++g++ln+pl +++gdee+ ++f+e+  
  gi|557694924|ref|YP_008797978.1| 160 AYVDIDAHHGDGVCYDFYSEKRVIFADIHQDGRTLYPGTGFRNETGEGEARGTKLNIPLLPYSGDEEFFQAFQEVE- 235
                                       ************************************************************************9976. PP

                                       HHHCCH--SEEEEEE-STTBTTSTT-S-BB-HHHHHHHHHHHCCCHGS-.G..EEEEE-S---HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Hist_deacetyl 232 pvleefkPdlilvsaGfDalkgdplgelnlsvegykeltkklaeladkv.k.kvvllleGGYnlealaravtavlsa 306
                                       + le+++ d++l+++G+D+l+gdpl +l+ s++ ++++ ++l+++a+k  + +++++++GGY++ ++a a+tav++a
  gi|557694924|ref|YP_008797978.1| 236 QFLEKHEFDFLLLQCGADGLMGDPLTNLQYSARAHGYAASRLLKIAEKKcGgRILAMGGGGYDPVNVAHAWTAVVKA 312
                                       999*********************************************9989**********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2548.30
//
Query:       gi|557694925|ref|YP_008797979.1|  [L=210]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-60  201.5   0.0    8.6e-60  201.3   0.0    1.0  1  DUF99          Protein of unknown function DUF99
  ------ inclusion threshold ------
       0.15   11.5   0.1        0.2   11.1   0.1    1.1  1  PrsW-protease  PrsW family intramembrane metalloprotease


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 !  201.3   0.0   9.5e-64   8.6e-60       1     182 [.      10     188 ..      10     189 .. 0.97

  Alignments for each domain:
  == domain 1  score: 201.3 bits;  conditional E-value: 9.5e-64
                                       GGSEEEEEEEEE.....-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEET CS
                             DUF99   1 keirvlGiddsfferkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGitia 77 
                                       k+ir+lG+++sf  rk+ ++++vl+Gvvmr+d +vdg++fg +tv+G+D+tea++e+++rl r di+vvll+G +i+
  gi|557694925|ref|YP_008797979.1|  10 KGIRALGVAESF--RKRLGSRAVLAGVVMRSDLLVDGFVFGACTVGGMDSTEAVLEMWQRLGRMDINVVLLSGSVIS 84 
                                       589*********..5688*********************************************************** PP

                                       TTEE--HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTH.HHHHHHHHHC.---EEETT....EEEEEESS-HH CS
                             DUF99  78 gFNvvDlerlheetglPviavtreepdlgklekaLrkhfpde.eeRlelieklgerieevektgeelyvravGiele 153
                                       +FNvvDl++lh+++g P+i++++++++ g le+  r++fp + e+Rl++  + ger  +v ktg+++yvr+ G+ ++
  gi|557694925|ref|YP_008797979.1|  85 WFNVVDLNKLHQTIGTPLICLSYRDSR-G-LEEVFRRRFPSDwEQRLSVHLRNGERSDVVLKTGYKVYVRCFGLLPT 159
                                       ***************************.8.*********9766********************************** PP

                                       HHHHHHHHC-SSSSS-HHHHHHHHHHHHH CS
                             DUF99 154 eaaklvrkltlegriPEPlRvAhliAsal 182
                                       +a+++++k+t++gr PEP+R+A+l+A+++
  gi|557694925|ref|YP_008797979.1| 160 DAKTVLDKFTVDGRFPEPVRLAKLLARGA 188
                                       **************************986 PP

>> PrsW-protease  PrsW family intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   2.3e-05       0.2      51     104 ..      16      69 ..      11      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.3e-05
                     PrsW-protease  51 glvEEllKalgvllllllrrrefdepldGivygaavglGFavlEnllYyvqalp 104
                                       g++E + K lg  ++l     + d  +dG+v+ga +  G + +E +l ++q l 
  gi|557694925|ref|YP_008797979.1|  16 GVAESFRKRLGSRAVLAGVVMRSDLLVDGFVFGACTVGGMDSTEAVLEMWQRLG 69 
                                       8999**********999889999************************9998764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1532.86
//
Query:       gi|557694926|ref|YP_008797980.1|  [L=349]
Description: bifunctional protein GlmU [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-31  109.9   0.0    1.7e-31  109.7   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    4.5e-15   56.4   0.0    5.7e-15   56.0   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    2.2e-10   39.9   3.4    0.00013   21.5   0.1    3.8  4  Hexapep          Bacterial transferase hexapeptide (six repea
    5.6e-05   23.0   0.0     0.0001   22.1   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.017   15.0   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
      0.094   11.7   0.0       0.14   11.1   0.0    1.2  1  SHR3_chaperone   ER membrane protein SH3
       0.75    9.6  10.2       0.28   10.9   0.9    4.0  4  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 !  109.7   0.0   6.8e-35   1.7e-31       1     245 [.       3     233 ..       3     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 6.8e-35
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kav+ a G+G+RL+PLt +++k  +pv+gk +li  ++++l+ +gi++ + vl  +h + + e lk+  + +  +++
  gi|557694926|ref|YP_008797980.1|   3 KAVVFAAGYGKRLRPLTINRPKHVLPVAGK-PLIRWVVEALSTAGIDD-VGVLVGYHGHDAVEALKNLHRPR--LTF 75 
                                       79****************************.*****************.999****************9866..*** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST.THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEE CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikd.ayeeavkkaiekaakgtvtfgivpveeateyGviea 153
                                       + +++  gt +A++  +e+le e+    +lv+ gD+ ++d  +++++ + +e +   + ++++v+ ee++++G i+ 
  gi|557694926|ref|YP_008797980.1|  76 IEQKKLLGTGQALKECREFLEGEDV---FLVVYGDVTVNDmVLRRLLGFWREGGF--DSVLAAVELEESKRFGSIKL 147
                                       ************************5...9******9999879999***9999999..89999*************** PP

                                       CTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE CS
                   NTP_transferase 154 deegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs 230
                                       d+e r  +++EK  + k   ++++GiY+f +++++ l + +  ++rge e+td+++++ ++g+     +f+ +  W 
  gi|557694926|ref|YP_008797980.1| 148 DGE-RLVKIEEKTGAGK---IVNAGIYIFSKNIFKAL-EMVGFSERGEIELTDAVNQLAAQGHIVGVKVFDRS-WWF 218
                                       *95.8889****76655...***************99.889****************9999988777677775.6** PP

                                       EXSSHHHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleanekl 245
                                       DvG + ++l++n  +
  gi|557694926|ref|YP_008797980.1| 219 DVGLPADYLRVNHVY 233
                                       *********998765 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 !   56.0   0.0   2.2e-18   5.7e-15       1     124 [.       4     135 ..       4     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 2.2e-18
                                       EEEEEESS-TTT.....TTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC.....HHHHHHTTCTS-EEE-TT CS
                      NTP_transf_3   1 aviLAGGrSsRm.....ggdKallplggkpllervldalraagvdevvvvggde.....evlaalarlgvrvveded 67 
                                       av+ A+G ++R+     +++K  lp++gkpl+++v++al+ ag+d+v v +g++     e l+ l r++++++e++ 
  gi|557694926|ref|YP_008797980.1|   4 AVVFAAGYGKRLrpltiNRPKHVLPVAGKPLIRWVVEALSTAGIDDVGVLVGYHghdavEALKNLHRPRLTFIEQK- 79 
                                       79**********5555557*******************************99965555555557788899999997. PP

                                       SS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESS CS
                      NTP_transf_3  68 pgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptye 124
                                       +  g++++l+   + ++++d +lv+ +D+  ++  +++rll  +++ g d v ++ e
  gi|557694926|ref|YP_008797980.1|  80 KLLGTGQALKECREFLEGEDVFLVVYGDV-TVNDMVLRRLLGFWREGGFDSVLAAVE 135
                                       589**************************.6799**********9998776666554 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.5   3.8e+03      15      23 ..     103     111 ..     100     112 .. 0.82
   2 !   18.1   0.1     6e-07    0.0015       3      36 .]     243     276 ..     241     276 .. 0.92
   3 !   21.5   0.1     5e-08   0.00013       3      36 .]     261     294 ..     259     294 .. 0.93
   4 !   14.5   0.0   8.4e-06     0.021       2      34 ..     295     326 ..     294     328 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                                       EEETTEEE- CS
                           Hexapep  15 viggnVkIG 23 
                                       v++g+V++ 
  gi|557694926|ref|YP_008797980.1| 103 VVYGDVTVN 111
                                       899***996 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 6e-07
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                        I +++++g  + + g+V + ++++I++g+v+ g
  gi|557694926|ref|YP_008797980.1| 243 SIDEGTVLGEDVELNGPVMVEEGCVIESGSVLEG 276
                                       57899**************************975 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 5e-08
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                                        ++++++I +++v+ g++ I  ++ Ig+ ++++g
  gi|557694926|ref|YP_008797980.1| 261 MVEEGCVIESGSVLEGPCYICQGSFIGRRSRVAG 294
                                       5899************************999976 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 8.4e-06
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       +v+ +++++gp++++ + V +G++++  +gv +
  gi|557694926|ref|YP_008797980.1| 295 SVVLEKCFLGPGSHLVNSV-LGEGSVFSEGVEV 326
                                       67789**************.**********987 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 !   22.1   0.0     4e-08    0.0001       3      63 ..       4      66 ..       2      78 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 4e-08
                                      EEEECTTSSCTT-...SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHH CS
                              IspD  3 vvipAAGsGkRmk...aglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqll 63
                                      +v+ AAG GkR++    ++pK  l ++g++l+ + v+al     +d + v+v  +  +++e+l 
  gi|557694926|ref|YP_008797980.1|  4 AVVFAAGYGKRLRpltINRPKHVLPVAGKPLIRWVVEALST-AGIDDVGVLVGYHGHDAVEALK 66
                                      89*********8533379*******************9987.8899999999877777777765 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 ?   15.0   0.0   6.5e-06     0.017      43     130 ..      62     148 ..      41     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.5e-06
                                       HHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS.EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEE CS
                   Glycos_transf_2  43 veileelakedprvrvirreenvGkagalnaglraatgd.yilflDaDdepdpdwleklvealekdgadvvlgqrpr 118
                                       ve l++l+  +pr+++i +++  G + al +  +   g+ ++l++  D+++++  l++l++++ ++g d vl+++  
  gi|557694926|ref|YP_008797980.1|  62 VEALKNLH--RPRLTFIEQKKLLGTGQALKECREFLEGEdVFLVVYGDVTVNDMVLRRLLGFWREGGFDSVLAAVEL 136
                                       56666665..7**************************************************************9988 PP

                                       EECCCCCCCHC- CS
                   Glycos_transf_2 119 ifgetdeiernk 130
                                        +++++   +  
  gi|557694926|ref|YP_008797980.1| 137 EESKRFGSIKLD 148
                                       887777666655 PP

>> SHR3_chaperone  ER membrane protein SH3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.6e-05      0.14      98     138 ..     167     207 ..     163     212 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.6e-05
                    SHR3_chaperone  98 vgvvvyitnivkglrtvtegawgevdredslkvlaasntil 138
                                       +g+ ++ +ni k+l++v  ++ ge++ +d ++ laa   i+
  gi|557694926|ref|YP_008797980.1| 167 AGIYIFSKNIFKALEMVGFSERGEIELTDAVNQLAAQGHIV 207
                                       699*********************************98876 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 ?   -1.4   0.1      0.79     2e+03      25      32 ..     164     171 ..     160     172 .. 0.84
   2 ?   10.9   0.9   0.00011      0.28       2      32 ..     242     274 ..     241     275 .. 0.87
   3 ?    1.4   0.0      0.11   2.7e+02       7      29 ..     300     306 ..     279     309 .. 0.54
   4 ?    1.8   0.1     0.083   2.1e+02       7      24 ..     300     318 ..     299     326 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.79
                                       EE-TT-EE CS
                         Hexapep_2  25 vvgaGvvi 32 
                                       +v aG++i
  gi|557694926|ref|YP_008797980.1| 164 IVNAGIYI 171
                                       7999*998 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00011
                                       EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
                         Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvgaGvvi 32 
                                       ++I + +++G + +   +v ++++cv+++G+v+
  gi|557694926|ref|YP_008797980.1| 242 ISIDEGTVLGEDVELngPVMVEEGCVIESGSVL 274
                                       678888999999998855*************98 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.11
                                       T-EE-TT-EESEEE-TT-EE-TT CS
                         Hexapep_2   7 nCliGanagiGvslGdncvvgaG 29 
                                        C++G+                G
  gi|557694926|ref|YP_008797980.1| 300 KCFLGP----------------G 306
                                       344444................4 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.083
                                       T-EE-TT-E.ESEEE-TT- CS
                         Hexapep_2   7 nCliGanag.iGvslGdnc 24 
                                        C++G+ +  +   lG+++
  gi|557694926|ref|YP_008797980.1| 300 KCFLGPGSHlVNSVLGEGS 318
                                       6999998864444455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); 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: 0.49u 0.20s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2666.71
//
Query:       gi|557694927|ref|YP_008797981.1|  [L=335]
Description: diphthine synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   86.0   0.0    4.9e-24   85.4   0.0    1.2  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
    1.4e-11   44.3   0.7    1.5e-10   41.0   0.3    2.7  3  DUF357        Protein of unknown function (DUF357)


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 !   85.4   0.0   5.5e-28   4.9e-24       2     207 ..       3     215 ..       2     220 .. 0.75

  Alignments for each domain:
  == domain 1  score: 85.4 bits;  conditional E-value: 5.5e-28
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal.aealr 77 
                                       l++VG G+G  e+lT++Al+++k+a+ ++ d+ +++ ++ d+ ++   l++  g+ +   ++  e+++ +l  ea++
  gi|557694927|ref|YP_008797981.1|   3 LTFVGGGLGRFEHLTIEALETVKNAEKIYVDT-YTSFWAADFFDK---LREAAGHVVAADRKMLEDNVHKLvSEAVE 75 
                                       89***************************999.988888888876...45555555555555577777777366666 PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerel 154
                                       +   +vll++GDP++++t+ ++   l+  +++++v+v+ Gvs+++aa +++g++++++g++ ++  ++++ +   e+
  gi|557694927|ref|YP_008797981.1|  76 NE--IVLLTPGDPFIATTHLAIR-TLAH-RKNVSVKVVHGVSAVSAAVSSSGLHIYKFGKTATIP-KTTDSNMLNEI 147
                                       65..*****************97.5554.589*********************************.33333333333 PP

                      TP_methylase 155 eallan.....gdtlvllkaprk...laelaelL....kea...lyddttpvavveragtedervvrg 207
                                        + +++      +tl+ll++ ++   ++e++++L    k++   + + +t +++ +r+g +d  +  +
  gi|557694927|ref|YP_008797981.1| 148 FKTIETnlsnnLHTLLLLDTSDNgltIPEAVKQLldysKQHgknFINQNTLMVALARLGFPDNMTLAA 215
                                       333333466679******88886778888888884444333555677777888888888877665555 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.51   4.6e+03       3      16 ..      14      27 ..      12      41 .. 0.66
   2 ?   -0.6   0.0      0.16   1.5e+03      39      57 ..     187     205 ..     168     207 .. 0.80
   3 !   41.0   0.3   1.7e-14   1.5e-10      28      69 ..     286     327 ..     267     330 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.51
                                      HHHHHHHHHHHH.. CS
                            DUF357  3 irlleealekvkia 16
                                      + l+ eale+vk a
  gi|557694927|ref|YP_008797981.1| 14 EHLTIEALETVKNA 27
                                      55666777777733 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.16
                                       HHHHHHHHTT-HHHHHHHH CS
                            DUF357  39 eDakyflekgdlvnAlasf 57 
                                       + +k f++++ l+ Ala +
  gi|557694927|ref|YP_008797981.1| 187 QHGKNFINQNTLMVALARL 205
                                       56999*****999999976 PP

  == domain 3  score: 41.0 bits;  conditional E-value: 1.7e-14
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHH CS
                            DUF357  28 eevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagar 69 
                                        ++l  + +Y+eDa++f++ g +v+Al ++ YaeG+LDa++ 
  gi|557694927|ref|YP_008797981.1| 286 TDYLGYVSRYVEDAERFVKDGNMVDALLAIGYAEGLLDALRL 327
                                       67888899*******************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2624.25
//
Query:       gi|557694928|ref|YP_008797982.1|  [L=151]
Description: glycerol-3-phosphate cytidylyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-18   65.3   0.0    9.4e-18   64.8   0.0    1.2  1  CTP_transf_like  Cytidylyltransferase-like
      1e-06   28.7   0.4    7.4e-06   25.9   0.3    2.1  2  FAD_syn          FAD synthetase


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 !   64.8   0.0   1.1e-21   9.4e-18       1     143 []       7     140 ..       7     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.1e-21
                                       EEEE--TT--HHHHHHHHHHHHHSSES..EEEEEESSTHCSST-..SCSSTHHHHHHHHHHHTTCTTEEEEEEESEH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleed..livgvpsdeppkkkk..kplasaeeRlemlelakevdevisvdpwelt 73 
                                       l+ G FD++HlGH+ +l+ akkl +    l+v v+sd++++++k   p++ a eR +ml+ +k vdev+   + ++ 
  gi|557694928|ref|YP_008797982.1|   7 LTTGAFDILHLGHMLMLKDAKKLAGPRgkLVVVVASDKTVRRNKgrAPIFGARERKKMLQFLKPVDEVLIGYDPVSF 83 
                                       578****************************************669*********************9988877777 PP

                                       HHHHHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHHH CS
                   CTP_transf_like  74 revlkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkirer 143
                                        ++l+k +pd  ++++g d+ + +    ++ +  +++k+ v+        v+++++ + n++Ss+++ +r
  gi|557694928|ref|YP_008797982.1|  84 EKILRKVRPD--IVAFGYDQRK-I--RDQFLRFCRERKVKVR--------VVTLRKHNVNPVSSSDVVKR 140
                                       78********..*****99733.3..4455555555555555........5568889999******9876 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.3   8.3e-10   7.4e-06       6      80 ..       3      74 ..       1     136 [. 0.82
   2 ?    0.7   0.0     0.047   4.2e+02      28      71 ..     107     150 ..     101     151 .] 0.72

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 8.3e-10
                           FAD_syn  6 egavvtlGnFDGvHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelg.vdav 80
                                      +++v+t G+FD +HlGH  +lk+a+++a  +g  +vvv  ++    +++++k +a +   +e+ ++l+ l  vd+v
  gi|557694928|ref|YP_008797982.1|  3 SRTVLTTGAFDILHLGHMLMLKDAKKLAGPRGKLVVVVASDK----TVRRNKGRAPIFGARERKKMLQFLKpVDEV 74
                                      689*****************************9999987554....444455555667777776666655446655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.047
                           FAD_syn  28 kaveaakekglpsvvvtFephPrevlakekaparLttleeklel 71 
                                       + ++  +e+++++ vvt  +h  + +++++   r+ +l +++++
  gi|557694928|ref|YP_008797982.1| 107 QFLRFCRERKVKVRVVTLRKHNVNPVSSSDVVKRVLSLGKRVRR 150
                                       56666788888899999888888888866666667777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1197.23
//
Query:       gi|557694929|ref|YP_008797983.1|  [L=199]
Description: riboflavin kinase, archaea type [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   98.5   0.1    3.8e-28   98.0   0.1    1.2  1  CTP-dep_RFKase  Domain of unknown function DUF120
    0.00053   19.9   0.7     0.0011   18.9   0.7    1.6  1  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0019   18.1   0.4     0.0037   17.1   0.4    1.5  1  MarR            MarR family
     0.0065   16.3   0.9      0.011   15.6   0.4    1.6  2  MarR_2          MarR family
  ------ inclusion threshold ------
      0.085   13.2   0.2       0.17   12.3   0.2    1.5  1  Rrf2            Transcriptional regulator
       0.12   12.5   0.2       0.29   11.2   0.2    1.7  1  HTH_20          Helix-turn-helix domain


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 !   98.0   0.1   1.3e-31   3.8e-28       1      96 [.      99     196 ..      99     198 .. 0.95

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 1.3e-31
                                       EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCC.GHHHHCHHHHS--EEE--EEETTEEE--EEEEEEE CS
                    CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldee.slelrkaleklkgieiegfedeertfgavkvypak 76 
                                       V++G geG yy+sl+ y +q++eklgf pypGTLN++l ++ s+e++  l+k+  iei+gf+de+rt+g+vk+++++
  gi|557694929|ref|YP_008797983.1|  99 VFTGYGEGVYYMSLPNYVKQMQEKLGFIPYPGTLNITLLSKdSIENKMLLQKYADIEIHGFRDEKRTYGDVKAVRVT 175
                                       799**********************************99888*********************************** PP

                                       ECCE.EEEEEEESS-SS.TTE CS
                    CTP-dep_RFKase  77 ieki.kaavvvperthyeedv 96 
                                       ++++ +a++++pert y+++v
  gi|557694929|ref|YP_008797983.1| 176 VNDTePAYMIFPERTLYDNSV 196
                                       **654899*********9986 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 !   18.9   0.7   3.6e-07    0.0011       5      54 ..       9      58 ..       8      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.6e-07
                                      HHHHHHHCTTTC.EEEEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2  5 rfLlrlaeragg.eielpltqeelAsmlGltretvsrilseLkreglisrg 54
                                      r+L++lae  g+ +  l++t   l++   +++++ sr+l  L++egli+r+
  gi|557694929|ref|YP_008797983.1|  9 RVLIYLAEA-GAiTSSLKITTPILSRQFSTSQQSASRLLILLEKEGLIERR 58
                                      568888775.5566789********************************64 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   1.2e-06    0.0037       8      50 ..      10      58 ..       7      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
                                      HHHHHHHSTTEEHH......HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  8 iLrilyeqgplsvs......eLakklgvskstvtrvldrLekkGlieRs 50
                                      +L  l+e g+++ s       L +++++s+ +++r+l  Lek+GlieR+
  gi|557694929|ref|YP_008797983.1| 10 VLIYLAEAGAITSSlkittpILSRQFSTSQQSASRLLILLEKEGLIERR 58
                                      7888889999998888888899**************************6 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   3.6e-06     0.011      10      54 ..      10      58 ..       7      64 .. 0.79
   2 ?   -3.6   0.0       3.6   1.1e+04      23      31 ..      69      77 ..      66      89 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.6e-06
                                      HHHHHHCTTTS.....EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 10 vLaaLgrrpgr.....dltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      vL +L+ ++       ++t   l r +  s++++sr+l  L++ GL+err
  gi|557694929|ref|YP_008797983.1| 10 VLIYLAEAG-AitsslKITTPILSRQFSTSQQSASRLLILLEKEGLIERR 58
                                      666666655.34665556777799999**********************9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.6
                                      EHHHHHHHH CS
                            MarR_2 23 tvgelarrl 31
                                      t++ +ar l
  gi|557694929|ref|YP_008797983.1| 69 TQKGVARLL 77
                                      444444433 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.2   5.7e-05      0.17      12      57 ..       9      57 ..       3      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.7e-05
                                      HHHHHHHHSSTCC-...B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 12 hallyLakeeeeep...vsseeiaerqnispsylekilakLrkaglvks 57
                                      ++l+yLa+    ++   +++  +++++++s++ ++++l  L+k+gl++ 
  gi|557694929|ref|YP_008797983.1|  9 RVLIYLAEAGAITSslkITTPILSRQFSTSQQSASRLLILLEKEGLIER 57
                                      6899998876654444599999*************************85 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   9.8e-05      0.29      30      61 .]      31      62 ..       6      62 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.8e-05
                                      HHHHHTS-HHHHHHHHHHHHHCTTEEEECTEE CS
                            HTH_20 30 laerldlskntlsyHLrvLeeagLvevvregr 61
                                      l +++++s++++s+ L  Le+ gL+e++ +gr
  gi|557694929|ref|YP_008797983.1| 31 LSRQFSTSQQSASRLLILLEKEGLIERRVVGR 62
                                      789999**********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 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:                         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 0.28s 00:00:00.68 Elapsed: 00:00:00.57
# Mc/sec: 1055.10
//
Query:       gi|557694930|ref|YP_008797984.1|  [L=201]
Description: proteasome beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-47  161.6   0.3    1.7e-47  161.4   0.3    1.0  1  Proteasome  Proteasome subunit
     0.0074   16.8   0.0        0.7   10.5   0.0    2.2  2  ATP-cone    ATP cone domain


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 !  161.4   0.3   1.9e-51   1.7e-47       4     187 ..       9     185 ..       6     187 .. 0.97

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 1.9e-51
                                       S-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTC CS
                        Proteasome   4 GttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrpip 80 
                                       G t++Gi+gkd vv+aa+kr  +g  ++sk+ ++K+fki++ +g+a+aG +aD++++++ + a ++lyrl+ g +++
  gi|557694930|ref|YP_008797984.1|   9 GATTLGIRGKDSVVIAAEKRFAYGYFVMSKQ-ARKVFKISNSVGAACAGVVADMQNMIKEVTAVVNLYRLEQGVEPS 84 
                                       89*************************7777.8******************************************** PP

                                       HHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHSTT CS
                        Proteasome  81 verlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyked 157
                                       v+     va+ l+ +++ ++  p+ ++++++g+d +g p++  +dp Gs+ie++ ++++G+g+e+a +++e++y++d
  gi|557694930|ref|YP_008797984.1|  85 VK----TVAKILSWNLFGNRYFPYFMETIVGGIDSQG-PHVIVLDPLGSMIEDD-YAVVGTGAEVAVGVIENLYRKD 155
                                       **....****************************888.***************6.********************** PP

                                       BSHHHHHHHHHHHHHHHHHHBTTSCSSEEE CS
                        Proteasome 158 ltleeavelavkalkealerdklsgkniev 187
                                       ++ +e+ +la ka+k+++ rd+ sg++i++
  gi|557694930|ref|YP_008797984.1| 156 MSATEIRDLATKAIKASIARDAGSGNGIDL 185
                                       ***************************986 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   7.8e-05       0.7      14      71 ..      42     102 ..      37     110 .. 0.78
   2 !    4.2   0.0     0.007        63      42      66 ..     146     170 ..     131     179 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 7.8e-05
                                       -HHHHHHHHHHHHHH-HHHHHHHHHHHHHHH.HHHHIIT..-BHHHHHHHHHHHHHHSS-H CS
                          ATP-cone  14 dvekIkraiekAcegseeeideiaeeveaev.rkrlrdg..isteeIqdlvektliehpdy 71 
                                       +v kI +++ +Ac g+ ++++++++ev a v   rl+ g  +s++ + +++  +l  ++++
  gi|557694930|ref|YP_008797984.1|  42 KVFKISNSVGAACAGVVADMQNMIKEVTAVVnLYRLEQGvePSVKTVAKILSWNLFGNRYF 102
                                       578************9999999999998888645566666699999999988777766665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.007
                                       HHHHHHHIIT-BHHHHHHHHHHHHH CS
                          ATP-cone  42 aevrkrlrdgisteeIqdlvektli 66 
                                         +++ +r+++s  eI+dl  k+++
  gi|557694930|ref|YP_008797984.1| 146 GVIENLYRKDMSATEIRDLATKAIK 170
                                       4567889999********9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1415.49
//
Query:       gi|557694931|ref|YP_008797985.1|  [L=360]
Description: RNA 3'-terminal phosphate cyclase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-75  252.0   0.3    4.1e-75  251.8   0.3    1.0  1  RTC         RNA 3'-terminal phosphate cyclase
    8.7e-19   68.0   0.1    1.5e-18   67.2   0.1    1.4  1  RTC_insert  RNA 3'-terminal phosphate cyclase (RTC), insert d
  ------ inclusion threshold ------
      0.056   12.9   0.0      0.083   12.3   0.0    1.2  1  APCDDC      Adenomatosis polyposis coli down-regulated 1


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 !  251.8   0.3   6.9e-79   4.1e-75       1     220 [.      11     335 ..      11     337 .. 0.99

  Alignments for each domain:
  == domain 1  score: 251.8 bits;  conditional E-value: 6.9e-79
                                       STTTSTHHHHHHHHHHHHH---EEEESTTTTSSS-S--HHHHHHHHHHHHHHT-EEE--STT-SEEEEE------SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC   1 lgegGgqiLRtalaLsaltgkpvrIenIRanRkkPGLraqhltavrllakitnaevegaeigsteleFkPgeikage 77 
                                       +gegGgq+LR ala+sa++++p++++nIR++R++PGLr+qhltavr+++  +++ev++a++gste+ F+Pg+i+  +
  gi|557694931|ref|YP_008797985.1|  11 IGEGGGQVLRVALAISAIIERPLHVYNIRKKRSNPGLRNQHLTAVRAVQLACGGEVRNAHVGSTEIFFSPGRITVDS 87 
                                       58*************************************************************************** PP

                                       EEEEEESSEBHHHHHHHHHHHHTTSSS-EEEEEEEBSBBTTS--HHHHHHTHHHHHHHHT.-EEEEEEEE--BTTTB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC  78 yevdigtAGsitlllqtllplllfakkpseltlkGgTnvsaapsvdylktvllpllkrfgvlelelelkkrGfypkG 154
                                       + +d+gtAGs++l+lq l+p+l fak++++ +++GgTn+++ap+++y++++++++l+ +g +e+ l+l +rGfyp+G
  gi|557694931|ref|YP_008797985.1|  88 LLLDTGTAGSTSLVLQSLIPVLCFAKARTQFRIRGGTNNPNAPTFEYFQQIFFHFLQTIG-VECGLRLLRRGFYPRG 163
                                       ************************************************************.7*************** PP

                                       -EEEEEEEE-.-S---EB........................................................... CS
                                       xxxxxxxxxxxxxxxxxx........................................................... RF
                               RTC 155 gGevelevepskklkpie........................................................... 172
                                       gGeve  + p+kk+++++                                                           
  gi|557694931|ref|YP_008797985.1| 164 GGEVEGYIIPVKKISAFSlterpqltkvsihaytsrlpahvakrmaesckqrlqaeditvietreevltesmhncai 240
                                       **********99999999*********************************************************** PP

                                       ...............................................BSS-HHHHHHHHHHHHHHT.-EEEEESS-- CS
                                       ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               RTC 173 ...............................................acvDehlqdqlilfmaLakgksrirvaelt 202
                                                                                      a+vD+hl d+l++++aLa+g s++rv+ lt
  gi|557694931|ref|YP_008797985.1| 241 dpgagifvagefdtirigvdklgekgvpaekvgqeaaesflkeyrsgAPVDTHLGDMLVIYAALAEGVSTYRVSTLT 317
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHSS-EE CS
                                       xxxxxxxxxxxxxxxxxx RF
                               RTC 203 lhtetairvieqflgvkf 220
                                       +ht t i+v++ +l++k 
  gi|557694931|ref|YP_008797985.1| 318 MHTLTSIEVCKALLEIKA 335
                                       **************9985 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 !   67.2   0.1   2.5e-22   1.5e-18       2     102 ..     184     284 ..     183     285 .. 0.89

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 2.5e-22
                                       S----SEEEEEEEEESS-THHHHHHHHHHHHHHTTT.SSEEEEEEE..EE-CGGC-SS-EEEEEEEEE-T.TS-EEE CS
                        RTC_insert   2 drGrvkrirGvafaarvspsvanrmveaargvLnkl.lpdvyiytdv.vkegkesgkspGfgisLvaetttegvllg 76 
                                       +r ++ ++++ a+++r++++va+rm+e+++++L++  +  ++   +v +++  +++  pG+gi++  e++t  +++g
  gi|557694931|ref|YP_008797985.1| 184 ERPQLTKVSIHAYTSRLPAHVAKRMAESCKQRLQAEdITVIETREEVlTESMHNCAIDPGAGIFVAGEFDT--IRIG 258
                                       78899****************************9984556666666666677779999***********76..**** PP

                                       EEEEE-TT--HHHHHHHHHHHHHHHH CS
                        RTC_insert  77 aealgekgvppedvGeeaaeeLleei 102
                                       ++ lgekgvp+e+vG+eaae +l+e 
  gi|557694931|ref|YP_008797985.1| 259 VDKLGEKGVPAEKVGQEAAESFLKEY 284
                                       ***********************985 PP

>> APCDDC  Adenomatosis polyposis coli down-regulated 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.4e-05     0.083      96     151 ..     187     238 ..     178     287 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.4e-05
                            APCDDC  96 qlhkvkivphseevaeklakrlnksCsgllkkerpyvpellyelleksekaesrdC 151
                                       ql+kv+i++++++   ++akr+ +sC++ l++e+  v e+  e l++s     ++C
  gi|557694931|ref|YP_008797985.1| 187 QLTKVSIHAYTSRLPAHVAKRMAESCKQRLQAEDITVIETREEVLTESM----HNC 238
                                       89************************88877777777776666666322....344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2693.22
//
Query:       gi|557694932|ref|YP_008797986.1|  [L=171]
Description: nicotinamide-nucleotide adenylyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.0    1.1e-11   45.1   0.0    1.9  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.13   12.1   0.0       0.23   11.3   0.0    1.4  1  FAD_syn          FAD synthetase


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 !   45.1   0.0   1.2e-15   1.1e-11       1      59 [.       5      62 ..       5     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.2e-15
                                      EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHH.T CS
                   CTP_transf_like  1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlela.k 59
                                      l+ G+F+p+HlGHlr +e ++k+ +e li+g+ s++ ++   +++++a eR+e + +  +
  gi|557694932|ref|YP_008797986.1|  5 LFIGRFQPFHLGHLRAVEHILKKEDE-LIIGIGSAQYSHTP-ENPFTAGERIEIIMKSlR 62
                                      699***********************.************99.***********9876644 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.6e-05      0.23      11      61 ..       6      55 ..       2      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.6e-05
                           FAD_syn 11 tlGnFDGvHlGHqallkkaveaakekglpsvvvtFephPrevlakekapar 61
                                       +G F  +HlGH   +++++++ +e  + +    +++ P++ +++  ++ +
  gi|557694932|ref|YP_008797986.1|  6 FIGRFQPFHLGHLRAVEHILKKEDELIIGIGSAQYSHTPENPFTAG-ERIE 55
                                      69*************************************9999953.3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1255.25
//
Query:       gi|557694933|ref|YP_008797987.1|  [L=263]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-72  242.6   0.1    4.1e-72  242.4   0.1    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 !  242.4   0.1   2.3e-76   4.1e-72       1     234 [.       6     256 ..       6     257 .. 0.92

  Alignments for each domain:
  == domain 1  score: 242.4 bits;  conditional E-value: 2.3e-76
                                       EEEEESSTSSSSHHHHHHHHHHHH-TTSEEEEEES-S-TT-HHHHHHHHHHHHGGS-TTEEEEEE--TTTTSS--EE CS
                   SAM_adeno_trans   1 itLlTDFGlkdpyvgamkgvilsiapdarivDitHdippfdvreaaflLaaalpyfpkgtvhlavVDpgvgterral 77 
                                       ++LlTD+G  d+yv+ +k+ il++ pd+ +vDitH++ p++++++aflL+ a+++fp++t+++avVDpgvg er +l
  gi|557694933|ref|YP_008797987.1|   6 VALLTDYGDMDTYVAEVKATILRETPDVVLVDITHQVHPQNIMQGAFLLMLAAKSFPSNTIFVAVVDPGVGGERASL 82 
                                       68*************************************************************************** PP

                                       EEEETTS.EEEEESSSTTHHHH...SEEEEEEGSSCC...--TS-HHHHTHHHHHHHHHCT--GGGCSEEESGGGS- CS
                   SAM_adeno_trans  78 vveakgg.yfvgPDNGlltlal...lleeaveieeee...ssatFhgrDvFapvaarlaagvsleelgeeldpeelv 147
                                        ve+ +g +f+gPDNGll +a+   +++++++i++e    +s+tFhgrDvFa+va   aa +++++l e++ +  +v
  gi|557694933|ref|YP_008797987.1|  83 FVETTSGkIFIGPDNGLLYPAAareKIRQVFRIKTELipnVSNTFHGRDVFAYVAGLAAADKDISHLTEPYVS--MV 157
                                       ****9988**************88877999999866699999**************99999********9987..55 PP

                                       SSS....E..CSCEEEEEEEE-TTS-EEEEEE...EHHHHHTTCEE......EEEEE.SSGGGSTTTSEEEEE-TTS CS
                   SAM_adeno_trans 148 rle....e..derlegevlyvDrFGNvitniskelleelekerkva......klkkv.etyaevaegellalvnssg 211
                                       +l+       d+r++   l+vDrFGNvit i+++l +++ k++  +      ++  v + yaev+ ge+++lv+ +g
  gi|557694933|ref|YP_008797987.1| 158 QLQiprpVlgDDRVDSVALHVDRFGNVITCIEGALPRDWLKAEV-YvndewrTVAAVgRFYAEVEIGEPILLVGGTG 233
                                       555546525689999999********************988766.2356778666777******************* PP

                                       EEEEEETTC-HHHHHT--TT-EE CS
                   SAM_adeno_trans 212 lleiavnkgsaaellglkvgdev 234
                                       +le+++n+g+a++++g+k+gd++
  gi|557694933|ref|YP_008797987.1| 234 YLELSINRGNASTTFGIKPGDKI 256
                                       *********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 00:00:00.41
# Mc/sec: 1925.97
//
Query:       gi|557694934|ref|YP_008797988.1|  [L=118]
Description: peptidyl-tRNA hydrolase, PTH2 family [Candidatus Caldiarchaeum subterraneum]
Scores for 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  139.4   0.0    6.9e-41  139.2   0.0    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2


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 !  139.2   0.0   3.8e-45   6.9e-41       2     117 .]       5     118 .]       4     118 .] 0.98

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 3.8e-45
                                       EEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-SE CS
                              PTH2   2 kmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglpa 78 
                                       k+v+vvr+DL ms Gk aaq++hAav ++++++++ ++ e++++W e+gqkk+vl+v+seeeL ++aa++ ++glp 
  gi|557694934|ref|YP_008797988.1|   5 KQVIVVRSDLRMSVGKTAAQAGHAAVLALERTRRM-RP-EWVRNWFETGQKKVVLRVSSEEELRRIAAECSRRGLPW 79 
                                       9*********************************9.88.8************************************* PP

                                       EEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                              PTH2  79 alirDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                       ++++Dag t+++pgt+T+l+igPap+++vdkvtg+L ll
  gi|557694934|ref|YP_008797988.1|  80 EIVEDAGLTELPPGTATALGIGPAPDEEVDKVTGSLPLL 118
                                       ************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 899.94
//
Query:       gi|557694935|ref|YP_008797989.1|  [L=227]
Description: rhomboid family protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-35  120.6  15.2    5.6e-35  120.6  15.2    2.0  2  Rhomboid  Rhomboid family
  ------ inclusion threshold ------
      0.015   15.8   3.2      0.015   15.8   3.2    3.0  3  DUF1751   Eukaryotic integral membrane protein (DUF1751)


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 ?    1.9   0.2     0.022     2e+02      99     117 ..      15      31 ..       5      48 .. 0.61
   2 !  120.6  15.2   6.2e-39   5.6e-35       5     148 ..      55     219 ..      51     221 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.022
                                       ---HC...CCCCCCCCCCH CS
                          Rhomboid  99 kliiallllllfillnlvl 117
                                       ++i+    +++++++n+v+
  gi|557694935|ref|YP_008797989.1|  15 VIIV--ANIVVWLFINIVF 31 
                                       3333..3666666666665 PP

  == domain 2  score: 120.6 bits;  conditional E-value: 6.2e-39
                                       C-TTHHHHGGG--SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-S.............. CS
                          Rhomboid   5 gelwrlltsmflHagwlHllfNmlallvfGsplerrlGslrflllyllsglagsllsllfsaeses........... 70 
                                       + l  l+++mf+H+++lH+++Nm+al++fG  +e+rlGs+ fl++y+lsg++++++++++ a  +s           
  gi|557694935|ref|YP_008797989.1|  55 QNLLSLISYMFIHVDFLHIFLNMYALFLFGRDVEERLGSALFLVVYFLSGVVAAVFHMIYYAVFMSlecspfvrplp 131
                                       56789**********************************************************999*********** PP

                                       .....-EESSHHHHHHHHHHHHHHHHCCCCGS----HC........CCCCCCCCCCHHHCTSSSTTTHHHHHHHHHH CS
                          Rhomboid  71 .....plvGaSGaifgllgallvlvprnrkllrkliia.....llllllfillnlvlgllpraggvsnlAHlgGlla 137
                                            p++GaSGaifg++g++lv++pr++  ++  +i+      ++++++il++++++l+ +++ +++ AH+gG++a
  gi|557694935|ref|YP_008797989.1| 132 avcvvPAIGASGAIFGIMGSYLVFFPRRPLAAFLYLIPiiapaYIVIAFIILIQTFFMLTMPFSTIAYTAHVGGFIA 208
                                       ******************************9998888889999999**************999************** PP

                                       HHHHHHHHCCH CS
                          Rhomboid 138 Glllgllllrr 148
                                       Gll++l +++r
  gi|557694935|ref|YP_008797989.1| 209 GLLTSLPFRNR 219
                                       ***99988765 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   1.0      0.19   1.7e+03      53      71 ..      14      32 ..      11      47 .. 0.61
   2 ?   15.8   3.2   1.7e-06     0.015       8      76 ..      57     121 ..      48     153 .. 0.82
   3 ?   -0.1   1.9      0.16   1.4e+03      47      79 ..     161     192 ..     138     214 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.19
                           DUF1751 53 vvnvitnllvvlltlllyl 71
                                      +v +++n++v+l+  ++++
  gi|557694935|ref|YP_008797989.1| 14 FVIIVANIVVWLFINIVFT 32
                                      4555667777666555443 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.7e-06
                           DUF1751   8 pwtlltasfveqnvwkvlvslltlllggkylErlWgskEllkFilvvnvitnllvvlltlllylvtkse 76 
                                         +l+ ++f+ + ++++ +++ +l+l+g+ +E+  gs  +    lvv ++++++++++++++y+v+ s 
  gi|557694935|ref|YP_008797989.1|  57 LLSLISYMFIHVDFLHIFLNMYALFLFGRDVEERLGSALF----LVVYFLSGVVAAVFHMIYYAVFMSL 121
                                       568999***************************9998644....5556666666666666666666554 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.16
                           DUF1751  47 llkFilvvnvitnllvvlltlllylvtkseell 79 
                                       l+ F+ ++ +i+   +v++ ++l  ++   + +
  gi|557694935|ref|YP_008797989.1| 161 LAAFLYLIPIIAPAYIVIAFIILIQTFFMLT-M 192
                                       5556555555555555544444444444444.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1629.11
//
Query:       gi|557694936|ref|YP_008797990.1|  [L=168]
Description: NADH dehydrogenase I subunit B [Candidatus Caldiarchaeum subterraneum]
Scores for 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-27   94.8   0.0    4.5e-27   94.4   0.0    1.1  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 !   94.4   0.0   2.5e-31   4.5e-27       3     129 ..      47     156 ..      46     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 94.4 bits;  conditional E-value: 2.5e-31
                                       HHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEE CS
                       Oxidored_q6   3 GcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviav 79 
                                       +cs++++a++++ +d      +r+++    +++    +   ++ dvlvveG+vt+k++++l+l++++++++k+via+
  gi|557694936|ref|YP_008797990.1|  47 CCSVEFAATHSPRYDP-----ERFGWLP--ATG----SL--RQSDVLVVEGTVTSKMAQRLRLVYDQMPEPKWVIAM 110
                                       49*************9.....8887644..444....12..389********************************* PP

                                       SHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHH CS
                       Oxidored_q6  80 GtCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetll 129
                                       G+CA++GG++a  + +  +  ++++++ +pvd+++pGCPp+p ++++++l
  gi|557694936|ref|YP_008797990.1| 111 GACAISGGLYAKDS-Y-NV--IQGIDDILPVDVYVPGCPPNPSTFFQAIL 156
                                       **********5544.3.34..579***********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1329.75
//
Query:       gi|557694937|ref|YP_008797991.1|  [L=161]
Description: NADH dehydrogenase I subunit C [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-35  122.6   0.0    1.7e-35  122.3   0.0    1.1  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
      0.095   13.0   0.2       0.14   12.4   0.2    1.2  1  RVT_N           N-terminal domain of reverse transcriptase
       0.16   11.8   0.1        8.2    6.3   0.0    2.1  2  Imm61           Immunity protein 61


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 !  122.3   0.0   2.8e-39   1.7e-35       1     120 [.      33     160 ..      33     161 .] 0.90

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 2.8e-39
                                       EE--HHHHHHHHHHHHH...TT--EEEEEEEEETT.....SSSEEEEEEEE--S-.....-EEEEEE....-S-BEE CS
                    Complex1_30kDa   1 lvvepedllevakflkdeeelgfdvlsdltavDek.....eerfevvyhllslekn....erirvkvevdeeepevp 68 
                                       +vv++++l++va+fl+d+  +g+d++  +t+vD +     e+++e++yhl s+++       i + +++d+++p++p
  gi|557694937|ref|YP_008797991.1|  33 IVVDAASLVAVARFLRDN--YGLDHVKAVTGVDLSrllkkEDKIEIIYHLGSYTRPelatADIALSTKLDKKSPRMP 107
                                       5899*************5..9************43455569************76667779999***9999****** PP

                                       --TTT-STHHHHHHHHHHHSHHBCTTSSTSS-SSSSTTS.SS-TTSTTS---- CS
                    Complex1_30kDa  69 SvtdlfpgadwyEREayDmfGivfeghpdlrrillpedf.eghPLRkdfplsg 120
                                       S++d++p+++++ERE+y+mfG+vfeghpdlrr+llpe +    P+ k+++ +g
  gi|557694937|ref|YP_008797991.1| 108 SLIDVWPSVEFHEREVYEMFGVVFEGHPDLRRLLLPEYWsDIPPMLKEYEPPG 160
                                       ***************************************5556*****98765 PP

>> RVT_N  N-terminal domain of reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   2.3e-05      0.14      11      83 .]       7      80 ..       3      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                             RVT_N 11 kkVfkLqkrIykAsqegdikkvkkLqklLtkSlsakllAvrrVtqdnkg....kktagvDgvksltpkerlelveeL 83
                                      + V+ L ++  kA  e+ ++  +kL k+++   +a l+Av r   dn g    k  +gvD    l++++++e++ +L
  gi|557694937|ref|YP_008797991.1|  7 TVVQELENKFGKALLEKAVD-TRKLVKIVVD--AASLVAVARFLRDNYGldhvKAVTGVDLSRLLKKEDKIEIIYHL 80
                                      67888888888888877665.5888888887..578*************9999999****************99876 PP

>> Imm61  Immunity protein 61
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0    0.0076        45      45      71 ..      27      53 ..       3      96 .. 0.71
   2 ?    6.3   0.0    0.0014       8.2      56      93 ..     114     151 ..      92     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0076
                                      TT---EEEEEESSHHHHHHHHHHHHHH CS
                             Imm61 45 raeeeevvlaAasldvverylwgllgd 71
                                        +  ++v+ Aasl +v+r+l +  g 
  gi|557694937|ref|YP_008797991.1| 27 TRKLVKIVVDAASLVAVARFLRDNYGL 53
                                      44444589999********99888774 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0014
                                       SSHHHHHHHHHHHHHHHHHHHTT---EE---SGGGS-T CS
                             Imm61  56 asldvverylwgllgddvrekreLprlklPvsaedias 93 
                                       +s++  er  ++++g   +++ +L+rl lP  + di +
  gi|557694937|ref|YP_008797991.1| 114 PSVEFHEREVYEMFGVVFEGHPDLRRLLLPEYWSDIPP 151
                                       6788889999************************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1283.63
//
Query:       gi|557694938|ref|YP_008797992.1|  [L=405]
Description: NADH dehydrogenase I subunit D [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-77  260.7   0.0    1.4e-74  250.6   0.0    2.3  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
  ------ inclusion threshold ------
      0.015   14.2   0.0      0.052   12.4   0.0    1.7  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 !  250.6   0.0   1.6e-78   1.4e-74       2     271 .]     133     405 .]     133     405 .] 0.98

  Alignments for each domain:
  == domain 1  score: 250.6 bits;  conditional E-value: 1.6e-78
                                       TT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---T...........................THHHH CS
                    Complex1_49kDa   2 lGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpe...........................gllek 51 
                                       lG  t+fl++f +Re+++dl   + G+R+t+sy+ +GGv++D+p+                           +l + 
  gi|557694938|ref|YP_008797992.1| 133 LGNSTMFLWCFGDREYLVDLTSLIGGQRITHSYFEPGGVRNDMPSrvpqdllkefnryyrmvmgrdlpgdadQLRKY 209
                                       699********************************************************************9999** PP

                                       HHHHHHHHHHHHHHHHHHHHSSSSHHHHHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS------ CS
                    Complex1_49kDa  52 ikeflkelekkldeleklltknrifkkRtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpv 128
                                       i+ +++ ++k+ld++ +l+ +n++f++Rt++vg+l+ e+a++lg++G +lRasG+k+D R ++pY+aY++l+f++p+
  gi|557694938|ref|YP_008797992.1| 210 ITYVCECFDKRLDDYWDLFFNNELFISRTRNVGILKPEDAIKLGVVGTTLRASGIKFDNRVNNPYDAYSQLKFEIPI 286
                                       ***************************************************************************** PP

                                       -SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEE CS
                    Complex1_49kDa 129 geegDvydRylvrveEmrqSlkIieqaleklpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevy 205
                                       ge+gD+ydR +v ++Emr+S++Ii qa e +p+gpv+++++ +                        +++vp+ge++
  gi|557694938|ref|YP_008797992.1| 287 GERGDCYDRAIVGFKEMRESCRIISQAAEMMPDGPVKVKQHPI------------------------NIRVPAGEAV 339
                                       ***********************************99977665........................3579****** PP

                                       EEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 206 aavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                       a++Ea++Ge+++y+ s+g++kpyr+ki +psf  + a+++ll+ge +a ++ i+ sl++   e+DR
  gi|557694938|ref|YP_008797992.1| 340 ARTEAARGEMMYYIRSEGGDKPYRVKISTPSFRLIPAIKYLLRGEEIANIPPIYWSLNYWPVEADR 405
                                       ***************************************************************998 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   5.8e-06     0.052      35      70 ..      91     126 ..      88     130 .. 0.95
   2 ?   -1.7   0.0      0.11     1e+03     417     442 ..     332     356 ..     300     360 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.8e-06
                                       HHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHH CS
                      NiFeSe_Hases  35 vravedAlgikipknarlirnliaaalllhdhivhF 70 
                                       v ave+ +gi+ p+ a+++r ++a  + + +h+ +F
  gi|557694938|ref|YP_008797992.1|  91 VLAVEKLMGIEAPERAKYLRVIMAELQRIASHLYWF 126
                                       689******************************999 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.11
                                       GS-SEEEEEEEEEETTEEEEEEEEEE CS
                      NiFeSe_Hases 417 evpkeakGvglveapRGaLsHwikik 442
                                       +vp+  + v+ +ea+RG +  +i+ +
  gi|557694938|ref|YP_008797992.1| 332 RVPA-GEAVARTEAARGEMMYYIRSE 356
                                       3444.889999*******99999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 00:00:00.41
# Mc/sec: 2938.51
//
Query:       gi|557694939|ref|YP_008797993.1|  [L=827]
Description: DNA polymerase I [Candidatus Caldiarchaeum subterraneum]
Scores for 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-58  196.8   0.0    8.2e-58  196.2   0.0    1.2  1  DNA_pol_B       DNA polymerase family B
    1.3e-26   93.6   0.0    2.6e-26   92.6   0.0    1.5  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    4.4e-06   26.8   0.0    1.7e-05   24.9   0.0    2.1  2  RNase_H_2       RNase_H superfamily
    0.00014   21.6   0.0    0.00037   20.2   0.0    1.7  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
     0.0053   15.4   0.0       0.01   14.4   0.0    1.5  1  DUF1744         Domain of unknown function (DUF1744)
  ------ inclusion threshold ------
       0.16   11.8   0.3       0.47   10.3   0.1    1.7  2  VHS             VHS domain


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 !  196.2   0.0   2.7e-61   8.2e-58       6     426 ..     402     790 ..     397     814 .. 0.84

  Alignments for each domain:
  == domain 1  score: 196.2 bits;  conditional E-value: 2.7e-61
                                       HHHS-HHHHHHHHHHHHHHHTTBE-B-.......----.--SS............-S----BE----EEESS-EEEE CS
                         DNA_pol_B   6 vledgqqirveslLlrlakeegfilpd.......rtekkgkeee...........gYqGatVlePkkglydkpvlvl 64 
                                       v  +g +  ++ lL+ +++ ++  +p        +                    +Y Ga+V+eP  g++  +v+vl
  gi|557694939|ref|YP_008797993.1| 402 VCRHGVSGWIKNLLYWELRGRNWLIPRkdelitaK--------GgtttkaiiegkKYRGALVVEPVPGIHF-NVTVL 469
                                       56667777888899999999999999544443330........2444556666646*************96.699** PP

                                       EETTHHHHHHHHTT-STTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHH CS
                         DNA_pol_B  65 DFaSLYPsiiqahNlcyttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelk 141
                                       DFaSLYPsi+ ++Nl+++t+ +s+e+ ++ +  +            + +  ++++g+ ++++  + + R +  k ++
  gi|557694939|ref|YP_008797993.1| 470 DFASLYPSILKEYNLSFETINCSHEKCRTNNIPE-----------TTHWVCREKRGVQSSIIGVIRDIRVRWYKPMA 535
                                       *************************998655433...........2345567889999999999999****999999 PP

                                       ..CS--HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS CS
                         DNA_pol_B 142 ..eekdefekalldkqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpe 216
                                         ++ d++++  ++  Q alKv+ N+ YG++G+++ +l+c +lA+s T+iGR++  ++ e  ++             
  gi|557694939|ref|YP_008797993.1| 536 snKSLDPVTRSWYEVVQRALKVFLNASYGVLGFEEFPLYCPPLAESTTAIGRYVFSSAVEKAKSL------------ 600
                                       66778999**********************************************98776666644............ PP

                                       .....T-EEEEEBSSEEEEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEEE.TTEEEEEEEEES CS
                         DNA_pol_B 217 eaeeeklkviYGDTDSvfielkvkdveellkigkelaeevseklfkkplklefekvykkllLis.KKkYaglkvekt 292
                                            ++ v+YGDTDS+f++ + +      ++ +el +  +e +f+  l lef+kvy  +++ + KK Y g++    
  gi|557694939|ref|YP_008797993.1| 601 -----GVTVVYGDTDSIFLKAEKQ------ELVHELIRWARE-KFR--LDLEFDKVYRYVVFSKrKKNYLGVTDR-- 661
                                       .....9*************98765......466777777777.444..69************863677***9999.. PP

                                       STTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEE CS
                         DNA_pol_B 293 skanklliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskel 369
                                          + +++KG+   +r+   ++ke  +++l++l +  + +++le++ +++++++++ +++l+++ ++++++ +  ++
  gi|557694939|ref|YP_008797993.1| 662 ---GVVDVKGLTGKKRNIPVFIKEAFDDMLKQLAEV-KSAEELETVKKNIRQVIATWYSRLKNRTFEIDQLAFRVMM 734
                                       ...999***************************999.8899************************************ PP

                                       SS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTE CS
                         DNA_pol_B 370 skepenyksknlphlevakrlkkrneeapevgdrisYvivekkkevkkknllasera 426
                                       sk+ e y++++  h+++ak+l++  + ++ +gd isYv +++k+ v+  +l ++e +
  gi|557694939|ref|YP_008797993.1| 735 SKTIERYEKTTPQHVKAAKKLQSL-GVKVGPGDIISYVKTKDKDGVTPLQLAKRENI 790
                                       ********************9988.799**************998844444333333 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 !   92.6   0.0   8.8e-30   2.6e-26       4     327 ..      32     320 ..      29     328 .. 0.81

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 8.8e-30
                                       TTSEEEEEEEE---EEEEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEESSTC CS
                    DNA_pol_B_exo1   4 egksvcvnvfgfkpyfYceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvsnpn 80 
                                       +++++ ++ +g+kpy++++ p     +e++++ +  + +  + ++      +++  s+ + +++   ++ ++ ++p 
  gi|557694939|ref|YP_008797993.1|  32 NTVEIHMDSTGHKPYCLTDRP----IDELEKNQALREAGATAFIK------VTKYDSIADRMRE---MTLIQATDPL 95 
                                       56777888999********99....44455555555555544444......3333355555555...999******* PP

                                       HHHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEE.TEEEEGCC--C-.SEEEEEETTTSCEETTT.. CS
                    DNA_pol_B_exo1  81 elkkirkelspleeivdvyeydvdylerflidnkivgfgwysvk.kylvraegkisncdveidcdvddliakpke.. 154
                                       ++   +k +   +e+v+ +e+d++y+ ++++d +++++  y+ k  +l ++ g  s+ +  ++   +dl a++ e  
  gi|557694939|ref|YP_008797993.1|  96 AVGGSKKSI---RELVTAWEADIPYHLNYVYDMRLTPSMIYEKKnGMLTPVFGEKSKVENILQQFFPDLPAEEREem 169
                                       ******998...678****************************9756666666666666677788899988887777 PP

                                       ........CC.S-EEEEEEEEEETEE.TTSEETTTT..--EEEEEEEE.CCTC.SS.SEEEEEEECCCTSS----EE CS
                    DNA_pol_B_exo1 155 ........se.pplrvlsFDIecksk.kgkfpdaensedpiiqIscvl.dglgekepearklftlrecaseeeedfe 220
                                               se p ++    DIe+ s+ + k p ++n+ d++++Is+    g g       k+++lr          +
  gi|557694939|ref|YP_008797993.1| 170 ekwlrmleSEhPAVDFTGLDIEILSDsPTKVPSPSNPVDRVVAISFSGtRGMG-------KVLVLRRDG------VD 233
                                       77777775449************9872566******************9****.......888888877......23 PP

                                       --SSTCSTTEEEEEESSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHCG.SCCSCTCEECCC CS
                    DNA_pol_B_exo1 221 ltpkpeypgvkvlefdsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvklsklgrlnkggrskvs 297
                                       +t  +   +  v  fd+E +lL++ +e++ +y   +++++N+d+FDlpY+ nRa+              k g+ k++
  gi|557694939|ref|YP_008797993.1| 234 MTFNG--GEYSVEVFDDETTLLSRCFEIMDSY--PIVVTFNGDDFDLPYLRNRAE--------------KLGIPKNR 292
                                       33333..3558888******************..*********************..............88888888 PP

                                       CESEEEEEECEEEETTSEEEEHHHHHHHHS CS
                    DNA_pol_B_exo1 298 eigfskqarekvkisgrihlDlyrvvkrkl 327
                                        +      re  +++  ihlDlyr++++k+
  gi|557694939|ref|YP_008797993.1| 293 IPITL--GREGASLRRGIHLDLYRFFNNKS 320
                                       87776..6899999************9987 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       4.6   1.4e+04      33      51 ..     140     158 ..     133     183 .. 0.60
   2 !   24.9   0.0   5.7e-09   1.7e-05      43     113 ..     248     341 ..     231     377 .. 0.81

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 4.6
                         RNase_H_2  33 ltqllaeepeeekailelf 51 
                                       lt ++ e+ + e++++++f
  gi|557694939|ref|YP_008797993.1| 140 LTPVFGEKSKVENILQQFF 158
                                       5566666666666666666 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 5.7e-09
                         RNase_H_2  43 eekailelflellekkkalvtfngksFDvpflkrlfkkyklde..............eefrhiDLlkelrkkkl... 102
                                       +e+ +l+   e++  ++ +vtfng  FD+p+l+++++k  +++              ++  h+DL++ +++k +   
  gi|557694939|ref|YP_008797993.1| 248 DETTLLSRCFEIMDSYPIVVTFNGDDFDLPYLRNRAEKLGIPKnripitlgregaslRRGIHLDLYRFFNNKSVqvy 324
                                       444445444599************************999999999999999988777677*******9987776556 PP

                         RNase_H_2 103 .......esysLksveke 113
                                              e   L  v+k+
  gi|557694939|ref|YP_008797993.1| 325 afdnryrEH-TLDGVAKA 341
                                       666666333.66666666 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 !   20.2   0.0   1.3e-07   0.00037      33      79 ..     245     290 ..     204     298 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.3e-07
                    DNA_pol_B_exo2  33 eessekelikkffegvekkkpqlVsfngrgfDlpvleyralkhgvsa 79 
                                         ++e++l+++ fe+++++ p +V+fng  fDlp l  ra k g+  
  gi|557694939|ref|YP_008797993.1| 245 VFDDETTLLSRCFEIMDSY-PIVVTFNGDDFDLPYLRNRAEKLGIPK 290
                                       334599********99876.8******************98877765 PP

>> DUF1744  Domain of unknown function (DUF1744)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   3.5e-06      0.01     308     392 ..     573     648 ..     561     658 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.5e-06
                           DUF1744 308 LyDpaLrrlvqnlmkKvflqLlaefkrlgskvvyAdfnkillkTsKksvenayaYveyilkairskelFkflelkik 384
                                       Ly p L +    + + vf+  +++ k lg +vvy+d+  i+lk +K+++      v+ +++  r+k  F+ l+l+++
  gi|557694939|ref|YP_008797993.1| 573 LYCPPLAESTTAIGRYVFSSAVEKAKSLGVTVVYGDTDSIFLKAEKQEL------VHELIRWAREK--FR-LDLEFD 640
                                       8888899999999999*******************************94......33333333333..32.566666 PP

                           DUF1744 385 kyWdlLlw 392
                                       k++++ ++
  gi|557694939|ref|YP_008797993.1| 641 KVYRYVVF 648
                                       66666665 PP

>> VHS  VHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.2   6.5e+03     107     133 ..     101     125 ..      79     126 .. 0.73
   2 ?   10.3   0.1   0.00016      0.47      84     124 ..     681     721 ..     677     730 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.2
                                       HHHHHHHHHHHHHHTTT-TTGHHHHHH CS
                               VHS 107 kkkvlelleeWadafknkpelkkisdv 133
                                       kk + el+  W+ ++     l++++d+
  gi|557694939|ref|YP_008797993.1| 101 KKSIRELVTAWEADI--PYHLNYVYDM 125
                                       778889999999998..4456666665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00016
                                       SHHHHHHHHHHHHCTTTCHCS.HHHHHHHHHHHHHHHTTT- CS
                               VHS  84 skeflnelvklilekknsklakvkkkvlelleeWadafknk 124
                                       ++ f + l++l++ k++++l++vkk++ +++  W+  +kn+
  gi|557694939|ref|YP_008797993.1| 681 KEAFDDMLKQLAEVKSAEELETVKKNIRQVIATWYSRLKNR 721
                                       56799999999999**********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (827 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      799  (0.0445647); 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: 0.78u 0.30s 00:00:01.08 Elapsed: 00:00:00.46
# Mc/sec: 5431.62
//
Query:       gi|557694940|ref|YP_008797994.1|  [L=295]
Description: agmatinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  235.4   0.0    1.1e-69  235.1   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 !  235.1   0.0   5.9e-74   1.1e-69       2     277 ..      29     288 ..      28     290 .. 0.93

  Alignments for each domain:
  == domain 1  score: 235.1 bits;  conditional E-value: 5.9e-74
                                       EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHH CS
                          Arginase   2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeava 77 
                                       + +++GvP+d++ s+rpG+r GP+a+r+ sa++e+    + ++g+  +++ki+dlgd+ +++ + +++l+++e+ v+
  gi|557694940|ref|YP_008797994.1|  29 RYCVFGVPYDLTSSFRPGCRYGPEAVRRFSANIEA-N--SYRKGFdISTAKIADLGDIIFEY-KLPKMLRKVEKVVE 101
                                       5789******************************6.2..3445667999*********9996.999*********** PP

                                       HHHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEE CS
                          Arginase  78 eilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvq 154
                                        i ++gk pi++GG+Hs +++++++laek     ++i +DAH+Dlr+++  g +++h++++rr + e+++ +k +++
  gi|557694940|ref|YP_008797994.1| 102 IISASGKSPIMIGGEHSFTYSCFKSLAEK---SSCIIVLDAHFDLRDEY-LGLRFNHASYLRRLV-EKFP-NKPVAV 172
                                       ****************************8...469**************.8**************.5555.59**** PP

                                       EEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-H CS
                          Arginase 155 iGirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltl 231
                                       +G+r++d+ e ++ak++gi +i++ e+d+++  +vv+ ++e+vg  ++  y+S+DiDv+Dp ++PG+G pep Gl++
  gi|557694940|ref|YP_008797994.1| 173 LGVRGFDPAEEKFAKDHGIMYIKASEMDDRR--RVVKILEEAVG--HGRPYISVDIDVVDPGFCPGVGNPEPEGLNP 245
                                       ****************************987..59999999998..5799*************************** PP

                                       HHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                          Arginase 232 rellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                        ++++l+  l +  + +g+DvvEvnP +d+ +  ta+laar+++e 
  gi|557694940|ref|YP_008797994.1| 246 TQVIDLVSILGA-FRPAGLDVVEVNPLFDN-G-ATAALAARIIFET 288
                                       **********88.99**************9.5.8*********994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2158.75
//
Query:       gi|557694941|ref|YP_008797995.1|  [L=737]
Description: hypothetical protein CSUB_C1514 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  10.7      0.017   15.0  10.7    2.5  1  Mannosyl_trans  Mannosyltransferase (PIG-M)


Domain annotation for each model (and alignments):
>> Mannosyl_trans  Mannosyltransferase (PIG-M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0  10.7   9.2e-07     0.017       5     196 ..     139     314 ..     134     349 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.2e-07
                    Mannosyl_trans   5 GnadsivailvlltlyllekrkiasaalvlGlavhlkiYPliyalalalslskkkeqsvaakllrllkiavlvlvlv 81 
                                       G  dsi  +l+l+ + l  +rk+a++a vlG+   +k+YPl  +l+l+++++  +  s++++ll ++          
  gi|557694941|ref|YP_008797995.1| 139 GMFDSIAVALSLFGVLLAYRRKYAASAFVLGFGGAVKLYPLFLMLPLLVYMRIGERISLKKSLLTIIAC-------- 207
                                       7789*********************************************99988877887777666554........ PP

                    Mannosyl_trans  82 alisllaltlllyklYGqefleeaylYhlvrkDhrhnfslyflllYleeaskvaassilkllaflPqlvllllvslk 158
                                         +s l+l  + y       le+ ++Yh+        f  y+  l l +     a  +l+   f+  l ++   + k
  gi|557694941|ref|YP_008797995.1| 208 --VSGLILPAAPYITNPIPLLEK-LFYHFGNIG---SFT-YWTALSLVSPPA--AIPALSYGFFAAILYIVYRRTQK 275
                                       ..344444455566666666654.457776432...333.444444444443..23445555555544444444444 PP

                    Mannosyl_trans 159 f.rrnlafalfvqtfvfvtfnkvctsqYfvWylvlLpll 196
                                         r  l     ++ ++f +    + +qY +W l++L++ 
  gi|557694941|ref|YP_008797995.1| 276 SnRPSLFDLSQLTLVAFLATSAKVNVQYVLWVLPFLTIS 314
                                       424444455555566677667777777777777777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (737 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); 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:                         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 0.24s 00:00:00.89 Elapsed: 00:00:00.42
# Mc/sec: 5308.30
//
Query:       gi|557694942|ref|YP_008797996.1|  [L=151]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.1   0.0       0.12   12.4   0.0    1.9  2  TruB-C_2  Pseudouridine synthase II TruB, C-terminal


Domain annotation for each model (and alignments):
>> TruB-C_2  Pseudouridine synthase II TruB, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       0.5     9e+03      28      36 ..      36      44 ..      33      46 .. 0.70
   2 ?   12.4   0.0   6.9e-06      0.12       3      55 ..      90     139 ..      89     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.5
                          TruB-C_2 28 eglVRvyde 36
                                      eg+VR  +e
  gi|557694942|ref|YP_008797996.1| 36 EGKVRALTE 44
                                      789998744 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.9e-06
                          TruB-C_2   3 veLseesakrflqGQrvklaaglpaeglVRvydeegrFlGvGeitddgvlaPk 55 
                                       veL++e a +++ G +vk+  ++ +         ++++lG++ ++ +gv  P+
  gi|557694942|ref|YP_008797996.1|  90 VELTKEDALKWMRGDPVKV-GKQNHKTVIG--RYREHLLGTAVVDINGVAYPQ 139
                                       9****************66.4444444333..44899***********99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1111.15
//
Query:       gi|557694943|ref|YP_008797997.1|  [L=320]
Description: tRNA and rRNA cytosine-C5-methylases [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-48  165.0   0.0    2.3e-48  164.5   0.0    1.2  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
    4.9e-13   49.4   0.0    9.7e-13   48.4   0.0    1.5  1  Methyltr_RsmF_N  N-terminal domain of 16S rRNA methyltransfer
    1.2e-06   28.7   0.0    2.6e-06   27.7   0.0    1.4  1  FtsJ             FtsJ-like methyltransferase
    0.00038   20.3   0.0    0.00064   19.5   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0015   19.2   0.0      0.003   18.2   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
       0.13   11.4   0.0       0.21   10.7   0.0    1.3  1  Fibrillarin      Fibrillarin
       0.23   10.8   0.0       0.52    9.6   0.0    1.5  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family


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 !  164.5   0.0   8.9e-52   2.3e-48       3     199 ..     111     316 ..     109     317 .. 0.97

  Alignments for each domain:
  == domain 1  score: 164.5 bits;  conditional E-value: 8.9e-52
                                       HH---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC.. CS
                   Methyltr_RsmB-F   3 lLapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggel 79 
                                       lL+ +++ ++lDlcaaPG+KTthia+ ++ +g+vvA+d++++R+k++ +n++r gv n  ++ aD+r++     g +
  gi|557694943|ref|YP_008797997.1| 111 LLDVEPGHWVLDLCAAPGSKTTHIAARLRGEGVVVANDVSRTRIKALSSNMQRCGVVNGVLTLADGRRFGYRYRG-M 186
                                       689999***************************************************************888887.9 PP

                                       EEEEEEEE--CCGGGTTT-TCHHHH--HHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEES--STTTTHHHHHHHHHH CS
                   Methyltr_RsmB-F  80 fDriLlDaPCsgtgvirrdpdvklrrkekdiaqlaklqkellsaaidllkkgGvlvYsTCsvlveEneevieeaLkk 156
                                       fDr+++DaPC+++g+ ++d +v  + +    a+l++lq  ll +    lk+gG+l+YsTC+ ++ Ene+v++++L+k
  gi|557694943|ref|YP_008797997.1| 187 FDRVMIDAPCTSLGIGSKDWSVLRNWTTGSSARLSRLQTSLLFSGYMALKPGGILIYSTCTFHPFENETVVNNLLEK 263
                                       **********************99999************************************************** PP

                                       -TTEEEESSBSTTSTTSSECEEC...........TSEEE-TTTTSS-SEEEEEE CS
                   Methyltr_RsmB-F 157 redvelvetelsepkglklgeea...........gtlrllPhtenkdgffiakl 199
                                        e++e+ +++l++  + + g ++           +t+r++P ++  +gf+iak+
  gi|557694943|ref|YP_008797997.1| 264 FEEAEVLPIKLNG-LECDWGFDEwggrifspevrKTVRIWPFQSGAEGFYIAKI 316
                                       *********9988.88899999899***************************98 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 !   48.4   0.0   3.8e-16   9.7e-13       6      89 ..      20     105 ..      15     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 3.8e-16
                                       HHHHHHHHGGGHHHHHHHHH-----EEE--TTS..TTHHHHHHH..-SS--B-TT-TTEEES---...TTSHHHHTT CS
                   Methyltr_RsmF_N   6 iekmkellgeeaeaflaaleeprkkglRvNtlKisveeleklse..efelepvpwceeGfyleeeerpgkhplheaG 80 
                                        + ++++++++++ +l+a+++p + ++RvNtlKi++e++  l +  + +++++p++ +Gfy e e   + + +h+ G
  gi|557694943|ref|YP_008797997.1|  20 RSFLEAIIPDKMDMLLEAYSRPLPDSFRVNTLKIDRENCLILLReeGLTVRRIPFTVDGFYAEPEGLLTDSLWHMLG 96 
                                       5557889999****************************99987778999**************************** PP

                                       S-EE--TTT CS
                   Methyltr_RsmF_N  81 lyYiQEpSa 89 
                                       ++Y Q p +
  gi|557694943|ref|YP_008797997.1|  97 YVYAQGPVS 105
                                       *****9865 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0     1e-09   2.6e-06      19     157 ..     114     269 ..     107     278 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1e-09
                                       S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS......HHHTTEEEECS-CCCSSHHHHHCHCHHHSSEE CS
                              FtsJ  19 fkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm......aplpgvttiqgditdpetiekikealserkvd 89 
                                       ++pg+ v+Dl+aaPG+ +  ++ rl  +g+vva D+         ++++++ +++g  t  + ++   ++  +  +d
  gi|557694943|ref|YP_008797997.1| 114 VEPGHWVLDLCAAPGSKTTHIAARLRGEGVVVANDVSRTrikalsSNMQRCGVVNGVLTLADGRRFGYRY--RGMFD 188
                                       45999********************878********8865554444445555555555555555544432..36799 PP

                                       EEEE--S-........SS-CHHHHHHHHH.........CCCCHHHHCCHCCCCECCCEEEECCCHCCCHH..HHHHH CS
                              FtsJ  90 lvvsDgap........dvsgvhdldeylq.........sqLllaalelalkllkpggtfvlkifrgeete..allkq 147
                                        v+ D           d s  +      +         s+L  + l  +   lkpgg+++  +++++ +e   ++++
  gi|557694943|ref|YP_008797997.1| 189 RVMIDAPCtslgigskDWSVLR------NwttgssarlSRLQTSLLFSGYMALKPGGILIYSTCTFHPFEneTVVNN 259
                                       9999975433333333333333......244555544455555555557789********98888666665377777 PP

                                       HHCCEEEEEE CS
                              FtsJ 148 lkkfFekvsv 157
                                       l ++Fe+ +v
  gi|557694943|ref|YP_008797997.1| 260 LLEKFEEAEV 269
                                       9999998876 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 !   19.5   0.0   2.5e-07   0.00064      64     150 ..     107     194 ..      95     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.5e-07
                                       HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGG.TTGG CS
                              PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrk.Gyee 139
                                       l++ell++++g  vL++ +  G +t  +a  ++ +g vv+ + ++  +++ + n+++ ++ n +++ +DGr  Gy  
  gi|557694943|ref|YP_008797997.1| 107 LVTELLDVEPGHWVLDLCAAPGSKTTHIAARLRGEGVVVANDVSRTRIKALSSNMQRCGVVNGVLTLADGRRfGYRY 183
                                       689******************************************999999*******************755**** PP

                                       G-SEEEEEESS CS
                              PCMT 140 kaPYdaihvga 150
                                       +  +d++++ a
  gi|557694943|ref|YP_008797997.1| 184 RGMFDRVMIDA 194
                                       ******99977 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   1.2e-06     0.003       1      70 [.     120     192 ..     120     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.2e-06
                                       EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSS.STTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpf.edgsfDlvvs 70 
                                       vLdl++ +G  t ++a+rl g++ v++ D+s + ++a  +++++ g+ n  +  +d +++ +   g fD v++
  gi|557694943|ref|YP_008797997.1| 120 VLDLCAAPGSKTTHIAARLrGEGVVVANDVSRTRIKALSSNMQRCGVvNGVLTLADGRRFGYrYRGMFDRVMI 192
                                       9******************889********************9999999999999999998635569999987 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   8.1e-05      0.21      66     118 ..     112     164 ..     105     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8.1e-05
                                       -S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTS CS
                       Fibrillarin  66 lpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkR 118
                                       l +++g+ vL l aa G+   H++  +  egvv a ++s + ++ l + +++ 
  gi|557694943|ref|YP_008797997.1| 112 LDVEPGHWVLDLCAAPGSKTTHIAARLRGEGVVVANDVSRTRIKALSSNMQRC 164
                                       56899************************************999998665543 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0002      0.52      41     120 ..     110     190 ..     105     196 .. 0.83
   2 ?   -3.4   0.0       1.9   4.7e+03     139     150 ..     231     242 ..     224     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0002
                                       HH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-.T- CS
                   Ubie_methyltran  41 klvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed.ds 116
                                       +l  v +g+ vlD+++  g  + +++  ++ +g vv  D++ + +k     +++ g++n  +  a++ ++ +   + 
  gi|557694943|ref|YP_008797997.1| 110 ELLDVEPGHWVLDLCAAPGSKTTHIAARLRGEGVVVANDVSRTRIKALSSNMQRCGVVNGVLTLADGRRFGYRYrGM 186
                                       5666789999************************************9999999999998777777777666654456 PP

                                       EEEE CS
                   Ubie_methyltran 117 fDvv 120
                                       fD v
  gi|557694943|ref|YP_008797997.1| 187 FDRV 190
                                       6655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.9
                                       HHHHEEEEEEEE CS
                   Ubie_methyltran 139 ayrvlkpGGrlv 150
                                        y  lkpGG+l+
  gi|557694943|ref|YP_008797997.1| 231 GYMALKPGGILI 242
                                       57889****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2232.62
//
Query:       gi|557694944|ref|YP_008797998.1|  [L=207]
Description: N-glycosylase/DNA lyase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   11.9   0.0       0.25   11.4   0.0    1.2  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 ?   11.4   0.0   1.4e-05      0.25      30      89 ..      94     151 ..      84     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.4e-05
                                       ESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEEEEEEEEECTCG CS
                               POR  30 gseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkpggiiiynseel 89 
                                       ++ ++ g + + vr +++ +v+ ++   +d++v+l ++++s +l ++  +g++i++ + l
  gi|557694944|ref|YP_008797998.1|  94 DALKMFGDVLAVVRSGRS-HVEIRR-FLVDVVVGLGMKEASHFLRNIGFDGLAILDRHIL 151
                                       67899999********97.777777.77****************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1523.68
//
Query:       gi|557694945|ref|YP_008797999.1|  [L=488]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-15   56.6   0.0    8.1e-15   55.5   0.0    1.5  2  DUF87          Helicase HerA, central domain
  ------ inclusion threshold ------
      0.019   14.8   0.0      0.039   13.8   0.0    1.5  1  CLP1_P         mRNA cleavage and polyadenylation factor CLP1 
      0.019   15.2   0.2         14    5.9   0.1    3.0  2  AAA_22         AAA domain
      0.022   14.5   0.5       0.77    9.5   0.1    2.4  2  AAA_29         P-loop containing region of AAA domain
      0.061   12.2   0.0       0.14   11.1   0.0    1.5  1  TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-


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 !   55.5   0.0   2.3e-18   8.1e-15      34     226 ..     168     346 ..     162     347 .. 0.89
   2 ?   -3.0   0.0       1.7   6.1e+03      13      30 ..     434     451 ..     424     452 .. 0.75

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 2.3e-18
                             DUF87  34 sGKSntvavLleellekkgatililDpHGEYgkal......ekllsekvkvitpspsakdkelkinpwsldpeelld 104
                                       sGKS+++++++e ++ ++g+t+++lD++GEY +++      ++ l++ + ++ p      ++++  ++ +  + + d
  gi|557694945|ref|YP_008797999.1| 168 SGKSHLAKIIVEGIV-SNGGTVVVLDVNGEYLSLDkrfdggKSDLADALTLLHPG-----RNFTASLRMMGLKTFHD 238
                                       8**************.*******************99999999999999999997.....69999999999999999 PP

                             DUF87 105 llee.ddkpaaavqrsvleealdqakakeekeklssdepveklleelkkekeelrklknqaiarlldkledllrkgg 180
                                       ++e  +++pa  ++ + l +++++++  +e +++  d+++  +++e          +++  +++ll++le++ ++g 
  gi|557694945|ref|YP_008797999.1| 239 IMEHvYGTPA--TSLRELGRIWKKLE--KECGDFCLDDLMDVVENEP---------MNEAVREALLSRLESINSSGF 302
                                       9999666665..56666788888887..9*********999555444.........588889999999999999998 PP

                             DUF87 181 sfsnsstdliallleklekegkitiidlsgvdelaqqlvvsvilrr 226
                                         +n++tdl +ll  k+  +g++t+++ls++  ++ +lvv ++l +
  gi|557694945|ref|YP_008797999.1| 303 ISDNDPTDLAELL--KPRPGGNVTVVNLSKLLPSTRRLVVEYLLSH 346
                                       88***********..999************************9986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                             DUF87  13 pvyldlnklvtrHlAilg 30 
                                       +v+l ++k+  r++++lg
  gi|557694945|ref|YP_008797999.1| 434 TVKLLVKKMPPRRCLVLG 451
                                       588888888889998888 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 ?   13.8   0.0   1.1e-05     0.039       1      30 [.     164     193 ..     164     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.1e-05
                            CLP1_P   1 GpkdsGKSTlarlLlNyalrkgrkpvyvDl 30 
                                       G+k+sGKS la+++++ ++++g ++v++D+
  gi|557694945|ref|YP_008797999.1| 164 GKKESGKSHLAKIIVEGIVSNGGTVVVLDV 193
                                       89***************************7 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.004        14       5      27 ..     157     179 ..     154     200 .. 0.87
   2 ?    5.8   0.0    0.0042        15      71     121 ..     336     385 ..     204     398 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.004
                            AAA_22   5 agilvvtGesGtGKTtllrrlle 27 
                                        +++++tG + +GK++l++ ++e
  gi|557694945|ref|YP_008797999.1| 157 GSLTIITGKKESGKSHLAKIIVE 179
                                       6789**************97766 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0042
                            AAA_22  71 erlsseellealeqalrarav.ielliiDEaqh.lrseealeeLrsllnlsrk 121
                                       +rl  e ll++l   l++ +  + +l+ +Ea+  l +e+ +e+L++++   + 
  gi|557694945|ref|YP_008797999.1| 336 RRLVVEYLLSHLSTLLSSNKIePLFLLAEEAHLyL-RETYWEDLVTRMR--HI 385
                                       44455555566666666666699**********99.9999999988877..44 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 ?    9.5   0.1   0.00021      0.77      22      38 ..     156     173 ..     148     175 .. 0.84
   2 ?    2.5   0.0     0.034   1.2e+02      33      48 ..     206     220 ..     185     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00021
                            AAA_29  22 kg.atlltGpsGsGKSTl 38 
                                       +g  t++tG+ +sGKS l
  gi|557694945|ref|YP_008797999.1| 156 DGsLTIITGKKESGKSHL 173
                                       4678************66 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.034
                            AAA_29  33 sGKSTllDAiqalLvp 48 
                                        GKS l DA++ l  p
  gi|557694945|ref|YP_008797999.1| 206 GGKSDLADALTLL-HP 220
                                       5********9754.44 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 ?   11.1   0.0   3.8e-05      0.14      17      57 ..     159     199 ..     147     211 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.8e-05
                     TrwB_AAD_bind  17 hilivGttGsGKtqalekllrairargdraivlDltGafvs 57 
                                        ++i+G   sGK+  ++ ++++i + g +++vlD +G+++s
  gi|557694945|ref|YP_008797999.1| 159 LTIITGKKESGKSHLAKIIVEGIVSNGGTVVVLDVNGEYLS 199
                                       5899**********************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3406.80
//
Query:       gi|557694946|ref|YP_008798000.1|  [L=362]
Description: hypothetical protein CSUB_C1519 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    0.00094   18.9   0.2      0.015   15.0   0.0    2.6  2  NurA          NurA domain
  ------ inclusion threshold ------
       0.17    9.7   0.1       0.26    9.1   0.1    1.1  1  Tenui_PVC2    Tenuivirus PVC2 protein
       0.21   12.0   1.1       0.47   10.9   1.1    1.5  1  H-kinase_dim  Signal transducing histidine kinase, homodimeri


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 ?   -1.3   0.0      0.24   1.4e+03     121     138 ..       8      28 ..       7      54 .. 0.74
   2 !   15.0   0.0   2.5e-06     0.015     189     241 ..     276     324 ..     115     325 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.24
                                       EEEEESS-SCTCCHCCC.... CS
                              NurA 121 lvgvaKsfrskellnll...l 138
                                       +++++K f++++l+ +l    
  gi|557694946|ref|YP_008798000.1|   8 CCAIFKYFNNSNLSVKLlniM 28 
                                       568999*********994431 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2.5e-06
                                       EEESSTTTTEEEEEHHHHHHCCHHHHHHHHHH..TTB-SSSBCCHHHHHHHHC CS
                              NurA 189 YvrlegggsilrleipaevstakdedvlsllasqrlsisGYprpLalAhelak 241
                                         +l++  +++r++    vs+a d  +l++l+s ++ i GYp++L lAh+lak
  gi|557694946|ref|YP_008798000.1| 276 VAHLSPRYFPFRVD----VSAADDIQLLNQLLSSEAIIYGYPESLILAHQLAK 324
                                       44568889999999....6789999***************************9 PP

>> Tenui_PVC2  Tenuivirus PVC2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   4.4e-05      0.26     276     308 ..      95     126 ..      89     135 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 4.4e-05
                        Tenui_PVC2 276 devsvdmstvrvvdeaeegllvvedsiapntnv 308
                                         v+ dmstv++ d ae gl  v  si  + nv
  gi|557694946|ref|YP_008798000.1|  95 PVVACDMSTVKIADSAEGGLWAVRGSIVRK-NV 126
                                       45899*********************9753.44 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 ?   10.9   1.1   7.8e-05      0.47      13      63 ..      23      71 ..      23      76 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.8e-05
                      H-kinase_dim 13 yLlnlvGElVitkarLnqsleefrfenglkasvtelksslqnlgrisgeLQ 63
                                      +Lln++++l i++  L+ +le+f   + +++s t lk  +  ++  s++ Q
  gi|557694946|ref|YP_008798000.1| 23 KLLNIMSNLTIQQHHLQTLLETFT--QTAQNSLTGLKNHTVAIETASTDSQ 71
                                      69**********************..7778888989888888877777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); 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:                         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: 2591.43
//
Query:       gi|557694947|ref|YP_008798001.1|  [L=134]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0077   16.6   0.1      0.019   15.3   0.0    1.6  1  Penicillinase_R  Penicillinase repressor


Domain annotation for each model (and alignments):
>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-06     0.019      13      65 ..      67     120 ..      60     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-06
                                       HHHS-EEHHHHHHT--GG.G---HHHHHHHHHHHHHTTS-EEEEETTEEEEE-- CS
                   Penicillinase_R  13 wekgeatvkevveeleee.kelaysTVktllrrLvkKgllsrekegrafiYspl 65 
                                       w +   t +evv+ele++      + V+ +l  Lv+ g l+r  e r++iY + 
  gi|557694947|ref|YP_008798001.1|  67 WLQTGRTLAEVVSELERRgFLYDTTAVAHVLLDLVREGKLERVGEPRRYIYLAK 120
                                       8888999***********44447777*************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1001.80
//
Query:       gi|557694948|ref|YP_008798002.1|  [L=159]
Description: hypothetical protein CSUB_C1521 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   16.2   0.1      0.016   15.2   0.1    1.5  1  HTH_1     Bacterial regulatory helix-turn-helix protein, lysR
  ------ inclusion threshold ------
      0.014   15.5   0.0       0.04   14.1   0.0    1.8  1  AbiEi_4   Transcriptional regulator, AbiEi antitoxin
      0.023   14.6   0.1       0.04   13.8   0.1    1.5  1  MarR_2    MarR family
      0.034   14.2   0.1      0.063   13.4   0.1    1.5  1  HTH_20    Helix-turn-helix domain
      0.037   14.2   0.0      0.089   13.0   0.0    1.6  2  Rio2_N    Rio2, N-terminal
        0.1   12.6   0.0       0.24   11.4   0.0    1.6  1  HTH_12    Ribonuclease R winged-helix domain
       0.14   12.3   0.0        0.3   11.3   0.0    1.6  1  Mrr_N     Mrr N-terminal domain


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 !   15.2   0.1   6.2e-06     0.016      17      59 ..     108     148 ..     106     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.2e-06
                                       HHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSE.EEE-HHH CS
                             HTH_1  17 trAAeeLglsqpavsrqikrLEeelgvpLfeRtgrg.lrLTeaG 59 
                                       ++AA +Lg   ++vs ++++   +++  L+ R grg  + T++G
  gi|557694948|ref|YP_008798002.1| 108 SEAASALGKPEKTVSGRLSE---LVQKSLLKRVGRGgYTITPYG 148
                                       79*************87775...5999*******955*****99 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.6e-05      0.04      16      48 ..     107     144 ..      99     145 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.6e-05
                           AbiEi_4  16 trelea.aGispsa....lrrLvrkGwLvrlrrGvYal 48 
                                        +e++  +G+++++    l++Lv+k +L r++rG Y++
  gi|557694948|ref|YP_008798002.1| 107 ASEAASaLGKPEKTvsgrLSELVQKSLLKRVGRGGYTI 144
                                       5788888*****999*******************8876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   1.6e-05      0.04      14      54 ..      97     137 ..      78     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.6e-05
                                       HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54 
                                       Lg+++ +++ ++e a +lg +  +vs +l +Lv++ L+ r+
  gi|557694948|ref|YP_008798002.1|  97 LGHSDSGEFLASEAASALGKPEKTVSGRLSELVQKSLLKRV 137
                                       78888889*****************************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 ?   13.4   0.1   2.4e-05     0.063      21      60 ..     101     140 ..      82     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                                       TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  21 raegltaselaerldlskntlsyHLrvLeeagLvevvreg 60 
                                       + +++ ase a +l+ + +t+s +L +L++  L+++v+ g
  gi|557694948|ref|YP_008798002.1| 101 DSGEFLASEAASALGKPEKTVSGRLSELVQKSLLKRVGRG 140
                                       667899*****************************99865 PP

>> Rio2_N  Rio2, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.3   1.1e+04      35      49 ..      43      58 ..      40      64 .. 0.58
   2 ?   13.0   0.0   3.5e-05     0.089      38      74 ..     118     152 ..     104     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.3
                            Rio2_N 35 rlk.eeevkkrlsrll 49
                                      +l+ + +v++ l+++ 
  gi|557694948|ref|YP_008798002.1| 43 KLRsSAGVEEILDKIK 58
                                      5554555666665554 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.5e-05
                            Rio2_N  38 eeevkkrlsrllkaklisrktakydGYkLtyeGyDyL 74 
                                       e+ v+ rls+l+++ l++r      GY +t  G+DyL
  gi|557694948|ref|YP_008798002.1| 118 EKTVSGRLSELVQKSLLKRVG--RGGYTITPYGLDYL 152
                                       678899************954..58***********9 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 ?   11.4   0.0   9.2e-05      0.24      32      66 .]     118     152 ..     106     152 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.2e-05
                            HTH_12  32 eravRyrLrkleergltrrvgyagreltEkGleeL 66 
                                       e++v  rL  l +++l +rvg++g ++t  Gl+ L
  gi|557694948|ref|YP_008798002.1| 118 EKTVSGRLSELVQKSLLKRVGRGGYTITPYGLDYL 152
                                       6778889999*********************9976 PP

>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00012       0.3      58      85 ..     125     152 ..     116     154 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00012
                             Mrr_N  58 rtyLkkagllespkrgvwkiTekGrevl 85 
                                       +++L++  ll++  rg ++iT+ G ++l
  gi|557694948|ref|YP_008798002.1| 125 LSELVQKSLLKRVGRGGYTITPYGLDYL 152
                                       57899*******************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1236.13
//
Query:       gi|557694949|ref|YP_008798003.1|  [L=156]
Description: hypothetical protein CSUB_C1522 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   17.3   0.0     0.0049   16.4   0.0    1.5  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.019   14.2   0.1      0.025   13.9   0.1    1.1  1  EAP30     EAP30/Vps36 family
      0.077   13.2   0.1        0.2   11.9   0.0    1.8  2  PaaX      PaaX-like protein


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 !   16.4   0.0   8.2e-07    0.0049      16      47 ..     103     134 ..      99     135 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.2e-07
                            HTH_24  16 prisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                        ++s + +A+ l++     ++rl +L++eG++
  gi|557694949|ref|YP_008798003.1| 103 DGLSPKRVAQILHIDEKVARARLSELWKEGVV 134
                                       589****************************8 PP

>> EAP30  EAP30/Vps36 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   4.2e-06     0.025     120     236 .]      25     138 ..      23     138 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.2e-06
                             EAP30 120 eelyalvnr...arggv.a...lvs.pdDllraiekl....lvlgsglsvlqvggkkvvrSvptelntdqvevl... 181
                                       ee++alvnr   +r g  +   ++s + Dl + +ek+     v ++g+ v+             e +t++  v+   
  gi|557694949|ref|YP_008798003.1|  25 EEVWALVNRyfsERLGPvEavaKLSgQVDLGKLLEKMigkvVVNNGGIDVVA------------EADTKKRIVYcla 89 
                                       5778888875553333323333333355666666666654344447777776............4444443344334 PP

                             EAP30 182 .evakrlvsllaekssgggvtaselaeeeenlgwsvarakeaLeelereGllwvDd 236
                                        ++a+r + +l++     g++ + +a+    l+++ ++a++ L el +eG++ +Dd
  gi|557694949|ref|YP_008798003.1|  90 gAYAGRRLGFLDS----DGLSPKRVAQI---LHIDEKVARARLSELWKEGVVDRDD 138
                                       4555555555544....4699****999...*********************9997 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.87   5.2e+03      12      28 ..      43      59 ..      42      69 .. 0.74
   2 ?   11.9   0.0   3.4e-05       0.2      31      60 ..     112     141 ..      85     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.87
                              PaaX 12 dyveprggaiwlgsLir 28
                                      ++v++  g++ lg+L++
  gi|557694949|ref|YP_008798003.1| 43 EAVAKLSGQVDLGKLLE 59
                                      56777778888888875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.4e-05
                              PaaX  31 aelGiseslvRaalsRlakaGwlvrekegr 60 
                                       + l i+e++ Ra ls l k+G ++r +egr
  gi|557694949|ref|YP_008798003.1| 112 QILHIDEKVARARLSELWKEGVVDRDDEGR 141
                                       55789************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 1073.57
//
Query:       gi|557694950|ref|YP_008798004.1|  [L=92]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   10.4   0.1       0.22   10.3   0.1    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
       0.99    9.8   5.0         13    6.1   5.0    2.0  1  DPM2             Dolichol phosphate-mannose biosynthesis regu


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   2.4e-05      0.22     382     445 ..      14      85 ..       3      90 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.4e-05
                           DUF2207 382 klsalglgliilglilillallllvll...........lvfllilllillliaiivlllfsrllgrrteeGaell 445
                                       +l+al+ ++ i+g+il  +al+l               l+ ++ ++ +l++ia+i + l+++  +++ ee  ++l
  gi|557694950|ref|YP_008798004.1|  14 TLGALLMIVSIAGIILYAWALFL---PpipgldtiilkLTAIVAVGGVLGIIAWIGYTLATTPPPKPLEEIEKEL 85 
                                       45555666666666655555555...2445999999999999999999999999999888877777766666655 PP

>> DPM2  Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   5.0    0.0015        13       2      32 ..      12      41 ..      11      76 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0015
                              DPM2  2 dklvGlllllvalllfvYYtiwvillPfvde 32
                                      d++ G+ll++v+++  + Y  w+++lP ++ 
  gi|557694950|ref|YP_008798004.1| 12 DQTLGALLMIVSIAGIILYA-WALFLPPIPG 41
                                      99************999996.7777776553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 706.48
//
Query:       gi|557694951|ref|YP_008798005.1|  [L=69]
Description: hypothetical protein CSUB_C1524 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 508.37
//
Query:       gi|557694952|ref|YP_008798006.1|  [L=399]
Description: coenzyme F420-dependent hydrogenase beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  129.2   0.0    2.3e-37  128.2   0.0    1.5  1  FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    8.5e-22   77.1   0.1    1.8e-21   76.0   0.0    1.6  1  FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta su
    7.8e-09   35.9   1.5      0.002   18.5   0.1    2.5  2  Fer4_8       4Fe-4S dicluster domain
    2.7e-08   33.3  14.6    0.00015   21.4   3.9    2.5  2  Fer4         4Fe-4S binding domain
    4.3e-08   33.1   9.9    1.1e-07   31.9   9.9    1.6  1  Fer4_10      4Fe-4S dicluster domain
    1.2e-07   31.8   9.4    1.2e-07   31.8   9.4    1.8  2  Fer4_9       4Fe-4S dicluster domain
    3.6e-07   31.0   5.2     0.0082   17.0   0.9    2.6  2  Fer4_16      4Fe-4S double cluster binding domain
    3.1e-06   27.7  13.7    3.1e-06   27.7  13.7    2.4  2  Fer4_7       4Fe-4S dicluster domain
    3.6e-06   26.8  13.8     0.0014   18.6   3.3    2.5  2  Fer4_6       4Fe-4S binding domain
    4.2e-06   27.2   7.8      0.012   16.1   0.4    2.9  2  Fer4_13      4Fe-4S single cluster domain of Ferredoxin I
    0.00024   21.0  22.4     0.0026   17.7   4.9    2.7  2  Fer4_2       4Fe-4S binding domain
    0.00035   21.3  18.7      0.072   14.1   3.9    2.6  2  Fer4_3       4Fe-4S binding domain
    0.00041   20.4  15.0      0.024   14.7  15.2    2.5  2  Fer4_21      4Fe-4S dicluster domain
    0.00046   20.5  16.9      0.016   15.6   0.4    3.0  3  Fer4_4       4Fe-4S binding domain
    0.00078   19.6  10.1      0.002   18.3  10.1    1.6  1  Fer4_18      4Fe-4S dicluster domain
     0.0013   19.3  14.2      0.048   14.2   0.8    2.7  2  Fer4_17      4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.27   12.0  11.5        1.5    9.6   2.4    2.6  2  Fer4_15      4Fe-4S single cluster domain
        4.4    8.2  12.1        5.7    7.8   3.6    2.5  4  Fer4_22      4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> FrhB_FdhB_C  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.2   0.0   2.4e-40   2.3e-37       2     152 ..     219     369 ..     218     372 .. 0.96

  Alignments for each domain:
  == domain 1  score: 128.2 bits;  conditional E-value: 2.4e-40
                       FrhB_FdhB_C   2 kkvavvGtPCqiaalrklqk........kklkekilltiglfCggnfspealrklleelgvdpedvkklefrgkgkf 70 
                                       +k++vvG+PCqi++lr lq+        + +k+ +++ iglfC+++f++ +l+k+ +e+gv+p+dv k++++  gk+
  gi|557694952|ref|YP_008798006.1| 219 DKLGVVGVPCQINGLRYLQHsvpeiryaEWFKQHVVFSIGLFCSEVFTYTGLMKYFNEIGVNPNDVAKINIK--GKV 293
                                       689****************999******99*****************************************5..*** PP

                       FrhB_FdhB_C  71 rvelkd..ekeislkeleefirpsCkvCkdktaelADisvGdvwgpekkgdddegvstvlvrtekgeellekaveag 145
                                       ++ lk+  e   +lk l++++rp+C++Ckd+ a +ADisvG             g+++ + rt  g+ l+e+av++g
  gi|557694952|ref|YP_008798006.1| 294 IISLKNgdEIVKPLKPLHKYERPACRFCKDYAADNADISVGGL--------ATHGWTITVLRTRVGKTLFEDAVSKG 362
                                       *****99877779******************************........589*********************** PP

                       FrhB_FdhB_C 146 eleleel 152
                                       +le++el
  gi|557694952|ref|YP_008798006.1| 363 YLEIKEL 369
                                       ****987 PP

>> FrhB_FdhB_N  Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.0   0.0   1.8e-24   1.8e-21       2      78 .]     134     211 ..     133     211 .. 0.95

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 1.8e-24
                       FrhB_FdhB_N   2 vaArstdkeirkkaqsGGivtallkylLeegiidgvivvaps.kdpwrpkpviattkeellaaaGskYtlspnlklL 77 
                                       +  rst++ei+k++q+GG vt+ll+y+L+e+ id++   + + ++p++p+p ++ +++++l +aGs+Yt++pnl +L
  gi|557694952|ref|YP_008798006.1| 134 FLSRSTNSEILKRSQDGGTVTSLLIYALKENVIDAAALSTTTsEQPLKPIPKLVFEPDDVLGCAGSRYTYAPNLLAL 210
                                       5679*******************************999998889******************************998 PP

                       FrhB_FdhB_N  78 k 78 
                                       k
  gi|557694952|ref|YP_008798006.1| 211 K 211
                                       6 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   1.1e-05     0.011      46      65 .]      57      76 ..      20      76 .. 0.80
   2 !   18.5   0.1     2e-06     0.002       2      25 ..      89     112 ..      88     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                            Fer4_8 46 ealwsCttcgaCtevCpvgi 65
                                       + ++C++c aC++vCp+++
  gi|557694952|ref|YP_008798006.1| 57 VGTGRCSGCAACVTVCPTNV 76
                                      46789************986 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 2e-06
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhl 25 
                                       l++CieC +C +aCp l+ +++++
  gi|557694952|ref|YP_008798006.1|  89 LNHCIECDLCVEACPELHLSDMEI 112
                                       689************888877554 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   3.9   1.5e-07   0.00015       5      22 ..      59      76 ..      56      78 .. 0.87
   2 !   16.8   3.0   4.2e-06    0.0042       7      19 ..      91     103 ..      88     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.5e-07
                                      TTTSSS-THHHHHSTTTE CS
                              Fer4  5 eekCigCGaCvevCPvgA 22
                                      + +C gC aCv vCP+++
  gi|557694952|ref|YP_008798006.1| 59 TGRCSGCAACVTVCPTNV 76
                                      679*************97 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.2e-06
                                       TSSS-THHHHHST CS
                              Fer4   7 kCigCGaCvevCP 19 
                                        Ci C +Cve+CP
  gi|557694952|ref|YP_008798006.1|  91 HCIECDLCVEACP 103
                                       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 !   31.9   9.9   1.1e-10   1.1e-07       7      56 .]      60     103 ..      56     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.1e-10
                           Fer4_10   7 dtCirCgkCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                        +C +C++Cv++CP+      +   + e+ +v++ + +C++c  CveaCP
  gi|557694952|ref|YP_008798006.1|  60 GRCSGCAACVTVCPT------NVFDYVEDHPVNTRLNHCIECDLCVEACP 103
                                       58*************......7777788889999***************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 !   31.8   9.4   1.2e-10   1.2e-07       1      48 [.      61     104 ..      61     107 .. 0.90
   2 ?   -2.5   0.0       6.2   6.2e+03      34      40 ..     316     322 ..     297     323 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 1.2e-10
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpk 48 
                                       +C gC aCv++Cp++v+ + + +  +   +     Ci+C  CveaCp+
  gi|557694952|ref|YP_008798006.1|  61 RCSGCAACVTVCPTNVFDYVEDHPVNTRLN----HCIECDLCVEACPE 104
                                       5****************9999999988644....6************6 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 6.2
                            Fer4_9  34 eaCigCg 40 
                                        aC +C+
  gi|557694952|ref|YP_008798006.1| 316 PACRFCK 322
                                       4688886 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 !   17.0   0.9   8.3e-06    0.0082       1      20 [.      61      80 ..      60      90 .. 0.78
   2 !   15.1   0.2   3.3e-05     0.032       1      19 [.      91     109 ..      91     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 8.3e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      rC +C +C+ vCPtn+++  
  gi|557694952|ref|YP_008798006.1| 61 RCSGCAACVTVCPTNVFDYV 80
                                      59999999999999998765 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 3.3e-05
                           Fer4_16   1 rCgtCgkCaevCPtnaike 19 
                                       +C++C  C+e+CP+ +++ 
  gi|557694952|ref|YP_008798006.1|  91 HCIECDLCVEACPELHLSD 109
                                       7************987765 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7  13.7   3.1e-09   3.1e-06       1      49 [.      61     103 ..      61     105 .. 0.93
   2 ?   -2.3   0.2         7   6.9e+03       5      11 ..     318     324 ..     316     329 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.1e-09
                            Fer4_7   1 rCigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCP 49 
                                       rC gC aCv +Cp++++++ e+      + v+ + + C+ C+ Cv++CP
  gi|557694952|ref|YP_008798006.1|  61 RCSGCAACVTVCPTNVFDYVED------HPVNTRLNHCIECDLCVEACP 103
                                       8******************997......448999*************** PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7
                            Fer4_7   5 CgaCvaa 11 
                                       C++C ++
  gi|557694952|ref|YP_008798006.1| 318 CRFCKDY 324
                                       9999876 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   3.3   1.5e-06    0.0014       8      23 ..      61      76 ..      59      77 .. 0.92
   2 !   13.2   2.9   7.1e-05     0.071       9      21 ..      92     104 ..      90     107 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.5e-06
                            Fer4_6  8 kCigCgdCvrvCPega 23
                                      +C gC +Cv+vCP+++
  gi|557694952|ref|YP_008798006.1| 61 RCSGCAACVTVCPTNV 76
                                      8*************97 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 7.1e-05
                            Fer4_6   9 CigCgdCvrvCPe 21 
                                       Ci C+ Cv +CPe
  gi|557694952|ref|YP_008798006.1|  92 CIECDLCVEACPE 104
                                       ************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 !   14.2   1.1   4.7e-05     0.047       5      25 ..      61      82 ..      57      87 .. 0.87
   2 !   16.1   0.4   1.2e-05     0.012       5      20 ..      91     106 ..      88     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.7e-05
                           Fer4_13  5 tCiacgaCvelaP.dvFeedde 25
                                      +C++c+aCv ++P +vF++ ++
  gi|557694952|ref|YP_008798006.1| 61 RCSGCAACVTVCPtNVFDYVED 82
                                      7************669*99887 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-05
                           Fer4_13   5 tCiacgaCvelaPdvF 20 
                                        Ci+c++Cve++P++ 
  gi|557694952|ref|YP_008798006.1|  91 HCIECDLCVEACPELH 106
                                       7************975 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   4.9   2.6e-06    0.0026       4      22 .]      56      74 ..      54      74 .. 0.91
   2 !   14.6   3.2   2.6e-05     0.026       8      22 .]      90     104 ..      84     104 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.6e-06
                            Fer4_2  4 vvdtdrCigCgaCvsaCPa 22
                                      vv t rC gC aCv++CP+
  gi|557694952|ref|YP_008798006.1| 56 VVGTGRCSGCAACVTVCPT 74
                                      57789*************7 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.6e-05
                            Fer4_2   8 drCigCgaCvsaCPa 22 
                                       ++Ci+C  Cv aCP+
  gi|557694952|ref|YP_008798006.1|  90 NHCIECDLCVEACPE 104
                                       59************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 !   12.5   7.0   0.00023      0.23       1      14 [.      62      75 ..      62      76 .. 0.94
   2 !   14.1   3.9   7.2e-05     0.072       1      13 [.      92     104 ..      92     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00023
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C gC aCv vCP++
  gi|557694952|ref|YP_008798006.1| 62 CSGCAACVTVCPTN 75
                                      99**********97 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 7.2e-05
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+ C +Cve+CP+
  gi|557694952|ref|YP_008798006.1|  92 CIECDLCVEACPE 104
                                       ************5 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   3.4   3.7e-05     0.037      36      53 ..      57      74 ..      35      81 .. 0.74
   2 !   14.7  15.2   2.4e-05     0.024       7      52 ..      61     103 ..      57     110 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                           Fer4_21 36 vvedeCvGCnlCssvCPv 53
                                      v + +C GC+ C++vCP+
  gi|557694952|ref|YP_008798006.1| 57 VGTGRCSGCAACVTVCPT 74
                                      34789************7 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.4e-05
                           Fer4_21   7 kCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCP 52 
                                       +C gC  C+++C+++  + +   +++ ++++ ++C+ C+lC++ CP
  gi|557694952|ref|YP_008798006.1|  61 RCSGCAACVTVCPTNVFDYV---EDHPVNTRLNHCIECDLCVEACP 103
                                       7************7655555...5666777899************* 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   4.4   0.00012      0.12       3      17 .]      61      75 ..      59      75 .. 0.92
   2 !   15.6   0.4   1.6e-05     0.016       2      15 ..      90     103 ..      89     118 .. 0.90
   3 ?   -1.3   0.4       4.4   4.4e+03       7      12 ..     318     323 ..     317     324 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      rC gC +Cv +CP++
  gi|557694952|ref|YP_008798006.1| 61 RCSGCAACVTVCPTN 75
                                      9************86 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.6e-05
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       + Ci+C+ Cv aCP
  gi|557694952|ref|YP_008798006.1|  90 NHCIECDLCVEACP 103
                                       56************ PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.4
                            Fer4_4   7 CgsCva 12 
                                       C+ C +
  gi|557694952|ref|YP_008798006.1| 318 CRFCKD 323
                                       999987 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3  10.1     2e-06     0.002      57      98 ..      58     105 ..      41     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2e-06
                           Fer4_18  57 gagdcidcescvkvcPtgi.dirkG....lql.eciscllcidacdkv 98 
                                       g+g c  c +cv+vcPt++ d  +      +l +ci+c lc++ac ++
  gi|557694952|ref|YP_008798006.1|  58 GTGRCSGCAACVTVCPTNVfDYVEDhpvnTRLnHCIECDLCVEACPEL 105
                                       7899*************98654443111133327***********875 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.8   4.9e-05     0.048      42      60 ..      58      76 ..      19      77 .. 0.74
   2 !   13.5   2.3   8.1e-05     0.081      41      58 ..      87     104 ..      75     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.9e-05
                           Fer4_17 42 kaslCieCgeCerkCPqgl 60
                                        ++C++C  C+++CP ++
  gi|557694952|ref|YP_008798006.1| 58 GTGRCSGCAACVTVCPTNV 76
                                      5678999999999999875 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 8.1e-05
                           Fer4_17  41 ekaslCieCgeCerkCPq 58 
                                       ++ + CieC +C+++CP+
  gi|557694952|ref|YP_008798006.1|  87 TRLNHCIECDLCVEACPE 104
                                       68899************6 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 ?    9.6   2.4    0.0015       1.5       7      23 ..      61      78 ..      56      90 .. 0.77
   2 ?    6.9   1.8     0.011        11       7      24 ..      91     108 ..      85     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
                           Fer4_15  7 aCigcglCvaeape.vfe 23
                                      +C gc++Cv+++p+ vf 
  gi|557694952|ref|YP_008798006.1| 61 RCSGCAACVTVCPTnVFD 78
                                      8***********741554 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.011
                           Fer4_15   7 aCigcglCvaeapevfel 24 
                                        Ci c lCv+++pe+   
  gi|557694952|ref|YP_008798006.1|  91 HCIECDLCVEACPELHLS 108
                                       7************98655 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   5.1      0.03        30      81      94 ..      61      74 ..      38      76 .. 0.70
   2 ?    7.8   3.6    0.0058       5.7       1      23 [.      61      83 ..      61      91 .. 0.76
   3 ?    4.7   1.0     0.057        56      79      93 ..      89     103 ..      76     106 .. 0.66
   4 ?    4.3   1.2     0.071        71       1      19 [.      91     109 ..      91     124 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.03
                           Fer4_22 81 gCvGCgRCieacpv 94
                                       C GC  C+++cp+
  gi|557694952|ref|YP_008798006.1| 61 RCSGCAACVTVCPT 74
                                      56666666666655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0058
                           Fer4_22  1 rClsCgaCtlvCptCsCfdvede 23
                                      rC +C+aC +vCpt +   ved+
  gi|557694952|ref|YP_008798006.1| 61 RCSGCAACVTVCPTNVFDYVEDH 83
                                      79999999999999766555555 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.057
                           Fer4_22  79 esgCvGCgRCieacp 93 
                                        ++C+ C  C+eacp
  gi|557694952|ref|YP_008798006.1|  89 LNHCIECDLCVEACP 103
                                       566677777777666 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.071
                           Fer4_22   1 rClsCgaCtlvCptCsCfd 19 
                                       +C++C  C  +Cp  +  d
  gi|557694952|ref|YP_008798006.1|  91 HCIECDLCVEACPELHLSD 109
                                       5999999999999766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); 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 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2804.36
//
Query:       gi|557694953|ref|YP_008798007.1|  [L=180]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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       0.22   11.6   0.0    1.6  1  Zincin_1       Zincin-like metallopeptidase
        0.1   12.4   0.2       0.19   11.6   0.2    1.4  1  Peptidase_M10  Matrixin
       0.12   12.2   0.1       0.18   11.6   0.1    1.5  1  UPF0054        Uncharacterized protein family UPF0054
       0.16   11.3   0.4       0.76    9.0   0.3    1.8  2  DUF5630        Family of unknown function (DUF5630)


Domain annotation for each model (and alignments):
>> Zincin_1  Zincin-like metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     5e-05      0.22      51      94 ..      77     123 ..      60     127 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5e-05
                                       EEEEHHHHHH...H--TT--HHHHHHHHHHHHHHHHHTT-HHHHHHH CS
                          Zincin_1  51 ivlyrrplla...vaetreeleeevretllHEighhfGlddedleel 94 
                                       iv+ ++ l a   + ++re ++    ++llHE  h +G+d+++ +el
  gi|557694953|ref|YP_008798007.1|  77 IVVNQAMLNAvysATKSREMVNSYLFVVLLHEYLHALGFDEKQTREL 123
                                       55555444443224447777999999***************987765 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   4.2e-05      0.19     104     130 ..      96     122 ..      64     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.2e-05
                                       SSSEEHHHHHHHHHHHHTTBESXSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M10 104 eqgvslflVaaHEiGHalGLeHssdkd 130
                                         +  lf+V +HE+ HalG +  + ++
  gi|557694953|ref|YP_008798007.1|  96 MVNSYLFVVLLHEYLHALGFDEKQTRE 122
                                       345569*************99866655 PP

>> UPF0054  Uncharacterized protein family UPF0054
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.1e-05      0.18      79     113 ..      88     122 ..      13     140 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.1e-05
                           UPF0054  79 eqaeeyghslerelafllvHgllHllGYDHeeeee 113
                                         a +  + +++ l ++l H  lH lG+D ++  e
  gi|557694953|ref|YP_008798007.1|  88 YSATKSREMVNSYLFVVLLHEYLHALGFDEKQTRE 122
                                       2333444566777779999**********997665 PP

>> DUF5630  Family of unknown function (DUF5630)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.11   4.8e+02     192     213 ..       4      25 ..       2      30 .. 0.79
   2 ?    9.0   0.3   0.00017      0.76     122     188 ..      81     146 ..      66     149 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.11
                                       HHHTTTSTTTCT-------HHH CS
                           DUF5630 192 hNAyfGkGLaesnsfklesise 213
                                        NAy+G+  + s +  + s++e
  gi|557694953|ref|YP_008798007.1|   4 ANAYIGRSVEVSGKVTVLSYAE 25 
                                       6******999998887777765 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00017
                                       HH...HHHHHHHHHHHSHHHHHHHHHHHHHHHHHT-SST......HHHHHHHHHHHHHHHHHTTSHH CS
                           DUF5630 122 eelaeilknleklaklygtpGYLllanayfrlakflqeldnealaeaalqlalkalelAekleeeSe 188
                                       + + +++++++k  +   ++ ++ l + y++ + f +++  e    +a+++al + ++A k+ ++S 
  gi|557694953|ref|YP_008798007.1|  81 QAMLNAVYSATKSREMVNSYLFVVLLHEYLHALGFDEKQTRELVR-EAVSSALPYDHVATKIASTSI 146
                                       4478899***************************99998666655.9***************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1273.94
//
Query:       gi|557694954|ref|YP_008798008.1|  [L=141]
Description: ferredoxin [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   47.1  14.3    1.6e-06   27.7   2.8    2.3  2  Fer4      4Fe-4S binding domain
    9.3e-10   39.0  24.9    9.2e-07   29.4   7.6    1.9  3  Fer4_7    4Fe-4S dicluster domain
    4.3e-07   29.9   5.0    1.1e-06   28.6   5.0    1.7  1  Fer4_10   4Fe-4S dicluster domain
    8.2e-07   29.1   6.4    2.2e-05   24.5   7.6    2.1  2  Fer4_9    4Fe-4S dicluster domain
      5e-06   26.6   6.1      0.017   15.2   1.1    2.2  2  Fer4_21   4Fe-4S dicluster domain
    4.2e-05   24.4   7.0       0.13   13.2   4.2    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    4.4e-05   23.4  14.2      0.017   15.2   2.4    2.2  2  Fer4_6    4Fe-4S binding domain
    6.1e-05   23.4   4.7    0.00025   21.4   5.1    1.7  2  Fer4_8    4Fe-4S dicluster domain
    0.00027   21.1   0.9       0.11   12.7   0.1    2.1  2  Fer4_18   4Fe-4S dicluster domain
    0.00071   20.3  13.0      0.017   16.0   4.6    2.4  2  Fer4_3    4Fe-4S binding domain
    0.00072   20.0   5.8     0.0068   16.9   6.7    1.9  2  Fer4_17   4Fe-4S dicluster domain
    0.00096   19.5   7.3      0.043   14.3   2.6    2.3  2  Fer4_4    4Fe-4S binding domain
     0.0026   17.9   0.8      0.057   13.6   0.8    2.1  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
  ------ inclusion threshold ------
      0.027   15.0  12.7       0.03   14.9   0.4    2.7  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.037   14.9   1.1        4.7    8.1   0.4    2.2  2  Fer4_22   4Fe-4S dicluster domain
      0.044   13.9  10.7       0.18   12.0   0.6    2.4  2  Fer4_2    4Fe-4S binding domain
      0.082   13.7   1.2      0.082   13.7   1.2    2.8  3  Fer4_15   4Fe-4S single cluster 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 !   27.7   2.8   1.5e-09   1.6e-06       2      23 ..      61      82 ..      60      83 .. 0.91
   2 !   25.2   3.8   9.4e-09   9.9e-06       3      24 .]     116     137 ..     114     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.5e-09
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       +d+e Ci+ G+C++vCPv++ 
  gi|557694954|ref|YP_008798008.1| 61 AVDWEACIADGICMDVCPVNVF 82
                                      69*****************986 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 9.4e-09
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                       i e +Ci+C+aC+  CP+ AI+
  gi|557694954|ref|YP_008798008.1| 116 IREADCIFCMACEASCPTKAIK 137
                                       77899****************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.4   3.7e-05     0.039      29      52 .]      58      81 ..      26      81 .. 0.76
   2 !   29.4   7.6   8.7e-10   9.2e-07       2      52 .]      67     135 ..      66     135 .. 0.66
   3 !   17.3   3.3     5e-06    0.0053       2      21 ..     121     140 ..     120     141 .] 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.7e-05
                            Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                      + v++d e C+  g C++vCP+++
  gi|557694954|ref|YP_008798008.1| 58 KIVAVDWEACIADGICMDVCPVNV 81
                                      66789999*************986 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 8.7e-10
                            Fer4_7   2 CigCgaCvaaCpvkaield................eeenekgt........ekveidpekClgCgaCvavCPtga 52 
                                       Ci  g C+++Cpv+++e+                                 ++  i++ +C++C aC+a CPt+a
  gi|557694954|ref|YP_008798008.1|  67 CIADGICMDVCPVNVFEWAlnpgrsgtgndlypleG------ElyekyrtdKSEPIREADCIFCMACEASCPTKA 135
                                       9999*************9944433333333332220......033222222555788899*************87 PP

  == domain 3  score: 17.3 bits;  conditional E-value: 5e-06
                            Fer4_7   2 CigCgaCvaaCpvkaielde 21 
                                       Ci C aC+a Cp+kai++++
  gi|557694954|ref|YP_008798008.1| 121 CIFCMACEASCPTKAIKINP 140
                                       99999999999999999876 PP

>> 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   5.0     1e-09   1.1e-06       4      56 .]      62     132 ..      59     132 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1e-09
                           Fer4_10   4 idddtCirCgkCvkaCPadl..................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d + Ci  g C+++CP+++                   + + ++++  ++ + +   +C++c aC ++CP
  gi|557694954|ref|YP_008798008.1|  62 VDWEACIADGICMDVCPVNVfewalnpgrsgtgndlypLEGELYEKYRTDKSEPIREADCIFCMACEASCP 132
                                       67799*************99****************9855555666666666666779************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 !    9.5   0.2     0.001       1.1      32      49 ..      63      80 ..      30      82 .. 0.71
   2 !   24.5   7.6   2.1e-08   2.2e-05       2      51 .]      67     136 ..      65     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.001
                            Fer4_9 32 seeaCigCgaCveaCpkg 49
                                      ++eaCi  g C+++Cp +
  gi|557694954|ref|YP_008798008.1| 63 DWEACIADGICMDVCPVN 80
                                      337899999999999986 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 2.1e-08
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase....................eaCigCgaCveaCpkgai 51 
                                       C+  g C+++Cp +v++   +++     ++ +                     +Ci+C+aC++ Cp++ai
  gi|557694954|ref|YP_008798008.1|  67 CIADGICMDVCPVNVFEWALNPGRSGTGNDLYplegelyekyrtdksepireADCIFCMACEASCPTKAI 136
                                       677789*********999998888777655458999****************99*************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 !   13.9   0.3   4.2e-05     0.045      33      53 ..      59      79 ..      52      83 .. 0.84
   2 !   15.2   1.1   1.6e-05     0.017      34      58 ..     114     137 ..     106     139 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.2e-05
                           Fer4_21 33 vlkvvedeCvGCnlCssvCPv 53
                                      +++v  + C++  +C++vCPv
  gi|557694954|ref|YP_008798008.1| 59 IVAVDWEACIADGICMDVCPV 79
                                      5677889*************9 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 1.6e-05
                           Fer4_21  34 lkvvedeCvGCnlCssvCPvedcie 58 
                                        +++e +C+ C  C + CP+ ++i+
  gi|557694954|ref|YP_008798008.1| 114 EPIREADCIFCMACEASCPT-KAIK 137
                                       56667777777777777775.5554 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 !   11.9   0.0   0.00033      0.34      54      67 .]      67      80 ..      33      91 .. 0.78
   2 !   13.2   4.2   0.00012      0.13       2      18 ..     121     137 ..     120     140 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00033
                           Fer4_16 54 itgCdiCqdvCPan 67
                                      ++  +iC+dvCP+n
  gi|557694954|ref|YP_008798008.1| 67 CIADGICMDVCPVN 80
                                      44445666666655 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00012
                           Fer4_16   2 CgtCgkCaevCPtnaik 18 
                                       C+ C +C  +CPt+aik
  gi|557694954|ref|YP_008798008.1| 121 CIFCMACEASCPTKAIK 137
                                       99**************8 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.4   1.6e-05     0.017       1      23 [.      59      81 ..      59      82 .. 0.90
   2 !   13.8   4.2   4.3e-05     0.045       9      24 .]     121     136 ..     116     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                            Fer4_6  1 vveidpdkCigCgdCvrvCPega 23
                                      +v++d ++Ci  g C++vCP ++
  gi|557694954|ref|YP_008798008.1| 59 IVAVDWEACIADGICMDVCPVNV 81
                                      5788899*************987 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 4.3e-05
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       Ci C++C++ CP++ai
  gi|557694954|ref|YP_008798008.1| 121 CIFCMACEASCPTKAI 136
                                       999***********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 !   10.2   0.3   0.00075      0.79      48      64 ..      64      80 ..      27      81 .. 0.71
   2 !   21.4   5.1   2.4e-07   0.00025       3      64 ..      65     134 ..      63     135 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00075
                            Fer4_8 48 lwsCttcgaCtevCpvg 64
                                      +++C + g C +vCpv+
  gi|557694954|ref|YP_008798008.1| 64 WEACIADGICMDVCPVN 80
                                      44555555566666555 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2.4e-07
                            Fer4_8   3 ekCieCgaCqsaCp..........vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       e+Ci  g C++ Cp            + t+++l+  +ge  e + ++++ +e      C  c+aC+  Cp++
  gi|557694954|ref|YP_008798008.1|  65 EACIADGICMDVCPvnvfewalnpGRSGTGNDLYPLEGELYE-KYRTDK-SEPIREADCIFCMACEASCPTK 134
                                       79***********95443333332222244555555555555.444444.34566789************97 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.1    0.0044       4.7      58      75 ..      64      81 ..      32      83 .. 0.82
   2 !   12.7   0.1   0.00011      0.11      48      74 ..     108     134 ..      91     139 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0044
                           Fer4_18 58 agdcidcescvkvcPtgi 75
                                         ci+ + c++vcP+++
  gi|557694954|ref|YP_008798008.1| 64 WEACIADGICMDVCPVNV 81
                                      5679999********976 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00011
                           Fer4_18  48 kekeerkekgagdcidcescvkvcPtg 74 
                                        ++++ +   ++dci c +c + cPt+
  gi|557694954|ref|YP_008798008.1| 108 YRTDKSEPIREADCIFCMACEASCPTK 134
                                       45566677789**************96 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   1.2    0.0022       2.3       6      14 ..      72      80 ..      66      81 .. 0.77
   2 !   16.0   4.6   1.7e-05     0.017       1      15 []     121     135 ..     121     135 .. 0.98

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0022
                            Fer4_3  6 aCvevCPvg 14
                                       C++vCPv+
  gi|557694954|ref|YP_008798008.1| 72 ICMDVCPVN 80
                                      5******98 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 1.7e-05
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       C+ C+aC+ +CP++A
  gi|557694954|ref|YP_008798008.1| 121 CIFCMACEASCPTKA 135
                                       *************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 !   10.0   0.1   0.00095         1      42      60 ..      63      81 ..      40      82 .. 0.82
   2 !   16.9   6.7   6.5e-06    0.0068       2      58 ..      67     133 ..      66     135 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00095
                           Fer4_17 42 kaslCieCgeCerkCPqgl 60
                                       ++ Ci  g C  +CP ++
  gi|557694954|ref|YP_008798008.1| 63 DWEACIADGICMDVCPVNV 81
                                      6899999999999999775 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 6.5e-06
                           Fer4_17   2 CiqCgyClpeCps..yeaydne.pkkllraakl...glleeaeke....ekaslCieCgeCerkCPq 58 
                                       Ci  g C+++Cp   +e+  n  +  + +++++   +l e+  ++     +  +Ci C  Ce++CP 
  gi|557694954|ref|YP_008798008.1|  67 CIADGICMDVCPVnvFEWALNPgRSGTGNDLYPlegELYEKYRTDksepIREADCIFCMACEASCPT 133
                                       99999*******73355555541445667766677533333222223234779*************7 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.2    0.0065       6.9       2      17 .]      65      80 ..      64      84 .. 0.84
   2 !   14.3   2.6   4.1e-05     0.043       4      16 ..     121     133 ..     112     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0065
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      e Ci  g C+++CP++
  gi|557694954|ref|YP_008798008.1| 65 EACIADGICMDVCPVN 80
                                      67888888******75 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.1e-05
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       Ci C++C+a+CP+
  gi|557694954|ref|YP_008798008.1| 121 CIFCMACEASCPT 133
                                       999*********8 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 !   13.6   0.8   5.4e-05     0.057      31      95 ..      58     141 .]      43     141 .] 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.4e-05
                                       TTHHHHTHHHHHS-THHHH-TTS-EEEEETTT...................TSSEEEEE-CCC--S--HHHHH-TT- CS
                            ETF_QO  31 aevavkvnlekyagpeqryCPagvyeivedee...................akekklqinaqnCvhCktCdikdpsq 88 
                                       + vav+ +    +g++  +CP +v+e++ +                      ++k   i  ++C+ C +C+   p++
  gi|557694954|ref|YP_008798008.1|  58 KIVAVDWEACIADGICMDVCPVNVFEWALNPGrsgtgndlyplegelyekyRTDKSEPIREADCIFCMACEASCPTK 134
                                       5555555666667778888888888887654334556667777777766656677778999**************** PP

                                       -EEE--- CS
                            ETF_QO  89 niewvvP 95 
                                        i+ ++P
  gi|557694954|ref|YP_008798008.1| 135 AIKINPP 141
                                       **98877 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 ?   14.9   0.4   2.8e-05      0.03       1      21 [.      62      83 ..      62      91 .. 0.88
   2 ?    3.8   5.4     0.082        86       4      17 ..     119     132 ..     116     134 .. 0.88
   3 ?    4.7   0.1     0.043        45      49      57 ..     129     137 ..     128     138 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.8e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP.dvFe 21
                                      VD + Cia+g+C +++P +vFe
  gi|557694954|ref|YP_008798008.1| 62 VDWEACIADGICMDVCPvNVFE 83
                                      8999*************55665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.082
                           Fer4_13   4 dtCiacgaCvelaP 17 
                                         Ci c+aC + +P
  gi|557694954|ref|YP_008798008.1| 119 ADCIFCMACEASCP 132
                                       57***********9 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.043
                           Fer4_13  49 daCPvesIg 57 
                                       ++CP+++I+
  gi|557694954|ref|YP_008798008.1| 129 ASCPTKAIK 137
                                       69******8 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   0.0     0.028        30      76      95 ..      61      80 ..      23      81 .. 0.66
   2 ?    8.1   0.4    0.0044       4.7       2      14 ..     121     133 ..     102     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.028
                           Fer4_22 76 kfgesgCvGCgRCieacpvk 95
                                       ++ ++C+  g C+++cpv+
  gi|557694954|ref|YP_008798008.1| 61 AVDWEACIADGICMDVCPVN 80
                                      44778899999999999986 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0044
                           Fer4_22   2 ClsCgaCtlvCpt 14 
                                       C+ C aC + Cpt
  gi|557694954|ref|YP_008798008.1| 121 CIFCMACEASCPT 133
                                       8888888888887 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.6   0.00017      0.18       3      21 ..      60      78 ..      58      79 .. 0.88
   2 ?    6.0   3.7     0.013        14      10      22 .]     121     133 ..     115     133 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                            Fer4_2  3 vvvdtdrCigCgaCvsaCP 21
                                      v+vd ++Ci+ g+C ++CP
  gi|557694954|ref|YP_008798008.1| 60 VAVDWEACIADGICMDVCP 78
                                      7899999*988******** PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.013
                            Fer4_2  10 CigCgaCvsaCPa 22 
                                       Ci C aC  +CP+
  gi|557694954|ref|YP_008798008.1| 121 CIFCMACEASCPT 133
                                       888****999**7 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   1.2   7.7e-05     0.082       1      19 [.      60      78 ..      60      86 .. 0.87
   2 ?   -0.8   4.5       2.5   2.6e+03       7      19 ..     120     132 ..     116     133 .. 0.86
   3 ?    3.5   0.9      0.12   1.2e+02      57      66 .]     129     138 ..     125     138 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.7e-05
                           Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                      V vD++aCi +g C++++p
  gi|557694954|ref|YP_008798008.1| 60 VAVDWEACIADGICMDVCP 78
                                      89****************8 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.5
                           Fer4_15   7 aCigcglCvaeap 19 
                                        Ci c +C a +p
  gi|557694954|ref|YP_008798008.1| 120 DCIFCMACEASCP 132
                                       7*******99998 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.12
                           Fer4_15  57 raCPvdAIrv 66 
                                       ++CP++AI +
  gi|557694954|ref|YP_008798008.1| 129 ASCPTKAIKI 138
                                       68******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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):              17  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1039.30
//
Query:       gi|557694955|ref|YP_008798009.1|  [L=226]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   92.0   0.0    5.1e-26   91.4   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 !   91.4   0.0   2.9e-30   5.1e-26       2     128 ..      64     192 ..      63     207 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 2.9e-30
                                       SSEEEEEEEES--.-----HHHHHHHHHTT---.--HHHHHHHHHHHHHT--EEEEEGGGTBTEEEEEE--TTEEEE CS
                              B3_4   2 cpryaarvlrgvkktapspewlqrrLrragirp.innvVDitNyvmlelgqPlhafDldkiqgdivvrlakegeklv 77 
                                       ++ +++r++ +++kt+ps e+l rr+ +    p in++VD++N+v+++   P+ afD++k++g++ +++a+ ge + 
  gi|557694955|ref|YP_008798009.1|  64 YRDFFWRIGIDPTKTRPSAEALLRRVLAGRDFPrINPLVDVYNVVSMQSLLPIAAFDVEKLKGELLMKFANVGELFL 140
                                       789************************************************************************** PP

                                       BTTS-.EEEE-TTSEEEETEEEEEEETTTEEBTTTB--TT--EEEEEEEE-- CS
                              B3_4  78 tldgk.ereldeedlviadsekpvslagvmggeeskvsedTknvfleaaafd 128
                                        ++ +  + l+++++v+ d+ek v+++++++ +++kv+ +T++vfl + ++ 
  gi|557694955|ref|YP_008798009.1| 141 GIGMDkPVALTGKEVVVRDDEKLVAIYPYRDADATKVTSATRHVFLMVCGVP 192
                                       **87735666************************************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 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:                        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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1567.63
//
Query:       gi|557694956|ref|YP_008798010.1|  [L=151]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  111.8   0.3    8.9e-16   58.1   0.1    2.1  2  CBS       CBS domain
      0.001   19.3   0.0       0.62   10.4   0.0    2.5  2  IF3_N     Translation initiation factor IF-3, N-terminal doma


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 !   52.1   0.0   7.3e-18   6.6e-14       1      54 [.      21      74 ..      21      77 .. 0.94
   2 !   58.1   0.1   9.9e-20   8.9e-16       2      54 ..      87     139 ..      86     142 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 7.3e-18
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54
                                      ++d+m+ ++v+v++d+t eea+++m ++gv++++V+d+dg lvGi+t+rD+l a
  gi|557694956|ref|YP_008798010.1| 21 ASDLMSYPPVVVSEDATAEEAAKTMWDNGVGSILVLDKDGTLVGIITERDILYA 74
                                      589*********************98888**********************977 PP

  == domain 2  score: 58.1 bits;  conditional E-value: 9.9e-20
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       +++m++++vt++pd++++ +le+m++ +++++PVVd +gk++G+++ rD+l++
  gi|557694956|ref|YP_008798010.1|  87 RSLMSKNLVTASPDEDVASVLEKMKDFNIRHIPVVDQEGKPLGVLSSRDILDF 139
                                       789*********************9999***********************87 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 !    6.7   0.0   0.00099       8.8       9      34 ..      52      77 ..      49     102 .. 0.90
   2 !   10.4   0.0   6.9e-05      0.62       7      30 ..     115     138 ..     111     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.00099
                                      EEEEE-SSS-EEEEEEHHHHHHHHHH CS
                             IF3_N  9 evrlvdedGeqlGvistreAlrlaee 34
                                       + + d+dG+ +G+i+ r++l  a +
  gi|557694956|ref|YP_008798010.1| 52 SILVLDKDGTLVGIITERDILYAASH 77
                                      58899****************99876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 6.9e-05
                                       SSEEEEE-SSS-EEEEEEHHHHHH CS
                             IF3_N   7 arevrlvdedGeqlGvistreAlr 30 
                                        r++ +vd++G+ lGv+s r++l+
  gi|557694956|ref|YP_008798010.1| 115 IRHIPVVDQEGKPLGVLSSRDILD 138
                                       589******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1080.19
//
Query:       gi|557694957|ref|YP_008798011.1|  [L=590]
Description: aldehyde:ferredoxin oxidoreductase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-64  216.6   0.0      7e-64  216.2   0.0    1.1  1  AFOR_C    Aldehyde ferredoxin oxidoreductase, domains 2 & 3
    1.8e-50  171.6   0.2    3.2e-50  170.8   0.2    1.4  1  AFOR_N    Aldehyde ferredoxin oxidoreductase, N-terminal doma


Domain annotation for each model (and alignments):
>> AFOR_C  Aldehyde ferredoxin oxidoreductase, domains 2 & 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.2   0.0   7.9e-68     7e-64      19     364 ..     234     574 ..     214     584 .. 0.91

  Alignments for each domain:
  == domain 1  score: 216.2 bits;  conditional E-value: 7.9e-68
                                       HHHHH-GGGHHHHHHHTT---BTTTTBS--TTGGGGSHHHHHHHTEEEE.E-TT-SS--EEEEE.......ETEE-- CS
                            AFOR_C  19 elrkyGTaelvnianetgalptknfqegtfekaekisgealeekylvknegCfsCpiaCgrevkveegkk.vkvegp 94 
                                        l+  GTa+  +++ +++a+p+kn++ +t ek+  ++g +++e++lv+++ C +Cp++C+re+      + v +egp
  gi|557694957|ref|YP_008798011.1| 234 LLAVHGTAVAAEALGSNEAIPVKNYTITTTEKYPLVGGRKMSETVLVRRMTCSYCPVSCRRETI----AYgVRGEGP 306
                                       67889**********************999999****************99***********98....344569*** PP

                                       -HHHHHHHTGGGT---HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSS-HHHHTS----TT-THHHHHHHHH CS
                            AFOR_C  95 eyetlaalGsnlgiddleailklnelcdelGlDtisaGntiafamelyekGllkkedtdglelefgdaeallellek 171
                                       +y  + +lG+n++i+dl++i ++ +lc e G+D i++Gnt+a++ +++e+Gl +k      +le+gd e + +l+++
  gi|557694957|ref|YP_008798011.1| 307 DYAQISSLGTNCMIFDLAQISYMTQLCYEVGVDPIEMGNTLAVYADISERGLAEK------KLEWGDFEMMCRLIHE 377
                                       *****************************************************99......89************** PP

                                       HHTT-TTHHHHTT-HHHHHHCTT-GGG--EETTEE--SS-GGG-HHHHHHHHH-TTS.S-SGGG-THHHH....... CS
                            AFOR_C 172 iAkregigdllAeGvkrlaeklgaeelamhvkGlelpaydprgakgmalaYatsnrG.acHlrayliale....... 240
                                       ++++ ++g +l+ G+ + a+++gaeela +vk ++++  dpr+ k++++  a++n G +cH+  y+  ++       
  gi|557694957|ref|YP_008798011.1| 378 TGHGGELGVILGRGAAYTARHYGAEELAPSVKNISIQNADPRAEKAWGVINAVENYGaGCHIWVYPNLIQsfrkigi 454
                                       ********************************************************6379***88888888888887 PP

                                       ..S---TT--HHHHHHHHHHHHHHHHHHHHT--GGGG-HHH......HHHHHHHHHT----HHHHHHHHHHHHHHHH CS
                            AFOR_C 241 ..ekvdpletegkaelvkwfqdltalvdslglCkftseaeerldlelyakllsavtGidvteeellkaGeRiynleR 315
                                            +  ++e  a  +   q   a++dslg+C f++     +d+ +y + + av+G +v ++ +l++Ge +  leR
  gi|557694957|ref|YP_008798011.1| 455 qtIFDNDASEEIIATCIYRKQCEVAALDSLGVCAFSR---LVFDIRDYLDGFDAVYGKEV-ADVFLEVGENVLRLER 527
                                       642222233355666666677799*************...6799**************99.689************* PP

                                       HHHHHHT--HHHS---HHHHHS---SSTTTT---..-HHHHHHHHHHHH CS
                            AFOR_C 316 lfnlreGltrkddtlperlleeplkegpakgkvledeleemldeyYelr 364
                                       ++n+  G++ +   lp++++eepl++g+++gkv+  ++ee l+ y ++r
  gi|557694957|ref|YP_008798011.1| 528 YLNNLYGVSDAGYMLPRKFTEEPLPTGKHRGKVC--NVEEILRHYRRVR 574
                                       *********************************9..89****9998776 PP

>> AFOR_N  Aldehyde ferredoxin oxidoreductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.8   0.2   3.6e-54   3.2e-50       2     196 ..       2     197 ..       1     199 [. 0.94

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 3.6e-54
                                       EEEEEETTTTEEEEEE--HHHHHHH-SCHHHHHHHHHHHS-TTS-TTSTTS-EEEEE-TTTTSSSTTB-EEEEEEE- CS
                            AFOR_N   2 kilrvdLstgkieveelpeelaekylGgrglaakllldevppgvdplspenplvfatGpltgtpapgsgrlvvvaks 78 
                                       +i+++dLs++++ v+e+p+ +   + Ggr l++ l++++     d+l+p+ plv+a+G l gt++p  +rl++v++s
  gi|557694957|ref|YP_008798011.1|   2 RIAEIDLSEKSVVVHEFPDLFEYGVWGGRCLGLGLIARN-SSVKDALDPDSPLVLAVGSLGGTGFPLGNRLTLVFRS 77 
                                       799***************65555589************5.4678********************************* PP

                                       TTTSSEEEEEEETCHHHHHHHCT-SEEEEES--SS-EEEEEETTEEEEEE-TTTTTS-HHHHHHHHHHHHTS.EEEE CS
                            AFOR_N  79 PltgtlgesnaGgrfgaelkraGydaivieGkaekpvylvieddkveiedaedlwgldtyettealkeelgd.kvav 154
                                       Pltgt++ ++ Gg++++ l+ +Gy+a+ i+G+ +k + +v +dd++++ d+e l gl++ et++a++  +gd +v++
  gi|557694957|ref|YP_008798011.1|  78 PLTGTIAWAHTGGYAAYTLAALGYSALYITGRLDKLSAMVMTDDGISFVDVEGLRGLGAVETCAAVRLLAGDaRVLA 154
                                       ********************************************************************88887999* PP

                                       E-HHHHTT-TTB-E.EETTEEE.-SSSHHHHHHHTTEEEEEEE CS
                            AFOR_N 155 iGpaGenlvrfAsisvddgraa.grgGlGavmgsKnlkaivvr 196
                                       iGpaGe+++++A+++ d gr+   r G+Gav+gsKnlkaiv+r
  gi|557694957|ref|YP_008798011.1| 155 IGPAGEKQLPIATVVNDMGRSSgVRHGVGAVFGSKNLKAIVLR 197
                                       **************6668886648*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4302.70
//
Query:       gi|557694958|ref|YP_008798012.1|  [L=323]
Description: aldo/keto reductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-69  234.0   0.0    2.4e-69  233.8   0.0    1.0  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 !  233.8   0.0   1.3e-73   2.4e-69       3     292 ..      17     302 ..      15     304 .. 0.96

  Alignments for each domain:
  == domain 1  score: 233.8 bits;  conditional E-value: 1.3e-73
                                       EEE-SSS-ST......TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SS CS
                      Aldo_ket_red   3 glGtwqlgsk.....eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrd 74 
                                        lGtwq+gs+     + + ++e le++ + +eaG+n +DtAevYg g se+++G+a+k+     + v+iatKv    
  gi|557694958|ref|YP_008798012.1|  17 WLGTWQFGSGswgfgKGYGEKECLEAVYASVEAGVNVIDTAEVYGGGVSEKIVGKAVKE---LGDRVLIATKV---- 86 
                                       58*******9**9999*******************************************...***********.... PP

                                       STTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.H CS
                      Aldo_ket_red  75 aeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.k 150
                                          + +l+ + ++e++e+sl rLg++++Dl+++H p+p  p i+ +++a+e+lvk Gkir+iGvSnfs +ql ka +
  gi|557694958|ref|YP_008798012.1|  87 --APHHLTYNGVIEACERSLNRLGVKTIDLYQIHFPNPLIP-ITQTMRAMEHLVKTGKIRYIGVSNFSLGQLIKArQ 160
                                       ..***************************************.*********************************77 PP

                                       HTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------.TS-HHHH CS
                      Aldo_ket_red 151 kkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrd.ertsknl 226
                                       + +  +iv++qv+ynll+++ ee+ll++c  +++ + ayspl++Glltgky+s +++ d  +r +   +   +++  
  gi|557694958|ref|YP_008798012.1| 161 ALRSEDIVSNQVRYNLLQRQPEEHLLPYCIREKINILAYSPLAQGLLTGKYTSTNPPRDIIRRINPLYTrRYLKRIE 237
                                       777788***************************************************99998877555578889999 PP

                                       HHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                      Aldo_ket_red 227 daaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                        ++ el++la+++g s+ q+al++++ +  + ++i g++n eq+  n++a +++l+ +e+++l +l
  gi|557694958|ref|YP_008798012.1| 238 PLLTELRNLAEKYGASVGQIALAWVF-AHEGCVAIAGSKNREQALNNAAAGNIQLTRDEMEKLTAL 302
                                       9*************************.5778999***************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 2454.09
//
Query:       gi|557694959|ref|YP_008798013.1|  [L=277]
Description: hypothetical protein CSUB_C1532 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   28.7   3.7    1.2e-05   25.2   4.4    2.0  2  DZR             Double zinc ribbon
     0.0015   18.2   1.6     0.0015   18.2   1.6    2.7  3  zinc_ribbon_2   zinc-ribbon domain
     0.0015   18.3   0.2     0.0015   18.3   0.2    2.5  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
  ------ inclusion threshold ------
      0.023   14.0   1.8      0.023   14.0   1.8    2.4  2  zf-RanBP        Zn-finger in Ran binding protein and others
        0.1   12.6   0.4       0.25   11.3   0.1    1.8  2  DUF1358         Protein of unknown function (DUF1358)
       0.13   12.3   4.4       0.28   11.2   4.3    1.6  1  zinc-ribbons_6  zinc-ribbons
       0.14   12.3  10.3       0.15   12.2   4.9    2.5  2  UPF0547         Uncharacterised protein family UPF0547
       0.42   10.5   7.0        2.6    8.0   0.2    2.9  3  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.54   10.2   4.1        9.3    6.2   1.1    2.3  2  Ribosomal_L40e  Ribosomal L40e family
       0.86   10.1   3.7          4    8.0   3.7    1.9  1  zf-CHY          CHY zinc finger
        1.3    9.3   4.9          3    8.1   0.1    2.3  2  FYVE            FYVE zinc finger
          2    8.5   5.5      1e+02    2.9   5.5    2.3  1  HypA            Hydrogenase/urease nickel incorporation, meta
        2.7    8.3   6.3        2.3    8.5   2.9    2.6  2  zf-LITAF-like   LITAF-like zinc ribbon domain
        3.3    7.8   6.7        4.5    7.3   1.1    2.5  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        4.9    7.3  10.1        9.5    6.4   0.6    3.2  3  Zn-ribbon_8     Zinc ribbon domain
        9.3    6.7   6.1    2.3e+02    2.2   6.1    2.6  1  C1_2            C1 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 !   25.2   4.4   1.1e-08   1.2e-05       1      49 []     216     269 ..     216     269 .. 0.83
   2 ?    5.2   1.0      0.02        22       1      23 [.     245     273 ..     245     277 .] 0.78

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.1e-08
                               DZR   1 CpqCgeelppdarfCseCgtklkavaaedrCpsCgekvdpearf......CpeCG 49 
                                       Cp+C++++p +ar+Cs Cg+ l  v+   +Cp C+++    ++       C+ CG
  gi|557694959|ref|YP_008798013.1| 216 CPKCRAANPLKARTCSGCGAILA-VEIGLKCPVCDAPFAYAKKLrmdryiCGICG 269
                                       **********************5.7779*******99655555445666688887 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.02
                               DZR   1 CpqCgee......lppdarfCseCgtklk 23 
                                       Cp C ++      l+ d   C+ Cg++l 
  gi|557694959|ref|YP_008798013.1| 245 CPVCDAPfayakkLRMDRYICGICGSTLV 273
                                       88888888887778888889999999875 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   1.6   1.3e-06    0.0015       2      21 ..     216     235 ..     215     237 .. 0.94
   2 ?   -0.9   0.3       1.3   1.5e+03       1       5 [.     244     248 ..     244     251 .. 0.71
   3 ?   -0.5   0.1         1   1.1e+03      16      21 ..     265     270 ..     261     272 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGt 21 
                                       Cp+C a ++ +a+ C+ CG+
  gi|557694959|ref|YP_008798013.1| 216 CPKCRAANPLKARTCSGCGA 235
                                       *******************8 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.3
                     zinc_ribbon_2   1 fCpnC 5  
                                       +Cp C
  gi|557694959|ref|YP_008798013.1| 244 KCPVC 248
                                       68888 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1
                     zinc_ribbon_2  16 CpyCGt 21 
                                       C  CG+
  gi|557694959|ref|YP_008798013.1| 265 CGICGS 270
                                       777776 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 ?   -2.9   4.3       6.2   6.9e+03       7      15 ..     216     221 ..     215     237 .. 0.59
   2 !   18.3   0.2   1.4e-06    0.0015       6      36 ..     244     274 ..     244     275 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.2
                    Zn_ribbon_SprT   7 CtgCgreyt 15 
                                       C+ C+    
  gi|557694959|ref|YP_008798013.1| 216 CPKCR---A 221
                                       77777...2 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.4e-06
                    Zn_ribbon_SprT   6 rCtgCgreythhlsirrhnYrCrrCkgtLrg 36 
                                       +C+ C+  + +  + r  +Y+C++C++tL+ 
  gi|557694959|ref|YP_008798013.1| 244 KCPVCDAPFAYAKKLRMDRYICGICGSTLVV 274
                                       6***************************986 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 ?   14.0   1.8   2.1e-05     0.023       6      26 ..     215     235 ..     209     235 .. 0.93
   2 ?    0.1   0.2      0.47   5.2e+02      20      26 ..     244     250 ..     243     251 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                                       E-SSS--EEESSSSB-TTT-- CS
                          zf-RanBP   6 dCskClvqNfawstkCvaCqa 26 
                                       +C+kC + N++++ +C  C+a
  gi|557694959|ref|YP_008798013.1| 215 TCPKCRAANPLKARTCSGCGA 235
                                       7******************97 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.47
                                       B-TTT-- CS
                          zf-RanBP  20 kCvaCqa 26 
                                       kC  C+a
  gi|557694959|ref|YP_008798013.1| 244 KCPVCDA 250
                                       5666666 PP

>> DUF1358  Protein of unknown function (DUF1358)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00022      0.25      67     100 ..      35      68 ..      28      82 .. 0.86
   2 ?   -2.9   0.0       5.9   6.6e+03      27      35 ..     160     168 ..     144     185 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                           DUF1358  67 aslalralGWGslyallGvGllsfaiWkllGvks 100
                                        s+ lralGW  +    GvG  s+ +  llGv  
  gi|557694959|ref|YP_008798013.1|  35 VSIVLRALGWRDVRRGTGVGSASYLVIFLLGVVT 68 
                                       6899**********************99999976 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 5.9
                           DUF1358  27 tvaaasala 35 
                                       + a a+a+a
  gi|557694959|ref|YP_008798013.1| 160 VSALAAAVA 168
                                       333333332 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   4.3   0.00025      0.28       2      56 ..     215     269 ..     214     276 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                                       --SSS-S--EE-SSEEE-TTT--..EEEEEEE-SSS-S---EEEETTEEEE--TTTT CS
                    zinc-ribbons_6   2 kCpeCqqelekrgeqyhCeaCqe..dlkkealCpeCeqelevlkaCgavdyfCnkcn 56 
                                       +Cp+C ++   +    +C+ C +   ++    Cp C+ +    k+     y+C  c 
  gi|557694959|ref|YP_008798013.1| 215 TCPKCRAANPLKA--RTCSGCGAilAVEIGLKCPVCDAPFAYAKKLRMDRYICGICG 269
                                       7****98766444..68******666677789***************99****9885 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   4.9   0.00014      0.15       1      21 [.     214     234 ..     214     234 .. 0.99
   2 ?    2.5   0.2      0.14   1.6e+02       2       9 ..     244     251 ..     244     257 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                           UPF0547   1 KvCPeCeakvPvaaqfCphCG 21 
                                       K+CP C+a  P+ a+ C+ CG
  gi|557694959|ref|YP_008798013.1| 214 KTCPKCRAANPLKARTCSGCG 234
                                       9*******************9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                           UPF0547   2 vCPeCeak 9  
                                       +CP C+a+
  gi|557694959|ref|YP_008798013.1| 244 KCPVCDAP 251
                                       7****986 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 ?    5.5   0.2     0.014        16      35      45 ..     210     221 ..     204     225 .. 0.79
   2 ?    8.0   0.2    0.0024       2.6      25      47 ..     229     252 ..     226     255 .. 0.87
   3 ?   -0.7   0.1       1.2   1.3e+03      36      44 ..     261     269 ..     255     273 .. 0.56

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.014
                                       H.TT-B-TTT-- CS
                        zf-C3HC4_3  35 k.rkkkCpiCrr 45 
                                       + ++k+Cp Cr+
  gi|557694959|ref|YP_008798013.1| 210 EgSQKTCPKCRA 221
                                       45799******7 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0024
                                       E-HHHHHHHHH.TT-B-TTT--B- CS
                        zf-C3HC4_3  25 lCeeCaekllk.rkkkCpiCrrpi 47 
                                       +C+ C   l      kCp+C +p 
  gi|557694959|ref|YP_008798013.1| 229 TCSGCGAILAVeIGLKCPVCDAPF 252
                                       79***9999878999*****9885 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.2
                                       TT-B-TTT- CS
                        zf-C3HC4_3  36 rkkkCpiCr 44 
                                        +  C iC 
  gi|557694959|ref|YP_008798013.1| 261 DRYICGICG 269
                                       555555554 PP

>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.1    0.0083       9.3      17      39 ..     214     234 ..     205     236 .. 0.89
   2 ?    4.4   0.1     0.031        35       9      27 ..     255     273 ..     252     276 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0083
                    Ribosomal_L40e  17 miCrkCYArlpprAtnCrkkkCg 39 
                                       + C kC A  p++A  C    Cg
  gi|557694959|ref|YP_008798013.1| 214 KTCPKCRAANPLKARTCS--GCG 234
                                       67***************8..776 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.031
                    Ribosomal_L40e   9 AqKyncdKmiCrkCYArlp 27 
                                       A+K ++d+ iC  C + l 
  gi|557694959|ref|YP_008798013.1| 255 AKKLRMDRYICGICGSTLV 273
                                       99*********99977775 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   3.7    0.0036         4      43      73 ..     215     269 ..     204     271 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0036
                            zf-CHY  43 lcllCeteq.ekavlCkkCkk.......................efaeyfCpiCk 73 
                                       +c +C++++  ka +C+ C+                        ++++y C iC 
  gi|557694959|ref|YP_008798013.1| 215 TCPKCRAANpLKARTCSGCGAilaveiglkcpvcdapfayakklRMDRYICGICG 269
                                       4667766663345567777666666555555555558888888888889999986 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.2      0.13   1.5e+02       8      35 ..     212     237 ..     206     241 .. 0.77
   2 ?    8.1   0.1    0.0027         3      11      34 ..     244     271 ..     239     275 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.13
                                       --SB-TTT--B--SSS--EE-TTT--EE CS
                              FYVE   8 evkkCeiCakkFsllrrrhhCrlCGkvv 35 
                                       + k+C++C+++  l  +   C  CG ++
  gi|557694959|ref|YP_008798013.1| 212 SQKTCPKCRAANPL--KARTCSGCGAIL 237
                                       56889999998876..556799998875 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0027
                                       B-TTT--B--SS....S--EE-TTT--E CS
                              FYVE  11 kCeiCakkFsll....rrrhhCrlCGkv 34 
                                       kC+ C+++F +     + r+ C +CG+ 
  gi|557694959|ref|YP_008798013.1| 244 KCPVCDAPFAYAkklrMDRYICGICGST 271
                                       7********8643334889*******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 ?    2.9   5.5     0.093     1e+02      65      95 ..     237     271 ..     195     275 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.093
                                       EEE--EEEETTTS-EEECHH..H..HHS-TTTSSS CS
                              HypA  65 eevpvkvrCreCgkefelee..k..alrCpkCgsa 95 
                                         v++ ++C +C++ f  ++  +  ++ C+ Cgs+
  gi|557694959|ref|YP_008798013.1| 237 LAVEIGLKCPVCDAPFAYAKklRmdRYICGICGST 271
                                       44566677777777777554342345577777775 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 ?   -0.7   0.1       1.6   1.8e+03      24      42 ..      54      71 ..      48      79 .. 0.59
   2 ?    8.5   2.9    0.0021       2.3       5      67 ..     213     273 ..     209     275 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.6
                     zf-LITAF-like 24 gkltwllalllclfgcllc 42
                                      g+  +l+++ll ++++l +
  gi|557694959|ref|YP_008798013.1| 54 GSASYLVIFLLGVVTFL-L 71
                                      55666666666666652.2 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0021
                     zf-LITAF-like   5 qvdCpaCqqrvvTsveyksgkltwlla.lllclfgcllccliPfcv.dslkdvehyCpnCgallg 67 
                                       q +Cp+C++    + ++ sg++++l++ + l +     +c  Pf + ++l+  ++ C+ Cg++l 
  gi|557694959|ref|YP_008798013.1| 213 QKTCPKCRAANPLKARTCSGCGAILAVeIGLKC----PVCDAPFAYaKKLRMDRYICGICGSTLV 273
                                       568*******************99887555443....346778876599999999******9986 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 ?    7.3   1.1     0.004       4.5      16      44 ..     211     234 ..     197     235 .. 0.75
   2 ?    2.9   0.4     0.097   1.1e+02      19      44 ..     243     269 ..     241     271 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.004
                     Zn_Tnp_IS1595  16 pngfvCPhCgsrkayriktrglfqCkeCr 44 
                                       ++  +CP+C  + + + +t     C+ C+
  gi|557694959|ref|YP_008798013.1| 211 GSQKTCPKCRAANPLKART-----CSGCG 234
                                       45578*****777777777.....88886 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.097
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayrikt...rglfqCkeCr 44 
                                         CP C        +++     ++ C  C+
  gi|557694959|ref|YP_008798013.1| 243 LKCPVCDAPfA---YAKklrMDRYICGICG 269
                                       57****95543...3333347888888886 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.6    0.0084       9.5      17      34 ..     207     221 ..     203     227 .. 0.73
   2 ?    0.6   0.2      0.56   6.3e+02      27      34 ..     228     235 ..     221     241 .. 0.70
   3 ?    5.3   0.2     0.019        21       7      35 ..     244     272 ..     242     275 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0084
                       Zn-ribbon_8  17 vlqsisdapltaCPeCgs 34 
                                       +l+   + ++++CP+C +
  gi|557694959|ref|YP_008798013.1| 207 PLR---EGSQKTCPKCRA 221
                                       444...566999****87 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.56
                       Zn-ribbon_8  27 taCPeCgs 34 
                                        +C  Cg+
  gi|557694959|ref|YP_008798013.1| 228 RTCSGCGA 235
                                       45999997 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.019
                       Zn-ribbon_8   7 rCeeCghefevlqsis.dapltaCPeCgs.e 35 
                                       +C  C+  f    +   d     C  Cgs  
  gi|557694959|ref|YP_008798013.1| 244 KCPVCDAPFAYAKKLRmD--RYICGICGStL 272
                                       799999999955554423..44599999944 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   6.1      0.21   2.3e+02      17      27 ..     241     251 ..     202     274 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.21
                              C1_2  17 esfnCsaCgrk 27 
                                       +  +C +C+ +
  gi|557694959|ref|YP_008798013.1| 241 IGLKCPVCDAP 251
                                       33445555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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):              16  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1893.17
//
Query:       gi|557694960|ref|YP_008798014.1|  [L=111]
Description: hypothetical protein CSUB_C1533 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       253  (0.0141112); expected 358.6 (0.02)
Passed bias filter:                      175  (0.00976072); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 846.24
//
Query:       gi|557694961|ref|YP_008798015.1|  [L=125]
Description: hypothetical protein CSUB_C1534 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 994.75
//
Query:       gi|557694962|ref|YP_008798016.1|  [L=134]
Description: hypothetical protein CSUB_C1535 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.6   0.4       0.56    9.9   0.1    2.1  2  DUF4364   Domain of unknown function (DUF4364)
      0.066   13.1   0.2      0.093   12.6   0.2    1.3  1  Vip3A_N   Vegetative insecticide protein 3A N terminal


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 ?    4.5   0.0    0.0029        26      35      78 ..       5      49 ..       4      74 .. 0.83
   2 ?    9.9   0.1   6.3e-05      0.56      30      80 ..      85     133 ..      54     134 .] 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0029
                           DUF4364 35 dlqqalseLvesglieee.ekenktlykiTekGketlelfenrip 78
                                      d+++ l +Lv ++ i+ e  ++ k ++++T+kG+ +  + ++++p
  gi|557694962|ref|YP_008798016.1|  5 DIKEKLRDLVIEEEISPEhVEKIKRFIRLTKKGQIVFVTPKEKLP 49
                                      577889999999999999666889999******999888888887 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 6.3e-05
                           DUF4364  30 ytnYfdlqqalseLvesglieeeekenktlykiTekGketlelfenripks 80 
                                        ++Yf+++  lseL +++++ +   e  +++ +  + ke+l+ +e+ i+++
  gi|557694962|ref|YP_008798016.1|  85 DADYFQVTARLSELKSQNYVLS--VERGEYIIVLARLKEILDRLESMIQEK 133
                                       579*****************98..467788888888899999999998875 PP

>> Vip3A_N  Vegetative insecticide protein 3A N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2     1e-05     0.093      95     143 ..      76     127 ..      54     134 .] 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1e-05
                           Vip3A_N  95 kldaintmlrvylpkitsmlsdvmkqnyalslq.ieyls..kqlqeisdkld 143
                                         + i   l     ++t+ ls++  qny+ls++  ey+    +l+ei d+l+
  gi|557694962|ref|YP_008798016.1|  76 SNEEISRGLDADYFQVTARLSELKSQNYVLSVErGEYIIvlARLKEILDRLE 127
                                       445666677777789****************9724776422789****9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1079.51
//
Query:       gi|557694963|ref|YP_008798017.1|  [L=133]
Description: hypothetical protein CSUB_C1536 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   49.0   0.0    4.9e-13   48.4   0.0    1.3  1  ArsA_HSP20  HSP20-like domain found in ArsA
    5.5e-13   49.0   0.0      9e-13   48.3   0.0    1.4  1  HSP20       Hsp20/alpha crystallin family
    0.00031   21.1   0.0    0.00047   20.5   0.0    1.3  1  PIH1_CS     PIH1 CS-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 !   48.4   0.0   8.2e-17   4.9e-13       2      62 ..      48     119 ..      47     120 .. 0.97

  Alignments for each domain:
  == domain 1  score: 48.4 bits;  conditional E-value: 8.2e-17
                        ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkig............nfrRqitLPsvlarkevtsAkfedgvLeIr 62 
                                       +eyv+++d+P++dke+idl+ +++ L++++             ++r  i LP++++  ++ +A++ +gvLeIr
  gi|557694963|ref|YP_008798017.1|  48 NEYVVTIDMPGADKEKIDLYADENRLIVEAPcrrdipsarygnRYRLMIELPTTVDTSNI-KARYLQGVLEIR 119
                                       89****************************************999999************.***********7 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   1.5e-16     9e-13       2      91 ..      43     126 ..      42     133 .] 0.88

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.5e-16
                                       --SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEET CS
                             HSP20   2 ikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslkd 78 
                                       i+++e+e+ v++d+pg +ke +++  ++nr++v++  +      +++ + r  + ++ +++LP  vd++++ka + +
  gi|557694963|ref|YP_008798017.1|  43 IMDTENEYVVTIDMPGADKEKIDLYADENRLIVEAPCR------RDIPSARYGNRYRLMIELPTTVDTSNIKARYLQ 113
                                       789********************************999......34444455678********************** PP

                                       TEEEEEEEBSS-- CS
                             HSP20  79 GvLtvtvpkkepe 91 
                                       GvL++ v kk++ 
  gi|557694963|ref|YP_008798017.1| 114 GVLEIRVSKKKTR 126
                                       *********9987 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   7.8e-08   0.00047      31      87 ..      48     113 ..      43     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.8e-08
                           PIH1_CS  31 kelaieielPllksikevklrvgerrlel..........eskkakyfLslkLpYpvdedkveAkFvk 87 
                                       +e++++i++P+    ++++l  +e+rl +          +  +++y+L ++Lp +vd ++++A++ +
  gi|557694963|ref|YP_008798017.1|  48 NEYVVTIDMPGA-DKEKIDLYADENRLIVeapcrrdipsARYGNRYRLMIELPTTVDTSNIKARYLQ 113
                                       79*********9.7899************99****998544449********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 991.00
//
Query:       gi|557694964|ref|YP_008798018.1|  [L=249]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  118.0   0.0    6.5e-34  117.8   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 !  117.8   0.0   3.6e-38   6.5e-34       1     211 [.      21     226 ..      21     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 3.6e-38
                                       EEEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETTEEE-SEEEEEETTT.SEEEEEEE... CS
                              PAC2   1 LilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveegrelepprlyakdsgsrdllvlqg... 74 
                                       L+lGfp++G+Vg++av++++e+l  e+ g++ds + lp     p+v v++g + e +r+y ++    ++l + +   
  gi|557694964|ref|YP_008798018.1|  21 LLLGFPDTGLVGSIAVSYMVEQLRPEEKGYVDSAE-LP-----PIVPVRRGYPKELIRIYESS----NFLTILSelp 87 
                                       79*********************************.9*.....********99999****775....56666666*5 PP

                                       E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHH.H..CT...-CEEEEH CS
                              PAC2  75 repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleel.e..es...eyggivg 145
                                       + p l  + f++a++dwa++ +v  + +L+g++  +r ++  ++p kv++ + +  ++eel +  ++   ++g+i+g
  gi|557694964|ref|YP_008798018.1|  88 IPPMLIRD-FSEAMIDWADDKKVGWIGCLTGVAEPRRLEI--DTP-KVFVLSAELRRAEELaKflDAevfQEGFITG 160
                                       55555555.************************9999765..677.7877775555555553344335799****** PP

                                       HHHHHHHHHHHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHH CS
                              PAC2 146 itglLlsaakergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqlee 211
                                       + + +l ++ +rgi++ +lla+++  +pdP aaa ll +l kl++  vd+++L e  e ++ ql  
  gi|557694964|ref|YP_008798018.1| 161 VHAEILRQGLRRGIEVDVLLAQAHLNYPDPGAAAQLLTRLPKLVNEHVDVKPLLESEENIRIQLRD 226
                                       ***********************************************************9988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1841.74
//
Query:       gi|557694965|ref|YP_008798019.1|  [L=667]
Description: acetyl-CoA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-91  306.9   0.0    2.1e-91  306.6   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    1.8e-27   96.1   0.2    4.2e-27   94.9   0.2    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    4.7e-18   64.9   2.8    1.1e-17   63.6   2.8    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 !  306.6   0.0   3.6e-95   2.1e-91       3     422 ..      86     535 ..      84     536 .. 0.86

  Alignments for each domain:
  == domain 1  score: 306.6 bits;  conditional E-value: 3.6e-95
                                       HHHHHST.TSEEEEE..........CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHH CS
                       AMP-binding   3 eqaaktp.dkvalvd..........sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallail 68 
                                       ++a+ ++ +kva+++            + +++TY el+++vnrlA++++slG++kgdr ai+lp+ pe+ +++la++
  gi|557694965|ref|YP_008798019.1|  86 RHAKSWRkNKVAYIWegepvdgdgkPLSIRKYTYYELYREVNRLAHVFLSLGLRKGDRAAIYLPMIPELPMTMLALA 162
                                       666666668899988888888887766789*********************************************** PP

                                       HTT-EEEEEETTS-HHHHHHHHHHHTESEEE.........ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHC CS
                       AMP-binding  69 kaGavvvplnptltaeelayiledseakvli.........atvdselleklleaaakleavklvivldadellkeee 136
                                       ++G++  ++ ++++ae la  ++d +ak+l+         +    ++l++++++a +  +v++++v+++++ + + +
  gi|557694965|ref|YP_008798019.1| 163 RIGVIFTVVFSGFSAENLAIRVNDLGAKILVtadgfyrrgR---LINLKEVADKALESTDVEKIVVVKRAGNEVAMK 236
                                       *******************************9877764321...233566666666667777788888766544433 PP

                                       CCHCCCCSCTTS.........-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-E CS
                       AMP-binding 137 lkeeeeseekae.........kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddv 204
                                       + +++ +    +           +e+e+l++ +++y++YTSGTTGkPKG+++ ++ ++  + s  ++  f+++++dv
  gi|557694965|ref|YP_008798019.1| 237 E-GRDFWL---HdllrtvpenLVVEPESLDSTHPLYVLYTSGTTGKPKGIIHDTGGYAVLLNST-MKWVFDIRDEDV 308
                                       2.233233...13456778885667789**************************8887776664.5555778899** PP

                                       EEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHC CS
                       AMP-binding 205 vlsilplahifglilelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkak 280
                                       +++++++ +++g+++ ++++l++Gat+v+++++++ ++ +++++ ie+++v+v++++P+++++l++ g++   +k++
  gi|557694965|ref|YP_008798019.1| 309 YFCTADIGWVTGHSYIVFGPLMAGATIVMYEGTPDyPTVERWWQIIERYGVNVFYTTPTAVRMLMRFGNEP--VKKH 383
                                       ***********************************777****************************55555..5788 PP

                                       CGTT-SEEEEESS-EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEE....CHCTTTCTSTTS-BEE-TTEEEEE CS
                       AMP-binding 281 dlsslrlvllggeplspellrffralfge...evlegYGlTEttgvvtv....lpleedkkklgsvGkplpgvevki 350
                                       d s lr++ ++gep++p+++r++ +++ge   +v  ++++TEt+g+++     l  +    k+g+ G plpg+++++
  gi|557694965|ref|YP_008798019.1| 384 DRSTLRIIHSVGEPINPAAWRWLFEVVGErrcPVGSTWWMTETGGILIShlpgL--MLTPLKPGTNGLPLPGIDAEV 458
                                       99**************************9******************5557653..3334479************** PP

                                       E-TTTSCBEETTSEEEEEEEET.....TS-SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEE CS
                       AMP-binding 351 vDeetgepvpdgeeGellvrgp.....gvmkgYlkkpeataeafdse.grwlrTGDlgrldedGyleivgRkkdlik 421
                                       vDe+ g+  ++g+ G l++r+p     g   g +k+pe+ +++++++ ++ + TGD ++ d dGy+++ gR+++++k
  gi|557694965|ref|YP_008798019.1| 459 VDEK-GNAAAPGQRGYLVIRKPwpgmpGPPTGMWKEPERYRQVYWEKvNGVFFTGDYAVKDFDGYIWVAGRADEVLK 534
                                       **98.99999************6655557889*************76888**************************9 PP

                                       E CS
                       AMP-binding 422 l 422
                                       +
  gi|557694965|ref|YP_008798019.1| 535 V 535
                                       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 !   94.9   0.2   6.9e-31   4.2e-27       1      76 []     544     622 ..     544     622 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 6.9e-31
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---.---...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-T CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg.sea...leeeLkahvrkelgpyavpkkvvfvdelpktr 73 
                                       e+Es+lvsh aVaeaaVvGvpde+kGe++vafVvlk+g +     ++++L+++vr++ g++a+p+ + fv++lpktr
  gi|557694965|ref|YP_008798019.1| 544 ELESVLVSHAAVAEAAVVGVPDEIKGETPVAFVVLKSGyQ-GggeMAQQLMKYVRETYGAIATPSSILFVSKLPKTR 619
                                       89*********************************99852.2345******************************** PP

                                       TS- CS
                     AMP-binding_C  74 sGK 76 
                                       sGK
  gi|557694965|ref|YP_008798019.1| 620 SGK 622
                                       **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 !   63.6   2.8   1.9e-21   1.1e-17       1      55 []      28      83 ..      28      83 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.9e-21
                                      HHHHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTC.T-EESTT-EE-HHHHH CS
                            ACAS_N  1 ykelykeSiedpeaFWaeqakeldWekpfdkvldgskgp.fikWFeGGklNicyNc 55
                                      yk++++  +ed+ +FW++ a++l+W++p+d+v+++ ++p  +kWF+GG+lN++y c
  gi|557694965|ref|YP_008798019.1| 28 YKRFWRTTVEDYIGFWEKEARNLEWFRPWDHVVEKGEHPfVFKWFVGGQLNMSYLC 83
                                      999************************************889************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (667 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); 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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.41
# Mc/sec: 4833.66
//
Query:       gi|557694966|ref|YP_008798020.1|  [L=241]
Description: 5-formyltetrahydrofolate cyclo-ligase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  112.9   0.0    1.9e-32  112.6   0.0    1.1  1  5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family


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 !  112.6   0.0   1.1e-36   1.9e-32       1     186 [.       9     201 ..       9     202 .. 0.90

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 1.1e-36
                                       HHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHTSHHHHH-SEE.........EE----TTS---HHHHHHHHHTTEE CS
                    5-FTHF_cyc-lig   1 KqelRkqllaalralseeevaaesealsqrieslkesqeakrv.........alyvsvkgeidtkelikklleegke 68 
                                       Kqe+R++   ++r+l+e++vaa + ++ +ri+++k+++ea ++         a +v+v+++ ++ ++++++l++gk+
  gi|557694966|ref|YP_008798020.1|   9 KQEIRQR---IWRLLEERGVAAFPTPVAGRIPNFKGAAEAANLlrtskhyidADVVKVNPDAPQAPVRRNVLRDGKK 82 
                                       899***9...******************************9999********************************* PP

                                       EEEEEECSSCTEECEEEEEECCCCCCCCCHCTS.SCE--TTECCBCGGGG-SEEEE--SEEETTS-EE-SSTTHHHH CS
                    5-FTHF_cyc-lig  69 vllPrvrlesgslkvvrlttlkeedslesgkyg.lkePeeeeerelalekldlvlvPgvAfdkeGaRlGkGkGyyDr 144
                                       +++P++r + g+l +     +++  + +++  g +  +++ e+r l+   +dlv+v++vA++  G R+GkG+Gy + 
  gi|557694966|ref|YP_008798020.1|  83 LIMPTPRIKHGFLMINPKKLPQRGLREAATIAGaYRYGVKVEPRDLP--GIDLVVVGSVAVSPSGWRIGKGEGYSEI 157
                                       **********9999888666655444443333335677777777777..9*************************** PP

                                       HHHHHTS.T-SS--EEEEE--GGGEES.-----ST----SEEE- CS
                    5-FTHF_cyc-lig 145 flarlkg.gagdkpltvglaldeqlve.rlPleehDvpvdevvt 186
                                       ++a l+   +  ++++v +++++ ++  ++P++++D  vd + t
  gi|557694966|ref|YP_008798020.1| 158 EYALLRTfCKVGEDTPVYTTVHDLQIVdKIPHQAYDLAVDRIFT 201
                                       *********************9987777*************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); 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: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1758.39
//
Query:       gi|557694967|ref|YP_008798021.1|  [L=338]
Description: mannose-6-phosphate isomerase / glucose-6-phosphate isomerase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  100.6   0.0    1.2e-28  100.0   0.0    1.2  1  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
  ------ inclusion threshold ------
       0.02   14.8   0.1      0.054   13.5   0.0    1.6  2  DUF4888     Domain of unknown function (DUF4888)
      0.035   14.0   0.1        9.1    6.1   0.1    2.9  2  SIS         SIS 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 !  100.0   0.0   2.1e-32   1.2e-28       9     149 ..     195     330 ..     189     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.0 bits;  conditional E-value: 2.1e-32
                                       HHHHTTSEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH..... CS
                        bact-PGI_C   9 AlelagklpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdeeehprv 85 
                                       A+ + g+ +vi++ ++ l++aA+R+k+qlnenAK+p+++++ pea hne+ g+     +  ++  v+lr++ e+  v
  gi|557694967|ref|YP_008798021.1| 195 ARPMLGRHVVIVS-ADNLYSAAYRLKCQLNENAKHPCHVATAPEAFHNEVEGW----TNLGNYCYVFLRSGYEQLMV 266
                                       7788999999999.999************************************....89****************** PP

                                       ...HHHHHHHHTTTSSEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S-TTTTHHHH CS
                        bact-PGI_C  86 kkraeivkelaeergvrvtevkaegesplerlaslillgDfvSvylAllrgvDPtpvpaIdelK 149
                                       +  ++ +ke+++++g+ v+e+  + +sp+++l++  l++D+ S+ lA l++vDP   ++I +l+
  gi|557694967|ref|YP_008798021.1| 267 SDGLDWMKEYLRSNGAAVIEIGVKSSSPVSELLKFLLIADLLSLGLACLKKVDPIMLHTIPKLR 330
                                       *********************************************************9999987 PP

>> DUF4888  Domain of unknown function (DUF4888)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.1e-06     0.054      21      66 ..      92     137 ..      85     141 .. 0.88
   2 ?   -3.0   0.0       1.1   6.7e+03      99     116 ..     279     296 ..     275     298 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.1e-06
                           DUF4888  21 sneyetinvtyllsngysssvsapgnddgghltqsidfkglkqidl 66 
                                       s   +t++ ++ + +g+s sv+  g   gg lt  ++++gl+ + +
  gi|557694967|ref|YP_008798021.1|  92 SYSGDTVETSWAFVDGFSKSVAVVGVSSGGRLTSLMEMRGLRVVKV 137
                                       5666899999*******************************98865 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.1
                           DUF4888  99 qngqkvsiyssdssspvs 116
                                        ng  v      ssspvs
  gi|557694967|ref|YP_008798021.1| 279 SNGAAVIEIGVKSSSPVS 296
                                       577777777888999998 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0015       9.1       6      69 ..      41     100 ..      38     115 .. 0.77
   2 ?    4.3   0.0    0.0058        34       7      96 ..     202     297 ..     200     306 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0015
                                       SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHH CS
                               SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdl 69 
                                       +ri++ G G s+ +++ +++   +   ++ve  ++        ++  +d+l+i +s+sg t ++
  gi|557694967|ref|YP_008798021.1|  41 RRIFIAGVGGSGIVGDIISAIRDHNLPPPVETLKTFR-LP---GYTGPDTLLIPVSYSGDTVET 100
                                       79*************9999887777766666555544.33...478888888888888887766 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0058
                                       EEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHH.HHHTGGGG-STTCEEEEEESSSHHHHHHHH....HH.HHH CS
                               SIS   7 riyvlGaGtsyaiakelalkleeiggivvevedase.lkhgvlalideddlvilisfsgetkdlvaa....ae.lak 77 
                                       +++++ a   y++a  l+ +l+e ++ +++v  a+e ++++v +  + +  + ++ +sg++  +v +     + +++
  gi|557694967|ref|YP_008798021.1| 202 HVVIVSADNLYSAAYRLKCQLNENAKHPCHVATAPEaFHNEVEGWTNLGNYCYVFLRSGYEQLMVSDgldwMKeYLR 278
                                       56666667789999999999999999999999999977888778888888888888888876655432222455888 PP

                                       HTTSEEEEEESSTTSHHHH CS
                               SIS  78 ergakiiaITdskgsplar 96 
                                       ++ga++i I  +++sp+++
  gi|557694967|ref|YP_008798021.1| 279 SNGAAVIEIGVKSSSPVSE 297
                                       8888888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); 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 0.28s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2508.61
//
Query:       gi|557694968|ref|YP_008798022.1|  [L=264]
Description: competence/damage-inducible protein CinA [Candidatus Caldiarchaeum subterraneum]
Scores for 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-34  117.4   0.0      6e-34  116.8   0.0    1.3  1  MoCF_biosynth  Probable molybdopterin 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 !  116.8   0.0   3.3e-38     6e-34       2     143 ..      10     182 ..       9     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.8 bits;  conditional E-value: 3.3e-38
                                       EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS.SEEEEESS-SSSTT--HHHH CS
                     MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea.dviittGGtGptpdDvtpea 77 
                                       vi vG+ell g++ +tn  +l+ +l+elg+ v++ t+v+Dd ++i+ al++al+++   ++++GG+Gpt+dD t++a
  gi|557694968|ref|YP_008798022.1|  10 VINVGNELLDGRTINTNLNWLCGKLSELGYVVKRATIVRDDLNDIAIALREALRRKpMWLFISGGLGPTHDDKTVQA 86 
                                       999**********************************************99999999******************** PP

                                       HHHHHSEE-HHHHHHHHHHHHHHCC...............................TTSHGGGGGGE.EETTEEEEE CS
                     MoCF_biosynth  78 laklfekelegfeeafrrvslkpgk...............................pvgvapgailsravgktiigL 123
                                       +a++++k+l+ ++ a++ +++++ +                                vg+apg+ l+++ g +i++L
  gi|557694968|ref|YP_008798022.1|  87 VARALGKRLKIDKTALESIRRRYIElfeagvikdpsltkerlkmaklpegsktlrnRVGTAPGVLLEKS-GVKIVCL 162
                                       **********************999***************************************99976.888**** PP

                                       -SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth 124 PGspkavkealeeillpale 143
                                       PG+pk+ ++++e+ l+p l+
  gi|557694968|ref|YP_008798022.1| 163 PGVPKELMDIFENELRPLLR 182
                                       ***************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1856.34
//
Query:       gi|557694969|ref|YP_008798023.1|  [L=217]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   64.6   0.0    2.2e-17   63.8   0.0    1.3  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    3.4e-17   62.6   0.1    4.7e-14   52.3   0.0    2.2  2  Metallophos_3  Metallophosphoesterase, calcineurin superfamil
    2.7e-16   60.7   0.0    3.6e-16   60.3   0.0    1.2  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 !   63.8   0.0   3.6e-21   2.2e-17       1     152 [.       2     201 ..       2     205 .. 0.68

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 3.6e-21
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepe...vleellela.pvlaVrGNnD......... 62 
                                       Mk++  SD+H++++a  a++e++ +   d ++++GD+   ++ p+   +l+++ +   pvl V+GN+D         
  gi|557694969|ref|YP_008798023.1|   2 MKVLQASDIHGSMAAASALAEKAMNY--DIVVLVGDIthFGAVPQaepILATVAKSGrPVLFVPGNCDhpsllgwrp 76 
                                       9*************************..********8663333322237777777669****************999 PP

                     Metallophos_2  63 ................eevveedvlreaaelgtdl...........peeaelel....agek......vlliHgdpl 102
                                                       +          + +lg+             +  +e+e        +      +l+ H  p 
  gi|557694969|ref|YP_008798023.1|  77 pnkniinihgaivrqgG--------YDFYGLGGGNlspfntliefsE--EEFESmlskF--NpasesfILISHTPPF 141
                                       88766655444433331........3333333333665554444321..2222123330..2444556777777766 PP

                     Metallophos_2 103 ...........gvkdalaellkeaeegsd.vvvcGHtHvp.evekeggvlvvnPGsvgeprdg 152
                                                   ++ a+++ +++  ++    v+cGH+H+  +++k+g+++vvn+G ++e+ ++
  gi|557694969|ref|YP_008798023.1| 142 gvdadigrgrhLGSTAIRKFVET--KR-PlAVCCGHIHEGrSISKIGETVVVNAGPAKEGFYA 201
                                       88888887554444444444444..44.35*********879***************998765 PP

>> Metallophos_3  Metallophosphoesterase, calcineurin superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1   0.00021       1.3       7      45 ..       3      39 ..       1      46 [. 0.85
   2 !   52.3   0.0   7.9e-18   4.7e-14      83     255 ..      50     213 ..      44     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00021
                                      EEEEEE--TT-GGGHHHHHHHHHHH--SEEEEES----- CS
                     Metallophos_3  7 kvlaisdlkgevellerlveviedkdpDllvlvGdlvka 45
                                      kvl +sd++g++     l e++   + D++vlvGd+ + 
  gi|557694969|ref|YP_008798023.1|  3 KVLQASDIHGSMAAASALAEKAM--NYDIVVLVGDITHF 39
                                      99*********999999999876..68********9765 PP

  == domain 2  score: 52.3 bits;  conditional E-value: 7.9e-18
                                       HHHHTT-SEEEEE--TTS--HHHHHHHHHHTTTT-TTEEE-SSEEEEETTTEEEEEE-SEEESS--BSSSS-EEEHH CS
                     Metallophos_3  83 relgeldvpafvvPGkrDaPlevflreayeaevvfpnlkvvhesfaekeGevliaGmGGeivdgekeeefrLkYPaw 159
                                        ++ + + p+++vPG+ D P           +    n+  +h++++ + G + + G+GG       + ++ +++   
  gi|557694969|ref|YP_008798023.1|  50 ATVAKSGRPVLFVPGNCDHPSLLGW------RPPNKNIINIHGAIVRQGG-YDFYGLGGGN---LSPFNTLIEFSEE 116
                                       56677778999********975544......455569999*****99988.*******953...345578899**** PP

                                       HHHHHGGGGGGS---EEEEEESS--S-.SSTBTTBS---S-HHHHHHHHHH--SEEEE-SS--EE..EEETTEEEEE CS
                     Metallophos_3 160 eveyrLkvlkelkdrrkvlllatpPig.elvadkglkekgsevvaelvktlnPevvvvghavkeh..eelgktlvvn 233
                                       e e +L  ++ +  +  +l+ +tpP g + ++ +g ++ gs  + ++v t +P  v +gh + ++   ++g+t+vvn
  gi|557694969|ref|YP_008798023.1| 117 EFESMLSKFNPA-SESFILISHTPPFGvDADIGRG-RHLGSTAIRKFVETKRPLAVCCGHIHEGRsiSKIGETVVVN 191
                                       ************.8899********8834457777.999***********************999999********* PP

                                       --BGGGTEEEEEETTTTEEEEE CS
                     Metallophos_3 234 PGaleeGdfavvdleekkvele 255
                                        G  +eG +a +++ +k+v+ e
  gi|557694969|ref|YP_008798023.1| 192 AGPAKEGFYASLEILGKEVKAE 213
                                       *******************975 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   6.1e-20   3.6e-16       1     203 [.       2     177 ..       2     178 .. 0.79

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 6.1e-20
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCH CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegf 77 
                                       +++l+ +D+H     g+++++ +l +++    + d+v+l+GD+++ g +++  +  la + k++ pv +++GN++  
  gi|557694969|ref|YP_008798023.1|   2 MKVLQASDIH-----GSMAAASALAEKA---MNYDIVVLVGDITHFGAVPQ-AEPILATVAKSGRPVLFVPGNCD-- 67 
                                       89********.....**********888...788*************9999.9999999999999**********.. PP

                                       HH.HHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE..EEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHH CS
                       Metallophos  78 ee.ellnkygylgifsepwrsdaevfnnlplaslgsgs..lkvlllhGgspellvsldklgslnleleapepgdewl 151
                                        + +             +wr ++  +n++++ + +  +  ++++ l Gg      +l++ ++l  + e++   + +l
  gi|557694969|ref|YP_008798023.1|  68 -HpS-----------LLGWRPPN--KNIINIHGAIVRQggYDFYGLGGG------NLSPFNTLIEFSEEEF--ESML 122
                                       .112...........23444442..255666554444457888888888......4555555555555444..4444 PP

                                       HHHHHHTTCSEEEEEESSESS.....CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 152 kdlekrekadwvivlgHsply.....rgsgylfgdealedllkkygvdlvisGHtHv 203
                                       ++       +  i+++H p+       g g + g+ a++++ + +++ +v++GH+H+
  gi|557694969|ref|YP_008798023.1| 123 SK--FNPASESFILISHTPPFgvdadIGRGRHLGSTAIRKFVETKRPLAVCCGHIHE 177
                                       44..45567899999*****************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1562.45
//
Query:       gi|557694970|ref|YP_008798024.1|  [L=192]
Description: hypothetical protein CSUB_C1543 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   87.1   8.4    2.5e-13   50.2   1.4    2.2  2  CBS             CBS domain
     0.0076   16.2   4.3      0.019   14.8   4.3    1.6  1  Prok-RING_1     Prokaryotic RING finger family 1
  ------ inclusion threshold ------
      0.034   14.2   3.1        1.2    9.3   1.0    2.3  2  zf-BED          BED zinc finger
      0.075   12.6   1.6      0.081   12.5   0.2    1.7  2  zf_C2H2_13      Zinc finger domain
       0.61    9.9   5.4        6.2    6.7   0.2    2.7  2  zinc_ribbon_2   zinc-ribbon domain
        4.7    7.4   7.8        6.2    7.0   1.7    2.3  2  zf-CHCC         Zinc-finger domain
        5.2    6.8   6.8        2.7    7.8   3.1    2.3  3  Ribosomal_S27e  Ribosomal protein S27


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 !   41.1   0.9     7e-14   1.8e-10       1      55 [.       7      60 ..       7      62 .. 0.93
   2 !   50.2   1.4   9.8e-17   2.5e-13       1      53 [.      72     123 ..      72     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 7e-14
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      V+d+  +++++v + +++ ea++ m+e+++s++ V+ + gk+vG+vt+rD+++++
  gi|557694970|ref|YP_008798024.1|  7 VKDVVKSPLISVEEGSSVIEAAKVMAERKISGI-VITNKGKPVGLVTERDIVSKV 60
                                      899**********************9888****.87789************9976 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 9.8e-17
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       V+++m+++++t++ ++tl ea++lm +k+v+rl+V+  d++++G++t rD+l 
  gi|557694970|ref|YP_008798024.1|  72 VKEVMSKPLITIDIEATLLEAVDLMNRKKVRRLLVT-RDDEVIGLFTIRDVLA 123
                                       89***********************9999****998.6677**********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 !   14.8   4.3   7.6e-06     0.019       6      43 ..     127     172 ..     124     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.6e-06
                       Prok-RING_1   6 kCpvCgkelkee........dDiVvCpeCgtpyHraCyekagkCvn 43 
                                       +C  Cgk++k+          Di++   Cg++y ++C +++  C+ 
  gi|557694970|ref|YP_008798024.1| 127 ICAYCGKPIKPLlpsqpqseADIIIECSCGAVYMQECAKTVVYCIY 172
                                       79*****99976677777779****99*****************86 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.014        35      18      26 ..     127     135 ..     117     137 .. 0.89
   2 ?    9.3   1.0   0.00045       1.2       8      26 ..     161     177 ..     158     180 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.014
                                       EETTTTEE- CS
                            zf-BED  18 vCryCgkil 26 
                                       +C yCgk +
  gi|557694970|ref|YP_008798024.1| 127 ICAYCGKPI 135
                                       7*****977 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00045
                                       ----GGSS--EETTTTEE- CS
                            zf-BED   8 tpvslkeqkavCryCgkil 26 
                                       +++   +++++C+yC ++l
  gi|557694970|ref|YP_008798024.1| 161 QECA--KTVVYCIYCSRKL 177
                                       5566..99*******9987 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.1       4.3   1.1e+04      24      29 ..      45      50 ..      44      51 .. 0.83
   2 ?   12.5   0.2   3.2e-05     0.081      18      28 ..     126     136 ..     120     137 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.3
                        zf_C2H2_13 24 GkPisl 29
                                      GkP+ l
  gi|557694970|ref|YP_008798024.1| 45 GKPVGL 50
                                      9**965 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.2e-05
                        zf_C2H2_13  18 RvCnkCGkPis 28 
                                       R+C  CGkPi+
  gi|557694970|ref|YP_008798024.1| 126 RICAYCGKPIK 136
                                       9********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 ?    6.7   0.2    0.0024       6.2      15      23 .]     127     135 ..     125     136 .. 0.78
   2 ?    4.5   1.2     0.012        30      10      19 ..     164     173 ..     154     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0024
                     zinc_ribbon_2  15 FCpyCGtpl 23 
                                        C yCG p+
  gi|557694970|ref|YP_008798024.1| 127 ICAYCGKPI 135
                                       699999885 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.012
                     zinc_ribbon_2  10 qdnakFCpyC 19 
                                        +++++C yC
  gi|557694970|ref|YP_008798024.1| 164 AKTVVYCIYC 173
                                       467889**** PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.5     0.028        72      29      35 ..     127     133 ..     125     134 .. 0.84
   2 ?    7.0   1.7    0.0024       6.2      18      36 ..     158     176 ..     157     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.028
                                       EETTTTE CS
                           zf-CHCC  29 dCgYCgl 35 
                                        C YCg+
  gi|557694970|ref|YP_008798024.1| 127 ICAYCGK 133
                                       5*****7 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0024
                                       EEEE--TTSEEEETTTTEE CS
                           zf-CHCC  18 vyieldkkgpvdCgYCglr 36 
                                       vy++  +k+ v C YC+++
  gi|557694970|ref|YP_008798024.1| 158 VYMQECAKTVVYCIYCSRK 176
                                       788878999*******985 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1       0.6   1.5e+03      29      36 ..     128     135 ..     125     137 .. 0.84
   2 ?   -1.9   0.1       1.1   2.9e+03      23      35 ..     147     158 ..     145     162 .. 0.68
   3 ?    7.8   3.1     0.001       2.7      22      38 ..     163     179 ..     151     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.6
                                       ESSSTCEE CS
                    Ribosomal_S27e  29 CisCgkvL 36 
                                       C  Cgk++
  gi|557694970|ref|YP_008798024.1| 128 CAYCGKPI 135
                                       999*9975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.1
                                       -SS-EEESSSTCE CS
                    Ribosomal_S27e  23 aatvvkCisCgkv 35 
                                       a  +++C sCg v
  gi|557694970|ref|YP_008798024.1| 147 ADIIIEC-SCGAV 158
                                       6667888.68877 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.001
                                       S-SS-EEESSSTCEEEE CS
                    Ribosomal_S27e  22 haatvvkCisCgkvLve 38 
                                        a+tvv Ci C++ Lv+
  gi|557694970|ref|YP_008798024.1| 163 CAKTVVYCIYCSRKLVT 179
                                       589**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1474.47
//
Query:       gi|557694971|ref|YP_008798025.1|  [L=314]
Description: D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding [Candidatus Caldiarchaeum subterraneum]
Scores for 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-41  139.3   0.0    1.3e-40  138.7   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    1.3e-12   47.6   0.0    1.6e-12   47.2   0.0    1.1  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
    4.1e-06   27.0   0.0    8.6e-06   25.9   0.0    1.5  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
    3.8e-05   23.3   0.0    0.00015   21.4   0.0    2.0  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
     0.0037   17.5   0.0     0.0083   16.3   0.0    1.6  1  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
  ------ inclusion threshold ------
      0.012   15.7   0.2      0.055   13.5   0.1    2.1  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
      0.012   16.2   0.2      0.025   15.1   0.2    1.5  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      0.039   14.4   0.2       0.11   12.9   0.0    1.9  2  NAD_binding_7  Putative NAD(P)-binding
       0.08   13.5   0.5       0.69   10.5   0.0    2.5  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
        0.1   11.6   0.0       0.19   10.7   0.0    1.4  1  PDH            Prephenate dehydrogenase
       0.16   11.3   0.1       0.31   10.4   0.1    1.4  1  ThiF           ThiF family


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 !  138.7   0.0   7.7e-44   1.3e-40       2     178 .]     100     275 ..      99     275 .. 0.94

  Alignments for each domain:
  == domain 1  score: 138.7 bits;  conditional E-value: 7.7e-44
                                       HHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHH CS
                      2-Hacid_dh_C   2 alllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeel 78 
                                       a++l++++++++++++vr+  +  e+++   +l+g+t+ i+G+G+IG +va++++ fgm+vi++ +s k++   +++
  gi|557694971|ref|YP_008798025.1| 100 AMILSIAKKIPHYYDRVRNAVF--ERDTEVLQLNGRTILIVGMGSIGVKVAEVARCFGMRVIGVTKSGKARG-HADK 173
                                       79******************99..9999999************************************99776.6666 PP

                                       TCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--S CS
                      2-Hacid_dh_C  79 gvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfe 155
                                        + ++ lee+l e+Di ++++plt+ tr ++n+++l ++kkg i++N++R+++v++e+L++ Lk+++   +a+Dv++
  gi|557694971|ref|YP_008798025.1| 174 ILPWTRLEEALPEADIMIIATPLTKYTRSMFNRNNLPLLKKGCIVVNVGRAEIVNREDLIAFLKERQDIVFATDVWW 250
                                       779*************************************************************************9 PP

                                       SS....SSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 156 ee....plpedspllelpnviltPHia 178
                                       e     p +  ++l++lpn++ tP+ia
  gi|557694971|ref|YP_008798025.1| 251 EVkrgePWE--TELIKLPNFMGTPWIA 275
                                       975542444..68************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 !   47.2   0.0   9.8e-16   1.6e-12       8     134 .]      12     309 ..       5     309 .. 0.93

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 9.8e-16
                                       CHHHHHHHHHTTE.EEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHT CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   8 reeelellkeegv.evevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaaker 83 
                                       ++e++  +++  + ev++k+++  ee ++    a+a+++ +   ++ + +++l++L++++  ++GvD v  + + e+
  gi|557694971|ref|YP_008798025.1|  12 EQESVSQIER--YaEVVTKNSPNFEESKK---TAEAVLCIT---LKPDEIAKLKNLRFVQVLSAGVDGVAWQHLPEH 80 
                                       5555555555..66788777666664444...566666555...44688**************************** PP

                                       T-EEEE-TTTTHHHHHHHH.......................................................... CS
                                       xxxxxxxxxxxxxxxxxxx.......................................................... RF
                        2-Hacid_dh  84 GilVtnvpgystesvAElt.......................................................... 102
                                        +lV+   g+++e+v E+t                                                          
  gi|557694971|ref|YP_008798025.1|  81 -VLVAGNMGSNAEAVSEHTwamilsiakkiphyydrvrnavferdtevlqlngrtilivgmgsigvkvaevarcfgm 156
                                       .**************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|557694971|ref|YP_008798025.1| 157 rvigvtksgkarghadkilpwtrleealpeadimiiatpltkytrsmfnrnnlpllkkgcivvnvgraeivnredli 233
                                       ***************************************************************************** PP

                                       ............................................T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBCS CS
                                       ............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ............................................aaTeeaqeniaeeaaenlvaflkgespanavn 134
                                                                                   + + e ++++ ++a++n++++++g++p+n +n
  gi|557694971|ref|YP_008798025.1| 234 aflkerqdivfatdvwwevkrgepweteliklpnfmgtpwiagaFGSPEVYKKMLKTAVQNIIKYFSGQTPDNLIN 309
                                       ********************************************99***************************987 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 !   25.9   0.0   5.3e-09   8.6e-06      14     114 ..     122     226 ..     115     255 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.3e-09
                                       HHHH-S-.-TTSEEEEE--SHHHHHHHHHHHHCT-EEE.EE-S-HHHHHHHHCTT-EE--HHHCTTT-SEEEE-SS. CS
                     AdoHcyase_NAD  14 kratdvl.laGkvavvaGyGdvGkGcaaslkglGarvi.vtevdPicalqaameGfevvtleevvkkadivvtttG. 87 
                                       +r t+vl l G++++++G G +G   a+  + +G rvi vt      a   a + +  ++lee++ +adi++ +t  
  gi|557694971|ref|YP_008798025.1| 122 ERDTEVLqLNGRTILIVGMGSIGVKVAEVARCFGMRVIgVTK--SGKARGHADKILPWTRLEEALPEADIMIIATPl 196
                                       6888887689**************************984555..44666777778899**************99863 PP

                                       ...SSSSB-HHHHCCS-TTEEEEE-SSTTT CS
                     AdoHcyase_NAD  88 ...nkdiitlehlkkmkddaivcniGhfds 114
                                          ++ + ++++l  +k+ +iv n+G  + 
  gi|557694971|ref|YP_008798025.1| 197 tkyTRSMFNRNNLPLLKKGCIVVNVGRAEI 226
                                       2235789999****************8654 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 ?   -1.4   0.0      0.91   1.5e+03      53      73 ..      32      54 ..       9      59 .. 0.61
   2 !   21.4   0.0   8.9e-08   0.00015       2      91 ..     130     218 ..     129     246 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.91
                                      EHHHHHHT-SEE..EE-S-HHHH CS
                              IlvN 53 tvaeavkkadvv..miliPDelq 73
                                      + +e  k+a+ v  ++l PDe+ 
  gi|557694971|ref|YP_008798025.1| 32 NFEESKKTAEAVlcITLKPDEIA 54
                                      45566666655511567799875 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 8.9e-08
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-.HHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliP.Delqkevy 77 
                                       l+g++i ++G+Gs G   a+  r  g+ v +g+ +++k   +A  + +  ++++ea  +ad+++i +P  ++ ++++
  gi|557694971|ref|YP_008798025.1| 130 LNGRTILIVGMGSIGVKVAEVARCFGMRV-IGVTKSGKARGHAD-KILPWTRLEEALPEADIMIIATPlTKYTRSMF 204
                                       789*************************8.57777776666664.5688999****************456789999 PP

                                       HHHTGGG--TT-EE CS
                              IlvN  78 eeeiepnlkegkal 91 
                                       +++  p lk+g ++
  gi|557694971|ref|YP_008798025.1| 205 NRNNLPLLKKGCIV 218
                                       99999999999766 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 !   16.3   0.0   5.1e-06    0.0083       2     108 ..     135     240 ..     134     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.1e-06
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       i ++G+G +G + a+     g++v+++  +  k++   a+++ + + +ee++ ++d++i+  + +k ++++ ++  l
  gi|557694971|ref|YP_008798025.1| 135 ILIVGMGSIGVKVAEVARCFGMRVIGVTKS-GKARGH-ADKILPWTRLEEALPEADIMIIATPLTKYTRSMFNRnNL 209
                                       6689***********999999999999876.444444.46789*****************************99999 PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHHHTT CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelkekg 108
                                       + lkkg i+++++ +++ + ++l + lke++
  gi|557694971|ref|YP_008798025.1| 210 PLLKKGCIVVNVGRAEIVNREDLIAFLKERQ 240
                                       *****************99999999888875 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.4e-05     0.055       9      86 ..     129     197 ..     122     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-05
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSS CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatas 85 
                                       +l+++++l++G G ++ +va+     g++ + v+     +a+  a++       +l+ + l+e+l ead++i+at  
  gi|557694971|ref|YP_008798025.1| 129 QLNGRTILIVGMGSIGVKVAEVARCFGMRVIGVTK--SGKARGHADK-------ILPWTRLEEALPEADIMIIATPL 196
                                       6999*****************98877877555543..3344444444.......5999****************965 PP

                                       S CS
                      Shikimate_DH  86 e 86 
                                       +
  gi|557694971|ref|YP_008798025.1| 197 T 197
                                       5 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.2   1.5e-05     0.025       2      39 ..     135     172 ..     134     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSS CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllD 39 
                                       +++vG G ig+ +A++++ +g +V  v  s k +   D
  gi|557694971|ref|YP_008798025.1| 135 ILIVGMGSIGVKVAEVARCFGMRVIGVTKSGKARGHAD 172
                                       89**********************99999988886655 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 ?   -3.1   0.0       6.8   1.1e+04      51      69 ..      29      47 ..      11      59 .. 0.53
   2 ?   12.9   0.0   6.9e-05      0.11       3      73 ..     128     198 ..     127     236 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.8
                     NAD_binding_7 51 aeeelekdlegadlviaat 69
                                      ++ ++e++ + a+ v+++t
  gi|557694971|ref|YP_008798025.1| 29 NSPNFEESKKTAEAVLCIT 47
                                      3333444445555555544 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 6.9e-05
                     NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapev..keeleelvklaeeelekdlegadlviaatddre 73 
                                       l+l+g+++l+vG G+++ + ++    +g +v+ v++       +++++ ++   le+ l +ad+ i+at+ ++
  gi|557694971|ref|YP_008798025.1| 128 LQLNGRTILIVGMGSIGVKVAEVARCFGMRVIGVTKSGkaRGHADKILPWT--RLEEALPEADIMIIATPLTK 198
                                       79****************999999999999999988842233333444444..46888888888888887655 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 ?    0.5   0.1      0.59   9.6e+02      27      61 ..      24      56 ..      13     116 .. 0.66
   2 ?   10.5   0.0   0.00042      0.69       2      77 ..     135     202 ..     134     222 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.59
                                      CEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH CS
                     F420_oxidored 27 eivvansrnpekaeelaeelgvkvtavdneeaaee 61
                                      e+v  ns+n e+ +++ae++   +++ +  e a+ 
  gi|557694971|ref|YP_008798025.1| 24 EVVTKNSPNFEESKKTAEAVL--CITLKPDEIAKL 56
                                      556566666666666666643..443344444443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00042
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHH CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveev 77 
                                       i i+G+G++g  +a+ +   g     ++ +   +  ka+  a+++     +   eea+ ead+ ++a + ++++  
  gi|557694971|ref|YP_008798025.1| 135 ILIVGMGSIGVKVAEVARCFG---MRVI-G-VTKSGKARGHADKIL--PWT-RLEEALPEADIMIIATPLTKYTRS 202
                                       6799***********888888...7777.6.888899999999975..444.58***************9998765 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00012      0.19       8     100 ..     152     243 ..     147     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00012
                                       TT--SEEEEE-SSHHHHHHHHHTTSSSEEES-GGGGCCGSEEEE-S-GGGHHH.HH.HHHHHHS-TT-EEEE--S-- CS
                               PDH   8 kgfkvtvigydideekaeaalelglvdeatddieavkeadivvlavPvevile.vl.kelaphlkedalitDvgsvK 82 
                                       ++f  +vig+ ++ +++ +a +  l +++ +  ea+ eadi ++a+P  +  + +  ++  p lk++++++ vg + 
  gi|557694971|ref|YP_008798025.1| 152 RCFGMRVIGVTKSGKARGHA-DKILPWTRLE--EALPEADIMIIATPLTKYTRsMFnRNNLPLLKKGCIVVNVGRAE 225
                                       68889999999999998888.5557777777..69************9875541552445679*********99876 PP

                                       CHHHHHHHHHCC..GCEE CS
                               PDH  83 ekvvreleellkegksfv 100
                                           ++l ++lke++ +v
  gi|557694971|ref|YP_008798025.1| 226 IVNREDLIAFLKERQDIV 243
                                       666666666666666655 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00019      0.31       6      47 ..     119     161 ..     113     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00019
                                       HHHHH.HHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEE CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   6 allge.dgqekLrdskvllvGaGglGsellknLalsGvgkltl 47 
                                       a++ +     +L+  ++l+vG+G +G  +++   + G++ + +
  gi|557694971|ref|YP_008798025.1| 119 AVFERdTEVLQLNGRTILIVGMGSIGVKVAEVARCFGMRVIGV 161
                                       456676778889999***************9999899888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2235.41
//
Query:       gi|557694972|ref|YP_008798026.1|  [L=116]
Description: transcriptional regulator, MarR family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-25   87.0   0.1    6.9e-25   86.7   0.1    1.1  1  HxlR       HxlR-like helix-turn-helix
    0.00088   19.1   0.0     0.0025   17.6   0.0    1.7  2  HTH_5      Bacterial regulatory protein, arsR family
     0.0023   17.8   0.0     0.0054   16.6   0.0    1.6  2  MarR       MarR family
      0.003   17.6   0.0      0.006   16.6   0.0    1.5  2  HTH_20     Helix-turn-helix domain
     0.0092   15.9   0.0      0.016   15.2   0.0    1.3  1  HTH_Crp_2  Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.017   15.0   0.0       0.03   14.2   0.0    1.3  1  MarR_2     MarR family
      0.033   13.8   1.2      0.038   13.7   0.2    1.7  2  Crp        Bacterial regulatory proteins, crp family
      0.036   13.9   0.0      0.049   13.5   0.0    1.2  1  TrmB       Sugar-specific transcriptional regulator TrmB
       0.14   11.7   0.1       0.27   10.8   0.1    1.5  1  HTH_24     Winged helix-turn-helix DNA-binding


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 !   86.7   0.1   3.5e-28   6.9e-25       1      89 [.      21     109 ..      21     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.7 bits;  conditional E-value: 3.5e-28
                                       HHHSTTHHHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHH CS
                              HxlR   1 liggkWkllilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlq 77 
                                       lig+ W+++i+  l++g+k f+el +a+p++  k+L+++L++L+++gl+er+v++ +P  v Yslt++ ++l+p+l+
  gi|557694972|ref|YP_008798026.1|  21 LIGSVWSMVIISYLVEGPKGFNELLKAVPGLNSKTLSRTLKNLQKKGLVERNVVSLQPFSVAYSLTPMAKELAPILE 97 
                                       6999************************************************************************* PP

                                       HHHHHHHHHHHC CS
                              HxlR  78 elkkwgeeylee 89 
                                       +l +wg++++++
  gi|557694972|ref|YP_008798026.1|  98 QLREWGSKWAMQ 109
                                       *********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 !   17.6   0.0   1.3e-06    0.0025       7      46 ..      30      70 ..      29      71 .. 0.97
   2 ?   -2.7   0.0       2.9   5.8e+03       7      14 ..      95     103 ..      95     105 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                                      HHHHHTTSSEEHHHHHHHH.TS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  7 ILklLaegelcvcelaeel.glsqstvShHLkkLreaGLVe 46
                                      I+++L eg++ + el +++ gl+  t+S+ Lk L + GLVe
  gi|557694972|ref|YP_008798026.1| 30 IISYLVEGPKGFNELLKAVpGLNSKTLSRTLKNLQKKGLVE 70
                                      99****************999*******************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.9
                                       HHHHHTT.S CS
                             HTH_5   7 ILklLae.g 14 
                                       IL +L+e g
  gi|557694972|ref|YP_008798026.1|  95 ILEQLREwG 103
                                       666776644 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.7e-06    0.0054      28      49 ..      50      71 ..      36      72 .. 0.89
   2 ?   -3.7   0.0       5.9   1.2e+04       8      16 ..      95     103 ..      95     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                                      TS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 28 gvskstvtrvldrLekkGlieR 49
                                      g+++ t++r+l+ L kkGl+eR
  gi|557694972|ref|YP_008798026.1| 50 GLNSKTLSRTLKNLQKKGLVER 71
                                      78999****************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.9
                                       HHHHHHHST CS
                              MarR   8 iLrilyeqg 16 
                                       iL++l+e+g
  gi|557694972|ref|YP_008798026.1|  95 ILEQLREWG 103
                                       788999988 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     3e-06     0.006      13      57 ..      28      72 ..      17      75 .. 0.88
   2 ?   -2.7   0.0       3.2   6.5e+03      30      34 ..      95      99 ..      84     112 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3e-06
                                      HHHHHHHSTCTTB-HHHHHHHH.TS-HHHHHHHHHHHHHCTTEEEE CS
                            HTH_20 13 rrilraLaraegltaselaerl.dlskntlsyHLrvLeeagLvevv 57
                                      + i ++L  +++  ++el +++ +l  +tls+ L+ L++ gLve+ 
  gi|557694972|ref|YP_008798026.1| 28 MVIISYL-VEGPKGFNELLKAVpGLNSKTLSRTLKNLQKKGLVERN 72
                                      6789999.99999999999*9999********************85 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.2
                                      HHHHH CS
                            HTH_20 30 laerl 34
                                      + e+l
  gi|557694972|ref|YP_008798026.1| 95 ILEQL 99
                                      33333 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 !   15.2   0.0   7.9e-06     0.016      32      54 ..      50      72 ..      47      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7.9e-06
                                      TSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 32 GltretvsrilseLkreglisrg 54
                                      Gl+  t+sr+l+ L+++gl++r+
  gi|557694972|ref|YP_008798026.1| 50 GLNSKTLSRTLKNLQKKGLVERN 72
                                      77889***************976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05      0.03      33      53 ..      51      71 ..      47      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                      SSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 33 lsksavsrilkrLvaaGLver 53
                                      l   ++sr+lk L+++GLver
  gi|557694972|ref|YP_008798026.1| 51 LNSKTLSRTLKNLQKKGLVER 71
                                      556689**************9 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   1.9e-05     0.038      18      31 ..      55      68 ..      50      69 .. 0.90
   2 ?   -2.9   0.0       2.9   5.8e+03      25      30 ..      98     103 ..      96     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHHHHHTTS CS
                               Crp 18 TVSRlLtrLrekGL 31
                                      T SR+L+ L++kGL
  gi|557694972|ref|YP_008798026.1| 55 TLSRTLKNLQKKGL 68
                                      88***********9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.9
                                       HHHHTT CS
                               Crp  25 rLrekG 30 
                                        Lre+G
  gi|557694972|ref|YP_008798026.1|  98 QLREWG 103
                                       799998 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.5e-05     0.049      20      58 ..      36      75 ..      30      89 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                                      HCCCHHCHHCCCT.TSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 20 lgpatadeiaeel.gvprskvYevLrsLedkGlVerekgr 58
                                      +gp+  +e+ +++ g+   +  ++L++L +kGlVer+  +
  gi|557694972|ref|YP_008798026.1| 36 EGPKGFNELLKAVpGLNSKTLSRTLKNLQKKGLVERNVVS 75
                                      5666666666665478888999*************98766 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 ?   10.8   0.1   0.00014      0.27      28      48 .]      50      70 ..      50      70 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                            HTH_24 28 glSpstvnrrlkrLeeeGlIk 48
                                      gl + t++r lk+L+++Gl++
  gi|557694972|ref|YP_008798026.1| 50 GLNSKTLSRTLKNLQKKGLVE 70
                                      8999***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); 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:                         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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 909.14
//
Query:       gi|557694973|ref|YP_008798027.1|  [L=170]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   53.6  10.4    2.5e-14   53.6  10.4    2.1  2  DoxX      DoxX
      2e-10   40.7  13.4    2.1e-10   40.6   4.6    2.5  2  DoxX_2    DoxX-like family
    0.00068   19.7   8.2    0.00068   19.7   8.2    2.1  2  FxsA      FxsA cytoplasmic membrane protein
     0.0097   15.8  10.9      0.029   14.3   0.1    2.6  2  DoxD      TQO small subunit DoxD


Domain annotation for each model (and alignments):
>> DoxX  DoxX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6  10.4   5.7e-18   2.5e-14       1      80 [.      26     103 ..      26     114 .. 0.96
   2 ?    1.6   1.1     0.098   4.4e+02      27      49 ..     136     158 ..     107     164 .. 0.52

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 5.7e-18
                              DoxX   1 lllllRlllgvlfiahGlqkltgfglegtaaslaalglpppellaylaalvElvgglllllGlltRlaAlalavtll 77 
                                       +ll+lR++lg ++++hG+ kl+g++ +++ + + ++g+  p  l  l++l+E+vgg++l++G+lt +a l++++ ++
  gi|557694973|ref|YP_008798027.1|  26 GLLVLRVVLGFIMVVHGAPKLFGPMRQQMRGGMSQMGI--PGGLFDLVGLLEFVGGIALIVGFLTQVAGLLFFIQMI 100
                                       69************************************..************************************* PP

                              DoxX  78 vat 80 
                                       +++
  gi|557694973|ref|YP_008798027.1| 101 GTI 103
                                       998 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.098
                              DoxX  27 egtaaslaalglpppellaylaa 49 
                                       +g+ ++ ++l +++++ll+++++
  gi|557694973|ref|YP_008798027.1| 136 AGVGGWEFDLLILAAALLLVFTG 158
                                       33333333444444444444333 PP

>> DoxX_2  DoxX-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   4.6   4.7e-14   2.1e-10       1      80 [.      29     105 ..      29     112 .. 0.94
   2 !    5.0   1.5    0.0056        25      18      54 ..     113     155 ..     104     167 .. 0.64

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 4.7e-14
                            DoxX_2   1 vltvllalffllsGvakllra..eevvakfaqlgfpssfvrllGvvellgalgLllplvtaprltplAavglallmv 75 
                                       vl v+l +++++ G+ kl+ +  +++  ++ q+g+p ++  l+G++e++g+++L++++     lt++A +++++ m+
  gi|557694973|ref|YP_008798027.1|  29 VLRVVLGFIMVVHGAPKLFGPmrQQMRGGMSQMGIPGGLFDLVGLLEFVGGIALIVGF-----LTQVAGLLFFIQMI 100
                                       6899***************998789999*****************************6.....9************* PP

                            DoxX_2  76 gAiat 80 
                                       g i  
  gi|557694973|ref|YP_008798027.1| 101 GTISL 105
                                       *9976 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0056
                            DoxX_2  18 llraeevvakfa..qlgfpssfvrllGvve....llgalgLll 54 
                                       ++ ++e+++++   + +f ++f+  +G +e    +l+a++Ll+
  gi|557694973|ref|YP_008798027.1| 113 FVPPPEMLQQMVagSRQFMRGFMAGVGGWEfdllILAAALLLV 155
                                       6677888887774455788999999999884443233333332 PP

>> FxsA  FxsA cytoplasmic membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   8.2   1.5e-07   0.00068      21      96 ..      19      98 ..       8     109 .. 0.79
   2 ?    0.2   0.7      0.18     8e+02      61      79 ..     135     154 ..     105     160 .. 0.55

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.5e-07
                              FxsA 21 iGvlatllllvltallGallvrrqgrralrrlqekla....qgelpaee.lldglllllggvLLllPGfvtdvlGllll 94
                                      +++++ + llvl ++lG+++v +   +++  ++++++    q ++p+    l gll ++gg+ L++ Gf+t v+Gll++
  gi|557694973|ref|YP_008798027.1| 19 LSGFMDVGLLVLRVVLGFIMVVHGAPKLFGPMRQQMRggmsQMGIPGGLfDLVGLLEFVGGIALIV-GFLTQVAGLLFF 96
                                      45667899*********************999999993222344455444344999********99.**********99 PP

                              FxsA 95 lP 96
                                      + 
  gi|557694973|ref|YP_008798027.1| 97 IQ 98
                                      85 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.18
                              FxsA  61 lpaeelld.glllllggvLL 79 
                                       + +    +  ll+l++++LL
  gi|557694973|ref|YP_008798027.1| 135 MAGVGGWEfDLLILAAALLL 154
                                       44444333123333444444 PP

>> DoxD  TQO small subunit DoxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   4.2    0.0031        14      70     102 ..      70     102 ..      43     110 .. 0.85
   2 !   14.3   0.1   6.4e-06     0.029     116     144 ..     140     168 ..     131     170 .] 0.92

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0031
                              DoxD  70 lftlvEiivGlllliGlltRlsslvafalalgi 102
                                       l++l+E + G+ l++G+lt +++l  f   +g 
  gi|557694973|ref|YP_008798027.1|  70 LVGLLEFVGGIALIVGFLTQVAGLLFFIQMIGT 102
                                       78999*****************99888776664 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 6.4e-06
                              DoxD 116 EyqiglllvaaelvliltgsgklslDyll 144
                                        ++  ll  aa+l+l++tg+g +s+D+ll
  gi|557694973|ref|YP_008798027.1| 140 GWEFDLLILAAALLLVFTGAGAFSVDSLL 168
                                       6999***********************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1434.83
//
Query:       gi|557694974|ref|YP_008798028.1|  [L=168]
Description: DtxR family iron dependent repressor [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   58.4   1.0    1.9e-15   56.8   0.2    2.2  2  Fe_dep_repress   Iron dependent repressor, N-terminal DNA bin
    3.5e-10   39.8   1.6    3.5e-10   39.8   1.6    1.8  1  Fe_dep_repr_C    Iron dependent repressor, metal binding and 
    1.1e-07   31.2   0.0    3.4e-07   29.7   0.0    1.9  1  HTH_24           Winged helix-turn-helix DNA-binding
      1e-05   25.3   0.1      6e-05   22.8   0.0    2.2  2  MarR_2           MarR family
    3.9e-05   24.1   0.8    0.00014   22.3   0.0    2.3  2  HTH_27           Winged helix DNA-binding domain
    0.00026   21.3   0.2    0.00066   20.0   0.2    1.9  1  Penicillinase_R  Penicillinase repressor
     0.0011   18.9   0.0     0.0038   17.1   0.0    1.9  1  MarR             MarR family
     0.0017   18.1   0.1     0.0063   16.2   0.0    1.8  2  DUF4423          Domain of unknown function (DUF4423)
     0.0017   18.2   1.2     0.0062   16.4   0.2    2.5  2  TrmB             Sugar-specific transcriptional regulator Trm
     0.0018   18.0   2.1     0.0038   17.0   0.0    2.7  2  HTH_IclR         IclR helix-turn-helix domain
     0.0049   15.9   0.0     0.0073   15.4   0.0    1.3  1  Topoisom_bac     DNA topoisomerase
     0.0055   16.5   0.0      0.016   15.0   0.0    1.9  1  HTH_23           Homeodomain-like domain
  ------ inclusion threshold ------
      0.011   15.8   0.6        1.1    9.4   0.0    3.3  3  HTH_29           Winged helix-turn helix
      0.011   16.0   0.1      0.074   13.4   0.0    2.2  2  Rrf2             Transcriptional regulator
      0.013   15.6   0.0       0.14   12.3   0.0    2.4  2  AbiEi_4          Transcriptional regulator, AbiEi antitoxin
      0.017   15.0   0.1       0.13   12.1   0.0    2.0  2  PAX              'Paired box' domain
      0.018   15.1   0.1       0.14   12.3   0.0    2.4  2  HTH_7            Helix-turn-helix domain of resolvase
       0.02   14.9   0.1      0.094   12.8   0.0    2.3  2  Cullin_Nedd8     Cullin protein neddylation domain
      0.021   14.8   0.0      0.054   13.5   0.0    1.8  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.036   13.8   0.3        0.1   12.3   0.3    1.9  1  Sigma54_DBD      Sigma-54, DNA binding domain
      0.036   13.8   0.0       0.14   11.9   0.0    1.9  2  LexA_DNA_bind    LexA DNA binding domain
      0.038   13.6   0.0      0.089   12.4   0.0    1.5  1  E3_UFM1_ligase   E3 UFM1-protein ligase 1
      0.041   13.7   1.4      0.069   13.0   0.1    2.2  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.054   13.1   0.6        2.4    7.7   0.1    2.0  2  Arfaptin         Arfaptin-like domain
      0.054   13.3   0.0       0.12   12.1   0.0    1.6  1  HTH_38           Helix-turn-helix domain
       0.06   13.5   0.1        0.2   11.9   0.1    1.8  2  DUF2789          Protein of unknown function (DUF2789)
      0.061   12.4   0.3      0.087   11.9   0.3    1.3  1  Exo70            Exo70 exocyst complex subunit
      0.062   13.3   0.0       0.21   11.6   0.0    1.9  1  HTH_11           HTH domain
      0.065   12.9   1.0       0.55    9.9   0.0    2.9  3  GntR             Bacterial regulatory proteins, gntR family
      0.098   12.6   0.0       0.24   11.3   0.0    1.6  1  CtsR             CtsR N-terminal HTH domain
       0.12   11.9   0.0       0.25   10.9   0.0    1.5  1  HTH_47           winged helix-turn-helix


Domain annotation for each model (and alignments):
>> 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 !   56.8   0.2   3.4e-18   1.9e-15       5      58 ..      24      78 ..      21      80 .. 0.95
   2 ?   -0.8   0.0       3.1   1.8e+03       2      22 ..     125     146 ..     124     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 3.4e-18
                                      HHHHHHHHHHHHHH.HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                    Fe_dep_repress  5 stEdYLetIYtlse.ekkvvktkdlaerLnvspssVsemlkkLekdGyveyekyk 58
                                       +E+YLe++Y++     + v++ d+a++Lnv+ps+V + + +L ++Gy+ y++yk
  gi|557694974|ref|YP_008798028.1| 24 LAEEYLEAVYEILQqRDGRVRPVDVAKALNVAPSTVKKVITRLCEKGYLRYQPYK 78
                                      58*********999899*************************************9 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.1
                                       --HHHHHHHHHHHHHHH.HHSS CS
                    Fe_dep_repress   2 LvestEdYLetIYtlse.ekkv 22 
                                       L+e+   +Le+++   e + +v
  gi|557694974|ref|YP_008798028.1| 125 LSETSTAVLEALLNTLEsDLEV 146
                                       6777778899988888855555 PP

>> 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 !   39.8   1.6   6.1e-13   3.5e-10       1      62 [.      83     143 ..      83     148 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 6.1e-13
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB- CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeec 62 
                                       Te+G    ++l++rh ++ +++ ++lg+d+  a+ eAer+Eh lse +   l++ll+ +e++
  gi|557694974|ref|YP_008798028.1|  83 TEEGLARVRQLKHRHDTVSKLF-QTLGLDELSAEVEAERMEHSLSETSTAVLEALLNTLESD 143
                                       9*********************.88********************************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 !   29.7   0.0   5.8e-10   3.4e-07       7      48 .]      31      73 ..      26      73 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 5.8e-10
                            HTH_24  7 kILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +++e+Lq+ ++r    ++A++l++ pstv++ + rL+e+G+++
  gi|557694974|ref|YP_008798028.1| 31 AVYEILQQrDGRVRPVDVAKALNVAPSTVKKVITRLCEKGYLR 73
                                      578899999********************************86 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0     1e-07     6e-05      14      55 ..      36      76 ..      30      78 .. 0.91
   2 ?   -1.2   0.0       3.4     2e+03      31      34 ..      93      96 ..      81     111 .. 0.51

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1e-07
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      L  r+gr +++ ++a++l++ +s+v +++ rL ++G+++++p
  gi|557694974|ref|YP_008798028.1| 36 LQQRDGR-VRPVDVAKALNVAPSTVKKVITRLCEKGYLRYQP 76
                                      6678886.9*****************************9986 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.4
                                      HTSS CS
                            MarR_2 31 lgls 34
                                      l++ 
  gi|557694974|ref|YP_008798028.1| 93 LKHR 96
                                      2223 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 !   22.3   0.0   2.4e-07   0.00014      13      68 .]      33      86 ..      27      86 .. 0.84
   2 ?   -1.0   0.1       4.6   2.7e+03      41      42 ..     135     136 ..      91     153 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.4e-07
                            HTH_27 13 r....hrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +     r++r++  d++++lnv  s++ +++ +L+ekG++  +       +k ++lT++G
  gi|557694974|ref|YP_008798028.1| 33 YeilqQRDGRVRPVDVAKALNVAPSTVKKVITRLCEKGYLRYQ------PYKVLELTEEG 86
                                      4444489999999***************************444......45799999998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 4.6
                            HTH_27  41 kL 42 
                                       +L
  gi|557694974|ref|YP_008798028.1| 135 AL 136
                                       33 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   1.1e-06   0.00066       8      54 ..      32      75 ..      23     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHHS-.EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEE CS
                   Penicillinase_R  8 vmeilwekge.atvkevveeleeekelaysTVktllrrLvkKgllsre 54
                                      v+eil +++  +   +v +      ++a+sTVk +++rL++Kg+l+ +
  gi|557694974|ref|YP_008798028.1| 32 VYEILQQRDGrVRPVDVAK----ALNVAPSTVKKVITRLCEKGYLRYQ 75
                                      4444444444344444444....45577*****************976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.6e-06    0.0038      18      48 ..      43      73 ..      30      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.6e-06
                                      EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR 18 lsvseLakklgvskstvtrvldrLekkGlie 48
                                       +  + ak+l+v +stv +v++rL +kG+++
  gi|557694974|ref|YP_008798028.1| 43 VRPVDVAKALNVAPSTVKKVITRLCEKGYLR 73
                                      666689***********************97 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-05    0.0063      20      82 ..      26      86 ..      12      97 .. 0.87
   2 ?   -0.4   0.0       1.4   8.2e+02      38      74 ..     117     153 ..      96     159 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                           DUF4423 20 sWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyrqteks 82
                                      + y  +++e+l+ +d++  p  +ak+l+  +  + v+k + +L++ g l+ +  + ++ te+ 
  gi|557694974|ref|YP_008798028.1| 26 EEYLEAVYEILQQRDGRVRPVDVAKALN--VAPSTVKKVITRLCEKGYLRYQPYKVLELTEEG 86
                                      668889**********************..******************998777666666665 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
                           DUF4423  38 dpeelakrlrpkisaeevekalefLl.klgllkkdedg 74 
                                       + e +++ l  + s++  e+ l++L+ +l++l++ ++g
  gi|557694974|ref|YP_008798028.1| 117 EAERMEHSLS-ETSTAVLEALLNTLEsDLEVLHRVRSG 153
                                       4566777777.777788888888887346777766665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   1.1e-05    0.0062      13      55 ..      32      75 ..      26      97 .. 0.88
   2 ?   -1.0   0.0       2.9   1.7e+03       6      24 ..     125     143 ..     121     158 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                                      HCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 13 vYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      vY  L  + g+ +  ++a++l+v  s+v +v+ +L +kG+ + +
  gi|557694974|ref|YP_008798028.1| 32 VYEILQqRDGRVRPVDVAKALNVAPSTVKKVITRLCEKGYLRYQ 75
                                      777777677899999************************98765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.9
                                       HHHHCCCHCHHHHHHCCCH CS
                              TrmB   6 LseyEakvYlaLlklgpat 24 
                                       Lse+   v  aLl+  +++
  gi|557694974|ref|YP_008798028.1| 125 LSETSTAVLEALLNTLESD 143
                                       7778888888888765555 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 !   17.0   0.0   6.5e-06    0.0038      10      52 .]      34      76 ..      31      76 .. 0.94
   2 ?   -2.5   0.0         8   4.7e+03      17      21 ..     105     109 ..      96     116 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.5e-06
                                      CT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE... CS
                          HTH_IclR 10 dalaeapqeltlselArrtglpkStvhRlLqtLvelGyveqdg 52
                                      ++l +++++++  ++A+++ +++Stv   +  L e Gy+++++
  gi|557694974|ref|YP_008798028.1| 34 EILQQRDGRVRPVDVAKALNVAPSTVKKVITRLCEKGYLRYQP 76
                                      67899999********************************976 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 8
                                       SS-BH CS
                          HTH_IclR  17 qeltl 21 
                                       q l+l
  gi|557694974|ref|YP_008798028.1| 105 QTLGL 109
                                       33444 PP

>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-05    0.0073     343     389 ..      56     103 ..      55     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
                      Topoisom_bac 343 paTraeiieklvergYverkk.kslvptelGkalvellekfkdlvspe 389
                                       p+T  ++i +l+e+gY++ +  k l  te G a v+ l++ +d vs+ 
  gi|557694974|ref|YP_008798028.1|  56 PSTVKKVITRLCEKGYLRYQPyKVLELTEEGLARVRQLKHRHDTVSKL 103
                                       8*******************99****************8776666654 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.7e-05     0.016       9      41 ..      34      66 ..      29      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.7e-05
                            HTH_23  9 rillllaeGlsvreIAreLgvsrrTvyrwlkry 41
                                      +il+  + + ++ ++A++L+v ++Tv +++ r 
  gi|557694974|ref|YP_008798028.1| 34 EILQQRDGRVRPVDVAKALNVAPSTVKKVITRL 66
                                      444444449999****************99885 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.35     2e+02      40      54 ..       7      21 ..       2      28 .. 0.64
   2 ?    9.4   0.0    0.0019       1.1      10      40 ..      40      70 ..      33      74 .. 0.80
   3 ?    0.3   0.0       1.2     7e+02      11      11 ..      96      96 ..      77     115 .. 0.53

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.35
                            HTH_29 40 Glaalld.rrrsgrpr 54
                                      +++al++ ++r  r++
  gi|557694974|ref|YP_008798028.1|  7 RIEALMRaHKR-ERGS 21
                                      399***98887.4443 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0019
                            HTH_29 10 eGvstvsqiAkllglsrrtvyrwlkrfeegG 40
                                      +G  ++ ++Ak+l++ ++tv +++ r  e+G
  gi|557694974|ref|YP_008798028.1| 40 DGRVRPVDVAKALNVAPSTVKKVITRLCEKG 70
                                      444489*****************99977666 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.2
                            HTH_29 11 G 11
                                       
  gi|557694974|ref|YP_008798028.1| 96 R 96
                                      2 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   0.00013     0.074      11      56 ..      29      73 ..      20      76 .. 0.88
   2 ?   -0.1   0.1       2.1   1.2e+03      26      50 ..     116     141 ..      92     146 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 11 lhallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      l a++++ ++++++ v+  ++a+  n+ ps ++k++++L ++g+++
  gi|557694974|ref|YP_008798028.1| 29 LEAVYEILQQRDGR-VRPVDVAKALNVAPSTVKKVITRLCEKGYLR 73
                                      56777777888877.9***************************997 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.1
                                       B-HHHHHHHH.TS-HHHHHHHHHHHH CS
                              Rrf2  26 vsseeiaerq.nispsylekilakLr 50 
                                       v++e + ++  ++s  +le +l++L+
  gi|557694974|ref|YP_008798028.1| 116 VEAERMEHSLsETSTAVLEALLNTLE 141
                                       45555554433788888888888886 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00024      0.14       9      38 ..      38      72 ..      30      73 .. 0.83
   2 ?    0.4   0.0       1.3   7.7e+02      12      21 ..      86      95 ..      79     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00024
                           AbiEi_4  9 rqvGlfttrelea.aGispsa....lrrLvrkGwL 38
                                      ++ G ++  ++++ +++ ps+    ++rL++kG L
  gi|557694974|ref|YP_008798028.1| 38 QRDGRVRPVDVAKaLNVAPSTvkkvITRLCEKGYL 72
                                      44477899999999*******************98 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.3
                           AbiEi_4 12 Glfttrelea 21
                                      Gl+++r+l+ 
  gi|557694974|ref|YP_008798028.1| 86 GLARVRQLKH 95
                                      7889999832 PP

>> PAX  'Paired box' domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00023      0.13      31      64 ..      40      73 ..      28      79 .. 0.86
   2 ?    0.5   0.0      0.93   5.4e+02      25      54 ..      78     104 ..      74     108 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00023
                               PAX 31 hsgvrpcvisrqlrvshgcvskilgryqetgsir 64
                                         vrp+++++ l+v+   v k+++r  e g +r
  gi|557694974|ref|YP_008798028.1| 40 DGRVRPVDVAKALNVAPSTVKKVITRLCEKGYLR 73
                                      5569**************************9887 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.93
                               PAX  25 kivelahsgvrpcvisrqlrvshgcvskil 54 
                                       k++el+++g+      rql+  h  vsk++
  gi|557694974|ref|YP_008798028.1|  78 KVLELTEEGLAR---VRQLKHRHDTVSKLF 104
                                       677777777643...599*********986 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 ?   12.3   0.0   0.00024      0.14      26      42 ..      47      63 ..      41      66 .. 0.91
   2 ?   -0.5   0.0       2.4   1.4e+03      14      23 ..      79      89 ..      74     103 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00024
                                      TTSSSS---SSSS--SS CS
                             HTH_7 26 kIAkevnisRsTvYRyl 42
                                      ++Ak++n+++sTv+++ 
  gi|557694974|ref|YP_008798028.1| 47 DVAKALNVAPSTVKKVI 63
                                      79*************96 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.4
                                      GGSSTTTT.-- CS
                             HTH_7 14 vvkLleeG.is 23
                                      v++L eeG   
  gi|557694974|ref|YP_008798028.1| 79 VLELTEEGlAR 89
                                      67777777333 PP

>> Cullin_Nedd8  Cullin protein neddylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00016     0.094      35      58 ..      50      73 ..      26      77 .. 0.84
   2 ?   -1.5   0.0       4.5   2.6e+03      18      29 ..     105     116 ..      88     134 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                      Cullin_Nedd8 35 krftpsiadikkrIesLiekeYle 58
                                      k  ++ ++ +kk+I +L ek+Yl+
  gi|557694974|ref|YP_008798028.1| 50 KALNVAPSTVKKVITRLCEKGYLR 73
                                      46778899**************97 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.5
                      Cullin_Nedd8  18 ktlshneLvsev 29 
                                       +tl  +eL +ev
  gi|557694974|ref|YP_008798028.1| 105 QTLGLDELSAEV 116
                                       444555555555 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 ?   13.5   0.0   9.3e-05     0.054      26      65 ..      47      87 ..      23      90 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.3e-05
                                      HHHHHTTSSHHHHHHHHHHHHHTTSEEET.EEEEES-HHHH CS
                         HTH_Crp_2 26 elAsmlGltretvsrilseLkreglisrg.rririldleaL 65
                                      + A  l++ ++tv +++++L ++g+++ + +++  l  e+L
  gi|557694974|ref|YP_008798028.1| 47 DVAKALNVAPSTVKKVITRLCEKGYLRYQpYKVLELTEEGL 87
                                      88************************954233555555555 PP

>> Sigma54_DBD  Sigma-54, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   0.00018       0.1      14      72 ..      11      65 ..       3     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHXSSXXXXXXXHHHHHTTSSSXHHHHHHHHHH CS
                       Sigma54_DBD 14 liksleqRketllkvaeeiverQkdflekgeealrpltlrevaealelhesTvSRvvsn 72
                                      l+++ ++R++  +k aee +e   + l++ +  +rp+   +va+al++  sTv +v++ 
  gi|557694974|ref|YP_008798028.1| 11 LMRA-HKRERGSVKLAEEYLEAVYEILQQRDGRVRPV---DVAKALNVAPSTVKKVITR 65
                                      5554.68999999***********************8...79************99985 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 ?   11.9   0.0   0.00025      0.14      30      62 ..      47      78 ..      43      79 .. 0.91
   2 ?   -1.5   0.0       3.8   2.2e+03      28      48 ..     125     138 ..     105     149 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00025
                                      HHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG- CS
                     LexA_DNA_bind 30 eiaralglkSpsaveehLkaLerKGyierdpgk 62
                                      ++a+al+++ ps+v++   +L  KGy++ +p k
  gi|557694974|ref|YP_008798028.1| 47 DVAKALNVA-PSTVKKVITRLCEKGYLRYQPYK 78
                                      579999999.******************99865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.8
                                       HHHHHHHHTS-.HHHHHHHHH CS
                     LexA_DNA_bind  28 ireiaralglkSpsaveehLk 48 
                                         e + a+        e  L+
  gi|557694974|ref|YP_008798028.1| 125 LSETSTAV-------LEALLN 138
                                       33333333.......333333 PP

>> E3_UFM1_ligase  E3 UFM1-protein ligase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00015     0.089      60      97 ..      32      69 ..      24      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00015
                    E3_UFM1_ligase 60 ikdelekagGRvnlvdLakilnvdlshiekkaeeivke 97
                                      + + l++++GRv  vd+ak+lnv  s ++k +++++++
  gi|557694974|ref|YP_008798028.1| 32 VYEILQQRDGRVRPVDVAKALNVAPSTVKKVITRLCEK 69
                                      6677999***********************99998765 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 ?   13.0   0.1   0.00012     0.069      13      40 ..      38      65 ..      34      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00012
                     HTH_AsnC-type 13 qedaRisyaeLAervGlSestvlrRvrr 40
                                      q+d+R    ++A+++++++stv + + r
  gi|557694974|ref|YP_008798028.1| 38 QRDGRVRPVDVAKALNVAPSTVKKVITR 65
                                      899*******************876666 PP

>> Arfaptin  Arfaptin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.061        35      37      69 ..       6      38 ..       2      41 .. 0.91
   2 ?    7.7   0.1    0.0042       2.4      51     124 ..      78     147 ..      73     150 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.061
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Arfaptin 37 aklevlreiketykelvklaknlskallklsqt 69
                                      +++e l + +++ ++ vkla+++++a+++++q+
  gi|557694974|ref|YP_008798028.1|  6 SRIEALMRAHKRERGSVKLAEEYLEAVYEILQQ 38
                                      699***************************996 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0042
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH..H-CCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Arfaptin  51 elvklaknlskallklsqtekelGdvfkdlskrekqealgeaftatgealrllakqgeallkalkrfiselntf 124
                                       ++++l+++ ++++ +l + +   ++ f+ l+      +l+++++a    ++l++   + l + l+++ s+l+++
  gi|557694974|ref|YP_008798028.1|  78 KVLELTEEGLARVRQLKHRHDTVSKLFQTLGL----DELSAEVEAERMEHSLSETSTAVLEALLNTLESDLEVL 147
                                       578899999999********************....77788899999999999999999************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 ?   12.1   0.0   0.00021      0.12      24      43 ..      46      65 ..      33      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00021
                            HTH_38 24 reIArrLgrspsTIsRElkR 43
                                       ++A+ L+++psT+ + + R
  gi|557694974|ref|YP_008798028.1| 46 VDVAKALNVAPSTVKKVITR 65
                                      489*************9998 PP

>> DUF2789  Protein of unknown function (DUF2789)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       4.8   2.8e+03      22      42 ..       6      26 ..       3      29 .. 0.83
   2 ?   11.9   0.1   0.00034       0.2       4      43 ..      96     135 ..      93     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.8
                                      HHHHHHHHHS.---TTS-STT CS
                           DUF2789 22 eaieaFiakhkpleeevklad 42
                                      ++iea +++hk+ + +vkla+
  gi|557694974|ref|YP_008798028.1|  6 SRIEALMRAHKRERGSVKLAE 26
                                      579999999999888998876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00034
                                       T-THHHHHHHHHTS---HHHHHHHHHHS.---TTS-STT- CS
                           DUF2789   4 sehtlseLFeqLGLdsseeaieaFiakhkpleeevkladA 43 
                                        + t+s+LF+ LGLd+ ++++ea   +h+  e+++++ +A
  gi|557694974|ref|YP_008798028.1|  96 RHDTVSKLFQTLGLDELSAEVEAERMEHSLSETSTAVLEA 135
                                       67789*****************999999877777777776 PP

>> Exo70  Exo70 exocyst complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   0.00015     0.087     139     214 ..      78     144 ..      46     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00015
                             Exo70 139 gvheltrnvmnylrkLleykdtlssllkdlkdeswssasssqssssesssadgesllalfladlisaLesnLeaka 214
                                        v elt + + ++r+L   +dt+s+l+++l+ ++         +s e + +  e +l++  + +++aL++ Le+  
  gi|557694974|ref|YP_008798028.1|  78 KVLELTEEGLARVRQLKHRHDTVSKLFQTLGLDE---------LSAEVEAERMEHSLSETSTAVLEALLNTLESDL 144
                                       699****************************986.........555666666677999999999999999999765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00036      0.21       3      44 ..      30      71 ..      29      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00036
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      ++++e+L + +g +   + A+ Lnv  +tv + I +L e+g+
  gi|557694974|ref|YP_008798028.1| 30 EAVYEILQQRDGRVRPVDVAKALNVAPSTVKKVITRLCEKGY 71
                                      5678899777777999999********************995 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00096      0.55      30      57 ..      48      75 ..      44      78 .. 0.90
   2 ?   -1.6   0.1       3.6   2.1e+03      47      58 ..      81      92 ..      80      94 .. 0.85
   3 ?   -0.5   0.1       1.7   9.9e+02      39      56 ..     131     148 ..     105     155 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00096
                                      HHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 30 LaaefgVsrttvReALrrLeaeglverr 57
                                      +a++++V  +tv +++ rL ++g++  +
  gi|557694974|ref|YP_008798028.1| 48 VAKALNVAPSTVKKVITRLCEKGYLRYQ 75
                                      6899*******************99866 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 3.6
                                      HHHHTTSEEEET CS
                              GntR 47 rLeaeglverrq 58
                                      +L++egl+ +rq
  gi|557694974|ref|YP_008798028.1| 81 ELTEEGLARVRQ 92
                                      699999999987 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHTTSEEE CS
                              GntR  39 ttvReALrrLeaeglver 56 
                                        ++   L++Le++  v  
  gi|557694974|ref|YP_008798028.1| 131 AVLEALLNTLESDLEVLH 148
                                       333333455555555555 PP

>> CtsR  CtsR N-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00042      0.24       6      54 ..      25      71 ..      22      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00042
                              CtsR  6 ieeyikelleeseeeeveikRnelaekfecvPsQinYVlktRFtaekGy 54
                                       eey++ + e  +++  +++  ++a+ ++++Ps +  V+ tR   ekGy
  gi|557694974|ref|YP_008798028.1| 25 AEEYLEAVYEILQQRDGRVRPVDVAKALNVAPSTVKKVI-TRL-CEKGY 71
                                      5889988888888888999*******************9.564.56777 PP

>> HTH_47  winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00043      0.25      31      76 ..      27      72 ..      16      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00043
                                      --HHHHHHHHHH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-E CS
                            HTH_47 31 qaemallwvLnlaDGkrsLldiAeriglpfdrvaaiaraLaeagll 76
                                      +  +a+ ++L   DG+   +d+A+ +++   +v++++ +L e+g l
  gi|557694974|ref|YP_008798028.1| 27 EYLEAVYEILQQRDGRVRPVDVAKALNVAPSTVKKVITRLCEKGYL 72
                                      5567778899999***************************999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1132  (0.0631379); expected 358.6 (0.02)
Passed bias filter:                      854  (0.0476323); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 1354.97
//
Query:       gi|557694975|ref|YP_008798029.1|  [L=462]
Description: 2-isopropylmalate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-45  153.9   0.1    9.1e-45  153.3   0.1    1.2  1  HMGL-like     HMGL-like
    7.7e-05   23.1   0.7       0.62   10.4   0.0    3.0  4  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.011   15.1   0.1      0.023   14.2   0.1    1.6  1  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 !  153.3   0.1   1.5e-48   9.1e-45       4     260 ..       5     262 ..       3     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 1.5e-48
                                       EEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B....--EE-SSHHHH CS
                         HMGL-like   4 ivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkar..ilalvrarekdi 78 
                                       ++d+tLR+Ge +    l+++ kl++++ L++ag++ +E+++     + +e+v+ ++k+ ++     +++ ra  +d+
  gi|557694975|ref|YP_008798029.1|   5 LLDSTLREGELF--RVLKLSTKLELVERLADAGLKRVEITVDYPPRTTREDVEPLVKKCNSLGveAVLHGRAIRQDL 79 
                                       78*******965..6788889**************************************887555889999999*** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHH.SSTHHHHHHHHHHHHHHHHHTT-E.TTT-BTTTBS--HHH....HH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkakl.kkdreevakkaeeavkaarslgkd.velsledasrtdlef....la 149
                                       +aa++      a+ v ++ia +e+h+ +kl +++ +e +++  +avk ar++g + v+  +edasr  le     l+
  gi|557694975|ref|YP_008798029.1|  80 EAAAK----YDAAGVGLYIALTEIHRTHKLhGISYQEGLERLMDAVKTAREMGFRyVRATVEDASRFYLEGqlppLV 152
                                       *****....99***************9997369********************99999********98775334489 PP

                                       HHHHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS CS
                         HMGL-like 150 evveaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnG 226
                                       + v+ +++aGat ++++Dt G+l+P++ +e i +l+e+++  ++l+ H+Hnd+G+A ant++Av aGad+  +tv G
  gi|557694975|ref|YP_008798029.1| 153 DAVNSVRKAGATLVSVPDTAGLLSPQKTREFITFLREKTD--APLAAHFHNDYGMASANTVEAVLAGADEAHVTVMG 227
                                       99**************************************..*********************************** PP

                                       --SSBBB-BHHHHHHHHHHTT.-B----HHHHHHH CS
                         HMGL-like 227 lGeraGnaaleelvaalealg.vdtgldlqklrsi 260
                                       +G+r+G a+l e+va le  + +d g+d +kl s+
  gi|557694975|ref|YP_008798029.1| 228 VGDRNGIADLYEVVAVLEDIHgIDLGVDRSKLNSL 262
                                       *****************98777******9999886 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0   0.00017         1     130     165 ..      24      59 ..      13      61 .. 0.88
   2 !   10.4   0.0    0.0001      0.62      88     144 ..      76     131 ..      58     137 .. 0.78
   3 ?   -2.7   0.0       1.1   6.6e+03      32      70 ..     212     244 ..     199     258 .. 0.55
   4 ?   -2.4   0.0       0.9   5.4e+03      55      75 ..     334     362 ..     305     402 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 130 vlealeklreagikrvvdrivglpGendeeleelle 165
                                        le++e+l++ag+krv +++  +p  ++e++e l++
  gi|557694975|ref|YP_008798029.1|  24 KLELVERLADAGLKRVEITVDYPPRTTREDVEPLVK 59 
                                       5899**************************998876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0001
                                       CHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  88 lpdeeklerllelgvdrvslgleaaddekvlklmn..rghtfeevlealeklreagikr 144
                                       + d e +++ + +g   +++ l  ++    +kl++   ++++e++++a++++re g++ 
  gi|557694975|ref|YP_008798029.1|  76 RQDLEAAAKYDAAG-VGLYIALTEIHRT--HKLHGisYQEGLERLMDAVKTAREMGFRY 131
                                       44467788888888.9999999999995..666666699******************94 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  32 eeileevkelkaekgvkevilgggepllypdfvellerl 70 
                                       e +l+ ++e+      ++ ++g g+ +  +d++e ++ l
  gi|557694975|ref|YP_008798029.1| 212 EAVLAGADEA------HVTVMGVGDRNGIADLYEVVAVL 244
                                       3344444333......45555555555555555554444 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 0.9
                                       STGGGSTTHHHHHHHHHHTC........C CS
                                       xxxxxxxxxxxxxxxxxxxx........x RF
                       Radical_SAM  55 gepllypdfvellerlakla........v 75 
                                       g p+ +p+   ++e+la++a         
  gi|557694975|ref|YP_008798029.1| 334 GLPSTDPRARSATEALARKArekkgrlsI 362
                                       44555555555555555555433343330 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 ?   14.2   0.1   3.8e-06     0.023       2      90 ..      29     135 ..      28     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-06
                                       HHHHHCT-SEEEEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHC.................HT CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypded.................er 61 
                                       +++a+aG + vE+  +++   +   +e+++ l k + +lg++ +++   +r    +                   +r
  gi|557694975|ref|YP_008798029.1|  29 ERLADAGLKRVEITVDYPPRTT---REDVEPLVKKCNSLGVEAVLHGRAIRQDL-EAAakydaagvglyialteiHR 101
                                       789******************9...69***************666666666555.4446**************9966 PP

                                       TCS.....HHHHHHHHHHHHHHHHHHTBSEEEEE CS
                      AP_endonuc_2  62 ear.....reesvdalkraielaaaLGapllvlh 90 
                                        ++      +e +++l +a+++a+++G +++   
  gi|557694975|ref|YP_008798029.1| 102 THKlhgisYQEGLERLMDAVKTAREMGFRYVRAT 135
                                       666777777999*****************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 3383.02
//
Query:       gi|557694976|ref|YP_008798030.1|  [L=140]
Description: signal-transduction protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-30  105.2  12.2    1.1e-16   61.0   2.8    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 !   50.0   2.0   1.7e-17     3e-13       1      55 [.       8      61 ..       8      63 .. 0.91
   2 !   61.0   2.8   6.2e-21   1.1e-16       1      56 [.      73     127 ..      73     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.7e-17
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTT.BEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedg.klvGivtlrDllral 55
                                      V+d+mt dvvtv+p+t++  a+++m+e++v++l VV   g k+vG++t+rD++r +
  gi|557694976|ref|YP_008798030.1|  8 VKDVMTADVVTVSPTTSVYAAAKIMAEEEVGSL-VVT-VGeKPVGVLTERDVVRRV 61
                                      89***********************9999****.773.5547***********986 PP

  == domain 2  score: 61.0 bits;  conditional E-value: 6.2e-21
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       V+d+mt++vv+v ++t+leea+ +m++++v+rl+VV  d+klvGivt +D++ral 
  gi|557694976|ref|YP_008798030.1|  73 VEDVMTSPVVVVGENTSLEEAVAIMASNRVRRLLVV-RDEKLVGIVTVTDIVRALG 127
                                       89***********************9999*******.6888************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      264  (0.0147247); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1040.33
//
Query:       gi|557694977|ref|YP_008798031.1|  [L=100]
Description: large subunit ribosomal protein L44e [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   49.1   2.7    6.1e-13   49.1   2.7    1.6  2  Ribosomal_L44  Ribosomal protein L44
  ------ inclusion threshold ------
      0.024   15.0   0.5       0.04   14.3   0.3    1.6  1  ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L


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 ?   -3.0   1.4       1.2   1.1e+04      56      56 ..      16      16 ..       4      38 .. 0.57
   2 !   49.1   2.7   6.8e-17   6.1e-13       2      45 ..      40      83 ..      39      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                                      E CS
                     Ribosomal_L44 56 C 56
                                      C
  gi|557694977|ref|YP_008798031.1| 16 C 16
                                      1 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 6.8e-17
                                      EEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.-- CS
                     Ribosomal_L44  2 HtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaK 45
                                      Hteh+v+ ykkgk+++la g+Rr++r+ +gygGq+ p+++k+ +
  gi|557694977|ref|YP_008798031.1| 40 HTEHTVSLYKKGKERKLALGARRHARELKGYGGQKYPIQRKNPR 83
                                      ****************************************9643 PP

>> ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   4.4e-06      0.04      29      53 ..      28      52 ..      19      68 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-06
                     ribosomal_L24 29 SnVmlvdpkcgkptrvgfrlkedgk 53
                                      S+Vm ++pkc+  t   + l ++gk
  gi|557694977|ref|YP_008798031.1| 28 SKVMTYCPKCNSHTEHTVSLYKKGK 52
                                      9**********99998887766776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); 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: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 762.89
//
Query:       gi|557694978|ref|YP_008798032.1|  [L=66]
Description: small subunit ribosomal protein S27e [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   66.2   1.1    1.8e-18   66.0   1.1    1.1  1  Ribosomal_S27e   Ribosomal protein S27
    0.00042   19.8   0.5    0.00058   19.3   0.5    1.2  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0013   18.1   2.0       0.71    9.4   0.2    2.2  2  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.7   1.3      0.014   15.3   1.3    1.2  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
      0.012   15.4   0.2        1.3    8.9   0.1    2.2  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
      0.019   14.8   4.8       0.02   14.7   0.7    2.0  2  DUF3797          Domain of unknown function (DUF3797)
      0.042   13.9   0.1        2.6    8.1   0.0    2.2  2  zf-BED           BED zinc finger
      0.048   13.7   0.2      0.058   13.4   0.2    1.1  1  Zn_Tnp_IS91      Transposase zinc-binding domain
      0.053   13.5   0.2      0.063   13.3   0.2    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.058   13.0   2.9       0.91    9.2   0.2    2.2  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.062   13.1   2.2      0.073   12.9   0.6    1.7  2  PADR1            PADR1 (NUC008) domain
      0.067   13.1   0.5      0.092   12.6   0.5    1.2  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.095   11.1   0.2       0.11   10.9   0.2    1.0  1  DUF4503          Domain of unknown function (DUF4503)
       0.11   12.2   2.2          6    6.7   0.4    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.11   12.6   0.6       0.21   11.7   0.6    1.4  1  Zn-ribbon_8      Zinc ribbon domain
       0.14   12.2   1.6       0.23   11.5   1.6    1.5  1  zinc_ribbon_6    Zinc-ribbon
       0.16   12.0   0.4       0.21   11.6   0.4    1.1  1  DUF1451          Zinc-ribbon containing domain
       0.18   11.8   0.3       0.18   11.8   0.3    2.0  2  zf-DNL           DNL zinc finger
       0.18   12.0   2.5        2.9    8.1   0.2    2.1  2  zf-AN1           AN1-like Zinc finger
       0.19   11.6   3.4        5.4    6.9   0.5    2.1  2  TFIIS_C          Transcription factor S-II (TFIIS)
       0.23   11.3   5.7          2    8.3   0.6    2.1  2  ZZ               Zinc finger, ZZ type
       0.24   11.2   5.0        0.4   10.4   5.0    1.4  1  A2L_zn_ribbon    A2L zinc ribbon domain
       0.24   11.5   3.5        2.3    8.4   0.1    2.3  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.31   11.0   4.5        8.4    6.4   0.3    2.1  2  Prok-RING_1      Prokaryotic RING finger family 1
       0.35   11.1   0.2       0.35   11.1   0.2    2.0  2  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r


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 !   66.0   1.1   2.5e-21   1.8e-18       1      46 [.      12      57 ..      12      65 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 2.5e-21
                                      -S--EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEE CS
                    Ribosomal_S27e  1 prskFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkakl 46
                                      p+skFl v C +C+n+++vF++a+ +vkC  Cg vL++P GGka +
  gi|557694978|ref|YP_008798032.1| 12 PQSKFLIVTCNECGNNQIVFDSAKIIVKCNVCGAVLAKPSGGKAII 57
                                      79*****************************************966 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.5     8e-07   0.00058       2      31 ..      20      49 ..      19      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8e-07
                                      EETTTTCEECHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVled 31
                                      +C +Cg+ ++v+D +   + C  CG+Vl  
  gi|557694978|ref|YP_008798032.1| 20 TCNECGNNQIVFDSAKIIVKCNVCGAVLAK 49
                                      7******99******************976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0018       1.3       3      11 ..      19      28 ..      18      35 .. 0.81
   2 !    9.4   0.2   0.00099      0.71       3      13 ..      38      49 ..      37      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0018
                       zf-ribbon_3  3 vrCPnCGa.p 11
                                      v+C++CG+ +
  gi|557694978|ref|YP_008798032.1| 19 VTCNECGNnQ 28
                                      68*****955 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00099
                       zf-ribbon_3  3 vrCPnCGa.pls 13
                                      v+C+ CGa +++
  gi|557694978|ref|YP_008798032.1| 38 VKCNVCGAvLAK 49
                                      79******5555 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 ?   15.3   1.3   1.9e-05     0.014      88     116 ..      19      45 ..      14      46 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                                       TSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  88 VlCkeCkspetelekeerllvlkCkaCga 116
                                       V+C+eC++ ++ +    +++ +kC+ Cga
  gi|557694978|ref|YP_008798032.1|  19 VTCNECGNNQIVFDSA-KII-VKCNVCGA 45 
                                       99******98876654.444.7******8 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 ?    8.9   0.1    0.0018       1.3       8      20 ..      13      25 ..       9      25 .. 0.93
   2 ?    4.7   0.0     0.037        27      13      21 ..      37      45 ..      28      50 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0018
                         zf-C2H2_3  8 qksfgasqCkeCg 20
                                      q++f  ++C+eCg
  gi|557694978|ref|YP_008798032.1| 13 QSKFLIVTCNECG 25
                                      99**********8 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.037
                         zf-C2H2_3 13 asqCkeCgM 21
                                       ++C++Cg 
  gi|557694978|ref|YP_008798032.1| 37 IVKCNVCGA 45
                                      367****95 PP

>> DUF3797  Domain of unknown function (DUF3797)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.7   2.9e-05      0.02      14      33 ..      19      38 ..      12      39 .. 0.90
   2 ?    3.6   0.3     0.086        61      14      33 ..      38      57 ..      37      61 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.9e-05
                           DUF3797 14 vqCPeCgNnkvlNsegkvii 33
                                      v C eCgNn++    +k+i+
  gi|557694978|ref|YP_008798032.1| 19 VTCNECGNNQIVFDSAKIIV 38
                                      79****************98 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.086
                           DUF3797 14 vqCPeCgNnkvlNsegkvii 33
                                      v+C +Cg      s+gk ii
  gi|557694978|ref|YP_008798032.1| 38 VKCNVCGAVLAKPSGGKAII 57
                                      78*****9999999999877 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.061        44      16      25 ..      18      27 ..       2      28 .. 0.81
   2 ?    8.1   0.0    0.0037       2.6      16      28 ..      37      49 ..      31      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.061
                                      --EETTTTEE CS
                            zf-BED 16 kavCryCgki 25
                                       ++C+ Cg++
  gi|557694978|ref|YP_008798032.1| 18 IVTCNECGNN 27
                                      689*****96 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0037
                                      --EETTTTEE--- CS
                            zf-BED 16 kavCryCgkilsr 28
                                       ++C+ Cg++l+ 
  gi|557694978|ref|YP_008798032.1| 37 IVKCNVCGAVLAK 49
                                      699******9975 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 ?   13.4   0.2   8.2e-05     0.058      37      66 ..      16      46 ..      11      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.2e-05
                       Zn_Tnp_IS91 37 faryeCeeCghekivyfsCksrh.CpsCqkk 66
                                      f  + C+eCg+++iv+ s k    C+ C++ 
  gi|557694978|ref|YP_008798032.1| 16 FLIVTCNECGNNQIVFDSAKIIVkCNVCGAV 46
                                      56789****************999****986 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   0.2   8.8e-05     0.063      70     106 ..      18      57 ..      11      62 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.8e-05
                                       EEEETTTS-EEE.CHH.H.HHS-TTTSSS-EEEEESSSEE CS
                              HypA  70 kvrCreCgkefe.lee.k.alrCpkCgsadveivsGeell 106
                                        v+C+eCg++    ++ k  ++C+ Cg+   +  +G+ + 
  gi|557694978|ref|YP_008798032.1|  18 IVTCNECGNNQIvFDSaKiIVKCNVCGAVLAKPSGGKAII 57 
                                       689****987663333335669*****9999988888776 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.2     0.036        26       9      14 ..      21      26 ..      16      33 .. 0.82
   2 ?    9.2   0.2    0.0013      0.91       7      15 ..      38      46 ..      34      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.036
                                      -TTT-- CS
                   Desulfoferrod_N  9 CevCGn 14
                                      C+ CGn
  gi|557694978|ref|YP_008798032.1| 21 CNECGN 26
                                      *****9 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0013
                                      EE-TTT--E CS
                   Desulfoferrod_N  7 YkCevCGni 15
                                       kC+vCG +
  gi|557694978|ref|YP_008798032.1| 38 VKCNVCGAV 46
                                      59*****87 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.6    0.0001     0.073      15      30 ..      20      37 ..      17      42 .. 0.79
   2 ?    0.8   0.2      0.61   4.4e+02      14      20 ..      38      44 ..      36      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                             PADR1 15 kCpeCkegqlvfdss..g 30
                                       C eC+++q+vfds    
  gi|557694978|ref|YP_008798032.1| 20 TCNECGNNQIVFDSAkiI 37
                                      7************99443 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.61
                             PADR1 14 ekCpeCk 20
                                       kC  C+
  gi|557694978|ref|YP_008798032.1| 38 VKCNVCG 44
                                      5899998 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 ?   12.6   0.5   0.00013     0.092      13      37 ..      20      46 ..      14      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                                      B-TTT-SB-.-S.SSS-EEEETTT--E CS
                              C1_1 13 fCkhCgefl.wg.kekqglkCswCkll 37
                                      +C++Cg+    +  +k ++kC++C+ +
  gi|557694978|ref|YP_008798032.1| 20 TCNECGNNQiVFdSAKIIVKCNVCGAV 46
                                      7****86543677***********975 PP

>> DUF4503  Domain of unknown function (DUF4503)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00015      0.11     282     314 ..      20      51 ..      13      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                           DUF4503 282 vCdrCgsekleqspedrgafsCgsCssvvtsPv 314
                                       +C++Cg++++   ++ +  ++C+ C  v+++P 
  gi|557694978|ref|YP_008798032.1|  20 TCNECGNNQIVF-DSAKIIVKCNVCGAVLAKPS 51 
                                       8*********85.566799***********996 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.4    0.0083         6       3      10 ..      21      28 ..      20      31 .. 0.83
   2 ?    5.4   0.1     0.022        15       3      12 ..      40      49 ..      39      52 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0083
                      Rubredoxin_2  3 CsqCGfes 10
                                      C++CG+ +
  gi|557694978|ref|YP_008798032.1| 21 CNECGNNQ 28
                                      *****986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.022
                      Rubredoxin_2  3 CsqCGfesak 12
                                      C+ CG++ ak
  gi|557694978|ref|YP_008798032.1| 40 CNVCGAVLAK 49
                                      9999987665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6    0.0003      0.21       8      35 ..      21      46 ..      18      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0003
                       Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgse 35
                                      C+eCg+   v+ s++    ++ C  Cg+ 
  gi|557694978|ref|YP_008798032.1| 21 CNECGNNQIVFDSAK---IIVkCNVCGAV 46
                                      *****8888888766...7777*****84 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.6   0.00032      0.23      23      54 ..      12      44 ..       1      46 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00032
                     zinc_ribbon_6 23 yknkkvkilCnDCekkse.vkfhvlglkCkeCg 54
                                       ++k   ++Cn C++++   +   + +kC+ Cg
  gi|557694978|ref|YP_008798032.1| 12 PQSKFLIVTCNECGNNQIvFDSAKIIVKCNVCG 44
                                      5678999*******9988567778899*****7 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.4   0.00029      0.21     116     140 ..      20      45 ..      17      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                           DUF1451 116 vCekCgk.elalkkteeippCpkCga 140
                                       +C++Cg+ ++ +++++ i +C+ Cga
  gi|557694978|ref|YP_008798032.1|  20 TCNECGNnQIVFDSAKIIVKCNVCGA 45 
                                       8****96268899***********96 PP

>> zf-DNL  DNL zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00025      0.18      27      46 ..      17      36 ..      11      39 .. 0.85
   2 ?    3.6   0.6     0.088        63      25      35 ..      34      44 ..      30      48 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00025
                            zf-DNL 27 VivqCpgCknrHliaDnLgw 46
                                       iv+C++C n+ ++ D  ++
  gi|557694978|ref|YP_008798032.1| 17 LIVTCNECGNNQIVFDSAKI 36
                                      79************998665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.088
                            zf-DNL 25 GvVivqCpgCk 35
                                        +iv+C+ C 
  gi|557694978|ref|YP_008798032.1| 34 AKIIVKCNVCG 44
                                      56899999996 PP

>> zf-AN1  AN1-like Zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.2     0.004       2.9       9      22 ..      14      27 ..      11      28 .. 0.85
   2 ?    4.4   0.2     0.057        41      12      21 ..      36      45 ..      27      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.004
                            zf-AN1  9 kdflpfkCryCgkv 22
                                      + fl+++C++Cg++
  gi|557694978|ref|YP_008798032.1| 14 SKFLIVTCNECGNN 27
                                      66899******986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.057
                            zf-AN1 12 lpfkCryCgk 21
                                      +++kC+ Cg 
  gi|557694978|ref|YP_008798032.1| 36 IIVKCNVCGA 45
                                      459*****96 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 ?    6.9   0.5    0.0076       5.4      27      36 ..      17      26 ..      14      28 .. 0.75
   2 ?    5.7   3.5     0.019        13       2      13 ..      20      31 ..      19      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0076
                           TFIIS_C 27 vfykCtkCgh 36
                                      ++++C++Cg+
  gi|557694978|ref|YP_008798032.1| 17 LIVTCNECGN 26
                                      5688999987 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.019
                           TFIIS_C  2 kCpkCgsreayf 13
                                      +C++Cg+++++f
  gi|557694978|ref|YP_008798032.1| 20 TCNECGNNQIVF 31
                                      799999998887 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.6    0.0028         2       5      15 ..      19      29 ..      18      36 .. 0.79
   2 ?    6.1   0.5     0.014       9.8       5      12 ..      38      45 ..      34      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0028
                                      EE-TTT-S..E CS
                                ZZ  5 ytCdgCseapl 15
                                      +tC++C++  +
  gi|557694978|ref|YP_008798032.1| 19 VTCNECGNNQI 29
                                      79*****9544 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.014
                                      EE-TTT-S CS
                                ZZ  5 ytCdgCse 12
                                      ++C++C++
  gi|557694978|ref|YP_008798032.1| 38 VKCNVCGA 45
                                      89****98 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 ?   10.4   5.0   0.00056       0.4       4      30 ..      19      46 ..      18      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00056
                     A2L_zn_ribbon  4 kvCsvCggngiln.seqgylvCieCgas 30
                                      ++C  Cg+n i+  s++ +  C+ Cga+
  gi|557694978|ref|YP_008798032.1| 19 VTCNECGNNQIVFdSAKIIVKCNVCGAV 46
                                      79***********9************97 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 ?    4.0   0.5     0.073        52       3       9 ..      20      26 ..      19      27 .. 0.83
   2 ?    8.4   0.1    0.0032       2.3       2      13 ..      38      49 ..      38      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.073
                            zf-ACC  3 KCpsCge 9 
                                       C++Cg+
  gi|557694978|ref|YP_008798032.1| 20 TCNECGN 26
                                      7****97 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0032
                            zf-ACC  2 tKCpsCgemlyk 13
                                      +KC+ Cg++l k
  gi|557694978|ref|YP_008798032.1| 38 VKCNVCGAVLAK 49
                                      7********976 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 ?    6.4   0.3     0.012       8.4      20      28 ..      18      26 ..      13      29 .. 0.88
   2 ?    6.0   4.7     0.016        11       6      29 ..      20      46 ..      19      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.012
                       Prok-RING_1 20 iVvCpeCgt 28
                                      iV+C eCg 
  gi|557694978|ref|YP_008798032.1| 18 IVTCNECGN 26
                                      9******96 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.016
                       Prok-RING_1  6 kCpvCgke...lkeedDiVvCpeCgtp 29
                                       C+ Cg++   +++++ iV C +Cg++
  gi|557694978|ref|YP_008798032.1| 20 TCNECGNNqivFDSAKIIVKCNVCGAV 46
                                      588888755558888999*******96 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 ?   11.1   0.2   0.00048      0.35      30      45 ..      13      28 ..       8      35 .. 0.84
   2 ?    0.9   0.6      0.71   5.1e+02      34      42 ..      36      44 ..      30      48 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00048
                    zinc_ribbon_13 30 nkkfitvsCknCgYte 45
                                      + kf++v+C++Cg  +
  gi|557694978|ref|YP_008798032.1| 13 QSKFLIVTCNECGNNQ 28
                                      579*********9665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.71
                    zinc_ribbon_13 34 itvsCknCg 42
                                      i+v C+ Cg
  gi|557694978|ref|YP_008798032.1| 36 IIVKCNVCG 44
                                      679999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 493.81
//
Query:       gi|557694979|ref|YP_008798033.1|  [L=254]
Description: translation initiation factor eIF-2 alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   50.6   0.3      4e-13   49.5   0.3    1.6  1  S1           S1 RNA binding domain
    6.7e-11   42.3   0.9    1.8e-10   40.9   0.2    1.9  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
     0.0007   20.4   0.6        1.2    9.9   0.2    2.6  2  PriA_C       Primosomal protein N C-terminal domain


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 !   49.5   0.3   6.7e-17     4e-13       2      75 .]       5      79 ..       4      79 .. 0.98

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 6.7e-17
                                      STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                      pe+ge v G V +v ++Ga+Ve++   g egfv++se+s +  v+++ e+lk+G++  +k+++v+ ++  ++lsi+
  gi|557694979|ref|YP_008798033.1|  5 PEVGELVIGRVREVKDYGAYVEIDeyPGYEGFVHVSEVSLK-WVRNIREHLKEGQRTVFKIIRVNPAAMQADLSIR 79
                                      899**********************99**************.********************************97 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 ?   -0.9   0.0      0.28   1.7e+03      72      84 ..      47      59 ..      34     100 .. 0.70
   2 !   40.9   0.2     3e-14   1.8e-10      10     113 ..     122     221 ..     113     225 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.28
                                      HHHHHHHHHHHST CS
                       EIF_2_alpha 72 veaIkeaLkagee 84
                                      v +I+e Lk+g++
  gi|557694979|ref|YP_008798033.1| 47 VRNIREHLKEGQR 59
                                      5556666664443 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 3e-14
                                       TTTTS-HHHHHHHHHSTTH...HHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHHHHHS CS
                       EIF_2_alpha  10 yekyghaydaFklaitdee...vldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaLkage 83 
                                        +  + +yd+F+ +  d+    ++ +  ++++  e+L   i++++++++++i+ di ++c +  Gv aI+ea  a+e
  gi|557694979|ref|YP_008798033.1| 122 TRDTDVLYDIFEQISADQPvkqFFPQ--LDDKESETLRRAIEHEIRVREHEIKKDIIMRCEARRGVMAIREAAAAAE 196
                                       333466*****877777773434555..67999***************************************99777 PP

                                       T.S..TTSSSEEEEEEEESSSSEEEEEEEE CS
                       EIF_2_alpha  84 easneeeveeeeevkikliapPeYvltvet 113
                                       e      +   e+v+i++ ++P Y + v++
  gi|557694979|ref|YP_008798033.1| 197 EL-----AGPGETVEIRTKGAPVYGVLVKS 221
                                       64.....45669************988765 PP

>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.2   0.00021       1.2      43      80 ..      73     110 ..      38     126 .. 0.71
   2 !    8.5   0.0    0.0006       3.6      36      81 ..     194     239 ..     151     250 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00021
                            PriA_C  43 papapiakikgryryqillksksrkalqkllkellekl 80 
                                        a   i ++++r r+  ll+ k+ ++++++lk l e+ 
  gi|557694979|ref|YP_008798033.1|  73 QADLSIRRVSQRERMEKLLEVKKASKVRRVLKILEEAS 110
                                       4556799************************9665544 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0006
                            PriA_C  36 eeveilgpapapiakikgryryqillksksrkalqkllkellekle 81 
                                        + e+ gp + +  + kg   y +l+ks++r++ ++ll+++lek+ 
  gi|557694979|ref|YP_008798033.1| 194 AAEELAGPGETVEIRTKGAPVYGVLVKSSTREKSEELLSKVLEKCG 239
                                       22358999999999999************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 1998.57
//
Query:       gi|557694980|ref|YP_008798034.1|  [L=110]
Description: hypothetical protein CSUB_C1553 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 887.13
//
Query:       gi|557694981|ref|YP_008798035.1|  [L=250]
Description: hypothetical protein CSUB_C1554 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-35  120.5  36.9    9.7e-35  120.3  36.9    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 !  120.3  36.9   5.4e-39   9.7e-35       2     236 .]      10     244 ..       9     244 .. 0.92

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 5.4e-39
                              TauE   2 llagllaGfvagllGiGggliavPlLll.l.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliG 76 
                                       +l++++  +v+++lG+Ggg+++vP+ +  + + p vav++sl +v+ +++s++l+ + ++++++r  l+l+l++   
  gi|557694981|ref|YP_008798035.1|  10 VLLAFFSALVGSMLGVGGGFVFVPVSVGiMgFRPFVAVPASLSLVLSNAFSATLTRLMKKAFNLRPNLWLILPASGL 86 
                                       689999*********************97789************************9999****999999999999* PP

                              TauE  77 allGallllllpsellkllfgvlllllallmllrkkrsrakgrerrptaillvliggl.vGllsGllGiGgGfllvp 152
                                       ++lGal +++l ++++k++fg +ll ++ll+l +++++++    + ++ ++  l+ ++ +G++s+llG+GgG l+vp
  gi|557694981|ref|YP_008798035.1|  87 SVLGALTSARLEAPVFKIMFGTFLLGSSLLLLKTRGEQEQ---GHSRGFAGRRLVVVVaAGFISSLLGVGGGLLMVP 160
                                       *******************************998874333...4555555555555666****************** PP

                              TauE 153 llllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertlrrlfalll 229
                                        ++ll +++ +++va+s +++ ++s++g+++y+l+g++ ++l + + +g+llG+++G+r+   lse++l+ ++ l  
  gi|557694981|ref|YP_008798035.1| 161 GFILLSKMSSRESVAVSQFITGFTSATGLATYLLQGSFFPSLYGSAFAGGLLGGFVGSRIQIGLSEKQLKTAISLGF 237
                                       *****************************************9999******************************99 PP

                              TauE 230 lvlgvkl 236
                                        ++g+ +
  gi|557694981|ref|YP_008798035.1| 238 SAIGLWM 244
                                       9999976 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:                      277  (0.0154498); 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: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1901.14
//
Query:       gi|557694982|ref|YP_008798036.1|  [L=210]
Description: peptidase M50 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0002   20.7  19.2     0.0012   18.2   1.1    3.5  3  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
        0.6   10.0   2.0        1.2    9.0   2.0    1.6  1  TMIE           TMIE protein
        2.8    8.3  10.4        8.3    6.8   0.0    3.0  3  2TM            2TM 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 ?   -1.1   0.1      0.16   9.4e+02      16     102 ..      32      54 ..      29      60 .. 0.48
   2 !    7.5   6.8   0.00037       2.2       2     106 ..      62     148 ..      61     153 .. 0.81
   3 !   18.2   1.1     2e-07    0.0012     191     219 ..     158     186 ..     150     197 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.16
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  16 GHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkkspwqrllivl 92 
                                       +H+lvA l                                                                 ++vl
  gi|557694982|ref|YP_008798036.1|  32 AHLLVATL-----------------------------------------------------------------VVVL 43 
                                       55555554.................................................................4455 PP

                                       XXX.XXXXXXX CS
                                       xxx.xxxxxxx RF
                     Peptidase_M50  93 AGp.lanfila 102
                                       AG  l +f++a
  gi|557694982|ref|YP_008798036.1|  44 AGVsLLGFVFA 54 
                                       55313344444 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00037
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeaka 78 
                                       +++ +  + + HEl+H +vA + g+   ef + f   l+++    ++  ++++   G V ++g +            
  gi|557694982|ref|YP_008798036.1|  62 LLIGFAASFLGHELAHKIVALRKGFGA-EFRVYFAGLLVTVLTSVLPIPFKVIMP-GSVVIRGIQ------------ 124
                                       5788999999***************99.9*****999999887766665555543.557788877............ PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  79 flkkspwqrllivlAGplanfilailvf 106
                                           s+     +++AGpl+n+ +a + +
  gi|557694982|ref|YP_008798036.1| 125 ----SLRDMGQVAVAGPLFNMAVAAVSL 148
                                       ....677789999999999999988765 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 2e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 191 flqllalisvnLgilNLlPipvLDGghll 219
                                       +l  +a+++  L ++N+lPi++LDG +++
  gi|557694982|ref|YP_008798036.1| 158 VLMAVASLNAFLMFFNMLPIMPLDGEKVF 186
                                       6778899******************9986 PP

>> TMIE  TMIE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.0    0.0002       1.2       2      26 ..     183     207 ..     182     210 .] 0.92

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0002
                              TMIE   2 ekevfaglrvWhviaivllvvlaiv 26 
                                       ek+ ++  +vW v+++++lvvl++v
  gi|557694982|ref|YP_008798036.1| 183 EKVFIWSKKVWTVVFVLSLVVLTLV 207
                                       78999*****************997 PP

>> 2TM  2TM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.7      0.13   7.9e+02      25      47 ..      38      67 ..      26      73 .. 0.44
   2 ?    6.8   0.0    0.0014       8.3       2      31 ..      75     104 ..      74     142 .. 0.85
   3 ?    5.2   2.0    0.0044        26      22      51 ..     164     200 ..     156     208 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.13
                               2TM 25 iflilinl.......gsswflwpilfWgig 47
                                      ++++++         + +  ++++l+ g++
  gi|557694982|ref|YP_008798036.1| 38 TLVVVLAGvsllgfvFAPTLFYAALLIGFA 67
                                      322222112113323444445555555544 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0014
                               2TM   2 kakkrvkeikgFyrhlvvYlivniflilin 31 
                                        a+k v  +kgF   + vY++  ++ +l +
  gi|557694982|ref|YP_008798036.1|  75 LAHKIVALRKGFGAEFRVYFAGLLVTVLTS 104
                                       68999****************999877764 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0044
                               2TM  22 ivniflilinl.......gsswflwpilfWgiglllh 51 
                                         n+fl+++n+       g   f+w   +W ++++l 
  gi|557694982|ref|YP_008798036.1| 164 SLNAFLMFFNMlpimpldGEKVFIWSKKVWTVVFVLS 200
                                       5799******99******6666666666666555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1609.90
//
Query:       gi|557694983|ref|YP_008798037.1|  [L=141]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   25.9   0.0    1.4e-05   25.2   0.0    1.4  1  HSP20       Hsp20/alpha crystallin family
    0.00014   21.4   0.0     0.0002   20.9   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 !   25.2   0.0   1.5e-09   1.4e-05      13      91 ..      55     134 ..      47     141 .] 0.80

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.5e-09
                                       EE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS--.-EEEEEE--STTB-TTT-EEEEETTEEEEEEEBS CS
                             HSP20  13 ldvpglkkeelkvkvednrvlvkgeheeeeedekglikerss.rkFsrkftLPenvdadkvkaslkdGvLtvtvpkk 88 
                                       ++v+g  ++ ++++ ++n+++v++e  +  + e    +  ++ +   r ++LP  +d++kv+a+++ G+L + ++  
  gi|557694983|ref|YP_008798037.1|  55 FEVAGCPRDKIELTAQENQIMVSAELVSPPSPEFSRLYPFTRgKGVHRVLRLPRAIDPSKVEAKYDSGLLFIRAEIA 131
                                       799999*******************994444444444444440557899***********************99987 PP

                                       S-- CS
                             HSP20  89 epe 91 
                                       +p 
  gi|557694983|ref|YP_008798037.1| 132 KPR 134
                                       775 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 !   20.9   0.0   2.2e-08    0.0002      10      62 ..      57     127 ..      48     127 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.2e-08
                        ArsA_HSP20  10 LPfvdkeeidlsrsgdeLtIkig...................nfrRqitLPsvlarkevtsAkfedgvLeIr 62 
                                       + +  +++i+l+ ++++++++++                     +R+  LP+ ++  +v  Ak+  g L Ir
  gi|557694983|ref|YP_008798037.1|  57 VAGCPRDKIELTAQENQIMVSAElvsppspefsrlypftrgkGVHRVLRLPRAIDPSKV-EAKYDSGLLFIR 127
                                       6678899****************************************************.*******99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1115.10
//
Query:       gi|557694984|ref|YP_008798038.1|  [L=529]
Description: DNA ligase 1 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-49  167.5   0.0    6.6e-49  166.3   0.0    1.6  2  DNA_ligase_A_M   ATP dependent DNA ligase domain
    2.8e-18   66.9   0.2    1.3e-10   41.9   0.2    2.4  2  DNA_ligase_A_N   DNA ligase N terminus
    2.5e-14   53.6   0.0    9.3e-14   51.8   0.0    2.1  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
     0.0077   16.2   0.6      0.056   13.4   0.1    2.7  3  HTH_15           Helix-turn-helix domain of alkylmercury lyas
  ------ inclusion threshold ------
      0.014   15.2   0.0      0.097   12.5   0.0    2.2  1  mRNA_cap_enzyme  mRNA capping enzyme, catalytic 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 !  166.3   0.0   1.9e-52   6.6e-49       1     204 []     196     391 ..     196     391 .. 0.95
   2 ?   -4.1   0.0       2.8     1e+04     130     156 ..     439     464 ..     437     471 .. 0.76

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 1.9e-52
                                       -EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEE CS
                    DNA_ligase_A_M   1 pmLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilD 77 
                                       pmLAe++ s e++++kl + ++++E K+DG+R+qvh  ++ vk+++R lkd+t++ p++v+++++a+ ++  ++ilD
  gi|557694984|ref|YP_008798038.1| 196 PMLAEYAYSPEEIFEKL-SPPVYLEPKIDGVRLQVHVGDGMVKVYTRGLKDVTESVPDIVEMVRQALSAE--KCILD 269
                                       9***************9.899**********************************************986..9**** PP

                                       EEEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEE CS
                    DNA_ligase_A_M  78 GElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrve 154
                                       GE ++vd++ g++ pfq++++r+ ++k+v e+lke  l++ +FDi++l+ge+l ++pl+eRr+ Lee +    ++  
  gi|557694984|ref|YP_008798038.1| 270 GEGYCVDEN-GRPTPFQETMRRIGREKNVDEALKELGLRIKFFDIIHLNGEDLWQKPLDERRQALEETV----EQPL 341
                                       *****9888.*************88888*****************************************....3444 PP

                                       E--EEEESSHHHHHHHHHHHHHTTECEEEEEETT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 155 laeslevkdveeleelleeaiseglEGlvvKnpdskYepgkrsknwlKvK 204
                                       +   +  ++ + ++e+le   s g+EGl++K+p+s+Y+pg+r+ +wlK+K
  gi|557694984|ref|YP_008798038.1| 342 INPLTIADNRDMVQEALETWTSLGYEGLMAKSPKSPYTPGRRGGHWLKMK 391
                                       566777888999*************************************9 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2.8
                                       HTTSCHHHHHHHHHHHB--BTTTEEE- CS
                    DNA_ligase_A_M 130 ltdeplkeRrklLeeilkesedrvela 156
                                       ltd +++++ +lL  i  +s++++ ++
  gi|557694984|ref|YP_008798038.1| 439 LTDDEFRKMTQLLLGIA-KSREEWGVV 464
                                       88999999999999988.666666554 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 !   25.5   0.0   3.8e-09   1.4e-05       2      69 ..       5      74 ..       4      76 .. 0.87
   2 !   41.9   0.2   3.6e-14   1.3e-10      94     173 .]      70     151 ..      66     151 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 3.8e-09
                                      CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH...SS-CCCS------HHHHHHHHH CS
                    DNA_ligase_A_N  2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrL...llPdydgreygigesllakala 69
                                      F+ela+l+ k+e+ tk+r ek++++++f+ k+  ++ +++++a+ L   l    ++   +ig+ +l++al 
  gi|557694984|ref|YP_008798038.1|  5 FSELADLCVKLES-TKSRREKIKHISDFLGKFGPEEADEAAAAANLlvgLSSGVRKLGVNIGPATLYRALR 74
                                      9************.999************888888888899999996777777777788999*****9986 PP

  == domain 2  score: 41.9 bits;  conditional E-value: 3.6e-14
                                       HHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHHHHHHHHCT---SS--HHHH CS
                    DNA_ligase_A_N  94 eevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEakyliriilkdlriglsektv 168
                                       +++l+++++  +++++lti+ev e+ +k ++  gkg  +++k++l++ll+ras++E  +l+ri+ +++r g+s + +
  gi|557694984|ref|YP_008798038.1|  70 YRALREQQSVlTPPTSLTISEVWETIEKASSLtGKGVIEARKALLSNLLSRASEKEREWLTRILMGEMRHGASVGIL 146
                                       45554454445******************87789***************************************9998 PP

                                       HHHHH CS
                    DNA_ligase_A_N 169 ldala 173
                                       ++ la
  gi|557694984|ref|YP_008798038.1| 147 VESLA 151
                                       88876 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 !   51.8   0.0   2.6e-17   9.3e-14       1      99 []     410     502 ..     410     502 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 2.6e-17
                                       GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEES CS
                    DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfa 75 
                                       r+g+++ + l+v +  +g ++ vgk+  G++d+e +++++ l  + ++++++           v veP++vve++f 
  gi|557694984|ref|YP_008798038.1| 410 RRGWLSNYHLAVLEsrGGGFTPVGKTFKGLTDDEFRKMTQLLLGIAKSREEW----------GVVVEPRIVVEIEFN 476
                                       689***********98999***********************8888888888..........2569*********** PP

                                       EEECTSSSTT..EECT-EEEEE-TTS CS
                    DNA_ligase_A_C  76 eitasgkyka..slRfPrfkrlReDk 99 
                                       e+++s++y++  +lRf+r+k +R+Dk
  gi|557694984|ref|YP_008798038.1| 477 EVQRSPTYPSgyALRFARIKAIRTDK 502
                                       *************************8 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 !   13.4   0.1   1.6e-05     0.056       9      55 ..     116     164 ..     110     168 .. 0.84
   2 ?   -1.3   0.0      0.58   2.1e+03      48      59 ..     253     264 ..     243     271 .. 0.82
   3 ?   -4.1   0.0       4.4   1.6e+04      50      64 ..     352     366 ..     348     367 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                            HTH_15   9 slakgeeggssaellrpLlrlLakGepVt..veeLAaatgrsveevrqa 55 
                                       +l +     +  +l r L+ ++ +G+ V   ve LA+ ++ ++e+v++a
  gi|557694984|ref|YP_008798038.1| 116 NLLSRASEKEREWLTRILMGEMRHGASVGilVESLAKYLNMPLEKVKAA 164
                                       455666677899***************97447**************986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.58
                            HTH_15  48 sveevrqaLaal 59 
                                        ve vrqaL+a+
  gi|557694984|ref|YP_008798038.1| 253 IVEMVRQALSAE 264
                                       5899*****986 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 4.4
                            HTH_15  50 eevrqaLaalpstEy 64 
                                       + v++aL++  s  y
  gi|557694984|ref|YP_008798038.1| 352 DMVQEALETWTSLGY 366
                                       789999999988776 PP

>> mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.7e-05     0.097      91     129 ..     306     344 ..     294     391 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.7e-05
                                       EEEEEEEEEEETTEEGTTSBHHHHHHHHHHHTHHHHHHH CS
                   mRNA_cap_enzyme  91 lryliyDivaingvtvaeeplskRleilkkelikprnee 129
                                       lr   +Di+++ng ++ ++pl++R ++l+  + +p  + 
  gi|557694984|ref|YP_008798038.1| 306 LRIKFFDIIHLNGEDLWQKPLDERRQALEETVEQPLINP 344
                                       67789************************9999887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (529 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); 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: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3621.81
//
Query:       gi|557694985|ref|YP_008798039.1|  [L=191]
Description: hypothetical protein CSUB_C1558 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); 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 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1448.43
//
Query:       gi|557694986|ref|YP_008798040.1|  [L=121]
Description: methionyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   75.3   0.0    3.5e-21   75.1   0.0    1.1  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 !   75.1   0.0     2e-25   3.5e-21       1      95 [.      26     118 ..      26     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 2e-25
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECC CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeel 77 
                                       +rvG+v++ae+++++dkLl+l v +G+ e +q+ +g++++y+p+   ++  v v nl+ +k+rG+ Se+M+l a e 
  gi|557694986|ref|YP_008798040.1|  26 MRVGRVVHAEKLKGSDKLLRLRVRFGDVE-KQVLTGLAEYYSPDHFTGRLFVFVTNLETRKIRGEVSEAMLLTAVE- 100
                                       79***************************.*********************************************8. PP

                                       ESSCEEEEEESST--TTC CS
                         tRNA_bind  78 dekevgilelpadveaGe 95 
                                       +e++   + ++++v  G+
  gi|557694986|ref|YP_008798040.1| 101 SEQKIVPIVPEGEVAEGT 118
                                       9999999****9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 895.71
//
Query:       gi|557694987|ref|YP_008798041.1|  [L=429]
Description: asparaginyl-tRNA synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-84  283.2   0.0    2.8e-84  282.9   0.0    1.0  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    9.6e-13   47.9   0.1    2.3e-12   46.7   0.1    1.7  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.002   17.6   0.1       0.27   10.7   0.0    2.4  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)


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 !  282.9   0.0   4.6e-88   2.8e-84       6     313 ..     115     423 ..     111     424 .. 0.96

  Alignments for each domain:
  == domain 1  score: 282.9 bits;  conditional E-value: 4.6e-88
                                       HHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....-E-S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxx RF
                       tRNA-synt_2   6 lknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....aLtqs 78 
                                        ++r+l +r++k  ++lr+rs+++k++r+++e++gf+e++ P+++++++e+ga+lF v       ++f    +Ltqs
  gi|557694987|ref|YP_008798041.1| 115 SDHRHLAIRSPKAAAILRFRSNLLKSIRNWFEREGFVEVHCPTFITAAVEGGATLFEV-------NYFgkkvYLTQS 184
                                       579*******************************************************.......55555556**** PP

                                       SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  79 pqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdief 155
                                        q+y e+ i + +++v++i ++FRaE+s+t+rhl+EF+++e em+f+  +d+m+v+e+l+ +   e+le+s++ ++ 
  gi|557694987|ref|YP_008798041.1| 185 VQFYQEAAIYS-LGKVYSIQPSFRAERSKTRRHLTEFWHVEGEMAFAGLDDLMKVVERLVGEASAETLENSRDVLKL 260
                                       ***********.**************************************************************999 PP

                                       TTTTTS.EE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTST CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 156 virrns.kdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddk 225
                                         r+ s ++++ p+ r++y+ea+++l ++      g dl  ++e++l+  e  +p+f+t+fP++ k Fy+  +  ++
  gi|557694987|ref|YP_008798041.1| 261 LGRERSpESVEPPYHRVKYSEALDILASKgvqlewGSDLGADEEKILTM-EFDKPFFLTHFPKKAKAFYHMPDPANP 336
                                       9998886777777*************9999***99999**********9.999************************ PP

                                       TBBSEEEEEET.TE.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT CS
                                       xxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 226 kltesyDllin.gv.ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllg 300
                                       +lt s Dll + g+ E+vg+ +Ri+d+++l +++ ++gl+   ++ ++wyl++++yG++ph+G+glG++Rlv++llg
  gi|557694987|ref|YP_008798041.1| 337 ELTLSADLLAPeGYgEIVGSGQRIHDYQQLLTRIVEEGLE---PSDYKWYLDLRKYGSVPHSGFGLGVERLVQWLLG 410
                                       **********9889**************************...********************************** PP

                                       -SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxx RF
                       tRNA-synt_2 301 sesIrdviaFPkl 313
                                       +++Ir +++FP++
  gi|557694987|ref|YP_008798041.1| 411 LKNIRSAVMFPRT 423
                                       ***********97 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 !   46.7   0.1   3.8e-16   2.3e-12       1      75 [.      17      95 ..      17      96 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 3.8e-16
                                      EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEE CS
                   tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrr...pggelelkvee 72
                                      V ++G+++s+  r++g+++fidlrDgtg +qv+l      e++++  ++  +++ + v+G v  +   pgg  e+k+ +
  gi|557694987|ref|YP_008798041.1| 17 VELRGWIRSK--RHHGRLMFIDLRDGTGVVQVTLKAaevpEADFQAVSSAGRESALVVRGVVVHDpraPGG-AEVKAGK 92
                                      7899******..*****************************************************999999.******* PP

                                      EEE CS
                   tRNA_anti-codon 73 iel 75
                                      +el
  gi|557694987|ref|YP_008798041.1| 93 VEL 95
                                      997 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 !    4.5   0.0    0.0036        21     103     150 ..     198     244 ..     182     253 .. 0.82
   2 !   10.7   0.0   4.6e-05      0.27     209     234 ..     392     417 ..     384     426 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0036
                                       EEEEEEEEEBSST.-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHH CS
                      tRNA-synt_2d 103 kiisigrvfRrda.vDathlaeFhqveglvvdenvsladlkgvleellk 150
                                       k+ si+  fR +  + ++hl eF  veg ++     l+dl++v+e l+ 
  gi|557694987|ref|YP_008798041.1| 198 KVYSIQPSFRAERsKTRRHLTEFWHVEGEMAFA--GLDDLMKVVERLVG 244
                                       78899999****978999**********88764..46788888877765 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 4.6e-05
                                       SEEEEEEEEHHHHHHHHHT-SSGHHH CS
                      tRNA-synt_2d 209 vsgfafGlGveRlamlkygieDiRel 234
                                       v+  +fGlGveRl    +g+++iR+ 
  gi|557694987|ref|YP_008798041.1| 392 VPHSGFGLGVERLVQWLLGLKNIRSA 417
                                       56678*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 3216.13
//
Query:       gi|557694988|ref|YP_008798042.1|  [L=184]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   46.0   0.0    1.4e-11   44.9   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
    2.1e-11   43.8   0.0    2.7e-11   43.5   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    3.1e-10   39.9   0.0    1.3e-09   37.8   0.0    1.7  1  MTS              Methyltransferase small domain
      5e-10   39.9   0.0    1.5e-09   38.4   0.0    1.7  2  Methyltransf_11  Methyltransferase domain
    8.9e-09   36.0   0.0    1.8e-08   35.0   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    1.8e-05   24.5   0.0    3.1e-05   23.7   0.0    1.4  1  UPF0020          Putative RNA methylase family UPF0020
    3.3e-05   23.8   0.0    4.5e-05   23.3   0.0    1.3  1  Methyltransf_23  Methyltransferase domain
    0.00051   19.5   0.0     0.0007   19.1   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00075   19.0   0.0     0.0014   18.1   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
    0.00084   19.1   0.0     0.0012   18.5   0.0    1.2  1  TPMT             Thiopurine S-methyltransferase (TPMT)
     0.0031   17.4   0.0      0.005   16.7   0.0    1.3  1  UPF0146          Uncharacterised protein family (UPF0146)
     0.0035   17.2   0.0      0.015   15.1   0.0    1.8  2  N6-adenineMlase  Probable N6-adenine methyltransferase
     0.0094   15.3   0.0      0.011   15.1   0.0    1.2  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
  ------ inclusion threshold ------
      0.013   15.0   0.1      0.022   14.2   0.0    1.4  2  Methyltransf_5   MraW methylase family
      0.026   14.1   0.0      0.034   13.7   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
      0.051   13.2   0.0      0.086   12.4   0.0    1.3  1  NodS             Nodulation protein S (NodS)
      0.061   13.3   0.1       0.46   10.4   0.0    1.9  2  Methyltransf_18  Methyltransferase domain
      0.097   12.4   0.2       0.34   10.6   0.0    1.9  2  N6_N4_Mtase      DNA methylase
       0.13   11.9   0.0       0.21   11.1   0.0    1.3  1  Carbam_trans_C   Carbamoyltransferase C-terminus
       0.13   11.5   0.0       0.54    9.5   0.0    1.8  1  N6_Mtase         N-6 DNA Methylase


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 !   44.9   0.0   1.5e-14   1.4e-11       1      71 [.      27      93 ..      27     102 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 1.5e-14
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvss 71
                                      v ++GcGtG++++ala++    +++g+Di++e+l++a+e++++ +   +++  +a+ lp+  +s D+vv++
  gi|557694988|ref|YP_008798042.1| 27 VAEVGCGTGEVLKALAEKS--DDIIGIDIDPEALRIAAEKLKDLK--PRLHLLNASLLPLRPRSLDMVVAN 93
                                      789**************95..********************7655..5555566667888899*****994 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0     3e-14   2.7e-11       7     127 ..      27     154 ..      21     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 3e-14
                   Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsn.. 81 
                                       v ++GCGtGe +++lae+     +++GiDi++ea++ A e++++l+     ++  ++  l+  l +++ D++++n  
  gi|557694988|ref|YP_008798042.1|  27 VAEVGCGTGEVLKALAEK---SDDIIGIDIDPEALRIAAEKLKDLKPR---LHLLNASLLP--LRPRSLDMVVANpp 95 
                                       679*************65...456*******************99995...9999999999..889*********66 PP

                   Methyltransf_31  82 ..........evl.....naladpdkileeiervlkpggilliedprllaelpakveeesk 127
                                                           +   ++i+e  +r+l+++ il+++  + l+++++ +++ s+
  gi|557694988|ref|YP_008798042.1|  96 ylpdepgfhdP-TihggpRGVELAEQIMEHSSRALRNQAILVLTASS-LSDVDDLLSKASR 154
                                       66666655542.1678889999999***********99999999888.8888877776666 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   1.5e-12   1.3e-09      27     151 ..      18     151 ..      10     158 .. 0.82

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.5e-12
                                       CHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEE CS
                               MTS  27 lpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdliv 102
                                       + k+ + + v+ +GcG+G +  ala++s++  +  +d+d +Al++a e l++ k ++++++ ++l   + +++d++v
  gi|557694988|ref|YP_008798042.1|  18 VAKTsHVQMVAEVGCGTGEVLKALAEKSDD--IIGIDIDPEALRIAAEKLKDLKPRLHLLNASLLPLRP-RSLDMVV 91 
                                       5555466789****************9999..99*****************************998887.******* PP

                                       E---.......STT....TCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHH CS
                               MTS 103 sNPP.......fha....gkatelavaeeliaeAkeaLkegGeLliVanrklgyesllee 151
                                        NPP       fh+    g     ++ae++++++ +aL+++  L++ a++  ++++ll++
  gi|557694988|ref|YP_008798042.1|  92 ANPPylpdepgFHDptihGGPRGVELAEQIMEHSSRALRNQAILVLTASSLSDVDDLLSK 151
                                       ****66666665652211334567899999999999999999999888888888877776 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   1.6e-12   1.5e-09       2      68 ..      29      93 ..      28     102 .. 0.95
   2 ?   -1.6   0.0         5   4.5e+03      77      95 ..     118     136 ..     107     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.6e-12
                                      EET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEE CS
                   Methyltransf_11  2 dvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvss 68
                                      +vGcGtG +++ala++  +++g+D+++e+l++a ek ++ +   +++  +a+ lp++  s D+vv++
  gi|557694988|ref|YP_008798042.1| 29 EVGCGTGEVLKALAEKSDDIIGIDIDPEALRIAAEKLKDLK--PRLHLLNASLLPLRPRSLDMVVAN 93
                                      79*************************************99..67899999999**********986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5
                                       HHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  77 pekalkeiaRvLkpgGllv 95 
                                        e++++   R L++  +lv
  gi|557694988|ref|YP_008798042.1| 118 AEQIMEHSSRALRNQAILV 136
                                       4667777777777777665 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0     2e-11   1.8e-08       2      72 ..      29      92 ..      28      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 2e-11
                   Methyltransf_12  2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvva 72
                                      e+GcGtG++l+al+ek    +++g+Di+p+a+  a+ekl++ ++    +++l + +ll l ++ s D+vva
  gi|557694988|ref|YP_008798042.1| 29 EVGCGTGEVLKALAEK--SDDIIGIDIDPEALRIAAEKLKDLKP----RLHLLNASLLPLRPR-SLDMVVA 92
                                      9***************..************************98....667776666655555.8888887 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   3.5e-08   3.1e-05      68     180 ..      37     153 ..      13     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 3.5e-08
                                       HHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE------........--- CS
                           UPF0020  68 eaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGe........rlg 136
                                        +++ a++   ++g+D+d+++++ a e+++  +     ++ +a    Lr ++ + d++v+npPY           ++
  gi|557694988|ref|YP_008798042.1|  37 VLKALAEKSDDIIGIDIDPEALRIAAEKLKDLKPR--LHLLNASLLPLR-PR-SLDMVVANPPYLPdepgfhdpTIH 109
                                       45566667777******************987765..556666677777.66.9**********8422222333688 PP

                                       -HHHHHHHHHHHHHHHHHH-TT..-EEEEEESSHHHHHCC---E CS
                           UPF0020 137 skkalekLYseflrelkrvlrgggrlvlltsenkalekaleera 180
                                         ++  +L +++++  +r lr+++ lvl +s+ +++ ++l++++
  gi|557694988|ref|YP_008798042.1| 110 GGPRGVELAEQIMEHSSRALRNQAILVLTASSLSDVDDLLSKAS 153
                                       88889999999999999999998888888888888888888764 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   5.1e-08   4.5e-05      27      62 ..      28      66 ..      17     132 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.1e-08
                   Methyltransf_23 27 LdiGcGtGillevlrengfsvtgvDlspeaveiae...k 62
                                       ++GcGtG++l+ l+e+  +++g+D++pea  ia+   k
  gi|557694988|ref|YP_008798042.1| 28 AEVGCGTGEVLKALAEKSDDIIGIDIDPEALRIAAeklK 66
                                      59****************************999975441 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   7.9e-07    0.0007     163     233 ..      25      93 ..      11      94 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.9e-07
                              PrmA 163 eevlDvGtGSG.iLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseell..keekadvivaN 233
                                       + v  vG+G+G +L   a     ++++++DiD+ A+++a+e +   +++ +l++ + ++ll  + ++ d++vaN
  gi|557694988|ref|YP_008798042.1|  25 QMVAEVGCGTGeVLKALA--EKSDDIIGIDIDPEALRIAAEKL--KDLKPRLHLLN-ASLLplRPRSLDMVVAN 93 
                                       4799*******6665444..45799***************965..57777777643.34332446889*****9 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.5e-06    0.0014       4      50 ..      26      70 ..      23      93 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.5e-06
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTT CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealel 50
                                      +v+e+GcG Ge+l alA+k    +++Gi+i  + ++ + +k ++l+ 
  gi|557694988|ref|YP_008798042.1| 26 MVAEVGCGTGEVLKALAEKS--DDIIGIDIDPEALRIAAEKLKDLKP 70
                                      789**************996..678*********9999999998843 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.4e-06    0.0012      45      86 ..      31      73 ..      16      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.4e-06
                                      T-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTT.SGGGG CS
                              TPMT 45 lCGkaldlvwlAeqgrevvGvelselAvekffeeanl.epkvk 86
                                      +CG ++ l++lAe+ ++++G+++ + A++ ++e+ +  +p+++
  gi|557694988|ref|YP_008798042.1| 31 GCGTGEVLKALAEKSDDIIGIDIDPEALRIAAEKLKDlKPRLH 73
                                      8***************************997665332366665 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   5.6e-06     0.005       5      66 ..      15      73 ..      12      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.6e-06
                                      HHHHHHHS-SSEEEEET-TT--HHHHHHHHHS-EEEEE-SS-S....STTEE---SSS--HH CS
                           UPF0146  5 akkiaeenargkvvEvGiGrkldvaealakrgvdlvatDikekkakegvrivrDDvtdPnle 66
                                      ++ +a++++ + v+EvG G+  +v +ala+++ d++ +Di+++  +   +  +D   +P+l+
  gi|557694988|ref|YP_008798042.1| 15 IDCVAKTSHVQMVAEVGCGT-GEVLKALAEKSDDIIGIDIDPEALRIAAEKLKD--LKPRLH 73
                                      56789999999********7.5899****************9966666666665..456655 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.87   7.8e+02      98     133 ..      12      45 ..      10      76 .. 0.70
   2 !   15.1   0.0   1.7e-05     0.015      87     152 ..      85     169 ..      67     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.87
                   N6-adenineMlase  98 Flseeclkklaktaklllkklilctgevmeelekll 133
                                       Fl+ +c+ k++++     +++ + tgev + l+++ 
  gi|557694988|ref|YP_008798042.1|  12 FLTIDCVAKTSHVQMV--AEVGCGTGEVLKALAEKS 45 
                                       8889999997764443..366677888888855554 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.7e-05
                   N6-adenineMlase  87 gkfdviviDPPF....................lseeclkklaktaklllkklilctgevmeelekll.gvkktkfep 142
                                        + d++v+ PP+                    l e+++++ +++++     ++++t +  +++++ll ++++  f+p
  gi|557694988|ref|YP_008798042.1|  85 RSLDMVVANPPYlpdepgfhdptihggprgveLAEQIMEHSSRALRNQ--AILVLTASSLSDVDDLLsKASRKGFRP 159
                                       678***************999999999999999999999988877765..89****999999**999788899**** PP

                   N6-adenineMlase 143 ehenklsnef 152
                                        h+  l+  f
  gi|557694988|ref|YP_008798042.1| 160 LHKLVLKSFF 169
                                       **98666555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.2e-05     0.011      39     103 ..      14      75 ..       9     149 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                       HHHH--S--T.TEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEE CS
                   Ubie_methyltran  39 veklvavkrg.akvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkiniefl 103
                                       ++++va+ +  + v +v +Gtg++  +    ++++ +++++Di+++ L+++ +klk+    ++++l
  gi|557694988|ref|YP_008798042.1|  14 TIDCVAKTSHvQMVAEVGCGTGEVLKA---LAEKSDDIIGIDIDPEALRIAAEKLKDLK-PRLHLL 75 
                                       4566665544146779******98655...5678899******************9853.344443 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.5e-05     0.022      36      77 ..      35      78 ..      15      91 .. 0.85
   2 ?   -3.3   0.0       5.3   4.8e+03     220     246 ..     119     144 ..     115     155 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                                      HHHHTT--TT..EEEEEES-HHHHHHHTT.....---EEEEES- CS
                    Methyltransf_5 36 ealLeqlsel..rligidrDksalarakerLkefekrltlvkgn 77
                                       ++L++l e+   +igid+D++al +a e+Lk+ + rl+l++++
  gi|557694988|ref|YP_008798042.1| 35 GEVLKALAEKsdDIIGIDIDPEALRIAAEKLKDLKPRLHLLNAS 78
                                      56777777665689***********************9998875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.3
                                       HHHHHHHHHHEEEEEEEEEEESSHHHH CS
                    Methyltransf_5 220 eelleaalellakggrlavisFhSled 246
                                       e+++e++ ++l+++++l v++  Sl d
  gi|557694988|ref|YP_008798042.1| 119 EQIMEHSSRALRNQAIL-VLTASSLSD 144
                                       55666666666666544.455555544 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   3.8e-05     0.034       8      53 ..      15      62 ..       8      94 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.8e-05
                              MetW  8 aelikpgsr...vldlGcGdGellellkeekqvdgrGleldeegvaecv 53
                                       + + + s+   v ++GcG Ge+l+ l+e k  d  G+++d e++  + 
  gi|557694988|ref|YP_008798042.1| 15 IDCVAKTSHvqmVAEVGCGTGEVLKALAE-KSDDIIGIDIDPEALRIAA 62
                                      555555554111679************87.5556677777766554333 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   9.6e-05     0.086      41      87 ..      21      67 ..       6      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.6e-05
                              NodS 41 qgsiadalevGcaaGalterlapyckrltvvdvveeaiararervke 87
                                        ++  + evGc +G + + la  ++ +  +d+ +ea+  a e++k+
  gi|557694988|ref|YP_008798042.1| 21 TSHVQMVAEVGCGTGEVLKALAEKSDDIIGIDIDPEALRIAAEKLKD 67
                                      56788899******************************999998876 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00051      0.46      13      62 ..      22      69 ..      14      92 .. 0.77
   2 ?    0.7   0.0      0.51   4.6e+02      92     119 ..     114     141 ..     111     165 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00051
                   Methyltransf_18 13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekag 62
                                      ++ + va +G+  g +  +l++  k + +i +Di +++l+ a e++++ +
  gi|557694988|ref|YP_008798042.1| 22 SHVQMVAEVGCGTGEVLKALAE--KSDDIIGIDIDPEALRIAAEKLKDLK 69
                                      446789************9995..7789*****************99754 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.51
                   Methyltransf_18  92 GgelileILeeakeklkkikklilqpns 119
                                       G el  +I+e++++ l++   l+l + s
  gi|557694988|ref|YP_008798042.1| 114 GVELAEQIMEHSSRALRNQAILVLTASS 141
                                       7788999***999999998889987654 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00038      0.34     200     230 ..      32      62 ..      18      63 .. 0.94
   2 ?   -1.3   0.1       1.7   1.5e+03       2      10 ..      88      96 ..      87     126 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00038
                                       -TTTHHHHHHHHTT-EEEEEESSHHHHHHHH CS
                       N6_N4_Mtase 200 aGSGtTavaakelgrkfiGieieeeyvelae 230
                                       +G+G  ++a +e + + iGi+i++e++++a 
  gi|557694988|ref|YP_008798042.1|  32 CGTGEVLKALAEKSDDIIGIDIDPEALRIAA 62 
                                       8**************************9986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.7
                                      EEEEE--SS CS
                       N6_N4_Mtase  2 dlivtdpPY 10
                                      d++v+ pPY
  gi|557694988|ref|YP_008798042.1| 88 DMVVANPPY 96
                                      788888888 PP

>> Carbam_trans_C  Carbamoyltransferase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00024      0.21      12      68 ..     117     173 ..     113     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00024
                    Carbam_trans_C  12 wfqgrmEfGpRALGnRSiladprk..eemkeklnekikkResfrPfApsvleeeaeeyf 68 
                                       ++++ mE  +RAL n +il    +  +++ + l+ k  +R+ frP+   vl++ +e++f
  gi|557694988|ref|YP_008798042.1| 117 LAEQIMEHSSRALRNQAILVLTASslSDVDDLLS-K-ASRKGFRPLHKLVLKSFFETVF 173
                                       56788*************9866551145556666.4.46************99998887 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0    0.0006      0.54      29     137 ..       5      98 ..       1     129 [. 0.72

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0006
                          N6_Mtase  29 fTPrevsklivell.epksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgiey 104
                                       +TPre + l ++ + ++++ + v    cG+g +l   ++         k+  i G ++++++ r+a     l++ + 
  gi|557694988|ref|YP_008798042.1|   5 YTPREDTFLTIDCVaKTSHVQMVAEVGCGTGEVLKALAE---------KSDDIIGIDIDPEALRIAAEK--LKDLKP 70 
                                       888888888888776677777888888998877644333.........445678888888888888764..677777 PP

                          N6_Mtase 105 kkvkirlgdtlekpkfekdkkfdvvvaNppfnq 137
                                            +l ++   p     +++d+vvaNpp+  
  gi|557694988|ref|YP_008798042.1|  71 R---LHLLNASLLPLRP--RSLDMVVANPPYLP 98 
                                       6...3344444445555..789********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1358.72
//
Query:       gi|557694989|ref|YP_008798043.1|  [L=624]
Description: basic amino acid/polyamine antiporter, APA family [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-33  116.2  43.0    2.8e-33  115.4  42.7    1.4  1  AA_permease_2  Amino acid permease
    2.4e-22   79.2  37.9    2.4e-22   79.2  37.9    1.6  2  AA_permease    Amino acid permease
  ------ inclusion threshold ------
       0.08   13.4   0.9        1.1    9.7   0.8    3.2  2  COX7a          Cytochrome c oxidase subunit VII


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 !  115.4  42.7   4.6e-37   2.8e-33       1     387 [.      13     414 ..      13     461 .. 0.78

  Alignments for each domain:
  == domain 1  score: 115.4 bits;  conditional E-value: 4.6e-37
                     AA_permease_2   1 lsllsafalvigsv.....igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf 72 
                                       +++++ fal +g+v     i +g++    ++++g a+ + + ia+l++  +v+l yaEl+ + p sgG+ vy+ +af
  gi|557694989|ref|YP_008798043.1|  13 IGWFGSFALGYGDVgpnifIALGVI----TLYAGGAAPIAFAIAALLY-ATVGLMYAELGPTYPYSGGVHVYGLKAF 84 
                                       89************76653333334....67899999999********.69********988*************** PP

                     AA_permease_2  73 gkkvaflsawfnwfayvpvlasilsvaasyllnalgp.......dlqgntwltyliaiail.ilvalinirgikesa 141
                                       + +v f+++w+ ++ay++ +++ +++aa+yl +++ p       ++ g t++++++ +++l  l++l+ni+gik sa
  gi|557694989|ref|YP_008798043.1|  85 NSVVSFVAGWAMLLAYIVCISLFAVAAAGYLRQLF-PvlmfpdiTVMGVTIPSIGVLAGLLaSLLILLNIVGIKYSA 160
                                       ******************99888888888887755.4454445533344777766666665167899********** PP

                     AA_permease_2 142 kiqnilgilkillpliiliilglitv.dgggfssl....stetdt...........ffpngwpgvllgllivlwsfd 202
                                        + + l+ + ++ + ++++ +g+++  d++ f  +         +           f+p   + +l +++ ++ sf+
  gi|557694989|ref|YP_008798043.1| 161 FMVSALVFVGLF-IEALILSTGFLLKfDPQLFLRQltefG----SsqlqrdvaylpFLPVETNNFLYAITLAMASFV 232
                                       ***********6.778888899888624455554454331....23455566766677777777899********** PP

                     AA_permease_2 203 Gfesaanvseevkk..kdvpkaifigllivlvlyllvniaflgvvpddeian.lsnlgsvaalffeavg.gkvvaii 275
                                       G+es+++ +ee ++    +pka+ +++++v+ + + ++++++g   +  ia   +n   +++l+      g  +  +
  gi|557694989|ref|YP_008798043.1| 233 GIESISQAAEETRRphISLPKAAKMVVVVVAASAIAFPVLAIGSTDWRVIAAaYEN--PIYTLVSTYPYvGELLMPL 307
                                       ***********7775469********************************651344..2344444443312566666 PP

                     AA_permease_2 276 vvilialsllgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfll 351
                                       v++++++ +  + nt v+g+sr+  +++r + lP +++ ++ +f +p+r+i ++  +   ++l+fl+    +++fl+
  gi|557694989|ref|YP_008798043.1| 308 VALAAFILCYSSSNTGVVGVSRLTASMGRFRLLPAWLQAIHpRFRTPVRTITVFGGIG--VGLAFLG----DVTFLA 378
                                       666666666669*********************************************9..4566755....7***** PP

                     AA_permease_2 352 svsslgliisyllliigalilrkkrphlkrpgkilv 387
                                       sv++++++isyl+l ++++ lr+ +    rp+ +++
  gi|557694989|ref|YP_008798043.1| 379 SVYAFSAVISYLILGFSYFRLRRLETTVYRPWCMPL 414
                                       ***********************9999999887543 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2  37.9     4e-26   2.4e-22      11     392 ..      26     401 ..      19     416 .. 0.81
   2 ?   -1.4   0.4      0.11   6.5e+02     335     370 ..     422     456 ..     409     466 .. 0.58

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 4e-26
                       AA_permease  11 iGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfswi 87 
                                       +G  +f++lgv++  aG+ +a +a+++a + ++ v+l+ +e+   +p sgg ++y  +   + ++fv G+  l+ +i
  gi|557694989|ref|YP_008798043.1|  26 VGPNIFIALGVITLYAGG-AAPIAFAIAALLYATVGLMYAELGPTYPYSGGVHVYGLKAFNSVVSFVAGWAMLLAYI 101
                                       68889*************.999*************************************************999999 PP

                       AA_permease  88 tvlaleltaasiliqfwelvtdlpkawvt............gavflvvlliinlvgvkvygeaefilalikiiaiia 152
                                       + + l  +aa+ ++  +  ++ l+  ++t            + ++  +l+++n+vg+k++++  ++ al+ +  +i 
  gi|557694989|ref|YP_008798043.1| 102 VCISLFAVAAAGYLRQL--FPVLMFPDITvmgvtipsigvlAGLLASLLILLNIVGIKYSAF--MVSALVFVGLFIE 174
                                       99988777777777666..333333333344556****9985577778999***********..7888888888898 PP

                       AA_permease 153 fiivgiillaggkpnkga......gfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiag 223
                                        +i++  +l + +p+ +       g + l+ +++  +  + p         + nf++++  ++ +f Gie++  +a+
  gi|557694989|ref|YP_008798043.1| 175 ALILSTGFLLKFDPQLFLrqltefGSSQLQRDVA--YLPFLPV-------ETNNFLYAITLAMASFVGIESISQAAE 242
                                       8888855666666555545477666666666666..3333333.......589************************ PP

                       AA_permease 224 EvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgv.svlaplinavilta 299
                                       E++ P  s+Pka ++vv+ ++ + + + +l++   ++    +++++ +  +++ ++ ++  v  +l pl++++ ++ 
  gi|557694989|ref|YP_008798043.1| 243 ETRRPHISLPKAAKMVVVVVAASAIAFPVLAIGSTDWR---VIAAAYEN-PIYTLVSTYPYVgELLMPLVALAAFIL 315
                                       ******************99998665555544444444...45544444.57777777655437899********** PP

                       AA_permease 300 alssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisali 375
                                       ++ss+n +++  sR+  s+ + +l+P +  + + + + P+r i+++  i++ + +l  +++          +++a++
  gi|557694989|ref|YP_008798043.1| 316 CYSSSNTGVVGVSRLTASMGRFRLLPaWLQAIHPRFRTPVRTITVFGGIGVGLAFLGDVTFL--------ASVYAFS 384
                                       **************************555677899******************988888777........7777777 PP

                       AA_permease 376 glivwlliilsylrfRk 392
                                       ++i +l+  +sy r+R+
  gi|557694989|ref|YP_008798043.1| 385 AVISYLILGFSYFRLRR 401
                                       77777777777777775 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.11
                       AA_permease 335 gvPlraillsmiisllalllaslnlaapivfnflla 370
                                        vP+ a++ ++ +++++ l+a + +    v++ l  
  gi|557694989|ref|YP_008798043.1| 422 EVPVLALMEVSGMAVILGLMAVFHAV-GRVMALLWV 456
                                       56666666666666666666655433.344443333 PP

>> COX7a  Cytochrome c oxidase subunit VII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         3   1.8e+04      17      37 ..     246     266 ..     241     273 .. 0.69
   2 ?    9.7   0.8   0.00019       1.1      32      50 ..     450     468 ..     446     471 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3
                             COX7a  17 plwlrgprsklylypyyalfa 37 
                                       + +   p+++ +++   a+ a
  gi|557694989|ref|YP_008798043.1| 246 RPHISLPKAAKMVVVVVAASA 266
                                       667777787777777766555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00019
                             COX7a  32 yyalfavgllgslygmyrm 50 
                                        +al++vg ++++y++yr+
  gi|557694989|ref|YP_008798043.1| 450 VMALLWVGAGLTFYALYRK 468
                                       69***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (624 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); 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):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4264.48
//
Query:       gi|557694990|ref|YP_008798044.1|  [L=91]
Description: transcriptional regulator, AsnC family [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   67.8   0.5      7e-19   67.6   0.5    1.1  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.12   12.4   0.0    1.1  1  CNOT1_HEAT       CCR4-NOT transcription complex subunit 1 HEA
       0.12   12.4   0.1       0.14   12.2   0.1    1.1  1  Spore_YhcN_YlaJ  Sporulation lipoprotein YhcN/YlaJ (Spore_Yhc


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 !   67.6   0.5   1.2e-22     7e-19       1      73 [.      10      79 ..      10      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 1.2e-22
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73
                                      v++ +e+++   +e++++++ +l+eV+ +y vtG++d++l v + d++ +++fl++k+ s+ gv++  tsivl
  gi|557694990|ref|YP_008798044.1| 10 VHIFVESNS---IEKVAKQVSKLDEVLDVYEVTGEFDLILLVQTSDIRGFREFLKNKILSVQGVKSAVTSIVL 79
                                      789999888...************************************************************9 PP

>> CNOT1_HEAT  CCR4-NOT transcription complex subunit 1 HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.1e-05      0.12      49     101 ..      17      69 ..       8      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
                                       SHHHHHHHHTT-HHHHHHHS-TTCHHHCHHHHHHHT---HHHHHHHH--TT.. CS
                        CNOT1_HEAT  49 srIldvaqelkilsellnklpfnfaldLaalasrreyldlekwledklkehge 101
                                       + I +va++  +l+e+l++  ++  +dL  l+   +  ++ ++l++k+ + + 
  gi|557694990|ref|YP_008798044.1|  17 NSIEKVAKQVSKLDEVLDVYEVTGEFDLILLVQTSDIRGFREFLKNKILSVQG 69 
                                       56889******************************************987654 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 ?   12.2   0.1   2.4e-05      0.14      62     106 ..      19      65 ..      10      81 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                   Spore_YhcN_YlaJ  62 aqniaqrverlegVedarvlvtgndvlVavqtde..sdnekvkkkVk 106
                                        +++a++v++l++V d++ ++ + d++  vqt +  + +e +k+k+ 
  gi|557694990|ref|YP_008798044.1|  19 IEKVAKQVSKLDEVLDVYEVTGEFDLILLVQTSDirGFREFLKNKIL 65 
                                       689******************************99988888888874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); 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: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 695.18
//
Query:       gi|557694991|ref|YP_008798045.1|  [L=412]
Description: molybdopterin biosynthesis protein MoeA [Candidatus Caldiarchaeum subterraneum]
Scores for 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  127.2   0.0    6.8e-37  126.7   0.0    1.3  1  MoeA_N         MoeA N-terminal region (domain I and II)
    4.8e-13   49.0   0.0    8.7e-13   48.2   0.0    1.4  1  MoCF_biosynth  Probable molybdopterin binding domain
    0.00013   22.0   0.0    0.00063   19.9   0.0    2.2  2  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 !  126.7   0.0   1.1e-40   6.8e-37       3     157 .]      11     174 ..       9     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 126.7 bits;  conditional E-value: 1.1e-40
                                       HHHHHHHHHHH-.HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--.............. CS
                            MoeA_N   3 veealaiilaal.eleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........s 69 
                                       v +a++++l++l ++ + e vp+  +a grv+ e+vv+p d+Pp+++S mDGYAv+++  ++as+++p         
  gi|557694991|ref|YP_008798045.1|  11 VWDAQRLLLEHLsPIGDYEvVPV-FQAFGRVVYEPVVSPADLPPHNASHMDGYAVNSSLLQNASPSNPvklktvgvC 86 
                                       6689999999*978866666***.99**************************************************6 PP

                                       .....-S---TT-.EEEE-TTSB--TT--EEEEGGGE..E....EETTE..S--STTTTEE-TTSSB-TTSEEE-TT CS
                            MoeA_N  70 aageeperllpgg.avrimTGaplPegadaVvpvEdte.eeeaketvev..kavkpgenvrraGedikaGevllrag 142
                                        ag++pe ++  g ++ri TGa lP+g+daVvp+E+++ e   +    v  ++++p + v  +G d++aG++l+++g
  gi|557694991|ref|YP_008798045.1|  87 YAGKKPEFKVGAGeTARILTGAYLPDGCDAVVPQENVTvEG--DYV--VftSPATPYQYVDMKGFDVAAGQTLFERG 159
                                       66666666666666***********************6432..222..1348999********************** PP

                                       BB--CCCHHHHHHCT CS
                            MoeA_N 143 trltpaeigllasvG 157
                                       ++l+ a+++l+a++G
  gi|557694991|ref|YP_008798045.1| 160 RVLKMADVALAAALG 174
                                       *************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 !   48.2   0.0   1.5e-16   8.7e-13       1     143 [.     187     322 ..     187     323 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.5e-16
                                       EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSST CS
                     MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptp 70 
                                       ++++vGdel+       +gk+ +t+++++a+l++++g e   +++vpD+ +++ + l++++++ d+++++ G ++++
  gi|557694991|ref|YP_008798045.1| 187 GIVAVGDELTddfseakRGKVLNTHSHVVARLVEAAGGEPLFLGIVPDNRTAFLQLLENQIRRLDLLLSIAGSSVSE 263
                                       699*********************************************************9**************** PP

                                       T--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  71 dDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpale 143
                                       +Dv   +la          e  +++++l+pg+   v+ ++ l+++   ++i+LPG   +   ++ ++ +pal+
  gi|557694991|ref|YP_008798045.1| 264 KDVSS-ILASEN-------ELFVHGLTLQPGR---VGGFTFLGDR---PFIFLPGLIMSTLNVFMFLAYPALR 322
                                       **864.344333.......4899*******99...7777778876...8********************9998 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 ?   -2.3   0.0      0.86   5.1e+03      36      48 ..     209     221 ..     206     223 .. 0.84
   2 !   19.9   0.0   1.1e-07   0.00063       2      65 ..     338     402 ..     337     407 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.86
                                       ---TT-GGGCTT- CS
                            MoeA_C  36 kqgSglLsslaeA 48 
                                       ++ S++++ l+eA
  gi|557694991|ref|YP_008798045.1| 209 NTHSHVVARLVEA 221
                                       678********99 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.1e-07
                                       EEESS-EE--S..SS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT- CS
                            MoeA_C   2 arlaedlksdp..grreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGe 65 
                                       a laed++  +  +    ++v+++e++ ++ ++p+  ++S+  s  ++++g+i  p+gt  l+aGe
  gi|557694991|ref|YP_008798045.1| 338 AALAEDITFRKyhDFVKVVWVRVEEDGEGLRCYPV-LGESSGMSIPSRSDGFITGPPGTSVLKAGE 402
                                       55666666555004455566666699999******.7777777888*******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2961.31
//
Query:       gi|557694992|ref|YP_008798046.1|  [L=283]
Description: carbon monoxide dehydrogenase F protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-30  105.7   0.0    3.3e-30  105.2   0.0    1.2  1  XdhC_C        XdhC Rossmann domain
    3.5e-16   59.1   0.0    6.5e-16   58.3   0.0    1.4  1  XdhC_CoxI     XdhC and CoxI family
  ------ inclusion threshold ------
      0.032   14.3   0.0      0.063   13.3   0.0    1.4  1  OTCace        Aspartate/ornithine carbamoyltransferase, Asp/O
      0.066   12.6   0.0       0.12   11.8   0.0    1.4  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 !  105.2   0.0   7.3e-34   3.3e-30       1     125 []     110     245 ..     110     245 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 7.3e-34
                                       EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE...........-EEEE--S-HHHHHHHHHHHSS CS
                            XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade...........tavvvlthdhklDaealeaalr 66 
                                       l+++G+g ++++la+++++l+++v+v+dp+  f++++ + +              + +vv++  hklD+++l+ al+
  gi|557694992|ref|YP_008798046.1| 110 LLLVGHGGIVESLAKIGKMLDYKVVVADPEGMFKDPSMVDQYVVdpdlkgvtidgNTAVVVSTMHKLDHKYLKIALD 186
                                       789******************************988888854448999*******899999999************9 PP

                                       S--SEEEESS-HHHHHHHCTTS.--.......TTEESS-S--S---SHHHHHHHHHHHH CS
                            XdhC_C  67 kkaayigllGSrkkaarrlerlraaglseeelarlhaPiGldigaktpeeIAvsilAei 125
                                       + a+yigl++S+k+a  ++e l + g++ee+++r+++P+G+diga++peeIA+si Aei
  gi|557694992|ref|YP_008798046.1| 187 GGARYIGLVASKKRAGIVFETLLRLGVPEESIRRISSPAGIDIGAEKPEEIALSIFAEI 245
                                       99********************999*********************************8 PP

>> XdhC_CoxI  XdhC and CoxI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   0.0   1.5e-19   6.5e-16       2      64 ..      14      77 ..      13      81 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 1.5e-19
                                      HHCT..EEEEEEEEEECSSSSGTT-EEEEETTS-E.EE-SSSSCHHHHHHHHHHHHHHCT--EE CS
                         XdhC_CoxI  2 laagrpvalaTVvdteGsaprplGakmlvrpdgrv.iGsvgggclEaavideArallaagrtal 64
                                      +a+++++ +aTVv+t G++  ++G+k ++ +dg+  +G+vgggc+E +v+ eA++ +++gr+++
  gi|557694992|ref|YP_008798046.1| 14 IAENKKFCIATVVKTIGHTSGKVGSKAIILEDGKGlFGWVGGGCVETTVLHEALKTIKEGRSRT 77
                                      7999****************************9956*************************996 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 ?   13.3   0.0   1.4e-05     0.063       4      49 ..     109     152 ..     107     176 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                                       EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHH CS
                            OTCace   4 kiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeak 49 
                                       ++ +vG  ++ +++sl+k+  +l+ +vv++ P+g+ +d+ ++++  
  gi|557694992|ref|YP_008798046.1| 109 QLLLVG--HGGIVESLAKIGKMLDYKVVVADPEGMFKDPSMVDQYV 152
                                       677888..568******************************99865 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 ?   11.8   0.0   2.6e-05      0.12      31      70 ..     102     141 ..      79     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.6e-05
                                       BS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C  31 gkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                          l +k++ ++G G I +++ak+ k ++ kv++ d+   
  gi|557694992|ref|YP_008798046.1| 102 EPVLPKKQLLLVGHGGIVESLAKIGKMLDYKVVVADPEGM 141
                                       5567899*****************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1900.95
//
Query:       gi|557694993|ref|YP_008798047.1|  [L=382]
Description: VWA containing CoxE family protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  165.2   0.1      2e-48  164.7   0.1    1.2  1  VWA_CoxE       VWA domain containing CoxE-like protein
  ------ inclusion threshold ------
      0.022   15.0   0.0       0.04   14.2   0.0    1.4  1  VWA            von Willebrand factor type A domain
      0.035   14.1   0.1      0.073   13.1   0.1    1.6  1  TetR_C_32      Tetracyclin repressor-like, C-terminal domain
      0.062   13.4   0.0        4.3    7.4   0.0    2.2  2  NAD_binding_6  Ferric reductase NAD binding domain


Domain annotation for each model (and alignments):
>> 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 !  164.7   0.1   4.4e-52     2e-48       3     222 ..     141     353 ..     136     354 .. 0.94

  Alignments for each domain:
  == domain 1  score: 164.7 bits;  conditional E-value: 4.4e-52
                          VWA_CoxE   3 kklaalllglarrrrrrkrrrrgrriDlrrtlranlrhggelvelvrrkprerkprelvllvDvSgSmaaysaifla 79 
                                       k+l+++l+ l+ rr    +++ ++ +D+r t+r +lr+ ge+++l   k r+++  +lv + DvSgSm++y+++ ++
  gi|557694993|ref|YP_008798047.1| 141 KRLRRRLALLPGRR---YTKSAKGYVDFRETIRTSLRTHGEILRLLHMK-RKVTRCKLVAIFDVSGSMDTYTEFLMQ 213
                                       45666666666666...899999**************************.999999********************* PP

                          VWA_CoxE  80 llhAllqqlprtevfaFdtrlvdlTralrerDpaeaLarvsaavedlgGgTrigaalaeflelvtrpaLsrravvvl 156
                                        ++Al +q   +evf+F+trl ++++ l+   p++a + +s++v+ +g+gTrig+ la+f++  +  + s+++vv++
  gi|557694993|ref|YP_008798047.1| 214 SMYALARQSVAVEVFVFSTRLLKVSSLLKYFGPKKAAELISREVNIWGSGTRIGNCLATFIDKYRGIV-SKGTVVMI 289
                                       *****************************************************************777.******** PP

                          VWA_CoxE 157 vsDglergdreellaelarlvrrarrlvwlnplsdagtpgydpearalrailphvdelrpleqlas 222
                                       vsDg+++gd e l++++++l++   r++w+np   a +pg++p++ +++ + p++d l+ ++ l+s
  gi|557694993|ref|YP_008798047.1| 290 VSDGWDTGDPEVLDRAMRSLKELVGRVIWINPH--ADKPGFKPRTIGMETAMPYIDVLAGMNALKS 353
                                       *********************************..99*******************9988777766 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 ?   14.2   0.0     9e-06      0.04       2     123 ..     194     302 ..     194     340 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 9e-06
                                       EEEEEE-STTSCHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSSEEEEEETTSHCHHHHHHHHHHTG.SGGGGS CS
                               VWA   2 ivfvlDgSgsmgeenfekvkefikklveklevgpegtrvglvqfssevktefslndysskeellsalnnl.kysggg 77 
                                       +v + D+Sgsm     ++  ef+ + +  l   ++++ v++  fs+    + sl +y   +++++ +++  ++ g+g
  gi|557694993|ref|YP_008798047.1| 194 LVAIFDVSGSM-----DTYTEFLMQSMYALA--RQSVAVEVFVFSTRLLKVSSLLKYFGPKKAAELISREvNIWGSG 263
                                       57889999999.....777777777777777..**************999999999998899999998855999999 PP

                                       SC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CSSHTHHH CS
                               VWA  78 ttntgkalkyaleklfkssagaRenakkviilltdGksndgdpkea 123
                                       t+ +g  l+  ++k+    ++       v+++++dG +++ dp+  
  gi|557694993|ref|YP_008798047.1| 264 TR-IGNCLATFIDKYRGIVSK-----GTVVMIVSDGWDTG-DPEVL 302
                                       99.**9999999999999999.....89**********98.44432 PP

>> TetR_C_32  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   0.1   1.6e-05     0.073      27      95 ..     119     191 ..     115     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                         TetR_C_32  27 kfmaREqlePtealeriyqeeirPlhealerivaellged....aedeevrlrtlsivGqclafriareavlr 95 
                                        fm RE+  Pt a+ r  ++++++l+++l+ + ++   ++     + +e+ +  l   G++l ++++++ v r
  gi|557694993|ref|YP_008798047.1| 119 VFMKRELPTPTLAFMRESKRVMKRLRRRLALLPGRRYTKSakgyVDFRETIRTSLRTHGEILRLLHMKRKVTR 191
                                       69***************************99988776666567667777777777777777777777776665 PP

>> NAD_binding_6  Ferric reductase NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0      0.01        47      40      64 ..      53      77 ..      40     119 .. 0.88
   2 ?    7.4   0.0   0.00096       4.3      29      82 ..     184     239 ..     127     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.01
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                     NAD_binding_6 40 iwvvressslewfkdvLneleeeks 64
                                       ++v+  +++e+f+++ +ele++k 
  gi|557694993|ref|YP_008798047.1| 53 LCMVKRLEDYEIFDKIFDELEKQKT 77
                                      5899*****************9986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00096
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxx RF
                     NAD_binding_6  29 kealktkkikliwvvressslewfkdvL.neleeekse.gnieihiYlTseyeaed 82 
                                         + k++++kl+ ++  s+s++ +++ L +++  + ++   +e+ ++ T+  ++++
  gi|557694993|ref|YP_008798047.1| 184 HMKRKVTRCKLVAIFDVSGSMDTYTEFLmQSMYALARQsVAVEVFVFSTRLLKVSS 239
                                       467899********************997888888888777888888888777644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2721.70
//
Query:       gi|557694994|ref|YP_008798048.1|  [L=289]
Description: ATPase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   49.7   0.0    6.9e-13   48.8   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
    1.5e-10   41.6   0.0    3.7e-10   40.3   0.0    1.6  1  AAA              ATPase family associated with various cellul
    3.7e-09   36.5   0.0     0.0013   18.5   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
    1.1e-06   29.2   0.0    3.3e-06   27.6   0.0    1.8  2  AAA_16           AAA ATPase domain
    1.2e-05   25.5   0.0    6.7e-05   23.2   0.0    2.1  1  AAA_22           AAA domain
    2.6e-05   24.0   0.1       0.12   12.1   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00066   20.2   0.0     0.0016   19.0   0.0    1.9  1  AAA_18           AAA domain
    0.00085   19.1   0.0        0.2   11.3   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
     0.0022   18.4   0.0      0.022   15.1   0.0    2.1  1  RNA_helicase     RNA helicase
     0.0034   17.3   0.1     0.0093   15.9   0.0    1.7  2  Rad17            Rad17 P-loop domain
     0.0043   17.0   0.4      0.016   15.1   0.4    2.0  1  NACHT            NACHT domain
  ------ inclusion threshold ------
      0.013   16.0   0.1      0.047   14.2   0.0    2.4  1  ABC_tran         ABC transporter
      0.014   15.5   0.0      0.058   13.5   0.0    2.0  2  Sigma54_activ_2  Sigma-54 interaction domain
      0.015   15.5   0.0      0.051   13.7   0.0    1.8  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.018   14.0   0.0      0.028   13.4   0.0    1.2  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
      0.025   14.0   0.0      0.046   13.1   0.0    1.4  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.042   13.9   0.0       0.27   11.3   0.0    2.1  1  AAA_14           AAA domain
       0.08   13.3   0.0       0.41   11.0   0.0    2.0  2  AAA_19           AAA domain
       0.09   12.5   0.0       0.14   12.0   0.0    1.3  1  AAA_11           AAA domain
       0.13   12.5   0.1       0.31   11.3   0.1    1.6  1  HHH_3            Helix-hairpin-helix motif
       0.13   11.5   0.0       0.25   10.6   0.0    1.4  1  Zeta_toxin       Zeta toxin
       0.18   11.3   0.0       0.27   10.7   0.0    1.2  1  AAA_7            P-loop containing dynein motor region
       0.18   10.9   0.0         22    4.0   0.0    2.9  3  MCM              MCM P-loop 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 !   48.8   0.0   8.9e-16   6.9e-13       2     137 ..      40     191 ..      39     192 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 8.9e-16
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--............--------........... CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik...ngttslvdsplvraar........... 64 
                                       +l+ G+pG+gK+e+a+ la++ln+e+   q+++++t+++ ++++++       + l+d++ v++++           
  gi|557694994|ref|YP_008798048.1|  40 LLIEGEPGCGKTEVAKVLARLLNTELIRLQCYEGITASQALYEWDYPrqlINIRLLEDKKSVDEITeeifsekfllk 116
                                       899*******************************************88776667778888888888999999999** PP

                                       ............G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT- CS
                             AAA_5  65 ............egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslne 129
                                                   ++ +l++DE++r + e  + Ll  l e ++ ++e+g+   +k+        vi t+n+ +    e
  gi|557694994|ref|YP_008798048.1| 117 rpllaallyegpNPPVLLIDEIDRSDEEFEGFLLEFLAEFQVTIPELGTIKAKKK------PVVIITSNRTR----E 183
                                       ************************************************9998888......58999999988....5 PP

                                       TTHHHHTT CS
                             AAA_5 130 lspalrsR 137
                                       +   lr+R
  gi|557694994|ref|YP_008798048.1| 184 VGDGLRRR 191
                                       55555555 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 !   40.3   0.0   4.8e-13   3.7e-10       1     124 [.      40     192 ..      40     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 4.8e-13
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS................STTHHHHHHHHHHHHHHHTS.... CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk................yvgesekkirelfkeakeka.... 57 
                                       +l+ G pG+GKT +ak +a+ l++e++++++ e +                   + e +k++ e+ +e+ +++    
  gi|557694994|ref|YP_008798048.1|  40 LLIEGEPGCGKTEVAKVLARLLNTELIRLQCYEGITAsqalyewdyprqliniRLLEDKKSVDEITEEIFSEKfllk 116
                                       5889*************************99998844589999******9999888999999999999988888888 PP

                                       ............TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.........SSTEEEEEEESSGG CS
                               AAA  58 ............kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk.........eskvivigatnrpd 113
                                                   +p +l+iDEid+  ++               Ll++l +++           ++k +vi+++nr +
  gi|557694994|ref|YP_008798048.1| 117 rpllaallyegpNPPVLLIDEIDRSDEE-----------FEGFLLEFLAEFQVTipelgtikaKKKPVVIITSNRTR 182
                                       88999999999999*********99444...........5999999999999999999999998889********** PP

                                       GSTHHHHSTTS CS
                               AAA 114 kldpallrgRf 124
                                       ++ + l+ +R+
  gi|557694994|ref|YP_008798048.1| 183 EVGDGLR-RRC 192
                                       **99999.587 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 !   18.5   0.0   1.7e-06    0.0013       2      34 ..      40      72 ..      39      82 .. 0.90
   2 !   15.7   0.0   1.3e-05      0.01      65     114 ..     132     182 ..     105     187 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-06
                             AAA_3  2 vllegvPGlaktllvkalakaldlefkriqftp 34
                                      +l+eg PG +kt ++k la+ l++e+ r+q+  
  gi|557694994|ref|YP_008798048.1| 40 LLIEGEPGCGKTEVAKVLARLLNTELIRLQCYE 72
                                      69****************************865 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.3e-05
                             AAA_3  65 llladeinrappktqsalleameerqvtveg.ethklpepflvlatqnPie 114
                                       +ll dei+r+    +  lle ++e qvt+ +  t k +++ +v+ t n   
  gi|557694994|ref|YP_008798048.1| 132 VLLIDEIDRSDEEFEGFLLEFLAEFQVTIPElGTIKAKKKPVVIITSNRTR 182
                                       89***************************7625788888899999999765 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   4.2e-09   3.3e-06      26     159 ..      39     154 ..      28     176 .. 0.79
   2 ?   -2.1   0.0       5.6   4.4e+03     108     131 ..     213     239 ..     195     265 .. 0.59

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 4.2e-09
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrekl 101
                                        +l+ Ge+G+GK+ +++ l+r l+++   ++r +c +    i+ s+ l +    ++l++  l e+++      +e  
  gi|557694994|ref|YP_008798048.1|  39 PLLIEGEPGCGKTEVAKVLARLLNTE---LIRLQCYEG---ITASQaLYEWDYPRQLINIRLLEDKK----SVDEIT 105
                                       589******************99999...899999999...66666699999999999999999555....333333 PP

                            AAA_16 102 eealaavpelagaeasrllellkrllallsrderplvlvlDdlqwadeaslql.laaLl 159
                                       ee ++          + +l +   l+all ++  p vl++D++++ de+   + l++L+
  gi|557694994|ref|YP_008798048.1| 106 EEIFS----------EKFLLKRPLLAALLYEGPNPPVLLIDEIDRSDEEFEGFlLEFLA 154
                                       34455..........67777766666888888999*************98888555554 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.6
                            AAA_16 108 vpelagaea...srllellkrllalls 131
                                       vp+l++++a     + ++l+++ +l++
  gi|557694994|ref|YP_008798048.1| 213 VPQLSPKLAaevVNFVQKLRQIGELAK 239
                                       455555555333334444443333333 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   8.6e-08   6.7e-05       6     115 ..      38     156 ..      35     184 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8.6e-08
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.......sskdllrellralglelka..... 70 
                                       + l++ Ge+G+GKT +++ l++ l         + e+++ ++ ++        +++  ++ +   l +++k+     
  gi|557694994|ref|YP_008798048.1|  38 KPLLIEGEPGCGKTEVAKVLARLL---------NTELIRLQCYEGItasqalyEWDYPRQLINIRLLEDKKSvdeit 105
                                       56899******************9.........66666555544443111123333333334444443333355555 PP

                            AAA_22  71 .erlsseell.ealeqalrarav.ielliiDEaqhlr...seealeeLrsl 115
                                        e  s++ ll + l  al   +  +++l+iDE+++ +   +  +le+L ++
  gi|557694994|ref|YP_008798048.1| 106 eEIFSEKFLLkRPLLAALLYEGPnPPVLLIDEIDRSDeefEGFLLEFLAEF 156
                                       544445555544444444444447999********9654447777777554 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   0.00015      0.12      36      61 ..      40      65 ..      10      76 .. 0.88
   2 !    9.6   0.0   0.00094      0.73      70     115 ..     115     160 ..     102     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                            RuvB_N 36 vllyGpPGlGkttlakiiakelgvkl 61
                                      +l+ G PG Gkt +ak++a+ l+++l
  gi|557694994|ref|YP_008798048.1| 40 LLIEGEPGCGKTEVAKVLARLLNTEL 65
                                      6899***************9998875 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00094
                            RuvB_N  70 ekagdlaalltnleekdvlfideihrlsraveevlysamedfrldi 115
                                        k   laall +  +  vl+idei r +++ e +l   + +f++ i
  gi|557694994|ref|YP_008798048.1| 115 LKRPLLAALLYEGPNPPVLLIDEIDRSDEEFEGFLLEFLAEFQVTI 160
                                       55666999****99**********************9999999877 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.1e-06    0.0016       2      66 ..      41      97 ..      40     177 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.1e-06
                            AAA_18  2 lltGtpGvGKttlakeLskrlgf...gvnlrdvakenglllevdpealdeskrldedkldklldalee 66
                                      l+ G pG+GKt++ak L+++l+               +++++ ++   +   + d +++  ++++le 
  gi|557694994|ref|YP_008798048.1| 41 LIEGEPGCGKTEVAKVLARLLNTeliR---------LQCYEGITAS--QALYEWDYPRQLINIRLLED 97
                                      699****************97445552.........3444444444..44444444444444444444 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   0.00026       0.2      18      45 ..      33      60 ..      23      81 .. 0.82
   2 ?    5.5   0.0     0.016        13      96     142 ..     132     180 ..     125     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00026
                                      HCTSSS-EEEECSTTSSHHHHHHHHHHH CS
                   Sigma54_activat 18 vaktdlsvlitGesGtGKellaraihea 45
                                      + k + ++li+Ge G+GK+ +a+ + + 
  gi|557694994|ref|YP_008798048.1| 33 ALKLEKPLLIEGEPGCGKTEVAKVLARL 60
                                      45677899**************998765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.016
                                       EEEEETGGGS-HHHHHHHHHHHHHSEEE..SBTSSSEEE--EEEEEEES CS
                   Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegeve..rvGsskeikvdvriiaatn 142
                                       +l++Dei + + e+   Ll++l e +v+   +G+ k +k  v ii++  
  gi|557694994|ref|YP_008798048.1| 132 VLLIDEIDRSDEEFEGFLLEFLAEFQVTipELGTIKAKKKPVVIITSNR 180
                                       799*******************997654338999999999988886543 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.8e-05     0.022       2      27 ..      41     106 ..      40     180 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.8e-05
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl........................................k 27 
                                       ++ G++g+GK+ +ak La+ l ++l                                        +
  gi|557694994|ref|YP_008798048.1|  41 LIEGEPGCGKTEVAKVLARLLNTELirlqcyegitasqalyewdyprqlinirlledkksvdeitE 106
                                       689****************99988866666665555555555555555555555555555555554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.2e-05    0.0093      42      74 ..      34      66 ..      23      77 .. 0.84
   2 ?   -2.8   0.0       6.5   5.1e+03     139     177 ..     102     140 ..      97     144 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-05
                             Rad17 42 srkkriLLisGPsGCgkstvvkvLskelgiklr 74
                                       + ++ LLi G +GCgk+ v kvL++ l ++l+
  gi|557694994|ref|YP_008798048.1| 34 LKLEKPLLIEGEPGCGKTEVAKVLARLLNTELI 66
                                      4555679*******************9988776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 6.5
                             Rad17 139 edlPnkfyrdsdalrevirkylrssealplilviteies 177
                                       +++ ++ + +   l+  ++ +l  +++ p +l+i ei+ 
  gi|557694994|ref|YP_008798048.1| 102 DEITEEIFSEKFLLKRPLLAALLYEGPNPPVLLIDEIDR 140
                                       555555555555666666677777777777888888865 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4     2e-05     0.016       2     100 ..      39     151 ..      38     229 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                                       CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-...-HCHHHCCCCTS--SSS-C....... CS
                             NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgnarsladllfsqlpepaapvse....... 71 
                                       +++++Ge+G+GKT  ++ la+++ ++    +  ++     +++l +      +++l+   l+e ++ v+e       
  gi|557694994|ref|YP_008798048.1|  39 PLLIEGEPGCGKTEVAKVLARLLNTELIRLQ--CYEGITASQALYEW---DYPRQLINIRLLEDKKSVDEiteeifs 110
                                       689******************9999876653..33333333333332...356777777777777777776667555 PP

                                       .........CHHHHCCSCCCEEEEEE-STT-SS-TCH.... CS
                             NACHT  72 .........vwavllelperlLlilDglDelvtdlgq...k 100
                                                  a+l e p+  +l++D +D+  ++++    +
  gi|557694994|ref|YP_008798048.1| 111 ekfllkrplLAALLYEGPNPPVLLIDEIDRSDEEFEGfllE 151
                                       55555555555555555555558888888877765555553 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     6e-05     0.047       6      38 ..      32      64 ..      29     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6e-05
                                      EEEETTSEEEEEESTTSSHHHHHHHHTTSS--S CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  6 lklkegekvaivGenGaGKStLlkllagllkpt 38
                                      l lk  + + i Ge G+GK+ ++k+la+ll+ +
  gi|557694994|ref|YP_008798048.1| 32 LALKLEKPLLIEGEPGCGKTEVAKVLARLLNTE 64
                                      67788888999*****************99863 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 ?   13.5   0.0   7.4e-05     0.058      19      45 ..      35      61 ..      25      83 .. 0.81
   2 ?   -1.5   0.0       3.1   2.4e+03     119     138 .]     144     163 ..     122     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.4e-05
                                      T-SS-EEEEEETT--HHHHHHCC--TT CS
                   Sigma54_activ_2 19 qsklpvfltGekGsgkelvArlLhkns 45
                                      + + p+++ Ge+G+gk+ vA++L+   
  gi|557694994|ref|YP_008798048.1| 35 KLEKPLLIEGEPGCGKTEVAKVLARLL 61
                                      6678*******************9765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.1
                                       -HHHHHHHHSSSEEEEE--- CS
                   Sigma54_activ_2 119 afdekLlkeLselrlhvPpL 138
                                       +f+  Ll+ L e+++ +P+L
  gi|557694994|ref|YP_008798048.1| 144 EFEGFLLEFLAEFQVTIPEL 163
                                       55556677777777777765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.6e-05     0.051       7      82 ..      41     143 ..      37     184 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.6e-05
                                       EEE--TTSSHHHHHHHHHHHTT-...........................-EEEEEGGG-------THHHH.HHHHH CS
                             AAA_2   7 lllgptgvGktelakalaellfv.......................kkekkliradaselleeeevehlvs.rliga 59 
                                       l+ g+ g+Gkte+ak la+ll+                        +                    +l++ rl+  
  gi|557694994|ref|YP_008798048.1|  41 LIEGEPGCGKTEVAKVLARLLNTelirlqcyegitasqalyewdypR--------------------QLINiRLLED 97 
                                       788999****************7555444444444333333332221....................2222111111 PP

                                       TTT-HHHHTTS...............................EEEEETGGG--- CS
                             AAA_2  60 ppgyvgaeegG...............................ivllDEidKihp 82 
                                       ++                                        ++l+DEid+  +
  gi|557694994|ref|YP_008798048.1|  98 KK--------SvdeiteeifsekfllkrpllaallyegpnppVLLIDEIDRSDE 143
                                       11........01122222245555555555556666668888999999998666 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 ?   13.4   0.0   3.6e-05     0.028      25      72 ..      30      77 ..      24      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                             AAA_6 25 ltqAlklklggapaGpagtGKtEtvkdLakalakqvvvfncsdqldyk 72
                                      +  Alkl+    ++G  g GKtE  k La+ l + ++ ++c ++++++
  gi|557694994|ref|YP_008798048.1| 30 VYLALKLEKPLLIEGEPGCGKTEVAKVLARLLNTELIRLQCYEGITAS 77
                                      5568888888899*****************************999875 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.9e-05     0.046      16      47 ..      31      62 ..      22      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.9e-05
                      Mg_chelatase 16 eiaaaGgHnlllvGppGsGKtmlakrlpsllp 47
                                       +a   +  ll+ G pG+GKt +ak l+ ll 
  gi|557694994|ref|YP_008798048.1| 31 YLALKLEKPLLIEGEPGCGKTEVAKVLARLLN 62
                                      5566666789*****************99985 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00035      0.27       3      90 ..      38     156 ..      36     171 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00035
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell...........vkkesilyinldderd.........kkladpe....kllel 55 
                                       k+l+i+G   +GKT ++k l++ l            +++++ ly ++d +r+         k     +      +e+
  gi|557694994|ref|YP_008798048.1|  38 KPLLIEGEPGCGKTEVAKVLARLLNtelirlqcyegITASQALY-EWDYPRQlinirlledK-----KsvdeITEEI 108
                                       789999999*****999888866556666666666544444333.34443335444333211.....1111122233 PP

                            AAA_14  56 ileklke................ekktylflDEiqev.pewekalkslvdeg 90 
                                       +     e                ++  +l++DEi ++ +e+e +l +++ e 
  gi|557694994|ref|YP_008798048.1| 109 FS----EkfllkrpllaallyegPNPPVLLIDEIDRSdEEFEGFLLEFLAEF 156
                                       33....2233346788889998888999******998345888887777665 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   0.00053      0.41      10      36 ..      37      63 ..      28      79 .. 0.84
   2 ?   -0.7   0.0         2   1.6e+03     105     124 ..     132     151 ..     116     160 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00053
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallve 36
                                      ek+ll+ + pG+GKT+v k   +ll+ 
  gi|557694994|ref|YP_008798048.1| 37 EKPLLIEGEPGCGKTEVAKVLARLLNT 63
                                      7899*************9988887765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2
                            AAA_19 105 llivDEfqdvdelqyrLlka 124
                                       +l++DE+   de    +l +
  gi|557694994|ref|YP_008798048.1| 132 VLLIDEIDRSDEEFEGFLLE 151
                                       799****9999555554433 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   0.00017      0.14       8      42 ..      28      62 ..      22     118 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                            AAA_11  8 eaiksalseseitliqGPPGtgKTktivellsqll 42
                                       a++ al+ ++  li+G PG+gKT +   l + l+
  gi|557694994|ref|YP_008798048.1| 28 LAVYLALKLEKPLLIEGEPGCGKTEVAKVLARLLN 62
                                      6778888888889***********66555554443 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1    0.0004      0.31      18      54 ..     212     245 ..     206     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0004
                             HHH_3  18 klpGlgpklAknIvayReknGpfksreeLlkvkglgp 54 
                                       k+p l+pklA ++v++    ++++ + eL k++g+++
  gi|557694994|ref|YP_008798048.1| 212 KVPQLSPKLAAEVVNFV---QKLRQIGELAKKPGISE 245
                                       79***************...899************97 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   0.00032      0.25      19      48 ..      40      67 ..      34      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00032
                        Zeta_toxin 19 illgGqpGAGKselaellkdelerqgnvvr 48
                                      +l+ G pG+GK+e+a+ l++ l  + + +r
  gi|557694994|ref|YP_008798048.1| 40 LLIEGEPGCGKTEVAKVLARLL--NTELIR 67
                                      5788*************99988..566665 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 ?   10.7   0.0   0.00035      0.27      28      60 ..      32      64 ..      24      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
                             AAA_7 28 lllknkkpvllvGptGtGKtviikdllkkldke 60
                                      l lk +kp+l+ G+ G+GKt ++k l + l++e
  gi|557694994|ref|YP_008798048.1| 32 LALKLEKPLLIEGEPGCGKTEVAKVLARLLNTE 64
                                      678899****************99988888755 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.19   1.5e+02      60      82 ..      40      62 ..      32      78 .. 0.84
   2 ?    4.0   0.0     0.028        22     124     156 ..     132     164 ..     128     182 .. 0.83
   3 ?    1.3   0.0      0.19   1.5e+02       3      50 ..     232     279 ..     230     287 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.19
                                      EEEEESSTSTHHHHHHHHHHHSS CS
                               MCM 60 vllvgdpgtaKsqlLkyveklap 82
                                      +l+ g+pg++K+++ k +++l++
  gi|557694994|ref|YP_008798048.1| 40 LLIEGEPGCGKTEVAKVLARLLN 62
                                      6888*********9999888765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.028
                                       EEEEESGGGSTCHHHHHHHHHHHHSEEEEESSS CS
                               MCM 124 vcciDefdkmkeedrsalhEamEqqtisiaKaG 156
                                       v++iDe+d+ +ee +  l+E + + +++i   G
  gi|557694994|ref|YP_008798048.1| 132 VLLIDEIDRSDEEFEGFLLEFLAEFQVTIPELG 164
                                       789*****************9999999987666 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.19
                                       HHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSS CS
                               MCM   3 eeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkled 50 
                                       ++i elak++ i e+l  + a +++g +++  +il + + +  k+++d
  gi|557694994|ref|YP_008798048.1| 232 RQIGELAKKPGISETLDWANALTVLGAREINPSILSSTLTCLIKNEDD 279
                                       7899********************************999999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 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:                        81  (0.00451782); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2085.13
//
Query:       gi|557694995|ref|YP_008798049.1|  [L=291]
Description: molybdopterin dehydrogenase FAD-binding [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-45  155.4   0.1    2.3e-45  154.4   0.0    1.5  2  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
    1.8e-26   92.3   2.0    2.3e-26   91.9   0.9    1.8  2  CO_deh_flav_C  CO dehydrogenase flavoprotein C-terminal domai
  ------ inclusion threshold ------
      0.076   13.1   0.1       0.15   12.2   0.1    1.5  1  LPD7           Large polyvalent protein-associated domain 7


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 !  154.4   0.0   3.9e-49   2.3e-45       2     170 ..       5     173 ..       4     174 .. 0.97
   2 ?   -2.3   0.0      0.54   3.2e+03      52      52 ..     219     219 ..     179     261 .. 0.55

  Alignments for each domain:
  == domain 1  score: 154.4 bits;  conditional E-value: 3.9e-49
                                       EEEEEE-SSHHHHHHHHHH.CTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHH CS
                     FAD_binding_5   2 kfeylrpasleealallaa.epdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlsel 77 
                                       kfey+ p++++ea++ll++ +++ak+++Gg +l+++mk++v++p+ +idi++i+ l++i+  ++ ++iGA+v+++++
  gi|557694995|ref|YP_008798049.1|   5 KFEYFAPTTVSEAVSLLRKyRDSAKILSGGMSLIPMMKLRVLSPQVIIDINNIKSLNYIKDGGKTVRIGALVRHADI 81 
                                       89*****************999******************************************************* PP

                                       HHHHHHHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETTE CS
                     FAD_binding_5  78 aaealvrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkgpgk 154
                                        ++++++e++p +++a+ +iA++q+Rn++T  G la+a+p++D+++  laldAe++ ++ + +r +++++f+kgp +
  gi|557694995|ref|YP_008798049.1|  82 EHSPIIKEKFPMMADAAPHIADMQVRNLGTFLGALAHADPAADWPASALALDAELVAQG-TAKRVIKATKFFKGPFE 157
                                       *******************************************************9986.569************** PP

                                       ESS-TT-EEEEEEEE- CS
                     FAD_binding_5 155 talepgelitaveiPa 170
                                       tal+p e++++  +P 
  gi|557694995|ref|YP_008798049.1| 158 TALKPTEMLVEAVLPV 173
                                       ***********99996 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.54
                                       T CS
                     FAD_binding_5  52 g 52 
                                        
  gi|557694995|ref|YP_008798049.1| 219 A 219
                                       3 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 ?   -2.9   0.0       1.3   7.6e+03      34      49 ..     135     150 ..     122     166 .. 0.64
   2 !   91.9   0.9   3.9e-30   2.3e-26       1     101 [.     181     281 ..     181     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.3
                                       EEEEESSSSS-EE-HH CS
                     CO_deh_flav_C  34 riafggvaptpvraek 49 
                                       +++  g a++++ a+k
  gi|557694995|ref|YP_008798049.1| 135 ELVAQGTAKRVIKATK 150
                                       4444444444444443 PP

  == domain 2  score: 91.9 bits;  conditional E-value: 3.9e-30
                                       EEE.EEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCH CS
                     CO_deh_flav_C   1 say.klsrrrendiaivnaAfrveleedgkiedariafggvaptpvraekaeaaLiGkplseelleeaakaleeels 76 
                                       +ay k++r+++ d+aiv++A +++l+ +++i++a ia+++v+p p ra+ ae++L+G+++s++l+e+aaka+++ ++
  gi|557694995|ref|YP_008798049.1| 181 QAYlKFERKAG-DYAIVGVASLLTLNRENVIQKAAIALTAVNPFPFRATDAEELLVGQKPSKDLIEQAAKAAAAMAD 256
                                       6899*******.**************999************************************************ PP

                                       HHTCTTC-HHHHHHHHHHHHHHHHH CS
                     CO_deh_flav_C  77 pasdprasaeYRrslavsllfrfll 101
                                       p+sd+r+saeY+r++a+++++r l+
  gi|557694995|ref|YP_008798049.1| 257 PSSDLRGSAEYKREMAKVFTRRSLN 281
                                       *********************9886 PP

>> LPD7  Large polyvalent protein-associated domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.6e-05      0.15      33      75 ..     237     280 ..     224     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.6e-05
                              LPD7  33 sddddeavaaalelAqakwg.sltvsGseeFkreaweaaaergl 75 
                                       ++ +++ ++ a ++A+a  + s ++ Gs+e+kre++++ ++r l
  gi|557694995|ref|YP_008798049.1| 237 QKPSKDLIEQAAKAAAAMADpSSDLRGSAEYKREMAKVFTRRSL 280
                                       555678899999999888866*****************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); 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: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 2453.45
//
Query:       gi|557694996|ref|YP_008798050.1|  [L=179]
Description: (2Fe-2S)-binding domain protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  109.0   1.3      2e-31  107.8   0.0    1.9  2  Fer2_2     [2Fe-2S] binding domain
    0.00014   21.8   0.1    0.00014   21.8   0.1    2.1  2  Fer2       2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
       0.13   12.3   0.1       0.25   11.4   0.1    1.6  1  Fer2_3     2Fe-2S iron-sulfur cluster binding domain
       0.15   11.9   0.0       0.29   10.9   0.0    1.5  1  DUF5634_N  Family of unknown function (DUF5634)


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 ?   -0.4   0.3      0.26   1.2e+03      22      31 ..      52      61 ..      44      67 .. 0.82
   2 !  107.8   0.0   4.4e-35     2e-31       1      75 [.      90     162 ..      90     163 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.26
                            Fer2_2 22 egasqCGyCt 31
                                      ++ + CG Ct
  gi|557694996|ref|YP_008798050.1| 52 CDTTNCGACT 61
                                      67889****9 PP

  == domain 2  score: 107.8 bits;  conditional E-value: 4.4e-35
                            Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                       T+egl++  ++lhp+q+af e++++qCGyCtpG++m+aa++l  n p+pteee+r+ +sgnlCRCtgY +iv+ +
  gi|557694996|ref|YP_008798050.1|  90 TIEGLAKG-DQLHPLQKAFWENHGLQCGYCTPGMIMAAAGFLMIN-PNPTEEEVRHGISGNLCRCTGYVNIVKSI 162
                                       9*****88.88*******************************999.99999*********************976 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 !   21.8   0.1   3.1e-08   0.00014       1      48 [.      18      65 ..      18      86 .. 0.81
   2 ?   -1.8   1.2      0.67     3e+03      39      44 ..     113     119 ..     110     165 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.1e-08
                                      EETTTEEEEEEEETTTHBHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEE CS
                              Fer2  1 itidgkevevevadgettlldaaee.nggidipysCggggCgtClvevl 48
                                      i i+g+++++ev++    l  + +e +g ++++ +C   +Cg+C+v ++
  gi|557694996|ref|YP_008798050.1| 18 IDINGTKYSYEVEPRLL-LVHFIREyAGLTGTHIGCDTTNCGACTVLME 65
                                      579********977776.99999999*******************9754 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.67
                                       S.SSTTE CS
                              Fer2  39 g.CgtCl 44 
                                         Cg C+
  gi|557694996|ref|YP_008798050.1| 113 LqCGYCT 119
                                       4588876 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 ?   11.4   0.1   5.6e-05      0.25      50      93 ..      50      96 ..      20     105 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.6e-05
                            Fer2_3 50 asCregiCGsca..vainGkp..tlaCtatikdlakqkseieleplpk 93
                                        C  + CG+c+  ++++Gk      Ct+   + + +   i++e l+k
  gi|557694996|ref|YP_008798050.1| 50 IGCDTTNCGACTvlMEVDGKWkaIKSCTHFAVQANGKR-IITIEGLAK 96
                                      58*********955579998722457888877776554.699998865 PP

>> DUF5634_N  Family of unknown function (DUF5634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.4e-05      0.29      54      77 ..     138     161 ..     135     177 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.4e-05
                                       EEEEEEEETTEEEEEEEE--SB-S CS
                         DUF5634_N  54 evsvrvgtggalyRCkgvvetved 77 
                                       e  vr g +g+l+RC g v+ v++
  gi|557694996|ref|YP_008798050.1| 138 EEEVRHGISGNLCRCTGYVNIVKS 161
                                       557999*************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); 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:                         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 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1341.91
//
Query:       gi|557694997|ref|YP_008798051.1|  [L=151]
Description: carbon monoxide dehydrogenase subunit G like protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-33  115.4   0.1    1.8e-33  115.2   0.1    1.0  1  COXG             Carbon monoxide dehydrogenase subunit G (Cox
    2.1e-12   47.5   0.0    2.4e-12   47.3   0.0    1.0  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
    0.00018   21.7   0.0    0.00027   21.2   0.0    1.4  1  AHSA1            Activator of Hsp90 ATPase homolog 1-like pro
     0.0015   18.7   0.0     0.0022   18.2   0.0    1.5  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.042   14.0   0.0       0.29   11.3   0.0    1.9  1  DUF1997          Protein of unknown function (DUF1997)


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 !  115.2   0.1   5.1e-37   1.8e-33       2     139 ..       6     143 ..       5     144 .. 0.91

  Alignments for each domain:
  == domain 1  score: 115.2 bits;  conditional E-value: 5.1e-37
                                       EEEESS-HHHHHHHHT-HHHHGGGSTTEEEEEEET.TEEEEEEEEESSSSEEEEEEEEEEEEEETTTEEE..EEEEE CS
                              COXG   2 efrvaapkeavwefLndpeklarciPGvksvekeg.deykvkvklkvGplkgsfkarvelselekensttieikGkG 77 
                                       +f v+ap+e+v++f++dp+ + ++iP ++s+ek + +++kv++k+++G +kg+++  ++++e+++++   ++i G G
  gi|557694997|ref|YP_008798051.1|   6 KFVVSAPREKVFKFVTDPDSFVKLIPDLQSYEKVDdKNFKVVFKIGLGMIKGNLNMAFRFEEVREPEF--VKISGHG 80 
                                       688********************************99******************************6..6777777 PP

                                       E-SSEEEEEEEEEEEEEETT.EEEEEEEEEEEEEHHHHS-HHHHHHHHHHHHHHHHHHHHHHH CS
                              COXG  78 rgagvaidfalvvlveeggg.trlswsakvnvggllaslGsrlidsaarklinelfecisskl 139
                                       +g+++++d +l++  +   g t++ w+a+v vggl+as+Gsrl++s++++ ++e++e ++++l
  gi|557694997|ref|YP_008798051.1|  81 SGMQSTADLTLNLNLNAADGgTEVAWDADVAVGGLVASVGSRLMESTTKSKVKEIVEGLKREL 143
                                       777777777777766665555**************************************9987 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 !   47.3   0.0   6.6e-16   2.4e-12       3     143 .]       2     144 ..       1     144 [. 0.85

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 6.6e-16
                                       EEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSE.STSSSTTTEEEEECCCS...SEEEEEEEEEETTTTEE CS
                   Polyketide_cyc2   3 kvtvsvviaappekVwalvsdfenwprWhpevarveleg.gggpargvegtvrvggr...gtvreelvevdpegrll 75 
                                       k++++ v+ ap ekV+++v+d++++ + +p ++++e ++ ++ +++++ g            +  +++ev++ + ++
  gi|557694997|ref|YP_008798051.1|   2 KLSDKFVVSAPREKVFKFVTDPDSFVKLIPDLQSYEKVDdKNFKVVFKIGLGM---IkgnLNMAFRFEEVRE-PEFV 74 
                                       5788899****************************988724444344444444...243466999*****96.8888 PP

                                       EEEEE...SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Polyketide_cyc2  76 syriv..kpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavkgdleagLerLkarle 143
                                       ++ +   + +++a+ + ++ + +++ggt+v w++++++g+l + +   ++++  k+ +++ +e+Lk++le
  gi|557694997|ref|YP_008798051.1|  75 KISGHgsGMQSTADLTLNLNLNAADGGTEVAWDADVAVGGLVASVGSRLMESTTKSKVKEIVEGLKRELE 144
                                       888855678999999**********************999999999**********************98 PP

>> AHSA1  Activator of Hsp90 ATPase homolog 1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   7.5e-08   0.00027       2      97 ..      11     117 ..      10     144 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7.5e-08
                                       S-HHHHHHHHH-HHHHHHHEEEEEEEE--ST.TEEEEE....EETTTSEEEEEEEEEEEEETTTEEEEEEEEETSET CS
                             AHSA1   2 apperVfraltdpellkrWftlteaemdlrp.Ggkfrl....rdspdgkefgnegeylevvpperlvytwrledepe 73 
                                       ap+e+Vf+  tdp+ + +   +++ ++  ++ +++f++      +   ++ ++  +++ev +pe ++++ +  + ++
  gi|557694997|ref|YP_008798051.1|  11 APREKVFKFVTDPDSFVKL--IPDLQSYEKVdDKNFKVvfkiGLGMIKGNLNMAFRFEEVREPEFVKISGHGSGMQS 85 
                                       8******************..66666666665667777654322333456666666*************76666666 PP

                                       EEEEEEEEEEEEETTEEEEEEEE........E CS
                             AHSA1  74 eeestvtieleeegggTrltlth........t 97 
                                       +++ t+ ++l +++ggT++   +        +
  gi|557694997|ref|YP_008798051.1|  86 TADLTLNLNLNAADGGTEVAWDAdvavgglvA 117
                                       99****************98888544444333 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 !   18.2   0.0   6.1e-07    0.0022       1      53 [.       9      63 ..       9     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 6.1e-07
                                      ESS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE.....EEEECSTTSSCEEE CS
                    Polyketide_cyc  1 vpapadqvyalvadvesypeflphcssvevleeaes..glsadlevgfggltesf 53
                                      v+ap ++v+++v+d +s+ +++p ++s e +++++    +++ l   +g l++ f
  gi|557694997|ref|YP_008798051.1|  9 VSAPREKVFKFVTDPDSFVKLIPDLQSYEKVDDKNFkvVFKIGLGMIKGNLNMAF 63
                                      79*****************************999954433333333333333333 PP

>> DUF1997  Protein of unknown function (DUF1997)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0     8e-05      0.29       5     142 ..      19     143 ..      15     146 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8e-05
                           DUF1997   5 YLrqpqrlvsaladperierlgeetfrltvgplkflglevePvvdlrvepeeegvvrlesedcelkgleavendrfs 81 
                                       +  +p++ v+ + d ++ e++++++f++   ++++  ++ +  ++ r+e       + e   +++ g +  ++   +
  gi|557694997|ref|YP_008798051.1|  19 FVTDPDSFVKLIPDLQSYEKVDDKNFKVVF-KIGLGMIKGNLNMAFRFEEVR----EPEF--VKISGHGSGMQ--ST 86 
                                       566777777777777777777777777744.344433333333333333322....3344..44444444423..44 PP

                           DUF1997  82 ldlkgaleleeegsrtelegdldlkvsvelppflallPesllestgnsvlkqvlkqvkprl 142
                                       +dl+ +l+l+  ++ te+ +d+d++v+  + ++       l+est +s +k++++ +k++l
  gi|557694997|ref|YP_008798051.1|  87 ADLTLNLNLNAADGGTEVAWDADVAVGGLVASV----GSRLMESTTKSKVKEIVEGLKREL 143
                                       555556666666666***********9966666....556666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1149.09
//
Query:       gi|557694998|ref|YP_008798052.1|  [L=728]
Description: elongation factor EF-2 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-59  199.3   0.0    6.8e-59  198.7   0.0    1.3  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    2.2e-24   85.6   0.1    8.6e-24   83.6   0.0    2.1  2  EFG_IV        Elongation factor G, domain IV
    1.3e-21   76.4   0.0    3.6e-21   75.0   0.0    1.8  1  EFG_C         Elongation factor G C-terminus
    9.1e-21   73.7   0.1    5.8e-20   71.2   0.0    2.4  3  EFG_II        Elongation Factor G, domain II
    9.1e-12   45.2   2.1    2.4e-11   43.9   2.1    1.8  1  GTP_EFTU_D2   Elongation factor Tu domain 2
     0.0025   17.9   0.1     0.0085   16.2   0.0    1.9  2  MMR_HSR1      50S ribosome-binding GTPase
  ------ inclusion threshold ------
       0.03   13.9   0.0      0.059   13.0   0.0    1.4  1  Ras           Ras family
       0.14   12.2   0.0       0.37   10.9   0.0    1.7  1  ADAM_spacer1  ADAM-TS Spacer 1


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 !  198.7   0.0     3e-62   6.8e-59       2     192 ..      19     255 ..      18     257 .. 0.89

  Alignments for each domain:
  == domain 1  score: 198.7 bits;  conditional E-value: 3e-62
                                       CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE..TTCSSEEEEEEE CS
                          GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle..ketkkylinliD 76 
                                       +irnigii+hvDhGKtT++d+Ll+++g  s   + a+ + +lD l+eE++r++Tik+a++sl+   ++k y inliD
  gi|557694998|ref|YP_008798052.1|  19 SIRNIGIIAHVDHGKTTTSDSLLAAAGLLSP--SLAGRALALDYLEEEQQRQMTIKAANVSLYyeMDGKPYIINLID 93 
                                       79*****************************..77888999**********************745*********** PP

                                       ESSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  77 tPGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk 153
                                       tPGHvdFs  v+r+lr++Dga++vvdaveGv++qte+v+r+al e+v++++ iNK+Drl +elk  +e+++++l r 
  gi|557694998|ref|YP_008798052.1|  94 TPGHVDFSGRVTRALRAIDGAIVVVDAVEGVMTQTETVIRQALGERVRPVLYINKIDRLVKELKLPPEKIQETLARI 170
                                       **************************************************************************777 PP

                                       ..............HHHHHHHHHTTT........TTEEEEEEBTTTTBTHH.......................... CS
                          GTP_EFTU 154 ..............eeklekygekge........kevpvvfgSalkgegvk.......................... 182
                                                     e          +         + +v+ gS+++ +g++                          
  gi|557694998|ref|YP_008798052.1| 171 vrevntlidmygepE----------QrekwkisfADNTVAIGSSKDRWGFTvkqaqqkgikfsdvidafsredvewl 237
                                       888855555444440..........2445555556668**********99999999999999999999999999999 PP

                                       ........HHHHHHHHHS CS
                          GTP_EFTU 183 ........tllealvell 192
                                               +lle+++++ 
  gi|557694998|ref|YP_008798052.1| 238 rqktplheALLEMVISKH 255
                                       999999988999998765 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 ?   -2.9   0.0       2.4   5.5e+03      74      89 ..     287     301 ..     277     308 .. 0.80
   2 !   83.6   0.0   3.9e-27   8.6e-24      11     120 ..     509     615 ..     500     616 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.4
                                       TS-TTTS--EESEEEE CS
                            EFG_IV  74 keGplagepvtdvkvt 89 
                                       ++Gp     vtdv+v 
  gi|557694998|ref|YP_008798052.1| 287 ENGPTV-MAVTDVRVD 301
                                       789999.99****995 PP

  == domain 2  score: 83.6 bits;  conditional E-value: 3.9e-27
                                       S-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEE CS
                            EFG_IV  11 kpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvk 87 
                                       ++ k+++++l +++g+d ++a+ +++i+      gn++vd+tkg q+++e +  +  Gfq +++eGpla e++++vk
  gi|557694998|ref|YP_008798052.1| 509 MDRKQVAKIL-REHGWDADEARNVWTIDGR----GNILVDATKGAQYLQESKMMILGGFQRVMQEGPLAAENMRGVK 580
                                       5566455555.559**************95....9****************************************** PP

                                       EEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                            EFG_IV  88 vtLldgslhe..vdsseaafkpaarralkeallkA 120
                                       ++L++++lhe  v+++ a++ pa+ r l++++l+A
  gi|557694998|ref|YP_008798052.1| 581 AVLTQVELHEdpVHRGYAQIAPATWRSLYASVLSA 615
                                       *******************************9998 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 !   75.0   0.0   1.6e-24   3.6e-21       1      88 [.     618     704 ..     618     721 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 1.6e-24
                                       EEEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEE CS
                             EFG_C   1 vllEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsg 77 
                                       vllEP+ k+e +v++e++g+v+s+++s+rG+++d++q  +  +++ +eiP++e++++++++rs+T G++ + +efs+
  gi|557694998|ref|YP_008798052.1| 618 VLLEPVLKIEAKVSQEFMGAVTSTITSKRGRVLDVKQA-EYVTVVVGEIPASETFDLSEAMRSATMGKAFWATEFSE 693
                                       59************************************.************************************** PP

                                       EEE--HHHHHH CS
                             EFG_C  78 Yeevpgdklde 88 
                                       +++vp ++ d+
  gi|557694998|ref|YP_008798052.1| 694 WKPVPASLRDK 704
                                       *****988765 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 ?   -2.5   0.0       2.6   5.7e+03      19      34 ..     161     176 ..     160     178 .. 0.84
   2 ?   -2.0   0.0       1.7   3.9e+03      18      33 ..     219     234 ..     212     235 .. 0.81
   3 !   71.2   0.0   2.6e-23   5.8e-20       1      71 [.     385     454 ..     385     458 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.6
                            EFG_II  19 dklskaLarlleEDpt 34 
                                       +k+++ Lar+++E  t
  gi|557694998|ref|YP_008798052.1| 161 EKIQETLARIVREVNT 176
                                       7999*******99666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                            EFG_II  18 edklskaLarlleEDp 33 
                                         k+s++++ +++ED 
  gi|557694998|ref|YP_008798052.1| 219 GIKFSDVIDAFSREDV 234
                                       5599**********95 PP

  == domain 3  score: 71.2 bits;  conditional E-value: 2.6e-23
                            EFG_II   1 fPePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvev 71 
                                       ++ePv+++++epk ++d  kl ++L++l+ EDptl + + +eT+e+++sGmG+lHlei+++ +++  ++ev
  gi|557694998|ref|YP_008798052.1| 385 VSEPVVTISVEPKYSRDLPKLVEFLNKLTIEDPTLVTVVRPETGEYLISGMGTLHLEIALTWIQKA-GLEV 454
                                       689**********************************************************99875.6666 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 !   43.9   2.1   1.1e-14   2.4e-11       1      73 [.     305     371 ..     305     372 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 1.1e-14
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G+va+gr++sGt+ +Gd v i+g n        +r++++ + +++ +e v   +aG+i a+ gl d +++Gdt+
  gi|557694998|ref|YP_008798052.1| 305 GVVATGRLFSGTISEGDSVIIVGrNI------SGRVQQVGVYMGPSREIVGSIPAGNIPAVLGLAD-VRAGDTI 371
                                       89*******************77554......4*********************************.******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 !   16.2   0.0   3.8e-06    0.0085       3     112 ..      24     146 ..      22     148 .. 0.53
   2 ?   -2.8   0.0       2.8   6.4e+03      49      65 ..     176     191 ..     160     239 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.8e-06
                                       EEEESTTSSHHHHHHHHHT................STEEESSSTTSSSSEEEEEEE..ETTEE.....EEEEECGGC CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg................ekaivsdkpgtTrdinegrvk..lkgke.....ielvDtpGl 56 
                                       +i+ +   GK+t   +l+                 +  + +++ + T++     +   +   +     i+l+DtpG 
  gi|557694998|ref|YP_008798052.1|  24 GIIAHVDHGKTTTSDSLLAaagllspslagralalDYLEEEQQRQMTIKAANVSLYyeM---DgkpyiINLIDTPGH 97 
                                       55555666666666666643333333333222211122334444445554444333332...0333559*******6 PP

                                       SSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEE CS
                          MMR_HSR1  57 iegaseekglgkaflaleeadlillvvdaseeklkpldeeleelleeakkplilvl 112
                                       ++        g+  +al+  d +++vvda e+ +++ +  + + l e+ +p+ l++
  gi|557694998|ref|YP_008798052.1|  98 VD------FSGRVTRALRAIDGAIVVVDAVEGVMTQTETVIRQALGERVRPV-LYI 146
                                       66......355666666668********996656666666666666555554.444 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.8
                                       EEEECGGCSSHHHHHHH CS
                          MMR_HSR1  49 elvDtpGliegaseekg 65 
                                       +l+D+ G   +++e+++
  gi|557694998|ref|YP_008798052.1| 176 TLIDMYGEP-EQREKWK 191
                                       678888833.3444442 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.6e-05     0.059      25      83 ..      64     122 ..      54     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                                       SSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTB CS
                               Ras  25 keeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvydits 83 
                                       +++ ++Ti +++ +   e+dgk + +++ DT G  +f+   +  +r  +g+++v d  +
  gi|557694998|ref|YP_008798052.1|  64 EQQRQMTIKAANVSLYYEMDGKPYIINLIDTPGHVDFSGRVTRALRAIDGAIVVVDAVE 122
                                       467889***********************************************987554 PP

>> ADAM_spacer1  ADAM-TS Spacer 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.37      60     113 ..     215     266 ..     192     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                      ADAM_spacer1  60 asek.lelagtvleysrsdeakesleatgplkesltvqvlvqkeknpgvkYeyvi 113
                                       a++k +++++++  +sr+d   e+l+ + pl+e l  +v+++ +++p+v+ +y i
  gi|557694998|ref|YP_008798052.1| 215 AQQKgIKFSDVIDAFSRED--VEWLRQKTPLHEALLEMVISK-HPPPHVAQKYRI 266
                                       3344699999999999994..6*******************9.999999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (728 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.40
# Mc/sec: 5441.90
//
Query:       gi|557694999|ref|YP_008798053.1|  [L=299]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   18.8  36.3      0.037   14.1  18.4    2.5  2  Nup54            Nucleoporin complex subunit 54
  ------ inclusion threshold ------
      0.028   14.8   4.0      0.028   14.8   4.0    5.5  4  ZapB             Cell division protein ZapB
        0.1   11.5  43.6      0.072   12.0  18.2    2.3  2  Spc7             Spc7 kinetochore protein
       0.12   12.3   0.5       0.35   10.8   0.0    2.0  2  DUF1298          Protein of unknown function (DUF1298)
       0.12   12.6   5.8        2.3    8.5   0.7    3.2  3  DUF948           Bacterial protein of unknown function (DUF94
       0.14   12.2  14.6        1.2    9.2   2.1    3.5  3  DUF1664          Protein of unknown function (DUF1664)
       0.31   11.1  24.0        1.7    8.6   6.6    3.5  3  Laminin_II       Laminin Domain II
       0.45   10.3  11.2        2.3    8.0   2.9    2.5  2  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
       0.59    8.4  49.2      0.003   16.0  33.9    2.0  2  MAD              Mitotic checkpoint protein
       0.84    9.7  37.5      0.075   13.1  11.1    3.6  3  Mod_r            Modifier of rudimentary (Mod(r)) protein
        1.1    9.5  40.1       0.16   12.2  14.1    3.0  3  ATG16            Autophagy protein 16 (ATG16)
        1.1    8.6  50.9       0.44    9.9  16.6    2.1  2  GAS              Growth-arrest specific micro-tubule binding
        1.4    7.9  38.5          3    6.9  15.9    2.3  2  Atg14            Vacuolar sorting 38 and autophagy-related su
        2.2    8.5  24.9       0.49   10.6   5.6    3.2  3  Fib_alpha        Fibrinogen alpha/beta chain family
          3    8.0   6.3         11    6.2   0.1    3.4  3  DUF695           Family of unknown function (DUF695)
          4    7.6  13.3        1.1    9.3   4.0    3.1  2  DUF2730          Protein of unknown function (DUF2730)
        4.3    7.4  44.5         28    4.8  23.2    3.7  2  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        6.1    7.5  26.3       0.18   12.4   1.6    4.2  4  DUF4665          Domain of unknown function (DUF4665)
        7.1    6.6   9.7        4.1    7.4   1.8    2.3  2  DUF2400          Protein of unknown function (DUF2400)
        7.3    7.0  41.7        2.9    8.3  19.2    2.2  2  Fez1             Fez1
        9.8    6.9  28.7        3.5    8.3   6.9    3.5  3  AATF-Che1        Apoptosis antagonizing transcription factor
         10    6.9  35.6       0.68   10.6   5.9    4.6  5  YabA             Initiation control protein YabA


Domain annotation for each model (and alignments):
>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1  18.4   4.6e-05     0.037      33     136 ..      22     161 ..      18     165 .. 0.83
   2 !   10.3   9.9   0.00069      0.57      33     118 ..     174     264 ..     168     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.6e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---S.. CS
                             Nup54  33 dLakRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyalda.. 107
                                       +L+k++   ++e++++ e+ ++++ r++e++ ++++ t++r+++++++ +e   Rl ++++k++  rs++ a+    
  gi|557694999|ref|YP_008798053.1|  22 ELRKKKLEHEEEAQKYYEKRESLHARIREIK-EKNAATLERVAQLRNELAEFRARLDEVTAKINEKRSQKEAILSqq 97 
                                       79999999***********************.9*********************************99988666667 PP

                                       ................................SHHHHHHHHHHHHHHHS...-HHH.HHHHHHH CS
                             Nup54 108 ................................eEeelrarletleaqln...dpaqlkgrvnel 136
                                                                       eE++++ +l++l++ l    +++++  ++ el
  gi|557694999|ref|YP_008798053.1|  98 vaenakgytgqeifrkirdleqrieteilrpeEEKRIYDELRQLNKLLAevqKREGVAEKLREL 161
                                       7778888888888888888888888888888888889887776655554111567778888777 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00069
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.TT-S CS
                             Nup54  33 dLakRvkaQqkevaqhrerlkeisdrleele......qkhqletsvrlekakkrhvelshRllrllrkleil.rsrg 102
                                        L++  k+ ++e++++re +++++d + +l+      ++  le+ ++ + +  +++ l++Rl++l    e + ++r 
  gi|557694999|ref|YP_008798053.1| 174 NLREQIKKKKEEIQAARETIQSVKDLIMQLKpeadeyHNAYLEAKKKAQMCEAEEILLTSRLVELQ---EFVkKRRE 247
                                       689999*************************88886666667888899999999999999988775...54449999 PP

                                       S---SSHHHHHHHHH.H CS
                             Nup54 103 yaldaeEeelrarle.t 118
                                         l+a E  ++++++ +
  gi|557694999|ref|YP_008798053.1| 248 FELRAREYMMKEKIKtK 264
                                       *******9999999933 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   5.4    0.0033       2.7      19      64 ..       5      50 ..       3      51 .. 0.92
   2 ?   14.8   4.0   3.5e-05     0.028      26      71 .]      40      85 ..      39      85 .. 0.88
   3 ?    0.4  15.4       1.1   9.2e+02      24      65 ..     155     196 ..     108     203 .. 0.76
   4 ?    0.0   7.2       1.4   1.2e+03      13      64 ..     186     237 ..     185     293 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0033
                              ZapB 19 titlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64
                                      ++++  +ei + +++ +el +++ e eee ++  e re++++r++ 
  gi|557694999|ref|YP_008798053.1|  5 NVAAIEEEIFQIRAKLAELRKKKLEHEEEAQKYYEKRESLHARIRE 50
                                      6778889*************************************86 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3.5e-05
                              ZapB 26 eieeLkeeneelkeenreleeeneqlkeereawqerlkkLLgklee 71
                                      + e L ++ +e ke+n++  e + ql++e +++++rl+ + +k++e
  gi|557694999|ref|YP_008798053.1| 40 KRESLHARIREIKEKNAATLERVAQLRNELAEFRARLDEVTAKINE 85
                                      5678888889999999999999999999999999999999999987 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.1
                              ZapB  24 qmeieeLkeeneelkeenreleeeneqlkeereawqerlkkL 65 
                                        ++++eL    + l ee+r+l+e++++ kee +a +e ++++
  gi|557694999|ref|YP_008798053.1| 155 AEKLRELNNSAAPLYEEARNLREQIKKKKEEIQAARETIQSV 196
                                       456677777777777777777777777777777777777664 PP

  == domain 4  score: 0.0 bits;  conditional E-value: 1.4
                              ZapB  13 iqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkk 64 
                                       iq+a +ti++ +  i +Lk e  e+ +   e +++ +  ++e   +++rl  
  gi|557694999|ref|YP_008798053.1| 186 IQAARETIQSVKDLIMQLKPEADEYHNAYLEAKKKAQMCEAEEILLTSRLVE 237
                                       899999****************999999999999999999888888888865 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0  18.2   8.8e-05     0.072     163     271 ..       7     113 ..       2     131 .. 0.61
   2 ?    3.9  19.0     0.025        20     150     263 ..     137     248 ..     122     284 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                              Spc7 163 eeldellpeleeekaelee.eleklqeaaeeles..idkeeLeelreelaelkaeieekkkelaelqeqleeleeki 236
                                       + ++e   +++++ ael++ +le+++ea++  e+  + +++++e++e+ a+  + ++++++elae +++l+e+++ki
  gi|557694999|ref|YP_008798053.1|   7 AAIEEEIFQIRAKLAELRKkKLEHEEEAQKYYEKreSLHARIREIKEKNAATLERVAQLRNELAEFRARLDEVTAKI 83 
                                       44555555566666666541455555544444442144667777777777777777777777777777777777777 PP

                              Spc7 237 eelkeqkseleeeiaeaervleeckgwsesevsrl 271
                                       +e ++qk+ +      +++v e+ kg + +e+ r 
  gi|557694999|ref|YP_008798053.1|  84 NEKRSQKEAIL-----SQQVAENAKGYTGQEIFRK 113
                                       55555554443.....5789999999999999874 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.025
                              Spc7 150 gleedkelLek..qeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelae 224
                                       +l++ ++lL++  ++e + e l el++  a l ee+++l+e+ ++    +kee++++re+++++k  i ++k e +e
  gi|557694999|ref|YP_008798053.1| 137 ELRQLNKLLAEvqKREGVAEKLRELNNSAAPLYEEARNLREQIKK----KKEEIQAARETIQSVKDLIMQLKPEADE 209
                                       222222222210022223333344444444444444444443333....4555555555555555555555555555 PP

                              Spc7 225 lqeqleeleekieelkeqkseleeeiaeaervleeckgw 263
                                         +   e ++k +  +++   l +++ e ++++++++++
  gi|557694999|ref|YP_008798053.1| 210 YHNAYLEAKKKAQMCEAEEILLTSRLVELQEFVKKRREF 248
                                       555555555555555555555555555555555555554 PP

>> DUF1298  Protein of unknown function (DUF1298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00043      0.35      12      61 ..      65     114 ..      55     125 .. 0.87
   2 ?   -1.5   0.1       2.7   2.2e+03      18      38 ..     174     194 ..     164     207 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                           DUF1298  12 LpidladPlerlrkakkamdrkKrsleavltylllelllkllpakvaaal 61 
                                       L  +la+   rl ++++++++k+++ ea+l+++++e +  ++++++++++
  gi|557694999|ref|YP_008798053.1|  65 LRNELAEFRARLDEVTAKINEKRSQKEAILSQQVAENAKGYTGQEIFRKI 114
                                       5566678889***************************9999999999887 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.7
                           DUF1298  18 dPlerlrkakkamdrkKrsle 38 
                                       +  e ++k k+ ++++++  +
  gi|557694999|ref|YP_008798053.1| 174 NLREQIKKKKEEIQAARETIQ 194
                                       344444444444444444443 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 ?    5.1   0.4     0.033        27      38      79 ..      44      85 ..      15     123 .. 0.73
   2 ?    5.3   0.1     0.029        24      40      72 ..     132     163 ..     105     179 .. 0.79
   3 ?    8.5   0.7    0.0028       2.3      21      86 ..     138     202 ..     132     205 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.033
                            DUF948 38 lekqvdpilkevedllakvnelledvneklekvdplteavad 79
                                      l  ++++i ++ +++l+ v +l +++ e  +++d++t+++++
  gi|557694999|ref|YP_008798053.1| 44 LHARIREIKEKNAATLERVAQLRNELAEFRARLDEVTAKINE 85
                                      555556666666666666666666666666666666665543 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.029
                            DUF948  40 kqvdpilkevedllakvnelledvneklekvdp 72 
                                       k++   l+++++lla+v++  e+v ekl ++++
  gi|557694999|ref|YP_008798053.1| 132 KRIYDELRQLNKLLAEVQK-REGVAEKLRELNN 163
                                       5666668899999999999.9999999999986 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0028
                            DUF948  21 llklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlgesvse 86 
                                       l++l+k+l e++++ e++ ++++++ + ++ l +++++l e++++k e++++  e ++ + + + +
  gi|557694999|ref|YP_008798053.1| 138 LRQLNKLLAEVQKR-EGVAEKLRELNNSAAPLYEEARNLREQIKKKKEEIQAARETIQSVKDLIMQ 202
                                       55667777777665.666788888888888888888888888888888888888888877766655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.6      0.15   1.2e+02      76     122 ..       7      53 ..       1      55 [. 0.62
   2 ?    6.4   1.1      0.01       8.5      80     112 ..      53      85 ..      43     131 .. 0.51
   3 ?    9.2   2.1    0.0015       1.2      49     114 ..     140     204 ..     129     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.15
                           DUF1664  76 deqkeiskeikeevtevredlseigedvesvkeavegleskleriee 122
                                        + +e + +i+++++e+r++  e +e+ ++  e  e+l +++++i+e
  gi|557694999|ref|YP_008798053.1|   7 AAIEEEIFQIRAKLAELRKKKLEHEEEAQKYYEKRESLHARIREIKE 53 
                                       44455555667777777777667777777777777777777777765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.01
                           DUF1664  80 eiskeikeevtevredlseigedvesvkeaveg 112
                                       e  +++ e v+++r++l+e++  +++v + +++
  gi|557694999|ref|YP_008798053.1|  53 EKNAATLERVAQLRNELAEFRARLDEVTAKINE 85 
                                       444444444444444444444444444333332 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0015
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       ql+++ ++++  ++  ++++ +++++     e +++++e++++ +e++++ +e ++svk+++++l+
  gi|557694999|ref|YP_008798053.1| 140 QLNKLLAEVQ-KREGVAEKLRELNNSAAPLYEEARNLREQIKKKKEEIQAARETIQSVKDLIMQLK 204
                                       3344444433.2455788888888888888888889999999999999999999999999888886 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.3     0.065        53      15      48 ..       2      35 ..       1      45 [. 0.74
   2 ?    8.6   6.6    0.0021       1.7       4      83 ..      47     122 ..      44     151 .. 0.67
   3 ?    6.2   7.2     0.012       9.7      21     101 ..     120     202 ..      95     211 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.065
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II 15 vleqlaplsqnlentkeklseinrsveetnekvk 48
                                      ++e +a++++++ ++++kl e++++  e +e+++
  gi|557694999|ref|YP_008798053.1|  2 TEENVAAIEEEIFQIRAKLAELRKKKLEHEEEAQ 35
                                      5778888899999999999988888555555555 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0021
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXX--TTTTTGGGHHHHH CS
                        Laminin_II   4 laaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankair.dArrsvkkLeklapqLldklkelk 79 
                                        ++e++e+ +++le +a+l ++l + ++ l e+ ++   +nek +++  ++  ++ ++ k    + ++++ k++ l+
  gi|557694999|ref|YP_008798053.1|  47 RIREIKEKNAATLERVAQLRNELAEFRARLDEVTAK---INEKRSQKEAILSqQVAENAKGY--TGQEIFRKIRDLE 118
                                       689*********************************...66666555444321233333333..2345555555555 PP

                                       HHHH CS
                        Laminin_II  80 qlee 83 
                                       q+ e
  gi|557694999|ref|YP_008798053.1| 119 QRIE 122
                                       5543 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.012
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHH....HHHHHHHH...HHHHHH CS
                        Laminin_II  21 plsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklk....elkqleeassslsdnis 93 
                                        +++++ +  e+ ++i +++++ n+++ + +k    A ++ ++L++ a  L +  +    ++k+++e+ ++  + i+
  gi|557694999|ref|YP_008798053.1| 120 RIETEILRP-EEEKRIYDELRQLNKLLAEVQKREGVA-EKLRELNNSAAPLYEEARnlreQIKKKKEEIQAARETIQ 194
                                       333333333.444677777777777777655554433.345555555555554433000126666666666888899 PP

                                       HHHHHHHH CS
                        Laminin_II  94 eikelIaq 101
                                        +k lI q
  gi|557694999|ref|YP_008798053.1| 195 SVKDLIMQ 202
                                       99998877 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   2.0    0.0091       7.4      98     158 ..      39      99 ..      15     123 .. 0.85
   2 ?    8.0   2.9    0.0028       2.3      95     171 ..     125     204 ..      98     210 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0091
                      Bacillus_HBL  98 kdkaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsg 158
                                       +++++l +++ +++e+     + v ql +eL +++ +l++ +++ +++ ++ ++il+ + +
  gi|557694999|ref|YP_008798053.1|  39 EKRESLHARIREIKEKNAATLERVAQLRNELAEFRARLDEVTAKINEKRSQKEAILSQQVA 99 
                                       5778888888888888777788888899999999999999999999999999999987755 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0028
                      Bacillus_HBL  95 v.dkkdkaellellekLqeeiqqnq..kevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneie 168
                                       +   ++ + + + l +L++ + + q  + v +++ eL++ +  l+++ +n+ +++++ ++ +++   +i+ ++  i 
  gi|557694999|ref|YP_008798053.1| 125 IlRPEEEKRIYDELRQLNKLLAEVQkrEGVAEKLRELNNSAAPLYEEARNLREQIKKKKEEIQAARETIQSVKDLIM 201
                                       25556666677777777776654441145888899999999999***********9999999999999999999998 PP

                      Bacillus_HBL 169 dlq 171
                                       +l+
  gi|557694999|ref|YP_008798053.1| 202 QLK 204
                                       876 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0  33.9   3.7e-06     0.003      76     246 ..      11     189 ..       1     198 [. 0.83
   2 ?   -2.3   8.4       1.3     1e+03      11      85 ..     196     266 ..     188     286 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.7e-06
                               MAD  76 Elarlkkknlealnkkekekesklaearevisalknelaelkrqiekqelelsekeseleelqerldllkkklsele 152
                                       E+  + + +l++l kk+ e+e++ ++  e  ++l+ +++e k++   +   + + ++el e++ rld+  +k++e  
  gi|557694999|ref|YP_008798053.1|  11 EEIFQIRAKLAELRKKKLEHEEEAQKYYEKRESLHARIREIKEKNAATLERVAQLRNELAEFRARLDEVTAKINEKR 87 
                                       3333455677889999999******************************************************9987 PP

                               MAD 153 qli.....qqlekkqkelaeae..qrikeLefeiqsqeddslivknskselaripelekelerlreenkklnelken 222
                                        ++     qq  ++ k  + +e   +i++Le++i+      ++ k + +el ++ +l +e+++ +   +kl+el++ 
  gi|557694999|ref|YP_008798053.1|  88 SQKeailsQQVAENAKGYTGQEifRKIRDLEQRIETEILRPEEEKRIYDELRQLNKLLAEVQKREGVAEKLRELNNS 164
                                       6664555555544444444444337**************************************************** PP

                               MAD 223 kelLkEevedlkkkLer.eEkaree 246
                                          L Ee+ +l++++++ +E++++ 
  gi|557694999|ref|YP_008798053.1| 165 AAPLYEEARNLREQIKKkKEEIQAA 189
                                       *************997526777775 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
                               MAD  11 leqlknelkqkelehkrarielekkasalkrqleeesdrnqelqkrikllekre.eekeealreqiElarlkkknl 85 
                                       + +l  +lk ++ e+++a +e++kka+  + +      r  elq+ +k+ ++ e  ++e  ++e+i  +      +
  gi|557694999|ref|YP_008798053.1| 196 VKDLIMQLKPEADEYHNAYLEAKKKAQMCEAEEILLTSRLVELQEFVKKRREFElRAREYMMKEKIKTKA-----M 266
                                       4556667777788888888888888777666666667888888888888888887777777777776544.....2 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 ?   13.1  11.1   9.2e-05     0.075      24      90 ..      29      97 ..      10     122 .. 0.86
   2 ?    1.1  16.9      0.48   3.9e+02      17     112 ..     140     225 ..     124     268 .. 0.46
   3 ?   -0.7   3.8       1.7   1.4e+03     106     133 ..     219     246 ..     209     296 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.2e-05
                             Mod_r 24 tl.pevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldell.qk 90
                                      +  +e +++ e++e+l a ++++ ekn +  +++ +lr+el+e +  l+e+ ++ +ek ++ +++l q+
  gi|557694999|ref|YP_008798053.1| 29 EHeEEAQKYYEKRESLHARIREIKEKNAATLERVAQLRNELAEFRARLDEVTAKINEKRSQKEAILsQQ 97
                                      343679********************************************************9999444 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.48
                             Mod_r  17 klealvktlpevkqlkeekeellaeneslaeknlslepeleelrselqekleelkelekefeekeqeldellqkfsp 93 
                                       +l++l+ ++++ + + e++ el ++   l e+  +l+++++++++e+q+++e+++++++   +++ e de+ + + +
  gi|557694999|ref|YP_008798053.1| 140 QLNKLLAEVQKREGVAEKLRELNNSAAPLYEEARNLREQIKKKKEEIQAARETIQSVKDLIMQLKPEADEYHNAYLE 216
                                       33333333333333333333333333333344444444444444444444444444444444444444443333322 PP

                             Mod_r  94 dallarLqtavaeaeeeSe 112
                                       +          ++  +++e
  gi|557694999|ref|YP_008798053.1| 217 A----------KKKAQMCE 225
                                       2..........22223333 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.7
                             Mod_r 106 eaeeeSealaeefl.egeieldeFvkefk 133
                                       +  +++ea +e +l +   el+eFvk+ +
  gi|557694999|ref|YP_008798053.1| 219 KKAQMCEA-EEILLtSRLVELQEFVKKRR 246
                                       44455555.33333233355555555433 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  14.1    0.0002      0.16      73     154 ..       3      84 ..       1     102 [. 0.85
   2 ?    1.4  18.8      0.39   3.2e+02      81     189 ..     136     236 ..      82     244 .. 0.49
   3 ?   -0.6   1.7       1.6   1.3e+03      77     110 ..     225     258 ..     201     279 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0002
                             ATG16  73 sakiqsleqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrek 149
                                       ++++++ e++++q+r+ lael k++ e+++  ++  e+ + l ++++e +e+ a+  +++a+l+ +l++ +++l e 
  gi|557694999|ref|YP_008798053.1|   3 EENVAAIEEEIFQIRAKLAELRKKKLEHEEEAQKYYEKRESLHARIREIKEKNAATLERVAQLRNELAEFRARLDEV 79 
                                       6789999*********************9999999999999999999999999999999999999998888888887 PP

                             ATG16 150 eklvq 154
                                       ++ ++
  gi|557694999|ref|YP_008798053.1|  80 TAKIN 84 
                                       66554 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.39
                             ATG16  81 qklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlq 157
                                       ++l ql++ lae++k+ g  a++l+eln++ + l e++++ +e++++ ++e++a        +e+++  + l+ +l+
  gi|557694999|ref|YP_008798053.1| 136 DELRQLNKLLAEVQKREG-VAEKLRELNNSAAPLYEEARNLREQIKKKKEEIQAA-------RETIQSVKDLIMQLK 204
                                       333444444444443332.233333333333333333333333333333333332.......233333334444555 PP

                             ATG16 158 DElsaLqlqlnqaEeklrklekENkeLveRWm 189
                                        E +  + ++  a +k + +e+E   L +R++
  gi|557694999|ref|YP_008798053.1| 205 PEADEYHNAYLEAKKKAQMCEAEEILLTSRLV 236
                                       55555555555555555555555555555555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1.6
                             ATG16  77 qsleqklaqlreelaelyksrgelaqrllelnee 110
                                       ++ e +l++   el+e  k+r e++ r +e + +
  gi|557694999|ref|YP_008798053.1| 225 EAEEILLTSRLVELQEFVKKRREFELRAREYMMK 258
                                       3333333333346666666666666666654443 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 ?    9.9  16.6   0.00053      0.44      57     153 ..       7     100 ..       1     109 [. 0.86
   2 ?    4.9  26.4     0.018        15      28     184 ..     114     271 ..     105     281 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00053
                               GAS  57 krlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaai 133
                                         ++e++ + +++++eLrk+  ++e++ q+     ++ ++l   ++++k+++    +r++++ +e  e++++ +++ 
  gi|557694999|ref|YP_008798053.1|   7 AAIEEEIFQIRAKLAELRKKKLEHEEEAQK---YYEKRESLHARIREIKEKNAATLERVAQLRNELAEFRARLDEVT 80 
                                       457788889999999999999888886665...556667788999999***************************** PP

                               GAS 134 qevqqktglknllLekklka 153
                                        ++ +k + k+ +L +++++
  gi|557694999|ref|YP_008798053.1|  81 AKINEKRSQKEAILSQQVAE 100
                                       ****************9976 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.018
                               GAS  28 IkslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdl 104
                                       I+ l + ie+   + e+ ++  +e+ q nk l  +++k e   e+Lr+  +      ++ +nl++++k+ ++e+++ 
  gi|557694999|ref|YP_008798053.1| 114 IRDLEQRIETEILRPEEEKRIYDELRQLNK-LLAEVQKREGVAEKLRELNNSAAPLYEEARNLREQIKKKKEEIQAA 189
                                       666666666666666666666666666665.66679999999*********************************** PP

                               GAS 105 kwehevleqrfekvekerdelykkfeaaiqevqqktglknllLekklkalqeelEkke...aqleevlaaanldpaa 178
                                       ++  +++++ + +++ e de ++ + +a ++  q ++ +++lL  +l +lqe + k+     + +e++ + +++++a
  gi|557694999|ref|YP_008798053.1| 190 RETIQSVKDLIMQLKPEADEYHNAYLEAKKK-AQMCEAEEILLTSRLVELQEFVKKRRefeLRAREYMMKEKIKTKA 265
                                       **************************97655.678*******************9985333566899*******999 PP

                               GAS 179 lsavse 184
                                       ++++s+
  gi|557694999|ref|YP_008798053.1| 266 MEKLSK 271
                                       999887 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 ?    3.5  18.9     0.039        32      23     111 ..      12      90 ..       3     145 .. 0.49
   2 ?    6.9  15.9    0.0036         3      43     138 ..     132     228 ..     114     277 .. 0.63

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.039
                             Atg14  23 rlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeiee 99 
                                        +++ r +la l+++k + +++ +k+ e++e          +++a+++e+k + a + er+++l+  l + +++++e
  gi|557694999|ref|YP_008798053.1|  12 EIFQIRAKLAELRKKKLEHEEEAQKYYEKRE----------SLHARIREIKEKNAATLERVAQLRNELAEFRARLDE 78 
                                       4555555666666666666666666666655..........445555555555555555555555555555555555 PP

                             Atg14 100 kkkklaklsdkl 111
                                         +k+ +++++ 
  gi|557694999|ref|YP_008798053.1|  79 VTAKINEKRSQK 90 
                                       555554444442 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0036
                             Atg14  43 kkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklkkRrsdle 119
                                       k+i ++l + ++   + +k +  ++kl+el +  a l e+ ++l++++++ k+ei+++++++++ +d + + + +++
  gi|557694999|ref|YP_008798053.1| 132 KRIYDELRQLNKLLAEVQKREGVAEKLRELNNSAAPLYEEARNLREQIKKKKEEIQAARETIQSVKDLIMQLKPEAD 208
                                       33333333333333333455556788888888888888899999999999999999999999999998887666654 PP

                             Atg14 120 s.lqneleerrkkqiaklqd 138
                                         ++  le+++k+q+ +  +
  gi|557694999|ref|YP_008798053.1| 209 EyHNAYLEAKKKAQMCEAEE 228
                                       41445566666666665544 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   5.6   0.00061      0.49      51     130 ..      10      88 ..       2      92 .. 0.80
   2 ?    6.0   6.9     0.015        13      36     126 ..     113     208 ..     106     213 .. 0.70
   3 ?    4.6   4.9     0.043        35      35      87 ..     170     222 ..     159     271 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00061
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  51 tkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirvLqnvlesneqkiqkLeqdidq 127
                                       ++e++++  ++ +  ++k ++++ + + + + +++l  +i ++ke+  a+ +++ +L+n l + + ++ +   +i++
  gi|557694999|ref|YP_008798053.1|  10 EEEIFQIRAKLAELRKKKLEHEE-EAQKYYEKRESLHARIREIKEKNAATLERVAQLRNELAEFRARLDEVTAKINE 85 
                                       45566666666666666666666.46777777899999************************************999 PP

                                       HHH CS
                         Fib_alpha 128 ker 130
                                       k++
  gi|557694999|ref|YP_008798053.1|  86 KRS 88 
                                       875 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                                       HHCCCCCCCCCC...CCHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHHH CS
                         Fib_alpha  36 dlekleneleei...snstkeaeelvkeikdslrekqkskkdn..dnvikksskeleeeilrlketidaqesnirvL 107
                                       ++++le+++e+     +++k +++  +++++ l+e qk +      + +++s+  l ee  +l+e+i+++ ++i++ 
  gi|557694999|ref|YP_008798053.1| 113 KIRDLEQRIETEilrPEEEKRIYDELRQLNKLLAEVQKREGVAekLRELNNSAAPLYEEARNLREQIKKKKEEIQAA 189
                                       56666666655311134566677777777777777777765432256678888888889999999999999999999 PP

                                       HHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 108 qnvlesneqkiqkLeqdid 126
                                       +++++s +  i +L+ + d
  gi|557694999|ref|YP_008798053.1| 190 RETIQSVKDLIMQLKPEAD 208
                                       9999999999999987665 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.043
                                       HHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  35 kdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskele 87 
                                       ++ ++l++++++ +++ + a+e+++++kd + + + ++++  n++ + +k+ +
  gi|557694999|ref|YP_008798053.1| 170 EEARNLREQIKKKKEEIQAARETIQSVKDLIMQLKPEADEYHNAYLEAKKKAQ 222
                                       44556666666666666666666666666666666666666666655555544 PP

>> DUF695  Family of unknown function (DUF695)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.2      0.62     5e+02      35      72 ..      13      50 ..       3      64 .. 0.78
   2 ?    2.6   0.2      0.18   1.5e+02      10      70 ..      65     125 ..      60     135 .. 0.70
   3 ?    6.2   0.1     0.013        11      55      98 ..     164     207 ..     160     232 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.62
                            DUF695 35 vvvvrveykapdenGlpseeeydkLekiedallealka 72
                                      ++++r ++ + + + l +eee++k +++ + l +++++
  gi|557694999|ref|YP_008798053.1| 13 IFQIRAKLAELRKKKLEHEEEAQKYYEKRESLHARIRE 50
                                      78888899999999999999999999999999888853 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.18
                            DUF695  10 lddkpaiirvnldlaefapsekykh.vvvvrveykapdenGlpseeeydkLekiedalleal 70 
                                       l++  a +r++ld   ++ +ek ++    ++ ++ + +++G  ++e + k+ + e+++++ +
  gi|557694999|ref|YP_008798053.1|  65 LRNELAEFRARLDEVTAKINEKRSQkEAILSQQVAE-NAKGYTGQEIFRKIRDLEQRIETEI 125
                                       556666677777666555555555534444445555.689******************9988 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.013
                            DUF695  55 eydkLekiedallealkakpnalyvGritsngtrdlyfytkdte 98 
                                       +++ L++ ++ l e++k+k++ + ++r t + + dl++ +k + 
  gi|557694999|ref|YP_008798053.1| 164 SAAPLYEEARNLREQIKKKKEEIQAARETIQSVKDLIMQLKPEA 207
                                       56779999999**************************9888765 PP

>> DUF2730  Protein of unknown function (DUF2730)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.0    0.0014       1.1      18     100 ..      13      97 ..       5      99 .. 0.79
   2 ?    2.1   1.7      0.24     2e+02      36      91 ..     142     198 ..     133     206 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                           DUF2730  18 vavilllldskYakredleklaekveendkrlte..letkvenLPtakdlekLkllladlrgelkaleaevrqlshq 92 
                                       ++ i+++l++   k+ ++e+ a+k  e+++ l++   e+k +n  t + +++L+ +la+ r++l++++a++++ + q
  gi|557694999|ref|YP_008798053.1|  13 IFQIRAKLAELRKKKLEHEEEAQKYYEKRESLHAriREIKEKNAATLERVAQLRNELAEFRARLDEVTAKINEKRSQ 89 
                                       5567778887778888888888887777777776224777789999**************************99999 PP

                           DUF2730  93 vdLLLene 100
                                        + +L ++
  gi|557694999|ref|YP_008798053.1|  90 KEAILSQQ 97 
                                       88888776 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.24
                           DUF2730  36 eklaekveend...krlteletkvenLPtakdlekLkllladlrgelkaleaevrqlsh 91 
                                       +kl  +v++ +   ++l el+   +  P  ++  +L+ ++++ + e++a+++++++++ 
  gi|557694999|ref|YP_008798053.1| 142 NKLLAEVQKREgvaEKLRELN--NSAAPLYEEARNLREQIKKKKEEIQAARETIQSVKD 198
                                       444444444441113344333..345577788888999999999999999998888875 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 ?    4.8  23.2     0.034        28       3     113 ..      13     122 ..      11     147 .. 0.84
   2 ?    4.8  13.8     0.034        28      11      94 ..     142     221 ..     138     247 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.034
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       + + ++++++l+++k e+e+++qk+ e+ e+ +++ +e ++k +  l   a+  +el+++r++l+e++a+i+e +++
  gi|557694999|ref|YP_008798053.1|  13 IFQIRAKLAELRKKKLEHEEEAQKYYEKRESLHARIREIKEKNAATLERVAQLRNELAEFRARLDEVTAKINEKRSQ 89 
                                       55778999*******************************************************************99 PP

                        TPR_MLP1_2  80 aesakaeleeseesweeqkeelekelselekrie 113
                                        e+  ++  ++ ++   + +e+ +++++le+rie
  gi|557694999|ref|YP_008798053.1|  90 KEAILSQQVAENAK-GYTGQEIFRKIRDLEQRIE 122
                                       99876664444433.3344445556777777765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.034
                        TPR_MLP1_2  11 kslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesakael 87 
                                       ++l++e ++ e  ++kl+e  ++ a +++ea +   +++ k++   +e+qa+re ++++k+ i +lk ea++ +++ 
  gi|557694999|ref|YP_008798053.1| 142 NKLLAEVQKREGVAEKLRELNNSAAPLYEEARN-LREQIKKKK---EEIQAARETIQSVKDLIMQLKPEADEYHNAY 214
                                       556666666666666666666666666666666.333333333...3556677777777777777777777777766 PP

                        TPR_MLP1_2  88 eeseesw 94 
                                        e++++ 
  gi|557694999|ref|YP_008798053.1| 215 LEAKKKA 221
                                       6666554 PP

>> DUF4665  Domain of unknown function (DUF4665)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   2.1     0.012        10      43      92 ..       2      51 ..       1      59 [. 0.82
   2 ?   12.4   1.6   0.00023      0.18      35      95 ..      50     110 ..      46     114 .. 0.88
   3 ?    3.9   2.5       0.1        84      47      97 ..     138     194 ..     130     203 .. 0.70
   4 ?   -0.8   0.6         3   2.4e+03      23      30 ..     257     264 ..     213     283 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.012
                           DUF4665 43 kkekvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnvdea 92
                                      ++e v+ +++++ +i+++l++l kk+  ++++ +k  +k+e  ++ + e 
  gi|557694999|ref|YP_008798053.1|  2 TEENVAAIEEEIFQIRAKLAELRKKKLEHEEEAQKYYEKRESLHARIREI 51
                                      6899*******************988888888888888888777777665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00023
                           DUF4665  35 nLKkinavkkekvenldkalvdiqkdlkslskklkletkkkekvkkkkekekvnvdeaael 95 
                                       ++K+ na + e+v++l ++l++ ++ l +++ k++ +  +ke + +++  e+++    +e 
  gi|557694999|ref|YP_008798053.1|  50 EIKEKNAATLERVAQLRNELAEFRARLDEVTAKINEKRSQKEAILSQQVAENAKGYTGQEI 110
                                       5688899999***********************************9999999887766665 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.1
                           DUF4665  47 venldkalvdiqk......dlkslskklkletkkkekvkkkkekekvnvdeaaella 97 
                                        ++l+k l+++qk      +l++l +++++  ++ ++++++ +k+k+++++a e+++
  gi|557694999|ref|YP_008798053.1| 138 LRQLNKLLAEVQKregvaeKLRELNNSAAPLYEEARNLREQIKKKKEEIQAARETIQ 194
                                       567777777777533333356777777777777777888888888888888888776 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 3
                           DUF4665  23 lKaKaKAk 30 
                                       +K K K+k
  gi|557694999|ref|YP_008798053.1| 257 MKEKIKTK 264
                                       23333333 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   1.3     0.068        56      84     135 ..      34      85 ..      23     105 .. 0.69
   2 ?    7.4   1.8     0.005       4.1      32     136 ..     109     218 ..     102     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.068
                           DUF2400  84 lkelleksgsLeeaflkaeeeeeeleealeafreaflekekrtrkleflips 135
                                        ++++ek +sL++ + + +e+++ + e+++++r++++e + r  ++++ i +
  gi|557694999|ref|YP_008798053.1|  34 AQKYYEKRESLHARIREIKEKNAATLERVAQLRNELAEFRARLDEVTAKINE 85 
                                       688999999***9999988888888888888888888844443333333332 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.005
                           DUF2400  32 qiikkleellelmdkspydfvleeeeekdlkelekf....kyRffnsedllallkalkelleksgsLeeaflkaeee 104
                                        i++k++ l ++++++  +   e++  ++l++l+k+    + R   +e+l +l ++   l+e+  +L+e ++k++ee
  gi|557694999|ref|YP_008798053.1| 109 EIFRKIRDLEQRIETEILRPEEEKRIYDELRQLNKLlaevQKREGVAEKLRELNNSAAPLYEEARNLREQIKKKKEE 185
                                       577777777777777666655555555555554443233379999999999999*******************9999 PP

                           DUF2400 105 eeeleealeafreafle.kekrtrkleflipsp 136
                                        +  +e+++++++ +++ k+++++  ++ +  +
  gi|557694999|ref|YP_008798053.1| 186 IQAARETIQSVKDLIMQlKPEADEYHNAYLEAK 218
                                       9999*********99996555544444444444 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  19.2    0.0036       2.9      26     163 ..       6     140 ..       2     150 .. 0.72
   2 ?    2.8  16.7      0.17   1.4e+02      18     124 ..     157     263 ..     137     289 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0036
                              Fez1  26 vtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelree 102
                                       v++  +ei++++a+l elr+k  e+eee++++ e++e+ ++ + +++++ + + +++  lr+++ ++ + l e+  +
  gi|557694999|ref|YP_008798053.1|   6 VAAIEEEIFQIRAKLAELRKKKLEHEEEAQKYYEKRESLHARIREIKEKNAATLERVAQLRNELAEFRARLDEVTAK 82 
                                       55556788999999999988888888888888888888888888888888888888888888888888888888887 PP

                              Fez1 103 lselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeerqkkeeqassFeqERr 163
                                       ++e+  +++ea+l+++   a++++  + +e  r++  l++++++e  + ee++  +++ R+
  gi|557694999|ref|YP_008798053.1|  83 INEKR-SQKEAILSQQV--AENAKGYTGQEIFRKIRDLEQRIETEILRPEEEKRIYDELRQ 140
                                       77744.33444333333..233334566777888888888988888888888888887776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.17
                              Fez1  18 QLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekveklee 94 
                                        L++  +  +   +e  +l+ q++  ++++++  e+i+++++ + + + e ++++n   ++k++a++ + +   l +
  gi|557694999|ref|YP_008798053.1| 157 KLRELNNSAAPLYEEARNLREQIKKKKEEIQAARETIQSVKDLIMQLKPEADEYHNAYLEAKKKAQMCEAEEILLTS 233
                                       56666666667777777777777777777777777777777777777777777777766666666666666666666 PP

                              Fez1  95 elkelreelselsleeeeaalesdeakaqr 124
                                        l el+e +++  + e +a++ +++ k + 
  gi|557694999|ref|YP_008798053.1| 234 RLVELQEFVKKRREFELRAREYMMKEKIKT 263
                                       666666655553333333322222222222 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4      0.22   1.8e+02      53      83 ..       4      35 ..       2      51 .. 0.46
   2 ?    8.3   6.9    0.0043       3.5      33     125 ..      26     121 ..      14     126 .. 0.60
   3 ?   -0.9  13.3       2.9   2.4e+03      46     113 ..     149     279 ..     130     299 .] 0.60

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.22
                         AATF-Che1 53 ealeeaekalkklleslleLreelleqne.ik 83
                                      e+++++e+++ ++  +l eLr++ le +e  +
  gi|557694999|ref|YP_008798053.1|  4 ENVAAIEEEIFQIRAKLAELRKKKLEHEEeAQ 35
                                      44445555555555555555555444443222 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0043
                         AATF-Che1  33 nqLpqpetlkeflesseefeealeeaekalkklleslleLreelleqne.ikklaeskeeeekkkskrkrkkk.... 104
                                       ++L ++e+++++ e+ e+++++++e++++  ++le + +Lr+el e    + +         ++k ++kr +k    
  gi|557694999|ref|YP_008798053.1|  26 KKLEHEEEAQKYYEKRESLHARIREIKEKNAATLERVAQLRNELAEFRArLDE--------VTAKINEKRSQKeail 94 
                                       57888999999999999999999999999999999999999999332222222........2222222222111111 PP

                         AATF-Che1 105 ......kkeetsleelwkeleklekal 125
                                             + +  + +e+ +++++le+++
  gi|557694999|ref|YP_008798053.1|  95 sqqvaeNAKGYTGQEIFRKIRDLEQRI 121
                                       111111222233344666666666655 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.9
                         AATF-Che1  46 esseefeealeeaekalkklleslleLreelleqne.ikkla................................... 86 
                                       ++ e ++e+l+e+ +++  l+e+  +Lre++ +++e i++++                                   
  gi|557694999|ref|YP_008798053.1| 149 QKREGVAEKLRELNNSAAPLYEEARNLREQIKKKKEeIQAARetiqsvkdlimqlkpeadeyhnayleakkkaqmce 225
                                       34677888888888888888888888888885555555544477777777777776666666655555555555555 PP

                         AATF-Che1  87 ...........................eskeeeekkkskrkrkkkkkeetslee 113
                                                                  ++   +ek k+k+ +k +k e+ s+ee
  gi|557694999|ref|YP_008798053.1| 226 aeeilltsrlvelqefvkkrrefelraREYMMKEKIKTKAMEKLSKGEKLSFEE 279
                                       555555555555555555555544444444444445555555555555555555 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.5       0.1        82       9      44 ..       5      40 ..       1      47 [. 0.65
   2 ?    9.7   4.6    0.0016       1.3      15      65 ..      39      89 ..      32     106 .. 0.72
   3 ?    3.4   0.8      0.15   1.2e+02      20      68 ..     110     160 ..     105     170 .. 0.47
   4 ?   10.6   5.9   0.00084      0.68       3      76 ..     131     203 ..     129     211 .. 0.87
   5 ?   -1.0   3.0       3.4   2.8e+03      16      53 ..     206     256 ..     193     288 .. 0.45

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.1
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA  9 kleeleeqleelleeleelkeelaelleenaeLele 44
                                      +++++ee++ ++ ++l+el+++  e  ee ++    
  gi|557694999|ref|YP_008798053.1|  5 NVAAIEEEIFQIRAKLAELRKKKLEHEEEAQKYYEK 40
                                      567777777777777777777777777776665444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0016
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.....XXXXXXXXXXXXX CS
                              YabA 15 eqleelleeleelkeelaelleenaeLeleneklrerl.....eeeekkekekkke 65
                                      e+ e+l+++++e+ke+ a++le+ a+L+ e  ++r rl     +      +ek+++
  gi|557694999|ref|YP_008798053.1| 39 EKRESLHARIREIKEKNAATLERVAQLRNELAEFRARLdevtaK-----INEKRSQ 89
                                      67789999******************************555431.....2222221 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXX CS
                              YabA  20 lleeleelkeelaell...eenaeLeleneklrerleeeekkekekkkelse 68 
                                       + +++++l++++++ +   ee++++  e ++l ++l+ e +k++   ++l+e
  gi|557694999|ref|YP_008798053.1| 110 IFRKIRDLEQRIETEIlrpEEEKRIYDELRQLNKLLA-EVQKREGVAEKLRE 160
                                       4445555555554433233555555566666666552.33333333334444 PP

  == domain 4  score: 10.6 bits;  conditional E-value: 0.00084
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   3 kkelfdkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLarl 76 
                                       +k ++d+l++l++ l+e+++  e + e+l el +  a L  e ++lre++++++++ ++ ++++++ k+ + +l
  gi|557694999|ref|YP_008798053.1| 131 EKRIYDELRQLNKLLAEVQK-REGVAEKLRELNNSAAPLYEEARNLREQIKKKKEEIQAARETIQSVKDLIMQL 203
                                       6789*******999998766.58899************************999998888888888888877766 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 3.4
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.............X CS
                              YabA  16 qleelleeleelkeelaelleenaeLeleneklrerl.............e 53 
                                       + +e ++   e k++ + +  e+  L+    +l+e +              
  gi|557694999|ref|YP_008798053.1| 206 EADEYHNAYLEAKKKAQMCEAEEILLTSRLVELQEFVkkrrefelrareyM 256
                                       555555555555555555555554454444444444433333333332221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3007  (0.167717); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                       143  (0.0079759); 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):              22  [number of targets reported over threshold]
# CPU time: 1.35u 0.34s 00:00:01.69 Elapsed: 00:00:00.51
# Mc/sec: 1759.46
//
Query:       gi|557695000|ref|YP_008798054.1|  [L=256]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-52  178.8   0.0    1.7e-52  178.6   0.0    1.0  1  ATP_bind_1   Conserved hypothetical ATP binding protein
     0.0033   17.8   0.0     0.0045   17.4   0.0    1.3  1  AAA_16       AAA ATPase domain
     0.0064   16.1   0.0        1.5    8.4   0.0    2.2  2  SRP54        SRP54-type protein, GTPase domain
     0.0066   16.5   0.1      0.065   13.3   0.1    2.1  1  MMR_HSR1     50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.085   13.1   0.0    2.2  2  AAA_22       AAA domain
       0.02   14.7   0.0        1.9    8.2   0.0    2.3  2  CLP1_P       mRNA cleavage and polyadenylation factor CLP1 P-
      0.024   13.6   0.1      0.088   11.8   0.0    1.9  3  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
      0.061   12.5   0.0      0.089   12.0   0.0    1.4  1  ArsA_ATPase  Anion-transporting ATPase
      0.068   13.7   0.0       0.11   13.0   0.0    1.4  1  AAA_18       AAA domain
        0.1   12.5   0.0        3.2    7.6   0.0    2.9  3  RsgA_GTPase  RsgA GTPase
        0.1   12.3   0.1       0.26   11.0   0.0    1.7  2  AAA_30       AAA domain
       0.11   12.4   0.1       0.26   11.2   0.1    1.9  1  NACHT        NACHT domain
       0.13   12.0   0.0       0.23   11.2   0.0    1.4  1  AAA_24       AAA domain
       0.16   12.5   0.0       0.22   12.0   0.0    1.5  1  ABC_tran     ABC transporter


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 !  178.6   0.0   1.3e-55   1.7e-52       1     238 [.       9     247 ..       9     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: 178.6 bits;  conditional E-value: 1.3e-55
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflre 77 
                                       vvG+aGsGK++++g +se+l++ ++s a+vNLDPAa +lpY+++vd+re++++e +m   +lgpngal+ ++  ++ 
  gi|557695000|ref|YP_008798054.1|   9 VVGTAGSGKSSLTGVFSEWLRDHEQSTATVNLDPAALSLPYDPDVDVREFVDYERIMSTRNLGPNGALIASVREVAR 85 
                                       89*************************************************************************** PP

                        ATP_bind_1  78 sldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlr 154
                                       ++d+++   e+ ++d+ll+DtPGQ+elf +++++++i ++++ +++   ++L+Ds +++ p ++  +l++++s++l+
  gi|557695000|ref|YP_008798054.1|  86 NIDEIAALAEETNADWLLVDTPGQLELFAFRKEGRIIARKIS-DGRKLLLFLLDSVICAHPRNYAASLFLSVSTILS 161
                                       ******99988899****************************.8********************************* PP

                        ATP_bind_1 155 lelPhvvvlnkfDllkek.lekeleffedvealslllekee.ekykklaeaiaelleefalvlrflplssekeesie 229
                                       l+lP v+vl+k+D +  + l + + + e  e++       + e + +l ++i++++ e +  + ++ +s+++ e+++
  gi|557695000|ref|YP_008798054.1| 162 LGLPAVNVLTKTDAVPPRnLARIFGWHESEESFAVSSSGSMnELQMTLSREIVQTVWEISNSIPLVAVSAKTYEGFT 238
                                       **************99998888999999888888877776679999******************************* PP

                        ATP_bind_1 230 dllslidea 238
                                       +l++ +  +
  gi|557695000|ref|YP_008798054.1| 239 ELYANLTRI 247
                                       **9887766 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   0.0   3.5e-06    0.0045      23      77 ..       3      57 ..       1     140 [. 0.65

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.5e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqala 77
                                      r+++++++G +G+GKssl   + + l++++  +++ + d    ++py++ +++ +
  gi|557695000|ref|YP_008798054.1|  3 RTRVLFVVGTAGSGKSSLTGVFSEWLRDHEQSTATVNLDPAALSLPYDPDVDVRE 57
                                      6799***************777754444445556666666666788866555553 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0012       1.5       2      38 ..       5      41 ..       4      44 .. 0.91
   2 !    5.9   0.0     0.007         9      74      96 ..      89     111 ..      76     175 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      +v+ +vG+ G+GK + ++  +++l++++++++ v +D
  gi|557695000|ref|YP_008798054.1|  5 RVLFVVGTAGSGKSSLTGVFSEWLRDHEQSTATVNLD 41
                                      57899**********************9999988877 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.007
                                       HHHHHHHHTTSSEEEEEE--SST CS
                             SRP54  74 eavekakeekidvvlvDTaGrlq 96 
                                       e    a+e ++d +lvDT G+l+
  gi|557695000|ref|YP_008798054.1|  89 EIAALAEETNADWLLVDTPGQLE 111
                                       4445678899**********987 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   5.1e-05     0.065       4      86 ..       9     140 ..       6     172 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-05
                                       EEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEE................................ CS
                          MMR_HSR1   4 ivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgke................................ 47 
                                       +vG   +GKS+L    ++  + + ++++ + +d+    + ++  +                                
  gi|557695000|ref|YP_008798054.1|   9 VVGTAGSGKSSLTGVFSEWlRDHEQSTATVNLDPAALSLPYD--Pdvdvrefvdyerimstrnlgpngaliasvrev 83 
                                       788888888888887777545555555566666655555533..123445555555666666666666666666666 PP

                                       .................EEEEECGGCSS...HHHHHHHHHHHHHHHHCTSEEEEEEETT CS
                          MMR_HSR1  48 .................ielvDtpGlie...gaseekglgkaflaleeadlillvvdas 86 
                                                        + lvDtpG +e     +e++ +++++ + +  +l+l+++d+ 
  gi|557695000|ref|YP_008798054.1|  84 arnideiaalaeetnadWLLVDTPGQLElfaFRKEGRIIARKISDGR--KLLLFLLDSV 140
                                       66666666666677777********7654333445556666666544..7999999955 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   6.7e-05     0.085       5      45 ..       4      38 ..       1     105 [. 0.82
   2 ?   -0.2   0.0      0.86   1.1e+03      23      66 ..     203     250 ..     199     254 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.7e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfv 45
                                       ++l+v+G +G+GK+ l   + e+l  +++       +++v
  gi|557695000|ref|YP_008798054.1|  4 TRVLFVVGTAGSGKSSLTGVFSEWLRDHEQS------TATV 38
                                      6899********************9765443......3333 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.86
                            AAA_22  23 rrlleqldeeakaee....erpevvfvtlpsstsskdllrellralgl 66 
                                       ++l+++l +e+ ++     ++ ++v v ++  ++ ++l+ +l r++++
  gi|557695000|ref|YP_008798054.1| 203 NELQMTLSREIVQTVweisNSIPLVAVSAKTYEGFTELYANLTRIYDE 250
                                       556666654444444666667777788888888999999999998886 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 ?    8.2   0.0    0.0015       1.9       1      33 [.      11      43 ..      11      49 .. 0.92
   2 ?    4.2   0.0     0.026        33      81     114 ..      77     110 ..      71     120 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0015
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                      G   sGKS+l+ +  +++  ++++++ v+lD+ 
  gi|557695000|ref|YP_008798054.1| 11 GTAGSGKSSLTGVFSEWLRDHEQSTATVNLDPA 43
                                      7789**************99999999*****95 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.026
                            CLP1_P  81 lalvkelareveekleenkkakasgliIntpGwv 114
                                       +a v+e+ar+++e  +  ++ +a+ l+++tpG  
  gi|557695000|ref|YP_008798054.1|  77 IASVREVARNIDEIAALAEETNADWLLVDTPGQL 110
                                       6779999*****9999999*************76 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 ?   11.8   0.0   6.9e-05     0.088      28      69 ..       3      44 ..       1      47 [. 0.94
   2 ?   -2.5   0.0       1.5   1.9e+03     106     131 ..      83     108 ..      75     111 .. 0.79
   3 ?   -2.3   0.0       1.4   1.8e+03     204     226 ..     223     245 ..     198     250 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.9e-05
                                      -SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                              MeaB 28 raqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                      r++v+ + G+ G+Gks l+  + + lr++ +  a + +DP++
  gi|557695000|ref|YP_008798054.1|  3 RTRVLFVVGTAGSGKSSLTGVFSEWLRDHEQSTATVNLDPAA 44
                                      789999**********************************85 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHHTT-SEEEEEEES CS
                              MeaB 106 laaktrevvllleaaGfDvvlietvG 131
                                       +a++  e+ +l e    D++l++t G
  gi|557695000|ref|YP_008798054.1|  83 VARNIDEIAALAEETNADWLLVDTPG 108
                                       67777788888888888999988866 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.4
                                       --EEEEEBCCCTBSHHHHHHHHH CS
                              MeaB 204 rpkvlktsavegeGidelvdaie 226
                                       + +++ +sa++ eG  el ++++
  gi|557695000|ref|YP_008798054.1| 223 SIPLVAVSAKTYEGFTELYANLT 245
                                       45788899999999999988766 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   6.9e-05     0.089       1      41 [.       4      44 ..       4     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.9e-05
                                      -EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTT CS
                       ArsA_ATPase  1 lkvilvgGKGGVGKttvsaatavklsekgkkvllistDPAh 41
                                      ++v++v G  G GK+++   ++ +l ++++++  + +DPA 
  gi|557695000|ref|YP_008798054.1|  4 TRVLFVVGTAGSGKSSLTGVFSEWLRDHEQSTATVNLDPAA 44
                                      689************************************94 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.9e-05      0.11       2      81 ..       8     106 ..       7     135 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.9e-05
                            AAA_18   2 lltGtpGvGKttlakeLskrl.gf.....................gvnlrdvakenglllevdpealdeskrldedk 56 
                                       ++ Gt+G+GK++l+   s+ l                        +++  +v +e+ +++ +  +  +  +++    
  gi|557695000|ref|YP_008798054.1|   8 FVVGTAGSGKSSLTGVFSEWLrDHeqstatvnldpaalslpydpdVDVREFVDYERIMSTRNLGP--NGALIASVRE 82 
                                       699***********999777533355566667777777777777777777777777777777777..5555555555 PP

                            AAA_18  57 ldklldaleenssaleegknlvidg 81 
                                       +++++d++ + ++ ++++++l++d 
  gi|557695000|ref|YP_008798054.1|  83 VARNIDEIAALAE-ETNADWLLVDT 106
                                       5555555555554.55566666664 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0025       3.2      99     120 ..       4      25 ..       1      41 [. 0.76
   2 ?    0.6   0.0      0.36   4.6e+02     150     161 ..      98     109 ..      89     113 .. 0.80
   3 ?   -0.4   0.0      0.74   9.4e+02      90      90 ..     202     202 ..     151     246 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0025
                                       TSEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinall 120
                                        ++ ++vG  G GKS+L  ++ 
  gi|557695000|ref|YP_008798054.1|   4 TRVLFVVGTAGSGKSSLTGVFS 25 
                                       578899***********87665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.36
                                       TTTEEEESS-SS CS
                       RsgA_GTPase 150 aegglliDtPGf 161
                                       +++ ll+DtPG 
  gi|557695000|ref|YP_008798054.1|  98 NADWLLVDTPGQ 109
                                       56899******5 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.74
                                       H CS
                       RsgA_GTPase  90 l 90 
                                       +
  gi|557695000|ref|YP_008798054.1| 202 M 202
                                       1 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0002      0.26      17      46 ..       3      32 ..       1      46 [. 0.81
   2 ?   -2.7   0.0       3.3   4.2e+03     103     123 ..      85     105 ..      71     111 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0002
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaag 46
                                      + rv +++G AG+GK+ + ++  e +++++
  gi|557695000|ref|YP_008798054.1|  3 RTRVLFVVGTAGSGKSSLTGVFSEWLRDHE 32
                                      45799*************999999888775 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.3
                            AAA_30 103 kqlaallkaaekagakvilvG 123
                                       ++++++++ ae+++a  +lv 
  gi|557695000|ref|YP_008798054.1|  85 RNIDEIAALAEETNADWLLVD 105
                                       344555555555555555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1    0.0002      0.26       1      30 [.       5      33 ..       5     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                                      SCEEEEC-TTTCHHHHHHHHHHHHCTS-SC CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklalawaegklp 30
                                      r++++ G aGsGK+ L  ++ ++w +++ +
  gi|557695000|ref|YP_008798054.1|  5 RVLFVVGTAGSGKSSLT-GVFSEWLRDHEQ 33
                                      789***********985.555566555544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00018      0.23       4      79 ..       6     112 ..       3     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                            AAA_24   4 kiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie......................swed 51 
                                        ++++G +g+GK++l   +       +++++ ++++  + sl  d  +d++                      s+ +
  gi|557695000|ref|YP_008798054.1|   6 VLFVVGTAGSGKSSLTGVFsewlrdhEQSTATVNLDPAALSLPYDPDVDVRefvdyerimstrnlgpngaliaSVRE 82 
                                       6789************999999****9**********9999999999999888888888888888888887776666 PP

                            AAA_24  52 fldevvel..aaeladyktlviDtidelee 79 
                                       +   ++e+   ae+ + ++l +Dt ++le 
  gi|557695000|ref|YP_008798054.1|  83 VARNIDEIaaLAEETNADWLLVDTPGQLEL 112
                                       555555557656677799*****9998875 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017      0.22      12      39 ..       5      32 ..       1     142 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                                      SEEEEEESTTSSHHHHHHHHTTSS--SE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 12 ekvaivGenGaGKStLlkllagllkpte 39
                                      +++ +vG  G+GKS+L  ++++ l++ e
  gi|557695000|ref|YP_008798054.1|  5 RVLFVVGTAGSGKSSLTGVFSEWLRDHE 32
                                      67899************99998776633 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 1813.63
//
Query:       gi|557695001|ref|YP_008798055.1|  [L=443]
Description: aspartyl-tRNA(Asn)/glutamyl-tRNA (Gln) amidotransferase subunit A [Candidatus Caldiarchaeum subterraneum]
Scores for 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-101  339.2   0.0   5.2e-101  338.8   0.0    1.1  1  Amidase   Amidase
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.18   11.2   0.0    1.3  1  PIN_5     PINc domain ribonuclease


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 !  338.8   0.0  5.8e-105  5.2e-101      44     451 .]      59     429 ..      51     429 .. 0.95

  Alignments for each domain:
  == domain 1  score: 338.8 bits;  conditional E-value: 5.8e-105
                                       ...TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT---BB CS
                           Amidase  44 ekgpLhGvPisvKDnidvkgvpttaGskalenypaekDatvverLkkaGavilgkTnmdefamgsstensvfgptrN 120
                                        + +L G+ + vKD +++kg+pttaGs+ l n ++++ a vv+r+ +aG  + gkTn++efa+g+s  n+++g+  N
  gi|557695001|ref|YP_008798055.1|  59 RRRFLRGISFGVKDVFHIKGYPTTAGSRLLSNMVSSRTAAVVSRILEAGGAVNGKTNLHEFAFGVSNINPFYGACLN 135
                                       5789************************************************************************* PP

                                       TTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEESSH CS
                           Amidase 121 PwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsfcglvGlKPtygrvSragvvalessldvvGplarsv 197
                                       P+d+sr++GGSSGGsA+avA g++++++GtDt+GS+R+PA+fcg+vG+KPt+g +S +gv++l++s+d+vG+l+r+v
  gi|557695001|ref|YP_008798055.1| 136 PFDTSRVSGGSSGGSAVAVALGMCDIGLGTDTAGSVRVPAAFCGVVGFKPTSGQLSTDGVIPLSWSMDHVGILSRNV 212
                                       ***************************************************************************** PP

                                       HHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHCTT-EEE CS
                           Amidase 198 edlalllrvilgedpkdstssvipeesedlaeelkkslkglriGvvkedgvasldpevqravekalkaLeeaGhevv 274
                                        +++l+++v++ +   +++  +               l+glriGv+++++ + ld  v++a+ek l++Le+ G+ ++
  gi|557695001|ref|YP_008798055.1| 213 WETILVYSVLVDKP-LKPDAIK------------PLPLDGLRIGVPRNYFLDLLDRHVEEAFEKGLRTLEQRGAVLE 276
                                       ***********554.4455554............34699************************************** PP

                                       EEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCC CS
                           Amidase 275 evelpsleealslyylilvaeassnlarylgvryerlsetkvlsellpksraellgeevkrrielgnyalsaeassk 351
                                       ev ++++e+a++    i++aea+++                  +  l++ r +++g+ v+ ri +g    +a     
  gi|557695001|ref|YP_008798055.1| 277 EVVVENVEKAARCRSVIAFAEAAAY------------------HLQLSRGRLHEYGQDVRDRIVRGLAIPAAA---- 331
                                       ***********************88..................778999******************999988.... PP

                                       CHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHHHHHGCCTTT...HHHHHTT--EEEEECC CS
                           Amidase 352 yylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsytvlynlldftavvvpvnlaglpalsvpag 428
                                        yl+a ++r++l ++f k+fe++Dvl++Pt+ +pa+r +e++ +i + + +    + ++++ p+nl g pa+s+pa+
  gi|557695001|ref|YP_008798055.1| 332 -YLNALRARKRLVKDFGKLFEKVDVLATPTTLIPAHRVDEENVEI-DGQLISVREASLKNTEPFNLYGVPAISLPAA 406
                                       .9***************************************9876.777788888888899**************** PP

                                       CCT.TECEEEEEEESTT-HHHHH CS
                           Amidase 429 ksedglPvGvqvigkafqeetlL 451
                                       ++++glPvG+q++g+++++ +lL
  gi|557695001|ref|YP_008798055.1| 407 ERARGLPVGIQLVGPYGEDLKLL 429
                                       ******************98876 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     2e-05      0.18      69     124 ..     286     341 ..     253     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2e-05
                             PIN_5  69 iakldtwlvkkspdryevkipaeilyeyveevrerinkGlrvaEeavreaaeesek 124
                                        a+ + ++   +   y++++    l+ey ++vr+ri +Gl +   a  +a +++++
  gi|557695001|ref|YP_008798055.1| 286 AARCRSVIAFAEAAAYHLQLSRGRLHEYGQDVRDRIVRGLAIPAAAYLNALRARKR 341
                                       467788899999999***************************99998888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3189.44
//
Query:       gi|557695002|ref|YP_008798056.1|  [L=244]
Description: proteasome alpha subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-49  167.3   0.0    3.2e-49  167.0   0.0    1.1  1  Proteasome      Proteasome subunit
    2.3e-13   49.6   0.7    7.4e-13   47.9   0.2    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 !  167.0   0.0   3.6e-53   3.2e-49       1     188 [.      32     214 ..      32     216 .. 0.95

  Alignments for each domain:
  == domain 1  score: 167.0 bits;  conditional E-value: 3.6e-53
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       v+ G+t++ i++++gvvla++ r+    kl++++   Kif+id+hig+a+aGl +Dar+lv+ ar+ aq+ rl+y++
  gi|557695002|ref|YP_008798056.1|  32 VRSGSTALSITCREGVVLAVEERMH--TKLQNPDFSWKIFQIDEHIGAAAAGLNSDARVLVDNARVYAQTLRLSYDE 106
                                       578**********************..*******999**************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                       ++ ve +++rv + +q ytq++g+rpfg +lli+gvd++g p+L++ +psG ++e+ +a aiG g++ +++++e +y
  gi|557695002|ref|YP_008798056.1| 107 EPLVEAVARRVGDIMQLYTQHAGVRPFGTALLIGGVDKTG-PRLFYAEPSGLILEY-NAWAIGRGADKVREIFETSY 181
                                       *************************************999.***************.7******************* PP

                                       STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEE CS
                        Proteasome 155 kedltleeavelavkalkealerdklsgknieva 188
                                       k d++l+ avel ++al  +++     g++++++
  gi|557695002|ref|YP_008798056.1| 182 KVDMSLDNAVELGLSALVDSVD-KIEEGWTVRLV 214
                                       *****************99998.44566666666 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 !   47.9   0.2   8.2e-17   7.4e-13       1      22 [.       9      30 ..       9      30 .. 0.98
   2 ?   -0.9   0.0      0.15   1.3e+03      13      18 ..      67      72 ..      67      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 8.2e-17
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmk 22
                                      YDr++t+FSP+GRL+QVEYA++
  gi|557695002|ref|YP_008798056.1|  9 YDRAITVFSPQGRLYQVEYALE 30
                                      ********************87 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.15
                    Proteasome_A_N 13 RLfQVE 18
                                      ++fQ++
  gi|557695002|ref|YP_008798056.1| 67 KIFQID 72
                                      79**97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1878.16
//
Query:       gi|557695003|ref|YP_008798057.1|  [L=232]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   75.1   0.1    5.7e-21   74.4   0.1    1.4  1  SBDS      Shwachman-Bodian-Diamond syndrome (SBDS) protein
    5.1e-19   68.4   0.0    8.2e-19   67.7   0.0    1.3  1  SBDS_C    SBDS protein C-terminal domain
     0.0035   17.4   0.0     0.0077   16.3   0.0    1.5  1  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 !   74.4   0.1   9.6e-25   5.7e-21       1      88 []       7      94 ..       7      94 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 9.6e-25
                                      T-EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSE CS
                              SBDS  1 nvsivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGe 79
                                      n +i+r+  g++++e++v+++++l+y+ g++i+++++l+ e++F++ +kG +as+sel+k fgt+++  ++++I+ +Ge
  gi|557695003|ref|YP_008798057.1|  7 NYTIARLGIGGTTYEVLVDPENALRYKMGEKIPITKILAYEEVFKDWKKGVRASESELKKNFGTTDVRVVAEKIMAEGE 85
                                      67899999*********************************************************************** PP

                                      EE--HHHHH CS
                              SBDS 80 iqvsaeerk 88
                                      +  ++e+r+
  gi|557695003|ref|YP_008798057.1| 86 VLITTEQRR 94
                                      *****9996 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 !   67.7   0.0   1.4e-22   8.2e-19       2     114 ..     101     217 ..     100     219 .. 0.88

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1.4e-22
                                       HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CC CS
                            SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikd 78 
                                       +++ii+++a+++++p+t++p+++++Ie al+++g sv++    k  al+++++L++ +pi+  +m+++i ++ +   
  gi|557695003|ref|YP_008798057.1| 101 KRQIIDFIARNAIDPRTNTPHPPQRIELALEQVGLSVEPFADPKVEALKAVEKLRRVLPIKIGNMKVEIRVAGEFMG 177
                                       799*********************************************************************88877 PP

                                       CHHHHHHHH.HH........S.EEEEEEEEGGGHHHHHHH CS
                            SBDS_C  79 kilklieqv.esqk..vae.kewevvvliePgaykeleef 114
                                       k+  li ++ +  +  + + ++w +v+ i+ g++ +l + 
  gi|557695003|ref|YP_008798057.1| 178 KVYGLIRSMgTMLEegWLGdGSWRCVAEIPTGVQADLIDR 217
                                       777777777544334555535599**99*99999998775 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 !   16.3   0.0   1.3e-06    0.0077       7      69 ..     165     226 ..     164     229 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-06
                                       EEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS- CS
                             EFG_C   7 vkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGeg 69 
                                       +kvei+v  e++gkv+  l +  G++++    ++g  +  aeiP+    ++ ++L+++  G+ 
  gi|557695003|ref|YP_008798057.1| 165 MKVEIRVAGEFMGKVY-GLIRSMGTMLEEGWLGDGSWRCVAEIPTGVQADLIDRLNKICGGRV 226
                                       89**************.67777899999999988899999******999*********99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1822.93
//
Query:       gi|557695004|ref|YP_008798058.1|  [L=223]
Description: exosome complex component RRP4 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   34.1   0.0    3.4e-08   33.2   0.0    1.5  1  ECR1_N    Exosome complex exonuclease RRP4 N-terminal region
    2.9e-06   27.0   0.0    6.7e-06   25.8   0.0    1.7  1  KH_1      KH domain
    0.00045   20.5   0.3     0.0012   19.2   0.2    1.8  2  KH_6      KH domain
     0.0011   18.7   0.3     0.0033   17.2   0.3    1.8  1  KH_2      KH domain
     0.0049   17.2   0.1      0.024   14.9   0.1    2.1  2  S1        S1 RNA binding domain
  ------ inclusion threshold ------
      0.034   14.0   0.3       0.21   11.4   0.2    2.4  2  DUF1953   Domain of unknown function (DUF1953)
      0.066   13.1   0.4       0.17   11.8   0.1    1.8  2  KH_4      KH 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 !   33.2   0.0   1.3e-11   3.4e-08       1      34 [.       9      41 ..       9      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.3e-11
                                      EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGt 34
                                      +V+PG+ l +d+   +G GTYvr+g++yAsv+G+
  gi|557695004|ref|YP_008798058.1|  9 LVVPGQLL-SDNPRQSGLGTYVRDGKVYASVMGF 41
                                      69******.88889*******************8 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   2.6e-09   6.7e-06       4      56 ..     136     182 ..     134     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2.6e-09
                                       EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE.SHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG.spea 56 
                                       ++v++ +v+riIG++Gs+++ +r+etg+   v  +      +  +++ G +p+ 
  gi|557695004|ref|YP_008798058.1| 136 VSVNAAKVPRIIGRKGSMLQILRRETGCDFWVG-R------NGLIVVNGpDPAH 182
                                       5789999*********************98864.3......2478888877665 PP

>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.6   9.2e+03       1      11 [.      68      78 ..      68      79 .. 0.84
   2 !   19.2   0.2   4.5e-07    0.0012       1      45 [.     133     180 ..     133     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.6
                              KH_6  1 GmlfeVslslv 11
                                      G++ +V+++ v
  gi|557695004|ref|YP_008798058.1| 68 GIVSDVKPNAV 78
                                      89999*99876 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 4.5e-07
                              KH_6   1 GmlfeVslslvrRllnhvLeeLg...kagpfeiavGlNGriWvksesp 45 
                                       G+l++V   +v+R++   +++L+    + +++  vG+NG i v++++p
  gi|557695004|ref|YP_008798058.1| 133 GILVSVNAAKVPRIIGRKGSMLQilrRETGCDFWVGRNGLIVVNGPDP 180
                                       99*************666666653225577***********9998876 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.3   1.3e-06    0.0033      24      68 ..     131     175 ..     118     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                                       SCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEE CS
                              KH_2  24 anrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkl 68 
                                       + ++ + + +++  ++IG++Gs+++ ++ e + d+ + +++ + +
  gi|557695004|ref|YP_008798058.1| 131 PSGILVSVNAAKVPRIIGRKGSMLQILRRETGCDFWVGRNGLIVV 175
                                       56788999*********************9998887777766665 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.83   2.1e+03      30      63 ..       9      41 ..       4      48 .. 0.71
   2 !   14.9   0.1   9.6e-06     0.024       2      36 ..      60      94 ..      59     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.83
                                      EEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEE CS
                                S1 30 gfvpaselsrdarvedpdevlkvGdevkvkvlkv 63
                                        vp  +ls++  ++++  ++  + +v++ v ++
  gi|557695004|ref|YP_008798058.1|  9 LVVPGQLLSDN-PRQSGLGTYVRDGKVYASVMGF 41
                                      67888899988.7777777777777777766665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 9.6e-06
                                      STTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGG CS
                                S1  2 pekgevveGeVtsvtkgGafVelgngvegfvpase 36
                                      p+ g+ v G+V++v + +++V++g++ ++ +  +e
  gi|557695004|ref|YP_008798058.1| 60 PQRGDKVLGIVSDVKPNAVEVDIGGETTAVIKPHE 94
                                      889*********************99998887665 PP

>> DUF1953  Domain of unknown function (DUF1953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.67   1.7e+03       8      24 ..      22      38 ..      20      46 .. 0.81
   2 ?   11.4   0.2     8e-05      0.21      16      44 ..      62      91 ..      55     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.67
                                      -TTEEEEEETTTEEEEE CS
                           DUF1953  8 qkGlcGfmrGdkvlviv 24
                                      q Gl  ++r  kv   v
  gi|557695004|ref|YP_008798058.1| 22 QSGLGTYVRDGKVYASV 38
                                      88999999*99998665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8e-05
                                      ETTTEEEEEESSS.S-EEEEEEEEEEETTT CS
                           DUF1953 16 rGdkvlvivktln.rdydieidGeytdvit 44
                                      rGdkvl iv  +     +++i Ge t vi 
  gi|557695004|ref|YP_008798058.1| 62 RGDKVLGIVSDVKpNAVEVDIGGETTAVIK 91
                                      9********998724579999*******96 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.4   3.6e+03      14      26 ..      74      85 ..      65      91 .. 0.62
   2 ?   11.8   0.1   6.8e-05      0.17      31      55 ..     134     158 ..     121     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.4
                              KH_4 14 dpeevevteeeee 26
                                      +p++vev++  +e
  gi|557695004|ref|YP_008798058.1| 74 KPNAVEVDIG-GE 85
                                      5777888775.33 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 6.8e-05
                              KH_4  31 ielnvegedlGrvIGkrGrtldAlq 55 
                                       i ++v+  ++ r+IG++G +l+ l+
  gi|557695004|ref|YP_008798058.1| 134 ILVSVNAAKVPRIIGRKGSMLQILR 158
                                       77999****************8665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); 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: 1658.47
//
Query:       gi|557695005|ref|YP_008798059.1|  [L=246]
Description: exosome complex component RRP41 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  114.5   0.0    6.2e-33  114.1   0.0    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    1.1e-15   57.3   0.2    2.2e-15   56.5   0.2    1.5  1  RNase_PH_C  3' exoribonuclease family, domain 2
  ------ inclusion threshold ------
      0.045   13.1   0.0      0.064   12.6   0.0    1.1  1  DUF4862     Domain of unknown function (DUF4862)


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 !  114.1   0.0     1e-36   6.2e-33       1     132 []      24     153 ..      24     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 1e-36
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeei 76 
                                       e+R++++e gvl++ +GSay+elG t ++a+v gp+e++p+  + +d  g++++++ +a+f+  er+     +++ei
  gi|557695005|ref|YP_008798059.1|  24 EMRKMRMEVGVLEKTDGSAYVELGGTRIYAGVIGPREVHPKHLElPDK-GVINCRYHMASFSVDERKP-LGMTRREI 98 
                                       79************************************8888887875.89***************77.669***** PP

                                       HHHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  77 elsrlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                       els+++ +al+ ++ le++p+  idi+++v+++dg ++  a i+aaslALadagip
  gi|557695005|ref|YP_008798059.1|  99 ELSKVIREALETVVFLEEFPRMMIDIFVEVIQADG-GTRTAGITAASLALADAGIP 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 !   56.5   0.2   3.6e-19   2.2e-15       1      66 [.     156     220 ..     156     221 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 3.6e-19
                                       S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHH CS
                        RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkk 66 
                                       ++++a++vgkvd+ +vlD + +E++++e+d+++a+a + ++++l++++g  +++e++ +++e+A++
  gi|557695005|ref|YP_008798059.1| 156 DMIAAIAVGKVDGVLVLDINEQEDKYGEADMPVAIAPHLNSIVLLQLNGR-MTPEEVDKGLEMAQQ 220
                                       689***********************************************.*************97 PP

>> DUF4862  Domain of unknown function (DUF4862)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.1e-05     0.064     196     283 ..     148     236 ..     142     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.1e-05
                           DUF4862 196 rdaetplehveelaaaglLaglmfSGasdedteyGaaWeDlhlplakdepa.asedSllteeriaetleaagdaals 271
                                        da  p++ + ++ a g++ g+++   ++++ +yG+a     ++++ ++    + +  +t+e++++ le+a++a ++
  gi|557695005|ref|YP_008798059.1| 148 ADAGIPMADMIAAIAVGKVDGVLVLDINEQEDKYGEADMPVAIAPHLNSIVlLQLNGRMTPEEVDKGLEMAQQAVQK 224
                                       58899999***************************877777777777777788999*******************99 PP

                           DUF4862 272 yvGikvavrpad 283
                                       ++ +++++  ++
  gi|557695005|ref|YP_008798059.1| 225 IHHMQIEALKRK 236
                                       999998876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1818.37
//
Query:       gi|557695006|ref|YP_008798060.1|  [L=271]
Description: exosome complex component RRP42 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  106.4   0.0      2e-30  106.0   0.0    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    4.8e-07   29.7   0.1    9.4e-07   28.8   0.1    1.5  1  RNase_PH_C  3' exoribonuclease family, domain 2
  ------ inclusion threshold ------
      0.053   13.4   0.0       0.15   12.0   0.0    1.7  1  DUF1421     UBA-like domain (DUF1421)


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 !  106.0   0.0   3.3e-34     2e-30       1     132 []      32     167 ..      32     167 .. 0.95

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 3.3e-34
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeie 77 
                                       ++R+++i+t+v+++a+GSa+++lG+tk+l+++++++ + p ++r ++eg+++v+ e+ p+as +++  g p++++ie
  gi|557695006|ref|YP_008798060.1|  32 QYRKIEIATNVVEKAHGSALVSLGKTKILTGIKVEVGT-PYPDR-PNEGVFTVNAELLPLASKTFEP-GPPDERAIE 105
                                       68**********************************98.89995.45899***************77.9******** PP

                                       HHHHHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  78 lsrlleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                       lsr+++r +r+s  +        e+++ + i id++vl++dg +++da++++a +AL +  +p
  gi|557695006|ref|YP_008798060.1| 106 LSRIVDRVIRESKAIeveklcivEGQKVYMIFIDCYVLDYDG-NYFDASVLSAVAALRTMTLP 167
                                       **************99999999999*9***************.**************998887 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 !   28.8   0.1   1.6e-10   9.4e-07       2      66 ..     191     255 ..     190     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.6e-10
                                       --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHH CS
                        RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkk 66 
                                       ++++vt++++ d++++Dp   Eed+++ ++t+ +++++   +++k+  + l+   ++e+++++++
  gi|557695006|ref|YP_008798060.1| 191 LPVSVTMALIRDKIIVDPLPAEEDVADTVVTIGYDSDGVLSAIQKSSPGLLPVNMFKEMVKIGLD 255
                                       89*********************************777555555555554999999999999987 PP

>> DUF1421  UBA-like domain (DUF1421)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.4e-05      0.15       3      24 ..     214     235 ..     213     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                           DUF1421   3 dlidkvasMGfrrDqVrsvvqr 24 
                                       d++d+v+++G+  D V s +q+
  gi|557695006|ref|YP_008798060.1| 214 DVADTVVTIGYDSDGVLSAIQK 235
                                       9***************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 2027.46
//
Query:       gi|557695007|ref|YP_008798061.1|  [L=76]
Description: large subunit ribosomal protein L37Ae [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   73.0   4.8    1.7e-20   72.9   4.8    1.1  1  Ribosomal_L37ae  Ribosomal L37ae protein family
    7.1e-05   22.7   3.3      9e-05   22.4   3.3    1.3  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    0.00011   22.0   0.9    0.00013   21.8   0.9    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0057   16.7   0.8       0.37   11.0   0.1    2.2  2  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.012   15.7   1.2      0.018   15.2   1.2    1.2  1  zf-RING_13       RING/Ubox like zinc-binding domain
      0.021   14.5   4.2       0.93    9.3   0.8    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
      0.023   14.6   1.7       0.43   10.5   0.2    2.2  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
      0.069   12.8   1.1        2.6    7.7   0.2    2.2  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.078   12.8   3.1        0.1   12.4   0.3    2.1  2  zf-C2H2_11       zinc-finger C2H2-type
      0.079   12.5   0.2       0.71    9.4   0.0    2.0  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.13   11.6   4.2        3.9    6.9   0.4    2.2  2  zf-RanBP         Zn-finger in Ran binding protein and others
        1.9    8.3   7.3        7.7    6.3   7.3    1.8  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
        5.7    6.5   6.1        6.3    6.4   1.1    2.2  2  zn-ribbon_14     Zinc-ribbon


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 !   72.9   4.8   1.2e-23   1.7e-20      10      70 ..      14      74 ..       6      76 .] 0.93

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 1.2e-23
                                      GGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS- CS
                   Ribosomal_L37ae 10 kygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpet 70
                                        g+rYG++lrk+++++    +a++ C +cg ++v+R++vg+w+C++cg+++aG Ay p+ 
  gi|557695007|ref|YP_008798061.1| 14 GLGPRYGSTLRKKWAEVVSVARANHVCDRCGAKRVRRVSVGVWQCRRCGYKFAGQAYAPKA 74
                                      569*******************************************************986 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 !   22.4   3.3   6.5e-08     9e-05      18      45 ..      37      63 ..      24      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.5e-08
                     Zn_Tnp_IS1595 18 gfvCPhCgsrkayriktrglfqCkeCrk 45
                                      ++vC +Cg ++++r++  g++qC++C++
  gi|557695007|ref|YP_008798061.1| 37 NHVCDRCGAKRVRRVSV-GVWQCRRCGY 63
                                      589*************7.********98 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 !   21.8   0.9   9.2e-08   0.00013      22      56 ..      31      65 ..      18      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9.2e-08
                    OrfB_Zn_ribbon 22 vnpayTSktCseCgsknkealsgrtfkCpnCgfea 56
                                      v+ a     C +Cg+k  +++s  +++C++Cg+++
  gi|557695007|ref|YP_008798061.1| 31 VSVARANHVCDRCGAKRVRRVSVGVWQCRRCGYKF 65
                                      555556678***********************996 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1   0.00027      0.37      24      39 ..      35      51 ..      22      52 .. 0.78
   2 ?    4.7   0.1     0.024        33       7      15 ..      57      65 ..      55      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00027
                       Zn-ribbon_8 24 apltaCPeCgs.evrrv 39
                                      +++ +C +Cg+ +vrrv
  gi|557695007|ref|YP_008798061.1| 35 RANHVCDRCGAkRVRRV 51
                                      34566**********97 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.024
                       Zn-ribbon_8  7 rCeeCghef 15
                                      +C++Cg +f
  gi|557695007|ref|YP_008798061.1| 57 QCRRCGYKF 65
                                      7*****998 PP

>> zf-RING_13  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   1.2   1.3e-05     0.018       3      33 ..      39      69 ..      37      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                                      --TTTSS--SEEETTS-EE-TTTHHHTTTSS CS
                        zf-RING_13  3 vctvcgaapvaksacggwfcgncvpyhaghc 33
                                      vc  cga  v + + g w c  c    ag  
  gi|557695007|ref|YP_008798061.1| 39 VCDRCGAKRVRRVSVGVWQCRRCGYKFAGQA 69
                                      9**********************99999976 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0048       6.6       1       9 [.      38      46 ..      38      51 .. 0.84
   2 ?    9.3   0.8   0.00068      0.93       1      10 [.      56      65 ..      55      67 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0048
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      +vC++CG++
  gi|557695007|ref|YP_008798061.1| 38 HVCDRCGAK 46
                                      69*****86 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00068
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      ++C++CG+++
  gi|557695007|ref|YP_008798061.1| 56 WQCRRCGYKF 65
                                      7899999976 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 ?    3.6   0.1     0.045        62      17      30 ..      35      46 ..      30      47 .. 0.71
   2 ?   10.5   0.2   0.00031      0.43      17      31 ..      55      65 ..      49      66 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.045
                                      SCCCEEEESSSS-E CS
                    RNA_POL_M_15KD 17 kegknfeCrqCgYe 30
                                      + + +  C+ Cg++
  gi|557695007|ref|YP_008798061.1| 35 RANHV--CDRCGAK 46
                                      45555..****986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00031
                                      SCCCEEEESSSS-EE CS
                    RNA_POL_M_15KD 17 kegknfeCrqCgYee 31
                                      +      Cr CgY++
  gi|557695007|ref|YP_008798061.1| 55 V----WQCRRCGYKF 65
                                      3....45******97 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.2    0.0019       2.6       2      10 ..      37      45 ..      36      46 .. 0.84
   2 ?    4.0   0.1     0.027        38       3      12 ..      56      65 ..      54      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0019
                            zf_UBZ  2 tylCerCgk 10
                                      +++C+rCg+
  gi|557695007|ref|YP_008798061.1| 37 NHVCDRCGA 45
                                      689****97 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.027
                            zf_UBZ  3 ylCerCgkei 12
                                      ++C rCg ++
  gi|557695007|ref|YP_008798061.1| 56 WQCRRCGYKF 65
                                      79****9765 PP

>> zf-C2H2_11  zinc-finger C2H2-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2      0.37   5.1e+02       7      13 ..      40      46 ..      36      46 .. 0.78
   2 ?   12.4   0.3   7.3e-05       0.1       6      17 ..      57      68 ..      54      69 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.37
                        zf-C2H2_11  7 CleCGlc 13
                                      C  CG +
  gi|557695007|ref|YP_008798061.1| 40 CDRCGAK 46
                                      9999975 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 7.3e-05
                        zf-C2H2_11  6 qCleCGlcftSq 17
                                      qC+ CG +f+ q
  gi|557695007|ref|YP_008798061.1| 57 QCRRCGYKFAGQ 68
                                      *********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 ?    9.4   0.0   0.00051      0.71      16      27 ..      34      45 ..      19      47 .. 0.86
   2 ?    1.0   0.1      0.22   3.1e+02      22      27 ..      58      63 ..      57      66 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00051
                                      STTCEEESSSSB CS
                      TF_Zn_Ribbon 16 ergelvCtdCGl 27
                                      +r+++vC +CG+
  gi|557695007|ref|YP_008798061.1| 34 ARANHVCDRCGA 45
                                      799********7 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.22
                                      ESSSSB CS
                      TF_Zn_Ribbon 22 CtdCGl 27
                                      C +CG+
  gi|557695007|ref|YP_008798061.1| 58 CRRCGY 63
                                      666665 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 ?    6.4   0.3    0.0041       5.7      20      28 ..      39      47 ..      35      48 .. 0.88
   2 ?    6.9   0.4    0.0028       3.9       2      12 ..      53      63 ..      52      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0041
                                      B-TTT--BT CS
                          zf-RanBP 20 kCvaCqapk 28
                                      +C +C+a++
  gi|557695007|ref|YP_008798061.1| 39 VCDRCGAKR 47
                                      7******97 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0028
                                      SSSEE-SSS-- CS
                          zf-RanBP  2 egdWdCskClv 12
                                       g W+C  C++
  gi|557695007|ref|YP_008798061.1| 53 VGVWQCRRCGY 63
                                      578******98 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 ?    6.3   7.3    0.0055       7.7       6      28 ..      39      62 ..      35      64 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0055
                           zf-RRN7  6 pCgvCgcrsftl.ddGfyyCrrCh 28
                                      +C+ Cg+++++    G + CrrC+
  gi|557695007|ref|YP_008798061.1| 39 VCDRCGAKRVRRvSVGVWQCRRCG 62
                                      8**********************9 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3     0.058        81       3       8 ..      40      45 ..      38      46 .. 0.87
   2 ?    6.4   1.1    0.0045       6.3       2       8 ..      57      63 ..      56      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.058
                      zn-ribbon_14  3 CerCGy 8 
                                      C rCG 
  gi|557695007|ref|YP_008798061.1| 40 CDRCGA 45
                                      ****95 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0045
                      zn-ribbon_14  2 kCerCGy 8 
                                      +C+rCGy
  gi|557695007|ref|YP_008798061.1| 57 QCRRCGY 63
                                      7*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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):              13  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 601.93
//
Query:       gi|557695008|ref|YP_008798062.1|  [L=83]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-11   44.7   0.4    1.2e-11   44.5   0.4    1.0  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.4   6.8e-16   1.2e-11       2      74 .]       4      78 ..       3      78 .. 0.96

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 6.8e-16
                                      EEEEEE-SSH.HHHHHHHHHHHHHCHC-TTE.CEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1  2 ltisvpfpte.rlAsialrtLqvDkelspla.vkrslslegnvLqveykAttnrmLRvavngfleslglvletme 74
                                      +tis++f+te  +As+ l++L+++    +++ +k s++  g  + v+ +A +  ++R+a n+++++l++ + tme
  gi|557695008|ref|YP_008798062.1|  4 VTISIEFSTEpDKASSLLNSLKPETDSIKSKrSKASIEKRGGEVSVKLEADDITAARAAANTVIRLLNVSMATME 78
                                      79*******989************88888888******************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 693.15
//
Query:       gi|557695009|ref|YP_008798063.1|  [L=121]
Description: prefoldin beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-23   80.3  12.9      1e-22   80.1  12.9    1.0  1  Prefoldin_2      Prefoldin subunit
  ------ inclusion threshold ------
      0.044   14.2  10.1       0.21   12.0   1.4    2.3  2  FlaC_arch        Flagella accessory protein C (FlaC)
      0.094   13.2  14.5        1.1    9.7   2.5    2.0  2  APG6_N           Apg6 coiled-coil region
       0.17   12.5   6.4       0.36   11.4   6.4    1.5  1  DUF2408          Protein of unknown function (DUF2408)
       0.18   11.6   6.9       0.26   11.1   6.9    1.2  1  DUF724           Protein of unknown function (DUF724)
       0.22   11.8   6.6      0.091   13.0   1.4    2.2  2  XhlA             Haemolysin XhlA
        1.5    7.3   4.6        1.6    7.1   4.6    1.0  1  FUSC             Fusaric acid resistance protein family
          2    9.2   8.8       0.62   10.8   2.7    2.5  2  Vir_act_alpha_C  Virulence activator alpha C-term
        2.1    8.3   8.0       0.15   12.0   0.7    1.9  2  Halogen_Hydrol   5-bromo-4-chloroindolyl phosphate hydrolysis
        4.8    7.5  11.3      7e+02    0.5  11.2    2.2  1  Spc24            Spc24 subunit of Ndc80
        5.1    7.8   9.8         16    6.2   4.2    2.2  2  YabA             Initiation control protein YabA
        6.5    5.5   4.8        7.2    5.4   4.8    1.0  1  LMBR1            LMBR1-like membrane protein


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 !   80.1  12.9   6.8e-26     1e-22       1     104 [.      11     114 ..      11     116 .. 0.98

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 6.8e-26
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketleke 77 
                                       q+++ ++qqlqq l+ l ++++ +e +l e++ +lee++++d+++  +k vG+vlv+++ke++ +eL erke ++++
  gi|557695009|ref|YP_008798063.1|  11 QQQVLRLQQLQQSLSLLLTEKQRIESELAEVNAALEEINKMDDSAVLFKAVGPVLVQTSKEKMVAELTERKELADTR 87 
                                       899************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                       Prefoldin_2  78 iktlekqleklekeleelkeelqkklq 104
                                       +k +e+q+++ ++++e l++e+qk+l 
  gi|557695009|ref|YP_008798063.1|  88 LKVIERQESRARAQIESLQKEVQKLLS 114
                                       ************************986 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 ?    7.0   1.9    0.0052       7.8       1      35 [.      16      50 ..      16      52 .. 0.90
   2 ?   12.0   1.4   0.00014      0.21      10      42 ..      82     114 ..      73     114 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0052
                         FlaC_arch  1 ridelEnklsklsteletvkkeneelsksveelke 35
                                      r+++l++ ls l te + +++e+ e++  +ee+++
  gi|557695009|ref|YP_008798063.1| 16 RLQQLQQSLSLLLTEKQRIESELAEVNAALEEINK 50
                                      77899999999999999999999999999999986 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00014
                         FlaC_arch  10 sklsteletvkkeneelsksveelkenVkdlls 42 
                                       +  +t+l+ ++++ +  + ++e l+++V++lls
  gi|557695009|ref|YP_008798063.1|  82 ELADTRLKVIERQESRARAQIESLQKEVQKLLS 114
                                       557899*************************96 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.5   0.00077       1.1      56      88 ..      17      49 ..       3      56 .. 0.58
   2 ?    9.4   4.3   0.00097       1.4      52      94 ..      70     112 ..      64     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00077
                            APG6_N 56 leklekeeeelleeLkelekereeleaelaale 88
                                      l++l++  + ll+e +++e+e +e++a+l+++ 
  gi|557695009|ref|YP_008798063.1| 17 LQQLQQSLSLLLTEKQRIESELAEVNAALEEIN 49
                                      555555555555555555555555555555544 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00097
                            APG6_N  52 leeeleklekeeeelleeLkelekereeleaelaaleeeleal 94 
                                        e+ +++l + +e + + Lk +e+++++ +a++++l++e ++l
  gi|557695009|ref|YP_008798063.1|  70 KEKMVAELTERKELADTRLKVIERQESRARAQIESLQKEVQKL 112
                                       4566778888888888888888888888888888888888876 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   6.4   0.00024      0.36       3     106 ..       5     100 ..       4     115 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00024
                           DUF2408   3 elspelepiyekLvsirrsLlslaakskaeeakeseevkeelkelkeeLkkieskrdeegkFkseegkevvekgqav 79 
                                       +++p++++ + +L ++++sL+ l++++++         ++el e+++ L++i++  d+   Fk      v+ +++++
  gi|557695009|ref|YP_008798063.1|   5 TIPPNVQQQVLRLQQLQQSLSLLLTEKQRI--------ESELAEVNAALEEINKMDDSAVLFKAVGPVLVQTSKEKM 73 
                                       69999***************9999998886........99**************99999999887776788888999 PP

                           DUF2408  80 lngLlddcfdlvedlkaqdgeekkvas 106
                                       +++L ++     + lk  + +e++ + 
  gi|557695009|ref|YP_008798063.1|  74 VAELTERKELADTRLKVIERQESRARA 100
                                       999998876655555544433333333 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   6.9   0.00018      0.26      91     186 ..      11     114 ..       8     115 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                            DUF724  91 qsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkil..........elerqlallk..ekkea 155
                                       q+++ +L +l+++ + ll+e++++e++++e +++ +++++     +   +          +  ++++++   e+ke 
  gi|557695009|ref|YP_008798063.1|  11 QQQVLRLQQLQQSLSLLLTEKQRIESELAEVNAALEEINKM----DDSAVlfkavgpvlvQTSKEKMVAEltERKEL 83 
                                       56666777888888888888888888888877766654433....2222222223333335555555555779**** PP

                            DUF724 156 adkeiarlkseaekleeeledveqeFeavas 186
                                       ad +++ ++ ++++++ ++e+ ++e+++++s
  gi|557695009|ref|YP_008798063.1|  84 ADTRLKVIERQESRARAQIESLQKEVQKLLS 114
                                       **************************99876 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3      0.24   3.5e+02      30      44 ..      34      48 ..      10      55 .. 0.53
   2 ?   13.0   1.4   6.1e-05     0.091      14      44 ..      81     112 ..      70     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.24
                              XhlA 30 aeekiknleedlkkl 44
                                       e+++ +++  l+++
  gi|557695009|ref|YP_008798063.1| 34 IESELAEVNAALEEI 48
                                      333333333333333 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.1e-05
                              XhlA  14 dnlee.rvdkleekaaeaeekiknleedlkkl 44 
                                       ++l + r++ +e+ +++a+++i++l++++ kl
  gi|557695009|ref|YP_008798063.1|  81 KELADtRLKVIERQESRARAQIESLQKEVQKL 112
                                       455666**********************9998 PP

>> FUSC  Fusaric acid resistance protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   4.6    0.0011       1.6     212     315 ..       8     113 ..       7     121 .] 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0011
                              FUSC 212 prirararalrrllsrmlallallsslarllarlraeeaaavpe..laallaelaal....eaaaaaealeaalaal 282
                                       p++++++ +l++l++ +  ll+  + ++++la+++a+ ++  +    a l++++  +    +++++ ++l+++ +  
  gi|557695009|ref|YP_008798063.1|   8 PNVQQQVLRLQQLQQSLSLLLTEKQRIESELAEVNAALEEINKMddSAVLFKAVGPVlvqtSKEKMVAELTERKELA 84 
                                       67899999***************************998887666778888888888777775566777777777777 PP

                              FUSC 283 rarlralrraleadadtaalllarlaellaela 315
                                       ++rl+ ++r+++    +a++ +++l+ ++++l+
  gi|557695009|ref|YP_008798063.1|  85 DTRLKVIERQES----RARAQIESLQKEVQKLL 113
                                       777777777777....55555555555555544 PP

>> Vir_act_alpha_C  Virulence activator alpha C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.4      0.23   3.5e+02      27      46 ..      16      37 ..       7      66 .. 0.69
   2 ?   10.8   2.7   0.00042      0.62      14      46 ..      67     104 ..      64     121 .] 0.79

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.23
                   Vir_act_alpha_C 27 rreeheekLaeyeeieerl..e 46
                                      r+++ ++ L+ +++ ++r+  e
  gi|557695009|ref|YP_008798063.1| 16 RLQQLQQSLSLLLTEKQRIesE 37
                                      5666777777777777766430 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00042
                   Vir_act_alpha_C  14 vldpealieeLerrreeheekLaeyeeieerl.....e 46 
                                       + ++e++++eL++r+e++  +L+ +e+ e r      +
  gi|557695009|ref|YP_008798063.1|  67 QTSKEKMVAELTERKELADTRLKVIERQESRAraqieS 104
                                       5789**********************999998555541 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.4      0.41   6.2e+02     153     178 ..      18      43 ..       9      52 .. 0.74
   2 ?   12.0   0.7    0.0001      0.15      35      87 ..      61     112 ..      51     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.41
                    Halogen_Hydrol 153 ealeetrqlLdelaealekdlqklle 178
                                       ++l+++ +lL + ++ +e++l ++++
  gi|557695009|ref|YP_008798063.1|  18 QQLQQSLSLLLTEKQRIESELAEVNA 43 
                                       57888888888888888888887765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.0001
                    Halogen_Hydrol  35 lggilvyvasrknkkkkhlkksglsrkelkyiretlkeakekikrlekalkrv 87 
                                       +g +lv   + k++ + + ++++l+++ lk+i+++ + a+++i++l+k+ +++
  gi|557695009|ref|YP_008798063.1|  61 VGPVLVQTSKEKMVAELT-ERKELADTRLKVIERQESRARAQIESLQKEVQKL 112
                                       444444444443333333.3479*************************99885 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5  11.2      0.47     7e+02       7      44 ..      18      62 ..      12     112 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.47
                             Spc24  7 friakelsdleselesleselaelkeeleeleeesee.......k 44
                                      ++++++ls l +e +++eselae ++ lee+++++ +        
  gi|557695009|ref|YP_008798063.1| 18 QQLQQSLSLLLTEKQRIESELAEVNAALEEINKMDDSavlfkavG 62
                                      678889999999999999999999999999999887755554440 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   4.2     0.011        16      16      58 ..       9      51 ..       3      85 .. 0.79
   2 ?    5.2   0.4     0.021        32       3      36 ..      80     114 ..      78     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXX CS
                              YabA 16 qleelleeleelkeelaelleenaeLeleneklrerleeeekk 58
                                      ++++ + +l++l+++l+ ll e +++e e  ++   lee +k 
  gi|557695009|ref|YP_008798063.1|  9 NVQQQVLRLQQLQQSLSLLLTEKQRIESELAEVNAALEEINKM 51
                                      678888999********************99999999444333 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.021
                                       HHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              YabA   3 kkelfd.kleeleeqleelleeleelkeelaelle 36 
                                       +kel d +l+ +e+q ++  +++e+l++e+++ll 
  gi|557695009|ref|YP_008798063.1|  80 RKELADtRLKVIERQESRARAQIESLQKEVQKLLS 114
                                       56666426899999999*************99986 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   4.8    0.0048       7.2     201     299 ..      16     114 ..       9     121 .] 0.84

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0048
                             LMBR1 201 elkklyfeaaklntekeeaereledllkevkklrksisesdp.lrkyleeilkkvPeeiaeklksnenkteeslakl 276
                                       +l++l+ +++ l tek+  e el +++ +++++ +++ +s+  ++ +   +++++ e++  +l + ++ +  +l+  
  gi|557695009|ref|YP_008798063.1|  16 RLQQLQQSLSLLLTEKQRIESELAEVNAALEEI-NKMDDSAVlFKAVGPVLVQTSKEKMVAELTERKELADTRLKVI 91 
                                       7899999*****************999999999.5555666647777788888888888888888899999999999 PP

                             LMBR1 277 ekqlikalqkrertekqwkrlle 299
                                       e+q  +a+++ e  +k+ ++ll 
  gi|557695009|ref|YP_008798063.1|  92 ERQESRARAQIESLQKEVQKLLS 114
                                       99999999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1952  (0.108874); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 855.43
//
Query:       gi|557695010|ref|YP_008798064.1|  [L=335]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   45.7   0.1    9.1e-12   45.1   0.1    1.3  1  DHH       DHH family
    0.00067   20.1   0.6     0.0037   17.7   0.2    2.3  3  DHHA1     DHHA1 domain


Domain annotation for each model (and alignments):
>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.1     1e-15   9.1e-12       2     101 .]      23     165 ..      22     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1e-15
                                       EEEE-ECSSSHHHHHHHHHHHH...........................................CECS--TCGGCG CS
                                       xxxxxxxxxxxxxxxxxxxxxx...........................................xxxxxxxxxxxx RF
                               DHH   2 ilivghknpDtDsigSaialan...........................................llvDhneksqav 35 
                                       + ++ h   D+Ds+gSa+++++                                           llvD+++++   
  gi|557695010|ref|YP_008798064.1|  23 VQVLSHWGGDADSVGSAYVMTRlltqnyeaseagflipeesalhvkaimqhlrfdeklletpevyLLVDVGSPHLLG 99 
                                       668899999*******99999967777777776666666666666666666666666666666666*******9877 PP

                                       CCH..HCCCSEEEEEEE-S---SS---SS--EEEE-SSS-HHHHHHHHHHHTT----HHHHHHHHHHH CS
                                       xxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  36 ege..akeeaedviiiDHHrlgeefetlapilflnepvgstaeivaelleekkeeiskeiaellllgi 101
                                       e +  +  +++ +i iDHH +   +e+ ++i+++++++ +taeiv +l+e+ +  i+ke+ae+l lgi
  gi|557695010|ref|YP_008798064.1| 100 EYKdkVYGSGKPIISIDHHVKT--AENSETITLVSTKYLATAEIVHDLVEYLNLVIDKEMAEALFLGI 165
                                       65455999*************6..8888889***********************************98 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.35   3.1e+03      47      85 ..      28      69 ..       8      72 .. 0.73
   2 ?   -1.2   0.0      0.28   2.5e+03      68      88 ..     155     175 ..     118     216 .. 0.59
   3 !   17.7   0.2   4.1e-07    0.0037      56     132 ..     237     320 ..     217     326 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.35
                                      CHCCHHHHHHHHH..HHHHHTHGBT.TCEEEEEEEECT.EEEE CS
                             DHHA1 47 vgeewdagalgia..adklksklkk.pvivfvakeegd.kvkv 85
                                         + da+ +g+a   ++l+++ ++  ++ f++ ee   +vk 
  gi|557695010|ref|YP_008798064.1| 28 H-WGGDADSVGSAyvMTRLLTQNYEaSEAGFLIPEESAlHVKA 69
                                      3.66777777777778999998888899999999998777776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.28
                                       BT.TCEEEEEEEECTEEEEEEE CS
                             DHHA1  68 kk.pvivfvakeegdkvkvsar 88 
                                       k+ ++++f+    + +v++s++
  gi|557695010|ref|YP_008798064.1| 155 KEmAEALFLGIYYD-TVRLSIG 175
                                       34444444444444.5554443 PP

  == domain 3  score: 17.7 bits;  conditional E-value: 4.1e-07
                                       HHHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSH.....SS-HH.HHHHHHHHHTTCCEEEETCEEEEEEE..H CS
                             DHHA1  56 lgiaadklksklkkpvivfvakeegdkvkvsarskkd.....gvdag.elakeaaaklgggGGGHdlAaGagip..a 124
                                       l ++a  l +    + +++va+e+g+   + ar + d     gv +g +l++ + + + g GGGH  Aa ++++   
  gi|557695010|ref|YP_008798064.1| 237 LSSVARTLVN--AGAHVALVAGEKGEYTILAARGSYDfqkfsGVGLGdDLVNYLLRRFEGDGGGHVGAARLRLKapV 311
                                       5677778888..6699999999999888899999999**********99****************999998886335 PP

                                       CH.HHHHHH CS
                             DHHA1 125 ek.leeale 132
                                       ek +eea++
  gi|557695010|ref|YP_008798064.1| 312 EKvIEEAVK 320
                                       555666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2399.14
//
Query:       gi|557695011|ref|YP_008798065.1|  [L=282]
Description: cobalt/nickel ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-29  101.1   0.0      1e-28  100.6   0.0    1.2  1  ABC_tran      ABC transporter
    2.5e-10   40.6   1.2    1.7e-05   24.8   0.1    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    4.9e-07   29.4   0.2    2.3e-06   27.2   0.2    1.9  1  SMC_N         RecF/RecN/SMC N terminal domain
    0.00032   20.3   0.0      0.058   13.0   0.0    2.9  3  AAA_25        AAA domain
    0.00082   19.1   0.0     0.0016   18.2   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
     0.0017   18.8   0.4     0.0027   18.1   0.3    1.7  1  AAA_16        AAA ATPase domain
     0.0027   18.0   0.1     0.0066   16.7   0.1    1.8  1  AAA_22        AAA domain
     0.0031   17.5   0.0     0.0063   16.4   0.0    1.5  1  RsgA_GTPase   RsgA GTPase
      0.006   16.0   0.0      0.011   15.2   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
  ------ inclusion threshold ------
      0.011   16.2   0.0       0.02   15.4   0.0    1.3  1  AAA_23        AAA domain
      0.028   14.6   0.0       0.37   11.0   0.0    2.1  2  AAA_28        AAA domain
      0.037   13.6   0.0      0.068   12.7   0.0    1.3  1  AAA_27        AAA domain
      0.041   14.3   0.8         10    6.5   0.1    2.5  2  AAA           ATPase family associated with various cellular 
       0.11   12.2   0.0       0.17   11.6   0.0    1.5  1  AAA_30        AAA domain
       0.13   12.2   0.0       0.23   11.4   0.0    1.4  1  Rad17         Rad17 P-loop domain
       0.15   12.0   0.2        1.8    8.6   0.0    2.2  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 !  100.6   0.0     9e-32     1e-28       1     137 []      21     172 ..      21     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 100.6 bits;  conditional E-value: 9e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlkeqeleslrkeigvlpqe..pql 70 
                                       lknvs+++++ge v +vG++G GKStLl++l gl+ +      +G++ +dg + ++++++++++ ig+++q+  +ql
  gi|557695011|ref|YP_008798065.1|  21 LKNVSFSVERGEFVLVVGPSGGGKSTLLRCLNGLVPQfyegeYSGKVVVDGLEPDKTPTHKMSQVIGMVFQNpqNQL 97 
                                       79*********************************99999999*****************************54444 PP

                                       -TTSBHHHH..........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  71 fpeltvren..........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       f  + v+             ++e i+++ +++gl ++++ + ++sp +LSgGq+qrva+a +l+ kpk+l +DEpt+
  gi|557695011|ref|YP_008798065.1|  98 FALS-VEADiafplenlglPREEIIQRVEETMGLLNIAHLR-DRSPFELSGGQQQRVAIASVLAMKPKILAMDEPTS 172
                                       4444.66669*******995555555555555555544444.4556*****************************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 !   15.3   0.1   1.2e-05     0.014       1      22 [.      33      54 ..      33      77 .. 0.83
   2 !   24.8   0.1   1.5e-08   1.7e-05     182     292 ..     104     195 ..      59     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      + +++Gp g GKS+LL++l +l
  gi|557695011|ref|YP_008798065.1| 33 FVLVVGPSGGGKSTLLRCLNGL 54
                                      6789***************998 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.5e-08
                            AAA_21 182 krllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkkg 258
                                        ++++ l++  +++e               ++ +  e+++ +l   + ++++++elS G+++  a+++ l+  +   
  gi|557695011|ref|YP_008798065.1| 104 ADIAFPLENLGLPRE---------------EIIQRVEETMGLLNIAHLRDRSPFELSGGQQQRVAIASVLAMKP--- 162
                                       333333333333333...............3333333477777777888899***********88888888877... PP

                            AAA_21 259 sllliDEpEngLHPkllrrllellkelsrngaQv 292
                                       ++l+ DEp ++L+P   + ll l+++ ++ + Q+
  gi|557695011|ref|YP_008798065.1| 163 KILAMDEPTSFLDPLTAAQLLSLIDDVRK-RLQL 195
                                       9**********************988877.6665 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 !   27.2   0.2     2e-09   2.3e-06      25     211 ..      32     214 ..      20     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2e-09
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--....BTTCSSTTEEEEEEEEEETTEESSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk....skekasvkkaeveitfdnedkklkiekeev 97 
                                       +f  +vGp G GKs ll  +  +  +        e   +++       k+  + ++  + ++f+n++++l   + e 
  gi|557695011|ref|YP_008798065.1|  32 EFVLVVGPSGGGKSTLLRCLNGLVPQ----FYEGEYSGKVVVDglepDKTPTHKMSQVIGMVFQNPQNQLFALSVEA 104
                                       5999**************99544442....22344444455445663555566666677899*******99999999 PP

                                       EEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDek 174
                                        i   +++ g  + +i ++  +   + ++ +  + s+ +LSgG+++ va+a ++A++   p+ +  +De  + LD  
  gi|557695011|ref|YP_008798065.1| 105 DIAFPLENLGLPREEIIQRVEETMGLLNIAHLRDRSPFELSGGQQQRVAIASVLAMK---PK-ILAMDEPTSFLDPL 177
                                       999999999987777777777777777777777778889************999975...44.779*********** PP

                                       HHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 175 nvkkvaellkeksknaQfivislreemlekadklvgv 211
                                         +++ +l++  +k+ Q+ v  +++++   a k  ++
  gi|557695011|ref|YP_008798065.1| 178 TAAQLLSLIDDVRKRLQLTVLLVEHRVEMAAAKADRI 214
                                       *****************98877666655555444444 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   5.2e-05     0.058      30      53 ..      28      51 ..       5     132 .. 0.74
   2 ?    3.8   0.0     0.034        38     165     188 ..     179     202 ..     167     204 .. 0.91
   3 ?   -0.8   0.0      0.84   9.4e+02      69      88 ..     258     277 ..     245     281 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.2e-05
                            AAA_25 30 lpagelallaGapgtGKttlaldl 53
                                      + +ge++l++G++g GK+tl+  l
  gi|557695011|ref|YP_008798065.1| 28 VERGEFVLVVGPSGGGKSTLLRCL 51
                                      589*****************8665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.034
                            AAA_25 165 vgalvealeriarrtgaavllvhH 188
                                       +++l++ ++++++r++ +vllv H
  gi|557695011|ref|YP_008798065.1| 179 AAQLLSLIDDVRKRLQLTVLLVEH 202
                                       4789999****************9 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.84
                            AAA_25  69 peqgkVlyvsaEdsedelrr 88 
                                        e+++ + +saE+ e+e+rr
  gi|557695011|ref|YP_008798065.1| 258 LEKWNRVCLSAEEFEAEVRR 277
                                       3899999********99998 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 !   18.2   0.0   1.4e-06    0.0016      15      39 ..      24      48 ..      20      57 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                       ++++++ +++l++GpsG GKSTll
  gi|557695011|ref|YP_008798065.1| 24 VSFSVERGEFVLVVGPSGGGKSTLL 48
                                      567777666***************8 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   0.3   2.4e-06    0.0027      23      45 ..      30      52 ..      21     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.4e-06
                            AAA_16 23 rpelvllsGesGvGKsslvrell 45
                                      r+e vl++G+sG GKs+l+r+l 
  gi|557695011|ref|YP_008798065.1| 30 RGEFVLVVGPSGGGKSTLLRCLN 52
                                      3489****************986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   5.9e-06    0.0066       4      43 ..      30      69 ..      28     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5.9e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43
                                      +  +++v+G+sG GK+tllr l    ++ ++ e+ ++ vv
  gi|557695011|ref|YP_008798065.1| 30 RGEFVLVVGPSGGGKSTLLRCLNGLVPQFYEGEYSGKVVV 69
                                      56799***************99988877666666333333 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   5.6e-06    0.0063      87     121 ..      18      53 ..       5      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 5.6e-06
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       k +l++++  ++  +++++vG+SG GKStL+  l++
  gi|557695011|ref|YP_008798065.1|  18 KPSLKNVSFSVERgEFVLVVGPSGGGKSTLLRCLNG 53 
                                       456777777777669999*************99986 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   9.4e-06     0.011      25      67 ..      34      76 ..      20     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.4e-06
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealevakiasvagkk 67
                                      +l+vGp+G GK+ l ++l++l+p+  e e      +  +   k
  gi|557695011|ref|YP_008798065.1| 34 VLVVGPSGGGKSTLLRCLNGLVPQFYEGEYSGKVVVDGLEPDK 76
                                      899*********************9999987777776666544 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.0   1.8e-05      0.02      12      40 ..      23      52 ..      19      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-05
                            AAA_23 12 dqeidFsk.gltlItGpNGaGKTTildAik 40
                                      ++++  ++  ++l++Gp G GK+T+l+++ 
  gi|557695011|ref|YP_008798065.1| 23 NVSFSVERgEFVLVVGPSGGGKSTLLRCLN 52
                                      55555555257899**************96 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   0.00033      0.37       2      42 ..      34      75 ..      33      97 .. 0.79
   2 ?    1.5   0.0      0.27     3e+02      48      82 ..     188     222 ..     171     264 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                            AAA_28  2 ivitGgestGKTtlleaLaargypvv.pEaareileeklakg 42
                                      + ++G++++GK+tll+ L+    + +  E+  +++ ++l+ +
  gi|557695011|ref|YP_008798065.1| 34 VLVVGPSGGGKSTLLRCLNGLVPQFYeGEYSGKVVVDGLEPD 75
                                      7899************99988777776777777777776555 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.27
                            AAA_28  48 wvedllafaervleeqleeeaaaaankvlfcDrgl 82 
                                       +v+++l++  +++e+++e +aa a++ ++++D  +
  gi|557695011|ref|YP_008798065.1| 188 DVRKRLQLTVLLVEHRVEMAAAKADRIMVISDGRV 222
                                       44677888888888898888888888888888765 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.1e-05     0.068      18      49 ..      23      54 ..      18      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-05
                            AAA_27 18 sldfsaeeadlhliyGpNEAGKstalrAisdl 49
                                      +++fs e+ ++ l++Gp   GKst+lr ++ l
  gi|557695011|ref|YP_008798065.1| 23 NVSFSVERGEFVLVVGPSGGGKSTLLRCLNGL 54
                                      6889999********************99876 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 ?    6.0   0.0     0.013        15       1      18 [.      34      51 ..      34      92 .. 0.91
   2 ?    6.5   0.1    0.0092        10      47     114 ..     149     206 ..     118     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.013
                                      EEEESSTTSSHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakav 18
                                      vl++Gp G GK++l + +
  gi|557695011|ref|YP_008798065.1| 34 VLVVGPSGGGKSTLLRCL 51
                                      79***********99865 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0092
                                       HHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGG CS
                               AAA  47 relfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdk 114
                                       ++ ++ a+  a kp+il +DE  ++              +++qLl+ +d+v+k+ + ++v+++ +r+++
  gi|557695011|ref|YP_008798065.1| 149 QQRVAIASVLAmKPKILAMDEPTSFLDPL----------TAAQLLSLIDDVRKRLQ-LTVLLVEHRVEM 206
                                       44444455555679999999999998888..........89************977.888887777665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00015      0.17      18      67 ..      31      87 ..      24     200 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaa.g....grvi..glAptgkaAkvLaeelg 67
                                        +++++Gp G GK+t+l+ l+ ++ +  +    g+v+  gl p ++  +++++ +g
  gi|557695011|ref|YP_008798065.1| 31 GEFVLVVGPSGGGKSTLLRCLNGLVPQFyEgeysGKVVvdGLEPDKTPTHKMSQVIG 87
                                      45899**************99877655422344533332356555555555555555 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0002      0.23      43      66 ..      29      52 ..      18      96 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                             Rad17 43 rkkriLLisGPsGCgkstvvkvLs 66
                                      ++ + +L+ GPsG gkst ++ L 
  gi|557695011|ref|YP_008798065.1| 29 ERGEFVLVVGPSGGGKSTLLRCLN 52
                                      445689**************9996 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 ?    8.6   0.0    0.0016       1.8       2      23 ..      34      55 ..      33      63 .. 0.85
   2 ?    1.3   0.0      0.28   3.2e+02      58      97 ..     155     194 ..     116     234 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                                      EEEE--SSSSHHHHHHHGGGGB CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal 23
                                      vl+vGp+G gKs+l + l  ++
  gi|557695011|ref|YP_008798065.1| 34 VLVVGPSGGGKSTLLRCLNGLV 55
                                      799***********99887766 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.28
                                       -------G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE.. CS
                             AAA_5  58 plvraaregeilvlDEverae.sevlnsLlslleerrllle 97 
                                       + v a  +++il +DE +    + +++ Llsl+++ r +l 
  gi|557695011|ref|YP_008798065.1| 155 ASVLA-MKPKILAMDEPTSFLdPLTAAQLLSLIDDVRKRLQ 194
                                       44423.36677777777776669999999999998665443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); 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 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2038.21
//
Query:       gi|557695012|ref|YP_008798066.1|  [L=268]
Description: cobalt/nickel ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-27   95.6   0.0    5.8e-27   94.9   0.0    1.4  1  ABC_tran      ABC transporter
    1.8e-08   34.6   0.1     0.0037   17.1   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    2.2e-06   27.3   0.1    4.3e-05   23.1   0.1    2.1  1  SMC_N         RecF/RecN/SMC N terminal domain
    2.3e-05   25.0   0.0    3.9e-05   24.2   0.0    1.3  1  AAA_23        AAA domain
    5.7e-05   22.8   0.0    0.00013   21.7   0.0    1.5  1  AAA_29        P-loop containing region of AAA domain
    0.00044   20.1   0.0     0.0031   17.3   0.0    1.9  2  AAA_15        AAA ATPase domain
      0.001   18.8   0.0     0.0029   17.3   0.0    1.7  2  AAA_30        AAA domain
     0.0013   18.7   0.1     0.0023   17.9   0.1    1.5  1  NACHT         NACHT domain
     0.0014   19.0   0.1     0.0023   18.4   0.1    1.6  1  AAA_16        AAA ATPase domain
     0.0021   17.7   0.1     0.0059   16.3   0.0    1.7  2  SRP54         SRP54-type protein, GTPase domain
     0.0024   16.8   0.1     0.0035   16.2   0.1    1.1  1  DLIC          Dynein light intermediate chain (DLIC)
      0.003   17.5   0.9       0.08   12.9   0.2    2.2  2  NTPase_1      NTPase
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.025   14.0   0.0    1.5  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
      0.025   14.5   0.0       0.06   13.3   0.0    1.6  1  Gag_p17       gag gene protein p17 (matrix protein)
      0.029   14.1   0.0      0.057   13.1   0.0    1.5  1  AAA_24        AAA domain
      0.032   14.5   0.0      0.083   13.2   0.0    1.7  2  AAA_22        AAA domain
      0.038   14.3   0.0       0.18   12.1   0.0    1.9  2  AAA_19        AAA domain
      0.041   13.1   0.3        0.1   11.8   0.0    1.7  2  NB-ARC        NB-ARC domain
      0.047   11.2   0.1      0.062   10.8   0.1    1.1  1  DUF3584       Protein of unknown function (DUF3584)
      0.056   13.4   0.0       0.12   12.4   0.0    1.5  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.077   12.6   0.1       0.15   11.7   0.1    1.5  1  cobW          CobW/HypB/UreG, nucleotide-binding domain
       0.08   12.9   0.8       0.19   11.6   0.2    1.9  2  RsgA_GTPase   RsgA GTPase
      0.086   12.6   0.1        0.2   11.4   0.1    1.5  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
      0.092   12.8   0.2       0.31   11.0   0.1    1.9  2  AAA_5         AAA domain (dynein-related subfamily)
      0.095   13.2   0.1       0.24   11.9   0.1    1.9  1  AAA_18        AAA domain
        0.1   12.1   0.0       0.28   10.7   0.0    1.7  1  AAA_25        AAA domain
       0.13   12.1   0.0       0.23   11.4   0.0    1.5  1  ATPase_2      ATPase domain predominantly from Archaea


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 !   94.9   0.0   8.8e-30   5.8e-27       1     136 [.      12     157 ..      12     158 .. 0.92

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 8.8e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltv 76 
                                       l+ vsl++++ge+va++GenG+GK+tLlk + gllkp +G++ ++g ++++ +  +l++  g ++q+ + +f e++v
  gi|557695012|ref|YP_008798066.1|  12 LRGVSLEFRPGELVALMGENGSGKTTLLKHINGLLKPVKGRVIVEGVETRTASVAQLSQVAGLVFQNaEDMFFESNV 88 
                                       678****************************************************************8677777778 PP

                                       HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                        ++               ++++e al+ ++l+  +++        LSgG+k+r+a+a +l+  p++++lDEpt
  gi|557695012|ref|YP_008798066.1|  89 FDEvafalrnfgygeeVVRKRVEWALKFFELDAYANQSP----FLLSGGEKKRLAMAIILAWSPRIICLDEPT 157
                                       8888999999*9987666677999999999999777776....*****************************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 !   15.7   0.1   1.5e-05      0.01       2      23 ..      25      46 ..      24      68 .. 0.82
   2 !   17.1   0.0   5.6e-06    0.0037     201     302 ..      81     192 ..      61     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       +l G NgsGK++LL+ + +l 
  gi|557695012|ref|YP_008798066.1| 25 VALMGENGSGKTTLLKHINGLL 46
                                      6899************999994 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 5.6e-06
                            AAA_21 201 dlgegeeliasvderlrer.............gvvflengdgqelparelSdGtkrllalltallralkkgsllliD 264
                                       d+ + ++  ++v+++lr                + f+e + + + +++ lS G k+ la++ +l+  +   +++++D
  gi|557695012|ref|YP_008798066.1|  81 DMFFESNVFDEVAFALRNFgygeevvrkrvewALKFFELDAYANQSPFLLSGGEKKRLAMAIILAWSP---RIICLD 154
                                       5555555555555555555777777777778889999999*****************99999999888...****** PP

                            AAA_21 265 EpEng...LHPkllrrllellkelsrngaQviltTHSplll 302
                                       Ep  g   L  + +++ +++l   ++ g  v+l+TH+ +++
  gi|557695012|ref|YP_008798066.1| 155 EPTIGqdsLQKEKMKHMIKML---NTQGRTVLLATHDVEFV 192
                                       ***994445556666666666...44478*******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 !   23.1   0.1   6.4e-08   4.3e-05      20     203 ..      17     193 ..       7     206 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6.4e-08
                                       EETTS.SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEE.EEEEETTEESSSSS CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                             SMC_N  20 lpfsk.sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeve.itfdnedkklkiek 94 
                                       l+f + ++ a++G+NGSGK+ ll  i    G    k ++ + + + +   ++ + ++  +v+ ++f+n ++ + +++
  gi|557695012|ref|YP_008798066.1|  17 LEFRPgELVALMGENGSGKTTLLKHIN---G--LLKPVKGRVIVEGVET-RTASVAQLSQVAgLVFQNAEDMFFESN 87 
                                       55555247899************9994...3..2334555555555554.677777777776356777777744444 PP

                                       ..SCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEE CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  95 ..eevsisrrvkrkgeseykingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyl 163
                                         +ev    r +  ge        ev +k v+  l+  +++        lLSgGek+ +a+a+++A     p+ + +
  gi|557695012|ref|YP_008798066.1|  88 vfDEVAFALRNFGYGE--------EVVRKRVEWALKFFELDAYanqspfLLSGGEKKRLAMAIILAWS---PR-IIC 152
                                       1133444433333333........33333333333333333333333339**************9964...54.566 PP

                                       ECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
                             SMC_N 164 lDeidaaLDeknvkkvaellkekskn.aQfivislreemle 203
                                       lDe     D  + +k+ +++k  +++   ++  +++ e+++
  gi|557695012|ref|YP_008798066.1| 153 LDEPTIGQDSLQKEKMKHMIKMLNTQgRTVLLATHDVEFVA 193
                                       89999999999999999999977766355666677666655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   5.9e-08   3.9e-05       6      41 ..       8      44 ..       5      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 5.9e-08
                            AAA_23  6 nfrsfrdqeidFsk.gltlItGpNGaGKTTildAikl 41
                                      n++ +r+++++F +  l+++ G+NG+GKTT+l  i  
  gi|557695012|ref|YP_008798066.1|  8 NVHALRGVSLEFRPgELVALMGENGSGKTTLLKHING 44
                                      89999*******9846****************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 !   21.7   0.0   1.9e-07   0.00013       8      50 ..       8      50 ..       2      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.9e-07
                            AAA_29  8 NWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      N + ++g ++e+++ + + l+G++GsGK+Tll  i+ lL p k
  gi|557695012|ref|YP_008798066.1|  8 NVHALRGVSLEFRPGELVALMGENGSGKTTLLKHINGLLKPVK 50
                                      6678889999***999****************99998888865 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.7e-06    0.0031      14      48 ..      12      47 ..       7      95 .. 0.82
   2 ?    0.7   0.0      0.51   3.4e+02     325     367 ..     149     190 ..     145     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.7e-06
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFln 48
                                      l+ v++++ +  l  l G+N+sGK+++l+ ++ +l+
  gi|557695012|ref|YP_008798066.1| 12 LRGVSLEFRPGeLVALMGENGSGKTTLLKHINGLLK 47
                                      6778888888889******************98887 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.51
                            AAA_15 325 villiEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                                        i++++EP + +  ++qk+ +k +++++n+    v++ TH   
  gi|557695012|ref|YP_008798066.1| 149 RIICLDEPTIGQ-DSLQKEKMKHMIKMLNTQGRTVLLATHDVE 190
                                       689999999999.78999999********99999******865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.4e-06    0.0029      19      67 ..      23      73 ..      17     115 .. 0.79
   2 ?   -1.6   0.0       2.8   1.9e+03      35      63 ..     168     196 ..     164     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.4e-06
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkv..Laeelg 67
                                       +++l G  G+GKtt+lk+++ +++  +grvi+   + + A v  L++ +g
  gi|557695012|ref|YP_008798066.1| 23 ELVALMGENGSGKTTLLKHINGLLKPVKGRVIVEGVETRTASVaqLSQVAG 73
                                      47899**********************999998888777776623555444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.8
                            AAA_30  35 lkalreaweaaggrviglAptgkaAkvLa 63 
                                       +k++ ++++++g++v+++++  +  ++L+
  gi|557695012|ref|YP_008798066.1| 168 MKHMIKMLNTQGRTVLLATHDVEFVAELR 196
                                       67777777777777777776666665555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   3.4e-06    0.0023       2      24 ..      24      46 ..      23      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.4e-06
                                      CEEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalaw 24
                                      lv+l Ge+GsGKTtLl+++  ++
  gi|557695012|ref|YP_008798066.1| 24 LVALMGENGSGKTTLLKHINGLL 46
                                      799***************97665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   3.4e-06    0.0023      23      63 ..      20      62 ..       9     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.4e-06
                            AAA_16 23 rp.elvllsGesGvGKsslvrellralekdggif.lrgkcdql 63
                                      rp elv l Ge G+GK++l++++   l+  +g + ++g  ++ 
  gi|557695012|ref|YP_008798066.1| 20 RPgELVALMGENGSGKTTLLKHINGLLKPVKGRViVEGVETRT 62
                                      55699***************99996555544555355554444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   8.9e-06    0.0059       4      53 ..      25      73 ..      23      97 .. 0.87
   2 ?   -1.8   0.0         3     2e+03      21      38 ..     171     188 ..     157     193 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.9e-06
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHH CS
                             SRP54  4 illvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlae 53
                                      ++l+G +G+GKTt l  +  llk  + +v++  + t R a v QL+++a 
  gi|557695012|ref|YP_008798066.1| 25 VALMGENGSGKTTLLKHINGLLKPVKGRVIVEGVET-RTASVAQLSQVAG 73
                                      789*************99999999888888777766.*********9985 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                                       HHHHHHHTTS-EEEEEES CS
                             SRP54  21 LaallkkegkkvllvaaD 38 
                                       + ++l+++g++vll++ D
  gi|557695012|ref|YP_008798066.1| 171 MIKMLNTQGRTVLLATHD 188
                                       556677777777777777 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   5.3e-06    0.0035      26      56 ..      23      53 ..      15      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.3e-06
                              DLIC 26 ksvlvlGedgsGkttliaklqGveeekkGrG 56
                                        v ++Ge+gsGkttl+  + G+ ++ kGr 
  gi|557695012|ref|YP_008798066.1| 23 ELVALMGENGSGKTTLLKHINGLLKPVKGRV 53
                                      56899************************95 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   0.00012      0.08       2      36 ..      25      61 ..      24      70 .. 0.81
   2 ?    3.1   0.0      0.12        82      96     150 ..     148     199 ..     125     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
                                      EEEE--TTSSHHHHHHHHHHHH.....GGGEEEEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkss..gvkvgGfyte 36
                                      v++ G+ G+GKtTl+k +  llk     v v+G+ t+
  gi|557695012|ref|YP_008798066.1| 25 VALMGENGSGKTTLLKHINGLLKPVkgRVIVEGVETR 61
                                      6789****************99843225778888775 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.12
                                       H-EEEE--..-STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT- CS
                          NTPase_1  96 adviviDE..iGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdv 150
                                       + +i +DE  iG+  l+ +k+k++++ + ++++ vl   h     ++v e+r r  v
  gi|557695012|ref|YP_008798066.1| 148 PRIICLDEptIGQDSLQKEKMKHMIKMLNTQGRTVLLATHDV---EFVAELRPR--V 199
                                       568999999999999*******99987777888888888877...689999887..4 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   0.0   3.7e-05     0.025      25      68 ..      25      70 ..      10      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-05
                      Mg_chelatase 25 lllvGppGsGKtmlakrlpsllpplseeealev..akiasvagkke 68
                                      + l+G  GsGKt l k +++ll p++ + ++e   ++ asva+ ++
  gi|557695012|ref|YP_008798066.1| 25 VALMGENGSGKTTLLKHINGLLKPVKGRVIVEGveTRTASVAQLSQ 70
                                      5799**********************99999851245566766555 PP

>> Gag_p17  gag gene protein p17 (matrix protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.1e-05      0.06      29      64 ..     229     264 ..     215     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.1e-05
                           Gag_p17  29 klkhlvwasrelerfavdeglleteeGckkileqle 64 
                                        +  lv+a ++le ++ d  +l+ +eG +++l++l+
  gi|557695012|ref|YP_008798066.1| 229 LMPQLVYAFKRLEDLGFDSHVLDVDEGVRQVLKVLR 264
                                       4678*****************************996 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.6e-05     0.057       5      37 ..      25      64 ..      23      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.6e-05
                            AAA_24  5 iliyGpsgiGKTtlakel.......gpkplfidtekGlks 37
                                      ++++G++g+GKTtl+k++       + ++++  +e  ++s
  gi|557695012|ref|YP_008798066.1| 25 VALMGENGSGKTTLLKHIngllkpvKGRVIVEGVETRTAS 64
                                      689**************97777766666666666665555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00012     0.083       7      29 ..      24      46 ..      20      82 .. 0.84
   2 ?   -2.1   0.0       6.5   4.3e+03     103     117 ..     163     176 ..     107     192 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                            AAA_22  7 ilvvtGesGtGKTtllrrlleql 29
                                      +++++Ge G+GKTtll+ +   l
  gi|557695012|ref|YP_008798066.1| 24 LVALMGENGSGKTTLLKHINGLL 46
                                      6899*************987666 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 6.5
                            AAA_22 103 lrseealeeLrslln 117
                                       l ++e +++  ++ln
  gi|557695012|ref|YP_008798066.1| 163 L-QKEKMKHMIKMLN 176
                                       3.3333333333333 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      0.18      10      39 ..      22      51 ..      16     133 .. 0.90
   2 ?    0.2   0.0       1.3   8.5e+02      27      62 ..     164     199 ..     137     262 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00027
                            AAA_19 10 ekvllvtaGpGtGKTrvlkhivallvelgg 39
                                       +++++++  G+GKT++lkhi  ll+ ++g
  gi|557695012|ref|YP_008798066.1| 22 GELVALMGENGSGKTTLLKHINGLLKPVKG 51
                                      578999***************999987775 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.3
                            AAA_19  27 lkhivallvelggvkpeeillvaftgrAakelrerl 62 
                                        k+++++++++ + + +++ll++     + elr r+
  gi|557695012|ref|YP_008798066.1| 164 QKEKMKHMIKMLNTQGRTVLLATHDVEFVAELRPRV 199
                                       566777777777777777777777666666666665 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   0.0   0.00015       0.1      22      45 ..      24      47 ..      16      55 .. 0.84
   2 ?   -2.2   0.0       2.8   1.9e+03     215     230 ..     166     181 ..     160     195 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                      EEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC 22 vvalvGmgGvGKttlakqilnksd 45
                                      +val+G  G+GKttl+k+i+  ++
  gi|557695012|ref|YP_008798066.1| 24 LVALMGENGSGKTTLLKHINGLLK 47
                                      799***************986655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.8
                                       CHHHHHHHHHHCTGCC CS
                            NB-ARC 215 eewkkvleklesklle 230
                                       e++k++++ l+++++ 
  gi|557695012|ref|YP_008798066.1| 166 EKMKHMIKMLNTQGRT 181
                                       5677777777766655 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   9.4e-05     0.062       4      36 ..       8      41 ..       7      43 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.4e-05
                           DUF3584  4 dsf.lkGrvaeldldghtnieGtNaaGKTtLlrL 36
                                      + + l+G+  e ++ + + + G N++GKTtLl+ 
  gi|557695012|ref|YP_008798066.1|  8 NVHaLRGVSLEFRPGELVALMGENGSGKTTLLKH 41
                                      5677899999*********************975 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00018      0.12      19      40 ..      22      43 ..       7      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                                      TEEEEEEESTTSSHHHHHHHHH CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrgla 40
                                      g++++L G+ G+GKTtl +++ 
  gi|557695012|ref|YP_008798066.1| 22 GELVALMGENGSGKTTLLKHIN 43
                                      788***************9985 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 ?   11.7   0.1   0.00022      0.15       4      23 ..      26      45 ..      23      67 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                                      EEEESTTCCHHHHHHHHHCT CS
                              cobW  4 vltGflGsGKTtLlnhllen 23
                                       l G  GsGKTtLl+h+   
  gi|557695012|ref|YP_008798066.1| 26 ALMGENGSGKTTLLKHINGL 45
                                      688999**********9744 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00028      0.19      99     122 ..      22      45 ..       8      75 .. 0.79
   2 ?   -1.9   0.0       4.1   2.7e+03      91      91 ..     193     193 ..     157     230 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00028
                                       TSEEEEECSTTSSHHHHHHHHCTT CS
                       RsgA_GTPase  99 dktsvlvGqSGvGKStLinallpe 122
                                       +++++l+G+ G GK+tL++++++ 
  gi|557695012|ref|YP_008798066.1|  22 GELVALMGENGSGKTTLLKHINGL 45 
                                       47899**************99885 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.1
                                       H CS
                       RsgA_GTPase  91 e 91 
                                       +
  gi|557695012|ref|YP_008798066.1| 193 A 193
                                       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 ?   11.4   0.1    0.0003       0.2       4      23 ..      25      44 ..      23      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0003
                         PduV-EutP  4 illiGkvgsGKttLtqalkg 23
                                      + l+G+ gsGKttL ++++g
  gi|557695012|ref|YP_008798066.1| 25 VALMGENGSGKTTLLKHING 44
                                      679**************998 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 ?   11.0   0.1   0.00046      0.31       2      24 ..      25      50 ..      24      82 .. 0.80
   2 ?   -1.7   0.0         4   2.6e+03      65      75 ..     147     157 ..     133     194 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                                      EEEE--SSSSHHHHHHHGGGGB...S CS
                             AAA_5  2 vlLvGppGtgKselaerlaaal...n 24
                                      v L G+ G+gK++l +++  +l   +
  gi|557695012|ref|YP_008798066.1| 25 VALMGENGSGKTTLLKHINGLLkpvK 50
                                      569***************99996541 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4
                                       G-SEEEEESGG CS
                             AAA_5  65 egeilvlDEve 75 
                                       +++i++lDE +
  gi|557695012|ref|YP_008798066.1| 147 SPRIICLDEPT 157
                                       67888888854 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00036      0.24       1      54 [.      25      91 ..      25     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00036
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf............gvnlrdvakenglllevdpealdeskrlde 54
                                      ++l+G  G+GKttl k+++ +l  +               + ++ +  gl++ + ++++ es+++de
  gi|557695012|ref|YP_008798066.1| 25 VALMGENGSGKTTLLKHINGLLkPVkgrvivegvetrTASVAQLSQVAGLVFQNAEDMFFESNVFDE 91
                                      679999************8877444877788877555333333333333333333335555555554 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   0.00042      0.28      32      50 ..      21      39 ..      10      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00042
                            AAA_25 32 agelallaGapgtGKttla 50
                                       gel++l+G  g+GKttl+
  gi|557695012|ref|YP_008798066.1| 21 PGELVALMGENGSGKTTLL 39
                                      59***************97 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 ?   11.4   0.0   0.00034      0.23      16      50 ..      18      52 ..      14     144 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00034
                          ATPase_2 16 erepneiyfiYGpegsGKtaLlkeiienledkdky 50
                                      e  p e + + G  gsGKt+Llk+i   l+  + +
  gi|557695012|ref|YP_008798066.1| 18 EFRPGELVALMGENGSGKTTLLKHINGLLKPVKGR 52
                                      66678888999*************97776554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      649  (0.0361983); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 1953.87
//
Query:       gi|557695013|ref|YP_008798067.1|  [L=265]
Description: cobalt/nickel ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  113.6  10.8    9.7e-33  113.6  10.8    1.4  2  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 !  113.6  10.8   5.4e-37   9.7e-33       2     217 ..      13     218 ..      12     219 .. 0.90
   2 ?   -4.1   0.1      0.55   9.9e+03     101     105 ..     234     238 ..     224     249 .. 0.47

  Alignments for each domain:
  == domain 1  score: 113.6 bits;  conditional E-value: 5.4e-37
                                       SCCCCS-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHTTS---HHHHHHHCCCHCHHHHHHHHHHE..... CS
                              CbiQ   2 ksvlhrldprvkliwlfllllalvlapnlvtlliiiallllllllvilprvlaqalilpllflllgllillfqlitt 78 
                                       k+++hrldprvkl++  ++l+ +v+   +v +l++ +l  l++l++ +  ++ + ++  + ++l+ +++++++    
  gi|557695013|ref|YP_008798067.1|  13 KTFIHRLDPRVKLATSTMVLITAVIHIDIVIILLLLILESLVILSAKVQNLWIKTIR--GALPLVAIVFAITF---- 83 
                                       89**************99999999999999998888888888888888888888888..77777777777773.... PP

                                       ..EECTTEEE...E-TTHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHCCCSS--HHHHHHHHHHHHHHHHHHH CS
                              CbiQ  79 egefvfagggqisitseGllrglllalRiltllslllllalTTppeeltsslerlgvPlelalillLayRfiflLle 155
                                            f++ ++  + s Gl ++l+ +lR l++ls  +l++lTT+p e++ +l++l+vP e ++++  a Rf ++++e
  gi|557695013|ref|YP_008798067.1|  84 -----FSQYSREPVISTGLGYALTYSLRLLVFLSSFSLFFLTTTPDEIALTLQQLRVPYEYTFAFVSAIRFTPVMAE 155
                                       .....444444556777788********************************************************* PP

                                       HHHHHHHHHHHTTTTS...SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS-SS.....S CS
                              CbiQ 156 evqrikqAqklRlgds.klgirrslrslgkliaalflralkraervalAmeaRGYtgseerth 217
                                       e+q+  +Aq++R+++  k ++ +++r l++++++l++ +++r+ ++a Ame++++  s++rt+
  gi|557695013|ref|YP_008798067.1| 156 ELQVVLDAQRSRGLEVdKGPFTKRIRNLIPVLVPLLVNVIRRSYELAEAMEVKCFGASRKRTS 218
                                       *******************************************************99888876 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.55
                                       HHHHH CS
                              CbiQ 101 lllal 105
                                       ++l+l
  gi|557695013|ref|YP_008798067.1| 234 VVLVL 238
                                       11111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.22s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2000.78
//
Query:       gi|557695014|ref|YP_008798068.1|  [L=187]
Description: transcription initiation factor TFIID TATA-box-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-59  195.9   0.2    7.7e-29   99.5   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
      4e-08   33.3   0.1      0.012   15.7   0.0    2.3  2  DUF3378   Domain of unknown function (DUF3378)
    0.00015   21.8   0.0      0.019   15.1   0.0    2.1  2  PAS_11    PAS domain
  ------ inclusion threshold ------
      0.026   14.8   0.0        5.1    7.5   0.0    2.2  2  DUF4061   Domain of unknown function (DUF4061)


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 !   94.9   0.1   4.8e-31   2.2e-27       2      84 ..       9      89 ..       8      90 .. 0.96
   2 !   99.5   0.0   1.7e-32   7.7e-29       2      83 ..     100     179 ..      99     180 .. 0.97

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 4.8e-31
                                      EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                               TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80
                                      ++iqNvv s++l ++ldL +++++    ++eY+p +fpglv+rl +pk++ liFssGk+v+tGakseee+ +a++++++
  gi|557695014|ref|YP_008798068.1|  9 VEIQNVVSSVTLFQKLDLAQIQRT--FPDVEYKPAQFPGLVFRLAKPKTATLIFSSGKMVCTGAKSEEESIRAVRTVVK 85
                                      79*******************766..5**************************************************** PP

                                      HHHH CS
                               TBP 81 ilkk 84
                                       lkk
  gi|557695014|ref|YP_008798068.1| 86 ALKK 89
                                      **97 PP

  == domain 2  score: 99.5 bits;  conditional E-value: 1.7e-32
                                       EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       ++iqN+vas++l+ ++dLe+ a+++  +n+ Yepe+fpgl+yr+++pkv++l+F+sGk+v+tGak e+++++a++k+
  gi|557695014|ref|YP_008798068.1| 100 IEIQNIVASIDLHGRIDLERAATTL--ENVMYEPEQFPGLIYRMNSPKVVILMFASGKLVCTGAKYEKDVYDAVNKL 174
                                       89*******************9888..************************************************** PP

                                       HHHHH CS
                               TBP  79 apilk 83 
                                        ++l+
  gi|557695014|ref|YP_008798068.1| 175 QQLLE 179
                                       99997 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.8e-06     0.012      10      60 ..      25      76 ..      16      89 .. 0.83
   2 !   15.6   0.0   2.9e-06     0.013      24      59 ..     131     166 ..     120     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.8e-06
                           DUF3378 10 tikkmkeyyksk.lrskkppyavfaakkndttItaYtSgKVlFQGknaeaeA 60
                                      ++ +++ ++ +   +  + p+ vf+  k++t   ++ SgK +  G++ e+e+
  gi|557695014|ref|YP_008798068.1| 25 DLAQIQRTFPDVeYKPAQFPGLVFRLAKPKTATLIFSSGKMVCTGAKSEEES 76
                                      5666666666654677899*****************************9986 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2.9e-06
                           DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeae 59 
                                        ++ p+ +++  +++++I ++ SgK++  G++ e++
  gi|557695014|ref|YP_008798068.1| 131 PEQFPGLIYRMNSPKVVILMFASGKLVCTGAKYEKD 166
                                       5789**************************999886 PP

>> PAS_11  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.0    0.0064        29      40     109 ..      17      85 ..       8      88 .. 0.86
   2 !   15.1   0.0   4.2e-06     0.019      42     108 ..     110     175 ..      98     182 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0064
                            PAS_11  40 iydLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfknqksneqdfimathtlls 109
                                         +L+++ dl ++++ + +v  ++ ++  +++RL   +++   +   +k+ ++  ++e ++i a+ t+++
  gi|557695014|ref|YP_008798068.1|  17 SVTLFQKLDLAQIQRTFPDVEYKPAQFPGLVFRLAK-PKTATLIFSSGKMVCTGAKSEEESIRAVRTVVK 85 
                                       56799999************999***********98.777777778888888889999999999999875 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.2e-06
                            PAS_11  42 dLchpqdlstlkshlrevissngeatsslyRLrlsqdkfvkvktksklfknqksneqdfimathtll 108
                                       dL+   dl+++++ l++v+ +++++  ++yR+ + +++++ + + +kl ++  + e d++ a++ l+
  gi|557695014|ref|YP_008798068.1| 110 DLHGRIDLERAATTLENVMYEPEQFPGLIYRMNS-PKVVILMFASGKLVCTGAKYEKDVYDAVNKLQ 175
                                       6777889**************************9.***********************999999876 PP

>> DUF4061  Domain of unknown function (DUF4061)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0011       5.1      17      56 ..      60      99 ..      57     132 .. 0.82
   2 ?    5.2   0.0    0.0057        25      17      47 ..     151     181 ..     139     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0011
                           DUF4061 17 FhsGklkafGkdcsleqleeiReqQekLarlhfeldaeee 56
                                      F sGk+   G++   e + ++R     L +  f + +e +
  gi|557695014|ref|YP_008798068.1| 60 FSSGKMVCTGAKSEEESIRAVRTVVKALKKEGFVIREEPQ 99
                                      99**********************9999999998887765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0057
                           DUF4061  17 FhsGklkafGkdcsleqleeiReqQekLarl 47 
                                       F sGkl   G++   +  +++ + Q+ L ++
  gi|557695014|ref|YP_008798068.1| 151 FASGKLVCTGAKYEKDVYDAVNKLQQLLEEK 181
                                       99*********************99988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1393.43
//
Query:       gi|557695015|ref|YP_008798069.1|  [L=225]
Description: lipoyl(octanoyl) transferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-11   42.7   0.0    7.2e-11   42.1   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 !   42.1   0.0     4e-15   7.2e-11      24     131 .]      62     159 ..      50     159 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 4e-15
                                       T-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH..........HHTT-TTEEEE CS
                     BPL_LplA_LipB  24 gglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealg..y..rdskpgiegipvfik 96 
                                       +++ v r ++gG++++h+p++ ++y ++++ +        ++ +v+ll+  v+++l   +   +   g++g++v+  
  gi|557695015|ref|YP_008798069.1|  62 RSVPVYRVERGGDATYHGPGQLVAYPVIDLNRL----AVTVAGFVHLLEEVVIKVLHdfSvdAERVEGYPGVWVK-- 132
                                       678899************************775....66688999999999999996542333378888898888.. PP

                                       TTTEEEETTEEEEEEEEEEEETTS-EEEEEEEEEE CS
                     BPL_LplA_LipB  97 wpnDlyvngrKlaGiavtstrgktlhhivigvgvn 131
                                               grK+a+i+  ++ ++t h+++++v+++
  gi|557695015|ref|YP_008798069.1| 133 --------GRKIASIGLAVKQWVTYHGVALNVNTD 159
                                       ........************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1732.90
//
Query:       gi|557695016|ref|YP_008798070.1|  [L=459]
Description: dihydrolipoamide dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-61  207.0   4.6    3.6e-61  207.0   4.6    1.9  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      5e-32  110.4   1.9    7.5e-32  109.9   0.8    1.9  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    1.3e-22   80.1   8.6    1.1e-20   73.9   0.6    3.4  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.9e-17   62.9   0.0    4.2e-17   62.4   0.0    1.3  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.7e-09   36.6   7.4    4.8e-09   35.8   3.0    2.6  3  GIDA            Glucose inhibited division protein A
    7.5e-08   32.5   2.7    2.1e-05   24.7   0.1    2.8  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    3.2e-07   30.1   2.4    3.2e-07   30.1   2.4    1.9  2  FAD_oxidored    FAD dependent oxidoreductase
    7.1e-07   28.6   8.3    2.6e-05   23.5   0.4    3.8  4  FAD_binding_2   FAD binding domain
    9.3e-06   25.1   6.5    0.00012   21.4   0.2    2.6  2  FAD_binding_3   FAD binding domain
    2.9e-05   23.8  15.8     0.0028   17.3   1.4    4.2  4  DAO             FAD dependent oxidoreductase
    0.00039   19.2   7.5       0.02   13.6   0.2    3.9  4  HI0933_like     HI0933-like protein
     0.0012   19.2   1.4       0.33   11.4   0.1    2.8  2  NAD_binding_7   Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.038   14.0   5.0       0.73    9.8   0.1    3.4  3  NAD_binding_9   FAD-NAD(P)-binding
      0.072   11.9   0.1      0.072   11.9   0.1    2.0  3  Trp_halogenase  Tryptophan halogenase
       0.26   10.5   6.9      0.043   13.1   0.7    2.8  4  Thi4            Thi4 family
       0.62    9.1   5.4       0.52    9.3   1.1    2.6  2  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 !  207.0   4.6   3.2e-64   3.6e-61       2     294 .]       4     320 ..       3     320 .. 0.93
   2 ?    0.5   0.1      0.25   2.8e+02     147     195 ..     403     452 ..     373     459 .] 0.72

  Alignments for each domain:
  == domain 1  score: 207.0 bits;  conditional E-value: 3.2e-64
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHC.HHHHHHHHHHHHH................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx.xxxxxxxxxxxxx................. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllsk.allgvaedaeias................. 57 
                                       d v++GgGp+G+a+a++l+q g+k++lve   l+g+c n+gc++sk  ++++++ ++ ++                 
  gi|557695016|ref|YP_008798070.1|   4 DAVIVGGGPGGYATAIRLSQLGVKTALVEkehLGGECTNWGCIPSKhLITHAKKIHSLMElsatglvtgqmtvnmsk 80 
                                       78**************************999*************9945666666666666***************** PP

                                       ......HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC....TCEEEEEESEEEE---EEE-BC...TCTTC.T CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxx...xxxxxxx RF
                       Pyr_redox_2  58 ......evvkklnqgielllgeevvkidpgkkkvklekkke....gdeekiaydklvlAtGssprdl...gipGvae 121
                                             +vv++l+qgi +ll++ +v+++ g++ +k + +++    g  e++++ ++v+AtG  +  l   + +G   
  gi|557695016|ref|YP_008798070.1|  81 itastqQVVQRLRQGISYLLKTYGVSVYVGEAVLKGSGEVKvvgeGGSESLEARNIVIATGTVQSSLsaaPYDGK-- 155
                                       *********************99*************9999999998889************86666632333344.. PP

                                       TBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 122 nvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGv 198
                                             r++   eal l+ +pk+++vvGgG+iGvEl  a++ lg++vt+ve +d+ll+++d+++++ l++ +ek Gv
  gi|557695016|ref|YP_008798070.1| 156 ------RIIGFREALYLEVVPKKMLVVGGGAIGVELGTAYRHLGSDVTVVELMDQLLPGMDPDAARLLKRGMEKIGV 226
                                       ......799999***************************************************************** PP

                                       EEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 199 evklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyai 274
                                       +++l+t+v+e +  +  +e vl++  +   d v+v vG rps   +   +lg++l e+g+++vd+++rt+ +g+ya+
  gi|557695016|ref|YP_008798070.1| 227 KIHLKTTVEETRYVDGGVEAVLSNDVKDVFDVVLVVVGKRPSEWVRMlADLGVKLSEKGYVLVDSRMRTSLDGVYAV 303
                                       ***********9999999*8888888889*************98888****************************** PP

                                       GGGCTECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 275 GDvaggkggpelaqaAvqqG 294
                                       GDv+   g p la++A +q+
  gi|557695016|ref|YP_008798070.1| 304 GDVT---GPPFLAHKAYKQA 320
                                       ****...99*******9997 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.25
                                       EES-SHHHHHHHHHHHHHT-E.EEEEESSSSSS..TTS-HHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 147 vvGgGyiGvElAaalaklgke.vtlveardrll..raldkelsaaleealek 195
                                       vvG  + ++E+ + l+ l k  +t+ ea +++   +++ +++++ ++ a+++
  gi|557695016|ref|YP_008798070.1| 403 VVG--PHATETVSILTTLIKLgATVEEASETIFihPTYSEAVAEVMHLAHKR 452
                                       333..555666666766644449999**999999999999999988887765 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 ?   -3.3   0.0       9.9   1.1e+04      66      86 ..     121     141 ..     114     150 .. 0.69
   2 !  109.9   0.8   6.7e-35   7.5e-32       1     108 [.     338     444 ..     338     446 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 9.9
                                       EEECTTHHHHHHHHHHHHHTT CS
                     Pyr_redox_dim  66 hivGpgageliqelavaikag 86 
                                       ++vG+g +e +++ +++i  g
  gi|557695016|ref|YP_008798070.1| 121 KVVGEGGSESLEARNIVIATG 141
                                       567777777776666666555 PP

  == domain 2  score: 109.9 bits;  conditional E-value: 6.7e-35
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       +p  vft peva+vGl+ e A+++g++   ++fp++a+gra+a++ ++gfvKl++d+kt+kvlGa++vGp+a+e ++
  gi|557695016|ref|YP_008798070.1| 338 VPFGVFTTPEVAAVGLSAETAREKGYDSAEARFPYAALGRAVAEN-EDGFVKLIFDKKTDKVLGATVVGPHATETVS 413
                                       57789**************************************97.9****************************** PP

                                       HHHHHHHTTSBHHHHHTSBSSSSSTGGGGHC CS
                     Pyr_redox_dim  78 elavaikagltvedladtihihPtlsealke 108
                                        l+++ik g+tve++ +ti+ihPt+sea+ e
  gi|557695016|ref|YP_008798070.1| 414 ILTTLIKLGATVEEASETIFIHPTYSEAVAE 444
                                       ****************************987 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.4    0.0012       1.3       2      31 ..       5      34 ..       4      39 .. 0.93
   2 ?   -2.8   0.0       8.9   9.9e+03      27      67 ..      51      93 ..      48     101 .. 0.69
   3 ?   -2.6   0.0       7.7   8.6e+03      49      69 ..      99     119 ..      86     125 .. 0.66
   4 !   73.9   0.6     1e-23   1.1e-20       1      77 [.     172     248 ..     172     252 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      +v+vGgG  g   A  l++lg k+ +ve +
  gi|557695016|ref|YP_008798070.1|  5 AVIVGGGPGGYATAIRLSQLGVKTALVEKE 34
                                      69*************************975 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 8.9
                                      EEESSSSSSTTSSHHHHHHHHHHHHHT..TEEEECSEEEEEEE CS
                         Pyr_redox 27 vversdkllrllDeeaskilqeklekn..gievllntkveeie 67
                                      ++  ++k+ +l++  a  +++ +++ n  +i+  ++++v++++
  gi|557695016|ref|YP_008798070.1| 51 LITHAKKIHSLMELSATGLVTGQMTVNmsKITASTQQVVQRLR 93
                                      6666667777777777777777776666677777777777665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.7
                                       HHHHTTEEEECSEEEEEEEEE CS
                         Pyr_redox  49 klekngievllntkveeiegs 69 
                                        l+  g+ v+ ++ v +  g+
  gi|557695016|ref|YP_008798070.1|  99 LLKTYGVSVYVGEAVLKGSGE 119
                                       456667777777777666555 PP

  == domain 4  score: 73.9 bits;  conditional E-value: 1e-23
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       k++vvGgG ig+El++a+++lg++Vtvve +d+ll+++D++a+++l++ +ek g++++l+t+vee +  + gve+v 
  gi|557695016|ref|YP_008798070.1| 172 KMLVVGGGAIGVELGTAYRHLGSDVTVVELMDQLLPGMDPDAARLLKRGMEKIGVKIHLKTTVEETRYVDGGVEAVL 248
                                       689****************************************************************9999999885 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 !   62.4   0.0   3.7e-20   4.2e-17       1     305 []       6     304 ..       6     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 3.7e-20
                       Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnignsiyrypk..emtfispsftsekleipdlnaiseetspafslke 75 
                                       +I+G+GP G a+ai l ++g++    +Ek+++g   +++    ++ +i+ +++ ++l       +++++  ++ +++
  gi|557695016|ref|YP_008798070.1|   6 VIVGGGPGGYATAIRLSQLGVK-TALVEKEHLGGECTNWGCipSKHLITHAKKIHSLMELSATGLVTGQM-TVNMSK 80 
                                       7********************5.789*************6433889999887766655544444444444.577889 PP

                       Pyr_redox_3  76 eklsrkealeYlre....vaksfelpiklfeeVesvkkedegfevetske..tyeAkkviiAtGefdkPnklnipGe 146
                                         +s++++++ lr+    + k++ +++   e   +v k +++ +v  + +  ++eA++++iAtG  +       p  
  gi|557695016|ref|YP_008798070.1|  81 ITASTQQVVQRLRQgisyLLKTYGVSVYVGE---AVLKGSGEVKVVGEGGseSLEARNIVIATGTVQSSL-SAAPYD 153
                                       9999999999999822224455555555555...5566666666666554349************77654.455555 PP

                       Pyr_redox_3 147 eklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvk 223
                                         + +       + ++  +k++V+Gg+  +v+  +     g++Vtvv   +++          + pd    l+++++
  gi|557695016|ref|YP_008798070.1| 154 G-KRIIGFREALYLEVVPKKMLVVGGGAIGVELGTAYRHLGSDVTVVELMDQLLP-------GMDPDAARLLKRGME 222
                                       5.3344444445558899*****************************99986554.......589************ PP

                       Pyr_redox_3 224 eekikvlfnaevkeikekeeeykvktedgkkvevkddvvla.tGykpd..lsflkkslfeldedgrpvlteeteetn 297
                                       +  +k++ +++v+e +  +  ++   ++   v+   dvvl+ +G +p+  +++l++ +++l+e+g++++++  + t 
  gi|557695016|ref|YP_008798070.1| 223 KIGVKIHLKTTVEETRYVDGGVEAVLSN--DVKDVFDVVLVvVGKRPSewVRMLADLGVKLSEKGYVLVDS-RMRTS 296
                                       955******************9988888..3444455555549****977899************999875.68999 PP

                       Pyr_redox_3 298 vpglflaG 305
                                       ++g++ +G
  gi|557695016|ref|YP_008798070.1| 297 LDGVYAVG 304
                                       *****998 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   3.0   4.3e-12   4.8e-09       1     153 [.       4     144 ..       4     163 .. 0.78
   2 ?    2.1   0.1     0.071        79       2      28 ..     173     199 ..     172     231 .. 0.85
   3 ?   -2.4   0.0       1.7   1.9e+03     349     386 ..     292     329 ..     287     332 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 4.3e-12
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfr 75 
                                       d +++GgG  G++ A+ +++lG+k++L+   h  +++ + +C ps   i  ++  + + +l +  + ++ + ++   
  gi|557695016|ref|YP_008798070.1|   4 DAVIVGGGPGGYATAIRLSQLGVKTALVekEHLGGECTNWGCIPSKHLITHAKKIHSLMEL-SATGLVTGQMTV--- 76 
                                       579*************************999999***************544433333333.667777888888... PP

                                       EESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-B CS
                              GIDA  76 ilNrskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtfl 152
                                         N sk  a  +       ++ ++ +   l++   +++  +e+      +++vk+v     e ++a+++viatGt +
  gi|557695016|ref|YP_008798070.1|  77 --NMSKITASTQQ----VVQRLRQGISYLLKT-YGVSVYVGEAVL--KGSGEVKVVGEGGSESLEARNIVIATGT-V 143
                                       ..66666665554....555566777777766.899999888654..4569************************.3 PP

                                       T CS
                              GIDA 153 k 153
                                       +
  gi|557695016|ref|YP_008798070.1| 144 Q 144
                                       3 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.071
                                       EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLi 28 
                                       + V+GgG  G+e   a   lG +v+ +
  gi|557695016|ref|YP_008798070.1| 173 MLVVGGGAIGVELGTAYRHLGSDVTVV 199
                                       67********************99987 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.7
                                       TSBBSSSBTEEE-CGGGTB-SHHHHHH..HHHHHHHHHHH CS
                              GIDA 349 tLetkkvkgLflAGqinGteGYeEaaa..qGllAGinaar 386
                                       +++t+  +g+++ G+++G   ++++ a  q  +A+ n+a 
  gi|557695016|ref|YP_008798070.1| 292 RMRTS-LDGVYAVGDVTGPP-FLAHKAykQAAVAAENIAG 329
                                       67776.8999*******987.7776666677777777765 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 !   24.7   0.1   1.9e-08   2.1e-05       1      38 [.       7      43 ..       7      61 .. 0.92
   2 !    7.2   0.3    0.0054       6.1       1      29 [.     175     203 ..     175     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.9e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                      IvG+G +G ++A +L++ g++  l+ek  +lGG ++ +
  gi|557695016|ref|YP_008798070.1|  7 IVGGGPGGYATAIRLSQLGVKTALVEKE-HLGGECTNW 43
                                      9**************************5.*****9975 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0054
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                                       +vG+G+ G  +  +++  g dv+++e  d
  gi|557695016|ref|YP_008798070.1| 175 VVGGGAIGVELGTAYRHLGSDVTVVELMD 203
                                       8***********************99755 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   2.4   2.8e-10   3.2e-07       1     109 [.       4     103 ..       4     145 .. 0.59
   2 ?   -1.2   0.3      0.89     1e+03       3      29 ..     174     200 ..     173     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.8e-10
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtgiareflerlrqrggarlkk 77 
                                       D v+vGGgp+G+a Ai   + G k++Lve+ ++lGG  t+ +  +  +  ++++ ++ +++     l    g+    
  gi|557695016|ref|YP_008798070.1|   4 DAVIVGGGPGGYATAIRLSQLGVKTALVEK-EHLGGECTNWGCIPSKHLITHAKKIHSLMELSATGLVT--GQ---- 73 
                                       779*************************97.69*******99988888665554444444444444422..11.... PP

                      FAD_oxidored  78 rskwntfepevakavleeml..aeagvtvllntr 109
                                            t++ +  +a  ++++   ++g+  ll+t 
  gi|557695016|ref|YP_008798070.1|  74 ----MTVNMSKITASTQQVVqrLRQGISYLLKTY 103
                                       ....123333333333333322122444444444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.89
                      FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLve 29 
                                       +VvGGg+ Gv    a    G  v +ve
  gi|557695016|ref|YP_008798070.1| 174 LVVGGGAIGVELGTAYRHLGSDVTVVE 200
                                       8*********99999999999999998 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.4   2.3e-08   2.6e-05       1      39 [.       4      42 ..       4      44 .. 0.88
   2 ?   -1.5   0.1      0.92     1e+03     182     204 ..     117     145 ..      55     154 .. 0.63
   3 ?    4.7   0.3     0.012        14       2      32 ..     173     203 ..     172     205 .. 0.93
   4 ?    3.0   0.0      0.04        45     383     403 ..     286     308 ..     272     320 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.3e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                                      D++++G+G +G+a A+++++ G k+a+veke+  g  t 
  gi|557695016|ref|YP_008798070.1|  4 DAVIVGGGPGGYATAIRLSQLGVKTALVEKEHLGGECTN 42
                                      89*****************************97443555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.92
                                       T......TTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 182 p......esgrevrirakavvlatgGfgr 204
                                       +       +g+ + ++a+++v+atg ++ 
  gi|557695016|ref|YP_008798070.1| 117 SgevkvvGEGGSESLEARNIVIATGTVQS 145
                                       14444445667778899999999998875 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.012
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeq 32 
                                        +V+G+G+ G   +++ ++ G +v+vve ++
  gi|557695016|ref|YP_008798070.1| 173 MLVVGGGAIGVELGTAYRHLGSDVTVVELMD 203
                                       59*************************9876 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.04
                                       BE..STTEEESSBTEEE-STCEE CS
                     FAD_binding_2 383 rv..ldadgqpipGLYAaGevaa 403
                                        v  +++  + ++G YA+G v++
  gi|557695016|ref|YP_008798070.1| 286 YVlvDSRMRTSLDGVYAVGDVTG 308
                                       5444555566**********994 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   1.1e-07   0.00012       2      33 ..       3      34 ..       2      37 .. 0.93
   2 !    5.2   1.6    0.0095        11       4      38 ..     173     207 ..     171     255 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                       d +IVG+Gp G  +a  Ls+ Gv++ lvek 
  gi|557695016|ref|YP_008798070.1|  3 FDAVIVGGGPGGYATAIRLSQLGVKTALVEKE 34
                                      5889**************************96 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0095
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCC CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvv 38 
                                        l+VG+G  G+ l++  +  G +v++ve +++  +
  gi|557695016|ref|YP_008798070.1| 173 MLVVGGGAIGVELGTAYRHLGSDVTVVELMDQLLP 207
                                       69**************************9887665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   1.4   2.5e-06    0.0028       1      37 [.       4      41 ..       4      66 .. 0.87
   2 ?    3.3   0.1     0.044        49     151     203 ..      95     143 ..      60     171 .. 0.68
   3 ?    4.8   0.5     0.016        18       3      27 ..     174     200 ..     172     205 .. 0.77
   4 !    6.9   0.1    0.0035         4     149     226 ..     214     289 ..     209     386 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.5e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaS 37
                                      d vi+GGG  G +tA  L++ g  ++l+ek+  +g +++
  gi|557695016|ref|YP_008798070.1|  4 DAVIVGGGPGGYATAIRLSQLGvkTALVEKE-HLGGECT 41
                                      78*****************************.6664554 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.044
                                       HHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGG CS
                               DAO 151 alaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGaw 203
                                       ++   +++ Gv ++ g+ v + +   g v+ v   + g++  +a+ +V+a+G  
  gi|557695016|ref|YP_008798070.1|  95 GISYLLKTYGVSVYVGEAVLKGS---GEVKVV--GEGGSEsLEARNIVIATGTV 143
                                       44455677899999999999863...445555..222555336799*****943 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.016
                                       EEECTSHHH..HHHHHHHHHTT..EEEEE CS
                               DAO   3 viiGGGiiG..lstAyeLarrg..Vtlle 27 
                                       +++GGG iG  l+tAy     g  Vt++e
  gi|557695016|ref|YP_008798070.1| 174 LVVGGGAIGveLGTAYRHL--GsdVTVVE 200
                                       8********5557777774..44699998 PP

  == domain 4  score: 6.9 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEEEEE--GGGHHHH.HTTCTTTSEEEEEEEE CS
                               DAO 149 taalaraaealGveilegtevtgleeedgkvwgve.rttpgendaadavVnaaGawsdll.gllkeldlpispvrgq 223
                                       ++ l r +e+ Gv+i+++t+v++ +  dg+v  v  +     +d +d v +  G   +++ ++l +l ++    +g+
  gi|557695016|ref|YP_008798070.1| 214 ARLLKRGMEKIGVKIHLKTTVEETRYVDGGVEAVLsN---DVKDVFDVVLVVVGKRPSEWvRMLADLGVK-LSEKGY 286
                                       5667788****************98888998888443...333446888888886666666777666445.666777 PP

                                       EEE CS
                               DAO 224 vlv 226
                                       vlv
  gi|557695016|ref|YP_008798070.1| 287 VLV 289
                                       776 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.2   1.8e-05      0.02       2      33 ..       4      35 ..       3      40 .. 0.92
   2 ?    2.2   0.1     0.053        59     109     164 ..      86     142 ..      74     152 .. 0.68
   3 ?    4.1   0.1     0.013        15       2      35 ..     172     205 ..     171     208 .. 0.92
   4 ?    0.6   0.0      0.16   1.8e+02     113     147 ..     215     249 ..     211     267 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      d +++GgG+ G  +Ai++++ g +++l+ek++
  gi|557695016|ref|YP_008798070.1|  4 DAVIVGGGPGGYATAIRLSQLGVKTALVEKEH 35
                                      89***************************985 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.053
                                       HHHHHHHHHH....HHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 109 edivdallke....lkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       +++v+ l +     lk  gv++++ ++v +    ++++  v   ++e+lea+++v+AtG 
  gi|557695016|ref|YP_008798070.1|  86 QQVVQRLRQGisylLKTYGVSVYVGEAVLKG---SGEVKVVGEGGSESLEARNIVIATGT 142
                                       5666666655111145667777777776665...3333344446999***********96 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.013
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                       +++v+GgGa G+    + ++ g++V+++e +++l
  gi|557695016|ref|YP_008798070.1| 172 KMLVVGGGAIGVELGTAYRHLGSDVTVVELMDQL 205
                                       689**************************99876 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.16
                                       HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE CS
                       HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvkt 147
                                       ++l++ +++ gvk++l+t+v++ ++ ++g+  v  
  gi|557695016|ref|YP_008798070.1| 215 RLLKRGMEKIGVKIHLKTTVEETRYVDGGVEAVLS 249
                                       6789999***************9888877544444 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 ?    6.2   0.1     0.012        14      10      41 ..       5      45 ..       2     127 .. 0.73
   2 !   11.4   0.1   0.00029      0.33       1      40 [.     164     203 ..     164     327 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                     NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvapev.........k 41
                                       ++vGgG+ ++  + +l + g k  +v +e          +
  gi|557695016|ref|YP_008798070.1|  5 AVIVGGGPGGYATAIRLSQLGVKTALVEKEHlggectnwgC 45
                                      79*************************99965444443332 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00029
                     NAD_binding_7   1 lfldlkgkkvlvvGgGevAarkvrklleagakvtvvapev 40 
                                       l+l++  kk+lvvGgG ++ +        g +vtvv    
  gi|557695016|ref|YP_008798070.1| 164 LYLEVVPKKMLVVGGGAIGVELGTAYRHLGSDVTVVELMD 203
                                       5788889**************999999999*****87662 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 ?    9.8   0.1   0.00065      0.73       1      39 [.       6      38 ..       6      62 .. 0.79
   2 ?    2.1   0.1      0.15   1.7e+02     129     155 ..     115     142 ..      82     143 .. 0.69
   3 ?    2.4   0.2      0.12   1.4e+02     105     154 ..     214     264 ..     212     266 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00065
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgag 39
                                      +ivG+Gp G a++ rL +       ++  l++++++g g
  gi|557695016|ref|YP_008798070.1|  6 VIVGGGPGGYATAIRLSQLG-----VKTALVEKEHLG-G 38
                                      7****************994.....777788887775.4 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.15
                     NAD_binding_9 129 eradgqavlladg.aslaadaVvLAlGh 155
                                       +  ++++v+ ++g +sl+a+++v+A+G 
  gi|557695016|ref|YP_008798070.1| 115 KGSGEVKVVGEGGsESLEARNIVIATGT 142
                                       34445677777774789**********6 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.12
                     NAD_binding_9 105 eellarlpegvtvevh.raevvdleeradgqavlladgaslaadaVvLAlG 154
                                       ++ll+r  e++ v++h +++v++ +  ++g++ +l+++ +  +d V + +G
  gi|557695016|ref|YP_008798070.1| 214 ARLLKRGMEKIGVKIHlKTTVEETRYVDGGVEAVLSNDVKDVFDVVLVVVG 264
                                       57888999999999997889999********999*9999999999998888 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   6.4e-05     0.072       3      37 ..       6      37 ..       4      67 .. 0.89
   2 ?   -2.8   0.3       1.8     2e+03       1      32 [.     172     200 ..     172     203 .. 0.80
   3 ?   -2.7   0.2       1.7   1.9e+03     157     195 ..     214     252 ..     212     262 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.4e-05
                                      EEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                    Trp_halogenase  3 vivGGGtaGwlaAaalakalkgklevtlveseeig 37
                                      vivGGG+ G+ +A+ l++ +   ++  lve+e++g
  gi|557695016|ref|YP_008798070.1|  6 VIVGGGPGGYATAIRLSQLG---VKTALVEKEHLG 37
                                      9****************999...999******987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.8
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlve 32 
                                       k+++vGGG  G    +a ++ +    +vt+ve
  gi|557695016|ref|YP_008798070.1| 172 KMLVVGGGAIGVELGTAYRHLG---SDVTVVE 200
                                       5789******998888888777...6788887 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS CS
                    Trp_halogenase 157 akfLrrvaearGvtrvegkvvevqldedgrveslrledg 195
                                       a++L+r  e+ Gv++   + ve +   dg ve++  +d 
  gi|557695016|ref|YP_008798070.1| 214 ARLLKRGMEKIGVKIHLKTTVEETRYVDGGVEAVLSNDV 252
                                       68899999999***9999998888888999999988773 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.7   3.8e-05     0.043      17      58 ..       2      41 ..       1      87 [. 0.80
   2 ?   -0.9   0.1       0.7   7.9e+02      22      57 ..     139     180 ..     131     207 .. 0.56
   3 ?   -3.3   0.0       3.8   4.3e+03     101     127 ..     214     240 ..     213     252 .. 0.71
   4 ?   -3.3   0.0       3.7   4.2e+03      75      93 ..     272     289 ..     256     294 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.8e-05
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTT CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGaw 58
                                      + D vivG+G+ G ++a  l++  ++k+a++e++  +GG   
  gi|557695016|ref|YP_008798070.1|  2 KFDAVIVGGGPGGYATAIRLSQL-GVKTALVEKEH-LGGECT 41
                                      5799******************9.********975.444433 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.7
                                       EE--SHHHHHHHHHHHHC.TTS-EE....EE.ESSSS--TTT CS
                              Thi4  22 ivGaGssGLtaayylakk.pdlkva....il.ersvspGGGa 57 
                                         G+  s L+aa y +k+  +++ a    ++  + + +GGGa
  gi|557695016|ref|YP_008798070.1| 139 ATGTVQSSLSAAPYDGKRiIGFREAlyleVVpKKMLVVGGGA 180
                                       456666666666665555444443310012212334445554 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.8
                                       HHHHHHHHTSTTEEEEESEEEEEEEEE CS
                              Thi4 101 stllskvlqlanvkllnavaveDlivr 127
                                       ++ll + +++ +vk+   ++ve+    
  gi|557695016|ref|YP_008798070.1| 214 ARLLKRGMEKIGVKIHLKTTVEETRYV 240
                                       567778888889999999999876544 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 3.7
                                       HHHHHTT---EEESSEEEE CS
                              Thi4  75 elLdelgikyedegdyvvv 93 
                                        +L +lg+k++++g yv+v
  gi|557695016|ref|YP_008798070.1| 272 RMLADLGVKLSEKG-YVLV 289
                                       58999999998876.4555 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.1   0.00047      0.52       1      50 [.       4      49 ..       4     170 .. 0.52
   2 ?   -0.4   0.2       0.4   4.5e+02       3      36 ..     174     205 ..     172     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00047
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefed 50
                                      D v++G+Gp g + A rl  ++ g+k  l+e   +l  +++   W +  + 
  gi|557695016|ref|YP_008798070.1|  4 DAVIVGGGPGGYATAIRL--SQLGVKTALVEKE-HL--GGECtNWGCIPSK 49
                                      88****************..**********543.33..5555477665443 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.4
                     Lycopene_cycl   3 vviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       +v+G+G+ g+ l       + g  v+++e  ++l
  gi|557695016|ref|YP_008798070.1| 174 LVVGGGAIGVELGTAY--RHLGSDVTVVELMDQL 205
                                       79**********9998..8888888888866665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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):              16  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3142.12
//
Query:       gi|557695017|ref|YP_008798071.1|  [L=324]
Description: 2-oxoisovalerate dehydrogenase E1 component, beta subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   0.0    2.2e-50  170.8   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    1.3e-37  128.4   0.2    2.6e-37  127.5   0.0    1.5  2  Transketolase_C  Transketolase, C-terminal domain
     0.0011   19.2   0.0     0.0021   18.4   0.0    1.5  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


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 !  170.8   0.0   3.7e-54   2.2e-50       2     176 ..       3     178 ..       2     179 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 3.7e-54
                                       EEEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEE CS
                      Transket_pyr   2 kiawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllvi 76 
                                       ++++++a+++al e++ +d++vv++g+Dv+  gg+f+ ++gl + +g++rvid+++sE++++g+a+G+a++g l+++
  gi|557695017|ref|YP_008798071.1|   3 QLNMAQALNLALREEMSRDERVVVLGEDVGrrGGVFLITEGLYELFGPERVIDTPLSEAGIIGVAAGMAMNG-LRPV 78 
                                       5789**************************99****************************************.9*** PP

                                       EEEEEHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHH CS
                      Transket_pyr  77 veaqFgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetk 151
                                       +e+qF+dF+ g+  qi+ + a+++++++g++ v++++r+p+g g +G   +s+++ea++ ++pglkvv+Ps+p+++k
  gi|557695017|ref|YP_008798071.1|  79 AEIQFADFIFGGfdQIVSNVAKIRYRTGGQFSVPLTIRAPVGGGVKGGMFHSQSPEAYFIHTPGLKVVTPSTPSDAK 155
                                       **********99***************************************************************** PP

                                       HHHHHHHHSSS.SEEEEEE-SSEEC CS
                      Transket_pyr 152 hllrrairredrkPvvlrlpksllr 176
                                       +ll   ir  d++Pv +++pk+ +r
  gi|557695017|ref|YP_008798071.1| 156 GLLISSIR--DDDPVLFFEPKRIYR 178
                                       ********..899*********998 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.1   6.8e+03      60      76 ..      21      37 ..      13      46 .. 0.65
   2 !  127.5   0.0   4.3e-41   2.6e-37       1     124 []     194     314 ..     194     314 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.1
                                      HHSEEEEEEEEESTTSH CS
                   Transketolase_C 60 ktgrlvvveeavkrgGi 76
                                        + +v+ e+  +rgG+
  gi|557695017|ref|YP_008798071.1| 21 DERVVVLGEDVGRRGGV 37
                                      44555555666666765 PP

  == domain 2  score: 127.5 bits;  conditional E-value: 4.3e-41
                                       TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       g a++ reg+dv l++y ++v+ +l+Aae++e+egi++eVvdlrt+ p+Dk+ +++ vkktgr v+v+ea k++G+g
  gi|557695017|ref|YP_008798071.1| 194 GVARVAREGSDVSLITYAATVHDCLRAAEKAEAEGITCEVVDLRTLLPFDKDAVEKTVKKTGRPVIVHEAPKMCGFG 270
                                       568999*********************************************************************** PP

                                       HHHHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                       +e+aa++ae+++ +l+apv+rv+g+d+  p++    e++++++  +i
  gi|557695017|ref|YP_008798071.1| 271 AELAAFIAERLLYDLEAPVLRVTGYDT--PFP-FVHEHHYMPNESRI 314
                                       ***************************..666.45899999998876 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 !   18.4   0.0   3.5e-07    0.0021       2      71 ..     204     274 ..     203     295 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.5e-07
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-.SEEEEEE-S--TT-G-HHH CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkv.kkvvvldrnisfgseGqlv 71 
                                       +v ++++++++ ++ +a++++ +egi   ++ lrtl PF ++++++ +kk+ + v+v +   + g+   l+
  gi|557695017|ref|YP_008798071.1| 204 DVSLITYAATVHDCLRAAEKAEAEGITCEVVDLRTLLPFDKDAVEKTVKKTgRPVIVHEAPKMCGFGAELA 274
                                       7889*****************************************99887625688888877777765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2468.77
//
Query:       gi|557695018|ref|YP_008798072.1|  [L=291]
Description: lipoic acid synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   47.2   0.1    4.5e-12   46.6   0.1    1.2  1  Radical_SAM  Radical SAM superfamily
      3e-07   30.8   0.0    4.3e-06   27.1   0.1    2.3  2  LIAS_N       N-terminal domain of lipoyl synthase of Radical_
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.041   13.7   0.0    1.4  1  DUF473       Protein of unknown function (DUF473)


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 !   46.6   0.1   7.6e-16   4.5e-12       4     166 ..      59     220 ..      56     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 7.6e-16
                                       ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC....CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xx RF
                       Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla....vp 76 
                                       +  C+++C+fCa++    +++++ +l+  e ++ ++++  e+g ++v+l++   ++  d    + ++  ++    +p
  gi|557695018|ref|YP_008798072.1|  59 GDICTRGCRFCAVK----TGKPSGFLDAKEPENVARAV-SEMGLRYVVLTSVCRDDLEDGGAGIYAETIRKikqtKP 130
                                       678***********....58999999999999999999.59999999999877777766555544444444456789 PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSET..EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx..xxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikr..vvdriv 150
                                       ++ + v ++ +  + e l++ +e+++d+v++++e++       l++ ++ ++e+ l++l++ ++   +   +++ i+
  gi|557695018|ref|YP_008798072.1| 131 EVLVEVLIPDFNAESEALKKVVEARPDVVAHNIETVRR--LTPLVRdPRASYEKSLRVLQLVKQM-SPTtyTKSSIM 204
                                       99999999999998************************..678888899***********99888.7888******* PP

                                       EBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleellel 166
                                       ++ Ge++ee++e l++
  gi|557695018|ref|YP_008798072.1| 205 VGLGESFEEVVEALRD 220
                                       ************9987 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 !   27.1   0.1   7.2e-10   4.3e-06      70     108 .]       3      41 ..       1      41 [. 0.94
   2 ?    1.1   0.0     0.088   5.3e+02      75      98 ..     197     222 ..     173     226 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7.2e-10
                            LIAS_N  70 rlrLPswlktkiPlGknynkikndlreLnLhtvCeeaRC 108
                                        l+ P+w++ ++P    y k++  lr+  LhtvCeea C
  gi|557695018|ref|YP_008798072.1|   3 TLHKPEWIRATLPGLGAYPKVRGILRKYGLHTVCEEALC 41 
                                       5889*********9899********************99 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.088
                            LIAS_N  75 swlktki..PlGknynkikndlreLn 98 
                                        + k +i   lG++++ + + lr+L+
  gi|557695018|ref|YP_008798072.1| 197 TYTKSSImvGLGESFEEVVEALRDLR 222
                                       57777661156899*********996 PP

>> DUF473  Protein of unknown function (DUF473)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   6.9e-06     0.041      28      73 ..      83     128 ..      75     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.9e-06
                            DUF473  28 rsahNvitllklevgdlvFlTsvsleDltkGteGiiaevlsveist 73 
                                       + ++Nv+ + +    ++v lTsv ++Dl++G +Gi ae +++   t
  gi|557695018|ref|YP_008798072.1|  83 KEPENVARAVSEMGLRYVVLTSVCRDDLEDGGAGIYAETIRKIKQT 128
                                       5678888887766679*********************976554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2343.69
//
Query:       gi|557695019|ref|YP_008798073.1|  [L=147]
Description: NUDIX hydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-17   61.7   0.9    8.8e-17   61.4   0.9    1.1  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
        0.2   11.2   0.0       0.25   10.8   0.0    1.1  1  PipA      PipA protein


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 !   61.4   0.9   9.8e-21   8.8e-17       5     122 ..       9     126 ..       6     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 9.8e-21
                                       EEEEE.EEETTSE..EEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEE.EEE.EEEEEEEEEEEEE CS
                             NUDIX   5 avgvv.llnekge..vLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGlea.ell.ellgrlhylapyd 75 
                                       ++g+v +++e +    Ll++      +g W++P+G++e +E+  +A++RE++EEtG++  el+  +  ++ y+++ +
  gi|557695019|ref|YP_008798073.1|   9 SAGAVlFIREGNGveYLLLKYG----AGhWDFPKGHIERNESELQAVVREVWEETGIQRmELVeGFRKVINYMFMKN 81 
                                       4444422222222466777533....556************777*************99899955555888888888 PP

                                       EEEEEEEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHH.HHHHTHC CS
                             NUDIX  76 gpygdeheilyvfleevegelepndenevsevrwvpleel.lkeklaa 122
                                       g+   ++e+++++ e ++  +++  + e+ ++ w+ple++  + +++ 
  gi|557695019|ref|YP_008798073.1|  82 GKLV-RKEVVFYLGEVFDRAVTL--SQEHLDFVWLPLEKAiERLTFKT 126
                                       8777.788876666777777665..59999999*******54444444 PP

>> PipA  PipA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   2.8e-05      0.25      60     117 ..      46     109 ..      17     112 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.8e-05
                              PipA  60 decrevlsrvledaytq....setfrrlmnyayekelhdveqrwllgageafettva..dedlk 117
                                        e + v+ +v e++  q     e fr+++ny + k+ + v +  ++  ge f+ +v+  +e+l+
  gi|557695019|ref|YP_008798073.1|  46 SELQAVVREVWEETGIQrmelVEGFRKVINYMFMKNGKLVRKEVVFYLGEVFDRAVTlsQEHLD 109
                                       455556666666655552222589*********************99*****976542288876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1023.21
//
Query:       gi|557695020|ref|YP_008798074.1|  [L=565]
Description: hypothetical protein CSUB_C1593 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-19   67.6  21.5    5.6e-09   36.2   1.5    5.8  5  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    3.1e-12   46.3  17.5     0.0028   17.6   0.1    5.5  5  Big_1            Bacterial Ig-like domain (group 1)
    2.3e-06   27.5   4.2      0.012   15.6   0.1    3.9  3  CarbopepD_reg_2  CarboxypepD_reg-like domain
     0.0001   22.4   4.8        1.2    9.3   0.1    5.0  5  MG4              Macroglobulin domain MG4
      0.006   16.8   2.2      0.052   13.8   0.3    3.2  3  SdrD_B           SdrD B-like domain
  ------ inclusion threshold ------
      0.011   15.7   1.9         14    5.7   0.0    4.1  4  bMG3             Bacterial alpha-2-macroglobulin MG3 domain
      0.025   14.9  15.9        1.3    9.4   2.0    5.3  6  Invasin_D3       Invasin, domain 3
      0.027   14.3   0.9        8.1    6.4   0.0    4.4  4  FlgD_ig          FlgD Ig-like domain
      0.033   14.5   3.0       0.37   11.2   0.2    3.1  4  SpaA             Prealbumin-like fold domain
       0.16   11.4   0.4         42    3.5   0.0    3.5  5  Dioxygenase_C    Dioxygenase
       0.17   11.9   0.0       0.77    9.8   0.0    2.0  3  PapC_N           PapC N-terminal domain


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 !   36.2   1.5   3.4e-12   5.6e-09       4      63 ..      30      87 ..      27      96 .. 0.89
   2 !   10.9   0.4   0.00027      0.44       2      47 ..     107     152 ..     106     197 .. 0.79
   3 !   21.5   0.1   1.3e-07   0.00021       4      80 ..     285     365 ..     282     366 .. 0.83
   4 !    7.8   0.3    0.0025       4.1       5      57 ..     372     422 ..     370     443 .. 0.73
   5 ?    2.6   0.1       0.1   1.7e+02       2      34 ..     449     480 ..     448     483 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 3.4e-12
                   CarboxypepD_reg  4 GrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatat 63
                                        Vt  +gap +g tVtv+  +++++ +++t+a+G+  lr+l pgty+vtvs ++ +  +
  gi|557695020|ref|YP_008798074.1| 30 VLVTTGDGAPRSGLTVTVQ--GENFRETAVTNATGYAVLRQLSPGTYQVTVSLQNIELIR 87
                                      568999*************..99****************************988766555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00027
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglpp 47 
                                       +  +V+d+ g+p+++  V + +  +  + s +t+ +G   +r++p 
  gi|557695020|ref|YP_008798074.1| 107 LYAKVVDTAGKPVSNFFVNLLSPTGLISVSQRTNGTGVAVFRDIPF 152
                                       5669*****************7555568999******999998875 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 1.3e-07
                   CarboxypepD_reg   4 GrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglpp....gtysvtvsapGyatatreevtltagqttt 76 
                                        +V d+ g+p++g+ + v +++ g  ++ +td++G+f++  +p     g+y++   + G     +e++tl++ + t 
  gi|557695020|ref|YP_008798074.1| 285 IKVLDPEGKPVKGVGILVGASGYGNFTGGVTDQEGQFSVGIVPLskvvGDYQLSL-FRGRSRIQVEQLTLSESRVTK 360
                                       58*****************999999999***********999889999*****99.666666666789998877653 PP

                   CarboxypepD_reg  77 .ldit 80 
                                        + +t
  gi|557695020|ref|YP_008798074.1| 361 eVKLT 365
                                       25555 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0025
                   CarboxypepD_reg   5 rVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsap 57 
                                       r++d +g p++ a ++++++ tg + +t t a G+ + +   pg+ +v v+++
  gi|557695020|ref|YP_008798074.1| 372 RIVDYTGSPLSSAMLSIKDTVTGRTVNT-TIAAGEASAD-FFPGSNEVSVTYK 422
                                       789***************5444444443.4578888875.6667777777665 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.1
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvasttt 34 
                                       ++ +V d+ g+ + g +V v+  d+ +  st++
  gi|557695020|ref|YP_008798074.1| 449 VTISVLDSLGNNVGGLRVKVYG-DGRELLSTVS 480
                                       6778*****************3.3334455555 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 !   13.5   3.4   3.4e-05     0.055       6      64 .]      25      78 ..      22      78 .. 0.84
   2 !   17.6   0.1   1.7e-06    0.0028       8      50 ..     106     147 ..     104     148 .. 0.93
   3 !   16.3   0.1   4.4e-06    0.0071       8      52 ..     282     325 ..     279     338 .. 0.87
   4 ?   -0.9   0.1       1.1   1.8e+03      22      50 ..     393     408 ..     370     411 .. 0.61
   5 ?    4.9   0.0     0.016        26       9      38 ..     449     479 ..     446     485 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.4e-05
                             Big_1  6 tntltatvkDangnpvagatVtfsvsggalsassgtTdanGkatvtltstkagtvtvtA 64
                                      + +lt+ v+  +g p +g tVt++  +   +  +++T+a G a+  l    +gt++vt+
  gi|557695020|ref|YP_008798074.1| 25 QQVLTVLVTTGDGAPRSGLTVTVQGEN---FRETAVTNATGYAV--LRQLSPGTYQVTV 78
                                      6789*******************9555...7889********98..5566778888875 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1.7e-06
                             Big_1   8 tltatvkDangnpvagatVtfsvsggalsassgtTdanGkatv 50 
                                       tl a v+D  g+pv++  V++ ++ g + + s++T+  G+a++
  gi|557695020|ref|YP_008798074.1| 106 TLYAKVVDTAGKPVSNFFVNLLSPTGLI-SVSQRTNGTGVAVF 147
                                       8889*********************999.99*********987 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 4.4e-06
                             Big_1   8 tltatvkDangnpvagatVtfsvsg.galsassgtTdanGkatvtl 52 
                                       +l + v D +g+pv+g+ + + +sg g+   + g+Td++G+++v +
  gi|557695020|ref|YP_008798074.1| 282 ELVIKVLDPEGKPVKGVGILVGASGyGNF--TGGVTDQEGQFSVGI 325
                                       56789********************9999..78*********9976 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 1.1
                             Big_1  22 agatVtfsvsggalsassgtTdanGkatv 50 
                                        g              +  tT a G+a++
  gi|557695020|ref|YP_008798074.1| 393 TG-------------RTVNTTIAAGEASA 408
                                       23.............44456666666665 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.016
                             Big_1   9 ltatvkDangnpvagatVtfsvsg.galsas 38 
                                       +t+ v D+ gn v g  V++  +g + ls+ 
  gi|557695020|ref|YP_008798074.1| 449 VTISVLDSLGNNVGGLRVKVYGDGrELLSTV 479
                                       899****************999995444444 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 !   15.6   0.1   7.4e-06     0.012       9      66 ..      35      94 ..      30     112 .. 0.80
   2 !   10.5   0.1   0.00029      0.47       4      42 ..     286     327 ..     285     365 .. 0.82
   3 ?   -0.4   0.0      0.74   1.2e+03       5      29 ..     373     396 ..     372     400 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.4e-06
                   CarbopepD_reg_2  9 etkeplpgatVyvkgtk..kgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvsk 66
                                      +++ p  g tV+v+g +    +vT++ G+  l++l +g+y+++vs    +   +++++ +
  gi|557695020|ref|YP_008798074.1| 35 GDGAPRSGLTVTVQGENfrETAVTNATGYAVLRQLSPGTYQVTVSLQNIELIRRTISFPE 94
                                      55667778888888886437899**********************998888888887755 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00029
                   CarbopepD_reg_2   4 tVvdketkeplpgatVyvkgtk....kgtvTdenGnFelknlp 42 
                                       +V+d e ++p+ g+ ++v  ++    +g vTd++G+F++  +p
  gi|557695020|ref|YP_008798074.1| 286 KVLDPE-GKPVKGVGILVGASGygnfTGGVTDQEGQFSVGIVP 327
                                       577765.68*******9976543344999********997666 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.74
                   CarbopepD_reg_2   5 VvdketkeplpgatVyvkgtkkgtv 29 
                                       +vd  t+ pl  a  ++k+t +g +
  gi|557695020|ref|YP_008798074.1| 373 IVD-YTGSPLSSAMLSIKDTVTGRT 396
                                       555.5789************99866 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.1   0.00074       1.2      18      61 ..      28      67 ..      27      84 .. 0.83
   2 ?    1.8   0.0      0.16   2.6e+02      20      59 ..     109     146 ..      94     150 .. 0.70
   3 !    6.4   0.0    0.0061        10      19      56 ..     284     319 ..     282     327 .. 0.77
   4 ?   -1.3   0.0       1.5   2.4e+03      21      58 ..     372     406 ..     369     422 .. 0.72
   5 ?    1.7   0.0      0.17   2.8e+02      16      39 ..     447     470 ..     433     494 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00074
                               MG4 18 ikVlvkdpdgspaknvpVkiealkseteekeslttdedGtakfs 61
                                      ++Vlv+  dg p ++ +V+++  +   ++ e+  t++ G a + 
  gi|557695020|ref|YP_008798074.1| 28 LTVLVTTGDGAPRSGLTVTVQG-E---NFRETAVTNATGYAVLR 67
                                      79********************.4...78899999999998775 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.16
                               MG4  20 VlvkdpdgspaknvpVkiea.lkseteekeslttdedGtak 59 
                                        +v+d+ g+p++n  V +   ++       s+ t+  G+a 
  gi|557695020|ref|YP_008798074.1| 109 AKVVDTAGKPVSNFFVNLLSpTG---LISVSQRTNGTGVAV 146
                                       689***********999877222...222334555666665 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0061
                               MG4  19 kVlvkdpdgspaknvpVkiealkseteekeslttdedG 56 
                                        ++v dp+g+p+k+v + + a  s+  +     td++G
  gi|557695020|ref|YP_008798074.1| 284 VIKVLDPEGKPVKGVGILVGA--SGYGNFTGGVTDQEG 319
                                       689****************99..344455556677777 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 1.5
                               MG4  21 lvkdpdgspaknvpVkiealkseteekeslttdedGta 58 
                                       +++d+ gsp++  +++i+     t +    tt + G a
  gi|557695020|ref|YP_008798074.1| 372 RIVDYTGSPLSSAMLSIKD-T-VTGR-TVNTTIAAGEA 406
                                       6889999999999999988.2.2223.33355566655 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.17
                               MG4  16 fsikVlvkdpdgspaknvpVkiea 39 
                                       f ++++v d++g+ +++  Vk+  
  gi|557695020|ref|YP_008798074.1| 447 FPVTISVLDSLGNNVGGLRVKVYG 470
                                       7899****************9977 PP

>> SdrD_B  SdrD B-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.3   3.2e-05     0.052      25      66 ..      41      80 ..      18      89 .. 0.86
   2 ?   -0.0   0.0      0.63     1e+03      18      54 ..     113     149 ..     111     170 .. 0.81
   3 ?   -0.8   0.0       1.1   1.7e+03      18      51 ..     289     322 ..     287     349 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.2e-05
                            SdrD_B 25 sgvtVtLkdakgevvatttTdasGkYkFtnltpGeYkVefta 66
                                      sg tVt+  + ++  +t +T+a+G+    +l+pG+Y+V+++ 
  gi|557695020|ref|YP_008798074.1| 41 SGLTVTV--QGENFRETAVTNATGYAVLRQLSPGTYQVTVSL 80
                                      6778887..44555589*********************9975 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.63
                            SdrD_B  18 dagekgisgvtVtLkdakgevvatttTdasGkYkFtn 54 
                                       d+  k +s+  V+L + +g +  ++ T+ +G   F +
  gi|557695020|ref|YP_008798074.1| 113 DTAGKPVSNFFVNLLSPTGLISVSQRTNGTGVAVFRD 149
                                       6667889999999999999888899999998877765 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.1
                            SdrD_B  18 dagekgisgvtVtLkdakgevvatttTdasGkYk 51 
                                       d + k ++gv + + ++     +  +Td++G+++
  gi|557695020|ref|YP_008798074.1| 289 DPEGKPVKGVGILVGASGYGNFTGGVTDQEGQFS 322
                                       6667899999998866666666889999999886 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 ?    4.6   0.3      0.02        32       7      60 ..      19      70 ..      17      84 .. 0.81
   2 ?    5.7   0.0    0.0088        14      25      58 ..     116     149 ..     112     212 .. 0.85
   3 ?    0.6   0.0      0.34   5.6e+02      24      54 ..     291     321 ..     279     325 .. 0.88
   4 ?   -1.1   0.0       1.2     2e+03       6      39 ..     337     370 ..     332     375 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.02
                              bMG3  7 haklgrdkllvwvtsLdsgkPvagaeVrlldkkgevlaegtTDaqGvarfaall 60
                                      +  ++++++l +  +  +g P +g +V++  ++ ++  ++ T+a+G+a + +l+
  gi|557695020|ref|YP_008798074.1| 19 TLSQSQQQVLTVLVTTGDGAPRSGLTVTVQGENFRE--TAVTNATGYAVLRQLS 70
                                      56677888877778889************9888885..7899999999998774 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0088
                              bMG3  25 gkPvagaeVrlldkkgevlaegtTDaqGvarfaa 58 
                                       gkPv++  V+ll+ +g    +++T+ +Gva f +
  gi|557695020|ref|YP_008798074.1| 116 GKPVSNFFVNLLSPTGLISVSQRTNGTGVAVFRD 149
                                       9*****************************9975 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.34
                              bMG3  24 sgkPvagaeVrlldkkgevlaegtTDaqGva 54 
                                       +gkPv+g+ + + +        g TD++G  
  gi|557695020|ref|YP_008798074.1| 291 EGKPVKGVGILVGASGYGNFTGGVTDQEGQF 321
                                       69********999999999999999999976 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.2
                              bMG3   6 lhaklgrdkllvwvtsLdsgkPvagaeVrlldkk 39 
                                       l+  +gr++++v   +L++ +  ++++++l++ +
  gi|557695020|ref|YP_008798074.1| 337 LSLFRGRSRIQVEQLTLSESRVTKEVKLTLIKTS 370
                                       778899999999999**************99876 PP

>> Invasin_D3  Invasin, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.0   0.00078       1.3      19      67 ..      23      79 ..      16      92 .. 0.73
   2 ?    6.6   0.1    0.0059       9.6      22      64 ..     105     145 ..      89     149 .. 0.80
   3 ?   -2.6   0.0       4.4   7.2e+03      40      64 ..     207     234 ..     185     256 .. 0.55
   4 ?    1.2   0.0      0.28   4.5e+02      25      62 ..     284     321 ..     279     339 .. 0.76
   5 ?   -0.9   0.1       1.3   2.1e+03      26      64 ..     371     408 ..     365     423 .. 0.72
   6 ?    3.4   0.0     0.058        95      24      53 ..     449     478 ..     436     491 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00078
                        Invasin_D3 19 kststltvtlkDangnpvsgltvtfstt..sagtlsavt......dngdGtytatLt 67
                                      +++++ltv ++  +g p sgltvt++ +   +++++++t      + + Gty++t++
  gi|557695020|ref|YP_008798074.1| 23 SQQQVLTVLVTTGDGAPRSGLTVTVQGEnfRETAVTNATgyavlrQLSPGTYQVTVS 79
                                      57899*********************7744222222222344444777788888874 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0059
                        Invasin_D3  22 stltvtlkDangnpvsgltvtfsttsagtlsavtdngdGtyta 64 
                                       stl +++ D++g+pvs+  v++ +  +g   +v++  +Gt  a
  gi|557695020|ref|YP_008798074.1| 105 STLYAKVVDTAGKPVSNFFVNLLSP-TGL-ISVSQRTNGTGVA 145
                                       79999*****************988.884.3455555555444 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.4
                        Invasin_D3  40 tvtfstt...sagtlsavtdngdGtyta 64 
                                        +++s++    ag +++  d  dG  ++
  gi|557695020|ref|YP_008798074.1| 207 RIKLSASlslRAGNVTERVDVVDGFASV 234
                                       3333333333344444444555565554 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.28
                        Invasin_D3  25 tvtlkDangnpvsgltvtfsttsag.tlsavtdngdGty 62 
                                        +++ D +g+pv+g  + + ++  g  +++vtd++ G  
  gi|557695020|ref|YP_008798074.1| 284 VIKVLDPEGKPVKGVGILVGASGYGnFTGGVTDQE-GQF 321
                                       57899*********999999886675445676655.665 PP

  == domain 5  score: -0.9 bits;  conditional E-value: 1.3
                        Invasin_D3  26 vtlkDangnpvsgltvtfsttsag.tlsavtdngdGtyta 64 
                                       + + D  g p+s +  +++ t +g t++  t+ ++G  +a
  gi|557695020|ref|YP_008798074.1| 371 FRIVDYTGSPLSSAMLSIKDTVTGrTVN--TTIAAGEASA 408
                                       6778888888888888888776665555..4566666665 PP

  == domain 6  score: 3.4 bits;  conditional E-value: 0.058
                        Invasin_D3  24 ltvtlkDangnpvsgltvtfsttsag..tlsa 53 
                                       +t+ + D  gn v+gl v++  +  g   ls+
  gi|557695020|ref|YP_008798074.1| 449 VTISVLDSLGNNVGGLRVKVYGD--GreLLST 478
                                       8999****************987..3234443 PP

>> FlgD_ig  FlgD Ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.18   2.9e+02      63      76 ..      68      81 ..      67      83 .. 0.85
   2 ?    6.4   0.0    0.0049       8.1      11      48 ..     269     306 ..     261     321 .. 0.80
   3 ?    0.6   0.0      0.33   5.3e+02      20      47 ..     379     408 ..     362     418 .. 0.82
   4 ?   -1.7   0.0       1.7   2.7e+03      24      38 ..     448     462 ..     430     472 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.18
                                      B--SEEEEEEEEEE CS
                           FlgD_ig 63 kladGaYtvkvtat 76
                                      +l++G+Y+v+v+ +
  gi|557695020|ref|YP_008798074.1| 68 QLSPGTYQVTVSLQ 81
                                      6899*******865 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0049
                                       -EEEEEE.ESSSEEEEEEEE-SS--EEEEEEEEESSSE CS
                           FlgD_ig  11 eaplgvelpeaadevtvtikDasGevVrtidlgaqsaG 48 
                                       +a+++++l+ ++ e+++++ D +G+ V+ +     ++G
  gi|557695020|ref|YP_008798074.1| 269 DAYGSFTLSPDVGELVIKVLDPEGKPVKGVGILVGASG 306
                                       6799*********************9997665555555 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.33
                                       SSSEEEEEEEE-S.S--EE.EEEEEEESSS CS
                           FlgD_ig  20 eaadevtvtikDa.sGevV.rtidlgaqsa 47 
                                       ++ +++ ++ikD  +G++V  ti +g+ sa
  gi|557695020|ref|YP_008798074.1| 379 SPLSSAMLSIKDTvTGRTVnTTIAAGEASA 408
                                       67788999****99*****66777777766 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.7
                                       EEEEEEE-SS--EEE CS
                           FlgD_ig  24 evtvtikDasGevVr 38 
                                        vt+++ D+ G+ V 
  gi|557695020|ref|YP_008798074.1| 448 PVTISVLDSLGNNVG 462
                                       589999999999885 PP

>> SpaA  Prealbumin-like fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00022      0.37      32      59 ..      50      77 ..      18      77 .. 0.74
   2 ?   -3.6   0.0       8.8   1.4e+04      39      53 ..     138     152 ..     113     165 .. 0.72
   3 ?    2.3   0.0      0.13   2.1e+02      36      58 ..     311     337 ..     218     338 .. 0.83
   4 ?   -2.2   0.1       3.2   5.3e+03      28      48 ..     383     408 ..     359     412 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
                                      CCEESEEE-BTTSEEEEEEEESEEEEEE CS
                              SpaA 32 gtevttlttdenGkatfegLplGtYllv 59
                                       +  +t++t+++G+a    L +GtY+++
  gi|557695020|ref|YP_008798074.1| 50 ENFRETAVTNATGYAVLRQLSPGTYQVT 77
                                      334499*******************985 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.8
                                       E-BTTSEEEEEEEES CS
                              SpaA  39 ttdenGkatfegLpl 53 
                                        t+ +G a f ++p 
  gi|557695020|ref|YP_008798074.1| 138 RTNGTGVAVFRDIPF 152
                                       578888888888776 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.13
                                       SEEE-BTTSEEEEEEEES....EEEEE CS
                              SpaA  36 ttlttdenGkatfegLpl....GtYll 58 
                                       t  +td++G+++++ +pl    G+Y+l
  gi|557695020|ref|YP_008798074.1| 311 TGGVTDQEGQFSVGIVPLskvvGDYQL 337
                                       5568*********98888777777876 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 3.2
                                       T......TTCCEESEEE-BTTSEEEE CS
                              SpaA  28 a.....kktgtevttlttdenGkatf 48 
                                       +     k+t+t  t  tt + G+a+ 
  gi|557695020|ref|YP_008798074.1| 383 SamlsiKDTVTGRTVNTTIAAGEASA 408
                                       13555667777778888888888875 PP

>> Dioxygenase_C  Dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.031        51      72     100 ..      50      78 ..      42      90 .. 0.87
   2 ?    3.5   0.0     0.026        42      32      52 ..     107     127 ..      99     191 .. 0.73
   3 ?   -2.7   0.0         2   3.3e+03      35      47 ..     286     298 ..     283     305 .. 0.85
   4 ?   -3.0   0.0       2.6   4.3e+03      79      88 ..     314     323 ..     307     327 .. 0.73
   5 ?   -1.7   0.0         1   1.7e+03      26      51 ..     363     388 ..     344     393 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.031
                                       TTTEEEEE--TTSEEEEEEE----EE--T CS
                     Dioxygenase_C  72 lnlrgriltdeeGryrirtikPapYpipn 100
                                        n+r + +t++ G+  +r + P++Y++  
  gi|557695020|ref|YP_008798074.1|  50 ENFRETAVTNATGYAVLRQLSPGTYQVTV 78 
                                       69************************875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.026
                                       EEEEEE-TTSSB-TT-EEEEE CS
                     Dioxygenase_C  32 lsGrvldeaGkplagalvelW 52 
                                       l  +v+d+aGkp+ +  v+l 
  gi|557695020|ref|YP_008798074.1| 107 LYAKVVDTAGKPVSNFFVNLL 127
                                       5679***********999986 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2
                                       EEE-TTSSB-TT- CS
                     Dioxygenase_C  35 rvldeaGkplaga 47 
                                       +vld +Gkp++g 
  gi|557695020|ref|YP_008798074.1| 286 KVLDPEGKPVKGV 298
                                       699*******986 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 2.6
                                       E--TTSEEEE CS
                     Dioxygenase_C  79 ltdeeGryri 88 
                                       +td+eG++++
  gi|557695020|ref|YP_008798074.1| 314 VTDQEGQFSV 323
                                       6889998876 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 1
                                       T--EEEEEEEEE-TTSSB-TT-EEEE CS
                     Dioxygenase_C  26 egerlvlsGrvldeaGkplagalvel 51 
                                       + + +  s r++d  G pl  a++ +
  gi|557695020|ref|YP_008798074.1| 363 KLTLIKTSFRIVDYTGSPLSSAMLSI 388
                                       44555567799********9998765 PP

>> PapC_N  PapC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00047      0.77      19      60 ..      62     103 ..      50     116 .. 0.81
   2 ?   -2.6   0.0         3   4.9e+03      29      60 ..     333     364 ..     330     372 .. 0.78
   3 ?   -3.2   0.0       4.8   7.8e+03      24      49 ..     408     433 ..     396     457 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00047
                                       HHHTT-SS-SEEEEEEEEETTEEEEEEEEEEEECCTCCCEEE CS
                            PapC_N  19 rFskgnavlpGeYrvdvyvNgkeigrqevefkaekkkkklep 60 
                                        ++   ++ pG+Y+v v + + e+ r++++f +++   +++p
  gi|557695020|ref|YP_008798074.1|  62 GYAVLRQLSPGTYQVTVSLQNIELIRRTISFPETSFIREVAP 103
                                       566667899**********************98776555555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3
                                       EEEEEEEEETTEEEEEEEEEEEECCTCCCEEE CS
                            PapC_N  29 GeYrvdvyvNgkeigrqevefkaekkkkklep 60 
                                       G+Y+++++  +++i+ +++++++++ +k++++
  gi|557695020|ref|YP_008798074.1| 333 GDYQLSLFRGRSRIQVEQLTLSESRVTKEVKL 364
                                       89999999999999999999888776666655 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.8
                                       -SS-SEEEEEEEEETTEEEEEEEEEE CS
                            PapC_N  24 navlpGeYrvdvyvNgkeigrqevef 49 
                                        ++ pG+++v+v+  ++ + ++ +e+
  gi|557695020|ref|YP_008798074.1| 408 ADFFPGSNEVSVTYKDRVVFQKVLEL 433
                                       56778999999888777776666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); 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):              11  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 3741.92
//
Query:       gi|557695021|ref|YP_008798075.1|  [L=99]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); 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:                         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: 00:00:00.40
# Mc/sec: 737.79
//
Query:       gi|557695022|ref|YP_008798076.1|  [L=254]
Description: F420-0:gamma-glutamyl ligase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-61  207.2   0.4    2.9e-61  206.9   0.4    1.0  1  F420_ligase  F420-0:Gamma-glutamyl ligase


Domain annotation for each model (and alignments):
>> F420_ligase  F420-0:Gamma-glutamyl ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.9   0.4   1.6e-65   2.9e-61       6     244 .]      17     231 ..      14     231 .. 0.98

  Alignments for each domain:
  == domain 1  score: 206.9 bits;  conditional E-value: 1.6e-65
                                       ---TT--HHHHHHCCS-.....--TT-EEEEEHHHHHHHTT-EEEGGGS---HHHHHHHHHH.TS-H.......... CS
                       F420_ligase   6 likegddlaeivvesvkkagleledgDivvvtekvvakaegnyvsledikpsekAeeiaeklkvidpilSrnrfsli 82 
                                       l kegdd+ae++++ vkk++l+ledgD+vvv++++v+kaeg++v+l++++ps++A+++a+++  +dp          
  gi|557695022|ref|YP_008798076.1|  17 LAKEGDDVAELIMDGVKKSSLTLEDGDVVVVAHSLVSKAEGKIVKLDEVTPSHHAIHLAKAT-AKDP---------- 82 
                                       679***********************************************************.****.......... PP

                                       ........HHHHHHHHTEEEEEE-...S-EEEE.......TTS-EEEGGG-B-TTS-TT.EEE---S-HHHHHHHHH CS
                       F420_ligase  83 Lkalakatrkvevvlsepsdevgn...qlidekytdevlvklGllgsnagidesnveeg.llkllPedpdksaeeik 155
                                               r+ve vl+++ ++++    ++i+e+       ++G++++nag+d+sn  ++ +l+ lP+dpd+sa++i+
  gi|557695022|ref|YP_008798076.1|  83 --------RHVETVLRNAAKILRVghgVIICET-------HHGFVCANAGVDASNSGGEaFLITLPDDPDASAHRIR 144
                                       ........*************9999999*****.......****************98889**************** PP

                                       HHHHHHHS---EEEE..EEEEEETTEECEEEEEEEEESB-SEEE-TT-B-TTS-B-S--EEEHHHHHHHHHHHHC-S CS
                       F420_ligase 156 kklkertgkdveVliygkDpegriweladpvvaigtsglealrdlrgkkdldgkelgttpravtdelgsladLvsGs 232
                                       + l++  g+dv+V+i  +D+ gr+++ + ++vaig+sg+++l dlrg+kdl+g+ l+     v+d+++++a Lv+G+
  gi|557695022|ref|YP_008798076.1| 145 SGLRRLAGVDVAVVI--TDSWGRPFRKGAVNVAIGCSGINPLIDLRGRKDLYGRVLRSKIICVADQIAAAAGLVMGE 219
                                       ***************..************************************************************ PP

                                       SSS---EEEEES CS
                       F420_ligase 233 adegtPvvlvrg 244
                                       adegtP+++v+g
  gi|557695022|ref|YP_008798076.1| 220 ADEGTPAAIVKG 231
                                       **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1924.35
//
Query:       gi|557695023|ref|YP_008798077.1|  [L=206]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00051   20.1   0.0    0.00087   19.3   0.0    1.3  1  Mrr_cat   Restriction endonuclease
      0.006   17.0   0.0      0.025   15.0   0.0    1.8  2  NERD      Nuclease-related domain


Domain annotation for each model (and alignments):
>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   9.7e-08   0.00087       4      71 ..      47     114 ..      44     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.7e-08
                                       T-TTCHHHHHHHHHHHHSSS...EEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHH CS
                           Mrr_cat   4 mspkeFeklvaellealGyk...eveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqelig 71 
                                       +s++e+e++vae+ ++ G+     ++ + +++ g +D++a  +      ++v +Kr++++ + k ++e++ 
  gi|557695023|ref|YP_008798077.1|  47 LSWREMEDFVAEACRRAGFLcrtGFRFSVEGKKGEVDVLAAGSS---ICLAVDCKRWSKRLSGKTLREIVE 114
                                       79*****************9777556777789999****98765...569********9999999999865 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   2.8e-06     0.025       6      88 ..      53     127 ..      48     147 .. 0.66
   2 ?   -0.7   0.0      0.22   1.9e+03      45      60 ..     156     171 ..     152     203 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.8e-06
                              NERD   6 EravakeLkelkedeylvlhdvrlrpg..tgeiDhlvispkgifviEvKnwsGwifgd.kegrwtqkikkgfknple 79 
                                       E  va++ +   + ++l  +++r+  +  +ge+D+l+ + + ++ +++K ws ++ g+          ++ ++  l+
  gi|557695023|ref|YP_008798077.1|  53 EDFVAEACR---RAGFLCRTGFRFSVEgkKGEVDVLAAGSSICLAVDCKRWSKRLSGKtL--------REIVEKSLH 118
                                       556666666...3367788888887776566**********8888*******99999821........122233444 PP

                              NERD  80 qakrhakal 88 
                                         k  +++l
  gi|557695023|ref|YP_008798077.1| 119 RTKLLKNYL 127
                                       444444444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.22
                              NERD  45 gifviEvKnwsGwifg 60 
                                       g+fv+ v +++G++++
  gi|557695023|ref|YP_008798077.1| 156 GVFVVPVHSIRGFLTS 171
                                       8999999999995543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1577.52
//
Query:       gi|557695024|ref|YP_008798078.1|  [L=163]
Description: histidine triad (HIT) protein (hit) [Candidatus Caldiarchaeum subterraneum]
Scores for 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-12   46.9   0.0    4.9e-12   46.4   0.0    1.1  1  HIT       HIT domain
    1.4e-07   31.4   0.0    2.4e-07   30.6   0.0    1.3  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1
    1.6e-07   31.8   0.0    2.2e-07   31.3   0.0    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding


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 !   46.4   0.0   8.3e-16   4.9e-12       7      95 ..      37     126 ..      31     129 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 8.3e-16
                                       CEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT- CS
                               HIT   7 tvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagq 83 
                                        vv + ++++++ +i p   gh+ v p +h+  l++l+++e+ ++++ +k v+k++ + ++ +g+++  n g++ag 
  gi|557695024|ref|YP_008798078.1|  37 YVVHRGKKSFIIMNIYPYNNGHVMVTPFRHVGSLEELDDDEMLEMMQQIKWVVKVISNIMRPEGFNIGANIGKSAGA 113
                                       57888899********************************************************************* PP

                                       SS.SS-EEEEEEC CS
                               HIT  84 sv.ahlHiHvipr 95 
                                        +  h+H+Hv+pr
  gi|557695024|ref|YP_008798078.1| 114 GIeDHIHFHVVPR 126
                                       9945*******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 !   30.6   0.0     4e-11   2.4e-07      12      81 ..      20      91 ..      13      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4e-11
                                      HH-S----SS---..SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHHHH CS
                          CwfJ_C_1 12 dsClfClsnpkle..khlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfrkalvkm 81
                                      + C fCl  ++ +  k+ +v  g+k ++ +   p ++gHv+++p  H+ +l +ld++++ e+ +  k +vk+
  gi|557695024|ref|YP_008798078.1| 20 SGCVFCLAAEEKDdrKRYVVHRGKKSFIIMNIYPYNNGHVMVTPFRHVGSLEELDDDEMLEMMQQIKWVVKV 91
                                      67*****87766522789**************************************9999998777766665 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 !   31.3   0.0   3.7e-11   2.2e-07       2     100 ..      22     124 ..      21     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.7e-11
                                       -HHHHHHTTSS.-B-E.EEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T CS
                            DcpS_C   2 wvfnilakgke.perv.vyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne 76 
                                       +vf+  a++k+ ++r  v++ +k  ++  i+p ++ h++v p r++ sl++L+++  ++l em++++k v++   n 
  gi|557695024|ref|YP_008798078.1|  22 CVFCLAAEEKDdRKRYvVHRGKKSFIIMNIYPYNNGHVMVTPFRHVGSLEELDDD--EML-EMMQQIKWVVKVISNI 95 
                                       8999988888865555255669999999************************844..445.5667788888888877 PP

                                       -EEEEE--SCCCT--S.....-S--EEEE CS
                            DcpS_C  77 vdaeelrvgvhyqPsv.....yhlHlHvi 100
                                       +++e +++g ++  s      +h+H+Hv+
  gi|557695024|ref|YP_008798078.1|  96 MRPEGFNIGANIGKSAgagieDHIHFHVV 124
                                       8999999999999954333348*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1271.12
//
Query:       gi|557695025|ref|YP_008798079.1|  [L=337]
Description: tRNA-modifying enzyme [Candidatus Caldiarchaeum subterraneum]
Scores for 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-21   75.9   0.1    1.3e-19   71.2   0.0    2.5  2  Radical_SAM   Radical SAM superfamily
    6.7e-19   68.0   0.0    1.3e-18   67.1   0.0    1.5  1  Wyosine_form  Wyosine base formation
     0.0031   17.8   0.2       0.11   12.8   0.2    2.3  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 !   71.2   0.0   2.1e-23   1.3e-19       3     162 ..      75     253 ..      73     258 .. 0.79
   2 ?   -3.2   0.0       1.6   9.7e+03      24      49 ..     282     305 ..     273     314 .. 0.67

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 2.1e-23
                                       EESEESS--TTTSCCTT..HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE........................ CS
                                       xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet..vrregrgrslsveeileevkelkaekgvkevilg........................ 53 
                                        ++ Cn++C+fC+r +t    + ++g+   +eeile + +       +++++g                        
  gi|557695025|ref|YP_008798079.1|  75 SVQYCNMMCVFCWRFHTlnRVQPYDGEWDKPEEILERMIAE-----QRQLLSGfggnpnvskerfreamepmhiais 146
                                       5678*************997777777777778777777444.....2333333344555557777777777777777 PP

                                       .SSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH...HHHHHHTCTSH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
                       Radical_SAM  54 .ggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaadde...kvlklmnrght 126
                                         gep+lyp ++e++  ++ +   g++++++tngt+p e+  e+l ++ ++ ++++l  +d+e   k+ k++  +++
  gi|557695025|ref|YP_008798079.1| 147 lDGEPTLYPYLAEFIQLASSR---GMTTFLVTNGTMP-ERLEELLQKAQPTSLYISLYGPDKEthvKTCKPL-IKDS 218
                                       799999999999999999998...************8.77777777777**************555444444.99** PP

                                       HHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 127 feevlealeklreagikrvvdrivglpGendeelee 162
                                       +e++l++le++ +  ++  ++r+++++ +n++  e+
  gi|557695025|ref|YP_008798079.1| 219 WERLLKSLELMGRFSCR-KIIRLTLVKDVNMHSPEK 253
                                       *****************.8***********987766 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHHHHHHHHHHHHTTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  24 grgrslsveeileevkelkaekgvke 49 
                                       +++ + s+eei + + el+a+  +++
  gi|557695025|ref|YP_008798079.1| 282 KKENMPSLEEINKFAAELAAS--IGF 305
                                       566777888888888888544..444 PP

>> Wyosine_form  Wyosine base formation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.0   2.2e-22   1.3e-18       2      63 .]     261     321 ..     260     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 2.2e-22
                                       HT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                      Wyosine_form   2 aepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                       a pdFvE K+yt+vG+s+ rL+++n+P+ ee+ +fa +l+ s++ +  +ae++ Srvvlla+
  gi|557695025|ref|YP_008798079.1| 261 ASPDFVECKGYTHVGESQLRLKKENMPSLEEINKFAAELAASIG-FIKVAEDEVSRVVLLAN 321
                                       79******************************************.***************96 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 !   12.8   0.2   1.8e-05      0.11      12      70 ..      76     132 ..      65     201 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeft..kelleeiiedlkkesiegltllGGEPllpenae 70 
                                       v+ Cn+ C +C    t +    ++++   +  eei+e++  e+++ l+ +GG P +   +e
  gi|557695025|ref|YP_008798079.1|  76 VQYCNMMCVFCWRFHTLNR--VQPYDgeWDKPEEILERMIAEQRQLLSGFGGNPNV--SKE 132
                                       899********97666643..34443224444566666666777777777777766..333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); 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: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2434.55
//
Query:       gi|557695026|ref|YP_008798080.1|  [L=289]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   50.7   0.1    9.5e-07   28.4   0.0    2.1  2  PfkB         pfkB family carbohydrate kinase
  ------ inclusion threshold ------
      0.065   12.7   0.0       0.11   11.9   0.0    1.4  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 !   20.4   0.0     3e-08   0.00027      33      91 ..      17      74 ..      10      79 .. 0.90
   2 !   28.4   0.0   1.1e-10   9.5e-07     174     281 ..     154     253 ..     108     258 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3e-08
                                      EEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTTEEETTEEEESSSEEE CS
                              PfkB 33 ksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkegvdtdyvkidedtrtg 91
                                      ++ GG++    +a+a+l ++v++++avG+D+  e ++++++k+g+++++v+  + +rt 
  gi|557695026|ref|YP_008798080.1| 17 NYIGGSPWYAGTAAASLSHEVSVCSAVGNDF-PENFITLMQKRGLNISRVVKIGSARTY 74
                                      6677777777899******************.*******************99999986 PP

  == domain 2  score: 28.4 bits;  conditional E-value: 1.1e-10
                                       HHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEETTEEEEEEE.SSSS CS
                              PfkB 174 keallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvvekdgelkvpavpkvk 250
                                         +++e+l+ +d+l +++eE+ a+tge+  d+ +a+++       g++ vv   +++G +++ + g+l   ++p v 
  gi|557695026|ref|YP_008798080.1| 154 SRDVSEILESVDVLHCSDEEALAVTGED--DVVSATRVFGL----GTEAVVLVGSADGLYIA-HRGSLSLLRLP-VS 222
                                       46799***********************..99999999765....99***************.55555666657.** PP

                                       -SBGTTHHHHHHHHHHHHHHTTHHHHHHHHH CS
                              PfkB 251 vvDttGAGDsfvggflaallegksleealrf 281
                                         D tGAGD+ +g fl  +++g +  ea++ 
  gi|557695026|ref|YP_008798080.1| 223 GHDLTGAGDMLTGFFLTLYTDGVNPFEAAAH 253
                                       ****************999998776666655 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.3e-05      0.11     140     214 ..     180     254 ..     166     264 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.3e-05
                                       CCSHHHHHHHHHHHHTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHH CS
                       Carb_kinase 140 eddrlelarelaqklnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaa 214
                                       edd++ + r +    +avvl+  +  + +++ g ++++    s+    G GD L+G  + l     +++eaa+ a
  gi|557695026|ref|YP_008798080.1| 180 EDDVVSATRVFGLGTEAVVLVGSADGLYIAHRGSLSLLRLPVSGHDLTGAGDMLTGFFLTLYTDGVNPFEAAAHA 254
                                       56666666777777778888888888999*******************************999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2176.07
//
Query:       gi|557695027|ref|YP_008798081.1|  [L=102]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); 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: 00:00:00.38
# Mc/sec: 802.93
//
Query:       gi|557695028|ref|YP_008798082.1|  [L=150]
Description: S-adenosylmethionine decarboxylase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-35  119.5   0.0    9.2e-35  119.1   0.0    1.1  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 !  119.1   0.0   5.1e-39   9.2e-35       1     105 [.      40     147 ..      40     148 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 5.1e-39
                                       EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-..SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEE CS
                         AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkf..epeGvsvvvliaeShlsiHtwpetgyaaiDvf 75 
                                       h++ +ly+c +++++d++ l++i++ea++++++t++s  +++f  e++Gvsv++li eSh+++Htw e++ya++D++
  gi|557695028|ref|YP_008798082.1|  40 HVFGNLYNCPENIISDEKYLRKIVREAIKQANMTLVSLRSWSFggEKGGVSVIALITESHVAVHTWREYNYATVDIY 116
                                       999****************************************88778***************************** PP

                                       EEST.HHHHHHHHHHHHHHT-SEEEEEEEEE CS
                         AdoMet_dc  76 tcge.ispekaleylieafkadrvtvdelkR 105
                                       tcge  +peka++y+++++++++vt   ++R
  gi|557695028|ref|YP_008798082.1| 117 TCGEeSNPEKAFDYIVQHLRPESVTRYFADR 147
                                       ************************9877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1189.97
//
Query:       gi|557695029|ref|YP_008798083.1|  [L=146]
Description: molybdenum cofactor biosynthesis protein E [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   79.4   0.1    2.7e-22   79.2   0.1    1.0  1  MoaE      MoaE protein


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 !   79.2   0.1   1.5e-26   2.7e-22      11     112 ..      23     125 ..      15     126 .. 0.94

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 1.5e-26
                                       HHHHH--TT--EEEEEEEE------.TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE-EEEETTSEE CS
                              MoaE  11 iealvaspkaGAvvlFvGtvRdsfd.gkkvteLeyeayepmaektleeiaeearerwelervavvHrlGelevgeas 86 
                                       ++a v++ ++GA ++F+G+v+ + + +  v++L +e+ye+ a+++l++i++e++++++l+ v ++H +G l+vge++
  gi|557695029|ref|YP_008798083.1|  23 VVARVSDGSCGAAAFFLGIVKRRGRgEVGVEKLFMESYEEHANRALKRICDEVMAEYSLKFVGIWHLVGMLDVGEPV 99 
                                       56778999*************77776669************************************************ PP

                                       EEEEEEESSHHHHHHHHHHHHHHHHH CS
                              MoaE  87 vvvavssahRkeafeaceylidelKk 112
                                       v+va++++ R+e f+  + ++++ K+
  gi|557695029|ref|YP_008798083.1| 100 VFVAAAGESRDEVFRGLRTAVERYKR 125
                                       ***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1074.38
//
Query:       gi|557695030|ref|YP_008798084.1|  [L=109]
Description: molybdenum cofactor biosynthesis protein D [Candidatus Caldiarchaeum subterraneum]
Scores for 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-20   71.6   0.0    7.3e-20   71.4   0.0    1.1  1  ThiS           ThiS family
  ------ inclusion threshold ------
      0.023   14.4   0.0      0.035   13.8   0.0    1.3  1  DUF2635        Protein of unknown function (DUF2635)
      0.024   14.7   0.0        4.4    7.4   0.0    2.2  2  TGS            TGS domain
      0.041   14.2   0.0      0.045   14.1   0.0    1.2  1  Lambda_tail_I  Bacteriophage lambda tail assembly protein I
       0.21   12.2   0.0        5.4    7.7   0.0    2.1  1  DUF4430        Domain of unknown function (DUF4430)


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 !   71.4   0.0     2e-23   7.3e-20       2      77 .]      11      97 ..      10      97 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 2e-23
                                      EETTCCHHHHT..CEEEEESSTSBHHHHHHHHHHHTCHHG........TTTTEEEEETTEEEGC.CTTTSB--TTCEEE CS
                              ThiS  2 llfaelrelag..eeelelaegstvaelleaLgerypela........lerrvavavNgeivpr.lwldtelkdgDeva 69
                                      +++a lre +g  +ee+el++gstv + le+L + y++          l+ ++a+a+Nge ++r lw++t+lkdgD+v+
  gi|557695030|ref|YP_008798084.1| 11 KYYAVLRERVGkaSEEFELPQGSTVIDFLEKLRQVYGGVLgdlfegdgLRTGFALALNGESLDRkLWASTRLKDGDVVV 89
                                      79***********************************999********99**************88************* PP

                                      EEESTTC- CS
                              ThiS 70 ilppVaGG 77
                                      +lpp+aGG
  gi|557695030|ref|YP_008798084.1| 90 VLPPIAGG 97
                                      *******9 PP

>> DUF2635  Protein of unknown function (DUF2635)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   9.9e-06     0.035      15      43 ..      62      90 ..      59      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.9e-06
                           DUF2635 15 gelLpaeGeevprtlyWlRRlkdGDvvev 43
                                      g  L   Ge  +r l+   RlkdGDvv+v
  gi|557695030|ref|YP_008798084.1| 62 GFALALNGESLDRKLWASTRLKDGDVVVV 90
                                      55677889999****************98 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0012       4.4       9      25 ..      25      41 ..      18      46 .. 0.81
   2 ?    5.3   0.0    0.0059        21      46      57 ..      78      89 ..      59      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0012
                                      SEEEEETTB-HHHHHHH CS
                               TGS  9 kvpdlprgatveDfAyk 25
                                      ++++lp+g+tv+Df  k
  gi|557695030|ref|YP_008798084.1| 25 EEFELPQGSTVIDFLEK 41
                                      5678*********9655 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0059
                                      TTSBB-SSEEEE CS
                               TGS 46 ldhvLedgdvve 57
                                       +++L+dgdvv 
  gi|557695030|ref|YP_008798084.1| 78 ASTRLKDGDVVV 89
                                      589*******96 PP

>> Lambda_tail_I  Bacteriophage lambda tail assembly protein I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.3e-05     0.045      46      86 .]      57      97 ..      16      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                     Lambda_tail_I 46 rskfavrvagvdVgesvpvdrya.etlkdgkvvtivpvpaGg 86
                                      ++ + ++    + ges  +  +a   lkdg vv + p  aGg
  gi|557695030|ref|YP_008798084.1| 57 DGLRTGFALALN-GESLDRKLWAsTRLKDGDVVVVLPPIAGG 97
                                      78889999999*.************************99998 PP

>> DUF4430  Domain of unknown function (DUF4430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0015       5.4      41      69 ..      60      89 ..      32      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
                           DUF4430 41 ksyWmyevNGepsdv.Gagsyklkdgdkiv 69
                                      +++  +  NGe+ d+    s++lkdgd++v
  gi|557695030|ref|YP_008798084.1| 60 RTGFALALNGESLDRkLWASTRLKDGDVVV 89
                                      488888899999998778899999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); 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:                         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 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 776.76
//
Query:       gi|557695031|ref|YP_008798085.1|  [L=172]
Description: dCTP deaminase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-21   74.1   0.0      1e-20   73.7   0.0    1.2  1  dUTPase   dUTPase
    5.2e-06   25.5   0.0    1.2e-05   24.3   0.0    1.5  1  DCD       2'-deoxycytidine 5'-triphosphate deaminase (DCD)
  ------ inclusion threshold ------
        0.1   12.4   0.0       0.15   11.9   0.0    1.1  1  DUF3821   Domain of unknown function (DUF3821)


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 !   73.7   0.0   1.7e-24     1e-20       7     125 ..      52     166 ..      45     168 .. 0.87

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 1.7e-24
                                       BESSTT-SSEEEE-SSSEEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE- CS
                           dUTPase   7 trkspesAgyDlsaakdltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnl 83 
                                       t+ks+ + +y ++ a+++++ p+e+vl+ t  +++lp++l+++++ RS+ a+ gl+++p++id+ ++Ge+ + l   
  gi|557695031|ref|YP_008798085.1|  52 TKKSDAANFYTIEEAEEFVINPHEHVLLHTLEYLALPKDLMGFVNLRSSYARIGLTIPPTIIDANFEGELTIEL--V 126
                                       566777779***********************************************************655555..5 PP

                                       SSS.-EEE-TT-EEEEEEEEEBECGEEEEESST.TTESSBTTXT CS
                           dUTPase  84 tkk.dvkikkgdRiAqLifariltaeleevetl.katergeggf 125
                                       +++ +vk+  gdR+++++far+       ve++   +++g++g+
  gi|557695031|ref|YP_008798085.1| 127 GGDfPVKLYSGDRFLHVVFARLSS----IVEKPyTGKYQGQRGV 166
                                       5555****************9999....5665557888888886 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 !   24.3   0.0     2e-09   1.2e-05       4     168 ..       2     153 ..       1     166 [. 0.83

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 2e-09
                               DCD   4 ilpdqeiealieegaikaeepleeeqiqPaslDLrLgkkayrvrasFlpgkgekvaekleelklheldLtegavlek 80 
                                       il+d ++ + i++g ++  ep++e+ +  + lDLr+g++     a F  +++   ++k ++ ++++++ +e+ v++ 
  gi|557695031|ref|YP_008798085.1|   2 ILSDFDLWNYIRNGRLR-IEPFSEDVVRENGLDLRIGRQI----ARFNKNSKVFDTKKSDAANFYTIEEAEEFVINP 73 
                                       67777778888888885.4789***************886....55655555555667788999************9 PP

                               DCD  81 gcvYivplleslaLpadlsaaanpksstGRlDvftRvitdkgeefdeveagYkGplyleisprsFsilvrkGsrLsq 157
                                           +++ le laLp+dl + +n +ss  R+ + +            ++a ++G+l +e++   F++++ +G+r   
  gi|557695031|ref|YP_008798085.1|  74 HEHVLLHTLEYLALPKDLMGFVNLRSSYARIGLTIP--------PTIIDANFEGELTIELVGGDFPVKLYSGDRFLH 142
                                       99999999***********************97542........3357899************************99 PP

                               DCD 158 irfrrgeakls 168
                                       + f r ++ ++
  gi|557695031|ref|YP_008798085.1| 143 VVFARLSSIVE 153
                                       99988776665 PP

>> DUF3821  Domain of unknown function (DUF3821)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.6e-05      0.15       8      56 ..      28      75 ..      26      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
                           DUF3821  8 gEegLdisnllnggtqiawwasgaev...kseepdksikisdpenFyvsPaa 56
                                       E+gLd+     +g qia +++ ++v   k++++++ ++i+++e+F+++P +
  gi|557695031|ref|YP_008798085.1| 28 RENGLDLR----IGRQIARFNKNSKVfdtKKSDAANFYTIEEAEEFVINPHE 75
                                      59999999....899*********9988889999999*************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1212.04
//
Query:       gi|557695032|ref|YP_008798086.1|  [L=262]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   67.3   0.1    1.7e-18   66.9   0.1    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    5.1e-13   49.5   0.2      7e-11   42.5   0.0    2.8  3  Lactamase_B    Metallo-beta-lactamase superfamily
    2.3e-05   24.4   0.2    4.6e-05   23.4   0.2    1.5  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 !   66.9   0.1   2.8e-22   1.7e-18       1     200 [.      30     225 ..      30     226 .. 0.87

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 2.8e-22
                                       SEEEES--TTHHHHHTCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCC...........C--EEEEEEEEHH CS
                     Lactamase_B_2   1 rriLiDagpdlrqqalral.qPvelrdelppidaVllthaHyDHlaglltlre...........lrpkklplyapkg 65 
                                       +r+LiD+gp++   + r+  +       + ++ aVl++h H DH+ +ll l              +pk+l+l++p g
  gi|557695032|ref|YP_008798086.1|  30 TRLLIDPGPGTIYKLIRLAvN-------PLSLTAVLISHFHLDHISDLLPLIMmwcydeegkpsSQPKNLHLIGPSG 99 
                                       79********77774444423.......4589*****************99998988889888777777******** PP

                                       HHHHCCTTCGHHHCHTT.......TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTE CS
                     Lactamase_B_2  66 vlavleanfvylaleee.......pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggk 135
                                       +++ +e+ ++ +a+           ++++ e+  g+  ++g  +++ita +++h  g           ++ i+  gk
  gi|557695032|ref|YP_008798086.1| 100 LHKLVEQVISIDAFSYLnkpmqvrRFLQIDEMRHGDMRQVG--ECKITAAEVEHLNGL----------AYKITHRGK 164
                                       ***99998776665555566779999**************9..578***********9..........********* PP

                                       EEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 136 rvyyigDtgyipeeigerlggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliH 200
                                       +++y+gDt   + ++ ++ +++dll++++ + +++       H + ++ +e+aa++++++  ++H
  gi|557695032|ref|YP_008798086.1| 165 NIVYSGDTVPDK-HLIDLAKNCDLLIHECSFPHQQLI---GKHTSEKQLAEIAAKTNPRKIAVTH 225
                                       *********655.6666*************9999884...57**********************9 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   1.2e-14     7e-11       7      63 ..      21      72 ..      16      74 .. 0.92
   2 ?    3.4   0.0     0.011        68     137     162 ..     158     183 ..     152     225 .. 0.72
   3 ?    0.2   0.0      0.11   6.6e+02      61     105 ..     209     249 ..     207     261 .. 0.72

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.2e-14
                                      EEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGG CS
                       Lactamase_B  7 nsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgg 63
                                      + ++ie +++ +LiD+G +t +++++     l ++p+ ++av+++H+HlDHi++l  
  gi|557695032|ref|YP_008798086.1| 21 SGVFIEAEETRLLIDPGPGTIYKLIR-----LAVNPLSLTAVLISHFHLDHISDLLP 72
                                      5689*********************8.....7*********************9865 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.011
                                       EEEETTCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 137 vveygggkvlftGDallagetgridl 162
                                        ++ +g++++++GD+++    +++ +
  gi|557695032|ref|YP_008798086.1| 158 KITHRGKNIVYSGDTVPDKHLIDLAK 183
                                       578899**********9877777666 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.11
                                       GGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCC CS
                       Lactamase_B  61 lgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsadk 105
                                       l++++ +t+  ++av + +p + ++e++  +  k++    + ++ 
  gi|557695032|ref|YP_008798086.1| 209 LAEIAAKTNPRKIAVTHLYPTWSGREHEITEALKQA----GIPPE 249
                                       577888999999999999999999999988888764....33333 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 !   23.4   0.2   7.8e-09   4.6e-05      10     134 ..      23     190 ..      20     225 .. 0.57

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 7.8e-09
                     Lactamase_B_3  10 flletagarilvDPfka....nlgyeppaeeaDlvlisqaledHahletlkql........................ 58 
                                       + +e +++r+l+DP+ +     + ++ ++ +  +vlis+ + dH     l+ +                        
  gi|557695032|ref|YP_008798086.1|  23 VFIEAEETRLLIDPGPGtiykLIRLAVNPLSLTAVLISHFHLDHISD-LLPLImmwcydeegkpssqpknlhligps 98 
                                       68999**********64322233444555889999999999999764.3555588*********9994444444444 PP

                     Lactamase_B_3  59 ..........................aenvkvleegeslevggleiravatshdavggsergenngflleqdgltiy 109
                                                                 + +++ +++g+  +vg+++i+a + +          ++ ++ ++ +g +i+
  gi|557695032|ref|YP_008798086.1|  99 glhklveqvisidafsylnkpmqvrrFLQIDEMRHGDMRQVGECKITAAEVE--------HLNGLAYKITHRGKNIV 167
                                       4444433333322222222222211111111111122222333333333333........35689************ PP

                     Lactamase_B_3 110 hlGhlahelsseelkelg.rvDvvlt 134
                                       + G+++    +++l  l+ + D+++ 
  gi|557695032|ref|YP_008798086.1| 168 YSGDTVP---DKHLIDLAkNCDLLIH 190
                                       *****98...5555444327788775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1963.91
//
Query:       gi|557695033|ref|YP_008798087.1|  [L=174]
Description: molybdenum cofactor biosynthesis protein B [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  115.8   0.0    1.4e-33  115.6   0.0    1.0  1  MoCF_biosynth    Probable molybdopterin binding domain
  ------ inclusion threshold ------
       0.19   11.9   0.0       0.31   11.2   0.0    1.2  1  Isochorismatase  Isochorismatase family


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 !  115.6   0.0   1.5e-37   1.4e-33       1     144 []      18     166 ..      18     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 1.5e-37
                                       EEEEE-HHHH.....TTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTS.SEEEEESS-SSSTT CS
                     MoCF_biosynth   1 avitvGdell.....sgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleea.dviittGGtGptpd 71 
                                       av+t +++++     ++ ++D++g   +++l++lg++v+ ++vv Dd+  i++++l+ale+  dv+++tGGtG++p+
  gi|557695033|ref|YP_008798087.1|  18 AVLTASSSRYykkirNEAYVDESGENAVQKLRDLGHNVEYLGVVNDDILMIRSTVLTALEKGfDVVVITGGTGLSPR 94 
                                       6999999999566656666************************************99988889************** PP

                                       --HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE....TTE.EEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  72 Dvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsrav....gkt.iigLPGspkavkealeeillpale 143
                                       Dvt eal++lf+ke+eg +e+fr  s+++     ++ +a lsr++    ++  ii+LPGsp av+ al+++  p+++
  gi|557695033|ref|YP_008798087.1|  95 DVTIEALRPLFDKEVEGWGELFRVESYRE-----IGSAAALSRTTagivNGRlIIALPGSPEAVRLALKLLG-PEIP 165
                                       ****************************9.....999999***99****666599****************9.9998 PP

                                       H CS
                     MoCF_biosynth 144 h 144
                                       h
  gi|557695033|ref|YP_008798087.1| 166 H 166
                                       7 PP

>> Isochorismatase  Isochorismatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.4e-05      0.31     127     153 ..      68      94 ..      66     109 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.4e-05
                   Isochorismatase 127 VeatardaldlGyevvvvsDAvaalsp 153
                                       +++t++ al++G++vvv++ +++ + +
  gi|557695033|ref|YP_008798087.1|  68 IRSTVLTALEKGFDVVVITGGTGLSPR 94 
                                       679***************998886664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); 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: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1472.98
//
Query:       gi|557695034|ref|YP_008798088.1|  [L=142]
Description: molybdenum cofactor biosynthesis protein C [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-42  144.7   2.0    1.9e-42  144.6   2.0    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 !  144.6   2.0   1.1e-46   1.9e-42       5     134 ..       2     136 ..       1     138 [. 0.97

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 1.1e-46
                                       TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEETTTT CS
                              MoaC   5 sekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkveveleleeeee 81 
                                       s+k+++kr+AvA gr+ l+++t+e+i++k+++kGd l+ a++agi++aK+t++l+plcHpl+l++ve++ e+   e+
  gi|557695034|ref|YP_008798088.1|   2 SAKPVQKREAVAVGRIILKHSTVEMIRKKAVEKGDPLQLAHVAGILGAKQTPTLLPLCHPLKLEHVEITEEVG--EN 76 
                                       78*****************************************************************988765..89 PP

                                       EEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEE CS
                              MoaC  82 sveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKs 134
                                        +e++++v + +ktGvemEALtav++a+l+++D+vK+++k+       + i+++r+v+K 
  gi|557695034|ref|YP_008798088.1|  77 YIEVRSKVVAYEKTGVEMEALTAVATALLNIWDVVKQYEKDeygqyptTAITDIRVVSKV 136
                                       *****************************************9****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1115.08
//
Query:       gi|557695035|ref|YP_008798089.1|  [L=147]
Description: small subunit ribosomal protein S11 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-38  131.2   1.7    3.1e-38  130.6   1.7    1.3  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 !  130.6   1.7   1.7e-42   3.1e-38       1     110 []      25     143 ..      25     143 .. 0.99

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 1.7e-42
                     Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg...... 70 
                                       Gv+hi++s+nn i+++tdl+Gae++++++Gg+ v a r +++Pya+++aa+ ++e+++  Gi+av++ v++      
  gi|557695035|ref|YP_008798089.1|  25 GVVHIYSSYNNIIVHLTDLTGAETIARASGGMFVDAGRlEPTPYAGMRAASFVMEAAKAAGITAVHILVRApggvks 101
                                       89*************************************************************************** PP

                     Ribosomal_S11  71 ..pGpGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                         pGp  +aa+r++ar+Gl igriedvtPiPhd++r++++rr
  gi|557695035|ref|YP_008798089.1| 102 rtPGPATQAAIRTIARSGLMIGRIEDVTPIPHDSVRKKGGRR 143
                                       ***************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1066.10
//
Query:       gi|557695036|ref|YP_008798090.1|  [L=170]
Description: small subunit ribosomal protein S4 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-16   59.6   0.1    3.7e-16   58.6   0.1    1.6  1  S4            S4 domain
    3.4e-06   27.9   1.5    5.2e-06   27.3   0.6    1.7  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 !   58.6   0.1   4.1e-20   3.7e-16       1      47 [.     109     155 ..     109     156 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 4.1e-20
                                       EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCE CS
                                S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDv 47 
                                       rRL+++++r gla ++ +ArqlI hG+VlV Gk+v+ psy Vk g++
  gi|557695036|ref|YP_008798090.1| 109 RRLQTIVFRTGLARTIFHARQLITHGKVLVGGKKVRAPSYHVKRGEE 155
                                       8******************************************9986 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 !   27.3   0.6   5.8e-10   5.2e-06      36      80 ..      21      66 ..       6     108 .. 0.80
   2 ?   -1.1   0.0      0.41   3.6e+03      11      41 ..     109     150 ..     100     161 .. 0.52

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 5.8e-10
                                      --CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHHH CS
                      Ribosomal_S4 36 lseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLlq 80
                                        +++   l+e+ kl+++Ygl+ +++++r+ +++r++r  ++++L +
  gi|557695036|ref|YP_008798090.1| 21 RHPWRReILEEELKLMGEYGLRnKREIWRAASQLRKYR-ALARRLFT 66
                                      45999999******************************.*****987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.41
                                       CHCTS-STSSS...........S-S-SSTTTTS.....-----CHCH CS
                      Ribosomal_S4  11 Rrvgfklflkg...........reyppGqhgkr.....rkklseYgk 41 
                                       Rr+++ +f +g                  hgk      + ++  Y +
  gi|557695036|ref|YP_008798090.1| 109 RRLQTIVFRTGlartifharqlI-----THGKVlvggkKVRAPSYHV 150
                                       66666666666665555442220.....3333333333444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       321  (0.017904); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1291.18
//
Query:       gi|557695037|ref|YP_008798091.1|  [L=379]
Description: geranylgeranyl reductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   53.7   1.4    3.5e-05   23.2   0.1    3.0  3  FAD_binding_3   FAD binding domain
    1.7e-10   40.7   0.2    2.9e-10   39.9   0.2    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    9.7e-10   38.2   1.8    0.00034   20.0   0.2    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      1e-09   38.5   0.4    0.00088   19.0   0.0    2.2  2  DAO             FAD dependent oxidoreductase
    1.7e-08   33.6   1.5      1e-05   24.4   0.3    2.3  2  HI0933_like     HI0933-like protein
    2.6e-07   30.1   1.0    0.00054   19.1   0.7    2.3  2  Lycopene_cycl   Lycopene cyclase protein
      7e-07   28.5   0.1      0.022   13.6   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
    7.3e-07   28.9   3.1    7.3e-07   28.9   3.1    2.4  2  FAD_oxidored    FAD dependent oxidoreductase
      6e-06   25.6   3.3    1.5e-05   24.3   3.3    1.8  1  GIDA            Glucose inhibited division protein A
    6.5e-05   22.3   0.4    0.00032   20.0   0.1    2.2  2  Thi4            Thi4 family
     0.0001   22.5   0.0     0.0001   22.5   0.0    2.2  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00012   21.3   0.7    0.00012   21.3   0.7    2.1  3  FAD_binding_2   FAD binding domain
     0.0032   17.5   0.3       0.93    9.5   0.0    2.5  2  NAD_binding_9   FAD-NAD(P)-binding
      0.004   17.7   0.9      0.025   15.1   0.1    2.4  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.018   14.3   0.6      0.044   13.1   0.1    1.9  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.11   12.4   0.0       0.62   10.0   0.0    2.1  2  DUF896          Bacterial protein of unknown function (DUF896


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   3.1e-08   3.5e-05       1      38 [.       3      40 ..       3      59 .. 0.86
   2 !   20.9   0.0   1.5e-07   0.00017     113     179 ..     101     162 ..      84     208 .. 0.74
   3 !    7.4   0.1    0.0021       2.3     284     319 ..     256     291 ..     224     309 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.1e-08
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCC CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvv 38
                                      e+dV++VG+GpaG+++a+  ++  v+v+l+ek+ t + 
  gi|557695037|ref|YP_008798091.1|  3 EYDVVVVGGGPAGVSAAKAAAMNSVSVLLLEKHPTIMA 40
                                      589******************************98654 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.5e-07
                                       HHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGG.EEEE CS
                     FAD_binding_3 113 ehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgie.fege 179
                                       ++a+e g++++  +ev+++ +++++    ++ k t ++ t +ak ++GaDG++Stv+++lg++ ++++
  gi|557695037|ref|YP_008798091.1| 101 AQAAEYGADIHVREEVTGVVRENSK----LLVK-T-NRDTYKAKVVIGADGYNSTVARSLGVTeRPEP 162
                                       5667777777777777777766655....3333.2.345899*******************9944443 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0021
                                       TTEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHH CS
                     FAD_binding_3 284 grvflaGDAaHihpPtgGqGlNtaiqDavnLawkLa 319
                                       +  +l+GDAa  + P +G G+ ++++     ++  a
  gi|557695037|ref|YP_008798091.1| 256 DGAMLIGDAAGHVIPLTGAGIHSSVSAGLAAGKVAA 291
                                       56689******************9998777776555 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 !   39.9   0.2   2.6e-13   2.9e-10       1     112 [.       4     149 ..       4     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 2.6e-13
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH.....HCHHHHHHHHHHHHH............... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxx............... RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll.....skallgvaedaeias............... 57 
                                       +dvvv+GgGpAG++aa+ +a +++ v+l+e+  t++ +++        + +++  ++    +               
  gi|557695037|ref|YP_008798091.1|   4 YDVVVVGGGPAGVSAAKAAAMNSVSVLLLEKHPTIMANKPCGeacskETLVTAGVKPSP--Rivmheayalvyspsm 78 
                                       69***************************955555555554434421222222222222..1346888888899999 PP

                                       ......................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE- CS
                                       ......................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ......................evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGsspr 112
                                                              +  +++++i+++ +  v+++ +++ k+ +++++     +++++ ++ A G ++ 
  gi|557695037|ref|YP_008798091.1|  79 ievkipqigyninksffiqeiaAQAAEYGADIHVREE--VTGVVRENSKLLVKTNR----DTYKAKVVIGADGYNST 149
                                       999*****************99778899999998888..********9*9996555....48999999999886554 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 !   17.6   0.1   1.6e-06    0.0018       1      30 [.       7      35 ..       7      43 .. 0.91
   2 !   20.0   0.2     3e-07   0.00034      90     134 ..     102     146 ..      66     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      +++G+GPaG++aa ++  + + ++l lEk+
  gi|557695037|ref|YP_008798091.1|  7 VVVGGGPAGVSAAKAAAMNSV-SVLLLEKH 35
                                      79*******************.7******8 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3e-07
                       Pyr_redox_3  90 vaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGe 134
                                        a+++  +i+  eeV+ v +e+++  v+t+++ty+Ak vi A G+
  gi|557695037|ref|YP_008798091.1| 102 QAAEYGADIHVREEVTGVVRENSKLLVKTNRDTYKAKVVIGADGY 146
                                       57788899**********************************998 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   7.8e-07   0.00088       1      31 [.       5      37 ..       5      63 .. 0.91
   2 !   17.9   0.1   1.6e-06    0.0018     147     266 ..      94     208 ..      86     292 .. 0.59

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 7.8e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                                      dvv++GGG +G+s+A ++a     V+llek++ 
  gi|557695037|ref|YP_008798091.1|  5 DVVVVGGGPAGVSAAKAAAMNSvsVLLLEKHPT 37
                                      9*****************988789******965 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTT.CTTT.SEEEEE CS
                               DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdllgll.keld.lpispv 220
                                        +++ +a++a++ G++i+ ++evtg+ +e+ k   v  +t+  +  +a+ v+ a G  s+ ++ l  + +  p  p+
  gi|557695037|ref|YP_008798091.1|  94 FFIQEIAAQAAEYGADIHVREEVTGVVRENSK-LLV--KTNrDT-YKAKVVIGADGYNSTVARSLgVTERpEP-IPT 165
                                       58899********************9776534.333..454333.2446688888888875555533333123.555 PP

                                       EEEEEEEEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEEE CS
                               DAO 221 rgqvlvlkplseklvspaailpvpetdddgrgvyvtprkdgrvlvG 266
                                         ++++ ++l++   s a  + +  ++ +g++  ++pr +    vG
  gi|557695037|ref|YP_008798091.1| 166 VQYIMANCRLKN---SDAVRFYLGNKIAPGGYAWIFPRTEKLAEVG 208
                                       555555555544...3333333333778888888888765533343 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.3   9.2e-09     1e-05       1      35 [.       4      38 ..       4      42 .. 0.93
   2 !    8.0   0.0    0.0009         1     115     167 ..      99     149 ..      91     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 9.2e-09
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakkl 35
                                      +dv+v+GgG+AG+ aA +aa +  +Vlllek +++
  gi|557695037|ref|YP_008798091.1|  4 YDVVVVGGGPAGVSAAKAAAMNSVSVLLLEKHPTI 38
                                      59*****************************9875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0009
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS- CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSi 167
                                       + +++ e g ++++++ev++v +e+++ + vkt ++++++a+ ++ A G +S 
  gi|557695037|ref|YP_008798091.1|  99 IAAQAAEYGADIHVREEVTGVVRENSK-LLVKT-NRDTYKAKVVIGADGYNST 149
                                       56788999*************887666.*****.9*******99999887774 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.7   4.8e-07   0.00054       1     140 [.       5     145 ..       5     160 .. 0.58
   2 !    8.9   0.0   0.00061      0.68     241     309 ..     242     312 ..     219     347 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 4.8e-07
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnny.vWsdefedlga.....leecvehsWsgtivyldd 71 
                                       Dvvv+G+GpAg+s A+    a   ++v+l+e  p ++  n+     + +e l +       ++v h  + + vy + 
  gi|557695037|ref|YP_008798091.1|   5 DVVVVGGGPAGVSAAKAA--AMNSVSVLLLEKHPTIMA-NKPcGEACSKETLVTagvkpSPRIVMHE-AYALVYSPS 77 
                                       9************99999..99************9954.4332222333332222444323333333.445566666 PP

                     Lycopene_cycl  72 gkkillg.raYgrvsskrlkeellerlvengv.klleakvesveeeeageslvvleggr.kirarlvvdarg 140
                                         ++++    Y  ++++ + +e++ + +e g+ + ++  v+ v+ e+       ++ +r + +a++v+ a g
  gi|557695037|ref|YP_008798091.1|  78 MIEVKIPqIGY-NINKSFFIQEIAAQAAEYGAdIHVREEVTGVVRENS---KLLVKTNRdTYKAKVVIGADG 145
                                       55555552334.466666666666666654441445666666666655...333333333667777777777 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00061
                     Lycopene_cycl 241 gviPvtlggslprleqk.vlaiGaaaglvhPaTGYsvarslae...apllasaiaaalresslsarawatlwp 309
                                       + +P+  gg +++      + iG aag v P TG  +  s+++   a ++a+  ++ +++s+++ ++  +l+ 
  gi|557695037|ref|YP_008798091.1| 242 APVPI--GGAISESVFDgAMLIGDAAGHVIPLTGAGIHSSVSAglaAGKVAATAVQEGDTSKRRLSEFYKLYE 312
                                       55777..99988877666999*************998888874111444444444444444555555555544 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1     3e-05     0.034       1      35 [.       5      36 ..       5      53 .. 0.82
   2 !   13.6   0.0     2e-05     0.022     146     371 ..      85     315 ..      64     334 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SS CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlvesee 35
                                      ++v+vGGG+aG  aA a a+     ++v+l+e+  
  gi|557695037|ref|YP_008798091.1|  5 DVVVVGGGPAGVSAAKAAAMNS---VSVLLLEKHP 36
                                      69***************99998...99***99853 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
                                       --EEEE-HHHHHHHHHHHHHHCT-EE.EE--EEEEEE-TTS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT--- CS
                    Trp_halogenase 146 syAyhldaalyakfLrrvaearGvtr.vegkvvevqldedgrveslrledgreveadlfiDcsGfrgllieqaLktg 221
                                       + +y ++++ + + + + a + G ++ v+ +v+ v+ +++   + l  ++  +++a  +i + G+++ +  +    g
  gi|557695037|ref|YP_008798091.1|  85 QIGYNINKSFFIQEIAAQAAEYGADIhVREEVTGVVRENS---KLLVKTNRDTYKAKVVIGADGYNSTVARSL---G 155
                                       56899999**************999614555555554444...44666677889**************99996...9 PP

                                       EEE-TTT----EEEEEEEE--H..---SSEEEEE-SSEEEEEEEETTEEEE.EEEE-TTTS.-HHHHHHHHH.HHCT CS
                    Trp_halogenase 222 fedwsdvLltdrAlavqvesee..lvepytrataekaGWtWkiPLqhrlgn.Gyvyssaha.dddeAlaell.aeld 293
                                       +++  + ++t + + ++++ ++  +v+ y +      G  W  P +++l + G+ ++ a a d  +A+ +l   el+
  gi|557695037|ref|YP_008798091.1| 156 VTERPEPIPTVQYIMANCRLKNsdAVRFYLGNKIAPGGYAWIFPRTEKLAEvGIGVRGAVAkDYLDAFVKLFsDELG 232
                                       *****************99888889************************999*****99995445777666515666 PP

                                       --TTTS-EEEE---E.EES-SEETTEEE-CCCTEE--CCCS-HHHHHHH...HHHHHHHT--BTT--.HHHHHHHHH CS
                    Trp_halogenase 294 gkleaeprkirfttG.rrkqawvknvvalGlasgfvePlestsihliqa...alrrLlallpdksde.paaiaefnr 365
                                        ++  + r  ++  G   +++   + +++G+a+g v Pl +++ih   +   a+ +++a+  +++d  +  ++ef +
  gi|557695037|ref|YP_008798091.1| 233 NAKIIDYRGAPVPIGgAISESVFDGAMLIGDAAGHVIPLTGAGIHSSVSaglAAGKVAATAVQEGDTsKRRLSEFYK 309
                                       66555559999887615788999999*******************98775555556655555444443556666666 PP

                                       HHHHHH CS
                    Trp_halogenase 366 evarel 371
                                        ++  l
  gi|557695037|ref|YP_008798091.1| 310 LYEPWL 315
                                       665555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   3.1   6.6e-10   7.3e-07       1      34 [.       5      38 ..       5     156 .. 0.60
   2 ?   -0.8   0.1      0.66   7.4e+02     402     420 ..     281     299 ..     278     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 6.6e-10
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvl 34
                                      DvvVvGGgpaGv AA aAa +  +vlL+e+++ +
  gi|557695037|ref|YP_008798091.1|  5 DVVVVGGGPAGVSAAKAAAMNSVSVLLLEKHPTI 38
                                      9*****************************9987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.66
                      FAD_oxidored 402 alGqAaGvaAalaleegva 420
                                       + G AaG +Aa a++eg +
  gi|557695037|ref|YP_008798091.1| 281 SAGLAAGKVAATAVQEGDT 299
                                       6799**********99865 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   3.3   1.3e-08   1.5e-05       1      45 [.       5      49 ..       5     161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.3e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsig 45
                                      dv+V+GgG AG+ AA aaa   ++vlL+ ++   +a+ +C ++  
  gi|557695037|ref|YP_008798091.1|  5 DVVVVGGGPAGVSAAKAAAMNSVSVLLLEKHPTIMANKPCGEACS 49
                                      79**************************99999999999988765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   2.8e-07   0.00032      17      50 ..       3      35 ..       1      46 [. 0.92
   2 ?   -0.9   0.0      0.72   8.1e+02     123     172 ..     109     150 ..      95     157 .. 0.66

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.8e-07
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailers 50
                                      e Dvv+vG+G++G++aa+  a +  + v++le++
  gi|557695037|ref|YP_008798091.1|  3 EYDVVVVGGGPAGVSAAKAAAMN-SVSVLLLEKH 35
                                      78*********************.********97 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.72
                                       EEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEEE--GSSSTT CS
                              Thi4 123 DlivregegvaGvvinwtlvelahdtqscvDPlvirakvvvdatGhdgei 172
                                       D+ vre  +v+Gvv + + + ++       +  + +akvv+ a G+++ +
  gi|557695037|ref|YP_008798091.1| 109 DIHVRE--EVTGVVRENSKLLVKT------NRDTYKAKVVIGADGYNSTV 150
                                       555666..7777776655444333......33566777777777776655 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 !   22.5   0.0   9.1e-08    0.0001       1      31 [.       8      38 ..       8      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.1e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                                      +vG+G +G +aA ++a + ++vlllek++ +
  gi|557695037|ref|YP_008798091.1|  8 VVGGGPAGVSAAKAAAMNSVSVLLLEKHPTI 38
                                      8***************************976 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.7   1.1e-07   0.00012       1      32 [.       5      36 ..       5      41 .. 0.95
   2 ?   -1.1   0.0      0.68   7.6e+02     171     199 ..     113     144 ..      90     166 .. 0.64
   3 ?   -3.3   0.1       3.1   3.5e+03     226     250 ..     272     296 ..     270     301 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.1e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                                      Dv+V+G+G AG +AA +aa +  +v+++ek +
  gi|557695037|ref|YP_008798091.1|  5 DVVVVGGGPAGVSAAKAAAMNSVSVLLLEKHP 36
                                      9****************************987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.68
                                       TTEEEEEEEEET...TTTCEEEEEESEEEE-- CS
                     FAD_binding_2 171 dgrvtGavvenp...esgrevrirakavvlat 199
                                        ++vtG+v en+    + ++ +++ak v+ a 
  gi|557695037|ref|YP_008798091.1| 113 REEVTGVVRENSkllVKTNRDTYKAKVVIGAD 144
                                       34677777776666633444445665555444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.1
                                       S-HHHHHHHCTTSSEES..TT-EEE CS
                     FAD_binding_2 226 tGdglalalragaalnddrmeevqf 250
                                       tG g+++ ++ag+a ++ +  +vq+
  gi|557695037|ref|YP_008798091.1| 272 TGAGIHSSVSAGLAAGKVAATAVQE 296
                                       7888888888888877766666665 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 !    9.5   0.0   0.00083      0.93       1      39 [.       7      41 ..       7      56 .. 0.80
   2 ?    5.6   0.1     0.013        14     104     154 ..      96     145 ..      92     147 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00083
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep.gag 39
                                      ++vG+Gp+G++++++ + ++     +++ l +++++ +a 
  gi|557695037|ref|YP_008798091.1|  7 VVVGGGPAGVSAAKAAAMNS-----VSVLLLEKHPTiMAN 41
                                      69************999985.....999999998875555 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.013
                     NAD_binding_9 104 feellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlG 154
                                       ++e++a++ e     ++r+ev+ + +++++  +++++ ++++a+ V+ A G
  gi|557695037|ref|YP_008798091.1|  96 IQEIAAQAAEYGADIHVREEVTGVVRENSKL-LVKTNRDTYKAKVVIGADG 145
                                       566666664433334579*******999986.77999999***99997766 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.2e-05     0.025       2      44 ..       6      50 ..       5      58 .. 0.85
   2 ?   -0.1   0.1       1.3   1.4e+03      47      72 ..     100     125 ..      95     134 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS..TTSSHHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll..rllDeeask 44
                                      vvvvGgG  g+ +A+a+a    +V ++e +++++  + ++e++sk
  gi|557695037|ref|YP_008798091.1|  6 VVVVGGGPAGVSAAKAAAMNSVSVLLLEKHPTIManKPCGEACSK 50
                                      8*********************************55555555554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.3
                                       HHHHHHTTEEEECSEEEEEEEEETTS CS
                         Pyr_redox  47 qeklekngievllntkveeiegsedg 72 
                                       + +  + g +++  ++v+ ++ ++++
  gi|557695037|ref|YP_008798091.1| 100 AAQAAEYGADIHVREEVTGVVRENSK 125
                                       45556667777777777777766666 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   0.1   3.9e-05     0.044      30      64 ..       5      39 ..       1     142 [. 0.90
   2 ?   -1.1   0.0      0.88   9.8e+02      34      80 ..     272     320 ..     258     339 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.9e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparl 64
                                       v+v+GgG aG++A+++a+    +V +l++ p+ +
  gi|557695037|ref|YP_008798091.1|  5 DVVVVGGGPAGVSAAKAAAMNSVSVLLLEKHPTIM 39
                                      69****************99999999999888765 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.88
                                       ESTSHHHHHHHHHHHHTT-E..EEEEESSHHHHHHHHHTTTCECEEHCH CS
                       AlaDh_PNT_C  34 iGgGvaGlqAiatakglgak..VtvlDvrparleqleslgakfvevlks 80 
                                        G+G+    ++  a+g  a   V+  D++++rl ++ +l + +++ +k+
  gi|557695037|ref|YP_008798091.1| 272 TGAGIHSSVSAGLAAGKVAAtaVQEGDTSKRRLSEFYKLYEPWLNRIKK 320
                                       5888888888888877766511444566677777666665555555554 PP

>> DUF896  Bacterial protein of unknown function (DUF896)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00055      0.62      26      57 ..     212     243 ..     199     246 .. 0.81
   2 ?   -0.6   0.1       1.1   1.2e+03      11      22 ..     323     335 ..     303     342 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00055
                            DUF896  26 qkkLRkeYlkafraslksqlenvkvvDeeGnd 57 
                                       + +  k Yl+af + + ++l n k++D  G  
  gi|557695037|ref|YP_008798091.1| 212 RGAVAKDYLDAFVKLFSDELGNAKIIDYRGAP 243
                                       6677799********************99975 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.1
                            DUF896  11 kkkkt.egLTeeE 22 
                                       k  ++ e+LT+eE
  gi|557695037|ref|YP_008798091.1| 323 KAMRAvEKLTDEE 335
                                       2222225666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2467.48
//
Query:       gi|557695038|ref|YP_008798092.1|  [L=436]
Description: peptidase M20 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-35  120.9   0.0    2.1e-34  119.1   0.0    1.8  1  Peptidase_M20  Peptidase family M20/M25/M40
      3e-19   69.0   0.0    4.9e-19   68.3   0.0    1.3  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 !  119.1   0.0   2.3e-38   2.1e-34       1     198 [.      70     422 ..      70     431 .. 0.90

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 2.3e-38
                                       EEEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTT CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   1 llgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrg 76 
                                       ll++H+Dv+p+e+ ++w+t pf+l e+dG l+GrG++d+kg ++a l+a+  +++  ++++ t+++l++++EE+g+ 
  gi|557695038|ref|YP_008798092.1|  70 LLYNHYDVQPPEPLEEWKTdPFQLVERDGLLFGRGVSDNKGEIIARLAAVDCVEKVLGELPVTVKWLIEGEEEVGSP 146
                                       79********99999**********************************************************9999 PP

                                       HHHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................... RF
                     Peptidase_M20  77 Gakallegleerekvdavfelhieepgileagklaigvv...................................... 115
                                       G++ ++    ++  +++v +++ e+++i    +  ++++                                      
  gi|557695038|ref|YP_008798092.1| 147 GIPDIVSR--NKGLFKGVPGCMWEGGDIDR-SG--PNLYlgvkgmlyieltlrtakadahsmyapiienaaekmlki 218
                                       99999992..24456666677766555555.44..333355779999999999999999999999999999999999 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|557695038|ref|YP_008798092.1| 219 irmikdergrvkvpgfyetvakptaaekrlmkslrksareyadslgverlaveggqvaeklvyeptcniaglysgyt 295
                                       9**************************************************************************** PP

                                       .......................................EEEEEEEEEESHEEEC.CHHHHHHHHHHHHHHHTSCEE CS
                                       .......................................xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 116 .......................................kvevelleggapvtln.dsplvkalaeaaeelfgekve 152
                                                                              +v+v+ +  ++p++++ ++plvka+ +aa +++g+++ 
  gi|557695038|ref|YP_008798092.1| 296 gpgsktivpstatvkidfrlvpnqdplkllktikkilpkDVDVKVYTVSYPARIShENPLVKAAVDAAVQVYGKRPS 372
                                       **************************************66****99***************************6644 PP

                                       EE.EESSSBHTHHHH..TTTEEEEE..EE.SSGGCTTSTTTEEEHHHHHHHH CS
                                       xx.xxxxxxxxxxxx..xxxxxxxx..xx.xxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 153 li.vsgpggtdarff..agiptvmi..fg.pgsglaHspnEyvdledlekgi 198
                                       +   ++ g+    +f  agipt+m+  +  pg +  H+pnE++  e++ k i
  gi|557695038|ref|YP_008798092.1| 373 VLpNMA-GTGPLYHFvkAGIPTAMLsaLAhPG-SKLHAPNENIYREHFIKSI 422
                                       443444.888888889999****998988799.99*********99998876 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   5.4e-23   4.9e-19       2     103 ..     182     334 ..     181     339 .. 0.97

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 5.4e-23
                                       EB-EEEEEEEE..EE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.............................. CS
                         M20_dimer   2 ghkGlaggkit..vkgkagHsgapgagaNAieklarllaeledeegdia............................ 48 
                                       g kG++  ++t  +   ++Hs +    +NA ek+ +++  ++de+g+++                            
  gi|557695038|ref|YP_008798092.1| 182 GVKGMLYIELTlrTAKADAHSMYAPIIENAAEKMLKIIRMIKDERGRVKvpgfyetvakptaaekrlmkslrksare 258
                                       6789999999999**************************************************************** PP

                                       ....................TCCTCCCCCEECCE-C....CCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTS CS
                         M20_dimer  49 .................eerslprttlnvtgiegGs....aknvipdeaeakidiRllpgedpeevleeieeilek 103
                                                        +e+ + ++t+n++g+++G+    +k+++p++a++kid+Rl+p++dp ++l++i++il k
  gi|557695038|ref|YP_008798092.1| 259 yadslgverlaveggqvAEKLVYEPTCNIAGLYSGYtgpgSKTIVPSTATVKIDFRLVPNQDPLKLLKTIKKILPK 334
                                       *************************************************************************977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2962.35
//
Query:       gi|557695039|ref|YP_008798093.1|  [L=196]
Description: isochorismatase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-40  137.7   0.0    4.7e-40  137.6   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 !  137.6   0.0   2.6e-44   4.7e-40       1     164 [.      19     179 ..      19     190 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.6 bits;  conditional E-value: 2.6e-44
                   Isochorismatase   1 talvviDmqndfv.eegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttga 76 
                                       ta++v+Dmqndf+ ++g   +++  +++++i ++l++ar++++ +++t+d h     k d++   + +h  +g++ga
  gi|557695039|ref|YP_008798093.1|  19 TAVIVVDMQNDFCkPSGKLFVPASVETIPKIGQVLEKARQSDVMIVYTQDWHM----KDDPEFAIWGEHALEGSWGA 91 
                                       79***********99999999********************************....99****************** PP

                   Isochorismatase  77 elvpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalsp 153
                                       e+v+el+p++gdvvv K r++af+gt+ld iL+ ++i++iv++G  +++CV++ta +a+ + y+v+++ D+v+al+ 
  gi|557695039|ref|YP_008798093.1|  92 EIVDELRPRAGDVVVKKLRYDAFYGTSLDHILRLRQIENIVVTGTVANICVLHTAGSAALRWYKVYLPIDCVSALND 168
                                       ****************************************************************************9 PP

                   Isochorismatase 154 elhdaalkrlk 164
                                        +++a l++++
  gi|557695039|ref|YP_008798093.1| 169 FDYRATLRQVS 179
                                       99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.44
# Mc/sec: 1348.07
//
Query:       gi|557695040|ref|YP_008798094.1|  [L=403]
Description: nicotinate phosphoribosyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   78.1   0.0    9.2e-22   77.6   0.0    1.2  1  QRPTase_C    Quinolinate phosphoribosyl transferase, C-termin
    0.00013   22.3   0.1    0.00046   20.6   0.0    1.8  1  NAPRTase_C   Nicotinate phosphoribosyltransferase C-terminal 
    0.00019   21.5   0.0     0.0024   17.9   0.0    2.5  3  QRPTase_N    Quinolinate phosphoribosyl transferase, N-termin
  ------ inclusion threshold ------
        0.1   12.0   0.0       0.43   10.0   0.0    1.9  2  BtpA         BtpA family
       0.22   11.3   0.0       0.43   10.3   0.0    1.5  1  T_hemolysin  Thermostable hemolysin


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 !   77.6   0.0   2.6e-25   9.2e-22       1     169 []     119     307 ..     119     307 .. 0.93

  Alignments for each domain:
  == domain 1  score: 77.6 bits;  conditional E-value: 2.6e-25
                                       HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSSHHHHH CS
                         QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaagsiveav 70 
                                       + t++ar++ aa+++ v +++ R  +P++ ++  +A+++GG+d          l+L+ + +++++ + ++g+ ++a+
  gi|557695040|ref|YP_008798094.1| 119 VSTKAARVKLAANGKPVLFFGIRCVHPAISPMVDRAAYVGGCDavsgvagAVMLELEPTGTMPHALMLVLGDEKKAW 195
                                       6799********************************************9999************************* PP

                                       HHHHHHHTTTSE..EEEEESSHHHHHHHHHHT.....-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEEEEE CS
                         QRPTase_C  71 ksvreavdkevk..ievevesleeleevleae.....adiimLDnfsv..eelkkaveel.keknkr....vlievS 133
                                       k + e+++++v+    v++ ++e +e+  +ae       +++LD++s+   +++k+v+e+ +  +++    v+i+vS
  gi|557695040|ref|YP_008798094.1| 196 KLFHEVMPENVPriALVDTFFDERVEALEAAEtlgknLYGVRLDTPSSrrGNMRKIVQEVrWTLDIHghrhVKIFVS 272
                                       ***********99778999999988877776666666889******997799*******988888888899****** PP

                                       SS--TTTHHHHHCTT-SEEEECHHCHTB----EEEE CS
                         QRPTase_C 134 GgvtlenveeyaksgvdvisvgalthsvkalDislk 169
                                       Gg+ ++nv e+ + + d ++vg+ +   +++D++l+
  gi|557695040|ref|YP_008798094.1| 273 GGLDEKNVMELVDLV-DGFGVGTSIAFPPSIDLALD 307
                                       *************98.*****************996 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 !   20.6   0.0   1.3e-07   0.00046      51      87 ..     354     390 ..     336     394 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.3e-07
                        NAPRTase_C  51 rvekLlkkvfkdGklvyelpsleeireyvkeqlaelr 87 
                                        ve+L k+++++Gklv +lp+ +++re+v  q+++l 
  gi|557695040|ref|YP_008798094.1| 354 PVEPLVKQILSKGKLVSDLPDAKKVREHVLGQVEKLA 390
                                       59********************************996 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 !   17.9   0.0   6.6e-07    0.0024      25      87 ..      55     115 ..      37     117 .. 0.89
   2 ?   -3.6   0.0       3.4   1.2e+04      46      60 ..     304     318 ..     302     321 .. 0.77
   3 ?    0.2   0.0      0.22     8e+02      26      59 ..     346     379 ..     343     390 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.6e-07
                                       SSSEEE-SHHHHHHHHHHHTTTEEE.ESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHHH CS
                         QRPTase_N  25 keegvvaGlevaeevfellpgleve.llvkDGervekgdvlleieGnarallsaERvaLnllqr 87 
                                        e++v+ Gle++  ++e   g+ v+ + +++G+ +++ + +++ieG + ++  +E  +L +l +
  gi|557695040|ref|YP_008798094.1|  55 YEWAVFTGLEEVVYLLE---GVPVDlYAMPEGTVFRAMEPVARIEGAYGDFGVYEPAILGMLRH 115
                                       5899*********9999...667776777********************************998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.4
                                       TEEEESS-TT-EEET CS
                         QRPTase_N  46 levellvkDGervek 60 
                                       l+ ++  kDGe ++k
  gi|557695040|ref|YP_008798094.1| 304 LALDIVEKDGEPLSK 318
                                       566788899999876 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.22
                                       SSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEE CS
                         QRPTase_N  26 eegvvaGlevaeevfellpglevellvkDGerve 59 
                                       e++vv+G +v   v ++l++ +     +D ++v+
  gi|557695040|ref|YP_008798094.1| 346 EKCVVCGGPVEPLVKQILSKGKLVSDLPDAKKVR 379
                                       799****987655555556666666667766665 PP

>> BtpA  BtpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.36   1.3e+03     117     141 ..      99     123 ..      93     166 .. 0.81
   2 ?   10.0   0.0   0.00012      0.43     200     230 ..     266     296 ..     249     308 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.36
                              BtpA 117 lsdeGilegkaaellrykkllesrv 141
                                         d+G+ e+ +  +lr+   +++++
  gi|557695040|ref|YP_008798094.1|  99 YGDFGVYEPAILGMLRHSTSVSTKA 123
                                       5799999999999999999996652 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00012
                              BtpA 200 kvkvlvgsGvseenlekllsiadGvivgtsi 230
                                       +vk++v  G +e+n+ +l+++ dG+ vgtsi
  gi|557695040|ref|YP_008798094.1| 266 HVKIFVSGGLDEKNVMELVDLVDGFGVGTSI 296
                                       489**************************98 PP

>> T_hemolysin  Thermostable hemolysin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00012      0.43      98     139 ..      38      79 ..      30     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00012
                       T_hemolysin  98 aarllilalarllaeaglewvvftatkqlrnllqrlglelte 139
                                       ++  +++ + ++   +g+ew+vft+ +++  ll+ + ++l +
  gi|557695040|ref|YP_008798094.1|  38 SSTRVVAEIHSYGLPEGYEWAVFTGLEEVVYLLEGVPVDLYA 79 
                                       5667889999999******************99988777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2772.85
//
Query:       gi|557695041|ref|YP_008798095.1|  [L=465]
Description: fumarate hydratase, class II [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-104  350.0   0.0   1.6e-104  349.6   0.0    1.1  1  Lyase_1      Lyase
    3.5e-17   62.6   0.8    4.4e-16   59.0   0.7    2.5  2  FumaraseC_C  Fumarase C C-terminus


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 !  349.6   0.0  1.8e-108  1.6e-104       1     312 []      11     341 ..      11     341 .. 0.99

  Alignments for each domain:
  == domain 1  score: 349.6 bits;  conditional E-value: 1.8e-108
                                       CEEEEETCHHHHHHHHHHHHHGGGHHHHHC.....HHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHHCG CS
                           Lyase_1   1 grftvkadklmgiftersrenfrlseedik.....alaalkkaaakanvdl....keeaaaiikaldevleegkldd 68 
                                       g++ v+ad+l+g++t+r+  nf +s+ + +     al++lk aaa+an+ l    k++ +ai ka+ ev+e gk+d+
  gi|557695041|ref|YP_008798095.1|  11 GEMRVPADALYGAQTARAVDNFPISGLRFQrafiwALGLLKHAAAEANMALglldKRIGEAISKAALEVAE-GKHDK 86 
                                       7899*********************999889****************************************.***** PP

                                       GHHHBSSSSSHHHHHHHHHHHHHH....HHTT......HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHH CS
                           Lyase_1  69 qfvlkviqegsgtavnmnlnevig....ellg......ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpal 135
                                       +fv++v+q+gsgt++nmn+nevi+    e+lg      ++++pnd+v++gqS+nD++pT +++a++ ++ +kLlpal
  gi|557695041|ref|YP_008798095.1|  87 HFVVDVFQTGSGTSTNMNANEVIAnralEILGlsrgdkKTIHPNDHVNMGQSTNDVIPTVMNVAAAYQIVKKLLPAL 163
                                       *************************9999999******9************************************** PP

                                       HHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC CS
                           Lyase_1 136 eqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadp 212
                                       e L + l +ka+efkd vk GrTh qdA+Pvt+gqe+s+ya+++++ r r+ ++l + l+el  ggta+gtglna+p
  gi|557695041|ref|YP_008798095.1| 164 ELLETELMKKAEEFKDFVKSGRTHFQDAVPVTFGQEFSGYATMVRKGRRRVLNAL-ESLYELPIGGTATGTGLNAHP 239
                                       *******************************************************.99999999************* PP

                                       THHHHHHHHHHHHHCST.EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSSC CS
                           Lyase_1 213 efaelvakelakvtglp.vkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssge.aglvelslaesepG 287
                                       efa+lv+++l+++tgl   +a+n+fea+ +rD  +e+++al+ la+sL k+++Dlr+lssg+ +g++e++l++ +pG
  gi|557695041|ref|YP_008798095.1| 240 EFARLVVEKLNEITGLRfRIADNRFEAMGTRDCCLEASAALRSLAVSLLKICNDLRILSSGPnTGINEIELPAVQPG 316
                                       ***************************************************************************** PP

                                       -TTSTTTEBTHHHHHHHHHHHHHHH CS
                           Lyase_1 288 SSiMPgKvNPvqlElltgvagrvvG 312
                                       SSiMPgKvNPv lE + +va++v+G
  gi|557695041|ref|YP_008798095.1| 317 SSIMPGKVNPVILESTMLVAAQVIG 341
                                       ***********************98 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.085   7.7e+02       7      14 ..     338     345 ..     332     347 .. 0.86
   2 !   59.0   0.7   4.9e-20   4.4e-16       1      52 [.     407     458 ..     407     460 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.085
                                       HHHHHHHH CS
                       FumaraseC_C   7 phIGYekA 14 
                                        +IGY++A
  gi|557695041|ref|YP_008798095.1| 338 QVIGYDRA 345
                                       68****98 PP

  == domain 2  score: 59.0 bits;  conditional E-value: 4.9e-20
                                       GGGGGHHHHHHHHHHHHHHHHHHHT--HHHHHHHTT-.-HHHHHHHT-HHHH CS
                       FumaraseC_C   1 LVTaLnphIGYekAakIAkeAlkegktlreavlelgllteeeldelldpekM 52 
                                       LVT+ +p IGY+kAa++Ak++l+e+kt+++a +e+  l+ +e+de+ld +k 
  gi|557695041|ref|YP_008798095.1| 407 LVTVVAPRIGYDKAARVAKKMLAENKTIKQALIEEAGLSPAEVDEILDLLKI 458
                                       8***********************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 3364.55
//
Query:       gi|557695042|ref|YP_008798096.1|  [L=343]
Description: glycerol-1-phosphate dehydrogenase [NAD(P)] [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-59  201.7   0.4    2.2e-59  201.2   0.2    1.3  2  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    9.3e-20   70.7   0.8    1.2e-18   67.1   0.8    2.0  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    1.5e-05   24.3   0.2    0.00029   20.1   0.2    2.5  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 !  201.2   0.2   3.7e-63   2.2e-59       1     250 []      13     265 ..      13     265 .. 0.88
   2 ?   -3.3   0.0         1     6e+03      36      75 ..     280     319 ..     277     323 .. 0.62

  Alignments for each domain:
  == domain 1  score: 201.2 bits;  conditional E-value: 3.7e-63
                          Fe-ADH_2   1 vigegaleklgellkelelkkvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketd 77 
                                       vig++  +++ e+lk +++k  l++++++ +++ g+k+e    e+gik+++++ +   +   + ekl    ++ ++d
  gi|557695042|ref|YP_008798096.1|  13 VIGHDLAQTIIEHLKLHGFKAPLMITSNTPYRVFGSKIEAL-MESGIKLSTIDVE---EVYGDLEKL---TKMGGFD 82 
                                       5899999*******************************865.5888***999733...333333333...34458** PP

                          Fe-ADH_2  78 lvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrll 154
                                       ++++vGgG+++Di+k+v+ k+++p++s+pT aS+DG+asp+ s +++gk  +  k  +Pl ++aD+dv++++Prr l
  gi|557695042|ref|YP_008798096.1|  83 VILGVGGGRVMDISKVVAEKTGRPFISIPTVASHDGIASPMTSYRQNGKAYSR-KSVMPLEIYADIDVISRSPRRYL 158
                                       ************************************************99986.999******************** PP

                          Fe-ADH_2 155 asGvGDllgkytaladwklan........evseplaklsaamvqeaaeklved..kketealeelleal.alsgigi 220
                                       +sG+GDl++k +a+ dw+la+        +++++la ls   ++ +a+++ ++  ++ ++++e+l++a  a++++g+
  gi|557695042|ref|YP_008798096.1| 159 MSGCGDLVAKHSAVRDWWLAHretgeyygRYAAHLAYLSGSVIVRSAKEIRNNsiEGVRTVVEALISAGvAMGVAGS 235
                                       **********************99999999999*****************974113335555666665358999999 PP

                          Fe-ADH_2 221 srpaSGsEHliSHaldmlalkqalHGeqVG 250
                                       srp+SG+EHli+Hal+ l  k+alHGe++G
  gi|557695042|ref|YP_008798096.1| 236 SRPCSGGEHLIAHALETLMDKPALHGERCG 265
                                       ****************************98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1
                          Fe-ADH_2  36 ekveeslkeagikvevveeveeea.dleeveklvealreke 75 
                                       ekv+eslk+ g  ++++++ + ++  ++e+ kl+ +lr ++
  gi|557695042|ref|YP_008798096.1| 280 EKVKESLKTIG-APNTLKDINVDEeLFTEAVKLAPNLRRER 319
                                       68889998887.55556555544414566667777666555 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   0.8     2e-22   1.2e-18       1     346 [.       9     312 ..       9     333 .. 0.78

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 2e-22
                                       -SEEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaala 77 
                                       P+ +v+g + ++ + e+lk +g+k +l++t++  +   +++   +e+l e+gi++ ++d    +  + ++e+++   
  gi|557695042|ref|YP_008798096.1|   9 PHFVVIGHDLAQTIIEHLKLHGFKAPLMITSNTPY---RVFGSKIEALMESGIKLSTID---VEEVYGDLEKLT--- 76 
                                       67899****************************99...999999****9******9655...455555555555... PP

                                       -TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEE CS
                            Fe-ADH  78 reegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegekl 154
                                       +  g+dv+++vGGG v+D+ K++a  ++                   p+i iPT+a+ +  ++p       ++   +
  gi|557695042|ref|YP_008798096.1|  77 KMGGFDVILGVGGGRVMDISKVVAEKTG------------------RPFISIPTVASHDGIASPMTSYR--QN--GK 131
                                       5789************************..................8************9999988777..33..34 PP

                                       EE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHH...HHH.HT---TTSSB--HHHHHHHHHHHHHHHHH CS
                            Fe-ADH 155 sifdpellPdlaivDpeltltlPkrvtaatglDalahalEa...yvs.kkanplsdalaleairliaknleravadg 227
                                       +++ ++++P  +  D +++   P+r+++++ +D +a+        ++ +++ ++  ++a + + l    + r+ ++ 
  gi|557695042|ref|YP_008798096.1| 132 AYSRKSVMPLEIYADIDVISRSPRRYLMSGCGDLVAKHSAVrdwWLAhRETGEYYGRYAAHLAYLSGSVIVRSAKEI 208
                                       666679*******************************9888333333344444555555555555555555555553 PP

                                       H..HHHHHHHHHHHHHHHHHHHHSS---.....HHHHHHHHHHC.CGGG..GGS-HHHHHHHHH..........HHH CS
                            Fe-ADH 228 e..dleareqmllastlaglafsnaglg.....avHalahalgalfgip..hglanaillpavlrfnaeaaperlaq 295
                                       +  ++e  + +++a + ag+a++ ag +       H +ahal  l++ p  hg+ ++i+  + lr            
  gi|557695042|ref|YP_008798096.1| 209 RnnSIEGVRTVVEALISAGVAMGVAGSSrpcsgGEHLIAHALETLMDKPalHGERCGIATIFTLRLHG--------- 276
                                       23366999999999999*999999999888889***********9998889*******9999994443......... PP

                                       HHHT.......T--HHHHHHHHHHHHHTT---SHHHHT-TT-HHHHHHHHH CS
                            Fe-ADH 296 laralggesdeeaaeeliealrellkelglptsLselgvdeedldklaeaa 346
                                          a              e+++e lk++g+p++L++++vdee + + ++ a
  gi|557695042|ref|YP_008798096.1| 277 ---A------------RWEKVKESLKTIGAPNTLKDINVDEELFTEAVKLA 312
                                       ...2............24566667777777777777777776555555444 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   4.8e-08   0.00029      32     247 ..      82     299 ..      61     311 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.8e-08
                                       -EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEEEETTEEEEEEEE---SEEEEEGGGGGGS CS
                      DHQ_synthase  32 sllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtainlplgKNliGafaqPkavlidlevLktL 108
                                       ++++ +GGG v+D+   vA     G  f+ +Pt  +a  D  +        ++gK       +P  +++d++v++  
  gi|557695042|ref|YP_008798096.1|  82 DVILGVGGGRVMDISKVVAEKT--GRPFISIPT--VASHDG-IASPMTSYRQNGKAYSRKSVMPLEIYADIDVISRS 153
                                       799****************866..669*****9..688875.666666667899*********************** PP

                                       -HHHHHHHHHH.HHHHHHHT-HHHHHHHHHHHHHHHC............TTTHHHHHHHHHHHHHHHHHHHHH.... CS
                      DHQ_synthase 109 perelraGlaE.viKyalikdeelfelleenaeallk............eeeeealeeliarsievkaevvee.... 168
                                       p+r l +G+++ v K+++++d  l ++ + +     +            +    +++e+ ++sie  ++vve+    
  gi|557695042|ref|YP_008798096.1| 154 PRRYLMSGCGDlVAKHSAVRDWWLAHRETGEYYGRYAahlaylsgsvivR----SAKEIRNNSIEGVRTVVEAlisa 226
                                       **********944699*999987766555444444336777888866652....33333344444444444330000 PP

                                       C...CTTTTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---ST CS
                      DHQ_synthase 169 D...ekekglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvsl 242
                                               + r +    H i+Ha+E+l++    lHGe   i  +++++l         ++ e++++ lk++g p +l
  gi|557695042|ref|YP_008798096.1| 227 GvamGVAGSSRPCSGGEHLIAHALETLMDK-PALHGERCGIATIFTLRLHG-------ARWEKVKESLKTIGAPNTL 295
                                       20002335556666666************9.9*****99998888888873.......3457788888888888888 PP

                                       TTT.- CS
                      DHQ_synthase 243 kelle 247
                                       k+  +
  gi|557695042|ref|YP_008798096.1| 296 KDI-N 299
                                       777.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2426.61
//
Query:       gi|557695043|ref|YP_008798097.1|  [L=276]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-35  120.6   0.0    8.5e-35  119.8   0.0    1.3  1  ThiP_synth      Thiamine-phosphate synthase
    0.00023   21.1   0.0    0.00053   20.0   0.0    1.5  1  Cro             Cro
     0.0013   18.6   0.3     0.0077   16.1   0.1    2.3  3  P22_Cro         DNA-binding transcriptional regulator Cro
     0.0037   17.3   0.4      0.032   14.3   0.0    2.3  2  HTH_3           Helix-turn-helix
  ------ inclusion threshold ------
       0.01   15.8   0.0      0.021   14.8   0.0    1.6  1  HTH_37          Helix-turn-helix domain
      0.016   15.1   0.2      0.066   13.2   0.0    2.1  3  HTH_1           Bacterial regulatory helix-turn-helix protein
      0.017   14.9   0.0      0.067   13.0   0.0    2.1  2  HTH_23          Homeodomain-like domain
      0.022   14.6   0.0      0.068   13.0   0.0    1.8  2  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
      0.036   13.6   0.1       0.12   11.9   0.0    1.9  2  Sigma70_r4      Sigma-70, region 4
      0.036   13.9   0.0       0.39   10.6   0.0    2.4  2  MarR_2          MarR family
       0.21   12.2   0.0       0.33   11.5   0.0    1.2  1  HNF-1_N         Hepatocyte nuclear factor 1 (HNF-1), N termin


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 !  119.8   0.0   5.2e-38   8.5e-35       2     131 ..     142     270 ..     141     275 .. 0.96

  Alignments for each domain:
  == domain 1  score: 119.8 bits;  conditional E-value: 5.2e-38
                                       HHHHHHHHHCC--.GCC--TT-B-EEEE-ST--SGGGEEEETT-EEE-TSSEEE-S-EEETS-CHHHHHHHHHHCC- CS
                        ThiP_synth   2 leralelleeeeefakliPevgsNiayalpdAksieDvaavpGRIvrvkgrvkvvgepefgasshvarvllaamkfd 78 
                                       le+ l++le +++f++liP+vg+N++y++ dA+++ Dva+v GRIv + ++vk+vg+p+fg+s+h+a++ll+a++f+
  gi|557695043|ref|YP_008798097.1| 142 LEDSLKKLETSPGFKRLIPQVGANLVYCIADASTEYDVAGVAGRIVLADDEVKAVGRPMFGGSRHLANILLTARNFN 218
                                       78899************************************************************************ PP

                                       TT--EEEEEE--HHHHHHHCCTTSEEEE--CCCS-CCCT-HHHHHHHHHHHCC CS
                        ThiP_synth  79 pevraainirydekilealeelglkvvefdreeepeevgstmewgvaeaieel 131
                                       +++raain++  +++ + le+ g+k++ +++++ep + ++ + + va+a++e 
  gi|557695043|ref|YP_008798097.1| 219 KRIRAAINLKHFPEMGKVLEKVGVKFAVVGARAEPIS-DDVVLEDVARAFKEK 270
                                       ***********************************99.788888899998875 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.3e-07   0.00053      13      41 ..      29      57 ..      26      68 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.3e-07
                                      HHHHHHHHHHTS-HHHHHHHHHCT-EEEE CS
                               Cro 13 vGQaktAkdlgvkqsaIsKAlkakRnIyl 41
                                      +GQ+ +Ak lg++qsa+s  l +  +I+ 
  gi|557695043|ref|YP_008798097.1| 29 FGQTMVAKVLGITQSAVSQILAKDEKIFY 57
                                      8***********************99985 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 !   16.1   0.1   4.7e-06    0.0077      11      28 ..      30      47 ..      28      53 .. 0.90
   2 ?   -2.1   0.0       2.2   3.5e+03       9      19 ..     201     211 ..     200     212 .. 0.89
   3 ?   -2.0   0.0         2   3.3e+03       7      28 ..     228     249 ..     226     254 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.7e-06
                                      SHHHHHHHHTS-HHHHHH CS
                           P22_Cro 11 gvekvAkalgvtksAVsq 28
                                      g++ vAk+lg+t+sAVsq
  gi|557695043|ref|YP_008798097.1| 30 GQTMVAKVLGITQSAVSQ 47
                                      5789*************9 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                                       HSSHHHHHHHH CS
                           P22_Cro   9 FGgvekvAkal 19 
                                       FGg + +A+ l
  gi|557695043|ref|YP_008798097.1| 201 FGGSRHLANIL 211
                                       9*******976 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2
                                       HHHSSHHHHHHHHTS-HHHHHH CS
                           P22_Cro   7 khFGgvekvAkalgvtksAVsq 28 
                                       khF +  kv + +gv  + V  
  gi|557695043|ref|YP_008798097.1| 228 KHFPEMGKVLEKVGVKFAVVGA 249
                                       8999999999999998766655 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0     2e-05     0.032       7      30 ..      26      49 ..      21      54 .. 0.85
   2 ?    0.1   0.1      0.54   8.8e+02       6      16 ..      61      71 ..      60      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                                      HTTHHHHHHHHHHTSSHHHHHHHH CS
                             HTH_3  7 qlglsqeeLAeklGvsrstisriE 30
                                        g  q+++A++lG+++s++s+i 
  gi|557695043|ref|YP_008798097.1| 26 SEGFGQTMVAKVLGITQSAVSQIL 49
                                      6666699***************96 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.54
                                      HHTTHHHHHHH CS
                             HTH_3  6 kqlglsqeeLA 16
                                      +q gls++e++
  gi|557695043|ref|YP_008798097.1| 61 EQMGLSRKEAS 71
                                      899*****987 PP

>> HTH_37  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   1.3e-05     0.021      23      56 ..      20      53 ..       4      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.3e-05
                                      HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT-- CS
                            HTH_37 23 iaeliekrelsqseaaqllgiaqPkvsrllrgkl 56
                                      +a  +++++  q+ +a+ lgi+q+ vs++l  + 
  gi|557695043|ref|YP_008798097.1| 20 VAHRLKSEGFGQTMVAKVLGITQSAVSQILAKDE 53
                                      677899999********************96544 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 ?   13.2   0.0     4e-05     0.066      18      45 ..      33      60 ..      26      72 .. 0.87
   2 ?   -2.2   0.0       2.6   4.3e+03      21      37 ..      61      77 ..      61      81 .. 0.80
   3 ?   -2.7   0.0       3.7     6e+03      33      42 ..     138     147 ..     136     151 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
                                      HHHHHHTS-HHHHHHHHHHHHHHHTS-S CS
                             HTH_1 18 rAAeeLglsqpavsrqikrLEeelgvpL 45
                                        A+ Lg++q+avs+ +++ E+ + + L
  gi|557695043|ref|YP_008798097.1| 33 MVAKVLGITQSAVSQILAKDEKIFYHSL 60
                                      579**************99888886665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.6
                                      HHHTS-HHHHHHHHHHH CS
                             HTH_1 21 eeLglsqpavsrqikrL 37
                                      e++gls + +s  + +L
  gi|557695043|ref|YP_008798097.1| 61 EQMGLSRKEASLLVETL 77
                                      68999999999888877 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.7
                                       HHHHHHHHHT CS
                             HTH_1  33 qikrLEeelg 42 
                                        +k+LE+ l+
  gi|557695043|ref|YP_008798097.1| 138 VLKKLEDSLK 147
                                       5788888775 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.1e-05     0.067       7      40 ..      17      51 ..      14      54 .. 0.88
   2 ?   -3.1   0.0       4.9   7.9e+03      15      23 ..      60      70 ..      55      71 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
                            HTH_23  7 Rlrillllae.GlsvreIAreLgvsrrTvyrwlkr 40
                                      R ++++ l+  G  ++ +A+ Lg++++ v+++l +
  gi|557695043|ref|YP_008798097.1| 17 RGLVAHRLKSeGFGQTMVAKVLGITQSAVSQILAK 51
                                      77888889977********************9976 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4.9
                            HTH_23 15 ae..GlsvreI 23
                                      +e  Gls++e+
  gi|557695043|ref|YP_008798097.1| 60 LEqmGLSRKEA 70
                                      33489999987 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 ?   13.0   0.0   4.2e-05     0.068      10      31 ..      30      51 ..      25      57 .. 0.88
   2 ?   -3.4   0.0       5.8   9.4e+03       9      18 ..     202     211 ..     200     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.2e-05
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkg 31
                                      gq+ +A+ lg++q+aVsq l+ 
  gi|557695043|ref|YP_008798097.1| 30 GQTMVAKVLGITQSAVSQILAK 51
                                      899***************9974 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.8
                    YdaS_antitoxin   9 GgqkaLAeal 18 
                                       Gg ++LA  l
  gi|557695043|ref|YP_008798097.1| 202 GGSRHLANIL 211
                                       9999**9865 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.5e-05      0.12      24      43 ..      32      51 ..      22      51 .. 0.86
   2 ?   -3.5   0.0       4.7   7.7e+03      28      35 ..      61      68 ..      61      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.5e-05
                                      HHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4 24 eEIgerlgiSrerVrqiekr 43
                                        ++++lgi++++V+qi+++
  gi|557695043|ref|YP_008798097.1| 32 TMVAKVLGITQSAVSQILAK 51
                                      569**************875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.7
                                      HHHTS-HH CS
                        Sigma70_r4 28 erlgiSre 35
                                      e++g+Sr 
  gi|557695043|ref|YP_008798097.1| 61 EQMGLSRK 68
                                      68999996 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00024      0.39      22      44 ..      29      51 ..      14      53 .. 0.85
   2 ?   -0.1   0.0      0.52   8.5e+02       2      18 ..      64      80 ..      63      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00024
                                      EEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2 22 ltvgelarrlglsksavsrilkr 44
                                      + ++ +a+ lg+++savs+il++
  gi|557695043|ref|YP_008798097.1| 29 FGQTMVAKVLGITQSAVSQILAK 51
                                      5577899**************87 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.52
                                      T--HHHHHHHHHHHCTT CS
                            MarR_2  2 gltpaqarvLaaLgrrp 18
                                      gl++ +a +L +  +++
  gi|557695043|ref|YP_008798097.1| 64 GLSRKEASLLVETLCNE 80
                                      89999*******99997 PP

>> HNF-1_N  Hepatocyte nuclear factor 1 (HNF-1), N terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0002      0.33     155     177 ..      30      52 ..      15      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                           HNF-1_N 155 sQrevvdvTGlsQShlSqwLlkG 177
                                        Q++v++v G+ QS +Sq L k 
  gi|557695043|ref|YP_008798097.1|  30 GQTMVAKVLGITQSAVSQILAKD 52 
                                       6******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2123.23
//
Query:       gi|557695044|ref|YP_008798098.1|  [L=123]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-09   35.8   0.1    6.4e-08   32.5   0.0    2.1  2  HTH_3           Helix-turn-helix
    4.1e-05   23.2   0.2    0.00073   19.3   0.1    2.2  2  HTH_23          Homeodomain-like domain
    6.6e-05   23.2   0.2    0.00012   22.3   0.2    1.5  1  HTH_31          Helix-turn-helix domain
    7.5e-05   22.2   0.8    0.00054   19.4   0.1    2.1  2  Sigma70_r4      Sigma-70, region 4
    0.00013   21.8   0.1    0.00023   21.0   0.0    1.6  2  HTH_37          Helix-turn-helix domain
    0.00037   20.3   0.0    0.00072   19.4   0.0    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
    0.00089   19.2   0.0     0.0016   18.5   0.0    1.5  1  Cro             Cro
     0.0018   17.9   0.1      0.063   13.0   0.0    2.2  2  Sigma70_r4_2    Sigma-70, region 4
     0.0025   17.6   0.2     0.0065   16.3   0.1    1.8  2  P22_Cro         DNA-binding transcriptional regulator Cro
     0.0033   17.9   0.0     0.0077   16.7   0.0    1.6  1  HTH_40          Helix-turn-helix domain
     0.0077   16.2   0.2       0.02   14.9   0.0    1.8  2  HTH_19          Helix-turn-helix domain
     0.0091   15.7   0.1       0.15   11.8   0.0    2.1  2  HTH_38          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.016   15.6   0.2      0.031   14.7   0.2    1.6  1  REV1_C          DNA repair protein REV1 C-terminal domain
      0.037   14.3   1.0       0.79   10.0   0.2    2.1  2  KORA            TrfB plasmid transcriptional repressor
       0.04   13.7   0.0      0.047   13.5   0.0    1.0  1  DUF3891         Protein of unknown function (DUF3891)
      0.059   13.2   1.3       0.16   11.8   0.1    2.3  2  LacI            Bacterial regulatory proteins, lacI family
      0.059   13.4   0.0      0.088   12.9   0.0    1.3  1  RepB            RepB plasmid partitioning protein
      0.062   12.9   0.1       0.13   11.9   0.1    1.7  1  HTH_50          Helix-turn-helix domain
      0.065   11.8   0.0      0.073   11.7   0.0    1.0  1  Cpn60_TCP1      TCP-1/cpn60 chaperonin family
       0.13   12.6   0.5        0.3   11.4   0.2    1.7  2  HTH_Tnp_1       Transposase
       0.13   12.4   0.6        4.2    7.6   0.1    2.2  2  HTH_28          Helix-turn-helix domain
       0.15   12.1   0.0       0.25   11.3   0.0    1.4  1  HTH_1           Bacterial regulatory helix-turn-helix protein
       0.15   11.9   0.0       0.34   10.8   0.0    1.6  1  HTH_10          HTH DNA binding domain


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 !   32.5   0.0   8.2e-11   6.4e-08       4      38 ..      22      58 ..      20      60 .. 0.88
   2 ?    1.1   0.0      0.54   4.2e+02      35      48 ..      81      94 ..      76     113 .. 0.69

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 8.2e-11
                                      HHH..HTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBH CS
                             HTH_3  4 lRk..qlglsqeeLAeklGvsrstisriEnGernPsl 38
                                      +R+  ++g++qe++A++lGv+++++s++ +G r +s 
  gi|557695044|ref|YP_008798098.1| 22 KRLvyERGYTQEKVAQVLGVTQAAVSNYLRGVRGISS 58
                                      455589*************************998875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.54
                                      CSBHHHHHHHHHHH CS
                             HTH_3 35 nPsletlkklakaL 48
                                      +P++e++ ++ +aL
  gi|557695044|ref|YP_008798098.1| 81 EPRQEIARRINDAL 94
                                      56666666666655 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   9.4e-07   0.00073      12      40 ..      23      52 ..      14      58 .. 0.80
   2 ?    2.0   0.0      0.25   1.9e+02      10      27 ..      73      90 ..      62      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.4e-07
                            HTH_23 12 lllae.GlsvreIAreLgvsrrTvyrwlkr 40
                                      +l+ e G++++++A+ Lgv++  v+++l+ 
  gi|557695044|ref|YP_008798098.1| 23 RLVYErGYTQEKVAQVLGVTQAAVSNYLRG 52
                                      455568*********************985 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.25
                            HTH_23 10 illllaeGlsvreIAreL 27
                                      ++ ++ +  +++eIAr+ 
  gi|557695044|ref|YP_008798098.1| 73 VVEAVVKNEPRQEIARRI 90
                                      6666667999*****986 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   0.2   1.6e-07   0.00012      13      55 ..      23      68 ..      14      77 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.6e-07
                            HTH_31 13 a.....GLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                      +     G +qe vA+ lgv+++ +s + +G rg    ++le+  +++ 
  gi|557695044|ref|YP_008798098.1| 23 RlvyerGYTQEKVAQVLGVTQAAVSNYLRGVRG-I-SSDLEKHDELVK 68
                                      444444**************************8.5.455555555555 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   6.9e-07   0.00054      14      39 ..      23      48 ..      23      52 .. 0.92
   2 ?    0.9   0.1      0.42   3.3e+02      33      49 ..      82      98 ..      77      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.9e-07
                                      HHHHTTT--HHHHHHHHTS-HHHHHH CS
                        Sigma70_r4 14 elrfgeglTleEIgerlgiSrerVrq 39
                                      +l++++g+T+e ++++lg+++ +V+ 
  gi|557695044|ref|YP_008798098.1| 23 RLVYERGYTQEKVAQVLGVTQAAVSN 48
                                      589********************985 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.42
                                      -HHHHHHHHHHHHHHHH CS
                        Sigma70_r4 33 SrerVrqiekrAlrkLR 49
                                      +r  + +++++Al+++R
  gi|557695044|ref|YP_008798098.1| 82 PRQEIARRINDALKNIR 98
                                      67778888999999887 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     3e-07   0.00023      13      54 ..       9      52 ..       1      79 [. 0.78
   2 ?   -2.1   0.0       5.1     4e+03      16      27 ..      83      94 ..      72      99 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3e-07
                                      HHHHHHHHHH..HHHHHHHCT--HHHHHHHHT--HHHHHHHHTT CS
                            HTH_37 13 lkaKaqlala..iaeliekrelsqseaaqllgiaqPkvsrllrg 54
                                       k++  l++a   ++l  +r+++q+++aq lg++q+ vs+ lrg
  gi|557695044|ref|YP_008798098.1|  9 SKIMIPLLRAmvAKRLVYERGYTQEKVAQVLGVTQAAVSNYLRG 52
                                      5566666666545788899*********************9986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.1
                                      HHHHHHHHHHHH CS
                            HTH_37 16 Kaqlalaiaeli 27
                                      + ++a++i++ +
  gi|557695044|ref|YP_008798098.1| 83 RQEIARRINDAL 94
                                      555666666655 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 !   19.4   0.0   9.3e-07   0.00072      10      36 ..      31      57 ..      27      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 9.3e-07
                    YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqvp 36
                                      +q ++A+ lgv+q+aVs+ l+g ++++
  gi|557695044|ref|YP_008798098.1| 31 TQEKVAQVLGVTQAAVSNYLRGVRGIS 57
                                      699********************9987 PP

>> Cro  Cro
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0     2e-06    0.0016      14      39 ..      31      56 ..      18      73 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2e-06
                                      HHHHHHHHHTS-HHHHHHHHHCT-EE CS
                               Cro 14 GQaktAkdlgvkqsaIsKAlkakRnI 39
                                       Q k+A+ lgv+q+a+s  l+  R I
  gi|557695044|ref|YP_008798098.1| 31 TQEKVAQVLGVTQAAVSNYLRGVRGI 56
                                      59****************99999988 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 !   13.0   0.0     8e-05     0.063      21      48 ..      24      51 ..      23      54 .. 0.92
   2 ?    2.8   0.0      0.12        92      23      37 ..      77      91 ..      71     100 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8e-05
                                      HHHTS---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 21 lryleglsykEIAellgisegtVksrls 48
                                      l y+ g++++ +A++lg++ ++V ++l+
  gi|557695044|ref|YP_008798098.1| 24 LVYERGYTQEKVAQVLGVTQAAVSNYLR 51
                                      77999*******************9985 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                                      HTS---HHHHHHHHT CS
                      Sigma70_r4_2 23 yleglsykEIAellg 37
                                       +++ + +EIA++++
  gi|557695044|ref|YP_008798098.1| 77 VVKNEPRQEIARRIN 91
                                      57788899****997 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 ?   -2.8   0.0       7.9   6.2e+03      33      39 ..      13      19 ..      12      24 .. 0.76
   2 !   16.3   0.1   8.3e-06    0.0065      11      28 ..      31      48 ..      29      53 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 7.9
                                      --HHHHH CS
                           P22_Cro 33 iPelray 39
                                      iP lra+
  gi|557695044|ref|YP_008798098.1| 13 IPLLRAM 19
                                      8999986 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 8.3e-06
                                      SHHHHHHHHTS-HHHHHH CS
                           P22_Cro 11 gvekvAkalgvtksAVsq 28
                                      ++ekvA++lgvt++AVs 
  gi|557695044|ref|YP_008798098.1| 31 TQEKVAQVLGVTQAAVSN 48
                                      689*************97 PP

>> HTH_40  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   9.9e-06    0.0077       9      84 ..      26     118 ..      18     122 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.9e-06
                            HTH_40   9 leeglsieeIAkerglkesTIegHL..aeliee.....geeidl.....erlvseeeekeIeeaiekvgsek..... 68 
                                       +e g++ e++A+  g++++ + ++L  ++ i +     +e +++     e +v+ e ++eI+  i+++ ++      
  gi|557695044|ref|YP_008798098.1|  26 YERGYTQEKVAQVLGVTQAAVSNYLrgVRGISSdlekhDELVKWadevvEAVVKNEPRQEIARRINDALKNIrvmri 102
                                       59***********************5555566644443355666543434456777777777777763322235557 PP

                            HTH_40  69 lkpikealpeevsyde 84 
                                       l + +++++++++ d 
  gi|557695044|ref|YP_008798098.1| 103 LCEYHKRVEPDIDVDS 118
                                       8888999999999876 PP

>> HTH_19  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      0.02      10      43 ..      27      59 ..      22      73 .. 0.82
   2 ?   -1.8   0.2       4.3   3.4e+03       2      10 ..      92     100 ..      87     102 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                            HTH_19 10 elgltqeelaerlgisrskisaiEngkkdvpsae 43
                                      e+g+tqe++a+ lg++++  s++  g +  +s++
  gi|557695044|ref|YP_008798098.1| 27 ERGYTQEKVAQVLGVTQAAVSNYLRGVR-GISSD 59
                                      79************************88.77633 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.3
                            HTH_19   2 erLkeaRee 10 
                                       + Lk +R +
  gi|557695044|ref|YP_008798098.1|  92 DALKNIRVM 100
                                       457777776 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0    0.0002      0.15      15      42 ..      23      51 ..      17      52 .. 0.87
   2 ?    1.8   0.0      0.26     2e+02      24      31 ..      84      91 ..      78      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                            HTH_38 15 rl.laeGlslreIArrLgrspsTIsRElk 42
                                      rl +++G+++ ++A+ Lg+    +s+ l+
  gi|557695044|ref|YP_008798098.1| 23 RLvYERGYTQEKVAQVLGVTQAAVSNYLR 51
                                      5559***************9999998776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.26
                            HTH_38 24 reIArrLg 31
                                       eIArr++
  gi|557695044|ref|YP_008798098.1| 84 QEIARRIN 91
                                      58899886 PP

>> REV1_C  DNA repair protein REV1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   3.9e-05     0.031      25      75 ..      45      96 ..      40     115 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.9e-05
                            REV1_C 25 alakyLkkvveeerdlekavavlkwlrvlleee.eeskeeeageaWekafre 75
                                      a+++yL+ v + ++dlek  +++kw + ++e   +++ ++e ++  ++a+++
  gi|557695044|ref|YP_008798098.1| 45 AVSNYLRGVRGISSDLEKHDELVKWADEVVEAVvKNEPRQEIARRINDALKN 96
                                      7899**************************9995445555555555555555 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2     0.001      0.79      30      55 ..      28      53 ..      13      70 .. 0.79
   2 ?    3.4   0.1      0.12        91      28      65 ..      77     112 ..      56     114 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                              KORA 30 egkkqadvatelgltkqavsqavkrv 55
                                       g +q++va+ lg+t+ avs+  + v
  gi|557695044|ref|YP_008798098.1| 28 RGYTQEKVAQVLGVTQAAVSNYLRGV 53
                                      4679****************987655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.12
                              KORA  28 LVegkkqadvatelgltkqavsqavkrvwaahaereep 65 
                                        V+++ ++++a+++  + +++   v r++  +++r ep
  gi|557695044|ref|YP_008798098.1|  77 VVKNEPRQEIARRINDALKNIR--VMRILCEYHKRVEP 112
                                       69999******99988888876..56777777777766 PP

>> DUF3891  Protein of unknown function (DUF3891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     6e-05     0.047     102     182 ..      15      95 ..       8     114 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6e-05
                           DUF3891 102 LLvSmHlssLyeekrgeseevaaFldeeeerqkellkelgiekeelernyellqlcDrlSLilcmnepgaereleis 178
                                       LL +m +++L+ e+  ++e+va+ l  +++  +++l+ ++    +le++ el+++ D++  ++  nep++e +++i+
  gi|557695044|ref|YP_008798098.1|  15 LLRAMVAKRLVYERGYTQEKVAQVLGVTQAAVSNYLRGVRGISSDLEKHDELVKWADEVVEAVVKNEPRQEIARRIN 91 
                                       8999999999977777999*********************9****************************99999886 PP

                           DUF3891 179 lfke 182
                                          +
  gi|557695044|ref|YP_008798098.1|  92 DALK 95 
                                       5444 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1    0.0002      0.16       5      30 ..      35      60 ..      31      64 .. 0.89
   2 ?   -0.6   0.1       1.5   1.2e+03      24      36 ..      88     101 ..      74     107 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                      HHHHCTS-HHHHHHHCTTSSSSTHHH CS
                              LacI  5 VArlAGVSkaTVSrvLnnkerVseet 30
                                      VA+  GV+ a+VS +L++ + +s ++
  gi|557695044|ref|YP_008798098.1| 35 VAQVLGVTQAAVSNYLRGVRGISSDL 60
                                      89999**************9999876 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
                                       SSSTHHHHH.HHHH CS
                              LacI  24 erVseetre.rVea 36 
                                       +r+ +++++ rV++
  gi|557695044|ref|YP_008798098.1|  88 RRINDALKNiRVMR 101
                                       34444444335555 PP

>> RepB  RepB plasmid partitioning protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.088      13      75 ..      20      87 ..      14      99 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                              RepB 13 faarl.eerGvdreeiasalgldkqtvskmva..raipegica..eevaLLkdvetgiaaiglakkig 75
                                       a rl  erG+++e++a+ lg+++++vs ++   r i  ++++  e v+  ++v+  ++  +++++i+
  gi|557695044|ref|YP_008798098.1| 20 VAKRLvYERGYTQEKVAQVLGVTQAAVSNYLRgvRGISSDLEKhdELVKWADEVVEAVVKNEPRQEIA 87
                                      55555259**********************99999999999541122233345555555555555555 PP

>> HTH_50  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00017      0.13      28      45 ..      34      51 ..       5      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                            HTH_50 28 klAkrLGvShtaianklr 45
                                      k+A+ LGv+++a+ n lr
  gi|557695044|ref|YP_008798098.1| 34 KVAQVLGVTQAAVSNYLR 51
                                      9************99876 PP

>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.3e-05     0.073      79     156 ..      23     100 ..      11     122 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.3e-05
                                       HHHHC.TXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  79 kliaa.gvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       +l+ + g +  ++ +++  + +++ ++L+ + + iss+ ++++eL+k a  ++   + ++ ++e+++ + dA+k i+
  gi|557695044|ref|YP_008798098.1|  23 RLVYErGYTQEKVAQVLGVTQAAVSNYLRGV-RGISSDLEKHDELVKWADEVVEAVVKNEPRQEIARRINDALKNIR 98 
                                       4444449999******************999.9*****9**********************************7776 PP

                                       CC CS
                        Cpn60_TCP1 155 en 156
                                         
  gi|557695044|ref|YP_008798098.1|  99 VM 100
                                       55 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00038       0.3      17      71 ..      23      77 ..      17      81 .. 0.85
   2 ?    0.4   0.1       1.1   8.2e+02       6      32 ..      68      89 ..      66      95 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                         HTH_Tnp_1 17 reslepgksvsevArrhgvspnqLykWrrqyregeeaspaefeltaleeenrelk 71
                                      r+++e g++   vA+ +gv +++ ++  r +r+ ++ ++  +el++ ++e+ e++
  gi|557695044|ref|YP_008798098.1| 23 RLVYERGYTQEKVAQVLGVTQAAVSNYLRGVRGISSDLEKHDELVKWADEVVEAV 77
                                      5789***************************977777777788999999988765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                         HTH_Tnp_1  6 rwsdefKariVreslepgksvsevArr 32
                                      +w de+ +++V+       +  e+Arr
  gi|557695044|ref|YP_008798098.1| 68 KWADEVVEAVVKNE-----PRQEIARR 89
                                      67777777777765.....55566665 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0053       4.2      10      34 ..      25      51 ..      16      61 .. 0.80
   2 ?    3.3   0.1      0.12        93       4      22 ..      72      90 ..      72      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0053
                            HTH_28 10 a..aGhsvreaArelgisrrtvyrWik 34
                                         +G ++  +A+ lg+++  v+  ++
  gi|557695044|ref|YP_008798098.1| 25 VyeRGYTQEKVAQVLGVTQAAVSNYLR 51
                                      443899**************9998877 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.12
                            HTH_28  4 eiikllaaGhsvreaArel 22
                                      e+++++ + +++ e+Ar+ 
  gi|557695044|ref|YP_008798098.1| 72 EVVEAVVKNEPRQEIARRI 90
                                      7999*************86 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      14      35 ..      29      51 ..      16      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
                                      S.SHHHHHHHHTS-HHHHHHHHH CS
                             HTH_1 14 g.sftrAAeeLglsqpavsrqik 35
                                      g +  + A+ Lg++q+avs  ++
  gi|557695044|ref|YP_008798098.1| 29 GyTQEKVAQVLGVTQAAVSNYLR 51
                                      5556689************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 ?   10.8   0.0   0.00043      0.34      20      46 ..      26      52 ..      25      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00043
                            HTH_10 20 yPRrvtlkeLAkelGIskstlsehLrk 46
                                      y R  t +++A+ lG++++++s++Lr 
  gi|557695044|ref|YP_008798098.1| 26 YERGYTQEKVAQVLGVTQAAVSNYLRG 52
                                      6788999******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      788  (0.0439511); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 933.80
//
Query:       gi|557695045|ref|YP_008798099.1|  [L=267]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-54  182.5   0.0    8.3e-54  182.2   0.0    1.1  1  tRNA_deacylase  D-aminoacyl-tRNA deacylase


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 !  182.2   0.0   4.6e-58   8.3e-54       4     204 ..      61     264 ..      58     265 .. 0.96

  Alignments for each domain:
  == domain 1  score: 182.2 bits;  conditional E-value: 4.6e-58
                                       --SEEEEEEEEE-TT---EEEEE--B-SS-.-TTSS-TT-B--B-HHHHHHHHHHHHGGG..GGSTT-EEEE--S-S CS
                    tRNA_deacylase   4 dvdliiflSrHssesgkplLTvHvtGnlge.aelGGkpeelapaaPrllkallralkkia..ekleefevtlEatHH 77 
                                       ++dl+i+ S+H se+g+++L vH tGn+g+ a++GGkp++l+ ++++++ ++l  l++    + +++ ev +EatHH
  gi|557695045|ref|YP_008798099.1|  61 EADLVIVPSKHVSETGRRCLLVHSTGNWGAtAPYGGKPRQLSETSAAAVYRALMGLRQAVenSGVRDVEVGMEATHH 137
                                       78***************************************************9999999777899*********** PP

                                       S-----S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH--.----EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE- CS
                    tRNA_deacylase  78 GPtelkvPslFvEiGSteeeWkdedaaeavaeavlellese.eekekvlvgiGGgHYaprftklvletevavGhils 153
                                       GP   ++P++FvE+GS+ + W+d+++aea ae+v++l+    ++  +++vg+GGgHY + + k v+  +++vGh++s
  gi|557695045|ref|YP_008798099.1| 138 GPH-SEKPLIFVEVGSDISAWRDSKMAEAAAETVYQLCFGVeTNLPEPAVGFGGGHYPRDILKPVFAGSYMVGHVAS 213
                                       ***.********************************98766578899****************************** PP

                                       GGGGGG--HHHHHHHHHHH..T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                    tRNA_deacylase 154 kyaleelkeevikqaleks.egadvalidkkslkseqkeaieelleelgiev 204
                                       k+ +  l+eevi+qa++++ e+ ++alid+ +l+se++ a++++l++ gi+v
  gi|557695045|ref|YP_008798099.1| 214 KH-HFPLDEEVIRQAFQRTvEQPRTALIDWDGLRSEHRTALIRALSSFGIDV 264
                                       **.778*******************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2076.18
//
Query:       gi|557695046|ref|YP_008798100.1|  [L=283]
Description: SAM-dependent methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   31.8   0.0    1.5e-07   31.2   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
    1.2e-05   25.2   0.0      2e-05   24.4   0.0    1.3  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
    1.4e-05   24.6   0.0    1.9e-05   24.1   0.0    1.3  1  Spermine_synth   Spermine/spermidine synthase domain
    3.3e-05   24.5   0.0    7.7e-05   23.3   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
     0.0002   21.0   0.0    0.00029   20.4   0.0    1.2  1  MTS              Methyltransferase small domain
     0.0003   21.4   0.0    0.00074   20.1   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
     0.0024   18.8   0.0     0.0066   17.4   0.0    1.7  2  Methyltransf_24  Methyltransferase domain
     0.0063   15.9   0.0     0.0088   15.5   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.008   15.4   0.0      0.017   14.3   0.0    1.5  1  Methyltrans_SAM  S-adenosylmethionine-dependent methyltransfe
  ------ inclusion threshold ------
      0.018   14.4   0.0       0.15   11.4   0.0    2.3  3  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      0.049   13.4   0.0      0.084   12.6   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.064   12.5   0.0      0.097   11.9   0.0    1.2  1  DUF43            Branched-chain polyamine synthase A C-termin
      0.096   12.5   0.0       0.17   11.7   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
       0.12   11.5   0.0       0.15   11.1   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase


Domain annotation for each model (and alignments):
>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.2e-10   1.5e-07      35     123 ..     127     213 ..     115     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.2e-10
                                       HHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHH.HCCCT--TTTEEEEES-HHHHCTS--S CS
                     Cons_hypoth95  35 ilaaeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilken.leelkleeetaelkedaleallklakk 110
                                       +l  e+ ga+ LD++ G G  ++  l  ga+++v vekd++ vk+   n +++  ++e+++ ++ da++ l+k    
  gi|557695046|ref|YP_008798100.1| 127 MLLRELGGAEALDICTGLGYTAIALLANGARRVVTVEKDPNIVKMATLNpWSRQLFTEKIERIVADAVDFLRKC--- 200
                                       566789999**********************************9666552333334457999999998888666... PP

                                       S-EEEEEEE--SS CS
                     Cons_hypoth95 111 keefdivflDPPy 123
                                       +eefd+v  DPP 
  gi|557695046|ref|YP_008798100.1| 201 GEEFDVVMHDPPS 213
                                       678*********4 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 !   24.4   0.0   1.6e-08     2e-05      34     115 ..     187     268 ..     172     272 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.6e-08
                                       EEEES-HHHHHHHC-T-EEEEEE-SS-TTTSGGGCSHHHHHHHHHHEEEEEEEEES---HHHHHHHHHTT-EEEEEE CS
                   Methyltransf_30  34 klligdarealkeldekadawFlDgFsPaknPelwseellkelarllkkkgtlatyssAgavrrgLkeaGfkvekrk 110
                                       + ++ da ++l ++ e++d++ +D+ s + + el+s e++++l+r+++ +g+++ y     v+rg + +   ve+ +
  gi|557695046|ref|YP_008798100.1| 187 ERIVADAVDFLRKCGEEFDVVMHDPPSFRVAGELYSTEFYRLLYRVVRRGGVVVHYVGQPGVKRGFALYRGVVERMR 263
                                       55799****************************************************99999999988777777777 PP

                                       -CTCS CS
                   Methyltransf_30 111 gfgrK 115
                                       ++g K
  gi|557695046|ref|YP_008798100.1| 264 KAGFK 268
                                       76655 PP

>> Spermine_synth  Spermine/spermidine synthase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   1.5e-08   1.9e-05      72     136 ..     183     246 ..     136     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.5e-08
                                       CTTEEEEESTCHHHHCTCSS-EEEEEEECCSTTCSSCGCSSHHHHHHHHHTEEEEEEEEEEEEET CS
                    Spermine_synth  72 darvklvlgdgfkflkayekkfdvvivdsldpvgpaenlFskeffdllkkvlkedGviilqaekp 136
                                        ++++ ++ d++ fl+++ ++fdvv+ d       a +l+s ef++ll++v++ +Gv++    +p
  gi|557695046|ref|YP_008798100.1| 183 TEKIERIVADAVDFLRKCGEEFDVVMHDPPS-FRVAGELYSTEFYRLLYRVVRRGGVVVHYVGQP 246
                                       567777899******************9887.677778*******************99766555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0     6e-08   7.7e-05       2      97 .]     138     237 ..     137     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6e-08
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT...TEEEEESBCCG.BSSSTTTEEEEEEEST. CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl...nvefvqgdaed.lpfedgsfDlvvssga. 73 
                                       Ld+++G G +++al+++ g+ +v+ v+ +++ ++ a  +  +++l   ++e +++da d l    ++fD+v+     
  gi|557695046|ref|YP_008798100.1| 138 LDICTGLGYTAIALLAN-GARRVVTVEKDPNIVKMATLNPWSRQLfteKIERIVADAVDfLRKCGEEFDVVMHDPPs 213
                                       9**************99.69*****************99988888899*********885788999******96666 PP

                                       GGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  74 lhhlsdedlekalkeiarvLkpgG 97 
                                       + +  +    ++++ ++rv++ gG
  gi|557695046|ref|YP_008798100.1| 214 FRVAGELYSTEFYRLLYRVVRRGG 237
                                       777777778899999999999998 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.3e-07   0.00029      32     108 ..     134     215 ..     119     238 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-07
                                       CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC......EEEEE-STTTTSTTS-EEEEE CS
                               MTS  32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle......vevvasdvleeveekkfdliv 102
                                         ++lD+++G G+ ++al+++  + +v+ v++d + +++a+ n  + +l       + + a d l +   ++fd+++
  gi|557695046|ref|YP_008798100.1| 134 GAEALDICTGLGYTAIALLANGAR-RVVTVEKDPNIVKMATLNPWSRQLFtekierIVADAVDFLRKCG-EEFDVVM 208
                                       4679**************997776.8**************99977666654564355566677777777.9****** PP

                                       E---.ST CS
                               MTS 103 sNPP.fh 108
                                         PP f+
  gi|557695046|ref|YP_008798100.1| 209 HDPPsFR 215
                                       ****444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.8e-07   0.00074       1      95 [.     138     240 ..     138     241 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.8e-07
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCC.TSS-TT-EEEEEEES-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl...kvefvvadaek.lpfednsfDlvvssevlh 72 
                                       Ld+ +G G+ a al  +g +rvv+v+ +++ +k+a  +   ++l   k+e +vada + l    + fD+v+     +
  gi|557695046|ref|YP_008798100.1| 138 LDICTGLGYTAIALLANGaRRVVTVEKDPNIVKMATLNPWSRQLfteKIERIVADAVDfLRKCGEEFDVVMHDPPSF 214
                                       89999**********9999****************9999999999998999******94466668*****9877555 PP

                                       C-...CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  73 hv...edpekalkeiaRvLkpgGllv 95 
                                        v       ++ + ++Rv++ gG++v
  gi|557695046|ref|YP_008798100.1| 215 RVageLYSTEFYRLLYRVVRRGGVVV 240
                                       5545447999*************986 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       9.5   1.2e+04      37      37 ..      88      88 ..      56     127 .. 0.41
   2 !   17.4   0.0   5.2e-06    0.0066       7     102 ..     144     240 ..     139     241 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9.5
                   Methyltransf_24 37 e 37
                                      +
  gi|557695046|ref|YP_008798100.1| 88 K 88
                                      1 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 5.2e-06
                   Methyltransf_24   7 sGvstlwllralrrngagrlvavdhdpg...aeeaaalareaglddrvrlikadseealaslaagsiDllfiDggha 80 
                                        G+++++ll    +nga r+v+v++dp      ++ + + ++ +++ ++ i+ad+ + l++   +++D+++ D + +
  gi|557695046|ref|YP_008798100.1| 144 LGYTAIALL----ANGARRVVTVEKDPNivkM-ATLNPWSRQLFTEKIERIVADAVDFLRKCG-EEFDVVMHDPP-S 213
                                       677776666....89999*********65532.23333334799999****************.99*******54.6 PP

                   Methyltransf_24  81 a....e.avledleallprlapggvvl 102
                                            e    e++++l +++++ggvv+
  gi|557695046|ref|YP_008798100.1| 214 FrvagElYSTEFYRLLYRVVRRGGVVV 240
                                       623221234556799999******997 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.9e-06    0.0088     161     230 ..     133     207 ..     121     210 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.9e-06
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk.....eekadvi 230
                                       +g+e lD+ tG G  aia +  ga++vv v  D+  vk+a  N    ++ + k+e +  +++++      e++dv+
  gi|557695046|ref|YP_008798100.1| 133 GGAEALDICTGLGYTAIALLANGARRVVTVEKDPNIVKMATLNPWSRQLFTeKIERI-VADAVDflrkcGEEFDVV 207
                                       57899************************************9965554433255432.233332222345566666 PP

>> Methyltrans_SAM  S-adenosylmethionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.3e-05     0.017     188     250 ..     195     255 ..     138     269 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
                   Methyltrans_SAM 188 gkikksg.pydlviidppsfqkgsfaltkdykkilrrlpellveggevlacvnspavspdflie 250
                                         ++k g ++d+v+ dppsf+      + ++ ++l r   ++  gg v+  v +p v   f + 
  gi|557695046|ref|YP_008798100.1| 195 DFLRKCGeEFDVVMHDPPSFRVAGELYSTEFYRLLYR---VVRRGGVVVHYVGQPGVKRGFALY 255
                                       3467777369**********98777777777777776...4789*************9999764 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.58   7.5e+02      54      94 ..      25      71 ..      14      80 .. 0.80
   2 ?   11.4   0.0   0.00011      0.15      45     150 ..     131     240 ..     119     256 .. 0.72
   3 ?   -2.3   0.0       1.7   2.2e+03     206     217 ..     260     271 ..     247     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.58
                                      ES-TT-HHHHHHHHHHHHHH......EEEEEES-HHHHHHHHHHHHH CS
                   Ubie_methyltran 54 vagGtgDlafklsdsvgekg......kvvvlDinenmLkvgekklke 94
                                      v +G  D++++l  s  + +       ++ + ++  mL+ + ++ ++
  gi|557695046|ref|YP_008798100.1| 25 VRCGEVDVSLDLGVSTSKGFvcnegvSIDDVRVSRWMLEKAAARPED 71
                                      56999999999998888777888877778888899999999887665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00011
                                       S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHH.HHHTSS.TEEEEE--TTT.-TTS-T-EE CS
                   Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekkl.keegki.nieflqanaee.LpfeddsfD 118
                                       ++ ga++lD+++G g  a++l+ +     +vv ++ ++n++k++      ++ ++ +ie ++a+a + L    + fD
  gi|557695046|ref|YP_008798100.1| 131 ELGGAEALDICTGLGYTAIALLANG--ARRVVTVEKDPNIVKMATLNPwSRQLFTeKIERIVADAVDfLRKCGEEFD 205
                                       56799**************998654..44677777788888887755413333335788888887762444457788 PP

                                       EEEE...ES-GGG-S-HHHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 119 vvtv...sfGlrnvtDklkaLkeayrvlkpGGrlv 150
                                       vv     sf +      ++  + +yrv++ GG +v
  gi|557695046|ref|YP_008798100.1| 206 VVMHdppSFRVAGELYSTEFYRLLYRVVRRGGVVV 240
                                       87643337777777777788899999999999875 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.7
                                       HHHHHTTEEEEE CS
                   Ubie_methyltran 206 eliedaGfksve 217
                                       e +++aGfk+v+
  gi|557695046|ref|YP_008798100.1| 260 ERMRKAGFKAVH 271
                                       5689****9986 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 ?   12.6   0.0   6.6e-05     0.084      73     117 ..     133     175 ..     108     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.6e-05
                                       TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHH CS
                              PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrn 117
                                        ga++L++ +G Gy +     l +   rvv++e+ +++v+ a+ n
  gi|557695046|ref|YP_008798100.1| 133 GGAEALDICTGLGYTAIA--LLANGARRVVTVEKDPNIVKMATLN 175
                                       5899**********8754..455666789***********99876 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 ?   11.9   0.0   7.6e-05     0.097      58     122 ..     148     213 ..     118     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.6e-05
                                       HHHHHHHT--SEEEEE-S-HHHHHH..HHHHHHHHT--.EEEE---TTS---TTTSS-BSEEEE---S CS
                             DUF43  58 slalaLtglpkkvvvvDiDeRlikf..iervakelglk.ieaivyDlrkplpeelkekFdvfitDPpe 122
                                       ++a  L++ +++vv v+ D+ ++k+  ++  +++l  + ie iv D  +    ++ e+Fdv++ DPp 
  gi|557695046|ref|YP_008798100.1| 148 AIA-LLANGARRVVTVEKDPNIVKMatLNPWSRQLFTEkIERIVADAVDF-LRKCGEEFDVVMHDPPS 213
                                       444.48999**************9844578899988878*******9875.57899**********96 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00013      0.17      11      62 ..     121     187 ..     110     226 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                   Methyltransf_23  11 dklerll.pklraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae.............k 62 
                                       d++++++  ++  g++ Ldi +G G+++  l +ng+  v+ v+ +p+ v++a              +
  gi|557695046|ref|YP_008798100.1| 121 DARQKVMlLRELGGAEALDICTGLGYTAIALLANGArRVVTVEKDPNIVKMATlnpwsrqlftekiE 187
                                       555554412355677*********************99********999988666655555554442 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00012      0.15      34      71 ..     137     175 ..     118     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                                       EEEES-TTTCCHHHH.HCC-SEEEEE-S-HHHHHHHHCH CS
                            RrnaAD  34 vleigpGkGilTeeL.akrakqvvvlElderLakllqkk 71 
                                        l+i +G G +   L a+ a+ vv +E+d++++k+ + +
  gi|557695046|ref|YP_008798100.1| 137 ALDICTGLGYTAIALlANGARRVVTVEKDPNIVKMATLN 175
                                       59**********99989999************9987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); 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):              14  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2155.84
//
Query:       gi|557695047|ref|YP_008798101.1|  [L=542]
Description: lysyl-tRNA synthetase, class I [Candidatus Caldiarchaeum subterraneum]
Scores for 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-100  334.8   0.0   7.5e-100  334.3   0.0    1.1  1  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> 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 !  334.3   0.0  4.2e-104  7.5e-100       2     340 ..      11     355 ..      10     372 .. 0.96

  Alignments for each domain:
  == domain 1  score: 334.3 bits;  conditional E-value: 4.2e-104
                      tRNA-synt_1f   2 aWadklaeklieerkkkka.ekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkv 77 
                                       +W+dkla ++i er+k+   + +++  e+Gi++SG iHiG+l + ++a++v  a++++g   ++i ++DdmDglR v
  gi|557695047|ref|YP_008798101.1|  11 TWIDKLAWEII-EREKQLGrSLENIRTEAGIAASGFIHIGSLSDSVRAYAVSLAIKNLGYGSEMIQFADDMDGLRSV 86 
                                       6**********.5555555599******************************************************* PP

                      tRNA-synt_1f  78 penlpekllekylgkpltsiPdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenreki 154
                                       p+++p++ +ek+l kp++ iPdp+++hesyaeh++ +l+++L++ g+e +f++  ++Y sgl++++i ++len + i
  gi|557695047|ref|YP_008798101.1|  87 PAEIPKE-YEKHLLKPVSLIPDPFNCHESYAEHMETMLLDTLAKTGVESKFYRGFHVYGSGLLKNQISKILENAKTI 162
                                       *******.********************************************************************* PP

                      tRNA-synt_1f 155 keilekyrgeereetyspylpvcekcgrvdttevvevdaeeeeieYkc..........eecGeeeevdiregngKLq 221
                                        e + + +g+++  + +py p+c +cgr+ tt+++++d+++++++Y+c          e cG+e+e+di++++gKL+
  gi|557695047|ref|YP_008798101.1| 163 GEKILELTGQQKFVETLPYFPLCASCGRIYTTHAESFDHKTGRVHYVCkgvsikkrwfEGCGYEGEADISKADGKLS 239
                                       ***************************************************************************** PP

                      tRNA-synt_1f 222 WkvdwamrWaalgVdfEpaGkDhaaaGgSvdvsskia.eilggeaPekvvYelillkggekmssSkGn.vltledwl 296
                                       Wkv+wa+rWaal+V+fE++GkD+aa   Sv v+++++ +ilg+++P++v+Yel+l++ ++k+s+SkG+ v+t+++w+
  gi|557695047|ref|YP_008798101.1| 240 WKVEWAARWAALDVRFEAYGKDLAA---SVMVNDWVSeNILGYKPPKHVQYELFLDESRRKISKSKGVsVFTPHEWF 313
                                       *************************...***************************************6489****** PP

                      tRNA-synt_1f 297 evaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf 340
                                       ++++p++l +l+l+ ++k    ++++  i++l+de d l ++  
  gi|557695047|ref|YP_008798101.1| 314 KYGSPQSLVLLFLK-RIKGTRVVSPQ-LIPALMDELDALGEQHR 355
                                       **************.**********9.9*********9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); 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: 0.54u 0.21s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 4188.37
//
Query:       gi|557695048|ref|YP_008798102.1|  [L=142]
Description: replication factor A1 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   26.3   0.0    7.2e-06   25.9   0.0    1.3  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
        0.1   12.7   0.1          6    7.0   0.0    2.1  2  PBP3             Penicillin Binding Protein 3 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 !   25.9   0.0     8e-10   7.2e-06       7      71 ..      31      92 ..       8      98 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 8e-10
                                      EEEEE.EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEEE CS
                   tRNA_anti-codon  7 vtsis.drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkve 71
                                      v+s + d+s+ ++  + + D+tg i++vl++    +  + + eGd ++v  G +k ++g+ ++l+  
  gi|557695048|ref|YP_008798102.1| 31 VVSSQyDQSEHRLTEALIADETGAITLVLWD----DNIDLVNEGDSIKVVnGFIKLFRGK-MQLNLG 92
                                      44444799999********************....99*********************99.999765 PP

>> PBP3  Penicillin Binding Protein 3 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0    0.0057        51      84     106 ..      36      59 ..       5      63 .. 0.65
   2 ?    7.0   0.0   0.00067         6      49      90 ..      67     108 ..      63     122 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0057
                              PBP3  84 stlvssad.talsaddeGAilLrl 106
                                       + ++++    al ad++GAi L l
  gi|557695048|ref|YP_008798102.1|  36 YDQSEHRLtEALIADETGAITLVL 59 
                                       33344433045779999***9987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00067
                              PBP3  49 vaagdGiKVlyGsitlkdeekkvrrplatkaftaastlvssa 90 
                                       v++gd iKV+ G i+l+  + + + + + k  ++++ +++++
  gi|557695048|ref|YP_008798102.1|  67 VNEGDSIKVVNGFIKLFRGKMQLNLGKFGKIEPSEEPVTEVN 108
                                       5789************99987777666666666666666553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); 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:                         2  (0.000111551); expected 0.2 (1e-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: 1127.28
//
Query:       gi|557695049|ref|YP_008798103.1|  [L=422]
Description: membrane-bound serine protease, ClpP class [Candidatus Caldiarchaeum subterraneum]
Scores for 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   38.6   0.2    3.2e-09   37.0   0.2    1.9  1  NfeD          NfeD-like C-terminal, partner-binding
    1.2e-06   28.6   0.1    1.9e-06   27.9   0.1    1.3  1  CLP_protease  Clp protease


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 !   37.0   0.2   3.6e-13   3.2e-09       3      84 .]     340     418 ..     334     418 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 3.6e-13
                                       XXXXXXXXXXXXXXS---SSS--S.S---GGTTSEEEEEE-BS-EEEEETTEEEEEE-.SSB-TT-EEEEEEE-SSS CS
                              NfeD   3 avvsvlllvllrplllkklkkkekktnaealiGkegvvledigtGrvkvdGeeWsarsegeiekgerVrVveveGlt 79 
                                       + v++ l +l+++ +lk+++kk  + +ae  +G+ ++ +e+ + G v v+Ge+W+a++  ++++++r++Vv+ e   
  gi|557695049|ref|YP_008798103.1| 340 VFVAAFLGFLIYK-ALKAQRKK--PMGAEPKLGRAAENIETGQIGYVFVEGEYWRAKAVKPVKENDRIKVVGKENGV 413
                                       3344444455555.44444332..37788778888888886657**************999**************** PP

                                       EEEEE CS
                              NfeD  80 liVep 84 
                                       l Vep
  gi|557695049|ref|YP_008798103.1| 414 LLVEP 418
                                       ***98 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.1   2.1e-10   1.9e-06      44     180 ..      48     179 ..      25     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 2.1e-10
                                       -SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEE...EEEETHHHHHHHTS-TTGEEEETTEEEEES-TEEE CS
                      CLP_protease  44 dpdkdillyinspGGsvtaglaIydtmqyikpdvsticl...GlaaSmgslllaagekgkRfalpnarimihqPlgg 117
                                       +  + +++ in+ GGs +a+l I ++++   ++v+ ++    G a S+g+ +l++ +    ++ p++ i   qP+ g
  gi|557695049|ref|YP_008798103.1|  48 SRYEAVVITINTLGGSADAMLRIVEAIERSPTPVIGFVYpvgGKALSAGTYILMSTHFA--AMAPETLIGSAQPVAG 122
                                       5567899**********************999997666555699***********9999..7889999999999988 PP

                                       EEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE-S CS
                      CLP_protease 118 aqgqasdieieaeellkikerlneilakhtgqslekiekdldrdtflsaeeAveyGLidevie 180
                                        +        e + l+   e++ ++ +++  +  e +++ l++ + ++++ A+e GLi+ v +
  gi|557695049|ref|YP_008798103.1| 123 GEP-----VTESKVLNFFAEKMGTLAESRGRNRDEAVKTVLENKN-FNPSSALEAGLIEAVAS 179
                                       777.....5678999999999999888888777888877777655.699**********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 3289.34
//
Query:       gi|557695050|ref|YP_008798104.1|  [L=270]
Description: membrane protease subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  114.3   5.5    7.9e-33  113.9   5.5    1.1  1  Band_7    SPFH domain / Band 7 family
    6.9e-05   22.6   0.2    0.00014   21.7   0.2    1.6  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 !  113.9   5.5   8.8e-37   7.9e-33       2     177 ..      40     209 ..      39     210 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.9 bits;  conditional E-value: 8.8e-37
                            Band_7   2 iieegevgvvvrfGklsrvlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapkl 78 
                                       ++ e e++v++r G+l +v++pG+  ilP +++  ++++r +t+dv++ + ++tkD++ v++d++v++rv +d+  +
  gi|557695050|ref|YP_008798104.1|  40 VVTEYERAVIFRLGRLIGVKGPGVVVILPVIDRRRIIDLRLVTFDVPK-QRIITKDNVTVDVDAIVYFRV-TDPMMA 114
                                       68899*******************************************.*********************.****** PP

                            Band_7  79 vaaveresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaq 155
                                       v++v    +++ +    +++ +lr vi++ +l++ll  reel++++++ l e+ + +G+ v+ v ++d+++p+  ++
  gi|557695050|ref|YP_008798104.1| 115 VLKV----KDYFTASALLAQTTLRDVIGQVELDDLLTRREELNKRIQQILDEATEPWGIKVTTVALRDVVIPEMMQR 187
                                       ****....999999999************************************************************ PP

                            Band_7 156 alaakqaaeaeaqaeiaraeae 177
                                       a+a+ ++ae+e++ +i  ae+e
  gi|557695050|ref|YP_008798104.1| 188 AIAKQAEAERERRSRIIAAEGE 209
                                       *****************99987 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 !   21.7   0.2   1.5e-08   0.00014     144     209 ..     132     195 ..      70     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.5e-08
                          Band_7_1 144 rlsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                       +l dv++  ++ + dl ++ eel +++++ l+e+ +  G++++ + ++++ +pe +++a+ k+a++
  gi|557695050|ref|YP_008798104.1| 132 TLRDVIG--QVELDDLLTRREELNKRIQQILDEATEPWGIKVTTVALRDVVIPEMMQRAIAKQAEA 195
                                       4566665..46678999*********************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); 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 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1855.21
//
Query:       gi|557695051|ref|YP_008798105.1|  [L=451]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0058   15.5  15.7     0.0058   15.5  15.7    4.0  5  Spc7             Spc7 kinetochore protein
     0.0084   16.3  14.8        3.4    8.0   0.4    4.6  4  DUF948           Bacterial protein of unknown function (DUF94
  ------ inclusion threshold ------
      0.015   15.4  18.1        2.6    8.1   0.1    4.9  5  DUF1664          Protein of unknown function (DUF1664)
       0.02   15.1   1.1       0.02   15.1   1.1    5.4  6  HALZ             Homeobox associated leucine zipper
      0.024   15.1  37.2       0.12   12.8  13.1    3.4  4  Fez1             Fez1
      0.058   13.6   1.8         11    6.2   0.0    2.7  2  Imm5             Immunity protein Imm5
       0.06   12.4  29.0       0.19   10.8   3.3    4.2  4  APG17            Autophagy protein Apg17
       0.11   12.8   7.4        6.4    7.1   0.0    4.6  4  WXG100           Proteins of 100 residues with WXG
       0.14   12.1  26.3       0.47   10.3   1.9    5.1  5  Sec34            Sec34-like family
        0.3   10.6  31.2        2.3    7.7   8.3    3.0  2  Exonuc_VII_L     Exonuclease VII, large subunit
       0.31   11.1  50.4       0.29   11.2  17.2    5.0  5  DHR10            Designed helical repeat protein 10 domain
       0.39   10.5   6.5        7.5    6.3   3.4    2.9  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
       0.68   10.3   2.3        3.9    7.8   1.4    2.9  2  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
       0.94    8.8  19.7          1    8.6  12.6    2.9  2  DUF4407          Domain of unknown function (DUF4407)
        1.1    8.6  35.5        1.5    8.2  14.8    4.0  5  Cluap1           Clusterin-associated protein-1
        1.5    8.8  23.1       0.12   12.4   0.6    4.9  5  DUF4446          Protein of unknown function (DUF4446)
        1.6    9.1  27.2        1.9    8.8   5.3    5.3  4  BLOC1_2          Biogenesis of lysosome-related organelles co
          2    8.9  13.1         16    6.0   0.0    4.9  5  ACP_PD           Acyl carrier protein phosphodiesterase
          2    8.7  35.4       0.15   12.3  11.2    5.0  5  FliJ             Flagellar FliJ protein
          2    8.9  17.0        5.6    7.5   0.5    5.4  6  NPV_P10          Nucleopolyhedrovirus P10 protein
        2.5    8.2  45.3        3.7    7.6   1.5    4.6  3  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
        3.2    8.1  39.7       0.63   10.4  11.8    4.2  4  OmpH             Outer membrane protein (OmpH-like)
        3.3    8.2  33.1        3.9    8.0   5.8    5.4  6  Snapin_Pallidin  Snapin/Pallidin
        3.4    7.9  36.4      0.054   13.7   6.4    4.9  5  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
        3.5    5.7  40.8        8.6    4.4   1.5    4.0  2  EzrA             Septation ring formation regulator, EzrA
        5.8    6.9  14.7        2.7    8.0   2.7    3.7  3  Halogen_Hydrol   5-bromo-4-chloroindolyl phosphate hydrolysis
        7.2    7.0   7.6        2.4    8.6   0.1    3.6  3  Flagellin_C      Bacterial flagellin C-terminal helical regio
        9.7    5.6   9.0       0.97    8.9   4.0    1.8  2  IpaC_SipC        Salmonella-Shigella invasin protein C (IpaC_


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 ?    1.0   1.3      0.25   1.6e+02     234     280 ..      47      93 ..      16     102 .. 0.68
   2 ?    2.6  12.8     0.081        52     152     238 ..      64     165 ..      49     168 .. 0.52
   3 !   10.8  17.0   0.00025      0.16     143     238 ..     120     210 ..     118     211 .. 0.85
   4 !   15.5  15.7   9.1e-06    0.0058     158     290 ..     169     296 ..     163     317 .. 0.80
   5 !    6.7   6.0    0.0045       2.9     174     302 ..     272     405 ..     261     413 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.25
                              Spc7 234 ekieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkalee 280
                                        k+e   ++  e + +i+e  rv++e+++ + + v+r+++  ++le+
  gi|557695051|ref|YP_008798105.1|  47 VKLEYSINELLEKRRKIEEDLRVYMEQQRLTLETVNRVNNIIRSLEK 93 
                                       34444445555556667777778888888888888888888888775 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.081
                              Spc7 152 eedkelLekqeeeldellpeleeekaelee......eleklqeaaeeles.........idkeeLeelreelaelka 213
                                       eed ++ ++q+ +  e ++++++   +le+       le+l + a+++++          + ++Lee+ ++l+e +a
  gi|557695051|ref|YP_008798105.1|  64 EEDLRVYMEQQRLTLETVNRVNNIIRSLEKygvnigHLENLAKVAAKVSEtgtdfkqvfETFAKLEEAENRLKETQA 140
                                       44444444444444444444444444444422211134444444444444443333343345667777777777777 PP

                              Spc7 214 eieekkkelaelqeqleeleekiee 238
                                        iee +k+l+e++++l+++ +++ e
  gi|557695051|ref|YP_008798105.1| 141 MIEENEKRLEEVETELQRKIARLRE 165
                                       7777777777777777776666655 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00025
                              Spc7 143 gleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekk 219
                                       ++ e++++lee +++L++ ++ ++e  ++lee ++el++++++l+e    ++ ++  ++e+l e+l++l +e+e ++
  gi|557695051|ref|YP_008798105.1| 120 QVFETFAKLEEAENRLKETQAMIEENEKRLEEVETELQRKIARLRE----VSGVE-PDIEKLSETLSKLRTEVELLE 191
                                       5668899999999999999999999999999999999999999999....44444.469999999999999999999 PP

                              Spc7 220 kelaelqeqleeleekiee 238
                                       k+ +el+++ +el+ + e+
  gi|557695051|ref|YP_008798105.1| 192 KREEELRQKNNELAREYEA 210
                                       9999999999999887765 PP

  == domain 4  score: 15.5 bits;  conditional E-value: 9.1e-06
                              Spc7 158 LekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleelee 234
                                       +e + e+l+e l +l++e + le++ e+l+++++el+  + e L  +r + a+l + ieek++el++l e+l+++++
  gi|557695051|ref|YP_008798105.1| 169 VEPDIEKLSETLSKLRTEVELLEKREEELRQKNNELAR-EYEALLGFRTDTASLLKLIEEKRNELNRLDEELARVRD 244
                                       56677888889999999999999999999998888766.67788899999999999999999999999999999999 PP

                              Spc7 235 kieelkeqkseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivsls 290
                                       ++++l+e+ +++++ +     +l++ + ++++++++l  ++ +l ++   ++ +l+
  gi|557695051|ref|YP_008798105.1| 245 TLQTLEEEVASARSLLL----LLQNPELVKKEDLETLSRQLANLSNIKAGQMPELK 296
                                       99999888888888877....89999999999999999999999988766665555 PP

  == domain 5  score: 6.7 bits;  conditional E-value: 0.0045
                              Spc7 174 eekaeleeeleklqe....aaeelesidkeeLeelreelaelkaeieekkke....laelqeqleeleekieelkeq 242
                                       e  ++l+++l++l +    +  el+++++  Le++r++++el   + + +       ++l+++ +e++++ ++l+e+
  gi|557695051|ref|YP_008798105.1| 272 EDLETLSRQLANLSNikagQMPELKALEPSLLENVRKRVVELVMPVIRSELVphwvFEKLEKEFKEVAARKAQLEEE 348
                                       4456999999999998777778899999***********99988887555431111456666666666666666666 PP

                              Spc7 243 kseleeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivslsgstleltyrsel 302
                                        ++l++e++   +++  + +   + v +l  +++ l+++t+++  s  +  l+++y ++ 
  gi|557695051|ref|YP_008798105.1| 349 NERLRNELN---QLRGTKPQTAVQAVPQLPRKFQLLKKKTELSTDSGIKIKLKCVYCQNS 405
                                       666666655...556666677889999999999999999999988777777777777765 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 !    8.0   0.4    0.0053       3.4      23      86 ..      48     120 ..      46     123 .. 0.77
   2 ?    6.2   1.0     0.019        12      23      74 ..     130     180 ..     120     184 .. 0.78
   3 ?    6.1   1.0     0.021        14      20      88 ..     179     250 ..     169     251 .. 0.65
   4 ?    4.5   0.0     0.065        42      20      53 ..     327     360 ..     322     378 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0053
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvne.........klekvdplteavadlgesvse 86 
                                       kl+  ++e+ +  +++e++++ ++++ + +l++vn++ + +++         +le++ ++ ++v ++g+ +++
  gi|557695051|ref|YP_008798105.1|  48 KLEYSINELLEKRRKIEEDLRVYMEQQRLTLETVNRVNNIIRSlekygvnigHLENLAKVAAKVSETGTDFKQ 120
                                       67778899999999**************999999994444444555777777778888888888777777665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.019
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplt 74 
                                       ++++ l+e++a+iee ek+++++ +e+++ +a  +e +++v+  +ek+ +  
  gi|557695051|ref|YP_008798105.1| 130 EAENRLKETQAMIEENEKRLEEVETELQRKIARLRE-VSGVEPDIEKLSETL 180
                                       457788899999999999999999999999999988.888888888877655 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.021
                            DUF948  20 vllklkktldeaaatieelekqvdpilkevedllakvne..........lledvneklekvdplteavadlgesvse 86 
                                       +l kl+  ++ ++++ eel+++ +++ +e e       +          ll+ ++ek +++++l e++a + +++++
  gi|557695051|ref|YP_008798105.1| 179 TLSKLRTEVELLEKREEELRQKNNELAREYE-------AllgfrtdtasLLKLIEEKRNELNRLDEELARVRDTLQT 248
                                       4445555555555555555555555555555.......444444445669999999999999999999999999988 PP

                            DUF948  87 ln 88 
                                       l+
  gi|557695051|ref|YP_008798105.1| 249 LE 250
                                       85 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.065
                            DUF948  20 vllklkktldeaaatieelekqvdpilkevedll 53 
                                       v+ kl+k ++e+aa+ ++le++ + + +e+++l 
  gi|557695051|ref|YP_008798105.1| 327 VFEKLEKEFKEVAARKAQLEEENERLRNELNQLR 360
                                       6789**************************9985 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.1      0.35   2.2e+02      71     115 ..      49      93 ..      37     101 .. 0.82
   2 ?    8.1   0.1    0.0041       2.6      67     124 .]      83     139 ..      81     139 .. 0.81
   3 ?    6.2   3.0     0.015       9.8      57     115 ..     142     199 ..     132     207 .. 0.42
   4 ?    4.8   0.8     0.043        28      79     111 ..     222     254 ..     190     287 .. 0.59
   5 ?    4.0   0.1     0.074        47      48      93 ..     329     375 ..     322     389 .. 0.71

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.35
                           DUF1664  71 vdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       ++ +++e  e  ++i+e++    e+ + + e v+ v++++++le+
  gi|557695051|ref|YP_008798105.1|  49 LEYSINELLEKRRKIEEDLRVYMEQQRLTLETVNRVNNIIRSLEK 93 
                                       566788888888899999998888888888999999999998886 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0041
                           DUF1664  67 ridrvdkkldeqkeiskeikeevtevredlseigedvesvkeaveglesklerieekQ 124
                                       r++++ ++l++    + ++ e++++v  ++se+g+d+++v e++ +le+  +r++e+Q
  gi|557695051|ref|YP_008798105.1|  83 RVNNIIRSLEKYGVNIGHL-ENLAKVAAKVSETGTDFKQVFETFAKLEEAENRLKETQ 139
                                       6666666666666655555.6799************************9999998887 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.015
                           DUF1664  57 laatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegles 115
                                       +++  ++L++   ++++k+    e+s  ++ ++++++e ls+++++ve +++  e+l +
  gi|557695051|ref|YP_008798105.1| 142 IEENEKRLEEVETELQRKIARLREVS-GVEPDIEKLSETLSKLRTEVELLEKREEELRQ 199
                                       33333333333333333333333332.23444444444444444444444444444444 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.043
                           DUF1664  79 keiskeikeevtevredlseigedvesvkeave 111
                                        ++++e ++e++++ e+l+++++ +++++e v 
  gi|557695051|ref|YP_008798105.1| 222 LKLIEEKRNELNRLDEELARVRDTLQTLEEEVA 254
                                       334444445555555555555555555555444 PP

  == domain 5  score: 4.0 bits;  conditional E-value: 0.074
                           DUF1664  48 kqleqvseslaatkrhLssridrvdkkldeqkeiskeik.eevtevr 93 
                                       ++le+  +++aa k +L+++ +r+ ++l++   ++ +++ + v ++ 
  gi|557695051|ref|YP_008798105.1| 329 EKLEKEFKEVAARKAQLEEENERLRNELNQLRGTKPQTAvQAVPQLP 375
                                       67888888889999999999999988888887777666523454554 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2       1.9   1.2e+03       2       8 ..      23      29 ..      22      60 .. 0.78
   2 ?   -2.4   0.5         9   5.8e+03      30      39 ..     155     164 ..     134     166 .. 0.61
   3 ?   -0.7   1.2       2.7   1.7e+03      29      41 ..     181     193 ..     172     200 .. 0.60
   4 ?   -0.5   3.4       2.4   1.6e+03      12      34 ..     185     207 ..     180     213 .. 0.49
   5 ?   -2.5   0.7       9.6   6.1e+03      27      41 ..     231     245 ..     220     253 .. 0.69
   6 ?   15.1   1.1   3.2e-05      0.02       8      41 ..     329     362 ..     328     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.9
                              HALZ  2 QLErDYd 8 
                                      QLE+ Y+
  gi|557695051|ref|YP_008798105.1| 23 QLEKQYG 29
                                      9999996 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 9
                              HALZ  30 kLkaelqeLk 39 
                                       +L+ ++++L+
  gi|557695051|ref|YP_008798105.1| 155 ELQRKIARLR 164
                                       4666666666 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.7
                              HALZ  29 ekLkaelqeLkek 41 
                                        kL++e++ L ++
  gi|557695051|ref|YP_008798105.1| 181 SKLRTEVELLEKR 193
                                       4666666666544 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 2.4
                              HALZ  12 asYdaLksdydsLkkenekLkae 34 
                                          + L  + + L++ n++L  e
  gi|557695051|ref|YP_008798105.1| 185 TEVELLEKREEELRQKNNELARE 207
                                       34444444445555555555555 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 9.6
                              HALZ  27 enekLkaelqeLkek 41 
                                       e ++L  el++ ++ 
  gi|557695051|ref|YP_008798105.1| 231 ELNRLDEELARVRDT 245
                                       444566666665555 PP

  == domain 6  score: 15.1 bits;  conditional E-value: 3.2e-05
                              HALZ   8 dvLKasYdaLksdydsLkkenekLkaelqeLkek 41 
                                       + L + +   +++  +L++ene+L++el++L++ 
  gi|557695051|ref|YP_008798105.1| 329 EKLEKEFKEVAARKAQLEEENERLRNELNQLRGT 362
                                       778899999999999****************975 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.2       2.6   1.7e+03      26      70 ..      39      83 ..       7     121 .. 0.61
   2 ?   12.8  13.1   0.00019      0.12      25     117 ..     106     201 ..     100     209 .. 0.76
   3 ?   10.4  14.7     0.001      0.64      18     153 ..     196     365 ..     186     372 .. 0.77
   4 ?    4.3   1.7     0.076        49      49      89 ..     330     371 ..     325     419 .. 0.53

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.6
                              Fez1 26 vtqklseivalkaqlrelrakleekeeeikeleesleektlelev 70
                                        ++  + v+l  ++ el +k ++ ee ++ + e+ +   + +++
  gi|557695051|ref|YP_008798105.1| 39 YEKRFRDSVKLEYSINELLEKRRKIEEDLRVYMEQQRLTLETVNR 83
                                      344444555555555555555555554444444444444444444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00019
                              Fez1  25 evtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrk...kseaellrekvekleeelke 98 
                                        v++k+se  +   q+ e+ aklee e+++ke+++ +ee ++ le++e elqrk     e++ ++  +ekl+e l++
  gi|557695051|ref|YP_008798105.1| 106 KVAAKVSETGTDFKQVFETFAKLEEAENRLKETQAMIEENEKRLEEVETELQRKiarLREVSGVEPDIEKLSETLSK 182
                                       57777777777778889999**********************************87766666667777777777777 PP

                              Fez1  99 lreelselsleeeeaales 117
                                       lr+e++ l+++eee +++ 
  gi|557695051|ref|YP_008798105.1| 183 LRTEVELLEKREEELRQKN 201
                                       7777776555544443333 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.001
                              Fez1  18 QLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekveklee 94 
                                        L++  +e+++  + ++  ++++  l + +eek +e+++l+e+l    + l+++e+e++ ++s   ll++     +e
  gi|557695051|ref|YP_008798105.1| 196 ELRQKNNELAREYEALLGFRTDTASLLKLIEEKRNELNRLDEELARVRDTLQTLEEEVASARSLLLLLQNPELVKKE 272
                                       58888888888888889999999999999999999999999999888889999999999888888888888888888 PP

                              Fez1  95 elkelreelselsleeeeaa...................................lesdeakaqrqeaeeleelkre 136
                                       +l+ l ++l++ls+ ++ ++                                    e+ e k+ ++ a + ++l++e
  gi|557695051|ref|YP_008798105.1| 273 DLETLSRQLANLSNIKAGQMpelkalepsllenvrkrvvelvmpvirselvphwvFEKLE-KEFKEVAARKAQLEEE 348
                                       888888888887766665558888888888888888888888888888888776433333.4444446788899999 PP

                              Fez1 137 verlraeLkeerqkkee 153
                                        erlr+eL++ r +k +
  gi|557695051|ref|YP_008798105.1| 349 NERLRNELNQLRGTKPQ 365
                                       9******9998877655 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.076
                              Fez1  49 ekeeeikeleesleektlelevcenelqrk.kseaellrekv 89 
                                       + e+e ke+ ++  + ++e+e++ nel++   ++ ++  + v
  gi|557695051|ref|YP_008798105.1| 330 KLEKEFKEVAARKAQLEEENERLRNELNQLrGTKPQTAVQAV 371
                                       344444444444444444444444444443222222223333 PP

>> Imm5  Immunity protein Imm5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.6     0.022        14      18      73 ..      57     112 ..      43     159 .. 0.71
   2 ?    6.2   0.0     0.017        11      42     106 ..     307     372 ..     257     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.022
                              Imm5  18 LplRvkllraigsprviqklaiecvkkvlplweevfaedqsplrlLekaedylye.k 73 
                                       L++R+k+   ++ +   q+l +e+v++v ++ ++ + +    ++ Le+  +++ + +
  gi|557695051|ref|YP_008798105.1|  57 LEKRRKIEEDLRVYMEQQRLTLETVNRVNNIIRS-LEKYGVNIGHLENLAKVAAKvS 112
                                       889****************************997.4455555555555555555543 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.017
                              Imm5  42 vkkvlplweevfaedqsplrlLekaedylye.ktdkeeiekeadklsndlendsgeeaeetvalag 106
                                        k+v++l   v++ +  p+ + ek e+   e  + k ++e+e ++l+n l++  g++ +++v +++
  gi|557695051|ref|YP_008798105.1| 307 RKRVVELVMPVIRSELVPHWVFEKLEKEFKEvAARKAQLEEENERLRNELNQLRGTKPQTAVQAVP 372
                                       5789999999999999*********99988889999***************988999999998875 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.7      0.31     2e+02     310     361 ..       8      59 ..       3      75 .. 0.81
   2 ?    8.8   2.8    0.0012      0.77     239     320 ..      83     166 ..      79     171 .. 0.78
   3 ?   10.8   3.3    0.0003      0.19     244     322 ..     173     251 ..     168     254 .. 0.95
   4 ?    7.6   0.3    0.0028       1.8      67     104 ..     329     369 ..     274     384 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 310 kekieekleeleeLrefYegFlsaYdklllEveRRraveekmekilkkarek 361
                                       +++++++++ +++Lr+  +++ + ++ l +E+e+R +   k e  ++++ ek
  gi|557695051|ref|YP_008798105.1|   8 QTQLKRYIKGVNKLRQLEKQYGKPFQVLFREYEKRFRDSVKLEYSINELLEK 59 
                                       5688999999**********************99988777777666666555 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHH CS
                             APG17 239 eledVvkelqerleem..ekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekeki 313
                                        + +++++l++   ++   +  + + +k +e+ +  +++ +++++lee +++l+e+ a++++ e+ le+ e+e ++ 
  gi|557695051|ref|YP_008798105.1|  83 RVNNIIRSLEKYGVNIghLENLAKVAAKVSETGTDFKQVFETFAKLEEAENRLKETQAMIEENEKRLEEVETELQRK 159
                                       5778888888888888887778889999999999999999*******99*********7777777777755555555 PP

                                       HHHHHHH CS
                             APG17 314 eekleel 320
                                        ++l+e+
  gi|557695051|ref|YP_008798105.1| 160 IARLREV 166
                                       5555554 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.0003
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHH CS
                             APG17 244 vkelqerleemekakkllsekkeeiekllsalkkaleeleevgkklpeylaifkaeeeflerweeekekieekleel 320
                                       +++l e+l+++ ++ +ll++++ee+++ +++l + +e l  +++  ++ l++++++++ l+r +ee +++ + l++l
  gi|557695051|ref|YP_008798105.1| 173 IEKLSETLSKLRTEVELLEKREEELRQKNNELAREYEALLGFRTDTASLLKLIEEKRNELNRLDEELARVRDTLQTL 249
                                       5789999******************************************************************9999 PP

                                       HH CS
                             APG17 321 ee 322
                                       ee
  gi|557695051|ref|YP_008798105.1| 250 EE 251
                                       86 PP

  == domain 4  score: 7.6 bits;  conditional E-value: 0.0028
                                       IIIIIIIIHH...HHHHHHHHHHHHHHHHHHHTSS-TTS.. CS
                             APG17  67 ekgkeefkdl...ikeldaanerLektlekLrktkvepsfr 104
                                       ek+++efk++    ++l++ nerL++ l++Lr tk + +++
  gi|557695051|ref|YP_008798105.1| 329 EKLEKEFKEVaarKAQLEEENERLRNELNQLRGTKPQTAVQ 369
                                       5556666555111567*****************99777765 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 ?    0.9   0.2      0.83   5.3e+02      56      85 ..     124     153 ..     111     154 .. 0.61
   2 ?    0.9   0.3      0.82   5.3e+02      12      35 ..     131     154 ..     124     165 .. 0.46
   3 ?    3.9   0.4       0.1        64      50      77 ..     229     256 ..     175     260 .. 0.61
   4 ?    7.1   0.0    0.0099       6.4       6      39 ..     328     361 ..     326     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  56 wkqaaqklvdaLeeisealkqaanafedaD 85 
                                         +++++  + L+e++  ++++ +++e+++
  gi|557695051|ref|YP_008798105.1| 124 TFAKLEEAENRLKETQAMIEENEKRLEEVE 153
                                       334556666667777777777777777666 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.82
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  12 aaarfqkqaeeledelqrlkaevd 35 
                                       a +r++++++ +e+  +rl+    
  gi|557695051|ref|YP_008798105.1| 131 AENRLKETQAMIEENEKRLEEVET 154
                                       444444444444444444443333 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            WXG100  50 qaefeewkqaaqklvdaLeeisealkqa 77 
                                       ++e+++++++++++ d L++++e++ +a
  gi|557695051|ref|YP_008798105.1| 229 RNELNRLDEELARVRDTLQTLEEEVASA 256
                                       3455666666666666666666665554 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0099
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGC CS
                            WXG100   6 peelrqaaarfqkqaeeledelqrlkaevdalqs 39 
                                       +e+l++  +++++ +++le+e +rl++e+++l++
  gi|557695051|ref|YP_008798105.1| 328 FEKLEKEFKEVAARKAQLEEENERLRNELNQLRG 361
                                       68899999999999**************999976 PP

>> Sec34  Sec34-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.4      0.22   1.4e+02       4      59 ..      10      65 ..       8     100 .. 0.63
   2 ?   10.3   1.9   0.00073      0.47       8      69 ..     100     161 ..      98     170 .. 0.91
   3 ?    6.1   2.0     0.015       9.8      11      61 ..     165     215 ..     155     227 .. 0.73
   4 ?    3.0   0.5      0.14        87       4      34 ..     224     254 ..     215     286 .. 0.65
   5 ?    6.0   0.1     0.016        10      26      59 ..     328     361 ..     325     383 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.22
                             Sec34  4 qLeskeeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrlee 59
                                      qL+++ + +++l +  ++  + ++ l  ++++   ++ +l+ + ++lle+++++ee
  gi|557695051|ref|YP_008798105.1| 10 QLKRYIKGVNKLRQLEKQYGKPFQVLFREYEKRFRDSVKLEYSINELLEKRRKIEE 65
                                      77777777777777777777788888888888888888888888888888777654 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00073
                             Sec34   8 keeecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleelaeeieekLk 69 
                                       + e++ ++ ++++e+ ++++++ e f + +e  ++l+e+   + e++krlee+  e++ k+ 
  gi|557695051|ref|YP_008798105.1| 100 HLENLAKVAAKVSETGTDFKQVFETFAKLEEAENRLKETQAMIEENEKRLEEVETELQRKIA 161
                                       567889999*********************************************99998875 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.015
                             Sec34  11 ecdelleqtdealeqLeeleekfksvsektsslheaceqlleeqkrleela 61 
                                       e+  +  +++++ e+L++l+++++  +++ ++l+++ ++l +e + l  + 
  gi|557695051|ref|YP_008798105.1| 165 EVSGVEPDIEKLSETLSKLRTEVELLEKREEELRQKNNELAREYEALLGFR 215
                                       445555678888888888888888888888888888888888888776555 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.14
                             Sec34   4 qLeskeeecdelleqtdealeqLeeleekfk 34 
                                        +e+k++e+++l e++ ++ ++L++lee++ 
  gi|557695051|ref|YP_008798105.1| 224 LIEEKRNELNRLDEELARVRDTLQTLEEEVA 254
                                       3444555555555555555555555555544 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.016
                             Sec34  26 Leeleekfksvsektsslheaceqlleeqkrlee 59 
                                       +e+le++fk+v+++  +l+e+ e+l +e ++l+ 
  gi|557695051|ref|YP_008798105.1| 328 FEKLEKEFKEVAARKAQLEEENERLRNELNQLRG 361
                                       689************************9999875 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 ?    5.9  20.3     0.013       8.1     158     259 ..     116     242 ..       6     251 .. 0.67
   2 ?    7.7   8.3    0.0035       2.3     162     297 ..     223     398 ..     214     404 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.013
                      Exonuc_VII_L 158 kaikrlleekkqrleklasrlkspeellerkrqrldeleerleralkkq.........lkkkrerleelkerlkekl 225
                                       + +k+ + e  ++le++++rlk+ ++++e++++rl+e+e++l+r++++          ++k +e+l++l++++ e l
  gi|557695051|ref|YP_008798105.1| 116 TDFKQVF-ETFAKLEEAENRLKETQAMIEENEKRLEEVETELQRKIARLrevsgvepdIEKLSETLSKLRTEV-ELL 190
                                       2223333.344679999999999999*************9999988877786665555444444444444333.344 PP

                      Exonuc_VII_L 226 eekkerlkklkerle..................lleekkerleeleekleal 259
                                       e+++e+l++ +++l+                  l+eek+++l++l e+l+ +
  gi|557695051|ref|YP_008798105.1| 191 EKREEELRQKNNELAreyeallgfrtdtasllkLIEEKRNELNRLDEELARV 242
                                       4444444444333334444555666666666667999999999999988765 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0035
                      Exonuc_VII_L 162 rlleekkqrleklasrlkspeellerkrqrldeleerleralkkqlkkkrerleelkerl.k......ekleekk.. 229
                                       +l+eek+++l++l+++l++ ++ l++ ++++ ++++ l   l++    k+e+le+l+++l +            +  
  gi|557695051|ref|YP_008798105.1| 223 KLIEEKRNELNRLDEELARVRDTLQTLEEEVASARSLLLL-LQNPELVKKEDLETLSRQLaNlsnikaG-----Qmp 293
                                       4567777777777777777777777777777765555554.4444334555555555555334222221.....234 PP

                      Exonuc_VII_L 230 .......................................erlkklkerlelleekkerleeleeklealsplkvLkr 267
                                                                              +++k++++r ++lee++erl++  ++l+ ++p+++ + 
  gi|557695051|ref|YP_008798105.1| 294 elkalepsllenvrkrvvelvmpvirselvphwvfekleKEFKEVAARKAQLEEENERLRNELNQLRGTKPQTAVQA 370
                                       444444555555556666666666666666666664444666777777779**********************9997 PP

                      Exonuc_VII_L 268 Gyaivrkedgkvvtsakdlkkgdeleirla 297
                                          + r  + ++++++++l++++ ++i+l+
  gi|557695051|ref|YP_008798105.1| 371 VPQLPR--KFQLLKKKTELSTDSGIKIKLK 398
                                       655555..4688888888888888888876 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 ?   -1.1   0.4         3   1.9e+03      49      59 ..      57      67 ..      33     102 .. 0.52
   2 ?   10.9   8.1   0.00058      0.37      28      82 ..     104     158 ..      98     166 .. 0.82
   3 ?    2.2   6.8      0.29   1.8e+02      43      90 ..     150     197 ..     149     200 .. 0.51
   4 ?   11.2  17.2   0.00045      0.29      12     103 ..     195     283 ..     177     297 .. 0.76
   5 ?    2.3   3.0      0.27   1.7e+02      67      98 ..     329     360 ..     327     386 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 3
                             DHR10 49 lakleeakkkl 59
                                      l+k ++ +++l
  gi|557695051|ref|YP_008798105.1| 57 LEKRRKIEEDL 67
                                      22222222222 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00058
                             DHR10  28 lqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeer 82 
                                       l++v + ++++ +  +++ +  akleea+ +lke+++ +ee+e++l+e+e++ +r
  gi|557695051|ref|YP_008798105.1| 104 LAKVAAKVSETGTDFKQVFETFAKLEEAENRLKETQAMIEENEKRLEEVETELQR 158
                                       66666667777777778888899***********************999998776 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.29
                             DHR10  43 eeieaelakleeakkklkelrdaleekeielrelerkeerlqrqlena 90 
                                       ee+e+el++     ++++  +  +e+++++l++l ++ e+l+++ e  
  gi|557695051|ref|YP_008798105.1| 150 EEVETELQRKIARLREVSGVEPDIEKLSETLSKLRTEVELLEKREEEL 197
                                       566666666555555555555555555555555555555555554433 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00045
                             DHR10  12 aelErkarelqakidalqvvekdlrsciklleeieaelakleeakkklkelrdaleekeielrelerkeerlqrqle 88 
                                       +el +k++el   ++al  + +d +s++kl+ee  +el++l+e+    ++ rd+l+++e+e++   +   +lq    
  gi|557695051|ref|YP_008798105.1| 195 EELRQKNNELAREYEALLGFRTDTASLLKLIEEKRNELNRLDEEL---ARVRDTLQTLEEEVASARSLLLLLQNPEL 268
                                       56677888888899****************************985...56677777777777777777778888888 PP

                             DHR10  89 naeeklerlreqaee 103
                                        ++e le l +q ++
  gi|557695051|ref|YP_008798105.1| 269 VKKEDLETLSRQLAN 283
                                       888888888877665 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.27
                             DHR10  67 eekeielrelerkeerlqrqlenaeeklerlr 98 
                                       e++e+e +e+ +++++l+   e+ + +l++lr
  gi|557695051|ref|YP_008798105.1| 329 EKLEKEFKEVAARKAQLEEENERLRNELNQLR 360
                                       45566666666666666666666666665555 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 ?    2.8   0.1      0.14        92      66     167 ..      28     127 ..      25     130 .. 0.71
   2 ?    6.3   3.4     0.012       7.5      80     161 ..     107     187 ..     101     206 .. 0.62
   3 ?    3.5   0.1     0.089        57      80     141 ..     197     257 ..     191     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.14
                                       CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH CS
                         MCPsignal  66 qGrGFaVVAdEVrkLAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevad 142
                                       +G+ F V   E  k  + s +    i++l+ e  ++i++ +++  e ++ + e+++ v++  ++l++   +++++++
  gi|557695051|ref|YP_008798105.1|  28 YGKPFQVLFREYEKRFRDSVKLEYSINELL-EKRRKIEEDLRVYMEQQRLTLETVNRVNNIIRSLEKYGVNIGHLEN 103
                                       578888888888888888888888888988.5566677777777777777777888888888888888888887765 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 143 lvqeiaaaseeqsasieevnqavee 167
                                        +  +aa ++e  +  ++v +++++
  gi|557695051|ref|YP_008798105.1| 104 -LAKVAAKVSETGTDFKQVFETFAK 127
                                       .456777777777777776666555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  80 LAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsa 156
                                       +A++  ++  + +++  e  ++ +++ + l+et+  +ee  +  ee +++l++  ++  ev+ +  +i + se +s+
  gi|557695051|ref|YP_008798105.1| 107 VAAKVSETGTDFKQVF-ETFAKLEEAENRLKETQAMIEENEKRLEEVETELQRKIARLREVSGVEPDIEKLSETLSK 182
                                       4555555555566655.555666666666677777777777777777777766666666666666666666666666 PP

                                       HHHHH CS
                         MCPsignal 157 sieev 161
                                         +ev
  gi|557695051|ref|YP_008798105.1| 183 LRTEV 187
                                       55554 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.089
                                       HHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH CS
                         MCPsignal  80 LAersaqaakeiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaeva 141
                                       L ++  + a+e eal+     ++ + ++ +ee r++ +   e+ ++ +++l+++ e+va+  
  gi|557695051|ref|YP_008798105.1| 197 LRQKNNELAREYEALL-GFRTDTASLLKLIEEKRNELNRLDEELARVRDTLQTLEEEVASAR 257
                                       6778888899999999.889999999999999998887777777777777777776666654 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 ?   -1.4   0.0       4.7     3e+03      16      44 ..      20      48 ..      15      51 .. 0.85
   2 ?    7.8   1.4     0.006       3.9      21      90 .]     371     434 ..     258     434 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 4.7
                                      H-HHHHHHHHHHHHHHHHHCT---SSTCC CS
                              Rpr2 16 aspalsrylakqlrevskkaqlrlppsvk 44
                                      ++ +l ++++k ++ + ++++ r  +svk
  gi|557695051|ref|YP_008798105.1| 20 KLRQLEKQYGKPFQVLFREYEKRFRDSVK 48
                                      67899999999999999999999999887 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.006
                                       HHHHHHHHHHHHHHCT---SSTCCCTB.-TTT--B--CTTTEEEEEE-SSS-E.........EEEEETTTT CS
                              Rpr2  21 srylakqlrevskkaqlrlppsvkrtv.CkkCgsvlipgvtcsvrvenkskkkkkkkkkadvlvvtClaCg 90 
                                         +l ++++ + kk++l+ +  +k ++ C  C++  +  +  + ++e++ +       ++dvlv+tC +Cg
  gi|557695051|ref|YP_008798105.1| 371 VPQLPRKFQLLKKKTELSTDSGIKIKLkCVYCQNSSLMILPNKQELEEAAS-------SNDVLVTTCGSCG 434
                                       456667888888999999888887665588887666666666666654333.......3489********7 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  12.6    0.0016         1     120     221 ..     138     283 ..      41     305 .. 0.62
   2 ?    2.0   0.7      0.16     1e+02     137     172 ..     330     365 ..     304     391 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0016
                           DUF4407 120 akelkeqlaaa....................ltaelaeleaqiaalqaeidaaear...ldalraeaqkeldgtkgt 173
                                       +++  e+ ++                      ++++++l + +++l++e++ +e+r   l+++++e+++e++   g 
  gi|557695051|ref|YP_008798105.1| 138 TQAMIEENEKRleevetelqrkiarlrevsgVEPDIEKLSETLSKLRTEVELLEKReeeLRQKNNELAREYEALLGF 214
                                       22222222222111122222224444444444444444444444666666555444111444444444444433333 PP

                           DUF4407 174 gttgvaGkgpaakekkaqldaaqaelaelkakld......................atarlaalraelae 221
                                       + t +a   +  +ek+++l+++++ela ++++l+                      ++++l++l ++la 
  gi|557695051|ref|YP_008798105.1| 215 R-TDTASLLKLIEEKRNELNRLDEELARVRDTLQtleeevasarslllllqnpelvKKEDLETLSRQLAN 283
                                       3.22555666666677777777777777666666666666666666666655555555555555555555 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.16
                           DUF4407 137 eleaqiaalqaeidaaearldalraeaqkeldgtk.g 172
                                       +le++ ++  a  +++e++ ++lr+e++ +l gtk +
  gi|557695051|ref|YP_008798105.1| 330 KLEKEFKEVAARKAQLEEENERLRNELN-QLRGTKpQ 365
                                       4455555555555555555555555555.33333323 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       2.9   1.9e+03     237     261 ..      32      56 ..      22      66 .. 0.73
   2 ?    8.2  14.8    0.0023       1.5     112     232 ..      91     210 ..      49     213 .. 0.79
   3 ?    5.4   1.6     0.016        10     172     220 ..     195     243 ..     194     247 .. 0.90
   4 ?    7.5   3.7    0.0036       2.3     168     238 ..     233     303 ..     218     313 .. 0.90
   5 ?    3.7   0.6     0.054        35     189     224 ..     329     364 ..     318     367 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.9
                            Cluap1 237 LqelyeeYvekfrnlsylekqlekk 261
                                        q l++eY ++fr    le  +++ 
  gi|557695051|ref|YP_008798105.1|  32 FQVLFREYEKRFRDSVKLEYSINEL 56 
                                       6789999999999988888766553 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0023
                            Cluap1 112 eldlssklsdlkaarqlaseitekgasLydlLekevelreartkalsrqleleeiekalkeaikkvkeelektkkal 188
                                         +   ++  l++  ++a+++ e+g+   + +e+  +l ea ++  ++q  +ee ek+l+e  +++++++++++ ++
  gi|557695051|ref|YP_008798105.1|  91 LEKYGVNIGHLENLAKVAAKVSETGTDFKQVFETFAKLEEAENRLKETQAMIEENEKRLEEVETELQRKIARLR-EV 166
                                       34455567778888999*****************************************************9985.79 PP

                            Cluap1 189 enlesdeanLeakiekkkqeleraqkrLqslqsvrPafmdeyek 232
                                       + +e d ++L++ + k ++e+e  +kr ++l++       eye 
  gi|557695051|ref|YP_008798105.1| 167 SGVEPDIEKLSETLSKLRTEVELLEKREEELRQKNNELAREYEA 210
                                       9**************************99999877777777765 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.016
                            Cluap1 172 eaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqslq 220
                                       e++++ ++el++  +al   ++d a+L + ie k++el+r  + L+ ++
  gi|557695051|ref|YP_008798105.1| 195 EELRQKNNELAREYEALLGFRTDTASLLKLIEEKRNELNRLDEELARVR 243
                                       5678889999999999*************************99998775 PP

  == domain 4  score: 7.5 bits;  conditional E-value: 0.0036
                            Cluap1 168 kalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqslqsvrPafmdeyekleeeLq 238
                                       ++l e++ +v+++l+++++++++ +s    L++    kk++le  +++L++l +++   m e + le  L 
  gi|557695051|ref|YP_008798105.1| 233 NRLDEELARVRDTLQTLEEEVASARSLLLLLQNPELVKKEDLETLSRQLANLSNIKAGQMPELKALEPSLL 303
                                       5688999999999999999999999999999999999*****************************98875 PP

  == domain 5  score: 3.7 bits;  conditional E-value: 0.054
                            Cluap1 189 enlesdeanLeakiekkkqeleraqkrLqslqsvrP 224
                                       e+le++ ++++a+  + ++e er ++ L++l+ ++P
  gi|557695051|ref|YP_008798105.1| 329 EKLEKEFKEVAARKAQLEEENERLRNELNQLRGTKP 364
                                       677888888888888888888888888888888888 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.9      0.45   2.9e+02      39      75 ..      45      74 ..       9      97 .. 0.46
   2 ?    4.5   2.2     0.049        32      39      81 ..     117     162 ..      87     167 .. 0.58
   3 ?   -0.3   6.3       1.5   9.8e+02      63      82 ..     144     163 ..     121     209 .. 0.52
   4 ?   12.4   0.6   0.00019      0.12      22      78 ..     199     256 ..     196     264 .. 0.91
   5 ?    2.8   0.1      0.16     1e+02      41      73 ..     329     361 ..     320     372 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.45
                           DUF4446 39 dgksleellkekleeveelkeeseelekeieeleekl 75
                                      d  +le  ++e le+ ++++e+        +   e++
  gi|557695051|ref|YP_008798105.1| 45 DSVKLEYSINELLEKRRKIEEDL-------RVYMEQQ 74
                                      22333333333333333333333.......3333333 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.049
                           DUF4446  39 dgksleel...lkekleeveelkeeseelekeieeleeklkkslqk 81 
                                       d k++ e+   l+e  ++++e ++  ee+ek++ee+e++l++++ +
  gi|557695051|ref|YP_008798105.1| 117 DFKQVFETfakLEEAENRLKETQAMIEENEKRLEEVETELQRKIAR 162
                                       3333333300034444555555555667777777777777777665 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.5
                           DUF4446  63 elekeieeleeklkkslqkv 82 
                                       e+ek++ee+e++l++++ ++
  gi|557695051|ref|YP_008798105.1| 144 ENEKRLEEVETELQRKIARL 163
                                       44444444444444444332 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 0.00019
                           DUF4446  22 vklkklkkkykklmkgk.dgksleellkekleeveelkeeseelekeieeleeklkks 78 
                                        k ++l ++y++l+  + d +sl +l++ek +e+++l+ee +++++++++lee+++++
  gi|557695051|ref|YP_008798105.1| 199 QKNNELAREYEALLGFRtDTASLLKLIEEKRNELNRLDEELARVRDTLQTLEEEVASA 256
                                       57899**********665***********************************99875 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.16
                           DUF4446  41 ksleellkekleeveelkeeseelekeieelee 73 
                                       ++le+ +ke  ++  +l+ee+e+l++e+++l+ 
  gi|557695051|ref|YP_008798105.1| 329 EKLEKEFKEVAARKAQLEEENERLRNELNQLRG 361
                                       567788888888888888888888888887765 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 ?    1.5   0.6      0.58   3.7e+02      45      87 ..      52      94 ..      33     102 .. 0.74
   2 ?    4.9   1.8     0.051        33      31      91 ..     113     156 ..      95     161 .. 0.42
   3 ?    8.8   5.3     0.003       1.9      12      80 ..     184     252 ..     176     258 .. 0.49
   4 ?    3.9   0.2       0.1        65      23      55 ..     329     361 ..     325     384 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.58
                           BLOC1_2 45 slekkleklnekyeelqpylqqidqiekqvteLeeavseLDey 87
                                      s+++ lek ++ +e l+ y++q     ++v++  +++  L++y
  gi|557695051|ref|YP_008798105.1| 52 SINELLEKRRKIEEDLRVYMEQQRLTLETVNRVNNIIRSLEKY 94
                                      5667777777777788888888888888888888888888777 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.051
                           BLOC1_2  31 aasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeeavseLDeyskeL 91 
                                       ++ + +k++ +  a+le+  ++l+e+++ ++++ ++++++e+                 eL
  gi|557695051|ref|YP_008798105.1| 113 ETGTDFKQVFETFAKLEEAENRLKETQAMIEENEKRLEEVET-----------------EL 156
                                       223333333334444444444444444444444444444444.................33 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.003
                           BLOC1_2  12 eaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvteLeea 80 
                                       + e+e   +  + L + N++ +++y++l     ++++ l+ ++ek +el+ + +++ ++ +++++Lee 
  gi|557695051|ref|YP_008798105.1| 184 RTEVELLEKREEELRQKNNELAREYEALLGFRTDTASLLKLIEEKRNELNRLDEELARVRDTLQTLEEE 252
                                       333333444444445555555555555555555555555555555555555555555555555555544 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.1
                           BLOC1_2  23 klLeklNeaasekykklkdvaaslekkleklne 55 
                                       + Lek  ++++++ ++l+++ + l+++l++l+ 
  gi|557695051|ref|YP_008798105.1| 329 EKLEKEFKEVAARKAQLEEENERLRNELNQLRG 361
                                       445555556666666666666666666666655 PP

>> ACP_PD  Acyl carrier protein phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.3     0.084        54      64     102 ..      35      73 ..       8      75 .. 0.85
   2 ?    6.0   0.0     0.025        16      46     100 ..      71     126 ..      67     130 .. 0.88
   3 ?    3.7   0.7      0.13        82      49      99 ..     157     211 ..     126     213 .. 0.69
   4 ?   -1.8   0.0       6.7   4.3e+03      46      46 ..     262     262 ..     225     305 .. 0.55
   5 ?    1.0   0.1      0.87   5.5e+02       7      48 ..     333     376 ..     329     388 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.084
                            ACP_PD  64 alqrmarrlkrasklaeaieeleenyaeleadFleffpe 102
                                        +++ ++r++ + kl+ +i+el e+ +++e+d + ++++
  gi|557695051|ref|YP_008798105.1|  35 LFREYEKRFRDSVKLEYSINELLEKRRKIEEDLRVYMEQ 73 
                                       5667789*************************9988876 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.025
                            ACP_PD  46 mieedw.LesYaelegieralqrmarrlkrasklaeaieeleenyaeleadFleff 100
                                       m ++++ Le  + +++i r+l++    + + ++la+ ++++ e  +++++ F++f 
  gi|557695051|ref|YP_008798105.1|  71 MEQQRLtLETVNRVNNIIRSLEKYGVNIGHLENLAKVAAKVSETGTDFKQVFETFA 126
                                       66665448899999***************************************995 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.13
                            ACP_PD  49 edwLesYaelegieralqrmarrlkras....klaeaieeleenyaeleadFlef 99 
                                       ++ +++ +e++g+e  ++++++ l++       l++  eel+++ +el+++++++
  gi|557695051|ref|YP_008798105.1| 157 QRKIARLREVSGVEPDIEKLSETLSKLRteveLLEKREEELRQKNNELAREYEAL 211
                                       4566777888888888888885555444344348899999999999999998875 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 6.7
                            ACP_PD  46 m 46 
                                       +
  gi|557695051|ref|YP_008798105.1| 262 L 262
                                       2 PP

  == domain 5  score: 1.0 bits;  conditional E-value: 0.87
                            ACP_PD   7 rnwsey..saepLeefvqrvyaqlekneealPerlqrllprmie 48 
                                       ++++e    + +Lee  +r++++l++ + + P+ + +++p++ +
  gi|557695051|ref|YP_008798105.1| 333 KEFKEVaaRKAQLEEENERLRNELNQLRGTKPQTAVQAVPQLPR 376
                                       55555522355688889999999999999999999998888755 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   1.2      0.77   4.9e+02      27      74 ..      35      84 ..       3      93 .. 0.66
   2 ?   12.3  11.2   0.00024      0.15       1     101 [.     129     230 ..     129     231 .. 0.82
   3 ?    6.5   7.6     0.014       9.1      19      95 ..     185     259 ..     174     278 .. 0.67
   4 ?   -1.1   0.0       3.3   2.1e+03      17      40 ..     270     294 ..     256     309 .. 0.70
   5 ?    4.1   1.6     0.079        51       1      40 [.     329     369 ..     329     381 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.77
                              FliJ 27 yrqeyqkqlsgea.qglsaaelrnyqafi.saldeaiaqqkqelaqaekq 74
                                       ++ey+k+++++     s++el   ++ i + l+  ++qq+ +l+  +++
  gi|557695051|ref|YP_008798105.1| 35 LFREYEKRFRDSVkLEYSINELLEKRRKIeEDLRVYMEQQRLTLETVNRV 84
                                      45677777777774477777766655555145777777777777776665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00024
                              FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeai...aqqkqelaqaekq 74 
                                       +ea+++L+e q+ ++++e++lee+e ++q+   +l++ + g+++ ++ ++++ +s+l++++   ++ ++el q++++
  gi|557695051|ref|YP_008798105.1| 129 EEAENRLKETQAMIEENEKRLEEVETELQRKIARLREVS-GVEP-DIEKLSETLSKLRTEVellEKREEELRQKNNE 203
                                       79************************************9.5554.45666666666666651115677899999999 PP

                              FliJ  75 vekareewqearqerkklekLkerekk 101
                                       + +  e+++  r    +l kL+e++++
  gi|557695051|ref|YP_008798105.1| 204 LAREYEALLGFRTDTASLLKLIEEKRN 230
                                       999999999999999999999999886 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.014
                              FliJ  19 ekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqearqerkklekL 95 
                                        ++e le+  +e+  q+++e  + + ++l  ++   ++l + i++ ++el+++ +++ + r+ +q  + e+ + + L
  gi|557695051|ref|YP_008798105.1| 185 TEVELLEKREEEL-RQKNNEL-AREYEALLGFRTDTASLLKLIEEKRNELNRLDEELARVRDTLQTLEEEVASARSL 259
                                       4444444444444.3333333.3555666667777788888888999999999999999888888888888877665 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3.3
                              FliJ  17 aeekleeleqyrqeyqkqlsgea.q 40 
                                       ++e le l ++++++++ ++g++ +
  gi|557695051|ref|YP_008798105.1| 270 KKEDLETLSRQLANLSNIKAGQMpE 294
                                       5677788888888888887777733 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.079
                              FliJ   1 deaareLaeaqrelqqaeekleeleqyrqeyqkqlsgea.q 40 
                                       ++ ++e++e+ ++++q ee+ e+l++++++++  + ++a q
  gi|557695051|ref|YP_008798105.1| 329 EKLEKEFKEVAARKAQLEEENERLRNELNQLRGTKPQTAvQ 369
                                       67899999999999999999999999999999888877744 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       3.3   2.1e+03      24      61 ..      50      87 ..      43      94 .. 0.66
   2 ?    4.0   0.3      0.11        68      23      61 ..     107     145 ..     101     157 .. 0.54
   3 ?    7.5   0.5    0.0088       5.6      12      59 ..     141     188 ..     131     205 .. 0.83
   4 ?    6.0   0.4     0.026        17      30      66 ..     225     261 ..     218     270 .. 0.81
   5 ?    0.7   0.2       1.2   7.5e+02      41      56 ..     271     286 ..     262     325 .. 0.79
   6 ?   -0.1   0.1       2.1   1.4e+03      28      53 ..     329     354 ..     299     376 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 3.3
                           NPV_P10 24 qqqvddvqenlpdvte.lnekLdaqsaqLaeletkvenI 61
                                      + +++++ e+ ++++e l   +++q  +L++++  v+nI
  gi|557695051|ref|YP_008798105.1| 50 EYSINELLEKRRKIEEdLRVYMEQQRLTLETVNR-VNNI 87
                                      5566666666666654377778888888888764.5555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.11
                           NPV_P10  23 lqqqvddvqenlpdvtelnekLdaqsaqLaeletkvenI 61 
                                       + ++v +  +++++v e  +kL++  + L+e ++ +e+ 
  gi|557695051|ref|YP_008798105.1| 107 VAAKVSETGTDFKQVFETFAKLEEAENRLKETQAMIEEN 145
                                       445555556666666666666666666666665555543 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0088
                           NPV_P10  12 dikavddkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkve 59 
                                        i++ +++++ +++++++  + l++v+ ++  ++++s++L +l t+ve
  gi|557695051|ref|YP_008798105.1| 141 MIEENEKRLEEVETELQRKIARLREVSGVEPDIEKLSETLSKLRTEVE 188
                                       567777788888888888888888899999999999999999999997 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.026
                           NPV_P10  30 vqenlpdvtelnekLdaqsaqLaeletkvenIqdiLn 66 
                                       ++e+ ++++ l e+L +  ++L++le++v +  ++L 
  gi|557695051|ref|YP_008798105.1| 225 IEEKRNELNRLDEELARVRDTLQTLEEEVASARSLLL 261
                                       667778889999*****************99999886 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 1.2
                           NPV_P10  41 nekLdaqsaqLaelet 56 
                                       +e L+ +s qLa+l++
  gi|557695051|ref|YP_008798105.1| 271 KEDLETLSRQLANLSN 286
                                       4678888888888877 PP

  == domain 6  score: -0.1 bits;  conditional E-value: 2.1
                           NPV_P10  28 ddvqenlpdvtelnekLdaqsaqLae 53 
                                       +++++++++v   +++L++ ++ L +
  gi|557695051|ref|YP_008798105.1| 329 EKLEKEFKEVAARKAQLEEENERLRN 354
                                       55666666666666666666666543 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 ?    6.5  11.2     0.013       8.3       3     116 ..      53     164 ..      48     169 .. 0.61
   2 ?    1.9  17.3      0.34   2.2e+02       4     103 ..     174     276 ..     172     286 .. 0.74
   3 ?    7.6   1.5    0.0058       3.7      61      90 ..     330     359 ..     327     374 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.013
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkae 79 
                                       +++l e+  +++e+   + ++++   e ++   +i +  ++ Y   + + ++ +k  +++ e   + k+  +   a+
  gi|557695051|ref|YP_008798105.1|  53 INELLEKRRKIEEDLRVYMEQQRLTLETVNRVNNIIRSLEK-YGVNIGHLENLAKVAAKVSETGTDFKQVFE-TFAK 127
                                       56677777777777777777777777777777777777766.665554444444444444444444443333.3356 PP

                        TPR_MLP1_2  80 aesakaeleeseesweeqkeelekelselekriedln 116
                                       +e+a++ l+e ++ +ee +++le+  +el+++i  l 
  gi|557695051|ref|YP_008798105.1| 128 LEEAENRLKETQAMIEENEKRLEEVETELQRKIARLR 164
                                       6666666666666666666666666666666666554 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.34
                        TPR_MLP1_2   4 ksleeeikslkeekeeaeaklqklqedlekqaeiakea...qqkYerelvkhaedvkelqalreelnelkaeiaelk 77 
                                       ++l e++++l++e e +e+++++l+++ ++ a+++++      + ++ l + +e  +el++l eel+++++++++l+
  gi|557695051|ref|YP_008798105.1| 174 EKLSETLSKLRTEVELLEKREEELRQKNNELAREYEALlgfRTDTASLLKLIEEKRNELNRLDEELARVRDTLQTLE 250
                                       56667777777777777777777777777777666653222666777999999999999999999999999999999 PP

                        TPR_MLP1_2  78 aeaesakaeleeseesweeqkeelek 103
                                       +e+ sa++ l   ++    +ke le+
  gi|557695051|ref|YP_008798105.1| 251 EEVASARSLLLLLQNPELVKKEDLET 276
                                       99999999988877777777776665 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0058
                        TPR_MLP1_2  61 alreelnelkaeiaelkaeaesakaelees 90 
                                       +l +e++e+ a+ a+l++e+e++++el++ 
  gi|557695051|ref|YP_008798105.1| 330 KLEKEFKEVAARKAQLEEENERLRNELNQL 359
                                       667777777777777777777777777765 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   2.3      0.55   3.5e+02      43     112 ..      22      77 ..       2      95 .. 0.42
   2 ?   10.4  11.8   0.00098      0.63       6      92 ..     117     206 ..     116     214 .. 0.75
   3 ?    7.8   1.0    0.0062         4      11     101 ..     222     313 ..     208     321 .. 0.54
   4 ?    5.3   2.3     0.036        23      22      72 ..     329     378 ..     326     392 .. 0.48

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.55
                                       HHHHHHHHHHTTTS.-HHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-S CS
                              OmpH  43 qklqeelqkkakklekeekeqe.lqkkeqelqqkqqqkaqelqkkqqellkpildkinkaikevakekgyd 112
                                       ++l             e+++ + +q + +e+++ + ++  +l+   +ell++   ki++ ++ +++++ ++
  gi|557695051|ref|YP_008798105.1|  22 RQL-------------EKQYGKpFQVLFREYEK-RFRDSVKLEYSINELLEK-RRKIEEDLRVYMEQQRLT 77 
                                       111.............12222233333333333.222223333333333332.344444444444444333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00098
                                       -HHHHHHHSHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHTTTS....-HHHHHHHHHHHHHHHHHH CS
                              OmpH   6 dvqkileespegkaaqeqlekkf...kklqaeleakekelqklqeelqkkakkle...keekeqelqkkeqelqqkq 76 
                                       d+++++e++ + ++a+++l++++   ++ ++ le+ e+elq+++++l + +        e+  + l k+++e++  +
  gi|557695051|ref|YP_008798105.1| 117 DFKQVFETFAKLEEAENRLKETQamiEENEKRLEEVETELQRKIARLREVSG--VepdIEKLSETLSKLRTEVEL-L 190
                                       7788999999999999988777766689999999999999999999974333..146677777778888888888.7 PP

                                       HHHHHHHHHHHHHHHH CS
                              OmpH  77 qqkaqelqkkqqellk 92 
                                       +++++el++k++el +
  gi|557695051|ref|YP_008798105.1| 191 EKREEELRQKNNELAR 206
                                       7777888888888765 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0062
                                       HHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.................-HHHHHHHHHHHHH CS
                              OmpH  11 leespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkle................keekeqelqkkeqe 71 
                                       l              k +++ ++el+++ +el + +++lq+ +++                  k+e+ + l ++ ++
  gi|557695051|ref|YP_008798105.1| 222 L--------------KLIEEKRNELNRLDEELARVRDTLQTLEEE-VasarslllllqnpelvKKEDLETLSRQLAN 283
                                       3..............444444555555555555555544432222.1234445556666644455555555555555 PP

                                       HHHHHHHHH.HHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  72 lqqkqqqka.qelqkkqqellkpildkinka 101
                                       l + ++  +  el++ +  ll+++ +++ + 
  gi|557695051|ref|YP_008798105.1| 284 LSNIKAG-QmPELKALEPSLLENVRKRVVEL 313
                                       5553333.24777777777777777776665 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.036
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHH CS
                              OmpH  22 eqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqel 72 
                                       e+lek+fk+ +a  +++e+e ++l++el++   ++  +++ q++ ++ +++
  gi|557695051|ref|YP_008798105.1| 329 EKLEKEFKEVAARKAQLEEENERLRNELNQLRGTK-PQTAVQAVPQLPRKF 378
                                       45666665544444444444444444444222332.344444444444444 PP

>> Snapin_Pallidin  Snapin/Pallidin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4      0.65   4.2e+02      26      59 ..      61      95 ..      48     123 .. 0.65
   2 ?    3.2   1.9      0.19   1.2e+02      59      88 ..     122     151 ..      99     167 .. 0.50
   3 ?    3.6   8.7      0.14        88      11      87 ..     131     202 ..     123     204 .. 0.83
   4 ?    8.0   5.8    0.0061       3.9      11      86 ..     176     253 ..     173     255 .. 0.88
   5 ?    4.2   0.4     0.088        56      34      75 ..     272     313 ..     262     315 .. 0.86
   6 ?    7.8   0.4    0.0069       4.4      15      71 ..     328     384 ..     323     393 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.65
                   Snapin_Pallidin 26 rqsQeeLleqldrlnekLkeleeaqe.aevlpdlk 59
                                      r+  e+L+  +++++  L+ ++++++   +l++  
  gi|557695051|ref|YP_008798105.1| 61 RKIEEDLRVYMEQQRLTLETVNRVNNiIRSLEKYG 95
                                      55567788888888888888888888444444444 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.19
                   Snapin_Pallidin  59 keyakKLvnikkrmsslnerlqklkkRaek 88 
                                        e  +KL ++++r+++ +  +++ +kR+e+
  gi|557695051|ref|YP_008798105.1| 122 FETFAKLEEAENRLKETQAMIEENEKRLEE 151
                                       333344444444444444444444444433 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.14
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkrmsslnerlqklkkRae 87 
                                        e  l+e+++ ++e ++  ee+  +l+r  ++L+e++ +++     d+++  + L++++ +++ l++r ++l+++ +
  gi|557695051|ref|YP_008798105.1| 131 AENRLKETQAMIEENEKRLEEVETELQRKIARLREVSGVEP-----DIEKLSETLSKLRTEVELLEKREEELRQKNN 202
                                       56778888888888888888999999999999998888888.....99999999999999***99999999888765 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.0061
                   Snapin_Pallidin  11 lepkldeldeklkelrqsQeeLleqldrlnekLkeleeaqe..aevlpdlkeyakKLvnikkrmsslnerlqklkkR 85 
                                       l+ +l +l+++++ l++  eeL+++ ++l+++++ l       a++l+ ++e ++ L+++  ++ ++ ++lq+l++ 
  gi|557695051|ref|YP_008798105.1| 176 LSETLSKLRTEVELLEKREEELRQKNNELAREYEALLGFRTdtASLLKLIEEKRNELNRLDEELARVRDTLQTLEEE 252
                                       678999******************999999999998876554778888899999*******************9986 PP

                   Snapin_Pallidin  86 a 86 
                                       +
  gi|557695051|ref|YP_008798105.1| 253 V 253
                                       5 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.088
                   Snapin_Pallidin  34 eqldrlnekLkeleeaqeaevlpdlkeya.kKLvnikkrmssl 75 
                                       e+l++l+++L++l++++   ++p+lk      L n++kr+ +l
  gi|557695051|ref|YP_008798105.1| 272 EDLETLSRQLANLSNIKA-GQMPELKALEpSLLENVRKRVVEL 313
                                       789*************99.778888877758889999999765 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0069
                   Snapin_Pallidin  15 ldeldeklkelrqsQeeLleqldrlnekLkeleeaqeaevlpdlkeyakKLvnikkr 71 
                                        ++l++++ke+ +   +L e+ +rl+++L++l+ ++++ +++ +++  +K + +kk+
  gi|557695051|ref|YP_008798105.1| 328 FEKLEKEFKEVAARKAQLEEENERLRNELNQLRGTKPQTAVQAVPQLPRKFQLLKKK 384
                                       68999***************************9999988888888888888777775 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 ?    2.5   2.5      0.26   1.7e+02       7      95 ..      36     130 ..      19     131 .. 0.75
   2 ?    7.2   8.3     0.009       5.8       9      98 ..     102     188 ..      88     191 .. 0.86
   3 ?   13.7   6.4   8.4e-05     0.054      26     100 ..     175     249 ..     169     254 .. 0.93
   4 ?   -1.6   0.0       4.8   3.1e+03      15      70 ..     270     275 ..     260     306 .. 0.56
   5 ?    4.9   0.4     0.046        30      71     100 ..     330     359 ..     318     390 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.26
                                       HHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTT......S-TCCCCCCCH CS
                      Seryl_tRNA_N   7 irenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkk......edaeeliaevk 77 
                                       +re  + +++++k     ++++++  +++e  r  + +     +  N++++ I ++ k +      e+ +++ a+v+
  gi|557695051|ref|YP_008798105.1|  36 FREYEKRFRDSVKLEYSINELLEKRRKIEEDLRVYMEQQRLTLETVNRVNNIIRSLEKYGvnighlENLAKVAAKVS 112
                                       45555555556655556666666666667776666666667777889999999999888888888888888889999 PP

                                       HHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  78 elkeelkaleaelkelea 95 
                                       e ++++k++ ++ ++le+
  gi|557695051|ref|YP_008798105.1| 113 ETGTDFKQVFETFAKLEE 130
                                       999988888888887775 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.009
                                       H-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHH CS
                      Seryl_tRNA_N   9 enpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelka 85 
                                       en+++v++k+ +      d+++++e  +k +e++++l e qa   e  k  ++   + + + + + ev+ +  ++++
  gi|557695051|ref|YP_008798105.1| 102 ENLAKVAAKVSET---GTDFKQVFETFAKLEEAENRLKETQAMIEENEKRLEEVETELQRKIARLREVSGVEPDIEK 175
                                       5777777777655...5889999999999999999999999999999999999999998888889999999999999 PP

                                       HHHHHHHHHHHHH CS
                      Seryl_tRNA_N  86 leaelkeleaele 98 
                                       l+++l++l++e+e
  gi|557695051|ref|YP_008798105.1| 176 LSETLSKLRTEVE 188
                                       9999999998876 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 8.4e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  26 advdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaelekl 100
                                       ++ ++l +l ++ + l+++ eel+++ Nel++e + +     d+++l++ ++e  +el++l++el+ +++ l++l
  gi|557695051|ref|YP_008798105.1| 175 KLSETLSKLRTEVELLEKREEELRQKNNELAREYEALLGFRTDTASLLKLIEEKRNELNRLDEELARVRDTLQTL 249
                                       56788999*******************************99****************************999976 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 4.8
                                       HHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TC CS
                      Seryl_tRNA_N  15 keklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedae 70 
                                       k+                                                  ed e
  gi|557695051|ref|YP_008798105.1| 270 KK--------------------------------------------------EDLE 275
                                       43..................................................3333 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.046
                                       CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  71 eliaevkelkeelkaleaelkeleaelekl 100
                                       +l +e ke+ ++ ++le+e + l++el++l
  gi|557695051|ref|YP_008798105.1| 330 KLEKEFKEVAARKAQLEEENERLRNELNQL 359
                                       455555566666666666666666655554 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7  31.0     0.022        14     218     423 ..      71     281 ..      48     322 .. 0.51
   2 ?    4.4   1.5     0.014       8.6      96     151 ..     328     384 ..     319     391 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.022
                                       TTTTTTSHHHHHHHHHHHHHSTTS--SGGGS....SSSSHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHH...HHH CS
                              EzrA 218 eelkkelpkqleelkegykemkeegYaleel....niekeieelekkieeilerlkeleledveeelktie...eei 287
                                        e + +  + ++ ++++++ +++ g ++ +l    ++  +++e+ ++ ++++e  ++l  e++e+ lk+++   ee 
  gi|557695051|ref|YP_008798105.1|  71 MEQQRLTLETVNRVNNIIRSLEKYGVNIGHLenlaKVAAKVSETGTDFKQVFETFAKL--EEAENRLKETQamiEEN 145
                                       3333334444555555555555555555554311222233333333333333333333..33333333333000333 PP

                                       HHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-TTTS-G.GGSSTTTSTTHHHHHHHHHHHHHHHHHH CS
                              EzrA 288 dsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeldrlkqs.YeLseeeleklrelekelkelekdyeel 363
                                       ++  +  e+E + k    ++++ ++  +e+l + +++l++e++ l+++  eL +++ e +re+e  l   ++d  +l
  gi|557695051|ref|YP_008798105.1| 146 EKRLEEVETELQRKIARLREVSGVEPDIEKLSETLSKLRTEVELLEKReEELRQKNNELAREYE-ALLGFRTDTASL 221
                                       3344444455555555555555555555555555555555555554431345555555555555.455555555555 PP

                                       HHHHS-SS---STTGGGTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EzrA 364 eekleekkvaYSelqeeleeleekleeieekqeeileslkslrkdEkrAreqldeikkel 423
                                        + +eek     +l eel ++ ++l+++ee++ + +  l  l++ E+  +e l++++++l
  gi|557695051|ref|YP_008798105.1| 222 LKLIEEKRNELNRLDEELARVRDTLQTLEEEVASARSLLLLLQNPELVKKEDLETLSRQL 281
                                       555555555555555555555555555555555555555555555555555555555555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.014
                                       HHHTTHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTTTTTH.HHHHHHHHHHHHHHHT CS
                              EzrA  96 fkkakkklaeleeeldeveekikkileelkelteseeknr.eeieklkekYrelrkk 151
                                       f k++k+ +e+ ++ +++ee+ +++++el++l+  + +   +++ +l  k++ l+kk
  gi|557695051|ref|YP_008798105.1| 328 FEKLEKEFKEVAARKAQLEEENERLRNELNQLRGTKPQTAvQAVPQLPRKFQLLKKK 384
                                       555556666666666666666666666666665544333314455555555555555 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1         1   6.5e+02      53      96 ..      64     107 ..      49     121 .. 0.73
   2 ?    8.0   2.7    0.0042       2.7     133     176 ..     120     163 ..     117     176 .. 0.91
   3 ?    4.3   1.1     0.057        37      55     100 ..     224     269 ..     183     273 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 1
                    Halogen_Hydrol  53 lkksglsrkelkyiretlkeakekikrlekalkrvrslevikqv 96 
                                       +++  +  +++++  et++   + i++lek+  ++ +le +++v
  gi|557695051|ref|YP_008798105.1|  64 EEDLRVYMEQQRLTLETVNRVNNIIRSLEKYGVNIGHLENLAKV 107
                                       44444445566777788888888888888888888888877666 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0042
                    Halogen_Hydrol 133 eltekYaeLskqpvksketrealeetrqlLdelaealekdlqkl 176
                                       ++ e +a+L++++++ ket+  +ee+++ L+e++ +l+++  +l
  gi|557695051|ref|YP_008798105.1| 120 QVFETFAKLEEAENRLKETQAMIEENEKRLEEVETELQRKIARL 163
                                       57899*******************************99988766 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.057
                    Halogen_Hydrol  55 ksglsrkelkyiretlkeakekikrlekalkrvrslevikqvreil 100
                                         + +r+el+ ++e l+  ++ +++le++  ++rsl ++ q+ e++
  gi|557695051|ref|YP_008798105.1| 224 LIEEKRNELNRLDEELARVRDTLQTLEEEVASARSLLLLLQNPELV 269
                                       4566788999999999999999999999999999988888877766 PP

>> Flagellin_C  Bacterial flagellin C-terminal helical region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.1    0.0037       2.4      23      50 ..     126     153 ..     101     162 .. 0.88
   2 ?    0.0   0.2       1.7   1.1e+03      23      48 ..     174     199 ..     172     202 .. 0.89
   3 ?   -0.6   0.0       2.8   1.8e+03       7      33 ..     334     360 ..     328     373 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0037
                                       HHHHHHHHHHHHHHCHHHHHHCHHCCHH CS
                       Flagellin_C  23 nRlesaitnlkaqsenlkaaesrledvD 50 
                                       ++le+a ++lk ++ +++++e+rle+v 
  gi|557695051|ref|YP_008798105.1| 126 AKLEEAENRLKETQAMIEENEKRLEEVE 153
                                       5799999*****************9985 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHHHHCHHHHHHCHHCC CS
                       Flagellin_C  23 nRlesaitnlkaqsenlkaaesrled 48 
                                       ++l+++ ++l + +e+l+++e++l++
  gi|557695051|ref|YP_008798105.1| 174 EKLSETLSKLRTEVELLEKREEELRQ 199
                                       68999999**********99999875 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.8
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Flagellin_C   7 aitdldkvrselGavqnRlesaitnlk 33 
                                         +++++ +++l    +Rl +  ++l 
  gi|557695051|ref|YP_008798105.1| 334 EFKEVAARKAQLEEENERLRNELNQLR 360
                                       455555555555555555555555554 PP

>> IpaC_SipC  Salmonella-Shigella invasin protein C (IpaC_SipC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   4.0    0.0015      0.97     153     254 ..     133     236 ..     106     249 .. 0.89
   2 ?   -2.2   0.2       3.5   2.3e+03     165     187 ..     338     360 ..     330     379 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0015
                         IpaC_SipC 153 kglseergalkknlaklakLkkesaevkleLnkqnkvklsadevsevkikrnagtsvlek..leldssneklsdeHk 227
                                       + l+e +  +++n ++l++ ++e++ + + L++   v+   +++se   k  +  + lek   el + n++l++e +
  gi|557695051|ref|YP_008798105.1| 133 NRLKETQAMIEENEKRLEEVETELQRKIARLREVSGVEPDIEKLSETLSKLRTEVELLEKreEELRQKNNELAREYE 209
                                       668899999****************************99999****999999999999762258************* PP

                         IpaC_SipC 228 avLsseaeslqdkidleqlameenklk 254
                                       a L+ ++        +e+++ e n+l+
  gi|557695051|ref|YP_008798105.1| 210 ALLGFRTDTASLLKLIEEKRNELNRLD 236
                                       ****99988887777888888888886 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 3.5
                         IpaC_SipC 165 nlaklakLkkesaevkleLnkqn 187
                                        +a+ a+L++e++  ++eLn+  
  gi|557695051|ref|YP_008798105.1| 338 VAARKAQLEEENERLRNELNQLR 360
                                       45566667777766666666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2263  (0.12622); expected 358.6 (0.02)
Passed bias filter:                      806  (0.0449551); expected 358.6 (0.02)
Passed Vit filter:                       179  (0.00998383); expected 17.9 (0.001)
Passed Fwd filter:                       111  (0.00619109); 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: 1.71u 0.34s 00:00:02.04 Elapsed: 00:00:00.58
# Mc/sec: 2330.51
//
Query:       gi|557695052|ref|YP_008798106.1|  [L=125]
Description: hypothetical protein CSUB_C1625 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 909.29
//
Query:       gi|557695053|ref|YP_008798107.1|  [L=142]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-17   62.9   0.0    6.8e-17   61.3   0.0    1.7  1  Hjc            Archaeal holliday junction resolvase (hjc)
     0.0044   16.6   0.0     0.0065   16.0   0.0    1.4  1  AHJR-like      REase_AHJR-like
  ------ inclusion threshold ------
      0.021   14.2   0.1      0.031   13.7   0.1    1.3  1  zf-ribbon_3    zinc-ribbon domain
       0.16   12.1   0.1       0.25   11.4   0.1    1.3  1  DUF1272        Protein of unknown function (DUF1272)
       0.16   11.9   0.1        0.3   11.1   0.1    1.4  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
       0.17   11.6   0.0        0.2   11.3   0.0    1.1  1  MmcB-like      DNA repair protein MmcB-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 !   61.3   0.0   2.3e-20   6.8e-17      10      90 ..      32     123 ..      25     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 2.3e-20
                                       HHHTT-EEEEBSCSSSSSSSS-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHH.......TC....EE CS
                               Hjc  10 LrergfavvRsagSggatkplpDviAirgdvvlviEvKsskkeriylkkeqvekllefarka.......gg....el 75 
                                        +e+gf++vR +gSg ++   pD+iA+ ++++l+iEvKss+k+    ++eqv +ll+f +++       gg    ++
  gi|557695053|ref|YP_008798107.1|  32 VEENGFYAVRTPGSGTGKMAKPDIIAVDKGELLAIEVKSSSKDYAAFSAEQVGRLLKFVERFmivcphcGGkihpKP 108
                                       5799*************88*******************************************666666632222256 PP

                                       EEEEEETTTEEEEEE CS
                               Hjc  76 llavklqgkewkllv 90 
                                       + av++ g+ w+++ 
  gi|557695053|ref|YP_008798107.1| 109 VAAVRFVGRGWEFID 123
                                       778888888888776 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.2e-06    0.0065      44      80 ..      52      91 ..      22      97 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-06
                         AHJR-like 44 rpDliarkdeeaviiEvksrrs...saseqyLqelakave 80
                                      +pD+ia  + e ++iEvks+++   + s ++  +l k ve
  gi|557695053|ref|YP_008798107.1| 52 KPDIIAVDKGELLAIEVKSSSKdyaAFSAEQVGRLLKFVE 91
                                      8******************998666677777777777776 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     1e-05     0.031      16      26 .]      94     104 ..      88     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1e-05
                       zf-ribbon_3  16 dnvCpyCGtkl 26 
                                       ++vCp+CG+k+
  gi|557695053|ref|YP_008798107.1|  94 MIVCPHCGGKI 104
                                       799*****986 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   8.5e-05      0.25      40      56 ..      93     109 ..      89     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.5e-05
                           DUF1272  40 lenvCPncgGelvkRPi 56 
                                       +  vCP cgG++ ++P+
  gi|557695053|ref|YP_008798107.1|  93 FMIVCPHCGGKIHPKPV 109
                                       5679**********996 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 ?   11.1   0.1   9.9e-05       0.3      19      32 ..      95     109 ..      88     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.9e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayri 32 
                                        vCPhCg++ ++  +
  gi|557695053|ref|YP_008798107.1|  95 IVCPHCGGKiHPKPV 109
                                       58*****99877655 PP

>> MmcB-like  DNA repair protein MmcB-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.6e-05       0.2      43      69 ..      52      77 ..      32      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.6e-05
                         MmcB-like 43 raDlvalskkgeiwiieikssveDfrt 69
                                      + D++a++ kge+  ie+kss +D+ +
  gi|557695053|ref|YP_008798107.1| 52 KPDIIAVD-KGELLAIEVKSSSKDYAA 77
                                      45999996.79*************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 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:                        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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 969.69
//
Query:       gi|557695054|ref|YP_008798108.1|  [L=148]
Description: transcriptional regulator, AsnC family [Candidatus Caldiarchaeum subterraneum]
Scores for 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   57.5   0.0    1.6e-15   56.6   0.0    1.5  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    3.4e-15   55.3   0.0    1.1e-13   50.5   0.0    2.5  2  HTH_24           Winged helix-turn-helix DNA-binding
    1.4e-12   47.4   0.0    1.9e-12   46.9   0.0    1.2  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    2.3e-05   24.4   0.0    7.6e-05   22.7   0.0    1.8  2  HTH_20           Helix-turn-helix domain
      6e-05   22.9   0.0     0.0034   17.2   0.0    2.4  2  TrmB             Sugar-specific transcriptional regulator Trm
    7.3e-05   22.4   0.3    0.00035   20.3   0.0    2.1  2  HTH_DeoR         DeoR-like helix-turn-helix domain
    7.8e-05   22.5   0.0    0.00077   19.3   0.0    2.5  3  HTH_5            Bacterial regulatory protein, arsR family
    0.00022   20.6   0.0      0.025   14.0   0.0    2.4  2  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
     0.0003   20.8   0.1    0.00047   20.2   0.1    1.2  1  NapD             NapD protein
    0.00038   20.3   0.0      0.011   15.5   0.0    2.3  2  MarR_2           MarR family
    0.00079   19.5   0.0     0.0012   19.0   0.0    1.3  1  AsnC_trans_reg2  AsnC-like ligand binding domain
     0.0016   17.9   0.0       0.03   13.9   0.0    2.5  2  Sigma70_r4       Sigma-70, region 4
     0.0023   17.9   1.1     0.0067   16.4   0.0    2.2  3  HTH_11           HTH domain
     0.0027   17.6   0.1      0.049   13.6   0.0    2.2  2  MarR             MarR family
     0.0032   17.2   0.0      0.034   13.9   0.0    2.3  2  HTH_38           Helix-turn-helix domain
     0.0036   17.1   0.0      0.045   13.6   0.0    2.4  2  HTH_IclR         IclR helix-turn-helix domain
     0.0048   16.5   0.0      0.012   15.3   0.0    1.7  1  Sigma70_r4_2     Sigma-70, region 4
     0.0057   16.6   0.0      0.063   13.2   0.0    2.3  2  HTH_36           Helix-turn-helix domain
     0.0066   16.4   0.0        1.5    8.8   0.0    2.3  2  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0069   16.4   0.0      0.072   13.2   0.0    2.2  2  FeoC             FeoC like transcriptional regulator
     0.0071   16.1   0.0      0.029   14.2   0.0    2.0  2  HTH_23           Homeodomain-like domain
  ------ inclusion threshold ------
      0.012   15.7   0.0        3.8    7.6   0.0    3.1  3  HTH_29           Winged helix-turn helix
      0.012   16.2   2.5       0.21   12.2   0.1    2.8  2  ACT_4            ACT domain
      0.014   15.3   0.7        1.2    9.0   0.0    2.3  2  TFIIE_alpha      TFIIE alpha subunit
      0.015   15.3   0.0      0.046   13.8   0.0    1.8  1  HTH_Mga          M protein trans-acting positive regulator (M
      0.022   14.3   0.0      0.097   12.2   0.0    2.0  3  GerE             Bacterial regulatory proteins, luxR family
      0.031   14.9   0.0       0.17   12.5   0.0    2.1  2  Mga              Mga helix-turn-helix domain
      0.047   13.3   0.1        1.9    8.2   0.0    2.3  2  CENP-B_N         CENP-B N-terminal DNA-binding domain
      0.055   13.7   0.0        1.2    9.4   0.0    2.2  2  Myb_DNA-binding  Myb-like DNA-binding domain
       0.06   13.7   0.0       0.17   12.3   0.0    1.7  1  FaeA             FaeA-like protein
      0.073   13.4   0.1        1.4    9.3   0.0    2.5  3  Rrf2             Transcriptional regulator
       0.12   12.9   0.1       0.24   11.9   0.1    1.5  1  DUF4089          Protein of unknown function (DUF4089)
       0.16   12.1   0.0       0.94    9.7   0.0    2.2  2  HTH_28           Helix-turn-helix domain


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 !   56.6   0.0     3e-18   1.6e-15       2      41 ..       3      42 ..       1      43 [. 0.98

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 3e-18
                     HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      De+D+kIL++L ed+R+s+a++++++G+Se+tv+ R ++L
  gi|557695054|ref|YP_008798108.1|  3 DELDLKILNILFEDGRASFADIGRKLGVSENTVRFRFQKL 42
                                      **************************************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 !   50.5   0.0   2.1e-16   1.1e-13       2      48 .]       3      49 ..       2      49 .. 0.98
   2 ?    2.3   0.0      0.23   1.3e+02      25      43 ..      68      86 ..      64      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 2.1e-16
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      de+d+kIL++L +++r s +++ ++lg+S +tv+ r ++L++ G+I+
  gi|557695054|ref|YP_008798108.1|  3 DELDLKILNILFEDGRASFADIGRKLGVSENTVRFRFQKLVKTGVIR 49
                                      89********************************************7 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.23
                            HTH_24 25 erlglSpstvnrrlkrLee 43
                                       +l + p+ +nr l++L++
  gi|557695054|ref|YP_008798108.1| 68 LMLKIDPTKINRVLDELKQ 86
                                      5799***********9975 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 !   46.9   0.0   3.6e-15   1.9e-12       3      74 ..      70     137 ..      68     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 3.6e-15
                                       EEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   3 vslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       ++++p +   ++++ ++l++l e+  +y+++Gd+d ++ ++ rdl+++++++++ + ++pg+ +++t++ l+
  gi|557695054|ref|YP_008798108.1|  70 LKIDPTK---INRVLDELKQLREIANIYQLSGDFDAIAVAYGRDLDHIREIVEQ-IKKIPGIISVNTLVTLR 137
                                       6778888...9****************************************999.**************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 !   22.7   0.0   1.4e-07   7.6e-05      11      58 ..       5      52 ..       1      54 [. 0.92
   2 ?   -1.4   0.0       4.7   2.5e+03      39      51 ..      78      91 ..      67      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.4e-07
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEEC CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvr 58
                                        ++il  L +++ ++++++ + l++s nt+++++++L++ g ++ v+
  gi|557695054|ref|YP_008798108.1|  5 LDLKILNILFEDGRASFADIGRKLGVSENTVRFRFQKLVKTGVIRKVT 52
                                      5589999999**********************************9987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.7
                                      HHHHHHHHHHHH.C CS
                            HTH_20 39 ntlsyHLrvLee.a 51
                                      n + + L++L+e a
  gi|557695054|ref|YP_008798108.1| 78 NRVLDELKQLREiA 91
                                      55778888888855 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   6.3e-06    0.0034       8      55 ..       4      51 ..       2      59 .. 0.94
   2 ?    3.3   0.0      0.14        78      31      47 ..      69      85 ..      58      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.3e-06
                                      HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB  8 eyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      e + k+   L + g+a+  +i ++lgv++++v    ++L++ G+++++
  gi|557695054|ref|YP_008798108.1|  4 ELDLKILNILFEDGRASFADIGRKLGVSENTVRFRFQKLVKTGVIRKV 51
                                      788999999************************************987 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                                      CTTSSCHCHHHHHHHHH CS
                              TrmB 31 elgvprskvYevLrsLe 47
                                      +l+++ +k+++vL +L+
  gi|557695054|ref|YP_008798108.1| 69 MLKIDPTKINRVLDELK 85
                                      6899*********9997 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 !   20.3   0.0   6.4e-07   0.00035       4      47 ..       8      51 ..       6      52 .. 0.95
   2 ?   -1.1   0.0       2.9   1.6e+03       4      18 ..     116     131 ..     108     139 .. 0.53

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.4e-07
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                      +il  l ++g  s  ++   lgvSe+T+R  +++L++ g+++++
  gi|557695054|ref|YP_008798108.1|  8 KILNILFEDGRASFADIGRKLGVSENTVRFRFQKLVKTGVIRKV 51
                                      79999***********************************9986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.9
                          HTH_DeoR   4 qilellkq.qgklsve 18 
                                       +i+e +k+  g +sv+
  gi|557695054|ref|YP_008798108.1| 116 EIVEQIKKiPGIISVN 131
                                       3444443313445555 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 !   19.3   0.0   1.4e-06   0.00077       5      47 .]       7      50 ..       3      50 .. 0.95
   2 ?   -1.6   0.0       4.7   2.5e+03      36      40 ..      84      88 ..      69      97 .. 0.62
   3 ?   -0.6   0.0       2.3   1.2e+03      18      33 ..     114     129 ..     113     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.4e-06
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      lkIL++L e g +++ ++ ++lg+s+ tv+  + kL + G+++k
  gi|557695054|ref|YP_008798108.1|  7 LKILNILFEdGRASFADIGRKLGVSENTVRFRFQKLVKTGVIRK 50
                                      8***************************************9986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4.7
                                      HHHHH CS
                             HTH_5 36 LkkLr 40
                                      Lk+Lr
  gi|557695054|ref|YP_008798108.1| 84 LKQLR 88
                                      33333 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 2.3
                                       HHHHHHHHTS-HHHHH CS
                             HTH_5  18 vcelaeelglsqstvS 33 
                                       + e++e++++ ++++S
  gi|557695054|ref|YP_008798108.1| 114 IREIVEQIKKIPGIIS 129
                                       5799999999999998 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 !   14.0   0.0   4.6e-05     0.025      27      48 ..      18      39 ..       9      43 .. 0.84
   2 ?    4.4   0.0     0.046        25      32      50 ..      65      83 ..      63      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.6e-05
                      HTH_Tnp_ISL3 27 srsvkavArqlgvSwtTVwril 48
                                      ++s++++ r lgvS++TV+ ++
  gi|557695054|ref|YP_008798108.1| 18 RASFADIGRKLGVSENTVRFRF 39
                                      38****************8655 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.046
                      HTH_Tnp_ISL3 32 avArqlgvSwtTVwrildr 50
                                      ++A +l +++t ++r+ld+
  gi|557695054|ref|YP_008798108.1| 65 SAALMLKIDPTKINRVLDE 83
                                      689**************97 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   8.7e-07   0.00047       6      68 ..      68     131 ..      66     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 8.7e-07
                              NapD   6 lvVqarperlaavkaalaalpg.vEvhasdeegklVvviEaesedeladtieaiealpgVlsas 68 
                                       l  +++p ++++v+++l++l + + +++ +++   + v  + + d + +++e+i+++pg++s++
  gi|557695054|ref|YP_008798108.1|  68 LMLKIDPTKINRVLDELKQLREiANIYQLSGDFDAIAVAYGRDLDHIREIVEQIKKIPGIISVN 131
                                       678999*************977379*************************************97 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   2.1e-05     0.011      13      57 ..      11      54 ..       7      57 .. 0.87
   2 ?    2.5   0.0      0.26   1.4e+02      28      47 ..      67      86 ..      65      91 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                                      HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESS CS
                            MarR_2 13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgp 57
                                      ++  ++gr  + +++ r+lg+s  +v  + ++Lv+ G +++++ +
  gi|557695054|ref|YP_008798108.1| 11 NILFEDGR-ASFADIGRKLGVSENTVRFRFQKLVKTGVIRKVTVL 54
                                      56667776.7******************************99865 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.26
                                      HHHHTSSHHHHHHHHHHHHH CS
                            MarR_2 28 arrlglsksavsrilkrLva 47
                                      a  l++++  ++r+l++L +
  gi|557695054|ref|YP_008798108.1| 67 ALMLKIDPTKINRVLDELKQ 86
                                      56799***********9986 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 !   19.0   0.0   2.2e-06    0.0012       1      80 [.      59     138 ..      59     140 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-06
                   AsnC_trans_reg2   1 klGfkanalvawkvpeerveevaevvaelpevtHcYeRewpynlyfmvharseeeveevlaeiaaatgledyevLps 77 
                                       klG k++a  ++k++ +++++v   +++l+e++ +Y+ + ++   ++  +r+ ++++e++++i++  g+ ++++L++
  gi|557695054|ref|YP_008798108.1|  59 KLGLKNSAALMLKIDPTKINRVLDELKQLREIANIYQLSGDFDAIAVAYGRDLDHIREIVEQIKKIPGIISVNTLVT 135
                                       79***999*******************************************************************99 PP

                   AsnC_trans_reg2  78 tre 80 
                                       +r 
  gi|557695054|ref|YP_008798108.1| 136 LRV 138
                                       885 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   5.5e-05      0.03      19      38 ..      17      36 ..       3      44 .. 0.82
   2 ?    1.3   0.0      0.46   2.5e+02      22      33 ..      86      97 ..      77      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-05
                                      TT--HHHHHHHHTS-HHHHH CS
                        Sigma70_r4 19 eglTleEIgerlgiSrerVr 38
                                         ++++Ig++lg+S+ +Vr
  gi|557695054|ref|YP_008798108.1| 17 GRASFADIGRKLGVSENTVR 36
                                      55799**************9 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.46
                                      -HHHHHHHHTS- CS
                        Sigma70_r4 22 TleEIgerlgiS 33
                                       l EI++++++S
  gi|557695054|ref|YP_008798108.1| 86 QLREIANIYQLS 97
                                      589*****9998 PP

>> HTH_11  HTH 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    0.0067       3      44 ..       7      47 ..       6      55 .. 0.87
   2 ?   -2.0   0.0       6.6   3.6e+03      35      42 ..      80      87 ..      70      98 .. 0.58
   3 ?   -1.4   0.0       4.5   2.4e+03       3      14 ..     115     126 ..     109     133 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      l+il +L+e     s +++ ++L+vS+ tvr + ++L ++gv
  gi|557695054|ref|YP_008798108.1|  7 LKILNILFEDGR-ASFADIGRKLGVSENTVRFRFQKLVKTGV 47
                                      589999976665.9******************9999999984 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.6
                            HTH_11 35 dIkaLeel 42
                                       +++L+ l
  gi|557695054|ref|YP_008798108.1| 80 VLDELKQL 87
                                      34444433 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.5
                            HTH_11   3 lqilelLlearg 14 
                                       + i+e++++  g
  gi|557695054|ref|YP_008798108.1| 115 REIVEQIKKIPG 126
                                       345555544333 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0     9e-05     0.049       6      49 ..       7      50 ..       4      54 .. 0.94
   2 ?    1.5   0.0      0.53   2.9e+02      26      42 ..      69      85 ..      67      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 9e-05
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      ++iL il e g +s +++++klgvs  tv     +L+k G i++
  gi|557695054|ref|YP_008798108.1|  7 LKILNILFEDGRASFADIGRKLGVSENTVRFRFQKLVKTGVIRK 50
                                      689*************************************9987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.53
                                      HHTS-HHHHHHHHHHHH CS
                              MarR 26 klgvskstvtrvldrLe 42
                                      +l+++++ + rvld+L 
  gi|557695054|ref|YP_008798108.1| 69 MLKIDPTKINRVLDELK 85
                                      5899**********995 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   0.0   6.3e-05     0.034      15      37 ..      12      35 ..       8      36 .. 0.87
   2 ?    0.5   0.0      0.95   5.2e+02      13      28 ..      77      92 ..      73      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.3e-05
                            HTH_38 15 rllaeG.lslreIArrLgrspsTI 37
                                      +l + G  s+++I+r+Lg+s +T+
  gi|557695054|ref|YP_008798108.1| 12 ILFEDGrASFADIGRKLGVSENTV 35
                                      56788889***************8 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.95
                            HTH_38 13 IerllaeGlslreIAr 28
                                      I r l+e + lreIA 
  gi|557695054|ref|YP_008798108.1| 77 INRVLDELKQLREIAN 92
                                      7778888899999996 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 !   13.6   0.0   8.2e-05     0.045       6      50 ..       7      50 ..       7      52 .. 0.94
   2 ?    0.4   0.1       1.1   5.9e+02      40      51 ..     131     142 ..     130     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.2e-05
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      l iL++l e +++ +++++ r++g++  tv+   q Lv+ G +++
  gi|557695054|ref|YP_008798108.1|  7 LKILNILFEDGRA-SFADIGRKLGVSENTVRFRFQKLVKTGVIRK 50
                                      68999**9*9998.9**************************9986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.1
                                       HHHHHTTSEE.. CS
                          HTH_IclR  40 qtLvelGyveqd 51 
                                       +tLv l+ v++d
  gi|557695054|ref|YP_008798108.1| 131 NTLVTLRVVKTD 142
                                       8********998 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 !   15.3   0.0   2.1e-05     0.012      28      49 ..      20      41 ..      14      45 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-05
                                      -HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 28 sykEIAellgisegtVksrlsR 49
                                      s ++I ++lg+se+tV+ r ++
  gi|557695054|ref|YP_008798108.1| 20 SFADIGRKLGVSENTVRFRFQK 41
                                      789**************99887 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00012     0.063      26      55 .]      19      48 ..      15      48 .. 0.94
   2 ?    0.6   0.0       1.1   5.8e+02      35      52 ..      70      87 ..      66      90 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                            HTH_36 26 psqetlakrlglsknTvsraikeLeqlGyi 55
                                      +s++++ ++lg+s+nTv+   ++L+++G i
  gi|557695054|ref|YP_008798108.1| 19 ASFADIGRKLGVSENTVRFRFQKLVKTGVI 48
                                      799************************976 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.1
                            HTH_36 35 lglsknTvsraikeLeql 52
                                      l+++  ++ r ++eL ql
  gi|557695054|ref|YP_008798108.1| 70 LKIDPTKINRVLDELKQL 87
                                      57888999*******997 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 !    8.8   0.0    0.0028       1.5      25      54 ..      22      51 ..      12      61 .. 0.86
   2 ?    5.4   0.0     0.033        18      28      48 ..      67      87 ..      63      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0028
                                      HHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 25 eelAsmlGltretvsrilseLkreglisrg 54
                                      +++++ lG++  tv   +++L + g+i++ 
  gi|557695054|ref|YP_008798108.1| 22 ADIGRKLGVSENTVRFRFQKLVKTGVIRKV 51
                                      79999**********************953 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.033
                                      HHHTTSSHHHHHHHHHHHHHT CS
                         HTH_Crp_2 28 AsmlGltretvsrilseLkre 48
                                      A ml + +  ++r+l eLk+ 
  gi|557695054|ref|YP_008798108.1| 67 ALMLKIDPTKINRVLDELKQL 87
                                      78999**************86 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00013     0.072       9      49 ..      13      53 ..       7      59 .. 0.90
   2 ?    1.0   0.0      0.86   4.7e+02       4      26 ..      83     102 ..      77     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00013
                              FeoC  9 leergrvslkeLsrhfkaspealeamLeqwvrkGrvekvaa 49
                                      l e gr+s+ ++ r++ +s+++++     +v+ G ++kv+ 
  gi|557695054|ref|YP_008798108.1| 13 LFEDGRASFADIGRKLGVSENTVRFRFQKLVKTGVIRKVTV 53
                                      56889*********************************986 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.86
                              FeoC   4 elkeyleergrvslkeLsrhfka 26 
                                       elk++   r+ +++ +Ls  f+a
  gi|557695054|ref|YP_008798108.1|  83 ELKQL---REIANIYQLSGDFDA 102
                                       44444...777777777777765 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   5.3e-05     0.029      16      36 ..      16      38 ..       7      49 .. 0.80
   2 ?   -1.8   0.0       5.4     3e+03      15      26 ..      82      93 ..      69      97 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.3e-05
                            HTH_23 16 e.GlsvreIAreLgvsrrTvy.r 36
                                      + ++s ++I r+Lgvs++Tv+ r
  gi|557695054|ref|YP_008798108.1| 16 DgRASFADIGRKLGVSENTVRfR 38
                                      4678999*************955 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.4
                            HTH_23 15 aeGlsvreIAre 26
                                      +e +  reIA +
  gi|557695054|ref|YP_008798108.1| 82 DELKQLREIANI 93
                                      446677788755 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0       0.2   1.1e+02      16      42 ..      22      49 ..      12      58 .. 0.77
   2 ?    7.6   0.0     0.007       3.8      15      39 ..      63      87 ..      50      97 .. 0.80
   3 ?    1.6   0.0      0.53   2.9e+02      17      35 ..     102     120 ..      99     123 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.2
                            HTH_29 16 sqiAkllglsrrtvy.rwlkrfeegGla 42
                                      ++i + lg+s+ tv+ r++k+  +g ++
  gi|557695054|ref|YP_008798108.1| 22 ADIGRKLGVSENTVRfRFQKLVKTGVIR 49
                                      566689********75888887777665 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.007
                            HTH_29 15 vsqiAkllglsrrtvyrwlkrfeeg 39
                                         +A +l +++++++r+l+   + 
  gi|557695054|ref|YP_008798108.1| 63 KNSAALMLKIDPTKINRVLDELKQL 87
                                      5679***************987776 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.53
                            HTH_29  17 qiAkllglsrrtvyrwlkr 35 
                                        iA ++g + ++++ +++ 
  gi|557695054|ref|YP_008798108.1| 102 AIAVAYGRDLDHIREIVEQ 120
                                       69***********998875 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3      0.23   1.2e+02      59      78 ..      74      93 ..      10      94 .. 0.86
   2 ?   12.2   0.1   0.00039      0.21      57      78 ..     109     130 ..     109     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.23
                             ACT_4 59 vehLsrviakLraipgVisV 78
                                        +++rv++ L++++++ ++
  gi|557695054|ref|YP_008798108.1| 74 PTKINRVLDELKQLREIANI 93
                                      46789999999999999876 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00039
                             ACT_4  57 kdvehLsrviakLraipgVisV 78 
                                       +d++h++++++++++ipg+isV
  gi|557695054|ref|YP_008798108.1| 109 RDLDHIREIVEQIKKIPGIISV 130
                                       799******************9 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0    0.0022       1.2      16      58 ..       7      49 ..       1      59 [. 0.90
   2 ?    5.2   0.3     0.033        18      34      59 ..      67      92 ..      46     129 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0022
                                      HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEE CS
                       TFIIE_alpha 16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvk 58
                                       ++l++L e+g  +  d+ ++l++  n +r    +L + +++ 
  gi|557695054|ref|YP_008798108.1|  7 LKILNILFEDGRASFADIGRKLGVSENTVRFRFQKLVKTGVIR 49
                                      689****************************999999999885 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.033
                                      HHHHTS-HHHHHHHHHHHHHCTSEEE CS
                       TFIIE_alpha 34 akelkidlnelrklLnrLyearlvky 59
                                      a  lkid++++ ++L +L++ r +  
  gi|557695054|ref|YP_008798108.1| 67 ALMLKIDPTKINRVLDELKQLREIAN 92
                                      5679**************99886655 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 ?   13.8   0.0   8.4e-05     0.046       6      44 ..       5      42 ..       3      52 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.4e-05
                           HTH_Mga  6 rklkLlelLteneksltldelakeLglseltlqsdiseL 44
                                       +lk+l++L+e +++ +  ++  +Lg se t++ + ++L
  gi|557695054|ref|YP_008798108.1|  5 LDLKILNILFE-DGRASFADIGRKLGVSENTVRFRFQKL 42
                                      689********.*******************99666655 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00018     0.097      21      40 ..      22      41 ..      13      45 .. 0.85
   2 ?   -2.9   0.0       9.4   5.1e+03      44      53 ..      59      68 ..      58      70 .. 0.80
   3 ?   -2.4   0.0       6.5   3.5e+03      21      30 ..      88      97 ..      85      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00018
                                      HHHHHHHTS-HHHHHHHHHH CS
                              GerE 21 keIAeelniSekTVkvhksn 40
                                       +I+++l++Se+TV++  + 
  gi|557695054|ref|YP_008798108.1| 22 ADIGRKLGVSENTVRFRFQK 41
                                      68*************97665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9.4
                                      HHT-SSHHHH CS
                              GerE 44 KLnvksrvel 53
                                      KL++k+ ++l
  gi|557695054|ref|YP_008798108.1| 59 KLGLKNSAAL 68
                                      8999998877 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 6.5
                                      HHHHHHHTS- CS
                              GerE 21 keIAeelniS 30
                                       eIA ++++S
  gi|557695054|ref|YP_008798108.1| 88 REIANIYQLS 97
                                      6899988887 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00032      0.17      16      50 ..       4      38 ..       1      46 [. 0.87
   2 ?   -0.4   0.0       3.4   1.8e+03      42      57 ..      72      87 ..      64      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00032
                                      SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHH CS
                               Mga 16 slkyqllkflfeeeevsieelaqelyiSestlkrk 50
                                       l++++l  lfe+ + s++++ ++l +Se t+   
  gi|557695054|ref|YP_008798108.1|  4 ELDLKILNILFEDGRASFADIGRKLGVSENTVRFR 38
                                      5789**************************99755 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 3.4
                                      --HHHHHHHHHHHHHH CS
                               Mga 42 iSestlkrkikelnkl 57
                                      i  ++++r+++el++l
  gi|557695054|ref|YP_008798108.1| 72 IDPTKINRVLDELKQL 87
                                      6667889999998875 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 ?    8.2   0.0    0.0035       1.9      19      40 ..      14      36 ..      12      38 .. 0.93
   2 ?    2.7   0.1      0.18        99      25      51 ..      63      89 ..      59      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0035
                                      HHCTT.-HHHHHHHHT--CCHHH CS
                          CENP-B_N 19 leege.Skaelarrfnvpestls 40
                                       e+g  S a+++r+++v e t++
  gi|557695054|ref|YP_008798108.1| 14 FEDGRaSFADIGRKLGVSENTVR 36
                                      599999***************97 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.18
                                      HHHHHHHHT--CCHHHHHHHCHHHHCC CS
                          CENP-B_N 25 kaelarrfnvpestlsdilknKkkllk 51
                                      k++ a ++ + ++ + ++l+  k+l++
  gi|557695054|ref|YP_008798108.1| 63 KNSAALMLKIDPTKINRVLDELKQLRE 89
                                      788899999************999996 PP

>> Myb_DNA-binding  Myb-like DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0022       1.2       7      45 ..       4      42 ..       3      43 .. 0.93
   2 ?    2.0   0.0      0.45   2.4e+02       7      31 ..      82     108 ..      81     116 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0022
                                      HHHHHHHHHHHHHT.TCHHHHHHHHTSS-HHHHHHHHHHH CS
                   Myb_DNA-binding  7 eEdelLleavkkhG.nrWkkIaerlggRtekqcrsrwrny 45
                                      e d+++l+ + + G  +++ I ++l g +e+ +r r++++
  gi|557695054|ref|YP_008798108.1|  4 ELDLKILNILFEDGrASFADIGRKL-GVSENTVRFRFQKL 42
                                      89999*******9*999********.6***********97 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.45
                                       HHHHHHHHHHHHHT..TCHHHHHHHHT CS
                   Myb_DNA-binding   7 eEdelLleavkkhG..nrWkkIaerlg 31 
                                       +E ++L e  + +   +++++Ia  +g
  gi|557695054|ref|YP_008798108.1|  82 DELKQLREIANIYQlsGDFDAIAVAYG 108
                                       799999999999999999****97664 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00031      0.17       6      50 ..      10      53 ..       6      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00031
                                      HHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE-- CS
                              FaeA  6 leylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrspv 50
                                      l+ l +  + +  ++i   lg+s   +R+  ++L k g i+++ v
  gi|557695054|ref|YP_008798108.1| 10 LNILFE-DGRASFADIGRKLGVSENTVRFRFQKLVKTGVIRKVTV 53
                                      555555.56666789***************************976 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0026       1.4      23      57 ..      16      50 ..       7      52 .. 0.85
   2 ?    0.7   0.0       1.3     7e+02      34      52 ..      69      87 ..      62      93 .. 0.83
   3 ?   -1.3   0.0       5.4   2.9e+03      29      51 ..     101     123 ..      90     131 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0026
                                      CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 23 eepvsseeiaerqnispsylekilakLrkaglvks 57
                                      ++ +s ++i ++ ++s++ ++  ++kL k g+++ 
  gi|557695054|ref|YP_008798108.1| 16 DGRASFADIGRKLGVSENTVRFRFQKLVKTGVIRK 50
                                      344899**************************986 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.3
                                      HHTS-HHHHHHHHHHHHHT CS
                              Rrf2 34 rqnispsylekilakLrka 52
                                      + +i p+ + ++l +L++ 
  gi|557695054|ref|YP_008798108.1| 69 MLKIDPTKINRVLDELKQL 87
                                      678999999*****99985 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 5.4
                                       HHHHHHHTS-HHHHHHHHHHHHH CS
                              Rrf2  29 eeiaerqnispsylekilakLrk 51 
                                       ++ia  ++    +++ i+++ +k
  gi|557695054|ref|YP_008798108.1| 101 DAIAVAYGRDLDHIREIVEQIKK 123
                                       56777777777888888887776 PP

>> DUF4089  Protein of unknown function (DUF4089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00043      0.24       5      34 ..      64      93 ..      62      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00043
                           DUF4089  5 taallgLeldpeyrpgVvanferiaaiAql 34
                                       +a+l L++dp+ ++ V++ + ++++iA +
  gi|557695054|ref|YP_008798108.1| 64 NSAALMLKIDPTKINRVLDELKQLREIANI 93
                                      578899**********************86 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0017      0.94      11      35 ..      16      41 ..       7      50 .. 0.80
   2 ?   -0.5   0.0       2.6   1.4e+03      15      25 ..      87      97 ..      65      99 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0017
                            HTH_28 11 aGh.svreaArelgisrrtvyrWikr 35
                                      +G+ s +++ r+lg+s+ tv+   ++
  gi|557695054|ref|YP_008798108.1| 16 DGRaSFADIGRKLGVSENTVRFRFQK 41
                                      7999****************976555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 2.6
                            HTH_28 15 vreaArelgis 25
                                       re+A+++++s
  gi|557695054|ref|YP_008798108.1| 87 LREIANIYQLS 97
                                      46677776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1059.21
//
Query:       gi|557695055|ref|YP_008798109.1|  [L=391]
Description: serine hydroxymethyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  123.0   0.0    3.3e-34  118.1   0.0    2.1  1  SHMT             Serine hydroxymethyltransferase
    0.00017   21.0   0.1    0.00031   20.2   0.1    1.4  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00038   19.1   0.0    0.00054   18.6   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00059   19.2   0.0      0.001   18.4   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0013   18.0   0.0     0.0027   16.9   0.0    1.6  1  Aminotran_1_2    Aminotransferase class I and II
     0.0014   17.7   0.0      0.002   17.2   0.0    1.2  1  SelA             L-seryl-tRNA selenium transferase
      0.006   15.6   0.1      0.009   15.0   0.1    1.2  1  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.096   13.0   0.0       0.28   11.5   0.0    1.8  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


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 !  118.1   0.0   1.5e-37   3.3e-34      14     398 ..      18     364 ..       7     365 .. 0.85

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 1.5e-37
                                       HHHHH.HHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTTEEEE CS
                              SHMT  14 keker.qkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpakwgvn 89 
                                       +e+er +++ ++l+asen+ s+av  alGs +  +y+       +yGG+ ++ ev +la +  + +f+++    +  
  gi|557695055|ref|YP_008798109.1|  18 REHERfRRRCVNLVASENVLSPAVRRALGSDMGSRYSLR---PEFYGGTRYIQEVWRLAEELGRLVFGAE----FCS 87 
                                       34444145679*************************964...47**************************....*** PP

                                       ---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHH CS
                              SHMT  90 vqplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkak 166
                                       v plsG  a +    a +  g++i  +d    G+   G ++++     + ++      k+++++  id +e  +  +
  gi|557695055|ref|YP_008798109.1|  88 VAPLSGHVALMMALYACVPRGGKIACVDPGFAGY--PGLEIDK-----IPQVMGYSVIKLTEKELCIDVEEAVEMVS 157
                                       ***********9999***********99877776..5788877.....55555666678889999************ PP

                                       HH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCT.SSEEEEESSSTT-S-S-EEE CS
                              SHMT 167 efkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfey.advvtttthktlrGprggli 242
                                       + kP  +v G+s     +  + l e  ++ g  ++ d +h+ Glva+gv+ +P++  ad++   thk++ Gp+gg+i
  gi|557695055|ref|YP_008798109.1| 158 REKPDAVVLGASLILYPMPVRELAETVHNYGGVVVYDASHVLGLVAGGVFQQPLKEgADIMIGSTHKSFFGPQGGII 234
                                       *************9999999**********************************7549******************* PP

                                       EEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHT CS
                              SHMT 243 llrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealkek 319
                                       l++             + +l+kki++  f       +   +aa+aval e  + + k+y+++v++na++lae l++ 
  gi|557695055|ref|YP_008798109.1| 235 LTN-------------DTHLAKKIEENTFHKFVDNIHFNRVAALAVALDEI-RRHGKMYATRVVDNARTLAESLEKA 297
                                       ***.............579*****************************985.6678********************* PP

                                       T-EEGGG...S-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTSSTTTT-SEEEEESHHHHHTT--HHHHH CS
                              SHMT 320 gyklvsg...GtdnhlvlvdlrekgldGkraekvlekvnitankntvPgdksalvtsGlrlGtpaltsrgfkeedle 393
                                       g k   +    t +h v +          +++++ + +n+  +kn +  d       G+r+Gt  +t+rg++  ++ 
  gi|557695055|ref|YP_008798109.1| 298 GLKPFRNrlgYTFSHQVYLP--------YSVDEAAHVCNV-LEKNHIIAD------IGVRFGTCEVTRRGMGLRQMG 359
                                       *9876651113455554443........334444444443.457766544......699999999999999999999 PP

                                       HHHHH CS
                              SHMT 394 kvakf 398
                                       ++ak+
  gi|557695055|ref|YP_008798109.1| 360 QIAKL 364
                                       99886 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 !   20.2   0.1   1.4e-07   0.00031      92     200 ..     140     251 ..      68     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.4e-07
                                       B-TTTSSB-GGGCGGG--TTE..EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT...EECCCSSS CS
                   DegT_DnrJ_EryC1  92 vdpdtynidpaaieaaitert..kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg...kkvGalgd 163
                                        +++ ++id++++ + + ++   + +l + l   ++ + +l +  +++g +v+ Da+h lG    g   +++ + +d
  gi|557695055|ref|YP_008798109.1| 140 LTEKELCIDVEEAVEMVSREKpdAVVLGASLILYPMPVRELAETVHNYGGVVVYDASHVLGLVAGGvfqQPLKEGAD 216
                                       578899*****999999988887778899***********************************999999******* PP

                                       EEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBT CS
                   DegT_DnrJ_EryC1 164 aavfSFyptKnlttGeGGavvtndeelaekarvlrnh 200
                                       + + S +  K +    GG+++tnd  la+k++    h
  gi|557695055|ref|YP_008798109.1| 217 IMIGSTH--KSFFGPQGGIILTNDTHLAKKIEENTFH 251
                                       *****87..8999*****************9965555 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 !   18.6   0.0   2.4e-07   0.00054      71     224 ..      88     246 ..      64     298 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.4e-07
                                       EEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHH.HHHTHHHTTCEEEEEST.....TSHHHHHHHCCTTEEEE CS
                   Cys_Met_Meta_PP  71 lavssGmaAiaaailallkaGdeivvsddlYggtqrl.lkkvlkklgievkfvdt.....sdleelekaikentklv 141
                                       +a  sG  A+++a+ a +  G +i + d  + g   l ++k+ + +g +v          + +e++e + +e+ ++v
  gi|557695055|ref|YP_008798109.1|  88 VAPLSGHVALMMALYACVPRGGKIACVDPGFAGYPGLeIDKIPQVMGYSVIKLTEkelciDVEEAVEMVSREKPDAV 164
                                       45569999999999999999999999999998876663455545455544332221334466788888888999999 PP

                                       EEESS-TTTT----HHHHHHHHHHTT-EEEEEGT.....TTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEE CS
                   Cys_Met_Meta_PP 142 ylEtptnpllkvvDiekiaklakkagvlvvvDnt.....faspllqrplklgaDivvhSaTKylgGhsdvvaGvivv 213
                                        l   ++  l  + ++++a+++++ g +vv D++     +a +++q+plk gaDi + S+ K   G +   +G+i++
  gi|557695055|ref|YP_008798109.1| 165 VLG--ASLILYPMPVRELAETVHNYGGVVVYDAShvlglVAGGVFQQPLKEGADIMIGSTHKSFFGPQ---GGIILT 236
                                       886..4566666779*****************973333245679******************999976...788998 PP

                                       SSCHHHHHHHH CS
                   Cys_Met_Meta_PP 214 kgkeelkkelk 224
                                       ++ ++l+k+++
  gi|557695055|ref|YP_008798109.1| 237 ND-THLAKKIE 246
                                       88.77777665 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   4.6e-07     0.001      44     241 ..      80     302 ..      43     379 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.6e-07
                                       HTT-SEEEEES.-HHHHHHHHHHHH--TTEEEEEETT..-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHH CS
                   Beta_elim_lyase  44 lfgkeaalfvp.qGtaAnsillkillqrgeevivtep..ahihfdetgaiaelagvklrdlknkeaGkmdlekleaa 117
                                       +fg+e    +p +G  A  ++l + + rg ++ + +p  a +   e   i ++ g  +++l+ ke   +d   +e+a
  gi|557695055|ref|YP_008798109.1|  80 VFGAEFCSVAPlSGHVALMMALYACVPRGGKIACVDPgfAGYPGLEIDKIPQVMGYSVIKLTEKE-LCID---VEEA 152
                                       56666444443377777777777777777777777776666666777777777777788888888.3444...5555 PP

                                       S--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEE CS
                   Beta_elim_lyase 118 ikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtm 194
                                       ++ v++  ek+ +++l           +++  +re+a+++++yg  +++D+  ++   ++ g+  + + +++D++  
  gi|557695055|ref|YP_008798109.1| 153 VEMVSR--EKPDAVVLGASLIL-----YPM-PVRELAETVHNYGGVVVYDASHVLG-LVAGGVFQQPLKEGADIMIG 220
                                       555555..78888888877764.....555.589******************9996.5699**************** PP

                                       ESSSTT--SS-EEEEE-HH.......................................HHHHHHHHHHHHT---SST CS
                   Beta_elim_lyase 195 slkKdllanvGgvlafrddel...................................edylaerveqrkylggglrqa 236
                                       s  K  + + Gg+++++d +l                                   + y  + v  +++l++ l++a
  gi|557695055|ref|YP_008798109.1| 221 STHKSFFGPQGGIILTNDTHLakkieentfhkfvdnihfnrvaalavaldeirrhgKMYATRVVDNARTLAESLEKA 297
                                       *******************8889999999988888888888888888888888888788777778888888888888 PP

                                       HHHHH CS
                   Beta_elim_lyase 237 gvlaa 241
                                       g++  
  gi|557695055|ref|YP_008798109.1| 298 GLKPF 302
                                       87654 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 !   16.9   0.0   1.2e-06    0.0027     167     324 ..     174     329 ..      28     353 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.2e-06
                                       HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTT.SSGGG-EEEEEEEH.HHHH CS
                     Aminotran_1_2 167 leeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKaf.GlaGeRvGyilgna.avvs 241
                                       +  +++l+++++ y+ +++ D  +  +      +      ++e+ + +  gs  K+f G  G   G+il n+ ++++
  gi|557695055|ref|YP_008798109.1| 174 PMPVRELAETVHNYGGVVVYDASHVLGLVAGGVF---QQPLKEGAD-IMIGSTHKSFfGPQG---GIILTNDtHLAK 243
                                       556899******************9777664433...567777777.99******988****...*****6547777 PP

                                       HHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEEEETHHC CS
                     Aminotran_1_2 242 qlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmflltdlsaet 316
                                        ++    +  +   +  +++a a+  ++ ++++ +  + r+ +++++l ++L+++glk + +  +  f+ +++ +++
  gi|557695055|ref|YP_008798109.1| 244 KIEENTFHKFVdNIHFNRVAALAVALDE-IRRHGKMYATRVVDNARTLAESLEKAGLKPFRNRlGYTFSHQVYLPYS 319
                                       7777766666665555555444443333.345***************************999966667777777775 PP

                                       HHHHHHH..H CS
                     Aminotran_1_2 317 akelskk..L 324
                                        +e++ +   
  gi|557695055|ref|YP_008798109.1| 320 VDEAAHVcnV 329
                                       5555555453 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0     9e-07     0.002     188     257 ..     199     270 ..     177     319 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 9e-07
                                       GT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-HH.HHHHHHHSTHHHHT.B--HHHHHHHHHHHH CS
                              SelA 188 yglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGkke.lieklkknplkraL.rvDkltlaaleatlr 257
                                        gl     +q+ l+eG+d++  s  k + gpq Gii+ +   l +k+++n +++ +  +   ++aal+ +l 
  gi|557695055|ref|YP_008798109.1| 199 LGLVAGGVFQQPLKEGADIMIGSTHKSFFGPQGGIILTNDThLAKKIEENTFHKFVdNIHFNRVAALAVALD 270
                                       478888899****************************98651667899999988641233334555555554 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1     4e-06     0.009     157     223 ..     176     247 ..     160     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4e-06
                                       -HHHHHHHHHHTT-EEEEE-TTTTTTS---H....HHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS.. CS
                       Aminotran_5 157 pveeigklakkkgalvlvDaaqavghipidv....kklgvDflafsghK.llgPtGiGvlyvrkelleklep 223
                                       pv e+++ ++++g +v+ Da+  +g     v     k g+D++  s+hK ++gP+G  +l   ++l +k+e 
  gi|557695055|ref|YP_008798109.1| 176 PVRELAETVHNYGGVVVYDASHVLGLVAGGVfqqpLKEGADIMIGSTHKsFFGPQGGIILTNDTHLAKKIEE 247
                                       99*******************988765544411114569*****************6666666666666655 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 ?   11.5   0.0   0.00013      0.28      14      68 ..     148     204 ..     140     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHHTT-.-EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G.- CS
                           PFOR_II  14 taksavdelReegi.kvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgse.G 68 
                                       ++++av+++ +e+   v l    +l+P P +el+e ++++  vvv+d ++ +g   G
  gi|557695055|ref|YP_008798109.1| 148 DVEEAVEMVSREKPdAVVLGASLILYPMPVRELAETVHNYGGVVVYDASHVLGLVaG 204
                                       5666776654444404444445689*************************9987663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); 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):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 2772.33
//
Query:       gi|557695056|ref|YP_008798110.1|  [L=320]
Description: diphosphomevalonate decarboxylase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-07   29.8   0.0      7e-07   29.2   0.0    1.2  1  MDD_C           Mevalonate 5-diphosphate decarboxylase C-term
     0.0012   19.1   0.8     0.0021   18.2   0.8    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain


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 !   29.2   0.0   7.8e-11     7e-07      19     130 ..     193     301 ..     189     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 7.8e-11
                             MDD_C  19 mqrsvetSeLlkhrakevvperieelekAikekdFetfaeitmkdSnqlhavcldtyPpifYlndtSraiielvhel 95 
                                        +r +e S++++ r+k   ++r++ le+ ik+ dF+ f++++  d+ +lh v  +    +   ++ S +i+elv+++
  gi|557695056|ref|YP_008798110.1| 193 AHREAELSAFFEARVKA-AQKRCDMLEQVIKDGDFTGFGQLVELDALELHGVTSTGPSRMILATKDSMRIVELVQDM 268
                                       56677899*******99.9*********************************998888888999************9 PP

                             MDD_C  96 NeaagkikvAYtFDAGpNavlyleekdveellsll 130
                                          ++++++ ++   Gp  ++ ++ +d e + + +
  gi|557695056|ref|YP_008798110.1| 269 R--RENVECYFSMQTGPTVFINCLPEDSEYVATRV 301
                                       8..77888889999999999999999888777655 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 !   18.2   0.8   2.4e-07    0.0021       2      41 ..      88     132 ..      87     150 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.4e-07
                                       EEEEESSHTTS..SSCHHHHHHHHHHHHHHHHTTEH.H..HHHHH CS
                    GHMP_kinases_N   2 ivikseiPvga..GLGSSAAlavalvaAllallgls.l..eeakl 41 
                                       +v+++ +P g+  GLG S+++ +al+aA++++ gl+ +   +++l
  gi|557695056|ref|YP_008798110.1|  88 MVSRNSMPKGSvkGLGFSSSAGAALAAAAYRAAGLDkMygWDYRL 132
                                       5789999*************************9976533222555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); 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 0.23s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2537.45
//
Query:       gi|557695057|ref|YP_008798111.1|  [L=57]
Description: hypothetical protein CSUB_C1630 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   16.6   0.1     0.0082   16.0   0.1    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
      0.017   15.3   0.0       0.02   15.0   0.0    1.1  1  Polo_box_2      Polo box domain
      0.039   14.4   0.0      0.043   14.3   0.0    1.2  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin


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 !   16.0   0.1   1.4e-06    0.0082       7      27 ..      19      39 ..      16      50 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-06
                                      EEEEE-CCCHHHCCEECTCEE CS
                    MazE_antitoxin  7 gavriPkevrfelgireGdev 27
                                      g+++iP e+r+  +i+ Gd++
  gi|557695057|ref|YP_008798111.1| 19 GRITIPEEIRKIFEIKDGDSL 39
                                      79*****************98 PP

>> Polo_box_2  Polo box domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   3.3e-06      0.02      16      56 ..      15      55 ..      13      57 .] 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.3e-06
                                      E-SSEEEEEEETTEEEEEEE-TTSBEEEEEEEEEET..TEE CS
                        Polo_box_2 16 vtaaGryiveddtlvvfevanksnlvkkilvveidergkvq 56
                                      vta+Gr  + ++ + +fe+    +l+ +i +v+  ++g  q
  gi|557695057|ref|YP_008798111.1| 15 VTAGGRITIPEEIRKIFEIKDGDSLLCRIRIVKRKSQGTDQ 55
                                      79******************************999888777 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 ?   14.3   0.0   7.2e-06     0.043       3      32 ..      14      42 ..      12      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.2e-06
                    PrlF_antitoxin  3 tltergqttiPasvRkaLklkkgrdkiayt 32
                                      ++t+ g  tiP+ +Rk+ ++k   d++  +
  gi|557695057|ref|YP_008798111.1| 14 EVTAGGRITIPEEIRKIFEIKD-GDSLLCR 42
                                      79999****************8.5566555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); 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: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 436.84
//
Query:       gi|557695058|ref|YP_008798112.1|  [L=91]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  102.1   1.2    1.4e-29  101.9   1.2    1.0  1  HTH_45    Winged helix-turn-helix
    0.00018   21.3   0.2    0.00024   20.9   0.2    1.3  1  DUF4364   Domain of unknown function (DUF4364)
     0.0054   16.6   0.2     0.0074   16.2   0.2    1.2  1  TrmB      Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.031   14.8   0.1       0.04   14.4   0.1    1.2  1  HTH_27    Winged helix DNA-binding 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 !  101.9   1.2   3.1e-33   1.4e-29       1      76 [.       5      84 ..       5      85 .. 0.96

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 3.1e-33
                            HTH_45  1 rRskleIiadILeais.egeakkTkimykanLsykllnkYLdmLvekgli...kkskekYvlTekGlelleklkeleel 75
                                      +Rsk++IiadILe+i+ +g+ak+Tki+++anLsy++l kYLdmLvek+l+   ++s+++YvlTekGle+l+++k++e++
  gi|557695058|ref|YP_008798112.1|  5 YRSKTKIIADILESINqQGHAKPTKILLDANLSYDRLVKYLDMLVEKKLVervENSETMYVLTEKGLEFLMEYKRFERF 83
                                      6**************9899******************************877799**********************98 PP

                            HTH_45 76 a 76
                                      a
  gi|557695058|ref|YP_008798112.1| 84 A 84
                                      6 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2   5.4e-08   0.00024      26      72 ..      31      76 ..      11      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 5.4e-08
                           DUF4364 26 leneytnYfdlqqalseLvesglieeeekenktlykiTekGketlel 72
                                      l +  ++Y  l ++l+ Lve++l+e  e +++t+y +TekG e l +
  gi|557695058|ref|YP_008798112.1| 31 LLDANLSYDRLVKYLDMLVEKKLVERVE-NSETMYVLTEKGLEFLME 76
                                      44556799*****************866.99**********998865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.2   1.6e-06    0.0074      19      64 ..      21      66 ..      10      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.6e-06
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYra 64
                                      ++g a+ ++i  ++++++ +  ++L  L++k lVer++ + ++Y+ 
  gi|557695058|ref|YP_008798112.1| 21 QQGHAKPTKILLDANLSYDRLVKYLDMLVEKKLVERVENSETMYVL 66
                                      68999999********************************999986 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 ?   14.4   0.1     9e-06      0.04       8      68 .]      15      70 ..       9      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 9e-06
                            HTH_27  8 vLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +L++i+ +++ +k + +    n+++   ++ l+ L+ek Lver +      e+ + lT+kG
  gi|557695058|ref|YP_008798112.1| 15 ILESIN-QQGHAKPTKILLDANLSYDRLVKYLDMLVEKKLVERVENS----ETMYVLTEKG 70
                                      688888.777777788888999*******************999988....9********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); 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: 683.00
//
Query:       gi|557695059|ref|YP_008798113.1|  [L=209]
Description: hypothetical protein CSUB_C1632 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.9   4.1     0.0075   15.9   4.1    2.1  2  MASE3     Membrane-associated sensor domain


Domain annotation for each model (and alignments):
>> MASE3  Membrane-associated sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   4.1   4.2e-07    0.0075      11      57 ..      10      56 ..       5      67 .. 0.91
   2 !    1.7  12.4     0.009   1.6e+02     102     219 ..      82     200 ..      58     205 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.2e-07
                             MASE3 11 tllElfsivvallifliawntrkftknnyllflGiaflfvglldllH 57
                                      +++E +s +++l+if++a+++ ++t ++ l +l+++fl ++l  ++ 
  gi|557695059|ref|YP_008798113.1| 10 IIFEAISFFISLAIFAVALAAARRTGSRSLTLLALGFLLMALAMFIR 56
                                      689**************************************988776 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.009
                             MASE3 102 lrayavflvyalvtlllllsifypkifPalfiegsGlTpfkiisEyliilllllalllllrrrkkfekkvl...rll 175
                                       l+ ++++++++ ++  ++++ + ++ +P+   e +Gl  +  ++ y   +  + alll +  ++  +++v+    ++
  gi|557695059|ref|YP_008798113.1|  82 LQIQELVYSVVRISGYVVFL-YLYSSYPSSKKEAEGLFAVAPVIIYNPLFEAVSALLLAFVVYQLARNRVYggsGYV 157
                                       45555666665565554444.447889**********9988877777666666666666666666666665222799 PP

                             MASE3 176 laalvllilsellftlyvsvydilnllGHlfkilsfyliykaiv 219
                                       l+ + ll +s llf l    +  + +l+++ ++ls +l++ a+ 
  gi|557695059|ref|YP_008798113.1| 158 LLGFSLLLFSHLLFLLLP-LSFAIYFLAQFTQLLSLILFLTAVL 200
                                       9999************55.55567799*************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1083  (0.0604049); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); 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):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1470.03
//
Query:       gi|557695060|ref|YP_008798114.1|  [L=166]
Description: hypothetical protein CSUB_C1633 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1272.23
//
Query:       gi|557695061|ref|YP_008798115.1|  [L=322]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit beta [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-30  106.1   0.1    2.6e-30  105.2   0.1    1.4  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    1.4e-16   60.3   0.3    2.3e-15   56.5   0.3    2.3  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit
  ------ inclusion threshold ------
      0.063   13.1   0.0       0.21   11.4   0.0    1.8  2  ATP13         Mitochondrial ATPase expression


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 !  105.2   0.1   4.4e-34   2.6e-30       2     153 .]      51     198 ..      50     198 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 4.4e-34
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       iGc+             ++y++  g+++ +G+ lp+A+Gakla+p+ +v+a+ GDG+ l i   ++++  rrn+++t
  gi|557695061|ref|YP_008798115.1|  51 IGCSGK----------TPHYINaYGIHTLHGRVLPFALGAKLANPSLTVIAVGGDGDGLGIgAGHFVNTGRRNVDFT 117
                                       677776..........889999888************************************99************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpa 149
                                       +v+++N++yg+t+gq   + p+g+k+ks p+++  + v++ +la   G + +ar   +d+  l+e +k+ ++++g+a
  gi|557695061|ref|YP_008798115.1| 118 YVLFDNGVYGLTKGQaspTLPRGMKTKSLPKPNVNDAVNPIALAVVSGYTfVARGYAYDTRYLKELIKKGIQHEGSA 194
                                       *****************999******************************9998889999***************** PP

                                       EEEE CS
                      TPP_enzyme_C 150 liev 153
                                       +i+v
  gi|557695061|ref|YP_008798115.1| 195 FIDV 198
                                       **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 !   56.5   0.3   3.8e-19   2.3e-15       1      63 [.     202     287 ..     202     289 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 3.8e-19
                                       XTTTXSSSXSXXXX...........X-EEEGGGST---EE...........HHHHHHHHT-----EEEEEEEE.TTS CS
                        PFO_beta_C   1 CvtFNkvnTfdwYk...........ervykleedgyDpsd...........lekAlekalewgdkiplGifYk.eek 54 
                                       C+t+N++ T +wY             r+ykle++gyD ++           + +A++k++ewgd+ip+G+fY+ +  
  gi|557695061|ref|YP_008798115.1| 202 CPTYNDIMTKEWYGgedrivegkplPRIYKLEDTGYDGEVksndpeevnskKLQAIAKSFEWGDRIPVGVFYQnKFI 278
                                       *************74433443434459******9****999************************************ PP

                                       --HHHHHHT CS
                        PFO_beta_C  55 ptyeerlee 63 
                                       p+yeer+++
  gi|557695061|ref|YP_008798115.1| 279 PSYEERISA 287
                                       ******975 PP

>> ATP13  Mitochondrial ATPase expression
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.46   2.7e+03       9      26 ..     169     186 ..     164     190 .. 0.86
   2 ?   11.4   0.0   3.6e-05      0.21      42      87 ..     239     285 ..     226     294 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.46
                             ATP13   9 lslgrsgqlelieklikk 26 
                                       ++ g++ +++++++likk
  gi|557695061|ref|YP_008798115.1| 169 VARGYAYDTRYLKELIKK 186
                                       6789999********986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.6e-05
                             ATP13  42 tkvksdsplyPtselLkaivssfsynneiesAlklvdkfskkYpe.i 87 
                                        +vks++p   +s+ L ai++sf   ++i  ++ + +kf+ +Y+e i
  gi|557695061|ref|YP_008798115.1| 239 GEVKSNDPEEVNSKKLQAIAKSFEWGDRIPVGVFYQNKFIPSYEErI 285
                                       578889999999*******************************9742 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); 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:                         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: 00:00:00.41
# Mc/sec: 2364.56
//
Query:       gi|557695062|ref|YP_008798116.1|  [L=651]
Description: 2-oxoglutarate ferredoxin oxidoreductase subunit alpha [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  204.7   0.0    2.5e-60  204.1   0.0    1.3  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    9.2e-33  113.8   0.1    1.8e-32  112.8   0.1    1.5  1  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
      7e-09   35.9   0.0    1.8e-08   34.6   0.0    1.8  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    5.1e-05   22.9   0.0    9.9e-05   22.0   0.0    1.4  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
     0.0074   16.2   0.0      0.018   14.9   0.0    1.6  1  Transketolase_C  Transketolase, C-terminal domain


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 !  204.1   0.0     7e-64   2.5e-60       2     230 ..     253     509 ..     252     510 .. 0.89

  Alignments for each domain:
  == domain 1  score: 204.1 bits;  conditional E-value: 7e-64
                                       HHHHCTEEEEEE--BTTTCC........HHHHHCHCCCCCTT.......EE.EEEE-SSHHHHHHHHHHHHCTT-EE CS
                             POR_N   2 aaiaagvdviaaYPITPsse........iaeelaellakgev.......gdvevvqmesEigaisaviGAaaaGara 63 
                                       ++iaag++++++YPITP+s+        ++ +l e ++ ++        g ++vvq+e+Ei+a+++v GAa+aGara
  gi|557695062|ref|YP_008798116.1| 253 GKIAAGCRFQTYYPITPASDesvyledhMVFNLREEYPHVKEmeeldghGSIVVVQTEDEISAVNMVSGAALAGARA 329
                                       789****************98776666666666666666655999****99************************** PP

                                       EEEEECCHHHHCCCCHHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHH CS
                             POR_N  64 aTaTSgqGllLmienlglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdla 135
                                        TaTSg+G+ Lm+e +g+a+++e+P+v+++++R++pstgl++r +q++l++ +     +++ iv+as++++eaf ++
  gi|557695062|ref|YP_008798116.1| 330 STATSGPGFDLMVEGIGYAGMNEIPIVVTLYQRGGPSTGLPTRHEQGELLFSIfgghgEFPRIVIASGDIEEAFYDV 406
                                       ***************************************************************************** PP

                                       HHHHHHHHHCTSEEEEEEEHHHH.HEEEEEEC-SGG.GS-----SBXXXXXXXX...........SXXXBXXTXXTS CS
                             POR_N 136 lvAfnlAekvrvPvivlfDgfllshevekvelpdeedelklikekleeyerkey...........aldpekpiargt 201
                                       ++Afn+Ae++++Pvi+++D+ l+ ++  +v++ d   ++ + + kl+ +++ +            +++ +  + ++ 
  gi|557695062|ref|YP_008798116.1| 407 AKAFNYAERYQTPVIHILDKALA-NSTMTVDVFDLS-KIVIDRGKLVTSWDNSLgeykrfkftedGISYRTVLGVEN 481
                                       ***********************.9999**999887.4444444444444444344455555999************ PP

                                       SXXEEESBXBXTTSXBXXXXHHHHHHHHH CS
                             POR_N 202 aanpdtglehrekgneaedaaekvveeve 230
                                         +++tg+eh+e g+++e+  +++++++e
  gi|557695062|ref|YP_008798116.1| 482 GIFWNTGDEHDELGHITEE-PSTRDRMME 509
                                       *******************.999999887 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.8   0.1   5.1e-36   1.8e-32       2     177 .]      15     219 ..      12     219 .. 0.94

  Alignments for each domain:
  == domain 1  score: 112.8 bits;  conditional E-value: 5.1e-36
                                       TSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEE CS
                               POR   2 GqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkp 78 
                                       G+Gv + ++++++aaa+ G+yv+++rey s+i+G hsy+ v isd  +v s   +e++ll  +d et+ +h+ ++ +
  gi|557695062|ref|YP_008798116.1|  15 GTGVDSSANVFSRAAASYGLYVFGKREYYSNIKGEHSYFSVVISDG-KVHSTM-DEVHLLATFDSETVVRHAWEVVE 89 
                                       99*******************************************8.899999.9********************** PP

                                       EEEEEEECTCGTT-CCHHHCTS-HHHHHHH......................T-EEEEE-HHHHHHHCCC....... CS
                               POR  79 ggiiiynseelkpdelkkakeeerelkerl......................gvrvygvdatkiakeiggn...... 127
                                       gg iiy+s  + ++      +e++ l++ +                      gvr+y++++ +++k+ g++      
  gi|557695062|ref|YP_008798116.1|  90 GGGIIYDSLAVGEKITSIPTLEKPVLERIQmrlskegvgdtigdvlevarrnGVRLYPIPYMELLKKVGDKtgekql 166
                                       ********8888888887777777777767999*********************************88888888899 PP

                                       ...CCHHHHHHHHHHHHHHTS-HHHHHHHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 128 ...eraaNtvmlGalaallglplealeeaikkrfpkkkeviekNlkafragye 177
                                          +r++Nt+++Ga++ ll++pl +le+a ++ f+ k+ v++ N+ a++a++e
  gi|557695062|ref|YP_008798116.1| 167 salARMTNTLAVGASLTLLSIPLTHLETAFSQVFRAKASVVKSNVIAAEAAHE 219
                                       999***********************************************985 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 !   34.6   0.0     5e-12   1.8e-08       1     101 [.     536     629 ..     536     630 .. 0.90

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 5e-12
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       A ++++  Gs+ g + +avd l  eg++  + ++++l PFP++ l++l+ ++k+ +v+++n++    Gql++ +ka 
  gi|557695062|ref|YP_008798116.1| 536 APYLVLSWGSTKGAIIDAVDYLASEGLRFAFAQIKVLNPFPTRFLQNLIPQYKRTIVVEQNFT----GQLATLIKAR 608
                                       568999********************************************************5....*******999 PP

                                       TGGGTSEEEEEE--GGG----HHH CS
                           PFOR_II  78 lkkskvkvvnfvaglgGrditved 101
                                       +     ++ +++ + +Gr ++ ++
  gi|557695062|ref|YP_008798116.1| 609 TGI---HTDHLIVKYNGRPFSFSE 629
                                       854...477888888888776665 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 !   22.0   0.0   2.8e-08   9.9e-05      31     156 ..     295     421 ..     287     436 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 2.8e-08
                                       HCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH. CS
                      TPP_enzyme_N  31 ldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg. 106
                                       +++l+ + +i vv++ +E +a+++ +g a a     +  +tsgpG+  ++ ++  A  + iP++v   +r+  ++g 
  gi|557695062|ref|YP_008798116.1| 295 MEELDGHGSIVVVQTEDEISAVNMVSGAALAGA--RASTATSGPGFDLMVEGIGYAGMNEIPIVVTLYQRGGPSTGl 369
                                       577888889**********************85..678899******************************999996 PP

                                       .S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHH...HHHHHHHSSS--EEE CS
                      TPP_enzyme_N 107 .qgvlqqeldqlalfrpvtkyaervtspeelpealr...rAirtalsgrpgPvy 156
                                        + + q+el   ++f  + ++ + v  + +++ea+    +A+  a ++ ++Pv 
  gi|557695062|ref|YP_008798116.1| 370 pTRHEQGEL-LFSIFGGHGEFPRIVIASGDIEEAFYdvaKAFNYA-ERYQTPVI 421
                                       544444344.55566666666555555555555544333888888.77888875 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   4.9e-06     0.018      13      71 ..     539     597 ..     537     616 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.9e-06
                                       EEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEE CS
                   Transketolase_C  13 tlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeav 71 
                                       +++++Gs+    ++A++ L++eg+++    +  ++p+ ++ +++++ +++r +vve++ 
  gi|557695062|ref|YP_008798116.1| 539 LVLSWGSTKGAIIDAVDYLASEGLRFAFAQIKVLNPFPTRFLQNLIPQYKRTIVVEQNF 597
                                       589*****************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); 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 0.32s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 4010.71
//
Query:       gi|557695063|ref|YP_008798117.1|  [L=191]
Description: small heat shock protein HSP20 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-13   49.5   3.8    9.7e-12   44.9   3.8    2.3  1  HSP20       Hsp20/alpha crystallin family
      3e-12   45.9   0.1    4.9e-12   45.2   0.1    1.4  1  ArsA_HSP20  HSP20-like domain found in ArsA
    0.00018   21.6   0.2    0.00027   21.1   0.2    1.2  1  GvpH        GvpH
      0.003   17.6   0.5        0.1   12.7   0.3    2.5  2  FKBP26_C    FKBP26_C-terminal
     0.0038   17.6   0.4     0.0087   16.5   0.1    1.6  2  PIH1_CS     PIH1 CS-like domain
     0.0092   17.0   1.4      0.014   16.4   1.4    1.2  1  CS          CS domain
  ------ inclusion threshold ------
      0.077   13.6   0.7         11    6.7   0.1    2.3  2  QIL1        MICOS complex subunit MIC13, QIL1
       0.18   11.6   0.6       0.24   11.2   0.6    1.1  1  DUF2807     Putative auto-transporter adhesin, head GIN domai


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 !   44.9   3.8   4.3e-15   9.7e-12       1     101 [.     105     190 ..     105     191 .] 0.91

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 4.3e-15
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslk 77 
                                       d+ ee+++ +v +++pg++ke+++++v+++++++k   e          +    rk+ ++++LP +v ++ vka+++
  gi|557695063|ref|YP_008798117.1| 105 DVFEEDQNVKVVAEIPGVRKEDIDLTVDEKMLTIKVDTE----------Q----RKYYKEVELPVEVSTTGVKATYN 167
                                       57799******************************9999..........4....889999***************** PP

                                       TTEEEEEEEBSS--..-------- CS
                             HSP20  78 dGvLtvtvpkkepekkkkerkiqi 101
                                       +GvL+vt+pkk++ k     ki+i
  gi|557695063|ref|YP_008798117.1| 168 NGVLEVTLPKKQASKP-RGEKIKI 190
                                       ************9976.6666666 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 !   45.2   0.1   2.2e-15   4.9e-12       2      63 .]     111     175 ..     110     175 .. 0.93

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 2.2e-15
                        ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkignfrRq....itLPsvlarkevtsAkfedgvLeIrF 63 
                                        ++++++++P+v ke+idl+ +++ LtIk++ ++R+    + LP  ++   v +A++++gvLe+++
  gi|557695063|ref|YP_008798117.1| 111 QNVKVVAEIPGVRKEDIDLTVDEKMLTIKVDTEQRKyykeVELPVEVSTTGV-KATYNNGVLEVTL 175
                                       6789***************************877777777**********99.***********96 PP

>> GvpH  GvpH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   1.2e-07   0.00027     100     167 ..     110     179 ..     105     186 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                              GvpH 100 sdelvvvadlpGvtdedvdvaletdeqaltlrvdddvverlv.lddp.dvait..dltlrnqvlelrlarse 167
                                        +++ vva++pGv  ed+d +++  e+ lt++vd +  +    ++ p +v+ t  + t +n vle+ l + +
  gi|557695063|ref|YP_008798117.1| 110 DQNVKVVAEIPGVRKEDIDLTVD--EKMLTIKVDTEQRKYYKeVELPvEVSTTgvKATYNNGVLEVTLPKKQ 179
                                       45678**************9998..9*******987543322122222344441145777888888776655 PP

>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.3   4.5e-05       0.1      12      44 ..     118     151 ..     109     155 .. 0.82
   2 ?    2.5   0.0     0.071   1.6e+02      16      37 ..     157     178 ..     154     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                                       H-TT--..--EEEEETTEEEEE--TTG.GGSTTH CS
                          FKBP26_C  12 yiPnidlekfkieiedktvtIelpeea.kFieni 44 
                                        iP + +e++++++++k +tI+++ e  k+++++
  gi|557695063|ref|YP_008798117.1| 118 EIPGVRKEDIDLTVDEKMLTIKVDTEQrKYYKEV 151
                                       48**********************7652677776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.071
                                       --..--EEEEETTEEEEE--TT CS
                          FKBP26_C  16 idlekfkieiedktvtIelpee 37 
                                       ++++ +k ++++++++++lp++
  gi|557695063|ref|YP_008798117.1| 157 VSTTGVKATYNNGVLEVTLPKK 178
                                       56677899999*********98 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.5   5.7e+03      24      40 ..      37      53 ..      24      55 .. 0.68
   2 !   16.5   0.1   3.9e-06    0.0087      34      96 ..     114     175 ..     108     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.5
                           PIH1_CS 24 skkenvpkelaieielP 40
                                         e vpkel+ e  +P
  gi|557695063|ref|YP_008798117.1| 37 RMMEYVPKELVKETRTP 53
                                      44678899998887777 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.9e-06
                           PIH1_CS  34 aieielPllksikevklrvgerrlel..eskkakyfLslkLpYpvdedkveAkFvkktklLkvkl 96 
                                       ++  e+P++   ++++l v+e++l +  ++++ ky  +++Lp +v+ + v+A++++    L+v+l
  gi|557695063|ref|YP_008798117.1| 114 KVVAEIPGV-RKEDIDLTVDEKMLTIkvDTEQRKYYKEVELPVEVSTTGVKATYNN--GVLEVTL 175
                                       566789999.5789********998833555599********************96..4555555 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.4   6.2e-06     0.014       7      76 .]     108     177 ..     104     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.2e-06
                                       EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECEBSS-BETTTEEEEEETTEEEEEEEB CS
                                CS   7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliegeLfgpIdpeesswtieskkveitLkK 76 
                                       +++++V+v  ++++v  +k+d++++  e+ l++k+  + +k ++e eL  ++ +   + t  +  +e+tL K
  gi|557695063|ref|YP_008798117.1| 108 EEDQNVKVVAEIPGV--RKEDIDLTVDEKMLTIKVdTEqRKYYKEVELPVEVSTTGVKATYNNGVLEVTLPK 177
                                       67899*********9..******************966699999999***********************88 PP

>> QIL1  MICOS complex subunit MIC13, QIL1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1    0.0048        11      16      47 ..      23      54 ..      18      60 .. 0.85
   2 ?    5.2   0.0     0.015        33      31      63 ..     144     173 ..     124     175 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0048
                              QIL1 16 lykkakeyipPyvdevkkklclevpklpsvee 47
                                      ++++++++i + + ++++++++e++k+ +++e
  gi|557695063|ref|YP_008798117.1| 23 MFEEMQREIMEEMRRMMEYVPKELVKETRTPE 54
                                      7899*******************888777665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                              QIL1  31 vkkklclevpklpsveevkf.slveyWNkgVkkv 63 
                                       ++k++  + ++lp   ev+   ++ ++N+gV +v
  gi|557695063|ref|YP_008798117.1| 144 QRKYY--KEVELP--VEVSTtGVKATYNNGVLEV 173
                                       45555..334444..466665799*******765 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 ?   11.2   0.6   0.00011      0.24      15      81 ..     107     176 ..      96     187 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                       EEE-SS-EEEEEEEHHHHCCEEEEEETTEEEEEE-...TTTTSSB.EEEEEEES--SEEEEECCEEEEE- CS
                           DUF2807  15 vtqgdeqsvviegdenllekvevevedgtLkirle...kefestktlkvtvtvpnleelelsgsgsieve 81 
                                       +++ ++ +vv e +    e++  +v++++L+i+ +   +++  + +l v+v+ + +++   +g  ++++ 
  gi|557695063|ref|YP_008798117.1| 107 FEEDQNVKVVAEIPGVRKEDIDLTVDEKMLTIKVDteqRKYYKEVELPVEVSTTGVKATYNNGVLEVTLP 176
                                       5667777****************************88856655557999999999999888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      682  (0.0380389); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1447.68
//
Query:       gi|557695064|ref|YP_008798118.1|  [L=384]
Description: glycosyl transferase family 2 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   86.5   0.0    2.7e-24   85.9   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    4.5e-19   69.3   0.0    6.3e-19   68.8   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    6.8e-13   48.5   0.1    1.6e-12   47.2   0.0    1.6  2  Glyco_transf_21  Glycosyl transferase family 21
    1.5e-07   31.8   0.2    3.4e-07   30.7   0.2    1.5  1  Glyco_tranf_2_4  Glycosyl transferase family 2
    1.1e-05   25.0   0.0    1.9e-05   24.3   0.0    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
     0.0048   16.8   4.3     0.0092   15.9   4.3    1.5  1  Glyco_trans_2_3  Glycosyl transferase family group 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 !   85.9   0.0   8.9e-28   2.7e-24       1     169 [.      46     214 ..      46     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 8.9e-28
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-.HHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak.edprvrvirreenv.Gkagalnagl 75 
                                       s++ p+ Ne +++  +++ ll+  +y ++e+ivvDD+StD+t+e++e+ a      vrv+  ee++ Gk +a   g 
  gi|557695064|ref|YP_008798118.1|  46 SIILPVRNELAYIHDSVRTLLSL-DYVEKEVIVVDDNSTDGTWEVVEKMAVeDLFVVRVVGDEEGWmGKCRACHIGY 121
                                       8**********************.*************************99777899******************** PP

                                       HH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCST CS
                   Glycos_transf_2  76 raatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnls 152
                                        +++g+++lf DaD+ ++p  l++ v+a+e+ g d     ++++f +  ++  +        + f + +    g ++
  gi|557695064|ref|YP_008798118.1| 122 LHSRGEWLLFTDADTDFAPTVLKDAVQAAEAFGLDFLSLYPRFRFRSFLHRAAMPV-LLTGFYLFGKPHLVHSGRSA 197
                                       *******************************8886554444444444444443332.23333444444555566899 PP

                                       TCSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 153 feigsaallrrealeel 169
                                       f  gs++l+rr a+e++
  gi|557695064|ref|YP_008798118.1| 198 FAFGSFMLFRRGAYEKI 214
                                       9************9997 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 !   68.8   0.0   2.1e-22   6.3e-19       3     202 ..      44     242 ..      41     267 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 2.1e-22
                   Glyco_tranf_2_3   3 dlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksral 79 
                                       +++++ p+ ne +++++ ++ ll+ +y + ev+vv+d+s+++t ev+e +a +   v vrvv  ++  g  gk ra 
  gi|557695064|ref|YP_008798118.1|  44 KVSIILPVRNELAYIHDSVRTLLSLDYVEKEVIVVDDNSTDGTWEVVEKMAVEDLFV-VRVV-GDE-EGWMGKCRAC 117
                                       69**********************************************986655443.6766.444.4889****** PP

                   Glyco_tranf_2_3  80 nealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrs....tlvsalgalefaerhlrflaar 152
                                         ++ + +++++l+ D+Dt   P++lk ++q++++ + +++    +++ rs    +++++l    f+     +l+++
  gi|557695064|ref|YP_008798118.1| 118 HIGYLHSRGEWLLFTDADTDFAPTVLKDAVQAAEAFGLDFLSLYPRFRFRSflhrAAMPVLLT-GFYLFGKPHLVHS 193
                                       *********************************888999999888888777554333444433.6778888888888 PP

                   Glyco_tranf_2_3 153 ralgvltlnGsgslirrevlkelegldp.lflltdDyelglrlrragfrta 202
                                        +  +++  Gs++l+rr  ++ ++g+++ +  l +D  l+l +r++g r+ 
  gi|557695064|ref|YP_008798118.1| 194 GRSAFAF--GSFMLFRRGAYEKIGGHTAvRDALLEDRALALHARSHGLRMG 242
                                       8888888..***************************************996 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 !   47.2   0.0   5.3e-16   1.6e-12       6     148 ..     101     246 ..      95     267 .. 0.82
   2 ?   -2.7   0.0       1.2   3.5e+03      61      86 ..     306     332 ..     295     351 .. 0.56

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 5.3e-16
                   Glyco_transf_21   6 llvsgdpvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaa 82 
                                       + v+gd++g   K  +++ ++   + ++l++ D+d+ ++p+ L++ ++a e  +  +++ +p+   ++ l++a   +
  gi|557695064|ref|YP_008798118.1| 101 VRVVGDEEGWMGKCRACHIGYLHSRGEWLLFTDADTDFAPTVLKDAVQAAEAFGLDFLSLYPRFRFRSFLHRAAMPV 177
                                       457789999999***************************************99999999999887777666666666 PP

                   Glyco_transf_21  83 flntl.....agvlqaklsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspa 148
                                       +l+ +     + ++ +  ++  fa+G++m++rr a e+iGG  a++d L eD al+ + r++Gl++ l +a
  gi|557695064|ref|YP_008798118.1| 178 LLTGFylfgkPHLVHS--GRSAFAFGSFMLFRRGAYEKIGGHTAVRDALLEDRALALHARSHGLRMGLFRA 246
                                       6633312223333333..7889*******************************************988776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.2
                   Glyco_transf_21  61 glVtslpvgsdakglaaaleaafl.nt 86 
                                        l t+++v+ +  g+ a+ +aa + n 
  gi|557695064|ref|YP_008798118.1| 306 LLSTGYVVAGAVVGWEARRHAASFlNG 332
                                       566777777777777777755555343 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 !   30.7   0.2   1.1e-10   3.4e-07       1      81 [.      52     135 ..      52     139 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.1e-10
                   Glyco_tranf_2_4   1 rneadiLpeflahhlalgf..drilvydndstDgtrailkel..pevkllhvdksyederrqvellkalla..ryae 71 
                                       rne +++   ++ +l+l++  ++++v+d++stDgt+++++++  +++ +++v+++    + ++   +a+     +++
  gi|557695064|ref|YP_008798118.1|  52 RNELAYIHDSVRTLLSLDYveKEVIVVDDNSTDGTWEVVEKMavEDLFVVRVVGDE---EGWMGKCRACHIgyLHSR 125
                                       8999**************86678******************833556666666654...556665555554115689 PP

                   Glyco_tranf_2_4  72 adwvlvvDaD 81 
                                       ++w+l+ DaD
  gi|557695064|ref|YP_008798118.1| 126 GEWLLFTDAD 135
                                       9********9 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 !   24.3   0.0   6.3e-09   1.9e-05       1      97 [.      46     141 ..      45     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 6.3e-09
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddk.ayslaaarNrG 76 
                                       s+++p+r+  e  yi++ v+   +    e e+ivvdd S++ + e+v+++    l v     d++   ++ +a   G
  gi|557695064|ref|YP_008798118.1|  46 SIILPVRN--ELAYIHDSVRTLLSLDYVEKEVIVVDDNSTDGTWEVVEKMAVEDLFVVRVVGDEEgWMGKCRACHIG 120
                                       56777776..5669*****77666644799********************999999954444455488999999*** PP

                   Glyco_tranf_2_2  77 askaesdlvlFlDaDcfissD 97 
                                         ++ ++ +lF DaD  +++ 
  gi|557695064|ref|YP_008798118.1| 121 YLHSRGEWLLFTDADTDFAPT 141
                                       ***************766555 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 !   15.9   4.3   3.1e-06    0.0092       1     142 [.     128     270 ..     128     346 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.1e-06
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvm..nvanwleelaalff.aedhgkdilvrealgrvvpsvG 74 
                                       + l+ DaDt   p +l+++++  +      + + +l+   + +++l++ a+    +  +++  +  + +gr ++ +G
  gi|557695064|ref|YP_008798118.1| 128 WLLFTDADTDFAPTVLKDAVQAAEA---FGLDFLSLYPrfRFRSFLHRAAMPVLlTGFYLFGKPHLVHSGRSAFAFG 201
                                       7789999***999999999998864...4555555553356689999999998556677777777789********* PP

                   Glyco_trans_2_3  75 sgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpes.lvkekspltlraalrQrkRway 142
                                       s +++rr a +++gg     +++ ED  ++l ++++G+r  +  +   v  +  ++ r  ++ + R ++
  gi|557695064|ref|YP_008798118.1| 202 SFMLFRRGAYEKIGGHTAVRDALLEDRALALHARSHGLRMGLFRALdRVTASWNDDSRSLWNGMLRIFM 270
                                       *************************************99998877644444444455555555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); 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:                         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: 00:00:00.39
# Mc/sec: 2923.59
//
Query:       gi|557695065|ref|YP_008798119.1|  [L=315]
Description: modification methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-06   28.5   0.0    0.00054   19.7   0.0    2.3  2  N6_N4_Mtase      DNA methylase
    0.00077   20.1   0.1       0.12   13.0   0.0    3.2  3  Methyltransf_11  Methyltransferase domain
  ------ inclusion threshold ------
      0.044   14.5   0.0         13    6.5   0.0    3.1  3  Methyltransf_25  Methyltransferase domain
      0.056   13.1   0.0      0.091   12.4   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020


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 !    6.8   0.0    0.0011         5     203     223 ..       2      22 ..       1      29 [. 0.89
   2 !   19.7   0.0   1.2e-07   0.00054       1      81 [.     170     287 ..     170     315 .] 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0011
                                       THHHHHHHHTT-EEEEEESSH CS
                       N6_N4_Mtase 203 GtTavaakelgrkfiGieiee 223
                                       GtT+  ++elg ++iG ++++
  gi|557695065|ref|YP_008798119.1|   2 GTTLLTCRELGINSIGLDVSP 22 
                                       9*****************987 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 1.2e-07
                                       EEEEEE--SSSSSCS.....................................GCCGCCHHHHHHHHHHHHHHHHHHH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy................................endeqyeeedsyeeyleflekvlkevrrv 45 
                                       vd ++t+pPY ++ +y                                  + ++e+      y+e +ekv+ ev+r+
  gi|557695065|ref|YP_008798119.1| 170 VDAVITSPPYLNKIEYtrcywpeyeiffphishtglrsylsmrpedveLSSLEEEAPLVARLYFEDMEKVCGEVYRI 246
                                       799***************************************9998766666677777799**************** PP

                                       EEEEEEEEEEE-CCCHHT......HHHHHHHHHTT-EEEEEE CS
                       N6_N4_Mtase  46 Lkddgsifiniddseikk......elkaladeifggffllnv 81 
                                       L ++g +++ ++   + +       ++  ++e  g +f+   
  gi|557695065|ref|YP_008798119.1| 247 LRPGGAAVMVVGGGVFPDrviqvdVAVSDIAERCG-LFVERI 287
                                       ********999988877766665544444444445.444444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.7   7.4e+03      16      31 ..      10      25 ..       2      52 .. 0.64
   2 ?    3.3   0.0      0.03   1.3e+02      41      67 ..     150     175 ..     105     179 .. 0.69
   3 !   13.0   0.0   2.7e-05      0.12      73      95 ..     232     254 ..     226     255 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
                                      HTTSEEEEEES-HHHH CS
                   Methyltransf_11 16 krgarvvgvDlskeml 31
                                      + g + +g+D+s+ ++
  gi|557695065|ref|YP_008798119.1| 10 ELGINSIGLDVSPLFV 25
                                      5567777888877655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.03
                                       HT-EEEETTEECCCT.SS-TT-EEEEEE CS
                   Methyltransf_11  41 eglkvefvvadaekl.pfednsfDlvvs 67 
                                       +  + + + +da+++  +e +s+D+v+ 
  gi|557695065|ref|YP_008798119.1| 150 A--SAKAMLGDARRMeSVETESVDAVIT 175
                                       2..3556788888887788899998875 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 2.7e-05
                                       C-CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  73 hvedpekalkeiaRvLkpgGllv 95 
                                       ++ed+ek++ e++R+L+pgG  v
  gi|557695065|ref|YP_008798119.1| 232 YFEDMEKVCGEVYRILRPGGAAV 254
                                       5799****************987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.99   4.4e+03      20      40 ..      12      31 ..       2      60 .. 0.59
   2 ?    4.1   0.0     0.018        79      32      71 ..     137     176 ..     133     189 .. 0.76
   3 ?    6.5   0.0     0.003        13      80      97 .]     234     251 ..     225     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.99
                                      TSSEEEEEESSHHHHHHHHHH CS
                   Methyltransf_25 20 gkakvtgvDiseemleaarer 40
                                      g  + +g+D+s+ ++ +   +
  gi|557695065|ref|YP_008798119.1| 12 G-INSIGLDVSPLFVFISVVK 31
                                      4.7778888888776554444 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHTTTTEEEEESBCCGBS.SSTTTEEEEEEE CS
                   Methyltransf_25  32 emleaareraeeeglnvefvqgdaedlp.fedgsfDlvvss 71 
                                       +m+e ++++    +++++ + gda++++  e +s+D+v+ s
  gi|557695065|ref|YP_008798119.1| 137 KMIEDVEKHPL-TDASAKAMLGDARRMEsVETESVDAVITS 176
                                       56666666653.34599999******9857999*****985 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.003
                                       HHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  80 edlekalkeiarvLkpgG 97 
                                       ed+ek++ e++r+L+pgG
  gi|557695065|ref|YP_008798119.1| 234 EDMEKVCGEVYRILRPGG 251
                                       5899*************9 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0     2e-05     0.091     110     148 ..     157     196 ..     140     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2e-05
                                       --GGG--.STTS---EEEE----------HHHHHHHHHHH CS
                           UPF0020 110 adaakLr.lkegevdvivtnpPYGerlgskkalekLYsef 148
                                        da+ ++  ++++vd+++t pPY ++++ ++  +  Y+ f
  gi|557695065|ref|YP_008798119.1| 157 GDARRMEsVETESVDAVITSPPYLNKIEYTRCYWPEYEIF 196
                                       678888876677***************9888776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2635.73
//
Query:       gi|557695066|ref|YP_008798120.1|  [L=170]
Description: protease I [Candidatus Caldiarchaeum subterraneum]
Scores for 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-56  188.5   0.0      8e-56  188.4   0.0    1.0  1  DJ-1_PfpI      DJ-1/PfpI family
     0.0013   18.4   0.0      0.002   17.8   0.0    1.4  1  Catalase_C     C-terminal domain found in long catalases
     0.0014   18.4   0.0     0.0015   18.3   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
     0.0069   16.0   0.0     0.0085   15.7   0.0    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.021   14.6   0.0    1.3  1  Peptidase_C26  Peptidase C26
      0.042   12.9   0.0      0.051   12.7   0.0    1.2  1  GATase_5       CobB/CobQ-like glutamine amidotransferase doma
      0.097   12.3   0.0       0.45   10.2   0.0    1.9  2  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 !  188.4   0.0   3.1e-59     8e-56       1     164 [.       4     166 ..       4     167 .. 0.99

  Alignments for each domain:
  == domain 1  score: 188.4 bits;  conditional E-value: 3.1e-59
                                       EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESSTSEEEETTSEEEE-SEEGGGCTCCG-SEEEE--BHHHHHHH CS
                         DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvdkeevkgsrGlkvtvdaslddvkaaeyDalvlpGGragperl 77 
                                       +k+++l++ ++ed+El++p+ +l+++g++v++v++d++ ++g++G ++t+d+s++++k++ey +l++pGG a p+rl
  gi|557695066|ref|YP_008798120.1|   4 MKAVILVGPEFEDLELFYPLIRLREEGYAVEIVGPDRKAYRGKHGIEITADKSVEEAKPEEYSCLIIPGGWA-PDRL 79 
                                       699*********************************************************************.**** PP

                                       HTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSEEEETTEEEESSGGG CS
                         DJ-1_PfpI  78 renekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrvvvdgnlvTsrgpga 154
                                       r++++vv++vk+f+e gk+vaaIC+gpqlL++a+vlkg ++Ts  a+kd++e+ag  y d +vvvd nl+Tsrgpg+
  gi|557695066|ref|YP_008798120.1|  80 RRDQRVVQFVKRFFETGKPVAAICHGPQLLISAKVLKGFKLTSASAIKDDVENAGGVYHDAPVVVDRNLITSRGPGD 156
                                       ***************************************************************************** PP

                                       HHHHHHHHHH CS
                         DJ-1_PfpI 155 aiefalelle 164
                                       +  f ++l+e
  gi|557695066|ref|YP_008798120.1| 157 LHVFVKALIE 166
                                       *******998 PP

>> Catalase_C  C-terminal domain found in long catalases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   7.8e-07     0.002      51     117 ..      57     114 ..      23     145 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.8e-07
                        Catalase_C  51 YstadaveFDaivvadgaeslfsakataasslfpagrplqllldayrhgKpigalGsgaealkaagi 117
                                          a+  e+  +++ +g          a+++l  ++r++q+++  ++ gKp++a+ +g ++l +a++
  gi|557695066|ref|YP_008798120.1|  57 VEEAKPEEYSCLIIPGG---------WAPDRLRRDQRVVQFVKRFFETGKPVAAICHGPQLLISAKV 114
                                       44555555555555555.........35678999************************998886665 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.8e-07    0.0015      30      87 ..      54     112 ..      25     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.8e-07
                                       TSHHHHHHHTHHSTSEEEEEEESSCTT...TTTHHHHHHHHCTSTS-EEEETHHHHHHHHH CS
                            GATase  30 dasaeeilellknpdgilvsgGpgspg...vegkieaikearenkiPiLGICLGmQllaie 87 
                                       d+s ee   + +++  ++++gG         +  ++++k+++e ++P+  IC G Qll+ +
  gi|557695066|ref|YP_008798120.1|  54 DKSVEEA--KPEEYSCLIIPGGWAPDRlrrDQRVVQFVKRFFETGKPVAAICHGPQLLISA 112
                                       3333333..5789999******987778888999***********************9876 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 !   15.7   0.0   3.3e-06    0.0085      34      89 ..      58     110 ..      16     120 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.3e-06
                          GATase_3  34 deslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLG 89 
                                       +e+ +e++  +i+pGg    +   l r++++ + +k++ e+g+pv +iC G q+L 
  gi|557695066|ref|YP_008798120.1|  58 EEAKPEEYSCLIIPGGW---APDRLRRDQRVVQFVKRFFETGKPVAAICHGPQLLI 110
                                       333347899******96...567899999************************995 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   8.4e-06     0.021      88     120 ..      79     111 ..      58     144 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.4e-06
                     Peptidase_C26  88 peRdalelaLiraalergvPilgiCrGlqllnv 120
                                        +Rd+  ++ +++  e g+P+ +iC G qll  
  gi|557695066|ref|YP_008798120.1|  79 LRRDQRVVQFVKRFFETGKPVAAICHGPQLLIS 111
                                       6899**************************954 PP

>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05     0.051      71     129 ..      78     135 ..      65     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                          GATase_5  71 slllneklrealekflnredtlaLGiCnGfqlLvklglvpggeieeaeksptltrNksg 129
                                       +l+  +++ + +++f++  ++ + +iC G qlL+  +++ g + ++a+     ++N+ g
  gi|557695066|ref|YP_008798120.1|  78 RLRRDQRVVQFVKRFFET-GKPVAAICHGPQLLISAKVLKGFKLTSASAIKDDVENAGG 135
                                       67778999999******9.********************99888877665555555555 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.25   6.3e+02      10      31 ..      18      39 ..      13      61 .. 0.80
   2 ?   10.2   0.0   0.00018      0.45      83     144 ..      63     115 ..      50     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.25
                         ThiJ_like 10 evaipwkvlkdagfsveFvtek 31
                                      e+  p+  l+++g+ ve v + 
  gi|557695066|ref|YP_008798120.1| 18 ELFYPLIRLREEGYAVEIVGPD 39
                                      67789999999***99998776 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00018
                         ThiJ_like  83 eeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpe 144
                                       eey+ + +pGG  +    l  ++r+ + ++ ++       e  k ++aic+g   l  ak  
  gi|557695066|ref|YP_008798120.1|  63 EEYSCLIIPGGWAPDR--LRRDQRVVQFVKRFF-------ETGKPVAAICHGPQLLISAKVL 115
                                       6899999999998865..778888888888888.......77899*******9999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       210  (0.0117129); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); 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 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1338.94
//
Query:       gi|557695067|ref|YP_008798121.1|  [L=117]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   70.5   1.3    1.3e-19   70.1   1.3    1.2  1  FeS_assembly_P  Iron-sulfur cluster assembly protein
  ------ inclusion threshold ------
      0.059   13.5   0.1       0.11   12.7   0.1    1.4  1  NifU            NifU-like domain
        0.1   12.6   0.1        0.2   11.7   0.0    1.4  1  GMP_synt_C      GMP synthase C terminal 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 !   70.1   1.3   2.2e-23   1.3e-19       2      72 ..      21      93 ..      20      95 .. 0.92

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 2.2e-23
                                      HHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.-EEEEEE--SSTT-TTHHHHHHHHHHHHC..STT--EEEE CS
                    FeS_assembly_P  2 eavlaaLrtVtDPelgvdlvslglvreidieg.gkVsvditltypacslaeairadaeaalr.alpgvevveV 72
                                      e+v++aL++ +DPe++v++v+lglv++++i +  +V+v++tlt p+c++ + +++++++a+   ++gve v V
  gi|557695067|ref|YP_008798121.1| 21 EQVMEALKNCYDPEIPVNIVDLGLVYDVKIIDdKTVYVKMTLTAPGCPVGAFVAEQVKEAIMtLVEGVERVDV 93
                                      79***************************98879****************************77889666665 PP

>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.8e-05      0.11      25      66 ..      51      91 ..      40      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                                      EETTEEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EE CS
                              NifU 25 vdegvVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeV 66
                                      +d+++V+v+++    gCp  +    e +++a++  v+ v++V
  gi|557695067|ref|YP_008798121.1| 51 IDDKTVYVKMTLTAPGCPVGAFVA-EQVKEAIMTLVEGVERV 91
                                      6889***************99988.99999999999999998 PP

>> 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 ?   11.7   0.0   3.3e-05       0.2      46      89 ..      59     102 ..      44     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                                       -------B----HHHHHHHHHHHHHHSTT---EEEE---TTTS- CS
                        GMP_synt_C  46 eDamtadvaelpyevLekissrivnevkgvnrvvyditskPpat 89 
                                       + ++ta  + + + v e++ + i+  v+gv rv  di   Pp t
  gi|557695067|ref|YP_008798121.1|  59 KMTLTAPGCPVGAFVAEQVKEAIMTLVEGVERVDVDIVFDPPWT 102
                                       55678888888888999*********************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 862.30
//
Query:       gi|557695068|ref|YP_008798122.1|  [L=775]
Description: valyl tRNA-synthetase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-111  373.4   0.0   5.3e-110  368.4   0.0    2.0  1  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    3.2e-32  111.6   0.1      6e-32  110.7   0.1    1.5  1  Anticodon_1     Anticodon-binding domain of tRNA
    8.1e-25   87.4   0.0    2.3e-12   46.4   0.0    3.6  2  tRNA-synt_1g    tRNA synthetases class I (M)
    0.00018   21.5   1.0      0.066   13.2   0.3    2.6  2  DZR             Double zinc ribbon
    0.00063   19.3   0.0     0.0018   17.8   0.0    1.7  1  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2
     0.0013   18.2   2.0        1.9    8.1   0.3    3.4  3  TF_Zn_Ribbon    TFIIB zinc-binding
     0.0059   16.0   6.9        4.8    6.7   0.1    3.4  3  zf-ribbon_3     zinc-ribbon domain
     0.0096   15.6   7.0        3.2    7.6   0.1    3.4  3  zinc_ribbon_2   zinc-ribbon domain
  ------ inclusion threshold ------
      0.016   15.1   4.9        6.8    6.7   0.0    3.0  2  Nudix_N_2       Nudix N-terminal
      0.018   15.2   1.7       0.28   11.3   0.5    2.6  2  Zn-ribbon_8     Zinc ribbon domain
      0.029   13.7   0.0       0.41    9.9   0.0    2.3  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
      0.036   13.0   0.0       0.13   11.2   0.0    1.8  2  tRNA-synt_1f    tRNA synthetases class I (K)
      0.037   13.3   1.9         20    4.6   0.0    3.5  3  zf-TFIIB        Transcription factor zinc-finger
       0.12   12.4   0.1       0.73    9.9   0.1    2.1  2  HypA            Hydrogenase/urease nickel incorporation, meta
        0.3   10.8   2.1         55    3.5   0.0    3.3  3  zf-NADH-PPase   NADH pyrophosphatase zinc ribbon domain
       0.37   10.9   5.0         85    3.4   0.1    4.2  4  zf-ACC          Acetyl-coA carboxylase zinc finger domain
        0.6   10.8   3.9        7.4    7.3   0.0    3.0  3  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
       0.84    9.8   4.0         48    4.2   0.0    3.4  3  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
        1.2    9.2   6.5         10    6.2   0.3    3.4  3  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        1.5    8.8   8.2         12    5.9   0.5    3.4  3  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
        2.6    8.1   5.0         34    4.6   0.2    3.2  3  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        3.9    7.2   9.9        1.1    8.9   0.2    3.2  3  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII


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 !  368.4   0.0  6.5e-113  5.3e-110       2     601 ..      20     573 ..      19     574 .. 0.95

  Alignments for each domain:
  == domain 1  score: 368.4 bits;  conditional E-value: 6.5e-113
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGsl.HiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaie 77 
                                       ++  We+ed+++ +   + ++k+f++  +PPy  G++ HiG a + +  d++ r++rm G+ +l+ +G+D  Gl++e
  gi|557695068|ref|YP_008798122.1|  20 ILRLWEKEDLYRFN--IRSRRKKFVIDTPPPYPSGRPwHIGAAAHYSQIDMIARTARMMGYMTLFPIGIDRNGLPVE 94 
                                       6889*******999..778899*************977*************************************** PP

                       tRNA-synt_1  78 akvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkg 154
                                          ekk+g+  +    +  re+f+e ++   +e  +e+ + +krlG s Df++ y T ++e+   ++++f +l ++g
  gi|557695068|ref|YP_008798122.1|  95 IYTEKKYGIAIR----DTPREKFIELCKTSLDELEAEMLEIMKRLGLSGDFKNRYRTDSPEYRRFTQNTFIKLWKNG 167
                                       *******99987....99*********************************************************** PP

                       tRNA-synt_1 155 liyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitke 231
                                       l+yr++++ n+++ + t+++++Evey+d  ++l +v+fpl+++    + iaTT+Pe +++  av  np         
  gi|557695068|ref|YP_008798122.1| 168 LVYRASRPNNYCPMCGTTIADAEVEYEDLPSTLHYVKFPLENGGY--IPIATTRPELIPACAAVIYNPA-------- 234
                                       ****************************************99876..9*********************........ PP

                       tRNA-synt_1 232 klilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkk 308
                                                              d r+++Le k+++ pl + k+piia   ++ ++GtG+V +  + d+ D ++ ++
  gi|557695068|ref|YP_008798122.1| 235 -----------------------DSRYAHLENKTATTPLFGDKVPIIARPEAKPDFGTGAVMVCSYGDHTDVRLFRE 288
                                       .......................9***************************************************** PP

                       tRNA-synt_1 309 ynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvk 385
                                        +l+   +++ +g+++e+a+  +gl+v++ark++ve+l + g ++k+e+i hs p+cersk+pi+    + ++ ++ 
  gi|557695068|ref|YP_008798122.1| 289 LKLPEKIVITLEGRMNENAGFLKGLRVEEARKAIVEKLIDAGYYIKSENIIHSTPVCERSKTPIEIIPMDEYYLNQL 365
                                       ***************************************************************************** PP

                       tRNA-synt_1 386 eladaalkavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeae 461
                                       ++ d++ k  ++++f p+ +++   +w+  ++ dW iSR r++ + +p+++ ++ +  v               + +
  gi|557695068|ref|YP_008798122.1| 366 DFLDDLRKIAHEMEFLPEHSRQLLLNWIDSVSiDWPISRRRYYATEVPVWYCNSCGTPVLP----------DDGQYH 432
                                       *****************************9877*********************9966663..........344555 PP

                       tRNA-synt_1 462 kkalekeakdkl.kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlill 537
                                       + + ek  +++  k++  +++ de ++D+W +S+ +p  ++    ++ +  ++ +p ++  +G  i+r W++  +l 
  gi|557695068|ref|YP_008798122.1| 433 QPWREKAPVERCpKCGSTSFRGDERTFDTWMDSSISPLFVIS-DRKTGKIHESLYPVSIRPQGKEIVRTWLYYTVLR 508
                                       56666666766668999*********************9999.55557777889*********************** PP

                       tRNA-synt_1 538 slaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdvgrdinl 601
                                          ltg++Pf++v ++gl +de+G KmSKs+gNvidp+ +++kygad  R++ + +++ g+d ++
  gi|557695068|ref|YP_008798122.1| 509 CYLLTGKRPFNKVWISGLGLDEHGEKMSKSKGNVIDPMPILEKYGADCFRFWNAqEASLGEDFRI 573
                                       *****************************************************999999999887 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 !  110.7   0.1   7.4e-35     6e-32       1     152 []     610     756 ..     610     756 .. 0.91

  Alignments for each domain:
  == domain 1  score: 110.7 bits;  conditional E-value: 7.4e-35
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedk.ra.aqevllevletllr 75 
                                       drwil+el+k+v+++ + ye ++f    +++  f+wn ++++y+e++kpr y++  +++ ++ a ++l++vl+t l 
  gi|557695068|ref|YP_008798122.1| 610 DRWILAELSKTVETCLAGYEGFNFFIPSNEIRRFIWNIFASHYVEMSKPRAYGQGFTESeQKsAFYTLHTVLRTTLL 686
                                       9*******************************************************9999777************** PP

                       Anticodon_1  76 llaPfmPfitEelwqreeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselkvv 151
                                       llaP++Pfit+++w    ++l + +si+l+ +p+ ++    k+l  +  e l e ++a+ +++++l+++ + e++++
  gi|557695068|ref|YP_008798122.1| 687 LLAPITPFITDYIW----RRLYGGKSIHLERFPKpAWP---KTL-TKYTEPLTEFNSAVWAKKKSLNLSLRDEISYE 755
                                       **************....9999999********74443...233.2356667779**************99998876 PP

                       Anticodon_1 152 i 152
                                       i
  gi|557695068|ref|YP_008798122.1| 756 I 756
                                       5 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 !   46.4   0.0   2.8e-15   2.3e-12       2     136 ..      42     192 ..      41     197 .. 0.83
   2 !   34.3   0.1   1.3e-11   1.1e-08     166     371 ..     342     578 ..     316     593 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 2.8e-15
                                       EEEE--B--SS--.-HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS....-HH....HHH. CS
                      tRNA-synt_1g   2 lvttalpYangkl.HlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gv....tpe....elv. 67 
                                       ++ t+ pY++g++ H+G ++++ + D++aR  r+ g+ +lf  g D  G p+e+  ek+ g+    tp+    el+ 
  gi|557695068|ref|YP_008798122.1|  42 VIDTPPPYPSGRPwHIGAAAHYSQIDMIARTARMMGYMTLFPIGIDRNGLPVEIYTEKKyGIairdTPRekfiELCk 118
                                       689999****9755***************************************998875455223344422223442 PP

                                       ...HHHHHHHHHHHHHTT--..-SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
                      tRNA-synt_1g  68 ...ekvheeikelfkklnis..fdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                                          ++ ++e+ e++k+l++s  f + +rt+s e ++++q+ f kl ++gl+y+ +    ycp ++++++d +ve
  gi|557695068|ref|YP_008798122.1| 119 tslDELEAEMLEIMKRLGLSgdFKNRYRTDSPEYRRFTQNTFIKLWKNGLVYRASRPNNYCPMCGTTIADAEVE 192
                                       222456777888999999974477899********************************************997 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 1.3e-11
                                       ...........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET.... CS
                      tRNA-synt_1g 166 npksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP.... 238
                                        p++  s++  e+   ++++++  +f ++l++   +e + l+e+ ++ +++w+++   d+ isr+  ++ +vP    
  gi|557695068|ref|YP_008798122.1| 342 TPVCERSKTPIEIIPMDEYYLNQLDFLDDLRKIA-HEMEFLPEHSRQLLLNWIDSVSIDWPISRRRYYATEVPvwyc 417
                                       478888888889999*****************99.444479**************99***************99899 PP

                                       ........TECCEEE-HHHH.HHHHHHHTTTTT-...TTSGGGG.G--S......EEEEE.GGGHHHHHTHHHHHHH CS
                      tRNA-synt_1g 239 ........gaekkvlYVWld.AligYisatkelakkkgeeekwkeyWakdkevelvhfig.kdiikFHtifwPaill 305
                                                +++++   W + A+++     + ++  +g+e++++++   d+ ++   +i+ +   k H  ++P  + 
  gi|557695068|ref|YP_008798122.1| 418 nscgtpvlPDDGQYHQPWREkAPVERCPKCGSTS-FRGDERTFDTWM--DSSISPLFVISdRKTGKIHESLYPVSIR 491
                                       8888888889999999**876******9999987.778999***999..45555555554277889*******9998 PP

                                       HTT--....................--S-EEEE--.EEE--------------HHHHHHHH-HHHHHHHHHHHS-TT CS
                      tRNA-synt_1g 306 gaelk....................lpkkvvahey.ltvegkKlSkSrgvvvkakealerldadllRYylaaeapek 361
                                        ++ +                      +kv  ++  l  +g+K+SkS+g+v+++  +le++ ad++R++ a+ea+  
  gi|557695068|ref|YP_008798122.1| 492 PQGKEivrtwlyytvlrcylltgkrPFNKVWISGLgLDEHGEKMSKSKGNVIDPMPILEKYGADCFRFWNAQEASLG 568
                                       7433334556666677777776665677887777647889************************************* PP

                                       S-EEE-HHHH CS
                      tRNA-synt_1g 362 kDldfswedf 371
                                       +D+ +s++ +
  gi|557695068|ref|YP_008798122.1| 569 EDFRISEARI 578
                                       **99998765 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.015        12      12      24 ..     176     188 ..     170     230 .. 0.84
   2 !   13.2   0.3   8.1e-05     0.066      14      37 ..     416     450 ..     412     457 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.015
                               DZR  12 arfCseCgtklka 24 
                                       +++C+ Cgt++  
  gi|557695068|ref|YP_008798122.1| 176 NNYCPMCGTTIAD 188
                                       679*****99864 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 8.1e-05
                               DZR  14 fCseCgtklkavaa...........edrCpsCgek 37 
                                       +C+ Cgt++ +               +rCp+Cg+ 
  gi|557695068|ref|YP_008798122.1| 416 YCNSCGTPVLPDDGqyhqpwrekapVERCPKCGST 450
                                       9*******7643337999**************985 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 !   17.8   0.0   2.2e-06    0.0018      85     146 ..     242     303 ..     235     327 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.2e-06
                     tRNA-synt_1_2  85 tglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedee 146
                                       ++ +a+ P+ g+k+pi        ++gtgavm +   d+ D +  ++ +lp k vi+ e++ 
  gi|557695068|ref|YP_008798122.1| 242 ENKTATTPLFGDKVPIIARPEAKPDFGTGAVMVCSYGDHTDVRLFRELKLPEKIVITLEGRM 303
                                       67899***************************************************987654 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   0.0    0.0068       5.5      10      35 ..     166     192 ..     163     195 .. 0.81
   2 ?    0.5   0.0      0.53   4.3e+02      21      32 ..     416     428 ..     415     437 .. 0.80
   3 !    8.1   0.3    0.0023       1.9       2      17 ..     443     458 ..     442     461 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0068
                                       E.CHEETSTTCEEESSSSBEEEECCCC CS
                      TF_Zn_Ribbon  10 n.lveDpergelvCtdCGlVlednsid 35 
                                       n lv+ ++r + +C+ CG+ + d  ++
  gi|557695068|ref|YP_008798122.1| 166 NgLVYRASRPNNYCPMCGTTIADAEVE 192
                                       55789999999*******999887665 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.53
                                       EESSS.SBEEEEC CS
                      TF_Zn_Ribbon  21 vCtdC.GlVledn 32 
                                       +C +C ++Vl d+
  gi|557695068|ref|YP_008798122.1| 416 YCNSCgTPVLPDD 428
                                       6****77888776 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0023
                                       EETTTTCEECHEETST CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDper 17 
                                       +CP+Cgst++  D+ +
  gi|557695068|ref|YP_008798122.1| 443 RCPKCGSTSFRGDERT 458
                                       6*******99666544 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   0.1     0.016        13       3      14 ..     177     189 ..     175     192 .. 0.77
   2 !    6.2   0.3    0.0086         7       4      16 ..     416     428 ..     415     430 .. 0.75
   3 !    6.7   0.1    0.0059       4.8       3      10 ..     442     449 ..     440     457 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
                       zf-ribbon_3   3 vrCPnCGa.plss 14 
                                       ++CP CG+ ++++
  gi|557695068|ref|YP_008798122.1| 177 NYCPMCGTtIADA 189
                                       79****9988665 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0086
                       zf-ribbon_3   4 rCPnCGaplssdd 16 
                                       +C++CG+p+ +dd
  gi|557695068|ref|YP_008798122.1| 416 YCNSCGTPVLPDD 428
                                       7******654443 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0059
                       zf-ribbon_3   3 vrCPnCGa 10 
                                        rCP+CG+
  gi|557695068|ref|YP_008798122.1| 442 ERCPKCGS 449
                                       58****98 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1     0.004       3.2       1       9 [.     178     186 ..     176     191 .. 0.62
   2 ?    5.5   0.2     0.018        15       1      10 [.     416     425 ..     416     428 .. 0.65
   3 ?    4.7   0.4     0.032        26       2       6 ..     444     448 ..     441     450 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.004
                     zinc_ribbon_2   1 fCpnCGael 9  
                                       +Cp CG+++
  gi|557695068|ref|YP_008798122.1| 178 YCPMCGTTI 186
                                       566666665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.018
                     zinc_ribbon_2   1 fCpnCGaelq 10 
                                       +C +CG+++ 
  gi|557695068|ref|YP_008798122.1| 416 YCNSCGTPVL 425
                                       6777777774 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.032
                     zinc_ribbon_2   2 CpnCG 6  
                                       Cp+CG
  gi|557695068|ref|YP_008798122.1| 444 CPKCG 448
                                       77777 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0083       6.8       1      11 [.     177     187 ..     177     196 .. 0.79
   2 ?    6.7   3.2    0.0083       6.8       2      31 ..     416     450 ..     415     452 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0083
                                       -B-TTT--B-E CS
                         Nudix_N_2   1 kFCsqCGtpve 11 
                                       ++C++CGt+++
  gi|557695068|ref|YP_008798122.1| 177 NYCPMCGTTIA 187
                                       7******9865 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0083
                                       B-TTT--B-E.....EE--TT-SS-EEEETTTTEE CS
                         Nudix_N_2   2 FCsqCGtpve.....lripdgDnreRlvCpaCgti 31 
                                       +C++CGtpv      ++ p  ++ +  +Cp+Cg +
  gi|557695068|ref|YP_008798122.1| 416 YCNSCGTPVLpddgqYHQPWREKAPVERCPKCGST 450
                                       9*******976777799999999999999999975 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.34   2.7e+02      24      34 ..     174     184 ..     168     188 .. 0.73
   2 ?   11.3   0.5   0.00034      0.28       8      35 ..     417     450 ..     409     453 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.34
                       Zn-ribbon_8  24 apltaCPeCgs 34 
                                       +p+  CP Cg 
  gi|557695068|ref|YP_008798122.1| 174 RPNNYCPMCGT 184
                                       45667999997 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00034
                       Zn-ribbon_8   8 CeeCghefe.....vlqsisdaplta.CPeCgse 35 
                                       C++Cg+          q+  ++++++ CP+Cgs+
  gi|557695068|ref|YP_008798122.1| 417 CNSCGTPVLpddgqYHQPWREKAPVErCPKCGST 450
                                       999999998888886777776666666*****94 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 ?    0.9   0.0      0.28   2.3e+02      23      47 ..      55      79 ..      25      84 .. 0.82
   2 ?    9.9   0.0    0.0005      0.41     237     281 ..     518     562 ..     509     581 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.28
                                      -BHHHHHHHHHHHHHHHHHHHTT-E CS
                      tRNA-synt_1e 23 shlGhaRslvafDilrrilqalgYd 47
                                       h+G a  +  +D+++r+ +++gY 
  gi|557695068|ref|YP_008798122.1| 55 WHIGAAAHYSQIDMIARTARMMGYM 79
                                      4888888888888888888888885 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0005
                                       -EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHH CS
                      tRNA-synt_1e 237 lvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllll 281
                                       + k ++    l  +gekmsks +n+i    +l+k+ +  +R+  +
  gi|557695068|ref|YP_008798122.1| 518 FNKVWISGLGLDEHGEKMSKSKGNVIDPMPILEKYGADCFRFWNA 562
                                       566777777778899***********************9998755 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 ?   -2.1   0.0       1.7   1.3e+03      33      59 ..      50      77 ..      35      82 .. 0.87
   2 ?   11.2   0.0   0.00016      0.13     275     310 ..     528     563 ..     490     580 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.7
                      tRNA-synt_1f 33 pSGli.HiGnlrevltadlvaralrkrg 59
                                      pSG++ HiG +    + d++ar  r +g
  gi|557695068|ref|YP_008798122.1| 50 PSGRPwHIGAAAHYSQIDMIARTARMMG 77
                                      899766***************9998776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00016
                      tRNA-synt_1f 275 llkggekmssSkGnvltledwlevaepevlrflilr 310
                                       l+++gekms+SkGnv+ +  +le +  +  rf  ++
  gi|557695068|ref|YP_008798122.1| 528 LDEHGEKMSKSKGNVIDPMPILEKYGADCFRFWNAQ 563
                                       577888*****************9999999998887 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.25   2.1e+02       1      13 [.     178     190 ..     178     197 .. 0.78
   2 ?    4.6   0.0     0.024        20      15      26 ..     410     421 ..     402     421 .. 0.83
   3 ?    4.2   0.1     0.034        28      18      26 ..     440     448 ..     436     459 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.25
                          zf-TFIIB   1 kCPkCqdeleese 13 
                                       +CP C+++  ++e
  gi|557695068|ref|YP_008798122.1| 178 YCPMCGTTIADAE 190
                                       7999999877665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.024
                          zf-TFIIB  15 ggveidyCpqCr 26 
                                        +v+++yC++C+
  gi|557695068|ref|YP_008798122.1| 410 TEVPVWYCNSCG 421
                                       68*********7 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.034
                          zf-TFIIB  18 eidyCpqCr 26 
                                       ++++Cp+C+
  gi|557695068|ref|YP_008798122.1| 440 PVERCPKCG 448
                                       566677665 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 ?   -0.8   0.0       1.8   1.5e+03      64      81 ..     170     187 ..     152     198 .. 0.66
   2 ?    9.9   0.1    0.0009      0.73      69      97 ..     413     452 ..     394     458 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.8
                                       EEEE--EEEETTTS-EEE CS
                              HypA  64 ieevpvkvrCreCgkefe 81 
                                       ++  + + +C  Cg+++ 
  gi|557695068|ref|YP_008798122.1| 170 YRASRPNNYCPMCGTTIA 187
                                       445555556666666555 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0009
                                       -EEEETTTS-EEECHH.HHH...........S-TTTSSS-E CS
                              HypA  69 vkvrCreCgkefelee.kal...........rCpkCgsadv 97 
                                        + +C++Cg+ +  ++ + +           rCpkCgs+++
  gi|557695068|ref|YP_008798122.1| 413 PVWYCNSCGTPVLPDDgQ-YhqpwrekapveRCPKCGSTSF 452
                                       4678*****999977533.345899999**********876 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 ?    2.3   0.0      0.17   1.4e+02       4      12 ..     177     185 ..     174     193 .. 0.79
   2 ?    3.5   0.0     0.068        55       5      20 ..     416     431 ..     416     433 .. 0.85
   3 ?    2.1   0.6      0.19   1.5e+02       6      11 ..     444     449 ..     443     453 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.17
                     zf-NADH-PPase   4 rFCgrCGap 12 
                                        +C+ CG+ 
  gi|557695068|ref|YP_008798122.1| 177 NYCPMCGTT 185
                                       69*****96 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.068
                     zf-NADH-PPase   5 FCgrCGaptepaeggw 20 
                                       +C  CG+p+ p +g++
  gi|557695068|ref|YP_008798122.1| 416 YCNSCGTPVLPDDGQY 431
                                       6889*****9999987 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.19
                     zf-NADH-PPase   6 CgrCGa 11 
                                       C++CG+
  gi|557695068|ref|YP_008798122.1| 444 CPKCGS 449
                                       666665 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 ?    3.2   0.1      0.12        98       4      17 ..     179     192 ..     177     193 .. 0.88
   2 ?   -0.5   0.0       1.7   1.4e+03       5      13 ..     224     232 ..     224     233 .. 0.91
   3 ?    3.1   0.0      0.13     1e+02       3      11 ..     416     424 ..     415     428 .. 0.83
   4 ?    3.4   0.1       0.1        85       3      10 ..     443     450 ..     443     455 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.12
                            zf-ACC   4 CpsCgemlykkeLe 17 
                                       Cp Cg+++   e+e
  gi|557695068|ref|YP_008798122.1| 179 CPMCGTTIADAEVE 192
                                       ********988887 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.7
                            zf-ACC   5 psCgemlyk 13 
                                       p+C +++y+
  gi|557695068|ref|YP_008798122.1| 224 PACAAVIYN 232
                                       89******7 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.13
                            zf-ACC   3 KCpsCgeml 11 
                                        C+sCg+ +
  gi|557695068|ref|YP_008798122.1| 416 YCNSCGTPV 424
                                       7*****987 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.1
                            zf-ACC   3 KCpsCgem 10 
                                       +Cp+Cg++
  gi|557695068|ref|YP_008798122.1| 443 RCPKCGST 450
                                       59***986 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 ?   -1.9   0.1       6.8   5.6e+03       5      11 ..     179     185 ..     177     189 .. 0.87
   2 ?    3.5   0.2      0.15   1.2e+02       3      24 ..     415     436 ..     413     437 .. 0.92
   3 ?    7.3   0.0    0.0091       7.4       3      19 ..     442     458 ..     440     468 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.8
                           zf-ISL3   5 CPnCgsk 11 
                                       CP Cg +
  gi|557695068|ref|YP_008798122.1| 179 CPMCGTT 185
                                       *****86 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.15
                           zf-ISL3   3 hrCPnCgsktvvkhgkkerrvr 24 
                                       + C  Cg +++ + g++++ +r
  gi|557695068|ref|YP_008798122.1| 415 WYCNSCGTPVLPDDGQYHQPWR 436
                                       77*******************9 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0091
                           zf-ISL3   3 hrCPnCgsktvvkhgkk 19 
                                        rCP+Cgs++ +   + 
  gi|557695068|ref|YP_008798122.1| 442 ERCPKCGSTSFRGDERT 458
                                       69*******98876655 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 ?    2.0   0.2      0.28   2.3e+02      15      23 ..     176     184 ..     175     189 .. 0.80
   2 ?    4.2   0.0     0.059        48      17      29 ..     416     428 ..     415     433 .. 0.81
   3 ?    2.7   0.1      0.17   1.4e+02      16      30 ..     442     454 ..     441     459 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.28
                     Auto_anti-p27  15 aetCpvCgv 23 
                                       + +Cp Cg+
  gi|557695068|ref|YP_008798122.1| 176 NNYCPMCGT 184
                                       578999976 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.059
                     Auto_anti-p27  17 tCpvCgvPLmrdr 29 
                                       +C  Cg+P + d 
  gi|557695068|ref|YP_008798122.1| 416 YCNSCGTPVLPDD 428
                                       7********9963 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.17
                     Auto_anti-p27  16 etCpvCgvPLmrdrk 30 
                                       e Cp+Cg+  +r  +
  gi|557695068|ref|YP_008798122.1| 442 ERCPKCGSTSFR--G 454
                                       57****998888..4 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 ?    1.2   0.0      0.44   3.6e+02      15      26 ..     164     184 ..     162     190 .. 0.68
   2 ?    3.0   0.3      0.13     1e+02      28      44 ..     406     421 ..     402     422 .. 0.71
   3 ?    6.2   0.3     0.013        10      15      28 ..     435     451 ..     434     459 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.44
                     Zn_Tnp_IS1595  15 Wpng.........fvCPhCgs 26 
                                       W+ng           CP Cg 
  gi|557695068|ref|YP_008798122.1| 164 WKNGlvyrasrpnNYCPMCGT 184
                                       666666666664344****95 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.13
                     Zn_Tnp_IS1595  28 kayriktrglfqCkeCr 44 
                                       ++y ++   ++ C++C+
  gi|557695068|ref|YP_008798122.1| 406 RYYATE-VPVWYCNSCG 421
                                       455555.589******8 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.013
                     Zn_Tnp_IS1595  15 Wpng...fvCPhCgsrk 28 
                                       W+++    +CP+Cgs++
  gi|557695068|ref|YP_008798122.1| 435 WREKapvERCPKCGSTS 451
                                       677775445*****875 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 ?    2.6   0.1      0.16   1.3e+02      24      33 ..     175     184 ..     175     188 .. 0.81
   2 ?    3.2   0.2       0.1        83      13      23 ..     416     426 ..     415     428 .. 0.91
   3 ?    5.9   0.5     0.014        12      27      36 ..     443     452 ..     440     453 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.16
                           DUF35_N  24 PravCphCgs 33 
                                       P ++Cp+Cg 
  gi|557695068|ref|YP_008798122.1| 175 PNNYCPMCGT 184
                                       6689****96 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.1
                           DUF35_N  13 rCpdCGtvqfP 23 
                                       +C +CGt + P
  gi|557695068|ref|YP_008798122.1| 416 YCNSCGTPVLP 426
                                       7******9988 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.014
                           DUF35_N  27 vCphCgsddl 36 
                                        Cp+Cgs+++
  gi|557695068|ref|YP_008798122.1| 443 RCPKCGSTSF 452
                                       5666666654 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 ?    4.2   0.0     0.055        45       2      10 ..     179     187 ..     178     194 .. 0.81
   2 ?   -1.3   0.1       2.9   2.4e+03       4       9 ..     419     424 ..     416     429 .. 0.81
   3 ?    4.6   0.2     0.042        34       1       8 [.     443     450 ..     443     456 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.055
                    DNA_ligase_ZBD   2 CPvCGsavv 10 
                                       CP CG+ + 
  gi|557695068|ref|YP_008798122.1| 179 CPMCGTTIA 187
                                       *****9875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.9
                    DNA_ligase_ZBD   4 vCGsav 9  
                                       +CG++v
  gi|557695068|ref|YP_008798122.1| 419 SCGTPV 424
                                       8***99 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.042
                    DNA_ligase_ZBD   1 hCPvCGsa 8  
                                       +CP CGs 
  gi|557695068|ref|YP_008798122.1| 443 RCPKCGST 450
                                       5*****95 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 ?   -2.9   0.2       6.9   5.7e+03      23      29 ..     178     184 ..     178     186 .. 0.80
   2 ?    3.4   0.8     0.074        60      22      29 ..     415     422 ..     415     422 .. 0.95
   3 ?    8.9   0.2    0.0014       1.1       4      16 ..     441     453 ..     439     456 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.9
                           zf-RRN7  23 yCrrCht 29 
                                       yC  C+t
  gi|557695068|ref|YP_008798122.1| 178 YCPMCGT 184
                                       8999998 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.074
                           zf-RRN7  22 yyCrrCht 29 
                                       +yC++C+t
  gi|557695068|ref|YP_008798122.1| 415 WYCNSCGT 422
                                       8******8 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.0014
                           zf-RRN7   4 gppCgvCgcrsft 16 
                                       +++C+ Cg++sf+
  gi|557695068|ref|YP_008798122.1| 441 VERCPKCGSTSFR 453
                                       68**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (775 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); 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: 0.71u 0.26s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 4953.91
//
Query:       gi|557695069|ref|YP_008798123.1|  [L=162]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   63.4   0.1    2.6e-17   63.1   0.1    1.1  1  NUDIX     NUDIX domain
  ------ inclusion threshold ------
      0.044   13.7   0.0      0.056   13.4   0.0    1.2  1  BphX      BphX-like


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 !   63.1   0.1   2.9e-21   2.6e-17       4     119 ..       6     120 ..       3     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 2.9e-21
                                       EEEEEEEEETTSEEEEEEESSSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   4 ravgvvllnekgevLlvrrskkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgpyg 79 
                                        +vg++++++ g++Llv +   ++   +++PgG+v+ gE++ +A++RE++EE+Gl+++ ++++++ +   p +++ +
  gi|557695069|ref|YP_008798123.1|   6 LTVGAFIIDDSGKLLLVVSP--KWGYlYSIPGGHVDHGEKIFQAVVREAWEEVGLKVKPVRVIAVQEVINPRHFKSR 80 
                                       689**********9999877..4444558**********888**********************9999999999999 PP

                                       EEEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHH CS
                             NUDIX  80 deheilyvfleevegelepndenevsevrwvpleellkek 119
                                       ++h++++ +l+++  +  + d +e+ ++ w ++  + + +
  gi|557695069|ref|YP_008798123.1|  81 RRHFVFVDVLCKALNDRVLVDGEEIVGYIWKEPGHAFELP 120
                                       888888777755555555556*****99998888874444 PP

>> BphX  BphX-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.3e-06     0.056      29      79 ..      25      78 ..       6     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-06
                              BphX 29 gllelly..PGveldqgepifk.llldawlvvGlqlaaiGvvalwGardPlryl 79
                                      ++   ly  PG ++d ge if+ ++++aw  vGl++  + v+a+    +P ++ 
  gi|557695069|ref|YP_008798123.1| 25 PKWGYLYsiPGGHVDHGEKIFQaVVREAWEEVGLKVKPVRVIAVQEVINPRHFK 78
                                      444444444999*********84578******************9999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); 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: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1221.58
//
Query:       gi|557695070|ref|YP_008798124.1|  [L=406]
Description: hypothetical protein CSUB_C1643 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.9        2.2    8.3   0.0    2.4  2  DUF2103   Predicted metal-binding protein (DUF2103)


Domain annotation for each model (and alignments):
>> DUF2103  Predicted metal-binding protein (DUF2103)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2    0.0084   1.5e+02      43      74 ..     163     195 ..     143     206 .. 0.77
   2 ?    8.3   0.0   0.00013       2.2      48      87 ..     259     299 ..     249     307 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0084
                           DUF2103  43 kgsssggglrvkvt.raderGnlrlllrdgssv 74 
                                       +g+++g++++v++   +++rG +++ +++++ +
  gi|557695070|ref|YP_008798124.1| 163 GGEVDGRQMEVSIAtVTTSRGEVKIYVTQETGT 195
                                       35677777777775246899******9998865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00013
                           DUF2103  48 ggglrvkvt.raderGnlrlllrdgssvQevfivttakdre 87 
                                       +++ +vkv  +  +rG +rl+l+++ss Q   i+ ++++  
  gi|557695070|ref|YP_008798124.1| 259 KTEYDVKVVeQGFDRGFIRLVLSSDSSEQGRLIILDVDKSI 299
                                       556667776244589*******************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       731  (0.0407719); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3030.67
//
Query:       gi|557695071|ref|YP_008798125.1|  [L=287]
Description: hypothetical protein CSUB_C1644 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-08   32.7   0.0    1.6e-07   31.2   0.0    1.7  2  HTH_20    Helix-turn-helix domain
    1.7e-07   31.0   0.0    5.4e-07   29.4   0.0    1.9  2  HTH_5     Bacterial regulatory protein, arsR family
    0.00021   20.8   0.0    0.00039   19.9   0.0    1.5  1  HTH_24    Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.024   14.6   0.0      0.047   13.6   0.0    1.5  1  HTH_11    HTH domain
      0.065   13.4   0.0       0.12   12.5   0.0    1.5  1  HTH_34    Winged helix DNA-binding domain
      0.099   12.7   0.0       0.21   11.7   0.0    1.5  1  HTH_Mga   M protein trans-acting positive regulator (MGA) HTH
       0.37   10.5  22.8       0.58    9.8  22.8    1.2  1  Yip1      Yip1 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 !   31.2   0.0   6.4e-11   1.6e-07       6      46 ..      28      68 ..      23      71 .. 0.92
   2 ?   -3.2   0.0       3.6   9.3e+03      24      41 ..     118     135 ..     118     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 6.4e-11
                                      HHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHH CS
                            HTH_20  6 ALahPvRrrilraLaraegltaselaerldlskntlsyHLr 46
                                      +L +PvRr i  +L++++ + as+l+++l++s  tl+yHL+
  gi|557695071|ref|YP_008798125.1| 28 LLKNPVRRQIITLLKENGSMAASDLKKLLGISVGTLYYHLE 68
                                      5778***********************************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.6
                                       TB-HHHHHHHHTS-HHHH CS
                            HTH_20  24 gltaselaerldlskntl 41 
                                       ++t+++l +r++l+ +tl
  gi|557695071|ref|YP_008798125.1| 118 AFTLNPLLQRIQLTNTTL 135
                                       589999999999988775 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 !   29.4   0.0   2.1e-10   5.4e-07       1      39 [.      31      70 ..      31      71 .. 0.96
   2 ?   -2.5   0.0       1.9     5e+03      15      31 ..      94     110 ..      90     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 2.1e-10
                                      SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHH CS
                             HTH_5  1 dptRlkILklLae.gelcvcelaeelglsqstvShHLkkL 39
                                      +p R++I+ lL e g++ +++l + lg+s +t+ +HL ++
  gi|557695071|ref|YP_008798125.1| 31 NPVRRQIITLLKEnGSMAASDLKKLLGISVGTLYYHLEFM 70
                                      699**********************************876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.9
                                       SEEHHHHHHHHTS-HHH CS
                             HTH_5  15 elcvcelaeelglsqst 31 
                                       +++v++  +e+ + +++
  gi|557695071|ref|YP_008798125.1|  94 SMKVSDFLAETSVAEPA 110
                                       68999999999888875 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 !   19.9   0.0   1.5e-07   0.00039       2      41 ..      31      70 ..      30      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.5e-07
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrL 41
                                      +  +r+I+ lL++n+++  ++L + lg+S++t+ ++l+ +
  gi|557695071|ref|YP_008798125.1| 31 NPVRRQIITLLKENGSMAASDLKKLLGISVGTLYYHLEFM 70
                                      6678********************************9865 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.8e-05     0.047       2      37 ..      34      68 ..      33      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                            HTH_11  2 llqilelLleargpisgeeLAeeLnvSrrtvrrdIk 37
                                      ++qi++lL+e+ + + +++L++ L++S  t + +++
  gi|557695071|ref|YP_008798125.1| 34 RRQIITLLKENGS-MAASDLKKLLGISVGTLYYHLE 68
                                      69******66666.****************998876 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 ?   12.5   0.0   4.8e-05      0.12       1      38 [.      33      70 ..      33      90 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.8e-05
                            HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkL 38
                                      vR +++++L ++ ++ +++lk+ l+++ g L+ hl+ +
  gi|557695071|ref|YP_008798125.1| 33 VRRQIITLLKENGSMAASDLKKLLGISVGTLYYHLEFM 70
                                      68899*****************************9865 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 ?   11.7   0.0     8e-05      0.21       9      45 ..      36      71 ..      35      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8e-05
                           HTH_Mga  9 kLlelLteneksltldelakeLglseltlqsdiseLn 45
                                      ++++lL e ++s+  ++l+k Lg+s  tl   +++++
  gi|557695071|ref|YP_008798125.1| 36 QIITLLKE-NGSMAASDLKKLLGISVGTLYYHLEFMQ 71
                                      67888888.****************999977777777 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8  22.8   0.00023      0.58      29     167 ..     138     277 ..     126     283 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00023
                              Yip1  29 lalltlllgllaslnlgqtlasgeevqgltlssllgaiiggylgl...llgllllalllhliakllggkgsfkqtls 102
                                       + l+++++     l l++ l++++ +  ++ + +   ++++++g    l+ l+l+a++l+        kg  + + +
  gi|557695071|ref|YP_008798125.1| 138 VSLASAMVY----LLLSWRLSNSQLILHFRPVGFPELALLYAVGNlvfLIVLMLVAGFLTT-----FKKGGEGLIAA 205
                                       333333333....455688888866666666666666666666652224444444444444.....24444445999 PP

                              Yip1 103 vvgyallPlilgaliaillllllgt.......llllvgllaliWslvllylglkaahnlskkkallaalill 167
                                        v +al+P+ l++ ++++++ ++         +++ v + + +W++++l+  l +a ++s++ka++a+++l 
  gi|557695071|ref|YP_008798125.1| 206 TVPLALTPSNLLLTVFAVFSGFGLLgngwfgtVSFGVYVFFHVWQMAALAAVLVSAKGVSWEKAVAAVVALS 277
                                       99999999999999999999998889999999************************************9833 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2033.47
//
Query:       gi|557695072|ref|YP_008798126.1|  [L=281]
Description: protoheme IX farnesyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-51  173.6  28.4    6.4e-51  173.1  28.4    1.2  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 !  173.1  28.4   3.6e-55   6.4e-51       4     250 ..      20     264 ..      16     278 .. 0.90

  Alignments for each domain:
  == domain 1  score: 173.1 bits;  conditional E-value: 3.6e-55
                              UbiA   4 palvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilg 80 
                                       +a+ + +l+a gsp   +++ lll+++l  ++a alN+++D++iD++m+rt  RP+++Gri p++a +++ ++++++
  gi|557695072|ref|YP_008798126.1|  20 FAASASFLSAEGSPA--NMIHLLLAGYLSVGGASALNHFLDADIDSRMRRTSGRPIPAGRIRPRTAALLGSIMVAAA 94 
                                       444456666666544..4899999***************************************************** PP

                              UbiA  81 llllalllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavfllt 156
                                       +l +++++nplta+++l + l+y +vYt ++lKrrt++++v+gg+a+ ++pl+gw a++ ++ +l+l++al+vfl+t
  gi|557695072|ref|YP_008798126.1|  95 VLYSYVMYNPLTAIFILSGALVYvFVYT-VWLKRRTVWNIVIGGVAGSFAPLAGWSAAGREIEALPLFMALLVFLWT 170
                                       ****************************.9*********************************************** PP

                              UbiA 157 waialandlrdregDrkagiktlpvvlGrkaaril.lalllavlllallllllalllllylllalllaalallraar 232
                                        ++++a + r ++++ +ag+++lpvv+G +++ i  l++ ++++ +all+++l    llyl++a+++ a++l+ +++
  gi|557695072|ref|YP_008798126.1| 171 PGHFWALASRAVKDYSAAGVPMLPVVYGVQTTSIAtLVSNVIAVAAALLMATLVSNPLLYLVIAAPFSAWLLIESIK 247
                                       **********************************7633333333333566888888888999999999999999999 PP

                              UbiA 233 lvrrrdakkaakfflfls 250
                                        + ++++++a+++f ++s
  gi|557695072|ref|YP_008798126.1| 248 PCIKYSPSAAWRAF-KIS 264
                                       999999**999999.665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       769  (0.0428914); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
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 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1897.31
//
Query:       gi|557695073|ref|YP_008798127.1|  [L=236]
Description: sugar fermentation stimulation protein A [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  112.3   0.0    2.2e-32  111.8   0.0    1.2  1  SfsA      Sugar fermentation stimulation protein RE domain
    3.8e-11   43.0   0.0    7.1e-11   42.1   0.0    1.5  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 !  111.8   0.0   2.5e-36   2.2e-32       2     137 ..      87     222 ..      86     223 .. 0.95

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 2.5e-36
                                       HHHHHHHHHHEE...........EEES-EETTEE-SEEEE-S.SSEEEEEEEE--EE...EEEEE-SS--HHHHHHH CS
                              SfsA   2 lpnklveealesgli.elagyeeikrevkygnsriDfllekeeeekcyvEVKsvtlee.ggialfPdapteRgqkhl 76 
                                       l+ +++eea++++li  l++++ +++ev +  sriD+ll+++ +ek+++E+Ks+     +g a++Pd++++Rg+ h+
  gi|557695073|ref|YP_008798127.1|  87 LQARCFEEAFNRRLIpWLQKFSGYRKEVFFMGSRIDYLLSSN-GEKAFLELKSAAYLGrDGAAMYPDTVSTRGRTHV 162
                                       67899**********99************************8.**********98885489**************** PP

                                       HHHHHHHHTT-EEEEEEEE-SSS--EEEE-TTT-HHHHHHHHHHHHHT-EEEEEEEEE-TT CS
                              SfsA  77 eeLaelvkegyravvlfvvqredarefkpnkeidpefaealreaaeaGVevlaydckvtpe 137
                                       ++Lae+++   +++++fv+  +dar f+p +e dp++  +l +a++aGVe+ ++++ +t +
  gi|557695073|ref|YP_008798127.1| 163 QKLAEIAAT-CQTYLVFVAALPDARFFTPCDEGDPDMRPLLIKARRAGVEIRCIKLYMTLD 222
                                       *******77.9********************************************999876 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 !   42.1   0.0   7.9e-15   7.1e-11       1      54 [.      20      74 ..      20      83 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 7.9e-15
                                      EEEEETTEEEEEEE.....EE----S--TTT--TT-EEEEE....ESSS-SEEEEEE CS
                            SfsA_N  1 lrRpnRFladveldg.t..vHvpntGrlkelllpGarvllsksdnpkrKtkytleav 54
                                      l R nRFl+++e +g +   H+ ntGrl +l++pGa++l++  + p  Kt+  l  v
  gi|557695073|ref|YP_008798127.1| 20 LTRLNRFLVEAEDNGeKvfLHLTNTGRLHDLIYPGATILYT--PRPSAKTAGVLAGV 74
                                      68**********9985378**********************..57889999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1758.32
//
Query:       gi|557695074|ref|YP_008798128.1|  [L=380]
Description: citrate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-128  428.9   0.0   1.7e-128  428.8   0.0    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain


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 !  428.8   0.0  9.3e-133  1.7e-128       1     361 []      11     363 ..      11     363 .. 0.97

  Alignments for each domain:
  == domain 1  score: 428.8 bits;  conditional E-value: 9.3e-133
                                       GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHH CS
                      Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlea 77 
                                       gl+++a+ et++s++dgekg+l+Y Gy+ieeLa e+ss+eev++lLl+g+lPt+ el++f+++l ++r lp++v++ 
  gi|557695074|ref|YP_008798128.1|  11 GLENIAIKETRLSSIDGEKGKLYYVGYSIEELA-EYSSYEEVCFLLLHGRLPTRTELENFSAMLVSERSLPRQVVDV 86 
                                       799******************************.8****************************************** PP

                                       HHCSSTTS-HHHHHHHHHHHHHHHSTTCTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHHHH CS
                      Citrate_synt  78 lealpkdahpmavlraavsalsaddeeseakeeseeaalrdalkliAklptiaaaiyrarlgreplepddklsyaen 154
                                       l++lp++a +m+ l ++v +ls +d+++e++++  e+ +++a +li+k++t++a++yr  +g ep+ep+++ls+a n
  gi|557695074|ref|YP_008798128.1|  87 LRTLPRTAPMMSWLKTGVDLLSLFDPDAEKTDD--ESRMKTATRLISKVATLTATAYRLARGLEPVEPRSDLSHAGN 161
                                       *************************97555555..777888889*************************99****** PP

                                       HHHHHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHHH CS
                      Citrate_synt 155 flymlrgkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmleei 231
                                       flym++g+k ++ e+k++d+a++lha+Hel aST aa vvaStl+dlysa++agigalkGplhggane++l+ml+ i
  gi|557695074|ref|YP_008798128.1| 162 FLYMVTGNKSSPLEEKIMDVAFILHAEHELPASTTAALVVASTLSDLYSAVSAGIGALKGPLHGGANERALEMLQTI 238
                                       *******999******************************************************************* PP

                                       SSGG.GHHHHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTCHTHHHHHHHHHHHHHHHHHHHHCHHGC CS
                      Citrate_synt 232 gsaeveveeylekvlakekerlpGfGHrvykksDpRakilkelaeelaeekgkdpllklaeeleevapevlkekeek 308
                                       gs++ +++ y+++ la+ k+r++GfGHrvy+++DpRa+i+k+++e+l+e+ g++ ll++ae++e+++ + +     k
  gi|557695074|ref|YP_008798128.1| 239 GSPD-KADGYVANELAA-KRRIMGFGHRVYRSFDPRARIFKRYLEQLSEKRGDKTLLQVAEAVENAVIKRMG--G-K 310
                                       ****.***********7.6**************************************************444..6.9 PP

                                       T-EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHHHT------E CS
                      Citrate_synt 309 nlypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileqladnkiiRPr 361
                                       +++pN+D+ysg +++ lg+ +e+ft++fa++R++GwlAh+le+ +dn++iRPr
  gi|557695074|ref|YP_008798128.1| 311 SIFPNIDLYSGPVFHLLGLGKEIFTPFFAAARTVGWLAHVLEYWRDNRLIRPR 363
                                       ******************************************88********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2905.92
//
Query:       gi|557695075|ref|YP_008798129.1|  [L=568]
Description: long-chain-fatty-acid--CoA ligase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-104  349.5   0.0   3.4e-104  348.8   0.0    1.3  2  AMP-binding    AMP-binding enzyme
    2.6e-18   66.8   1.8    2.6e-18   66.8   1.8    2.0  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
        0.1   12.7   1.5        2.8    8.1   0.2    3.0  3  Thioredoxin_3  Thioredoxin 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 !  348.8   0.0  5.6e-108  3.4e-104       1     421 [.      37     464 ..      37     466 .. 0.87
   2 ?   -3.6   0.0      0.54   3.2e+03      73      97 ..     504     528 ..     503     542 .. 0.86

  Alignments for each domain:
  == domain 1  score: 348.8 bits;  conditional E-value: 5.6e-108
                                       HHHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEE CS
                       AMP-binding   1 leeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpl 77 
                                       +++++ k+p+kva ++   ++ +T++ l++ ++r+A++Lr+lGv+kg+rV+i+lpns++++v++++ilk Ga+vvp+
  gi|557695075|ref|YP_008798129.1|  37 FDDTCSKYPKKVAAIF--LDTPVTFEALKNFSDRFASALRKLGVGKGSRVMIVLPNSIQFIVSYYGILKTGATVVPV 111
                                       678999**********..99********************************************************* PP

                                       ETTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSC..C-EECEEEEESCCS-HCCHCCCHCCCCSCTTS.... CS
                       AMP-binding  78 nptltaeelayiledseakvliatvdselleklleaaak..leavklvivldadellkeeelkeeeeseekae.... 148
                                       np +t +e++ + + seakv++  + +  ++++  a ++  +++v ++ + d+ ++lk +  k+ ++ ++k+     
  gi|557695075|ref|YP_008798129.1| 112 NPLSTGQEIKELAKLSEAKVIV--TLDLFIDEVMGALGEttVKHVVVTNIADHLPALKRTLGKILKKIPSKQLpsns 186
                                       **********************..44444666655555411355555666677777777666666666666525677 PP

                                       ..............-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH..HHHCSCCTTT-EEEESS CS
                       AMP-binding 149 ..............kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslk..letrfklkeddvvlsil 209
                                                     +  e++ + ++dla i++T+GTTG PKGVml+h n+v+n+ +++  ++++ + ++++++ + l
  gi|557695075|ref|YP_008798129.1| 187 simsyvemisgpveR-IEADVNPEKDLASIQFTGGTTGFPKGVMLTHHNIVSNIFQMYefIRPYLD-EANERFAALL 261
                                       888899999999962.344456789*******************************9987666644.3699****** PP

                                       -TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-S CS
                       AMP-binding 210 plahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslr 286
                                       p++hi+g+++ l + ll G t+v++p+ +   +  +++++ek+ vt+++gvP++++ + +++  +    + + ++l+
  gi|557695075|ref|YP_008798129.1| 262 PFYHIYGQSVILGAGLLMGNTLVVFPRLEL--E-KFMRDLEKYDVTIFPGVPTLFNLMSNHRLAD----QLRYPKLK 331
                                       ********999***************7776..3.367*********************9986555....557889** PP

                                       EEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTS CS
                       AMP-binding 287 lvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdge 363
                                       +v++g++ l+pe+++ f+++fg++++egYGl+E+++v++ ++ + dk+k+gs G p+p + ++i+++et e +++ge
  gi|557695075|ref|YP_008798129.1| 332 MVISGADMLPPEVAENFEKKFGRKIVEGYGLSEASPVTH-VN-PPDKVKRGSFGIPIPSTLAAIINPETREFLGPGE 406
                                       **************************************9.77.4555899*************************** PP

                                       EEEEEEEETTS-SEBTT-HHHHHHHEEET.CC.EEEEEEEEEEETTSEEEEEEECCCEEE CS
                       AMP-binding 364 eGellvrgpgvmkgYlkkpeataeafdse.gr.wlrTGDlgrldedGyleivgRkkdlik 421
                                       +Ge+ v+gp+vm+gYl++   ++ +f  e gr wlrTGD+g +d dGy++++ R+kd+ik
  gi|557695075|ref|YP_008798129.1| 407 VGEIIVSGPQVMQGYLGQ--DNSNVFLYEaGRkWLRTGDMGQMDSDGYFYFTERAKDIIK 464
                                       *****************9..4555666455777**************************9 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.54
                                       EEEEEETTS-HHHHHHHHHHHTESE CS
                       AMP-binding  73 vvvplnptltaeelayiledseakv 97 
                                       ++v+l p++++e+++ + e + +k+
  gi|557695075|ref|YP_008798129.1| 504 AAVVLKPGYGPEQVKTLHELCHSKL 528
                                       689999*******999999988876 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 ?   -2.4   0.0       1.7     1e+04      42      42 ..     151     151 ..     108     177 .. 0.58
   2 !   66.8   1.8   4.3e-22   2.6e-18       1      76 []     474     550 ..     474     550 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.7
                                       H CS
                     AMP-binding_C  42 l 42 
                                       +
  gi|557695075|ref|YP_008798129.1| 151 V 151
                                       2 PP

  == domain 2  score: 66.8 bits;  conditional E-value: 4.3e-22
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE----.--HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgs.ealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                       e+E +l +++aV+eaaVvG+pd+v Ge +va Vvlk+g+ ++  ++L + + ++l++y++p+++++vdelpk   GK
  gi|557695075|ref|YP_008798129.1| 474 EIEKVLYESDAVKEAAVVGIPDPVVGEKIVAAVVLKPGYgPEQVKTLHELCHSKLAEYKRPSEIILVDELPKSLVGK 550
                                       8***********************************99533468****************************98887 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.048   2.9e+02      35      64 ..     119     148 ..     112     156 .. 0.85
   2 ?   -1.3   0.0      0.39   2.4e+03      36      53 ..     292     309 ..     288     312 .. 0.82
   3 ?    8.1   0.2   0.00047       2.8      18      61 ..     457     504 ..     454     505 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.048
                                       CCTTHHHHHHCT-SSSSEEECTTCEEEESS CS
                     Thioredoxin_3  35 kvtdfeeiekygVmsvPalvidgkvvvsGk 64 
                                       +++++ ++++ +V+ +  l+id+++ + G+
  gi|557695075|ref|YP_008798129.1| 119 EIKELAKLSEAKVIVTLDLFIDEVMGALGE 148
                                       77899999***************9988884 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.39
                                       CTTHHHHHHCT-SSSSEE CS
                     Thioredoxin_3  36 vtdfeeiekygVmsvPal 53 
                                        + ++++eky V+  P++
  gi|557695075|ref|YP_008798129.1| 292 EKFMRDLEKYDVTIFPGV 309
                                       5678999*****999986 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00047
                                       HHHHHHCHCCTCEC...EEECC.TTHHHHHHCT-SSSSEEECTTCEEE CS
                     Thioredoxin_3  18 kavkeaaaekgika...evekv.tdfeeiekygVmsvPalvidgkvvv 61 
                                       + +k +++ kg+++   e+ekv ++++ +++  V  +P  v+ +k+v+
  gi|557695075|ref|YP_008798129.1| 457 ERAKDIIKHKGFTVfpaEIEKVlYESDAVKEAAVVGIPDPVVGEKIVA 504
                                       56788899999887788*****9999999***************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 4281.88
//
Query:       gi|557695076|ref|YP_008798130.1|  [L=120]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   0.2     0.0082   15.9   0.2    1.2  1  Hs1pro-1_N  Hs1pro-1 N-terminus


Domain annotation for each model (and alignments):
>> Hs1pro-1_N  Hs1pro-1 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.2   4.6e-07    0.0082     136     175 ..      74     116 ..      55     120 .] 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.6e-07
                        Hs1pro-1_N 136 rgtaPvadlsasngvlar...vvsktseasLLprlatwqksed 175
                                       ++ aP+a+ s+  +v+     +v ++s +sLL+++a w ks+ 
  gi|557695076|ref|YP_008798130.1|  74 VSFAPMANYSSMLSVEKGpeaMVINVSRSSLLTQVARWLKSKL 116
                                       6789****99998888767789*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       292  (0.0162865); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 930.09
//
Query:       gi|557695077|ref|YP_008798131.1|  [L=260]
Description: SAM-dependent methyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-49  166.6   0.0    7.2e-49  166.3   0.0    1.1  1  Met_10           Met-10+ like-protein
    1.6e-06   27.8   0.0    2.8e-06   27.0   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    2.5e-05   23.8   0.0    3.7e-05   23.2   0.0    1.2  1  DNA_methylase    C-5 cytosine-specific DNA methylase
    5.9e-05   22.8   0.0     0.0001   22.0   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
    0.00034   20.4   0.0     0.0013   18.5   0.0    1.8  2  N6_N4_Mtase      DNA methylase
    0.00041   19.8   0.0    0.00059   19.3   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0013   18.3   0.0     0.0021   17.6   0.0    1.3  1  MTS              Methyltransferase small domain
     0.0043   16.2   0.0     0.0066   15.5   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0053   17.4   0.0     0.0098   16.6   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.077   12.2   0.0      0.094   11.9   0.0    1.2  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
      0.089   12.6   0.0       0.13   12.1   0.0    1.2  1  PRMT5            PRMT5 arginine-N-methyltransferase
       0.17   11.5   0.1       0.36   10.4   0.1    1.6  1  GCD14            tRNA methyltransferase complex GCD14 subunit


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 !  166.3   0.0   4.8e-52   7.2e-49       6     199 .]       8     204 ..       4     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 166.3 bits;  conditional E-value: 4.8e-52
                                       ETTEEEEEB-TTSSHHHHHHHHHHHHHS.S-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS CS
                            Met_10   6 iGdvvilnlreelkeykkvigevildkt.kvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskv 81 
                                        G v+i++++   +   ++ ++vi+ ++  v+tvl+ + ++eg fR++ ++++aGs +t+t +kE g+ + +D s+ 
  gi|557695077|ref|YP_008798131.1|   8 LGRVAIVRVPRGSNIDLREFARVIMMRNnGVETVLEIE-RIEGPFRVPVIRHVAGSPDTVTTVKEDGIVYTFDASRL 83 
                                       688888888776665566778888877779****9865.56**************999******************* PP

                                       ---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES CS
                            Met_10  82 yfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpile 158
                                       +fs ++ +Er+r+ +l ++ge+Vvd+fAG+G+f++p+ak s a+ v++ ++n e++kyl +ni+lN+ve++v+++ +
  gi|557695077|ref|YP_008798131.1|  84 MFSLGNFEERRRIRRLPRPGEIVVDMFAGVGQFTLPAAK-SAANHVYSFEINEEAYKYLVKNIRLNHVEHKVTAFHT 159
                                       **************************************9.99999******************************** PP

                                       -GGG---...TT-EEEEEE--TTTGGGGHHHHHHHEEEE.EEEEE CS
                            Met_10 159 Dgrevir...eqladrvvmnlpksaieFldkvlaalkdg.gvihy 199
                                       D+r+ ++   +  adrv+m++ + + e+  ++l+ l+d  g+ih+
  gi|557695077|ref|YP_008798131.1| 160 DCRNAVNmglRGCADRVLMGYFRGTAEYFPTALQLLRDVgGFIHF 204
                                       ****99888899*************************96489998 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 !   27.0   0.0   1.9e-09   2.8e-06       2      82 ..     104     183 ..     103     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.9e-09
                   Methyltransf_15   2 rvilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvfl 77 
                                       ++++D+f+G G  +   a++  ++v++ ein+e  +   +N ++  v++k+t  + d+ ++++      +  d v++
  gi|557695077|ref|YP_008798131.1| 104 EIVVDMFAGVGQFTLPAAKSaANHVYSFEINEEAYKYLVKNIRLNHVEHKVTAFHTDCRNAVNMGLRG-C-ADRVLM 178
                                       689***********9999986889************************************99874433.3.366666 PP

                   Methyltransf_15  78 SpPwG 82 
                                           G
  gi|557695077|ref|YP_008798131.1| 179 GYFRG 183
                                       55555 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 !   23.2   0.0   2.5e-08   3.7e-05       3      54 ..     106     158 ..     105     171 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 2.5e-08
                                       EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-..-SEEEES-TTT CS
                     DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk.kvsigDitkid 54 
                                       ++d+faG+G f+l  ++   ++v++ ei+++a k + +n++ +++++++t + 
  gi|557695077|ref|YP_008798131.1| 106 VVDMFAGVGQFTLPAAKSAANHVYSFEINEEAYKYLVKNIRlNHVEHKVTAFH 158
                                       69**************************************9999999888765 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   6.7e-08    0.0001      42     104 ..     103     165 ..      90     177 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.7e-08
                                       C-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHH CS
                     Cons_hypoth95  42 garvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleal 104
                                       g+ v+D+faG G   l A+   a++++ +e ++ea+k l +n++  ++e++++++  d  +a+
  gi|557695077|ref|YP_008798131.1| 103 GEIVVDMFAGVGQFTLPAAKSAANHVYSFEINEEAYKYLVKNIRLNHVEHKVTAFHTDCRNAV 165
                                       5679*****************************************999999988888776655 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   8.9e-07    0.0013     183     229 ..      94     141 ..      93     144 .. 0.88
   2 ?   -1.2   0.0      0.88   1.3e+03     182     200 ..     237     256 ..     233     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.9e-07
                                       HHHHHHS-TT-EEEETT-TTTH.HHHHHHHTT-EEEEEESSHHHHHHH CS
                       N6_N4_Mtase 183 rlIklstkkgdivlDpFaGSGt.TavaakelgrkfiGieieeeyvela 229
                                       r I+ + ++g+iv+D FaG G  T+ aak+   + +++ei+ee+++  
  gi|557695077|ref|YP_008798131.1|  94 RRIRRLPRPGEIVVDMFAGVGQfTLPAAKSAANHVYSFEINEEAYKYL 141
                                       56888889************966********************99854 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.88
                                       HHHHHHHS-T.T-EEEETT- CS
                       N6_N4_Mtase 182 erlIklstkk.gdivlDpFa 200
                                       +r++k +++k   +vlD Fa
  gi|557695077|ref|YP_008798131.1| 237 KRVVKTYSPKlSHWVLDLFA 256
                                       7999****99999*****97 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0     4e-07   0.00059     158     215 ..      99     156 ..      93     176 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4e-07
                              PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklev 215
                                       l ++ge v+D+ +G G  ++ aak +a++v+   i+e A k   +N++lN+ve+k++ 
  gi|557695077|ref|YP_008798131.1|  99 LPRPGEIVVDMFAGVGQFTLPAAKSAANHVYSFEINEEAYKYLVKNIRLNHVEHKVTA 156
                                       66899*************************************************9865 PP

>> MTS  Methyltransferase small 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    0.0021      29      94 ..     101     166 ..      80     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.4e-06
                                       CCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST CS
                               MTS  29 kelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve 94 
                                           + v+D+ +G+G  ++ +ak   + +v  ++++ +A +   +n++ n++e  v+++++d+ ++v+
  gi|557695077|ref|YP_008798131.1| 101 R-PGEIVVDMFAGVGQFTLPAAKSAAN-HVYSFEINEEAYKYLVKNIRLNHVEhkVTAFHTDCRNAVN 166
                                       4.45669***************97777.8***********************9889999999988876 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   4.4e-06    0.0066      30      87 ..     102     163 ..      95     167 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.4e-06
                                       TTSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCG CS
                            RrnaAD  30 ekltvleigpGkGilTeeLakra.kqvvvlElderLakllqkkls...kdeklkvvhqDflk 87 
                                       +   v+++ +G+G +T + ak a ++v ++E+ e+ +k l k+++    ++k++  h+D  +
  gi|557695077|ref|YP_008798131.1| 102 PGEIVVDMFAGVGQFTLPAAKSAaNHVYSFEINEEAYKYLVKNIRlnhVEHKVTAFHTDCRN 163
                                       66779******************888889*************99998999*********876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   6.6e-06    0.0098       1      70 [.     106     178 ..     106     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.6e-06
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBS.S.STTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlp.f.edgsfDlvvs 70 
                                       v+d+ +G G++tl +ak   + +v+ ++i+ee+ ++  ++++ +++  +v+  + d+++       g  D v++
  gi|557695077|ref|YP_008798131.1| 106 VVDMFAGVGQFTLPAAKSA-ANHVYSFEINEEAYKYLVKNIRLNHVehKVTAFHTDCRNAVnMgLRGCADRVLM 178
                                       899***************7.8********************998889999999999987421224456666655 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.3e-05     0.094      54     113 ..     107     164 ..      67     201 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.3e-05
                                       EESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHH CS
                               TRM  54 ldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvl 113
                                       +d +++ G  ++  a+    +++v+  +i+e+A++ + +N++ln+ve+ v++ ++d +  
  gi|557695077|ref|YP_008798131.1| 107 VDMFAGVGQFTLPAAKS--AANHVYSFEINEEAYKYLVKNIRLNHVEHKVTAFHTDCRNA 164
                                       56666666666666665..67889999********************9887776676544 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.8e-05      0.13      88     134 ..     123     166 ..     105     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.8e-05
                                       HHCCCEEEEEEEES-HHHHHHHHHHHHHHTTCCGCEEEES-CCCCCH CS
                             PRMT5  88 etkvtkvkivavEKnpnavvtLqkkvneekWeekveviksdmrelka 134
                                       +      +++  E n++a+ +L k+++ ++ e+kv+ +++d r+  +
  gi|557695077|ref|YP_008798131.1| 123 S---AANHVYSFEINEEAYKYLVKNIRLNHVEHKVTAFHTDCRNAVN 166
                                       3...34689*********************************98654 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00024      0.36      40     119 ..     102     178 ..      65     202 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                             GCD14  40 pGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtvthrDvckeGfdeevsgkvDa 116
                                       pG  vv+  +G g ++   a++     h+++fe  e+ ++  +++ r +++++ vt  h D c++  + ++ g +D 
  gi|557695077|ref|YP_008798131.1| 102 PGEIVVDMFAGVGQFTLPAAKSA--ANHVYSFEINEEAYKYLVKNIRLNHVEHKVTAFHTD-CRNAVNMGLRGCADR 175
                                       67777777777776665555554..57*********************************9.677778899999998 PP

                             GCD14 117 vfL 119
                                       v++
  gi|557695077|ref|YP_008798131.1| 176 VLM 178
                                       876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); 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: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1769.04
//
Query:       gi|557695078|ref|YP_008798132.1|  [L=121]
Description: small subunit ribosomal protein S25e [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   57.9   0.5    9.5e-16   57.9   0.5    2.0  2  Ribosomal_S25    S25 ribosomal protein
    0.00027   20.7   0.1    0.00042   20.1   0.1    1.3  1  MarR_2           MarR family
     0.0032   17.3   0.3     0.0055   16.6   0.3    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0059   16.6   0.0     0.0097   16.0   0.0    1.3  1  FeoC             FeoC like transcriptional regulator
     0.0087   16.4   0.1      0.014   15.7   0.1    1.3  1  Rrf2             Transcriptional regulator
  ------ inclusion threshold ------
      0.026   14.6   0.1      0.062   13.4   0.1    1.8  1  DUF2250          Uncharacterized protein conserved in archaea
      0.034   14.5   0.1      0.046   14.1   0.1    1.3  1  Penicillinase_R  Penicillinase repressor


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 !   57.9   0.5   3.7e-19   9.5e-16      15      99 ..       5      90 ..       1      91 [. 0.84
   2 ?   -0.4   4.2       0.5   1.3e+03       8      28 ..      98     118 ..      93     121 .] 0.41

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 3.7e-19
                     Ribosomal_S25 15 aggkakkKKwskgkvkdklnnavl.fdketydkllkevpkyklitpsvvserlkingslArraLreleekgliklvskh 92
                                      a++k+ k K + +k+++ +++ v+ +   +++++ + v+ +k++tp+ ++er+k+++s+A+++Lr+l +kgl+k+v+ +
  gi|557695078|ref|YP_008798132.1|  5 AKKKGGKEKKAPEKKEEVVERGVMgVAAPSLEEVREYVKGVKVLTPASIAERFKVRLSVAKALLRDLVSKGLVKEVVGS 83
                                      22333355666777777777777648899************************************************** PP

                     Ribosomal_S25 93 raqviYt 99
                                      ++ ++Y+
  gi|557695078|ref|YP_008798132.1| 84 NRLRVYA 90
                                      ******7 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.5
                     Ribosomal_S25   8 akaaaakaggkakkKKwskgk 28 
                                       a+a+aa+  +k +k K s++k
  gi|557695078|ref|YP_008798132.1|  98 AEAKAAATEEKPAKAKRSSKK 118
                                       333333334444444444444 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.1   1.7e-07   0.00042      22      61 ..      48      87 ..      26      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.7e-07
                                      EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2 22 ltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      lt++ +a+r+++  s +  +l++Lv++GLv ++ g++ +R
  gi|557695078|ref|YP_008798132.1| 48 LTPASIAERFKVRLSVAKALLRDLVSKGLVKEVVGSNRLR 87
                                      799*****************************99988776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.3   2.1e-06    0.0055      22      64 ..      47      91 ..      36     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.1e-06
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST..TTEEEE CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgr..pklYra 64
                                       +t   iae+ +v  s +   Lr L++kGlV+ + g+   ++Y +
  gi|557695078|ref|YP_008798132.1| 47 VLTPASIAERFKVRLSVAKALLRDLVSKGLVKEVVGSnrLRVYAP 91
                                      578999***************************998854446665 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.8e-06    0.0097       1      47 [.      34      80 ..      34      87 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.8e-06
                              FeoC  1 iLtelkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekv 47
                                      +L e++ey++  +      ++ +fk+  +  +a+L  +v kG v++v
  gi|557695078|ref|YP_008798132.1| 34 SLEEVREYVKGVKVLTPASIAERFKVRLSVAKALLRDLVSKGLVKEV 80
                                      699*****************************************987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   5.6e-06     0.014      26      62 ..      48      84 ..      39      85 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.6e-06
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT- CS
                              Rrf2 26 vsseeiaerqnispsylekilakLrkaglvksvrGkg 62
                                      ++ ++iaer+++  s+++ +l+ L  +glvk v G +
  gi|557695078|ref|YP_008798132.1| 48 LTPASIAERFKVRLSVAKALLRDLVSKGLVKEVVGSN 84
                                      67789**************************999975 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 ?   13.4   0.1   2.4e-05     0.062      13      57 ..      38      82 ..      31     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                           DUF2250 13 vlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerveg 57
                                      v +++k ++v  + sia++++++l+ ++ ll++L + GL+++v g
  gi|557695078|ref|YP_008798132.1| 38 VREYVKGVKVLTPASIAERFKVRLSVAKALLRDLVSKGLVKEVVG 82
                                      56788888888899***************************9875 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.8e-05     0.046      23      77 ..      53     104 ..      33     114 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                       HHHT--GGG---HHHHHHHHHHHHHTTS-EEEEE.TTEEEEE----XXXXXXXXXX CS
                   Penicillinase_R  23 vveeleeekelaysTVktllrrLvkKgllsreke.grafiYsplvseeeavasavk 77 
                                       + e+++ +     s  k llr Lv Kgl+++    +r  +Y+pl++ + a a+a+ 
  gi|557695078|ref|YP_008798132.1|  53 IAERFKVR----LSVAKALLRDLVSKGLVKEVVGsNRLRVYAPLIQTTTAEAKAAA 104
                                       44444444....455589************987769999*******9999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 886.66
//
Query:       gi|557695079|ref|YP_008798133.1|  [L=124]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-11   42.3   0.0      7e-11   42.0   0.0    1.1  1  Cyclophil_like   Cyclophilin-like
    4.4e-05   23.4   0.0    7.2e-05   22.7   0.0    1.4  1  Cyclophil_like2  Cyclophilin-like family


Domain annotation for each model (and alignments):
>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.0   7.8e-15     7e-11       5     101 ..      10     102 ..       5     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 7.8e-15
                                       EEET.TEEEEEEEETT...HHHHHHHHC-SEEEEEEECTTEEEEE-S-----SSSEESSB-TTEEEEECCCTEEEEE CS
                    Cyclophil_like   5 idie.sseveveLddt...etaraikealPiesrvntWgeEiYfstpvklekeenakevveagdiaywppGkalclf 77 
                                       +++e   eve eL+      t++++++ lPie+ v++W++ +Y  t+++ +  e++  ++e+gdi yw p +al + 
  gi|557695079|ref|YP_008798133.1|  10 VHVEgLEEVEGELHRFaapLTVDEVVKRLPIEGFVARWQNAVYIITEIRRG-VEKSVTKLEKGDIFYWSPEQALGIA 85 
                                       555556788888877666789*****************************9.778888****************998 PP

                                       SS--TT-TTSB--SSSEEEEEEEE CS
                    Cyclophil_like  78 fGktPisddeirpaspvnviGriv 101
                                         +         + s+  +iG + 
  gi|557695079|ref|YP_008798133.1|  86 LSQH-------AAPSQTIKIGSVG 102
                                       8777.......3334444455554 PP

>> Cyclophil_like2  Cyclophilin-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   8.1e-09   7.2e-05      48     100 ..      62     108 ..      25     119 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.1e-09
                   Cyclophil_like2  48 ptddapegssikaGdlayyapwgnlvlfykdfeesysygltrlGrieedaeel 100
                                       +    +++++ ++Gd++y++p++ l +   ++    +++ +++G++ + a+e+
  gi|557695079|ref|YP_008798133.1|  62 E----KSVTKLEKGDIFYWSPEQALGIALSQHAA--PSQTIKIGSVGRGADEI 108
                                       3....3567999********************55..99********4333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 888.94
//
Query:       gi|557695080|ref|YP_008798134.1|  [L=409]
Description: phosphoglycerate mutase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  190.9   0.1    3.5e-56  189.7   0.0    1.6  2  PhosphMutase   2,3-bisphosphoglycerate-independent phosphogly
    2.2e-33  115.7   0.0    2.5e-33  115.5   0.0    1.0  1  Metalloenzyme  Metalloenzyme superfamily
     0.0019   17.8   0.0     0.0044   16.6   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 !  189.7   0.0   5.8e-60   3.5e-56       1     170 []      37     208 ..      37     208 .. 0.97
   2 ?   -2.4   0.0      0.62   3.7e+03     142     165 ..     307     330 ..     278     333 .. 0.64

  Alignments for each domain:
  == domain 1  score: 189.7 bits;  conditional E-value: 5.8e-60
                                       HHTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTG CS
                      PhosphMutase   1 AkkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrra 77 
                                       A++GetGl+d v++gi+ gSd+++l++lGydp ++ytGRGp+EAlg+Gl+l+ +dvafRcn++tv+ edg++idrra
  gi|557695080|ref|YP_008798134.1|  37 AAEGETGLVDVVARGIPNGSDTGHLALLGYDPSTCYTGRGPFEALGAGLDLSLDDVAFRCNFATVA-EDGTVIDRRA 112
                                       899**************************************************************7.6********* PP

                                       GG-.-TTHHHHHHHT-EEE..TTEEEEEEE-STTEEEEEE....--S-B--S--..SSTTS------BS..SGGGHH CS
                      PhosphMutase  78 gristeeakeLikalneel.eegvevkfypgveyrhllvl....lsdkitdtdpphdkegkeikellpl.kseeake 148
                                       gristee++eL+++++++  + gv+++f+++ve+r +l++     s++++++dp  + +   +++ +pl +s+e+ +
  gi|557695080|ref|YP_008798134.1| 113 GRISTEESRELAESIQTMEiD-GVQFTFRHTVEHRGVLIMrgkgISHRVSNVDP--HGKTSTVQKPMPLdDSPESIK 186
                                       *****************9854.9*********************9*********..899999*******99****** PP

                                       HHHHHHHHHHHHHHHHHHSHHH CS
                      PhosphMutase 149 taellnelieksqeiLedhpvN 170
                                       ta++l++++ek ++iL+ hp+N
  gi|557695080|ref|YP_008798134.1| 187 TAQALEKFLEKTRQILQTHPIN 208
                                       *********************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.62
                                       .SGGGHHHHHHHHHHHHHHHHHHH CS
                      PhosphMutase 142 kseeaketaellnelieksqeiLe 165
                                       ++++ +e+ae++n++ e++ ++Le
  gi|557695080|ref|YP_008798134.1| 307 HDKKPREKAEMINRVGEALGKMLE 330
                                       244457777777777777766665 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   0.0   4.2e-37   2.5e-33       1     244 [.       1     396 [.       1     400 [. 0.98

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 4.2e-37
                                       -EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH....... CS
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                     Metalloenzyme   1 kkvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel....... 67 
                                       +k+vlvvlDGlG++    l+    +++A+  +ld+L++e       +++g+   ++ ++ ++s++gHl+l       
  gi|557695080|ref|YP_008798134.1|   1 MKAVLVVLDGLGDRRCRSLGYmtpLQYARNRVLDRLAAE-------GETGLVDVVARGIPNGSDTGHLALlgydpst 70 
                                       589*************99988889***************.......899**************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|557695080|ref|YP_008798134.1|  71 cytgrgpfealgagldlslddvafrcnfatvaedgtvidrragristeesrelaesiqtmeidgvqftfrhtvehrg 147
                                       ***************************************************************************** PP

                                       ..............................................................HHHHTT-----EEEE CS
                                       ..............................................................xxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 ..............................................................lrisetvkfahvtff 82 
                                                                                                     +r+++   +a+++++
  gi|557695080|ref|YP_008798134.1| 148 vlimrgkgishrvsnvdphgktstvqkpmplddspesiktaqalekflektrqilqthpiniKRREKNLPPANYILT 224
                                       **************************************************************999************ PP

                                       EEEE-S---SSHHHHHT--EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  83 wnggrsgyfnpleereeipsdtvitfdl....................qpemkavevaekaldailsgkfdlvvvni 139
                                       +++gr +++ p+e+++++++++v+   l                    + +++  ++++++++ + ++  d+v++++
  gi|557695080|ref|YP_008798134.1| 225 RGAGRLPNLLPFEKKFGLKAAVVAGGALykgvcraagfdvvnvegatgTVNTNLGNKINAVIESL-KT-RDFVLLHV 299
                                       ***********************************************9999**************.44.7******* PP

                                       -HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEEEESTT- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 140 knaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkgl 216
                                       k +D ++H++++ +++++i ++ ea++++l++++++  +++vt+DH +++++ +        H  +pVP+li+g+++
  gi|557695080|ref|YP_008798134.1| 300 KATDTLSHDKKPREKAEMINRVGEALGKMLEQLSSDT-YVAVTGDHTTPSEIGD--------HRGDPVPVLIWGPDV 367
                                       ********************************99988.****************........*************** PP

                                       ---S--S.SHHHHTT-TTEEEEGGGHHHH CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 217 apdkvke.gakfrekggLanvaatllnll 244
                                       + d+v++ ++ ++  ggL+++++  l+ +
  gi|557695080|ref|YP_008798134.1| 368 RGDSVTRfDEISCMCGGLGRIRGVELMPI 396
                                       **********************9988866 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0      0.81   4.8e+03       2      31 ..       4      40 ..       3      43 .. 0.84
   2 !   16.6   0.0   7.4e-07    0.0044     169     234 ..     288     346 ..     229     358 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.81
                                      EEEEETT-B......TTHHHHHG.STSHHHHHHHHHS CS
                      Phosphodiest  2 lvislDGlr......adlldrla.ellpnlaaLakeg 31
                                      ++++lDGl         ++ +l+  +   l++La eg
  gi|557695080|ref|YP_008798134.1|  4 VLVVLDGLGdrrcrsLGYMTPLQyARNRVLDRLAAEG 40
                                      8899999998888888999999888999999999887 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7.4e-07
                                       CTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES--- CS
                      Phosphodiest 169 elekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGm 234
                                       +l++ d++l+++ +tDt +H   p +   ++ + rv +a+g++le+l  +     t + +++DH  
  gi|557695080|ref|YP_008798134.1| 288 SLKTRDFVLLHVKATDTLSHDKKPRE--KAEMINRVGEALGKMLEQLSSD-----TYVAVTGDHTT 346
                                       33888***************996654..569******************9.....88*******65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); 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:                         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: 2884.17
//
Query:       gi|557695081|ref|YP_008798135.1|  [L=320]
Description: DNA repair protein RadA [Candidatus Caldiarchaeum subterraneum]
Scores for 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-86  288.2   0.0    6.4e-86  287.8   0.0    1.1  1  Rad51          Rad51
    1.1e-10   41.3   0.1    1.9e-10   40.5   0.1    1.5  1  ATPase         KaiC
    1.6e-10   40.9   0.4      1e-09   38.3   0.1    1.9  2  RecA           recA bacterial DNA recombination protein
    7.8e-09   36.0   0.1    2.4e-08   34.5   0.1    1.9  1  HHH_5          Helix-hairpin-helix domain
    2.4e-07   30.5   0.0      4e-07   29.8   0.0    1.3  1  AAA_25         AAA domain
     0.0019   18.4   0.0     0.0034   17.6   0.0    1.4  1  Cdd1           Pathogenicity locus
  ------ inclusion threshold ------
      0.016   15.1   0.0        1.4    8.9   0.0    2.7  2  HHH            Helix-hairpin-helix motif
      0.037   14.3   0.0      0.077   13.3   0.0    1.5  1  AAA_22         AAA domain
       0.04   13.7   0.0      0.072   12.8   0.0    1.4  1  AAA_24         AAA domain
      0.045   14.1   0.0       0.13   12.6   0.0    1.9  1  IMS_HHH        IMS family HHH motif
      0.065   12.9   0.0       0.22   11.2   0.0    2.0  1  GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-te
      0.087   13.4   0.1        0.4   11.2   0.1    2.1  1  AAA_18         AAA domain


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 !  287.8   0.0   4.3e-89   6.4e-86       3     254 ..      66     315 ..      64     316 .. 0.98

  Alignments for each domain:
  == domain 1  score: 287.8 bits;  conditional E-value: 4.3e-89
                                       -EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEES CS
                             Rad51   3 fvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidt 79 
                                        v+a el+e + ++ ++ttGs++lD l+gGG+et++ite fGef+sGk+qlch+l+v vqlp+  gG +g a+yidt
  gi|557695081|ref|YP_008798135.1|  66 WVTAKELAEIKTNIGRITTGSTRLDLLIGGGVETQAITEFFGEFGSGKSQLCHQLAVNVQLPVRRGGLDGSALYIDT 142
                                       6899************************************************************************* PP

                                       SS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------TH CS
                             Rad51  80 egtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgela 156
                                       e tfrper++++a+  +l+ +evle++ ya ayt++hq  l+++a + ++e++++l+ivDs+t+++R+++ gr+ l 
  gi|557695081|ref|YP_008798135.1| 143 ENTFRPERVTSMANSLGLNADEVLERIIYAEAYTSDHQILLVEKADKIIKEKNVKLIIVDSLTSHFRSEYLGRQLLP 219
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-ST.TEEEEEE CS
                             Rad51 157 kRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkg.eeRivkv 232
                                       +Rqqkl+k++++L +l   f++a v+tnqv++++d    +fs+ +  PigG++++h+s+ R+ lrk  g   Ri+++
  gi|557695081|ref|YP_008798135.1| 220 ERQQKLNKHMHKLIRLCRAFNIAAVVTNQVMSRPDD---IFSTMAVYPIGGHIVGHTSHNRVFLRKVAGkPLRIARL 293
                                       ***********************************9...9*****************************457***** PP

                                       ES-SSS-S-EEEEEEETTEEE- CS
                             Rad51 233 vdsPnlpeleavfaigeeGied 254
                                       v+sP lpe eavf i+e+G+ed
  gi|557695081|ref|YP_008798135.1| 294 VSSPYLPEGEAVFKITERGVED 315
                                       ********************99 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.1   1.3e-13   1.9e-10       2     224 ..      83     313 ..      82     320 .] 0.73

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.3e-13
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikg...aeky..gepgvfvtveepa..edlrenakslG 71 
                                        tg   lD ++ gG+  ++++   Ge G+GK+ ++ q +++    +++   +   +++ +e +   e +   a+slG
  gi|557695081|ref|YP_008798135.1|  83 TTGSTRLDLLIGGGVETQAITEFFGEFGSGKSQLCHQLAVNVqlpVRRGglDGSALYIDTENTFrpERVTSMANSLG 159
                                       689999**********************************9622234431144669*****98666*********** PP

                            ATPase  72 wdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl.aye........ekeav 139
                                        + +++ e+  +++ +a++s+++            l+e+  ++ike+++k +++Ds+t++   e        e++++
  gi|557695081|ref|YP_008798135.1| 160 LNADEVLER--IIYAEAYTSDHQ----------ILLVEKADKIIKEKNVKLIIVDSLTSHfRSEylgrqllpERQQK 224
                                       *********..999999999765..........46999********************9853222333333357888 PP

                            ATPase 140 aReilrqlvrvlkklgvTailvsekssseeaaggygveefivdgvivLdlkeiee....elvRtleivkmRgtk.hs 211
                                       + + +++l+r  +  ++ a+ ++++ s      +   + + + g iv +   ++        + l+i  + +++   
  gi|557695081|ref|YP_008798135.1| 225 LNKHMHKLIRLCRAFNIAAVVTNQVMS-RPDDIFSTMAVYPIGGHIVGHTSHNRVflrkVAGKPLRIARLVSSPyLP 300
                                       9999********************766.3444444444455555555444444333333333344444444444134 PP

                            ATPase 212 kkehpfeIteegi 224
                                         e +f+Ite+g+
  gi|557695081|ref|YP_008798135.1| 301 EGEAVFKITERGV 313
                                       4566666666665 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.18   2.8e+02      71     106 ..      30      65 ..      26      71 .. 0.87
   2 !   38.3   0.1   6.9e-13     1e-09      28     198 ..      76     258 ..      67     286 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.18
                                       HHHHHHHHHTT--EEEEESS----HHHHHHTT--GG CS
                              RecA  71 lhaiaeaqkkggvaafidaehaldpkyakklGvdid 106
                                       ++ ia a  +  vaa +d eha     a++ G++i 
  gi|557695081|ref|YP_008798135.1|  30 VESIATATVSELVAAGVDEEHASRIISAAREGIEIA 65 
                                       6778999999999*********99999999999985 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 6.9e-13
                                       -----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHH...HTT...--EEEEESS----HH.. CS
                              RecA  28 klkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaq...kkg...gvaafidaehaldpk.. 96 
                                       k+++  i++Gs  ld+ +G GG+    i+e +G   sGk+ l+ ++ +++q   ++g   g a +id+e ++ p+  
  gi|557695081|ref|YP_008798135.1|  76 KTNIGRITTGSTRLDLLIG-GGVETQAITEFFGEFGSGKSQLCHQLAVNVQlpvRRGgldGSALYIDTENTFRPErv 151
                                       679999*************.**********************9999999985554552226799********99633 PP

                                       ..HHHHTT--GGG-E....EE--SSHH.HHH..HHHHHHHTTT--SEEEEE-TTT---STT-----------HHHHH CS
                              RecA  97 ..yakklGvdidell....vsqpdtGe.qal..eiadalvrsgaidlivvdsvaalvpkaeieGemgdskvglqarl 164
                                          a+ lG++ de+l     ++  t + q l  e ad++++   + li+vds+++   ++e    +g + +  + + 
  gi|557695081|ref|YP_008798135.1| 152 tsMANSLGLNADEVLeriiYAEAYTSDhQILlvEKADKIIKEKNVKLIIVDSLTSHF-RSEY---LGRQLLPERQQK 224
                                       336899****99976442234443333133323889****************98865.4443...445555555556 PP

                                       HHHHHHHHHHHHTTT--EEEEEEE---------- CS
                              RecA 165 msqalrkltgaisksntvvifinqirekiGvmfg 198
                                       + + + kl    +  n++++  nq+  +   +f 
  gi|557695081|ref|YP_008798135.1| 225 LNKHMHKLIRLCRAFNIAAVVTNQVMSRPDDIFS 258
                                       6788888888888889999999998776655555 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   1.6e-11   2.4e-08       3      57 .]       7      60 ..       5      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.6e-11
                                      HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                             HHH_5  3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                      ++ +++G+ +k+A +l + G+++ve +a a+v eL ++ G+ ++ A rii ++++
  gi|557695081|ref|YP_008798135.1|  7 DIEELPGVSAKLAEKLRELGYSTVESIATATVSELVAA-GVDEEHASRIISAARE 60
                                      67899*********************************.*************996 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   2.7e-10     4e-07       8     186 ..      75     246 ..      68     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.7e-10
                            AAA_25   8 savsvadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsed 84 
                                        ++ ++++ +  ++++ l++g +  ++++ ++G  g+GK+ l+ +la+ v +            g  ly+++E++  
  gi|557695081|ref|YP_008798135.1|  75 IKTNIGRITTGSTRLDLLIGGGVETQAITEFFGEFGSGKSQLCHQLAVNVQLPVRR----GGLDGSALYIDTENTF- 146
                                       3457888999999*******999***************************964432....2368***********8. PP

                            AAA_25  85 elrrRlravgealrddarllvldlagveslpLfak.drggtlltadvdaleaaieevegvrlvviDplsralgg... 157
                                         ++R+  +   l ++a++ +        +  +++ ++++++    v++ ++ i+e ++v+l+++D+l++ ++    
  gi|557695081|ref|YP_008798135.1| 147 -RPERVTSMANSLGLNADEVLER------IIYAEAyTSDHQI--LLVEKADKIIKE-KNVKLIIVDSLTSHFRSeyl 213
                                       .6788888887775555554433......3333331345555..357788999999.99**********98877444 PP

                            AAA_25 158 ....densnsdvgalvealeriarrtgaavllv 186
                                            ++++ + ++ + +l r++r++++a +++
  gi|557695081|ref|YP_008798135.1| 214 grqlLPERQQKLNKHMHKLIRLCRAFNIAAVVT 246
                                       444445555557777777888888888766665 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.3e-06    0.0034       3      43 ..       3      43 ..       1      52 [. 0.89

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.3e-06
                              Cdd1  3 kalkelqdiPniGkalaedlvelGirsveelkgedpeelye 43
                                      ++ ++++++P++  +lae+l+elG+++ve ++  +  el++
  gi|557695081|ref|YP_008798135.1|  3 QRYNDIEELPGVSAKLAEKLRELGYSTVESIATATVSELVA 43
                                      567899*************************9999888876 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00093       1.4      11      28 ..       6      23 ..       3      25 .. 0.87
   2 ?    3.3   0.0     0.056        84       2      15 ..      30      43 ..      29      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00093
                                      HHHHTSTT-SHHHHHHHH CS
                               HHH 11 eeLlalPGVGpktAeaIl 28
                                       ++++lPGV  k Ae+ +
  gi|557695081|ref|YP_008798135.1|  6 NDIEELPGVSAKLAEKLR 23
                                      5899***********976 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.056
                                      HHHHHTSSHHHHHT CS
                               HHH  2 leglipasreeLla 15
                                      +e++ +a++ eL+a
  gi|557695081|ref|YP_008798135.1| 30 VESIATATVSELVA 43
                                      799*********86 PP

>> AAA_22  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     0.077       4      99 ..      99     203 ..      97     245 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.1e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...erpevvfvtlpsstsskdllrellralglelka....... 70 
                                       t+ i+  +Ge G+GK+ l+ +l+ + +      +    + + ++++  +   ++ + + +++ lgl++++       
  gi|557695081|ref|YP_008798135.1|  99 TQAITEFFGEFGSGKSQLCHQLAVNVQLP-V--RrggLDGSALYIDTENTFRPERV-TSMANSLGLNADEvleriiy 171
                                       7788899***************9997432.2..14578888888888888855444.66677777666666667888 PP

                            AAA_22  71 ...erlsseell.ealeqalraravielliiDE 99 
                                          ++ + + ll e+  + ++++ v +l+i+D 
  gi|557695081|ref|YP_008798135.1| 172 aeaYTSDHQILLvEKADKIIKEKNV-KLIIVDS 203
                                       8888889999997777777777777.9999995 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   4.8e-05     0.072       8      78 ..     106     208 ..     103     251 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.8e-05
                            AAA_24   8 yGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie.....swedfldevvel....... 59 
                                       +G+ g+GK+ l+ +l               ++l+idte+ +    + ++ ++      + +++l+ + +        
  gi|557695081|ref|YP_008798135.1| 106 FGEFGSGKSQLCHQLavnvqlpvrrgglDGSALYIDTENTF---RPERVTSMAnslglNADEVLERIIYAeaytsdh 179
                                       79*************************99**********66...555555555556888888888888887777777 PP

                            AAA_24  60 ..........aaeladyktlviDtidele 78 
                                                   ++++ k +++D+++   
  gi|557695081|ref|YP_008798135.1| 180 qillvekadkIIKEKNVKLIIVDSLTSHF 208
                                       77777777775556668888888887664 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.9e-05      0.13      12      32 .]       7      27 ..       7      27 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.9e-05
                           IMS_HHH 12 pitkipGiGgklgekLeklGi 32
                                      +i ++pG+  kl+ekL+ lG+
  gi|557695081|ref|YP_008798135.1|  7 DIEELPGVSAKLAEKLRELGY 27
                                      699****************95 PP

>> GalP_UDP_tr_C  Galactose-1-phosphate uridyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00015      0.22      71     103 ..     237     270 ..     173     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHH.HHHHHHHHHCTS---EEEEEE-- CS
                     GalP_UDP_tr_C  71 ekedlaailk.klarkydnlfetsfeysmGlhqa 103
                                          ++aa+++ +++++ d++f+t + y++G h  
  gi|557695081|ref|YP_008798135.1| 237 RAFNIAAVVTnQVMSRPDDIFSTMAVYPIGGHIV 270
                                       55699998873699****************9865 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00027       0.4       5      91 ..     107     213 ..     104     218 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                            AAA_18   5 GtpGvGKttlakeLskrlgf.....................gvnlrdvakenglllevdpe.......aldeskrld 53 
                                       G  G+GK++l++ L+   ++                      ++++++a   gl  ++  e        ++++++l 
  gi|557695081|ref|YP_008798135.1| 107 GEFGSGKSQLCHQLAVNVQLpvrrggldgsalyidtentfrPERVTSMANSLGLNADEVLEriiyaeaYTSDHQILL 183
                                       778***********554333445555577777777777777555555555555555555553322222222233333 PP

                            AAA_18  54 edkldklldaleenssaleegknlvidghlaeleseaa 91 
                                              +++ ++++ ++ + k +++d++ ++++se++
  gi|557695081|ref|YP_008798135.1| 184 -------VEKADKII-KEKNVKLIIVDSLTSHFRSEYL 213
                                       .......33333333.35556899********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 2282.71
//
Query:       gi|557695082|ref|YP_008798136.1|  [L=122]
Description: hypothetical protein CSUB_C1655 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   18.5   0.0     0.0038   17.7   0.0    1.4  1  TPR_19    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.098   13.3   0.1        0.2   12.4   0.1    1.5  1  TPR_6     Tetratricopeptide repeat
       0.16   12.8   0.1       0.34   11.9   0.1    1.5  1  TPR_14    Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> 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   6.3e-07    0.0038      39      64 ..      19      44 ..      16      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.3e-07
                            TPR_19 39 gqldeAealLdalpeedpddaryasL 64
                                      ++l+eAe++L++l e++p d+ry  +
  gi|557695082|ref|YP_008798136.1| 19 NRLTEAERILQQLTEKYPEDSRYLHA 44
                                      89******************766543 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.3e-05       0.2      13      32 ..      19      37 ..      10      38 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                                      HHHHHHHHHHHHHHHHH-TT CS
                             TPR_6 13 lgdtdkAlealerlikeYPd 32
                                        + ++A ++l++l ++YP+
  gi|557695082|ref|YP_008798136.1| 19 N-RLTEAERILQQLTEKYPE 37
                                      4.889**************7 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.7e-05      0.34      15      41 ..      19      45 ..      11      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.7e-05
                            TPR_14 15 GdpdeAiallrralalaPddaeawlll 41
                                       ++ eA+++l+++ +++P+d +++ +l
  gi|557695082|ref|YP_008798136.1| 19 NRLTEAERILQQLTEKYPEDSRYLHAL 45
                                      6899****************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      712  (0.0397122); 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: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 900.95
//
Query:       gi|557695083|ref|YP_008798137.1|  [L=91]
Description: hypothetical protein CSUB_C1656 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   15.5   6.6      0.024   15.2   6.6    1.1  1  Rab5ip    Rab5-interacting protein (Rab5ip)
      0.027   14.2   0.3      0.027   14.2   0.3    1.8  2  CbtA      Probable cobalt transporter subunit (CbtA)


Domain annotation for each model (and alignments):
>> Rab5ip  Rab5-interacting protein (Rab5ip)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   6.6   2.6e-06     0.024       2      82 .]       6      85 ..       5      85 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.6e-06
                            Rab5ip  2 lsnlrsltalllGvvaGilgLeslsGflfylllsllvsllfyalkvkgkskk...yfrgalkelwteglvnglagFvLt 77
                                      +++ + +++l  Gv+a  l+  + + ++ yll+     l+++   ++ +++    + r   ++ +++gl      F+L+
  gi|557695083|ref|YP_008798137.1|  6 VYWTKFVVGLGYGVLAAWLAASNPTPLITYLLIIGAALLYVI--VAEVFWRLfdkKLRR--RQSYLNGLGGYAGMFLLV 80
                                      799***************************876544443333..455555443325555..68899************* PP

                            Rab5ip 78 WtlfY 82
                                      W+l+Y
  gi|557695083|ref|YP_008798137.1| 81 WILMY 85
                                      ****9 PP

>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.5      0.05   4.5e+02      10      31 ..      12      33 ..       6      37 .. 0.61
   2 ?   14.2   0.3     3e-06     0.027      78     124 ..      34      80 ..      28      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.05
                              CbtA 10 laGllAGllaflvqrlvvePli 31
                                      ++Gl  G+la+ +++   +Pli
  gi|557695083|ref|YP_008798137.1| 12 VVGLGYGVLAAWLAASNPTPLI 33
                                      4555556666666666666655 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3e-06
                              CbtA  78 nvltgvalglllaavfallegrlgklsaralalllalagflavvlvP 124
                                       + l+ ++ +ll+++v+ ++++ + k   r++++l +l+g++ ++l  
  gi|557695083|ref|YP_008798137.1|  34 TYLLIIGAALLYVIVAEVFWRLFDKKLRRRQSYLNGLGGYAGMFLLV 80 
                                       56777999**********************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 685.04
//
Query:       gi|557695084|ref|YP_008798138.1|  [L=628]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-40  136.8   0.0    1.3e-39  136.2   0.0    1.1  1  FbpA           Fibronectin-binding protein A N-terminus (FbpA
    3.3e-17   63.1   0.0      7e-17   62.1   0.0    1.5  1  NFACT-R_1      NFACT protein RNA binding domain
    8.7e-06   26.2   0.0    2.7e-05   24.6   0.0    1.8  2  Ribosomal_S13  Ribosomal protein S13/S18
    4.4e-05   23.6   0.0    0.00013   22.1   0.0    1.8  1  NFACT-R_2      NFACT protein RNA binding domain
  ------ inclusion threshold ------
      0.021   15.2   3.8        0.4   11.1   0.3    3.5  3  CLZ            C-terminal leucine zipper domain of cyclic nuc
       0.11   12.8   0.3       0.11   12.8   0.3    2.2  2  TSC22          TSC-22/dip/bun family
       0.26   11.3   3.4       0.29   11.1   0.3    2.5  2  Prefoldin_2    Prefoldin subunit
       0.35   10.6   1.3        3.2    7.5   0.2    2.1  2  zf-CpG_bind_C  CpG binding protein zinc finger C terminal dom
        1.1    9.7   3.5          2    8.9   3.5    1.4  1  AAA_23         AAA domain
        6.6    7.3  11.0        8.1    7.0   0.1    2.8  3  APG6_N         Apg6 coiled-coil region


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 !  136.2   0.0   7.4e-43   1.3e-39       8     414 ..      12     409 ..       8     413 .. 0.85

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 7.4e-43
                                       HHHHHHHHHTTXEEEEEEEEETTEEEEEEE.ETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHHHHHTTX CS
                              FbpA   8 vvaELqkellggridkiyqpekdelvltlr.anrgrhkLllsahpsyarihltekpkenpkeppnFcmlLRkyLkga 83 
                                       +vaE ++++l++ ++++y  +++ + l++     g+  L l a   y+ +++ +++ e++++p++ + +LR+++ g+
  gi|557695084|ref|YP_008798138.1|  12 LVAECRDRVLDSYVRNVYGFGSRAILLKVWkPSIGSGELWLTA--GYSVFYI-DQSVEKESTPSTHVLQLRRKVVGK 85 
                                       7999**************************88888888*****..5555555.666668****************** PP

                                       EEEEEEEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXXX CS
                              FbpA  84 rivsieqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpgekYel 160
                                       ri++i+q+g +R v l+++           +L+vE m   +Ni+L+ +++ +  ++++ ++   ++R +  gekY++
  gi|557695084|ref|YP_008798138.1|  86 RITDIKQVGGERLVTLGLDGF---------ELVVECMPP-GNIVLM-KDGVVEWLLEKFES---STRILKVGEKYHP 148
                                       *********************.........9********.******.57788888888855...59*********** PP

                                       SXXXSXBXTTSXXH.HHHHHHHHH..S.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHH CS
                              FbpA 161 PpsqdklnPleaeeleefkellsk..kekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyeal 235
                                       Pp+  k++    e+   +  ll++  +++ +v aL++ + Gl++ +aeel++ragldk++++++ls+e+++rl++ +
  gi|557695084|ref|YP_008798138.1| 149 PPA--KHSHTLGEA---WPVLLKDlnPKTGVVVALARDL-GLGGKFAEELVARAGLDKNKRVEQLSDEEVNRLNTVW 219
                                       ***..443333333...344444444889999*******.************************************* PP

                                       HHHHTXXX....XXEE.....XSSSEESSX.XTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHHHHH CS
                              FbpA 236 qelleeleeekfepqlvlkeekpeefsvvp.lkslselekesfdslsealdeyYakkaerdrveqkrsdlekrvene 311
                                       +el++ele  + +p+l+ ++   e++ + + ++ ls+l+ +++ s+sea+   Y ++ ++ rv++ +++ +k +e+ 
  gi|557695084|ref|YP_008798138.1| 220 SELMRELE--HPRPRLYRRDG--EAIPCATeFQTLSSLQVREVGSFSEAVFLAYLEEMQSLRVREVEEKGRKQLES- 291
                                       *******9..79****98885..5555554488888999************************9988888888554. PP

                                       HHHHHHHHHHHHHHHHCCGGH................HHHHCCHH-----------------------.-------- CS
                              FbpA 312 leklekklkklekelekaeka................enyrligelltaylyaikkgmsevelenyydegeevtIpL 372
                                       l++++  +    ++lek ++a                  +++ +e l  +++    +++  + +  ++ + +++++L
  gi|557695084|ref|YP_008798138.1| 292 LAREKGYRMHTLENLEKRKNAleffisgveqasafweTIWQKPAEALEKIRQTTGLDAEMRNGKVLLT-KDGLKVTL 367
                                       4444444444444555555555666666666699998889***********99988888877787788.99****** PP

                                       ---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FbpA 373 dprkspsenAqkyfkkykKlkraveaveeqieetkeeleyle 414
                                       + + sp++     +++ k +k+ave++ ++i+e +++++ l 
  gi|557695084|ref|YP_008798138.1| 368 SRDTSPVKMLGPVYEELKTVKKAVEKLRQEIAEIEKKMNTLS 409
                                       **************************************9885 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 !   62.1   0.0   3.9e-20     7e-17       2     109 .]     430     538 ..     429     538 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 3.9e-20
                         NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia. 77 
                                       ++ F +s g+  + G+D+ +n +l+k++l e+d+++h ++ +s+ ++l   +g   + +e+ ++e+aq++ ++S+a 
  gi|557695084|ref|YP_008798138.1| 430 FREFVTSGGFRALLGRDARSNIMLLKRHLGENDLVLHTEIPGSPAAVLI--NGV--KASETDVQECAQMVGCYSRAw 502
                                       66799999*************************************9999..555..789****************** PP

                         NFACT-R_1  78 gnklssvdvvyvpasnlsktap....ldtGsvgfkg 109
                                       ++++s+v+v+ v+a+++s t+p    l++Gs++++g
  gi|557695084|ref|YP_008798138.1| 503 RENFSNVSVYAVKAEQVSFTPPsgqyLPKGSFMVYG 538
                                       *********************************986 PP

>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.5e-08   2.7e-05       5      60 ..     166     221 ..     163     257 .. 0.86
   2 ?   -3.3   0.1       6.1   1.1e+04      49      60 ..     389     400 ..     381     412 .. 0.46

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.5e-08
                     Ribosomal_S13   5 tdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeiven 60 
                                        d++ k  v++al+   G+G + a++++++a++d++kr+++l++ee+++++++ ++
  gi|557695084|ref|YP_008798138.1| 166 KDLNPKTGVVVALARDLGLGGKFAEELVARAGLDKNKRVEQLSDEEVNRLNTVWSE 221
                                       58899999*****************************************9987665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.1
                     Ribosomal_S13  49 eeiekieeiven 60 
                                       + +ek+++++++
  gi|557695084|ref|YP_008798138.1| 389 KAVEKLRQEIAE 400
                                       333344444333 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 !   22.1   0.0   7.5e-08   0.00013       2      85 ..     431     517 ..     431     527 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.5e-08
                         NFACT-R_2   2 RhfrlsekaklIvgReeeEnkflkgll..kkdfvslrakshkGplvli.dg.elseedlelaarivarYskgkeeee 74 
                                       R f++s +++   gR+++ n +l +    ++d+v l+++   +p +++ +g ++se+d++ +a++v+ Ys++ +e+ 
  gi|557695084|ref|YP_008798138.1| 431 REFVTSGGFRALLGRDARSNIMLLKRHlgENDLV-LHTEIPGSPAAVLiNGvKASETDVQECAQMVGCYSRAWRENF 506
                                       8999**************9998766555777777.88888777877775898999****************999888 PP

                         NFACT-R_2  75 vevkvkkkege 85 
                                        +v+v   + e
  gi|557695084|ref|YP_008798138.1| 507 SNVSVYAVKAE 517
                                       88877665554 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 ?   -1.5   0.0       1.9   3.5e+03       8      16 ..     119     127 ..     116     141 .. 0.62
   2 ?    2.8   0.1     0.085   1.5e+02      29      64 ..     200     236 ..     186     237 .. 0.81
   3 ?   11.1   0.3   0.00022       0.4       4      59 ..     353     417 ..     351     425 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.9
                               CLZ   8 ILlKdglLD 16 
                                       +L+Kdg  +
  gi|557695084|ref|YP_008798138.1| 119 VLMKDGVVE 127
                                       677777655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.085
                               CLZ  29 leekverL.essLeaLqtrlarLlaeyessqrkLkqR 64 
                                        +++ve+L +++++ L+t    L++e+e+   +L +R
  gi|557695084|ref|YP_008798138.1| 200 KNKRVEQLsDEEVNRLNTVWSELMRELEHPRPRLYRR 236
                                       467788883468****************998888777 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00022
                               CLZ   4 kGreILlKdgl...LDee...aakag...aeqkeleekverLessLeaLqtrlarLlaeyessqr 59 
                                        G+ +L+Kdgl   L ++   ++  g   +e k++++ ve+L +++  ++++++ L +eye s +
  gi|557695084|ref|YP_008798138.1| 353 NGKVLLTKDGLkvtLSRDtspVKMLGpvyEELKTVKKAVEKLRQEIAEIEKKMNTLSGEYEPSPT 417
                                       69999999998666655543444444788999****************************98765 PP

>> TSC22  TSC-22/dip/bun family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.3       4.4   7.8e+03      14      30 ..     210     226 ..     209     228 .. 0.83
   2 ?   12.8   0.3   6.4e-05      0.11      11      36 ..     386     411 ..     384     414 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.4
                             TSC22  14 EeVevLkekIkeLeern 30 
                                       EeV+ L +   eL+ + 
  gi|557695084|ref|YP_008798138.1| 210 EEVNRLNTVWSELMREL 226
                                       99999999999999765 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.4e-05
                             TSC22  11 AVrEeVevLkekIkeLeernseleeE 36 
                                       +V+  Ve L+++I+e e+++++l  E
  gi|557695084|ref|YP_008798138.1| 386 TVKKAVEKLRQEIAEIEKKMNTLSGE 411
                                       79999****************99766 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.65   1.2e+03      63      82 ..     302     321 ..     278     343 .. 0.73
   2 ?   11.1   0.3   0.00016      0.29      41      86 ..     367     413 ..     348     417 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  63 vkeeLeerketlekeiktle 82 
                                       ++e+Le+rk+ le  i+ +e
  gi|557695084|ref|YP_008798138.1| 302 TLENLEKRKNALEFFISGVE 321
                                       56677777777766665555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00016
                                       S-TT--EEEEETTEEEEE.-HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  41 ldedtkvyklvGdvlvkq.dkeevkeeLeerketlekeiktlekqle 86 
                                       l  dt   k+ G+v  +  +++++ e+L ++++++ek+++tl+ ++e
  gi|557695084|ref|YP_008798138.1| 367 LSRDTSPVKMLGPVYEELkTVKKAVEKLRQEIAEIEKKMNTLSGEYE 413
                                       67789999999999987559999999999999999999999988776 PP

>> zf-CpG_bind_C  CpG binding protein zinc finger C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2    0.0018       3.2      21      66 ..     279     324 ..     265     341 .. 0.85
   2 ?    1.7   0.1       0.1   1.8e+02      29      56 ..     382     409 ..     369     428 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0018
                     zf-CpG_bind_C  21 svaeeenkkklekirkeqeeakkklkelekklkkLeeliekakkls 66 
                                        ++ee+ +k+le++ +e+    ++l++lek+++ Le +i+  +++s
  gi|557695084|ref|YP_008798138.1| 279 REVEEKGRKQLESLAREKGYRMHTLENLEKRKNALEFFISGVEQAS 324
                                       4789***********************************9877764 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.1
                     zf-CpG_bind_C  29 kklekirkeqeeakkklkelekklkkLe 56 
                                       ++l++++k +e+++++++e+ekk+++L 
  gi|557695084|ref|YP_008798138.1| 382 EELKTVKKAVEKLRQEIAEIEKKMNTLS 409
                                       6788888888888888888888888876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.5    0.0011         2     100     199 ..     281     405 ..     245     406 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0011
                            AAA_23 100 kgkttkkaklelleideleqfisellgskkiilnlilflgqer...feefelkdkkerleelekeleeledekk... 170
                                        +++ +k+ ++l +++  +  + e+l+++k+ l++++  g e+   f+e  ++++ e+le++++ +    ++++   
  gi|557695084|ref|YP_008798138.1| 281 VEEKGRKQLESLAREKGYRMHTLENLEKRKNALEFFIS-GVEQasaFWETIWQKPAEALEKIRQTTGLDAEMRNgkv 356
                                       33444555555566677777777788888777766553.3333457999999*************999999999887 PP

                            AAA_23 171 llekl....................eqekekekeleeleeeleeilkel 199
                                       ll k                     e++k  +k+ e+l++e+ ei+k++
  gi|557695084|ref|YP_008798138.1| 357 LLTKDglkvtlsrdtspvkmlgpvyEELKTVKKAVEKLRQEIAEIEKKM 405
                                       7888899******************9********************996 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.3       2.8     5e+03      35      71 ..     192     227 ..     187     228 .. 0.59
   2 ?    6.4   1.3    0.0068        12      29      82 ..     267     315 ..     260     349 .. 0.82
   3 ?    7.0   0.1    0.0045       8.1      68      97 ..     382     411 ..     378     414 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2.8
                            APG6_N  35 lkkekkeeekqdeeleeleeeleklekeeeelleeLk 71 
                                       l +++  ++ ++  ++ ++ee+ +l+   +el++eL+
  gi|557695084|ref|YP_008798138.1| 192 LVARAGLDK-NKRVEQLSDEEVNRLNTVWSELMRELE 227
                                       555544443.344556667777777777777777776 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0068
                            APG6_N  29 eeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereelea 82 
                                       +++l+++++ ++     +e +e+ +++le l +e+   +  L++lek + +le 
  gi|557695084|ref|YP_008798138.1| 267 LAYLEEMQSLRV-----REVEEKGRKQLESLAREKGYRMHTLENLEKRKNALEF 315
                                       445555555544.....4567899999**********************99985 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0045
                            APG6_N  68 eeLkelekereeleaelaaleeelealeee 97 
                                       eeLk ++k+ e+l++e+a++e++ + l  e
  gi|557695084|ref|YP_008798138.1| 382 EELKTVKKAVEKLRQEIAEIEKKMNTLSGE 411
                                       789999999999999999999988877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      977  (0.0544927); expected 358.6 (0.02)
Passed Vit filter:                       148  (0.00825478); 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):              10  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.48
# Mc/sec: 3948.04
//
Query:       gi|557695085|ref|YP_008798139.1|  [L=196]
Description: CBS-domain-containing protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-26   91.2   5.3    1.2e-12   48.1   0.6    2.2  2  CBS       CBS domain
  ------ inclusion threshold ------
      0.094   12.9   0.1       0.17   12.0   0.1    1.3  1  DUF2318   Predicted membrane protein (DUF2318)


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 !   48.1   0.6   1.3e-16   1.2e-12       1      55 [.      13      66 ..      13      68 .. 0.96
   2 !   45.5   0.4   8.5e-16   7.6e-12       1      54 [.      78     130 ..      78     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.3e-16
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55
                                      V+d+m+++vv ++ +++  e++elmr++g++++ V+ ++gk+vGi+t++Dl+ ++
  gi|557695085|ref|YP_008798139.1| 13 VRDVMSSPVVEADAEASAVEVAELMRRYGIGSV-VISSQGKPVGIITKTDLVTKV 66
                                      89*******************************.**9**************9875 PP

  == domain 2  score: 45.5 bits;  conditional E-value: 8.5e-16
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       ++dimt+++ tv pd t+ +al +m + ++srl VV   ++l Givt +D+l++
  gi|557695085|ref|YP_008798139.1|  78 ARDIMTTPLQTVEPDVTIDDALSKMNKLKLSRLVVV-YKERLAGIVTIKDILQV 130
                                       58***********************6555****778.7789***********86 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.9e-05      0.17      28      62 ..     151     187 ..     142     191 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                           DUF2318  28 gklrvaldaCevC.ekkgYv.qegeelvCknCgvrfa 62 
                                       ++ +va   Ce+C e + Y    +++l C+ C  +++
  gi|557695085|ref|YP_008798139.1| 151 SNQTVAEGYCELCgEWSDYLvRVEDQLLCEDCRIELE 187
                                       556688889****8778998789*********98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1397.00
//
Query:       gi|557695086|ref|YP_008798140.1|  [L=145]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-30  106.5   6.4    4.8e-29  101.3   6.4    2.0  1  Mut7-C          Mut7-C RNAse domain
    8.9e-08   31.8   0.1    1.3e-07   31.2   0.1    1.3  1  DUF5615         Domain of unknown function (DUF5615)
    0.00035   20.9   0.4    0.00057   20.2   0.4    1.3  1  PIN_9           PIN like domain
     0.0075   16.3   0.0      0.011   15.7   0.0    1.2  1  ADH_zinc_N      Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.031   14.3   1.1       0.05   13.6   1.1    1.3  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.042   13.8   1.8      0.099   12.6   0.2    2.2  2  ADK_lid         Adenylate kinase, active site lid
      0.046   13.7   1.4      0.046   13.7   1.4    1.7  1  zf-BED          BED zinc finger
      0.054   12.9   0.0      0.063   12.7   0.0    1.1  1  ZnuA            Zinc-uptake complex component A periplasmic
       0.12   12.6   0.3       0.68   10.2   0.2    2.2  2  PIN_10          PIN like domain
       0.12   12.0   0.1       0.18   11.4   0.1    1.2  1  DUF188          Uncharacterized BCR, YaiI/YqxD family COG1671
       0.15   12.1   1.7       0.26   11.3   1.7    1.4  1  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
       0.22   11.7   5.4       0.39   10.9   5.4    1.4  1  zf-Dof          Dof domain, zinc finger
       0.29   11.1   2.6       0.64   10.0   1.6    2.0  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
        1.7    8.8   4.2          5    7.3   0.2    2.9  3  SR1P            SR1 protein
        3.2    7.9   5.9         56    3.9   5.7    2.1  2  zf-Sec23_Sec24  Sec23/Sec24 zinc finger


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 !  101.3   6.4     4e-32   4.8e-29       1     145 [.       1     134 [.       1     135 [. 0.94

  Alignments for each domain:
  == domain 1  score: 101.3 bits;  conditional E-value: 4e-32
                            Mut7-C   1 krfllDamlgklakyLRllGydalyasdvedeellalaakekrillTrdreLlkraklkkg..vlltsrdveeqlre 75 
                                       ++fllD+m+g++ ++LRllGyd+ly ++++d+el++l+++ekr+++Trd+ L+++ k+     vll++ d+ e l++
  gi|557695086|ref|YP_008798140.1|   1 MKFLLDTMMGHMVTWLRLLGYDTLYVREASDDELIELSVAEKRVVVTRDKTLAAKLKKLGVktVLLETVDTVETLAK 77 
                                       69****************************************************998875577999*********** PP

                            Mut7-C  76 viarlglklslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwerveel 145
                                       + ++ g++l ++p  +rC  Cn+ le+ +++              ++ + C+ C+k +W G hw++++++
  gi|557695086|ref|YP_008798140.1|  78 IGSETGVELVFNPLNTRCPVCNTLLEHFQEN-------------REHRWICRGCGKTYWIGGHWRNITKV 134
                                       *************************987655.............5678******************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 !   31.2   0.1   1.1e-10   1.3e-07       1      57 [.       1      51 [.       1      66 [. 0.91

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.1e-10
                           DUF5615  1 mklllDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDkD 57
                                      mk+llD  +    v++lr +g+d+l+vre     asD+e +e+  +e+r++vT+Dk 
  gi|557695086|ref|YP_008798140.1|  1 MKFLLDTMMG-HMVTWLRLLGYDTLYVRE-----ASDDELIELSVAEKRVVVTRDKT 51
                                      9******999.89**************55.....78*******************85 PP

>> PIN_9  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.4   4.8e-07   0.00057      72     113 ..      27      66 ..      16      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 4.8e-07
                             PIN_9  72 eeekaDdailelakeldaavlvTnDreLkkrllekgipvilL 113
                                       + e+ Dd ++el+ + +  v+vT+D+ L  +l++ g++++lL
  gi|557695086|ref|YP_008798140.1|  27 R-EASDDELIELSVAEK-RVVVTRDKTLAAKLKKLGVKTVLL 66 
                                       4.789*********998.5666*****************998 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   9.5e-06     0.011      18      67 ..      44      92 ..      37     102 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.5e-06
                                      EEEESSHHHHHHHHHTTESEEEETTTC.HHHHHHHHHTTTSSEEEEEESSC CS
                        ADH_zinc_N 18 iavdsseeklelakklGadevinykea.dlverikeltggegvdvvfecvG 67
                                      ++v +++  ++++kklG++ v+ +  + d ve ++++  + gv +vf+ ++
  gi|557695086|ref|YP_008798140.1| 44 VVVTRDKTLAAKLKKLGVKTVLLE--TvDTVETLAKIGSETGVELVFNPLN 92
                                      6788888889**************..55*******************9876 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 ?   13.6   1.1   4.2e-05      0.05      19      46 .]      93     121 ..      85     121 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.2e-05
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCrkq 46 
                                        +CP C    ++++ ++  ++ C+ C+k+
  gi|557695086|ref|YP_008798140.1|  93 TRCPVCNTLlEHFQENREHRWICRGCGKT 121
                                       56*****99*9999999*********985 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 ?   -0.6   0.1       1.1   1.3e+03      24      29 ..      95     100 ..      91     102 .. 0.65
   2 ?   12.6   0.2   8.3e-05     0.099       1      11 [.     112     122 ..     112     137 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.1
                                       -TTT-- CS
                           ADK_lid  24 CDkCGe 29 
                                       C +C+ 
  gi|557695086|ref|YP_008798140.1|  95 CPVCNT 100
                                       666654 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 8.3e-05
                                       EEE-TTT--EE CS
                           ADK_lid   1 RrvCpkCGrsY 11 
                                       R++C+ CG++Y
  gi|557695086|ref|YP_008798140.1| 112 RWICRGCGKTY 122
                                       9********** PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.4   3.9e-05     0.046       5      30 ..     103     129 ..      99     135 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.9e-05
                                       SSS----GGSS--EETTTTEE----...S CS
                            zf-BED   5 kyftpvslkeqkavCryCgkilsrg...g 30 
                                       ++f+++   e +++Cr Cgk++  g   +
  gi|557695086|ref|YP_008798140.1| 103 EHFQENR--EHRWICRGCGKTYWIGghwR 129
                                       79****9..************98875554 PP

>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.3e-05     0.063     187     229 ..      49      90 ..      17     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.3e-05
                                       HHHHHHHHHHTT-SEEEEETTS-THHHHHHHHHHT-EEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 187 iaalieeikeagvkaifveplaspklaetlaeeagvkvatlys 229
                                        + l+ ++k++gvk++++e++ + ++++++ +e+gv++ ++++
  gi|557695086|ref|YP_008798140.1|  49 DKTLAAKLKKLGVKTVLLETVDTVETLAKIGSETGVEL-VFNP 90 
                                       578999******************************96.3433 PP

>> PIN_10  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.2   0.00057      0.68       1      63 [.       1      53 [.       1      64 [. 0.76
   2 ?   -2.5   0.0       5.2   6.2e+03      15      27 ..     100     112 ..      95     118 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00057
                            PIN_10  1 MkfflDenlppalakaLrelleeeghevvhlrdkfaagtkDeeWiaalaeggwvvltkDrrir 63
                                      Mkf+lD  +++ +   Lr         +  +  ++ ++ +D e+i++  +++ vv+t+D+ ++
  gi|557695086|ref|YP_008798140.1|  1 MKFLLDTMMGH-MVTWLR---------LLGYDTLYVREASDDELIELSVAEKRVVVTRDKTLA 53
                                      56666655555.555555.........444566678899********99**********7664 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.2
                            PIN_10  15 kaLrelleeeghe 27 
                                         L++++e+++h+
  gi|557695086|ref|YP_008798140.1| 100 TLLEHFQENREHR 112
                                       5566666666654 PP

>> DUF188  Uncharacterized BCR, YaiI/YqxD family COG1671
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00015      0.18      39      71 ..      28      61 ..      21      67 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                            DUF188 39 daaDdaIve.raeagDlvvTqDipLAarvlekga 71
                                      +a Dd+++e +++++ +vvT+D  LAa++ + g+
  gi|557695086|ref|YP_008798140.1| 28 EASDDELIElSVAEKRVVVTRDKTLAAKLKKLGV 61
                                      5677777772578899***********9866665 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   1.7   0.00022      0.26       1      15 [.      94     108 ..      94     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00022
                    DNA_ligase_ZBD   1 hCPvCGsavvReege 15 
                                       +CPvC++ +++ ++ 
  gi|557695086|ref|YP_008798140.1|  94 RCPVCNTLLEHFQEN 108
                                       5*********98873 PP

>> zf-Dof  Dof domain, zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.4   0.00033      0.39       5      48 ..      94     132 ..      91     143 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                            zf-Dof   5 kCprCestntkFcYyNNyslsqPRyfCkaCrryWtkgGklRnvp 48 
                                       +Cp C   nt   ++        R++C+ C + +  gG+ Rn+ 
  gi|557695086|ref|YP_008798140.1|  94 RCPVC---NTLLEHFQE--NREHRWICRGCGKTYWIGGHWRNIT 132
                                       45555...555555543..3456*******887778******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 ?   -0.3   0.0       0.9   1.1e+03       7      25 ..      51      69 ..      49      81 .. 0.80
   2 ?   10.0   1.6   0.00054      0.64      30      55 ..      94     121 ..      70     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.9
                    OrfB_Zn_ribbon  7 qleykakeyGikveevnpa 25
                                       l+ k k+ G+k+++ +  
  gi|557695086|ref|YP_008798140.1| 51 TLAAKLKKLGVKTVLLETV 69
                                      588899999*999877655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00054
                    OrfB_Zn_ribbon  30 tCseCgsknke..alsgrtfkCpnCgfe 55 
                                       +C++C   +++  ++ + ++ C+ Cg +
  gi|557695086|ref|YP_008798140.1|  94 RCPVCNTLLEHfqENREHRWICRGCGKT 121
                                       8**********99999999*******87 PP

>> SR1P  SR1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       1.4   1.6e+03      11      18 ..      67      74 ..      67      75 .. 0.88
   2 ?    7.3   0.2    0.0042         5       6      20 ..      95     109 ..      95     110 .. 0.92
   3 ?    1.3   0.0      0.33   3.9e+02       5      12 ..     114     121 ..     113     122 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                              SR1P 11 atIdhfed 18
                                      +t+d++e+
  gi|557695086|ref|YP_008798140.1| 67 ETVDTVET 74
                                      69****97 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0042
                              SR1P   6 CqtCnatIdhfedek 20 
                                       C  Cn++ +hf +++
  gi|557695086|ref|YP_008798140.1|  95 CPVCNTLLEHFQENR 109
                                       889********9986 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.33
                              SR1P   5 vCqtCnat 12 
                                       +C+ C++t
  gi|557695086|ref|YP_008798140.1| 114 ICRGCGKT 121
                                       8****997 PP

>> zf-Sec23_Sec24  Sec23/Sec24 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3     0.074        89      23      32 ..      92     101 ..      84     107 .. 0.75
   2 ?    3.9   5.7     0.047        56      17      31 ..     105     120 ..      94     127 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.074
                    zf-Sec23_Sec24  23 rwiCnfCnhk 32 
                                         +C+ Cn+ 
  gi|557695086|ref|YP_008798140.1|  92 NTRCPVCNTL 101
                                       568****985 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.047
                    zf-Sec23_Sec24  17 idfg.gkrwiCnfCnh 31 
                                       ++++  +rwiC  C++
  gi|557695086|ref|YP_008798140.1| 105 FQENrEHRWICRGCGK 120
                                       4444379*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1081.50
//
Query:       gi|557695087|ref|YP_008798141.1|  [L=216]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-48  163.0   0.0    5.5e-48  162.7   0.0    1.1  1  AMMECR1   AMMECR1


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 !  162.7   0.0   3.1e-52   5.5e-48       1     166 []       4     177 ..       4     177 .. 0.94

  Alignments for each domain:
  == domain 1  score: 162.7 bits;  conditional E-value: 3.1e-52
                                       HHHHHHHHHHHTTSS-S-HH---HHHHSEEEEEEEEE.EE..CCECCCECEEEEEEHHHHHHHHHHHHHHT-TTS-- CS
                           AMMECR1   1 lklareaieealkeekkleeeakeelkekaglFVtlk.ekkgeLRGCiGtleperpLaeevaenAlaaAfeDpRFsp 76 
                                       ++lar+a+e++l++++  ++ a ++l ek+g+FV++    ++eLRGCiG+  p+ pL+e+ +++A+a+A+eDpRF+p
  gi|557695087|ref|YP_008798141.1|   4 VQLARRAVETFLETGNLEKAPAADWLMEKRGVFVSIYtYPDKELRGCIGYPLPTLPLGEATVRAAVASAVEDPRFPP 80 
                                       689**************999****************998889*********************************** PP

                                       --HHHHTTEEEEEEEE---EE--.......GGG--TTT-EEEEEETTEEEEE-THHHHHTT--HHHHHHHHHHHHTS CS
                           AMMECR1  77 vtaeElpeleveVsvLtepepiv.......ledlevgkhGliiekgsrsatlLPqvaveqgwdkeeflasllrKagl 146
                                       ++++Elp++ +eVsvL++p +i+       ++ +evg++Gliie+   s++lLPqv+ve+gw+ eefl++l+ Kagl
  gi|557695087|ref|YP_008798141.1|  81 LSPDELPHVVFEVSVLSKPVEIDvsnrkslPDLVEVGVDGLIIETPLGSGLLLPQVPVEYGWNAEEFLSHLCIKAGL 157
                                       **********************43444444555***********999****************************** PP

                                       -TTCCCSTTSEEEEE-EEEE CS
                           AMMECR1 147 rpdewkdseikltryevekf 166
                                       +p++w + +++l ++++ +f
  gi|557695087|ref|YP_008798141.1| 158 NPTYWLHGKMRLLKFTADVF 177
                                       *****9*********99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       201  (0.0112109); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1750.63
//
Query:       gi|557695088|ref|YP_008798142.1|  [L=382]
Description: glycosyltransferase family 28 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-21   74.7   0.0    2.5e-20   73.0   0.0    1.7  1  Glyco_trans_1_3  Glycosyl transferase family 1
    2.4e-15   56.9   0.0    1.5e-14   54.3   0.0    2.0  2  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
    7.9e-07   28.2   0.0    1.2e-05   24.3   0.0    2.1  2  UDPGT            UDP-glucoronosyl and UDP-glucosyl transferas


Domain annotation for each model (and alignments):
>> Glyco_trans_1_3  Glycosyl transferase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.0   4.1e-24   2.5e-20       3     317 ..       3     345 ..       1     352 [. 0.77

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 4.1e-24
                   Glyco_trans_1_3   3 ilYgvsGeGaGhasRsrvvlehL.arghevkvvvsgraldvLekef.dvneivglsi.vyeenrvrklktllknlqv 76 
                                       i  +v G G Gha+Rs +v+e L  rgh++ + ++g++ ++L+k+  +  +++++   v  +  ++  kt+++nl++
  gi|557695088|ref|YP_008798142.1|   3 IHLAVCGIGLGHATRSYAVAEELwRRGHTLTFSSYGQGFEFLSKNGcEPAHVPSVGYgVGVDGAISVKKTIVHNLFL 79 
                                       66799******************555*****************99779999988865378999************99 PP

                   Glyco_trans_1_3  77 aaklaknvkalvelvedfrpdlvvtDFealtallakrhkLPvisvdnqqv..vnrtdyelell.....akkdallak 146
                                         k+a +  a    + d   d+vv+D  a ++l+ak  + Pv ++ nq    ++  +++ + +     ++  +l+ +
  gi|557695088|ref|YP_008798142.1|  80 PVKVAAQTLAEASIIGD--ADVVVSDTRASATLAAKLCRKPVATILNQYNllLQSEKHQRAAEviqpmLQTPQLVWN 154
                                       77776665555666665..8*************************99875115666777766622333445555555 PP

                   Glyco_trans_1_3 147 avvkaklPkadl.y.lvttFfqapvrkkertt....lvPpilR..keilaakptege.....hlLvYlt.segneal 209
                                       +  k ++P  +  y l     q p +  er++    l+ pil   ++i  +++ +g+      lLv+    e ++al
  gi|557695088|ref|YP_008798142.1| 155 LSDKIIIPDLPPpYtLSEHTLQLPDKLMERVVytgpLTKPILHshQQIEDVRSIHGAldkpfVLLVFSGgVEEKKAL 231
                                       5567888875431325555567787778888733335567775335666666666653333357888877789999* PP

                   Glyco_trans_1_3 210 pevLkklgvef...vvYglrrdteeekegnltykafseegFleDL....ataraviagagftLmtealyLkkPlLav 279
                                       +e+ k +g+++    vY +    + ++e++ +  +     ++ DL     +a  v++ +g tL+   +  +kP +++
  gi|557695088|ref|YP_008798142.1| 232 VEMFKMFGEKLssdFVYVMST-ADPSTETDRRQGPLHMRSWIPDLdlyiEAADLVVCRGGLTLLLKCILYGKPAVVI 307
                                       ******997653336899988.77788888888888888888887333358999*********************** PP

                   Glyco_trans_1_3 280 PvarqFeqvlnalyLerlgyGaavdakdldkedvkdFl 317
                                       P  +  eq  na+  e++g+  +v++++l+++  ++ +
  gi|557695088|ref|YP_008798142.1| 308 PPPQHGEQLANAIKAEKMGVAKMVEQRKLSPAGFEEAV 345
                                       *****************************987666554 PP

>> 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 ?    0.0   0.1      0.12   7.4e+02      65     102 ..      89     126 ..      67     141 .. 0.63
   2 !   54.3   0.0   2.5e-18   1.5e-14      56     153 ..     265     360 ..     218     378 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.12
                                       SHHHHHHHH-EEEECS-CHHHHHHHHTT--EEEE--TT CS
                   Glyco_tran_28_C  65 kmaeaikaadLvIsRAGagtiaEllalgkplIlvplpe 102
                                         a++i +ad+v+s   a++ + +    kp  ++ +++
  gi|557695088|ref|YP_008798142.1|  89 AEASIIGDADVVVSDTRASATLAAKLCRKPVATILNQY 126
                                       44788888888888555555555555555555555555 PP

  == domain 2  score: 54.3 bits;  conditional E-value: 2.5e-18
                                       EEEEEESSSSHHHHHHHH-EEEECS-CHHHHHHHHTT--EEEE--TT....S-HHHHHHHHHHHHHHSSEEEE-STT CS
                   Glyco_tran_28_C  56 kvevfefidkmaeaikaadLvIsRAGagtiaEllalgkplIlvplpeaaenhqdnNakelekagaalvleqkeltpe 132
                                       ++++ + i++++ +i+aadLv++R+G + ++ +  +gkp++++p p+   ++q  Na + ek g+a ++eq++l+p 
  gi|557695088|ref|YP_008798142.1| 265 PLHMRSWIPDLDLYIEAADLVVCRGGLTLLLKCILYGKPAVVIPPPQ--HGEQLANAIKAEKMGVAKMVEQRKLSPA 339
                                       4567789999*************************************..78************************** PP

                                       CHHHHHHHHCCS---S---SS CS
                   Glyco_tran_28_C 133 kLeeallelaaeklrlaeksk 153
                                         eea++ l+ + + +++ ++
  gi|557695088|ref|YP_008798142.1| 340 GFEEAVKSLLRNVEVAERVKH 360
                                       *********999887666655 PP

>> UDPGT  UDP-glucoronosyl and UDP-glucosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.013        78     118     181 ..      96     161 ..      77     228 .. 0.84
   2 !   24.3   0.0     2e-09   1.2e-05     325     421 ..     267     364 ..     170     367 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.013
                             UDPGT 118 kfdvvladpvlpcgellAellkiptvyllrdvp...gqaaekvsGkllsppsyvpvvlselsdkmtf 181
                                         dvv++d+ ++ ++l A+l + p+  +l++     ++  ++ + ++++p+   p+++ +lsdk++ 
  gi|557695088|ref|YP_008798142.1|  96 DADVVVSDTRAS-ATLAAKLCRKPVATILNQYNlllQSEKHQRAAEVIQPMLQTPQLVWNLSDKIII 161
                                       568999998877.99999**9999999888754111445555667999***************9986 PP

  == domain 2  score: 24.3 bits;  conditional E-value: 2e-09
                             UDPGT 325 llvkWlPqndlLgHPktkAFvtHaGangvyEaisnGvPmvglP..lFgdqrdNikrmeakgaavtlnvkemtsedll 399
                                        +  W+P  dl     +   v  +G   ++  i  G P v++P    g+q  N+ + e+ g a  ++ ++++ ++++
  gi|557695088|ref|YP_008798142.1| 267 HMRSWIPDLDLYIE-AADLVVCRGGLTLLLKCILYGKPAVVIPppQHGEQLANAIKAEKMGVAKMVEQRKLSPAGFE 342
                                       56689999998765.5678899*****************99953389****************************** PP

                             UDPGT 400 nAlkevindksykenimrLssl 421
                                       +A+k+++++    e + +Ls++
  gi|557695088|ref|YP_008798142.1| 343 EAVKSLLRNVEVAERVKHLSEI 364
                                       *******************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); 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: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 3126.60
//
Query:       gi|557695089|ref|YP_008798143.1|  [L=172]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   93.5   0.3    1.8e-26   93.0   0.3    1.1  1  AAA_assoc_C  C-terminal AAA-associated domain


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 !   93.0   0.3   9.8e-31   1.8e-26       3     119 .]      36     154 ..      35     154 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.0 bits;  conditional E-value: 9.8e-31
                       AAA_assoc_C   3 LaeelelevddLlpiveaaelLglveveegdielTelGrkfveadikerKeifreqllklvplaaairrvLderenk 79 
                                       +a+el++evd++lp+ +aaelLgl+ev++g+   T+lG+k+ ++  k +K+i++eql +l+p++++i+   ++++ k
  gi|557695089|ref|YP_008798143.1|  36 IARELQMEVDQILPASNAAELLGLLEVHDGEGAATQLGIKVSKSLAKGKKKILKEQLPHLEPFKTIIEL--AKTKPK 110
                                       799****************************************************************95..69**** PP

                       AAA_assoc_C  80 rlpeerfldeLeekls....eeeaertletaieWgrYaelfeyd 119
                                        ++ e+++++L++k +    ++e e+  e +++W +Y+e+++yd
  gi|557695089|ref|YP_008798143.1| 111 GFNIEDLINVLANKTElveyTQEPEKLRELILDWLIYSEILSYD 154
                                       **************999999***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1479.86
//
Query:       gi|557695090|ref|YP_008798144.1|  [L=253]
Description: sulfonate/nitrate/taurine ABC transporter ATP binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-35  122.0   0.0    2.9e-34  118.5   0.0    2.1  2  ABC_tran     ABC transporter
    1.3e-08   35.0   0.4     0.0039   17.0   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0042   16.8   0.2     0.0099   15.6   0.2    1.6  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.013   15.9   0.1       0.36   11.2   0.1    2.3  1  AAA          ATPase family associated with various cellular a
      0.014   15.7   0.1      0.031   14.6   0.1    1.7  1  AAA_22       AAA domain
      0.029   14.2   0.5      0.059   13.3   0.2    1.7  2  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.055   12.6   0.4        0.1   11.8   0.4    1.4  1  NB-ARC       NB-ARC domain
      0.076   12.9   0.3       0.17   11.8   0.1    1.7  2  RsgA_GTPase  RsgA GTPase
      0.078   12.9   1.1       0.17   11.8   0.3    1.8  2  NACHT        NACHT domain
       0.11   13.0   0.2       0.17   12.4   0.2    1.2  1  AAA_23       AAA domain
       0.19   11.5   0.4       0.62    9.7   0.2    1.8  2  AAA_24       AAA domain
       0.24   11.1   0.2       0.39   10.4   0.2    1.3  1  AAA_30       AAA domain
       0.43   10.7   1.3       0.86    9.7   0.3    2.3  2  MMR_HSR1     50S ribosome-binding GTPase


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 !  118.5   0.0   2.1e-37   2.9e-34       2     136 ..      27     166 ..      26     167 .. 0.95
   2 ?    1.3   0.0      0.33   4.5e+02      56      77 ..     176     197 ..     169     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 2.1e-37
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       kn+s+++k ge ++ivG++G+GK+tLlk++agl kp +G +l++gk+++          i+ ++qep lfp ltv e
  gi|557695090|ref|YP_008798144.1|  27 KNMSFDVKYGEFLGIVGQSGSGKTTLLKIMAGLIKPLSGMVLYKGKPVTG-----PTPAISLVFQEPVLFPWLTVLE 98 
                                       8***********************************************99.....999******************* PP

                                       H..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       n              e+ ++++ +l+ +gl++++++       +LSgG+kqrv+laral+++p++ll+DEp+
  gi|557695090|ref|YP_008798144.1|  99 NvvlalkrveniskeEMIVKAQSFLDMVGLSGFENSYP----GELSGGMKQRVVLARALVTNPDVLLMDEPF 166
                                       *********998777777779999******99999998....*****************************7 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.33
                                       HCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  56 slrkeigvlpqepqlfpeltvr 77 
                                       slr+ei +l q+++l p++ v 
  gi|557695090|ref|YP_008798144.1| 176 SLRREIDMLRQHETLPPTSVVL 197
                                       6799999999999999988643 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 !   16.4   0.1   4.3e-06     0.006       2      23 ..      39      60 ..      38      87 .. 0.84
   2 !   17.0   0.0   2.9e-06    0.0039     235     299 ..     137     202 ..     117     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.3e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldlla 23
                                       +++G  gsGK++LL+++ +l 
  gi|557695090|ref|YP_008798144.1| 39 LGIVGQSGSGKTTLLKIMAGLI 60
                                      689***************9984 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.9e-06
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr....ngaQviltTHSp 299
                                        elS G+k+   +l+  l +++  ++ll DEp ++L+P    +l + ++ l++      + v+l++H+ 
  gi|557695090|ref|YP_008798144.1| 137 GELSGGMKQR-VVLARALVTNP--DVLLMDEPFSNLDPLTAISLRREIDMLRQhetlPPTSVVLVSHNV 202
                                       6788899888.55555555555..9*************999888877755555555999********95 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   0.2   7.2e-06    0.0099      16      41 ..      30      55 ..      24      66 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.2e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDA 41
                                      +++++  ++  ++G+sGsGK+Tll  
  gi|557695090|ref|YP_008798144.1| 30 SFDVKYGEFLGIVGQSGSGKTTLLKI 55
                                      45555555777************955 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 ?   11.2   0.1   0.00026      0.36       3      66 ..      41     164 ..      39     167 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00026
                                       EESSTTSSHHHHHHHHHHHHT..HE.................................................... CS
                               AAA   3 lyGppGtGKTllakavakelg..ve.................................................... 25 
                                       ++G  G GKT+l k +a  ++  +                                                     
  gi|557695090|ref|YP_008798144.1|  41 IVGQSGSGKTTLLKIMAGLIKplSGmvlykgkpvtgptpaislvfqepvlfpwltvlenvvlalkrveniskeemiv 117
                                       68999***********9997543113333444555666666677777777777777777766666655555554444 PP

                                       ....EEEEETTTCSSS.........STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  26 ....fleisgsellsk.........yvgesekkirelfkeakeka.kpsilfiDE 66 
                                           fl         +         y ge +  +++ +  a++   +p +l++DE
  gi|557695090|ref|YP_008798144.1| 118 kaqsFLD--------MvglsgfensYPGELSGGMKQRVVLARALVtNPDVLLMDE 164
                                       4444444........0444444444888888888887777777667789999998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.2e-05     0.031       5      28 ..      36      59 ..      32     165 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleq 28
                                        +l ++G+sG+GKTtll+ ++  
  gi|557695090|ref|YP_008798144.1| 36 GEFLGIVGQSGSGKTTLLKIMAGL 59
                                      567889************987765 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 ?   13.3   0.2   4.3e-05     0.059       2      19 ..      39      56 ..      38      65 .. 0.84
   2 ?   -3.3   0.0       5.8     8e+03      79     100 ..     110     132 ..      99     135 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.3e-05
                              MobB  2 lgivgksgsGKTtLlekl 19
                                      lgivg+sgsGKTtLl+ +
  gi|557695090|ref|YP_008798144.1| 39 LGIVGQSGSGKTTLLKIM 56
                                      89************9855 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.8
                              MobB  79 lsleellarlse.vDlvlvEGfk 100
                                       +s ee++ + ++ +D+v   Gf 
  gi|557695090|ref|YP_008798144.1| 110 ISKEEMIVKAQSfLDMVGLSGFE 132
                                       34444444443337888777776 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   0.4   7.4e-05       0.1       7      38 ..      24      54 ..      18      60 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.4e-05
                                      HHHHHHHCTTTSCSEEEEEEESTTSSHHHHHH CS
                            NB-ARC  7 kviekLlekdelqslvvalvGmgGvGKttlak 38
                                      +vi++++   + +  ++++vG  G+GKttl+k
  gi|557695090|ref|YP_008798144.1| 24 EVIKNMSFDVKYG-EFLGIVGQSGSGKTTLLK 54
                                      5666666444555.79**************86 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00012      0.17      99     121 ..      35      58 ..       9      70 .. 0.80
   2 ?   -3.4   0.0       5.9   8.1e+03      49      69 ..     100     120 ..      95     131 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                       T.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  99 d.ktsvlvGqSGvGKStLinallp 121
                                         ++  +vGqSG GK+tL++ +++
  gi|557695090|ref|YP_008798144.1|  35 YgEFLGIVGQSGSGKTTLLKIMAG 58 
                                       4467789************98765 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.9
                                       EEEEEE-GGG--HHHHHHHHH CS
                       RsgA_GTPase  49 pvivlnKiDlleeeeeleelk 69 
                                       +v++l +++ +++ee + + +
  gi|557695090|ref|YP_008798144.1| 100 VVLALKRVENISKEEMIVKAQ 120
                                       566666777776666444444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00012      0.17       5      21 ..      41      57 ..      37      63 .. 0.83
   2 ?   -1.1   0.0       1.1   1.6e+03      73      84 ..     202     213 ..     162     229 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                      EEC-TTTCHHHHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlqkla 21
                                      + G++GsGKTtLl+ +a
  gi|557695090|ref|YP_008798144.1| 41 IVGQSGSGKTTLLKIMA 57
                                      89***********8665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
                                       HHHHCCSCCCEE CS
                             NACHT  73 wavllelperlL 84 
                                       +++++el +r+L
  gi|557695090|ref|YP_008798144.1| 202 VEEIVELSDRVL 213
                                       233444444444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   0.00012      0.17      23      37 ..      40      54 ..      26      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00012
                            AAA_23 23 lItGpNGaGKTTild 37
                                       I+G+ G+GKTT+l 
  gi|557695090|ref|YP_008798144.1| 40 GIVGQSGSGKTTLLK 54
                                      6************96 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2   0.00045      0.62       6      22 ..      40      56 ..      38      68 .. 0.86
   2 ?   -1.2   0.0         1   1.4e+03     115     141 ..     184     211 ..     177     250 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00045
                            AAA_24  6 liyGpsgiGKTtlakel 22
                                       i+G+sg+GKTtl+k +
  gi|557695090|ref|YP_008798144.1| 40 GIVGQSGSGKTTLLKIM 56
                                      599**********9987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1
                            AAA_24 115 lkklqelrk.nvifiahektrkdedpeg 141
                                       l++ + l+   v++++h  ++ +e  ++
  gi|557695090|ref|YP_008798144.1| 184 LRQHETLPPtSVVLVSHNVEEIVELSDR 211
                                       5555555556788888877777766544 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00028      0.39      21      44 ..      39      62 ..      33      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00028
                            AAA_30 21 avltGpAGtGKttalkalreawea 44
                                        ++G  G+GKtt+lk ++ +++ 
  gi|557695090|ref|YP_008798144.1| 39 LGIVGQSGSGKTTLLKIMAGLIKP 62
                                      5699************99888765 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.5   4.8e+03      77      92 ..       3      18 ..       2      30 .. 0.61
   2 ?    9.7   0.3   0.00062      0.86       2      21 ..      39      58 ..      38     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.5
                                      SEEEEEEETTTTCSHH CS
                          MMR_HSR1 77 dlillvvdaseeklkp 92
                                      d+il vvd+s++ +++
  gi|557695090|ref|YP_008798144.1|  3 DAILKVVDVSHSYYTR 18
                                      7899999988443433 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00062
                                      EEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltg 21
                                       +ivG++ +GK+tL++ + g
  gi|557695090|ref|YP_008798144.1| 39 LGIVGQSGSGKTTLLKIMAG 58
                                      58*************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 2031.35
//
Query:       gi|557695091|ref|YP_008798145.1|  [L=517]
Description: sulfonate/nitrate/taurine ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   89.7  38.9    4.9e-17   62.2   8.1    3.1  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 !   39.2  15.0   3.4e-14     6e-10       2     174 ..      33     208 ..      28     215 .. 0.92
   2 ?   -1.2   0.4     0.078   1.4e+03      51     120 ..     268     287 ..     237     320 .. 0.61
   3 !   62.2   8.1   2.8e-21   4.9e-17       2     173 ..     332     499 ..     327     508 .. 0.85

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.4e-14
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrs 78 
                                       i++G  a+   nk + k+  p+ ++l+s+P++ ++++ + vf+  s +  + l++i+l+++s+++ +++ +++  r 
  gi|557695091|ref|YP_008798145.1|  33 IVVGTAAG--VNKSFEKVAVPVLDILQSIPILGFFPVAIQVFYAASPVFGAELAAIFLIFTSQVWNITFAVYESTRF 107
                                       45555555..*****************************9**99999999*************************** PP

                      BPD_transp_1  79 lpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG........lgtllleailg 147
                                       ++ +l  +a  + +s +++fr++ lP+ lp i+  +  ++++ +   v +e+l+   G        +gtl+ e+  +
  gi|557695091|ref|YP_008798145.1| 108 IQPELLDVANSMRMSAFERFRHIYLPACLPRIVRNFQPSWANGMFFIVGAEILAF--GdvelklfgVGTLVSEFAVA 182
                                       *****************************************************94..33589999999999999999 PP

                      BPD_transp_1 148 ydyseisnggvlalviavlllnlvadi 174
                                        d+  i+ +++l+lv+a++ +n++++i
  gi|557695091|ref|YP_008798145.1| 183 GDLLGII-TVLLVLVAATIMVNFLVFI 208
                                       9999999.9999999999999999876 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.078
                      BPD_transp_1  51 hlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafgg 120
                                       +l+                                                    ++  i+ g++ ++++
  gi|557695091|ref|YP_008798145.1| 268 SLVRN--------------------------------------------------LIFLILIGFLATLAI 287
                                       33333..................................................333333333333332 PP

  == domain 3  score: 62.2 bits;  conditional E-value: 2.8e-21
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilg.hlilpviillllsaapyvrlirraalr 77 
                                       i++++ +a  r+  l+ +++++++v+ s+P+ ++ +l+         l+ +  l +++++l  + +yv++ + a+l+
  gi|557695091|ref|YP_008798145.1| 332 IPAAVAIA--RRPQLSTAVTTVFQVVASIPVTIVYPLFA------ETLKdQPELRAFVMILAATQWYVFFQVLAGLK 400
                                       45555555..999**************************......8999566666********************** PP

                      BPD_transp_1  78 slpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                       ++p++  e+a +l +++w+++r v lP alp +itg i a+gg+++g v++e l     lg+l+ e+ l     + s
  gi|557695091|ref|YP_008798145.1| 401 NIPRSELEVADMLQLKTWTRIRMVYLPRALPALITGCITAAGGAWNGLVVAERLV----LGDLVAETDLPGLGKLLS 473
                                       *******************************************************....999999988877777777 PP

                      BPD_transp_1 155 .......nggvlalviavlllnlvad 173
                                                g++ ++i++  ++++++
  gi|557695091|ref|YP_008798145.1| 474 qltyagdLLGSVSVLIVMSSIVVLMN 499
                                       67787774444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (517 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); 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: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 4063.12
//
Query:       gi|557695092|ref|YP_008798146.1|  [L=312]
Description: octaprenyl-diphosphate synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  133.8   0.2    7.2e-39  133.4   0.2    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 !  133.4   0.2     4e-43   7.2e-39      11     206 ..      41     224 ..      36     272 .. 0.88

  Alignments for each domain:
  == domain 1  score: 133.4 bits;  conditional E-value: 4e-43
                                       HHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHHHHHH CS
                   polyprenyl_synt  11 lveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklAindg 87 
                                        v +gGKrlRp+l+l +++ l+   +++ ka+++a+++el h+asLvhDDi+D +++RRG+ +   ++G  +Ai +g
  gi|557695092|ref|YP_008798146.1|  41 AV-RGGKRLRPILLLTVFKTLG--GTDYTKALDVAVALELAHSASLVHDDIVDFDKVRRGKVSLWYQIGAGKAIIQG 114
                                       56.8******************..4479************************************************* PP

                                       HHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHH CS
                   polyprenyl_synt  88 dfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaal 164
                                         + ++af+++ ++  ++ e++++f e+  +  +G l ++ ++    l+   +  yl +++ KTa+lf+++++++a+
  gi|557695092|ref|YP_008798146.1| 115 HRIINLAFNIVLDI--GE-EMTRIFVEAWDRASKGILDEVVNK--AALT---ERLYLLMIREKTASLFEAAAQAGAV 183
                                       **************..77.****************99999555..7888...9************************ PP

                                       HTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS- CS
                   polyprenyl_synt 165 lagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKp 206
                                       lagas+e++++++++g e+G+++Q+ DD+     + ++lg+ 
  gi|557695092|ref|YP_008798146.1| 184 LAGASPEMVQHMRRYGSEVGTVYQLADDLTENI-KRKNLGRM 224
                                       ****************************99877.44666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); 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 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2502.33
//
Query:       gi|557695093|ref|YP_008798147.1|  [L=135]
Description: thioredoxin 1 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  105.7   0.0    1.4e-30  105.3   0.0    1.1  1  Thioredoxin    Thioredoxin
    1.3e-08   35.2   0.1    1.1e-07   32.3   0.1    2.1  1  Thioredoxin_2  Thioredoxin-like domain
    1.2e-07   32.0   0.0    1.8e-05   25.0   0.0    2.3  2  Thioredoxin_8  Thioredoxin-like
    2.2e-06   27.2   0.0    2.9e-06   26.9   0.0    1.1  1  OST3_OST6      OST3 / OST6 family, transporter family
     0.0005   20.0   0.0     0.0022   17.9   0.0    1.8  2  AhpC-TSA       AhpC/TSA family
     0.0011   19.0   0.0     0.0018   18.2   0.0    1.4  1  Thioredoxin_3  Thioredoxin domain
     0.0013   18.5   0.1     0.0068   16.1   0.1    1.9  2  Redoxin        Redoxin
     0.0018   18.0   0.0     0.0034   17.2   0.0    1.3  1  Thioredoxin_9  Thioredoxin
     0.0039   17.1   0.0     0.0061   16.5   0.0    1.4  1  HyaE           Hydrogenase-1 expression protein HyaE
     0.0054   16.6   0.1      0.031   14.1   0.0    1.9  2  TraF           F plasmid transfer operon protein
  ------ inclusion threshold ------
      0.017   15.3   0.0      0.028   14.6   0.0    1.3  1  Thioredoxin_7  Thioredoxin-like
      0.018   14.9   0.4       0.14   11.9   0.0    2.1  2  DSBA           DSBA-like thioredoxin domain
      0.028   14.0   0.1       0.19   11.3   0.1    2.2  1  DUF953         Eukaryotic protein of unknown function (DUF953
      0.047   13.5   0.1       0.06   13.1   0.1    1.1  1  Amidohydro_2   Amidohydrolase


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 !  105.3   0.0   1.1e-33   1.4e-30       3     102 ..      34     132 ..      32     133 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 1.1e-33
                                       EESSHHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEE CS
                       Thioredoxin   3 lvltkenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklf 79 
                                       ++lt+++F+e v + ++ v+v+F+A+wC++C+a+aP++++la++++++v + k++vden+ +a+ +++ giPtl++f
  gi|557695093|ref|YP_008798147.1|  34 VELTDQSFDEFVGS-HDFVVVDFWAEWCAPCRAIAPVVKELAKQYAGRVYFGKLNVDENPRTASAFGIMGIPTLLFF 109
                                       789***********.************************************************************** PP

                                       ETTEEEEEEESS-HHHHHHHHHH CS
                       Thioredoxin  80 kngkevkkyegarekeklaaflk 102
                                       kng+ v+ ++ga +k  l+a ++
  gi|557695093|ref|YP_008798147.1| 110 KNGRVVDMVVGAVPKRVLEARIN 132
                                       ****************9999886 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   0.1   8.4e-11   1.1e-07       4     107 ..      47     129 ..      45     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 8.4e-11
                     Thioredoxin_2   4 ngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrg 80 
                                       ++  v+v+f++++C  C+++  ++kel               ++++a +++  k        ++en   a ++g+ g
  gi|557695093|ref|YP_008798147.1|  47 SHDFVVVDFWAEWCAPCRAIAPVVKEL---------------AKQYAGRVYFGKLN------VDENPRTASAFGIMG 102
                                       67889**********************...............66777777777766......47777889******* PP

                     Thioredoxin_2  81 tPt.ivfldgkeivarlpGyvpaeelea 107
                                        Pt ++f +g+ +v++++G+vp+  lea
  gi|557695093|ref|YP_008798147.1| 103 IPTlLFFKNGR-VVDMVVGAVPKRVLEA 129
                                       ***55577777.**********988876 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.4e-08   1.8e-05       3      31 ..      50      78 ..      48      92 .. 0.86
   2 ?    5.3   0.0     0.019        25      72      92 ..      92     112 ..      78     115 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.4e-08
                                      EEEEEE--SSSHHHHHHHHHHHHHHHHHH CS
                     Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklk 31
                                       v++ f+a+wc+pc+a+ p +kel +++ 
  gi|557695093|ref|YP_008798147.1| 50 FVVVDFWAEWCAPCRAIAPVVKELAKQYA 78
                                      699***********************997 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.019
                                       HHHTT-S--TT-SEEEEE-TT CS
                     Thioredoxin_8  72 nklkkkynvkaiPtlvvldkn 92 
                                          ++ +++++iPtl+  ++ 
  gi|557695093|ref|YP_008798147.1|  92 PRTASAFGIMGIPTLLFFKNG 112
                                       456889********9876654 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 !   26.9   0.0   2.2e-09   2.9e-06      13     104 ..      33     111 ..      18     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 2.2e-09
                         OST3_OST6  13 viklndenykellkgprdysvvvllTatspqfkCelCrefepefelvakswrkdekskskklfFakvdfdegkdvFq 89 
                                        ++l+d++++e++ g+ d+ vvv + a+     C++Cr ++p ++ +ak++          ++F+k+++de++ + +
  gi|557695093|ref|YP_008798147.1|  33 PVELTDQSFDEFV-GSHDF-VVVDFWAE----WCAPCRAIAPVVKELAKQYAGR-------VYFGKLNVDENPRTAS 96 
                                       6899999999999.68887.55566665....6****************99988.......9*************** PP

                         OST3_OST6  90 klglnsaPhlllfpp 104
                                        +g+  +P ll+f+ 
  gi|557695093|ref|YP_008798147.1|  97 AFGIMGIPTLLFFKN 111
                                       *************86 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.8e-06    0.0022      16      56 ..      37      78 ..      23      90 .. 0.81
   2 ?   -0.3   0.0      0.72   9.3e+02      88     117 ..      88     111 ..      85     117 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-06
                                      EEEECHHHTT..SEEEEEEESTST-CCHHHHHHHHHHCHHHCC CS
                          AhpC-TSA 16 etvslsdykg..kpvvlffypkdwcpvCttelpalaklyeefk 56
                                      ++ s++++ g  + vv+ f+++ wc +C++ +p  ++l+++++
  gi|557695093|ref|YP_008798147.1| 37 TDQSFDEFVGshDFVVVDFWAE-WCAPCRAIAPVVKELAKQYA 78
                                      45566677555599********.*************9999987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.72
                                       E-TTSHHHHHTT-EETTTTECSCEEEEE-T CS
                          AhpC-TSA  88 sDeegkvakaygvlkeekglalratfvidk 117
                                        De+  +a a+g++       +++  ++++
  gi|557695093|ref|YP_008798147.1|  88 VDENPRTASAFGIM------GIPTLLFFKN 111
                                       68999999999999......6777666654 PP

>> Thioredoxin_3  Thioredoxin 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    0.0018      10      67 ..      60     124 ..      51     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.4e-06
                                       STTCHHHHHHHHHHCHCC.T.CECEEECCTTHHHH.HHCT-SSSSEE..ECTTCEE..EESS--- CS
                     Thioredoxin_3  10 CakCpklekavkeaaaek.g.ikaevekvtdfeei.ekygVmsvPal..vidgkvv..vsGkvps 67 
                                       Ca C++++ +vke+a++  g +++   +v +++   + +g+m +P+l  + +g+vv  v+G+vp+
  gi|557695093|ref|YP_008798147.1|  60 CAPCRAIAPVVKELAKQYaGrVYFGKLNVDENPRTaSAFGIMGIPTLlfFKNGRVVdmVVGAVPK 124
                                       ******************756777667775555555***********867799997557888876 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   5.3e-06    0.0068       7      59 ..      27      78 ..      21      98 .. 0.77
   2 ?    0.7   0.0      0.29   3.7e+02      92     140 ..      89     128 ..      84     135 .] 0.65

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-06
                                      ---ECCEETTCEEEEEHHHHTTSE..EEEEEESTTT-HHHHHTHHHHHTHHHHHH CS
                           Redoxin  7 Pdftlplaatdgnsvslsefkgkk..vvvnfvpgafcPtCsaehpyleklaellk 59
                                      P+++  + + + ++ s +ef g    vvv f++  +c +C+a +p +++la++++
  gi|557695093|ref|YP_008798147.1| 27 PTVVA-E-PVELTDQSFDEFVGSHdfVVVDFWAE-WCAPCRAIAPVVKELAKQYA 78
                                      55553.2.4677777788855554469999****.***************99976 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.29
                                       -TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT.ST CS
                           Redoxin  92 DgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet.ee 140
                                       D++   ++a+G+          ++p++ ++ ++g+vv + v++ p++  e
  gi|557695093|ref|YP_008798147.1|  89 DENPRTASAFGIM---------GIPTL-LFFKNGRVVDMVVGAVPKRvLE 128
                                       5555555555522.........66654.6679999999999998855544 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.6e-06    0.0034      49     123 ..      56     128 ..      46     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.6e-06
                                       --TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--EEEEEESS-HHHHH CS
                     Thioredoxin_9  49 tedwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildeegeelgvwgerPaevqe 123
                                        ++wC  ++++ Pv++++a +++ ++ +  l  den+ +   +   g   iPtl++++++  + +v g  P++v e
  gi|557695093|ref|YP_008798147.1|  56 WAEWCAPCRAIAPVVKELAkQYAGRVYFGKLNVDENPRTASAF---GIMGIPTLLFFKNGRVVDMVVGAVPKRVLE 128
                                       579***************9567889999999********9999...7799*******9995555599999999866 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.7e-06    0.0061      44      99 ..      64     118 ..      28     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.7e-06
                                       S-HCHHHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEEEE CS
                              HyaE  44 sDvaVvlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylgvl 99 
                                          a v+ El k++  + +   ++  +++ + a+ fg++  P+llf+++g+++ ++
  gi|557695093|ref|YP_008798147.1|  64 RAIAPVVKELAKQYAGRVYFGKLN-VDENPRTASAFGIMGIPTLLFFKNGRVVDMV 118
                                       55567899***********99999.8888999*******************99876 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.31     4e+02      41      77 ..       6      42 ..       2      53 .. 0.84
   2 !   14.1   0.0   2.4e-05     0.031     131     218 ..      50     126 ..      46     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.31
                              TraF 41 saaelrkeleelldkAilnPteenveaylrlqrvald 77
                                      ++++++ + ++ l  A  nP+++ v++ ++l ++ +d
  gi|557695093|ref|YP_008798147.1|  6 ELEKIKMRKMRELMSASKNPSPTVVAEPVELTDQSFD 42
                                      6677888888888999999999999999999988877 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.4e-05
                              TraF 131 ygLlfFyrgkcpyceaqapilqafadkyglevra..VsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqk 205
                                       +  + F ++ c  c+a ap+++++a++y   v +   +vd++p   +++         ++g+  +P+l++++    +
  gi|557695093|ref|YP_008798147.1|  50 FVVVDFWAEWCAPCRAIAPVVKELAKQYAGRVYFgkLNVDENPR--TAS---------AFGIMGIPTLLFFKNG--R 113
                                       5556688899******************9888862266666666..677.........9*********999887..5 PP

                              TraF 206 vvpvaaGllslde 218
                                       vv   +G++    
  gi|557695093|ref|YP_008798147.1| 114 VVDMVVGAVPKRV 126
                                       5544555555555 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.2e-05     0.028      20      82 ..      51     110 ..      46     111 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                                       EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT---SSEEEEE- CS
                     Thioredoxin_7  20 vlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanileldeqgvPvvafld 82 
                                       v v+f a+wc +C+a++ ++ +    k+ +a+++ + +++v+e+ +   ++   g+P+++f++
  gi|557695093|ref|YP_008798147.1|  51 VVVDFWAEWCAPCRAIAPVVKEL--AKQ-YAGRVYFGKLNVDENPRTASAFGIMGIPTLLFFK 110
                                       789**************999554..777.************99999774555589****9985 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.23     3e+02       2      28 ..      53      78 ..      52      85 .. 0.81
   2 ?   11.9   0.0   0.00011      0.14     152     192 ..      87     131 ..      83     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.23
                                      EEEEEBTTBHHHHHHHHHHHHHHHHCC CS
                              DSBA  2 vdeffDvlCPyCylgkerleklaarsp 28
                                      vd++ +  C  C + ++++++la+++ 
  gi|557695093|ref|YP_008798147.1| 53 VDFWAEW-CAPCRAIAPVVKELAKQYA 78
                                      7777774.888************9994 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHTT-SSSSEEEE..TTC..EEEESSSSHHHHHHHH CS
                              DSBA 152 avrentaaaqslgvtGvPtvvv..dgk..rmvfGadrldtladal 192
                                        v+en + a + g+ G+Pt ++  +g+   mv+Ga +   l+ ++
  gi|557695093|ref|YP_008798147.1|  87 NVDENPRTASAFGIMGIPTLLFfkNGRvvDMVVGAVPKRVLEARI 131
                                       799****************99988888889*****9988887765 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00015      0.19      36      98 ..      58     111 ..      32     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                                       BSSHHHHHHHHHHHHHHHH-SS-EEEEEEE---HHHHT-TTSHHHH..TS---SSSEEEEETS CS
                            DUF953  36 sWCPdCvkaepvieealkeapedvklvrvdvGdrevWkdpanpfRkdpklkltgvPtLlrwkg 98 
                                        WC  C +  pv++e  k+ +  v + + +v + +         R+ + + ++g+PtLl +k+
  gi|557695093|ref|YP_008798147.1|  58 EWCAPCRAIAPVVKELAKQYAGRVYFGKLNVDENP---------RTASAFGIMGIPTLLFFKN 111
                                       6******************9998888777775544.........8889999999999998876 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.7e-05      0.06      33      99 ..      30      95 ..      15      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.7e-05
                                      CHHTSSECCCEHCHHHHHHHHTSHHCHHHHHHHHHHHHHHHHHHHHHHCTTCBECEEECTSSHCHHH CS
                      Amidohydro_2 33 kragvdpqlaspeallvlnaaagiaravivaalcrgannrvlaeaakrpdrfvggaavvpldpedaa 99
                                       + +v  +++s++++  +++  ++++++ ++a c +a + v++e ak+++++v ++ +++ + +++a
  gi|557695093|ref|YP_008798147.1| 30 VAEPVELTDQSFDEFVGSHDFVVVDFWAEWCAPC-RAIAPVVKELAKQYAGRVYFGKLNVDENPRTA 95
                                      567888899*************************.77788999999999999999999877766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); 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: 00:00:00.40
# Mc/sec: 1002.00
//
Query:       gi|557695094|ref|YP_008798148.1|  [L=94]
Description: hypothetical protein CSUB_C1667 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 682.70
//
Query:       gi|557695095|ref|YP_008798149.1|  [L=360]
Description: histidinol-phosphate aminotransferase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-45  155.3   0.0    3.2e-45  154.9   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    2.1e-08   33.5   0.0    4.8e-07   29.1   0.0    2.1  2  Aminotran_5      Aminotransferase class-V
    2.1e-07   29.8   0.0    4.1e-07   28.9   0.0    1.4  2  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00034   19.6   0.0     0.0011   17.9   0.0    1.7  2  Alliinase_C      Allinase
     0.0036   16.7   0.0      0.006   15.9   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.027   13.3   0.0      0.048   12.5   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 !  154.9   0.0   1.1e-48   3.2e-45      35     351 ..      60     345 ..      38     351 .. 0.92

  Alignments for each domain:
  == domain 1  score: 154.9 bits;  conditional E-value: 1.1e-48
                                       TSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHH CS
                     Aminotran_1_2  35 gtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilr 111
                                         +n y+++  +  ++e++  + g      l ++ +v+vg+G +++i ++ +++ l++g + ++++pty+ +  +++
  gi|557695095|ref|YP_008798149.1|  60 MAINLYPDTS-YRRFREKVSNYTG------LSAD-NVLVGNGGDECIMIVCQAF-LEKGLNTVISSPTYSYFRIAAE 127
                                       56899*****.*************......8899.*******************.********************** PP

                                       HTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEE CS
                     Aminotran_1_2 112 lsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDe 188
                                       ++ +e + ++ +  +d + d+++++e +++       t  i+++sp+NPtG+  +l++++k+   a +  + ++vDe
  gi|557695095|ref|YP_008798149.1| 128 INSAEARLVKRR--PDGSDDVDKILETVDK------NTGAIFLCSPNNPTGVTTSLQDIRKI---AAEAPCPVIVDE 193
                                       **********55..999*************......89************************...9999******** PP

                                       TTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHH CS
                     Aminotran_1_2 189 aYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaals 265
                                       aY +   +     ++ ++++ +pn+++ ++lsKaf+laG R+Gy+l+ ++ ++ l+k+  p   s +  a++ +a+s
  gi|557695095|ref|YP_008798149.1| 194 AYYEYSGK-----TAASLLSSYPNIIVIRTLSKAFSLAGARIGYALAAEETINILNKVRPPNSLSIISLALAEKAMS 265
                                       ****9999.....3499********************************************999************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTST CS
                     Aminotran_1_2 266 dallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftvp 341
                                        + l+++++e+++    ++r++l +++ ++ g+ v +s+++++llt  ++  a ++ +kL e+ g  +t++   t+p
  gi|557695095|ref|YP_008798149.1| 266 QVGLVKRWVEATV----AERRRLASAIGKIpGIVVKESEANFLLLTFKTHD-AGKIHEKLMEK-G-FITRNLGNTIP 335
                                       ***9776776666....68****************************9999.99*********.3.45666677889 PP

                                       TEEEEECTTS CS
                     Aminotran_1_2 342 grlRitvAgl 351
                                       + lR+tvA+ 
  gi|557695095|ref|YP_008798149.1| 336 NTLRVTVAAP 345
                                       *******764 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   1.6e-10   4.8e-07      44     177 ..      69     194 ..      63     199 .. 0.91
   2 ?    2.2   0.0     0.023        70     253     340 ..     249     333 ..     231     350 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.6e-10
                                       HHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEE CS
                       Aminotran_5  44 aveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvip 120
                                        ++  rekv +  + +  +++++  G+ e i +v +++   l++g + v+++  +   +  ++e++    a+ + ++
  gi|557695095|ref|YP_008798149.1|  69 SYRRFREKVSNYTGLSA-DNVLVGNGGDECIMIVCQAF---LEKGLNTVISSPTYSYFR-IAAEIN---SAEARLVK 137
                                       57889**********96.********************...9*******9988765555.777776...57888899 PP

                                       BETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 121 ldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                         ++g+ d+d++ ++++++t +++++  +n tG+   +++i k+a ++ + v+vD a
  gi|557695095|ref|YP_008798149.1| 138 RRPDGSDDVDKILETVDKNTGAIFLCSPNNPTGVTTSLQDIRKIAAEAPCPVIVDEA 194
                                       999****************************************************76 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.023
                                       --HHHHHHHHHHHHHHHCHHHHHHHHHHH.HHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHH CS
                       Aminotran_5 253 pnvagiiglgaaleyleeigleaiekhek.elaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlL 328
                                       pn  +ii+l++a + ++++gl + + +++ + + +l +++ ++pg+ +  +   e +a+ + ++fk+++a ++   L
  gi|557695095|ref|YP_008798149.1| 249 PNSLSIISLALAEKAMSQVGLVKRWVEATvAERRRLASAIGKIPGIVV--K---ESEANFLLLTFKTHDAGKIHEKL 320
                                       788899999999999*99999887766662556789999*******99..3...78999999999999999999999 PP

                                       HHTTEEEEE.E-T CS
                       Aminotran_5 329 deegIavrs.Ghh 340
                                        e+g   r  G++
  gi|557695095|ref|YP_008798149.1| 321 MEKGFITRNlGNT 333
                                       9998877766665 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 !   28.9   0.0   1.4e-10   4.1e-07      67     176 ..      85     195 ..      71     203 .. 0.89
   2 ?   -3.4   0.0       0.9   2.7e+03     109     163 ..     261     320 ..     257     335 .. 0.56

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 1.4e-10
                                       -SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.TSHHHHHHHCCTTEEEEE CS
                   Cys_Met_Meta_PP  67 geaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.sdleelekaikentklvy 142
                                       ++++l+ + G   i+ + +a+l++G + v+s+  Y+  +   +    +  +  +  d  +d++++ + +++nt +++
  gi|557695095|ref|YP_008798149.1|  85 ADNVLVGNGGDECIMIVCQAFLEKGLNTVISSPTYSYFRIAAEINSAEARLVKRRPDGsDDVDKILETVDKNTGAIF 161
                                       6778888999999*99****************999998888888777777777777763789*************** PP

                                       EESS-TTTT----HHHHHHHHHHTT-EEEEEGTT CS
                   Cys_Met_Meta_PP 143 lEtptnpllkvvDiekiaklakkagvlvvvDntf 176
                                       l +p np+  ++ +++i k+a +a ++v+vD ++
  gi|557695095|ref|YP_008798149.1| 162 LCSPNNPTGVTTSLQDIRKIAAEAPCPVIVDEAY 195
                                       *******************************876 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.9
                                       HHTHHHTTCEEEEEST..TSHHHHHHHCCTTEEEEEEESS-TTTT...----HHHHHHHH CS
                   Cys_Met_Meta_PP 109 kkvlkklgievkfvdt..sdleelekaikentklvylEtptnpll...kvvDiekiakla 163
                                       +k ++++g+  ++v+   ++  +l++ai +   +v  E+ +n ll   k++D  ki +  
  gi|557695095|ref|YP_008798149.1| 261 EKAMSQVGLVKRWVEAtvAERRRLASAIGKIPGIVVKESEANFLLltfKTHDAGKIHEKL 320
                                       556666666666666522334456677777777777777777543122555555555544 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       0.3   8.9e+02     121     155 ..      14      52 ..       5      68 .. 0.66
   2 !   17.9   0.0   3.7e-07    0.0011     140     213 ..     159     240 ..      89     247 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.3
                                       EEEEEESTT-.....--S..S-EEEEEESS-TTT----- CS
                       Alliinase_C 121 ykweGdaaayv....kkknpeefielvtsPnnPdgllre 155
                                       y we  +++ +     k ++   ++l tsP  P g lr 
  gi|557695095|ref|YP_008798149.1|  14 YSWEASSEEIArrygLKVEQIVRMDLNTSPYQPRGWLRS 52 
                                       566655444432111333333456899********9996 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.7e-07
                                       EEEEESS-TTT----.....-----TT-EEEEEE-TT-ST.T..TS---S-B--SEEEEEHHHHHS-GGG-EEEEEE CS
                       Alliinase_C 140 ielvtsPnnPdgllr.....eavvkgseakviyDlayYWP.h..ytpitskadedimLftlskltGhaGsrlGWalv 208
                                         +  sPnnP g+       +++ ++    vi+D ayY       + + s   + i++ tlsk    aG+r+G+al 
  gi|557695095|ref|YP_008798149.1| 159 AIFLCSPNNPTGVTTslqdiRKIAAEAPCPVIVDEAYYEYsGktAASLLSSYPNIIVIRTLSKAFSLAGARIGYALA 235
                                       34678******9754221223566777788*******9431211233445556678889*****************9 PP

                                       S-HHH CS
                       Alliinase_C 209 kdkev 213
                                        ++++
  gi|557695095|ref|YP_008798149.1| 236 AEETI 240
                                       99876 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 !   15.9   0.0     2e-06     0.006      23     146 ..      68     194 ..      55     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-06
                                       HHHHHHHHHHHHHHT..-SEEEEESSHHHHHHHHHHHTTTTTT-EEE.EESSS-THHHHHHHHTT-EEEEE-B-TTT CS
                   DegT_DnrJ_EryC1  23 peveeFEkafaaylg..vkhaiavssGtaAlhlaLralgvgpgdeVI.vpsltFvatanavlelgakpvfvDvdpdt 96 
                                          ++F +++++y+g  +++++  + G + ++++ +a+  +  ++VI  p+++++  a+ +  + a+ v       +
  gi|557695095|ref|YP_008798149.1|  68 TSYRRFREKVSNYTGlsADNVLVGNGGDECIMIVCQAFLEKGLNTVIsSPTYSYFRIAAEINSAEARLV--KRR-PD 141
                                       56799**********955666666667789999999955554555552578888888888877666655..444.45 PP

                                       SSB-GGGCGGG--TTEEEEE...EB-GGGB---HHHHHHHHHHCT-EEEEE-T CS
                   DegT_DnrJ_EryC1  97 ynidpaaieaaitertkaIl...pVhlyGqvadmdalkaiaakhglkvieDaA 146
                                          d+++i + + ++t aI+   p +  G    ++ +++iaa+   +vi D A
  gi|557695095|ref|YP_008798149.1| 142 GSDDVDKILETVDKNTGAIFlcsPNNPTGVTTSLQDIRKIAAEAPCPVIVDEA 194
                                       778****************933345789*********************9976 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05     0.048     126     275 ..     111     245 ..     102     253 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                                       EEEEEES--HHHHHHHHHHT-EEEEEEEETTEE-.HHHHHHHHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT- CS
                    Aminotran_MocR 126 kllvtvpGydrhfllleelGielltvdlqddGpd.vdaveklvaedasvkGilavpkysnptGetiseevarrlaal 201
                                         ++++p y    +  e    e   v+ ++dG d vd++ + v ++    G +++    nptG t s + +r++aa 
  gi|557695095|ref|YP_008798149.1| 111 NTVISSPTYSYFRIAAEINSAEARLVKRRPDGSDdVDKILETVDKN---TGAIFLCSPNNPTGVTTSLQDIRKIAA- 183
                                       5678999998777778888999999*******75277776666555...5888889999**************985. PP

                                       --SSTT-EEEEE-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHHHH CS
                    Aminotran_MocR 202 kaaapdfrifaddayavhdlvaeedkdanivalardaGhpdrafvlastskitfaGaGvafvassedniawlkk 275
                                          ap   + +d+ay  ++     + +a ++     + +p+  ++ + +   ++aGa +++  ++e+ i+ l+k
  gi|557695095|ref|YP_008798149.1| 184 --EAPC-PVIVDEAYYEYSG----KTAASLL-----SSYPNIIVIRTLSKAFSLAGARIGYALAAEETINILNK 245
                                       ..4443.4678899865432....3333333.....35666543333333356777777776666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2696.70
//
Query:       gi|557695096|ref|YP_008798150.1|  [L=168]
Description: transcription factor E [Candidatus Caldiarchaeum subterraneum]
Scores for 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   63.9   0.4    1.5e-17   63.3   0.4    1.2  1  TFIIE_alpha     TFIIE alpha subunit
      0.001   19.2   0.1     0.0019   18.3   0.1    1.4  1  Acetyltransf_6  Acetyltransferase (GNAT) domain
     0.0038   17.4   0.2      0.006   16.8   0.2    1.3  1  IBR             IBR domain, a half RING-finger domain
     0.0082   16.0   0.2      0.045   13.6   0.0    2.1  2  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.017   15.2   0.0      0.028   14.5   0.0    1.4  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.033   14.2   0.1       0.06   13.4   0.1    1.4  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.05   13.6   0.1      0.071   13.1   0.1    1.2  1  DUF977          Bacterial protein of unknown function (DUF977
       0.11   12.1   0.0       0.32   10.6   0.0    1.8  1  zf_C2H2_13      Zinc finger domain
       0.14   12.3   0.6       0.27   11.3   0.1    1.6  2  Sigma70_r3      Sigma-70 region 3


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 !   63.3   0.4   7.8e-21   1.5e-17       6     104 ..      13     111 ..      10     112 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 7.8e-21
                                       HHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHC CS
                       TFIIE_alpha   6 vvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklv 82 
                                       +v+ ++geeav+++  Ll k  +t+ed++  +++d++ +r++L rL e + v+y  +rd +++ + + wr+++e+lv
  gi|557695096|ref|YP_008798150.1|  13 IVGMIAGEEAVKIVGLLLDKPGLTDEDVSSMTSLDIKDVRRVLHRLNEVGAVSYEVHRDKDTGHRIFRWRVQQEQLV 89 
                                       8999************************************************************************* PP

                                       CCHHHHHHHHHHHHHHHHCCCT CS
                       TFIIE_alpha  83 dvvkrkleevvkkLeeklekee 104
                                          k  +++v+ +L+  le e+
  gi|557695096|ref|YP_008798150.1|  90 GYAKTMIRKVLERLKARLEYES 111
                                       *******************987 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   9.7e-07    0.0019       5      70 ..      49     112 ..      47     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.7e-07
                    Acetyltransf_6   5 knlrrkrrkleelgevrfrvatdpedleallelfraqwarrpdvfadpltraflrdllaalaarga 70 
                                       k++rr + +l e+g+v+++v++d ++ ++++++ ++q +   ++ a+   r+ l++l a+l+ + +
  gi|557695096|ref|YP_008798150.1|  49 KDVRRVLHRLNEVGAVSYEVHRDKDTGHRIFRWRVQQEQLV-GY-AKTMIRKVLERLKARLEYESS 112
                                       689*******************************9998888.55.589999999999999977665 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 !   16.8   0.2     3e-06     0.006       4      46 ..     101     143 ..      98     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3e-06
                               IBR   4 eklklkkslesdpnlkwCprpdCeaiieksegcksvtCskCgf 46 
                                       e+lk + ++es++++ wC +p+C+++  +++ +   +C++Cg+
  gi|557695096|ref|YP_008798150.1| 101 ERLKARLEYESSNQMYWCGTPGCGKYGFETAMELLFKCKTCGK 143
                                       67777778999999**********9999999877789****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 !   13.6   0.0   2.3e-05     0.045      17      55 ..      29      67 ..      20      80 .. 0.89
   2 ?   -0.1   0.0      0.45   8.9e+02      33      48 ..      90     105 ..      86     106 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                      Ll +  +t +++++++ ++   v +vL +L + G V  e
  gi|557695096|ref|YP_008798150.1| 29 LLDKPGLTDEDVSSMTSLDIKDVRRVLHRLNEVGAVSYE 67
                                      789999*****************************9866 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.45
                                       TSSCHCHHHHHHHHHH CS
                              TrmB  33 gvprskvYevLrsLed 48 
                                       g  ++ + +vL++L+ 
  gi|557695096|ref|YP_008798150.1|  90 GYAKTMIRKVLERLKA 105
                                       66689999****9975 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 ?   14.5   0.0   1.4e-05     0.028      11      59 ..      18      66 ..      10      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.4e-05
                                      STTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEEE CS
                             HTH_9 11 FGevvakVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVqy 59
                                       Ge + k+v++Ll+k  lt  + ++ t+L+ + V+++L  L   + V+y
  gi|557695096|ref|YP_008798150.1| 18 AGEEAVKIVGLLLDKPGLTDEDVSSMTSLDIKDVRRVLHRLNEVGAVSY 66
                                      5999**********************************88877666666 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   0.1     3e-05      0.06      39      95 ..      83     144 ..      79     156 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                                       --HHHHHHHHHHHHCC.T.TTT-EEEEEEE--EEEETT..TS-EEECHH.H.HHS-TTTSSS CS
                              HypA  39 vepeaLefafellaegtv.legaeLeieevpvkvrCre..Cgkefelee.k.alrCpkCgsa 95 
                                       v++e+L  + +++ ++ +   +a+Le+e+ +  ++C +  Cgk + +++ +  ++C++Cg+ 
  gi|557695096|ref|YP_008798150.1|  83 VQQEQLVGYAKTMIRKVLeRLKARLEYESSNQMYWCGTpgCGKYGFETAmElLFKCKTCGKP 144
                                       6777787777888777664448**************754499776544425677******85 PP

>> DUF977  Bacterial protein of unknown function (DUF977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   3.6e-05     0.071      16      93 ..      24     102 ..      19     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.6e-05
                            DUF977  16 riiGlvkkneritisdleritGvgrtsvrkylvdvlerGdlirpGkyGvfrdervvrvwrkaaekat..dqtlirkl 90 
                                       +i+Gl+ ++  +t +d+  +t  + + vr++l    e G +  + +    + +r++r wr   e+ +   +t+irk+
  gi|557695096|ref|YP_008798150.1|  24 KIVGLLLDKPGLTDEDVSSMTSLDIKDVRRVLHRLNEVGAVSYEVHRDKDTGHRIFR-WRVQQEQLVgyAKTMIRKV 99 
                                       79***************************************999999999999***9.**999987522689***98 PP

                            DUF977  91 pdg 93 
                                        + 
  gi|557695096|ref|YP_008798150.1| 100 LER 102
                                       654 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.32      20      30 ..     138     148 ..     134     160 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                        zf_C2H2_13  20 CnkCGkPisle 30 
                                       C+ CGkP+ ++
  gi|557695096|ref|YP_008798150.1| 138 CKTCGKPLTIY 148
                                       ********985 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00014      0.27      22      60 ..      36      74 ..      36      77 .. 0.95
   2 ?   -2.6   0.1       3.2   6.3e+03       7      20 ..      97     110 ..      95     114 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                      XHHHHHHHHTXXHHHHHHHHHHHXXXEETTXBSSSSTTX CS
                        Sigma70_r3 22 tpeEiAeeLglseekVrevleaarepvSldlpvgeeedt 60
                                      t+e++   + l++++Vr+vl   +e+ +++++v  ++dt
  gi|557695096|ref|YP_008798150.1| 36 TDEDVSSMTSLDIKDVRRVLHRLNEVGAVSYEVHRDKDT 74
                                      7899********************************997 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.2
                                       HHHHHHHHHHHSSX CS
                        Sigma70_r3   7 kraqreLeqelgre 20 
                                       +++ ++L  +l++e
  gi|557695096|ref|YP_008798150.1|  97 RKVLERLKARLEYE 110
                                       44444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      966  (0.0538792); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); 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: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1207.44
//
Query:       gi|557695097|ref|YP_008798151.1|  [L=188]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  153.7   0.1    2.7e-45  153.1   0.1    1.3  1  Trm56            tRNA ribose 2'-O-methyltransferase, aTrm56
  ------ inclusion threshold ------
      0.091   13.2   0.1       0.18   12.3   0.1    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1


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 !  153.1   0.1     3e-49   2.7e-45       1     118 [.      54     170 ..      54     171 .. 0.97

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 3e-49
                                       H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE...EEEEE------TCHHHHSSEEEESS CS
                             Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkek..dllvvvGaekvprevyeladynvsvg 75 
                                       wGg fk+e+++s+k+l+k+++   g++vhltmyG+++++vieei++  +  dllv+vG+ekv+ ev+++adynv+v+
  gi|557695097|ref|YP_008798151.1|  54 WGGAFKIEYTSSWKTLVKTWS---GKIVHLTMYGLPLKTVIEEIRAIMRqfDLLVIVGGEKVEGEVFQVADYNVAVT 127
                                       *********************...*********************9665569************************* PP

                                       SS---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EE CS
                             Trm56  76 nqPhsevaalaifldrllegkelekefedaklkviPsergkkv 118
                                       +qPhse aala+fld +++g+e+++ + da ++viPs++gk v
  gi|557695097|ref|YP_008798151.1| 128 SQPHSEAAALAVFLDWVFQGSEMDRVYPDAAISVIPSTKGKVV 170
                                       *****************************************98 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 ?   12.3   0.1     2e-05      0.18      18      82 ..      88     167 ..      70     173 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                                       HHHHHHHHHHH.H.HEEEEEES---...HHHHHHHT.T-..........T.TEEEE---...THHHHHHHH-SEEEE CS
                   Glyco_trans_1_4  18 dllleavpllrkk.dvrlvivGdgp.rpeeleelaa.gl..........eerveftGfv...edlaellaaadvfva 78 
                                       + ++e++ ++ ++ d  lvivG+++ +  e+ + a+ ++          ++  +f+ +v   +++++++ +a + v+
  gi|557695097|ref|YP_008798151.1|  88 KTVIEEIRAIMRQfD-LLVIVGGEKvEG-EVFQVADyNVavtsqphseaAALAVFLDWVfqgSEMDRVYPDAAISVI 162
                                       456777766664423.499999544443.444333343333444443323449*******9889************* PP

                                       --.-- CS
                   Glyco_trans_1_4  79 Ps.eg 82 
                                       Ps +g
  gi|557695097|ref|YP_008798151.1| 163 PStKG 167
                                       **433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1418.44
//
Query:       gi|557695098|ref|YP_008798152.1|  [L=679]
Description: V-type H+-transporting ATPase subunit I [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   82.0   5.5    1.9e-11   42.7   0.0    3.4  3  V_ATPase_I   V-type ATPase 116kDa subunit family
  ------ inclusion threshold ------
      0.016   15.4   1.0        2.9    8.1   0.2    2.4  2  TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
       0.02   14.5   0.0      0.052   13.1   0.0    1.7  1  DUF374       Domain of unknown function (DUF374)
       0.18   10.4   0.9        0.3    9.7   0.9    1.3  1  AAA_13       AAA domain


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 !   42.7   0.0   4.1e-15   1.9e-11     202     415 ..     183     390 ..      72     414 .. 0.86
   2 !   14.5   3.2   1.4e-06    0.0061     515     560 ..     458     504 ..     444     509 .. 0.86
   3 !   22.3   0.9   6.2e-09   2.8e-05     775     811 ..     631     667 ..     574     669 .. 0.69

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 4.1e-15
                        V_ATPase_I 202 gekveksvfiiffqgeqlkekikkicesfgaklyelp.eseeereeklkeveeriedlekvleqteealkevleeia 277
                                        + +e +  +++++ ++  e +++++++fg k+ + p   +++ +e++++++e+i+ l++ +++  ++l  +le+  
  gi|557695098|ref|YP_008798152.1| 183 TQPLENTNLVVIISKRSDGEDVERVVKGFGLKIVTTPpGYPKNVSEAVARLDEEIQTLKREVDSLGSELAGLLERER 259
                                       4566788899999999999***************9873567788888899999999888888888888888888888 PP

                        V_ATPase_I 278 keleewklkvkkekaiyhtLnlfnldvtkkvliaegWvpkeeleeiqkalkeateessssvpsilneie..tketpP 352
                                        ++ + +   +  k+  + +      + +++ i+eg++p+e+ ee  k++ ++        + +++e    ++e+ P
  gi|557695098|ref|YP_008798152.1| 260 LRIIAARDGYQLVKETLSRIAGA--GELRSFAISEGYIPAEKKEEFLKVIGSKY-------HVVVKEDAhgHHEEKP 327
                                       88888888887777777777666..67799*************99877776644.......333333331146899* PP

                        V_ATPase_I 353 TyfrtnkfteafQeivdaYGiarYrEvNpalftiitFPFlFavMFGDiGHGlllllfalllvl 415
                                          r  +  + f ++    G ++  E+ p++f  i F   +++MF D+GHGl++l f++++  
  gi|557695098|ref|YP_008798152.1| 328 VLLRNPSPVKPFENVTLIQGPPKSGEIDPTPFVSIFFTVFYGLMFADLGHGLVILGFGAFMYK 390
                                       ***********************************************************9965 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.4e-06
                        V_ATPase_I 515 lsvilGviqMlfgvllslvNalyfkkkldiilefiPqllf.llsifg 560
                                       + ++lGv++M++g++ls+v  + +k+  + ++  +P ll+ ++ if+
  gi|557695098|ref|YP_008798152.1| 458 FTILLGVVHMIVGYILSIVKLVKEKELAEAFTVKLPTLLMyVFGIFF 504
                                       579*********************************98751445555 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 6.2e-09
                        V_ATPase_I 775 vLllmeglsafLHaLRLhWVEfqsKFykgdGykFepf 811
                                        ++++egl  f+ a+RLh  Ef sKFy g+G++F+ +
  gi|557695098|ref|YP_008798152.1| 631 GVIVLEGLLVFIQAMRLHVYEFFSKFYDGTGTPFRKL 667
                                       35689*****************************976 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 ?    8.1   0.2   0.00066       2.9      16      68 ..      95     147 ..      87     174 .. 0.88
   2 ?    5.4   0.0    0.0044        20      16      44 ..     225     253 ..     221     282 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00066
                       TMF_TATA_bd  16 rlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkelee 68 
                                        l s + +lE+E + + e++++l + +++a++ + ++++  ++lk+lk+   +
  gi|557695098|ref|YP_008798152.1|  95 DLLSLLDKLEAESRPVVESINTLLNRKKAAEDKLSQIIALYDSLKALKELKLS 147
                                       5778999******************************9999999998876554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0044
                       TMF_TATA_bd  16 rlsseirrlEgElaslkeelerleaerde 44 
                                       + s ++ rl+ E+++lk+e+ +l +e   
  gi|557695098|ref|YP_008798152.1| 225 NVSEAVARLDEEIQTLKREVDSLGSELAG 253
                                       56778888888888888888877666543 PP

>> DUF374  Domain of unknown function (DUF374)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05     0.052       5      34 ..     188     217 ..     186     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                            DUF374   5 kkklaaliSrsrDGeliarvlerlGiktir 34 
                                       + +l+++iS+  DGe + rv++ +G+k + 
  gi|557695098|ref|YP_008798152.1| 188 NTNLVVIISKRSDGEDVERVVKGFGLKIVT 217
                                       5789**********************9986 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.9   6.7e-05       0.3     286     492 ..      59     275 ..      50     293 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 6.7e-05
                            AAA_13 286 erLekliekv.eskkselleklkavsdeasensafeed...keelkaeaealeeqLkglqraleaKrkepfksvele 358
                                       ++++ li+++  +++  +le+l ++++ + +n+ + +     ++l+ae + + e++++l ++ +a  +++++ + l 
  gi|557695098|ref|YP_008798152.1|  59 STIQALIQELnIKESVGILEQLSKPVEIDAKNFSASDLlslLDKLEAESRPVVESINTLLNRKKAAEDKLSQIIALY 135
                                       6789999998556666899********9999887666667789999999999999999999999999999**99**9 PP

                            AAA_13 359 svkakiesikklvaeineliakhNekvanleeekeeakkklelhlv....eeleseldeyk........kkykklek 423
                                       ++ + ++++k +++++ +l   h   ++  ++e +e++k+l ++ v           ++ +        ++ +++e+
  gi|557695098|ref|YP_008798152.1| 136 DSLKALKELKLSLDQFTNLKWFHVFVTTASTSELSELRKALPKSAVitqpL------ENTNlvviiskrSDGEDVER 206
                                       99999999***********************************98744441......33222233333345555555 PP

                            AAA_13 424 aieklekelkeee.aelkkleeeikeLekqlrdekpaaeeinkeLkafGlgeleLkfeeekkgYrivrkg 492
                                        ++    ++        k++ e ++ L +++++ k+ ++ + +eL+   l++  L+++++  gY++v++ 
  gi|557695098|ref|YP_008798152.1| 207 VVKGFGLKIVTTPpGYPKNVSEAVARLDEEIQTLKREVDSLGSELAGL-LERERLRIIAARDGYQLVKET 275
                                       55655555544431455777888*************************.*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1307  (0.0728987); expected 358.6 (0.02)
Passed bias filter:                      819  (0.0456802); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); 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: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.46
# Mc/sec: 4401.68
//
Query:       gi|557695099|ref|YP_008798153.1|  [L=82]
Description: hypothetical protein CSUB_C1672 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   41.2  11.8    1.3e-10   41.2  11.8    1.6  2  Oxidored_q3      NADH-ubiquinone/plastoquinone oxidoreductase
     0.0048   17.0  16.4     0.0066   16.6  16.4    1.2  1  DUF4040          Domain of unknown function (DUF4040)
  ------ inclusion threshold ------
      0.034   14.1   1.5      0.047   13.7   1.5    1.3  1  SLATT_fungal     SMODS and SLOG-associating 2TM effector doma
       0.89    7.8   9.9        0.9    7.8   9.9    1.0  1  DUF2070          Predicted membrane protein (DUF2070)
          6    6.0   9.4        8.1    5.5   9.4    1.2  1  CitMHS           Citrate transporter
        6.2    6.9   7.9        1.6    8.8   4.5    1.6  2  SLATT_3          SMODS and SLOG-associating 2TM effector doma


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 ?   -0.3   0.3      0.27   8.2e+02     127     139 ..       4      16 ..       1      21 [. 0.49
   2 !   41.2  11.8   4.4e-14   1.3e-10       2      60 ..      19      77 ..      18      82 .] 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHH CS
                       Oxidored_q3 127 felasllLLvali 139
                                       +el+ ++LL+a  
  gi|557695099|ref|YP_008798153.1|   4 LELLEMVLLIAAA 16 
                                       5555555555432 PP

  == domain 2  score: 41.2 bits;  conditional E-value: 4.4e-14
                                      HHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHS CS
                       Oxidored_q3  2 allvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimll 60
                                      a++++ + ++v+s+++L+  +  + ++f++lga+ +a+lq+lvY+G+i+ lf+Fvi+l+
  gi|557695099|ref|YP_008798153.1| 19 AVAAVEQGRLVRSVIALLGYTATLGVIFFVLGAYPVAILQLLVYAGGIIALFIFVILLT 77
                                      6778888899************************************************6 PP

>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6  16.4   2.2e-06    0.0066       3      63 ..      15      75 ..       9      78 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-06
                           DUF4040  3 lvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvllllalr 63
                                      ++++a+aav + +++++vi+l  +   + ++f++lgA  vA+ q++v +g +++l+++++ 
  gi|557695099|ref|YP_008798153.1| 15 AAVFAVAAVEQGRLVRSVIALLGYTATLGVIFFVLGAYPVAILQLLVYAGGIIALFIFVIL 75
                                      567788888888*********************************************9985 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 ?   13.7   1.5   1.6e-05     0.047      27      58 ..      10      42 ..       2      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.6e-05
                      SLATT_fungal 27 QvllgAlltaLgalssgr.tqvaitvLGalnTv 58
                                       +l++A++ a++a+++gr  + +i++LG  +T+
  gi|557695099|ref|YP_008798153.1| 10 VLLIAAAVFAVAAVEQGRlVRSVIALLGYTATL 42
                                      5799**************************997 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   9.9    0.0003       0.9     105     178 ..       6      79 ..       1      82 [] 0.85

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0003
                           DUF2070 105 vlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifalavylfivvvdrp 178
                                       +l ++l +a  ++ + av + +l ++v+  l +++++ ++++++ ++  ++l ll+ +  ++a+++f++++++ 
  gi|557695099|ref|YP_008798153.1|   6 LLEMVLLIAAAVFAVAAVEQGRLVRSVIALLGYTATLGVIFFVLGAYPVAILQLLVYAGGIIALFIFVILLTKG 79 
                                       56799999************************************777777777777777788888888887765 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   9.4    0.0027       8.1     215     279 ..       9      75 ..       4      82 .] 0.63

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0027
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 215 vlllfaGvfllvgaleqtGilealadllga.ggplval..alvlgliallsafisnvavaalmapial 279
                                       ++ll+a+++ +v+a+eq  ++ ++++llg  +  l ++  +l+++ +a+l +++    + al+++++l
  gi|557695099|ref|YP_008798153.1|   9 MVLLIAAAVFAVAAVEQGRLVRSVIALLGYtA-TLGVIffVLGAYPVAILQLLVYAGGIIALFIFVIL 75 
                                       45566666666677777778888888874321.22222234557777777777777777777777765 PP

>> SLATT_3  SMODS and SLOG-associating 2TM effector domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.5   0.00054       1.6      24      65 ..       7      47 ..       1      55 [. 0.84
   2 ?    3.4   1.4     0.026        76      21      64 ..      28      70 ..      27      81 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00054
                           SLATT_3 24 lrlvllvvAAlaaalslkvgsvdlaallaalafllalvievv 65
                                      l++vll++AA+ a+++++ g++ + +++a+l++ ++l++ ++
  gi|557695099|ref|YP_008798153.1|  7 LEMVLLIAAAVFAVAAVEQGRL-VRSVIALLGYTATLGVIFF 47
                                      7899************999766.8999999999999988765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.026
                           SLATT_3 21 llrlrlvllvvAAlaaalslkvgsvdlaallaalafllalviev 64
                                      l+r+ ++ll   A+++++ + +g   ++a+l++l++++ +++ +
  gi|557695099|ref|YP_008798153.1| 28 LVRSVIALLGYTATLGVIFFVLG-AYPVAILQLLVYAGGIIALF 70
                                      67778888888999999998885.55889999999987766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1090  (0.0607954); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); 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):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 605.48
//
Query:       gi|557695100|ref|YP_008798154.1|  [L=86]
Description: hypothetical protein CSUB_C1673 [Candidatus Caldiarchaeum subterraneum]
Scores for 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    8.4   7.0        2.7    8.0   1.1    2.5  2  TNFR_16_TM  Tumor necrosis factor receptor member 16 trans-me


Domain annotation for each model (and alignments):
>> 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 ?    8.0   1.1   0.00015       2.7      13      27 ..       6      20 ..       5      23 .. 0.95
   2 ?    3.2   0.5    0.0047        85       8      23 ..      62      76 ..      58      77 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00015
                        TNFR_16_TM 13 ILaaVvvgLlaYvif 27
                                      IL+aV   Lla+v+f
  gi|557695100|ref|YP_008798154.1|  6 ILGAVTALLLAFVVF 20
                                      9*************9 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0047
                        TNFR_16_TM  8 PiYcSILaaVvvgLla 23
                                      P ++S  ++Vv++L++
  gi|557695100|ref|YP_008798154.1| 62 PLFVS-FGLVVLTLVI 76
                                      55666.599*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 0.31u 0.30s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 636.85
//
Query:       gi|557695101|ref|YP_008798155.1|  [L=105]
Description: NADH dehydrogenase I subunit K [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   73.0   5.7    1.6e-20   72.7   5.7    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha


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 !   72.7   5.7     9e-25   1.6e-20       2     105 .]       8     102 ..       7     104 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 9e-25
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHH CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaiviga 78 
                                       + l + +lf+iG+y++ +r++++k++igle++ na++l +v+++++           + ++dp+++ ++++ + +ga
  gi|557695101|ref|YP_008798155.1|   8 YVLAASFLFIIGAYCLATRKSIIKQIIGLEIMVNAAHLSFVALSSKA---------GNGVVDPYAMSFIIMSLGVGA 75 
                                       6788899**************************************99.........6789***************** PP

                                       HHHHHHHHHHHHHHHHSSS-BCCG--X CS
                       Oxidored_q2  79 aetavgLallvrlyreygtddvqelrr 105
                                        ++a++L l+v++yr y+t+dv elrr
  gi|557695101|ref|YP_008798155.1|  76 TVVALALLLTVQVYRVYRTTDVTELRR 102
                                       ************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 836.69
//
Query:       gi|557695102|ref|YP_008798156.1|  [L=218]
Description: hypothetical protein CSUB_C1675 [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1564.86
//
Query:       gi|557695103|ref|YP_008798157.1|  [L=252]
Description: calcineurin superfamily phosphohydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-16   58.8   0.1    1.4e-15   57.9   0.1    1.4  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.1e-14   54.5   0.3    3.1e-14   54.0   0.3    1.3  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 !   57.9   0.1   1.5e-19   1.4e-15       2     161 ..       3     220 ..       3     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 1.5e-19
                     Metallophos_2   2 klaiiSDlH.........snldaleavlealkevgvdaiihaGDl..eeeepe...vleellela.pvlaVrGNnD. 62 
                                       +l++iSD+H         ++lda  ++++ l+ + ++ +ih+GDl  +++  +   ++e++ e + ++++V+GN+D 
  gi|557695103|ref|YP_008798157.1|   3 RLVHISDTHisrfgmflpDRLDACIRIVNSLDPA-PQFVIHTGDLtdYGILMDyemAVEKMDEFEpDIIYVPGNHDe 78 
                                       589*******************************.*********8666666553345555555558**********8 PP

                     Metallophos_2  63 ......................eevveedvlreaaelgtdlp.eeaelelagek........vlliHgdpl...... 102
                                                             ++vv    ++ +   +++l   ++++  ++++        +  +H++        
  gi|557695103|ref|YP_008798157.1|  79 knygdslfremvsqvdvlnsfgKIVVLTLGSAIPDSDNGRLGrGRQQMIKQRMRgfgddilkIVAFHHHLIpvpfag 155
                                       88887777776666666655533334444444555555555433333332333355566667667777644899999 PP

                     Metallophos_2 103 ......gvkdalaellkeaeegsdvvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe..tyaild 161
                                             +++ ++ + + e  +g+++v++GH Hv+++ k g++l+vn+G v+  r++ +   ++ i+d
  gi|557695103|ref|YP_008798157.1| 156 rekdilEDAGDVLRIILE--SGVNMVLMGHRHVRNAIKVGETLLVNAGTVSCVRTRGRLgnSFNIID 220
                                       999888777788888887..9*****************************98877665555666665 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.3   3.5e-18   3.1e-14       2     203 ..       3     186 ..       2     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 3.5e-18
                                       EEEEEESBTB.TTCCTHHHHHHHHHHHHHHH.TTESEEEEESTSSSSS...HHHHHHHHHHHHHHHHTSEEEEEC-T CS
                       Metallophos   2 rilvigDlHl.algggqlddllkllddllre.ekpdlvllaGDlvdrg...dlekellellaalvkypipvylllGN 73 
                                       r+++i+D+H+   g    d+l+++++ +++  + p +v+++GDl+d g   d+e   +e ++++ +    ++ ++GN
  gi|557695103|ref|YP_008798157.1|   3 RLVHISDTHIsRFGMFLPDRLDACIRIVNSLdPAPQFVIHTGDLTDYGilmDYEM-AVEKMDEFEP---DIIYVPGN 75 
                                       789*******9777777777777777774444589*************9877777.4444588888...89****** PP

                                       TSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHHHHHHSCHHHHCC... CS
                       Metallophos  74 HegfeeellnkygylgifsepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklgslnleleapepg... 147
                                       H+    e    yg       ++r  ++ ++ l++++      k+++l  g                   +p+++   
  gi|557695103|ref|YP_008798157.1|  76 HD----EK--NYG-----DSLFREMVSQVDVLNSFG------KIVVLTLG-----------------SAIPDSDngr 118
                                       **....22..222.....222222233333333333......22222222.................1111111112 PP

                                       .....HHHHHH.HHHHTTCSEEEEEESSESS......CSSSCSCCHHHHHHHHHHTTESEEEEESSSS CS
                       Metallophos 148 .....dewlkd.lekrekadwvivlgHsply......rgsgylfgdealedllkkygvdlvisGHtHv 203
                                            ++++k+  + ++++  +iv +H+ l       r +  l +   + ++  + gv +v++GH Hv
  gi|557695103|ref|YP_008798157.1| 119 lgrgrQQMIKQrMRGFGDDILKIVAFHHHLIpvpfagREKDILEDAGDVLRIILESGVNMVLMGHRHV 186
                                       22333888888888899999999999999998999998888888888888999*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1931.31
//
Query:       gi|557695104|ref|YP_008798158.1|  [L=147]
Description: coenzyme A-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-39  132.9   0.2    8.4e-39  132.7   0.2    1.1  1  CoA_binding_2  CoA binding domain
    1.1e-07   32.4   0.0    2.1e-07   31.6   0.0    1.4  2  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 !  132.7   0.2   9.4e-43   8.4e-39       1     115 [.      19     133 ..      19     134 .. 0.98

  Alignments for each domain:
  == domain 1  score: 132.7 bits;  conditional E-value: 9.4e-43
                                       --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkeala 77 
                                       r +aVvGas +p+k++++v+r+l +hg++v+pVnp ++eilg+kvy++l+e p++v++vdvf+p+ea+ e++++a++
  gi|557695104|ref|YP_008798158.1|  19 RVVAVVGASREPTKPAHYVPRFLMRHGYEVIPVNPFADEILGQKVYKTLEEIPKQVEIVDVFRPSEAVYEVAESAAK 95 
                                       679***********************************************968************************ PP

                                       H--SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHHHH CS
                     CoA_binding_2  78 lgakavwlqpgsedeeaaelaeeagirvvgdrCilveg 115
                                       + +k++w+q+g++++eaael++++g++vv +rC++ e+
  gi|557695104|ref|YP_008798158.1|  96 ILPKVFWMQEGIYNREAAELLKSKGVTVVWNRCMMKEH 133
                                       ***********************************998 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   2.3e-11   2.1e-07       5      84 ..      20      95 ..      16     103 .. 0.90
   2 ?   -3.3   0.0       1.8   1.6e+04      80      92 ..     113     126 ..     110     127 .. 0.63

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 2.3e-11
                                      EEEEETTTSHHHHHH.HHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHH CS
                       CoA_binding  5 kviviGagglgiagl.yhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdel 82
                                       v+v+Ga+++ ++ + y+ ++ ++ +  +v++vnp   ++e+lg +vyk+++e++++  v++  ++ P+e+++e+++ +
  gi|557695104|ref|YP_008798158.1| 20 VVAVVGASREPTKPAhYVPRFLMR-HGYEVIPVNPF--ADEILGQKVYKTLEEIPKQ--VEIVDVFRPSEAVYEVAESA 93
                                      599************999998887.56689*****9..*******************..99988999*********999 PP

                                      HH CS
                       CoA_binding 83 ve 84
                                      ++
  gi|557695104|ref|YP_008798158.1| 94 AK 95
                                      86 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.8
                                       HHHHH.TT-SEEEE CS
                       CoA_binding  80 delve.agikgivi 92 
                                        el++ +g+ ++++
  gi|557695104|ref|YP_008798158.1| 113 AELLKsKGVTVVWN 126
                                       45555488888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1171.81
//
Query:       gi|557695105|ref|YP_008798159.1|  [L=360]
Description: pyruvate formate-lyase activating enzyme [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   38.5   0.0    2.4e-09   37.8   0.0    1.4  1  Radical_SAM    Radical SAM superfamily
  ------ inclusion threshold ------
      0.016   15.2   0.1      0.016   15.2   0.1    2.8  3  DZR            Double zinc ribbon
       0.11   11.9   7.3        2.9    7.4   0.2    3.7  3  zf-ribbon_3    zinc-ribbon domain
       0.17   11.6   0.2       0.17   11.6   0.2    1.9  2  zf-CCHC_5      GAG-polyprotein viral zinc-finger
          1   10.0   0.0          1   10.0   0.0    3.3  4  zf-ISL3        zinc-finger of transposase IS204/IS1001/IS1096
        2.4    8.0  11.3        3.8    7.4   0.2    3.6  4  zinc_ribbon_2  zinc-ribbon domain
        3.6    7.7   6.4        1.7    8.8   0.1    2.8  3  zf-ACC         Acetyl-coA carboxylase zinc finger 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 !   37.8   0.0   9.5e-13   2.4e-09       3     150 ..      84     226 ..      82     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 9.5e-13
                                       EESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgi 78 
                                        t gCn  C +C++    +rr + g + s+e+++e++ ++      +++  +  ep+   +++ ++  +a++  +g+
  gi|557695105|ref|YP_008798159.1|  84 ATTGCNWLCAYCQNFDIsQRRKVEGVEASPEMVVELALRYG----SDGIAYTYNEPSIFMEYAHDIGVIARR--KGL 154
                                       689************99***********************8....***************************..7** PP

                                       EEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH.HHHHHHTCTSHHHHHHHHHHHHHHTTSET...EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx RF
                       Radical_SAM  79 ritvetngtlpdeeklerllelgvdrvslgleaadde.kvlklmnrghtfeevlealeklreagikr...vvdriv 150
                                        + ++tng++  ++ ++   e  +d  +++ +   +   v++ + + ++ e v ++l  +r++  +    ++d iv
  gi|557695105|ref|YP_008798159.1| 155 INIFVTNGYWT-PDAVKMAGEF-LDCATVDFKGSGEQsFVQRFI-GIPSAEPVFDTLLEIRRK-TRIhleITDLIV 226
                                       **********7.6666665554.599999999999887788888.999999999999999998.443344555544 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.3      0.22   5.5e+02      10      39 ..      18      31 ..       7      41 .. 0.60
   2 ?   -1.8   0.2       1.3   3.3e+03      31      35 ..      92      96 ..      77     102 .. 0.72
   3 ?   15.2   0.1   6.4e-06     0.016       8      38 ..     298     338 ..     277     342 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.22
                               DZR 10 pdarfCseCgtklkavaaedrCpsCgekvd 39
                                      ++ +                 C +C + + 
  gi|557695105|ref|YP_008798159.1| 18 DGRI----------------ECTACARYCR 31
                                      4444................4555555544 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                               DZR 31 CpsCg 35
                                      C  C+
  gi|557695105|ref|YP_008798159.1| 92 CAYCQ 96
                                      33333 PP

  == domain 3  score: 15.2 bits;  conditional E-value: 6.4e-06
                               DZR   8 lppdarfCseCgtklkavaa..........edrCpsCgekv 38 
                                       +p ++ +C+ Cg+ +                +rCp+Cg+ +
  gi|557695105|ref|YP_008798159.1| 298 HPLENTYCPGCGEMVVGRHGfdivdwrlvdDNRCPRCGYRI 338
                                       577899********975555******************976 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2      0.15   3.8e+02      19      24 ..      92      97 ..      91      98 .. 0.81
   2 ?    5.7   0.2    0.0039        10       2      12 ..     302     313 ..     301     315 .. 0.80
   3 ?    7.4   0.2    0.0011       2.9      15      26 .]     327     338 ..     326     338 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.15
                       zf-ribbon_3 19 CpyCGt 24
                                      C+yC+ 
  gi|557695105|ref|YP_008798159.1| 92 CAYCQN 97
                                      ****86 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0039
                       zf-ribbon_3   2 tvrCPnCGa.pl 12 
                                        ++CP CG+ ++
  gi|557695105|ref|YP_008798159.1| 302 NTYCPGCGEmVV 313
                                       589*****9775 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0011
                       zf-ribbon_3  15 ddnvCpyCGtkl 26 
                                       ddn Cp CG+++
  gi|557695105|ref|YP_008798159.1| 327 DDNRCPRCGYRI 338
                                       788899999876 PP

>> zf-CCHC_5  GAG-polyprotein viral zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2       2.3     6e+03       5       9 ..     305     309 ..     303     310 .. 0.87
   2 ?   11.6   0.2   6.8e-05      0.17       2      14 ..     328     340 ..     327     342 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.3
                                       -TTT- CS
                         zf-CCHC_5   5 CpRCk 9  
                                       Cp C+
  gi|557695105|ref|YP_008798159.1| 305 CPGCG 309
                                       ****8 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 6.8e-05
                                       --B-TTT-SSBS- CS
                         zf-CCHC_5   2 pglCpRCkkgkHw 14 
                                       +++CpRC+ + H 
  gi|557695105|ref|YP_008798159.1| 328 DNRCPRCGYRIHI 340
                                       59********995 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 ?   -4.5   1.2         7   1.8e+04       4       9 ..      22      27 ..      20      33 .. 0.61
   2 ?   -2.3   0.0       2.9   7.5e+03       3      10 ..      90      97 ..      89     106 .. 0.73
   3 ?   10.0   0.0   0.00041         1       5      27 ..     305     327 ..     301     329 .. 0.91
   4 ?    4.5   1.0     0.023        58       4      14 ..     330     341 ..     327     349 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 7
                           zf-ISL3  4 rCPnCg 9 
                                       C  C+
  gi|557695105|ref|YP_008798159.1| 22 ECTACA 27
                                      455565 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.9
                           zf-ISL3  3 hrCPnCgs 10
                                      + C +C++
  gi|557695105|ref|YP_008798159.1| 90 WLCAYCQN 97
                                      67889986 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00041
                           zf-ISL3   5 CPnCgsktvvkhgkkerrvrhlp 27 
                                       CP+Cg+ +v +hg   + +r ++
  gi|557695105|ref|YP_008798159.1| 305 CPGCGEMVVGRHGFDIVDWRLVD 327
                                       *******************9875 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.023
                           zf-ISL3   4 rCPnCgsk.tvv 14 
                                       rCP+Cg + + v
  gi|557695105|ref|YP_008798159.1| 330 RCPRCGYRiHIV 341
                                       8*****986655 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.44   1.1e+03       8      19 ..      15      26 ..      14      29 .. 0.83
   2 ?   -2.8   0.7       2.3   5.9e+03      16      19 ..      92      95 ..      91      95 .. 0.87
   3 ?    7.4   0.2    0.0015       3.8      12      21 ..     301     310 ..     298     312 .. 0.83
   4 ?    6.7   0.1    0.0023         6      15      21 ..     330     336 ..     327     338 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.44
                     zinc_ribbon_2  8 elqdnakFCpyC 19
                                      +l+d+   C+ C
  gi|557695105|ref|YP_008798159.1| 15 PLPDGRIECTAC 26
                                      688999999999 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                     zinc_ribbon_2 16 CpyC 19
                                      C yC
  gi|557695105|ref|YP_008798159.1| 92 CAYC 95
                                      9999 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0015
                     zinc_ribbon_2  12 nakFCpyCGt 21 
                                       ++++Cp CG+
  gi|557695105|ref|YP_008798159.1| 301 ENTYCPGCGE 310
                                       689******7 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0023
                     zinc_ribbon_2  15 FCpyCGt 21 
                                        Cp+CG+
  gi|557695105|ref|YP_008798159.1| 330 RCPRCGY 336
                                       5666665 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 ?   -2.6   0.3       2.5   6.3e+03       2       7 ..      21      26 ..      21      27 .. 0.76
   2 ?    8.8   0.1   0.00067       1.7       2      11 ..     303     312 ..     303     315 .. 0.90
   3 ?    1.7   0.1      0.11   2.8e+02       3       8 ..     330     335 ..     329     338 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.5
                            zf-ACC  2 tKCpsC 7 
                                      + C++C
  gi|557695105|ref|YP_008798159.1| 21 IECTAC 26
                                      569999 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00067
                            zf-ACC   2 tKCpsCgeml 11 
                                       t Cp+Cgem+
  gi|557695105|ref|YP_008798159.1| 303 TYCPGCGEMV 312
                                       68*******8 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.11
                            zf-ACC   3 KCpsCg 8  
                                       +Cp+Cg
  gi|557695105|ref|YP_008798159.1| 330 RCPRCG 335
                                       69***8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2810.80
//
Query:       gi|557695106|ref|YP_008798160.1|  [L=270]
Description: hypothetical protein CSUB_C1679 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2181.70
//
Query:       gi|557695107|ref|YP_008798161.1|  [L=468]
Description: hypothetical protein CSUB_C1680 [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-37  128.5   0.2    5.4e-20   72.0   0.0    2.1  2  Thy1      Thymidylate synthase complementing protein
  ------ inclusion threshold ------
       0.15   12.2   0.0         13    6.0   0.0    2.5  2  MerR_1    MerR HTH family regulatory 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 !   72.0   0.0     6e-24   5.4e-20      32     187 ..      58     212 ..      35     213 .. 0.89
   2 !   54.8   0.0   1.2e-18     1e-14      61     188 .]     292     427 ..     265     427 .. 0.89

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 6e-24
                                       GCCHHHHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-TTSEEEE--TTTSGCCCTCBS--GGGCC.HHHHH CS
                              Thy1  32 eekkeklikkllkhghgsplehasftfeiegvSravlrqlvrHRiasfsqqSqRYvesskeafvippeieqkeelee 108
                                        ++++k+ ++  ++gh s+    sf++e++++Sra++  lv     s+ q+SqR   ++    ++pp  ++  +  +
  gi|557695107|ref|YP_008798161.1|  58 AKTAAKVHRESTQRGHASITTSLSFQLEVRECSRALSMLLVAPPFGSYLQESQRRAIVTHSSLITPPLPSE--HHVK 132
                                       366778999999******************************************99999955999999885..4568 PP

                                       HHHHHHHHHHHHHHHHHHTTCHHHHHGGGSBTTBEEEEEEEEEHHHHHHHHHHHS.STTS-HHHHHHHHHHHHHHHH CS
                              Thy1 109 lyeeamekaleaykelleagvarEdaryvLPlatktklvvtmNlrsLlhflelra.csrAqwEirelaeemleelkk 184
                                       ++ee+  + ++ yk+l+e+gv  EdaryvLPl+tkt+l +++ l ++  f+++ +  ++   E+ e+ae+ + + k+
  gi|557695107|ref|YP_008798161.1| 133 IFEETAHRLVDGYKQLIENGVTLEDARYVLPLCTKTSLFISCSLETYAPFIQHSNvGEHLPSEVHEFAEKFYSLAKN 209
                                       8************************************************9999884778****************** PP

                                       HSH CS
                              Thy1 185 vaP 187
                                       vaP
  gi|557695107|ref|YP_008798161.1| 210 VAP 212
                                       **9 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 1.2e-18
                                       EEEEHHHHHHHTT-TTSEEEE--TTTSGCCCTC.....BS--GGGCC..HHHHHHHHHHHHHHHHHHHHHHHTTCHH CS
                              Thy1  61 egvSravlrqlvrHRiasfsqqSqRYvesskea.....fvippeieq.keeleelyeeamekaleaykelleagvar 131
                                       e +S ++ +q +rHR++   ++S  Y+  +++       +ipp+  + +++  +l+++ + ++le y++l++ g   
  gi|557695107|ref|YP_008798161.1| 292 EPLSLVAYHQAIRHRTVPTAVESI-YTAAERALknpekNIIPPPDVKtNPRNMKLFTQLCIESLECYDKLVKDGCRL 367
                                       66899***********88777764.676655224678888999988767888899********************** PP

                                       HHHGGGSBTTBEEEEEEEEEHHHHHH...HHHHHSSTTS-HHHHHHHHHHHHHHHHHSHH CS
                              Thy1 132 EdaryvLPlatktklvvtmNlrsLlh...flelracsrAqwEirelaeemleelkkvaPe 188
                                        da  +LP+a+k  +v   N  +Ll    f++ r+cs AqwE r++a ++l e+ k aPe
  gi|557695107|ref|YP_008798161.1| 368 GDAALILPQALKLYVVRAYNGFNLLYpsgFVATRTCSYAQWEERAIAYKLLHEVVKRAPE 427
                                       ************************97788*****************************96 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 ?    3.4   0.0    0.0089        80      27      66 ..     122     162 ..     117     164 .. 0.74
   2 ?    6.0   0.0    0.0014        13      24      67 ..     329     375 ..     327     377 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0089
                                       S-EE.-TTS-EEEEHHHHHHHHHHHHHHHTT--GGG---XX CS
                            MerR_1  27 kpkr.teggrryYtdedierLklikyLlkrGltlkgikkll 66 
                                        p+  +e+   ++ ++  + +   k+L ++G+tl++++ +l
  gi|557695107|ref|YP_008798161.1| 122 TPPLpSEHHVKIFEETAHRLVDGYKQLIENGVTLEDARYVL 162
                                       555533333467777777778889*************9887 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0014
                                       TT-S-EE...-TTS-EEEEHHHHHHHHHHHHHHHTT--GGG---XXX CS
                            MerR_1  24 gllkpkr...teggrryYtdedierLklikyLlkrGltlkgikklln 67 
                                         ++p+    + +++ ++t+  ie L+   +L k G  l +++ +l 
  gi|557695107|ref|YP_008798161.1| 329 NIIPPPDvktNPRNMKLFTQLCIESLECYDKLVKDGCRLGDAALILP 375
                                       458888889899999*********************99999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3665.45
//
Query:       gi|557695108|ref|YP_008798162.1|  [L=156]
Description: 6-pyruvoyl tetrahydrobiopterin synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-23   81.0   0.0      9e-23   80.6   0.0    1.1  1  PTPS      6-pyruvoyl tetrahydropterin synthase


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 !   80.6   0.0     5e-27     9e-23       6     119 ..      16     153 ..      13     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.6 bits;  conditional E-value: 5e-27
                                       EEEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEEC..CCC-CCHHCCS. CS
                              PTPS   6 feFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkfl..naddpeleell. 79 
                                       ++Fd+aH+l++++ kc+ lHGH+ +v vtv g+    ++mvv fgelk+++k++++ +Dhk++   +   +l     
  gi|557695108|ref|YP_008798162.1|  16 INFDYAHFLPSSP-KCGVLHGHSSTVSVTVVGK--VVDEMVVEFGELKKIVKKVVDAMDHKLIvcRKYLSHL---Ed 86 
                                       58********877.*******************..7889************************533444444...45 PP

                                       .............................--HHHHHHHHHHHHHHHHGCCCGCEEEEEEEEETTEEEE CS
                              PTPS  80 ............................spTaEnlaklifeelkerlqekevklskvrvwEtpnswae 119
                                                                   ++T+En++++i+++l+e l +++v+  +vr++E  +++a+
  gi|557695108|ref|YP_008798162.1|  87 gkvkvefdgvgghyefilpinsvyvierDSTVENISEHIAARLREML-PPNVQRIHVRMSEGFGKYAT 153
                                       559*************************99*****************.9999999******9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      607  (0.0338558); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1210.16
//
Query:       gi|557695109|ref|YP_008798163.1|  [L=216]
Description: transcription regulator ExsB related protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-39  136.0   0.0    1.4e-39  135.8   0.0    1.0  1  QueC             Queuosine biosynthesis protein QueC
    6.7e-06   25.8   0.0    1.4e-05   24.8   0.0    1.5  1  ThiI             Thiamine biosynthesis protein (ThiI)
    0.00015   20.7   0.0    0.00019   20.3   0.0    1.2  1  tRNA_Me_trans    tRNA methyl transferase
  ------ inclusion threshold ------
      0.036   13.8   0.0       0.16   11.7   0.0    1.9  2  ATP_bind_3       PP-loop family
       0.13   11.1   0.0       0.17   10.7   0.0    1.1  1  Not1             CCR4-Not complex component, Not1
       0.18   11.4   0.0       0.25   11.0   0.0    1.2  1  Asn_synthase     Asparagine synthase
       0.22   11.0   0.0       0.33   10.4   0.0    1.3  1  Diphthami_syn_2  Diphthamide synthase


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 !  135.8   0.0   5.4e-43   1.4e-39       1     209 [.       2     205 ..       2     206 .. 0.93

  Alignments for each domain:
  == domain 1  score: 135.8 bits;  conditional E-value: 5.4e-43
                                       EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG----- CS
                              QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeei 77 
                                       k+v l+SGG+DSt++l+  ++eg+ +  lt+   +r+ +e+eaakki+k++  +e  + d+++l+el +     +e 
  gi|557695109|ref|YP_008798163.1|   2 KIVALVSGGIDSTVMLWKLRSEGHSILPLTLLTFRRNPREIEAAKKISKAASGREPIVYDVSFLRELYDYPQHIKER 78 
                                       6799*************************************************9***********998876555543 PP

                                       ------...--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH.HTS--E CS
                              QueC  78 evpkeeleeeelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg.edkkie 153
                                        v +   +  +lpn  +p RN+if+s+aa  a +  aeai+ G ++ed++  PD  +ef++ l+k+ln +   ++++
  gi|557695109|ref|YP_008798163.1|  79 -VFQ---QFPSLPNIVIPYRNIIFYSVAAYVACHEAAEAIAGGHTREDMERIPDVGEEFFADLEKILNKStPFHRVK 151
                                       .444...3589**********************************************************965689** PP

                                       EE-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHHH CS
                              QueC 154 ieaPlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfeea 209
                                       i +P+  l K ei++lg elg+p+ et+sC++  e  k+Cg+C+ C  Rk+ f+++
  gi|557695109|ref|YP_008798163.1| 152 ILTPVAGLWKPEIMRLGVELGAPIGETWSCWSVFE--KHCGKCPGCLSRKEVFRAV 205
                                       *********************************44..6*************99875 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   5.5e-09   1.4e-05       5     160 ..       2     172 ..       1     192 [. 0.71

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.5e-09
                              ThiI   5 kvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqt...slevklvvvdfkevlke 78 
                                       k++aL+SgGiDS V  + l + G  +  ++l  +   ++++ie  +k+ +  +  +     +++    +d+ + +ke
  gi|557695109|ref|YP_008798163.1|   2 KIVALVSGGIDSTVMLWKLRSEGHSILPLTLL-TFRRNPREIEAAKKISKAASGREPivyDVSFLRELYDYPQHIKE 77 
                                       689**********************9887775.55556666666666666655444310023444457888776665 PP

                              ThiI  79 .ilekvkekltivl.lk.rkmlriAekvaeeegakalvtG......esLgqVaSqtleNlrvisavv....nllilr 142
                                        + ++ +    iv+ ++   ++ +A  va +e a+a+  G      e +  V    +  l+ i + +     + il 
  gi|557695109|ref|YP_008798163.1|  78 rVFQQFPSLPNIVIpYRnIIFYSVAAYVACHEAAEAIAGGhtredmERIPDVGEEFFADLEKILNKStpfhRVKILT 154
                                       2666777766666623314689***************9994443334577888888888877766553444678999 PP

                              ThiI 143 PLigldKeeiiklAkeig 160
                                       P+ gl K ei++l  e+g
  gi|557695109|ref|YP_008798163.1| 155 PVAGLWKPEIMRLGVELG 172
                                       999999999999888877 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   7.6e-08   0.00019       1      82 [.       1      83 [.       1     126 [. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.6e-08
                     tRNA_Me_trans  1 kkvvvalSgGVDSsvaaallkeqgyevigvflklwee.edeegkeccaeedlkdaervaeklgiplevvdfekeykekv 78
                                      +k+v+++SgG+DS+v +  l+++g+++  ++l +  +   e + +++ ++ ++  e +   ++   e  d+ ++ ke+v
  gi|557695109|ref|YP_008798163.1|  1 MKIVALVSGGIDSTVMLWKLRSEGHSILPLTLLTFRRnPREIEAAKKISKAASGREPIVYDVSFLRELYDYPQHIKERV 79
                                      699***************************9988887344444566667777777888888888899999999999999 PP

                     tRNA_Me_trans 79 feef 82
                                      f++f
  gi|557695109|ref|YP_008798163.1| 80 FQQF 83
                                      9987 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.1e-05      0.16       2      24 ..       3      25 ..       2      62 .. 0.73
   2 ?   -0.5   0.0      0.35   8.9e+02      91     109 ..     105     123 ..      95     170 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.1e-05
                                      EEEE--SCHHHHHHHHHHHHHCT CS
                        ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkk 24
                                      +++ vSgG+DS+++l+ l ++ +
  gi|557695109|ref|YP_008798163.1|  3 IVALVSGGIDSTVMLWKLRSEGH 25
                                      45569***********9998755 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.35
                                       CHHCCT.CEEE---BHHHH CS
                        ATP_bind_3  91 alkkegievlllAhhadDq 109
                                       ++ +e +e ++ +h+++D 
  gi|557695109|ref|YP_008798163.1| 105 VACHEAAEAIAGGHTREDM 123
                                       5556667777777777764 PP

>> Not1  CCR4-Not complex component, Not1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   6.8e-05      0.17     107     177 ..      69     139 ..      63     150 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.8e-05
                              Not1 107 hDfPeFLaenhyslcdaippsciqLrNlilsAfPkkmklpdpftpglkvdrleeikeaPkilsdvteaLee 177
                                        D+P+ + e  ++   ++p+ +i  rN+i  ++   + + +  +     ++ e++++ P + +++ ++Le+
  gi|557695109|ref|YP_008798163.1|  69 YDYPQHIKERVFQQFPSLPNIVIPYRNIIFYSVAAYVACHEAAEAIAGGHTREDMERIPDVGEEFFADLEK 139
                                       6******************************************999999**************99999965 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   9.7e-05      0.25      21      97 ..       4      77 ..       1      92 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.7e-05
                      Asn_synthase 21 GalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhlee 97
                                       al SGG+DS++    ++ + +s l    ++f  +   e+++ak+++++   +  e ++    +l++l d+++h+ e
  gi|557695109|ref|YP_008798163.1|  4 VALVSGGIDSTVMLWKLRSEGHSILPLTLLTF-RRNPREIEAAKKISKAASGR--EPIVYDVSFLRELYDYPQHIKE 77
                                      6899*****************99999999999.89999********9998877..4444444577777777777776 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00013      0.33       1      23 [.       1      23 [.       1      37 [. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                   Diphthami_syn_2  1 mkvavlysGGkDsilaLykalke 23
                                      mk ++l+sGG Ds++ L+k   e
  gi|557695109|ref|YP_008798163.1|  1 MKIVALVSGGIDSTVMLWKLRSE 23
                                      89****************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1583.96
//
Query:       gi|557695110|ref|YP_008798164.1|  [L=267]
Description: NAD+ kinase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-36  126.4   0.6    1.4e-36  126.2   0.6    1.0  1  NAD_kinase  ATP-NAD kinase


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 !  126.2   0.6   7.6e-41   1.4e-36      68     290 ..      38     247 ..       4     249 .. 0.86

  Alignments for each domain:
  == domain 1  score: 126.2 bits;  conditional E-value: 7.6e-41
                                       ECCC-TTTTTSSS.EEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEE CS
                        NAD_kinase  68 rkaleafadagvd.liivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrev 143
                                       ++++e+  ++ vd ++ ++GGDGT+l++ r+++  ++ v+gvn G++gfl ++epe++ ++ +kl ++++ ve+ ++
  gi|557695110|ref|YP_008798164.1|  38 LSEFEQISQSPVDdVLMILGGDGTVLRATRHIKSPNVRVVGVNFGRAGFLCVIEPEELETAVKKLAAEDYHVEEIMR 114
                                       5667777777775155679********************************************************** PP

                                       EEEEEEETTE......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE CS
                        NAD_kinase 144 ldavimrskgeediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgpli 220
                                       l+  ++ +++      +v++  +lne+++   ++ t+ie  ++ + e+l++d++dg+i+stP Gstay++s Ggp++
  gi|557695110|ref|YP_008798164.1| 115 LS--LYVDDK------YVGD--ALNEIYVSSTRPGTVIEYRVQ-QREVLASDVADGVILSTPVGSTAYAFSSGGPIV 180
                                       99..666666......6644..59***************9998.67999**************************** PP

                                       -TT---EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEE CS
                        NAD_kinase 221 sPgvlailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfkli 290
                                       + +++ +++vp+   +   rp+V+s    l++ v  + +a + +dG+  + +++ +evrv +s ++ ++i
  gi|557695110|ref|YP_008798164.1| 181 DERLETVVVVPMASMTN-LRPMVISIATPLQVSVV-KGRAQALVDGHTVTPVEK-GEVRVEKSLHSIHMI 247
                                       ***********998765.69999999888886654.67788889**99998876.689*****9999888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); 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: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1972.28
//
Query:       gi|557695111|ref|YP_008798165.1|  [L=168]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   61.1   0.1    1.8e-16   60.4   0.1    1.3  1  PIN_6            PIN domain of ribonuclease
     0.0032   17.6   0.8     0.0055   16.8   0.8    1.4  1  NOB1_Zn_bind     Nin one binding (NOB1) Zn-ribbon like
  ------ inclusion threshold ------
      0.018   15.1   3.0      0.054   13.6   3.0    1.8  1  Zn-ribbon_8      Zinc ribbon domain
       0.07   13.2   0.2      0.099   12.7   0.2    1.5  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.11   12.8   0.0       0.81   10.0   0.0    2.0  2  PIN_4            PIN domain
       0.15   11.5   1.0          2    7.8   0.2    2.1  2  PIN_5            PINc domain ribonuclease
       0.16   12.5   3.3       0.26   11.8   0.7    2.2  2  zf-C2H2          Zinc finger, C2H2 type
       0.36   10.8   6.7        1.3    8.9   6.7    1.8  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.69    9.7   3.0        1.1    9.0   3.0    1.4  1  Rubredoxin_2     Rubredoxin metal binding 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 !   60.4   0.1   9.1e-20   1.8e-16       2      88 ..       8      94 ..       7      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 9.1e-20
                             PIN_6  2 VlDagaliknslsslqnlaeklyttpeVvaEird...kkarerlellplelevrePspesvkkvtefakktGDlsvLSk 77
                                      VlD++al+++   +++    +l+t++e v+E+     + +r + +l ++ +++++Psp+++k+v+e+a+ktGDl+ LSk
  gi|557695111|ref|YP_008798165.1|  8 VLDTTALLSA---QFEPGPAELVTVQEAVDEVMYgglAPQRVSTALSTQAVKLKKPSPQAIKHVEEAARKTGDLPKLSK 83
                                      9*******87...99999**************87211334445555557****************************** PP

                             PIN_6 78 tDievlALtye 88
                                      tD+ +lAL+ye
  gi|557695111|ref|YP_008798165.1| 84 TDLALLALAYE 94
                                      **********7 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   0.8   2.8e-06    0.0055       1      32 [.     130     160 ..     130     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.8e-06
                      NOB1_Zn_bind   1 ikrvkswvlrChaCfkvtkdmtkkFCpkCGnk 32 
                                       ++++++wv+rC  C kv+++   + C  CG +
  gi|557695111|ref|YP_008798165.1| 130 VREIREWVYRCLVCGKVYTRPVNR-CRDCGGE 160
                                       799**************9885544.****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 ?   13.6   3.0   2.7e-05     0.054       6      40 .]     138     165 ..     136     165 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.7e-05
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgsevrrvi 40 
                                       YrC  Cg+++++       p   C +Cg+ev+r++
  gi|557695111|ref|YP_008798165.1| 138 YRCLVCGKVYTR-------PVNRCRDCGGEVERIV 165
                                       *******99993.......3345**********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 ?   12.7   0.2   4.9e-05     0.099      64     100 ..     131     165 ..      49     167 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                                       EEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EEEE CS
                              HypA  64 ieevpvkvrCreCgkefeleekalrCpkCgsadveiv 100
                                        e  + ++rC +Cgk ++   +  rC +Cg++  +iv
  gi|557695111|ref|YP_008798165.1| 131 REIREWVYRCLVCGKVYTRPVN--RCRDCGGEVERIV 165
                                       56778899******99997644..9*****9866665 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.31   6.2e+02       1      10 [.       7      16 ..       7      19 .. 0.90
   2 ?   10.0   0.0   0.00041      0.81      84     125 ..      81     120 ..      27     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.31
                             PIN_4  1 fVlDTnvlLh 10
                                      fVlDT  lL+
  gi|557695111|ref|YP_008798165.1|  7 FVLDTTALLS 16
                                      8*******98 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00041
                             PIN_4  84 seknDnrIlavalelkeekpdrkvvLvskDinlrikAkalgi 125
                                        +k+D + la  l+++e+    +vv v++D  l++ A  lg+
  gi|557695111|ref|YP_008798165.1|  81 LSKTDLALLA--LAYEERVGGAEVVVVTDDYSLQNTALRLGL 120
                                       4577777765..567788889****************99987 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.051     1e+02       2      15 ..       7      20 ..       6      41 .. 0.75
   2 ?    7.8   0.2     0.001         2     156     190 ..      82     121 ..      69     137 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.051
                             PIN_5  2 fvlDTsaltdpevr 15
                                      fvlDT+al  ++  
  gi|557695111|ref|YP_008798165.1|  7 FVLDTTALLSAQFE 20
                                      9*******988765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.001
                             PIN_5 156 saeDldvllLAkE.....LdaavvssDeGikkwaeklGlr 190
                                       s+ Dl +l LA+E      + +vv++D  +++ a +lGl 
  gi|557695111|ref|YP_008798165.1|  82 SKTDLALLALAYEervggAEVVVVTDDYSLQNTALRLGLG 121
                                       899********9955433456899*************985 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   0.00013      0.26       1      15 [.     138     152 ..     138     155 .. 0.90
   2 ?    1.1   0.6      0.34   6.7e+02       2       7 ..     153     158 ..     152     168 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                                       EEETTTTEEESSHHH CS
                           zf-C2H2   1 ykCpdCgksFkrksn 15 
                                       y+C +Cgk+++r+ n
  gi|557695111|ref|YP_008798165.1| 138 YRCLVCGKVYTRPVN 152
                                       9***********977 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.34
                                       EETTTT CS
                           zf-C2H2   2 kCpdCg 7  
                                       +C dCg
  gi|557695111|ref|YP_008798165.1| 153 RCRDCG 158
                                       7****9 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 ?    8.9   6.7   0.00068       1.3       3      33 ..     136     160 ..     134     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00068
                    Zn_ribbon_SprT   3 yvYrCtgCgreythhlsirrhnYrCrrCkgt 33 
                                       +vYrC  Cg+   +++ ++r    Cr C+g+
  gi|557695111|ref|YP_008798165.1| 136 WVYRCLVCGK--VYTRPVNR----CRDCGGE 160
                                       9********5..45555577....9999886 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.0   0.00057       1.1       1      21 [.     138     158 ..     138     159 .. 0.97

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00057
                      Rubredoxin_2   1 YvCsqCGfesakwfGrCpsCg 21 
                                       Y+C  CG ++ + + rC++Cg
  gi|557695111|ref|YP_008798165.1| 138 YRCLVCGKVYTRPVNRCRDCG 158
                                       9*******************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1260.79
//
Query:       gi|557695112|ref|YP_008798166.1|  [L=184]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   53.3  30.8    2.9e-14   53.1  30.8    1.1  1  DUF998        Protein of unknown function (DUF998)
  ------ inclusion threshold ------
      0.023   13.8   0.7      0.032   13.4   0.7    1.3  1  Dicty_CAR     Slime mold cyclic AMP receptor


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 !   53.1  30.8   3.3e-18   2.9e-14       2     183 ..      13     176 ..       7     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 3.3e-18
                            DUF998   2 aaallalavilaaallrpgydplrhaiSeLgaeggpggwlfnaglvllgllvlalavgllraargragragrlllav 78 
                                       ++++ +l++  +a   +pgy++  ++iS+Lg   g  + +fn+ +  lg++v+a a++        ++r+ ++l+a+
  gi|557695112|ref|YP_008798166.1|  13 IGVAQFLFFLRVAESIYPGYSVSGNYISDLGV--GVAAPVFNTSVSFLGVCVIAAAYLS---LAVVGSRVFAALVAA 84 
                                       78899999999*********************..********************99966...77899********** PP

                            DUF998  79 aglglvlagvfptdpgggspslsglvHglasavaflalavavl.llasaarrrawallrlvggvallllvaalvwll 154
                                       ag+g++++g+fp++          ++H+++s ++f+   +a++  l       + +l+ +++ v+ l ++aal+++ 
  gi|557695112|ref|YP_008798166.1|  85 AGVGAFGVGLFPENVP--------VLHTVFSFITFFFAGLAAVyGLR-----VFNRLMGVFSMVCGLTALAALALFA 148
                                       **************99........5**99999888766666653444.....5556666666666666666666666 PP

                            DUF998 155 aaaldgslllGlaerllvlaitawllala 183
                                           + +l+ G  erl+v+ ++ w l+l+
  gi|557695112|ref|YP_008798166.1| 149 SG-NYLGLGHGGMERLIVYPVLSWGLLLS 176
                                       66.6669999**************99885 PP

>> Dicty_CAR  Slime mold cyclic AMP receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.7   3.5e-06     0.032     226     267 ..      90     131 ..      55     148 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-06
                         Dicty_CAR 226 nglnlfpalvnilhtylsvshgfyasvtfiynnplmwrylgs 267
                                        g++lfp  v +lht +s    f+a ++ +y   ++ r +g 
  gi|557695112|ref|YP_008798166.1|  90 FGVGLFPENVPVLHTVFSFITFFFAGLAAVYGLRVFNRLMGV 131
                                       4899***************************98888887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1509.93
//
Query:       gi|557695113|ref|YP_008798167.1|  [L=177]
Description: hypothetical protein CSUB_C1686 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   13.0   0.1       0.18   11.5   0.1    1.9  1  DUF3481   C-terminal domain of neuropilin glycoprotein
       0.61   10.5  12.2       0.87   10.0   8.2    2.8  2  CPBP      CPBP intramembrane metalloprotease


Domain annotation for each model (and alignments):
>> DUF3481  C-terminal domain of neuropilin glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1     2e-05      0.18      18      41 ..      13      37 ..       7      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2e-05
                           DUF3481 18 itiiamsa.lGvllGaicGvvlyca 41
                                      ++iia+sa + vl+Gai G+vl  a
  gi|557695113|ref|YP_008798167.1| 13 LSIIALSAaFYVLMGAISGLVLPAA 37
                                      57999996378**********9766 PP

>> CPBP  CPBP intramembrane metalloprotease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.14   1.2e+03      38      53 ..      13      28 ..       2      40 .. 0.61
   2 ?   10.0   8.2   9.7e-05      0.87      22      70 ..      44      97 ..      42     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.14
                                      HHHHHHHHHHHHHCSG CS
                              CPBP 38 tlailissilFglaHl 53
                                      + +i++s+++++l+ +
  gi|557695113|ref|YP_008798167.1| 13 LSIIALSAAFYVLMGA 28
                                      5566666666666544 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 9.7e-05
                                      HHTTCHHHH...HHHH.S-.HHHHHHHHHHHHHCSGGGHHH.HHHHHHHHHHHH CS
                              CPBP 22 lfRglllql...lqergss.tlailissilFglaHlpngps.vllaalaGlvlg 70
                                      +fRgl +++    ++r +s t+  lis+ilF ++  +++p+ ++ +++aGl++ 
  gi|557695113|ref|YP_008798167.1| 44 FFRGLAMSAagaYTRRMWSvTVMSLISGILFLVLVPAPAPYlLFSTVAAGLLYD 97
                                      89****99844455558999******************9999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1291.92
//
Query:       gi|557695114|ref|YP_008798168.1|  [L=126]
Description: hypothetical protein CSUB_C1687 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   18.9   5.7     0.0014   18.9   5.7    1.8  2  CopD      Copper resistance protein D
     0.0062   16.8   0.5     0.0091   16.3   0.5    1.3  1  DUF4149   Domain of unknown function (DUF4149)


Domain annotation for each model (and alignments):
>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0      0.85   7.6e+03      60      69 ..      10      19 ..       3      29 .. 0.62
   2 !   18.9   5.7   1.6e-07    0.0014       3     104 ..      35     124 ..      33     126 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.85
                              CopD 60 lnrfrlvprl 69
                                      +  f+ +p+l
  gi|557695114|ref|YP_008798168.1| 10 HLAFAAIPQL 19
                                      3344555555 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.6e-07
                              CopD   3 alrrFsrlalaavavvlvtGvvnallrvglagllttayGrlllaKlalllvllalaalnrfrlvprleaatgaggqa 79 
                                       +++r+  +a+ a+ +++++ ++++l       + +t+   l +++la l  +++l  l+ f l pr+    ++g+++
  gi|557695114|ref|YP_008798168.1|  35 MMKRYNPVAWTAIPILIASTTYLTLHS-----AGKTP---LPIITLAILYTAAVLDFLHSFILGPRA----ASGKTH 99 
                                       799********************6555.....44555...6699***********************....667777 PP

                              CopD  80 lrhrlrrsaalelvlalvvlllaaa 104
                                       +r    ++a++e++lal+  ll+a 
  gi|557695114|ref|YP_008798168.1| 100 ARTLALTVARVETALALALPLLIAG 124
                                       7778999**********99887665 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.5     1e-06    0.0091       5      98 ..       3      98 ..       1     102 [. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-06
                           DUF4149  5 lllGsqlwvtfvvapvlfrsLprhqfgelqsklFplyfglg.lalsvlllltevavg.seklaseellqlllllvvlll 81
                                      +++G++  + f + p l +  + ++  +l++ +  +y+ +  +a+++l++ t+ +   s+  ++    +l +l ++++l
  gi|557695114|ref|YP_008798168.1|  3 FWVGGIAHLAFAAIPQLAKLENIADRTRLMGGMMKRYNPVAwTAIPILIASTTYLTLhSAGKTPLPIITLAILYTAAVL 81
                                      899999999999999999987777788999999999998651455555555555544889999999************* PP

                           DUF4149 82 tllnafylepritslke 98
                                       +l++f+l+pr++s k+
  gi|557695114|ref|YP_008798168.1| 82 DFLHSFILGPRAASGKT 98
                                      ************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); 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 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 959.14
//
Query:       gi|557695115|ref|YP_008798169.1|  [L=510]
Description: GMP synthase (glutamine-hydrolysing) [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  132.6   0.0      2e-38  132.1   0.0    1.2  1  GATase         Glutamine amidotransferase class-I
    4.7e-32  109.9   0.0      1e-31  108.8   0.0    1.6  1  GMP_synt_C     GMP synthase C terminal domain
    1.2e-08   34.3   0.1      0.001   18.3   0.0    2.2  2  NAD_synthase   NAD synthase
    7.8e-08   32.3   0.1    2.4e-07   30.7   0.1    1.9  1  Peptidase_C26  Peptidase C26
    0.00042   19.2   0.0      0.035   12.9   0.0    2.1  2  tRNA_Me_trans  tRNA methyl transferase
     0.0015   18.1   0.0     0.0051   16.4   0.0    1.7  2  ThiI           Thiamine biosynthesis protein (ThiI)
      0.003   17.1   0.0      0.055   13.0   0.0    2.2  2  QueC           Queuosine biosynthesis protein QueC
     0.0036   17.1   0.0      0.016   15.0   0.0    1.9  2  ATP_bind_3     PP-loop family
  ------ inclusion threshold ------
      0.038   13.7   0.0      0.053   13.2   0.0    1.2  1  Asn_synthase   Asparagine synthase


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 !  132.1   0.0     1e-41     2e-38       2     189 ..       7     185 ..       6     186 .. 0.91

  Alignments for each domain:
  == domain 1  score: 132.1 bits;  conditional E-value: 1e-41
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEET CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGIC 78 
                                       ++D++ ++ + + ++++++gvk++v+p++   ++     + + g+++sgGp s++  +++++  e +  ++P+LGIC
  gi|557695115|ref|YP_008798169.1|   7 VVDFGGQYAHLISRRIRSIGVKTHVIPHSMLPDTD---ISIYRGVVFSGGPASVYENNAPKVDMEKLR-GKPLLGIC 79 
                                       89*************************99844444...368**********************99998.9******* PP

                                       HHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEE CS
                            GATase  79 LGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelm 155
                                       +G+Ql+a+ +g++v +e+ +e+  ++  l++ +++l++gl++++ ++++H++ v++    p+g+e +a ++++   +
  gi|557695115|ref|YP_008798169.1|  80 YGHQLIAYLLGGEVRRERAREYGRAELFLKH-GCRLFQGLPDRFMVWMSHGDHVEK---IPQGFETAASTNTS-PHA 151
                                       ******************99*******9999.9***********************...*******8888554.666 PP

                                       EEEEETTTEEEESSBTTSTTSTTHHHHHHHHHHH CS
                            GATase 156 eiiekknpfvgvQFHPEststpegpellfnflik 189
                                       +i ++  +++gvQFHPE+ +t++g ++l+nf+++
  gi|557695115|ref|YP_008798169.1| 152 AICNEAGNIYGVQFHPEVAHTEHGLKILKNFVFD 185
                                       66666668***********************875 PP

>> 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 !  108.8   0.0   5.2e-35     1e-31       1      91 [.     418     508 ..     418     509 .. 0.99

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 5.2e-35
                                       CCCCTTT-GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT--- CS
                        GMP_synt_C   1 eelkkaglykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnr 77 
                                       eel+kagl +++wQafav+ + k++Gv+gd+R+ +y+v++R+v+s D+mtad+++lpy+vL++i+sri ne+++v+ 
  gi|557695115|ref|YP_008798169.1| 418 EELEKAGLLDEVWQAFAVVGDDKATGVRGDRRSLGYIVTVRVVSSVDGMTADYVKLPYTVLDRIASRIANELDKVSW 494
                                       799************************************************************************** PP

                                       EEEE---TTTS-S- CS
                        GMP_synt_C  78 vvyditskPpatiE 91 
                                       v+y ++skPpatiE
  gi|557695115|ref|YP_008798169.1| 495 VTYAVSSKPPATIE 508
                                       *************9 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     5e-07     0.001       4      45 ..     198     239 ..     195     280 .. 0.83
   2 !   13.8   0.0   1.2e-05     0.024     148     177 ..     358     387 ..     353     409 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5e-07
                                       HHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCG CS
                      NAD_synthase   4 elvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgke 45 
                                       +l++ + e v+  g   v+  +SGG+DS+++aa+  ka+gk 
  gi|557695115|ref|YP_008798169.1| 198 YLEKAVSEVVEVVGPGRVLCAVSGGIDSTVTAAIVSKAVGKR 239
                                       5678889999999999***********************864 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 1.2e-05
                                       BETTTTS-HHHHHHHHHHTT--HHHHCS-- CS
                      NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpP 177
                                       ++p+ el+K ev++La+ ++ P+ ++k++P
  gi|557695115|ref|YP_008798169.1| 358 VEPLRELYKDEVRQLAEMMGLPRWLVKRHP 387
                                       68**************************99 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1   1.2e-10   2.4e-07     104     216 .]      71     168 ..      61     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.2e-10
                     Peptidase_C26 104 rgvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaike 180
                                       rg+P+lgiC G+ql++  lGG++ ++              ++  + ++ +++g  l + l  ++++v   H   +++
  gi|557695115|ref|YP_008798169.1|  71 RGKPLLGICYGHQLIAYLLGGEVRRERA------------REYGRAELFLKHGCRLFQGLP-DRFMVWMSHGDHVEK 134
                                       79*******************9876655............344578899999999999999.9************** PP

                     Peptidase_C26 181 laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       + ++++  A ++     ai  e+    ++gvQ+HPE
  gi|557695115|ref|YP_008798169.1| 135 IPQGFETAASTNTSPHAAICNEA--GNIYGVQFHPE 168
                                       ********999999988988887..56********9 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   1.8e-05     0.035       2      30 ..     214     242 ..     213     264 .. 0.79
   2 !    4.2   0.0     0.008        16     163     186 ..     356     379 ..     350     386 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigv 30 
                                       +v++a+SgG+DS+v+aa++ ++  +  ++
  gi|557695115|ref|YP_008798169.1| 214 RVLCAVSGGIDSTVTAAIVSKAVGKRLKC 242
                                       79***************998876555444 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.008
                     tRNA_Me_trans 163 kllfPlgeltKeevrkiAkeagla 186
                                       kl+ Pl el K+evr++A+ +gl+
  gi|557695115|ref|YP_008798169.1| 356 KLVEPLRELYKDEVRQLAEMMGLP 379
                                       5677***************99986 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.6e-06    0.0051       4      56 ..     213     266 ..     211     275 .. 0.85
   2 ?   -2.4   0.0       1.4   2.9e+03     125     160 ..     342     377 ..     326     378 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.6e-06
                              ThiI   4 gkvlaLlSgGiDSpVaaylllkR.Gcrvvlvhlknepgtseeaiekveklaell 56 
                                       g+vl+ +SgGiDS V+a ++ k  G r ++++++  +  ++e ++++e+l +++
  gi|557695115|ref|YP_008798169.1| 213 GRVLCAVSGGIDSTVTAAIVSKAvGKRLKCLFVNHGLLRKNEPEKVLETLRKIV 266
                                       89*************999988744999***999888888888888888887776 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                              ThiI 125 tleNlrvisavvnllilrPLigldKeeiiklAkeig 160
                                       t +N+  + ++  + +++PL  l K+e+ +lA  +g
  gi|557695115|ref|YP_008798169.1| 342 THHNVGGMPQNFGMKLVEPLRELYKDEVRQLAEMMG 377
                                       666777777778888999999999999999998776 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   2.7e-05     0.055       2      59 ..     215     272 ..     214     289 .. 0.71
   2 ?    1.7   0.0     0.079   1.6e+02     147     176 ..     347     379 ..     317     384 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                                       EEEE--SSHHHHHHHHHH.HHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEE CS
                              QueC   2 avvllSGGlDSttvlala.kkegkevealtfdYgqrhkkeleaakkiakelgveehkil 59 
                                       +++ +SGG+DSt+ +a++ k+ gk++++l ++ g  +k+e e++ +  +++   e++i+
  gi|557695115|ref|YP_008798169.1| 215 VLCAVSGGIDSTVTAAIVsKAVGKRLKCLFVNHGLLRKNEPEKVLETLRKIV-GEDNII 272
                                       67899*******988776155679*********9987777776655555442.244444 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.079
                                       H...HTS--EEE-TTTT--HHHHHHHHHHTTHH CS
                              QueC 147 g...edkkieieaPlidlsKaeivklgkelgvp 176
                                       g   ++  ++++ Pl +l K e+ +l++ +g+p
  gi|557695115|ref|YP_008798169.1| 347 GgmpQNFGMKLVEPLRELYKDEVRQLAEMMGLP 379
                                       343366678999****************99987 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     8e-06     0.016       2      58 ..     215     270 ..     214     306 .. 0.79
   2 ?   -0.7   0.0      0.53   1.1e+03     131     159 ..     351     376 ..     327     381 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8e-06
                                       EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSS..TCHHHHHHHHHHHHHHTT CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglr..eeskeeaelvkelckkln 58 
                                       vl AvSgG+DS++   ++ k     g +l ++ v+hgl   +e ++  e++++++ + n
  gi|557695115|ref|YP_008798169.1| 215 VLCAVSGGIDSTVTAAIVSKAV---GKRLKCLFVNHGLLrkNEPEKVLETLRKIVGEDN 270
                                       799**********999988884...55999******98523444555566666665555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.53
                                       SEEEETTCCEE-CCCT--HHHHHHHHHHT CS
                        ATP_bind_3 131 easeiasirlvRPlLkvskeeleeylkek 159
                                       +     +++lv Pl +++k+e++++++  
  gi|557695115|ref|YP_008798169.1| 351 Q---NFGMKLVEPLRELYKDEVRQLAEMM 376
                                       3...26899*************9998765 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.6e-05     0.053       3      48 ..     196     243 ..     194     288 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.6e-05
                      Asn_synthase   3 relLedaVkrrl..radvpvGalLSGGlDSSliaalaarqsksplktF 48 
                                       ++ Le+aV + +  ++  +v +  SGG+DS++ aa+ ++   ++lk+ 
  gi|557695115|ref|YP_008798169.1| 196 EDYLEKAVSEVVevVGPGRVLCAVSGGIDSTVTAAIVSKAVGKRLKCL 243
                                       567888888766557888999****************99888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3814.14
//
Query:       gi|557695116|ref|YP_008798170.1|  [L=268]
Description: enoyl-CoA hydratase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  242.5   0.1    4.5e-72  242.4   0.1    1.0  1  ECH_1            Enoyl-CoA hydratase/isomerase
    6.6e-41  140.9   0.2    1.1e-38  133.6   0.1    2.0  2  ECH_2            Enoyl-CoA hydratase/isomerase
     0.0026   17.7   0.0     0.0061   16.5   0.0    1.6  1  Peptidase_S49    Peptidase family S49
     0.0038   16.3   0.0     0.0099   14.9   0.0    1.6  2  SDH_sah          Serine dehydrogenase proteinase
  ------ inclusion threshold ------
      0.018   15.4   0.0      0.041   14.3   0.0    1.5  1  SeleniumBinding  Selenium binding protein
      0.027   13.8   0.0      0.044   13.1   0.0    1.3  1  NucS             Endonuclease NucS
      0.044   13.6   0.2      0.044   13.6   0.2    1.5  2  DUF3731          DNA-K related protein
       0.11   13.5   0.5        3.9    8.5   0.0    2.5  2  AMP-binding_C    AMP-binding enzyme C-terminal domain


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 !  242.4   0.1     2e-75   4.5e-72       2     250 ..      16     267 ..      15     268 .] 0.95

  Alignments for each domain:
  == domain 1  score: 242.4 bits;  conditional E-value: 2e-75
                                       EETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHH CS
                             ECH_1   2 ieagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevl 78 
                                       +e gva i ln+P   Nal+ el+ El  ale++  d ++r+v + G ++ F+aGad+++ +e  +ak  ++ +ev 
  gi|557695116|ref|YP_008798170.1|  16 KEGGVASIVLNNPSRYNALELELRRELRRALEEAARDDEARVVLIRGAGGNFSAGADIRAFLEWDPAKCVSIANEVG 92 
                                       5789******************************9999*************************99988777776664 PP

                                       H...HHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHH CS
                             ECH_1  79 e...lwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeei 152
                                           l + +++++kpvia v+G+++gGG+ela+ cD+++aa++a+fg++e++lGlipg ggtq+lar vG+++A+++
  gi|557695116|ref|YP_008798170.1|  93 TsmvLANIIRSMQKPVIAVVEGYCLGGGFELAMSCDMIVAAEDAVFGQPEINLGLIPGGGGTQRLARLVGEKRAKQL 169
                                       4111667799******************************************************************* PP

                                       HHHT-EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
                             ECH_1 153 lllgkkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfs 229
                                       +++g++isa e++k+G+v+ vvp++ l+e   el+ekl++k++ al+++kea+n ++e  l ++l ae +lf s+f+
  gi|557695116|ref|YP_008798170.1| 170 VMTGDRISARELEKMGVVNVVVPRDRLEEAVKELVEKLLSKPRMALAAAKEAVNLAMETGLLAGLRAELMLFASLFA 246
                                       ***************************************************************************** PP

                                       SHHHHHHHHHHHTCSH----- CS
                             ECH_1 230 kddikeGlqaflEkrkpefed 250
                                       ++d keG  aflEkrkp +++
  gi|557695116|ref|YP_008798170.1| 247 TEDQKEGARAFLEKRKPVWKG 267
                                       *******************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 !  133.6   0.1     5e-42   1.1e-38       2     191 ..      21     210 ..      20     227 .. 0.91
   2 !   10.9   0.0    0.0001      0.23     247     318 ..     198     266 ..     197     268 .] 0.91

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 5e-42
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYk 78 
                                       + i Ln+p+  NaL+le+ r+l++al+e ++dde+++v+++gag   f+AG D+ra+ e   ++  + ++ + +   
  gi|557695116|ref|YP_008798170.1|  21 ASIVLNNPSRYNALELELRRELRRALEEAARDDEARVVLIRGAG-GNFSAGADIRAFLEWDPAKCVSIANEVGTSMV 96 
                                       5799**************************************99.79****************976667889999** PP

                                       HHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH- CS
                             ECH_2  79 lnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTG 154
                                       l + i +++kpv+a+++G+++GgG  l++++ + v+ e++vf  PE+++Gl+P  Gg+  L+rl g + ++ l +TG
  gi|557695116|ref|YP_008798170.1|  97 LANIIRSMQKPVIAVVEGYCLGGGFELAMSCDMIVAAEDAVFGQPEINLGLIPGGGGTQRLARLVGeKRAKQLVMTG 173
                                       ***************************************************************977588******** PP

                                       --B-HHHHHHTTS--EE--GGGHHHHHHHHHTT.... CS
                             ECH_2 155 arlkgadalaaglathyvpseklealeeaLaelessd 191
                                       +r++++++ ++g+ + +vp+++le+  ++L e   s+
  gi|557695116|ref|YP_008798170.1| 174 DRISARELEKMGVVNVVVPRDRLEEAVKELVEKLLSK 210
                                       ************************9999999865554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS-------S CS
                             ECH_2 247 ewakktletlkkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkWk 318
                                       e +k+ +e+l ++  ++l+++ e+++ + ++  l   lr El l ++l+a++D  eG ra l +  +kP Wk
  gi|557695116|ref|YP_008798170.1| 198 EAVKELVEKLLSKPRMALAAAKEAVNLAMETG-LLAGLRAELMLFASLFATEDQKEGARAFLEK--RKPVWK 266
                                       567889999999*******************5.***************************9954..689997 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.7e-06    0.0061       3      40 ..     102     139 ..     100     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.7e-06
                                       HHTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                     Peptidase_S49   3 kkakkPvvasaenvaaSggYylasaadkivanpstivg 40 
                                       ++ +kPv+a++e++   gg+ la+ +d iva+  ++ g
  gi|557695116|ref|YP_008798170.1| 102 RSMQKPVIAVVEGYCLGGGFELAMSCDMIVAAEDAVFG 139
                                       5779****************************999876 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.45     1e+03      71     125 ..      32      87 ..      25      95 .. 0.75
   2 !   14.9   0.0   4.4e-06    0.0099     110     221 ..      96     207 ..      86     217 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.45
                           SDH_sah  71 kfitiedseevlrairltp.kdkpidliihtpGGlvlaatqiakalkehkaktrvi 125
                                       + +++e   e+ ra+  +  +d    ++i   GG   a  +i   l+  +ak   i
  gi|557695116|ref|YP_008798170.1|  32 NALELELRRELRRALEEAArDDEARVVLIRGAGGNFSAGADIRAFLEWDPAKCVSI 87 
                                       55666777788888876651555666788999999999999999898888887665 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.4e-06
                           SDH_sah 110 qiakalkehkaktrvivphyamsGGtlialaadeiildenavlGpvdpqlgqypaasilkvvekkeakdiddktlil 186
                                        +a+ +++ + ++  +v  y + GG  +a++ d i+  e+av+G  + +lg +p     + + +   ++   + ++ 
  gi|557695116|ref|YP_008798170.1|  96 VLANIIRSMQKPVIAVVEGYCLGGGFELAMSCDMIVAAEDAVFGQPEINLGLIPGGGGTQRLARLVGEKRAKQLVMT 172
                                       568888888999999***************************************99998888888877766665555 PP

                           SDH_sah 187 ad.iakkaikqveefvyellkdkydeekakeiakkl 221
                                        d i+ + ++++  + + + +d+++ e  ke+ +kl
  gi|557695116|ref|YP_008798170.1| 173 GDrISARELEKMGVVNVVVPRDRLE-EAVKELVEKL 207
                                       5558888888876444444466664.5566666555 PP

>> SeleniumBinding  Selenium binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.8e-05     0.041       7      58 ..     168     219 ..     163     229 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.8e-05
                   SeleniumBinding   7 fiittaneiPGvelyylgivsavvesdnvdkilkaleekvkekkglaligfk 58 
                                        ++ t + i   el  +g+v  vv  d +++ +k l ek ++k  +al + k
  gi|557695116|ref|YP_008798170.1| 168 QLVMTGDRISARELEKMGVVNVVVPRDRLEEAVKELVEKLLSKPRMALAAAK 219
                                       58899******************************************98765 PP

>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     2e-05     0.044      22     107 ..      51     135 ..      43     143 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                              NucS  22 rLeegerlivikpdGaflvhkd.rkvePvnWqppkssltaevedgslilksirrkpeeeLkveieevehasayeled 97 
                                       r +e++ +++  + G f+  +d r+   + W p+k+ ++a++ + s++l  i r  +  +  ++e+  +   +el  
  gi|557695116|ref|YP_008798170.1|  51 RDDEARVVLIRGAGGNFSAGADiRA--FLEWDPAKCVSIANEVGTSMVLANIIRSMQKPVIAVVEGYCLGGGFELAM 125
                                       4455555555568899*****9665..59***********************9999999999999999999999988 PP

                              NucS  98 veelvldGse 107
                                         +++++  +
  gi|557695116|ref|YP_008798170.1| 126 SCDMIVAAED 135
                                       8888877655 PP

>> DUF3731  DNA-K related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.1       4.9   1.1e+04     195     216 ..      31      52 ..      27      58 .. 0.66
   2 ?   13.6   0.2     2e-05     0.044     124     191 ..     157     228 ..     152     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 4.9
                           DUF3731 195 ardlseelrekvlekLkaakap 216
                                        + l+ elr+++ ++L++a   
  gi|557695116|ref|YP_008798170.1|  31 YNALELELRRELRRALEEAARD 52 
                                       5566777777777777766544 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
                           DUF3731 124 lkrlkkkkekaqslwalgRlgaRep.lygsahkvvppeeveawlekllaldwkkkek...aafaavqlarlt 191
                                       l+rl  +k+ +q + +  R++aRe+  +g ++ vvp+++ e+ +++l+++   k ++   aa  av+la  t
  gi|557695116|ref|YP_008798170.1| 157 LARLVGEKRAKQLVMTGDRISARELeKMGVVNVVVPRDRLEEAVKELVEKLLSKPRMalaAAKEAVNLAMET 228
                                       677777889999999999******9357999**********9999999998887777333455567777666 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 ?    8.5   0.0    0.0017       3.9      29      66 ..      19      58 ..      13      60 .. 0.81
   2 ?    2.4   0.2      0.15   3.3e+02      29      55 ..     186     209 ..     177     225 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0017
                                      -EEEEEE---..---HHHHHHHHHHHHT-TTTS-SEEEE- CS
                     AMP-binding_C 29 lvafVvlkdg..sealeeeLkahvrkelgpyavpkkvvfv 66
                                       va +vl++   ++ale eL++ +r++l++ a+ +++++v
  gi|557695116|ref|YP_008798170.1| 19 GVASIVLNNPsrYNALELELRRELRRALEEAARDDEARVV 58
                                      6999***53332255*****************99988876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
                                       -EEEEEE------HHHHHHHHHHHHT- CS
                     AMP-binding_C  29 lvafVvlkdgsealeeeLkahvrkelg 55 
                                       +v +Vv++d    lee++k+ v+k l 
  gi|557695116|ref|YP_008798170.1| 186 VVNVVVPRDR---LEEAVKELVEKLLS 209
                                       6778889644...45666666665444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); 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 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2107.01
//
Query:       gi|557695117|ref|YP_008798171.1|  [L=175]
Description: hypothetical protein CSUB_C1690 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1402.51
//
Query:       gi|557695118|ref|YP_008798172.1|  [L=132]
Description: S-adenosylmethionine decarboxylase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-36  122.7   0.0    9.1e-36  122.3   0.0    1.1  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 !  122.3   0.0   5.1e-40   9.1e-36       1     106 []       7     114 ..       7     114 .. 0.98

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 5.1e-40
                                       EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-.SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEE CS
                         AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkf.epeGvsvvvliaeShlsiHtwpetgyaaiDvft 76 
                                       hl+++l gcd++ll+d ++l ++lt+aa a+gat++  ++ +f + +Gvs++++++eSh+siHtwpe gyaa+D++t
  gi|557695118|ref|YP_008798172.1|   7 HLILELTGCDQRLLSDVDFLDDLLTKAAVASGATIVGKYSERFdHGQGVSAIIVLKESHISIHTWPELGYAALDIYT 83 
                                       9******************************************5456****************************** PP

                                       EST.HHHHHHHHHHHHHHT-SEEEEEEEEEE CS
                         AdoMet_dc  77 cge.ispekaleylieafkadrvtvdelkRG 106
                                       cge i+p+ka++++i ++++++v + e++RG
  gi|557695118|ref|YP_008798172.1|  84 CGEnIDPWKAYDLIIARLEPENVGAFEVVRG 114
                                       ******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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: 1016.48
//
Query:       gi|557695119|ref|YP_008798173.1|  [L=303]
Description: spermidine synthase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-43  146.0   0.0    1.2e-42  145.5   0.0    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
    3.3e-11   42.9   0.0    5.6e-11   42.2   0.0    1.4  1  Spermine_synt_N  Spermidine synthase tetramerisation domain
  ------ inclusion threshold ------
      0.022   14.6   0.0      0.042   13.7   0.0    1.4  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
       0.16   11.6   0.0       0.32   10.6   0.0    1.4  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 !  145.5   0.0   2.7e-46   1.2e-42       1     170 [.      61     232 ..      61     246 .. 0.91

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 2.7e-46
                                       THHHHHHHHHHHHCCSSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEE CS
                    Spermine_synth   1 efaykemiahvplmlhknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvkl 77 
                                       e++y+e+++h +++l  +p++v iiGGg G +lrev+++ tve++ ++d+D++v+++++k+lp+l+++afnd+r+ l
  gi|557695119|ref|YP_008798173.1|  61 EHIYHETLVHPAMCLSGEPRRVVIIGGGEGATLREVLRWRTVEEAYMIDLDREVVELCQKYLPTLSAGAFNDQRLRL 137
                                       789************************************************************************** PP

                                       EESTCHHHHCTCSS.-EEEEEEECCS..TTCSSCGCSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHHH CS
                    Spermine_synth  78 vlgdgfkflkayek.kfdvvivdsld..pvgpaenlFskeffdllkkvlkedGviilqaekpelekelvinvdksgk 151
                                       + +dg   +++ ++   dv i d +d  + gp+  l+++ef++ll ++l e+Gvi +qa +p  +    ++++k+++
  gi|557695119|ref|YP_008798173.1| 138 FFMDGRRWVAEKLEdSVDVFIIDVTDplEQGPSYLLYTREFYQLLSSKLSENGVIATQATSPTHTPLAYQSIKKTMQ 214
                                       *******99987777***********444555555****************************************** PP

                                       TTSSCEEEEEEEETTTSCS CS
                    Spermine_synth 152 qvfalqvepsavlvPtyls 170
                                       ++f+ +v+  a++v +++ 
  gi|557695119|ref|YP_008798173.1| 215 TIFP-YVSELATYVVSFSA 232
                                       ****.88888877766654 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 !   42.2   0.0   1.3e-14   5.6e-11       2      50 ..       7      55 ..       6      57 .. 0.97

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.3e-14
                                      EEEEEEETTEEEEEEEEEEEEEEEESSSEEEEEEETTTEEEEEETTEEE CS
                   Spermine_synt_N  2 WfteisdpglalelkVekvLyeekSeyQdieifesktfGkvLvLDgvvq 50
                                      W++e +++ l  ++kV   +y +k++yQ++ei++++ fG  L LDg+ q
  gi|557695119|ref|YP_008798173.1|  7 WYREQISESLLESYKVVRHIYSGKTRYQKVEILDTEPFGSCLLLDGKMQ 55
                                      ***********************************************99 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 ?   13.7   0.0   9.4e-06     0.042      29      90 ..     131     196 ..     110     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.4e-06
                                       TTEEEEEEES-HHHHH.HHC-T-EEEEEE-SS-T.TTSGG..GCSHHHHHHHHHHEEEEEEEEES- CS
                   Methyltransf_30  29 eevtlklligdareal.keldekadawFlDgFsP.aknPe..lwseellkelarllkkkgtlatys 90 
                                       ++ +l+l ++d r  + ++l+ ++d++  D   P ++ P   l++ e++++l+ +l+++g++at +
  gi|557695119|ref|YP_008798173.1| 131 NDQRLRLFFMDGRRWVaEKLEDSVDVFIIDVTDPlEQGPSylLYTREFYQLLSSKLSENGVIATQA 196
                                       5689*******9877625788*************445565669********************965 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   7.1e-05      0.32      50     167 ..      87     211 ..      72     220 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 7.1e-05
                                       -TTSHHHHHHHH.TT-SEEEEEES-HHHHHHHHHHHCCCT--T....TTEEEEES-HHHHCTS--SS-EEEEEEE-- CS
                     Cons_hypoth95  50 aGsGalglEAlS.Rgakkavlvekdkeavkilkenleelklee....etaelkedaleallklakkkeefdivflDP 121
                                       +G Ga   E l  R +++a++++ d+e+v+++++ l +l + +    + + + +d  + + ++ + +  + i+ ++ 
  gi|557695119|ref|YP_008798173.1|  87 GGEGATLREVLRwRTVEEAYMIDLDREVVELCQKYLPTLSAGAfndqRLRLFFMDGRRWVAEKLEDSVDVFIIDVTD 163
                                       566666667664499***********************998777778899999999999999988888888888889 PP

                                       SSSTTCH....HHHHHHHHHTT-EEEEEEEEEEEECCSSS--.-TTEEE CS
                     Cons_hypoth95 122 Pyakell...ieevlelleekkllkenalvvvetekekelpespenlel 167
                                       P +++     + + + +l  ++ l+en+++ ++  + ++ p   + +++
  gi|557695119|ref|YP_008798173.1| 164 PLEQGPSyllYTREFYQLL-SSKLSENGVIATQATSPTHTPLAYQSIKK 211
                                       9999866556555555555.37899999999999888777776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); 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:                         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: 00:00:00.39
# Mc/sec: 2326.87
//
Query:       gi|557695120|ref|YP_008798174.1|  [L=214]
Description: phosphonate ABC transporter permese [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   64.3  19.1    1.7e-17   63.8  19.1    1.3  1  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 !   63.8  19.1   9.3e-22   1.7e-17       4     177 ..      37     203 ..      13     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 9.3e-22
                      BPD_transp_1   4 lGilaa.lnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrsl 79 
                                       +++la  ++++ +l+ ++r ++ +++++P++ +a+++v       ++g + l++ +++++++++y   i+++a++++
  gi|557695120|ref|YP_008798174.1|  37 FSALAMrNMFSHTLTTVVRAFFGFVRTIPVLFWAVVFV------IAVGLGPLAGTLAIAVYTFGYLSKIYYEAFEAV 107
                                       333333799999**************************......99******************************* PP

                      BPD_transp_1  80 pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseisng 156
                                       + +   a r+  a+r  i+r+ ++P ++ +ii++l++ f +++  +++l f+g++ G+g+l+++ i++ +ys+ + +
  gi|557695120|ref|YP_008798174.1| 108 DPEVLDAIRVTKAPRLLIVRHAIIPESMNTIISQLLFMFEYNIRSSTVLGFVGAG-GIGLLMISYIESLQYSSLT-T 182
                                       *****************************************************76.7***************888.5 PP

                      BPD_transp_1 157 gvlalviavlllnlvadilqr 177
                                       ++l +++ v+++ l++  l +
  gi|557695120|ref|YP_008798174.1| 183 ALLLTLVTVVAIDLLSGYLRK 203
                                       555555555555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1636.53
//
Query:       gi|557695121|ref|YP_008798175.1|  [L=238]
Description: phosphonate ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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    1.7e-29  103.1   0.0    1.2  1  ABC_tran     ABC transporter
    0.00025   20.7   0.2    0.00053   19.7   0.2    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0004   20.3   0.0       0.73    9.6   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
     0.0042   16.5   0.1       0.26   10.7   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
     0.0068   16.9   0.1     0.0097   16.4   0.1    1.2  1  AAA_23       AAA domain
  ------ inclusion threshold ------
      0.011   16.1   0.5      0.019   15.3   0.5    1.7  1  AAA_16       AAA ATPase domain
      0.012   15.5   0.3      0.022   14.6   0.0    1.5  2  RsgA_GTPase  RsgA GTPase
      0.043   13.7   0.1       0.09   12.7   0.1    1.5  1  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.046   13.3   0.2       0.19   11.3   0.0    1.9  2  AAA_25       AAA domain
       0.06   13.9   0.1       0.11   13.1   0.1    1.4  1  AAA_18       AAA domain
      0.064   13.2   0.1       0.14   12.0   0.1    1.6  1  NACHT        NACHT domain
       0.11   12.2   0.2       0.23   11.2   0.2    1.5  1  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
       0.12   12.1   0.5       0.21   11.3   0.1    1.6  2  AAA_30       AAA domain
       0.12   12.6   1.5       0.37   11.0   0.2    2.0  2  AAA_22       AAA domain
       0.14   11.7   1.2       0.18   11.4   0.3    1.6  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.28   11.1   1.5       0.96    9.3   0.3    2.0  2  NTPase_1     NTPase


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 !  103.1   0.0   1.5e-32   1.7e-29       1     134 [.      21     161 ..      21     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 1.5e-32
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ ++l+l++ge++ai+G +G+GK+tLlk++agll p +G++          +++ ++  ig++pq+  l ++lt+ 
  gi|557695121|ref|YP_008798175.1|  21 LDGLDLDLSAGETLAIMGYSGSGKTTLLKIVAGLLYPYQGTV----------KTHDAKGGIGYIPQNVGLVKNLTAV 87 
                                       6889**************************************..........56789******************88 PP

                                       HH.....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xx.....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllD 133
                                       +n                     e  ++++++l+ lgl e +d+++      LSgG++qrva+aral+++p++ll+D
  gi|557695121|ref|YP_008798175.1|  88 QNvahgalgkigifpglfgkfpqEVFVKAYQLLEDLGLAEAADRKA----GLLSGGERQRVAVARALMQNPSILLAD 160
                                       889****************999989999****************99....*************************** PP

                                       S CS
                                       x RF
                          ABC_tran 134 E 134
                                       E
  gi|557695121|ref|YP_008798175.1| 161 E 161
                                       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 !   19.7   0.2   4.7e-07   0.00053      13      50 ..      22      59 ..      19      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.7e-07
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      dg +++++  ++  ++G sGsGK+Tll  ++ lL+p +
  gi|557695121|ref|YP_008798175.1| 22 DGLDLDLSAGETLAIMGYSGSGKTTLLKIVAGLLYPYQ 59
                                      55667787556999**************9999**9977 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 !    9.0   0.0     0.001       1.1       6      23 ..      38      55 ..      34      76 .. 0.82
   2 !    9.6   0.0   0.00065      0.73     234     303 .]     133     200 ..      96     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.001
                            AAA_21  6 GpNgsGKSnLLdaldlla 23
                                      G  gsGK++LL++  +l 
  gi|557695121|ref|YP_008798175.1| 38 GYSGSGKTTLLKIVAGLL 55
                                      667***********9985 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00065
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSpllld 303
                                       a  lS G ++  a++ al + +   s+ll DE+ + L+     +++el  k+++rn++ +++t H+++l++
  gi|557695121|ref|YP_008798175.1| 133 AGLLSGGERQRVAVARALMQNP---SILLADEFVSDLDVINAYEVMELTtKICRRNNIALVMTMHDTYLVN 200
                                       5678888888878888888777...**************9999999999999999*************986 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 ?    4.0   0.0     0.025        28      26      42 ..      33      49 ..      19      57 .. 0.84
   2 !   10.7   0.0   0.00023      0.26     136     212 ..     135     209 ..      78     216 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.025
                                      EEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlld 42
                                        ai+G  GSGK+ ll 
  gi|557695121|ref|YP_008798175.1| 33 TLAIMGYSGSGKTTLLK 49
                                      458**********9976 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00023
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHH..HCTTSEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellke..ksknaQfivislreemlekadklvg 210
                                       lLSgGe++ va+a       ++  ++ l De+ + LD  n  +v el  +  +++n  ++++ +++ +++k    v 
  gi|557695121|ref|YP_008798175.1| 135 LLSGGERQRVAVARA----LMQNPSILLADEFVSDLDVINAYEVMELTTKicRRNNIALVMTMHDTYLVNKFADRVA 207
                                       8*******9998755....3566678899************999999875224556666666666667777665555 PP

                                       EE CS
                                       xx RF
                             SMC_N 211 vt 212
                                       v 
  gi|557695121|ref|YP_008798175.1| 208 VL 209
                                       55 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   8.6e-06    0.0097      11      48 ..      22      60 ..      12      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.6e-06
                            AAA_23 11 rdqeidFskglt.lItGpNGaGKTTildAiklaLygetp 48
                                      ++ ++d+s g t +I G  G+GKTT+l  +   Ly   +
  gi|557695121|ref|YP_008798175.1| 22 DGLDLDLSAGETlAIMGYSGSGKTTLLKIVAGLLYPYQG 60
                                      67788998876637**************99999997544 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   0.5   1.7e-05     0.019      19      45 ..      28      52 ..      14     189 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                            AAA_16 19 vrsgrpelvllsGesGvGKsslvrell 45
                                      +++g  e + + G+sG+GK++l++ ++
  gi|557695121|ref|YP_008798175.1| 28 LSAG--ETLAIMGYSGSGKTTLLKIVA 52
                                      3455..7899************98665 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      96     137 ..      27      69 ..      10      71 .. 0.80
   2 ?   -3.4   0.0       6.9   7.7e+03      18      31 ..     186     199 ..     165     210 .. 0.54

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                                       HCTT.SEEEEECSTTSSHHHHHHHHCTT-----S--------- CS
                       RsgA_GTPase  96 llkd.ktsvlvGqSGvGKStLinallpelelktgevseklgrG 137
                                        l+  +t +++G SG GK+tL++ +++ l    g v++++ +G
  gi|557695121|ref|YP_008798175.1|  27 DLSAgETLAIMGYSGSGKTTLLKIVAGLLYPYQGTVKTHDAKG 69 
                                       5555499****************99998877777777777776 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 6.9
                                       EEEEEEESTTTT-- CS
                       RsgA_GTPase  18 qllivvslkepels 31 
                                       ++ +v+++++  l 
  gi|557695121|ref|YP_008798175.1| 186 NIALVMTMHDTYLV 199
                                       33444444444444 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 ?   12.7   0.1     8e-05      0.09       2      20 ..      34      52 ..      33      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 8e-05
                              MobB  2 lgivgksgsGKTtLlekli 20
                                      l+i+g+sgsGKTtLl+ + 
  gi|557695121|ref|YP_008798175.1| 34 LAIMGYSGSGKTTLLKIVA 52
                                      79*************8665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.19      19      50 ..      14      48 ..       3      53 .. 0.78
   2 ?   -0.8   0.0      0.85   9.6e+02     168     188 ..     174     194 ..     163     196 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                            AAA_25 19 ppprrwlvkg...llpagelallaGapgtGKttla 50
                                         rr++++g    l age+ +++G +g+GKttl+
  gi|557695121|ref|YP_008798175.1| 14 YDGRRKILDGldlDLSAGETLAIMGYSGSGKTTLL 48
                                      55667777774445799****************97 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.85
                            AAA_25 168 lvealeriarrtgaavllvhH 188
                                       ++e   +i+rr ++a+++++H
  gi|557695121|ref|YP_008798175.1| 174 VMELTTKICRRNNIALVMTMH 194
                                       56667799***********99 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   9.6e-05      0.11       2      40 ..      35      75 ..      34      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 9.6e-05
                            AAA_18  2 lltGtpGvGKttlakeLskrl.gf.gvnlrdvakengllle 40
                                      +++G++G+GKttl k ++ +l  + g++ ++ ak +  +++
  gi|557695121|ref|YP_008798175.1| 35 AIMGYSGSGKTTLLKIVAGLLyPYqGTVKTHDAKGGIGYIP 75
                                      599*************9988755576666666665555555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00013      0.14       2      21 ..      33      52 ..      32      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                                      CEEEEC-TTTCHHHHHHHHH CS
                             NACHT  2 lvilqGeaGsGKTtLlqkla 21
                                      ++++ G +GsGKTtLl+ +a
  gi|557695121|ref|YP_008798175.1| 33 TLAIMGYSGSGKTTLLKIVA 52
                                      789*************9776 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00021      0.23       5      33 ..      35      63 ..      32      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                         PduV-EutP  5 lliGkvgsGKttLtqalkgeelkYkktqa 33
                                       ++G +gsGKttL + + g    Y+ t  
  gi|557695121|ref|YP_008798175.1| 35 AIMGYSGSGKTTLLKIVAGLLYPYQGTVK 63
                                      589****************9999998855 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00019      0.21      20      42 ..      33      55 ..      26      92 .. 0.86
   2 ?   -2.1   0.0       2.4   2.6e+03     121     133 ..     136     148 ..     114     182 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                            AAA_30 20 vavltGpAGtGKttalkalreaw 42
                                      + ++ G+ G+GKtt+lk ++ ++
  gi|557695121|ref|YP_008798175.1| 33 TLAIMGYSGSGKTTLLKIVAGLL 55
                                      67899************998766 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.4
                            AAA_30 121 lvGDerQlasVea 133
                                       l G erQ  +V +
  gi|557695121|ref|YP_008798175.1| 136 LSGGERQRVAVAR 148
                                       3344444444333 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   0.00033      0.37       8      26 ..      34      52 ..      28      75 .. 0.87
   2 ?    0.4   0.1      0.63   7.1e+02      59     126 ..     118     190 ..     114     201 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00033
                            AAA_22  8 lvvtGesGtGKTtllrrll 26
                                      l+++G sG+GKTtll+ ++
  gi|557695121|ref|YP_008798175.1| 34 LAIMGYSGSGKTTLLKIVA 52
                                      79*************9776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.63
                            AAA_22  59 ellralglelkaerlsseellealeqalrarav.....ielliiDEaqh.lr..s.eealeeLrsllnlsrkgvqli 126
                                       +ll++lgl   a  +++  ll+  e++  a a+     +++l+ DE+   l+  +  e++e   ++    r +++l+
  gi|557695121|ref|YP_008798175.1| 118 QLLEDLGLAEAA--DRKAGLLSGGERQRVAVARalmqnPSILLADEFVSdLDviNaYEVMELTTKICR--RNNIALV 190
                                       566677766666..666666666666555555556778889999998777755523444444455555..5666655 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 ?   11.4   0.3   0.00016      0.18       3      19 ..      34      50 ..      32      62 .. 0.87
   2 ?   -2.4   0.0       2.8   3.1e+03     139     149 ..     191     201 ..     157     218 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00016
                                      EEEEESTTCCHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnh 19
                                      + + G+ GsGKTtLl+ 
  gi|557695121|ref|YP_008798175.1| 34 LAIMGYSGSGKTTLLKI 50
                                      6799***********85 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.8
                                       HHTSSEEEEE- CS
                              cobW 139 laaadllvlnK 149
                                       +++ d+ ++nK
  gi|557695121|ref|YP_008798175.1| 191 MTMHDTYLVNK 201
                                       23333333333 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.3   0.00086      0.96       2      33 ..      34      61 ..      33     103 .. 0.86
   2 ?    0.8   0.1      0.36     4e+02     119     154 ..     179     216 ..     140     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00086
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGf 33
                                      ++i G +G+GKtTl+k v+ ll    ++++G 
  gi|557695121|ref|YP_008798175.1| 34 LAIMGYSGSGKTTLLKIVAGLL----YPYQGT 61
                                      57899*************9999....666665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.36
                                       HHHHT.TTSEEEEE--SS-.-SHHHHHHHT-TT-EEEE CS
                          NTPase_1 119 eevLk.sekpvlavihrrk.dlalveeirerkdvkvfe 154
                                       +++ + ++  +++++h +   +++ +++   kd+k+++
  gi|557695121|ref|YP_008798175.1| 179 TKICRrNNIALVMTMHDTYlVNKFADRVAVLKDGKIMT 216
                                       55555567788999999988888888888888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1752.04
//
Query:       gi|557695122|ref|YP_008798176.1|  [L=318]
Description: phosphonate ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-50  169.8   0.1    9.1e-50  169.5   0.1    1.0  1  Phosphonate-bd  ABC transporter, phosphonate, periplasmic sub
    2.1e-06   27.4   0.0    3.4e-06   26.7   0.0    1.3  1  NMT1_3          NMT1-like family
    0.00013   22.0   0.0     0.0012   18.9   0.0    2.5  1  NMT1            NMT1/THI5 like
    0.00015   21.3   0.0     0.0088   15.5   0.0    2.2  2  SBP_bac_3       Bacterial extracellular solute-binding protei
     0.0013   18.1   0.1        1.7    8.0   0.0    2.5  2  LysR_substrate  LysR substrate binding domain


Domain annotation for each model (and alignments):
>> Phosphonate-bd  ABC transporter, phosphonate, periplasmic substrate-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.5   0.1   2.5e-53   9.1e-50       1     239 [.      42     294 ..      42     297 .. 0.91

  Alignments for each domain:
  == domain 1  score: 169.5 bits;  conditional E-value: 2.5e-53
                                       EEE--SS-HHHHHHHHHHHHHHHHHHH.SSEEEEE--SSHHHHHHHHHTTS-SEEE--HHHHHHHHHHS-EEEEEEE CS
                    Phosphonate-bd   1 igvlPsespaelkeayqpladyLseel.GvevelvvatdyaavvealragqvDiaflgplayvqardqagveplatr 76 
                                       i+v P+ s+ae+ ++++p+ ++L+++l +++ve+ v t+yaavve+lr g+++ af+++ + + a + a++e+++++
  gi|557695122|ref|YP_008798176.1|  42 IAVQPTLSAAEVLQRAKPIEAFLEQKLpDIDVEIYVPTSYAAVVESLRRGHAHAAFMSAWPSYLAWKLADAEVVLAE 118
                                       6899************************************************************************* PP

                                       EETT--S.......EEEEEEEEETTSS--SHHHHGG-EEEE--TT-TTTTHHHHHHTCCCCT-.........-HHHH CS
                    Phosphonate-bd  77 vrsdGsa.......syrsviivradsdiqsledLkgktiafvspsStsGylvpaalLvkeagl.........dpedd 137
                                        r+ G+        +y+s+++v +ds+i+s+edL+gk++a++sp StsGy++p+a Lv e g+         dp+++
  gi|557695122|ref|YP_008798176.1| 119 IRTVGEGdkiveapQYYSYWVVLPDSPIKSIEDLRGKKVALPSPISTSGYVAPLAKLV-ELGYiqvkqgseaDPSTF 194
                                       99666423355555*******************************************7.7777788888788999** PP

                                       SSEEEE--HHHHHHHHHTTSSSEEEEEHHHHHHHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS-HHHHHHHHHHH CS
                    Phosphonate-bd 138 fsevfsgshdaavlavlsgdadaaavsadaledlvaegpedkdelrviassppipndpvvvrkelseelkekiqdal 214
                                       f+ vf+g++ ++  a+ +gd+daa++  d+ e+l +e    ++ +rvias  pip++ vv++kel+e l++++ +al
  gi|557695122|ref|YP_008798176.1| 195 FQVVFTGGYAQSWTALKNGDVDAAVIAGDIPESLYRE---VMSNTRVIASQGPIPSHAVVFSKELKEPLRSRLINAL 268
                                       **********************************997...79*********************************** PP

                                       HH---SHHHHHHHHHT...TEEEEEE-- CS
                    Phosphonate-bd 215 lslaeteegkklleal...giegfvpad 239
                                        +l+  + + +l++++    + +f+p++
  gi|557695122|ref|YP_008798176.1| 269 QELG--DREPALMKQFvsaLFVRFEPTT 294
                                       ***9..6999999999533356666655 PP

>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   9.5e-10   3.4e-06      23     182 ..      66     236 ..      57     242 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 9.5e-10
                            NMT1_3  23 eklakdqkvkasaqssaGsveNiqllkkgeadlailqsdvayeAy...eGegefegkkplknlraitmlyaevfqlv 96 
                                       +kl  d  v++ + +s ++v  ++ l+ g a++a++++ + y A+   ++e ++++ + + +   i+   + + ++v
  gi|557695122|ref|YP_008798176.1|  66 QKL-PDIDVEIYVPTSYAAV--VESLRRGHAHAAFMSAWPSYLAWklaDAEVVLAEIRTVGEGDKIVEAPQYYSYWV 139
                                       555.3556777777777766..899*******************9444589999**9******************** PP

                            NMT1_3  97 vskdsgigsiadlkgkrvsvGpegsGteg..sarailealglsekd.........lklleelgygesadalkdgqld 162
                                       v  ds i+si+dl gk+v++ ++ s++       ++ e   ++ k+         ++++   gy++s +alk+g +d
  gi|557695122|ref|YP_008798176.1| 140 VLPDSPIKSIEDLRGKKVALPSPISTSGYvaPLAKLVELGYIQVKQgseadpstfFQVVFTGGYAQSWTALKNGDVD 216
                                       ********************999887743222222222222332223344566667777778*************** PP

                            NMT1_3 163 gaalvaGvPvsavtqlaase 182
                                       +a++++ +P s   +++ ++
  gi|557695122|ref|YP_008798176.1| 217 AAVIAGDIPESLYREVMSNT 236
                                       **********9999988765 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.2e-07    0.0012      20     103 ..      70     163 ..      67     286 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.2e-07
                                       TEEEEEE--SSTTHHHHHHHCTS-SEEEE-H.HHHHHHHHTT--EE.....EEE...EEE-S-..-EEEEEECCC-- CS
                              NMT1  20 GldVeivepadpsdatelvasgkadfgvsyq.esllaarakglpvv.....sva...allqep..lsglivlkdsgi 85 
                                       ++dVei  p+  + ++e + +g a+ ++ +  +s la + ++++vv     +v+   ++++ p   s ++vl ds+i
  gi|557695122|ref|YP_008798176.1|  70 DIDVEIYVPTSYAAVVESLRRGHAHAAFMSAwPSYLAWKLADAEVVlaeirTVGegdKIVEAPqyYSYWVVLPDSPI 146
                                       688888888888888888888888887644315555555566555411111444222344444114679******** PP

                                       SSGGGGTTSEEEE-S-TT CS
                              NMT1  86 kspkDLkGkrigyvgspf 103
                                       ks++DL+Gk+++++  p+
  gi|557695122|ref|YP_008798176.1| 147 KSIEDLRGKKVALPS-PI 163
                                       ***********9776.33 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   0.0    0.0096        35     116     159 ..      55      99 ..      31     135 .. 0.68
   2 !   15.5   0.0   2.4e-06    0.0088      94     209 ..     143     271 ..     128     275 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0096
                                       ETTSHHHHHHHHHHHCTSEEEEE..SSHHHHHHHHHTTSSSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 116 qagstaeellkeelkkgaeivef..dtleealqaLkngrvdavvad 159
                                       q++   e++l+++l+ ++++  +   +++++++ L+ g + a++++
  gi|557695122|ref|YP_008798176.1|  55 QRAKPIEAFLEQKLP-DIDVEIYvpTSYAAVVESLRRGHAHAAFMS 99 
                                       333334445555444.666654322566666899******999876 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.4e-06
                                       TTSHGTCCHSSCGCGTTSEEEEETT.SHHHHHHHHHHHC.....TSEE..............EEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx.....xxxx..............xxxxxxxxxxxxxxx RF
                         SBP_bac_3  94 kdaskissiksladLkgkkvgvqag.staeellkeelkk.....gaei..............vefdtleealqaLkn 150
                                       +     s iks++dL gkkv+     st+  +++  l+k      +++              v +  +++  +aLkn
  gi|557695122|ref|YP_008798176.1| 143 D-----SPIKSIEDLRGKKVALPSPiSTSG-YVAP-LAKlvelgYIQVkqgseadpstffqvVFTGGYAQSWTALKN 212
                                       3.....3477777********999955544.5443.2223445533334444445555555377899999999**** PP

                                       TSSSEEEEEHHHHHHHHHHCCGCCEEEEECGGCECEEEEEEETTTHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 151 grvdavvadspvlaylvkknpdkkvvlveeplsseeyaiavrkgdseLrkainkalael 209
                                       g vda+v    + + l ++   +++v++++   ++ ++++ ++ +++Lr  +  al+el
  gi|557695122|ref|YP_008798176.1| 213 GDVDAAVIAGDIPESLYREVMSNTRVIASQGPIPSHAVVFSKELKEPLRSRLINALQEL 271
                                       *****999888887777777777777756666666667777777888888888888876 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0   0.00056         2      28      66 ..      64     106 ..      34     122 .. 0.71
   2 !    8.0   0.0   0.00046       1.7      41      82 ..     200     239 ..     188     278 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00056
                                       HHHHSTTEEEEEEEESH.HHHHHHHHTTSSSEEEEESSS...C CS
                    LysR_substrate  28 fraryPevelelvegds.eelldllaegelDlairagpp...e 66 
                                       + ++ P++++e+ + +s +++++ l++g++++a+++ +p   +
  gi|557695122|ref|YP_008798176.1|  64 LEQKLPDIDVEIYVPTSyAAVVESLRRGHAHAAFMSAWPsylA 106
                                       45678*******9999989****************88774442 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00046
                                       EESHHHHHHHHHTTSSSEEEEESSSCCTTEEEEEEEEEEEEE CS
                    LysR_substrate  41 egdseelldllaegelDlairagppedsglearpLaeeplvl 82 
                                       +g  ++   +l++g++D+a++ag++++s   +r+++++ +v+
  gi|557695122|ref|YP_008798176.1| 200 TGGYAQSWTALKNGDVDAAVIAGDIPESL--YREVMSNTRVI 239
                                       4555788889***************9998..77777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2349.01
//
Query:       gi|557695123|ref|YP_008798177.1|  [L=247]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   24.2   0.1     0.0065   16.5   0.1    2.8  2  HTH_3          Helix-turn-helix
    0.00079   19.6   0.4     0.0017   18.5   0.4    1.6  1  Ferritin_2     Ferritin-like domain
     0.0048   17.3   5.0      0.014   15.8   2.8    2.7  2  Rubrerythrin   Rubrerythrin
  ------ inclusion threshold ------
      0.045   13.6   0.1       0.31   10.9   0.1    2.3  2  HTH_23         Homeodomain-like domain
      0.053   13.1   0.1       0.44   10.1   0.0    2.2  2  Phenol_Hydrox  Methane/Phenol/Toluene Hydroxylase
      0.059   13.2   0.1       0.36   10.7   0.0    2.2  2  P22_Cro        DNA-binding transcriptional regulator Cro
       0.14   12.5   1.3        9.3    6.6   0.2    3.2  4  KORA           TrfB plasmid transcriptional repressor
       0.17   12.2   2.2       0.45   10.9   1.2    2.4  2  DUF1840        Domain of unknown function (DUF1840)
       0.25   11.7   0.3       0.25   11.7   0.3    3.3  3  HTH_31         Helix-turn-helix domain


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 !   16.5   0.1   3.3e-06    0.0065       9      46 ..      26      69 ..      21      77 .. 0.81
   2 ?    4.6   0.0     0.017        33      23      42 ..     165     187 ..     161     191 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.3e-06
                                      THHHHHHHHHHTSSHHHHHHHHTT......SSCSBHHHHHHHHH CS
                             HTH_3  9 glsqeeLAeklGvsrstisriEnG......ernPsletlkklak 46
                                      gl ++e+A++l +++++++++ +G      + + s+++lk++ +
  gi|557695123|ref|YP_008798177.1| 26 GLKKAEVARLLSITPQAVTQYVRGvraggrQIALSQQRLKEMVR 69
                                      8999********************77776666666666666665 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.017
                                       HHHHHHHHTT...SSCSBHHHHH CS
                             HTH_3  23 rstisriEnG...ernPsletlk 42 
                                       ++tis+iE++      P++e+l+
  gi|557695123|ref|YP_008798177.1| 165 QTTISAIEKNfsgSVLPDPERLQ 187
                                       89*******99999999999997 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.4   8.6e-07    0.0017       4     133 ..     118     234 ..     115     237 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.6e-07
                        Ferritin_2   4 diLnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaaleGaaavakptfdfafdpfa 80 
                                       ++L   l++E+ +a+ + + +        ++ d+ v  ++++ia++ + H+++ +++++      +++ +f+ + + 
  gi|557695123|ref|YP_008798177.1| 118 RVLRNRLAAEQEAAELFLNEAI-------KAKDEMVSLLFRQIASDSIRHADIVQTTIS------AIEKNFSGSVLP 181
                                       6777778889988888887775.......678999999********************4......577899999999 PP

                        Ferritin_2  81 deksflalaavlEdvgvsAYlgaapllsnkelltaaasIlsvEArHaavirtl 133
                                       d++ +  l +  E+  ++++  + +ll+n+ l+ +  sI ++EA+H+ +i++l
  gi|557695123|ref|YP_008798177.1| 182 DPERLQMLRQHEEKSHAQGFETVKQLLKNDVLKILLDSIDADEAKHDMIIEKL 234
                                       999999999999***********************************999887 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       1.2   2.3e+03      94     108 ..      62      76 ..      22      94 .. 0.63
   2 !   15.8   2.8   7.2e-06     0.014       3     136 ..     120     234 ..     118     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                                       HHHHCHHHHHHHHHH CS
                      Rubrerythrin  94 aeeeemyrfyeelae 108
                                       ++ +em r++++   
  gi|557695123|ref|YP_008798177.1|  62 QRLKEMVREFARKIA 76 
                                       334444444443333 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 7.2e-06
                                       HHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTG CS
                      Rubrerythrin   3 LekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkfl 79 
                                       L + +a+E +a +l+ + a kak   + ++ lF+++A +  +Ha+i+   ++++e++                 ++l
  gi|557695123|ref|YP_008798177.1| 120 LRNRLAAEQEAAELFLNEAIKAK--DEMVSLLFRQIASDSIRHADIVQTTISAIEKNFS--------------GSVL 180
                                       55667899999999999999999..88889***********************888877..............7777 PP

                                       GHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  80 ttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrkl 136
                                         ++ L+++++ +++ + + +++ ++l++   n+  k l++++  +E kH  + +kl
  gi|557695123|ref|YP_008798177.1| 181 PDPERLQMLRQHEEKSHAQGFETVKQLLK---NDVLKILLDSIDADEAKHDMIIEKL 234
                                       88888998888888888887777777777...6667789999999999998777665 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00016      0.31       7      45 ..      14      54 ..      11      59 .. 0.80
   2 ?   -1.3   0.0         1   2.1e+03       6      16 ..     184     194 ..     182     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                            HTH_23  7 Rlrillllae..GlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      R+ ++  l    Gl ++e+Ar+L ++++ v ++++  r++G
  gi|557695123|ref|YP_008798177.1| 14 RAMVATELVTtyGLKKAEVARLLSITPQAVTQYVRGVRAGG 54
                                      5555555555789********************99876665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1
                            HTH_23   6 eRlrillllae 16 
                                       eRl++l+ + e
  gi|557695123|ref|YP_008798177.1| 184 ERLQMLRQHEE 194
                                       799**999886 PP

>> Phenol_Hydrox  Methane/Phenol/Toluene Hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00022      0.44     191     225 ..     136     170 ..     127     174 .. 0.89
   2 ?    0.5   0.0      0.18   3.6e+02     200     223 ..     212     235 ..     189     239 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00022
                                       HHGGGGT-SHHHHHHHHHHHHHHHHHHHHHHHHII CS
                     Phenol_Hydrox 191 evaaangDeltpslissaqsdearharwgdallkv 225
                                       ++a +  De++++l++++ sd+ rha +++ ++ +
  gi|557695123|ref|YP_008798177.1| 136 NEAIKAKDEMVSLLFRQIASDSIRHADIVQTTISA 170
                                       5788899***********************99976 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.18
                                       HHHHHHHHHHHHHHHHHHHHHHHH CS
                     Phenol_Hydrox 200 ltpslissaqsdearharwgdall 223
                                       ++  l++s+ +dea+h  ++++l 
  gi|557695123|ref|YP_008798177.1| 212 VLKILLDSIDADEAKHDMIIEKLA 235
                                       677899999999999998888776 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 ?    1.3   0.0      0.16   3.1e+02      31      51 ..       8      29 ..       5      31 .. 0.81
   2 ?   10.7   0.0   0.00018      0.36      11      29 ..      28      46 ..      18      51 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.16
                                      TC--HHHHH.HHHHHTTTSS-- CS
                           P22_Cro 31 eeiPelray.qierlTaGkLkv 51
                                      e iP lra+   e +T + Lk 
  gi|557695123|ref|YP_008798177.1|  8 ELIPLLRAMvATELVTTYGLKK 29
                                      679****973679999999996 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00018
                                      SHHHHHHHHTS-HHHHHHH CS
                           P22_Cro 11 gvekvAkalgvtksAVsqW 29
                                      +++ vA++l +t++AV q 
  gi|557695123|ref|YP_008798177.1| 28 KKAEVARLLSITPQAVTQY 46
                                      4678*************96 PP

>> KORA  TrfB plasmid transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2    0.0047       9.3      31      55 ..      26      50 ..      13      70 .. 0.86
   2 ?   -1.1   0.0       1.2   2.3e+03      40      54 ..      56      70 ..      51      81 .. 0.75
   3 ?    3.0   0.0     0.064   1.3e+02      56      77 ..     189     210 ..     186     215 .. 0.86
   4 ?   -3.5   0.0       6.5   1.3e+04       4      20 ..     225     241 ..     224     243 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0047
                              KORA 31 gkkqadvatelgltkqavsqavkrv 55
                                      g k+a+va+ l +t qav q v+ v
  gi|557695123|ref|YP_008798177.1| 26 GLKKAEVARLLSITPQAVTQYVRGV 50
                                      5689*****************9877 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                              KORA 40 elgltkqavsqavkr 54
                                      +++l++q+ +++v+ 
  gi|557695123|ref|YP_008798177.1| 56 QIALSQQRLKEMVRE 70
                                      678888888888864 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.064
                              KORA  56 waahaereepaglerVsvllpe 77 
                                       +  h+e+  ++g+e V+ ll +
  gi|557695123|ref|YP_008798177.1| 189 LRQHEEKSHAQGFETVKQLLKN 210
                                       6789*************99866 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 6.5
                              KORA   4 eeFeeiikgleelaeqt 20 
                                       ++ + ii++l el e+ 
  gi|557695123|ref|YP_008798177.1| 225 AKHDMIIEKLAELSERQ 241
                                       56778888998888765 PP

>> DUF1840  Domain of unknown function (DUF1840)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.2   0.00023      0.45      18      62 ..      89     133 ..      75     228 .. 0.90
   2 ?   -0.8   0.1      0.94   1.9e+03      22      61 ..     187     228 ..     178     245 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00023
                           DUF1840  18 dvakqllkllgkslterGaitaedlpaaiakLeaaiaaekaeeae 62 
                                       d a ++l +lgk+ + r ai +e   +a++ L++ +aae+++++ 
  gi|557695123|ref|YP_008798177.1|  89 DLAYEVLMILGKPSPDRQAIPEEAKSQALRVLRNRLAAEQEAAEL 133
                                       67899*********************************9988754 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.94
                           DUF1840  22 qllkllgkslterGaitaedl..paaiakLeaaiaaekaeea 61 
                                       q+l+   ++ +++G  t+++l  +++++ L   i+a++a+++
  gi|557695123|ref|YP_008798177.1| 187 QMLRQHEEKSHAQGFETVKQLlkNDVLKILLDSIDADEAKHD 228
                                       555555555666666666665334566666667766666654 PP

>> HTH_31  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   0.00013      0.25       7      39 ..      14      51 ..       8      70 .. 0.81
   2 ?    0.2   1.8      0.51     1e+03       5      20 ..     116     131 ..     114     192 .. 0.63
   3 ?   -1.1   0.0       1.3   2.6e+03       4      19 ..     184     199 ..     183     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00013
                            HTH_31  7 ralRera.....GLsqeevAerlgvsestlsrlEqGrr 39
                                      ra+ + +     GL+++evA++l +++  ++++ +G r
  gi|557695123|ref|YP_008798177.1| 14 RAMVATElvttyGLKKAEVARLLSITPQAVTQYVRGVR 51
                                      444444466666***********************876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.51
                            HTH_31   5 lLralReraGLsqeev 20 
                                        Lr lR+r    qe++
  gi|557695123|ref|YP_008798177.1| 116 ALRVLRNRLAAEQEAA 131
                                       6788888876665554 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1.3
                            HTH_31   4 alLralReraGLsqee 19 
                                       ++L+ lR+ +  s+++
  gi|557695123|ref|YP_008798177.1| 184 ERLQMLRQHEEKSHAQ 199
                                       589****999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1058  (0.0590105); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1643.97
//
Query:       gi|557695124|ref|YP_008798178.1|  [L=277]
Description: manganese/iron ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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-72  243.2  38.3    3.4e-72  243.1  38.3    1.0  1  ABC-3     ABC 3 transport family
  ------ inclusion threshold ------
       0.12   11.3  38.9       0.17   10.9  38.2    1.5  1  FecCD     FecCD transport family


Domain annotation for each model (and alignments):
>> ABC-3  ABC 3 transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  243.1  38.3   3.8e-76   3.4e-72       2     256 ..      13     266 ..      12     268 .. 0.99

  Alignments for each domain:
  == domain 1  score: 243.1 bits;  conditional E-value: 3.8e-76
                             ABC-3   2 yeflqrallasilvslacallgsfvvlrrqsllgdalsHaalpGvalayllgvnlllgailvgliaavalellkrkt 78 
                                       y f+q a+++si+v++ ++ l++ +vlr+++llgda+sHa+lpG ala +++++l+lg +++g+i ++a++l+++kt
  gi|557695124|ref|YP_008798178.1|  13 YRFMQSAFITSIAVGILASTLSVVIVLRGWALLGDAISHAVLPGLALAAVFNIPLTLGGAMAGIISSFAIGLIEQKT 89 
                                       89*************************************************************************** PP

                             ABC-3  79 klkedtaigivlsvflalglvlvslikkskvdldsyLfGniltisqedliliaiieavvllllllfwkelllitfde 155
                                       ++++dtaigivl+ ++alglv++s+ +    d++++LfGn+l++s e+l l+a+++  vll + lf ke++++tfd+
  gi|557695124|ref|YP_008798178.1|  90 RVRNDTAIGIVLTGAFALGLVAISKLR-PTLDVFHILFGNVLAVSTEELQLTAAVATAVLLFFGLFLKEIVAYTFDP 165
                                       ***************************.99*********************************************** PP

                             ABC-3 156 elAkveglsvkllkllllalialavvvalqavGviLvialliiPaatArrltrslesllivAillglvsvvaGlllS 232
                                        +A v+gl+ +ll+ +l+++i+lav ++lq+vG+iLv++lli+P+atA++++++l +++i+++ +g+ s+v+Gl+lS
  gi|557695124|ref|YP_008798178.1| 166 VFASVAGLPANLLHHILMVMISLAVIASLQTVGIILVVSLLITPGATAQLVAKNLLQMFIISVTVGVSSAVTGLYLS 242
                                       ***************************************************************************** PP

                             ABC-3 233 yyldlatGavivlvatllfllall 256
                                       +yl +++G++i+l at++f++++l
  gi|557695124|ref|YP_008798178.1| 243 FYLAASSGGTIALTATAIFFAVFL 266
                                       ********************9986 PP

>> FecCD  FecCD transport family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  38.2   1.9e-05      0.17      83     311 ..      43     267 ..      23     268 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.9e-05
                             FecCD  83 aalgavlallll.lgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsaltsllllllnee 158
                                       a lg +++ ++l  ++l ++  + + + ga+++++  +++   +++++      +Gi+++  ++     l+++++ +
  gi|557695124|ref|YP_008798178.1|  43 ALLGDAISHAVLpGLALAAVFNIPLTLGGAMAGIISSFAIGLIEQKTRVRNDTAIGIVLTGAFAL---GLVAISKLR 116
                                       55555555555552333333333344455555555555555455555555555667776654433...333333445 PP

                             FecCD 159 alesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllllllvalltava 235
                                        + ++ ++l+G++  +s +++ l +++++++ll++ l+ +++ +++++   A+  G++ + +  +l+++++l++ ++
  gi|557695124|ref|YP_008798178.1| 117 PTLDVFHILFGNVLAVSTEELQLTAAVATAVLLFFGLFLKEIVAYTFDPVFASVAGLPANLLHHILMVMISLAVIAS 193
                                       67899************************************************************************ PP

                             FecCD 236 valvGpigFvGL.ivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliGapffiylll 311
                                          vG+i  v L i P    +lv ++  ++ ++s+ +G+   +   +l+ +l++++    g +  +  a+ff+++l+
  gi|557695124|ref|YP_008798178.1| 194 LQTVGIILVVSLlITPGATAQLVAKNLLQMFIISVTVGVSSAVTGLYLSFYLAASSG---GTIALTATAIFFAVFLA 267
                                       **********97367999999*****************************9998777...77777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); 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):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1940.95
//
Query:       gi|557695125|ref|YP_008798179.1|  [L=251]
Description: ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-32  111.3   0.0      7e-32  110.8   0.0    1.2  1  ABC_tran     ABC transporter
    8.1e-14   52.1   1.1    2.2e-06   27.7   0.2    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    7.6e-08   32.1   0.5    0.00014   21.4   0.1    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    6.4e-06   26.1   0.0     0.0033   17.2   0.0    2.1  2  AAA_15       AAA ATPase domain
    1.1e-05   25.0   0.0    2.2e-05   24.1   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
    3.3e-05   24.5   0.2     0.0001   22.9   0.0    1.7  2  AAA_23       AAA domain
     0.0038   17.3   0.0     0.0063   16.6   0.0    1.6  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0038   17.1   0.1      0.015   15.2   0.0    1.9  2  RsgA_GTPase  RsgA GTPase
     0.0039   17.6   0.0       0.17   12.3   0.0    2.3  2  AAA          ATPase family associated with various cellular a
     0.0092   16.2   0.8        0.2   11.9   0.8    2.3  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
     0.0098   15.7   0.1      0.083   12.7   0.0    2.0  2  ATP_bind_1   Conserved hypothetical ATP binding protein
       0.01   16.1   0.6      0.021   15.1   0.1    1.8  2  AAA_22       AAA domain
  ------ inclusion threshold ------
      0.011   16.3   0.0       0.54   10.8   0.0    2.2  2  AAA_18       AAA domain
      0.013   14.3   0.1      0.075   11.8   0.1    1.9  2  ABC_ATPase   Predicted ATPase of the ABC class
      0.013   15.6   0.1      0.032   14.4   0.1    1.8  1  AAA_33       AAA domain
      0.026   14.9   0.8      0.074   13.4   0.8    1.9  1  AAA_16       AAA ATPase domain
      0.035   13.7   0.1      0.076   12.6   0.0    1.5  2  AAA_27       AAA domain
      0.049   13.3   0.1       0.11   12.2   0.1    1.5  1  AAA_30       AAA domain
      0.053   13.6   0.8        2.1    8.4   0.1    2.7  2  AAA_14       AAA domain
      0.056   13.7   0.0       0.14   12.3   0.0    1.6  2  Roc          Ras of Complex, Roc, domain of DAPkinase
       0.13   12.0   0.1        7.9    6.2   0.0    2.3  2  IstB_IS21    IstB-like ATP binding protein
       0.13   11.9   0.0        1.8    8.1   0.0    2.1  1  Zot          Zonular occludens toxin (Zot)
       0.13   12.1   0.0       0.75    9.7   0.0    1.9  2  ATPase_2     ATPase domain predominantly from Archaea
       0.15   11.7   0.1        2.2    8.0   0.0    2.2  2  AAA_24       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 !  110.8   0.0   9.4e-35     7e-32       1     136 [.      20     164 ..      20     165 .. 0.95

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 9.4e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpelt 75 
                                       l++vs+k+ +g+++a+vG+nG+GKStL+k+l gl+kp  G i++ g d+++     +r +i+++pq      ++ lt
  gi|557695125|ref|YP_008798179.1|  20 LEDVSFKIFRGSITAVVGPNGSGKSTLFKALVGLVKPRRGVIKILGLDVSD-----ARGKIAYVPQReeVYWDYPLT 91 
                                       689***************************************999999998.....**********95555567788 PP

                                       HHHH................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       v +                 ++de++ +al+k gl++l  +++    s+LSgGq+qrv +ara++++++++llDEp 
  gi|557695125|ref|YP_008798179.1|  92 VWDVvamgrirdvgylrsvkKDDERVLAALEKTGLSGLMRRKI----SELSGGQQQRVFIARAIAQEAEIYLLDEPL 164
                                       9999***************999999*****************9....*****************************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 !   27.7   0.2   2.9e-09   2.2e-06       1      22 [.      32      53 ..      32     136 .. 0.78
   2 !   24.1   0.1   3.8e-08   2.8e-05     234     299 ..     134     196 ..      97     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 2.9e-09
                            AAA_21  1 lnvliGpNgsGKSnLLdaldll 22
                                      +++++GpNgsGKS+L++al +l
  gi|557695125|ref|YP_008798179.1| 32 ITAVVGPNGSGKSTLFKALVGL 53
                                      79*****************998 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 3.8e-08
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       ++elS G+++  +++ a+++ +    ++l+DEp +g++ +   rl+++l+el+r g  vi+tTH+ 
  gi|557695125|ref|YP_008798179.1| 134 ISELSGGQQQRVFIARAIAQEA---EIYLLDEPLTGIDAESEDRLFDILSELRRMGKTVIMTTHDL 196
                                       6789999999978888888777...9**************************************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 !   21.4   0.1   1.9e-07   0.00014      22      44 ..      28      50 ..      16      56 .. 0.88
   2 !    9.0   0.0    0.0011      0.83     134     198 ..     134     195 ..     104     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.9e-07
                                      TTSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 22 fsksftaivGpNGSGKsnlldAi 44
                                      f  s+ta+vGpNGSGKs l+ A+
  gi|557695125|ref|YP_008798179.1| 28 FRGSITAVVGPNGSGKSTLFKAL 50
                                      77899****************98 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0011
                                       TTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N 134 kelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkekskn.aQfivislr 198
                                       +++LSgG+++ v +a       ++ a +yllDe    +D++   ++ ++l e +     +i+++++
  gi|557695125|ref|YP_008798179.1| 134 ISELSGGQQQRVFIARA----IAQEAEIYLLDEPLTGIDAESEDRLFDILSELRRMgKTVIMTTHD 195
                                       4589****997766655....457889************************999873445555554 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.4e-06    0.0033      23      48 ..      31      55 ..      18      75 .. 0.78
   2 !    7.1   0.0    0.0053         4     319     365 ..     150     195 ..     111     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.4e-06
                            AAA_15 23 eeltvliGkNnsGKSsilealdlFln 48
                                      + +t ++G+N+sGKS++ +al  + +
  gi|557695125|ref|YP_008798179.1| 31 S-ITAVVGPNGSGKSTLFKALVGLVK 55
                                      3.9*****************976666 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0053
                            AAA_15 319 ekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                        + ++  i+l++EP + +  +    l++ l el + +k  vi+tTH 
  gi|557695125|ref|YP_008798179.1| 150 AIAQEAEIYLLDEPLTGIDAESEDRLFDILSELRRMGK-TVIMTTHD 195
                                       23445689*****************************9.9******6 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 !   24.1   0.0     3e-08   2.2e-05      17      49 ..      25      57 ..      19      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 3e-08
                            AAA_29 17 ieidlkg.atlltGpsGsGKSTllDAiqalLvpa 49
                                      ++i + g +t ++Gp+GsGKSTl+ A+  l  p+
  gi|557695125|ref|YP_008798179.1| 25 FKIFR-GsITAVVGPNGSGKSTLFKALVGLVKPR 57
                                      55654.559*****************99988876 PP

>> AAA_23  AAA 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    0.0001      17      39 ..      28      50 ..      14      53 .. 0.82
   2 ?   -1.1   0.0       3.1   2.3e+03     118     148 ..     131     161 ..     100     213 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 1.4e-07
                            AAA_23 17 FskgltlItGpNGaGKTTildAi 39
                                      F   +t+++GpNG+GK+T++ A+
  gi|557695125|ref|YP_008798179.1| 28 FRGSITAVVGPNGSGKSTLFKAL 50
                                      36689****************98 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.1
                            AAA_23 118 eqfisellgskkiilnlilflgqerfeefel 148
                                       +++isel g ++++  +   ++qe + ++++
  gi|557695125|ref|YP_008798179.1| 131 RRKISELSGGQQQRVFIARAIAQEAEIYLLD 161
                                       4556666666666666666666665433333 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   8.4e-06    0.0063       3      55 ..      34      97 ..      32     192 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.4e-06
                                      EEEESTTSSHHHHHHHHHT.........S..TEEESSSTTSSSSE.EEEEEEETTEEEEEEECGG CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltg.........e..kaivsdkpgtTrdi.negrvklkgkeielvDtpG 55
                                      a+vG   +GKStL++al+g         +     vsd  g+   + ++++v ++  +++++D++ 
  gi|557695125|ref|YP_008798179.1| 34 AVVGPNGSGKSTLFKALVGlvkprrgviKilGLDVSDARGKIAYVpQREEVYWD-YPLTVWDVVA 97
                                      89****************955444333322223444444433332244444444.3667776666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   2.1e-05     0.015      90     124 ..      20      55 ..       4      74 .. 0.77
   2 ?   -0.8   0.0       1.7   1.2e+03      53      88 ..     164     198 ..     136     216 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-05
                                       HHHHHHH.CTTSEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  90 leelkel.lkdktsvlvGqSGvGKStLinallpele 124
                                       le+++ + ++++++++vG+ G GKStL +al++  +
  gi|557695125|ref|YP_008798179.1|  20 LEDVSFKiFRGSITAVVGPNGSGKSTLFKALVGLVK 55 
                                       566655514669******************998654 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                                       EE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHT CS
                       RsgA_GTPase  53 lnKiDlleeeeeleelkeelealgyevllvsaktke 88 
                                       l+ iD  +e++ l ++ +el+++g +v+++  + ++
  gi|557695125|ref|YP_008798179.1| 164 LTGIDAESEDR-LFDILSELRRMGKTVIMTTHDLSS 198
                                       66677777777.888888889998888888666554 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   0.0   0.00023      0.17       3      37 ..      35      74 ..      33     120 .. 0.80
   2 ?    3.3   0.0      0.14   1.1e+02      14      62 ..     147     190 ..     144     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00023
                                      EESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCSSS CS
                               AAA  3 lyGppGtGKTllakavakelg.....vefleisgsellsk 37
                                      ++Gp G GK++l ka++  ++     +++l +++s+ + k
  gi|557695125|ref|YP_008798179.1| 35 VVGPNGSGKSTLFKALVGLVKprrgvIKILGLDVSDARGK 74
                                      79***************99975545555666666666655 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.14
                                       HHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEE CS
                               AAA  14 lakavakelgvefleisgsellskyvgesekkirelfkeakekakpsil 62 
                                       +a+a+a+e+++++l   ++ +      ese+++ ++++e++++  ++++
  gi|557695125|ref|YP_008798179.1| 147 IARAIAQEAEIYLLDEPLTGID----AESEDRLFDILSELRRMG-KTVI 190
                                       89*******9999999999999....899999999999999887.5555 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 !   11.9   0.8   0.00027       0.2      19      89 ..     123     180 ..     110     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00027
                           SbcCD_C  19 edgkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatllelle 89 
                                       ++g ++ ++r++++lSGG++q ++   +a a+a   ++        ++ +LDE   ++D+es ++l+++l 
  gi|557695125|ref|YP_008798179.1| 123 KTGLSGLMRRKISELSGGQQQRVF---IARAIA---QE-------AEIYLLDEPLTGIDAESEDRLFDILS 180
                                       567777799***********6544...443333...33.......35789999999999999999999875 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   0.00011     0.083       1      33 [.      35      67 ..      35      81 .. 0.84
   2 ?    0.8   0.0      0.46   3.5e+02     115     158 ..     176     219 ..     168     246 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNLD 33
                                      vvGp GsGK+t+ +al+ +++ r   ++++ LD
  gi|557695125|ref|YP_008798179.1| 35 VVGPNGSGKSTLFKALVGLVKPRRGVIKILGLD 67
                                      89**************99999887777888887 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.46
                        ATP_bind_1 115 veeLesefalvvvyLvDsqrltdptkfisgllsalsamlrlelP 158
                                       ++ L++  +++ ++++ ++ l+++ +f++++l+  + ++  + P
  gi|557695125|ref|YP_008798179.1| 176 FDILSELRRMGKTVIMTTHDLSSTFEFFDNILLLRNRVIAFGSP 219
                                       34444444688888999999999999**9999888777777666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   2.8e-05     0.021       5      27 ..      30      52 ..      26      73 .. 0.86
   2 ?   -2.0   0.1       5.2   3.9e+03      97      97 ..     160     160 ..     113     197 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.8e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlle 27
                                       +i++v+G+ G+GK+tl + l+ 
  gi|557695125|ref|YP_008798179.1| 30 GSITAVVGPNGSGKSTLFKALVG 52
                                      689***************99976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.2
                            AAA_22  97 i 97 
                                       +
  gi|557695125|ref|YP_008798179.1| 160 L 160
                                       2 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00072      0.54       3      19 ..      35      51 ..      34     103 .. 0.80
   2 ?    3.5   0.0      0.13        98      24      84 ..     137     196 ..     119     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00072
                            AAA_18  3 ltGtpGvGKttlakeLs 19
                                      + G+ G+GK+tl k+L 
  gi|557695125|ref|YP_008798179.1| 35 VVGPNGSGKSTLFKALV 51
                                      89*************94 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.13
                            AAA_18  24 f.......gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghla 84 
                                       +       +++ r +a+e +++l ++p        +d +  d+l+d+l e +   + gk++++  h  
  gi|557695125|ref|YP_008798179.1| 137 LsggqqqrVFIARAIAQEAEIYLLDEPL-----TGIDAESEDRLFDILSELR---RMGKTVIMTTHDL 196
                                       2555566688899999999999999999.....5666666666777777764...5799999998865 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 ?   11.8   0.1    0.0001     0.075     243     265 ..      28      51 ..      23      57 .. 0.88
   2 ?   -0.3   0.0      0.48   3.6e+02     324     348 ..     138     162 ..     132     168 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                                       -SS.EEEEEE-TTSSHHHHHHHHH CS
                        ABC_ATPase 243 pkG.vtlIvGggfhGKsTLLeAle 265
                                        +G +t++vG++  GKsTL +Al 
  gi|557695125|ref|YP_008798179.1|  28 FRGsITAVVGPNGSGKSTLFKALV 51 
                                       5677******************96 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.48
                                       -HHHHHHHHHHHHHHTT-SEEEEEG CS
                        ABC_ATPase 324 SGStsqAanimealeagakllLiDE 348
                                       SG   q + i++a+  +a++ L+DE
  gi|557695125|ref|YP_008798179.1| 138 SGGQQQRVFIARAIAQEAEIYLLDE 162
                                       9999999*****************9 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.3e-05     0.032       3      21 ..      34      52 ..      32     235 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.3e-05
                            AAA_33  3 llvGlpGsGKstlaerllk 21
                                       +vG++GsGKstl + l+ 
  gi|557695125|ref|YP_008798179.1| 34 AVVGPNGSGKSTLFKALVG 52
                                      589************9853 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   0.8   9.9e-05     0.074      23      55 ..      29      61 ..      16     200 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.9e-05
                            AAA_16 23 rpelvllsGesGvGKsslvrellralekdggif 55
                                      r++++ ++G+ G+GKs+l ++l   ++ ++g+ 
  gi|557695125|ref|YP_008798179.1| 29 RGSITAVVGPNGSGKSTLFKALVGLVKPRRGVI 61
                                      448999*************99986666664333 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0    0.0001     0.076      24      49 ..      28      53 ..      18      54 .. 0.80
   2 ?   -2.5   0.0       4.3   3.2e+03     106     144 ..     159     196 ..     118     200 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0001
                            AAA_27 24 eeadlhliyGpNEAGKstalrAisdl 49
                                       + +++ ++GpN +GKst+++A+  l
  gi|557695125|ref|YP_008798179.1| 28 FRGSITAVVGPNGSGKSTLFKALVGL 53
                                      4667889***************9765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.3
                            AAA_27 106 vlaallggldretFealFgLdherLreGGealleaegel 144
                                       +l++ l g+d e  ++lF + + +Lr+ G++++ ++ +l
  gi|557695125|ref|YP_008798179.1| 159 LLDEPLTGIDAESEDRLFDILS-ELRRMGKTVIMTTHDL 196
                                       4555566666666666666543.4666666666555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.11      19      46 ..      31      58 ..      26      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaag 46
                                       +++++Gp G+GK+t+ kal+ +++ + 
  gi|557695125|ref|YP_008798179.1| 31 SITAVVGPNGSGKSTLFKALVGLVKPRR 58
                                      4789****************99988773 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0028       2.1       3      23 ..      31      51 ..      29      81 .. 0.81
   2 ?    2.8   0.1      0.15   1.1e+02      10      21 ..     182     193 ..     177     210 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0028
                            AAA_14  3 kilvitGaRrvGKTtllkqli 23
                                       i +++G+  +GK+tl k l+
  gi|557695125|ref|YP_008798179.1| 31 SITAVVGPNGSGKSTLFKALV 51
                                      6889************99887 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.15
                            AAA_14  10 aRrvGKTtllkq 21 
                                       +Rr+GKT+++ +
  gi|557695125|ref|YP_008798179.1| 182 LRRMGKTVIMTT 193
                                       6*******9964 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 ?   12.3   0.0   0.00019      0.14       4      70 ..      35     102 ..      33     113 .. 0.76
   2 ?   -2.4   0.0       6.9   5.2e+03       9      15 ..     184     190 ..     139     195 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                                       EESSTTSSHHHHHHCHCT-CC.C-EEETTTTEEEEEEECGGSGGCT.TBTTTTCEEEEEEEE-SGGCTT CS
                               Roc   4 lvGdsgvGKtsllkrfvedkf.sekekstigvdfltkevtkikgve.ndkkvkkvklniWDtaGqerfr 70 
                                       +vG +g+GK++l+k +v     ++   +++g+d+++ +  ki  v   ++   ++ l +WD+    r+r
  gi|557695125|ref|YP_008798179.1|  35 VVGPNGSGKSTLFKALVGLVKpRRGVIKILGLDVSDARG-KIAYVPqREEVYWDYPLTVWDVVAMGRIR 102
                                       89***************7544145678999****99886.56655414445567899****97766655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.9
                                       TSSHHHH CS
                               Roc   9 gvGKtsl 15 
                                       ++GKt +
  gi|557695125|ref|YP_008798179.1| 184 RMGKTVI 190
                                       3455554 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 ?    6.2   0.0     0.011       7.9      37      67 ..      19      50 ..      10      62 .. 0.77
   2 ?    3.7   0.0     0.062        46     108     149 ..     154     196 ..     130     211 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.011
                         IstB_IS21 37 eLatlsf.iekkenivllGpsGvGKshlaial 67
                                      +L   sf i +    +++Gp G GKs l  al
  gi|557695125|ref|YP_008798179.1| 19 ALEDVSFkIFRGSITAVVGPNGSGKSTLFKAL 50
                                      55555554556667799**********99887 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.062
                         IstB_IS21 108 kvdllilDdlgllpldqaeaellfeviek..ryerrsiiitsnl 149
                                       ++++ +lD+  l+ +d +++  lf+++++  r +++ i+ t +l
  gi|557695125|ref|YP_008798179.1| 154 EAEIYLLDE-PLTGIDAESEDRLFDILSElrRMGKTVIMTTHDL 196
                                       445666776.58899************97324555555555444 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0025       1.8      63     128 ..     136     197 ..      31     202 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
                               Zot  63 pegaetlkefakwatidkga.llviDEcqeifpvrakegrkdpevinaftehRhlgwDivlltqdis 128
                                       +++  +++++++ + i+++a + ++DE  +   ++++     +  ++ + e+R++g +++++t d+s
  gi|557695125|ref|YP_008798179.1| 136 ELSGGQQQRVFIARAIAQEAeIYLLDEPLTGIDAESE-----DRLFDILSELRRMGKTVIMTTHDLS 197
                                       4444444444444444433313355555555444444.....56889999************99987 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 ?    9.7   0.0     0.001      0.75      21      42 ..      31      52 ..      21      71 .. 0.87
   2 ?    0.1   0.0      0.87   6.5e+02      31      82 ..     124     179 ..     113     216 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.001
                          ATPase_2 21 eiyfiYGpegsGKtaLlkeiie 42
                                      +i  + Gp gsGK++L+k ++ 
  gi|557695125|ref|YP_008798179.1| 31 SITAVVGPNGSGKSTLFKALVG 52
                                      678899************9886 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.87
                          ATPase_2  31 sGKtaLlkeiienledkdkyviyyial..reesiskldefie..eeeekkklekal 82 
                                        G + L+++ i++l+  +++++++     +e +i  lde +   + e++++l + l
  gi|557695125|ref|YP_008798179.1| 124 TGLSGLMRRKISELSGGQQQRVFIARAiaQEAEIYLLDEPLTgiDAESEDRLFDIL 179
                                       56677888888888777777777765311334444444444455555555555444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0029       2.2       5      22 ..      33      50 ..      29      79 .. 0.83
   2 ?    1.4   0.0      0.29   2.2e+02     110     137 ..     174     201 ..     169     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0029
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                       +++Gp+g+GK+tl k l
  gi|557695125|ref|YP_008798179.1| 33 TAVVGPNGSGKSTLFKAL 50
                                      5799**********9988 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.29
                            AAA_24 110 efrrllkklqelrknvifiahektrkde 137
                                       ++ ++l  l+ ++k+vi++ h    ++e
  gi|557695125|ref|YP_008798179.1| 174 RLFDILSELRRMGKTVIMTTHDLSSTFE 201
                                       55567888899999*******8888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 1661.81
//
Query:       gi|557695126|ref|YP_008798180.1|  [L=307]
Description: manganese/iron ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-73  245.1   0.0    9.2e-73  244.8   0.0    1.0  1  ZnuA      Zinc-uptake complex component A periplasmic


Domain annotation for each model (and alignments):
>> ZnuA  Zinc-uptake complex component A periplasmic
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  244.8   0.0   5.1e-77   9.2e-73       3     254 ..      37     300 ..      36     302 .. 0.91

  Alignments for each domain:
  == domain 1  score: 244.8 bits;  conditional E-value: 5.1e-77
                                       ESSHHHHHHHHHHHGGGCEEEECS-TTSTTTT----HHHHHHHHHSSEEEESSTTTSGTHHHHHHHHTTCCCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA   3 attsplgdlvrqvaGdrvevtvLvppgadpHsyeptprdvrklaeAdllvynglelEtwldkllasssqatrvevid 79 
                                       atts+++dl+r+v+G   +v+++v pg++pH+yeptp+d+ k+++A++++yng  +++w+ kll s ++ ++  +  
  gi|557695126|ref|YP_008798180.1|  37 ATTSIICDLARNVVGRLWDVECIVAPGQSPHTYEPTPEDMVKASKAKVILYNGFAVDAWVVKLLGSQNN-EK--LYR 110
                                       9**************************************************************976664.33..333 PP

                                       TTTTC.........CSEBCSSESTGGGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                                       xxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA  80 lsegv.........eeeeeeeDpHiWlspknaiamveniadaLveadpanadtyeanaaayiekLeeldaeireela 147
                                       ++eg+         ++   +eDpH+W+++ +ai++ve i+d ++e dp+na+ y+anaaayi++Leeld++ire+++
  gi|557695126|ref|YP_008798180.1| 111 VTEGLepyllkvpdGPYAGKEDPHMWMDVGLAIKYVEHIRDIFIEQDPDNAEIYKANAAAYIRELEELDKWIRETVS 187
                                       444442223333333455566******************************************************** PP

                                       TSSGTEGEEEESSSTTHHHHHHTT-EEEEEE.SSSSS....HHHHHHHHHHHHHTT-SEEEEETTS-THHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ZnuA 148 eipeekrklvtthdafgylarayglevagia.giste....aaqiaalieeikeagvkaifveplaspklaetlaee 219
                                       ++p ekr+lvt+++af+y+arayg++v + + +i te    + ++ + +e++k++gv + fve++ s++l+++l +e
  gi|557695126|ref|YP_008798180.1| 188 QLPTEKRILVTQENAFQYFARAYGFRVGAYFySIATEiepsPIDMVHAVEKVKQLGVCVFFVESTLSSRLLDSLVRE 264
                                       ***************************999999*999**99************************************ PP

                                       HT-EE.EEE-STSSSTSTTS.TTSHHHHHHHHHHHHH CS
                                       xxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                              ZnuA 220 agvkv.atlysldslgdegs.aetYidmmranleslk 254
                                       ag ++ ++ly  d++g++gs ae+Y++mm+ n+ +++
  gi|557695126|ref|YP_008798180.1| 265 AGGRLaGPLYV-DGVGPRGSgAESYVSMMKVNVGTIV 300
                                       *9998467***.*******99************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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: 00:00:00.42
# Mc/sec: 2196.48
//
Query:       gi|557695127|ref|YP_008798181.1|  [L=382]
Description: DNA primase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   46.3   0.1    1.5e-11   44.6   0.1    1.9  1  Toprim_4  Toprim domain
    1.5e-05   25.3   0.0    5.6e-05   23.5   0.0    2.0  2  Toprim_2  Toprim-like
      4e-05   23.8   0.1    0.00029   21.0   0.1    2.4  1  Toprim    Toprim domain
  ------ inclusion threshold ------
      0.072   11.6   2.6      0.082   11.4   0.1    2.1  3  Aldedh    Aldehyde dehydrogenase family


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 !   44.6   0.1   3.3e-15   1.5e-11       1      78 [.     169     234 ..     169     242 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 3.3e-15
                          Toprim_4   1 seiiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerlael 77 
                                       +e+iiVEg+aD ++l ++g+kn++av g  + p++ ++++k+k+           +vi +ldgD  G+   ++l++ 
  gi|557695127|ref|YP_008798181.1| 169 DELIIVEGRADIINLLRYGYKNTIAVEGVKI-PKSIAGLTKRKK-----------RVIAFLDGDRGGDLILQELLQN 233
                                       589****************************.999999666555...........9************999999885 PP

                          Toprim_4  78 l 78 
                                       +
  gi|557695127|ref|YP_008798181.1| 234 C 234
                                       5 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   1.2e-08   5.6e-05       1      68 [.     172     234 ..     172     252 .. 0.85
   2 ?   -3.0   0.0       2.2     1e+04      20      41 ..     328     348 ..     321     355 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 1.2e-08
                          Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaell 68 
                                       +++Eg  D + l+++g k   n +a+ G+++++  + l +r+  k+v+  lD D+ G+   ++l +  
  gi|557695127|ref|YP_008798181.1| 172 IIVEGRADIINLLRYGYK---NTIAVEGVKIPKSIAGLTKRK--KRVIAFLDGDRGGDLILQELLQNC 234
                                       69***************9...********9988888888888..99*************999887665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.2
                          Toprim_2  20 ktnvvalgGtalteaalkller 41 
                                       + ++v   G+ +t+++++l ++
  gi|557695127|ref|YP_008798181.1| 328 DAKYVVFDGV-VTQRLVDLAAS 348
                                       6789999999.88877776554 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   6.4e-08   0.00029       1      93 [.     170     241 ..     170     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.4e-08
                                       EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHH CS
                            Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGe 77 
                                       el+ivEg +d +++ ++   g+++++a+ G  +                      ++ l kr +++i  +D+Dr G 
  gi|557695127|ref|YP_008798181.1| 170 ELIIVEGRADIINLLRY---GYKNTIAVEGVKIPKS-------------------IAGLTKRKKRVIAFLDGDRGGD 224
                                       69***************...9********9766544...................899******************* PP

                                       HHHHHHHHHHT.HHHTT CS
                            Toprim  78 aiawellevlk.ellen 93 
                                        i  ell+++k +++ +
  gi|557695127|ref|YP_008798181.1| 225 LILQELLQNCKiDAVAR 241
                                       ********999644444 PP

>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0     0.095   4.2e+02     395     431 ..      29      64 ..      26      67 .. 0.86
   2 ?   11.4   0.1   1.8e-05     0.082       8      67 ..      89     149 ..      83     163 .. 0.91
   3 ?   -3.6   0.1      0.64   2.9e+03      23      65 ..     248     293 ..     245     305 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.095
                                       EESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--T CS
                            Aldedh 395 yGLaagvftkdleraervaerleaGnvyiNdsttgaa 431
                                       +G + g+f++dl+ ++++ +  + G + iN +t+g+ 
  gi|557695127|ref|YP_008798181.1|  29 FGQTEGIFSSDLD-LRELQKTGRIGRIEINVTTQGNK 64 
                                       89999****9965.78999999********9988775 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 1.8e-05
                                       EEEEEETT.TCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHT CS
                            Aldedh   8 tievinPa.tgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleer 67 
                                       +i+ + P+  + vi k+++   e+ ++++++Ake   aw+k +++e   iLr++ d++ + 
  gi|557695127|ref|YP_008798181.1|  89 SIDRVGPYqARAVIEKIEDTRLEKRKRIIERAKEILAAWEKQKVPENDLILRELEDAIVKT 149
                                       5788889978899*******************************************99765 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 0.64
                                       EE-B-HHHHHHHHHHHHH...HHHHHTTS-HHHHHHHHHHHHHHHH CS
                            Aldedh  23 vpaataedvdaavaaAke...afkawaklpaeeRaeiLrkaadlle 65 
                                       v++ ta ++++a+++A     a +a +    +eR+ +  ++ ++++
  gi|557695127|ref|YP_008798181.1| 248 VEQLTAREIHEALEHAVPpseALRAKEMAAGAERKTVPSELKNYVK 293
                                       6677777777777777541113333444444555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2712.90
//
Query:       gi|557695128|ref|YP_008798182.1|  [L=359]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-17   64.0   0.0    3.9e-17   62.7   0.0    1.7  1  eRF1_3    eRF1 domain 3
    1.2e-13   51.2   0.2      2e-13   50.4   0.2    1.3  1  eRF1_1    eRF1 domain 1


Domain annotation for each model (and alignments):
>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.0   4.4e-21   3.9e-17       3     113 .]     255     350 ..     253     350 .. 0.94

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 4.4e-21
                                       HHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHHH CS
                            eRF1_3   3 qekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenve 79 
                                        ++  +ee+++ l +++gka  G+ e+l+al+mgAve++Lvse++  sr+  k+              + elve +e
  gi|557695128|ref|YP_008798182.1| 255 ADVMDVEELMRVLVTEPGKASLGFVETLNALRMGAVEKVLVSEDFLWSRYMDKD--------------VWELVERAE 317
                                       567789*******************************************88765..............689****** PP

                                       HTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS-- CS
                            eRF1_3  80 esgakveiisseseeGeqlvkafgGiaaiLRykv 113
                                         ga+v ++s+ se+  +l +++gG+aa+LRy+v
  gi|557695128|ref|YP_008798182.1| 318 AHGASVRVVSTGSEATDKL-NGLGGVAAFLRYSV 350
                                       *******************.************86 PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.2   2.3e-17     2e-13      14     114 ..      11     112 ..       1     122 [. 0.92

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.3e-17
                                       CEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECTTSSEEEEEEEEEEG CS
                            eRF1_1  14 gsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdkdagvlrisGkviee 90 
                                        +vt++pe+  dl  +y +++ gd v a+t+r+ ++e+  gs++s rv ++L ++v +  +d+  ++l + G +  e
  gi|557695128|ref|YP_008798182.1|  11 RLVTVVPESTLDLLNIYRVLEVGDVVYAVTSRELKKERRDGSVDSVRVAVELGVEVLEKSLDPMLKRLDLLGVIRYE 87 
                                       689************************************************************************99 PP

                                       GGG.--TTSEEEEEE-TTSEEEEEE CS
                            eRF1_1  91 neh.vklgafhtldlelkrpftiik 114
                                       +++   +g++h++ + +++++t++ 
  gi|557695128|ref|YP_008798182.1|  88 SRElGLVGKHHSIHVSVGDELTVES 112
                                       9985678**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); 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: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2617.67
//
Query:       gi|557695129|ref|YP_008798183.1|  [L=232]
Description: maleate isomerase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  102.3   0.0    3.1e-29  102.2   0.0    1.0  1  Amdase        Arylmalonate decarboxylase
      9e-18   64.9   0.0    1.9e-17   63.9   0.0    1.5  2  Asp_Glu_race  Asp/Glu/Hydantoin racemase


Domain annotation for each model (and alignments):
>> Amdase  Arylmalonate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.2   0.0   3.4e-33   3.1e-29      21     208 ..      36     220 ..      21     229 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.2 bits;  conditional E-value: 3.4e-33
                            Amdase  21 lkelskegydevidrvveaArelaerGaqavslmGtsLsFyRGaafneeLvarleeatgLPattmssavvealralg 97 
                                       l+++  +  +   d+ v  Ar+l ++G+++++   ts sF +G++  + ++++le+  g Pa   s av++al +lg
  gi|557695129|ref|YP_008798183.1|  36 LENVMVSELTVLEDEAVREARKLVTAGVDVLVYGCTSGSFVKGPQQYSGIEEKLEK-LGKPAVATSGAVIRALTHLG 111
                                       56666666667779999************************************986.689***************** PP

                            Amdase  98 arRvAvataYidevnerLvayLeesglevaalesLdiedveavakvtaeelvelgkkavaaapeadallisCGGLrt 174
                                       a ++ + t Y+ ++ e  +a+L+++g+ev +  + +i +  ++  v+++e++e +++ +  +p++da++isC  L+t
  gi|557695129|ref|YP_008798183.1| 112 AGKISLITPYTRDITEVEKAFLAKHGFEVLSTFHASIVANLDIGMVKDDEVAEWATENT--HPDSDAIFISCTNLST 186
                                       *****************************************************998876..899************* PP

                            Amdase 175 ldvvreledelglpvvssalAGlwdavrlaglda 208
                                        ++++++e+++g+pvvss  A lw+++++++++ 
  gi|557695129|ref|YP_008798183.1| 187 FKAIKRIEENTGKPVVSSNSATLWNVLQKLNKKI 220
                                       ***************************9998765 PP

>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.0   2.1e-21   1.9e-17       1     223 [.       4     212 ..       4     213 .. 0.87
   2 ?   -1.1   0.0      0.16   1.4e+03      83      98 ..     212     227 ..     208     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 2.1e-21
                                       EEECSCCCCHHHHHHHHHHBTTSSGGGS..EEEEE-CCS-TCHHHHHCH.T..THH.HHHHHHHHHHCTTESEEEE- CS
                      Asp_Glu_race   1 IGgmgpeatlsvlrklveatpaesdqehlplivlndsaipdrteaieeesgddpvl.klleaakkLekagadaivia 76 
                                       IG + p++++++ r+++e ++++    h  ++ l++  + + t           ++ +  ++a+kL +ag+d++v+ 
  gi|557695129|ref|YP_008798183.1|   4 IGLIVPSSNTTMEREFWESLNGHAT-IHAGRVFLENVMVSELTV----------LEdEAVREARKLVTAGVDVLVYG 69 
                                       8999********************5.578889999999554443..........44489****************** PP

                                       -CHHHHHHHHHH.........HH-SSEEEECHHHHHHHHHHHSS-EEEEEE-HHHHHCTHHHHHHHHHGT.EEE... CS
                      Asp_Glu_race  77 CnTahavadelq.........kkikiPvlgiveataealkatgvkkvglLgTrgtlksglyqkeleanqgievvvps 144
                                       C++  +++++ q         +k+  P +    a+++al   g++k+ l+++++   +++ +++l++ +g+      
  gi|557695129|ref|YP_008798183.1|  70 CTSG-SFVKGPQqysgieeklEKLGKPAVATSGAVIRALTHLGAGKISLITPYTRDITEVEKAFLAK-HGF------ 138
                                       ****.999999967565555555555566666677889999**************************.9**...... PP

                                       .T-CCCHHCCHCHHHHTT-TTSHHHHHHHHHHHHHHTTT-SEEEE-STTHHHHHHHHHHCC-TT.SEEEEHHHHHHH CS
                      Asp_Glu_race 145 eelqssvnqaiyeelkaGevteearrailkllerlaergadaviLGCTelplllekaealekeksvpvidptdilar 221
                                        e+ s+ + +i + l  G v++++ ++ +++       + da+++ CT+l+++ ++++++e+++++pv+++++++ +
  gi|557695129|ref|YP_008798183.1| 139 -EVLSTFHASIVANLDIGMVKDDEVAEWATENT---HPDSDAIFISCTNLSTF-KAIKRIEENTGKPVVSSNSATLW 210
                                       .99999******8888*******7777777777...89*************99.9999999999***********99 PP

                                       HH CS
                      Asp_Glu_race 222 et 223
                                       ++
  gi|557695129|ref|YP_008798183.1| 211 NV 212
                                       75 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.16
                                       HHHHHHHH-SSEEEEC CS
                      Asp_Glu_race  83 vadelqkkikiPvlgi 98 
                                       v+++l kki++P+lg+
  gi|557695129|ref|YP_008798183.1| 212 VLQKLNKKIDLPLLGM 227
                                       5677889********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1650.06
//
Query:       gi|557695130|ref|YP_008798184.1|  [L=683]
Description: N-methylhydantoinase A [Candidatus Caldiarchaeum subterraneum]
Scores for 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-92  308.3   3.7    4.8e-92  308.3   3.7    2.5  3  Hydantoinase_A  Hydantoinase/oxoprolinase
    2.6e-46  157.6   0.0    6.8e-46  156.2   0.0    1.7  1  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
  ------ inclusion threshold ------
      0.025   14.1   0.0       0.13   11.8   0.0    2.2  3  ROK             ROK family
       0.04   12.5   0.8        1.5    7.3   0.0    2.4  2  MutL            MutL protein


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 ?    1.7   0.1     0.028   1.3e+02      81      98 ..       5      22 ..       1      35 [. 0.81
   2 ?   -3.5   0.0       1.1   4.9e+03     186     218 ..     132     165 ..     129     179 .. 0.66
   3 !  308.3   3.7   1.1e-95   4.8e-92       1     288 [.     204     498 ..     204     501 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.028
                    Hydantoinase_A 81 vItfDmGGTstDvslikd 98
                                      v  +D+GGT tD+ ++++
  gi|557695130|ref|YP_008798184.1|  5 VAAVDVGGTFTDLVAVDE 22
                                      6689********999875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.1
                    Hydantoinase_A 186 gdqkldvelarrafeelakelnlk.veevAegil 218
                                       g++++ +e  +r++e la+++++   e vA  +l
  gi|557695130|ref|YP_008798184.1| 132 GKGEVLKEVDERELEALAEQIEKIgTESVAICFL 165
                                       6666666777777777777776543666665555 PP

  == domain 3  score: 308.3 bits;  conditional E-value: 1.1e-95
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       rt+t+vvnA+l+p++++y+ sv++ l+  g+++++++m+s Gglv++dea ++pv +i+SGPaaGv+gaa++++  g
  gi|557695130|ref|YP_008798184.1| 204 RTSTTVVNAALAPVVSRYIASVRQGLDGLGITCPVQIMSSAGGLVDVDEAVNRPVACIESGPAAGVIGAAKVAEAIG 280
                                       89*************************************************************************** PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsletei............agvkvrlpaldirtvgagGgsilvvdeggklrv 142
                                        k+vI fDmGGT+++  ++ dg ++++ e e+            +g++vr+p++d+++v+agGg+i+ v+++g l+v
  gi|557695130|ref|YP_008798184.1| 281 LKRVISFDMGGTTAKTGVVVDGLPATVPEIEVggrvhmgriikgSGYPVRFPSIDLAEVSAGGGTIIQVSKTGGLQV 357
                                       ***************************************************************************** PP

                    Hydantoinase_A 143 gpesagadpgpacyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegils 219
                                       gp sagadpgpacy+ Gg e+t+TDan +LGr+++  +l   +g++kld  la++a+e++ak+l++++ e++++ l 
  gi|557695130|ref|YP_008798184.1| 358 GPLSAGADPGPACYGMGGVEPTITDANHLLGRVEH--LL---GGEMKLDTVLAEKAMEKVAKQLGQNLVETSWNSLV 429
                                       *********************************87..79...9********************************** PP

                    Hydantoinase_A 220 vavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvr 288
                                       +a+  ma+av  ++ ergldp+e+tlv+fGGaG++haa+la+++g++k+++pp++g++s lG+++ d++
  gi|557695130|ref|YP_008798184.1| 430 LANLHMARAVHIVTLERGLDPTEFTLVAFGGAGPMHAAELAQQIGISKIVIPPSPGLFSSLGLLMTDMK 498
                                       *****************************************************************9987 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 !  156.2   0.0   1.5e-49   6.8e-46       3     176 ..       7     183 ..       5     185 .. 0.95

  Alignments for each domain:
  == domain 1  score: 156.2 bits;  conditional E-value: 1.5e-49
                        Hydant_A_N   3 gIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkg... 76 
                                       ++DvGGTfTD+va+de ++++ ++K+ stp+ ++eg+++a++++le+    +++ + +++  T+ tN +  +     
  gi|557695130|ref|YP_008798184.1|   7 AVDVGGTFTDLVAVDESDGRLYKVKTRSTPHRPEEGFLDAVQKLLENFS--PKDFELIIHVNTIGTNLFRGQLAlkm 81 
                                       79******************************************99855..7***************9988866777 PP

                        Hydant_A_N  77 ervaLittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagve 151
                                       + v+L+ttkgfrd++eigrqnrp+l++   +  +p+v++e+++ev+erv+ +gevlk++de e+++ ++++ + g e
  gi|557695130|ref|YP_008798184.1|  82 PAVSLVTTKGFRDVVEIGRQNRPELYNIFYRrpDPIVPRERRFEVSERVDGKGEVLKEVDERELEALAEQIEKIGTE 158
                                       *************************99544489******************************************** PP

                        Hydant_A_N 152 siavvllhSylnpehElrvaeiare 176
                                       s+a+++l+Sylnp +E+r++e++r+
  gi|557695130|ref|YP_008798184.1| 159 SVAICFLNSYLNPVNEKRAKEVLRR 183
                                       **********************997 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.8e-05      0.13       2      51 ..       6      55 ..       5      74 .. 0.87
   2 ?   -2.4   0.0       0.6   2.7e+03      23      68 ..     198     240 ..     187     251 .. 0.73
   3 ?   -2.9   0.0      0.82   3.7e+03     176     195 ..     401     420 ..     398     440 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.8e-05
                                      EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCH CS
                               ROK  2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeae 51
                                      +++d+Ggt + l  vde+   l++ k   +   +ee+  da+++l+++  
  gi|557695130|ref|YP_008798184.1|  6 AAVDVGGTFTDLVAVDESDGRLYKVKTRSTPHRPEEGFLDAVQKLLENFS 55
                                      69*************************99999************998754 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.6
                                       EEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEE CS
                               ROK  23 larekvetptetteetlvdaiaelvdeaerkadeliavgigspGli 68 
                                       ++re+  t+t+ ++ +l  +++  +++  + +d   ++gi  p  i
  gi|557695130|ref|YP_008798184.1| 198 EHREYERTSTTVVNAALAPVVSRYIASVRQGLD---GLGITCPVQI 240
                                       456666778889999999999999999988777...7777776666 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.82
                                       HHCCSHHHHHHCHTCCGTTS CS
                               ROK 176 Etlasgralekraqqkgekl 195
                                       +t+++++a+ek+a+q g++l
  gi|557695130|ref|YP_008798184.1| 401 DTVLAEKAMEKVAKQLGQNL 420
                                       55666666666666644443 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00034       1.5       3      56 ..       7      55 ..       5      71 .. 0.77
   2 ?    2.8   0.5    0.0081        36     207     269 ..     240     304 ..     237     312 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00034
                              MutL  3 viDiGSttTkvtlvdlekvderllgqaeapTtveeedvleGleealeeleeklg 56
                                      ++D+G t+T +++vd+++  +rl+      T        eG+  a+++l e+ +
  gi|557695130|ref|YP_008798184.1|  7 AVDVGGTFTDLVAVDESD--GRLYKVKTRSTPHRP---EEGFLDAVQKLLENFS 55
                                      7999**********9966..888877777777664...4788888888887754 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.0081
                              MutL 207 iv.kakglskleelvsaeimp...TPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvaegsp 269
                                       i+  a gl ++ e v++++++    PaA + ++  +ae  + gl  ++ +D+GG+T     v++g p
  gi|557695130|ref|YP_008798184.1| 240 IMsSAGGLVDVDEAVNRPVACiesGPAAGVIGAAKVAE--AIGLKRVISFDMGGTTAKTGVVVDGLP 304
                                       55567777777777777765511156666666666666..67888***********98877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (683 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); 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 0.26s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 4913.03
//
Query:       gi|557695131|ref|YP_008798185.1|  [L=522]
Description: N-methylhydantoinase B [Candidatus Caldiarchaeum subterraneum]
Scores for 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-186  618.9   0.0     7e-186  618.6   0.0    1.0  1  Hydantoinase_B   Hydantoinase B/oxoprolinase
  ------ inclusion threshold ------
       0.14   11.8   0.0       0.26   11.0   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase


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 !  618.6   0.0  7.8e-190    7e-186       6     515 ..       6     519 ..       3     520 .. 0.97

  Alignments for each domain:
  == domain 1  score: 618.6 bits;  conditional E-value: 7.8e-190
                    Hydantoinase_B   6 evfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekf..eg.elk 79 
                                       ev++ +l  i eemg +l+++a+Spni+er D sca++d +g+l+ qa+hipvh+gs+++ +k++l+++  +g e++
  gi|557695131|ref|YP_008798185.1|   6 EVVKYSLLYISEEMGVALRKSAFSPNIRERADHSCAILDWRGRLIGQAEHIPVHIGSLPHGLKNTLAYLekKGvEMS 82 
                                       89999*************************************************************888543378** PP

                    Hydantoinase_B  80 pGDvlltNdPyaggtHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveege 156
                                       pGD++++NdPy  gtHl+Dit+i+P+f++gelv++va++aHh+D+GGi p s++ +a+++ +EG++ippvkl++e++
  gi|557695131|ref|YP_008798185.1|  83 PGDMYVLNDPYIAGTHLNDITTIRPIFYRGELVAYVANKAHHVDVGGIDPSSISIRAETLLQEGIVIPPVKLMKENK 159
                                       ***************************************************************************** PP

                    Hydantoinase_B 157 leedvlelllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpdgtye 233
                                         edv+++l++n+R p+ +lgDl+Aqiaan +ge++l +lie+++l ++++a+++i++++++ vr+++a+lp g+  
  gi|557695131|ref|YP_008798185.1| 160 IMEDVVDILRNNTRIPDITLGDLRAQIAANLIGEKKLLDLIEKVSLPVFREAVEQIIEKTNQLVRQEVAQLPWGRAV 236
                                       ***************************************************************************** PP

                    Hydantoinase_B 234 aedyl..dd.gipikvtvtidgdeatvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievkl 307
                                        ed+l  d+ ++ ik  v++  + ++v+f+gt++qv++++Na+l vt +a++y++r+l+++di lNeG+ + +++++
  gi|557695131|ref|YP_008798185.1| 237 GEDFLelDErDLVIKADVEVGSQGFRVNFAGTDRQVNKPLNAVLGVTIAATTYTIRTLLGPDILLNEGFTETLSIHA 313
                                       ***997666569*******99999***************************************************** PP

                    Hydantoinase_B 308 pegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetiagGaGA 384
                                       peg+l+np +pa+v++gn etsqr+vd+++kal++++ +r++Aas g+mnnl++gg+++++g+++++yeti+gG GA
  gi|557695131|ref|YP_008798185.1| 314 PEGTLVNPVKPAPVAAGNLETSQRIVDTIYKALSEIMHDRIPAASTGSMNNLMMGGIHPETGKAWAFYETIGGGGGA 390
                                       ***************************************************************************** PP

                    Hydantoinase_B 385 rpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserrvfa 461
                                       rpg+dG++++h+hmtnt nt++E++E+ yPvl+ ++++r++sgG G++rGG+G++r++++l+p ++v+++++r++++
  gi|557695131|ref|YP_008798185.1| 391 RPGMDGVDGIHCHMTNTLNTPIEVIEHYYPVLFMSYRFRDGSGGVGRWRGGMGIERSLKALAP-IHVAVMGDRSRHR 466
                                       **************************************************************9.************* PP

                    Hydantoinase_B 462 pwGlaGGepGargrvvlnllvr..geeenlggkatvelkagdvlvietpGGGGyGd 515
                                       pwGl+GG++Ga++++++   ++  g++++l++k+ ++l++gd+++i+t+GGGGyG+
  gi|557695131|ref|YP_008798185.1| 467 PWGLKGGGEGAPSEYLI---KKvdGTIIKLSSKDVATLNPGDIIIIRTAGGGGYGR 519
                                       **************554...334599*****************************6 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.8e-05      0.26      81     129 ..     208     254 ..     201     261 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.8e-05
                   Methyltransf_16  81 llellkknielnknalkskvkvevLdWgeeleedllekeevDlilaaDc 129
                                         e +++ ie  +++++++  v +L Wg  + ed+le  e Dl++ aD+
  gi|557695131|ref|YP_008798185.1| 208 FREAVEQIIEKTNQLVRQE--VAQLPWGRAVGEDFLELDERDLVIKADV 254
                                       5677888888877555555..579************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 3694.13
//
Query:       gi|557695132|ref|YP_008798186.1|  [L=202]
Description: small subunit ribosomal protein S7 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-38  129.6   1.1    8.8e-38  129.3   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 !  129.3   1.1   4.9e-42   8.8e-38      17     149 .]      61     202 .]      51     202 .] 0.95

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 4.9e-42
                                       STTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEE CS
                      Ribosomal_S7  17 kynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpv 89 
                                       k + ++ e+l n+lm+     Gkks+A   v++al ii+ +t+k+plevl++A+en++P ++v+++ +GG+ y  +v
  gi|557695132|ref|YP_008798186.1|  61 KSQLNIAERLANMLMRpgknGGKKSKALAAVRNALWIIHLRTGKNPLEVLVRAVENSAPLEDVTRLSYGGIVYFKAV 137
                                       567799**********999999******************************************************* PP

                                       EE-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                      Ribosomal_S7  90 evrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                       +++p+Rr++lAlr+i++aa   ++r+ +++ e+LaeE+i A+e++  + avk+r e++r+A a+r
  gi|557695132|ref|YP_008798186.1| 138 DISPQRRVDLALRNIAQAArenSFRTRRTIDEALAEEIILASEKDskSFAVKRRIELERVALASR 202
                                       *******************888889999****************98899************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1473.55
//
Query:       gi|557695133|ref|YP_008798187.1|  [L=522]
Description: phosphoenolpyruvate carboxylase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-156  520.5   0.0     4e-156  520.4   0.0    1.0  1  PEPcase_2  Phosphoenolpyruvate carboxylase
  ------ inclusion threshold ------
       0.11   12.6   0.4       0.62   10.2   0.0    2.4  3  UPF0147    Uncharacterised protein family (UPF0147)
       0.15   10.1   0.0       0.22    9.6   0.0    1.3  1  PEPcase    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 !  520.4   0.0  6.8e-160    4e-156       1     494 []       8     522 .]       8     522 .] 0.95

  Alignments for each domain:
  == domain 1  score: 520.4 bits;  conditional E-value: 6.8e-160
                                       --SEEEE--ST-.......SS--B-TTTHHHHHHHHHSS----EEEEE-SSB---TTHHHHHHHHHHC..TT--TTT CS
                         PEPcase_2   1 iprtmsTQHPDnakvPefaeeevisgedEveEAykalselgvdEvMwDfEGKevdehvvrkllseyeeffkekvlGe 77 
                                       iprtms QHPDn+  P +  +  i+g+dEveE y+  ++lg++E MwD+EGK+vd +vvrkll++ +e+f+ek++G+
  gi|557695133|ref|YP_008798187.1|   8 IPRTMSSQHPDNVSSPPWLDTPLIEGDDEVEEVYQSWVTLGCEEAMWDAEGKDVDLNVVRKLLTTHPEYFREKIIGR 84 
                                       9**************************************************************************** PP

                                       SSEEEEE---TTTS-HHHHHHHHHHHHHHHHH.HHHHH....SS-S-SEEEESS--SHHHHHHHHHHHHHHHH.... CS
                         PEPcase_2  78 dvfltlRvPnpkvEkaerkvlaetlesipnsydlaekf...eetkpifevilPmttsaeelievakyyekvvagkee 151
                                       d flt+R+Pnp++Ek++rkv+ etl+sip+ +d+ e+f   + ++p+fevilP+tts+++li+v+++y+k+v + ee
  gi|557695133|ref|YP_008798187.1|  85 DHFLTYRIPNPSMEKSDRKVFFETLQSIPKHFDACEAFygrQVNPPVFEVILPFTTSVNQLIRVVNTYRKAVVQLEE 161
                                       **************************************9855899***************************98888 PP

                                       .......HHHHH-SS---TTSSEEEEEE-SHHHHHTHHHHHHHHHHHT--SEEEEEEESHHHHHHH-HHHHHHHHHH CS
                         PEPcase_2 152 lelad..lkvkelvgelkpesievIPLiEdkesllnideiveeyvkekklkelRvflarSDpAlnyGlisavllvkv 226
                                       + +    +++ +++g+++pe+ievIPL+Ed +s+ln+d+i+ ++++ ++++++R f+arSDpAln Gl++a+l++k+
  gi|557695133|ref|YP_008798187.1| 162 IVIDYpnITLGDIIGKISPEKIEVIPLFEDLDSMLNADTILGRFIELTSPRYVRAFIARSDPALNNGLVAATLMAKL 238
                                       7776568********************************************************************** PP

                                       HHHHHHHHHHHHT-EEEEEEE-BSSGGGT---TTGHHHHHHHTTT-SEEEE-HHHHHTTHHHHHHHHHHHHHHGGG- CS
                         PEPcase_2 227 AlselykleeelgvkiyPilGvGslpfRGhlspenveevleeYagvkTfTvQSafkYdyeeeevkeairkineaevk 303
                                       A+++l +l+ ++g++++ i+GvG+lpfRG+lsp+++e++ eeY gv T+T+QSaf+Ydy+++ vkeai++in++   
  gi|557695133|ref|YP_008798187.1| 239 AIDKLQNLSTNTGIPVHTIIGVGTLPFRGGLSPTHLEKFYEEYGGVSTVTIQSAFRYDYPQNIVKEAIKSINNTLPI 315
                                       *************************************************************************8888 PP

                                       ------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS---S-B----------EEE--HE---HHHHHHHHH CS
                         PEPcase_2 304 kprelseeeeelllevieklseaYqekiekladvinevaklipkrRaRklhiglfgYsReieevelPRAIsftgalY 380
                                       ++r +  e+ e++l+vi+k s+aY++  e  a+ i++v+ l p rR+Rklh+g f YsR +++velPRAI +  ++Y
  gi|557695133|ref|YP_008798187.1| 316 EKRSTIIESVETVLKVIAKGSQAYRAFAEVAAPSIARVSALTPARRRRKLHVGAFAYSRVLGGVELPRAIPYACSFY 392
                                       88888888889****************************************************************** PP

                                       HTT--GGGTTHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHTT--SS............TTTTTS-HHHHHHHHHHHH CS
                         PEPcase_2 381 siGlPpellgissllelaeeelevllevykalkedlaeaarylnle............ksklkldeetvkkikedle 445
                                       ++GlPpe +g++ l +l+eee +vl+e+y +l edl+  a  ++ +            k++l+  +e++  + edle
  gi|557695133|ref|YP_008798187.1| 393 TLGLPPEFIGLRFLYQLSEEEFDVLKEFY-NLAEDLRRVAPLVCFDnintllseeskdKHELQPLREALPLYVEDLE 468
                                       **************************999.5899****999999998999999888776777777888999999*** PP

                                       HHHHHTT--.....HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-- CS
                         PEPcase_2 446 iveeildlk.....yeeeeheeltsellkalkekkdeelkelilemaklRkflG 494
                                       ++++ l++k     ++e++ +++ +++l a  e++ ee++  +l++a +R+ lG
  gi|557695133|ref|YP_008798187.1| 469 AAQDLLNIKpgpktSSERKYSNILNNFLIAYMEENLEEARLELLRAAGIRRCLG 522
                                       ********998776566666677777777788888888**************99 PP

>> UPF0147  Uncharacterised protein family (UPF0147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.6   9.6e+03      49      62 ..     154     168 ..     152     170 .. 0.70
   2 ?   10.2   0.0    0.0001      0.62      20      67 ..     209     256 ..     193     260 .. 0.90
   3 ?   -1.4   0.1      0.42   2.5e+03      22      47 ..     298     324 ..     295     333 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.6
                                       HHHHHHHHHHT-.TT CS
                           UPF0147  49 taisiLdeisnD.pn 62 
                                       +a+  L+ei+ D pn
  gi|557695133|ref|YP_008798187.1| 154 KAVVQLEEIVIDyPN 168
                                       578888888866455 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0001
                                       TS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHH CS
                           UPF0147  20 svPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlha 67 
                                       + Pr +R  +  +  +L++   + ++ a  ai  L ++s +  +P+h+
  gi|557695133|ref|YP_008798187.1| 209 TSPRYVRAFIARSDPALNNGLVAATLMAKLAIDKLQNLSTNTGIPVHT 256
                                       459********************************************7 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.42
                                       -HHH.HHHHHHHHHHHT-TTS-HHHHH CS
                           UPF0147  22 Prni.RraakeakekLkdekeslavra 47 
                                       P+ni + a+k ++++L  ek+s  + +
  gi|557695133|ref|YP_008798187.1| 298 PQNIvKEAIKSINNTLPIEKRSTIIES 324
                                       777624456667777777777766655 PP

>> PEPcase  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   3.6e-05      0.22     400     495 ..     181     268 ..     167     392 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 3.6e-05
                                       S---EEEEE-SHHHHHHHHHHHHHHHHSHHHHHHTTT...EEEEEE-HHHHHHHH-HHHHHHHHHHHHHHHHHHHHH CS
                           PEPcase 400 aelrvvPLfEtvedLknapevleellslplyrelvkksgelqevMlGYSDSnKdaGfltsnWelykaqealvkvaee 476
                                       ++++v+PLfE ++ + na+++l ++++l+  r  v++        +  SD + + G+++++     a ++l+++ ++
  gi|557695133|ref|YP_008798187.1| 181 EKIEVIPLFEDLDSMLNADTILGRFIELTSPRY-VRA-------FIARSDPALNNGLVAATLMAKLAIDKLQNLSTN 249
                                       689*********************999876553.333.......466688888888888888888888888888888 PP

                                       HT-EEEEEE-SSTGGGS-H CS
                           PEPcase 477 agvklrlFHGrGGsvgRGG 495
                                       +g+ ++   G G    RGG
  gi|557695133|ref|YP_008798187.1| 250 TGIPVHTIIGVGTLPFRGG 268
                                       8888777777776666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); 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: 00:00:00.43
# Mc/sec: 3651.88
//
Query:       gi|557695134|ref|YP_008798188.1|  [L=324]
Description: simple sugar ABC transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for 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  114.2  37.7      8e-33  113.7  37.7    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 !  113.7  37.7   4.4e-37     8e-33       4     252 ..      11     280 ..       8     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: 113.7 bits;  conditional E-value: 4.4e-37
                      BPD_transp_2   4 nlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsllllallvallvgaavglllgllvlrl 80 
                                         +++++++++a+lG ++   +aGv+nlg +g+m++Ga ++ +  ++l+    +a++  llvgaa+gl+ +l ++ l
  gi|557695134|ref|YP_008798188.1|  11 GAVASGTVFLLASLGETVAE-RAGVLNLGMEGMMIMGASLSYIFTNALGH--GWAIATVLLVGAALGLMHALFTVSL 84 
                                       56788999************.****************************6..8999********************* PP

                      BPD_transp_2  81 kvdeliitllllsvlvgltlllltgitsgvkgqs...svkellgfagallsflsaviv................... 135
                                       ++++++++l+++++ +gl  ll  + ++g    +   + ++++  +++ +      i                    
  gi|557695134|ref|YP_008798188.1|  85 RLNQVVVGLAFTVLGLGLSGLLASNEIRGRIILAlnpEASPAVIASQEAAKLPPIPIPglvnipiigpmifshnilv 161
                                       ********************9999999998777633322223333333333333333377999************99 PP

                      BPD_transp_2 136 llalllvlavllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallalllgsipp.nigvg 211
                                       ++ l+l+ +++++l +t+fG+ lr vgen+++a+alG+nv+ ++ +++ i gal+ laGa l   ++  ++  + +g
  gi|557695134|ref|YP_008798188.1| 162 YISLILAGVLWFILFKTSFGLSLRSVGENPSMADALGVNVFLIRYIAMTICGALGSLAGAYLFIGYQPFWVeGMTQG 238
                                       999999*********************************************************************** PP

                      BPD_transp_2 212 lgfnaiaavvlGgagsllgtviGaliigvvksllltllgi..p 252
                                        gf a+a v+l+ + ++l +++Ga+++g v++l   l  +  +
  gi|557695134|ref|YP_008798188.1| 239 RGFIALALVILATW-NPLRAILGAYLFGGVEALQFRLQLVgvA 280
                                       **************.****************965555444331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); 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):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2608.51
//
Query:       gi|557695135|ref|YP_008798189.1|  [L=354]
Description: simple sugar transporter permease [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  109.4  30.9    1.6e-31  109.4  30.9    1.5  2  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 ?   -3.2   0.4       0.2   3.6e+03      60      73 ..      25      31 ..      11      47 .. 0.46
   2 !  109.4  30.9   9.2e-36   1.6e-31       3     264 ..      60     339 ..      58     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.2
                      BPD_transp_2 60 lvallvgaavglll 73
                                      ++++lv        
  gi|557695135|ref|YP_008798189.1| 25 AASFLV-------A 31
                                      111111.......1 PP

  == domain 2  score: 109.4 bits;  conditional E-value: 9.2e-36
                      BPD_transp_2   3 lnlltlaailaiaAlGlalvfgiaGvinlghggfmalGayvaalllalllsl........lllallvallvgaavgl 71 
                                       l+ + ++++l++aAlGl++ f +++ +n+g++g++ lG+++a+ ++ l            l+l+++ ++l+g++  +
  gi|557695135|ref|YP_008798189.1|  60 LEAALRGLPLGFAALGLTVAF-KMNFWNIGAEGQIYLGMVAATGVVLLHVYYglvpdflvLPLMVVSSFLAGGLYCA 135
                                       56678899*************.****************66555555554444699********************** PP

                      BPD_transp_2  72 llgllvlrlkvdeliitllllsvlvgltlllltgitsgvkgqssvkellgfagallsflsaviv....llalllvla 144
                                       l ++l+++l+v+e++ tl+l++v++ ++++l +g+++++kg   +  +++ ++a l ++ ++ +      a++++ +
  gi|557695135|ref|YP_008798189.1| 136 LPAFLKAKLGVNEILPTLMLNYVAYHFVNYLIHGPWRDPKGFGFPLSIVFPPYARLDTILGHTAyvgvPAAFIIAGL 212
                                       **********************************************9999999999999999997776566666667 PP

                      BPD_transp_2 145 vllllrrtrfGralravgeneeaaralGinvkrvklltfvisgalAglaGallall.lgsipp.nigvglgfnaiaa 219
                                       ++ ++++t+ G+ +r++g+n eaar++G++++r+ ll  +i+g+lAgl G+ +++  lg   p ++ vg+g++ai++
  gi|557695135|ref|YP_008798189.1| 213 LYGFMLYTPAGFEMRVLGQNYEAARYAGVRIGRTLLLGSLIAGGLAGLGGLSIVAGiLGRMRPpSAYVGYGYTAIII 289
                                       888999*********************************************9987514555557************* PP

                      BPD_transp_2 220 vvlGgagsllgtviGaliigvvksllltllgi.......ptelarvllgall 264
                                       ++l+ + ++  +v +a+ +g +   ++ ++++       + +  ++ +++++
  gi|557695135|ref|YP_008798189.1| 290 AFLAAL-NPWLAVPAAIFFGGLLV-AGDVIQAtlnlpfpAIQILQATIFLMI 339
                                       ******.*************9999.666666656664432333333444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); 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: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2829.76
//
Query:       gi|557695136|ref|YP_008798190.1|  [L=510]
Description: simple sugar transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-51  174.7   0.0    2.7e-31  108.9   0.0    2.2  2  ABC_tran     ABC transporter
    4.2e-08   33.3   0.0     0.0031   17.4   0.0    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.7e-05   23.4   0.5      0.012   15.5   0.0    3.1  3  RsgA_GTPase  RsgA GTPase
     0.0001   22.0   0.0     0.0045   16.7   0.0    2.7  3  AAA_29       P-loop containing region of AAA domain
     0.0023   17.4   0.9        1.7    8.0   0.1    2.6  3  SMC_N        RecF/RecN/SMC N terminal domain
  ------ inclusion threshold ------
      0.012   16.2   0.0      0.034   14.6   0.0    1.7  1  AAA_23       AAA domain
      0.047   13.8   0.1        0.5   10.5   0.0    2.6  2  MMR_HSR1     50S ribosome-binding GTPase
      0.059   13.7   0.3        1.3    9.4   0.0    2.7  2  AAA_16       AAA ATPase domain
      0.098   12.9   0.9         14    5.9   0.0    3.3  4  AAA_22       AAA domain
       0.14   11.8   0.0       0.26   10.8   0.0    1.4  1  AAA_27       AAA domain
       0.21   11.3   1.0       0.87    9.3   0.0    2.4  4  AAA_30       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 !  108.9   0.0   1.6e-34   2.7e-31       2     137 .]      24     171 ..      23     171 .. 0.96
   2 !   63.7   0.0   1.5e-20   2.5e-17       2     123 ..     276     417 ..     275     432 .. 0.89

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 1.6e-34
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvr 77 
                                       +nv+++l++ge++a++GenGaGKStL+++l+g ++p++Gei++ gk+++   ++  l   ig+++q+ +l p +tv+
  gi|557695136|ref|YP_008798190.1|  24 DNVNFTLRPGEVHALLGENGAGKSTLMNILYGIYRPDAGEIWVYGKKVDIrGPRDALTLGIGMVHQQFKLIPVHTVA 100
                                       79******************************************999998889************************ PP

                                       HH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       en               + ++e++++++++g +  ++ +v     +LS G+kq v+l +al +k ++l+lDEpt+
  gi|557695136|ref|YP_008798190.1| 101 ENvilglrelgfvinerKINNELTQLIQTYGWTISPNARV----WQLSAGEKQQVELLKALYRKVRILILDEPTS 171
                                       *************998888888999999999999999998....*****************************96 PP

  == domain 2  score: 63.7 bits;  conditional E-value: 1.5e-20
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS..--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe..pqlfpelt 75 
                                       +nvs+kl++ge+++i G +G G + Ll++lagl k   G+++ldg d+++ ++ e+ ++ ++++p e      pe+t
  gi|557695136|ref|YP_008798190.1| 276 RNVSFKLYRGEILGIAGVSGNGQTELLEALAGLRKIVRGKVWLDGVDITNrHPQEIIDAGVSYIPAEalRYSAPEMT 352
                                       79***********************************************9899**************888899**** PP

                                       HHHH....................HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHH CS
                                       xxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren....................esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalaral 123
                                       v+en                    + + ++e++++ ++++     +++++ ++LSgG  qr++lar l
  gi|557695136|ref|YP_008798190.1| 353 VAENlvlkayrnhlfgnrflirwrDVNLKAEELVKAFRIVT---PTISNKVANLSGGNIQRLVLAREL 417
                                       **********9999999999985544455999999999988...44557779*************976 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 !   17.4   0.0   1.9e-06    0.0031       2      67 ..      36      89 ..      35      92 .. 0.77
   2 !   13.8   0.0   2.4e-05     0.039     234     298 ..     140     201 ..     114     205 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.9e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieefls 67
                                       +l G Ng+GKS+L+ +l+++ r            ++ g+i+++ ++ d + p+ + +++i  +++
  gi|557695136|ref|YP_008798190.1| 36 HALLGENGAGKSTLMNILYGIYR------------PDAGEIWVYGKKVDIRGPRDALTLGIGMVHQ 89
                                      689*****************976............6677777777777777777777777666655 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.4e-05
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                                       +++lS G k+   ll al+r     ++l++DEp + L P+    l++ l++ ++ g  v+l TH 
  gi|557695136|ref|YP_008798190.1| 140 VWQLSAGEKQQVELLKALYRKV---RILILDEPTSVLTPQESVALFQTLRKMATQGLGVVLITHK 201
                                       7899****************88...************************666666*********5 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   7.6e-06     0.012      92     121 ..      25      55 ..      14      69 .. 0.82
   2 ?    4.4   0.1     0.019        31      87     123 ..     272     309 ..     226     318 .. 0.76
   3 ?   -2.3   0.0       2.3   3.7e+03      57      85 ..     436     463 ..     407     477 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.6e-06
                                       HHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  92 elkellkd.ktsvlvGqSGvGKStLinallp 121
                                       +++  l+  ++ +l+G+ G+GKStL+n l +
  gi|557695136|ref|YP_008798190.1|  25 NVNFTLRPgEVHALLGENGAGKSTLMNILYG 55 
                                       566677766999***************9987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.019
                                       HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinallpel 123
                                        e++++++ +l   ++  ++G SG G + L++al++  
  gi|557695136|ref|YP_008798190.1| 272 LEAVRNVSFKLYRgEILGIAGVSGNGQTELLEALAGLR 309
                                       36677777777655999****************99854 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.3
                                       GG--HHHHHHHHHHHHHHTTSEEEE--TT CS
                       RsgA_GTPase  57 Dlleeeeeleelkeelealgyevllvsak 85 
                                       D++++e+ +++   + ++ g++vllvs++
  gi|557695136|ref|YP_008798190.1| 436 DIASTEQ-IHQELVRRAEKGVAVLLVSEE 463
                                       5556666.666666666677777777665 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 !   16.7   0.0   2.8e-06    0.0045      15      39 ..      26      50 ..      20      59 .. 0.85
   2 ?   -3.7   0.0       6.3     1e+04      38      51 ..     165     178 ..     165     180 .. 0.80
   3 ?    1.8   0.0      0.12     2e+02      18      43 ..     281     306 ..     273     308 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.8e-06
                            AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                                        +++++ +++ l G++G+GKSTl+
  gi|557695136|ref|YP_008798190.1| 26 VNFTLRPGEVHALLGENGAGKSTLM 50
                                      6778888889**************8 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 6.3
                            AAA_29  38 llDAiqalLvpakk 51 
                                       +lD  + +L+p+++
  gi|557695136|ref|YP_008798190.1| 165 ILDEPTSVLTPQES 178
                                       6788899****985 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.12
                            AAA_29  18 eidlkgatlltGpsGsGKSTllDAiq 43 
                                       ++ + ++  ++G sG+G + ll A++
  gi|557695136|ref|YP_008798190.1| 281 KLYRGEILGIAGVSGNGQTELLEALA 306
                                       5554447779************9986 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 !    8.0   0.1     0.001       1.7      25      42 ..      34      51 ..      13      56 .. 0.75
   2 !    7.3   0.0    0.0018       2.9     113     213 ..     114     217 ..      98     224 .. 0.76
   3 ?   -3.0   0.0       2.4     4e+03      27      44 ..     288     305 ..     281     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.001
                                      SEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlld 42
                                      ++ a++G+NG+GKs l++
  gi|557695136|ref|YP_008798190.1| 34 EVHALLGENGAGKSTLMN 51
                                      5789**********9986 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0018
                                       ETTEEE-HHHHHHHHHCTT-STT......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 113 ingkevtkkevsellesagiske......lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaell 183
                                       in+++++ +e+++l+++ g +++      +LS Gek+   + Ll A+  +++  + +lDe  + L  ++  ++ + l
  gi|557695136|ref|YP_008798190.1| 114 INERKIN-NELTQLIQTYGWTISpnarvwQLSAGEKQQ--VELLKAL--YRKVRILILDEPTSVLTPQESVALFQTL 185
                                       5555543.56777777766666677888899****985..5677666..677889********************** PP

                                       HHHCTT.SEEEEE-SS.HHHCCC-SCEEEEEE CS
                                       xxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxx RF
                             SMC_N 184 kekskn.aQfivislr.eemlekadklvgvtk 213
                                       ++  ++   ++ i+++ ee+++ ad++  ++ 
  gi|557695136|ref|YP_008798190.1| 186 RKMATQgLGVVLITHKlEEVFNVADRVTVMRA 217
                                       98876668899999985678888888876665 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.4
                                       EEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAi 44 
                                         i G  G G + ll+A+
  gi|557695136|ref|YP_008798190.1| 288 LGIAGVSGNGQTELLEAL 305
                                       569999**********98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.1e-05     0.034      13      38 ..      26      52 ..      14      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                            AAA_23 13 qeidFsk.gltlItGpNGaGKTTildA 38
                                      +++ + +  + ++ G+NGaGK+T+++ 
  gi|557695136|ref|YP_008798190.1| 26 VNFTLRPgEVHALLGENGAGKSTLMNI 52
                                      4445555258899***********985 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00031       0.5       3      21 ..      37      55 ..      35      74 .. 0.88
   2 ?   -0.5   0.0      0.79   1.3e+03       3      26 ..     289     312 ..     287     326 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                                      EEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1  3 aivGrpNvGKStLinaltg 21
                                      a++G   +GKStL+n l g
  gi|557695136|ref|YP_008798190.1| 37 ALLGENGAGKSTLMNILYG 55
                                      799************9976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.79
                                       EEEESTTSSHHHHHHHHHTSTEEE CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltgekaiv 26 
                                       +i+G +  G + L+ al g + iv
  gi|557695136|ref|YP_008798190.1| 289 GIAGVSGNGQTELLEALAGLRKIV 312
                                       899**************9987776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00081       1.3      25      63 ..      34      73 ..      24     198 .. 0.75
   2 ?    1.7   0.1      0.18   2.9e+02      24      45 ..     285     306 ..     272     472 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00081
                            AAA_16 25 elvllsGesGvGKsslvrellralekd.ggiflrgkcdql 63
                                      e+  l Ge G GKs+l++ l+  ++ d g i+++gk ++ 
  gi|557695136|ref|YP_008798190.1| 34 EVHALLGENGAGKSTLMNILYGIYRPDaGEIWVYGKKVDI 73
                                      556799*************998888885456677777766 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.18
                            AAA_16  24 pelvllsGesGvGKsslvrell 45 
                                       +e++ + G sG G + l+++l+
  gi|557695136|ref|YP_008798190.1| 285 GEILGIAGVSGNGQTELLEALA 306
                                       4778889999999999998887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0087        14       9      24 ..      37      52 ..      31      64 .. 0.87
   2 ?    3.1   0.0     0.065   1.1e+02      86     128 ..     154     198 ..     137     206 .. 0.70
   3 ?   -1.8   0.0       2.1   3.4e+03       7      27 ..     287     307 ..     283     325 .. 0.84
   4 ?   -1.1   0.0       1.3   2.1e+03      80     104 ..     441     468 ..     375     479 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0087
                            AAA_22  9 vvtGesGtGKTtllrr 24
                                      ++ Ge G+GK+tl++ 
  gi|557695136|ref|YP_008798190.1| 37 ALLGENGAGKSTLMNI 52
                                      688**********975 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.065
                            AAA_22  86 lrarav.ielliiDEaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                       l+a ++ +++li+DE    l+   s +++++Lr+++    +g+ ++L+
  gi|557695136|ref|YP_008798190.1| 154 LKALYRkVRILILDEPTSvLTpqeSVALFQTLRKMAT---QGLGVVLI 198
                                       444444568*********6655444666666666655...88888887 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.1
                            AAA_22   7 ilvvtGesGtGKTtllrrlle 27 
                                       il + G sG G T ll+ l+ 
  gi|557695136|ref|YP_008798190.1| 287 ILGIAGVSGNGQTELLEALAG 307
                                       666889999999999998875 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 1.3
                            AAA_22  80 ealeqalrarav...ielliiDEaqhlr 104
                                       e+++q l +ra     +ll+ +E + l+
  gi|557695136|ref|YP_008798190.1| 441 EQIHQELVRRAEkgvAVLLVSEELEELI 468
                                       5666666666666655666667776664 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   0.00016      0.26      16      51 ..      23      54 ..      19      67 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                            AAA_27 16 drsldfsaeeadlhliyGpNEAGKstalrAisdllf 51
                                      + +++f     ++h ++G N AGKst+++    +l+
  gi|557695136|ref|YP_008798190.1| 23 NDNVNFTLRPGEVHALLGENGAGKSTLMN----ILY 54
                                      567888888999**************986....444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00053      0.87      17      50 ..      32      65 ..      25      75 .. 0.82
   2 ?   -2.5   0.0       2.1   3.5e+03      87     109 ..     158     182 ..     121     199 .. 0.59
   3 ?   -2.0   0.0       1.6   2.6e+03      21      41 ..     288     308 ..     282     318 .. 0.78
   4 ?   -4.0   0.1       6.3     1e+04     106     122 ..     445     460 ..     438     461 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00053
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrvi 50
                                      +  v++l G  G+GK+t+++ l  +++ + g++ 
  gi|557695136|ref|YP_008798190.1| 32 PGEVHALLGENGAGKSTLMNILYGIYRPDAGEIW 65
                                      556999**************99999988766665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.1
                            AAA_30  87 epg.tllivDEagmv.....dtkqlaall 109
                                        ++ ++li DE   v     +     al+
  gi|557695136|ref|YP_008798190.1| 158 YRKvRILILDEPTSVltpqeS----VALF 182
                                       334478888886666333322....3333 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.6
                            AAA_30  21 avltGpAGtGKttalkalrea 41 
                                         + G+ G G t +l+al+ +
  gi|557695136|ref|YP_008798190.1| 288 LGIAGVSGNGQTELLEALAGL 308
                                       568899999999999998765 PP

  == domain 4  score: -4.0 bits;  conditional E-value: 6.3
                            AAA_30 106 aallkaaekagakvilv 122
                                       ++l+++aek g+ v+lv
  gi|557695136|ref|YP_008798190.1| 445 QELVRRAEK-GVAVLLV 460
                                       578999988.8888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.53
# Mc/sec: 2880.31
//
Query:       gi|557695137|ref|YP_008798191.1|  [L=449]
Description: simple sugar ABC transporter substrate-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  113.6   0.4    8.3e-33  113.6   0.4    1.3  2  Bmp              ABC transporter substrate-binding protein Pn
     0.0012   18.1   1.0     0.0012   18.1   1.0    2.3  2  UCR_Fe-S_N       Ubiquitinol-cytochrome C reductase Fe-S subu
     0.0022   16.8   0.2     0.0043   15.8   0.2    1.4  1  SpoVAD           Stage V sporulation protein AD (SpoVAD)
  ------ inclusion threshold ------
        1.2    9.2   9.5      0.071   13.1   1.1    2.6  2  CytB6-F_Fe-S     Cytochrome B6-F complex Fe-S subunit


Domain annotation for each model (and alignments):
>> Bmp  ABC transporter substrate-binding protein PnrA-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.2       1.2   5.5e+03     130     156 ..      21      47 ..      16      56 .. 0.77
   2 !  113.6   0.4   1.9e-36   8.3e-33       3     252 ..      79     338 ..      77     348 .. 0.90

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.2
                                       EECSS-SCCCHHCHHHHHHHHHHH-TT CS
                               Bmp 130 fvgGveipvvksfingFeaGikyvnpd 156
                                       +vgGv    v   ++g+ +G+ ++ p+
  gi|557695137|ref|YP_008798191.1|  21 AVGGVAAGAVVGGLAGYFLGASQAAPA 47 
                                       577888888888888888888877665 PP

  == domain 2  score: 113.6 bits;  conditional E-value: 1.9e-36
                                       EEEEECSS-TTTSCHHHHHHHHHHHHHHHC.TTEEEEEEEEC.GGGHHHHHHHHHHCTT-SEEEEESCCHHHHHHHH CS
                               Bmp   3 kvavlvegtidDksfnessyeGirrlkkeq.nieliskesslltdedyiadlknlkeegsdlivatgfalqdalqev 78 
                                       kv+ +++g++ D +++  ++eG++ +   + n+++ + es+   +++   +++ l ++g dl+++t+f ++d + ev
  gi|557695137|ref|YP_008798191.1|  79 KVGYIYVGPVGDYGWTFAHNEGRKFADAAYkNVDSFYIESVP--EAQSAGAIESLINQGADLVITTSFGYMDSTAEV 153
                                       78999*************************************..7999***************************** PP

                                       HHH-TTS-EEEESS--TT-S....TTEEEEEE-HHHHHHHHHHHHHHHHHCTTTTEECSS-SCCCHHCHHHHHHHHH CS
                               Bmp  79 ssdfpkvkFliiDavvekey....knvlsvaFrseegaFLaGvaaAlmsktnkigfvgGveipvvksfingFeaGik 151
                                       ++++p+ +F++i+++ +       +n++s++   ++  +L G+aa+++++t+  g+v++ +ip+v + in+F +G+ 
  gi|557695137|ref|YP_008798191.1| 154 AAKYPDKYFVHISGYRSGAAgnapQNMSSAFAEFYQLYYLNGLAAGAVTQTGVVGYVAAFPIPEVVRHINAFVLGAN 230
                                       ****************99999999****************************************************9 PP

                                       HH.....-TT-EEEEEE-SSSS-HHHHHHHHHHHHH.CT--EEEEE-GGGHHHHHHHHHHHCHCT....EEEEEES- CS
                               Bmp 152 yv.....npdievvvkvagtfsDakkgkslAsslyk.egvdvifpaagkagkgvieaakelglsn....yvIgvdkd 218
                                       y+     + +i+ +v+++  + D+ k++++A  l++ + +dv +     + +  ++ a+e   ++    ++    +d
  gi|557695137|ref|YP_008798191.1| 231 YAykkrtGRNIKAYVSWLFAWFDPGKAREAAVALIEqSNADVLAF--TEDTPTTLQVAEEYTTQKgrrvWSFSHYND 305
                                       9633333778**************************9******99..4444555555555444444456******** PP

                                       -CGCSTTCCEEEEEEEHHHHHHHHHHHHHCCT-- CS
                               Bmp 219 qsylapenvitsiiknvedlvvsiiekvakgevl 252
                                       +s  +p++++t  i+n++ ++  +   va g+ +
  gi|557695137|ref|YP_008798191.1| 306 MSSYGPNAHLTGQIVNWGPIYLDFYRMVATGT-W 338
                                       *******************9999998888887.4 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   1.0   2.7e-07    0.0012       7      31 ..       6      31 ..       1      34 [. 0.82
   2 ?   -4.9   3.4         4   1.8e+04      19      25 ..     204     210 ..     196     213 .. 0.43

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.7e-07
                        UCR_Fe-S_N  7 deptRRDFLyiATg.avgaVGaaaaa 31
                                         +RR FL + Tg avg+V+a+a++
  gi|557695137|ref|YP_008798191.1|  6 SRISRRKFLAVSTGaAVGGVAAGAVV 31
                                      5679*********7358999999987 PP

  == domain 2  score: -4.9 bits;  conditional E-value: 4
                        UCR_Fe-S_N  19 TgavgaV 25 
                                       Tg+vg V
  gi|557695137|ref|YP_008798191.1| 204 TGVVGYV 210
                                       3333333 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 !   15.8   0.2   9.6e-07    0.0043     157     213 ..      56     115 ..      44     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.6e-07
                                       --EE--EEEEEEEE...SS--SEEEEEEE----B-S----TT-HHHHHHHHHHHHHHHHH CS
                            SpoVAD 157 aqwtvtgagavlla...kegegpkitavtiGkvvDlglkdplnmGaamapaavdtieahl 213
                                        + tvtg ga++ +     +++ k+ ++ +G v D+g + ++n G   a aa + + +++
  gi|557695137|ref|YP_008798191.1|  56 VTRTVTGPGATVTTtvqAPAKRLKVGYIYVGPVGDYGWTFAHNEGRKFADAAYKNVDSFY 115
                                       4679******9976221455689*****************************99988766 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 ?   13.1   1.1   1.6e-05     0.071       7      36 ..       9      39 ..       7      42 .. 0.81
   2 ?   -0.7   1.9      0.34   1.5e+03      18      37 ..     197     216 ..     193     216 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                      CytB6-F_Fe-S  7 srRqllNlllvGaialtaaaaLyP.vvkFFi 36
                                      srR +l   +++a++++aa+a+++  + +F+
  gi|557695137|ref|YP_008798191.1|  9 SRRKFLAVSTGAAVGGVAAGAVVGgLAGYFL 39
                                      8****************99998752555665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.34
                      CytB6-F_Fe-S  18 GaialtaaaaLyPvvkFFiP 37 
                                       +a+a+t ++ +  v++F iP
  gi|557695137|ref|YP_008798191.1| 197 AAGAVTQTGVVGYVAAFPIP 216
                                       66677777766666667665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3150.71
//
Query:       gi|557695138|ref|YP_008798192.1|  [L=596]
Description: adenine deaminase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-65  217.7   0.0    1.1e-64  216.9   0.0    1.4  1  Adenine_deam_C  Adenine deaminase C-terminal domain
      7e-24   84.8   0.1    6.8e-22   78.2   0.1    2.2  1  Amidohydro_1    Amidohydrolase family
    5.3e-13   49.2   0.7      3e-06   27.0   0.0    2.5  2  Amidohydro_3    Amidohydrolase family


Domain annotation for each model (and alignments):
>> Adenine_deam_C  Adenine deaminase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.9   0.0   1.8e-68   1.1e-64       2     169 .]     422     589 ..     421     589 .. 0.99

  Alignments for each domain:
  == domain 1  score: 216.9 bits;  conditional E-value: 1.8e-68
                                       SS-EEEEEEEEEETTEEE-..-TTEEEEEEE--SSSS--EEEEEEESS--BSSEEEES--TTT--EEEEESSHHHHH CS
                    Adenine_deam_C   2 liTkelevelpvkdgvvvadlekdllkiavveRhgktgnvgvgfvkgfglkkgAiAssvahDshniivvGtndedma 78 
                                       +iTk+++++l v++g+v++d+++ + kiavveRhgk+g +++gf  gfg++kgA+As+vahDshn++v+G +++dma
  gi|557695138|ref|YP_008798192.1| 422 VITKHRIERLMVENGEVKPDPDRSIFKIAVVERHGKHGGMSTGFAAGFGFRKGAVASTVAHDSHNLLVIGFDEKDMA 498
                                       89*************************************************************************** PP

                                       HHHHHHHHTTSEEEEEETTEEEEEEE-TBTTTBBSS-HHHHHHHHHHHHHHHHTTS-TTTBSGGGGGSTT-TTSSSE CS
                    Adenine_deam_C  79 lAvnrvielgGGivvvedgkvlaelpLpiaGlmSdepaeevaekleeleaalkelgvkledpfmtlsflalpviPel 155
                                       +A+n+ ++++GGiv v+dg+vla ++Lp+aGlmS epae vaekl++  ++ ++lg++  +pfmtls+l+l+viPel
  gi|557695138|ref|YP_008798192.1| 499 VAANENARINGGIVTVADGEVLARVELPLAGLMSPEPAEVVAEKLNKTYEVWRRLGCEWVSPFMTLSLLSLSVIPEL 575
                                       ***************************************************************************** PP

                                       EEETTSEEETTTTE CS
                    Adenine_deam_C 156 kltdkGlvdvkkfe 169
                                       ++tdkGl+d+ +f+
  gi|557695138|ref|YP_008798192.1| 576 RITDKGLLDTVTFQ 589
                                       *********99885 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.1   1.1e-25   6.8e-22       1     344 []      78     365 ..      78     365 .. 0.80

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 1.1e-25
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEE CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplgl 77 
                                       +++PGl D HvH+e+s++            ++a+  l +g+++ + +++++ + +g     g+++++e++++lpl++
  gi|557695138|ref|YP_008798192.1|  78 FLVPGLLDPHVHVESSMV---------SVTQFARIILPHGTTAVFIDPHEIGNVFGLD---GVKLMIEESRNLPLKV 142
                                       689***********9988.........999***************************7...**************** PP

                                       EEEEESSEGGS..GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEE CS
                      Amidohydro_1  78 rilggkvsldr..gsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkealkeakkrdlpvaiH 151
                                       ++  ++++++   +++     + e++++ +      k d+v+   +++  + + + de +++ + e  k+++ v  H
  gi|557695138|ref|YP_008798192.1| 143 YVTYPSCVPAApgYETAGAVVTPEEVAEAM------KLDEVIAlGEMMNFPGVLAADEKVHAEIAETLKAGKLVEGH 213
                                       **********98866666666666665555......577888889999999999999999999999999******** PP

                                       E..TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEE.HHHHHHHHHHHHHHCEEHHHHHHHHS CS
                      Amidohydro_1 152 a..letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhlt.pteaellkerlkeagvahcpfsnsil 225
                                          l  ++  +++ a++ +t+e+ t +  +e           l  g+++   + +++l+ +     v        + 
  gi|557695138|ref|YP_008798192.1| 214 DsgLLGRELSAYVAAGILSTHESVTKQQTLER----------LRNGMYVYlREGSAWLDIK---ETVR------AYT 271
                                       96545555666666666666666666666555..........9999999974433333322...1111......345 PP

                                       EHHHHHHHHHHHHTSC..EEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-T CS
                      Amidohydro_1 226 rsgrealrkaldeGvk..vglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrmaTingAkalgld 300
                                       ++g+++   +l  + k   ++  D  ++ + +     +r a+           + g++++ a++maT+n+A+ ++l+
  gi|557695138|ref|YP_008798192.1| 272 ETGIDPRHICLCTDDKepASILRD--GHVDHC-----VRRAI-----------QEGVDPLTAIQMATLNPAERYRLS 330
                                       555555555554433334444444..666677.....99999...........899********************* PP

                                       TTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 301 dkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkGklv 344
                                       +++Gsi +G+ AD+ +v          +   + v +v+ +G+lv
  gi|557695138|ref|YP_008798192.1| 331 HELGSISPGRVADILLV---------SDLARFRVETVFADGELV 365
                                       *****************.........88888**********987 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   6.7e-08    0.0004       2      29 ..      71      99 ..      70     111 .. 0.84
   2 !   27.0   0.0   5.1e-10     3e-06     402     459 ..     304     360 ..     289     373 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.7e-08
                      Amidohydro_3  2 viDakGrlvlPGFvDsHtHlagggvnl.r 29
                                      v+Da+G++++PG+ D+H H+ +  v + +
  gi|557695138|ref|YP_008798192.1| 71 VVDASGKFLVPGLLDPHVHVESSMVSVtQ 99
                                      8******************8777766644 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 5.1e-10
                      Amidohydro_3 402 lrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelae 459
                                       + + e ++  +a+++ T +pA++++l+++ G++ +G  AD+ + + d++++  ++++ 
  gi|557695138|ref|YP_008798192.1| 304 RAIQEGVDPLTAIQMATLNPAERYRLSHELGSISPGRVADILLVS-DLARFRVETVFA 360
                                       567899999*********************************996.777777665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); 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 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 4243.88
//
Query:       gi|557695139|ref|YP_008798193.1|  [L=335]
Description: F420-dependent N5,N10-methenyltetrahydromethanopterin reductase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  228.3   0.9    1.8e-67  228.0   0.9    1.0  1  Bac_luciferase  Luciferase-like monooxygenase
  ------ inclusion threshold ------
      0.081   12.9   0.0       0.17   11.9   0.0    1.5  1  DUF179          Uncharacterized ACR, COG1678


Domain annotation for each model (and alignments):
>> Bac_luciferase  Luciferase-like monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.0   0.9     2e-71   1.8e-67      20     313 ..      14     314 ..       2     315 .. 0.88

  Alignments for each domain:
  == domain 1  score: 228.0 bits;  conditional E-value: 2e-71
                    Bac_luciferase  20 aslrylvelaraaEelGfdavwvaehhggpggaldaftllaalaaaTerirlgtavtplytrhPavlAqqaatLdhl 96 
                                       + +r++v++a+ aE++Gfd++w+ae+ +     +da+t+++a+a +T+ri++g++v +++tr+ a++Aq++at+d+l
  gi|557695139|ref|YP_008798193.1|  14 MHVRDMVRHAQFAEQHGFDSAWIAESRLA----RDALTPMTAIATVTSRIKVGAGVINTWTRNAALIAQTFATMDEL 86 
                                       6899************************9....******************************************** PP

                    Bac_luciferase  97 sgGRfglglgtggpaveerrfGvdhderyarlrEfvevlrrlwrgeevdfeGeffsvkgalllprpgqgp....iPv 169
                                       s+GR+ lglg+++++    + G+++ e++  +rE+v+v+rrl+r eev+feG+f++++g++l    g g+    iP+
  gi|557695139|ref|YP_008798193.1|  87 SDGRVMLGLGAWWDPLA-WKVGIERKEPLTCMREYVTVIRRLFRMEEVTFEGKFVKMRGVRLDVLHGAGEkprnIPI 162
                                       ****************9.777**********************99*********99944444444433334477*** PP

                    Bac_luciferase 170 yvaaaspaglelaarhadglllag.eppeeaaelierlragaaeagrdpadirvgisltvivadteeeAraearali 245
                                       y++a++ +++ela++++dg+ll+   +p+    ++e++raga++agr+ +di+    + +++ +++++A + a++++
  gi|557695139|ref|YP_008798193.1| 163 YIGATGWKMMELAGEIGDGVLLNYlVSPKYNDTALEHIRAGASKAGRRLEDIDRPQLIACSMHPDADKAIKLAKKHV 239
                                       *************************************************************************8888 PP

                    Bac_luciferase 246 agld.........fyaldsegagreaeaaeiqeeedanlwagaadavpdelvaatalvGtpeqvaerlaayaeagvd 313
                                         ++          +   se    e +    + + ++++ ++aa+ vpd++v+ +++ Gtp +v++++++y + g +
  gi|557695139|ref|YP_008798193.1| 240 --TMtlgqqphimKASGVSEDLIEEVQKVMGGWPAKPGGIEKAAEIVPDDVVKMITASGTPSDVVAKVKEYMAHGCT 314
                                       ..44468776653333333333333333378****************************************998866 PP

>> DUF179  Uncharacterized ACR, COG1678
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.8e-05      0.17     100     132 ..     150     183 ..     117     201 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.8e-05
                                       H.CSTTSCSSEEEEEEEEEECTTHHHHHHHTTSE CS
                            DUF179 100 l.agkagpeklrvflGyagWeagQLeeEieegaW 132
                                       l   +++p+++ +++G +gW+ ++L  Ei +g  
  gi|557695139|ref|YP_008798193.1| 150 LhGAGEKPRNIPIYIGATGWKMMELAGEIGDGVL 183
                                       3334899**********************99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2634.66
//
Query:       gi|557695140|ref|YP_008798194.1|  [L=410]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-61  207.3   0.0    4.6e-61  207.0   0.0    1.0  1  Amidohydro_1  Amidohydrolase family
    1.4e-18   67.7   0.0    2.2e-12   47.2   0.0    2.4  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
      0.059   12.7   0.0      0.097   12.0   0.0    1.3  1  TatD_DNase    TatD related DNase


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 !  207.0   0.0   7.8e-65   4.6e-61       1     341 [.      59     395 ..      59     397 .. 0.91

  Alignments for each domain:
  == domain 1  score: 207.0 bits;  conditional E-value: 7.8e-65
                                       EEEE-EEEEEEECETTECSSS.....GHHHHH.............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSS CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga.....tledwl.............vppetaaealesgiktalksGtttvadmgatt 59 
                                       +v+PGl++aH+Hl++ +lrga     ++ d+l             ++ e+a++++  +++++  +Gttt+ad++ + 
  gi|557695140|ref|YP_008798194.1|  59 FVMPGLVCAHTHLYGIALRGAslrirPTTDFLenlqriwwplderMDNEDAYATALAACMEMALNGTTTFADTYSAP 135
                                       79************************6666667779***************************************87 PP

                                       TH...HHHHHHHHHHTSSSEEEEEEESSEGGS.GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHH CS
                      Amidohydro_1  60 st...giealleaaeelplglrilggkvsldr.gsaetskasreklkagaaetikgkadgvvkvalapheapafsde 132
                                       ++   +++a+++a+ e+  g+r ++++   +r +++e ++ + e++ +     + + ++g+ k  +  h+ +++sd+
  gi|557695140|ref|YP_008798194.1| 136 PRpegSLDAIAKAVNEV--GIRGVISFEATERrSVEEGRRGLEENI-RF----LSKGGEGLAKGMISLHASFTISDD 205
                                       77**************8..*******88888843333333333333.33....34455566669999********** PP

                                       HHHHHHHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHH CS
                      Amidohydro_1 133 elkealkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellker 209
                                       ++   +++akk ++p++iH++e +++v + ++ +g   ++   +e++ + gll++  ++lah+vhl   e+ ll e 
  gi|557695140|ref|YP_008798194.1| 206 LIVRGVEAAKKFNAPITIHVSEGPNDVYHNIERYG---KR--TVERLRDTGLLGP-SAVLAHCVHLNRREIQLLTET 276
                                       ***********************************...77..99999********.********************* PP

                                       HHHHCEEHHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHH CS
                      Amidohydro_1 210 lkeagvahcpfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkeal 286
                                         +++vah p sn+  + g+++l ++l++Gv+vg+g D    g  ++ +e +  a++++r + ++d+   ls+ ++l
  gi|557695140|ref|YP_008798194.1| 277 --GTSVAHNPMSNMLNAVGVMKLPEMLEAGVNVGIGND----GYIFDGFENMCTAFLIHR-VDRRDPSI-LSPQKVL 345
                                       ..************************************....999999999999999999.77779999.******* PP

                                       HHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSEEEEEEEETT CS
                      Amidohydro_1 287 rmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdgnvkkvivkG 341
                                       +maT ++A+a+gl ++vGs+evGk+AD++vv     +++  +  d+nv +  v+G
  gi|557695140|ref|YP_008798194.1| 346 EMATVDAARAYGL-RDVGSLEVGKKADIIVV----RPEVKATPMDRNVYGYLVNG 395
                                       *************.6****************....*****************999 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.2e-07    0.0013       1      39 [.      51      87 ..      51      96 .. 0.83
   2 !   47.2   0.0   3.6e-16   2.2e-12     328     451 ..     276     381 ..     190     397 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.2e-07
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvt 39
                                      +v D +Gr+v+PG+v +HtHl+g  +  + lr ++   t
  gi|557695140|ref|YP_008798194.1| 51 RVLDVSGRFVMPGLVCAHTHLYGIALRGASLRIRP--TT 87
                                      689********************998777777776..55 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 3.6e-16
                      Amidohydro_3 328 lqvaagvqpvfnfedelldsrlgperargstpvkellnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrp 404
                                        +   +  p++n             +a g+  + e+l+agv+v  g+D  + +fd +  + +a+          +r+
  gi|557695140|ref|YP_008798194.1| 276 TGTSVAHNPMSNM-----------LNAVGVMKLPEMLEAGVNVGIGND--GYIFDGFENMCTAFLIHR----VDRRD 335
                                       4444444444444...........2455668899**************..99*******999996444....68899 PP

                      Amidohydro_3 405 deelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpld 451
                                          ls +++l + T ++A+a+gl+d  G+LevG++AD++v + +  +
  gi|557695140|ref|YP_008798194.1| 336 PSILSPQKVLEMATVDAARAYGLRDV-GSLEVGKKADIIVVRPEVKA 381
                                       999**********************9.*************9855433 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.6e-05     0.097     115     181 ..     209     287 ..     194     302 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHTTEEEEEEEES-HHHHHHHHHHCGGCCS............EEEETT--S-HHHHHHHHHTTEEEEE-GG CS
                        TatD_DNase 115 eqlrlAkelklplviHlrkaeedlleilkeaaeaka............kvvlHsfsgsaeeakkflklgyyislsgl 179
                                       + +++Ak+++ p+ iH  +  +d+++ +++++++ +            +v  H+   +  e++ ++++g +++ + +
  gi|557695140|ref|YP_008798194.1| 209 RGVEAAKKFNAPITIHVSEGPNDVYHNIERYGKRTVerlrdtgllgpsAVLAHCVHLNRREIQLLTETGTSVAHNPM 285
                                       6689***************98888888877666666666666667778999*****999999999999988887766 PP

                                       GG CS
                        TatD_DNase 180 lt 181
                                       ++
  gi|557695140|ref|YP_008798194.1| 286 SN 287
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 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:                        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: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3357.29
//
Query:       gi|557695141|ref|YP_008798195.1|  [L=277]
Description: carbon monoxide dehydrogenase medium subunit [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-32  111.9   0.1    3.7e-32  111.4   0.1    1.1  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
    1.3e-08   34.9   0.0    2.8e-08   33.8   0.0    1.6  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 !  111.4   0.1   4.1e-36   3.7e-32       3     151 ..      12     158 ..      10     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 111.4 bits;  conditional E-value: 4.1e-36
                                       EEEEE-SSHHHHHHHHHHCTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHHHH CS
                     FAD_binding_5   3 feylrpasleealallaaepdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlselaa 79 
                                       +e++ p+s+eeal+ll+++pda ++a gt +++++++++ r +++idi+++ +l++i+++ g   +G++vt++el  
  gi|557695141|ref|YP_008798195.1|  12 IEVMIPSSVEEALNLLQTHPDAEILAAGTHIITQLTLGIKRTRKYIDINNLHQLRKISHHHGTASVGSLVTHQEL-- 86 
                                       67899**********************************************************************.. PP

                                       HHHHHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEE CS
                     FAD_binding_5  80 ealvrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkg 151
                                        a++ +++pa++  l+k  sp++ n+aT+GG+++ +    Dl+p+Ll+ldAe++ ++ eg +++pl+ fl +
  gi|557695141|ref|YP_008798195.1|  87 AATLMNQVPAFTAFLQKYSSPAVANRATVGGSIMLRLAGEDLIPILLTLDAELSFATLEGVKNIPLKAFLAR 158
                                       688889***************************************************************865 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 !   33.8   0.0   3.2e-12   2.8e-08      41     102 ..     213     274 ..     204     275 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 3.2e-12
                                       SSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHHHTCTTC-HHHHHHHHHHHHHHHHHH CS
                     CO_deh_flav_C  41 aptpvraekaeaaLiGkplseelleeaakaleeelspasdprasaeYRrslavsllfrflle 102
                                       ++tp r+ ++e++L    lsee++e+a +++++ ++p+sd+ as  YRr+ a +ll+r l++
  gi|557695141|ref|YP_008798195.1| 213 GSTPGRVAAVEKFLSMHGLSEEVVEKASRLMMDSINPESDVLASSWYRRRAAGVLLKRLLQN 274
                                       57899*****************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2038.05
//
Query:       gi|557695142|ref|YP_008798196.1|  [L=151]
Description: carbon-monoxide dehydrogenase small subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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   77.4   0.0    6.1e-22   77.4   0.0    1.5  2  Fer2_2    [2Fe-2S] binding domain
    1.6e-06   28.0   0.4    1.6e-06   28.0   0.4    2.0  2  Fer2      2Fe-2S iron-sulfur cluster binding domain
     0.0016   18.4   0.0     0.0028   17.7   0.0    1.4  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.029   14.4   0.7      0.052   13.6   0.2    1.9  2  Fer2_4    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 ?   -5.4   1.7         4   1.8e+04      26      30 ..      43      47 ..      39      48 .. 0.72
   2 !   77.4   0.0   1.4e-25   6.1e-22       1      75 [.      73     145 ..      73     146 .. 0.94

  Alignments for each domain:
  == domain 1  score: -5.4 bits;  conditional E-value: 4
                            Fer2_2 26 qCGyC 30
                                       CG C
  gi|557695142|ref|YP_008798196.1| 43 DCGLC 47
                                      69999 PP

  == domain 2  score: 77.4 bits;  conditional E-value: 1.4e-25
                            Fer2_2   1 TveglgeeleelhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                       Tveg+g+  ++lhp+q+af++ ga+qCG+C p  ++ +++l e+n p+ ++ee+r+al+  lCRC++Y ++ +A+
  gi|557695142|ref|YP_008798196.1|  73 TVEGMGDG-SRLHPLQQAFIDVGAVQCGFCIPAALLVLKHLHENN-PDASREEVRHALRSVLCRCGSYLRFEEAF 145
                                       9*****88.78******************************9999.88888*****************9999986 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 !   28.0   0.4   3.5e-10   1.6e-06       2      61 ..       6      53 ..       5      70 .. 0.86
   2 ?    0.3   0.3      0.15   6.8e+02      23      44 ..      86     102 ..      65     135 .. 0.67

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.5e-10
                                      ETTTEEEEEEEETTTHBHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTH CS
                              Fer2  2 tidgkevevevadgettlldaaee.nggidipysCggggCgtClvevlegevqsdeteleg 61
                                      ++++ ++ vev+++e+ l d++++  g + ++ +Cg g Cg C v ++            g
  gi|557695142|ref|YP_008798196.1|  6 MVNDVKYVVEVEPNER-LSDVLRRkLGFVSVKEGCGVGDCGLCIVLID------------G 53
                                      789999**********.******99********************877............3 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.15
                                       HHHTTTTTSTTSSSSSSSSTTE CS
                              Fer2  23 aeenggidipysCggggCgtCl 44 
                                       ++++  id+    g+ +Cg C 
  gi|557695142|ref|YP_008798196.1|  86 LQQA-FIDV----GAVQCGFCI 102
                                       5544.5555....445599996 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 !   17.7   0.0   6.2e-07    0.0028      37      82 ..      24      69 ..       7      91 .. 0.70

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 6.2e-07
                            Fer2_3 37 kikeevdptlafrasCregiCGscavainGkptlaCtatikdlakq 82
                                       + ++    ++ +  C+ g CG c v i+G+p   C     +   +
  gi|557695142|ref|YP_008798196.1| 24 DVLRRKLGFVSVKEGCGVGDCGLCIVLIDGRPVNSCLVLAYQASGH 69
                                      33344556677889**********************8877665544 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 ?   13.6   0.2   1.2e-05     0.052      44      73 ..      37      65 ..       4      76 .. 0.88
   2 ?   -2.3   0.0       1.1   4.7e+03      25      49 ..     112     136 ..     105     137 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                            Fer2_4 44 elcaggeCrnClVevegepnvracstpved 73
                                      e c +g C  C+V ++g+p v++c + +++
  gi|557695142|ref|YP_008798196.1| 37 EGCGVGDCGLCIVLIDGRP-VNSCLVLAYQ 65
                                      56999**************.*****98875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                            Fer2_4  25 llangvdvprsckygrprgelcagg 49 
                                       l +n+ d  r    ++ r  lc  g
  gi|557695142|ref|YP_008798196.1| 112 LHENNPDASREEVRHALRSVLCRCG 136
                                       5666667777777788888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1137.31
//
Query:       gi|557695143|ref|YP_008798197.1|  [L=774]
Description: carbon-monoxide dehydrogenase large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-167  556.1   1.0   1.2e-166  555.5   1.0    1.2  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    3.5e-27   94.9   0.0      8e-27   93.8   0.0    1.7  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 !  555.5   1.0  1.3e-170  1.2e-166       6     550 .]     160     709 ..     157     709 .. 0.96

  Alignments for each domain:
  == domain 1  score: 555.5 bits;  conditional E-value: 1.3e-170
                                       STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHHT CS
                     Ald_Xan_dh_C2   6 pdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevlg 80 
                                       +dnv+   ki+kGdve++f+e+d+v+e+++rt+ ++  +lEt+ a+  + +++g++t  +stq+ + v + v ++lg
  gi|557695143|ref|YP_008798197.1| 160 RDNVVThfKIRKGDVEKGFKESDVVIERTYRTQFITGLPLETEIAYSFL-EDGGRITCIVSTQNLYDVYNKVVKILG 235
                                       56777768899**************************************.88************************* PP

                                       --GGGEEEE-SB-S--TTTTSS--H..HHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EE CS
                     Ald_Xan_dh_C2  81 lpenkvrvivprvGGGFGgKtqsvp..levlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkit 155
                                       +p++k+rvi+   GGGFG K+++ p  ++++a+la++ tg+p    ++R+e m+ ++krhpf+i+  vga++dGk++
  gi|557695143|ref|YP_008798197.1| 236 VPSEKLRVIQAATGGGFGPKSDETPidVAAYACLATYFTGKPALAAFSRSEAMTVQCKRHPFEITNMVGARNDGKLL 312
                                       ********************665551156778999999*************************************** PP

                                       EEEEEEEEEESSTHHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 156 aldvdlladaGayadlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeel 232
                                       a++ +l+ d+Gay + ++ v+ ra++h++gpY++pnv ++g++v tN++ ++  RGfG+pqa fa+E++++elAeel
  gi|557695143|ref|YP_008798197.1| 313 AWRSTLIEDTGAYISKGHLVIGRATFHCTGPYEVPNVWADGYCVLTNNTMAGSTRGFGAPQAHFAAESVLNELAEEL 389
                                       ***************************************************************************** PP

                                       T--HHHHHHHHBCECGCC.SEEETEESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCT..ECEEEEEEEEEEEEBS-- CS
                     Ald_Xan_dh_C2 233 gldplelRrrNlikpgeltpygqpvydsgdlpelldklkessdyeerraeqaefnag..wkkrGiglapvvegiglg 307
                                       gl+ple+R++N+++pg+lt + q+  ++ +l ++++++ e+s++e+r +e++efn++    k+Gig+a+ ++g +lg
  gi|557695143|ref|YP_008798197.1| 390 GLSPLEIREINMLRPGSLTATSQK-IEDDGLLKCYQRAVEESEWEKRVREIQEFNKTnkVLKKGIGIAMLYHGNTLG 465
                                       ******************999999.689***************************8776778************999 PP

                                       S.EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHHH CS
                     Ald_Xan_dh_C2 308 ftakflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstdl 384
                                       ++    + +++   v+ dG+v+v+tg+te G+G+ t+la + ae+Lg+pl++v+++  dt+ vpn+++t+aSr+t++
  gi|557695143|ref|YP_008798197.1| 466 PEG--DDFATVVTYVERDGKVVVQTGLTEYGTGALTSLAIVTAETLGLPLSMVKLERPDTAAVPNAGPTVASRTTVI 540
                                       943..56678999999************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEETEEEECHHHHHHHHHHTTSSEEEEEEE.......EEE CS
                     Ald_Xan_dh_C2 385 ngnAvkkAaeklrerllkiaaellevspedleledgkvvvkeksvslaelaaaaylervslsatgfykt....ldee 457
                                       +g+A+++Aa k+r+ ++++aa++l  +p+dle++dg v +++++v+++e++++++ e++sl   g+y +    +d e
  gi|557695143|ref|YP_008798197.1| 541 GGQAALDAALKIRAMVAQVAAKMLSSNPADLEFRDGLVKANGRAVTWNEVVNQCFEENISLRVVGYYMApptkWDPE 617
                                       *******************************************************************88******** PP

                                       ETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEES CS
                     Ald_Xan_dh_C2 458 tgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqll 534
                                       tg+g p+++++yga vaeV+vDtetg vkv+r+++++DvG++iNp       eGG ++G G+almE++v  +dG ++
  gi|557695143|ref|YP_008798197.1| 618 TGQGAPYNQYTYGALVAEVTVDTETGMVKVDRLTAAYDVGRAINPLGLVAVYEGGSIMGQGYALMEKIVH-DDGVVI 693
                                       ********************************************************************99.5***** PP

                                       S-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 535 tasladYkiPtaadiP 550
                                       + +l++Y iPta+d+P
  gi|557695143|ref|YP_008798197.1| 694 NPNLHTYIIPTASDAP 709
                                       **************98 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 !   93.8   0.0     9e-31     8e-27       2     110 .]      36     141 ..      35     141 .. 0.95

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 9e-31
                                       T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEES CS
                      Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkvr 78 
                                       G+  Y+ D+   ++ly++ vrS+++h++i +id+s+a + +GVv+v+t+ d+p+ n+ + s ++d +  lla +kvr
  gi|557695143|ref|YP_008798197.1|  36 GKPLYTADLVSGKTLYVKAVRSKIPHGYIRKIDTSQAASRQGVVKVLTHRDIPGVNDGG-SLISDRP--LLAFEKVR 109
                                       8999***************************************************9988.5777766..******** PP

                                       STT-EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                      Ald_Xan_dh_C  79 svgqavaavvAedeetArkAaklvkveYeelp 110
                                       +vg+ava+vv e+ e+A++Aa+ v+++Y++lp
  gi|557695143|ref|YP_008798197.1| 110 HVGEAVALVVGESLEAAEEAAEHVEIDYDPLP 141
                                       ****************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (774 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 5166.31
//
Query:       gi|557695144|ref|YP_008798198.1|  [L=98]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-10   40.9   0.0    2.4e-10   40.6   0.0    1.2  1  NTP_transf_2    Nucleotidyltransferase domain
    3.1e-05   24.0   0.0    4.2e-05   23.6   0.0    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0048   17.1   0.0     0.0055   16.9   0.0    1.1  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
      0.013   14.4   0.0      0.016   14.1   0.0    1.1  1  Pox_A51         Poxvirus A51 protein
       0.17   10.9   0.0       0.19   10.7   0.0    1.0  1  DUF3626         Protein of unknown function (DUF3626)


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 !   40.6   0.0   6.6e-14   2.4e-10       5      58 ..      27      75 ..      23      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 6.6e-14
                                      HHHHHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHH CS
                      NTP_transf_2  5 leelkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklae 58
                                       e +++  ++++++l GSyarG+++  SD+Dllvv+p++++ +     l++  +
  gi|557695144|ref|YP_008798198.1| 27 VELVEKIVGPVSAALIGSYARGDFNQWSDVDLLVVSPRFAPTP-----LNRFDQ 75
                                      566788888******************************8744.....333333 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   1.2e-08   4.2e-05       8      54 ..      31      82 ..      25      92 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.2e-08
                                      HHHHHHHSTTEEEEEE-S------EEEEEEEESS-.....--HHHHHHHHHH CS
                           Polbeta  8 ekekeielaylFGSrakgkareeSDiDlavllkek.....ldleeelelaae 54
                                      ek  +   a l GS+a+g++++ SD+Dl v+  +      +++++ +++ ++
  gi|557695144|ref|YP_008798198.1| 31 EKIVGPVSAALIGSYARGDFNQWSDVDLLVVSPRFaptplNRFDQVADVLKK 82
                                      5556677899*********************998876666666666555555 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 !   16.9   0.0   1.5e-06    0.0055      10      70 ..      23      83 ..      13      97 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.5e-06
                                      HHHHHHHHHHHH-TT-EEEE-HHHHTT-.SEESSEEEEEEBTTBSTTSS--HHHHHHHHHHH CS
                    DNA_pol_B_palm 10 lealvkkaakeldpevevivcGSYRRga.essGDvDvlitkkdakseskklkklleklvkkl 70
                                        ++v + ++++   v++   GSY Rg  ++  DvD+l+  ++++ +  ++ + +++++kk 
  gi|557695144|ref|YP_008798198.1| 23 AVEAV-ELVEKIVGPVSAALIGSYARGDfNQWSDVDLLVVSPRFAPTPLNRFDQVADVLKKF 83
                                      33333.56778888899*********9746789*********99986544555555555554 PP

>> Pox_A51  Poxvirus A51 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.5e-06     0.016     256     302 ..       3      49 ..       1      54 [. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.5e-06
                           Pox_A51 256 essicvldkeellkksvCesirggltiivkdiGefsasivGkypefd 302
                                       e+++ v++k+++++k+  e+  +++ ++ k +G  sa+++G y + d
  gi|557695144|ref|YP_008798198.1|   3 EVEMGVFEKRKMMRKAAVEAAVEAVELVEKIVGPVSAALIGSYARGD 49 
                                       57789**************************************8877 PP

>> DUF3626  Protein of unknown function (DUF3626)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.3e-05      0.19     148     211 ..       9      72 ..       2      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.3e-05
                           DUF3626 148 lkvaklvellaalreselververepsrnLdhyieaqihGdvsLerDveaLvaDpsfkgtdige 211
                                       ++ +k++++ a ++  e ve ve+ ++ +   +i +   Gd +  +Dv+ Lv+ p f+ t++++
  gi|557695144|ref|YP_008798198.1|   9 FEKRKMMRKAAVEAAVEAVELVEKIVGPVSAALIGSYARGDFNQWSDVDLLVVSPRFAPTPLNR 72 
                                       5678899999999999999999999999999***************************999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 711.97
//
Query:       gi|557695145|ref|YP_008798199.1|  [L=339]
Description: ornithine carbamoyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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  126.5   0.0    1.4e-36  125.7   0.0    1.4  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    2.1e-36  125.3   0.0      3e-36  124.9   0.0    1.2  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 !  125.7   0.0   1.6e-40   1.4e-36       1     148 []       9     159 ..       9     159 .. 0.92

  Alignments for each domain:
  == domain 1  score: 125.7 bits;  conditional E-value: 1.6e-40
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       r+l+s +d+s eei++ +dla++lk ++++ + ++l+k++t+++lF+++StRTr+Sfe+Aa+ lGg++ +++ a  +
  gi|557695145|ref|YP_008798199.1|   9 RDLISSQDWSIEEIDAAMDLARSLKIARASGNVPELFKNRTMFMLFYNTSTRTRASFEAAATMLGGHAQFIDFA--T 83 
                                       89***************************9******************************************55..2 PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEE..........ESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviR..........hpgaeeleelakyasvpviNagdgdgeHPtQaLaDll 144
                                         +  ++g  Es++D+a++ +r+++++ +R           +g++ ++e a++a++pviN+   d+ HP Qa++Dl+
  gi|557695145|ref|YP_008798199.1|  84 TRG--AEG--ESVKDIAKMYERLGHVLGVRilesavdyvyGRGNAVVREYAEHAKIPVINMA-DDMFHPSQAITDLY 155
                                       223..556..********************8888877754336677****************.99************ PP

                                       HHHH CS
                          OTCace_N 145 tire 148
                                       t+re
  gi|557695145|ref|YP_008798199.1| 156 TLRE 159
                                       **97 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 !  124.9   0.0   3.4e-40     3e-36      16     156 ..     185     334 ..     165     335 .. 0.88

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 3.4e-40
                                       HHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SSETTC....... CS
                            OTCace  16 anslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvwvsmge....... 85 
                                       +++ + +++r+gmdvvl+ P+g++ d+++++ akkna++sgg++ti+++++ea+++aD v++++w+s +        
  gi|557695145|ref|YP_008798199.1| 185 IQDEMLIATRYGMDVVLAYPPGFDIDENLVKLAKKNAEESGGTLTISHNYKEALENADAVFPRSWASHECvitgmnr 261
                                       4566789***********************************************************88889**9999 PP

                                       .CGGHH.HHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
                            OTCace  86 .ekere.erlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                                         +ere e  +k++d+++t+el +l++ + iv H LP++rg+E +d+V+d+prsv+++qaeN l++++A+l l
  gi|557695145|ref|YP_008798199.1| 262 fGREREiELHNKYRDWKLTRELTDLMSRHGIVTHVLPVFRGQEADDDVMDGPRSVIYDQAENLLYVRAAILSL 334
                                       955555477889999*******************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2545.66
//
Query:       gi|557695146|ref|YP_008798200.1|  [L=318]
Description: carbamate kinase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  115.0   0.1    7.2e-33  114.2   0.1    1.4  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
       0.13   12.0   0.0         11    5.8   0.0    2.5  2  GntR       Bacterial regulatory proteins, gntR 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 !  114.2   0.1     8e-37   7.2e-33       2     240 ..       6     299 ..       5     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 114.2 bits;  conditional E-value: 8e-37
                                       EEEEEE-TTCCC.CTCC.......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....... CS
                         AA_kinase   2 rvVvKlGGsslt.dkee.......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa...... 64 
                                       ++Vv+lGG++l   +++       +++ ++a+ +a+++e+g++lv+ hG+g+++ + l + ++  ++ +++      
  gi|557695146|ref|YP_008798200.1|   6 LIVVALGGNALLrRGDKgsfeeqyKNVGEAAKYLADIVEAGHRLVITHGNGPQVGATLLR-HDAGQKLHNIpafpmd 81 
                                       79*******777466669*********************************999999999.6666666555677788 PP

                                       .............E..HHHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE................ CS
                         AA_kinase  65 ..........glrstleeagevatrdalaslgerlvaallaaglpavglsaaaldateagr................ 115
                                                 g   +++ ++e+ +r     + + +++ ++++  pa++ + ++++++ ++                 
  gi|557695146|ref|YP_008798200.1|  82 acgaetqgfiGYIIQQNLRNELKRRGIDKYVITVVTRVIVDKNDPAFSNPTKPIGPFYKKEemekikaehpeyvfve 158
                                       88888899988888888888888885555555555555555555666666666666666656668888888888888 PP

                                       ...........HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE.......EEEE-HHHHHHHHHHHCTSSEE CS
                         AA_kinase 116 .........degsdgnvesvdaeaieelleagvvpvltgfigldeege.......lgrgssDtiaallAealgAdkl 176
                                                 ++s+++    ++ ai++l+++g+++v +g++g++  +e        +++++D +   lAe++gAd+ 
  gi|557695146|ref|YP_008798200.1| 159 dkarggwrrVVPSPDPKIIAERHAIRKLVDEGFIVVASGGGGIPIVEEngkaygvEAVIDKDLAGERLAELIGADRF 235
                                       888899999999999999999******************998888888888999988******************** PP

                                       EEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEE CS
                         AA_kinase 177 iiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvIt 240
                                       iiltdVdG y + +k +   ++l+++s+ ea+   +++++++g+m +k++a++++++ gg ++vI+
  gi|557695146|ref|YP_008798200.1| 236 IILTDVDGAYLNFGKPD--QKKLEKVSAAEARRylEQGHFGSGSMLPKVLACIRFIEAGGKEAVIA 299
                                       *************9876..7*****************************************99996 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0012        11      42      61 ..     180     199 ..     180     201 .. 0.94
   2 ?    3.3   0.0    0.0074        66      10      27 ..     265     282 ..     260     284 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHTTSEEEETTCE CS
                              GntR  42 ReALrrLeaeglverrqgrG 61 
                                       R A+r+L+ eg +++ +g+G
  gi|557695146|ref|YP_008798200.1| 180 RHAIRKLVDEGFIVVASGGG 199
                                       88**************9998 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0074
                                       HHHHHTTSS-TTSB---H CS
                              GntR  10 redIlsgelrpGdkLPse 27 
                                       r+ + +g++  G++LP++
  gi|557695146|ref|YP_008798200.1| 265 RRYLEQGHFGSGSMLPKV 282
                                       67799***********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2273.50
//
Query:       gi|557695147|ref|YP_008798201.1|  [L=414]
Description: threonine synthase [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-74  251.3   0.1    1.5e-74  251.0   0.1    1.0  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 !  251.0   0.1   8.6e-79   1.5e-74       4     293 ..      76     383 ..      74     384 .. 0.94

  Alignments for each domain:
  == domain 1  score: 251.0 bits;  conditional E-value: 8.6e-79
                                       CSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT- CS
                              PALP   4 gigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGl 79 
                                        +g+TPl++++rl  elgv+ lflK+E  npt SfKdR+++   a++ e  g++ vv assGN++ +lAa++a lGl
  gi|557695147|ref|YP_008798201.1|  76 SEGNTPLLHAQRLGGELGVKrLFLKDETRNPTASFKDRAMAVGAAKAVEM-GRRDVVIASSGNAASSLAAYSASLGL 151
                                       689***********************************************.************************** PP

                                       EEEEEEETTS-HHHHHHHHHTT-EEEEE...CCHHHHHHHHHHHHHHHSTTCEE--TTT..SHHHHHHHHTHHHHHH CS
                              PALP  80 kvtivvpadaspekvallrllGaevvev...ggdydeavaaaaelaaegegaylvsqfd..nptviegygtiglEil 151
                                       ++t +vp+d+  +k+ +l l+Ga+v +v   +++ d +v+++++  +e  g+y +++f+  np+ +eg +ti++E++
  gi|557695147|ref|YP_008798201.1| 152 RCTAFVPEDVAMGKASQLLLYGARVLRVkqvEEGRDPTVDLMMQTVKE-LGWYPCPSFGpfNPYQVEGPKTIVYEMV 227
                                       ***********************9999988888899999999999999.9*************************** PP

                                       HHTT.TTEEEEEEE-SSSHHHHHHHHHHHH....HSTT..-EEEEEEECTTCGGTTCCS..S.SS..B.....SSS. CS
                              PALP 152 eqlg.gkpdavvvpvGgGgliaGiaaglke....rrpd..vrvigvepegsdalarslragrrvtvpvs....dtia 217
                                       eq+g g+pd v+ p+G+G l++Gi+++lke    +  +  ++++ v+p+g+++l r++ +g+r +  ++    ++ia
  gi|557695147|ref|YP_008798201.1| 228 EQMGwGVPDFVFIPTGSGCLATGIWKALKElrllGLIEsyPKLVPVQPSGNMPLVRAILQGKRFEEVEPekwpKSIA 304
                                       ******************************8876333368******************9999998888856666666 PP

                                       CCSTCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEE CS
                              PALP 218 dglavg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvvi 291
                                       +gl  +   +++ a+e ++ +++++v+v ++e+ ea+++lar eg+++eps+a+++aa+ kl+e+g ++++d+vvv+
  gi|557695147|ref|YP_008798201.1| 305 SGLLDPypWDGDAAMEGVRTTGGTAVAVEEDEIREAVKKLARLEGVFAEPSGAVGVAAVqKLLEQGVVEASDTVVVL 381
                                       666666888888888899**********************************************************9 PP

                                       E- CS
                              PALP 292 lt 293
                                       +t
  gi|557695147|ref|YP_008798201.1| 382 VT 383
                                       98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3103.30
//
Query:       gi|557695148|ref|YP_008798202.1|  [L=143]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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   46.9   3.2    3.2e-12   46.3   3.2    1.3  1  V4R       V4R domain


Domain annotation for each model (and alignments):
>> V4R  V4R domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   3.2   1.8e-16   3.2e-12       2      60 ..      82     140 ..      81     142 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 1.8e-16
                                       -EEEEEES-S-TT---SS---HHHHHHHHHHHHHHHSSEEEEEEEE-GGGT-SSEEEEE CS
                               V4R   2 elsieespelaglpgkeePvCyleaGllagalsellgkrveveEveCaaeGhdhCeFev 60 
                                       ++  e++++++gl  ++ P+C +  G++ag+++  +g+ v v E  C+a G++ C+F +
  gi|557695148|ref|YP_008798202.1|  82 VVVFENCVFCEGLEHEKTPACSFLSGIIAGIAESVYGRGVTVQEELCRAAGGGVCRFSI 140
                                       66779****************************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 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:                        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 0.21s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1133.27
//
Query:       gi|557695149|ref|YP_008798203.1|  [L=342]
Description: cysteine synthase A [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-68  231.9   0.0    1.2e-68  231.7   0.0    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
       0.14   12.0   0.0        0.3   10.9   0.0    1.5  1  NifZ      NifZ 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 !  231.7   0.0   1.4e-72   1.2e-68       3     294 .]       9     297 ..       7     297 .. 0.94

  Alignments for each domain:
  == domain 1  score: 231.7 bits;  conditional E-value: 1.4e-72
                                       GCSSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHH CS
                              PALP   3 lgigpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaa 74 
                                       + ig+TPl+rl+ ++k++gv+  +++KlE+ np+gS KdR    +++++ e    ++++ ++e s+GN+g+a+ +++
  gi|557695149|ref|YP_008798203.1|   9 DLIGNTPLLRLRHIEKQHGVEaeIWAKLEFYNPSGSLKDRIYREMITKAIERgdlRPGMEILEVSTGNAGIACTFVG 85 
                                       689*********************************************77766************************ PP

                                       HHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEE...CCHHHHHHHHHHHHHHH.STTCEE--TTTSHHHHHH.HHTH CS
                              PALP  75 allGlkvtivvpadaspekvallrllGaevvev...ggdydeavaaaaelaae.gegaylvsqfdnptvieg.ygti 146
                                        +lG++vtiv+p+++s+e+++l++++G ++v++   ++d+d ++++a+e+ ++  +++ + +qf np++i++  +t+
  gi|557695149|ref|YP_008798203.1|  86 THLGYRVTIVMPEGMSEERKQLIKAFGGNLVFTpgaESDVDLSLRKAEEMMRQnPGKYWFPNQFTNPDNIQAhIKTT 162
                                       *********************************87777788889999999999677788999999************ PP

                                       HHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS CS
                              PALP 147 glEileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg 223
                                       g+Ei+eq++gk+da+v++ G+Gg+++G++++lke++p+v+++ vep++++ + +++          +++ ++g++ g
  gi|557695149|ref|YP_008798203.1| 163 GPEIWEQTKGKVDAFVMSQGSGGTVSGVGKFLKEKNPSVKIYTVEPSEAPIISEGR---------WGSHKIEGIGDG 230
                                       ********************************************************.........89********** PP

                                       .CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 224 .spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                         p +l++ ++    d +vt +++e ++++r+lar egi+ + ss++++aa+  + a++ ++  ++v+++++
  gi|557695149|ref|YP_008798203.1| 231 fIPRNLDLGVC----DGVVTTTSDESIAMARQLARLEGIFGGISSGCNVAAA-VKVAKKHPNLRKIVTLICD 297
                                       88888888877....55777********************************.9999999998999999996 PP

>> NifZ  NifZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.3e-05       0.3      26      56 ..     173     207 ..     168     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.3e-05
                              NifZ  26 eigelLvkkGdvGvvvsvGtflq....nqeiYlVe 56 
                                       +++++++ +G+ G+v  vG fl+    + +iY+Ve
  gi|557695149|ref|YP_008798203.1| 173 KVDAFVMSQGSGGTVSGVGKFLKeknpSVKIYTVE 207
                                       68999*****************9776667899997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2686.90
//
Query:       gi|557695150|ref|YP_008798204.1|  [L=297]
Description: ornithine carbamoyltransferase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-43  147.4   0.0    5.7e-43  146.7   0.0    1.3  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    7.4e-29  100.7   0.0    1.1e-28  100.1   0.0    1.3  1  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 !  146.7   0.0   6.4e-47   5.7e-43       4     156 ..     130     292 ..     128     293 .. 0.94

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 6.4e-47
                                       EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE-- CS
                            OTCace   4 kiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdv 79 
                                        +a++G+ k+  v++s i + +++ mdvvl++P+g+e + +v+e +kkn++++ggs+tit+d++ea++gaD+vy++ 
  gi|557695150|ref|YP_008798204.1| 130 SYAYSGGlKPLAVPQSCILIGTQFAMDVVLAHPPGFELEDHVIEACKKNVEQYGGSFTITNDMKEAFEGADFVYPKA 206
                                       5799**99********************************************************************* PP

                                       SSETTC.........CGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTT.BHHHHHHHHH CS
                            OTCace  80 wvsmge.........ekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdspr.svvfeqaeNr 146
                                       w + +          ++  ++   ++k++  t el++l++   +++Hc Pa+rg+Ev deV+dspr s++f+qaeNr
  gi|557695150|ref|YP_008798204.1| 207 WSPKKFfppynstvdKEGAMKYQDQFKNWITTPELMDLTNR-GKYMHCGPADRGQEVVDEVIDSPRySLYFQQAENR 282
                                       **777799*9999865566688899************8765.9***********************9********** PP

                                       HHHHHHHHHH CS
                            OTCace 147 lhtikAllvl 156
                                       lh++kA++ +
  gi|557695150|ref|YP_008798204.1| 283 LHVQKAVMSM 292
                                       ********86 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 !  100.1   0.0   1.2e-32   1.1e-28      44     147 ..       1     116 [.       1     117 [. 0.84

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 1.2e-32
                                       EEESS--HHHHHHHHHHHHHTTSEEEEEESTT....TSCT.TTGGSTTSSCHHHHHHHHHHHTSEEEEE........ CS
                          OTCace_N  44 llFeepStRTrvSfevAakrlGgkvlslseae....diql.ssvskgrkEsleDtarvlsryvdaiviR........ 107
                                       +lF+++S+RTr Sfe+++++lGg++ +ls ++    +  l + +   ++Es++D+arvls y+dai++R        
  gi|557695150|ref|YP_008798204.1|   1 MLFYNRSLRTRNSFEAGIYQLGGHAHFLSPSDvytpT--LpEDMIPYQTESIADVARVLSTYGDAIAVRiygdaakw 75 
                                       89***************************55555332..2433433346********************77777666 PP

                                       ES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                          OTCace_N 108 hp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                       h   g++ ++e+ak+a++pv+N++  d +HP QaLaD++ i+
  gi|557695150|ref|YP_008798204.1|  76 HIgrGHRVIQEFAKWATIPVLNME-DDIYHPFQALADMMAIQ 116
                                       22447777****************.999***********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); 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 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2217.24
//
Query:       gi|557695151|ref|YP_008798205.1|  [L=417]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-33  114.1  18.7    6.4e-33  114.1  18.7    1.6  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
       0.23   10.6   0.0       0.33   10.1   0.0    1.1  1  CymA      Putative cyclodextrin porin


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 !  114.1  18.7   7.1e-37   6.4e-33       3     229 ..     129     369 ..     127     380 .. 0.88

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 7.1e-37
                              UbiA   3 ipalvg.lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadme.......rtpnRPlvsGrispkeali 71 
                                        p+l+g  ++a  g +d+ll++l+l+g+ l+++a n+ Ndy+D + +ad +           R l  G+++pk++l+
  gi|557695151|ref|YP_008798205.1| 129 APVLIGvGTAAYLGYFDPLLFILTLIGASLIHLALNMANDYYDTKLGADPAnitptpfSGGSRILHYGLMTPKQLLT 205
                                       689999999999*************************************77888888755678899*********** PP

                              UbiA  72 faivllilgllll...allln.pltallgllalllyvvYt.g.lrlKrrtllgtvvggiafglppllgwaavtgsl. 141
                                       ++++++ +g++++   a+l +  ++++++  ++l+ ++Yt + l l +r+l g+v +gi fg +++lg  +v+ ++ 
  gi|557695151|ref|YP_008798205.1| 206 LIVLFYGVGIAIGlylAFLRGlIPILAVMTTGVLISIFYTaPpLKLAYRGL-GEVAVGIGFGPIIVLGSHYVQTQFf 281
                                       *************88755555355566666777777*****99********.*******************666666 PP

                              UbiA 142 sllalllalavflltwaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylll 218
                                       s++all+++++++l++ i+++n ++d   D++ag++tl+++l +++++  + l la++++++++++++ l+++++l+
  gi|557695151|ref|YP_008798205.1| 282 SPEALLASIPIGILIMLILYVNEIPDAPYDKAAGKHTLVTRLSKENVLKGYKLSLAATYAVIVAAVVLRLAPPTTLI 358
                                       ******************************************9999999866667777777889************* PP

                              UbiA 219 alllaalallr 229
                                       al+ ++ a+  
  gi|557695151|ref|YP_008798205.1| 359 ALATIPKAIST 369
                                       **999888766 PP

>> CymA  Putative cyclodextrin porin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   3.7e-05      0.33     190     244 ..      53     106 ..      42     116 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 3.7e-05
                              CymA 190 gereeegysllfkpykrfgqwelalelyyqvkenkdktangslneisdftekyie 244
                                       ge   eg +++fkpyk++g w+   + ++q  e++  +a+  +  +s+   + ++
  gi|557695151|ref|YP_008798205.1|  53 GEAVTEGNTIIFKPYKQYG-WDEKTKPFFQYCEERVPQAKSYVRRLSEAVGRQVK 106
                                       788899************9.88888999999999999999888888877666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3075.81
//
Query:       gi|557695152|ref|YP_008798206.1|  [L=147]
Description: hypothetical protein CSUB_C1725 [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0013   18.9   0.0     0.0019   18.3   0.0    1.2  1  Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
  ------ inclusion threshold ------
      0.018   14.6   0.0      0.022   14.4   0.0    1.1  1  Pyrid_ox_like   Pyridoxamine 5'-phosphate oxidase like


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   2.2e-07    0.0019      17      86 ..       9      84 ..       2      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2.2e-07
                                      EEEEETTSEEEEEEEEEEEETTT.TEEEEEEETTSHHHHHHHHH-EEEEEEEETT.....GSEEEEEEEEEEEESC CS
                    Putative_PNPOx 17 lATvdedGrPnvspvllkagdgr.dgivfatnadsrklrnleenprvallfldde.....lgrgvrieGtaelvsd 86
                                      l+ ++++G +   p+l  +  +r +++ +++   s+k   +++np+v++lf  ++      +  ++++G a++ ++
  gi|557695152|ref|YP_008798206.1|  9 LSVITPSGEVLTNPMLPLYSRERkKLYMTSSILFSKKINYIKQNPKVGVLFSGRPfiktpRYSLLHVKGDAKIYEE 84
                                      66678999999999998888888556666677788***********************99999999*****99876 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.4e-06     0.022      18     102 ..       9      97 ..       1     112 [. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-06
                     Pyrid_ox_like  18 LttteadgklksrPMatqkveedgdlwfltk.kdsdkvkeirkdsqvnlafsde.....skkkyvsvsGtaevvedr 88 
                                       L +++ +g++   PM     +e  +l+  ++   s+k++ i+++++v ++fs++        + ++v+G a+++e++
  gi|557695152|ref|YP_008798206.1|   9 LSVITPSGEVLTNPMLPLYSRERKKLYMTSSiLFSKKINYIKQNPKVGVLFSGRpfiktPRYSLLHVKGDAKIYEEN 85 
                                       556667889999***************9987357****************997522211466779999***999875 PP

                     Pyrid_ox_like  89 akieelWspvvkaw 102
                                         ++  W+ +v+ w
  gi|557695152|ref|YP_008798206.1|  86 --LHSGWEWLVELW 97 
                                       ..566677677666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); 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: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1152.96
//
Query:       gi|557695153|ref|YP_008798207.1|  [L=368]
Description: major facilitator superfamily MFS [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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  116.6  58.3    2.6e-26   92.4  30.0    2.1  2  MFS_1       Major Facilitator Superfamily
    0.00032   19.7  11.0      0.041   12.7   0.0    2.4  2  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
       0.22   10.3   0.5       0.42    9.4   0.5    1.5  1  DUF5423     Family of unknown function (DUF5423)


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 !   92.4  30.0   4.3e-30   2.6e-26       7     177 ..       7     177 ..       5     195 .. 0.90
   2 !   29.7  20.7   5.1e-11   3.1e-07       4     172 ..     199     365 ..     192     368 .] 0.88

  Alignments for each domain:
  == domain 1  score: 92.4 bits;  conditional E-value: 4.3e-30
                             MFS_1   7 lsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfa 82 
                                       +++l++ +++pa p +la++++i  s++g+l +++ lg a+++lp++ l+ rfG++++ llgl++++++ +l++l  
  gi|557695153|ref|YP_008798207.1|   7 VYTLNWLAISPAQP-FLATEFNIGLSALGILGAVFLLGVALFQLPAAILAARFGAKKIALLGLFFSSFFaGLCGL-- 80 
                                       67889999******.******************************************************666666.. PP

                             MFS_1  83 sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyila 158
                                       ++ + +llvlr+l+G++ +++f  g++++a +f+ +erg a+g+++agf  G++++ ++ + ++s++gWr+  ++ +
  gi|557695153|ref|YP_008798207.1|  81 APAFeYLLVLRFLTGVFLSFFFGPGITFFAPLFTAKERGTAVGVYNAGFHTGTLVTLGVWPTVMSLYGWRLGLLVPG 157
                                       56666************************************************************************ PP

                             MFS_1 159 ivsllafvlfllll.peepp 177
                                       +++ll++ + +++  ++e+p
  gi|557695153|ref|YP_008798207.1| 158 VAGLLLAFVTYWVSrWVEDP 177
                                       ******77544443444444 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 5.1e-11
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdr.fGrrrvlllglllfalgllll 79 
                                       ++ ++++a++ l+ +  l+l+++  +++  +g ++++ +lg++v++++ Grl dr   r+r+l l  ll +++ l++
  gi|557695153|ref|YP_008798207.1| 199 GLGFAGAAWYPLTQFGILYLTSEAKLDVGIAGAMVSVLSLGSVVGAPLSGRLYDRaRDRKRLLYLLNLLNSVS-LAA 274
                                       5555666666666666669999999******************************556777************.444 PP

                             MFS_1  80 l.fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                       + + s++ +++   +++Gl++ a++ + ++    +++++e +  ++ +++   l+a   p + +++a+ +g+ a ++
  gi|557695153|ref|YP_008798207.1| 275 FsL-SPVQAIMPIVFMTGLFYTASNNLYYVTPMMVVNQSEIAVTVATVNMVHLLAASAIPYVFSAVAEGWGYFAGWM 350
                                       425.9999********************************************************************* PP

                             MFS_1 156 ilaivsllafvlfllll 172
                                       ++ +vslla+++  ++ 
  gi|557695153|ref|YP_008798207.1| 351 MMVFVSLLAVLC--VWR 365
                                       *********998..444 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 !    8.2   6.7   0.00017         1     260     361 ..      31     133 ..      15     144 .. 0.83
   2 !   12.7   0.0   6.9e-06     0.041      24      85 ..     216     278 ..     205     285 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00017
                        MFS_1_like 260 tllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaave 336
                                       + lG+l a+  ++   + + a  l  ++G+ k+ +++l++  +   l ++   +  +l++ +L g+ +  +++ +++
  gi|557695153|ref|YP_008798207.1|  31 SALGILGAVFLLGVALFQLPAAILAARFGAKKIALLGLFFSSFFAGLCGLAPAFEYLLVLRFLTGVFLSFFFGPGIT 107
                                       55666666666666666677888999************99999999999999999********************** PP

                        MFS_1_like 337 yvskiapksleatgqglls.glyfgl 361
                                       + + +++ + ++t  g+++ g++ g 
  gi|557695153|ref|YP_008798207.1| 108 FFAPLFTAKERGTAVGVYNaGFHTGT 133
                                       *****************962577665 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 6.9e-06
                        MFS_1_like  24 iylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfi 85 
                                       +yl+ +  l++ + g ++++l l s++++p+ g l Dr + rk ++ l  ll+ v+++++ + 
  gi|557695153|ref|YP_008798207.1| 216 LYLTsEAKLDVGIAGAMVSVLSLGSVVGAPLSGRLYDRARDRKRLLYLLNLLNSVSLAAFSLS 278
                                       68885678***********************************************99987754 PP

>> DUF5423  Family of unknown function (DUF5423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.5     7e-05      0.42      74     107 ..     311     344 ..     267     363 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 7e-05
                           DUF5423  74 skeiadtvaavslpfiltgtaaglmfsaiavggg 107
                                         eia tva+v +  +l+ +a   +fsa+a g g
  gi|557695153|ref|YP_008798207.1| 311 QSEIAVTVATVNMVHLLAASAIPYVFSAVAEGWG 344
                                       569***************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2530.01
//
Query:       gi|557695154|ref|YP_008798208.1|  [L=466]
Description: V-type H+-transporting ATPase subunit B [Candidatus Caldiarchaeum subterraneum]
Scores for 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  232.8   0.0    4.4e-69  232.4   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    4.5e-11   43.1   6.2    4.5e-11   43.1   6.2    1.8  2  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
     0.0001   22.4   5.0    0.00056   20.0   2.1    2.7  3  HAS-barrel     HAS barrel domain


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 !  232.4   0.0   7.4e-73   4.4e-69       1     213 []     137     355 ..     137     355 .. 0.98

  Alignments for each domain:
  == domain 1  score: 232.4 bits;  conditional E-value: 7.4e-73
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrt 72 
                                       Gi+++D + ++v+Gq++ i++++g++++++++++++q++      + a+i++++G +++e++ + ++++e++++kr+
  gi|557695154|ref|YP_008798208.1| 137 GISAIDGMNSLVRGQKLPIFSGAGLPHNMLAAQIARQATVPgkeeEfAVIFAAVGVQNDEARYFRRSLEESGAIKRS 213
                                       89***********************************8665888768****************************** PP

                                       EEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  73 vlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklasl 148
                                        l++n +++p+++r+ ++++++tlAEy++  qg++vl+i+++++++aeAlre+s++ +e+p+++gyp+y++++lasl
  gi|557695154|ref|YP_008798208.1| 214 ALFLNLADDPAIERIVTPRIALTLAEYLAFkQGYHVLVIITDITNYAEALREVSAAREEVPGRKGYPGYMYTDLASL 290
                                       *****************************99********************************************** PP

                                       HTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 149 yERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       yERag+++  +Gs+t+++++s++++D+++p+++ t +it+g+ivL+++l +++++P+invl+S+S
  gi|557695154|ref|YP_008798208.1| 291 YERAGRIKGLKGSLTQMPILSMPSDDITHPIPDLTGYITEGQIVLSRDLYRKGIYPPINVLMSLS 355
                                       ********99*****************************************************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 !   43.1   6.2   7.5e-15   4.5e-11       1      69 []      14      80 ..      14      80 .. 0.97
   2 ?   -3.5   0.0       2.6   1.6e+04      49      64 ..     137     152 ..     136     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 7.5e-15
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVkrTG 69
                                      i ++ Gp++ v++++g   g+++++eve v+ g+ +lg +++++e++++v+v+++t+Gl   Gt+ +++G
  gi|557695154|ref|YP_008798208.1| 14 IQEIKGPLMVVGGVSG--VGYDELVEVETVD-GERRLGRVIEVSEGRAVVQVFEGTQGLGIaGTKARFLG 80
                                      6799************..**********99*.*****************************9****9998 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
                                       EEEESS-STTBBTTSE CS
                     ATP-synt_ab_N  49 rvivmgstdGlsrGte 64 
                                       ++ +++++  l+rG++
  gi|557695154|ref|YP_008798208.1| 137 GISAIDGMNSLVRGQK 152
                                       6778899999999985 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   2.1   9.3e-08   0.00056      11      83 ..      18      75 ..       8      96 .. 0.80
   2 ?    1.9   0.0     0.043   2.5e+02      22      52 ..     234     265 ..     224     276 .. 0.71
   3 ?   -2.8   0.0       1.2   7.1e+03      50      73 ..     399     425 ..     391     426 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 9.3e-08
                        HAS-barrel 11 sslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalatedt....... 82
                                       +++++v g+ +v++ e+Ve+e+ dge++lG+v  +++                       + +v++++e+t       
  gi|557695154|ref|YP_008798208.1| 18 KGPLMVVGGVSGVGYDELVEVETVDGERRLGRVIEVSE-----------------------GRAVVQVFEGTqglgiag 73
                                      78999*********************************.......................888888888887666666 PP

                        HAS-barrel 83 .g 83
                                        
  gi|557695154|ref|YP_008798208.1| 74 tK 75
                                      63 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.043
                        HAS-barrel  22 dvkvGeyVeielpdgeivlGmvtdirrgn...se 52 
                                        + + ey+ ++  +g +vl ++tdi ++     e
  gi|557695154|ref|YP_008798208.1| 234 ALTLAEYLAFK--QGYHVLVIITDITNYAealRE 265
                                       56666899999..4799999*******7644433 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.2
                        HAS-barrel  50 n...selsndlalvlsleeleeangdd 73 
                                       +   ++ +++l++ + +e+++  +g +
  gi|557695154|ref|YP_008798208.1| 399 SglsETDLKYLEFGDLFEQRFLRQGSN 425
                                       345678889999999999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); 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:                         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: 00:00:00.39
# Mc/sec: 3572.70
//
Query:       gi|557695155|ref|YP_008798209.1|  [L=596]
Description: V-type H+-transporting ATPase subunit A [Candidatus Caldiarchaeum subterraneum]
Scores for 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-92  306.8   0.0    9.7e-92  306.4   0.0    1.1  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    1.1e-43  147.9   0.0    1.9e-43  147.2   0.0    1.4  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    1.7e-12   47.7   1.3    2.5e-12   47.1   0.3    1.9  2  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
      0.049   13.9   0.0       0.13   12.6   0.0    1.7  1  AAA_22           AAA domain


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 !  306.4   0.0   2.2e-95   9.7e-92       1     213 []     215     438 ..     215     438 .. 0.98

  Alignments for each domain:
  == domain 1  score: 306.4 bits;  conditional E-value: 2.2e-95
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imk 70 
                                       G+rvlD++fpi +G++ +ipgafg+Gktv +++l+k+s+++ +i  vg+Gergne +evl+efp+      g+ +m+
  gi|557695155|ref|YP_008798209.1| 215 GQRVLDTFFPISKGGTACIPGAFGTGKTVTLHQLAKWSDTR-VIFHVGCGERGNEESEVLTEFPHlkdpatGRpLME 290
                                       9************************************9877.***********************988865228*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       rtvl+antsn+pvaareasiytg+t+AEyfrd+g++vll+ads+srwaeAlreis+rl+empa++gyp+yl+++la+
  gi|557695155|ref|YP_008798209.1| 291 RTVLIANTSNMPVAAREASIYTGVTMAEYFRDMGYDVLLVADSTSRWAEALREISGRLEEMPAEEGYPSYLASRLAE 367
                                       ***************************************************************************** PP

                                       HHTTSEEE.....TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagka.....pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       +yERag++     p+r Gsvt v avsp+ggDf++pvtt+t++++ +f+ Ld +la  +h+Pain+ +S+S
  gi|557695155|ref|YP_008798209.1| 368 FYERAGRVvtlgnPERIGSVTLVGAVSPPGGDFTEPVTTHTMRFIRTFWALDANLAYTRHYPAINWITSYS 438
                                       *************9********************************************************9 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 !  147.2   0.0   4.3e-47   1.9e-43       1     121 []      86     206 ..      86     206 .. 0.97

  Alignments for each domain:
  == domain 1  score: 147.2 bits;  conditional E-value: 4.3e-47
                                       EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--T.T-EEEEE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvpp.kvegkvk 76 
                                       yDG+qrpL++i ++s  fi+rG+kv++l r+kkw+f+p vk+gd+v +gdi+G+v+et l+  kimvpp + +gk++
  gi|557695155|ref|YP_008798209.1|  86 YDGVQRPLDAIGKISTGFIKRGIKVDPLPRNKKWKFTPVVKKGDEVGPGDIIGEVPETPLVVSKIMVPPyAKRGKLT 162
                                       9*******************************************************************94559**** PP

                                       EE--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEEE CS
                   ATP-synt_ab_Xtn  77 eiaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkekl 121
                                       +ia+egeyt+edt+a++et+eg +++l+l+++wPvr++rp++++l
  gi|557695155|ref|YP_008798209.1| 163 YIAPEGEYTIEDTVATLETREG-STDLRLYHNWPVRRARPFNRRL 206
                                       ******************9996.9*****************9986 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 !   47.1   0.3   5.7e-16   2.5e-12       1      69 []       8      70 ..       8      70 .. 0.97
   2 ?   -3.7   0.0         4   1.8e+04      20      40 ..     570     591 ..     564     594 .. 0.68

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 5.7e-16
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      iv v Gp v+++++ g   ++y+ + v+  e  + l+g+++ l +d++ ++v+++t+Gl++G++V++TG
  gi|557695155|ref|YP_008798209.1|  8 IVWVAGPAVKADGMMG--AKMYETVYVG--E--ERLIGEIIKLTGDVAFIQVYENTSGLRPGEPVESTG 70
                                      56799******9999*..**********..8..9**********************************9 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4
                                       CTTEEEEECCET.CSTEEEEEE CS
                     ATP-synt_ab_N  20 giynalevelve.fgtlllgva 40 
                                       ++++ le  +v+ f++l +g+ 
  gi|557695155|ref|YP_008798209.1| 570 ELLDELEKAMVDtFEKLAYGEK 591
                                       5666677777777888888875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.8e-05      0.13       5      48 ..     228     263 ..     225     295 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlp 48 
                                        g  ++ G  GtGKT++l +l+++          + +v+ +v + 
  gi|557695155|ref|YP_008798209.1| 228 GGTACIPGAFGTGKTVTLHQLAKWS---------DTRVIfHVGCG 263
                                       677899******************9.........56666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); 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 0.26s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 4537.38
//
Query:       gi|557695156|ref|YP_008798210.1|  [L=325]
Description: ABC transporter ATP-binding protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-27   96.5   0.0    3.2e-27   95.7   0.0    1.4  1  ABC_tran      ABC transporter
    6.8e-09   36.0   0.1      0.004   17.0   0.1    2.2  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    7.8e-05   22.3   0.2    0.00025   20.7   0.0    1.9  2  AAA_29        P-loop containing region of AAA domain
     0.0003   21.5   0.0      0.001   19.8   0.0    1.9  2  DUF4162       Domain of unknown function (DUF4162)
     0.0018   18.8   0.7     0.0038   17.8   0.2    1.5  1  AAA_23        AAA domain
     0.0034   17.8   0.3      0.036   14.5   0.3    2.2  1  AAA           ATPase family associated with various cellular 
     0.0088   16.0   0.0      0.047   13.6   0.0    1.9  2  Rad17         Rad17 P-loop domain
     0.0094   15.7   0.5        0.5   10.1   0.1    2.3  2  AAA_30        AAA domain
  ------ inclusion threshold ------
      0.017   15.5   0.0      0.054   13.9   0.0    1.9  1  AAA_16        AAA ATPase domain
       0.02   14.8   0.1      0.048   13.6   0.0    1.5  1  ATPase_2      ATPase domain predominantly from Archaea
       0.02   14.8   0.0      0.044   13.7   0.0    1.6  1  RsgA_GTPase   RsgA GTPase
      0.043   13.7   0.1      0.099   12.6   0.1    1.7  1  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 
      0.045   12.4   0.0      0.076   11.6   0.0    1.3  1  AAA_13        AAA domain
      0.073   12.8   0.0       0.84    9.3   0.0    2.0  2  AAA_15        AAA ATPase domain
      0.077   12.5   0.1        2.4    7.7   0.0    2.2  2  NIR_SIR       Nitrite and sulphite reductase 4Fe-4S domain
      0.093   12.7   0.1       0.25   11.4   0.1    1.7  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
      0.099   12.9   0.2       0.32   11.3   0.1    2.0  2  AAA_22        AAA domain
       0.13   11.6   0.0       0.26   10.6   0.0    1.4  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
       0.14   12.0   0.0       0.29   11.0   0.0    1.5  1  Ph1570        Ph1570 protein
       0.16   11.2   0.0         18    4.5   0.0    2.4  2  Zeta_toxin    Zeta toxin
       0.16   12.5   0.4       0.37   11.4   0.3    2.1  1  AAA_18        AAA domain
        0.2   11.3   0.5        1.6    8.3   0.1    2.2  2  SRP54         SRP54-type protein, GTPase domain
       0.24   10.8   0.0          4    6.8   0.0    2.1  2  SMC_N         RecF/RecN/SMC N terminal 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 !   95.7   0.0   4.2e-30   3.2e-27       1     136 [.      24     168 ..      24     169 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 4.2e-30
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSB.H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpelt.v 76 
                                       l++v+l +++g++++++G+nGaGK+tL+k+l+ ll pt Ge  + g d+++ e ++ r  i  ++  ++  ++l  v
  gi|557695156|ref|YP_008798210.1|  24 LEKVNLRIEKGQIYGLLGPNGAGKTTLVKILTTLLLPTTGEAYVYGYDVSK-EASKIRPLINLVSGADTPGYGLItV 99 
                                       689***********************************************9.9999999******99888888766* PP

                                       HHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  77 ren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ren             +++e+i+++++++glke++++ +    ++LS G +qr+ lar l+++p +l+lDEpt
  gi|557695156|ref|YP_008798210.1| 100 RENlwfysmlygldkeTAKERINRLVEEVGLKEVENELL----RNLSTGYRQRMNLARGLVNDPLVLFLDEPT 168
                                       **************9999999******************....*****************************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 !   17.0   0.1   5.2e-06     0.004       2      22 ..      37      57 ..      36      86 .. 0.86
   2 !   17.0   0.0   5.3e-06    0.0041     259     298 ..     160     201 ..     137     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 5.2e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldll 22
                                       +l GpNg+GK++L ++l  l
  gi|557695156|ref|YP_008798210.1| 37 YGLLGPNGAGKTTLVKILTTL 57
                                      689***************766 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 5.3e-06
                            AAA_21 259 sllliDEpEngLHP...kllrrll.ellkelsrngaQviltTHS 298
                                        +l++DEp  gL+    +++rrl+ ++++  s     vilt+H 
  gi|557695156|ref|YP_008798210.1| 160 LVLFLDEPTIGLDAvsaRRIRRLIkDWVRVDSG--RTVILTSHY 201
                                       69************5555555555555566655..********6 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 !   20.7   0.0   3.2e-07   0.00025      16      50 ..      28      62 ..      22      67 .. 0.82
   2 ?   -2.5   0.0       5.6   4.4e+03       4      17 ..     274     287 ..     273     297 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.2e-07
                            AAA_29 16 tieidlkg.atlltGpsGsGKSTllDAiqalLvpak 50
                                       ++i+ kg ++ l Gp+G+GK+Tl+  +++lL+p++
  gi|557695156|ref|YP_008798210.1| 28 NLRIE-KGqIYGLLGPNGAGKTTLVKILTTLLLPTT 62
                                      56777.445999**********************98 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.6
                            AAA_29   4 lqlvNWgtfdghti 17 
                                       + + NW +  + + 
  gi|557695156|ref|YP_008798210.1| 274 VVVNNWDETADIVE 287
                                       67899*88776444 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       6.7   5.2e+03      43      59 ..     127     143 ..     109     148 .. 0.60
   2 !   19.8   0.0   1.3e-06     0.001       1      81 []     224     314 ..     224     314 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 6.7
                                       EE--------------- CS
                           DUF4162  43 kledeeaanellkalts 59 
                                       ++  +e+ nell+ l++
  gi|557695156|ref|YP_008798210.1| 127 EVGLKEVENELLRNLST 143
                                       44445667777777755 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.3e-06
                                       E-HHHHHTTS-SSEEEEE.....-------...--.-EEEE-TT..S-EEEEE-------------.----EEEEEE CS
                           DUF4162   1 GtleeiKrsygknrieve.....adaeellee.pg.veeveeeg..gelelkledeeaanellkal.tsgveirsFe 67 
                                       Gt+ e+++  +++++ v      +dae +l+  ++  ++ + ++   ++++ +++ +   ++ +++ ++g+++ s+ 
  gi|557695156|ref|YP_008798210.1| 224 GTPAELRSLVAGKTVAVMevwlpTDAEHVLDKlESaYRTHDPATniYRIRVVVNNWDETADIVEHItSHGGKVLSLV 300
                                       99********99999977799886666666552443555555553444666666888999******77********* PP

                                       EE---HHHHHHHHH CS
                           DUF4162  68 eeePsLndIFiekv 81 
                                          Ps +d+++++v
  gi|557695156|ref|YP_008798210.1| 301 KAMPSFEDVYVKLV 314
                                       ***********987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   4.9e-06    0.0038      18      43 ..      33      58 ..      15      65 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.9e-06
                            AAA_23 18 skgltlItGpNGaGKTTildAiklaL 43
                                      +  ++ + GpNGaGKTT++  ++  L
  gi|557695156|ref|YP_008798210.1| 33 KGQIYGLLGPNGAGKTTLVKILTTLL 58
                                      3468999************9999876 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   0.3   4.6e-05     0.036       3     118 ..      39     208 ..      37     217 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-05
                                       EESSTTSSHHHHHHHHHHHH.....THE................................................. CS
                               AAA   3 lyGppGtGKTllakavakel.....gve................................................. 25 
                                       l Gp G GKT+l+k + + l     +++                                                 
  gi|557695156|ref|YP_008798210.1|  39 LLGPNGAGKTTLVKILTTLLlpttgEAYvygydvskeaskirplinlvsgadtpgyglitvrenlwfysmlygldke 115
                                       78**************9997666553442222233333344444444444444455555555555555555555555 PP

                                       .........EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEET....GGGHHHHHTTCCCHHHHHHHHH CS
                               AAA  26 .........fleisgsellskyvgesekkirelfkeakeka.kpsilfiDE....idalaksrsgseseeeervvnq 88 
                                                + e+ ++e+ ++++ + +   r+ ++ a+    +p +lf+DE    +da+  +r           +  
  gi|557695156|ref|YP_008798210.1| 116 takerinrlVEEVGLKEVENELLRNLSTGYRQRMNLARGLVnDPLVLFLDEptigLDAVSARR-----------IRR 181
                                       554544444444444444444666666666777766665557889999999666666666666...........777 PP

                                       HHHHHHHTTTSSSTEEEEEEESSGGGSTHH CS
                               AAA  89 Llteldgvkkkeskvivigatnrpdkldpa 118
                                       L++ + +v++     +vi++++++ ++++ 
  gi|557695156|ref|YP_008798210.1| 182 LIKDWVRVDS---GRTVILTSHYMAEVEEM 208
                                       7777777777...35778888777777665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   6.1e-05     0.047      33      70 ..      22      59 ..      15      74 .. 0.86
   2 ?   -0.3   0.0       1.1   8.8e+02     147     170 ..     174     197 ..     126     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.1e-05
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70
                                      ++l+   L  +k +i  + GP G gk+t vk+L+  l 
  gi|557695156|ref|YP_008798210.1| 22 QALEKVNLRIEKGQIYGLLGPNGAGKTTLVKILTTLLL 59
                                      67888888889999*******************97765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                             Rad17 147 rdsdalrevirkylrssealplil 170
                                        +++++r +i+ ++r+    ++il
  gi|557695156|ref|YP_008798210.1| 174 VSARRIRRLIKDWVRVDSGRTVIL 197
                                       46699999****999877655554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00064       0.5      17      42 ..      33      58 ..      21      79 .. 0.78
   2 ?    3.9   0.1     0.048        38      68     160 ..     174     265 ..     149     296 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00064
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaw 42
                                      + ++  l Gp G+GKtt++k l+ ++
  gi|557695156|ref|YP_008798210.1| 33 KGQIYGLLGPNGAGKTTLVKILTTLL 58
                                      44688899************998765 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.048
                            AAA_30  68 ieastiakllkrlkgrarlepgtllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaGgvlrdlvea. 143
                                       + a++i +l+   k+++r+++g+ +i     m+  +++ a ++ ++k   +v+  G ++ l s  aG++++ +  + 
  gi|557695156|ref|YP_008798210.1| 174 VSARRIRRLI---KDWVRVDSGRTVILTSHYMAEVEEMCARVAVLNK--GRVVAEGTPAELRSLVAGKTVAVM--Ev 243
                                       3566666666...5556789999999999999999999888888877..9******************99988..33 PP

                            AAA_30 144 .....agigtaeLtevvRqkes 160
                                            a++   +L++ +R +++
  gi|557695156|ref|YP_008798210.1| 244 wlptdAEHVLDKLESAYRTHDP 265
                                       4555467777778888888765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.9e-05     0.054      10      75 ..      22      88 ..      14     196 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.9e-05
                            AAA_16 10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekd..ggif....lrgkcdqlesaipysalaqa 75
                                      ++L+ +  r+ +g  ++  l G+ G GK++lv+ l + l  +  ++++    ++ ++ +    +p++ l++ 
  gi|557695156|ref|YP_008798210.1| 22 QALEKVNLRIEKG--QIYGLLGPNGAGKTTLVKILTTLLLPTtgEAYVygydVSKEASKI---RPLINLVSG 88
                                      4444444445555..688899***********9999877777432333212222222222...444333333 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 ?   13.6   0.0   6.2e-05     0.048       1      60 [.      14      75 ..      14      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.2e-05
                          ATPase_2  1 FfdRekelkeleei.lerepneiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialree 60
                                      F +R   ++ le++ l+ e+ +iy + Gp g GKt+L+k + + l    ++  +y +++++e
  gi|557695156|ref|YP_008798210.1| 14 FRNRGSMVQALEKVnLRIEKGQIYGLLGPNGAGKTTLVKILTTLLlPTTGEAYVYGYDVSKE 75
                                      667777777777764667889******************99998855666677777777665 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   5.7e-05     0.044      88     129 ..      22      64 ..       5      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-05
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelelktge 129
                                       ++le+++ ++++ ++  l+G+ G+GK+tL++ l+  l   tge
  gi|557695156|ref|YP_008798210.1|  22 QALEKVNLRIEKgQIYGLLGPNGAGKTTLVKILTTLLLPTTGE 64 
                                       66788888888779*****************998765555554 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00013     0.099       1      13 [.     219     231 ..     219     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00013
                      BCA_ABC_TP_C   1 rvIAeGtPaEvrn 13 
                                       rv AeGtPaE r+
  gi|557695156|ref|YP_008798210.1| 219 RVVAEGTPAELRS 231
                                       89********985 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.8e-05     0.076       4      39 ..      13      57 ..      11      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.8e-05
                            AAA_13  4 ifdfrgaeledfkriNl......iYG...wNGaGKTtLSrllrsl 39
                                      +f  rg +++ ++++Nl      iYG    NGaGKTtL ++l  l
  gi|557695156|ref|YP_008798210.1| 13 VFRNRGSMVQALEKVNLriekgqIYGllgPNGAGKTTLVKILTTL 57
                                      566678888888888887777778853337***********9987 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0011      0.84      15      47 ..      25      58 ..      22      83 .. 0.81
   2 ?    1.4   0.0      0.26     2e+02     322     364 ..     157     200 ..     113     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0011
                            AAA_15 15 kdveidlsee.ltvliGkNnsGKSsilealdlFl 47
                                      ++v + +++  +  l G+N++GK++++++l  +l
  gi|557695156|ref|YP_008798210.1| 25 EKVNLRIEKGqIYGLLGPNGAGKTTLVKILTTLL 58
                                      5555555555677799**************8776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.26
                            AAA_15 322 eknvilliEEPEahLHpqaqkvlikllkelandnkt.QviitTH 364
                                       +++ +l+++EP + L     + + +l+k+ ++ +++  vi+t+H
  gi|557695156|ref|YP_008798210.1| 157 NDPLVLFLDEPTIGLDAVSARRIRRLIKDWVRVDSGrTVILTSH 200
                                       67899***************************999989999999 PP

>> 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 ?    7.7   0.0    0.0031       2.4     122     151 ..     108     137 ..      73     143 .. 0.82
   2 ?    2.5   0.0      0.12        91      96     135 ..     235     274 ..     229     281 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0031
                                       HHHS-CSSGGG-SHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR 122 rdhgdrknrkkeRlkylverlGvekFrekv 151
                                       + +g  k+ +keR+  lve++G+++  +++
  gi|557695156|ref|YP_008798210.1| 108 MLYGLDKETAKERINRLVEEVGLKEVENEL 137
                                       4589999****************9988776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.12
                                       TCEEEEE.EEEEGGGHHHHHHHHHHHHHHHS-CSSGGG-SH CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  96 kktsarl.gfvpeeevlevveaivevyrdhgdrknrkkeRl 135
                                       +kt a++ +++p++    v++++   yr h+ ++n ++ R+
  gi|557695156|ref|YP_008798210.1| 235 GKTVAVMeVWLPTD-AEHVLDKLESAYRTHDPATNIYRIRV 274
                                       56677668999999.99***********9999999887775 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00032      0.25       8      41 ..      25      56 ..       8      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00032
                                      HHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHH CS
                              TsaE  8 ealgkklakalgdvilLeGdLGaGKTtlvrglak 41
                                      e++  ++ k  g++  L G+ GaGKTtlv+ l  
  gi|557695156|ref|YP_008798210.1| 25 EKVNLRIEK--GQIYGLLGPNGAGKTTLVKILTT 56
                                      333344444..88899*************98875 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   0.00041      0.32       5      30 ..      34      59 ..      30     197 .. 0.75
   2 ?   -1.6   0.0         4   3.1e+03      42      56 ..     238     252 ..     189     295 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00041
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqld 30
                                       +i  + G+ G+GKTtl++ l+  l 
  gi|557695156|ref|YP_008798210.1| 34 GQIYGLLGPNGAGKTTLVKILTTLLL 59
                                      6677789************9999883 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 4
                            AAA_22  42 vvfvtlpsstsskdl 56 
                                       v+ +++  +t+ + +
  gi|557695156|ref|YP_008798210.1| 238 VAVMEVWLPTDAEHV 252
                                       223333333333333 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00033      0.26      27      52 ..      39      64 ..      27      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00033
                      Mg_chelatase 27 lvGppGsGKtmlakrlpsllpplsee 52
                                      l+Gp G+GKt l k l++ll p + e
  gi|557695156|ref|YP_008798210.1| 39 LLGPNGAGKTTLVKILTTLLLPTTGE 64
                                      78****************99887765 PP

>> Ph1570  Ph1570 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00037      0.29      18      61 ..      26      77 ..      16     103 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                            Ph1570 18 kfnleie...vyg.....kdarklllalirelylpeygeeyvypfecakefw 61
                                      k nl+ie   +yg     + ++  l+ ++  l lp  ge yvy ++++ke  
  gi|557695156|ref|YP_008798210.1| 26 KVNLRIEkgqIYGllgpnGAGKTTLVKILTTLLLPTTGEAYVYGYDVSKEAS 77
                                      556665422245533333467889999**********************965 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.029        23      17      38 ..      35      56 ..      22      72 .. 0.78
   2 ?    4.5   0.0     0.024        18      56     105 ..     178     227 ..     164     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.029
                        Zeta_toxin 17 klillgGqpGAGKselaellkd 38
                                       ++ l G  GAGK++l + l++
  gi|557695156|ref|YP_008798210.1| 35 QIYGLLGPNGAGKTTLVKILTT 56
                                      566677999*******998875 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.024
                        Zeta_toxin  56 elhPeyeeilkadpkkaseltqkdaselvekllqeaiengyniivegtlr 105
                                       +  +  ++  + d+ ++++lt+  + e+ e+    a+ n+  ++ egt +
  gi|557695156|ref|YP_008798210.1| 178 RIRRLIKDWVRVDSGRTVILTSHYMAEVEEMCARVAVLNKGRVVAEGTPA 227
                                       444445677789999********************************955 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00047      0.37       3      34 ..      39      78 ..      38     268 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00047
                            AAA_18  3 ltGtpGvGKttlakeLskrlgf.........gvnlrdvake 34
                                      l G+ G+GKttl k L  +l +         g+ +++ a++
  gi|557695156|ref|YP_008798210.1| 39 LLGPNGAGKTTLVKILTTLL-LpttgeayvyGYDVSKEASK 78
                                      78**************7775.23366666665555555555 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1    0.0021       1.6       6      32 ..      39      65 ..      35      78 .. 0.75
   2 ?    0.6   0.0      0.48   3.7e+02     153     183 ..     290     324 ..     282     325 .] 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0021
                                      EEESTTSSHHHHHHHHHHHHHHTTS-E CS
                             SRP54  6 lvGlqGaGKTttlaKLaallkkegkkv 32
                                      l+G++GaGKTt +  L  ll     ++
  gi|557695156|ref|YP_008798210.1| 39 LLGPNGAGKTTLVKILTTLLLPTTGEA 65
                                      89*********9998888776665555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.48
                                       SSSTTHHHHHHHHH....TS-EEEEE-SSSTTGEE CS
                             SRP54 153 dakgGaalsiaael....klPikfigvGekiedle 183
                                       +++gG++ls+++++    ++ +k++g Ge + ++e
  gi|557695156|ref|YP_008798210.1| 290 TSHGGKVLSLVKAMpsfeDVYVKLVGGGEVVSEFE 324
                                       6899*****99987333346799999999998876 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 ?    6.8   0.0    0.0052         4      25      42 ..      35      52 ..      21      59 .. 0.76
   2 ?    1.8   0.0      0.18   1.4e+02     161     211 ..     161     212 ..     108     221 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0052
                                      SEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlld 42
                                      ++  ++GpNG+GK+ l+ 
  gi|557695156|ref|YP_008798210.1| 35 QIYGLLGPNGAGKTTLVK 52
                                      456799********9986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.18
                                       EEEECTTTTTS-HHHHHHHHHHHHHHCTT...SEEEEE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 161 lyllDeidaaLDeknvkkvaellkekskn...aQfivislreemlekadklvgv 211
                                       + +lDe    LD+   +++ +l+k          +i +s+    +e+   + +v
  gi|557695156|ref|YP_008798210.1| 161 VLFLDEPTIGLDAVSARRIRRLIKDWVRVdsgRTVILTSHYMAEVEE--MCARV 212
                                       3468*******************954322211444445544444444..44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       749  (0.0417759); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                       121  (0.00674884); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2251.13
//
Query:       gi|557695157|ref|YP_008798211.1|  [L=272]
Description: ABC-2 type transport system protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   33.1  24.0    3.1e-08   33.1  24.0    1.4  2  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.076   12.3  21.1      0.081   12.2  17.8    2.2  1  ABC2_membrane_2  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 ?   -2.0   0.0      0.16   1.4e+03       4      26 ..      31      52 ..      29      57 .. 0.75
   2 !   33.1  24.0   3.5e-12   3.1e-08     178     344 ..      76     251 ..      45     252 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.16
                   ABC2_membrane_3  4 liitlllPiilvlllglifsnsv 26
                                      l ++ ++P+++v+ +++++  s 
  gi|557695157|ref|YP_008798211.1| 31 L-TESVIPLLIVFAAATLYRVSG 52
                                      4.888999999999888876554 PP

  == domain 2  score: 33.1 bits;  conditional E-value: 3.5e-12
                   ABC2_membrane_3 178 fiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll...afglgipfg..nlglllllfllfg 249
                                        +a+ +  Ekes+ + l +++++s+ +++l+  lg+ ++  + +lli+ll   +++  ip++  + +++ll+f+l +
  gi|557695157|ref|YP_008798211.1|  76 LMASQFYWEKESGNLDLYIIAPISKMSILLGMSLGSIINTSIRALLIFLLatfVLH--IPVSiaDPLAVLLVFVLTL 150
                                       344456679*************************************9996555888..666666************* PP

                   ABC2_membrane_3 250 layialgyllsslfknset.aqilifivil....llsgffgglfp.ledlpsalkwifsiiPffapglgllrli.tg 319
                                        a+  lg+l+ssl   ++  a++ +  v++    llsg++++++   + +p +++ + s+iP++  ++gl r i  g
  gi|557695157|ref|YP_008798211.1| 151 TALYGLGMLMSSLYMLYGRgAYQ-LNEVFSepvyLLSGLYFPTIGrYSPFPAIIQFLVSLIPLTFGIDGLRRTIiLG 226
                                       *************8888662555.444444455569*******99555479**********************6699 PP

                   ABC2_membrane_3 320 dplweillsliilalfavvylllal 344
                                       + l +++l++ +l++++vv++ la+
  gi|557695157|ref|YP_008798211.1| 227 EGLEQVMLHIYVLLALTVVLIPLAW 251
                                       99999***************99997 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 ?   12.2  17.8   9.1e-06     0.081     100     281 ..      84     254 ..      74     259 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.1e-06
                   ABC2_membrane_2 100 EkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledllllvvasvlllllvv 176
                                       Eke+g l l    P+s+++illg  +g+++    + + +l +   +l+ + +l i+++++d l +++++vl+l+++ 
  gi|557695157|ref|YP_008798211.1|  84 EKESGNLDLYIIAPISKMSILLGMSLGSIIN---TSIRALLI---FLLATFVLHIPVSIADPLAVLLVFVLTLTAL- 153
                                       9******************************...66655555...677999999****************999955. PP

                   ABC2_membrane_2 177 flalglllSsvarssreaaalalglfvvlailvpivlyg.vaellagpavpqeindflsllsptsayntllneilag 252
                                         +lg+l+Ss+     + a     +f   + l +++ ++ ++     pa+   i+ ++sl++ t  ++ l+++i+ g
  gi|557695157|ref|YP_008798211.1| 154 -YGLGMLMSSLYMLYGRGAYQLNEVFSEPVYLLSGLYFPtIGRYSPFPAI---IQFLVSLIPLTFGIDGLRRTIILG 226
                                       .9********9764444333333333333333333333313333333333...555566666666677777777777 PP

                   ABC2_membrane_2 253 sdlnalgstatnllilllllavllvlgy..v 281
                                       ++   l + + ++ +ll+l++vl+ l++   
  gi|557695157|ref|YP_008798211.1| 227 EG---LEQVMLHIYVLLALTVVLIPLAWrvL 254
                                       76...34677777777777777777777544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); 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: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1982.61
//
Query:       gi|557695158|ref|YP_008798212.1|  [L=279]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00015   21.3  20.9    0.00015   21.3  20.9    1.6  2  ABC2_membrane    ABC-2 type transporter
    0.00034   20.0  17.5    0.00043   19.7  17.5    1.1  1  ABC2_membrane_2  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 !   21.3  20.9   1.7e-08   0.00015      11     208 ..      20     233 ..      10     234 .. 0.75
   2 ?   -1.9   0.0       0.2   1.8e+03      23      41 ..     243     261 ..     238     273 .. 0.58

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.7e-08
                     ABC2_membrane  11 flqrwrdpslgllwrliqplllalvfgtvfgnlgnsedglnr..............pgllffsvlflafsaltsvap 73 
                                       + + w  p++++ +++i+pl  +l+f +++        g+n+              +g  ff+   +a + + ++++
  gi|557695158|ref|YP_008798212.1|  20 VESNWTEPFIFIGLQVIRPLASTLLFPLLYL------VGMNFigrpvdpnylgyifVGTAFFTPYIFA-AETGGTIV 89 
                                       5567999999999******************......3454456677778886664444444444444.77888899 PP

                     ABC2_membrane  74 vferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv....gldls.rf...flflllllltal 142
                                       + +rer  +++  +  ++sls y+l+++l+ +++sl+ +l  ++ +y l+    g+ +  r    + ++l+l ++++
  gi|557695158|ref|YP_008798212.1|  90 SQDRERYGVMKSIYITTSSLSIYFLGRFLAVAAISLFSTLSSFAAAYALIvwgiGYSMPlRLenlLDAFLALGAIYI 166
                                       ***********************************************998664444444733545555555555555 PP

                     ABC2_membrane 143 aasslgllisalapsfedas.qlaslvllpllllsGffipidsm.pkwlqwiaylnPltyavealrsn 208
                                        + ++++++ +++      +  l+  +l +l ll+ +++p++s+ p     +ay++P   a++ lr +
  gi|557695158|ref|YP_008798212.1| 167 GSFAIFFILPSINLLTNKLQwSLTYYFLGLLYLLGDIIFPVQSLsP-LAEPLAYILPTNQALNTLRDA 233
                                       555555555444444444431445556677789999********88.***************999976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.2
                     ABC2_membrane  23 lwrliqplllalvfgtvfg 41 
                                       ++  +  +l+a +  +vf 
  gi|557695158|ref|YP_008798212.1| 243 AAAYLASILWAALGYFVFK 261
                                       4445555555555555555 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 !   19.7  17.5   4.8e-08   0.00043      80     285 ..      71     262 ..      27     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.8e-08
                   ABC2_membrane_2  80 imavlipvi.aalfgadaiagEker.gTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalg 153
                                        +a++ p i aa +g ++++ ++er g +k  + +  s + + lg f++ +ai+l+ ++ ++ a++ l +++  +++
  gi|557695158|ref|YP_008798212.1|  71 GTAFFTPYIfAAETGGTIVSQDRERyGVMKSIYITTSSLSIYFLGRFLAVAAISLFsTLSSFAAAYAL-IVWGIGYS 146
                                       5677777545999***********9899*************************************999.******** PP

                   ABC2_membrane_2 154 ivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavpqein 230
                                       ++l+le+ll  ++a  ++ + + f+ +++l S+ + +++ +  l   ++ +l++l +i+  +v +l   +++     
  gi|557695158|ref|YP_008798212.1| 147 MPLRLENLLDAFLALGAIYI-GSFAIFFILPSINLLTNKLQWSLTYYFLGLLYLLGDIIF-PVQSLSPLAEP----- 216
                                       **********9999996666.455666666677777777777777666667888887776.88888888888..... PP

                   ABC2_membrane_2 231 dflsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkr 285
                                         l ++ pt   n++ln++    +    ++t+ n ++  l  +   +lgy++Fkr
  gi|557695158|ref|YP_008798212.1| 217 --LAYILPT---NQALNTLRDALG----LPTTYNTAAAYLASILWAALGYFVFKR 262
                                       ..5555555...455555544443....444555555555555556799999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); 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):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1906.08
//
Query:       gi|557695159|ref|YP_008798213.1|  [L=339]
Description: L-iditol 2-dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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   75.5   0.0    5.7e-21   74.8   0.0    1.3  1  ADH_zinc_N    Zinc-binding dehydrogenase
    1.2e-18   67.0   0.2    2.2e-18   66.1   0.2    1.4  1  ADH_N         Alcohol dehydrogenase GroES-like domain
      2e-06   28.9   0.0    3.4e-06   28.2   0.0    1.4  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    2.4e-06   27.2   0.1    4.5e-06   26.3   0.1    1.5  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
    2.5e-05   24.1   0.4    9.8e-05   22.2   0.4    1.8  1  ADH_N_2       N-terminal domain of oxidoreductase
     0.0025   17.9   0.7     0.0062   16.6   0.7    1.6  1  NADH_4Fe-4S   NADH-ubiquinone oxidoreductase-F iron-sulfur bi
  ------ inclusion threshold ------
      0.036   13.4   0.0      0.065   12.6   0.0    1.4  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   2.2e-24   5.7e-21       2     128 ..     171     299 ..     170     301 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 2.2e-24
                                       HHHHHHHHHHHTT-EEEE.EESSHHHHHHHHHTTESEEEET.TTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                        ADH_zinc_N   2 vGlaavqlAkalGaevia.vdsseeklelakklGadeviny.keadlverikeltggegvdvvfecvGsgatleaal 76 
                                        G++ + +Aka+Ga v+a    s+ ++++a ++Gad+++++ +e d+ ++++elt+g gvd+++ ++ + + l++al
  gi|557695159|ref|YP_008798213.1| 171 TGTIFIVMAKAFGAPVVAvSELSKYRRDMALENGADAAVDPlSE-DFAKKCRELTDGLGVDIAVLATPAAKPLSTAL 246
                                       69999*********88883566788****************655.*****************9999888******** PP

                                       HCEEEEEEEEECSCTSSEEE..EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N  77 kllkpgGrlvvvGggkgeee..fdlrnlllkeksilGsllgslreefkealdll 128
                                       ++l++gG+l ++G+++++e+  +d+++l+ +ek+i+ s   +   e  ++l++l
  gi|557695159|ref|YP_008798213.1| 247 DSLRRGGTLLLFGAPEKGEKteVDFSRLFIEEKNIVTSYSTT-EAETNTVLHML 299
                                       **************66666667***************99998.77777777766 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 !   66.1   0.2   8.5e-22   2.2e-18       2     105 ..      25     121 ..      24     124 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 8.5e-22
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-G CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegee 78 
                                       ge+l++++++g+ g+Dl+ + g    +  +p +lGHE+vG+v+e   + ++++ GdrV+v+++++cg+C++C+eg++
  gi|557695159|ref|YP_008798213.1|  25 GELLVEMRMCGVDGTDLEKAFG----RPLTPPMLGHEVVGVVAES--RAEGFEEGDRVFVHHHVTCGKCYYCREGSP 95 
                                       799***************9999....3555669**********95..5789************************** PP

                                       GG-TTBEETTTSS-SSSBSEEEECGGG CS
                             ADH_N  79 nlCeeakllgvsldGgfaeyvvvpekk 105
                                       ++C+    ++++ + gfae + vp+ +
  gi|557695159|ref|YP_008798213.1|  96 TMCPLFLQTSID-PCGFAEFFRVPRVN 121
                                       ***998888888.78899999988765 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 !   28.2   0.0   1.3e-09   3.4e-06       2     133 .]     204     337 ..     203     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.3e-09
                                       T-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEE CS
                      ADH_zinc_N_2   2 GAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvk 74 
                                       GAd ++d  +edf+    + t+g gvD+++ ++  ++ l+ +l+ l+ gG+l+  g+p    + +++++   +r + 
  gi|557695159|ref|YP_008798213.1| 204 GADAAVDPLSEDFAkkcrELTDGLGVDIAVLATPAAKPLSTALDSLRRGGTLLLFGAP----EKGEKTEVDFSRLFI 276
                                       9*****************99********99999955556999999*777***988864....666666767788888 PP

                                       E--GGG...-..-HHHHHHHHHHHHHHH..----EEEEEEGGGHHHHHHHHHSS--SSEEEE CS
                      ADH_zinc_N_2  75 yeflfsmkas.aqadileelaalieeGk..lrpvvdrvfpleeaaeAhrylesgrarGKiVl 133
                                        e  + ++++   + + +++++++ ++   l+  ++++++le+a eA+++ +   +  K+Vl
  gi|557695159|ref|YP_008798213.1| 277 EEKNI-VTSYsTTEAETNTVLHMLTKKVftLKQLITHTYSLEKAEEAFQRARDPNTSLKVVL 337
                                       88888.77778556669**********88899******************999999888887 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 !   26.3   0.1   1.8e-09   4.5e-06      36     210 ..     165     337 ..     137     338 .. 0.64

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.8e-09
                       Glu_dehyd_C  36 vlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatY.vds.re...tpvdeipeaseemdlvvEa 107
                                       ++GaG+ G + +++ +a    +    v++  +  + + d+  e Ga   vd  +e   ++  e+      +d+ v a
  gi|557695159|ref|YP_008798213.1| 165 LVGAGPTGTIFIVMAKA----FG-APVVAVSELSKYRRDMALENGADAaVDPlSEdfaKKCREL-TDGLGVDIAVLA 235
                                       45777777666444433....32.2344444444444444444444321222012000222222.234579****** PP

                       Glu_dehyd_C 108 TGsakhafeaiealapnGvaaLlGvpeds.evevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpeslld 183
                                       T +ak +  a++ l+  G   L G pe+  + evd ++l     +e k +v s  +  ++ ++ ++ L+  +   l+
  gi|557695159|ref|YP_008798213.1| 236 TPAAKPLSTALDSLRRGGTLLLFGAPEKGeKTEVDFSRLF----IEEKNIVTSYSTTEAETNTVLHMLT-KKVFTLK 307
                                       **************************986599***99875....5699999998777776665555554.455669* PP

                       Glu_dehyd_C 184 elvtkvvdldeleeAfe...dddetiKtvv 210
                                       +l+t+ + l+++eeAf+   d ++++K+v+
  gi|557695159|ref|YP_008798213.1| 308 QLITHTYSLEKAEEAFQrarDPNTSLKVVL 337
                                       ****************84445567888876 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 !   22.2   0.4   3.8e-08   9.8e-05      19      91 ..      13      79 ..      10      86 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 3.8e-08
                           ADH_N_2 19 eleeeelpelkdGevlvralylSvDPymRgrmndaksyvepvelgdvmrgg.avgeVveSknpdfkvGdlVvgl 91
                                      e++++++pe+++Ge+lv+++  +vD +    +  +k      +l  +m g+ +vg V eS+++ f++Gd V  +
  gi|557695159|ref|YP_008798213.1| 13 EVVDVDVPEVGEGELLVEMRMCGVDGTD---L--EKA--FGRPLTPPMLGHeVVGVVAESRAEGFEEGDRVFVH 79
                                      78899********************653...2..222..2245677888862689999***********99765 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 !   16.6   0.7   2.4e-06    0.0062      11      29 ..      80      98 ..      76     104 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.4e-06
                                      HHH--S--HHHHIIIIHHH CS
                       NADH_4Fe-4S 11 aaesCGkCtpCreGtkrll 29
                                      ++ +CGkC  CreG++ + 
  gi|557695159|ref|YP_008798213.1| 80 HHVTCGKCYYCREGSPTMC 98
                                      5789***********9986 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 ?   12.6   0.0   2.6e-05     0.065      35      72 ..     159     196 ..     152     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.6e-05
                                       TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHH CS
                      2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkke 72 
                                       +g t+ ++G+G  G+ ++ ++kafg+ v+a++   k +
  gi|557695159|ref|YP_008798213.1| 159 AGHTLSLVGAGPTGTIFIVMAKAFGAPVVAVSELSKYR 196
                                       589***************************99876644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      663  (0.0369792); 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):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2360.87
//
Query:       gi|557695160|ref|YP_008798214.1|  [L=366]
Description: dehydrogenase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-28   96.4   0.6    1.7e-27   95.4   0.1    1.7  2  ADH_N         Alcohol dehydrogenase GroES-like domain
    7.7e-27   93.8   0.0    1.3e-26   93.1   0.0    1.3  1  ADH_zinc_N    Zinc-binding dehydrogenase
    4.1e-09   37.6   0.0    7.1e-09   36.8   0.0    1.3  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    7.5e-09   35.4   0.0    1.4e-08   34.5   0.0    1.5  1  Glu_dehyd_C   Glucose dehydrogenase C-terminus
  ------ inclusion threshold ------
      0.077   13.3   0.1       0.13   12.5   0.1    1.4  1  TrkA_N        TrkA-N domain
      0.084   12.2   0.2       0.13   11.5   0.2    1.2  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-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 !   95.4   0.1   5.7e-31   1.7e-27       2     104 ..      46     149 ..      45     155 .. 0.93
   2 ?   -2.6   0.0       1.7   5.1e+03      47      62 ..     179     194 ..     171     198 .. 0.76

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 5.7e-31
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-G CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegee 78 
                                       gevl+++ ++  Cg+Dl+++    ++ +++p+i+GHE++G+v+evg+ev+ ++vGd+Vv+    +cg C +Ck g+ 
  gi|557695160|ref|YP_008798214.1|  46 GEVLVRTFVTLTCGTDLKMFLR-GHPYARPPVIMGHEFAGVVVEVGEEVDWVNVGDEVVAANSAPCGYCIYCKLGRF 121
                                       79***************99998.69**************************************************** PP

                                       GG-TT..BEETTTSS-SSSBSEEEECGG CS
                             ADH_N  79 nlCee..akllgvsldGgfaeyvvvpek 104
                                       nlCe+  ++++g+s+dG++aey+ +p++
  gi|557695160|ref|YP_008798214.1| 122 NLCENlgETIIGFSVDGAYAEYIKLPRR 149
                                       ***87335678888*********99976 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
                                       STT-CS--TT-EEEE- CS
                             ADH_N  47 gpevkklkvGdrVvve 62 
                                       g+++ ++ vGd V+v 
  gi|557695160|ref|YP_008798214.1| 179 GQRLIHIDVGDAVAVV 194
                                       6777789999999985 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.0   4.2e-30   1.3e-26       1     129 [.     198     328 ..     198     329 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 4.2e-30
                                       HHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaal 76 
                                       ++Gl+ + l + +Ga +vi+ d++ ++l++a +lGad v+n+ e+d  +r+ e tgg g+dvv+e+vG ++t+e+al
  gi|557695160|ref|YP_008798214.1| 198 PIGLLHMLLSRLSGArKVIVLDVNWNRLRFASELGADIVVNSGEEDARKRVLEETGGIGADVVIEAVGLPETWERAL 274
                                       79****************************************666******************************** PP

                                       HCEEEEEEEEECSCTSSEEE..EEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                        ADH_zinc_N  77 kllkpgGrlvvvGggkgeee..fdlrnlllkeksilGsllgslreefkealdlla 129
                                       +l+++gG++ ++Gg+ g+++   d+  +++ e+s+ Gs+  + ++++ +al+ll+
  gi|557695160|ref|YP_008798214.1| 275 TLVRKGGTVLFFGGPPGGTKltADTHTIHYGELSLHGSFHHT-PQDVVRALRLLE 328
                                       **************7777775588888**************9.888888999876 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 !   36.8   0.0   2.4e-12   7.1e-09       1     127 [.     231     359 ..     231     361 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.4e-12
                                       TT-SEEEETTSTTHH....HHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EE CS
                      ADH_zinc_N_2   1 lGAdevidyrtedfe....aatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsv 73 
                                       lGAd v+++ +ed++    ++tgg g Dvv+++vg +++ e++l+++++gG+++  ggpp  ++l + +     + +
  gi|557695160|ref|YP_008798214.1| 231 LGADIVVNSGEEDARkrvlEETGGIGADVVIEAVGLPETWERALTLVRKGGTVLFFGGPPGGTKLTADTHTIHYGEL 307
                                       8*********9999999999***************77777*******888*******98655555555554444444 PP

                                       EE--GGG...-.-HHHHHHHHHHHHHHH..----EEEEEEGGGHHHHHHHHHSS-- CS
                      ADH_zinc_N_2  74 kyeflfsmkasaqadileelaalieeGk..lrpvvdrvfpleeaaeAhrylesgra 127
                                       +++  f  +++ ++d   + ++l+e++k  ++  ++ +  le++ + ++ l++g++
  gi|557695160|ref|YP_008798214.1| 308 SLHGSF--HHT-PQD-VVRALRLLESKKlpFEKLITGEARLEDIHRVFEELRQGKH 359
                                       444444..233.667.99**********4445678888999999999999999998 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 !   34.5   0.0   4.7e-12   1.4e-08      32     210 ..     189     364 ..     165     366 .] 0.76

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 4.7e-12
                       Glu_dehyd_C  32 esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYv.dsretpv.deipeas..eemdlv 104
                                       + + v+GaG++GLL  +ll+ + +g  +v vl+    +  ++++ +elGa  v +s e++  +++ e++     d+v
  gi|557695160|ref|YP_008798214.1| 189 DAVAVVGAGPIGLLH-MLLS-RLSGARKVIVLDV---NWNRLRFASELGADIVvNSGEEDArKRVLEETggIGADVV 260
                                       46789**********.5554.5799999****96...4457888999999765244443330334333311468*** PP

                       Glu_dehyd_C 105 vEaTGsakhafeaiealapnGvaaLlGvpeds.evevdggelhrelvleNkalvGsvNanrrhfeaavdtLaalpes 180
                                       +Ea G ++    a++ ++  G +   G p +  ++  d+ ++h         l Gs     +    a++ L++ +  
  gi|557695160|ref|YP_008798214.1| 261 IEAVGLPETWERALTLVRKGGTVLFFGGPPGGtKLTADTHTIHYG----ELSLHGSFHHTPQDVVRALRLLESKK-L 332
                                       *********************999988887653888998888875....67789*********999999887655.4 PP

                       Glu_dehyd_C 181 lldelvtkvvdldeleeAfe..dddetiKtvv 210
                                        +++l+t+++ l+++++ fe  ++ ++iK+++
  gi|557695160|ref|YP_008798214.1| 333 PFEKLITGEARLEDIHRVFEelRQGKHIKVAI 364
                                       579****************9555778999998 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.4e-05      0.13       1      75 [.     191     269 ..     191     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.4e-05
                                       EEEES-SHHH..HHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-T...TSHHHHHHTTGGGESEEEE-SSS CS
                            TrkA_N   1 iiiiGlGrvG..rslaeeLseggkdvvvidkdeerveelreeglevvvgda...tdeevLeeagiekadaviaatgd 72 
                                       ++++G+G +G    l+ +Ls +  +v+v d + +r++ ++e g+++vv ++   +++ vLee g   ad+vi a+g 
  gi|557695160|ref|YP_008798214.1| 191 VAVVGAGPIGllHMLLSRLSGAR-KVIVLDVNWNRLRFASELGADIVVNSGeedARKRVLEETGGIGADVVIEAVGL 266
                                       689*******3335777787766.5******************9988866622245789999999999999988776 PP

                                       HHH CS
                            TrkA_N  73 dea 75 
                                        e+
  gi|557695160|ref|YP_008798214.1| 267 PET 269
                                       665 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 ?   11.5   0.2   4.4e-05      0.13      31     102 ..     191     267 ..     183     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.4e-05
                                       EEEESTSHHHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH.....-SEEEE---B CS
                       AlaDh_PNT_C  31 vlviGgGvaGlqAiatakglga.kVtvlDvrparleqleslgakfvevlksqeellaeavke.....advvigtvli 101
                                       v v+G+G  Gl  +  ++  ga kV vlDv+ +rl+  ++lga  + v + +e++ ++ ++e     advvi +v +
  gi|557695160|ref|YP_008798214.1| 191 VAVVGAGPIGLLHMLLSRLSGArKVIVLDVNWNRLRFASELGAD-IVVNSGEEDARKRVLEEtggigADVVIEAVGL 266
                                       89************9999999857********************.76644444443333333222338999988877 PP

                                       T CS
                       AlaDh_PNT_C 102 p 102
                                       p
  gi|557695160|ref|YP_008798214.1| 267 P 267
                                       7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); 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: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2598.92
//
Query:       gi|557695161|ref|YP_008798215.1|  [L=172]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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    1.6e-29  102.5   0.0    1.1  1  tRNA_edit  Aminoacyl-tRNA editing domain
  ------ inclusion threshold ------
       0.02   14.4   0.0      0.029   13.9   0.0    1.2  1  Flu_NS1    Influenza non-structural protein (NS1)


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 !  102.5   0.0   1.8e-33   1.6e-29       2     122 ..      45     161 ..      44     162 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 1.8e-33
                         tRNA_edit   2 pgtktieelaaalgvdpsaiaKtlvlkdkkgelvlvllpgdreldlkklakllgakklrlaseeelrellgvepGgv 78 
                                       ++++t+e +a a+g++ ++iaK++vlk   +++++v+l gdr++dlkk++k++g   +rla+++e++  +g+++G+v
  gi|557695161|ref|YP_008798215.1|  45 EQARTSESAANAVGCELGQIAKSIVLKG--SRTYVVVLAGDRRIDLKKFSKVVG-EPVRLAKPDEVLSETGYPVGAV 118
                                       6899***********************5..668*********************.********************** PP

                         tRNA_edit  79 gPlglkaagvpvllDeslkeyptvvvgagengatlelspedlrk 122
                                       +P+g+  + +++++D+sl++++ v++++g+ + +l+l +++l++
  gi|557695161|ref|YP_008798215.1| 119 PPFGH-IRPLKTFIDASLLRHKVVYASGGSDSFLLKLGVDTLLN 161
                                       ****9.7*****************************99998875 PP

>> Flu_NS1  Influenza non-structural protein (NS1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.2e-06     0.029     146     185 ..      25      64 ..      13      71 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-06
                                       EEEEEETTS-EEEEEEE-TTSS---HHHHHHHHHHHHHHH CS
                           Flu_NS1 146 llrafteegaivaeisplpslpghtaedvknavgvliggl 185
                                        lr f e+g +v+e + lp     t+e   navg  +g +
  gi|557695161|ref|YP_008798215.1|  25 RLRRFMESGGLVGEFVELPPEQARTSESAANAVGCELGQI 64 
                                       589*******************************988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       212  (0.0118244); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1275.11
//
Query:       gi|557695162|ref|YP_008798216.1|  [L=243]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for complete 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-26   93.0  41.3    2.5e-26   92.8  41.3    1.0  1  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
        3.2    8.0   6.4       0.23   11.7   0.6    2.0  2  DUF3093   Protein of unknown function (DUF3093)


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 !   92.8  41.3   2.7e-30   2.5e-26       3     236 .]      12     239 ..       8     239 .. 0.87

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 2.7e-30
                              TauE   3 lagllaGfvagllGiGggliavPlLlll.lppavavatsllavvatslsgalahrrrgnvdw.rlllllllgsliGa 77 
                                       l+g+ a f+  l G++gg +++ +Ll++ +p+ +a+ + l+ +++++ s++l++r     ++ r +l++++gs++ a
  gi|557695162|ref|YP_008798216.1|  12 LLGA-AAFFYTLGGFAGGSVFIAILLAAsVPAGQAALAGLVFNTVSTSSSILRWRI----HFsREMLWFVAGSVPMA 83 
                                       4444.88********************659**************999999999876....45489999********* PP

                              TauE  78 llGallllllpsellkllfgvlllllallmllrkkrsrakgrerrptaillvligglvGllsGllGiGgGfllvpll 154
                                       ++G+ll  ++p+ell+ ++gv++l+ ++ +l+  + +    ++ + + ++ vl+g+++Gll+Gl+GiGgG+ l+pll
  gi|557695162|ref|YP_008798216.1|  84 FVGGLL--YVPDELLRRVMGVAILVGGFTVLTATF-Q---LKKVYLGIPARVLVGCGIGLLAGLTGIGGGVYLAPLL 154
                                       ******..99***************9999998776.2...23567777778999999******************** PP

                              TauE 155 llllglplkkavatslllilvislagalgyal..agavdwpllllllpgallGallGarl.arrlsertlrrlfall 228
                                       ++l   ++k+++at+++lil++slag+l+ +      +  p++l+++  ++l+a+lG+++ a+ +s++t+rr++al+
  gi|557695162|ref|YP_008798216.1| 155 IMLDIANPKTTAATTTTLILLNSLAGILARLPrlPTLLPNPVILAAISLIILTAQLGSYTgAKLFSQKTVRRVIALI 231
                                       **99**********************9997445555566666777888899999999996255559*********** PP

                              TauE 229 llvlgvkl 236
                                       l+ +g++l
  gi|557695162|ref|YP_008798216.1| 232 LISIGLYL 239
                                       *****996 PP

>> DUF3093  Protein of unknown function (DUF3093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.6   2.6e-05      0.23      21     104 ..      31     112 ..      14     117 .. 0.79
   2 ?   -1.5   0.3       0.3   2.7e+03      32      32 ..     192     192 ..     126     238 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.6e-05
                           DUF3093  21 laaalvaaevglavavlvaavlvalavvallalsrtrieVtdgeLrvgrarlplavvgrvealdaeakraalgrqld 97 
                                       ++a+l+aa v  + a+l+   lv  +v    ++ r ri+ +++ L+    ++p+a+vg    +++e  r+ +g ++ 
  gi|557695162|ref|YP_008798216.1|  31 FIAILLAASVPAGQAALA--GLVFNTVSTSSSILRWRIHFSREMLWFVAGSVPMAFVGGLLYVPDELLRRVMGVAIL 105
                                       235555666655555554..77888888999999***************************************9887 PP

                           DUF3093  98 paAfvvl 104
                                          f vl
  gi|557695162|ref|YP_008798216.1| 106 VGGFTVL 112
                                       7777765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.3
                           DUF3093  32 l 32 
                                       l
  gi|557695162|ref|YP_008798216.1| 192 L 192
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); 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):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1841.00
//
Query:       gi|557695163|ref|YP_008798217.1|  [L=166]
Description: hypothetical protein CSUB_C1736 [Candidatus Caldiarchaeum subterraneum]
Scores for 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 ------
      0.069   13.4   3.9          5    7.4   0.0    2.7  2  TrbC      TrbC/VIRB2 family
      0.082   12.9   0.5      0.082   12.9   0.5    2.3  3  DUF2116   Uncharacterized protein containing a Zn-ribbon (DUF
        2.2    8.6   7.3       0.48   10.7   0.3    2.4  2  DUF3382   Domain of unknown function (DUF3382)


Domain annotation for each model (and alignments):
>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00083         5       9      42 ..       4      35 ..       1      48 [. 0.82
   2 ?    4.9   2.2    0.0052        31      53      95 ..     112     154 ..     110     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00083
                              TrbC  9 rrlllalalalvllllaspalAqaaggdpvetvl 42
                                      r+++++++++++++++ +p++A+++  + v++ l
  gi|557695163|ref|YP_008798217.1|  4 RSTKTLALILMLFVFSIQPVFADGG--EEVNKEL 35
                                      67889999999***********876..6766655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0052
                              TrbC  53 lakviatiaiivaGimlafgrlswrtlvmvviGiviifgAssi 95 
                                       l+ ++++ a++v+G+ l+    +  +++  vi + i++ A  i
  gi|557695163|ref|YP_008798217.1| 112 LSLTVVIAAVMVSGYFLMLVSNRYSKALNKVIHTQIVITALLI 154
                                       567999**********999988888888888888888777555 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 ?   -0.5   0.1      0.22   1.3e+03      44      53 ..       9      18 ..       2      24 .. 0.59
   2 ?   -3.2   0.2       1.5   8.7e+03      45      53 ..     116     122 ..     112     127 .. 0.46
   3 ?   12.9   0.5   1.4e-05     0.082      26      56 ..     133     163 ..     131     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.22
                           DUF2116 44 gililllavv 53
                                      ++lil+l v+
  gi|557695163|ref|YP_008798217.1|  9 LALILMLFVF 18
                                      4555555555 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.5
                           DUF2116  45 ililllavv 53 
                                       ++i+  av+
  gi|557695163|ref|YP_008798217.1| 116 VVIA--AVM 122
                                       2222..222 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 1.4e-05
                           DUF2116  26 eeyekkrkkvarsqqilfgililllavvlvl 56 
                                       ++y+k+ +kv+++q+++++ li+l+++ +++
  gi|557695163|ref|YP_008798217.1| 133 NRYSKALNKVIHTQIVITALLIVLIILHVIT 163
                                       68*********************88877765 PP

>> DUF3382  Domain of unknown function (DUF3382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3     8e-05      0.48      12      52 ..       9      49 ..       7      88 .. 0.88
   2 ?    0.8   1.8     0.098   5.9e+02      76      95 ..     136     157 ..      91     160 .. 0.56

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 8e-05
                           DUF3382 12 lalvlfvpilGlqleldgtrlvleprwglvaiavavvfvgq 52
                                      lal+l+++++ +q +  ++  ++++++g++ai+++v +   
  gi|557695163|ref|YP_008798217.1|  9 LALILMLFVFSIQPVFADGGEEVNKELGWLAIGAGVLATLP 49
                                      89********************************9987665 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.098
                           DUF3382  76 dgvlvl..tqrwiillllvvAl 95 
                                       +++l++  +++++i +ll+v +
  gi|557695163|ref|YP_008798217.1| 136 SKALNKviHTQIVITALLIVLI 157
                                       2222223345555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1394.60
//
Query:       gi|557695164|ref|YP_008798218.1|  [L=232]
Description: transcriptional regulator [Candidatus Caldiarchaeum subterraneum]
Scores for 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-06   26.2   0.1    0.00013   21.9   0.0    2.3  2  HTH_19    Helix-turn-helix domain
    1.1e-05   25.4   0.2    4.1e-05   23.5   0.2    2.0  2  HTH_3     Helix-turn-helix
    0.00012   22.3   0.0    0.00049   20.4   0.0    2.0  2  HTH_31    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.1e-08   0.00013       1      52 [.      21      72 ..      21      72 .. 0.97
   2 ?    1.7   0.0     0.044   2.6e+02      11      41 ..      80     106 ..      78     120 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.1e-08
                            HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaeal 52
                                      Ge Lk+ R  + l+q+ +a++ +is s +s +E+ +++ p+ + +++++eal
  gi|557695164|ref|YP_008798218.1| 21 GEVLKKWRTLFELSQKSIAREMSISSSVLSDYEKSRRKSPGTDFIRRYVEAL 72
                                      899********************************999***********986 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.044
                            HTH_19  11 lgltqeelaerlgisrskisaiEngkkdvps 41 
                                        gl+++e a+++++    +s    g +++++
  gi|557695164|ref|YP_008798218.1|  80 GGLKIREFASDVQT----LSDVVLGMSEYTT 106
                                       699*******9999....6666666444555 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   6.9e-09   4.1e-05       1      48 [.      24      72 ..      24      74 .. 0.95
   2 ?   -1.8   0.0      0.57   3.4e+03      23      40 ..      91     109 ..      79     118 .. 0.60

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.9e-09
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaL 48
                                      lk++R    lsq+ +A+++ +s s +s++E+  + +P  + + ++ +aL
  gi|557695164|ref|YP_008798218.1| 24 LKKWRTLFELSQKSIAREMSISSSVLSDYEKSrRKSPGTDFIRRYVEAL 72
                                      89******************************99999999999999887 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.57
                                       HHHHHHHHTT..SSCSBHHH CS
                             HTH_3  23 rstisriEnG..ernPslet 40 
                                       ++t+s+   G  e   +++t
  gi|557695164|ref|YP_008798218.1|  91 VQTLSDVVLGmsEY-TTPKT 109
                                       46777776665422.44444 PP

>> HTH_31  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   8.1e-08   0.00049       3      54 ..      21      72 ..      21      80 .. 0.95
   2 ?   -1.8   0.0       0.7   4.2e+03      33      40 ..     168     175 ..     166     205 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 8.1e-08
                            HTH_31  3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                      G+ L+ +R+   Lsq+  A+   +s s ls++E  rr  p  ++++++++al
  gi|557695164|ref|YP_008798218.1| 21 GEVLKKWRTLFELSQKSIAREMSISSSVLSDYEKSRRKSPGTDFIRRYVEAL 72
                                      899*********************************************9997 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.7
                            HTH_31  33 rlEqGrrg 40 
                                        +E+Gr +
  gi|557695164|ref|YP_008798218.1| 168 NVERGRSP 175
                                       67888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 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:                        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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1762.13
//
Query:       gi|557695165|ref|YP_008798219.1|  [L=145]
Description: hypothetical protein CSUB_C1738 [Candidatus Caldiarchaeum subterraneum]
Scores for 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   14.1   0.7      0.023   13.8   0.7    1.1  1  DUF898    Bacterial protein of unknown function (DUF898)
      0.093   12.4   0.9       0.12   12.1   0.9    1.2  1  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF898  Bacterial protein of unknown function (DUF898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.7   2.6e-06     0.023      62     118 ..       8      67 ..       4      86 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-06
                            DUF898  62 ellkGflialvllvlysvasala...pllglllllllflllpwaivramrFrlrntswRG 118
                                         + Gf ++++ll+++  as +    p +  l+l+++++ll + + +a++ +l  + w +
  gi|557695165|ref|YP_008798219.1|   8 GSFSGFWLLMLLLIAVATASFFIrlsPGILGLALAAMAILLTLYWAKAVKNSLGSSAWDD 67 
                                       5699************98888887778899999999999*******************76 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.9   1.3e-05      0.12       6      66 ..      12      76 ..       8     108 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.3e-05
                           DUF4131  6 alvllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqlles.......g 66
                                       ++ll+lll++ +++ ++   r ++ + l+l+l+++++ll +++  + +n+   s + ++       g
  gi|557695165|ref|YP_008798219.1| 12 GFWLLMLLLIAVATASFFI--RLSPGI-LGLALAAMAILLTLYWAKAVKNSLGSSAWDDYllelrqeG 76
                                      5788888888888887775..333333.3333333333333333333333333333333322243322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1127.32
//
Query:       gi|557695166|ref|YP_008798220.1|  [L=931]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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-40  137.8   1.8    3.9e-40  137.8   1.8    2.5  2  UPF0182   Uncharacterised protein family (UPF0182)


Domain annotation for each model (and alignments):
>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   3.8      0.17   3.1e+03       3      57 ..      18      72 ..      14     150 .. 0.46
   2 !  137.8   1.8   2.2e-44   3.9e-40     230     753 ..     248     748 ..     180     753 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 0.17
                           UPF0182  3 lllavlavlllllellarlytellwfkelgylsvfltrlltrlllfvvvflllal 57
                                      +ll++l+++ l++  +++++ +++ f +l  +  ++  +   +l f++ f l ++
  gi|557695166|ref|YP_008798220.1| 18 VLLVLLLFTGLFIGSFINIWLNVMEFGDLFIRPFYFSLIGGLTLSFIALFRLDFV 72
                                      3444444444556666666777777666666666655555555555544433333 PP

  == domain 2  score: 137.8 bits;  conditional E-value: 2.2e-44
                           UPF0182 230 lpaktilavialvvavlllvaivlkk..lklplialallvllaillgvvlpalvqkfiVkPnelekEkpYiernIea 304
                                         +k++++++ ++ avl ++ ++  +    l  ++l l +l++i l ++   +vq++i + +++e   pY+ ++I++
  gi|557695166|ref|YP_008798220.1| 248 YNTKVLIVAAFTASAVLAFYGYLDLRgkRFLNNVWLRLGLLVIIGLLTASVVTVQNTIADAQKIEYKGPYVLQEIHV 324
                                       334444444455556666665533331222334444444445554556666789*********************** PP

                           UPF0182 305 TreAygLdkveveefeaeael.....taedleenaetienirLlDprplletfrqlqqirnYYkFedldvdrYtidg 376
                                        r   +L + ++ +++ ++++      ++ +++n++ ++  rL+D+++  +  r    + +Y +Fed d+ rY+ + 
  gi|557695166|ref|YP_008798220.1| 325 NRFLADL-NFKILPYNFSKTTvsaanASAIVNANEDILSRARLWDWDAAFAKLRPEIGLIPYVDFEDSDILRYNGSL 400
                                       **98888.4444444444444345535667799****************************************8765 PP

                           UPF0182 377 eerqvviaaREldysalpeeaktwvnkhlvYTH.GyGvvaspvnkvteeGlpeflvkdipseeeeslkieepriYfG 452
                                              + + +   ++ + a+ w n+hlvYTH   G+ +  + + +   + +                +e riY+G
  gi|557695166|ref|YP_008798220.1| 401 Y---WSASMKPVLPPTV-TPADAWYNRHLVYTHiPQGFLMLDAHTGEIVDSSK--------------FFNERRIYYG 459
                                       4...5556677777777.4679***********6689*999998765433333..............35689***** PP

                           UPF0182 453 eltndyvivgt.kvkEfdypsgeenvyntYdGkgGvkigsllrrllfaiklkdlklllsseitseskilfrRnikeR 528
                                       e  ++  + +  +   +  + ++e   ++Y+G+gGvkig +l+  l+     d+ ++ls + ++e  +l +R+i++R
  gi|557695166|ref|YP_008798220.1| 460 EGGPRSLFSSDwAAIIMGKDVSDEIGGSRYSGSGGVKIGPPLSW-LY-----DVTFFLS-YPDKEILLLRYRDIHDR 529
                                       **88888888844445666666667889**********977764.33.....5555554.4567777899******* PP

                           UPF0182 529 vekvaPfLtl...Ds..dpYlvvadgrlyWivD..aYTtsdrYPySepeeatsgeeevnYiRNSVKvvvDAydGtvk 598
                                       v+ + P++++   D+  d ++v+   r yW++   a   +++ P+S+            ++R    ++vDAy+G+++
  gi|557695166|ref|YP_008798220.1| 530 VQLLFPYFSYvykDEyvDMFPVTDGTRTYWMMPliAILPTENVPWSNG---------NPFVRFVGLALVDAYNGEIR 597
                                       ********98544333366788888******9744777799*****87.........269999999*********** PP

                           UPF0182 599 lYvvdeeDPiikawskiFpglfkplsempeeLrshlrYPedlFkvqsellakYHvtdpevFYnredlWevpkeeeeq 675
                                       l +   +D   k ++ ++ + ++   ++p+ L++++rYP +lF+ q+++++ YH++dp  F +  ++ e+p+     
  gi|557695166|ref|YP_008798220.1| 598 LITLG-DDMFTKLFEAVYADKVSR--DVPNWLHNQIRYPAELFDYQTRMFSIYHIDDPAIFIQARQFYEIPSG---- 667
                                       *8887.89************9875..9*********************************************9.... PP

                           UPF0182 676 pvePyYlilklpgeekeefillspftp..ssrenliawlaarsdgenygklllyelpkqelv..yGpeqiearinqd 748
                                        ve y++++klp++++ ef+ ++ +    s+  nl+++ ++r+d  + g++  y++ +++ +   Gp+ + + ++ d
  gi|557695166|ref|YP_008798220.1| 668 -VEVYFVVTKLPNHSQLEFVGILSLELrgSRGLNLAGYAVVRNDYPHTGEMYFYRVAEDSPIklLGPSAALQALQRD 743
                                       .******************87666665215667*************************98762269*9999999999 PP

                           UPF0182 749 peisq 753
                                       p+ ++
  gi|557695166|ref|YP_008798220.1| 744 PDFRT 748
                                       98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (931 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       605  (0.0337442); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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):               1  [number of targets reported over threshold]
# CPU time: 0.73u 0.25s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 6261.15
//
Query:       gi|557695167|ref|YP_008798221.1|  [L=561]
Description: acetolactate synthase I/II/III large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-43  147.2   0.0    2.7e-42  144.3   0.0    2.1  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    5.2e-16   58.8   0.0    1.4e-15   57.4   0.0    1.7  1  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
  ------ inclusion threshold ------
      0.034   13.0   0.2      0.068   12.0   0.2    1.5  1  XFP_N         XFP N-terminal domain
       0.16   11.7   0.0       0.33   10.7   0.0    1.6  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 !  144.3   0.0     6e-46   2.7e-42       3     169 ..      11     188 ..       9     190 .. 0.97
   2 ?    0.3   0.0       0.1   4.7e+02     113     148 ..     511     546 ..     432     559 .. 0.75

  Alignments for each domain:
  == domain 1  score: 144.3 bits;  conditional E-value: 6e-46
                                       HHHHHHHHHHHCT--EEEE---CCCHH.HHCCHHCT...TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHH CS
                      TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilp.lldalseeq..girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGa 76 
                                       ++ +l+  L+++gv+++f++ G+++   lld+++ ++  + ++v++++E +a++aA gy+ +  +  +v+v++ pG+
  gi|557695167|ref|YP_008798221.1|  11 GGGLLLVSLRKAGVDRFFINSGTEYSGlLLDYMHLSPsqRPEMVVCLSETTAVAAAYGYSLMNENASAVMVHTVPGV 87 
                                       67789999*******************999999999999************************************** PP

                                       HHCHHHHHHHHHHT--EEEEEEE--CCCHH........S..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHH CS
                      TPP_enzyme_N  77 tnaltalaeAkvdriPllvlsgdrptslrg........qgvlqqeldqlalfrpvtkyaervtspeelpealrrAir 145
                                       ++al++l++A++++iP++++sg +++s+rg         ++ q++ d+ +l+r+++k+ + v++++e+pea+ rA++
  gi|557695167|ref|YP_008798221.1|  88 ASALPNLFNAYTAGIPIILISGVTSYSSRGrrgsrqirVHWGQDVRDIRGLVRQFVKWDYVVNESAEIPEAVSRAVE 164
                                       *******************************************999******************************* PP

                                       HHHSSS--EEEEEEEHHHCC-EEE CS
                      TPP_enzyme_N 146 talsgrpgPvylelpkdvlleevd 169
                                       +a+s+++gPvyl + +++++++ +
  gi|557695167|ref|YP_008798221.1| 165 VAMSPPQGPVYLGIHREHFMANLE 188
                                       *******************99876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.1
                                       -T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHH CS
                      TPP_enzyme_N 113 eldqlalfrpvtkyaervtspeelpealrrAirtal 148
                                        ld  ++ r +   ++  ++p++++ealr+A++  l
  gi|557695167|ref|YP_008798221.1| 511 PLDVYSMGRGMGFSSYVAEKPRQAAEALREAVADVL 546
                                       556666666666677888999999999999998775 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 !   57.4   0.0   3.2e-19   1.4e-15      13     148 ..     410     550 ..     405     555 .. 0.83

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 3.2e-19
                                       HTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT..GGGHHHHHHTT-SEEEEEEE-SBCCC CS
                      TPP_enzyme_C  13 lkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi..lqelatavrrnlpitvvvlnNegygm 87 
                                       l + +p++y+ +   g++G+gl+aA+G+klakp+  v ++ GDG+f ++  ++  + +  ++lp+++ v+n++++  
  gi|557695167|ref|YP_008798221.1| 410 LLFDEPGTYFGEPPGGSLGWGLGAALGIKLAKPEVFVSVVLGDGSFVFNnpVSGAVLSKWYRLPVLLTVFNDGCWWD 486
                                       567899*****99**********************************997667777888899*************** PP

                                       HHHHHHHHTCCTTTTSBB....BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH...CSSSE CS
                      TPP_enzyme_C  88 tggqqepfggkrksgpagk...dlkpvdfaklaealGakgarvekadveeleealkeal...ekkgp 148
                                       +++    +g + + + + +     +p+d+  + +++G + ++ ek+   + +eal+ea+    k+ +
  gi|557695167|ref|YP_008798221.1| 487 VKKSLADMGFSEFGK-KVEgvdFPEPLDVYSMGRGMGFSSYVAEKP--RQAAEALREAVadvLKGVT 550
                                       ****66666544433.3234655999*************9997888..**********955444445 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   1.5e-05     0.068     139     169 ..     424     454 ..     412     552 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                             XFP_N 139 GGelGyalshayGavldnPdlivacvvGdGe 169
                                       GG lG+ l  a G  l +P+++v  v+GdG 
  gi|557695167|ref|YP_008798221.1| 424 GGSLGWGLGAALGIKLAKPEVFVSVVLGDGS 454
                                       9*****************************6 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 ?   10.7   0.0   7.3e-05      0.33       1      45 [.     209     253 ..     209     333 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 7.3e-05
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEE CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvtt 45 
                                       ++k+ae+l++a  pvil  +  ++++  + l++lae l + v   
  gi|557695167|ref|YP_008798221.1| 209 VKKIAERLASANYPVILTRSAGRNAKSFHLLKSLAEMLCARVNYA 253
                                       689**********************************99888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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 0.24s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3902.95
//
Query:       gi|557695168|ref|YP_008798222.1|  [L=512]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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   21.9  20.0    0.00016   21.9  20.0    3.1  3  PMT_2            Dolichyl-phosphate-mannose-protein mannosylt
     0.0034   16.7   5.7     0.0034   16.7   5.7    2.8  3  Glyco_transf_22  Alg9-like mannosyltransferase family
     0.0072   15.9  15.2     0.0072   15.9  15.2    3.5  3  PMT              Dolichyl-phosphate-mannose-protein mannosylt
  ------ inclusion threshold ------
        0.3   10.7   1.4        7.3    6.2   0.3    2.9  2  ATP-synt_J       ATP synthase j chain


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 !   21.9  20.0   3.6e-08   0.00016       4     158 ..      70     221 ..      67     227 .. 0.89
   2 ?   -2.7   0.0       1.3     6e+03      78      97 ..     247     266 ..     240     269 .. 0.75
   3 ?    2.0   6.3     0.049   2.2e+02       4      65 ..     375     435 ..     339     453 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 3.6e-08
                             PMT_2   4 Pliawllalftklfgfselairlvsalagvltilllyllarrlfg.kraallaalllavvplfvalsalftpdaplv 79 
                                       Pl+ w+l+ ++ l +     +rl+s l++v ++++++ll+ +lf+  +a++l+++++ ++ +fv+++  + +da   
  gi|557695168|ref|YP_008798222.1|  70 PLFWWMLTGVYLL-NAPVEYARLLSPLLTVAATVVMFLLVSKLFKsLMAGILSSVFTIALNYFVQTTSYILTDASGS 145
                                       9999*****9999.889999*************************89999**99999999999999998999***** PP

                             PMT_2  80 llwalalylllraleknklkywllagvlfGlgflsKytaallliaallyllisarrilkekkpylalllalllfspv 156
                                       +l  lal+ +   l  + +  + ++g l ++++l +   +lll+ +ll + +   r+ k++k+++ +ll+++++++v
  gi|557695168|ref|YP_008798222.1| 146 MLAFLALLSFSLGLRYGPF--LWVSGGLTAVSILARDQNLLLLPVMLLSMGWI-ARVSKTMKILYLALLGAVAAAAV 219
                                       *****************96..7789999****************999977777.68888877777777777777666 PP

                             PMT_2 157 li 158
                                       ++
  gi|557695168|ref|YP_008798222.1| 220 VM 221
                                       65 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                             PMT_2  78 lvllwalalylllraleknk 97 
                                       l+++++ +l+++++++++++
  gi|557695168|ref|YP_008798222.1| 247 LIVFTTVTLLAVHKVHQQKN 266
                                       67788888888888887665 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.049
                             PMT_2   4 Pliawllalftklfgfselairlvsalagvltilllyllarrlfgkraallaalllavvplf 65 
                                       Pli w++  ++ ++ f+    r+++  ++  ++l+ y++ r + +++ a++aa  + v+ +f
  gi|557695168|ref|YP_008798222.1| 375 PLILWFALTVAYIILFTHIEYRFLAPAVQPAAALAAYAITRVR-KRWLAFIAAGVILVYVVF 435
                                       7777777777777777777777777777777777777777775.667777777666655544 PP

>> Glyco_transf_22  Alg9-like mannosyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0  10.7       1.5   6.6e+03     116     219 ..      95     217 ..      72     234 .. 0.65
   2 ?   -1.5   0.2      0.24   1.1e+03     322     348 ..     241     271 ..     240     300 .. 0.46
   3 !   16.7   5.7   7.5e-07    0.0034     267     374 ..     344     448 ..     339     459 .. 0.74

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 1.5
                   Glyco_transf_22 116 lllslsswglfvfstrtfsnslemllts...ialyllsellsrenksss.................nekylvavlli 172
                                       ll    ++++f+  +++f + ++ +l s   ial ++ ++ s+  +  s                 +   l ++  +
  gi|557695168|ref|YP_008798222.1|  95 LLTVAATVVMFLLVSKLFKSLMAGILSSvftIALNYFVQTTSYILTDASgsmlaflallsfslglrYGPFLWVSGGL 171
                                       45556677888888888888888777651114444444444444444448888888899888888755567788889 PP

                   Glyco_transf_22 173 avlavliRptsallwlplvlf..lllrlvkkrsktflfliialvllvll 219
                                       +++++l R  ++ll+ +++l+  ++ r+ k+ ++++l l+ a+    ++
  gi|557695168|ref|YP_008798222.1| 172 TAVSILARDQNLLLLPVMLLSmgWIARVSKTMKILYLALLGAVA---AA 217
                                       99999999999999877776633566666666655533222222...22 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.24
                   Glyco_transf_22 322 pvl.Plillsaavlltrls...resakvskk 348
                                       pv+ Pl++++ +v+l ++    +++ + sk+
  gi|557695168|ref|YP_008798222.1| 241 PVYiPLLIVFTTVTLLAVHkvhQQKNLLSKR 271
                                       5666777777777766665444222222222 PP

  == domain 3  score: 16.7 bits;  conditional E-value: 7.5e-07
                   Glyco_transf_22 267 qnlpnilgvlllavllgllvl.lsrkvsrlllllltilltLlvysllpHKElRFllpvlPlillsaavlltrlsres 342
                                       +++p +l v ll ++++ + l l+ ++++ ++l+l ++lt++   l+ H E RFl p +     +aa+++tr+ r++
  gi|557695168|ref|YP_008798222.1| 344 SAFPSLLTVPLLTAAVAGAILaLKNRIEEAKPLILWFALTVAYIILFTHIEYRFLAPAVQPAAALAAYAITRV-RKR 419
                                       56777766655555555444415667777999*************************99667777899*****.566 PP

                   Glyco_transf_22 343 akvskklsllvllllfnvvlalllglvhqagv 374
                                       +++        ++l++ v+ + l+g+v + + 
  gi|557695168|ref|YP_008798222.1| 420 WLAFIA---AGVILVYVVFPTQLYGVVPEFSE 448
                                       665444...77888888888888887766655 PP

>> PMT  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9  15.2   1.6e-06    0.0072      63     156 ..      69     171 ..      60     265 .. 0.75
   2 ?    0.2   0.0       0.1   4.5e+02     139     162 ..     246     270 ..     240     291 .. 0.66
   3 ?   -3.2   3.4       1.1     5e+03     139     155 ..     375     391 ..     342     443 .. 0.50

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.6e-06
                               PMT  63 dgnftfesigaeyypenvpyvslRlfsallgslivplvyltllelgfskltallaallvllenslitlsryilld.. 137
                                       ++ f++   g  y ++ +p+  +Rl+s ll++ ++++++l++ +l +s  +++l++++ +  n ++  + yil+d  
  gi|557695168|ref|YP_008798222.1|  69 QPLFWWMLTG-VYLLN-APVEYARLLSPLLTVAATVVMFLLVSKLFKSLMAGILSSVFTIALNYFVQTTSYILTDas 143
                                       6788888886.56666.**********************************************************77 PP

                               PMT 138 .spLlfftllsmyclvkfe........r 156
                                        s+L+f  lls+ + +++         +
  gi|557695168|ref|YP_008798222.1| 144 gSMLAFLALLSFSLGLRYGpflwvsggL 171
                                       779********99888876555555551 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                               PMT 139 pLlfftllsmyclvkfe.rkapfsr 162
                                        L+ ft+++++ + k++ +k+ +s+
  gi|557695168|ref|YP_008798222.1| 246 LLIVFTTVTLLAVHKVHqQKNLLSK 270
                                       6899999999999999953333333 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.1
                               PMT 139 pLlfftllsmyclvkfe 155
                                       pL+++ +l++++ + f 
  gi|557695168|ref|YP_008798222.1| 375 PLILWFALTVAYIILFT 391
                                       44444444444444443 PP

>> ATP-synt_J  ATP synthase j chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.037   1.7e+02      15      32 ..      99     116 ..      87     118 .. 0.82
   2 ?    6.2   0.3    0.0016       7.3       4      24 ..     414     434 ..     413     441 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHHHHHHHST CS
                        ATP-synt_J  15 aaglivlygvnkaqnamm 32 
                                       aa ++++ +v+k+ +++m
  gi|557695168|ref|YP_008798222.1|  99 AATVVMFLLVSKLFKSLM 116
                                       788899999999877766 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0016
                                       --SSSSSHHHHHHHHHHHHHH CS
                        ATP-synt_J   4 tpvlkpmwPFfaaglivlygv 24 
                                       t v k  + F+aag+i +y v
  gi|557695168|ref|YP_008798222.1| 414 TRVRKRWLAFIAAGVILVYVV 434
                                       678899999**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); 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:                         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: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3485.18
//
Query:       gi|557695169|ref|YP_008798223.1|  [L=440]
Description: hypothetical protein CSUB_C1742 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3046.92
//
Query:       gi|557695170|ref|YP_008798224.1|  [L=384]
Description: hypothetical protein CSUB_C1743 [Candidatus Caldiarchaeum subterraneum]
Scores for 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  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2791.94
//
Query:       gi|557695171|ref|YP_008798225.1|  [L=142]
Description: hypothetical protein CSUB_C1744 [Candidatus Caldiarchaeum subterraneum]
Scores for 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-05   23.3   0.4    8.1e-05   22.6   0.4    1.4  1  PRC              PRC-barrel domain
     0.0061   16.9   1.4     0.0095   16.3   1.4    1.3  1  Lar_restr_allev  Restriction alleviation protein Lar
  ------ inclusion threshold ------
      0.023   14.6   4.0      0.033   14.2   4.0    1.2  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.35   11.0   3.4       0.25   11.5   1.5    1.7  2  DUF2256          Uncharacterized protein conserved in bacteri


Domain annotation for each model (and alignments):
>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.4   1.8e-08   8.1e-05       7      74 ..      10      70 ..       4      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.8e-08
                                      ---TT-EEEETTSSEEEEEEEEEEETTTTEEEEEEEEETTT.....-EEEEEGG.CEECCCTEEEETT CS
                               PRC  7 sdliGkeVytedGeklGkVkDvvidekegrvralvvsvggflgigekevliPfdlavkigkdriivda 74
                                       +l+G++Vy+ dG  +G+V+D+ + +++g++   ++s+ +          +P+   v + +d+ii+++
  gi|557695171|ref|YP_008798225.1| 10 GKLVGMQVYSPDGSLVGVVQDIELPIGSGEIGLQILSKYNV------VERVPWS-MVAAAGDIIILKE 70
                                      589*****************************999999976......4589999.9999999999886 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   1.4   2.1e-06    0.0095       4      35 ..     115     139 ..     112     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                   Lar_restr_allev   4 kpCPfCggravlersqrvvaeigqcvyCadCg 35 
                                       +pCP Cg + ++++++++++       C +Cg
  gi|557695171|ref|YP_008798225.1| 115 NPCPTCGRDLTWIEQYQRWY-------CYNCG 139
                                       7**************99997.......66666 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 ?   14.2   4.0   7.3e-06     0.033      21      45 ..     117     140 ..     106     141 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.3e-06
                     Zn_Tnp_IS1595  21 CPhCgsrkayriktrglfqCkeCrk 45 
                                       CP Cg r ++ i++ +++ C+ C+k
  gi|557695171|ref|YP_008798225.1| 117 CPTCG-RDLTWIEQYQRWYCYNCGK 140
                                       *****.99999999*********97 PP

>> DUF2256  Uncharacterized protein conserved in bacteria (DUF2256)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.5   5.6e-05      0.25       7      25 ..     114     132 ..     110     135 .. 0.81
   2 ?   -1.5   0.2      0.65   2.9e+03       9      15 ..     134     140 ..     127     141 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.6e-05
                           DUF2256   7 sKiCavCgrpftwRkkWek 25 
                                       + +C++Cgr +tw  ++++
  gi|557695171|ref|YP_008798225.1| 114 KNPCPTCGRDLTWIEQYQR 132
                                       458**********777665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.65
                           DUF2256   9 iCavCgr 15 
                                        C  Cg+
  gi|557695171|ref|YP_008798225.1| 134 YCYNCGK 140
                                       6999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1023.21
//
Query:       gi|557695172|ref|YP_008798226.1|  [L=797]
Description: carbon monoxide dehydrogenase large subunit [Candidatus Caldiarchaeum subterraneum]
Scores for 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-185  616.4   0.0   4.8e-185  616.2   0.0    1.0  1  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
      3e-28   98.4   0.0    5.8e-28   97.4   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 !  616.2   0.0  5.4e-189  4.8e-185       2     550 .]     160     725 ..     159     725 .. 0.97

  Alignments for each domain:
  == domain 1  score: 616.2 bits;  conditional E-value: 5.4e-189
                                       TTT-STTEEE..EEEEE-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHH CS
                     Ald_Xan_dh_C2   2 heeapdnvla..kiekGdveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlva 76 
                                       ++++p+n ++  + + Gdve+af+ ad+vv++++ ++r +++++Et+a+la++++ ++e tvy ++q+ph +r l++
  gi|557695172|ref|YP_008798226.1| 160 YDDVPNNTAFvwRASGGDVEKAFDGADVVVSQRLVNSRLQPTPMETRAVLADYNPTTDEATVYLTSQNPHVHRLLLS 236
                                       5789999999555557************************************************************* PP

                                       HHHT--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS- CS
                     Ald_Xan_dh_C2  77 evlglpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGk 153
                                        v+g pe+k+rv++ +vGGGFG K++ ++ ev++ ++Ak +++pVk++++R e+++at ++++++++++++ad+ G 
  gi|557695172|ref|YP_008798226.1| 237 LVTGHPEHKLRVVSYDVGGGFGAKIHLYSPEVVLLHLAKTLKKPVKWMETRMENFTATIHGRDHIQYVDLAADRTGL 313
                                       ***************************************************************************** PP

                                       EEEEEEEEEEEESST.HHHCHCCHCCTTGGGT.TTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 154 italdvdlladaGay.adlspavleralshld.gpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdel 228
                                       +++l+v+ +a++Gay ++++p++++  ++ +  gpY+ip+++ve+ ++ tNt+p++a+RG+G+p+a+++lEr++d l
  gi|557695172|ref|YP_008798226.1| 314 VLGLRVKSYANMGAYlSTAAPGIPTILFGPVLsGPYRIPAISVEVVGALTNTAPVDAYRGAGRPEATYILERMIDIL 390
                                       ***************8899******99999988******************************************** PP

                                       HHHHT--HHHHHHHHBCECGCC.SEEET....EESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEE CS
                     Ald_Xan_dh_C2 229 AeelgldplelRrrNlikpgeltpygqp....vydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvv 301
                                        ++lg dp+e+R +N+ik++ + py       vydsgd+++++ k++e s+y e+r++q+e++a++k +Gig++ ++
  gi|557695172|ref|YP_008798226.1| 391 SRRLGKDPAEVRLKNFIKKEMF-PYSAMpiglVYDSGDYEKAFMKALELSRYSEWRKKQEEMRAKGKLIGIGISSYI 466
                                       ******************9999.995544999*******************************88899********* PP

                                       EEBS--S.....EETTEE.......EEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBT CS
                     Ald_Xan_dh_C2 302 egiglgf....takflnq.......egalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdt 367
                                       e +glg+          +       e+  +rv+++G+v+v++gg+++GqG et++aqi+a++L++p+edv++ +gdt
  gi|557695172|ref|YP_008798226.1| 467 EICGLGPssvaR----ATgfglglwESTIIRVHPTGKVSVYIGGHPHGQGEETTFAQIVADRLQIPIEDVEILHGDT 539
                                       *******64331....334677788**************************************************** PP

                                       TSSS----S-TT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-CCCEEEETTEEEET...EEEECHHHHHHHHHH. CS
                     Ald_Xan_dh_C2 368 dkvpngsgtaaSrstdlngnAvkkAaeklrerllkiaaellevspedleledgkvvvk...eksvslaelaaaayl. 440
                                       + +p+g+gt++Sr+t ++g++v+  ++++ e+++kiaa+lle+ ++d+e+  gk++v+   eks+s+ae+a aay  
  gi|557695172|ref|YP_008798226.1| 540 AMIPFGMGTYGSRTTPVAGASVAIGCDRILEKARKIAAHLLEAGEKDIEYVAGKFYVRempEKSKSFAEVAYAAYGa 616
                                       ************************************************************9999**********999 PP

                                       ........TTSSEEEEEEE...EEEETHCHCSBBEEEEEEEEEEEEETTT--EEEEEEEEEEE-BS-S-HHHHHHHH CS
                     Ald_Xan_dh_C2 441 ........ervslsatgfyktldeetgkgppfayfaygaavaeVevDtetgevkvlrvvivhDvGksiNpaivegQi 509
                                                +++l++t f+         +pp+++f++g++++  evD+etg+vkvl++++v+D+G+ iNp+ivegQi
  gi|557695172|ref|YP_008798226.1| 617 ganelpqgLEPGLETTVFF---------DPPNFTFPFGTHICITEVDPETGKVKVLEYYAVDDCGNRINPMIVEGQI 684
                                       99999999999********.........9************************************************ PP

                                       HHHHHHHHHHHHT---EEETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 510 eGGfvqGiGlalmEelvydedGqlltasladYkiPtaadiP 550
                                       +GG++qG+++al+Ee  yd+dGqllt++l++Y++Pta++iP
  gi|557695172|ref|YP_008798226.1| 685 HGGIAQGLAQALYEEASYDSDGQLLTSNLTEYLVPTAMEIP 725
                                       ****************************************9 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 !   97.4   0.0   6.5e-32   5.8e-28       1     110 []      27     143 ..      27     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 97.4 bits;  conditional E-value: 6.5e-32
                                       TT-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCT...TSSS-EE....EE CS
                      Ald_Xan_dh_C   1 tGeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaig...siledee....da 70 
                                       tG+++Y+  +++pg++y++fvrS++ahAkiv +dvsaa+++ GV+ v+t+++l+++   i    +i++++      +
  gi|557695172|ref|YP_008798226.1|  27 TGRGRYTHNLSLPGMVYACFVRSPHAHAKIVGVDVSAAEKSSGVLGVFTGAELADKLGPIPcawQIPNSDIkvprYM 103
                                       8*****************************************************99777666653444433556568 PP

                                       SS-SSEESSTT-EEEEEEESSHHHHHHHHHT-EEEEEE-- CS
                      Ald_Xan_dh_C  71 llaedkvrsvgqavaavvAedeetArkAaklvkveYeelp 110
                                        la dk+r+vg++va+vvA++ ++A +Aa+lvkveYe+lp
  gi|557695172|ref|YP_008798226.1| 104 PLAVDKARFVGDPVAVVVATSYAEALDAASLVKVEYEKLP 143
                                       9************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (797 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); 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:                         2  (0.000111551); expected 0.2 (1e-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 0.28s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 5471.07
//
Query:       gi|557695173|ref|YP_008798227.1|  [L=223]
Description: conserved hypothetical protein [Candidatus Caldiarchaeum subterraneum]
Scores for 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:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1637.38
//
Query:       gi|557695174|ref|YP_008798228.1|  [L=97]
Description: MazG nucleotide pyrophosphohydrolase [Candidatus Caldiarchaeum subterraneum]
Scores for 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-10   38.6   0.0    1.2e-09   38.2   0.0    1.1  1  MazG      MazG nucleotide pyrophosphohydrolase domain


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 !   38.2   0.0   6.6e-14   1.2e-09       3      66 ..      23      80 ..      21      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 6.6e-14
                                      HHHHHHHHHHHHHHHHHH.HHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHH CS
                              MazG  3 petllaylleEvgEvaea.IkkedrdeleeELGDvLlqvlflaniaeeeggidledvaetileKl 66
                                      +e + ++l+ E+gE+ +a Ik++  ++l+eE +DvL ++l+++n+    + idle+++   l+K+
  gi|557695174|ref|YP_008798228.1| 23 LERTFLWLVSEMGELSDAyIKNKGPRQLDEEAADVLAWLLSFCNV----ASIDLEKAF---LNKY 80
                                      678899***********97999**********************9....*******99...6666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 672.57
//
Query:       gi|557695175|ref|YP_008798229.1|  [L=77]
Description: sec-independent protein translocase protein TatA [Candidatus Caldiarchaeum subterraneum]
Scores for 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   29.5   4.9    1.7e-06   27.3   4.9    2.2  1  MttA_Hcf106  mttA/Hcf106 family
  ------ inclusion threshold ------
       0.08   11.8   0.0      0.094   11.6   0.0    1.1  1  DUF677       Protein of unknown function (DUF677)


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 !   27.3   4.9   1.8e-10   1.7e-06       1      45 [.       3      49 ..       3      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.8e-10
                                      S-HHHHHHHHHHHHH..HS-TTTHHHHHHHHHHHHHHHHHHHHHHHH CS
                       MttA_Hcf106  1 lgapelliIlvVall..lFGpkkLPEvaraLGktLreFkkavkelee 45
                                      ++++e++iI+ ++l+     p kLP +a++LG++ reF ka k +e 
  gi|557695175|ref|YP_008798229.1|  3 ISLTEIAIIAAIILIaiYILPGKLPKLAKSLGEAKREFEKASKREEV 49
                                      6999******9999842235**********************98876 PP

>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     1e-05     0.094     221     268 ..      27      74 ..       2      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1e-05
                            DUF677 221 eavgkwvasawkkyeealkrqkeivssmekgievakkdvenisilver 268
                                         ++k +++a ++ e+a kr++ +    e gi v  k++e+i+ +++r
  gi|557695175|ref|YP_008798229.1|  27 PKLAKSLGEAKREFEKASKREEVLERARELGIDVTGKTLEEIEEEIRR 74 
                                       4455667899*********************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1286  (0.0717274); expected 358.6 (0.02)
Passed bias filter:                      897  (0.0500307); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 542.72
//
[ok]
